Alignment last updated: 11/20/2008 16:56:50

Join Legend

Serious alignment problem, requires review. (details...)
- Zero, or more than one, overlaps
- Half dove-tail >50 bp
- Alignment identity <98%
- Alignment length <50 bp
- >2 gaps, each gap >25 bp, not marked as an SSR
- >0 gaps, each gap >50 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, marked as an SSR
Minor alignment problem. (details...)
- Exactly one overlap
- Half dove-tail >0 bp and <=50bp
- Alignment identity <99.1%
- Alignment length <2000 bp
- >0 gaps, each gap >25 bp, not marked as an SSR
- >0 gaps, each gap >50 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, marked as an SSR
Excellent alignment, meets all defined criteria. (details...)
- Exactly one RuleInfo
- Half dove-tail <=0 bp
- Alignment identity >=99.1%
- Alignment length >=2000 bp
- <=0 gaps, each gap >25 bp, not marked as an SSR
- <=0 gaps, each gap >50 bp, not marked as an SSR
- <=0 gaps, each gap >500 bp, not marked as an SSR
- <=0 gaps, each gap >500 bp, marked as an SSR
Certificate submitted, not yet approved.
Certificate submitted and approved.
Valid, contained clone
Join not evaluated due to one accession not being finished.

Alignment for AL662868.15 and AL732587.8

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AL662868.15 Mouse DNA sequence from clone RP23-144P24 on chromosome 11, complete sequence [htgs_phase3]

Length: 198,647 bp

AL732587.8 Mouse DNA sequence from clone RP23-268K22 on chromosome 11, complete sequence [htgs_phase3]

Length: 132,671 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 239
Total Length: 2000
Aligned Length: 2000
Percent Identity: 100
Number of Gaps: 0
Number of Mismatches: 0
Source: CtgOverlap Seq-Align
Valid Switchpoint: true (A)

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time	Id	Alignment	Releases
A	198647	2001	+	+	chenhc	Taxid 10090 chrom 11 Primary assembly	2008-11-20 16:56:50.940	63555	239	GRCm39, GRCm38, MGSCv37

Alignment 1 of 1

 AL662868.15 : + : 196648..198647
 AL732587.8 : + : 1..2000
 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  1 BAC and 13 Fosmid bridging clones.
  1 BAC and 12 Fosmid concordant clones.
  0 BAC and 1 Fosmid discordant clones.

AL662868.15 >196648  tacctctcattaccagaggagagagagagaacataaagcctccgcctcagcctcagcagc 196707 
AL732587.8  >1       ............................................................ 60     

AL662868.15 >196708  cagcacatttactgcccaagaggagcagtcgtgtggagggtcctttcgtgagaatgaggt 196767 
AL732587.8  >61      ............................................................ 120    

AL662868.15 >196768  ggtggaccactgagtttaactctgtttctgtggacattcgggagggctattttcatcctc 196827 
AL732587.8  >121     ............................................................ 180    

AL662868.15 >196828  caaaaggagagcacctcccctccctctttttcttctcccctctaataggaacacaagaac 196887 
AL732587.8  >181     ............................................................ 240    

AL662868.15 >196888  ttccaccgagatcccagcgtggcttttgtctgtgaatccattaacacctccaggcgtggc 196947 
AL732587.8  >241     ............................................................ 300    

AL662868.15 >196948  tggctctgccctcattaatgattagacattatggagcctgaggactctgcctggggagaa 197007 
AL732587.8  >301     ............................................................ 360    

AL662868.15 >197008  agctactcttgagtcctttcctttttcttcactattgtcaaagtcctccgggctttgagg 197067 
AL732587.8  >361     ............................................................ 420    

AL662868.15 >197068  gtccctctgaggtcagtccacatctgtacttggatttgacttacacagtctagcaggcag 197127 
AL732587.8  >421     ............................................................ 480    

AL662868.15 >197128  tcttacctgcatttttttgtgtgacgaagaggacacaagtactcacaatggctgctttga 197187 
AL732587.8  >481     ............................................................ 540    

AL662868.15 >197188  gtgccttgcagtcgtgctcaaagaaaatggggaataccggcatctcagtcttcagagacc 197247 
AL732587.8  >541     ............................................................ 600    

AL662868.15 >197248  cacaaggaaagctaaactctgaggcgtcagccagcccacagctgcatgaagggatagcat 197307 
AL732587.8  >601     ............................................................ 660    

AL662868.15 >197308  tgggttgtgaacagttcccaaacaagtacagtgacacaggccactgcatcaagcacagtg 197367 
AL732587.8  >661     ............................................................ 720    

AL662868.15 >197368  acataggccactgtcattgagcacagtgacacaggccactgtcattgagcacaatgacac 197427 
AL732587.8  >721     ............................................................ 780    

AL662868.15 >197428  aggccactgcatcaagcacagtgacataggccactgtcattgagcaccgtgacacaggcc 197487 
AL732587.8  >781     ............................................................ 840    

AL662868.15 >197488  actgtcattgagcacagtgacataggccactgcagggccagctgtcagccatcactggca 197547 
AL732587.8  >841     ............................................................ 900    

AL662868.15 >197548  ccgattagctgtgggagtgaaatgaccacagaagtcgtgaagaatcaggataggagcctc 197607 
AL732587.8  >901     ............................................................ 960    

AL662868.15 >197608  tctctagatctttccctccaggtccttaataatcaggaagacgctcccacacaagggaat 197667 
AL732587.8  >961     ............................................................ 1020   

AL662868.15 >197668  ctgtccacaggcaaataaatggaagccatgcaccaggaatcctgactcagtgggtgaaga 197727 
AL732587.8  >1021    ............................................................ 1080   

AL662868.15 >197728  gaacaaaacagtaaaactaaccccaagtgcatccaacgcttgtcacacgctgctgtccat 197787 
AL732587.8  >1081    ............................................................ 1140   

AL662868.15 >197788  ctggggatacctggtgcaagggcatttctgtaattctacgtgtatgtatgcatctgtgtg 197847 
AL732587.8  >1141    ............................................................ 1200   

AL662868.15 >197848  tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttatagctagtgcatgctaaacaa 197907 
AL732587.8  >1201    ............................................................ 1260   

AL662868.15 >197908  atgctctaccactacccaacatctgtagcctctaactatttaacccatgtgtcacagtta 197967 
AL732587.8  >1261    ............................................................ 1320   

AL662868.15 >197968  gaaatgcagtggccatctcaatccagtacacagctgtgtgcacacagtaggactaagcca 198027 
AL732587.8  >1321    ............................................................ 1380   

AL662868.15 >198028  tgcttcctgacattttgcttgtaacagaatctgctgtctcgtgagttggggttaatagtc 198087 
AL732587.8  >1381    ............................................................ 1440   

AL662868.15 >198088  actgttctgcagacttgcatgcatccatgtatgtatgtacacacacacacacacacacac 198147 
AL732587.8  >1441    ............................................................ 1500   

AL662868.15 >198148  acatttcaccactcacctacccacctggaggtcatgacttcagattaaaaaggcaggcac 198207 
AL732587.8  >1501    ............................................................ 1560   

AL662868.15 >198208  aaatgctgttttgtgaagaattctgtatggcttgatgaaatgtgggcccgacccttctct 198267 
AL732587.8  >1561    ............................................................ 1620   

AL662868.15 >198268  ggccctccagcctgcattgcacgtcttgaacatgatccttaatccttgaccctgagccat 198327 
AL732587.8  >1621    ............................................................ 1680   

AL662868.15 >198328  aggctccccagcacagcccatctgctcctcgggacagatcattgaccccacagtgaccct 198387 
AL732587.8  >1681    ............................................................ 1740   

AL662868.15 >198388  cctgaagcgctcagagctccctgtgggaacaacatggggggctcagaccagcactgggat 198447 
AL732587.8  >1741    ............................................................ 1800   

AL662868.15 >198448  ccttgtagtagattgggcacagtgactcccaggcttaaaagagaccacaacatgaactgg 198507 
AL732587.8  >1801    ............................................................ 1860   

AL662868.15 >198508  gtggaggccccgcttactgtcttgaatcactcagcctatagcattccacgctctgcctgc 198567 
AL732587.8  >1861    ............................................................ 1920   

AL662868.15 >198568  ttaccttccagcttgggaactcaggacatgcctgctccctcttgcacagtttgggctgtt 198627 
AL732587.8  >1921    ............................................................ 1980   

AL662868.15 >198628  taaaaactcaagctgaattc 198647 
AL732587.8  >1981    .................... 2000

Events

Id	Type	Date	Whodid	Comment
472	ImportOldDb	09/02/2005 07:45:00	f_old_db
473	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174312	CreateSwitchPt	11/20/2008 16:56:50	chenhc	tpf_builder 1.6 Toolkit wrapper version: built Nov 19 2008 using /netopt/ncbi_tools64/c++.by-date/20081119/GCC401-Release64/lib

BAC Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
C3H-156O7	AL732587.8	99.06%	pos 66681 (R+)
C3H-156O7	AL732587.8	99.24%	pos 66737 (R+)
C3H-191O1				AL662868.15	99.5%	pos 161819 (F-)
CH29-585F7	AL732587.8	99.32%	pos 61381 (R-)
CH29-599L19	AL662868.15	99.25%	pos 45520 (R+)
CH29-611D23				AL732587.8	99.14%	pos 40386 (F+)
RP23-132C23	AL732587.8	99.38%	pos 125391 (R-)
RP24-126N17	AL732587.8	99.36%	pos 96318 (R-)
RP24-210G18	AL732587.8	99.29%	pos 129268 (R-)	AL662868.15	99.43%	pos 175396 (F+)
RP24-244I15				AL662868.15	99.53%	pos 140797 (F-)
RP24-338K3	AL662868.15	99.22%	pos 76838 (R+)
RP24-341K1	AL662868.15	99.54%	pos 4357 (R-)
RP24-361J5				AL662868.15	99.86%	pos 17637 (F-)
RP24-362E19				AL662868.15	99.78%	pos 37322 (F-)
RP24-362K8				AL662868.15	99.55%	pos 37337 (F-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1042H8	AL732587.8	100%	pos 103997 (R-)	AL732587.8	100%	pos 73632 (F+)
WI1-1047G4	AL662868.15	99.61%	pos 163403 (R-)	AL662868.15	99.81%	pos 117745 (F+)
WI1-104A10	AL662868.15	100%	pos 2515 (R+)	AL662868.15	100%	pos 44665 (F-)
WI1-1090H13	AL662868.15	100%	pos 162494 (R+)	AL732587.8	100%	pos 10638 (F-)
WI1-1111B24	AL662868.15	99.12%	pos 77764 (R-)
WI1-1145B19	AL662868.15	99.68%	pos 162503 (R+)	AL732587.8	99.73%	pos 10599 (F-)
WI1-1160O4	AL732587.8	100%	pos 42145 (R-)	AL662868.15	100%	pos 196207 (F+)
WI1-1187L23	AL662868.15	100%	pos 65630 (R+)	AL662868.15	100%	pos 107023 (F-)
WI1-1189A12	AL662868.15	100%	pos 133285 (R+)	AL662868.15	100%	pos 175404 (F-)
WI1-1213O14	AL662868.15	99.62%	pos 77794 (R-)	AL662868.15	99.85%	pos 38313 (F+)
WI1-1220N19	AL662868.15	99.73%	pos 183081 (R-)
WI1-1240M24	AL662868.15	99.15%	pos 86581 (R+)	AL662868.15	100%	pos 126183 (F-)
WI1-1247E4	AL662868.15	100%	pos 184448 (R-)	AL662868.15	99.18%	pos 141750 (F+)
WI1-1283D16	AL662868.15	99.5%	pos 114399 (R-)	AL662868.15	99.7%	pos 79105 (F+)
WI1-1289F20	AL662868.15	99.78%	pos 144863 (R-)	AL662868.15	100%	pos 101897 (F+)
WI1-1304E15	AL662868.15	100%	pos 143661 (R-)	AL662868.15	99.82%	pos 105309 (F+)
WI1-1318K18	AL732587.8	99.78%	pos 27319 (R-)	AL662868.15	100%	pos 184179 (F+)
WI1-1356E23	AL732587.8	99.69%	pos 22137 (R-)	AL662868.15	99.83%	pos 174558 (F+)
WI1-1444G5	AL662868.15	100%	pos 65855 (R-)	AL662868.15	99.3%	pos 23470 (F+)
WI1-146I20	AL662868.15	99.71%	pos 167218 (R+)	AL732587.8	99.8%	pos 5956 (F-)
WI1-146P15	AL662868.15	100%	pos 167200 (R+)	AL732587.8	99.35%	pos 5955 (F-)
WI1-1472D9	AL662868.15	99.78%	pos 168914 (R+)	AL732587.8	99.75%	pos 16489 (F-)
WI1-1476H20				AL732587.8	99.42%	pos 11484 (F-)
WI1-1526K16	AL662868.15	100%	pos 94179 (R-)	AL662868.15	100%	pos 56281 (F+)
WI1-1546B3	AL732587.8	99.02%	pos 42811 (R-)	AL732587.8	100%	pos 6017 (F+)
WI1-1597I22	AL662868.15	99.5%	pos 37611 (R+)
WI1-1610O8	AL662868.15	100%	pos 196226 (R-)	AL662868.15	99.07%	pos 157649 (F+)
WI1-1668D22	AL732587.8	100%	pos 66622 (R+)	AL732587.8	100%	pos 105484 (F-)
WI1-1668L10	AL732587.8	100%	pos 66622 (R+)	AL732587.8	100%	pos 105484 (F-)
WI1-1682B8	AL662868.15	100%	pos 147188 (R-)
WI1-1731J2				AL662868.15	99.09%	pos 73415 (F+)
WI1-1751P21	AL662868.15	100%	pos 77190 (R+)	AL662868.15	99.72%	pos 115124 (F-)
WI1-1762M6	AL732587.8	100%	pos 42145 (R-)	AL662868.15	99.61%	pos 196218 (F+)
WI1-1779I17	AL732587.8	100%	pos 24387 (R-)	AL662868.15	99.67%	pos 177169 (F+)
WI1-1796P4	AL662868.15	99.66%	pos 45974 (R-)	AL662868.15	99.55%	pos 8642 (F+)
WI1-1873D6	AL662868.15	100%	pos 60464 (R+)	AL662868.15	100%	pos 99962 (F-)
WI1-1909F11	AL662868.15	100%	pos 196308 (R-)	AL662868.15	100%	pos 158204 (F+)
WI1-1926D20	AL662868.15	100%	pos 177105 (R+)
WI1-1957A13	AL732587.8	100%	pos 125107 (R-)	AL732587.8	100%	pos 85163 (F+)
WI1-1960L16	AL732587.8	100%	pos 128431 (R+)
WI1-1961I17				AL662868.15	99.83%	pos 9420 (F-)
WI1-1990B9	AL662868.15	100%	pos 195479 (R-)	AL662868.15	100%	pos 154492 (F+)
WI1-2018G1	AL732587.8	100%	pos 131535 (R-)	AL732587.8	100%	pos 90188 (F+)
WI1-2022O16	AL662868.15	100%	pos 42654 (R-)
WI1-2032I10	AL662868.15	100%	pos 24510 (R+)	AL662868.15	99.71%	pos 62882 (F-)
WI1-2033P17				AL662868.15	100%	pos 23595 (F-)
WI1-2038E5	AL662868.15	99.84%	pos 49198 (R+)
WI1-204A13	AL662868.15	100%	pos 47354 (R-)	AL662868.15	100%	pos 91 (F+)
WI1-2060C11	AL662868.15	100%	pos 107098 (R+)	AL662868.15	100%	pos 145911 (F-)
WI1-2096I7	AL662868.15	100%	pos 56827 (R+)	AL662868.15	99.66%	pos 99394 (F-)
WI1-212M5				AL662868.15	99.17%	pos 183896 (F-)
WI1-2138G4	AL732587.8	100%	pos 103453 (R-)	AL732587.8	99.64%	pos 62077 (F+)
WI1-2142G6	AL662868.15	99.7%	pos 12479 (R-)
WI1-2178J7	AL662868.15	100%	pos 123078 (R-)	AL662868.15	99.12%	pos 84162 (F+)
WI1-2178N7	AL662868.15	100%	pos 123078 (R-)	AL662868.15	100%	pos 84176 (F+)
WI1-2181K3	AL662868.15	100%	pos 145282 (R+)
WI1-229L21	AL662868.15	99.81%	pos 21926 (R-)
WI1-229N7	AL662868.15	99.68%	pos 21906 (R-)
WI1-2382B3	AL662868.15	99.7%	pos 109112 (R+)	AL662868.15	100%	pos 150080 (F-)
WI1-2398N19	AL732587.8	100%	pos 71879 (R-)	AL732587.8	100%	pos 42010 (F+)
WI1-2425O20	AL732587.8	100%	pos 86470 (R-)	AL732587.8	99.73%	pos 46891 (F+)
WI1-2446E4	AL662868.15	100%	pos 177183 (R+)	AL732587.8	100%	pos 20604 (F-)
WI1-2461N12				AL732587.8	100%	pos 95590 (F+)
WI1-2515H4	AL662868.15	99.41%	pos 177183 (R+)	AL732587.8	99.47%	pos 18062 (F-)
WI1-2568N15	AL662868.15	100%	pos 3908 (R-)
WI1-2685G12				AL662868.15	100%	pos 146324 (F-)
WI1-2837K1	AL662868.15	100%	pos 10995 (R+)	AL662868.15	100%	pos 47282 (F-)
WI1-2837L21				AL732587.8	99.82%	pos 103223 (F+)
WI1-2850F24				AL662868.15	99.55%	pos 153071 (F-)
WI1-2862F22	AL732587.8	100%	pos 56318 (R+)	AL732587.8	100%	pos 95070 (F-)
WI1-340P15	AL732587.8	100%	pos 89753 (R-)	AL732587.8	99.68%	pos 46196 (F+)
WI1-354M20	AL662868.15	99.8%	pos 142544 (R-)	AL662868.15	100%	pos 103845 (F+)
WI1-461I5	AL732587.8	100%	pos 34970 (R+)
WI1-472K9	AL662868.15	99.74%	pos 140272 (R+)
WI1-624F22	AL732587.8	99.3%	pos 130569 (R+)
WI1-64E14	AL662868.15	100%	pos 186183 (R-)	AL662868.15	100%	pos 147818 (F+)
WI1-692O11	AL662868.15	99.81%	pos 117266 (R+)
WI1-697P12	AL662868.15	99.76%	pos 181287 (R+)
WI1-814B18				AL662868.15	100%	pos 170631 (F+)
WI1-844I13	AL662868.15	100%	pos 52395 (R-)	AL662868.15	99.37%	pos 13243 (F+)
WI1-870D23				AL662868.15	100%	pos 35494 (F-)
WI1-871M15	AL662868.15	99.1%	pos 115899 (R-)	AL662868.15	100%	pos 115962 (F-)
WI1-904H8	AL662868.15	99.49%	pos 178688 (R+)	AL662868.15	99.38%	pos 154491 (F+)
WI1-915L24	AL662868.15	99.08%	pos 175543 (R-)	AL662868.15	99.81%	pos 134564 (F+)
WI1-917H10	AL662868.15	99.12%	pos 175540 (R-)	AL662868.15	100%	pos 134554 (F+)
WI1-919P15	AL732587.8	99.39%	pos 101288 (R-)	AL732587.8	99.64%	pos 61501 (F+)
WI1-920F7	AL732587.8	99.83%	pos 73981 (R-)
WI1-98F10	AL662868.15	99.74%	pos 178532 (R+)	AL732587.8	99.03%	pos 11393 (F-)
WI1-992D23	AL662868.15	99.22%	pos 178492 (R+)

Repeats

Too repeats, not showing repeat table.

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Curator Links

Alignment for AL662868.15 and AL732587.8

Alignment Summary

Alignment 1 of 1