Alignment last updated: 11/20/2008 16:56:51

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 AL845465.2 and AL596185.12

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AL845465.2 Mouse DNA sequence from clone RP23-119B10 on chromosome 11, complete sequence [htgs_phase3]

Length: 37,402 bp

AL596185.12 Mouse DNA sequence from clone RP23-172M21 on chromosome 11, complete sequence [htgs_phase3]

Length: 248,203 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 2375
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	37402	2001	+	+	chenhc	Taxid 10090 chrom 11 Primary assembly	2008-11-20 16:56:51.393	63788	2375	GRCm39, GRCm38, MGSCv37

Alignment 1 of 1

 AL845465.2 : + : 35403..37402
 AL596185.12 : + : 1..2000
 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  3 BAC and 4 Fosmid bridging clones.
  3 BAC and 4 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL845465.2  >35403   gaattccaatcctagccaggcagtggtggtgcaagcttttgatcccagcacttgggaggc 35462  
AL596185.12 >1       ............................................................ 60     

AL845465.2  >35463   agaggcaagtggatttctgagttccgaggccagcctggtccacagagtgagttccaggac 35522  
AL596185.12 >61      ............................................................ 120    

AL845465.2  >35523   agccagggctacacagagaaaccctgtctcaaagaaccaaaaaagagagagagagagaga 35582  
AL596185.12 >121     ............................................................ 180    

AL845465.2  >35583   gagagagagagagagagagagagagagagagagagagttccaaacctctctgttccttgc 35642  
AL596185.12 >181     ............................................................ 240    

AL845465.2  >35643   cagtgctaggcttgcaggcctgatccaccaaacccagcccctgatagtttatttagaatt 35702  
AL596185.12 >241     ............................................................ 300    

AL845465.2  >35703   gggaacctacattgtgggtgtagctcagctgtagatcccttgttgttgtggttattggtt 35762  
AL596185.12 >301     ............................................................ 360    

AL845465.2  >35763   ttttttgttgttgttgttttttcagacagggtttctctgtgtagccctggctgtcctgga 35822  
AL596185.12 >361     ............................................................ 420    

AL845465.2  >35823   actcactttgtagaccaggctggcctcgaactcagaaatctgcctgcctctgcctcccaa 35882  
AL596185.12 >421     ............................................................ 480    

AL845465.2  >35883   gtgctgggattaaaggtgtgcgccaccatgctcagcttattattattattattattatta 35942  
AL596185.12 >481     ............................................................ 540    

AL845465.2  >35943   ttattattattattattattattattattattttgatagggttcctctatgtatccctgg 36002  
AL596185.12 >541     ............................................................ 600    

AL845465.2  >36003   cagtcctggaacttgctatgttgtagatcaggctggccttgaactcatagagatatgcct 36062  
AL596185.12 >601     ............................................................ 660    

AL845465.2  >36063   atttctgcctcccctgagctgggattaaaggagcgtgccattgtgccagatgttttatta 36122  
AL596185.12 >661     ............................................................ 720    

AL845465.2  >36123   ttaccttctaacatagtatgcagttatttagttactgatctgtttgtctgtctttgctga 36182  
AL596185.12 >721     ............................................................ 780    

AL845465.2  >36183   ctaagggttgtatcttgatgtacttcatatacaatacacaatcattattgatccgagaat 36242  
AL596185.12 >781     ............................................................ 840    

AL845465.2  >36243   attcaactggttgggtttagctgagacagttgtcttcttacctgctccaggtcttaaatg 36302  
AL596185.12 >841     ............................................................ 900    

AL845465.2  >36303   cattgctggcacgtttgaaaagatgtccttccattaccaagccactaggcccctccttta 36362  
AL596185.12 >901     ............................................................ 960    

AL845465.2  >36363   ggcttggctctggctcctcgccacctagctcctagaagcatgagaggatcaaagacaact 36422  
AL596185.12 >961     ............................................................ 1020   

AL845465.2  >36423   gggataggcagagaccaaagccatagctggttttcctctggcctccataccagcccttac 36482  
AL596185.12 >1021    ............................................................ 1080   

AL845465.2  >36483   cttctgcttcagtaacacatgcctctgttccatgtctctcttctgtcgagctgagttcaa 36542  
AL596185.12 >1081    ............................................................ 1140   

AL845465.2  >36543   gaccaggttgtgcaactgggcataggagggtcctctcagatgtctgagtttgtcccaacc 36602  
AL596185.12 >1141    ............................................................ 1200   

AL845465.2  >36603   agtccagaagagtcatcttagtgtatcctaacctctctgctccaactttctagagtcctt 36662  
AL596185.12 >1201    ............................................................ 1260   

AL845465.2  >36663   acctgggtacccaattccttccgatactgagccagcctgtttagctcttcatggccctgc 36722  
AL596185.12 >1261    ............................................................ 1320   

AL845465.2  >36723   tggaaataagtggcctgggcctcaaccaaacgcagtacctgatggtgggcgggaggcaga 36782  
AL596185.12 >1321    ............................................................ 1380   

AL845465.2  >36783   actgaggaaggacactcctctctctccctcttccctcccactgtcagcccgttcctctcc 36842  
AL596185.12 >1381    ............................................................ 1440   

AL845465.2  >36843   atcttggctgcccctgaaactcacgaattccatgatgtcaaacttcctcttatcctcaat 36902  
AL596185.12 >1441    ............................................................ 1500   

AL845465.2  >36903   cacattgacctgaaggccccaaaagacctcaggtcagtctagaaaccacagcaccccccc 36962  
AL596185.12 >1501    ............................................................ 1560   

AL845465.2  >36963   attacaccctaggaactccccttctcccgaacaccttcaaggtatgcaggtatcctggag 37022  
AL596185.12 >1561    ............................................................ 1620   

AL845465.2  >37023   gatgggttggggtaggcacctacctgcagggcataatctaatgcccgactccggtaccca 37082  
AL596185.12 >1621    ............................................................ 1680   

AL845465.2  >37083   gctcgagcggtcctcaaagcagttccagcctcctctgcttcttggacacggcgcctgggg 37142  
AL596185.12 >1681    ............................................................ 1740   

AL845465.2  >37143   acctctgcattgtgggtaagagcagcctccaggttctcagcccctcgccagaaatccctg 37202  
AL596185.12 >1741    ............................................................ 1800   

AL845465.2  >37203   cgagcctctcggaagccccggagacctctagagttaggggagacaaaacaaaaccacaga 37262  
AL596185.12 >1801    ............................................................ 1860   

AL845465.2  >37263   tttacccttctgctttaggaaagaaaaatctcaggataaggcccacctatctcctgtcag 37322  
AL596185.12 >1861    ............................................................ 1920   

AL845465.2  >37323   cctgtgtagagaggaaacgccaggcaatcccaggataggaagacagaagccaggccactt 37382  
AL596185.12 >1921    ............................................................ 1980   

AL845465.2  >37383   cccaccctcatagctcctcc 37402  
AL596185.12 >1981    .................... 2000

Events

Id	Type	Date	Whodid	Comment
4555	ImportOldDb	09/02/2005 14:16:00	f_old_db
4556	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174545	CreateSwitchPt	11/20/2008 16:56:51	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-26G8	AL596185.12	99.41%	pos 230123 (R-)	AL596185.12	99.01%	pos 71134 (F+)
C3H-26H7	AL596185.12	99.07%	pos 230117 (R-)
C3H-55O14	AL845465.2	99.48%	pos 13024 (R-)
C3H-76O6				AL596185.12	99.28%	pos 220861 (F+)
C3H-83O5	AL596185.12	99.85%	pos 16971 (R+)	AL596185.12	99.77%	pos 161201 (F-)
CH29-186C11	AL596185.12	99.73%	pos 73636 (R+)
CH29-2I4				AL596185.12	100%	pos 123870 (F+)
CH29-606J8	AL596185.12	100%	pos 137054 (R-)	AL845465.2	100%	pos 23286 (F+)
CH29-620B4	AL845465.2	99.28%	pos 2087 (R+)
CH29-622M4				AL596185.12	99.42%	pos 229805 (F+)
CH29-76M20	AL596185.12	100%	pos 103931 (R-)
RP24-127J23	AL596185.12	99.6%	pos 104896 (R-)
RP24-166E17	AL596185.12	99.31%	pos 132538 (R+)
RP24-212B17	AL596185.12	100%	pos 187569 (R-)
RP24-271F5	AL596185.12	99.09%	pos 71077 (R-)
RP24-297N24	AL845465.2	99.16%	pos 27794 (R+)	AL596185.12	99.6%	pos 147498 (F-)
RP24-306K19	AL596185.12	99.4%	pos 136434 (R-)
RP24-310D12				AL596185.12	99.28%	pos 94347 (F-)
RP24-368D9	AL596185.12	99.5%	pos 180139 (R+)
RP24-372D12	AL845465.2	99.52%	pos 5094 (R+)	AL596185.12	99.64%	pos 166963 (F-)
RP24-391M12	AL596185.12	99.08%	pos 174810 (R+)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1018C3	AL845465.2	100%	pos 24129 (R-)
WI1-1122P13	AL596185.12	99.21%	pos 92337 (R+)	AL596185.12	100%	pos 127129 (F-)
WI1-1182A4				AL596185.12	99.59%	pos 176720 (F+)
WI1-1183M6	AL845465.2	99.85%	pos 28846 (R-)
WI1-1206K1				AL596185.12	99.35%	pos 191913 (F+)
WI1-1217K11	AL596185.12	99.67%	pos 227255 (R-)	AL596185.12	99.85%	pos 187697 (F+)
WI1-1230M16	AL596185.12	100%	pos 47346 (R-)	AL596185.12	100%	pos 14450 (F+)
WI1-1243I15				AL596185.12	99.55%	pos 237305 (F+)
WI1-1257C18	AL845465.2	100%	pos 518 (R+)	AL596185.12	100%	pos 7339 (F-)
WI1-1364F4	AL596185.12	100%	pos 12806 (R+)	AL596185.12	99.45%	pos 52495 (F-)
WI1-1378I18	AL596185.12	100%	pos 3448 (R-)
WI1-139K12	AL845465.2	100%	pos 24145 (R+)	AL596185.12	100%	pos 32870 (F-)
WI1-1434D24	AL596185.12	100%	pos 185087 (R-)	AL596185.12	99.47%	pos 143390 (F+)
WI1-1434D24				AL596185.12	100%	pos 143431 (F+)
WI1-149F4				AL596185.12	100%	pos 186531 (F+)
WI1-1508I12				AL845465.2	100%	pos 12431 (F+)
WI1-1575K15	AL596185.12	100%	pos 139219 (R+)	AL596185.12	100%	pos 177557 (F-)
WI1-1689N14	AL596185.12	100%	pos 39095 (R+)
WI1-1709J9				AL596185.12	100%	pos 232901 (F+)
WI1-1735A16	AL596185.12	100%	pos 153474 (R+)	AL596185.12	100%	pos 189039 (F-)
WI1-1802M8	AL596185.12	99.58%	pos 155759 (R+)	AL596185.12	100%	pos 196521 (F-)
WI1-1867M19	AL596185.12	99.49%	pos 170912 (R-)
WI1-1887A7	AL596185.12	100%	pos 52907 (R-)
WI1-1903F9	AL845465.2	100%	pos 23788 (R+)	AL596185.12	100%	pos 25627 (F-)
WI1-197I8	AL596185.12	100%	pos 107355 (R+)	AL596185.12	100%	pos 147816 (F-)
WI1-2006E22				AL596185.12	99.7%	pos 63107 (F+)
WI1-2011F15				AL596185.12	100%	pos 61725 (F+)
WI1-2032G1				AL845465.2	100%	pos 9502 (F-)
WI1-2060K15	AL845465.2	100%	pos 26213 (R+)	AL596185.12	100%	pos 33342 (F-)
WI1-2066F12	AL596185.12	99.77%	pos 55619 (R+)	AL596185.12	100%	pos 92482 (F-)
WI1-2066I11	AL596185.12	100%	pos 207309 (R-)	AL596185.12	99.85%	pos 161596 (F+)
WI1-2066J24				AL596185.12	99.81%	pos 194380 (F-)
WI1-2068N19	AL596185.12	99.8%	pos 79751 (R-)	AL596185.12	100%	pos 40129 (F+)
WI1-2071L12	AL596185.12	100%	pos 127087 (R-)	AL596185.12	100%	pos 83633 (F+)
WI1-2162M12	AL596185.12	99.72%	pos 198069 (R+)
WI1-2183N3	AL596185.12	100%	pos 214790 (R-)	AL596185.12	99.63%	pos 179113 (F+)
WI1-2206A9	AL596185.12	99.85%	pos 182536 (R-)	AL596185.12	100%	pos 140642 (F+)
WI1-2248P11				AL845465.2	99.69%	pos 9488 (F-)
WI1-2249B14	AL596185.12	100%	pos 52907 (R-)
WI1-2252M6	AL596185.12	99.77%	pos 63369 (R+)	AL596185.12	100%	pos 103274 (F-)
WI1-2271F19	AL596185.12	99.37%	pos 227434 (R+)
WI1-2323P8	AL596185.12	99.7%	pos 117217 (R-)	AL596185.12	100%	pos 78135 (F+)
WI1-2405F11	AL596185.12	100%	pos 222483 (R+)
WI1-2406J11	AL596185.12	100%	pos 174286 (R-)
WI1-2448D21				AL596185.12	100%	pos 100745 (F-)
WI1-2541F9	AL596185.12	100%	pos 141356 (R+)	AL596185.12	100%	pos 177560 (F-)
WI1-2555A14	AL596185.12	99.73%	pos 95893 (R-)	AL596185.12	100%	pos 53853 (F+)
WI1-2590J6	AL596185.12	99.75%	pos 179791 (R+)	AL596185.12	100%	pos 218015 (F-)
WI1-2643G12	AL596185.12	100%	pos 156398 (R+)	AL596185.12	100%	pos 195989 (F-)
WI1-2808H17	AL845465.2	100%	pos 32701 (R-)
WI1-2816M13	AL596185.12	100%	pos 53723 (R-)	AL596185.12	100%	pos 13205 (F+)
WI1-2840O16				AL596185.12	100%	pos 6473 (F-)
WI1-2888E16	AL596185.12	99.07%	pos 39539 (R+)
WI1-295I10	AL596185.12	100%	pos 80681 (R+)
WI1-30A10	AL596185.12	100%	pos 60981 (R+)	AL596185.12	100%	pos 104065 (F-)
WI1-466C17	AL596185.12	99.86%	pos 232571 (R+)
WI1-562B10	AL596185.12	99.79%	pos 92310 (R-)	AL596185.12	99.58%	pos 49483 (F+)
WI1-788K21	AL845465.2	99.74%	pos 24233 (R-)
WI1-792E22	AL845465.2	100%	pos 24874 (R-)
WI1-813G19	AL596185.12	100%	pos 90762 (R-)	AL596185.12	99.44%	pos 49051 (F+)
WI1-899B24	AL596185.12	99.54%	pos 208332 (R+)
WI1-921D7	AL596185.12	100%	pos 178361 (R-)	AL596185.12	99.19%	pos 141134 (F+)
WI1-930D3	AL845465.2	100%	pos 25974 (R-)

Repeats

Too repeats, not showing repeat table.

Join Legend

Curator Links

Alignment for AL845465.2 and AL596185.12

Alignment Summary

Alignment 1 of 1