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 AL646091.4 and AL669943.9

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AL646091.4 Mouse DNA sequence from clone RP23-101K9 on chromosome 11, complete sequence [htgs_phase3]

Length: 133,477 bp

AL669943.9 Mouse DNA sequence from clone RP23-286C19 on chromosome 11, complete sequence [htgs_phase3]

Length: 204,312 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 397
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	133477	2001	+	+	chenhc	Taxid 10090 chrom 11 Primary assembly	2008-11-20 16:56:50.973	63571	397	GRCm39, GRCm38, MGSCv37

Alignment 1 of 1

 AL646091.4 : + : 131478..133477
 AL669943.9 : + : 1..2000
 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  5 BAC and 0 Fosmid bridging clones.
  5 BAC and 0 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL646091.4 >131478  gaattcagtagtctcttagtccacgatgctggatatctcaacaatcccagtttgatattg 131537 
AL669943.9 >1       ............................................................ 60     

AL646091.4 >131538  aaggcttaaaagattcccatagaaatactggttttcattttatattagaatcctaaggaa 131597 
AL669943.9 >61      ............................................................ 120    

AL646091.4 >131598  gctggtttaatatctgtaatggaatgcagcagccatggaataggtgacctggccagcaag 131657 
AL669943.9 >121     ............................................................ 180    

AL646091.4 >131658  agtgaaggcaaacaagcaaaagcgtggctttttgtctgggctgacattagaaggggccac 131717 
AL669943.9 >181     ............................................................ 240    

AL646091.4 >131718  acgtattagggttggtcttcccttttcaagaaatctaatcccaaaagtctctcacaggag 131777 
AL669943.9 >241     ............................................................ 300    

AL646091.4 >131778  tgcccaatggcttgcgttttagttaatcccagcgtccatcaaattcacaatcaagattaa 131837 
AL669943.9 >301     ............................................................ 360    

AL646091.4 >131838  ccagcacactccctcaatactgcacaggtgcaggtgtccctgtttctgctgacagttttg 131897 
AL669943.9 >361     ............................................................ 420    

AL646091.4 >131898  tatcattgtatttttgttgtggtgttttgtatcattttatttttgttgtggttgcatggg 131957 
AL669943.9 >421     ............................................................ 480    

AL646091.4 >131958  actctacctgcagctattcagttcccctgcctttgcagctctcttgaccaaatggctttg 132017 
AL669943.9 >481     ............................................................ 540    

AL646091.4 >132018  ctcaataacaacacgtttacagcagtaattcctcatccctttcacttttttcctgaagaa 132077 
AL669943.9 >541     ............................................................ 600    

AL646091.4 >132078  taaccaaaggctgccattactgcattactctctattattccttcataaaaagaggaaagt 132137 
AL669943.9 >601     ............................................................ 660    

AL646091.4 >132138  gatgtaattataactagtttaacatgcaaagggaaatgatagatgacccatcatagattt 132197 
AL669943.9 >661     ............................................................ 720    

AL646091.4 >132198  ttgcaagttatttttctgtttttattttataacatatttagttatgtatgtatgtatgta 132257 
AL669943.9 >721     ............................................................ 780    

AL646091.4 >132258  tgtgtggggagccgcactcacatttgccattacaagatggcgctgacagctgtgttctaa 132317 
AL669943.9 >781     ............................................................ 840    

AL646091.4 >132318  gtagtaaataatctgcacatgtgcaggggcagttttcccgccatgtgctctgcctttctc 132377 
AL669943.9 >841     ............................................................ 900    

AL646091.4 >132378  gtgatgacaactgggccgatgggctgcagccaatcagggagtgacatgtcctaggcggag 132437 
AL669943.9 >901     ............................................................ 960    

AL646091.4 >132438  gataattctccttaaaagggacggggttgtggcactccctctcctcttcgtctcttcctc 132497 
AL669943.9 >961     ............................................................ 1020   

AL646091.4 >132498  ttcgtcttttcctctgctctcttcctctgctctctgcctctctctctgcgtctctctctc 132557 
AL669943.9 >1021    ............................................................ 1080   

AL646091.4 >132558  tcttcctctctgcctctctctgccgcgctcttcctctcttgctcctgagtaagcaataaa 132617 
AL669943.9 >1081    ............................................................ 1140   

AL646091.4 >132618  gctttgctgcagaagattctggtttgttgcgtctttcctggcctgtcgcgaacgagtgta 132677 
AL669943.9 >1141    ............................................................ 1200   

AL646091.4 >132678  agatgtatgtatgtacatatgtatgtattatgtagactctgtgtgtgtgtgtgtttgtga 132737 
AL669943.9 >1201    ............................................................ 1260   

AL646091.4 >132738  atgtgtgtgttacctgcaaagatcaaaaaaggtcaccaggtaccctggaactggaattgc 132797 
AL669943.9 >1261    ............................................................ 1320   

AL646091.4 >132798  atgtggttgtgagtcaccatgcacactgtgagaacctgagtactctgttaggcagcaggt 132857 
AL669943.9 >1321    ............................................................ 1380   

AL646091.4 >132858  ggggttaactgctgaattatctctcaatcaccagcaaggcattttcttatacaggcttgt 132917 
AL669943.9 >1381    ............................................................ 1440   

AL646091.4 >132918  attaatagcacccaggtttttctaatgtaaaacattttttctaatgtaaaacaatggctt 132977 
AL669943.9 >1441    ............................................................ 1500   

AL646091.4 >132978  taccataaaatgaatattatcattgtaggatgaagcaaatgtcttttgctagtcccttaa 133037 
AL669943.9 >1501    ............................................................ 1560   

AL646091.4 >133038  tttgtttttcagtgttctggatgagattccatgctatttacaatcaagggagtgatttcc 133097 
AL669943.9 >1561    ............................................................ 1620   

AL646091.4 >133098  cactgacatatgatgcaaccttttagagatctctaggaaatattgacaaccatctgaaat 133157 
AL669943.9 >1621    ............................................................ 1680   

AL646091.4 >133158  tatttatttgtccaactgtttttcatgaagtcaactagtgtagccaaaaaagttttgttt 133217 
AL669943.9 >1681    ............................................................ 1740   

AL646091.4 >133218  gtttgttcttgttaaatttcccagtttacttttctttgtcagtaatttgtcatcacatat 133277 
AL669943.9 >1741    ............................................................ 1800   

AL646091.4 >133278  atattttgaattctcttatacttttaatgtgtacactttataattcaagtatatctacag 133337 
AL669943.9 >1801    ............................................................ 1860   

AL646091.4 >133338  aatcatgcaattggggcctttattacttgaaaacataaggagagctttttaataaaacta 133397 
AL669943.9 >1861    ............................................................ 1920   

AL646091.4 >133398  ttgatgcccttgaacttgtcttctgccaagtgagataaatagatagtctaccctagatgc 133457 
AL669943.9 >1921    ............................................................ 1980   

AL646091.4 >133458  tggcctctgtatcacagact 133477 
AL669943.9 >1981    .................... 2000

Events

Id	Type	Date	Whodid	Comment
775	ImportOldDb	09/02/2005 08:18:00	f_old_db
776	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174328	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-191P4				AL669943.9	99.38%	pos 123710 (F-)
C3H-231J24				AL669943.9	99.55%	pos 172946 (F+)
CH29-14O9	AL646091.4	99.04%	pos 73639 (R+)	AL669943.9	99.31%	pos 184563 (F-)
CH29-172C5	AL669943.9	99.52%	pos 103995 (R-)	AL646091.4	99.61%	pos 39096 (F+)
CH29-186L1				AL669943.9	99.86%	pos 14804 (F-)
CH29-26D13	AL646091.4	99.16%	pos 56407 (R+)	AL669943.9	100%	pos 167396 (F-)
CH29-530L12	AL646091.4	100%	pos 18668 (R+)	AL669943.9	99.64%	pos 68466 (F-)
CH29-548E17				AL646091.4	99.3%	pos 54728 (F-)
CH29-548E17				AL646091.4	100%	pos 54949 (F-)
CH29-554O17				AL646091.4	99.72%	pos 38904 (F-)
CH29-595C8	AL646091.4	99.52%	pos 55037 (R-)
RP23-139K11				AL646091.4	99.19%	pos 121272 (F-)
RP23-25C12				AL669943.9	99.71%	pos 88819 (F-)
RP23-25G12	AL646091.4	99.3%	pos 65768 (R+)
RP23-8M22	AL669943.9	99.86%	pos 117106 (R-)
RP24-158I20				AL646091.4	99.5%	pos 117299 (F-)
RP24-189O7	AL646091.4	99.6%	pos 57003 (R+)	AL669943.9	99.51%	pos 91276 (F-)
RP24-201I15				AL646091.4	100%	pos 87305 (F-)
RP24-254G18	AL669943.9	99.55%	pos 6230 (R-)
RP24-394H8	AL669943.9	99.46%	pos 113596 (R+)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1463A14	AL646091.4	99.65%	pos 27877 (R-)
WI1-1553H17				AL646091.4	100%	pos 20738 (F+)
WI1-1624N22				AL646091.4	99.83%	pos 20744 (F+)
WI1-1750E15	AL669943.9	100%	pos 113598 (R-)	AL669943.9	100%	pos 75565 (F+)
WI1-1762F22	AL669943.9	100%	pos 194115 (R-)	AL669943.9	100%	pos 161182 (F+)
WI1-1769P10	AL646091.4	100%	pos 54945 (R-)	AL646091.4	99.77%	pos 17062 (F+)
WI1-1790G6	AL646091.4	100%	pos 28475 (R+)
WI1-1844F21	AL669943.9	99.4%	pos 120443 (R-)
WI1-2063I10	AL669943.9	100%	pos 166261 (R-)
WI1-2106J9				AL646091.4	100%	pos 11416 (F-)
WI1-2199A11	AL646091.4	99.78%	pos 115595 (R-)	AL646091.4	99.8%	pos 79998 (F+)
WI1-2509J11	AL646091.4	100%	pos 107158 (R+)
WI1-2634K21				AL669943.9	99.83%	pos 190147 (F+)
WI1-2748B12	AL669943.9	99.8%	pos 75435 (R-)	AL669943.9	99.83%	pos 35486 (F+)
WI1-2799G11	AL669943.9	100%	pos 124970 (R-)	AL669943.9	100%	pos 82452 (F+)
WI1-2832J8				AL669943.9	100%	pos 174309 (F+)
WI1-2868F2				AL669943.9	99.85%	pos 17579 (F-)
WI1-2882I21	AL669943.9	99.3%	pos 188806 (R+)
WI1-362F19	AL646091.4	99.79%	pos 43015 (R+)	AL646091.4	99.78%	pos 81857 (F-)
WI1-392N20	AL646091.4	100%	pos 18088 (R+)	AL646091.4	99.74%	pos 55299 (F-)
WI1-460F11	AL669943.9	100%	pos 83229 (R+)
WI1-504E3	AL669943.9	99.78%	pos 35590 (R+)	AL669943.9	100%	pos 79953 (F-)
WI1-560H18	AL646091.4	100%	pos 66171 (R+)	AL646091.4	100%	pos 104797 (F-)
WI1-691I1	AL669943.9	100%	pos 134651 (R+)	AL669943.9	100%	pos 175044 (F-)
WI1-712I20				AL669943.9	99.64%	pos 60548 (F-)
WI1-792C7	AL646091.4	100%	pos 120647 (R-)
WI1-896N19	AL669943.9	99.81%	pos 191586 (R+)
WI1-976M6	AL646091.4	99.61%	pos 3039 (R+)	AL646091.4	99.58%	pos 43035 (F-)
WI1-997I18	AL646091.4	100%	pos 89272 (R-)	AL646091.4	100%	pos 50052 (F+)

Repeats

Too repeats, not showing repeat table.

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Curator Links

Alignment for AL646091.4 and AL669943.9

Alignment Summary

Alignment 1 of 1