Join Evaluation Legend

Serious alignment problem, requires review. (details...)
- Zero, or more than one, overlaps
- Half dove-tail >50 bp
- Alignment identity <98%
- Alignment length <100 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.

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Alignment for AL672029.7 and BX842239.2

AL672029.7 Mouse DNA sequence from clone RP23-416F22 on chromosome X, complete sequence [htgs_phase3]

Length: 189,958 bp

BX842239.2 Mouse DNA sequence from clone RP23-454A1 on chromosome X Contains a CpG island, complete sequence [htgs_phase3]

Length: 58,222 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 15859
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)

Alignment 1 of 1

 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  1 BAC and 2 Fosmid bridging clones.
  1 BAC and 2 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL672029.7 >187959  tacaacattttgatgattacaggaaactcatctcagagaaaaagatagacactacctcag 188018 
BX842239.2 >1       ............................................................ 60     

AL672029.7 >188019  aatgaaaggctggaaaacaattttccaagcaaatggtctgaagaaacaagctggagtagc 188078 
BX842239.2 >61      ............................................................ 120    

AL672029.7 >188079  cattctaatatcgaataaaatcgacttccaatccaaagtcatcaataaagtcaaggagag 188138 
BX842239.2 >121     ............................................................ 180    

AL672029.7 >188139  gcacttcatactcatcaaaggtaaaatcctccaagaggaactatcaattctgaatatcta 188198 
BX842239.2 >181     ............................................................ 240    

AL672029.7 >188199  tgctccaaatacaaggacagccacaatcactaaagaaactttagtaaagctcaaagcaca 188258 
BX842239.2 >241     ............................................................ 300    

AL672029.7 >188259  cattgcaccacacacaataatagtgggagacttcaacacatgactttcaacaatggacag 188318 
BX842239.2 >301     ............................................................ 360    

AL672029.7 >188319  acatggaaacagaaactaaacaggaacacagtgaaactaacagaagttatgaaacaaatg 188378 
BX842239.2 >361     ............................................................ 420    

AL672029.7 >188379  gatctaacagatatctatggaacattttatccgaaaacaaaaggatataccttcttctca 188438 
BX842239.2 >421     ............................................................ 480    

AL672029.7 >188439  gtacctcatggtaccttctccaaaattgaccacataattcgtcacaaaaaacaagcctca 188498 
BX842239.2 >481     ............................................................ 540    

AL672029.7 >188499  gcatatacaaaaatattgaaattgtcacatacatcctatcagatcaccatggactaaggc 188558 
BX842239.2 >541     ............................................................ 600    

AL672029.7 >188559  tgatcttcaataacaacataaataatagaaatccatcattcacatggaaactgaacaaca 188618 
BX842239.2 >601     ............................................................ 660    

AL672029.7 >188619  ctcttctcaatgacaccttggtcaaggaaggaataaagaaagaaattaagaacttttcgg 188678 
BX842239.2 >661     ............................................................ 720    

AL672029.7 >188679  agtttaatgaaaatgaagccacaacatacccaaacttatgggaaacaatgaaagcatttc 188738 
BX842239.2 >721     ............................................................ 780    

AL672029.7 >188739  taagaggaacccaaatagctctgagtgcctccaaaaagaaactagagagagtacacatta 188798 
BX842239.2 >781     ............................................................ 840    

AL672029.7 >188799  gcagcttggcaacacacctaaaagctctaaagcaaaaggaagcaaattcacccaagagga 188858 
BX842239.2 >841     ............................................................ 900    

AL672029.7 >188859  gtagacagcaggaaataatcaaactcagcggcaaaatccaccaagttgaaacgagaacta 188918 
BX842239.2 >901     ............................................................ 960    

AL672029.7 >188919  ttcaaagaatcaaacaaatggggagctggttctttgagaaaatcaacaagatagataaac 188978 
BX842239.2 >961     ............................................................ 1020   

AL672029.7 >188979  ccttatccagactcactacagggcacagggaaagcatcctaattaacaaaatcagaaatg 189038 
BX842239.2 >1021    ............................................................ 1080   

AL672029.7 >189039  aaaagggagacatagcaacagatcctgaagaaatccaaaacaccatcagatccttctata 189098 
BX842239.2 >1081    ............................................................ 1140   

AL672029.7 >189099  acaggctatagtcaacaaaactggagaacctggatgaaatggacaagtttctggacagat 189158 
BX842239.2 >1141    ............................................................ 1200   

AL672029.7 >189159  accaggtaccaaagttaaatcaagatcaggttaatgatctaaacagtcctatatccctta 189218 
BX842239.2 >1201    ............................................................ 1260   

AL672029.7 >189219  agaaaaaagaagcagtcattaatagtctcccaaacaaaaaaagcccaggaccagatgggt 189278 
BX842239.2 >1261    ............................................................ 1320   

AL672029.7 >189279  ttagtgcagagttctatcagaccttcaaagaagatctaattccagttcttcacaaactat 189338 
BX842239.2 >1321    ............................................................ 1380   

AL672029.7 >189339  tccacaaaatagaagcagaaggtactacagagtaattgtgataaaaactacatgatactg 189398 
BX842239.2 >1381    ............................................................ 1440   

AL672029.7 >189399  gtatagtgagagacaagtagacaagaccaatggagtagaattgaagacccagagatgaac 189458 
BX842239.2 >1441    ............................................................ 1500   

AL672029.7 >189459  ccacacacctatggtcacttgttctttgacaagggagctaaaacaatcctgtggaaaaaa 189518 
BX842239.2 >1501    ............................................................ 1560   

AL672029.7 >189519  gcattttcaacaaatggtgttggcacaactggtggttatcatatagacgaatgtgaattg 189578 
BX842239.2 >1561    ............................................................ 1620   

AL672029.7 >189579  atccattcctatctccttgtactaatgtcaaatctaagtggattaaggaactccacataa 189638 
BX842239.2 >1621    ............................................................ 1680   

AL672029.7 >189639  aaccagagacactgaaacttatagaggagaaagtagggaaaaccctcgaagagggaaaaa 189698 
BX842239.2 >1681    ............................................................ 1740   

AL672029.7 >189699  ttcctgaataggacagcaatggcttgtgctgtaagattgagaatcgataaatgggacctc 189758 
BX842239.2 >1741    ............................................................ 1800   

AL672029.7 >189759  ataaagtttcaaagcttctgcaaggcaaaagacaccttcaataagacaaaaggaccacca 189818 
BX842239.2 >1801    ............................................................ 1860   

AL672029.7 >189819  acagattgggaaaggatatttacctatcctaaatcagataagggactaatatccaatata 189878 
BX842239.2 >1861    ............................................................ 1920   

AL672029.7 >189879  tataaagaacacaagaaggtggactccagaaaagcatataaccccattaaaaatggggct 189938 
BX842239.2 >1921    ............................................................ 1980   

AL672029.7 >189939  cagatctcaacaaagaattc 189958 
BX842239.2 >1981    .................... 2000

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	189958	2001	+	+	chenhc	Taxid 10090 chrom X Reference assembly	2008-11-20 17:02:11.660

Events

Id	Type	Date	Whodid	Comment
23900	ImportOldDb	09/04/2005 15:52:00	f_old_db
23901	ReSetShortOvlp	09/04/2008 10:31:48	dbo
179650	CreateSwitchPt	11/20/2008 17:02:11	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-119D9				AL672029.7	99.55%	pos 120479 (F+)
C3H-153E23	AL672029.7	99.6%	pos 135320 (R-)
C3H-153E24	AL672029.7	99.58%	pos 135271 (R-)
C3H-210I1	AL672029.7	99.35%	pos 18454 (R+)
C3H-24B23				AL672029.7	99.15%	pos 175648 (F+)
C3H-24B24				AL672029.7	99.18%	pos 175660 (F+)
C3H-24B24				AL672029.7	99.41%	pos 175634 (F+)
CH29-47I21	AL672029.7	100%	pos 181796 (R+)
CH29-528B18				AL672029.7	100%	pos 94475 (F-)
CH29-585P13	AL672029.7	99.87%	pos 177926 (R+)
CH29-590C3	AL672029.7	99.86%	pos 54786 (R-)
CH29-618G7	BX842239.2	99.06%	pos 48208 (R-)	AL672029.7	99.25%	pos 36601 (F+)
CH29-7D13				AL672029.7	100%	pos 127718 (F+)
RP24-123J19	AL672029.7	99.39%	pos 112814 (R-)
RP24-283A9				AL672029.7	99.48%	pos 108586 (F-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1061A11	AL672029.7	99.82%	pos 127295 (R-)	AL672029.7	99.38%	pos 86457 (F+)
WI1-1160L24	AL672029.7	99.6%	pos 56373 (R+)	AL672029.7	100%	pos 94385 (F-)
WI1-1164O24	AL672029.7	100%	pos 34323 (R+)
WI1-1374E16				BX842239.2	99.82%	pos 16141 (F-)
WI1-1394I23	AL672029.7	100%	pos 151552 (R+)	BX842239.2	100%	pos 3038 (F-)
WI1-1394O15	AL672029.7	99.78%	pos 151548 (R+)	BX842239.2	100%	pos 3069 (F-)
WI1-1426N23	AL672029.7	100%	pos 167587 (R-)
WI1-148M7	AL672029.7	100%	pos 184922 (R-)	AL672029.7	99.81%	pos 147815 (F+)
WI1-1674L10	AL672029.7	100%	pos 126345 (R+)	AL672029.7	100%	pos 164735 (F-)
WI1-1797O3	BX842239.2	99.36%	pos 49978 (R-)	BX842239.2	99.59%	pos 7602 (F+)
WI1-1823C14	AL672029.7	100%	pos 137452 (R+)	AL672029.7	99.12%	pos 175730 (F-)
WI1-1865O5	AL672029.7	100%	pos 136117 (R+)
WI1-2039P4	AL672029.7	99.77%	pos 8295 (R-)
WI1-2089P1	AL672029.7	99.83%	pos 71169 (R+)	AL672029.7	100%	pos 114828 (F-)
WI1-2138C7	AL672029.7	99.78%	pos 181752 (R-)
WI1-2304M21	AL672029.7	100%	pos 64565 (R+)
WI1-2334D4	BX842239.2	99.8%	pos 49984 (R-)	BX842239.2	99.29%	pos 7593 (F+)
WI1-2368P16	AL672029.7	99.83%	pos 74549 (R+)	AL672029.7	100%	pos 114190 (F-)
WI1-2749A6	AL672029.7	99.8%	pos 77846 (R-)	AL672029.7	99.82%	pos 38612 (F+)
WI1-2749G12	AL672029.7	99.55%	pos 77845 (R-)	AL672029.7	100%	pos 38610 (F+)
WI1-2851F10	AL672029.7	100%	pos 54050 (R+)	AL672029.7	100%	pos 89597 (F-)
WI1-400N6	AL672029.7	100%	pos 62542 (R-)	AL672029.7	100%	pos 22060 (F+)
WI1-54O11	AL672029.7	100%	pos 112778 (R+)	AL672029.7	99.7%	pos 150650 (F-)
WI1-57J14	AL672029.7	99.66%	pos 47788 (R-)	AL672029.7	100%	pos 9054 (F+)
WI1-884N20				AL672029.7	100%	pos 161490 (F+)

NCBI

Join Evaluation Legend

Curator Links

Alignment for AL672029.7 and BX842239.2

Alignment Summary

Alignment 1 of 1