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 AL672004.12 and AL672049.13

AL672004.12 Mouse DNA sequence from clone RP23-200C21 on chromosome 11 Contains part of the Murr2 gene for U2af1-rs1 region 2, complete sequence [htgs_phase3]

Length: 101,730 bp

AL672049.13 Mouse DNA sequence from clone RP23-188K3 on chromosome 11 Contains the 3' end of the Murr2 gene for U2af1-rs1 region 2, a novel gene (1110064P04Rik), a novel gene (1700030C12Rik), a novel gene (1700093K21Rik), a novel gene, a novel gene (0610010F05Rik), the Pex13 gene for peroxisomal biogenesis factor 13, the 5' end of a novel gene (4933435A13Rik) and three CpG islands, complete sequence [htgs_phase3]

Length: 224,034 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 108
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
  5 BAC and 5 Fosmid bridging clones.
  5 BAC and 5 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL672004.12 >99731   gaattcgctataaatcaaatcatcagttagtatggtcttgagagaacaaggtgaaaggca 99790  
AL672049.13 >1       ............................................................ 60     

AL672004.12 >99791   cagaaatggaggcttgataaaaccaaatgtttttgttttgtagctttagttttgaatcct 99850  
AL672049.13 >61      ............................................................ 120    

AL672004.12 >99851   gtaaatgttttgtataatttatataagaagcagtattttaaagtcaaagtggaggtgata 99910  
AL672049.13 >121     ............................................................ 180    

AL672004.12 >99911   cagtatcgcagaggaattaaagaacatgttaactgtcagttttcaacaggatgtacataa 99970  
AL672049.13 >181     ............................................................ 240    

AL672004.12 >99971   aggagaagacgtaattgcaaaatattttaagctgtcttaataatcgtgttgttattaata 100030 
AL672049.13 >241     ............................................................ 300    

AL672004.12 >100031  taattagaattattctggaagtattatgtgttcaggtactgggcaagaagtgagtaagat 100090 
AL672049.13 >301     ............................................................ 360    

AL672004.12 >100091  tcttggaatggtcttatttatttatttattttgtttttgagaagcatggagactaaacag 100150 
AL672049.13 >361     ............................................................ 420    

AL672004.12 >100151  actattctggggttcatgtttaaaggactcaacagtgtactgtaggagtttctgttgctt 100210 
AL672049.13 >421     ............................................................ 480    

AL672004.12 >100211  ttgtgttggacaaggtacacatcaaaattaagaataactgtgctggaatgtaaaacacat 100270 
AL672049.13 >481     ............................................................ 540    

AL672004.12 >100271  caagatgcttacattgataatcccagaatggtaccagaaaagaaaacttgaaaaacttgt 100330 
AL672049.13 >541     ............................................................ 600    

AL672004.12 >100331  tggcaacgtttgaaatatactgagacatgaaatctttcttttgaaaactgataaaaggaa 100390 
AL672049.13 >601     ............................................................ 660    

AL672004.12 >100391  atggtgtaaaggatatgtttatcttactgcaaaaaataaacgttcatgtcaactgagtgg 100450 
AL672049.13 >661     ............................................................ 720    

AL672004.12 >100451  cgaatgatacatcgataacagatgtttcaactaataaatgagcaaggagtgttggaatta 100510 
AL672049.13 >721     ............................................................ 780    

AL672004.12 >100511  gaaaaatcactattttgtgaccctaaatgagataatgcttccaaggtcatcacgggtgga 100570 
AL672049.13 >781     ............................................................ 840    

AL672004.12 >100571  accccttctttatgtgtttccctgaggaaagtccacatcacagcctacaaaatatccctg 100630 
AL672049.13 >841     ............................................................ 900    

AL672004.12 >100631  attaaaaagtgaagcctaaatctgatcaagtctttagatctgtctactattttacaggaa 100690 
AL672049.13 >901     ............................................................ 960    

AL672004.12 >100691  cagaggaatgtgctaaaacatcaccatcaggattcacttagcaaaccataaatattggaa 100750 
AL672049.13 >961     ............................................................ 1020   

AL672004.12 >100751  ttgctacaggacaaacaagctgctttcttcaaaggataaattgcagtaaagttccaaggg 100810 
AL672049.13 >1021    ............................................................ 1080   

AL672004.12 >100811  aacccagtagattaaacattttaaagacattaaaagcaattgtaacaacagactttgatt 100870 
AL672049.13 >1081    ............................................................ 1140   

AL672004.12 >100871  caggtccagactgaaacaaattaactataaagttttttagacagtttaggaaatgtgtac 100930 
AL672049.13 >1141    ............................................................ 1200   

AL672004.12 >100931  acctaataatacaaggtagaaaagattggctacgttaggcgtgaataatggtattgcggt 100990 
AL672049.13 >1201    ............................................................ 1260   

AL672004.12 >100991  tacatttttttgaaatttacctgagatgatgtattgagatttatggattaaatggtaaaa 101050 
AL672049.13 >1261    ............................................................ 1320   

AL672004.12 >101051  acaaccaaacacctggaatttgcctcagcataatgtatattgaatgactggtggtaaaag 101110 
AL672049.13 >1321    ............................................................ 1380   

AL672004.12 >101111  tgaaataggattgcttcaggggaatttgaacttgagtgatagaatacttgacattccctt 101170 
AL672049.13 >1381    ............................................................ 1440   

AL672004.12 >101171  attttttaaaaaatatacctgaatttttatataggttaaacatacttcctttaaattata 101230 
AL672049.13 >1441    ............................................................ 1500   

AL672004.12 >101231  cagtaaaactaatatttcttagaatttcagaaaaaatagctgtcaaaataaaataacacc 101290 
AL672049.13 >1501    ............................................................ 1560   

AL672004.12 >101291  cattttagcattttaatatattaattttattgatttaatgaaatagaaataaggtaaact 101350 
AL672049.13 >1561    ............................................................ 1620   

AL672004.12 >101351  cagtgttccatggtgcagtcttggaaaattgcctaagatgcttagtaagaaaatctagca 101410 
AL672049.13 >1621    ............................................................ 1680   

AL672004.12 >101411  atcaaacacttctcctgtccccaaattttatggtggcaggttgatatggttataatagac 101470 
AL672049.13 >1681    ............................................................ 1740   

AL672004.12 >101471  ttgacaggtttcatgcatgtcatgctgttaatagctaaaagctagtccacatgggaaaga 101530 
AL672049.13 >1741    ............................................................ 1800   

AL672004.12 >101531  tttatttccactaatattttcttttaggcatttgacattgtcacagactgacatggctgc 101590 
AL672049.13 >1801    ............................................................ 1860   

AL672004.12 >101591  attaacaggaggaaaggtaatacctttactaagattaaacaattcagtcattctaaaaat 101650 
AL672049.13 >1861    ............................................................ 1920   

AL672004.12 >101651  gatatagtagttctcaaacgaacaacttgtgtttttaacagggatttcccttcttatttc 101710 
AL672049.13 >1921    ............................................................ 1980   

AL672004.12 >101711  aacacattcgtgatggcatc 101730 
AL672049.13 >1981    .................... 2000

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	101730	2001	+	+	chenhc	Taxid 10090 chrom 11 Reference assembly	2008-11-20 16:56:36.940

Events

Id	Type	Date	Whodid	Comment
211	ImportOldDb	09/02/2005 07:34:00	f_old_db
212	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174071	CreateSwitchPt	11/20/2008 16:56:36	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-106A9				AL672049.13	99.3%	pos 17809 (F-)
C3H-12C17				AL672049.13	99.43%	pos 89733 (F+)
C3H-143C6				AL672004.12	100%	pos 11681 (F-)
C3H-144E18				AL672049.13	99.33%	pos 113904 (F-)
C3H-238B10				AL672049.13	99.87%	pos 35845 (F-)
C3H-90G23	AL672049.13	99.5%	pos 207734 (R+)
CH29-115B17				AL672004.12	99.22%	pos 98864 (F-)
CH29-178N19				AL672049.13	99.51%	pos 145353 (F-)
CH29-181A20	AL672049.13	99.14%	pos 38259 (R-)
CH29-35H19	AL672004.12	99.26%	pos 63694 (R+)
CH29-37O12	AL672004.12	99.61%	pos 28612 (R+)	AL672049.13	99.8%	pos 156208 (F-)
CH29-38C11				AL672049.13	99.75%	pos 49651 (F-)
CH29-491F16				AL672004.12	100%	pos 35681 (F-)
CH29-499I16				AL672049.13	100%	pos 103100 (F-)
CH29-500H17	AL672049.13	99.37%	pos 141830 (R-)
CH29-533C19				AL672004.12	100%	pos 63260 (F-)
CH29-555C10	AL672049.13	100%	pos 163073 (R-)	AL672004.12	99.01%	pos 28619 (F+)
CH29-560N8				AL672049.13	99.87%	pos 209405 (F+)
CH29-564H6				AL672049.13	99.87%	pos 108469 (F+)
CH29-564K6				AL672049.13	99.29%	pos 108418 (F+)
CH29-566C12	AL672049.13	99.59%	pos 89053 (R-)
CH29-579B19	AL672004.12	99.87%	pos 98977 (R+)	AL672049.13	100%	pos 191992 (F-)
CH29-605K22	AL672049.13	99.23%	pos 215499 (R-)
RP23-342K2				AL672049.13	99.19%	pos 217275 (F-)
RP24-118G13	AL672049.13	99.82%	pos 169766 (R+)
RP24-212A2	AL672004.12	99.37%	pos 44309 (R+)
RP24-290O7	AL672049.13	100%	pos 36308 (R-)
RP24-291C8	AL672049.13	99.66%	pos 89854 (R-)	AL672004.12	99.08%	pos 15634 (F+)
RP24-297N11	AL672049.13	99.17%	pos 116788 (R+)
RP24-342K12	AL672049.13	99.23%	pos 90122 (R-)	AL672004.12	99.03%	pos 35933 (F+)
RP24-363F17				AL672049.13	99.34%	pos 49533 (F-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1037B16				AL672004.12	100%	pos 21062 (F-)
WI1-108B7	AL672049.13	99.73%	pos 201575 (R-)	AL672049.13	99.54%	pos 160897 (F+)
WI1-110M23	AL672049.13	99.36%	pos 42176 (R+)	AL672049.13	100%	pos 78394 (F-)
WI1-1179M3	AL672004.12	100%	pos 53145 (R+)	AL672004.12	100%	pos 91854 (F-)
WI1-1196H10	AL672049.13	100%	pos 7910 (R-)	AL672004.12	99.78%	pos 70371 (F+)
WI1-1210C15	AL672049.13	99.44%	pos 25851 (R-)
WI1-1224E15	AL672004.12	100%	pos 76300 (R-)	AL672004.12	100%	pos 37037 (F+)
WI1-1228B17	AL672004.12	100%	pos 66096 (R-)
WI1-1244J19	AL672049.13	100%	pos 32921 (R+)	AL672049.13	99.21%	pos 63401 (F-)
WI1-1300G20	AL672004.12	99.77%	pos 89239 (R+)
WI1-1300L7	AL672004.12	100%	pos 89256 (R+)
WI1-1310C14	AL672004.12	99.5%	pos 13165 (R+)	AL672004.12	100%	pos 51594 (F-)
WI1-1382F16	AL672049.13	100%	pos 24956 (R+)	AL672049.13	99.71%	pos 64495 (F-)
WI1-1397P11	AL672004.12	99.7%	pos 53612 (R-)	AL672004.12	100%	pos 15031 (F+)
WI1-142O7	AL672004.12	100%	pos 40776 (R-)
WI1-1444B6	AL672049.13	99.63%	pos 2087 (R+)	AL672049.13	100%	pos 42083 (F-)
WI1-1612L21	AL672049.13	99.86%	pos 9060 (R-)	AL672004.12	99.85%	pos 74009 (F+)
WI1-1622E3	AL672049.13	100%	pos 135187 (R+)	AL672049.13	100%	pos 174842 (F-)
WI1-1647D6	AL672004.12	99.58%	pos 80336 (R+)	AL672049.13	100%	pos 19251 (F-)
WI1-1653L13	AL672004.12	100%	pos 17732 (R+)
WI1-1703F18	AL672049.13	99.57%	pos 126982 (R-)	AL672049.13	99.81%	pos 83235 (F+)
WI1-1843P4	AL672004.12	100%	pos 64433 (R+)	AL672004.12	100%	pos 101009 (F-)
WI1-1843P4				AL672049.13	100%	pos 1279 (F-)
WI1-1944G19	AL672049.13	100%	pos 73600 (R+)	AL672049.13	99.72%	pos 115370 (F-)
WI1-1970M15	AL672049.13	99.5%	pos 210698 (R-)
WI1-2043L12	AL672004.12	99.73%	pos 72989 (R-)	AL672004.12	99.5%	pos 31980 (F+)
WI1-2080D17	AL672049.13	100%	pos 162900 (R-)	AL672049.13	100%	pos 123161 (F+)
WI1-2197L20	AL672049.13	99.82%	pos 112644 (R-)	AL672049.13	99.67%	pos 71446 (F+)
WI1-2219P7	AL672049.13	99.78%	pos 60596 (R+)	AL672049.13	100%	pos 99657 (F-)
WI1-2283P12	AL672004.12	99.57%	pos 38849 (R+)	AL672004.12	100%	pos 81704 (F-)
WI1-2312C20				AL672049.13	99.8%	pos 194123 (F+)
WI1-2331H15				AL672004.12	99.69%	pos 13471 (F+)
WI1-245F16	AL672049.13	99.69%	pos 89650 (R+)	AL672049.13	100%	pos 135245 (F-)
WI1-2622D4	AL672049.13	100%	pos 210698 (R-)	AL672049.13	99.66%	pos 177677 (F+)
WI1-272O14				AL672049.13	100%	pos 167869 (F-)
WI1-2785L9	AL672049.13	100%	pos 165694 (R-)	AL672049.13	99.82%	pos 126019 (F+)
WI1-289C11	AL672049.13	100%	pos 4666 (R+)	AL672049.13	99.78%	pos 43070 (F-)
WI1-324H16	AL672049.13	99.61%	pos 42289 (R+)	AL672049.13	99.81%	pos 80651 (F-)
WI1-348O16				AL672004.12	99.65%	pos 17301 (F-)
WI1-519E23	AL672004.12	100%	pos 38871 (R-)
WI1-547L19				AL672049.13	99.79%	pos 2683 (F+)
WI1-588P16	AL672049.13	99.25%	pos 217857 (R-)	AL672049.13	99.11%	pos 177828 (F+)
WI1-620F8	AL672049.13	100%	pos 80472 (R-)	AL672049.13	100%	pos 41556 (F+)
WI1-680B12	AL672049.13	99.32%	pos 42206 (R+)	AL672049.13	100%	pos 78726 (F-)
WI1-879G4	AL672004.12	99.5%	pos 84326 (R+)	AL672049.13	99.84%	pos 24116 (F-)
WI1-879G4	AL672004.12	100%	pos 84327 (R+)	AL672049.13	100%	pos 24117 (F-)
WI1-946K7	AL672004.12	100%	pos 43554 (R+)	AL672004.12	100%	pos 83643 (F-)

NCBI

Join Evaluation Legend

Curator Links

Alignment for AL672004.12 and AL672049.13

Alignment Summary

Alignment 1 of 1