BAC Information

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BAC

Clone NameMSMg01-089C09
Chromosome12 (Build37)
Map Location 62,498,756 - 62,594,796
singlet/doubletdoublet
Overlap geneNanog-ps2
Upstream geneLOC665665, Ppia-ps12_475.1, LOC100040300, LOC665677
Downstream geneLrfn5, LOC665699, LOC665707, LOC100040403, LOC665713, LOC622746, LOC100040438
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-089C09.T7 (MSMg01no089_c09.b1)MSMg01-089C09.TJ (MSMg01no089_c09.g1)
ACCAG307721AG307722
length714678
length of high quality
(start - end)
337 (36 - 372)233 (105 - 337)
definitionCHROMAT_FILE: MSMg01no089_c09.b1 PHD_FILE: MSMg01no089_c09.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:41:51 2005CHROMAT_FILE: MSMg01no089_c09.g1 PHD_FILE: MSMg01no089_c09.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:41:51 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(62,498,756 - 62,499,089)(62,594,564 - 62,594,796)
sequence
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAATTCCATAC
ATCTATCTGAGCTATTGACATTGTTCATTGTGTTAAGATACTGGTTTTGA
GGATAACATATTTCTGAGTCATAGATCATGGGGAAATCAAACTTTCCATC
TAGTGCAATTAGCTCATGACATATGAAAACTGGTAGAGATCTGATTGCAG
TATTCTTATTACAGAGGGCCTTAATTTCAGTCATTATTATAAAGGGCACA
ATAATTATTAATATAAATTTAGGAATTATCATTGAATCATCATTAAAAAT
TAAGAAATCATTTTTCTACGTAGCATCATTATATTACAGTACATCTTTAT
TGATCTGTACAAAATCTGGCCAATAGGGTGGCCTAATACCCAGGAATTTT
TATATCAACCCAACAATTAATGTACGGACATATCAATAACAAGAATCTAC
CCTGAGATTAGCTTATCAAGCCTCCACAGGGTCAAGGTTCTAGTCTCCCA
TTGATGCTGGATAAGTCACATCTCTGCTACTTATGTTGCCAGAGCAATCG
ATAGCTTTTTTGCACCCTTCGTCCTGCTGTTTTACCCTTTTGTTTACCCC
TTTTCCCCTTTTTTTCACCTTTATCCTCTTTCGCTTCCCCCTTATCTTCT
TTTTTTTTTTATTTTTTTCCCCCCCTTCTTCCATCTCTCTAATTTATTCC
CCCCCCCCCCTTCT
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXCTTTCAATCACAGTGAGAGAAATAGGACTCATTTTTAAAGTTTAC
CCTTTTACATATATGCACACACACATGCAGTTAGCCATACATGCATGCAC
ACACACATACATGTGAGCACACATGCACACACATGTTCAGCATGCTTACA
CATCAGAGAAATGCAAATCAAAACAAGCCTCAAGTTTGTTATAGTTTGAC
TTAATGGACATAAGAACAAACAGCCCTTTATATTTTTATCTTTCTACACA
GAGTTTAGAGTAGTTTTCAGATCTAATCACAGAATGTCTTTGTGTTCATC
CGGCCCCCAAACATTGAAGCATACAATTGATAATAACATGAAGAACAAAT
GACTATGAAGTATACTATCATCAATGGCACATTATATTATTATATTATAA
CACCCTACCTAAAGGATCAGATCACGAGCATCTTGTAATAGGGAACGCAA
AGAGCGTATAAGATAGGAAAAACAGAGAAAAAATAATTTTTCTTGACATG
ATAGAAGCACTATATCCTTCCTCTCATACCACCTGTGGTTATCTGTCAAA
GATCTACATACAACTCATCTAAGCTTATATTCCATCATGCCTCACACCTT
TCATGTCCTCACTCCTAACTGATGACTA
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no089_c09.b1 MSMg01no089_c09.b1 CHROMAT_FILE:
MSMg01no089_c09.b1 PHD_FILE: MSMg01no089_c09.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:41:51 2005
         (337 letters)



>mm_chr12_62498553_62499289
          Length = 737

 Score =  607 bits (314), Expect = e-178
 Identities = 329/334 (98%)
 Strand = Plus / Plus

                                                                       
Query: 4   ggaattccatacatctatctgagctattgacattgttcattgtgttaagatactggtttt 63
           |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Sbjct: 204 ggaattccatacatctatatgagctattgacattgttcattgtgttaagatactggtttt 263

                                                                       
Query: 64  gaggataacatatttctgagtcatagatcatggggaaatcaaactttccatctagtgcaa 123
           ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 264 gaggataacatatttttgagtcatagatcatggggaaatcaaactttccatctagtgcaa 323

                                                                       
Query: 124 ttagctcatgacatatgaaaactggtagagatctgattgcagtattcttattacagaggg 183
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 324 ttagctcatgacatatgaaaactggtagagatctgattgcagtattcttattacagaggg 383

                                                                       
Query: 184 ccttaatttcagtcattattataaagggcacaataattattaatataaatttaggaatta 243
           ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct: 384 ccttaatttcagtcattattataaagggcacaataattattaatacaaatttaggaatta 443

                                                                       
Query: 244 tcattgaatcatcattaaaaattaagaaatcatttttctacgtagcatcattatattaca 303
           ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 444 tcattgaatcatcattaaaaattaagaaatcatttttctccgtagcatcattatattaca 503

                                             
Query: 304 gtacatctttattgatctgtacaaaatctggcca 337
           ||||||||||||||||||||| ||||||||||||
Sbjct: 504 gtacatctttattgatctgtaaaaaatctggcca 537


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.34    0.600     1.10 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 2, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 16
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 337
Length of database: 737
Length adjustment: 9
Effective length of query: 328
Effective length of database: 728
Effective search space:   238784
Effective search space used:   238784
X1: 8 (15.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 8 (16.4 bits)
S2: 8 (16.2 bits)
Query= MSMg01no089_c09.g1 MSMg01no089_c09.g1 CHROMAT_FILE:
MSMg01no089_c09.g1 PHD_FILE: MSMg01no089_c09.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:41:51 2005
         (233 letters)



>mm_chr12_62594232_62594864
          Length = 633

 Score =  404 bits (209), Expect = e-117
 Identities = 227/233 (97%)
 Strand = Plus / Minus

                                                                       
Query: 1   ttacatatatgcacacacacatgcagttagccatacatgcatgcacacacacatacatgt 60
           |||||||||||||||||| |||||||||||||||||||||| ||||||||||||||||||
Sbjct: 565 ttacatatatgcacacacgcatgcagttagccatacatgcacgcacacacacatacatgt 506

                                                                       
Query: 61  gagcacacatgcacacacatgttcagcatgcttacacatcagagaaatgcaaatcaaaac 120
           ||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||
Sbjct: 505 gagcacacatgcacacacatgttcagcatgcttacccatcagagtaatgcaaatcaaaac 446

                                                                       
Query: 121 aagcctcaagtttgttatagtttgacttaatggacataagaacaaacagccctttatatt 180
           |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct: 445 aagcctcaagtttgttatagtttgacttaatggacataagaacaaacaaccctttatatt 386

                                                                
Query: 181 tttatctttctacacagagtttagagtagttttcagatctaatcacagaatgt 233
           |||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 385 tttatctttctacacagagtttagtgtagttttcagatctaatcacagaatgt 333


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.34    0.600     1.10 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 2, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 8
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 233
Length of database: 633
Length adjustment: 9
Effective length of query: 224
Effective length of database: 624
Effective search space:   139776
Effective search space used:   139776
X1: 7 (13.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 7 (14.4 bits)
S2: 7 (14.3 bits)