BAC Information

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BAC

Clone NameMSMg01-336J03
Chromosome2 (Build37)
Map Location 74,415,241 - 74,564,943
singlet/doubletdoublet
Overlap geneLnp, LOC100040519, Evx2, Hoxd13, Hoxd12, Hoxd11, Hoxd10, Hoxd9, Hoxd8, 1700109F18Rik, Hoxd3, Hoxd4
Upstream geneChrna1, Chn1, Atf2, Atp5g3, LOC667729, LOC100040172
Downstream geneLOC667804, Hoxd1, Mtx2, LOC667817, A330043C09Rik, LOC667739, LOC545423, LOC100040324, LOC667828, Hnrpa3, Nfe2l2, E030042O20Rik
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-336J03.T7 (MSMg01no336_j03.b1)MSMg01-336J03.TJ (MSMg01no336_j03.g1)
ACCAG451557AG451558
length728725
length of high quality
(start - end)
422 (44 - 465)323 (307 - 629)
definitionCHROMAT_FILE: MSMg01no336_j03.b1 PHD_FILE: MSMg01no336_j03.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 22:24:40 2005CHROMAT_FILE: MSMg01no336_j03.g1 PHD_FILE: MSMg01no336_j03.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 22:24:40 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(74,564,526 - 74,564,943)(74,415,241 - 74,415,563)
sequence
ATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAA
TTCTCCTACTGGGGTGCAAAATAAGGAAGAATGAGTGTGGGCAATGTGGC
CTCCGAGTTGGGTAGAGTCCTAGGCAGGCAGGCAGGCTGCCCGGCCAGCT
GGCAGGAGTCCTGGACTCTGACATACAAAGACCTGTCTTGGCTTTGTCTT
CATCAGGGTCACCCAAAAGTTACCAGAATCTGGCGGACCTGAATTGAGTT
AGGCAATGAGTAACCACTATGCTTTTCTGCCAATGCCCAGGCTGGGGTGT
TTCTAGTTGAAGTTGGATCTTTCTGCAGGAGGCCCTCACAGTTCTGAGTC
TGGTGGCTGAGGGGTTGGGTCATATTGGGATGGTGGGGAGGGGGACCTTA
ACCTTGCCTAAATGTACCCCAACGGTCTCCGATGGCCTATCTTTCAGTTT
GTCTTCTTCCCACACAAGGGCAGGTGAGCCCCATTTGGGAACCTTTGTGT
CTCATGCTCCTTCAGAGCAGGGCTTCTGCTGGAGCTTTCTGGCCTTTCCC
CTCACTCTCTAATACCCTACAAGCTGGCCCTCTGGNTTTACACTCAAACA
ACCACTTGAGTACCTACTGGAAGATCCATAGGAGATTCTTCTGGAAATTG
CCGTACATTTCCCCCCGNGCAAATCCAGTTCCCTCGCCGTTCATGTCACG
TAACAAGAACACGTTGTATCCCCCCCCA
TGCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXTCAACTCACTTCAAATCACATTAAAACAA
TGGGATAAGGATTCAAAACATGGCTCAGCCATTTACCAGCTATATGATCT
TAAACTTAGAGAGTTCTTAAACTCTGAGCTTTGGCTAATAAAGCAGTTAG
AATATTTACATTCCTTGGAATTGTATAAATTTAGTGAACTTATTTATCAC
TTGGCACAGTATTTAGCACATAGTATTTAGGTAATTTTXXXXXXXXXXXX
XXXXXXTACCAAAACCACATGTAATATCTAAATGAAGCATGTGCCTAACA
TTCCATTAAATGAGTGCATATTTTAATTATTTCATAATTTAAAATCTGTA
AGTATAAAATAAGTTTGTGTTTTTACTAAAAATATTTTTCTCATTTACCC
TAGCATGGAAATAAATAAATGGAGTATTTTTCAAGCACTTCCCATTATAA
TAAACGTATAAGCCTTCATAGAAAACAACAAAAGAAATGGAGTTTTGTGG
TTTTTAACCTTTGATTCCAAACTTAAATATAAACTAGTCACCTTTAACAG
CATCTCCACATTATACTACACAATTTGGGTTTAGATGTGATTTGTTCGAA
ATCGCTTTCCAATGTCCAAATAGGCAACTCTGAAATATCTTACACCAGGG
TTATTGCCCAAAAAAAAAAACAAAN
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no336_j03.b1 MSMg01no336_j03.b1 CHROMAT_FILE:
MSMg01no336_j03.b1 PHD_FILE: MSMg01no336_j03.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 22:24:40 2005
         (422 letters)



>mm_chr2_74564322_74565143
          Length = 822

 Score =  801 bits (414), Expect = 0.0
 Identities = 417/418 (99%)
 Strand = Plus / Minus

                                                                       
Query: 5   gaattctcctactggggtgcaaaataaggaagaatgagtgtgggcaatgtggcctccgag 64
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 622 gaattctcctactggggtgcaaaataaggaagaatgagtgtgggcaatgtggcctccgag 563

                                                                       
Query: 65  ttgggtagagtcctaggcaggcaggcaggctgcccggccagctggcaggagtcctggact 124
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 562 ttgggtagagtcctaggcaggcaggcaggctgcccggccagctggcaggagtcctggact 503

                                                                       
Query: 125 ctgacatacaaagacctgtcttggctttgtcttcatcagggtcacccaaaagttaccaga 184
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 502 ctgacatacaaagacctgtcttggctttgtcttcatcagggtcacccaaaagttaccaga 443

                                                                       
Query: 185 atctggcggacctgaattgagttaggcaatgagtaaccactatgcttttctgccaatgcc 244
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
Sbjct: 442 atctggcggacctgaattgagttaggcaatgagtaaccactatgcttttctgccaatgcg 383

                                                                       
Query: 245 caggctggggtgtttctagttgaagttggatctttctgcaggaggccctcacagttctga 304
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 382 caggctggggtgtttctagttgaagttggatctttctgcaggaggccctcacagttctga 323

                                                                       
Query: 305 gtctggtggctgaggggttgggtcatattgggatggtggggagggggaccttaaccttgc 364
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 322 gtctggtggctgaggggttgggtcatattgggatggtggggagggggaccttaaccttgc 263

                                                                     
Query: 365 ctaaatgtaccccaacggtctccgatggcctatctttcagtttgtcttcttcccacac 422
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 262 ctaaatgtaccccaacggtctccgatggcctatctttcagtttgtcttcttcccacac 205


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: 19
Number of extensions: 2
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: 422
Length of database: 822
Length adjustment: 9
Effective length of query: 413
Effective length of database: 813
Effective search space:   335769
Effective search space used:   335769
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= MSMg01no336_j03.g1 MSMg01no336_j03.g1 CHROMAT_FILE:
MSMg01no336_j03.g1 PHD_FILE: MSMg01no336_j03.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 22:24:40 2005
         (323 letters)



>mm_chr2_74415041_74415763
          Length = 723

 Score =  625 bits (323), Expect = 0.0
 Identities = 323/323 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   taccaaaaccacatgtaatatctaaatgaagcatgtgcctaacattccattaaatgagtg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 201 taccaaaaccacatgtaatatctaaatgaagcatgtgcctaacattccattaaatgagtg 260

                                                                       
Query: 61  catattttaattatttcataatttaaaatctgtaagtataaaataagtttgtgtttttac 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 261 catattttaattatttcataatttaaaatctgtaagtataaaataagtttgtgtttttac 320

                                                                       
Query: 121 taaaaatatttttctcatttaccctagcatggaaataaataaatggagtatttttcaagc 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 321 taaaaatatttttctcatttaccctagcatggaaataaataaatggagtatttttcaagc 380

                                                                       
Query: 181 acttcccattataataaacgtataagccttcatagaaaacaacaaaagaaatggagtttt 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 381 acttcccattataataaacgtataagccttcatagaaaacaacaaaagaaatggagtttt 440

                                                                       
Query: 241 gtggtttttaacctttgattccaaacttaaatataaactagtcacctttaacagcatctc 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 441 gtggtttttaacctttgattccaaacttaaatataaactagtcacctttaacagcatctc 500

                                  
Query: 301 cacattatactacacaatttggg 323
           |||||||||||||||||||||||
Sbjct: 501 cacattatactacacaatttggg 523


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: 323
Length of database: 723
Length adjustment: 9
Effective length of query: 314
Effective length of database: 714
Effective search space:   224196
Effective search space used:   224196
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)