BAC Information

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BAC

Clone NameMSMg01-403F12
Chromosome9 (Build37)
Map Location 42,030,947 - 42,209,292
singlet/doubletdoublet
Overlap geneSc5d, Tecta
Upstream geneLOC100042464, EG667566, 6720432D03Rik, Sorl1
Downstream geneTbcel, Grik4, Arhgef12, LOC545339, Tmem136, Pou2f3, LOC628726, Oaf, D630033O11Rik, Trim29
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-403F12.T7 (MSMg01no403_f12.b1)MSMg01-403F12.TJ (MSMg01no403_f12.g1)
ACCAG502276AG502277
length766750
length of high quality
(start - end)
399 (62 - 460)243 (69 - 311)
definitionCHROMAT_FILE: MSMg01no403_f12.b1 PHD_FILE: MSMg01no403_f12.b1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:17:35 2005CHROMAT_FILE: MSMg01no403_f12.g1 PHD_FILE: MSMg01no403_f12.g1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:17:36 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(42,030,947 - 42,031,345)(42,209,050 - 42,209,292)
sequence
TXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAATT
CATTTTTACCAAAAGGGAACAATTAAAATAAAGAGAGAAAGGAAGGAAGA
AAGGAAGAAAGAAAGGAAGGAAGAAGGAAGGAAGGGAAAAGGGAGGGAAG
GAAATCCTCTCTTACCCCCAGAGATTGGGTAAATCTATAGCTATAGTACC
AATCCTAGGAAAGACCTAGCTTGAAATCAGACAGACAAAGGTGACTAATG
ATGCTTCCTATGAGGCTTGCCAGCTCTCTAGCCCCAGATACTTCTTCACA
TGGTCTTGCTTGTTTGTCAATGGCTTATTTGGTCTTTCTCCTTGTTACTC
TCCATTTGATTCTACTTTGGCAATGGTGGTCATATTCACCTCAATGCTCT
CAGTTAAAGAATTTATTTAATTTTTAATTATGTGTATATATGTGTGTTGG
TGGGTATGTGCACAGGAGTGTAGTGTCCCCCGAGGCTTTAAAAGGACTTC
ATATTTCCCCCCGCTGGAGCCTCACATGGTTGTGAGCTGCCCAACGTTTT
TGCCTTGCCTCCCTTTTTCCGTCTGCCGTTCTTTATTGTCTGACGCTTTC
CCCTTTCTTTCCATCCCCTTTTTCCCTCGGCCCCTCCTCCTCCCGCTTTT
TCTTCTCTCTTCTCCTTCGCCCACGTTTTCTTCCTCTCTCGTTTTTCCTC
CATTTTTCCGTTTTTTCTCCCCCCTCCTCCCCTTTTTCCCTCTTCTCCCC
GTTTTCTCCTTTTCTT
GCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXTGCCTCAAGAAATTCACGTTACCAGCGAAAGAATGAACACATTG
TGTAATGCCTACACAGCTATCACAGGGCTTTGGCTGAAGACGGGGAAACG
TATGGCAAAGACCAGGTTCTCCCAACACTCTTGGCCTTTAGCACAGCATA
TGCAAAGCTGGGTTGTTTTGATTCAGTTCTTATTTCTGGTCTAGGTAACA
CATCAGGGTCTGGCCAGAGAAAGATCTGGACAGATTTAAAATTCCAATCG
ATTTGATTTACTAATGNATCTTTCCTGCTGCATCCAAATTATTTCTTCTT
GTTCTTTTTATGAATGCCCCTTTGAGTATTTTAATTTCTGCGGTACTTTC
ACAGTCTTCTGCATGTTTAAATTTTTCTTAGAGATGTTTGTACATGAGGA
GTGTGTCTCCACCACTCCTTCCTTCAAACTTCCCCTTCCAGATTCATGAG
CTCTTCTTTAATTTTTATTCTTACATAGACACACATACATGTATGTGTGT
GTGTGCGTGTGCGCCCTACTCCCTCCTCCCCCCTTTTTTTTCATTCCTCC
CCCCCTCCCCCCCCCCCCTTCCCCCCCCCCCACCCGTTCTTTTTTTTTTT
TTTTTTTCCCCTTTCCTCCCTCCTTTTTCCCCCTTTCCTCTTCCCCCCCT
CCCTATCCCCTTTTTTCTTCCCTTTTCTCCCTTAAACCCTCTTTACCCCT

quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no403_f12.b1 MSMg01no403_f12.b1 CHROMAT_FILE:
MSMg01no403_f12.b1 PHD_FILE: MSMg01no403_f12.b1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 18:17:35 2005
         (399 letters)



>mm_chr9_42030747_42031545
          Length = 799

 Score =  772 bits (399), Expect = 0.0
 Identities = 399/399 (100%)
 Strand = Plus / Plus

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

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

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

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

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

                                                                       
Query: 301 ctactttggcaatggtggtcatattcacctcaatgctctcagttaaagaatttatttaat 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 501 ctactttggcaatggtggtcatattcacctcaatgctctcagttaaagaatttatttaat 560

                                                  
Query: 361 ttttaattatgtgtatatatgtgtgttggtgggtatgtg 399
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 561 ttttaattatgtgtatatatgtgtgttggtgggtatgtg 599


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: 23
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: 399
Length of database: 799
Length adjustment: 9
Effective length of query: 390
Effective length of database: 790
Effective search space:   308100
Effective search space used:   308100
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= MSMg01no403_f12.g1 MSMg01no403_f12.g1 CHROMAT_FILE:
MSMg01no403_f12.g1 PHD_FILE: MSMg01no403_f12.g1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 18:17:36 2005
         (243 letters)



>mm_chr9_42208850_42209492
          Length = 643

 Score =  439 bits (227), Expect = e-128
 Identities = 239/243 (98%)
 Strand = Plus / Minus

                                                                       
Query: 1   ttcacgttaccagcgaaagaatgaacacattgtgtaatgcctacacagctatcacagggc 60
           |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct: 443 ttcacgttaccagcgaaagaatgaacacattgtgtaatgcctacacagttatcacagggc 384

                                                                       
Query: 61  tttggctgaagacggggaaacgtatggcaaagaccaggttctcccaacactcttggcctt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 383 tttggctgaagacggggaaacgtatggcaaagaccaggttctcccaacactcttggcctt 324

                                                                       
Query: 121 tagcacagcatatgcaaagctgggttgttttgattcagttcttatttctggtctaggtaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Sbjct: 323 tagcacagcatatgcaaagctgggttgttttgattcagttcttatttctggtctaggcaa 264

                                                                       
Query: 181 cacatcagggtctggccagagaaagatctggacagatttaaaattccaatcgatttgatt 240
           |||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||
Sbjct: 263 cacatcagggtctggccagagaaagacctggacagatttaaaattccaattgatttgatt 204

              
Query: 241 tac 243
           |||
Sbjct: 203 tac 201


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: 9
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: 243
Length of database: 643
Length adjustment: 9
Effective length of query: 234
Effective length of database: 634
Effective search space:   148356
Effective search space used:   148356
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)