BAC Information

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BAC

Clone NameMSMg01-058F04
Chromosome4 (Build37)
Map Location 66,349,807 - 66,505,800
singlet/doubletdoublet
Overlap geneLOC667499, Tlr4
Upstream geneAstn2
Downstream geneLOC100039379, Hmgb1-rs18
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-058F04.T7 (MSMg01no058_f04.b1)MSMg01-058F04.TJ (MSMg01no058_f04.g1)
ACCAG285265AG285266
length718721
length of high quality
(start - end)
280 (37 - 316)288 (66 - 353)
definitionCHROMAT_FILE: MSMg01no058_f04.b1 PHD_FILE: MSMg01no058_f04.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:00:32 2005CHROMAT_FILE: MSMg01no058_f04.g1 PHD_FILE: MSMg01no058_f04.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:00:32 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(66,349,807 - 66,350,083)(66,505,513 - 66,505,800)
sequence
TGCGGCCGCTATACGACTCCTATTTCGAGAGGAGCCGCGGAATTCTTATT
ATTATCTTGTCAAGGGTTCCTCAGAATAAAATTTTATCCTGAGTGCCCAA
TTTCTAGGACTACTTCCAATTCCAATTGTCTTCCCCTGAAATTTCCCAAA
AGCATATTCAGGTACCAAGCTCAACCCAAAGTGAATTTGTAGTTATAAAT
TCCCAGAAGTATGGCTAGAGAGATGACTAGAAGTTAAAGGCTCCTGCTAC
ACTTGCCGATGACGGGGAGTTCAGTTCTCAGCATCCAGGCTGTGATGTTC
ACAAACACCTAAATTGTATCTCAAGAGGATCTGAAACCTTCTTCTGCTCT
CTGTGTGCACCTTTATATGCCACAAATGTACCTGCACACAGACAGCCTGA
CAGACAGACTCTCGTTATATTCTTTTTCATTGATAAAAGAGGCCCACCAA
CCGATGAATTACAGCGAGCTACTACTTGGCTGAGTGGTGAGCCGTTACTT
ATTGTATGCCATTAACGGTTGTACATTCTCGCCCACCCCTCCCCCAAAAA
CAAACTTTTCAGTATGTTGAAACCCGCATATGACCCATTACGAATAGCCC
CGCTGCACTATGGTATTCGTATATACCGTCCCCCCCCACCCAACCCCAAT
TTAACAACCCCACCATTTTATAACCACTAAATCCCCATATCAAACCCCGC
AACCTTTCACCGTTTTGN
GTGAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXTCACAATAGCAAACAATAAATAATTAAAAATACAG
AACAGTGCCATTCAACTCTTGACATAAAACAAAAGAGAACAGTAGAGAAA
CTATTAAATAAAGTCAGTTTGATAATTAGTTTTGCCCATTTAATGCCTGT
GTACTTTGGATGTGTTAAGAAAAATCTTGAAGCCTGTGATTTTGTGAATG
TTTATCAAATCGGCATAGCATGCAAAACTTACTCAAATATTAACCAGCTG
AATATAATTTTAATGTATCCATTATAGAACACTATTGTTAGAACTACGCC
CCCCTTCCATACACACCTTCCACAAAATTTTAGAATACATGGCGTTAAGC
ACCCACGCCACTAAGCTATTTATATCATCCATACAAAGGGAAAGACAGGG
AAAACTAATTTGACCGCTAAGATCCCTATTACTTTACATTCTGAACTGGA
ATGTATCTAGGACAATAGTACACCATGACAAAATGCCCCACTGATTCTCT
TTCTTCTTCACGAATACATGCAAATGTCTGCTTCCCTCCGTTACGGAATG
ATGTCTCTAATACCACGACGCCCATACATATGGCCATATAAATGGCCCCT
CCCATATCCCCATTTGAACCCACCGACAAACCTTAGTAACACACTATGAC
TAATTGCTTTCTCTTTTAACT
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no058_f04.b1 MSMg01no058_f04.b1 CHROMAT_FILE:
MSMg01no058_f04.b1 PHD_FILE: MSMg01no058_f04.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:00:32 2005
         (280 letters)



>mm_chr4_66349604_66350283
          Length = 680

 Score =  489 bits (253), Expect = e-143
 Identities = 271/277 (97%)
 Strand = Plus / Plus

                                                                       
Query: 4   gaattcttattattatcttgtcaagggttcctcagaataaaattttatcctgagtgccca 63
           ||||||||||||| || |||||||||| ||||||||||||||||||||||||||||||||
Sbjct: 204 gaattcttattatgatattgtcaagggctcctcagaataaaattttatcctgagtgccca 263

                                                                       
Query: 64  atttctaggactacttccaattccaattgtcttcccctgaaatttcccaaaagcatattc 123
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 264 atttctaggactacttccaattccaattgtcttcccctgaaatttcccaaaagcatattc 323

                                                                       
Query: 124 aggtaccaagctcaacccaaagtgaatttgtagttataaattcccagaagtatggctaga 183
           |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 324 aggtaccaagctcaacccaaagtgaatttgtagttacaaattcccagaagtatggctaga 383

                                                                       
Query: 184 gagatgactagaagttaaaggctcctgctacacttgccgatgacggggagttcagttctc 243
           ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Sbjct: 384 gagatgactagaagttaaaggctcctgctacacttgcagatgacggggagttcagttctc 443

                                                
Query: 244 agcatccaggctgtgatgttcacaaacacctaaattg 280
            ||||||||||||||||||||||||||||||||||||
Sbjct: 444 ggcatccaggctgtgatgttcacaaacacctaaattg 480


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: 10
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: 280
Length of database: 680
Length adjustment: 9
Effective length of query: 271
Effective length of database: 671
Effective search space:   181841
Effective search space used:   181841
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)
Query= MSMg01no058_f04.g1 MSMg01no058_f04.g1 CHROMAT_FILE:
MSMg01no058_f04.g1 PHD_FILE: MSMg01no058_f04.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:00:32 2005
         (288 letters)



>mm_chr4_66505313_66506000
          Length = 688

 Score =  487 bits (252), Expect = e-142
 Identities = 279/288 (96%)
 Strand = Plus / Minus

                                                                       
Query: 1   tcacaatagcaaacaataaataattaaaaatacagaacagtgccattcaactcttgacat 60
           |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct: 488 tcacaatagcaaacaataaataattaaaaatacagaacagtggcattcaactcttgacat 429

                                                                       
Query: 61  aaaacaaaagagaacagtagagaaactattaaataaagtcagtttgataattagttttgc 120
           ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct: 428 aaaacaaaagagaacagtagagaaactattaaataaagtcagtttgatatttagttttgc 369

                                                                       
Query: 121 ccatttaatgcctgtgtactttggatgtgttaagaaaaatcttgaagcctgtgattttgt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 368 ccatttaatgcctgtgtactttggatgtgttaagaaaaatcttgaagcctgtgattttgt 309

                                                                       
Query: 181 gaatgtttatcaaatcggcatagcatgcaaaacttactcaaatattaaccagctgaatat 240
           |||||||||||||||||| ||||||||||||||||| |||||||||||  ||||||||||
Sbjct: 308 gaatgtttatcaaatcggtatagcatgcaaaacttaatcaaatattaattagctgaatat 249

                                                           
Query: 241 aattttaatgtatccattatagaacactattgttagaactacgccccc 288
            ||||||||||||||| || ||||||||||||||||||||||||||||
Sbjct: 248 gattttaatgtatccactagagaacactattgttagaactacgccccc 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: 10
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: 288
Length of database: 688
Length adjustment: 9
Effective length of query: 279
Effective length of database: 679
Effective search space:   189441
Effective search space used:   189441
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)