Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_027407
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 666081
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Found at i:3921 original size:36 final size:36
Alignment explanation
Indices: 3879--4419 Score: 1082
Period size: 36 Copynumber: 15.0 Consensus size: 36
3869 CCTATGTCTT
3879 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3915 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3951 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
3987 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4023 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4059 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4095 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4131 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4167 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4203 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4239 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4275 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4311 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4347 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4383 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
1 TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
4419 T
1 T
4420 TTTCTTGGTA
Statistics
Matches: 505, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 505 1.00
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (36 bp):
TCGGAAAAACAAATGCCATGAAGGACTTAGGAAAGA
Left flanking sequence: Indices 3379 -- 3878
AAAACAGGTACTGATAACAAAGTACAAGCCCTAGCTTTTAAGCCGAAGAAAGAAGCAATCATACT
CCTTAAACAGAAAGATATTGCACTTCAAAATCGTTACTAGAAGCACTACAAGCGCACTTCCTATC
TAAACAAACCAAAGCAGAAAAAGCACCTCCCTCCCGGATAAAGAGCAAGTGTGCGAGAGAATAGA
ACTGAGCATCAAGGCTGCAAGACAGAAGGAAGGTTCCTGCGTGCAGGAAAGCTTTTTCACCGTCC
ATTGGGTATTTGTCTTTATCTCGCTCTCCCAACTAACTCAGACTTATGATAGGCGGGCTCAATTC
CAGATATTGACCTCTGGGGATCCTTCTCTTTGAATTCCCGGTCTTCCGTTTTCTTCCTTGGTTCC
ACCCTTCCATTCATGAAGCAGATCGCCGGGAAGGCTTTTTCTCAAGCATAAAACGAGAGACCCGA
TCACATTGATCGACAAACAAAACTCCCGATAGAAGCCTATGTCTT
Right flanking sequence: Indices 4420 -- 4919
TTTCTTGGTATTCACGCTCATCGGACTGAAGTTGGTCCTCATTTATCTCAGCAGAAGTCTTTCAT
GATCTTTTCATAAAGTTGAATCTAGCCAATGCAAACTCAACTCAGTTAGTACTCCTATATCAATC
GTTGTCGCTGCCTTCTCAAGATGACGGGTAACCCCTTTCTTTAGGAGGATCCATCTCTTTATCGC
AGCATGGTAGGAGCCTTGCATTATTTAAGCATGACAGGGCCGGACATTGCCTTTGCCGTAAGCAT
TTGAAGCCAATTCCTCAATTGCCGCCCAGTACATCGTAAAGTGGATCGATCGATATCTTAAGGGA
ACTTCTCATTATGTCTTTTACCTCTTCTTCTGAGCTAGAGTTACATGCTTATGCTGATTGGGGTC
CTTGTCTTGATAGTCGACGTTCTCTTTCTGGGTATGCTCTCCTTTTTCTTGCCTAATCTCCTTTC
CTAAAACTCTGCGCTTCTCTTTTGAATCTTCTCACCCCGCCTAGC
Found at i:80394 original size:24 final size:24
Alignment explanation
Indices: 80352--80400 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
80342 ATTCGGATTC
* *
80352 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
80376 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
80400 G
1 G
80401 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 79852 -- 80351
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTCGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 80401 -- 80900
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:97777 original size:26 final size:26
Alignment explanation
Indices: 97743--97800 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
97733 TTCCATACTT
* *
97743 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
97769 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
97795 A-AGAAA
1 AGAGAAA
97801 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Left flanking sequence: Indices 97243 -- 97742
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 97801 -- 98300
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:155795 original size:21 final size:21
Alignment explanation
Indices: 155769--155815 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
155759 TTAAGGGATG
155769 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
155790 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
155811 TAACA
1 TAACA
155816 ATCGATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (21 bp):
TAACAGAAGTTTCAAGAGAAC
Left flanking sequence: Indices 155269 -- 155768
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTTAAATTGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTAAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 155816 -- 156315
ATCGATGGACTGGAAGGGCGAGAGACAGAACAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:165891 original size:13 final size:13
Alignment explanation
Indices: 165873--165899 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
165863 CCACACATTA
165873 CCGGTGGATGCTC
1 CCGGTGGATGCTC
165886 CCGGTGGATGCTC
1 CCGGTGGATGCTC
165899 C
1 C
165900 AGCCGCTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.33, G:0.37, T:0.22
Consensus pattern (13 bp):
CCGGTGGATGCTC
Left flanking sequence: Indices 165373 -- 165872
TTGTGTTATGATGTAGACGTGTGTTATGATTTAGTTAGGACTTTGTCTCCCTTTCGTTATCTTCC
GCTTCCCTTATATAGGTTGGGGAAGGGCCGGGTGGATTACCTTTGGGGGGCTAAGTCGAAGATCT
TGGTGGTCTTGTGAGTGGTTGATAAACTACGATTGCAGTTTTATTTAGGAAGTCCCATAGCTGTG
AGGCTTAACAGACAAAGAAAACGGTGGATACTTCCACTAGTTGGGTAGAAGGTGACGACCCTAAT
GAATCGACTATGAAGGTGGCTGTTAGCTACATCAGCGCTCAAATTCCTTCATCGTTATTGCCCTG
GCTTCGATGATCAACCCCTGGCACATTTAGGTTTTTATTTTTGATCTTCGGCCATCCTGGTCCTC
AGGACCCAACACAATATTATTATTTTTAGATATTTCCTTTAAAATTAAAAGATGCAAAAGGTGTT
GATACGTCCTATCCACATAGAAAGCTTACCCTCTTCCACACATTA
Right flanking sequence: Indices 165900 -- 166399
AGCCGCTATCACTTTGGCTGCAGGAGGGGAATGGTTAAGTGAAACTCTCGACGTCTTGTTTGGTA
AACGGGATGTTTACCCAGGCGCCGTAGTCTTGCCTAACCGTTCGGCCGGAGATGCCTTTGTATGG
TATAGCAAGCTGTTTAGCTACTTGTATCGATTTGCCACAGTGTGGTTAGATACAATGCGCTGGCA
GCCTCAGCTTGGCAGGATGGGAATGAAGGTCGAGGAAGCAGGGAAGAAAAGGTTATTCGCTATTG
GCTCACCCTTGTATCAGGCCTTGGTACGGCCTATACATGATTGAGTCATGACGGTTTTGACAAAG
TTCAGAATGGATGGTACCTATAACCAGACCCAACCGTTGCAGTACTTGAGAGGAAAGAAAAAATG
ATTTTCTTTTGATCTCAAGGCTGCTATCGATTCCTTACCTGTTATCCTGACGTCCTGTATGATTG
CAGGGTTTTTCGGAAATCCCTTTCCCTTTGCAACTTCCTGGGCGT
Found at i:259474 original size:17 final size:17
Alignment explanation
Indices: 259454--259489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
259444 ATATCCTTAG
259454 CTTTCCTGTATCTCTTT
1 CTTTCCTGTATCTCTTT
* *
259471 CTTTCTTGTCTCTCTTT
1 CTTTCCTGTATCTCTTT
259488 CT
1 CT
259490 CTATCTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTCCTGTATCTCTTT
Left flanking sequence: Indices 258954 -- 259453
GGCAAGAAATGAAATCGAATAATTGTATGCCGATCGCGCCCTCTCTTTCAATTGAGCTGATCCCC
TCGCTTCTTTACCCGGTGACTTAAATTTCTATTCATTACTGGGCTATTCCCACGTACTCACTGAC
GAACTGTACTAATTGGTGGGTTGATCCAGGTAGCTCAGATCTGGGAATGTACTACAGGGAGCATC
CTGACTAGTCTCATTGACATTTAAATGAGCATCCTGTTCCCTTCTGCTTCAGCATAGTAGACCTA
TTCTCCGAGAAGGAAGACCCTGTCCAGAAAAGTGGATTTCCCTGCTGTAGTATGAGTTGAGAGGA
TCAGACTTACGGGGGAACCTTCTCTAGTCTAGGAGCATTTCCACTATGTCTGTGTTCTTTCAATG
CCCCTTCCCAAAGCAAAGCAGGAAGAAACCTATGGCGCATTCTTCTCTTTCAAAAAAGCTTTGGT
ATTGCGCCTTTCTGTGCTCCCTTTCGCCCTTCGTTATATCCTTAG
Right flanking sequence: Indices 259490 -- 259989
CTATCTTCCCATTCCTTGTAAGAAGTCCTAGGAGCCAAGACAGTAAGTAAGCCAGTCTTTGGTCT
TTTAGTAAGTCTTTCCCTTCCTTGTACTAAGTAAGTAGGGGATCCTTTCTTTCTTTTTAATATTC
TTTCTCTCCAGGCAAGCAAGGAAGTAAGCAAGTAAGGAAGGGGGTCTGTGATTAATAGGTAAGCC
TGTGCTGCTAGTGTTAAGCTAGTGGTAAGGCAGCAGTAGGCCAATAATCCTTCTTTATAAGAGTC
CTAAATCCTAGGGTCCTCGTAGTCCATTAGGAAGAAGGCAAAAGAGCTTACCTCTGAAGACTGAA
GGAACAAGCGATTACTCTAAACCAAAGCGAACGCGAAGGGGTATCGGTAGTCCCTTTACTTTATT
CCTTGGCAGGAATAGCGGAAATGGTAACTCCAAACCCTTGAGTGGCTGGTTGAATGGATTTGGGC
GTATCTTAAATAAGGTAATTGATTGATTGAGTTGTTTCTGGATAA
Found at i:301813 original size:16 final size:17
Alignment explanation
Indices: 301781--301826 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
301771 CATCCCTTGG
301781 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
301798 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
301814 GCTTAGTTTATTC
1 GGTTAGTTCATTC
301827 CATTTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Left flanking sequence: Indices 301281 -- 301780
CTTCTATCCCCTTACCGAATTCTCTGTCTGTAATATTAAGTGTTGTAATAAATGTTATAGTTGAA
AGAAATTCCACCTCCTCCTTTTTTTTTCTCATCCCTTAGCCTTAGCTCTTTGATGAGCTCTTCGA
GAGTAATGAAATAGGCGTAGGCTCGATGATTCTTGAAAGTGAATATCGCTCGCAATGGCCGCCCT
GAGAGTTGAACCCTTCAACGGATAATTTCGTATGCTAGCTCCAATGAGTAGTAGAGGAAAGCTCG
GCCTCAGTGCGTCCTACTTGTGTCGTGTTTTAAGCCTGCTATGCATTCTTGCTCCATCTACCATT
CCTGACAAGCCATTTCTGGTATGCCCGCTGCTTCGTCCAAAATGACTTAAAATCCATCCTATCTT
TATTGGGATCATACCCCCTTGGACTTTACTTTTTTTTTCTGTTTTAGGAATTTATCCCTGGGCTT
TCAATGGGACCATGCCTTGGATTTCAATCCGAGATCATCCCTTGG
Right flanking sequence: Indices 301827 -- 302326
CATTTACTGCCCCTCTTTTGCTTGATGAAAGACATCCTGGCAAAGGCCTTGTATATTAGTAAAAA
AGGGGACTTTAATGGGTCCGATGGCTCTTTGACTGGTGTGCCTGAAAATGTGATTGATAAATGGG
CTTTTGAAACTCGATTTGTCGCAACAAGAGGTATTGTCTCCGCCTTTTCAAGTAGGGATCATCTC
TCAAGTGTTATGATCCTCCATTTCTGCTCGGTAGTGGCCTAAGGCTCAATGATGGATCTTCCTAG
CTAAGGCTAGCATCTCATCCCAGCTTTCATCTTATTGCTTTGAGCTCTCTTTGCTTTGGGAAAGT
GTAAAAGTGTAACCTGCTGCTCCTTGATTTCACATAAACAACTGAGTGTCTTCTGCTCCTTTTGC
TCTTCGCTTTCTGTGTTTATTGATCTCCTGCCCACTCACATTCTCTTTCTTTATCGAATCCTTAT
AGGCAGATAGGACTACTCCTGCTTGCTCTTGGCCTTGGCTGCTTA
Found at i:328884 original size:26 final size:26
Alignment explanation
Indices: 328848--328900 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
328838 GGGACAAAGG
328848 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
328874 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
328900 C
1 C
328901 ATAGCGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.30
Consensus pattern (26 bp):
CCTCGAATCCTGTCTTTGACGGCGAT
Left flanking sequence: Indices 328348 -- 328847
TCGCAGTGAGCGCTACCTAAGCACTGTTGAAGGCACTCAGAGAAGAGTGGAAAGAGTCCTAAGAG
GGCTTCTCACTAAGACTTTCGACTCACTGCCAAAAGCTCCTTCTTGTGCGCTAACGCTGGAAGGG
ATGGTTTTGGGTGGGGGAGAGATCACTGGAAGACTTAGTCGTTTAGATAGAGATAACATTTCTAT
AATAAAAAATATGGAACTCAGTACCCCCAGGCGTTCGCTAAATGCATTTCGCTTACAGTCACTAG
GAAGGGGTTCTAGTAACGAAAGATTCCTTCCATAGATAGGCCACATTTCTCATATTCATTTCAGT
GCTTTTGGTCTACCGTTTTGGAAAGCAGGGGCAAGTCAGGCATCATGCTTTCCTGGGGAGATCGT
TTCAATTTACATAATAGTTAAGCTTCGTGCTTGCTGTGAAAGTGATCTTCGTAATCAAGAGATGG
GGCGTTCTCTCTCCCTACTTAACTAACAAGCAATGGGGACAAAGG
Right flanking sequence: Indices 328901 -- 329400
ATAGCGTGTCACGCTGGGAAACTGATCGAATGTTTTCTGTCTCAATGTCAGTGTGAAAGTCCTAA
TATCTTTACGAGGTCGAAATAGCATCACAGAAAGAGCAGCCAGAACCTACTCCCAGTTGGCCAGC
ATCAAAGCATTCAAATGAAGAAGGAGTCCCCGTCCAACGGAGCACTAAGAAGCAAGGGACACATG
GACAAGAAATGGGTAAGGGGAAAATGAACTCATCGGTTAATAACCCAGTGTTTGGGACCAGAAGG
AAGGCATGGAACTCGAACTAGTGATTCCCTTGCGATCTTGTCTTCCTACTATAGAAGGATCAGAG
CCAGAAGTCCCTATAAAAGAAAAAAGTCCTAGGTGAATTTTTAGTTTTATTTGAAGAGTCTTACC
CCTACGGAATGAAAGAAAGTTTTATTCCGTAGGGGATAGTATCTGCATTTGCGTCTACTGAATAC
TATATTTCACATTGGGACGGCTATAGTCAATAGAGCCACTACCAC
Found at i:337434 original size:14 final size:14
Alignment explanation
Indices: 337415--337445 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
337405 TTTGAATTAT
337415 AATGCCACTAATCC
1 AATGCCACTAATCC
*
337429 AATGCCGCTAATCC
1 AATGCCACTAATCC
337443 AAT
1 AAT
337446 AGTTTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGCCACTAATCC
Left flanking sequence: Indices 336915 -- 337414
CTACGACATTCTGCTGGGCGTACTACCGCACTACCGGGATCCGACGCCGCTTCTTGTCTTGGGAA
AGATGCCTCGAAATTTCAAGGCCAAGCGCGAAGAAACTCGTTCCATGGTAGGACCGGTGGATGAA
GCCATCGCTATACTCCTAGACTCAAAGCCTAACGGAGACCAGCGCCCTATAAGCCCGCCATATGC
TTGGGAGGTAGACGAAAACCCCTTTCCGATAGGGTACCCGTTACCCAGCTTAAAAATCGTTAGAG
GCTTCGGCTTTTGTCAATGCCTGTCCATTTCCTGTTGTGGGCTGGGTTGTCAGGAAGTGAGCCCG
AGAGGGGCGTCCAGACGCGGGTCGAGTATGAATGCTTCCTTTATCCAAACAAGCTGTACTATTCC
TTTTCCACCGACCTTGGCTATTTGAGCTGCGGGTAACTAAGGCTCTACCCTTTCTGCCTTTCCTG
ATTACCTGATTGTTTTCCTGCTTCGCGAAAGTCTTTTTGAATTAT
Right flanking sequence: Indices 337446 -- 337945
AGTTTAGATATCCATGCACAGAGAAGCTGCTAGTCTTTTCGACTATGCCTTCCTTTCTAATTTTC
CTTCTTACAGGGCACGAACGGGAGCCTTTCTTTCCTAAGAAGGAATGTGGCGAAGAACCTGAAAG
TCTTTCTTCTTTTAATGCCCACAGATCCGCTGGAGGAAGGAAGCCAGGGAGACTTAGCATCCGAT
TATCGCAATATACTCTTTCTGGGAAATGTGCATGAAGAGTAATTCCATGTAGGCAGCTTATAGCC
TTCTTTCCTTGTTTTGTTGCACTCATTCACTCCGCAATTCCCTAAAGAAAGGGCAAGATAGAGTC
AAAAGGCAGAAGAAGAAGGGCTTTTCTTTGCTCTTCTTTCCAGGATTCCTTCTCATCGAGAGATG
CGGCATTACCGCTGTTGTCTCTATGCCTTTTTGCCTATCTTACTCTTTCTCGAGGGACAGATGCC
GATTATCCTACAATGCTTTTTTTAACATCTGAAAAAGCTTTTCTT
Found at i:387674 original size:15 final size:15
Alignment explanation
Indices: 387654--387710 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
387644 TTGGCCAAAA
387654 ACCGCTGGTTCTGCT
1 ACCGCTGGTTCTGCT
*
387669 ACCGCTGGTTTTGCT
1 ACCGCTGGTTCTGCT
*
387684 ATCGCTGGTT-TAGCT
1 ACCGCTGGTTCT-GCT
387699 ACCGCTGGTTCT
1 ACCGCTGGTTCT
387711 TCTAATGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.09, C:0.28, G:0.26, T:0.37
Consensus pattern (15 bp):
ACCGCTGGTTCTGCT
Left flanking sequence: Indices 387154 -- 387653
GTAAATCATCGCACCTACGGTCCAACCAATTGGGAGAGAATCAATAGATTCCTTTTCGGGAGCGA
TTCATCCTTCCCTTCACTTTGCTTTGCCCAGCTAAACGCAAAGAGAACAATTGCTTCCTTCCTTA
ACTAAGTCAAAGAGCGGATTCGTACCATCCTGTTAAACAGTCGAGTTGCGGGAAAGAGATAGCAT
TCGCCACGTTCAAGCTAAAAACTAGTTCGAACTAAAGTATTTATTCTATTAGGTAATTAGAAATA
TCGTAAGAGAAGAAGAAATGCCCAAAGACTCCCATGCTTTCCGTTGGTCAACAACCAATAAAAGT
AAACTATAGCACTACTCCTACAGGAAGGACTCGCTTTCTCTTTCTGTCTGGAGGGAATCCTTTTT
TCTCAATCTCAACATGAATGATTTAATTCTTAACTATCTTTTCGATACAATTTCCGGTTCAAAAT
TCAAAAGATTTTTTTTCAAAATGTTTGTCTTGGCCTTGGCCAAAA
Right flanking sequence: Indices 387711 -- 388210
TCTAATGACCTGGGGGTGGGGGGGCAAATGGAACCACCCCAACCACCCATCGTCCCCAGCCCCCT
TGAGCAATTTGAGATTGTGCCATTGATTGATTTGAAGATTGGAAACTTGTATTTCTCATTCACAA
ATCCATCTTTGTTTATGCTGCTAACTCTCAGTTTGTTCCTACTTCTGGTTCATTTTGTTACTAAA
AAGGGAGGAGGAAAGTTAGTACCAAATGCTTGGCAATCCTTGGTAGAGCTTATTTATGATTTCGT
GCTGAACCCGGTAAACGAACAAATAGGCGGTCTTTCCAGTAATGTGAAACAAAAGTATTTCCCTT
GCATCTCGGTCACTTTTACTTTTTCGTTATTTCGTAATCCCCAGGGTATGATACCTTATAGCTTC
ACAGTTACAAGTCATTTTCTCATTACTTTGGGTCTCTCATTTTCTCTTTTTATTGGCATTACTAT
AGTGGGATTTCAAAGAAATGGGATACATTTTTTAAGCTTTTTATT
Found at i:568039 original size:26 final size:26
Alignment explanation
Indices: 568003--568053 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
567993 TTTTCTTTTT
* *
568003 TTTTTTTTTTTTTTGGAAAGGGGGGG
1 TTTTTTTTTTTTATGGAAAGAGGGGG
568029 TTTTTTTTTTTTATGGAAAGAGGGG
1 TTTTTTTTTTTTATGGAAAGAGGGG
568054 ATGATACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (26 bp):
TTTTTTTTTTTTATGGAAAGAGGGGG
Left flanking sequence: Indices 567503 -- 568002
CAGAGAGGAACGTGCCCGCGAGGGCACCACCAGATGTTGTAGATGAACCTACTAAAGAAGAAGGT
TGAGTATATCATAGCTGACCGCACCATGGGCTAGCCCATACACCCACTGCACGAGTGAAATACTA
CTTAGTCAAGTAGAAGGGCCAACCTGAGAGCGAGGCGAGCTGGGAACGGGCTGAAACTTACGATT
CGAAGACCAAGTCAGAGATTACTGGACCTTTCGCAGAGCGACTCTCAACGAGGACATTAAGACTT
AAAAAAAAAATGTTTTCTTAATCCGCCTTTACTAAAGATCAAGGAGTATACTTGTACTCCGGCTA
ATAAAGGAAAGGTATTTTTTCATTTTAAATTGAAGTTTGACTCTGATTAGATCCTTAGCGCAAGC
GCTAAGTAAGCAAGCTACCTTATGTAATGTAAAAAAAACCGAGGAAAATAACGTCAAGTAGAAAC
GAACAAGGTCTTACGGCACGATCGATCACTATATCTTTTCTTTTT
Right flanking sequence: Indices 568054 -- 568553
ATGATACGTGGCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCC
ATGTATATGTTCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACG
AATATGGCTCAAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGC
CAGCCGGTGTGGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGA
TATAGAAAGTGTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATTATTTTATTTC
ACTTAATTTTATTTCACTTAGCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGC
CCTCGCAAGTCTCTCTGCATTTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCT
TAGAAGAATTCCACTTTGAACGGCACGACTCTTTCTATTTTTTCG
Found at i:568389 original size:15 final size:15
Alignment explanation
Indices: 568369--568398 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
568359 CCAGTATATT
568369 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
568384 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
568399 GCCTGCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTCACTTA
Left flanking sequence: Indices 567869 -- 568368
TCTGATTAGATCCTTAGCGCAAGCGCTAAGTAAGCAAGCTACCTTATGTAATGTAAAAAAAACCG
AGGAAAATAACGTCAAGTAGAAACGAACAAGGTCTTACGGCACGATCGATCACTATATCTTTTCT
TTTTTTTTTTTTTTTTTTGGAAAGGGGGGGTTTTTTTTTTTTATGGAAAGAGGGGATGATACGTG
GCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCCATGTATATGT
TCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACGAATATGGCTC
AAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGCCAGCCGGTGT
GGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGATATAGAAAGT
GTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATT
Right flanking sequence: Indices 568399 -- 568898
GCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGCCCTCGCAAGTCTCTCTGCAT
TTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCTTAGAAGAATTCCACTTTGAA
CGGCACGACTCTTTCTATTTTTTCGCTGGAATTCATTTTGTCTCCCCTCCTCTTTCAATCGACAC
ACTCGACGCAGATAGCTCCGGTGGCCCCGGCTTCTGCCTCTATCAGGCGGCGGGAGCCTCCCTCG
GGGGGGCGCCCCCCCCACCTCCCCAGCCACAGCATGGAGGAGCAGCTCCTTAATCCGCACTACAA
CCAATCCAAATTATCTCCGGATCGATATATGATGATGCTAAACCGAGACCGAGATAGAGAAAGAG
GGCTGTCCCTTTGTTGGCTTTTCGAAAAAAAGCACTCATAGGAATGGTGCGAATTCCCATGTTCT
TTTTAGTCTCGCTTGGTTTCGAGAGCCTCCCCCTCCCCGTCTCTT
Found at i:581269 original size:19 final size:19
Alignment explanation
Indices: 581233--581274 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
581223 CTTCAGATAT
*
581233 TTTTATTTCTTTTATTTTA
1 TTTTATTTCTTTGATTTTA
*
581252 TTTTATTT-TTTGACTTTTC
1 TTTTATTTCTTTGA-TTTTA
581271 TTTT
1 TTTT
581275 GGTGCTGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTTCTTTGATTTTA
Left flanking sequence: Indices 580733 -- 581232
TGAAGCAGCCTAGCATCACTTTAGATAGAAGCAGAATGGATAACTTACAACTGAAAGTAAGTTCT
TCGGATCGATATCTCGTACGACGTAATGGAGATCTTGGTCTAGATCCGGTGGTTCGCAGAATTCG
GGACCTAACGATGTTCGGTTCGTCCCATGAACGGGAGCGGACAATTCCCTTTTCGGGGAATGGCT
GCAATCACAAGCAAGTGATTGAATGAGTGGGGGGCTCCGAAAGCACATGCGGGATAAGCAGGTAT
TTCAGGAGACGGTCTAAAAATGGGTCCGATTCAAAAAAAAAAAAGAGAACTCTCAACAAGCTGGA
ACTAATCAAGATCAATAGGAAGAGGAGTTAGCTAGGAATCTATTGACAAAGTTCATGCACCTATA
TGGAAGGGCTGTTTTGTTGATGTATTCCTGTCGAGAATGAAGAAGAAGAAAAAGAGCCTTTTCAA
CCGGCCCAGATCTATTATCACGAACCCTAAAATTTCTTCAGATAT
Right flanking sequence: Indices 581275 -- 581774
GGTGCTGCTACTGTTCAACTCCATACTAACATTTTTAAATTCCTATCATCATCGTCGCAGCTTGC
GAGTTTGAGGAAGATAAGGTCGATTCGATGGAGGTGCAGCAAGCCCTCCCCCCGGTGCCGGAAGC
TTCTGAGCCACTACCACTAGCTCAGGAGCCTGTTTCTCCTTCGTTTGAAATCCAAGCTGCTGAAG
TCAACCAAGAGGACATCTGGAGGGAGTTGGAGCAGCAGGAGCAACCGGCACCAACGGGTGGAGCT
AAGCTAACAAGGCCTCACATATGCGAAAGCTCACCCCATTGGAAAATCAGGTAGCTGACCTTATT
ATCGATTTACGAAAATCCGAAGTACCCTCACCTAATAAGATTCAACAAATCGTCGAAATGCTCGA
AGAAGAAAGAATATGGTCTGGAAAAGCTGCGCACAATCAAAAAGCACAACCAACAATATGGCAGA
AAGAGGGGATTTTTTAGGAACTCCAAGGAGTGCTTTAATATGTTC
Done.