Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 131 of 131
Found at i:43135079 original size:2 final size:2
Alignment explanation
Indices: 43135072--43135101 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
43135062 ACACCATGCT
*
43135072 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
43135102 AGGATGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43140297 original size:329 final size:331
Alignment explanation
Indices: 43139692--43140351 Score: 1252
Period size: 329 Copynumber: 2.0 Consensus size: 331
43139682 GTGTCAATTC
43139692 GGGTTGACATGTATTCAAAATTTTTGAAGTAGAAAAATAGAAATATTAATATTAGTGGAGAGGGT
1 GGGTTGACATGTATTCAAAATTTTTGAAGTAGAAAAATAGAAATATTAATATTAGTGGAGAGGGT
43139757 GGTTAGATATTATAAGAAATTAAAAAAAAAAACTTCCGAACTCAAGGAAAATTAATTTAAGGAAT
66 GGTTAGATATTATAAGAAATT-AAAAAAAAAACTTCCGAACTCAAGGAAAATTAATTTAAGGAAT
43139822 GGATTAAATTGTAGAATTGTGAAGAGTGTTCGGTCATAGTGTGAAAATTTAAAATAAGAGATTAT
130 GGATTAAATTGTAGAATTGTGAAGAGTGTTCGGTCATAGTGTGAAAATTTAAAATAAGAGATTAT
43139887 GGAATTAAATGGATAAGAAAAAGAGGAACACCTTAACGAATAAATTAATCATGAAAGTACATGGA
195 GGAATTAAATGGATAAGAAAAAGAGGAACACCTTAACGAATAAATTAATCATGAAAGTACATGGA
43139952 GATGTTGATAGTAGTGAAAGTGATTAGACACCATTTATATTTAATGATGATTAGATTTTTAATAA
260 GATGTTGATAGTAGTGAAAGTGATTAGACACCATTTATATTTAATGATGATTAGATTTTTAATAA
43140017 -TATATT
325 TTATATT
43140023 GGGTTGACATGTATTCAAAATTTTTGAAGTAGAAAAATAGAAATATTAATATTAGTGGAGAGGGT
1 GGGTTGACATGTATTCAAAATTTTTGAAGTAGAAAAATAGAAATATTAATATTAGTGGAGAGGGT
*
43140088 GGTTAGATATTATAAGAAATT-AAAAAAAAACTTTCGAACTCAAGGAAAATTAATTTAAGGAATG
66 GGTTAGATATTATAAGAAATTAAAAAAAAAACTTCCGAACTCAAGGAAAATTAATTTAAGGAATG
*
43140152 GATTAAATTGTAGAATTGTGAGGAGTGTTCGGTCATAGTGTGAAAATTTAAAATAAGAGATTATG
131 GATTAAATTGTAGAATTGTGAAGAGTGTTCGGTCATAGTGTGAAAATTTAAAATAAGAGATTATG
*
43140217 GAATTAAATGGATAAGAAAAAGAGGAACGCCTTAACGAATAAATTAATCATGAAAGTACATGGAG
196 GAATTAAATGGATAAGAAAAAGAGGAACACCTTAACGAATAAATTAATCATGAAAGTACATGGAG
* *
43140282 ATGTTGATGGTAGTGAAAGTGATTAGACACCATTTATATTTAATGATGATTTGATTTTTAATAAT
261 ATGTTGATAGTAGTGAAAGTGATTAGACACCATTTATATTTAATGATGATTAGATTTTTAATAAT
43140347 TATAT
326 TATAT
43140352 ATATATATAT
Statistics
Matches: 323, Mismatches: 5, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
329 232 0.72
330 5 0.02
331 86 0.27
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (331 bp):
GGGTTGACATGTATTCAAAATTTTTGAAGTAGAAAAATAGAAATATTAATATTAGTGGAGAGGGT
GGTTAGATATTATAAGAAATTAAAAAAAAAACTTCCGAACTCAAGGAAAATTAATTTAAGGAATG
GATTAAATTGTAGAATTGTGAAGAGTGTTCGGTCATAGTGTGAAAATTTAAAATAAGAGATTATG
GAATTAAATGGATAAGAAAAAGAGGAACACCTTAACGAATAAATTAATCATGAAAGTACATGGAG
ATGTTGATAGTAGTGAAAGTGATTAGACACCATTTATATTTAATGATGATTAGATTTTTAATAAT
TATATT
Found at i:43141440 original size:21 final size:22
Alignment explanation
Indices: 43141394--43141449 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
43141384 CGATAATGGT
* *
43141394 ACTACGGTGCAAGTGAAAGTGGC
1 ACTACAGTGCAAGTG-AAGTGAC
*
43141417 ACTACTGTGCAAGTG-AGTGAC
1 ACTACAGTGCAAGTGAAGTGAC
*
43141438 ACTTCAGTGCAA
1 ACTACAGTGCAA
43141450 AGAGATACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 15 0.52
23 14 0.48
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (22 bp):
ACTACAGTGCAAGTGAAGTGAC
Found at i:43143735 original size:2 final size:2
Alignment explanation
Indices: 43143728--43143759 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
43143718 ACCACTTAAC
43143728 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
43143760 ATTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43147162 original size:18 final size:18
Alignment explanation
Indices: 43147139--43147173 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43147129 TATGTCAAAA
*
43147139 TGGTATCGATATTTAATT
1 TGGTATCGATATCTAATT
43147157 TGGTATCGATATCTAAT
1 TGGTATCGATATCTAAT
43147174 AACAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (18 bp):
TGGTATCGATATCTAATT
Found at i:43147868 original size:14 final size:15
Alignment explanation
Indices: 43147849--43147881 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
43147839 AAAATCAAAT
43147849 AAAATTACATT-ATA
1 AAAATTACATTAATA
43147863 AAAATTACATTAATA
1 AAAATTACATTAATA
43147878 AAAA
1 AAAA
43147882 ATCACAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTACATTAATA
Found at i:43148127 original size:106 final size:103
Alignment explanation
Indices: 43147862--43148262 Score: 492
Period size: 106 Copynumber: 3.9 Consensus size: 103
43147852 ATTACATTAT
*
43147862 AAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAA-TTATAACCTAATCA
1 AAAAATTACATTAATAAAAAACCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATCA
* * *
43147926 TAAATTACTAACAAAATAATTATAAAATAATTTTTTAA
66 TAAATTACTAACAAAATAACTATAAAATTATTTTTTTA
* * * *
43147964 AAAACATTTACATCACTAAAAAATCACAAAACACTAAACTAACCACTAACAATTTATAACCTAAT
1 AAAA-A-TTACATTAATAAAAAACCACAAAACACTAAACTAAACACTAACAATTTATAACCTAAT
* * * *
43148029 CGTAAATTATTAACAAAATAACTACAAAATTATGTTTTTTTTG
64 CATAAATTACTAACAAAATAACTATAAAATTA---TTTTTTTA
* * * * * *
43148072 AAAAATTAAATTACTAAAAAACCACAAATCACTAAACTAAATACTAACAAGTTATAACCTAATTA
1 AAAAATTACATTAATAAAAAACCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATCA
43148137 TAAATTACTAACAAAATAACTATAAAATTA----TTTA
66 TAAATTACTAACAAAATAACTATAAAATTATTTTTTTA
* * * *
43148171 AAAAATTACATTAATAAAAAATCC-CAAAACACAAAACTAAACAC-ACCGATTTATAACCTAATA
1 AAAAATTACATTAATAAAAAA-CCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATC
*
43148234 ATAAATTATTAACAAAATAACTATAAAAT
65 ATAAATTACTAACAAAATAACTATAAAAT
43148263 AATTAAAAAA
Statistics
Matches: 260, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
98 43 0.17
99 39 0.15
100 2 0.01
102 4 0.02
103 1 0.00
104 42 0.16
105 39 0.15
106 79 0.30
107 1 0.00
108 10 0.04
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.28
Consensus pattern (103 bp):
AAAAATTACATTAATAAAAAACCACAAAACACTAAACTAAACACTAACAATTTATAACCTAATCA
TAAATTACTAACAAAATAACTATAAAATTATTTTTTTA
Found at i:43150005 original size:22 final size:21
Alignment explanation
Indices: 43149957--43150005 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
43149947 TTCAAGTTAG
43149957 ATAAAACAATTAAAATAAATA
1 ATAAAACAATTAAAATAAATA
* *
43149978 ACTAAAATAATTAAAATGGAATA
1 A-TAAAACAATTAAAAT-AAATA
43150001 ATAAA
1 ATAAA
43150006 TCTACTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (21 bp):
ATAAAACAATTAAAATAAATA
Found at i:43155150 original size:16 final size:16
Alignment explanation
Indices: 43155129--43155192 Score: 110
Period size: 16 Copynumber: 4.0 Consensus size: 16
43155119 TGTTATTATG
43155129 ATTGATTAAAAAACAA
1 ATTGATTAAAAAACAA
43155145 ATTGATTAAAAAACAA
1 ATTGATTAAAAAACAA
*
43155161 CTTGATTAAAAAACAA
1 ATTGATTAAAAAACAA
*
43155177 CTTGATTAAAAAACAA
1 ATTGATTAAAAAACAA
43155193 GTATTTTGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.25
Consensus pattern (16 bp):
ATTGATTAAAAAACAA
Found at i:43155243 original size:6 final size:6
Alignment explanation
Indices: 43155232--43155267 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
43155222 AAATATTCAT
43155232 TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA
1 TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA
43155268 AGTTCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTTAA
Found at i:43159168 original size:15 final size:15
Alignment explanation
Indices: 43159133--43159174 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43159123 TTAAGAATTT
*
43159133 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43159147 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43159161 TATTTAATAATAAT
1 TATTTAATTATAAT
43159175 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43159418 original size:16 final size:16
Alignment explanation
Indices: 43159397--43159448 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
43159387 TTGATTTGCT
43159397 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
43159413 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
43159429 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
43159445 ATTA
1 ATTA
43159449 TGTTTCTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:43159438 original size:32 final size:32
Alignment explanation
Indices: 43159397--43159461 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
43159387 TTGATTTGCT
43159397 ATTACGCCTCTATTCCATTACGCTTCTATTCC
1 ATTACGCCTCTATTCCATTACGCTTCTATTCC
* *
43159429 ATTACGCCTCTATTCCATTATGTTTCTATTCC
1 ATTACGCCTCTATTCCATTACGCTTCTATTCC
43159461 A
1 A
43159462 ATACAGTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (32 bp):
ATTACGCCTCTATTCCATTACGCTTCTATTCC
Found at i:43159456 original size:16 final size:16
Alignment explanation
Indices: 43159397--43159461 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
43159387 TTGATTTGCT
*
43159397 ATTACGCCTCTATTCC
1 ATTACGCTTCTATTCC
43159413 ATTACGCTTCTATTCC
1 ATTACGCTTCTATTCC
*
43159429 ATTACGCCTCTATTCC
1 ATTACGCTTCTATTCC
* *
43159445 ATTATGTTTCTATTCC
1 ATTACGCTTCTATTCC
43159461 A
1 A
43159462 ATACAGTGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTACGCTTCTATTCC
Found at i:43159792 original size:12 final size:12
Alignment explanation
Indices: 43159771--43159803 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
43159761 TTGCAAAGTA
43159771 AGAA-TTCTCGT
1 AGAACTTCTCGT
43159782 AGAACTTCTCGT
1 AGAACTTCTCGT
43159794 AGAACTTCTC
1 AGAACTTCTC
43159804 CAAGGCATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (12 bp):
AGAACTTCTCGT
Found at i:43161984 original size:231 final size:231
Alignment explanation
Indices: 43161581--43162043 Score: 926
Period size: 231 Copynumber: 2.0 Consensus size: 231
43161571 GGCCTGTCTG
43161581 TATCCTTTATTTAACAAAATGAGGAGTTCGTCAAGAATATCTCACAGTTCTGCTTCAAAAGAAGA
1 TATCCTTTATTTAACAAAATGAGGAGTTCGTCAAGAATATCTCACAGTTCTGCTTCAAAAGAAGA
43161646 ACACTGAGGCAAATGATTTTTATTTATAGTAAAAAAATGGTAGAATAATTAATCTGAACAATTAT
66 ACACTGAGGCAAATGATTTTTATTTATAGTAAAAAAATGGTAGAATAATTAATCTGAACAATTAT
43161711 ATTAATCGGAAGTGATTAAAATGGAAAAAATTAAGTGACAAAAATAGGGCAAATCACATTTACTA
131 ATTAATCGGAAGTGATTAAAATGGAAAAAATTAAGTGACAAAAATAGGGCAAATCACATTTACTA
43161776 TTCAAGTAACCACCTTAAATTTATGTGACAAAAAAA
196 TTCAAGTAACCACCTTAAATTTATGTGACAAAAAAA
43161812 TATCCTTTATTTAACAAAATGAGGAGTTCGTCAAGAATATCTCACAGTTCTGCTTCAAAAGAAGA
1 TATCCTTTATTTAACAAAATGAGGAGTTCGTCAAGAATATCTCACAGTTCTGCTTCAAAAGAAGA
43161877 ACACTGAGGCAAATGATTTTTATTTATAGTAAAAAAATGGTAGAATAATTAATCTGAACAATTAT
66 ACACTGAGGCAAATGATTTTTATTTATAGTAAAAAAATGGTAGAATAATTAATCTGAACAATTAT
43161942 ATTAATCGGAAGTGATTAAAATGGAAAAAATTAAGTGACAAAAATAGGGCAAATCACATTTACTA
131 ATTAATCGGAAGTGATTAAAATGGAAAAAATTAAGTGACAAAAATAGGGCAAATCACATTTACTA
43162007 TTCAAGTAACCACCTTAAATTTATGTGACAAAAAAA
196 TTCAAGTAACCACCTTAAATTTATGTGACAAAAAAA
43162043 T
1 T
43162044 TAGAATTCTT
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 232 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (231 bp):
TATCCTTTATTTAACAAAATGAGGAGTTCGTCAAGAATATCTCACAGTTCTGCTTCAAAAGAAGA
ACACTGAGGCAAATGATTTTTATTTATAGTAAAAAAATGGTAGAATAATTAATCTGAACAATTAT
ATTAATCGGAAGTGATTAAAATGGAAAAAATTAAGTGACAAAAATAGGGCAAATCACATTTACTA
TTCAAGTAACCACCTTAAATTTATGTGACAAAAAAA
Found at i:43166464 original size:16 final size:17
Alignment explanation
Indices: 43166433--43166473 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
43166423 AAATAATTTT
43166433 AAATATA-ATTTATTGA
1 AAATATATATTTATTGA
*
43166449 AAATTTATATTT-TTGA
1 AAATATATATTTATTGA
43166465 AAATATATA
1 AAATATATA
43166474 AGTAAAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
AAATATATATTTATTGA
Found at i:43172093 original size:44 final size:44
Alignment explanation
Indices: 43172036--43172132 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
43172026 TGAGATTTTG
*
43172036 TGTAAGACTACGTCTAGGACGTTAGCATCGATTTGAGACTTTCA
1 TGTAAGACCACGTCTAGGACGTTAGCATCGATTTGAGACTTTCA
* * *
43172080 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGACTTTCG
1 TGTAAGACCACGTCTAGGACGTTAGCATCGATTTGAGACTTTCA
43172124 TGTAAGACC
1 TGTAAGACC
43172133 CTATCTGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTAGGACGTTAGCATCGATTTGAGACTTTCA
Found at i:43172140 original size:44 final size:43
Alignment explanation
Indices: 43172052--43172194 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 43
43172042 ACTACGTCTA
* *
43172052 GGACGTTAGCATCGATTTGAGACTTTCATGTAAGACCACGTCTG
1 GGACGTTGGCATCGATTTGAGACTTTCATGTAAGACC-CATCTG
*
43172096 GGACGTTGGCATCGATTTGAGACTTTCGTGTAAGACCCTATCTG
1 GGACGTTGGCATCGATTTGAGACTTTCATGTAAGACCC-ATCTG
* * *
43172140 GGACAGTT-GCATCGATATT-TGA-TTACATGTAAGACCAAATCTG
1 GGAC-GTTGGCATCGAT-TTGAGACTTTCATGTAAGACC-CATCTG
*
43172183 AGACGTTGGCAT
1 GGACGTTGGCAT
43172195 TGTACGAACT
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
42 3 0.03
43 25 0.29
44 53 0.62
45 5 0.06
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
GGACGTTGGCATCGATTTGAGACTTTCATGTAAGACCCATCTG
Found at i:43177398 original size:102 final size:102
Alignment explanation
Indices: 43177213--43177664 Score: 518
Period size: 102 Copynumber: 4.4 Consensus size: 102
43177203 GTGAAAGTGA
* * * * * *
43177213 TGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGCGTACTGGA-ACGA-AA-GGTCACATGTG
1 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-AATCGATA-AATAATGGTCACATGTG
43177275 TAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
64 TAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
43177314 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTA
1 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTA
* * *
43177379 GTACTAAGTGACGTCTACAATATGTACCGAGAAGCTT
66 GTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
* * * * * *
43177416 TGGTCACTTGTGTAGTACAGTGTGAAGGCTACTACATGAATTGATAAATGATGGTTACATGTGTA
1 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTA
* * *
43177481 GTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTT
66 GTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
* * * * * *
43177518 TAGTCACATATGTGTAGTACTGTGTGAAGGCTACTACATGAATTGATAAATGATGGTTACATGTG
1 TGGTCAC--GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTG
* * * * * * *
43177583 TAGTGCTATGTGAAAGCTACAACGTGAACCGTACAA--AT
64 TAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTT
* * *
43177621 TGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
43177665 ATGATAATAG
Statistics
Matches: 305, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
100 5 0.02
101 70 0.23
102 143 0.47
103 6 0.02
104 78 0.26
105 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTA
GTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
Found at i:43177570 original size:104 final size:102
Alignment explanation
Indices: 43177268--43177655 Score: 528
Period size: 102 Copynumber: 3.8 Consensus size: 102
43177258 ACGAAAGGTC
*
43177268 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACT
1 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACTTGTGTAGTACT
* * * *
43177333 GTGTGAAGGCTACTACGTGAATCGATAAATAATGGTC
66 GTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
* * * *
43177370 ACATGTGTAGTACTAAGTGACGTCTACAATATGTACCGAGAAGCTTTGGTCACTTGTGTAGTACA
1 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACTTGTGTAGTACT
43177435 GTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
66 GTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
* * * *
43177472 ACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTAGTCACATATGTGTAGTA
1 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCAC-T-TGTGTAGTA
43177537 CTGTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
64 CTGTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
* * * * * * * * *
43177576 ACATGTGTAGTGCTATGTGAAAGCTACAACGTGAACCGTACAA--ATTGATCACGTGTGTAGTAC
1 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACTTGTGTAGTAC
*
43177639 TATGTGAAGGCTACTAC
65 TGTGTGAAGGCTACTAC
43177656 GTGTATCGAA
Statistics
Matches: 253, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
101 26 0.10
102 139 0.55
103 7 0.03
104 78 0.31
105 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACTTGTGTAGTACT
GTGTGAAGGCTACTACATGAATTGATAAATGATGGTT
Found at i:43177595 original size:51 final size:51
Alignment explanation
Indices: 43177210--43177655 Score: 271
Period size: 51 Copynumber: 8.7 Consensus size: 51
43177200 AAAGTGAAAG
* * ** * * *
43177210 TGATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGCGTACTG--GAA
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAA
* * * * ** * * *
43177259 CGAAAGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGC
1 TG-ATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAA-A
* * * * *
43177312 T-TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAA
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAA
* * * * * * * * *
43177362 TAATGGTCACATGTGTAGTACTAAGTGACGTCTACAATATGTACCGAGAAGC
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAA-A
* * **
43177414 T-TTGGTCACTTGTGTAGTAC-AGTGTGAAGGCTACTACATGAATTGATAAA
1 TGATGGTCACATGTGTAGTACTA-TGTGAAGGCTACTACATGAACCGATAAA
* * ** * *
43177464 TGATGGTTACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGA-AAA
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAA
* * * **
43177514 -GCTTTAGTCACATATGTGTAGTACTGTGTGAAGGCTACTACATGAATTGATAAA
1 TG--ATGGTCAC--ATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAA
* * * * * *
43177568 TGATGGTTACATGTGTAGTGCTATGTGAAAGCTACAACGTGAACCGTACAAA
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCG-ATAAA
* *
43177620 T--TGATCACGTGTGTAGTACTATGTGAAGGCTACTAC
1 TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTAC
43177656 GTGTATCGAA
Statistics
Matches: 299, Mismatches: 82, Indels: 31
0.73 0.20 0.08
Matches are distributed among these distances:
49 2 0.01
50 71 0.24
51 178 0.60
52 8 0.03
53 36 0.12
54 3 0.01
55 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
TGATGGTCACATGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAA
Found at i:43178574 original size:5 final size:5
Alignment explanation
Indices: 43178564--43178626 Score: 72
Period size: 5 Copynumber: 12.6 Consensus size: 5
43178554 TGCTTGATGA
* * * * *
43178564 AATGG AATGG AATGG TATGA AATGG AATAG TATGG AATGG AGTGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
*
43178614 TATGG AATGG AAT
1 AATGG AATGG AAT
43178627 ATATATATAT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.37, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:43189657 original size:37 final size:37
Alignment explanation
Indices: 43189607--43189935 Score: 631
Period size: 37 Copynumber: 8.9 Consensus size: 37
43189597 NNNNNNNNNN
*
43189607 ACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189644 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189681 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189718 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189755 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189792 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
43189829 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
*
43189866 ACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
*
43189903 ACAAAGTGATAAGTGGCTACACTTATCTGATCA
1 ACAAATTGATAAGTGGCTACACTTATCTGATCA
43189936 GGGACAAGTG
Statistics
Matches: 290, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 290 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (37 bp):
ACAAATTGATAAGTGGCTACACTTATCTGATCAAGAA
Found at i:43195377 original size:21 final size:21
Alignment explanation
Indices: 43195354--43195395 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
43195344 TAAATGATGA
43195354 AGAATAGAAAATAAAAGTAAAAG
1 AGAA-AGAAAA-AAAAGTAAAAG
43195377 AGAAAGAAAAAAAAGTAAA
1 AGAAAGAAAAAAAAGTAAA
43195396 TAAATAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (21 bp):
AGAAAGAAAAAAAAGTAAAAG
Found at i:43195404 original size:22 final size:22
Alignment explanation
Indices: 43195353--43195404 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
43195343 ATAAATGATG
43195353 AAGAATAGAAAATAAAAGTAAAA
1 AAGAA-AGAAAATAAAAGTAAAA
*
43195376 GAGAAAGAAAA-AAAAGTAAATA
1 AAGAAAGAAAATAAAAGTAAA-A
*
43195398 AATAAAG
1 AAGAAAG
43195405 TCAAAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (22 bp):
AAGAAAGAAAATAAAAGTAAAA
Found at i:43198258 original size:40 final size:40
Alignment explanation
Indices: 43198198--43198368 Score: 306
Period size: 40 Copynumber: 4.3 Consensus size: 40
43198188 CGTTTGGACA
* *
43198198 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
43198238 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
43198278 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
1 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
* *
43198318 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
43198358 AAAAACGCCGC
1 AAAAACGCCGC
43198369 AAAAAGTCTA
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 127 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCTC
Done.