Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold183
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: 216225
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12553 original size:14 final size:14
Alignment explanation
Indices: 12534--12560 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12524 TGCATCTCCC
12534 CATGCATGAATCTA
1 CATGCATGAATCTA
12548 CATGCATGAATCT
1 CATGCATGAATCT
12561 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:15946 original size:25 final size:24
Alignment explanation
Indices: 15918--15964 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
15908 TTTTATTACT
* *
15918 CATTTTTTTCTTTTCTTCTTTTCTA
1 CATTATTTTC-TTTATTCTTTTCTA
15943 CATTATTTTCTTTATTCTTTTC
1 CATTATTTTCTTTATTCTTTTC
15965 ATTTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (24 bp):
CATTATTTTCTTTATTCTTTTCTA
Found at i:19174 original size:14 final size:14
Alignment explanation
Indices: 19155--19181 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19145 TGCATCTCCC
19155 CATGCATGAATCTA
1 CATGCATGAATCTA
19169 CATGCATGAATCT
1 CATGCATGAATCT
19182 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:22481 original size:17 final size:19
Alignment explanation
Indices: 22461--22495 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22451 ATAATCAAAT
22461 TTTTTTTC-AA-TTTTTTG
1 TTTTTTTCTAACTTTTTTG
22478 TTTTTTTCTAACTTTTTT
1 TTTTTTTCTAACTTTTTT
22496 TCAAGCTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTAACTTTTTTG
Found at i:26015 original size:21 final size:21
Alignment explanation
Indices: 25982--26021 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25972 CATAGAAAAC
* *
25982 TCAACTACTCTCGTTTCTTTT
1 TCAACGACACTCGTTTCTTTT
26003 TCAACGACACTCGTTTCTT
1 TCAACGACACTCGTTTCTT
26022 GCATACTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (21 bp):
TCAACGACACTCGTTTCTTTT
Found at i:26116 original size:21 final size:21
Alignment explanation
Indices: 26058--26116 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
26048 TCACTCTCTT
26058 TTTCAA-TTTCTTTCTC-TTTC
1 TTTCAATTTTCTTT-TCATTTC
*
26078 TCTTC-TTTTTCTTTTTCATTTC
1 T-TTCAATTTTC-TTTTCATTTC
26100 TTTCAATTTTCTTTTCA
1 TTTCAATTTTCTTTTCA
26117 ATGTTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 18 0.56
22 13 0.41
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCAATTTTCTTTTCATTTC
Found at i:26747 original size:18 final size:18
Alignment explanation
Indices: 26726--26760 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26716 TAAATTAGAA
*
26726 AGAAAAATAATCCTCACT
1 AGAAAAAAAATCCTCACT
*
26744 AGAAAAAAAATTCTCAC
1 AGAAAAAAAATCCTCAC
26761 AAGTTCTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.20, G:0.06, T:0.20
Consensus pattern (18 bp):
AGAAAAAAAATCCTCACT
Found at i:27197 original size:14 final size:13
Alignment explanation
Indices: 27176--27208 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
27166 CAAAATAAAC
27176 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
27189 TTCTTTTTTTGAAT
1 TT-TTTTTTTGAAT
27203 TTTTTT
1 TTTTTT
27209 ACAATCTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:30833 original size:17 final size:18
Alignment explanation
Indices: 30801--30837 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
30791 TTTTGAGCTA
30801 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
30819 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
30836 AA
1 AA
30838 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:32999 original size:15 final size:14
Alignment explanation
Indices: 32979--33024 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
32969 TGAAATCTCA
32979 TTTTCATTTTCATCT
1 TTTTCATTTTCAT-T
32994 TTTTCATTTTCATT
1 TTTTCATTTTCATT
*
33008 TCTTTCAATTTC-TT
1 T-TTTCATTTTCATT
33022 TTT
1 TTT
33025 CAATGTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 22 0.76
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCATTTTCATT
Found at i:35513 original size:12 final size:13
Alignment explanation
Indices: 35496--35529 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
35486 TCTTTCTTTC
35496 TTTTTTTTGAAAT
1 TTTTTTTTGAAAT
35509 TTTTTTTTGAAAT
1 TTTTTTTTGAAAT
35522 TTTTTTTT
1 TTTTTTTT
35530 CAATTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTTTTTTGAAAT
Found at i:35534 original size:12 final size:12
Alignment explanation
Indices: 35496--35534 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35486 TCTTTCTTTC
*
35496 TTTTTTTTGAAA
1 TTTTTTTTTAAA
35508 TTTTTTTTTGAAA
1 TTTTTTTTT-AAA
*
35521 TTTTTTTTTCAA
1 TTTTTTTTTAAA
35533 TT
1 TT
35535 ACAATATCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:38281 original size:29 final size:29
Alignment explanation
Indices: 38249--38372 Score: 124
Period size: 29 Copynumber: 4.3 Consensus size: 29
38239 GGTTGTCACC
* **
38249 ATCCCTTTTCATAATTGATAGTTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
*
38278 ATCCCTTTTCATAATCGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
* * * * * *
38307 ATTCCTTTTCATATTCGATGGTCGTCATC-
1 ATCCCTTTTCATAATCGATAGCCG-AAGCT
* *
38336 ATCCCTTTTCATAGTCGATAGCTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCT
38365 ATCCCTTT
1 ATCCCTTT
38373 CCATTGGTTG
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
28 2 0.03
29 71 0.95
30 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCT
Found at i:38464 original size:12 final size:12
Alignment explanation
Indices: 38447--38476 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
38437 AAATGATAAC
38447 ATTTAAAACAGT
1 ATTTAAAACAGT
38459 ATTTAAAACAGT
1 ATTTAAAACAGT
38471 ATTTAA
1 ATTTAA
38477 TGTACGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTTAAAACAGT
Found at i:40733 original size:120 final size:119
Alignment explanation
Indices: 40511--40773 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 119
40501 TCCTCGTTCA
* * **
40511 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * *
40576 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
40629 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
40694 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
40750 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40774 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 36 0.30
120 80 0.66
121 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:40734 original size:40 final size:40
Alignment explanation
Indices: 40511--40720 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
40501 TCCTCGTTCA
* * * ** *
40511 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
40550 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
40590 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
40630 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
40670 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
40710 AAGGCCTTCGG
1 AATGCCTTCGG
40721 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 33 0.21
40 126 0.79
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:40757 original size:80 final size:80
Alignment explanation
Indices: 40514--40773 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 80
40504 TCGTTCAAAT
* * * ** * * *
40514 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
40578 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
* * *
40593 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
40658 ACAACTCGCACGAAT
66 ACAACTAGCACGAAA
** * **
40673 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
*
40737 ATTC-ACTTAGCAC-AAA
65 A-ACAAC-TAGCACGAAA
*
40753 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
40774 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 33 0.21
80 120 0.75
81 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ACAACTAGCACGAAA
Found at i:40782 original size:41 final size:41
Alignment explanation
Indices: 40705--40782 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40695 TTAGTATCTC
* * *
40705 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40746 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40783 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:48544 original size:40 final size:40
Alignment explanation
Indices: 48453--48715 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
48443 TCCTCGTTCA
* * * * *
48453 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
48492 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
48532 AATGCCTTCGGGACTTAACCCGGATTTAAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
48572 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
48612 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
48652 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
48692 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
48716 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 36 0.18
40 155 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:48724 original size:41 final size:41
Alignment explanation
Indices: 48647--48724 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
48637 TTAGTATCTC
* * *
48647 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
48688 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
48725 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54323 original size:25 final size:25
Alignment explanation
Indices: 54290--54347 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
54280 GCTCGAGAGA
*
54290 GAGCTTACCGATATTCAACTCGCAT
1 GAGCTTACCGATAGTCAACTCGCAT
* * *
54315 GAGCTTACCGTTAGTCAGCTCGTAT
1 GAGCTTACCGATAGTCAACTCGCAT
54340 GAGCTTAC
1 GAGCTTAC
54348 TGATTATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGATAGTCAACTCGCAT
Found at i:55432 original size:26 final size:26
Alignment explanation
Indices: 55383--55432 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
55373 TTTGGTATCT
*
55383 TGATGGTATAATGGCAAAGTTTGGCA
1 TGATGGTATAATGGCAAAGCTTGGCA
*
55409 TGATGGTATGATGGACAAA-CTTGG
1 TGATGGTATAATGG-CAAAGCTTGG
55433 ATTGTTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (26 bp):
TGATGGTATAATGGCAAAGCTTGGCA
Found at i:55924 original size:7 final size:7
Alignment explanation
Indices: 55908--55945 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
55898 TAAAACCCTA
55908 AAACTTT
1 AAACTTT
*
55915 AAACTCT
1 AAACTTT
55922 AAACTTT
1 AAACTTT
55929 AAACTTT
1 AAACTTT
*
55936 AAACCTT
1 AAACTTT
55943 AAA
1 AAA
55946 ATCCTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (7 bp):
AAACTTT
Found at i:60583 original size:20 final size:20
Alignment explanation
Indices: 60549--60588 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
60539 TAGCTCAACG
* *
60549 AGCTCATTTTTAGCTCATTT
1 AGCTCATCTTAAGCTCATTT
*
60569 AGCTCATCTTAAGCTTATTT
1 AGCTCATCTTAAGCTCATTT
60589 TAGTTTGCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (20 bp):
AGCTCATCTTAAGCTCATTT
Found at i:65270 original size:20 final size:20
Alignment explanation
Indices: 65235--65273 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65225 TCAGCTCAAC
65235 TTTAGCTCAATGAGCTCATT
1 TTTAGCTCAATGAGCTCATT
* *
65255 TTTAGCTCATTTAGCTCAT
1 TTTAGCTCAATGAGCTCAT
65274 CTTAAGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTAGCTCAATGAGCTCATT
Found at i:65281 original size:20 final size:20
Alignment explanation
Indices: 65217--65286 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
65207 AGTCTACTTC
* * *
65217 AAGCTCACTCAGCTCAACTT
1 AAGCTCATTTAGCTCATCTT
* * * *
65237 TAGCTCAATGAGCTCATTTT
1 AAGCTCATTTAGCTCATCTT
*
65257 TAGCTCATTTAGCTCATCTT
1 AAGCTCATTTAGCTCATCTT
*
65277 AAGCTTATTT
1 AAGCTCATTT
65287 TAGGTTGCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (20 bp):
AAGCTCATTTAGCTCATCTT
Found at i:66942 original size:146 final size:146
Alignment explanation
Indices: 66678--66972 Score: 536
Period size: 146 Copynumber: 2.0 Consensus size: 146
66668 ATCACTTGCA
* *
66678 AGAAGGCCAAGTCCAAGATTAATTCACATGGACTCTACAAAGCATTGCCCATATCAAATGCACCA
1 AGAAGGCCAAGTCCAAGATTAATCCACATGGACTCTACAAACCATTGCCCATATCAAATGCACCA
66743 TGGGTCGATCTTTCTATGGATTTTGTCCTAGGTCTTCCAAGAACTAAAACGGGGAAGGATTCTAT
66 TGGGTCGATCTTTCTATGGATTTTGTCCTAGGTCTTCCAAGAACTAAAACGGGGAAGGATTCTAT
*
66808 CTTTGTTGTTGTAGGT
131 CTTTGTTGTTGTAGAT
* *
66824 AGAAGGCCAAGTCCAAGATTAATCCACATGGACTCTACAAACCATTGGCCATATCCAATGCACCA
1 AGAAGGCCAAGTCCAAGATTAATCCACATGGACTCTACAAACCATTGCCCATATCAAATGCACCA
*
66889 TGGGTCGATCTTTCTATGGATTTTGTCCTAGGTCTTCCTAGAACTAAAACGGGGAAGGATTCTAT
66 TGGGTCGATCTTTCTATGGATTTTGTCCTAGGTCTTCCAAGAACTAAAACGGGGAAGGATTCTAT
66954 CTTTGTTGTTGTAGAT
131 CTTTGTTGTTGTAGAT
66970 AGA
1 AGA
66973 TTTTCCAAAA
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 143 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (146 bp):
AGAAGGCCAAGTCCAAGATTAATCCACATGGACTCTACAAACCATTGCCCATATCAAATGCACCA
TGGGTCGATCTTTCTATGGATTTTGTCCTAGGTCTTCCAAGAACTAAAACGGGGAAGGATTCTAT
CTTTGTTGTTGTAGAT
Found at i:78627 original size:20 final size:19
Alignment explanation
Indices: 78604--78668 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
78594 AAGCTCAAAC
78604 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
78624 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
78644 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
78664 GAGCT
1 GAGCT
78669 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:85464 original size:10 final size:10
Alignment explanation
Indices: 85432--85488 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
85422 ATAAAATAAA
*
85432 TGAGCTGAAT
1 TGAGCTCAAT
*
85442 TGTAGCTAAAT
1 TG-AGCTCAAT
*
85453 TGAGCTCGAT
1 TGAGCTCAAT
* *
85463 TGAGCTAAAA
1 TGAGCTCAAT
85473 TGAGCTCAAT
1 TGAGCTCAAT
85483 TGAGCT
1 TGAGCT
85489 GGTCGGAGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:85468 original size:20 final size:19
Alignment explanation
Indices: 85428--85488 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
85418 ACCAATAAAA
85428 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
85448 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
*
85468 TAAAATGAGCTCAATTGAGC
1 T-AAATGAGCTCGATTGAGC
85488 T
1 T
85489 GGTCGGAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 23 0.62
21 13 0.35
22 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:91536 original size:20 final size:20
Alignment explanation
Indices: 91489--91536 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
91479 AGTAAGCTCG
91489 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
91509 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
91529 GTTGAGCT
1 GTTGAGCT
91537 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:93209 original size:13 final size:12
Alignment explanation
Indices: 93175--93206 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
93165 TTTTTCACTC
93175 CTCTTTTTCAAA
1 CTCTTTTTCAAA
93187 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
93199 TTCTTTTT
1 CTCTTTTT
93207 TCACTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:93219 original size:15 final size:13
Alignment explanation
Indices: 93199--93248 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
93189 CTTTTTCAAA
93199 TTCTTTTTTCACTT
1 TTCTTTTTTCA-TT
93213 TT-TCTTTTTCAATT
1 TTCT-TTTTTC-ATT
93227 TTCTTTTCTTCATT
1 TTCTTTT-TTCATT
93241 TTCTTTTT
1 TTCTTTTT
93249 CTCTCACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.06
14 25 0.78
15 5 0.16
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTTTTTCATT
Found at i:93220 original size:14 final size:13
Alignment explanation
Indices: 93188--93249 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
93178 TTTTTCAAAC
*
93188 TCTTTTTCAA-AT
1 TCTTTTTCAATTT
*
93200 TCTTTTTTCACTTTT
1 TC-TTTTTCA-ATTT
93215 TCTTTTTCAATTT
1 TCTTTTTCAATTT
93228 TCTTTTCTTC-ATTT
1 TC-TTT-TTCAATTT
93242 TCTTTTTC
1 TCTTTTTC
93250 TCTCACTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 5 0.12
13 15 0.36
14 16 0.38
15 6 0.14
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTTTTCAATTT
Found at i:93222 original size:27 final size:27
Alignment explanation
Indices: 93188--93249 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
93178 TTTTTCAAAC
93188 TCTTTTTCAA-ATTCTTTT-TTCACTTTT
1 TCTTTTTCAATATTCTTTTCTTCA--TTT
*
93215 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATATTCTTTTCTTCATTT
93242 TCTTTTTC
1 TCTTTTTC
93250 TCTCACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 21 0.66
28 7 0.22
29 4 0.12
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATATTCTTTTCTTCATTT
Found at i:93330 original size:6 final size:6
Alignment explanation
Indices: 93210--93317 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
93200 TCTTTTTTCA
* * * **
93210 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
93261 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
93309 -GTTTT CTTT
1 CTTTTT CTTT
93318 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:94400 original size:11 final size:10
Alignment explanation
Indices: 94376--94414 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
94366 TTGTCACTTC
*
94376 TTTTTTTTCC
1 TTTTTTTTCA
94386 TTTTTTTTCGA
1 TTTTTTTTC-A
*
94397 TTTTTTTTAA
1 TTTTTTTTCA
94407 TTTTTTTT
1 TTTTTTTT
94415 GAATTTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:94518 original size:12 final size:12
Alignment explanation
Indices: 94501--94531 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
94491 CAACTCAAAA
*
94501 TTTTTTTTGATT
1 TTTTTTTTGACT
94513 TTTTTTTTGACT
1 TTTTTTTTGACT
94525 TTTTTTT
1 TTTTTTT
94532 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTGACT
Found at i:95746 original size:21 final size:22
Alignment explanation
Indices: 95722--95766 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
95712 TCATATAATT
* *
95722 ATAATTTAAAAT-ATTAACTAA
1 ATAACTTAAAATCACTAACTAA
*
95743 ATAACTTAATATCACTAACTAA
1 ATAACTTAAAATCACTAACTAA
95765 AT
1 AT
95767 TTGAACACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAACTTAAAATCACTAACTAA
Found at i:98934 original size:13 final size:13
Alignment explanation
Indices: 98916--98961 Score: 60
Period size: 12 Copynumber: 3.7 Consensus size: 13
98906 TAGTTTCTCG
98916 AAAAAAACTC-AA
1 AAAAAAACTCGAA
* *
98928 AAAAAAATTTGAA
1 AAAAAAACTCGAA
98941 AAAAAAA-TCGAA
1 AAAAAAACTCGAA
98953 AAAAAAACT
1 AAAAAAACT
98962 AGTTTCCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAAAAACTCGAA
Found at i:99021 original size:14 final size:13
Alignment explanation
Indices: 99000--99048 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
98990 TATCAAGTTG
99000 TGAAAAAAAAATT
1 TGAAAAAAAAATT
99013 TGAAAAAAAAATT
1 TGAAAAAAAAATT
99026 GTGAAAAAAAAA-T
1 -TGAAAAAAAAATT
99039 TGAAAAAAAA
1 TGAAAAAAAA
99049 GAGAGAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.29
13 14 0.40
14 11 0.31
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.18
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:99027 original size:27 final size:26
Alignment explanation
Indices: 98997--99048 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
98987 GGATATCAAG
98997 TTGTGAAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAAA-TTGAAAAAAAAA
99024 TTGTGAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
99049 GAGAGAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (26 bp):
TTGTGAAAAAAAAATTGAAAAAAAAA
Found at i:103232 original size:21 final size:22
Alignment explanation
Indices: 103203--103253 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
103193 TCTCTCTCGC
*
103203 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
103224 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
103246 TTT-ATTTT
1 TTTCATTTT
103254 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:103259 original size:21 final size:22
Alignment explanation
Indices: 103215--103256 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
103205 TCCTTTTCGC
103215 CTTTTTCA-TTTTCA-TTTTCTT
1 CTTTTTCACTTTT-ATTTTTCTT
103236 CTTTTTCACTTTTATTTTTCT
1 CTTTTTCACTTTTATTTTTCT
103257 CTTCTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTTCACTTTTATTTTTCTT
Found at i:107365 original size:20 final size:19
Alignment explanation
Indices: 107301--107365 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
107291 TATAAACGCA
107301 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGCTG
* *
107321 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAGCT-G
107342 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
107361 AATGA
1 AATGA
107366 ACTTGAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 5 0.14
20 31 0.84
21 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:115268 original size:18 final size:17
Alignment explanation
Indices: 115234--115267 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
115224 AGACCGTATA
115234 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTTCTTTT
*
115251 CAATTTTTTTTTATTTT
1 CAATTTTTTTTTCTTTT
115268 TTTTCGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
CAATTTTTTTTTCTTTT
Found at i:115271 original size:21 final size:20
Alignment explanation
Indices: 115237--115282 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
115227 CCGTATACAA
115237 TTTTTTTTTCTTTTCAATTT
1 TTTTTTTTTCTTTTCAATTT
* *
115257 TTTTTTATTTTTTTTCGATTT
1 TTTTTT-TTTCTTTTCAATTT
115278 TTTTT
1 TTTTT
115283 CAGAAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTCTTTTCAATTT
Found at i:115283 original size:11 final size:11
Alignment explanation
Indices: 115242--115284 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
115232 TACAATTTTT
115242 TTTTCTTTTCAA
1 TTTT-TTTTCAA
*
115254 TTTTTTTT-TA
1 TTTTTTTTCAA
*
115264 TTTTTTTTCGA
1 TTTTTTTTCAA
115275 TTTTTTTTCA
1 TTTTTTTTCA
115285 GAAATCTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.33
11 14 0.52
12 4 0.15
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:121408 original size:18 final size:18
Alignment explanation
Indices: 121387--121430 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
121377 AAAAGAAGAC
121387 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
121405 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
121423 AGAGAAAA
1 AGA-AAAA
121431 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:123181 original size:33 final size:33
Alignment explanation
Indices: 123109--123182 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
123099 GAGTTAGTTT
*
123109 ATTAAATTTAGTTTAGCTCAAATAAGTGTTAGA
1 ATTAATTTTAGTTTAGCTCAAATAAGTGTTAGA
*
123142 ATTAATTTTAGTTTAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTTAGCTCAAATAAGTGTTAG-A
123176 A-TAATTT
1 ATTAATTT
123183 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (33 bp):
ATTAATTTTAGTTTAGCTCAAATAAGTGTTAGA
Found at i:127405 original size:20 final size:20
Alignment explanation
Indices: 127354--127407 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
127344 TAATTCATGT
*
127354 TTTAATTTAAGACATACTTAA
1 TTTAA-TTAAGACACACTTAA
** * *
127375 TAAAATCAAGACACATTTAA
1 TTTAATTAAGACACACTTAA
127395 TTTAATTAAGACA
1 TTTAATTAAGACA
127408 AGACAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAATTAAGACACACTTAA
Found at i:127488 original size:21 final size:22
Alignment explanation
Indices: 127463--127508 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
127453 TAAAAAACAA
127463 ATTAAACACTT-AACTAAATTT
1 ATTAAACACTTAAACTAAATTT
* *
127484 ATTAAATACTTAAACTAATTTT
1 ATTAAACACTTAAACTAAATTT
127506 ATT
1 ATT
127509 CCAGCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAACACTTAAACTAAATTT
Found at i:127574 original size:20 final size:20
Alignment explanation
Indices: 127549--127589 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
127539 ATTTAAACCG
127549 AGCTCAAACGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
***
127569 AGCTCATGTGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
127589 A
1 A
127590 AATTAGGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAAATA
Found at i:131297 original size:23 final size:22
Alignment explanation
Indices: 131245--131297 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
131235 TCCACGTCTT
*
131245 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
131267 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
131290 TTTCTTTT
1 TTTCTTTT
131298 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:139544 original size:21 final size:21
Alignment explanation
Indices: 139518--139580 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
139508 TTGGTATTTG
139518 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
139539 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
139560 GGTATTTGGTAC-AAATTGGTA
1 GG-AATTGGTACGAAA-TGGTA
139581 AAGGTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:139549 original size:11 final size:11
Alignment explanation
Indices: 139529--139561 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
139519 GAATTGGTAC
139529 GAAATGGTATG
1 GAAATGGTATG
*
139540 GAATTGGTAT-
1 GAAATGGTATG
139550 GAAATGGTATG
1 GAAATGGTATG
139561 G
1 G
139562 TATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:144811 original size:16 final size:16
Alignment explanation
Indices: 144790--144821 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
144780 GTTTTGTTGC
*
144790 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
144806 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
144822 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:147509 original size:26 final size:26
Alignment explanation
Indices: 147480--147536 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
147470 TCAACTTCTC
*
147480 TTTTTAGTT-AATAAATTCTCTTTGAG
1 TTTTTAGTTCAAGAAATTCT-TTTGAG
** *
147506 TTTTTCTTTCAAGAATTTCTTTTGAG
1 TTTTTAGTTCAAGAAATTCTTTTGAG
147532 TTTTT
1 TTTTT
147537 TTAGAAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.60
Consensus pattern (26 bp):
TTTTTAGTTCAAGAAATTCTTTTGAG
Found at i:147544 original size:25 final size:27
Alignment explanation
Indices: 147495--147544 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
147485 AGTTAATAAA
*
147495 TTCTCTTTGAGTTTTTCTTTCAAGAAT
1 TTCTCTTTGAGTTTTTCTTACAAGAAT
*
147522 TTCT-TTTGAGTTTTT-TTAGAAGA
1 TTCTCTTTGAGTTTTTCTTACAAGA
147545 GTTTTAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 11 0.52
27 4 0.19
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTTCTTACAAGAAT
Found at i:154909 original size:11 final size:11
Alignment explanation
Indices: 154874--154912 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
154864 AGCTCGATCC
*
154874 AGCTCAA-TCG
1 AGCTCAATTCT
154884 AGCTCAATT-T
1 AGCTCAATTCT
154894 AGCTCAATTCT
1 AGCTCAATTCT
154905 AGCTCAAT
1 AGCTCAAT
154913 GAGCTCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (11 bp):
AGCTCAATTCT
Found at i:154910 original size:21 final size:20
Alignment explanation
Indices: 154874--154912 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
154864 AGCTCGATCC
154874 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
*
154894 AGCTCAATTCTAGCTCAAT
1 AGCTCAA-TCGAGCTCAAT
154913 GAGCTCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:154917 original size:20 final size:20
Alignment explanation
Indices: 154874--154918 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
154864 AGCTCGATCC
*
154874 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTG
*
154894 AGCTCAATTCTAGCTCAA-TG
1 AGCTCAA-TCGAGCTCAATTG
154914 AGCTC
1 AGCTC
154919 GTTCCTAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTG
Found at i:160013 original size:30 final size:30
Alignment explanation
Indices: 159979--160075 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
159969 TAAACTAAAA
*
159979 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
160009 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* *
160039 TGAGCTGAGGTTTAGCTCATGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
160068 ATGAGCTA
1 -TGAGCTA
160076 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.90
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:164292 original size:21 final size:21
Alignment explanation
Indices: 164247--164309 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
164237 TTTGAACCAT
* *
164247 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
164269 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
164290 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
164310 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:166020 original size:54 final size:54
Alignment explanation
Indices: 165957--166059 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
165947 ATAAGTATTT
* *
165957 AGTTGCTGGAATAAATTACTCGA-CTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTC-ATCTTAGTTAATTAAGTTCAACTTAGTTAATTA
166011 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCAACTTAGTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCAACTTAGTT
166060 CGCTTAGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 45 0.98
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCAACTTAGTTAATTA
Found at i:166069 original size:54 final size:53
Alignment explanation
Indices: 165955--166079 Score: 171
Period size: 54 Copynumber: 2.3 Consensus size: 53
165945 GAATAAGTAT
* *
165955 TTAGTTGCTGGAATAAATTACTCGACTTAGTTAATTGAGTTCATCTTAGTTAA
1 TTAGTTGCTGGAATAAATTACTCGACTTAGTTAATTAAGTTCAACTTAGTTAA
**
166008 TTAAGTTGCTGGAATAAATTACTC-ATCTTAGTTAATTAAGTTCAACTTAGTTCGC
1 TT-AGTTGCTGGAATAAATTACTCGA-CTTAGTTAATTAAGTTCAACTTAGTT-AA
*
166063 TTAGTTGCTGGATTAAA
1 TTAGTTGCTGGAATAAA
166080 CTTTTAATGT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 3 0.05
54 59 0.92
55 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (53 bp):
TTAGTTGCTGGAATAAATTACTCGACTTAGTTAATTAAGTTCAACTTAGTTAA
Found at i:172826 original size:21 final size:21
Alignment explanation
Indices: 172784--172828 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
172774 TCATGTCTCA
* * *
172784 TATAATTGCTCTCTCTCGAGC
1 TATAATTGCTCTCACACAAGC
172805 TATAATTGCTCTCACACAAGC
1 TATAATTGCTCTCACACAAGC
172826 TAT
1 TAT
172829 CAGTCAGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (21 bp):
TATAATTGCTCTCACACAAGC
Found at i:173305 original size:20 final size:20
Alignment explanation
Indices: 173282--173328 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
173272 AGCTTCTTTC
* *
173282 AGCTCCAATCAGCTCATTTG
1 AGCTCAAATCAGCTCATTTA
* *
173302 AGCTTAAATCAGCTCGTTTA
1 AGCTCAAATCAGCTCATTTA
173322 AGCTCAA
1 AGCTCAA
173329 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
AGCTCAAATCAGCTCATTTA
Found at i:174655 original size:10 final size:10
Alignment explanation
Indices: 174640--174695 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
174630 TGCAAGATGA
*
174640 AGCTCACTTG
1 AGCTCACTTC
*
174650 AGCTCAATTC
1 AGCTCACTTC
*
174660 AGCTCACTCC
1 AGCTCACTTC
**
174670 AGCTCAAGTC
1 AGCTCACTTC
174680 AGCTCA-TTC
1 AGCTCACTTC
174689 GAGCTCA
1 -AGCTCA
174696 AGTCAGCTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
9 2 0.05
10 35 0.95
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (10 bp):
AGCTCACTTC
Found at i:174665 original size:20 final size:20
Alignment explanation
Indices: 174640--174733 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
174630 TGCAAGATGA
*
174640 AGCTCACTTGAGCTCAATTC
1 AGCTCACTTGAGCTCAAGTC
**
174660 AGCTCACTCCAGCTCAAGTC
1 AGCTCACTTGAGCTCAAGTC
174680 AGCTCA-TTCGAGCTCAAGTC
1 AGCTCACTT-GAGCTCAAGTC
* ** * *
174700 AGCTCCCACGAGCTTAATTC
1 AGCTCACTTGAGCTCAAGTC
174720 AGCTCA-TTGAGCTC
1 AGCTCACTTGAGCTC
174734 GTTATTAGCT
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
19 6 0.10
20 52 0.90
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (20 bp):
AGCTCACTTGAGCTCAAGTC
Found at i:174695 original size:40 final size:39
Alignment explanation
Indices: 174640--174733 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
174630 TGCAAGATGA
* *
174640 AGCTCACTTGAGCTCAATTCAGCTCACTCCAGCTCAAGTC
1 AGCTCA-TTGAGCTCAAGTCAGCTCACACCAGCTCAAGTC
* * * *
174680 AGCTCATTCGAGCTCAAGTCAGCTCCCACGAGCTTAATTC
1 AGCTCATT-GAGCTCAAGTCAGCTCACACCAGCTCAAGTC
174720 AGCTCATTGAGCTC
1 AGCTCATTGAGCTC
174734 GTTATTAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.17
40 39 0.83
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (39 bp):
AGCTCATTGAGCTCAAGTCAGCTCACACCAGCTCAAGTC
Found at i:174703 original size:10 final size:10
Alignment explanation
Indices: 174650--174704 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
174640 AGCTCACTTG
*
174650 AGCTCAATTC
1 AGCTCAAGTC
*
174660 AGCTC-ACTCC
1 AGCTCAAGT-C
174670 AGCTCAAGTC
1 AGCTCAAGTC
*
174680 AGCTC-ATTC
1 AGCTCAAGTC
174689 GAGCTCAAGTC
1 -AGCTCAAGTC
174700 AGCTC
1 AGCTC
174705 CCACGAGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.14
10 27 0.73
11 5 0.14
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (10 bp):
AGCTCAAGTC
Found at i:176668 original size:27 final size:28
Alignment explanation
Indices: 176610--176672 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
176600 AAAAAAAATC
* ***
176610 AAAAAAAATTCGAAAAAAAAATTGATTGA
1 AAAAAAAATTC-AAAAAAAAATCGAGCAA
176639 AAAAAAAATTC-AAAAAAAATCGAGCAA
1 AAAAAAAATTCAAAAAAAAATCGAGCAA
176666 AAAAAAA
1 AAAAAAA
176673 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 19 0.63
29 11 0.37
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (28 bp):
AAAAAAAATTCAAAAAAAAATCGAGCAA
Found at i:177721 original size:6 final size:6
Alignment explanation
Indices: 177693--177832 Score: 57
Period size: 6 Copynumber: 22.3 Consensus size: 6
177683 CCATTGAGCG
* * * * * * *
177693 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * * ** *
177744 AGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAATC A-AAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGAAAA
* * *
177792 AGAGAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
177833 CGAAAAAAGA
Statistics
Matches: 94, Mismatches: 32, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
5 1 0.01
6 71 0.76
7 15 0.16
8 7 0.07
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:177721 original size:18 final size:18
Alignment explanation
Indices: 177693--177832 Score: 74
Period size: 18 Copynumber: 7.8 Consensus size: 18
177683 CCATTGAGCG
* *
177693 AGAAAAGGAAAAAGAGAT
1 AGAAAAAGAAAAAGAAAT
* **
177711 TGAAAAAGAAATTG-AA-
1 AGAAAAAGAAAAAGAAAT
* *
177727 AG-AAAACAAAAAGAAAA
1 AGAAAAAGAAAAAGAAAT
177744 AGAAAAAGAAAAAGAAAT
1 AGAAAAAGAAAAAGAAAT
* *
177762 TGCAAAAGAAAAAGAAAT
1 AGAAAAAGAAAAAGAAAT
** *
177780 CA-AAAAAGTGAGAGAGAA-
1 -AGAAAAAGAAAAAGA-AAT
*
177798 AGAAAATGAAGAAAAGAAAAT
1 AGAAAAAG-A-AAAAG-AAAT
*
177819 TGAAAAAGAAAAAG
1 AGAAAAAGAAAAAG
177833 CGAAAAAAGA
Statistics
Matches: 88, Mismatches: 24, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
15 8 0.09
16 3 0.03
17 4 0.05
18 53 0.60
19 7 0.08
20 6 0.07
21 7 0.08
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (18 bp):
AGAAAAAGAAAAAGAAAT
Found at i:177743 original size:39 final size:40
Alignment explanation
Indices: 177712--177850 Score: 108
Period size: 39 Copynumber: 3.4 Consensus size: 40
177702 AAAAGAGATT
177712 GAAAAAGAAATTG-AAAGAAAACAAAAAGAAAAAGAAAAA
1 GAAAAAGAAATTGAAAAGAAAACAAAAAGAAAAAGAAAAA
** *
177751 GAAAAAGAAATTGCAAAAGAAAA-AGAAATCA-AAAAAGTGAGA
1 GAAAAAGAAATTG-AAAAGAAAACA-AAA--AGAAAAAGAAAAA
* * * *
177793 GAGAAAGAAAATG--AAGAAAAGAAAATTGAAAAAGAAAAA
1 GAAAAAGAAATTGAAAAGAAAACAAAA-AGAAAAAGAAAAA
177832 GCGAAAAAAGAAATTGAAA
1 --G-AAAAAGAAATTGAAA
177851 GAGAGCTTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
39 31 0.41
40 2 0.03
41 12 0.16
42 29 0.38
43 1 0.01
44 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.08
Consensus pattern (40 bp):
GAAAAAGAAATTGAAAAGAAAACAAAAAGAAAAAGAAAAA
Found at i:182028 original size:33 final size:33
Alignment explanation
Indices: 181990--182052 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
181980 GATTACTCAC
181990 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
182023 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
182053 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:182075 original size:15 final size:13
Alignment explanation
Indices: 182049--182105 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
182039 TCAAGCTCTC
*
182049 TTTCAATTTCTTT
1 TTTCATTTTCTTT
182062 TTTCACTTTT-TCTT
1 TTTCA-TTTTCT-TT
182076 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
182090 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
182104 TT
1 TT
182106 CTCTCACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 26 0.68
15 5 0.13
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:182079 original size:27 final size:27
Alignment explanation
Indices: 182049--182106 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
182039 TCAAGCTCTC
182049 TTTCAA-TTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTTCTTTTCTTCA--TTTTCTT
182076 TTTCAATTTTCTTTTCTTCATTTTCTT
1 TTTCAATTTTCTTTTCTTCATTTTCTT
182103 TTTC
1 TTTC
182107 TCTCACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.59
28 8 0.28
29 4 0.14
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTCAATTTTCTTTTCTTCATTTTCTT
Found at i:182165 original size:18 final size:18
Alignment explanation
Indices: 182067--182205 Score: 88
Period size: 18 Copynumber: 7.7 Consensus size: 18
182057 TCTTTTTTCA
182067 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
182086 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
182106 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
182124 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
182142 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
182160 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCATTTT
** * *
182175 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCATTTT
*
182193 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
182206 TCGCTCAATG
Statistics
Matches: 91, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.08
16 5 0.05
17 6 0.07
18 54 0.59
19 3 0.03
20 8 0.09
21 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:182187 original size:6 final size:6
Alignment explanation
Indices: 182067--182174 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
182057 TCTTTTTTCA
* * * **
182067 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
182118 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
182166 -GTTTT CTTT
1 CTTTTT CTTT
182175 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:182206 original size:81 final size:83
Alignment explanation
Indices: 182052--182206 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
182042 AGCTCTCTTT
* * **
182052 CAATTTCTTTTTTCACTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTT
1 CAATTTCTTTTTT-ACTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTT
*
182117 TCGATTTCTTTTTCTTTTG
65 TCCATTTCTTTTTCTTTTG
* * *
182136 CAATTTC-TTTTT-CTTTTTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTT
1 CAATTTCTTTTTTACTTTTTCGTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTT
*
182198 TCCTTTTCT
65 TCCATTTCT
182207 CGCTCAATGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 9 0.15
81 40 0.66
83 5 0.08
84 7 0.11
ACGTcount: A:0.09, C:0.20, G:0.03, T:0.68
Consensus pattern (83 bp):
CAATTTCTTTTTTACTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTTT
CCATTTCTTTTTCTTTTG
Found at i:183264 original size:28 final size:28
Alignment explanation
Indices: 183188--183267 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
183178 GCAAGACTTT
* **
183188 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCAC-TTTTTTTCACTTTTTTTTTTTTGC
*
183217 TCACTTTTTTTC-TTTCTTTTTTTTTTGC
1 TCACTTTTTTTCACTT-TTTTTTTTTTGC
183245 TCGA-TTTTTTTCACTTTTTTTTT
1 TC-ACTTTTTTTCACTTTTTTTTT
183268 GAATTTCGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 2 0.05
28 34 0.79
29 7 0.16
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTCACTTTTTTTTTTTTGC
Found at i:184083 original size:20 final size:20
Alignment explanation
Indices: 184029--184083 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
184019 AACTTAAGCC
184029 AAGCTCAAA-CGAGCTAAAGT
1 AAGCT-AAATCGAGCTAAAGT
** * *
184049 AAGCTAAATTAAGCTCATGT
1 AAGCTAAATCGAGCTAAAGT
184069 AAGCTAAATCGAGCT
1 AAGCTAAATCGAGCT
184084 GGGAAAAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGCTAAATCGAGCTAAAGT
Found at i:185617 original size:11 final size:11
Alignment explanation
Indices: 185601--185648 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
185591 AGTCATTGTG
*
185601 AAAAAAATTGA
1 AAAAAAATTCA
185612 AAAAAAA-TC-
1 AAAAAAATTCA
185621 -AAAAAATTCA
1 AAAAAAATTCA
185631 AAAAAAATTCA
1 AAAAAAATTCA
185642 AAAAAAA
1 AAAAAAA
185649 GTTTATTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 1 0.03
11 24 0.73
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:185626 original size:19 final size:20
Alignment explanation
Indices: 185602--185646 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
185592 GTCATTGTGA
*
185602 AAAAAATTGAAAAAAAA-TC
1 AAAAAATTCAAAAAAAATTC
185621 AAAAAATTCAAAAAAAATTC
1 AAAAAATTCAAAAAAAATTC
185641 AAAAAA
1 AAAAAA
185647 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAATTCAAAAAAAATTC
Found at i:186774 original size:36 final size:36
Alignment explanation
Indices: 186729--186812 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
186719 AGAAATGAAA
*
186729 GAAAAAGAAGATGAATGTGAGAATAAAAAGAAAATT
1 GAAAAAGAAGATGAATGTGAGAACAAAAAGAAAATT
* *
186765 GAAAAAGAAGATGAGTGTGAGAACGAAAAGAAAATT
1 GAAAAAGAAGATGAATGTGAGAACAAAAAGAAAATT
*
186801 GAAAAAAAAGAT
1 GAAAAAGAAGAT
186813 AAGTTTGGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.61, C:0.01, G:0.24, T:0.14
Consensus pattern (36 bp):
GAAAAAGAAGATGAATGTGAGAACAAAAAGAAAATT
Found at i:186851 original size:18 final size:18
Alignment explanation
Indices: 186828--186888 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
186818 TGGTGAAATG
*
186828 AAAGAAAAAGACATTGAA
1 AAAGAAAAAGAAATTGAA
*
186846 AAAGAAAAAGAAATTGCA
1 AAAGAAAAAGAAATTGAA
* *
186864 AAAGAACAGGAAATTGAA
1 AAAGAAAAAGAAATTGAA
186882 AAAGAAA
1 AAAGAAA
186889 TTGAAAGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.67, C:0.05, G:0.18, T:0.10
Consensus pattern (18 bp):
AAAGAAAAAGAAATTGAA
Found at i:186867 original size:30 final size:30
Alignment explanation
Indices: 186843--186899 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
186833 AAAAGACATT
186843 GAAAAAGAAAAAGAAATTGCAAAAGAACAG
1 GAAAAAGAAAAAGAAATTGCAAAAGAACAG
**
186873 GAAATTGAAAAAGAAATTG-AAAGAGAA
1 GAAAAAGAAAAAGAAATTGCAAA-AGAA
186900 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.65, C:0.04, G:0.21, T:0.11
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAATTGCAAAAGAACAG
Found at i:188648 original size:20 final size:20
Alignment explanation
Indices: 188618--188683 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
188608 TGCGGTTCAC
*
188618 CTCACTCGAGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
188638 CTCATTTGAGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*** *
188658 CTCCCACGAGCTCAATTCAG
1 CTCATTCGAGCTCAAGTCAG
188678 CTCATT
1 CTCATT
188684 GCTGGAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:191728 original size:20 final size:20
Alignment explanation
Indices: 191705--191758 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
191695 AGTTTTTCCC
*
191705 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
191725 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
191745 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
191759 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:191749 original size:30 final size:30
Alignment explanation
Indices: 191705--191778 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
191695 AGTTTTTCCC
191705 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
191735 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
191765 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
191779 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:191768 original size:20 final size:20
Alignment explanation
Indices: 191705--191769 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
191695 AGTTTTTCCC
* * * *
191705 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
191725 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
191744 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
191765 AGCTC
1 AGCTC
191770 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:200219 original size:10 final size:10
Alignment explanation
Indices: 200204--200230 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
200194 TGTAGATTCA
200204 AAAAAAATCG
1 AAAAAAATCG
200214 AAAAAAATCG
1 AAAAAAATCG
200224 AAAAAAA
1 AAAAAAA
200231 AATTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:200220 original size:12 final size:12
Alignment explanation
Indices: 200203--200257 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
200193 TTGTAGATTC
200203 AAAAAAAATCG-
1 AAAAAAAATCGA
200214 -AAAAAAATCGA
1 AAAAAAAATCGA
*
200225 AAAAAAAATTGA
1 AAAAAAAATCGA
*
200237 AAAAAAAATTGA
1 AAAAAAAATCGA
200249 AAAAAAAAT
1 AAAAAAAAT
200258 TGCATACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
10 10 0.24
12 31 0.76
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:200258 original size:12 final size:12
Alignment explanation
Indices: 200214--200259 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
200204 AAAAAAATCG
*
200214 AAAAAAATCGAA
1 AAAAAAATTGAA
200226 AAAAAAATTGAA
1 AAAAAAATTGAA
200238 AAAAAAATTGAA
1 AAAAAAATTGAA
200250 AAAAAAATTG
1 AAAAAAATTG
200260 CATACGGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:211241 original size:10 final size:10
Alignment explanation
Indices: 211226--211276 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
211216 TAGTAGTTTC
211226 TTCAAAAAAA
1 TTCAAAAAAA
211236 TTCAAAAAAA
1 TTCAAAAAAA
*
211246 ATC-AAAAAA
1 TTCAAAAAAA
211255 TTCAAAAAAAAA
1 TTC--AAAAAAA
211267 TTCAAAAAAA
1 TTCAAAAAAA
211277 AATTGGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 8 0.22
10 19 0.53
12 9 0.25
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:211254 original size:19 final size:21
Alignment explanation
Indices: 211230--211275 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
211220 AGTTTCTTCA
211230 AAAAAATTC-AAAAAAAA-TC
1 AAAAAATTCAAAAAAAAATTC
211249 AAAAAATTCAAAAAAAAATTC
1 AAAAAATTCAAAAAAAAATTC
211270 AAAAAA
1 AAAAAA
211276 AAATTGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAATTCAAAAAAAAATTC
Found at i:211275 original size:9 final size:9
Alignment explanation
Indices: 211230--211263 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
211220 AGTTTCTTCA
211230 AAAAAATTC
1 AAAAAATTC
*
211239 AAAAAAAATC
1 -AAAAAATTC
211249 AAAAAATTC
1 AAAAAATTC
211258 AAAAAA
1 AAAAAA
211264 AAATTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAATTC
Found at i:211280 original size:12 final size:11
Alignment explanation
Indices: 211229--211277 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
211219 TAGTTTCTTC
211229 AAAAAAATTCA
1 AAAAAAATTCA
211240 AAAAAAA-TC-
1 AAAAAAATTCA
211249 -AAAAAATTCAA
1 AAAAAAATTC-A
211260 AAAAAAATTCA
1 AAAAAAATTCA
211271 AAAAAAA
1 AAAAAAA
211278 ATTGGTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 2 0.06
11 15 0.44
12 9 0.26
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:211336 original size:14 final size:14
Alignment explanation
Indices: 211317--211355 Score: 69
Period size: 14 Copynumber: 2.7 Consensus size: 14
211307 GATATCAAGT
211317 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
211331 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
211345 TGAGAAAAAAA
1 TGA-AAAAAAA
211356 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.18
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Done.