Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3332
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: 12649
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:399 original size:15 final size:15
Alignment explanation
Indices: 379--431 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
369 TTTCCTTTTT
379 TTTTTTAAACACAAA
1 TTTTTTAAACACAAA
*
394 TTTTTTAAAATACAAGAA
1 TTTTTT-AAACAC-A-AA
**
412 TTTTAGAAACACAAA
1 TTTTTTAAACACAAA
427 TTTTT
1 TTTTT
432 AAAAAAACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 12 0.40
16 6 0.20
17 6 0.20
18 6 0.20
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (15 bp):
TTTTTTAAACACAAA
Found at i:399 original size:16 final size:16
Alignment explanation
Indices: 378--435 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
368 TTTTCCTTTT
*
378 TTTTTTTAAACACAAA
1 TTTTTTAAAACACAAA
*
394 TTTTTTAAAATACAAGA
1 TTTTTTAAAACACAA-A
*
411 -ATTTTAGAAACACAAA
1 TTTTTTA-AAACACAAA
427 -TTTTTAAAA
1 TTTTTTAAAA
436 AAACACGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.09
16 24 0.69
17 8 0.23
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTTTTAAAACACAAA
Found at i:415 original size:17 final size:16
Alignment explanation
Indices: 385--436 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
375 TTTTTTTTTT
*
385 AAACACAAATTTTTTA
1 AAACACAAATTTTTAA
* * *
401 AAATACAAGAATTTTAG
1 AAACACAA-ATTTTTAA
418 AAACACAAATTTTTAA
1 AAACACAAATTTTTAA
434 AAA
1 AAA
437 AACACGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (16 bp):
AAACACAAATTTTTAA
Found at i:560 original size:17 final size:18
Alignment explanation
Indices: 537--785 Score: 173
Period size: 17 Copynumber: 14.2 Consensus size: 18
527 ACGGGAATTT
537 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
554 ATTTTGAAAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
**
572 -TTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
* *
589 TTTTT-TAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* *
606 -ATTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
*
623 TTTTTG--AATACGAAAA
1 TTTTTGAAAACACGAAAA
*
639 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
656 TTTTTG-AAACAC-AGAAG
1 TTTTTGAAAACACGA-AAA
673 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* * * *
692 -ATTTGAAAA-ATTGGAAT
1 TTTTTGAAAACA-CGAAAA
*
709 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
727 TTTTTGAAAAACATGAAAA
1 TTTTTG-AAAACACGAAAA
* **
746 TTTTTG-CAACACGGGAA
1 TTTTTGAAAACACGAAAA
763 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-AAAA
782 TTTT
1 TTTT
786 CCAATTTTTA
Statistics
Matches: 178, Mismatches: 37, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
16 19 0.11
17 84 0.47
18 42 0.24
19 32 0.18
20 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:611 original size:34 final size:32
Alignment explanation
Indices: 573--660 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
563 ACACTGGAAT
* *
573 TTTGAAAACACGAGGATTTTTTAAATACGAAAAA
1 TTTGAAAACACGA-AAATTTTTAAATACG-AAAA
* *
607 TTTGAAAACAAGAAAATTTTTGAATACGAAAA
1 TTTGAAAACACGAAAATTTTTAAATACGAAAA
*
639 TTTTAGAAACACGAAAATTTTT
1 TTTGA-AAACACGAAAATTTTT
661 GAAACACAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 8 0.17
33 27 0.57
34 12 0.26
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (32 bp):
TTTGAAAACACGAAAATTTTTAAATACGAAAA
Found at i:633 original size:33 final size:33
Alignment explanation
Indices: 590--663 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
580 ACACGAGGAT
*
590 TTTTTAAATACGAAAAATTTGA-AAACAAGAAAA
1 TTTTTGAATACG-AAAATTTGAGAAACAAGAAAA
* *
623 TTTTTGAATACGAAAATTTTAGAAACACGAAAA
1 TTTTTGAATACGAAAATTTGAGAAACAAGAAAA
656 TTTTTGAA
1 TTTTTGAA
664 ACACAGAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 8 0.22
33 29 0.78
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (33 bp):
TTTTTGAATACGAAAATTTGAGAAACAAGAAAA
Found at i:731 original size:54 final size:55
Alignment explanation
Indices: 632--777 Score: 142
Period size: 54 Copynumber: 2.7 Consensus size: 55
622 ATTTTTGAAT
* **
632 ACGAAAAT-TTTAGAAACACGAAAATTTTTG-AAACAC-AGAAGTTTTT-AGAAAAC
1 ACGAAAATATTT-GAAAAACGGGAATTTTTGAAAACACGAGAAGTTTTTGA-AAAAC
**
685 ACGAAAA-ATTTGAAAAATTGGAATTTTTTGAAAACACGAGAA-TTTTTGAAAAAC
1 ACGAAAATATTTGAAAAACGGGAA-TTTTTGAAAACACGAGAAGTTTTTGAAAAAC
* * * *
739 ATGAAAATTTTTGCAACACGGGAATTTTTGAAAACACGA
1 ACGAAAATATTTGAAAAACGGGAATTTTTGAAAACACGA
778 AAAATTTTCC
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
52 7 0.09
53 16 0.21
54 37 0.49
55 16 0.21
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (55 bp):
ACGAAAATATTTGAAAAACGGGAATTTTTGAAAACACGAGAAGTTTTTGAAAAAC
Found at i:757 original size:36 final size:37
Alignment explanation
Indices: 537--785 Score: 154
Period size: 35 Copynumber: 7.1 Consensus size: 37
527 ACGGGAATTT
* * *
537 TTTTTG-AAACACGAAAAATTTTG-AAAACACTG-GAA
1 TTTTTGAAAACACGAGAATTTTTGAAAAACA-TGAAAA
* * *
572 -TTTTGAAAACACGAGGATTTTTTAAATAC--GAAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
* * * *
606 -ATTTGAAAACAAGAAAATTTTTG-AATAC--GAAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
* * * *
639 TTTTAG-AAACACGAAAATTTTTGAAACACA-G-AAG
1 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
** * * *
673 TTTTTAGAAAACACGA-AAAATTTGAAAAA-TTGGAAT
1 TTTTT-GAAAACACGAGAATTTTTGAAAAACATGAAAA
709 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
* * *
746 TTTTTG-CAACACGGGAATTTTTG-AAAACACGAAAA
1 TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
*
781 ATTTT
1 TTTTT
786 CCAATTTTTA
Statistics
Matches: 171, Mismatches: 31, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
33 27 0.16
34 38 0.22
35 51 0.30
36 45 0.26
37 10 0.06
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (37 bp):
TTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAA
Found at i:929 original size:20 final size:22
Alignment explanation
Indices: 889--931 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
879 TGTTACCTTA
889 TTTTTGAAAAACACGAGAAATT
1 TTTTTGAAAAACACGAGAAATT
*
911 TTTTTG-AAGACACGA-AAATT
1 TTTTTGAAAAACACGAGAAATT
931 T
1 T
932 CGAAACCCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TTTTTGAAAAACACGAGAAATT
Found at i:1121 original size:17 final size:17
Alignment explanation
Indices: 1092--1141 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1082 AAAATTATTT
*
1092 AAAA-TAAAATAAAATA
1 AAAATTAAATTAAAATA
*
1108 AAAATTAAATTAAATTA
1 AAAATTAAATTAAAATA
1125 AAAATATAAATATAAAA
1 AAAAT-TAAAT-TAAAA
1142 ATGCATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 5 0.18
19 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTAAATTAAAATA
Found at i:1294 original size:19 final size:19
Alignment explanation
Indices: 1272--1332 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 19
1262 ATTGAACCTC
1272 TTTTTTTCTTTTTTCCTTCT
1 TTTTTTTCTTTTTT-CTTCT
1292 TTTTTCCTTCTCTTTTTCTTCT
1 TTTTT--TTCT-TTTTTCTTCT
1314 TTTTCTTTCTTTTTT-TTCT
1 TTTT-TTTCTTTTTTCTTCT
1333 CTGCTGGGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.11
20 10 0.27
21 4 0.11
22 13 0.35
23 6 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTTTTTTCTTCT
Found at i:1305 original size:13 final size:11
Alignment explanation
Indices: 1277--1328 Score: 72
Period size: 11 Copynumber: 4.8 Consensus size: 11
1267 ACCTCTTTTT
1277 TTCTTTTTTCC
1 TTCTTTTTTCC
1288 TTCTTTTTTCC
1 TTCTTTTTTCC
1299 TTCTCTTTTT-C
1 TTCT-TTTTTCC
*
1310 TTC-TTTTTCT
1 TTCTTTTTTCC
1320 TTCTTTTTT
1 TTCTTTTTT
1329 TTCTCTGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 5 0.14
10 3 0.08
11 24 0.65
12 5 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTTTCC
Found at i:1332 original size:22 final size:22
Alignment explanation
Indices: 1272--1329 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1262 ATTGAACCTC
*
1272 TTTT-TTTCTTTTTTCCTTCTT
1 TTTTCTTTCTTTTTTTCTTCTT
* *
1293 TTTTCCTTCTCTTTTTCTTC-T
1 TTTTCTTTCTTTTTTTCTTCTT
1314 TTTTCTTTCTTTTTTT
1 TTTTCTTTCTTTTTTT
1330 TCTCTGCTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTCTTTCTTTTTTTCTTCTT
Found at i:1614 original size:13 final size:13
Alignment explanation
Indices: 1596--1631 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1586 TCTTTTTTTT
1596 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
1609 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
1622 T-TCTTCTTCT
1 TCT-TTCTTCT
1632 CTTCAAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTTTCTTCTTCC
Found at i:2081 original size:29 final size:30
Alignment explanation
Indices: 2039--2105 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2029 AAGTTAGGTG
*
2039 TGAAATTAAAG-AAAGTTTAAGGGTCAAAA
1 TGAAATTTAAGAAAAGTTTAAGGGTCAAAA
* *
2068 TGAAATTTAGGAAAAGTTTAGGGGTCAAAA
1 TGAAATTTAAGAAAAGTTTAAGGGTCAAAA
*
2098 TGCAATTT
1 TGAAATTT
2106 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.28
Consensus pattern (30 bp):
TGAAATTTAAGAAAAGTTTAAGGGTCAAAA
Found at i:2557 original size:54 final size:55
Alignment explanation
Indices: 2371--2588 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
2361 CACGTGAGCC
* *
2371 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
2426 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
2477 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
2531 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
2586 AAG
1 AAG
2589 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:2586 original size:14 final size:14
Alignment explanation
Indices: 2567--2601 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2557 GAGTTGATTT
2567 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
2581 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
2595 TTGAAAA
1 TTGAAAA
2602 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2844 original size:85 final size:86
Alignment explanation
Indices: 2692--2938 Score: 306
Period size: 85 Copynumber: 2.8 Consensus size: 86
2682 AAACAGAAAT
* * *
2692 TAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 TAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
2757 TTGATTTGAAAAG-TAGAATT-A
65 TTGATTTGAAAAGATAG-ATTGA
* * *
2778 GTAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAA
1 -TAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGA
2841 GTTGATTTTTGAAAAGCATAGATTGA
64 GTTGA--TTTGAAAAG-ATAGATTGA
* *
2867 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 TAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
2931 GTTGATTT
64 GTTGATTT
2939 TTGAAAAACA
Statistics
Matches: 139, Mismatches: 11, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 33 0.24
88 30 0.22
89 4 0.03
90 33 0.24
92 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (86 bp):
TAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGA
Found at i:2926 original size:90 final size:88
Alignment explanation
Indices: 2693--2945 Score: 322
Period size: 90 Copynumber: 2.9 Consensus size: 88
2683 AACAGAAATT
* * *
2693 AAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
*
2758 TGA--TTTGAAAAGTAGAATTAGT
65 TGATTTTTGAAAAGTAGAATTAGA
* * *
2780 AAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAGT
1 AAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAGT
2843 TGATTTTTGAAAAGCATAG-ATT-GAA
65 TGATTTTTGAAAAG--TAGAATTAG-A
*
2868 AAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGAG
2932 TTGATTTTTGAAAA
64 TTGATTTTTGAAAA
2946 ACAAAATTAA
Statistics
Matches: 145, Mismatches: 11, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 33 0.23
88 27 0.19
89 3 0.02
90 43 0.30
92 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (88 bp):
AAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGTT
GATTTTTGAAAAGTAGAATTAGA
Found at i:3087 original size:122 final size:122
Alignment explanation
Indices: 2868--3184 Score: 519
Period size: 122 Copynumber: 2.6 Consensus size: 122
2858 ATAGATTGAA
* * * * * *
2868 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTAAAAATACCTCGGC--GTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGT
2933 TGATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
64 TGATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
* *
2992 AAAACATAAACTAAAAATACCTCGGCGTGTCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
3057 -TTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
66 ATTTTTGAAAAAC-AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
3114 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
3179 ATTTTT
66 ATTTTT
3185 TTTTAAAAAA
Statistics
Matches: 181, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
121 12 0.07
122 141 0.78
123 5 0.03
124 23 0.13
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (122 bp):
AAAACATAAACTAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:3639 original size:190 final size:193
Alignment explanation
Indices: 3003--3818 Score: 1400
Period size: 190 Copynumber: 4.3 Consensus size: 193
2993 AAACATAAAC
** ** *
3003 TAAAAATACCTCGGCGTGTCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGTTTTTGAAAAA
1 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
3068 CAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATA
66 CAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATA
3133 CCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAAAATT
131 CCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTTAAAAAAATT
3198 TAAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTG----
1 T-AAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAA
3259 ---AAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTC-------AACATAAACTAAAAAT
65 ACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAAT
3314 ACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAAATT
130 ACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATT
*
3377 TAAAAATACCTCAACATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
1 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
3442 CAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACT-AAAATA
66 CAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATA
3506 CCTCGGCGTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTAAAAAAATT
131 CCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATT
*
3567 TAAAAAT-CCTCAACGTGTCTTGAGGCTCAGCTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
1 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
3631 CAAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAAT
66 C-AAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAAT
3696 ACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATT
130 ACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATT
3760 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
3819 CCTTGGAAAG
Statistics
Matches: 592, Mismatches: 9, Indels: 41
0.92 0.01 0.06
Matches are distributed among these distances:
178 58 0.10
179 16 0.03
182 64 0.11
185 39 0.07
189 95 0.16
190 115 0.19
191 32 0.05
192 46 0.08
193 22 0.04
194 50 0.08
195 1 0.00
196 54 0.09
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (193 bp):
TAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA
CAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATA
CCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATT
Found at i:3662 original size:123 final size:123
Alignment explanation
Indices: 3520--3747 Score: 291
Period size: 123 Copynumber: 1.9 Consensus size: 123
3510 GGCGTGCCCG
* * * **
3520 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAA-A-AATTTAAAAAT-CCTCAACG
1 AGGCTCAACTCACCTCTCGCAATATGAG-TCA--ATTTAAAACATAAACTAAAAATACCTCAACG
* ** * *
3582 TGTCTTGAGGCTCAGCTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAATTAAA
63 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAATTAAA
* **
3643 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
3708 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
66 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
3748 TTTAAAAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
120 7 0.08
121 1 0.01
122 11 0.12
123 70 0.79
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (123 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAACGTGC
CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAATTAAA
Found at i:11602 original size:26 final size:27
Alignment explanation
Indices: 11570--11621 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
11560 GTAATTATTG
11570 AAAATTTGAAAACTG-AATCTCGATTA
1 AAAATTTGAAAACTGAAATCTCGATTA
11596 AAAATTTGAAAACTGAAATCTCGATT
1 AAAATTTGAAAACTGAAATCTCGATT
11622 TATTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (27 bp):
AAAATTTGAAAACTGAAATCTCGATTA
Found at i:11958 original size:16 final size:16
Alignment explanation
Indices: 11936--11986 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
11926 CCTTTTTTTT
**
11936 AACACAAATTTTTTAA
1 AACACAAATTTTAGAA
*
11952 AATACAAGAATTTTAGAA
1 AACAC-A-AATTTTAGAA
11970 AACACAAATTTTA-AA
1 AACACAAATTTTAGAA
11985 AA
1 AA
11987 AACACGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 2 0.07
18 12 0.41
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (16 bp):
AACACAAATTTTAGAA
Found at i:11987 original size:16 final size:16
Alignment explanation
Indices: 11936--11987 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
11926 CCTTTTTTTT
11936 AACACAAATTTTTTAAAA
1 AACACAAA--TTTTAAAA
* *
11954 TACA-AGAATTTTAGAA
1 AACACA-AATTTTAAAA
11970 AACACAAATTTTAAAA
1 AACACAAATTTTAAAA
11986 AA
1 AA
11988 ACACGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 21 0.75
17 2 0.07
18 5 0.18
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.29
Consensus pattern (16 bp):
AACACAAATTTTAAAA
Found at i:12040 original size:17 final size:17
Alignment explanation
Indices: 11986--12333 Score: 181
Period size: 18 Copynumber: 19.9 Consensus size: 17
11976 AATTTTAAAA
11986 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
12002 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
12020 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
12037 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
* * *
12056 AAACGCGAAAGTTTTGG
1 AAACACGAAAATTTTTG
* **
12073 AAAAACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
12094 AAACA-GAAAA-ATTTG
1 AAACACGAAAATTTTTG
*
12109 AAAACACTG-GAA-TTTTG
1 -AAACAC-GAAAATTTTTG
** *
12126 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* *
12144 AAATACGAAAA-ATTTG
1 AAACACGAAAATTTTTG
*
12160 AAACAAGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
12176 AAATACGAAAATTTTAAG
1 AAACACGAAAATTTT-TG
12194 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
**
12211 AAACACAGAAGTTTTTTAG
1 AAACAC-GAAAATTTTT-G
*
12230 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* * *
12248 AAA-ATTGGAATTTTTTG
1 AAACA-CGAAAATTTTTG
*
12265 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
12283 AAAACATGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* **
12301 CAACACGGGAATTTTTG
1 AAACACGAAAATTTTTG
12318 AAACACGAAAAATTTT
1 AAACACG-AAAATTTT
12334 CCATTTTTAT
Statistics
Matches: 247, Mismatches: 63, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
15 4 0.02
16 41 0.17
17 78 0.32
18 91 0.37
19 18 0.07
20 6 0.02
21 9 0.04
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:12185 original size:32 final size:34
Alignment explanation
Indices: 12137--12213 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 34
12127 AAACACGAGG
*
12137 ATTTTTTAAATACGAAAAATTT-GAAACAAGAAA
1 ATTTTTGAAATACGAAAAATTTAGAAACAAGAAA
* *
12170 A-TTTTGAAATACGAAAATTTTAAGAAACACGAAA
1 ATTTTTGAAATACGAAAAATTT-AGAAACAAGAAA
12204 ATTTTTGAAA
1 ATTTTTGAAA
12214 CACAGAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 18 0.47
33 1 0.03
34 11 0.29
35 8 0.21
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (34 bp):
ATTTTTGAAATACGAAAAATTTAGAAACAAGAAA
Found at i:12306 original size:35 final size:36
Alignment explanation
Indices: 12088--12333 Score: 139
Period size: 35 Copynumber: 7.1 Consensus size: 36
12078 CGGGAATTTT
* *
12088 TTTTTG-AAACA-GAAAA-ATTTGAAAACACTG-GAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACA-TGAAAA
** *
12121 -TTTTGAAAACACGAGGATTTTTTAAATAC--GAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAA-ACATGAAAA
* *
12155 -ATTTG-AAACAAGAAAA-TTTTGAAATAC--GAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAA-ACATGAAAA
* **
12187 -TTTTAAGAAACACGAAAATTTTTGAAACACA-GAAGT
1 TTTTTGA-AAACACGAAAATTTTTGAAA-ACATGAAAA
* * * *
12223 TTTTTAGAAAACACGAAAAATTTTGAAAA-TTGGAAT
1 TTTTT-GAAAACACGAAAATTTTTGAAAACATGAAAA
*
12259 TTTTTGAAAACACGAGAATTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACATGAAAA
* ** *
12295 TTTTTG-CAACACGGGAATTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAACATGAAAA
*
12329 ATTTT
1 TTTTT
12334 CCATTTTTAT
Statistics
Matches: 170, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
32 23 0.14
33 14 0.08
34 33 0.19
35 52 0.31
36 24 0.14
37 23 0.14
38 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (36 bp):
TTTTTGAAAACACGAAAATTTTTGAAAACATGAAAA
Found at i:12462 original size:22 final size:21
Alignment explanation
Indices: 12435--12477 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
12425 TTACCCCTTA
12435 TTTTTGAAAACACGAGAAATTT
1 TTTTTGAAAACACGA-AAATTT
*
12457 TTTTTGAAGACACGAAAATTT
1 TTTTTGAAAACACGAAAATTT
12478 CGAAACCCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TTTTTGAAAACACGAAAATTT
Done.