Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_175
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: 143653
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:6908 original size:669 final size:670
Alignment explanation
Indices: 5630--7131 Score: 2943
Period size: 669 Copynumber: 2.2 Consensus size: 670
5620 GTGGCTGTTC
5630 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
1 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
5695 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
66 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
5760 AGATGAAATATTTGAATTGTGAGCTATCCAATTGTTTTTTAAATTATGCTTCTTTAATTAAACTA
131 AGATGAAATATTTGAATTGTGAGCTATCCAATTGTTTTTTAAATTATGCTTCTTTAATTAAACTA
*
5825 TTTGCTGGAATAATTATTGCATATATGTTTTAGTTCATTTATTTAAGTAAGTTTAATGTTTGTTA
196 GTTGCTGGAATAATTATTGCATATATGTTTTAGTTCATTTATTTAAGTAAGTTTAATGTTTGTTA
5890 TGATTAATAAGTGTTTTCATTTGTTTAATAAACTCATTTTAATGAGTTTATTGCAGGTGACTTTT
261 TGATTAATAAGTGTTTTCATTTGTTTAATAAACTCATTTTAATGAGTTTATTGCAGGTGACTTTT
5955 TAGCTTATAGTGGTTACAATTCAAGGCTGTTACACATTTAATTAAGTGGCTGTTCAAGTTCTTTT
326 TAGCTTATAGTGGTTACAATTCAAGGCTGTTACACATTTAATTAAGTGGCTGTTCAAGTTCTTTT
*
6020 GAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAATCATTAAAGGAGTTTTTAAAGGGCA
391 GAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAATCATTAAAGGAGTTTTTAAAGAGCA
6085 TTTTATGCCCTTTAAAATTCAGCAGCAACTCTTCCACTTCCAGCCGTTTTTGGAGCTTTCAAGAG
456 TTTTATGCCCTTTAAAATTCAGCAGCAACTCTTCCACTTCCAGCCGTTTTTGGAGCTTTCAAGAG
6150 AAATTAATCAAGCCTTTGAATGTCATTAAGAAGCTGGTTAAGAGATGGTGTCTATTCAACTAGCC
521 AAATTAATCAAGCCTTTGAATGTCATTAAGAAGCTGGTTAAGAGATGGTGTCTATTCAACTAGCC
*
6215 AAAGACAACTCAAGAGTCATTTTCTAAGCCATTAAAGACATTCAAATTAGCTGAAGTAAAGTGAT
586 AAAGACAACTCAAGAGTCATTTTCTAAGCCATTAAAGACATTCAAATCAGCTGAAGTAAAGTGAT
6280 TTTATGGAAGGAGTTATTTG
651 TTTATGGAAGGAGTTATTTG
6300 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
1 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
6365 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGA-GGAACTTTTTGCTGAATAT
66 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
6429 AGATGAAATATTTGAATTGTGAGCTATCCAATTGTTTTTTAAATTATGCTTCTTTAATTAAACTA
131 AGATGAAATATTTGAATTGTGAGCTATCCAATTGTTTTTTAAATTATGCTTCTTTAATTAAACTA
6494 GTTGCTGGAATAATTATTGCATATATGTTTTAGTTCATTTATTTAAGTAAGTTTAATGTTTGTTA
196 GTTGCTGGAATAATTATTGCATATATGTTTTAGTTCATTTATTTAAGTAAGTTTAATGTTTGTTA
*
6559 TGATTAATAAGTTTTTTCATTTGTTTAATAAACTCATTTTAATGAGTTTATTGCAGGTGACTTTT
261 TGATTAATAAGTGTTTTCATTTGTTTAATAAACTCATTTTAATGAGTTTATTGCAGGTGACTTTT
6624 TAGCTTATAGTGGTTACAATTCAAGGCTGTTACACATTTAATTAAGTGGCTGTTCAAGTTCTTTT
326 TAGCTTATAGTGGTTACAATTCAAGGCTGTTACACATTTAATTAAGTGGCTGTTCAAGTTCTTTT
6689 GAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAATCATTAAAGGAGTTTTTAAAGAGCA
391 GAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAATCATTAAAGGAGTTTTTAAAGAGCA
6754 TTTTATGCCCTTTAAAATTCAGCAGCAACTCTTCCACTTCCAGCCGTTTTTGGAGCTTTCAAGAG
456 TTTTATGCCCTTTAAAATTCAGCAGCAACTCTTCCACTTCCAGCCGTTTTTGGAGCTTTCAAGAG
6819 AAATTAATCAAGCCTTTGAATGTCATTAAGAAGCTGGTTAAGAGATGGTGTCTATTCAACTAGCC
521 AAATTAATCAAGCCTTTGAATGTCATTAAGAAGCTGGTTAAGAGATGGTGTCTATTCAACTAGCC
* *
6884 AAGGACAACTCAAGAGTCATTTTCTAAGCCATTAAAGACATTCAAATCAGCTGAATTAAAGTGAT
586 AAAGACAACTCAAGAGTCATTTTCTAAGCCATTAAAGACATTCAAATCAGCTGAAGTAAAGTGAT
6949 TTTATGGAAGGAGTTATTTG
651 TTTATGGAAGGAGTTATTTG
6969 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
1 GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
7034 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
66 TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
7099 AGATGAAATATTTGAATTGTGAGCTATCCAATT
131 AGATGAAATATTTGAATTGTGAGCTATCCAATT
7132 CTCTTTGTTC
Statistics
Matches: 825, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
669 663 0.80
670 162 0.20
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (670 bp):
GTTCAAAGAATAAGAAAAGACATCAGTTTTTATGGCTCATTAAGTGGATGTTTTTGACCATTCGG
TTACCTTGTTTTAGCATTATAAATAGATGTAATCAGCCATAGAGAGGGAACTTTTTGCTGAATAT
AGATGAAATATTTGAATTGTGAGCTATCCAATTGTTTTTTAAATTATGCTTCTTTAATTAAACTA
GTTGCTGGAATAATTATTGCATATATGTTTTAGTTCATTTATTTAAGTAAGTTTAATGTTTGTTA
TGATTAATAAGTGTTTTCATTTGTTTAATAAACTCATTTTAATGAGTTTATTGCAGGTGACTTTT
TAGCTTATAGTGGTTACAATTCAAGGCTGTTACACATTTAATTAAGTGGCTGTTCAAGTTCTTTT
GAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAATCATTAAAGGAGTTTTTAAAGAGCA
TTTTATGCCCTTTAAAATTCAGCAGCAACTCTTCCACTTCCAGCCGTTTTTGGAGCTTTCAAGAG
AAATTAATCAAGCCTTTGAATGTCATTAAGAAGCTGGTTAAGAGATGGTGTCTATTCAACTAGCC
AAAGACAACTCAAGAGTCATTTTCTAAGCCATTAAAGACATTCAAATCAGCTGAAGTAAAGTGAT
TTTATGGAAGGAGTTATTTG
Found at i:7781 original size:22 final size:22
Alignment explanation
Indices: 7730--7795 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
7720 GGTATTTGGG
* *
7730 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
7751 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
7773 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
7796 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:9615 original size:13 final size:13
Alignment explanation
Indices: 9597--9621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9587 GTATTGATCA
9597 TGTGTTCACACCT
1 TGTGTTCACACCT
9610 TGTGTTCACACC
1 TGTGTTCACACC
9622 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:10955 original size:13 final size:12
Alignment explanation
Indices: 10897--10952 Score: 94
Period size: 12 Copynumber: 4.7 Consensus size: 12
10887 TAGTTTCTCG
* *
10897 AAAAAAAACTCG
1 AAAAAAAATTCA
10909 AAAAAAAATTCA
1 AAAAAAAATTCA
10921 AAAAAAAATTCA
1 AAAAAAAATTCA
10933 AAAAAAAATTCA
1 AAAAAAAATTCA
10945 AAAAAAAA
1 AAAAAAAA
10953 ATTGGTTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:11015 original size:16 final size:15
Alignment explanation
Indices: 10992--11032 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
10982 GATATCAAGT
10992 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
*
11007 TGAAAAAAAAATTTG
1 TGAAAAAAAAATTCG
11022 TGAAAAAAAAA
1 TGAAAAAAAAA
11033 GAAGAAGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:18128 original size:20 final size:20
Alignment explanation
Indices: 18105--18151 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18095 GGGTTAAGAT
*
18105 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
18125 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
18145 TGAGCTG
1 TGAGCTG
18152 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:20587 original size:11 final size:10
Alignment explanation
Indices: 20562--20622 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
20552 ACCAATAAAA
20562 TAAA-TGAGC
1 TAAATTGAGC
*
20571 TGAATTGTAGC
1 TAAATTG-AGC
20582 TAAATTGAGC
1 TAAATTGAGC
**
20592 TCGATTGAGC
1 TAAATTGAGC
20602 TGAAA-TGAGC
1 T-AAATTGAGC
*
20612 TCAATTGAGC
1 TAAATTGAGC
20622 T
1 T
20623 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:20623 original size:20 final size:20
Alignment explanation
Indices: 20563--20623 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20553 CCAATAAAAT
*
20563 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
20583 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
20604 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
20624 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:22713 original size:18 final size:18
Alignment explanation
Indices: 22692--22726 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22682 TTTTTCTTTT
22692 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
22710 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
22727 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:24658 original size:13 final size:13
Alignment explanation
Indices: 24642--24719 Score: 52
Period size: 12 Copynumber: 5.6 Consensus size: 13
24632 CAAAAAAATC
24642 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
24655 AAAAAAAATTTGATTGAA
1 AAAAAAAA--T--TCG-A
24673 AAAAAAAATTC-A
1 AAAAAAAATTCGA
*
24685 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
*
24697 AAAAAAAAATCGA
1 AAAAAAAATTCGA
24710 GCAAAAAAAA
1 --AAAAAAAA
24720 AAGGTGACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
12 20 0.38
13 10 0.19
14 1 0.02
15 9 0.17
16 1 0.02
17 2 0.04
18 9 0.17
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:24717 original size:25 final size:25
Alignment explanation
Indices: 24642--24706 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 25
24632 CAAAAAAATC
24642 AAAAAAAATTCGAAAAAAAAATTTGATTGAA
1 AAAAAAAATTC-AAAAAAAAA---G--TGAA
24673 AAAAAAAATTCAAAAAAAAAGTGAA
1 AAAAAAAATTCAAAAAAAAAGTGAA
24698 AAAAAAAAT
1 AAAAAAAAT
24707 CGAGCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.38
27 1 0.03
30 9 0.26
31 11 0.32
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (25 bp):
AAAAAAAATTCAAAAAAAAAGTGAA
Found at i:30542 original size:11 final size:10
Alignment explanation
Indices: 30517--30577 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
30507 ACCAATAAAA
30517 TAAA-TGAGC
1 TAAATTGAGC
*
30526 TGAATTGTAGC
1 TAAATTG-AGC
30537 TAAATTGAGC
1 TAAATTGAGC
**
30547 TCGATTGAGC
1 TAAATTGAGC
30557 TGAAA-TGAGC
1 T-AAATTGAGC
*
30567 TCAATTGAGC
1 TAAATTGAGC
30577 T
1 T
30578 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:30578 original size:20 final size:20
Alignment explanation
Indices: 30518--30578 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
30508 CCAATAAAAT
*
30518 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
30538 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
30559 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
30579 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:31326 original size:48 final size:48
Alignment explanation
Indices: 31274--31379 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
31264 TTGTCTTTTC
*
31274 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
31322 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
*
31370 TGTCTTTTTC
1 TTTCTTTTTC
31380 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.03, T:0.58
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:34003 original size:20 final size:20
Alignment explanation
Indices: 33980--34026 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33970 GGGTTAAGAT
*
33980 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
34000 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
34020 TGAGCTG
1 TGAGCTG
34027 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40574 original size:13 final size:13
Alignment explanation
Indices: 40553--40591 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
40543 GGATATCAAG
*
40553 TTGTAAAAAAAAA
1 TTGTGAAAAAAAA
40566 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
40579 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
40592 GAGCTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:41532 original size:18 final size:17
Alignment explanation
Indices: 41511--41555 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
41501 GAGTGACGAG
41511 AGAAAAAGAAATCGAAAA
1 AGAAAAA-AAATCGAAAA
*
41529 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAATCGAAAA
41547 AGAGAAAAA
1 AGA-AAAAA
41556 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAATCGAAAA
Found at i:41560 original size:18 final size:18
Alignment explanation
Indices: 41509--41560 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
41499 AAGAGTGACG
*
41509 AGAGAAAAAGAAATCGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
41529 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
41547 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
41561 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:64755 original size:12 final size:11
Alignment explanation
Indices: 64728--64797 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 11
64718 AACCGTATGC
64728 AATTTTTTTTT
1 AATTTTTTTTT
*
64739 -CTTTTTTTTT
1 AATTTTTTTTT
64749 AAATTTTTTTTTT
1 -AA-TTTTTTTTT
64762 CAATTTTTTTTT
1 -AATTTTTTTTT
64774 CGAACTCTTTTTTTT
1 --AA-T-TTTTTTTT
*
64789 GATTTTTTT
1 AATTTTTTT
64798 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 9 0.19
11 6 0.12
12 10 0.21
13 14 0.29
14 1 0.02
15 8 0.17
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:64797 original size:13 final size:13
Alignment explanation
Indices: 64740--64797 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
64730 TTTTTTTTTC
*
64740 TTTTTTTTTAAAT
1 TTTTTTTTTGAAT
*
64753 TTTTTTTTTCAAT
1 TTTTTTTTTGAAT
*
64766 TTTTTTTTCGAACT
1 TTTTTTTTTGAA-T
*
64780 CTTTTTTTTG-AT
1 TTTTTTTTTGAAT
64792 TTTTTT
1 TTTTTT
64798 GTTACTCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
12 6 0.16
13 23 0.61
14 9 0.24
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:71750 original size:20 final size:20
Alignment explanation
Indices: 71703--71750 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
71693 AGTAAGCTCG
71703 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
71723 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
71743 GTTGAGCT
1 GTTGAGCT
71751 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:73442 original size:13 final size:12
Alignment explanation
Indices: 73424--73542 Score: 70
Period size: 12 Copynumber: 10.0 Consensus size: 12
73414 TTATTTCGCT
73424 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
73437 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
73451 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
73462 TCTCACTTTTTGA
1 T-TTTCTTTTTCA
73475 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
73485 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
73498 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
73510 TTTTCTTTTT-G
1 TTTTCTTTTTCA
73521 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
73531 ATTTCTTTTTCA
1 TTTTCTTTTTCA
73543 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 17 0.20
12 35 0.42
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:73453 original size:14 final size:14
Alignment explanation
Indices: 73424--73460 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
73414 TTATTTCGCT
73424 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
73437 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
73451 TTTTCTTTTT
1 TTTTCTTTTT
73461 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:73514 original size:18 final size:18
Alignment explanation
Indices: 73422--73524 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
73412 TCTTATTTCG
73422 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
73441 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* ** *
73461 CTCTCACTTTTTGA-TTT
1 CTTTTTCTTTTTCATTTT
* *
73478 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
73496 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
73514 CTTTTTGTTTT
1 CTTTTTCTTTT
73525 CTTTCAATTT
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 12 0.19
18 33 0.52
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:73541 original size:6 final size:6
Alignment explanation
Indices: 73422--73528 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
73412 TCTTATTTCG
* * * **
73422 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
73473 -GATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
73520 -GTTTT CTTT
1 CTTTTT CTTT
73529 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
5 7 0.10
6 53 0.74
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:75661 original size:30 final size:30
Alignment explanation
Indices: 75627--75723 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
75617 TAAACTAAAA
*
75627 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
75657 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
75687 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
75716 ATGAGCTA
1 -TGAGCTA
75724 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:77998 original size:6 final size:6
Alignment explanation
Indices: 77982--78031 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
77972 TTTCTTTTTA
*
77982 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
78031 T
1 T
78032 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:78014 original size:37 final size:37
Alignment explanation
Indices: 77971--78041 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
77961 CTTGCCTCTC
77971 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
78008 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
78042 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:78042 original size:16 final size:16
Alignment explanation
Indices: 77967--78027 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
77957 GCCTCTTGCC
*
77967 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
77983 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
77999 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
78015 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
78028 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:79011 original size:11 final size:10
Alignment explanation
Indices: 78968--79007 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
78958 TTTTTCACTT
**
78968 TTTTTTTTCC
1 TTTTTTTTGA
*
78978 TTTTTTTCGA
1 TTTTTTTTGA
78988 TTTTTTTTGA
1 TTTTTTTTGA
78998 TTTTTTTTGA
1 TTTTTTTTGA
79008 ATTTCTTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:80766 original size:30 final size:30
Alignment explanation
Indices: 80732--80828 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
80722 TAAACTAAAA
*
80732 TGAGCTAAGTTTTAGCCCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCCCGTGAGCTAAAGT
* * * * * **
80762 TGAGCTGAGGCTAAACTCC-TAAGCTGGAGT
1 TGAGCTAAGGTTTAGC-CCGTGAGCTAAAGT
*
80792 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCCCGTGAGCTAAAGT
80821 ATGAGCTA
1 -TGAGCTA
80829 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.92
31 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCCCGTGAGCTAAAGT
Found at i:84046 original size:21 final size:21
Alignment explanation
Indices: 84006--84064 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
83996 AATCTTGAAT
*
84006 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
84027 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
84048 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
84065 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:84056 original size:15 final size:14
Alignment explanation
Indices: 84017--84064 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
84007 AAATTGAGAG
84017 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
84031 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
84046 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
84061 AAGA
1 AAGA
84065 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:87794 original size:11 final size:12
Alignment explanation
Indices: 87778--87808 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
87768 AACTCAAACT
87778 TTTTTTTTTGA-
1 TTTTTTTTTGAC
87789 TTTTTTTTTGAC
1 TTTTTTTTTGAC
87801 TTTTTTTT
1 TTTTTTTT
87809 CGTTACGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAC
Found at i:89273 original size:20 final size:20
Alignment explanation
Indices: 89226--89273 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
89216 AGTAAGCTCG
89226 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
** * *
89246 AATAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
89266 GTTGAGCT
1 GTTGAGCT
89274 GGACGGTGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:90945 original size:11 final size:12
Alignment explanation
Indices: 90915--90946 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
90905 TTTCACTCTT
90915 CTCTTTTTCAAA
1 CTCTTTTTCAAA
90927 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
90939 TTCTTTTT
1 CTCTTTTT
90947 TCGCTTTTTC
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:90958 original size:27 final size:27
Alignment explanation
Indices: 90928--90989 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
90918 TTTTTCAAAC
*
90928 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
90955 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
90982 TCTTTTTC
1 TCTTTTTC
90990 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:90968 original size:13 final size:12
Alignment explanation
Indices: 90952--91071 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
90942 TTTTTTCGCT
90952 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
90965 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
90979 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
90990 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
91004 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
91014 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
91027 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
91039 TTTTCTTTTT-G
1 TTTTCTTTTTCA
91050 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
91060 ATTTCTTTTTCA
1 TTTTCTTTTTCA
91072 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 15 0.18
12 32 0.39
13 17 0.20
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:90981 original size:14 final size:14
Alignment explanation
Indices: 90930--90988 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
90920 TTTCAAACTC
*
90930 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
90943 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
90956 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
90971 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
90985 TTTT
1 TTTT
90989 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:91070 original size:6 final size:6
Alignment explanation
Indices: 90950--91057 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
90940 TCTTTTTTCG
* * * **
90950 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
91001 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
91049 -GTTTT CTTT
1 CTTTTT CTTT
91058 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:92253 original size:10 final size:11
Alignment explanation
Indices: 92238--92266 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
92228 CAACTCAATT
92238 TTTTTTTTGA-
1 TTTTTTTTGAC
92248 TTTTTTTTGAC
1 TTTTTTTTGAC
92259 TTTTTTTT
1 TTTTTTTT
92267 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:93731 original size:20 final size:20
Alignment explanation
Indices: 93684--93731 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
93674 AGTAAGCTCG
93684 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
93704 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
93724 GTTGAGCT
1 GTTGAGCT
93732 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:96454 original size:16 final size:15
Alignment explanation
Indices: 96432--96485 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 15
96422 GAATATTTAC
*
96432 ATAAAAATTAAACTAA
1 ATAAAAAATAAA-TAA
*
96448 GTAAAAAATAAATAA
1 ATAAAAAATAAATAA
96463 AT--AAAAT-AA-AA
1 ATAAAAAATAAATAA
96474 ATAAAAAATAAA
1 ATAAAAAATAAA
96486 ACTTTACAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 4 0.12
12 2 0.06
13 10 0.31
14 2 0.06
15 4 0.12
16 10 0.31
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
ATAAAAAATAAATAA
Found at i:96475 original size:19 final size:18
Alignment explanation
Indices: 96451--96486 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
96441 AAACTAAGTA
96451 AAAAATAAATAAATAAAAT
1 AAAAATAAA-AAATAAAAT
96470 AAAAATAAAAAATAAAA
1 AAAAATAAAAAATAAAA
96487 CTTTACAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAAATAAAAT
Found at i:106677 original size:21 final size:21
Alignment explanation
Indices: 106652--106698 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
106642 GATTGTGGGA
106652 GCCATCTTCAGCCTTCTTCTT
1 GCCATCTTCAGCCTTCTTCTT
106673 GCCATCTTCAGCCTTCTTCTT
1 GCCATCTTCAGCCTTCTTCTT
106694 GCCAT
1 GCCAT
106699 TGATATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.11, C:0.38, G:0.11, T:0.40
Consensus pattern (21 bp):
GCCATCTTCAGCCTTCTTCTT
Found at i:110066 original size:9 final size:9
Alignment explanation
Indices: 110052--110085 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
110042 CATTTTAGAA
110052 AAAAAATTC
1 AAAAAATTC
*
110061 AAAAAAATC
1 AAAAAATTC
110070 AAAAAAATTC
1 -AAAAAATTC
110080 AAAAAA
1 AAAAAA
110086 AGTTTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
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:110066 original size:10 final size:10
Alignment explanation
Indices: 110051--110086 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
110041 GCATTTTAGA
110051 AAAAAAATTC
1 AAAAAAATTC
110061 AAAAAAA-TC
1 AAAAAAATTC
110070 AAAAAAATTC
1 AAAAAAATTC
110080 AAAAAAA
1 AAAAAAA
110087 GTTTCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:110143 original size:13 final size:14
Alignment explanation
Indices: 110122--110157 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
110112 GATATCAAGT
*
110122 TGAAAAAAAATTTG
1 TGAAAAAAAATTCG
110136 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
110150 TGAAAAAA
1 TGAAAAAA
110158 GAAGAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Found at i:111109 original size:18 final size:17
Alignment explanation
Indices: 111088--111132 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
111078 GAGTGACGAG
111088 AGAAAAATAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
111106 AGAAATAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
111124 AGAGAAAAA
1 AGA-AAAAA
111133 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:116201 original size:11 final size:11
Alignment explanation
Indices: 116166--116200 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
116156 CGTAAATTGT
116166 AAATCGAAAAA
1 AAATCGAAAAA
116177 AAATCGAAAAA
1 AAATCGAAAAA
116188 AAATC-AAAAA
1 AAATCGAAAAA
116198 AAA
1 AAA
116201 AGAGTCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.09
Consensus pattern (11 bp):
AAATCGAAAAA
Found at i:120522 original size:19 final size:19
Alignment explanation
Indices: 120492--120561 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
120482 CCACTCTTTC
120492 CTTTTCTTCTTTTTCAATCT
1 CTTTTCTTC-TTTTCAATCT
*
120512 CTTTT-TTCTTTTCACTCT
1 CTTTTCTTCTTTTCAATCT
**
120530 CTTTTCTT-TTTGAAATCT
1 CTTTTCTTCTTTTCAATCT
*
120548 CATTTTCATCTTTT
1 C-TTTTCTTCTTTT
120562 TCTTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 22 0.54
19 11 0.27
20 8 0.20
ACGTcount: A:0.11, C:0.23, G:0.01, T:0.64
Consensus pattern (19 bp):
CTTTTCTTCTTTTCAATCT
Found at i:120576 original size:15 final size:14
Alignment explanation
Indices: 120556--120603 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
120546 CTCATTTTCA
120556 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
120571 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
120585 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
120600 TCTT
1 TCTT
120604 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:120608 original size:22 final size:21
Alignment explanation
Indices: 120556--120614 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
120546 CTCATTTTCA
* *
120556 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
120577 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
120598 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
120615 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:121635 original size:12 final size:12
Alignment explanation
Indices: 121609--121668 Score: 70
Period size: 11 Copynumber: 5.0 Consensus size: 12
121599 GAATACAAAC
*
121609 TTTTTTTTCGGAT
1 TTTTTTTTC-AAT
121622 TTTTTTTTCAAT
1 TTTTTTTTCAAT
121634 TTTATTTTT-AAT
1 TTT-TTTTTCAAT
121646 TTTTTTTTC-AT
1 TTTTTTTTCAAT
*
121657 TTTTTTTACAAT
1 TTTTTTTTCAAT
121669 ACCGTAATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 15 0.36
12 13 0.31
13 14 0.33
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:121636 original size:11 final size:11
Alignment explanation
Indices: 121622--121668 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
121612 TTTTTCGGAT
121622 TTTTTTTTCAA
1 TTTTTTTTCAA
*
121633 TTTTATTTTTAA
1 TTTT-TTTTCAA
121645 TTTTTTTTTC-A
1 -TTTTTTTTCAA
121656 TTTTTTTTACAA
1 TTTTTTTT-CAA
121668 T
1 T
121669 ACCGTAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.27
11 6 0.20
12 12 0.40
13 4 0.13
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:121647 original size:24 final size:22
Alignment explanation
Indices: 121620--121663 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
121610 TTTTTTTCGG
121620 ATTTTTTTTTCAATTTTATTTTTA
1 ATTTTTTTTTC-ATTTT-TTTTTA
121644 ATTTTTTTTTCATTTTTTTT
1 ATTTTTTTTTCATTTTTTTT
121664 ACAATACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (22 bp):
ATTTTTTTTTCATTTTTTTTTA
Found at i:130048 original size:307 final size:307
Alignment explanation
Indices: 129494--130109 Score: 939
Period size: 307 Copynumber: 2.0 Consensus size: 307
129484 TAAAGTCTAA
* * *
129494 ATGATACGAGTCACAAAGGCCCAATTCAAGCTCAAGGACGTGATGGGCTCAAATTACCACAAGGC
1 ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAGAACATGATGGGCTCAAATTACCACAAGGC
* * * * * *
129559 CCAATAATGAGGTCAAAGGCCAGGCAAATGCGTATGAAACTAAATGGAATCATTCAAGCCTTCAT
66 CCAATAACGAGATCAAAGGCCAGACAAATGCGTATCAAACTAAATGGAACCATTCAAGACTTCAT
* *
129624 TAGCAAGGCCTTAGATGCGTATACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTATTTTCAAG
131 TAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTATTTTCAAG
* * *
129689 AAAATCAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCGATTTCAAGAATCAAGAAAAT
196 AAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
129754 CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
261 CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
*
129801 ATGATACGAGTCACAAAGGCCCAATCCAAGTTCAAGAACATGATGGGCTCAAATTACCACAAGGC
1 ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAGAACATGATGGGCTCAAATTACCACAAGGC
* * * *
129866 CCAATAACGAGATCAAAGGCCCGACAAATGCGT-TCCAAACTAAATAGG-ACCATTCAGGAGTTT
66 CCAATAACGAGATCAAAGGCCAGACAAATGCGTAT-CAAACTAAAT-GGAACCATTCAAGACTTC
* * * * *
129929 GTTAGCAAGGCCTTAGATGCATACACGAAGGAACAAGAAAATCAAGATTCCCTTTCTTGTTTTCA
129 ATTAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTATTTTCA
* *
129994 AGAAAATCAAGAAACCGAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGACTCAAGAAA
194 AGAAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAAA
* **
130059 ATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCTTGC
259 ATCAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
130108 AT
1 AT
130110 CTAAAACGCA
Statistics
Matches: 278, Mismatches: 29, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
306 1 0.00
307 275 0.99
308 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (307 bp):
ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAGAACATGATGGGCTCAAATTACCACAAGGC
CCAATAACGAGATCAAAGGCCAGACAAATGCGTATCAAACTAAATGGAACCATTCAAGACTTCAT
TAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTATTTTCAAG
AAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
Done.