Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014229.1 Kokia drynarioides strain JFW-HI SEQ_129262, whole genome shotgun sequence
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: 552652
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 140 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:15631 original size:23 final size:21
Alignment explanation
Indices: 15595--15657 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
15585 TTATTTTGGA
** *
15595 ATTTTTATAATATTCTATTAT
1 ATTTTTATTTTATTATATTAT
*
15616 ATTTATTAATTTTATTATTTTAT
1 ATTT-TT-ATTTTATTATATTAT
*
15639 ATTTTTATTTTATTTTATT
1 ATTTTTATTTTATTATATT
15658 TTTTTGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.44
22 4 0.12
23 15 0.44
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTATTTTATTATATTAT
Found at i:15662 original size:13 final size:13
Alignment explanation
Indices: 15624--15661 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
15614 ATATTTATTA
15624 ATTTTATTATTTT
1 ATTTTATTATTTT
15637 ATATTT-TTATTTT
1 AT-TTTATTATTTT
15650 ATTTTATT-TTTT
1 ATTTTATTATTTT
15662 TGAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.30
13 13 0.57
14 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTTATTATTTT
Found at i:16673 original size:28 final size:28
Alignment explanation
Indices: 16642--16736 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
16632 AATTAAGTAA
16642 AAATAGGAAAGATATATAATATATTCCT
1 AAATAGGAAAGATATATAATATATTCCT
* * *
16670 AAATAGGAAAGATAAATAATAAATTTCT
1 AAATAGGAAAGATATATAATATATTCCT
* *
16698 AAATA-TATAGATATATAATATATTCTCCT
1 AAATAGGAAAGATATATAATATA-T-TCCT
16727 AAATAGGAAA
1 AAATAGGAAA
16737 AAAAAAAGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 13 0.24
28 31 0.57
29 8 0.15
30 2 0.04
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (28 bp):
AAATAGGAAAGATATATAATATATTCCT
Found at i:17682 original size:16 final size:16
Alignment explanation
Indices: 17652--17689 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
17642 TTGGAATTAA
17652 ATTTTTT-ATAAAAAT
1 ATTTTTTGATAAAAAT
*
17667 ATTTTTTGATAGAAAT
1 ATTTTTTGATAAAAAT
17683 -TTTTTTG
1 ATTTTTTG
17690 GACTAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
ATTTTTTGATAAAAAT
Found at i:18765 original size:6 final size:6
Alignment explanation
Indices: 18754--18799 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
18744 CTGGTGGTGG
18754 AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGA
1 AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGAGC AAGA
18800 AGTAGAGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGAGC
Found at i:18891 original size:189 final size:189
Alignment explanation
Indices: 18589--18942 Score: 611
Period size: 189 Copynumber: 1.9 Consensus size: 189
18579 ATGGTGGTGG
* * *
18589 AAGAGGAAGAGGAAGAGCAAGAGGTAGAGATGACAGCGCTGATCATCAGGGTCCTTATCAGGCGG
1 AAGAGCAAGAGCAAGAGCAAGAAGTAGAGATGACAGCGCTGATCATCAGGGTCCTTATCAGGCGG
*
18654 CCATAGGCCAAAGGCAAAGTGGGGCCAACTGGAACCCAACTGACTCTCAAGTGGGTCCTTATCAG
66 CCATAGGCCAAAGGCAAAGTGGGGCCAACTGGAACCCAACTAACTCTCAAGTGGGTCCTTATCAG
* * *
18719 GACGGCGATGCGAGGGGTGGTCAGTCTGGTGGTGGAAGAGCAAGAGCAAGAGCAAGAGC
131 GACGGCGATGAGAGGGGCGGTCAGGCTGGTGGTGGAAGAGCAAGAGCAAGAGCAAGAGC
*
18778 AAGAGCAAGAGCAAGAGCAAGAAGTAGAGATTACAGCGCTGATCATCAGGGTCCTTATCAGGCGG
1 AAGAGCAAGAGCAAGAGCAAGAAGTAGAGATGACAGCGCTGATCATCAGGGTCCTTATCAGGCGG
*
18843 CCATAGGCC-AAGAGCAAAGTGGGGCCAACTGGAACCGAACTAACTCTCAAGTGGGTCCTTATCA
66 CCATAGGCCAAAG-GCAAAGTGGGGCCAACTGGAACCCAACTAACTCTCAAGTGGGTCCTTATCA
18907 GGACGGCGATGAGAGGGGCGGTCAGGCTGGTGGTGG
130 GGACGGCGATGAGAGGGGCGGTCAGGCTGGTGGTGG
18943 TCGTGGTAGA
Statistics
Matches: 155, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
188 3 0.02
189 152 0.98
ACGTcount: A:0.30, C:0.20, G:0.35, T:0.15
Consensus pattern (189 bp):
AAGAGCAAGAGCAAGAGCAAGAAGTAGAGATGACAGCGCTGATCATCAGGGTCCTTATCAGGCGG
CCATAGGCCAAAGGCAAAGTGGGGCCAACTGGAACCCAACTAACTCTCAAGTGGGTCCTTATCAG
GACGGCGATGAGAGGGGCGGTCAGGCTGGTGGTGGAAGAGCAAGAGCAAGAGCAAGAGC
Found at i:24500 original size:6 final size:6
Alignment explanation
Indices: 24489--24518 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24479 CAAGGGTTAG
*
24489 AAAAAC AAAAAC AAAAAA AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
24519 CATCCATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:31264 original size:29 final size:29
Alignment explanation
Indices: 31227--31289 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
31217 TTTTTTCATG
* * *
31227 TCAACATTTTTGTTTAAATGGATGTCACA
1 TCAACATTTTTATTTAAATGAATGCCACA
*
31256 TCAATATTTTTATTTAAATGAATGCCACA
1 TCAACATTTTTATTTAAATGAATGCCACA
31285 TCAAC
1 TCAAC
31290 CGAACACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (29 bp):
TCAACATTTTTATTTAAATGAATGCCACA
Found at i:35385 original size:21 final size:21
Alignment explanation
Indices: 35361--35420 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
35351 GTTTATTTTT
35361 TTAAGTTAAAAGTTAAAATCA
1 TTAAGTTAAAAGTTAAAATCA
35382 TTAAGTTAAAAGTTAAAATCA
1 TTAAGTTAAAAGTTAAAATCA
*
35403 TTAAGTTAAAAGATAAAA
1 TTAAGTTAAAAGTTAAAA
35421 CTACGTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32
Consensus pattern (21 bp):
TTAAGTTAAAAGTTAAAATCA
Found at i:36513 original size:32 final size:32
Alignment explanation
Indices: 36477--36540 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
36467 TAGTTAAGTT
36477 AATCTTAACTTTTTATCAAATAACTATTTTTA
1 AATCTTAACTTTTTATCAAATAACTATTTTTA
*
36509 AATCTTAACTTTTTATCGAATAACTATTTTTA
1 AATCTTAACTTTTTATCAAATAACTATTTTTA
36541 TTATTCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (32 bp):
AATCTTAACTTTTTATCAAATAACTATTTTTA
Found at i:37576 original size:19 final size:19
Alignment explanation
Indices: 37554--37604 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
37544 TACTATAAAA
37554 TATATATTATTAAT-ATATT
1 TATATATTA-TAATAATATT
37573 TATA-ATTATAATAAATATT
1 TATATATTATAAT-AATATT
*
37592 TAT-TATTAAAATA
1 TATATATTATAATA
37605 TTAATATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 5 0.18
19 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATTATAATAATATT
Found at i:37605 original size:15 final size:15
Alignment explanation
Indices: 37549--37606 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
37539 CTTTATACTA
*
37549 TAAAATATATATTAT
1 TAAAATATTTATTAT
*
37564 TAATATATTTATAATTAT
1 TAAAATA-TT-T-ATTAT
*
37582 AATAAATATTTATTAT
1 TA-AAATATTTATTAT
37598 TAAAATATT
1 TAAAATATT
37607 AATATTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 13 0.38
16 7 0.21
17 2 0.06
18 8 0.24
19 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:37612 original size:14 final size:15
Alignment explanation
Indices: 37585--37664 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 15
37575 TAATTATAAT
*
37585 AAATATTTATTATT-A
1 AAATA-TTAATATTGA
37600 AAATATTAATATTGA
1 AAATATTAATATTGA
* *
37615 ATATTTTCAATATTTGA
1 AAATATT-AATA-TTGA
*
37632 AGAATATT-AT-TTAA
1 A-AATATTAATATTGA
*
37646 AAATATTATTATT-A
1 AAATATTAATATTGA
37660 AAATA
1 AAATA
37665 AAAATAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
13 6 0.12
14 18 0.35
15 13 0.25
16 6 0.12
17 5 0.10
18 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (15 bp):
AAATATTAATATTGA
Found at i:37788 original size:13 final size:13
Alignment explanation
Indices: 37772--37797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37762 TCGAAAAATA
37772 TAATATTTTATAT
1 TAATATTTTATAT
37785 TAATATTTTATAT
1 TAATATTTTATAT
37798 ATTTTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATATTTTATAT
Found at i:41909 original size:30 final size:30
Alignment explanation
Indices: 41873--41935 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
41863 TTTATCCTTA
* *
41873 TTTATATTATGATCTAAAAAAATGCATTTG
1 TTTATATTATGATATAAAAAAATGCATATG
* *
41903 TTTATATTATGGTATAAAAAAGTGCATATG
1 TTTATATTATGATATAAAAAAATGCATATG
41933 TTT
1 TTT
41936 TGACAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTATATTATGATATAAAAAAATGCATATG
Found at i:49326 original size:145 final size:145
Alignment explanation
Indices: 49060--49349 Score: 562
Period size: 145 Copynumber: 2.0 Consensus size: 145
49050 AAGCAATACG
*
49060 AACCTAAGACACTAGCAAAGCCAACCCCACTAAAATGGAAATTTTCACGTTTAGTCCTTTTATAA
1 AACCTAAGACACTAGCAAAACCAACCCCACTAAAATGGAAATTTTCACGTTTAGTCCTTTTATAA
49125 TTTTAAAAATTTTAAATTAGTATATAGTAAAATTACACTTTGATCCCTCAACAATGAGAAAAAAA
66 TTTTAAAAATTTTAAATTAGTATATAGTAAAATTACACTTTGATCCCTCAACAATGAGAAAAAAA
49190 AATGATTTAGTCCTT
131 AATGATTTAGTCCTT
49205 AACCTAAGACACTAGCAAAACCAACCCCACTAAAATGGAAATTTTCACGTTTAGTCCTTTTATAA
1 AACCTAAGACACTAGCAAAACCAACCCCACTAAAATGGAAATTTTCACGTTTAGTCCTTTTATAA
*
49270 TTTTAAAAATTTTAAATTAGTATATAGTAAAATTACACTTTGATCCCTCAAGAATGAGAAAAAAA
66 TTTTAAAAATTTTAAATTAGTATATAGTAAAATTACACTTTGATCCCTCAACAATGAGAAAAAAA
49335 AATGATTTAGTCCTT
131 AATGATTTAGTCCTT
49350 TAAAAATTAT
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (145 bp):
AACCTAAGACACTAGCAAAACCAACCCCACTAAAATGGAAATTTTCACGTTTAGTCCTTTTATAA
TTTTAAAAATTTTAAATTAGTATATAGTAAAATTACACTTTGATCCCTCAACAATGAGAAAAAAA
AATGATTTAGTCCTT
Found at i:52591 original size:97 final size:98
Alignment explanation
Indices: 52401--52600 Score: 321
Period size: 97 Copynumber: 2.0 Consensus size: 98
52391 AACTTTTTAG
*
52401 TGAGTGAAAAGAATAAAGGGTCTGTTGTCTCAAAAGTGAAACAGTCAGTCGTACTGCTCTTGTTT
1 TGAGTGAAAAGAATAAAAGGTCTGTTGTCTCAAAAGTGAAACAGTCA---GTACTGCTCTTGTTT
* *
52466 CAGGATTTTATTAGAACGCTACATATCCTTTTAGCC
63 CAGGATTTTATTAGAACACTACACATCCTTTTAGCC
*
52502 TGAGTGAAAAGAATAAAAGTTCTGTTGTCTCAAAAGTGAAACAGTCA-TACTGCTCTTGTTTCAG
1 TGAGTGAAAAGAATAAAAGGTCTGTTGTCTCAAAAGTGAAACAGTCAGTACTGCTCTTGTTTCAG
*
52566 GATTTTGTTAGAACACTACACATCCTTTTAGCC
66 GATTTTATTAGAACACTACACATCCTTTTAGCC
52599 TG
1 TG
52601 TCTTTGCATT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
97 49 0.52
101 45 0.48
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (98 bp):
TGAGTGAAAAGAATAAAAGGTCTGTTGTCTCAAAAGTGAAACAGTCAGTACTGCTCTTGTTTCAG
GATTTTATTAGAACACTACACATCCTTTTAGCC
Found at i:59867 original size:7 final size:7
Alignment explanation
Indices: 59855--59968 Score: 74
Period size: 7 Copynumber: 16.6 Consensus size: 7
59845 TTTAAATTTC
59855 AAGGTTT
1 AAGGTTT
59862 AAGGTTT
1 AAGGTTT
*
59869 -ATGTTT
1 AAGGTTT
* *
59875 GAGATTT
1 AAGGTTT
*
59882 AAGATTT
1 AAGGTTT
59889 AAGGTTT
1 AAGGTTT
59896 -AGGATTT
1 AAGG-TTT
*
59903 GAGGTTT
1 AAGGTTT
*
59910 AATGTTT
1 AAGGTTT
59917 -AGGTTT
1 AAGGTTT
59923 AAGGTTT
1 AAGGTTT
*
59930 ATAGTTTT
1 A-AGGTTT
* *
59938 GAGGATT
1 AAGGTTT
*
59945 -AGGGTT
1 AAGGTTT
*
59951 AAAGTTT
1 AAGGTTT
*
59958 AGGGTTT
1 AAGGTTT
59965 AAGG
1 AAGG
59969 GTTTGAGATT
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
6 18 0.22
7 57 0.69
8 8 0.10
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (7 bp):
AAGGTTT
Found at i:59893 original size:27 final size:27
Alignment explanation
Indices: 59858--59923 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
59848 AAATTTCAAG
*
59858 GTTTAAGGTTTATG-TTTGAGATTTAA
1 GTTTAAGGTTTAGGATTTGAGATTTAA
*
59884 GATTTAAGGTTTAGGATTTGAGGTTTAA
1 G-TTTAAGGTTTAGGATTTGAGATTTAA
59912 TGTTT-AGGTTTA
1 -GTTTAAGGTTTA
59924 AGGTTTATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 14 0.40
29 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (27 bp):
GTTTAAGGTTTAGGATTTGAGATTTAA
Found at i:59901 original size:21 final size:21
Alignment explanation
Indices: 59859--59968 Score: 86
Period size: 21 Copynumber: 5.3 Consensus size: 21
59849 AATTTCAAGG
*
59859 TTTAAGGTTT-ATGTTT-GAGA
1 TTTAAGGTTTAAGGTTTAG-GA
*
59879 TTTAAGATTTAAGGTTTAGGA
1 TTTAAGGTTTAAGGTTTAGGA
* *
59900 TTTGAGGTTTAATGTTTAGG-
1 TTTAAGGTTTAAGGTTTAGGA
*
59920 TTTAAGGTTTATAGTTTTGAGGA
1 TTTAAGGTTTA-AGGTTT-AGGA
* * *
59943 -TT-AGGGTTAAAGTTTAGGG
1 TTTAAGGTTTAAGGTTTAGGA
59962 TTTAAGG
1 TTTAAGG
59969 GTTTGAGATT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.04
20 25 0.35
21 37 0.52
22 6 0.08
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAAGGTTTAGGA
Found at i:59922 original size:13 final size:13
Alignment explanation
Indices: 59855--59968 Score: 61
Period size: 13 Copynumber: 8.3 Consensus size: 13
59845 TTTAAATTTC
59855 AAGGTTTAAGGTTT
1 AAGGTTT-AGGTTT
* *
59869 -ATGTTTGAGATTT
1 AAGGTTT-AGGTTT
*
59882 AAGATTTAAGGTTT
1 AAGGTTT-AGGTTT
59896 -AGGATTTGAGGTTT
1 AAGG-TTT-AGGTTT
*
59910 AATGTTTAGGTTT
1 AAGGTTTAGGTTT
*
59923 AAGGTTTATAGTTTT
1 AAGG-TT-TAGGTTT
* * *
59938 GAGGATTAGGGTT
1 AAGGTTTAGGTTT
*
59951 AAAGTTTAGGGTTT
1 AAGGTTTA-GGTTT
59965 AAGG
1 AAGG
59969 GTTTGAGATT
Statistics
Matches: 73, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
13 31 0.42
14 31 0.42
15 11 0.15
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (13 bp):
AAGGTTTAGGTTT
Found at i:67562 original size:6 final size:6
Alignment explanation
Indices: 67548--67581 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
67538 AGGATAAAAA
* *
67548 AAGAAG AAGATG AAGATG AAGATG AAGAAG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGA
67582 AGAGGGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (6 bp):
AAGATG
Found at i:67568 original size:12 final size:12
Alignment explanation
Indices: 67548--67581 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
67538 AGGATAAAAA
67548 AAGAAGAAGATG
1 AAGAAGAAGATG
*
67560 AAGATGAAGATG
1 AAGAAGAAGATG
67572 AAGAAGAAGA
1 AAGAAGAAGA
67582 AGAGGGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (12 bp):
AAGAAGAAGATG
Found at i:67640 original size:21 final size:21
Alignment explanation
Indices: 67601--67640 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
67591 TGTGGAAATG
***
67601 AGTTTAGGGTTTTTTAATTGA
1 AGTTTAGGGTTTAAAAATTGA
67622 AGTTTAGGGTTTAAAAATT
1 AGTTTAGGGTTTAAAAATT
67641 TTAATTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
AGTTTAGGGTTTAAAAATTGA
Found at i:73181 original size:33 final size:34
Alignment explanation
Indices: 73122--73185 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
73112 ATGATTCATC
73122 AAAAGTCAAAAAATATAATATATAATATATTATT
1 AAAAGTCAAAAAATATAATATATAATATATTATT
* *
73156 AAAAGTCAAAATAT-TCATATATAATATATT
1 AAAAGTCAAAAAATATAATATATAATATATT
73186 TTGTGTTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (34 bp):
AAAAGTCAAAAAATATAATATATAATATATTATT
Found at i:73303 original size:157 final size:160
Alignment explanation
Indices: 72997--73309 Score: 456
Period size: 157 Copynumber: 2.0 Consensus size: 160
72987 ATGATTTATC
*
72997 AAAGTCAAAATAATTCATATATAATATATTTTGTGTTGCACATTTCTTCAAGTACTTGATATTTT
1 AAAGTCAAAATAATTCATATATAATATATTTTGTGTTACACATTTCTTCAAGTACTTGATATTTT
73062 TTCAAATCAGGAATAATCCAATTTTGACAGATTATTGAACTATGTGTTTTATGATTCATCAAAAG
66 TTCAAATCAGGAATAATCCAATTTTGACAGATTATTGAACTATGTGTTTTATGATTCATCAAAAG
73127 TCAAAAAATATAATATATAATATATTATTA
131 TCAAAAAATATAATATATAATATATTATTA
* * *
73157 AAAGTCAAAAT-ATTCATATATAATATATTTTGTGTTACGCATTTCTTCAATTA-TTTATATTTT
1 AAAGTCAAAATAATTCATATATAATATATTTTGTGTTACACATTTCTTCAAGTACTTGATATTTT
* * ** * * *
73220 TT-AAATCGGGAATAAAT-GAATTTTGATGGATTATTGAACTATGTGTTTTATGATTTATTAAGA
66 TTCAAATCAGGAAT-AATCCAATTTTGACAGATTATTGAACTATGTGTTTTATGATTCATCAAAA
* *
73283 GTCAAAATAAT-TCATGTATAATATATT
130 GTCAAAA-AATATAATATATAATATATT
73310 TTGTGTCAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
157 71 0.51
158 17 0.12
159 39 0.28
160 11 0.08
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (160 bp):
AAAGTCAAAATAATTCATATATAATATATTTTGTGTTACACATTTCTTCAAGTACTTGATATTTT
TTCAAATCAGGAATAATCCAATTTTGACAGATTATTGAACTATGTGTTTTATGATTCATCAAAAG
TCAAAAAATATAATATATAATATATTATTA
Found at i:73308 original size:124 final size:127
Alignment explanation
Indices: 73151--73427 Score: 341
Period size: 128 Copynumber: 2.2 Consensus size: 127
73141 ATATAATATA
* * *
73151 TTATTAAAAGTCAAAAT-ATTCATATATAATATATTTTGTGT-TACGCATTTCTTCAAT-TATTT
1 TTATTAAAAGTCAAAATAATTCATATATAATATATTTTGTGTAGACACATTTCTTC-ATGTACTT
* * * * * * *
73213 ATA-TTTT-TTAAATCGGGAATAAATGAATTTTGATGGATTATTGAACTATGTGTTTTA-TGAT
65 ATATTTTTCTTAAATCAGGAATAAATCAATTCTGATGGATGATTAAACCATGCGTTTTAGT-AT
* *
73274 TTATTAAGAGTCAAAATAATTCATGTATAATATATTTTGTGTCAGACACATTTCTTCATGTACTT
1 TTATTAAAAGTCAAAATAATTCATATATAATATATTTTGTGT-AGACACATTTCTTCATGTACTT
* *
73339 ATATTTTTCTTAAATCAGTAATAAATCAATTCTGATGGGTGATTAAACCATGCGTTTTAGTAT
65 ATATTTTTCTTAAATCAGGAATAAATCAATTCTGATGGATGATTAAACCATGCGTTTTAGTAT
* *
73402 TTATTAAAAGTTAAAATAATCCATAT
1 TTATTAAAAGTCAAAATAATTCATAT
73428 TTTGTGTTAC
Statistics
Matches: 129, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
123 16 0.12
124 23 0.18
125 2 0.02
126 18 0.14
127 4 0.03
128 65 0.50
129 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (127 bp):
TTATTAAAAGTCAAAATAATTCATATATAATATATTTTGTGTAGACACATTTCTTCATGTACTTA
TATTTTTCTTAAATCAGGAATAAATCAATTCTGATGGATGATTAAACCATGCGTTTTAGTAT
Found at i:87338 original size:96 final size:96
Alignment explanation
Indices: 87161--87345 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
87151 GAAAAGGATG
** *
87161 TTCGATTATTACGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATTACGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
* *
87226 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAGAAACATTGCCTCGATTAAGGGTA
* *
87257 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTT-TGAAACTC
1 TTCGATTATTACGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TC
*
87321 -AAAATAAA-AGAATATTGCCTCGATT
64 GAAAATAAAGA-AACATTGCCTCGATT
87346 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 74 0.95
97 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTATTACGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AAATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:87730 original size:29 final size:29
Alignment explanation
Indices: 87698--88134 Score: 326
Period size: 29 Copynumber: 14.9 Consensus size: 29
87688 AATCGGGATC
87698 AAAAATGGAATTTTTGGACA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGGT
* * * *
87727 -AAAAGGGTAATTTTTTGAAGTTTTAGGGTT
1 AAAAATGG-AATTTTTGGAAG-TTTGGGGGT
87757 AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* ** * *
87786 -AGAATGGTAATTTTAAG-AGTTTCGAGGTT
1 AAAAATGG-AATTTTTGGAAGTTT-GGGGGT
* * * ** *
87815 AAAATTGGGATTTTTGAAAGTTCAGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
87844 AAAAATGTAATTTTTGGAAGTTTAGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * * *
87873 TAAAATGAAATTTTTAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * *
87902 AAAAATGTAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
87931 CAAAATGGAATTTTTGAAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
87960 GAAAATGTAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
87989 AAAAAATGGAA-TTTTGAAAGTTCGAGGCT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
88018 AAAAATGTAATTTTTAGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-GGGGGT
* * *
88048 AAAAATGGAATTTTTGGAAGTTCGAGTGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
88077 AAAAATGTAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGGT
** *
88107 AAAAATATAATTTTGGAGAAGTTTGGGG
1 AAAAATGGAATTTTTG-GAAGTTTGGGG
88135 ACCTCCAGGA
Statistics
Matches: 317, Mismatches: 78, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
28 27 0.09
29 194 0.61
30 86 0.27
31 10 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:87836 original size:58 final size:59
Alignment explanation
Indices: 87698--88112 Score: 468
Period size: 58 Copynumber: 7.1 Consensus size: 59
87688 AATCGGGATC
* * ** * *
87698 AAAAATGGAATTTTTGGACA-TTTGGGGGTAAAAGGGTAATTTTTTGAAGTTT-TAGGGTT
1 AAAAATGGAATTTTT-GAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGA-GGTT
* * * **
87757 AAAAATGGAATTTTTGGAAGTTTGGGGGT-AGAATGGTAATTTTAAG-AGTTTCGAGGTT
1 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAAT-GTAATTTTTGGAAGTTTCGAGGTT
* * * * *
87815 AAAATTGGGATTTTTGAAAGTTCAGAGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTT
1 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* *
87874 -AAAATGAAATTTTT-AGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGG-T
1 AAAAATGGAATTTTTGA-AAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* * * *
87931 CAAAATGGAATTTTTGAAAGTTTGGGGGTGAAAATGTAATTTTTGGAAGTTTCGAGGTA
1 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* * *
87990 AAAAATGGAA-TTTTGAAAGTTCGAGGCTAAAAATGTAATTTTTAGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* * * * *
88048 AAAAATGGAATTTTTGGAAGTTCGAGTGTAAAAATGTAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
88107 AAAAAT
1 AAAAAT
88113 ATAATTTTGG
Statistics
Matches: 303, Mismatches: 43, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.01
58 194 0.64
59 107 0.35
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
Found at i:90001 original size:17 final size:17
Alignment explanation
Indices: 89976--90030 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
89966 AATTGGATTT
*
89976 TTTTTAATTAATTTAAA
1 TTTTAAATTAATTTAAA
*
89993 TTTTAAATTCAAATTAAA
1 TTTTAAATT-AATTTAAA
90011 -TTTAAACTTAATTTAAA
1 TTTTAAA-TTAATTTAAA
90028 TTT
1 TTT
90031 AAACTTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAAATTAATTTAAA
Found at i:90021 original size:23 final size:23
Alignment explanation
Indices: 89981--90046 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
89971 GATTTTTTTT
*
89981 AATT-AATTTAAATTTTAAATTCA
1 AATTAAATTTAAA-CTTAAATTCA
*
90004 AATTAAATTTAAACTT-AATTTA
1 AATTAAATTTAAACTTAAATTCA
*
90026 AATTTAAACTTAAAC-TAAATT
1 AA-TTAAATTTAAACTTAAATT
90047 TAAACCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 8 0.22
23 21 0.57
24 8 0.22
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTAAATTTAAACTTAAATTCA
Found at i:90023 original size:11 final size:11
Alignment explanation
Indices: 90009--90051 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
89999 ATTCAAATTA
90009 AATTTAAACTT
1 AATTTAAACTT
*
90020 AATTTAAATTT
1 AATTTAAACTT
* *
90031 AAACTTAAACTA
1 -AATTTAAACTT
90043 AATTTAAAC
1 AATTTAAAC
90052 CCAAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (11 bp):
AATTTAAACTT
Found at i:90031 original size:17 final size:17
Alignment explanation
Indices: 89983--90051 Score: 86
Period size: 17 Copynumber: 4.0 Consensus size: 17
89973 TTTTTTTTAA
*
89983 TTAATTTAAATTTTAAA-
1 TTAAATTAAA-TTTAAAC
90000 TTCAAATTAAATTTAAAC
1 TT-AAATTAAATTTAAAC
*
90018 TTAATTTAAATTTAAAC
1 TTAAATTAAATTTAAAC
*
90035 TTAAACTAAATTTAAAC
1 TTAAATTAAATTTAAAC
90052 CCAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 37 0.80
18 9 0.20
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:90050 original size:6 final size:6
Alignment explanation
Indices: 89985--90050 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
89975 TTTTTTAATT
* *
89985 AATTTA AATTTTA AATTCA AA-TTA AATTTA AACTT- AATTTA AATTTA
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
90032 AACTTA AA-CTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
90051 CCCAAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 12 0.24
6 31 0.63
7 6 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:90061 original size:17 final size:17
Alignment explanation
Indices: 90024--90063 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
90014 AAACTTAATT
** *
90024 TAAATTTAAACTTAAAC
1 TAAATTTAAACCCAAAA
90041 TAAATTTAAACCCAAAA
1 TAAATTTAAACCCAAAA
90058 TAAATT
1 TAAATT
90064 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATTTAAACCCAAAA
Found at i:92708 original size:18 final size:19
Alignment explanation
Indices: 92681--92716 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
92671 ATTTTATCTC
92681 ATATTATAATATTATTATA
1 ATATTATAATATTATTATA
92700 ATATT-TAATATTATTAT
1 ATATTATAATATTATTAT
92717 CATCGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATAATATTATTATA
Found at i:93539 original size:22 final size:23
Alignment explanation
Indices: 93487--93539 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
93477 TCATCTTAAT
*
93487 ATTATTTTA-ATATTTACAATAA
1 ATTATATTATATATTTACAATAA
**
93509 ATTAGTATTATATATTTAGTATAA
1 ATTA-TATTATATATTTACAATAA
93533 ATT-TATT
1 ATTATATT
93540 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.31
23 4 0.15
24 14 0.54
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTATATTATATATTTACAATAA
Found at i:98241 original size:8 final size:9
Alignment explanation
Indices: 98220--98261 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
98210 AAAAAAGTAT
98220 TTTTTATAA
1 TTTTTATAA
98229 TTTTTATAA
1 TTTTTATAA
98238 TTTTTGA-AA
1 TTTTT-ATAA
*
98247 TTTTTTATGA
1 -TTTTTATAA
98257 TTTTT
1 TTTTT
98262 CAATTTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (9 bp):
TTTTTATAA
Found at i:98550 original size:39 final size:39
Alignment explanation
Indices: 98496--98574 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
98486 CAAAAATCAC
*
98496 ATCAAAACTCTTCATAATCATAATCTTCCCTATAACCAT
1 ATCAAAACTCTTCATAATCATAATCTTCCCAATAACCAT
* * **
98535 ATCAATACTCTTCATATTCATTTTCTTCCCAATAACCAT
1 ATCAAAACTCTTCATAATCATAATCTTCCCAATAACCAT
98574 A
1 A
98575 CTCCTCCTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (39 bp):
ATCAAAACTCTTCATAATCATAATCTTCCCAATAACCAT
Found at i:104697 original size:16 final size:16
Alignment explanation
Indices: 104678--104708 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104668 CGATACTAAG
104678 GAAAAAAAAAATTGCA
1 GAAAAAAAAAATTGCA
*
104694 GAAAAGAAAAATTGC
1 GAAAAAAAAAATTGC
104709 TGTAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.13
Consensus pattern (16 bp):
GAAAAAAAAAATTGCA
Found at i:107096 original size:12 final size:12
Alignment explanation
Indices: 107079--107103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107069 TCTCAAGTTT
107079 AGAAACCCTCAA
1 AGAAACCCTCAA
107091 AGAAACCCTCAA
1 AGAAACCCTCAA
107103 A
1 A
107104 TTGCCTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (12 bp):
AGAAACCCTCAA
Found at i:116854 original size:33 final size:32
Alignment explanation
Indices: 116783--116851 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
116773 AACTTTAATG
116783 ATATATAAAATATTTTAAAAACTTGAAACATA
1 ATATATAAAATATTTTAAAAACTTGAAACATA
* *
116815 AT-TATAAATTATATTT-AAAA-TTGTAACATA
1 ATATATAAAATAT-TTTAAAAACTTGAAACATA
*
116845 TTATATA
1 ATATATA
116852 TAACATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 10 0.31
31 17 0.53
32 5 0.16
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (32 bp):
ATATATAAAATATTTTAAAAACTTGAAACATA
Found at i:122851 original size:23 final size:22
Alignment explanation
Indices: 122807--122852 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
122797 TCATCGGTGC
*
122807 ATTAATATATTTGACTACATTA
1 ATTAATATATTTCACTACATTA
* *
122829 ATTATATATATTTCATTATATTA
1 ATTA-ATATATTTCACTACATTA
122852 A
1 A
122853 ATTTATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATATATTTCACTACATTA
Found at i:124146 original size:19 final size:19
Alignment explanation
Indices: 124124--124161 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
124114 TATGTAATCC
124124 TAAAGATTTGACATTCCTT
1 TAAAGATTTGACATTCCTT
124143 TAAAGATTTGACATTCCTT
1 TAAAGATTTGACATTCCTT
124162 AAAAAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TAAAGATTTGACATTCCTT
Found at i:138459 original size:6 final size:6
Alignment explanation
Indices: 138448--138482 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
138438 TAAACTCGTT
* *
138448 AGAAAA AGAAAA GGAAAA AAAAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
138483 GAAAGCTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:141540 original size:2 final size:2
Alignment explanation
Indices: 141498--141525 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
141488 TTTGTATTTG
141498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141526 GAGTAGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141968 original size:27 final size:27
Alignment explanation
Indices: 141915--141968 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
141905 AAATTTAATC
**
141915 ATTTTTAATTTAAAAAAATATTTTTAA
1 ATTTTTAATTTAAAAAAATATAATTAA
*
141942 ATTTTTAAATTTTAAAAAAT-TAATTAA
1 ATTTTT-AATTTAAAAAAATATAATTAA
141969 TTGCTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTTTAATTTAAAAAAATATAATTAA
Found at i:142879 original size:10 final size:10
Alignment explanation
Indices: 142856--142911 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
142846 TTAAATTTTA
142856 AAAAAAT-AT
1 AAAAAATCAT
*
142865 TAAAAATCAT
1 AAAAAATCAT
142875 AAAAAA-CAT
1 AAAAAATCAT
**
142884 AAAAAAATGTT
1 -AAAAAATCAT
*
142895 ATAAAATCAT
1 AAAAAATCAT
142905 AAAAAAT
1 AAAAAAT
142912 ATTATTAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
9 9 0.25
10 26 0.72
11 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:142889 original size:20 final size:20
Alignment explanation
Indices: 142866--142929 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
142856 AAAAAATATT
142866 AAAAATCATAAAAAACATAA
1 AAAAATCATAAAAAACATAA
** *
142886 AAAAATGTTATAAAATCATAA
1 AAAAATCATA-AAAAACATAA
* *
142907 AAAATATTATTAAAAA-ATAA
1 AAAA-ATCATAAAAAACATAA
142927 AAA
1 AAA
142930 TTTTGATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 15 0.43
21 17 0.49
22 3 0.09
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATCATAAAAAACATAA
Found at i:142890 original size:21 final size:21
Alignment explanation
Indices: 142866--142929 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 21
142856 AAAAAATATT
142866 AAAAATCATAAAAAACAT-AA
1 AAAAATCATAAAAAACATAAA
** *
142886 AAAAATGTTATAAAATCATAAA
1 AAAAATCATA-AAAAACATAAA
* * *
142908 AAATATTATTAAAAA-ATAAA
1 AAAAATCATAAAAAACATAAA
142928 AA
1 AA
142930 TTTTGATCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 15 0.44
21 11 0.32
22 8 0.24
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAATCATAAAAAACATAAA
Found at i:153367 original size:21 final size:20
Alignment explanation
Indices: 153343--153385 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
153333 ACGTCACGTG
153343 ATAAACATAAATTAAAAATAT
1 ATAAA-ATAAATTAAAAATAT
* *
153364 AT-AAATTAATTAAAAATGT
1 ATAAAATAAATTAAAAATAT
153383 ATA
1 ATA
153386 TTTTTCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 15 0.79
20 2 0.11
21 2 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATAAATTAAAAATAT
Found at i:153522 original size:8 final size:8
Alignment explanation
Indices: 153491--153590 Score: 80
Period size: 8 Copynumber: 11.9 Consensus size: 8
153481 ATTATTTTGA
153491 AAATATAT
1 AAATATAT
153499 AAA-ATAT
1 AAATATAT
153506 AAATTTATAT
1 AAA--TATAT
*
153516 AAATATACA
1 AAATATA-T
153525 AAATACTAT
1 AAATA-TAT
*
153534 AACATATGTAA
1 AA-ATA--TAT
153545 AAATATAT
1 AAATATAT
153553 AAATATAT
1 AAATATAT
153561 AAATATAT
1 AAATATAT
*
153569 ATATATAT
1 AAATATAT
153577 ATAAT-TAT
1 A-AATATAT
153585 -AATATA
1 AAATATA
153591 CAAGTTTATA
Statistics
Matches: 76, Mismatches: 7, Indels: 19
0.75 0.07 0.19
Matches are distributed among these distances:
6 3 0.04
7 9 0.12
8 36 0.47
9 9 0.12
10 15 0.20
11 4 0.05
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (8 bp):
AAATATAT
Found at i:155800 original size:61 final size:61
Alignment explanation
Indices: 155730--155912 Score: 318
Period size: 61 Copynumber: 3.0 Consensus size: 61
155720 CGCAGCATAA
*
155730 AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAGAGCATTCTCAATATGAC
1 AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAGAGCATTCTCAATAAGAC
*
155791 AACTGTGTT---AACTCTCCATGTCCTTACACATCAAGCACAAGAGCATTCTCAATAAGAC
1 AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAGAGCATTCTCAATAAGAC
*
155849 AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAAAGCATTCTCAATAAGAC
1 AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAGAGCATTCTCAATAAGAC
155910 AAC
1 AAC
155913 AATGATGCCT
Statistics
Matches: 115, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
58 56 0.49
61 59 0.51
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (61 bp):
AACTGTGTTAGAAACTCTCTATGTCCTTACACATCAAGCACAAGAGCATTCTCAATAAGAC
Found at i:165158 original size:29 final size:30
Alignment explanation
Indices: 165119--165243 Score: 121
Period size: 29 Copynumber: 4.2 Consensus size: 30
165109 TTAATATAAT
165119 ATTTGATATTTAAATTTGATATTTTTT-TA
1 ATTTGATATTTAAATTTGATATTTTTTCTA
* * *
165148 GTTTGGTATTTAAATTT--TTTTTTTATCTA
1 ATTTGATATTTAAATTTGATATTTTT-TCTA
* * * *
165177 ATTTGGTACTTAAACTTGACATTTTTTCATA
1 ATTTGATATTTAAATTTGATATTTTTTC-TA
* *
165208 ATTTGATATTTAAATTTGACTCTTTTTCCTA
1 ATTTGATATTTAAATTTGA-TATTTTTTCTA
165239 ATTTG
1 ATTTG
165244 GTACCTAATC
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
27 6 0.08
28 1 0.01
29 31 0.41
30 2 0.03
31 30 0.39
32 6 0.08
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (30 bp):
ATTTGATATTTAAATTTGATATTTTTTCTA
Found at i:165210 original size:31 final size:29
Alignment explanation
Indices: 165167--165247 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 29
165157 TTAAATTTTT
165167 TTTTTATCTAATTTGGTACTTAAACTTGAC
1 TTTTT-TCTAATTTGGTACTTAAACTTGAC
* * *
165197 ATTTTTTCATAATTTGATATTTAAATTTGAC
1 -TTTTTTC-TAATTTGGTACTTAAACTTGAC
165228 TCTTTTTCCTAATTTGGTAC
1 T-TTTTT-CTAATTTGGTAC
165248 CTAATCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 3 0.07
31 38 0.90
32 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (29 bp):
TTTTTTCTAATTTGGTACTTAAACTTGAC
Found at i:165534 original size:51 final size:51
Alignment explanation
Indices: 165477--165577 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
165467 TAAATTGGGT
* ** * *
165477 AAAAAAATAGTTTATGTACCAAATTAAGAAAAAAGGTCAAGTTTAAGTACA
1 AAAAAAAAAGTTTAAATACCAAATTAAAAAAAAAGGTCAAGTTCAAGTACA
*
165528 AAAAAAAAAGTTTAAATACCAAATTAAAAAAAAATGTCAAGTTCAAGTAC
1 AAAAAAAAAGTTTAAATACCAAATTAAAAAAAAAGGTCAAGTTCAAGTAC
165578 CAAATGTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (51 bp):
AAAAAAAAAGTTTAAATACCAAATTAAAAAAAAAGGTCAAGTTCAAGTACA
Found at i:165550 original size:21 final size:21
Alignment explanation
Indices: 165515--165559 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
165505 AAAAAAGGTC
*
165515 AAGTTTAAGTACAAA-AAAAA
1 AAGTTTAAATACAAATAAAAA
165535 AAGTTTAAATACCAAATTAAAAA
1 AAGTTTAAATA-CAAA-TAAAAA
165558 AA
1 AA
165560 AATGTCAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
23 7 0.33
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (21 bp):
AAGTTTAAATACAAATAAAAA
Found at i:166896 original size:28 final size:30
Alignment explanation
Indices: 166834--166897 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
166824 AAAAAGTTGG
166834 TTGTTTAGTGTTGGAGTTTAGGAGGAAAAAA
1 TTGTTTAGTGTTGGAGTTTA-GAGGAAAAAA
* *
166865 TTGTTT-GTGTTGGAGTTT-TAGGAATAAA
1 TTGTTTAGTGTTGGAGTTTAGAGGAAAAAA
166893 TTGTT
1 TTGTT
166898 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 13 0.42
30 12 0.39
31 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.44
Consensus pattern (30 bp):
TTGTTTAGTGTTGGAGTTTAGAGGAAAAAA
Found at i:168770 original size:8 final size:8
Alignment explanation
Indices: 168757--168880 Score: 56
Period size: 8 Copynumber: 15.0 Consensus size: 8
168747 TTATTTTAGA
168757 AAATTTTT
1 AAATTTTT
168765 AAATTTTT
1 AAATTTTT
*
168773 AAAATTTT
1 AAATTTTT
*
168781 AACTTTTT
1 AAATTTTT
*
168789 ---TTTAT
1 AAATTTTT
**
168794 ATTTTTTT
1 AAATTTTT
168802 AGAATTTTT
1 A-AATTTTT
*
168811 ATATTTTTTT
1 A-A-ATTTTT
** *
168821 AAAAATAT
1 AAATTTTT
*
168829 AAATTTTG
1 AAATTTTT
168837 AAATTTTTAT
1 AAA-TTTT-T
168847 AAATATTTT
1 AAAT-TTTT
* *
168856 AAAATTTG
1 AAATTTTT
168864 AAATTATTT
1 AAATT-TTT
168873 AAATTTTT
1 AAATTTTT
168881 GAGAATTATT
Statistics
Matches: 85, Mismatches: 22, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
5 4 0.05
8 45 0.53
9 24 0.28
10 12 0.14
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (8 bp):
AAATTTTT
Found at i:168858 original size:27 final size:25
Alignment explanation
Indices: 168828--168880 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
168818 TTTAAAAATA
* *
168828 TAAATTTTGAAATTTTTATAAATATTT
1 TAAAATTTGAAATTATT-TAAAT-TTT
168855 TAAAATTTGAAATTATTTAAATTTT
1 TAAAATTTGAAATTATTTAAATTTT
168880 T
1 T
168881 GAGAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 5 0.21
27 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
TAAAATTTGAAATTATTTAAATTTT
Found at i:168895 original size:20 final size:19
Alignment explanation
Indices: 168831--168897 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
168821 AAAAATATAA
*
168831 ATTTTGAAATTTTT-ATAAAT
1 ATTTT-AAATTTTTGA-AATT
*
168851 ATTTTAAA-ATTTGAAATT
1 ATTTTAAATTTTTGAAATT
168869 A-TTTAAATTTTTGAGAATT
1 ATTTTAAATTTTTGA-AATT
168888 ATTTTAAATT
1 ATTTTAAATT
168898 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.15
18 12 0.30
19 9 0.22
20 13 0.32
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTTTAAATTTTTGAAATT
Found at i:168902 original size:10 final size:10
Alignment explanation
Indices: 168831--168902 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
168821 AAAAATATAA
168831 ATTTTGAAATT
1 ATTTT-AAATT
168842 -TTTATAAA-T
1 ATTT-TAAATT
168851 ATTTTAAA--
1 ATTTTAAATT
*
168859 ATTTGAAATT
1 ATTTTAAATT
168869 A-TTTAAATT
1 ATTTTAAATT
*
168878 -TTTGAGAATT
1 ATTTTA-AATT
168888 ATTTTAAATT
1 ATTTTAAATT
168898 ATTTT
1 ATTTT
168903 GTAATTTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 7 0.14
9 15 0.30
10 23 0.46
11 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:179312 original size:71 final size:70
Alignment explanation
Indices: 179237--179453 Score: 162
Period size: 71 Copynumber: 3.1 Consensus size: 70
179227 TATATAGTTA
179237 ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTTATG
1 ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTT-CAAAAGAATATTAATTTTTATG
*
179302 TCTTTT
65 TATTTT
** * * * * * ** *
179308 ATATTTTG-A-CCA--AAATTAATTAATATAAATGTTTA-T-ATT-AATA-AATTTGATAAAATA
1 ATATTTTGTATGAATCAAATTAA-T-ATATTAAT-TATATTCTTTCAAAAGAATAT--TAATTTT
* * *
179365 TATATAATTA
61 TATGTATTTT
* *
179375 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTTCAAAAGAATATTAATTTTCATG
1 ATATTTTGTATGAATCAAATTAATATATTAATTATATTC-TTTCAAAAGAATATTAATTTTTATG
*
179440 TTTTTT
65 TATTTT
179446 ATATTTTG
1 ATATTTTG
179454 ACTGAAATTA
Statistics
Matches: 102, Mismatches: 30, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
65 4 0.04
66 3 0.03
67 25 0.25
68 7 0.07
69 18 0.18
70 5 0.05
71 33 0.32
72 3 0.03
73 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (70 bp):
ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTTCAAAAGAATATTAATTTTTATGT
ATTTT
Found at i:179323 original size:138 final size:138
Alignment explanation
Indices: 179149--179549 Score: 649
Period size: 138 Copynumber: 2.9 Consensus size: 138
179139 AAAAGGAATT
*
179149 ATATTAATTTTTATGTCTTTTATATTTTTACTAAAATTAATTAATATAATTGTTTATATTAATAA
1 ATATTAATTTTTATGTCTTTTATATTTTGACTAAAATTAATTAATATAATTGTTTATATTAATAA
* ** * *
179214 AGTCAATAAATTATATATAGTTAATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTT
66 ATTTGATAAAATATATATAATTAATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTT
179279 CCAAAAGA
131 CCAAAAGA
* *
179287 ATATTAATTTTTATGTCTTTTATATTTTGACCAAAATTAATTAATATAAATGTTTATATTAATAA
1 ATATTAATTTTTATGTCTTTTATATTTTGACTAAAATTAATTAATATAATTGTTTATATTAATAA
*
179352 ATTTGATAAAATATATATAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTT
66 ATTTGATAAAATATATATAATTAATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTT
*
179417 TCAAAAGA
131 CCAAAAGA
* * * *
179425 ATATTAATTTTCATGTTTTTTATATTTTGACTGAAATTAATTAATATAATTTTTTATATTAATAA
1 ATATTAATTTTTATGTCTTTTATATTTTGACTAAAATTAATTAATATAATTGTTTATATTAATAA
* * *
179490 ATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTTATATATTAATTATAT
66 ATTTGATAAAATATATATAATTAATATTTTGTATGAATCAAATTAATATATTAATTATAT
179550 CTATGTTCTT
Statistics
Matches: 244, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 244 1.00
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.49
Consensus pattern (138 bp):
ATATTAATTTTTATGTCTTTTATATTTTGACTAAAATTAATTAATATAATTGTTTATATTAATAA
ATTTGATAAAATATATATAATTAATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTT
CCAAAAGA
Found at i:190906 original size:13 final size:13
Alignment explanation
Indices: 190885--190923 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
190875 AATATAAAAA
190885 ACATAATTTTATG
1 ACATAATTTTATG
*
190898 ACATTATTTTAATG
1 ACATAATTTT-ATG
*
190912 AAATAATTTTAT
1 ACATAATTTTAT
190924 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (13 bp):
ACATAATTTTATG
Found at i:193219 original size:15 final size:15
Alignment explanation
Indices: 193201--193236 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
193191 TGGTTACAAA
*
193201 TTTTTT-TTTTACTT
1 TTTTTTATTTTAATT
193215 TTTTTTATTTTAATT
1 TTTTTTATTTTAATT
193230 TTTTTTA
1 TTTTTTA
193237 AAAAAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTATTTTAATT
Found at i:205634 original size:20 final size:20
Alignment explanation
Indices: 205603--205657 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
205593 AAAAATATTA
205603 TTTAAT-ATTTTTATAATTT
1 TTTAATAATTTTTATAATTT
205622 TTTAATAA-TTTT-TAATTT
1 TTTAATAATTTTTATAATTT
*
205640 TTAAAAATAATTTTTATA
1 TT--TAATAATTTTTATA
205658 TATATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 6 0.20
21 4 0.13
22 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATAATTTTTATAATTT
Found at i:205645 original size:49 final size:53
Alignment explanation
Indices: 205571--205673 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 53
205561 TACGTCAGCA
205571 TTTAATTAATGTTTTAAATTATAAAAAT-ATTATTTA-ATAT-TTTTATAATTT
1 TTTAATTAATGTTTTAAATTATAAAAATAATT-TTTATATATATTTTATAATTT
* * *
205622 TTTAA-TAAT-TTTTAATTTTTAAAAATAATTTTTATATATATTTTTTAATTT
1 TTTAATTAATGTTTTAAATTATAAAAATAATTTTTATATATATTTTATAATTT
205673 T
1 T
205674 CAAAAATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
49 19 0.41
50 11 0.24
51 16 0.35
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (53 bp):
TTTAATTAATGTTTTAAATTATAAAAATAATTTTTATATATATTTTATAATTT
Found at i:205653 original size:31 final size:33
Alignment explanation
Indices: 205615--205685 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
205605 TAATATTTTT
*
205615 ATAATTTTT-TA-ATAATTTTTAATTTTTAAAA
1 ATAATTTTTATATATAATTTTTAATTTTCAAAA
*
205646 ATAATTTTTATATATATTTTTTAATTTTCAAAA
1 ATAATTTTTATATATAATTTTTAATTTTCAAAA
205679 ATTAATT
1 A-TAATT
205686 AAATATTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 9 0.26
32 2 0.06
33 19 0.54
34 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
ATAATTTTTATATATAATTTTTAATTTTCAAAA
Found at i:206087 original size:16 final size:16
Alignment explanation
Indices: 206066--206097 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
206056 GATAAATTTA
206066 AAATTTTCAATTAATT
1 AAATTTTCAATTAATT
*
206082 AAATTTTTAATTAATT
1 AAATTTTCAATTAATT
206098 TATTTAATGA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTCAATTAATT
Found at i:207998 original size:16 final size:18
Alignment explanation
Indices: 207966--207998 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
207956 TGAAAAAATA
207966 TTTTAAATAAGAATTAAT
1 TTTTAAATAAGAATTAAT
207984 TTTTAAA-AA-AATTAA
1 TTTTAAATAAGAATTAA
207999 ATATGAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTTAAATAAGAATTAAT
Found at i:212676 original size:17 final size:18
Alignment explanation
Indices: 212650--212684 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
212640 GAAGCAAAGC
212650 AAAAGAGAAAAA-ATAAA
1 AAAAGAGAAAAACATAAA
*
212667 AAAAGGGAAAAACATAAA
1 AAAAGAGAAAAACATAAA
212685 GAGGAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAGAAAAACATAAA
Found at i:213321 original size:10 final size:10
Alignment explanation
Indices: 213303--213345 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
213293 AACTGGAAAG
213303 AAAGAAAATA
1 AAAGAAAATA
*
213313 AAAGGAAATA
1 AAAGAAAATA
213323 AAAG--AATA
1 AAAGAAAATA
213331 AAAGAAAATCA
1 AAAGAAAAT-A
213342 AAAG
1 AAAG
213346 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
10 16 0.55
11 5 0.17
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.09
Consensus pattern (10 bp):
AAAGAAAATA
Found at i:213332 original size:18 final size:19
Alignment explanation
Indices: 213309--213356 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
213299 AAAGAAAGAA
*
213309 AATAAAAGGAAAT-AAAAG
1 AATAAAAGAAAATCAAAAG
213327 AATAAAAGAAAATCAAAAG
1 AATAAAAGAAAATCAAAAG
*
213346 -TTAAAAGAAAA
1 AATAAAAGAAAA
213357 ATATAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (19 bp):
AATAAAAGAAAATCAAAAG
Found at i:214026 original size:16 final size:16
Alignment explanation
Indices: 214005--214042 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
213995 TTCTTAAGTC
214005 CAAAAAAAA-AAAGAAA
1 CAAAAAAAACAAA-AAA
214021 CAAAAAAAACAAAAAA
1 CAAAAAAAACAAAAAA
214037 CTAAAA
1 C-AAAA
214043 TTTTCTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (16 bp):
CAAAAAAAACAAAAAA
Found at i:214416 original size:6 final size:6
Alignment explanation
Indices: 214405--214448 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
214395 CCCAGACAGT
*
214405 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC ATGAGC AG
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AG
214449 ATACATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.48, T:0.02
Consensus pattern (6 bp):
AGGAGC
Found at i:218748 original size:45 final size:45
Alignment explanation
Indices: 218697--218814 Score: 114
Period size: 44 Copynumber: 2.6 Consensus size: 45
218687 GTTATCGTGT
* *
218697 CAAAAACACTTATAAAACTTAAAGCTCGCCAATATGAGGATCTCG
1 CAAAAACACTTATAAAACTTAGAGCTCGCCAATATGAGGAGCTCG
** ** * * *
218742 CAAAAACTTTTAT-TCA-TATAGAGCACACCAATATGATGAGCTCG
1 CAAAAACACTTATAAAACT-TAGAGCTCGCCAATATGAGGAGCTCG
* *
218786 CAAAAGCACTTATAAAACATAGAGCTCGC
1 CAAAAACACTTATAAAACTTAGAGCTCGC
218815 ACAACATGGT
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
43 1 0.02
44 32 0.60
45 20 0.38
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (45 bp):
CAAAAACACTTATAAAACTTAGAGCTCGCCAATATGAGGAGCTCG
Found at i:221567 original size:19 final size:19
Alignment explanation
Indices: 221529--221568 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
221519 GCATATACCC
* * *
221529 AAAAATAATAGTTATTATT
1 AAAAATAATAATCATAATT
221548 AAAAATAATAATCATAATT
1 AAAAATAATAATCATAATT
221567 AA
1 AA
221569 TAAGAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAAATAATAATCATAATT
Found at i:221579 original size:22 final size:21
Alignment explanation
Indices: 221529--221579 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
221519 GCATATACCC
* *
221529 AAAAATAATAGTTATTATTAA
1 AAAAATAATAGTAATTAATAA
221550 AAATAATAATCA-TAATTAATAA
1 AAA-AATAAT-AGTAATTAATAA
221572 GAAAAATA
1 -AAAAATA
221580 TGCCAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 3 0.12
22 18 0.72
23 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATAATAGTAATTAATAA
Found at i:222130 original size:14 final size:16
Alignment explanation
Indices: 222100--222138 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
222090 GTATTTGACA
*
222100 AAAGAGAAAATGAGAG
1 AAAGAAAAAATGAGAG
222116 AAA-AAAAAATG-GAG
1 AAAGAAAAAATGAGAG
222130 AAAGAAAAA
1 AAAGAAAAA
222139 GAGGGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 12 0.57
16 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (16 bp):
AAAGAAAAAATGAGAG
Found at i:230092 original size:36 final size:37
Alignment explanation
Indices: 230052--230126 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 37
230042 GTTCCTGTAA
*
230052 TTGCTGATGCTGCAGCTGC-TGTAACTGTTGCTGTTG
1 TTGCTGATGCTGCAACTGCATGTAACTGTTGCTGTTG
*
230088 TTGCTGATTCTGCAACTGCAGTTGTAACTGTTGCTGTTG
1 TTGCTGATGCTGCAACTGCA--TGTAACTGTTGCTGTTG
230127 ATGGGTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 17 0.50
39 17 0.50
ACGTcount: A:0.13, C:0.19, G:0.28, T:0.40
Consensus pattern (37 bp):
TTGCTGATGCTGCAACTGCATGTAACTGTTGCTGTTG
Found at i:230671 original size:12 final size:12
Alignment explanation
Indices: 230617--230672 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
230607 CATTTGTGTC
230617 TGCTGCTGTTGT
1 TGCTGCTGTTGT
* *
230629 TG-TAGCCGTTGC
1 TGCT-GCTGTTGT
* *
230641 TGCTGCCGTGGT
1 TGCTGCTGTTGT
230653 TGCTGCTGTTGT
1 TGCTGCTGTTGT
230665 TGCTGCTG
1 TGCTGCTG
230673 CTGCTGTATC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.94
13 1 0.03
ACGTcount: A:0.02, C:0.21, G:0.36, T:0.41
Consensus pattern (12 bp):
TGCTGCTGTTGT
Found at i:238714 original size:55 final size:55
Alignment explanation
Indices: 238651--238764 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
238641 GGACTTTCAT
238651 TTTGTAAATAAGCAATAATCTCAGTCGTTGATGTAATTCGATCTGTACCATTGGA
1 TTTGTAAATAAGCAATAATCTCAGTCGTTGATGTAATTCGATCTGTACCATTGGA
238706 TTTGTAAATAAGCAATAATCTCAGTCGTTGATGTAATTCGATCTGTACCATTGGA
1 TTTGTAAATAAGCAATAATCTCAGTCGTTGATGTAATTCGATCTGTACCATTGGA
238761 TTTG
1 TTTG
238765 AGGAAGCTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (55 bp):
TTTGTAAATAAGCAATAATCTCAGTCGTTGATGTAATTCGATCTGTACCATTGGA
Found at i:242424 original size:26 final size:26
Alignment explanation
Indices: 242395--242446 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
242385 AAACTTGACA
242395 TTTTTA-TTAATTTTG-TATTTAAATT
1 TTTTTATTTAA-TTTGATATTTAAATT
*
242420 TTTTTATTTAATTTGATATTTGAATT
1 TTTTTATTTAATTTGATATTTAAATT
242446 T
1 T
242447 GATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTTATTTAATTTGATATTTAAATT
Found at i:242445 original size:13 final size:12
Alignment explanation
Indices: 242424--242453 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
242414 TAAATTTTTT
242424 TATTTAATTTGA
1 TATTTAATTTGA
242436 TATTTGAATTTGA
1 TATTT-AATTTGA
242449 TATTT
1 TATTT
242454 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (12 bp):
TATTTAATTTGA
Found at i:242786 original size:30 final size:31
Alignment explanation
Indices: 242750--242837 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
242740 AGATTCCAAA
* *
242750 AAGTTTAAGTGGCAACTTA-AAAAAAGTGTC
1 AAGTTTAAGTAGCAAATTAGAAAAAAGTGTC
* * *
242780 AAGTTTAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTAGCAAATTAGAAAAAAGTGTC
* * *
242811 AAGTTTGAGTACCAAATTGGACAAAAA
1 AAGTTTAAGTAGCAAATTAGA-AAAAA
242838 AAGTTTAGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 15 0.33
31 26 0.57
32 5 0.11
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTAGCAAATTAGAAAAAAGTGTC
Found at i:242807 original size:31 final size:31
Alignment explanation
Indices: 242770--242870 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
242760 GGCAACTTAA
242770 AAAAAGTGTCAAGTTTAGGTATCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTATCAAATTAGG
*
242801 AAAAAGTGTCAAGTTT-GAGTACCAAATT-GG
1 AAAAAGTGTCAAGTTTAG-GTATCAAATTAGG
* * *
242831 ACAAAA----AAAGTTTAGATATCAAATTAAG
1 A-AAAAGTGTCAAGTTTAGGTATCAAATTAGG
242859 AAAAAGTGTCAA
1 AAAAAGTGTCAA
242871 TATCAAGTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
27 18 0.32
28 3 0.05
30 4 0.07
31 31 0.55
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTATCAAATTAGG
Found at i:243823 original size:11 final size:11
Alignment explanation
Indices: 243807--243846 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
243797 TATTACCCAA
243807 CAAACCCAAAC
1 CAAACCCAAAC
243818 CAAACCCAAAC
1 CAAACCCAAAC
*
243829 CAAACTCAAAC
1 CAAACCCAAAC
*
243840 TAAACCC
1 CAAACCC
243847 CAAGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.53, C:0.42, G:0.00, T:0.05
Consensus pattern (11 bp):
CAAACCCAAAC
Found at i:243902 original size:29 final size:28
Alignment explanation
Indices: 243870--243936 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
243860 CAAGTACGTG
243870 TAAACCCAAAACAATAAAAACCCAATA-CC
1 TAAACCCAAAACAA-AAAAACCCAA-ACCC
* **
243899 TAAACCCTAAAACCAAATCACCCAAACCC
1 TAAACCC-AAAACAAAAAAACCCAAACCC
243928 TAAACCCAA
1 TAAACCCAA
243937 TTCTATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 24 0.73
30 6 0.18
ACGTcount: A:0.54, C:0.36, G:0.00, T:0.10
Consensus pattern (28 bp):
TAAACCCAAAACAAAAAAACCCAAACCC
Found at i:243912 original size:21 final size:22
Alignment explanation
Indices: 243886--243937 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
243876 CAAAACAATA
*
243886 AAAACCCAAT-ACCTAAACCCT
1 AAAACCCAATCACCCAAACCCT
*
243907 AAAACCAAATCACCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
243929 -AAACCCAAT
1 AAAACCCAAT
243938 TCTATTTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAACCCAATCACCCAAACCCT
Found at i:243936 original size:22 final size:21
Alignment explanation
Indices: 243887--243936 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
243877 AAAACAATAA
*
243887 AAACCC-AATACCTAAACCCT
1 AAACCCAAATACCCAAACCCT
*
243907 AAAACCAAATCACCCAAACCCT
1 AAACCCAAAT-ACCCAAACCCT
243929 AAACCCAA
1 AAACCCAA
243937 TTCTATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 3 0.12
22 17 0.68
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (21 bp):
AAACCCAAATACCCAAACCCT
Found at i:244013 original size:14 final size:14
Alignment explanation
Indices: 243991--244036 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
243981 GACCGAACCC
* *
243991 GACCGTTGACCATT
1 GACCATTGATCATT
244005 GACCATTGATCATT
1 GACCATTGATCATT
244019 GA-CAGTTGATCATT
1 GACCA-TTGATCATT
244033 GACC
1 GACC
244037 GTTAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 25 0.89
15 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (14 bp):
GACCATTGATCATT
Found at i:244401 original size:14 final size:14
Alignment explanation
Indices: 244382--244432 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
244372 GTTACATCTC
*
244382 TTTGTGTGATATTG
1 TTTGTGTGATATTA
244396 TTTGTGTTGA-ATTA
1 TTTGTG-TGATATTA
* *
244410 ATTGGGTGATATTA
1 TTTGTGTGATATTA
244424 TTT-TGTGAT
1 TTTGTGTGAT
244433 GTAAAATGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 8 0.27
14 19 0.63
15 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTTGTGTGATATTA
Found at i:248136 original size:51 final size:51
Alignment explanation
Indices: 248060--248161 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
248050 AGGACGATGA
248060 CTACCCTAATTCTATAAATAAGCTCATTTAGCACTTGTTTAACGACAACTT
1 CTACCCTAATTCTATAAATAAGCTCATTTAGCACTTGTTTAACGACAACTT
*
248111 CTACCTTAATTCTATAAATAAGCTCATTTAGCACTTGTTTAACGACAACTT
1 CTACCCTAATTCTATAAATAAGCTCATTTAGCACTTGTTTAACGACAACTT
248162 TTCATACTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (51 bp):
CTACCCTAATTCTATAAATAAGCTCATTTAGCACTTGTTTAACGACAACTT
Found at i:251030 original size:24 final size:24
Alignment explanation
Indices: 251002--251063 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
250992 AATATTTTTG
251002 AAATTATAATTAAAATAATA-TATT
1 AAATTATAATTAAAATAATACT-TT
* *
251026 TAATT-TTATTAAAAATAATACTTT
1 AAATTATAATT-AAAATAATACTTT
251050 AAATATATAATTAA
1 AAAT-TATAATTAA
251064 CAAAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 4 0.13
24 18 0.60
25 4 0.13
26 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATTATAATTAAAATAATACTTT
Found at i:251794 original size:134 final size:131
Alignment explanation
Indices: 251557--251824 Score: 455
Period size: 134 Copynumber: 2.0 Consensus size: 131
251547 CTCTAGCACA
*
251557 TTTTATCGATTATAATGAAAGCATCTTCTTCTAATATGACATTTTGACCCATATCTACTGCAATC
1 TTTTATCGATTATAATGAAAGCATCTTCTTCTAATATGACATTTTGACCCAAATCTACTGCAATC
*
251622 TTCAAAGCATGGAGACATGCAATTGCTTCAATCACCATATGAGTAGAGAAAAAAAAGAAGAAAAG
66 TTCAAAGCATGGAGAAATGCAATTGCTTCAATCACCATATGAGTAGAGAAAAAAAAGAAGAAAAG
251687 T
131 T
* *
251688 TTTTATTGATTATGATGAAAGCATCTTCTTCTAATATGACATTTTGATGACCCAAATCTACTGCA
1 TTTTATCGATTATAATGAAAGCATCTTCTTCTAATATGACA-TTT--TGACCCAAATCTACTGCA
* *
251753 ATCTTCAAAGCATGGAGAAATGCAATTGTTTCAATCACCATATGAGTAGAGAACAAAAAGAAGAA
63 ATCTTCAAAGCATGGAGAAATGCAATTGCTTCAATCACCATATGAGTAGAGAAAAAAAAGAAGAA
251818 AAGT
128 AAGT
251822 TTT
1 TTT
251825 GTTGAGATGA
Statistics
Matches: 128, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
131 39 0.30
132 3 0.02
134 86 0.67
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (131 bp):
TTTTATCGATTATAATGAAAGCATCTTCTTCTAATATGACATTTTGACCCAAATCTACTGCAATC
TTCAAAGCATGGAGAAATGCAATTGCTTCAATCACCATATGAGTAGAGAAAAAAAAGAAGAAAAG
T
Found at i:256707 original size:13 final size:13
Alignment explanation
Indices: 256689--256718 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
256679 TAGAAGGTTT
*
256689 TTTTTATTTTACA
1 TTTTTATTTTAAA
256702 TTTTTATTTTAAA
1 TTTTTATTTTAAA
256715 TTTT
1 TTTT
256719 GGTAGAACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTATTTTAAA
Found at i:262212 original size:2 final size:2
Alignment explanation
Indices: 262205--262237 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
262195 CCAGGTTTGT
262205 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
262238 ATCATCTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:267830 original size:22 final size:22
Alignment explanation
Indices: 267805--267857 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
267795 CTCTATTTTT
* *
267805 TTTTTTCTTTAAAGTCTTTATA
1 TTTTTCCTTTAAAGGCTTTATA
267827 TTTTTCCTTTAAAGGCTTTATA
1 TTTTTCCTTTAAAGGCTTTATA
267849 TTTTTCCTT
1 TTTTTCCTT
267858 AATCTCTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTTCCTTTAAAGGCTTTATA
Found at i:282138 original size:6 final size:6
Alignment explanation
Indices: 282127--282158 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
282117 CAACCTTTTA
282127 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TC
282159 ACGATAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCCC
Found at i:286891 original size:14 final size:15
Alignment explanation
Indices: 286858--286898 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
286848 ATTTGTTTTA
286858 TTTTACATTATTTCACT
1 TTTTAC-TT-TTTCACT
286875 TTTTACTTTTT-ACT
1 TTTTACTTTTTCACT
286889 TTTTA-TTTTT
1 TTTTACTTTTT
286899 TTTTCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 3 0.12
16 2 0.08
17 6 0.25
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTACTTTTTCACT
Found at i:290796 original size:218 final size:218
Alignment explanation
Indices: 290418--290860 Score: 814
Period size: 218 Copynumber: 2.0 Consensus size: 218
290408 AACAAGCTAG
* *
290418 TAAATTTTCTTCAGATTCATCTACTAAATTTCTTTGTTCAAATCATATAGAGGTGTTGCTTAAGA
1 TAAATTTTCTTCAGATTCATCGACTAAATTTCTTTGTTCAAATCATATACAGGTGTTGCTTAAGA
290483 ATTTCTAATTAAAAATTTTGCTTATTTGAGTTCATACTCTTTGAAAAATGGTAAAAAAGGAGCTT
66 ATTTCTAATTAAAAATTTTGCTTATTTGAGTTCATACTCTTTGAAAAATGGTAAAAAAGGAGCTT
*
290548 CTTGCTTTGGCATGTATTTTTTTGGTGTTTGATTATTTGAGTAGATCTTGAATGATGCGCTATTT
131 CTTGCTTTGGCATGTATTTTTTTGGTGTTTGATTATTTGAGTAGATCTTGAATGATGCACTATTT
290613 TCCTCTATGAAAGTTGAATGCTT
196 TCCTCTATGAAAGTTGAATGCTT
* * *
290636 TAAATTTTCTTCAGATTCATCGACTAATTTTTTTTGTTCAAATCATATACAGGTTTTGCTTAAGA
1 TAAATTTTCTTCAGATTCATCGACTAAATTTCTTTGTTCAAATCATATACAGGTGTTGCTTAAGA
290701 ATTTCTAATTAAAAATTTTGCTTATTTGAGTTCATACTCTTTGAAAAATGGTAAAAAAGGAGCTT
66 ATTTCTAATTAAAAATTTTGCTTATTTGAGTTCATACTCTTTGAAAAATGGTAAAAAAGGAGCTT
* *
290766 CTTGCTTTGGCATGTATTTTTTTGGTGTTTGATTATTTGAGTAGATCTTGCATGATGCATTATTT
131 CTTGCTTTGGCATGTATTTTTTTGGTGTTTGATTATTTGAGTAGATCTTGAATGATGCACTATTT
290831 TCCTCTATGAAAGTTGAATGCTT
196 TCCTCTATGAAAGTTGAATGCTT
290854 TAAATTT
1 TAAATTT
290861 CTTTTTGTAA
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 217 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (218 bp):
TAAATTTTCTTCAGATTCATCGACTAAATTTCTTTGTTCAAATCATATACAGGTGTTGCTTAAGA
ATTTCTAATTAAAAATTTTGCTTATTTGAGTTCATACTCTTTGAAAAATGGTAAAAAAGGAGCTT
CTTGCTTTGGCATGTATTTTTTTGGTGTTTGATTATTTGAGTAGATCTTGAATGATGCACTATTT
TCCTCTATGAAAGTTGAATGCTT
Found at i:302055 original size:19 final size:18
Alignment explanation
Indices: 302026--302063 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
302016 ATATATTAGT
302026 TTTTGTCTTTTATTTTATTA
1 TTTTGTCTTTT-TTTT-TTA
302046 TTTT-TCTTTTTTTTTTA
1 TTTTGTCTTTTTTTTTTA
302063 T
1 T
302064 CACAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
19 6 0.33
20 4 0.22
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTGTCTTTTTTTTTTA
Found at i:311145 original size:20 final size:20
Alignment explanation
Indices: 311107--311145 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
311097 AAAAATTCAT
*
311107 AATATAAAAAATTTCAAAAA
1 AATATAAAAAATTTAAAAAA
311127 AATAT-AAAAATATTAAAAA
1 AATATAAAAAAT-TTAAAAA
311146 TCCTAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATATAAAAAATTTAAAAAA
Found at i:315220 original size:10 final size:10
Alignment explanation
Indices: 315182--315221 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
315172 TAGTGGTACA
315182 TTATATATTAT
1 TTAT-TATTAT
*
315193 TTATTATCAT
1 TTATTATTAT
*
315203 CTATTATTAT
1 TTATTATTAT
315213 TTATTATTA
1 TTATTATTA
315222 CATTGGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATTAT
Found at i:316767 original size:19 final size:19
Alignment explanation
Indices: 316727--316768 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
316717 ACTATACACC
*
316727 AAAAATAAATAAATAATAA
1 AAAAATAAATAAATAAGAA
*
316746 AAAACATAAA-AAATAAGCA
1 AAAA-ATAAATAAATAAGAA
316765 AAAA
1 AAAA
316769 TAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAATAAATAAATAAGAA
Found at i:317428 original size:47 final size:46
Alignment explanation
Indices: 317332--317421 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 46
317322 ATGGAATTAA
317332 TGAATTTTTATTTTTATATTTTATATACTTTTTTCTTATTATTTTAT
1 TGAATTTTTATTTTTATATTTTATATA-TTTTTTCTTATTATTTTAT
*
317379 TGAATTTTTAATATTTT-TATTTT-TAT-TTTTTTGTTATT-TTTTA
1 TGAATTTTT-AT-TTTTATATTTTATATATTTTTTCTTATTATTTTA
317422 AAATTGATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
44 5 0.12
45 11 0.28
47 12 0.30
48 8 0.20
49 4 0.10
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (46 bp):
TGAATTTTTATTTTTATATTTTATATATTTTTTCTTATTATTTTAT
Found at i:334487 original size:12 final size:13
Alignment explanation
Indices: 334462--334486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334452 AAACCAAAGT
334462 TTTTTAATTAAAA
1 TTTTTAATTAAAA
334475 TTTTTAATTAAA
1 TTTTTAATTAAA
334487 TAAATATAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAATTAAAA
Found at i:334499 original size:21 final size:19
Alignment explanation
Indices: 334473--334514 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
334463 TTTTAATTAA
334473 AATTTTTAATTAAATAAATAT
1 AATTTTT-A-TAAATAAATAT
*
334494 AATTTTTATATATAAATAT
1 AATTTTTATAAATAAATAT
334513 AA
1 AA
334515 AATATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 1 0.05
21 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTTTATAAATAAATAT
Found at i:338676 original size:41 final size:41
Alignment explanation
Indices: 338527--338716 Score: 152
Period size: 41 Copynumber: 4.7 Consensus size: 41
338517 TTGGGATAAA
* * * * * * *
338527 TGTCGCAAAAGGT-AAAGCAATAGCGGTGTTTATAGAAAAAA
1 TGTCGCTAAAGGTCAGAGCATTAGCGGCGCTTAT-GGAAAAG
* * * *
338568 TGTCGCTAAAAGACAGAGCATTAGTGACGCTTATGGAAAAG
1 TGTCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
* * * *
338609 CGCCGCTAAAGGTCAAAGAATTAGCGGCGCTTATGGAAAAG
1 TGTCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
* ** *
338650 TGTCGTTAAAGGTCAGAGCATTAGCGGCATTTATTAGAAAA-
1 TGTCGCTAAAGGTCAGAGCATTAGCGGCGCTTA-TGGAAAAG
* *
338691 TGTCGCTAAAGGTTA-AGCAATAGCGG
1 TGTCGCTAAAGGTCAGAGCATTAGCGG
338717 GGTTTTCAAA
Statistics
Matches: 117, Mismatches: 30, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
40 10 0.09
41 87 0.74
42 20 0.17
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (41 bp):
TGTCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
Found at i:341819 original size:31 final size:31
Alignment explanation
Indices: 341781--341849 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 31
341771 AGTGTGATCA
341781 AAATTTACTAATAGTTCAGTAATCAAATT-T
1 AAATTTACTAATAGTTCAGTAATCAAATTGT
341811 GAAATTTACTAATAGTTCAGTAATCAAATTGT
1 -AAATTTACTAATAGTTCAGTAATCAAATTGT
341843 AAATTTA
1 AAATTTA
341850 TTCATCCCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (31 bp):
AAATTTACTAATAGTTCAGTAATCAAATTGT
Found at i:343975 original size:206 final size:210
Alignment explanation
Indices: 343613--344030 Score: 740
Period size: 206 Copynumber: 2.0 Consensus size: 210
343603 TGGATACCCT
* *
343613 ATTAGATTTGACTCTAATCTGGTGGATTTATGTTGTCCTATTTCTAGGATTGCATGAACTCCACT
1 ATTAGATTTGACTCTAATCTGGTGGATTTATGTCGTCCTATTTCTAAGATTGCATGAACTCCACT
343678 CAATTATACTAGATCTACTCTTAAATAGGATCTATTCCTCCTCTAATTTAAGCACATCAAACATG
66 CAATTATACTAGATCTACTCTTAAATAGGATCTATTCCTCCTCTAATTTAAGCACATCAAACATG
*
343743 GATTAATATCCTGAAAATATTAAACTAATGATTAATCACACATAATTGAGAATAAGATCTAAGTA
131 GATTAATATCCTAAAAATATTAAACTAATGATTAATCACACATAATTGAGAATAAGATCTAAGTA
*
343808 TTTATTGTGTAAAAC
196 TTTATTGTATAAAAC
343823 ATTAGATTTGACTCTAATCTGGTGGATTTATGTCGTCCTATTTCTAAGATTGCATGAACTCCACT
1 ATTAGATTTGACTCTAATCTGGTGGATTTATGTCGTCCTATTTCTAAGATTGCATGAACTCCACT
343888 CAA-T-TA-TAGATC-ACTCTTAAATA-GAGTCTATTCCTCCTCTAATTTAAGCACATCAAACAT
66 CAATTATACTAGATCTACTCTTAAATAGGA-TCTATTCCTCCTCTAATTTAAGCACATCAAACAT
343948 GGATTAATAT-CTCAAAAATATTAAACTAATGATTAATCACACATAATTGAGAATAAGATCTAAG
130 GGATTAATATCCT-AAAAATATTAAACTAATGATTAATCACACATAATTGAGAATAAGATCTAAG
344012 TATTTATTGTATAAAAC
194 TATTTATTGTATAAAAC
344029 AT
1 AT
344031 AAATCAAAAG
Statistics
Matches: 202, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
205 4 0.02
206 123 0.61
207 6 0.03
208 2 0.01
209 1 0.00
210 66 0.33
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (210 bp):
ATTAGATTTGACTCTAATCTGGTGGATTTATGTCGTCCTATTTCTAAGATTGCATGAACTCCACT
CAATTATACTAGATCTACTCTTAAATAGGATCTATTCCTCCTCTAATTTAAGCACATCAAACATG
GATTAATATCCTAAAAATATTAAACTAATGATTAATCACACATAATTGAGAATAAGATCTAAGTA
TTTATTGTATAAAAC
Found at i:359024 original size:19 final size:19
Alignment explanation
Indices: 359000--359039 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
358990 TTCAAATAAT
359000 AAACAAAAGAAAATACATA
1 AAACAAAAGAAAATACATA
359019 AAACAAAAGAAAATACATA
1 AAACAAAAGAAAATACATA
359038 AA
1 AA
359040 TTGTGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (19 bp):
AAACAAAAGAAAATACATA
Found at i:366428 original size:25 final size:26
Alignment explanation
Indices: 366399--366447 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
366389 TGGAAAAGGC
*
366399 AATTA-AAAAAAATTCATAATTCTTT
1 AATTATAAAAAAAGTCATAATTCTTT
**
366424 AATTATGGAAAAAGTCATAATTCT
1 AATTATAAAAAAAGTCATAATTCT
366448 GGTAAGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (26 bp):
AATTATAAAAAAAGTCATAATTCTTT
Found at i:372248 original size:18 final size:16
Alignment explanation
Indices: 372225--372260 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
372215 GTTTAAAATT
372225 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
372243 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
372259 TT
1 TT
372261 CTCATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:372532 original size:30 final size:30
Alignment explanation
Indices: 372496--372555 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
372486 CAACTTAATA
*
372496 AATAATAGCTTATATTACATGCCCATAGGG
1 AATAATAGCTTATATTACATGCCAATAGGG
* *
372526 AATAATAGCTTATTTTATATGCCAATAGGG
1 AATAATAGCTTATATTACATGCCAATAGGG
372556 TTGTTGTGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (30 bp):
AATAATAGCTTATATTACATGCCAATAGGG
Found at i:373101 original size:3 final size:3
Alignment explanation
Indices: 373093--373121 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
373083 CTTTTCAAGC
373093 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
373122 AGGTTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:383409 original size:19 final size:20
Alignment explanation
Indices: 383381--383418 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
383371 CCGGTTTCAA
383381 TTAAATAAAT-TATTAAAAAT
1 TTAAATAAATATA-TAAAAAT
383401 TTAAA-AAATATATAAAAA
1 TTAAATAAATATATAAAAA
383419 AATTATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAATAAATATATAAAAAT
Found at i:383418 original size:20 final size:20
Alignment explanation
Indices: 383381--383419 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
383371 CCGGTTTCAA
*
383381 TTAAATAAATTATTAAAAAT
1 TTAAATAAATTATAAAAAAT
383401 TTAAA-AAATATATAAAAAA
1 TTAAATAAAT-TATAAAAAA
383420 ATTATAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAATAAATTATAAAAAAT
Done.