Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014101.1 Kokia drynarioides strain JFW-HI SEQ_129132, 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: 273957
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:5384 original size:19 final size:20
Alignment explanation
Indices: 5349--5387 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5339 AGGGTTTCCA
5349 AAAAAAGTCAACTAGTCAAC
1 AAAAAAGTCAACTAGTCAAC
5369 AAAAAAGTCAAC-AGTCAAC
1 AAAAAAGTCAACTAGTCAAC
5388 GATCGATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAAAAGTCAACTAGTCAAC
Found at i:6703 original size:17 final size:17
Alignment explanation
Indices: 6681--6714 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6671 TTACCGTACA
*
6681 TGAACTTTTAAATAATT
1 TGAACTTTTAAACAATT
6698 TGAACTTTTAAACAATT
1 TGAACTTTTAAACAATT
6715 CAACAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (17 bp):
TGAACTTTTAAACAATT
Found at i:6763 original size:21 final size:22
Alignment explanation
Indices: 6728--6770 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6718 CAATAGTGCA
6728 AATTCTTACCGATACAAATGAC
1 AATTCTTACCGATACAAATGAC
* *
6750 AATTC-TATCGATACAAGTGAC
1 AATTCTTACCGATACAAATGAC
6771 TCTTTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (22 bp):
AATTCTTACCGATACAAATGAC
Found at i:11338 original size:51 final size:49
Alignment explanation
Indices: 11265--11446 Score: 167
Period size: 51 Copynumber: 3.6 Consensus size: 49
11255 ATTTCATTTA
** *
11265 ATACTCA-GATGACA-TATAGTCATCGGACCTCTTGTTCCGT-ATAGGAATTC
1 ATACTCATGATGACACT-TAGTCATCGGACCT-TTAATCCATCAT-GG-ATTC
11315 ATACTCATGATGACACTGT-GTCATCGGACCTTTAATCCATCATGGATTC
1 ATACTCATGATGACACT-TAGTCATCGGACCTTTAATCCATCATGGATTC
* * * *
11364 ATTTACTCATGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTC
1 A--TACTCATGATGACACTTAGTCATCGGACCTTTAATCCATCATGGATTC
*
11415 ATTTACTCACT-ATAACACTTAGTCATCGGACC
1 A--TACTCA-TGATGACACTTAGTCATCGGACC
11447 CTTTCGTTTA
Statistics
Matches: 115, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
49 5 0.04
50 16 0.14
51 91 0.79
52 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (49 bp):
ATACTCATGATGACACTTAGTCATCGGACCTTTAATCCATCATGGATTC
Found at i:16785 original size:116 final size:116
Alignment explanation
Indices: 16659--16874 Score: 324
Period size: 116 Copynumber: 1.9 Consensus size: 116
16649 TGCGAACCAC
* * * * *
16659 TGATATTTTTAAATACATGACTACCGATACTTGTTATTCCTCTACCGATACAACCCAAGTCAGTG
1 TGATACTTTTAAACACATGACTACCAATACTTGTTATTCATCTACCAATACAACCCAAGTCAGTG
* *
16724 TACAACCTCTTTCCTACCATGTACTTCTACCGATATAAATATGCAAAATAT
66 AACAACCTCTTTCCTACCATATACTTCTACCGATATAAATATGCAAAATAT
16775 TGATACTTTTAAACACATGACTACCAATACTTGTTATTCATCTACCAATACAACCCAAGTCAGTG
1 TGATACTTTTAAACACATGACTACCAATACTTGTTATTCATCTACCAATACAACCCAAGTCAGTG
* * ** *
16840 AATAACTTCTTTCCTACTTTATACTTCTATCGATA
66 AACAACCTCTTTCCTACCATATACTTCTACCGATA
16875 CATGCATGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
116 88 1.00
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (116 bp):
TGATACTTTTAAACACATGACTACCAATACTTGTTATTCATCTACCAATACAACCCAAGTCAGTG
AACAACCTCTTTCCTACCATATACTTCTACCGATATAAATATGCAAAATAT
Found at i:18553 original size:20 final size:20
Alignment explanation
Indices: 18517--18559 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18507 TTATTAAGCT
*
18517 TTAATTAATCACTTTTAATC
1 TTAATTAAACACTTTTAATC
*
18537 TTAATTAAAC-CTATTTACTC
1 TTAATTAAACACT-TTTAATC
18557 TTA
1 TTA
18560 GTATAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTAAACACTTTTAATC
Found at i:25374 original size:16 final size:16
Alignment explanation
Indices: 25346--25392 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
25336 ATAATTAAAG
*
25346 TAAAATAA-CATTATT
1 TAAAATAATAATTATT
*
25361 TAAAATAATAATTAGT
1 TAAAATAATAATTATT
*
25377 TAATATAATTAATTAT
1 TAAAATAA-TAATTAT
25393 AATTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAAATAATAATTATT
Found at i:30504 original size:21 final size:21
Alignment explanation
Indices: 30478--30537 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
30468 TGTAGTGCTG
30478 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * * *
30499 AGTTCTATCGATAAAAGTGGC
1 ACTTCTACCGATACAAGTGAC
* *
30520 ACATCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
30538 CTTACTTCTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:37563 original size:10 final size:11
Alignment explanation
Indices: 37535--37567 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
37525 GTTCCATTCA
37535 TCTTTAAGACT
1 TCTTTAAGACT
*
37546 TATTTAAGA-T
1 TCTTTAAGACT
37556 TCTTTAAGACT
1 TCTTTAAGACT
37567 T
1 T
37568 TTTGAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (11 bp):
TCTTTAAGACT
Found at i:43841 original size:21 final size:20
Alignment explanation
Indices: 43796--43842 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
43786 TCAGAATTAG
*
43796 ATGCAGCCATACCAAAATTGG
1 ATGCAGCCATA-CAAAATTGA
43817 ATGCAGCCATA-AAAATCTGCA
1 ATGCAGCCATACAAAAT-TG-A
43838 ATGCA
1 ATGCA
43843 AAATCAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.22
20 2 0.09
21 16 0.70
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ATGCAGCCATACAAAATTGA
Found at i:47795 original size:18 final size:18
Alignment explanation
Indices: 47751--47803 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
47741 GCGTAGCCTG
*
47751 ATCAGTTGCAATCACATA
1 ATCAGATGCAATCACATA
* * * *
47769 CTCAAATGCAGTCATATA
1 ATCAGATGCAATCACATA
47787 ATCAGATGCAATCACAT
1 ATCAGATGCAATCACAT
47804 GCTCGAATGC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (18 bp):
ATCAGATGCAATCACATA
Found at i:53415 original size:12 final size:12
Alignment explanation
Indices: 53398--53440 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
53388 TTAAAGAGGA
53398 AGAAGAGAAAAG
1 AGAAGAGAAAAG
*
53410 AGAAGAG-GAA-
1 AGAAGAGAAAAG
*
53420 AGAAGAGAGAAG
1 AGAAGAGAAAAG
53432 AGAAGAGAA
1 AGAAGAGAA
53441 GGAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 5 0.19
12 15 0.56
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (12 bp):
AGAAGAGAAAAG
Found at i:53425 original size:22 final size:21
Alignment explanation
Indices: 53391--53438 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
53381 GCGGGTGTTA
53391 AAGAGGAAGAAGAGAAAAGAG
1 AAGAGGAAGAAGAGAAAAGAG
*
53412 AAGAGGAAAGAAGAGAGAAGAG
1 AAGAGG-AAGAAGAGAAAAGAG
53434 AAGAG
1 AAGAG
53439 AAGGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (21 bp):
AAGAGGAAGAAGAGAAAAGAG
Found at i:53886 original size:21 final size:19
Alignment explanation
Indices: 53842--53886 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
53832 TCAGTACATA
53842 GTTTAGTTGCATACATTTC
1 GTTTAGTTGCATACATTTC
* *
53861 ATTTAGTTGTCATTACATTTT
1 GTTTAGTTG-CA-TACATTTC
53882 GTTTA
1 GTTTA
53887 TCTTTGCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.53
Consensus pattern (19 bp):
GTTTAGTTGCATACATTTC
Found at i:60464 original size:21 final size:21
Alignment explanation
Indices: 60435--60486 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
60425 TGTAGATTAC
60435 TACCGATACAAGTGATC-GTTT
1 TACCGATACAAGTGA-CAGTTT
*
60456 TACTGATACAAGTGACAGTTT
1 TACCGATACAAGTGACAGTTT
60477 TACCGATACA
1 TACCGATACA
60487 TGTCTTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (21 bp):
TACCGATACAAGTGACAGTTT
Found at i:61204 original size:40 final size:40
Alignment explanation
Indices: 61149--61240 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
61139 GTTCATGTGT
* *
61149 CTTCC-TTATAACAATCTTATGCTCTATCGAGTCATAACT
1 CTTCCTTTTTAACAATCTTATGCTCTATCGAGTCATAACA
* *
61188 TTTCCTTTTTAACAATCTTATGCTCTATCGAGTCATAAGA
1 CTTCCTTTTTAACAATCTTATGCTCTATCGAGTCATAACA
61228 CTTCCTTTTTAAC
1 CTTCCTTTTTAAC
61241 CATTCTCACG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 4 0.09
40 43 0.91
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (40 bp):
CTTCCTTTTTAACAATCTTATGCTCTATCGAGTCATAACA
Found at i:61274 original size:42 final size:41
Alignment explanation
Indices: 61175--61325 Score: 117
Period size: 41 Copynumber: 3.7 Consensus size: 41
61165 TTATGCTCTA
* * * * * * * *
61175 TCGAGTCATAACTTTTCCTTTTTAACAATCTTATGCT-CTA
1 TCGAGTCATGAGTCTTCCTTTTTAACATTCTCACGCTAATC
* * *
61215 TCGAGTCATAAGACTTCCTTTTTAACCATTCTCACGCTAATT
1 TCGAGTCATGAGTCTTCCTTTTTAA-CATTCTCACGCTAATC
* * ** *
61257 TCGAGTCATGAGTCTTCCTTTATCACATTCTCATTCTCATC
1 TCGAGTCATGAGTCTTCCTTTTTAACATTCTCACGCTAATC
*
61298 TCGA-TACATGAGTCTTCCTTTTAAACAT
1 TCGAGT-CATGAGTCTTCCTTTTTAACAT
61326 CAAGAAAATT
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
40 23 0.26
41 44 0.49
42 22 0.25
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (41 bp):
TCGAGTCATGAGTCTTCCTTTTTAACATTCTCACGCTAATC
Found at i:65322 original size:6 final size:6
Alignment explanation
Indices: 65311--65338 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
65301 AAAAATTATA
65311 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
65339 AATATAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:72053 original size:29 final size:29
Alignment explanation
Indices: 72016--72085 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
72006 AAGTTTTCGT
* *
72016 TTTAGTCACTTAATTAAAAAAAGTTTTAA
1 TTTAATCACTAAATTAAAAAAAGTTTTAA
** * *
72045 TTTAATCACTAAATTATGAAATGTTTTCA
1 TTTAATCACTAAATTAAAAAAAGTTTTAA
72074 TTTAAGTCACTA
1 TTTAA-TCACTA
72086 GGTTGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 28 0.82
30 6 0.18
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTAATCACTAAATTAAAAAAAGTTTTAA
Found at i:72169 original size:15 final size:15
Alignment explanation
Indices: 72149--72181 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
72139 TTGAAATTTC
72149 TCTTTCTGCTCCTTT
1 TCTTTCTGCTCCTTT
72164 TCTTTCTGCTCCTTT
1 TCTTTCTGCTCCTTT
72179 TCT
1 TCT
72182 ACAATTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.06, T:0.61
Consensus pattern (15 bp):
TCTTTCTGCTCCTTT
Found at i:74891 original size:19 final size:17
Alignment explanation
Indices: 74863--74902 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
74853 ATGATAATAA
74863 ATTTAGTTTTTAATATTT
1 ATTTAGTTTTT-ATATTT
*
74881 ATTTAAGTTTTTATTTTT
1 ATTT-AGTTTTTATATTT
74899 ATTT
1 ATTT
74903 TTCGAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
ATTTAGTTTTTATATTT
Found at i:75052 original size:21 final size:20
Alignment explanation
Indices: 75018--75064 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
75008 TGTAACTCAT
75018 AAAAAT-TTTAAAAAATAATA
1 AAAAATATTTAAAAAATAA-A
75038 ATAAAATATTT-AAAAATAAA
1 A-AAAATATTTAAAAAATAAA
75058 AAAAATA
1 AAAAATA
75065 AAAAAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 13 0.52
22 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATATTTAAAAAATAAA
Found at i:82917 original size:36 final size:36
Alignment explanation
Indices: 82844--82948 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
82834 TTATCGTTAT
* *
82844 TCGTTTTACTCTCTATTGACCTCAAAGGTCATGATGC
1 TCGTTTTACTCCCTATTGACC-CAAAGGTCATTATGC
*
82881 TCGTTTTACTCCCTATTGACCCAAAGTTCATTATGC
1 TCGTTTTACTCCCTATTGACCCAAAGGTCATTATGC
* * * *
82917 TCATTTTTCTCCATGTTGACCCAAAGGTCATT
1 TCGTTTTACTCCCTATTGACCCAAAGGTCATT
82949 CCTGTTACCA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 40 0.67
37 20 0.33
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (36 bp):
TCGTTTTACTCCCTATTGACCCAAAGGTCATTATGC
Found at i:86260 original size:22 final size:22
Alignment explanation
Indices: 86232--86275 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
86222 TTGGGAAATA
86232 GAAAAACTGAATCGGGTTGGAT
1 GAAAAACTGAATCGGGTTGGAT
86254 GAAAAACTGAATCGGGTTGGAT
1 GAAAAACTGAATCGGGTTGGAT
86276 CACATTACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (22 bp):
GAAAAACTGAATCGGGTTGGAT
Found at i:86657 original size:88 final size:88
Alignment explanation
Indices: 86508--86684 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
86498 ATTAATGACA
*
86508 CCGATAGAGTTATTAATACAACTTTGATTAGTTGTTATTCTATCGAAAAATAGAGAGAATTTATT
1 CCGATAGAGTTATTAATACAACTTTGATTAGTTGTTATTCTACCGAAAAATAGAGAGAATTTATT
*
86573 CTCAATTATTACATATATTTTTC
66 CTCAACTATTACATATATTTTTC
86596 CCGATAGAGTTATTAATACAACTTTGATTAGTTGTTATTCTACCGAAAAATAGAGAGAATTTATT
1 CCGATAGAGTTATTAATACAACTTTGATTAGTTGTTATTCTACCGAAAAATAGAGAGAATTTATT
86661 CTCAACTATTACATATATTTTTC
66 CTCAACTATTACATATATTTTTC
86684 C
1 C
86685 GGAATAACAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (88 bp):
CCGATAGAGTTATTAATACAACTTTGATTAGTTGTTATTCTACCGAAAAATAGAGAGAATTTATT
CTCAACTATTACATATATTTTTC
Found at i:89664 original size:24 final size:24
Alignment explanation
Indices: 89624--89673 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
89614 AAAATTCAAA
*
89624 AACTATATTAAACTTAAGCCCATG
1 AACTATATTAAAATTAAGCCCATG
* *
89648 AACTA-ATTGAAAATTAATCCTATG
1 AACTATATT-AAAATTAAGCCCATG
89672 AA
1 AA
89674 AAAAAGCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (24 bp):
AACTATATTAAAATTAAGCCCATG
Found at i:95615 original size:19 final size:19
Alignment explanation
Indices: 95580--95619 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
95570 CATGTCAATG
*
95580 ACATATGTTATGAAAGATAT
1 ACATATGTTAAGAAAGA-AT
95600 ACATAT-TTAAGAAAGAAT
1 ACATATGTTAAGAAAGAAT
95618 AC
1 AC
95620 TCAAGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (19 bp):
ACATATGTTAAGAAAGAAT
Found at i:96102 original size:17 final size:17
Alignment explanation
Indices: 96070--96112 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
96060 AGGAAAAAGT
*
96070 AGTTACAAGAATATGAAA
1 AGTTA-AAGAAGATGAAA
*
96088 GGTTAAAGAAGATGAAA
1 AGTTAAAGAAGATGAAA
96105 AGTTAAAG
1 AGTTAAAG
96113 GTCAAGAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.21
Consensus pattern (17 bp):
AGTTAAAGAAGATGAAA
Found at i:96741 original size:22 final size:22
Alignment explanation
Indices: 96695--96741 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
96685 ATAAAATCAT
* *
96695 TAAATATTAAAATAATATAATA
1 TAAATATTAAAAAAATATAAAA
96717 TAAATATTTAAAAAAAT-TAAAA
1 TAAATA-TTAAAAAAATATAAAA
96739 TAA
1 TAA
96742 TATCGACGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATATTAAAAAAATATAAAA
Found at i:106575 original size:20 final size:21
Alignment explanation
Indices: 106538--106581 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
106528 AAAGTTGAAG
*
106538 AAAATGCAAATGAAATTTCCT
1 AAAATGCAAATGAAATTTACT
*
106559 AAAATGCAAGT-AAATTTACT
1 AAAATGCAAATGAAATTTACT
106579 AAA
1 AAA
106582 GTACAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATGCAAATGAAATTTACT
Found at i:111236 original size:21 final size:21
Alignment explanation
Indices: 111212--111259 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
111202 AAGTAAGACC
111212 TGTATCGGTAGAA-GAGTCACT
1 TGTATCGGTAGAATGA-TCACT
*
111233 TGTATCGGTAGAATTATCACT
1 TGTATCGGTAGAATGATCACT
111254 TGTATC
1 TGTATC
111260 AATAGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
TGTATCGGTAGAATGATCACT
Found at i:113442 original size:5 final size:5
Alignment explanation
Indices: 113432--113458 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
113422 TATAGTTAAA
113432 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
113459 TGGTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:119346 original size:51 final size:52
Alignment explanation
Indices: 119239--119364 Score: 209
Period size: 51 Copynumber: 2.4 Consensus size: 52
119229 TAAAATGTGG
* * *
119239 ATGCAATTCATATGTACTCAAATATCACCTGCTCTGAATGCTTTTCATGTAA
1 ATGCAATTCATATGTACTCAAATATCACCTACTCTGAATGCTTTTAACGTAA
*
119291 ATGCAATTCATATGTACTCAGATATCACC-ACTCTGAATGCTTTTAACGTAA
1 ATGCAATTCATATGTACTCAAATATCACCTACTCTGAATGCTTTTAACGTAA
119342 ATGCAATTCATATGTACTCAAAT
1 ATGCAATTCATATGTACTCAAAT
119365 CCAAACCCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 41 0.59
52 28 0.41
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (52 bp):
ATGCAATTCATATGTACTCAAATATCACCTACTCTGAATGCTTTTAACGTAA
Found at i:121805 original size:32 final size:32
Alignment explanation
Indices: 121769--121833 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
121759 GATGGTTCTA
121769 TCTATCAATTCAGTCAGTGTCATGTTTTCGTG
1 TCTATCAATTCAGTCAGTGTCATGTTTTCGTG
121801 TCTATCAATTCAGTCAGTGTCATGTTTTCGTG
1 TCTATCAATTCAGTCAGTGTCATGTTTTCGTG
121833 T
1 T
121834 GAGGCCGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (32 bp):
TCTATCAATTCAGTCAGTGTCATGTTTTCGTG
Found at i:130721 original size:13 final size:13
Alignment explanation
Indices: 130703--130754 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
130693 AATTTAGCAT
130703 TGTTTTTGAAAAA
1 TGTTTTTGAAAAA
130716 TGTTTTT-AAAAA
1 TGTTTTTGAAAAA
* *
130728 GTGTTGTAGAAAAA
1 -TGTTTTTGAAAAA
130742 TGTTTTTGAAAAA
1 TGTTTTTGAAAAA
130755 AATTTGGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 5 0.15
13 23 0.70
14 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (13 bp):
TGTTTTTGAAAAA
Found at i:132374 original size:31 final size:31
Alignment explanation
Indices: 132312--132370 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
132302 AAATTTAAAG
* *
132312 TCTAAAATTTCAAAACTAACGTATCTAAATT
1 TCTAAAAATTCAAAACTAACATATCTAAATT
*
132343 TCTAAAAATTCAAAAC-AATATATCTAAA
1 TCTAAAAATTCAAAACTAACATATCTAAA
132371 ATTTACTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (31 bp):
TCTAAAAATTCAAAACTAACATATCTAAATT
Found at i:132453 original size:21 final size:22
Alignment explanation
Indices: 132420--132481 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
132410 TTTATTTAGT
132420 TTTAGGGTT-TTTTAAATTAGGG
1 TTTA-GGTTATTTTAAATTAGGG
* *
132442 TTTTGG-TATTTTAAATAAGGG
1 TTTAGGTTATTTTAAATTAGGG
*
132463 TTTAGGTTAATTTAAATTA
1 TTTAGGTTATTTTAAATTA
132482 ATGGCTATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 19 0.58
22 13 0.39
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (22 bp):
TTTAGGTTATTTTAAATTAGGG
Found at i:132518 original size:11 final size:11
Alignment explanation
Indices: 132502--132542 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
132492 AAAATATTTA
132502 ATTATTTAATT
1 ATTATTTAATT
132513 ATTATTT--TT
1 ATTATTTAATT
*
132522 ATAATTTAATT
1 ATTATTTAATT
*
132533 ATTTTTTAAT
1 ATTATTTAAT
132543 CTGTCGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTATTTAATT
Found at i:134062 original size:52 final size:52
Alignment explanation
Indices: 133970--134162 Score: 269
Period size: 52 Copynumber: 3.7 Consensus size: 52
133960 ATTTCATTTC
* *
133970 ATTCATATACTCACGATGACACATAGCCATTGGACTTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * * * * *
134022 GTTCATATTCTTACGATAACACATAACCATCGGGCCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * *
134074 ATTCATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTGAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
*
134126 ATTCATATACTCACGATGACACATAGTCATCGGACCT
1 ATTCATATACTCACGATGACACATAGCCATCGGACCT
134163 TTTTTCATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:136364 original size:22 final size:22
Alignment explanation
Indices: 136338--136395 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
136328 TATACTAAAT
136338 TTTAATTCAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
136360 TTTAATTCAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
136382 TTTAATTCAA-AATT
1 TTTAATTCAATAATT
136396 CCATATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAATTCAATAATTAAAATTC
Found at i:136766 original size:28 final size:29
Alignment explanation
Indices: 136702--136770 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
136692 ATTCATCTCG
* * * *
136702 TCAAAATAATTTTTTCAGAACCCATCTTC
1 TCAAATTATTTTTTTCAGAACACATCATC
*
136731 TCAAAATTATTTTTTTCAGAACACATCATG
1 TC-AAATTATTTTTTTCAGAACACATCATC
136761 TC-AATTATTT
1 TCAAATTATTT
136771 AGATATATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 8 0.24
29 2 0.06
30 24 0.71
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (29 bp):
TCAAATTATTTTTTTCAGAACACATCATC
Found at i:147261 original size:18 final size:18
Alignment explanation
Indices: 147238--147274 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
147228 ACAATTCATA
147238 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
147256 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
147274 T
1 T
147275 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:147595 original size:6 final size:6
Alignment explanation
Indices: 147584--147612 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
147574 TTCTATTCAA
147584 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
147613 TACATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:171845 original size:31 final size:31
Alignment explanation
Indices: 171769--171878 Score: 134
Period size: 30 Copynumber: 3.6 Consensus size: 31
171759 CTTTGGCAGA
* * * *
171769 CTCGTACTTTTGGCTTACTATCTTCAATAGT
1 CTCGCACTTTTGGCTTACTGTCTTCAACAGG
171800 CTCGCAC-TTTGGCTTACTGTCTTCAACAGG
1 CTCGCACTTTTGGCTTACTGTCTTCAACAGG
* *
171830 CTTGCACTTTTGGCTTATTGTCTTCAACAGG
1 CTCGCACTTTTGGCTTACTGTCTTCAACAGG
* *
171861 ATCGCA-TGTTGGCTTACT
1 CTCGCACTTTTGGCTTACT
171879 AACTATTGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
30 36 0.53
31 32 0.47
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (31 bp):
CTCGCACTTTTGGCTTACTGTCTTCAACAGG
Found at i:172273 original size:10 final size:10
Alignment explanation
Indices: 172255--172301 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
172245 ACCAACTGCT
172255 TGCTC-ATGC
1 TGCTCGATGC
172264 TGCTCGATGC
1 TGCTCGATGC
* *
172274 TGCTTGATGA
1 TGCTCGATGC
*
172284 TACTCGATGC
1 TGCTCGATGC
172294 TGCTCGAT
1 TGCTCGAT
172302 ACTTGCTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.34
Consensus pattern (10 bp):
TGCTCGATGC
Found at i:176937 original size:30 final size:30
Alignment explanation
Indices: 176901--176976 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
176891 GGTTTGCACT
176901 TTTGGCTTACTGTCTTCAAAAGACTCGTAC
1 TTTGGCTTACTGTCTTCAAAAGACTCGTAC
** *
176931 TTTGGCTTACTGTCTTCAACTGGCTCGTAC
1 TTTGGCTTACTGTCTTCAAAAGACTCGTAC
* *
176961 TTTAGCTTACTATCTT
1 TTTGGCTTACTGTCTT
176977 TGACAGGCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTGGCTTACTGTCTTCAAAAGACTCGTAC
Found at i:176986 original size:30 final size:30
Alignment explanation
Indices: 176905--176987 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
176895 TGCACTTTTG
* * * *
176905 GCTTACTGTCTTCAAAAGACTCGTACTTTG
1 GCTTACTATCTTCAACAGGCTCGTACTTTA
* *
176935 GCTTACTGTCTTCAACTGGCTCGTACTTTA
1 GCTTACTATCTTCAACAGGCTCGTACTTTA
**
176965 GCTTACTATCTTTGACAGGCTCG
1 GCTTACTATCTTCAACAGGCTCG
176988 CAGTTTGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.37
Consensus pattern (30 bp):
GCTTACTATCTTCAACAGGCTCGTACTTTA
Found at i:181103 original size:36 final size:36
Alignment explanation
Indices: 181036--181104 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
181026 ATATCCAATG
*
181036 GAGGAATTATTTGTTCTTCATCAATGCCAATATCAA
1 GAGGAATTATTTGTTCTTCATCAATACCAATATCAA
* * *
181072 GAGGAATTGTTTGTTCTTCATTAATATCAATAT
1 GAGGAATTATTTGTTCTTCATCAATACCAATAT
181105 TTTCAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (36 bp):
GAGGAATTATTTGTTCTTCATCAATACCAATATCAA
Found at i:181563 original size:23 final size:23
Alignment explanation
Indices: 181509--181563 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
181499 AATAAACATT
*
181509 GTAACTAACTAAAAAATTAAATGA
1 GTAAC-AAATAAAAAATTAAATGA
181533 --AATGCAAATAAAAAATTAAATGA
1 GTAA--CAAATAAAAAATTAAATGA
181556 GTAACAAA
1 GTAACAAA
181564 AACATAGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
22 2 0.08
23 21 0.81
24 1 0.04
25 2 0.08
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (23 bp):
GTAACAAATAAAAAATTAAATGA
Found at i:182395 original size:5 final size:6
Alignment explanation
Indices: 182378--182402 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
182368 AGCCCAAAGT
182378 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
182403 AATTCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:186990 original size:23 final size:23
Alignment explanation
Indices: 186964--187014 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
186954 TTTATTCATA
*
186964 TGCCACATGGTAGAATTTTAAGT
1 TGCCACATGGTAAAATTTTAAGT
*
186987 TGCCACATGTTAAAATTTTAAGT
1 TGCCACATGGTAAAATTTTAAGT
187010 T-CCAC
1 TGCCAC
187015 GTATGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (23 bp):
TGCCACATGGTAAAATTTTAAGT
Found at i:187025 original size:22 final size:23
Alignment explanation
Indices: 186977--187026 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
186967 CACATGGTAG
* *
186977 AATTTTAAGTTGCCACATGTTAA
1 AATTTTAAGTTGCCACATATGAA
* *
187000 AATTTTAAGTT-CCACGTATGAT
1 AATTTTAAGTTGCCACATATGAA
187022 AATTT
1 AATTT
187027 CTTTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
AATTTTAAGTTGCCACATATGAA
Found at i:187801 original size:4 final size:4
Alignment explanation
Indices: 187794--187818 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
187784 TCGGTATTTA
187794 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
187819 TAATTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:194164 original size:21 final size:22
Alignment explanation
Indices: 194140--194186 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
194130 CGATCTAAGG
194140 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
194161 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAACAGAATT
194183 AAAA
1 AAAA
194187 GAACTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:195030 original size:19 final size:19
Alignment explanation
Indices: 195006--195048 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
194996 AAACATAAAT
195006 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
195025 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
195044 TAAAT
1 TAAAT
195049 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:197347 original size:57 final size:57
Alignment explanation
Indices: 197249--197358 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
197239 AAGTTGATGA
* * *
197249 TAAAAGAATGGAATCGATTCGTAAGAAACTAGGCTATGTGCATGGCATTGATGTAGG
1 TAAAAGAATGGAATCGATTCATAAGAAACTAAGCTACGTGCATGGCATTGATGTAGG
* *
197306 TAAAAGAATGGAATCGATTCATAGGAAATTAAGCTACGTGCATGGCATTGATG
1 TAAAAGAATGGAATCGATTCATAAGAAACTAAGCTACGTGCATGGCATTGATG
197359 CAAGTGATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (57 bp):
TAAAAGAATGGAATCGATTCATAAGAAACTAAGCTACGTGCATGGCATTGATGTAGG
Found at i:197583 original size:2 final size:2
Alignment explanation
Indices: 197576--197603 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
197566 ATATGGTTCC
197576 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
197604 GAGACTTCAA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:212349 original size:23 final size:24
Alignment explanation
Indices: 212307--212365 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
212297 ATTTTTTATC
212307 ATATTATTAAATTGATATTTAAAA
1 ATATTATTAAATTGATATTTAAAA
* *
212331 ATATTATTATATTTA-ATTTAAAA
1 ATATTATTAAATTGATATTTAAAA
*
212354 TTATTAATTAAA
1 ATATT-ATTAAA
212366 AATTTTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATTATTAAATTGATATTTAAAA
Found at i:212422 original size:17 final size:18
Alignment explanation
Indices: 212384--212422 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
212374 CTTAAAATAT
*
212384 AATTATACATTTAAAAGT
1 AATTATACATTTAAAAGA
*
212402 AATTATA-ATTTAATAGA
1 AATTATACATTTAAAAGA
212419 AATT
1 AATT
212423 GTGATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTATACATTTAAAAGA
Found at i:214032 original size:18 final size:16
Alignment explanation
Indices: 214001--214044 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
213991 AGATTTAGGT
*
214001 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
214018 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
214032 TTAAAAATTTATT
1 TTAAAAATTTATT
214045 CTCATCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:223626 original size:26 final size:26
Alignment explanation
Indices: 223583--223644 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
223573 ATGATAATTA
* * *
223583 AATTAAATT-AATTATTATGTAATTT
1 AATTAAATTAAAATATTATATAATAT
* *
223608 GATTAAATTAAAATGTTATATAATAT
1 AATTAAATTAAAATATTATATAATAT
223634 AATTAAATTAA
1 AATTAAATTAA
223645 GTTAATGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
AATTAAATTAAAATATTATATAATAT
Found at i:226808 original size:105 final size:105
Alignment explanation
Indices: 226669--226875 Score: 245
Period size: 105 Copynumber: 2.0 Consensus size: 105
226659 CCCACAAACC
** * * * * * * *
226669 GATCAGCAAGAGAAGCATAAGCGTTTGAGTTCAACTGCAGAGCTCGATAATATGGCCTACGATAT
1 GATCAGCAAGAGAAGCATAAGCCATTGAGCTCAACTACAGAGCTCGACAACATGGCCCACAAGAT
* *
226734 CGACAATGAAGCAAACCAGAGAGAAGATACGGAAGCATCA
66 CGACAATGAAGAAAACCAGAGACAAGATACGGAAGCATCA
* * *
226774 GATCAGCAAGAGAAGCATAAGCACATT-AGCTCAACTACGGAGCTTGACAGCATGGCCCACAAGA
1 GATCAGCAAGAGAAGCATAAGC-CATTGAGCTCAACTACAGAGCTCGACAACATGGCCCACAAGA
* * *
226838 TCGACAATGAAGAAAACGAGAGCCAAGATATGGAAGCA
65 TCGACAATGAAGAAAACCAGAGACAAGATACGGAAGCA
226876 CTGCAAAAGG
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
105 82 0.98
106 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (105 bp):
GATCAGCAAGAGAAGCATAAGCCATTGAGCTCAACTACAGAGCTCGACAACATGGCCCACAAGAT
CGACAATGAAGAAAACCAGAGACAAGATACGGAAGCATCA
Found at i:230118 original size:42 final size:42
Alignment explanation
Indices: 230072--230163 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
230062 ACGGGATGAG
*
230072 ACAGAAGCAATAGGG-CCTTGTTGAGA-CTGATTTTGGGCTTC-A
1 ACAGAAGCAA-AGGGACCTTGTTG-GACCTGACTTTGGGC-TCGA
* *
230114 ACAGAAGCAAGGGGACCTTGTTGGACCTGGCTTTGGGCTCGA
1 ACAGAAGCAAAGGGACCTTGTTGGACCTGACTTTGGGCTCGA
230156 ACAGAAGC
1 ACAGAAGC
230164 TTCACCACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 7 0.16
42 37 0.84
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (42 bp):
ACAGAAGCAAAGGGACCTTGTTGGACCTGACTTTGGGCTCGA
Found at i:235522 original size:17 final size:18
Alignment explanation
Indices: 235489--235523 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
235479 TTTATGAGAT
*
235489 ATCGATACTCCTTTGATA
1 ATCGATACTCCTCTGATA
235507 ATCGATAC-CCTCTGATA
1 ATCGATACTCCTCTGATA
235524 TTTTCAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (18 bp):
ATCGATACTCCTCTGATA
Found at i:235607 original size:111 final size:111
Alignment explanation
Indices: 235409--235622 Score: 329
Period size: 111 Copynumber: 1.9 Consensus size: 111
235399 AAATGGTATC
* * *
235409 GATATTTTCAAACAAGTTAGAATTGCTTCAAGACAAAAAGTATCGATACTTTTTGTCTAAATATT
1 GATATTTTCAAACAAGTTAGAATTGCTTCAAGACAAAAAATATCGATACATTTTGTCTAAATATC
* * * *
235474 GGTATTTTATGAGATATCGATACTCCTTTGATAATCGATACCCTCT
66 GATATTTTATAAGATATCGATACCCCTCTGATAATCGATACCCTCT
* * *
235520 GATATTTTCAAACAAGTTAGAATTGCTTCAGGACAAAAAATATCGGTACATTTTGTCTAAGTATC
1 GATATTTTCAAACAAGTTAGAATTGCTTCAAGACAAAAAATATCGATACATTTTGTCTAAATATC
*
235585 GATATTTTATAAGATATTGATACCCCTCTGATAATCGA
66 GATATTTTATAAGATATCGATACCCCTCTGATAATCGA
235623 GACCAAATTG
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 92 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (111 bp):
GATATTTTCAAACAAGTTAGAATTGCTTCAAGACAAAAAATATCGATACATTTTGTCTAAATATC
GATATTTTATAAGATATCGATACCCCTCTGATAATCGATACCCTCT
Found at i:235704 original size:20 final size:21
Alignment explanation
Indices: 235665--235706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
235655 CAAACAATGA
*
235665 CAAAAAGTATCGATACCTTTT
1 CAAAAAATATCGATACCTTTT
*
235686 CAAAAAATATCGATACTTTTT
1 CAAAAAATATCGATACCTTTT
235707 ATTAGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
CAAAAAATATCGATACCTTTT
Found at i:238832 original size:21 final size:21
Alignment explanation
Indices: 238806--238857 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
238796 TTCAAATAAT
238806 GATACCTTTTCAAAAAGTATC
1 GATACCTTTTCAAAAAGTATC
238827 GATACCTTTTCAAAAAGTATC
1 GATACCTTTTCAAAAAGTATC
238848 GATACCTTTT
1 GATACCTTTT
238858 ATTAGATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (21 bp):
GATACCTTTTCAAAAAGTATC
Found at i:239898 original size:3 final size:3
Alignment explanation
Indices: 239885--239914 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
239875 ACTATGATTG
239885 ATT ATTT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT
239915 AAGAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:240139 original size:3 final size:3
Alignment explanation
Indices: 240131--240157 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
240121 TAGCTCAATC
240131 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
240158 TTCTGGACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:246242 original size:38 final size:38
Alignment explanation
Indices: 246183--246330 Score: 152
Period size: 38 Copynumber: 3.9 Consensus size: 38
246173 AAAGTGGAAT
** *
246183 ACTAATTATACTGAACATTTGCTCCAACGAGCGAATCC
1 ACTAATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * **
246221 ACTAATTATACTGAATGTTTGCTAAAACAATTGAATCC
1 ACTAATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * * *
246259 ATTGATTATACTGCATGTTTGCTTAAACGAGCAAATCC
1 ACTAATTATACTGAATGTTTGCTCAAACGAGCGAATCC
* * * *
246297 ACTGATTTTATTAAATGTTTGCTCAAACGAGCGA
1 ACTAATTATACTGAATGTTTGCTCAAACGAGCGA
246331 TAACTACTGG
Statistics
Matches: 88, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 88 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (38 bp):
ACTAATTATACTGAATGTTTGCTCAAACGAGCGAATCC
Found at i:246564 original size:31 final size:31
Alignment explanation
Indices: 246528--246590 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
246518 TGGTAAGATA
246528 ATCATTTAATTTAACGAACTTACTAAGCTTC
1 ATCATTTAATTTAACGAACTTACTAAGCTTC
246559 ATCATTTAATTTAACGAACTTACTAAGCTTC
1 ATCATTTAATTTAACGAACTTACTAAGCTTC
246590 A
1 A
246591 AGTAAGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (31 bp):
ATCATTTAATTTAACGAACTTACTAAGCTTC
Found at i:253011 original size:29 final size:30
Alignment explanation
Indices: 252952--253075 Score: 151
Period size: 30 Copynumber: 4.1 Consensus size: 30
252942 TGTTTTCATT
* *
252952 AAAATTATATTTTGACCCCTAAATTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* *
252982 AAAATCACATTTTGA-CCCTAAACTTCTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* **
253011 AAAATTACATTTTTGACCCCTAAGCTTTTTT
1 AAAATTACA-TTTTGACCCCTAAACTTTTCC
* *
253042 AAAATTACATTTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
253072 AAAA
1 AAAA
253076 AATTATGTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.26
30 39 0.50
31 19 0.24
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:259848 original size:49 final size:49
Alignment explanation
Indices: 259791--259924 Score: 137
Period size: 49 Copynumber: 2.7 Consensus size: 49
259781 ATCAAGGAAA
* * *
259791 CATGAAGATGTGATAGGAAATGTTGAGGTCACAATGACAAACCCAGTAC
1 CATGAAGATATGATAGGAAAGGTTGAGGTCACAACGACAAACCCAGTAC
* * * **
259840 CATGAAGATTTGA-AGGGAAAGGTTGAGGTTACAACGACGAACCTGGTAC
1 CATGAAGATATGATA-GGAAAGGTTGAGGTCACAACGACAAACCCAGTAC
* *
259889 C-TCAAAAGATATGATGGGAAAGGTTGAGGTCACAAC
1 CAT--GAAGATATGATAGGAAAGGTTGAGGTCACAAC
259925 AGTGAACCTA
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
48 2 0.03
49 41 0.59
50 27 0.39
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (49 bp):
CATGAAGATATGATAGGAAAGGTTGAGGTCACAACGACAAACCCAGTAC
Found at i:260397 original size:82 final size:81
Alignment explanation
Indices: 260255--260486 Score: 315
Period size: 82 Copynumber: 2.8 Consensus size: 81
260245 AAGCAGCATC
* * *
260255 ATTCTAATCTTTTACCCCTAATTAAAAGGGACAGATTGAAGA-TCCAATCTTTTACCCCTAATCA
1 ATTCTAGTCTTTTACCCCTAATCAAAAGGG-CAAATTGAAGATTCCAATCTTTTACCCCTAATCA
*
260319 AGAGGGGCAAATTGAAT
65 AGAGGGGCAAATTAAAT
* * *
260336 ATTCTAGTTTTTTACCCCTAACCAAGAAGGGCAAATTGAAAATTCCAATCTTTTACCCCTAATCA
1 ATTCTAGTCTTTTACCCCTAATCAA-AAGGGCAAATTGAAGATTCCAATCTTTTACCCCTAATCA
*
260401 AGAGGGGCAGATTAAAT
65 AGAGGGGCAAATTAAAT
* *
260418 ATT-TCAGTCTTTTACCCCAAATCAATAAGGGCAAATTGAAGATTACAATCTTTTATCCCCTAAT
1 ATTCT-AGTCTTTTACCCCTAATCAA-AAGGGCAAATTGAAGATTCCAATCTTTTA-CCCCTAAT
260482 CAAGA
63 CAAGA
260487 AGGGTAGATT
Statistics
Matches: 133, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
81 31 0.23
82 89 0.67
83 13 0.10
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (81 bp):
ATTCTAGTCTTTTACCCCTAATCAAAAGGGCAAATTGAAGATTCCAATCTTTTACCCCTAATCAA
GAGGGGCAAATTAAAT
Found at i:260509 original size:42 final size:41
Alignment explanation
Indices: 260255--260510 Score: 282
Period size: 41 Copynumber: 6.2 Consensus size: 41
260245 AAGCAGCATC
* * *
260255 ATTCTAATCTTTTACCCCTAATTAA-AAGGGACAGATTGAAG
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGG-CAAATTGAAG
* *
260296 A-TCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAT
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAG
* * * * *
260336 ATTCTAGTTTTTTACCCCTAACCAAGAAGGGCAAATTGAAA
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAG
* * * *
260377 ATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTAAAT
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAG
* * * *
260418 ATTTCAGTCTTTTACCCCAAATCAATAAGGGCAAATTGAAG
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAG
* * *
260459 ATTACAATCTTTTATCCCCTAATCAAGAAGGGTAGATTGAAG
1 ATTCCAATCTTTTA-CCCCTAATCAAGAAGGGCAAATTGAAG
*
260501 ATCCCAATCT
1 ATTCCAATCT
260511 CCTACCTTTA
Statistics
Matches: 177, Mismatches: 35, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
40 30 0.17
41 116 0.66
42 31 0.18
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (41 bp):
ATTCCAATCTTTTACCCCTAATCAAGAAGGGCAAATTGAAG
Found at i:260571 original size:46 final size:46
Alignment explanation
Indices: 260504--260694 Score: 197
Period size: 46 Copynumber: 4.2 Consensus size: 46
260494 ATTGAAGATC
* ** *
260504 CCAATCTCCTACCTTTAAGTCAAGAAAGGTAGATTAAAGTCATCATT
1 CCAATCTCATACCCCTAAGTCAAGAAAGGCAGATTAAAGTCATCA-T
* ** * *
260551 TC-ATCTCATACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATCAT
1 CCAATCTCATACCCCTAAGTCAAGAAAGGCAGATTAAAGTCATCAT
* * * * *
260596 CCAATCTCATACACATAAGTCAAG-AAGGATAGATTGAAGTCATGAT
1 CCAATCTCATACCCCTAAGTCAAGAAAGG-CAGATTAAAGTCATCAT
**
260642 CCAATCTCATACCCCTAAGTCAAGAGGGGCAGATTAAAGTCATCAT
1 CCAATCTCATACCCCTAAGTCAAGAAAGGCAGATTAAAGTCATCAT
*
260688 CCGATCT
1 CCAATCT
260695 TATCCCAGTC
Statistics
Matches: 116, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
45 4 0.03
46 109 0.94
47 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (46 bp):
CCAATCTCATACCCCTAAGTCAAGAAAGGCAGATTAAAGTCATCAT
Found at i:260636 original size:92 final size:91
Alignment explanation
Indices: 260474--260694 Score: 267
Period size: 92 Copynumber: 2.5 Consensus size: 91
260464 AATCTTTTAT
* * * *
260474 CCCCTAA-TCAAGAAGGGTAGATTGAAG-ATC--CCAATCTCCTACCTTTAAGTCAAGAAAGGTA
1 CCCCTAAGTCAAGAGGGGCAGATTGAAGCATCATCCAATCTCATACCTATAAGTCAAGAAAGGTA
*
260535 GATTAAAGTCATCATTTC-ATCTCATA
66 GATTAAAGTCATCA-TCCAATCTCATA
260561 CCCCTAAGTCAAGAGGGGCAGATTGAAGCCATCATCCAATCTCATACAC-ATAAGTCAAG-AAGG
1 CCCCTAAGTCAAGAGGGGCAGATTGAAG-CATCATCCAATCTCATAC-CTATAAGTCAAGAAAGG
* *
260624 ATAGATTGAAGTCATGATCCAATCTCATA
64 -TAGATTAAAGTCATCATCCAATCTCATA
* *
260653 CCCCTAAGTCAAGAGGGGCAGATTAAAGTCATCATCCGATCT
1 CCCCTAAGTCAAGAGGGGCAGATTGAAG-CATCATCCAATCT
260695 TATCCCAGTC
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
87 7 0.06
88 18 0.16
90 3 0.03
91 6 0.05
92 81 0.70
93 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (91 bp):
CCCCTAAGTCAAGAGGGGCAGATTGAAGCATCATCCAATCTCATACCTATAAGTCAAGAAAGGTA
GATTAAAGTCATCATCCAATCTCATA
Found at i:260872 original size:85 final size:85
Alignment explanation
Indices: 260768--260933 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 85
260758 GATTAAACCT
* * ** * * *
260768 CATCTTTCTGATGAGATACAGAGAAGTGGGTCGAAGCATTAAAACGGTCATCTTCTTGATGAGAT
1 CATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATAAAACGGTCATCTTCTTGATGAGAT
260833 ACATAA-AAGTGGACCAAATC
66 ACA-AAGAAGTGGACCAAATC
** *
260853 CATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATAAAGTGGTCATCTTTTTGATGAGAT
1 CATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATAAAACGGTCATCTTCTTGATGAGAT
260918 ACAAAGAAGTGGACCA
66 ACAAAGAAGTGGACCA
260934 GAATATGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
84 2 0.03
85 68 0.97
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (85 bp):
CATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATAAAACGGTCATCTTCTTGATGAGAT
ACAAAGAAGTGGACCAAATC
Found at i:261726 original size:22 final size:22
Alignment explanation
Indices: 261696--261749 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
261686 GAATATATTA
*
261696 AAAAATAAAAAACCTCAAAAAG
1 AAAAATAAAAAAACTCAAAAAG
* *
261718 AAAATTAAAAAAATTCAAAAAG
1 AAAAATAAAAAAACTCAAAAAG
*
261740 ATAAA-AAAAA
1 AAAAATAAAAA
261750 CTATAACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAAAACTCAAAAAG
Found at i:262330 original size:30 final size:30
Alignment explanation
Indices: 262290--262478 Score: 236
Period size: 30 Copynumber: 6.3 Consensus size: 30
262280 ACCTCCAAAT
* ** *
262290 TTTTCTAAAATTACATTTTAACCTTTATAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
*
262320 TTTTCCAAAATTACATTTTGACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
*
262350 TTTTCCAAAATTACATTTTAACCCTTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* ** * *
262380 TTTTCCGAAATCCCATTTTCA-CCTTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
* * *
262409 TTCTCTAAAATTACTTTTTAACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
*
262439 TTCTCCAAAATTACATTTTAACCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAAC
262469 TTTTCCAAAA
1 TTTTCCAAAA
262479 AATATGTTTT
Statistics
Matches: 136, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
29 22 0.16
30 114 0.84
ACGTcount: A:0.34, C:0.25, G:0.01, T:0.40
Consensus pattern (30 bp):
TTTTCCAAAATTACATTTTAACCCCTAAAC
Found at i:262337 original size:59 final size:60
Alignment explanation
Indices: 262258--262478 Score: 236
Period size: 60 Copynumber: 3.7 Consensus size: 60
262248 TTTGACCACG
* * *
262258 AACTTTTCTAAAAATT-CA-TTTGACCTCCAAATTTTTCTAAAATTACATTTTAACCTTTA
1 AACTTTTC-CAAAATTACATTTTGACCTCCAAACTTTTCTAAAATTACATTTTAACCCTTA
* *
262317 TACTTTTCCAAAATTACATTTTGACC-CCTAAACTTTTCCAAAATTACATTTTAACCCTTA
1 AACTTTTCCAAAATTACATTTTGACCTCC-AAACTTTTCTAAAATTACATTTTAACCCTTA
* ** * * * * *
262377 AACTTTTCCGAAATCCCATTTTCACCT-TAAACTTCTCTAAAATTACTTTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCTCCAAACTTTTCTAAAATTACATTTTAACCCTTA
* * *
262436 AACTTCTCCAAAATTACATTTTAACC-CCTAAACTTTTCCAAAA
1 AACTTTTCCAAAATTACATTTTGACCTCC-AAACTTTTCTAAAA
262479 AATATGTTTT
Statistics
Matches: 133, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
58 6 0.05
59 59 0.44
60 68 0.51
ACGTcount: A:0.34, C:0.25, G:0.01, T:0.39
Consensus pattern (60 bp):
AACTTTTCCAAAATTACATTTTGACCTCCAAACTTTTCTAAAATTACATTTTAACCCTTA
Found at i:262419 original size:89 final size:90
Alignment explanation
Indices: 262303--262474 Score: 265
Period size: 89 Copynumber: 1.9 Consensus size: 90
262293 TCTAAAATTA
* * * *
262303 CATTTTAACCTTTATACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTT
1 CATTTTAACCTTTAAACTTCTCCAAAATTACATTTTAACCCCTAAACTTCTCCAAAATTACATTT
*
262368 TAACCCTTAAACTTTTCCGAAATCC
66 TAACCCCTAAACTTTTCCGAAATCC
* * *
262393 CATTTTCACC-TTAAACTTCTCTAAAATTACTTTTTAACCCCTAAACTTCTCCAAAATTACATTT
1 CATTTTAACCTTTAAACTTCTCCAAAATTACATTTTAACCCCTAAACTTCTCCAAAATTACATTT
262457 TAACCCCTAAACTTTTCC
66 TAACCCCTAAACTTTTCC
262475 AAAAAATATG
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 65 0.88
90 9 0.12
ACGTcount: A:0.32, C:0.27, G:0.01, T:0.40
Consensus pattern (90 bp):
CATTTTAACCTTTAAACTTCTCCAAAATTACATTTTAACCCCTAAACTTCTCCAAAATTACATTT
TAACCCCTAAACTTTTCCGAAATCC
Found at i:263114 original size:18 final size:17
Alignment explanation
Indices: 263087--263139 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
263077 ACTTTATTTC
263087 TATTACTTTAGTCATTTTT
1 TATTA-TTTA-TCATTTTT
**
263106 TATTATTTATTTTTATTT
1 TATTATTTATCATT-TTT
263124 TATTATTT-TCATTTTT
1 TATTATTTATCATTTTT
263140 AAATAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 3 0.10
17 6 0.21
18 15 0.52
19 5 0.17
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.72
Consensus pattern (17 bp):
TATTATTTATCATTTTT
Found at i:268150 original size:16 final size:16
Alignment explanation
Indices: 268126--268157 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
268116 GTTTTTTTTT
268126 TTAAATTGAAAAAAAA
1 TTAAATTGAAAAAAAA
*
268142 TTAATTTGAAAAAAAA
1 TTAAATTGAAAAAAAA
268158 AATTGAAAAG
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:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
TTAAATTGAAAAAAAA
Found at i:268205 original size:12 final size:11
Alignment explanation
Indices: 268188--268253 Score: 59
Period size: 12 Copynumber: 6.1 Consensus size: 11
268178 AATTAGTATA
268188 TTTATTTTCAAT
1 TTTATTTT-AAT
*
268200 TTTATTCTCAAT
1 TTTATT-TTAAT
268212 TTTA-TTT--T
1 TTTATTTTAAT
*
268220 TTTATCTT-AT
1 TTTATTTTAAT
268230 TTTATTTTTAAT
1 TTTA-TTTTAAT
268242 TTTATTTTAAT
1 TTTATTTTAAT
268253 T
1 T
268254 ATGCACTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.11
9 2 0.04
10 6 0.13
11 12 0.27
12 19 0.42
13 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:268237 original size:17 final size:18
Alignment explanation
Indices: 268210--268250 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
268200 TTTATTCTCA
*
268210 ATTTTATTTTTTTATCTT
1 ATTTTATTTTTTAATCTT
*
268228 ATTTTA-TTTTTAATTTT
1 ATTTTATTTTTTAATCTT
268245 ATTTTA
1 ATTTTA
268251 ATTATGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTATTTTTTAATCTT
Found at i:269197 original size:11 final size:11
Alignment explanation
Indices: 269183--269240 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
269173 AGTCGAAAAG
269183 AAAAAAATGAA
1 AAAAAAATGAA
**
269194 AAAAATTTGAA
1 AAAAAAATGAA
* *
269205 AAATAATTGAA
1 AAAAAAATGAA
269216 AAAAAAA--AA
1 AAAAAAATGAA
269225 AAGAAAAA-GAA
1 AA-AAAAATGAA
269236 AAAAA
1 AAAAA
269241 GAGGAAGACA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 4 0.10
10 8 0.21
11 27 0.69
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:269207 original size:12 final size:11
Alignment explanation
Indices: 269183--269221 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
269173 AGTCGAAAAG
269183 AAAAAAA-TGA
1 AAAAAAATTGA
*
269193 AAAAAATTTGA
1 AAAAAAATTGA
*
269204 AAAATAATTGA
1 AAAAAAATTGA
269215 AAAAAAA
1 AAAAAAA
269222 AAAAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:269248 original size:14 final size:14
Alignment explanation
Indices: 269213--269242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
269203 AAAAATAATT
*
269213 GAAAAAAAAAAAAA
1 GAAAAAGAAAAAAA
269227 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
269241 GA
1 GA
269243 GGAAGACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:270227 original size:23 final size:25
Alignment explanation
Indices: 270201--270246 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
270191 CCAATTAGGG
270201 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
270224 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
270247 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:273364 original size:31 final size:32
Alignment explanation
Indices: 273309--273377 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
273299 TCTTTTAAAA
*
273309 AAATATATAATTTAGAATTGTTATATTATTTT
1 AAATATATAATTTAGAATTGTTATATAATTTT
* *
273341 CAATATAT-TTTTAGTAATT-TTATATAATTTT
1 AAATATATAATTTAG-AATTGTTATATAATTTT
273372 AAATAT
1 AAATAT
273378 TTGAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (32 bp):
AAATATATAATTTAGAATTGTTATATAATTTT
Done.