Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011583.1 Kokia drynarioides strain JFW-HI SEQ_126572, 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: 133090
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:519 original size:29 final size:29
Alignment explanation
Indices: 477--888 Score: 322
Period size: 29 Copynumber: 14.1 Consensus size: 29
467 AGGGTCCCGA
*
477 AACTTCCAAAAATCCCGTTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
**
506 AACTTTTAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* * *
535 AAGCTTCTAAAAATCCCATTTTGACTC-CG
1 AA-CTTCCAAAAATCCCATTTTTACCCTCG
* **
564 AAACTTTCAAAAATCCCATTTTTGACCCTAA
1 -AACTTCCAAAAATCCCATTTTT-ACCCTCG
* * *
595 AACTTCCAAAAATCTCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
624 AACTTTCAAAAATCCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCTC-G
* *
654 AACCTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
683 AACTTCTAAAAATCCCATTTTTGATCC-CG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
* * *
712 AAACTTCCAAAAATCCCGTTTTTACCCCCA
1 -AACTTCCAAAAATCCCATTTTTACCCTCG
* * *
742 AACTTCTAAAAATCCCATTTTTGACCTTGG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
** *
772 AACTTCC-AAAATTTCATTTTAACCC-CG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* * *
799 AAACTTCTAAAAATTCCATTTTTAGCCCT-A
1 -AACTTCCAAAAATCCCATTTTTA-CCCTCG
* ** *
829 AACTTCCCAAAATTTCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
858 AA-TGTCCAAAAAAT-CCATTTTTAACCC-CG
1 AACT-TCC-AAAAATCCCATTTTT-ACCCTCG
887 AA
1 AA
889 TTTTCCCAAA
Statistics
Matches: 308, Mismatches: 54, Indels: 42
0.76 0.13 0.10
Matches are distributed among these distances:
27 1 0.00
28 13 0.04
29 179 0.58
30 115 0.37
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:576 original size:59 final size:59
Alignment explanation
Indices: 474--855 Score: 422
Period size: 59 Copynumber: 6.5 Consensus size: 59
464 CTGAGGGTCC
* *
474 CGAAACTTCCAAAAATCCCGTTTTTACCCTCG-AACTTTTAAAAATCCCATTTTTGACCT
1 CGAAACTTCCAAAAATCCCATTTTTACCC-CGAAACTTCTAAAAATCCCATTTTTGACCT
* * * *
533 CGAAGCTTCTAAAAATCCCATTTTGACTCCGAAACTT-TCAAAAATCCCATTTTTGACC-
1 CGAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCT-AAAAATCCCATTTTTGACCT
* * *
591 CTAAAACTTCCAAAAATCTCATTTTTACCCCCAAACTT-TCAAAAATCCCATTTTTGACCT
1 C-GAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCT-AAAAATCCCATTTTTGACCT
* * *
651 CAAAACCTCCAAAAATTCCATTTTTACCCTCG-AACTTCTAAAAATCCCATTTTTGATCC-
1 CGAAACTTCCAAAAATCCCATTTTTACCC-CGAAACTTCTAAAAATCCCATTTTTGA-CCT
* *
710 CGAAACTTCCAAAAATCCCGTTTTTACCCCCAAACTTCTAAAAATCCCATTTTTGACCT
1 CGAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCTAAAAATCCCATTTTTGACCT
* * ** * *
769 TGGAACTTCC-AAAATTTCATTTTAACCCCGAAACTTCTAAAAATTCCATTTTT-AGCC-
1 CGAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCTAAAAATCCCATTTTTGA-CCT
* * **
826 CTAAACTTCCCAAAATTTCATTTTTACCCC
1 CGAAACTTCCAAAAATCCCATTTTTACCCC
856 CGAATGTCCA
Statistics
Matches: 279, Mismatches: 33, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
57 8 0.03
58 64 0.23
59 202 0.72
60 5 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
CGAAACTTCCAAAAATCCCATTTTTACCCCGAAACTTCTAAAAATCCCATTTTTGACCT
Found at i:687 original size:118 final size:118
Alignment explanation
Indices: 476--856 Score: 477
Period size: 118 Copynumber: 3.2 Consensus size: 118
466 GAGGGTCCCG
* * * * *
476 AAACTTCCAAAAATCCCGTTTTTACCCTCGAACTTTTAAAAATCCCATTTTTGACCTCGAAGCTT
1 AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCTCGAAACTT
* * * *
541 CTAAAAATCCCATTTTGACTCCGAAACTT-TCAAAAATCCCATTTTTGA-CCCT
66 CCAAAAATTCCATTTTAACCCCGAAACTTCT-AAAAATCCCATTTTTGAGCCCT
* * *
593 AAAACTTCCAAAAATCTCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCTCAAAACC
1 -AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCTCGAAACT
* * *
658 TCCAAAAATTCCATTTTTACCCTCG-AACTTCTAAAAATCCCATTTTTGATCCCG
65 TCCAAAAATTCCATTTTAACCC-CGAAACTTCTAAAAATCCCATTTTTGAGCCCT
* * *
712 AAACTTCCAAAAATCCCGTTTTTACCCCCAAAC-TTCTAAAAATCCCATTTTTGACCTTGGAACT
1 AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTTC-AAAAATCCCATTTTTGACCTCGAAACT
* *
776 TCC-AAAATTTCATTTTAACCCCGAAACTTCTAAAAATTCCATTTTT-AGCCCT
65 TCCAAAAATTCCATTTTAACCCCGAAACTTCTAAAAATCCCATTTTTGAGCCCT
* **
828 AAACTTCCCAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
857 GAATGTCCAA
Statistics
Matches: 230, Mismatches: 28, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
116 31 0.13
117 40 0.17
118 153 0.67
119 6 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (118 bp):
AAACTTCCAAAAATCCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCTCGAAACTT
CCAAAAATTCCATTTTAACCCCGAAACTTCTAAAAATCCCATTTTTGAGCCCT
Found at i:895 original size:59 final size:58
Alignment explanation
Indices: 513--901 Score: 227
Period size: 59 Copynumber: 6.6 Consensus size: 58
503 TCGAACTTTT
* * ** ** * * *
513 AAAAATCCCATTTTTGACCTCGAAGCTTCTAAAAATCCCATTTTGACTCCGAAACTTTC-
1 AAAAAT-CCATTTTT-ACCCCGAAACTTCCCAAAATTTCATTTTAACCCCGAAACTTCCA
** * * * * *
572 AAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACCCCCAAACTTTC-
1 AAAAAT-CCATTTTT-ACCCCGAAACTTCCCAAAATTTCATTTTAACCCCGAAACTTCCA
* * * * * * *
631 AAAAATCCCATTTTTGACCTCAAAACCTCCAAAAATTCCATTTTTACCCTCG-AACTT-CT
1 AAAAAT-CCATTTTT-ACCCCGAAACTTCCCAAAATTTCATTTTAACCC-CGAAACTTCCA
* * ** * * * *
690 AAAAATCCCATTTTTGATCCCGAAACTTCCAAAAATCCCGTTTTTACCCCCAAACTT-CT
1 AAAAAT-CCATTTTT-ACCCCGAAACTTCCCAAAATTTCATTTTAACCCCGAAACTTCCA
** * *
749 AAAAATCCCATTTTTGACCTTGGAACTT-CCAAAATTTCATTTTAACCCCGAAACTTCTA
1 AAAAAT-CCATTTTT-ACCCCGAAACTTCCCAAAATTTCATTTTAACCCCGAAACTTCCA
* * * *
808 AAAATTCCATTTTTAGCCCTAAACTTCCCAAAATTTCATTTTTACCCCCG-AA-TGTCCA
1 AAAAATCCATTTTTACCCCGAAACTTCCCAAAATTTCA-TTTTAACCCCGAAACT-TCCA
**
866 AAAAATCCATTTTTAACCCCGAATTTTCCCAAAATT
1 AAAAATCCATTTTT-ACCCCGAAACTTCCCAAAATT
902 ACCGTTTCAC
Statistics
Matches: 275, Mismatches: 47, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
57 8 0.03
58 61 0.22
59 205 0.75
60 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAAATCCATTTTTACCCCGAAACTTCCCAAAATTTCATTTTAACCCCGAAACTTCCA
Found at i:2948 original size:22 final size:22
Alignment explanation
Indices: 2910--2953 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2900 CTTGTTTTAC
*
2910 TGTTTTGTTGTTTTTTTCTTAT
1 TGTTTTCTTGTTTTTTTCTTAT
*
2932 TGTTTTCTT-TTTATTTTGTTAT
1 TGTTTTCTTGTTT-TTTTCTTAT
2954 CATTTCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.07, C:0.05, G:0.11, T:0.77
Consensus pattern (22 bp):
TGTTTTCTTGTTTTTTTCTTAT
Found at i:7991 original size:18 final size:19
Alignment explanation
Indices: 7963--8014 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
7953 ATTAGTTTAT
7963 TTATAATTTTTAAATATTA
1 TTATAATTTTTAAATATTA
**
7982 TTAT-ATTTTTATTTATTA
1 TTATAATTTTTAAATATTA
*
8000 TT-TAATTTATAAATA
1 TTATAATTTTTAAATA
8015 AATATATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.04
18 22 0.81
19 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATAATTTTTAAATATTA
Found at i:11391 original size:53 final size:53
Alignment explanation
Indices: 11311--11416 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
11301 CGTCCCATCT
11311 TCATCCCATTGTTTAAGAATGTTTCTGTTTTTTTCTGTGTTTTAGTACTACTA
1 TCATCCCATTGTTTAAGAATGTTTCTGTTTTTTTCTGTGTTTTAGTACTACTA
*
11364 TCATCCCATTGTTTAAGAATGTTTCTGTTTTTTTCTTTGTTTTAGTACTACTA
1 TCATCCCATTGTTTAAGAATGTTTCTGTTTTTTTCTGTGTTTTAGTACTACTA
11417 ACTGCAACTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (53 bp):
TCATCCCATTGTTTAAGAATGTTTCTGTTTTTTTCTGTGTTTTAGTACTACTA
Found at i:22775 original size:29 final size:28
Alignment explanation
Indices: 22711--22775 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
22701 CCTTTCCGTA
22711 TTTTAAAATTATTTTTACTCCTAAACTT
1 TTTTAAAATTATTTTTACTCCTAAACTT
* *
22739 TCTAAAAATTATGTTTTGAC-CCTCAAA-TT
1 TTTTAAAATTAT-TTTT-ACTCCT-AAACTT
22768 TTTTAAAA
1 TTTTAAAA
22776 ATTTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 10 0.33
29 15 0.50
30 5 0.17
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTTAAAATTATTTTTACTCCTAAACTT
Found at i:22777 original size:30 final size:28
Alignment explanation
Indices: 22711--22778 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
22701 CCTTTCCGTA
22711 TTTT-AAAATTATTTTTACTCCTAAACT
1 TTTTAAAAATTATTTTTACTCCTAAACT
* *
22738 TTCTAAAAATTATGTTTTGAC-CCTCAAATT
1 TTTTAAAAATTAT-TTTT-ACTCCT-AAACT
22768 TTTTAAAAATT
1 TTTTAAAAATT
22779 TAAATTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 8 0.24
29 7 0.21
30 16 0.47
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTAAAAATTATTTTTACTCCTAAACT
Found at i:22957 original size:31 final size:30
Alignment explanation
Indices: 22884--22959 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
22874 TTTAATCCTA
* * *
22884 AATTTTCCAAAATTTTTGATTTGACCCTTG
1 AATTTTCAAAAAATTTTGATTTGACACTTG
**
22914 AATTTTTTAAAAATTTTGATTTGACACTTG
1 AATTTTCAAAAAATTTTGATTTGACACTTG
*
22944 AGGTTTTCAAAAAATT
1 A-ATTTTCAAAAAATT
22960 CAAATTTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 27 0.71
31 11 0.29
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (30 bp):
AATTTTCAAAAAATTTTGATTTGACACTTG
Found at i:23035 original size:10 final size:10
Alignment explanation
Indices: 23010--23058 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
23000 TTATCCTATA
*
23010 TGTATATTAT
1 TGTATTTTAT
*
23020 TTTATTTTAT
1 TGTATTTTAT
23030 TGTATTTTA-
1 TGTATTTTAT
*
23039 TGTA-TATAT
1 TGTATTTTAT
23048 TGTATTTTAT
1 TGTATTTTAT
23058 T
1 T
23059 ATGTATACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.09
9 8 0.25
10 21 0.66
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (10 bp):
TGTATTTTAT
Found at i:25889 original size:23 final size:23
Alignment explanation
Indices: 25859--25962 Score: 129
Period size: 23 Copynumber: 4.4 Consensus size: 23
25849 ACACTATAGC
*
25859 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
25882 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* * *
25907 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
25930 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
25953 GCTCTCTGTT
1 GCTCTCTGTT
25963 ACCCAGCACT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 48 0.70
24 1 0.01
25 17 0.25
26 3 0.04
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:25979 original size:71 final size:69
Alignment explanation
Indices: 25860--26009 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 69
25850 CACTATAGCG
** * *
25860 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTACCAGCACTGTATGTGCTCACTG-TTAGTACTT
25925 TGTGTA
65 TG-GTA
*
25931 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTGTTACCCAGCACT-TATGTGCTCACTGTTAGTACT
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTA-CCAGCACTGTATGTGCTCACTGTTAGTACT
25994 TTGGTA
64 TTGGTA
26000 CTCTCTGTTT
1 CTCTCTGTTT
26010 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
69 13 0.18
70 11 0.15
71 39 0.54
72 9 0.12
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTACCAGCACTGTATGTGCTCACTGTTAGTACTTT
GGTA
Found at i:26007 original size:21 final size:22
Alignment explanation
Indices: 25893--26008 Score: 85
Period size: 23 Copynumber: 5.1 Consensus size: 22
25883 CTCTCTGTTA
* *
25893 TTAGCACTGTGTGTGCTCTCTG
1 TTAGCACTTTGTGTACTCTCTG
*
25915 ATTAGTACTTTGTGTACTCTCTG
1 -TTAGCACTTTGTGTACTCTCTG
* *
25938 TTTAGCACTGTGTGTGCTCTCTG
1 -TTAGCACTTTGTGTACTCTCTG
*
25961 TTACCCAGCACTTATGTG--CTCACTG
1 TT----AGCACTT-TGTGTACTCTCTG
*
25986 TTAGTACTTTG-GTACTCTCTG
1 TTAGCACTTTGTGTACTCTCTG
26007 TT
1 TT
26009 TGTTCCGTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 14 0.19
22 2 0.03
23 38 0.51
25 8 0.11
26 6 0.08
27 4 0.05
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (22 bp):
TTAGCACTTTGTGTACTCTCTG
Found at i:32164 original size:15 final size:14
Alignment explanation
Indices: 32140--32173 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
32130 TTCTCTAATG
*
32140 ATATATGAATTATT
1 ATATAGGAATTATT
32154 AGTATAGGAATTATT
1 A-TATAGGAATTATT
32169 ATATA
1 ATATA
32174 AGTACATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (14 bp):
ATATAGGAATTATT
Found at i:33030 original size:23 final size:23
Alignment explanation
Indices: 32928--33031 Score: 95
Period size: 23 Copynumber: 4.4 Consensus size: 23
32918 ACACTAGCGC
*
32928 GCTCTCTGTTTAGCACGTCTCGT-T
1 GCTCTCTGTTTAGCAC-TAT-GTGT
* *
32952 -CTCTCAGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTATGTGT
* * *
32976 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTATGTGT
*
32999 ACTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGTTTAGCACTATGTGT
33022 GCTCTCTGTT
1 GCTCTCTGTT
33032 ACCCAACACT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
23 48 0.74
24 4 0.06
25 13 0.20
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTATGTGT
Found at i:36610 original size:9 final size:9
Alignment explanation
Indices: 36582--36644 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
36572 ATTTCTCCCT
*
36582 AAAAAATAG
1 AAAAAAAAG
36591 AAAAAGAAAAG
1 -AAAA-AAAAG
*
36602 AAAAGAAAG
1 AAAAAAAAG
36611 AAAGAAAAATG
1 AAA-AAAAA-G
*
36622 -AAAAAAAT
1 AAAAAAAAG
36630 AAAAAAAAG
1 AAAAAAAAG
36639 AAAAAA
1 AAAAAA
36645 GAAAAAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 25 0.57
10 14 0.32
11 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.05
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:36618 original size:24 final size:23
Alignment explanation
Indices: 36581--36650 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 23
36571 AATTTCTCCC
*
36581 TAAAAAATAGAAAAAGAAAAGAAA
1 TAAAAAAAAGAAAAAGAAAA-AAA
*
36605 -AGAAAGAAAGAAAAATGAAAAAAA
1 TA-AAAAAAAGAAAAA-GAAAAAAA
36629 TAAAAAAAAGAAAAAAGAAAAA
1 TAAAAAAAAG-AAAAAGAAAAA
36651 GAGAGGTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.03
24 27 0.69
25 11 0.28
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (23 bp):
TAAAAAAAAGAAAAAGAAAAAAA
Found at i:36619 original size:32 final size:31
Alignment explanation
Indices: 36583--36650 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
36573 TTTCTCCCTA
* *
36583 AAAAATAGAAAAAGA-AAAGAAAAGAAAGAAAG
1 AAAAAT-GAAAAAAATAAAAAAAAGAAA-AAAG
36615 AAAAATGAAAAAAATAAAAAAAAGAAAAAAG
1 AAAAATGAAAAAAATAAAAAAAAGAAAAAAG
36646 AAAAA
1 AAAAA
36651 GAGAGGTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (31 bp):
AAAAATGAAAAAAATAAAAAAAAGAAAAAAG
Found at i:37151 original size:112 final size:112
Alignment explanation
Indices: 36954--37155 Score: 318
Period size: 112 Copynumber: 1.8 Consensus size: 112
36944 TTGATCAATG
*
36954 TTTAATTTTCTCATTCATGCGAGCTTTGCCTCCAATAAAATCCAATTTTATCCACCTCACAACCT
1 TTTAATTTTCTCATTCATGCGAGCTTTGCCTCAAATAAAATCCAATTTTATCCACCTCACAACCT
*
37019 TGTTCAAGCATTTTTGCATTGAAATAACGGTTAGTGGATTAATGATT
66 TGTTCAAGCATTTTTACATTGAAATAACGGTTAGTGGATTAATGATT
* * * *
37066 TTTAATCTTT-TCATTCATGCGAGCTTTGCCTCAAATCAAATTCAATTTTATCCACTTTACAATC
1 TTTAAT-TTTCTCATTCATGCGAGCTTTGCCTCAAATAAAATCCAATTTTATCCACCTCACAA-C
37130 C-TGTTCAAGCATTTTTACATTGAAAT
64 CTTGTTCAAGCATTTTTACATTGAAAT
37156 GGCAGTTAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
112 77 0.94
113 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (112 bp):
TTTAATTTTCTCATTCATGCGAGCTTTGCCTCAAATAAAATCCAATTTTATCCACCTCACAACCT
TGTTCAAGCATTTTTACATTGAAATAACGGTTAGTGGATTAATGATT
Found at i:37694 original size:50 final size:50
Alignment explanation
Indices: 37594--37727 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 50
37584 GACGAGTCAT
* *
37594 ATACACCTAAAGCTGTAGAGGGGCAAATTTGAAGCCTCAATGGCAAATCTC
1 ATACACCTAAAGCTGTAAAGGGGCATA-TTGAAGCCTCAATGGCAAATCTC
* **
37645 ATACACCTAAAGTTGTAAAGGGGCATATTGAAG-CTACAATGGTGAATCTC
1 ATACACCTAAAGCTGTAAAGGGGCATATTGAAGCCT-CAATGGCAAATCTC
* *
37695 ATTCACCTAAAGCTATAGAA-GGGCATATTGAAG
1 ATACACCTAAAGCTGTA-AAGGGGCATATTGAAG
37728 TCGTAAGGAC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 2 0.03
50 45 0.62
51 26 0.36
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (50 bp):
ATACACCTAAAGCTGTAAAGGGGCATATTGAAGCCTCAATGGCAAATCTC
Found at i:37879 original size:79 final size:79
Alignment explanation
Indices: 37784--38229 Score: 488
Period size: 79 Copynumber: 5.6 Consensus size: 79
37774 TACAACCCCG
* * *
37784 AATCTTTTACCTCGACCATGGGGCAGATTAAAGCAACCCAATCTTTTACCCTAATCAGAGGGAAA
1 AATCTTTTACCTCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAA
37849 ATTGAAGACCATTT
66 ATTGAAGACCATTT
* * *
37863 AATCTTTTACCTCGACCATGGGACAGATTGAAA-CAATCCAATCTTTTACCCTAATCAGACGGCA
1 AATCTTTTACCTCGACCATGGGGCAGATT-AAAGCAATCCAATCTTTTACCCTAACCAGAGGGCA
37927 AATTGAAGACCATTT
65 AATTGAAGACCATTT
* * * * *
37942 AATC-TTTAACTCCGACCTTGTGGCAGATTGAAGCAATCTAATCTTTTACCCTAACCAGAGGGCA
1 AATCTTTTACCT-CGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCA
* * *
38006 GATTGAAGACTATCCT
65 AATTGAAGACCAT-TT
* * * * * *
38022 -ATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTGCCTTAACCAGAGGGCAA
1 AATCTTTTACCTCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAA
**
38086 ATTGAAGACCATCC
66 ATTGAAGACCATTT
* * * * * * *
38100 GATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACTAGAGAGCAG
1 AATCTTTTACCTCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAA
* * *
38165 CTTAAAGACCA-TC
66 ATTGAAGACCATTT
* * * *
38178 AGATCTTCTACCTCGACCATGGGGTAGATTGAAA-CAATCAAATATTTTACCC
1 A-ATCTTTTACCTCGACCATGGGGCAGATT-AAAGCAATCCAATCTTTTACCC
38230 CTAAAGCTAT
Statistics
Matches: 315, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
78 10 0.03
79 295 0.94
80 10 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (79 bp):
AATCTTTTACCTCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAA
ATTGAAGACCATTT
Found at i:38228 original size:237 final size:237
Alignment explanation
Indices: 37798--38229 Score: 584
Period size: 237 Copynumber: 1.8 Consensus size: 237
37788 TTTTACCTCG
* **
37798 ACCATGGGGCAGATTAAAGCAACCCAATCTTTTACCCTAATCAGAGGGAAAATTGAAGACCATTT
1 ACCATGGGGCAGATTAAAGCAACCCAATCTTTTACCCTAACCAGAGGGAAAATTGAAGACCATCC
* *
37863 AATCTTTTACCTCGACCATGGGACAGATTGAAACAATCCAATCTTTTACCCTAATCAGACGGCAA
66 AATCTCTTACCCCGACCATGGGACAGATTGAAACAATCCAATCTTTTACCCTAATCAGACGGCAA
* * * * * * *
37928 ATTGAAGACCATTTAATCTTTAACTCCGACCTTGTGGCAGATTGAAGCAATCTAATCTTTTACCC
131 ATTAAAGACCATTCAATCTTTAACTCCGACCATGGGGCAGATTGAAACAATCAAATATTTTACCC
37993 TAACCAGAGGGCAGATTGAAGACTATCCTATCTCTTACCCCA
196 TAACCAGAGGGCAGATTGAAGACTATCCTATCTCTTACCCCA
* * * * *
38035 ACCATGGGGCAGATTGAAGCAATCCAATCTTTTGCCTTAACCAGAGGGCAAATTGAAGACCATCC
1 ACCATGGGGCAGATTAAAGCAACCCAATCTTTTACCCTAACCAGAGGGAAAATTGAAGACCATCC
* * *
38100 GATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAA-CTAGA-GAGC
66 AATCTCTTACCCCGACCATGGGACAGATTGAAACAATCCAATCTTTTACCCTAATC-AGACG-GC
** * *
38163 AGCTTAAAGACCA-TCAGATCTTCTACCT-CGACCATGGGGTAGATTGAAACAATCAAATATTTT
129 AAATTAAAGACCATTCA-ATCTT-TAACTCCGACCATGGGGCAGATTGAAACAATCAAATATTTT
38226 ACCC
192 ACCC
38230 CTAAAGCTAT
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
236 4 0.02
237 159 0.95
238 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (237 bp):
ACCATGGGGCAGATTAAAGCAACCCAATCTTTTACCCTAACCAGAGGGAAAATTGAAGACCATCC
AATCTCTTACCCCGACCATGGGACAGATTGAAACAATCCAATCTTTTACCCTAATCAGACGGCAA
ATTAAAGACCATTCAATCTTTAACTCCGACCATGGGGCAGATTGAAACAATCAAATATTTTACCC
TAACCAGAGGGCAGATTGAAGACTATCCTATCTCTTACCCCA
Found at i:39943 original size:29 final size:29
Alignment explanation
Indices: 39911--40094 Score: 106
Period size: 30 Copynumber: 6.2 Consensus size: 29
39901 AACGTATTTT
*
39911 AAAATTAT-TTTTGACCCCTATATTTTCCA
1 AAAATTATGTTTTGACCCC-AAATTTTCCA
* *
39940 AAAATTATGTTTTGACCTCAAATTTTCTA
1 AAAATTATGTTTTGACCCCAAATTTTCCA
** * *
39969 AAAATTTAAATTTT-ATCTCAAATTTTCCA
1 AAAA-TTATGTTTTGACCCCAAATTTTCCA
*** * * *
39998 ATAAATTCA-AAATTGATCCCTAAACTCTCCA
1 A-AAATT-ATGTTTTGA-CCCCAAATTTTCCA
* * *
40029 AAAATTTTGTTCTGACCCCTAAAATTTCCA
1 AAAATTATGTTTTGACCCC-AAATTTTCCA
* *
40059 AAAATT-TGAATTTGACCCCAAAATTTTTCA
1 AAAATTATG-TTTTGACCCC-AAATTTTCCA
40089 AAAATT
1 AAAATT
40095 CCAAATTGAC
Statistics
Matches: 119, Mismatches: 27, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
29 44 0.37
30 65 0.55
31 10 0.08
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAATTATGTTTTGACCCCAAATTTTCCA
Found at i:40104 original size:30 final size:30
Alignment explanation
Indices: 40041--40116 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
40031 AATTTTGTTC
* ** *
40041 TGACCCCTAAAA-TTTCCAAAAATTTGAATT
1 TGACCCC-AAAATTTTTCAAAAATTCCAAAT
40071 TGACCCCAAAATTTTTCAAAAATTCCAAAT
1 TGACCCCAAAATTTTTCAAAAATTCCAAAT
**
40101 TGACCCTTAAATTTTT
1 TGACCCCAAAATTTTT
40117 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (30 bp):
TGACCCCAAAATTTTTCAAAAATTCCAAAT
Found at i:49303 original size:25 final size:25
Alignment explanation
Indices: 49249--49304 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
49239 AATATATATT
* *
49249 ATTA-TTATTAGTTGAAGAAATTTA
1 ATTATTTATTAGTTAAAGAAAGTTA
49273 ATTATTTATTAGTTAAAGAAAGGTTA
1 ATTATTTATTAGTTAAAGAAA-GTTA
49299 A-TATTT
1 ATTATTT
49305 TGCATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (25 bp):
ATTATTTATTAGTTAAAGAAAGTTA
Found at i:51029 original size:15 final size:15
Alignment explanation
Indices: 51009--51039 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50999 AGAGTCCAAC
51009 CACCATCACCACCAT
1 CACCATCACCACCAT
*
51024 CACCATCACCATCAT
1 CACCATCACCACCAT
51039 C
1 C
51040 TTCCTCTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (15 bp):
CACCATCACCACCAT
Found at i:51934 original size:2 final size:2
Alignment explanation
Indices: 51929--51956 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51919 ATTTTATTAA
51929 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
51957 TAAAAATGAT
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:52485 original size:53 final size:53
Alignment explanation
Indices: 52424--52525 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
52414 ATTTAATGTT
* *
52424 AAGCATGATGATAAATTTGAAGCAAAATAGAATTTTGGTTTAGCTTATTTCCA
1 AAGCATGATGATAAATTTGAACCAAAATAGAAATTTGGTTTAGCTTATTTCCA
52477 AAGCATGATGATAAATTTGAACCAAAATAGAAATTTGGTTTAGCTTATT
1 AAGCATGATGATAAATTTGAACCAAAATAGAAATTTGGTTTAGCTTATT
52526 GTTTTTATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (53 bp):
AAGCATGATGATAAATTTGAACCAAAATAGAAATTTGGTTTAGCTTATTTCCA
Found at i:56017 original size:58 final size:58
Alignment explanation
Indices: 55955--56069 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
55945 ACCCACCAAC
*
55955 AAACTAAACCCAAATACTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAA
1 AAACTAAACCCAAATACTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAA
* * * *
56013 AAACTAAACCTAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCA
1 AAACTAAACCCAAATACTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCA
56070 TGAACAACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (58 bp):
AAACTAAACCCAAATACTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAA
Found at i:69033 original size:17 final size:17
Alignment explanation
Indices: 69011--69044 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
69001 TAAATGATTA
*
69011 TTGGACTTAGAGAATAT
1 TTGGACCTAGAGAATAT
69028 TTGGACCTAGAGAATAT
1 TTGGACCTAGAGAATAT
69045 AAATACAAGT
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:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (17 bp):
TTGGACCTAGAGAATAT
Found at i:88095 original size:18 final size:18
Alignment explanation
Indices: 88072--88111 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
88062 AACTTGCTAT
*
88072 TGCAGCAAGCATACGAGC
1 TGCAGCAAGCATACAAGC
*
88090 TGCAGCATGCATACAAGC
1 TGCAGCAAGCATACAAGC
88108 TGCA
1 TGCA
88112 AGCTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.15
Consensus pattern (18 bp):
TGCAGCAAGCATACAAGC
Found at i:96827 original size:21 final size:21
Alignment explanation
Indices: 96803--96857 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
96793 GAAATTTAAA
96803 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
96824 ACAAA-ATATTATGAGGAGAGTT
1 ACAAACATA--ATGAGGAGAGTT
96846 ACAAACATAATG
1 ACAAACATAATG
96858 TTTTGTAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.10
21 8 0.26
22 17 0.55
23 3 0.10
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:101780 original size:81 final size:81
Alignment explanation
Indices: 101645--101808 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
101635 TAAAGGCTTA
* * *
101645 CAGATGAACAAAAGTATGGGACAATGAGGAAGAAGAACATTTGTAACACCCAGGTTTTTAAGTTT
1 CAGATGAACAAAAATATGGAACAATGAGGAAGAAAAACATTTGTAACACCCAGGTTTTTAAGTTT
101710 GATTTTTAAAAATTTT
66 GATTTTTAAAAATTTT
* * *
101726 CAGATGAACAAAAATATGGAACAATGAGGAAGAAAAAGATTTGTAATACTCAGGTTTTTAAGTTT
1 CAGATGAACAAAAATATGGAACAATGAGGAAGAAAAACATTTGTAACACCCAGGTTTTTAAGTTT
* *
101791 GGTTTTTAACAATTTT
66 GATTTTTAAAAATTTT
101807 CA
1 CA
101809 TATTTCAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (81 bp):
CAGATGAACAAAAATATGGAACAATGAGGAAGAAAAACATTTGTAACACCCAGGTTTTTAAGTTT
GATTTTTAAAAATTTT
Found at i:101985 original size:158 final size:158
Alignment explanation
Indices: 101726--102618 Score: 1336
Period size: 158 Copynumber: 5.7 Consensus size: 158
101716 TAAAAATTTT
* * *
101726 CAGATGAACAAAAATATGGAACAATGAGGAAGAAAAAGATTTGTAATA-CTCAGGTTTTTAAGTT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCT-AGGTTTTTAAGTT
* * * * * *
101790 TGGTTTTTAACAATTTTCATATTTCAAAAACCCAATTTTTATTTTTTAAAATTTGAGTTTTTGAA
65 TGATTTTTAAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGAA
*
101855 ATTTGAAAATTAGTGTTTCTAAAAGCTTA
130 ATTTGAAAATTAGTGTTTCTAAAGGCTTA
*
101884 CAGATGAACAAAAGTATGGAACAATAAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
* * *
101949 GA-TTTTAAAAAATTTCAGCTTTCAAAAACTCAAATTTTATTTTTAAAAATTTGGGTTTTTGAAA
66 GATTTTTAAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGAAA
102013 TTTGAAAATTAGTGTTTCTAAAGGCTTA
131 TTTGAAAATTAGTGTTTCTAAAGGCTTA
* * * * *
102041 CGGATGAACAAGAGTATGGAATAATGAGGAAGAAGAAGATTTGTAACACTTGGGTTTTTAAGTTT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
*
102106 GATTTTTAAAAATTTTCAGATTTCAAAAACTCAAA---T-TTTTATAAAATTTGGGTTTTTGAAA
66 GATTTTTAAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGAAA
*
102167 TTTGAAAATTAGTGTATCTAAAGGCTTA
131 TTTGAAAATTAGTGTTTCTAAAGGCTTA
* * * *
102195 CAGATGAACAAAAGTATGGAACAATGAGAAAGAATAATATTTGTAACACCCAGGTTTTTAAGTTT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
* *
102260 GATTTTTAAAAATTTTCAGATTTCAAAAACCCAAATTTTATTTTTAAAAATTTGGGTTTTTGAAA
66 GATTTTTAAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGAAA
* *
102325 TTTGAAAATTAATGTTTCTAAAAGCTTA
131 TTTGAAAATTAGTGTTTCTAAAGGCTTA
* * *
102353 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAATA-CTAAGGTTTTGAAATT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCT-AGGTTTTTAAGTT
102417 TGATTTTTAAAAAATTTT-AGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGA
65 TGATTTTT-AAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGA
*
102481 AATTTGAAAATTAGTGTTTTTAAAGGCTTA
129 AATTTGAAAATTAGTGTTTCTAAAGGCTTA
* * * * *
102511 CAGATGAACAAAAATATGAAACAATGAGGAAAAAGAATATTTGTAACACCCAGGTTTTTAAGTTT
1 CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
*
102576 GATTTTTAAAAATTTTCAAATTTCAAAAA-TCTAAATTTTATTT
66 GATTTTTAAAAATTTTCAGATTTCAAAAACTC-AAATTTTATTT
102619 GGTGGATTAA
Statistics
Matches: 663, Mismatches: 61, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
154 140 0.21
155 1 0.00
157 155 0.23
158 355 0.54
159 12 0.02
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (158 bp):
CAGATGAACAAAAGTATGGAACAATGAGGAAGAAGAAGATTTGTAACACCTAGGTTTTTAAGTTT
GATTTTTAAAAATTTTCAGATTTCAAAAACTCAAATTTTATTTTTTAAAATTTGGGTTTTTGAAA
TTTGAAAATTAGTGTTTCTAAAGGCTTA
Found at i:105032 original size:21 final size:21
Alignment explanation
Indices: 105006--105055 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
104996 GAGACAATAT
105006 TACCGATACAAGT-ATGACTTC
1 TACCGATACAAGTCATG-CTTC
* *
105027 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
105048 TA-CGATAC
1 TACCGATAC
105056 TAAAAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 17 0.68
22 3 0.12
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:106761 original size:10 final size:10
Alignment explanation
Indices: 106746--106774 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
106736 CTTTAACATG
106746 AAAATTACTA
1 AAAATTACTA
106756 AAAATTACTA
1 AAAATTACTA
106766 AAAATTACT
1 AAAATTACT
106775 TTACAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTACTA
Found at i:108513 original size:30 final size:31
Alignment explanation
Indices: 108472--108608 Score: 90
Period size: 30 Copynumber: 4.5 Consensus size: 31
108462 TTTTGGGATC
*
108472 AATTTAATATTTAATCTTGATA-TTTTTTTT
1 AATTTAGTATTTAATCTTGATACTTTTTTTT
* * *
108502 AATTTAGTATTTGAA-CTTGATAGTTATTCTT
1 AATTTAGTATTT-AATCTTGATACTTTTTTTT
* *
108533 AATTT-GATATTTAATATT--T-TTTTTTGTTT
1 AATTTAG-TATTTAATCTTGATACTTTTT-TTT
* * *
108562 CATTTTAATATTTGAAT-TTAATACTTTTTTTT
1 -AATTTAGTATTT-AATCTTGATACTTTTTTTT
*
108594 AATTTAGTATCTAAT
1 AATTTAGTATTTAAT
108609 ATTTTGTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
28 4 0.05
29 3 0.04
30 35 0.42
31 32 0.39
32 4 0.05
33 5 0.06
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (31 bp):
AATTTAGTATTTAATCTTGATACTTTTTTTT
Found at i:108574 original size:61 final size:61
Alignment explanation
Indices: 108504--108619 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
108494 TTTTTTTTAA
* * * * *
108504 TTTAGTATTTGAACTTGATAGTTATTCTTAATTT-GATATTTAATATTTTTTTTTGTTTCAT
1 TTTAATATTTGAACTTAATACTTATTCTTAATTTAG-TATCTAATATTTTGTTTTGTTTCAT
* * *
108565 TTTAATATTTGAATTTAATACTTTTTTTTAATTTAGTATCTAATATTTTGTTTTG
1 TTTAATATTTGAACTTAATACTTATTCTTAATTTAGTATCTAATATTTTGTTTTG
108620 GTCTGAATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 45 0.98
62 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (61 bp):
TTTAATATTTGAACTTAATACTTATTCTTAATTTAGTATCTAATATTTTGTTTTGTTTCAT
Found at i:108609 original size:38 final size:37
Alignment explanation
Indices: 108534--108612 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
108524 GTTATTCTTA
** *
108534 ATTTGATATTTAATATTTTTTTTTGTTTCATTTTAAT
1 ATTTGATATTTAATATTTTTTTTAATTTCATTCTAAT
108571 ATTTGA-ATTTAATACTTTTTTTTAATTT-AGTATCTAAT
1 ATTTGATATTTAATA-TTTTTTTTAATTTCA-T-TCTAAT
108609 ATTT
1 ATTT
108613 TGTTTTGGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 9 0.25
37 18 0.50
38 9 0.25
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (37 bp):
ATTTGATATTTAATATTTTTTTTAATTTCATTCTAAT
Found at i:118767 original size:60 final size:57
Alignment explanation
Indices: 118694--118824 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 57
118684 CAAAAAAGAC
* * *
118694 AAAATTGACTAATACTTGAGTGACTATTTTGTAACTATTCATAGTTGGGTGACCGAAAA
1 AAAATTGATTAATAATTGAGTGACCATTTTGTAACTATTCATAGTTGGGTGACC--AAA
**
118753 AGAAATTGATTAATAATTGAGTGACCATTTTGTAACTATTTGTAGTTGGGTGACCAAA
1 A-AAATTGATTAATAATTGAGTGACCATTTTGTAACTATTCATAGTTGGGTGACCAAA
*
118811 AAAATTAATTAATA
1 AAAATTGATTAATA
118825 GTTAAGAGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 12 0.18
58 4 0.06
59 1 0.02
60 48 0.74
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (57 bp):
AAAATTGATTAATAATTGAGTGACCATTTTGTAACTATTCATAGTTGGGTGACCAAA
Found at i:120499 original size:5 final size:5
Alignment explanation
Indices: 120483--120515 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
120473 AGAGGAGGGC
120483 TTCTT CTTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT -TTCTT TTCTT TTCTT TTCTT TTCTT TT
120516 TTTCTGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:120509 original size:15 final size:16
Alignment explanation
Indices: 120483--120520 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
120473 AGAGGAGGGC
120483 TTCTTCTTCTTTTCTT
1 TTCTTCTTCTTTTCTT
120499 TTCTT-TTCTTTTCTT
1 TTCTTCTTCTTTTCTT
*
120514 TTTTTCT
1 TTCTTCT
120521 GGGTCAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTCTTCTTTTCTT
Found at i:123732 original size:51 final size:51
Alignment explanation
Indices: 123685--124111 Score: 233
Period size: 50 Copynumber: 8.5 Consensus size: 51
123675 TGAAGACATG
* *
123685 AAGGGAAAGGTCTAAGTCGCAACAGCAGGACCGTGTACCTCAAAAGACACA
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGTGTACCTCAAAAGACACA
* * * * * * *
123736 AAGGAAAAAATTTAAG-CTGCAACGAC-GGATCC-AGTACCAC-AAAGATACAA
1 AAGGGAAAGATCTAAGTC-GCAACGGCAGGA-CCGTGTACCTCAAAAGACAC-A
* * * *
123786 AAGGGAAAGGTCTAAGTCGCAACGGCAGGATCGTGTACCTCAGAAGACACG
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGTGTACCTCAAAAGACACA
* * * * * *
123837 AAGGGAAAGATTTAAGTCGTAACGGC-GAATCC-AGTACCAC-AAAGATACAA
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGA-CCGTGTACCTCAAAAGACAC-A
* * *
123887 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGA
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGTGTACCTCAAAAGACAC-A
* * * * * * **
123939 AA-GGAAAGATTTAAGCCGCAACGAC-GAATC-TAGTA-C-CATGAAGACATG
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGT-GTACCTCA-AAAGACACA
* * * * *
123987 AAGGGAAAGATCTAAGACCACAACGGCA-GATCC-AGTACCAC-AAAGATACAA
1 AAGGGAAAGATCTAAG-TCGCAACGGCAGGA-CCGTGTACCTCAAAAGACAC-A
* * * * *
124038 AAGGGAAAGGTTTAAGTCGCAACGG-TGGACCATGTACCTCAGAAGACA-A
1 AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGTGTACCTCAAAAGACACA
* *
124087 GAAAGGAAAGATTTAAG-CAGCAACG
1 -AAGGGAAAGATCTAAGTC-GCAACG
124112 ACAAATCTAG
Statistics
Matches: 280, Mismatches: 70, Indels: 53
0.69 0.17 0.13
Matches are distributed among these distances:
48 4 0.01
49 38 0.14
50 121 0.43
51 101 0.36
52 16 0.06
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (51 bp):
AAGGGAAAGATCTAAGTCGCAACGGCAGGACCGTGTACCTCAAAAGACACA
Found at i:123869 original size:101 final size:101
Alignment explanation
Indices: 123685--124061 Score: 453
Period size: 101 Copynumber: 3.7 Consensus size: 101
123675 TGAAGACATG
* * * *
123685 AAGGGAAAGGTCTAAGTCGCAACAGCAGGACCGTGTACCTCAAAAGACACAAAGGAAAAAATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACACAAAGGGAAAGATTTA
*
123750 AG-CTGCAACGACGGATCCAGTACCACAAAGATACAA
66 AGTC-GCAACGACGAATCCAGTACCACAAAGATACAA
* *
123786 AAGGGAAAGGTCTAAGTCGCAACGGCAGGATCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACACAAAGGGAAAGATTTA
* *
123851 AGTCGTAACGGCGAATCCAGTACCACAAAGATACAA
66 AGTCGCAACGACGAATCCAGTACCACAAAGATACAA
*
123887 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAA-GGAAAGATTT
1 AAGGGAAAGGTCTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACAC-AAAGGGAAAGATTT
* * ** *
123951 AAGCCGCAACGACGAATCTAGTACCATGAAG--ACATG
65 AAGTCGCAACGACGAATCCAGTACCACAAAGATACA-A
* * * * * * *
123987 AAGGGAAAGATCTAAGACCACAACGGCA-GATCC-AGTACCACA-AAGATACAAAAGGGAAAGGT
1 AAGGGAAAGGTCTAAG-TCGCAACGGCAGGA-CCGTGTACCTCAGAAGACAC-AAAGGGAAAGAT
124049 TTAAGTCGCAACG
63 TTAAGTCGCAACG
124062 GTGGACCATG
Statistics
Matches: 242, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
99 12 0.05
100 43 0.18
101 184 0.76
102 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.14
Consensus pattern (101 bp):
AAGGGAAAGGTCTAAGTCGCAACGGCAGGACCGTGTACCTCAGAAGACACAAAGGGAAAGATTTA
AGTCGCAACGACGAATCCAGTACCACAAAGATACAA
Found at i:124024 original size:50 final size:49
Alignment explanation
Indices: 123929--124132 Score: 119
Period size: 50 Copynumber: 4.1 Consensus size: 49
123919 GTGTACCTCA
* * *
123929 GAAGACACGAAAGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAT
1 GAAGACACGAAAGGAAAGATCTAAGCCACAACGACGAATCCAGTACCAT
* * * *
123978 GAAGACATGAAGGGAAAGATCTAAGACCACAACGGC-AGATCCAGTACCAC
1 GAAGACACGAAAGGAAAGATCTAAG-CCACAACGACGA-ATCCAGTACCAT
* * * * * * * ** *
124028 AAAGATACAAAAGGGAAAGGTTTAAGTCGCAACGGTGGA-CCATGTACC-T
1 GAAGACACGAAA-GGAAAGATCTAAGCCACAACGACGAATCCA-GTACCAT
* * * * *
124077 CAGAAGACAAGAAAGGAAAGATTTAAG-CAGCAACGACAAATCTAGTACCAC
1 --GAAGACACGAAAGGAAAGATCTAAGCCA-CAACGACGAATCCAGTACCAT
124128 GAAGA
1 GAAGA
124133 TTTGAAGGGG
Statistics
Matches: 114, Mismatches: 31, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
49 32 0.28
50 61 0.54
51 21 0.18
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (49 bp):
GAAGACACGAAAGGAAAGATCTAAGCCACAACGACGAATCCAGTACCAT
Found at i:124110 original size:150 final size:150
Alignment explanation
Indices: 123828--124141 Score: 461
Period size: 150 Copynumber: 2.1 Consensus size: 150
123818 GTGTACCTCA
* * * **
123828 GAAGACACGAAGGGAAAGATTTAAGTCGTAACGGCGAATCCAGTACCACAAAGATACAAAAGGGA
1 GAAGACATGAAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTACCACAAAGATACAAAAGGGA
* * *
123893 AAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAAGGAAAGATTTAAGCCGC
66 AAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACAAGAAAGGAAAGATTTAAGCAGC
* *
123958 AACGACGAATCTAGTACCAT
131 AACGACAAATCTAGTACCAC
123978 GAAGACATGAAGGGAAAGATCTAAGACCACAACGGC-AGATCCAGTACCACAAAGATACAAAAGG
1 GAAGACATGAAGGGAAAGATCTAAG-CCACAACGGCGA-ATCCAGTACCACAAAGATACAAAAGG
* **
124042 GAAAGGTTTAAGTCGCAACGG-TGGACCATGTACCTCAGAAGACAAGAAAGGAAAGATTTAAGCA
64 GAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACAAGAAAGGAAAGATTTAAGCA
124106 GCAACGACAAATCTAGTACCAC
129 GCAACGACAAATCTAGTACCAC
**
124128 GAAGATTTGAAGGG
1 GAAGACATGAAGGG
124142 GAAATGTTTA
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
150 94 0.64
151 53 0.36
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (150 bp):
GAAGACATGAAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTACCACAAAGATACAAAAGGGA
AAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACAAGAAAGGAAAGATTTAAGCAGC
AACGACAAATCTAGTACCAC
Found at i:131053 original size:2 final size:2
Alignment explanation
Indices: 131046--131073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
131036 TAGAATGCTT
131046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
131074 AAGTTTATAA
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):
TA
Done.