Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002433.1 Hibiscus syriacus cultivar Beakdansim tig00004976_pilon, 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: 96677
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2062 original size:11 final size:11
Alignment explanation
Indices: 2048--2078 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2038 ATTATGTTAA
*
2048 ATTTTATTTTT
1 ATTTTATTATT
2059 ATTTTATTATT
1 ATTTTATTATT
2070 ATTTTATTA
1 ATTTTATTA
2079 AAAATTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:17855 original size:17 final size:17
Alignment explanation
Indices: 17830--17870 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
17820 AACTACAATA
* *
17830 TGCTTGAAAGGGCTCCT
1 TGCTCGAAAGGGATCCT
17847 TGCTCGAAAGGGATCCT
1 TGCTCGAAAGGGATCCT
17864 TG-TCGAA
1 TGCTCGAA
17871 GGTCGGCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (17 bp):
TGCTCGAAAGGGATCCT
Found at i:18917 original size:16 final size:16
Alignment explanation
Indices: 18896--18936 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
18886 CAATGGACTC
18896 GACTCGAATCGAGCTT
1 GACTCGAATCGAGCTT
18912 GACTCGAATCGAGCTT
1 GACTCGAATCGAGCTT
18928 GACTCGAAT
1 GACTCGAAT
18937 TCTTAACGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (16 bp):
GACTCGAATCGAGCTT
Found at i:19720 original size:28 final size:29
Alignment explanation
Indices: 19669--19725 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
19659 GAAAAAATAT
19669 TTTTTAAAAAATATAAAAATTATTTGTTTA
1 TTTTTAAAAAATATAAAAATTATTT-TTTA
*
19699 TTTTT-AAAATTATAAAAA-TATTTTTTA
1 TTTTTAAAAAATATAAAAATTATTTTTTA
19726 ATTATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 12 0.46
30 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTTAAAAAATATAAAAATTATTTTTTA
Found at i:29884 original size:25 final size:25
Alignment explanation
Indices: 29856--29904 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29846 ATAATCATAT
29856 TTAATATAAAAATAAGAATTTATAA
1 TTAATATAAAAATAAGAATTTATAA
* * * *
29881 TTAATTTAAACATTATAATTTATA
1 TTAATATAAAAATAAGAATTTATA
29905 TAAATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAATATAAAAATAAGAATTTATAA
Found at i:35142 original size:11 final size:11
Alignment explanation
Indices: 35126--35151 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35116 ATATTAACTC
35126 TTTAATATGTA
1 TTTAATATGTA
35137 TTTAATATGTA
1 TTTAATATGTA
35148 TTTA
1 TTTA
35152 TGCGAATCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTTAATATGTA
Found at i:49191 original size:17 final size:17
Alignment explanation
Indices: 49169--49208 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
49159 GAGGTACTCT
49169 GGTGCAATATGCCCAAC
1 GGTGCAATATGCCCAAC
49186 GGTGCAATATGCCCAAC
1 GGTGCAATATGCCCAAC
*
49203 AGTGCA
1 GGTGCA
49209 GTGGTCACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (17 bp):
GGTGCAATATGCCCAAC
Found at i:54712 original size:102 final size:102
Alignment explanation
Indices: 54536--54739 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
54526 ATTTCCCCAG
*
54536 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGACTGGTA
1 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
54601 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
66 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
*
54638 GAGCTGCACGATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
1 GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
54703 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
66 CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
54740 TTTACTGCTC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (102 bp):
GAGCTGCACAATAAATTACAACCAAAATTGAGCTTTCAAATTGAAGTTCTCATTGTTGAATGGTA
CCTCCAAAAAATTACCTCATAATTATCTTCCTACTTA
Found at i:67629 original size:29 final size:29
Alignment explanation
Indices: 67568--67629 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
67558 GGGGGTAGGT
**
67568 CGCCATGCACGCCCAGCGACCTACCAGGT
1 CGCCATGCACGCCCAGCGACCTACCAGCA
67597 CGCCATGCACGCCCAGCGACCT-CCATGCA
1 CGCCATGCACGCCCAGCGACCTACCA-GCA
67626 CGCC
1 CGCC
67630 CAGCTCGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (29 bp):
CGCCATGCACGCCCAGCGACCTACCAGCA
Found at i:67983 original size:29 final size:29
Alignment explanation
Indices: 67936--68019 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
67926 TGCAACGTGG
*
67936 GTAGGTCGCCAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAAGGAATCCCAGCGACATT
*
67965 GTAGGTCGCCAAGGCATCCCAGCGACATT
1 GTAGGTCGCCAAGGAATCCCAGCGACATT
* *
67994 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCCAAGGAATCCCAGCGAC
68020 CTATGCCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (29 bp):
GTAGGTCGCCAAGGAATCCCAGCGACATT
Found at i:68351 original size:8 final size:9
Alignment explanation
Indices: 68321--68358 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
68311 GGTAATTTTT
68321 TTTTAATTA
1 TTTTAATTA
68330 TTTTAATTA
1 TTTTAATTA
*
68339 GTTT-ATTA
1 TTTTAATTA
68347 TTTTAAATTA
1 TTTT-AATTA
68357 TT
1 TT
68359 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:68480 original size:28 final size:27
Alignment explanation
Indices: 68441--68493 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
68431 ATATTAAAAA
68441 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
68469 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
68494 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:68499 original size:27 final size:29
Alignment explanation
Indices: 68440--68504 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
68430 TATATTAAAA
68440 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
68469 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
68495 AAATAGTTAA
1 AAATAATTAA
68505 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:68642 original size:18 final size:18
Alignment explanation
Indices: 68619--68673 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
68609 AATAATTATT
68619 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
68637 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
68649 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
68666 TAAATTAG
1 TAAATTAG
68674 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:68726 original size:21 final size:21
Alignment explanation
Indices: 68701--68740 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
68691 GTTAATTAGT
68701 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
68722 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
68741 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:68988 original size:30 final size:30
Alignment explanation
Indices: 68920--69023 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
68910 ATTAGTTAAT
* *
68920 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAATTAT-ATTAAAGAA
*
68951 TCA-TTTATTAGTTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATATTAAAGAA
*
68981 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-ATTATATTAAAGAA
69011 TAGTTTATTAGTT
1 TAGTTTATTAGTT
69024 GTTTAAGGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.17
30 42 0.66
31 10 0.16
32 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATATTAAAGAA
Found at i:71354 original size:14 final size:14
Alignment explanation
Indices: 71335--71382 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
71325 TTCAAGTCGT
71335 AAATCATTACTATC
1 AAATCATTACTATC
71349 AAATCATTAC--T-
1 AAATCATTACTATC
*
71360 AAATCATTAATATC
1 AAATCATTACTATC
71374 AAATCATTA
1 AAATCATTA
71383 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:71407 original size:49 final size:49
Alignment explanation
Indices: 71354--71696 Score: 292
Period size: 60 Copynumber: 6.3 Consensus size: 49
71344 CTATCAAATC
* *
71354 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAATTCATT
*
71403 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATT-C--ATT
*
71462 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAATTCATT
* *
71512 ATTACTAATCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATT-C--ATT
* *
71571 ATTACTAATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAATTCATT
* *
71620 ATTACTAATCATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATT
1 ATTACTAATCA-T--T--A-C-----TATCAAATCATTAAAAATTAATAATAAATTCATT
71680 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
71697 AATCATTAAT
Statistics
Matches: 247, Mismatches: 14, Indels: 66
0.76 0.04 0.20
Matches are distributed among these distances:
48 32 0.13
49 55 0.22
50 10 0.04
51 1 0.00
52 4 0.02
53 3 0.01
54 4 0.02
55 6 0.02
56 2 0.01
57 2 0.01
58 1 0.00
59 50 0.20
60 77 0.31
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:71464 original size:35 final size:35
Alignment explanation
Indices: 71423--71525 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
71413 ATTACTATCA
71423 AATCATTAAAAATTAATAATAATTTTATTATTACT
1 AATCATTAAAAATTAATAATAATTTTATTATTACT
* * * *
71458 AATCATT----ACT-A-AATCA--TTACTA-T-CA
1 AATCATTAAAAATTAATAATAATTTTATTATTACT
*
71483 AATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTAAAAATTAATAATAATTTTATTATTACT
71518 AATCATTA
1 AATCATTA
71526 CTATCAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 20
0.63 0.12 0.26
Matches are distributed among these distances:
25 8 0.16
26 1 0.02
27 5 0.10
29 6 0.12
30 2 0.04
31 6 0.12
33 4 0.08
34 1 0.02
35 16 0.33
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.42
Consensus pattern (35 bp):
AATCATTAAAAATTAATAATAATTTTATTATTACT
Found at i:71478 original size:60 final size:59
Alignment explanation
Indices: 71403--71866 Score: 646
Period size: 60 Copynumber: 8.1 Consensus size: 59
71393 ATAAATTATT
*
71403 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
71462 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
71522 ATTACT-ATCA--A--AT----T-ATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
71571 ATTACTAATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
71630 ATTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
71690 ATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
71750 ---A-T--T-A-T--TATCAAATCATTAAAAAATAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
71799 ATTACT-ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
71859 ATTACTAA
1 ATTACTAA
71867 ATCTTATAAA
Statistics
Matches: 366, Mismatches: 15, Indels: 46
0.86 0.04 0.11
Matches are distributed among these distances:
49 82 0.22
50 5 0.01
51 1 0.00
52 3 0.01
53 2 0.01
54 5 0.01
56 2 0.01
57 2 0.01
58 6 0.02
59 46 0.13
60 211 0.58
61 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (59 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:71554 original size:109 final size:109
Alignment explanation
Indices: 71350--71865 Score: 770
Period size: 109 Copynumber: 4.7 Consensus size: 109
71340 ATTACTATCA
* *
71350 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
71414 TTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
66 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
71458 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
71523 TTACTATCAAATTATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
71567 AATCATTACT-AATCATTACTATCAAATCATTAAAAAATAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
*
71631 TTACTAAATCATTATTATCAAATCATTAAAAATTAATAATGATTTCATTATTACT
66 -T--T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
71686 AATCATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
71751 TTATTATCAAATCATTAAAAAATAATAATAATTTCATTATTACT
66 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
71795 AATCATTACT--ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAAT
1 AATCATTACTAAATC--ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
71858 CATTACTA
64 CATTACTA
71866 AATCTTATAA
Statistics
Matches: 374, Mismatches: 19, Indels: 29
0.89 0.05 0.07
Matches are distributed among these distances:
107 3 0.01
108 100 0.27
109 167 0.45
111 1 0.00
113 1 0.00
114 1 0.00
115 1 0.00
117 1 0.00
119 49 0.13
120 50 0.13
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (109 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:71574 original size:10 final size:10
Alignment explanation
Indices: 71561--71587 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
71551 TAATTTCATT
71561 ATTACTAATC
1 ATTACTAATC
71571 ATTACTAATC
1 ATTACTAATC
71581 ATTACTA
1 ATTACTA
71588 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:71663 original size:24 final size:24
Alignment explanation
Indices: 71615--71663 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
71605 AATAATAATT
* *
71615 TCATTATTACTAATCATTACTAAA
1 TCATTATTACAAATCATTACAAAA
71639 TCATTATTATCAAATCATTA-AAAA
1 TCATTATTA-CAAATCATTACAAAA
71663 T
1 T
71664 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCATTATTACAAATCATTACAAAA
Found at i:71760 original size:49 final size:49
Alignment explanation
Indices: 71690--71813 Score: 194
Period size: 49 Copynumber: 2.5 Consensus size: 49
71680 ATTACTAATC
* *
71690 ATTACTAAATCATTAATATCAAATTATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTAATATCAAATTATTAAAAAATAATAATAATTTCATT
* *
71740 ATTACTAATCATTATTATCAAATCATTAAAAAATAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATTATTAAAAAATAATAATAATTTCATT
*
71789 ATTACTAATCATTACTATCAAATTA
1 ATTACTAATCATTAATATCAAATTA
71814 CTATCAAATC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 62 0.91
50 6 0.09
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATTATTAAAAAATAATAATAATTTCATT
Found at i:74970 original size:28 final size:28
Alignment explanation
Indices: 74939--74992 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
74929 ATAATCTAAT
*
74939 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
74967 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
74993 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:74999 original size:28 final size:28
Alignment explanation
Indices: 74935--74999 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
74925 TTATATAATC
*
74935 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
74963 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
74991 TAATTTATA
1 TAATATATA
75000 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:75002 original size:21 final size:21
Alignment explanation
Indices: 74969--75017 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
74959 TTAATATAAT
74969 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
74990 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
75011 ATTAACT
1 A-TAACT
75018 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:75742 original size:29 final size:29
Alignment explanation
Indices: 75643--75777 Score: 117
Period size: 29 Copynumber: 4.5 Consensus size: 29
75633 GGACGCCAGC
* *
75643 GTGCATGGCGACCTATAAGGTCGCTGGGC
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
* * * *
75672 GTACATGACGACCTACCATCTTGGTCGCCGGGA
1 GTGCATGGCGACCTA-CA---AGGTCGCTGGGA
* *
75705 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*** *
75734 GTGCATGGCGACCTTGTAGGTCGCTTGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*
75763 GTGCTTGGCGACCTA
1 GTGCATGGCGACCTA
75778 TGTTTGGATG
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 59 0.72
30 1 0.01
32 2 0.02
33 20 0.24
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.24
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCTGGGA
Done.