Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003119.1 Hibiscus syriacus cultivar Beakdansim tig00006533_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: 58093
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2761 original size:19 final size:19
Alignment explanation
Indices: 2737--2810 Score: 55
Period size: 19 Copynumber: 4.0 Consensus size: 19
2727 AATTAATTAC
2737 ATTAATTTTATAAAAATAT
1 ATTAATTTTATAAAAATAT
* * *
2756 ATTAATTATACATAAAT-T
1 ATTAATTTTATAAAAATAT
* ** *
2774 A-T-ATATCTATTTATATAT
1 ATTAAT-TTTATAAAAATAT
2792 ATTAATTTTATAAAAATAT
1 ATTAATTTTATAAAAATAT
2811 TTATAATTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
16 2 0.05
17 8 0.20
18 4 0.10
19 24 0.60
20 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATTTTATAAAAATAT
Found at i:7463 original size:13 final size:13
Alignment explanation
Indices: 7447--7471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7437 TAATTATAAA
7447 ATAAAATTTTTAT
1 ATAAAATTTTTAT
7460 ATAAAATTTTTA
1 ATAAAATTTTTA
7472 ATTAATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAAATTTTTAT
Found at i:7627 original size:186 final size:186
Alignment explanation
Indices: 7388--7766 Score: 661
Period size: 186 Copynumber: 2.0 Consensus size: 186
7378 ATAAAAATTA
*
7388 AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTTTAATAATATATAATTATAAAATAAAA
1 AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAA
*
7453 TTTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
66 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
* *
7518 ATTAATTAAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATACATAATATATTT
131 ATTAATTAAGTTTTAAATGGTTTAGGCTGAACCCATATGTTATACATAATATATTT
**
7574 AATATTTTTTAATTCAAAAAAATTGTTTAC-AATTAATTTAAATAATATATAATTATAAAATAAA
1 AATATTTTTTAATTCAAAAAAACAGTTT-CTAATTAATTTAAATAATATATAATTATAAAATAAA
7638 AATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
65 AATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
* *
7703 TATTAATTGAGTTTTAAATGGTTTAGGCTGAACCCATATGTTATATATAATATATTT
130 TATTAATTAAGTTTTAAATGGTTTAGGCTGAACCCATATGTTATACATAATATATTT
*
7760 AAAATTT
1 AATATTT
7767 AAAATTTAAT
Statistics
Matches: 183, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
186 182 0.99
187 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (186 bp):
AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAA
ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
ATTAATTAAGTTTTAAATGGTTTAGGCTGAACCCATATGTTATACATAATATATTT
Found at i:9693 original size:14 final size:14
Alignment explanation
Indices: 9674--9700 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9664 CTGAACCCGA
9674 CCGATCCCGAGAAC
1 CCGATCCCGAGAAC
9688 CCGATCCCGAGAA
1 CCGATCCCGAGAA
9701 AAAATTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.41, G:0.22, T:0.07
Consensus pattern (14 bp):
CCGATCCCGAGAAC
Found at i:10086 original size:9 final size:9
Alignment explanation
Indices: 10074--10157 Score: 69
Period size: 9 Copynumber: 8.6 Consensus size: 9
10064 TATATAATTA
10074 ATATAAAAT
1 ATATAAAAT
10083 ATATAAAAT
1 ATATAAAAT
*
10092 ATATATAATT
1 ATATA-AAAT
*
10102 GATATAAAAA
1 -ATATAAAAT
10112 ATATAAAATT
1 ATATAAAA-T
10122 ATATATATAATT
1 ATATA-A-AA-T
*
10134 AATATAAAAA
1 -ATATAAAAT
*
10144 ATGTAAAAT
1 ATATAAAAT
10153 ATATA
1 ATATA
10158 TAATCAGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
9 33 0.54
10 10 0.16
11 8 0.13
12 5 0.08
13 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (9 bp):
ATATAAAAT
Found at i:10106 original size:29 final size:29
Alignment explanation
Indices: 10064--10161 Score: 142
Period size: 29 Copynumber: 3.3 Consensus size: 29
10054 AGGTTTGTAT
*
10064 TATATAATTAATATAAAATATATAAAATA
1 TATATAATTAATATAAAAAATATAAAATA
*
10093 TATATAATTGATATAAAAAATATAAAATTATA
1 TATATAATTAATATAAAAAATAT-AAA--ATA
*
10125 TATATAATTAATATAAAAAATGTAAAATA
1 TATATAATTAATATAAAAAATATAAAATA
10154 TATATAAT
1 TATATAAT
10162 CAGGGCGGTG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
29 32 0.52
30 3 0.05
31 3 0.05
32 24 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TATATAATTAATATAAAAAATATAAAATA
Found at i:10480 original size:2 final size:2
Alignment explanation
Indices: 10475--10508 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10465 TTAGTGTGTG
10475 TA TA TA 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 TA TA TA
10509 AAGTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10660 original size:15 final size:16
Alignment explanation
Indices: 10640--10673 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10630 GACACCATCT
10640 AAAATAT-TTAAAAAC
1 AAAATATATTAAAAAC
*
10655 AAAATATATTATAAAC
1 AAAATATATTAAAAAC
10671 AAA
1 AAA
10674 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATATATTAAAAAC
Found at i:13867 original size:30 final size:30
Alignment explanation
Indices: 13833--13893 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
13823 TTTGGAAGTT
13833 ACTGTAGCAGTTACTATAGCGTATCAATGC
1 ACTGTAGCAGTTACTATAGCGTATCAATGC
* *
13863 ACTGTAGCAGTTACTGTAGCGTATCGATGC
1 ACTGTAGCAGTTACTATAGCGTATCAATGC
13893 A
1 A
13894 TAATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (30 bp):
ACTGTAGCAGTTACTATAGCGTATCAATGC
Found at i:13989 original size:22 final size:22
Alignment explanation
Indices: 13962--14015 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
13952 GATGCACTGT
13962 TCACTGTTCACGGTATTGTTCA
1 TCACTGTTCACGGTATTGTTCA
13984 TCACTGTTCACGGTATTGTTCA
1 TCACTGTTCACGGTATTGTTCA
*
14006 TCACTATTCA
1 TCACTGTTCA
14016 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
TCACTGTTCACGGTATTGTTCA
Found at i:22438 original size:14 final size:13
Alignment explanation
Indices: 22421--22489 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
22411 AATTAATTTT
22421 TAAATTAAAATATA
1 TAAATT-AAATATA
22435 TAAA-TAACATATA
1 TAAATTAA-ATATA
22448 T-AATTAAATAATA
1 TAAATTAAAT-ATA
*
22461 AAAATTAAATA-A
1 TAAATTAAATATA
22473 TAAAATTAAATATA
1 T-AAATTAAATATA
22487 TAA
1 TAA
22490 CTTGCATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
12 7 0.15
13 26 0.55
14 14 0.30
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATTAAATATA
Found at i:26358 original size:50 final size:50
Alignment explanation
Indices: 26299--26414 Score: 223
Period size: 50 Copynumber: 2.3 Consensus size: 50
26289 AATATCGGTT
*
26299 ATGAACCGTTAACGGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
26349 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
1 ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
26399 ATGAACCGTTAACAGT
1 ATGAACCGTTAACAGT
26415 TAACAAGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (50 bp):
ATGAACCGTTAACAGTCACCGACCACGACTCTCTATCTAAATGAAAAGGA
Found at i:29118 original size:31 final size:31
Alignment explanation
Indices: 29069--29160 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
29059 TCAATTTTGC
*
29069 CTATTCCG-GGGCTTAAAGAAGAACTGTACT
1 CTATTCCGAGGACTTAAAGAAGAACTGTACT
29099 CTATTCCGAGGACTTAAAGAAGAACTGTACT
1 CTATTCCGAGGACTTAAAGAAGAACTGTACT
*
29130 -TGATGCCGAGGACTTAAAGAAGAACTGTACT
1 CT-ATTCCGAGGACTTAAAGAAGAACTGTACT
29161 TGATGTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 9 0.16
31 49 0.84
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (31 bp):
CTATTCCGAGGACTTAAAGAAGAACTGTACT
Found at i:29161 original size:31 final size:31
Alignment explanation
Indices: 29080--29165 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
29070 TATTCCGGGG
*
29080 CTTAAAGAAGAACTGTACTCT-ATTCCGAGGA
1 CTTAAAGAAGAACTGTACT-TGATGCCGAGGA
29111 CTTAAAGAAGAACTGTACTTGATGCCGAGGA
1 CTTAAAGAAGAACTGTACTTGATGCCGAGGA
29142 CTTAAAGAAGAACTGTACTTGATG
1 CTTAAAGAAGAACTGTACTTGATG
29166 TTTTAGAGTA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (31 bp):
CTTAAAGAAGAACTGTACTTGATGCCGAGGA
Found at i:32395 original size:17 final size:18
Alignment explanation
Indices: 32364--32397 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
32354 TGTATTTAAT
32364 TTATTTAAGTATTTTACA
1 TTATTTAAGTATTTTACA
32382 TTATTTAA-TATTTTAC
1 TTATTTAAGTATTTTAC
32398 TAATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTTAAGTATTTTACA
Found at i:32654 original size:111 final size:111
Alignment explanation
Indices: 32460--32679 Score: 368
Period size: 111 Copynumber: 2.0 Consensus size: 111
32450 TAAAAATCAT
* * *
32460 ATATCTCTACACTTTGCTGATACAGTAAAATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAAAATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
*
32525 TAAGTAGTTGATTTATTTAATGCATGATTAGTAGATTAAGAATTAA
66 TAAGTAGTTGATTTATTTAATGCATGATTAGTAAATTAAGAATTAA
* *
32571 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACAGTAAAATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
* *
32636 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATT
66 TAAGTAGTTGATTTATTTAATGCATGATTAGTAAATTAAGAATT
32680 CCCCTTGAAC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACAGTAAAATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
TAAGTAGTTGATTTATTTAATGCATGATTAGTAAATTAAGAATTAA
Found at i:33997 original size:49 final size:48
Alignment explanation
Indices: 33919--34020 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 48
33909 TATCCCGGGC
* *
33919 GCGCTATACCCCACGTGTAACCCAGTCAGCGTATAGCGCGGAACAGGGG
1 GCGCTATACCCCACGTG-AACCCAATCAGCATATAGCGCGGAACAGGGG
* **
33968 GCGCTATACTCCACGTG-ACGCCAAATCAGCATATAGCGCGGTTCAGGGG
1 GCGCTATACCCCACGTGAAC-CC-AATCAGCATATAGCGCGGAACAGGGG
34017 GCGC
1 GCGC
34021 GCTTTACTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 2 0.04
48 2 0.04
49 42 0.91
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (48 bp):
GCGCTATACCCCACGTGAACCCAATCAGCATATAGCGCGGAACAGGGG
Found at i:34081 original size:29 final size:29
Alignment explanation
Indices: 34039--34113 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
34029 GCTATGGGTG
*
34039 TTAGATCGGGAAATATAATCTGACC-GATA
1 TTAGATCGAGAAATATAATCTGACCAG-TA
34068 TTAGATCGAGAAATATAATCTGACCAGTA
1 TTAGATCGAGAAATATAATCTGACCAGTA
* *
34097 TTAAATCGATAAATATA
1 TTAGATCGAGAAATATA
34114 CCGATCACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 41 0.98
30 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (29 bp):
TTAGATCGAGAAATATAATCTGACCAGTA
Found at i:37034 original size:16 final size:16
Alignment explanation
Indices: 36994--37037 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
36984 ACCGGACGTG
*
36994 ATCATTTCCCTAATCA
1 ATCATTTCTCTAATCA
37010 ATCATTTCTCTAATCA
1 ATCATTTCTCTAATCA
37026 ATCATTTCTCTA
1 ATCATTTCTCTA
37038 TATTAACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (16 bp):
ATCATTTCTCTAATCA
Found at i:38788 original size:22 final size:22
Alignment explanation
Indices: 38763--38804 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38753 ATTTTGAAAG
*
38763 AAAAAAATAAAAGAAAAAAGAA
1 AAAAAAAGAAAAGAAAAAAGAA
*
38785 AAAAAAAGGAAAGAAAAAAG
1 AAAAAAAGAAAAGAAAAAAG
38805 TTGGTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAAAAGAAAAAAGAA
Found at i:38801 original size:12 final size:12
Alignment explanation
Indices: 38758--38804 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
38748 AATCTATTTT
*
38758 GAAAGAAAAAAAT
1 GAAAG-AAAAAAG
*
38771 AAAAGAAAAAA-
1 GAAAGAAAAAAG
38782 GAAA-AAAAAAG
1 GAAAGAAAAAAG
38793 GAAAGAAAAAAG
1 GAAAGAAAAAAG
38805 TTGGTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.20
11 7 0.23
12 13 0.43
13 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
GAAAGAAAAAAG
Found at i:48278 original size:14 final size:14
Alignment explanation
Indices: 48259--48286 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48249 AATAAATAAT
48259 GAACATAAACGAAC
1 GAACATAAACGAAC
48273 GAACATAAACGAAC
1 GAACATAAACGAAC
48287 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:48364 original size:10 final size:10
Alignment explanation
Indices: 48349--48408 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
48339 CATTTAATAA
48349 ATAAACGAAC
1 ATAAACGAAC
48359 ATAAACGAAC
1 ATAAACGAAC
** *
48369 ACGAAC-ATAA
1 ATAAACGA-AC
48379 ATGAATACGAAAC
1 AT-AA-ACG-AAC
48392 ATAAACGAAC
1 ATAAACGAAC
48402 ATAAACG
1 ATAAACG
48409 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
9 1 0.03
10 26 0.67
11 4 0.10
12 4 0.10
13 3 0.08
14 1 0.03
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:48374 original size:16 final size:16
Alignment explanation
Indices: 48353--48402 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
48343 TAATAAATAA
48353 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
48369 ACGAACATAAATGAAT
1 ACGAACATAAACGAAC
48385 ACGAAACATAAACGAAC
1 ACG-AACATAAACGAAC
48402 A
1 A
48403 TAAACGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:49150 original size:10 final size:10
Alignment explanation
Indices: 49135--49195 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 10
49125 ATAAATGAAT
49135 GAACATAAAC
1 GAACATAAAC
49145 GAACATAATCGAAC
1 GAACAT-A---AAC
49159 GAACATAAAC
1 GAACATAAAC
49169 GAACATAACCAAC
1 GAACAT-A--AAC
*
49182 GAACATAATC
1 GAACATAAAC
49192 GAAC
1 GAAC
49196 GTTCACGAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
10 21 0.49
11 2 0.05
12 1 0.02
13 10 0.23
14 9 0.21
ACGTcount: A:0.54, C:0.23, G:0.11, T:0.11
Consensus pattern (10 bp):
GAACATAAAC
Found at i:49159 original size:14 final size:13
Alignment explanation
Indices: 49142--49196 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
49132 AATGAACATA
49142 AACGAACATAATCG
1 AACGAACATAA-CG
49156 AACGAACAT-A--
1 AACGAACATAACG
*
49166 AACGAACATAACC
1 AACGAACATAACG
49179 AACGAACATAATCG
1 AACGAACATAA-CG
49193 AACG
1 AACG
49197 TTCACGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 12 0.33
14 14 0.39
ACGTcount: A:0.53, C:0.24, G:0.13, T:0.11
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:49162 original size:24 final size:24
Alignment explanation
Indices: 49122--49195 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
49112 GATTGGGTTA
*
49122 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
49146 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
49170 AACATAA-CCAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
49193 AAC
1 AAC
49196 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 20 0.43
24 26 0.57
ACGTcount: A:0.55, C:0.20, G:0.11, T:0.14
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:49871 original size:22 final size:22
Alignment explanation
Indices: 49846--50162 Score: 466
Period size: 22 Copynumber: 14.6 Consensus size: 22
49836 CTATTTTAAA
49846 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* **
49868 ATTTATTTTAAAATGTGGA-AA
1 ATTTATTTTAAAATATGGATTG
49889 ATTT-TATTTAAAATATGGATTG
1 ATTTAT-TTTAAAATATGGATTG
*
49911 ATTTATTTTAAAATATGGA--A
1 ATTTATTTTAAAATATGGATTG
*
49931 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
49953 ATTTATTTT-AAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
49974 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
49996 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
50018 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* **
50040 ATTTATTTTAAAATATAGA-AA
1 ATTTATTTTAAAATATGGATTG
50061 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
50084 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
50106 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
50128 ATTTATTTTAAATTTTGGATTG
1 ATTTATTTTAAAATATGGATTG
50150 ATTTATTTTAAAA
1 ATTTATTTTAAAA
50163 AAATTATTAT
Statistics
Matches: 264, Mismatches: 23, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
20 19 0.07
21 37 0.14
22 206 0.78
23 2 0.01
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:50243 original size:31 final size:31
Alignment explanation
Indices: 50186--50244 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
50176 AGTTGTATGG
*
50186 ATTATTTAAATTTCAATATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
* *
50217 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
50245 CTTAAGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:57471 original size:31 final size:32
Alignment explanation
Indices: 57433--57499 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
57423 TCGAATTTTC
57433 CTGTTCAAGGACTTC-TTTTCTATCACCAATG
1 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
57464 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
1 CTGTTCAAGGACTTCTTTTTCTATCACCAATG
57496 CTGT
1 CTGT
57500 CACCGCTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (32 bp):
CTGTTCAAGGACTTCTTTTTCTATCACCAATG
Done.