Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004059.1 Hibiscus syriacus cultivar Beakdansim tig00008876_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: 68541
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:2667 original size:15 final size:16
Alignment explanation
Indices: 2647--2704 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
2637 ATTAATAAAG
2647 TAAAATAATAATA-AT
1 TAAAATAATAATACAT
*
2662 TAAAATATTAA-ACAT
1 TAAAATAATAATACAT
*
2677 ATAAAATTAA-AATATAT
1 -TAAAA-TAATAATACAT
*
2694 TTAAATAATAA
1 TAAAATAATAA
2705 CTAAAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
14 1 0.03
15 15 0.44
16 13 0.38
17 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATAATAATACAT
Found at i:4548 original size:22 final size:22
Alignment explanation
Indices: 4523--4602 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 22
4513 AATAAAGCTT
4523 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
4545 TCATCTTT--AAAGAGATAGGCTA
1 TCATCTTTGAAAAGAGA-A-TCTA
*
4567 TCATCTTTGAAGAA-AGAGTCTA
1 TCATCTTTGAA-AAGAGAATCTA
4589 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
4603 TGTAGATGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
20 7 0.14
21 3 0.06
22 33 0.67
24 4 0.08
25 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5063 original size:54 final size:54
Alignment explanation
Indices: 4973--5084 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
4963 TGACTGGTTC
* * * *
4973 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * * * *
5027 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGCTG
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
5081 GTAA
1 GTAA
5085 GGGAGGATCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
Found at i:6176 original size:75 final size:75
Alignment explanation
Indices: 5926--6179 Score: 298
Period size: 75 Copynumber: 3.4 Consensus size: 75
5916 AAGATGATAT
* * * *
5926 GGGCCTTCAGCGTGCCCC-GACATTTGCTGATACGAACATTCAAAATGCA-CAAACATTCCTGAT
1 GGGCTTTCAGCATGCCCCAG-CATTTGCTGATACAAACGTTCAAAATGCATC-AACATTCCTGAT
5989 TCTTGATTGAAAG
64 TC-TGATTGAAAG
* * * ** * *
6002 GTGCTTTCAGCATGCCCCAGCATTGGCTAATACAAACGTTCAAAATGTGTCAATATTCCTCATTC
1 GGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACGTTCAAAATGCATCAACATTCCTGATTC
6067 TGATTGAAAG
66 TGATTGAAAG
* * * *
6077 GGGCTTTCAGCATGCCCCAGCATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTC
1 GGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACGTTCAAAATGCATCAACATTCCTGATTC
6142 TGATT-AAGAG
66 TGATTGAA-AG
* *
6152 GGGTTTTCAGTATGCCCCAGCATTTGCT
1 GGGCTTTCAGCATGCCCCAGCATTTGCT
6180 TTCTTGTTAA
Statistics
Matches: 151, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
74 2 0.01
75 97 0.64
76 50 0.33
77 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (75 bp):
GGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACGTTCAAAATGCATCAACATTCCTGATTC
TGATTGAAAG
Found at i:9608 original size:8 final size:8
Alignment explanation
Indices: 9595--9647 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
9585 CTTGGTTCAA
9595 TTTTTCCC
1 TTTTTCCC
9603 TTTTTCCC
1 TTTTTCCC
9611 TTTTTCCC
1 TTTTTCCC
*
9619 TTTTTTCC
1 TTTTTCCC
*
9627 TTTTTTCC
1 TTTTTCCC
9635 TTTTTCCC
1 TTTTTCCC
9643 TTTTT
1 TTTTT
9648 TTTCTTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTCCC
Found at i:9648 original size:16 final size:16
Alignment explanation
Indices: 9595--9677 Score: 84
Period size: 16 Copynumber: 5.4 Consensus size: 16
9585 CTTGGTTCAA
*
9595 TTTTTCCCTTTTTCCC
1 TTTTTTCCTTTTTCCC
* *
9611 TTTTTCCCTTTTTTCC
1 TTTTTTCCTTTTTCCC
9627 TTTTTTCCTTTTTCCC
1 TTTTTTCCTTTTTCCC
9643 TTTTTT--TTCTTT--C
1 TTTTTTCCTT-TTTCCC
* *
9656 TTTTTTCTTTTTTTCC
1 TTTTTTCCTTTTTCCC
9672 TTTTTT
1 TTTTTT
9678 TTCAAGTATA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.12
14 5 0.08
15 5 0.08
16 42 0.71
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCCTTTTTCCC
Found at i:9651 original size:11 final size:10
Alignment explanation
Indices: 9619--9680 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
9609 CCTTTTTCCC
9619 TTTTTTCC--
1 TTTTTTCCTT
9627 TTTTTTCC--
1 TTTTTTCCTT
*
9635 TTTTTCCCTT
1 TTTTTTCCTT
9645 TTTTTT-CTT
1 TTTTTTCCTT
*
9654 TCTTTTTTC-T
1 T-TTTTTCCTT
9664 TTTTTTCCTT
1 TTTTTTCCTT
9674 TTTTTTC
1 TTTTTTC
9681 AAGTATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.33
9 10 0.22
10 20 0.43
11 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:9662 original size:7 final size:7
Alignment explanation
Indices: 9618--9668 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
9608 CCCTTTTTCC
9618 CTTTTTT
1 CTTTTTT
9625 CCTTTTTT
1 -CTTTTTT
*
9633 CCTTTTTCC
1 -CTTTTT-T
9642 CTTTTTT
1 CTTTTTT
*
9649 -TTCTTT
1 CTTTTTT
9655 CTTTTTT
1 CTTTTTT
9662 CTTTTTT
1 CTTTTTT
9669 TCCTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 5 0.14
7 12 0.32
8 20 0.54
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
CTTTTTT
Found at i:9666 original size:19 final size:18
Alignment explanation
Indices: 9619--9680 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
9609 CCTTTTTCCC
*
9619 TTTTTTCCTTTTTTCC-T
1 TTTTTTCTTTTTTTCCTT
** *
9636 TTTTCCCTTTTTTTTCTTT
1 TTTTTTC-TTTTTTTCCTT
9655 CTTTTTTCTTTTTTTCCTT
1 -TTTTTTCTTTTTTTCCTT
9674 TTTTTTC
1 TTTTTTC
9681 AAGTATAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 5 0.14
18 14 0.40
19 11 0.31
20 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTTTTTTCCTT
Found at i:12396 original size:12 final size:13
Alignment explanation
Indices: 12372--12400 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12362 AAAATGAAAA
12372 AAATGCAAAATGT
1 AAATGCAAAATGT
12385 AAATGC-AAATGT
1 AAATGCAAAATGT
12397 AAAT
1 AAAT
12401 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:14902 original size:23 final size:24
Alignment explanation
Indices: 14863--14911 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
14853 AATCATAAAG
14863 AATAATATATAAAATAT-TACAAA
1 AATAATATATAAAATATGTACAAA
* *
14886 AATAATA-ATAAGTATATGTATAAA
1 AATAATATATAA-AATATGTACAAA
14910 AA
1 AA
14912 ATTTGAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (24 bp):
AATAATATATAAAATATGTACAAA
Found at i:15666 original size:6 final size:7
Alignment explanation
Indices: 15638--15665 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
15628 AATAATATGT
15638 ATAAAAA
1 ATAAAAA
15645 ATAAAAA
1 ATAAAAA
15652 ATAAAAA
1 ATAAAAA
15659 ATAAAAA
1 ATAAAAA
15666 TTATTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:15707 original size:27 final size:26
Alignment explanation
Indices: 15676--15746 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
15666 TTATTAGTTT
15676 ATAAAATTAATCATATAAT-ATATATTA
1 ATAAAATTAA-CATATAATAATA-ATTA
* *
15703 ATAAAAGTAAAATAATAATAATAATTA
1 ATAAAATTAACAT-ATAATAATAATTA
*
15730 A-AATATTAAACATATAA
1 ATAAAATT-AACATATAA
15747 AATTAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 10 0.28
27 23 0.64
28 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (26 bp):
ATAAAATTAACATATAATAATAATTA
Found at i:15770 original size:24 final size:22
Alignment explanation
Indices: 15716--15757 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
15706 AAAGTAAAAT
15716 AATAATAATAATTAAAATATTA
1 AATAATAATAATTAAAATATTA
*
15738 AACATATAA-AATTAAAATAT
1 AATA-ATAATAATTAAAATAT
15758 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATAATAATTAAAATATTA
Found at i:17223 original size:3 final size:3
Alignment explanation
Indices: 17208--17245 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
17198 ATATTTAATT
*
17208 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
17246 TAGTGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:17232 original size:21 final size:21
Alignment explanation
Indices: 17208--17247 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17198 ATATTTAATT
*
17208 TAATAATATTAATAATATATA
1 TAATAATAATAATAATATATA
17229 TAATAATAATAATAATATA
1 TAATAATAATAATAATATA
17248 GTGAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATAATAATAATAATATATA
Found at i:17879 original size:18 final size:19
Alignment explanation
Indices: 17844--17881 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
17834 CTCTATTATT
*
17844 TTTATTTAAATTGCTTTTA
1 TTTATTTAAATCGCTTTTA
17863 TTTATTT-AATCGCTTTTA
1 TTTATTTAAATCGCTTTTA
17881 T
1 T
17882 CACTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTTAAATCGCTTTTA
Found at i:23271 original size:4 final size:4
Alignment explanation
Indices: 23262--23288 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23252 CAATGCATGT
23262 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
23289 CATAGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:24345 original size:13 final size:15
Alignment explanation
Indices: 24327--24374 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
24317 TAGACATTTT
24327 TCTTCCAA-AG-CAG
1 TCTTCCAACAGCCAG
24340 TCTTCCAAGCAGCCAG
1 TCTTCCAA-CAGCCAG
*
24356 TCTTCCAAGTAGCCAG
1 TCTTCCAA-CAGCCAG
24372 TCT
1 TCT
24375 ATTATTCAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 8 0.26
15 2 0.06
16 21 0.68
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (15 bp):
TCTTCCAACAGCCAG
Found at i:24358 original size:16 final size:16
Alignment explanation
Indices: 24337--24374 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
24327 TCTTCCAAAG
24337 CAGTCTTCCAAGCAGC
1 CAGTCTTCCAAGCAGC
*
24353 CAGTCTTCCAAGTAGC
1 CAGTCTTCCAAGCAGC
24369 CAGTCT
1 CAGTCT
24375 ATTATTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (16 bp):
CAGTCTTCCAAGCAGC
Found at i:31575 original size:4 final size:4
Alignment explanation
Indices: 31566--31596 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
31556 CAATGCATGT
*
31566 ATAA ATAA ATAA ATAA ATAA ATAA AAAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
31597 CATAGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:54901 original size:3 final size:3
Alignment explanation
Indices: 54893--54962 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
54883 ATGGGAAATA
**
54893 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- ATT
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
54940 AAG AAG AAG AA- AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG
54963 TTCAATTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:55059 original size:166 final size:166
Alignment explanation
Indices: 54776--55087 Score: 563
Period size: 166 Copynumber: 1.9 Consensus size: 166
54766 AGCGTATTGT
*
54776 AAGACGAAGAAGAAGAAGAAGTTCAATTATTAGAATTTTAATGATAAAAAGGAATATAAAATTAG
1 AAGAAGAAGAAGAAGAAGAAGTTCAATTATTAGAATTTTAATGATAAAAAGGAATATAAAATTAG
*
54841 GAAGCGTATTGTAAGACCACGTGCCATTATTTCTCTGGTTTGATGGGAAATAAAGAAGAAGAAGA
66 GAAGCGTATTGTAAGACCACGTGCCATTATTCCTCTGGTTTGATGGGAAATAAAGAAGAAGAAGA
54906 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAATTAAG
131 AGAA-AAGAAGAAGAAGAAGAAGAAGAAGAAATTAAG
*
54943 AAGAAGAA-AAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATTAG
1 AAGAAGAAGAAGAAGAAGAAGTTCAATTATTAGAATTTTAATGATAAAAAGGAATATAAAATTAG
* *
55007 GAAGCGTATTGTAAGACGACGTGCCATTATTCCTCTGGTTTGATGGGAAATAAATAAGAAGAAGA
66 GAAGCGTATTGTAAGACCACGTGCCATTATTCCTCTGGTTTGATGGGAAATAAAGAAGAAGAAGA
55072 AGAAAAGAAGAAGAAG
131 AGAAAAGAAGAAGAAG
55088 TTCAATTATT
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
165 12 0.09
166 121 0.86
167 7 0.05
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.22
Consensus pattern (166 bp):
AAGAAGAAGAAGAAGAAGAAGTTCAATTATTAGAATTTTAATGATAAAAAGGAATATAAAATTAG
GAAGCGTATTGTAAGACCACGTGCCATTATTCCTCTGGTTTGATGGGAAATAAAGAAGAAGAAGA
AGAAAAGAAGAAGAAGAAGAAGAAGAAGAAATTAAG
Found at i:55079 original size:125 final size:122
Alignment explanation
Indices: 54940--55283 Score: 602
Period size: 125 Copynumber: 2.8 Consensus size: 122
54930 AGAAGAAATT
54940 AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
1 AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
* *
55005 AGGAAGCGTATTGTAAGACGACGTGCCATTATTCCTCTGGTTTGATGGGAAATAAATAAG
66 AGGAAGCGTATTGTAAGACCACATGCCATTATTCCTCTGGTTTGATGGGAAAT--A-AAG
*
55065 AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGAAATATAAAATT
1 AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
*
55130 AGGAATCGTATTGTAAGACCACATGCCATTATTCCTCTGGTTTGATGGGAAATAAAG
66 AGGAAGCGTATTGTAAGACCACATGCCATTATTCCTCTGGTTTGATGGGAAATAAAG
*
55187 AATAAGAAG--AAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
1 AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
55250 AGGAAGCGTATTGTAAGACCACATGCCATTATTC
66 AGGAAGCGTATTGTAAGACCACATGCCATTATTC
55284 AATATAAAAT
Statistics
Matches: 212, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
120 86 0.41
122 11 0.05
123 1 0.00
125 114 0.54
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (122 bp):
AAGAAGAAGAAAAGAAGAAGAAGTTCAATTATTAGATTTTTAATGATAAAAAGGAATATAAAATT
AGGAAGCGTATTGTAAGACCACATGCCATTATTCCTCTGGTTTGATGGGAAATAAAG
Found at i:55303 original size:45 final size:45
Alignment explanation
Indices: 55239--55328 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
55229 GATAAAAAGG
55239 AATATAAAATTAGGAAGCGTATTGTAAGACCACATGCCATTATTC
1 AATATAAAATTAGGAAGCGTATTGTAAGACCACATGCCATTATTC
55284 AATATAAAATTAGGAAGCGTATTGTAAGACCACATGCCATTATTC
1 AATATAAAATTAGGAAGCGTATTGTAAGACCACATGCCATTATTC
55329 CTCTGGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (45 bp):
AATATAAAATTAGGAAGCGTATTGTAAGACCACATGCCATTATTC
Found at i:58403 original size:35 final size:33
Alignment explanation
Indices: 58363--58447 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
58353 GTATTTCAGT
*
58363 TAATTTTGTT-TATTATCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
58398 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
58433 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
58448 TAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Done.