Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009217.1 Hibiscus syriacus cultivar Beakdansim tig00112805_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: 97350
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11102 original size:63 final size:64
Alignment explanation
Indices: 10999--11142 Score: 175
Period size: 63 Copynumber: 2.3 Consensus size: 64
10989 AAATAAGCCT
* ** * * **
10999 GGAGTGCATCAATGCATGGTTTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATT-A
1 GGAGTGCATCGATGCATGCCTTGTGCATCGATACACAAAATGCATTCGAAATTCAAATTATTAA
* * *
11062 GGAGTGCATCGATGCATGCCTTGTTCATCGGTACACAAAATGCATTCGAAATTCAATTTATTCAA
1 GGAGTGCATCGATGCATGCCTTGTGCATCGATACACAAAATGCATTCGAAATTCAAATTATT-AA
11127 GG-GTGCATCGATGCAT
1 GGAGTGCATCGATGCAT
11143 TATATAGTGC
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 52 0.75
64 14 0.20
65 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
GGAGTGCATCGATGCATGCCTTGTGCATCGATACACAAAATGCATTCGAAATTCAAATTATTAA
Found at i:16500 original size:28 final size:28
Alignment explanation
Indices: 16455--16576 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
16445 ATAATAGTTT
*
16455 TGAATCATTCAA-AATGTACTTTAATGC
1 TGAATCATTCAACAATGTATTTTAATGC
* * *
16482 TAAATAATTCAACAATGTATTTTAATGT
1 TGAATCATTCAACAATGTATTTTAATGC
* *
16510 TGAATCATTCAACAGTGTATTTTAATGT
1 TGAATCATTCAACAATGTATTTTAATGC
* *
16538 TGAATCATTTAACAGTGTATTTTAATGC
1 TGAATCATTCAACAATGTATTTTAATGC
16566 TGAATCATTCA
1 TGAATCATTCA
16577 GTGTACTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 10 0.12
28 74 0.88
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (28 bp):
TGAATCATTCAACAATGTATTTTAATGC
Found at i:16590 original size:25 final size:27
Alignment explanation
Indices: 16455--16592 Score: 120
Period size: 28 Copynumber: 5.1 Consensus size: 27
16445 ATAATAGTTT
* * * *
16455 TGAATCATTCAAAATGTACTTTAATGC
1 TGAATCATTTACAGTGTATTTTAATGC
* * * * *
16482 TAAATAATTCAACAATGTATTTTAATGT
1 TGAATCATT-TACAGTGTATTTTAATGC
* *
16510 TGAATCATTCAACAGTGTATTTTAATGT
1 TGAATCATT-TACAGTGTATTTTAATGC
16538 TGAATCATTTAACAGTGTATTTTAATGC
1 TGAATCATTT-ACAGTGTATTTTAATGC
16566 TGAATCA-TT-CAGTGTACTTTT-ATGC
1 TGAATCATTTACAGTGTA-TTTTAATGC
16591 TG
1 TG
16593 CAGTATTTTG
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
25 13 0.13
26 4 0.04
27 9 0.09
28 71 0.73
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (27 bp):
TGAATCATTTACAGTGTATTTTAATGC
Found at i:17457 original size:18 final size:21
Alignment explanation
Indices: 17411--17451 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
17401 GAAATTAATA
17411 ATAAATAAATTATTTTCAATTT
1 ATAAATAAATTA-TTTCAATTT
17433 ATAAATAAATTA-TTCAATT
1 ATAAATAAATTATTTCAATT
17452 AAAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAATAAATTATTTCAATTT
Found at i:17980 original size:37 final size:37
Alignment explanation
Indices: 17932--18029 Score: 178
Period size: 37 Copynumber: 2.6 Consensus size: 37
17922 TTCGGGTCGA
* *
17932 GTTTTTTAGAGTAGAAGTTTGGGTCAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
17969 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
18006 GTTTTTCAGAGTAGAAGTTCGGGT
1 GTTTTTCAGAGTAGAAGTTCGGGT
18030 TGAGTTCGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (37 bp):
GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
Found at i:22262 original size:19 final size:19
Alignment explanation
Indices: 22238--22288 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
22228 GCTGCTGGAA
*
22238 AACCGGTTTGACCAGTTTG
1 AACCGGTTTGACCAGTCTG
*
22257 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGTCTG
*
22276 AACCGGGTTGACC
1 AACCGGTTTGACC
22289 CGACCCGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCAGTCTG
Found at i:22267 original size:10 final size:10
Alignment explanation
Indices: 22238--22286 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
22228 GCTGCTGGAA
22238 AACCGGTTTG
1 AACCGGTTTG
*
22248 -ACCAGTTTG
1 AACCGGTTTG
22257 AACCGGTTTG
1 AACCGGTTTG
*
22267 -ACCGGTCTG
1 AACCGGTTTG
*
22276 AACCGGGTTG
1 AACCGGTTTG
22286 A
1 A
22287 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:22304 original size:17 final size:17
Alignment explanation
Indices: 22282--22322 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
22272 TCTGAACCGG
22282 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
22299 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
22316 ATTGACC
1 GTTGACC
22323 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:22322 original size:7 final size:7
Alignment explanation
Indices: 22312--22355 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
22302 GACCCGACCC
*
22312 GACCATT
1 GACCGTT
22319 GACCGTT
1 GACCGTT
22326 GACCG-T
1 GACCGTT
22332 GACCGTT
1 GACCGTT
22339 GACCGTT
1 GACCGTT
*
22346 GACCATT
1 GACCGTT
22353 GAC
1 GAC
22356 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:22340 original size:20 final size:20
Alignment explanation
Indices: 22312--22349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22302 GACCCGACCC
22312 GACCATTGACCGTTGACCGT
1 GACCATTGACCGTTGACCGT
*
22332 GACCGTTGACCGTTGACC
1 GACCATTGACCGTTGACC
22350 ATTGACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (20 bp):
GACCATTGACCGTTGACCGT
Found at i:29555 original size:20 final size:19
Alignment explanation
Indices: 29530--29618 Score: 74
Period size: 19 Copynumber: 4.6 Consensus size: 19
29520 GCTGCTGGAA
* *
29530 AACCGGTTTGAGCAGTTTTG
1 AACCGGTTTGA-CAGGTTCG
*
29550 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACAGGTTCG
*
29569 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACAGGTTC-G
* *
29588 AACCAGTTTGACCGG-TCTG
1 AACCGGTTTGACAGGTTC-G
*
29607 AACCGGGTTGAC
1 AACCGGTTTGAC
29619 CCGACCCGAC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
18 2 0.03
19 49 0.79
20 11 0.18
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACAGGTTCG
Found at i:29559 original size:10 final size:10
Alignment explanation
Indices: 29530--29617 Score: 83
Period size: 10 Copynumber: 9.1 Consensus size: 10
29520 GCTGCTGGAA
29530 AACCGGTTTG
1 AACCGGTTTG
* * *
29540 AGCAGTTTTG
1 AACCGGTTTG
29550 AACCGGTTTG
1 AACCGGTTTG
*
29560 -ACCGGTTCG
1 AACCGGTTTG
29569 AACCGGTTTG
1 AACCGGTTTG
*
29579 -ACCGGTCTG
1 AACCGGTTTG
*
29588 AACCAGTTTG
1 AACCGGTTTG
*
29598 -ACCGGTCTG
1 AACCGGTTTG
*
29607 AACCGGGTTG
1 AACCGGTTTG
29617 A
1 A
29618 CCCGACCCGA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
9 23 0.38
10 37 0.62
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:29573 original size:19 final size:19
Alignment explanation
Indices: 29548--29619 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
29538 TGAGCAGTTT
29548 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
29566 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
*
29586 TGAACCAGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
29605 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
29620 CGACCCGACT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
18 1 0.02
19 47 0.96
20 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:29597 original size:38 final size:38
Alignment explanation
Indices: 29530--29619 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
29520 GCTGCTGGAA
* * * *
29530 AACCGGTTTGAGCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGA-CCGGTCTGAACCAGTTTGACCGGTCT-G
29569 AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
*
29607 AACCGGGTTGACC
1 AACCGGTTTGACC
29620 CGACCCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 33 0.73
39 12 0.27
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
Found at i:29635 original size:17 final size:17
Alignment explanation
Indices: 29613--29670 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
29603 TCTGAACCGG
*
29613 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
29630 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
29647 GTTGACCCGACCCGTCC
1 GTTGACCCGACCCGACC
29664 GTTGACC
1 GTTGACC
29671 GTTAACCGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:29672 original size:7 final size:7
Alignment explanation
Indices: 29662--29696 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
29652 CCCGACCCGT
29662 CCGTTGA
1 CCGTTGA
*
29669 CCGTTAA
1 CCGTTGA
29676 CCG-TGA
1 CCGTTGA
29682 CCGTTGA
1 CCGTTGA
29689 CCGTTGA
1 CCGTTGA
29696 C
1 C
29697 TTTCTTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:31406 original size:21 final size:21
Alignment explanation
Indices: 31380--31424 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31370 CAATAAAAAA
* *
31380 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
31401 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
31422 TCA
1 TCA
31425 TAGCTCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:39858 original size:21 final size:21
Alignment explanation
Indices: 39834--39877 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39824 ACTTATTCAG
39834 ACTATAAACATTTCCTTTGCC
1 ACTATAAACATTTCCTTTGCC
39855 ACTATAAACATTTCCTTTGCC
1 ACTATAAACATTTCCTTTGCC
39876 AC
1 AC
39878 GACATTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (21 bp):
ACTATAAACATTTCCTTTGCC
Found at i:42299 original size:30 final size:29
Alignment explanation
Indices: 42242--42299 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
42232 GTATGGTTTG
*
42242 AAAATAAATGAAAGTTTAGATACTAAAAT
1 AAAATAAATGAAAGTTTACATACTAAAAT
*
42271 AAAATAAAATTAATAGTTTACA-ACTAAAA
1 AAAAT-AAATGAA-AGTTTACATACTAAAA
42300 GTGTAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 13 0.52
31 7 0.28
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (29 bp):
AAAATAAATGAAAGTTTACATACTAAAAT
Found at i:43263 original size:54 final size:55
Alignment explanation
Indices: 43115--43308 Score: 225
Period size: 55 Copynumber: 3.6 Consensus size: 55
43105 CCTGTTTTTT
* * * * * *
43115 AGATGTATTCGATTCCGGGATCTCTATTTTTATGCTTCTTAATAGCAACAACTGA
1 AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
43170 TAGATATACTCGATTTTGGG-CCCCTATTTTTATGCTTATTAATGGCAACAACTG-
1 -AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
** *
43224 AGATATATTCGATTTCGGGACCCCTATTTTTATAATTATTAATGG-AACAATTGA
1 AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
43278 TACATATATTCGA-TTCGGGGCCCCTATTTTT
1 -AGATATATTCGATTTCGGGACCCCTATTTTT
43309 TGGGGCCGTT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
53 24 0.20
54 40 0.33
55 41 0.34
56 15 0.12
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (55 bp):
AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
Found at i:65072 original size:19 final size:21
Alignment explanation
Indices: 65027--65074 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
65017 TGTACTATAC
*
65027 TTGAAATT-TATGTTAGAGTG
1 TTGAAATTGTATGTTAGAATG
65047 TTGAAATTGT-TGTTAGAATG
1 TTGAAATTGTATGTTAGAATG
65067 -TGAAATTG
1 TTGAAATTG
65075 GGTTATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (21 bp):
TTGAAATTGTATGTTAGAATG
Found at i:66153 original size:2 final size:2
Alignment explanation
Indices: 66146--66179 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
66136 CTTGAACCAA
66146 AT AT AT 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 AT AT AT
66180 TAAAATAAAG
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):
AT
Found at i:74053 original size:11 final size:12
Alignment explanation
Indices: 74024--74058 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
74014 TTAGGTGCTG
74024 GAAACAAGATAA
1 GAAACAAGATAA
*
74036 GAAACAAGATTA
1 GAAACAAGATAA
74048 -AAACAAGATAA
1 GAAACAAGATAA
74059 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:76294 original size:23 final size:21
Alignment explanation
Indices: 76251--76294 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
76241 AGAAATTATC
**
76251 GAAGAAAAGGGGATTTTAGAA
1 GAAGAAAAGGGGATTACAGAA
76272 GAAGAAGAAGGGAGATTACAGAA
1 GAAGAA-AAGGG-GATTACAGAA
76295 AAAGGATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.34, T:0.14
Consensus pattern (21 bp):
GAAGAAAAGGGGATTACAGAA
Found at i:76654 original size:21 final size:21
Alignment explanation
Indices: 76625--76674 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
76615 CATTCCCAAA
*
76625 TCATGTTCGTTCCTCCGTTCT
1 TCATCTTCGTTCCTCCGTTCT
76646 TCATCTTCGTTCCTCCGTTCT
1 TCATCTTCGTTCCTCCGTTCT
76667 TCATCTTC
1 TCATCTTC
76675 TTCTCCAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.36, G:0.10, T:0.48
Consensus pattern (21 bp):
TCATCTTCGTTCCTCCGTTCT
Found at i:81843 original size:21 final size:21
Alignment explanation
Indices: 81817--81861 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
81807 CCAAATCCTG
81817 TTCGTTCCTCCGTTCTTCATC
1 TTCGTTCCTCCGTTCTTCATC
81838 TTCGTTCCTCCGTTCTTCATC
1 TTCGTTCCTCCGTTCTTCATC
81859 TTC
1 TTC
81862 TTCTCCAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.38, G:0.09, T:0.49
Consensus pattern (21 bp):
TTCGTTCCTCCGTTCTTCATC
Found at i:87833 original size:22 final size:22
Alignment explanation
Indices: 87808--87859 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
87798 GGGGTATCAA
87808 TTCCCCTAAAAGGGGGAATCGG
1 TTCCCCTAAAAGGGGGAATCGG
* *
87830 TTCCCCTTCAAATGGGGAATCGG
1 TTCCCC-TAAAAGGGGGAATCGG
87853 TTCCCCT
1 TTCCCCT
87860 TCAAGGGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (22 bp):
TTCCCCTAAAAGGGGGAATCGG
Found at i:87872 original size:21 final size:23
Alignment explanation
Indices: 87820--87863 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
87810 CCCCTAAAAG
87820 GGGGAATCGGTTCCCCTTCAAAT
1 GGGGAATCGGTTCCCCTTCAAAT
87843 GGGGAATCGGTTCCCCTTCAA
1 GGGGAATCGGTTCCCCTTCAA
87864 GGGGTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAT
Found at i:91571 original size:20 final size:21
Alignment explanation
Indices: 91533--91572 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
91523 GAAGTTTTAA
* *
91533 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACCTTTGAT
91554 GATCATC-ATTTACCTTTGA
1 GATCATCAATTTACCTTTGA
91573 AAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACCTTTGAT
Done.