Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000224.1 Hibiscus syriacus cultivar Beakdansim tig00000394_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: 65677
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1917 original size:16 final size:16
Alignment explanation
Indices: 1896--1947 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
1886 ATTTGCACTA
1896 ATATCTTAAATCAATC
1 ATATCTTAAATCAATC
1912 ATATCTTAAATCAATC
1 ATATCTTAAATCAATC
*
1928 ATATCTTAAATCAATT
1 ATATCTTAAATCAATC
1944 ATAT
1 ATAT
1948 GGACATGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATCTTAAATCAATC
Found at i:3349 original size:9 final size:10
Alignment explanation
Indices: 3318--3357 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
3308 TTCATCACAC
3318 CAAATTCTCT
1 CAAATTCTCT
3328 CAAATTCTCT
1 CAAATTCTCT
3338 CAAATT-TCT
1 CAAATTCTCT
*
3347 CAAATACTCT
1 CAAATTCTCT
3357 C
1 C
3358 TCTGTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3359 original size:21 final size:20
Alignment explanation
Indices: 3318--3357 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3308 TTCATCACAC
3318 CAAATTCTCTCAAATTCTCT
1 CAAATTCTCTCAAATTCTCT
*
3338 CAAATT-TCTCAAATACTCT
1 CAAATTCTCTCAAATTCTCT
3357 C
1 C
3358 TCTGTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (20 bp):
CAAATTCTCTCAAATTCTCT
Found at i:3429 original size:17 final size:18
Alignment explanation
Indices: 3392--3432 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3382 AAATTATGTA
*
3392 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
3410 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
3427 TTTACT
1 TTTACT
3433 AATATAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:5128 original size:18 final size:18
Alignment explanation
Indices: 5105--5161 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
5095 ACAGCAGCCA
5105 CCGTAGCCATTTATGATG
1 CCGTAGCCATTTATGATG
*
5123 CCGTAGCTATTTATGATG
1 CCGTAGCCATTTATGATG
* * *
5141 CTGCAGCCATATATGATG
1 CCGTAGCCATTTATGATG
5159 CCG
1 CCG
5162 CCATCGCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (18 bp):
CCGTAGCCATTTATGATG
Found at i:8635 original size:18 final size:18
Alignment explanation
Indices: 8608--8648 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
8598 CGAAATATTC
*
8608 GTTATTAGCTCCTAAAGA
1 GTTATCAGCTCCTAAAGA
*
8626 GTTATCAGCTCCTCAAGA
1 GTTATCAGCTCCTAAAGA
8644 GTTAT
1 GTTAT
8649 GTTTCTCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (18 bp):
GTTATCAGCTCCTAAAGA
Found at i:11915 original size:170 final size:168
Alignment explanation
Indices: 11631--12113 Score: 617
Period size: 170 Copynumber: 2.8 Consensus size: 168
11621 TCGAATAACT
* *
11631 CAGAATAATTCAATCGAAATTAAGCAAAAAGGAGGACAAAATAGCAACTAGCAAATAATGAGAAA
1 CAGAATAATTCAATCGAAATTAAGC-AAAA--AGGAC-AAATAGCAAGTAGCAAATCATGAGAAA
* * * *
11696 CAGC-AAAGCAAAGATATTTAATCCCCTGATGAAAGAACAATTCAATCAAACTCGTTCAAATTCT
62 CAACAAAAGCAAAGATCTTTAAT-CCCTAATGAAAGAACAATTCAATCAAACTCGTACAAATTCT
* * **
11760 AATAGCATAAGAAGATCAAACAGTTAACTTTCTTTAAAAAACA
126 AATAGCATAAGAAGAGCAAACAGCTAACTTTCTGAAAAAAACA
*
11803 CAGAATAATTCAATCGAAATTAAGCAAAAAGGACAAATTAGCAAGTAGCAAATCATGAGAAACAC
1 CAGAATAATTCAATCGAAATTAAGCAAAAAGGACAAA-TAGCAAGTAGCAAATCATGAGAAACAA
* *
11868 CAAAAGCAAAGGTCTTTAATCACCTAATGAAAGAACTATTCAATCAAACTCGTACAAATTCTAAT
65 CAAAAGCAAAGATCTTTAATC-CCTAATGAAAGAACAATTCAATCAAACTCGTACAAATTCTAAT
* * *
11933 ATCATGAGAAGAGCAGACAGCTAACTTTCTGAAAAAAACA
129 AGCATAAGAAGAGCAAACAGCTAACTTTCTGAAAAAAACA
*
11973 CAGAATAATTCAATCAAAATTAAGCAAAAAGGACACAATAGCAAGTAGCAAATCATGATTCATGA
1 CAGAATAATTCAATCGAAATTAAGCAAAAAGGACA-AATAGCAAGTAGC--A--A--A-TCATGA
* * * *
12038 GAAACAACAAAAGCAAAGATCTTTAATCCCAAAATAAAAGAACCATTCAATCAAACTCGTAGAAA
58 GAAACAACAAAAGCAAAGATCTTTAATCCC-TAATGAAAGAACAATTCAATCAAACTCGTACAAA
*
12103 TTATAATAGCA
122 TTCTAATAGCA
12114 AACTGCGAAC
Statistics
Matches: 275, Mismatches: 24, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
168 3 0.01
169 31 0.11
170 134 0.49
171 6 0.02
172 26 0.09
174 1 0.00
176 3 0.01
177 71 0.26
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (168 bp):
CAGAATAATTCAATCGAAATTAAGCAAAAAGGACAAATAGCAAGTAGCAAATCATGAGAAACAAC
AAAAGCAAAGATCTTTAATCCCTAATGAAAGAACAATTCAATCAAACTCGTACAAATTCTAATAG
CATAAGAAGAGCAAACAGCTAACTTTCTGAAAAAAACA
Found at i:12145 original size:2 final size:2
Alignment explanation
Indices: 12138--12164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12128 AACTTTCCAA
12138 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
12165 ATAATTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13848 original size:21 final size:21
Alignment explanation
Indices: 13809--13849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13799 ACAATACTGA
* * *
13809 CATGATAATTTATAGTATTAT
1 CATGATAATTCACAATATTAT
13830 CATGATAATTCACAATATTA
1 CATGATAATTCACAATATTA
13850 ATGAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
CATGATAATTCACAATATTAT
Found at i:14561 original size:49 final size:48
Alignment explanation
Indices: 14475--14571 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 48
14465 ACTATATGAC
* * * *
14475 CAAACAGACTCTGACCCATGGCTTCATATTGGGGATGAACCAGACTCG
1 CAAACAGACCCTGACCCATGGCTCCAAATTGGAGATGAACCAGACTCG
* *
14523 CAAATAGACCCTGACCCCGTGGCTCCAAATTGGAGATGAACCAGACTCG
1 CAAACAGACCCTGA-CCCATGGCTCCAAATTGGAGATGAACCAGACTCG
14572 AATTGTATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 12 0.29
49 30 0.71
ACGTcount: A:0.30, C:0.29, G:0.23, T:0.19
Consensus pattern (48 bp):
CAAACAGACCCTGACCCATGGCTCCAAATTGGAGATGAACCAGACTCG
Found at i:14657 original size:59 final size:58
Alignment explanation
Indices: 14530--14708 Score: 164
Period size: 59 Copynumber: 3.0 Consensus size: 58
14520 TCGCAAATAG
* * * * * **
14530 ACCCTGACCCCGTGGCTCCAAATTGGAGATGAACCAGACTCGAATTGTATGACCAGGCAGA
1 ACCCTGA-CCCATGACTCCATA-TGGAGATGAACCAGACTTGAACTGTATGACCAAACA-A
** * * * *
14591 A-TTTGACCCATTACTCCATATTAGG-GATGAACCAGACTTGAATTGTCTGATCAAACAA
1 ACCCTGACCCATGACTCCATA-T-GGAGATGAACCAGACTTGAACTGTATGACCAAACAA
*
14649 ACCCTGACCCATGGCTCCATATGGTAGATGAACCAGACTTGAACTGTATGACCAAACAA
1 ACCCTGACCCATGACTCCATATGG-AGATGAACCAGACTTGAACTGTATGACCAAACAA
14708 A
1 A
14709 TGGACATGTA
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 85 0.89
60 5 0.05
61 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (58 bp):
ACCCTGACCCATGACTCCATATGGAGATGAACCAGACTTGAACTGTATGACCAAACAA
Found at i:17704 original size:15 final size:15
Alignment explanation
Indices: 17684--17712 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17674 TGCATCCACG
17684 TCACCTTAAAAATAC
1 TCACCTTAAAAATAC
17699 TCACCTTAAAAATA
1 TCACCTTAAAAATA
17713 TCCATGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (15 bp):
TCACCTTAAAAATAC
Found at i:18443 original size:2 final size:2
Alignment explanation
Indices: 18436--18486 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
18426 TTTATAGTGT
*
18436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18478 TA TA T- TA TA
1 TA TA TA TA TA
18487 GTTTTGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27512 original size:6 final size:6
Alignment explanation
Indices: 27476--27500 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27466 ACCTTTTGTA
27476 TTGCAT TTGCAT TTGCAT TTGCAT T
1 TTGCAT TTGCAT TTGCAT TTGCAT T
27501 CCACATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTGCAT
Found at i:30558 original size:20 final size:21
Alignment explanation
Indices: 30513--30566 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
30503 TACACAGTCA
*
30513 AGTATCGATACCCCAACACCAG
1 AGTATCGATA-CTCAACACCAG
*
30535 AGTATCGATACTCAAC-CTAG
1 AGTATCGATACTCAACACCAG
30555 AGTATCGATACT
1 AGTATCGATACT
30567 TCCTTAACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.50
21 5 0.17
22 10 0.33
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (21 bp):
AGTATCGATACTCAACACCAG
Found at i:30662 original size:20 final size:20
Alignment explanation
Indices: 30618--30670 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
30608 CAATAGGTGG
30618 GTATCGATAC-CAAGGGTAC
1 GTATCGATACTCAAGGGTAC
*
30637 GATATCGATACTGAAGGGTTA-
1 G-TATCGATACTCAAGGG-TAC
*
30658 GTATCAATACTCA
1 GTATCGATACTCA
30671 TGATCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 19 0.68
21 6 0.21
22 2 0.07
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCAAGGGTAC
Found at i:34347 original size:16 final size:16
Alignment explanation
Indices: 34326--34356 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34316 ATAGAATGTA
34326 CCGAAGGACCACGTAC
1 CCGAAGGACCACGTAC
*
34342 CCGAAGGACCGCGTA
1 CCGAAGGACCACGTA
34357 GAACCCTCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.35, G:0.29, T:0.06
Consensus pattern (16 bp):
CCGAAGGACCACGTAC
Found at i:34429 original size:2 final size:2
Alignment explanation
Indices: 34422--34488 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
34412 TGGGTTTTAC
34422 TA TA TA TA 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 TA TA TA TA
34464 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34489 TTCATATGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34623 original size:5 final size:5
Alignment explanation
Indices: 34613--34671 Score: 118
Period size: 5 Copynumber: 11.8 Consensus size: 5
34603 ATAATCACGT
34613 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
34663 ATATC ATAT
1 ATATC ATAT
34672 AGCTTATATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:35778 original size:166 final size:167
Alignment explanation
Indices: 35504--35838 Score: 615
Period size: 165 Copynumber: 2.0 Consensus size: 167
35494 ACTCCTAAAC
35504 ATCCAATTTCTCAATAGCATACTTGGAATAAAAAATCTTACCAAATTTCAACTTTGTTATAAAAT
1 ATCCAATTTCTCAATAGCATACTTGGAATAAAAAATCTTACCAAATTTCAACTTTGTTATAAAAT
35569 CTTTCTACCTCATAAATCTCTTATTCTAATCGATGCCAAGTT-AATTTAACCCTC-AACTTCATT
66 CTTTCTACCTCATAAATCTCTTATTCTAATCGATGCCAAGTTAAATTTAA-CCTCAAACTTCATT
35632 TACTAACTCTTTCTCAACAATTCACTTAAAAACCT-TT
130 TACTAACTCTTTCTCAACAATTCACTTAAAAACCTCTT
35669 ATCCAATTTCTCAATAGCATACTTGGAAT-AAAAATCTTACCAAAATTTCAACTTTGTTATAAAA
1 ATCCAATTTCTCAATAGCATACTTGGAATAAAAAATCTTACC-AAATTTCAACTTTGTTATAAAA
35733 TCTTTCTAACCTCATAAATCTCTTATTCTAATCGATGCCAAGTTAAATTTAACCTCAAACTTCAT
65 TCTTTCT-ACCTCATAAATCTCTTATTCTAATCGATGCCAAGTTAAATTTAACCTCAAACTTCAT
35798 TTACTAACTCTTTCTCAACAATTCACTTAAAAACCTCTT
129 TTACTAACTCTTTCTCAACAATTCACTTAAAAACCTCTT
35837 AT
1 AT
35839 ATTCAATCGC
Statistics
Matches: 165, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
164 12 0.07
165 58 0.35
166 40 0.24
167 51 0.31
168 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (167 bp):
ATCCAATTTCTCAATAGCATACTTGGAATAAAAAATCTTACCAAATTTCAACTTTGTTATAAAAT
CTTTCTACCTCATAAATCTCTTATTCTAATCGATGCCAAGTTAAATTTAACCTCAAACTTCATTT
ACTAACTCTTTCTCAACAATTCACTTAAAAACCTCTT
Found at i:51327 original size:18 final size:18
Alignment explanation
Indices: 51304--51372 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
51294 TGAATATTTA
51304 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* * *
51322 TCCCGAAGGAGCTCTATA
1 TCCCGAAGGACCACTATG
51340 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
51358 TCCTGAAGGACCACT
1 TCCCGAAGGACCACT
51373 GATAATCACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:52039 original size:19 final size:19
Alignment explanation
Indices: 52015--52066 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
52005 TTTAAGGGGG
52015 TGCATCGATGCACTCTTCA
1 TGCATCGATGCACTCTTCA
52034 TGCATCGATGCACTCTTCA
1 TGCATCGATGCACTCTTCA
*
52053 TGCATCGATACACT
1 TGCATCGATGCACT
52067 AATTGCATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCTTCA
Found at i:53605 original size:11 final size:11
Alignment explanation
Indices: 53589--53628 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
53579 AACTCGTATC
53589 CGGGTTGGGTA
1 CGGGTTGGGTA
53600 CGGGTTGGGTA
1 CGGGTTGGGTA
53611 CGGGTTGGGTA
1 CGGGTTGGGTA
53622 CGGGTTG
1 CGGGTTG
53629 AGGGTGTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.07, C:0.10, G:0.55, T:0.28
Consensus pattern (11 bp):
CGGGTTGGGTA
Found at i:56446 original size:21 final size:20
Alignment explanation
Indices: 56420--56476 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
56410 TTCTATAGCG
56420 CAAAGGATTGATCCCTTTGA
1 CAAAGGATTGATCCCTTTGA
*
56440 CCAAAGGATCGATCCC-TTGA
1 -CAAAGGATTGATCCCTTTGA
* *
56460 AAAAAGATTGATCCCTT
1 CAAAGGATTGATCCCTT
56477 GGATAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 12 0.39
20 5 0.16
21 14 0.45
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
CAAAGGATTGATCCCTTTGA
Found at i:56474 original size:19 final size:20
Alignment explanation
Indices: 56425--56477 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
56415 TAGCGCAAAG
* *
56425 GATTGATCCCTTTGACCAAAG
1 GATTGATCCC-TTGACAAAAA
*
56446 GATCGATCCCTTGA-AAAAA
1 GATTGATCCCTTGACAAAAA
56465 GATTGATCCCTTG
1 GATTGATCCCTTG
56478 GATAATAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.54
20 4 0.14
21 9 0.32
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (20 bp):
GATTGATCCCTTGACAAAAA
Found at i:59504 original size:27 final size:27
Alignment explanation
Indices: 59444--59507 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
59434 ATATGATATA
59444 ATTA-ATATATATTAAAAGATATAATT
1 ATTATATATATATTAAAAGATATAATT
*
59470 AGTATATATATATATTAAAAGATA-CATT
1 A-T-TATATATATATTAAAAGATATAATT
59498 CATTATATAT
1 -ATTATATAT
59508 TTTATTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 1 0.03
27 8 0.24
28 6 0.18
29 18 0.55
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (27 bp):
ATTATATATATATTAAAAGATATAATT
Found at i:60277 original size:21 final size:21
Alignment explanation
Indices: 60245--60305 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
60235 TAAAAGGATT
60245 CACTCA-TTTTTCTAAATTCG
1 CACTCATTTTTTCTAAATTCG
60265 CACTCATTTTTTCTAAATTCG
1 CACTCATTTTTTCTAAATTCG
60286 CACTCATTTTTTCTAAATTC
1 CACTCATTTTTTCTAAATTC
60306 ATCGAGTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 6 0.15
21 34 0.85
ACGTcount: A:0.25, C:0.25, G:0.03, T:0.48
Consensus pattern (21 bp):
CACTCATTTTTTCTAAATTCG
Found at i:61308 original size:51 final size:50
Alignment explanation
Indices: 61253--61379 Score: 143
Period size: 51 Copynumber: 2.5 Consensus size: 50
61243 GTAGCAGTAA
** *
61253 AGCGCGCTCCCTGTCTCGCGCTATATGCTGATTTGGC-GCCACGTGTGGTAT
1 AGCGCGC-CCCTGTCTCGCGCTATATGCTGACATGGCTGACACGTG-GGTAT
*
61304 AGCGCGCCCCCTGTAC-CGCGCTATATGCTGACATGGCTTACACGTGGGTAT
1 AGCGCG-CCCCTGT-CTCGCGCTATATGCTGACATGGCTGACACGTGGGTAT
61355 AGCGCGGCCCCTGATCT-GCGCTATA
1 AGCGC-GCCCCTG-TCTCGCGCTATA
61380 GTTGTTTATC
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
51 56 0.85
52 10 0.15
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.25
Consensus pattern (50 bp):
AGCGCGCCCCTGTCTCGCGCTATATGCTGACATGGCTGACACGTGGGTAT
Done.