Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007859.1 Hibiscus syriacus cultivar Beakdansim tig00110221_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: 3538007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3499515 original size:21 final size:21
Alignment explanation
Indices: 3499491--3499534 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3499481 GTTTGATGCT
*
3499491 TTCTC-TTTGATTCTCTTTTGA
1 TTCTCTTTTGATTCT-TGTTGA
3499512 TTCTCTTTTGATTCTTGTTGA
1 TTCTCTTTTGATTCTTGTTGA
3499533 TT
1 TT
3499535 GTCATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.09, C:0.16, G:0.11, T:0.64
Consensus pattern (21 bp):
TTCTCTTTTGATTCTTGTTGA
Found at i:3500024 original size:19 final size:20
Alignment explanation
Indices: 3500000--3500039 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3499990 AATTTAATCG
*
3500000 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
3500019 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
3500039 A
1 A
3500040 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:3502437 original size:22 final size:23
Alignment explanation
Indices: 3502406--3502487 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
3502396 AAACCCCATG
* *
3502406 GGGGGTATCGATT-CCCTCCAAT
1 GGGGGAATCGATTCCCCTCCAAA
* *
3502428 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTCCAAA
** *
3502451 GGGGGAATCGGCTCCCCTGC-AA
1 GGGGGAATCGATTCCCCTCCAAA
*
3502473 -GGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
3502488 TCTGTACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
21 12 0.24
22 13 0.26
23 25 0.50
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (23 bp):
GGGGGAATCGATTCCCCTCCAAA
Found at i:3502445 original size:23 final size:22
Alignment explanation
Indices: 3502406--3502476 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
3502396 AAACCCCATG
* *
3502406 GGGGGTATCGATT-CCCTCCAA
1 GGGGGAATCGGTTCCCCTCCAA
*
3502427 TGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGGTTCCCC-TCCAA
* *
3502451 GGGGGAATCGGCTCCCCTGCAA
1 GGGGGAATCGGTTCCCCTCCAA
3502473 GGGG
1 GGGG
3502477 TATCGATTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.44
23 19 0.46
24 4 0.10
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTCCAA
Found at i:3508899 original size:19 final size:19
Alignment explanation
Indices: 3508872--3508927 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
3508862 AAATGACCAA
*
3508872 ATAAATCGCAATGCGATCG
1 ATAATTCGCAATGCGATCG
*
3508891 ATAATTCGCAATGCGATAG
1 ATAATTCGCAATGCGATCG
*
3508910 ATAATTCGCAACGCGATC
1 ATAATTCGCAATGCGATC
3508928 TCCGGTATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
ATAATTCGCAATGCGATCG
Found at i:3509004 original size:21 final size:21
Alignment explanation
Indices: 3508975--3509027 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3508965 ATTCTGACTA
3508975 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
3508996 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
3509017 TCGCAATGCGA
1 TCGCATTGCGA
3509028 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3509102 original size:20 final size:20
Alignment explanation
Indices: 3509017--3509092 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
3509007 TTTTCCGAAT
3509017 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
3509037 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
3509057 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
3509077 TCGCAATGCGATTATG
1 TCGCAATGCGAATATG
3509093 ACTATCGCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:3509107 original size:20 final size:20
Alignment explanation
Indices: 3509076--3509193 Score: 103
Period size: 20 Copynumber: 6.4 Consensus size: 20
3509066 GAATATGTAA
* *
3509076 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
3509096 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3509116 AT--C-A--C-----TGACT
1 ATCGCAACGCGATTCTGACT
* * *
3509126 ATCGCAACGAGGTTCTGATT
1 ATCGCAACGCGATTCTGACT
* *
3509146 ATCGCAACGAGGTTCTGACT
1 ATCGCAACGCGATTCTGACT
3509166 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3509186 ATCGCAAC
1 ATCGCAAC
3509194 ACTGAATTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.09
12 1 0.01
13 1 0.01
15 1 0.01
17 1 0.01
18 1 0.01
20 69 0.85
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3509127 original size:30 final size:30
Alignment explanation
Indices: 3509091--3509148 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3509081 AATGCGATTA
*
3509091 TGACTATCGCAACGCGATTCTGACTATCAC
1 TGACTATCGCAACGAGATTCTGACTATCAC
* *
3509121 TGACTATCGCAACGAGGTTCTGATTATC
1 TGACTATCGCAACGAGATTCTGACTATC
3509149 GCAACGAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (30 bp):
TGACTATCGCAACGAGATTCTGACTATCAC
Found at i:3510060 original size:24 final size:24
Alignment explanation
Indices: 3510009--3510062 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3509999 GTATTCGAAA
*
3510009 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
3510033 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
3510057 TTTGAT
1 TTTGAT
3510063 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:3512342 original size:18 final size:18
Alignment explanation
Indices: 3512327--3512361 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3512317 TCAAAATCGT
*
3512327 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
3512345 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
3512362 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:3512354 original size:12 final size:12
Alignment explanation
Indices: 3512315--3512354 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3512305 AGAAAAAGGC
*
3512315 AATCAAAATCGT
1 AATCAAAATCGA
*
3512327 AATCAAAATCGC
1 AATCAAAATCGA
*
3512339 AATCAAAATCAA
1 AATCAAAATCGA
3512351 AATC
1 AATC
3512355 CCAATCACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (12 bp):
AATCAAAATCGA
Found at i:3512361 original size:12 final size:12
Alignment explanation
Indices: 3512313--3512348 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3512303 CAAGAAAAAG
3512313 GCAATCAAAATC
1 GCAATCAAAATC
*
3512325 GTAATCAAAATC
1 GCAATCAAAATC
3512337 GCAATCAAAATC
1 GCAATCAAAATC
3512349 AAAATCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.19
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:3512484 original size:20 final size:20
Alignment explanation
Indices: 3512455--3512628 Score: 182
Period size: 20 Copynumber: 9.1 Consensus size: 20
3512445 GAAATAATCA
*
3512455 CAACGTGAATTTGACTATCG
1 CAACGCGAATTTGACTATCG
3512475 CAACGCGAATTTGACTATCG
1 CAACGCGAATTTGACTATCG
3512495 CAACGCGAATTTGACTATCG
1 CAACGCGAATTTGACTATCG
* *
3512515 CAACGAGAATTTAACTATCG
1 CAACGCGAATTTGACTATCG
* *
3512535 CAACGTGAATTTGATTATCG
1 CAACGCGAATTTGACTATCG
* * *
3512555 CAACGGGTATTCGACTATCG
1 CAACGCGAATTTGACTATCG
*
3512575 CAACGAGAA----A--ATCG
1 CAACGCGAATTTGACTATCG
* * *
3512589 CAAAGCGTATTAGACTATCG
1 CAACGCGAATTTGACTATCG
*
3512609 CAACGCGAA-TTGACTTTCG
1 CAACGCGAATTTGACTATCG
3512628 C
1 C
3512629 GTTGCGATTT
Statistics
Matches: 129, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 9 0.07
20 108 0.84
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
CAACGCGAATTTGACTATCG
Found at i:3512647 original size:20 final size:20
Alignment explanation
Indices: 3512622--3512660 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3512612 CGCGAATTGA
*
3512622 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
3512642 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
3512661 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:3512813 original size:29 final size:28
Alignment explanation
Indices: 3512779--3512833 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
3512769 ATAAGAATTA
*
3512779 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
3512808 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
3512834 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:3512834 original size:14 final size:14
Alignment explanation
Indices: 3512774--3512835 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
3512764 CACAAATAAG
*
3512774 AATTATTTACACATC
1 AATT-TTTACAAATC
**
3512789 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
3512804 AACTTTTACAAATC
1 AATTTTTACAAATC
3512818 AATTTTTACAAATC
1 AATTTTTACAAATC
3512832 AATT
1 AATT
3512836 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:3514854 original size:18 final size:18
Alignment explanation
Indices: 3514831--3514897 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 18
3514821 GAAACTTAAA
*
3514831 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
3514849 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
3514869 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
3514889 ATCGCAACG
1 ATCGCAACG
3514898 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.27
20 32 0.73
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:3514867 original size:20 final size:20
Alignment explanation
Indices: 3514842--3514897 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3514832 TCGCAACACG
3514842 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
3514862 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
3514882 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
3514898 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:3514965 original size:20 final size:20
Alignment explanation
Indices: 3514940--3514987 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3514930 GCGATTCTTT
3514940 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3514960 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3514980 CGTTGCGA
1 CGTTGCGA
3514988 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3515159 original size:18 final size:18
Alignment explanation
Indices: 3515136--3515185 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
3515126 TTTACTAAGC
3515136 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
3515154 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
3515172 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
3515186 TATGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:3516178 original size:20 final size:20
Alignment explanation
Indices: 3516132--3516187 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3516122 TATGAAACTT
*
3516132 AAAACCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
3516152 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
3516172 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
3516188 TTTGACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3516193 original size:20 final size:20
Alignment explanation
Indices: 3516137--3516206 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
3516127 AACTTAAAAC
* **
3516137 CGCAACACGAAAATGAAAAT
1 CGCAACGCGAAAATGACTAT
*
3516157 CGCAACACGAAAATGACTAT
1 CGCAACGCGAAAATGACTAT
**
3516177 CGCAACGCGAATTTGACTAT
1 CGCAACGCGAAAATGACTAT
* *
3516197 TGTAACGCGA
1 CGCAACGCGA
3516207 GAATCGCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAT
Found at i:3516646 original size:22 final size:22
Alignment explanation
Indices: 3516619--3516660 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3516609 GAGATAGACG
3516619 GATTTC-TCCGGAGATGGGGACT
1 GATTTCGT-CGGAGATGGGGACT
3516641 GATTTCGTCGGAGATGGGGA
1 GATTTCGTCGGAGATGGGGA
3516661 TGGATGTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.19, C:0.14, G:0.40, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACT
Found at i:3516851 original size:20 final size:20
Alignment explanation
Indices: 3516822--3516894 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
3516812 CGCTTTGAAA
*
3516822 ATCGCATTGCGATAGTCAGC
1 ATCGCGTTGCGATAGTCAGC
3516842 ATCGCGTTGCGATAGTCAGC
1 ATCGCGTTGCGATAGTCAGC
** *
3516862 ATCTAGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGC
3516882 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
3516895 TTACATATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGC
Found at i:3516906 original size:20 final size:20
Alignment explanation
Indices: 3516883--3516966 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
3516873 ATAGTCAGAA
*
3516883 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
3516903 TCGCATTGCAATTTACATAT
1 TCGCATTGCGATTTACATAT
*
3516923 TTGCATTGC-A--T--AT-T
1 TCGCATTGCGATTTACATAT
3516937 T-GCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
3516956 TCGCATTGCGA
1 TCGCATTGCGA
3516967 ATTCGGAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.13
14 3 0.06
15 2 0.04
16 1 0.02
17 1 0.02
18 2 0.04
19 3 0.06
20 35 0.65
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:3516936 original size:13 final size:13
Alignment explanation
Indices: 3516918--3516944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3516908 TTGCAATTTA
3516918 CATATTTGCATTG
1 CATATTTGCATTG
3516931 CATATTTGCATTG
1 CATATTTGCATTG
3516944 C
1 C
3516945 GATTTACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (13 bp):
CATATTTGCATTG
Found at i:3516942 original size:33 final size:33
Alignment explanation
Indices: 3516898--3516964 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3516888 TTGCGATTTA
*
3516898 CATATTCGCATTGCAATTTACATATTTGCATTG
1 CATATTCGCATTGCAATTTACATATTCGCATTG
* *
3516931 CATATTTGCATTGCGATTTACATATTCGCATTG
1 CATATTCGCATTGCAATTTACATATTCGCATTG
3516964 C
1 C
3516965 GAATTCGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (33 bp):
CATATTCGCATTGCAATTTACATATTCGCATTG
Found at i:3516987 original size:21 final size:21
Alignment explanation
Indices: 3516963--3517008 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3516953 TATTCGCATT
3516963 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
3516984 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
3517005 GCGA
1 GCGA
3517009 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:3520329 original size:30 final size:31
Alignment explanation
Indices: 3520267--3520330 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
3520257 CAAAGGTGTT
*
3520267 AAATAAAAATAAAATTTGAATAATATCCGGC
1 AAATAAAAATAAAATTTGAACAATATCCGGC
* * *
3520298 AAATAAAAAT-AAGTTTGAACAGTATCGGGC
1 AAATAAAAATAAAATTTGAACAATATCCGGC
3520328 AAA
1 AAA
3520331 AATAAGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (31 bp):
AAATAAAAATAAAATTTGAACAATATCCGGC
Found at i:3521237 original size:25 final size:24
Alignment explanation
Indices: 3521209--3521284 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 24
3521199 TTTTAATGAA
3521209 TAATTATAAATTTTTATATAAATCT
1 TAATTATAAATTTTTATAT-AATCT
*
3521234 TAA-T-TAAATTTTT-T-TAATCGA
1 TAATTATAAATTTTTATATAATC-T
3521255 TAATCTATAAA-TTTTATATGAATCT
1 TAAT-TATAAATTTTTATAT-AATCT
*
3521280 CAATT
1 TAATT
3521285 GAATCTTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
20 4 0.10
21 4 0.10
22 1 0.02
23 14 0.34
24 7 0.17
25 7 0.17
26 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.50
Consensus pattern (24 bp):
TAATTATAAATTTTTATATAATCT
Found at i:3521258 original size:46 final size:47
Alignment explanation
Indices: 3521198--3521332 Score: 145
Period size: 46 Copynumber: 2.9 Consensus size: 47
3521188 TTTATTATTA
3521198 TTTTTAATGAATAATTATAAATTTTTATATAAATCTTAATTAAAT-T
1 TTTTTAATGAATAATTATAAATTTTTATATAAATCTTAATTAAATCT
* * *
3521244 TTTTTAATCG-ATAATCTATAAA-TTTTATATGAATCTCAATTGAATCT
1 TTTTTAAT-GAATAAT-TATAAATTTTTATATAAATCTTAATTAAATCT
* * *
3521291 TCTTGAA-GAATAATTTATAAATTTTCATATAAAT-TCTAATTA
1 TTTTTAATGAATAA-TTATAAATTTTTATATAAATCT-TAATTA
3521333 GGTTATCACA
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
45 1 0.01
46 44 0.60
47 28 0.38
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (47 bp):
TTTTTAATGAATAATTATAAATTTTTATATAAATCTTAATTAAATCT
Found at i:3523573 original size:2 final size:2
Alignment explanation
Indices: 3523566--3523598 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3523556 TTGTAGGTAT
3523566 TA TA TA TA 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 TA TA TA TA T
3523599 GCAAACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3536931 original size:14 final size:14
Alignment explanation
Indices: 3536914--3536958 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3536904 AGTGAAAATG
3536914 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
**
3536928 AAAAATAAAAAATG
1 AAAAATAAAAAAAA
3536942 AAAAATGGAAAAAAAA
1 AAAAAT--AAAAAAAA
3536958 A
1 A
3536959 GGGTTCAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 18 0.72
16 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (14 bp):
AAAAATAAAAAAAA
Found at i:3536948 original size:7 final size:7
Alignment explanation
Indices: 3536908--3536947 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3536898 AAAATGAGTG
*
3536908 AAAATGA
1 AAAATAA
3536915 AAAATAA
1 AAAATAA
*
3536922 AAAAAAA
1 AAAATAA
3536929 AAAATAA
1 AAAATAA
*
3536936 AAAATGA
1 AAAATAA
3536943 AAAAT
1 AAAAT
3536948 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (7 bp):
AAAATAA
Done.