Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005050.1 Hibiscus syriacus cultivar Beakdansim tig00011339_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: 81114
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:521 original size:42 final size:42
Alignment explanation
Indices: 263--575 Score: 357
Period size: 43 Copynumber: 7.4 Consensus size: 42
253 AGCAAAAGAT
*
263 CCTGGGGAAACTGTAAGGCTTACCC-TGCACACAA-AAAGGAA
1 CCTGGGG-AACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
* * * *
304 CATGGGAAAATGTAAGGCTTACCCTTGCACACAACAAAGGAA
1 CCTGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
* * * * *
346 ACTGGGAGAACTATAAGGTTTATCCTTGCACACAGCAAAGGTG-
1 CCTGGG-GAACTGTAAGGCTTACCCTTGCACACAACAAAGG-GA
* *
389 CCTGGGGGAATTATAAGGCTTACCCTTGCACACAACAAAGGGA
1 CCT-GGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
* *
432 CCTAAGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
1 CCT-GGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
* *
475 CCTGGGCGAACTGTAAGGCTTACCC-TGCACACAGCAAAGGGG
1 CCTGGG-GAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
*
517 CCTGGGGAAACTGTAAGGC-TACCCTTGAACACAACAAAGGGA
1 CCTGGGG-AACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
559 CCTGGGGGAAACTGTAA
1 CCT-GGGG-AACTGTAA
576 CGTAATTAAT
Statistics
Matches: 235, Mismatches: 27, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
40 16 0.07
41 20 0.09
42 64 0.27
43 132 0.56
44 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (42 bp):
CCTGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGA
Found at i:3330 original size:13 final size:13
Alignment explanation
Indices: 3308--3337 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3298 TTTCAGTCAA
3308 CGGG-CAACGGGT
1 CGGGTCAACGGGT
3320 CGGGTCAACGGGT
1 CGGGTCAACGGGT
3333 CGGGT
1 CGGGT
3338 TATGACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.13, C:0.23, G:0.50, T:0.13
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:5284 original size:43 final size:42
Alignment explanation
Indices: 5141--5285 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 42
5131 AGGTCTTATA
* * * *
5141 CTTGCACATAGCAAAAGAGCCATGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGA-ACATTGGAAACTGTAAGGCTTACC
* *
5184 CTTGCACACAGCAAAGGAACCTTGGAAACTGTAAGGCTTAGC
1 CTTGCACACAGCAAAGGAACATTGGAAACTGTAAGGCTTACC
*
5226 CTTGCACACAGCAAAGGAA-ATTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACATT--GGAAACTGTAAGGCTTACC
5269 CTTGCACACAGCAAAGG
1 CTTGCACACAGCAAAGG
5286 TGTCTGGGGG
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
41 2 0.02
42 39 0.43
43 50 0.55
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (42 bp):
CTTGCACACAGCAAAGGAACATTGGAAACTGTAAGGCTTACC
Found at i:5294 original size:43 final size:43
Alignment explanation
Indices: 5168--5304 Score: 188
Period size: 43 Copynumber: 3.2 Consensus size: 43
5158 AGCCATGGGA
* * *
5168 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-TGGA
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGAATCTGGGGG
*
5210 AACTGTAAGGCTTAGCCTTGCACACAGCAAAGGAAAT-TGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGG-AATCTGGGGG
**
5253 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGTGTCTGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGAATCTGGGGG
5296 AAACTGTAA
1 -AACTGTAA
5305 CTGTAATTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
42 34 0.40
43 42 0.50
44 8 0.10
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (43 bp):
AACTGTAAGGCTTACCCTTGCACACAGCAAAGGAATCTGGGGG
Found at i:5383 original size:28 final size:27
Alignment explanation
Indices: 5316--5383 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
5306 TGTAATTAAT
* *
5316 CTATATTTAGAAATCATGTACAAAAATA
1 CTATA-TTAGAAACCATATACAAAAATA
*
5344 CTGTAATTAGAAACCATAT-CAAAATATA
1 CTAT-ATTAGAAACCATATACAAAA-ATA
5372 CTATATTCAGAA
1 CTATATT-AGAA
5384 CATCGGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.24
28 24 0.73
29 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (27 bp):
CTATATTAGAAACCATATACAAAAATA
Found at i:8131 original size:5 final size:5
Alignment explanation
Indices: 8110--8149 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
8100 GTCAGGTAAA
* *
8110 CGGGT CGGTT TGGGT CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT
8150 TATGACAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.25
Consensus pattern (5 bp):
CGGGT
Found at i:11976 original size:19 final size:19
Alignment explanation
Indices: 11952--11989 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11942 TTTATTGGAT
*
11952 GTCCGATAATGGGAAAGAC
1 GTCCGACAATGGGAAAGAC
11971 GTCCGACAATGGGAAAGAC
1 GTCCGACAATGGGAAAGAC
11990 CGACGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.13
Consensus pattern (19 bp):
GTCCGACAATGGGAAAGAC
Found at i:13659 original size:7 final size:7
Alignment explanation
Indices: 13647--13672 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13637 AAAATAGCAT
13647 CGGTCAA
1 CGGTCAA
13654 CGGTCAA
1 CGGTCAA
13661 CGGTCAA
1 CGGTCAA
13668 CGGTC
1 CGGTC
13673 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:20791 original size:29 final size:29
Alignment explanation
Indices: 20747--20814 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
20737 ATTTTTGCAG
*
20747 AAATAGCACCTTTTTTAAATTAATTACTA
1 AAATAGCACCTATTTTAAATTAATTACTA
*
20776 AAATAGCACCTATTTTGAATTAATTACTA
1 AAATAGCACCTATTTTAAATTAATTACTA
20805 AAATAGCACC
1 AAATAGCACC
20815 GGTCAACGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATAGCACCTATTTTAAATTAATTACTA
Found at i:39159 original size:23 final size:23
Alignment explanation
Indices: 39120--39163 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39110 AGGGTTTTTT
39120 TAAAGTTATTTTGAATTAATAAA
1 TAAAGTTATTTTGAATTAATAAA
*
39143 TAAAG-TATTATTTAATTAATA
1 TAAAGTTATT-TTGAATTAATA
39164 CAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
TAAAGTTATTTTGAATTAATAAA
Found at i:49070 original size:24 final size:24
Alignment explanation
Indices: 49043--49113 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
49033 AAACAAAACT
49043 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
49067 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* * * *
49091 CATGTCAAATATTATAACAGAAT
1 CAGGTCAAGTATCATATCAGAAT
49114 TCAAATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:64155 original size:24 final size:23
Alignment explanation
Indices: 64128--64215 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
64118 ATTTCTGACT
*
64128 TGAATTCTGTTATGATACATTACC
1 TGAATTCTGTTATGATAC-TTATC
* * *
64152 TGAATTCTGTTTTGATTTCTGATC
1 TGAATTCTGTTATGA-TACTTATC
* *
64176 TGGATTCTGCTATGATATCTTATC
1 TGAATTCTGTTATGATA-CTTATC
*
64200 TGAATTCTGTTTTGAT
1 TGAATTCTGTTATGAT
64216 TTCTGATATC
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 47 0.94
25 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTATGATACTTATC
Found at i:64190 original size:48 final size:49
Alignment explanation
Indices: 64118--64222 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 49
64108 ATTTTATCTA
*
64118 ATTTCTGA-CTTGAATTCTGTTATGATA-CATTACCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGCTATGATATC-TTACCTGAATTCTGTTTTG
* *
64166 ATTTCTGATC-TGGATTCTGCTATGATATCTTATCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTCTGCTATGATATCTTACCTGAATTCTGTTTTG
64214 ATTTCTGAT
1 ATTTCTGAT
64223 ATCTCCATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTCTGCTATGATATCTTACCTGAATTCTGTTTTG
Found at i:68613 original size:24 final size:24
Alignment explanation
Indices: 68578--68649 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
68568 GATACATTAC
* *
68578 CTGAATTTTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
68602 CTGGATTCTGTTATGATATCTTAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
68626 CTGAATTCCGTTTTGATTTTTGAT
1 CTGAATTCTGTTATGATTTCTGAT
68650 ATCTCCATTT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:68643 original size:48 final size:48
Alignment explanation
Indices: 68558--68649 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
68548 TTCAACTTGA
**
68558 ATTCTGCTATGATACATTACCTGAATTTTGTTCTGATTTCTGATCTGG
1 ATTCTGCTATGATACATTACCTGAATTCCGTTCTGATTTCTGATCTGG
* * * *
68606 ATTCTGTTATGATATC-TTATCTGAATTCCGTTTTGATTTTTGAT
1 ATTCTGCTATGATA-CATTACCTGAATTCCGTTCTGATTTCTGAT
68650 ATCTCCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
48 36 0.97
49 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
ATTCTGCTATGATACATTACCTGAATTCCGTTCTGATTTCTGATCTGG
Found at i:68813 original size:2 final size:2
Alignment explanation
Indices: 68806--68836 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68796 AGGATATGGG
68806 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 T
68837 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77439 original size:38 final size:38
Alignment explanation
Indices: 77365--77439 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
77355 TCGTTCCGAG
**
77365 TTTATGAAATCGAGCTCTCCGCGGTCAAAGTTTTTGAT
1 TTTATGAAATCGAGCTCTCCGCGGTCAAAGAATTTGAT
*
77403 TTTATGAAATCGAGCTCTCCGCCGTTCAAA-AATTTGA
1 TTTATGAAATCGAGCTCTCCG-CGGTCAAAGAATTTGA
77440 ACCGATCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 26 0.79
39 7 0.21
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (38 bp):
TTTATGAAATCGAGCTCTCCGCGGTCAAAGAATTTGAT
Found at i:77631 original size:7 final size:7
Alignment explanation
Indices: 77619--77650 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
77609 ACCCGACCCA
77619 TTGACCG
1 TTGACCG
77626 TTGACCG
1 TTGACCG
*
77633 TTGACCA
1 TTGACCG
77640 TTGACCG
1 TTGACCG
77647 TTGA
1 TTGA
77651 TCGTGTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (7 bp):
TTGACCG
Found at i:77642 original size:21 final size:22
Alignment explanation
Indices: 77616--77659 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
77606 TTGACCCGAC
77616 CCATTGACCGTTGACCGT-TGA
1 CCATTGACCGTTGACCGTGTGA
*
77637 CCATTGACCGTTGATCGTGTGA
1 CCATTGACCGTTGACCGTGTGA
77659 C
1 C
77660 ATTTTAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (22 bp):
CCATTGACCGTTGACCGTGTGA
Found at i:77709 original size:29 final size:29
Alignment explanation
Indices: 77654--77709 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
77644 CCGTTGATCG
* * *
77654 TGTGACATTTTAGTAATTATTTTGAAACT
1 TGTGACATTTGAGTAATTAATTCGAAACT
77683 TGTGACATATTGAG-AATTAATTCGAAA
1 TGTGACAT-TTGAGTAATTAATTCGAAA
77710 AGGGTGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (29 bp):
TGTGACATTTGAGTAATTAATTCGAAACT
Found at i:77756 original size:27 final size:27
Alignment explanation
Indices: 77714--77769 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
77704 TCGAAAAGGG
* *
77714 TGTTATTTTTTGTAATTTTTTTAAAAAA
1 TGTTATTTTTCGTAA-TTTTTGAAAAAA
77742 TGTTA-TTTTCGTAATTTTTGAAAAAA
1 TGTTATTTTTCGTAATTTTTGAAAAAA
77768 TG
1 TG
77770 ACATTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 8 0.31
28 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (27 bp):
TGTTATTTTTCGTAATTTTTGAAAAAA
Found at i:77775 original size:26 final size:27
Alignment explanation
Indices: 77720--77781 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
77710 AGGGTGTTAT
* * **
77720 TTTTTGTAATTTTTTTAAAAAATGTTA
1 TTTTAGTAATTTTTTGAAAAAATGACA
*
77747 TTTTCGTAA-TTTTTGAAAAAATGACA
1 TTTTAGTAATTTTTTGAAAAAATGACA
77773 TTTTAGTAA
1 TTTTAGTAA
77782 ATATTTTGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (27 bp):
TTTTAGTAATTTTTTGAAAAAATGACA
Done.