Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008344.1 Hibiscus syriacus cultivar Beakdansim tig00111071_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: 332991
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:277453 original size:5 final size:5
Alignment explanation
Indices: 277430--277477 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
277420 AGACCTGGAT
*
277430 AATAA AACAA AA-AA TAATAA AATAA AATAA AAT-A AAT-A AAT-A AATAA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATAA
277477 A
1 A
277478 TAACTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
4 14 0.36
5 23 0.59
6 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:277572 original size:35 final size:36
Alignment explanation
Indices: 277506--277602 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 36
277496 TTATTATAAT
*
277506 AAAAATATTTTCCAAAAAACTATATAATATATATTTCAA
1 AAAAATATTTT-C--AAAATTATATAATATATATTTCAA
* ***
277545 AAAAATATTTT-AAAATTATATATTATATATTTTTT
1 AAAAATATTTTCAAAATTATATAATATATATTTCAA
*
277580 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
277603 GTTTTCGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 29 0.57
36 11 0.22
39 11 0.22
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAAATATTTTCAAAATTATATAATATATATTTCAA
Found at i:277643 original size:25 final size:25
Alignment explanation
Indices: 277603--277652 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
277593 AAATTATATA
*
277603 GTTTTCGAAAATATTTTAAAACTAT
1 GTTTTCGAAAATATTTCAAAACTAT
277628 GTTTTC-AAAATGATTTCAAAACTAT
1 GTTTTCGAAAAT-ATTTCAAAACTAT
277653 ATATTATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (25 bp):
GTTTTCGAAAATATTTCAAAACTAT
Found at i:277706 original size:38 final size:37
Alignment explanation
Indices: 277629--277855 Score: 172
Period size: 38 Copynumber: 6.2 Consensus size: 37
277619 TAAAACTATG
* * *
277629 TTTTCAAAATG-ATTTC-AAAACTATATATTATA-AGTA
1 TTTTCAAAATGTTTTTCAAAAACCATATAATATATA--A
277665 TTTTCAAAATGTTTTTCAAAAACCATATAATATATACA
1 TTTTCAAAATGTTTTTCAAAAACCATATAATATATA-A
*
277703 TTTTTAAAATGTTTTTCAAAAA--ATAT-ATA-AT-A
1 TTTTCAAAATGTTTTTCAAAAACCATATAATATATAA
* * *
277735 TTTTC-AAACGTTTTTCAAAAACTATATATTATATATAC
1 TTTTCAAAATGTTTTTCAAAAACCATATA--ATATATAA
* * *
277773 TTTTCAAAATATTTTT--AAAATCATATATTATATAA
1 TTTTCAAAATGTTTTTCAAAAACCATATAATATATAA
* * *
277808 GTTTTCTAAAAATATTTTT-AAAAGCCATATATTATATAA
1 -TTTTC--AAAATGTTTTTCAAAAACCATATAATATATAA
*
277847 TTTCCAAAA
1 TTTTCAAAA
277856 ATGATTTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 30
0.77 0.08 0.15
Matches are distributed among these distances:
31 15 0.09
32 5 0.03
33 4 0.03
34 2 0.01
35 9 0.06
36 27 0.17
37 15 0.09
38 56 0.35
39 26 0.16
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTCAAAATGTTTTTCAAAAACCATATAATATATAA
Found at i:277728 original size:31 final size:31
Alignment explanation
Indices: 277693--277762 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
277683 AAAACCATAT
*
277693 AATATATACAT-TTTTAAAATGTTTTTCAAAA
1 AATATATA-ATATTTTAAAACGTTTTTCAAAA
*
277724 AATATATAATATTTTCAAACGTTTTTCAAAA
1 AATATATAATATTTTAAAACGTTTTTCAAAA
*
277755 ACTATATA
1 AATATATA
277763 TTATATATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (31 bp):
AATATATAATATTTTAAAACGTTTTTCAAAA
Found at i:277755 original size:69 final size:70
Alignment explanation
Indices: 277657--277792 Score: 188
Period size: 69 Copynumber: 1.9 Consensus size: 70
277647 AACTATATAT
* * *
277657 TATAAGTATTTTCAAAATGTTTTTCAAAAACCATATA-ATATATACATTTTTAAAATGTTTTTCA
1 TATAAGTATTTTCAAAACGTTTTTCAAAAACCATATATATATATAC-TTTTCAAAATATTTTT-A
277721 AAAAATA
64 AAAAATA
*
277728 TATAA-TATTTTC-AAACGTTTTTCAAAAACTATATATTATATATACTTTTCAAAATATTTTTAA
1 TATAAGTATTTTCAAAACGTTTTTCAAAAACCATATA-TATATATACTTTTCAAAATATTTTTAA
277791 AA
65 AA
277793 TCATATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
69 25 0.42
70 21 0.36
71 13 0.22
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (70 bp):
TATAAGTATTTTCAAAACGTTTTTCAAAAACCATATATATATATACTTTTCAAAATATTTTTAAA
AAATA
Found at i:277931 original size:2 final size:2
Alignment explanation
Indices: 277924--277981 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
277914 AATGAGTGTC
277924 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
277966 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
277982 AATCAAAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278398 original size:390 final size:392
Alignment explanation
Indices: 277969--278753 Score: 1414
Period size: 391 Copynumber: 2.0 Consensus size: 392
277959 ATATATATAT
277969 ATATATATATATAAATCAAAAGAATTATTATGATTTAAG-TTTGATATATTTTAATTATCATTCT
1 ATATATATATATAAATCAAAAGAATTATTATGATTTAAGTTTTGATATATTTTAATTATCATTCT
278033 ATTTAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTTGG
66 ATTTAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTTGG
278098 CAATTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAA
131 CAATTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAA
* *
278163 TTTTAATTTTAATCATAAATCTGAATTTAATTAAATAACGTCATTTAATTTTTATTAT-TGATAA
196 TTTTAATTTTAATCAGAAATCTAAATTTAATTAAATAACGTCATTTAATTTTTATTATAT-ATAA
* *
278227 ACTAAATCATTCATATTAATATAAGGGCAAATTATATATTTAGTACCTAATCTATCAGTTTTGAT
260 ACTAAATCATTCATATTAATAAAAGGGCAAATTATATATTTAGTACCTAAACTATCAGTTTTGAT
* *
278292 CTGTTTTAGTACCTAAACTTTTAATTTTTTTAAAACCATATCTAAAGTTTACTTTTTGTTTCATT
325 CTGTTTTAGTACCTAAACTTTTAATTTTTTTAAAACCATACCTAAAGTTTACTTTTTATTTCATT
278357 TTA
390 TTA
*
278360 ATATATATAT-TAAATCAAAAGAATTATTATGATTTAAGTTTTGATATATTTTAATTATCATTTT
1 ATATATATATATAAATCAAAAGAATTATTATGATTTAAGTTTTGATATATTTTAATTATCATTCT
*
278424 ATTTAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTGTCACTTTTTTTTGG
66 ATTTAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTTGG
**
278489 CAATTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTTGTATTTTAAATCATTAATTTAA
131 CAATTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAA
* *
278554 TTTTAATTTTAATCAGAAGTCTAAATTTAATTAAATAACTTCATTTAATTTTTATTATATATAAA
196 TTTTAATTTTAATCAGAAATCTAAATTTAATTAAATAACGTCATTTAATTTTTATTATATATAAA
*
278619 CTAAATCATTCATGTTAATAAAAGGGCAAATTATATATTTAGTACCTAAACTATCAGTTTTGATC
261 CTAAATCATTCATATTAATAAAAGGGCAAATTATATATTTAGTACCTAAACTATCAGTTTTGATC
*
278684 TGTTTTAGTACCTAAACTTTTAATTTTTTTAAAACCATACCTAAAGTTTATTTTTTATTTCATTT
326 TGTTTTAGTACCTAAACTTTTAATTTTTTTAAAACCATACCTAAAGTTTACTTTTTATTTCATTT
278749 TA
391 TA
278751 ATA
1 ATA
278754 CACCGTCGTT
Statistics
Matches: 378, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
390 28 0.07
391 349 0.92
392 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (392 bp):
ATATATATATATAAATCAAAAGAATTATTATGATTTAAGTTTTGATATATTTTAATTATCATTCT
ATTTAATTGAAAGATTTCGTTAGATGTCAATGCCTAATGGCATGCCTTTTATCACTTTTTTTTGG
CAATTTATACGTGGATCGCTTCCATAAAAAGAATGGATGATTCATATTTTAAATCATTAATTTAA
TTTTAATTTTAATCAGAAATCTAAATTTAATTAAATAACGTCATTTAATTTTTATTATATATAAA
CTAAATCATTCATATTAATAAAAGGGCAAATTATATATTTAGTACCTAAACTATCAGTTTTGATC
TGTTTTAGTACCTAAACTTTTAATTTTTTTAAAACCATACCTAAAGTTTACTTTTTATTTCATTT
TA
Found at i:288591 original size:56 final size:57
Alignment explanation
Indices: 288520--288638 Score: 215
Period size: 56 Copynumber: 2.1 Consensus size: 57
288510 ATAGGAGATG
*
288520 AAAT-TATAAAATTGTAGGGAACGAAAATGTATTATCAAACATAAAATGTT-AAAAA
1 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
288575 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
1 AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
288632 AAATCTA
1 AAATCTA
288639 AACTGTACAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 4 0.07
56 45 0.74
57 12 0.20
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.26
Consensus pattern (57 bp):
AAATCTATAAAATTGTAGGGAACGAAAACGTATTATCAAACATAAAATGTTAAAAAA
Found at i:290089 original size:58 final size:57
Alignment explanation
Indices: 289966--290075 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
289956 GATTATAGGA
* * * *
289966 CATTATTTTGTTTAGTCATCCGACTATTAAGAGTTACAAAATGATCTTTGACTATAAG
1 CATTGTTTTGTTGAGTCATCCGACTATTAAAAGTTACAAAATAATCTTTGAC-ATAAG
290024 CATTGTTTTGTTGAGTCCAT-CGACTATTAAAAGTTACAAAATAATCATTTGA
1 CATTGTTTTGTTGAGT-CATCCGACTATTAAAAGTTACAAAATAATC-TTTGA
290076 ATATTCATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
58 38 0.83
59 8 0.17
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (57 bp):
CATTGTTTTGTTGAGTCATCCGACTATTAAAAGTTACAAAATAATCTTTGACATAAG
Found at i:296901 original size:105 final size:105
Alignment explanation
Indices: 296727--297390 Score: 1169
Period size: 105 Copynumber: 6.4 Consensus size: 105
296717 GTGTTGTTTC
*
296727 GAGTCCAATACCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
296792 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
296832 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
296897 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGCCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
296937 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
297002 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
297042 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
297107 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* * *
297147 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
297212 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
297252 GAGTCCAATATCCTTCG-T-T---G-TGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
297311 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
297351 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
297391 GGTAAAACCT
Statistics
Matches: 538, Mismatches: 15, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
99 96 0.18
100 2 0.00
101 1 0.00
103 1 0.00
104 2 0.00
105 436 0.81
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:319635 original size:22 final size:22
Alignment explanation
Indices: 319607--319652 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
319597 CATTATGCCC
319607 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
319629 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
319651 AT
1 AT
319653 GCTTCTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (22 bp):
ATAGTTAACACAACACAGAACA
Found at i:325823 original size:21 final size:21
Alignment explanation
Indices: 325798--325837 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
325788 GTATTTTTGG
*
325798 GTGTCAGTAACGGTATTGTAT
1 GTGTCAGTAACGATATTGTAT
*
325819 GTGTCAGTATCGATATTGT
1 GTGTCAGTAACGATATTGT
325838 TCTTATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40
Consensus pattern (21 bp):
GTGTCAGTAACGATATTGTAT
Done.