Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001614.1 Hibiscus syriacus cultivar Beakdansim tig00003205_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: 56176
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6826 original size:15 final size:15
Alignment explanation
Indices: 6806--6835 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6796 GAATTGCCTG
6806 AAATGGAGACCTTTT
1 AAATGGAGACCTTTT
6821 AAATGGAGACCTTTT
1 AAATGGAGACCTTTT
6836 GGCAAACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
AAATGGAGACCTTTT
Found at i:8431 original size:29 final size:30
Alignment explanation
Indices: 8389--8445 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
8379 CTAAGATACC
*
8389 TATTTTGACCAAAAA-TAATTTTAGGTATT
1 TATTTTGACCAAAAATTAACTTTAGGTATT
*
8418 TATTTTGATCAAAAATTAACTTTAGGTA
1 TATTTTGACCAAAAATTAACTTTAGGTA
8446 CCTATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (30 bp):
TATTTTGACCAAAAATTAACTTTAGGTATT
Found at i:8452 original size:30 final size:29
Alignment explanation
Indices: 8385--8453 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
8375 CCTACTAAGA
*
8385 TACCTATTTTGACCAAAAATAATTTTAGG
1 TACCTATTTTGACCAAAAATAACTTTAGG
** *
8414 TATTTATTTTGATCAAAAATTAACTTTAGG
1 TACCTATTTTGACCAAAAA-TAACTTTAGG
8444 TACCTATTTT
1 TACCTATTTT
8454 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
TACCTATTTTGACCAAAAATAACTTTAGG
Found at i:14784 original size:29 final size:29
Alignment explanation
Indices: 14750--14842 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
14740 AATGATACTG
*
14750 ATTTAAGGATTAATATAAAATATTCTAAA
1 ATTTAAGAATTAATATAAAATATTCTAAA
* * * *
14779 ATTTAAGAATCAATTTAAAATGAGATC-ATA
1 ATTTAAGAATTAATATAAAAT-A-TTCTAAA
*
14809 ATTTAAGAATTAATATAAAATATTATAAA
1 ATTTAAGAATTAATATAAAATATTCTAAA
14838 ATTTA
1 ATTTA
14843 TAAACCAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.02
29 26 0.51
30 22 0.43
31 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (29 bp):
ATTTAAGAATTAATATAAAATATTCTAAA
Found at i:20895 original size:2 final size:2
Alignment explanation
Indices: 20890--20917 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20880 ATATATATAT
20890 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20918 TTAACGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21590 original size:25 final size:26
Alignment explanation
Indices: 21535--21599 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
21525 TATAAATTTT
*
21535 AATTAAATTATTTTTTTTCAATAATA
1 AATTAAATTATTATTTTTCAATAATA
* *
21561 AATTAAATTATTATTTTT-ATTGATA
1 AATTAAATTATTATTTTTCAATAATA
*
21586 GATTAAATTATTAT
1 AATTAAATTATTAT
21600 GGCTGAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 18 0.51
26 17 0.49
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (26 bp):
AATTAAATTATTATTTTTCAATAATA
Found at i:23265 original size:77 final size:78
Alignment explanation
Indices: 23092--23437 Score: 565
Period size: 78 Copynumber: 4.5 Consensus size: 78
23082 AGGTTGTACT
* * * * *
23092 TCAGCATTGTCTTCCTTTTGTCGTTCCGAAACATTTACTGTCTCC-TTTGTTTTGCCTCGCTTCT
1 TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
23156 TTTCCCTTGATCC
66 TTTCCCTTGATCC
23169 TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
1 TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
23234 TTTCCCTTGATCC
66 TTTCCCTTGATCC
23247 TCAGCATTGTCTTC-TTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
1 TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
23311 TTTCCCTTGATCC
66 TTTCCCTTGATCC
* *
23324 TCATCATTGTCTTCTTTTTGTCGTTCTGAAACAGTTT-CAGTCTCCTTTTGTTTTACCTCGTTTC
1 TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACA-TTTGCAGTCTCCTTTTGTTTTGCCTCGTTTC
*
23388 TTTTCCCTTGACCC
65 TTTTCCCTTGATCC
*
23402 TCAGCATTGTCTTCTTTTTGTCATT-TGGAAACATTT
1 TCAGCATTGTCTTCTTTTTGTCGTTCT-GAAACATTT
23438 CTTGTACCTT
Statistics
Matches: 255, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
77 121 0.47
78 131 0.51
79 3 0.01
ACGTcount: A:0.12, C:0.26, G:0.13, T:0.49
Consensus pattern (78 bp):
TCAGCATTGTCTTCTTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCT
TTTCCCTTGATCC
Found at i:23355 original size:155 final size:154
Alignment explanation
Indices: 23092--23437 Score: 561
Period size: 155 Copynumber: 2.2 Consensus size: 154
23082 AGGTTGTACT
* *
23092 TCAGCATTGTCTTCCTTTTGTCGTTCCGAAACATTTACTGTCTCCTTTGTTTTGCCTCGCTTCTT
1 TCAGCATTGTCTT-CTTTTGTCGTTCTGAAACATTTACAGTCTCCTTTGTTTTGCCTCGCTTCTT
23157 TTCCCTTGATCCTCAGCATTGTCTTCTTTTTGTCGTTCTGAAACA-TTTGCAGTCTCCTTTTGTT
65 TTCCCTTGATCCTCAGCATTGTCTTCTTTTTGTCGTTCTGAAACAGTTT-CAGTCTCCTTTTGTT
* *
23221 TTGCCTCGTTTCTTTTCCCTTGATCC
129 TTACCTCGTTTCTTTTCCCTTGACCC
* *
23247 TCAGCATTGTCTTCTTTTGTCGTTCTGAAACATTTGCAGTCTCCTTTTGTTTTGCCTCGTTTCTT
1 TCAGCATTGTCTTCTTTTGTCGTTCTGAAACATTTACAGTCTCC-TTTGTTTTGCCTCGCTTCTT
*
23312 TTCCCTTGATCCTCATCATTGTCTTCTTTTTGTCGTTCTGAAACAGTTTCAGTCTCCTTTTGTTT
65 TTCCCTTGATCCTCAGCATTGTCTTCTTTTTGTCGTTCTGAAACAGTTTCAGTCTCCTTTTGTTT
23377 TACCTCGTTTCTTTTCCCTTGACCC
130 TACCTCGTTTCTTTTCCCTTGACCC
*
23402 TCAGCATTGTCTTCTTTTTGTCATT-TGGAAACATTT
1 TCAGCATTGTCTTC-TTTTGTCGTTCT-GAAACATTT
23438 CTTGTACCTT
Statistics
Matches: 179, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
154 28 0.16
155 130 0.73
156 21 0.12
ACGTcount: A:0.12, C:0.26, G:0.13, T:0.49
Consensus pattern (154 bp):
TCAGCATTGTCTTCTTTTGTCGTTCTGAAACATTTACAGTCTCCTTTGTTTTGCCTCGCTTCTTT
TCCCTTGATCCTCAGCATTGTCTTCTTTTTGTCGTTCTGAAACAGTTTCAGTCTCCTTTTGTTTT
ACCTCGTTTCTTTTCCCTTGACCC
Found at i:24156 original size:2 final size:2
Alignment explanation
Indices: 24149--24175 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24139 ATGAAAGTAC
24149 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
24176 AATTAATGAG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28598 original size:16 final size:16
Alignment explanation
Indices: 28577--28612 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28567 TCAGCAAAAG
28577 TACATTCATGAACTAT
1 TACATTCATGAACTAT
*
28593 TACATTGATGAACTAT
1 TACATTCATGAACTAT
28609 TACA
1 TACA
28613 GCAAAAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (16 bp):
TACATTCATGAACTAT
Found at i:30226 original size:29 final size:29
Alignment explanation
Indices: 30193--30266 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
30183 TATCGATAAT
30193 TTTAATGACCAAAATATAACTTTTGAAAC
1 TTTAATGACCAAAATATAACTTTTGAAAC
* * **
30222 TTTAATGACCAAAATGTAAGTTTTGACCC
1 TTTAATGACCAAAATATAACTTTTGAAAC
* *
30251 TTCAATGATCAAAATA
1 TTTAATGACCAAAATA
30267 AAAAATCGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (29 bp):
TTTAATGACCAAAATATAACTTTTGAAAC
Found at i:30665 original size:2 final size:2
Alignment explanation
Indices: 30658--30761 Score: 92
Period size: 2 Copynumber: 54.5 Consensus size: 2
30648 TAAAAATAAT
30658 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
* * * * * * *
30700 TA T- TA -A TA AA TT TA -A TT TA AA TA -A AA AA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
30738 -A TT TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30762 CCGGCCCGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
1 5 0.06
2 77 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30738 original size:19 final size:19
Alignment explanation
Indices: 30714--30753 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30704 AATAAATTTA
30714 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
30733 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
30752 AT
1 AT
30754 ATATATATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:31132 original size:29 final size:27
Alignment explanation
Indices: 31099--31158 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
31089 AAATCACATT
31099 AATATTTTAAACATAAAATTATTATAATA
1 AATATTTTAAACATAAAA-TATTATAA-A
* *
31128 AATATTTTAAATATAAAATATTTTAAA
1 AATATTTTAAACATAAAATATTATAAA
31155 AATA
1 AATA
31159 AATATCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 7 0.24
29 17 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATTTTAAACATAAAATATTATAAA
Found at i:31148 original size:16 final size:15
Alignment explanation
Indices: 31099--31160 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 15
31089 AAATCACATT
31099 AATATTTTAAACATAA
1 AATATTTTAAA-ATAA
* *
31115 AAT-TATTATAAT-A
1 AATATTTTAAAATAA
31128 AATATTTTAAATATAA
1 AATATTTTAAA-ATAA
31144 AATATTTTAAAAATAA
1 AATATTTT-AAAATAA
31160 A
1 A
31161 TATCATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.11
14 7 0.18
15 7 0.18
16 17 0.45
17 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATTTTAAAATAA
Found at i:38712 original size:23 final size:23
Alignment explanation
Indices: 38680--38750 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
38670 TCGAAAAATA
* * *
38680 TGTCATAAAGACAGAGATAAACG
1 TGTCACAAAGACAAACATAAACG
* *
38703 TGTCACAAAGACAAATATAAGCG
1 TGTCACAAAGACAAACATAAACG
*
38726 TG-CAACACAGACAAACATAAACG
1 TGTC-ACAAAGACAAACATAAACG
38749 TG
1 TG
38751 CAACACATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (23 bp):
TGTCACAAAGACAAACATAAACG
Found at i:38751 original size:23 final size:23
Alignment explanation
Indices: 38696--38757 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
38686 AAAGACAGAG
* *
38696 ATAAACGTGTC-ACAAAGACAAAT
1 ATAAACGTG-CAACACAGACAAAC
*
38719 ATAAGCGTGCAACACAGACAAAC
1 ATAAACGTGCAACACAGACAAAC
38742 ATAAACGTGCAACACA
1 ATAAACGTGCAACACA
38758 TGTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.13
Consensus pattern (23 bp):
ATAAACGTGCAACACAGACAAAC
Found at i:41635 original size:15 final size:16
Alignment explanation
Indices: 41615--41649 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41605 TTTTAGTTCA
*
41615 GAATGATT-AAGTGTT
1 GAATGATTCAAATGTT
41630 GAATGATTCAAATGTT
1 GAATGATTCAAATGTT
41646 GAAT
1 GAAT
41650 AATTTAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (16 bp):
GAATGATTCAAATGTT
Found at i:48619 original size:16 final size:16
Alignment explanation
Indices: 48598--48629 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48588 AGAGAGCCTC
48598 TGAATCATTCAACATT
1 TGAATCATTCAACATT
48614 TGAATCATTCAACATT
1 TGAATCATTCAACATT
48630 AAATCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACATT
Done.