Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003194.1 Hibiscus syriacus cultivar Beakdansim tig00006723_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: 105788
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:724 original size:29 final size:30
Alignment explanation
Indices: 656--712 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
646 ATTTAAGGCA
656 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
686 AAAATGTTTTTGGACTT-AATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
713 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:931 original size:21 final size:21
Alignment explanation
Indices: 892--966 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 21
882 ATGCAATTAG
892 TGCATCGATGCAT-CTTGCTA
1 TGCATCGATGCATCCTTGCTA
*
912 TGCATCGACGCATCCTTGCTA
1 TGCATCGATGCATCCTTGCTA
*
933 TGCATCGATGCATCC-TGCGA
1 TGCATCGATGCATCCTTGCTA
*
953 TGCATCCATGCATC
1 TGCATCGATGCATC
967 AAGGCTGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCTA
Found at i:1736 original size:2 final size:2
Alignment explanation
Indices: 1729--1761 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1719 ATAATTTCAC
*
1729 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1762 GTGATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3914 original size:2 final size:2
Alignment explanation
Indices: 3907--3936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3897 AATTTACAGT
3907 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
3937 AACAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10179 original size:16 final size:16
Alignment explanation
Indices: 10136--10185 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
10126 TACATTATTC
10136 ATAATTCAGAAAAATA
1 ATAATTCAGAAAAATA
*
10152 TTTAA-TCA-AAAAATA
1 -ATAATTCAGAAAAATA
*
10167 ATAATTCAGAAAAAAA
1 ATAATTCAGAAAAATA
10183 ATA
1 ATA
10186 CAATCATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
16 12 0.43
17 3 0.11
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAATTCAGAAAAATA
Found at i:10355 original size:31 final size:31
Alignment explanation
Indices: 10283--10356 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
10273 AATGTAATCG
* * **
10283 TTAACATAA-ATGCGCATATATTTAATTTCT
1 TTAATATAATATGCGCATATATTAAATTAAT
*
10313 TTGATATAATATGCGCATATATTAAATTAAT
1 TTAATATAATATGCGCATATATTAAATTAAT
10344 TTAAT-TAAATATG
1 TTAATAT-AATATG
10357 AAATTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 8 0.22
31 28 0.78
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (31 bp):
TTAATATAATATGCGCATATATTAAATTAAT
Found at i:18349 original size:21 final size:20
Alignment explanation
Indices: 18325--18363 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18315 CAGATTACTC
18325 GGAGGGAGCCGATTCCCCCCA
1 GGAGGGA-CCGATTCCCCCCA
*
18346 GGAGGTACCGATTCCCCC
1 GGAGGGACCGATTCCCCC
18364 ATCTCATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.38, G:0.31, T:0.13
Consensus pattern (20 bp):
GGAGGGACCGATTCCCCCCA
Found at i:20804 original size:22 final size:22
Alignment explanation
Indices: 20701--20804 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 22
20691 TTATATAACG
* * * *
20701 AAAGTGCCTTAGCACTAATACT
1 AAAGTGCCATCGCACTGATACA
*
20723 AAAGTGCCATAGCACTGATACA
1 AAAGTGCCATCGCACTGATACA
20745 AAAGTG-CATTCGCACTGA-ATCA
1 AAAGTGCCA-TCGCACTGATA-CA
* * *
20767 AAAGAG-CATTCACACTGATACT
1 AAAGTGCCA-TCGCACTGATACA
20789 AAAGTGCCATCGCACT
1 AAAGTGCCATCGCACT
20805 CGGGAAGAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
21 3 0.04
22 63 0.91
23 3 0.04
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAGTGCCATCGCACTGATACA
Found at i:21101 original size:18 final size:21
Alignment explanation
Indices: 21054--21106 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
21044 TATACAGGAC
21054 GTCAGTATCGATACTGAGCCT
1 GTCAGTATCGATACTGAGCCT
*
21075 GTCAGTATCGATACT-AGTCT
1 GTCAGTATCGATACTGAGCCT
21095 -T-AGTATCGATAC
1 GTCAGTATCGATAC
21107 CGGTTGAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 11 0.35
19 1 0.03
20 4 0.13
21 15 0.48
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
GTCAGTATCGATACTGAGCCT
Found at i:22817 original size:14 final size:14
Alignment explanation
Indices: 22798--22825 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22788 TAGGCATTTA
22798 TAAATATATAATAT
1 TAAATATATAATAT
22812 TAAATATATAATAT
1 TAAATATATAATAT
22826 AGTTATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATATATAATAT
Found at i:23216 original size:13 final size:13
Alignment explanation
Indices: 23198--23224 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23188 ACAAACATCC
23198 TTCTTTATTTGTT
1 TTCTTTATTTGTT
23211 TTCTTTATTTGTT
1 TTCTTTATTTGTT
23224 T
1 T
23225 CATGTATTTA
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:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (13 bp):
TTCTTTATTTGTT
Found at i:23247 original size:23 final size:23
Alignment explanation
Indices: 23218--23264 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23208 GTTTTCTTTA
* *
23218 TTTGTTTCATGTA-TTTATTTATT
1 TTTGTTTAAT-TATTTTATATATT
23241 TTTGTTTAATTATTTTATATATT
1 TTTGTTTAATTATTTTATATATT
23264 T
1 T
23265 CTCCAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (23 bp):
TTTGTTTAATTATTTTATATATT
Found at i:28115 original size:6 final size:6
Alignment explanation
Indices: 28104--28138 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
28094 GACTTAGCTT
*
28104 TACCTC TACCTC TACCTC TACCTC TACATC TACCT
1 TACCTC TACCTC TACCTC TACCTC TACCTC TACCT
28139 TTACGTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (6 bp):
TACCTC
Found at i:28707 original size:135 final size:135
Alignment explanation
Indices: 28465--28733 Score: 439
Period size: 135 Copynumber: 2.0 Consensus size: 135
28455 CGGGATCGTT
*
28465 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAACGAAACTCGGAATAT
1 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
*
28530 ATGATTGGCGACTCAGTTGTGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
66 ATGATTGGCAACTCAGTTGTGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
28595 TTCCG
131 TTCCG
* ** *
28600 GCCATCACAAAGTGCTGCAACTGATTTAAGAACACGTTGGCTGTTACGAAATAAACTCGGAATAT
1 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
* * * * *
28665 ATGATTGGCAATTCAGTTGTGAAAGCTTACCTAAAGTTTGTTTTTTAGAAGATGGAACTATTGTC
66 ATGATTGGCAACTCAGTTGTGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
28730 TTCC
131 TTCC
28734 CATCCTTCGC
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 123 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (135 bp):
GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
ATGATTGGCAACTCAGTTGTGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
TTCCG
Found at i:40743 original size:19 final size:21
Alignment explanation
Indices: 40706--40748 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40696 TAACTTTTTC
*
40706 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
40726 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
40746 TTT
1 TTT
40749 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:42388 original size:2 final size:2
Alignment explanation
Indices: 42383--42410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42373 GAAAAAAAAA
42383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42411 TTCTGCATAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49338 original size:32 final size:32
Alignment explanation
Indices: 49295--49356 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
49285 ATACTTAAAT
* *
49295 TTTTTATATTTAAAATATTTGCAACCTAAAAA
1 TTTTAATATTTAAAATATTTACAACCTAAAAA
49327 TTTTAATATTTAAAATATTTACAACCTAAA
1 TTTTAATATTTAAAATATTTACAACCTAAA
49357 CACATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTTAATATTTAAAATATTTACAACCTAAAAA
Found at i:59471 original size:18 final size:18
Alignment explanation
Indices: 59448--59498 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
59438 ATGGATTATC
59448 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
59466 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
59484 AGTGATCATTCGGGA
1 AGTGGTCCTTCGGGA
59499 AAAATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:82086 original size:24 final size:24
Alignment explanation
Indices: 82054--82104 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
82044 ATATAGGTGA
82054 ACTAATCAACGACCTAGTGCAGTT
1 ACTAATCAACGACCTAGTGCAGTT
82078 ACTAATCAACGACCTAGTGCAGTT
1 ACTAATCAACGACCTAGTGCAGTT
82102 ACT
1 ACT
82105 CTCGACCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (24 bp):
ACTAATCAACGACCTAGTGCAGTT
Found at i:83247 original size:27 final size:30
Alignment explanation
Indices: 83185--83240 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
83175 AAAATAAGTG
* *
83185 TAAATTATATTATTATTTTAAATAGGTATT
1 TAAATTATATTATTATTTTAAATAGATATC
83215 TAAATTATATTA-T-TTTTAAATAGATA
1 TAAATTATATTATTATTTTAAATAGATA
83241 CTCAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
29 1 0.04
30 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
TAAATTATATTATTATTTTAAATAGATATC
Found at i:83417 original size:28 final size:27
Alignment explanation
Indices: 83386--83446 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
83376 TTATATTTGA
**
83386 AAAAAAACACAATTTTTTTGAATACTTT
1 AAAAAAACACAAAATTTTTGAAT-CTTT
* *
83414 AAAAAACCTCAAAATTTTTGAATCTTT
1 AAAAAAACACAAAATTTTTGAATCTTT
*
83441 TAAAAA
1 AAAAAA
83447 TACTTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.36
Consensus pattern (27 bp):
AAAAAAACACAAAATTTTTGAATCTTT
Found at i:84966 original size:16 final size:17
Alignment explanation
Indices: 84929--84966 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
84919 TGATAAAAAA
*
84929 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
84946 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
84962 TTAAA
1 TTAAA
84967 TTAATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:85138 original size:29 final size:29
Alignment explanation
Indices: 85105--85181 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
85095 AAAAAATCAG
85105 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
85134 TTAATTCGATTC-AGTTAATAATTTTCAAA
1 TTAATTCGGTTCGA-TTAATAATTTTCAAA
* *
85163 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
85182 CATAACTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 10 0.24
31 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Done.