Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007223.1 Hibiscus syriacus cultivar Beakdansim tig00019110_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: 75537
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5071 original size:2 final size:2
Alignment explanation
Indices: 5064--5096 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5054 AAATAAATAA
5064 AT AT AT 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 AT AT AT A
5097 ATTTTAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5965 original size:20 final size:20
Alignment explanation
Indices: 5929--5966 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5919 ATCCTATTCC
**
5929 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTACATTCTCA
5949 CTGATAATCTTACATTCT
1 CTGATAATCTTACATTCT
5967 GTGTACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
CTGATAATCTTACATTCTCA
Found at i:10292 original size:2 final size:2
Alignment explanation
Indices: 10285--10316 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10275 AGCATCTTAC
10285 AT AT 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 AT AT
10317 TGTAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12853 original size:22 final size:22
Alignment explanation
Indices: 12815--12858 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12805 GAGCACTAAG
* *
12815 AATATCAGATGTATGAACGTTA
1 AATATCAAATGTATGAAAGTTA
12837 AATATCAAATAGT-TGAAAGTTA
1 AATATCAAAT-GTATGAAAGTTA
12859 TCTTCGAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (22 bp):
AATATCAAATGTATGAAAGTTA
Found at i:13148 original size:15 final size:17
Alignment explanation
Indices: 13119--13150 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
13109 AATTTTGAAA
13119 TATATATTTTATAAAAT
1 TATATATTTTATAAAAT
13136 TATA-ATTTT-TAAAAT
1 TATATATTTTATAAAAT
13151 AGTTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATTTTATAAAAT
Found at i:18988 original size:2 final size:2
Alignment explanation
Indices: 18981--19006 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18971 GGAAAATGTC
18981 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
19007 TTGAAAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20269 original size:32 final size:31
Alignment explanation
Indices: 20233--20308 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 31
20223 ATCTATAATT
* *
20233 TTGAAATAAAAAAAATTTGAAAGTCAGAGTGA
1 TTGAAATAAAAAAAATTGGAAAGTCA-AGTAA
* **
20265 TTGAATTAAAAGTAATTGGAAAGTCAAGTAA
1 TTGAAATAAAAAAAATTGGAAAGTCAAGTAA
*
20296 TT-AAATTAAAAAA
1 TTGAAATAAAAAAA
20309 TTTAAACTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 7 0.20
31 6 0.17
32 22 0.63
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.28
Consensus pattern (31 bp):
TTGAAATAAAAAAAATTGGAAAGTCAAGTAA
Found at i:20306 original size:31 final size:32
Alignment explanation
Indices: 20246--20306 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
20236 AAATAAAAAA
* * *
20246 AATTTGAAAGTCAGAGTGATTGAATTAAAAGT
1 AATTGGAAAGTCAGAGTAATTAAATTAAAAGT
20278 AATTGGAAAGTCA-AGTAATTAAATTAAAA
1 AATTGGAAAGTCAGAGTAATTAAATTAAAA
20307 AATTTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (32 bp):
AATTGGAAAGTCAGAGTAATTAAATTAAAAGT
Found at i:21251 original size:31 final size:31
Alignment explanation
Indices: 21210--21269 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
21200 AGATAAGGAA
*
21210 AAAAGAGTAAACTACACCACGAGTCATTAGG
1 AAAAGAGTAAACTACACCACAAGTCATTAGG
* * * *
21241 AAAAGGGTAAATTATACCATAAGTCATTA
1 AAAAGAGTAAACTACACCACAAGTCATTA
21270 AACTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (31 bp):
AAAAGAGTAAACTACACCACAAGTCATTAGG
Found at i:32143 original size:29 final size:28
Alignment explanation
Indices: 32101--32171 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
32091 AAGAATAAAT
* *
32101 TAAAATTAAAAATTATTTTTTCTATTAG
1 TAAAATTAAAAATTATTTATTCTATTAA
*
32129 TAAAAGTTAAGAATTATTTATTCTATTAA
1 TAAAA-TTAAAAATTATTTATTCTATTAA
*
32158 TAAAAATTAGAAAT
1 T-AAAATTAAAAAT
32172 AATAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.14
29 27 0.75
30 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (28 bp):
TAAAATTAAAAATTATTTATTCTATTAA
Found at i:32510 original size:22 final size:19
Alignment explanation
Indices: 32484--32524 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 19
32474 CGTGTCATCA
32484 TTTAATTAGAAATTAAATTTAT
1 TTTAATTA-AAA-T-AATTTAT
32506 TTTAATTAAAATAATTTAT
1 TTTAATTAAAATAATTTAT
32525 AAATATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 3 0.16
22 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTAATTAAAATAATTTAT
Found at i:33054 original size:16 final size:16
Alignment explanation
Indices: 33033--33083 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
33023 TAAATAATAA
33033 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33049 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
33065 AC--A-ATAAATGAAC
1 ACGAACATAAACGAAC
33078 ACGAAC
1 ACGAAC
33084 TGACAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 1 0.03
16 18 0.58
ACGTcount: A:0.57, C:0.24, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:37690 original size:32 final size:32
Alignment explanation
Indices: 37620--37691 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
37610 TTATGTTACT
* * *
37620 TAATATATGTCATGTCATTTAAAATAATGATA
1 TAATATATATCATATCATTTAAAATAATGACA
* * * *
37652 TGATATATATTATATCATTTAAAGTGATGACA
1 TAATATATATCATATCATTTAAAATAATGACA
37684 TAATATAT
1 TAATATAT
37692 GATATGTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (32 bp):
TAATATATATCATATCATTTAAAATAATGACA
Found at i:45446 original size:60 final size:60
Alignment explanation
Indices: 45379--45500 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
45369 ATTTATTTTT
45379 GAAGGTCAGAGTTT-GAAGATTGA-TACAAAACATCTTAAAATTTAAAGACTAATTTAAAAC
1 GAAGGTCAGAGTTTAG-AGATT-ACTACAAAACATCTTAAAATTTAAAGACTAATTTAAAAC
* * ** * * * *
45439 GAAGGTCATAGTTTAGGGATTACTGTAAAATATTTTAAAATTTAAAGATTAATTTAGAAC
1 GAAGGTCAGAGTTTAGAGATTACTACAAAACATCTTAAAATTTAAAGACTAATTTAAAAC
45499 GA
1 GA
45501 GAGTTATAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
59 1 0.02
60 50 0.96
61 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.32
Consensus pattern (60 bp):
GAAGGTCAGAGTTTAGAGATTACTACAAAACATCTTAAAATTTAAAGACTAATTTAAAAC
Found at i:55571 original size:30 final size:30
Alignment explanation
Indices: 55537--55596 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
55527 CTTAAACTAT
55537 TTTTAAAACAATTTTACAAAGTATTTCGAA
1 TTTTAAAACAATTTTACAAAGTATTTCGAA
55567 TTTTAAAACAATTTTACAAAGTATTTCGAA
1 TTTTAAAACAATTTTACAAAGTATTTCGAA
55597 CCGTTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTAAAACAATTTTACAAAGTATTTCGAA
Found at i:55744 original size:21 final size:20
Alignment explanation
Indices: 55713--55762 Score: 91
Period size: 21 Copynumber: 2.5 Consensus size: 20
55703 AGGGGTATAG
55713 ATTCCCCCCAGGGGGAACAA
1 ATTCCCCCCAGGGGGAACAA
55733 ATTCCACCCCAGGGGGAACAA
1 ATTCC-CCCCAGGGGGAACAA
55754 ATTCCCCCC
1 ATTCCCCCC
55763 CCAAGGGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.28, C:0.40, G:0.20, T:0.12
Consensus pattern (20 bp):
ATTCCCCCCAGGGGGAACAA
Found at i:57588 original size:13 final size:13
Alignment explanation
Indices: 57535--57588 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
57525 ATCCCAAAAT
*
57535 GTCACCGGGTCGG
1 GTCAACGGGTCGG
*
57548 GTCAATGGGTCGG
1 GTCAACGGGTCGG
* *
57561 GTTAACAGGTC-G
1 GTCAACGGGTCGG
*
57573 GTCAACGGGTCAG
1 GTCAACGGGTCGG
57586 GTC
1 GTC
57589 GAACCGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.20
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:58022 original size:15 final size:15
Alignment explanation
Indices: 58002--58057 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
57992 CGGATGTTAC
58002 GGGTACCCGGTAATT
1 GGGTACCCGGTAATT
* **
58017 GGGTACTCGGATTTTGT
1 GGGTACCCGG-TAAT-T
*
58034 GGGTACCCGGTAATC
1 GGGTACCCGGTAATT
58049 GGGTACCCG
1 GGGTACCCG
58058 ATACCCGGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 18 0.56
16 4 0.12
17 10 0.31
ACGTcount: A:0.16, C:0.21, G:0.36, T:0.27
Consensus pattern (15 bp):
GGGTACCCGGTAATT
Found at i:58028 original size:32 final size:32
Alignment explanation
Indices: 57992--58054 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
57982 TGTCCCGACC
*
57992 CGGATGTTACGGGTACCCGGTAATTGGGTACT
1 CGGATGTTACGGGTACCCGGTAATCGGGTACT
* **
58024 CGGATTTTGTGGGTACCCGGTAATCGGGTAC
1 CGGATGTTACGGGTACCCGGTAATCGGGTAC
58055 CCGATACCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (32 bp):
CGGATGTTACGGGTACCCGGTAATCGGGTACT
Found at i:65518 original size:57 final size:56
Alignment explanation
Indices: 65446--65596 Score: 171
Period size: 57 Copynumber: 2.6 Consensus size: 56
65436 AAATTACAAA
* *
65446 ATCACCTTTATTAAAAATAATTACCAAAATATCATCGTTATCAAATAAATCCCAAAAT
1 ATCACCTTT-TTAAAAATAATTACCAAAATGTCATCGTT-TCAAAAAAATCCCAAAAT
* * * *
65504 GTCA-TTATTTTAAAAATAATTAGCAGAAATGTCA-CTGTTTTAAAAAAATCCCAAAAT
1 ATCACCT-TTTTAAAAATAATTACCA-AAATGTCATC-GTTTCAAAAAAATCCCAAAAT
* *
65561 ATCACCTTTTTCAAAATAATTCCCAAAATGTCATCG
1 ATCACCTTTTTAAAAATAATTACCAAAATGTCATCG
65597 GGTCGGGTCA
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
56 9 0.12
57 52 0.68
58 16 0.21
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.32
Consensus pattern (56 bp):
ATCACCTTTTTAAAAATAATTACCAAAATGTCATCGTTTCAAAAAAATCCCAAAAT
Found at i:69159 original size:21 final size:21
Alignment explanation
Indices: 69133--69194 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
69123 TAGAATGTCC
*
69133 AGGGGGTACAGATTCCCCTCA
1 AGGGGGTACAGATTCCCCCCA
*
69154 AGGGGGAACAGATTCCCCCCCA
1 AGGGGGTACAGATT-CCCCCCA
*
69176 AGGGGGTACCGATTCCCCC
1 AGGGGGTACAGATTCCCCC
69195 TGATCAACGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.23, C:0.34, G:0.29, T:0.15
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCCA
Found at i:69172 original size:22 final size:22
Alignment explanation
Indices: 69133--69195 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
69123 TAGAATGTCC
69133 AGGGGGTACAGATT-CCCCTCA
1 AGGGGGTACAGATTCCCCCTCA
* *
69154 AGGGGGAACAGATTCCCCCCCA
1 AGGGGGTACAGATTCCCCCTCA
*
69176 AGGGGGTACCGATTCCCCCT
1 AGGGGGTACAGATTCCCCCT
69196 GATCAACGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (22 bp):
AGGGGGTACAGATTCCCCCTCA
Found at i:71759 original size:25 final size:26
Alignment explanation
Indices: 71708--71759 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
71698 ATAACATGGG
*
71708 CATTTTCACTTATCTCATTTCACTATA
1 CATTTTCAC-TATCACATTTCACTATA
71735 CATTTTCA-TATCACATGTTCA-TATA
1 CATTTTCACTATCACAT-TTCACTATA
71760 AGCTCATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 11 0.48
26 4 0.17
27 8 0.35
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46
Consensus pattern (26 bp):
CATTTTCACTATCACATTTCACTATA
Found at i:72463 original size:20 final size:22
Alignment explanation
Indices: 72438--72495 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
72428 TTCCCCTTGA
72438 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
72458 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
72481 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
72496 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:73087 original size:27 final size:25
Alignment explanation
Indices: 73049--73098 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
73039 TAGCACCCCT
73049 AGAATTAAAACT-AAACTTAAACTCA
1 AGAATTAAAACTGAAA-TTAAACTCA
73074 AGAATTAACCAACTGAAATTAAACT
1 AGAATTAA--AACTGAAATTAAACT
73099 TACCTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (25 bp):
AGAATTAAAACTGAAATTAAACTCA
Done.