Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004456.1 Hibiscus syriacus cultivar Beakdansim tig00009809_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: 41421
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:6555 original size:24 final size:24
Alignment explanation
Indices: 6521--6592 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
6511 AAACGGAGAT
* *
6521 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
6545 AAT-AGATATCAGAACAGAATCCAG
1 -ATCAGAAATCAGAACAGAATTCAG
6569 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
6593 GTAATGTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:6592 original size:12 final size:12
Alignment explanation
Indices: 6533--6592 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
6523 CATAAATCAA
6533 AACAGAATTCAG
1 AACAGAATTCAG
*
6545 AATAG-ATATCAG
1 AACAGAAT-TCAG
*
6557 AACAGAATCCAG
1 AACAGAATTCAG
* *
6569 ATCAGAAATCAG
1 AACAGAATTCAG
6581 AACAGAATTCAG
1 AACAGAATTCAG
6593 GTAATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:6603 original size:24 final size:25
Alignment explanation
Indices: 6528--6615 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 25
6518 GATATCATAA
*
6528 ATCAAAACAGAATTCA-G-AATAGAT
1 ATCAGAACAGAATTCAGGTAAT-GAT
* * * *
6552 ATCAGAACAGAATCCAGATCA-GAA
1 ATCAGAACAGAATTCAGGTAATGAT
6576 ATCAGAACAGAATTCAGGTAATG-T
1 ATCAGAACAGAATTCAGGTAATGAT
*
6600 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
6616 AGTCGGAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
24 49 0.96
25 1 0.02
26 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (25 bp):
ATCAGAACAGAATTCAGGTAATGAT
Found at i:6625 original size:48 final size:48
Alignment explanation
Indices: 6521--6629 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
6511 AAACGGAGAT
* * *
6521 ATCATAAATCAAAACAGAATTCAGAATAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAATAGATATCAGAACAGAATCAAG
*
6569 ATCAGAAATCAGAACAGAATTCAGGTAAT-G-TATCAGAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCA-G-AATAGATATCAGAACAGAA-TCAAG
*
6618 -TCGGAAATCAGA
1 ATCAGAAATCAGA
6630 TAAAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
48 44 0.83
49 6 0.11
50 3 0.06
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAATAGATATCAGAACAGAATCAAG
Found at i:9087 original size:8 final size:8
Alignment explanation
Indices: 9054--9111 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 8
9044 TCAAAGTTTT
9054 GGTCAACAG
1 GGTCAAC-G
9063 TGGTCAACGG
1 -GGTCAAC-G
9073 TGGTCAACG
1 -GGTCAACG
9082 GGTCAACG
1 GGTCAACG
*
9090 GGTCAGGTCG
1 GGTCA--ACG
9100 GGTCAACG
1 GGTCAACG
9108 GGTC
1 GGTC
9112 GGGTAAACAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
8 19 0.44
9 1 0.02
10 23 0.53
ACGTcount: A:0.21, C:0.22, G:0.40, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:9087 original size:18 final size:20
Alignment explanation
Indices: 9053--9090 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
9043 GTCAAAGTTT
9053 TGGTCAACAGTGGTCAACGG
1 TGGTCAACAGTGGTCAACGG
9073 TGGTCAAC-G-GGTCAACGG
1 TGGTCAACAGTGGTCAACGG
9091 GTCAGGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.24, C:0.21, G:0.37, T:0.18
Consensus pattern (20 bp):
TGGTCAACAGTGGTCAACGG
Found at i:9111 original size:13 final size:13
Alignment explanation
Indices: 9093--9130 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
9083 GTCAACGGGT
9093 CAGGTCGGGTCAA
1 CAGGTCGGGTCAA
* *
9106 CGGGTCGGGTAAA
1 CAGGTCGGGTCAA
9119 CAGGTCGGGTCA
1 CAGGTCGGGTCA
9131 GGTAAACGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (13 bp):
CAGGTCGGGTCAA
Found at i:9127 original size:18 final size:18
Alignment explanation
Indices: 9106--9151 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
9096 GTCGGGTCAA
9106 CGGGTCGGGTAAACAGGT
1 CGGGTCGGGTAAACAGGT
* *
9124 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
*
9142 TGGGTCGGGT
1 CGGGTCGGGT
9152 TATGACCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:9139 original size:31 final size:31
Alignment explanation
Indices: 9080--9146 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
9070 CGGTGGTCAA
* * * *
9080 CGGGTCAACGGGTCAGGTCGGGTCAACGGGT
1 CGGGTAAACAGGTCAGGTCAGGTAAACGGGT
*
9111 CGGGTAAACAGGTCGGGTCAGGTAAACGGGT
1 CGGGTAAACAGGTCAGGTCAGGTAAACGGGT
*
9142 TGGGT
1 CGGGT
9147 CGGGTTATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.18, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTAAACAGGTCAGGTCAGGTAAACGGGT
Found at i:11233 original size:24 final size:24
Alignment explanation
Indices: 11199--11291 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
11189 AACCGAAGAT
*
11199 ATCATAAATCAAAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* * * *
11223 AACATATATCATAACAGAATCCAG
1 ATCATAAATCAGAACAGAATTCAG
* *
11247 ATCAGAAATTAGAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* **
11271 GTCATGTATCAGAACAGAATT
1 ATCATAAATCAGAACAGAATT
11292 TAAGTCGGAA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCATAAATCAGAACAGAATTCAG
Found at i:13777 original size:13 final size:13
Alignment explanation
Indices: 13759--13788 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
13749 GTCGGTCAAC
13759 GGTCAACGGGTCA
1 GGTCAACGGGTCA
13772 GGTCAACGGGTCA
1 GGTCAACGGGTCA
13785 GGTC
1 GGTC
13789 GTTTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:15370 original size:29 final size:29
Alignment explanation
Indices: 15333--15522 Score: 267
Period size: 29 Copynumber: 6.6 Consensus size: 29
15323 CACATTCGAA
*
15333 AATTCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
15362 AATTCCCAAAATGTCACCTCTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
15391 AATTCCCAAAATGTCA-C-TTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
15418 AATTCCTAAAATATCACTTTTTTTTCAAAAT
1 AATTCCCAAAATGTCAC--CTTTTTCAAAAT
* *
15449 AATTCCCAGAATGTCACCTTTGTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
15478 AATTCTCAAAATGTCACTTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
15507 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
15523 TCGGGTCGGG
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.16
28 1 0.01
29 93 0.66
31 24 0.17
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:18171 original size:44 final size:44
Alignment explanation
Indices: 18119--18210 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
18109 TTTGTGGCAT
* *
18119 TTTG-TCCCAAAAACGCCGTTAAATATTATGA-CATATAGTGGTG
1 TTTGTTCCCAAAAACGCCGCTAAATATTAT-ATCATATAGTGGCG
*
18162 TTTGTTCCCAAAAACGCCGCTAAATGTTATATCATATAGTGGCG
1 TTTGTTCCCAAAAACGCCGCTAAATATTATATCATATAGTGGCG
18206 TTTGT
1 TTTGT
18211 GAATGTAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 5 0.11
44 39 0.89
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (44 bp):
TTTGTTCCCAAAAACGCCGCTAAATATTATATCATATAGTGGCG
Found at i:18451 original size:21 final size:21
Alignment explanation
Indices: 18425--18483 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
18415 ATTATCCAAT
*
18425 AAACTTGACATCAATAACAAC
1 AAACTTGAAATCAATAACAAC
*
18446 AAACTTGAAATTCAA-AACAAG
1 AAACTTGAAA-TCAATAACAAC
*
18467 AAACTTGAAATCTATAA
1 AAACTTGAAATCAATAA
18484 TAATAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 26 0.79
22 4 0.12
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCAATAACAAC
Found at i:26997 original size:3 final size:3
Alignment explanation
Indices: 26989--27040 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
26979 TATTTATATA
* * * * *
26989 ATT ATT ATT ATT ATT ATA ATT ATA ATA ATA ATT ATT ATT AAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
27035 ATT ATT
1 ATT ATT
27041 TAATATTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:27822 original size:30 final size:30
Alignment explanation
Indices: 27788--27868 Score: 103
Period size: 28 Copynumber: 2.7 Consensus size: 30
27778 TCTCTGTTTT
* *
27788 AGAGAGAAGTGAGAGTGAAAATTCTCTCTC
1 AGAGAGAAGAGAGAGAGAAAATTCTCTCTC
27818 --AGAGAAGAGAGAGAGAAAATTCTCTCTC
1 AGAGAGAAGAGAGAGAGAAAATTCTCTCTC
27846 AGAGAAGAGAGAGAGAGGAGAAA
1 AGAG-AGA-AGAGAGA-GAGAAA
27869 CTGAGAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 26 0.59
30 2 0.05
31 3 0.07
32 7 0.16
33 6 0.14
ACGTcount: A:0.44, C:0.10, G:0.31, T:0.15
Consensus pattern (30 bp):
AGAGAGAAGAGAGAGAGAAAATTCTCTCTC
Found at i:27830 original size:28 final size:28
Alignment explanation
Indices: 27790--27861 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
27780 TCTGTTTTAG
* *
27790 AGAGAAGTGAGAGTGAAAATTCTCTCTC
1 AGAGAAGAGAGAGAGAAAATTCTCTCTC
27818 AGAGAAGAGAGAGAGAAAATTCTCTCTC
1 AGAGAAGAGAGAGAGAAAATTCTCTCTC
27846 AGAGAAGAGAGAGAGA
1 AGAGAAGAGAGAGAGA
27862 GGAGAAACTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (28 bp):
AGAGAAGAGAGAGAGAAAATTCTCTCTC
Found at i:29181 original size:29 final size:26
Alignment explanation
Indices: 29120--29183 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 26
29110 TTTATAAGTC
*
29120 TTTTTTTTATATACATATTATTTTCA
1 TTTTATTTATATACATATTATTTTCA
** *
29146 TAGTATTTATATATATTATTAATATTTCA
1 TTTTATTTATATACA-TATT-AT-TTTCA
29175 TTTTATTTA
1 TTTTATTTA
29184 CAAGTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 11 0.38
27 4 0.14
28 2 0.07
29 12 0.41
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTATTTATATACATATTATTTTCA
Found at i:32483 original size:15 final size:15
Alignment explanation
Indices: 32463--32494 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32453 ATCAATACCT
32463 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
32478 TTTTGCATACATTCA
1 TTTTGCATACATGCA
32493 TT
1 TT
32495 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:39731 original size:4 final size:4
Alignment explanation
Indices: 39717--39761 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
39707 ATGCTTGAAG
39717 AGAA A-AA AGAA AGAA AGAA A-AA A-AA AGAA AGAA A-AA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
39761 A
1 A
39762 AAGGAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 12 0.32
4 26 0.68
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:39751 original size:11 final size:11
Alignment explanation
Indices: 39722--39772 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
39712 TGAAGAGAAA
39722 AAAGAAAGAAAG
1 AAAGAAA-AAAG
39734 AAA-AAAAAAG
1 AAAGAAAAAAG
39744 AAAGAAAAAAG
1 AAAGAAAAAAG
*
39755 AAAGAAAAAGG
1 AAAGAAAAAAG
39766 AAA-AAAA
1 AAAGAAAA
39773 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 11 0.30
11 23 0.62
12 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:39771 original size:18 final size:15
Alignment explanation
Indices: 39717--39761 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
39707 ATGCTTGAAG
39717 AGAAAAAAGAAAGAA
1 AGAAAAAAGAAAGAA
39732 AGAAAAAA-AAAGAA
1 AGAAAAAAGAAAGAA
39746 AGAAAAAAGAAAGAA
1 AGAAAAAAGAAAGAA
39761 A
1 A
39762 AAGGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 14 0.48
15 15 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAGAA
Found at i:41295 original size:79 final size:80
Alignment explanation
Indices: 41117--41407 Score: 363
Period size: 92 Copynumber: 3.5 Consensus size: 80
41107 GAACAAATGC
41117 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACAATCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA-CTGATCT-GTTTGGTAAAACAATCA
**
41182 TTGAATTTGGAAGAATA
64 TTGAATTTGGAAGAGGA
* *
41199 ATGTGCTCATAGAATCTTCT-GAAGTGTTCTTTTGAGTTA-TGATCTGATTGGTAAAATCAATCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTC-TTTGAGTTACTGATCTGTTTGGTAAAA-CAATCA
41262 TTGAATTTGGAA-AGGA
64 TTGAATTTGGAAGAGGA
41278 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA-CTGATCTG-TTTGGTA--AA--AC-
*
41343 GAACCAGTTATTGAATTTGGAAGAGGA
59 --A--A-TCATTGAATTTGGAAGAGGA
*
41370 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
41408 CTCTGATTTG
Statistics
Matches: 184, Mismatches: 8, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
79 40 0.22
80 33 0.18
81 16 0.09
82 34 0.18
84 2 0.01
85 1 0.01
86 1 0.01
88 1 0.01
90 1 0.01
91 14 0.08
92 41 0.22
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (80 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTACTGATCTGTTTGGTAAAACAATCATT
GAATTTGGAAGAGGA
Done.