Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001220.1 Hibiscus syriacus cultivar Beakdansim tig00002409_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: 61900
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:5483 original size:17 final size:16
Alignment explanation
Indices: 5457--5493 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
5447 TTGACCAAAA
5457 TCCTTTCTTCTCCTTC
1 TCCTTTCTTCTCCTTC
5473 TCCTCTTCTTCTCCTTC
1 TCCT-TTCTTCTCCTTC
5490 TCCT
1 TCCT
5494 ATTGCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (16 bp):
TCCTTTCTTCTCCTTC
Found at i:10933 original size:69 final size:70
Alignment explanation
Indices: 10805--10934 Score: 174
Period size: 70 Copynumber: 1.9 Consensus size: 70
10795 TTTAAGATTA
* * *
10805 GTCTTCGAAACCTTTTTATTTTCACCTTGGTTGCTTGAACTGAGCAGATTTGCAGGCGAGAATTG
1 GTCTTCAAAACCTTTTTATTTTCACCTTAGTTGCTTGAACTGAGCAGATTTACAGGCGAGAATTG
10870 GTGTT
66 GTGTT
* * * *
10875 GTCTTCAAAACCTTTTTCTTTTCATCTTAG-TGCTTGAA-TTAGGTAGATTTACAGGCGAGA
1 GTCTTCAAAACCTTTTTATTTTCACCTTAGTTGCTTGAACTGA-GCAGATTTACAGGCGAGA
10935 GTGAATTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 2 0.04
69 24 0.46
70 26 0.50
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (70 bp):
GTCTTCAAAACCTTTTTATTTTCACCTTAGTTGCTTGAACTGAGCAGATTTACAGGCGAGAATTG
GTGTT
Found at i:11526 original size:29 final size:30
Alignment explanation
Indices: 11493--11568 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 30
11483 TTCAATCTAC
*
11493 AAAGTTCAGTGAGTAAAT-TGAAAAAAA-T
1 AAAGTTCAGTGAGTAAATAGGAAAAAAAGT
*
11521 GAAAG-TC-GATGAGTAAAATAGGAGAAAAAGT
1 -AAAGTTCAG-TGAGT-AAATAGGAAAAAAAGT
*
11552 AAAGTTCAGTGAATAAA
1 AAAGTTCAGTGAGTAAA
11569 CATGTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
27 1 0.03
28 7 0.18
29 8 0.21
30 14 0.37
31 7 0.18
32 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (30 bp):
AAAGTTCAGTGAGTAAATAGGAAAAAAAGT
Found at i:14674 original size:2 final size:2
Alignment explanation
Indices: 14667--14691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14657 TAATACTTTC
14667 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 A
14692 ATCAACAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15091 original size:28 final size:28
Alignment explanation
Indices: 15051--15115 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
15041 TTGACTATTG
15051 AAAGTTACAAAATAGTATATCGCTAATA
1 AAAGTTACAAAATAGTATATCGCTAATA
15079 AAAGTTACAAAATAGTATATCGCTAATA
1 AAAGTTACAAAATAGTATATCGCTAATA
15107 AAAGTTACA
1 AAAGTTACA
15116 CAATGGTCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAGTTACAAAATAGTATATCGCTAATA
Found at i:26295 original size:8 final size:8
Alignment explanation
Indices: 26282--26309 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
26272 AGATTCTCCC
26282 ATATGTAT
1 ATATGTAT
26290 ATATGTAT
1 ATATGTAT
26298 ATATGTAT
1 ATATGTAT
26306 ATAT
1 ATAT
26310 ATCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:29846 original size:9 final size:9
Alignment explanation
Indices: 29827--29856 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29817 AGTGAAAATG
29827 AAAAAAT-A
1 AAAAAATAA
29835 AAAAAATAA
1 AAAAAATAA
29844 AAAAAATAA
1 AAAAAATAA
29853 AAAA
1 AAAA
29857 TGAAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:29866 original size:8 final size:8
Alignment explanation
Indices: 29821--29873 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
29811 AAAATGAGTG
29821 AAAATGAA
1 AAAATGAA
*
29829 AAAATAAA
1 AAAATGAA
*
29837 AAAATAAAA
1 AAAAT-GAA
29846 AAAAT-AA
1 AAAATGAA
29853 AAAATGAA
1 AAAATGAA
29861 AAAATGGAA
1 AAAAT-GAA
29870 AAAA
1 AAAA
29874 AAGAAGGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
7 7 0.17
8 19 0.46
9 15 0.37
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAATGAA
Found at i:30860 original size:55 final size:55
Alignment explanation
Indices: 30796--31296 Score: 835
Period size: 55 Copynumber: 9.1 Consensus size: 55
30786 AGGTTTCCCA
* *
30796 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
30851 ACAATTGTTGAAGATTATTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
30906 ACGATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
30961 ACAATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
31016 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
31071 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
31126 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAACAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
31181 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
31236 ACGATTATCG-AGAATCGTTCGAGTCTTATACTCTCTGAA-AAATAGGGAGCAGAC
1 ACGATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
31290 ACGATTG
1 ACGATTG
31297 ACGAAGATAT
Statistics
Matches: 422, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
54 22 0.05
55 400 0.95
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:34287 original size:13 final size:13
Alignment explanation
Indices: 34267--34298 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
34257 TCCATAATTC
34267 TCTTCTTTTCCTT
1 TCTTCTTTTCCTT
*
34280 TTTTCTTTTCCTT
1 TCTTCTTTTCCTT
34293 TCTTCT
1 TCTTCT
34299 CCTTCACGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TCTTCTTTTCCTT
Found at i:35827 original size:32 final size:32
Alignment explanation
Indices: 35786--35924 Score: 108
Period size: 32 Copynumber: 4.4 Consensus size: 32
35776 AGTCGAGGGT
35786 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* * * * *
35818 TTACCTATG-TCTTTCGGGAGATATGCACATAA
1 TTACCTATGTTC-TACGGAACATATGGACAGAA
***
35850 TTACCTATG-TCTTTTGAGACATATGGAC--AA
1 TTACCTATGTTCTACGGA-ACATATGGACAGAA
* * *
35880 TATACCTGTGTTCTACGGAGCATATGGACAG-T
1 T-TACCTATGTTCTACGGAACATATGGACAGAA
*
35912 TTACCTAGGTTCT
1 TTACCTATGTTCT
35925 TTGGGACCTA
Statistics
Matches: 83, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
30 3 0.04
31 31 0.37
32 49 0.59
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:40023 original size:32 final size:32
Alignment explanation
Indices: 39948--40023 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
39938 GTTCTACGGA
* *
39948 ACATATGGACATAATTAACTATGTCTTTCGGG
1 ACATATGGACAGAATTAACTATGTCTTTCGAG
* *
39980 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAATTAACTATGTCTTTCGAG
* *
40012 ATATATAGACAG
1 ACATATGGACAG
40024 CGTACCTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (32 bp):
ACATATGGACAGAATTAACTATGTCTTTCGAG
Found at i:43651 original size:2 final size:2
Alignment explanation
Indices: 43604--43637 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43594 TTAAATATTC
43604 AT 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 AT
43638 TGAATCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50823 original size:129 final size:129
Alignment explanation
Indices: 50659--50916 Score: 498
Period size: 129 Copynumber: 2.0 Consensus size: 129
50649 CTAGGTGCTG
50659 AAAATTATGGCTAATACCATTAGAATTACAAAAATCAGTAAATCCAAGATTTTCAAATTCAGTTC
1 AAAATTATGGCTAATACCATTAGAATTACAAAAATCAGTAAATCCAAGATTTTCAAATTCAGTTC
* *
50724 CATGATCACTCCTAACACTAGTTATAGATTAACCTTTTTCGTTTTGGATTATTTTTGAAAACGT
66 CATGATCACTCCTAACACTAGTTATAGAGTAACCTTTTTCATTTTGGATTATTTTTGAAAACGT
50788 AAAATTATGGCTAATACCATTAGAATTACAAAAATCAGTAAATCCAAGATTTTCAAATTCAGTTC
1 AAAATTATGGCTAATACCATTAGAATTACAAAAATCAGTAAATCCAAGATTTTCAAATTCAGTTC
50853 CATGATCACTCCTAACACTAGTTATAGAGTAACCTTTTTCATTTTGGATTATTTTTGAAAACGT
66 CATGATCACTCCTAACACTAGTTATAGAGTAACCTTTTTCATTTTGGATTATTTTTGAAAACGT
50917 GATGAATTTT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (129 bp):
AAAATTATGGCTAATACCATTAGAATTACAAAAATCAGTAAATCCAAGATTTTCAAATTCAGTTC
CATGATCACTCCTAACACTAGTTATAGAGTAACCTTTTTCATTTTGGATTATTTTTGAAAACGT
Found at i:54147 original size:65 final size:65
Alignment explanation
Indices: 54077--54198 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
54067 TGACCGTTGG
* * *
54077 ATCCTTAGTGCATCGGTGCACTAAG-A-GTGCATCGATGCATCAAGTGCATTCAATGTTTTCATA
1 ATCCTTAATGCATCGGTG-AAT-AGTATGTGCATCGATGCATCAAATGCATTCAATGTTTTCATA
54140 AA
64 AA
* * *
54142 ATCCTTAATGCATCGGTGAATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTTAATGCATCGGTGAATAGTATGTGCATCGATGCATCAAATGCATTCAATGTT
54199 CAATTTAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.02
64 3 0.06
65 45 0.92
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (65 bp):
ATCCTTAATGCATCGGTGAATAGTATGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA
Found at i:55647 original size:18 final size:18
Alignment explanation
Indices: 55616--55653 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55606 AAGCTATTTG
55616 GTGAAAGAGAAACAAATT
1 GTGAAAGAGAAACAAATT
* *
55634 GTGAAGGAGGAACAAATT
1 GTGAAAGAGAAACAAATT
55652 GT
1 GT
55654 TGAATAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.29, T:0.18
Consensus pattern (18 bp):
GTGAAAGAGAAACAAATT
Found at i:57373 original size:102 final size:102
Alignment explanation
Indices: 57150--57365 Score: 389
Period size: 102 Copynumber: 2.1 Consensus size: 102
57140 GTAGAGGGTC
57150 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
57215 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
*
57253 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
*
57318 TGATCC-TAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
57354 TATGTGGTCCTT
1 TATGTGGTCCTT
57366 ATGGACATTA
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
101 40 0.36
102 57 0.52
103 13 0.12
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:57419 original size:23 final size:23
Alignment explanation
Indices: 57389--57444 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
57379 TATGGTACTA
57389 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* * *
57412 CGGTGCAATTCTACGTGTCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
57435 AGGTGCAATT
1 CGGTGCAATT
57445 ATATGAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Done.