Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002909.1 Hibiscus syriacus cultivar Beakdansim tig00006011_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: 58683
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2437 original size:20 final size:21
Alignment explanation
Indices: 2399--2463 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 21
2389 TACGTAACGT
2399 CCGCAACATCCGCAACCGCAA
1 CCGCAACATCCGCAACCGCAA
* *
2420 CCGCAACA-CCGTAACCGCAT
1 CCGCAACATCCGCAACCGCAA
2440 CCGCAACAAAATCCGCAACCGCAA
1 CCGCAAC---ATCCGCAACCGCAA
2464 TTTGATACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.47
21 8 0.22
23 1 0.03
24 10 0.28
ACGTcount: A:0.35, C:0.45, G:0.14, T:0.06
Consensus pattern (21 bp):
CCGCAACATCCGCAACCGCAA
Found at i:6599 original size:4 final size:4
Alignment explanation
Indices: 6546--6579 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
6536 ACATCCACAT
6546 AATA TAATA AATA AATA AATA AATA AATA AATA A
1 AATA -AATA AATA AATA AATA AATA AATA AATA A
6580 CGAAATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:6609 original size:20 final size:20
Alignment explanation
Indices: 6570--6609 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6560 ATAAATAAAT
** *
6570 AAATAAATAACGAAATACTA
1 AAATAAATAAAAAAACACTA
6590 AAATAAATAAAAAAACACTA
1 AAATAAATAAAAAAACACTA
6610 TGAATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (20 bp):
AAATAAATAAAAAAACACTA
Found at i:6992 original size:6 final size:6
Alignment explanation
Indices: 6983--7148 Score: 269
Period size: 6 Copynumber: 27.7 Consensus size: 6
6973 CATACACATA
6983 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
*
7031 TACACG TACACG TACACG TACATG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
* ** * * *
7079 TACACG TACACA TACATA TACACG TACACG TACATG TACACA TATACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
7127 TACACG TACACG TACACG TACA
1 TACACG TACACG TACACG TACA
7149 TATACATATA
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 148 1.00
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (6 bp):
TACACG
Found at i:16053 original size:16 final size:17
Alignment explanation
Indices: 16028--16063 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
16018 TTAAGCAATC
16028 AAAAGCAATAAACA-AA
1 AAAAGCAATAAACATAA
*
16044 AAAAGTAATAAACATAA
1 AAAAGCAATAAACATAA
16061 AAA
1 AAA
16064 TATCAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAGCAATAAACATAA
Found at i:23933 original size:27 final size:27
Alignment explanation
Indices: 23893--24041 Score: 266
Period size: 27 Copynumber: 5.6 Consensus size: 27
23883 CTATAGGAAT
23893 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
23918 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
23945 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
23972 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
23999 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
24026 TATAGAGATATGATTT
1 TATAGAGATATGATTT
24042 TGTAAATAGA
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
25 7 0.06
27 113 0.94
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:27781 original size:27 final size:27
Alignment explanation
Indices: 27741--27889 Score: 248
Period size: 27 Copynumber: 5.6 Consensus size: 27
27731 GTGTAGGAAT
27741 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
27766 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
27793 TATAGAGATATGATTTGTTACTATTCC
1 TATAGAGATATGATTTGTTACCATTCC
27820 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
* *
27847 TATAGAGGTATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
27874 TATAGAGATATGATTT
1 TATAGAGATATGATTT
27890 TGTAAATAGA
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
25 7 0.06
27 109 0.94
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:33708 original size:36 final size:36
Alignment explanation
Indices: 33661--33763 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
33651 TCTGCAGGAG
*
33661 ATAGTTATTCTTCTAAATATCTCATGCATCTATGG-T
1 ATAGTTATTCTTCGAAATATCTCATGCATCT-TGGAT
*
33697 ATAGTTATTCTTCGAAATATCTCATGAATC-TGGAAT
1 ATAGTTATTCTTCGAAATATCTCATGCATCTTGG-AT
33733 ATAGTTATTCTTCGAAATATCTCATGCATCT
1 ATAGTTATTCTTCGAAATATCTCATGCATCT
33764 GAGGATTGCA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 3 0.05
36 58 0.95
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (36 bp):
ATAGTTATTCTTCGAAATATCTCATGCATCTTGGAT
Found at i:37794 original size:16 final size:16
Alignment explanation
Indices: 37772--37812 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
37762 CAACCTTATC
*
37772 CTAATAAATAACCCTT
1 CTAATAAATAACCCTA
* *
37788 GTAATAAATAATCCTA
1 CTAATAAATAACCCTA
37804 CTAATAAAT
1 CTAATAAAT
37813 TGGGTAGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (16 bp):
CTAATAAATAACCCTA
Found at i:39072 original size:37 final size:37
Alignment explanation
Indices: 39027--39137 Score: 143
Period size: 37 Copynumber: 3.0 Consensus size: 37
39017 ATTCCAGTCT
* * **
39027 AATATAAATTTAT-AATAATTTGTTTGTATTTTAATTG
1 AATATAAATTTATAAATAATATATTTGTA-TTTAATCA
*
39064 AATGTAAATTTATAAATAATATATTTGTATTTAATCA
1 AATATAAATTTATAAATAATATATTTGTATTTAATCA
*
39101 AATATAAATTTATAAATAATATATTTATATTTCAATC
1 AATATAAATTTATAAATAATATATTTGTATTT-AATC
39138 GATTATATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
37 48 0.74
38 17 0.26
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (37 bp):
AATATAAATTTATAAATAATATATTTGTATTTAATCA
Found at i:47698 original size:60 final size:60
Alignment explanation
Indices: 47616--47775 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 60
47606 CGAAAGATCT
* * * * **
47616 AAAAGTTTAGGGACCAAATTAGAATGAGATTCATAGTTTGAGGATGAAATTGGAATATTC
1 AAAAGTTTAAGGACTAATTTAGAATGAGATTCATAGTTTGAGGATAAAATTAAAATATTC
* * * * *
47676 AAAAGTTTAAGGACTAATTTAGAATGAAAGTCCTATTTTGAGGATAAAATTAAAATATTT
1 AAAAGTTTAAGGACTAATTTAGAATGAGATTCATAGTTTGAGGATAAAATTAAAATATTC
* *
47736 AGAAGTTTAAAGACTAATTTCA-AATGAG-TGTCATAGTTTG
1 AAAAGTTTAAGGACTAATTT-AGAATGAGAT-TCATAGTTTG
47776 GGGACATATG
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
60 80 0.99
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAGAATGAGATTCATAGTTTGAGGATAAAATTAAAATATTC
Found at i:48112 original size:15 final size:15
Alignment explanation
Indices: 48092--48120 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48082 TTTATACTCC
48092 TTTTTACTATTGTTG
1 TTTTTACTATTGTTG
48107 TTTTTACTATTGTT
1 TTTTTACTATTGTT
48121 ATCTAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTTACTATTGTTG
Found at i:50322 original size:12 final size:11
Alignment explanation
Indices: 50304--50369 Score: 64
Period size: 12 Copynumber: 6.0 Consensus size: 11
50294 TTTAGTAAAA
50304 AATAATATTTT
1 AATAATATTTT
50315 AGATAATATTTT
1 A-ATAATATTTT
* *
50327 AATAAAAATATT
1 AAT-AATATTTT
50339 AAT-AT-TTTT
1 AATAATATTTT
50348 AATAATATTTT
1 AATAATATTTT
**
50359 TTTAATATTTT
1 AATAATATTTT
50370 TTTATCTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 6 0.13
10 3 0.07
11 16 0.36
12 20 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATAATATTTT
Found at i:50353 original size:32 final size:30
Alignment explanation
Indices: 50287--50358 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 30
50277 CGTCTAATAT
*
50287 TAATATTTTTAGTAAAAAATAATATTTTAGA
1 TAATA-TTTTAATAAAAAATAATATTTTAGA
50318 TAATATTTTAATAAAAATATTAATATTTTTA-A
1 TAATATTTTAATAAAAA-A-TAATA-TTTTAGA
50350 TAATATTTT
1 TAATATTTT
50359 TTTAATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 11 0.30
31 6 0.16
32 15 0.41
33 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
TAATATTTTAATAAAAAATAATATTTTAGA
Found at i:50356 original size:18 final size:19
Alignment explanation
Indices: 50318--50356 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
50308 ATATTTTAGA
50318 TAATATTTTAATAAAAATAT
1 TAATATTTT-ATAAAAATAT
*
50338 TAATATTTT-TAATAATAT
1 TAATATTTTATAAAAATAT
50356 T
1 T
50357 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTTTATAAAAATAT
Found at i:50364 original size:11 final size:11
Alignment explanation
Indices: 50337--50373 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
50327 AATAAAAATA
50337 TTAATATTTTT
1 TTAATATTTTT
*
50348 AATAATATTTTT
1 -TTAATATTTTT
50360 TTAATATTTTT
1 TTAATATTTTT
50371 TTA
1 TTA
50374 TCTATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:53289 original size:2 final size:2
Alignment explanation
Indices: 53282--53335 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
53272 ATATGGAACG
53282 AT AT AT AT 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 AT AT AT AT
53324 AT AT AT AT AT AT
1 AT AT AT AT AT AT
53336 GGGAAGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57330 original size:21 final size:21
Alignment explanation
Indices: 57301--57353 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
57291 ATTCTGACTA
57301 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
57322 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTCCCAAAT
*
57343 TCGCAATGCGA
1 TCGCATTGCGA
57354 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:57368 original size:20 final size:20
Alignment explanation
Indices: 57343--57529 Score: 286
Period size: 20 Copynumber: 9.3 Consensus size: 20
57333 TTTTCCGAAT
57343 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
57363 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
57384 TTGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
57404 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
57424 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
57444 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
57464 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
57484 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
57504 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
57524 TCGCAA
1 TCGCAA
57530 CGAGATTCTG
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 136 0.90
21 14 0.09
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:58410 original size:24 final size:24
Alignment explanation
Indices: 58383--58436 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
58373 GTATTCGAAA
58383 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
58407 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
58431 TTTGAT
1 TTTGAT
58437 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.