Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005003.1 Hibiscus syriacus cultivar Beakdansim tig00011224_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: 74883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:432 original size:20 final size:20
Alignment explanation
Indices: 367--436 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
357 CACATGATCA
367 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
**
387 AAATCAAAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
407 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATATGT
427 AAATCGCAAC
1 AAATCGCAAC
437 ACAGAAGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:485 original size:20 final size:20
Alignment explanation
Indices: 326--485 Score: 75
Period size: 20 Copynumber: 8.0 Consensus size: 20
316 AAAATGACCA
* *
326 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAATTT
* * *
346 CAATTTCGCAACAC--ATGAT
1 CAAATTCGCAACGCGAAT-TT
*
365 CAAAATCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAAT-T-T
**
387 -AAA-TCAAAACGCGAATATGT
1 CAAATTCGCAACGCGAAT-T-T
407 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
* * *
425 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACGC-GAATTT
* *
445 CAAATTCGTAACACGGAATTT
1 CAAATTCGCAACGC-GAATTT
466 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
486 ATTTTTCATA
Statistics
Matches: 109, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.02
19 15 0.14
20 70 0.64
21 21 0.19
22 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:2724 original size:20 final size:20
Alignment explanation
Indices: 2674--2724 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2664 ATAAGTCAGT
*
2674 AGTATCGATACCCAGAGGTT
1 AGTATCGATACCCAGAGGTC
* *
2694 AATATTGATACCCAGAGGTC
1 AGTATCGATACCCAGAGGTC
*
2714 AGTATCAATAC
1 AGTATCGATAC
2725 TGAAGAGCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTATCGATACCCAGAGGTC
Found at i:6521 original size:3 final size:3
Alignment explanation
Indices: 6515--6587 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
6505 ACGTAGTAGA
6515 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
6562 ACT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
6588 GAGTTCCTAG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13456 original size:15 final size:15
Alignment explanation
Indices: 13436--13466 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13426 CAAAACGCTG
13436 GTCTAAACTTTTGAA
1 GTCTAAACTTTTGAA
13451 GTCTAAACTTTTGAA
1 GTCTAAACTTTTGAA
13466 G
1 G
13467 CAATAGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (15 bp):
GTCTAAACTTTTGAA
Found at i:21657 original size:21 final size:21
Alignment explanation
Indices: 21590--21663 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 21
21580 AGGTCATTAC
*
21590 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCAAGATGA
* * **
21611 CTAAATCTTTCGTGTC-ATCT-A
1 -TAAGTCTTTCGAG-CAAGATGA
21632 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCTTTCGAGCAAGATGA
*
21653 TAAGTCCTTCG
1 TAAGTCTTTCG
21664 GGCTGTCTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.33
21 12 0.31
22 12 0.31
23 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TAAGTCTTTCGAGCAAGATGA
Found at i:23392 original size:18 final size:18
Alignment explanation
Indices: 23371--23408 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
23361 ATGATATAAG
23371 ATATAAATAATA-TAATTA
1 ATAT-AATAATATTAATTA
*
23389 ATATTATAATATTAATTA
1 ATATAATAATATTAATTA
23407 AT
1 AT
23409 GGTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATAATATTAATTA
Found at i:24765 original size:36 final size:36
Alignment explanation
Indices: 24661--24802 Score: 214
Period size: 36 Copynumber: 3.9 Consensus size: 36
24651 TAATCTGATC
24661 TTGCTTCACTACTCTTTTTGTGAAGGC-TGAATTTGCA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTTG-ATTTGCA
*
24698 TTGCTTCACTACTATTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACT-CTTTTGTGAAGGCTTGATTTGCA
* *
24735 TTGCTTTACTACTCTTTTATGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
*
24771 TTGCTTCACTACTCTTTTGTGAAGACTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
24803 GACTTGAGAA
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
36 50 0.52
37 44 0.46
38 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
Found at i:24781 original size:73 final size:73
Alignment explanation
Indices: 24661--24802 Score: 216
Period size: 73 Copynumber: 1.9 Consensus size: 73
24651 TAATCTGATC
* * *
24661 TTGCTTCACTACTCTTTTTGTGAAGGCTGAATTTGCATTGCTTCACTACTATTTTTGTGAAGGCT
1 TTGCTTCACTACTCTTTTTATGAAGGCTGAATTTGCATTGCTTCACTACT-CTTTTGTGAAGACT
24726 TGATTTGCA
65 TGATTTGCA
*
24735 TTGCTTTACTACTC-TTTTATGAAGGCTTG-ATTTGCATTGCTTCACTACTCTTTTGTGAAGACT
1 TTGCTTCACTACTCTTTTTATGAAGGC-TGAATTTGCATTGCTTCACTACTCTTTTGTGAAGACT
24798 TGATT
65 TGATT
24803 GACTTGAGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
72 17 0.27
73 31 0.49
74 15 0.24
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (73 bp):
TTGCTTCACTACTCTTTTTATGAAGGCTGAATTTGCATTGCTTCACTACTCTTTTGTGAAGACTT
GATTTGCA
Found at i:35421 original size:23 final size:23
Alignment explanation
Indices: 35395--35475 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
35385 TGCTAAGTAT
35395 CGATACCCCCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
*
35418 CGATACCCTCTTTGAATGGGTAC
1 CGATACCCCCTTTGAATGGGTAC
* *
35441 CGATACCCTCTTTGAATGGGTAT
1 CGATACCCCCTTTGAATGGGTAC
*
35464 CAATACCCCCTT
1 CGATACCCCCTT
35476 AGGGTTCTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (23 bp):
CGATACCCCCTTTGAATGGGTAC
Found at i:48843 original size:42 final size:43
Alignment explanation
Indices: 48777--48874 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 43
48767 TAATGAGCTT
* * *
48777 TTTTGCGGCTTTTGTATCAAAAAACACTGCTATAGATATGAGC
1 TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATATGACC
*
48820 TTTTGCGGCGTTTGTATC-AAAAACGCCGCTATAGATATGACC
1 TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATATGACC
* *
48862 ATTTGCGGTGTTT
1 TTTTGCGGCGTTT
48875 ACACGCCGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 32 0.65
43 17 0.35
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (43 bp):
TTTTGCGGCGTTTGTATCAAAAAACACCGCTATAGATATGACC
Found at i:48954 original size:43 final size:43
Alignment explanation
Indices: 48903--49099 Score: 232
Period size: 43 Copynumber: 4.5 Consensus size: 43
48893 GACCTTTTAC
** * *
48903 GGCGTTTGTTCTAAAAACGCCGCTAAATATGAACACCTATTGT
1 GGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGT
* * *
48946 GGTGTTTGTTGGACAAACGTCGCTAAATATCAACACCTATTGC
1 GGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGT
* * *
48989 GGCGTTTGTTGGACAAATGCCGCTAAATATCAACATCTATTGC
1 GGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGT
* * **
49032 GTCGTTTGTTGGACAAACGCCGCTATATATCATTACCTATTGT
1 GGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGT
* *
49075 GGCGTTTTTTGTTGCCAAACGCCGC
1 GGCGTTTGTTG--GACAAACGCCGC
49100 GAACTTTAGC
Statistics
Matches: 131, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 120 0.92
45 11 0.08
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (43 bp):
GGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGT
Found at i:49569 original size:3 final size:3
Alignment explanation
Indices: 49561--49600 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
49551 TAGTTGAGAT
49561 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
49601 AATTGAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:50515 original size:2 final size:2
Alignment explanation
Indices: 50508--50535 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50498 TAGAAATCTC
50508 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
50536 CCCACCATTA
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:50622 original size:20 final size:19
Alignment explanation
Indices: 50591--50639 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
50581 ATTAAAGGAA
50591 ATTTATTATTAACTTTCTTTAT
1 ATTTATT-TTAA--TTCTTTAT
*
50613 -TTTATTTTAATTCTTTTT
1 ATTTATTTTAATTCTTTAT
50631 ATTTATTTT
1 ATTTATTTT
50640 GTAAAACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 4 0.16
21 6 0.24
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTATTTTAATTCTTTAT
Found at i:52059 original size:27 final size:27
Alignment explanation
Indices: 52027--52090 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
52017 CATAAAATAT
52027 ATATTTTTAAATAAAAATAAAAATAAA
1 ATATTTTTAAATAAAAATAAAAATAAA
** **
52054 ATATTTTTAAATTCAGTTAAAAATAAA
1 ATATTTTTAAATAAAAATAAAAATAAA
*
52081 ATATATTTAA
1 ATATTTTTAA
52091 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATTTTTAAATAAAAATAAAAATAAA
Found at i:54605 original size:18 final size:17
Alignment explanation
Indices: 54584--54617 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54574 TTATGTTGAA
*
54584 TTTAGATTTTAATTTTAT
1 TTTAAATTTT-ATTTTAT
54602 TTTAAATTTTATTTTA
1 TTTAAATTTTATTTTA
54618 ATAAAATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAAATTTTATTTTAT
Found at i:54609 original size:12 final size:12
Alignment explanation
Indices: 54589--54618 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54579 TTGAATTTAG
54589 ATTTT-AATTTT
1 ATTTTAAATTTT
54600 ATTTTAAATTTT
1 ATTTTAAATTTT
54612 ATTTTAA
1 ATTTTAA
54619 TAAAATAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTAAATTTT
Found at i:62194 original size:9 final size:9
Alignment explanation
Indices: 62180--62212 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
62170 TCTATCTACT
62180 TTCATTTTC
1 TTCATTTTC
62189 TTCATTTT-
1 TTCATTTTC
62197 TT-ATTTTC
1 TTCATTTTC
62205 TTCATTTT
1 TTCATTTT
62213 TCATTCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.23
8 4 0.18
9 13 0.59
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TTCATTTTC
Found at i:62204 original size:16 final size:16
Alignment explanation
Indices: 62183--62213 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62173 ATCTACTTTC
62183 ATTTTCTTCATTTTTT
1 ATTTTCTTCATTTTTT
62199 ATTTTCTTCATTTTT
1 ATTTTCTTCATTTTT
62214 CATTCTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTCTTCATTTTTT
Found at i:64505 original size:21 final size:21
Alignment explanation
Indices: 64437--64497 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
64427 AATAGTATTG
64437 ATACTCCTAATAGGTGTACCA
1 ATACTCCTAATAGGTGTACCA
*
64458 ATAATCCTAATAGGTGTACCA
1 ATACTCCTAATAGGTGTACCA
64479 ATACTCCTAATAGGTGTAC
1 ATACTCCTAATAGGTGTAC
64498 TGATACTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (21 bp):
ATACTCCTAATAGGTGTACCA
Done.