Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007264.1 Hibiscus syriacus cultivar Beakdansim tig00019254_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: 56817
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:633 original size:2 final size:2
Alignment explanation
Indices: 626--653 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
616 TTCACCGTTA
626 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
654 TGTTGCTAGT
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:9375 original size:20 final size:20
Alignment explanation
Indices: 9342--9398 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
9332 CGGCTAAATT
*
9342 AATATATTTT-ATAATAATTG
1 AATATATTTTAATAATAA-AG
*
9362 CATAT-TTTTAATAATTAAAG
1 AATATATTTTAATAA-TAAAG
9382 AATATATTTTAATAATA
1 AATATATTTTAATAATA
9399 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 15 0.48
21 12 0.39
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATATTTTAATAATAAAG
Found at i:9393 original size:21 final size:21
Alignment explanation
Indices: 9342--9406 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
9332 CGGCTAAATT
*
9342 AATATATTTT-ATAA-TAATTG
1 AATATATTTTAATAATTAA-AG
*
9362 CATAT-TTTTAATAATTAAAG
1 AATATATTTTAATAATTAAAG
9382 AATATATTTTAATAATATAAA-
1 AATATATTTTAATAAT-TAAAG
9403 AATA
1 AATA
9407 AAAAATCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.11
20 13 0.34
21 17 0.45
22 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
AATATATTTTAATAATTAAAG
Found at i:12137 original size:50 final size:51
Alignment explanation
Indices: 12000--12179 Score: 199
Period size: 51 Copynumber: 3.5 Consensus size: 51
11990 GTAACAGTAA
* * *
12000 AGCGCGCCCCCTGAAT-CGCGCTATATGCTGATTTGGCG-T-CACGTGGAGTAT
1 AGCGCGCCCCCTG-CTCCGCGCTATACGCTGA-TTGG-GTTACACGTGGGGTAT
* * * * *
12051 AGCGCTCCCCCTG-TATCGCGTTATATGCTGACTGGGTTACACGTGGGGTAT
1 AGCGCGCCCCCTGCT-CCGCGCTATACGCTGATTGGGTTACACGTGGGGTAT
* *
12102 AACGC-ACCCCTGCTCCGCGCTATACGCTGATTGGGTTACACGTGGGGTAT
1 AGCGCGCCCCCTGCTCCGCGCTATACGCTGATTGGGTTACACGTGGGGTAT
12152 AGCGCGCCCCCTGCTCCGCGCTATACGC
1 AGCGCGCCCCCTGCTCCGCGCTATACGC
12180 CACGTAGGGG
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
49 2 0.02
50 46 0.41
51 63 0.57
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.24
Consensus pattern (51 bp):
AGCGCGCCCCCTGCTCCGCGCTATACGCTGATTGGGTTACACGTGGGGTAT
Found at i:15368 original size:111 final size:111
Alignment explanation
Indices: 15045--15377 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
15035 ATTACAAAAA
*
15045 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
15110 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTATCAAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
15156 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
15221 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
15267 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
15332 AATTAAACCGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
15378 ATGATTTCCA
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:15527 original size:10 final size:11
Alignment explanation
Indices: 15509--15544 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
15499 AAGATAGAGT
15509 ATTTGAGAGAA
1 ATTTGAGAGAA
15520 ATTT-AGAG-A
1 ATTTGAGAGAA
15529 ATTTGAGAG-A
1 ATTTGAGAGAA
15539 ATTTGA
1 ATTTGA
15545 TGTGATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 15 0.62
11 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:15720 original size:50 final size:50
Alignment explanation
Indices: 15666--15791 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
15656 AGATACCCAT
* * *
15666 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTTGCGCCAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCAACGTGGCGCCAAATCACC
* * ** *
15716 GTATATCACGGGA-CAGGGGATGCGCTATACCAACGTGGCGCCAAATCAGC
1 GTATAGCGC-GGATCAGGGGGCGCGCTATACCAACGTGGCGCCAAATCACC
* * *
15766 GTATAGAGCGGTTCAGGGGGCTCGCT
1 GTATAGCGCGGATCAGGGGGCGCGCT
15792 TTACTGCTAC
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.03
50 54 0.92
51 3 0.05
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCAACGTGGCGCCAAATCACC
Found at i:22416 original size:15 final size:15
Alignment explanation
Indices: 22396--22425 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22386 ATTGCCAATG
*
22396 GAACCAGCGGCACCC
1 GAACCAGCAGCACCC
22411 GAACCAGCAGCACCC
1 GAACCAGCAGCACCC
22426 CAGACAGACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (15 bp):
GAACCAGCAGCACCC
Found at i:26153 original size:21 final size:22
Alignment explanation
Indices: 26108--26154 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
26098 CATATAATTA
*
26108 TAAATTAGTTTAAATTTAAAAG
1 TAAATTAGTTTAAATATAAAAG
26130 TAAATTA-TTTAAA-ATAAAAGG
1 TAAATTAGTTTAAATATAAAA-G
26151 TAAA
1 TAAA
26155 CTATGTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
TAAATTAGTTTAAATATAAAAG
Found at i:28755 original size:23 final size:23
Alignment explanation
Indices: 28729--28776 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28719 ATAAAGTACA
*
28729 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
28752 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
28775 AT
1 AT
28777 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:29226 original size:23 final size:23
Alignment explanation
Indices: 29200--29262 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
29190 ATATAACCAC
29200 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
29223 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
29246 TACCTATTACATCATAT
1 TACCTATTACATTATAT
29263 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:29736 original size:39 final size:39
Alignment explanation
Indices: 29682--29767 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
29672 CAAGTTGTAG
*
29682 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
29721 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
29760 ATTTTGAT
1 ATTTTGAT
29768 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:30047 original size:18 final size:18
Alignment explanation
Indices: 30024--30060 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30014 CGAAATATAT
30024 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
30042 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
30060 A
1 A
30061 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:30514 original size:23 final size:23
Alignment explanation
Indices: 30482--30630 Score: 219
Period size: 23 Copynumber: 6.5 Consensus size: 23
30472 GATAGATACT
*
30482 TTACAATATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
* *
30505 TTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTA
30528 TTACATTATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
*
30551 TTACATTATATAAGC-ACTACCTA
1 TTACATTATATAAACGA-TACCTA
30574 TTACATTATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
* *
30597 TTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTA
*
30620 TTACATCATAT
1 TTACATTATAT
30631 GTTTACCTAT
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.01
23 112 0.98
24 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.35
Consensus pattern (23 bp):
TTACATTATATAAACGATACCTA
Found at i:30532 original size:46 final size:46
Alignment explanation
Indices: 30482--30630 Score: 271
Period size: 46 Copynumber: 3.2 Consensus size: 46
30472 GATAGATACT
*
30482 TTACAATATATAAACGATACCTATTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTA
*
30528 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTA
30574 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTA
*
30620 TTACATCATAT
1 TTACATTATAT
30631 GTTTACCTAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.35
Consensus pattern (46 bp):
TTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTA
Found at i:31032 original size:25 final size:25
Alignment explanation
Indices: 30975--31040 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
30965 CACTCAAAAG
*
30975 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
31000 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
31025 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
31041 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:32307 original size:17 final size:18
Alignment explanation
Indices: 32285--32327 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
32275 ATATATCCGG
32285 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
32302 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
32322 TATCAT
1 TATCAT
32328 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:32345 original size:20 final size:19
Alignment explanation
Indices: 32290--32336 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
32280 TCCGGTATCA
32290 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
32309 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
32330 TTTTACC
1 TTTTACC
32337 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:32484 original size:20 final size:20
Alignment explanation
Indices: 32458--32503 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
32448 CACTTTTAAA
32458 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
32477 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
32498 TTTACC
1 TTTACC
32504 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:33860 original size:2 final size:2
Alignment explanation
Indices: 33853--33889 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33843 AAAATTTACT
33853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33890 TATTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34464 original size:3 final size:3
Alignment explanation
Indices: 34456--34497 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
34446 CGTAGCCCTC
34456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34498 GTAAATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34966 original size:2 final size:2
Alignment explanation
Indices: 34959--34984 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34949 TATGCATTTA
34959 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
34985 TCCCTTTTTA
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:49902 original size:29 final size:29
Alignment explanation
Indices: 49859--49941 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
49849 CTCACCTAAC
49859 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
* **
49889 TAAATGATGCAAGCAATGACATTTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
49918 TAAATGATATAAGCAATGATATCA
1 TAAATGATGTAAGCAATGACATCA
49942 ATTTAGTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 41 0.91
30 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Done.