Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005342.1 Hibiscus syriacus cultivar Beakdansim tig00012102_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: 42217
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2340 original size:2 final size:2
Alignment explanation
Indices: 2329--2377 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2319 ACAAATAAAA
2329 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2370 AG AG AG AG
1 AG AG AG AG
2378 GTTGCGCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4204 original size:17 final size:17
Alignment explanation
Indices: 4147--4204 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
4137 TTATATCAAG
4147 TTATATTT-AATGTTATT
1 TTATATTTAAATG-TATT
* * * *
4164 TTTTAATTAAATTTCATG
1 TTATATTTAAATGT-ATT
4182 TTATATTTAAATGTATT
1 TTATATTTAAATGTATT
4199 TTATAT
1 TTATAT
4205 ATTCTATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (17 bp):
TTATATTTAAATGTATT
Found at i:8649 original size:23 final size:23
Alignment explanation
Indices: 8619--8671 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
8609 TGAACCGGTA
*
8619 AGGAGGCGATGAACGGAAACGGC
1 AGGAGGCGATGAACAGAAACGGC
*
8642 AGGAGGCGATGAATAGAAACGGC
1 AGGAGGCGATGAACAGAAACGGC
*
8665 TGGAGGC
1 AGGAGGC
8672 AGGCAAGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.43, T:0.08
Consensus pattern (23 bp):
AGGAGGCGATGAACAGAAACGGC
Found at i:10159 original size:47 final size:48
Alignment explanation
Indices: 10089--10185 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
10079 GGCCATACTT
*
10089 ATTGTTTATATTGATGACATTATCATAATAGGAGATGACTTTGAAGAA
1 ATTGTTTATATTGATGACATTATCATAATAGGAGATGACTATGAAGAA
* * *
10137 ATTG-TTATGTTGATGACATTATCGTAATAGGAGATGACTATGGAGAA
1 ATTGTTTATATTGATGACATTATCATAATAGGAGATGACTATGAAGAA
10184 AT
1 AT
10186 CAATAAGCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 41 0.91
48 4 0.09
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (48 bp):
ATTGTTTATATTGATGACATTATCATAATAGGAGATGACTATGAAGAA
Found at i:22604 original size:26 final size:27
Alignment explanation
Indices: 22575--22629 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
22565 AGATTGTAAA
22575 CAAAC-TCTAAACAACCTGCTAACTAG
1 CAAACATCTAAACAACCTGCTAACTAG
*
22601 CAAACAGATTCTAAACCACCTGCTAACTA
1 CAAAC--A-TCTAAACAACCTGCTAACTA
22630 TTCTTCAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
30 19 0.79
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.20
Consensus pattern (27 bp):
CAAACATCTAAACAACCTGCTAACTAG
Found at i:24867 original size:2 final size:2
Alignment explanation
Indices: 24860--24923 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
24850 ATGCATCCAA
24860 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
24902 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
24924 CAGGTACATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26053 original size:2 final size:2
Alignment explanation
Indices: 26042--26102 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
26032 ATATTATACT
26042 TA TA -A TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
26082 TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
26103 TACTTAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30989 original size:19 final size:20
Alignment explanation
Indices: 30956--31001 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
30946 ATACTCATCT
30956 ATATATTATTGAATAAAAATA
1 ATAT-TTATTGAATAAAAATA
*
30977 ATATTTATT-AATAAATATA
1 ATATTTATTGAATAAAAATA
*
30996 TTATTT
1 ATATTT
31002 TGGGTCGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 5 0.22
21 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTTATTGAATAAAAATA
Found at i:34240 original size:39 final size:39
Alignment explanation
Indices: 34196--34277 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
34186 TAAATTCTAA
34196 ATTTAATCCTAATCTTATTTAGAGGGAGAGAAAAAATAG
1 ATTTAATCCTAATCTTATTTAGAGGGAGAGAAAAAATAG
34235 ATTTAATCCTAATCTTATTTAGAGGGAGAGAAAAAATAG
1 ATTTAATCCTAATCTTATTTAGAGGGAGAGAAAAAATAG
34274 ATTT
1 ATTT
34278 TAGATTAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (39 bp):
ATTTAATCCTAATCTTATTTAGAGGGAGAGAAAAAATAG
Found at i:34797 original size:2 final size:2
Alignment explanation
Indices: 34790--34840 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
34780 AACCAAAAGA
34790 AT AT AT AT AT AT AT AT A- 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
*
34831 AT CT AT AT AT
1 AT AT AT AT AT
34841 CGCGTTCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35115 original size:2 final size:2
Alignment explanation
Indices: 35110--35136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35100 CTTGTGTGTG
35110 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 T
35137 TCGAGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35287 original size:20 final size:20
Alignment explanation
Indices: 35262--35308 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
35252 AGTTTCCAAT
*
35262 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTATAAA
*
35282 TCGCAATGCGAATTTATAAA
1 TCGCAACGCGAATTTATAAA
35302 TCGCAAC
1 TCGCAAC
35309 ACAGAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTATAAA
Found at i:35325 original size:20 final size:20
Alignment explanation
Indices: 35302--35367 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
35292 AATTTATAAA
*
35302 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAATCAAAT
*
35322 TCGCAACACA-AAATCAATT
1 TCGCAACACAGAAATCAAAT
* *
35341 TCGCAA-ACTGAATTTCAAAT
1 TCGCAACACAGAA-ATCAAAT
35361 TCGCAAC
1 TCGCAAC
35368 TGAATTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.05
19 15 0.39
20 21 0.55
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAATCAAAT
Found at i:35338 original size:19 final size:19
Alignment explanation
Indices: 35302--35386 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
35292 AATTTATAAA
*
35302 TCGCAACACAGAAGTCAAAT
1 TCGCAACACA-AATTCAAAT
* *
35322 TCGCAACACAAAATCAATT
1 TCGCAACACAAATTCAAAT
*
35341 TCGCAA-ACTGAATTTCAAAT
1 TCGCAACAC--AAATTCAAAT
** *
35361 TCGCAACTGAATTTCAAAT
1 TCGCAACACAAATTCAAAT
35380 TCGCAAC
1 TCGCAAC
35387 TCGATTTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.04
19 30 0.55
20 23 0.42
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (19 bp):
TCGCAACACAAATTCAAAT
Found at i:35393 original size:19 final size:19
Alignment explanation
Indices: 35316--35387 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
35306 AACACAGAAG
** **
35316 TCAAATTCGCAACACAAAA
1 TCAAATTCGCAACTGAATT
*
35335 TCAATTTCGCAAACTGAATT
1 TCAAATTCGC-AACTGAATT
35355 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
35374 TCAAATTCGCAACT
1 TCAAATTCGCAACT
35388 CGATTTTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 32 0.70
20 14 0.30
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:38594 original size:18 final size:18
Alignment explanation
Indices: 38567--38603 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38557 GTGCCAAGCA
*
38567 AAAATCAAAATCGCAATC
1 AAAATCAAAATCCCAATC
*
38585 AAAATTAAAATCCCAATC
1 AAAATCAAAATCCCAATC
38603 A
1 A
38604 CAACCGGGCT
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:0.57, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAATCAAAATCCCAATC
Found at i:38920 original size:20 final size:20
Alignment explanation
Indices: 38897--38934 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38887 AAAACCGCAA
*
38897 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTATCGCGT
38917 TGCGAATTTGACTATCGC
1 TGCGAATTTGACTATCGC
38935 AACGAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TGCGAATTTGACTATCGCGT
Found at i:40237 original size:21 final size:22
Alignment explanation
Indices: 40201--40249 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
40191 ATGGAGATAG
40201 ACGGATTTCGTCGGAGATGGGA
1 ACGGATTTCGTCGGAGATGGGA
*
40223 ACGGATTTC-TCGGAGATGGGG
1 ACGGATTTCGTCGGAGATGGGA
40244 ACGGAT
1 ACGGAT
40250 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.22
Consensus pattern (22 bp):
ACGGATTTCGTCGGAGATGGGA
Found at i:40356 original size:19 final size:19
Alignment explanation
Indices: 40332--40378 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
40322 CTGTTTACAT
40332 TTGTGTTTCTCAATTAATA
1 TTGTGTTTCTCAATTAATA
40351 TTGTGTTTCTCAATTAATA
1 TTGTGTTTCTCAATTAATA
40370 TTGTGTTTC
1 TTGTGTTTC
40379 GAATTCGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (19 bp):
TTGTGTTTCTCAATTAATA
Found at i:40422 original size:19 final size:19
Alignment explanation
Indices: 40384--40425 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40374 GTTTCGAATT
**
40384 CGAAAATAAATTCGCGTTG
1 CGAAAATAAACGCGCGTTG
*
40403 CGAAAATAAACGCGCTTTG
1 CGAAAATAAACGCGCGTTG
40422 CGAA
1 CGAA
40426 TTTGACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (19 bp):
CGAAAATAAACGCGCGTTG
Found at i:40444 original size:20 final size:20
Alignment explanation
Indices: 40419--40568 Score: 221
Period size: 20 Copynumber: 7.5 Consensus size: 20
40409 TAAACGCGCT
*
40419 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
*
40439 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
* *
40459 TTGCAAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGTG
*
40479 TTGCGAATTTGACTTCTATG
1 TTGCGAATTTGACTTCTGTG
*
40499 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
*
40519 TTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
40539 TTGC-AATTTGACATCTGTG
1 TTGCGAATTTGACTTCTGTG
40558 TTGCGAATTTG
1 TTGCGAATTTG
40569 TTGTCATTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 18 0.15
20 99 0.85
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Done.