Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005508.1 Hibiscus syriacus cultivar Beakdansim tig00012713_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: 77693
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:279 original size:113 final size:111
Alignment explanation
Indices: 81--297 Score: 346
Period size: 113 Copynumber: 1.9 Consensus size: 111
71 GATGATGCAG
* * *
81 TTCATCTTTCAATTCCAATGATCGGTTCTGGGTTCCTACCGAATCAGATCAGATAACTCAAAGAA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGTTCATACCAAATCA-ATCAGATAACTCAAAGAA
146 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 CACTTCCAGAAGATGCTATTGGGTCTCCTTA-TTCTACTATGAGCAAA
* *
194 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAATC-ATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGG-TTCT-GGGTTCATACCAAATCAATCAGATAACTCAAAGA
258 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTCTACTA
64 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTCTACTA
298 CGAGAACATG
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
112 8 0.08
113 72 0.74
114 3 0.03
115 14 0.14
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (111 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGTTCATACCAAATCAATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTCCTTATTCTACTATGAGCAAA
Found at i:2555 original size:21 final size:18
Alignment explanation
Indices: 2519--2588 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 18
2509 ATTTTTTTCC
*
2519 TTTTCTTTTTT--GTTTT
1 TTTTCTTTTTTCCTTTTT
2535 TTTTCTATTTCATTCCTTTTT
1 TTTTCT-TTT--TTCCTTTTT
*
2556 TTTTCTTTTTTCC-TCTT
1 TTTTCTTTTTTCCTTTTT
2573 TTTTCTTTTTTCCTTT
1 TTTTCTTTTTTCCTTT
2589 CTTTGCTGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 6 0.13
17 19 0.42
18 5 0.11
19 2 0.04
20 3 0.07
21 10 0.22
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTTTCCTTTTT
Found at i:2603 original size:22 final size:22
Alignment explanation
Indices: 2578--2621 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2568 CTCTTTTTTC
2578 TTTTTTCCTTTCTTTGCTGGAT
1 TTTTTTCCTTTCTTTGCTGGAT
* *
2600 TTTTTTTCTTTCTTTGTTGGAT
1 TTTTTTCCTTTCTTTGCTGGAT
2622 GAGTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.05, C:0.14, G:0.14, T:0.68
Consensus pattern (22 bp):
TTTTTTCCTTTCTTTGCTGGAT
Found at i:5788 original size:14 final size:14
Alignment explanation
Indices: 5750--5803 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
5740 CATAAAAATA
* *
5750 CAAATGCAAAGATG
1 CAAATGTAAATATG
5764 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
5779 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
5793 TAAATGTAAAT
1 CAAATGTAAAT
5804 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:7527 original size:37 final size:37
Alignment explanation
Indices: 7456--7529 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
7446 AATACCTGAA
7456 AAAAATATTAACAACAAAATATAAAAATAATAAATAAT
1 AAAAATATTAACAACAAAATATAAAAAT-ATAAATAAT
* *
7494 AAAAATTTTAA-AAGAAAATAATTAAAAAT-TAAATAA
1 AAAAATATTAACAACAAAAT-A-TAAAAATATAAATAA
7530 ATGAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 14 0.44
38 11 0.34
39 7 0.22
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (37 bp):
AAAAATATTAACAACAAAATATAAAAATATAAATAAT
Found at i:9620 original size:3 final size:3
Alignment explanation
Indices: 9591--9672 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
9581 TTGAGTTTTG
* * * * *
9591 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
9638 TAA TAA TAA TAA TAA -ATA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
9673 TAAATAACGT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
2 1 0.01
3 59 0.88
4 7 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:9646 original size:24 final size:24
Alignment explanation
Indices: 9591--9678 Score: 97
Period size: 24 Copynumber: 3.6 Consensus size: 24
9581 TTGAGTTTTG
* *
9591 TAATATTAATAAATAATATATATTAA
1 TAATAATAATAAAT-AT-TATAATAA
* *
9617 TAATAATAATAATTATTATTATAA
1 TAATAATAATAAATATTATAATAA
* *
9641 TAATAATAATAAATATAATGATAA
1 TAATAATAATAAATATTATAATAA
9665 TAATAAT-ATAAATA
1 TAATAATAATAAATA
9679 ACGTTTAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 7 0.13
24 34 0.62
25 2 0.04
26 12 0.22
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (24 bp):
TAATAATAATAAATATTATAATAA
Found at i:14933 original size:20 final size:21
Alignment explanation
Indices: 14904--14943 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
14894 TGATAGAACG
*
14904 CTACTTAAAATATT-ATTTTT
1 CTACTGAAAATATTAATTTTT
14924 CTACTGAAAATATTAATTTT
1 CTACTGAAAATATTAATTTT
14944 GTTACCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
CTACTGAAAATATTAATTTTT
Found at i:22470 original size:13 final size:13
Alignment explanation
Indices: 22452--22476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22442 CGGCAACAGC
22452 TGGTTTGACATGA
1 TGGTTTGACATGA
22465 TGGTTTGACATG
1 TGGTTTGACATG
22477 TACCTCGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.40
Consensus pattern (13 bp):
TGGTTTGACATGA
Found at i:28151 original size:42 final size:42
Alignment explanation
Indices: 28092--28187 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
28082 TTTGGGAGCC
* *
28092 GGAACTGGAATCGGAACCTGTTGC-ACCGGTTCCTAAAAAATG
1 GGAACCGGAACCGGAACCTGTT-CAACCGGTTCCTAAAAAATG
* *
28134 GGAACCGGAACCGGAACCTGTTCAACCGGTTCCTAGAAATTG
1 GGAACCGGAACCGGAACCTGTTCAACCGGTTCCTAAAAAATG
28176 GGAACCGGAACC
1 GGAACCGGAACC
28188 TGTAGGTACC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (42 bp):
GGAACCGGAACCGGAACCTGTTCAACCGGTTCCTAAAAAATG
Found at i:28216 original size:13 final size:13
Alignment explanation
Indices: 28198--28229 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28188 TGTAGGTACC
28198 GGTACCGGTTCCA
1 GGTACCGGTTCCA
28211 GGTACCGGTTCCA
1 GGTACCGGTTCCA
28224 GGTACC
1 GGTACC
28230 CTGTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GGTACCGGTTCCA
Found at i:34135 original size:30 final size:30
Alignment explanation
Indices: 34099--34157 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
34089 TATATTTAGG
34099 ACCTATGAGAAAGATATG-TCAATATCAAGC
1 ACCTATGAGAAAGATATGCT-AATATCAAGC
34129 ACCTATGAGAAAGATATGCTAATATCAAG
1 ACCTATGAGAAAGATATGCTAATATCAAG
34158 AACGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (30 bp):
ACCTATGAGAAAGATATGCTAATATCAAGC
Found at i:34614 original size:69 final size:69
Alignment explanation
Indices: 34535--34677 Score: 277
Period size: 69 Copynumber: 2.1 Consensus size: 69
34525 GAATGCAGTA
*
34535 GAAGGCAAATAAATAGAATAACATCACATAATATAATATTTATTTAGAGTGGCGGATTCACATGT
1 GAAGGCAAATAAATAGAATAACATCACATAACATAATATTTATTTAGAGTGGCGGATTCACATGT
34600 ATCC
66 ATCC
34604 GAAGGCAAATAAATAGAATAACATCACATAACATAATATTTATTTAGAGTGGCGGATTCACATGT
1 GAAGGCAAATAAATAGAATAACATCACATAACATAATATTTATTTAGAGTGGCGGATTCACATGT
34669 ATCC
66 ATCC
34673 GAAGG
1 GAAGG
34678 TGGGCAAGTG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (69 bp):
GAAGGCAAATAAATAGAATAACATCACATAACATAATATTTATTTAGAGTGGCGGATTCACATGT
ATCC
Found at i:40203 original size:6 final size:6
Alignment explanation
Indices: 40192--40226 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
40182 CTTGAGCTGA
40192 TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TTCTG
1 TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TTCTG
40227 ACTCTACCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.31, T:0.51
Consensus pattern (6 bp):
TTCTGG
Found at i:51887 original size:2 final size:2
Alignment explanation
Indices: 51880--51915 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
51870 TAGTTTTTAA
51880 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
51916 GGTTTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58944 original size:23 final size:23
Alignment explanation
Indices: 58914--58973 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
58904 ATTATTATAT
58914 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
58937 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
58960 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
58974 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:65410 original size:16 final size:16
Alignment explanation
Indices: 65389--65421 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
65379 TACATCTCAT
*
65389 TTTGAAAGTTTGAGAG
1 TTTGAAAGATTGAGAG
65405 TTTGAAAGATTGAGAG
1 TTTGAAAGATTGAGAG
65421 T
1 T
65422 CTTATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (16 bp):
TTTGAAAGATTGAGAG
Found at i:65879 original size:14 final size:14
Alignment explanation
Indices: 65855--65888 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
65845 TAGCTGGAGT
65855 AATAATGGAAGGGG
1 AATAATGGAAGGGG
* *
65869 GATAATTGAAGGGG
1 AATAATGGAAGGGG
65883 AATAAT
1 AATAAT
65889 ATGTTGATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (14 bp):
AATAATGGAAGGGG
Found at i:68866 original size:23 final size:24
Alignment explanation
Indices: 68840--68886 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
68830 CTTTACACTT
*
68840 GTCCAA-ATTTGACCTTTCTTTAA
1 GTCCAACATGTGACCTTTCTTTAA
*
68863 GTCCAACTATGTGCCCTTTCTTTA
1 GTCCAAC-ATGTGACCTTTCTTTA
68887 TAAAAGACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.43
Consensus pattern (24 bp):
GTCCAACATGTGACCTTTCTTTAA
Found at i:75615 original size:1 final size:1
Alignment explanation
Indices: 75609--75643 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
75599 TTTGTTTGCA
*
75609 TTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
75644 GTATAGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:75617 original size:16 final size:15
Alignment explanation
Indices: 75592--75635 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
75582 AAGAGCATTT
*
75592 ATTTTATTTTGTTTGC
1 ATTTT-TTTTTTTTGC
**
75608 ATTTTTTTTTTTTTT
1 ATTTTTTTTTTTTGC
75623 ATTTTTTTTTTTT
1 ATTTTTTTTTTTT
75636 TTTTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (15 bp):
ATTTTTTTTTTTTGC
Done.