Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004376.1 Hibiscus syriacus cultivar Beakdansim tig00009585_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: 90784
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:770 original size:31 final size:31
Alignment explanation
Indices: 735--811 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
725 TCAGAAAACA
*
735 TAAGATATGAACACTTTCATTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
**
766 TAAGATATGATCACTTTTGTTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
*
797 TAAGATGTGATCACT
1 TAAGATATGATCACT
812 CCGAGTTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.48
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTATTTAAT
Found at i:1843 original size:31 final size:31
Alignment explanation
Indices: 1769--1848 Score: 128
Period size: 30 Copynumber: 2.6 Consensus size: 31
1759 TGACCACATC
1769 TTAATTAAAT-AAAACGAAAATAACCATATT
1 TTAATTAAATAAAAACGAAAATAACCATATT
* *
1799 TTAATT-AATAAAAACGAAAATGATCATATT
1 TTAATTAAATAAAAACGAAAATAACCATATT
1829 TTAATTAAATAAAAACGAAA
1 TTAATTAAATAAAAACGAAA
1849 GTTATATCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 3 0.07
30 30 0.65
31 13 0.28
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAATAACCATATT
Found at i:2166 original size:2 final size:2
Alignment explanation
Indices: 2154--2187 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2144 TCAACCGTTT
2154 TA TA T- TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2188 CTTTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5300 original size:20 final size:22
Alignment explanation
Indices: 5266--5308 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5256 TTGATTAATT
5266 TTAATATAAAATTTTT-ATATG
1 TTAATATAAAATTTTTAATATG
*
5287 TTAA-ATAAATTTTTTAATATG
1 TTAATATAAAATTTTTAATATG
5308 T
1 T
5309 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTAATATAAAATTTTTAATATG
Found at i:5624 original size:12 final size:11
Alignment explanation
Indices: 5592--5630 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
5582 TATTAGTTGA
*
5592 ATAAAATTAAT
1 ATAAAAATAAT
5603 -TAAAAATAAT
1 ATAAAAATAAT
5613 ATAAATAATAAT
1 ATAAA-AATAAT
5625 ATAAAA
1 ATAAAA
5631 TTTGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:13955 original size:5 final size:5
Alignment explanation
Indices: 13945--14087 Score: 119
Period size: 5 Copynumber: 28.4 Consensus size: 5
13935 TGATGACTCG
* * * *
13945 CAGAT CAGAT CAGAT CATAT CAGAT CATAT CATAT CAGAT CAAAT CAGAT
1 CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT
* * * * *
13995 CATAT CATG-T CAGAT CAAAT CAGAT CATAT CATG-T CATAT CAAAT CAGAT
1 CAGAT CA-GAT CAGAT CAGAT CAGAT CAGAT CA-GAT CAGAT CAGAT CAGAT
* * * * *
14045 CATAT CATAT CATAT CAAAT CAGAT CATAT CAGAT CAAGAT CA
1 CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT CAGAT C-AGAT CA
14088 CCAGAACGAC
Statistics
Matches: 113, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
4 1 0.01
5 107 0.95
6 5 0.04
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (5 bp):
CAGAT
Found at i:13982 original size:25 final size:25
Alignment explanation
Indices: 13948--14087 Score: 208
Period size: 25 Copynumber: 5.6 Consensus size: 25
13938 TGACTCGCAG
* *
13948 ATCAGATCAGATCATATCAGATCAT
1 ATCATATCAGATCAAATCAGATCAT
13973 ATCATATCAGATCAAATCAGATCAT
1 ATCATATCAGATCAAATCAGATCAT
*
13998 ATCATGTCAGATCAAATCAGATCAT
1 ATCATATCAGATCAAATCAGATCAT
* *
14023 ATCATGTCATATCAAATCAGATCAT
1 ATCATATCAGATCAAATCAGATCAT
*
14048 ATCATATCATATCAAATCAGATCAT
1 ATCATATCAGATCAAATCAGATCAT
*
14073 ATCAGATCAAGATCA
1 ATCATATC-AGATCA
14088 CCAGAACGAC
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 102 0.95
26 5 0.05
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (25 bp):
ATCATATCAGATCAAATCAGATCAT
Found at i:28565 original size:22 final size:22
Alignment explanation
Indices: 28537--28579 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28527 GCCCTTTGAG
28537 CCCAAAGTAATTCTTCATGTCA
1 CCCAAAGTAATTCTTCATGTCA
28559 CCCAAAGTAATTCTTCATGTC
1 CCCAAAGTAATTCTTCATGTC
28580 TCAAAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (22 bp):
CCCAAAGTAATTCTTCATGTCA
Found at i:30319 original size:23 final size:23
Alignment explanation
Indices: 30282--30344 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
30272 ATCAAATTGA
30282 TTATTTATTTTAAAAATAGATTTG
1 TTATTT-TTTTAAAAATAGATTTG
30306 TTATTTTTTTAAAAATAGATTTG
1 TTATTTTTTTAAAAATAGATTTG
30329 TTATTTTTTTTAAAAA
1 TTA-TTTTTTTAAAAA
30345 AAAACTAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTATTTTTTTAAAAATAGATTTG
Found at i:31365 original size:2 final size:2
Alignment explanation
Indices: 31358--31395 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31348 CGAACACATC
*
31358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31396 TCATAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33953 original size:22 final size:23
Alignment explanation
Indices: 33925--33968 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
33915 AATACAATAA
* *
33925 AATTTTAGTGTGAACAC-CATAG
1 AATTTTAATGTAAACACACATAG
33947 AATTTTAATGTAAACACACATA
1 AATTTTAATGTAAACACACATA
33969 CATTGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (23 bp):
AATTTTAATGTAAACACACATAG
Found at i:39440 original size:20 final size:20
Alignment explanation
Indices: 39404--39441 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39394 ATCATATTCC
**
39404 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
39424 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
39442 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:43692 original size:25 final size:25
Alignment explanation
Indices: 43639--43692 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
43629 TTCTCTAAAT
* *
43639 AATT-TTATTTTAATATAATTTATA
1 AATTATTATTTTAAAAGAATTTATA
*
43663 TATTATTATTTTAAAAGAATTGTA-A
1 AATTATTATTTTAAAAGAATT-TATA
43688 AATTA
1 AATTA
43693 ATTTAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.12
25 19 0.79
26 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
AATTATTATTTTAAAAGAATTTATA
Found at i:44688 original size:33 final size:33
Alignment explanation
Indices: 44651--44722 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
44641 TTTGATAGAA
44651 AAATAAAATTTTA-AGTAAAAATAAT-AATATTTT
1 AAATAAAATTTTATA--AAAAATAATAAATATTTT
** *
44684 AAATAACGTTTTATAAAAAATATTAAATATTTT
1 AAATAAAATTTTATAAAAAATAATAAATATTTT
44717 AAATAA
1 AAATAA
44723 CGTCTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 8 0.24
33 25 0.74
34 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (33 bp):
AAATAAAATTTTATAAAAAATAATAAATATTTT
Found at i:55590 original size:16 final size:16
Alignment explanation
Indices: 55569--55616 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
55559 CGAGTATTTT
55569 TATTTGGATTTAAAAA
1 TATTTGGATTTAAAAA
* *
55585 TATTTGGGTTTTAAAA
1 TATTTGGATTTAAAAA
55601 TATTAATGGATTTAAA
1 TATT--TGGATTTAAA
55617 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 18 0.69
18 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (16 bp):
TATTTGGATTTAAAAA
Found at i:67792 original size:15 final size:15
Alignment explanation
Indices: 67772--67803 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
67762 TGCAAGATCG
*
67772 AAATCCAGAACGGGA
1 AAATCCAGAACGAGA
67787 AAATCCAGAACGAGA
1 AAATCCAGAACGAGA
67802 AA
1 AA
67804 GAAGGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.06
Consensus pattern (15 bp):
AAATCCAGAACGAGA
Found at i:72237 original size:29 final size:30
Alignment explanation
Indices: 72163--72237 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
72153 ATTCAAAGAA
* *
72163 GTTACATTTTGGTCGCTTAAGTTATCGATTT
1 GTTAAATTTTGGTC-ATTAAGTTATCGATTT
* *
72194 ATTAAATTTTGGTCATTACGTTATCGA-TT
1 GTTAAATTTTGGTCATTAAGTTATCGATTT
*
72223 GTTATATTTTGGTCA
1 GTTAAATTTTGGTCA
72238 CTGAACAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 15 0.39
30 11 0.29
31 12 0.32
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (30 bp):
GTTAAATTTTGGTCATTAAGTTATCGATTT
Found at i:72473 original size:2 final size:2
Alignment explanation
Indices: 72466--72501 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
72456 TCTAACAATA
*
72466 AT AT AT AT AT AT AT AT AT AT AA 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
72502 TCATATTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:73603 original size:30 final size:29
Alignment explanation
Indices: 73556--73656 Score: 116
Period size: 30 Copynumber: 3.3 Consensus size: 29
73546 GATTACTTAT
73556 TAATTTGACCTTTAAACTTTAGATAGAATA
1 TAATTTGA-CTTTAAACTTTAGATAGAATA
*
73586 CTAATTTGACGTTAAACTTTAGAT-GAAATA
1 -TAATTTGACTTTAAACTTTAGATAG-AATA
*
73616 TCATTTGACTTCTAAACTTTAGATA-ATATA
1 TAATTTGACTT-TAAACTTTAGATAGA-ATA
73646 TTAATTTGACT
1 -TAATTTGACT
73657 CCCTAAATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
29 11 0.18
30 33 0.54
31 17 0.28
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (29 bp):
TAATTTGACTTTAAACTTTAGATAGAATA
Found at i:74787 original size:3 final size:3
Alignment explanation
Indices: 74779--74803 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74769 AAAACATGGT
74779 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
74804 GACCCAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:76605 original size:12 final size:12
Alignment explanation
Indices: 76588--76613 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
76578 ATTATTCGTA
76588 TTTTTTTAATCT
1 TTTTTTTAATCT
76600 TTTTTTTAATCT
1 TTTTTTTAATCT
76612 TT
1 TT
76614 CTTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTAATCT
Found at i:81897 original size:22 final size:22
Alignment explanation
Indices: 81871--81919 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
81861 GGTTTTAATC
*
81871 GGTTTCGGTTCTTT-TTTATTTG
1 GGTTTCGGTT-TTTATTTAGTTG
*
81893 GGTTTGGGTTTTTATTTAGTTG
1 GGTTTCGGTTTTTATTTAGTTG
81915 GGTTT
1 GGTTT
81920 TGGGAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.06, C:0.04, G:0.29, T:0.61
Consensus pattern (22 bp):
GGTTTCGGTTTTTATTTAGTTG
Found at i:81929 original size:23 final size:22
Alignment explanation
Indices: 81885--81929 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
81875 TCGGTTCTTT
* **
81885 TTTATTTGGGTTTGGGTTTTTA
1 TTTAGTTGGGTTTGGGAGTTTA
81907 TTTAGTTGGGTTTTGGGAGTTTA
1 TTTAGTTGGG-TTTGGGAGTTTA
81930 AAAATGGTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.11, C:0.00, G:0.31, T:0.58
Consensus pattern (22 bp):
TTTAGTTGGGTTTGGGAGTTTA
Found at i:86005 original size:36 final size:36
Alignment explanation
Indices: 85938--86008 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
85928 AATATTAATA
* **
85938 TTTAATAAGAAAATACCCAATTTTTTTTATGAAACT
1 TTTAATAAGAAAATACCCAATATTTCGTATGAAACT
*
85974 TTTAATAAGAAAAATACTCAA-ATTTCGTATGAAAC
1 TTTAATAAG-AAAATACCCAATATTTCGTATGAAAC
86009 CTAAATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (36 bp):
TTTAATAAGAAAATACCCAATATTTCGTATGAAACT
Found at i:86456 original size:17 final size:18
Alignment explanation
Indices: 86431--86467 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
86421 TATGTTTTTT
86431 AAATCACAAAATAAC-GA
1 AAATCACAAAATAACTGA
*
86448 AAATGACAAAATAACTGA
1 AAATCACAAAATAACTGA
86466 AA
1 AA
86468 TACCCCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.65, C:0.14, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATCACAAAATAACTGA
Found at i:87474 original size:32 final size:31
Alignment explanation
Indices: 87433--87492 Score: 111
Period size: 32 Copynumber: 1.9 Consensus size: 31
87423 TAAATTAAAT
87433 TATTATAAATCAATCTTTAAATTGTATCAAAC
1 TATTATAAATCAATCTTTAAATT-TATCAAAC
87465 TATTATAAATCAATCTTTAAATTTATCA
1 TATTATAAATCAATCTTTAAATTTATCA
87493 CTATTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (31 bp):
TATTATAAATCAATCTTTAAATTTATCAAAC
Found at i:87891 original size:17 final size:19
Alignment explanation
Indices: 87849--87893 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
87839 CATTAATAAA
87849 TTATTAAAAATGATTTAAT
1 TTATTAAAAATGATTTAAT
* *
87868 TT-GTAAAAAT-A-TTATT
1 TTATTAAAAATGATTTAAT
87884 TTATTAAAAA
1 TTATTAAAAA
87894 ACACCTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 7 0.32
19 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TTATTAAAAATGATTTAAT
Done.