Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002717.1 Hibiscus syriacus cultivar Beakdansim tig00005607_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: 72156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2549 original size:24 final size:24
Alignment explanation
Indices: 2510--2599 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 24
2500 TATCGATCTG
2510 TTTATCGACT-AGTTTATAATATTA
1 TTTATCGACTCA-TTTATAATATTA
*
2534 TTTATCGACTCATTTAT--TGACTA
1 TTTATCGACTCATTTATAAT-ATTA
* * ** *
2557 GTTATCGAATCGCTTATAATATCA
1 TTTATCGACTCATTTATAATATTA
* *
2581 TTTATCGGCTCTTTTATAA
1 TTTATCGACTCATTTATAA
2600 GCTTGTTTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
22 1 0.02
23 16 0.32
24 31 0.62
25 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (24 bp):
TTTATCGACTCATTTATAATATTA
Found at i:2902 original size:41 final size:40
Alignment explanation
Indices: 2831--2915 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
2821 ATAAAGTCTG
* *
2831 GCCTATTTAGTAAAAAGGCCAGGCTCAGGCCTTTTTAAAA
1 GCCTATTTAGTAAAAAGGCCAGGCTCAGGCCTATTAAAAA
* * * *
2871 GCCTATTTAATTAAACAGGTCAGGCTTAGGCCTATTAAAAA
1 GCCTATTT-AGTAAAAAGGCCAGGCTCAGGCCTATTAAAAA
2912 GCCT
1 GCCT
2916 TATAAGCCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (40 bp):
GCCTATTTAGTAAAAAGGCCAGGCTCAGGCCTATTAAAAA
Found at i:3057 original size:12 final size:12
Alignment explanation
Indices: 3033--3066 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3023 AATGTTATTG
*
3033 TTAAACAGGCTT
1 TTAAACAGACTT
*
3045 TTAAATAGACTT
1 TTAAACAGACTT
3057 TTAAACAGAC
1 TTAAACAGAC
3067 CAGGCTAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (12 bp):
TTAAACAGACTT
Found at i:17983 original size:6 final size:6
Alignment explanation
Indices: 17972--18059 Score: 122
Period size: 6 Copynumber: 14.7 Consensus size: 6
17962 CAATCTAATG
* * * * *
17972 CATATA CATATA CATGTA CATATA CAAATA CAAATA CATGTA CATGTA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
*
18020 CATATA CATGTA CATATA CATATA CATATA CATATA CATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATA
18060 CCTTGGAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (6 bp):
CATATA
Found at i:19987 original size:22 final size:23
Alignment explanation
Indices: 19945--19988 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19935 TCTTTTTTGC
*
19945 TTTATTTTTTAAAAATAAAAATA
1 TTTATTTGTTAAAAATAAAAATA
*
19968 TTTATTTGTTAAAAAGAAAAA
1 TTTATTTGTTAAAAATAAAAA
19989 AGTTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTATTTGTTAAAAATAAAAATA
Found at i:22563 original size:13 final size:13
Alignment explanation
Indices: 22545--22569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22535 AAGTTTAGGG
22545 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
22558 TTTTTCTTTTCT
1 TTTTTCTTTTCT
22570 AATCTCGGCA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:29896 original size:18 final size:18
Alignment explanation
Indices: 29873--29908 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29863 ATTATTTTTA
* *
29873 ATTTAAACATTTAATAAT
1 ATTTAAAAACTTAATAAT
29891 ATTTAAAAACTTAATAAT
1 ATTTAAAAACTTAATAAT
29909 TGTATTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAAAACTTAATAAT
Found at i:44485 original size:48 final size:47
Alignment explanation
Indices: 44418--44513 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 47
44408 TATATAGTAT
* * *
44418 ATGCTATTTATATTTAAATATTTTGAATTTAAAATTATTATAAAATA
1 ATGCCATTTAAATTTAAATAATTTGAATTTAAAATTATTATAAAATA
44465 ATGCCATTTAAATTTGAAATAATTTGAATTTAAAATTATTATAAAATA
1 ATGCCATTTAAATTT-AAATAATTTGAATTTAAAATTATTATAAAATA
44513 A
1 A
44514 AATGAGGCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 13 0.29
48 32 0.71
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (47 bp):
ATGCCATTTAAATTTAAATAATTTGAATTTAAAATTATTATAAAATA
Found at i:45156 original size:2 final size:2
Alignment explanation
Indices: 45149--45178 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45139 GTATATTTTA
45149 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
45179 TCAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46100 original size:17 final size:17
Alignment explanation
Indices: 46078--46111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46068 TGGAATATAA
46078 TGAATAGTCAGGTGACT
1 TGAATAGTCAGGTGACT
*
46095 TGAATAGTCGGGTGACT
1 TGAATAGTCAGGTGACT
46112 ATTTTGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (17 bp):
TGAATAGTCAGGTGACT
Found at i:52625 original size:21 final size:21
Alignment explanation
Indices: 52599--52644 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52589 TCATAAATAT
*
52599 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATAATTTAAA
52620 TAAAAATAATAATAATTTAAA
1 TAAAAATAATAATAATTTAAA
52641 TAAA
1 TAAA
52645 TTTTTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAATAATAATAATTTAAA
Found at i:59298 original size:26 final size:26
Alignment explanation
Indices: 59269--59351 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
59259 TCATTTTATA
59269 TTAGTAAAAAGGGGTAAATTACACGT
1 TTAGTAAAAAGGGGTAAATTACACGT
*** * ** *
59295 TTAGTACCTAGGCGATCATTTTATA--T
1 TTAGTAAAAAGG-GGT-AAATTACACGT
59321 -TAGTAAAAAGGGGTAAATTACACGT
1 TTAGTAAAAAGGGGTAAATTACACGT
59346 TTAGTA
1 TTAGTA
59352 CCTAGGCGAT
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
23 5 0.13
24 2 0.05
25 9 0.24
26 15 0.39
27 2 0.05
28 5 0.13
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (26 bp):
TTAGTAAAAAGGGGTAAATTACACGT
Found at i:59314 original size:51 final size:51
Alignment explanation
Indices: 59258--59368 Score: 213
Period size: 51 Copynumber: 2.2 Consensus size: 51
59248 TTATATTGTA
59258 ATCATTTTATATTAGTAAAAAGGGGTAAATTACACGTTTAGTACCTAGGCG
1 ATCATTTTATATTAGTAAAAAGGGGTAAATTACACGTTTAGTACCTAGGCG
59309 ATCATTTTATATTAGTAAAAAGGGGTAAATTACACGTTTAGTACCTAGGCG
1 ATCATTTTATATTAGTAAAAAGGGGTAAATTACACGTTTAGTACCTAGGCG
59360 ATCAATTTT
1 ATC-ATTTT
59369 GGTCTGTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 54 0.92
52 5 0.08
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (51 bp):
ATCATTTTATATTAGTAAAAAGGGGTAAATTACACGTTTAGTACCTAGGCG
Found at i:60619 original size:22 final size:22
Alignment explanation
Indices: 60594--60882 Score: 472
Period size: 22 Copynumber: 13.2 Consensus size: 22
60584 TATTTTAAAT
*
60594 TTTATTTTAAAATATGTATTGA
1 TTTATTTTAAAATATGGATTGA
60616 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
60638 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
***
60660 TTTATTTTAAAATAT-GAAAAA
1 TTTATTTTAAAATATGGATTGA
60681 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
60703 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
60725 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
60747 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
60769 TTTGTTTTAAAATATGGAAAAA
1 TTTATTTTAAAATATGGATTGA
60791 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
60813 TTTATTTTAAAATATGGATTTA
1 TTTATTTTAAAATATGGATTGA
*
60835 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
60857 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
60879 TTTA
1 TTTA
60883 CGTTGGGATT
Statistics
Matches: 245, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
21 18 0.07
22 227 0.93
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:62378 original size:22 final size:22
Alignment explanation
Indices: 62353--62467 Score: 160
Period size: 22 Copynumber: 5.2 Consensus size: 22
62343 GAAATGTTTA
62353 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
* ***
62375 AAAATATGAAAAAAATTTATTTT
1 AAAATATG-GATTGATTTATTTT
62398 AAAA-ATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
62419 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
*
62441 AAAATATAGATTGATTTATTTTT
1 AAAATATGGATTGATTTA-TTTT
62464 AAAA
1 AAAA
62468 AATTATTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
21 14 0.17
22 45 0.56
23 22 0.27
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.46
Consensus pattern (22 bp):
AAAATATGGATTGATTTATTTT
Found at i:62527 original size:31 final size:31
Alignment explanation
Indices: 62489--62549 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
62479 TAGTTGTATG
*
62489 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
62520 AATTATTTAAATTTCAGTATTGCAAAACTA
1 AATTATTTAAATTTCAGTATTACAAAACTA
62550 TTTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:69027 original size:183 final size:182
Alignment explanation
Indices: 68719--69084 Score: 660
Period size: 183 Copynumber: 2.0 Consensus size: 182
68709 TTTATGATTT
68719 ACCATAACCATTCTCTACATTTTTGTTGGTTGGTTTCTATGGCAATTCAGAAAGAGCTTGACATT
1 ACCATAACCATTCTCTACATTTTTGTTGGTTGGTTTCTATGGCAATTCAGAAAGAGCTTGACATT
* *
68784 CAAGGCAAGCAGAACGTTAAGCTTCTGTTACGAAGGACCTCCACCAACTGTTGAGCTGAAAATGG
66 CAAGGCAAGCAGAACGTTAAGCTTCTGTCACGAAGGACCACCACCAACTGTTGAGCTGAAAATGG
* *
68849 TATACTGCAAATTCTTTTTATTGTCATTTAGCATGGTTAAAAATATATCAGAA
131 TATACTGCAAATTCCTTTTAATGTCATTTAGCATGGTT-AAAATATATCAGAA
*
68902 ACCATAACCATTTTCTACATTTTTGTTGGTTGGTTTCTATGGCAATTCAGAAAGAGCTTGACATT
1 ACCATAACCATTCTCTACATTTTTGTTGGTTGGTTTCTATGGCAATTCAGAAAGAGCTTGACATT
*
68967 CAAGGCAAGCCGAACGTTAAGCTTCTGTCACGAAGGACCACCACCAACTGTTGAGCTGAAAATGG
66 CAAGGCAAGCAGAACGTTAAGCTTCTGTCACGAAGGACCACCACCAACTGTTGAGCTGAAAATGG
*
69032 TATACTGCAAATTCCTTTTAATGTCATTTAGCATGGTTAAATTATATCAGAA
131 TATACTGCAAATTCCTTTTAATGTCATTTAGCATGGTTAAAATATATCAGAA
69084 A
1 A
69085 TAAGTGCCTG
Statistics
Matches: 176, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
182 14 0.08
183 162 0.92
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (182 bp):
ACCATAACCATTCTCTACATTTTTGTTGGTTGGTTTCTATGGCAATTCAGAAAGAGCTTGACATT
CAAGGCAAGCAGAACGTTAAGCTTCTGTCACGAAGGACCACCACCAACTGTTGAGCTGAAAATGG
TATACTGCAAATTCCTTTTAATGTCATTTAGCATGGTTAAAATATATCAGAA
Found at i:70071 original size:2 final size:2
Alignment explanation
Indices: 70064--70117 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
70054 GGATCATTCG
70064 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
70106 AT AT AT AT AT AT
1 AT AT AT AT AT AT
70118 GGTGACATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71697 original size:15 final size:15
Alignment explanation
Indices: 71659--71701 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
71649 GGTGTGCAAA
71659 TCCGGGTACCCGGATT
1 TCCGGGTACCC-GATT
* *
71675 TTCAGGTACCCGATT
1 TCCGGGTACCCGATT
71690 TCCGGGTACCCG
1 TCCGGGTACCCG
71702 GAACTTCCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.26
Consensus pattern (15 bp):
TCCGGGTACCCGATT
Found at i:71788 original size:16 final size:16
Alignment explanation
Indices: 71740--71792 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
71730 CCGTGTCCCA
*
71740 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
71757 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
71772 ACCCGGAT-TTGCGGGT
1 ACCCGGATATT-CGGGT
71788 ACCCG
1 ACCCG
71793 ATACCCGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.39
16 13 0.42
17 6 0.19
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Done.