Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005468.1 Hibiscus syriacus cultivar Beakdansim tig00012525_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: 65496
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10685 original size:17 final size:18
Alignment explanation
Indices: 10652--10685 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10642 CCATAGTTTT
10652 GAAAATAAATATTTATAC
1 GAAAATAAATATTTATAC
*
10670 GAAAATTAAT-TTTATA
1 GAAAATAAATATTTATA
10686 AAAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
GAAAATAAATATTTATAC
Found at i:11600 original size:11 final size:11
Alignment explanation
Indices: 11584--11612 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11574 CTCACTATTA
11584 TAAGCTTTTGC
1 TAAGCTTTTGC
11595 TAAGC-TTTGC
1 TAAGCTTTTGC
11605 TAAGCTTT
1 TAAGCTTT
11613 ACTCAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (11 bp):
TAAGCTTTTGC
Found at i:11639 original size:31 final size:30
Alignment explanation
Indices: 11597--11684 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 30
11587 GCTTTTGCTA
*
11597 AGCTTTGCTAAGCTTTACTCAATTCTCTCAT
1 AGCTTTTCTAAGCTTTACTCAATTCTCTC-T
* *
11628 AGCTTTTCTAAGCTAT-CTCAAATTTTCTCT
1 AGCTTTTCTAAGCTTTACTC-AATTCTCTCT
11658 AGCTTTTCTAAGCTTTCACTCATATTC
1 AGCTTTTCTAAGCTTT-ACTCA-ATTC
11685 CATCTCATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 19 0.40
31 23 0.48
32 6 0.12
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.44
Consensus pattern (30 bp):
AGCTTTTCTAAGCTTTACTCAATTCTCTCT
Found at i:11671 original size:10 final size:11
Alignment explanation
Indices: 11585--11673 Score: 50
Period size: 10 Copynumber: 8.6 Consensus size: 11
11575 TCACTATTAT
11585 AAGCTTTTGCT-
1 AAGCTTTT-CTC
*
11596 AAGCTTTGCT-
1 AAGCTTTTCTC
*
11606 AAGCTTTACTC
1 AAGCTTTTCTC
*
11617 AA--TTCTCTC
1 AAGCTTTTCTC
11626 ATAGCTTTTCT-
1 A-AGCTTTTCTC
*
11637 AAGC-TATCTC
1 AAGCTTTTCTC
*
11647 AA-ATTTTCTC
1 AAGCTTTTCTC
*
11657 TAGCTTTTCT-
1 AAGCTTTTCTC
11667 AAGCTTT
1 AAGCTTT
11674 CACTCATATT
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
9 10 0.17
10 29 0.48
11 16 0.27
12 5 0.08
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (11 bp):
AAGCTTTTCTC
Found at i:14677 original size:35 final size:35
Alignment explanation
Indices: 14638--14753 Score: 103
Period size: 35 Copynumber: 3.3 Consensus size: 35
14628 GTTGTATTTT
14638 GTGTTTGGTTGATTTAGCAGGAATATAAGATTATC
1 GTGTTTGGTTGATTTAGCAGGAATATAAGATTATC
* * * * *
14673 GTGTTT-GTCGTATTTGGTTAAAGGAATA-AATATT-TT
1 GTGTTTGGTTG-ATTTAG---CAGGAATATAAGATTATC
* * *
14709 GTGTTTGGTTGGTTTAACAGGAATATAAGATTACC
1 GTGTTTGGTTGATTTAGCAGGAATATAAGATTATC
14744 GTGTTTGGTT
1 GTGTTTGGTT
14754 AAAGGAATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
33 7 0.11
34 8 0.13
35 21 0.34
36 10 0.16
37 8 0.13
38 7 0.11
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.43
Consensus pattern (35 bp):
GTGTTTGGTTGATTTAGCAGGAATATAAGATTATC
Found at i:25071 original size:23 final size:23
Alignment explanation
Indices: 25044--25089 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
25034 CTTGGAACAT
25044 AAAAGTGAGTAGGGATGGCAAAC
1 AAAAGTGAGTAGGGATGGCAAAC
25067 AAAAGTGAGTAGGGATGGCAAAC
1 AAAAGTGAGTAGGGATGGCAAAC
25090 GGACGGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.35, T:0.13
Consensus pattern (23 bp):
AAAAGTGAGTAGGGATGGCAAAC
Found at i:25982 original size:15 final size:15
Alignment explanation
Indices: 25962--26013 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
25952 ATATTTAGCT
*
25962 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGAG
25977 GGGCGGGCGGATGAG
1 GGGCGGGCGGATGAG
*
25992 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGAG
26007 GGGCGGG
1 GGGCGGG
26014 TAATGTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.08, C:0.15, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGAG
Found at i:26703 original size:31 final size:28
Alignment explanation
Indices: 26661--26749 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 28
26651 CACAAAAATA
26661 ATATAAT-AAATATTAAAAAAAATTATC
1 ATATAATGAAATATTAAAAAAAATTATC
* *
26688 ATGAGTAATGAAAATATTATAAACACAAA-AATA
1 AT-A-TAATG-AAATATTA-AAA-A-AAATTATC
26721 ATATAATG-AATATTAAAAAAAATTATC
1 ATATAATGAAATATTAAAAAAAATTATC
26748 AT
1 AT
26750 TAAAATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
26 3 0.06
27 7 0.14
28 4 0.08
29 11 0.22
31 13 0.26
32 4 0.08
33 5 0.10
34 3 0.06
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
ATATAATGAAATATTAAAAAAAATTATC
Found at i:27756 original size:17 final size:18
Alignment explanation
Indices: 27719--27756 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27709 ATATTATGTA
27719 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
27737 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
27754 TTT
1 TTT
27757 GCTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:30941 original size:51 final size:50
Alignment explanation
Indices: 30837--30945 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 50
30827 GATACACAAA
* * * * * * *
30837 TATAGCGCGGTTCAGGGGGTGCGCTATACCCCACGTGTAACTTAGTTAGCG
1 TATAGCGCGGTGCAGGGGGTACACTATACCCCACGTG-AACTAAATCAACG
30888 TATAGCGCGGTGCAGGGGGTACACTATACCCCACGTG-ACGTCAAATCAACG
1 TATAGCGCGGTGCAGGGGGTACACTATACCCCACGTGAAC-T-AAATCAACG
30939 TATAGCG
1 TATAGCG
30946 TGAGTCAGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
49 2 0.04
50 1 0.02
51 46 0.94
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (50 bp):
TATAGCGCGGTGCAGGGGGTACACTATACCCCACGTGAACTAAATCAACG
Found at i:31183 original size:28 final size:28
Alignment explanation
Indices: 31144--31204 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
31134 AAAGATGAGG
*
31144 AAAAAAAGGAACAAGTGGCGGGTTAGAA
1 AAAAAAAAGAACAAGTGGCGGGTTAGAA
31172 AAAAAAAAGAACAAGTGGCGGGTTAGAA
1 AAAAAAAAGAACAAGTGGCGGGTTAGAA
31200 AAAAA
1 AAAAA
31205 GGACGGCGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.56, C:0.07, G:0.28, T:0.10
Consensus pattern (28 bp):
AAAAAAAAGAACAAGTGGCGGGTTAGAA
Found at i:31422 original size:20 final size:17
Alignment explanation
Indices: 31395--31438 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
31385 TTTTATAATA
* *
31395 ATTATATATATATATAT
1 ATTATTTATATATTTAT
31412 GATTATTTATATATTTAT
1 -ATTATTTATATATTTAT
31430 ATTATTTAT
1 ATTATTTAT
31439 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTTATATATTTAT
Found at i:40769 original size:16 final size:16
Alignment explanation
Indices: 40748--40781 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40738 AGTATATATG
40748 TATACACACACAAACA
1 TATACACACACAAACA
* *
40764 TATACACATACATACA
1 TATACACACACAAACA
40780 TA
1 TA
40782 CATAAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (16 bp):
TATACACACACAAACA
Found at i:43633 original size:23 final size:23
Alignment explanation
Indices: 43607--43659 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
43597 TATATATTAC
**
43607 ATTTTAAT-TTAATATTTTAAATA
1 ATTTTAATATTAA-ATTAAAAATA
*
43630 ATTTGAATATTAAATTAAAAATA
1 ATTTTAATATTAAATTAAAAATA
*
43653 AATTTAA
1 ATTTTAA
43660 AATCAGATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTAATATTAAATTAAAAATA
Found at i:47644 original size:16 final size:16
Alignment explanation
Indices: 47625--47655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47615 GTGATGTGTG
47625 TATATGCATATGTATA
1 TATATGCATATGTATA
*
47641 TATATGTATATGTAT
1 TATATGCATATGTAT
47656 GAGAGATACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (16 bp):
TATATGCATATGTATA
Found at i:50169 original size:2 final size:2
Alignment explanation
Indices: 50162--50199 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
50152 ATAAATTACA
50162 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
50200 TTTTTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53287 original size:38 final size:37
Alignment explanation
Indices: 53236--53314 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 37
53226 AAACCCGAAT
53236 CCGACCCGACCCGAATATCACACTTAAAAGAACCTGAC
1 CCGACCCGACCCGAATATCACACTTAAAA-AACCTGAC
*
53274 CCGACTCGACCCGAATATCACACTTAAAAAACCTGAC
1 CCGACCCGACCCGAATATCACACTTAAAAAACCTGAC
53311 CCGA
1 CCGA
53315 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 12 0.30
38 28 0.70
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Consensus pattern (37 bp):
CCGACCCGACCCGAATATCACACTTAAAAAACCTGAC
Found at i:54001 original size:29 final size:29
Alignment explanation
Indices: 53959--54028 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
53949 GTGTTTGACG
53959 TAGGTCGCCATGCTATCCGGGCGACCTAC
1 TAGGTCGCCATGCTATCCGGGCGACCTAC
*
53988 TAGGTCGCCATGCTATCCGGTCGACCTAC
1 TAGGTCGCCATGCTATCCGGGCGACCTAC
*
54017 TAGGTCGTCATG
1 TAGGTCGCCATG
54029 TCTTCCCGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCTATCCGGGCGACCTAC
Found at i:54240 original size:29 final size:29
Alignment explanation
Indices: 54139--54221 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
54129 GGAGCAGGAG
*
54139 GGAGTGCATGACGACTTACAAGGTCGTCA
1 GGAGTGCATGACGACTTACAAGGTCGCCA
* * * *
54168 GGAGTGCATGGCGACCTACAAGATCGCCT
1 GGAGTGCATGACGACTTACAAGGTCGCCA
54197 GGAGTGCATGACGACTTACAAGGTC
1 GGAGTGCATGACGACTTACAAGGTC
54222 ACCCGGAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (29 bp):
GGAGTGCATGACGACTTACAAGGTCGCCA
Found at i:57195 original size:14 final size:14
Alignment explanation
Indices: 57176--57206 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
57166 TTAAATGATA
57176 AACGAACACAAACG
1 AACGAACACAAACG
*
57190 AACGAACATAAACG
1 AACGAACACAAACG
57204 AAC
1 AAC
57207 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:57203 original size:10 final size:10
Alignment explanation
Indices: 57190--57241 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
57180 AACACAAACG
57190 AACGAACATA
1 AACGAACATA
57200 AACGAACATAATA
1 AACGAAC---ATA
*
57213 AATGAACATA
1 AACGAACATA
57223 AACGAACATA
1 AACGAACATA
57233 TAACGAACA
1 -AACGAACA
57242 ACACAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 19 0.53
11 8 0.22
13 9 0.25
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:62207 original size:2 final size:2
Alignment explanation
Indices: 62202--62227 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62192 CTTCAAACGA
62202 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
62228 TGTAAATCTC
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
Done.