Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003086.1 Hibiscus syriacus cultivar Beakdansim tig00006442_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: 56866
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:3435 original size:16 final size:16
Alignment explanation
Indices: 3410--3440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3400 AAAGGAGATC
*
3410 GATTGTAGTAAGGATT
1 GATTGGAGTAAGGATT
3426 GATTGGAGTAAGGAT
1 GATTGGAGTAAGGAT
3441 CTTAGCTTGG
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:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (16 bp):
GATTGGAGTAAGGATT
Found at i:4411 original size:16 final size:15
Alignment explanation
Indices: 4371--4412 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
4361 ATAAAAAGAA
4371 AAAAATAAAA-AAAT
1 AAAAATAAAACAAAT
*
4385 AAAATCTAAAACAAAT
1 AAAA-ATAAAACAAAT
4401 AAAAATGAAAAC
1 AAAAAT-AAAAC
4413 TAATCTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 13 0.57
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (15 bp):
AAAAATAAAACAAAT
Found at i:7520 original size:18 final size:17
Alignment explanation
Indices: 7484--7525 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
7474 CTTGTTTGTG
*
7484 TATATTATACTAGTATA
1 TATATTAGACTAGTATA
*
7501 TATATTAGACTATTTATA
1 TATATTAGACTA-GTATA
7519 TATATTA
1 TATATTA
7526 TAGTTGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
TATATTAGACTAGTATA
Found at i:7754 original size:19 final size:20
Alignment explanation
Indices: 7722--7760 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
7712 TTCCTTAATT
7722 AATTAATTATTTATT-TATA
1 AATTAATTATTTATTATATA
7741 AATTAATCTA-TTATTATATA
1 AATTAAT-TATTTATTATATA
7761 TTAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTAATTATTTATTATATA
Found at i:13363 original size:5 final size:4
Alignment explanation
Indices: 13320--13362 Score: 50
Period size: 4 Copynumber: 9.8 Consensus size: 4
13310 CTAAAAAACA
13320 AAAT GAAAT AAAAT AAAT AAAT AAAT AAAT AAACT AAACT AAA
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAA-T AAA-T AAA
13363 CAGGCATGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 19 0.53
5 17 0.47
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:15765 original size:211 final size:211
Alignment explanation
Indices: 15401--15824 Score: 794
Period size: 211 Copynumber: 2.0 Consensus size: 211
15391 CTTATTTCTC
15401 CCTCCAAACTCAACATCCTCAAAAATAATGTTATATACCTCACCTTGAAAATATTCCTAATTATA
1 CCTCCAAACTCAACATCCTCAAAAATAATGTTATATACCTCACCTTGAAAATATTCCTAATTATA
* *
15466 AGATCATAAAACTTATAACCCCCTAAATTGCTCAGAATAACCAAAGTAGTTGCTTACTGTTGTGG
66 AGATCATAAAACTTATAACCCCCTAAATTACTCAGAATAACCAAAGTAGTTGCTTACTGTCGTGG
*
15531 AATTCAATTTCTCATTATATGTCCTAATTTATCTCAAGAGAATAACCCTGTATAACATATTATTG
131 AATTCAATTTCTCATTATATGTCCTAATTTATCTCAAGAAAATAACCCTGTATAACATATTATTG
15596 TCTCTTTTGAGTTGGA
196 TCTCTTTTGAGTTGGA
*
15612 CCTCCAATCTCAACATCCTCAAAAATAATGTTATATACCTCACCTTGAAAATATTCCTAATTATA
1 CCTCCAAACTCAACATCCTCAAAAATAATGTTATATACCTCACCTTGAAAATATTCCTAATTATA
15677 AGATCATAAAACTTATAACCCCCTAAATTACTCAGAATAACCAAAGTAGTTGCTTACTGTCGTGG
66 AGATCATAAAACTTATAACCCCCTAAATTACTCAGAATAACCAAAGTAGTTGCTTACTGTCGTGG
* *
15742 AATTCAATTTCTCATTATATGTCCTAATTTATCTCAAGAAAATAACCCTTTATAACATATTGTTG
131 AATTCAATTTCTCATTATATGTCCTAATTTATCTCAAGAAAATAACCCTGTATAACATATTATTG
15807 TCTCTTTTGAGTTGGA
196 TCTCTTTTGAGTTGGA
15823 CC
1 CC
15825 CTTAACAACT
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
211 207 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (211 bp):
CCTCCAAACTCAACATCCTCAAAAATAATGTTATATACCTCACCTTGAAAATATTCCTAATTATA
AGATCATAAAACTTATAACCCCCTAAATTACTCAGAATAACCAAAGTAGTTGCTTACTGTCGTGG
AATTCAATTTCTCATTATATGTCCTAATTTATCTCAAGAAAATAACCCTGTATAACATATTATTG
TCTCTTTTGAGTTGGA
Found at i:20008 original size:14 final size:14
Alignment explanation
Indices: 19989--20015 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19979 CCTTACTCAG
19989 TGGGTATTTTACCA
1 TGGGTATTTTACCA
20003 TGGGTATTTTACC
1 TGGGTATTTTACC
20016 TACTGATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (14 bp):
TGGGTATTTTACCA
Found at i:20471 original size:59 final size:59
Alignment explanation
Indices: 20282--20679 Score: 595
Period size: 59 Copynumber: 6.8 Consensus size: 59
20272 TTTCCCATAT
* * ** *
20282 GGAAATTCATACACTTAGTATGAATCTCTAAAC-GGTTTGCACACAAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* *
20340 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACACGAAGTTCTCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* * * *
20398 GGAAATTCATACACTTAGTATGAATTCCTTAACAATTTTACACACGAAGTGTCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
20457 GGAAA-TCAATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTC-ATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
*
20516 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* *
20575 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGTAGTGCCCAATATA
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATA-C
** * *
20635 AAAAATTCATACACTTAGTATGAATTTCTTGACATTTTTACACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
20680 TTAGTGCCAT
Statistics
Matches: 311, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
58 85 0.27
59 183 0.59
60 43 0.14
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
Found at i:21221 original size:95 final size:96
Alignment explanation
Indices: 21017--21234 Score: 276
Period size: 95 Copynumber: 2.3 Consensus size: 96
21007 TCAGTATCTT
* * ** *
21017 TACCCTTAACATTGTATCGATACTACCATACTATGGTATCGATACCCCCTTTTTGGTATCGATAC
1 TACCCTTAACATGGTATCGATACTACCATACTATGGTATCGATACCCCCATTCCGGTACCGATAC
21082 CAATTTTAGATTCAATGTGACCTGGTATCGA
66 CAATTTTAGATTCAATGTGACCTGGTATCGA
* * * * * * * *
21113 TACCCTTACCATGGTATCAATACTACCATACTGTGGTATTGATA-CCTCATTCCGTTGCCGATAT
1 TACCCTTAACATGGTATCGATACTACCATACTATGGTATCGATACCCCCATTCCGGTACCGATAC
* **
21177 CAATTTTAGATTCGATGTTTCCTGGTATCGA
66 CAATTTTAGATTCAATGTGACCTGGTATCGA
*
21208 TACCCTTATCATGGTATCGATACTACC
1 TACCCTTAACATGGTATCGATACTACC
21235 TCGTCGGTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
95 65 0.62
96 39 0.38
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (96 bp):
TACCCTTAACATGGTATCGATACTACCATACTATGGTATCGATACCCCCATTCCGGTACCGATAC
CAATTTTAGATTCAATGTGACCTGGTATCGA
Found at i:24183 original size:179 final size:179
Alignment explanation
Indices: 23842--24293 Score: 626
Period size: 179 Copynumber: 2.5 Consensus size: 179
23832 TTTCCCATAT
* * ** * *
23842 GGAAATTCATACACTTAGTATGAATCTCTAAAC-GGTTTGCACACAAAGTGCCCAATATGGAAAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
* *
23906 TCATACACTTAGTATGAATTTCTTAAC---TTTTTGCACACGAAGTGCCCAATACTAAAATTCAT
66 TCATACACTTAGTATGAATTTCTTAACATTTTTTTGCACACGAACTGCCCAATACGAAAATTCAT
* *
23968 ACACTTAGTATGAATTCCTGAACATTTTTTCACACGAAGTGCATAATAC
131 ACACTTAGTATGAATTCCTGAACATTTTTGCACACGAAGTGCACAATAC
* *
24017 GGAAATTCATACTCTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGAAAAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
* *
24082 TCATACACTTAGTATGAATTTCTTAACATTTTTTTTCACACGAACTGCCCAATACGGAAATTCAT
66 TCATACACTTAGTATGAATTTCTTAACATTTTTTTGCACACGAACTGCCCAATACGAAAATTCAT
* * * *
24147 ACACTTAGTATGATTTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
131 ACACTTAGTATGAATTCCTGAACATTTTTGCACACGAAGTGCACAATAC
* * * * *
24196 AGAAATTCATACACTTATTATAAATGTT-TTAACATTTTTGCACAGGTAGTGCCCAATACGGAAA
1 GGAAATTCATACACTTAGTATGAAT-TTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAA
* **
24260 TACATACACTTAGTATGAATTTCTTGTCATTTTT
65 TTCATACACTTAGTATGAATTTCTTAACATTTTT
24294 GCACACTTAG
Statistics
Matches: 244, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
175 30 0.12
176 53 0.22
179 159 0.65
180 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (179 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
TCATACACTTAGTATGAATTTCTTAACATTTTTTTGCACACGAACTGCCCAATACGAAAATTCAT
ACACTTAGTATGAATTCCTGAACATTTTTGCACACGAAGTGCACAATAC
Found at i:24305 original size:59 final size:59
Alignment explanation
Indices: 23842--24299 Score: 634
Period size: 59 Copynumber: 7.8 Consensus size: 59
23832 TTTCCCATAT
* * ** * *
23842 GGAAATTCATACACTTAGTATGAATCTCTAAAC-GGTTTGCACACAAAGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
23900 GGAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
** * * * **
23958 TAAAATTCATACACTTAGTATGAATTCCTGAACATTTTTTCACACGAAGTGCATAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
*
24017 GGAAATTCATACTCTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* * *
24076 GAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTTTTCACACGAACTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACA--TTTTTGCACACGAAGTGCCCAATAC
*
24137 GGAAATTCATACACTTAGTATGATTTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* * * * *
24196 AGAAATTCATACACTTATTATAAATGTT-TTAACATTTTTGCACAGGTAGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAAT-TTCTTAACATTTTTGCACACGAAGTGCCCAATAC
* **
24255 GGAAATACATACACTTAGTATGAATTTCTTGTCATTTTTGCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
24300 TTAGTGATAT
Statistics
Matches: 353, Mismatches: 42, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
58 83 0.24
59 213 0.60
60 2 0.01
61 55 0.16
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATAC
Found at i:24673 original size:22 final size:20
Alignment explanation
Indices: 24628--24681 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
24618 TAGCTCTTTA
*
24628 GTATCGATACCCCTACCATG
1 GTATCGATACCCATACCATG
*
24648 GTATCGATACTACCATACTATG
1 GTATCGATAC--CCATACCATG
24670 GTATCGATACCC
1 GTATCGATACCC
24682 CCTTCCGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCATACCATG
Found at i:24771 original size:75 final size:75
Alignment explanation
Indices: 24648--24846 Score: 278
Period size: 75 Copynumber: 2.7 Consensus size: 75
24638 CCCTACCATG
*
24648 GTATCGATACTACCATACTATGGTATCGATACCCCCTTCCGGTATCGATACCAATTTTAGATTCC
1 GTATCGATACTACCATACTATGGTATCGATACCCCCTTTCGGTATCGATACCAATTTTAGATTCC
24713 ATGTGGCCTA
66 ATGTGGCCTA
* *
24723 GTATCGACACTACCATACTATGGTATCGATACCCCCTTTCGGTATCGATACCAATTTTAGATTCG
1 GTATCGATACTACCATACTATGGTATCGATACCCCCTTTCGGTATCGATACCAATTTTAGATTCC
** *
24788 ATGTTTCCTG
66 ATGTGGCCTA
* * **
24798 GTATTGATAC--CCTTAC-ATGGTATCGATACTACCTTGTCGGTATCGATAC
1 GTATCGATACTACCATACTATGGTATCGATACCCCCTT-TCGGTATCGATAC
24847 TGATTGAATC
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
72 17 0.15
73 18 0.16
75 77 0.69
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (75 bp):
GTATCGATACTACCATACTATGGTATCGATACCCCCTTTCGGTATCGATACCAATTTTAGATTCC
ATGTGGCCTA
Found at i:31746 original size:15 final size:15
Alignment explanation
Indices: 31728--31757 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31718 AATAGGTGAT
*
31728 TAATTTGTTTTATTG
1 TAATTTATTTTATTG
31743 TAATTTATTTTATTG
1 TAATTTATTTTATTG
31758 CGTGTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
TAATTTATTTTATTG
Found at i:32836 original size:13 final size:13
Alignment explanation
Indices: 32820--32847 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
32810 CAAACAATAC
32820 TACATAACATTTT
1 TACATAACATTTT
32833 TACATAACATTTT
1 TACATAACATTTT
32846 TA
1 TA
32848 GATGACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
TACATAACATTTT
Found at i:35853 original size:14 final size:14
Alignment explanation
Indices: 35834--35861 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35824 AAAAAGGGCT
35834 ACTCGTATATACAC
1 ACTCGTATATACAC
35848 ACTCGTATATACAC
1 ACTCGTATATACAC
35862 TTTGTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
ACTCGTATATACAC
Found at i:36583 original size:2 final size:2
Alignment explanation
Indices: 36576--36644 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
36566 TTATAAGTCA
36576 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
*
36618 AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
36645 ATACTACAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54514 original size:23 final size:23
Alignment explanation
Indices: 54478--54521 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54468 GCATAATTGC
* *
54478 ACTAATATAGGAGTTCACAAAGA
1 ACTAATATAAGAGTACACAAAGA
*
54501 ACTAATGTAAGAGTACACAAA
1 ACTAATATAAGAGTACACAAA
54522 TGCACTGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (23 bp):
ACTAATATAAGAGTACACAAAGA
Done.