Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009257.1 Hibiscus syriacus cultivar Beakdansim tig00112905_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: 57802
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:376 original size:82 final size:82
Alignment explanation
Indices: 239--394 Score: 294
Period size: 82 Copynumber: 1.9 Consensus size: 82
229 GAGTGGATGC
*
239 TGCTATCATATTTAACTTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTACATCTT
1 TGCTATCACATTTAACTTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTACATCTT
304 GAACGGTTTTACATGAT
66 GAACGGTTTTACATGAT
*
321 TGCTATCACATTTAACTTACCGAAACATGAAAGCACTCTGATTTCCTATGTCGTAACTACATCTT
1 TGCTATCACATTTAACTTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTACATCTT
386 GAACGGTTT
66 GAACGGTTT
395 CATAGATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (82 bp):
TGCTATCACATTTAACTTACCGAAACATGAAAGCAATCTGATTTCCTATGTCGTAACTACATCTT
GAACGGTTTTACATGAT
Found at i:2500 original size:32 final size:33
Alignment explanation
Indices: 2426--2526 Score: 161
Period size: 32 Copynumber: 3.1 Consensus size: 33
2416 TGAAACTATT
*
2426 TAACTAACAAACTAATTAAATATTTTTTATATA
1 TAACTAACAAACTAATTAAATAATTTTTATATA
*
2459 TAACCAACAAACTAATTAAATAATTTTT-TATA
1 TAACTAACAAACTAATTAAATAATTTTTATATA
*
2491 TAACTAACAAACTAATTAAAT-ATTTTTATTTA
1 TAACTAACAAACTAATTAAATAATTTTTATATA
2523 TAAC
1 TAAC
2527 ATCACTTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 6 0.10
32 31 0.49
33 26 0.41
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (33 bp):
TAACTAACAAACTAATTAAATAATTTTTATATA
Found at i:2673 original size:14 final size:15
Alignment explanation
Indices: 2654--2687 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2644 TTCACCCGGG
*
2654 TTCTTCCTTTC-TTC
1 TTCTTCCTTCCTTTC
2668 TTCTTCCTTCCTTTC
1 TTCTTCCTTCCTTTC
2683 TTCTT
1 TTCTT
2688 TTTGCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTTCCTTCCTTTC
Found at i:3370 original size:21 final size:20
Alignment explanation
Indices: 3309--3413 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 20
3299 TTCATGAAAA
* *
3309 AAAAGTTAAGTTTTTTCATG
1 AAAAGTTAAGTCTTTTCATC
**
3329 AAAAGTTGTTAAGTCACTTCATCC
1 AAAA---GTTAAGTCTTTTCAT-C
3353 AAAAGTTAAGTCTTTTCAT-
1 AAAAGTTAAGTCTTTTCATC
3372 ----GTTAAGTCTTTTCATC
1 AAAAGTTAAGTCTTTTCATC
* * *
3388 AAAAGGTTATGTTTTTTAATC
1 AAAA-GTTAAGTCTTTTCATC
3409 AAAAG
1 AAAAG
3414 GTCTTAACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
15 15 0.23
20 5 0.08
21 30 0.45
23 12 0.18
24 4 0.06
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (20 bp):
AAAAGTTAAGTCTTTTCATC
Found at i:3377 original size:15 final size:15
Alignment explanation
Indices: 3357--3386 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3347 TCATCCAAAA
3357 GTTAAGTCTTTTCAT
1 GTTAAGTCTTTTCAT
3372 GTTAAGTCTTTTCAT
1 GTTAAGTCTTTTCAT
3387 CAAAAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
GTTAAGTCTTTTCAT
Found at i:3793 original size:28 final size:27
Alignment explanation
Indices: 3733--3793 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
3723 CAAAACTCTT
*
3733 CTTTTTATTCAATTTTATCCTATTACA
1 CTTTCTATTCAATTTTATCCTATTACA
*
3760 -TGTTCTATTCTAATTTTA-CCTTTTACAA
1 CT-TTCTATTC-AATTTTATCCTATTAC-A
3788 CTTTCT
1 CTTTCT
3794 TATTGTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 1 0.04
27 14 0.50
28 12 0.43
29 1 0.04
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.56
Consensus pattern (27 bp):
CTTTCTATTCAATTTTATCCTATTACA
Found at i:9621 original size:28 final size:28
Alignment explanation
Indices: 9588--9643 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
9578 AGGTAAAAGT
9588 TCAGTTGAAGACTACTACAAGGAGATGC
1 TCAGTTGAAGACTACTACAAGGAGATGC
9616 TCAGTTGAAGACTACTACAAGGAGATGC
1 TCAGTTGAAGACTACTACAAGGAGATGC
9644 AATCCTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
TCAGTTGAAGACTACTACAAGGAGATGC
Found at i:12513 original size:12 final size:13
Alignment explanation
Indices: 12489--12517 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12479 TTGTTTATCT
12489 TTTCTTAATCTTG
1 TTTCTTAATCTTG
12502 TTTCTT-ATCTTG
1 TTTCTTAATCTTG
12514 TTTC
1 TTTC
12518 CAGCACCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTCTTAATCTTG
Found at i:18260 original size:44 final size:45
Alignment explanation
Indices: 18197--18355 Score: 166
Period size: 44 Copynumber: 3.6 Consensus size: 45
18187 TATTCGACTA
** * *
18197 GAGCTAGACAGGCATCTCTAGCAATTTATTCATTTGTTATA-C-AC
1 GAGCTAGATTGGCACCTCTAGCAATTTATTCACTTGTTA-AGCTAC
18241 GAGCTAGATTGGCACCTCTAGCAATTTATTCACTTGTTAAGCTAAC
1 GAGCTAGATTGGCACCTCTAGCAATTTATTCACTTGTTAAGCT-AC
* * * * *
18287 -ATC-ATATTAGTACCTCTAGTAATTTATTCACTTGTTAAGCTA-
1 GAGCTAGATTGGCACCTCTAGCAATTTATTCACTTGTTAAGCTAC
* *
18329 TAGCTAGATTGACACCTCTAGCAATTT
1 GAGCTAGATTGGCACCTCTAGCAATTT
18356 TTCTAGGAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
43 4 0.04
44 87 0.92
45 2 0.02
46 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (45 bp):
GAGCTAGATTGGCACCTCTAGCAATTTATTCACTTGTTAAGCTAC
Found at i:31434 original size:192 final size:192
Alignment explanation
Indices: 31107--31486 Score: 751
Period size: 192 Copynumber: 2.0 Consensus size: 192
31097 GATGAATGAC
31107 ACCCATGGAAAGAAACAAATCATAACAAAATGAACTAAAGAATTCAATTCCATTGTCAATCTTAA
1 ACCCATGGAAAGAAACAAATCATAACAAAATGAACTAAAGAATTCAATTCCATTGTCAATCTTAA
31172 TAAACTTGACATTGGCAAAAAACTATGTTTGAATATAGGCAAAGAACTATTTAAGATAAAGGATG
66 TAAACTTGACATTGGCAAAAAACTATGTTTGAATATAGGCAAAGAACTATTTAAGATAAAGGATG
31237 GTGTCAGACTTCAACCTCAACAAATAAACCTATGTCATTCTAGTGTTGTCATCCACAAATAA
131 GTGTCAGACTTCAACCTCAACAAATAAACCTATGTCATTCTAGTGTTGTCATCCACAAATAA
*
31299 ACCCATGGAAAGAAACGAATCATAACAAAATGAACTAAAGAATTCAATTCCATTGTCAATCTTAA
1 ACCCATGGAAAGAAACAAATCATAACAAAATGAACTAAAGAATTCAATTCCATTGTCAATCTTAA
31364 TAAACTTGACATTGGCAAAAAACTATGTTTGAATATAGGCAAAGAACTATTTAAGATAAAGGATG
66 TAAACTTGACATTGGCAAAAAACTATGTTTGAATATAGGCAAAGAACTATTTAAGATAAAGGATG
31429 GTGTCAGACTTCAACCTCAACAAATAAACCTATGTCATTCTAGTGTTGTCATCCACAA
131 GTGTCAGACTTCAACCTCAACAAATAAACCTATGTCATTCTAGTGTTGTCATCCACAA
31487 TTCTAAGGGA
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 187 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (192 bp):
ACCCATGGAAAGAAACAAATCATAACAAAATGAACTAAAGAATTCAATTCCATTGTCAATCTTAA
TAAACTTGACATTGGCAAAAAACTATGTTTGAATATAGGCAAAGAACTATTTAAGATAAAGGATG
GTGTCAGACTTCAACCTCAACAAATAAACCTATGTCATTCTAGTGTTGTCATCCACAAATAA
Found at i:35572 original size:54 final size:53
Alignment explanation
Indices: 35504--35807 Score: 180
Period size: 54 Copynumber: 5.5 Consensus size: 53
35494 GGTGCTTGAT
*
35504 TTTAGATTGTAGCACAGAGGTGCTCAATCAT-TCCGATGCACAGAGGTGCCAG
1 TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
* ** * *
35556 AATTTAGATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAG
1 --TTTAGATTGAAGCACAGAGGTGCTCAATCATA-TCCGATGCACAGAGGTGCCAG
* * * ** * * *
35612 TCCTCGATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAG
1 T-TTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
*** ** * * *** *
35666 CTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAG
1 -TTTAGATTGAAGCACAGAGGTGCTCAATCA---TATCCGA-TGCACAGAGGTGCCAG
* * ** * * *
35724 TTCTCGATT-AAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG
1 TT-TAGATTGAAGCACAGAGGTGCTCAATCA-TATCCGATGCACAGAGGTGCCAG
* *
35778 CTCTCGATTGAAGCACAGAGGTGCTCAATC
1 -TTTAGATTGAAGCACAGAGGTGCTCAATC
35808 GTTAATTCTA
Statistics
Matches: 207, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
54 95 0.46
55 53 0.26
56 17 0.08
57 24 0.12
58 18 0.09
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (53 bp):
TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
Found at i:35764 original size:112 final size:109
Alignment explanation
Indices: 35565--35804 Score: 347
Period size: 112 Copynumber: 2.2 Consensus size: 109
35555 GAATTTAGAT
**
35565 TGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
1 TGAAGCACAGAGGTGCTCAGTCATAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
*
35630 AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGGC
66 AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGAC
** *
35674 TGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATT-AAGCA
1 TGAAGCACAGAGGTGCTCAGTCA---TAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCA
* * * *
35738 CAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTCGAT
63 CAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCCCGAC
35786 TGAAGCACAGAGGTGCTCA
1 TGAAGCACAGAGGTGCTCA
35805 ATCGTTAATT
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
109 23 0.20
111 21 0.18
112 73 0.62
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (109 bp):
TGAAGCACAGAGGTGCTCAGTCATAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGAC
Found at i:36058 original size:81 final size:81
Alignment explanation
Indices: 35923--36080 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
35913 GCGAGTTACA
*
35923 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
35988 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
* *
36004 AAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
36069 CCGAGCCAGTTG
66 CCGAGCCAGTTG
36081 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:52868 original size:23 final size:23
Alignment explanation
Indices: 52842--52886 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52832 GATCATAATC
* *
52842 AATGTAATTTAAGTTTGAATTTT
1 AATGTAATGTAAATTTGAATTTT
*
52865 AATGTAATGTAAATTTGTATTT
1 AATGTAATGTAAATTTGAATTT
52887 GAATTTGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (23 bp):
AATGTAATGTAAATTTGAATTTT
Found at i:53350 original size:15 final size:15
Alignment explanation
Indices: 53330--53370 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
53320 CGCGTAATAT
53330 AGAAGTTGAACTTCA
1 AGAAGTTGAACTTCA
53345 AGAAGTTGAACTTCA
1 AGAAGTTGAACTTCA
53360 AGAAGTTGAAC
1 AGAAGTTGAAC
53371 CTTTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (15 bp):
AGAAGTTGAACTTCA
Found at i:57290 original size:24 final size:26
Alignment explanation
Indices: 57254--57301 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
57244 CTATTCTTTC
*
57254 GCTTCAATTGAGC-TC-AAATTTTAG
1 GCTTCAATCGAGCTTCTAAATTTTAG
57278 GCTTCAATCGAGCTTCTAAATTTT
1 GCTTCAATCGAGCTTCTAAATTTT
57302 TTGAGTTCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 2 0.10
26 7 0.33
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (26 bp):
GCTTCAATCGAGCTTCTAAATTTTAG
Done.