Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022903.1 Corchorus olitorius cultivar O-4 contig22936, 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: 13581
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:1450 original size:14 final size:15
Alignment explanation
Indices: 1431--1466 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1421 ACTCAACTTT
*
1431 TTGAAAAC-CTTTTC
1 TTGAAAACAATTTTC
1445 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
1460 TTGAAAA
1 TTGAAAA
1467 ACGTCTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Found at i:4300 original size:43 final size:41
Alignment explanation
Indices: 4206--4526 Score: 319
Period size: 41 Copynumber: 7.8 Consensus size: 41
4196 AGGGAATAGG
* *
4206 AACAACGCCTTCCGATGAGGAAGGGCAAACTGAGAAATGAT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGAT
* *
4247 AAACAACACCTTCCGGTGAGGAAGGGCAGACTTGGGAAATGAT
1 -AACAACACCTTCCGATGAGGAAGGGCAAAC-TGGGAAATGAT
* * *
4290 AAACAACACCTTCCGATGAGAAAGGCCAAACTGAG-AATGAT
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGAT
* * * * * *
4331 GACAACACCTTCCAACGAAGAAGGGCAAA-TTGGAAATGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGAT
* * **
4371 GACAACACCTTCCGATGAGGAAGGGCAAACT-GGACAAAGGC
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGA-AATGAT
* * * * *
4412 AACAACACCTCCCGATGAGGAAGGGCATATTGGGAAAAGCT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGAT
* * * *
4453 AACAATACCTTCCGATGAGGAAGGGCAAACT-GAACAAAGGT
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGGA-AATGAT
4494 AACAACA-CTTCCCGATGAGGAAGGGCAAACTGG
1 AACAACACCTT-CCGATGAGGAAGGGCAAACTGG
4527 ACAAGGGCAA
Statistics
Matches: 234, Mismatches: 37, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
39 2 0.01
40 62 0.26
41 99 0.42
42 34 0.15
43 37 0.16
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (41 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATGAT
Found at i:4475 original size:82 final size:82
Alignment explanation
Indices: 4206--4522 Score: 361
Period size: 82 Copynumber: 3.9 Consensus size: 82
4196 AGGGAATAGG
* * * * *
4206 AACAACGCCTTCCGATGAGGAAGGGCAAACTGAGA-AATGATAAACAACACCTTCCGGTGAGGAA
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GACAAAGGT-AACAACACCTCCCGATGAGGAA
* *
4270 GGGCAGACTTGGGAAATGAT
64 GGGCA-AATTGGGAAATGCT
* * * * * * * * * *
4290 AAACAACACCTTCCGATGAGAAAGGCCAAACT-GAGAATGATGACAACACCTTCCAACGAAGAAG
1 -AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGTAACAACACCTCCCGATGAGGAAG
4354 GGCAAATT-GGAAATGCT
65 GGCAAATTGGGAAATGCT
* *
4371 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGTAACAACACCTCCCGATGAGGAAGG
* *
4436 GCATATTGGGAAAAGCT
66 GCAAATTGGGAAATGCT
* * *
4453 AACAATACCTTCCGATGAGGAAGGGCAAACTGAACAAAGGTAACAACACTTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGTAACAACACCTCCCGATGAGGAAGG
4518 GCAAA
66 GCAAA
4523 CTGGACAAGG
Statistics
Matches: 199, Mismatches: 30, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
80 28 0.14
81 38 0.19
82 75 0.38
83 24 0.12
84 6 0.03
85 28 0.14
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (82 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGTAACAACACCTCCCGATGAGGAAGG
GCAAATTGGGAAATGCT
Found at i:5476 original size:4 final size:4
Alignment explanation
Indices: 5467--5506 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
5457 AAAATTATTA
* *
5467 AAAT AAAT AAAT AAAT AAAT AAAT AAGT -AAT AGAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
5507 TCTCTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 2 0.06
4 29 0.94
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:6897 original size:54 final size:54
Alignment explanation
Indices: 6838--7454 Score: 617
Period size: 54 Copynumber: 11.4 Consensus size: 54
6828 TGGATCAAAT
* * * * *
6838 TGGAGATCAAATCTGATCTTCGAAAACTTCTTAAAATGACTGCACCGAATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
6892 TGGAGATCAACTTTGATCTTCGAAAACTTCTTGAAACGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * ***
6946 TGGAGATCAACAT-TGATCTTCGAAAACTTCATGAAACGACCACACCAAATCATC
1 TGGAGATCAAC-TCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
** *
7000 TGGAGATCAACTCTTTTCTTCGAAAACTTCTTGGAAA-GACCGCACTGGATCATT
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTT-GAAATGACCGCACTGGATCATC
* * * *
7054 TGGAGATCAACTCTGATCATT-GAAAACTTCTTGGAAGGACCACACTGGATCATA
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * **
7108 TGGAGATTAACTCT-AGTCTTCGAAAACTTCTTGAAAGGACTGCACCAGATCATC
1 TGGAGATCAACTCTGA-TCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
7162 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACCGCACTGGATCATT
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * * **
7216 TGGAGATCAACTCTAATGATT-GAAATCTTTTTGGAATGACCATACTGGATCATC
1 TGGAGATCAACTCTGAT-CTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
7270 TGG-GATCAATTCTGATC-ACTGAAAACTTCTTGAAATGACCGCACTGGATTATC
1 TGGAGATCAACTCTGATCTTC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * ** *
7323 TGGGGATCAACTCTGATCATT-GAAAACGTT-TTTAGAATGACCGCGTTGGATCATG
1 TGGAGATCAACTCTGATC-TTCGAAAAC-TTCTTGA-AATGACCGCACTGGATCATC
* * * *
7378 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACCGCACTAGATCATT
1 T-GGAGATCAACTCTGATCTTC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
*
7432 TGGAGAACAACTCTGATCTTCGA
1 TGGAGATCAACTCTGATCTTCGA
7455 CCGCATTGGA
Statistics
Matches: 471, Mismatches: 70, Indels: 44
0.81 0.12 0.08
Matches are distributed among these distances:
53 51 0.11
54 366 0.78
55 52 0.11
56 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:7575 original size:145 final size:147
Alignment explanation
Indices: 7306--7731 Score: 376
Period size: 145 Copynumber: 2.8 Consensus size: 147
7296 TTCTTGAAAT
*** * ** *
7306 GACCGCACTGGATTATCTGGGGATCAACTCTGATCATTGAAAACGTTTTTAGAATGACCGCGTTG
1 GACCGCACTGGATTATCTAAAGATCAACTCTGATCATTGAAAACGTTTTGAGAATGACCGCACTA
* * ** * *
7371 GATCATGTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTAGATCATTTGGA
66 GAGCATCTAGGGATCAACTCTGATCTAAAAAAACTTCTTGGAATGACCGCACTAAATCATCTGGA
*
7436 GAACAACTCTGATCTTC
131 GAACAACTATGATCTTC
* *
7453 GACCGCATTGGATTATCTAAAGATCAACTCTGATCATTGAAAAC-TTATTGA-AATGACTGCACT
1 GACCGCACTGGATTATCTAAAGATCAACTCTGATCATTGAAAACGTT-TTGAGAATGACCGCACT
7516 AGAGCATCT-GGGATCAACTCTGATC-AAAGAAAACTTCTTGGAATGACCGCACTAAATCATCTG
65 AGAGCATCTAGGGATCAACTCTGATCTAAA-AAAACTTCTTGGAATGACCGCACTAAATCATCTG
* * *
7579 GGGATCAACTATGATCACTGAAAACTTATTGAAAT
129 GAGAACAACTATG---A-T-----C---TT----C
* * * *** *
7614 GACCGCACTAGATCATTTGGGGATCAACTCTGATCATTGAAAACTTCTTTG-GAATGACCGCACT
1 GACCGCACTGGATTATCTAAAGATCAACTCTGATCATTGAAAACGT-TTTGAGAATGACCGCACT
* * **
7678 GGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACT
65 AGAGCATCTAGGGATCAACTCTGATCTAAAAAAACTTCTTGGAATGACCGCACT
7732 GGGTCATCTG
Statistics
Matches: 225, Mismatches: 31, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
144 1 0.00
145 58 0.26
146 17 0.08
147 43 0.19
148 1 0.00
149 1 0.00
154 1 0.00
157 2 0.01
161 37 0.16
162 22 0.10
163 41 0.18
164 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (147 bp):
GACCGCACTGGATTATCTAAAGATCAACTCTGATCATTGAAAACGTTTTGAGAATGACCGCACTA
GAGCATCTAGGGATCAACTCTGATCTAAAAAAACTTCTTGGAATGACCGCACTAAATCATCTGGA
GAACAACTATGATCTTC
Found at i:7604 original size:54 final size:53
Alignment explanation
Indices: 7474--7902 Score: 435
Period size: 54 Copynumber: 7.8 Consensus size: 53
7464 ATTATCTAAA
* * * * *
7474 GATCAACTCTGATCATTGAAAACTTATTGAAATGACTGCACTAGAGCATCTGG
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCTGG
* *
7527 GATCAACTCTGATCAAAGAAAACTTCTTGGAATGACCGCACTAAATCATCTGGG
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCT-GG
* * * * *
7581 GATCAACTATGATCACTGAAAACTTATTGAAATGACCGCACTAGATCATTTGGG
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCT-GG
* *
7635 GATCAACTCTGATCATTGAAAACTTCTTTGGAATGACCGCACTGGATCATCTAGG
1 GATCAACTCTGATCAATGAAAACTTC-TTGGAATGACCGCACTAGATCATCT-GG
** * * *
7690 GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGGTCATCTGG
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCTGG
* *
7743 GATCAACTCTTGATCAAAGAAAACTTCTTAAAATGACTTTGGAATGACCGCACTGGATCATCTAG
1 GATCAACTC-TGATCAATGAAAA---C-T----T--C-TTGGAATGACCGCACTAGATCATCT-G
7808 G
53 G
* ** * ** *
7809 GATCAACTTTGATCTCTAAAAACTTCTTGGAATGACCGCACTAGGCCATATGG
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCTGG
* *
7862 GATCAACTCTGATCAAAGAAAACTTCTTGGAATCACCGCAC
1 GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCAC
7903 CTGGTTATCT
Statistics
Matches: 316, Mismatches: 45, Indels: 30
0.81 0.12 0.08
Matches are distributed among these distances:
53 92 0.29
54 126 0.40
55 48 0.15
57 2 0.01
58 1 0.00
61 1 0.00
62 2 0.01
64 1 0.00
65 33 0.10
66 10 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (53 bp):
GATCAACTCTGATCAATGAAAACTTCTTGGAATGACCGCACTAGATCATCTGG
Found at i:7622 original size:199 final size:201
Alignment explanation
Indices: 7273--7648 Score: 522
Period size: 199 Copynumber: 1.9 Consensus size: 201
7263 GATCATCTGG
* * * **
7273 GATCAATTCTGATCACTGAAAACTTCTTGAAATGACCGCACTGGATTATCTGGGGATCAACTCTG
1 GATCAACTCTGATCACTGAAAACTTATTGAAATGACCGCACTAGAGCATCTGGGGATCAACTCTG
** * ** ** * * *
7338 ATCATTGAAAACGTTTTTAGAATGACCGCGTTGGATCATGTAGGGATCAACTCTGATCTCTAAAA
66 ATCAAAGAAAACGTTCTTAGAATGACCGCACTAAATCATCTAGGGATCAACTATGATCACTAAAA
* *
7403 ACTTCTTGGAATGACCGCACTAGATCATTTGGAGAACAACTCTGATCTTCGACCGCATTGGATTA
131 ACTTATTGAAATGACCGCACTAGATCATTTGGAGAACAACTCTGATCTTCGACCGCATTGGATTA
7468 TCTAAA
196 TCTAAA
* *
7474 GATCAACTCTGATCATTGAAAACTTATTGAAATGACTGCACTAGAGCATCT-GGGATCAACTCTG
1 GATCAACTCTGATCACTGAAAACTTATTGAAATGACCGCACTAGAGCATCTGGGGATCAACTCTG
* * *
7538 ATCAAAGAAAAC-TTCTTGGAATGACCGCACTAAATCATCTGGGGATCAACTATGATCACTGAAA
66 ATCAAAGAAAACGTTCTTAGAATGACCGCACTAAATCATCTAGGGATCAACTATGATCACTAAAA
* *
7602 ACTTATTGAAATGACCGCACTAGATCATTTGGGGATCAACTCTGATC
131 ACTTATTGAAATGACCGCACTAGATCATTTGGAGAACAACTCTGATC
7649 ATTGAAAACT
Statistics
Matches: 151, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
199 84 0.56
200 23 0.15
201 44 0.29
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (201 bp):
GATCAACTCTGATCACTGAAAACTTATTGAAATGACCGCACTAGAGCATCTGGGGATCAACTCTG
ATCAAAGAAAACGTTCTTAGAATGACCGCACTAAATCATCTAGGGATCAACTATGATCACTAAAA
ACTTATTGAAATGACCGCACTAGATCATTTGGAGAACAACTCTGATCTTCGACCGCATTGGATTA
TCTAAA
Found at i:7835 original size:119 final size:118
Alignment explanation
Indices: 7660--7889 Score: 415
Period size: 119 Copynumber: 1.9 Consensus size: 118
7650 TTGAAAACTT
7660 CTTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGA
1 CTTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGA
* * *
7725 CCGCACTGGGTCATCTGGGATCAACTCTTGATCAAAGAAAACTTCTTAAAATGA
66 CCGCACTAGGCCATATGGGATCAACTC-TGATCAAAGAAAACTTCTTAAAATGA
*
7779 CTTTGGAATGACCGCACTGGATCATCTAGGGATCAACTTTGATCTCTAAAAACTTCTTGGAATGA
1 CTTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGA
7844 CCGCACTAGGCCATATGGGATCAACTCTGATCAAAGAAAACTTCTT
66 CCGCACTAGGCCATATGGGATCAACTCTGATCAAAGAAAACTTCTT
7890 GGAATCACCG
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
118 19 0.18
119 88 0.82
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (118 bp):
CTTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTTGGAATGA
CCGCACTAGGCCATATGGGATCAACTCTGATCAAAGAAAACTTCTTAAAATGA
Found at i:8062 original size:54 final size:54
Alignment explanation
Indices: 7998--8100 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
7988 GGGCTTTATG
*
7998 AAAGACCGCACATGGTCATCAGAAAATCAACTTAGATCACTGAAAACTTCTATC
1 AAAGACCGCACAGGGTCATCAGAAAATCAACTTAGATCACTGAAAACTTCTATC
* ** *
8052 AAAGACCGCACAGGGTCATCTGAACGTCAACTTAGATCTCTGAAAACTT
1 AAAGACCGCACAGGGTCATCAGAAAATCAACTTAGATCACTGAAAACTT
8101 TAAAAGATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (54 bp):
AAAGACCGCACAGGGTCATCAGAAAATCAACTTAGATCACTGAAAACTTCTATC
Done.