Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022561.1 Corchorus olitorius cultivar O-4 contig22594, 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: 35587
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--60 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
**
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GGG T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
43 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
61 AAAGTTATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1222 original size:107 final size:105
Alignment explanation
Indices: 1049--1311 Score: 413
Period size: 107 Copynumber: 2.5 Consensus size: 105
1039 AAGTTTAACC
*
1049 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
*
1114 TAATAATTTGTTGTTATAGGGTTTTAGAAATAAAATACAAAA
66 TAATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAA
*
1156 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAAT
1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
* *
1221 TAATAATATTGTTATAGGGTTTTAGAAATAAAATATATAA
66 TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAA
* ** *
1261 CTAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
1312 TCGAAAAATC
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
103 30 0.20
104 14 0.10
105 34 0.23
107 69 0.47
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
TAATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAA
Found at i:2017 original size:18 final size:19
Alignment explanation
Indices: 1978--2017 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1968 GTGCTCCCGT
1978 TGTGATGCTCCCATTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
1999 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
2017 T
1 T
2018 TCTGATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:6376 original size:121 final size:121
Alignment explanation
Indices: 6161--6398 Score: 379
Period size: 121 Copynumber: 2.0 Consensus size: 121
6151 GCGACAGCTC
* *
6161 AGTGGTTAAAGCTTAGAACTTCTTGTGGGTCGGATTTGAATCCTGAGATGGGCAGAGTGGGATTA
1 AGTGGTTAAAGCTTAGAACTTCTTGTGGGTCGGATTCGAATCCTGAGATGGGCAGAGTGAGATTA
*
6226 TGGGAGAGGAAAGAGTTACCTCCTGATGTGGAACTCATCTAAACATCATGTTCCTT
66 TGGGAGAGGAAAGAGTTACCTCCTAATGTGGAACTCATCTAAACATCATGTTCCTT
* *
6282 AGTGGTTAAAGCTTAGAACTTCTTGTGGGTCGGATTCGAATCCTGCGATGGG-TGAAGTGAGATT
1 AGTGGTTAAAGCTTAGAACTTCTTGTGGGTCGGATTCGAATCCTGAGATGGGCAG-AGTGAGATT
* * * *
6346 ATGGGAGAGGAGAGAGTTACCTCCTAATGTGGAACTCATTTCAATATCATGTT
65 ATGGGAGAGGAAAGAGTTACCTCCTAATGTGGAACTCATCTAAACATCATGTT
6399 AATGAGTAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
120 1 0.01
121 106 0.99
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (121 bp):
AGTGGTTAAAGCTTAGAACTTCTTGTGGGTCGGATTCGAATCCTGAGATGGGCAGAGTGAGATTA
TGGGAGAGGAAAGAGTTACCTCCTAATGTGGAACTCATCTAAACATCATGTTCCTT
Found at i:7071 original size:31 final size:31
Alignment explanation
Indices: 6954--7127 Score: 213
Period size: 31 Copynumber: 5.6 Consensus size: 31
6944 CGAGGCATGT
** ** * *
6954 CACGTGTAACTTTTTGGTACACATGGAGTGA
1 CACGTGTCGCTTTTTGGTACATGTGGCGTGC
* *
6985 CACGTGTCACTTTTTCGTACATGTGGCGTGC
1 CACGTGTCGCTTTTTGGTACATGTGGCGTGC
* *
7016 CACGTGTCACTTTTTGGTAGATGTGGCGTGC
1 CACGTGTCGCTTTTTGGTACATGTGGCGTGC
*
7047 CATGTGTCGCTTTTTGGTACATGTGGCGTGC
1 CACGTGTCGCTTTTTGGTACATGTGGCGTGC
* *
7078 CACATATCGCTTTTTGGTACATGTGGCGTGC
1 CACGTGTCGCTTTTTGGTACATGTGGCGTGC
* *
7109 CACATATCGCTTTTTGGTA
1 CACGTGTCGCTTTTTGGTA
7128 TACATGGCAT
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (31 bp):
CACGTGTCGCTTTTTGGTACATGTGGCGTGC
Found at i:7141 original size:62 final size:62
Alignment explanation
Indices: 7025--7142 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
7015 CCACGTGTCA
* ** * ** *
7025 CTTTTTGGTAGATGTGGCGTGCCATGTGTCGCTTTTTGGTACATGTGGCGTGCCACATATCG
1 CTTTTTGGTACATGTGGCGTGCCACATATCGCTTTTTGGTACACATGGCATGCCACATATCG
*
7087 CTTTTTGGTACATGTGGCGTGCCACATATCGCTTTTTGGTATACATGGCATGCCAC
1 CTTTTTGGTACATGTGGCGTGCCACATATCGCTTTTTGGTACACATGGCATGCCAC
7143 GTCGGGTACC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.36
Consensus pattern (62 bp):
CTTTTTGGTACATGTGGCGTGCCACATATCGCTTTTTGGTACACATGGCATGCCACATATCG
Found at i:13833 original size:31 final size:31
Alignment explanation
Indices: 13633--13825 Score: 181
Period size: 31 Copynumber: 6.2 Consensus size: 31
13623 CCTTTTTATG
* * *
13633 CACGAGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* *
13664 CACATGGCGTGACACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* * *
13695 CACATGACGTGACACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* * * * **
13726 CATGTGGTGTGCCACATGGCGCTTTTTAATA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* * **
13757 CATGTGACGTGCCA-AGTGTCACTTTTTAATA
1 CACGTGGCGTGCCACA-TGTCACTTTTTGGTA
* * *
13788 CACGTAGCGTGCCACATATCGCTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
13819 CACGTGG
1 CACGTGG
13826 TATGCCACGT
Statistics
Matches: 133, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
30 1 0.01
31 131 0.98
32 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (31 bp):
CACGTGGCGTGCCACATGTCACTTTTTGGTA
Found at i:15231 original size:31 final size:31
Alignment explanation
Indices: 15196--15272 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 31
15186 TTGAATTTGG
* * **
15196 GAAGTTTATGGGGCAAAATGTCCTGATTTTA
1 GAAGTTCATGGGACAAAATAACCTGATTTTA
*
15227 GAAGTTCATTGGACAAAATAACCTGA-TTT-
1 GAAGTTCATGGGACAAAATAACCTGATTTTA
*
15256 GATGTTCAT-GGACAAAA
1 GAAGTTCATGGGACAAAA
15273 CGTCCTTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.20
29 8 0.20
30 3 0.08
31 21 0.52
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (31 bp):
GAAGTTCATGGGACAAAATAACCTGATTTTA
Found at i:21748 original size:60 final size:59
Alignment explanation
Indices: 21670--21799 Score: 197
Period size: 60 Copynumber: 2.2 Consensus size: 59
21660 TGATTAATGA
* * * *
21670 TCAAACTTTTAGACCTAATTAGATTCAATCTAAGAAATTATGCCTAATTTGAGTATTTC
1 TCAAACTTTTAAACCTAATTAGATTCAATCTAAGAAATTATACCTAATTTGAGCACTTC
* *
21729 TCTAAACTTTTAAATCTAATTAGATTCAATCTAAGAAATTATACCTTATTTGAGCACTTC
1 TC-AAACTTTTAAACCTAATTAGATTCAATCTAAGAAATTATACCTAATTTGAGCACTTC
21789 TCAAACTTTTA
1 TCAAACTTTTA
21800 GTTTTTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 11 0.17
60 53 0.83
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (59 bp):
TCAAACTTTTAAACCTAATTAGATTCAATCTAAGAAATTATACCTAATTTGAGCACTTC
Found at i:31299 original size:47 final size:47
Alignment explanation
Indices: 31230--31370 Score: 255
Period size: 47 Copynumber: 3.0 Consensus size: 47
31220 AGATTCAAAT
*
31230 CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACAGCAACTTCTAG
1 CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACACCAACTTCTAG
* *
31277 CTACCTTTGAAATCCTCCAAAGATCAACTTGAAACACCTACTTCTAG
1 CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACACCAACTTCTAG
31324 CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACACCAACTTCTAG
1 CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACACCAACTTCTAG
31371 ACTTGATGAA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 89 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.25
Consensus pattern (47 bp):
CTACCCTTGAAATCCTCCAAAGATCAACTTGAAACACCAACTTCTAG
Found at i:32039 original size:6 final size:6
Alignment explanation
Indices: 32022--32052 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
32012 ATCTTTGAAT
32022 CTCTTAG CTCTTG CTCTTG CTCTTG CTCTTG
1 CTCTT-G CTCTTG CTCTTG CTCTTG CTCTTG
32053 TCATCGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.03, C:0.32, G:0.16, T:0.48
Consensus pattern (6 bp):
CTCTTG
Done.