Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016038.1 Corchorus olitorius cultivar O-4 contig16071, 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: 30988
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:1366 original size:6 final size:6
Alignment explanation
Indices: 1355--1398 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
1345 TAGGTAAAAA
1355 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT AT
1399 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:1589 original size:14 final size:14
Alignment explanation
Indices: 1570--1612 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1560 CCTTATAATT
1570 ATTTTATTTTTACC
1 ATTTTATTTTTACC
1584 ATTTTATTATTTTA-C
1 ATTTTA-T-TTTTACC
1599 ATTTATATTTTTAC
1 ATTT-TATTTTTAC
1613 TCAACTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.44
15 7 0.28
16 7 0.28
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:1856 original size:14 final size:14
Alignment explanation
Indices: 1837--1876 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
1827 TTTTATAAAT
1837 ATTTTATTTTTACC
1 ATTTTATTTTTACC
1851 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
1865 ATTTTAATTTTA
1 ATTTTATTTTTA
1877 AAAATGGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:2090 original size:13 final size:13
Alignment explanation
Indices: 2072--2096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2062 TTGGAATTCC
2072 AAATAATATTTAT
1 AAATAATATTTAT
2085 AAATAATATTTA
1 AAATAATATTTA
2097 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:3263 original size:36 final size:36
Alignment explanation
Indices: 3216--3285 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
3206 AGGTTTTGGG
3216 TTCTACTCTCACGAAATATGAGTTTTCTTTGTAATT
1 TTCTACTCTCACGAAATATGAGTTTTCTTTGTAATT
* *
3252 TTCTACTCTCACGGAATGTGAGTTTTCTTTGTAA
1 TTCTACTCTCACGAAATATGAGTTTTCTTTGTAA
3286 ATAGGGAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (36 bp):
TTCTACTCTCACGAAATATGAGTTTTCTTTGTAATT
Found at i:4005 original size:13 final size:13
Alignment explanation
Indices: 3987--4011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3977 CATGTGTCCC
3987 TTTGAATATTAAT
1 TTTGAATATTAAT
4000 TTTGAATATTAA
1 TTTGAATATTAA
4012 AGACATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTGAATATTAAT
Found at i:4936 original size:127 final size:127
Alignment explanation
Indices: 4789--5045 Score: 376
Period size: 127 Copynumber: 2.0 Consensus size: 127
4779 ATGGAGTGAA
* * *
4789 TAAATAATAGTACATGATTTTATGGTCAATAAATG-TGTTTACATTGAACTGGTTAAAAACCCTT
1 TAAATAATAATACATGATTTTATGGTCAATAAATGCT-TTCACATTGAACTAGTTAAAAACCCTT
* * *
4853 GTAATTACAAAAAAAGGC-AGA-GAGAAAAGGAATGGTGAGAAACTAATTGAGGGTCTTTTTAG
65 GCAATTACAAAAAAAGGCTAGAGGAG-AAAGGAATGGTGAGAAACTAATTGAGGATCTTCTTAG
*
4915 TAAATAAATAATACATGATTTTATGGTCAATAAATGCTTTCACATTTAACTAGTTAAAAACCCTT
1 TAAAT-AATAATACATGATTTTATGGTCAATAAATGCTTTCACATTGAACTAGTTAAAAACCCTT
* * *
4980 GCAATTACAAAAAAGGGCTTGAGGAGAAGGGAATGGTGAGAAACTAATTGAGGATCTTCTTAG
65 GCAATTACAAAAAAAGGCTAGAGGAGAAAGGAATGGTGAGAAACTAATTGAGGATCTTCTTAG
5043 TAA
1 TAA
5046 TTAACCAAGT
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
126 5 0.04
127 69 0.59
128 40 0.34
129 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.30
Consensus pattern (127 bp):
TAAATAATAATACATGATTTTATGGTCAATAAATGCTTTCACATTGAACTAGTTAAAAACCCTTG
CAATTACAAAAAAAGGCTAGAGGAGAAAGGAATGGTGAGAAACTAATTGAGGATCTTCTTAG
Found at i:5174 original size:16 final size:16
Alignment explanation
Indices: 5153--5184 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5143 TTCAAATAAC
5153 ATATACTATATATTAT
1 ATATACTATATATTAT
5169 ATATACTATATATTAT
1 ATATACTATATATTAT
5185 TTTTAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATACTATATATTAT
Found at i:5519 original size:205 final size:205
Alignment explanation
Indices: 5165--5577 Score: 675
Period size: 205 Copynumber: 2.0 Consensus size: 205
5155 ATACTATATA
*
5165 TTATATATACTATATATTATTTTTAATGACAATGGAAATTACTTAAAGGTCAAATTGAGGATTAA
1 TTATATATACTATATATTATTTTTAATGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAA
* * * *
5230 TGTAGTGTCTCCTTTTGACTTTTTTTGGTCTTTTCGCACTTTTCGGGTGACTAAAAAGGCACTCG
66 TGTAGTGCCTCCTTTTGACTTTTTTTGGTATTTTCACACTTTTCAGGTGACTAAAAAGGCACTCG
* ** *
5295 ATGAATTTTCTTCCTTACTTTTCCTGTTGCCCTTTTTGGTAATTTAATATTTTTATATTTATGAT
131 ATGAATTTTCCTCCTTACTTTTCCTACTGCCCTTTTTGGTAATTTAATATTTCTATATTTATGAT
5360 TAAGTGTGTT
196 TAAGTGTGTT
*
5370 TTATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAA
1 TTATATATACTATATATTATTTTTAATGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAA
* * *
5435 TGTGGTGCCTCCTTTTGGCTTTTTTTGGTATTTTCACACTTTTCAGGTGACTAAAAAGGCCCTCG
66 TGTAGTGCCTCCTTTTGACTTTTTTTGGTATTTTCACACTTTTCAGGTGACTAAAAAGGCACTCG
* *
5500 ATGAA-TTTCCTCACTTACTTTTCCTACTGCCCTTTTTTGTAATTTACTATTTCTATATTTATGA
131 ATGAATTTTCCTC-CTTACTTTTCCTACTGCCCTTTTTGGTAATTTAATATTTCTATATTTATGA
5564 TTAAGTGTGTT
195 TTAAGTGTGTT
5575 TTA
1 TTA
5578 ATTAATTACA
Statistics
Matches: 192, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
204 6 0.03
205 186 0.97
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (205 bp):
TTATATATACTATATATTATTTTTAATGACAATGGAAATTACTTAAAGGCCAAATTGAGGATTAA
TGTAGTGCCTCCTTTTGACTTTTTTTGGTATTTTCACACTTTTCAGGTGACTAAAAAGGCACTCG
ATGAATTTTCCTCCTTACTTTTCCTACTGCCCTTTTTGGTAATTTAATATTTCTATATTTATGAT
TAAGTGTGTT
Found at i:8840 original size:38 final size:39
Alignment explanation
Indices: 8789--8866 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
8779 TGGCCTCGGG
*
8789 TATCGGGTCGGGTGAAGCCGAAG-ATTAGTTGAAAAGGC
1 TATCGGGTCGGGTGAAGCCGAAGAAATAGTTGAAAAGGC
8827 TATCGGGTCGGGTGAAGCCGAAGAAATAGTTGAAAAGGC
1 TATCGGGTCGGGTGAAGCCGAAGAAATAGTTGAAAAGGC
8866 T
1 T
8867 TCCCGGGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 23 0.61
39 15 0.39
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (39 bp):
TATCGGGTCGGGTGAAGCCGAAGAAATAGTTGAAAAGGC
Found at i:19314 original size:14 final size:14
Alignment explanation
Indices: 19295--19325 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19285 TGAATCGTTA
19295 AATTGATGACGTAG
1 AATTGATGACGTAG
*
19309 AATTGATGATGTAG
1 AATTGATGACGTAG
19323 AAT
1 AAT
19326 GTTAAGTGAT
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:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (14 bp):
AATTGATGACGTAG
Found at i:20072 original size:34 final size:34
Alignment explanation
Indices: 20029--20093 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
20019 AGTTATTAGC
* *
20029 TCAACTGGTAGGTGTACTGTGTCTAGACCGTGAG
1 TCAACTGGTAGGTATACTGTGCCTAGACCGTGAG
* *
20063 TCAACTGGTAGGTATATTGTGCCTGGACCGT
1 TCAACTGGTAGGTATACTGTGCCTAGACCGT
20094 TAGGTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (34 bp):
TCAACTGGTAGGTATACTGTGCCTAGACCGTGAG
Found at i:21159 original size:2 final size:2
Alignment explanation
Indices: 21152--21191 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21142 TCTTCCACAA
21152 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21192 ATCTATCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23300 original size:15 final size:14
Alignment explanation
Indices: 23280--23311 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
23270 TGAGTGATTG
23280 ACTAATGTTTTATTA
1 ACTAATGTTTTA-TA
23295 ACTAATGTTTTATA
1 ACTAATGTTTTATA
23309 ACT
1 ACT
23312 GTAGATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (14 bp):
ACTAATGTTTTATA
Found at i:24357 original size:42 final size:42
Alignment explanation
Indices: 24302--24410 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
24292 TACAAATTGA
** **
24302 AACGCTTGAAAAATGTTAGAATCAACTGACTAGTATGATCTAT
1 AACGCTT-AAAAATGTTAGAATCAACCAACTAGTACAATCTAT
*
24345 AACG-TCTAAAAATATTAGAATCAACCAACTAGTACAATCTAT
1 AACGCT-TAAAAATGTTAGAATCAACCAACTAGTACAATCTAT
* *
24387 AATGCTTGAAAATGTTAGAATCAA
1 AACGCTTAAAAATGTTAGAATCAA
24411 TCAATCAGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 50 0.89
43 6 0.11
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (42 bp):
AACGCTTAAAAATGTTAGAATCAACCAACTAGTACAATCTAT
Found at i:24432 original size:42 final size:42
Alignment explanation
Indices: 24311--24441 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 42
24301 AAACGCTTGA
* ** ** * *
24311 AAAATGTTAGAATCAACTGACTAGTATGATCTATAACGTC-TA
1 AAAATATTAGAATCAACCAACTAGTACAATCTATAATG-CATG
*
24353 AAAATATTAGAATCAACCAACTAGTACAATCTATAATGCTTG
1 AAAATATTAGAATCAACCAACTAGTACAATCTATAATGCATG
* * *
24395 AAAATGTTAGAATCAATCAA-TCAGTATAATC-ATTAATGCATG
1 AAAATATTAGAATCAACCAACT-AGTACAATCTA-TAATGCATG
24437 AAAAT
1 AAAAT
24442 CAGCATGTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
41 3 0.04
42 72 0.96
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (42 bp):
AAAATATTAGAATCAACCAACTAGTACAATCTATAATGCATG
Found at i:28120 original size:6 final size:6
Alignment explanation
Indices: 28109--28158 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
28099 TGCTAAACGT
28109 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG
28157 GA
1 GA
28159 TAGTTCCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:30003 original size:52 final size:52
Alignment explanation
Indices: 29920--30019 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
29910 AGGTAATCAA
* * *
29920 ATCTGACTTATCTATTGCTTTTATTTCAAATTATATATTCTGAAATTGGATT
1 ATCTAACTTATCTATTCCTTTCATTTCAAATTATATATTCTGAAATTGGATT
* *
29972 ATCTAACTTATTTATTCCTTTCATTTCAAATTATTTATTCTGAAATTG
1 ATCTAACTTATCTATTCCTTTCATTTCAAATTATATATTCTGAAATTG
30020 ATCCCTACCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (52 bp):
ATCTAACTTATCTATTCCTTTCATTTCAAATTATATATTCTGAAATTGGATT
Done.