Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014657.1 Corchorus olitorius cultivar O-4 contig14690, 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: 78906
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1899 original size:14 final size:14
Alignment explanation
Indices: 1880--1912 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1870 CTTGTAGTAG
1880 TGTAT-ATAATTAAT
1 TGTATAATAA-TAAT
1894 TGTATAATAATAAT
1 TGTATAATAATAAT
1908 TGTAT
1 TGTAT
1913 TATTAGACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (14 bp):
TGTATAATAATAAT
Found at i:13755 original size:30 final size:30
Alignment explanation
Indices: 13727--14112 Score: 547
Period size: 30 Copynumber: 12.7 Consensus size: 30
13717 TACTTACAAA
* * *
13727 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
13757 TGACACCAGAAAAGTTGTCATAATCTCGCAAT
1 TGACACCAG--AAGTTGTCATGATCTTGCAAT
*
13789 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
13819 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
13849 TGACACCAGAAGTTGTCATAATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
13879 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
13909 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
13939 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
13969 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
13999 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
14029 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* ** * * * *
14059 TGATACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
14091 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
14113 AAATTTCCAA
Statistics
Matches: 322, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
30 273 0.85
31 3 0.01
32 46 0.14
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:13889 original size:90 final size:90
Alignment explanation
Indices: 13727--14180 Score: 566
Period size: 90 Copynumber: 4.9 Consensus size: 90
13717 TACTTACAAA
* * * *
13727 TGACACCAGAAGTTGTCATGGTCTTACAAATGACACCAGAAAAGTTGTCATAATCTCGCAATTGA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAG--AAGTTGTCATAATCTTGCAATTGA
* *
13792 CACCAGAAGTTGTCATGCTCTTGCAAT
64 CACCAGAAGTTGTCATGATTTTGCAAT
*
13819 TGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACA
13884 CCAGAAGTTGTCATGATTTTGCAAT
66 CCAGAAGTTGTCATGATTTTGCAAT
* * * *
13909 TGACACCAAAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATGTTGCAATTGACA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACA
*
13974 CCAGAAGTTGTCATGATGTTGCAAT
66 CCAGAAGTTGTCATGATTTTGCAAT
* * *
13999 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCATAAGTTGTCATGATCTTGCAATTGATA
1 TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACA
** * * *
14064 CTTGAAGATGTCATAATTTTATTCAAT
66 CCAGAAGTTGTCATGA-TTT-TGCAAT
* * * *** * * *
14091 TGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAATTGACACCAGAAGTTGTCATAA-TCT-TGCAAT
14156 TGACACCAGAAGTTGTCATGATTTT
61 TGACACCAGAAGTTGTCATGATTTT
14181 ACCTTTCAAA
Statistics
Matches: 316, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
90 204 0.65
91 2 0.01
92 63 0.20
95 21 0.07
96 5 0.02
97 21 0.07
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (90 bp):
TGACACCAGAAGTTGTCATGATCTTGCAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACA
CCAGAAGTTGTCATGATTTTGCAAT
Found at i:14092 original size:32 final size:32
Alignment explanation
Indices: 13785--14181 Score: 193
Period size: 30 Copynumber: 12.9 Consensus size: 32
13775 CATAATCTCG
* ** * *
13785 CAATTGACACCAGAAGTTGTCAT-GCTCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* ** * *
13815 CAATTGACACCAGAAGTTGTCAT-GCTCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * *
13845 CAATTGACACCAGAAGTTGTCATAA-TCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * *
13875 CAATTGACACCAGAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * * *
13905 CAATTGACACCAAAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * * *
13935 CAATTGACACCAGAAGTTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * * *
13965 CAATTGACACCAGAAGTTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * * *
13995 CAATTGACACCAGAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* * * * *
14025 CAATTGACACCATAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* **
14055 CAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* ** *
14087 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACCAGAAGATGTCAT-A-ATTTTATT
* ***
14120 CAATAGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGATGTCATAATTTTATT
* *
14152 CAATTGACACCAGAAGTTGTCATGATTTTA
1 CAATTGACACCAGAAGATGTCATAATTTTA
14182 CCTTTCAAAA
Statistics
Matches: 324, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
30 250 0.77
31 5 0.02
32 46 0.14
33 20 0.06
34 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
CAATTGACACCAGAAGATGTCATAATTTTATT
Found at i:14154 original size:65 final size:62
Alignment explanation
Indices: 13785--14177 Score: 316
Period size: 60 Copynumber: 6.4 Consensus size: 62
13775 CATAATCTCG
* * * ** * ** * *
13785 CAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCAT-GCTCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * *
13845 CAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * * ** * * * *
13905 CAATTGACACCAAAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * * *
13965 CAATTGACACCAGAAGTTGTCATGATGTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * *
14025 CAATTGACACCATAAGTTGTCATGATCTTGCAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* *
14087 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTATT
14152 CAATTGACACCAGAAGTTGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
14178 TTTACCTTTC
Statistics
Matches: 301, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
60 216 0.72
61 2 0.01
62 26 0.09
65 57 0.19
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
Found at i:21068 original size:3 final size:3
Alignment explanation
Indices: 21060--21093 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
21050 CTCATGCAAA
*
21060 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21094 GTATTAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21436 original size:14 final size:13
Alignment explanation
Indices: 21417--21469 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
21407 ATCACAACAC
21417 ATTCATTAATCATT
1 ATTCATTAAT-ATT
21431 ATTCA-T-ATATT
1 ATTCATTAATATT
21442 ATT-ATTAATATT
1 ATTCATTAATATT
*
21454 AAT-ATATAATATT
1 ATTCAT-TAATATT
21467 ATT
1 ATT
21470 AGCATATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 11 0.32
13 10 0.29
14 5 0.15
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTCATTAATATT
Found at i:21466 original size:22 final size:24
Alignment explanation
Indices: 21421--21470 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
21411 CAACACATTC
* *
21421 ATTAATCATTATTCATATATTATT
1 ATTAATCATTAATCATATAATATT
21445 ATTAAT-ATTAAT-ATATAATATT
1 ATTAATCATTAATCATATAATATT
21467 ATTA
1 ATTA
21471 GCATATACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.54
23 5 0.21
24 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAATCATTAATCATATAATATT
Found at i:23646 original size:7 final size:7
Alignment explanation
Indices: 23634--23659 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23624 CTGCGTTGTG
23634 TGTGAAT
1 TGTGAAT
23641 TGTGAAT
1 TGTGAAT
23648 TGTGAAT
1 TGTGAAT
23655 TGTGA
1 TGTGA
23660 TGTCCGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (7 bp):
TGTGAAT
Found at i:25353 original size:4 final size:4
Alignment explanation
Indices: 25329--25366 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
25319 ATCACTTCAC
*
25329 TTAA TTAA TCTAA ATAA -TAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA T-TAA TTAA TTAA TTAA TTAA TTAA TTAA TT
25367 GCTAGACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:25774 original size:27 final size:27
Alignment explanation
Indices: 25736--25813 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
25726 GCGGAGAACA
25736 GAGGTGGGCGAAGACAGAGAAGAGTCG
1 GAGGTGGGCGAAGACAGAGAAGAGTCG
*
25763 GAGGCGGGCGAAGACAGAGAAGAGTCG
1 GAGGTGGGCGAAGACAGAGAAGAGTCG
* *
25790 GAGGTGGGCGATGAGAGAGAAGAG
1 GAGGTGGGCGAAGACAGAGAAGAG
25814 CAAGGCGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.33, C:0.10, G:0.50, T:0.06
Consensus pattern (27 bp):
GAGGTGGGCGAAGACAGAGAAGAGTCG
Found at i:45387 original size:6 final size:6
Alignment explanation
Indices: 45378--45412 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
45368 TGTTAGCCTA
*
45378 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAC TGAGA
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT TGAGA
45413 GGAAGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (6 bp):
TGAGAT
Found at i:48294 original size:5 final size:5
Alignment explanation
Indices: 48284--48317 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
48274 GTTTTCAGGT
48284 TTCTG TTCTG TTCTG TTCTG TTCTG TTCTTG TTC
1 TTCTG TTCTG TTCTG TTCTG TTCTG TTC-TG TTC
48318 AGTTAGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.00, C:0.21, G:0.18, T:0.62
Consensus pattern (5 bp):
TTCTG
Found at i:67633 original size:29 final size:28
Alignment explanation
Indices: 67589--67644 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
67579 TTCTTCAAAC
*
67589 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
67617 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
67645 GTGAAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:67766 original size:33 final size:33
Alignment explanation
Indices: 67722--67822 Score: 175
Period size: 33 Copynumber: 3.1 Consensus size: 33
67712 AAAAATAACC
*
67722 GGTGCCGCCCTCCTAGGGCAGCATGACCATGGT
1 GGTGCCGCCCTCCTAGGGCGGCATGACCATGGT
*
67755 GGTGCCTCCCTCCTAGGGCGGCATGACCATGGT
1 GGTGCCGCCCTCCTAGGGCGGCATGACCATGGT
*
67788 GGTGCCGCCCTCCTTGGGCGGCATGACCATGGT
1 GGTGCCGCCCTCCTAGGGCGGCATGACCATGGT
67821 GG
1 GG
67823 GCGGCACCGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.12, C:0.33, G:0.36, T:0.20
Consensus pattern (33 bp):
GGTGCCGCCCTCCTAGGGCGGCATGACCATGGT
Found at i:69298 original size:5 final size:5
Alignment explanation
Indices: 69288--69312 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
69278 TCTTTTAGAA
69288 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
69313 CTAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:74212 original size:3 final size:3
Alignment explanation
Indices: 74200--74233 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
74190 CATGAAAAAA
* *
74200 AAG AAT AAG AAG AAG AAG AAG AAA AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
74234 GGGAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (3 bp):
AAG
Done.