Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020168.1 Corchorus olitorius cultivar O-4 contig20201, 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: 41296
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:119 original size:31 final size:31
Alignment explanation
Indices: 52--120 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
42 TAGAGTTTGT
*
52 CTTTA-TTTTCTTATTTAGATTATTATTAGG
1 CTTTATTTTTCTTATTTAGATTAGTATTAGG
*
82 CTTTTATTTTTCTTATTTTAG-TTAGTATTGGG
1 C-TTTATTTTTCTTA-TTTAGATTAGTATTAGG
114 CTTTATT
1 CTTTATT
121 GGCTGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 10 0.29
32 18 0.53
33 5 0.15
ACGTcount: A:0.19, C:0.07, G:0.12, T:0.62
Consensus pattern (31 bp):
CTTTATTTTTCTTATTTAGATTAGTATTAGG
Found at i:5729 original size:22 final size:23
Alignment explanation
Indices: 5704--5747 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5694 TGAAAAGAGG
5704 AATTGAGAA-AGT-GATTGAAGAA
1 AATTGAGAAGAGTCGA-TGAAGAA
*
5726 AATTTAGAAGAGTCGATGAAGA
1 AATTGAGAAGAGTCGATGAAGA
5748 TTGAAGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.23
Consensus pattern (23 bp):
AATTGAGAAGAGTCGATGAAGAA
Found at i:15079 original size:72 final size:72
Alignment explanation
Indices: 15001--15147 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
14991 TTAACCATTC
*
15001 TAAATTATCATTTATTCAATAAAATTTTTATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATTATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
15066 ATGAATA
66 ATGAATA
15073 TAAATTATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATTATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
15138 ATGAATA
66 ATGAATA
15145 TAA
1 TAA
15148 GTATTAAATC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (72 bp):
TAAATTATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
ATGAATA
Found at i:15645 original size:16 final size:16
Alignment explanation
Indices: 15626--15660 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15616 AAGTCGAAAA
15626 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
*
15642 ACCCAAAACCCGAGTG
1 ACCCAAAACCCGAATG
15658 ACC
1 ACC
15661 TGAAGCCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.40, G:0.14, T:0.06
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:16384 original size:22 final size:22
Alignment explanation
Indices: 16359--16403 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
16349 TTTAGTTGAA
*
16359 TAAAACTA-TAAAAGTAAAATAG
1 TAAAA-TAGTAAAAATAAAATAG
16381 TAAAATAGTAAAAATAAAATAG
1 TAAAATAGTAAAAATAAAATAG
16403 T
1 T
16404 TATAAGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (22 bp):
TAAAATAGTAAAAATAAAATAG
Found at i:16396 original size:9 final size:8
Alignment explanation
Indices: 16371--16403 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
16361 AAACTATAAA
16371 AGTAAAAT
1 AGTAAAAT
16379 AGTAAAAT
1 AGTAAAAT
16387 AGTAAAA-
1 AGTAAAAT
16394 A-TAAAAT
1 AGTAAAAT
16401 AGT
1 AGT
16404 TATAAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.22
7 2 0.09
8 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AGTAAAAT
Found at i:16535 original size:31 final size:31
Alignment explanation
Indices: 16500--16561 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
16490 ATATTCGAAA
* *
16500 AATAAGGGTATGATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGACGATTCAAAAGTTT
*
16531 AATAAGGGTATAATAGACGATTTAAAAGTTT
1 AATAAGGGTATAATAGACGATTCAAAAGTTT
16562 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.31
Consensus pattern (31 bp):
AATAAGGGTATAATAGACGATTCAAAAGTTT
Found at i:20498 original size:71 final size:69
Alignment explanation
Indices: 20381--20534 Score: 263
Period size: 71 Copynumber: 2.2 Consensus size: 69
20371 ATCACAACAA
*
20381 TTTAGTCACTATAACATTAATAATCTGAAGAGAAGGTAATGTGGGATCGCTTTGATTCCCCGTTC
1 TTTAGTCACTATAACATTAATAATCTGAAGAGAAGGTAATGTGGGATCGATTTGATTCCCCGTTC
20446 GAGT
66 GAGT
*
20450 TAATTAGTCACTATAACATTAATAATCTGAAGAGAAGGTTATGTGGGATCGATTTGATTCCCCGT
1 T--TTAGTCACTATAACATTAATAATCTGAAGAGAAGGTAATGTGGGATCGATTTGATTCCCCGT
20515 TCGAGT
64 TCGAGT
20521 TTTATGTCACTATA
1 TTTA-GTCACTATA
20535 TTAAAGGCAA
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
69 4 0.05
70 9 0.11
71 67 0.84
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (69 bp):
TTTAGTCACTATAACATTAATAATCTGAAGAGAAGGTAATGTGGGATCGATTTGATTCCCCGTTC
GAGT
Found at i:36918 original size:29 final size:29
Alignment explanation
Indices: 36885--36943 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
36875 GTTACCTCTA
*
36885 ATGGCTCGGGCTACTTTCATTCTCAAGCT
1 ATGGCTCAGGCTACTTTCATTCTCAAGCT
36914 ATGGCTCAGGCTACTTTCATTCTCAAGCT
1 ATGGCTCAGGCTACTTTCATTCTCAAGCT
36943 A
1 A
36944 AGCATGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (29 bp):
ATGGCTCAGGCTACTTTCATTCTCAAGCT
Found at i:37237 original size:153 final size:153
Alignment explanation
Indices: 36959--37266 Score: 555
Period size: 153 Copynumber: 2.0 Consensus size: 153
36949 GCAATAGATT
* *
36959 TGTTGTCCTATGTTGGACTTACAGATTCAAAGGTTACTTCCACTCCACTTGAAGCAAATCAAAAG
1 TGTTGTCCTATGTTGGACTTACAGATGCAAAGGTTACTCCCACTCCACTTGAAGCAAATCAAAAG
**
37024 CTTTCTCCATTAGATGGAAACCTCTAGATTTTCCTACTCTCTATCGCCAGCTAGTTGGGAGTCTT
66 CTTTCTCCATTAGATGGAAACCTCTAGATAATCCTACTCTCTATCGCCAGCTAGTTGGGAGTCTT
*
37089 ATCTATCTTACTGTGACTTGCCC
131 ATCTATCTTACTGTGACTCGCCC
37112 TGTTGTCCTATGTTGGACTTACAGATGCAAAGGTTAC-CCCACTCCACTTGAAGCAAATCAAAAG
1 TGTTGTCCTATGTTGGACTTACAGATGCAAAGGTTACTCCCACTCCACTTGAAGCAAATCAAAAG
37176 CTTTCTCCATTAGATGGCAAACCTCTAGATAATCCTACTCTCTATCGCCAGCTAGTTGGGAGTCT
66 CTTTCTCCATTAGATGG-AAACCTCTAGATAATCCTACTCTCTATCGCCAGCTAGTTGGGAGTCT
37241 TATCTATCTTACTGTGACTCGCCC
130 TATCTATCTTACTGTGACTCGCCC
37265 TG
1 TG
37267 ACATAGCACA
Statistics
Matches: 149, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
152 43 0.29
153 106 0.71
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (153 bp):
TGTTGTCCTATGTTGGACTTACAGATGCAAAGGTTACTCCCACTCCACTTGAAGCAAATCAAAAG
CTTTCTCCATTAGATGGAAACCTCTAGATAATCCTACTCTCTATCGCCAGCTAGTTGGGAGTCTT
ATCTATCTTACTGTGACTCGCCC
Found at i:37922 original size:11 final size:11
Alignment explanation
Indices: 37906--37936 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
37896 GGTGTTAAAA
37906 TATTATTATGT
1 TATTATTATGT
*
37917 TATTATTATTT
1 TATTATTATGT
37928 TATTATTAT
1 TATTATTAT
37937 CTTGGCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTATTATGT
Done.