Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018420.1 Corchorus olitorius cultivar O-4 contig18453, 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: 34951
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1264 original size:25 final size:25
Alignment explanation
Indices: 1236--1284 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1226 CGTGCTTATT
*
1236 CTTTCTCCAGGCCCTGCGCCACTTC
1 CTTTATCCAGGCCCTGCGCCACTTC
*
1261 CTTTATTCAGGCCCTGCGCCACTT
1 CTTTATCCAGGCCCTGCGCCACTT
1285 TTCTCTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.10, C:0.43, G:0.16, T:0.31
Consensus pattern (25 bp):
CTTTATCCAGGCCCTGCGCCACTTC
Found at i:1405 original size:40 final size:40
Alignment explanation
Indices: 1361--1443 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
1351 GTTCGCCTCG
*
1361 TTATCTCAAATTTGCTCCGTGCAACAACTAAGCTCCATGC
1 TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCATGC
* *
1401 TTATCTCAAACTTGCTCCGTGCAACAACTAATCTCCGTGC
1 TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCATGC
1441 TTA
1 TTA
1444 CCTTATCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (40 bp):
TTATCTCAAACTTGCTCCGTGCAACAACTAAGCTCCATGC
Found at i:2578 original size:12 final size:12
Alignment explanation
Indices: 2563--2606 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2553 CATATATATC
2563 TCGATATATCCG
1 TCGATATATCCG
*
2575 TCGATATATCTG
1 TCGATATATCCG
*
2587 TTCGATATATGCG
1 -TCGATATATCCG
*
2600 TAGATAT
1 TCGATAT
2607 TTATATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:4405 original size:13 final size:13
Alignment explanation
Indices: 4387--4412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4377 AAAAATGTAT
4387 ATAATTTAAACCC
1 ATAATTTAAACCC
4400 ATAATTTAAACCC
1 ATAATTTAAACCC
4413 TATTAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATTTAAACCC
Found at i:4762 original size:2 final size:2
Alignment explanation
Indices: 4755--4828 Score: 51
Period size: 2 Copynumber: 42.0 Consensus size: 2
4745 CGTTTAGTAC
* *
4755 TA TA TA TA -A T- TA AA TA TA TA T- TT TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4792 TA T- TA GA TA TA TA TA -A T- TA TA TA TA TA -A TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4829 ATTATTAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
1 10 0.18
2 47 0.82
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4815 original size:31 final size:30
Alignment explanation
Indices: 4763--4825 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
4753 ACTATATATA
*
4763 ATTAAATATATATTTTATATATATAATAAT
1 ATTAAATATATATATTATATATATAATAAT
*
4793 ATTAGATATATATAATTATATATATAATAAT
1 ATTAAATATATAT-ATTATATATATAATAAT
4824 AT
1 AT
4826 ATAATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTAAATATATATATTATATATATAATAAT
Found at i:5263 original size:21 final size:21
Alignment explanation
Indices: 5237--5277 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5227 AAAACTTAAA
5237 TAATTGTATAAAATAAAATAC
1 TAATTGTATAAAATAAAATAC
* *
5258 TAATTGTATTAAATTAAATA
1 TAATTGTATAAAATAAAATA
5278 ATAAATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAATTGTATAAAATAAAATAC
Found at i:6678 original size:20 final size:19
Alignment explanation
Indices: 6655--6696 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
6645 TTTTTCTCGC
6655 TTTTGATATTAATTTTTGTT
1 TTTTGATATTAATTTTT-TT
**
6675 TTTTTTTATTAATTTTTTT
1 TTTTGATATTAATTTTTTT
6694 TTT
1 TTT
6697 CTTATACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTGATATTAATTTTTTT
Found at i:18059 original size:109 final size:108
Alignment explanation
Indices: 17815--18078 Score: 360
Period size: 109 Copynumber: 2.5 Consensus size: 108
17805 AGTTTAGCCT
* * ** *
17815 TAATTTCACTAAGTTTAGCCCTAAATTAAAATTTTATTTTTATTTTAAGGGTTCATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCCAAAATT
17880 AATAATTTATTGTTATATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA-TTATTGTTATATAGGGTTTTAGAAATAAAATACAAAAC
* *
17924 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCCAAAATT
* *
17989 AATAA-TATTG-T-TATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATTATTGTTATATAGGGTTTTAGAAATAAAATACAAAAC
* **
18029 TAA-TTCACTAAGTTTAG-CCTAAATTAAAATTAAAATTT-TATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAAATTAAAATT-TTATTTCTATTTTAAGGGT
18079 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
103 25 0.17
104 18 0.13
105 30 0.21
106 1 0.01
107 5 0.03
109 64 0.45
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (108 bp):
TAATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCCAAAATT
AATAATTATTGTTATATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:24913 original size:21 final size:20
Alignment explanation
Indices: 24887--24928 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
24877 TTAAGGCACC
*
24887 ATTAACAATAGTTTAGCCCCA
1 ATTAACAA-AGTTTAACCCCA
*
24908 ATTAACTAAGTTTAACCCCA
1 ATTAACAAAGTTTAACCCCA
24928 A
1 A
24929 ATCATTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (20 bp):
ATTAACAAAGTTTAACCCCA
Found at i:25164 original size:101 final size:102
Alignment explanation
Indices: 24989--25175 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 102
24979 GAATTTAAAA
* * * *
24989 TTGAGCCTCAAATCACTAAGATTTAGCCCCAATTTATATAAAAAACATTTTAAGGGTATGTCTTG
1 TTGAGCCCCAAATCACTAAGATTTAACCCCAAATTATATAAAAAACATTTTAAAGGTATGTCTTG
25054 AATTAAAAATATTTATTTCTAGGTTTTGAAATTTTAG
66 AATTAAAAATATTTATTTCTAGGTTTTGAAATTTTAG
* * *
25091 TTGAGCCCCAAATCATTTAGATTTAACCTCAAATTATATAAAAATA-A-TTTAAAGGTATGTCTT
1 TTGAGCCCCAAATCACTAAGATTTAACCCCAAATTATATAAAAA-ACATTTTAAAGGTATGTCTT
*
25154 GAATTTAAAATATTTATTTCTA
65 GAATTAAAAATATTTATTTCTA
25176 AAATTTTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
101 36 0.47
102 39 0.51
103 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (102 bp):
TTGAGCCCCAAATCACTAAGATTTAACCCCAAATTATATAAAAAACATTTTAAAGGTATGTCTTG
AATTAAAAATATTTATTTCTAGGTTTTGAAATTTTAG
Found at i:28815 original size:25 final size:23
Alignment explanation
Indices: 28768--28816 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
28758 TTCTATGAAA
**
28768 TTTTGATAACCTCTATATGATTT
1 TTTTGATAACCTCTATAAAATTT
28791 TTTTGATAACCTCTCTATAAAATTT
1 TTTTGATAA-C-CTCTATAAAATTT
28816 T
1 T
28817 ATTACTCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 1 0.05
25 12 0.55
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (23 bp):
TTTTGATAACCTCTATAAAATTT
Found at i:28816 original size:23 final size:23
Alignment explanation
Indices: 28735--28816 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
28725 ACTGACCTAA
* * *
28735 CTATGAAATTTTTTAATAAACTTTT
1 CTATGAAA-TTTTTGAT-AACCTCT
28760 CTATGAAA-TTTTGATAACCTCT
1 CTATGAAATTTTTGATAACCTCT
* **
28782 ATATGATTTTTTTGATAACCTCT
1 CTATGAAATTTTTGATAACCTCT
*
28805 CTATAAAATTTT
1 CTATGAAATTTT
28817 ATTACTCTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
22 10 0.22
23 28 0.61
25 8 0.17
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (23 bp):
CTATGAAATTTTTGATAACCTCT
Found at i:30802 original size:46 final size:45
Alignment explanation
Indices: 30720--30811 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 45
30710 ATTTTAGTAA
30720 TGGCAATTTTATATATATTTTAATAATGACATAATTAAAACATAT
1 TGGCAATTTTATATATATTTTAATAATGACATAATTAAAACATAT
* *
30765 TGGCAATTTTATATAT-TTTAATAATAATGGCATAATTAAAATATAT
1 TGGCAATTTTATATATATTT--TAATAATGACATAATTAAAACATAT
30811 T
1 T
30812 TTAATAATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 3 0.07
45 16 0.37
46 24 0.56
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (45 bp):
TGGCAATTTTATATATATTTTAATAATGACATAATTAAAACATAT
Found at i:32463 original size:22 final size:21
Alignment explanation
Indices: 32438--32484 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
32428 AATACTTATT
32438 AAAAGATAAAAAGAAATTAAAA
1 AAAAGATAAAAAG-AATTAAAA
** *
32460 AAAATCTAAAAAGATTTAAAA
1 AAAAGATAAAAAGAATTAAAA
32481 AAAA
1 AAAA
32485 CGCAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAAGATAAAAAGAATTAAAA
Found at i:33157 original size:14 final size:14
Alignment explanation
Indices: 33138--33164 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33128 AGGCCTATAT
33138 TCTAATACTAATAG
1 TCTAATACTAATAG
33152 TCTAATACTAATA
1 TCTAATACTAATA
33165 CTAACAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
TCTAATACTAATAG
Found at i:34540 original size:15 final size:15
Alignment explanation
Indices: 34520--34551 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34510 CAATTTGGCT
34520 CAATATTACCATGAA
1 CAATATTACCATGAA
34535 CAATATTACCATGAA
1 CAATATTACCATGAA
34550 CA
1 CA
34552 GATGTCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (15 bp):
CAATATTACCATGAA
Done.