Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023615.1 Corchorus olitorius cultivar O-4 contig23648, 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: 28081
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1264 original size:86 final size:86
Alignment explanation
Indices: 1119--1652 Score: 717
Period size: 87 Copynumber: 6.2 Consensus size: 86
1109 TGCCTTGTCT
1119 AATTCCCAGTTTGCCCTTCCTCA-CGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
1 AATT-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTT
1183 CCCCACCGGAAGGTGTTGTTTA
65 CCCCACCGGAAGGTGTTGTTTA
* *
1205 AATTCCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTCTAAGTATACTTTACCCAATTTGCCCTTC
1 AATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTTC
1270 CCCACCGGAAGGTGTTGTTTAA
66 CCCACCGGAAGGTGTTGTTT-A
* * * * *
1292 AATCCCAATTTGCCCTTCCTCAACGGAAGGTGTTCTCTAAGTCTACTTTACCCAGTTTGCCCTTC
1 AATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTTC
*
1357 CCCACCGGAAGGTGTTGTCTA
66 CCCACCGGAAGGTGTTGTTTA
* * *
1378 AATTCCTAGTTTGCCCTTCCTTATCGGAAGGTATTGTTTAAG--T-C--TA-CCAAGTTTGCCCT
1 AATTCC-AGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAA-TTTGCCCT
*
1437 TCCCCACCGGAAGGTGTTGTCTA
64 TCCCCACCGGAAGGTGTTGTTTA
* *
1460 AATTCCCAGTTTTCCCTT-CTCCATCGGAAGGTGTTGTCTAAGTCTAGTTTACCCAATTTGCCCT
1 AATT-CCAGTTTGCCCTTCCT-CATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCT
* *
1524 TCCTCACCGGAAGGTTTTGTTTA
64 TCCCCACCGGAAGGTGTTGTTTA
* * * * *
1547 AATTCCAGTTTGCTCTTCCTCATCGAAAGGTGTTGTTTAAGTTTAGTTTA-CCAATTTGCCCTTC
1 AATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTTC
* *
1611 CCCACTGGAAGGTGTTATTTA
66 CCCACCGGAAGGTGTTGTTTA
**
1632 AATTCCCAACTTGCCCTTCCT
1 AATT-CCAGTTTGCCCTTCCT
1653 AACTGGAAGG
Statistics
Matches: 396, Mismatches: 38, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
81 5 0.01
82 65 0.16
83 2 0.01
84 2 0.01
85 54 0.14
86 121 0.31
87 143 0.36
88 4 0.01
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.35
Consensus pattern (86 bp):
AATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTTGCCCTTC
CCCACCGGAAGGTGTTGTTTA
Found at i:1310 original size:40 final size:40
Alignment explanation
Indices: 1255--1706 Score: 305
Period size: 40 Copynumber: 10.8 Consensus size: 40
1245 GTATACTTTA
*
1255 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAAAT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* * * *
1295 CCCAATTTGCCCTTCCTCAACGGAAGGTGTTCTCTAAGTCTACTTT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----A--TT
* *
1341 ACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATT
1 -CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* * ** * * *
1382 CCTAGTTTGCCCTTCCTTATCGGAAGGTATTGTTTAAGTCT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAAT-T
* *
1423 ACCAAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATT
1 CCCAA-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* * * * *
1464 CCCAGTTTTCCCTTCTCCATCGGAAGGTGTTGTCTAAGTCTAGTTT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----A--TT
* *
1510 ACCCAATTTGCCCTTCCTCACCGGAAGGTTTTGTTTAAATT
1 -CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* * * * *
1551 -CCAGTTTGCTCTTCCTCATCGAAAGGTGTTGTTTAAGTTTAGTTT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----A--TT
* * *
1596 ACCAATTTGCCCTTCCCCACTGGAAGGTGTTATTTAAATT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* ** * * *
1636 CCCAACTTGCCCTTCCTAACTGGAAGGCGTTGTTTGAATT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
* * * * * *
1676 TCCAGTCTACCCTTCCTCATC-GAAGGTGTTG
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTG
1707 ATCCTACTCC
Statistics
Matches: 324, Mismatches: 65, Indels: 47
0.74 0.15 0.11
Matches are distributed among these distances:
39 40 0.12
40 142 0.44
41 11 0.03
42 29 0.09
43 3 0.01
44 2 0.01
45 2 0.01
46 32 0.10
47 63 0.19
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (40 bp):
CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATT
Found at i:3576 original size:21 final size:21
Alignment explanation
Indices: 3551--3592 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3541 GATTGCATTG
3551 TGTTAATAGTGGTTCAAATTT
1 TGTTAATAGTGGTTCAAATTT
3572 TGTTAATAGTGGTTCAAATTT
1 TGTTAATAGTGGTTCAAATTT
3593 GGTGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48
Consensus pattern (21 bp):
TGTTAATAGTGGTTCAAATTT
Found at i:4161 original size:28 final size:28
Alignment explanation
Indices: 4121--4217 Score: 185
Period size: 28 Copynumber: 3.5 Consensus size: 28
4111 TTTATTTAAG
4121 TTGCATATTCCATTTTAAGAAGTTACAT
1 TTGCATATTCCATTTTAAGAAGTTACAT
*
4149 TTGCATATACCATTTTAAGAAGTTACAT
1 TTGCATATTCCATTTTAAGAAGTTACAT
4177 TTGCATATTCCATTTTAAGAAGTTACAT
1 TTGCATATTCCATTTTAAGAAGTTACAT
4205 TTGCATATTCCAT
1 TTGCATATTCCAT
4218 GTTTGATTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (28 bp):
TTGCATATTCCATTTTAAGAAGTTACAT
Found at i:8653 original size:14 final size:13
Alignment explanation
Indices: 8623--8679 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
8613 TGAGAAACAT
**
8623 TTTTCAAAAAAAA
1 TTTTCAAAAAAGG
8636 TTTTCAACAAAAGG
1 TTTTCAA-AAAAGG
*
8650 TTTTCAAAAATGAG
1 TTTTCAAAAAAG-G
8664 TTTTC-AAAAAGG
1 TTTTCAAAAAAGG
8676 TTTT
1 TTTT
8680 TAGTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
12 5 0.13
13 16 0.42
14 17 0.45
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:9382 original size:7 final size:7
Alignment explanation
Indices: 9370--9439 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
9360 TGAAGCAAAA
9370 AAAAATC
1 AAAAATC
*
9377 AAAAATA
1 AAAAATC
9384 AAAAATC
1 AAAAATC
*
9391 AAAAATA
1 AAAAATC
9398 AAAAATC
1 AAAAATC
* *
9405 AAAAGTA
1 AAAAATC
9412 AAAAAT-
1 AAAAATC
9418 AAAAA--
1 AAAAATC
9423 AATAAAT-
1 AA-AAATC
9430 AAAAATC
1 AAAAATC
9437 AAA
1 AAA
9440 TCAAAAAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 2 0.04
6 12 0.23
7 39 0.74
ACGTcount: A:0.79, C:0.06, G:0.01, T:0.14
Consensus pattern (7 bp):
AAAAATC
Found at i:9388 original size:14 final size:14
Alignment explanation
Indices: 9369--9435 Score: 95
Period size: 14 Copynumber: 5.0 Consensus size: 14
9359 GTGAAGCAAA
9369 AAAAAATCAAAAAT
1 AAAAAATCAAAAAT
9383 AAAAAATCAAAAAT
1 AAAAAATCAAAAAT
*
9397 AAAAAATCAAAAGT
1 AAAAAATCAAAAAT
9411 AAAAAAT-AAAAA-
1 AAAAAATCAAAAAT
*
9423 AATAAAT-AAAAAT
1 AAAAAATCAAAAAT
9436 CAAATCAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 34 0.69
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (14 bp):
AAAAAATCAAAAAT
Found at i:9400 original size:28 final size:27
Alignment explanation
Indices: 9369--9451 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
9359 GTGAAGCAAA
9369 AAAAAATCAAAAATAAAAAATCAAAAAT
1 AAAAAATCAAAAA-AAAAAATCAAAAAT
*
9397 AAAAAATCAAAAGTAAAAAAT-AAAAA-
1 AAAAAATCAAAA-AAAAAAATCAAAAAT
* ** *
9423 AATAAAT--AAAAATCAAATCAAAAAG
1 AAAAAATCAAAAAAAAAAATCAAAAAT
9448 AAAA
1 AAAA
9452 GAAAAAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.11
24 8 0.17
25 3 0.07
26 6 0.13
27 5 0.11
28 19 0.41
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.13
Consensus pattern (27 bp):
AAAAAATCAAAAAAAAAAATCAAAAAT
Found at i:9968 original size:20 final size:20
Alignment explanation
Indices: 9943--9982 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9933 GGCAATTGGG
9943 ACATTGTATTCATATTGCAA
1 ACATTGTATTCATATTGCAA
*
9963 ACATTGTATTTATATTGCAA
1 ACATTGTATTCATATTGCAA
9983 GCATGCCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
ACATTGTATTCATATTGCAA
Found at i:24843 original size:38 final size:38
Alignment explanation
Indices: 24801--24875 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
24791 ACTCGTAACA
24801 ACATCCTTCACTTACAAAAGGACAAAAACAGTTAGACT
1 ACATCCTTCACTTACAAAAGGACAAAAACAGTTAGACT
*
24839 ACATCCTTCACTTACAAAAGGACAAAAACGGTTAGAC
1 ACATCCTTCACTTACAAAAGGACAAAAACAGTTAGAC
24876 AAAGGAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.20
Consensus pattern (38 bp):
ACATCCTTCACTTACAAAAGGACAAAAACAGTTAGACT
Found at i:25431 original size:21 final size:23
Alignment explanation
Indices: 25407--25449 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
25397 ATCATGTGAT
25407 GGTT-GAGAGAAGAA-CAACACG
1 GGTTAGAGAGAAGAAGCAACACG
*
25428 GGTTCAGGGAGAAGAAGCAACA
1 GGTT-AGAGAGAAGAAGCAACA
25450 GAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
23 9 0.50
24 5 0.28
ACGTcount: A:0.42, C:0.14, G:0.35, T:0.09
Consensus pattern (23 bp):
GGTTAGAGAGAAGAAGCAACACG
Found at i:27846 original size:20 final size:20
Alignment explanation
Indices: 27821--27858 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
27811 GCAAGCTTCA
27821 AGGGACAAAGTGCTCAAGGT
1 AGGGACAAAGTGCTCAAGGT
27841 AGGGACAAAGTGCTCAAG
1 AGGGACAAAGTGCTCAAG
27859 CAAGACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.34, T:0.13
Consensus pattern (20 bp):
AGGGACAAAGTGCTCAAGGT
Done.