Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019541.1 Corchorus olitorius cultivar O-4 contig19574, 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: 12073
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:217 original size:18 final size:18
Alignment explanation
Indices: 194--228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
184 TTGTTAAATC
*
194 CGAACCGATTCGATCGGT
1 CGAACCGATTCAATCGGT
*
212 CGAACCGGTTCAATCGG
1 CGAACCGATTCAATCGG
229 AACCCGGAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (18 bp):
CGAACCGATTCAATCGGT
Found at i:1483 original size:3 final size:3
Alignment explanation
Indices: 1475--1504 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1465 GCAGTGGAAA
1475 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1505 GAAAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1629 original size:13 final size:12
Alignment explanation
Indices: 1611--1678 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 12
1601 CCCAAGCCAG
1611 AAAAAAGAAAGAA
1 AAAAAAGAAA-AA
1624 AAAAAAGGAGAAAA
1 AAAAAA-GA-AAAA
*
1638 GAAAAAGAAAAA
1 AAAAAAGAAAAA
* *
1650 GAAAAAGGAAAAG
1 -AAAAAAGAAAAA
*
1663 GAAAAAGAAAAGA
1 AAAAAAGAAAA-A
1676 AAA
1 AAA
1679 TAAATAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
12 13 0.30
13 19 0.44
14 9 0.21
15 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:1645 original size:6 final size:6
Alignment explanation
Indices: 1612--1678 Score: 73
Period size: 6 Copynumber: 10.7 Consensus size: 6
1602 CCAAGCCAGA
* *
1612 AAAAAG AAAGAAA AAAAAGG AGAAAAG AAAAAG AAAAAG AAAAAGG AAAAGG
1 AAAAAG AAA-AAG AAAAA-G A-AAAAG AAAAAG AAAAAG AAAAA-G AAAAAG
1664 AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAA
1679 TAAATAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
5 5 0.10
6 30 0.58
7 13 0.25
8 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1708 original size:10 final size:9
Alignment explanation
Indices: 1684--1723 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
1674 GAAAATAAAT
1684 AAATAAGGA
1 AAATAAGGA
1693 AAATAAGGA
1 AAATAAGGA
1702 GAAATAAGGA
1 -AAATAAGGA
*
1712 AATAAAAGGA
1 AA-ATAAGGA
1722 AA
1 AA
1724 TTTGGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (9 bp):
AAATAAGGA
Found at i:1985 original size:26 final size:26
Alignment explanation
Indices: 1930--1986 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1920 TCTTAAGACC
* *
1930 GTAAATTCCCGTTTTACCCATAAGTG
1 GTAAATTACCGTTTTACCCATAAGTA
* *
1956 GTAAATTACC-TTATTACCCCTAATTA
1 GTAAATTACCGTT-TTACCCATAAGTA
1982 GTAAA
1 GTAAA
1987 AGTGTACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (26 bp):
GTAAATTACCGTTTTACCCATAAGTA
Found at i:2618 original size:13 final size:13
Alignment explanation
Indices: 2569--2623 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
2559 TTGAGGAACT
*
2569 ATTTTATT-ACTG
1 ATTTTATTAAATG
2581 -TTTTATTAAATTG
1 ATTTTATTAAA-TG
*
2594 TTTTTA-TAAATG
1 ATTTTATTAAATG
2606 ATTTTATTAAATG
1 ATTTTATTAAATG
2619 ATTTT
1 ATTTT
2624 GGGTGCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 7 0.19
12 8 0.22
13 17 0.46
14 5 0.14
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (13 bp):
ATTTTATTAAATG
Found at i:3493 original size:10 final size:10
Alignment explanation
Indices: 3478--3505 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3468 CCTTGATCTT
3478 CATGCTTCTC
1 CATGCTTCTC
3488 CATGCTTCTC
1 CATGCTTCTC
3498 CATGCTTC
1 CATGCTTC
3506 CTTGCAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.11, T:0.39
Consensus pattern (10 bp):
CATGCTTCTC
Found at i:7470 original size:109 final size:109
Alignment explanation
Indices: 7279--7493 Score: 403
Period size: 109 Copynumber: 2.0 Consensus size: 109
7269 CTATTATATA
*
7279 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATAGAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
*
7344 AGTGCAATGAATTATTGGATTTAAAGAAAAATACAAGCACCTAT
66 AGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTAT
*
7388 TATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
7453 AGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
7494 AAAATGACTA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (109 bp):
TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
AGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTAT
Found at i:8425 original size:5 final size:5
Alignment explanation
Indices: 8415--8440 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
8405 ATCTATTGTG
8415 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
8441 TATCTTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:10178 original size:48 final size:48
Alignment explanation
Indices: 10055--10195 Score: 130
Period size: 48 Copynumber: 3.0 Consensus size: 48
10045 CAAGCAATCC
* ** *
10055 TTTACTTTTCACT-GCACTTTTTCA-CAATTTTTACCACAAAATTGAACT
1 TTTA-TTTTCACTCACACTTTTT-ATCAATTTTTAAGACAAAATTGATCT
* ** *
10103 TTTATTTTTACTTGCA-TCTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTCACTCACACT-TTTTATCAATTTTTAAGACAAAATTGATCT
*
10151 TTTAATTTTCA-TCACACTTTTTATCAATTTTT-TGACAAAATTGAT
1 TTT-ATTTTCACTCACACTTTTTATCAATTTTTAAGACAAAATTGAT
10196 TGGCACGCTC
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
47 20 0.26
48 51 0.65
49 7 0.09
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (48 bp):
TTTATTTTCACTCACACTTTTTATCAATTTTTAAGACAAAATTGATCT
Found at i:10777 original size:18 final size:18
Alignment explanation
Indices: 10738--10788 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
10728 AACAACACAA
* *
10738 TCGCACCGCACCAAGTAT
1 TCGCACCGCACCAAATAG
*
10756 TCGCACCGCACCAAATGG
1 TCGCACCGCACCAAATAG
*
10774 TCGCACCACACCAAA
1 TCGCACCGCACCAAA
10789 AGTTGCCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.31, C:0.41, G:0.16, T:0.12
Consensus pattern (18 bp):
TCGCACCGCACCAAATAG
Found at i:12046 original size:15 final size:15
Alignment explanation
Indices: 12026--12064 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12016 AGAAGATGAT
12026 GGCACC-AACATCGAC
1 GGCACCGAA-ATCGAC
*
12041 GGCACCGAAATTGAC
1 GGCACCGAAATCGAC
12056 GGCACCGAA
1 GGCACCGAA
12065 GATGATGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.08
Consensus pattern (15 bp):
GGCACCGAAATCGAC
Done.