Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020561.1 Corchorus olitorius cultivar O-4 contig20594, 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: 26101
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:813 original size:40 final size:40
Alignment explanation
Indices: 740--816 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
730 TGTTACATGA
* * *
740 GTGGATTAGAACAAATTGTTTTTAATTCCATTTTTAACGT
1 GTGGATTAAAACAAATTGTTTTGAATTACATTTTTAACGT
* *
780 GTGGATTAAAACAAATTGTTTTGGATTATATTTTTAA
1 GTGGATTAAAACAAATTGTTTTGAATTACATTTTTAA
817 TGTGAATGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (40 bp):
GTGGATTAAAACAAATTGTTTTGAATTACATTTTTAACGT
Found at i:1115 original size:89 final size:90
Alignment explanation
Indices: 959--1159 Score: 352
Period size: 89 Copynumber: 2.3 Consensus size: 90
949 CAAACGGCCT
*
959 GTGGTGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCCATGGCTTACGTTG
1 GTGGTGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCCACGGCTTACGTTG
* *
1024 CTATATAATTTATACCAACAGC-GG
66 CTATAGAATGTATACCAACAGCAGG
*
1048 GTGGCGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCCACGGCTTACGTTG
1 GTGGTGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCCACGGCTTACGTTG
1113 CTATAGAATGTATACCAACAGCAGG
66 CTATAGAATGTATACCAACAGCAGG
1138 G-GGTGTTGGTATAGCCATAAAC
1 GTGGTGTTGGTATAGCCATAAAC
1160 AGCCAACAGG
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 103 0.97
90 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (90 bp):
GTGGTGTTGGTATAGCCATAAACCAAAAAATGGTATGATTGGAGATATACCCACGGCTTACGTTG
CTATAGAATGTATACCAACAGCAGG
Found at i:2372 original size:16 final size:16
Alignment explanation
Indices: 2344--2378 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2334 ATATTATTTT
2344 AATATTATAATATCTA
1 AATATTATAATATCTA
2360 AATA-TATATATATCTA
1 AATATTATA-ATATCTA
2376 AAT
1 AAT
2379 TTTAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTATAATATCTA
Found at i:3518 original size:2 final size:2
Alignment explanation
Indices: 3455--3499 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3445 TACTAGTATC
*
3455 TA TA TA TA TA TA TA TA TA TT TA TA TA TA -A TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3494 TA TA TA
1 TA TA TA
3500 CTAAGTTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5342 original size:13 final size:14
Alignment explanation
Indices: 5324--5358 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5314 ATCGGGTTTT
5324 AGTCAGTTTGTT-G
1 AGTCAGTTTGTTCG
*
5337 AGTCAGTTTTTTCG
1 AGTCAGTTTGTTCG
5351 AGTCAGTT
1 AGTCAGTT
5359 AGTGTTGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (14 bp):
AGTCAGTTTGTTCG
Found at i:6455 original size:31 final size:31
Alignment explanation
Indices: 6420--6481 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6410 GGTAGGGCCT
6420 ATATTGTAATATAATAAATTTCTTTCATTTA
1 ATATTGTAATATAATAAATTTCTTTCATTTA
*
6451 ATATTGTAATGTAATAAATTTCTTTCATTTA
1 ATATTGTAATATAATAAATTTCTTTCATTTA
6482 TAAAAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (31 bp):
ATATTGTAATATAATAAATTTCTTTCATTTA
Found at i:8025 original size:18 final size:19
Alignment explanation
Indices: 8002--8042 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
7992 ATCAATCAAT
8002 TCATTTTC-TGACTTT-TAA
1 TCATTTTCAT-ACTTTATAA
8020 TCATTTTCATACTTTATAA
1 TCATTTTCATACTTTATAA
8039 TCAT
1 TCAT
8043 CTAATCTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (19 bp):
TCATTTTCATACTTTATAA
Found at i:10508 original size:17 final size:16
Alignment explanation
Indices: 10468--10514 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
10458 CATGTAATCT
**
10468 TTGATCACCGGTGATC
1 TTGATCACTAGTGATC
10484 TTGCATCACTAGTGATC
1 TTG-ATCACTAGTGATC
10501 TTAGATCACTAGTG
1 TT-GATCACTAGTG
10515 GTGATCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 3 0.11
17 23 0.85
18 1 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (16 bp):
TTGATCACTAGTGATC
Found at i:10847 original size:13 final size:13
Alignment explanation
Indices: 10829--10853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10819 AAGATCTCAA
10829 CAAAAATCATCAT
1 CAAAAATCATCAT
10842 CAAAAATCATCA
1 CAAAAATCATCA
10854 CTCATGCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
CAAAAATCATCAT
Found at i:11600 original size:2 final size:2
Alignment explanation
Indices: 11593--11618 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11583 CTAATTTTAT
11593 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11619 GGCCGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15835 original size:20 final size:20
Alignment explanation
Indices: 15781--15829 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
15771 GAGAAAATAA
15781 GCACGGAGCTTGTTTTTTTT
1 GCACGGAGCTTGTTTTTTTT
*
15801 GCACAGAGCTTGTTTTTTTT
1 GCACGGAGCTTGTTTTTTTT
15821 GCACGGAGC
1 GCACGGAGC
15830 AAGTTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (20 bp):
GCACGGAGCTTGTTTTTTTT
Found at i:23339 original size:21 final size:21
Alignment explanation
Indices: 23310--23352 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23300 AGTTGCTACT
*
23310 GCTTAATATTATTCGAAAAAA
1 GCTTAATATTAATCGAAAAAA
* *
23331 GCTTTATATTAATCGAATAAA
1 GCTTAATATTAATCGAAAAAA
23352 G
1 G
23353 TTAGCAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (21 bp):
GCTTAATATTAATCGAAAAAA
Found at i:24890 original size:18 final size:18
Alignment explanation
Indices: 24867--24916 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
24857 GCTGTTTGAT
24867 AAACCATTGAAAATTTTC
1 AAACCATTGAAAATTTTC
24885 AAACCATTGAAAATTTTC
1 AAACCATTGAAAATTTTC
24903 AAACCATTGAAAAT
1 AAACCATTGAAAAT
24917 GAAAAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (18 bp):
AAACCATTGAAAATTTTC
Found at i:25778 original size:24 final size:24
Alignment explanation
Indices: 25739--25790 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
25729 CTGCTGGGCC
25739 GGCCTGGCGCGGCCCA-GCGCACG
1 GGCCTGGCGCGGCCCAGGCGCACG
* *
25762 GGCCTGTGCGTGGCCCAGGCGCGCG
1 GGCCTG-GCGCGGCCCAGGCGCACG
25787 GGCC
1 GGCC
25791 AGGCCAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 9 0.36
25 10 0.40
ACGTcount: A:0.06, C:0.40, G:0.46, T:0.08
Consensus pattern (24 bp):
GGCCTGGCGCGGCCCAGGCGCACG
Found at i:25845 original size:6 final size:6
Alignment explanation
Indices: 25823--25881 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
25813 GGCCCAAGCC
* * *
25823 AGGAAA A-GAAA A-AAAA AGGAAA AGGAAA AGGAAG AGGAAA AAGAAA
1 AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA
* *
25869 AAGAAA AAGAAA A
1 AGGAAA AGGAAA A
25882 TAAAATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 9 0.19
6 38 0.81
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AGGAAA
Found at i:25880 original size:18 final size:18
Alignment explanation
Indices: 25826--25881 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
25816 CCAAGCCAGG
25826 AAAAGAAAAA-AAAAGGA
1 AAAAGAAAAAGAAAAGGA
* * *
25843 AAAGGAAAAGGAAGAGGA
1 AAAAGAAAAAGAAAAGGA
*
25861 AAAAGAAAAAGAAAAAGA
1 AAAAGAAAAAGAAAAGGA
25879 AAA
1 AAA
25882 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGA
Done.