Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016080.1 Corchorus olitorius cultivar O-4 contig16113, 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: 42492
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:983 original size:18 final size:18
Alignment explanation
Indices: 962--1002 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
952 GTTGAGCAAT
*
962 ATGATTTTGTCAGAGGTG
1 ATGATTCTGTCAGAGGTG
* *
980 ATGACTCTGTCAGTGGTG
1 ATGATTCTGTCAGAGGTG
998 ATGAT
1 ATGAT
1003 ATGCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (18 bp):
ATGATTCTGTCAGAGGTG
Found at i:1339 original size:9 final size:8
Alignment explanation
Indices: 1325--1390 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
1315 ACGACTTAAG
1325 TTATTTATA
1 TTATTT-TA
1334 TTATTTTA
1 TTATTTTA
**
1342 TGGTTTTA
1 TTATTTTA
*
1350 ATATTTATA
1 TTATTT-TA
1359 TTATTTTA
1 TTATTTTA
**
1367 TGGTTTTA
1 TTATTTTA
*
1375 ATATTTATA
1 TTATTT-TA
1384 TTATTTT
1 TTATTTT
1391 CTGATTACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
8 23 0.53
9 20 0.47
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (8 bp):
TTATTTTA
Found at i:1356 original size:25 final size:25
Alignment explanation
Indices: 1326--1390 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
1316 CGACTTAAGT
1326 TATTTATATTATTTTATGGTTTTAA
1 TATTTATATTATTTTATGGTTTTAA
1351 TATTTATATTATTTTATGGTTTTAA
1 TATTTATATTATTTTATGGTTTTAA
1376 TATTTATATTATTTT
1 TATTTATATTATTTT
1391 CTGATTACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (25 bp):
TATTTATATTATTTTATGGTTTTAA
Found at i:2582 original size:10 final size:10
Alignment explanation
Indices: 2569--2609 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
2559 CCCCAATATA
2569 CATAAAAATC
1 CATAAAAATC
*
2579 CATAAAAATA
1 CATAAAAATC
2589 CATAAAAATC
1 CATAAAAATC
*
2599 CATACAAATC
1 CATAAAAATC
2609 C
1 C
2610 CAAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.20
Consensus pattern (10 bp):
CATAAAAATC
Found at i:2589 original size:20 final size:20
Alignment explanation
Indices: 2566--2607 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2556 ATACCCCAAT
2566 ATACATAAAAATCCATAAAA
1 ATACATAAAAATCCATAAAA
*
2586 ATACATAAAAATCCATACAA
1 ATACATAAAAATCCATAAAA
2606 AT
1 AT
2608 CCCAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (20 bp):
ATACATAAAAATCCATAAAA
Found at i:4706 original size:39 final size:33
Alignment explanation
Indices: 4659--4740 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
4649 GCACCAGCAC
4659 CAGCCTCCCTCTCCCTATACATCCGAGCAGCCT
1 CAGCCTCCCTCTCCCTATACATCCGAGCAGCCT
4692 CAGCCTCCCTCTCCCTATACATCCGAGCAGCCT
1 CAGCCTCCCTCTCCCTATACATCCGAGCAGCCT
*
4725 CAGCCTCTCTCTCCCT
1 CAGCCTCCCTCTCCCT
4741 TTGCAACTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.16, C:0.50, G:0.11, T:0.23
Consensus pattern (33 bp):
CAGCCTCCCTCTCCCTATACATCCGAGCAGCCT
Found at i:7670 original size:13 final size:13
Alignment explanation
Indices: 7644--7681 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
7634 AGTTCTTTGA
7644 TTTCTTTTTCTTTC
1 TTTCTTTTT-TTTC
7658 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
7671 TTT-TTTTTTTT
1 TTTCTTTTTTTT
7682 TTGTGGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.33
13 7 0.29
14 9 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:7670 original size:17 final size:15
Alignment explanation
Indices: 7648--7683 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
7638 CTTTGATTTC
7648 TTTTTCTTTCTTTCTTT
1 TTTTTCTTT-TTT-TTT
7665 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
7680 TTTT
1 TTTT
7684 GTGGTGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 3 0.16
17 9 0.47
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:7682 original size:13 final size:13
Alignment explanation
Indices: 7648--7682 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
7638 CTTTGATTTC
*
7648 TTTTTCTTTCTTT
1 TTTTTTTTTCTTT
*
7661 CTTTTTTTTCTTT
1 TTTTTTTTTCTTT
7674 TTTTTTTTT
1 TTTTTTTTT
7683 TGTGGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:8059 original size:2 final size:2
Alignment explanation
Indices: 8052--8082 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8042 ATTCACTTCT
8052 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8083 ATGCCCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17297 original size:19 final size:20
Alignment explanation
Indices: 17273--17310 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17263 GTGATTAACT
*
17273 AACTGAC-TCAAACTCAACA
1 AACTGACTTAAAACTCAACA
17292 AACTGACTTAAAACTCAAC
1 AACTGACTTAAAACTCAAC
17311 TAACCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.18
Consensus pattern (20 bp):
AACTGACTTAAAACTCAACA
Found at i:19722 original size:21 final size:20
Alignment explanation
Indices: 19682--19763 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 20
19672 CCGTTTAGTA
19682 ATATT-TATA-ATAAAATAT
1 ATATTATATATATAAAATAT
19700 ATATTATATATATAAAATA-
1 ATATTATATATATAAAATAT
* *
19719 ATATTAAATATATATAAT-T
1 ATATTATATATATAAAATAT
* *
19738 ACA-TATATA-ATAATATAT
1 ATATTATATATATAAAATAT
19756 ATAATTAT
1 AT-ATTAT
19764 TAAATGGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 23 0.45
20 11 0.22
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTATATATATAAAATAT
Found at i:19738 original size:14 final size:14
Alignment explanation
Indices: 19681--19762 Score: 50
Period size: 12 Copynumber: 6.0 Consensus size: 14
19671 ACCGTTTAGT
* *
19681 AATATTTATAATAA
1 AATATATATAATTA
19695 AATATATATTATATATA
1 AATATATA-TA-AT-TA
*
19712 TAAAATA-AT-ATTA
1 -AATATATATAATTA
19725 AATATATATAATT-
1 AATATATATAATTA
*
19738 -ACATATATAA-T-
1 AATATATATAATTA
19749 AATATATATAATTA
1 AATATATATAATTA
19763 TTAAATGGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
11 1 0.02
12 23 0.43
13 5 0.09
14 12 0.23
15 2 0.04
16 3 0.06
17 2 0.04
18 5 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATAATTA
Found at i:19745 original size:12 final size:12
Alignment explanation
Indices: 19728--19762 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
19718 AATATTAAAT
19728 ATATATAATTAC
1 ATATATAATTAC
* *
19740 ATATATAATAAT
1 ATATATAATTAC
19752 ATATATAATTA
1 ATATATAATTA
19763 TTAAATGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATAATTAC
Found at i:32457 original size:13 final size:13
Alignment explanation
Indices: 32439--32464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32429 GAACATTCTT
32439 TAAGTTGATCAAA
1 TAAGTTGATCAAA
32452 TAAGTTGATCAAA
1 TAAGTTGATCAAA
32465 GAAACTTTAA
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:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TAAGTTGATCAAA
Found at i:37261 original size:2 final size:2
Alignment explanation
Indices: 37254--37325 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
37244 AGTGAAACAC
* *
37254 AG AG AG AG AG GG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37296 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37326 TGATCAAATG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41126 original size:2 final size:2
Alignment explanation
Indices: 41119--41149 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
41109 CTTATACCAA
41119 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
41150 TATTTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.