Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001112.1 Corchorus capsularis cultivar CVL-1 contig01112, 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: 9168
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:2689 original size:115 final size:117
Alignment explanation
Indices: 2544--2758 Score: 389
Period size: 115 Copynumber: 1.8 Consensus size: 117
2534 ACATTAGAGC
2544 GTTGGTTTAAAAAAACAAGAAAATCATTATGATCATTTTCAAATAAATAATGTTTCGCGCAAAAA
1 GTTGGTTT-AAAAAACAAGAAAATCATTATGATCATTTTCAAATAAATAATGTTTCGCGCAAAAA
* *
2609 CGCACAAAATTGTGAAGTTGAGGTTTTAGGCTTTGTCATGTATCAAAGTCAGT
65 CGCACAAAATTATGAAGTTGAGGTTTTAGACTTTGTCATGTATCAAAGTCAGT
2662 GTTGGTTT-AAAAA-AAGAAAATCATTATGATCATTTTCAAATAAATAATGTTTCGCGCAAAAAC
1 GTTGGTTTAAAAAACAAGAAAATCATTATGATCATTTTCAAATAAATAATGTTTCGCGCAAAAAC
2725 GCACAAAATTATGAAGTTGAGGTTTTAGACTTTG
66 GCACAAAATTATGAAGTTGAGGTTTTAGACTTTG
2759 AAGAAAACTT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
115 82 0.86
116 5 0.05
118 8 0.08
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (117 bp):
GTTGGTTTAAAAAACAAGAAAATCATTATGATCATTTTCAAATAAATAATGTTTCGCGCAAAAAC
GCACAAAATTATGAAGTTGAGGTTTTAGACTTTGTCATGTATCAAAGTCAGT
Found at i:3315 original size:22 final size:22
Alignment explanation
Indices: 3226--3488 Score: 100
Period size: 22 Copynumber: 12.0 Consensus size: 22
3216 TCCAATGTAG
* *
3226 AAATATTGATAACCTCATTTTGA
1 AAAT-TTGATAACCTCACTATGA
**
3249 AAATTTGATAACCTCTTTATG-
1 AAATTTGATAACCTCACTATGA
* *
3270 AAATTTCGATAATCTCCCTATGA
1 AAATTT-GATAACCTCACTATGA
* *
3293 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCTCACTATGA
* * *
3315 AATTTTGGTAACCAT-ACTACG-
1 AAATTTGATAACC-TCACTATGA
* * *
3336 AAATTTCAATAACCTCAGTA-CA
1 AAATTT-GATAACCTCACTATGA
**
3358 AAAGTTTGATAATATGC-CTAT-A
1 AAA-TTTGATAACCT-CACTATGA
* * *
3380 AAATTTTAATAATCACACTAAAT-A
1 AAA-TTTGATAACCTCACT--ATGA
** *
3404 AAA-TTGGCAACCGCACTATGA
1 AAATTTGATAACCTCACTATGA
3425 AAATTTTGATAACCTCA-TA--A
1 AAA-TTTGATAACCTCACTATGA
* * * *
3445 TATTTTGATAACCACACAATG-
1 AAATTTGATAACCTCACTATGA
*
3466 AAATTTCGATAACCTCCCTATGA
1 AAATTT-GATAACCTCACTATGA
3489 GAATAAAACT
Statistics
Matches: 176, Mismatches: 44, Indels: 40
0.68 0.17 0.15
Matches are distributed among these distances:
19 12 0.07
20 5 0.03
21 21 0.12
22 109 0.62
23 23 0.13
24 6 0.03
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTTGATAACCTCACTATGA
Found at i:3549 original size:22 final size:22
Alignment explanation
Indices: 3517--3576 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
3507 CTCTCTATGT
3517 ATTTTCGATAACCTCTCCATA-AA
1 ATTTTCGATAA-C-CTCCATATAA
3540 ATTTTC-ATAACCTCCATATAA
1 ATTTTCGATAACCTCCATATAA
* *
3561 ATTTTTGTTAACCTCC
1 ATTTTCGATAACCTCC
3577 CTAGGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 12 0.36
23 6 0.18
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (22 bp):
ATTTTCGATAACCTCCATATAA
Found at i:3556 original size:20 final size:24
Alignment explanation
Indices: 3517--3575 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
3507 CTCTCTATGT
3517 ATTTTCGATAACCTCTCCATA-AA
1 ATTTTCGATAACCTCTCCATATAA
3540 ATTTTC-ATAA-C-CTCCATATAA
1 ATTTTCGATAACCTCTCCATATAA
* *
3561 ATTTTTGTTAACCTC
1 ATTTTCGATAACCTC
3576 CCTAGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 7 0.23
21 8 0.27
22 7 0.23
23 7 0.23
24 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (24 bp):
ATTTTCGATAACCTCTCCATATAA
Found at i:3707 original size:22 final size:22
Alignment explanation
Indices: 3595--3805 Score: 122
Period size: 22 Copynumber: 9.5 Consensus size: 22
3585 TGATAAGCAC
*
3595 AAATTTTGGTAACCTCCCTCCCTATA
1 AAATTTTGGTAACCT--CT--CTATG
* * *
3621 AAATTTTGTTAA-CTTTCATAAG
1 AAATTTTGGTAACCTCTC-TATG
** * * *
3643 AAATTTTATTAACATCCCTAAG
1 AAATTTTGGTAACCTCTCTATG
* * *
3665 AAA-TTTGGTAAACTTTTTATG
1 AAATTTTGGTAACCTCTCTATG
*
3686 AAATTTTGGTAACCTCTGTATG
1 AAATTTTGGTAACCTCTCTATG
* *
3708 AAATTTTGATAA-CTACACTATG
1 AAATTTTGGTAACCT-CTCTATG
* * *
3730 AAGTTTTGATAACCTCTATATG
1 AAATTTTGGTAACCTCTCTATG
* *
3752 AAATTTTGGTAACCACACTATG
1 AAATTTTGGTAACCTCTCTATG
* * * *
3774 AAATTTTGATAATCTTTTTATG
1 AAATTTTGGTAACCTCTCTATG
*
3796 TAATTTTGGT
1 AAATTTTGGT
3806 TTGATTGTCA
Statistics
Matches: 142, Mismatches: 38, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
21 16 0.11
22 108 0.76
23 5 0.04
25 2 0.01
26 11 0.08
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
AAATTTTGGTAACCTCTCTATG
Found at i:3804 original size:44 final size:44
Alignment explanation
Indices: 3682--3805 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 44
3672 GTAAACTTTT
* * * *
3682 TATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACAC
*
3726 TATGAAGTTTTGATAACCTCTATATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACAC
* * * *
3770 TATGAAATTTTGATAATCTTTTTATGTAATTTTGGT
1 TATGAAATTTTGATAACCTCTATATGAAATTTTGGT
3806 TTGATTGTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACAC
Found at i:8932 original size:21 final size:22
Alignment explanation
Indices: 8888--8935 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
8878 CTTAAGGGGG
*
8888 TTGCTAAATACCGCCCCAATTT
1 TTGCTAAATACCACCCCAATTT
*
8910 TTGCTAAATACCACCCCATTTT
1 TTGCTAAATACCACCCCAATTT
8932 TTGC
1 TTGC
8936 ACTTTTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (22 bp):
TTGCTAAATACCACCCCAATTT
Done.