Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015770.1 Corchorus capsularis cultivar CVL-1 contig15791, 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: 12063
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Found at i:2330 original size:2 final size:2
Alignment explanation
Indices: 2323--2348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2313 TAGTTAGATA
2323 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2349 GTTGAATAGA
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):
AT
Found at i:3391 original size:31 final size:30
Alignment explanation
Indices: 3315--3393 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
3305 TCCAAAAAGT
* *
3315 AAAAAAGGCAATCAGTAATTAAGTTCAATA
1 AAAAAAAGTAATCAGTAATTAAGTTCAATA
*
3345 AAAAAAAGTAATCAGTGATTAAGTTCAATA
1 AAAAAAAGTAATCAGTAATTAAGTTCAATA
*
3375 AGAAAGATA-TAATCAGTAA
1 A-AAA-AAAGTAATCAGTAA
3394 AAGCTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 28 0.67
31 12 0.29
32 2 0.05
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (30 bp):
AAAAAAAGTAATCAGTAATTAAGTTCAATA
Found at i:3423 original size:22 final size:22
Alignment explanation
Indices: 3389--3444 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3379 AGATATAATC
*
3389 AGTAAA-AGCTAAAATGGCAATT
1 AGTAAAGAG-TAAAATGACAATT
* * *
3411 AGTAAAGAGTAAAGTGATAGTT
1 AGTAAAGAGTAAAATGACAATT
3433 AGTAAAGAGTAA
1 AGTAAAGAGTAA
3445 TAGAAATCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.23
Consensus pattern (22 bp):
AGTAAAGAGTAAAATGACAATT
Found at i:3481 original size:129 final size:128
Alignment explanation
Indices: 3385--3677 Score: 453
Period size: 129 Copynumber: 2.3 Consensus size: 128
3375 AGAAAGATAT
* * *
3385 AATCAGTAAAAGCTAAAATGGCAATTAGTAAAGAGTAAAGTGATAGTTAGTAAAGAGTAATAGAA
1 AATCAGTAAAAGCTAAAATGGCAATTAGTAAAGAGTAAAGTGATAATCAATAAAGAGTAATAGAA
*
3450 ATCAGTAAGAAGTAATAGTAAACAGCAAAAAGGTAAAAAGGTAATGAGTAAAAAAGTAAAAAGG
66 ATCAGTAAGAAGTAATAGTAAACAGCAAAAA-GTAAAAAGGTAATAAGTAAAAAAGTAAAAAGG
* *
3514 AATCAGTAAAAGGTAAAATGGCAATTAGTAAAGAGTAAAGTGATAATCAATGAAGAGTAATAGAA
1 AATCAGTAAAAGCTAAAATGGCAATTAGTAAAGAGTAAAGTGATAATCAATAAAGAGTAATAGAA
* *
3579 ATCAGTAAGAAGTAATAGTAAACAGTAAAAAGGTAAAAAGGTAATCAGTAAAAAAGTAAAAAGG
66 ATCAGTAAGAAGTAATAGTAAACAGCAAAAA-GTAAAAAGGTAATAAGTAAAAAAGTAAAAAGG
* * * *
3643 TATCTG-AAAGGGTAAAATGGCAATTAGTAAAGAGT
1 AATCAGTAAAAGCTAAAATGGCAATTAGTAAAGAGT
3678 TAAGAATAAG
Statistics
Matches: 154, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 28 0.18
129 126 0.82
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (128 bp):
AATCAGTAAAAGCTAAAATGGCAATTAGTAAAGAGTAAAGTGATAATCAATAAAGAGTAATAGAA
ATCAGTAAGAAGTAATAGTAAACAGCAAAAAGTAAAAAGGTAATAAGTAAAAAAGTAAAAAGG
Found at i:3502 original size:22 final size:21
Alignment explanation
Indices: 3477--3545 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
3467 GTAAACAGCA
*
3477 AAAAGGTAAAAAGGTAATGAGT
1 AAAAGGTAAAAAGG-AATCAGT
*
3499 AAAAAAGTAAAAAGGAATCAGT
1 -AAAAGGTAAAAAGGAATCAGT
* *
3521 AAAAGGTAAAATGGCAATTAGT
1 AAAAGGTAAAAAGG-AATCAGT
3543 AAA
1 AAA
3546 GAGTAAAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
21 12 0.30
22 15 0.38
23 13 0.32
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (21 bp):
AAAAGGTAAAAAGGAATCAGT
Found at i:3592 original size:20 final size:20
Alignment explanation
Indices: 3569--3606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3559 ATCAATGAAG
3569 AGTAATAG-AAATCAGTAAGA
1 AGTAATAGTAAA-CAGTAAGA
3589 AGTAATAGTAAACAGTAA
1 AGTAATAGTAAACAGTAA
3607 AAAGGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21
Consensus pattern (20 bp):
AGTAATAGTAAACAGTAAGA
Found at i:3616 original size:8 final size:8
Alignment explanation
Indices: 3603--3644 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3593 ATAGTAAACA
3603 GTAAAAAG
1 GTAAAAAG
3611 GTAAAAAG
1 GTAAAAAG
**
3619 GTAATCA-
1 GTAAAAAG
*
3626 GTAAAAAA
1 GTAAAAAG
3634 GTAAAAAG
1 GTAAAAAG
3642 GTA
1 GTA
3645 TCTGAAAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (8 bp):
GTAAAAAG
Found at i:7847 original size:3 final size:3
Alignment explanation
Indices: 7839--7905 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
7829 ATTTGCATTA
7839 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7886 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
7906 AGGGATAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.