Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000934.1 Corchorus capsularis cultivar CVL-1 contig00934, 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: 3570
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1510 original size:12 final size:11
Alignment explanation
Indices: 1495--1584 Score: 76
Period size: 12 Copynumber: 7.5 Consensus size: 11
1485 GGGAAGATAG
1495 AGATGCAGATGA
1 AGATG-AGATGA
1507 AGATAGAGATGA
1 AGAT-GAGATGA
1519 AGATGAAGAT-A
1 AGATG-AGATGA
1530 GAGATGAAGAT-A
1 -AGATG-AGATGA
1542 GAGATGCAGATGA
1 -AGATG-AGATGA
1555 AGATAGAGATGA
1 AGAT-GAGATGA
*
1567 AGATAGAGATGC
1 AGAT-GAGATGA
1579 AGATGA
1 AGATGA
1585 AGCTGAGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
11 4 0.06
12 64 0.90
13 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.33, T:0.17
Consensus pattern (11 bp):
AGATGAGATGA
Found at i:1521 original size:30 final size:30
Alignment explanation
Indices: 1501--1586 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
1491 ATAGAGATGC
1501 AGATGAAGATAGAGATGAAGATGAAGATAG
1 AGATGAAGATAGAGATGAAGATGAAGATAG
*
1531 AGATGAAGATAGAGATGCAGATGAAGATAG
1 AGATGAAGATAGAGATGAAGATGAAGATAG
*
1561 AGATGAAGATAGAGATGCAGATGAAG
1 AGATGAAGATAGAGATGAAGATGAAG
1587 CTGAGTTGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.48, C:0.02, G:0.34, T:0.16
Consensus pattern (30 bp):
AGATGAAGATAGAGATGAAGATGAAGATAG
Found at i:1586 original size:18 final size:18
Alignment explanation
Indices: 1456--1570 Score: 127
Period size: 18 Copynumber: 6.7 Consensus size: 18
1446 GGAGTATTGA
1456 AGAGATGCAGATGAAGAT
1 AGAGATGCAGATGAAGAT
**
1474 AGAG-TGGGCAGGGGAAGAT
1 AGAGAT--GCAGATGAAGAT
1493 AGAGATGCAGATGAAGAT
1 AGAGATGCAGATGAAGAT
*
1511 AGAGATGAAGATGAAGAT
1 AGAGATGCAGATGAAGAT
1529 ----A-G-AGATGAAGAT
1 AGAGATGCAGATGAAGAT
1541 AGAGATGCAGATGAAGAT
1 AGAGATGCAGATGAAGAT
*
1559 AGAGATGAAGAT
1 AGAGATGCAGAT
1571 AGAGATGCAG
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.12
13 1 0.01
14 1 0.01
16 1 0.01
17 2 0.02
18 52 0.63
19 14 0.17
20 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.37, T:0.16
Consensus pattern (18 bp):
AGAGATGCAGATGAAGAT
Found at i:3292 original size:2 final size:2
Alignment explanation
Indices: 3285--3329 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
3275 AGCTTCAGTA
3285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
3328 AT
1 AT
3330 TATTTTTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3485 original size:11 final size:11
Alignment explanation
Indices: 3469--3511 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
3459 TATACTATAT
3469 CTAATTAATAG
1 CTAATTAATAG
*
3480 CTAATTAATAT
1 CTAATTAATAG
3491 CTAATTAATAG
1 CTAATTAATAG
*
3502 TTAATTAATA
1 CTAATTAATA
3512 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:3490 original size:22 final size:22
Alignment explanation
Indices: 3465--3511 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3455 CCATTATACT
3465 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
3487 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
3509 ATA
1 ATA
3512 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.