Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013870.1 Corchorus olitorius cultivar O-4 contig13903, 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: 7427
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:358 original size:31 final size:31
Alignment explanation
Indices: 315--373 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
305 ACTCACACTC
*
315 AACTTCTTCAATTTACCCCTCCATTTTTATT
1 AACTTCTCCAATTTACCCCTCCATTTTTATT
346 AACTTCTCCAATTTACCCCTCCATTTTT
1 AACTTCTCCAATTTACCCCTCCATTTTT
374 TTATGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (31 bp):
AACTTCTCCAATTTACCCCTCCATTTTTATT
Found at i:2067 original size:25 final size:25
Alignment explanation
Indices: 2033--2084 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2023 ATTCTGTATT
2033 TTGCTTCTTATTGGTTGTTGACAGG
1 TTGCTTCTTATTGGTTGTTGACAGG
2058 TTGCTTCTTATTGGTTGTTGACAGG
1 TTGCTTCTTATTGGTTGTTGACAGG
2083 TT
1 TT
2085 TATCTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (25 bp):
TTGCTTCTTATTGGTTGTTGACAGG
Found at i:6291 original size:22 final size:22
Alignment explanation
Indices: 6261--6479 Score: 182
Period size: 22 Copynumber: 10.0 Consensus size: 22
6251 GCTAACGTAG
6261 AAATATTGATAACCACACTATGA
1 AAAT-TTGATAACCACACTATGA
* **
6284 AAATTTGATAACCTCGTTATG-
1 AAATTTGATAACCACACTATGA
*
6305 AAATTTCAATAACCTA-A-TATGA
1 AAATTT-GATAACC-ACACTATGA
*
6327 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACACTATGA
*
6349 AATTTTGATAACCACACTATGA
1 AAATTTGATAACCACACTATGA
* * * *
6371 AATTTTGATAACCCCAATGTGA
1 AAATTTGATAACCACACTATGA
* * *
6393 AATTTTGATAATCACACAAT-A
1 AAATTTGATAACCACACTATGA
* *
6414 AAA-TTGGTAACCGCACTATGA
1 AAATTTGATAACCACACTATGA
6435 AAATTTTGATAACCACA-TCATG-
1 AAA-TTTGATAACCACACT-ATGA
* *
6457 AAATTTCGATAACCTCCCTATGA
1 AAATTT-GATAACCACACTATGA
6480 GAATGAAACT
Statistics
Matches: 157, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
20 13 0.08
21 27 0.17
22 99 0.63
23 18 0.11
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:6332 original size:43 final size:44
Alignment explanation
Indices: 6269--6479 Score: 164
Period size: 43 Copynumber: 4.8 Consensus size: 44
6259 AGAAATATTG
* **
6269 ATAACCACACTATGAAAATTTGATAACCTCGTTATGAAATTTCA
1 ATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCA
* **
6313 ATAACCTA-A-TATGAAAATTTGATAACCACACTGTGAAATTTTG
1 ATAACC-ACACTATGAAAATTTGATAACCACACTATGAAATTTCA
* * * * **
6356 ATAACCACACTATGAAATTTTGATAACCCCAATGTGAAATTTTG
1 ATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCA
* * * * **
6400 ATAATCACACAAT-AAAA-TTGGTAACCGCACTATGAAAATTTTG
1 ATAACCACACTATGAAAATTTGATAACCACACTATG-AAATTTCA
* *
6443 ATAACCACA-TCATG-AAATTTCGATAACCTCCCTATGA
1 ATAACCACACT-ATGAAAATTT-GATAACCACACTATGA
6480 GAATGAAACT
Statistics
Matches: 138, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
42 14 0.10
43 59 0.43
44 52 0.38
45 13 0.09
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (44 bp):
ATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCA
Found at i:6368 original size:87 final size:86
Alignment explanation
Indices: 6260--6472 Score: 229
Period size: 87 Copynumber: 2.5 Consensus size: 86
6250 TGCTAACGTA
* **
6260 GAAATATTGATAACCACACTATGAAAATTTGATAACCTCGTTATGAAATTTCAATAA-C-CTA-A
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATATGAAATTTCAATAATCAC-ACA
*
6322 TATGAAAATTTGATAACCACACTGT
65 -AT-AAAA-TTGATAACCACACTAT
* * * **
6347 GAAATTTTGATAACCACACTATGAAATTTTGATAACCCCAATGTGAAATTTTGATAATCACACAA
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATATGAAATTTCAATAATCACACAA
* *
6412 TAAAATTGGTAACCGCACTAT
66 TAAAATTGATAACCACACTAT
6433 GAAAATTTTGATAACCACA-TCATG-AAATTTCGATAACCTC
1 G-AAATTTTGATAACCACACT-ATGAAAATTT-GATAACCTC
6473 CCTATGAGAA
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
86 20 0.19
87 81 0.76
88 4 0.04
89 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (86 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATATGAAATTTCAATAATCACACAA
TAAAATTGATAACCACACTAT
Found at i:6370 original size:65 final size:66
Alignment explanation
Indices: 6261--6479 Score: 196
Period size: 65 Copynumber: 3.3 Consensus size: 66
6251 GCTAACGTAG
* ** *
6261 AAATATTGATAACCACACTATGAAAATTTGATAACCTCGTTATGAAATTTCAATAA-CCTAATAT
1 AAAT-TTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCCCAATAT
6325 GA
65 GA
* * ** *
6327 AAATTTGATAACCACACTGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCCCAATGTG
1 AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCCCAATATG
6392 A
66 A
* * * * * ** *
6393 AATTTTGATAATCACACAAT-AAAA-TTGGTAACCGCACTATGAAAATTTTGATAACCAC-ATCA
1 AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATG-AAATTTCAATAACCCCAAT-A
6455 TG-
64 TGA
* *
6457 AAATTTCGATAACCTCCCTATGA
1 AAATTT-GATAACCACACTATGA
6480 GAATGAAACT
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
64 22 0.18
65 74 0.59
66 29 0.23
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (66 bp):
AAATTTGATAACCACACTATGAAAATTTGATAACCACACTATGAAATTTCAATAACCCCAATATG
A
Done.