Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024690.1 Corchorus olitorius cultivar O-4 contig24723, 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: 4199
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Found at i:2048 original size:22 final size:21
Alignment explanation
Indices: 2023--2151 Score: 78
Period size: 22 Copynumber: 5.9 Consensus size: 21
2013 TTATATAGGA
2023 AGGTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATA-AG
* * *
2045 AGGTTACCGAAATTTCATAGGG
1 AGGTTATCAAAATTTCATA-AG
* * *
2067 AGGTTAACAAAATTTTATATG
1 AGGTTATCAAAATTTCATAAG
* * * * *
2088 AAGATGATCGAAATTTTATATTG
1 -AGGTTATCAAAATTTCATA-AG
* *
2111 TGCTTATCAAAATTTCATAAG
1 AGGTTATCAAAATTTCATAAG
* *
2132 AATGTTAACAAAATTTCATA
1 -AGGTTATCAAAATTTCATA
2152 GGGACTGAAG
Statistics
Matches: 82, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
21 2 0.02
22 78 0.95
23 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAAG
Found at i:2264 original size:22 final size:22
Alignment explanation
Indices: 2204--2271 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
2194 TGGAGGTTAA
* * *
2204 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTACATAGAGAGATTAT
* *
2226 GAAAATTATAT-GAAGAGATTAT
1 CAAAATTACATAG-AGAGATTAT
*
2248 CAAAATTACATAGAGAGAATAT
1 CAAAATTACATAGAGAGATTAT
2270 CA
1 CA
2272 CAGTTTCATT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (22 bp):
CAAAATTACATAGAGAGATTAT
Found at i:2339 original size:22 final size:22
Alignment explanation
Indices: 2288--2350 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
2278 CATTCTCATA
*
2288 GGGAGGTTATCGAAA-TTTAAT
1 GGGAGGTTATCAAAATTTTAAT
*
2309 GGTGTGGTTATCAAAATTTTAA-
1 GG-GAGGTTATCAAAATTTTAAT
2331 GAGGAGGTTATCAAAATTTT
1 G-GGAGGTTATCAAAATTTT
2351 CACAGTGTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.06
22 28 0.78
23 6 0.17
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTAAT
Found at i:2408 original size:16 final size:16
Alignment explanation
Indices: 2387--2418 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2377 GTGATTATCA
2387 AAACTTCACACTGAGG
1 AAACTTCACACTGAGG
2403 AAACTTCACACTGAGG
1 AAACTTCACACTGAGG
2419 TTATCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
AAACTTCACACTGAGG
Found at i:2457 original size:22 final size:22
Alignment explanation
Indices: 2429--2510 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
2419 TTATCAAAAA
*
2429 TTTCATAGTGTGGTTATCGAAT
1 TTTCATAGTGTGGTTATTGAAT
* *
2451 TTTCATAGGGTGGTTATTGAAA
1 TTTCATAGTGTGGTTATTGAAT
* ** *
2473 TTTCATAATAAGGTTATTAAAT
1 TTTCATAGTGTGGTTATTGAAT
*
2495 TTTCACAGTGTGGTTA
1 TTTCATAGTGTGGTTA
2511 ACACGTTGGA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (22 bp):
TTTCATAGTGTGGTTATTGAAT
Found at i:2488 original size:44 final size:44
Alignment explanation
Indices: 2426--2510 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
2416 AGGTTATCAA
* ** * *
2426 AAATTTCATAGTGTGGTTATCGAATTTTCATAGGGTGGTTATTG
1 AAATTTCATAATAAGGTTATCAAATTTTCACAGGGTGGTTATTG
* *
2470 AAATTTCATAATAAGGTTATTAAATTTTCACAGTGTGGTTA
1 AAATTTCATAATAAGGTTATCAAATTTTCACAGGGTGGTTA
2511 ACACGTTGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (44 bp):
AAATTTCATAATAAGGTTATCAAATTTTCACAGGGTGGTTATTG
Found at i:3776 original size:31 final size:31
Alignment explanation
Indices: 3718--3778 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3708 CTTGAGGTCA
*
3718 AAACCCGAACCCGTACGACCCTAAACCCAGC
1 AAACCCGAACCCGAACGACCCTAAACCCAGC
* *
3749 AAACCCGAGACCCGAATGA-CCTGAACCCAG
1 AAACCCGA-ACCCGAACGACCCTAAACCCAG
3779 ATGAGCCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (31 bp):
AAACCCGAACCCGAACGACCCTAAACCCAGC
Found at i:3798 original size:16 final size:15
Alignment explanation
Indices: 3758--3800 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3748 CAAACCCGAG
*
3758 ACCCGAATGACCTGA
1 ACCCGAATGACCGGA
3773 ACCC-AGATGAGCCGGA
1 ACCCGA-ATGA-CCGGA
3789 ACCCGAATGACC
1 ACCCGAATGACC
3801 CACGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.33, C:0.35, G:0.23, T:0.09
Consensus pattern (15 bp):
ACCCGAATGACCGGA
Done.