Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013738.1 Corchorus olitorius cultivar O-4 contig13771, 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: 29684
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Found at i:1400 original size:253 final size:253
Alignment explanation
Indices: 952--1457 Score: 967
Period size: 253 Copynumber: 2.0 Consensus size: 253
942 CTTCTAATAA
952 ATCAAGATTAGGACTAAAAGCAACCAACTTTTCTTTTCGACCCAGTAGATCTAGTTAGACTAGAG
1 ATCAAGATTAGGACTAAAAGCAACCAACTTTTCTTTTCGACCCAGTAGATCTAGTTAGACTAGAG
* * *
1017 GTATCGTCACTTGACGGGCGACTCGGGGGTGCTAATCCTTCCCCGAGCGTAATCAACTCCCGAAC
66 GTACCGTCACTTGACGGGCGACTCGAGGGTGCTAATCATTCCCCGAGCGTAATCAACTCCCGAAC
*
1082 CTAGATTCAGGTTACAAGACCGGACCTTAGGTTTAGTGGGTCCATTGCCAAGTTTTGGACCTTAC
131 CTAGATTCAGGTTACAAGACCGGACCTTAGGTTTAGTGGGTCCATTGCCAAGCTTTGGACCTTAC
1147 TTAGCTTAGATAGCCTTTAGGTGACTAATCACACCTTTAAAAAGATTAGTGGCGACTC
196 TTAGCTTAGATAGCCTTTAGGTGACTAATCACACCTTTAAAAAGATTAGTGGCGACTC
1205 ATCAAGATTAGGACTAAAAGCAACCAACTTTTCTTTTCGACCCAGTAGATCTAGTTAGACTAGAG
1 ATCAAGATTAGGACTAAAAGCAACCAACTTTTCTTTTCGACCCAGTAGATCTAGTTAGACTAGAG
*
1270 GTACCGTCACTTGACGGGCGACTCGAGGGTGCTAATCATTCCCCGAGCGTAATCGACTCCCGAAC
66 GTACCGTCACTTGACGGGCGACTCGAGGGTGCTAATCATTCCCCGAGCGTAATCAACTCCCGAAC
1335 CTAGATTCAGGTTACAAGACCGGACCTTAGGTTTAGTGGGTCCATTGCCAAGCTTTGGACCTTAC
131 CTAGATTCAGGTTACAAGACCGGACCTTAGGTTTAGTGGGTCCATTGCCAAGCTTTGGACCTTAC
1400 TTAGCTTAGATAGCCTTTAGGTGACTAATCACACCTTTAAAAAGATTAGTGGCGACTC
196 TTAGCTTAGATAGCCTTTAGGTGACTAATCACACCTTTAAAAAGATTAGTGGCGACTC
1458 CTTCTTTTCC
Statistics
Matches: 248, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
253 248 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (253 bp):
ATCAAGATTAGGACTAAAAGCAACCAACTTTTCTTTTCGACCCAGTAGATCTAGTTAGACTAGAG
GTACCGTCACTTGACGGGCGACTCGAGGGTGCTAATCATTCCCCGAGCGTAATCAACTCCCGAAC
CTAGATTCAGGTTACAAGACCGGACCTTAGGTTTAGTGGGTCCATTGCCAAGCTTTGGACCTTAC
TTAGCTTAGATAGCCTTTAGGTGACTAATCACACCTTTAAAAAGATTAGTGGCGACTC
Found at i:7084 original size:65 final size:65
Alignment explanation
Indices: 6976--7099 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
6966 GCTTGCTATT
* ** *
6976 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGTTAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCAAGCATGGGTTGGAC
*
7041 GATTCAAACTTTTTGCACTAAG-CCAGGCGTGGGTAGGCCAAGGGTACCCCAAGCATGGG
1 GATTCAAACTTTCTGCACT-AGCCCAGGCGTGGGTAGGCCAAGGGTACCCCAAGCATGGG
7100 CAGGACCAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
65 51 0.96
66 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.23
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCAAGCATGGGTTGGAC
Found at i:8518 original size:21 final size:20
Alignment explanation
Indices: 8478--8519 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
8468 TTTTTCTTTC
*
8478 TAATTTGGCCCCCTTTTTTT
1 TAATTTGGCCCCCTTATTTT
8498 TAATTT-GCTCCCCTTAATTTT
1 TAATTTGGC-CCCCTT-ATTTT
8519 T
1 T
8520 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.14, C:0.24, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATTTGGCCCCCTTATTTT
Found at i:11697 original size:18 final size:16
Alignment explanation
Indices: 11668--11701 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
11658 CTACTTTCCC
11668 TTTTTTTCTTTCTTTT
1 TTTTTTTCTTTCTTTT
11684 TTTTTTTCCTTTTCTTTT
1 TTTTTTT-C-TTTCTTTT
11702 GGTCAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTCTTTCTTTT
Found at i:12027 original size:21 final size:21
Alignment explanation
Indices: 12003--12043 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11993 AAGATCCACA
12003 AGTCATCAAAATATAAATTCT
1 AGTCATCAAAATATAAATTCT
12024 AGTCATCAAAATATAAATTC
1 AGTCATCAAAATATAAATTC
12044 AAGATGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (21 bp):
AGTCATCAAAATATAAATTCT
Found at i:27385 original size:27 final size:27
Alignment explanation
Indices: 27347--27405 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
27337 GTACTTGAAG
*
27347 TGACCAAAATGCCCCTGGACATGTAAA
1 TGACCAAAATGCCCCTGAACATGTAAA
27374 TGACCAAAATGCCCCTGAACATGTAAA
1 TGACCAAAATGCCCCTGAACATGTAAA
27401 TGACC
1 TGACC
27406 GAAACAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGAACATGTAAA
Found at i:29651 original size:2 final size:2
Alignment explanation
Indices: 29644--29684 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29634 CTTCTACAAA
29644 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.