Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022303.1 Corchorus olitorius cultivar O-4 contig22336, 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: 43003
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:11678 original size:17 final size:16
Alignment explanation
Indices: 11632--11674 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
11622 GATCACCACT
11632 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
11649 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
11666 GGTGATCAA
1 AGTGATCAA
11675 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:14215 original size:37 final size:37
Alignment explanation
Indices: 14166--14309 Score: 225
Period size: 37 Copynumber: 3.9 Consensus size: 37
14156 ATTAAGAACT
* *
14166 AAAACCTGATGGGAACTTTCCCAATTTGAAAACTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
14203 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
* * *
14240 GAAACTTGATGGGAACTTTCCCATTTTTGAAAACTTTG
1 AAAACTTGATGGGAACTTTCCCA-ATTTAAAAACTTTG
*
14278 ATAACTTGATGGGAACTTTCCCAATTTAAAAA
1 AAAACTTGATGGGAACTTTCCCAATTTAAAAA
14310 GAGCTAAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 64 0.66
38 33 0.34
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (37 bp):
AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTG
Found at i:14284 original size:75 final size:74
Alignment explanation
Indices: 14167--14309 Score: 250
Period size: 75 Copynumber: 1.9 Consensus size: 74
14157 TTAAGAACTA
14167 AAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAACTTGATGGGAACTTTCCCAATTTAA
1 AAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAACTTGATGGGAACTTTCCCAATTTAA
14232 AAACTTTGG
66 AAACTTTGG
* * *
14241 AAACTTGATGGGAACTTTCCCATTTTTGAAAACTTTGATAACTTGATGGGAACTTTCCCAATTTA
1 AAACCTGATGGGAACTTTCCCA-ATTTGAAAACTTTGAAAACTTGATGGGAACTTTCCCAATTTA
14306 AAAA
65 AAAA
14310 GAGCTAAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 21 0.32
75 44 0.68
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (74 bp):
AAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAACTTGATGGGAACTTTCCCAATTTAA
AAACTTTGG
Found at i:14381 original size:51 final size:51
Alignment explanation
Indices: 14266--14406 Score: 237
Period size: 51 Copynumber: 2.7 Consensus size: 51
14256 TTTCCCATTT
* *
14266 TTGAAAACTTTGATAACTTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCC-ATTTAAAAAGAGCTAAA
* *
14318 TTGAATAGTTTGAAAACTTGTTGGGAACTTTCCCATTTAAAAAGAGCTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCATTTAAAAAGAGCTAAA
14369 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCATTT
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCATTT
14407 TGAAAACTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 53 0.64
52 30 0.36
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (51 bp):
TTGAATACTTTGAAAACTTGATGGGAACTTTCCCATTTAAAAAGAGCTAAA
Found at i:33991 original size:40 final size:40
Alignment explanation
Indices: 33947--34992 Score: 1236
Period size: 40 Copynumber: 26.4 Consensus size: 40
33937 CTGATGAGGC
* * * *
33947 AGGGCAAACTCGGTATTTAAACAACACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
**
33987 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGACGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* *
34027 AGGGCAAACTGGAAATTTGGACAGCACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* *
34067 AGGGCAAA-TTGGAATTTAGACAGCACCTTCCGGTGGAGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
*
34106 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGATGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * * * * *
34146 AGCGCAAACTAGGAATTTAAACAACACCTTCTGGTCGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * * * *
34186 AGGGCAAACTTGGAATTTAAACAACACCTTCCGATGCGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * * * * *
34226 AGGGCAAACTAGGAATCTAAACAACACCTTTCGGTGAGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34266 AAGGCAAACTAGGAATTTAGACAGCACCTTCCGGCGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34306 AGGGCAAACTAGGAATTTGGATAGCACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34346 AGGGCAAACTGGGAATTTAGACAGCACCTTTCTGCGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * **
34386 AGGGCAAACTGGGTATTTTGACAGCACCTTCTAGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * * *
34426 AGGGCAAACTAGGAATTTAGAGAGCACCTTCCAGCGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34466 ATGGCAAACTGGGTATTTGGACAGCACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34506 AGGGCAAACTTGGATTTTAGACAGCACCTTCGGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34546 AGGGCAAATTTGGAATTTAGACAGCACCTTCTGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* *
34586 AGGGCAAACTGGGTATTTAGACAGCACCTTCCCGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34626 AGGGCAAATTGGGAATCTAGACAGCAGCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34666 AGGACAAAC--------T----AGCACTTTCCCGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* *
34694 AGGGCAAATTGGGAATCTAGACAGCACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34734 AGGGCAAACTGGGAATTTAAACAACACCTTCCGATGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * *
34774 AGCGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* ** * * *
34814 AGGGCTAACTAAGAATTTAAACAACACCTTCCGATGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* * * * *
34854 AGGGCAAACTGGGAATCTAAACAACACCTTCCCGTGAGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
*
34894 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGCGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
* *
34934 AGGGCAAACTGAGTATTTAGACAGCACCTTCCGGTGGGGA
1 AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
34974 AGGGCAAACTGGGATATTT
1 AGGGCAAACTGGGA-ATTT
34993 GGGCTAGACG
Statistics
Matches: 863, Mismatches: 129, Indels: 27
0.85 0.13 0.03
Matches are distributed among these distances:
28 22 0.03
32 1 0.00
36 1 0.00
39 35 0.04
40 800 0.93
41 4 0.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (40 bp):
AGGGCAAACTGGGAATTTAGACAGCACCTTCCGGTGGGGA
Found at i:34717 original size:68 final size:68
Alignment explanation
Indices: 34608--34743 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
34598 GTATTTAGAC
*
34608 AGCACCTTCCCGTGGGGAAGGGCAAATTGGGAATCTAGACAGCAGCTTCCGGTGGGGAAGGACAA
1 AGCACCTTCCCGTGGGGAAGGGCAAATTGGGAATCTAGACAGCACCTTCCGGTGGGGAAGGACAA
34673 ACT
66 ACT
* *
34676 AGCACTTTCCCGTGGGGAAGGGCAAATTGGGAATCTAGACAGCACCTTCCGGTGGGGAAGGGCAA
1 AGCACCTTCCCGTGGGGAAGGGCAAATTGGGAATCTAGACAGCACCTTCCGGTGGGGAAGGACAA
34741 ACT
66 ACT
34744 GGGAATTTAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.27, C:0.22, G:0.34, T:0.17
Consensus pattern (68 bp):
AGCACCTTCCCGTGGGGAAGGGCAAATTGGGAATCTAGACAGCACCTTCCGGTGGGGAAGGACAA
ACT
Found at i:36496 original size:72 final size:72
Alignment explanation
Indices: 36379--36513 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
36369 TGTATTCATA
* *
36379 AATTAGCTAAATTTAGAACATTTACATGCATAAATCATCAAATCAACTTTT-AAATCAACTCAAC
1 AATTAGCTAAATTTAGAAAATTTACATGCATAAATCACCAAATCAACTTTTAAAAT-AACTCAAC
36443 CAACCAAC
65 CAACCAAC
*
36451 AATTAGCTAAATTTAGAAAATTTACATGCATCAATCACCAAATCAACTTTTAAAATAACTCAA
1 AATTAGCTAAATTTAGAAAATTTACATGCATAAATCACCAAATCAACTTTTAAAATAACTCAA
36514 ATAACAAACA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 55 0.93
73 4 0.07
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (72 bp):
AATTAGCTAAATTTAGAAAATTTACATGCATAAATCACCAAATCAACTTTTAAAATAACTCAACC
AACCAAC
Done.