Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016693.1 Corchorus olitorius cultivar O-4 contig16726, 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: 31630
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1760 original size:14 final size:14
Alignment explanation
Indices: 1741--1770 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1731 ATAAGGCTAC
1741 ATTTGGCTAAAAGA
1 ATTTGGCTAAAAGA
1755 ATTTGGCTAAAAGA
1 ATTTGGCTAAAAGA
1769 AT
1 AT
1771 GCTTTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (14 bp):
ATTTGGCTAAAAGA
Found at i:4034 original size:9 final size:8
Alignment explanation
Indices: 4021--4053 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
4011 AAATTGTTGG
4021 GTTTTTTT
1 GTTTTTTT
4029 GTTTTTTT
1 GTTTTTTT
4037 GTTTTTTT
1 GTTTTTTT
*
4045 GTTCTTTT
1 GTTTTTTT
4053 G
1 G
4054 GAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (8 bp):
GTTTTTTT
Found at i:7759 original size:65 final size:65
Alignment explanation
Indices: 7642--7855 Score: 311
Period size: 65 Copynumber: 3.3 Consensus size: 65
7632 CAATTTTATT
* * * * ** ** * *
7642 GTGTGATTATCAAAATTTCACATTGGGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAC
1 GTGTGGTTATCAAATTTTCATATT-AGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCAC
7707 A
65 A
7708 GTGTGGTTATCAAATTTTCATATTAGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACA
1 GTGTGGTTATCAAATTTTCATATTAGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACA
7773 GTGTGGTTATCAAATTTTCATATTAGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACA
1 GTGTGGTTATCAAATTTTCATATTAGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACA
*
7838 GTTTGGTTATCAATATTT
1 GTGTGGTTATCAA-ATTT
7856 CTACGTTAGC
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
65 111 0.82
66 25 0.18
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (65 bp):
GTGTGGTTATCAAATTTTCATATTAGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACA
Found at i:7845 original size:22 final size:22
Alignment explanation
Indices: 7574--7855 Score: 170
Period size: 22 Copynumber: 13.0 Consensus size: 22
7564 AGTTTCATTC
* *
7574 TCATAGGGAGGTTATCGAAA-TC
1 TCATAGTGAGGTTATC-AAATTT
*
7596 TCAT-GATGTGGTTATCAAAATTT
1 TCATAG-TGAGGTTATC-AAATTT
* *
7619 TCATAGTG-CG-TA-CCAATTT
1 TCATAGTGAGGTTATCAAATTT
* * * *
7638 T-ATTGTGTGATTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
* * * *
7659 TCACATTGGGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
* *
7681 TCATAGTGTGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAATTT
* *
7703 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
* *
7725 TCATA-TTAGGTTATTGAAA-TT
1 TCATAGTGAGGTTA-TCAAATTT
**
7746 TCATAACGAGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
* *
7768 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
* *
7790 TCATA-TTAGGTTATTGAAA-TT
1 TCATAGTGAGGTTA-TCAAATTT
**
7811 TCATAACGAGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAATTT
* **
7833 TCACAGTTTGGTTATCAATATTT
1 TCATAGTGAGGTTATCAA-ATTT
7856 CTACGTTAGC
Statistics
Matches: 202, Mismatches: 44, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
18 5 0.02
19 6 0.03
20 3 0.01
21 43 0.21
22 133 0.66
23 11 0.05
24 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (22 bp):
TCATAGTGAGGTTATCAAATTT
Found at i:9307 original size:17 final size:18
Alignment explanation
Indices: 9263--9309 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
9253 GGCAAAGTAT
*
9263 TATATAATAAAATAAATA
1 TATATAATATAATAAATA
*
9281 TATATTATATAAT-AATA
1 TATATAATATAATAAATA
*
9298 TATGTAATATAA
1 TATATAATATAA
9310 ATATCTAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TATATAATATAATAAATA
Found at i:10921 original size:15 final size:15
Alignment explanation
Indices: 10901--10930 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10891 ATTTAGATAC
10901 CTTTATAAACAGGAA
1 CTTTATAAACAGGAA
10916 CTTTATAAACAGGAA
1 CTTTATAAACAGGAA
10931 GAGGTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
CTTTATAAACAGGAA
Found at i:20502 original size:26 final size:26
Alignment explanation
Indices: 20453--20503 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20443 ATTATTAAGA
20453 TAAAGAAAAAAAACAAAAATAATAGC
1 TAAAGAAAAAAAACAAAAATAATAGC
* *
20479 TAAAGAATTAAAAACGAAAA-AATAG
1 TAAAGAA-AAAAAACAAAAATAATAG
20504 AATCAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.14
Consensus pattern (26 bp):
TAAAGAAAAAAAACAAAAATAATAGC
Found at i:21517 original size:21 final size:20
Alignment explanation
Indices: 21484--21522 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
21474 GCAGTGAGGA
*
21484 AAGAAAACAAAAGTGAAACG
1 AAGAAAACAAAAGAGAAACG
*
21504 AAGAAGAAGAAAAGAGAAA
1 AAGAA-AACAAAAGAGAAA
21523 TGACGACTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.69, C:0.05, G:0.23, T:0.03
Consensus pattern (20 bp):
AAGAAAACAAAAGAGAAACG
Done.