Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015011.1 Corchorus olitorius cultivar O-4 contig15044, 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: 20245
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9387 original size:12 final size:12
Alignment explanation
Indices: 9370--9412 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
9360 GCTGCTCCTC
9370 CACCTCCGGCTG
1 CACCTCCGGCTG
*
9382 CACCTCCAGCTG
1 CACCTCCGGCTG
* *
9394 CACCCCCGGCAG
1 CACCTCCGGCTG
9406 CACCTCC
1 CACCTCC
9413 TCCTCCTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.14, C:0.56, G:0.19, T:0.12
Consensus pattern (12 bp):
CACCTCCGGCTG
Found at i:9556 original size:18 final size:18
Alignment explanation
Indices: 9523--9558 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9513 AGAGGAAATA
*
9523 GTGCTTCTGGTAGTGGAG
1 GTGCTTCTGCTAGTGGAG
*
9541 GTGCTTCTGCTTGTGGAG
1 GTGCTTCTGCTAGTGGAG
9559 ATGAAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.14, G:0.42, T:0.36
Consensus pattern (18 bp):
GTGCTTCTGCTAGTGGAG
Found at i:18554 original size:75 final size:75
Alignment explanation
Indices: 18427--18571 Score: 245
Period size: 75 Copynumber: 1.9 Consensus size: 75
18417 CTAAATTGAT
* * * *
18427 AAAAGACCAAAACGTGACGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCTATTGGTAATTT
1 AAAAGACCAAAACGGGACGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCAATTAGTAATCT
18492 CCAGAGTGAG
66 CCAGAGTGAG
*
18502 AAAAGACCAAAACGGGACGAAAAGGTTCTCCCACGTTAAAAGTTGATTGGAGCAATTAGTAATCT
1 AAAAGACCAAAACGGGACGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCAATTAGTAATCT
18567 CCAGA
66 CCAGA
18572 TAGTATATAA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (75 bp):
AAAAGACCAAAACGGGACGAAAAGGTTCTCCCACGTTAAAAGTTGATGGGAGCAATTAGTAATCT
CCAGAGTGAG
Found at i:20155 original size:222 final size:222
Alignment explanation
Indices: 19767--20245 Score: 913
Period size: 222 Copynumber: 2.2 Consensus size: 222
19757 GCCATGCTTG
*
19767 TGAGAATTAATAACGAAGTAATTGACGACTATATATATCCTATCTCAATCATTCTAATGAACTAA
1 TGAGAATTAATAACGAAGTAATTGATGACTATATATATCCTATCTCAATCATTCTAATGAACTAA
19832 CTCAAGACTTTTCAGCATTCCTATTAGGTATATAGTACTACTTTCAAGCTCATATTATCAACCCT
66 CTCAAGACTTTTCAGCATTCCTATTAGGTATATAGTACTACTTTCAAGCTCATATTATCAACCCT
*
19897 CACATTTACACTGCTAATAAATCTTTAATGTTTTTTGATAAGTATGACTAAATAAAAGTTAGAAA
131 CACATTTACACTGCTAATAAATCTTTAATATTTTTTGATAAGTATGACTAAATAAAAGTTAGAAA
*
19962 ATAGAGTTGACTATTTTAGTTACCACA
196 ATAGAGTTAACTATTTTAGTTACCACA
19989 TGAGAATTAATAACGAAGTAATTGATGACTATATATATCCTATCTCAATCATTCTAATGAACTAA
1 TGAGAATTAATAACGAAGTAATTGATGACTATATATATCCTATCTCAATCATTCTAATGAACTAA
20054 CTCAAGACTTTTCAGCATTCCTATTAGGTATATAGTACTACTTTCAAGCTCATATTATCAACCCT
66 CTCAAGACTTTTCAGCATTCCTATTAGGTATATAGTACTACTTTCAAGCTCATATTATCAACCCT
* *
20119 CACATTTACACTGCTAATAAATGTTTGATATTTTTTGATAAGTATGACTAAATAAAAGTTAGAAA
131 CACATTTACACTGCTAATAAATCTTTAATATTTTTTGATAAGTATGACTAAATAAAAGTTAGAAA
20184 ATAGAGTTAACTATTTTAGTTACCACA
196 ATAGAGTTAACTATTTTAGTTACCACA
20211 TGAGAATTAATAACGAAGTAATTGATGACTATATA
1 TGAGAATTAATAACGAAGTAATTGATGACTATATA
Statistics
Matches: 252, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 252 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (222 bp):
TGAGAATTAATAACGAAGTAATTGATGACTATATATATCCTATCTCAATCATTCTAATGAACTAA
CTCAAGACTTTTCAGCATTCCTATTAGGTATATAGTACTACTTTCAAGCTCATATTATCAACCCT
CACATTTACACTGCTAATAAATCTTTAATATTTTTTGATAAGTATGACTAAATAAAAGTTAGAAA
ATAGAGTTAACTATTTTAGTTACCACA
Done.