Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005314.1 Corchorus capsularis cultivar CVL-1 contig05332, 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: 7595
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:1294 original size:22 final size:21
Alignment explanation
Indices: 1264--1322 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
1254 AATTCTTGCT
* *
1264 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
1286 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
1305 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
1323 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:1309 original size:11 final size:11
Alignment explanation
Indices: 1292--1323 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1282 ATTGTCTTCA
1292 AATCTTCAAAT
1 AATCTTCAAAT
*
1303 TATCTTCAAAT
1 AATCTTCAAAT
1314 AATCTTCAAA
1 AATCTTCAAA
1324 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:1323 original size:22 final size:22
Alignment explanation
Indices: 1264--1323 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
1254 AATTCTTGCT
* *
1264 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
1286 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
1305 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
1324 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:5837 original size:7 final size:7
Alignment explanation
Indices: 5825--5850 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5815 TAGACTCTTT
5825 TTATTAA
1 TTATTAA
5832 TTATTAA
1 TTATTAA
5839 TTATTAA
1 TTATTAA
5846 TTATT
1 TTATT
5851 TACTTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:6847 original size:25 final size:25
Alignment explanation
Indices: 6808--6863 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
6798 CAATTCTCAC
6808 TTTTAGGTTTCGAATTTTAATCATA
1 TTTTAGGTTTCGAATTTTAATCATA
* *
6833 TTTTAGTTTTTGAATTTTAATCATA
1 TTTTAGGTTTCGAATTTTAATCATA
6858 TCTTTA
1 T-TTTA
6864 TTATTTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTTAGGTTTCGAATTTTAATCATA
Found at i:6967 original size:66 final size:66
Alignment explanation
Indices: 6874--6998 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
6864 TTATTTAGTC
*
6874 TCCCACAAATTGGCAAGACCCCAAATTAT-TATTTAATTAATTATGTTT-TTATGATTTTTCTAG
1 TCCCACAAATTGGCAAGAACCCAAATTATCT-TTTAATTAATTAT-TTTATTATGATTTTTCTAG
6937 ACT
64 ACT
* * * *
6940 TCCCACAAATTGGCAA-AATCTAGAATTATCTTTTAATTATTTATTTTATTATTATTTTT
1 TCCCACAAATTGGCAAGAACCCA-AATTATCTTTTAATTAATTATTTTATTATGATTTTT
6999 ATAATTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 6 0.12
66 44 0.86
67 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (66 bp):
TCCCACAAATTGGCAAGAACCCAAATTATCTTTTAATTAATTATTTTATTATGATTTTTCTAGAC
T
Done.