Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008035.1 Corchorus capsularis cultivar CVL-1 contig08056, 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: 9964
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:3339 original size:8 final size:9
Alignment explanation
Indices: 3325--3359 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
3315 GTTCCTGGGT
3325 TTTTCTTTC
1 TTTTCTTTC
3334 -TTTCTTTC
1 TTTTCTTTC
3342 TTTTCTTTTC
1 TTTTC-TTTC
3352 TTTTCTTT
1 TTTTCTTT
3360 AAATCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:5346 original size:48 final size:48
Alignment explanation
Indices: 5275--5369 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
5265 CTCAAGTAAA
*
5275 TTCAATGTGTTTTATGGTATGTATTTTAATTTATGAGAAAATATGTTC
1 TTCAATGTGTTTTATGCTATGTATTTTAATTTATGAGAAAATATGTTC
5323 TTCAATGTGTTTTATGCTATGTATTTTAATTTATGAGAAAATATGTT
1 TTCAATGTGTTTTATGCTATGTATTTTAATTTATGAGAAAATATGTT
5370 ATTGATGTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (48 bp):
TTCAATGTGTTTTATGCTATGTATTTTAATTTATGAGAAAATATGTTC
Found at i:7646 original size:2 final size:2
Alignment explanation
Indices: 7641--7678 Score: 58
Period size: 2 Copynumber: 18.0 Consensus size: 2
7631 AATATCAGTG
7641 TA TA TA TA TA TA TA TA CTA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
7679 AAATTACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 30 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7663 original size:13 final size:13
Alignment explanation
Indices: 7641--7678 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
7631 AATATCAGTG
7641 TATA-TATATATA
1 TATACTATATATA
7653 TATACTATATATA
1 TATACTATATATA
7666 TATACTATATATA
1 TATACTATATATA
7679 AAATTACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (13 bp):
TATACTATATATA
Found at i:7742 original size:31 final size:31
Alignment explanation
Indices: 7707--7771 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
7697 AACTTAATGT
*
7707 TTTCCGATTGTA-CTCTTATTTTT-AAAACATA
1 TTTCCAATTGTATC-CTT-TTTTTCAAAACATA
7738 TTTCCAATTGTATCCTTTTTTTCAAAACATA
1 TTTCCAATTGTATCCTTTTTTTCAAAACATA
7769 TTT
1 TTT
7772 ATAAATTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 5 0.16
31 25 0.81
32 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTCCAATTGTATCCTTTTTTTCAAAACATA
Found at i:7844 original size:15 final size:15
Alignment explanation
Indices: 7800--7847 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
7790 ATAATATTTA
7800 AATTATTCCATTATT
1 AATTATTCCATTATT
* *
7815 --TT-TT-AATTATA
1 AATTATTCCATTATT
7826 AATTATTCCATTATT
1 AATTATTCCATTATT
7841 AATTATT
1 AATTATT
7848 AGATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
11 5 0.20
12 2 0.08
13 4 0.16
14 2 0.08
15 12 0.48
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTATTCCATTATT
Found at i:8621 original size:45 final size:46
Alignment explanation
Indices: 8542--8629 Score: 160
Period size: 45 Copynumber: 1.9 Consensus size: 46
8532 GATTACTTCT
8542 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
*
8588 CCAGCTCATCATTAATTC-GGGGTAGGGATCTTTTAGTAATTC
1 CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTC
8630 TACTACTCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 24 0.59
46 17 0.41
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (46 bp):
CCAGCTCATCATTAATCCTGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:9634 original size:14 final size:14
Alignment explanation
Indices: 9617--9654 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
9607 TTAAATTGAC
*
9617 ATTATTAAAAATTT
1 ATTATTAAAAATTA
9631 ATTATTTAAAAATTA
1 ATTA-TTAAAAATTA
9646 ATTA-TAAAA
1 ATTATTAAAA
9655 TTTCAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 4 0.18
15 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTATTAAAAATTA
Found at i:9641 original size:15 final size:15
Alignment explanation
Indices: 9617--9650 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9607 TTAAATTGAC
*
9617 ATTA-TTAAAAATTT
1 ATTATTTAAAAATTA
9631 ATTATTTAAAAATTA
1 ATTATTTAAAAATTA
9646 ATTAT
1 ATTAT
9651 AAAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTTAAAAATTA
Done.