Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013528.1 Corchorus capsularis cultivar CVL-1 contig13549, 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: 34016
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:5283 original size:17 final size:16
Alignment explanation
Indices: 5261--5292 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5251 GGTCGAAATT
5261 TTTTTATTTTGTTTTTA
1 TTTTTATTTT-TTTTTA
5278 TTTTTATTTTTTTTT
1 TTTTTATTTTTTTTT
5293 CGATATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTTTATTTTTTTTTA
Found at i:9115 original size:30 final size:30
Alignment explanation
Indices: 9079--9137 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9069 GTCTTCAAGT
9079 CCATGATAAGTCCTT-GGCACATCATTCCCC
1 CCATGATAAG-CCTTGGGCACATCATTCCCC
*
9109 CCATGATAAGCCTTGGGCGCATCATTCCC
1 CCATGATAAGCCTTGGGCACATCATTCCC
9138 TTCCCCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (30 bp):
CCATGATAAGCCTTGGGCACATCATTCCCC
Found at i:11680 original size:15 final size:15
Alignment explanation
Indices: 11647--11691 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
11637 GGACCTGCCC
*
11647 GACCTGAGACCCGAAT
1 GACCTGAAACCC-AAT
11663 GACCTGAAACCCAAT
1 GACCTGAAACCCAAT
* *
11678 GACCCGTAACCCAA
1 GACCTGAAACCCAA
11692 GTGTCTCGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.11
Consensus pattern (15 bp):
GACCTGAAACCCAAT
Found at i:12591 original size:16 final size:16
Alignment explanation
Indices: 12557--12643 Score: 88
Period size: 16 Copynumber: 5.5 Consensus size: 16
12547 AACCCGCCCA
*
12557 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
12573 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
12589 ACCCGAAACCCGAATA
1 ACCCGAGACCCGAATG
**
12605 ACCCGA-ACCAAAATG
1 ACCCGAGACCCGAATG
*
12620 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
12636 ACTCGAGA
1 ACCCGAGA
12644 AAACTGCCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.20
16 46 0.78
17 1 0.02
ACGTcount: A:0.37, C:0.36, G:0.21, T:0.07
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:15867 original size:17 final size:19
Alignment explanation
Indices: 15835--15870 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
15825 ATTGGGCCTT
15835 TTATTCTATCTTAGTTTAG
1 TTATTCTATCTTAGTTTAG
15854 TTATT-TAT-TTAGTTTAG
1 TTATTCTATCTTAGTTTAG
15871 AAGACATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (19 bp):
TTATTCTATCTTAGTTTAG
Found at i:20554 original size:22 final size:22
Alignment explanation
Indices: 20517--20560 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20507 GAATTTCAGG
*
20517 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
20539 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
20561 TACGGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:29000 original size:37 final size:37
Alignment explanation
Indices: 28912--29000 Score: 133
Period size: 38 Copynumber: 2.4 Consensus size: 37
28902 CTTTTTGTTC
*
28912 CCAACGTCCTATTTAATTTTGCCTTTTGTCTTTGTTT
1 CCAACGTCCTATTTAATTTTGCCTTTTGTCTTTGTCT
** *
28949 CCAATCGTTGTATTTAATTTTGCTTTTTGTCTTTGTCT
1 CCAA-CGTCCTATTTAATTTTGCCTTTTGTCTTTGTCT
28987 CCAACGTCCTATTT
1 CCAACGTCCTATTT
29001 GGGCTTAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 12 0.27
38 33 0.73
ACGTcount: A:0.15, C:0.21, G:0.11, T:0.53
Consensus pattern (37 bp):
CCAACGTCCTATTTAATTTTGCCTTTTGTCTTTGTCT
Found at i:29566 original size:37 final size:37
Alignment explanation
Indices: 29516--29589 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
29506 AAAAGACCTC
*
29516 AATTTGATGAATGGTAACAAGTTAAATCACTTTCTTT
1 AATTTGATGAATGGTAACAAGTCAAATCACTTTCTTT
*
29553 AATTTGATGAATGGTAAGAAGTCAAATCACTTTCTTT
1 AATTTGATGAATGGTAACAAGTCAAATCACTTTCTTT
29590 TATGAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (37 bp):
AATTTGATGAATGGTAACAAGTCAAATCACTTTCTTT
Done.