Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007145.1 Corchorus capsularis cultivar CVL-1 contig07166, 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: 36751
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:13073 original size:3 final size:3
Alignment explanation
Indices: 13065--13092 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13055 CTACCCTTTC
13065 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
13093 ACTCTTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:13518 original size:6 final size:6
Alignment explanation
Indices: 13507--13550 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
13497 TTCCTTTCCA
13507 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
13551 CTAAACTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:18331 original size:17 final size:16
Alignment explanation
Indices: 18311--18343 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
18301 GTAACATGAA
18311 AAAAAAAACCAAAAAAC
1 AAAAAAAA-CAAAAAAC
18328 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
18344 CCTTAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:18354 original size:21 final size:21
Alignment explanation
Indices: 18330--18369 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18320 CAAAAAACAA
18330 AAAAAACAAAAAACCCTTAAC
1 AAAAAACAAAAAACCCTTAAC
18351 AAAAAACAAAAAACCCTTA
1 AAAAAACAAAAAACCCTTA
18370 CCATGAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAAAACAAAAAACCCTTAAC
Found at i:22292 original size:7 final size:7
Alignment explanation
Indices: 22280--22310 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22270 ACTATTCCAG
22280 TAAATTA
1 TAAATTA
22287 TAAATTA
1 TAAATTA
22294 TAAATTA
1 TAAATTA
22301 TAAA-TA
1 TAAATTA
22307 TAAA
1 TAAA
22311 GGGGAGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAATTA
Found at i:22688 original size:15 final size:15
Alignment explanation
Indices: 22668--22700 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
22658 GTGCGTTTGT
22668 AATCCCAAACCAAGA
1 AATCCCAAACCAAGA
22683 AATCCCAAACCAAGA
1 AATCCCAAACCAAGA
22698 AAT
1 AAT
22701 GAAAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.30, G:0.06, T:0.09
Consensus pattern (15 bp):
AATCCCAAACCAAGA
Found at i:23619 original size:13 final size:14
Alignment explanation
Indices: 23591--23625 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
23581 CACAAGGAAA
*
23591 TTAAAGAAAAATCT
1 TTAAAGAAAAACCT
23605 TTAAA-AAAAACCT
1 TTAAAGAAAAACCT
23618 TTAAAGAA
1 TTAAAGAA
23626 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (14 bp):
TTAAAGAAAAACCT
Found at i:23649 original size:15 final size:15
Alignment explanation
Indices: 23620--23660 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
23610 AAAAACCTTT
23620 AAAGAAGAA-AAAAA
1 AAAGAAGAAGAAAAA
23634 AAAGAAGAAGAAAAA
1 AAAGAAGAAGAAAAA
23649 AAAGAAGAAGAA
1 AAAGAAGAAGAA
23661 CAGCGGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAAAA
Found at i:23653 original size:12 final size:13
Alignment explanation
Indices: 23620--23657 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
23610 AAAAACCTTT
*
23620 AAAGAAGAAAAAAA
1 AAAGAAG-AAGAAA
23634 AAAGAAGAAGAAA
1 AAAGAAGAAGAAA
23647 AAA-AAGAAGAA
1 AAAGAAGAAGAA
23658 GAACAGCGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAGAAA
Found at i:24034 original size:19 final size:20
Alignment explanation
Indices: 24012--24050 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24002 AAAATAGTCC
24012 AAGGGGG-GGTATCTAGTAA
1 AAGGGGGCGGTATCTAGTAA
*
24031 AAGGGGGCGGTATTTAGTAA
1 AAGGGGGCGGTATCTAGTAA
24051 TCCTCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.41, T:0.23
Consensus pattern (20 bp):
AAGGGGGCGGTATCTAGTAA
Found at i:26026 original size:7 final size:7
Alignment explanation
Indices: 26014--26044 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
26004 GGATGGACTA
26014 TGCCCAT
1 TGCCCAT
26021 TGCCCAT
1 TGCCCAT
*
26028 TGCCTAT
1 TGCCCAT
26035 TGCCCAT
1 TGCCCAT
26042 TGC
1 TGC
26045 TAAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.39, G:0.16, T:0.32
Consensus pattern (7 bp):
TGCCCAT
Found at i:33648 original size:6 final size:6
Alignment explanation
Indices: 33637--33662 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
33627 TGATTAATAT
33637 GTAGGA GTAGGA GTAGGA GTAGGA GT
1 GTAGGA GTAGGA GTAGGA GTAGGA GT
33663 GTAGGACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
GTAGGA
Done.