Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014203.1 Corchorus capsularis cultivar CVL-1 contig14224, 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: 20231
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:753 original size:16 final size:16
Alignment explanation
Indices: 728--758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
718 TCTACATATT
728 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
744 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
759 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:3404 original size:17 final size:17
Alignment explanation
Indices: 3384--3417 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3374 GCTAATCATA
3384 ATTATGAAATAATTATT
1 ATTATGAAATAATTATT
**
3401 ATTATTCAATAATTATT
1 ATTATGAAATAATTATT
3418 CCTAAAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATGAAATAATTATT
Found at i:6654 original size:24 final size:24
Alignment explanation
Indices: 6627--6682 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
6617 TTGCTTCTTC
* *
6627 CTGTTGCTTATTCTTTTTCTTCTG
1 CTGTTGCTCACTCTTTTTCTTCTG
*
6651 CTGTTGCTCACTCTTTTTCTTCTT
1 CTGTTGCTCACTCTTTTTCTTCTG
*
6675 CTGCTGCT
1 CTGTTGCT
6683 GTTTTGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.04, C:0.27, G:0.12, T:0.57
Consensus pattern (24 bp):
CTGTTGCTCACTCTTTTTCTTCTG
Found at i:14444 original size:19 final size:18
Alignment explanation
Indices: 14420--14455 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14410 TGAAGATTTA
14420 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
14439 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
14456 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15079 original size:18 final size:17
Alignment explanation
Indices: 15052--15087 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
15042 TTTCTCTTCA
15052 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
15069 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
15087 T
1 T
15088 TTAGGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:17734 original size:16 final size:16
Alignment explanation
Indices: 17713--17743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17703 TTGCTTTGTT
17713 TTGCTTTGAGTGATTA
1 TTGCTTTGAGTGATTA
*
17729 TTGCTTTGATTGATT
1 TTGCTTTGAGTGATT
17744 GTCTATTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (16 bp):
TTGCTTTGAGTGATTA
Found at i:17852 original size:21 final size:19
Alignment explanation
Indices: 17827--17865 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
17817 TATGACTCAT
17827 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
17848 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
17866 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Found at i:19465 original size:19 final size:18
Alignment explanation
Indices: 19441--19476 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19431 TGAAGATTTA
19441 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19460 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
19477 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19609 original size:10 final size:10
Alignment explanation
Indices: 19596--19620 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19586 TATATTCAGC
19596 CCATATAAGT
1 CCATATAAGT
19606 CCATATAAGT
1 CCATATAAGT
19616 CCATA
1 CCATA
19621 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:20110 original size:18 final size:17
Alignment explanation
Indices: 20083--20118 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
20073 TTTCTTTTCA
20083 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
20100 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
20118 T
1 T
20119 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Done.