Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005448.1 Corchorus capsularis cultivar CVL-1 contig05466, 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: 28594
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:81 original size:2 final size:2
Alignment explanation
Indices: 74--111 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
64 AGAAATGAAT
*
74 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112 ATAATGATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2621 original size:1 final size:1
Alignment explanation
Indices: 2615--2643 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2605 TTATGCAAGC
2615 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2644 CTAAAATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3306 original size:22 final size:22
Alignment explanation
Indices: 3281--3324 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3271 CAAAGGATAT
* *
3281 ATCAACAAATAATGAAGGACAA
1 ATCAACAAATAATCAAGAACAA
3303 ATCAACAAATAATCAAGAACAA
1 ATCAACAAATAATCAAGAACAA
3325 TCTCGGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (22 bp):
ATCAACAAATAATCAAGAACAA
Found at i:4279 original size:2 final size:2
Alignment explanation
Indices: 4272--4309 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4262 ATGGTAGGCC
4272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4310 CAGACTGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7334 original size:17 final size:17
Alignment explanation
Indices: 7312--7366 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
7302 ATCACCCCCC
7312 AGATCACTAGTGATCTA
1 AGATCACTAGTGATCTA
*
7329 AGATCACTAGTGATGTA
1 AGATCACTAGTGATCTA
** *
7346 AGATCACCGGTGATCAA
1 AGATCACTAGTGATCTA
7363 AGAT
1 AGAT
7367 TACATGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (17 bp):
AGATCACTAGTGATCTA
Found at i:9077 original size:2 final size:2
Alignment explanation
Indices: 9043--9069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9033 AGATCAAATA
9043 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9070 AGATATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9616 original size:2 final size:2
Alignment explanation
Indices: 9569--9602 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9559 TATTGTCCTA
9569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9603 TGGAAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11631 original size:11 final size:11
Alignment explanation
Indices: 11615--11655 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
11605 TGGACATGCA
11615 TTGCACGTACG
1 TTGCACGTACG
* *
11626 TTGCACGTGCA
1 TTGCACGTACG
11637 TTGCACGTACG
1 TTGCACGTACG
11648 TTGCACGT
1 TTGCACGT
11656 GTTTTATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (11 bp):
TTGCACGTACG
Found at i:11654 original size:22 final size:22
Alignment explanation
Indices: 11596--11656 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
11586 TACTCACTTC
* * *
11596 CACGTGCGTTGGACATGCATTG
1 CACGTACGTTGCACGTGCATTG
11618 CACGTACGTTGCACGTGCATTG
1 CACGTACGTTGCACGTGCATTG
11640 CACGTACGTTGCACGTG
1 CACGTACGTTGCACGTG
11657 TTTTATTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
CACGTACGTTGCACGTGCATTG
Done.