Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015238.1 Corchorus capsularis cultivar CVL-1 contig15259, 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: 31549
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Found at i:1316 original size:6 final size:6
Alignment explanation
Indices: 1305--1334 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1295 GAGGCAACCC
1305 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
1335 TGTTTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:5833 original size:22 final size:22
Alignment explanation
Indices: 5801--5846 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5791 CTAAAATTCA
*
5801 GGACAAGTTCTGCCCAGAACTT
1 GGACAACTTCTGCCCAGAACTT
*
5823 GGACAACTTCTGCCCAGGACTT
1 GGACAACTTCTGCCCAGAACTT
5845 GG
1 GG
5847 CCTGTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (22 bp):
GGACAACTTCTGCCCAGAACTT
Found at i:5913 original size:22 final size:22
Alignment explanation
Indices: 5877--5920 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5867 AATTTCAGGA
*
5877 CAACTTCGGCCCTGAACTTGTT
1 CAACTTCGGCACTGAACTTGTT
* *
5899 CAACTTCGGGACTGAAGTTGTT
1 CAACTTCGGCACTGAACTTGTT
5921 ACGCAGGATA
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:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
CAACTTCGGCACTGAACTTGTT
Found at i:5935 original size:52 final size:52
Alignment explanation
Indices: 5872--5972 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
5862 ACGAAAATTT
* * *
5872 CAGGACAACTTCGGCCCTGAACTTGTTCAACTTCGGGACTGAAGTTGTTACG
1 CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTTACG
* *
5924 CAGGATAACTTCGGCCCAGAACTTGTAGAACTTCGGGACAGAAGTTGTT
1 CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTT
5973 GCGGGAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (52 bp):
CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTTACG
Found at i:5965 original size:22 final size:22
Alignment explanation
Indices: 5930--5971 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5920 TACGCAGGAT
*
5930 AACTTCGGCCCAGAACTTGTAG
1 AACTTCGGCACAGAACTTGTAG
* *
5952 AACTTCGGGACAGAAGTTGT
1 AACTTCGGCACAGAACTTGT
5972 TGCGGGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (22 bp):
AACTTCGGCACAGAACTTGTAG
Found at i:8591 original size:12 final size:12
Alignment explanation
Indices: 8574--8605 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
8564 GCAGCGCAAC
8574 ACCGGCCACATG
1 ACCGGCCACATG
8586 ACCGGCCACATG
1 ACCGGCCACATG
8598 ACCGGCCA
1 ACCGGCCA
8606 TCGCATGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.44, G:0.25, T:0.06
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:22065 original size:42 final size:42
Alignment explanation
Indices: 22002--22090 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
21992 TGATGGGATC
* * *
22002 GCACATGACCGGCCATTGCATGGGGCAACCGCACAAGACCGG
1 GCACATCACCGGCCATGGCATGGAGCAACCGCACAAGACCGG
* * *
22044 GCACATCACCGGCCATGGCATGGAGCAATCGCATATGACCGG
1 GCACATCACCGGCCATGGCATGGAGCAACCGCACAAGACCGG
22086 GCACA
1 GCACA
22091 ACCCGGGCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.11
Consensus pattern (42 bp):
GCACATCACCGGCCATGGCATGGAGCAACCGCACAAGACCGG
Found at i:24723 original size:33 final size:32
Alignment explanation
Indices: 24606--24712 Score: 160
Period size: 33 Copynumber: 3.2 Consensus size: 32
24596 CTAATTGTGA
* *
24606 TGAAAACAAATCTGTTTTAGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTT-GTTGATCATAGCAT
*
24639 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTT-GTTGATCATAGCAT
24672 TGAAAATAATTCTGTTTTGCTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTG-TTGATCATAGCAT
24705 TGAAAATA
1 TGAAAATA
24713 GGACTGTTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
32 1 0.01
33 67 0.99
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (32 bp):
TGAAAATAATTCTGTTTTGTTGATCATAGCAT
Found at i:28426 original size:42 final size:42
Alignment explanation
Indices: 28356--28443 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
28346 TTACCCGGGT
* * *
28356 TGTGCCCGGTCATATGCGATTGCTCCATGCCATGGTCGGTCA
1 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
* * * *
28398 TGTGCTCGGTCTTGTGCGGTTGCCCCATGCAATGGCCGGTCA
1 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
28440 TGTG
1 TGTG
28444 TGATCCCATC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.11, C:0.27, G:0.32, T:0.30
Consensus pattern (42 bp):
TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
Done.