Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006823.1 Corchorus capsularis cultivar CVL-1 contig06844, 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: 36236
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:11105 original size:30 final size:30
Alignment explanation
Indices: 11070--11132 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
11060 CGTTTGGAAG
*
11070 TTTCTATAGAAAGTAAAAAAGTAGAAAGTT
1 TTTCTATAGAAAGTAAAAAACTAGAAAGTT
** *
11100 TTTCTATAGAAAGTTTAAGACTAGAAAGTT
1 TTTCTATAGAAAGTAAAAAACTAGAAAGTT
11130 TTT
1 TTT
11133 TCTTAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTCTATAGAAAGTAAAAAACTAGAAAGTT
Found at i:12121 original size:51 final size:50
Alignment explanation
Indices: 12052--12154 Score: 161
Period size: 50 Copynumber: 2.0 Consensus size: 50
12042 CACCATATCA
12052 TCCTGATCAATTCAGATTTTTTTTTCTATAATTACTAAAACCTTCTAAATC
1 TCCTGATCAATTCAGA-TTTTTTTTCTATAATTACTAAAACCTTCTAAATC
* ** *
12103 TCCTGATCCATTTGGATTTTTTTTCTATAATTACTAAAACTTTCTAAATC
1 TCCTGATCAATTCAGATTTTTTTTCTATAATTACTAAAACCTTCTAAATC
12153 TC
1 TC
12155 GAAACTACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
50 35 0.73
51 13 0.27
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (50 bp):
TCCTGATCAATTCAGATTTTTTTTCTATAATTACTAAAACCTTCTAAATC
Found at i:30227 original size:30 final size:30
Alignment explanation
Indices: 30201--30273 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
30191 TGGGTGCCAT
* *
30201 CATCTTTGGTGCCGTTGATTTCGGTGCCGC
1 CATCTTTGGTGCCGATAATTTCGGTGCCGC
*
30231 CATCTTTGGTGCAGATAATTTCGGTGCCGC
1 CATCTTTGGTGCCGATAATTTCGGTGCCGC
30261 CATCTTTGGTGCC
1 CATCTTTGGTGCC
30274 ATCATCTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.11, C:0.26, G:0.27, T:0.36
Consensus pattern (30 bp):
CATCTTTGGTGCCGATAATTTCGGTGCCGC
Found at i:30279 original size:15 final size:15
Alignment explanation
Indices: 30173--30281 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
30163 GCAGTAAACA
*
30173 CTTTCGGTGCAATCAT
1 CTTT-GGTGCCATCAT
*
30189 CTTGGGTGCCATCAT
1 CTTTGGTGCCATCAT
* *
30204 CTTTGGTGCCGTTGAT
1 CTTTGGTGCC-ATCAT
* **
30220 -TTCGGTGCCGCCAT
1 CTTTGGTGCCATCAT
* *
30234 CTTTGGTGCAGATAAT
1 CTTTGGTGC-CATCAT
* **
30250 -TTCGGTGCCGCCAT
1 CTTTGGTGCCATCAT
30264 CTTTGGTGCCATCAT
1 CTTTGGTGCCATCAT
30279 CTT
1 CTT
30282 CTTCCATGAC
Statistics
Matches: 67, Mismatches: 22, Indels: 9
0.68 0.22 0.09
Matches are distributed among these distances:
14 4 0.06
15 55 0.82
16 8 0.12
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.37
Consensus pattern (15 bp):
CTTTGGTGCCATCAT
Found at i:31556 original size:18 final size:18
Alignment explanation
Indices: 31507--31589 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 18
31497 AAGTGTGGCA
* * *
31507 ACTTGGTGCGTTGCGGCC
1 ACTTGGTGTGGTGCGACC
* **
31525 ACTAGGTGCAGTGCGACC
1 ACTTGGTGTGGTGCGACC
31543 ACTTGGTGTGGTGCGACC
1 ACTTGGTGTGGTGCGACC
* * * *
31561 ATTTGGTATAGTGCGGCC
1 ACTTGGTGTGGTGCGACC
*
31579 ACTGGGTGTGG
1 ACTTGGTGTGG
31590 CTTCTTGAAT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.13, C:0.22, G:0.39, T:0.27
Consensus pattern (18 bp):
ACTTGGTGTGGTGCGACC
Done.