Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023094.1 Corchorus olitorius cultivar O-4 contig23127, 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: 15137
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:4962 original size:10 final size:10
Alignment explanation
Indices: 4949--4984 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
4939 TAATCTTTAG
*
4949 GAGAATCGAA
1 GAGAAGCGAA
4959 GAGAAGCGAA
1 GAGAAGCGAA
4969 GAGAAGCGAA
1 GAGAAGCGAA
4979 GAGAAG
1 GAGAAG
4985 GTAAGGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.39, T:0.03
Consensus pattern (10 bp):
GAGAAGCGAA
Found at i:5493 original size:31 final size:31
Alignment explanation
Indices: 5456--5522 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
5446 CCTTTTCTAG
5456 ACGCCACTAATTAGCGGCGTCTGATGTCAAA
1 ACGCCACTAATTAGCGGCGTCTGATGTCAAA
*
5487 ACGCCACTAATTAGCGGCGTCTGATTTCAAA
1 ACGCCACTAATTAGCGGCGTCTGATGTCAAA
5518 ACGCC
1 ACGCC
5523 GCTATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (31 bp):
ACGCCACTAATTAGCGGCGTCTGATGTCAAA
Found at i:5686 original size:31 final size:31
Alignment explanation
Indices: 5649--5709 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5639 TTTTCTAGAC
5649 GCCACTAATTAGCGGCGTCTGATGTCAAAAG
1 GCCACTAATTAGCGGCGTCTGATGTCAAAAG
*
5680 GCCACTAATTAGCGGCGTTTGATGTCAAAA
1 GCCACTAATTAGCGGCGTCTGATGTCAAAA
5710 CGCCGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (31 bp):
GCCACTAATTAGCGGCGTCTGATGTCAAAAG
Found at i:5710 original size:191 final size:190
Alignment explanation
Indices: 5295--5860 Score: 884
Period size: 192 Copynumber: 3.0 Consensus size: 190
5285 CCTTTCCTAG
* *
5295 ACGCCACTAATTAGCGGCGTCTAATGTCAAAACGCCGTTATATATTATCGGCGTAGAGTTGGAAA
1 ACGCCACTAATTAGCGGCGTCTGATGTCAAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAA
* *
5360 CTTTCTTTGTTTTAAGGGAGAGGGAATTTTTCCTTAAAAAAAGGAAAAAAAAAACTCTCCCTCCA
66 CTTTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTAAAAAAA--AAAAAAAAAACTCTCCCTCCA
5425 TATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAGCGGCGTCTGATGTCAAA
129 TATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAGCGGCGTCTGATGTCAAA
* *
5487 ACGCCACTAATTAGCGGCGTCTGATTTCAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAA
1 ACGCCACTAATTAGCGGCGTCTGATGTCAAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAA
* *
5552 CTTTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTAAAAAAAAAGGAAAAAAACTCTCCATCCAT
66 CTTTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTAAAAAAAAA-AAAAAAAACTCTCCCTCCAT
5617 ATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAGCGGCGTCTGATGTCAAA
130 ATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAGCGGCGTCTGATGTCAAA
* *
5678 AGGCCACTAATTAGCGGCGTTTGATGTCAAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAA
1 ACGCCACTAATTAGCGGCGTCTGATGTCAAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAA
* *
5743 CTTTCTTTGTTTTAGGGGGGAGGG-ATTTTTCCCTCCAAAAAAAATAAAAAAAATCTCTCCCTCC
66 CTTTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCT--AAAAAAAA-AAAAAAAAACTCTCCCTCC
* * * * * * *
5807 ATATATTAATATGGCGGCATCTTTC-TATCGAAACGCCACTAAATAGCGGCGTCT
128 ATATATTAAAATGGCGGCGT-TTCCTTTTCTAGACGCCACTAATTAGCGGCGTCT
5861 TCATGTCAGA
Statistics
Matches: 346, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
190 12 0.03
191 163 0.47
192 167 0.48
193 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (190 bp):
ACGCCACTAATTAGCGGCGTCTGATGTCAAAACGCCGTTATATATTATAGGCGTAGAGTTGGAAA
CTTTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTAAAAAAAAAAAAAAAAACTCTCCCTCCATA
TATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAGCGGCGTCTGATGTCAAA
Found at i:10186 original size:14 final size:14
Alignment explanation
Indices: 10167--10200 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
10157 TTTTATAATT
10167 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
10181 ATTTTATTTTTACT
1 ATTTTATTTTTACC
10195 ATTTTA
1 ATTTTA
10201 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:13875 original size:33 final size:33
Alignment explanation
Indices: 13820--14048 Score: 379
Period size: 33 Copynumber: 7.0 Consensus size: 33
13810 CTCTTACAAC
* *
13820 CAATGAAGTT-GCGGGCCTTCATCACGCCGTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
*
13852 CAATGAAGTTCACAGGCCTTCATCACGCCTTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
13885 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
* * *
13918 CAATGAAGTTCACGGGCGTTCATCACACCGTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
*
13951 CAATGAAGTTCACAGGCCTTCATCACGCCTTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
*
13984 CAATGAAGTTCACAGGCCTTCATCACGCCTTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
14017 CAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 CAATGAAGTTCACGGGCCTTCATCACGCCTTT
14049 ACATGTTGAG
Statistics
Matches: 184, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 10 0.05
33 174 0.95
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (33 bp):
CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
Done.