Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014710.1 Corchorus olitorius cultivar O-4 contig14743, 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: 5266
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Found at i:305 original size:2 final size:2
Alignment explanation
Indices: 298--326 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
288 CTTCTTCCTA
298 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
327 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:472 original size:10 final size:10
Alignment explanation
Indices: 459--545 Score: 52
Period size: 10 Copynumber: 7.9 Consensus size: 10
449 TACCTTCGTG
459 TCTGTCTTCC
1 TCTGTCTTCC
469 TCTGTCTT-C
1 TCTGTCTTCC
*
478 TCGTGTTCCTTCGTG
1 TC-TG-T-CTTC--C
493 TCTGTCTTCC
1 TCTGTCTTCC
503 TCTGTCTT-C
1 TCTGTCTTCC
*
512 TCGTGTTCCTTCGTG
1 TC-TG-T-CTTC--C
527 TCTGTCTTCC
1 TCTGTCTTCC
537 TCTGTCTTC
1 TCTGTCTTC
546 TCGTGTACCT
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
9 6 0.10
10 29 0.48
11 2 0.03
12 14 0.23
13 2 0.03
14 4 0.07
15 4 0.07
ACGTcount: A:0.00, C:0.33, G:0.16, T:0.51
Consensus pattern (10 bp):
TCTGTCTTCC
Found at i:474 original size:34 final size:34
Alignment explanation
Indices: 436--560 Score: 232
Period size: 34 Copynumber: 3.7 Consensus size: 34
426 TGGAGCACCA
436 CTGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCT
1 CTGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCT
*
470 CTGTCTTCTCGTGTTCCTTCGTGTCTGTCTTCCT
1 CTGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCT
*
504 CTGTCTTCTCGTGTTCCTTCGTGTCTGTCTTCCT
1 CTGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCT
538 CTGTCTTCTCGTGTACCTTCGTG
1 CTGTCTTCTCGTGTACCTTCGTG
561 CCTGCTGGCC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 89 1.00
ACGTcount: A:0.02, C:0.32, G:0.18, T:0.48
Consensus pattern (34 bp):
CTGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCT
Found at i:702 original size:63 final size:62
Alignment explanation
Indices: 532--979 Score: 756
Period size: 62 Copynumber: 7.2 Consensus size: 62
522 TCGTGTCTGT
*
532 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTGTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
594 CTT-C-CTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
654 CTTCCTCTGTCTTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTC-TTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
717 CTTCCTCTGTCTTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTC-TTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* * * *
780 CTTCCTCTGTCTTCCCGTCTACCTTAGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* * * *
842 CTTCCTCTGTCTTCCCGTCTACCTTAGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* * *
904 CTTCCTCTGTCTTCCCGTCTACCTTAGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
966 CTTCCTCTGTCTTC
1 CTTCCTCTGTCTTC
980 CTTCCTCTGT
Statistics
Matches: 377, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
60 58 0.15
61 2 0.01
62 192 0.51
63 125 0.33
ACGTcount: A:0.04, C:0.40, G:0.22, T:0.34
Consensus pattern (62 bp):
CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
Found at i:980 original size:14 final size:14
Alignment explanation
Indices: 961--991 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
951 TGCGGAGGCC
961 TCTTCCTTCCTCTG
1 TCTTCCTTCCTCTG
975 TCTTCCTTCCTCTG
1 TCTTCCTTCCTCTG
989 TCT
1 TCT
992 GTCGTGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.06, T:0.52
Consensus pattern (14 bp):
TCTTCCTTCCTCTG
Found at i:3204 original size:56 final size:56
Alignment explanation
Indices: 3118--3230 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
3108 CGAGCATCTG
3118 AATCTTGTTTCGATTTAATTATAAATAAATTCGGGGAAAAATGGGAAAACGATATT
1 AATCTTGTTTCGATTTAATTATAAATAAATTCGGGGAAAAATGGGAAAACGATATT
3174 AATCTTGTTTCGATTTAATTATAAATAAATTCGGGGAAAAATGGGAAAACGATATT
1 AATCTTGTTTCGATTTAATTATAAATAAATTCGGGGAAAAATGGGAAAACGATATT
3230 A
1 A
3231 GAAGCATGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.34
Consensus pattern (56 bp):
AATCTTGTTTCGATTTAATTATAAATAAATTCGGGGAAAAATGGGAAAACGATATT
Done.