Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005243.1 Corchorus capsularis cultivar CVL-1 contig05261, 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: 12664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:7040 original size:155 final size:154
Alignment explanation
Indices: 6613--7156 Score: 640
Period size: 155 Copynumber: 3.5 Consensus size: 154
6603 GGTTCGAGCC
* *
6613 CTCCTTCATGGTGAACTAGGTTTCACACCTCAAACTGTCCTTAAATGAAAAATATGCATAAGTTT
1 CTCCTTGATGGTGAACT-GGTTTCTCACCTCAAACTGTCCTTAAATGAAAAAT-TGCATAAGTTT
** * * *
6678 TTCATCTTAAGTCCGTTTGACATGAAACTTTGCCACA-AGACTTAGACTATCTTCATAAGTCTAT
64 TTCATCTTAAGTCTATTTGAGATGAAA-TTTGCCACAGAGACTTAGACTATCTCCATAAGACTAT
*
6742 GGAAAAAATTCTAAGTAAAACCGAGCT
128 GGAAAAAATTCTAAGTAAAACCGAACT
* * *
6769 CTCCTTGATGGTGAAATTGGTTTCTCTCC-CTAAATTGTCCTTAAATGAAAAATTAGCATAAGTT
1 CTCCTTGATGGTG-AACTGGTTTCTCACCTC-AAACTGTCCTTAAATGAAAAATT-GCATAAGTT
* * * * * *
6833 TTTCAT-TCTAAGTCTA-ATAAGGCTG--ATTTTCCACCAGTAGGCTTAGATTATCTCCATAAGA
63 TTTCATCT-TAAGTCTATTTGA-GATGAAATTTGCCA-CAG-AGACTTAGACTATCTCCATAAGA
*
6894 CTATGGAAAAAATTCTAAGTAAAACTGAACT
124 CTATGGAAAAAATTCTAAGTAAAACCGAACT
* ** *
6925 CTCCTTGATAGTGAACTGACTTCTCACCTCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTT
1 CTCCTTGATGGTGAACTGGTTTCTCACCTCAAACTGTCCTTAAATGAAAAA-TTGCATAAGTTTT
6990 TCAT-TCTAAGTCTATTTGAGATGAAATTTGGCCA-AGAGACTTAGACTATCTCCATAAGACTAT
65 TCATCT-TAAGTCTATTTGAGATGAAATTT-GCCACAGAGACTTAGACTATCTCCATAAGACTAT
7053 -GAGAAAAATTCTAAGTAAAACCGAACT
128 GGA-AAAAATTCTAAGTAAAACCGAACT
* * * *
7080 C-CCTATCATGGTGAAGTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTT
1 CTCCT-TGATGGTGAACTGGTTTCTCACCTCAAACTGTCCTTAAATGAAAAA-TTGCATAAGTTT
7144 TTCATCTTAAGTC
64 TTCATCTTAAGTC
7157 CGCTTGAGAT
Statistics
Matches: 333, Mismatches: 38, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
153 6 0.02
154 8 0.02
155 176 0.53
156 133 0.40
157 7 0.02
158 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (154 bp):
CTCCTTGATGGTGAACTGGTTTCTCACCTCAAACTGTCCTTAAATGAAAAATTGCATAAGTTTTT
CATCTTAAGTCTATTTGAGATGAAATTTGCCACAGAGACTTAGACTATCTCCATAAGACTATGGA
AAAAATTCTAAGTAAAACCGAACT
Found at i:7950 original size:25 final size:25
Alignment explanation
Indices: 7922--7981 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
7912 AGTCCTTGAT
7922 TAAAAGGAAAGTATTTGAGCTTGTA
1 TAAAAGGAAAGTATTTGAGCTTGTA
7947 TAAAAGGAAAGTATTTGAGCTTGTA
1 TAAAAGGAAAGTATTTGAGCTTGTA
7972 TAAAAGGAAA
1 TAAAAGGAAA
7982 TTGGTCTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.28
Consensus pattern (25 bp):
TAAAAGGAAAGTATTTGAGCTTGTA
Done.