Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013696.1 Corchorus capsularis cultivar CVL-1 contig13717, 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: 22495
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2808 original size:30 final size:30
Alignment explanation
Indices: 2739--2808 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
2729 TGGACTGACA
*
2739 AATCATTAAAAAAATCCATACTTTCATTTT
1 AATCATCAAAAAAATCCATACTTTCATTTT
* * *
2769 -TTGAACAAAAAATAT-CATACTTTCATTTT
1 AATCATCAAAAAA-ATCCATACTTTCATTTT
2798 AATCATCAAAA
1 AATCATCAAAA
2809 TTATCCTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (30 bp):
AATCATCAAAAAAATCCATACTTTCATTTT
Found at i:6110 original size:64 final size:64
Alignment explanation
Indices: 6009--6128 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
5999 AGGTGCCTAC
6009 TTAGTTTTGTTAATCGGGAGGCTAATGTGTTAGTTCATAATATTGCTAAGTCATATGATCTCCT
1 TTAGTTTTGTTAATCGGGAGGCTAATGTGTTAGTTCATAATATTGCTAAGTCATATGATCTCCT
*
6073 TTAGTTTTGTTAATTGGGAGGCTAATGTGTTAGTTCATAATATTGCTAAGTCATAT
1 TTAGTTTTGTTAATCGGGAGGCTAATGTGTTAGTTCATAATATTGCTAAGTCATAT
6129 TGTATTGAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (64 bp):
TTAGTTTTGTTAATCGGGAGGCTAATGTGTTAGTTCATAATATTGCTAAGTCATATGATCTCCT
Found at i:10424 original size:45 final size:46
Alignment explanation
Indices: 10340--10431 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
10330 TAAGTTTGTT
*
10340 ATCTAAATTATCAGTATTCTGTAAAGGGAACATGTCAGGTCCCTAA
1 ATCTAAATTATCAGTATTATGTAAAGGGAACATGTCAGGTCCCTAA
* *
10386 ATCTCAATTATCTGTATTATGT-AAGGGAACATGTCAGGTCCCTAA
1 ATCTAAATTATCAGTATTATGTAAAGGGAACATGTCAGGTCCCTAA
10431 A
1 A
10432 ACTTTACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 24 0.56
46 19 0.44
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (46 bp):
ATCTAAATTATCAGTATTATGTAAAGGGAACATGTCAGGTCCCTAA
Found at i:11129 original size:27 final size:27
Alignment explanation
Indices: 11099--11241 Score: 153
Period size: 27 Copynumber: 5.3 Consensus size: 27
11089 TTCCGCCTTC
* * * *
11099 GGCACTCCTTCTTCTACGCCAGCGTTT
1 GGCACTCCCTCTTCGACTCCGGCGTTT
*
11126 GGCACTCCCTCTTCGACTCCGGCATTT
1 GGCACTCCCTCTTCGACTCCGGCGTTT
* *
11153 GGTACTCCCTCTTCGACGCCGGCGTTT
1 GGCACTCCCTCTTCGACTCCGGCGTTT
* * * *
11180 GGAACTCCGTCTTCTACTCCTGC-TTT
1 GGCACTCCCTCTTCGACTCCGGCGTTT
* *
11206 CGGTACTCCATCTTCGACTCCGGCGTTT
1 -GGCACTCCCTCTTCGACTCCGGCGTTT
11234 GGCACTCC
1 GGCACTCC
11242 GTCAACTTCA
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
26 3 0.03
27 90 0.94
28 3 0.03
ACGTcount: A:0.10, C:0.38, G:0.20, T:0.31
Consensus pattern (27 bp):
GGCACTCCCTCTTCGACTCCGGCGTTT
Found at i:11242 original size:54 final size:55
Alignment explanation
Indices: 11096--11244 Score: 194
Period size: 54 Copynumber: 2.7 Consensus size: 55
11086 AGCTTCCGCC
* * * * *
11096 TTCGGCACTCCTTCTTCTACGCCAGCGTTTGGCACTCCCTCTTCGACTCCGGCAT
1 TTCGGTACTCCATCTTCGACGCCGGCGTTTGGCACTCCGTCTTCGACTCCGGCAT
* * * *
11151 TT-GGTACTCCCTCTTCGACGCCGGCGTTTGGAACTCCGTCTTCTACTCCTGC-T
1 TTCGGTACTCCATCTTCGACGCCGGCGTTTGGCACTCCGTCTTCGACTCCGGCAT
*
11204 TTCGGTACTCCATCTTCGACTCCGGCGTTTGGCACTCCGTC
1 TTCGGTACTCCATCTTCGACGCCGGCGTTTGGCACTCCGTC
11245 AACTTCATCT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
53 3 0.04
54 77 0.94
55 2 0.02
ACGTcount: A:0.10, C:0.38, G:0.20, T:0.32
Consensus pattern (55 bp):
TTCGGTACTCCATCTTCGACGCCGGCGTTTGGCACTCCGTCTTCGACTCCGGCAT
Found at i:15831 original size:2 final size:2
Alignment explanation
Indices: 15826--15858 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15816 ATAGTGTGTG
15826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15859 GTTTCATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16318 original size:2 final size:2
Alignment explanation
Indices: 16313--16337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16303 CTCTCTCGCT
16313 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16338 TATGTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18280 original size:2 final size:2
Alignment explanation
Indices: 18273--18298 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18263 AAAAGAAGAT
18273 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18299 AAACTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21703 original size:21 final size:21
Alignment explanation
Indices: 21677--21733 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
21667 CATTGAAGAG
21677 AAAAATTAACACCACTCAGGC
1 AAAAATTAACACCACTCAGGC
*
21698 AAAAATTAATACCACTCAGGC
1 AAAAATTAACACCACTCAGGC
*
21719 AAAAGTTAACACCAC
1 AAAAATTAACACCAC
21734 CACATTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAATTAACACCACTCAGGC
Done.