Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010672.1 Corchorus capsularis cultivar CVL-1 contig10693, 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: 17962
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Found at i:319 original size:30 final size:30
Alignment explanation
Indices: 279--337 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
269 CAAGGGGGAG
279 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
* *
309 GGAATTATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
338 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:6057 original size:10 final size:10
Alignment explanation
Indices: 6044--6114 Score: 52
Period size: 10 Copynumber: 6.5 Consensus size: 10
6034 TAGCCGGTTG
6044 TGGCCGGGCA
1 TGGCCGGGCA
*
6054 TGGCCGAGTCAA
1 TGGCCG-GGC-A
6066 GTGGCCGGGCA
1 -TGGCCGGGCA
*
6077 TGGCCGAGTCAA
1 TGGCCG-GGC-A
**
6089 GTGGCCGGGTG
1 -TGGCCGGGCA
6100 TGGCCGGGCA
1 TGGCCGGGCA
6110 TGGCC
1 TGGCC
6115 ATGTCGCGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
10 25 0.53
11 5 0.11
12 5 0.11
13 12 0.26
ACGTcount: A:0.13, C:0.27, G:0.46, T:0.14
Consensus pattern (10 bp):
TGGCCGGGCA
Found at i:6072 original size:13 final size:13
Alignment explanation
Indices: 6054--6095 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
6044 TGGCCGGGCA
6054 TGGCCGAGTCAAG
1 TGGCCGAGTCAAG
*
6067 TGGCCG-GGC-A-
1 TGGCCGAGTCAAG
6077 TGGCCGAGTCAAG
1 TGGCCGAGTCAAG
6090 TGGCCG
1 TGGCCG
6096 GGTGTGGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.17, C:0.26, G:0.43, T:0.14
Consensus pattern (13 bp):
TGGCCGAGTCAAG
Found at i:6073 original size:33 final size:32
Alignment explanation
Indices: 6066--6176 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 32
6056 GCCGAGTCAA
6066 GTGGCCGGGCATGGCCGA-GTCAAGTGGCCGGGT
1 GTGGCCGGGCATGGCC-ATGTCAAGTGGCC-GGT
**
6099 GTGGCCGGGCATGGCCATGTCGCGTGGCCGGT
1 GTGGCCGGGCATGGCCATGTCAAGTGGCCGGT
** *
6131 GATGGCCGGGCATCTCCATGTCGCA-TGGCCGGT
1 G-TGGCCGGGCATGGCCATGTC-AAGTGGCCGGT
*
6164 GTTGCGCGGGCAT
1 GTGGC-CGGGCAT
6177 CTCCAAGTCG
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
32 8 0.12
33 59 0.88
ACGTcount: A:0.10, C:0.27, G:0.44, T:0.19
Consensus pattern (32 bp):
GTGGCCGGGCATGGCCATGTCAAGTGGCCGGT
Found at i:6105 original size:23 final size:23
Alignment explanation
Indices: 6043--6097 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
6033 GTAGCCGGTT
6043 GTGGCCGGGCATGGCCGAGTCAA
1 GTGGCCGGGCATGGCCGAGTCAA
6066 GTGGCCGGGCATGGCCGAGTCAA
1 GTGGCCGGGCATGGCCGAGTCAA
6089 GTGGCCGGG
1 GTGGCCGGG
6098 TGTGGCCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.47, T:0.13
Consensus pattern (23 bp):
GTGGCCGGGCATGGCCGAGTCAA
Found at i:6177 original size:33 final size:33
Alignment explanation
Indices: 6089--6196 Score: 130
Period size: 33 Copynumber: 3.3 Consensus size: 33
6079 GCCGAGTCAA
* **
6089 GTGGCCGGGTGTGGC-CGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTTGCGCGGGCATCTCCATGTCGC
*
6122 GTGGCCGGTGATG-GCCGGGCATCTCCATGTCGC
1 GTGGCCGGTGTTGCG-CGGGCATCTCCATGTCGC
* *
6155 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTTGCGCGGGCATCTCCATGTCGC
6188 GTGGCCGGT
1 GTGGCCGGT
6197 CACTCTCGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.08
33 58 0.91
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.43, T:0.20
Consensus pattern (33 bp):
GTGGCCGGTGTTGCGCGGGCATCTCCATGTCGC
Found at i:10815 original size:33 final size:32
Alignment explanation
Indices: 10779--10918 Score: 145
Period size: 33 Copynumber: 4.2 Consensus size: 32
10769 AAGGATCATG
** * *
10779 TGGCCGGTTGTGGCCGGGCATGGCCATGTCGCG
1 TGGCCGG-TGTGGCCGGGCATCTCCAAGTCGCA
*
10812 TGGCCGATGATGGCCGGGCATCTCCAAGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCCAAGTCGCA
*
10845 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCA
1 TGGCCGGTGTGGC-CGGGCATCTCCAAGTCGCA
** * *
10878 TGGCCGGCATTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTGGC-CGGGCATCTCCAAGTCGCA
*
10911 TGGTCGGT
1 TGGCCGGT
10919 CACAAGTGCT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 5 0.05
33 88 0.95
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.21
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATCTCCAAGTCGCA
Found at i:12908 original size:21 final size:21
Alignment explanation
Indices: 12884--12943 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
12874 GCATATCTTG
*
12884 GAATCGATTGGAATATTCCTA
1 GAATCGATTGGAATATTCATA
* * **
12905 GAATCGATTGTAGTAGACATA
1 GAATCGATTGGAATATTCATA
12926 GAATCGATTGGAATATTC
1 GAATCGATTGGAATATTC
12944 TTGCCCCAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (21 bp):
GAATCGATTGGAATATTCATA
Found at i:13949 original size:23 final size:23
Alignment explanation
Indices: 13919--13972 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
13909 CCGACCATCA
* *
13919 CCGGCCACGCGACTTGGAGATGC
1 CCGGCCACGCGACATGGACATGC
13942 CCGGCCACGCGACATGGACATGC
1 CCGGCCACGCGACATGGACATGC
13965 CCGGCCAC
1 CCGGCCAC
13973 AACCGGCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.41, G:0.31, T:0.09
Consensus pattern (23 bp):
CCGGCCACGCGACATGGACATGC
Found at i:16024 original size:33 final size:33
Alignment explanation
Indices: 15959--16030 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
15949 AAAGGATCGA
* *
15959 GTGGCCGGTTGTGGCCGGGCATGGTCATGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGCTCAAGTCGC
15992 GTGGCCGG-TGATGGCCGGGCAT-CTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGCT-CAAGTCGC
*
16025 ATGGCC
1 GTGGCC
16031 TGATGCGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.10, C:0.28, G:0.42, T:0.21
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGGCATGCTCAAGTCGC
Found at i:16188 original size:12 final size:12
Alignment explanation
Indices: 16171--16202 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
16161 GCCGCGCAAC
*
16171 ACCGGCCACATT
1 ACCGGCCACATG
16183 ACCGGCCACATG
1 ACCGGCCACATG
16195 ACCGGCCA
1 ACCGGCCA
16203 TCGCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.44, G:0.22, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:17221 original size:8 final size:8
Alignment explanation
Indices: 17208--17241 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
17198 CACCTTCTTA
17208 AAAAATTC
1 AAAAATTC
17216 AAAAATTC
1 AAAAATTC
*
17224 AGAAACTTC
1 A-AAAATTC
17233 AAAAATTC
1 AAAAATTC
17241 A
1 A
17242 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:17343 original size:14 final size:14
Alignment explanation
Indices: 17320--17349 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17310 ATCGAAAAAT
17320 ATAAAAAAAATAAA
1 ATAAAAAAAATAAA
*
17334 ATAAATAAAATAAA
1 ATAAAAAAAATAAA
17348 AT
1 AT
17350 TTTCGACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Done.