Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013575.1 Corchorus capsularis cultivar CVL-1 contig13596, 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: 39295
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:998 original size:11 final size:11
Alignment explanation
Indices: 955--992 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
945 TTCCTATATA
*
955 AAATAAATTAT
1 AAATTAATTAT
966 CAAA-TAATTAT
1 -AAATTAATTAT
977 AAATTAATTAT
1 AAATTAATTAT
988 AAATT
1 AAATT
993 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:15006 original size:306 final size:306
Alignment explanation
Indices: 14453--15068 Score: 1223
Period size: 306 Copynumber: 2.0 Consensus size: 306
14443 GCCTTTCAAA
14453 AGATACACCACCAAAAGAATCAAAACAAAGTCAACCAAGTGAAAGCTAGCACAATAGAAAAAATG
1 AGATACACCACCAAAAGAATCAAAACAAAGTCAACCAAGTGAAAGCTAGCACAATAGAAAAAATG
14518 ATATAGAATAAAGCATTAGAGACCTGCGGTATTTAAGCAAATTCCAAGTACTTTACTGACTAGCC
66 ATATAGAATAAAGCATTAGAGACCTGCGGTATTTAAGCAAATTCCAAGTACTTTACTGACTAGCC
14583 ATTAAACCCAGCAATAACAAAATTTTGCTAGCTTAAGTACTTGAAATGTTATTTACTCAAACATC
131 ATTAAACCCAGCAATAACAAAATTTTGCTAGCTTAAGTACTTGAAATGTTATTTACTCAAACATC
14648 ACACATTAACCAAACATTAAGCCATGGATATGTGTTAGCATTAAGAACCATGGGTAGGAGGACAG
196 ACACATTAACCAAACATTAAGCCATGGATATGTGTTAGCATTAAGAACCATGGGTAGGAGGACAG
*
14713 AAGAACATCAAAGAGGCGGAAAAATATCATGGAAAATTGTTGCATG
261 AAGAACATCAAAAAGGCGGAAAAATATCATGGAAAATTGTTGCATG
14759 AGATACACCACCAAAAGAATCAAAACAAAGTCAACCAAGTGAAAGCTAGCACAATAGAAAAAATG
1 AGATACACCACCAAAAGAATCAAAACAAAGTCAACCAAGTGAAAGCTAGCACAATAGAAAAAATG
14824 ATATAGAATAAAGCATTAGAGACCTGCGGTATTTAAGCAAATTCCAAGTACTTTACTGACTAGCC
66 ATATAGAATAAAGCATTAGAGACCTGCGGTATTTAAGCAAATTCCAAGTACTTTACTGACTAGCC
14889 ATTAAACCCAGCAATAACAAAATTTTGCTAGCTTAAGTACTTGAAATGTTATTTACTCAAACATC
131 ATTAAACCCAGCAATAACAAAATTTTGCTAGCTTAAGTACTTGAAATGTTATTTACTCAAACATC
14954 ACACATTAACCAAACATTAAGCCATGGATATGTGTTAGCATTAAGAACCATGGGTAGGAGGACAG
196 ACACATTAACCAAACATTAAGCCATGGATATGTGTTAGCATTAAGAACCATGGGTAGGAGGACAG
15019 AAGAACATCAAAAAGGCGGAAAAATATCATGGAAAATTGTTGCATG
261 AAGAACATCAAAAAGGCGGAAAAATATCATGGAAAATTGTTGCATG
15065 AGAT
1 AGAT
15069 GTCAATGACC
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
306 309 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (306 bp):
AGATACACCACCAAAAGAATCAAAACAAAGTCAACCAAGTGAAAGCTAGCACAATAGAAAAAATG
ATATAGAATAAAGCATTAGAGACCTGCGGTATTTAAGCAAATTCCAAGTACTTTACTGACTAGCC
ATTAAACCCAGCAATAACAAAATTTTGCTAGCTTAAGTACTTGAAATGTTATTTACTCAAACATC
ACACATTAACCAAACATTAAGCCATGGATATGTGTTAGCATTAAGAACCATGGGTAGGAGGACAG
AAGAACATCAAAAAGGCGGAAAAATATCATGGAAAATTGTTGCATG
Found at i:22257 original size:6 final size:6
Alignment explanation
Indices: 22246--22291 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
22236 CTTTGATAGT
*
22246 ATATAC ATATAC ATATAC ATATAC ATATAC TTATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
22292 TCGAATTGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:23064 original size:13 final size:13
Alignment explanation
Indices: 23046--23070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23036 ATAAGTTACT
23046 CTTTTTTTTTTGG
1 CTTTTTTTTTTGG
23059 CTTTTTTTTTTG
1 CTTTTTTTTTTG
23071 CAATCTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTTGG
Found at i:24251 original size:27 final size:26
Alignment explanation
Indices: 24202--24253 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
24192 TTTCTATTAT
24202 TATAATAATGGAATAATTAAAATATTG
1 TATAATAATGGAAT-ATTAAAATATTG
24229 TATAATAATGGCAAT-TTAGAAATAT
1 TATAATAATGG-AATATTA-AAATAT
24254 ATTTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (26 bp):
TATAATAATGGAATATTAAAATATTG
Found at i:27844 original size:27 final size:27
Alignment explanation
Indices: 27793--27844 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
27783 CTTAACAATA
**
27793 TCCCAATTTTTCTTAAAAATTAAAAGG
1 TCCCAATTTTTCTTAAAAAGGAAAAGG
27820 TCCCAATTTTTCTTAAAAAGGAAAA
1 TCCCAATTTTTCTTAAAAAGGAAAA
27845 AGGTTGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (27 bp):
TCCCAATTTTTCTTAAAAAGGAAAAGG
Found at i:34001 original size:33 final size:33
Alignment explanation
Indices: 33959--34034 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
33949 TTACACTGAA
**
33959 CCTCCCCACTA-GGACAGCTCAGTCACGGCGGAG
1 CCTCCCCACTAGGGA-AGCTCAACCACGGCGGAG
*
33992 CCTCCCCACTAGGGAGGCTCAACCACGGCGGAG
1 CCTCCCCACTAGGGAAGCTCAACCACGGCGGAG
34025 CCTCCCCACT
1 CCTCCCCACT
34035 GGGGCGGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.20, C:0.43, G:0.25, T:0.12
Consensus pattern (33 bp):
CCTCCCCACTAGGGAAGCTCAACCACGGCGGAG
Found at i:34077 original size:20 final size:21
Alignment explanation
Indices: 34035--34077 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34025 CCTCCCCACT
*
34035 GGGGCGGCTTCACCATGGGCA
1 GGGGCGGCTTCACCATCGGCA
*
34056 GGGGCGGCTTCGCCA-CGGCA
1 GGGGCGGCTTCACCATCGGCA
34076 GG
1 GG
34078 CCGCCCCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.12, C:0.30, G:0.47, T:0.12
Consensus pattern (21 bp):
GGGGCGGCTTCACCATCGGCA
Found at i:34198 original size:32 final size:31
Alignment explanation
Indices: 34149--34234 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
34139 AAAATAGCCG
* *
34149 AGTCGCCCCACCGGGGCGGCTTG-CCGTGGCGA
1 AGTCGCCCCA-GGGGGCGGCCTGACC-TGGCGA
34181 AGTCGCCCCAGGAGGGCGGCCTGACCTGGCGA
1 AGTCGCCCCAGG-GGGCGGCCTGACCTGGCGA
**
34213 AACCGCCCCAGTGGGGCGGCCT
1 AGTCGCCCCAG-GGGGCGGCCT
34235 TTTTATGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 1 0.02
32 43 0.91
33 3 0.06
ACGTcount: A:0.13, C:0.37, G:0.40, T:0.10
Consensus pattern (31 bp):
AGTCGCCCCAGGGGGCGGCCTGACCTGGCGA
Found at i:34780 original size:111 final size:107
Alignment explanation
Indices: 34607--34810 Score: 293
Period size: 111 Copynumber: 1.9 Consensus size: 107
34597 TCAAATCAGA
34607 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
34672 TATAATATATTAAAATTATTATTAGTTATTCCATATCATAACGT
66 TATAAT-TATTAAAATTATTATTA-TTATTCCATATCATAACGT
* * * **
34716 TTTTCTTTCCATATTACAAAA-TCTAAAATAATAGTAACAATTTTTTTTACGTTAAACCTCTTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAAT-A-A-TAACAATTATTTTTACGTTAAACAACTTAT
* *
34780 TATTATAATTATTAAACTTCTTATTATTATT
63 TATTATAATTATTAAAATTATTATTATTATT
34811 ATTTTAATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
108 8 0.09
109 25 0.29
110 16 0.19
111 36 0.42
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (107 bp):
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTAT
TATAATTATTAAAATTATTATTATTATTCCATATCATAACGT
Found at i:34801 original size:24 final size:23
Alignment explanation
Indices: 34767--34817 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
34757 TTTTTTTACG
34767 TTAAACCTCTTATTATTATAATT
1 TTAAACCTCTTATTATTATAATT
* *
34790 ATTAAACTTCTTATTATTATTATT
1 -TTAAACCTCTTATTATTATAATT
34814 TTAA
1 TTAA
34818 TTATTATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAACCTCTTATTATTATAATT
Found at i:37263 original size:265 final size:268
Alignment explanation
Indices: 36774--37264 Score: 713
Period size: 265 Copynumber: 1.8 Consensus size: 268
36764 ATGTTACTTA
*
36774 AAACTTAAAAGTGTTTATGGTTATTACGAAAAATAAAATTATCACATCCACTATCAGTGTAGTTT
1 AAACCTAAAAGTGTTTATGGTTATTACGAAAAATAAAATTATCACATCCACTATCAGTGTAGTTT
* *
36839 ACTATTAGATTGTACAAACGGGGTTAAAAGTTTGACATGTGTCTTTTTAGTGTATATTTTTTAAG
66 ACTATTAGATTGTACAAAC-GGG-----AG--TGACATGTGTCTTTTTAGCGTATACTTTTTAAG
* *** * *
36904 GAAAAATATTTTATCCATTGTTACTGAAGTTTAGCAGACTGCACATGCAGGGTTACGGTTAAAGG
123 GAAAAATATCTTATCCACCATTACTGAAGTTTAGCAGACTACACATGCAAGGTTACGGTTAAAGG
* * *
36969 GTTGATATGTGTACCCTTAGGGAATAGTTTTAATTTTTGAACATTAATTAAGTAAAAAGCCATAA
188 GTCGACATGTATACCCTTAGGGAATAGTTTTAATTTTTGAACATTAATTAAGTAAAAAGCCATAA
37034 TGATGTTATTTAAATT
253 TGATGTTATTTAAATT
*
37050 AAACCTAAAAGTGTTTATGGTTATTAC-AAAAAGTAAAATTATCACATCCACTATTAGTGTAGTT
1 AAACCTAAAAGTGTTTATGGTTATTACGAAAAA-TAAAATTATCACATCCACTATCAGTGTAGTT
*
37114 TACTATTAGATTGTACAAAC-GG-G-GACATGTGTCTTTTTAGCGTATACTTTTTAAGGAAAATT
65 TACTATTAGATTGTACAAACGGGAGTGACATGTGTCTTTTTAGCGTATACTTTTTAAGGAAAAAT
* *
37176 ATCTTATCCACCATTAGTGAAGTTTAGCAGACTACACATGCAAGGTTAGGGTTAAAGGGTCGACA
130 ATCTTATCCACCATTACTGAAGTTTAGCAGACTACACATGCAAGGTTACGGTTAAAGGGTCGACA
37241 TGTAT-CTCCTTAGGGAATAGTTTT
195 TGTATAC-CCTTAGGGAATAGTTTT
37265 GAACATAAAT
Statistics
Matches: 197, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
264 1 0.01
265 112 0.57
268 1 0.01
274 2 0.01
275 5 0.03
276 76 0.39
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (268 bp):
AAACCTAAAAGTGTTTATGGTTATTACGAAAAATAAAATTATCACATCCACTATCAGTGTAGTTT
ACTATTAGATTGTACAAACGGGAGTGACATGTGTCTTTTTAGCGTATACTTTTTAAGGAAAAATA
TCTTATCCACCATTACTGAAGTTTAGCAGACTACACATGCAAGGTTACGGTTAAAGGGTCGACAT
GTATACCCTTAGGGAATAGTTTTAATTTTTGAACATTAATTAAGTAAAAAGCCATAATGATGTTA
TTTAAATT
Done.