Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013773.1 Corchorus capsularis cultivar CVL-1 contig13794, 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: 59455
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1941 original size:10 final size:10
Alignment explanation
Indices: 1926--1974 Score: 80
Period size: 10 Copynumber: 4.9 Consensus size: 10
1916 TTTGAAGGTT
1926 GAGAGAATTC
1 GAGAGAATTC
*
1936 GAGAGAATTT
1 GAGAGAATTC
1946 GAGAGAATTC
1 GAGAGAATTC
*
1956 GAGAGAATTT
1 GAGAGAATTC
1966 GAGAGAATT
1 GAGAGAATT
1975 GAAAAGTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.31, T:0.24
Consensus pattern (10 bp):
GAGAGAATTC
Found at i:1949 original size:20 final size:20
Alignment explanation
Indices: 1924--1974 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1914 AGTTTGAAGG
1924 TTGAGAGAATTCGAGAGAAT
1 TTGAGAGAATTCGAGAGAAT
1944 TTGAGAGAATTCGAGAGAAT
1 TTGAGAGAATTCGAGAGAAT
1964 TTGAGAGAATT
1 TTGAGAGAATT
1975 GAAAAGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGAGAATTCGAGAGAAT
Found at i:8957 original size:165 final size:167
Alignment explanation
Indices: 8677--9123 Score: 592
Period size: 165 Copynumber: 2.6 Consensus size: 167
8667 GGAAGAGATA
*
8677 AATGTTGAGGGAAGTTCAGGTTTTGTGGCTGCTAAAGAGGGAGAAAGTGGAGAGAAATTGGAGGA
1 AATGTTGAGGGAAGTTCCGGTTTTGTGGCTGCTAAAGAGGGAGAAAGTGGAGAGAAATTGGAGGA
* ** * *
8742 AAACGAGGTTCAATCCAAAGGTTTTGTTGAGATAGCAAAGGGGGATGATGGAGCTTGTATGAAAG
66 AAATGAGGTTCAATCCAAAGGTTTTGTTGAGATTCCAGAGGGGAATGATGGAGCTTGTATGAAAG
**
8807 TGGATGCTGATTCTGTGAAGGTCAAAAGAGAGATT-G
131 TGGATGCTGATTCTAAGAAGGTCAAAAGAGAGATTGG
* * *
8843 -ATGTAGAGGGAAGTTCCGGTTTTGTTGCTGCTAAAGAGGGAGAAAATGGAGAGAAATTGGAGGA
1 AATGTTGAGGGAAGTTCCGGTTTTGTGGCTGCTAAAGAGGGAGAAAGTGGAGAGAAATTGGAGGA
* * *
8907 AAATGGGGTTCAATCTAGAGGTTTTGTTGAGATTCCAGAGGGGAATGATGGAGCTTGTATGAAAG
66 AAATGAGGTTCAATCCAAAGGTTTTGTTGAGATTCCAGAGGGGAATGATGGAGCTTGTATGAAAG
* * *
8972 TTGATGCTGCTTCTAAGAGGGTCAAAAGAGAGATTGCGGAAG
131 TGGATGCTGATTCTAAGAAGGTCAAAAGAGAGATT---G--G
* *
9014 ACATCAATGTTGAGGGAAGTTGCGGTTTTGTGGCTCCTAAAGAGGGAGAAAGTGGAGAGAAATTG
1 -----AATGTTGAGGGAAGTTCCGGTTTTGTGGCTGCTAAAGAGGGAGAAAGTGGAGAGAAATTG
* * *
9079 GTGGAAAATGAAGTTCAATCCAAAGGTTTTGTTGAGAATCCAGAG
61 GAGGAAAATGAGGTTCAATCCAAAGGTTTTGTTGAGATTCCAGAG
9124 ACAGCAGATG
Statistics
Matches: 241, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
165 147 0.61
171 1 0.00
177 93 0.39
ACGTcount: A:0.32, C:0.08, G:0.34, T:0.25
Consensus pattern (167 bp):
AATGTTGAGGGAAGTTCCGGTTTTGTGGCTGCTAAAGAGGGAGAAAGTGGAGAGAAATTGGAGGA
AAATGAGGTTCAATCCAAAGGTTTTGTTGAGATTCCAGAGGGGAATGATGGAGCTTGTATGAAAG
TGGATGCTGATTCTAAGAAGGTCAAAAGAGAGATTGG
Found at i:11349 original size:11 final size:12
Alignment explanation
Indices: 11320--11349 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
11310 TGTTGTTTTT
11320 TTTTTTTGTTAA
1 TTTTTTTGTTAA
11332 TTTTTTT-TTAA
1 TTTTTTTGTTAA
11343 TTTTTTT
1 TTTTTTT
11350 ATAAAGTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTAA
Found at i:25997 original size:1 final size:1
Alignment explanation
Indices: 25993--26019 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
25983 TTTTTTGAAC
25993 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
26020 GCTTGTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34581 original size:17 final size:18
Alignment explanation
Indices: 34549--34588 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
34539 TTTCCAATCC
34549 ATTCCTTATTAGAATTAGA
1 ATTCCTTA-TAGAATTAGA
*
34568 ATTCCTTA-AGAATTGGA
1 ATTCCTTATAGAATTAGA
34585 ATTC
1 ATTC
34589 TTTCCGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
ATTCCTTATAGAATTAGA
Found at i:38439 original size:25 final size:23
Alignment explanation
Indices: 38411--38488 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
38401 AATCCCTCTC
38411 TCTTTCTCTCACTCTATCCTCACTT
1 TCTTTCTCTC-CTCTAT-CTCACTT
38436 TCTTTCTCTCC-C--TCT--CTT
1 TCTTTCTCTCCTCTATCTCACTT
* *
38454 TTTTTCTCTCTCTCTATTTTCACTT
1 TCTTTCTCTC-CTCTA-TCTCACTT
38479 TCTTTCTCTC
1 TCTTTCTCTC
38489 TGTTTTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
18 12 0.28
19 1 0.02
20 3 0.07
21 1 0.02
23 3 0.07
24 1 0.02
25 22 0.51
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.56
Consensus pattern (23 bp):
TCTTTCTCTCCTCTATCTCACTT
Found at i:38454 original size:18 final size:18
Alignment explanation
Indices: 38428--38468 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38418 CTCACTCTAT
*
38428 CCTCACTTTCTTTCTCTC
1 CCTCTCTTTCTTTCTCTC
*
38446 CCTCTCTTTTTTTCTCTC
1 CCTCTCTTTCTTTCTCTC
*
38464 TCTCT
1 CCTCT
38469 ATTTTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTCTCTTTCTTTCTCTC
Found at i:38823 original size:14 final size:14
Alignment explanation
Indices: 38782--38828 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 14
38772 ACTCTGTTTG
*
38782 TTTCTCGAGAAAATG
1 TTTCTCG-GAAAATC
38797 TTTCTCGGGAAAATC
1 TTTCTC-GGAAAATC
38812 TTTCTCGGAAAATC
1 TTTCTCGGAAAATC
38826 TTT
1 TTT
38829 ATGTTTGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 11 0.37
15 18 0.60
16 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTCTCGGAAAATC
Found at i:39528 original size:25 final size:25
Alignment explanation
Indices: 39447--39558 Score: 79
Period size: 25 Copynumber: 4.6 Consensus size: 25
39437 ACAAGAATCC
* * * *
39447 CACTCTCTTTCTCTCACTCTAATCT
1 CACTTTCTTTCTCTCTCTCTATTAT
* *
39472 CACTTTCTTTCTCTCCCTCTCTT-T
1 CACTTTCTTTCTCTCTCTCTATTAT
*
39496 ---TTTTTTTCTCTCTCTCTATTAT
1 CACTTTCTTTCTCTCTCTCTATTAT
* * *
39518 CACTTTCTTTCTCTTTGTCTTTTTAAT
1 CACTTTCTTTCTCTCTCTC-TATT-AT
*
39545 CACTTTCTTACTCT
1 CACTTTCTTTCTCT
39559 GTTTTTTCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
21 17 0.25
22 1 0.01
24 1 0.01
25 32 0.46
26 3 0.04
27 15 0.22
ACGTcount: A:0.11, C:0.32, G:0.01, T:0.56
Consensus pattern (25 bp):
CACTTTCTTTCTCTCTCTCTATTAT
Found at i:39876 original size:14 final size:14
Alignment explanation
Indices: 39835--39877 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
39825 ACTCTGTTTG
39835 TTTCTCGAGAAAATA
1 TTTCTCG-GAAAATA
*
39850 TTTCTTAGGAAAATA
1 TTTC-TCGGAAAATA
39865 TTTCTCGGAAAAT
1 TTTCTCGGAAAAT
39878 CTTTATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 15 0.60
16 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (14 bp):
TTTCTCGGAAAATA
Found at i:45275 original size:107 final size:107
Alignment explanation
Indices: 45089--45286 Score: 369
Period size: 107 Copynumber: 1.9 Consensus size: 107
45079 AGACTAACAC
* * *
45089 CAATGACCTATACAATAATTAGCAAATGCAAAAAGTGCAGCAGATCAGGAGATACACAAGGAAGA
1 CAATGACCTATAAAATAATTAGCAAATGCAAAAAGTGCAGCAGATCAGAAAATACACAAGGAAGA
45154 AAGAAAGTGAGCGAGTGCAAGGCCTAACACCAATGACCTATA
66 AAGAAAGTGAGCGAGTGCAAGGCCTAACACCAATGACCTATA
45196 CAATGACCTATAAAATAATTAGCAAATGCAAAAAGTGCAGCAGATCAGAAAATACACAAGGAAGA
1 CAATGACCTATAAAATAATTAGCAAATGCAAAAAGTGCAGCAGATCAGAAAATACACAAGGAAGA
45261 AAGAAAGTGAGCGAGTGCAAGGCCTA
66 AAGAAAGTGAGCGAGTGCAAGGCCTA
45287 CTTCAGCATT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 88 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (107 bp):
CAATGACCTATAAAATAATTAGCAAATGCAAAAAGTGCAGCAGATCAGAAAATACACAAGGAAGA
AAGAAAGTGAGCGAGTGCAAGGCCTAACACCAATGACCTATA
Found at i:46868 original size:1 final size:1
Alignment explanation
Indices: 46832--46859 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
46822 CCAAAGAGCC
46832 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
46860 CCCCTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:48899 original size:50 final size:50
Alignment explanation
Indices: 48823--48924 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
48813 AACTGAATTG
*
48823 GCACCATTATACCTTTATGTACAATAGGAATGACATTGTTTGTGTCTTCT
1 GCACCATTATACCTTTATGTACAATAGGAATGACACTGTTTGTGTCTTCT
* *
48873 GCACCATTATACCTTTATGTATAATAGGAATGCCACTGTTTGTGTCTTCT
1 GCACCATTATACCTTTATGTACAATAGGAATGACACTGTTTGTGTCTTCT
48923 GC
1 GC
48925 TGCATATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (50 bp):
GCACCATTATACCTTTATGTACAATAGGAATGACACTGTTTGTGTCTTCT
Found at i:49043 original size:89 final size:89
Alignment explanation
Indices: 48872--49092 Score: 198
Period size: 89 Copynumber: 2.5 Consensus size: 89
48862 TTGTGTCTTC
* * ** * * *
48872 TGCACCATTATACCTTTATGTATAATAGGAATGCCACTGTTTGTGTCTTCTGCTGCATATTAAGA
1 TGCACCATTATACCTTGATGTATAAGAGGAATGCCACTCATTATGCCTTCTACTGCATATTAAGA
48937 ATCTAATACCAACTTTTATTCGGA
66 ATCTAATACCAACTTTTATTCGGA
** *
48961 TGCACCATTATACCTTGATGTATAAGAGGAATGCTTC-CATTATGCCTTTTACTGCATGA-TAAG
1 TGCACCATTATACCTTGATGTATAAGAGGAATGCCACTCATTATGCCTTCTACTGCAT-ATTAAG
* ***
49024 AATTACTAATAGCAA-TTTTAATATAAAA
65 AA-T-CTAATACCAACTTTT-AT-TCGGA
* * * * *
49052 TGCACCATCATACCATGATGTATGATAAGAATGCCA-TCATT
1 TGCACCATTATACCTTGATGTATAAGAGGAATGCCACTCATT
49093 GTGTCTTTTG
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
88 20 0.19
89 39 0.37
90 11 0.10
91 35 0.33
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (89 bp):
TGCACCATTATACCTTGATGTATAAGAGGAATGCCACTCATTATGCCTTCTACTGCATATTAAGA
ATCTAATACCAACTTTTATTCGGA
Found at i:49378 original size:232 final size:234
Alignment explanation
Indices: 48945--49399 Score: 707
Period size: 232 Copynumber: 2.0 Consensus size: 234
48935 GAATCTAATA
* *
48945 CCAACTTTTATTCGGATGCACCATTATACCTTGATGTATAAGAGGAATGCTTCCATTATGCCTTT
1 CCAACTTTTATTCGGATGCACCATTATACCTTGATGTATAACAGGAATGCATCCATTATGCCTTT
* * * * *
49010 TACTGCATGATAAGAATTACTAATAGCAATTTTAATATAAAATGCACCATCATACCATGATGTAT
66 TACTACATGATAAGAATTACCAACAACAACTTTAATATAAAATGCACCATCATACCATGATGTAT
* * * *
49075 GATAAGAATGCCATCATTGTGTCTTTTGCACCATATTAGAATCAATCCAAGAAGCTATATTCAGG
131 GATAAGAATGCCATAATTGTGCCCTTTGCACCATATTAGAATCAATCCAAAAAGCTATATTCAGG
* *
49140 GGAAAGTAATAAAATAAAACCGAAAGAAATTCCCATTAC
196 GGAAAGTAATAAAACAAAACAGAAAGAAATTCCCATTAC
*
49179 CCAAC-TTTATTCGGATGCACCATTATACCTTGATTTATAACAGGAATGCATCCATTATGCCTTT
1 CCAACTTTTATTCGGATGCACCATTATACCTTGATGTATAACAGGAATGCATCCATTATGCCTTT
* * *
49243 TACTACATGATAAGAATTACCACCAACAACTTTCATAT-AAATGCACCATCATATCATGATGTAT
66 TACTACATGATAAGAATTACCAACAACAACTTTAATATAAAATGCACCATCATACCATGATGTAT
* * *
49307 GATAGGAATGCCATAATTGTGCCCTTTGCAGCATATTAGGATCAATCCAAAAAGCTATATTCAGG
131 GATAAGAATGCCATAATTGTGCCCTTTGCACCATATTAGAATCAATCCAAAAAGCTATATTCAGG
*
49372 GGAAAGTAATAAAACAAAGCAGAAAGAA
196 GGAAAGTAATAAAACAAAACAGAAAGAA
49400 GACATAGCTG
Statistics
Matches: 200, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
232 108 0.54
233 87 0.44
234 5 0.03
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (234 bp):
CCAACTTTTATTCGGATGCACCATTATACCTTGATGTATAACAGGAATGCATCCATTATGCCTTT
TACTACATGATAAGAATTACCAACAACAACTTTAATATAAAATGCACCATCATACCATGATGTAT
GATAAGAATGCCATAATTGTGCCCTTTGCACCATATTAGAATCAATCCAAAAAGCTATATTCAGG
GGAAAGTAATAAAACAAAACAGAAAGAAATTCCCATTAC
Found at i:50020 original size:2 final size:2
Alignment explanation
Indices: 50013--50056 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
50003 TTTCAAGAAA
50013 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50055 AG
1 AG
50057 TAGATTTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54297 original size:61 final size:60
Alignment explanation
Indices: 54222--54344 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 60
54212 AACGCCAGAA
54222 TACATCACTATCTTCAGAAATTCAGGGTTTCACAGTCAAGAACAATCAACCCCAATGCTCC
1 TACATCACTATCTTCAGAAATTCAGGGTTTCACAGTCAAGAACAATCAA-CCCAATGCTCC
*
54283 TACATCACTATCTTCAGAAATTCAGGGTTTCGCAGTCAAGAACAATCAACCCAATGCTCC
1 TACATCACTATCTTCAGAAATTCAGGGTTTCACAGTCAAGAACAATCAACCCAATGCTCC
54343 TA
1 TA
54345 AGAAGTTTTC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 13 0.21
61 48 0.79
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (60 bp):
TACATCACTATCTTCAGAAATTCAGGGTTTCACAGTCAAGAACAATCAACCCAATGCTCC
Found at i:56680 original size:2 final size:2
Alignment explanation
Indices: 56673--56698 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56663 TCCATTAGTG
56673 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
56699 CTGCAGCTTT
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
Done.