Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015539.1 Corchorus capsularis cultivar CVL-1 contig15560, 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: 25505
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:446 original size:29 final size:29
Alignment explanation
Indices: 408--475 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
398 CGGTTTATCC
* * *
408 TGCAACAACAAACTCAACAGCCATAAATT
1 TGCAAGAACAAACTCAACAACCATAAACT
*
437 TGCAGGAACAAACTCAACAACCATAAACT
1 TGCAAGAACAAACTCAACAACCATAAACT
466 TGCAAGAACA
1 TGCAAGAACA
476 CCTAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (29 bp):
TGCAAGAACAAACTCAACAACCATAAACT
Found at i:782 original size:17 final size:17
Alignment explanation
Indices: 760--792 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
750 CGACGGGAAG
*
760 GAAGAAGTGGAGAAGAT
1 GAAGAAGTCGAGAAGAT
777 GAAGAAGTCGAGAAGA
1 GAAGAAGTCGAGAAGA
793 AGAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.39, T:0.09
Consensus pattern (17 bp):
GAAGAAGTCGAGAAGAT
Found at i:4375 original size:41 final size:41
Alignment explanation
Indices: 4317--4394 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
4307 AACTAGGGGT
* *
4317 TAAACCTGAATTCAATTTCTTACTTTAATTATTAGGAGGGC
1 TAAACCTGAATTCAATTTATTACCTTAATTATTAGGAGGGC
* * *
4358 TAAACCTGGATTTAATTTATTTCCTTAATTATTAGGA
1 TAAACCTGAATTCAATTTATTACCTTAATTATTAGGA
4395 TGATCAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (41 bp):
TAAACCTGAATTCAATTTATTACCTTAATTATTAGGAGGGC
Found at i:5396 original size:17 final size:17
Alignment explanation
Indices: 5374--5407 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5364 ATGTTATTCT
5374 AAAGAAAAAAGAAAAGG
1 AAAGAAAAAAGAAAAGG
*
5391 AAAGAAAAGAGAAAAGG
1 AAAGAAAAAAGAAAAGG
5408 TAAGGGTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAGG
Found at i:21752 original size:47 final size:48
Alignment explanation
Indices: 21679--21781 Score: 127
Period size: 48 Copynumber: 2.2 Consensus size: 48
21669 GAAGCGAACT
* *
21679 TGCCTTTCGTCCGGAAAAGGCATTTTA-AAAAAAGCAAGTGAAACTAA
1 TGCCTTTCATCCGGAAAAGGCATTTTAGAAAAAAGCAAGTAAAACTAA
* * * * * *
21726 TGCCTTTCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAATTAG
1 TGCCTTTCATCCGGAAAAGGCATTTTAGAAAAAAGCAAGTAAAACTAA
21774 TGCCTTTC
1 TGCCTTTC
21782 TGTTGGGGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 23 0.49
48 24 0.51
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (48 bp):
TGCCTTTCATCCGGAAAAGGCATTTTAGAAAAAAGCAAGTAAAACTAA
Found at i:21778 original size:48 final size:48
Alignment explanation
Indices: 21707--22215 Score: 288
Period size: 49 Copynumber: 10.3 Consensus size: 48
21697 GGCATTTTAA
* * * *
21707 AAAAAGCAAGTGAAACTAATGCCTTTCATCCGGGAAGGGCGTTTTAGG
1 AAAAAGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
** ** * ** *
21755 AAAAAGCAAGTAAAATTAGTGCCTTTCTGTTGGGGGAGGGCACTTTGGG
1 AAAAAGCAAGTAAAATTAGTGCC-TTCCATCCGGGAAGGGCGTTTTAGG
* *** * * ** *
21804 GAAAAGTGGGTAAAAGTGAGCGTTTTCCATCCGGGAAGGGCGTTTTCGG
1 AAAAAGCAAGTAAAA-TTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
* * * * * * *
21853 AAAATAACAAGTAAAATAAGTGCCTTCCGTCCGGGGAGAGCATTCT-GAG
1 AAAA-AGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAG-G
* * * *
21902 AAAAA-CAGGTAGAGATTAGTGCCTTCCATCCGGGAATGGCGCTTTAGG
1 AAAAAGCAAGTA-AAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
* * * ** *
21950 ACAAAGCAAGTAAAAATCAGTGCCTTCTATCCGGGAAGGGCACTTTGGG
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
*
21999 AAAAATGCAAGTAAAGATTAGTGCCTTCCATCTGGGAAGGGCGTTTTAGG
1 AAAAA-GCAAGTAAA-ATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
* * * * * *
22049 AAAAA-CAGGTAAAAATAAATGCC-TGCAGTCCGGGAAGGGCATTTTGAGAAAA
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCA-TCCGGGAAGGGCGTTTT-AG---G
* * * * * * *
22101 AAAAAGCAAGTAAAAATAAATGACTTCCGTCTGGGAAGGGCGCTTTGGG
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
* * * * * * *
22150 AAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGG
1 AAAAAGCAAGT-AAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTT-AGG
*
22200 GAAAAGCAAGTGAAAA
1 AAAAAGCAAGT-AAAA
22216 CCGAAAATTG
Statistics
Matches: 352, Mismatches: 90, Indels: 36
0.74 0.19 0.08
Matches are distributed among these distances:
47 8 0.02
48 77 0.22
49 162 0.46
50 67 0.19
52 6 0.02
53 30 0.09
54 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (48 bp):
AAAAAGCAAGTAAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTAGG
Found at i:21966 original size:97 final size:96
Alignment explanation
Indices: 21679--22190 Score: 356
Period size: 98 Copynumber: 5.2 Consensus size: 96
21669 GAAGCGAACT
* * * * * * * *
21679 TGCCTTTC-GTCCGGAAAAGGCATTTTAAAAAAAGCAAGTGAA-ACTAATGCCTTTCATCCGGGA
1 TGCC-TTCAGTCCGGGAAGGGCATTTGAGAAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGA
*
21742 AGGGCGTTTTAGGAAAAAGCAAGT-AAAATTAG
65 AGGGCGTTTTAGGAAAAA-CAAGTAAAAATAAG
* ** * * * *** * * **
21774 TGCCTTTCTGTTGGGGGAGGGCACTTTGGGGAAAAGTGGGTAAA-AGTGAGCGTTTTCCATCCGG
1 TGCC-TTCAGTCCGGGAAGGGCA-TTTGAGAAAAAGCAAGTAAAGA-TTAGTGCCTTCCATCCGG
*
21838 GAAGGGCGTTTTCGGAAAATAACAAGT-AAAATAAG
63 GAAGGGCGTTTTAGG-AAA-AACAAGTAAAAATAAG
* * * * *
21873 TGCCTTCCGTCCGGGGAGAGCATTCTGAGAAAAA-CAGGTAGAGATTAGTGCCTTCCATCCGGGA
1 TGCCTTCAGTCCGGGAAGGGCATT-TGAGAAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGA
* * * *
21937 ATGGCGCTTTAGGACAAAGCAAGTAAAAATCAG
65 AGGGCGTTTTAGGA-AAAACAAGTAAAAATAAG
* *
21970 TGCCTTCTA-TCCGGGAAGGGCACTTTGGGAAAAATGCAAGTAAAGATTAGTGCCTTCCATCTGG
1 TGCCTTC-AGTCCGGGAAGGGCA-TTTGAGAAAAA-GCAAGTAAAGATTAGTGCCTTCCATCCGG
* *
22034 GAAGGGCGTTTTAGGAAAAACAGGTAAAAATAAA
63 GAAGGGCGTTTTAGGAAAAACAAGTAAAAATAAG
* * * * * * *
22068 TGCCTGCAGTCCGGGAAGGGCATTTTGAGAAAAAAAAAGCAAGTAAAAATAAATGACTTCCGTCT
1 TGCCTTCAGTCCGGGAAGGGCA-TTTGAG----AAAAAGCAAGTAAAGATTAGTGCCTTCCATCC
* * *
22133 GGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAA-
61 GGGAAGGGCGTTTTAGGAAA-AACAAGTAAAAAT-AAG
* * *
22170 TGGCTTCCGTCTGGGAAGGGC
1 TGCCTTCAGTCCGGGAAGGGC
22191 GTTTTGGGGG
Statistics
Matches: 328, Mismatches: 69, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
95 8 0.02
96 16 0.05
97 82 0.25
98 87 0.27
99 58 0.18
100 2 0.01
101 40 0.12
102 33 0.10
103 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (96 bp):
TGCCTTCAGTCCGGGAAGGGCATTTGAGAAAAAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAA
GGGCGTTTTAGGAAAAACAAGTAAAAATAAG
Found at i:22066 original size:195 final size:195
Alignment explanation
Indices: 21726--22101 Score: 456
Period size: 195 Copynumber: 1.9 Consensus size: 195
21716 GTGAAACTAA
* * * * ** *
21726 TGCCTTTCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAATTAGTGCCTTTCTGTTGGGGG
1 TGCCTTCCATCCGGGAAGGGCGCTTTAGGAAAAAGCAAGTAAAATCAGTGCCTTTCTATCCGGGA
* * ** *
21791 AGGGCACTTTGGGGAAAAGTGGGTAAAAGTGAGCGTTTTCCATCCGGGAAGGGCGTTTTCGGAAA
66 AGGGCACTTTGGGGAAAAATGAGTAAAAGTGAGCGCCTTCCATCCGGGAAGGGCGTTTTAGGAAA
* * * *
21856 ATAACAAGTAAAATAAGTGCCTTCCGTCCGGGGAGAGCATTCTGAGAAAAACAGGTAGAGATTAG
131 ATAACAAGTAAAATAAATGCCTGCAGTCCGGGAAGAGCATTCTGAGAAAAACAGGTAGAGATTAG
* *
21921 TGCCTTCCATCCGGGAATGGCGCTTTAGGACAAAGCAAGTAAAAATCAGTGCC-TTCTATCCGGG
1 TGCCTTCCATCCGGGAAGGGCGCTTTAGGAAAAAGCAAGT-AAAATCAGTGCCTTTCTATCCGGG
* * *
21985 AAGGGCACTTT-GGGAAAAATGCAAGT-AAAGATTAGTGCCTTCCATCTGGGAAGGGCGTTTTAG
65 AAGGGCACTTTGGGGAAAAATG--AGTAAAAG-TGAGCGCCTTCCATCCGGGAAGGGCGTTTTAG
* * *
22048 G-AAA-AACAGGTAAAAATAAATGCCTGCAGTCCGGGAAGGGCATTTTGAGAAAAA
127 GAAAATAACAAGT-AAAATAAATGCCTGCAGTCCGGGAAGAGCATTCTGAGAAAAA
22102 AAAAGCAAGT
Statistics
Matches: 152, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
194 15 0.10
195 97 0.64
196 40 0.26
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.23
Consensus pattern (195 bp):
TGCCTTCCATCCGGGAAGGGCGCTTTAGGAAAAAGCAAGTAAAATCAGTGCCTTTCTATCCGGGA
AGGGCACTTTGGGGAAAAATGAGTAAAAGTGAGCGCCTTCCATCCGGGAAGGGCGTTTTAGGAAA
ATAACAAGTAAAATAAATGCCTGCAGTCCGGGAAGAGCATTCTGAGAAAAACAGGTAGAGATTAG
Found at i:25117 original size:20 final size:21
Alignment explanation
Indices: 25088--25135 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
25078 CAAAGCTACT
25088 ACCC-AAAGCCCAAGTTT-AA
1 ACCCAAAAGCCCAAGTTTAAA
25107 ACCCAAAAGCCCAAGTTTAAA
1 ACCCAAAAGCCCAAGTTTAAA
25128 ACCCAAAA
1 ACCCAAAA
25136 TGATGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.48, C:0.31, G:0.08, T:0.12
Consensus pattern (21 bp):
ACCCAAAAGCCCAAGTTTAAA
Done.