Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020615.1 Corchorus olitorius cultivar O-4 contig20648, 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: 3508
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:162 original size:14 final size:13
Alignment explanation
Indices: 100--164 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
90 ATAAAGGATT
100 TTTTCAAAAATGA
1 TTTTCAAAAATGA
113 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
127 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
141 TTTTCAAAAATGA
1 TTTTCAAAAATGA
154 GTTTTCAAAAA
1 -TTTTCAAAAA
165 GGTTTTGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.31
14 31 0.65
15 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:818 original size:6 final size:6
Alignment explanation
Indices: 807--842 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
797 GAATCAATCT
*
807 AAAGAA AAAGAA AAAG-C AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
843 GAAAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:854 original size:23 final size:22
Alignment explanation
Indices: 807--860 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
797 GAATCAATCT
*
807 AAAGAAAAAGAAAAAGCAAAGAA
1 AAAGAAAAAGAAAAA-CAAACAA
830 AAAGAAAAAGAAAGAA-AAATCAA
1 AAAGAAAAAGAAA-AACAAA-CAA
*
853 AAGGAAAA
1 AAAGAAAA
861 GGTTCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 22 0.81
24 2 0.07
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAAAACAAACAA
Found at i:855 original size:16 final size:17
Alignment explanation
Indices: 807--848 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
797 GAATCAATCT
807 AAAGAAAAAGAAAAAGC
1 AAAGAAAAAGAAAAAGC
824 AAAGAAAAAGAAAAAG-
1 AAAGAAAAAGAAAAAGC
840 AAAGAAAAA
1 AAAGAAAAA
849 TCAAAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGC
Found at i:859 original size:17 final size:16
Alignment explanation
Indices: 807--859 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
797 GAATCAATCT
*
807 AAAGAAAAAGAAAAAGC
1 AAAGAAAAA-AAAAAGG
824 AAAGAAAAAGAAAAA-G
1 AAAGAAAAA-AAAAAGG
*
840 AAAGAAAAATCAAAAGG
1 AAAGAAAAA-AAAAAGG
857 AAA
1 AAA
860 AGGTTCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAAAAAGG
Found at i:1127 original size:87 final size:87
Alignment explanation
Indices: 981--1149 Score: 259
Period size: 87 Copynumber: 1.9 Consensus size: 87
971 TGTTTGAAGG
* *
981 TTTCTTAAGATGAAAAACTGATCCGGAAACATCAATTAAGTTGGGAATATCAATGCATGA-TCAA
1 TTTCTTAAGATGAAAAACTGATCCAGAAACATCAATGAAGTTGGGAATATCAATGCATGACT-AA
1045 ATTGGAGGAAGAATTGGGAAACA
65 ATTGGAGGAAGAATTGGGAAACA
* * * *
1068 TTTCTTAAGGTGAGAAGCTGATCCAGAACCATCAATGAAGTTGGGAATATCAATGCATGACTAAA
1 TTTCTTAAGATGAAAAACTGATCCAGAAACATCAATGAAGTTGGGAATATCAATGCATGACTAAA
*
1133 TTGGAGGAAGATTTGGG
66 TTGGAGGAAGAATTGGG
1150 GCATCAATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 73 0.99
88 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (87 bp):
TTTCTTAAGATGAAAAACTGATCCAGAAACATCAATGAAGTTGGGAATATCAATGCATGACTAAA
TTGGAGGAAGAATTGGGAAACA
Found at i:1950 original size:37 final size:37
Alignment explanation
Indices: 1908--2025 Score: 137
Period size: 37 Copynumber: 3.2 Consensus size: 37
1898 AATTCATCTC
*
1908 ATCAAAACCTTGTTCAAGATTTCTGTTTAGGTGTCTT
1 ATCAAAACCTTGTTCAAGATTCCTGTTTAGGTGTCTT
* * * * * *
1945 ATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTC
1 ATCAAAACCTTGTTCAAGATTCCTGTTTAGGTGTCTT
* * *
1982 ATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTT
1 ATCAAAACCTTGTTCAAGATTCCTGTTTAGGTGTCTT
*
2019 ATTAAAA
1 ATCAAAA
2026 TTTAAGGTAC
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCAAAACCTTGTTCAAGATTCCTGTTTAGGTGTCTT
Found at i:1994 original size:74 final size:69
Alignment explanation
Indices: 1904--2059 Score: 204
Period size: 74 Copynumber: 2.2 Consensus size: 69
1894 ACAAAATTCA
* * * *
1904 TCTCATCAAAACCTTGTTCAAGATTTCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCT
1 TCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTGTCTTATCAAA-----ATTTAAGGTACCT
1969 GTTTAGGTG
61 GTTTAGGTG
* *
1978 TCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAAATTTAAGGTACCTGTTTA
1 TCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTGTCTTATCAAAATTTAAGGTACCTGTTTA
2043 GGTG
66 GGTG
*
2047 TCTCTTCAAAATC
1 TCTCATCAAAATC
2060 CCAGTTTAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 33 0.44
74 42 0.56
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (69 bp):
TCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTGTCTTATCAAAATTTAAGGTACCTGTTTA
GGTG
Found at i:2240 original size:54 final size:54
Alignment explanation
Indices: 2156--2400 Score: 339
Period size: 54 Copynumber: 4.5 Consensus size: 54
2146 TCTCTCTAGA
* * * *
2156 AAGTTGATCTTAAGTTGACCCCGTGCGGTCTTTCATTGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
2210 AAGTTGATCTTAAGATGGCCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
2264 AAGTTGATCTTAAGATGACCCAGTGTGGTATTTCATAGAAGCTTTT-AGAGGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
* * * * *
2318 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
2372 AAGTTGATCTTAAGTTGATCCAGTGTGGT
1 AAGTTGATCTTAAGATGACCCAGTGTGGT
2401 TATTCCAAGA
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 4 0.02
54 161 0.96
55 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (54 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:2345 original size:108 final size:108
Alignment explanation
Indices: 2156--2466 Score: 355
Period size: 108 Copynumber: 2.9 Consensus size: 108
2146 TCTCTCTAGA
* * * *
2156 AAGTTGATCTTAAGTTGACCCCGTGCGGTCTTTCATTGAAGTTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCTTAAGTTGACCCAGTGTGGTATTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
* * * *
2221 AAGATGGCCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCT
66 AAGATGACCCAGTGTGGTCTTCCATAGAAGTTGTCAAAAATCT
* *
2264 AAGTTGATCTTAAGATGACCCAGTGTGGTATTTCATAGAAGCTTTT-AGAGGTCTAAGTTGATCT
1 AAGTTGATCTTAAGTTGACCCAGTGTGGTATTTCATAGAAG-TTTTCAGAGATCTAAGTTGATCT
* * *
2328 TCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
65 TAAGATGACCCAGTGTGGTCTTCCATAGAAGTTGTCAAAAATCT
* * *
2372 AAGTTGATCTTAAGTTGATCCAGTGTGGTTATTCCA-AGAAGTTTAC-GATGATC-AGAGTTGAT
1 AAGTTGATCTTAAGTTGACCCAGTGTGG-TATTTCATAGAAGTTTTCAGA-GATCTA-AGTTGAT
* *
2434 CTCTAA-ACTGACCCATTGCGGTCATTCCA-AGAA
63 CT-TAAGA-TGACCCAGTGTGGTC-TTCCATAGAA
2467 AGGTTTCCAT
Statistics
Matches: 173, Mismatches: 22, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
107 6 0.03
108 134 0.77
109 28 0.16
110 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (108 bp):
AAGTTGATCTTAAGTTGACCCAGTGTGGTATTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTT
AAGATGACCCAGTGTGGTCTTCCATAGAAGTTGTCAAAAATCT
Found at i:2412 original size:54 final size:53
Alignment explanation
Indices: 2156--2448 Score: 317
Period size: 54 Copynumber: 5.4 Consensus size: 53
2146 TCTCTCTAGA
* * * *
2156 AAGTTGATCTTAAGTTGACCCCGTGCGGTCTTTCATTGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGT-TTTCATAGAAGTTTTCAGAGATCT
* *
2210 AAGTTGATCTTAAGATGGCCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGT-TTTCATAGAAGTTTTCAGAGATCT
*
2264 AAGTTGATCTTAAGATGACCCAGTGTGGTATTTCATAGAAGCTTTT-AGAGGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGT-TTTCATAGAAG-TTTTCAGAGATCT
* * * * *
2318 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGT-TTTCATAGAAGTTTTCAGAGATCT
* * *
2372 AAGTTGATCTTAAGTTGATCCAGTGTGGTTATTCCA-AGAAGTTTAC-GATGATC-
1 AAGTTGATCTTAAGATGACCCAGTGTGGTT-TT-CATAGAAGTTTTCAGA-GATCT
2425 AGAGTTGATCTCTAA-ACTGACCCA
1 A-AGTTGATCT-TAAGA-TGACCCA
2449 TTGCGGTCAT
Statistics
Matches: 204, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
53 7 0.03
54 183 0.90
55 14 0.07
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (53 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTTTTCATAGAAGTTTTCAGAGATCT
Found at i:2433 original size:162 final size:163
Alignment explanation
Indices: 2156--2448 Score: 384
Period size: 162 Copynumber: 1.8 Consensus size: 163
2146 TCTCTCTAGA
* * * * *
2156 AAGTTGATCTTAAGTTGACCCCGTGCGGTCTTTCATTGAAGTTTTCAGAGATCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGACCCCGTGCGGTCTTCCATAGAAGTTTTCAAAAATCTAAGTTGATCTT
*
2221 AAGATGGCCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCTAAGTTGATCT-TAAGA-TGACC
66 AAGATGACCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCTAAGTTGATCTCTAA-ACTGACC
2284 CAGTGTGGTATTTCATAGAAGCTTTTAGAGGTCT
130 CAGTGTGGTATTTCATAGAAGCTTTTAGAGGTCT
* * *
2318 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGACCCCGTGCGGTCTTCCATAGAAGTTTTCAAAAATCTAAGTTGATCTT
* *
2383 AAGTTGATCCAGTGTGGT-TATTCCA-AGAAGTT-T-ACGATGATC-AGAGTTGATCTCTAAACT
66 AAGATGACCCAGTGTGGTCT-TT-CATAGAAGTTGTCA-GA-GATCTA-AGTTGATCTCTAAACT
2443 GACCCA
126 GACCCA
2449 TTGCGGTCAT
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
160 1 0.01
161 5 0.04
162 95 0.84
163 12 0.11
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (163 bp):
AAGTTGATCTTAAGATGACCCCGTGCGGTCTTCCATAGAAGTTTTCAAAAATCTAAGTTGATCTT
AAGATGACCCAGTGTGGTCTTTCATAGAAGTTGTCAGAGATCTAAGTTGATCTCTAAACTGACCC
AGTGTGGTATTTCATAGAAGCTTTTAGAGGTCT
Found at i:2561 original size:33 final size:33
Alignment explanation
Indices: 2519--2596 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
2509 ATTAATTAAG
* * * * *
2519 AAGTTCAAAATTTGCATTTAATTTCAAAATTTA
1 AAGTTCAAAATCTGCATATAATATCAAAACTCA
*
2552 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATAATATCAAAACTCA
2585 AAGTTCAAAATC
1 AAGTTCAAAATC
2597 CACAGTTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATAATATCAAAACTCA
Found at i:2720 original size:7 final size:7
Alignment explanation
Indices: 2708--2741 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2698 CATTGCTCAG
2708 AATTCAA
1 AATTCAA
2715 AATTCAA
1 AATTCAA
2722 AATTCAA
1 AATTCAA
*
2729 AATTCAG
1 AATTCAA
2736 AATTCA
1 AATTCA
2742 GAACTCAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (7 bp):
AATTCAA
Found at i:2874 original size:7 final size:7
Alignment explanation
Indices: 2732--2870 Score: 233
Period size: 7 Copynumber: 19.9 Consensus size: 7
2722 AATTCAAAAT
*
2732 TCAGAAT
1 TCAGAAC
2739 TCAGAAC
1 TCAGAAC
2746 TCAGAAC
1 TCAGAAC
2753 TCAGAAC
1 TCAGAAC
2760 TCAGAAC
1 TCAGAAC
2767 TCAGAAC
1 TCAGAAC
*
2774 TCATAAC
1 TCAGAAC
2781 TCAGAAC
1 TCAGAAC
*
2788 TCATAAC
1 TCAGAAC
*
2795 TCATAAC
1 TCAGAAC
2802 TCAGAAC
1 TCAGAAC
2809 TCAGAAC
1 TCAGAAC
2816 TCAGAAC
1 TCAGAAC
2823 TCAGAAC
1 TCAGAAC
2830 TCAGAAC
1 TCAGAAC
2837 TCAGAAC
1 TCAGAAC
2844 TCAGAAC
1 TCAGAAC
2851 TCAGAAC
1 TCAGAAC
*
2858 TCAGAAT
1 TCAGAAC
2865 TCAGAA
1 TCAGAA
2871 TTCAAAATTC
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 126 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (7 bp):
TCAGAAC
Found at i:2879 original size:7 final size:7
Alignment explanation
Indices: 2862--2895 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2852 CAGAACTCAG
*
2862 AATTCAG
1 AATTCAA
2869 AATTCAA
1 AATTCAA
2876 AATTCAA
1 AATTCAA
2883 AATTCAA
1 AATTCAA
2890 AATTCA
1 AATTCA
2896 TGGCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (7 bp):
AATTCAA
Found at i:2978 original size:7 final size:7
Alignment explanation
Indices: 2944--2976 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2934 TTTCATTCTC
2944 CAAAAGT
1 CAAAAGT
2951 CAAAAGT
1 CAAAAGT
2958 CAAAAGT
1 CAAAAGT
*
2965 CAAAATT
1 CAAAAGT
2972 CAAAA
1 CAAAA
2977 TTTGCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (7 bp):
CAAAAGT
Done.