Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009665.1 Corchorus olitorius cultivar O-4 contig09697, 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: 6095
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Found at i:993 original size:22 final size:22
Alignment explanation
Indices: 968--1015 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
958 GAAATTATAC
968 GGAGATTTACAAAATCTCACAG
1 GGAGATTTACAAAATCTCACAG
990 GGAGATTTACAAAATCTCACAG
1 GGAGATTTACAAAATCTCACAG
1012 GGAG
1 GGAG
1016 GTTATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (22 bp):
GGAGATTTACAAAATCTCACAG
Found at i:1024 original size:22 final size:22
Alignment explanation
Indices: 977--1089 Score: 88
Period size: 22 Copynumber: 5.2 Consensus size: 22
967 CGGAGATTTA
* *
977 CAAAATCTCACAGGGAGATT-T
1 CAAAATCTCACAGGAAGGTTAT
*
998 ACAAAATCTCACAGGGAGGTTAT
1 -CAAAATCTCACAGGAAGGTTAT
* *
1021 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATCTCACAGGAAGGTTAT
*
1041 CAAAATTTCACAGGAAGGTTTAT
1 CAAAATCTCACAGGAAGG-TTAT
* * * **
1064 TAAAATTTCATAGTTAGGTTAT
1 CAAAATCTCACAGGAAGGTTAT
1086 CAAA
1 CAAA
1090 GTTTCATATG
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.07
21 22 0.29
22 34 0.45
23 15 0.20
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (22 bp):
CAAAATCTCACAGGAAGGTTAT
Found at i:1082 original size:23 final size:22
Alignment explanation
Indices: 999--1119 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
989 GGGAGATTTA
* * *
999 CAAAATCTCACAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
1021 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
*
1041 CAAAATTTCACAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
1064 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
1086 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
*
1108 CACAATTTCATA
1 CAAAATTTCATA
1120 ATGTTGAGCA
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
20 5 0.06
21 22 0.28
22 38 0.47
23 15 0.19
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:2138 original size:76 final size:75
Alignment explanation
Indices: 2012--2248 Score: 314
Period size: 76 Copynumber: 3.1 Consensus size: 75
2002 CTCGTCTCCG
* * * *
2012 ACGGCTGAGTGTCTAGACTGGCGCCTCCGTTCAACTCTCAGTGAGGCTGAGCGCCCATGCAGACG
1 ACGGCTGAATGCCTAGACTGGCGCCCCCGTTCAACTCT-AGTGAGGCTGAGCGTCCATGCAGACG
2077 CCACTCGCTCA
65 CCACTCGCTCA
* *
2088 ACGGCTGAATGCCTAGACTGGCGCCCCCGTTCAACCCTATGTGAGGCTGAGCGTCCACGCAGACG
1 ACGGCTGAATGCCTAGACTGGCGCCCCCGTTCAACTCTA-GTGAGGCTGAGCGTCCATGCAGACG
2153 CCACTCGCTCA
65 CCACTCGCTCA
* * * *
2164 ACGGCTGAGTGCTTAGACTGGCGCCCCCGTTTC-ACTCTAAATGAGGCCGAGCGTCCATGCAGAC
1 ACGGCTGAATGCCTAGACTGGCGCCCCCG-TTCAACTCT-AGTGAGGCTGAGCGTCCATGCAGAC
**
2228 GCCACTCATTCA
64 GCCACTCGCTCA
*
2240 ACAGCTGAA
1 ACGGCTGAA
2249 CACCAAGGAT
Statistics
Matches: 142, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
75 1 0.01
76 137 0.96
77 4 0.03
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (75 bp):
ACGGCTGAATGCCTAGACTGGCGCCCCCGTTCAACTCTAGTGAGGCTGAGCGTCCATGCAGACGC
CACTCGCTCA
Found at i:2490 original size:102 final size:101
Alignment explanation
Indices: 2310--2581 Score: 427
Period size: 102 Copynumber: 2.7 Consensus size: 101
2300 AAAGAGTGGT
* * *
2310 CTCCGAGTTTAAGTTGCACGAGGACGTTCGTCTGGCCAAGAGACTCCCTCGTTGGGACGGAAGAA
1 CTCCGCGTTTAAGTTG-ACGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGGACGGAAGAA
* *
2375 CGCTAAGGGTGGATGTTCGTCTCACGAAGAGAATGTC
65 CGCTAAGGGTGGATGTTCATCTCACGAAGAGAATATC
*
2412 CTCCGCGTTTAAGTTGATCGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGTACGGAAGAA
1 CTCCGCGTTTAAGTTGA-CGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGGACGGAAGAA
* *
2477 CGCTAAGGTTGGATGTTCATCTCACTAAGAGAATATC
65 CGCTAAGGGTGGATGTTCATCTCACGAAGAGAATATC
* *
2514 ATCCGCGTTTAAGTTGACCGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGGACAGAAGAA
1 CTCCGCGTTTAAGTTGA-CGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGGACGGAAGAA
2579 CGC
65 CGC
2582 CAAGAGTAGC
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
101 1 0.01
102 156 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (101 bp):
CTCCGCGTTTAAGTTGACGAGGATGTTCGTCTCGCCAAGAGACTCCCTCGTTGGGACGGAAGAAC
GCTAAGGGTGGATGTTCATCTCACGAAGAGAATATC
Found at i:3554 original size:53 final size:52
Alignment explanation
Indices: 3472--3596 Score: 151
Period size: 53 Copynumber: 2.3 Consensus size: 52
3462 AGAACGATGG
** * *
3472 TCTCCCGTATGAAGAACGAGAGTTTGACATAATAACTTCATAAACACAGCCGA
1 TCTCCC-TATGAAGAACGAGAGTCCGACATAATAAATTCATAAACACAGACGA
* * *
3525 TCTCCCATATGAAGAACGAGAGTCCGACATGATAAATTCATAAGCACTGACGA
1 TCTCCC-TATGAAGAACGAGAGTCCGACATAATAAATTCATAAACACAGACGA
*
3578 TCTCCTCCATGAAGAACGA
1 TCTCC-CTATGAAGAACGA
3597 TGGTTTCCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 61 0.98
54 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (52 bp):
TCTCCCTATGAAGAACGAGAGTCCGACATAATAAATTCATAAACACAGACGA
Found at i:4431 original size:22 final size:22
Alignment explanation
Indices: 4406--4466 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
4396 CATAGGTAAA
*
4406 TTATCAAAATTTCATAA-CGTGG
1 TTATCAAAATTTCATAAGC-TAG
*
4428 TTATCAAAATTTAATAAGCTAG
1 TTATCAAAATTTCATAAGCTAG
4450 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
4467 AAATATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGCTAG
Found at i:4856 original size:18 final size:18
Alignment explanation
Indices: 4833--4916 Score: 65
Period size: 18 Copynumber: 5.0 Consensus size: 18
4823 ATCAGGCAGA
4833 AAACAGGACCAAAAGGTC
1 AAACAGGACCAAAAGGTC
**
4851 AAACAGGACCAAGGGGTC
1 AAACAGGACCAAAAGGTC
*
4869 AAAACAGG--C---A--TA
1 -AAACAGGACCAAAAGGTC
*
4881 AAACAGGACCGAAAGGTC
1 AAACAGGACCAAAAGGTC
*
4899 AAACAGGACCAAGAGGTC
1 AAACAGGACCAAAAGGTC
4917 GAATAAGCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
11 7 0.14
12 1 0.02
13 1 0.02
16 1 0.02
17 1 0.02
18 33 0.65
19 7 0.14
ACGTcount: A:0.46, C:0.21, G:0.26, T:0.06
Consensus pattern (18 bp):
AAACAGGACCAAAAGGTC
Found at i:4949 original size:47 final size:46
Alignment explanation
Indices: 4804--4995 Score: 221
Period size: 47 Copynumber: 4.1 Consensus size: 46
4794 AGCGCTAAAA
* *
4804 AAACAGGACCGAA-AGGTCAATCAGGCAGAAAACAGGACCAAAAGGTC
1 AAACAGGACC-AAGAGGTCAAT-AAGCAGAAAACAGGACCGAAAGGTC
* * *
4851 AAACAGGACCAAGGGGTCAAAACAGGCATAAAACAGGACCGAAAGGTC
1 AAACAGGACCAAGAGGTCAATA-A-GCAGAAAACAGGACCGAAAGGTC
*
4899 AAACAGGACCAAGAGGTCGAATAAGCAGAAAACAGGAGC-AAAGGGTC
1 AAACAGGACCAAGAGGTC-AATAAGCAGAAAACAGGACCGAAA-GGTC
*
4946 AAACAGGACCAAGAGGTCAA-ACAGGCAGAAAATAGGA-CGAAAGGTC
1 AAACAGGACCAAGAGGTCAATA-A-GCAGAAAACAGGACCGAAAGGTC
4992 AAAC
1 AAAC
4996 GGAGCAAACT
Statistics
Matches: 127, Mismatches: 10, Indels: 17
0.82 0.06 0.11
Matches are distributed among these distances:
45 1 0.01
46 18 0.14
47 66 0.52
48 39 0.31
49 3 0.02
ACGTcount: A:0.47, C:0.19, G:0.27, T:0.06
Consensus pattern (46 bp):
AAACAGGACCAAGAGGTCAATAAGCAGAAAACAGGACCGAAAGGTC
Found at i:4951 original size:18 final size:18
Alignment explanation
Indices: 4928--4970 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4918 AATAAGCAGA
4928 AAACAGGAGCAAAG-GGTC
1 AAACAGGA-CAAAGAGGTC
*
4946 AAACAGGACCAAGAGGTC
1 AAACAGGACAAAGAGGTC
4964 AAACAGG
1 AAACAGG
4971 CAGAAAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.47, C:0.19, G:0.30, T:0.05
Consensus pattern (18 bp):
AAACAGGACAAAGAGGTC
Found at i:5115 original size:13 final size:13
Alignment explanation
Indices: 5097--5122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5087 TACACTTGGA
5097 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
5110 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
5123 TAGATGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:5163 original size:29 final size:28
Alignment explanation
Indices: 5116--5194 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
5106 CAACGGTCAA
* *
5116 AGTCAACTAGATGATGTGGCAGATTAACCC
1 AGTCAAC-GGATGACGTGGCAGATTAA-CC
* * *
5146 AGTCAACGGATGACGTGGCAGGTTGACT
1 AGTCAACGGATGACGTGGCAGATTAACC
*
5174 GGTCAACGGATGACGTGGCAG
1 AGTCAACGGATGACGTGGCAG
5195 CATGATATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 21 0.49
29 15 0.35
30 7 0.16
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (28 bp):
AGTCAACGGATGACGTGGCAGATTAACC
Found at i:5261 original size:49 final size:49
Alignment explanation
Indices: 5175--5274 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
5165 AGGTTGACTG
* *
5175 GTCAACGGATGACGTGGCAGCATGATATGGCAGGTTGACTCGGTCAACA
1 GTCAACGGATGACGTGGCAGCATGACATGGCAGGTTGACTCAGTCAACA
* * * *
5224 GTCAATGGATGACGTGGCAGGATGACGTGGC-GTGTTGACTTAGTCAACA
1 GTCAACGGATGACGTGGCAGCATGACATGGCAG-GTTGACTCAGTCAACA
5273 GT
1 GT
5275 GATGATGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 43 0.98
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (49 bp):
GTCAACGGATGACGTGGCAGCATGACATGGCAGGTTGACTCAGTCAACA
Found at i:5262 original size:13 final size:13
Alignment explanation
Indices: 5230--5254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5220 AACAGTCAAT
5230 GGATGACGTGGCA
1 GGATGACGTGGCA
5243 GGATGACGTGGC
1 GGATGACGTGGC
5255 GTGTTGACTT
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:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
GGATGACGTGGCA
Done.