Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010764.1 Corchorus olitorius cultivar O-4 contig10796, 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: 51481
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:37 original size:5 final size:5
Alignment explanation
Indices: 29--73 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
19 AGAAAGAAAT
29 TAAAA TAAAA T--AA TAATAA TAATAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAA-AA TAA-AA TAAAA TAAAA TAAAA TAAAA
74 AGAATGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
5 23 0.62
6 11 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:45 original size:3 final size:3
Alignment explanation
Indices: 32--71 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
22 AAGAAATTAA
32 AAT AA- AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
72 AAAGAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.24
3 25 0.76
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:1286 original size:24 final size:23
Alignment explanation
Indices: 1259--1314 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
1249 CTCGTTGAGG
*
1259 AAATGTTTTATAACTGCTTTATAT
1 AAATGTTTTATAAATGCTTTA-AT
* *
1283 AAATGCTTTATAAATGTTTTAAT
1 AAATGTTTTATAAATGCTTTAAT
1306 AAATGTTTT
1 AAATGTTTT
1315 GGGTGCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (23 bp):
AAATGTTTTATAAATGCTTTAAT
Found at i:1289 original size:13 final size:12
Alignment explanation
Indices: 1259--1314 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
1249 CTCGTTGAGG
1259 AAATG-TTTTAT
1 AAATGCTTTTAT
*
1270 AACTGCTTTATAT
1 AAATGCTTT-TAT
1283 AAATGC-TTTAT
1 AAATGCTTTTAT
1294 AAATG-TTTTAAT
1 AAATGCTTTT-AT
1306 AAATG-TTTT
1 AAATGCTTTT
1315 GGGTGCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 15 0.38
12 16 0.41
13 8 0.21
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (12 bp):
AAATGCTTTTAT
Found at i:5809 original size:181 final size:184
Alignment explanation
Indices: 5480--5983 Score: 638
Period size: 184 Copynumber: 2.8 Consensus size: 184
5470 GTATTTTTAC
* * **
5480 AGTGTTATTATGAATATCACATTTATGAGATTCACAATTAAGAACAAAGTCTACGTTTGCACAAA
1 AGTGTTATTATGAATATCACCTTTATGAGATTCGCAATTAAGAACAAAGGATACGTTTGCACAAA
* * * * * * *
5545 CACAATTTATATCACAAGTGACGCTCACAGTCGTCTGCAATTTCAGAAATCAACGTTCAAACACC
66 CACAATCTATATCACAGGTGACGCTCACGGTCGCCTGCAATTTCAGAAATCAAGGTTCAGACACT
* ** * * * **
5610 CTATCATGTCTGGGTGTAATAAT-C-TAAAT-TTTTTTTTTCAATGTTTCTGAT
131 CTGTTGTGTCTCGGTGTAAAAATCCGAAAATCTCATTTTTTCAATGTTTCTGAT
* * * * *
5661 AGTTTTATTATGAATATCACCTTTACGAGATTCGTAATCAAGAACAAAGGATACATTTGCACAAA
1 AGTGTTATTATGAATATCACCTTTATGAGATTCGCAATTAAGAACAAAGGATACGTTTGCACAAA
*
5726 CACAATCTATATCACGGGTGACGCTCACGGTCGCCTGCAATTTCAGAAATCAAGGTTCAGACACT
66 CACAATCTATATCACAGGTGACGCTCACGGTCGCCTGCAATTTCAGAAATCAAGGTTCAGACACT
* *
5791 CTGTTGTGTGTCGGTGTAAAAATCCGAAAATCTCATTTTTTGAATGTTTCTGAT
131 CTGTTGTGTCTCGGTGTAAAAATCCGAAAATCTCATTTTTTCAATGTTTCTGAT
*
5845 AGTGTTATTATGAATATCACCTTTATTAGATTCGCAATTAAGAACAAAGGATACGTTT-CTACAA
1 AGTGTTATTATGAATATCACCTTTATGAGATTCGCAATTAAGAACAAAGGATACGTTTGC-ACAA
* * * * * ** * *
5909 ACACAATCTATATCACAGGCGATGATCACGGTCGCCCGTAATTTCAGAGGTCAGGGTTCAGACGC
65 ACACAATCTATATCACAGGTGACGCTCACGGTCGCCTGCAATTTCAGAAATCAAGGTTCAGACAC
5974 TCTGTTGTGT
130 TCTGTTGTGT
5984 TTGTATATAT
Statistics
Matches: 276, Mismatches: 43, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
181 130 0.47
182 1 0.00
183 5 0.02
184 140 0.51
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (184 bp):
AGTGTTATTATGAATATCACCTTTATGAGATTCGCAATTAAGAACAAAGGATACGTTTGCACAAA
CACAATCTATATCACAGGTGACGCTCACGGTCGCCTGCAATTTCAGAAATCAAGGTTCAGACACT
CTGTTGTGTCTCGGTGTAAAAATCCGAAAATCTCATTTTTTCAATGTTTCTGAT
Found at i:12283 original size:59 final size:58
Alignment explanation
Indices: 12194--12307 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 58
12184 TCATACGACC
12194 TAGTGGGCATCCCCACACGAGCAATAAGAACGATCGAGCATCCCTCGGTCGCACGGCT
1 TAGTGGGCATCCCCACACGAGCAATAAGAACGATCGAGCATCCCTCGGTCGCACGGCT
*
12252 TAGTGGGCATCCCCCACACGAGTAATAAGAACGATCGAGCATCCCTCGGTCGCACG
1 TAGTGGGCAT-CCCCACACGAGCAATAAGAACGATCGAGCATCCCTCGGTCGCACG
12308 ATACTCATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 10 0.19
59 44 0.81
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.16
Consensus pattern (58 bp):
TAGTGGGCATCCCCACACGAGCAATAAGAACGATCGAGCATCCCTCGGTCGCACGGCT
Found at i:12831 original size:18 final size:18
Alignment explanation
Indices: 12810--12847 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12800 CACATGACAA
*
12810 CATAAGAGCGCACGATGC
1 CATAAGAGCACACGATGC
12828 CATAAGAGCACACGATGC
1 CATAAGAGCACACGATGC
12846 CA
1 CA
12848 CGCTTTGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.29, G:0.24, T:0.11
Consensus pattern (18 bp):
CATAAGAGCACACGATGC
Found at i:14401 original size:16 final size:15
Alignment explanation
Indices: 14380--14409 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
14370 GTCCATTGTA
14380 ATTGTGCCAAAAAAAT
1 ATTGTG-CAAAAAAAT
14396 ATTGTGCAAAAAAA
1 ATTGTGCAAAAAAA
14410 AAAAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
ATTGTGCAAAAAAAT
Found at i:14410 original size:16 final size:16
Alignment explanation
Indices: 14380--14410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14370 GTCCATTGTA
*
14380 ATTGTGCCAAAAAAAT
1 ATTGTGCAAAAAAAAT
14396 ATTGTGCAAAAAAAA
1 ATTGTGCAAAAAAAA
14411 AAAAAAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (16 bp):
ATTGTGCAAAAAAAAT
Found at i:16167 original size:28 final size:28
Alignment explanation
Indices: 16127--16181 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
16117 CTAAGATTAA
*
16127 GGAAACAACATGGGGCACATATGCTTAG
1 GGAAACAACATGGGGAACATATGCTTAG
*
16155 GGAAAGAACATGGGGAACATATGCTTA
1 GGAAACAACATGGGGAACATATGCTTA
16182 ATTAATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (28 bp):
GGAAACAACATGGGGAACATATGCTTAG
Found at i:25691 original size:184 final size:183
Alignment explanation
Indices: 25368--25702 Score: 449
Period size: 184 Copynumber: 1.8 Consensus size: 183
25358 GTAATAATTT
* * *
25368 GAAAATCTCGTTTGTTCAATGTTTCTGACAATGTTATTATGAATATCACCTTTGTCAAATTCGCA
1 GAAAATCTCGTTTGTTCAATGTTTCTGACAATGTTATTATGAATATCAACTTTATCAAATTCACA
* * * * * *
25433 CTTAAGAATAAAGGATACGTTTGCACAAACACAATCTATATCAGAAGTGACGCTCACGGTCGCCT
66 ATTAAGAACAAAAGATACGTTTGCACAAACACAATCTATATCAGAAGCGACACTCACGATCGCCT
25498 GCAATTTTAGAAATCAGGGTTTAAATGCCATGTTACGTGTCAGTGTAAAAAATA
131 G-AATTTTAGAAATCAGGGTTTAAATGCCATGTTACGTGTCAGTGTAAAAAATA
* * * * *
25552 GAAAATCTCGTTTTTTGAATGTTTCTGACAGTGTTATTATGAATATCAACTTTATTAGATTCACA
1 GAAAATCTCGTTTGTTCAATGTTTCTGACAATGTTATTATGAATATCAACTTTATCAAATTCACA
* * * *
25617 ATTAAGAACAAAAGATACGTTTGCACAAACACCATCTATTTCATG-GGCGACACTCGCGATCGCC
66 ATTAAGAACAAAAGATACGTTTGCACAAACACAATCTATATCA-GAAGCGACACTCACGATCG-C
*
25681 CATG-ATTTTAGAAATTAGGGTT
129 C-TGAATTTTAGAAATCAGGGTT
25703 CAGATGCCCT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
184 124 0.96
185 3 0.02
186 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (183 bp):
GAAAATCTCGTTTGTTCAATGTTTCTGACAATGTTATTATGAATATCAACTTTATCAAATTCACA
ATTAAGAACAAAAGATACGTTTGCACAAACACAATCTATATCAGAAGCGACACTCACGATCGCCT
GAATTTTAGAAATCAGGGTTTAAATGCCATGTTACGTGTCAGTGTAAAAAATA
Found at i:28927 original size:11 final size:11
Alignment explanation
Indices: 28888--28921 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
28878 AATGATCAAA
28888 TAATTATAAAT
1 TAATTATAAAT
28899 TAATTATAAAT
1 TAATTATAAAT
28910 TAATTATAAAT
1 TAATTATAAAT
28921 T
1 T
28922 TGTTATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:39089 original size:8 final size:8
Alignment explanation
Indices: 39067--39100 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
39057 ACCTTTTCCA
39067 TCAAATTT
1 TCAAATTT
39075 CTCAAATTT
1 -TCAAATTT
39084 TCAAATTT
1 TCAAATTT
*
39092 TCAAGTTT
1 TCAAATTT
39100 T
1 T
39101 GGAGAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (8 bp):
TCAAATTT
Found at i:48415 original size:108 final size:109
Alignment explanation
Indices: 48220--48440 Score: 365
Period size: 108 Copynumber: 2.0 Consensus size: 109
48210 AAGAGGGAAT
* *
48220 TTAATAAACTACTCCGCTGTTTTTGGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCGCTATTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAAC
* *
48285 CTTCGCGTCAGTCACGAACCAAAATTATGAGTATGCAAAGCATC
66 CTTCGCGTCAGTCACGAACCAAAATTACGAGTATGCAAAGCACC
*
48329 TTAATAAACTACTCCTCTATTTTT-GGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAAC
1 TTAATAAACTACTCCGCTATTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAAC
*
48393 CTTCGCGTCAGTCAC-AACCCAAAATTACGAGTATGCAAGGCACC
66 CTTCGCGTCAGTCACGAA-CCAAAATTACGAGTATGCAAAGCACC
48437 TTAA
1 TTAA
48441 ATGCGTAAGT
Statistics
Matches: 105, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
107 2 0.02
108 81 0.77
109 22 0.21
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (109 bp):
TTAATAAACTACTCCGCTATTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAAC
CTTCGCGTCAGTCACGAACCAAAATTACGAGTATGCAAAGCACC
Found at i:49539 original size:20 final size:21
Alignment explanation
Indices: 49500--49541 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
49490 CCTCTCATGG
**
49500 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
49521 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
49541 A
1 A
49542 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Done.