Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016304.1 Corchorus olitorius cultivar O-4 contig16337, 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: 25081
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:7679 original size:13 final size:13
Alignment explanation
Indices: 7661--7687 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7651 CAGCCGATCA
7661 ATTAAATTTTACC
1 ATTAAATTTTACC
7674 ATTAAATTTTACC
1 ATTAAATTTTACC
7687 A
1 A
7688 GTGTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTTTACC
Found at i:10415 original size:12 final size:12
Alignment explanation
Indices: 10398--10423 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10388 TCAATATTTT
10398 TACCACTTTAAG
1 TACCACTTTAAG
10410 TACCACTTTAAG
1 TACCACTTTAAG
10422 TA
1 TA
10424 ACAATTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (12 bp):
TACCACTTTAAG
Found at i:11013 original size:17 final size:16
Alignment explanation
Indices: 10991--11027 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
10981 CATTACAAGT
10991 GGCCAAAATCGGACTCA
1 GGCCAAAA-CGGACTCA
11008 GGCC--AACGGACTCA
1 GGCCAAAACGGACTCA
11022 GGCCAA
1 GGCCAA
11028 CGTTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.67
15 2 0.11
17 4 0.22
ACGTcount: A:0.32, C:0.32, G:0.27, T:0.08
Consensus pattern (16 bp):
GGCCAAAACGGACTCA
Found at i:11019 original size:14 final size:14
Alignment explanation
Indices: 11000--11029 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
10990 TGGCCAAAAT
11000 CGGACTCAGGCCAA
1 CGGACTCAGGCCAA
11014 CGGACTCAGGCCAA
1 CGGACTCAGGCCAA
11028 CG
1 CG
11030 TTGAAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.37, G:0.30, T:0.07
Consensus pattern (14 bp):
CGGACTCAGGCCAA
Found at i:11133 original size:14 final size:14
Alignment explanation
Indices: 11114--11143 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11104 ATTGAAATTA
11114 TTCAATATTACTTC
1 TTCAATATTACTTC
*
11128 TTCAATATTATTTC
1 TTCAATATTACTTC
11142 TT
1 TT
11144 TTGGTGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCAATATTACTTC
Found at i:13245 original size:18 final size:18
Alignment explanation
Indices: 13222--13308 Score: 96
Period size: 18 Copynumber: 5.2 Consensus size: 18
13212 TTTTTTGCAC
13222 CGGATGATGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
* *
13240 CGGATGATGTTTTTGCAA
1 CGGATGATGTTTCTGAAA
13258 CGG-T--TGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
* *
13273 CGGATGATGTTTTTGCAA
1 CGGATGATGTTTCTGAAA
13291 CGG-T--TGTTTCTGAAA
1 CGGATGATGTTTCTGAAA
13306 CGG
1 CGG
13309 TGCCAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
15 24 0.41
16 1 0.02
17 2 0.03
18 31 0.53
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.37
Consensus pattern (18 bp):
CGGATGATGTTTCTGAAA
Found at i:13269 original size:33 final size:33
Alignment explanation
Indices: 13229--13308 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
13219 CACCGGATGA
13229 TGTTTCTGAAACGGATGATGTTTTTGCAACGGT
1 TGTTTCTGAAACGGATGATGTTTTTGCAACGGT
13262 TGTTTCTGAAACGGATGATGTTTTTGCAACGGT
1 TGTTTCTGAAACGGATGATGTTTTTGCAACGGT
13295 TGTTTCTGAAACGG
1 TGTTTCTGAAACGG
13309 TGCCAATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (33 bp):
TGTTTCTGAAACGGATGATGTTTTTGCAACGGT
Found at i:13274 original size:15 final size:16
Alignment explanation
Indices: 13228--13309 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 16
13218 GCACCGGATG
13228 ATGTTTCTGAAACGGAT
1 ATGTTTCTGAAACGG-T
* *
13245 GATGTTTTTGCAACGGT
1 -ATGTTTCTGAAACGGT
13262 -TGTTTCTGAAACGGAT
1 ATGTTTCTGAAACGG-T
* *
13278 GATGTTTTTGCAACGGT
1 -ATGTTTCTGAAACGGT
13295 -TGTTTCTGAAACGGT
1 ATGTTTCTGAAACGGT
13310 GCCAATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
15 25 0.47
16 1 0.02
17 2 0.04
18 25 0.47
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (16 bp):
ATGTTTCTGAAACGGT
Found at i:15660 original size:440 final size:440
Alignment explanation
Indices: 14839--15720 Score: 1719
Period size: 440 Copynumber: 2.0 Consensus size: 440
14829 ATTGCACTTA
14839 TCAAATTCCCCCACACTTGGCTTTTTGCTTGTCCTCAAGTAAAACTAAAACAAAAATAAAATCCT
1 TCAAATTCCCCCACACTTGGCTTTTTGCTTGTCCTCAAGTAAAACTAAAACAAAAATAAAATCCT
14904 AAACTAAAGCAAGATATTAATTCCACTTTCGTAGGTGTACGACGGCAATTAGCACGTGACGCAAG
66 AAACTAAAGCAAGATATTAATTCCACTTTCGTAGGTGTACGACGGCAATTAGCACGTGACGCAAG
14969 CCTTTAAACCTTTAATCGAAGACATTAAAGGAGGAGTTATAGTCTCCTGAGGGTTTACTTAACTA
131 CCTTTAAACCTTTAATCGAAGACATTAAAGGAGGAGTTATAGTCTCCTGAGGGTTTACTTAACTA
*
15034 GAACGACACCCACAAACATTGCTACATATGAAAGTTAGTTCCAAAAACAATTTAAGAACAATTTT
196 GAACGACACCCACAAACATTGCTACATATGAAAGTTAATTCCAAAAACAATTTAAGAACAATTTT
*
15099 CAAAAATTCTTTTCTAGTAGGCCTCAAACTTTAAAGTGTTGGATACTTCTCAAAACAAATCATTA
261 CAAAAATTCTTTTCTAGTAGGCCTCAAACTTCAAAGTGTTGGATACTTCTCAAAACAAATCATTA
15164 TTTAACAAAGTAAAGCACAAATGGTTAGTTTATCATCCAAATCATTTGCCTCAAAAGAGCAATAG
326 TTTAACAAAGTAAAGCACAAATGGTTAGTTTATCATCCAAATCATTTGCCTCAAAAGAGCAATAG
15229 AAAACTATTGTAAAGAGCTACTTACCATAGGCTTGTATCTCATCTACATC
391 AAAACTATTGTAAAGAGCTACTTACCATAGGCTTGTATCTCATCTACATC
15279 TCAAATTCCCCCACACTTGGCTTTTTGCTTGTCCTCAAGTAAAACTAAAACAAAAATAAAATCCT
1 TCAAATTCCCCCACACTTGGCTTTTTGCTTGTCCTCAAGTAAAACTAAAACAAAAATAAAATCCT
*
15344 AAACTAAAGCAAGATATTAATTCCACTTTCGTAGGTGTACGACGGCACTTAGCACGTGACGCAAG
66 AAACTAAAGCAAGATATTAATTCCACTTTCGTAGGTGTACGACGGCAATTAGCACGTGACGCAAG
15409 CCTTTAAACCTTTAATCGAAGACATTAAAGGAGGAGTTATAGTCTCCTGAGGGTTTACTTAACTA
131 CCTTTAAACCTTTAATCGAAGACATTAAAGGAGGAGTTATAGTCTCCTGAGGGTTTACTTAACTA
*
15474 GAACGACACCCACAAACATTTCTACATATGAAAGTTAATTCCAAAAACAATTTAAGAACAATTTT
196 GAACGACACCCACAAACATTGCTACATATGAAAGTTAATTCCAAAAACAATTTAAGAACAATTTT
15539 CAAAAATTCTTTTCTAGTAGGCCTCAAACTTCAAAGTGTTGGATACTTCTCAAAACAAATCATTA
261 CAAAAATTCTTTTCTAGTAGGCCTCAAACTTCAAAGTGTTGGATACTTCTCAAAACAAATCATTA
15604 TTTAACAAAGTAAAGCACAAATGGTTAGTTTATCATCCAAATCATTTGCCTCAAAAGAGCAATAG
326 TTTAACAAAGTAAAGCACAAATGGTTAGTTTATCATCCAAATCATTTGCCTCAAAAGAGCAATAG
*
15669 AAAATTATTGTAAAGAGCTACTTACCATAGGCTTGTATCTCATCTACATC
391 AAAACTATTGTAAAGAGCTACTTACCATAGGCTTGTATCTCATCTACATC
15719 TC
1 TC
15721 CACTACAACC
Statistics
Matches: 437, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
440 437 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (440 bp):
TCAAATTCCCCCACACTTGGCTTTTTGCTTGTCCTCAAGTAAAACTAAAACAAAAATAAAATCCT
AAACTAAAGCAAGATATTAATTCCACTTTCGTAGGTGTACGACGGCAATTAGCACGTGACGCAAG
CCTTTAAACCTTTAATCGAAGACATTAAAGGAGGAGTTATAGTCTCCTGAGGGTTTACTTAACTA
GAACGACACCCACAAACATTGCTACATATGAAAGTTAATTCCAAAAACAATTTAAGAACAATTTT
CAAAAATTCTTTTCTAGTAGGCCTCAAACTTCAAAGTGTTGGATACTTCTCAAAACAAATCATTA
TTTAACAAAGTAAAGCACAAATGGTTAGTTTATCATCCAAATCATTTGCCTCAAAAGAGCAATAG
AAAACTATTGTAAAGAGCTACTTACCATAGGCTTGTATCTCATCTACATC
Done.