Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019193.1 Corchorus olitorius cultivar O-4 contig19226, 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: 25694
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1442 original size:18 final size:18
Alignment explanation
Indices: 1419--1453 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1409 GGCCTGCATA
1419 TATAAGCTTGTTAATTAG
1 TATAAGCTTGTTAATTAG
1437 TATAAGCTTGTTAATTA
1 TATAAGCTTGTTAATTA
1454 CAGTTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (18 bp):
TATAAGCTTGTTAATTAG
Found at i:5774 original size:438 final size:440
Alignment explanation
Indices: 4908--5922 Score: 1232
Period size: 438 Copynumber: 2.3 Consensus size: 440
4898 GTATTTTCTT
* * *
4908 TTCTATTTGTCTGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTACAATTTT
1 TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
* * * * * *
4973 CAT-CAGGAACTCAAAAACCAATTTTAATGTTTTGATTCTAAAAAATGCTTCCGAAATTTTGTGA
66 CATAAAGG-ACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGTGA
* * * * * *
5037 TTTTGATTACCGGTCAATTTAATATCGTCTAATTTTTTGTCCACATGTCCGATTGAAGTTATTGA
130 TTTCGATTACCGGTCAATTTAATACCATATAATTTTTCGTCCACATGTCCGATTAAAGTTATTGA
* * * *
5102 AGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGATCCAAAAGTTAAATTTGA
195 AGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCAAAAGTTAAATTTGA
*
5167 TCTACAAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATCTCTATTAACAAACAT
260 TCTACAAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCTATTAACAAACAT
* * * *
5232 TTTCTTATTTGGATTATTTATCAAATGACTCTCATATTTTTCTACTTTATACCACTTAGTCCTTT
325 TTTCTTATTTGAATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACCACTTAGTCATTT
* * *
5297 ACAGATTCTATCTTAATCTAACGTTTAAGATTTA-TTTTTTT-A-TTATTTG
390 ACAAATTCTATCTTAATCT-ACGTTTAACATTCATTTTTTTTCATTTATTTG
* * *
5346 TTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGTTAATTTCATGATCTACAACTTT
1 TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
* *
5411 CATAAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATGCTTCCTAAATTTGGTCG-
66 CATAAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGT-GA
** * *
5475 TTTCGATTATTGGTCTATTTAATACCATATAA-TTTTCGTACCACATGTCCGATTAAAGTTATTT
130 TTTCGATTACCGGTCAATTTAATACCATATAATTTTTCGT-CCACATGTCCGATTAAAGTTATTG
* * *
5539 AAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAGAACCCCAAAGTT-AATTTG
194 AAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCAAAAGTTAAATTTG
* * * * * *
5603 ATCTGCGAGTTTCATGAAA-GGTTCAAAGGGGAATTTTTATGTTTCAAGATATCTATTAAGAAAT
259 ATCTACAAGTTTCAT-AAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCTATTAACAAAC
* * *
5667 ATTTTCTTATTTGAATTATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATGCTACTTAGT
323 ATTTTCTTATTTGAATTA-T--TTATCAAATGACCCTCATACTTTTCTACTTTATACCACTTAGT
*
5732 CATTTACAAATTCTATCTT-AT-T-CGATTTAACACTTCATTTTTTTTTCATTTTCTTTG
385 CATTTACAAATTCTATCTTAATCTACG-TTTAACA-TTCA-TTTTTTTTCA-TTTATTTG
* * * * * *
5789 TTTTATTTTTCCAATTAAGGTAAATCAAGTG--TATTAAAAGGTAATTTTATGATCTACAACTTT
1 TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
* * * * * * * *
5852 TATGAAA-AACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAAAA-ACTTCTGAAATTTTGTG
66 CAT-AAAGGACTCAAAAGCAAATTTTAATGTTTTAATTC-AAAAAAATGCTTCCGAAATTTGGTG
5915 ATTTCGAT
129 ATTTCGAT
5923 CGACAATCTA
Statistics
Matches: 493, Mismatches: 67, Indels: 31
0.83 0.11 0.05
Matches are distributed among these distances:
436 2 0.00
437 88 0.18
438 215 0.44
439 6 0.01
440 63 0.13
441 79 0.16
442 10 0.02
443 30 0.06
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (440 bp):
TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
CATAAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCCGAAATTTGGTGAT
TTCGATTACCGGTCAATTTAATACCATATAATTTTTCGTCCACATGTCCGATTAAAGTTATTGAA
GTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCAAAAGTTAAATTTGAT
CTACAAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCTATTAACAAACATT
TTCTTATTTGAATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACCACTTAGTCATTTA
CAAATTCTATCTTAATCTACGTTTAACATTCATTTTTTTTCATTTATTTG
Found at i:8858 original size:53 final size:53
Alignment explanation
Indices: 8796--9061 Score: 247
Period size: 53 Copynumber: 5.1 Consensus size: 53
8786 TCTTTAAATC
* *
8796 CAATAGTTCATTGCATTTTGTATTATTTGGGATGTGTGCTTAATTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
8849 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
* ** *** *** * * ** * * * * ** *
8902 CAATTGAATAAACAACACAAT-TAATA-ATAATA-ATAT-ATAATAGAATTA--TC
1 CAA-T-AGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAA-TAGGTT
* *
8952 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGTTTATTTAATAAGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
9005 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
9058 CAAT
1 CAAT
9062 TGAATAAACA
Statistics
Matches: 160, Mismatches: 44, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
48 6 0.04
49 5 0.03
50 7 0.04
51 9 0.06
52 9 0.06
53 113 0.71
54 5 0.03
55 6 0.04
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:9077 original size:156 final size:156
Alignment explanation
Indices: 8793--9106 Score: 583
Period size: 156 Copynumber: 2.0 Consensus size: 156
8783 ATTTCTTTAA
*
8793 ATCCAATAGTTCATTGCATTTTGTATTATTTGGGATGTGTGCTTAATTAATAGGTTCAATAGTTC
1 ATCCAATAGTTCATTGCATTTTGTATTATTTGGGATGTGTGCTTAATTAATAAGTTCAATAGTTC
8858 ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTTCAATTGAATAAACAACACAAT
66 ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTTCAATTGAATAAACAACACAAT
8923 TAATAATAATAATATATAATAGAATT
131 TAATAATAATAATATATAATAGAATT
* * *
8949 ATCCAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGTTTATTTAATAAGTTCAATAGTTC
1 ATCCAATAGTTCATTGCATTTTGTATTATTTGGGATGTGTGCTTAATTAATAAGTTCAATAGTTC
9014 ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTTCAATTGAATAAACAACACAAT
66 ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTTCAATTGAATAAACAACACAAT
*
9079 TAATAATAATATTATATAATAGAATT
131 TAATAATAATAATATATAATAGAATT
9105 AT
1 AT
9107 TATTTTATAA
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (156 bp):
ATCCAATAGTTCATTGCATTTTGTATTATTTGGGATGTGTGCTTAATTAATAAGTTCAATAGTTC
ATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTTCAATTGAATAAACAACACAAT
TAATAATAATAATATATAATAGAATT
Found at i:9277 original size:16 final size:16
Alignment explanation
Indices: 9253--9296 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9243 TAATAGTAGG
9253 TATATATAAT-AT-A-
1 TATATATAATAATAAT
9266 TATATATAATAATAAT
1 TATATATAATAATAAT
*
9282 TATATATAAAAATAA
1 TATATATAATAATAA
9297 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 1 0.04
16 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATAATAATAAT
Found at i:9296 original size:22 final size:22
Alignment explanation
Indices: 9261--9302 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9251 GGTATATATA
* * *
9261 ATATATATATATAATAATAATT
1 ATATATAAAAATAAAAATAATT
9283 ATATATAAAAATAAAAATAA
1 ATATATAAAAATAAAAATAA
9303 AAAATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATATAAAAATAAAAATAATT
Found at i:17324 original size:17 final size:19
Alignment explanation
Indices: 17291--17325 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
17281 TGTAATTAAA
17291 AAATGTTGAAGTTAGTTTT
1 AAATGTTGAAGTTAGTTTT
17310 AAATGTT-AA-TTAGTTT
1 AAATGTTGAAGTTAGTTT
17326 CCCTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (19 bp):
AAATGTTGAAGTTAGTTTT
Found at i:20740 original size:30 final size:29
Alignment explanation
Indices: 20686--20763 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
20676 CTGATATAAG
*
20686 AGACGTGCATGGGAACCCCATTCAACTGAC
1 AGACGAGCATGGGAA-CCCATTCAACTGAC
*
20716 AGACGAGCATGGGAACCCAGTTCAATTGAC
1 AGACGAGCATGGGAACCCA-TTCAACTGAC
* * * *
20746 CGATGAACATGGCAACCC
1 AGACGAGCATGGGAACCC
20764 TGTTTATGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.15
Consensus pattern (29 bp):
AGACGAGCATGGGAACCCATTCAACTGAC
Done.