Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021689.1 Corchorus olitorius cultivar O-4 contig21722, 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: 52403
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1050 original size:14 final size:15
Alignment explanation
Indices: 1026--1057 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1016 ATAAAAGCCC
1026 AAATGAAAGGGAGCT
1 AAATGAAAGGGAGCT
1041 AAAT-AAAGGGAGCT
1 AAATGAAAGGGAGCT
1055 AAA
1 AAA
1058 GACCCAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.12
Consensus pattern (15 bp):
AAATGAAAGGGAGCT
Found at i:1065 original size:90 final size:90
Alignment explanation
Indices: 964--1133 Score: 331
Period size: 90 Copynumber: 1.9 Consensus size: 90
954 AAATCATAAA
964 TAAAGACCCAATAGTAAATAGAAGCCCAAACCTAGATGAAAAAAATAAATAAATAAAAGCCCAAA
1 TAAAGACCCAATAGTAAATAGAAGCCCAAACCTAGATGAAAAAAATAAATAAATAAAAGCCCAAA
1029 TGAAAGGGAGCTAAATAAAGGGAGC
66 TGAAAGGGAGCTAAATAAAGGGAGC
*
1054 TAAAGACCCAATAGTAAATAGAAGCCCAAACCTAGATGAAATAAATAAATAAATAAAAGCCCAAA
1 TAAAGACCCAATAGTAAATAGAAGCCCAAACCTAGATGAAAAAAATAAATAAATAAAAGCCCAAA
1119 TGAAAGGGAGCTAAA
66 TGAAAGGGAGCTAAA
1134 GGCCCAGAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.55, C:0.15, G:0.16, T:0.14
Consensus pattern (90 bp):
TAAAGACCCAATAGTAAATAGAAGCCCAAACCTAGATGAAAAAAATAAATAAATAAAAGCCCAAA
TGAAAGGGAGCTAAATAAAGGGAGC
Found at i:4765 original size:22 final size:22
Alignment explanation
Indices: 4697--4778 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
4687 TTTATGGAGT
* *
4697 TTATCACAATTTTAT-AGGTAA
1 TTATCAAAATTTTATAAGATAA
* * **
4718 TTATCAAAATTTCATATGATGG
1 TTATCAAAATTTTATAAGATAA
*
4740 TTATCAAAATTTAATAAGATAA
1 TTATCAAAATTTTATAAGATAA
*
4762 TTATTAAAATTTTATAA
1 TTATCAAAATTTTATAA
4779 AAATATTCAA
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
21 13 0.27
22 35 0.73
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGATAA
Found at i:5469 original size:3 final size:3
Alignment explanation
Indices: 5461--5503 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
5451 TGGTGCCGCG
* *
5461 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGA GGA GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
5504 CACGTGGCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.05, C:0.00, G:0.67, T:0.28
Consensus pattern (3 bp):
GGT
Found at i:16225 original size:20 final size:20
Alignment explanation
Indices: 16202--16242 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16192 CAAGGATAAC
*
16202 GGTTTGGAGTCAAGAATTGG
1 GGTTCGGAGTCAAGAATTGG
*
16222 GGTTCGGAGTTAAGAATTGG
1 GGTTCGGAGTCAAGAATTGG
16242 G
1 G
16243 ATGTCATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.41, T:0.29
Consensus pattern (20 bp):
GGTTCGGAGTCAAGAATTGG
Found at i:17089 original size:2 final size:2
Alignment explanation
Indices: 17082--17114 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17072 AGGATTTAAC
*
17082 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17115 CTAGTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17757 original size:23 final size:25
Alignment explanation
Indices: 17696--17757 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
17686 GTGGATTGTA
* * *
17696 AAATAAATTGAATATTTAAGACATT
1 AAATAAATTCAAGAATTAAGACATT
*
17721 AAATAAATTTAAGAATTAA-ACATT
1 AAATAAATTCAAGAATTAAGACATT
17745 AAA-AAATTCAAGA
1 AAATAAATTCAAGA
17758 CTGACCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 9 0.27
24 8 0.24
25 16 0.48
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAAATTCAAGAATTAAGACATT
Found at i:22152 original size:6 final size:6
Alignment explanation
Indices: 22142--22178 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
22132 GATCGTCCCT
*
22142 GGCAGT GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA G
1 GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA G
22179 ATGACATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.51, T:0.03
Consensus pattern (6 bp):
GGCAGA
Found at i:35425 original size:60 final size:60
Alignment explanation
Indices: 35272--35466 Score: 234
Period size: 60 Copynumber: 3.3 Consensus size: 60
35262 GCAAAACATG
* * * * *
35272 GCAAAA-CTGACCCTTTGACCGGAAGGGTACTT-TTGGAAAGTGAAAAATTAAACTTGATAT
1 GCAAAAGCTGACCCTTCGACCGGAAGGGTA-TTACTGGAAAGT-AAAAGTTGAACTTGAAAT
* * *
35332 GCAAAGGCTGACCCTTCAACCGGAAGGGTATTACTGGAAAGTAAAAGTTGAACTCGAAAT
1 GCAAAAGCTGACCCTTCGACCGGAAGGGTATTACTGGAAAGTAAAAGTTGAACTTGAAAT
* * * *
35392 GTAAAAGCTGACCCTTCGACCGGAAGCGCATTACTGGAAAGTGAAAGTTG-ACTTGAAAT
1 GCAAAAGCTGACCCTTCGACCGGAAGGGTATTACTGGAAAGTAAAAGTTGAACTTGAAAT
*
35451 GCAAAGGCTGACCCTT
1 GCAAAAGCTGACCCTT
35467 TGACTGAAAT
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
59 22 0.19
60 65 0.56
61 29 0.25
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (60 bp):
GCAAAAGCTGACCCTTCGACCGGAAGGGTATTACTGGAAAGTAAAAGTTGAACTTGAAAT
Found at i:48393 original size:118 final size:118
Alignment explanation
Indices: 48181--48413 Score: 405
Period size: 118 Copynumber: 2.0 Consensus size: 118
48171 TATGCGACTA
* *
48181 GGAGATGCTTTATGGGCATATCGAACATCTTATAAGACACCCTTGGTATGTCCCCATATGAGATT
1 GGAGATGCTTTATGGGCATATCGAACAGCCTATAAGACACCCTTGGTATGTCCCCATATGAGATT
*
48246 GTGTTTGGAAAACCATGCCATTTACCTGTGCAGATAGAACACAAAGCTTGTTT
66 GTGTTTGGAAAACCATGCCATTTAACTGTGCAGATAGAACACAAAGCTTGTTT
*
48299 GGAGATGCTTTATGGGCATATCGAACAGCCTATAAGACACCCCTTGGTATGTCCCCATAT-AGGT
1 GGAGATGCTTTATGGGCATATCGAACAGCCTATAAGACA-CCCTTGGTATGTCCCCATATGAGAT
*
48363 TGTGTTTGGAAAACCATGCCATTTAACTGTGGAGATAGAACACAAAGCTTG
65 TGTGTTTGGAAAACCATGCCATTTAACTGTGCAGATAGAACACAAAGCTTG
48414 GTGGACAGTG
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 89 0.82
119 20 0.18
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (118 bp):
GGAGATGCTTTATGGGCATATCGAACAGCCTATAAGACACCCTTGGTATGTCCCCATATGAGATT
GTGTTTGGAAAACCATGCCATTTAACTGTGCAGATAGAACACAAAGCTTGTTT
Done.