Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023184.1 Corchorus olitorius cultivar O-4 contig23217, 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: 26248
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:607 original size:20 final size:20
Alignment explanation
Indices: 582--620 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
572 AAAGACTCGG
582 CTAGGTGAAAGAGAGAGAGT
1 CTAGGTGAAAGAGAGAGAGT
602 CTAGGTGAAAGAGAGAGAG
1 CTAGGTGAAAGAGAGAGAG
621 AGCCTGCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.13
Consensus pattern (20 bp):
CTAGGTGAAAGAGAGAGAGT
Found at i:2373 original size:8 final size:8
Alignment explanation
Indices: 2360--2392 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2350 TAATAGCTTC
2360 AAAAAAAT
1 AAAAAAAT
2368 -AAAAAAT
1 AAAAAAAT
2375 AAAAAAAT
1 AAAAAAAT
2383 AAAAAGAAT
1 AAAAA-AAT
2392 A
1 A
2393 CCTGAGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 12 0.52
9 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3075 original size:41 final size:41
Alignment explanation
Indices: 3012--3137 Score: 173
Period size: 41 Copynumber: 3.1 Consensus size: 41
3002 TTCAATATGA
3012 TCCCTAATTTAGGA-TTCTATTTACTATTTGATACAATTTAG
1 TCCCTAATTTAGGATTTC-ATTTACTATTTGATACAATTTAG
* *
3053 TCCCTAATTTAGTATTTCATTTATTATTTGATACAATTTAG
1 TCCCTAATTTAGGATTTCATTTACTATTTGATACAATTTAG
* * * * *
3094 TCCCTGATTTAGGATTTTAGTTACTATTTGATCCAATTTGG
1 TCCCTAATTTAGGATTTCATTTACTATTTGATACAATTTAG
3135 TCC
1 TCC
3138 TTATTTTTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
41 72 0.96
42 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (41 bp):
TCCCTAATTTAGGATTTCATTTACTATTTGATACAATTTAG
Found at i:5195 original size:19 final size:20
Alignment explanation
Indices: 5171--5213 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5161 AAATGATACA
5171 CAAGGA-AAACAATTCAAT-T
1 CAAGGAGAAACAA-TCAATCT
5190 CAAGGAGTAAACAATCAATCT
1 CAAGGAG-AAACAATCAATCT
5211 CAA
1 CAA
5214 TATGCATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 10 0.48
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (20 bp):
CAAGGAGAAACAATCAATCT
Found at i:11958 original size:20 final size:20
Alignment explanation
Indices: 11933--12009 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
11923 AACTACCCAT
11933 AAAGCCCAAATGCATAAATA
1 AAAGCCCAAATGCATAAATA
* *
11953 AAAGCCTAAAT-CCTAAAATA
1 AAAGCCCAAATGCAT-AAATA
11973 AAA-CCC-AA-GACATAAATA
1 AAAGCCCAAATG-CATAAATA
* *
11991 AAAGGTCCAAATACATAAA
1 AAA-GCCCAAATGCATAAA
12010 AGAATAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
18 10 0.23
19 6 0.14
20 20 0.45
21 8 0.18
ACGTcount: A:0.57, C:0.19, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAGCCCAAATGCATAAATA
Found at i:14131 original size:22 final size:22
Alignment explanation
Indices: 14103--14152 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
14093 AAAAGGATGG
14103 ATGCAAAAGATACCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
* *
14125 ATGCAAAAGGTGCCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
14147 ATGCAA
1 ATGCAA
14153 CTATTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
ATGCAAAAGATACCATGCAAAA
Found at i:14543 original size:28 final size:28
Alignment explanation
Indices: 14511--14611 Score: 148
Period size: 28 Copynumber: 3.6 Consensus size: 28
14501 GCACTTGAAG
* *
14511 TGACCAAAATGCCCCTAGATGTGTAAAA
1 TGACCAAAATGCCCCTAGATATGCAAAA
* *
14539 TGACCAAAATGCCCTTGGATATGCAAAA
1 TGACCAAAATGCCCCTAGATATGCAAAA
*
14567 TGACCAAAATGCCCCTGGATATGCAAAA
1 TGACCAAAATGCCCCTAGATATGCAAAA
*
14595 TGACCAAAATCCCCCTA
1 TGACCAAAATGCCCCTA
14612 AATGACCTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.20
Consensus pattern (28 bp):
TGACCAAAATGCCCCTAGATATGCAAAA
Found at i:15015 original size:102 final size:102
Alignment explanation
Indices: 14882--15447 Score: 943
Period size: 102 Copynumber: 5.5 Consensus size: 102
14872 AATCTAATAT
* * *
14882 TAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTACCAGTTCAATCTTAAAAGGATCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
*
14947 CCGCTTATCCTTTGAACTGTCTACCAAGTCAATTCTA
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
* *
14984 TAAAAGGACCATCTTCCGCTTATCCTTTGAACTGTTTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
*
15049 CCGCTTATCATTTGAACTGTCTACCAATTCAATTCTA
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
* *
15086 TAAAAGGACCGTATTCAGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
** *
15151 CTACTTATCCTTTGAACTGTCTACCAAGTCAATTCTA
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
* *
15188 TAAAAGGACCATCTTCCGCTTATCCTTTGAACTGTTTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
*
15253 CCGCTTATCATTTGAACTGTCTACCAATTCAATTCTA
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
* *
15290 TAAAAGGACCGTATTCAGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
**
15355 CTACTTATCCTTTGAACTGTCTACCAATTCAATTCTA
66 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
*
15392 TAAAAGGACCGTCTTCTGCTTATCCTTTGAACTGTCTACCAATTCAATCTTGAAAA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-AAAA
15448 AAGGTAATGC
Statistics
Matches: 431, Mismatches: 32, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
102 427 0.99
103 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (102 bp):
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
Found at i:15566 original size:50 final size:50
Alignment explanation
Indices: 15503--15690 Score: 358
Period size: 50 Copynumber: 3.8 Consensus size: 50
15493 AGGTTTGAAA
* *
15503 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
15553 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
15603 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
15653 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
15691 AAAACATTCG
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 136 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
Found at i:17799 original size:12 final size:12
Alignment explanation
Indices: 17782--17813 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17772 ATTCACTCTG
*
17782 GATTTGAACTTT
1 GATTTGAACTAT
17794 GATTTGAACTAT
1 GATTTGAACTAT
17806 GATTTGAA
1 GATTTGAA
17814 TTACTTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (12 bp):
GATTTGAACTAT
Found at i:18118 original size:12 final size:12
Alignment explanation
Indices: 18101--18137 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 12
18091 TTGAAAACCC
18101 AAAACCTTTTTG
1 AAAACCTTTTTG
18113 AAAACCTATTTTTG
1 AAAACC--TTTTTG
18127 AAAACCTTTTT
1 AAAACCTTTTT
18138 CTTGAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (12 bp):
AAAACCTTTTTG
Found at i:18126 original size:14 final size:14
Alignment explanation
Indices: 18107--18146 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
18097 ACCCAAAACC
18107 TTTTTGAAAACCTA
1 TTTTTGAAAACCTA
*
18121 TTTTTGAAAACCTT
1 TTTTTGAAAACCTA
18135 TTTCTTGAAAAC
1 TTT-TTGAAAAC
18147 AATTTTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACCTA
Found at i:18142 original size:15 final size:15
Alignment explanation
Indices: 18110--18160 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
18100 CAAAACCTTT
*
18110 TTGAAAACCTATTT-
1 TTGAAAACCTTTTTC
18124 TTGAAAACCTTTTTC
1 TTGAAAACCTTTTTC
**
18139 TTGAAAACAATTTTC
1 TTGAAAACCTTTTTC
18154 TTGAAAA
1 TTGAAAA
18161 ACGTCTCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (15 bp):
TTGAAAACCTTTTTC
Found at i:21827 original size:20 final size:20
Alignment explanation
Indices: 21802--21878 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
21792 TTATACCAAT
21802 AAAGCCCAAATGCATAAATA
1 AAAGCCCAAATGCATAAATA
* *
21822 AAAGCCTAAAT-CCTAAAATA
1 AAAGCCCAAATGCAT-AAATA
21842 AAA-CCC-AA-GACATAAATA
1 AAAGCCCAAATG-CATAAATA
* *
21860 AAAGGTCCAAATACATAAA
1 AAA-GCCCAAATGCATAAA
21879 AGAATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
18 10 0.23
19 6 0.14
20 20 0.45
21 8 0.18
ACGTcount: A:0.57, C:0.19, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAGCCCAAATGCATAAATA
Found at i:26221 original size:11 final size:11
Alignment explanation
Indices: 26205--26229 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26195 GGGGAATAAT
26205 CAATCCAAAAA
1 CAATCCAAAAA
26216 CAATCCAAAAA
1 CAATCCAAAAA
26227 CAA
1 CAA
26230 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Done.