Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012332.1 Corchorus olitorius cultivar O-4 contig12365, 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: 30590
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2771 original size:22 final size:21
Alignment explanation
Indices: 2746--2793 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2736 ATGGAAACAG
* *
2746 AAAAACAGAATCAAGGATGTCT
1 AAAAACAGAAAC-AGAATGTCT
*
2768 AAAAACATAAACAGAATGTCT
1 AAAAACAGAAACAGAATGTCT
2789 AAAAA
1 AAAAA
2794 TAGTTTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAAACAGAAACAGAATGTCT
Found at i:4221 original size:18 final size:18
Alignment explanation
Indices: 4198--4232 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4188 CTTACCGTCA
4198 TCGAGAAAGGAGAGAAAG
1 TCGAGAAAGGAGAGAAAG
* *
4216 TCGAGAGATGAGAGAAA
1 TCGAGAAAGGAGAGAAA
4233 AAGAAAAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.37, T:0.09
Consensus pattern (18 bp):
TCGAGAAAGGAGAGAAAG
Found at i:4329 original size:16 final size:16
Alignment explanation
Indices: 4310--4340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4300 TGAATTATAA
*
4310 ATTTATATATTTAATT
1 ATTTATATATATAATT
4326 ATTTATATATATAAT
1 ATTTATATATATAAT
4341 AAAACTAAAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATATATAATT
Found at i:6216 original size:12 final size:12
Alignment explanation
Indices: 6199--6223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6189 CAACAAATTA
6199 AAATACATATTT
1 AAATACATATTT
6211 AAATACATATTT
1 AAATACATATTT
6223 A
1 A
6224 GTAAATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATACATATTT
Found at i:8326 original size:22 final size:20
Alignment explanation
Indices: 8301--8344 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
8291 ATCTGTGGTA
*
8301 GCCCGCGCGCGGGGCAACTCTT
1 GCCCACGCGC-GGGCAAC-CTT
*
8323 GCCCATGCGCGGGCAACCTT
1 GCCCACGCGCGGGCAACCTT
8343 GC
1 GC
8345 TTTCAGACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.11, C:0.41, G:0.34, T:0.14
Consensus pattern (20 bp):
GCCCACGCGCGGGCAACCTT
Found at i:17692 original size:32 final size:34
Alignment explanation
Indices: 17630--17694 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
17620 GTCCAACCTA
17630 ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
1 ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
*
17664 ACTTGTTCTG-CT-TTAATTG-CTTCTTCAATCT
1 ACTTG-TCTGCCTATTAATTGTCTGCTTCAATCT
17695 AACCTCTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 11 0.38
33 7 0.24
34 7 0.24
35 4 0.14
ACGTcount: A:0.17, C:0.23, G:0.12, T:0.48
Consensus pattern (34 bp):
ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
Found at i:19253 original size:16 final size:17
Alignment explanation
Indices: 19232--19278 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
19222 TTATTAAGTA
*
19232 ATTATTGAATAA-TATT
1 ATTATTCAATAATTATT
19248 ATTATTCAATAATTATT
1 ATTATTCAATAATTATT
*
19265 ATTAAGTCAATAAT
1 ATT-ATTCAATAAT
19279 AGTGGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
17 7 0.26
18 9 0.33
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (17 bp):
ATTATTCAATAATTATT
Found at i:20163 original size:12 final size:12
Alignment explanation
Indices: 20146--20177 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
20136 CCAAAATTAG
20146 CAGAATCGCAAT
1 CAGAATCGCAAT
20158 CAGAATCGCAAT
1 CAGAATCGCAAT
20170 CAGAATCG
1 CAGAATCG
20178 ATATCTGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.16
Consensus pattern (12 bp):
CAGAATCGCAAT
Found at i:25470 original size:33 final size:34
Alignment explanation
Indices: 25433--25499 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
25423 AGCATTTGGC
25433 AGTTGGTGTGTGGTAGAGTCAACCCA-TTTCTTT
1 AGTTGGTGTGTGGTAGAGTCAACCCATTTTCTTT
25466 AGTTGGTGTGTGGTAGAGTCAACCCATTTTCTTT
1 AGTTGGTGTGTGGTAGAGTCAACCCATTTTCTTT
25500 GTTTCTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (34 bp):
AGTTGGTGTGTGGTAGAGTCAACCCATTTTCTTT
Found at i:28106 original size:53 final size:53
Alignment explanation
Indices: 28042--28151 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
28032 TCTTTAAATC
*
28042 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGCTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
28095 CAATAGCTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGCTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
28148 CAAT
1 CAAT
28152 TGAATAAACA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (53 bp):
CAATAGCTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
Found at i:28337 original size:45 final size:45
Alignment explanation
Indices: 28280--28366 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
28270 TACCTAAATT
* * *
28280 CTACTCATTCTCTAGGTTATTCATCAAAATAGAGCTAATATTCTA
1 CTACTCATTCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA
* * *
28325 CTACTCCA-TCTCTATATAATTCGTCAAAATAAAGTTAATATT
1 CTACT-CATTCTCTAGATAATTCATCAAAATAAAGCTAATATT
28367 AATTGTTGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 33 0.94
46 2 0.06
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (45 bp):
CTACTCATTCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA
Found at i:29709 original size:16 final size:17
Alignment explanation
Indices: 29670--29712 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
29660 TTCAGAGACG
29670 TAATGGTTTCTAATAGCT
1 TAATGGTTTCTAATA-CT
29688 TAATGGTGTTCTAAT-C-
1 TAATGGT-TTCTAATACT
29704 TAATGGTTT
1 TAATGGTTT
29713 AAAGATTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 7 0.29
17 1 0.04
18 7 0.29
19 7 0.29
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (17 bp):
TAATGGTTTCTAATACT
Done.