Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023554.1 Corchorus olitorius cultivar O-4 contig23587, 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: 12411
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:503 original size:14 final size:14
Alignment explanation
Indices: 484--510 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
474 ATTATCATTT
484 CCTTCTTTTTTTTC
1 CCTTCTTTTTTTTC
498 CCTTCTTTTTTTT
1 CCTTCTTTTTTTT
511 TGCCACACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
CCTTCTTTTTTTTC
Found at i:638 original size:37 final size:38
Alignment explanation
Indices: 570--644 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
560 CTTTTTGAAA
* *
570 AACATTTTTCCTCTTTTGAAAAGACTGCACTTTGAGGAG
1 AACATTTTT-CTCTTTTGAAAAGACTACACTTGGAGGAG
609 AACATTTTT-TCTTTTGAAAAGA-TCACACTTGGAGGA
1 AACATTTTTCTCTTTTGAAAAGACT-ACACTTGGAGGA
645 AAGTTTCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.03
37 23 0.70
39 9 0.27
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (38 bp):
AACATTTTTCTCTTTTGAAAAGACTACACTTGGAGGAG
Found at i:896 original size:14 final size:14
Alignment explanation
Indices: 858--896 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
848 CGAAAACCGA
*
858 TTTTTTGAAAACCC
1 TTTTTTGAAAACAC
*
872 TTTTCTGAAAACAC
1 TTTTTTGAAAACAC
*
886 TTTTTTTAAAA
1 TTTTTTGAAAA
897 GCATTTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (14 bp):
TTTTTTGAAAACAC
Found at i:4497 original size:31 final size:29
Alignment explanation
Indices: 4424--4509 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 29
4414 AGCAAAACCA
* * *
4424 TAACGTTATATCCTGAAAT-CACACTTTTG
1 TAACGTTATATCCTGAATTGAACA-TTGTG
4453 TAACGTT-TCATCCTGAATTGAACATTCGTG
1 TAACGTTAT-ATCCTGAATTGAACATT-GTG
4483 TAAACGTTATATCCTGAATTGAACATT
1 T-AACGTTATATCCTGAATTGAACATT
4510 TAGCCTGCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.02
29 18 0.37
30 6 0.12
31 23 0.47
32 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (29 bp):
TAACGTTATATCCTGAATTGAACATTGTG
Found at i:5265 original size:19 final size:20
Alignment explanation
Indices: 5156--5407 Score: 108
Period size: 19 Copynumber: 12.8 Consensus size: 20
5146 AAAAAAAATA
5156 AAATA-ATAAA-AAA-AGAT
1 AAATAGATAAATAAATAGAT
5173 AAATAGGTATAGAGATAAATAGAT
1 AAATA-G-ATA-A-ATAAATAGAT
* * *
5197 ACAGAGA-ATAATAAATAAAT
1 AAATAGATA-AATAAATAGAT
** *
5217 AGGTAGCTAAA-AAA-AGAT
1 AAATAGATAAATAAATAGAT
5235 AATAATA-ATAAATAAATAGAT
1 -A-AATAGATAAATAAATAGAT
* * *
5256 -AATAGCTAAATTAATAAAT
1 AAATAGATAAATAAATAGAT
* * *
5275 AAAAAGATAAAT-AGTAAAT
1 AAATAGATAAATAAATAGAT
5294 AAATAGAT-AAT-AAT---T
1 AAATAGATAAATAAATAGAT
*
5309 AAATTA-ATAAATAAAAAGAT
1 AAA-TAGATAAATAAATAGAT
*
5329 AAATAG-CAAATAAATAGAT
1 AAATAGATAAATAAATAGAT
*
5348 AATAGTTAAAAATAAATAAATAGAT
1 AA-A--T--AGATAAATAAATAGAT
5373 AAATAG-TAAATAAATAGAT
1 AAATAGATAAATAAATAGAT
* *
5392 -AATAGTTAAAAAAATA
1 AAATAGATAAATAAATA
5408 AAAAAATAAA
Statistics
Matches: 180, Mismatches: 27, Indels: 54
0.69 0.10 0.21
Matches are distributed among these distances:
15 6 0.03
16 5 0.03
17 7 0.04
18 17 0.09
19 69 0.38
20 37 0.21
21 8 0.04
22 4 0.02
23 4 0.02
24 9 0.05
25 14 0.08
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.25
Consensus pattern (20 bp):
AAATAGATAAATAAATAGAT
Found at i:5270 original size:27 final size:27
Alignment explanation
Indices: 5240--5437 Score: 96
Period size: 27 Copynumber: 7.5 Consensus size: 27
5230 AAGATAATAA
*
5240 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
5267 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
5291 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
5313 TAATAAATAAAAAGATAAATAGCAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* * * * *
5340 AAATAGAT-AATAGTTAAA-AATAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* * *
5365 AAATAGATAAATAGTAAATAAATAGATAATAGT
1 TAATAAATAAA-A--AGATAAATAG-TAA-A-T
* * *
5398 TAAAAAAATAAAAAAATAAATAGTGAAT
1 T-AATAAATAAAAAGATAAATAGTAAAT
*
5426 AAAT-AATAAAAA
1 TAATAAATAAAAA
5438 AAATCTTTTT
Statistics
Matches: 131, Mismatches: 22, Indels: 37
0.69 0.12 0.19
Matches are distributed among these distances:
19 1 0.01
21 4 0.03
22 2 0.02
23 20 0.15
24 2 0.02
25 17 0.13
26 18 0.14
27 28 0.21
28 6 0.05
29 6 0.05
30 3 0.02
31 13 0.10
32 1 0.01
33 2 0.02
34 8 0.06
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.26
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:5312 original size:46 final size:44
Alignment explanation
Indices: 5227--5434 Score: 278
Period size: 46 Copynumber: 4.7 Consensus size: 44
5217 AGGTAGCTAA
* *
5227 AAAAAGATAATAATAATAAATAAATAGATAATAGCTAAATTAATAAAT
1 AAAAAGAT-A-AATAGTAAATAAATAGATAATAGTTAAA--AATAAAT
*
5275 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAAT
*
5321 AAAAAGATAAATAGCAAATAAATAGATAATAGTTAAAAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAT
*
5365 AAATAGATAAATAGTAAATAAATAGATAATAGTT-AAAA-AAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAT
* *
5407 AAAAAAATAAATAGTGAATAAATA-ATAA
1 AAAAAGATAAATAGTAAATAAATAGATAA
5435 AAAAAATCTT
Statistics
Matches: 150, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
41 4 0.03
42 25 0.17
43 4 0.03
44 39 0.26
46 69 0.46
47 1 0.01
48 8 0.05
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (44 bp):
AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAT
Found at i:5330 original size:12 final size:11
Alignment explanation
Indices: 5268--5419 Score: 67
Period size: 11 Copynumber: 13.7 Consensus size: 11
5258 TAGCTAAATT
5268 AATAAATAAAA
1 AATAAATAAAA
**
5279 AGATAAATAGTA
1 A-ATAAATAAAA
* *
5291 AATAAATAGAT
1 AATAAATAAAA
* *
5302 AATAATTAAATT
1 AATAAATAAA-A
5314 AATAAATAAAA
1 AATAAATAAAA
**
5325 AGATAAATAGCA
1 A-ATAAATAAAA
* *
5337 AATAAATAGAT
1 AATAAATAAAA
* *
5348 AAT-AGTTAAA
1 AATAAATAAAA
5358 AATAAATAAATA
1 AATAAATAAA-A
* **
5370 GATAAATAGTA
1 AATAAATAAAA
* *
5381 AATAAATAGAT
1 AATAAATAAAA
**
5392 AATAGTTAAAA
1 AATAAATAAAA
*
5403 AA-ATA-AAAA
1 AATAAATAAAA
5412 AATAAATA
1 AATAAATA
5420 GTGAATAAAT
Statistics
Matches: 103, Mismatches: 31, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
9 6 0.06
10 9 0.09
11 52 0.50
12 36 0.35
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:5393 original size:8 final size:8
Alignment explanation
Indices: 5169--5384 Score: 68
Period size: 8 Copynumber: 28.1 Consensus size: 8
5159 TAATAAAAAA
5169 AGATAAAT
1 AGATAAAT
* * *
5177 AGGTATAG
1 AGATAAAT
5185 AGATAAAT
1 AGATAAAT
* *
5193 AGATACAG
1 AGATAAAT
5201 AGA-ATAAT
1 AGATA-AAT
*
5209 AAATAAAT
1 AGATAAAT
* **
5217 AGGTAGCT
1 AGATAAAT
*
5225 A-A-AAAA
1 AGATAAAT
5231 AGAT-AAT
1 AGATAAAT
5238 A-AT-AAT
1 AGATAAAT
*
5244 AAATAAAT
1 AGATAAAT
5252 AGAT-AAT
1 AGATAAAT
*
5259 AGCTAAATT
1 AGATAAA-T
5268 A-ATAAAT
1 AGATAAAT
5275 --A-AAA-
1 AGATAAAT
5279 AGATAAAT
1 AGATAAAT
5287 AG-TAAAT
1 AGATAAAT
* *
5294 AAATAGAT
1 AGATAAAT
*
5302 A-ATAATT
1 AGATAAAT
* *
5309 AAATTAAT
1 AGATAAAT
* *
5317 AAATAAAA
1 AGATAAAT
5325 AGATAAAT
1 AGATAAAT
5333 AGCAAATAAAT
1 AG---ATAAAT
5344 AGAT-AAT
1 AGATAAAT
*
5351 AGTTAAAAAT
1 AG--ATAAAT
*
5361 AAATAAAT
1 AGATAAAT
5369 AGATAAAT
1 AGATAAAT
5377 AG-TAAAT
1 AGATAAAT
5384 A
1 A
5385 AATAGATAAT
Statistics
Matches: 151, Mismatches: 37, Indels: 41
0.66 0.16 0.18
Matches are distributed among these distances:
5 3 0.02
6 10 0.07
7 39 0.26
8 83 0.55
9 4 0.03
10 4 0.03
11 8 0.05
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:5431 original size:4 final size:4
Alignment explanation
Indices: 5241--5419 Score: 88
Period size: 4 Copynumber: 46.0 Consensus size: 4
5231 AGATAATAAT
* ** *
5241 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * *
5287 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
** * * * *
5333 AGCA AATA AATA GATA ATAGTT AA-A AATA AATA AATA GATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA
* ** * *
5381 AATA AATA GAT- AATA GTTA AAAA AATA AAAA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
5420 GTGAATAAAT
Statistics
Matches: 124, Mismatches: 38, Indels: 26
0.66 0.20 0.14
Matches are distributed among these distances:
3 17 0.14
4 99 0.80
5 6 0.05
6 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:5860 original size:17 final size:17
Alignment explanation
Indices: 5840--5873 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5830 AAACTAATGC
5840 TAAGTTAATTATGAAAT
1 TAAGTTAATTATGAAAT
5857 TAAGTTAATTATGAAAT
1 TAAGTTAATTATGAAAT
5874 AGAAGCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TAAGTTAATTATGAAAT
Done.