Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016132.1 Corchorus olitorius cultivar O-4 contig16165, 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: 35060
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:341 original size:33 final size:33
Alignment explanation
Indices: 299--418 Score: 105
Period size: 33 Copynumber: 3.6 Consensus size: 33
289 AAATGGTCGG
*
299 TGCCGCCCTCGGAGGGCGGCATGGCCATGGGGA
1 TGCCGCCCTCAGAGGGCGGCATGGCCATGGGGA
* * ** **
332 TGCCGCCCTCAGTGGGCGGCCTAACCATTAGGA
1 TGCCGCCCTCAGAGGGCGGCATGGCCATGGGGA
*** * **
365 TGCCGCCCTCCTTGGGCGGCACGGCCATGGCCA
1 TGCCGCCCTCAGAGGGCGGCATGGCCATGGGGA
* *
398 TGCTGCCCTTAGAGGGCGGCA
1 TGCCGCCCTCAGAGGGCGGCA
419 CCAATAAATA
Statistics
Matches: 65, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.13, C:0.34, G:0.37, T:0.16
Consensus pattern (33 bp):
TGCCGCCCTCAGAGGGCGGCATGGCCATGGGGA
Found at i:6065 original size:45 final size:45
Alignment explanation
Indices: 6001--6090 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
5991 CAGCAGCAGC
*
6001 CTCCCTCTCCCTATACATCCGAGCAGTCTCAGCCTCCCTCTCCCT
1 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCTCTCCCT
*
6046 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCTCTCTCCCT
1 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCTCTCCCT
6091 TTGCAACTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.13, C:0.51, G:0.09, T:0.27
Consensus pattern (45 bp):
CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCTCTCCCT
Found at i:6690 original size:19 final size:19
Alignment explanation
Indices: 6666--6704 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6656 CATGATGTTC
6666 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
6685 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
6704 T
1 T
6705 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:7279 original size:25 final size:26
Alignment explanation
Indices: 7251--7302 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
7241 ATTTTAATGC
7251 TTTAATT-TTATTTT-TTATTAAAAAA
1 TTTAATTATTATTTTATT-TTAAAAAA
7276 TTTAATTATTATTTTATTTTAAAAAA
1 TTTAATTATTATTTTATTTTAAAAAA
7302 T
1 T
7303 AAATATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 7 0.28
26 16 0.64
27 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTAATTATTATTTTATTTTAAAAAA
Found at i:7309 original size:24 final size:25
Alignment explanation
Indices: 7258--7309 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
7248 TGCTTTAATT
*
7258 TTATTTTTTATTAAAAAATTTAATTA
1 TTATTTTTTATTAAAAAA-TTAAATA
7284 TTATTTTATT-TTAAAAAA-TAAATA
1 TTATTTT-TTATTAAAAAATTAAATA
7308 TT
1 TT
7310 GGCGGGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.29
26 15 0.62
27 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTTTTTATTAAAAAATTAAATA
Found at i:8115 original size:11 final size:11
Alignment explanation
Indices: 8101--8138 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8091 ATTCATAACA
8101 AATTTATAATT
1 AATTTATAATT
8112 AATTTATAATT
1 AATTTATAATT
8123 -ATTTGATAATT
1 AATTT-ATAATT
*
8134 TATTT
1 AATTT
8139 CATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15901 original size:41 final size:40
Alignment explanation
Indices: 15842--15921 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
15832 TGCTTTTCAC
* *
15842 TATTCTGTAAGTTTTGTTTACATAAATTTCAAGCTGAGTTT
1 TATTCTGTAAGTTGTGTTTACATAAA-CTCAAGCTGAGTTT
*
15883 TATTCTGTAAGTTGTGTTTACCTAAACTCAAGCTGAGTT
1 TATTCTGTAAGTTGTGTTTACATAAACTCAAGCTGAGTT
15922 CTGCTGGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 12 0.33
41 24 0.67
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.45
Consensus pattern (40 bp):
TATTCTGTAAGTTGTGTTTACATAAACTCAAGCTGAGTTT
Found at i:18650 original size:17 final size:18
Alignment explanation
Indices: 18624--18657 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18614 TCAGTTATTG
18624 TTTTTACTAAC-ACTTTT
1 TTTTTACTAACAACTTTT
*
18641 TTTTTTCTAACAACTTT
1 TTTTTACTAACAACTTT
18658 GAACTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTACTAACAACTTTT
Found at i:19442 original size:19 final size:19
Alignment explanation
Indices: 19418--19483 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
19408 GTTTTGACAT
19418 TAAAACTCAATATGATATA
1 TAAAACTCAATATGATATA
** * *
19437 TAAAACAGGAAAGTTTTGACAT-
1 TAAAAC--TCAA--TATGATATA
19459 TAAAACTCAATATGATATA
1 TAAAACTCAATATGATATA
19478 TAAAAC
1 TAAAAC
19484 ATGAAAGGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 6 0.18
19 12 0.35
20 2 0.06
21 2 0.06
22 6 0.18
23 6 0.18
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (19 bp):
TAAAACTCAATATGATATA
Found at i:19451 original size:41 final size:41
Alignment explanation
Indices: 19406--19490 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
19396 AATATATTAT
19406 AAGTTTTGACATTAAAACTCAATATGATATATAAAACAGGA
1 AAGTTTTGACATTAAAACTCAATATGATATATAAAACAGGA
*
19447 AAGTTTTGACATTAAAACTCAATATGATATATAAAACATGA
1 AAGTTTTGACATTAAAACTCAATATGATATATAAAACAGGA
19488 AAG
1 AAG
19491 GTATAACTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.29
Consensus pattern (41 bp):
AAGTTTTGACATTAAAACTCAATATGATATATAAAACAGGA
Found at i:31621 original size:30 final size:29
Alignment explanation
Indices: 31585--31646 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
31575 CATACATACA
* *
31585 AATCACTGAAATTAGAATACTTAAAACTTC
1 AATCACTGAAATCAGAAAACTT-AAACTTC
*
31615 AATCACTGAAGTCAGAAAACTTAAACTTC
1 AATCACTGAAATCAGAAAACTTAAACTTC
31644 AAT
1 AAT
31647 AGCTAGCTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (29 bp):
AATCACTGAAATCAGAAAACTTAAACTTC
Done.