Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012258.1 Corchorus olitorius cultivar O-4 contig12291, 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: 33540
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9546 original size:26 final size:26
Alignment explanation
Indices: 9510--9561 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9500 CACATTACTG
9510 GGTGATACCCAGGTATTTACTTGGCC
1 GGTGATACCCAGGTATTTACTTGGCC
9536 GGTGATACCCAGGTATTTACTTGGCC
1 GGTGATACCCAGGTATTTACTTGGCC
9562 ATCTCCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (26 bp):
GGTGATACCCAGGTATTTACTTGGCC
Found at i:12296 original size:26 final size:26
Alignment explanation
Indices: 12267--12340 Score: 62
Period size: 31 Copynumber: 2.7 Consensus size: 26
12257 AGTAATATTT
12267 ATAATTAAATATATATTATATATAAA
1 ATAATTAAATATATATTATATATAAA
* *
12293 ATAATATTATATATATATAATTACATATATA
1 AT-A-ATTA-A-ATATAT-ATTATATATAAA
*
12324 ATAA-TATATATA-ATTAT
1 ATAATTAAATATATATTAT
12341 TAAACGGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
24 4 0.10
26 7 0.18
27 1 0.03
28 6 0.15
29 2 0.05
30 7 0.18
31 12 0.31
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAATTAAATATATATTATATATAAA
Found at i:12310 original size:28 final size:28
Alignment explanation
Indices: 12270--12342 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
12260 AATATTTATA
* *
12270 ATTAAATATATATTA-TATATAAAATAAT
1 ATTATATATATATTATTACAT-AAATAAT
* *
12298 ATTATATATATATAATTACATATATAAT
1 ATTATATATATATTATTACATAAATAAT
*
12326 AATATATATA-ATTATTA
1 ATTATATATATATTATTA
12343 AACGGTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 6 0.16
28 28 0.74
29 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTATATATATATTATTACATAAATAAT
Found at i:16942 original size:26 final size:27
Alignment explanation
Indices: 16887--16942 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 27
16877 GTTAACTTTC
* *
16887 AAAAAAAGAAAAGAAGAAAATGATTTAA
1 AAAAAAAAAAAAGAAGAAAA-GATTGAA
16915 AAAAACAAAAAAAGAAGAAAA-A-TGAA
1 AAAAA-AAAAAAAGAAGAAAAGATTGAA
16941 AA
1 AA
16943 TATTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.20
27 1 0.04
28 5 0.20
29 14 0.56
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (27 bp):
AAAAAAAAAAAAGAAGAAAAGATTGAA
Found at i:17092 original size:19 final size:18
Alignment explanation
Indices: 17068--17119 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
17058 TCCTTGACCC
17068 AATTTTTTAAAAAAATAAT
1 AATTTTTTAAAAAAAT-AT
17087 AATTTTTTTAATAAAAATAT
1 AA-TTTTTTAA-AAAAATAT
17107 -ATTTTTTAAAAAA
1 AATTTTTTAAAAAA
17120 TATTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 3 0.10
20 10 0.32
21 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTTTAAAAAAATAT
Found at i:17105 original size:18 final size:17
Alignment explanation
Indices: 17069--17135 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 17
17059 CCTTGACCCA
* *
17069 ATTTTTTAAAAAAATAAT
1 ATTTTTTTAATAAA-AAT
17087 AATTTTTTTAATAAAAAT
1 -ATTTTTTTAATAAAAAT
17105 ATATTTTTT-A-AAAAAT
1 AT-TTTTTTAATAAAAAT
17121 A-TTTTTTAATAAAAA
1 ATTTTTTTAATAAAAA
17136 AAATGACATG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
14 6 0.14
15 1 0.02
16 12 0.28
17 3 0.07
18 9 0.21
19 12 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTTTAATAAAAAT
Found at i:17134 original size:15 final size:15
Alignment explanation
Indices: 17081--17134 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
17071 TTTTTAAAAA
17081 AATAATAAT-TTTTTT
1 AATAA-AATATTTTTT
17096 AATAAAAATATATTTTTT
1 AAT--AAA-ATATTTTTT
17114 AA-AAAATATTTTTT
1 AATAAAATATTTTTT
17128 AATAAAA
1 AATAAAA
17135 AAAATGACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 11 0.32
15 10 0.29
16 1 0.03
17 4 0.12
18 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAAATATTTTTT
Found at i:17137 original size:18 final size:18
Alignment explanation
Indices: 17069--17137 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 18
17059 CCTTGACCCA
17069 ATTTTTTAA-AAAAATAAT
1 ATTTTTTAATAAAAA-AAT
*
17087 AATTTTTTTAATAAAAATAT
1 -A-TTTTTTAATAAAAAAAT
17107 A-TTTTT--T-AAAAAAT
1 ATTTTTTAATAAAAAAAT
17121 ATTTTTTAATAAAAAAA
1 ATTTTTTAATAAAAAAA
17138 ATGACATGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
14 7 0.17
15 6 0.14
17 6 0.14
18 6 0.14
19 2 0.05
20 10 0.24
21 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTTAATAAAAAAAT
Found at i:23443 original size:25 final size:25
Alignment explanation
Indices: 23410--23459 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
23400 TGCCTAATGG
23410 TATATTTACTTTATGACTAAATATA
1 TATATTTACTTTATGACTAAATATA
23435 TATATTTACTTTATGACTAAATATA
1 TATATTTACTTTATGACTAAATATA
23460 CAATACACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (25 bp):
TATATTTACTTTATGACTAAATATA
Found at i:24536 original size:356 final size:353
Alignment explanation
Indices: 24082--24791 Score: 1305
Period size: 357 Copynumber: 2.0 Consensus size: 353
24072 TCTTAACGTG
*
24082 AAAAAAAAAGTCGCCTTATAAGAAAAAATTGAAATTTATTAAAAAAAAGTCACGTTGCAAGTTAA
1 AAAAAAAAAGTCGCCTTATAAGAAAAAATTGAAATTTATTAAAAAAAAGTCACGTTGCAAGTAAA
*
24147 AAAAAAAGAAGTAAGTTAAAAATAAAATTTATTAATAAAATTATTCAATTTTAACTAAGATTAAA
66 AAAAAAAGAAGTAAGTTAAAAATAAAATTTATTAATAAAATTAATCAATTTTAACTAAGATTAAA
24212 ATTATGTTAAGGTAATTAATAAAAA-TTTAATTAGGTGTGGTAGGATGTAAATTAGGATTTGATG
131 ATTATGTTAAGGTAATTAATAAAAACTTTAATTAGGTGTGGTAGGATGTAAATTAGGATTTGATG
*
24276 ATGATTCAAATTTGATTAGGTGGCATCATCTTAATGGAATCCTAAAAACACCCATTTTTAAGATG
196 ATGATTCAAATTTGATTAGGTGACATCATCTTAATGGAATCCTAAAAACACCCATTTTTAAGATG
*
24341 ATCTTAATAGAATTTAAACCCTTTATTGATTGATTGCAAACAAATAAATAGGGGGTAATTATTTG
261 ATCTTAATAGAATTTAAACCCTTTATTGATTAATTGCAAACAAATAAATAGGGGGTAATTATTTG
24406 ATACACCGATGGTGTAAATTTTAGACTCC
326 ATACACCGATGGTGTAAA-TTTAGACTCC
*
24435 AAAAAAAGAAGTCGCGTTATAAGAAAAAATTGAAATTTATTAAAAAAAAAGTCACGTTGCAAGTA
1 AAAAAAA-AAGTCGCCTTATAAGAAAAAATTGAAATTTATT-AAAAAAAAGTCACGTTGCAAGT-
24500 AAAAAAAAAAGAAGTAAGTTAAAAATAAAATTTATTAATAAAATTAATCAATTTTAACTAAGATT
63 AAAAAAAAAAGAAGTAAGTTAAAAATAAAATTTATTAATAAAATTAATCAATTTTAACTAAGATT
24565 AAAATTATGTTAAGGTAATTAATAAAAACTTTAATTAGGTGTGGTAGGATGTAAATTAGGATTTG
128 AAAATTATGTTAAGGTAATTAATAAAAACTTTAATTAGGTGTGGTAGGATGTAAATTAGGATTTG
* **
24630 ATGATGATTCAAATTTGATTAGGTGACATCATCTTAATGGAATCCTTAAAACATTCATTTTTAAG
193 ATGATGATTCAAATTTGATTAGGTGACATCATCTTAATGGAATCCTAAAAACACCCATTTTTAAG
24695 ATGATCTTAATAGAATTTAAACCCTTTATTGATTAATTGCAAACAAATAAATAGGGGGTAATTAT
258 ATGATCTTAATAGAATTTAAACCCTTTATTGATTAATTGCAAACAAATAAATAGGGGGTAATTAT
24760 TTGATACACCGATGGTGTAAATTTAGACTCC
323 TTGATACACCGATGGTGTAAATTTAGACTCC
24791 A
1 A
24792 CAAGCGGATT
Statistics
Matches: 345, Mismatches: 8, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
353 7 0.02
354 32 0.09
355 22 0.06
356 102 0.30
357 182 0.53
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (353 bp):
AAAAAAAAAGTCGCCTTATAAGAAAAAATTGAAATTTATTAAAAAAAAGTCACGTTGCAAGTAAA
AAAAAAAGAAGTAAGTTAAAAATAAAATTTATTAATAAAATTAATCAATTTTAACTAAGATTAAA
ATTATGTTAAGGTAATTAATAAAAACTTTAATTAGGTGTGGTAGGATGTAAATTAGGATTTGATG
ATGATTCAAATTTGATTAGGTGACATCATCTTAATGGAATCCTAAAAACACCCATTTTTAAGATG
ATCTTAATAGAATTTAAACCCTTTATTGATTAATTGCAAACAAATAAATAGGGGGTAATTATTTG
ATACACCGATGGTGTAAATTTAGACTCC
Found at i:33540 original size:1 final size:1
Alignment explanation
Indices: 33505--33531 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
33495 CTATTAATAT
33505 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
33532 TTGAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.