Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013226.1 Corchorus olitorius cultivar O-4 contig13259, 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: 2871
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:97 original size:54 final size:54
Alignment explanation
Indices: 1--134 Score: 234
Period size: 54 Copynumber: 2.5 Consensus size: 54
*
1 CACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCA
1 CACTGGGTCATCTTAAGATCAACTTAGACCTCTGAAAACTTCTATGAAAGACCA
55 CACTGGGTCATCTTAAGATCAACTTAGACCTCT-AAAAGCTTCTATGAAAGACCA
1 CACTGGGTCATCTTAAGATCAACTTAGACCTCTGAAAA-CTTCTATGAAAGACCA
109 CACTGGGGTCATCTTAAGATCAACTT
1 CACT-GGGTCATCTTAAGATCAACTT
135 TCTAGAGAGA
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
53 4 0.05
54 52 0.68
55 21 0.27
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (54 bp):
CACTGGGTCATCTTAAGATCAACTTAGACCTCTGAAAACTTCTATGAAAGACCA
Found at i:287 original size:37 final size:37
Alignment explanation
Indices: 245--551 Score: 269
Period size: 37 Copynumber: 8.3 Consensus size: 37
235 TTGAAGAGAC
* * *
245 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * ** * * *
282 ACCTAAACATGAATTTTGAACAA-GATTTTGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAGAA
*
319 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * ** *
356 ACCTAAACATGAATCTTAAACAAAAATTTTGACAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAGAA
* *
394 ACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * *
431 ACCTAAACAGGGATCTTAAACAA-GATCTTGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGAT-TTGATAAGAA
* * * * * * *
468 ACTTAAATAGGGATCTTGAACCA-GATTTCGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAA
* * *
505 ACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAC
1 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
542 ACCTAAACAG
1 ACCTAAACAG
552 AAATCTTGAA
Statistics
Matches: 216, Mismatches: 48, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
36 7 0.03
37 172 0.80
38 37 0.17
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (37 bp):
ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
Found at i:320 original size:74 final size:74
Alignment explanation
Indices: 231--474 Score: 353
Period size: 74 Copynumber: 3.3 Consensus size: 74
221 CCTAAACTGG
* * *
231 GATTTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
* *
296 TTTGAACAA
66 CTTAAACAA
*
305 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
370 CTTAAACAAA
66 CTTAAAC-AA
* ** * * *
380 AATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
445 CTTAAACAA
66 CTTAAACAA
* *
454 GATCTTGATGAGACACTTAAA
1 GATTTTGATGAGACACCTAAA
475 TAGGGATCTT
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 84 0.56
75 67 0.44
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
CTTAAACAA
Found at i:421 original size:75 final size:74
Alignment explanation
Indices: 232--453 Score: 320
Period size: 75 Copynumber: 3.0 Consensus size: 74
222 CTAAACTGGG
* * *
232 ATTTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAATT
1 ATTTTGAA-AGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATC
* *
297 TTGAAC-AAG
65 TTAAACAAAA
* *
306 ATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATC
1 ATTTTGA-AAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATC
371 TTAAACAAAA
65 TTAAACAAAA
* * *
381 ATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGATC
1 ATTTTGA-AAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATC
446 TTAAACAA
65 TTAAACAA
454 GATCTTGATG
Statistics
Matches: 134, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
74 65 0.49
75 69 0.51
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (74 bp):
ATTTTGAAAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATCT
TAAACAAAA
Found at i:509 original size:149 final size:149
Alignment explanation
Indices: 232--513 Score: 388
Period size: 149 Copynumber: 1.9 Consensus size: 149
222 CTAAACTGGG
* * * *
232 ATTTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAATT
1 ATTTTGAAGAGAAACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATC
* * *
297 TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAA
66 TTAAACAAGATCTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAA
362 ACATGAATCTTAAACAAAA
131 ACATGAATCTTAAACAAAA
* *
381 ATTTTGACA-AGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 ATTTTGA-AGAGAAACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
* * * * * * *
445 CTTAAACAAGATCTTGATGAGACACTTAAATAGGGATCTTGAACCA-GATTTCGATGAGACACCT
65 CTTAAACAAGATCTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAAACCT
509 AAACA
129 AAACA
514 GGGACCTTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
148 5 0.04
149 109 0.95
150 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (149 bp):
ATTTTGAAGAGAAACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATC
TTAAACAAGATCTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAA
ACATGAATCTTAAACAAAA
Found at i:987 original size:26 final size:26
Alignment explanation
Indices: 926--980 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
916 TGCCCCCCTT
926 ATCAATCCAAATTGACAACATTTGTC
1 ATCAATCCAAATTGACAACATTTGTC
952 ATCAATCCAAATTGACAACATTTGTC
1 ATCAATCCAAATTGACAACATTTGTC
978 ATC
1 ATC
981 TTTCCAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCAATCCAAATTGACAACATTTGTC
Found at i:1568 original size:19 final size:20
Alignment explanation
Indices: 1544--1597 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1534 AACCTTTTGA
*
1544 TTTTTCTTTCTTT-TTCTTT
1 TTTTTCTTTCTTTCTCCTTT
1563 TTTTTCTTTGCTTTCTCCTTT
1 TTTTTCTTT-CTTTCTCCTTT
*
1584 TTTCTTTTTTCTTT
1 TTT-TTCTTTCTTT
1598 AGATTGCTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
21 12 0.40
22 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTCCTTT
Found at i:1593 original size:9 final size:9
Alignment explanation
Indices: 1544--1593 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
1534 AACCTTTTGA
1544 TTTTTCTTT
1 TTTTTCTTT
1553 CTTTTTCTTT
1 -TTTTTCTTT
1563 TTTTTCTTT
1 TTTTTCTTT
** *
1572 GCTTTCTCCT
1 TTTTTCT-TT
1582 TTTTTCTTT
1 TTTTTCTTT
1591 TTT
1 TTT
1594 CTTTAGATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 18 0.55
10 15 0.45
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1982 original size:5 final size:6
Alignment explanation
Indices: 1964--1990 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1954 AAGAACAATC
1964 TTCTTT TTCTTT TTCTTT TTCTTT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC
1991 CCCCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:2274 original size:13 final size:13
Alignment explanation
Indices: 2247--2311 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
2237 ACTCAAAACC
2247 TTTTTGAAAACTCA
1 TTTTTGAAAA-TCA
2261 TTTTTGAAAATCA
1 TTTTTGAAAATCA
2274 TTTCTTGAAAA-CAA
1 TTT-TTGAAAATC-A
*
2288 TTTCTTGAAAATAA
1 TTT-TTGAAAATCA
2302 TTTTTGAAAA
1 TTTTTGAAAA
2312 ACGTCCTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
13 14 0.30
14 33 0.70
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:2313 original size:28 final size:27
Alignment explanation
Indices: 2247--2311 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
2237 ACTCAAAACC
* *
2247 TTTTTGAAAACTCATTTTTGAAAATCA
1 TTTTTGAAAACTAATTTTTGAAAATAA
2274 TTTCTTGAAAAC-AATTTCTTGAAAATAA
1 TTT-TTGAAAACTAATTT-TTGAAAATAA
2302 TTTTTGAAAA
1 TTTTTGAAAA
2312 ACGTCCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTTTGAAAACTAATTTTTGAAAATAA
Done.