Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011390.1 Corchorus olitorius cultivar O-4 contig11423, 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: 37415
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:3189 original size:14 final size:15
Alignment explanation
Indices: 3164--3193 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3154 CTAAGTCCAA
3164 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
3179 TCCTT-TTTATTTAT
1 TCCTTGTTTATTTAT
3193 T
1 T
3194 TTTTCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:4511 original size:18 final size:19
Alignment explanation
Indices: 4475--4517 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4465 TTTTCTTAAT
*
4475 AAGAAATACTAAAAATAAA
1 AAGAAAAACTAAAAATAAA
*
4494 AAGAAAAAC-AAAACTAAA
1 AAGAAAAACTAAAAATAAA
*
4512 AGGAAA
1 AAGAAA
4518 GTAAAATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (19 bp):
AAGAAAAACTAAAAATAAA
Found at i:6300 original size:5 final size:5
Alignment explanation
Indices: 6290--6370 Score: 162
Period size: 5 Copynumber: 16.2 Consensus size: 5
6280 TTGTATAGAG
6290 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
6340 TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
6371 GAATAATAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 76 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:8450 original size:5 final size:5
Alignment explanation
Indices: 8440--8473 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
8430 AATTTATAAA
8440 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
8474 ATTTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:12293 original size:13 final size:13
Alignment explanation
Indices: 12275--12301 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12265 AAACAATTGA
12275 AAAGCACTTCTGG
1 AAAGCACTTCTGG
12288 AAAGCACTTCTGG
1 AAAGCACTTCTGG
12301 A
1 A
12302 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:15380 original size:6 final size:6
Alignment explanation
Indices: 15369--15395 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15359 AATGCTAGTT
15369 CAATTC CAATTC CAATTC CAATTC CAA
1 CAATTC CAATTC CAATTC CAATTC CAA
15396 AAATTAGTTA
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:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (6 bp):
CAATTC
Found at i:16108 original size:57 final size:57
Alignment explanation
Indices: 16009--16126 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
15999 TGTCGTGCAC
* * * * *
16009 CTGATTTTGATGGGTGAATCTACCAACAAGGATAGCTGCGTATAGGAAGTATCGAAT
1 CTGATTTTGATGAGTGAATCTACCAACAAGGACAGCTACGTATACGAAATATCGAAT
16066 CTGATTTTGATGAGTGAATCTACCAACGAA-GACAGCTACGTATACGAAATATCGAAT
1 CTGATTTTGATGAGTGAATCTACCAAC-AAGGACAGCTACGTATACGAAATATCGAAT
16123 CTGA
1 CTGA
16127 GACCGACCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 53 0.96
58 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (57 bp):
CTGATTTTGATGAGTGAATCTACCAACAAGGACAGCTACGTATACGAAATATCGAAT
Found at i:17195 original size:109 final size:109
Alignment explanation
Indices: 17004--17221 Score: 391
Period size: 109 Copynumber: 2.0 Consensus size: 109
16994 TAGTCATTTT
* *
17004 GGTGCTTGTATTTTTCTTTGAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTT
*
17069 ATTTAATAGGTTCAATTGAATAAACAACATAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
*
17113 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTT
*
17178 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
17222 TATATAATAG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTATTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:17380 original size:3 final size:3
Alignment explanation
Indices: 17372--17416 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
17362 AGGTATAATA
17372 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17417 ATCGTAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21417 original size:36 final size:36
Alignment explanation
Indices: 21373--21445 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
21363 ACTAATTTTC
21373 TTAAACTTGATGATATAGTTAAAAGGAACTTATATT
1 TTAAACTTGATGATATAGTTAAAAGGAACTTATATT
21409 TTAAACTTGATGATATAGTTAAAAGGAACTTATATT
1 TTAAACTTGATGATATAGTTAAAAGGAACTTATATT
21445 T
1 T
21446 ATGGACAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (36 bp):
TTAAACTTGATGATATAGTTAAAAGGAACTTATATT
Found at i:21430 original size:18 final size:18
Alignment explanation
Indices: 21373--21431 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
21363 ACTAATTTTC
21373 TTAAACTTGATGATATAG
1 TTAAACTTGATGATATAG
** * *
21391 TTAAA-AGGAACTTATAT-T
1 TTAAACTTG-A-TGATATAG
21409 TTAAACTTGATGATATAG
1 TTAAACTTGATGATATAG
21427 TTAAA
1 TTAAA
21432 AGGAACTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (18 bp):
TTAAACTTGATGATATAG
Found at i:21443 original size:19 final size:19
Alignment explanation
Indices: 21385--21443 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
21375 AAACTTGATG
21385 ATATAGTTAAAAGGAACTT
1 ATATAGTTAAAAGGAACTT
* ** *
21404 ATAT-TTTAAACTTG-A-TG
1 ATATAGTTAAA-AGGAACTT
21421 ATATAGTTAAAAGGAACTT
1 ATATAGTTAAAAGGAACTT
21440 ATAT
1 ATAT
21444 TTATGGACAG
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (19 bp):
ATATAGTTAAAAGGAACTT
Found at i:24012 original size:41 final size:40
Alignment explanation
Indices: 23964--24087 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 40
23954 ACCCAATAAC
*
23964 CAAAGTCCCCAAACAAAATTATAAAACAGGGTCAATTCTCT
1 CAAAGTCCCCAAACAAAATTATAACACAGGG-CAATTCTCT
* * * * * * *
24005 CCAAGTCCTCAAACACATTTATAACACAAAGGC-ATCTATAT
1 CAAAGTCCCCAAACAAAATTATAACAC-AGGGCAAT-TCTCT
* *
24046 CAAAGTCCCCAAGCATAATTATAACACAGGGGCAATTCTCT
1 CAAAGTCCCCAAACAAAATTATAACACA-GGGCAATTCTCT
24087 C
1 C
24088 TCTCAAAGTC
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
40 3 0.05
41 55 0.87
42 5 0.08
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (40 bp):
CAAAGTCCCCAAACAAAATTATAACACAGGGCAATTCTCT
Found at i:24055 original size:82 final size:85
Alignment explanation
Indices: 23964--24145 Score: 246
Period size: 85 Copynumber: 2.2 Consensus size: 85
23954 ACCCAATAAC
* *
23964 CAAAGTCCCCAAACAAAATTATAAAACAGGGTCAA-T-TCTCTC-C-AAGTCCTCAAACACATTT
1 CAAAGTCCCCAAACAAAATTATAAAACAGGGGCAATTCTCTCTCTCAAAGT-CTCAAACAAATTT
24025 ATAACACAAAGGCATCTATAT
65 ATAACACAAAGGCATCTATAT
* * * *
24046 CAAAGTCCCCAAGCATAATTATAACACAGGGGCAATTCTCTCTCTCAAAGTCTCAAGCAAATTTA
1 CAAAGTCCCCAAACAAAATTATAAAACAGGGGCAATTCTCTCTCTCAAAGTCTCAAACAAATTTA
*
24111 TAACGCAAAGGCATCTATAT
66 TAACACAAAGGCATCTATAT
* *
24131 TAAAGTCCCTAAACA
1 CAAAGTCCCCAAACA
24146 CATGTAACAC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 31 0.36
83 1 0.01
84 6 0.07
85 44 0.51
86 4 0.05
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (85 bp):
CAAAGTCCCCAAACAAAATTATAAAACAGGGGCAATTCTCTCTCTCAAAGTCTCAAACAAATTTA
TAACACAAAGGCATCTATAT
Found at i:26376 original size:21 final size:21
Alignment explanation
Indices: 26328--26379 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
26318 AACTCATCTT
*
26328 GATGATATGAAGTCCATTAGA
1 GATGATTTGAAGTCCATTAGA
*
26349 GATGATTTGAAGT-CATTTGGA
1 GATGATTTGAAGTCCA-TTAGA
26370 GATGATTTGA
1 GATGATTTGA
26380 GCAAGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.35
Consensus pattern (21 bp):
GATGATTTGAAGTCCATTAGA
Found at i:27771 original size:18 final size:19
Alignment explanation
Indices: 27742--27777 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27732 GAGAGGAAGG
*
27742 AAGAGTAAAAAATAAGAAA
1 AAGAGTAAAAAAGAAGAAA
27761 AAGAG-AAAAAAGAAGAA
1 AAGAGTAAAAAAGAAGAA
27778 CTAAGGTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
AAGAGTAAAAAAGAAGAAA
Found at i:33788 original size:21 final size:21
Alignment explanation
Indices: 33762--33803 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33752 GCATCTTAGG
33762 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
33783 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
33804 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:34937 original size:52 final size:52
Alignment explanation
Indices: 34877--34979 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
34867 CAAGAATTGC
*
34877 AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGGCAGAAGTTGTTGCGT
1 AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCGT
34929 AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCG
1 AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCG
34980 GAAAGAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (52 bp):
AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCGT
Found at i:34969 original size:22 final size:22
Alignment explanation
Indices: 34933--34976 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34923 TTGCGTAGGA
*
34933 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
34955 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
34977 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:35446 original size:22 final size:22
Alignment explanation
Indices: 35415--35458 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35405 TTCTTTCCGC
*
35415 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
35437 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
35459 TCCTGCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Done.