Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011880.1 Corchorus olitorius cultivar O-4 contig11913, 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: 72762
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:5121 original size:18 final size:18
Alignment explanation
Indices: 5083--5128 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5073 CTCATTATTA
* *
5083 TTCAGATTATTCACGTTG
1 TTCAGATTATTCACATAG
*
5101 TTCAGGTTATTCACATAG
1 TTCAGATTATTCACATAG
*
5119 TTCACATTAT
1 TTCAGATTAT
5129 CTGCCATCGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (18 bp):
TTCAGATTATTCACATAG
Found at i:15393 original size:22 final size:22
Alignment explanation
Indices: 15367--15408 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
15357 CTTGTCTTGA
15367 CAATGTATTTATGGTTGTGAGC
1 CAATGTATTTATGGTTGTGAGC
15389 CAATGTATTTATGGTTGTGA
1 CAATGTATTTATGGTTGTGA
15409 TGTTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (22 bp):
CAATGTATTTATGGTTGTGAGC
Found at i:16498 original size:2 final size:2
Alignment explanation
Indices: 16491--16518 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16481 AAAATGCTTT
16491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16519 ATGTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22695 original size:37 final size:37
Alignment explanation
Indices: 22627--22697 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
22617 ACGTTACAAT
* * *
22627 CCTTGAGTGGCCCCTTAGCAACATTTTCGGTAACCAA
1 CCTTGAGTGGCCCATTAGCAACAATTCCGGTAACCAA
* * *
22664 CCTTTAGTGGCCCATTAGCTATAATTCCGGTAAC
1 CCTTGAGTGGCCCATTAGCAACAATTCCGGTAAC
22698 AAATCCTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (37 bp):
CCTTGAGTGGCCCATTAGCAACAATTCCGGTAACCAA
Found at i:25572 original size:14 final size:16
Alignment explanation
Indices: 25540--25572 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25530 CATCAAAATA
25540 AAAATAAATAGATATT
1 AAAATAAATAGATATT
25556 AAAA-AAATAGA-ATT
1 AAAATAAATAGATATT
25570 AAA
1 AAA
25573 TAGATGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATAAATAGATATT
Found at i:26817 original size:3 final size:3
Alignment explanation
Indices: 26809--26854 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
26799 TATTACTATT
26809 ATA ATA ATA A-A ATA ATA ATA ATA AT- ATA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26854 A
1 A
26855 ATAGAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:26839 original size:19 final size:19
Alignment explanation
Indices: 26809--26853 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
26799 TATTACTATT
26809 ATAATAATAAAATAATAATA
1 ATAAT-ATAAAATAATAATA
26829 ATAATATAAAATAATAATA
1 ATAATATAAAATAATAATA
26848 ATAATA
1 ATAATA
26854 AATAGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATATAAAATAATAATA
Found at i:26869 original size:19 final size:19
Alignment explanation
Indices: 26809--26869 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 19
26799 TATTACTATT
26809 ATAAT-AATAAA-ATAATA
1 ATAATAAATAAATATAATA
26826 ATAATAATATAAAATAATAATA
1 ATAATAA-AT-AAAT-ATAATA
26848 ATAATAAATAGAATATAA-A
1 ATAATAAATA-AATATAATA
26867 ATA
1 ATA
26870 TTGAATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.13
18 1 0.03
19 6 0.16
20 8 0.21
21 5 0.13
22 13 0.34
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAATAAATAAATATAATA
Found at i:26967 original size:32 final size:31
Alignment explanation
Indices: 26920--26982 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
26910 ACCAATTTTT
*
26920 ATTTATTATTATAAATTTTAAAATATAAATTA
1 ATTTATTATTATAAATATT-AAATATAAATTA
* * *
26952 ATTTTTTATTTTAAATATTAAATTTAAATTA
1 ATTTATTATTATAAATATTAAATATAAATTA
26983 TACAGGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTATTATTATAAATATTAAATATAAATTA
Found at i:34587 original size:13 final size:11
Alignment explanation
Indices: 34540--34592 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
34530 GTTGAGGAAC
* *
34540 TGTTTTATTAC
1 TGTTTTATAAA
34551 TGTTTTATAATA
1 TGTTTTATAA-A
34563 TGTTTTATAAA
1 TGTTTTATAAA
34574 TGGTTTTAATAAA
1 T-GTTTT-ATAAA
34587 TTGTTT
1 -TGTTT
34593 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 11 0.31
12 15 0.42
13 9 0.25
14 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.58
Consensus pattern (11 bp):
TGTTTTATAAA
Found at i:44233 original size:127 final size:127
Alignment explanation
Indices: 44089--44347 Score: 400
Period size: 127 Copynumber: 2.0 Consensus size: 127
44079 CCATGTTTAA
*
44089 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
44151 A-ATTTTTACCATTTTACTATTTTATTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATA
66 ATATTTTTACCATTTTACTA--TT-TTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATA
44215 T
127 T
44216 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
*
44281 TATTTTATTTTTACTATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
44346 T
127 T
44347 A
1 A
44348 TTTCTTAAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
127 55 0.45
128 3 0.02
129 2 0.02
131 37 0.30
132 6 0.05
133 2 0.02
135 17 0.14
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:45997 original size:18 final size:19
Alignment explanation
Indices: 45946--46002 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
45936 ATTAAATAAT
45946 AATGAATAGATTAAAATTA
1 AATGAATAGATTAAAATTA
45965 AATGAATAGATTAAAATTA
1 AATGAATAGATTAAAATTA
45984 AATGAATA-ATTAAAATTA
1 AATGAATAGATTAAAATTA
46002 A
1 A
46003 CTTGTATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 11 0.29
19 27 0.71
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
AATGAATAGATTAAAATTA
Found at i:46013 original size:19 final size:18
Alignment explanation
Indices: 45933--46002 Score: 97
Period size: 19 Copynumber: 3.8 Consensus size: 18
45923 TTTTTACTTT
*
45933 ATAATT-AAATAATAATGA
1 ATAATTAAAATTA-AATGA
45951 ATAGATTAAAATTAAATGA
1 ATA-ATTAAAATTAAATGA
45970 ATAGATTAAAATTAAATGA
1 ATA-ATTAAAATTAAATGA
45989 ATAATTAAAATTAA
1 ATAATTAAAATTAA
46003 CTTGTATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 14 0.29
19 30 0.61
20 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
ATAATTAAAATTAAATGA
Found at i:46128 original size:19 final size:19
Alignment explanation
Indices: 46088--46124 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
46078 AATTTTTAAG
46088 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
46107 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
46125 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:49329 original size:40 final size:40
Alignment explanation
Indices: 49284--49366 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
49274 TTGAAAAACA
49284 TGGGAGAGCCTTTTTGCCTTGTTTCGGTCTTTTCTGACTC
1 TGGGAGAGCCTTTTTGCCTTGTTTCGGTCTTTTCTGACTC
*
49324 TGGGAGAGCCTTTTTGCCTTGTTTTGGTCTTTTCTGACTC
1 TGGGAGAGCCTTTTTGCCTTGTTTCGGTCTTTTCTGACTC
49364 TGG
1 TGG
49367 ATTTTACTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.07, C:0.20, G:0.27, T:0.46
Consensus pattern (40 bp):
TGGGAGAGCCTTTTTGCCTTGTTTCGGTCTTTTCTGACTC
Found at i:49448 original size:75 final size:74
Alignment explanation
Indices: 49322--49584 Score: 196
Period size: 75 Copynumber: 3.5 Consensus size: 74
49312 CTTTTCTGAC
* * * * *
49322 TCTGGGAGAGCCTTTT-TGCCTTGTTTTGGTCTTTTCTGACTCTGGATTTTACTGATAGCTCCTA
1 TCTGGGAGAACCTTTTCTACC--GTTTTGATCTTTTCTCACTCTGGAATTTACTGATAGCTCCTA
49386 TCAACTTTTAA
64 TCAACTTTTAA
* * **
49397 TCTGGGAGAACCTTTTCGTACCGTTTTGATCTTTTCTCACACTAGAATTTACCAATAGCTCCCT-
1 TCTGGGAGAACCTTTTC-TACCGTTTTGATCTTTTCTCACTCTGGAATTTACTGATAGCT-CCTA
*
49461 GCAACTTTTAA
64 TCAACTTTTAA
* * * * * * *
49472 -CATGGGAGAGCCTTTTC-ACCTCGTTTCGGTC-TTTGTCATTCTGGAATTTACTGATAGCCCCC
1 TC-TGGGAGAACCTTTTCTA-C-CGTTTTGATCTTTTCTCACTCTGGAATTTACTGATAGCTCCT
*
49534 ATCAACTCTTAA
63 ATCAACTTTTAA
* * ** *
49546 TGTTGGAG-ATTTTTTCCATCCCGTTTTGATCTTTTCTCA
1 TCTGGGAGAACCTTTT-C-TACCGTTTTGATCTTTTCTCA
49585 ATTTATTAGT
Statistics
Matches: 144, Mismatches: 32, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
73 7 0.05
74 46 0.32
75 85 0.59
76 3 0.02
77 3 0.02
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (74 bp):
TCTGGGAGAACCTTTTCTACCGTTTTGATCTTTTCTCACTCTGGAATTTACTGATAGCTCCTATC
AACTTTTAA
Found at i:57356 original size:30 final size:30
Alignment explanation
Indices: 57320--57381 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
57310 AGGCTTTAAA
* *
57320 TTCCCTGCTTTCTCTTAAAACCCGAAGATT
1 TTCCCTGCTCTCTCTTAAAACCCAAAGATT
*
57350 TTCCCTGCTCTCTCTTAAAACCCAAATATT
1 TTCCCTGCTCTCTCTTAAAACCCAAAGATT
57380 TT
1 TT
57382 ATATTAAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.39
Consensus pattern (30 bp):
TTCCCTGCTCTCTCTTAAAACCCAAAGATT
Found at i:57851 original size:23 final size:23
Alignment explanation
Indices: 57825--57869 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
57815 ACGTGTTTTG
*
57825 TGTCTTAACGATTAAGAAAATCA
1 TGTCATAACGATTAAGAAAATCA
*
57848 TGTCATCACGATTAAGAAAATC
1 TGTCATAACGATTAAGAAAATC
57870 GTGTTCCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (23 bp):
TGTCATAACGATTAAGAAAATCA
Found at i:59430 original size:18 final size:18
Alignment explanation
Indices: 59382--59422 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
59372 AATCATCACT
*
59382 TCCATAATACTAACAAAA
1 TCCATAACACTAACAAAA
59400 TCCATAACACTAACAAAA
1 TCCATAACACTAACAAAA
59418 -CCATA
1 TCCATA
59423 CTGACTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.20
Consensus pattern (18 bp):
TCCATAACACTAACAAAA
Found at i:64105 original size:17 final size:17
Alignment explanation
Indices: 64083--64121 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
64073 TTGGCCAATG
64083 GCCACGAAAGTATAGAA
1 GCCACGAAAGTATAGAA
64100 GCCACGAAAGTATAGAA
1 GCCACGAAAGTATAGAA
64117 GCCAC
1 GCCAC
64122 ATCAAGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (17 bp):
GCCACGAAAGTATAGAA
Found at i:72318 original size:131 final size:128
Alignment explanation
Indices: 72158--72425 Score: 360
Period size: 131 Copynumber: 2.1 Consensus size: 128
72148 TTGTTTAAAC
* * * *
72158 TTTTATAGTTTTATTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACCAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
* * *
72223 TTTTATTTTTACCATTTTATTATTTTAATTTAAAAAAAACTT-ATATATTAGAACTTTTTAATAT
66 TTTTA-TTTTACCATTTTACTAATTTAA-TT--AAAAAACTTAATATATTAGAA-TTTTTAAAAT
72287 AT-
126 ATA
* * * *
72289 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCATATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACCAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
72354 TTTTATTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATA
66 TTTTATTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATATA
*
72418 TTTCATAA
1 TTTTATAA
72426 ATGACATTAT
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
127 9 0.07
128 11 0.09
129 20 0.16
130 20 0.16
131 62 0.51
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (128 bp):
TTTTATAATTTTACTCAACCAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
TTTTATTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATA
Done.