Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012642.1 Corchorus olitorius cultivar O-4 contig12675, 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: 23130
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1013 original size:14 final size:14
Alignment explanation
Indices: 994--1035 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
984 AAATAGAGAG
**
994 GAAGAAGAAGGAAA
1 GAAGAAGAAAAAAA
1008 GAAGAAGAAAAAAA
1 GAAGAAGAAAAAAA
1022 GAAGAAGAAAAAAA
1 GAAGAAGAAAAAAA
1036 TCTGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAAAAA
Found at i:5124 original size:38 final size:38
Alignment explanation
Indices: 5078--5263 Score: 139
Period size: 37 Copynumber: 4.6 Consensus size: 38
5068 CTAGAAGCTG
*
5078 ATGGGAACTTTCCCAATTTAAAAACTTTTGCAAACTGA
1 ATGGGAACTTTCCCAATTTAAAAACTTTTGAAAACTGA
** *
5116 ATGGGAACTTTCCCAATTTTAAAAAAAAAAAAAAAAAACTCTGAAAACTGAA
1 ATGGGAACTTTCCCAA-TTT------------AAAAACTTTTGAAAACTG-A
5168 ATGGGAACTTTCCCAATTTAAAAA-TTTTGAAAACTGA
1 ATGGGAACTTTCCCAATTTAAAAACTTTTGAAAACTGA
* *
5205 ATGGGAACTTTCCCAATTTGAAAAC--TTAAAAACGTG-
1 ATGGGAACTTTCCCAATTTAAAAACTTTTGAAAAC-TGA
*
5241 -TGGGAACTTTCCCAATTTGAAAA
1 ATGGGAACTTTCCCAATTTAAAAA
5264 TTTCGAAGAC
Statistics
Matches: 124, Mismatches: 8, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
35 23 0.19
36 7 0.06
37 26 0.21
38 26 0.21
39 8 0.06
51 17 0.14
52 17 0.14
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (38 bp):
ATGGGAACTTTCCCAATTTAAAAACTTTTGAAAACTGA
Found at i:5217 original size:37 final size:37
Alignment explanation
Indices: 5157--5275 Score: 154
Period size: 37 Copynumber: 3.2 Consensus size: 37
5147 AAAAAAACTC
*
5157 TGAAAACTGAAATGGGAACTTTCCCAATTTAAAAATTT
1 TGAAAACTG-AATGGGAACTTTCCCAATTTGAAAATTT
*
5195 TGAAAACTGAATGGGAACTTTCCCAATTTGAAAA-CT
1 TGAAAACTGAATGGGAACTTTCCCAATTTGAAAATTT
*
5231 TAAAAACGTG--TGGGAACTTTCCCAATTTGAAAATTT
1 TGAAAAC-TGAATGGGAACTTTCCCAATTTGAAAATTT
* *
5267 CGAAGACTG
1 TGAAAACTG
5276 GTTCTTGATT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
35 25 0.35
36 12 0.17
37 26 0.36
38 9 0.12
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (37 bp):
TGAAAACTGAATGGGAACTTTCCCAATTTGAAAATTT
Found at i:5949 original size:25 final size:25
Alignment explanation
Indices: 5921--5979 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
5911 CCCACATTAT
5921 AACTAAAAACT-AGAGCCCAAACCTA
1 AACTAAAAACTAAG-GCCCAAACCTA
* *
5946 AACTAAGAACTAAGGTCCAAACCTA
1 AACTAAAAACTAAGGCCCAAACCTA
*
5971 AACAAAAAA
1 AACTAAAAA
5980 AAACCCAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (25 bp):
AACTAAAAACTAAGGCCCAAACCTA
Found at i:7103 original size:1 final size:1
Alignment explanation
Indices: 7097--7122 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
7087 GTTGTTGTTG
7097 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
7123 GCGGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8876 original size:32 final size:33
Alignment explanation
Indices: 8839--8943 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 33
8829 GACCCAGTTA
8839 AAAGAAATGAATTAGAAGAAAACTAATGGGAT-
1 AAAGAAATGAATTAGAAGAAAACTAATGGGATG
8871 AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGG
1 AAAGAAATGAATTAGAAGAAAACTAATGGGAT----G
8908 CAAAAAGAAATGAATTAGAAGAAAACTAATGGGATG
1 ---AAAGAAATGAATTAGAAGAAAACTAATGGGATG
8944 GAGGCAAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
32 32 0.49
36 1 0.02
40 32 0.49
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.17
Consensus pattern (33 bp):
AAAGAAATGAATTAGAAGAAAACTAATGGGATG
Found at i:8913 original size:21 final size:21
Alignment explanation
Indices: 8889--8951 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
8879 GAATTAGAAG
8889 AAAACTAATGGGATGGAGGCA
1 AAAACTAATGGGATGGAGGCA
** * * *
8910 AAAAGAAAT-GAAT-TA-GAA
1 AAAACTAATGGGATGGAGGCA
8928 GAAAACTAATGGGATGGAGGCA
1 -AAAACTAATGGGATGGAGGCA
8950 AA
1 AA
8952 TTAATCGATA
Statistics
Matches: 28, Mismatches: 10, Indels: 8
0.61 0.22 0.17
Matches are distributed among these distances:
18 2 0.07
19 8 0.29
20 6 0.21
21 10 0.36
22 2 0.07
ACGTcount: A:0.51, C:0.06, G:0.29, T:0.14
Consensus pattern (21 bp):
AAAACTAATGGGATGGAGGCA
Found at i:8926 original size:40 final size:40
Alignment explanation
Indices: 8871--8951 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
8861 CTAATGGGAT
8871 AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGGCAA
1 AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGGCAA
8911 AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGGCAA
1 AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGGCAA
8951 A
1 A
8952 TTAATCGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.05, G:0.27, T:0.15
Consensus pattern (40 bp):
AAAGAAATGAATTAGAAGAAAACTAATGGGATGGAGGCAA
Found at i:9293 original size:36 final size:35
Alignment explanation
Indices: 9208--9534 Score: 305
Period size: 35 Copynumber: 9.2 Consensus size: 35
9198 CCTGGATCAT
* * *
9208 TGAAATGAATTGAAGAAAGACCGCCCTGGGTCAAC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCAAC
* * * *
9243 TGACATAAATTGAAGAATGACCACCCTCGATCATTC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCA-AC
* * **
9279 GGACATAAGCTGAAGAAAAGACCACCC-CGGGTCAAC
1 TGAAATAAATTGAAG-AAAGACCACCCTC-GGTCAAC
* * *
9315 TGAAATAAGTTGAAGAAAGACCGCCCTGGGTCAAC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCAAC
* * * *
9350 TGAAATGAATTGAAGAACGACCACCCTCGATCATTC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCA-AC
* * *
9386 TGACATAAACTGAAGAAAAGACCACCCTGGGTCAAC
1 TGAAATAAATTGAAG-AAAGACCACCCTCGGTCAAC
* * *
9422 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAAC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCAAC
* * * *
9457 TGAAATGAATTGAAGAACGACCACCCTCGATCATTC
1 TGAAATAAATTGAAGAAAGACCACCCTCGGTCA-AC
* * *
9493 TGACATAAAATGAAGAAAAGACCACCCTGGGTCAAC
1 TGAAATAAATTGAAG-AAAGACCACCCTCGGTCAAC
9529 TGAAAT
1 TGAAAT
9535 TTGTGAAGAT
Statistics
Matches: 235, Mismatches: 49, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
35 117 0.50
36 74 0.31
37 44 0.19
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (35 bp):
TGAAATAAATTGAAGAAAGACCACCCTCGGTCAAC
Found at i:9328 original size:72 final size:70
Alignment explanation
Indices: 9184--9534 Score: 332
Period size: 72 Copynumber: 4.9 Consensus size: 70
9174 TAACTGAAAG
* * * * *
9184 TGAAGAATGGCCACCCTGGATCA-T-TGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACTGAC
1 TGAAGAAAGACCACCCTGGATCATTCTGAAAT-AACTGAAGAAAGACCACCCTGGGTCAACTGAA
9247 ATAAAT
65 ATAAAT
* * * * *
9253 TGAAGAATGACCACCCTCGATCATTCGGACATAAGCTGAAGAAAAGACCACCCCGGGTCAACTGA
1 TGAAGAAAGACCACCCTGGATCATTCTGAAATAA-CTGAAG-AAAGACCACCCTGGGTCAACTGA
*
9318 AATAAGT
64 AATAAAT
* * * * * * * *
9325 TGAAGAAAGACCGCCCTGGGTCA-ACTGAAATGAATTGAAGAACGACCACCCTCGATCATTCTGA
1 TGAAGAAAGACCACCCTGGATCATTCTGAAAT-AACTGAAGAAAGACCACCCTGGGTCA-ACTGA
* *
9389 CATAAAC
64 AATAAAT
* * *
9396 TGAAGAAAAGACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGA
1 TGAAG-AAAGACCACCCTGGATCATTCTGAAAT-AACTGAAGAAAGACCACCCTGGGTCAACTGA
*
9460 AATGAAT
64 AATAAAT
* * * *
9467 TGAAGAACGACCACCCTCGATCATTCTGACATAAAATGAAGAAAAGACCACCCTGGGTCAACTGA
1 TGAAGAAAGACCACCCTGGATCATTCTGAAAT-AACTGAAG-AAAGACCACCCTGGGTCAACTGA
9532 AAT
64 AAT
9535 TTGTGAAGAT
Statistics
Matches: 230, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
69 21 0.09
70 32 0.14
71 59 0.26
72 118 0.51
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (70 bp):
TGAAGAAAGACCACCCTGGATCATTCTGAAATAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
TAAAT
Found at i:9399 original size:107 final size:106
Alignment explanation
Indices: 9194--9534 Score: 558
Period size: 107 Copynumber: 3.2 Consensus size: 106
9184 TGAAGAATGG
* * * *
9194 CCACCCTGGATC-ATTGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACTGACATAAATTGAAG
1 CCACCCTGGGTCAACTGAAAT-AATTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAG
* * *
9258 AATGACCACCCTCGATCATTCGGACATAAGCTGAAGAAAAGA
65 AACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGA
*
9300 CCACCCCGGGTCAACTGAAATAAGTTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAG
1 CCACCCTGGGTCAACTGAAATAA-TTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAG
9365 AACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGA
65 AACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGA
*
9407 CCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAG
1 CCACCCTGGGTCAACTGAAAT-AATTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAG
*
9472 AACGACCACCCTCGATCATTCTGACATAAAATGAAGAAAAGA
65 AACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGA
9514 CCACCCTGGGTCAACTGAAAT
1 CCACCCTGGGTCAACTGAAAT
9535 TTGTGAAGAT
Statistics
Matches: 221, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
106 12 0.05
107 207 0.94
108 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (106 bp):
CCACCCTGGGTCAACTGAAATAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATGAATTGAAGA
ACGACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGA
Found at i:14538 original size:23 final size:23
Alignment explanation
Indices: 14508--14553 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
14498 TGACTACCAT
14508 GGCAAGTAAGACACGAATGGAGG
1 GGCAAGTAAGACACGAATGGAGG
14531 GGCAAGTAAGACACGAATGGAGG
1 GGCAAGTAAGACACGAATGGAGG
14554 ATTTTATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.39, T:0.09
Consensus pattern (23 bp):
GGCAAGTAAGACACGAATGGAGG
Found at i:15020 original size:19 final size:19
Alignment explanation
Indices: 14996--15033 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14986 AGCCTTCCTG
14996 TTTGTTCGGCAAAGAAAGT
1 TTTGTTCGGCAAAGAAAGT
15015 TTTGTTCGGCAAAGAAAGT
1 TTTGTTCGGCAAAGAAAGT
15034 CTGTACGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
TTTGTTCGGCAAAGAAAGT
Found at i:15206 original size:55 final size:55
Alignment explanation
Indices: 15071--15256 Score: 333
Period size: 55 Copynumber: 3.4 Consensus size: 55
15061 AGAAAAAAGG
*
15071 TGGGAACTTTCCCAATTTG-AAA-AAGAGCTAGATTGAATGCTTTGAAAACTG-A
1 TGGGAACTTTCCCAATTTGAAAACAAGAGATAGATTGAATGCTTTGAAAACTGAA
*
15123 TGGGAACTTTCCCAATTTGAAAAAAAGAGATAGATTGAATGCTTTGAAAACTGAA
1 TGGGAACTTTCCCAATTTGAAAACAAGAGATAGATTGAATGCTTTGAAAACTGAA
15178 TGGGAACTTTCCCAATTTGAAAACAAGAGATAGATTGAATGCTTTGAAAACTGAA
1 TGGGAACTTTCCCAATTTGAAAACAAGAGATAGATTGAATGCTTTGAAAACTGAA
15233 TGGGAACTTTCCCAATTTGAAAAC
1 TGGGAACTTTCCCAATTTGAAAAC
15257 TTAAAAAAAC
Statistics
Matches: 129, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
52 19 0.15
53 3 0.02
54 28 0.22
55 79 0.61
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (55 bp):
TGGGAACTTTCCCAATTTGAAAACAAGAGATAGATTGAATGCTTTGAAAACTGAA
Found at i:15274 original size:37 final size:38
Alignment explanation
Indices: 15224--15295 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
15214 GAATGCTTTG
*
15224 AAAACTGAATGGGAACTTTCCCAATTTGAAAACTTAAA
1 AAAACTGAATGGGAACTTTCCCAATTTAAAAACTTAAA
*
15262 AAAACTG-GTGGGAACTTTCCCAATTTAAAAACTT
1 AAAACTGAATGGGAACTTTCCCAATTTAAAAACTT
15296 GAACCTGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (38 bp):
AAAACTGAATGGGAACTTTCCCAATTTAAAAACTTAAA
Found at i:16608 original size:14 final size:14
Alignment explanation
Indices: 16589--16619 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16579 TTTATAATTC
16589 CTAACTCTATAACT
1 CTAACTCTATAACT
*
16603 CTAACTTTATAACT
1 CTAACTCTATAACT
16617 CTA
1 CTA
16620 GTTGAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (14 bp):
CTAACTCTATAACT
Found at i:22038 original size:38 final size:37
Alignment explanation
Indices: 21990--22180 Score: 190
Period size: 38 Copynumber: 5.0 Consensus size: 37
21980 CTAGAAGTTG
* *
21990 ATGGGAACTTTCCCAATTTAAAAATTTTTGCAAACTGA
1 ATGGGAACTTTCCCAATTTAAAAA-CTTTGAAAACTGA
* *
22028 ATGGGAACTTTCCCAAATTAAAAAAAAAAAACTCTGAAAACTGAA
1 ATGGGAACTTTCCC-AATT------TAAAAACTTTGAAAACTG-A
22073 ATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTGA
1 ATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTGA
* *
22110 ATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACGTG-
1 ATGGGAACTTTCCCAATTTAAAAACTTTGAAAAC-TGA
* * *
22146 -TGGGAACTTTCCCAATTTGAAAACTTCGAAGACTG
1 ATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTG
22181 GTTCTTGATT
Statistics
Matches: 132, Mismatches: 11, Indels: 23
0.80 0.07 0.14
Matches are distributed among these distances:
35 26 0.20
36 12 0.09
37 27 0.20
38 30 0.23
39 4 0.03
44 13 0.10
45 20 0.15
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (37 bp):
ATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTGA
Found at i:22122 original size:37 final size:37
Alignment explanation
Indices: 22054--22180 Score: 161
Period size: 37 Copynumber: 3.5 Consensus size: 37
22044 ATTAAAAAAA
*
22054 AAAAACTCTGAAAACTGAAATGGGAACTTTCCCAATTT
1 AAAAACTTTGAAAACTG-AATGGGAACTTTCCCAATTT
22092 AAAAACTTTGAAAACTGAATGGGAACTTTCCCAATTT
1 AAAAACTTTGAAAACTGAATGGGAACTTTCCCAATTT
* *
22129 GAAAAC-TTAAAAACGTG--TGGGAACTTTCCCAATTT
1 AAAAACTTTGAAAAC-TGAATGGGAACTTTCCCAATTT
* * *
22164 GAAAACTTCGAAGACTG
1 AAAAACTTTGAAAACTG
22181 GTTCTTGATT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
35 26 0.32
36 12 0.15
37 27 0.33
38 16 0.20
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (37 bp):
AAAAACTTTGAAAACTGAATGGGAACTTTCCCAATTT
Found at i:22854 original size:25 final size:25
Alignment explanation
Indices: 22826--22884 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
22816 CCCACATTAT
22826 AACTAAAAACT-AGAGCCCAAACCTA
1 AACTAAAAACTAAG-GCCCAAACCTA
* *
22851 AACTAAGAACTAAGGTCCAAACCTA
1 AACTAAAAACTAAGGCCCAAACCTA
22876 ATA-TAAAAA
1 A-ACTAAAAA
22885 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.54, C:0.22, G:0.08, T:0.15
Consensus pattern (25 bp):
AACTAAAAACTAAGGCCCAAACCTA
Done.