Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013093.1 Corchorus olitorius cultivar O-4 contig13126, 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: 34562
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:3045 original size:108 final size:106
Alignment explanation
Indices: 2840--3050 Score: 307
Period size: 108 Copynumber: 2.0 Consensus size: 106
2830 AAGTTGATCG
** * * *
2840 GCTCACGCTGGCGCATCGAGCATTCTTGATTTGTGGCTAGCAAATTATTTTAGTTTTAGAGTTTT
1 GCTCACGCTGGCGCATCGAGCATTCTTGAAATGTGGCTAGCAAATCATTTTACTTATAGAGTTTT
2905 TTTTCTCGGTTCTTATCATATATGTGAGTAGGTGGTTACCA
66 TTTTCTCGGTTCTTATCATATATGTGAGTAGGTGGTTACCA
* * *
2946 GCTCGCGCTGGCGCGTTGAGCATT-TTGAAATGTGGCTAGCAAATCATTTTACTTATAGAGTTTT
1 GCTCACGCTGGCGCATCGAGCATTCTTGAAATGTGGCTAGCAAATCATTTTACTTATAGAG-TTT
*
3010 TTTTCCTCTCGGTTCTTATCATATATTTGAGTAGGTGGTTA
65 TTTT--TCTCGGTTCTTATCATATATGTGAGTAGGTGGTTA
3051 GCAAATTCGA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 31 0.33
106 28 0.30
108 34 0.37
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (106 bp):
GCTCACGCTGGCGCATCGAGCATTCTTGAAATGTGGCTAGCAAATCATTTTACTTATAGAGTTTT
TTTTCTCGGTTCTTATCATATATGTGAGTAGGTGGTTACCA
Found at i:4235 original size:42 final size:42
Alignment explanation
Indices: 4176--4256 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
4166 GCTAAGTCTT
4176 GAAAATTCTCTGTAAATTAAGAAATACTCTA-CTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTC-AGCTCAAATCATA
* * *
4218 GAAAATTCTTTGTAAATTAATAAATGCTCAGCTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAGCTCAAATC
4257 CTAAGCCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAGCTCAAATCATA
Found at i:4386 original size:55 final size:56
Alignment explanation
Indices: 4325--4435 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
4315 ATTTTGTAGA
*
4325 ATAATTAAGTAGAGATAG-GAGGATA-TGATTTATTATAACATTTATTGTGTGAAAG
1 ATAATTAAGTAAAGATAGAGAGGATAGT-ATTTATTATAACATTTATTGTGTGAAAG
*
4380 ATAATTAAGTAAAGATAGAGGGGATAGTATTTATTATAACATTTATTGTGTGAAAG
1 ATAATTAAGTAAAGATAGAGAGGATAGTATTTATTATAACATTTATTGTGTGAAAG
4436 GAAACGGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
55 17 0.33
56 34 0.65
57 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.36
Consensus pattern (56 bp):
ATAATTAAGTAAAGATAGAGAGGATAGTATTTATTATAACATTTATTGTGTGAAAG
Found at i:10267 original size:31 final size:31
Alignment explanation
Indices: 10226--10304 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
10216 CGTTTATGTT
10226 TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
*
10257 TTTAGACTCAAATTGAG-CAACTTTTGAAAGG
1 TTTAGGCTCAAATTG-GTCAACTTTTGAAAGG
* *
10288 GTTAGGCTTAAATTGGT
1 TTTAGGCTCAAATTGGT
10305 GGCTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.02
31 40 0.95
32 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (31 bp):
TTTAGGCTCAAATTGGTCAACTTTTGAAAGG
Found at i:11035 original size:30 final size:30
Alignment explanation
Indices: 10999--11058 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
10989 CGCAACTTTT
10999 TTTTTCTTAACTCAACCCAAACACTATTTA
1 TTTTTCTTAACTCAACCCAAACACTATTTA
11029 TTTTTCTTAACTCAACCCAAACACTATTTA
1 TTTTTCTTAACTCAACCCAAACACTATTTA
11059 ATATTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTTTCTTAACTCAACCCAAACACTATTTA
Found at i:17840 original size:236 final size:235
Alignment explanation
Indices: 17365--17840 Score: 749
Period size: 236 Copynumber: 2.0 Consensus size: 235
17355 AGAATTCCGA
17365 ACCAATCCTCTATACTCATAATTTCCAAAACAGTAACAGTAGAATTAAATAAATGAAAGTTCTCA
1 ACCAATCCTCTATACTCATAATTTCCAAAACAGTAACAGTAGAATTAAATAAATGAAAGTTCTCA
* *
17430 TAAGTAAAGGTTAACATGTTACCCATGTGAAAACGAAAACAGAAATTCAGGCTATGTTCGGTGGT
66 TAAGTAAAGGTTAACATGTTACCCATGTGAAAACGAAAACAGAAATT----CTAGGTTCGGTGAT
* * * * *
17495 GGAGAACATTCTTCATTTTTCATCTCCGAAAAATTCAAAGAAATTAGATAGTGACACAATATGTG
127 GGAGAACATTCTCCATTTTCCATCTCCAAAAAAATCAAAGAAATTAGATAGTGACACAACATGTG
* * *
17560 TCAATGAAAACAAGTATATTGTTAGAGAATGGAGATGACAATGG
192 TAAATGAAAACAAGCATATTGTTAGAGAATGAAGATGACAATGG
*
17604 ACCAATCCTCTATACTCATAATTTCCAAAACAGTAATAGTAGAATTAAATAAATGAAAGTTCTCA
1 ACCAATCCTCTATACTCATAATTTCCAAAACAGTAACAGTAGAATTAAATAAATGAAAGTTCTCA
*
17669 TAAGTAAAGGTTAACGTGTTAACCCCATGTGAAAACAGAAAACAGAAATT-TAGGTT-GGTGATG
66 TAAGTAAAGGTTAACATGTT-A-CCCATGTGAAAAC-GAAAACAGAAATTCTAGGTTCGGTGATG
* *
17732 GAGAACATTCTCCCTTTTCCATTTCCAAAAAAATCAAAGAAATTAGATAGTGACACAACATGTGT
128 GAGAACATTCTCCATTTTCCATCTCCAAAAAAATCAAAGAAATTAGATAGTGACACAACATGTGT
17797 AAATGAAAACAAGCATATTGTTAGAGAATGAAGATGACAATGG
193 AAATGAAAACAAGCATATTGTTAGAGAATGAAGATGACAATGG
17840 A
1 A
17841 GTGACAATCT
Statistics
Matches: 220, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
236 105 0.48
237 5 0.02
239 83 0.38
240 1 0.00
241 13 0.06
242 13 0.06
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (235 bp):
ACCAATCCTCTATACTCATAATTTCCAAAACAGTAACAGTAGAATTAAATAAATGAAAGTTCTCA
TAAGTAAAGGTTAACATGTTACCCATGTGAAAACGAAAACAGAAATTCTAGGTTCGGTGATGGAG
AACATTCTCCATTTTCCATCTCCAAAAAAATCAAAGAAATTAGATAGTGACACAACATGTGTAAA
TGAAAACAAGCATATTGTTAGAGAATGAAGATGACAATGG
Found at i:20709 original size:2 final size:2
Alignment explanation
Indices: 20702--20742 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20692 ACATTTATGT
*
20702 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20743 TATTGGCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22290 original size:43 final size:44
Alignment explanation
Indices: 22242--22344 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
22232 TATAGTTAGG
* * * * *
22242 TTATCAAAGTTTCATATGGCGTTTATCATAATTTCATA-GATAA
1 TTATCAAAATTTCATATGGCGGTCATCAAAATTTAATAGGATAA
* * *
22285 TTATCAAAATTTCATATGGTGGTCATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATATGGCGGTCATCAAAATTTAATAGGATAA
22329 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
22345 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 32 0.63
44 19 0.37
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGCGGTCATCAAAATTTAATAGGATAA
Found at i:22315 original size:22 final size:22
Alignment explanation
Indices: 22287--22344 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
22277 ATAGATAATT
* *
22287 ATCAAAATTTCATATGGTGGTC
1 ATCAAAATTTCATAGGGTAGTC
* *
22309 ATCAAAATTTAATAGGGTAGTT
1 ATCAAAATTTCATAGGGTAGTC
22331 ATCAAAATTTCATA
1 ATCAAAATTTCATA
22345 AAAATATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGTAGTC
Found at i:22443 original size:2 final size:2
Alignment explanation
Indices: 22403--22429 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22393 CTAAAACTCT
22403 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
22430 CTTCATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22658 original size:29 final size:30
Alignment explanation
Indices: 22593--22665 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
22583 TTATTTTTAC
*
22593 ACGTTAAACATCTTTTCTCTTTTAGATATT
1 ACGTTAAACATCTTTTCTCTTTGAGATATT
*
22623 ACATTAAACATCTTTGT-T-TTTGAGATATT
1 ACGTTAAACATCTTT-TCTCTTTGAGATATT
22652 ACGTTAAACATCTT
1 ACGTTAAACATCTT
22666 AGTATGATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 23 0.59
30 15 0.38
31 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (30 bp):
ACGTTAAACATCTTTTCTCTTTGAGATATT
Found at i:22691 original size:26 final size:27
Alignment explanation
Indices: 22654--22706 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
22644 GAGATATTAC
22654 GTTAAACATCTTAGTATGAT-ATAATT
1 GTTAAACATCTTAGTATGATAATAATT
* * *
22680 GTTAAACTTCTTATTATTATAATAATT
1 GTTAAACATCTTAGTATGATAATAATT
22707 ATATATTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (27 bp):
GTTAAACATCTTAGTATGATAATAATT
Found at i:23174 original size:48 final size:48
Alignment explanation
Indices: 23103--23194 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
23093 AAAAACTAAT
* *
23103 TTGATTCATGAGTGTTATGATTTGCTCTAATCTCATAATATTTTTGTA
1 TTGATTCATAAGTGTTATAATTTGCTCTAATCTCATAATATTTTTGTA
23151 TTGATTCATAAGTGTTATAATTTGCTCTAATCTCATAATATTTT
1 TTGATTCATAAGTGTTATAATTTGCTCTAATCTCATAATATTTT
23195 GGAATTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (48 bp):
TTGATTCATAAGTGTTATAATTTGCTCTAATCTCATAATATTTTTGTA
Found at i:27234 original size:2 final size:2
Alignment explanation
Indices: 27227--27256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27217 CATTAGCTAG
27227 TA 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 TA
27257 ATAAAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28768 original size:178 final size:178
Alignment explanation
Indices: 28394--28849 Score: 501
Period size: 178 Copynumber: 2.6 Consensus size: 178
28384 AAGGTTAGTT
* * *
28394 AAGTGTCTATTAAAAGGTTATTCCATGATTTACAACTTTCATGAAAGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGGTTATTTCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * * * * *
28459 ATGTTTCAAGTATCAAAAAGA-ACTTCCGAAAAATGAGTTGTTTCAGTTAACGGGAATGGACGAT
66 ATATTTCAAGTAT-AAAAA-ATGCTTCTGAAAAATTAATTCTTTCAGTTAACGGGAATGGACGAT
* * *
28523 CCACTTAATATTACAATACTTTTGCTCCGGATGTCTCATTGAGGTTATTC
129 CCACTTAATAATACAATACTTTTGCTCCAGATGTCTCATTGAGGTGATTC
* * * * * *
28573 AAGTGTCTCTCAAAAGGTTATTTTATGATCTACAACTTTTATGCAGGACTCGAAAGCTAAATTTA
1 AAGTGTCTATTAAAAGGTTATTTCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * *
28638 ATATTTCAAGTATAAAAAATGCTTCTAAAAAATTAATTCTTTC-GTT-TCGCGAGAATGGACGGT
66 ATATTTCAAGTATAAAAAATGCTTCTGAAAAATTAATTCTTTCAGTTAACG-G-GAATGGACGAT
*
28701 CCACTTAATAATAC-ATAATTTTTGCTCCAGATGTC-CGATTGAGGTGATTC
129 CCACTTAATAATACAAT-ACTTTTGCTCCAGATGTCTC-ATTGAGGTGATTC
* * * * * * *
28751 AAGTGTTTGTTAAAAGGTTGTTTCGTGATCTGCAACTTTCATGGAGCACAT-GAAAACTAAATTT
1 AAGTGTCTATTAAAAGGTTATTTCATGATCTACAACTTTCATGAAGGAC-TCGAAAACTAAATTT
* * * **
28815 GATTTTTCAAATACCAAAAATGCTTCTGAAAAATT
65 AATATTTCAAGTATAAAAAATGCTTCTGAAAAATT
28850 TATTTTCGGT
Statistics
Matches: 232, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
176 2 0.01
177 8 0.03
178 153 0.66
179 69 0.30
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (178 bp):
AAGTGTCTATTAAAAGGTTATTTCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
ATATTTCAAGTATAAAAAATGCTTCTGAAAAATTAATTCTTTCAGTTAACGGGAATGGACGATCC
ACTTAATAATACAATACTTTTGCTCCAGATGTCTCATTGAGGTGATTC
Found at i:29833 original size:2 final size:2
Alignment explanation
Indices: 29828--29869 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
29818 TTTAACATAC
29828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29870 TCTATAAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32855 original size:6 final size:6
Alignment explanation
Indices: 32840--32899 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
32830 CCCAAGCCAG
* * *
32840 AAAGAGA AAAGAA AAAAAA AAAGAA AAGGAA GAAAGAA AAGGAA AAAGAA
1 AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA
*
32890 TAAGATA AAA
1 AAAGA-A AAA
32900 AAATGGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 30 0.70
7 13 0.30
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAGAA
Done.