Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018219.1 Corchorus olitorius cultivar O-4 contig18252, 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: 53981
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:248 original size:4 final size:4
Alignment explanation
Indices: 241--460 Score: 62
Period size: 4 Copynumber: 55.5 Consensus size: 4
231 AAAGATTTTT
* * **
241 TTTA TTTA TTTA -CTA TTTA TATT- TTTA TTTA TTAA TTTA ACTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * **
287 TCTA TTTA TTTA -CTA TTTA TCCT- TTTA TTTA TTAA TTTA GCTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * ** **
333 TCTA GTTA TTTA CTATTA TCTA CTT- TTT- TTTA CCTA ACTA TTTA TCTTA
1 TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* * ** * * * *
382 -TTA TCTA TATA CCTA TTTA TCTTT TTTA TTTA TCTA TTATT TTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TT-TA TTTA TTTA
* *
431 TTTA TCTA TTTA TTTA TTTA TTTA TCTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
461 ACTTTTTTTA
Statistics
Matches: 152, Mismatches: 49, Indels: 30
0.66 0.21 0.13
Matches are distributed among these distances:
3 19 0.12
4 116 0.76
5 14 0.09
6 3 0.02
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (4 bp):
TTTA
Found at i:272 original size:27 final size:27
Alignment explanation
Indices: 235--298 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
225 GACCAAAAAG
*
235 ATTTTT-TTTATTTATTT-ACTATTTAT
1 ATTTTTATTTATTAATTTAACTA-TTAT
261 ATTTTTATTTATTAATTTAACTATTAT
1 ATTTTTATTTATTAATTTAACTATTAT
* *
288 CTATTTATTTA
1 ATTTTTATTTA
299 CTATTTATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 23 0.70
28 4 0.12
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTATTTATTAATTTAACTATTAT
Found at i:287 original size:19 final size:18
Alignment explanation
Indices: 265--303 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
255 ATTTATATTT
*
265 TTATTTATTAATTTAACTA
1 TTATCTATTAATTT-ACTA
*
284 TTATCTATTTATTTACTA
1 TTATCTATTAATTTACTA
302 TT
1 TT
304 TATCCTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATCTATTAATTTACTA
Found at i:313 original size:46 final size:46
Alignment explanation
Indices: 243--364 Score: 181
Period size: 46 Copynumber: 2.6 Consensus size: 46
233 AGATTTTTTT
*
243 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* *
289 TATTTATTTACTATTTATCCTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* * *
335 TAGTTATTTACTATTATCTACTTTTTTTTA
1 TATTTATTTACTATT-TATACTTTTATTTA
365 CCTAACTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
46 57 0.84
47 11 0.16
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (46 bp):
TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
Found at i:470 original size:20 final size:19
Alignment explanation
Indices: 398--470 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 19
388 ATATACCTAT
398 TTATCTTTTTTATTTATCTA
1 TTAT-TTTTTTATTTATCTA
418 TTATTTTTACTTATTTATCTA
1 TTATTTTT--TTATTTATCTA
*
439 TTTATTTATTTATTTATCTA
1 -TTATTTTTTTATTTATCTA
459 TTACTTTTTTTA
1 TTA-TTTTTTTA
471 ATATTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.15
20 22 0.47
21 11 0.23
22 7 0.15
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTTTTATTTATCTA
Found at i:11401 original size:38 final size:38
Alignment explanation
Indices: 11348--11573 Score: 337
Period size: 38 Copynumber: 5.9 Consensus size: 38
11338 GAATTTATTA
11348 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
11386 GTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
11424 GTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
*
11462 GTCTTGGTCCCAAGCGAATAAAGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
11500 GTCTTGATCCCAAGCGAATAAAGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* ** *
11538 GTCTTGATCAAAAGCGAATAAT-AAATTTGGTCGCTT
1 GTCTTGGTCCCAAGCGAATAATGAAA-TTGATCGCTT
11574 TGTTGCAAGT
Statistics
Matches: 177, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
37 3 0.02
38 174 0.98
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (38 bp):
GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
Found at i:24499 original size:55 final size:57
Alignment explanation
Indices: 24423--24537 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 57
24413 TTATCTGTTC
24423 CTTTCACACAATAAATGTTATAATAAATCATAT-CCCC-TATCTATACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTTATCTATACTTAATTATT
* * *
24478 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTTTTCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATAT-CCCCCTTATCTATACTTAATTATT
24536 CT
1 CT
24538 ATAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 32 0.59
57 4 0.07
58 18 0.33
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTTATCTATACTTAATTATT
Found at i:24649 original size:21 final size:21
Alignment explanation
Indices: 24625--24691 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
24615 AGTATTCTTA
24625 ATTTACAAAGAATTTTCTATG
1 ATTTACAAAGAATTTTCTATG
*** * *
24646 ATTTGA-GTTGAGTATTTCT-TA
1 ATTT-ACAAAGAAT-TTTCTATG
24667 ATTTACAAAGAATTTTCTATG
1 ATTTACAAAGAATTTTCTATG
24688 ATTT
1 ATTT
24692 GAGTTGAGTA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (21 bp):
ATTTACAAAGAATTTTCTATG
Found at i:24676 original size:42 final size:42
Alignment explanation
Indices: 24604--24725 Score: 219
Period size: 42 Copynumber: 2.9 Consensus size: 42
24594 TAAGGATCAG
*
24604 GATTTCAGTTGAGTA-TTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
24645 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
24687 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
24726 AAGACTTAGC
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
41 14 0.18
42 64 0.82
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:33979 original size:61 final size:63
Alignment explanation
Indices: 33880--34013 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 63
33870 AGTTTGCATG
* * *
33880 ATGCAT-CCTGATTTGCATCCATACATGCATACATTTATCCATCAATCATATCT-ATGTCTGC
1 ATGCATACCTGATTTACATCCATACATGCATACAGTTATCCATCAATCATATCTAATGCCTGC
* *
33941 ATGCATACCTTATTTACATCCATACATG-ATACAGTTATCCATCAATTATATCTACATGCCTGC
1 ATGCATACCTGATTTACATCCATACATGCATACAGTTATCCATCAATCATATCTA-ATGCCTGC
34004 ATGCATACCT
1 ATGCATACCT
34014 ACATACCAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 29 0.45
62 19 0.29
63 17 0.26
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (63 bp):
ATGCATACCTGATTTACATCCATACATGCATACAGTTATCCATCAATCATATCTAATGCCTGC
Found at i:37304 original size:35 final size:37
Alignment explanation
Indices: 37262--37335 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 37
37252 AAAATTCTTG
37262 AAACCATTTG-TT-CCATTTTTTTTTTTGAAAAGCAA
1 AAACCATTTGTTTACCATTTTTTTTTTTGAAAAGCAA
37297 AAACCATTTGTTTGAAACCATTTTTTTTTTTGAAAAGCA
1 AAACCATTTGTTT---ACCATTTTTTTTTTTGAAAAGCA
37336 TTTGTTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 10 0.29
36 2 0.06
40 22 0.65
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (37 bp):
AAACCATTTGTTTACCATTTTTTTTTTTGAAAAGCAA
Found at i:39202 original size:16 final size:16
Alignment explanation
Indices: 39181--39212 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39171 TCCACTATGG
39181 CTAAAAAATCATTTTA
1 CTAAAAAATCATTTTA
*
39197 CTAAAAAATCGTTTTA
1 CTAAAAAATCATTTTA
39213 GGGATATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (16 bp):
CTAAAAAATCATTTTA
Found at i:41419 original size:3 final size:3
Alignment explanation
Indices: 41404--41474 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
41394 GAATCTATCT
*
41404 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41452 TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
41475 GGGAAATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42238 original size:2 final size:2
Alignment explanation
Indices: 42196--42226 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42186 AATTTTGGAG
42196 TA TA 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 TA TA T
42227 TAACTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44386 original size:13 final size:14
Alignment explanation
Indices: 44368--44397 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
44358 ATAAATCATT
44368 TATTAAAT-AAATA
1 TATTAAATAAAATA
44381 TATTAAATAAAATA
1 TATTAAATAAAATA
44395 TAT
1 TAT
44398 AATTTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTAAATAAAATA
Found at i:46090 original size:29 final size:29
Alignment explanation
Indices: 46057--46120 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
46047 TAATCATTAA
* * * *
46057 AATTCCGTCTACCAATATATGTGTTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
46086 AATTCCATCTACCAATAAACGTGCTACAT
1 AATTCCATCTACCAATAAACGTGCTACAT
46115 AATTCC
1 AATTCC
46121 TTATAGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (29 bp):
AATTCCATCTACCAATAAACGTGCTACAT
Found at i:47367 original size:15 final size:15
Alignment explanation
Indices: 47347--47375 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47337 ATACAACAAA
47347 GTAAGTCTTGATTCG
1 GTAAGTCTTGATTCG
47362 GTAAGTCTTGATTC
1 GTAAGTCTTGATTC
47376 ATGAAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (15 bp):
GTAAGTCTTGATTCG
Found at i:47551 original size:24 final size:24
Alignment explanation
Indices: 47519--47569 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
47509 CTACTACTAA
*
47519 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
47543 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
47567 TAA
1 TAA
47570 CGTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:52924 original size:21 final size:21
Alignment explanation
Indices: 52898--52960 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
52888 TTCAACAGAC
52898 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
*
52919 CAAGTCCTGGGTAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
52940 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
52961 TCTGATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.25
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:52984 original size:92 final size:92
Alignment explanation
Indices: 52826--53032 Score: 315
Period size: 92 Copynumber: 2.2 Consensus size: 92
52816 TTTTCGGCAA
*
52826 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAAGACTTCTTCTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGACAAGACTTCTTCTGAATTTTCTTCCGTCTTTC
52891 AACAGACCAAGTCCTGGGCAGGAGTTGT
65 AACAGACCAAGTCCTGGGCAGGAGTTGT
* * * * * *
52919 CAAGTCCTGGGTAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGACAAGACTTCTTCTGAATTTTCTTCCGTCTTTCA
* *
52984 ACAGACTAGGTCCTGGGCAGGAGTTGT
66 ACAGACCAAGTCCTGGGCAGGAGTTGT
*
53011 CAAGTCCTGGGCAGGACTTGTC
1 CAAGTCCTGGGCAGGAGTTGTC
53033 CTGTTTTTAG
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
92 83 0.81
93 20 0.19
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.30
Consensus pattern (92 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGACAAGACTTCTTCTGAATTTTCTTCCGTCTTTCA
ACAGACCAAGTCCTGGGCAGGAGTTGT
Found at i:53019 original size:21 final size:21
Alignment explanation
Indices: 52993--53032 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52983 AACAGACTAG
*
52993 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
53014 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
53033 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Done.