Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019146.1 Corchorus olitorius cultivar O-4 contig19179, 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: 52336
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4763 original size:24 final size:24
Alignment explanation
Indices: 4736--4808 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
4726 TGGTGTTTGA
*
4736 CTTCTGCGGTAGAATAGTGATTGG
1 CTTCTGCGGTAGAATAGTGGTTGG
* * * *
4760 CTTCTACAGTAGAATGGTGGTTAG
1 CTTCTGCGGTAGAATAGTGGTTGG
*
4784 CCTCTGCGGTAGAATAGTGGTTGG
1 CTTCTGCGGTAGAATAGTGGTTGG
4808 C
1 C
4809 ATCATTCCAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.32
Consensus pattern (24 bp):
CTTCTGCGGTAGAATAGTGGTTGG
Found at i:5254 original size:29 final size:29
Alignment explanation
Indices: 5220--5320 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
5210 ACTCCCGTAA
*
5220 TTGGGACTCACGCTATGCAGCTTCCGCGG
1 TTGGGACTCACGCTATGAAGCTTCCGCGG
* * *
5249 TTGGGACTCACGCTATGTAGCTTTCTCGG
1 TTGGGACTCACGCTATGAAGCTTCCGCGG
* * *
5278 TTGGGACTCATGCTA--AAGCTCCCGCAG
1 TTGGGACTCACGCTATGAAGCTTCCGCGG
*
5305 TTGGGACTCACACTAT
1 TTGGGACTCACGCTAT
5321 AAAACTCCCA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 20 0.33
29 40 0.67
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.28
Consensus pattern (29 bp):
TTGGGACTCACGCTATGAAGCTTCCGCGG
Found at i:5307 original size:27 final size:27
Alignment explanation
Indices: 5183--5530 Score: 201
Period size: 27 Copynumber: 12.9 Consensus size: 27
5173 AAAAAGAGAT
* * *
5183 GCTCCCGCAATTGGGACTTATGCTGGAA
1 GCTCCCGCAGTTGGGACTCATGCT-AAA
* * * *
5211 -CTCCCGTAATTGGGACTCACGCTATGCA
1 GCTCCCGCAGTTGGGACTCATGCTA--AA
* * * *
5239 GCTTCCGCGGTTGGGACTCACGCTATGTA
1 GCTCCCGCAGTTGGGACTCATGCTA--AA
** * *
5268 GCTTTCTCGGTTGGGACTCATGCTAAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
**
5295 GCTCCCGCAGTTGGGACTCACACTATAAA
1 GCTCCCGCAGTTGGGACTCATGC--TAAA
* * ****
5324 ACT-CC-CA--TAGGACTCATAAGGAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
* * *
5347 GCTCCCGCAGTTGGGATTTATGCTGAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
* * *
5374 GCTCTCGCAGTTGAGACTCATGCCAAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
* *
5401 GC-CTCCGCAGTTGGGACTCATGTTGAA
1 GCTC-CCGCAGTTGGGACTCATGCTAAA
* * *
5428 GCTCCCGCAGTCGGGGCTCATGCCAAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
*
5455 GC-CTCCGCAGTTGGGACTCATGCTGAA
1 GCTC-CCGCAGTTGGGACTCATGCTAAA
5482 GCT-CCGCAGTTGGGACTCATGCTAAA
1 GCTCCCGCAGTTGGGACTCATGCTAAA
* * * *
5508 GAT-CTGCATTTGGGACTAATGCT
1 GCTCCCGCAGTTGGGACTCATGCT
5531 GAAGGACTCA
Statistics
Matches: 249, Mismatches: 58, Indels: 28
0.74 0.17 0.08
Matches are distributed among these distances:
23 4 0.02
24 2 0.01
25 11 0.04
26 43 0.17
27 134 0.54
28 4 0.02
29 51 0.20
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (27 bp):
GCTCCCGCAGTTGGGACTCATGCTAAA
Found at i:5416 original size:54 final size:53
Alignment explanation
Indices: 5351--5534 Score: 244
Period size: 54 Copynumber: 3.5 Consensus size: 53
5341 AAGGAAGCTC
* * *
5351 CCGCAGTTGGGATTTATGCTGAAGCTCTCGCAGTTGAGACTCATGCCAAAGCCT
1 CCGCAGTTGGGACTCATGCTGAAGCTC-CGCAGTTGGGACTCATGCCAAAGCCT
* * *
5405 CCGCAGTTGGGACTCATGTTGAAGCTCCCGCAGTCGGGGCTCATGCCAAAGCCT
1 CCGCAGTTGGGACTCATGCTGAAGCT-CCGCAGTTGGGACTCATGCCAAAGCCT
* *
5459 CCGCAGTTGGGACTCATGCTGAAGCTCCGCAGTTGGGACTCATGCTAAAG-AT
1 CCGCAGTTGGGACTCATGCTGAAGCTCCGCAGTTGGGACTCATGCCAAAGCCT
* * *
5511 CTGCATTTGGGACTAATGCTGAAG
1 CCGCAGTTGGGACTCATGCTGAAG
5535 GACTCATGTC
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
52 22 0.19
53 21 0.18
54 71 0.62
55 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (53 bp):
CCGCAGTTGGGACTCATGCTGAAGCTCCGCAGTTGGGACTCATGCCAAAGCCT
Found at i:8403 original size:11 final size:12
Alignment explanation
Indices: 8380--8409 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
8370 CTTTAATGGG
8380 TATATTAATATA
1 TATATTAATATA
8392 TATATTATATATA
1 TATATTA-ATATA
8405 TATAT
1 TATAT
8410 GTTAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATTAATATA
Found at i:27725 original size:26 final size:26
Alignment explanation
Indices: 27695--27749 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
27685 GCCATCTTGA
*
27695 TCATTTTTGTCTCAGGGGCATTTTGG
1 TCATTTTTGCCTCAGGGGCATTTTGG
*
27721 TCATTTTTGCCTTAGGGGCATTTTGG
1 TCATTTTTGCCTCAGGGGCATTTTGG
27747 TCA
1 TCA
27750 AAATTATTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.45
Consensus pattern (26 bp):
TCATTTTTGCCTCAGGGGCATTTTGG
Found at i:30521 original size:16 final size:15
Alignment explanation
Indices: 30483--30524 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
30473 ACAGAGATTG
*
30483 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
30498 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30513 ACTAGAAAACAA
1 AC-AGAAAACAA
30525 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:31299 original size:11 final size:11
Alignment explanation
Indices: 31283--31308 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31273 CCTTTGCCTA
31283 AAAACTAGAAG
1 AAAACTAGAAG
31294 AAAACTAGAAG
1 AAAACTAGAAG
31305 AAAA
1 AAAA
31309 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:44105 original size:54 final size:54
Alignment explanation
Indices: 44036--44431 Score: 575
Period size: 54 Copynumber: 7.4 Consensus size: 54
44026 AAATCAGAGC
* *
44036 AATTAAACTAAAGAGTAAAAGAGGAAGTAAAGAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
*
44090 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCCGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * *
44144 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTATTTCCGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
*
44198 AATTAAACTAAAGAATAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
*
44252 AATTAAACTAAAGAGTAAAAGAGGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * * *
44306 AATTAAACTGAAGAGTAAAAGAAG-AGTAAACAGTA-ATTAGTTTTATTCTGGGC
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AGGTTAGTTTAATTCTGGGT
* * * * * *
44359 GATTAAACTAAATAGTAAAA-AAGGAGTAAACGGTA-ATTAGTTGAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AGGTTAGTTTAATTCTGGGT
*
44412 AATTAAACTAAACAGTAAAA
1 AATTAAACTAAAGAGTAAAA
44432 TTAAGCAGTA
Statistics
Matches: 315, Mismatches: 25, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
52 3 0.01
53 84 0.27
54 228 0.72
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (54 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
Found at i:50187 original size:17 final size:17
Alignment explanation
Indices: 50165--50203 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
50155 TTTATTTATT
*
50165 ATTTTTTTATTTGTTTG
1 ATTTTTTAATTTGTTTG
* *
50182 ATTTTTTAATTTTTTTT
1 ATTTTTTAATTTGTTTG
50199 ATTTT
1 ATTTT
50204 CTAAAAAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
ATTTTTTAATTTGTTTG
Done.