Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023904.1 Corchorus olitorius cultivar O-4 contig23937, 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: 5568
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Found at i:138 original size:43 final size:43
Alignment explanation
Indices: 71--318 Score: 318
Period size: 43 Copynumber: 5.8 Consensus size: 43
61 GTTTTCTCTC
*
71 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
* * * *
114 TTTAAAAAAATGCTCCTTCTTGGTTGGAAGGTCCTTATTTTCT
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
* * * * *
157 TCT-GAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCT
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
* * *
199 TTTCAAAAAATGCCCCTTCCTGTTTGGAAGGTCCCTGTTTTCA
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
* * *
242 TTTCCAAAAATGCCCCTTCCTTGTTGGAAGGTCCTTGTTTTCA
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
* * *
285 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
1 TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCC
319 AGTTTTCCTT
Statistics
Matches: 178, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 36 0.20
43 142 0.80
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (43 bp):
TTTCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCT
Found at i:179 original size:85 final size:86
Alignment explanation
Indices: 71--318 Score: 338
Period size: 85 Copynumber: 2.9 Consensus size: 86
61 GTTTTCTCTC
* * *
71 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTTAAAAAAATGCTCCTTCTTG
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTTCAAAAAATGCCCCTTCCTG
*
136 GTTGGAAGGTCCTTATTTTC-
66 GTTGGAAGGTCCCTATTTTCA
* * * *
156 -TTCTGAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAAATGCCCCTTCCT
1 TTTC-CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTTCAAAAAATGCCCCTTCCT
* *
220 GTTTGGAAGGTCCCTGTTTTCA
65 GGTTGGAAGGTCCCTATTTTCA
* * * *
242 TTTCCAAAAATGCCCCTTCCTTGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCCG
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTTCAAAAAATGCCCCTTCCTG
*
307 GTCGGAAGGTCC
66 GTTGGAAGGTCC
319 AGTTTTCCTT
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
84 3 0.02
85 71 0.51
86 63 0.45
87 3 0.02
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (86 bp):
TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCTTTTCAAAAAATGCCCCTTCCTG
GTTGGAAGGTCCCTATTTTCA
Found at i:238 original size:128 final size:129
Alignment explanation
Indices: 27--317 Score: 358
Period size: 128 Copynumber: 2.2 Consensus size: 129
17 CCCTGTTCTA
* * * * *
27 TTCCGAAAATG-CCCTTCCCAGTCGGAAGGTCACAGTT-TTCTCTCTTTCCAAAAATGCCCCTTC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGT--C-TTTATTGTCT-TTTCAAAAAATGCCCCTTC
* * *
90 CTGGTTGGAAGGTCCTTGTTTTCTTTTAAAAAAATGCTCCTT-CTTGGTTGGAAGGTCCTTATTT
62 CTGGTTGGAAGGTCCCTGTTTTCATTTAAAAAAATGCCCCTTCCTT-GTTGGAAGGTCCTTATTT
154 TC--
126 TCAT
* * *
156 TTCTGAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAAATGCCCCTTCCTG
1 TTC-CAAAAATGCCCCTTCCCGGTCGGAAGGTCTTTATTGTCTTTTCAAAAAATGCCCCTTCCTG
* ** *
221 TTTGGAAGGTCCCTGTTTTCATTTCCAAAAATGCCCCTTCCTTGTTGGAAGGTCCTTGTTTTCAT
65 GTTGGAAGGTCCCTGTTTTCATTTAAAAAAATGCCCCTTCCTTGTTGGAAGGTCCTTATTTTCAT
286 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC
318 CAGTTTTCCT
Statistics
Matches: 138, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
128 75 0.54
129 38 0.28
130 9 0.07
131 16 0.12
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (129 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTTTATTGTCTTTTCAAAAAATGCCCCTTCCTGG
TTGGAAGGTCCCTGTTTTCATTTAAAAAAATGCCCCTTCCTTGTTGGAAGGTCCTTATTTTCAT
Found at i:394 original size:41 final size:41
Alignment explanation
Indices: 340--542 Score: 320
Period size: 41 Copynumber: 5.0 Consensus size: 41
330 GATAATTCTC
340 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
* * *
381 AGTTTGCCGTTCCTCATCAGAAGGTGTTGTTTAAACTCCC-
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
* *
421 AGTTTGCCTTTCCTCATCGGAAGGTGTTGTTTAAATTCTC-
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
*
461 AGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTAAATTCCCA
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
* *
502 AGTTTGCCCTTCCTCATCGGAAGGCGTTGTTTAAACTCCCA
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
543 GTGATGCGCC
Statistics
Matches: 148, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.49
41 75 0.51
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (41 bp):
AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
Found at i:436 original size:40 final size:40
Alignment explanation
Indices: 333--544 Score: 325
Period size: 40 Copynumber: 5.2 Consensus size: 40
323 TTCCTTCGAT
*
333 AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* *
373 AATTCCCAAGTTTGCCGTTCCTCATCAGAAGGTGTTGTTTA
1 AATTCCC-AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* *
414 AACTCCCAGTTTGCCTTTCCTCATCGGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* *
454 AATTCTCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
*
494 AATTCCCAAGTTTGCCCTTCCTCATCGGAAGGCGTTGTTTA
1 AATTCCC-AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
*
535 AACTCCCAGT
1 AATTCCCAGT
545 GATGCGCCAA
Statistics
Matches: 156, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 82 0.53
41 74 0.47
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (40 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
Found at i:506 original size:81 final size:81
Alignment explanation
Indices: 339--542 Score: 320
Period size: 81 Copynumber: 2.5 Consensus size: 81
329 CGATAATTCT
*
339 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAGTTTGCCGTTCCTCATCAGAAG
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAGTTTGCCCTTCCTCATCAGAAG
404 GTGTTGTTTAAACTCC
66 GTGTTGTTTAAACTCC
* * * *
420 CAGTTTGCCTTTCCTCATCGGAAGGTGTTGTTTAAATTCTC-AGTTTGCCCTTCCTTATCGGAAG
1 CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAGTTTGCCCTTCCTCATCAGAAG
*
484 GTGTTGTTTAAATTCC
66 GTGTTGTTTAAACTCC
* *
500 CAAGTTTGCCCTTCCTCATCGGAAGGCGTTGTTTAAACTCCCA
1 C-AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCA
543 GTGATGCGCC
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 36 0.32
81 75 0.68
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.37
Consensus pattern (81 bp):
CAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAGTTTGCCCTTCCTCATCAGAAG
GTGTTGTTTAAACTCC
Found at i:3652 original size:21 final size:21
Alignment explanation
Indices: 3626--3666 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3616 TTGAAGCCCT
3626 ATTGGATAC-AAGTGGTACTAA
1 ATTGGAT-CTAAGTGGTACTAA
3647 ATTGGATCTAAGTGGTACTA
1 ATTGGATCTAAGTGGTACTA
3667 GGGTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (21 bp):
ATTGGATCTAAGTGGTACTAA
Found at i:4083 original size:23 final size:24
Alignment explanation
Indices: 4041--4093 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
4031 CAAGAAGTAC
4041 CAAATCAAGCCAAAGATTTAAGGA
1 CAAATCAAGCCAAAGATTTAAGGA
4065 CAAATCAAGCC-AAGATTTAAGGA
1 CAAATCAAGCCAAAGATTTAAGGA
4088 CAAATC
1 CAAATC
4094 TTCTTCAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (24 bp):
CAAATCAAGCCAAAGATTTAAGGA
Done.