Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013645.1 Corchorus olitorius cultivar O-4 contig13678, 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: 44455
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:354 original size:16 final size:17
Alignment explanation
Indices: 335--368 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
325 AAGGGTAGTT
*
335 AAAAAA-AATTGCTTTC
1 AAAAAAGAAGTGCTTTC
351 AAAAAAGAAGTGCTTTC
1 AAAAAAGAAGTGCTTTC
368 A
1 A
369 TGCAAGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (17 bp):
AAAAAAGAAGTGCTTTC
Found at i:7599 original size:303 final size:298
Alignment explanation
Indices: 7057--7640 Score: 808
Period size: 303 Copynumber: 1.9 Consensus size: 298
7047 GTCGTTTCAG
* * * * *
7057 CTGCAGAAAACACAGACTTGATTATTAAGCAAAATAATTGCAAGACAAGGTCTGGCCTGTTCCAG
1 CTGCAGAAAACACAGACTTGATTATTAAGCAAAACAATTGCAAGAAAAGGACTGCCCTGTGCCAG
* * * * *
7122 GGAAGTTTTCACAAGTATATCCTATACCAGAGCTGTCACTAAGAAGTGTTGCGGTGAACTCATGG
66 GGAAGTTTTCACAAGTATATCCAAAACCAGAGCTGTCACTAAGAAGTGTTGCGGTCAACTCAAGC
* * * * * *
7187 TATTGGGTAAACATTCTCACGATGCATTTGTTAAGAAGACTCATGAAGATCATTTATATATAGAC
131 AATTGGGTAAACATTCTAACGATGCATTTGTTAAGAAGACTCATGAAGACCATATATATAAAAAC
* *
7252 TTAAGCGAGACAACAATTACGAAGAAGAGTATAAAAACATGGAACACATGTGCCTCAGTCATCGA
196 TTAAGCGAGACAACAATTACAAAGAAGAGTAGAAAAACATGGAACACATGTGCCTCAGTCATCGA
7317 CATTTCACCATCTTCTTCTGCAAGCGAAGTTATTTATC
261 CATTTCACCATCTTCTTCTGCAAGCGAAGTTATTTATC
* * *
7355 CTGCAGAAAACCCGGACTTGATTATTAAGGAAAACAATTGCAAAATGAAAATGGCACTGCCCTGT
1 CTGCAGAAAACACAGACTTGATTATTAAGCAAAACAATTGC--AA-GAAAA-GG-ACTGCCCTGT
* * * *
7420 GCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAAGAAGTTTTGCGGTCAGCT
61 GCCAGGGAAGTTTTCACAAGTATATCCAAAACCAGAGCTGTCACTAAGAAGTGTTGCGGTCAACT
** * * * *
7485 CAAGCAATTGGGTAAAGTTTGTAACGATGCTTTTGTTAAGAAGACTCTTGAAGACCCTATATATA
126 CAAGCAATTGGGTAAACATTCTAACGATGCATTTGTTAAGAAGACTCATGAAGACCATATATATA
* * * *
7550 AAAACTTAAGTGAGTCAGCAATTGCAAAGAAGAGTAGAAAAACATGGAACACATGTGCCTCAGTC
191 AAAACTTAAGCGAGACAACAATTACAAAGAAGAGTAGAAAAACATGGAACACATGTGCCTCAGTC
7615 ATCGACATTTCACCATCTTCTTCTGC
256 ATCGACATTTCACCATCTTCTTCTGC
7641 TTGAGTAGCA
Statistics
Matches: 246, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
298 37 0.15
300 2 0.01
301 4 0.02
302 2 0.01
303 201 0.82
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (298 bp):
CTGCAGAAAACACAGACTTGATTATTAAGCAAAACAATTGCAAGAAAAGGACTGCCCTGTGCCAG
GGAAGTTTTCACAAGTATATCCAAAACCAGAGCTGTCACTAAGAAGTGTTGCGGTCAACTCAAGC
AATTGGGTAAACATTCTAACGATGCATTTGTTAAGAAGACTCATGAAGACCATATATATAAAAAC
TTAAGCGAGACAACAATTACAAAGAAGAGTAGAAAAACATGGAACACATGTGCCTCAGTCATCGA
CATTTCACCATCTTCTTCTGCAAGCGAAGTTATTTATC
Found at i:9097 original size:11 final size:11
Alignment explanation
Indices: 9081--9128 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
9071 GAAGTTCGTG
9081 TTTGAAGACTA
1 TTTGAAGACTA
9092 TTTGAAGA-TAA
1 TTTGAAGACT-A
9103 TTTGAAGAC--
1 TTTGAAGACTA
9112 -TTGAAGACTA
1 TTTGAAGACTA
9122 -TTGAAGA
1 TTTGAAGA
9129 ATTATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:15875 original size:302 final size:303
Alignment explanation
Indices: 15272--15877 Score: 910
Period size: 302 Copynumber: 2.0 Consensus size: 303
15262 CTTGTTTTAA
* * * *
15272 CAAGCGGAGTCGTTTCAACTGCAGAAAACCCAGACTTGATTATTAAGCAACATAATTGCAAGACA
1 CAAGCGGAGTCATTTCAACTGCACAAAACCCAGACTTGATTATTAAGCAACACAATTGCAAAACA
* ** * * * *
15337 AGAATGGGTCTGGCCTGTTCCAGGGAAGTTTTCACAAGTATATTCTATATCGGAGCTGTCACTAA
66 AAAATGGAACTGGCCTGTGCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
*
15402 GAAGTGTTGCGGTGAACTCATGGAATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
131 GAAGTGTTGCGGTGAACTAATGGAATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
* * * * *
15467 ATGAAGATCCTTTATATAAAGACTTAAGCGAGTCAACAATTGCGAAGAAGAGTATAAAAACATGG
196 ATGAAGACCCTATATATAAAAACTTAAGCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATGG
*
15532 AACACATGTGCCTCAGTCATCGACATTTCACCATCTTCTTCTG
261 AACACATGTGCCTCAGTCATCGACATTTCACCATATTCTTCTG
* * * * *
15575 CAAGCGGGGTCATTTCACCTGTACAAAACCCGGACTTGATTATTAAGGAA-ACAATTGCAAAACA
1 CAAGCGGAGTCATTTCAACTGCACAAAACCCAGACTTGATTATTAAGCAACACAATTGCAAAACA
15639 AAAATGGAACT-GCCATGTGCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTA
66 AAAATGGAACTGGCC-TGTGCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTA
* * *
15703 AGAATTGTTGCGTTGAACTAATGGTATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACT
130 AGAAGTGTTGCGGTGAACTAATGGAATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACT
* * * *
15768 CTTGAAGACCCTATATATAAAAACTTAAGTGAGTCAGCAATTGCAAAGAAGAGTACAAAAACGTG
195 CATGAAGACCCTATATATAAAAACTTAAGCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATG
*
15833 GAACACTTGTGCCTCAGTCATCGACATTTCACCATATTCTTCTG
260 GAACACATGTGCCTCAGTCATCGACATTTCACCATATTCTTCTG
15877 C
1 C
15878 TTGAGAAGCA
Statistics
Matches: 271, Mismatches: 31, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
301 3 0.01
302 225 0.83
303 43 0.16
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (303 bp):
CAAGCGGAGTCATTTCAACTGCACAAAACCCAGACTTGATTATTAAGCAACACAATTGCAAAACA
AAAATGGAACTGGCCTGTGCCAGGGAAGTTTTCACAAGTATATTCAAAACCGGAGCTGTCACTAA
GAAGTGTTGCGGTGAACTAATGGAATTGGGTAAAGTTTGTCACGATGCATTTGTTAAGAAGACTC
ATGAAGACCCTATATATAAAAACTTAAGCGAGTCAACAATTGCAAAGAAGAGTACAAAAACATGG
AACACATGTGCCTCAGTCATCGACATTTCACCATATTCTTCTG
Found at i:32445 original size:19 final size:18
Alignment explanation
Indices: 32421--32456 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32411 TGAAGACTTA
32421 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
32440 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
32457 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:32463 original size:30 final size:30
Alignment explanation
Indices: 32409--32468 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
32399 GAAGTTCGTG
* *
32409 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
32439 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
32469 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:33777 original size:22 final size:22
Alignment explanation
Indices: 33735--33777 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
33725 CTTTTAATTA
**
33735 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
33757 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
33778 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Done.