Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017701.1 Corchorus olitorius cultivar O-4 contig17734, 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: 46435
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6145 original size:435 final size:435
Alignment explanation
Indices: 5332--6190 Score: 1362
Period size: 435 Copynumber: 2.0 Consensus size: 435
5322 GTCCACTTGG
* *
5332 AAATTTTAGGAAACAAAACGGAATCCATGTGAAACCAATTCAGTGAAATGTTAGGGAAGACGAAA
1 AAATTTTAGAAAACAAAACGGAATCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGACGAAA
*
5397 ACAACCCAAATAGAAATGAAAACGAAAGGAAAACAGAACTGAAATGTCAATAGCTTACCCATGAA
66 ACAACCCAAATAGAAACGAAAACGAAAGGAAAACAGAACTGAAATGTCAATAGCTTACCCATGAA
* * * * *
5462 TCAATGATTATTGGAGATACATTTATAGCCCAAATCCCTTGGAATTCCGGCAAAGGAGTTGAACC
131 TCAATCATTATTGCAGATACATTGATAGCCCAAATCCCTTGAAATTCCGGCAAAGGAGTTAAACC
* **
5527 GGTAAATCCTAATATCCACACACAATTAATATGTAATTAGAACACACTTAATCTTAAATATAAAA
196 GGTAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCACAAATATAAAA
* * * *
5592 ATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGGAAATTCGTCGAGGGTCTTTCTAG
261 ATAGTAAATTACAAAAAAGGGCAACAAGAAAAGCAAGGGAGGAAATTCATCGAGGGTCTTTCTAG
* *
5657 ACACCCGAAAAGTGAGAAAAGACCAAAAAAGAGCCAAAAGGAGGCACCACATTAATCCTCAATTT
326 ACACCCGAAAAGTGAGAAAAGACAAAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTT
5722 GGCCTTTAAGTAATTTCCATAGTCACTAAAAATACGTCTACCTAA
391 GGCCTTTAAGTAATTTCCATAGTCACTAAAAATACGTCTACCTAA
* * * *
5767 AAATTTTAGAAAACAAAATGGAGTCCATTTGAAACCAATTTAGAGAAATGTTAGGGAAGACGAAA
1 AAATTTTAGAAAACAAAACGGAATCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGACGAAA
* * * * *
5832 ACCACCCGAATAGAAACGAAGACGAAAGGAAAACAGAACTGGAATGTCAATAGTTTACCCATGAA
66 ACAACCCAAATAGAAACGAAAACGAAAGGAAAACAGAACTGAAATGTCAATAGCTTACCCATGAA
* * * *
5897 TCAATCATTATTGCTGATACATTGATAGCACC-TATCCTTTGAAATTCCGGCAGAGGAGTTAAAC
131 TCAATCATTATTGCAGATACATTGATAGC-CCAAATCCCTTGAAATTCCGGCAAAGGAGTTAAAC
*
5961 CGGTAAATCCTAATATCCACATACAATTAATATGTAATTAAAACACACTTAATCACAAATATAAA
195 CGGTAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCACAAATATAAA
*
6026 AATAGTAAATTACAAAAAAAGGGCAACAAGAAAAGCAAGGGAGGAAATTCATCGAGGGTCTTTTT
260 AATAGTAAATTAC-AAAAAAGGGCAACAAGAAAAGCAAGGGAGGAAATTCATCGAGGGTCTTTCT
* * * *
6091 AGTCACCCGAAAAGTGAGAAAAGA-AAAAAAAAAGTCAAAAGGAGGCAGCACATTAATTCTCAAT
324 AGACACCCGAAAAGTGAGAAAAGACAAAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAAT
6155 TTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
389 TTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
6191 ATATATAGTA
Statistics
Matches: 386, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
435 315 0.82
436 71 0.18
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (435 bp):
AAATTTTAGAAAACAAAACGGAATCCATGTGAAACCAATTCAGAGAAATGTTAGGGAAGACGAAA
ACAACCCAAATAGAAACGAAAACGAAAGGAAAACAGAACTGAAATGTCAATAGCTTACCCATGAA
TCAATCATTATTGCAGATACATTGATAGCCCAAATCCCTTGAAATTCCGGCAAAGGAGTTAAACC
GGTAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAATCACAAATATAAAA
ATAGTAAATTACAAAAAAGGGCAACAAGAAAAGCAAGGGAGGAAATTCATCGAGGGTCTTTCTAG
ACACCCGAAAAGTGAGAAAAGACAAAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATTT
GGCCTTTAAGTAATTTCCATAGTCACTAAAAATACGTCTACCTAA
Found at i:17587 original size:18 final size:18
Alignment explanation
Indices: 17564--17600 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17554 AAGGGTAGTT
*
17564 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
17582 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
17600 T
1 T
17601 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:30420 original size:2 final size:2
Alignment explanation
Indices: 30413--30438 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30403 TGAATAGTTA
30413 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
30439 CTTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37603 original size:38 final size:38
Alignment explanation
Indices: 37519--37654 Score: 211
Period size: 38 Copynumber: 3.6 Consensus size: 38
37509 TTGACCCGTA
* * *
37519 CCTCAGGGGGTTAAACTGATGGTAAAGAGTGGACTCATA
1 CCTCAGGGGGTTAAACTGTTGGT-AAGAGTGGACCCATG
*
37558 CCACAGGGGGTTAAACTGTTGGTAAGAGTGGACCCATG
1 CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCATG
*
37596 CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCGTG
1 CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCATG
37634 CCTCAGGGGGTT-AACTGTTGG
1 CCTCAGGGGGTTAAACTGTTGG
37655 CTAGACTCGA
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 9 0.10
38 61 0.67
39 21 0.23
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (38 bp):
CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCATG
Found at i:37695 original size:6 final size:6
Alignment explanation
Indices: 37684--37727 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
37674 CGTTAACGGA
37684 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
37728 GTCACTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:37824 original size:22 final size:22
Alignment explanation
Indices: 37799--37850 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
37789 TATATGATTT
37799 TCTGAAATTTACTATAGCGGCG
1 TCTGAAATTTACTATAGCGGCG
37821 TCTGAAATTTACTATAGCGGCG
1 TCTGAAATTTACTATAGCGGCG
37843 TCTGAAAT
1 TCTGAAAT
37851 AGCGACGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (22 bp):
TCTGAAATTTACTATAGCGGCG
Found at i:43907 original size:27 final size:27
Alignment explanation
Indices: 43779--43897 Score: 202
Period size: 27 Copynumber: 4.4 Consensus size: 27
43769 GACTGTTACC
* *
43779 GCAGTGGATCCTTCCGCTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
43806 GTAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
43833 GCAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
43860 GCAGTGGATCCTCACACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
43887 GCAGTGGATCC
1 GCAGTGGATCC
43898 AGTTATTTCG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.20
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:46324 original size:32 final size:31
Alignment explanation
Indices: 46283--46408 Score: 146
Period size: 32 Copynumber: 4.0 Consensus size: 31
46273 AGCATGTGTG
* *
46283 AAAAGAAAACGCACTTATTTAGCGGTGTCTA
1 AAAACAAAACGCACTTATTTAGCGGCGTCTA
*
46314 CAAAACAAAACGCCCTTATTTAGCGGCGTCTA
1 -AAAACAAAACGCACTTATTTAGCGGCGTCTA
* * *
46346 TAGAACAAAACGCCCTTATTTGGCGGCGTCTA
1 -AAAACAAAACGCACTTATTTAGCGGCGTCTA
*
46378 AAGAACGAAACGCCAC-TATTTAGCGGCGTCT
1 AA-AACAAAACG-CACTTATTTAGCGGCGTCT
46409 TCAACACGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
31 1 0.01
32 79 0.96
33 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (31 bp):
AAAACAAAACGCACTTATTTAGCGGCGTCTA
Found at i:46377 original size:64 final size:64
Alignment explanation
Indices: 46288--46408 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
46278 GTGTGAAAAG
*
46288 AAAACGCACTTATTTAGCGGTGTCTACAA-AACAAAACGCC-CTTATTTAGCGGCGTCTATAGAA
1 AAAACGCACTTATTTAGCGGCGTCTA-AAGAACAAAACGCCAC-TATTTAGCGGCGTCTATAGAA
46351 C
64 C
* * *
46352 AAAACGCCCTTATTTGGCGGCGTCTAAAGAACGAAACGCCACTATTTAGCGGCGTCT
1 AAAACGCACTTATTTAGCGGCGTCTAAAGAACAAAACGCCACTATTTAGCGGCGTCT
46409 TCAACACGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 2 0.04
64 48 0.94
65 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (64 bp):
AAAACGCACTTATTTAGCGGCGTCTAAAGAACAAAACGCCACTATTTAGCGGCGTCTATAGAAC
Found at i:46418 original size:32 final size:32
Alignment explanation
Indices: 46283--46435 Score: 141
Period size: 32 Copynumber: 4.8 Consensus size: 32
46273 AGCATGTGTG
* * * *
46283 AAAAGAAAACGCACTTATTTAGCGGTGTCTAC
1 AAAACAAAACGCCCTTATTTAGCGGCGTCTTC
46315 AAAACAAAACGCCCTTATTTAGCGGCGTCTAT-
1 AAAACAAAACGCCCTTATTTAGCGGCGTCT-TC
* * *
46347 AGAACAAAACGCCCTTATTTGGCGGCGTC-TA
1 AAAACAAAACGCCCTTATTTAGCGGCGTCTTC
*
46378 AAGAACGAAACGCCAC-TATTTAGCGGCGTCTTC
1 AA-AACAAAACGCC-CTTATTTAGCGGCGTCTTC
* * * * *
46411 AACACGAAACACCGTTATTTGGCGG
1 AAAACAAAACGCCCTTATTTAGCGG
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 95 0.94
33 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (32 bp):
AAAACAAAACGCCCTTATTTAGCGGCGTCTTC
Found at i:46429 original size:64 final size:64
Alignment explanation
Indices: 46296--46435 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 64
46286 AGAAAACGCA
* * *
46296 CTTATTTAGCGGTGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTATAGAACAAAACGCC
1 CTTATTTGGCGGCGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTATAGAACAAAACACC
* *
46360 CTTATTTGGCGGCGTCTA-AAGAACGAAACGCCAC-TATTTAGCGGCGTCT-TCA-ACACGAAAC
1 CTTATTTGGCGGCGTCTACAA-AACAAAACGCC-CTTATTTAGCGGCGTCTAT-AGA-ACAAAAC
46421 ACC
62 ACC
*
46424 GTTATTTGGCGG
1 CTTATTTGGCGG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.06
64 61 0.92
65 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (64 bp):
CTTATTTGGCGGCGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTATAGAACAAAACACC
Done.