Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023621.1 Corchorus olitorius cultivar O-4 contig23654, 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: 33593
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:14499 original size:351 final size:351
Alignment explanation
Indices: 13846--14530 Score: 978
Period size: 351 Copynumber: 2.0 Consensus size: 351
13836 ACCAAACCAT
* * * *
13846 ATGTTTTGACGTCTAAATCTGATATTCTTAGACCCAATTCGTTACTATGGAAGCCCAAAGAAGGA
1 ATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTAATATGGAAGCCCAAAGAAGGA
* * ** * *
13911 GTCAAAGTCCAATCAGTAATTATGATGTGGTAATGATTCAGCTCTGATGTAACATTGTTAAATCA
66 GTCAAAGTCCAACCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAACATTGTTAAATCA
* * * * * * *
13976 TATTCGAAGGAGGACTTCACAAGAATAGTTTTTGAAGAAAATTCATGATTTTGTATCCGGAACTC
131 TATTCAAAAGAGGACTTCACAAGAACAGTTTTGGAAAAAAATTCATAATTTTGTATCCAGAACTC
* * ***
14041 AGAAAAATGCAAATGAGGTACTGTTAGAAAGAGGATTCCAAGGTTTACAACTTTTATGTTTACCT
196 AGAAAAATGCAAATGAGATACCGTTAGAAAGAGGATTCCAAGACCTACAACTTTTATGTTTACCT
* *
14106 TGAGACCTAATTCTGCAATTCTGGTGGACAATTTTGCCCTTGAAAATTCTGGACAGAATTGATCT
261 CGAGACCTAATTCTGCAATTCTGGTGGACAATTTTGCCCTTGAAAATTATGGACAGAATTGATCT
14171 TCTCCTAAATCGGCTTGGAGAGCCAA
326 TCTCCTAAATCGGCTTGGAGAGCCAA
14197 ATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTAATATGGAA-CCTCAAAGAAGG
1 ATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTAATATGGAAGCC-CAAAGAAGG
* *
14261 AGTCCAAGTCCAACCAGTAATTATAATGCAGTAATTATTCAGCCCTGATGCAACATTGTTAAATC
65 AGTCAAAGTCCAACCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAACATTGTTAAATC
* * * * *
14326 CTATTCAAAAGAGGGCTTCACAAGAGCAGTTTTGGAAAAAAATTCATAACTTTTG-ATCTAGACC
130 ATATTCAAAAGAGGACTTCACAAGAACAGTTTTGGAAAAAAATTCATAA-TTTTGTATCCAGAAC
* * *
14390 TCAGAAAATTGCAAATGAGATACCGTTATAAAGAGGATTTCAAGACCTACAACTTTTATGTTTAC
194 TCAGAAAAATGCAAATGAGATACCGTTAGAAAGAGGATTCCAAGACCTACAACTTTTATGTTTAC
* * ** * *
14455 CTCGAGACCTAATTTTGCAGTTCTGGTGGATGATTTTGCCCTTGAAATTTATGGACATAATTGAT
259 CTCGAGACCTAATTCTGCAATTCTGGTGGACAATTTTGCCCTTGAAAATTATGGACAGAATTGAT
14520 CTTCTCCTAAA
324 CTTCTCCTAAA
14531 CTGACTTGGA
Statistics
Matches: 292, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
350 2 0.01
351 285 0.98
352 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (351 bp):
ATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTAATATGGAAGCCCAAAGAAGGA
GTCAAAGTCCAACCAGTAATTATAATGCAGTAATGATTCAGCCCTGATGCAACATTGTTAAATCA
TATTCAAAAGAGGACTTCACAAGAACAGTTTTGGAAAAAAATTCATAATTTTGTATCCAGAACTC
AGAAAAATGCAAATGAGATACCGTTAGAAAGAGGATTCCAAGACCTACAACTTTTATGTTTACCT
CGAGACCTAATTCTGCAATTCTGGTGGACAATTTTGCCCTTGAAAATTATGGACAGAATTGATCT
TCTCCTAAATCGGCTTGGAGAGCCAA
Found at i:14760 original size:2 final size:2
Alignment explanation
Indices: 14749--14784 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
14739 TTCGTACTTT
14749 TA TA TA -A 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 TA TA TA T
14785 CAAAATCGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14850 original size:23 final size:23
Alignment explanation
Indices: 14816--14869 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
14806 TTCAGCATCA
14816 ATATACTAATAT-ATATATGATA-T
1 ATATA-TAATATCATATATG-TACT
14839 ATATATACATATGCATATATGTACT
1 ATATATA-ATAT-CATATATGTACT
14864 ATATAT
1 ATATAT
14870 TATTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 2 0.07
25 14 0.52
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATATAATATCATATATGTACT
Found at i:24753 original size:17 final size:17
Alignment explanation
Indices: 24713--24753 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
24703 TATTTTTCAG
24713 TAAC-TTTTTTTTTATT
1 TAACATTTTTTTTTATT
24729 TAATCATTTTTTTTCT-TT
1 TAA-CATTTTTTTT-TATT
24747 TAACATT
1 TAACATT
24754 CAACATCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 5 0.23
18 13 0.59
19 1 0.05
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (17 bp):
TAACATTTTTTTTTATT
Found at i:26449 original size:18 final size:18
Alignment explanation
Indices: 26426--26472 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
26416 AAAGGTTTTG
26426 GCAGAGGTAATTTTGATC
1 GCAGAGGTAATTTTGATC
* *
26444 GCAGAGGCAACTTTGATC
1 GCAGAGGTAATTTTGATC
* *
26462 GAAAAGGTAAT
1 GCAGAGGTAAT
26473 ACTGATCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (18 bp):
GCAGAGGTAATTTTGATC
Found at i:28400 original size:18 final size:18
Alignment explanation
Indices: 28366--28409 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28356 CGAAAATTAT
*
28366 TAATTATTTATTAAATAA
1 TAATTATTTATCAAATAA
28384 TAATTATTT-TCAGAATAA
1 TAATTATTTATCA-AATAA
*
28402 TTATTATT
1 TAATTATT
28410 AAATACCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTTATCAAATAA
Found at i:33442 original size:66 final size:66
Alignment explanation
Indices: 33364--33494 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
33354 GACTTCCTTT
*
33364 TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTAAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
33429 A
66 A
33430 TTATTAAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTAAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
33495 CAATGCTAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (66 bp):
TTATTAAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
A
Done.