Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014890.1 Corchorus olitorius cultivar O-4 contig14923, 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: 28560
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:14623 original size:29 final size:30
Alignment explanation
Indices: 14573--14633 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
14563 CTTTGGCCAT
*
14573 ATAAATATATATATATATATAA-TAAATAA
1 ATAAATATAAATATATATATAATTAAATAA
*
14602 ATAAATATAAATACTATA-ATAATTAATTAA
1 ATAAATATAAATA-TATATATAATTAAATAA
14632 AT
1 AT
14634 CATCTAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAATATAAATATATATATAATTAAATAA
Found at i:14632 original size:26 final size:25
Alignment explanation
Indices: 14573--14633 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
14563 CTTTGGCCAT
* *
14573 ATAAATATATATATATATATAATAA
1 ATAAATAAATATAAATATATAATAA
14598 ATAAATAAATATAAATACTATAATAA
1 ATAAATAAATATAAATA-TATAATAA
* *
14624 TTAATTAAAT
1 ATAAATAAAT
14634 CATCTAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAAATAAATATAAATATATAATAA
Found at i:20506 original size:18 final size:18
Alignment explanation
Indices: 20480--20519 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20470 CCTCCTGTAA
* *
20480 CACAAATCACATACTTTT
1 CACAAATCAAATAATTTT
*
20498 CACACATCAAATAATTTT
1 CACAAATCAAATAATTTT
20516 CACA
1 CACA
20520 TAGATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (18 bp):
CACAAATCAAATAATTTT
Found at i:21335 original size:15 final size:16
Alignment explanation
Indices: 21302--21341 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
21292 TTACTTTGCT
21302 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
21318 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
21333 TTGCTTTCT
1 TTGTTTTCT
21342 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:26996 original size:178 final size:178
Alignment explanation
Indices: 26662--27044 Score: 488
Period size: 178 Copynumber: 2.2 Consensus size: 178
26652 TTCCACCATA
* * * **
26662 AGCACAAATTATGTAATATTAAGTAGAACATCTATTTCCGTTAATCGAAACAATGAATTCTTTGG
1 AGCACAAATTATATAATATTAAGTAGAACATCTATTCCCGTTAACCGAAACAACAAATTCTTTGG
* *
26727 AAGCATTTTTTATACTTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCAT
66 AAGCATTTTTGATACTTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCAT
* *
26792 AGAACAACCTTTCAAAAGATACTTAAATCATCTCAATCAGACATCTGG
131 AGAACAACCTTTCAAAAGACACTTAAATCACCTCAATCAGACATCTGG
* * *
26840 AGCA-AAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTC
1 AGCACAAA-TTATATAATATTAAGTAGAACATCTATTCCCGTTAACCGAAACAACAAATTCTTT-
26903 GGAAGCATTTTTGATACTT-GAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAAT
64 GGAAGCATTTTTGATACTTCG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAAT
* * * * * * * * *
26967 GATGGAACAATCTTTTAATAGACACTTAAATCACCTTAATCAGATAACCAGAG
128 CATAGAACAACCTTTCAAAAGACACTTAAATCACCTCAATCAGA-CATCTG-G
*
27020 AG-A-AAATTATATAATATTAAATAGA
1 AGCACAAATTATATAATATTAAGTAGA
27045 TCGTTTAACC
Statistics
Matches: 177, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
177 7 0.04
178 160 0.90
179 7 0.04
180 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGTAGAACATCTATTCCCGTTAACCGAAACAACAAATTCTTTGG
AAGCATTTTTGATACTTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCAT
AGAACAACCTTTCAAAAGACACTTAAATCACCTCAATCAGACATCTGG
Found at i:28001 original size:34 final size:34
Alignment explanation
Indices: 27958--28024 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
27948 AATGGACTGA
27958 TAATATCATCAGTATAGGATTTAGATTTAATTTC
1 TAATATCATCAGTATAGGATTTAGATTTAATTTC
*
27992 TAATATCATCAGTATAGGATTTAGCTTTAATTT
1 TAATATCATCAGTATAGGATTTAGATTTAATTT
28025 TTACTTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (34 bp):
TAATATCATCAGTATAGGATTTAGATTTAATTTC
Found at i:28244 original size:42 final size:42
Alignment explanation
Indices: 28175--28257 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
28165 GCTAAGTCTT
* *
28175 GAAAATTCTCTGTAAATTTAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTAAAATCATA
* *
28217 GAAACTTCTTTGTAAATTAAGAAATACTCAACTAAAATCAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTAAAATCAT
28258 GATCCTTAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTAAAATCATA
Done.