Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014601.1 Corchorus olitorius cultivar O-4 contig14634, 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: 36104
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:273 original size:31 final size:31
Alignment explanation
Indices: 238--333 Score: 183
Period size: 31 Copynumber: 3.1 Consensus size: 31
228 GAGTTTTGAT
238 GTTGTTTTACTTGAATGATTAAGCTTTGAAA
1 GTTGTTTTACTTGAATGATTAAGCTTTGAAA
269 GTTGTTTTACTTGAATGATTAAGCTTTGAAA
1 GTTGTTTTACTTGAATGATTAAGCTTTGAAA
*
300 GTTGTTTTACTTGAATGATTAAGTTTTGAAA
1 GTTGTTTTACTTGAATGATTAAGCTTTGAAA
331 GTT
1 GTT
334 TGAAGGTTGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (31 bp):
GTTGTTTTACTTGAATGATTAAGCTTTGAAA
Found at i:12938 original size:5 final size:5
Alignment explanation
Indices: 12928--12953 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12918 GAAATATAGC
12928 TTGGG TTGGG TTGGG TTGGG TTGGG T
1 TTGGG TTGGG TTGGG TTGGG TTGGG T
12954 CTTAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
TTGGG
Found at i:14085 original size:16 final size:17
Alignment explanation
Indices: 14043--14091 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
14033 AGTTTGTGAC
*
14043 AGTTTTTTCTAAAATTGGT
1 AGTTTTTT-T-AAATAGGT
14062 AGTTTTTTTAAATAGGT
1 AGTTTTTTTAAATAGGT
*
14079 ATTTTTTTTAAAT
1 AGTTTTTTTAAAT
14092 GATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 19 0.68
18 1 0.04
19 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (17 bp):
AGTTTTTTTAAATAGGT
Found at i:17924 original size:32 final size:32
Alignment explanation
Indices: 17883--17943 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
17873 TGTAAAACTT
* *
17883 TTGAATCGACTATTATATCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
17915 TTGAATCGACCATTATACCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
17944 AAACATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:20790 original size:26 final size:26
Alignment explanation
Indices: 20761--20812 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20751 TGTACTCTCA
20761 TTCATTTTTTATTTTGATAAAAACAC
1 TTCATTTTTTATTTTGATAAAAACAC
20787 TTCATTTTTTATTTTGATAAAAACAC
1 TTCATTTTTTATTTTGATAAAAACAC
20813 ATCAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50
Consensus pattern (26 bp):
TTCATTTTTTATTTTGATAAAAACAC
Found at i:20827 original size:26 final size:26
Alignment explanation
Indices: 20768--20828 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
20758 TCATTCATTT
* ***
20768 TTTATTTTGATAAAAACACTTCATTT
1 TTTATTTTGATAAAAACACATCAAAG
20794 TTTATTTTGATAAAAACACATCAAAAG
1 TTTATTTTGATAAAAACACATC-AAAG
*
20821 TTTTTTTT
1 TTTATTTT
20829 TTTTTCATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (26 bp):
TTTATTTTGATAAAAACACATCAAAG
Found at i:22704 original size:19 final size:18
Alignment explanation
Indices: 22680--22719 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
22670 AATGTGATCT
*
22680 CTATGGCCACTGATACTAA
1 CTATGGCCACTCATAC-AA
*
22699 CTATGGCCTCTCATACAA
1 CTATGGCCACTCATACAA
22717 CTA
1 CTA
22720 ATTCGTCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (18 bp):
CTATGGCCACTCATACAA
Found at i:27743 original size:24 final size:23
Alignment explanation
Indices: 27716--27761 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
27706 TAATAATTTT
*
27716 AATACTAATAAAAAATCAGTATAA
1 AATACTAAGAAAAAAT-AGTATAA
* *
27740 AATATTCAGAAAAAATAGTATA
1 AATACTAAGAAAAAATAGTATA
27762 TAAAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (23 bp):
AATACTAAGAAAAAATAGTATAA
Found at i:29882 original size:1 final size:1
Alignment explanation
Indices: 29876--29924 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
29866 GTGGGAATTT
* * * * *
29876 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29925 GCCAATGATT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:31031 original size:18 final size:18
Alignment explanation
Indices: 31008--31042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30998 TAACTGGTTC
*
31008 AAACATTAACAACCTCAG
1 AAACATCAACAACCTCAG
*
31026 AAACATCAACAATCTCA
1 AAACATCAACAACCTCA
31043 TTAACCCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.17
Consensus pattern (18 bp):
AAACATCAACAACCTCAG
Done.