Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011489.1 Corchorus olitorius cultivar O-4 contig11522, 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: 17079
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1880 original size:22 final size:22
Alignment explanation
Indices: 1854--1905 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1844 CTAGAGATAG
*
1854 AAAAAGATCAAAATAAAGAAAA-
1 AAAAAGATAAAAAT-AAGAAAAT
* *
1876 AAAAAGAGAAAAATCAGAAAAT
1 AAAAAGATAAAAATAAGAAAAT
1898 AAAAAGAT
1 AAAAAGAT
1906 GCAATAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAGATAAAAATAAGAAAAT
Found at i:4447 original size:34 final size:38
Alignment explanation
Indices: 4404--4480 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
4394 AGGGTTTTCA
4404 TAATTGTTTT-C-T-AGTTTATTCATTGCTTTCTTA-T
1 TAATTGTTTTCCTTAAGTTTATTCATTGCTTTCTTAGT
* * *
4438 TAATTGTTTTCCTTAATTTTCTTGATTGCTTTCTTAGT
1 TAATTGTTTTCCTTAAGTTTATTCATTGCTTTCTTAGT
4476 TAATT
1 TAATT
4481 TTAATTGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 10 0.28
35 1 0.03
36 1 0.03
37 18 0.50
38 6 0.17
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (38 bp):
TAATTGTTTTCCTTAAGTTTATTCATTGCTTTCTTAGT
Found at i:8673 original size:2 final size:2
Alignment explanation
Indices: 8666--8705 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
8656 GAATCAACAA
*
8666 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8706 CCAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9727 original size:43 final size:43
Alignment explanation
Indices: 9643--9856 Score: 182
Period size: 43 Copynumber: 4.9 Consensus size: 43
9633 AAGTTGGTCA
* *
9643 GAAATTATAATAAGAAAATAATATTTAGAAATGATATATGTAAT
1 GAAATTATAATTAG-AAATAATATTTAGAAATTATATATGTAAT
* * * * *
9687 CAAATTATAATTAGGAATTATATTTATAAATTATACATGTAAT
1 GAAATTATAATTAGAAATAATATTTAGAAATTATATATGTAAT
* * * * *
9730 GAAA-TATTATTTAGAAAATCATATCTAAAAACTATATATGTGAA-
1 GAAATTA-TAATTAG-AAATAATATTTAGAAATTATATATGT-AAT
* * * * * *
9774 AAAATAATAATTAGGAATTATATTTATAAATTATGTATGTAAT
1 GAAATTATAATTAGAAATAATATTTAGAAATTATATATGTAAT
* *
9817 GAAA-TATAATTTAAAAATAATATTTAGAAATTATAAATGT
1 GAAATTATAA-TTAGAAATAATATTTAGAAATTATATATGT
9857 TTAGAAATTA
Statistics
Matches: 132, Mismatches: 32, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
42 8 0.06
43 80 0.61
44 41 0.31
45 3 0.02
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (43 bp):
GAAATTATAATTAGAAATAATATTTAGAAATTATATATGTAAT
Found at i:9974 original size:16 final size:16
Alignment explanation
Indices: 9953--9985 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9943 CATTTATTAA
*
9953 ATAAAAATATATAAAT
1 ATAAAAATATACAAAT
9969 ATAAAAATATACAAAT
1 ATAAAAATATACAAAT
9985 A
1 A
9986 GTGGCGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAATATACAAAT
Found at i:10941 original size:15 final size:15
Alignment explanation
Indices: 10921--10956 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
10911 GAGGGGATAA
10921 AGGAACTAAAGTAAT
1 AGGAACTAAAGTAAT
10936 AGGAACTAAAGTAAT
1 AGGAACTAAAGTAAT
10951 AGGAAC
1 AGGAAC
10957 CTTACCACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.08, G:0.22, T:0.17
Consensus pattern (15 bp):
AGGAACTAAAGTAAT
Found at i:12941 original size:20 final size:21
Alignment explanation
Indices: 12902--12946 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
12892 TTCCAATCAA
12902 TCAAGAACCCTAATTTTGAAC
1 TCAAGAACCCTAATTTTGAAC
*
12923 TCAAGAACCCTAA-TTTGAAT
1 TCAAGAACCCTAATTTTGAAC
12943 TCAA
1 TCAA
12947 TAAGCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (21 bp):
TCAAGAACCCTAATTTTGAAC
Found at i:16153 original size:2 final size:2
Alignment explanation
Indices: 16146--16175 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16136 AGAATTGTTC
16146 AT AT 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 AT AT
16176 TTTTGAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.