Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016048.1 Corchorus olitorius cultivar O-4 contig16081, 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: 19360
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:1938 original size:21 final size:20
Alignment explanation
Indices: 1914--1952 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1904 TAATGGAAAT
1914 TATAAAACAAAAACTAATAAA
1 TATAAAACAAAAAC-AATAAA
*
1935 TATAAAACAAGAACAATA
1 TATAAAACAAAAACAATA
1953 TTAGAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (20 bp):
TATAAAACAAAAACAATAAA
Found at i:2778 original size:7 final size:7
Alignment explanation
Indices: 2766--2795 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2756 CCGAAAAAAG
2766 AATTCAA
1 AATTCAA
2773 AATTCAA
1 AATTCAA
2780 AATTCAA
1 AATTCAA
*
2787 AAATCAA
1 AATTCAA
2794 AA
1 AA
2796 AAGAATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (7 bp):
AATTCAA
Found at i:2888 original size:52 final size:52
Alignment explanation
Indices: 2816--2946 Score: 172
Period size: 52 Copynumber: 2.5 Consensus size: 52
2806 TTCAAAGTTT
* * **
2816 TCAAGTCTTCATAGTTTTCAATTTAGGACTTTTCAAACTGGGAAAGATCCCA
1 TCAAGTTTTCAAAGTTTTCAATTTAGGACTTTTCAAACTAAGAAAGATCCCA
* * * *
2868 TCAAGTTTTCAAAGTATTCAATTTAGGAGTTTTCAAATTAAGAAAGTTCCCA
1 TCAAGTTTTCAAAGTTTTCAATTTAGGACTTTTCAAACTAAGAAAGATCCCA
* *
2920 TCAGGTTTTCTAAGTTTTCAATTTAGG
1 TCAAGTTTTCAAAGTTTTCAATTTAGG
2947 GAAAGATCCC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (52 bp):
TCAAGTTTTCAAAGTTTTCAATTTAGGACTTTTCAAACTAAGAAAGATCCCA
Found at i:2957 original size:38 final size:40
Alignment explanation
Indices: 2895--2997 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
2885 TCAATTTAGG
* * *
2895 AGTTTTCAAATTA-AGAAAGTTCCCATC-AGGTTTTCT-A
1 AGTTTTCAATTTAGGGAAAGATCCCATCAAGGTTTTCTAA
* *
2932 AGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTTTAA
1 AGTTTTCAATTTAGGGAAAGATCCCATCAAGGTTTTCTAA
*
2972 AGTTTTCAATTCAGGGAAAGATCCCA
1 AGTTTTCAATTTAGGGAAAGATCCCA
2998 CTCTTTTTGC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 12 0.21
38 12 0.21
39 7 0.12
40 26 0.46
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (40 bp):
AGTTTTCAATTTAGGGAAAGATCCCATCAAGGTTTTCTAA
Found at i:3049 original size:31 final size:32
Alignment explanation
Indices: 2984--3064 Score: 119
Period size: 31 Copynumber: 2.5 Consensus size: 32
2974 TTTTCAATTC
* *
2984 AGGGAAAGATCCCACTCTTTTTGCTCTCGATTT
1 AGGGAAAGATCCCA-TCATTTTACTCTCGATTT
*
3017 AGGGAAAGATCCCAT-ATTTTACTCTCGTTTT
1 AGGGAAAGATCCCATCATTTTACTCTCGATTT
3048 AGGGAAAGATCCCATCA
1 AGGGAAAGATCCCATCA
3065 AAAAGCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.64
32 2 0.05
33 14 0.32
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (32 bp):
AGGGAAAGATCCCATCATTTTACTCTCGATTT
Found at i:7989 original size:13 final size:13
Alignment explanation
Indices: 7967--8008 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
7957 TATATAAAAT
7967 AAAGTAAAAATTA
1 AAAGTAAAAATTA
*
7980 AAATTAAAAATT-
1 AAAGTAAAAATTA
7992 AAAGTAAAAATTTA
1 AAAGTAAAAA-TTA
8006 AAA
1 AAA
8009 AGAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 13 0.52
14 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
AAAGTAAAAATTA
Found at i:8014 original size:25 final size:23
Alignment explanation
Indices: 7962--8008 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 23
7952 TTAACTATAT
7962 AAAATAAAGTAAAAATTAAAATTA
1 AAAATAAAGTAAAAATTAAAA-TA
7986 AAAATTAAAGTAAAAATTTAAAA
1 AAAA-TAAAGTAAAAA-TTAAAA
8009 AGAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAATAAAGTAAAAATTAAAATA
Found at i:15539 original size:25 final size:25
Alignment explanation
Indices: 15511--15562 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
15501 CCCAAATTGT
15511 TCCATTAGTCTAATTTTTTTACTAG
1 TCCATTAGTCTAATTTTTTTACTAG
15536 TCCATTAGTCTAATTTTTTTACTAG
1 TCCATTAGTCTAATTTTTTTACTAG
15561 TC
1 TC
15563 AAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (25 bp):
TCCATTAGTCTAATTTTTTTACTAG
Found at i:15575 original size:26 final size:25
Alignment explanation
Indices: 15521--15575 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
15511 TCCATTAGTC
* * * *
15521 TAATTTTTTTACTAGTCCATTAGTC
1 TAATTTTTTTACTAGTCAAATAATA
15546 TAATTTTTTTACTAGTCAAATAATAA
1 TAATTTTTTTACTAGTCAAATAAT-A
15572 TAAT
1 TAAT
15576 AATGATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (25 bp):
TAATTTTTTTACTAGTCAAATAATA
Done.