Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013052.1 Corchorus olitorius cultivar O-4 contig13085, 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: 40850
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:104 original size:7 final size:7
Alignment explanation
Indices: 77--150 Score: 53
Period size: 7 Copynumber: 10.0 Consensus size: 7
67 TACTAATTTG
*
77 TATATAA
1 TATATAT
*
84 TATAAAT
1 TATATAT
91 TATTATAT
1 TA-TATAT
99 TATATAT
1 TATATAT
106 TATATA-
1 TATATAT
*
112 TATATAA
1 TATATAT
119 TATA-ACT
1 TATATA-T
126 TATATAAGTTT
1 TATAT-A---T
137 TATATAT
1 TATATAT
144 TATATAT
1 TATATAT
151 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
6 7 0.13
7 34 0.62
8 6 0.11
9 1 0.02
10 1 0.02
11 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:113 original size:9 final size:9
Alignment explanation
Indices: 77--151 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
67 TACTAATTTG
*
77 TATATAATA
1 TATATTATA
*
86 TAAATTAT-
1 TATATTATA
94 TATATTATA
1 TATATTATA
103 TAT-TATATA
1 TATAT-TATA
*
112 TATATAATA
1 TATATTATA
121 TA-ACTTATA
1 TATA-TTATA
*
130 TA-AGTTTTA
1 TATA-TTATA
139 TATATTATA
1 TATATTATA
148 TATA
1 TATA
152 AAAATAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 9 0.17
9 42 0.79
10 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
TATATTATA
Found at i:18842 original size:4 final size:4
Alignment explanation
Indices: 18786--18860 Score: 63
Period size: 4 Copynumber: 20.0 Consensus size: 4
18776 AAAAGGTAGG
* * *
18786 TTCT CTCT TTCT CTCT TTCT TT-T TTCC TTC- TTC- TTC- TTC- TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
18829 TCTTT TTCT TTCT TTCT TTCT TTCT TT-T TTCT
1 T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
18861 CTTTTTTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
3 18 0.30
4 39 0.65
5 3 0.05
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:18871 original size:13 final size:13
Alignment explanation
Indices: 18797--18870 Score: 63
Period size: 12 Copynumber: 6.1 Consensus size: 13
18787 TCTCTCTTTC
18797 TCTCTTTCTTTTT
1 TCTCTTTCTTTTT
*
18810 TC-C-TTC-TTCT
1 TCTCTTTCTTTTT
18820 TCT-TCTTCTTCTTT
1 TCTCT-TTCTT-TTT
*
18834 T-TCTTTCTTTCT
1 TCTCTTTCTTTTT
18846 T-TCTTTCTTTTT
1 TCTCTTTCTTTTT
18858 TCTCTTT-TTTTT
1 TCTCTTTCTTTTT
18870 T
1 T
18871 TTTTTTTCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 5 0.10
11 3 0.06
12 24 0.48
13 14 0.28
14 4 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTCTTTCTTTTT
Found at i:18875 original size:17 final size:17
Alignment explanation
Indices: 18799--18873 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 17
18789 TCTCTTTCTC
18799 TCTTTCTTTTTTC-C-T
1 TCTTTCTTTTTTCTCTT
18814 TC-TTCTTCTTCTTCT-TCT
1 TCTTTCTT-TT-TTCTCT-T
*
18832 T-TTTCTTTCTT-TCTT
1 TCTTTCTTTTTTCTCTT
18847 TCTTTCTTTTTTCTCTT
1 TCTTTCTTTTTTCTCTT
18864 T-TTT-TTTTTT
1 TCTTTCTTTTTT
18874 TTTTCTCTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
14 5 0.10
15 13 0.27
16 18 0.37
17 6 0.12
18 7 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTCTTTTTTCTCTT
Found at i:18880 original size:19 final size:20
Alignment explanation
Indices: 18793--18881 Score: 78
Period size: 19 Copynumber: 4.3 Consensus size: 20
18783 AGGTTCTCTC
18793 TTTCTC-TCTTTCTTTTTTCCT
1 TTTCTCTTCTTTCTTTTTT--T
18814 TCTTCTTCTTC-TTCTTCTTTTT
1 T-TTC-TCTTCTTTCTT-TTTTT
*
18836 CTTTCT-TTCTTTCTTTCTTT
1 -TTTCTCTTCTTTCTTTTTTT
*
18856 TTTCTCTT-TTTTTTTTTTT
1 TTTCTCTTCTTTCTTTTTTT
18875 TTTCTCT
1 TTTCTCT
18882 CAGTATGTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
19 21 0.36
20 9 0.16
21 7 0.12
22 7 0.12
23 8 0.14
24 6 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTTTTTTT
Found at i:26708 original size:2 final size:2
Alignment explanation
Indices: 26701--26726 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26691 TAAGGTTATC
26701 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
26727 TACCTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29174 original size:2 final size:2
Alignment explanation
Indices: 29167--29205 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29157 GTCGTCGAGT
29167 TA TA TA TA TA 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 TA T
29206 GCGGCCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.