Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002279.1 Corchorus capsularis cultivar CVL-1 contig02285, 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, 610
Length: 1017
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:32 original size:21 final size:21
Alignment explanation
Indices: 8--82 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 21
1 ATGATAA
8 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
* *
29 TTCATCATTATTGATTATTATATGATAA
1 TTCAT--TT-TTGA-AATT-TA-GA-AT
57 TTCATTTTTGAAATTTAGAAT
1 TTCATTTTTGAAATTTAGAAT
78 TTCAT
1 TTCAT
83 CATTATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 11 0.26
22 2 0.05
23 4 0.09
24 7 0.16
25 7 0.16
26 4 0.09
27 2 0.05
28 6 0.14
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (21 bp):
TTCATTTTTGAAATTTAGAAT
Found at i:37 original size:24 final size:24
Alignment explanation
Indices: 9--91 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
1 ATGATAAT
*
9 TCATTTTTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
* *
33 TCATTATTGATTATTATATGATAATTCA
1 TCATTATTGA-AATT-TA-GA-ATTTCA
61 T--TT-TTGAAATTTAGAATTTCA
1 TCATTATTGAAATTTAGAATTTCA
82 TCATTATTGA
1 TCATTATTGA
92 TTATTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 4 0.09
24 16 0.34
25 7 0.15
26 4 0.09
27 2 0.04
28 6 0.13
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (24 bp):
TCATTATTGAAATTTAGAATTTCA
Found at i:61 original size:25 final size:25
Alignment explanation
Indices: 33--116 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
23 TAGAATTTCA
33 TCATTATTGATTATTATATGATAAT
1 TCATTATTGATTATTATATGATAAT
* * *
58 TCATTTTTGA-AATT-TA-GA-ATTT
1 TCATTATTGATTATTATATGATA-AT
80 CATCATTATTGATTATTATATGATAAT
1 --TCATTATTGATTATTATATGATAAT
*
107 TCATTTTTGA
1 TCATTATTGA
117 ATGATGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.02
22 3 0.07
23 2 0.04
24 12 0.27
25 21 0.47
26 2 0.04
27 3 0.07
28 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (25 bp):
TCATTATTGATTATTATATGATAAT
Found at i:73 original size:49 final size:49
Alignment explanation
Indices: 1--117 Score: 234
Period size: 49 Copynumber: 2.4 Consensus size: 49
1 ATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTAT
1 ATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTAT
50 ATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTAT
1 ATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTAT
99 ATGATAATTCATTTTTGAA
1 ATGATAATTCATTTTTGAA
118 TGATGATTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (49 bp):
ATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTGATTATTAT
Found at i:970 original size:17 final size:18
Alignment explanation
Indices: 950--991 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
940 TATTTAAAAG
*
950 TAAATATA-CGATAAATA
1 TAAATATATCAATAAATA
967 TAAATA-ATCAATAAATA
1 TAAATATATCAATAAATA
984 TAAATATA
1 TAAATATA
992 AATAATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAATATATCAATAAATA
Found at i:986 original size:23 final size:23
Alignment explanation
Indices: 960--1012 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
950 TAAATATACG
960 ATAAATATAAATAATCAATAAAT
1 ATAAATATAAATAATCAATAAAT
983 ATAAATATAAATAATCAATAAAT
1 ATAAATATAAATAATCAATAAAT
1006 ATAAATA
1 ATAAATA
1013 AATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAATATAAATAATCAATAAAT
Done.