Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002152.1 Corchorus capsularis cultivar CVL-1 contig02156, 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, 769
Length: 1283
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Found at i:558 original size:25 final size:21
Alignment explanation
Indices: 518--580 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
508 TTCGCCTTTA
518 TGAATGAAAACAAAAGAAAGG
1 TGAATGAAAACAAAAGAAAGG
539 TGAATGAAAACAAAAGAAAGG
1 TGAATGAAAACAAAAGAAAGG
560 TGAATGAAAACAAAAGAAAGG
1 TGAATGAAAACAAAAGAAAGG
581 AGTCTCTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.62, C:0.05, G:0.24, T:0.10
Consensus pattern (21 bp):
TGAATGAAAACAAAAGAAAGG
Found at i:762 original size:11 final size:11
Alignment explanation
Indices: 746--781 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
736 ATTTATTCAT
746 TATTAATTA-A
1 TATTAATTAGA
756 CTATTAATTAGA
1 -TATTAATTAGA
768 TATTAATTAGA
1 TATTAATTAGA
779 TAT
1 TAT
782 AGTATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:909 original size:20 final size:20
Alignment explanation
Indices: 876--920 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
866 CATTCTAATT
876 ATTTAGACTTATAATGTATC
1 ATTTAGACTTATAATGTATC
896 ATTTA-ACTTAATAATGTATC
1 ATTTAGACTT-ATAATGTATC
916 ATTTA
1 ATTTA
921 TATAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTTAGACTTATAATGTATC
Found at i:1007 original size:19 final size:19
Alignment explanation
Indices: 983--1089 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 19
973 AATGTAAATA
*
983 ATACATATCTAAATTATAT
1 ATACATATATAAATTATAT
1002 ATACATATATAAATTATAT
1 ATACATATATAAATTATAT
*
1021 AATATATAAATATAAATTATAT
1 -ATACAT--ATATAAATTATAT
* *
1043 -TAAAT-TATATAATATATAA
1 ATACATATATA-AAT-TATAT
* *
1062 ATCCATTTAT-AA-TATAT
1 ATACATATATAAATTATAT
*
1079 ATAAATATATA
1 ATACATATATA
1090 TGAATTGAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
17 15 0.21
18 3 0.04
19 24 0.34
20 12 0.17
21 3 0.04
22 13 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATACATATATAAATTATAT
Found at i:1011 original size:8 final size:8
Alignment explanation
Indices: 998--1089 Score: 73
Period size: 8 Copynumber: 10.9 Consensus size: 8
988 TATCTAAATT
*
998 ATATATAC
1 ATATATAA
1006 ATATATAA
1 ATATATAA
1014 AT-TATATA
1 ATATATA-A
1022 ATATATAA
1 ATATATAA
1030 ATATA-AA
1 ATATATAA
*
1037 TTATATTAA
1 ATATA-TAA
1046 AT-TATATA
1 ATATATA-A
1054 ATATATAA
1 ATATATAA
1062 ATCCATTTATAA
1 AT--A--TATAA
1074 TATATATAA
1 -ATATATAA
1083 ATATATA
1 ATATATA
1090 TGAATTGAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
7 12 0.17
8 33 0.47
9 16 0.23
10 1 0.01
11 1 0.01
12 5 0.07
13 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAA
Found at i:1033 original size:22 final size:25
Alignment explanation
Indices: 999--1063 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 25
989 ATCTAAATTA
999 TATATACATATATAAATTATA-T-AA
1 TATATA-ATATATAAATTATATTAAA
1023 TATATAA-ATATAAATTATATTAAA
1 TATATAATATATAAATTATATTAAA
1047 TTATATAATATATAAAT
1 -TATATAATATATAAAT
1064 CCATTTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.32
23 2 0.05
24 8 0.22
25 7 0.19
26 8 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATAATATATAAATTATATTAAA
Found at i:1148 original size:24 final size:24
Alignment explanation
Indices: 1116--1163 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1106 TTATTATATT
1116 AAATATGTCATTATAAACTAGAAA
1 AAATATGTCATTATAAACTAGAAA
1140 AAATATGTCATTATAAACTAGAAA
1 AAATATGTCATTATAAACTAGAAA
1164 TTCTAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
AAATATGTCATTATAAACTAGAAA
Done.