Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001689.1 Corchorus capsularis cultivar CVL-1 contig01689, 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, 736
Length: 1228
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1038 original size:15 final size:16
Alignment explanation
Indices: 1008--1083 Score: 84
Period size: 15 Copynumber: 4.7 Consensus size: 16
998 TTAGAAATTA
*
1008 TATTATATATATATTTC
1 TATT-TATAAATATTTC
1025 TATTTA-AAATATTTC
1 TATTTATAAATATTTC
*
1040 TATTTA-GAATATTTC
1 TATTTATAAATATTTC
*
1055 TATTTTATAAATTATATC
1 TA-TTTATAAA-TATTTC
1073 TATTTATAAAT
1 TATTTATAAAT
1084 TATCTAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
15 24 0.46
16 7 0.13
17 14 0.27
18 7 0.13
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTTATAAATATTTC
Found at i:1052 original size:30 final size:33
Alignment explanation
Indices: 1002--1078 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
992 ATGAAATTAG
* *
1002 AAATTATAT-TATATA-TATATTTCTA-TTTA-
1 AAATTATATCTATTTAGAATATTTCTATTTTAT
*
1031 AAA-TATTTCTATTTAGAATATTTCTATTTTAT
1 AAATTATATCTATTTAGAATATTTCTATTTTAT
1063 AAATTATATCTATTTA
1 AAATTATATCTATTTA
1079 TAAATTATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.10
29 8 0.21
30 9 0.23
31 4 0.10
32 3 0.08
33 11 0.28
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (33 bp):
AAATTATATCTATTTAGAATATTTCTATTTTAT
Found at i:1119 original size:14 final size:13
Alignment explanation
Indices: 1100--1195 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 13
1090 ATAATATATT
1100 ATTATTAAATTAA
1 ATTATTAAATTAA
*
1113 GATTATTAAGTTATTAT
1 -ATTATTAA---ATTAA
*
1130 ATTATTAAGTTATA
1 ATTATTAAATTA-A
1144 ATTTATTAAATTTAA
1 A-TTATTAAA-TTAA
*
1159 ATTACTAAATT--
1 ATTATTAAATTAA
1170 ATTATTATAATTAA
1 ATTATTA-AATTAA
*
1184 ATTACTAAATTA
1 ATTATTAAATTA
1196 TTATTATAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
13 10 0.15
14 22 0.33
15 9 0.14
16 11 0.17
17 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (13 bp):
ATTATTAAATTAA
Found at i:1135 original size:16 final size:16
Alignment explanation
Indices: 1114--1212 Score: 66
Period size: 16 Copynumber: 6.4 Consensus size: 16
1104 TTAAATTAAG
*
1114 ATTATTAAGTTATTAT
1 ATTATTAAGTTATAAT
1130 ATTATTAAGTTATAAT
1 ATTATTAAGTTATAAT
*
1146 -TTATTAAATT-TAA-
1 ATTATTAAGTTATAAT
* * *
1159 ATTACTAAATTATTATT
1 ATTATTAAGTTA-TAAT
* *
1176 ATAATTAAATTACTAA-
1 ATTATTAAGTTA-TAAT
1192 ATTATT-A-TTATAAT
1 ATTATTAAGTTATAAT
*
1206 AATATTA
1 ATTATTA
1213 GATATTAGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
13 3 0.04
14 20 0.30
15 10 0.15
16 22 0.33
17 12 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTATTAAGTTATAAT
Found at i:1212 original size:25 final size:25
Alignment explanation
Indices: 1097--1205 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
1087 CTAATAATAT
*
1097 ATTATTATTA-AATTAAGATTATTAA
1 ATTATTATTATAATTAA-ATTACTAA
* * *
1122 GTTATTA-TATTATTAAGTTA-T-A
1 ATTATTATTATAATTAAATTACTAA
1144 A-T-TTATTA-AATTTAAATTACTAA
1 ATTATTATTATAA-TTAAATTACTAA
1167 ATTATTATTATAATTAAATTACTAA
1 ATTATTATTATAATTAAATTACTAA
1192 ATTATTATTATAAT
1 ATTATTATTATAAT
1206 AATATTAGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.06
21 10 0.14
22 2 0.03
23 3 0.04
24 6 0.09
25 43 0.61
26 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
ATTATTATTATAATTAAATTACTAA
Done.