Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002256.1 Corchorus capsularis cultivar CVL-1 contig02262, 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, 842
Length: 1404
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Found at i:1114 original size:13 final size:13
Alignment explanation
Indices: 1098--1146 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
1088 TTACTGTTTA
1098 ATATTATAATTAT
1 ATATTATAATTAT
*
1111 ATATT-TAA-TCT
1 ATATTATAATTAT
1122 AT-TTATAATTAT
1 ATATTATAATTAT
1134 ATA-TATTAATTAT
1 ATATTA-TAATTAT
1147 TAATTCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.07
11 7 0.23
12 9 0.30
13 12 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTATAATTAT
Found at i:1130 original size:23 final size:23
Alignment explanation
Indices: 1101--1176 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
1091 CTGTTTAATA
1101 TTATAATTATATAT-TTAATCTAT
1 TTATAATTATATATATTAAT-TAT
1124 TTATAATTATATATATTAATTA-
1 TTATAATTATATATATTAATTAT
* *
1146 -T-TAATTCTATATTTCTAATTAT
1 TTATAATTATATATAT-TAATTAT
1168 TTAT-ATTAT
1 TTATAATTAT
1177 TTCGAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 11 0.24
21 7 0.16
23 21 0.47
24 6 0.13
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATAATTATATATATTAATTAT
Found at i:1156 original size:20 final size:21
Alignment explanation
Indices: 1100--1168 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
1090 ACTGTTTAAT
1100 ATTA-TAATTATATATTTAATCTA
1 ATTATTAATTATATA--T-ATCTA
*
1123 TTTA-TAATTATATATAT-TA
1 ATTATTAATTATATATATCTA
* *
1142 ATTATTAATTCTATATTTCTA
1 ATTATTAATTATATATATCTA
1163 ATTATT
1 ATTATT
1169 TATATTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.12
20 13 0.32
21 9 0.22
23 13 0.32
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTAATTATATATATCTA
Found at i:1168 original size:28 final size:28
Alignment explanation
Indices: 1137--1190 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1127 TAATTATATA
*
1137 TATTAATTATTAATTC-TATATTTCTAAT
1 TATTAA-TATTAATTCGAATATTTCTAAT
* *
1165 TATTTATATTATTTCGAATATTTCTA
1 TATTAATATTAATTCGAATATTTCTA
1191 TTTCATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (28 bp):
TATTAATATTAATTCGAATATTTCTAAT
Found at i:1174 original size:16 final size:16
Alignment explanation
Indices: 1121--1174 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1111 ATATTTAATC
*
1121 TATTTATAATTATATA
1 TATTTATAATTATTTA
* *
1137 TATTAATTATTAATTCTA
1 TATTTATAATT-ATT-TA
*
1155 TATTTCTAATTATTTA
1 TATTTATAATTATTTA
1171 TATT
1 TATT
1175 ATTTCGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 15 0.50
17 5 0.17
18 10 0.33
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATAATTATTTA
Found at i:1192 original size:18 final size:19
Alignment explanation
Indices: 1145--1192 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1135 TATATTAATT
* *
1145 ATTAATTCTA-TATTTCTA
1 ATTATTTCTATTATTTCGA
*
1163 ATTATTTATATTATTTCGA
1 ATTATTTCTATTATTTCGA
1182 A-TATTTCTATT
1 ATTATTTCTATT
1193 TCATTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTATTTCTATTATTTCGA
Done.