Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002682.1 Corchorus capsularis cultivar CVL-1 contig02690, 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, 759
Length: 1266
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Found at i:684 original size:26 final size:26
Alignment explanation
Indices: 650--701 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
640 ACAATATAAC
* *
650 AATTTAATTCTTT-AATTTTTTTATT
1 AATTTAATTATTTAAATATTTTTATT
675 AATTTCAATTATTTAAATATTTTTATT
1 AATTT-AATTATTTAAATATTTTTATT
702 TAAACGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 7 0.30
27 11 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
AATTTAATTATTTAAATATTTTTATT
Found at i:940 original size:18 final size:18
Alignment explanation
Indices: 909--943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
899 GGTGAAATGG
*
909 GTCGGTTGAGTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
*
927 GTCGGGTGATTCGGTTT
1 GTCGGGTGAGTCGGTTT
944 GTGAAGTCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.11, G:0.40, T:0.43
Consensus pattern (18 bp):
GTCGGGTGAGTCGGTTTT
Found at i:1179 original size:22 final size:22
Alignment explanation
Indices: 1151--1193 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1141 ATATTTTTAT
1151 TAAATAAGAATATATATATATG
1 TAAATAAGAATATATATATATG
1173 TAAATAAGAATATATATATAT
1 TAAATAAGAATATATATATAT
1194 ATATATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TAAATAAGAATATATATATATG
Found at i:1227 original size:7 final size:7
Alignment explanation
Indices: 1215--1256 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1205 AATTTTATTT
1215 TAATATA
1 TAATATA
1222 TAATATA
1 TAATATA
*
1229 TATTAT-
1 TAATATA
*
1235 TAATATG
1 TAATATA
1242 TAATATA
1 TAATATA
1249 T-ATATA
1 TAATATA
1255 TA
1 TA
1257 TGTGTGTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:1239 original size:20 final size:19
Alignment explanation
Indices: 1210--1251 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1200 GTAAGAATTT
1210 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
1229 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
1249 TAT
1 TAT
1252 ATATATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:1249 original size:22 final size:22
Alignment explanation
Indices: 1123--1253 Score: 66
Period size: 22 Copynumber: 6.1 Consensus size: 22
1113 AATCATTTTT
* *
1123 TATTTTTAATATGTAA-AAATA
1 TATTATTAATATGTAATATATA
* *
1144 TTTTTATTAAATAAG-AATATATA
1 -TATTATT-AATATGTAATATATA
*
1167 TA-TATGTAAATAAG-AATATATA
1 TATTAT-T-AATATGTAATATATA
* *
1189 TA-TA-TATATATGTAAGA-ATTT
1 TATTATTA-ATATGTAATATA-TA
*
1210 TATT-TTAATATAT-A-ATATA
1 TATTATTAATATGTAATATATA
1229 TATTATTAATATGTAATATATA
1 TATTATTAATATGTAATATATA
1251 TAT
1 TAT
1254 ATATGTGTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
19 7 0.08
20 16 0.19
21 15 0.17
22 39 0.45
23 9 0.10
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTATTAATATGTAATATATA
Done.