Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023392.1 Corchorus olitorius cultivar O-4 contig23425, 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, 1000
Length: 4219
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Found at i:187 original size:20 final size:21
Alignment explanation
Indices: 145--187 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
135 TCCTTTGTTG
145 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
166 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
186 AT
1 AT
188 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:743 original size:154 final size:154
Alignment explanation
Indices: 428--1090 Score: 1118
Period size: 154 Copynumber: 4.3 Consensus size: 154
418 TGGCGCATCA
* *
428 ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTCTTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
*
493 TTAGTTCGGTTCTG-A--ATCTTCGATTTGGCAAACGACAATGCTTTTCTTTCCATTGTTTATGG
66 TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
555 CCTAACTATAATCATTTTGGTAAG
131 CCTAACTATAATCATTTTGGTAAG
*
579 ATTAGTCCATTGTGAAGTTTCTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
*
644 TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAGTGCTTTTCTTTCCATTGTTTATGG
66 TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
709 CCTAACTATAATCATTTTGGTAAG
131 CCTAACTATAATCATTTTGGTAAG
**
733 ATTAGTCCATTGTTCA-TTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
* * * * * *
797 TTAGTTCGGTTTTAATAATCGTCTTCAATTTAGCAAACCACAATGCTTTTCTTTCCATTGTTTAA
66 TTAGTTCGGTTCT--GAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTAT
*
862 GGCCTAACTATAATTATTTTGGTAAG
129 GGCCTAACTATAATCATTTTGGTAAG
888 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
* * *
953 TTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTTCATTGTTTATGG
66 TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
*
1018 GCTAACTATAATCATTTTGGTAAG
131 CCTAACTATAATCATTTTGGTAAG
1042 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTG
1 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTG
1091 TGATGCGCCA
Statistics
Matches: 479, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
151 76 0.16
152 1 0.00
153 59 0.12
154 200 0.42
155 83 0.17
156 60 0.13
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (154 bp):
ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
TTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTAAG
Found at i:1000 original size:309 final size:305
Alignment explanation
Indices: 428--1090 Score: 1121
Period size: 309 Copynumber: 2.2 Consensus size: 305
418 TGGCGCATCA
*
428 ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTCTTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
* * * *
493 TTAGTTCGGTTCTGAATCTTCGATTTGGCAAACGACAATGCTTTTCTTTCCATTGTTTATGGCCT
66 TTAGTTCGGTTCTGAATCTTCAATTTAGCAAACCACAATGCTTTTCTTTCCATTGTTTAAGGCCT
558 AACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTCTAGCTCATTTTGAACACTTGTTA
131 AACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTCTAGCTCATTTTGAACACTTGTTA
* *
623 TTTTGGGCCATTCGGGGCCCATTAGTTCGGTTCTGAATCATCTTCGATTTGGCAAACCACAGTGC
196 TTTTGGGCCATTCGGGGCCCATTAGTTCCGTTCTGAATCATCTTCGATTTGGCAAACCACAATGC
688 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAG
261 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAG
**
733 ATTAGTCCATTGTTCA-TTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
1 ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
* *
797 TTAGTTCGGTTTTAATAATCGTCTTCAATTTAGCAAACCACAATGCTTTTCTTTCCATTGTTTAA
66 TTAGTTCGGTTCT--GAA---TCTTCAATTTAGCAAACCACAATGCTTTTCTTTCCATTGTTTAA
* *
862 GGCCTAACTATAATTATTTTGGTAAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACT
126 GGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTCTAGCTCATTTTGAACACT
*
927 TGTTATTTTGGGCCATTCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCAC
191 TGTTATTTTGGGCCATTCGGGGCCCATTAGTTCCGTTCTGAATCATCTTCGATTTGGCAAACCAC
* *
992 AATGCTTTTCTTTTCATTGTTTATGGGCTAACTATAATCATTTTGGTAAG
256 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAG
*
1042 ATTAGTCCATTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTG
1 ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTATTTTG
1091 TGATGCGCCA
Statistics
Matches: 334, Mismatches: 18, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
304 59 0.18
305 14 0.04
306 2 0.01
309 227 0.68
310 32 0.10
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (305 bp):
ATTAGTCCATTGTGAACTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCATTCGGGGCCCA
TTAGTTCGGTTCTGAATCTTCAATTTAGCAAACCACAATGCTTTTCTTTCCATTGTTTAAGGCCT
AACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTTTCTAGCTCATTTTGAACACTTGTTA
TTTTGGGCCATTCGGGGCCCATTAGTTCCGTTCTGAATCATCTTCGATTTGGCAAACCACAATGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAG
Found at i:1226 original size:21 final size:21
Alignment explanation
Indices: 1200--1241 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1190 TAAGGAAGAA
1200 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
1221 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
1242 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:2321 original size:153 final size:154
Alignment explanation
Indices: 2037--2723 Score: 1180
Period size: 154 Copynumber: 4.5 Consensus size: 154
2027 GATTCGTATC
2037 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
1 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
* *
2102 CTTTTCTTTCCATTGTTTATGGGCTAAGTATAATCATTTTGGTAAGATTAGTCTATTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
* *
2167 TTTAACTCATTTCGAACACTTGTT
131 TTTAGCTCATTTTGAACACTTGTT
* *
2191 ATTTT-GGCCATTCGGGGCACATAAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
1 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
2255 CTTTTCTTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
2320 TTTAGCTCATTTTGAACACTTGTT
131 TTTAGCTCATTTTGAACACTTGTT
* * *
2344 CTTTTGGGCCATTCGGGGCCCATTAGTTCGGTTCTGAATCGTCTTCGATTTGCCAAACCACAATG
1 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
* *
2409 CTTTTCTTTCTATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
*
2474 TTTAGCTCGTTTTGAACACTTGTT
131 TTTAGCTCATTTTGAACACTTGTT
* * *
2498 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCATCTTCGATTTGGTAAACCACAATA
1 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
2563 CTTTTCTTTCCATTGTTTAT-GGCTTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGT
66 CTTTTCTTTCCATTGTTTATGGGC-TAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGT
2627 TTTTAGCTCATTTTGAACACTTGTT
130 TTTTAGCTCATTTTGAACACTTGTT
* * * *
2652 ATTTTGGGTCATTCGGGACCCATTAGTTCGGTTTTGAATTGTCTTCGATTTGGTAAACCACAATG
1 ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
2717 CTTTTCT
66 CTTTTCT
2724 CTTATCTCCT
Statistics
Matches: 503, Mismatches: 28, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
153 148 0.29
154 355 0.71
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (154 bp):
ATTTTGGGCCATTCGGGGCCCATTAGTTCGGTTTTGAATCGTCTTCGATTTGGCAAACCACAATG
CTTTTCTTTCCATTGTTTATGGGCTAACTATAATCATTTTGGTAAGATTAGTCCATTGTGAAGTT
TTTAGCTCATTTTGAACACTTGTT
Done.