Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011795.1 Corchorus olitorius cultivar O-4 contig11828, 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, 694
Length: 1157
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:351 original size:154 final size:154
Alignment explanation
Indices: 1--1157 Score: 1812
Period size: 154 Copynumber: 7.5 Consensus size: 154
* *
1 TTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATGATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
*
66 GAGATCAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTTGTTATTTTGGGCCTATCAGGG
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC-TTGTTATTTTGGGCCTATCAGGG
*
131 CCTATT-GCTGACGTTTTGAATCGTC
130 CCCATTAG-TGACGTTTTGAATCGTC
*
156 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTTTTTATGGCCTAACTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* *
221 GAGATCAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTATGGGCCTATCAGGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
*
286 CCATTAGTGACGTTTTAAATCGTC
131 CCATTAGTGACGTTTTGAATCGTC
* * * *
310 TTCGATTTGGCAAACCTTAATGGTTTTCTTTCCATTGTTTATGGCCTAAGTAAAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* * *
375 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTAGGGCCTATCAGGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
*
440 CCATTAGTGACGTTTTGAACCGTC
131 CCATTAGTGACGTTTTGAATCGTC
** *
464 TTCGATTTCACAAACTTCAATGCTTTTCTTTCCATTGTTTATGATGGCCTAACTATAATCATTTT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTG-TT-T-ATGGCCTAACTATAATCATTTT
* * * * * *
529 AGTGAGATTAGTCCACTGTGAAGTTTTAAGCTCATTTGGAACACTTGTTATTTTGTGCTTTTCGG
63 AGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAG
** * *
594 GGCCCATTAGTTCCATTTGGAATCGTC
128 GGCCCATTAGTGACGTTTTGAATCGTC
621 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
686 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGG
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCA-GGG
*
751 CCCATTACTGACGTTTTTGAATCGTC
130 CCCATTAGTGACG-TTTTGAATCGTC
* * * *
777 TTCGATTTGGCAAACCTCGATGCGTTTCTTTCCATTGTTTATGGCCTAAGTTTAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* * *
842 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGTGCCTTTCGGGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
** *
907 CCATTAGTTCCATTTTGAATCGTC
131 CCATTAGTGACGTTTTGAATCGTC
* *
931 TTCGATTTGGCAAACCTCGATGCTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* *
996 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
*
1061 CCATTAATGACGTTTTGAATCGTC
131 CCATTAGTGACGTTTTGAATCGTC
* * *
1085 TTCGATTTCGCAAACCTCAATGCTTTTCTTTCCTTTGTTTATGGCCTAAGTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
1150 GAGATCAG
66 GAGATCAG
Statistics
Matches: 913, Mismatches: 83, Indels: 13
0.90 0.08 0.01
Matches are distributed among these distances:
154 517 0.57
155 129 0.14
156 133 0.15
157 134 0.15
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
CCATTAGTGACGTTTTGAATCGTC
Found at i:946 original size:310 final size:308
Alignment explanation
Indices: 1--1157 Score: 1873
Period size: 310 Copynumber: 3.7 Consensus size: 308
* *
1 TTCGATTTGGCAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATGATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
*
66 GAGATCAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTTGTTATTTTGGGCCTATCAGGG
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC-TTGTTATTTTGGGCCTATCAGGG
* * * *
131 CCTATTGCTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTTTTT
130 CCCATTACTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTGTTT
*
196 ATGGCCTAACTATAATCATTTTAGTGAGATCAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACA
195 ATGGCCTAACTATAATCATTTTAGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* * * * ** * *
261 CTTGTTATTATGGGCCTATCAGGGCCCATTAGTGACGTTTTAAATCGTC
260 CTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTC
* * * *
310 TTCGATTTGGCAAACCTTAATGGTTTTCTTTCCATTGTTTATGGCCTAAGTAAAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* * *
375 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGTTATTTAGGGCCTATCAGGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
* * * *
440 CCATTAGTGACGTTTTGAACCGTCTTCGATTTCACAAACTTCAATGCTTTTCTTTCCATTGTTTA
131 CCATTACTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTG-TT-
* *
505 TGATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTAAGCTCATTTGGAA
194 T-ATGGCCTAACTATAATCATTTTAGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* *
570 CACTTGTTATTTTGTGCTTTTCGGGGCCCATTAGTTCCATTTGGAATCGTC
258 CACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTC
621 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
686 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGG
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCA-GGG
* * *
751 CCCATTACTGACGTTTTTGAATCGTCTTCGATTTGGCAAACCTCGATGCGTTTCTTTCCATTGTT
130 CCCATTACTGACG-TTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTGTT
* *
816 TATGGCCTAAGTTTAATCATTTTAGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
194 TATGGCCTAACTATAATCATTTTAGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
881 ACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTC
259 ACTTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTC
* *
931 TTCGATTTGGCAAACCTCGATGCTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
1 TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
* *
996 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAAGGC
66 GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
* *
1061 CCATTAATGACGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCTTTGTTTA
131 CCATTACTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
*
1126 TGGCCTAAGTATAATCATTTTAGTGAGATCAG
196 TGGCCTAACTATAATCATTTTAGTGAGATCAG
Statistics
Matches: 782, Mismatches: 61, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
308 155 0.20
309 114 0.15
310 232 0.30
311 221 0.28
312 17 0.02
313 43 0.05
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (308 bp):
TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTAGT
GAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCAGGGC
CCATTACTGACGTTTTGAATCGTCTTCGATTTCGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
TGGCCTAACTATAATCATTTTAGTGAGATCAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
TTGTTATTTTGTGCCTTTCGGGGCCCATTAGTTCCATTTTGAATCGTC
Done.