Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1056 ID=scaffold_1056-JGI_221_v2.0
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, 740
Length: 1234
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Found at i:1182 original size:303 final size:303
Alignment explanation
Indices: 1--1234 Score: 2088
Period size: 303 Copynumber: 4.1 Consensus size: 303
1 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
1 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
*
66 CTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
66 CTAGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
*
131 TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTGACAAAACG
131 TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTCACAAAACG
*
196 CAAATAACGAATGAGTTACACCACATCGAGAAAGTGCAACTAAAAAAAACATTATATGAAATAAA
196 CAAATAACGAATGAGTTACACCACATCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAA
261 ATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
261 ATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
* *
304 CCTAGTACTGCTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGAATTAGTG
1 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
* * * * *
369 CTGGTATGATCGCACACGTCAACTCTTACGCAATATATTCATATAAAGGCTGCCCCTTATCGCAT
66 CTAGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
* *
434 TTGCGCCTCG------AATGCAAATTCGACCAAATATCGTTTC-AAGTTATTTATTTCAGAAAAC
131 TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAA-TTATTTATTTCACAAAAC
* *
492 GCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAAACTAAAAAAAATATTATATGAAATA
195 GCAAATAACGAATGAGTTACACCACATCGAGAAAATGC-AACTAAAAAAAACATTATATGAAATA
* *
557 AAATGGGAGGGGTGGAACACGAGAACTTCCCAGGAGGTCACCCAT
259 AAATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
** * * *
602 CCTAGTACTACTCTCGCCCAATAACGCTTAGCTGCGGAGTTCTGATGGGATCCGGAGCAATAGTG
1 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
* *
667 C-AGGTATGATCGCACCCGTCAACTCTTTCGCAATCTATTCATATAAAAGGCTTCCCCTTTATCG
66 CTA-GTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATAT-AAAGGCTGCCCC-TTATCG
*
731 CAGTTGCGCCTCGAATTTAAAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTGACAA
128 CAGTTGCGCCTCGAATTT-AAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTCACAA
* *
796 AACGCAAATAACGAATGAGTTACAACACATCGAGAAAGTGCAACTAAAAAAAACATTATATGAAA
192 AACGCAAATAACGAATGAGTTACACCACATCGAGAAAATGCAACTAAAAAAAACATTATATGAAA
861 TAAAATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
257 TAAAATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
*
908 CCTAGTACTGCTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
1 CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
973 CTAGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
66 CTAGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
* *
1038 TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAATTGTTTATTTCCCAAAACG
131 TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTCACAAAACG
1103 CAAATAACGAATGAGTTACACCACATCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAA
196 CAAATAACGAATGAGTTACACCACATCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAA
*
1168 ATGGGAGGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCAT
261 ATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
1211 CCTAGTACTACTCTCGCCCAAGCA
1 CCTAGTACTACTCTCGCCCAAGCA
Statistics
Matches: 866, Mismatches: 51, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
296 2 0.00
297 78 0.09
298 165 0.19
299 11 0.01
300 18 0.02
303 309 0.36
304 24 0.03
305 11 0.01
306 168 0.19
307 78 0.09
308 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (303 bp):
CCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG
CTAGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAG
TTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTGCTAATTATTTATTTCACAAAACG
CAAATAACGAATGAGTTACACCACATCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAA
ATGGGAGGGGTGCAACACGAGAACTTCCCAAGAGGTCACCCAT
Done.