Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1919
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, 724
Length: 1207
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Found at i:587 original size:303 final size:303
Alignment explanation
Indices: 37--1207 Score: 1755
Period size: 303 Copynumber: 3.9 Consensus size: 303
27 TATAAAGGTT
* ** * *
37 GCCTCGAATTTAAATGTAAATTCGACGAAATATCGTTTCAAATTATTCACTTCACAAAACGCAAA
1 GCCTCGAATTTGAATACAAATTCGACCAAATATCGTTTCAAATTATTTACTTCACAAAACGCAAA
* *
102 TAATGAATGAGTTACACCACGTCGAGGAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
66 TAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
*
167 GAGGGGAGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
131 GAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
*
232 CTTAACTGCGGAGTTCTGATGGTATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCT
196 CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCT
297 TGCGCAATCTATTCATATAAAGGCTGCCGCTTATCGCACTTGC
261 TGCGCAATCTATTCATATAAAGGCTGCCGCTTATCGCACTTGC
* * *
340 GCCTCGAAATTGAATACAAATTCGACCAAATATCGTTCCAAATTATTTATTTCACAAAACGCAAA
1 GCCTCGAATTTGAATACAAATTCGACCAAATATCGTTTCAAATTATTTACTTCACAAAACGCAAA
*
405 TAACGAATGAGTTACACCACGTCGAGAAAACACAACTAAAAAAACCATTATATGAAATAAAAAGG
66 TAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
470 GAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
131 GAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
* * *
535 CTTAACTGCGGAGTTCTGATGGTATCCGGTGCATTAGTGCTGGTAGGATCGCACCCGTCTACTC-
196 CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCT
* * *
599 TGACGCAATCTTTTCA-ATAAAGGCTCGCC-CTTATTGCACTGGC
261 TG-CGCAATCTATTCATATAAAGGCT-GCCGCTTATCGCACTTGC
* * *
642 GCCTCGAATTTAAATGA-AAATTCGACAAAAAATCGTTTCAAATTATTTACTTCACAAAACGCAA
1 GCCTCGAATTTGAAT-ACAAATTCGACCAAATATCGTTTCAAATTATTTACTTCACAAAACGCAA
* * *
706 ATAATGAATGAGTTACACCACCTCGAGAAAACGCAACT-AAAAAA-CATTATATGAAATAAAATG
65 ATAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAG
* * * * * * *
769 GGAGGGGTGCTACAAGAGGACTTCTCAGGAGGTCACCCATTCTAGTACTACTCTCGCCCAAGCAC
130 GGAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCAC
* *
834 GCTTAACTGCGGAGTTTTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCAACTC
195 GCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTC
* * * *
899 TTGCGCAACCTATTCATA-AAAGGCTG-CGTCTTATCGTATTTGA
260 TTGCGCAATCTATTCATATAAAGGCTGCCG-CTTATCGCACTTGC
* * * * *
942 GCCTCGAATTTGAATACAAATTCGACCAAATATTGTTTCAAATTATTTATTTCACAAAATGTAAG
1 GCCTCGAATTTGAATACAAATTCGACCAAATATCGTTTCAAATTATTTACTTCACAAAACGCAAA
* * * *
1007 TAACGAATGAGTTACACCACTTCGAGAAAATGCAACTAAATAAAAACATTATATGAAATAAAATG
66 TAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAA-AAAACCATTATATGAAATAAAAAG
* * * *
1072 GGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGGAC
130 GGAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCAC
* * *
1137 GCTTAACTGCGGACTTCTGATGGGATCCGATGCATTATTGCTGGTATGATCGCACCCGTCAACTC
195 GCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTC
1202 TTGCGC
260 TTGCGC
Statistics
Matches: 790, Mismatches: 67, Indels: 22
0.90 0.08 0.03
Matches are distributed among these distances:
298 1 0.00
299 2 0.00
300 252 0.32
301 11 0.01
302 118 0.15
303 406 0.51
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (303 bp):
GCCTCGAATTTGAATACAAATTCGACCAAATATCGTTTCAAATTATTTACTTCACAAAACGCAAA
TAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
GAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCT
TGCGCAATCTATTCATATAAAGGCTGCCGCTTATCGCACTTGC
Found at i:1190 original size:603 final size:605
Alignment explanation
Indices: 37--1202 Score: 1899
Period size: 603 Copynumber: 1.9 Consensus size: 605
27 TATAAAGGTT
* * *
37 GCCTCGAATTTAAATGTAAATTCGACGAAATATCGTTTCAAATTATTCACTTCACAAAACGCAAA
1 GCCTCGAATTTAAATGAAAATTCGACAAAAAATCGTTTCAAATTATTCACTTCACAAAACGCAAA
* *
102 TAATGAATGAGTTACACCACGTCGAGGAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
66 TAATGAATGAGTTACACCACCTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
*
167 GAGGGGAGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
131 GAGGGGAGCAACAAGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
* *
232 CTTAACTGCGGAGTTCTGATGGTATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCT
196 CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCAACTCT
* *
297 TGCGCAATCTATTCATATAAAGGCTGCCGCTTATCGCACTTGCGCCTCGAAATTGAATACAAATT
261 TGCGCAACCTATTCATATAAAGGCTGCCGCTTATCGCACTTGAGCCTCGAAATTGAATACAAATT
362 CGACCAAATATCGTTCCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGT
326 CGACCAAATATCGTTCCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGT
*
427 CGAGAAAACACAACTAAAAAAACCATTATATGAAATAAAAAGGGAGGGGTGCAACACGAGAACAT
391 CGAGAAAACACAACTAAAAAAAACATTATATGAAATAAAAAGGGAGGGGTGCAACACGAGAACAT
*
492 CCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGG
456 CCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGACTTCTGATGG
* * *
557 TATCCGGTGCATTAGTGCTGGTAGGATCGCACCCGTCTACTCTGACGCAATCTTTTCAATAAAGG
521 GATCCGATGCATTAGTGCTGGTAGGATCGCACCCGTCAACTCTGACGCAATCTTTTCAATAAAGG
622 CTCGCCCTTATTGCACTGGC
586 CTCGCCCTTATTGCACTGGC
*
642 GCCTCGAATTTAAATGAAAATTCGACAAAAAATCGTTTCAAATTATTTACTTCACAAAACGCAAA
1 GCCTCGAATTTAAATGAAAATTCGACAAAAAATCGTTTCAAATTATTCACTTCACAAAACGCAAA
*
707 TAATGAATGAGTTACACCACCTCGAGAAAACGCAACT-AAAAAA-CATTATATGAAATAAAATGG
66 TAATGAATGAGTTACACCACCTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
* * * * * * *
770 GAGGGGTGCTACAAGAGGACTTCTCAGGAGGTCACCCATTCTAGTACTACTCTCGCCCAAGCACG
131 GAGGGGAGCAACAAGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
*
835 CTTAACTGCGGAGTTTTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCAACTCT
196 CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCAACTCT
* * *
900 TGCGCAACCTATTCATA-AAAGGCTG-CGTCTTATCGTATTTGAGCCTCGAATTTGAATACAAAT
261 TGCGCAACCTATTCATATAAAGGCTGCCG-CTTATCGCACTTGAGCCTCGAAATTGAATACAAAT
* * * * * *
963 TCGACCAAATATTGTTTCAAATTATTTATTTCACAAAATGTAAGTAACGAATGAGTTACACCACT
325 TCGACCAAATATCGTTCCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACG
** * *
1028 TCGAGAAAATGCAACTAAATAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGAC
390 TCGAGAAAACACAACTAAA-AAAAACATTATATGAAATAAAAAGGGAGGGGTGCAACACGAGAAC
* * *
1093 TTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGGACGCTTAACTGCGGACTTCTGAT
454 ATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGACTTCTGAT
* *
1158 GGGATCCGATGCATTATTGCTGGTATGATCGCACCCGTCAACTCT
519 GGGATCCGATGCATTAGTGCTGGTAGGATCGCACCCGTCAACTCT
1203 TGCGC
Statistics
Matches: 516, Mismatches: 43, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
601 2 0.00
602 115 0.22
603 297 0.58
604 6 0.01
605 96 0.19
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (605 bp):
GCCTCGAATTTAAATGAAAATTCGACAAAAAATCGTTTCAAATTATTCACTTCACAAAACGCAAA
TAATGAATGAGTTACACCACCTCGAGAAAACGCAACTAAAAAAACCATTATATGAAATAAAAAGG
GAGGGGAGCAACAAGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACG
CTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCAACTCT
TGCGCAACCTATTCATATAAAGGCTGCCGCTTATCGCACTTGAGCCTCGAAATTGAATACAAATT
CGACCAAATATCGTTCCAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGT
CGAGAAAACACAACTAAAAAAAACATTATATGAAATAAAAAGGGAGGGGTGCAACACGAGAACAT
CCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGACTTCTGATGG
GATCCGATGCATTAGTGCTGGTAGGATCGCACCCGTCAACTCTGACGCAATCTTTTCAATAAAGG
CTCGCCCTTATTGCACTGGC
Done.