Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_860 ID=scaffold_860-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, 1000
Length: 5102
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.15
Warning! 2071 characters in sequence are not A, C, G, or T
Found at i:570 original size:303 final size:303
Alignment explanation
Indices: 1--2017 Score: 3080
Period size: 303 Copynumber: 6.7 Consensus size: 303
* *
1 CTTCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCGGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
* * * * *
66 TGGGATCCGGTGCAATAGTT-CTGGTATGATCGTACCCGTCAACTCTTGTGTAACCTATTCATAT
66 TGGGATCCGGTGCATTA-TTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATAT
* * **
130 AAAGCCTGCCTCTTATCGCACTT-CAGCCTCGATTTTGAATACAAATAT-GAAAAAATATCGTTC
130 AAAGGCTGCCTCTTATCGCACTTGC-GCCTCGAATTTGAATACAAAT-TCGACCAAATATCGTTC
* *
193 CAAATTATTTATTTCACAAAACCCAAAAAACGAATGAGTTACACCACGTCGAGAAAATGCAACTA
193 CAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTA
*
258 AAAAAAACATTATATGAAATAAAATGGGACGGGTGCAACACGAGGA
258 AAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
* * *
304 CTTCCGAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGGACGCTTAACTGTGGAGTTCTGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
369 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
66 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
*
434 AAGGCTGCCTCTTATCACACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
131 AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
* * ** * * *
499 ATTATGTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAGCGCAACCATAT
196 ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
564 AAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
261 AAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
* *
607 CTTCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCGGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
* *
672 TGGGATCCGGTGCAATAGTT-CTGGTATGATCGTACCCGTCAACTCTTGCGCAA-CTTATTCATA
66 TGGGATCCGGTGCATTA-TTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATC-TATTCATA
* * * ** *
735 TAATGGCTGCCTCTTATCGCACTT-CAGCCTCGATTTTGAATACAAATACGAAAAAATATCGTTT
129 TAAAGGCTGCCTCTTATCGCACTTGC-GCCTCGAATTTGAATACAAATTCGACCAAATATCGTTC
* *
799 CAAATTATTTATTTCACAAAACGCAAAAAACGAATGAGTTACACCACGTCGAGAAAATGCAACAA
193 CAAATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTA
*
864 AAAAAAACATTATATGAAATAAAATGGGACGGGTGCAACACGAGGA
258 AAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
* * * * * *
910 CTTCCGAGGAGGTCACCCATCCAAGTACTACTCTCGCCCAAGGATGCTTAACTGTGGTGTTCTGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
*
975 TGGGATCTGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
66 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
*
1040 AAGGCTGCCTCTTATCACACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
131 AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
* * * *
1105 ATTATGTATTTCATAAAACGCAAATAACGAATGAGTTACACCACGTGGAGAAAACGCAACT-AAA
196 ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
*
1169 AAAACATTATATGAAATAAAATGGGAAGGGTGCAACACGAGGA
261 AAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
* * * * *
1212 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCTAGCACGCTTCACTTCGAAGTTCAGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
* * *
1277 TGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGACAATTCTTGCGCAATCTATTCATATA
66 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
* * * * * *
1342 AAGGCTGCCCCTTATCGCACTTGCTCCTCGAATTTAAAGGA-AAATTCGACCAAATATTGTTTCA
131 AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAA-TACAAATTCGACCAAATATCGTTCCA
1406 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAA
195 AATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACT-AA
*
1471 AAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACACAAGGA
259 AAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
* * * * * *
1516 CTTCCCAAGAGGTCACCTATCCTAGTGCTAGTCTCGCCCAAGCACGCTTAACTACAGAGTTCTGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
** * * *
1581 TATGATCCGGTGCATTAGTGCTGGTATTATCGCACCCGTCAACTGTTGCGCAATCTATTCATATA
66 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
* * * *
1646 AGGGCTGCCTCTTATCGCACTTGCGCGTCGAATTTGAATACAAATTCGACAAAATATCGTTTCAA
131 AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
1711 ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
196 ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
*
1776 AAATA-TTTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
261 AAA-ACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
1819 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
1 CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
** * * * *
1884 TATGATCCGGTGCATTAGTGCTGGTATTATCGCACCCGTCAACTGTTGCGCAATCTATTAATATA
66 TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
* *
1949 AGGGCTGCCTCTTATCGCACTTGCGCGTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
131 AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
2014 ATTA
196 ATTA
2018 NNNNNNNNNN
Statistics
Matches: 1564, Mismatches: 136, Indels: 28
0.91 0.08 0.02
Matches are distributed among these distances:
302 280 0.18
303 1004 0.64
304 280 0.18
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (303 bp):
CTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGA
TGGGATCCGGTGCATTATTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATTCATATA
AAGGCTGCCTCTTATCGCACTTGCGCCTCGAATTTGAATACAAATTCGACCAAATATCGTTCCAA
ATTATTTATTTCACAAAACGCAAATAACGAATGAGTTACACCACGTCGAGAAAATGCAACTAAAA
AAAACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGA
Found at i:4943 original size:302 final size:301
Alignment explanation
Indices: 4089--5102 Score: 1475
Period size: 302 Copynumber: 3.4 Consensus size: 301
4079 NNNNNNNNNN
* * * *
4089 CTTGCGCCTCGAAATTGAATACAAATTCGACCAAATATCGTTCCAAATTATTTATTTCACAAAAC
1 CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTATTTATTTCACAAAAC
*
4154 GCAAATAACGAATGAGTTACACCACGTCGAGAAAACACAACTAAAAAAACCATTATATGAAATAA
66 GCAAATAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAA-CATTATATGAAATAA
* * * *
4219 AAAGGGAGGGGTGCAACACGAGAACATCCCAAGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
130 AAAGGGAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * *
4284 GCACGCTTAACTGCGGAGTTCTGATGGTATCCGGTGCATTAGTGCTGGTAGGATCGCACCCGTCT
195 GCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
* *
4349 ACTC-TGACGCAATCTTTTCA-ATAAAGGCTCGCCCTTATTGCA
260 ACTCTTG-CGCAATCTATTCATATAAAGGCT-GCCCTTATCGCA
* * * * *
4391 CTGGCGCCTCGAATTTAAATGAAAATTCGACAAAAAATCGTTTCAAATTATTTACTTCACAAAAC
1 CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTATTTATTTCACAAAAC
* *
4456 GCAAATAATGAATGAGTTACACCACCTCGAGAAAACGCAACT-AAAAAACATTATATGAAATAAA
66 GCAAATAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACATTATATGAAATAAA
* * * *
4520 ATGGGAGGGGTGCTACAAGAGGACTT-CTCAGGAGGTCACCCATTCTAGTACTACTCTCGCCCAA
131 AAGGGAGGGGTGCAACACGAGGACTTCCT-AGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* *
4584 GCACGCTTAACTGCGGAGTTTTGATGGGATCCGGTGCATTAGTGCAGGTATGATCGCACCCGTCA
195 GCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
4649 ACTCTTGCGCAATCTATTCATATAAAGGCTGTCCCTTATCGCA
260 ACTCTTGCGCAATCTATTCATATAAAGGCTG-CCCTTATCGCA
* *
4692 CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAATTTATTTATTTCAGAAAAC
1 CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTATTTATTTCACAAAAC
* * *
4757 GCAAATAACGAATGAGTTACACCACGTCTAGAAAATGCAACTAAAAAAAAATTATTAT-AAATAA
66 GCAAATAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACATTA-TATGAAATAA
* * *
4821 AAGGGGAGGGGTGCAACCCGAGGACTTCCTAGGAGGTCACCCATCCTAGAACTACTCTCGCCCAA
130 AAAGGGAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAA
* * * *
4886 GTACGGTTAACTGCGGAGTTCTGAAGGGATCCGGTGCATTAGGGCTGGTATGATCGCACCCGTCA
195 GCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCA
4951 ACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCA
260 ACTCTTGCGCAATCTATTCATATAAAGGCTG-CCCTTATCGCA
* * * *
4994 CTTGCGCCTCGAATTGAAATGCAAACTCGACCAAATATCGTTTCCAA-TAGTTTATGTCACAAAA
1 CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTA-TTTATTTCACAAAA
* * * *
5058 CGCTAATGACG-ATAGAGTTACACCACGGCGAGAAAATGCAACTAA
65 CGCAAATAACGAAT-GAGTTACACCACGTCGAGAAAACGCAACTAA
Statistics
Matches: 641, Mismatches: 62, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
299 1 0.00
300 147 0.23
301 127 0.20
302 361 0.56
303 5 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (301 bp):
CTTGCGCCTCGAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTATTTATTTCACAAAAC
GCAAATAACGAATGAGTTACACCACGTCGAGAAAACGCAACTAAAAAAACATTATATGAAATAAA
AAGGGAGGGGTGCAACACGAGGACTTCCTAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAG
CACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAA
CTCTTGCGCAATCTATTCATATAAAGGCTGCCCTTATCGCA
Done.