Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_999 ID=scaffold_999-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, 964
Length: 1607
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Found at i:603 original size:303 final size:303
Alignment explanation
Indices: 1--1593 Score: 2534
Period size: 302 Copynumber: 5.2 Consensus size: 303
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
* *
66 GTCCTCGTGTTGTACCCCTCCCATTTGATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACG
66 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACG
* * * *
131 TGGTGTAACTCATTCCTTA-TTTGCGTTTTGTGAAATAAACTATTTGAAACGATATTGGGTCAAA
131 TGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTCGGCCAAA
* * *
195 TTTGCATTTAAATTCGATGCGCAAGTGCGATAAAG-GGCAGCCTTTATATGAATAGATTGCGCAA
196 TTTGCATTTAAATTCGAGGCGCAAGTGCGAT-CAGCGGCAACCTTTATATGAATAGATTGCGCAA
* *
259 GAGTTGACGGGTGCGATCATACCAGCACTAATGAACCGGATCCC
260 GAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
*
303 ATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
*
368 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTGGTTGCATTTTCTCGACG
66 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACG
*
433 TGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGCCAAA
131 TGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTCGGCCAAA
*
498 TTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTGTATATGAATAGATTGCGCAAG
196 TTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATTGCGCAAG
563 AGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
261 AGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
606 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
* * *
671 GTCCTCGTGTTGTACCCCTCCCATTTTATTTCATGTAATTTTTTTTTAGTTGTATTTTCTCGACG
66 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACG
*
736 TGGTGTAACTCATTCGTTA-TTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGCCAAA
131 TGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTCGGCCAAA
800 TTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATTGCGCAAG
196 TTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATTGCGCAAG
865 AGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
261 AGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
* * *
908 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGTGAGAGTAGTACTATGTGA-GGGTGACATCCCTTG
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTA-G-GATGGGTGACCT-CCTGG
* * * * * * * * * * ** *
972 GAAGTCTTCCTGTCGCTCCCCCCCCCCACTTTATATCTGAGAAAATTTATTTGCACTTGCATTTT
63 GAAGTCCTCGTGTTG--CACCCCTCCCA-TTT-TATTTCATATAATTTTTTTTTAGTTGCATTTT
* * * * * *
1037 CTCGACGTAGTGTAACTCATTCGTCATTTT-CGTTTTGTGAAATGAATAATTAGGAACGATATTC
124 CTCGACGTGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTC
*** *
1101 GGTTGAATTTGCATTTAAATTCGAGGCGCAATTGCGATCAGCGGCAACCTTTATATGAATAGATT
189 GGCCAAATTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATT
1166 GCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
254 GCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
1216 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
* * *
1281 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTTTACTTGCCTTTTCTCGA
66 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAA--TTTTTTTTTAGTTGCATTTTCTCGA
* * * * * * *
1346 CGTAGTGTAACTCATTCGTTATTTT-CGTTTTGTGAAATGAATAATTAGGAACGATATTCAG-TA
129 CGTGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTCGGCCA
*
1409 GAATTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTGTATATGAATAGATTGCGC
194 -AATTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATTGCGC
1474 AAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
258 AAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
1520 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1 ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
1585 GTCCTCGTG
66 GTCCTCGTG
1594 CTTTGAAACC
Statistics
Matches: 1206, Mismatches: 71, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
302 349 0.29
303 298 0.25
304 289 0.24
306 26 0.02
307 12 0.01
308 229 0.19
309 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (303 bp):
ATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACG
TGGTGTAACTCATTCGTTATTTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTCGGCCAAA
TTTGCATTTAAATTCGAGGCGCAAGTGCGATCAGCGGCAACCTTTATATGAATAGATTGCGCAAG
AGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGC
Done.