Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_907 ID=scaffold_907-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: 9487
ACGTcount: A:0.07, C:0.05, G:0.06, T:0.08
Warning! 6983 characters in sequence are not A, C, G, or T
Found at i:701 original size:302 final size:301
Alignment explanation
Indices: 1--1387 Score: 2278
Period size: 301 Copynumber: 4.6 Consensus size: 301
* *
1 TAAACAATTTGAAACAATATTTGGTCGAATTTGCATTTAAATTTGAGGCGCAACTGCGATAA-GG
1 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
65 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
66 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
* * *
130 GGATCCCATCAGAACTCCGCAGTTAAGCGCGCCTGGGCGAGAGTAGTACTACGATGGGTGACCTC
131 GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTC
*
195 CTGGGAAGTCCTCGTGTTGCACCCCTCCCATTATATTTCATATAATTTTTTTTAGTTGCATTTTC
196 CTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTAGTTGCATTTTC
*
260 TCGACGTGGTGTAACTCAATCGTTATTTGCGTTTTGTGAAA
261 TCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAA
* * *
301 TAAACAATTTGCAACGATATTTGGTCGAATTTGCATTTAAATTCGTGGCGCAACTGCAATAAGGG
1 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
* *
366 GCAGCCTTTATATGAATAGATTGTGCAAGAGTTGACGGTTGCGATCATACCAGCACTAATGCACC
66 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
*
431 GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTT
131 GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTC
*
496 CTTGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTT
196 CTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAT-TTTTTTTAGTTGCATTTT
* * * *
561 CTCGACTTGGTGTAAGTCATTCGTTATTTACGTTTTCTGAAA
260 CTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAA
603 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
1 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
*
668 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGGCGGGTGCGATCATACCAGCACTAATGCACC
66 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
* * *
733 GGATCCCATCAGAACTCCAG-AGTTAAGCGTGCTTGGGCGAGAGCAGTAGTAAGATGGGTGACCT
131 GGATCCCATCAGAACTCC-GCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCT
797 CCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTAGTTGCATTTT
195 CCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTAGTTGCATTTT
**
862 CTCGACGTGGTGTAACTCATTCGTTATTTTTGTTTTGTGAAA
260 CTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAA
* *
904 TAAACAATTTGAAACAATATTTGGTCGAATTTGCATTTAAATTCGTGGCGCAACTGCGATAAGGG
1 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
* *** ** ****
969 GCAGCCTTTATATGAATAGATTACGCAACCCCTTCTCGGGTGCGATCATACCAGCACCCCCCGCA
66 GCAGCCTTTATATGAATAGATTGCGCAA-GAGTTGACGGGTGCGATCATACCAGCA-CTAATGCA
* *
1034 CCGGATCCCATCTGAACTCCGCAGTTAAGCGTGGTTGGGCGAGAGTAGTACTAGGATGGGTGACC
129 CCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACC
*
1099 TCCTGGGAAGTCCTCGTGTTGCACCCCTCTCATTTTATTTCATATAATGTTTTTTTTAGTTGCAT
194 TCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAA--TTTTTTTTAGTTGCAT
* * *
1164 TTTCTAGACGTGATGTAACTCATTCGTTATCTGCGTTTTGTG-AA
257 TTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAA
* *
1208 T-AATAACTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
1 TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
*
1272 GCAGCCTTTATATCAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
66 GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
*
1337 GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTCGGGCGAGAGTAGTACTA
131 GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTA
1388 NNNNNNNNNN
Statistics
Matches: 1004, Mismatches: 75, Indels: 15
0.92 0.07 0.01
Matches are distributed among these distances:
300 57 0.06
301 369 0.37
302 328 0.33
303 194 0.19
304 3 0.00
305 53 0.05
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (301 bp):
TAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGG
GCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACC
GGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTC
CTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTAGTTGCATTTTC
TCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAA
Found at i:8938 original size:303 final size:302
Alignment explanation
Indices: 8371--9462 Score: 1622
Period size: 303 Copynumber: 3.6 Consensus size: 302
8361 NNNNNNNNNN
* * *
8371 ACCCCTCTCATTTTAATTTCATATAATGGTTTTTTTAGTTGCATTTTCTAGACGTGATGTAACTC
1 ACCCCTCCCATTTT-ATTTCATATAAT-GTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTC
*
8436 ATTCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCCTTTAAA
64 ATTCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAA
*
8501 TTCGAGACGCAACTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTG
129 TTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTG
* *
8566 CGATCATACCAGCACTAATGCACTGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCAAG
194 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAG
*
8631 AGTAGCACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
259 AGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
*
8675 ATCCCTCCCATTTTATTTCATATAAT-TTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCAT
1 ACCCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCAT
* * * * *
8739 TCGTTATTTTCATTTTGTGAAATAAATAATTTGGAACGATATTCGGGGTCGAATTTGCATTTAAA
66 TCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATT--TGGTCGAATTTGCATTTAAA
** * *
8804 TTCGAGGCGCATGTGCGATCAGGGGCAGCTTTTATATGAATAGATTGCGCAAGAGTTGACGGGTG
129 TTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTG
* * *
8869 CGATCATACCAGCACTAATGCACCGGATCCCTTCAGAACTCCGCAGTTAACCCTGCTTGGGCGAG
194 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAG
8934 AGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
259 AGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
* *
8978 ACCCCTCTCATTTTATTTCATATAA-ATTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCAT
1 ACCCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCAT
*
9042 TCGTTATTTGCGTTTTGTGAAATAGACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATT
66 TCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATT
* *
9107 CGAGGCGCAAGTGCGATAAGGGGCAACCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCG
131 CGAGGCGCAACTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCG
* **
9172 ATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGGTCTGCGTGCTTGGGCGAGA-
196 ATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAG
*
9236 TAGTACTAGGATGGGTGACCTCAT-GGAAGTCCTCGTGTTGC
261 TAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
* * * ** ***
9277 ACCCCTCCAATTTTATTTTCATAT-ATGTTTTTTTAATTGCATTTTCGCGGGGGTGGTGGCGCTC
1 ACCCCTCCCATTTTA-TTTCATATAATGTTTTTTTAGTTGCATTTTCTC-GACGTGGTGTAACTC
* * * * * *
9341 ATCCGTTAATTGCGTTTTGGGGAAT-AACAAATTTG-AACTATATTTTGGTCGAATTTGCTTTTT
64 ATTCGTTATTTGCGTTTTGTGAAATAAAC-AATTTGAAACGATA-TTTGGTCGAATTTGC-ATTT
* *
9404 AAATTCCAGGCGCAACTGCGATAAGGGGCAGTCCTTTATATTAATAAGATTGCGCAAGA
126 AAATTCGAGGCGCAACTGCGATAAGGGGCAG-CCTTTATATGAAT-AGATTGCGCAAGA
9463 TTTTACTGGG
Statistics
Matches: 716, Mismatches: 61, Indels: 22
0.90 0.08 0.03
Matches are distributed among these distances:
299 31 0.04
300 58 0.08
301 267 0.37
302 31 0.04
303 304 0.42
304 25 0.03
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (302 bp):
ACCCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCAT
TCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATT
CGAGGCGCAACTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCG
ATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAG
TAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGC
Done.