Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_827 ID=scaffold_827-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: 3469
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.26
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:779 original size:42 final size:42
Alignment explanation
Indices: 720--804 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
710 TGTCTCGCGG
720 AACTTTTCCGACAGGAAAATCTTATTCAGCGGGGCAATTCCA
1 AACTTTTCCGACAGGAAAATCTTATTCAGCGGGGCAATTCCA
762 AACTTTTCCGACAGGAAAATCTTATTCAGCGGGGCAATTCCA
1 AACTTTTCCGACAGGAAAATCTTATTCAGCGGGGCAATTCCA
804 A
1 A
805 GCGAGCTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
AACTTTTCCGACAGGAAAATCTTATTCAGCGGGGCAATTCCA
Found at i:3316 original size:332 final size:332
Alignment explanation
Indices: 2590--3270 Score: 1265
Period size: 332 Copynumber: 2.1 Consensus size: 332
2580 ATGTAGGTAC
2590 TGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGG
1 TGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGG
* * *
2655 TCAAAAACTCCAGTATTTTTGACCGTTTCGCGAATGTTCACCGACCGCGCGTTTTTCGCCGATCC
66 TCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCATTTTTCGCCGATCC
2720 AGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAG
131 AGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAG
*
2785 GGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATT
196 GGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATG
** *
2850 CTTCCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTT
261 CAACCCCTGTCAATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTT
2915 ACATAGT
326 ACATAGT
2922 TGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGG
1 TGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGG
*
2987 TCAAAAACTCCACTGTTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCATTTTTCGCCGAT-C
66 TCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCATTTTTCGCCGATCC
3051 AGGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
131 A-GCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
3116 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
195 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
*
3181 GGAACCCCTGTCAATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
260 GCAACCCCTGTCAATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
3246 TACATAGT
325 TACATAGT
3254 TGGAGGCGTAGAATCGA
1 TGGAGGCGTAGAATCGA
3271 CTCCGCACGG
Statistics
Matches: 339, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
331 2 0.01
332 337 0.99
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.26
Consensus pattern (332 bp):
TGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACGG
TCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCATTTTTCGCCGATCC
AGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAAG
GGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCATG
CAACCCCTGTCAATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCTT
ACATAGT
Done.