Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_476 ID=scaffold_476-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: 8426
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.26
Warning! 1797 characters in sequence are not A, C, G, or T
Found at i:273 original size:100 final size:100
Alignment explanation
Indices: 95--457 Score: 604
Period size: 100 Copynumber: 3.6 Consensus size: 100
85 ATGAAACCAT
* * *
95 AGATTTTACTTCTTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
160 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
*
195 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
260 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
* *
295 GGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
* *
360 GATATTACAATTAAAAAGATTGAAGCTACAACGGC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
* *
395 AGATCTTACTTCTCTAATG--GTGCAGTGGAACAGATTGAAGCCACGACGGCGGATCTGGTTTCC
1 AGATCTTACTTC-CTTA-GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCC
458 TCGACATTGC
Statistics
Matches: 248, Mismatches: 13, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
100 244 0.98
101 3 0.01
102 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (100 bp):
AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
Found at i:469 original size:50 final size:50
Alignment explanation
Indices: 115--484 Score: 266
Period size: 50 Copynumber: 7.4 Consensus size: 50
105 TCTTTAGCAG
* *
115 TGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCC-CTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTC-GACAT
* ** * * * * *** * *
165 TGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCT-TAGCAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTCGA-CAT
* *
215 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTCGACAT
* ** * * * ** * * *
265 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAG-CAG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATC-TGGTTTCCTCGACAT
*
315 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCC-CTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTC-GACAT
* * ** * * * *** *
365 TACAATTAAAAAGATTGAAGCTACAACGGCAGATCTTACTT-CTCTA-AT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTCGACAT
*
413 GGTGCAGTGGAACAGATTGAAGCCACGACGGCGGATCTGGTTTCCTCGACAT
1 --TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTCGACAT
* *
465 TGCAGTTGAACAAATTGAAG
1 TGCAGTGGAACAGATTGAAG
485 ATTACAGATC
Statistics
Matches: 235, Mismatches: 74, Indels: 22
0.71 0.22 0.07
Matches are distributed among these distances:
48 2 0.01
49 9 0.04
50 210 0.89
51 12 0.05
52 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCTCGACAT
Found at i:2348 original size:21 final size:22
Alignment explanation
Indices: 2308--2352 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2298 ATTATACTTG
* *
2308 TTTATTATTGTTATTTATTATT
1 TTTAATATTGTTAATTATTATT
2330 TTTAATATTG-TAATTATTATT
1 TTTAATATTGTTAATTATTATT
2351 TT
1 TT
2353 CGTGTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTAATATTGTTAATTATTATT
Done.