Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_757 ID=scaffold_757-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: 4117
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:555 original size:47 final size:47
Alignment explanation
Indices: 477--566 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 47
467 AAAGGTACTC
* * * *
477 TAGTTTTAAATAGGAATACATTAATATTCAATTATTTCGATTCATTA
1 TAGTTTTAAATAGGAAAACAGTAATAGTCAATTATTCCGATTCATTA
* * *
524 TAGTTTTTAATAGGAAAACAGTGATGGTCAATTATTCCGATTC
1 TAGTTTTAAATAGGAAAACAGTAATAGTCAATTATTCCGATTC
567 TTCACCGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (47 bp):
TAGTTTTAAATAGGAAAACAGTAATAGTCAATTATTCCGATTCATTA
Found at i:3357 original size:318 final size:319
Alignment explanation
Indices: 2757--3400 Score: 1157
Period size: 318 Copynumber: 2.0 Consensus size: 319
2747 GAATCCAAGT
*
2757 AGTCACAAAAGATCAAAACACATGCATGTAAAGTATCATTTTTCTAGAGAACAGGTAGAAAAAGG
1 AGTCGCAAAAGATCAAAACACATGCATGTAAAGTATCATTTTTCTAGAGAACAGGTAGAAAAAGG
2822 GCTAAAAAATGTGAAATATGTTCCAACAGGTGATCAGCTAGCCGATTTACTGACCAAACCGTTAT
66 GCTAAAAAATGTGAAATATGTTCCAACAGGTGATCAGCTAGCCGATTTACTGACCAAACCGTTAT
* *
2887 CCACCATAAAATTCAAGAAATTAAGACCAGGGCTGGATCTTCAAAATTAGCAAAATTAGAAATTA
131 CCACCACAAAATTCAAGAAATTAAGACCAGAGCTGGATCTTCAAAATTAGCAAAATTAGAAATTA
* * *
2952 GCAAGTCAAAATGCAAGTGGACTCGTCAAAATAAGTCTCCTTTGAATATATCCTTCAGCGCTCTC
196 ACAAGTCAAAATGCAAGGGGACTCGTCAAAATAACTCTCCTTTGAATATATCCTTCAGCGCTCTC
* *
3017 TAAGTGTTTTCTTTGCTCTCCTCTATCGAGTTGAAACGTAAGCTAAGGAAACAGACAAA
261 TAAGTGTTTACTTTGATCTCCTCTATCGAGTTGAAACGTAAGCTAAGGAAACAGACAAA
*
3076 AGTCGCAAAAGATCAAAACACATAG-ATGTAAAGTATCCTTTTTCTAGAGAACAGGTAGAAAAAG
1 AGTCGCAAAAGATCAAAACACAT-GCATGTAAAGTATCATTTTTCTAGAGAACAGGTAGAAAAAG
3140 GGCTAAAAAATGTGAAATATGTTCCAACAGGTGATCAGCTAGCCGATTTACTGACCAAACCGTT-
65 GGCTAAAAAATGTGAAATATGTTCCAACAGGTGATCAGCTAGCCGATTTACTGACCAAACCGTTA
* *
3204 TTCACCACAAAATTCAAGAAATTAAGACCAGAGCTGGGTCTTCAAAATTAGCAAAATTAGAAATT
130 TCCACCACAAAATTCAAGAAATTAAGACCAGAGCTGGATCTTCAAAATTAGCAAAATTAGAAATT
*
3269 AACAAGTCAAAATTCAAGGGGACTCGTCAAAATAACTCTCCTTTGAATATATCCTTCAGCGCTCT
195 AACAAGTCAAAATGCAAGGGGACTCGTCAAAATAACTCTCCTTTGAATATATCCTTCAGCGCTCT
3334 CTAAGTGTTTACTTTGATCTCCTCTATCGAGTTGAAACGTAAGCTAAGGAAACAGACAAA
260 CTAAGTGTTTACTTTGATCTCCTCTATCGAGTTGAAACGTAAGCTAAGGAAACAGACAAA
3394 AGTCGCA
1 AGTCGCA
3401 GGGAGCTAAA
Statistics
Matches: 312, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
318 187 0.60
319 124 0.40
320 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (319 bp):
AGTCGCAAAAGATCAAAACACATGCATGTAAAGTATCATTTTTCTAGAGAACAGGTAGAAAAAGG
GCTAAAAAATGTGAAATATGTTCCAACAGGTGATCAGCTAGCCGATTTACTGACCAAACCGTTAT
CCACCACAAAATTCAAGAAATTAAGACCAGAGCTGGATCTTCAAAATTAGCAAAATTAGAAATTA
ACAAGTCAAAATGCAAGGGGACTCGTCAAAATAACTCTCCTTTGAATATATCCTTCAGCGCTCTC
TAAGTGTTTACTTTGATCTCCTCTATCGAGTTGAAACGTAAGCTAAGGAAACAGACAAA
Done.