Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A04G000700.1.v1.1
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, 694
Length: 1157
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Found at i:196 original size:28 final size:29
Alignment explanation
Indices: 147--201 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
137 TCTCGGAATC
*
147 GAGAGGCGTGGCGGAGTGGGAC-GCTGGT
1 GAGAGGCGTGGCGGAGCGGGACTGCTGGT
*
175 GAGAGGCGT-GCGGCGCGAGGACTGCTG
1 GAGAGGCGTGGCGGAGCG-GGACTGCTG
202 TTGTTTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 13 0.57
29 4 0.17
ACGTcount: A:0.15, C:0.18, G:0.55, T:0.13
Consensus pattern (29 bp):
GAGAGGCGTGGCGGAGCGGGACTGCTGGT
Found at i:720 original size:45 final size:45
Alignment explanation
Indices: 662--1003 Score: 163
Period size: 45 Copynumber: 7.6 Consensus size: 45
652 AAAATTTGAT
*
662 CTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
* * * ** **
707 CTGTTCCACTCCTGCTCAGTGAAGATAAG-GCTGGT-GGCTGAAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATG-TTTAGC
* * * * ** ** *
751 CTGCTCTATTGCC-GATACA-TGGAGATAAGA-CTTGCCAAAATTT-GAT
1 CTGCTCCACT-CCTGCT-CAGTGAAGATAAGATC-TG-GTATGTTTAG-C
*
797 CTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
* * **
842 CTGCTCCACTCCTGCTCAGTGAAGATAAG-GCT-G-ATGATTGGAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATG-TT-TAGC
* * * ** *** * *
886 CTGCTCCA-TCGTCGGT-ACGTGGAGATAAGAT-TCATCAAAATTCGAT
1 CTGCTCCACTCCT-GCTCA-GTGAAGATAAGATCTGGT-ATGTTTAG-C
* * *
932 CTGCTTCACTCCTACACAGTGAAGATAAGATCTGGT-T-TTTAGC
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
975 CTGCTCCACTCCTGCTCAGTGAAGATAAG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG
1004 GCTGATGATA
Statistics
Matches: 212, Mismatches: 61, Indels: 50
0.66 0.19 0.15
Matches are distributed among these distances:
42 3 0.01
43 34 0.16
44 53 0.25
45 69 0.33
46 45 0.21
47 8 0.04
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (45 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGC
Found at i:743 original size:135 final size:135
Alignment explanation
Indices: 520--1007 Score: 745
Period size: 135 Copynumber: 3.6 Consensus size: 135
510 GGTCTGCTGT
* * *
520 AATTTGATCTGC-TCTACTCCTAATCAGCGAAGATAAGATCT-GTATGTTTAGCCTGCTTCACTC
1 AATTTGATCTGCTTC-ACTCCTACTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTC
*
583 CTGCTCAGTGAAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCGATACATGGAGATAAGACT
65 CTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACT
648 TGCCAA
130 TGCCAA
* *
654 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGTTCCACTCC
1 AATTTGATCTGCTTCACTCCTACTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
*
719 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCTATTGCCGATACATGGAGATAAGACTT
66 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTT
784 GCCAA
131 GCCAA
*
789 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTACTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
* ** * * * * *
854 TGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGTCGGTACGTGGAGATAAGA-TT
66 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTT
918 -CATCAA
131 GC--CAA
* *
924 AATTCGATCTGCTTCACTCCTACACAGTGAAGATAAGATCTGGT-T-TTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTACTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
987 TGCTCAGTGAAGATAAGGCTG
66 TGCTCAGTGAAGATAAGGCTG
1008 ATGATATCTG
Statistics
Matches: 330, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
133 40 0.12
134 38 0.12
135 252 0.76
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (135 bp):
AATTTGATCTGCTTCACTCCTACTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTT
GCCAA
Done.