Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A04G072100.1.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, 862
Length: 1437
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Found at i:696 original size:18 final size:18
Alignment explanation
Indices: 675--720 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
665 CCTAAGAAAG
* *
675 AAGATGCCGGTGAGAAGA
1 AAGACGCCGGAGAGAAGA
*
693 AAGACGGCGGAGAGAAGA
1 AAGACGCCGGAGAGAAGA
*
711 ATGACGCCGG
1 AAGACGCCGG
721 CGGTGATAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.41, T:0.07
Consensus pattern (18 bp):
AAGACGCCGGAGAGAAGA
Found at i:789 original size:21 final size:20
Alignment explanation
Indices: 764--830 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
754 TGCTGCGGGC
764 GGAGGCGAGAAGGAGGAAGGA
1 GGAGGCGAGAA-GAGGAAGGA
*
785 GGAGGTG-GAA-A-GAAGGAA
1 GGAGGCGAGAAGAGGAAGG-A
*
803 GGCGGCGAGAAGAAGGAAGGA
1 GGAGGCGAGAAG-AGGAAGGA
824 GGAGGCG
1 GGAGGCG
831 GGGAGAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 5 0.14
18 7 0.19
19 3 0.08
20 3 0.08
21 14 0.38
22 5 0.14
ACGTcount: A:0.37, C:0.06, G:0.55, T:0.01
Consensus pattern (20 bp):
GGAGGCGAGAAGAGGAAGGA
Found at i:817 original size:18 final size:19
Alignment explanation
Indices: 794--888 Score: 86
Period size: 18 Copynumber: 4.7 Consensus size: 19
784 AGGAGGTGGA
794 AAGAAGGAAGGCGGCGAGAAG
1 AAGAAGGAAGGCGGCG-G-AG
815 AAGGAAGGAGGAGGCGG-GGAG
1 AA-GAAGGA--AGGCGGCGGAG
*
836 AAGAAAGAAGGCGGCGGAGAG
1 AAGAAGGAAGGCGGC-G-GAG
*
857 AAGAAGGAAGGTGG-GGAG
1 AAGAAGGAAGGCGGCGGAG
*
875 AAGAAAGAAGGCGG
1 AAGAAGGAAGGCGG
889 TGGTGAAGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
18 21 0.33
19 1 0.02
20 6 0.10
21 21 0.33
22 7 0.11
23 1 0.02
24 6 0.10
ACGTcount: A:0.41, C:0.06, G:0.52, T:0.01
Consensus pattern (19 bp):
AAGAAGGAAGGCGGCGGAG
Found at i:821 original size:39 final size:39
Alignment explanation
Indices: 767--888 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 39
757 TGCGGGCGGA
* *
767 GGCGAGAAGGAGGAAGGAGGAGGTGGA-AAGAAGGAAGGC
1 GGCGAGAAGAAGGAAGGAGGAGG-GGAGAAGAAAGAAGGC
806 GGCGAGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAAGAAGGC
1 GGCGAGAAGAAGGAAGGAGGA---GGGGAGAAGAAAGAAGGC
*
848 GGCG-GAGAGAA-GAAGGAAGGTGGGGAGAAGAAAGAAGGC
1 GGCGAGA-AGAAGGAAGG-AGGAGGGGAGAAGAAAGAAGGC
887 GG
1 GG
889 TGGTGAAGCC
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
39 40 0.54
41 10 0.14
42 24 0.32
ACGTcount: A:0.39, C:0.06, G:0.53, T:0.02
Consensus pattern (39 bp):
GGCGAGAAGAAGGAAGGAGGAGGGGAGAAGAAAGAAGGC
Found at i:837 original size:21 final size:21
Alignment explanation
Indices: 770--877 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 21
760 GGGCGGAGGC
*
770 GAGAAGG-AGGAAGGAGGAGGTG
1 GAGAAGGAAGG-AGGAGGCGG-G
* *
792 GA-AA-GAAGGAAGGCGGCGAG
1 GAGAAGGAAGG-AGGAGGCGGG
*
812 AAGAAGGAAGGAGGAGGCGGG
1 GAGAAGGAAGGAGGAGGCGGG
* * * *
833 GAGAAGAAAGAAGGCGGCGGA
1 GAGAAGGAAGGAGGAGGCGGG
*
854 GAGAA-GAAGGA--AGGTGGG
1 GAGAAGGAAGGAGGAGGCGGG
872 GAGAAG
1 GAGAAG
878 AAAGAAGGCG
Statistics
Matches: 66, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
18 9 0.14
20 7 0.11
21 43 0.65
22 7 0.11
ACGTcount: A:0.40, C:0.05, G:0.54, T:0.02
Consensus pattern (21 bp):
GAGAAGGAAGGAGGAGGCGGG
Found at i:879 original size:21 final size:21
Alignment explanation
Indices: 794--885 Score: 93
Period size: 21 Copynumber: 4.3 Consensus size: 21
784 AGGAGGTGGA
*
794 AAGAAGGAAGGCGGCGAGAAG
1 AAGAAGGAAGGCGGGGAGAAG
815 AAGGAAGGAGGAGGCGGGGAGAAG
1 AA-GAAGGA--AGGCGGGGAGAAG
839 -A-AA-GAAGGCGGCGGAG-AG
1 AAGAAGGAAGGCGG-GGAGAAG
*
857 AAGAAGGAAGGTGGGGAGAAG
1 AAGAAGGAAGGCGGGGAGAAG
878 AAAGAAGG
1 -AAGAAGG
886 CGGTGGTGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
18 8 0.13
19 5 0.08
20 8 0.13
21 13 0.22
22 13 0.22
23 1 0.02
24 12 0.20
ACGTcount: A:0.42, C:0.05, G:0.51, T:0.01
Consensus pattern (21 bp):
AAGAAGGAAGGCGGGGAGAAG
Done.