Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00803.F2
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, 849
Length: 1416
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Found at i:698 original size:18 final size:18
Alignment explanation
Indices: 677--722 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
667 CCTAAGAAAG
* *
677 AAGATGCCGGTGAGAAGA
1 AAGACGCCGGAGAGAAGA
*
695 AAGACGGCGGAGAGAAGA
1 AAGACGCCGGAGAGAAGA
*
713 ATGACGCCGG
1 AAGACGCCGG
723 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:791 original size:21 final size:20
Alignment explanation
Indices: 766--832 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
756 TGCTGCGGGC
766 GGAGGCGAGAAGGAGGAAGGA
1 GGAGGCGAGAA-GAGGAAGGA
*
787 GGAGGTG-GAA-A-GAAGGAA
1 GGAGGCGAGAAGAGGAAGG-A
*
805 GGCGGCGAGAAGAAGGAAGGA
1 GGAGGCGAGAAG-AGGAAGGA
826 GGAGGCG
1 GGAGGCG
833 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:819 original size:18 final size:19
Alignment explanation
Indices: 796--890 Score: 86
Period size: 18 Copynumber: 4.7 Consensus size: 19
786 AGGAGGTGGA
796 AAGAAGGAAGGCGGCGAGAAG
1 AAGAAGGAAGGCGGCG-G-AG
817 AAGGAAGGAGGAGGCGG-GGAG
1 AA-GAAGGA--AGGCGGCGGAG
*
838 AAGAAAGAAGGCGGCGGAGAG
1 AAGAAGGAAGGCGGC-G-GAG
*
859 AAGAAGGAAGGTGG-GGAG
1 AAGAAGGAAGGCGGCGGAG
*
877 AAGAAAGAAGGCGG
1 AAGAAGGAAGGCGG
891 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:823 original size:39 final size:39
Alignment explanation
Indices: 769--890 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 39
759 TGCGGGCGGA
* *
769 GGCGAGAAGGAGGAAGGAGGAGGTGGA-AAGAAGGAAGGC
1 GGCGAGAAGAAGGAAGGAGGAGG-GGAGAAGAAAGAAGGC
808 GGCGAGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAAGAAGGC
1 GGCGAGAAGAAGGAAGGAGGA---GGGGAGAAGAAAGAAGGC
*
850 GGCG-GAGAGAA-GAAGGAAGGTGGGGAGAAGAAAGAAGGC
1 GGCGAGA-AGAAGGAAGG-AGGAGGGGAGAAGAAAGAAGGC
889 GG
1 GG
891 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:839 original size:21 final size:21
Alignment explanation
Indices: 772--879 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 21
762 GGGCGGAGGC
*
772 GAGAAGG-AGGAAGGAGGAGGTG
1 GAGAAGGAAGG-AGGAGGCGG-G
* *
794 GA-AA-GAAGGAAGGCGGCGAG
1 GAGAAGGAAGG-AGGAGGCGGG
*
814 AAGAAGGAAGGAGGAGGCGGG
1 GAGAAGGAAGGAGGAGGCGGG
* * * *
835 GAGAAGAAAGAAGGCGGCGGA
1 GAGAAGGAAGGAGGAGGCGGG
*
856 GAGAA-GAAGGA--AGGTGGG
1 GAGAAGGAAGGAGGAGGCGGG
874 GAGAAG
1 GAGAAG
880 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:881 original size:21 final size:21
Alignment explanation
Indices: 796--887 Score: 93
Period size: 21 Copynumber: 4.3 Consensus size: 21
786 AGGAGGTGGA
*
796 AAGAAGGAAGGCGGCGAGAAG
1 AAGAAGGAAGGCGGGGAGAAG
817 AAGGAAGGAGGAGGCGGGGAGAAG
1 AA-GAAGGA--AGGCGGGGAGAAG
841 -A-AA-GAAGGCGGCGGAG-AG
1 AAGAAGGAAGGCGG-GGAGAAG
*
859 AAGAAGGAAGGTGGGGAGAAG
1 AAGAAGGAAGGCGGGGAGAAG
880 AAAGAAGG
1 -AAGAAGG
888 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.