Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_503 ID=scaffold_503-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: 6678
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.34
Warning! 330 characters in sequence are not A, C, G, or T
Found at i:193 original size:41 final size:41
Alignment explanation
Indices: 148--377 Score: 230
Period size: 41 Copynumber: 5.6 Consensus size: 41
138 GCTTTTAGCA
* *
148 GCATTTTTAAAAAAGCGCCGCTAATGCTCTGGG-GTTTAACG
1 GCATTTTTGAAAAAGCGCCGCTAATGCTC-GGGCCTTTAACG
** * * *
189 GCATTTTTGAAAAAGCGTTGCTACTGCTCGGGGCTTTAGCG
1 GCATTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAACG
* * *
230 GCATTTTTGAAAAAGTGCCGCTAATGCTCGGGCCTTTAGCT
1 GCATTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAACG
* * *
271 GCGTTTTTGAAATAGCGCCGCTAATGCTTGGGCCTTTAACG
1 GCATTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAACG
* * ** * * **
312 TCGTTTTTGAAGTAGCGCCACTAATGTTCGGGCCTTTAGTG
1 GCATTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAACG
*
353 G-AGTTTTTGAAAAAGCGCCACTAAT
1 GCA-TTTTTGAAAAAGCGCCGCTAAT
378 AATAATAAAA
Statistics
Matches: 158, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 3 0.02
41 155 0.98
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
GCATTTTTGAAAAAGCGCCGCTAATGCTCGGGCCTTTAACG
Found at i:360 original size:123 final size:123
Alignment explanation
Indices: 136--377 Score: 281
Period size: 123 Copynumber: 2.0 Consensus size: 123
126 ACGAGTTTTT
* *
136 GGGCTTTTAGCAGCATTTTTAAAAAAGCGCCGCTAATGCTCTGGGGTTTAACGGCATTTTTGAAA
1 GGGCCTTTAGCAGCATTTTTAAAAAAGCGCCGCTAATGCTCTGGGCTTTAACGGCATTTTTGAAA
*** * * * *
201 AAGCGTTGCTACTGCTCGGGGCTTTAGCGGCATTTTTGAAAAAGTGCCGCTAATGCTC
66 AAGCGCCACTAATGCTCGGGCCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTC
* * * * * *
259 GGGCCTTTAGCTGCGTTTTTGAAATAGCGCCGCTAATGCT-TGGGCCTTTAACGTCGTTTTTGAA
1 GGGCCTTTAGCAGCATTTTTAAAAAAGCGCCGCTAATGCTCTGGG-CTTTAACGGCATTTTTGAA
** * *
323 GTAGCGCCACTAATGTTCGGGCCTTTAGTGG-AGTTTTTGAAAAAGCGCCACTAAT
65 AAAGCGCCACTAATGCTCGGGCCTTTAGCGGCA-TTTTTGAAAAAGCGCCACTAAT
378 AATAATAAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
122 5 0.05
123 93 0.95
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (123 bp):
GGGCCTTTAGCAGCATTTTTAAAAAAGCGCCGCTAATGCTCTGGGCTTTAACGGCATTTTTGAAA
AAGCGCCACTAATGCTCGGGCCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTC
Found at i:953 original size:15 final size:13
Alignment explanation
Indices: 931--987 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 13
921 GGGGTTAGAA
931 GGTTTAGGTGTTAG
1 GGTTTAGGT-TTAG
*
945 GGATTTAGGATTTAA
1 GG-TTTAGG-TTTAG
960 GGTTTAGGGTTTTAG
1 GGTTTA-GG-TTTAG
975 GGTTTAGGGTTTA
1 GGTTTA-GGTTTA
988 AGTTTAGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.27
15 26 0.70
16 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (13 bp):
GGTTTAGGTTTAG
Found at i:963 original size:29 final size:28
Alignment explanation
Indices: 929--994 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
919 TAGGGGTTAG
929 AAGGTTTAGGTGTTAGGGATTTAGGATTT
1 AAGGTTTAGGTGTTAGGG-TTTAGGATTT
* *
958 AAGGTTTAGGGTTTTAGGGTTTAGGGTTT
1 AAGGTTTA-GGTGTTAGGGTTTAGGATTT
987 AA-GTTTAG
1 AAGGTTTAG
995 CTTAATTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 5 0.15
29 19 0.56
30 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (28 bp):
AAGGTTTAGGTGTTAGGGTTTAGGATTT
Found at i:966 original size:22 final size:22
Alignment explanation
Indices: 936--987 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
926 TAGAAGGTTT
936 AGGTGTTAGGGATTTAGGATTTA
1 AGGT-TTAGGGATTTAGGATTTA
* *
959 AGGTTTAGGGTTTTAGGGTTTA
1 AGGTTTAGGGATTTAGGATTTA
*
981 GGGTTTA
1 AGGTTTA
988 AGTTTAGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (22 bp):
AGGTTTAGGGATTTAGGATTTA
Found at i:4026 original size:47 final size:49
Alignment explanation
Indices: 3955--4089 Score: 202
Period size: 47 Copynumber: 2.8 Consensus size: 49
3945 AAAACTAATC
*
3955 TCGAGCCGATGCCATGTCCTAGACATGGTCTTACACTGACTCT-C-ATA
1 TCGAGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTATA
* *
4002 TCGAGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTG
1 TCGAGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTATA
* *
4051 TCCGTGACGATGCCATGTCCCAGACATGGTCTTACACTG
1 T-CGAGCCGATGCCATGTCCCAGACATGGTCTTACACTG
4090 GCACACTCAC
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
47 42 0.52
48 1 0.01
49 2 0.03
50 35 0.44
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.27
Consensus pattern (49 bp):
TCGAGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCCTATA
Done.