Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_463 ID=scaffold_463-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: 8145
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.29
Warning! 1393 characters in sequence are not A, C, G, or T
Found at i:102 original size:16 final size:17
Alignment explanation
Indices: 81--115 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
71 ATCTAATAAT
81 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
97 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
114 TT
1 TT
116 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:2781 original size:73 final size:72
Alignment explanation
Indices: 2636--2794 Score: 210
Period size: 73 Copynumber: 2.2 Consensus size: 72
2626 ACAATAAGCA
* * * *
2636 TTAGCGGCGTTTTTTAAAAAGCGCCACAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTT
1 TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCCAAACGACACCATTTTCTGAGCTTT
2701 TGGGGAT
66 TGGGGAT
* * ** * * *
2708 TTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCTT
1 TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCC-AAACGACACCATTTTCTGAGCTT
2773 TTGGGGAT
65 TTGGGGAT
2781 TTAGCAGCGTTTTT
1 TTAGCAGCGTTTTT
2795 AAGTAAGTGC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 35 0.47
73 40 0.53
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (72 bp):
TTAGCAGCGTTTTTGAAAAAGAGCCACAAAAAACCTAAGCCAAACGACACCATTTTCTGAGCTTT
TGGGGAT
Found at i:2855 original size:114 final size:114
Alignment explanation
Indices: 2707--3213 Score: 780
Period size: 114 Copynumber: 4.4 Consensus size: 114
2697 CTTTTGGGGA
* * * *
2707 TTTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
* * * *
2772 TTTGGGGATTTAGCAGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
*
2821 TTTAGCGGCGTTTTTGAGAAAGTGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
*
2886 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGTTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
* *
2935 TTTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
1 -TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
*
3000 TTTCGGGGATTTAGCGGCGTTTTTAAGCAAGCGCCGCTAAAGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGGAA-----GC----GCCGCTAATGCTCAGGGC
*
3059 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
*
3124 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
*
3173 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGC
3214 GCTTTCGGGG
Statistics
Matches: 363, Mismatches: 20, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
114 162 0.45
115 90 0.25
118 2 0.01
120 2 0.01
123 90 0.25
124 17 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
Found at i:3126 original size:238 final size:228
Alignment explanation
Indices: 2707--3213 Score: 791
Period size: 238 Copynumber: 2.2 Consensus size: 228
2697 CTTTTGGGGA
* * * *
2707 TTTAGCTGCGTTTTTGAGAAAGAGCCGTAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
* *
2772 TTTGGGGATTTAGCAGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCAGCGTTTTTAAGCAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* *
2837 AGAAAGTGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
131 AGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
2902 CGTTTTTAAGGAAGCGCCGCTAATG-TTCAGGGC
196 CGTTTTTAAGGAAGCGCCGCTAATGCTT-AGGGC
* *
2935 TTTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATGACGCCGTTTTGTGAGC
1 -TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGC
*
3000 TTTCGGGGATTTAGCGGCGTTTTTAAGCAAGCGCCGCTAAAGCCGCTAATGCTCAGGGCTTTAGC
65 TTTCGGGGATTTAGCAGCGTTTTTAAGCAA-----G-T---GCCGCTAATGCTCAGGGCTTTAGC
3065 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGG
121 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGG
3130 GATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
186 GATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
* *
3173 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGC
1 TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGC
3214 GCTTTCGGGG
Statistics
Matches: 254, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
229 85 0.33
234 1 0.00
235 1 0.00
237 38 0.15
238 127 0.50
239 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (228 bp):
TTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTGTGAGCT
TTCGGGGATTTAGCAGCGTTTTTAAGCAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
AGAAAGCGCCGCAAAAAACCTAAGCCAAAATAACGCCGTTTTGTGAGCTTTCGGGGATTTAGCGG
CGTTTTTAAGGAAGCGCCGCTAATGCTTAGGGC
Found at i:3574 original size:29 final size:29
Alignment explanation
Indices: 3540--3621 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
3530 TTTAAAGGCT
3540 GGGTTTAAGG-TTTAGAGG-TTATGAGTTAA
1 GGGTTTAAGGTTTTA-AGGTTTA-GAGTTAA
* *
3569 GGGTTTAGGGTTTTAAGGTTTAGAGTTTA
1 GGGTTTAAGGTTTTAAGGTTTAGAGTTAA
* *
3598 GGGTTTTAAGAGTATTAGGGTTTA
1 GGG-TTTAAG-GTTTTAAGGTTTA
3622 CGTTTTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 21 0.48
30 12 0.27
31 11 0.25
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (29 bp):
GGGTTTAAGGTTTTAAGGTTTAGAGTTAA
Found at i:3590 original size:15 final size:16
Alignment explanation
Indices: 3565--3621 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
3555 AGGTTATGAG
*
3565 TTAAGGGTTTAGGGTT
1 TTAAGGGTTTAGAGTT
3581 TTAA-GGTTTAGAG-T
1 TTAAGGGTTTAGAGTT
*
3595 TT-AGGGTTTTAAGAGTA
1 TTAAGGG-TTT-AGAGTT
3612 TT-AGGGTTTA
1 TTAAGGGTTTA
3622 CGTTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 12 0.34
16 11 0.31
17 6 0.17
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.44
Consensus pattern (16 bp):
TTAAGGGTTTAGAGTT
Found at i:3596 original size:22 final size:24
Alignment explanation
Indices: 3571--3629 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 24
3561 TGAGTTAAGG
3571 GTTTAGGGTTTTAAG-GT-TTAGA
1 GTTTAGGGTTTTAAGAGTATTAGA
*
3593 GTTTAGGGTTTTAAGAGTATTAGG
1 GTTTAGGGTTTTAAGAGTATTAGA
*
3617 GTTTA-CGTTTTAA
1 GTTTAGGGTTTTAA
3630 TAAGTACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 15 0.45
23 9 0.27
24 9 0.27
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.46
Consensus pattern (24 bp):
GTTTAGGGTTTTAAGAGTATTAGA
Found at i:3696 original size:12 final size:12
Alignment explanation
Indices: 3679--3716 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3669 GATATCCCTT
*
3679 TTTTTAATAAGA
1 TTTTTAATAAAA
3691 TTTTT-ATAAAA
1 TTTTTAATAAAA
*
3702 TTTTTAAAAAAA
1 TTTTTAATAAAA
3714 TTT
1 TTT
3717 CATTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTTAATAAAA
Found at i:6094 original size:54 final size:54
Alignment explanation
Indices: 6036--6145 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
6026 TCAATACAAT
6036 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
1 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
6090 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
1 TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
6144 TA
1 TA
6146 TGTTGTGTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (54 bp):
TAGCGGTGGTGCCATTTTTTTCTTACTTGAGTAGCTCCTACACAAAACTGATGC
Done.