Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00988.N2
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: 1693
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Found at i:1176 original size:84 final size:83
Alignment explanation
Indices: 1052--1374 Score: 313
Period size: 84 Copynumber: 4.0 Consensus size: 83
1042 TGAACGAGTG
* * * * * *
1052 AGGCATAGTCTTGACAGAC-AAGTGGTAGGGGTGCTAAGAACCATAAATGATAACTTGTATTACA
1 AGGCATAGTCTTGACAGACAAAG-GGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACA
*
1116 CGTATGAGCATGAGCAAGCA
65 CG-ATGAGCATAAGCAAGCA
* *
1136 AGGCATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGGTAACTCGTATT--AC
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
* *
1199 -AT--GCATAAGGATG-A
66 GATGAGCATAAGCAAGCA
* * * *
1213 A--AATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAT
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
* * *
1276 GCATGAGCACAAGCCAGCG
66 G-ATGAGCATAAGCAAGCA
* * * * * *
1295 AGGCATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGAATGGTAACTTGTACTACAT
1 AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACA-
* *
1360 GGATGAGCATGAGCA
65 CGATGAGCATAAGCA
1375 TGAACTTGCC
Statistics
Matches: 197, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
75 53 0.27
77 3 0.02
78 8 0.04
79 2 0.01
80 2 0.01
81 7 0.04
82 3 0.02
84 115 0.58
85 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (83 bp):
AGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACAC
GATGAGCATAAGCAAGCA
Found at i:1240 original size:75 final size:75
Alignment explanation
Indices: 1140--1279 Score: 244
Period size: 75 Copynumber: 1.9 Consensus size: 75
1130 CAAGCAAGGC
* * *
1140 ATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1205 AAGGATGAAA
66 AAGGATGAAA
*
1215 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1280 GAGCACAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (75 bp):
ATAGTCTTGACAGACAAAGGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
AAGGATGAAA
Found at i:1345 original size:159 final size:159
Alignment explanation
Indices: 1056--1360 Score: 414
Period size: 159 Copynumber: 1.9 Consensus size: 159
1046 CGAGTGAGGC
* * * * * * *
1056 ATAGTCTTGACAGACAAGTGGTAGGGGTGCTAAGAACCATAAATGATAACTTGTATTACACGTAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
** *
1121 GAGCATGAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGGTGCCAAGAACCTTACATGG
66 GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTACATGG
*
1186 TAACTCGTATTACATGCATAAGGATGAAA
131 TAACTCGTACTACATGCATAAGGATGAAA
* * *
1215 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCTTAAATGGTAACTCGTATTACATGCAT
1 ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
* * * * *
1280 GAGCACAAGCCAGCGAGGCATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGA-ATG
66 GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTT-ACATG
*
1344 GTAACTTGTACTACATG
130 GTAACTCGTACTACATG
1361 GATGAGCATG
Statistics
Matches: 125, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
159 124 0.99
160 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (159 bp):
ATAGTCTTGACAGACAAATGATAGAGATGCCAAGAACCATAAATGATAACTCGTATTACACGCAT
GAGCACAAGCAAGCAAGGCATAGTCTTGACAGACAAAGGGTAGAGATGCCAAGAACCTTACATGG
TAACTCGTACTACATGCATAAGGATGAAA
Done.