Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00989.N3
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: 2527
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:1771 original size:93 final size:93
Alignment explanation
Indices: 1612--1780 Score: 257
Period size: 93 Copynumber: 1.8 Consensus size: 93
1602 CTAGGAAGCT
* * * * * * *
1612 TGAGGCATGGTCTTGACAGACAATTGGTAGAGGTGCCGAGAACCTTGAATGGTAACTTGCCTTAC
1 TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
1677 ATGCATGAGCACAAGCATGAGCATGAAG
66 ATGCATGAGCACAAGCATGAGCATGAAG
* *
1705 TGAGGCATAGTCTTGACAGACAAGTGGTAGGGGTGCCAAGAACCATAAATGATAACTTGTATTAC
1 TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
1770 ATGCATGAGCA
66 ATGCATGAGCA
1781 TGAAAATAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (93 bp):
TGAGGCATAGTCTTGACAGACAAGTGGTAGAGGTGCCAAGAACCATAAATGATAACTTGCATTAC
ATGCATGAGCACAAGCATGAGCATGAAG
Found at i:1820 original size:75 final size:75
Alignment explanation
Indices: 1711--1855 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 75
1701 GAAGTGAGGC
* * * * * **
1711 ATAGTCTTGACAGACAAGTGGTAGGGGTGCCAAGAACCATAAATGATAACTTGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
1776 GAGCATGAAA
66 GAGCATGAAA
* *
1786 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
1851 GAGCA
66 GAGCA
1856 CAAGCCAGCG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (75 bp):
ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCATAAATGATAACACGTATTACATGCAT
GAGCATGAAA
Found at i:1930 original size:84 final size:84
Alignment explanation
Indices: 1786--1939 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 84
1776 GAGCATGAAA
* *
1786 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGTATTACATGCAT
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGAACTACATGCAT
1851 GAGCACAAGCCAGCGAGGC
66 GAGCACAAGCCAGCGAGGC
* * * * * *
1870 ATAGTGTTGACAGACAAATGGTAGAGATGCCAAGAGCCTTGAATGGTAACTTC-AACTACATGCA
1 ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAAC-ACGAACTACATGCA
1934 TGAGCA
65 TGAGCA
1940 TGAGCATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 60 0.98
85 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (84 bp):
ATAGTCTTGACAGAAAAATGATAGAGATGCCAAGAACCTTAAATGGTAACACGAACTACATGCAT
GAGCACAAGCCAGCGAGGC
Found at i:2324 original size:78 final size:78
Alignment explanation
Indices: 2237--2397 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
2227 TATCTTTGGT
* * *
2237 TGCTTTGCTTTACTTGATGTTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGATTACATC
1 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
2302 TAAACAAGTTGCA
66 TAAACAAGTTGCA
*
2315 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGACTACATC
1 TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
2380 TAAACAAGTTGCA
66 TAAACAAGTTGCA
2393 TGCTT
1 TGCTT
2398 ACATGGATAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (78 bp):
TGCTTTGCTTTACTCGATGCTTAGTGCCTAACTAATTCTAAATTCATATGATTAATGACTACATC
TAAACAAGTTGCA
Done.