Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g03449.F6
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: 3091
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Found at i:1968 original size:126 final size:126
Alignment explanation
Indices: 1802--2045 Score: 316
Period size: 126 Copynumber: 1.9 Consensus size: 126
1792 GCCATGACAG
* *
1802 TAAATAGCTCCACTGAGGAGATGAAAAGAGAGACAACTACA-ATAAA-GAGCTCAGCGGAGAAGA
1 TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTACAGA-AAATG-GCTCAGCGGAAAAGA
* *
1865 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGAAGAAAGAAACATCAT
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGAAACATCAT
* * * *
1928 TAAATAGCT-CAGCTGAGAAGATGAGACA-AGAGACAGCTACAGAAAATGGTTCAGCTGAAAAGA
1 TAAATAGCTCCA-CTGAGAAGATGA-AAAGAGAGACAACTACAGAAAATGGCTCAGCGGAAAAGA
* * * *
1991 TGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGATGAACAAAGA
64 TGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGA
2046 GACAGCCTTG
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
125 2 0.02
126 96 0.94
127 4 0.04
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (126 bp):
TAAATAGCTCCACTGAGAAGATGAAAAGAGAGACAACTACAGAAAATGGCTCAGCGGAAAAGATG
AACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAAAAGATGAACAAAGAAACATCAT
Found at i:2188 original size:177 final size:174
Alignment explanation
Indices: 1738--2315 Score: 611
Period size: 177 Copynumber: 3.3 Consensus size: 174
1728 GAAGGCAAAC
* * **
1738 AAAGAGATGGCCTCGACAGTGAATAGCTCAGCTGAGAAGATGAAGA-ACGAGATGGCCATGACAG
1 AAAGAGATGGCC-AGACAGTGAATAGCTCAGCTGAGAAGATG-AGACAAGAGACAG-C-T-ACAG
* * ** *
1802 TAAATAGCTCCA-CTGAGGAGATGAA-AAGAGAGACAAC-T-ACAATAAAGAGCTCAGCGGAGAA
61 TAAATGGCT-CAGCTGAGAAGATGAAGAA-AGAGACGCCTTGACAGTAAAGAGCTCAGC-GAGAA
*
1863 GATGAACAAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGAAG
123 GATGAACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
* * * * *
1915 AAAGA-A---ACA-TCATTAAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGAAAAT
1 AAAGAGATGGCCAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGTAAAT
* * * * *
1975 GGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGATGAA
66 GGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAGAGCTCAGC-GAGAAGATGAA
2040 CAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
129 CAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
* *
2086 AAAGAGATGGCCAGGACAGTGAATAGCTCAGCTGAGAAGACGAGACAAGAGACAGCTACAGTTAA
1 AAAGAGATGGCCA-GACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGTAAA
* * *
2151 TGGCTCGGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAGAGCTCGAACGAGAAGGTGA
65 TGGCTCAGCTGAGAAGATGAAGAAAGAGAC-GCCTTGACAGTAAAGAGCTC-AGCGAGAAGATGA
* * * * * * *
2216 AGAAAGAAACAGCCTTGACAGTAAATAACTCGGCTGAGAAGGTTAAT
128 ACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
* * * * *
2263 AAAGAGATTGCTTCACA-AGTGAATGGCTCAGCTGAGAAGATGAAAAAAGAGAC
1 AAAGAGATGGC--CAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGAC
2316 CACTGTGGCA
Statistics
Matches: 336, Mismatches: 50, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
167 2 0.01
168 27 0.08
169 4 0.01
170 5 0.01
171 104 0.31
172 1 0.00
173 1 0.00
175 2 0.01
176 1 0.00
177 184 0.55
178 3 0.01
179 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (174 bp):
AAAGAGATGGCCAGACAGTGAATAGCTCAGCTGAGAAGATGAGACAAGAGACAGCTACAGTAAAT
GGCTCAGCTGAGAAGATGAAGAAAGAGACGCCTTGACAGTAAAGAGCTCAGCGAGAAGATGAACA
AAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
Found at i:2202 original size:45 final size:45
Alignment explanation
Indices: 1738--2315 Score: 478
Period size: 45 Copynumber: 13.2 Consensus size: 45
1728 GAAGGCAAAC
** * *
1738 AAAGAGATGGCCTCGACAGTGAATAGCTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* ** * *
1783 AACGAGATGGCCATGACAGTAAATAGCTCCA-CTGAGGAGATGAA-
1 AAAGAGACAGCCTTGACAGTAAATAGCT-CAGCTGAGAAGATGAAG
* * * * *
1827 AAGAGAGACA-AC-T-ACAATAAAGAGCTCAGCGGAGAAGATGAAC
1 AA-AGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
1870 AAAGAGACAGCCTTGAAAATAAATAACTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* *
1915 AAAGA-A-A--CAT--CATTAAATAGCTCAGCTGAGAAGATG-AG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * *
1953 ACAAGAGACAG-C-T-ACAGAAAATGGTTCAGCTGAAAAGATGAAG
1 A-AAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
1996 AAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGATGAAC
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* *
2041 AAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
** ** * *
2086 AAAGAGATGGCCAGGACAGTGAATAGCTCAGCTGAGAAGACG-AG
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
2130 ACAAGAGACAG-C-T-ACAGTTAATGGCTCGGCTGAGAAGATGAAG
1 A-AAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * * *
2173 AAAGAGACGGCCTTGACAGTAAAGAGCTCGAAC-GAGAAGGTGAAG
1 AAAGAGACAGCCTTGACAGTAAATAGCTC-AGCTGAGAAGATGAAG
* * * * * *
2218 AAAGAAACAGCCTTGACAGTAAATAACTCGGCTGAGAAGGTTAAT
1 AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
** * * * *
2263 AAAGAGATTG-CTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAA
1 AAAGAGACAGCCTTGAC-AGTAAATAGCTCAGCTGAGAAGATGAAG
2308 AAAGAGAC
1 AAAGAGAC
2316 CACTGTGGCA
Statistics
Matches: 430, Mismatches: 79, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
38 3 0.01
39 27 0.06
40 1 0.00
41 6 0.01
42 91 0.21
43 13 0.03
44 17 0.04
45 269 0.63
46 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (45 bp):
AAAGAGACAGCCTTGACAGTAAATAGCTCAGCTGAGAAGATGAAG
Found at i:2268 original size:132 final size:135
Alignment explanation
Indices: 1978--2315 Score: 312
Period size: 132 Copynumber: 2.5 Consensus size: 135
1968 AGAAAATGGT
* * * * ** * *
1978 TCAGCTGAAAAGATGA-AGAAAGAGACAGCCTTGAC-AGTAAATATCTCAGCTGAAAAGATGAAC
1 TCAGCTGAGAAGACGAGA-AAAGAGACAG-CTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAA
* * * **
2041 AAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGT
64 AAAGAGACAGCCTTGACAATAAAGAACTCAACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGT
* *
2106 GAATAGC
129 AAATAAC
* * * *
2113 TCAGCTGAGAAGACGAGACAAGAGACAGC-T-AC-AGTTAATGGCTCGGCTGAGAAGATGAAGAA
1 TCAGCTGAGAAGACGAGAAAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAAA
* * * * **
2175 AGAGACGGCCTTGACAGTAAAGAGCTCGAAC-GAGAAGGTGAAGAAAGAAACAGCCTTGACAGTA
66 AGAGACAGCCTTGACAATAAAGAACTC-AACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGTA
2239 AATAAC
130 AATAAC
* *** **
2245 TCGGCTGAGAAGGTTA-ATAAAGAGATTGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAA
1 TCAGCTGAGAAGACGAGA-AAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAA
2309 AAGAGAC
65 AAGAGAC
2316 CACTGTGGCA
Statistics
Matches: 165, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
131 1 0.01
132 100 0.61
133 4 0.02
134 3 0.02
135 56 0.34
136 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16
Consensus pattern (135 bp):
TCAGCTGAGAAGACGAGAAAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAAA
AGAGACAGCCTTGACAATAAAGAACTCAACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGTAA
ATAAC
Done.