Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g02062.F1
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: 5223
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Found at i:1848 original size:66 final size:66
Alignment explanation
Indices: 1742--2120 Score: 607
Period size: 66 Copynumber: 5.7 Consensus size: 66
1732 AGGGTTGACC
* *
1742 TTGAGGAATCAAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTACAAAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
1807 T
66 T
* * *
1808 TTGAGGAATCCAAGAAAA-AGGAAAGTGCAAGGTTTGAATCTATTTTGCAAAAGAAGGAACTTGA
1 TTGAGGAATCCAA-AAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGA
1872 GT
65 GT
* *
1874 TTGAGGAATCCAAAAAACAGGAAAGTGAAAGGTTTGAATCTACTTTGCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
1939 T
66 T
* * * *
1940 TTGAGGAATCCAAGAAACAGGAAAGTGAAAGGTTTGAATCTACTTTCCACAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
2005 T
66 T
* **
2006 TTGAGGAATCCAAAAACCAGGAAAGTGCAAGGTTTGAATCTACTACGCAAAAGATGCAACTTGAG
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
2071 T
66 T
*
2072 TTGAGGAATCCAAAAAACAGGAAAGAGCAAGGTTTGAATCTACTTTGCA
1 TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCA
2121 CAGAAAGGAA
Statistics
Matches: 288, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
65 4 0.01
66 280 0.97
67 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (66 bp):
TTGAGGAATCCAAAAAACAGGAAAGTGCAAGGTTTGAATCTACTTTGCAAAAGATGCAACTTGAG
T
Found at i:2264 original size:66 final size:66
Alignment explanation
Indices: 2173--2319 Score: 249
Period size: 66 Copynumber: 2.2 Consensus size: 66
2163 GAAACTACAG
*
2173 CTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
1 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
2238 A
66 A
* * * *
2239 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGTACAAGAAGGA
1 CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
2304 A
66 A
2305 CTTGAGTTTCAGGAA
1 CTTGAGTTTCAGGAA
2320 CTGCAAGTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (66 bp):
CTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAAGGA
A
Found at i:2289 original size:174 final size:174
Alignment explanation
Indices: 1996--2361 Score: 500
Period size: 174 Copynumber: 2.1 Consensus size: 174
1986 CCACAAGATG
* * * *** * *
1996 CAACTTGAGTTTGAGGAATCCAAAAACCAGGAAAGTGCAAGGTTTGAATCTACTACGCAAAAGAT
1 CAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAAGAA
* **
2061 GCAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGCAAGGTTTGAATCTACTTTGCAC-AGA
66 GCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACAAG-
* *
2125 AAGGAACTTCAGTTTCAGCAACTGCAATTTGAGTTGCAGAAACTA
130 AAGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAAATA
* ** *
2170 CAGCTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTTTGCACAAGAA
1 CAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAAGAA
* *
2235 GGAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGTACAAGA
66 GCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACAAGA
* * * *
2300 AGGAACTTGAGTTTCAGGAACTGCAAGTTGAGTTTCAGAAAATG
131 AGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAAATA
*
2344 CAACTTGAGCTTGAGGAA
1 CAACTTGAGTTTGAGGAA
2362 ACAAAAGAGT
Statistics
Matches: 166, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
174 164 0.99
175 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (174 bp):
CAACTTGAGTTTGAGGAATCCAAAAAACAGGAAAGAGAAACACTAGAATCTACTACGCAAAAGAA
GCAACTTGAGTTTCAGGAATCCAAAAAACAGGAAAGAGCAACATTTGAATCTACTTTGCACAAGA
AGGAACTTCAGTTTCAGCAACTGCAAGTTGAGTTGCAGAAAATA
Found at i:2332 original size:21 final size:21
Alignment explanation
Indices: 2303--2362 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2293 TACAAGAAGG
*
2303 AACTTGAGTTTCAGGAACTGC
1 AACTTGAGTTTCAGGAAATGC
* *
2324 AAGTTGAGTTTCAGAAAATGC
1 AACTTGAGTTTCAGGAAATGC
* *
2345 AACTTGAGCTTGAGGAAA
1 AACTTGAGTTTCAGGAAA
2363 CAAAAGAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (21 bp):
AACTTGAGTTTCAGGAAATGC
Found at i:2792 original size:33 final size:33
Alignment explanation
Indices: 2744--2872 Score: 222
Period size: 33 Copynumber: 3.9 Consensus size: 33
2734 GCAGAGATCC
* * *
2744 CCGTTGTTGACGATGAATCAATGAATAAACCTA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
2777 CCGTTATTGAAGATGAATCAATGAATAAACATA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
2810 CCGTTATTGAAGATGAATCAATGAATAAACATA
1 CCGTTATTGAAGATGAATCAATGAATAAACATA
*
2843 CCGTTATTGATGATGAATCAATGAATAAAC
1 CCGTTATTGAAGATGAATCAATGAATAAAC
2873 TTACTCCTGA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 92 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
CCGTTATTGAAGATGAATCAATGAATAAACATA
Found at i:3132 original size:186 final size:185
Alignment explanation
Indices: 2812--3270 Score: 765
Period size: 186 Copynumber: 2.5 Consensus size: 185
2802 TAAACATACC
* *
2812 GTTATTGAAGATGAATCAATGAATAAACATACCGTTATTGATGATGAATCAATGAATAAACTTAC
1 GTTATTGAA-ATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
*
2877 TCCTGAAAATGAACAGCTGAAGATTTTGGACATGGGAGCTGAGGACCAGAAACCACAGCAGCAGG
65 TGCTGAAAATGAACAGCTGAAGATTTTGGACATGGGAGCTGAGGACCAGAAACCACAGCAGCAGG
* * *
2942 CCATGCTGAGTTCACTGAGTACTACCATTTCAGAGGTGACATCTGCAGAGATCCCT
130 CCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGAGATCCCT
*
2998 GTTATTGAGAATGAATCAATGAATAAACCTACCGTTAATGACGATGAATCAATGAATAAACTTAC
1 GTTATTGA-AATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
* *
3063 TGCTGAAAAAGAACAGCTGAAGATTTTGGACATGGGAGCTGAGGACCAGAAACCACAGCAGCTGG
65 TGCTGAAAATGAACAGCTGAAGATTTTGGACATGGGAGCTGAGGACCAGAAACCACAGCAGCAGG
3128 CCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGAGATCCCT
130 CCATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGAGATCCCT
* * * *
3184 GTTATTGACAATGAATCAATGAATAAACCTACCGTTATTGACGATGGATCAATAAATAGACTTAT
1 GTTATTGA-AATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTAC
*
3249 TGCTGAAAATGAGCAGCTGAAG
65 TGCTGAAAATGAACAGCTGAAG
3271 GCTCTGGTAA
Statistics
Matches: 255, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
186 254 1.00
187 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (185 bp):
GTTATTGAAATGAATCAATGAATAAACCTACCGTTATTGACGATGAATCAATGAATAAACTTACT
GCTGAAAATGAACAGCTGAAGATTTTGGACATGGGAGCTGAGGACCAGAAACCACAGCAGCAGGC
CATGCCGAGTTCACTGAGTACAACCATGTCAGAGGTGACATCTGCAGAGATCCCT
Done.