Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g01474.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, 690
Length: 1151
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Found at i:190 original size:66 final size:66
Alignment explanation
Indices: 55--205 Score: 160
Period size: 66 Copynumber: 2.3 Consensus size: 66
45 TATACCGCCG
* * * * * * * *
55 AGAAAGCCAAGGAGGCAAGAGATACCACAGCCCAAAAGGCTTCTGAGTATACAGATTACGCTACC
1 AGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAAGGCTTCCGAGTATACAGACTACGCTACA
120 C
66 C
* * * *
121 AGAAAGCTAAGGACGCAAAAGACACCACTGCACAGAAGGCTTCCGAGTATACAGGCTATGC-AGC
1 AGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAAGGCTTCCGAGTATACAGACTACGCTA-C
185 AC
65 AC
* *
187 AGAAAACTAAGGATGCAAA
1 AGAAAGCTAAGGACGCAAA
206 GGATGCTACA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
65 1 0.01
66 69 0.99
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (66 bp):
AGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAAGGCTTCCGAGTATACAGACTACGCTACA
C
Found at i:256 original size:66 final size:66
Alignment explanation
Indices: 177--407 Score: 198
Period size: 66 Copynumber: 3.5 Consensus size: 66
167 GTATACAGGC
* * * * *
177 TATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGGGGAAAGCGGCTGAATATAAGGA
1 TATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTGAATATAAGGA
242 T
66 T
* * * * ** ** ** * *
243 TATACAGCTCAGAAAGCCAAGGAGGC-AAGAGATACTACAGCCCAAAAAGCTTCTGAGTACACA-
1 TATGCAGCACAGAAAGCCAAGGATGCAAAG-GATGCTACAATCGGAAAAGCGACTGAATATA-AG
306 GAT
64 GAT
* ** *
309 TATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCCGCAATTGGAAAAGCGACTGAATATAAGGA
1 TATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTGAATATAAGGA
*
374 C
66 T
**
375 TATGCAGCTGAGAAAGCCAAGGGA-GCAAAGGAT
1 TATGCAGCACAGAAAGCCAA-GGATGCAAAGGAT
408 ACGACAGCGC
Statistics
Matches: 124, Mismatches: 36, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
65 4 0.03
66 113 0.91
67 7 0.06
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (66 bp):
TATGCAGCACAGAAAGCCAAGGATGCAAAGGATGCTACAATCGGAAAAGCGACTGAATATAAGGA
T
Found at i:442 original size:66 final size:66
Alignment explanation
Indices: 247--538 Score: 176
Period size: 66 Copynumber: 4.4 Consensus size: 66
237 AAGGATTATA
* * * * * ** * * * *
247 CAGCTCAGAAAGCCAAGGAGGC-AAGAGATACTACAGCCCAAAAAGCTTCTGAGTACACAGATTA
1 CAGCTGAGAAAGCCAAGGAAGCAAAG-GATACGACAACGCAAAAAGCGACCGAGTATAAAGACTA
311 TG
65 TG
** * * * * * * * *
313 CAGCACAGAAAGCTAAGGATGCAAAGGATGCCG-CAATTG-GAAAAGCGACTGAATATAAGGACT
1 CAGCTGAGAAAGCCAAGGAAGCAAAGGAT-ACGACAA-CGCAAAAAGCGACCGAGTATAAAGACT
376 ATG
64 ATG
* * * * ** * * *
379 CAGCTGAGAAAGCCAAGGGAGCAAAGGATACGACAGCGCAGAAGGCTTCCGAGTTTACAGACTAC
1 CAGCTGAGAAAGCCAAGGAAGCAAAGGATACGACAACGCAAAAAGCGACCGAGTATAAAGACTAT
444 G
66 G
** * * * * *
445 CAGCACAGAAAGCTAAGGAAGCAAAAGATACTACAATGGAAAAAGCGACCGAGTATAAAGACTAT
1 CAGCTGAGAAAGCCAAGGAAGCAAAGGATACGACAACGCAAAAAGCGACCGAGTATAAAGACTAT
510 G
66 G
* * *
511 CAGCTGAAAAAGCGAAGGAAGCGAAGGA
1 CAGCTGAGAAAGCCAAGGAAGCAAAGGA
539 CGTGACAGCT
Statistics
Matches: 164, Mismatches: 57, Indels: 10
0.71 0.25 0.04
Matches are distributed among these distances:
65 3 0.02
66 157 0.96
67 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (66 bp):
CAGCTGAGAAAGCCAAGGAAGCAAAGGATACGACAACGCAAAAAGCGACCGAGTATAAAGACTAT
G
Found at i:546 original size:132 final size:129
Alignment explanation
Indices: 153--547 Score: 434
Period size: 132 Copynumber: 3.0 Consensus size: 129
143 CACCACTGCA
* *
153 CAGAAGGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
* * * * * *
218 GGGGAAAGCGGCTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACT-ACA
66 -GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGCAAG-G--ACTGACA
282 GCC
127 GCC
* * * * * **
285 CAAAAAGCTTCTGAGTACACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCCGCAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAA-
*
350 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGGAGCAAAGGA-TACGACA
65 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGC-AAGGACT--GACA
*
414 GCG
127 GCC
* * * * *
417 CAGAAGGCTTCCGAGTTTACAGACTACGCAGCACAGAAAGCTAAGGAAGCAAAAGATACTACAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
* * * * *
482 GGAAAAAGCGACCGAGTATAAAGACTATGCAGCTGAAAAAGCGAAGGAAGCGAAGGACGTGACAG
66 GG-AAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGC-AAGGAC-TGACAG
547 C
128 C
548 TGAGAAGACA
Statistics
Matches: 219, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 3 0.01
132 209 0.95
133 4 0.02
134 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (129 bp):
CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGCAAGGACTGACAGCC
Done.