Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g00111.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, 491
Length: 819
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.22
Found at i:364 original size:75 final size:75
Alignment explanation
Indices: 243--383 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
233 CCAGGCTATG
* *
243 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTCGTCATCCTCC-GAGTCCACCACA
1 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAG-GTCCACCACA
307 TGCTGAGCATC
65 TGCTGAGCATC
* * * *
318 CTCCTCCAAGGCCAAGT-CTCTATGTGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTACA
1 CTCCTCCAAGGCCAAGTCCTC-AAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACA
382 TG
65 TG
384 AGCATCCTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
74 3 0.05
75 54 0.93
76 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.18
Consensus pattern (75 bp):
CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACAT
GCTGAGCATC
Found at i:404 original size:99 final size:99
Alignment explanation
Indices: 287--481 Score: 275
Period size: 99 Copynumber: 2.0 Consensus size: 99
277 AGGACCTCGT
* * * *
287 CATCCTCCGAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCA-AGTCTCTATGTGCCACCAC
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGA-TCCCCATGCGCCACCAC
* *
351 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
65 CAAGACCAGGTCATCCTCCAAGTCCACCACATGAG
* ***
386 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTT
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
*
451 AGGACCAGGTCATCCTCCAAGTCCACCACAT
66 AAGACCAGGTCATCCTCCAAGTCCACCACAT
482 AATAATCATC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 83 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
AAGACCAGGTCATCCTCCAAGTCCACCACATGAG
Found at i:420 original size:27 final size:24
Alignment explanation
Indices: 362--407 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
352 AAGACCAGGT
* *
362 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
386 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
408 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:499 original size:99 final size:99
Alignment explanation
Indices: 296--574 Score: 254
Period size: 99 Copynumber: 2.9 Consensus size: 99
286 TCATCCTCCG
* * *
296 AGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAAGTCTCTATGTGCCACCACCAAGACCAGG
1 AGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAAGTCCCCATGCGCCACCACCAAGACCAGG
* * * * *
361 TCATCCTCCAGGTCCACTACATGAGCATCCTCCA
66 TCATCCTCCAAGTCCACCACATAAGAATCATCCA
* *** *
395 AGTCCACCACATGTTGAGCATCCTCCTCCAAGGCC-AGATCCCCATGCGCCACCGTTAGGACCAG
1 AGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAAG-TCCCCATGCGCCACCACCAAGACCAG
* **
459 GTCATCCTCCAAGTCCACCACATAATAATCATCTT
65 GTCATCCTCCAAGTCCACCACATAAGAATCATCCA
* * *
494 CGTCCAGGC-CA---T--GC-TCCTCCTCC-AGGACCAAGTCCCCATGCTCCACCACC-AGAACC
1 AGTCCA-CCACATGCTGAGCATCCTCCTCCAAGG-CCAAGTCCCCATGCGCCACCACCAAG-ACC
* * *
550 AGGCCATCTTCCAAGTCAACCACAT
63 AGGTCATCCTCCAAGTCCACCACAT
575 CTTGGTCATC
Statistics
Matches: 149, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
92 4 0.03
93 50 0.34
94 4 0.03
96 1 0.01
98 2 0.01
99 87 0.58
100 1 0.01
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.19
Consensus pattern (99 bp):
AGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAAGTCCCCATGCGCCACCACCAAGACCAGG
TCATCCTCCAAGTCCACCACATAAGAATCATCCA
Found at i:563 original size:93 final size:93
Alignment explanation
Indices: 415--638 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 93
405 ATGTTGAGCA
* *** * * *
415 TCCTCCTCCAAGGCC-AGATCCCCATGCGCCACCGTTAGGACCAGGTCATCCTCCAAGTCCACCA
1 TCCTCCTCCAAGGCCAAG-TCCCCATGCACCACCACCAGAACCAGGCCATCCTCCAAGTCAACCA
* * *
479 CATAATAATCATCTTCGTCCAGGCCATGC
65 CATAATAATCATCCTCATCCAGGCCACGC
* *
508 TCCTCCTCC-AGGACCAAGTCCCCATGCTCCACCACCAGAACCAGGCCATCTTCCAAGTCAACCA
1 TCCTCCTCCAAGG-CCAAGTCCCCATGCACCACCACCAGAACCAGGCCATCCTCCAAGTCAACCA
** ** *
572 CATCTTGGTCATCCTCATCCAGGCCACGG
65 CATAATAATCATCCTCATCCAGGCCACGC
* * *
601 TCCCCCTCCAAGGCCAGGTCCCCATGCACCACTACCAG
1 TCCTCCTCCAAGGCCAAGTCCCCATGCACCACCACCAG
639 GTCTAGGTCA
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
92 3 0.03
93 100 0.93
94 5 0.05
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (93 bp):
TCCTCCTCCAAGGCCAAGTCCCCATGCACCACCACCAGAACCAGGCCATCCTCCAAGTCAACCAC
ATAATAATCATCCTCATCCAGGCCACGC
Done.