Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g00920.F2
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, 883
Length: 1473
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Found at i:296 original size:42 final size:42
Alignment explanation
Indices: 237--367 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
227 TCCTCCAAAG
237 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA
1 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA
* * * * *
279 CCACCGAAGCCACCGGTGGTGAAGCCACCGTATCACCCTAAA
1 CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA
321 CCACCTAAGCCTCCGGTGGTGAAACCC-CCATATCACCCTAAA
1 CCACCTAAGCCTCCGGTGGT-AAACCCACCATATCACCCTAAA
363 CCACC
1 CCACC
368 AAAACATCCA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 74 0.95
43 4 0.05
ACGTcount: A:0.29, C:0.41, G:0.15, T:0.15
Consensus pattern (42 bp):
CCACCTAAGCCTCCGGTGGTAAACCCACCATATCACCCTAAA
Found at i:472 original size:69 final size:69
Alignment explanation
Indices: 399--572 Score: 249
Period size: 69 Copynumber: 2.5 Consensus size: 69
389 CAAGCCACCT
*
399 GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCGTATACACCCAAACC
1 GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCATATACACCCAAACC
*
464 TCCG
66 GCCG
* ** * *
468 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
1 GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCATATACACCCAAACC
533 GCCG
66 GCCG
*
537 GTTGTGAAGCCTCCGCCATATACACCCAAGCCACCT
1 GTTGTGAAGCCT---CCATATATACCCAAGCCACCT
573 TACTATCCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
69 74 0.80
72 18 0.20
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.20
Consensus pattern (69 bp):
GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCATATACACCCAAACC
GCCG
Found at i:478 original size:36 final size:35
Alignment explanation
Indices: 387--571 Score: 198
Period size: 36 Copynumber: 5.3 Consensus size: 35
377 ACCGCATCAT
* * *
387 CCCAAGCCACCTGTTGTGAAGCCTCCA--TATATA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCTATACA
* ** *
420 CCCAAGCCACCTATTGTAAAGCCTCCACCGTATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACC-TATACA
* *
456 CCCAAACCTCCGGTTGTGAAGCCTCCA--TATATA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCTATACA
*
489 CCCAAACCACCGGTTGTGAAGCCTCCGCCATATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACC-TATACA
* *
525 CCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACC-TATACA
*
561 CCCAAGCCACC
1 CCCAAACCACC
572 TTACTATCCA
Statistics
Matches: 131, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
33 55 0.42
36 76 0.58
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.19
Consensus pattern (35 bp):
CCCAAACCACCGGTTGTGAAGCCTCCACCTATACA
Found at i:692 original size:168 final size:168
Alignment explanation
Indices: 490--836 Score: 651
Period size: 168 Copynumber: 2.1 Consensus size: 168
480 CCATATATAC
*
490 CCAA-ACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
554 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
66 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
* *
619 AGCCACCAGTCTACCCCAGTCCACCAATAGTGAATCCA
131 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
657 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
*
722 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAATACTGCCTCCAA
66 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
787 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
131 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
825 CCAACACCGCCG
1 CCAACACCGCCG
837 ATTCTACCAC
Statistics
Matches: 175, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
167 4 0.02
168 171 0.98
ACGTcount: A:0.28, C:0.42, G:0.14, T:0.16
Consensus pattern (168 bp):
CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
Found at i:709 original size:36 final size:37
Alignment explanation
Indices: 657--733 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
647 AGTGAATCCA
657 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
694 CCAA-ACCGCCGGTTGTGAAGCCTCCGCCATATACAC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
730 CCAA
1 CCAA
734 GCCACCTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.90
37 4 0.10
ACGTcount: A:0.26, C:0.40, G:0.18, T:0.16
Consensus pattern (37 bp):
CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
Found at i:873 original size:24 final size:24
Alignment explanation
Indices: 846--904 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
836 GATTCTACCA
*
846 CCACCATCACCACCTATTGTGAAG
1 CCACCATCACCACCTATCGTGAAG
* * *
870 CCACCAACGCCTCCTATCGTGAAG
1 CCACCATCACCACCTATCGTGAAG
*
894 CCACCTTCACC
1 CCACCATCACC
905 GGAAACACCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.44, G:0.12, T:0.19
Consensus pattern (24 bp):
CCACCATCACCACCTATCGTGAAG
Done.