Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g00920.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, 905
Length: 1509
ACGTcount: A:0.28, C:0.32, G:0.17, 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--601 Score: 298
Period size: 69 Copynumber: 2.9 Consensus size: 69
389 CAAGCCACCT
* ** * * *
399 GTTGTGAAGCCTCCATATATACCCAAGCCACCTATTGTAAAGCCTCCACCGTATACACCCAAACC
1 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
*
464 TCCG
66 GCCG
468 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
1 GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
533 GCCG
66 GCCG
* *
537 GTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAA
1 GTTGTGAAGCCT---CCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAA
602 GCCACCTTAC
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
69 74 0.61
72 48 0.39
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (69 bp):
GTTGTGAAGCCTCCATATATACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACC
GCCG
Found at i:478 original size:36 final size:36
Alignment explanation
Indices: 387--607 Score: 256
Period size: 36 Copynumber: 6.3 Consensus size: 36
377 ACCGCATCAT
* * *
387 CCCAAGCCACCTGTTGTGAAGCCT---CCATATATA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
* ** * *
420 CCCAAGCCACCTATTGTAAAGCCTCCACCGTATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
* *
456 CCCAAACCTCCGGTTGTGAAGCCT---CCATATATA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
*
489 CCCAAACCACCGGTTGTGAAGCCTCCGCCATATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
* *
525 CCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
* *
561 CCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACA
1 CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
*
597 CCCAAGCCACC
1 CCCAAACCACC
608 TTACTATCCA
Statistics
Matches: 166, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
33 52 0.31
36 114 0.69
ACGTcount: A:0.27, C:0.38, G:0.16, T:0.19
Consensus pattern (36 bp):
CCCAAACCACCGGTTGTGAAGCCTCCACCATATACA
Found at i:717 original size:168 final size:168
Alignment explanation
Indices: 526--872 Score: 660
Period size: 168 Copynumber: 2.1 Consensus size: 168
516 CCATATACAC
526 CCAA-ACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
590 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
66 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
* *
655 AGCCACCAGTCTACCCCAGTCCACCAATAGTGAATCCA
131 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
693 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCC
*
758 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAATACTGCCTCCAA
66 ATATACACCCAAGCCACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAA
823 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
131 AGCCACCAGTCCACCCCAGTCCACCAATAGTGAACCCA
861 CCAACACCGCCG
1 CCAACACCGCCG
873 ATTCTACCAC
Statistics
Matches: 176, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
167 4 0.02
168 172 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:745 original size:36 final size:37
Alignment explanation
Indices: 693--769 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
683 AGTGAATCCA
693 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
730 CCAA-ACCGCCGGTTGTGAAGCCTCCGCCATATACAC
1 CCAACACCGCCGGTTGTGAAGCCTCCGCCATATACAC
766 CCAA
1 CCAA
770 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:909 original size:24 final size:24
Alignment explanation
Indices: 882--940 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
872 GATTCTACCA
*
882 CCACCATCACCACCTATTGTGAAG
1 CCACCATCACCACCTATCGTGAAG
* * *
906 CCACCAACGCCTCCTATCGTGAAG
1 CCACCATCACCACCTATCGTGAAG
*
930 CCACCTTCACC
1 CCACCATCACC
941 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.