Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01335.N1
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: 2983
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Found at i:659 original size:27 final size:27
Alignment explanation
Indices: 616--782 Score: 219
Period size: 27 Copynumber: 6.2 Consensus size: 27
606 GAGGAAGCGT
*
616 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
643 TCTGGTGGCTCTACCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
670 TCTGGTGGCTCTGCCATAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
697 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
724 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
752 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
778 TCTGG
1 TCTGG
783 CAGCCATGCT
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 5 0.04
27 105 0.84
28 15 0.12
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1379 original size:26 final size:26
Alignment explanation
Indices: 1316--1391 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
1306 AAAAGTAGCT
* * * *
1316 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-GTGCA
1344 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGGTGCA
1370 AAATTACTGTTATACCCCTAGG
1 AAATTACTGTTATACCCCTAGG
1392 GTTAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.57
27 1 0.02
28 18 0.41
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTGCA
Found at i:1537 original size:27 final size:27
Alignment explanation
Indices: 1494--1660 Score: 228
Period size: 27 Copynumber: 6.2 Consensus size: 27
1484 GAGGAAGCGT
*
1494 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
1521 TCTGGTGGCTCTACCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
1548 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1575 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1602 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
1630 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
1656 TCTGG
1 TCTGG
1661 CAGCCATGCT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
26 5 0.04
27 107 0.84
28 15 0.12
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1831 original size:878 final size:878
Alignment explanation
Indices: 137--1893 Score: 3460
Period size: 878 Copynumber: 2.0 Consensus size: 878
127 TCGCAAACAG
*
137 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAAG
1 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCAAAAAG
202 TCGGTATTTTGGGAATTTGCGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
66 TCGGTATTTTGGGAATTTGCGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
267 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
131 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
332 AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCCGGTAAGTGTTCTGATAGTA
196 AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCCGGTAAGTGTTCTGATAGTA
397 CGTAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
261 CGTAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
462 TGGAAAATTACTGTTATACCCCTAGGTGCAAAATTACCGTTATACCCCTAGGGTTAATTTTGACT
326 TGGAAAATTACTGTTATACCCCTAGGTGCAAAATTACCGTTATACCCCTAGGGTTAATTTTGACT
527 GAAAAGCATGACGATCTGATTCTGTATGATGTATGCCATGATTATATATCTGTTGCATGGGGACA
391 GAAAAGCATGACGATCTGATTCTGTATGATGTATGCCATGATTATATATCTGTTGCATGGGGACA
592 TGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTAC
456 TGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTAC
*
657 CACAAATATCTGATCTGGTGGCTCTGCCATAAATATCTGATCTGGTGGCTCTGCCACATATATCT
521 CACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
722 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCTGGCAGC
586 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCTGGCAGC
787 CATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTCGAGTTGTCTCCCCACACGGTGTAAG
651 CATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTCGAGTTGTCTCCCCACACGGTGTAAG
*
852 GTTGGTACGGGGGTGTATACGGTTGGATATTGTTGGGTTTCTGCATAAACATGTAATATCTGTTC
716 GTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAATATCTGTTC
917 TGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAACTTATTCTA
781 TGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAACTTATTCTA
982 TTTCTGTGGTTTGAGCTAATATAGGCTATGGTT
846 TTTCTGTGGTTTGAGCTAATATAGGCTATGGTT
1015 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCAAAAAG
1 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCAAAAAG
1080 TCGGTATTTTGGGAATTTGCGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
66 TCGGTATTTTGGGAATTTGCGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
1145 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
131 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
1210 AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCCGGTAAGTGTTCTGATAGTA
196 AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCCGGTAAGTGTTCTGATAGTA
1275 CGTAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
261 CGTAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
*
1340 TGGAAAATTACTGTTATACCCCTAGGTGCAAAATTACTGTTATACCCCTAGGGTTAATTTTGACT
326 TGGAAAATTACTGTTATACCCCTAGGTGCAAAATTACCGTTATACCCCTAGGGTTAATTTTGACT
* *
1405 GAAAAGCATGATGATCTGATTCTGTATGATGTATGCCTTGATTATATATCTGTTGCATGGGGACA
391 GAAAAGCATGACGATCTGATTCTGTATGATGTATGCCATGATTATATATCTGTTGCATGGGGACA
1470 TGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTAC
456 TGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTAC
1535 CACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
521 CACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1600 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCTGGCAGC
586 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCTGGCAGC
1665 CATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTCGAGTTGTCTCCCCACACGGTGTAAG
651 CATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTCGAGTTGTCTCCCCACACGGTGTAAG
1730 GTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAATATCTGTTC
716 GTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAATATCTGTTC
1795 TGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAACTTATTCTA
781 TGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAACTTATTCTA
1860 TTTCTGTGGTTTGAGCTAATATAGGCTATGGTT
846 TTTCTGTGGTTTGAGCTAATATAGGCTATGGTT
1893 G
1 G
1894 GGTTAATTTA
Statistics
Matches: 873, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
878 873 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (878 bp):
GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCAAAAAG
TCGGTATTTTGGGAATTTGCGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCCGGTAAGTGTTCTGATAGTA
CGTAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
TGGAAAATTACTGTTATACCCCTAGGTGCAAAATTACCGTTATACCCCTAGGGTTAATTTTGACT
GAAAAGCATGACGATCTGATTCTGTATGATGTATGCCATGATTATATATCTGTTGCATGGGGACA
TGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTAC
CACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCTGGCAGC
CATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTCGAGTTGTCTCCCCACACGGTGTAAG
GTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAATATCTGTTC
TGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAACTTATTCTA
TTTCTGTGGTTTGAGCTAATATAGGCTATGGTT
Done.