Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01334.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: 2793
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Found at i:683 original size:27 final size:26
Alignment explanation
Indices: 634--746 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
624 GAGGAAGCGT
* * *
634 TCTGGTGGCTATGCTACAAATATCTGA
1 TCTGGTGGCTCTGCCAC-ATTATCTGA
* *
661 TCTGGTCGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAT-TATCTGA
688 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCAC-ATTATCTG-A
* * *
716 TCTGGTGACTCTGTCACATTATCTGT
1 TCTGGTGGCTCTGCCACATTATCTGA
742 TCTGG
1 TCTGG
747 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.68
28 17 0.23
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
TCTGGTGGCTCTGCCACATTATCTGA
Found at i:739 original size:54 final size:54
Alignment explanation
Indices: 632--746 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
622 TGGAGGAAGC
*
632 GTTCTGGTGGCTATGCTACAAATATCTGATCTGGTCGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCCACATATATCT
* * * *
686 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGT-GACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTCG-CTCTGCCACATATATCT
740 GTTCTGG
1 GTTCTGG
747 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCCACATATATCT
Found at i:1562 original size:27 final size:26
Alignment explanation
Indices: 1458--1572 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
1448 TGGAGGAAGC
* * *
1458 GTTCTGGTGGTTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
1485 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
*
1512 GTTCTGGTGGTTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
1539 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
1566 GTTCTGG
1 GTTCTGG
1573 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:1565 original size:54 final size:54
Alignment explanation
Indices: 1458--1572 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
1448 TGGAGGAAGC
*
1458 GTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
1512 GTTCTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGTTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
1566 GTTCTGG
1 GTTCTGG
1573 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:1756 original size:826 final size:823
Alignment explanation
Indices: 156--1807 Score: 3162
Period size: 826 Copynumber: 2.0 Consensus size: 823
146 GTCGCAAACA
*
156 GGTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGTCGAAAAGCCGAAATGCCGAAAA
1 GGTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAA
221 GTCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGT
66 GTCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGT
286 AATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGC
131 AATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGC
351 CAAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGT
196 CAAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGT
*
416 ACGTAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
261 ACATAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
481 TGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTG
326 TGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTG
546 AAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACAT
391 AAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACAT
*
611 GGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCTACAAATATCTGATCTGGTCGCTCTGCC
456 GGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCC
676 ACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTG
521 ACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTG
741 TTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACA
586 TTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACA
*
806 CGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAA
651 CGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATGTAA
871 TATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAA
716 TATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAA
936 CTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTTG
781 CTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTTG
979 GGTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAA
1 GGTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAA
* *
1044 GTCGGTATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGT
66 GTCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGT
1109 AATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGC
131 AATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGC
1174 CAAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAG
196 CAAAGATCGGGTTCATGGGCCAACGGG-CCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAG
1239 TACATAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATG
260 TACATAAATAGTTAGGATATGCAT-AAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATG
1304 TATGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCCTAGGGTTAATTTTGA
324 TATGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATA-CCCTAGGGTTAATTTTGA
1369 CTGAAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGA
388 CTGAAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGA
* *
1434 CATGGGTTATATTATGGAGGAAGCGTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGGCTCT
453 CATGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCT
*
1499 GCCACATATATCTGTTCTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTAT
518 GCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTAT
* *
1564 CTGTTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTTGAGTTGTCTCCC
583 CTGTTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAG-TCGGTGGGTTGAGTTGTCTCCC
1629 CACACGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACAT
647 CACACGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACAT
1694 GTAATATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCT-GGCTAAGG
712 GTAATATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGG
1758 CCAACTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTTG
777 CCAACTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTTG
1805 GGT
1 GGT
1808 TAATTTACAC
Statistics
Matches: 814, Mismatches: 11, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
823 219 0.27
824 60 0.07
825 86 0.11
826 308 0.38
827 141 0.17
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (823 bp):
GGTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAA
GTCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGT
AATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGC
CAAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGT
ACATAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTA
TGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTG
AAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACAT
GGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCC
ACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTG
TTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACA
CGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATGTAA
TATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAA
CTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTTG
Done.