Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01334.N2
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: 2791
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:1560 original size:27 final size:26
Alignment explanation
Indices: 1456--1570 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
1446 TGGAGGAAGC
* * *
1456 GTTCTGGTGGTTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
1483 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
*
1510 GTTCTGGTGGTTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
1537 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
1564 GTTCTGG
1 GTTCTGG
1571 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:1563 original size:54 final size:54
Alignment explanation
Indices: 1456--1570 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
1446 TGGAGGAAGC
*
1456 GTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
1510 GTTCTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGTTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
1564 GTTCTGG
1 GTTCTGG
1571 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:1754 original size:824 final size:821
Alignment explanation
Indices: 157--1802 Score: 3150
Period size: 824 Copynumber: 2.0 Consensus size: 821
147 TCGCAAACAG
*
157 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGTCGAAAAGCCGAAATGCCGAAAAG
1 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAAG
222 TCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGTA
66 TCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGTA
287 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
131 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
352 AAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGTA
196 AAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGTA
*
417 CGTAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTAT
261 CATAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTAT
482 GGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTGA
326 GGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTGA
547 AAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACATG
391 AAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACATG
*
612 GGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCTACAAATATCTGATCTGGTCGCTCTGCCA
456 GGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCCA
677 CATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGT
521 CATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGT
742 TCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACAC
586 TCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACAC
*
807 GGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTGCATAAACATGTAAT
651 GGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATGTAAT
872 ATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAAC
716 ATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAAC
937 TTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTT
781 TTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTT
978 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAAG
1 GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAAG
* *
1043 TCGGTATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTGGGTTTGTATATTTGGTA
66 TCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGTA
1108 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
131 ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
1173 AAAGATCGGGTTCATGGGCCAACGGGCCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGT
196 AAAGATCGGGTTCATGGGCCAACGGG-CCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGT
1238 ACATAAATAGTTAGGATATGCATGAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGT
260 ACATAAATAGTTAGGATATGCAT-AAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGT
1303 ATGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCCTAGGGTTAATTTTGAC
324 ATGGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATA-CCCTAGGGTTAATTTTGAC
1368 TGAAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGAC
388 TGAAAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGAC
* *
1433 ATGGGTTATATTATGGAGGAAGCGTTCTGGTGGTTATGCCACAAATATCTGATCTGGTGGCTCTG
453 ATGGGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTG
*
1498 CCACATATATCTGTTCTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATC
518 CCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATC
* *
1563 TGTTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCGGTTGGGTGGGTTGAGTTGTCTCCCC
583 TGTTCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAG-TCGGTGGGTTGAGTTGTCTCCCC
1628 ACACGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATG
647 ACACGGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATG
1693 TAATATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCT-GGCTAAGGC
712 TAATATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGC
1757 CAACTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTT
777 CAACTTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTT
1802 G
1 G
1803 GGTTAATTTA
Statistics
Matches: 810, Mismatches: 11, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
821 218 0.27
822 60 0.07
823 86 0.11
824 305 0.38
825 141 0.17
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (821 bp):
GTGTGTAACTGACACCCTCTCATAGACTAGATTGGCAAAAGCCGAAAAGCCGAAATGCCGAAAAG
TCGATATTTTGGAAATTTACGAGTGTGCGAATGCTCGTAAGATAGTTAGGTTTGTATATTTGGTA
ATCTAAAGTAATAAACTGCAGTACGCGCGATTTCGTACATTTTGATAATTTGGGCTTAATGGGCC
AAAGATCGGGTTCATGGGCCAACGGGCCAATTCGGTAAGTATGCGCGGTAAGTGTTCTGATAGTA
CATAAATAGTTAGGATATGCATAAAACCCTAAAAGTAGCTAAATTACTATAATACCCCTATGTAT
GGAAAATTACTGTTATACCCCTAGGTACAAAATTACCGTTATACCCTAGGGTTAATTTTGACTGA
AAAGCATGACGATCTGATTTTGTATAATGTATGCCATGATTATATATCTGTTGCATGGGGACATG
GGTTATATTATGGAGGAAGCGTTCTGGTGGCTATGCCACAAATATCTGATCTGGTCGCTCTGCCA
CATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTGT
TCTGGCAGCCATGCTGCAAATTCTGTGGTGTGTAGCAGTCGGTGGGTTGAGTTGTCTCCCCACAC
GGTGTAAGGTTGGTACGGGGGTGTATACGGTTGGATATGGTTGGGTTTCTACATAAACATGTAAT
ATCTGTTCTGTTCTGTTATGGGCCTATGGGCTTTATTCTGAATTCTGTTCTGGGCTAAGGCCAAC
TTATTCTATTTCTGTGGTTTGAGCTGATATAGGCTATGGTT
Done.