Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3097
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: 31946
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:13570 original size:43 final size:42
Alignment explanation
Indices: 13508--13646 Score: 113
Period size: 43 Copynumber: 3.2 Consensus size: 42
13498 GTACAATTCC
*
13508 ATATCCCAGATATGGTCTTAAATGTAAATACAT-AT-CGATGCCA
1 ATATCCCAGA-AAGGTCTTAAATG-AAAT-CATAATACGATGCCA
* * *
13551 CTATCCCAGACAAGGTCTTACATGAAATTATAATACGATGCCA
1 ATATCCCAGA-AAGGTCTTAAATGAAATCATAATACGATGCCA
* * * * *
13594 ATGTCCCAGAAATGGTCTTACACGTAATC-TCAATACAATGCCA
1 ATATCCCAGAAA-GGTCTTAAATGAAATCAT-AATACGATGCCA
*
13637 ATGTCCCAGA
1 ATATCCCAGA
13647 CTTGGTCTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.02
42 9 0.11
43 70 0.86
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (42 bp):
ATATCCCAGAAAGGTCTTAAATGAAATCATAATACGATGCCA
Found at i:13653 original size:43 final size:43
Alignment explanation
Indices: 13582--13665 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
13572 ATGAAATTAT
*
13582 AATACGATGCCAATGTCCCAGAAATGGTCTTACACGTAATCTC
1 AATACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATCTC
** *
13625 AATACAATGCCAATGTCCCAGACTTGGTCTTACATGTAATC
1 AATACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATC
13666 ACATCTCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
AATACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATCTC
Found at i:19362 original size:41 final size:40
Alignment explanation
Indices: 19317--19402 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
19307 ATATGTGTGT
*
19317 GCATTAGAATTGAGAGTTATATCCGGGCTAAGTCCCGAAGA
1 GCATTAGAACTG-GAGTTATATCCGGGCTAAGTCCCGAAGA
* ** *
19358 GCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGA
1 GCATTAGAACTGGAGTTATATCCGGGCTAAGTCCCGAAGA
19398 GCATT
1 GCATT
19403 CGTGCTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 32 0.80
41 8 0.20
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
GCATTAGAACTGGAGTTATATCCGGGCTAAGTCCCGAAGA
Found at i:19376 original size:40 final size:40
Alignment explanation
Indices: 19332--19452 Score: 188
Period size: 40 Copynumber: 3.0 Consensus size: 40
19322 AGAATTGAGA
19332 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
19372 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
* ** * * *
19412 GTTACATATGGGCTAAGTCCTGAAGGGCATTCGTGCCGGT
1 GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
19452 G
1 G
19453 ATGTGTAATC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.27
Consensus pattern (40 bp):
GTTATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
Found at i:19512 original size:43 final size:43
Alignment explanation
Indices: 19441--19571 Score: 172
Period size: 43 Copynumber: 3.0 Consensus size: 43
19431 CTGAAGGGCA
* ** *
19441 TTCGTGCCGGTGATGTGTAATCATGCCTTCATGCCTAGCAGGC
1 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
* * * *
19484 TTTGTGCTGGTGATGTGTATTCGGGCCTTCGTTCCTACCAGGC
1 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
* *
19527 TTCGTGCCGGTGATGTGTATTTGGGTCTTCGTGCCTAGCAGGC
1 TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
19570 TT
1 TT
19572 AATACCGGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.35
Consensus pattern (43 bp):
TTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
Found at i:19755 original size:25 final size:25
Alignment explanation
Indices: 19701--19756 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
19691 ATGTGTAATA
19701 ACGAATGAATATAGGCACTATGGGT
1 ACGAATGAATATAGGCACTATGGGT
* * *
19726 GCGAATGAAT-TGAGGCACTGTGTGT
1 ACGAATGAATAT-AGGCACTATGGGT
19751 ACGAAT
1 ACGAAT
19757 TCTTTAACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.25
Consensus pattern (25 bp):
ACGAATGAATATAGGCACTATGGGT
Found at i:19773 original size:53 final size:53
Alignment explanation
Indices: 19715--19838 Score: 169
Period size: 53 Copynumber: 2.3 Consensus size: 53
19705 ATGAATATAG
* * *
19715 GCACTATGGGTGCGA-ATGAATTGAGGCACTGTGTGTACGAATTCTTTAACCGA
1 GCACTATGTGTGCGAGAT-AAGTCAGGCACTGTGTGTACGAATTCTTTAACCGA
* * *
19768 GCACTATGTGTGCGAGATAGGTCAGGCACTGTGTGTGCGAATTCTTTAATCGA
1 GCACTATGTGTGCGAGATAAGTCAGGCACTGTGTGTACGAATTCTTTAACCGA
*
19821 GCAATATGTGTGCGAGAT
1 GCACTATGTGTGCGAGAT
19839 CGGTCAGTGG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
53 61 0.97
54 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (53 bp):
GCACTATGTGTGCGAGATAAGTCAGGCACTGTGTGTACGAATTCTTTAACCGA
Found at i:19844 original size:53 final size:53
Alignment explanation
Indices: 19738--19866 Score: 186
Period size: 53 Copynumber: 2.4 Consensus size: 53
19728 GAATGAATTG
* *
19738 AGGCACTGTGTGTACGAATTCTTTAACCGAGCACTATGTGTGCGAGATAGGTC
1 AGGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATAGGTC
* *
19791 AGGCACTGTGTGTGCGAATTCTTTAATCGAGCAATATGTGTGCGAGATCGGTC
1 AGGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATAGGTC
*
19844 AGTGGGCAATGTGTGTGCGAATT
1 A---GGCACTGTGTGTGCGAATT
19867 TCGTTTCATG
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
53 50 0.74
56 18 0.26
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.29
Consensus pattern (53 bp):
AGGCACTGTGTGTGCGAATTCTTTAACCGAGCAATATGTGTGCGAGATAGGTC
Done.