Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold544
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: 28698
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Found at i:2892 original size:40 final size:40
Alignment explanation
Indices: 2808--2989 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
2798 TTGAATGCTG
* * * *
2808 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
2847 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
2888 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
2928 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
2967 TCCGGGTTAAGT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2990 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 11 0.09
39 16 0.13
40 85 0.70
41 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:2945 original size:80 final size:80
Alignment explanation
Indices: 2808--2986 Score: 217
Period size: 80 Copynumber: 2.3 Consensus size: 80
2798 TTGAATGCTG
* * *
2808 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
2872 TGTGCGAGTTATTAAT
66 CGTGCGAGTT-TTAAA
**
2888 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
2949 ATTCGTGCGAGTTTTAAA
63 ATTCGTGCGAGTTTTAAA
2967 TCCGGGTTAAGT-CCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
2987 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
78 8 0.09
79 18 0.20
80 53 0.60
81 9 0.10
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAA
Found at i:3010 original size:38 final size:38
Alignment explanation
Indices: 2888--3036 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
2878 AGTTATTAAT
* ** * *
2888 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAA
** *
2928 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAA
*
2967 TCCGGGTTAAGT-CCGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTA-AA
* *
3006 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
3037 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
37 6 0.06
38 22 0.24
39 30 0.32
40 35 0.38
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAA
Found at i:10894 original size:40 final size:40
Alignment explanation
Indices: 10732--10883 Score: 227
Period size: 40 Copynumber: 3.8 Consensus size: 40
10722 GGATGATAAT
*
10732 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTC
* *
10772 CGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTAATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTC
*
10812 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTAAT-TC
*
10852 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTG
10884 GCTATATCCG
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
39 4 0.04
40 96 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTC
Found at i:17378 original size:12 final size:12
Alignment explanation
Indices: 17361--17385 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17351 CTAGCAGCGG
17361 TGATTTTTGCGT
1 TGATTTTTGCGT
17373 TGATTTTTGCGT
1 TGATTTTTGCGT
17385 T
1 T
17386 AAAATTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TGATTTTTGCGT
Found at i:19833 original size:15 final size:15
Alignment explanation
Indices: 19813--19842 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19803 CAACACTTGT
19813 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
19828 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
19843 AATACATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Done.