Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1284
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: 20360
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1769 original size:46 final size:45
Alignment explanation
Indices: 1718--1880 Score: 147
Period size: 46 Copynumber: 3.6 Consensus size: 45
1708 AGCATCCAAA
* *
1718 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCGAG
* * * * *
1763 CTTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCGAA
1 C-TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCGAG
* * *
1810 CTCGTTGAGTTGAGTCCGAGTTCATTTATGG--GCGAACGCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCGAG
*
1853 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTA
1881 GGGCGGGTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 18
0.73 0.12 0.14
Matches are distributed among these distances:
43 36 0.38
45 5 0.05
46 43 0.46
47 9 0.10
49 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCGAG
Found at i:3339 original size:46 final size:45
Alignment explanation
Indices: 3289--3453 Score: 174
Period size: 46 Copynumber: 3.6 Consensus size: 45
3279 AGCATCCAAA
* *
3289 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTC-GAGTTCACTTATGGATGCAAACGTCTGAG
* * * * *
3335 CTCGTTGAGTTGAGTCGAGTTC-GTGA--GATGTAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCAA--A--CGTCTGAG
* *
3381 CTCGTTGAGTTGAGTCGAGTTCATTTATGGATGCGAACGTCTGAG
1 CTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCAAACGTCTGAG
3426 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTC-GAGTTCACTTA
3454 GGGGCGGGTT
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
42 6 0.06
44 3 0.03
45 28 0.29
46 52 0.54
47 3 0.03
49 5 0.05
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.33
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCAAACGTCTGAG
Found at i:4914 original size:46 final size:46
Alignment explanation
Indices: 4864--5030 Score: 187
Period size: 46 Copynumber: 3.6 Consensus size: 46
4854 AGCATCCAAA
* *
4864 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
* * * * * *
4910 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A--CGTCTGAG
* *
4957 CTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACGTCTGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
5003 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTA
5031 GGGCGGGTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 55 0.56
47 26 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCTGAG
Found at i:6517 original size:46 final size:46
Alignment explanation
Indices: 6447--6614 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
6437 TTGAGCATCC
*
6447 AACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
* * * *
6492 AACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCATCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCCG
* *
6539 AACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-G
* *
6585 AGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
6615 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.06
45 21 0.21
46 37 0.37
47 29 0.29
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCG
Found at i:9655 original size:46 final size:46
Alignment explanation
Indices: 9605--9775 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 46
9595 TGGTTGAGCA
*
9605 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * ** *
9651 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGGATGC-AAACG
* *
9697 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
9743 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
9776 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
45 13 0.13
46 87 0.85
47 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:9759 original size:92 final size:91
Alignment explanation
Indices: 9602--9770 Score: 284
Period size: 92 Copynumber: 1.8 Consensus size: 91
9592 GGATGGTTGA
* *
9602 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9667 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGT-CGAGTTCGTGAATGTAACTAG
* * *
9694 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
9759 TGAGTCGAGTTC
66 TGAGTCGAGTTC
9771 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
91 7 0.10
92 65 0.90
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAATGTAACTAG
Found at i:11228 original size:46 final size:46
Alignment explanation
Indices: 11178--11344 Score: 187
Period size: 46 Copynumber: 3.6 Consensus size: 46
11168 GAGCATCCAA
*
11178 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAG
* * * * * *
11224 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCGAA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A--CGTCCGAG
* * *
11271 CTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACGTCTGAG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAG
11317 CTCGTTGAGTTGAGTCTGAGTTCACTTA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTA
11345 GGGGCGGTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 54 0.55
47 27 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAG
Found at i:11338 original size:93 final size:92
Alignment explanation
Indices: 11170--11339 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
11160 GGATGGTTGA
*
11170 GCATCCAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAGCTCGTTGAGTT
1 GCATCCAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGTT
11235 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
* * *
11262 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGCGAACGTCTGAGCTCGTTGAGT
1 GCATCC-AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGT
*
11327 TGAGTCTGAGTTC
65 TGAGTCCGAGTTC
11340 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 6 0.08
93 66 0.92
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (92 bp):
GCATCCAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Done.