Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1515
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: 23354
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Found at i:288 original size:46 final size:46
Alignment explanation
Indices: 238--409 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 46
228 TGGTTGAGCA
*
238 TCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
284 TCCGAACTCGTTGAGTTGAGT-CGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
328 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
376 -CCAGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
410 GGGGGGGTTC
Statistics
Matches: 106, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
44 3 0.03
45 9 0.08
46 71 0.67
47 7 0.07
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:392 original size:92 final size:93
Alignment explanation
Indices: 235--404 Score: 290
Period size: 92 Copynumber: 1.8 Consensus size: 93
225 GGATGGTTGA
* *
235 GCATCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
300 TGAGT-CGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
327 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCAGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
391 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
405 ACTTAGGGGG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
91 2 0.03
92 64 0.88
93 7 0.10
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:10579 original size:12 final size:12
Alignment explanation
Indices: 10562--10601 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
10552 TACCAAACTT
10562 ATCATACATTTA
1 ATCATACATTTA
*
10574 ATCATACATTTC
1 ATCATACATTTA
10586 A-CATACAATTTA
1 ATCATAC-ATTTA
10598 ATCA
1 ATCA
10602 ATTCAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 17 0.71
13 2 0.08
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (12 bp):
ATCATACATTTA
Found at i:10611 original size:20 final size:20
Alignment explanation
Indices: 10583--10621 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10573 AATCATACAT
*
10583 TTCACATACAATTT-AATCAA
1 TTCAAATAC-ATTTCAATCAA
10603 TTCAAATACATTTCAATCA
1 TTCAAATACATTTCAATCA
10622 CAACTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (20 bp):
TTCAAATACATTTCAATCAA
Found at i:12878 original size:40 final size:40
Alignment explanation
Indices: 12777--12921 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
12767 TACTCGAATG
* *
12777 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCAACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
12818 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
12858 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
12898 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
12922 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:21595 original size:40 final size:40
Alignment explanation
Indices: 21501--21645 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
21491 TACTCGAATG
*
21501 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
21542 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
21582 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
21622 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
21646 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Done.