Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1202
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: 15650
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:201 original size:15 final size:16
Alignment explanation
Indices: 181--217 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
171 CAAACTTTTG
181 GCTTTT-GGCATTTCA
1 GCTTTTCGGCATTTCA
*
196 GCTTTTCGGCATTTCG
1 GCTTTTCGGCATTTCA
212 GCTTTT
1 GCTTTT
218 TCTAATAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.49
Consensus pattern (16 bp):
GCTTTTCGGCATTTCA
Found at i:4432 original size:45 final size:45
Alignment explanation
Indices: 4368--4457 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4358 CGAATTCATC
*
4368 ATCAAGACTGAAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGG
1 ATCAAGACTAAAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGG
4413 ATCAAGACTAAAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGG
1 ATCAAGACTAAAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGG
4458 TTTTCTTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (45 bp):
ATCAAGACTAAAGATCTCCCTTCAAGTTCCTTCAGGAGTTTTGGG
Found at i:5503 original size:27 final size:27
Alignment explanation
Indices: 5321--5506 Score: 210
Period size: 27 Copynumber: 6.9 Consensus size: 27
5311 ACATACATCA
* * *
5321 CATAAGGGTAAAACAGTCATCTTACCA
1 CATAAGGGAAAAACAGTCATTTTACCC
* * * * *
5348 TAAAAGGGCAAAACAGTAATTTTACCT
1 CATAAGGGAAAAACAGTCATTTTACCC
* *
5375 CACAAGGGAAAAACAGTCATTTTAGCC
1 CATAAGGGAAAAACAGTCATTTTACCC
* *
5402 CATAAGGGCAAAATAGTCATTTTACCC
1 CATAAGGGAAAAACAGTCATTTTACCC
* *
5429 CATAAGGGAAAAATAATCATTTTACCC
1 CATAAGGGAAAAACAGTCATTTTACCC
**
5456 CATAAGGGAAAAACAGTCATTTTACGT
1 CATAAGGGAAAAACAGTCATTTTACCC
* *
5483 CATAAGGGTAAAACAATCATTTTA
1 CATAAGGGAAAAACAGTCATTTTA
5507 TTAATTTGGG
Statistics
Matches: 135, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (27 bp):
CATAAGGGAAAAACAGTCATTTTACCC
Found at i:6955 original size:46 final size:45
Alignment explanation
Indices: 6905--7076 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
6895 TGGTTGAGCA
6905 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
6951 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
6997 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
7043 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
7077 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 96 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:7059 original size:92 final size:92
Alignment explanation
Indices: 6902--7071 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
6892 GGATGGTTGA
* *
6902 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
6967 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
6994 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
7059 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
7072 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:14441 original size:45 final size:44
Alignment explanation
Indices: 14392--14558 Score: 182
Period size: 45 Copynumber: 3.8 Consensus size: 44
14382 TGGTTGAGCA
14392 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AATG
* * *
14437 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T--G
*
14481 CATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCAA-C
1 --T-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
* *
14526 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
14559 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
41 2 0.02
42 23 0.22
43 12 0.12
44 3 0.03
45 28 0.27
46 8 0.08
47 21 0.20
49 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (44 bp):
TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
Done.