Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold452
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: 32996
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Found at i:2291 original size:16 final size:16
Alignment explanation
Indices: 2272--2302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2262 TGGATAAAAT
*
2272 TTGGTTTTTAAAAGAA
1 TTGGTTTTCAAAAGAA
2288 TTGGTTTTCAAAAGA
1 TTGGTTTTCAAAAGA
2303 TTTAAGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (16 bp):
TTGGTTTTCAAAAGAA
Found at i:6385 original size:12 final size:12
Alignment explanation
Indices: 6368--6393 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6358 AGAAGTAGAA
6368 ATAATTATTTTT
1 ATAATTATTTTT
6380 ATAATTATTTTT
1 ATAATTATTTTT
6392 AT
1 AT
6394 GAATAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATAATTATTTTT
Found at i:7637 original size:46 final size:47
Alignment explanation
Indices: 7587--7755 Score: 168
Period size: 46 Copynumber: 3.6 Consensus size: 47
7577 GGTTGAGCAT
*
7587 CGAACTCGTTGAGTTGAG-CCGAGTTCACTTATGGATGCAAAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAACGTC
* * * * *
7633 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A-ACGTC
* * *
7680 CGAAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-GAACGCC
1 CG-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAACGTC
*
7727 CGAGCTCGTTGAGTTGAGTCGCGAGTTCA
1 CGAACTCGTTGAGTTGAGTC-CGAGTTCA
7756 TTAGGGGCGG
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
44 6 0.06
46 38 0.38
47 24 0.24
48 26 0.26
49 2 0.02
51 4 0.04
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAACGTC
Found at i:14994 original size:46 final size:46
Alignment explanation
Indices: 14944--15069 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
14934 TGGTTGAGCA
*
14944 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
14990 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
15036 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
15070 GGGGCGGGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:18309 original size:39 final size:40
Alignment explanation
Indices: 18239--18459 Score: 353
Period size: 39 Copynumber: 5.6 Consensus size: 40
18229 TATTCGAATG
18239 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
18279 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
18318 ATAT-CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
18357 ATATCCGGGCTAAGTCCC-AAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
18396 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
18436 ATATCC-GGCTAAATCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCA
18460 CTTGGGTTTG
Statistics
Matches: 169, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
38 10 0.06
39 107 0.63
40 49 0.29
41 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:18447 original size:118 final size:118
Alignment explanation
Indices: 18239--18459 Score: 365
Period size: 118 Copynumber: 1.9 Consensus size: 118
18229 TATTCGAATG
*
18239 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCGAAGGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGCCCGAAGGCAT
* * *
18304 TTGTGCTATTGACTATATCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
66 TTGTGCGATTGACTATATCCGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
*
18357 ATATCCGGGCTAAGTCCC-AAGGCTTTTGTGCTATTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAG-CCCGAAGGCA
18421 TTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAGGCA
65 TTTGTGCGA-TTGACTATATCCGGCTAAATCCCGAAGGCA
18460 CTTGGGTTTG
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
117 34 0.35
118 59 0.61
119 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (118 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGCCCGAAGGCAT
TTGTGCGATTGACTATATCCGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:26535 original size:38 final size:40
Alignment explanation
Indices: 26428--26607 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
26418 TATTCGAATG
26428 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
26468 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
26508 ATATCCGGGCT-AGT-CCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
26546 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
26586 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
26608 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
38 35 0.27
39 19 0.15
40 74 0.56
41 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:26559 original size:78 final size:80
Alignment explanation
Indices: 26428--26607 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 80
26418 TATTCGAATG
* *
26428 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGACCCGAAGGCA
*
26493 TTTGTGCTA-TTGACT
66 TTTGTGCGAGTTG-CT
*
26508 ATATCCGGGCT-AGT-CCGAAGGCTTTTGTGCTATTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGACCCGAAGGCA
26571 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
*
26586 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
26608 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
77 4 0.04
78 64 0.70
79 13 0.14
80 11 0.12
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Done.