Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2632
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, 535
Length: 893
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Found at i:55 original size:14 final size:14
Alignment explanation
Indices: 19--55 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9 ATTGGCGTGA
*
19 AGTAGATCAAAGAT
1 AGTAGATCTAAGAT
33 AGTAGATCTAAGAT
1 AGTAGATCTAAGAT
47 AGTAGATCT
1 AGTAGATCT
56 TGTCTTCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (14 bp):
AGTAGATCTAAGAT
Found at i:140 original size:44 final size:44
Alignment explanation
Indices: 76--322 Score: 269
Period size: 44 Copynumber: 5.6 Consensus size: 44
66 TACTGGTGAC
* * *
76 GAAGTGGATCCAAGAAAGCAGATATTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* *** * * *
120 GAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
*
165 GAAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * *** * * *
209 GAAGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
* *
254 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* *
298 GAAGTAGATCAAAGATAGTAGATCT
1 GAAGTAGATCAAAGAAAGCAGATCT
323 AAGATAGTAG
Statistics
Matches: 161, Mismatches: 40, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
44 91 0.57
45 70 0.43
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
Found at i:184 original size:89 final size:89
Alignment explanation
Indices: 33--322 Score: 517
Period size: 89 Copynumber: 3.3 Consensus size: 89
23 GATCAAAGAT
* * *
33 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGACGAAGTGGATCCAAGAAAGCAGA
1 AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
*
98 TATTGTCTTCATGTATTGGCGTGA
66 TCTTGTCTTCATGTATTGGCGTGA
*
122 AGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
1 AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
187 TCTTGTCTTCATGTATTGGCGTGA
66 TCTTGTCTTCATGTATTGGCGTGA
*
211 AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGA
1 AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
*
276 TCTTGTCTTCATGTATTAGCGTGA
66 TCTTGTCTTCATGTATTGGCGTGA
300 AGTAGATCAAAGATAGTAGATCT
1 AGTAGATCAAAGATAGTAGATCT
323 AAGATAGTAG
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 193 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (89 bp):
AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
TCTTGTCTTCATGTATTGGCGTGA
Found at i:185 original size:45 final size:45
Alignment explanation
Indices: 33--285 Score: 276
Period size: 45 Copynumber: 5.7 Consensus size: 45
23 GATCAAAGAT
* * * *
33 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGACGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
* * * *** * * *
78 AGTGGATCCAAGAAAGCAGATATTGTCTTCATGTATTGG-CGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
*
122 AGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
* *** * * *
167 AGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
* *
211 AGTAGATCAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
*
256 AGTAGATCGAAGAAAGCAGATCTTGTCTTC
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTC
286 ATGTATTAGC
Statistics
Matches: 164, Mismatches: 42, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
44 68 0.41
45 96 0.59
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
AGTAGATCAAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGCGA
Found at i:229 original size:103 final size:103
Alignment explanation
Indices: 122--602 Score: 828
Period size: 103 Copynumber: 4.8 Consensus size: 103
112 ATTGGCGTGA
* *
122 AGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
1 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
*
187 TCTTGTCTTCATGTATTGGCGTGAAGTAGATC------
66 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
*
219 -----A---AAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGA
1 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
276 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
66 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
314 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
1 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
379 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
66 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
417 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
1 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
482 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
66 TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
520 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
1 AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
585 TCTTGTCTTCATGTATTA
66 TCTTGTCTTCATGTATTA
603 AATTGTAGCA
Statistics
Matches: 366, Mismatches: 4, Indels: 22
0.93 0.01 0.06
Matches are distributed among these distances:
89 85 0.23
92 1 0.00
100 1 0.00
103 279 0.76
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (103 bp):
AGTAGATCTAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGA
TCTTGTCTTCATGTATTAGCGTGAAGTAGATCAAAGAT
Found at i:336 original size:14 final size:14
Alignment explanation
Indices: 300--336 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
290 ATTAGCGTGA
*
300 AGTAGATCAAAGAT
1 AGTAGATCTAAGAT
314 AGTAGATCTAAGAT
1 AGTAGATCTAAGAT
328 AGTAGATCT
1 AGTAGATCT
337 TGTCTTCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (14 bp):
AGTAGATCTAAGAT
Found at i:439 original size:14 final size:14
Alignment explanation
Indices: 403--439 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
393 ATTAGCGTGA
*
403 AGTAGATCAAAGAT
1 AGTAGATCTAAGAT
417 AGTAGATCTAAGAT
1 AGTAGATCTAAGAT
431 AGTAGATCT
1 AGTAGATCT
440 TGTCTTCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (14 bp):
AGTAGATCTAAGAT
Found at i:542 original size:14 final size:14
Alignment explanation
Indices: 506--542 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
496 ATTAGCGTGA
*
506 AGTAGATCAAAGAT
1 AGTAGATCTAAGAT
520 AGTAGATCTAAGAT
1 AGTAGATCTAAGAT
534 AGTAGATCT
1 AGTAGATCT
543 TGTCTTCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (14 bp):
AGTAGATCTAAGAT
Done.