Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3048
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, 483
Length: 805
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Found at i:122 original size:40 final size:42
Alignment explanation
Indices: 78--219 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 42
68 CTTATCCCTT
* * *
78 TGAAGTTGCAGTGAGCAGA-T-CGCATCTAGTCTTAT-CTCCC
1 TGAAGTTGCAGTGAGCAGACTACGAAGCAAGTCTTATCCT-CC
*
118 TGAAGTTGCAGTGGAGCAGACTAACTAAGCAAGTCTTATCCTCC
1 TGAAGTTGCAGT-GAGCAGACT-ACGAAGCAAGTCTTATCCTCC
* * *
162 TGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAATCTTATCTCTCC
1 TGAAGTTGCAGTG-AGCAGACT-ACGA-AGCAAGTCTTATC-CTCC
208 -GAAGTTGCAGTG
1 TGAAGTTGCAGTG
220 GAACAGATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
40 12 0.14
41 7 0.08
42 1 0.01
43 1 0.01
44 35 0.41
45 25 0.29
46 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (42 bp):
TGAAGTTGCAGTGAGCAGACTACGAAGCAAGTCTTATCCTCC
Found at i:164 original size:44 final size:45
Alignment explanation
Indices: 105--226 Score: 144
Period size: 45 Copynumber: 2.7 Consensus size: 45
95 GATCGCATCT
*
105 AGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AA-CTAAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCA
* *
149 AGTCTTATCCTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
* *
194 AATCTTATCTCTCC-GAAGTTGCAGTGGAACAGA
1 AGTCTTATC-CTCCTGAAGTTGCAGTGGAGCAGA
227 TTAAAGCCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
44 31 0.46
45 32 0.47
46 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (45 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Found at i:215 original size:45 final size:45
Alignment explanation
Indices: 107--219 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
97 TCGCATCTAG
* * *
107 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTAACTAAGCAAG
1 TCTTATCTCTCCTGAAGTTGCAGTGAAGCAGACTAAATAAGCAAA
*
151 TCTTATC-CTCCTGAAGTTGCAGTGAAGCAGACTGAAGAT-GGCAAA
1 TCTTATCTCTCCTGAAGTTGCAGTGAAGCAGACT-AA-ATAAGCAAA
196 TCTTATCTCTCC-GAAGTTGCAGTG
1 TCTTATCTCTCCTGAAGTTGCAGTG
220 GAACAGATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 30 0.49
45 25 0.41
46 5 0.08
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCTCCTGAAGTTGCAGTGAAGCAGACTAAATAAGCAAA
Found at i:361 original size:44 final size:44
Alignment explanation
Indices: 277--805 Score: 459
Period size: 44 Copynumber: 12.0 Consensus size: 44
267 CAGGTTAAAA
* * *
277 ATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
* * * * *
321 ATAGCAGGTCCTGTCTTCCTATATTAGTAGGGAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG
* * * *
365 AT-GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAA
1 ATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
* * * *
409 AAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
* * * * *
453 ATAGCAGGTCCTGTCTTCCTATATTAGTAGGGAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG
* * *
497 AT-GTAGATCTTGTCTTCCCATACTGGT-GGCAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGG--AAGTAGATCGAAG
* * * *
541 AAAGCAGATGTTGTCTTCATGTATTCGCGT--GAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATT-G-GTAGGAAGTAGATCGAAG
* * *
585 ATAGCAGATCCTGTCTTCCTATGTTGGTAGGAAGTGGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG
* * *
629 AT-GCAGATCTTGTC-TCCCATACTGGTGGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
* * * * * *
672 AAAGCATATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG
* *
716 ATAGCAGAT-TCTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAG
1 ATAGCAGATCT-TGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
* * * * *
761 AT-GTAGATCTTGTATTCCCATACTGGTGGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG
805 A
1 A
Statistics
Matches: 382, Mismatches: 86, Indels: 34
0.76 0.17 0.07
Matches are distributed among these distances:
42 14 0.04
43 67 0.18
44 237 0.62
45 60 0.16
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (44 bp):
ATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAG
Found at i:437 original size:132 final size:132
Alignment explanation
Indices: 273--803 Score: 866
Period size: 132 Copynumber: 4.0 Consensus size: 132
263 GGAGCAGGTT
*
273 AAAAATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTT
1 AAAAA-AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTT
*
338 CCTATATTAGTAGGGAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
65 CCTATATTAGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
403 TCG
130 TCG
*
406 AAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTC
1 AAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
* * *
471 CTATATTAGTAGGGAGTGGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGCAAAGTAGAT
66 CTATATTAGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
536 CG
131 CG
* * *
538 AAGAAAGCAGATGTTGTCTTCATGTATTCGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
1 AAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
* *
603 CTATGTTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTC-TCCCATACTGGTGGCGAAGTAGAT
66 CTATATTAGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
667 CG
131 CG
* * * *
669 AAGAAAGCATATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAGATTCTGTCTTC
1 AAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
* * * *
734 CTATATTGGTAGCGAAGTGGATCAAAGATGTAGATCTTGTATTCCCATACTGGTGGCGAAGTAGA
66 CTATATTAGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
799 TCG
130 TCG
802 AA
1 AA
804 GA
Statistics
Matches: 376, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 96 0.26
132 247 0.66
133 33 0.09
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (132 bp):
AAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTC
CTATATTAGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
CG
Done.