Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4672
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, 301
Length: 502
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Found at i:235 original size:76 final size:76
Alignment explanation
Indices: 1--430 Score: 720
Period size: 76 Copynumber: 5.6 Consensus size: 76
* *
1 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATTTAAAAAAATACCTAA
1 CTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAGCAGAAATTT--AAAAATACCTCA
66 GCGTGACCCGAGG
64 GCGTGACCCGAGG
* *
79 CTCAACTCACATCTGTATTATGAGTTGATTTTTTGAAAAAAAACAGAAATTTAAAAATACCTCAG
1 CTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAAAGCAGAAATTTAAAAATACCTCAG
144 CGTGACCCGAGG
65 CGTGACCCGAGG
* *
156 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATTTAAAAATACCTCAGA
1 CTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAGCAGAAATTTAAAAATACCTCAGC
221 GTGACCCGAGG
66 GTGACCCGAGG
*
232 CTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGCAGAAATTTAAAAATACCTCAGC
1 CTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAGCAGAAATTTAAAAATACCTCAGC
297 GTGACCCGAGG
66 GTGACCCGAGG
*
308 CTCAACTCACCTCTGTATTATGAGTTGATTTTTG-AAAAAAGCAGAAATTAAAAAAAATACCTCA
1 CTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAGCAGAAATT--TAAAAATACCTCA
372 GCGTGACCCGAGG
64 GCGTGACCCGAGG
385 CTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAA-CAGA
1 CTCAACTCACCTCTGTATTATGAGTTGA-TTTTTGAAAAAAAGCAGA
431 TTTTTTTTAA
Statistics
Matches: 334, Mismatches: 13, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
75 15 0.04
76 151 0.45
77 104 0.31
78 37 0.11
79 27 0.08
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (76 bp):
CTCAACTCACCTCTGTATTATGAGTTGATTTTTGAAAAAAAGCAGAAATTTAAAAATACCTCAGC
GTGACCCGAGG
Found at i:364 original size:153 final size:153
Alignment explanation
Indices: 1--430 Score: 758
Period size: 153 Copynumber: 2.8 Consensus size: 153
*
1 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATTTAAAAAAATACCTAA
1 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAA-TTAAAAAAATACCTCA
*
66 GCGTGACCCGAGGCTCAACTCACATCTGTATTATGAGTTGATTTTTTGAAAAAAAACAGAAATTT
65 GCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG-AAAAAAACAGAAATTT
131 AAAAATACCTCAGCGTGACCCGAGG
129 AAAAATACCTCAGCGTGACCCGAGG
*
156 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATT-TAAAAATACCTCAG
1 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATTAAAAAAATACCTCAG
*
220 AGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT-AAAAAAAGCAGAAATTTA
66 CGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAA-CAGAAATTTA
284 AAAATACCTCAGCGTGACCCGAGG
130 AAAATACCTCAGCGTGACCCGAGG
*
308 CTCAACTCACCTCTGTATTATGAGTTGATTTTTG-AAAAAAGCAGAAATTAAAAAAAATACCTCA
1 CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATT-AAAAAAATACCTCA
372 GCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGA
65 GCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGA
431 TTTTTTTTAA
Statistics
Matches: 264, Mismatches: 7, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
151 22 0.08
152 67 0.25
153 118 0.45
154 9 0.03
155 48 0.18
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (153 bp):
CTCAACTCACCTCTGTATTATGAGTTGATATTTGAAAAAAAGCAGAAATTAAAAAAATACCTCAG
CGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAACAGAAATTTAA
AAATACCTCAGCGTGACCCGAGG
Done.