Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2409
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, 573
Length: 956
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.20
Warning! 252 characters in sequence are not A, C, G, or T
Found at i:158 original size:88 final size:88
Alignment explanation
Indices: 4--460 Score: 643
Period size: 88 Copynumber: 5.2 Consensus size: 88
1 CTG
* * * * * *
4 TTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGC-AGCGCTTGTGTCTACGA-TCTGATACAC
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG-GTTTGTGTCTTCGACT-TGCTTCGC
* * *
67 TGTCAATGTAGGAAGGTAAGATTTT
64 TGTCAATGCAGGAAGGCAAGATCTT
* * *
92 TTGTCTTCAACCAGCTCCATCACAACTGAGGGAGGTAAGGTTTGTGTCTTCGACTTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTG
* * *
157 TCGATACAGGAAGGCAGGATCTT
66 TCAATGCAGGAAGGCAAGATCTT
* *
180 TTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTG
* *
245 TCAA-GCAGGATGGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTT
267 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGA-TCTGCTTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACT-TGCTTCGCT
* *
331 GTCAATGTAGGAAGACAAGATCTT
65 GTCAATGCAGGAAGGCAAGATCTT
* * *
355 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCATCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTG
420 TCAATGCAGGAAGGCAAGATCTT
66 TCAATGCAGGAAGGCAAGATCTT
443 TTGTCTTCAACCAGCTCC
1 TTGTCTTCAACCAGCTCC
461 CNNNNNNNNN
Statistics
Matches: 330, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
87 80 0.24
88 247 0.75
89 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (88 bp):
TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACTTGCTTCGCTG
TCAATGCAGGAAGGCAAGATCTT
Found at i:328 original size:175 final size:176
Alignment explanation
Indices: 4--460 Score: 668
Period size: 175 Copynumber: 2.6 Consensus size: 176
1 CTG
* * * * * * *
4 TTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGC-AGCGCTTGTGTCTACGATCTGATACACT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG-GTTTGTGTCTTCGACCTGCTTCGCT
* * * * * *
68 GTCAATGTAGGAAGGTAAGATTTTTTGTCTTCAACCAGCTCCATCACAACTGAGGGAGGTAAGGT
65 GTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGT
* * *
133 TTGTGTCTTCGACTTGCTTCGCTGTCGATACAGGAAGGCAGGATCTT
130 TTGTGTCTTCGACTTGCTTCGCTGTCAATACAGGAAGACAAGATCTT
*
180 TTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* *
245 TCAA-GCAGGATGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTT
66 TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTT
**
309 TGTGTCTTCGA-TCTGCTTCGCTGTCAATGTAGGAAGACAAGATCTT
131 TGTGTCTTCGACT-TGCTTCGCTGTCAATACAGGAAGACAAGATCTT
* *
355 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCATCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
420 TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCC
66 TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCC
461 CNNNNNNNNN
Statistics
Matches: 252, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
174 1 0.00
175 157 0.62
176 92 0.37
177 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (176 bp):
TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTT
TGTGTCTTCGACTTGCTTCGCTGTCAATACAGGAAGACAAGATCTT
Found at i:853 original size:44 final size:43
Alignment explanation
Indices: 720--941 Score: 107
Period size: 44 Copynumber: 5.1 Consensus size: 43
710 NNNNGGAGGT
* *
720 AAGG-TTGTGTCTTCGATCTGCTTCGCTATCAATGCAGGAAGGT
1 AAGGTTTGTGTCTTCGACCTGCTTCGCTATCAA-GCAGGAAGGC
* * * * * *
763 AAGATCTTTTGTCTTCAACCGGC-TC-C-ATCACAACCGAGAGAGGC
1 AAGGT-TTGTGTCTTCGACCTGCTTCGCTATCA-AGCAG-GA-AGGC
*
807 AAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGC
1 AAGGTTTGTGTCTTCGACCTGCTTCGCTATCAA-GCAGGAAGGC
* * ** * ** * *
851 AAGATCTGCTGTCTTTAACCAGC-TCAATCA-CAACCAAGAGAGGC
1 AAGGTTTG-TGTCTTCGACCTGCTTCGCT-ATCAAGCAGGA-AGGC
* * *
895 AAGGTTTGTGTCGTCGATCT-CATTCGCTGTCAACGCAGGAAGGC
1 AAGGTTTGTGTCTTCGACCTGC-TTCGCTATCAA-GCAGGAAGGC
939 AAG
1 AAG
942 ATCTTTTGTC
Statistics
Matches: 126, Mismatches: 37, Indels: 31
0.65 0.19 0.16
Matches are distributed among these distances:
42 7 0.06
43 32 0.25
44 50 0.40
45 32 0.25
46 5 0.04
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (43 bp):
AAGGTTTGTGTCTTCGACCTGCTTCGCTATCAAGCAGGAAGGC
Found at i:881 original size:88 final size:88
Alignment explanation
Indices: 715--956 Score: 335
Period size: 88 Copynumber: 2.8 Consensus size: 88
705 NNNNNNNNNG
* * * **
715 GAGGTAAGG-TTGTGTCTTCGATCTGCTTCGCTATCAATGCAGGAAGGTAAGATCTTTTGTCTTC
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTC
* * *
779 AACCGGCTCCATCACAACCGAGA
66 AACCAGCTCAATCACAACCAAGA
* *
802 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTT
1 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTC
867 AACCAGCTCAATCACAACCAAGA
66 AACCAGCTCAATCACAACCAAGA
* * **
890 GAGGCAAGGTTTGTGTCGTCGATCT-CATTCGCTGTCAACGCAGGAAGGCAAGATCTTTTGTCTT
1 GAGGCAAGGTTTGTGTCTTCGATCTGC-TTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTT
954 CAA
65 CAA
Statistics
Matches: 137, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
87 9 0.07
88 128 0.93
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (88 bp):
GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTC
AACCAGCTCAATCACAACCAAGA
Done.