Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold772
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: 6766
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.25
Warning! 242 characters in sequence are not A, C, G, or T
Found at i:23 original size:7 final size:7
Alignment explanation
Indices: 1--444 Score: 398
Period size: 7 Copynumber: 61.6 Consensus size: 7
1 ACCCTAAA
1 ACCCT-AA
9 ACCCTAA
1 ACCCTAA
*
16 AACCTAA
1 ACCCTAA
23 ACCCTAA
1 ACCCTAA
30 ACCCTAAA
1 ACCCT-AA
38 ACCC--A
1 ACCCTAA
*
43 ACCC-CA
1 ACCCTAA
*
49 ACCC-CA
1 ACCCTAA
55 ACCCTAA
1 ACCCTAA
*
62 ACCC-CA
1 ACCCTAA
68 ACCCTAA
1 ACCCTAA
75 ACCCTAA
1 ACCCTAA
82 ACCCTAA
1 ACCCTAA
89 ACCCTAA
1 ACCCTAA
96 ACCCTAA
1 ACCCTAA
103 ACCCTAA
1 ACCCTAA
110 ACCCTAA
1 ACCCTAA
*
117 ACCCTAG
1 ACCCTAA
*
124 ACCCTAG
1 ACCCTAA
131 ACCCTAAA
1 ACCCT-AA
139 ACCCTAA
1 ACCCTAA
*
146 AACCTAAA
1 ACCCT-AA
*
154 ACCCTAG
1 ACCCTAA
161 ACCCTAA
1 ACCCTAA
168 ACCCTAAA
1 ACCCT-AA
176 ACCCTAAA
1 ACCCT-AA
184 ACCCTAAA
1 ACCCT-AA
* *
192 AACCTAG
1 ACCCTAA
199 ACCCTAAA
1 ACCCT-AA
*
207 ACCCTAG
1 ACCCTAA
*
214 ACCCTAG
1 ACCCTAA
*
221 ACCCTAG
1 ACCCTAA
228 ACCCTAAA
1 ACCCT-AA
*
236 ACCCTAG
1 ACCCTAA
243 ACCCTAAA
1 ACCCT-AA
*
251 ACCCTAG
1 ACCCTAA
258 ACCCTAAA
1 ACCCT-AA
266 ACCCTAA
1 ACCCTAA
* *
273 AACCTAG
1 ACCCTAA
280 ACCCTAAA
1 ACCCT-AA
288 ACCCTAAA
1 ACCCT-AA
296 ACCCTAAA
1 ACCCT-AA
*
304 ACCCTAG
1 ACCCTAA
*
311 ACCCTAG
1 ACCCTAA
*
318 ACCCTAG
1 ACCCTAA
325 ACCCTAGA
1 ACCCTA-A
333 ACCCTAGA
1 ACCCTA-A
341 ACCCTAGA
1 ACCCTA-A
*
349 ACCCTAG
1 ACCCTAA
*
356 ACCCTAG
1 ACCCTAA
*
363 ACCCTAG
1 ACCCTAA
*
370 ACCCTAG
1 ACCCTAA
377 ACCCTAGA
1 ACCCTA-A
*
385 CCCCTAA
1 ACCCTAA
*
392 CCCCTAA
1 ACCCTAA
*
399 CCCCTAA
1 ACCCTAA
*
406 CCCCTAA
1 ACCCTAA
413 ACCCT-A
1 ACCCTAA
*
419 ACCCCAA
1 ACCCTAA
426 ACCCCTAGA
1 A-CCCTA-A
435 ACCC-AA
1 ACCCTAA
441 ACCC
1 ACCC
445 CTAGAANNNN
Statistics
Matches: 386, Mismatches: 33, Indels: 36
0.85 0.07 0.08
Matches are distributed among these distances:
5 5 0.01
6 26 0.07
7 228 0.59
8 125 0.32
9 2 0.01
ACGTcount: A:0.40, C:0.43, G:0.05, T:0.12
Consensus pattern (7 bp):
ACCCTAA
Found at i:232 original size:97 final size:96
Alignment explanation
Indices: 54--449 Score: 396
Period size: 97 Copynumber: 4.2 Consensus size: 96
44 CCCCAACCCC
* * * *
54 AACCCTAAACCC--CAACCCTAAACCCTAAACCCTAAACCCTAAACCCT-AAACCCT-AAACCCT
1 AACCCTAAACCCTAAAACCCTAGACCCTAAACCCTAAAACCTAAACCCTAAAAACCTAAAACCCT
115 --AA------ACCCTAGACCCTAGACCCTAA
66 AAAACCCTAGACCCTAGACCCTAGACCCTAA
* *
138 AACCCTAAAACCTAAAACCCTAGACCCTAAACCCTAAAACCCTAAAACCCTAAAAACCT-AGACC
1 AACCCTAAACCCTAAAACCCTAGACCCTAAACCCTAAAA-CCT-AAACCCTAAAAACCTAAAACC
202 CTAAAACCCTAGACCCTAGACCCTAGACCCTAA
64 CTAAAACCCTAGACCCTAGACCCTAGACCCTAA
* * *
235 AACCCTAGACCCTAAAACCCTAGACCCTAAAACCCTAAAACCTAGACCCTAAAACCCTAAAACCC
1 AACCCTAAACCCTAAAACCCTAGACCCT-AAACCCTAAAACCTAAACCCTAAAAACCTAAAACCC
*
300 TAAAACCCTAGACCCTAGACCCTAGACCCTAG
65 TAAAACCCTAGACCCTAGACCCTAGACCCTAA
* * * * * * ** *
332 AACCCTAGAACCCTAGAACCCTAGACCCTAGACCCTAGACCCTAGACCCTAGACCCCT-AACCCC
1 AACCCTA-AACCCTAAAACCCTAGACCCTAAACCCTAAAACCTAAACCCTAAAAACCTAAAACCC
* * *
396 T-AACCCCTA-ACCCCTAAACCCTA-ACCCCAA
65 TAAAACCCTAGA-CCCTAGACCCTAGACCCTAA
* *
426 ACCCCTAGAACCC-AAACCCCTAGA
1 AACCCTA-AACCCTAAAACCCTAGA
450 ANNNNNNNNN
Statistics
Matches: 268, Mismatches: 27, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
84 11 0.04
86 22 0.08
87 3 0.01
88 7 0.03
89 12 0.04
91 2 0.01
93 9 0.03
94 18 0.07
95 18 0.07
96 19 0.07
97 117 0.44
98 30 0.11
ACGTcount: A:0.39, C:0.42, G:0.06, T:0.13
Consensus pattern (96 bp):
AACCCTAAACCCTAAAACCCTAGACCCTAAACCCTAAAACCTAAACCCTAAAAACCTAAAACCCT
AAAACCCTAGACCCTAGACCCTAGACCCTAA
Found at i:708 original size:7 final size:7
Alignment explanation
Indices: 696--990 Score: 80
Period size: 7 Copynumber: 42.4 Consensus size: 7
686 NNNNNNNAAC
*
696 CCCCCAA
1 CCCCAAA
*
703 CCCCCAA
1 CCCCAAA
*
710 CCCTAAA
1 CCCCAAA
* *
717 ACCCTAA
1 CCCCAAA
*
724 CCCC-TA
1 CCCCAAA
730 CCCCAAA
1 CCCCAAA
737 CCCCAAA
1 CCCCAAA
744 CCCCAAA
1 CCCCAAA
751 CCCCAAA
1 CCCCAAA
*
758 CCCTCTAA
1 CCC-CAAA
*
766 -CCCTAA
1 CCCCAAA
*
772 CCCC-TA
1 CCCCAAA
* *
778 GCCCTAA
1 CCCCAAA
*
785 CCCC-TA
1 CCCCAAA
**
791 GGCCAAA
1 CCCCAAA
* *
798 GCCCTAA
1 CCCCAAA
* *
805 GCCCTAA
1 CCCCAAA
812 CCCCAAA
1 CCCCAAA
*
819 CCACTAAAA
1 CC-C-CAAA
828 CCCCCAAA
1 -CCCCAAA
*
836 CCCTCGAA
1 CCC-CAAA
* *
844 CCCGAAC
1 CCCCAAA
851 CCCCAAA
1 CCCCAAA
*
858 -CCCGAA
1 CCCCAAA
864 CCCCAAAA
1 CCCC-AAA
*
872 CCCC-CA
1 CCCCAAA
*
878 CCCCCAA
1 CCCCAAA
885 CCCCTAAA
1 CCCC-AAA
893 CTCCC--A
1 C-CCCAAA
899 CCCCTTAAA
1 CCCC--AAA
908 CCCCAAA
1 CCCCAAA
*
915 CACCAAAA
1 C-CCCAAA
**
923 CCTTAAAA
1 CC-CCAAA
931 CCCCAAA
1 CCCCAAA
*
938 -CAC-AA
1 CCCCAAA
*
943 CCCCCAA
1 CCCCAAA
950 -CCC-AA
1 CCCCAAA
955 -CCC-AA
1 CCCCAAA
*
960 CCCCCAA
1 CCCCAAA
967 -CCCAAA
1 CCCCAAA
973 CCCCCAAA
1 -CCCCAAA
*
981 CCCCTAA
1 CCCCAAA
988 CCC
1 CCC
991 AAGAAAAAGA
Statistics
Matches: 220, Mismatches: 42, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
5 12 0.05
6 43 0.20
7 111 0.50
8 40 0.18
9 12 0.05
10 2 0.01
ACGTcount: A:0.36, C:0.55, G:0.03, T:0.07
Consensus pattern (7 bp):
CCCCAAA
Found at i:726 original size:21 final size:21
Alignment explanation
Indices: 696--891 Score: 98
Period size: 21 Copynumber: 9.3 Consensus size: 21
686 NNNNNNNAAC
* *
696 CCCCCAACCCCCAACCCTAAA
1 CCCCTAACCCCCAACCCCAAA
* *
717 ACCCTAA-CCCCTACCCCAAA
1 CCCCTAACCCCCAACCCCAAA
* *
737 CCCCAAACCCCAAACCCCAAA
1 CCCCTAACCCCCAACCCCAAA
* *
758 CCCTCTAA-CCCTAACCCC-TA
1 CCC-CTAACCCCCAACCCCAAA
* * **
778 GCCCTAA-CCCCTAGGCCAAA
1 CCCCTAACCCCCAACCCCAAA
* * *
798 GCCCTAAGCCCTAACCCCAAA
1 CCCCTAACCCCCAACCCCAAA
* *
819 CCACTAAAACCCCCAAACCCTCGAA
1 CCCCT--AACCCCC-AACCC-CAAA
* * *
844 -CCCGAACCCCCAAACCCGAA
1 CCCCTAACCCCCAACCCCAAA
* *
864 CCCCAAAACCCCC-ACCCCCAA
1 CCCC-TAACCCCCAACCCCAAA
885 CCCCTAA
1 CCCCTAA
892 ACTCCCACCC
Statistics
Matches: 132, Mismatches: 33, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
19 10 0.08
20 33 0.25
21 57 0.43
22 17 0.13
23 5 0.04
24 7 0.05
25 3 0.02
ACGTcount: A:0.34, C:0.55, G:0.04, T:0.07
Consensus pattern (21 bp):
CCCCTAACCCCCAACCCCAAA
Found at i:732 original size:20 final size:20
Alignment explanation
Indices: 698--757 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
688 NNNNNAACCC
* *
698 CCCAACCCCCAACCCTAAAA
1 CCCAAACCCCAACCCCAAAA
* * *
718 CCCTAACCCCTACCCCAAAC
1 CCCAAACCCCAACCCCAAAA
738 CCCAAACCCCAAACCCCAAA
1 CCCAAACCCC-AACCCCAAA
758 CCCTCTAACC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 24 0.75
21 8 0.25
ACGTcount: A:0.38, C:0.57, G:0.00, T:0.05
Consensus pattern (20 bp):
CCCAAACCCCAACCCCAAAA
Found at i:733 original size:27 final size:27
Alignment explanation
Indices: 697--756 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
687 NNNNNNAACC
* * *
697 CCCCAACCCCCAACCCTAAAACCCTAA
1 CCCCAACCCCAAACCCCAAAACCCAAA
* *
724 CCCCTACCCCAAACCCCAAACCCCAAA
1 CCCCAACCCCAAACCCCAAAACCCAAA
751 CCCCAA
1 CCCCAA
757 ACCCTCTAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.58, G:0.00, T:0.05
Consensus pattern (27 bp):
CCCCAACCCCAAACCCCAAAACCCAAA
Found at i:768 original size:48 final size:48
Alignment explanation
Indices: 696--788 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
686 NNNNNNNAAC
* *
696 CCCCCAACCCCCAACCCTAAAACCCTAACCCCTACCCCAAACCCCAAA
1 CCCCAAACCCCAAACCCTAAAACCCTAACCCCTACCCCAAACCCCAAA
** * *
744 CCCCAAACCCCAAACCCTCTAACCCTAACCCCTAGCCCTAACCCC
1 CCCCAAACCCCAAACCCTAAAACCCTAACCCCTACCCCAAACCCC
789 TAGGCCAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.32, C:0.58, G:0.01, T:0.09
Consensus pattern (48 bp):
CCCCAAACCCCAAACCCTAAAACCCTAACCCCTACCCCAAACCCCAAA
Found at i:784 original size:13 final size:13
Alignment explanation
Indices: 756--815 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
746 CCAAACCCCA
*
756 AACCCTCTAACCCT
1 AACCC-CTAGCCCT
770 AACCCCTAGCCCT
1 AACCCCTAGCCCT
* *
783 AACCCCTAGGCCA
1 AACCCCTAGCCCT
*
796 AAGCCCTAAGCCCT
1 AACCCCT-AGCCCT
810 AACCCC
1 AACCCC
816 AAACCACTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 24 0.63
14 14 0.37
ACGTcount: A:0.28, C:0.50, G:0.08, T:0.13
Consensus pattern (13 bp):
AACCCCTAGCCCT
Found at i:873 original size:22 final size:23
Alignment explanation
Indices: 824--877 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
814 CCAAACCACT
824 AAAACCCCCAAACCCTCGAACCC
1 AAAACCCCCAAACCCTCGAACCC
*
847 -GAACCCCCAAA-CC-CGAACCCC
1 AAAACCCCCAAACCCTCGAA-CCC
868 AAAACCCCCA
1 AAAACCCCCA
878 CCCCCAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 18 0.67
ACGTcount: A:0.39, C:0.54, G:0.06, T:0.02
Consensus pattern (23 bp):
AAAACCCCCAAACCCTCGAACCC
Found at i:965 original size:12 final size:13
Alignment explanation
Indices: 950--979 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
940 CAACCCCCAA
950 CCCAACCC-AACC
1 CCCAACCCAAACC
962 CCCAACCCAAACC
1 CCCAACCCAAACC
975 CCCAA
1 CCCAA
980 ACCCCTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.37, C:0.63, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCAACCCAAACC
Found at i:3646 original size:21 final size:21
Alignment explanation
Indices: 3622--3672 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
3612 TACAAAAAAT
3622 CTGAACCGGACACTAAAACAG
1 CTGAACCGGACACTAAAACAG
3643 CTGAACCGGACACTAAAACAG
1 CTGAACCGGACACTAAAACAG
3664 CTGAACCGG
1 CTGAACCGG
3673 GACGGGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.29, G:0.22, T:0.10
Consensus pattern (21 bp):
CTGAACCGGACACTAAAACAG
Done.