Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
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: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:324459 original size:31 final size:31
Alignment explanation
Indices: 324422--324480 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
324412 AAATTAAATT
*
324422 TTAAATTTTATTACTCAACT-TTGATTTTTTA
1 TTAAATTTTATCACTCAA-TATTGATTTTTTA
*
324453 TTAAATTTTATCACTTAATATTGATTTT
1 TTAAATTTTATCACTCAATATTGATTTT
324481 AAATAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (31 bp):
TTAAATTTTATCACTCAATATTGATTTTTTA
Found at i:333046 original size:29 final size:29
Alignment explanation
Indices: 333000--334221 Score: 945
Period size: 28 Copynumber: 41.5 Consensus size: 29
332990 TCTTTGAAAT
*
333000 CCTTTTAAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333029 CCTTTCAAAAGACTACAAATCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
**
333058 CCTTTCAAAAGCCCACAAGTCAGTGATAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333087 CATTTC-AAAGCCCATAAGTTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333115 GCTTTC-AAAGCCCACAAGTTAGTGGCAT
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * * *
333143 CCTTTCAAAAGGCCATAAGTTAGTAGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
*
333172 CCTTT-TAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* *
333200 CTTTTTCAAAA-CCCATAAG-CTAGTGGCAC
1 C-CTTTCAAAAGCCCACAAGTC-AGTGGCAC
*
333229 TCTTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* *
333258 CTTTTCAAAAGCCCACAAGTTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * * *
333287 CCTTTC-AAAGTCCATAAGTTAGTGGCAT
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333315 CCTTTCAAAAGCCCATAAGTTAGTGGCAT
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * **
333344 CGTTT-TAAAGCCCACAAGTTTGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333372 CATTT-TAAAGCCCACAAGTTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
333400 CCTTTTCAAAA-CCCACAAG-CTAGTGGCAC
1 CC-TTTCAAAAGCCCACAAGTC-AGTGGCAC
*
333429 CCTTTCAAAAGCCCACAAGTCATTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
** *
333458 ATTTTCAAAAGCCCACAAGTGAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
*
333487 CCTTTC-AAAGCCCACAAGTTAGTGGCATCCTTTC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCA------C
* *
333521 AATCCTTTCAAAAGCCCACAAGTGAATGGCAC
1 ---CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
333553 CCTTT-TAAAGCCTACAAGTTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* **
333581 TCTTTTGAAA-CCCACAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* **
333609 CCTTT-TAAAGCCCACAAGTTTGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* *
333637 CCTTT-TAAAGCCCATAAG-CTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTC-AGTGGCAC
* *
333665 CCTTTTC-AATGCCCACAAGTCAATGGCAC
1 CC-TTTCAAAAGCCCACAAGTCAGTGGCAC
* *
333694 CCTTTGAAAAGCCCACAAGTCAATGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
333723 CCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCA------C
*
333757 AATCCTTTCAAAA-CCCTCTAAGTCAGTGGCAC
1 ---CCTTTCAAAAGCCCAC-AAGTCAGTGGCAC
* *
333789 CCTTT-TAAAGCCCACAAGTCAGTGACAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* *
333817 CCTTT-GAAAGCCCACAAGTCAATGGCATCCTTTC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCA------C
*
333851 AATCCTTTCAAAAGCCCACAAGTTAGTGGCAC
1 ---CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * * *
333883 CATTTTAAAA-CCCATAAGTTAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
*
333911 CCTTTTCAAAAGCCCACAAGTCAGTAGCA-
1 CC-TTTCAAAAGCCCACAAGTCAGTGGCAC
* ** *
333940 CTTTTTTAAAGCCCATAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
*
333969 CCTTTC-AAAGCCCACAAGTTAGTGGCATCC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCA--C
* *
333999 TTTCAATCTTTTCAAAAGCCCATAAGTCAGTGGTAC
1 ---C---C-TTTCAAAAGCCCACAAGTCAGTGGCAC
* ** *
334035 TCTTTTC-AAAGCCCATGAGCCAGTGGCAC
1 -CCTTTCAAAAGCCCACAAGTCAGTGGCAC
** ** * *
334064 TTTTTTTAAAGCCCACGAGCCAGTGGCA-
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
** * * *
334092 CCTTTTTAAAGCCCACGAGTCAGTGACAT
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
*
334121 CCTTT-TAAAGCCCACAAGTCAGTGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* * *
334149 CCTTT-TAACGCCCACAAGTCAATGGCAC
1 CCTTTCAAAAGCCCACAAGTCAGTGGCAC
* *
334177 CCATTTC-AAAGCCTACAAGTCAGTGGCAAA
1 CC-TTTCAAAAGCCCACAAGTCAGTGGC-AC
334207 CCTTTCAAAAGCCCA
1 CCTTTCAAAAGCCCA
334222 TACAAGTTGG
Statistics
Matches: 988, Mismatches: 135, Indels: 139
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.00
28 456 0.46
29 384 0.39
30 38 0.04
32 3 0.00
33 1 0.00
34 5 0.01
36 2 0.00
37 25 0.03
38 71 0.07
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
CCTTTCAAAAGCCCACAAGTCAGTGGCAC
Found at i:333159 original size:57 final size:57
Alignment explanation
Indices: 333007--334251 Score: 965
Period size: 57 Copynumber: 21.1 Consensus size: 57
332997 AATCCTTTTA
* * * *
333007 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGACTACAAATCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
** * * *
333064 AAAAGCCCACAAGTCAGTGATACCATTTC-AAAGCCCATAAGTTAGTGGCACGCTTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* * * * * *
333121 AAAGCCCACAAGTTAGTGGCATCCTTTCAAAAGGCCATAAGTTAGTAGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* * * *
333178 AAAGCCCACAAGTCAGTGGCACCTTTTTCAAAA-CCCATAAGCTAGTGGCACTCTTTC
1 AAAGCCCACAAGTCAGTGGCACC-CTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
*
333235 AAAAGCCCACAAGTCAGTGGCACCTTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* * * * * * * *
333293 AAAGTCCATAAGTTAGTGGCATCCTTTCAAAAGCCCATAAGTTAGTGGCATCGTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
** * *
333350 AAAGCCCACAAGTTTGTGGCACCATTT-TAAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCC-TTTC
* * * **
333407 AAAACCCACAAG-CTAGTGGCACCCTTTCAAAAGCCCACAAGTCATTGGCACATTTTC
1 AAAGCCCACAAGTC-AGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
*
333464 AAAAGCCCACAAGTGAGTGGCACCCTTTC-AAAGCCCACAAGTTAGTGGCATCCTTTCAATCCTT
1 -AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCA------C---CCTT
333528 TC
56 TC
* * * * * *
333530 AAAAGCCCACAAGTGAATGGCACCCTTT-TAAAGCCTACAAGTTAGTGGCACTCTTTTG
1 -AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCAC-CCTTTC
* * *
333588 AAA-CCCACAAGTCAGTGGCACCCTTT-TAAAGCCCACAAGTTTGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* * * * *
333643 AAAGCCCATAAG-CTAGTGGCACCCTTTTC-AATGCCCACAAGTCAATGGCACCCTTTGA
1 AAAGCCCACAAGTC-AGTGGCACCC-TTTCAAAAGCCCACAAGTTAGTGGCACCCTTT-C
* *
333701 AAAGCCCACAAGTCAATGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAATCCTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCA------C---CCTTT
333765 C
57 C
* * * * * *
333766 AAAACCCTCTAAGTCAGTGGCACCCTTT-TAAAGCCCACAAGTCAGTGACACCCTTTG
1 AAAGCCCAC-AAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* *
333823 AAAGCCCACAAGTCAATGGCATCCTTTCAATCCTTTCAAAAGCCCACAAGTTAGTGGCACCATTT
1 AAAGCCCACAAGTCAGTGGCA------C---CCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTT
*
333888 T
57 C
* * * * * ** *
333889 AAAACCCATAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTAGCACTTTTTT
1 AAAGCCCACAAGTCAGTGGCACCC-TTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
*
333947 AAAGCCCATAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTTAGTGGCATCCTTTCAATCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCA--C---C---C-TTT
334011 C
57 C
* * * ** ** ** *
334012 AAAAGCCCATAAGTCAGTGGTACTCTTTTC-AAAGCCCATGAGCCAGTGGCACTTTTTTT
1 -AAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAAGCCCACAAGTTAGTGGCAC-CCTTTC
* * ** * * * * *
334071 AAAGCCCACGAGCCAGTGGCA-CCTTTTTAAAGCCCACGAGTCAGTGACATCCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
* * * *
334127 AAAGCCCACAAGTCAGTGGCACCCTTT-TAACGCCCACAAGTCAATGGCACCCATTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCC-TTTC
* * * *
334184 AAAGCCTACAAGTCAGTGGCAAACCTTTCAAAAGCCCATACAAGTTGGTGGCATCTCTTTC
1 AAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAAGCCC--ACAAGTTAGTGGCA-CCCTTTC
334245 TAAAGCC
1 -AAAGCC
334252 TGGAAATGCT
Statistics
Matches: 971, Mismatches: 149, Indels: 130
0.78 0.12 0.10
Matches are distributed among these distances:
55 8 0.01
56 180 0.19
57 328 0.34
58 222 0.23
59 10 0.01
60 3 0.00
61 15 0.02
62 9 0.01
63 3 0.00
65 16 0.02
66 155 0.16
67 22 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTC
Found at i:333596 original size:94 final size:94
Alignment explanation
Indices: 333429--333613 Score: 248
Period size: 94 Copynumber: 2.0 Consensus size: 94
333419 CTAGTGGCAC
*
333429 CCTTTCAAAAGCCCACAAGTCATTGGCACATTTTCAAAAGCCCACAAGTGAGTGGCACCCTTTCA
1 CCTTTCAAAAGCCCACAAGTCAATGGCACATTTT-AAAAGCCCACAAGTGAGTGGCACCCTTTCA
* *
333494 AAGCCCACAAGTTAGTGGCATCCTTTCAAT
65 AAGCCCACAAGTCAGTGGCACCCTTTCAAT
* * * * * *
333524 CCTTTCAAAAGCCCACAAGTGAATGGCACCCTTTT-AAAGCCTACAAGTTAGTGGCACTCTTTTG
1 CCTTTCAAAAGCCCACAAGTCAATGGCA-CATTTTAAAAGCCCACAAGTGAGTGGCAC-CCTTTC
333588 AAA-CCCACAAGTCAGTGGCACCCTTT
64 AAAGCCCACAAGTCAGTGGCACCCTTT
333614 TAAAGCCCAC
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
94 41 0.52
95 33 0.42
96 5 0.06
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (94 bp):
CCTTTCAAAAGCCCACAAGTCAATGGCACATTTTAAAAGCCCACAAGTGAGTGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACCCTTTCAAT
Found at i:333827 original size:94 final size:94
Alignment explanation
Indices: 333675--334214 Score: 402
Period size: 94 Copynumber: 5.9 Consensus size: 94
333665 CCTTTTCAAT
* * * *
333675 GCCCACAAGTCAATGGCACCCTTTGAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAA
1 GCCCACAAGTCAGTGGCACCCTTT-TAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACAA
333740 GTCAGTGGCATCCTTTCAATCCTTTCAAAA
65 GTCAGTGGCATCCTTTCAATCCTTTCAAAA
* * *
333770 -CCCTCTAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGACACCCTTTGAAAGCCCACAA
1 GCCCAC-AAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACAA
*
333834 GTCAATGGCATCCTTTCAATCCTTTCAAAA
65 GTCAGTGGCATCCTTTCAATCCTTTCAAAA
* * * * *
333864 GCCCACAAGTTAGTGGCACCATTTTAAAACCCATAAGTTAGTGGCACCCTTTTCAAAAGCCCACA
1 GCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCC-TTT-AAAAGCCCACA
*
333929 AGTCAGTAGCA--C-TT---T--TTT--AAA
64 AGTCAGTGGCATCCTTTCAATCCTTTCAAAA
* * *
333950 GCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAATCTTTTCAAA
1 GCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCA--C---C---C-TTT-AAA
* *
334015 AGCCCATAAGTCAGTGG--TAC--TC--T--TTTC-AAA
56 AGCCCACAAGTCAGTGGCATCCTTTCAATCCTTTCAAAA
** * ** * * * * *
334045 GCCCATGAGCCAGTGGCACTTTTTTTAAAGCCCACGAGCCAGTGGCACCTTTTTAAAGCCCACGA
1 GCCCACAAGTCAGTGGCAC-CCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACAA
*
334110 GTCAGT-G-A------C-ATCCTTT-TAAA
65 GTCAGTGGCATCCTTTCAATCCTTTCAAAA
* * * *
334130 GCCCACAAGTCAGTGGCACCCTTTTAACGCCCACAAGTCAATGGCACCCATTTCAAAGCCTACAA
1 GCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCC-TTTAAAAGCCCACAA
*
334195 GTCAGTGGCAAACCTTTCAA
65 GTCAGTGGC-ATCCTTTCAA
334215 AAGCCCATAC
Statistics
Matches: 362, Mismatches: 50, Indels: 66
0.76 0.10 0.14
Matches are distributed among these distances:
82 1 0.00
83 1 0.00
84 23 0.06
85 41 0.11
86 59 0.16
87 3 0.01
88 5 0.01
90 1 0.00
91 2 0.01
93 3 0.01
94 138 0.38
95 45 0.12
96 40 0.11
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (94 bp):
GCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCACAAG
TCAGTGGCATCCTTTCAATCCTTTCAAAA
Found at i:333921 original size:152 final size:152
Alignment explanation
Indices: 333116--334153 Score: 659
Period size: 152 Copynumber: 7.0 Consensus size: 152
333106 TAGTGGCACG
* * * ** *
333116 CTTTC-AAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAAGGCCATAAGTTAGTAGCACCCTTTT-
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAA-CCCATAAGCCAGTGGCACCCTTTTC
* * * * *
333178 AAAGCCCACAAGTCAGTGGCACCTTTTTCAAAACCCATAAG-CTAGTGGCACTCTTTCAAAAGCC
65 AAAACCCACAAGTCAGTGGCACCTTTTT-AAAGCCCACAAGTC-AGTGACACCCTTTC-AAAGCC
333242 CACAAGTCAGTGGCA--C---C--T-
127 CACAAGTCAGTGGCATCCTTTCAATC
* * ** ** *
333260 -TTTCAAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGTCCATAAGTTAGTGGCATCC-TTTCA
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAACCCATAAGCCAGTGGCACCCTTTTCA
* * * * ** * * *
333322 AAAGCCCATAAGTTAGTGGCATCGTTTTAAAGCCCACAAGTTTGTGGCACCATTTTAAAGCCCAC
66 AAA-CCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCAC
*
333387 AAGTTAGTGGCA-CC---C--T-
130 AAGTCAGTGGCATCCTTTCAATC
* * * * *
333403 -TTTCAAAA-CCCACAAG-CTAGTGGCAC-CCTTTCAAAAGCCCACAAGTCATTGGCA-CATTTT
1 CTTTCAAAAGCCCACAAGTC-AGTGGCACTCTTTTCAAAA-CCCATAAGCCAGTGGCACCCTTTT
* * * * *
333463 CAAAAGCCCACAAGTGAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAATCCTT
64 CAAAA-CCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGT-G-A------C-ACCCTT
* *
333528 TCAAAAGCCCACAAGTGAATGGCA-CC---C--T-
119 TC-AAAGCCCACAAGTCAGTGGCATCCTTTCAATC
* * * * *
333556 -TTT--AAAGCCTACAAGTTAGTGGCACTCTTTT-GAAACCCACAAGTCAGTGGCACCCTTTT-A
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAACCCATAAGCCAGTGGCACCCTTTTCA
* ** * * * *
333616 AAGCCCACAAGTTTGTGGCACCCTTTTAAAGCCCATAAG-CTAGTGGCACCCTTTTCAATGCCCA
66 AAACCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTC-AGTGACACCC-TTTCAAAGCCCA
*
333680 CAAGTCAATGGCA------C---C
129 CAAGTCAGTGGCATCCTTTCAATC
* * * * * *
333695 CTTTGAAAAGCCCACAAGTCAATGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAA
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAACCCATAAGCCAGTGGCA-CC---C--
* * *
333759 TCCTTTCAAAACCCTCTAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGACACCCTTTGA
60 T--TTTCAAAACCCAC-AAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGACACCCTTTCA
*
333824 AAGCCCACAAGTCAATGGCATCCTTTCAATC
122 AAGCCCACAAGTCAGTGGCATCCTTTCAATC
* **
333855 CTTTCAAAAGCCCACAAGTTAGTGGCAC-CATTTT-AAAACCCATAAGTTAGTGGCACCCTTTTC
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTC-TTTTCAAAACCCATAAGCCAGTGGCACCCTTTTC
* * * *
333918 AAAAGCCCACAAGTCAGTAGCACTTTTTTAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCA
65 AAAA-CCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCA
*
333983 CAAGTTAGTGGCATCCTTTCAATC
129 CAAGTCAGTGGCATCCTTTCAATC
* * * * * ** *
334007 TTTTCAAAAGCCCATAAGTCAGTGGTACTCTTTTCAAAGCCCATGAGCCAGTGGCACTTTTTTTA
1 CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAACCCATAAGCCAGTGGCACCCTTTTCA
* * * * * *
334072 AAGCCCACGAGCCAGTGGCACCTTTTTAAAGCCCACGAGTCAGTGACATCCTTTTAAAGCCCACA
66 AAACCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACA
*
334137 AGTCAGTGGCACCCTTT
131 AGTCAGTGGCATCCTTT
334154 TAACGCCCAC
Statistics
Matches: 735, Mismatches: 105, Indels: 100
0.78 0.11 0.11
Matches are distributed among these distances:
139 1 0.00
140 3 0.00
141 26 0.04
142 92 0.13
143 114 0.16
144 51 0.07
146 1 0.00
148 1 0.00
149 1 0.00
150 38 0.05
151 53 0.07
152 240 0.33
153 61 0.08
154 1 0.00
156 1 0.00
157 1 0.00
159 2 0.00
160 45 0.06
161 3 0.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (152 bp):
CTTTCAAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAACCCATAAGCCAGTGGCACCCTTTTCA
AAACCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACA
AGTCAGTGGCATCCTTTCAATC
Found at i:333947 original size:58 final size:58
Alignment explanation
Indices: 333856--334221 Score: 296
Period size: 58 Copynumber: 6.2 Consensus size: 58
333846 CTTTCAATCC
* ** * *
333856 TTTCAAAAGCCCACAAGTTAGTGGCAC-CATTTTAAAACCCATAAGTTAGTGGCACCCT
1 TTTC-AAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGCACCCT
*
333914 TTTCAAAAGCCCACAAGTCAGTAGCAC-TTTTTTAAAGCCCATAAGTCAGTGGCACCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGCACCCT
* * *
333971 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAATCTTTTCAAAAGCCCATAAGTCAGTGGTACT
1 TTTCAAAGCCCACAAGTCAGTGGCA--C-TT---T-TTTT--AAAGCCCATAAGTCAGTGGCACC
334036 CT
57 CT
** * ** *
334038 TTTCAAAGCCCATGAGCCAGTGGCACTTTTTTTAAAGCCCACGAGCCAGTGGCA-CCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGCACCCT
* * * ** *
334095 TTTTAAAGCCCACGAGTCAGTGACA-TCCTTTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGCACCCT
* * *** * * * *
334152 TTT-AACGCCCACAAGTCAATGGCACCCATTTCAAAGCCTACAAGTCAGTGGCAAACC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGC-ACCCT
334209 TTTCAAAAGCCCA
1 TTTC-AAAGCCCA
334222 TACAAGTTGG
Statistics
Matches: 255, Mismatches: 37, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
56 60 0.24
57 59 0.23
58 72 0.28
59 7 0.03
60 5 0.02
61 1 0.00
63 1 0.00
64 6 0.02
65 1 0.00
66 22 0.09
67 21 0.08
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (58 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTTTTTTTAAAGCCCATAAGTCAGTGGCACCCT
Found at i:334298 original size:31 final size:30
Alignment explanation
Indices: 334263--334341 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 30
334253 GGAAATGCTG
** *
334263 GTGGCAACCCTTCTACCGCCCACACATGTTT
1 GTGGCAACCCTTCTAAAGCCCACACAAG-TT
*
334294 GTGGCAACCTTCTCTAAAGCCCACACAAGTT
1 GTGGCAACCCT-TCTAAAGCCCACACAAGTT
334325 GATGGCAACCCTTCTAA
1 G-TGGCAACCCTTCTAA
334342 GCCTAATGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 18 0.44
32 23 0.56
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24
Consensus pattern (30 bp):
GTGGCAACCCTTCTAAAGCCCACACAAGTT
Found at i:334477 original size:52 final size:52
Alignment explanation
Indices: 334394--334498 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
334384 AAATCTTTTT
* *
334394 TCTTGAAGTCCGATATCGCTGGCCTTGAATCAACATATTGACACCTTTATCA
1 TCTTGAAGTCCAATATCGCTGGACTTGAATCAACATATTGACACCTTTATCA
* ** *
334446 TCTTTAAGTCCAATATCGCTGGACTTGAATCAGTATATTGGCACCTTTATCA
1 TCTTGAAGTCCAATATCGCTGGACTTGAATCAACATATTGACACCTTTATCA
334498 T
1 T
334499 TTTTCTTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
TCTTGAAGTCCAATATCGCTGGACTTGAATCAACATATTGACACCTTTATCA
Found at i:334730 original size:173 final size:174
Alignment explanation
Indices: 334529--334850 Score: 450
Period size: 174 Copynumber: 1.9 Consensus size: 174
334519 ATGTCGTTGG
* * * * *
334529 CCTTGAATCAACATATTGGCAGTTGTCAAATCTTCTTTCTTTCAAGCTCGATATCGAT-GGCTTG
1 CCTTGAATCAACACATTAGCACTTGTCAAATCTTCTTTCTTTCAAGCCCGATATCGATAGCCTTG
* * * *
334593 AATCAACATATCAACACCCTTATTATTCTTT-TCATCTTTAAGTTCAATGTCACTGACCTTGAAT
66 AATCAACATATCAACACCCTTATCATT-TTTCACATCATTAAGTCCAATGTCACTGACCTTGAAT
*
334657 TAGCACATTGGCACTCTTCTCATCCTTGTCATCTTTAAGTCTAGA
130 CAGCACATTGGCACTCTTCTCATCCTTGTCATCTTTAAGTCTAGA
* * *
334702 CCTTGAATCAACACCTTAGCACTTGTCAAATCTTCTTTCTTTCAAGCCCTATATCGCTAGCCTTG
1 CCTTGAATCAACACATTAGCACTTGTCAAATCTTCTTTCTTTCAAGCCCGATATCGATAGCCTTG
* * * ** *
334767 AATCAGCATATCGACACCTTTATCATTTTTCACATCATTAAGTCCAATGTCGTTGATCTTGAATC
66 AATCAACATATCAACACCCTTATCATTTTTCACATCATTAAGTCCAATGTCACTGACCTTGAATC
334832 AGCACATTGGCACTCTTCT
131 AGCACATTGGCACTCTTCT
334851 TATCTTTAAG
Statistics
Matches: 128, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
173 54 0.42
174 74 0.58
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (174 bp):
CCTTGAATCAACACATTAGCACTTGTCAAATCTTCTTTCTTTCAAGCCCGATATCGATAGCCTTG
AATCAACATATCAACACCCTTATCATTTTTCACATCATTAAGTCCAATGTCACTGACCTTGAATC
AGCACATTGGCACTCTTCTCATCCTTGTCATCTTTAAGTCTAGA
Found at i:339821 original size:201 final size:199
Alignment explanation
Indices: 339463--339836 Score: 479
Period size: 201 Copynumber: 1.9 Consensus size: 199
339453 TTTTTTTATT
* *
339463 TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTTTATAATTATTTAATATATTTTGCAC
1 TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTGTATAATTATTTAATATAATTTGCAC
* *
339528 ATGAAACAAATTTGACATTTTACTGCAAAATTTTTTTAATATGCACTTTATTAATTTATTTATGT
66 ATGAAACAAATTTGACA-TTGAATGC-AAATTTTTTTAATAT-CACTTTATTAATTTATTTATGT
* * *
339593 TTAAAATATATAATTATATATTCAAAAATAAGTAAATCAATCAGCATTCACATGTGAATGCATGT
128 TTAAAATATAAAATTATATATTCAAAAATAAATAAAACAATCAGCATTCACATGTGAATGCATGT
339658 GGTAATC
193 GGTAATC
* * * * *
339665 TTTGTAATTAATTTTGCATTAGTTTTAAAATTAATAAATTGTATTA-TACTTTGATATAATTTGT
1 TTTGTAATTAATTTTGCATTAATATTAAAA-TAATAAATTGTATAATTA-TTTAATATAATTTGC
* * *
339729 ACATGTAACAAAGTTT-ACA-TGAATGC-AATTTTTAGTTAAATAT-ATTTTATTAGTTTCATTT
64 ACATGAAACAAA-TTTGACATTGAATGCAAATTTTT--TT-AATATCACTTTATTAATTT-ATTT
*
339790 ATTTTTAAAATATAAAATTATATATTCAAAAATAAATAAAACAATCA
124 ATGTTTAAAATATAAAATTATATATTCAAAAATAAATAAAACAATCA
339837 TTCAAATGCA
Statistics
Matches: 149, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
199 7 0.05
200 11 0.07
201 54 0.36
202 35 0.23
203 39 0.26
204 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (199 bp):
TTTGTAATTAATTTTGCATTAATATTAAAATAATAAATTGTATAATTATTTAATATAATTTGCAC
ATGAAACAAATTTGACATTGAATGCAAATTTTTTTAATATCACTTTATTAATTTATTTATGTTTA
AAATATAAAATTATATATTCAAAAATAAATAAAACAATCAGCATTCACATGTGAATGCATGTGGT
AATC
Found at i:341080 original size:15 final size:15
Alignment explanation
Indices: 341060--341090 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
341050 AATAATGCCA
*
341060 TTTTTTCTTTTTATT
1 TTTTTTCTTTATATT
341075 TTTTTTCTTTATATT
1 TTTTTTCTTTATATT
341090 T
1 T
341091 CAACTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTATATT
Found at i:342709 original size:154 final size:155
Alignment explanation
Indices: 342241--342712 Score: 392
Period size: 155 Copynumber: 3.0 Consensus size: 155
342231 ACTAGAAAAA
* * ** *
342241 GATGAACCTATCCTAAA--CACATTCCTTTTG-CATAAAAGTATCCCGGTGACAA-CTAGGACTC
1 GATGAACCTATCCTAAATGCACA--CC-TTCGACATAAAAGCATCCTAGTGACAACCTAGGACTT
* * * * * * * *
342302 AGTTTTAGGAAAAATTACTAAAATACCACATATGGATGTACCTTCAACATGAAAGTATCCCGGTA
63 AGTTATAAG-AAAATTACAAAAATACCTC-TAAGG-TATACCTTTAACATGAAAGTAT-CTGGTA
* * *
342367 ACTCTAATGGACATTAAAATGATCATAAATGG
124 ACCCTAATGAACACTAAAATGATCATAAATGG
* * *
342399 GGTGAACCTATCCTAAATGCACACCTTCGACATAAAAGTATCCTAGTGACAACCTATGACTTAGT
1 GATGAACCTATCCTAAATGCACACCTTCGACATAAAAGCATCCTAGTGACAACCTAGGACTTAGT
* * * * * * * *
342464 TCTAAGAAAATTACAAAAATATCTCTAAGGTATACTTTTGATATAAAAGTATCTAGTAATCCTAA
66 TATAAGAAAATTACAAAAATACCTCTAAGGTATACCTTTAACATGAAAGTATCTGGTAACCCTAA
*
342529 T-AGACACTAAAATGGTCATAAATGG
131 TGA-ACACTAAAATGATCATAAATGG
*
342554 GATGAACCTATCCTAAATGCACACCCTT-GGCAT-AAAGCCATCGC-A-TGACAACCTAGGACTT
1 GATGAACCTATCCTAAATGCACA-CCTTCGACATAAAAG-CATC-CTAGTGACAACCTAGGACTT
* ** * * * *
342615 GGTTATAA-AAAATTATGAAAATGCC-CTTAGGGTATGCCTTTAACATGAAAGTATTTGGGTAAC
63 AGTTATAAGAAAATTACAAAAATACCTC-TAAGGTATACCTTTAACATGAAAGTATCT-GGTAAC
* *
342678 CCTAATGAATACTAAAATGAACA-AAGATGG
126 CCTAATGAACACTAAAATGATCATAA-ATGG
342708 GATGA
1 GATGA
342713 CTTTTACCCT
Statistics
Matches: 255, Mismatches: 47, Indels: 28
0.77 0.14 0.08
Matches are distributed among these distances:
152 1 0.00
153 37 0.15
154 56 0.22
155 61 0.24
156 21 0.08
157 7 0.03
158 54 0.21
159 14 0.05
160 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (155 bp):
GATGAACCTATCCTAAATGCACACCTTCGACATAAAAGCATCCTAGTGACAACCTAGGACTTAGT
TATAAGAAAATTACAAAAATACCTCTAAGGTATACCTTTAACATGAAAGTATCTGGTAACCCTAA
TGAACACTAAAATGATCATAAATGG
Found at i:343566 original size:19 final size:18
Alignment explanation
Indices: 343542--343604 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
343532 AAACCGTAAC
343542 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
343561 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
343574 TATATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
343593 TGTATCGATACA
1 TGTATCGATACA
343605 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:343585 original size:32 final size:32
Alignment explanation
Indices: 343544--343612 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
343534 ACCGTAACTG
343544 TATCGATACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
* *
343576 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATA
343608 TATCG
1 TATCG
343613 CTACGAAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:343675 original size:13 final size:13
Alignment explanation
Indices: 343657--343683 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
343647 ATTACTCAAA
343657 TGTATCGATACAT
1 TGTATCGATACAT
343670 TGTATCGATACAT
1 TGTATCGATACAT
343683 T
1 T
343684 TGATCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347424 original size:165 final size:164
Alignment explanation
Indices: 347179--347574 Score: 438
Period size: 165 Copynumber: 2.4 Consensus size: 164
347169 CTTATCGAAT
* * * * * * * ** *
347179 TAAAACACAAAATTAAACATCCAAGAAATCAAAGTCAACATAAAAAAGACATCCA-AAAGTTACA
1 TAAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAA-TTACA
* * * *
347243 A-AGAAGATTTGGCCATGTAAC-TTTGGCCTTGGAACAAAATTTCCAATATTTATACTTGAATCC
65 AGA-AAGATTCGGCCATGT-ACTTTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCC
* * * * *
347306 CTGAACTTTCTGAAATCATAAATTGGTCTTTATATAA
128 CTAAACTTTCTAAAATCACAAATTAGTCTCTATATAA
* ** *
347343 CTAAAACACAAAATTAAATATCAAACCTATCAAAATCCACACAAAAATTTGATCCACAAATTAGA
1 -TAAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACA
* * **
347408 AGAAAGATTCGGCCATGTACTTTTGGCCTTAGAATAAAATTTTCAATATTTACACTTAAATGTCT
65 AGAAAGATTCGGCCATGTACTTTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCCCT
*
347473 AAACTTTCTAAAATTACAAATTAGTCTCTATATAA
130 AAACTTTCTAAAATCACAAATTAGTCTCTATATAA
* * * * *
347508 TTAAACACAAAATTAAATATCGAACATATCAAAATTCAGACAAAAATCAGTTCCACAAATTACAA
1 TAAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACAA
347573 GA
66 GA
347575 GTTCGGCCAA
Statistics
Matches: 192, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
164 60 0.31
165 128 0.67
166 4 0.02
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (164 bp):
TAAAACACAAAATTAAATATCAAACATATCAAAATCCACACAAAAATCAGATCCACAAATTACAA
GAAAGATTCGGCCATGTACTTTTGGCCTTAGAACAAAATTTCCAATATTTACACTTAAATCCCTA
AACTTTCTAAAATCACAAATTAGTCTCTATATAA
Found at i:349324 original size:153 final size:149
Alignment explanation
Indices: 348874--349311 Score: 400
Period size: 153 Copynumber: 2.9 Consensus size: 149
348864 AAACTATTAG
* * * * *
348874 AATAAATTGAATTTTCACAAACTAATTTAATATAAATTTAATAAAAATATTTGATGGATTTT-AA
1 AATAAATTGAATTTTCA-AAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
* * ** *
348938 AATTTTTAAACTGAGAAAAATCTAACCAA-AAAAATTTATAGAGTAGAAAACTCTATATCTT-AA
65 AA-TTATAAACTTAGAAAAATCT-A-CAAGAAAAATTTACGGAGTAG-AAACTCTATATTTTGAA
* **
349001 AACAAGAAAAATTCTAAAACTTATAA
126 AA-TAGAAAAATT-TAAAACACATAA
* * * * * ** * * *
349027 AACATATTGAATTTTTTAAAATTGAATTAATACGAATTAGACAACAATATTTGAAGAATTTTGGA
1 AATAAATTGAA-TTTTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
* *** * * * **
349092 AATTATAAATTTAGAAAAATCCT-TTTGAAAAAATTTACGAAGTAAAAAACTCTATATTTGGGTA
65 AATTATAAACTTAGAAAAAT-CTACAAG-AAAAATTTACGGAGT-AGAAACTCTATATTTTGAAA
349156 ATAGAAAAATTTTAAAACACATAA
127 ATAGAAAAA-TTTAAAACACATAA
*
349180 AATAAATTGAATTATTCAAAACTGATTTAATATAAATTAAACAATAATATTTGAAGAATTTTGAA
1 AATAAATTGAATT-TTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAA
*
349245 AATTATAAACTTAAAAAAATCATACAAGAAAAATTTACGGAGTAGAAACTAC-ATATTTTGAAAA
65 AATTATAAACTTAGAAAAATC-TACAAGAAAAATTTACGGAGTAGAAACT-CTATATTTTGAAAA
349309 TAG
128 TAG
349312 GAAAGCCCTT
Statistics
Matches: 221, Mismatches: 52, Indels: 25
0.74 0.17 0.08
Matches are distributed among these distances:
152 21 0.10
153 184 0.83
154 16 0.07
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.33
Consensus pattern (149 bp):
AATAAATTGAATTTTCAAAACTGATTTAATATAAATTAAACAAAAATATTTGAAGAATTTTGAAA
ATTATAAACTTAGAAAAATCTACAAGAAAAATTTACGGAGTAGAAACTCTATATTTTGAAAATAG
AAAAATTTAAAACACATAA
Found at i:350268 original size:20 final size:20
Alignment explanation
Indices: 350234--350279 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
350224 CAGATTATGC
*
350234 TTAATTGAATTAAAATATAAA
1 TTAATTGAATAAAAAT-TAAA
*
350255 -TAATTTAATAAAAATTAAA
1 TTAATTGAATAAAAATTAAA
350274 TTAATT
1 TTAATT
350280 ACATGCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TTAATTGAATAAAAATTAAA
Found at i:351583 original size:155 final size:155
Alignment explanation
Indices: 351293--351593 Score: 390
Period size: 155 Copynumber: 1.9 Consensus size: 155
351283 CAAAGTTTAA
* * * *
351293 GAAAAATTATGAAAATGCCCTTAGGGGATACCTTTGATGTAAAAGCGCCTCATACCCCTAAATGA
1 GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAACACCTCATACCCCTAAAGGA
* * * * ** *
351358 CTAAAAAAGGATTATAAATGGGATGGACCTATCCTAAATACCCATATTCGGCATAAAAGTGAAAT
66 CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAAC
**
351423 CGGTGATGACCTAGGAGTTAAATTT
131 CGGTGACAACCTAGGAGTTAAATTT
* * * *
351448 GAAAAATTATGAAAATGCCCTTAGGTGAGACCTTTGATGTAAAAATACTTGATACCCCTAAAGGA
1 GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAACACCTCATACCCCTAAAGGA
* * *
351513 TTTAAAAAGGTTTAGAAACGGAATGAACCTATCCTAAATACCCACT-TTCGGCATAAAA-CCAAA
66 CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCA-TATTCGGCATAAAAGCCAAA
351576 CCTGGTGACAACCTAGGA
130 CC-GGTGACAACCTAGGA
351594 CTCCGTTCTA
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
154 4 0.03
155 119 0.96
156 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (155 bp):
GAAAAATTATGAAAATGCCCTTAGGGGAGACCTTTGATGTAAAAACACCTCATACCCCTAAAGGA
CTAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAAC
CGGTGACAACCTAGGAGTTAAATTT
Found at i:351636 original size:155 final size:154
Alignment explanation
Indices: 351294--351638 Score: 363
Period size: 155 Copynumber: 2.2 Consensus size: 154
351284 AAAGTTTAAG
* * *
351294 AAAAATTATGAAAATGCCCTTAGGGGATACCTTTGATGTAAAAGCGCCTCATACCCCTAAATGAC
1 AAAAATTATGAAAATGCCCTTA-GGGATACCTTTGATGTAAAAACACCTCATACCCCTAAAGGAC
* * * * ** *
351359 TAAAAAAGGATTATAAATGGGATGGACCTATCCTAAATACCCATATTCGGCATAAAAGTGAAATC
65 TAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAACC
** * *
351424 GGTGATGACCTAGGAGTTAAATTTG
130 GGTGACAACCTAGGAGCTAAATTTA
* * * * *
351449 AAAAATTATGAAAATGCCCTTAGGTGAGACCTTTGATGTAAAAATACTTGATACCCCTAAAGGAT
1 AAAAATTATGAAAATGCCCTTAGG-GATACCTTTGATGTAAAAACACCTCATACCCCTAAAGGAC
* *
351514 TTAAAAAGGTTTAGAAACGGAATGAACCTATCCTAAATACCCACT-TTCGGCATAAAA-CCAAAC
65 TAAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCA-TATTCGGCATAAAAGCCAAAC
***
351577 CTGGTGACAACCTAGGA-CTCCGTTCTA
129 C-GGTGACAACCTAGGAGCTAAATT-TA
** * *
351604 AAAAATTACAAAAATGCTCATAGAGGATACCTTTG
1 AAAAATTATGAAAATGCCCTTAG-GGATACCTTTG
351639 TCGTGAAAGT
Statistics
Matches: 156, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
154 9 0.06
155 145 0.93
156 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (154 bp):
AAAAATTATGAAAATGCCCTTAGGGATACCTTTGATGTAAAAACACCTCATACCCCTAAAGGACT
AAAAAAGGATTAGAAACGGAATGAACCTATCCTAAATACCCATATTCGGCATAAAAGCCAAACCG
GTGACAACCTAGGAGCTAAATTTA
Found at i:351694 original size:155 final size:151
Alignment explanation
Indices: 351535--352441 Score: 866
Period size: 151 Copynumber: 5.9 Consensus size: 151
351525 TAGAAACGGA
* * * * **
351535 ATGAACCTATCCTAAATACCCACTTTCGGCATAAAACCAAACCTGGTGACAACCTAGGACTCCGT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACT-CGT
* * * * * * *
351600 TCTAAAAAATTACAAAAATGCTCATAGAGGATACCTTTGTCGT-GAAAGTATCCCGGTACCTTTA
65 TCTAAAAAATTACTAAAATGCCCCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGATACCTCTA
* *
351664 AAGGACTTAAAAAAGATATAGCTGAG
128 AAGGACTT-AAAAAGA-AAAGTTGAG
* * * ** *
351690 ATGAACTTATCCTAACTACCCACCTTCTGCATGAAAGTGGACCCAGTGACAACCTAAGACTCGAT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCG-T
* * * * *
351755 TTTGAAAAATTACTAAAATACCCCTAGAGGGATATCTTCAACGTAGAAGTACCCGATACCTCTAA
65 TCTAAAAAATTACTAAAATGCCCCTAGA-GGATACCTTCGACGTAGAAGTACCCGATACCTCTAA
* *
351820 AGGCCTTAAAAAGAAAAGCTGAG
129 AGGACTTAAAAAGAAAAGTTGAG
* * * * * *
351843 ATGAACCTACCCTAACTACCCACCTTTGGCATAAAAACGGATCCAGTGACAACCTAGGACTCGGT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGTT
** * * * * * *
351908 -TAAAAAAAAACCAAAATGCCTCTAAAAGATATCTTCGATGTAGAAGTACCCGATACCTCTAAAG
66 CTAAAAAATTACTAAAATGCCCCTAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAAAG
*
351972 GACTTAAAAGGAAAAGTTGAG
131 GACTTAAAAAGAAAAGTTGAG
* * *
351993 ATGAACCTATCCTAACTACCCACCTTTGGCATAAAAGCGGACCTAGTGACAACCTAGGACTCGAT
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCG-T
* * * * * *
352058 TCT-AAAAATTA-TCGAAATGCCCTTAGGGGATATCTTCAACGTAGAAGTACCTGATACCTCTAA
65 TCTAAAAAATTACT-AAAATGCCCCTAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAA
*
352121 AGGACTTAAAATGAAAAGTTGAG
129 AGGACTTAAAAAGAAAAGTTGAG
* * * *
352144 ATGAGCCTACCCTAACTACCCACCTTCGGCATAAAAGCAGACCC-GATGACAACTTAGGACTTAG
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAG-TGACAACCTAGGAC-TCG
* * * * * * * * *
352208 TTTTGAAAAATTA-TGAAATGCCCTTAGGGGAGACCTTTGACAT-GAAAGTATCTC-ACTAGCC-
64 TTCTAAAAAATTACTAAAATGCCCCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGA-TA-CCT
*
352269 CTAAAGGACTTAAAAAGGATATAGTTGAG
125 CTAAAGGACTTAAAAA-GA-AAAGTTGAG
* * *
352298 ATGGACCTATCCTAACTACCCACCTTC-GCATAAAAACAGACCC-GCTGACAACCTAAGACTCGG
1 ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAG-TGACAACCTAGGACTC-G
* * * *
352361 TTCTAAGAAAATTATTAAAATGCCCCTAGAGGATACCTTCGACGT-GAAAGTATCCTGGTACCCC
64 TTCTAA-AAAATTACTAAAATGCCCCTAGAGGATACCTTCGACGTAG-AAGTA-CCCGATACCTC
352425 TAAAGGACTTAAAAAGA
126 TAAAGGACTTAAAAAGA
352442 TTATAGGTGG
Statistics
Matches: 629, Mismatches: 103, Indels: 41
0.81 0.13 0.05
Matches are distributed among these distances:
150 114 0.18
151 174 0.28
152 32 0.05
153 99 0.16
154 52 0.08
155 141 0.22
156 16 0.03
157 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (151 bp):
ATGAACCTATCCTAACTACCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGACTCGTT
CTAAAAAATTACTAAAATGCCCCTAGAGGATACCTTCGACGTAGAAGTACCCGATACCTCTAAAG
GACTTAAAAAGAAAAGTTGAG
Found at i:354332 original size:14 final size:13
Alignment explanation
Indices: 354313--354376 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 13
354303 TATTAATTCA
*
354313 AAAAATTATACTAT
1 AAAAATTA-AATAT
*
354327 AAAAATT-AATAA
1 AAAAATTAAATAT
354339 AAATAATTAAATTAT
1 AAA-AATTAAA-TAT
*
354354 AAAAATTAAAATTT
1 AAAAATT-AAATAT
354368 AAAAATTAA
1 AAAAATTAA
354377 GATAAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
12 6 0.14
13 6 0.14
14 22 0.52
15 8 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:354334 original size:27 final size:27
Alignment explanation
Indices: 354312--354362 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
354302 ATATTAATTC
*
354312 AAAA-AATTATACTATAAAAATTAATA
1 AAAATAATTAAACTATAAAAATTAATA
*
354338 AAAATAATTAAATTATAAAAATTAA
1 AAAATAATTAAACTATAAAAATTAA
354363 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATAATTAAACTATAAAAATTAATA
Found at i:354780 original size:166 final size:164
Alignment explanation
Indices: 354608--355015 Score: 385
Period size: 166 Copynumber: 2.4 Consensus size: 164
354598 TTTTAAATCG
* * ** * *
354608 AAGAAAATCTTTTAAAAAATATTTATGGAGTAGAAAACT-TGATTTTTCGGGAAAA-AGG-TATT
1 AAGAAAATCTTTCAAAAAA-ATTGACAGAGTAGAAAACTCTG-TTTTTC--AAAAAGAGGAAATT
* * * *
354670 TCGAAGAAAAAAAATCTAAAACATATGAAAATAAATTAATTTTTTAAAAATAATTTAATA-GGAA
62 T-GAAGAAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATATGAAA
* *
354734 TGAAATTATGATATTTGATGAATTTTAAAAATTAAAAACC
126 T-AAATAATAATATTTGATGAATTTTAAAAATTAAAAACC
* ** * *
354774 AAGAAAAATCCTTCCGAAAAATTGGCAGAGTAGAAAACTCTGTTTTTCAAAAAGAGGAAAATTTT
1 AAG-AAAATCTTTCAAAAAAATTGACAGAGTAGAAAACTCTGTTTTTCAAAAAGAGG-AAATTTG
* * * **
354839 AAGGAAAAAATTCAAAAACACATGAAAATGAATGAATTTTTTAAAAATGGTTTAATATGAAATAA
64 AAGAAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATATGAAATAA
*
354904 ATAATAATATTTGATGAGTTTTAAAAATTAAAAACC
129 ATAATAATATTTGATGAATTTTAAAAATTAAAAACC
* * * * * * *
354940 ATAAAAAATCTTCCTGAAAAAATTTAC-GAAGAAAAAAACTCTGTTTTTCAAAAATAGGAAAATT
1 A-AGAAAATCTTTC-AAAAAAATTGACAG-AGTAGAAAACTCTGTTTTTCAAAAAGAGG-AAATT
* *
355004 TCAAGGAAAAAA
62 TGAAGAAAAAAA
355016 GAAAACATTC
Statistics
Matches: 199, Mismatches: 34, Indels: 17
0.80 0.14 0.07
Matches are distributed among these distances:
164 4 0.02
165 3 0.02
166 118 0.59
167 74 0.37
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (164 bp):
AAGAAAATCTTTCAAAAAAATTGACAGAGTAGAAAACTCTGTTTTTCAAAAAGAGGAAATTTGAA
GAAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATATGAAATAAAT
AATAATATTTGATGAATTTTAAAAATTAAAAACC
Found at i:355012 original size:167 final size:166
Alignment explanation
Indices: 354667--355015 Score: 454
Period size: 166 Copynumber: 2.1 Consensus size: 166
354657 GGAAAAAGGT
* * * * *
354667 ATTTCGAAGAAAAAAAATCTAAAACATATGAAAATAAATTAATTTTTTAAAAATAATTTAATAGG
1 ATTTC-AAGGAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATAGA
* *
354732 AATGAAATTATGATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATT
65 AATGAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATT
* * *
354797 GGCAGAGTAGAAAACTCTGTTTTTCAAAAAGAGGAAA
130 GACAGAGAAAAAAACTCTGTTTTTCAAAAAGAGGAAA
* * * **
354834 ATTTTAAGGAAAAAATTCAAAAACACATGAAAATGAATGAATTTTTTAAAAATGGTTTAATATGA
1 ATTTCAAGGAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATA-GA
*
354899 AAT-AAATAATAATATTTGATGAGTTTTAAAAATTAAAAACCATA-AAAAAT-CTTCCTGAAAAA
65 AATGAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA-AGAAAAATCCTTCC-G-AAAA
* *
354961 ATTTAC-GAAGAAAAAAACTCTGTTTTTCAAAAATAGGAAA
127 ATTGACAG-AGAAAAAAACTCTGTTTTTCAAAAAGAGGAAA
355001 ATTTCAAGGAAAAAA
1 ATTTCAAGGAAAAAA
355016 GAAAACATTC
Statistics
Matches: 158, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
165 5 0.03
166 93 0.59
167 60 0.38
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (166 bp):
ATTTCAAGGAAAAAAATCAAAAACACATGAAAATAAATGAATTTTTTAAAAATAATTTAATAGAA
ATGAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATTG
ACAGAGAAAAAAACTCTGTTTTTCAAAAAGAGGAAA
Found at i:355066 original size:167 final size:163
Alignment explanation
Indices: 354678--355091 Score: 431
Period size: 166 Copynumber: 2.5 Consensus size: 163
354668 TTTCGAAGAA
* * * * * * * *
354678 AAAAAATCTAAAACATATGAAAATAAATTAATTTTTTAAAAATAATTTAATAGGAATGAAATTAT
1 AAAAAAT-AAAAACACATGAAAATGAATGAATTTTTGAAAAATGATTTAATATGAAT-AAATAAT
* * * *
354743 GATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATTGGCAGAGTAGA
64 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATTGACAGAGAAAA
*
354808 AAACTCTGTTTTTCAAAAAGAGGAAAATTTTAAGG
129 AAACTCTGTTTTTCAAAAAGAGGAAAATTTCAAGG
* *
354843 AAAAAATTCAAAAACACATGAAAATGAATGAATTTTTTAAAAATGGTTTAATATGAAATAAATAA
1 AAAAAA-T-AAAAACACATGAAAATGAATGAATTTTTGAAAAATGATTTAATATG-AATAAATAA
* *
354908 TAATATTTGATGAGTTTTAAAAATTAAAAACCATA-AAAAAT-CTTCCTGAAAAAATTTAC-GAA
63 TAATATTTGATGAATTTTAAAAATTAAAAACCA-AGAAAAATCCTTCC-G-AAAAATTGACAG-A
*
354970 GAAAAAAACTCTGTTTTTCAAAAATAGGAAAATTTCAAGG
124 GAAAAAAACTCTGTTTTTCAAAAAGAGGAAAATTTCAAGG
* * *** * * * * *
355010 AAAAAA-GAAAACATTCATGACAATTTTGTGAGTTTTTGGAAACTGATTTTATATGAATTAATAA
1 AAAAAATAAAAACA--CATGA-AAATGAATGAATTTTTGAAAAATGATTTAATATGAATAAATAA
*
355074 TAATATTTGAAGAATTTT
63 TAATATTTGATGAATTTT
355092 GATGTATAAA
Statistics
Matches: 210, Mismatches: 30, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
164 6 0.03
165 11 0.05
166 114 0.54
167 79 0.38
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.32
Consensus pattern (163 bp):
AAAAAATAAAAACACATGAAAATGAATGAATTTTTGAAAAATGATTTAATATGAATAAATAATAA
TATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTTCCGAAAAATTGACAGAGAAAAAA
ACTCTGTTTTTCAAAAAGAGGAAAATTTCAAGG
Found at i:356229 original size:13 final size:13
Alignment explanation
Indices: 356211--356236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
356201 TACAGCAAGT
356211 ATGTATCGATACA
1 ATGTATCGATACA
356224 ATGTATCGATACA
1 ATGTATCGATACA
356237 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:358487 original size:21 final size:21
Alignment explanation
Indices: 358454--358498 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
358444 TTGCAAGTTG
*
358454 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
358476 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
358496 AAA
1 AAA
358499 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:360322 original size:15 final size:15
Alignment explanation
Indices: 360302--360340 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
360292 TAAAAATGTC
*
360302 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
360317 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
360332 CCAAATGAA
1 CAAAATGAA
360341 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:362428 original size:20 final size:20
Alignment explanation
Indices: 362349--362428 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
362339 AATGTCCAAA
*
362349 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
362369 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
362394 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
362414 TTGTATCGATACATT
1 ATGTATCGATACATT
362429 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:362432 original size:13 final size:13
Alignment explanation
Indices: 362414--362452 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
362404 ACATTTTTCT
362414 TTGTATCGATACA
1 TTGTATCGATACA
362427 TTGTATCGATACA
1 TTGTATCGATACA
*
362440 CTGTATCGATACA
1 TTGTATCGATACA
362453 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:362597 original size:21 final size:21
Alignment explanation
Indices: 362573--362619 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
362563 AAATCTTTTG
362573 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
362594 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
362614 CAAAAT
1 CAAAAT
362620 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:362616 original size:20 final size:19
Alignment explanation
Indices: 362575--362617 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
362565 ATCTTTTGCA
362575 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
362595 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
362615 AAA
1 AAA
362618 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:363699 original size:20 final size:19
Alignment explanation
Indices: 363644--363699 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
363634 AAAACCCTTA
*
363644 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
363664 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
363684 AATGTATCGATACATG
1 AAAGTATCGATACATG
363700 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:363776 original size:13 final size:13
Alignment explanation
Indices: 363758--363783 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
363748 TACAGCAAGT
363758 ATGTATCGATACA
1 ATGTATCGATACA
363771 ATGTATCGATACA
1 ATGTATCGATACA
363784 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:365758 original size:50 final size:51
Alignment explanation
Indices: 365683--365799 Score: 173
Period size: 50 Copynumber: 2.3 Consensus size: 51
365673 TTTCACAATT
* * *
365683 TGTATCGATACATCCTTCATTGTATCGATACATTTTAGGTTTT-ACCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTAACCCAGA
* * *
365733 TGTATCAATACATTTTTCATTGTATCGATACATTCTAGGTTTTAACCCATA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTAACCCAGA
365784 TGTATCGATACATTCT
1 TGTATCGATACATTCT
365800 AGGTTTTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 39 0.67
51 19 0.33
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (51 bp):
TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTAACCCAGA
Found at i:365788 original size:31 final size:31
Alignment explanation
Indices: 365753--365828 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
365743 CATTTTTCAT
365753 TGTATCGATACATTCTAGGTTTTAACCCATA
1 TGTATCGATACATTCTAGGTTTTAACCCATA
365784 TGTATCGATACATTCTAGGTTTTAACCCATA
1 TGTATCGATACATTCTAGGTTTTAACCCATA
365815 TGTATCGATACATT
1 TGTATCGATACATT
365829 TTTCAATGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (31 bp):
TGTATCGATACATTCTAGGTTTTAACCCATA
Found at i:368334 original size:79 final size:78
Alignment explanation
Indices: 368201--368904 Score: 620
Period size: 79 Copynumber: 9.0 Consensus size: 78
368191 AATTCATGTT
* ** * * * * * *
368201 TTTTATTTCTAAAATACTGATTACCCACCATCGAGGATAC-CCTAAACCCGTTATTTTTGAAGGG
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTC-AACCCCATTATTTTTGAGGGG
368265 ATACTCCAACCCCAG
65 ATACTCCAACCCC-G
* * * * *
368280 TTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTTCAACCCTATTATTTTTTAGGGGA
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGGA
368345 TACTCCAACCCCG
66 TACTCCAACCCCG
* * * *
368358 ATTTTCTTT-TGAGAACACCGATTTTCCACAATCGGGGATAC-TCTAACCCCATTA-TTTCGAGG
1 -TTTTATTTCT-AAAACACTGATTTTCCACAATCGGGGATACTTC-AACCCCATTATTTTTGAGG
*
368420 GGATACTCCAACCCTGG
63 GGATACTCCAACCC-CG
** * * * * *
368437 TTTTATTTCTAAAACACAAATTTTCCACCATCGTGGATACTTCAACCCCATTGTTTTTAAGGGTA
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGGA
*
368502 TACTCCAACCTCG
66 TACTCCAACCCCG
* ** * ** * ***
368515 ATTTTATTTCCAAAACACCAATTTTTCACAATCGAAGATACTCCAACCTTGTTATTTTTGAGGGG
1 -TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGG
* *
368580 ATACTCTAACCTCGG
65 ATACTCCAACC-CCG
** * **
368595 TTTTATTTCTAAAACACCAATTTTCCACTATCGGGGATAC-TCTAACCCCATTATTTCCGAGGGG
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTC-AACCCCATTATTTTTGAGGGG
*
368659 ATACTCCAACCCTG
65 ATACTCCAACCCCG
* * *
368673 ATTTTATTTCCAAAACA-TCGATTTTCCACAATCTGGGATAC-TCTAACCCCATTATTTTCGAGG
1 -TTTTATTTCTAAAACACT-GATTTTCCACAATCGGGGATACTTC-AACCCCATTATTTTTGAGG
368736 GTG-TACT-CAACCCCGG
63 G-GATACTCCAACCCC-G
* * * * *
368752 CTTTATTTCTAAAACATTGATTTTTCACAATCGAGGATACTCCAACCCCATTATTTTTGA-GGGA
1 TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGGA
* **
368816 TACTTCAACCCTAA
66 TACTCCAACCC-CG
* * * * * * *
368830 TTTTATTTCTAAAACA-TCGATTTTTCACCATCAGGGATACTCCAACCTCGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACACT-GATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGG
368894 ATACTCCAACC
65 ATACTCCAACC
368905 TCGATTTTGT
Statistics
Matches: 518, Mismatches: 85, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
76 1 0.00
77 7 0.01
78 181 0.35
79 326 0.63
80 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
TTTTATTTCTAAAACACTGATTTTCCACAATCGGGGATACTTCAACCCCATTATTTTTGAGGGGA
TACTCCAACCCCG
Found at i:368620 original size:236 final size:233
Alignment explanation
Indices: 368201--368917 Score: 811
Period size: 236 Copynumber: 3.0 Consensus size: 233
368191 AATTCATGTT
* ** * * * *
368201 TTTTATTTCTAAAATACTGATTACCCACCATCGAGGATACCCTAAACCCGTTATTTTTGAAGGG-
1 TTTTATTTCTAAAACAC-GATTTTCCACCATCGTGGATACTCTAACCCCATTATTTTT-AAGGGT
* * * * *
368265 ATACTCCAACCCCAGTTTTATTTCTAAAATACTGATTTTTCACCATCGGGGATACTTCAACCCTA
64 ATACTCCAACCCGA-TTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTCCAACCCTA
* * * *
368330 TTATTTTTTAGGGGATACTCCAACCCCGATTTTCTTT-TGAGAACACCGATTTTCCACAATCGGG
128 TTATTTTTGAGGGGATACTCTAA-CCCGATTTTATTTCT-AAAACACCGATTTTCCACAATCGGG
*
368394 GATACTCTAACCCCATTATTTCGAGGGGATACTCCAACCCTGG
191 GATACTCTAACCCCATTATTTCGAGGGGATACTCCAACCCTGA
* *
368437 TTTTATTTCTAAAACACAAATTTTCCACCATCGTGGATACT-TCAACCCCATTGTTTTTAAGGGT
1 TTTTATTTCTAAAACAC-GATTTTCCACCATCGTGGATACTCT-AACCCCATTATTTTTAAGGGT
* ** * * *
368501 ATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAAGATACTCCAACCTTG
64 ATACTCCAACC-CGATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTCCAACCCTA
* * *
368566 TTATTTTTGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACTATCGGGG
128 TTATTTTTGAGGGGATACTCTAACC-CGATTTTATTTCTAAAACACCGATTTTCCACAATCGGGG
368631 ATACTCTAACCCCATTATTTCCGAGGGGATACTCCAACCCTGA
192 ATACTCTAACCCCATTATTT-CGAGGGGATACTCCAACCCTGA
* * **
368674 TTTTATTTCCAAAACATCGATTTTCCACAATC-TGGGATACTCTAACCCCATTATTTTCGAGGGT
1 TTTTATTTCTAAAACA-CGATTTTCCACCATCGT-GGATACTCTAACCCCATTATTTTTAAGGGT
* ** * *
368738 GTACT-CAACCCCGGCTTTATTTCTAAAACATTGATTTTTCACAATCGAGGATACTCCAACCCCA
64 ATACTCCAA-CCCGATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTCCAACCCTA
* * * * *
368802 TTATTTTTGA-GGGATACT-TCAACCCTAATTTTATTTCTAAAACATCGATTTTTCACCATCAGG
128 TTATTTTTGAGGGGATACTCT-AACCC-GATTTTATTTCTAAAACACCGATTTTCCACAATCGGG
* * *
368865 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAA-CCTCGA
191 GATACTCTAACCCCATTA-TTTCGAGGGGATACTCCAACCCT-GA
*
368909 TTTTGTTTC
1 TTTTATTTC
368918 CCAAATATTG
Statistics
Matches: 410, Mismatches: 57, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
234 5 0.01
235 91 0.22
236 230 0.56
237 82 0.20
238 2 0.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (233 bp):
TTTTATTTCTAAAACACGATTTTCCACCATCGTGGATACTCTAACCCCATTATTTTTAAGGGTAT
ACTCCAACCCGATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTCCAACCCTATTA
TTTTTGAGGGGATACTCTAACCCGATTTTATTTCTAAAACACCGATTTTCCACAATCGGGGATAC
TCTAACCCCATTATTTCGAGGGGATACTCCAACCCTGA
Found at i:371018 original size:4 final size:4
Alignment explanation
Indices: 371009--371046 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
370999 TTTGAGGTGC
371009 TTAT TTAT TTAT TTAT TCT-T TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TT
371047 TGTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.03
4 30 0.94
5 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:371867 original size:19 final size:19
Alignment explanation
Indices: 371843--371905 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
371833 AAACTATAAC
371843 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
371862 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
371875 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
371894 TGTATCGATACA
1 TGTATCGATACA
371906 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:371880 original size:13 final size:13
Alignment explanation
Indices: 371862--371919 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
371852 ACATAAGTGT
371862 TGTATCGATACAA
1 TGTATCGATACAA
371875 TGTATCGATACATAA
1 TGTATCGATAC--AA
371890 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
371907 TGTATCGCTACAA
1 TGTATCGATACAA
371920 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:371884 original size:32 final size:32
Alignment explanation
Indices: 371843--371918 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
371833 AAACTATAAC
371843 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
371875 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
371907 TGTATCGCTACA
1 TGTATCGATACA
371919 AAGCTACTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:371976 original size:13 final size:14
Alignment explanation
Indices: 371958--371986 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
371948 ATTACTCAAA
371958 TGTATCG-ATACAT
1 TGTATCGAATACAT
371971 TGTATCGAATACAT
1 TGTATCGAATACAT
371985 TG
1 TG
371987 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (14 bp):
TGTATCGAATACAT
Found at i:377411 original size:33 final size:33
Alignment explanation
Indices: 377374--377440 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
377364 TTCAACGATT
377374 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
377407 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
377440 T
1 T
377441 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:377412 original size:13 final size:13
Alignment explanation
Indices: 377394--377418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377384 CATAAAATGT
377394 TGTATCGATACAA
1 TGTATCGATACAA
377407 TGTATCGATACA
1 TGTATCGATACA
377419 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:377502 original size:13 final size:13
Alignment explanation
Indices: 377484--377508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377474 ATTACTCACA
377484 TGTATCGATACAT
1 TGTATCGATACAT
377497 TGTATCGATACA
1 TGTATCGATACA
377509 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:377573 original size:52 final size:52
Alignment explanation
Indices: 377517--377637 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
377507 CACTGATCTT
*
377517 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
377569 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
377621 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
377638 TAACTCTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:381840 original size:81 final size:81
Alignment explanation
Indices: 381676--381913 Score: 191
Period size: 81 Copynumber: 2.9 Consensus size: 81
381666 ACAAGTTAAG
* * *
381676 GGGGTTTGACTAGGGCAAAATTGATAAAGTCAACAAGTTAGAGGGTTGGCCACGACAAAACAGAT
1 GGGG-TTGACTAGGGCAAAATCGATAAAGTCAACAAGTTAAAGGGTTGGCAACGACAAAACAGAT
*
381741 AAAGCCAATAACAGAGA
65 AAAGCCAACAACAGAGA
* * * *
381758 GGGGTTGACTAGGGCAAAATCGATAAAGTCAATCGA-TTAAAGGGTTGGTTAAGGA-AAAATAGA
1 GGGGTTGACTAGGGCAAAATCGATAAAGTCAA-CAAGTTAAAGGGTTGG-CAACGACAAAACAGA
* ****
381821 TAAAGTCAACAGGTTAGA
64 TAAAGCCAACAACAGAGA
* * * **
381839 GGGGTTCACTAAGGTG-AAACT-AATAAAGTCAACTAA-TTAAAGGGGTTGGGCAGTG-CAAAAC
1 GGGGTTGACT-AGG-GCAAAATCGATAAAGTCAAC-AAGTTAAA-GGGTT-GGCAACGACAAAAC
*
381900 AAATAAAGCCAACA
61 AGATAAAGCCAACA
381914 GATTTAATGG
Statistics
Matches: 125, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
80 1 0.01
81 82 0.66
82 39 0.31
83 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (81 bp):
GGGGTTGACTAGGGCAAAATCGATAAAGTCAACAAGTTAAAGGGTTGGCAACGACAAAACAGATA
AAGCCAACAACAGAGA
Found at i:381979 original size:82 final size:81
Alignment explanation
Indices: 381780--381981 Score: 212
Period size: 82 Copynumber: 2.5 Consensus size: 81
381770 GGCAAAATCG
** * * * * * *
381780 ATAAAGTCAATCGATTAAAGGGTTGGTTAAGGAAAAATAGATAAAGTCAACAGGTTAGAGGGGTT
1 ATAAAGTCAATTAATTAAAGGGTTGGCTAGGGCAAAACAAATAAAGCCAACAGGTTAGAGGGGTT
381845 CACTAAGGTGAAACTA
66 CACTAAGGTGAAACTA
* * * *
381861 ATAAAGTCAACTAATTAAAGGGGTTGGGC-AGTGCAAAACAAATAAAGCCAACAGATTTA-ATGG
1 ATAAAGTCAATTAATTAAA-GGGTT-GGCTAGGGCAAAACAAATAAAGCCAACAG-GTTAGAGGG
* *
381924 GTTGACTCAGGTGAATAC-A
63 GTTCACTAAGGTGAA-ACTA
381943 ATAAAGTCAATTAATTAGAAGGGTTGGCTAGGGCAAAAC
1 ATAAAGTCAATTAATTA-AAGGGTTGGCTAGGGCAAAAC
381982 TGATAAAACT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
81 19 0.19
82 71 0.72
83 9 0.09
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (81 bp):
ATAAAGTCAATTAATTAAAGGGTTGGCTAGGGCAAAACAAATAAAGCCAACAGGTTAGAGGGGTT
CACTAAGGTGAAACTA
Found at i:381988 original size:41 final size:40
Alignment explanation
Indices: 381685--381988 Score: 133
Period size: 41 Copynumber: 7.5 Consensus size: 40
381675 GGGGGTTTGA
*
381685 CTAGGGCAAAATTGATAAAGTCAACAAGTTAG-AGGGTTGG
1 CTAGGGCAAAACTGATAAAGTCAACAA-TTAGAAGGGTTGG
* * * * * * * *
381725 CCACGACAAAACAGATAAAGCCAATAA-CAGAGAGGGGTTGA
1 CTAGGGCAAAACTGATAAAGTCAACAATTAGA-A-GGGTTGG
*
381766 CTAGGGCAAAA-TCGATAAAGTCAATCGATTA-AAGGGTTGG
1 CTAGGGCAAAACT-GATAAAGTCAA-CAATTAGAAGGGTTGG
* * * * * **
381806 TTAAGG-AAAAATAGATAAAGTCAACAGGTTAGAGGGGTTCA
1 CTAGGGCAAAACT-GATAAAGTCAACA-ATTAGAAGGGTTGG
* ** *
381847 CTAAGGTGAAACTAATAAAGTCAACTAATTA-AAGGGGTTGGG
1 CTAGGGCAAAACTGATAAAGTCAAC-AATTAGAA-GGGTT-GG
* ** * * *
381889 C-AGTGCAAAACAAATAAAGCCAACAGATTTA-ATGGGTTGA
1 CTAGGGCAAAACTGATAAAGTCAACA-A-TTAGAAGGGTTGG
* * *
381929 CTCAGGTG-AATAC-AATAAAGTCAATTAATTAGAAGGGTTGG
1 CT-AGG-GCAAAACTGATAAAGTCAA-CAATTAGAAGGGTTGG
381970 CTAGGGCAAAACTGATAAA
1 CTAGGGCAAAACTGATAAA
381989 ACTAATAGGT
Statistics
Matches: 192, Mismatches: 50, Indels: 43
0.67 0.18 0.15
Matches are distributed among these distances:
38 2 0.01
39 6 0.03
40 60 0.31
41 103 0.54
42 19 0.10
43 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (40 bp):
CTAGGGCAAAACTGATAAAGTCAACAATTAGAAGGGTTGG
Found at i:382564 original size:20 final size:20
Alignment explanation
Indices: 382539--382615 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
382529 TTTTACCCAG
*
382539 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
382559 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
382579 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
382599 ATGTATTGATACATTTT
1 ATGTATCGATACATTTT
382616 GTCTTTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:385848 original size:41 final size:40
Alignment explanation
Indices: 385739--385850 Score: 102
Period size: 41 Copynumber: 2.8 Consensus size: 40
385729 GACCATGGCA
* * **
385739 AAACTAATAAAGTTAAC-AATTAAAAGGGTTGGCCAAGGT
1 AAACTAATAAAGTCAACTAATTAAAGGGGTTCACCAAGGT
* * ** *
385778 AAAATCAATAAAGCCAA-TAGATTTGAGGGGTTCACTAAGGT
1 AAACT-AATAAAGTCAACTA-ATTAAAGGGGTTCACCAAGGT
385819 GAAACTAATAAAGTCAACTAATTAAAGGGGTT
1 -AAACTAATAAAGTCAACTAATTAAAGGGGTT
385851 GGGCAGTGCA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
39 4 0.07
40 10 0.18
41 35 0.64
42 6 0.11
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (40 bp):
AAACTAATAAAGTCAACTAATTAAAGGGGTTCACCAAGGT
Found at i:385874 original size:82 final size:81
Alignment explanation
Indices: 385739--385935 Score: 247
Period size: 82 Copynumber: 2.4 Consensus size: 81
385729 GACCATGGCA
* * * * *
385739 AAACTAATAAAGTTAAC-AATTAAAAGGGTTGGCCAAGGTAAAATCAATAAAGCCAATAGATTTG
1 AAACTAATAAAGTCAACTAATT-AAAGGGTTGGCCAAGGCAAAACCAATAAAGCCAACAGATTTA
385803 AGGGGTTCACTAAGGTG
65 AGGGGTTCACTAAGGTG
*
385820 AAACTAATAAAGTCAACTAATTAAAGGGGTTGGGC-AGTGCAAAACCAATAAAGCCAACAGATTT
1 AAACTAATAAAGTCAACTAATTAAA-GGGTTGGCCAAG-GCAAAACCAATAAAGCCAACAGATTT
* *
385884 AATGGGTTGACTAAGGTG
64 AAGGGGTTCACTAAGGTG
*
385902 AATAC-AATAAAGTCAATTAATTAGAAGGGTTGGC
1 AA-ACTAATAAAGTCAACTAATTA-AAGGGTTGGC
385936 TAGGGCGAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
81 21 0.21
82 76 0.75
83 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (81 bp):
AAACTAATAAAGTCAACTAATTAAAGGGTTGGCCAAGGCAAAACCAATAAAGCCAACAGATTTAA
GGGGTTCACTAAGGTG
Found at i:385910 original size:41 final size:40
Alignment explanation
Indices: 385764--385913 Score: 110
Period size: 41 Copynumber: 3.6 Consensus size: 40
385754 ACAATTAAAA
* * * * *
385764 GGGTTGGCCAAGGTAAAATCAATAAAGCCAATAGATTTGAG
1 GGGTTGACTAAGGTGAAA-CAATAAAGCCAACAGATTTAAG
* * *
385805 GGGTTCACTAAGGTGAAACTAATAAAGTCAACTA-ATTAAAG
1 GGGTTGACTAAGGTGAAAC-AATAAAGCCAAC-AGATTTAAG
* *
385846 GGGTTGGGC--A-GTGCAAAACCAATAAAGCCAACAGATTTAAT
1 GGGTT-GACTAAGGTG--AAA-CAATAAAGCCAACAGATTTAAG
385887 GGGTTGACTAAGGTGAATACAATAAAG
1 GGGTTGACTAAGGTGAA-ACAATAAAG
385914 TCAATTAATT
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
39 3 0.04
40 5 0.06
41 68 0.81
42 5 0.06
43 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (40 bp):
GGGTTGACTAAGGTGAAACAATAAAGCCAACAGATTTAAG
Found at i:386529 original size:20 final size:20
Alignment explanation
Indices: 386504--386579 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
386494 TTTACCCAGC
*
386504 TGTATCGATATATTTTTCAA
1 TGTATCGATACATTTTTCAA
* * *
386524 TGTATCGATACATGTATGAA
1 TGTATCGATACATTTTTCAA
386544 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAA
*
386564 TGTATTGATACATTTT
1 TGTATCGATACATTTT
386580 ATCTTTTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAA
Found at i:389866 original size:82 final size:81
Alignment explanation
Indices: 389675--390131 Score: 208
Period size: 81 Copynumber: 5.6 Consensus size: 81
389665 TCGTTGTGAA
* * * * * *
389675 AATAGGTTAGAAGGGTTGACCATGGCAAAACTAATAAAGTTAACAATTAAAAGGGTTGGCCAAGG
1 AATAGGTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATCAACAATTAAAAGGATTAGCCAAGG
* *
389740 TAAAATCAATAAAGCC
66 CAAAATCAATAAAACC
* * * * * *
389756 AATAGATTTGAGGGGTTGACCAATGCAAAA-TCGATAAAATCAACCAATTAAAAGGATTAGCGAG
1 AATAGGTTAGAGGGGTTGACCAAGGCAAAACT-AATAAAATCAA-CAATTAAAAGGATTAGCCAA
** *
389820 GGCAAAATTGATAAAACT
64 GGCAAAATCAATAAAACC
* * * ** * *
389838 TATAGGTTAGAGGGGTTGACCAGGGCAAATC-AATAATGTCAACTAATT-AGAGGAGTTGGCCAA
1 AATAGGTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATCAAC-AATTAAAAGGA-TTAGCCAA
* * * * *
389901 TGCGAAACCGATAAAGCC
64 GGCAAAATCAATAAAACC
* ** ** * * * * * * *
389919 AACAAATTTA-AGGGGTTGATTAGGGAAAAACCAATAAAGTTAACTATTAAAAGGGTTAGCCAAG
1 AA-TAGGTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATCAACAATTAAAAGGATTAGCCAAG
* **
389983 GCAAAA-CTGATAAAGTC
65 GCAAAATC-AATAAAACC
* * * * * * * **
390000 AACAGATTTA-AGGGGTTGACCAGGGCAAAATTGAT-AAAGCTAACCAATTAGAAGGATTAGTTA
1 AATAG-GTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATC-AA-CAATTAAAAGGATTAGCCA
* *
390063 GGGCAAAATCAATAAAGCC
63 AGGCAAAATCAATAAAACC
* * * *** * *
390082 AATAAGTTAGAGAGGTAGACTTGGGTAAAACTAATAAAGTCAACCAATTA
1 AATAGGTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATCAA-CAATTA
390132 GAGAGGTTAA
Statistics
Matches: 277, Mismatches: 84, Indels: 29
0.71 0.22 0.07
Matches are distributed among these distances:
80 11 0.04
81 133 0.48
82 129 0.47
83 4 0.01
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.22
Consensus pattern (81 bp):
AATAGGTTAGAGGGGTTGACCAAGGCAAAACTAATAAAATCAACAATTAAAAGGATTAGCCAAGG
CAAAATCAATAAAACC
Found at i:390028 original size:41 final size:40
Alignment explanation
Indices: 389687--390038 Score: 133
Period size: 41 Copynumber: 8.7 Consensus size: 40
389677 TAGGTTAGAA
* * * * *
389687 GGGTTGACCATGGCAAAACTAATAAAGTTAACAATTAAAA
1 GGGTTGACCAAGGCAAAACTGATAAAGTCAACAATTTAAG
* * * * * *
389727 GGGTTGGCCAAGGTAAAA-TCAATAAAGCCAATAGATTTGAG
1 GGGTTGACCAAGGCAAAACT-GATAAAGTCAACA-ATTTAAG
* * * *
389768 GGGTTGACCAATGCAAAA-TCGATAAAATCAACCAATTAAAA
1 GGGTTGACCAAGGCAAAACT-GATAAAGTCAA-CAATTTAAG
* * * * * * * **
389809 GGATT-AGCGAGGGCAAAATTGATAAA-ACTTATAGGTTAGAG
1 GGGTTGA-CCAAGGCAAAACTGATAAAGTC-AACAATTTA-AG
* * * *
389850 GGGTTGACCAGGGCAAATC-AATAATGTCAACTAA-TTAGAG
1 GGGTTGACCAAGGCAAAACTGATAAAGTCAAC-AATTTA-AG
* * * * * *
389890 GAGTTGGCCAATGCGAAACCGATAAAGCCAACAAATTTAAG
1 GGGTTGACCAAGGCAAAACTGATAAAGTCAAC-AATTTAAG
** * * ** * * * *
389931 GGGTTGATTAGGGAAAAACCAATAAAGTTAACTATTAAAA
1 GGGTTGACCAAGGCAAAACTGATAAAGTCAACAATTTAAG
389971 GGGTT-AGCCAAGGCAAAACTGATAAAGTCAACAGATTTAAG
1 GGGTTGA-CCAAGGCAAAACTGATAAAGTCAACA-ATTTAAG
* *
390012 GGGTTGACCAGGGCAAAATTGATAAAG
1 GGGTTGACCAAGGCAAAACTGATAAAG
390039 CTAACCAATT
Statistics
Matches: 221, Mismatches: 76, Indels: 29
0.68 0.23 0.09
Matches are distributed among these distances:
39 2 0.01
40 82 0.37
41 130 0.59
42 7 0.03
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (40 bp):
GGGTTGACCAAGGCAAAACTGATAAAGTCAACAATTTAAG
Found at i:390037 original size:81 final size:81
Alignment explanation
Indices: 389687--390059 Score: 297
Period size: 81 Copynumber: 4.6 Consensus size: 81
389677 TAGGTTAGAA
* * * *
389687 GGGTTGACCATGGCAAAA-CTAATAAAGTTAACAATTAAAAGGGTTGGCCAAGGTAAAA-TCAAT
1 GGGTTGACCAGGGCAAAATC-AATAAAGTTAACAATTAAAAGGGTTAGCCAAGGCAAAACT-GAT
* *
389750 AAAGCCAATAGATTTGAG
64 AAAGCCAACAGATTTAAG
** * * * * * * *
389768 GGGTTGACCAATGCAAAATCGATAAAATCAACCAATTAAAAGGATTAGCGAGGGCAAAATTGATA
1 GGGTTGACCAGGGCAAAATCAATAAAGTTAA-CAATTAAAAGGGTTAGCCAAGGCAAAACTGATA
* ** * *
389833 AAACTTATAG-GTTAGAG
65 AAGCCAACAGATTTA-AG
* * * * * * *
389850 GGGTTGACCAGGGC-AAATCAATAATGTCAACTAATT-AGAGGAGTTGGCCAATGCGAAACCGAT
1 GGGTTGACCAGGGCAAAATCAATAAAGTTAAC-AATTAAAAGG-GTTAGCCAAGGCAAAACTGAT
*
389913 AAAGCCAACAAATTTAAG
64 AAAGCCAACAGATTTAAG
** * * *
389931 GGGTTGATTAGGGAAAAACCAATAAAGTTAACTATTAAAAGGGTTAGCCAAGGCAAAACTGATAA
1 GGGTTGACCAGGGCAAAATCAATAAAGTTAACAATTAAAAGGGTTAGCCAAGGCAAAACTGATAA
*
389996 AGTCAACAGATTTAAG
66 AGCCAACAGATTTAAG
** * * *
390012 GGGTTGACCAGGGCAAAATTGATAAAGCTAACCAATTAGAAGGATTAG
1 GGGTTGACCAGGGCAAAATCAATAAAGTTAA-CAATTAAAAGGGTTAG
390060 TTAGGGCAAA
Statistics
Matches: 222, Mismatches: 60, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
80 5 0.02
81 135 0.61
82 81 0.36
83 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (81 bp):
GGGTTGACCAGGGCAAAATCAATAAAGTTAACAATTAAAAGGGTTAGCCAAGGCAAAACTGATAA
AGCCAACAGATTTAAG
Found at i:392136 original size:80 final size:79
Alignment explanation
Indices: 391923--392385 Score: 429
Period size: 80 Copynumber: 5.8 Consensus size: 79
391913 TTTAAAAGTG
* * * *
391923 GGGTTGGAGTATCCTTTCAGAAGAA-A-GGGGTTAGAGTATCCCCGATGATGAAAAATTTGATAT
1 GGGTTGGAGTATCCTCTCA-AAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATA-
* *
391986 TTTTGGAAGTAAAAAT
64 TTTTGGAAATAAAAAA
* * * * * * * * * *
392002 GAGTTTAGAGTATTCTCTTAGAAATA-ATGAGGTTGGAGTATCCTCGATGATGAAAAATTTGATA
1 G-GGTTGGAGTATCCTCTCA-AAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATA
*
392066 TTTAGGAAATAAAAATA
64 TTTTGGAAATAAAAA-A
* *
392083 GGGTTGGAGTATCTTCTCAAAAAAGATGGGGTTGGAGTATCCCCAATGGTGAAAAA-TTGATATT
1 GGGTTGGAGTATCCTCTCAAAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATATT
392147 TTGGAAATAAAAAA
66 TTGGAAATAAAAAA
* * * * * *** **
392161 GGGTTGGAGTATCCCCTCGAAAATGATAGGGTTAGAATATCCTTGATGGTGAAAAA-TCAATATT
1 GGGTTGGAGTATCCTCTCAAAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATATT
* *
392225 TTGGAAATGAAAAC
66 TTGGAAATAAAAAA
* * * * * * *
392239 GAGGTTGTAGTAACCCCTCGAAAATGATGGGGTTAGAGTATCCCCAATGGTGAAAAAATCGATAT
1 G-GGTTGGAGTATCCTCTCAAAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATAT
392304 TTT-GAAA-AAAATACA
65 TTTGGAAATAAAA-A-A
* *
392319 GGGTTGGAGTATCCCTCTCAAAAAATATGGGGTTAGAGTATCCCCAATGGTGAAAAATCT-ATAT
1 GGGTTGGAGTAT-CCTCTCAAAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATAT
392383 TTT
65 TTT
392386 TTTATGTAAA
Statistics
Matches: 318, Mismatches: 57, Indels: 18
0.81 0.15 0.05
Matches are distributed among these distances:
78 69 0.22
79 94 0.30
80 121 0.38
81 34 0.11
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
GGGTTGGAGTATCCTCTCAAAAAAGATGGGGTTAGAGTATCCCCAATGGTGAAAAATTTGATATT
TTGGAAATAAAAAA
Found at i:392515 original size:98 final size:99
Alignment explanation
Indices: 392336--392533 Score: 353
Period size: 98 Copynumber: 2.0 Consensus size: 99
392326 AGTATCCCTC
**
392336 TCAAAAAATATGGGGTTAGAGTATCCCCAATGGTGAAAAATCTATATTTTTTTATGTAAAAAATT
1 TCAAAAAATATGGGGTTAGAGTATCCCCAATGGTGAAAAATCTATATTTTTTTATCCAAAAAATT
392401 GACGTGAACGAGGATGGTAAAGATATAAAAATAT
66 GACGTGAACGAGGATGGTAAAGATATAAAAATAT
*
392435 TCAAAAAATATGTGGTTAGAGTATCCCCAATGGTGAAAAATCTATA-TTTTTTATCCAAAAAATT
1 TCAAAAAATATGGGGTTAGAGTATCCCCAATGGTGAAAAATCTATATTTTTTTATCCAAAAAATT
*
392499 GACGTGAACGAGGATGGTAAAGATATAAAAGTAT
66 GACGTGAACGAGGATGGTAAAGATATAAAAATAT
392533 T
1 T
392534 TATGCATTGA
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
98 50 0.53
99 45 0.47
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (99 bp):
TCAAAAAATATGGGGTTAGAGTATCCCCAATGGTGAAAAATCTATATTTTTTTATCCAAAAAATT
GACGTGAACGAGGATGGTAAAGATATAAAAATAT
Found at i:393192 original size:50 final size:51
Alignment explanation
Indices: 393133--393244 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
393123 TGAACAGTAC
393133 ATGTATCGATAAATT-T-TGTTTTTTACCTAGATGTATCGATACATTTTTCA
1 ATGTATCGATAAATTCTAT-TTTTTTACCTAGATGTATCGATACATTTTTCA
* *
393183 ATGTATCGATATATTCTATTTTTTTACCTAGATGTATTGATACATTTTTCA
1 ATGTATCGATAAATTCTATTTTTTTACCTAGATGTATCGATACATTTTTCA
393234 ATGTATCGATA
1 ATGTATCGATA
393245 CATCTAGTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 14 0.24
51 43 0.74
52 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (51 bp):
ATGTATCGATAAATTCTATTTTTTTACCTAGATGTATCGATACATTTTTCA
Found at i:398450 original size:51 final size:51
Alignment explanation
Indices: 398386--398482 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
398376 ATTTAGGTCA
**
398386 AAAACCCAAAATGTATCGATAAAATGAAAAATGTATTGATACATTTGTGCT
1 AAAACCCAAAATGTATCGATAAAATGAAAAATGTATCAATACATTTGTGCT
* **
398437 AAAACCCAGAATGTATCGATGTAATGAAAAATGTATCAATACATTT
1 AAAACCCAAAATGTATCGATAAAATGAAAAATGTATCAATACATTT
398483 TCTTTTCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (51 bp):
AAAACCCAAAATGTATCGATAAAATGAAAAATGTATCAATACATTTGTGCT
Found at i:398562 original size:20 final size:21
Alignment explanation
Indices: 398539--398592 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
398529 CATTTCAGAC
*
398539 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCAATGT
398559 ATGTATCGATACATTCAATGT
1 ATGTATCGATACATTCAATGT
*
398580 TTGTATCGATACA
1 ATGTATCGATACA
398593 AATTGTGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCAATGT
Found at i:400470 original size:21 final size:20
Alignment explanation
Indices: 400446--400519 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
400436 TTTTATGATT
400446 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATTAGTGAA
* *
400467 TGTATTGATACATAAGTGAA
1 TGTATCGATACATTAGTGAA
** *
400487 TGTATCGATACATGTCTTAAA
1 TGTATCGATACAT-TAGTGAA
400508 TGTATCGATACA
1 TGTATCGATACA
400520 AAACCATCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 20 0.44
21 25 0.56
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTAGTGAA
Found at i:400486 original size:20 final size:20
Alignment explanation
Indices: 400446--400499 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
400436 TTTTATGATT
*
400446 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
*
400467 TGTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
400487 TGTATCGATACAT
1 TGTATCGATACAT
400500 GTCTTAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:405176 original size:20 final size:20
Alignment explanation
Indices: 405153--405216 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
405143 ACACCTAGAT
405153 GTATCGATACAAATTGCTAA
1 GTATCGATACAAATTGCTAA
405173 GTATCGATAC--ATTG-T-A
1 GTATCGATACAAATTGCTAA
405189 -T-T-GATACAAATTGCTAA
1 GTATCGATACAAATTGCTAA
405206 GTATCGATACA
1 GTATCGATACA
405217 TTATATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 5 0.14
16 2 0.05
17 2 0.05
18 5 0.14
19 1 0.03
20 16 0.43
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACAAATTGCTAA
Found at i:405195 original size:33 final size:33
Alignment explanation
Indices: 405152--405229 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
405142 CACACCTAGA
405152 TGTATCGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCGATACAT
*
405185 TGTATTGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCGATACAT
*
405218 TATATCGATACA
1 TGTATCGATACA
405230 CAATAAAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCGATACAT
Found at i:405820 original size:34 final size:32
Alignment explanation
Indices: 405747--405839 Score: 132
Period size: 34 Copynumber: 2.8 Consensus size: 32
405737 GATTGAGAGA
* *
405747 TTCTATCTTAGCCTTTGAAAAAGATAGGGGAGG
1 TTCTATCTTAGCCTGTG-AAAAGATAGGGAAGG
405780 TTCTATCTTAGCCTGTGAAAAGATAGGGAAAAGG
1 TTCTATCTTAGCCTGTGAAAAGATAGGG--AAGG
*
405814 TTCTATCTTAGCTTGTGAAAAGATAG
1 TTCTATCTTAGCCTGTGAAAAGATAG
405840 AGTTGTAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 11 0.20
33 16 0.29
34 28 0.51
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (32 bp):
TTCTATCTTAGCCTGTGAAAAGATAGGGAAGG
Found at i:406506 original size:19 final size:19
Alignment explanation
Indices: 406479--406533 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
406469 TGGTCACATG
406479 AAGTTTATATTTGTTTAT-A
1 AAGTTTATATTT-TTTATAA
***
406498 TTTTTTATATTTTTTATAA
1 AAGTTTATATTTTTTATAA
406517 AAGTTTATATTTTTTAT
1 AAGTTTATATTTTTTAT
406534 CATACATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
AAGTTTATATTTTTTATAA
Found at i:406533 original size:9 final size:9
Alignment explanation
Indices: 406482--406515 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
406472 TCACATGAAG
406482 TTTATATTT
1 TTTATATTT
406491 GTTTATATTT
1 -TTTATATTT
406501 TTTATATTT
1 TTTATATTT
406510 TTTATA
1 TTTATA
406516 AAAGTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTATATTT
Found at i:406695 original size:21 final size:21
Alignment explanation
Indices: 406671--406713 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
406661 GATGTTTAAA
*
406671 TGATCTTGTATTGTTAATTGT
1 TGATCTTGTATGGTTAATTGT
* *
406692 TGATGTTGTGTGGTTAATTGT
1 TGATCTTGTATGGTTAATTGT
406713 T
1 T
406714 CATGAATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.02, G:0.26, T:0.56
Consensus pattern (21 bp):
TGATCTTGTATGGTTAATTGT
Found at i:407425 original size:40 final size:40
Alignment explanation
Indices: 407381--407504 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
407371 TACTTAATCA
407381 TATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCT
1 TATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCT
* * * * *
407421 TATGCTT-T-CATGAA-TTTATTATCTTAAATGCTAA--T-CA
1 TATGCTTGTACTTGAACTTTCTT-TGTTGAATG--AATGTCCT
407458 TATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCT
1 TATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCT
407498 TATGCTT
1 TATGCTT
407505 TCATGAATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
37 15 0.23
38 14 0.22
39 14 0.22
40 22 0.34
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (40 bp):
TATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCT
Found at i:407502 original size:77 final size:77
Alignment explanation
Indices: 407375--407529 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
407365 TGATTATACT
407375 TAATCATATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCTTATGCTTTCATGAATTTAT
1 TAATCATATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCTTATGCTTTCATGAATTTAT
407440 TATCTTAAATGC
66 TATCTTAAATGC
407452 TAATCATATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCTTATGCTTTCATGAATTTAT
1 TAATCATATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCTTATGCTTTCATGAATTTAT
*
407517 TCTCTTAAATGC
66 TATCTTAAATGC
407529 T
1 T
407530 CTGGTATTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (77 bp):
TAATCATATGCTTGTACTTGAACTTTCTTTGTTGAATGAATGTCCTTATGCTTTCATGAATTTAT
TATCTTAAATGC
Found at i:413169 original size:22 final size:19
Alignment explanation
Indices: 413144--413198 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
413134 GCCAAGGAAA
413144 TGTATCGATACATGCTTGCAAT
1 TGTATCGATACATGC-TG--AT
* *
413166 TGTATTGATACAATTCTGAT
1 TGTATCGATAC-ATGCTGAT
413186 TGTATCGATACAT
1 TGTATCGATACAT
413199 TTTGGGCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
22 12 0.41
23 3 0.10
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGCTGAT
Found at i:416415 original size:19 final size:21
Alignment explanation
Indices: 416373--416424 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
416363 ACACCTAGAC
*
416373 GTATCGATACAT-TATGCTTT
1 GTATCGATACATGTATGCATT
416393 GTATCGATACATGT-T-CATT
1 GTATCGATACATGTATGCATT
416412 GTATCGATACATG
1 GTATCGATACATG
416425 AAACTGGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.53
20 13 0.43
21 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
GTATCGATACATGTATGCATT
Found at i:420324 original size:25 final size:25
Alignment explanation
Indices: 420295--420345 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
420285 AATCTTGGTA
*
420295 AATTTGATGCTAAAAGTGAAGAAGG
1 AATTTAATGCTAAAAGTGAAGAAGG
*
420320 AATTTAATGCTAAAAGTGATGAAGG
1 AATTTAATGCTAAAAGTGAAGAAGG
420345 A
1 A
420346 GTTTTTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (25 bp):
AATTTAATGCTAAAAGTGAAGAAGG
Found at i:421771 original size:242 final size:242
Alignment explanation
Indices: 421346--421823 Score: 911
Period size: 242 Copynumber: 2.0 Consensus size: 242
421336 ATGAATCCTT
*
421346 GTGTCAAGAATTTTCTAAGTTAATGTAGGTGAATTCGAGATGAGCATGATGGGAGAATTAACATT
1 GTGTCAAGAATTTTCTAAGTTAATGTAGGTGAATTCGAGATGAGCATGATGGGAGAACTAACATT
*
421411 CTTTTTGGGGCTTCAAGTGAAGCAAACAAAGGACGGGATCTTCATCAATCAAGCAAAATATACAA
66 CTTTTTGGGGCTTCAAGTGAAGCAAACAAAAGACGGGATCTTCATCAATCAAGCAAAATATACAA
421476 AGCAGCTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATATAAAACACCGATGAGTACTTCA
131 AGCAGCTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATATAAAACACCGATGAGTACTTCA
*
421541 ACAAAGCTTGAAAGGATGAAGGAGGTAATTTTATCGATACCTTTTGA
196 ACAAAGCTTGAAAGGATGAAAGAGGTAATTTTATCGATACCTTTTGA
421588 GTGTCAAGAATTTTCTAAGTTAATGTAGGTGAATTCGAGATGAGCATGATGGGAGAACTAACATT
1 GTGTCAAGAATTTTCTAAGTTAATGTAGGTGAATTCGAGATGAGCATGATGGGAGAACTAACATT
421653 CTTTTTGGGGCTTCAAGTGAAGCAAACAAAAGACGGGATCTTCATCAATCAAGCAAAATATACAA
66 CTTTTTGGGGCTTCAAGTGAAGCAAACAAAAGACGGGATCTTCATCAATCAAGCAAAATATACAA
* *
421718 AGGAGCTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTAAAACACCGATGAGTACTTCA
131 AGCAGCTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATATAAAACACCGATGAGTACTTCA
421783 ACAAAGCTTGAAAGGATGAAAGAGGTAATTTTATCGATACC
196 ACAAAGCTTGAAAGGATGAAAGAGGTAATTTTATCGATACC
421824 AAACTCTATA
Statistics
Matches: 231, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
242 231 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (242 bp):
GTGTCAAGAATTTTCTAAGTTAATGTAGGTGAATTCGAGATGAGCATGATGGGAGAACTAACATT
CTTTTTGGGGCTTCAAGTGAAGCAAACAAAAGACGGGATCTTCATCAATCAAGCAAAATATACAA
AGCAGCTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATATAAAACACCGATGAGTACTTCA
ACAAAGCTTGAAAGGATGAAAGAGGTAATTTTATCGATACCTTTTGA
Found at i:423936 original size:284 final size:284
Alignment explanation
Indices: 423426--423997 Score: 862
Period size: 284 Copynumber: 2.0 Consensus size: 284
423416 CACCTCAAAC
* *
423426 CATTCCTATGGCTCCTCGAATTAAACTACCTTCTCAAAAACACATTCGAGGTGCTTCTTCATCAA
1 CATTCCTATGGCTCCTCGAATGAAACTACCTTCTCAAAAACACACTCGAGGTGCTTCTTCATCAA
*
423491 ATCCCCAAAATCAAACTTTTTGCGAAGGTTGTTTTCAAACTCAAGCCAACCTCGAGCATTTCAAC
66 ATCCCCAAAATCAAACTTTTTGCGAAGGTTGTTTTCAAACTCAAGCCAACCTCGACCATTTCAAC
*** *
423556 CAAACCTATTCCCAATTAGTTGTCCAATCATGTCGCGTAGTCAACATGAAGTTCCTTAGATCCTT
131 CAAACCTATTCCCAATTAGCCATCCAATCATGTCGCGCAGTCAACATGAAGTTCCTTAGATCCTT
* *
423621 TGACTTTGTCTACCTCCCTACTATTGAGATGTTCGGATGGATT-CCTTTTCTCAGCTTAAATATT
196 TGACTTTATCTACCTCCCTACTATTGAGATGTTCGGATGGATTACC-TTTCTCAACTTAAATATT
* *
423685 TTAGTTTGCGAGAACCTAGTCTGAG
260 TTAGTTCGCGAGAACCTAGTCCGAG
* * ** *
423710 CATTCCTATGGCTCCTTGAATGAAACTACCTTCTGAAAAATGCACTCGATGTGCTTCTTCATCAA
1 CATTCCTATGGCTCCTCGAATGAAACTACCTTCTCAAAAACACACTCGAGGTGCTTCTTCATCAA
**
423775 ATCCCCAAAATCAAACTTTCTT-CGAAGGTTGTTTTCGGACTCAAGCCAACCTCGACCATTTCAA
66 ATCCCCAAAATCAAACTTT-TTGCGAAGGTTGTTTTCAAACTCAAGCCAACCTCGACCATTTCAA
** * * *
423839 CCAAACCTATTCCCGGTTGGCCATCCGATCATGTCGCGCAGTCGACATGAAGTTCCTTAGATCCT
130 CCAAACCTATTCCCAATTAGCCATCCAATCATGTCGCGCAGTCAACATGAAGTTCCTTAGATCCT
*
423904 TTGACTTTATCTACCTCCCTACTCA-TGAGATGTTTGGATGGATTACCTTTCTCAACTTAAATAT
195 TTGACTTTATCTACCTCCCTACT-ATTGAGATGTTCGGATGGATTACCTTTCTCAACTTAAATAT
* *
423968 TTTGGTTCGTGAGAACCTAGTCCGAG
259 TTTAGTTCGCGAGAACCTAGTCCGAG
423994 CATT
1 CATT
423998 TCTCAGCAAT
Statistics
Matches: 259, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
284 254 0.98
285 5 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (284 bp):
CATTCCTATGGCTCCTCGAATGAAACTACCTTCTCAAAAACACACTCGAGGTGCTTCTTCATCAA
ATCCCCAAAATCAAACTTTTTGCGAAGGTTGTTTTCAAACTCAAGCCAACCTCGACCATTTCAAC
CAAACCTATTCCCAATTAGCCATCCAATCATGTCGCGCAGTCAACATGAAGTTCCTTAGATCCTT
TGACTTTATCTACCTCCCTACTATTGAGATGTTCGGATGGATTACCTTTCTCAACTTAAATATTT
TAGTTCGCGAGAACCTAGTCCGAG
Found at i:425755 original size:20 final size:19
Alignment explanation
Indices: 425710--425764 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
425700 TGTATTGATA
* * *
425710 CATTATATCGATATATGCT
1 CATTGTATCGATACATACT
425729 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
425748 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
425765 GAAACTGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:427344 original size:20 final size:20
Alignment explanation
Indices: 427319--427397 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
427309 ACTGCCAAGG
427319 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTACT
427339 AAATGTATCGATACATGCTTAC-
1 AAATGTATCGATACA---TTACT
* * *
427361 AATTGTATCAATACATTTCT
1 AAATGTATCGATACATTACT
* *
427381 CATTGTATCGATACATT
1 AAATGTATCGATACATT
427398 CTAGGTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.06
20 30 0.60
22 13 0.26
23 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTACT
Found at i:428712 original size:49 final size:49
Alignment explanation
Indices: 428640--428751 Score: 224
Period size: 49 Copynumber: 2.3 Consensus size: 49
428630 TAATGATACA
428640 ATGTATCGATACATAAGTTTTGTATCGATACATCTGGTATTTTACCCAG
1 ATGTATCGATACATAAGTTTTGTATCGATACATCTGGTATTTTACCCAG
428689 ATGTATCGATACATAAGTTTTGTATCGATACATCTGGTATTTTACCCAG
1 ATGTATCGATACATAAGTTTTGTATCGATACATCTGGTATTTTACCCAG
428738 ATGTATCGATACAT
1 ATGTATCGATACAT
428752 GATTCAATGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (49 bp):
ATGTATCGATACATAAGTTTTGTATCGATACATCTGGTATTTTACCCAG
Found at i:434375 original size:13 final size:14
Alignment explanation
Indices: 434339--434376 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
434329 ACATTTCATG
*
434339 CATTGCATTGCATTT
1 CATTGCATTAC-TTT
434354 CATTGCATTACTTT
1 CATTGCATTACTTT
434368 CA-TGCATTA
1 CATTGCATTA
434377 AAGTTACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 5 0.23
15 10 0.45
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (14 bp):
CATTGCATTACTTT
Found at i:434763 original size:23 final size:23
Alignment explanation
Indices: 434734--434780 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
434724 CAAAGAATAT
434734 AAAAGAGAATGGACAACAACTCA
1 AAAAGAGAATGGACAACAACTCA
* *
434757 AAAAGAGGATGGACAACAGCTCA
1 AAAAGAGAATGGACAACAACTCA
434780 A
1 A
434781 GAGATCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.21, T:0.09
Consensus pattern (23 bp):
AAAAGAGAATGGACAACAACTCA
Found at i:444944 original size:23 final size:23
Alignment explanation
Indices: 444915--444961 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
444905 CAAAGAATAT
*
444915 AAAAGAGAATGGACAGCAGCTCA
1 AAAAGAGAATGAACAGCAGCTCA
* *
444938 AAAAGAGGATGAACAGTAGCTCA
1 AAAAGAGAATGAACAGCAGCTCA
444961 A
1 A
444962 GAGATCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.26, T:0.11
Consensus pattern (23 bp):
AAAAGAGAATGAACAGCAGCTCA
Found at i:447403 original size:21 final size:19
Alignment explanation
Indices: 447379--447431 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
447369 TTCAACAATT
447379 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* * *
447400 TGTATCAATACATAAGTAT
1 TGTATCGATACAAAAGTAA
447419 TGTATCGATACAA
1 TGTATCGATACAA
447432 TGTATCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:447437 original size:13 final size:13
Alignment explanation
Indices: 447419--447444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
447409 ACATAAGTAT
447419 TGTATCGATACAA
1 TGTATCGATACAA
447432 TGTATCGATACAA
1 TGTATCGATACAA
447445 AGTGCCCTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:451958 original size:55 final size:54
Alignment explanation
Indices: 451875--452575 Score: 880
Period size: 55 Copynumber: 12.4 Consensus size: 54
451865 CTCCTTCCGC
*
451875 TTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
451929 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
451984 TTTTCCAGTCTTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
452039 TTTTCCAATCCTTAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452094 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
452155 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452210 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452265 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452326 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGGCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
452381 TTTTCCAGTCCTCAAAGGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452436 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * **
452497 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACAGGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
452552 CTTTTTACTCCTCAATGAGCAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
452576 TACAGTTCAT
Statistics
Matches: 572, Mismatches: 51, Indels: 47
0.85 0.08 0.07
Matches are distributed among these distances:
54 10 0.02
55 400 0.70
56 12 0.02
57 3 0.01
59 3 0.01
61 144 0.25
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:452202 original size:171 final size:171
Alignment explanation
Indices: 451875--452575 Score: 1150
Period size: 171 Copynumber: 4.1 Consensus size: 171
451865 CTCCTTCCGC
* * * *
451875 TTTT-CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
* * * * *
451939 CTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCTTC
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTC
451997 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
130 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452039 TTTTCCAATCCTTAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
452104 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
452169 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
131 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
452210 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
452275 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
*
452340 AAGAGCAGGACACCTTTCAAAGGCCACACAAGTTGGTGGCA
131 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
452381 TTTTCCAGTCCTCAAAGGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
1 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
452446 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
66 CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
* **
452511 AAGAGCAGGACGCCTTTCAAAGCCCACAGGAGTTGGTGGCA
131 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
452552 CTTTT-TACTCCTCAATGAGCAGGA
1 -TTTTCCAGTCCTCAAAGAGCAGGA
452576 TACAGTTCAT
Statistics
Matches: 505, Mismatches: 23, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
164 4 0.01
165 68 0.13
167 1 0.00
171 425 0.84
172 7 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (171 bp):
TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTC
CTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCA
AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:452360 original size:226 final size:220
Alignment explanation
Indices: 451874--452575 Score: 933
Period size: 226 Copynumber: 3.1 Consensus size: 220
451864 TCTCCTTCCG
*
451874 CTTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* *
451939 CTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGC
66 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
* * * * *
452004 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTTAAAGAGCAGGACACCTT
131 AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA-GCCTT
*
452069 TT-AAAGCCCACACAGGTTGGTGGCA
195 TTCAAAGCCCACACAAGTTGGTGGCA
* * * *
452094 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTT
452159 T-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
59 TCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
*
452223 AAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGG
124 AAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGG
452288 ATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
189 A-GC-----CTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
452326 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGGCCACACAAGTTGGTGGCATTTTCCAGTC
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * *
452391 CTCAAAGGGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGC
66 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
** **
452456 AGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
131 AGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA
**
452521 CGCC-TTTCAAAGCCCACAGGAGTTGGTGGCA
190 -GCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
452552 CTTTTTACTCCTCAATGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
452576 TACAGTTCAT
Statistics
Matches: 425, Mismatches: 37, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
220 22 0.05
222 1 0.00
225 3 0.01
226 293 0.69
227 4 0.01
228 1 0.00
230 1 0.00
231 10 0.02
232 90 0.21
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (220 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGAGCCTTT
TCAAAGCCCACACAAGTTGGTGGCA
Found at i:453278 original size:19 final size:19
Alignment explanation
Indices: 453254--453321 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
453244 AATTCAACGA
453254 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
453273 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
453288 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
453305 ATTGTATCAATACATAA
1 TTTGTATCGATACATAA
453322 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:453292 original size:32 final size:32
Alignment explanation
Indices: 453256--453318 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
453246 TTCAACGATT
* *
453256 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
453288 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
453319 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:453293 original size:13 final size:13
Alignment explanation
Indices: 453275--453299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453265 ACATAAGTTT
453275 TGTATCGATACAA
1 TGTATCGATACAA
453288 TGTATCGATACA
1 TGTATCGATACA
453300 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:453379 original size:13 final size:13
Alignment explanation
Indices: 453361--453386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
453351 CATTTTTCTG
453361 TGTATCGATACAT
1 TGTATCGATACAT
453374 TGTATCGATACAT
1 TGTATCGATACAT
453387 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:453380 original size:33 final size:33
Alignment explanation
Indices: 453341--453407 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
453331 GCCAAGGAAA
***
453341 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
453374 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
453407 T
1 T
453408 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:455807 original size:51 final size:53
Alignment explanation
Indices: 455738--456079 Score: 196
Period size: 52 Copynumber: 6.5 Consensus size: 53
455728 AGTTTATCAA
* * * * *
455738 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
455789 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * ** *** * *
455843 TTCTTCACAATCGGGGATACTCCAAC-CCCA-TTAATCAACGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
455901 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * *
455950 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
456003 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
456055 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
456080 CTCGTTATTT
Statistics
Matches: 222, Mismatches: 40, Indels: 57
0.70 0.13 0.18
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 6 0.03
51 35 0.16
52 79 0.36
53 35 0.16
54 29 0.13
55 19 0.09
56 2 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:456063 original size:104 final size:103
Alignment explanation
Indices: 455743--456078 Score: 288
Period size: 104 Copynumber: 3.2 Consensus size: 103
455733 ATCAATTCTC
* * *
455743 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGAGGATACTCCAA-TCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
455807 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * *** * * * ** * *
455848 CACAATCGGGGATACTCCAACCCCA-TTAATCAACGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGAGGATACTCCAATCCGATTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * *
455910 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
* * *
455954 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
456019 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
456059 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
456079 CCTCGTTATT
Statistics
Matches: 175, Mismatches: 40, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
103 5 0.03
104 45 0.26
105 35 0.20
106 19 0.11
107 38 0.22
108 6 0.03
109 27 0.15
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (103 bp):
CACAATCGAGGATACTCCAATCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:456099 original size:28 final size:28
Alignment explanation
Indices: 456063--456139 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
456053 ATTTTTCACA
* * *
456063 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
456091 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
456119 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
456140 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:456108 original size:212 final size:212
Alignment explanation
Indices: 455741--456146 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
455731 TTATCAATTC
* *
455741 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
455806 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
455871 CATTAATCAACGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATC
131 CATTAATCAACGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
455936 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * *
455953 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
456017 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
456080 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCATTA-ATCAACGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
456145 AT
193 AT
456147 TCCCAAAATA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 30 0.17
212 110 0.63
213 35 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CATTAATCAACGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:456206 original size:107 final size:107
Alignment explanation
Indices: 455801--456218 Score: 287
Period size: 107 Copynumber: 3.9 Consensus size: 107
455791 TTCTATAATC
* * * * *
455801 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * * * *
455866 AACCCCATTAATCAACGGGGATACTCCAACCCCGTTATTTCCGA
64 AACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * * *
455910 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
* * * ***** * * ** * *
455973 AATCCTGGT-TTTATTTTCAAAACGCCAATTTTCCTTTA-AT-C--
64 AACCCCGTTATTTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
456014 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
456079 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
456122 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
456186 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
456219 ATTTTTTTTC
Statistics
Matches: 237, Mismatches: 58, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
104 45 0.19
105 24 0.10
106 24 0.10
107 97 0.41
108 30 0.13
109 17 0.07
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:456272 original size:78 final size:79
Alignment explanation
Indices: 456093--456294 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 79
456083 GTTATTTCAT
* * * *
456093 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
456158 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * ** *
456172 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCC-GATTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
456235 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
456250 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
456295 TGTTATTATC
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 8 0.08
78 55 0.53
79 41 0.39
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:458616 original size:30 final size:30
Alignment explanation
Indices: 458453--458628 Score: 104
Period size: 30 Copynumber: 5.6 Consensus size: 30
458443 GTAGCACCCC
* * * *
458453 TTTTAAAGTCCATGACTCTCTAGCACCCTT
1 TTTTTAAGTCCATAACTCTATGGCACCCTT
* * ** *
458483 TTTTTAAGCCCACAACTCCGTGGCATCCC-A
1 TTTTTAAGTCCATAACTCTATGGCA-CCCTT
* * *
458513 TTTTAAAGTCCACAACTCTATGGCATCCTT
1 TTTTTAAGTCCATAACTCTATGGCACCCTT
*
458543 TCCCTTTTAAAGTCCATAACT-TAATGGCACCTTTTTT
1 T---TTTT-AAGTCCATAACTCT-ATGGCACC---CTT
*
458580 CTTTTTAAGTCCATGACTCTATGGCACCCTT
1 -TTTTTAAGTCCATAACTCTATGGCACCCTT
* *
458611 TTTTTAAGCCCACAACTC
1 TTTTTAAGTCCATAACTC
458629 CGTTGGCATC
Statistics
Matches: 111, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
29 2 0.02
30 55 0.50
31 5 0.05
33 4 0.04
34 37 0.33
35 5 0.05
37 2 0.02
38 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36
Consensus pattern (30 bp):
TTTTTAAGTCCATAACTCTATGGCACCCTT
Found at i:458619 original size:128 final size:130
Alignment explanation
Indices: 458452--458743 Score: 453
Period size: 129 Copynumber: 2.3 Consensus size: 130
458442 AGTAGCACCC
* * *
458452 CTTTTAAAGTCCATGACTCTCTAGCACCCTTTTTTTAAGCCCACAACTCCG-TGGCATCCCATTT
1 CTTTTTAAGTCCATGACTCTATGGCACCCTTTTTTTAAGCCCACAACTCCGTTGGCATCCCATTT
* * *
458516 TAAAGTCCACAACTCTATGGCATCCTTTCCCTTTTAAAGTCCATAACTTAATGGCAC-CTTTTTT
66 TAAAGTCCACAACTCTATGGCACCCTTTCCCCTTTAAAGTCCATAACTCAATGGCACACTTTTTT
*
458580 CTTTTTAAGTCCATGACTCTATGGCACCCTTTTTTTAAGCCCACAACTCCGTTGGCATCTCATTT
1 CTTTTTAAGTCCATGACTCTATGGCACCCTTTTTTTAAGCCCACAACTCCGTTGGCATCCCATTT
* * * *
458645 TAAAGTCCACAACTTTGTGGCACCCTTTCCCCTTTAAAGTCCATAACTCGATGGCACATTTTTTT
66 TAAAGTCCACAACTCTATGGCACCCTTTCCCCTTTAAAGTCCATAACTCAATGGCACACTTTTTT
**
458710 CTTTTTAAGTCCATGACTCCGTGGCACCCTTTTT
1 CTTTTTAAGTCCATGACTCTATGGCACCCTTTTT
458744 CTTTTTAAGT
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 48 0.32
129 63 0.42
130 38 0.26
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (130 bp):
CTTTTTAAGTCCATGACTCTATGGCACCCTTTTTTTAAGCCCACAACTCCGTTGGCATCCCATTT
TAAAGTCCACAACTCTATGGCACCCTTTCCCCTTTAAAGTCCATAACTCAATGGCACACTTTTTT
Found at i:458851 original size:33 final size:33
Alignment explanation
Indices: 458513--459008 Score: 332
Period size: 34 Copynumber: 14.9 Consensus size: 33
458503 TGGCATCCCA
** **
458513 TTTTAAAGTCCACAACTCTATGGCATCC-TTTCCC
1 TTTT-AAGTCCACAACTCCGTGGCA-CCTTTTTTC
* ***
458547 TTTTAAAGTCCATAACTTAATGGCACCTTTTTTC
1 TTTT-AAGTCCACAACTCCGTGGCACCTTTTTTC
** ** *
458581 TTTTTAAGTCCATGACTCTATGGCACC--CTTT-
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* * **
458612 TTTTAAGCCCACAACTCCGTTGGCA--TCTCAT-
1 TTTTAAGTCCACAACTCCG-TGGCACCTTTTTTC
* ** ***
458643 TTTAAAGTCCACAACTTTGTGGCACCCTTTCCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCTTTTTTC
* * *
458677 TTTAAAGTCCATAACT-CGATGGCACATTTTTTTC
1 TTTTAAGTCCACAACTCCG-TGGCAC-CTTTTTTC
** *
458711 TTTTTAAGTCCATGACTCCGTGGCACCCTTTTTC
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* * * *
458745 TTTTTAAGTCCATAACTTCGTAGCACCATTTTTC
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* * *
458779 TTTTTCAA-TCCACAACTCTGTGACAGCTTTTTTC
1 -TTTT-AAGTCCACAACTCCGTGGCACCTTTTTTC
*
458813 TTTTTAAGTCCACAACTCCATGGCACCTTTTTTC
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
458847 TTTTAAGTCCACAACTCCGTGGCA-CTTTTTTC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* * * *
458879 TTTTAAAGTCTACAACTCTGTGGCATC-TTTTCC
1 TTTT-AAGTCCACAACTCCGTGGCACCTTTTTTC
*
458912 TTTTAAGTCCACAACTCTGTGGCACC-TTTTTC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* * * *
458944 TTTTTAAGTCAACAACTCCGTAGCACATTTTTCC
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
* *
458978 TTTTAAGTCCACAATTCTGTGGCATCCTTTT
1 TTTTAAGTCCACAACTCCGTGGCA-CCTTTT
459009 CTAAACCCCA
Statistics
Matches: 376, Mismatches: 66, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
30 19 0.05
31 21 0.06
32 40 0.11
33 101 0.27
34 167 0.44
35 26 0.07
36 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (33 bp):
TTTTAAGTCCACAACTCCGTGGCACCTTTTTTC
Found at i:458935 original size:98 final size:97
Alignment explanation
Indices: 458706--459010 Score: 371
Period size: 98 Copynumber: 3.1 Consensus size: 97
458696 TGGCACATTT
** * *
458706 TTTTCTTTTTAAGTCCATGACTCCGTGGCACCCTTTTTCTTTTTAAGTCCATAACTTCGTAGCAC
1 TTTTCTTTTTAAGTCCACAACTCCGTGGCA-CCTTTTTCTTTTTAAGTCCACAACTCCGTAGCA-
* * *
458771 CATTTTTCTTTTTCAA-TCCACAACTCTGTGACAGCTT
64 CTTTTTTC-TTTT-AAGTCCACAACTCTGTGGCA--TC
* *
458808 TTTTCTTTTTAAGTCCACAACTCCATGGCACCTTTTT-TCTTTTAAGTCCACAACTCCGTGGCAC
1 TTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCT-TTTTAAGTCCACAACTCCGTAGCAC
*
458872 TTTTTTCTTTTAAAGTCTACAACTCTGTGGCATC
65 TTTTTTCTTTT-AAGTCCACAACTCTGTGGCATC
* * *
458906 TTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTTAAGTCAACAACTCCGTAGCACA
1 TTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTAGCAC-
* *
458971 TTTTTCCTTTTAAGTCCACAATTCTGTGGCATCC
65 TTTTTTCTTTTAAGTCCACAACTCTGTGGCAT-C
459005 TTTTCT
1 TTTTCT
459011 AAACCCCACA
Statistics
Matches: 178, Mismatches: 20, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
98 77 0.43
99 23 0.13
100 23 0.13
101 28 0.16
102 27 0.15
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.43
Consensus pattern (97 bp):
TTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTAGCACT
TTTTTCTTTTAAGTCCACAACTCTGTGGCATC
Found at i:459023 original size:98 final size:98
Alignment explanation
Indices: 458483--459010 Score: 360
Period size: 98 Copynumber: 5.3 Consensus size: 98
458473 TAGCACCCTT
* * * ** * ** **
458483 TTTTTAAGCCCACAACTCCGTGGCATCCCATT-TTAAAGTCCACAACTCTATGGCATCCTTTCCC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTCTTTAAGTCCACAACTCCGTGGCA-CCTTTTTC
* * *** * * *
458547 TTTTAAAGTCCATAACTTAATGGCACCTTTTTTC
65 TTTTTAAGTCCACAACTCCGTAGCACATTTTTCC
* ** * * * *
458581 TTTTTAAGTCCATGACTCTATGGCACCCTTTT-TTTAAGCCCACAACTCCGTTGGCA----TCTC
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTCTTTAAGTCCACAACTCCG-TGGCACCTTTTTC
* ** * ** *
458641 ATTTTAAAGTCCACAACTTTGTGGCACCCTTTCCC
65 -TTTTTAAGTCCACAACTCCGTAGCACATTTTTCC
* * ** **
458676 CTTTAAAGTCCATAACTC-GATGGCACATTTTTTTCTTTTTAAGTCCATGACTCCGTGGCACCCT
1 TTTTAAAGTCCACAACTCTG-TGG--CATCCTTTTC--TTTAAGTCCACAACTCCGTGGCA-CCT
* * *
458740 TTTTCTTTTTAAGTCCATAACTTCGTAGCACCATTTTTCT
60 TTTTCTTTTTAAGTCCACAACTCCGTAGCA-CATTTTTCC
* * * * *
458780 TTTTCAA-TCCACAACTCTGTGACAGCTTTTTTCTTTTTAAGTCCACAACTCCATGGCACCTTTT
1 TTTTAAAGTCCACAACTCTGTGGCATC-CTTTTC--TTTAAGTCCACAACTCCGTGGCACCTTTT
* *
458844 T-TCTTTTAAGTCCACAACTCCGTGGCAC-TTTTTTC
63 TCT-TTTTAAGTCCACAACTCCGTAGCACATTTTTCC
* *
458879 TTTTAAAGTCTACAACTCTGTGGCAT-CTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTT-C-TTTAAGTCCACAACTCCGTGGCACCTTTTT
*
458943 CTTTTTAAGTCAACAACTCCGTAGCACATTTTTCC
64 CTTTTTAAGTCCACAACTCCGTAGCACATTTTTCC
*
458978 TTTT-AAGTCCACAATTCTGTGGCATCCTTTTCT
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTCT
459011 AAACCCCACA
Statistics
Matches: 344, Mismatches: 64, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
94 3 0.01
95 46 0.13
97 7 0.02
98 114 0.33
99 38 0.11
100 32 0.09
101 30 0.09
102 28 0.08
103 32 0.09
104 14 0.04
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.40
Consensus pattern (98 bp):
TTTTAAAGTCCACAACTCTGTGGCATCCTTTTCTTTAAGTCCACAACTCCGTGGCACCTTTTTCT
TTTTAAGTCCACAACTCCGTAGCACATTTTTCC
Found at i:459081 original size:33 final size:33
Alignment explanation
Indices: 459015--459624 Score: 546
Period size: 33 Copynumber: 18.7 Consensus size: 33
459005 TTTTCTAAAC
* * * *
459015 CCCACACAAATCGGTGGCATCCC-CCTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTC-TCAAAAG
* * ** * *
459048 CCAACATAAGTAAGTGGCAACCCTTCCCTAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
*** *
459081 CCTGGACAAGTTGGTGGCAA-CCTTTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* * * *
459113 CCCATATAAGTTAGTGGCAACCCTTCACAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
*
459146 CCCACCCAAGTTGGTGGCAA-CC-TCTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTC-TCAAAAG
* * * *
459178 CCCTCACAAGTCGGTGGCAACGCTTCTCTAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
459211 CCCACACAAGTTGGTGGCAA-CC-TCTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTC-TCAAAAG
* * * ***
459243 TCCGCACCAGTCAATGGCAAACCCTTCTCAAAAG
1 CCCACACAAGTTGGTGGC-AACCCTTCTCAAAAG
* **
459277 CCC-CTAAAAGTTGGTGGCAACCCTTCTGTAAAG
1 CCCAC-ACAAGTTGGTGGCAACCCTTCTCAAAAG
459310 CCCACACAAGTTGGTGGCAA-CC-TCTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTC-TCAAAAG
* * *
459342 CCCACACAAGGTAGTGGCAACCCTTCTCTAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* ***
459375 CCTACACAAGTCAATGGCAACCCTTCTC-AAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
** *
459407 CCCACACAAGTCAGTGCCAACCCTTCTC-AAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* * * *
459439 CCCACGCAAGTCGATGGCAACCCCTCTTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTC-TCAAAAG
*
459473 CCCACACAAGTCGGTGGCAACCCTTCTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* * * **
459506 CCCACATAAGTCGGTGGCAACCCTTTTTTAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
*
459539 CCCACACAAGTTGGTGGCAACCCTT-T-TAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* *
459570 CCTACACAAGTCGGTGGCAACCC-TCTCAAAAG
1 CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
* *
459602 CTCACACAAGTCGGTGGCAACCC
1 CCCACACAAGTTGGTGGCAACCC
459625 AATATCGCTG
Statistics
Matches: 474, Mismatches: 85, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
30 1 0.00
31 33 0.07
32 173 0.36
33 213 0.45
34 52 0.11
35 2 0.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (33 bp):
CCCACACAAGTTGGTGGCAACCCTTCTCAAAAG
Found at i:459110 original size:65 final size:65
Alignment explanation
Indices: 459009--459623 Score: 430
Period size: 65 Copynumber: 9.4 Consensus size: 65
458999 GCATCCTTTT
* * * * * *
459009 CTAAACCCCACACAAATCGGTGGCATCCCCCTTCAAAAGCCAACATAAGTAAGTGGCAACCCTTC
1 CTAAAGCCCACACAAGTTGGTGGCA-ACCTCTTCAAAAGCCCACATAAGTAAGTGGCAACCCTTC
*
459074 C
65 A
*** * * *
459075 CTAAAGCCTGGACAAGTTGGTGGCAACCTTTTCAAAAGCCCATATAAGTTAGTGGCAACCCTTCA
1 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACATAAGTAAGTGGCAACCCTTCA
* * * * ** * *
459140 CAAAAGCCCACCCAAGTTGGTGGCAACCTCTTCAAAAGCCCTCACAAGTCGGTGGCAACGCTTCT
1 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACATAAGTAAGTGGCAACCCTTCA
* * **
459205 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGTCCGCACCAGTCAA-TGGCAAACCCTT
1 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACATAAGT-AAGTGGC-AACCCTT
*
459269 CT
64 CA
* * * * **
459271 CAAAAGCCC-CTAAAAGTTGGTGGCAACC-CTTCTGTAAAGCCCACACAAGTTGGTGGCAACCTC
1 CTAAAGCCCAC-ACAAGTTGGTGGCAACCTCTTC--AAAAGCCCACATAAGTAAGTGGCAACC-C
459334 TTCA
62 TTCA
* * * * *
459338 --AAAGCCCACACAAGGTAGTGGCAACC-CTTCTCTAAAGCCTACACAAGTCAA-TGGCAACCCT
1 CTAAAGCCCACACAAGTTGGTGGCAACCTC-T-TCAAAAGCCCACATAAGT-AAGTGGCAACCCT
*
459399 TCT
63 TCA
** * * ** * *
459402 C-AAAGCCCACACAAGTCAGTGCCAACC-CTTCTCAAAGCCCACGCAAGT-CGATGGCAACCCCT
1 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTC-AAAAGCCCACATAAGTAAG-TGGCAACCCTT
*
459464 CTT
64 C-A
* * **
459467 CAAAAGCCCACACAAGTCGGTGGCAACC-CTTCTCAAAAGCCCACATAAGTCGGTGGCAACCCTT
1 CTAAAGCCCACACAAGTTGGTGGCAACCTC-T-TCAAAAGCCCACATAAGTAAGTGGCAACCCTT
**
459531 TT
64 CA
* ** * * **
459533 TTAAAGCCCACACAAGTTGGTGGCAACC-CTTTTAAAGCCTACACAAGTCGGTGGCAACCCTCTC
1 CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACATAAGTAAGTGGCAACCCT-TC
459597 A
65 A
* *
459598 --AAAGCTCACACAAGTCGGTGGCAACC
1 CTAAAGCCCACACAAGTTGGTGGCAACC
459624 CAATATCGCT
Statistics
Matches: 451, Mismatches: 77, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
63 26 0.06
64 56 0.12
65 211 0.47
66 109 0.24
67 46 0.10
68 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.19
Consensus pattern (65 bp):
CTAAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACATAAGTAAGTGGCAACCCTTCA
Found at i:459312 original size:164 final size:162
Alignment explanation
Indices: 459101--459624 Score: 553
Period size: 164 Copynumber: 3.2 Consensus size: 162
459091 TTGGTGGCAA
* * * * ** *
459101 CCTTTTCAAAAGCCCATATAAGTTAGTGGCAACCCTTCACAAAAGCCCACCCAAGTTGGTGGCAA
1 CCTTCTCAAAAGCCCCTAAAAGTTGGTGGCAACCCTTC-TTAAAGCCCACACAAGTTGGTGGCAA
* *
459166 CCTCTTCAAAAGCCCTCACAAGTCGGTGGCAACGCTTCTCTAAAGCCCACACAAGTTGGTGGCAA
65 CCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAA
* * *
459231 CCTCTTC-AAAAGTCCGCACCAGTCAATGGCAAAC
130 CC-CTTCTAAAAGCCCACACAAGTCAAT-GCAAAC
459265 CCTTCTCAAAAGCCCCTAAAAGTTGGTGGCAACCCTTCTGTAAAGCCCACACAAGTTGGTGGCAA
1 CCTTCTCAAAAGCCCCTAAAAGTTGGTGGCAACCCTTCT-TAAAGCCCACACAAGTTGGTGGCAA
* * ***
459330 CCTCTTCAAAAGCCCACACAAGGT-AGTGGCAACCCTTCTCTAAAGCCTACACAAGTCAATGGCA
65 CCTCTTCAAAAGCCCACACAA-GTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCA
* * *
459394 ACCCTTCTCAAAGCCCACACAAGTCAGTGCCAAC
129 ACCCTTCTAAAAGCCCACACAAGTCAATGCAAAC
** * * * *
459428 CCTTCTC-AAAGCCCAC-GCAAGTCGATGGCAACCCCTCTTCAAAAGCCCACACAAGTCGGTGGC
1 CCTTCTCAAAAGCCC-CTAAAAGTTGGTGGCAACCCTTCTT--AAAGCCCACACAAGTTGGTGGC
* * *
459491 AACC-CTTCTCAAAAGCCCACATAAGTCGGTGGCAACCCTTTTTTAAAGCCCACACAAGTTGGTG
63 AACCTC-T-TCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTG
* * **
459555 GCAACCCTT-TTAAAGCCTACACAAGTCGGTGGC-AAC
126 GCAACCCTTCTAAAAGCCCACACAAGTCAAT-GCAAAC
* * *
459591 CC-TCTCAAAAGCTCAC-ACAAGTCGGTGGCAACCC
1 CCTTCTCAAAAGC-CCCTAAAAGTTGGTGGCAACCC
459625 AATATCGCTG
Statistics
Matches: 308, Mismatches: 40, Indels: 25
0.83 0.11 0.07
Matches are distributed among these distances:
161 1 0.00
162 29 0.09
163 90 0.29
164 186 0.60
165 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (162 bp):
CCTTCTCAAAAGCCCCTAAAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTTGGTGGCAAC
CTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAAC
CCTTCTAAAAGCCCACACAAGTCAATGCAAAC
Found at i:459723 original size:61 final size:61
Alignment explanation
Indices: 459626--459767 Score: 178
Period size: 61 Copynumber: 2.3 Consensus size: 61
459616 TGGCAACCCA
* * * *
459626 ATATCGCTGGCCTTGAATCAACATATTGACATTTTTATCATTTTTCTCATCTTTAAGCCCG
1 ATATCGCTGGCCTTGAATCAACATATTGACACTTTTATCATTCTTCGCATCCTTAAGCCCG
* * *
459687 ATATCGCTGG-CTGTGAATCAACATATTGGCACTTTTATCATTCTTCGCATCCTTAAGTCCA
1 ATATCGCTGGCCT-TGAATCAACATATTGACACTTTTATCATTCTTCGCATCCTTAAGCCCG
** *
459748 ACGTCGCTGACCTTGAATCA
1 ATATCGCTGGCCTTGAATCA
459768 GCACATTGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 2 0.03
61 65 0.94
62 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (61 bp):
ATATCGCTGGCCTTGAATCAACATATTGACACTTTTATCATTCTTCGCATCCTTAAGCCCG
Found at i:459776 original size:61 final size:60
Alignment explanation
Indices: 459622--459780 Score: 174
Period size: 61 Copynumber: 2.6 Consensus size: 60
459612 TCGGTGGCAA
* * * * * *
459622 CCCAATATCGCTGGCCTTGAATCAACATATTGACATTTTTATCATTTTTCTCATCTTTAAG
1 CCCAACATCGCT-GCCTTGAATCAACATATTGGCACTTTTATCATTCTTCGCATCCTTAAG
* * *
459683 CCCGATATCGCTGGCTGTGAATCAACATATTGGCACTTTTATCATTCTTCGCATCCTTAAG
1 CCCAACATCGCTGCCT-TGAATCAACATATTGGCACTTTTATCATTCTTCGCATCCTTAAG
* * * *
459744 TCCAACGTCGCTGACCTTGAATCAGCACATTGGCACT
1 CCCAACATCGCTG-CCTTGAATCAACATATTGGCACT
459781 CTTCTCATCT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 3 0.04
61 77 0.94
62 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (60 bp):
CCCAACATCGCTGCCTTGAATCAACATATTGGCACTTTTATCATTCTTCGCATCCTTAAG
Found at i:460494 original size:20 final size:20
Alignment explanation
Indices: 460441--460494 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
460431 TTTTATGATT
*
460441 TGTATCGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
* *
460462 TGTATTGATACATAAGTGTA
1 TGTATCGATACATAAGTGAA
*
460482 TGTATCAATACAT
1 TGTATCGATACAT
460495 GTCTCAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:474176 original size:28 final size:30
Alignment explanation
Indices: 474148--474327 Score: 88
Period size: 31 Copynumber: 6.0 Consensus size: 30
474138 CAACTCTCTT
*
474148 TTCAAAGTCCACGACTCAGTGGCATCTTTTC
1 TTCAAAGTCCACAACTCAGTGGCATC-TTTC
* * *
474179 TTCAAAGTCCACAACTCTGTGGC-TTTTTT
1 TTCAAAGTCCACAACTCAGTGGCATCTTTC
**
474208 TTCATCTTTAAGTCCATGACTCAGTGGCAATCTCTT-
1 TTCA-----AAGTCCACAACTCAGTGGC-ATCT-TTC
* * *
474244 TTCAAAGTCCATAACTCCGTAGCA-CTTT-
1 TTCAAAGTCCACAACTCAGTGGCATCTTTC
* * * *
474272 TT-TAAGTCCACAACTCTGTGGCACCCTT-
1 TTCAAAGTCCACAACTCAGTGGCATCTTTC
* *
474300 TT--AAGCCCACAACTCCGTGGCATTCTTT
1 TTCAAAGTCCACAACTCAGTGGCA-TCTTT
474328 TTCCTTTTAA
Statistics
Matches: 119, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
27 35 0.29
28 12 0.10
29 9 0.08
30 2 0.02
31 37 0.31
34 16 0.13
36 6 0.05
37 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (30 bp):
TTCAAAGTCCACAACTCAGTGGCATCTTTC
Found at i:474185 original size:31 final size:32
Alignment explanation
Indices: 474148--474254 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 32
474138 CAACTCTCTT
474148 TTCAAAGTCCACGACTCAGTGGC-ATCTTTTC
1 TTCAAAGTCCACGACTCAGTGGCAATCTTTTC
* * ** *
474179 TTCAAAGTCCACAACTCTGTGGCTTTTTTTTC
1 TTCAAAGTCCACGACTCAGTGGCAATCTTTTC
** * *
474211 ATCTTTAAGTCCATGACTCAGTGGCAATCTCTT-
1 -T-TCAAAGTCCACGACTCAGTGGCAATCTTTTC
474244 TTCAAAGTCCA
1 TTCAAAGTCCA
474255 TAACTCCGTA
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
31 29 0.50
32 7 0.12
33 1 0.02
34 21 0.36
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.36
Consensus pattern (32 bp):
TTCAAAGTCCACGACTCAGTGGCAATCTTTTC
Found at i:474255 original size:31 final size:30
Alignment explanation
Indices: 474142--474328 Score: 120
Period size: 27 Copynumber: 6.3 Consensus size: 30
474132 ATGTCTCAAC
*
474142 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
* *
474172 TCTTTTCTTCAAAGTCCACAACTCTGTGGC-
1 TCTCTT-TTCAAAGTCCACAACTCAGTGGCA
* * **
474202 TTTTTTTTCATCTTTAAGTCCATGACTCAGTGGCAA
1 TCTCTTTTCA-----AAGTCCACAACTCAGTGGC-A
* * *
474238 TCTCTTTTCAAAGTCCATAACTCCGTAGCA
1 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
* *
474268 -CT-TTTT-TAAGTCCACAACTCTGTGGCA
1 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
* * *
474295 -CCCTTTT--AAGCCCACAACTCCGTGGCA
1 TCTCTTTTCAAAGTCCACAACTCAGTGGCA
474322 T-TCTTTT
1 TCTCTTTT
474329 TCCTTTTAAG
Statistics
Matches: 127, Mismatches: 20, Indels: 23
0.75 0.12 0.14
Matches are distributed among these distances:
27 41 0.32
28 8 0.06
29 6 0.05
30 11 0.09
31 37 0.29
34 16 0.13
36 8 0.06
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.36
Consensus pattern (30 bp):
TCTCTTTTCAAAGTCCACAACTCAGTGGCA
Found at i:474273 original size:65 final size:65
Alignment explanation
Indices: 474152--474274 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 65
474142 TCTCTTTTCA
* * * **
474152 AAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCTGTGGCTTTTTTTTCATCTTT
1 AAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCCGTAGCACTTTTTTCATCTTT
* *
474217 AAGTCCATGACTCAGTGGCAATCTCTT-TTCAAAGTCCATAACTCCGTAGCACTTTTTT
1 AAGTCCACGACTCAGTGGC-ATCTCTTCTTCAAAGTCCACAACTCCGTAGCACTTTTTT
474275 AAGTCCACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 44 0.88
66 6 0.12
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (65 bp):
AAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCCGTAGCACTTTTTTCATCTTT
Found at i:474339 original size:34 final size:34
Alignment explanation
Indices: 474296--474506 Score: 192
Period size: 34 Copynumber: 6.5 Consensus size: 34
474286 TCTGTGGCAC
474296 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
* * *
474330 CCTTTTAAGCCCACAACTCCATGGTACTTTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TTCTTTTT
* * *
474365 CCTTTTAAACCCACAACTTCATGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
* * * * *
474399 CCTTTTAAGTCCACAAGTTCGTGG--TGCGTTGTT
1 CCTTTTAAGCCCACAACTCCGTGGCATTC-TTTTT
*
474432 CCTTTTAAGTCCACAACTCCGTGGCA--C-----
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
* *
474459 CCTTTT-AGTCCACAACTCCGTGGCA-TCTTTCT
1 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
*
474491 CCTTTTACGCCCACAA
1 CCTTTTAAGCCCACAA
474507 GTCAATGGAA
Statistics
Matches: 149, Mismatches: 17, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
26 19 0.13
27 7 0.05
32 8 0.05
33 34 0.23
34 51 0.34
35 30 0.20
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.37
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
Found at i:474471 original size:26 final size:27
Alignment explanation
Indices: 474432--474483 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
474422 GTGCGTTGTT
474432 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
474459 CCTTTT-AGTCCACAACTCCGTGGCA
1 CCTTTTAAGTCCACAACTCCGTGGCA
474484 TCTTTCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.21, C:0.37, G:0.15, T:0.27
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:474567 original size:29 final size:30
Alignment explanation
Indices: 474499--474621 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 30
474489 CTCCTTTTAC
* * *
474499 GCCCACAAGTCAATGGAACCCTTTTTAAAA
1 GCCCACAAGTCAATGGCACCCCTTTCAAAA
* * **
474529 TCCCAGAAGTCGGTGGCACCCCTTTCAAAA
1 GCCCACAAGTCAATGGCACCCCTTTCAAAA
*
474559 -CCCACAAGTCAATGGCA-ACC-TTCAAAA
1 GCCCACAAGTCAATGGCACCCCTTTCAAAA
* * *** *
474586 GCACACATGTTGGT-GCAACCCTTTCAAAA
1 GCCCACAAGTCAATGGCACCCCTTTCAAAA
474615 GCCCACA
1 GCCCACA
474622 TAAGTTGGTG
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
27 10 0.14
28 12 0.17
29 27 0.38
30 23 0.32
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (30 bp):
GCCCACAAGTCAATGGCACCCCTTTCAAAA
Done.