Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
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: 4418299
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 127125 characters in sequence are not A, C, G, or T
File 19 of 28
Found at i:2768312 original size:216 final size:210
Alignment explanation
Indices: 2767898--2768644 Score: 861
Period size: 216 Copynumber: 3.5 Consensus size: 210
2767888 TCTTCAAATC
*
2767898 TCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTCT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCA--TCT
* * * * *
2767963 TTTCTCAAAGTCCACAACTCAGTGGCCTCTCTTTTCTCAAAGTCTACGACTCAGTGGCAT-TTTT
64 TTTCTCAAAGTCCACAACTCAGTGGCAT-T-TTTTTTCTAAGTCCATGACTCAGTGGCATCTTTT
* ** * *
2768027 TTCTTAGTCCACAACTCAGTGGCAATCTCTT-CTCAAAGTCCACGACTCAGTGGCATCTTATCCC
127 CTCAAAGTCCACGACTCAGTGGC-ATCT-TTCCTCAAAGTCCACGACTCAGTGGCATCTTTTCCC
2768091 AAAGTCCACAACTCAGTGGCA
190 AAAGTCCACAACTCAGTGGCA
* * *
2768112 TCTCTTTTCAAAGTCCACAACTCAGTGGCATCACTTTTTTCAAAGTCCACAACTCAGTGGCATCT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCAT--CTCTTCTCAAAGTCCACAACTCAGTGGCA--T
* * * *
2768177 CTTTTCTCAAAGTCCACGACTCAATGGCATTTTTTTTCTTAGTCCATGACTCAGTGGCAATCTCT
62 CTTTTCTCAAAGTCCACAACTCAGTGGCATTTTTTTTCTAAGTCCATGACTCAGTGGC-ATCTTT
* * * *
2768242 TCTCAAAGTCCATGACTCGGTGGCATCTTGTCCT-AAAGTCCACGACTCAGTAGCATCTTTTCTT
126 TCTCAAAGTCCACGACTCAGTGGCATCTT-TCCTCAAAGTCCACGACTCAGTGGCATCTTTTC-C
2768306 CAAAGTCCACAACTCAGTGGCA
189 CAAAGTCCACAACTCAGTGGCA
* * * * *
2768328 TCTCTTTTCTAAGTCCACTACCCAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAGTGGCATCT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCAT-CTCTTC-TCAAAGTCCACAACTCAGTGGCATCT
* * * *
2768393 TTTCTTTAAAGTTCACAACTCAGTGGCATCTCTTTTCTAAGTCCATGACTCAGTGGCATCCTTTT
64 TTTC-TCAAAGTCCACAACTCAGTGGCATTTTTTTTCTAAGTCCATGACTCAGTGGCAT-CTTTT
* * * * *
2768458 CTTCCAAGTCCACGACTCAGTGGCATCTTTTTTCTTCAAAGTCCATGACTTAGTGGCATCTCTTC
127 C-TCAAAGTCCACGACTCAGTGGCATC---TTTCCTCAAAGTCCACGACTCAGTGGCATCTTTTC
*
2768523 CCAAAGTCCACGACTCAGTGGCA
188 CCAAAGTCCACAACTCAGTGGCA
* * *
2768546 TCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTTAGTGGCATCT
1 TCTCTT-TTCAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCT
* ** * *
2768611 TTTCCCAAAGTCCATGACTCTGTGGCACTTTTTT
64 TTTCTCAAAGTCCACAACTCAGTGGCATTTTTTT
2768645 CTTTTTAAAG
Statistics
Matches: 453, Mismatches: 63, Indels: 31
0.83 0.12 0.06
Matches are distributed among these distances:
214 61 0.13
215 89 0.20
216 173 0.38
217 21 0.05
218 56 0.12
219 51 0.11
220 2 0.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.33
Consensus pattern (210 bp):
TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTTT
TCTCAAAGTCCACAACTCAGTGGCATTTTTTTTCTAAGTCCATGACTCAGTGGCATCTTTTCTCA
AAGTCCACGACTCAGTGGCATCTTTCCTCAAAGTCCACGACTCAGTGGCATCTTTTCCCAAAGTC
CACAACTCAGTGGCA
Found at i:2768436 original size:93 final size:93
Alignment explanation
Indices: 2767905--2769217 Score: 819
Period size: 94 Copynumber: 14.0 Consensus size: 93
2767895 ATCTCTCTTC
* * *
2767905 TCAAAGTCCACGACTCAGTGGCATCTCTTC-TCAAAGTCCACAACTCAGTGGCATCTCTTTTCTC
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCT-
*
2767969 AAAGTCCACAACTCAGTGGCCTCTCTTTTC-
65 -AAGTCCACAACTCAGTGGCATC-CTTTTCT
* * * *
2767999 TCAAAGTCTACGACTCAGTGGCAT-TTTT-TTCT-TAGTCCACAACTCAGTGGCAATCTCTTCTC
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTT-TAAAGTCCACAACTCAGTGGC-ATCTCTTTTC
* * *
2768061 AAAGTCCACGACTCAGTGGCAT-CTTATC-
64 TAAGTCCACAACTCAGTGGCATCCTTTTCT
* * * *
2768089 CCAAAGTCCACAACTCAGTGGCATCTCTT-TTCAAAGTCCACAACTCAGTGGCATCACTTTTTTC
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTCAGTGGCAT--CTCTTTTC
*
2768153 AAAGTCCACAACTCAGTGGCATCTCTTTTC-
64 TAAGTCCACAACTCAGTGGCATC-CTTTTCT
* * ** ** *
2768183 TCAAAGTCCACGACTCAATGGCAT-TTTT-TTTCTTAGTCCATGACTCAGTGGCAATCTCTTCTC
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTT-AAAGTCCACAACTCAGTGGC-ATCTCTTTTC
* ** * * *
2768246 AAAGTCCATGACTCGGTGGCAT-CTTGTCC
64 TAAGTCCACAACTCAGTGGCATCCTTTTCT
* * *
2768275 T-AAAGTCCACGACTCAGTAGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTA
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCTA
* *
2768339 AGTCCACTACCCAGTGGCATCCTTTTCT
66 AGTCCACAACTCAGTGGCATCCTTTTCT
* *
2768367 TCCAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTTCACAACTCAGTGGCATCTCTTTTCTA
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCTA
**
2768432 AGTCCATGACTCAGTGGCATCCTTTTCT
66 AGTCCACAACTCAGTGGCATCCTTTTCT
* * * ** * **
2768460 TCCAAGTCCACGACTCAGTGGCATCTTTTTTCTTCAAAGTCCATGACTTAGTGGCATCTCTTCCC
1 TCAAAGTCCACAACTCAGTGGCATC--TTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTC
* *
2768525 AAAGTCCACGACTCAGTGGCAT-CTTTTCT
64 TAAGTCCACAACTCAGTGGCATCCTTTTCT
* * * * * *
2768554 TCAAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGTCCACGACTTAGTGGCATCT-TTTCCC
1 TCAAAGTCCACAACTCAGTGGC-ATCTTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTT-TC
* ** * *
2768617 AAAGTCCATGACTCTGTGGCA-CTTTTTTCTTT
64 TAAGTCCACAACTCAGTGGCATC-CTTTTC--T
* * * * * *
2768649 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCGCAACTCTGTGGCA-CT-TTTT
1 TCAAAGTCCACAACTCAGTGGCA-TC-TTTT-CTTTAAAGTCCACAACTCAGTGGCATCTCTTTT
* * * * *
2768712 TTAAGTTCACAACTCCGTAGCATCTTTTTCCT
63 CTAAGTCCACAACTCAGTGGCATCCTTTT-CT
** * * * * * *
2768744 TTTAAGTCCACAACTCCGTGGTACCTTTTTCTTTTAAGTCCACAACTCTGTGGCA-C-C-CTT-T
1 TCAAAGTCCACAACTCAGTGGCATC-TTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCT
* *
2768805 AAGTCCACAACTCCGTGGCATCTTTTTCTTT
65 AAGTCCACAACTCAGTGGCATCCTTTTC--T
** * * *
2768836 TTTAAG-CTCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCATAACTCTA-TGGCA-C-CTT
1 TCAAAGTC-CACAACTCAGTGGCA-TC-TTTT-CTTTAAAGTCCACAACTC-AGTGGCATCTCTT
2768897 TT-TAAGTCCACAACTCCA-TGGCAT-CTTTCTCCT
61 TTCTAAGTCCACAACT-CAGTGGCATCCTTT-T-CT
** * * * * ** *
2768930 TTTAAGTCTACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTCTGGCA-CCCTTTT
1 TCAAAGTCCACAACTCAGTGGCATCTT-TTC--TTTAAAGTCCACAACTCAGTGGCATCTC-TTT
*
2768994 TCCTTTTAAGTCCACAACTTC-GTGGCA-CC-CTT-T
62 T-C---TAAGTCCACAAC-TCAGTGGCATCCTTTTCT
* * *
2769027 T--AAGTCCACAACTTC-GTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCT-TGTT
1 TCAAAGTCCACAAC-TCAGTGGCATC-TTTTC-TTTAAAGTCCACAACTCAGTGGCATCTCT-TT
* *
2769088 CTCTTTAAAGCCCACAACTCTA-TGGCACTCTTTTTCCT
62 -TC--T-AAGTCCACAACTC-AGTGGCA-TCCTTTT-CT
** * * * *
2769126 TTTAAGTCCACAACTCCGTGGCACCTTTTC----AAGTCCACAACTCTA-TGGCACCTTGTTCCT
1 TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTC-AGTGGCATC-TCTT--T
* * *
2769186 TTTAAGTTCACAACTCCGTGGCA-CCTTTTCT
62 TCTAAGTCCACAACTCAGTGGCATCCTTTTCT
2769217 T
1 T
2769218 TTTAAGTCTA
Statistics
Matches: 1009, Mismatches: 132, Indels: 159
0.78 0.10 0.12
Matches are distributed among these distances:
90 29 0.03
91 106 0.11
92 150 0.15
93 210 0.21
94 232 0.23
95 165 0.16
96 36 0.04
97 14 0.01
98 18 0.02
99 3 0.00
100 8 0.01
101 37 0.04
102 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (93 bp):
TCAAAGTCCACAACTCAGTGGCATCTTTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCTA
AGTCCACAACTCAGTGGCATCCTTTTCT
Found at i:2768671 original size:34 final size:33
Alignment explanation
Indices: 2768618--2769306 Score: 466
Period size: 34 Copynumber: 21.5 Consensus size: 33
2768608 TCTTTTCCCA
** * *
2768618 AAGTCCATGACTCTGTGGCACTTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
*
2768651 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
* *
2768686 AAGTCCGCAACTCTGTGGCAC---TTT--TTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
2768714 AAGTTCACAACTCCGTAGCA-TCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
* *
2768747 AAGTCCACAACTCCGTGGTACCTTTTT-CTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
*
2768779 AAGTCCACAACTCTGTGGCAC------CC-TTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
*
2768805 AAGTCCACAACTCCGTGGCA-TCTTTTTCTTTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTC-CTTTT
2768839 AAG-CTCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGTC-CACAACTCCGTGGCACT-TTTTTCCTTTT
* ** *
2768873 AAGTCCATAACTCTATGGCAC------CTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
2768900 AAGTCCACAACTCCATGGCA-TCTTTCTCCTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
* * * *
2768933 AAGTCTACAACTCCGTGGCACCTTGTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
2768966 AAAGCCCACAACTCTC-TGGCACCCTTTTTCCTTTT
1 -AAGTCCACAACTC-CGTGGCA-CTTTTTTCCTTTT
*
2769001 AAGTCCACAACTTCGTGGCAC------CCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* *
2769028 AAGTCCACAACTTCGTGGCA-TCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
* * *
2769061 AAGTCCACAACTCCGTGGCACCTTGTTCTCTTTA
1 AAGTCCACAACTCCGTGGCACTTTTTTC-CTTTT
* **
2769095 AAGCCCACAACTCTATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACT-TTTTTCCTTTT
*
2769129 AAGTCCACAACTCCGTGGCAC-CTTTT-C----
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
** * *
2769156 AAGTCCACAACTCTATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* * *
2769189 AAGTTCACAACTCCGTGGCAC-CTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
* ** * *
2769221 AAGTCTATGACTCCGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CTTTTTTCCTTTT
** * * *
2769255 AAACCCACACCTTCGTGGCATCCTTTTTT-CTTGT
1 AAGTCCACAACTCCGTGGCA--CTTTTTTCCTTTT
* *
2769289 AAGTCCATAACTCTGTGG
1 AAGTCCACAACTCCGTGG
2769307 TACCTTTAAG
Statistics
Matches: 514, Mismatches: 89, Indels: 104
0.73 0.13 0.15
Matches are distributed among these distances:
26 22 0.04
27 69 0.13
28 23 0.04
29 1 0.00
30 3 0.01
31 4 0.01
32 53 0.10
33 108 0.21
34 189 0.37
35 42 0.08
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACTTTTTTCCTTTT
Found at i:2768811 original size:187 final size:188
Alignment explanation
Indices: 2768618--2769152 Score: 570
Period size: 187 Copynumber: 2.8 Consensus size: 188
2768608 TCTTTTCCCA
** *
2768618 AAGTCCATGACTCTGTGGCA-CTTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAGTCCACAACTCCGTGGCATC-TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
* * * * * *
2768682 TTTTAAGTCCGCAACTCTGTGGCACTTTTTTTAAGTTCACAACTCCGTAGCATCTTTTTCCTTTT
65 TTTTAAGTCCACAACTCTATGGCAC-CTTTTTAAGTCCACAACTCCATAGCATCTTTCTCCTTTT
* * * *
2768747 AAGTCCACAACTCCGTGGTACCTTTTTC-TTTT-AAGTCCACAACTCTGTGGCACCCTTT
129 AAGTCCACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTCTGGCACCCTTT
* *
2768805 AAGTCCACAACTCCGTGGCATCTTTTTCTTTTTTAAGCTCACAACTCCGTGGCACTCTTTTTCCT
1 AAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* *
2768870 TTTAAGTCCATAACTCTATGGCACCTTTTTAAGTCCACAACTCCATGGCATCTTTCTCCTTTTAA
66 TTTAAGTCCACAACTCTATGGCACCTTTTTAAGTCCACAACTCCATAGCATCTTTCTCCTTTTAA
*
2768935 GTCTACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTCTGGCACCCTTTTTCCTTT
131 GTCCACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTCTGGCA--C-----CC-TT
2769000 T
188 T
* * * * *
2769001 AAGTCCACAACTTCGTGGCA-C-----CCTTTT-AAGTCCACAACTTCGTGGCA-TCTTTTTCTT
1 AAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
** * * * *
2769058 TTTAAGTCCACAACTCCGTGGCACCTTGTTCTCTTTAAAGCCCACAACTCTATGGCACTCTTTTT
66 TTTAAGTCCACAACTCTATGGCACC----T-T-TTT-AAGTCCACAACTCCATAGCA-TCTTTCT
2769123 CCTTTTAAGTCCACAACTCCGTGGCACCTT
123 CCTTTTAAGTCCACAACTCCGTGGCACCTT
2769153 TTCAAGTCCA
Statistics
Matches: 298, Mismatches: 31, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
186 59 0.20
187 83 0.28
188 50 0.17
189 17 0.06
190 6 0.02
192 1 0.00
193 1 0.00
194 3 0.01
195 21 0.07
196 57 0.19
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (188 bp):
AAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TTTAAGTCCACAACTCTATGGCACCTTTTTAAGTCCACAACTCCATAGCATCTTTCTCCTTTTAA
GTCCACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTCTGGCACCCTTT
Found at i:2768813 original size:58 final size:59
Alignment explanation
Indices: 2768744--2768864 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 59
2768734 TCTTTTTCCT
* *
2768744 TTTAAGTCCACAACTCCGTGGTACCTTTTTC-TTTTAAG-TCCACAACTCTGTGGCACCC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCT-CACAACTCCGTGGCACCC
* *
2768802 TTTAAGTCCACAACTCCGTGGCATCTTTTTCTTTTTTAAGCTCACAACTCCGTGGCACTC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTC-TTTTTAAGCTCACAACTCCGTGGCACCC
2768862 TTT
1 TTT
2768865 TTCCTTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 29 0.52
60 26 0.46
61 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (59 bp):
TTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGCTCACAACTCCGTGGCACCC
Found at i:2768901 original size:27 final size:27
Alignment explanation
Indices: 2768869--2769179 Score: 102
Period size: 27 Copynumber: 10.0 Consensus size: 27
2768859 CTCTTTTTCC
* *
2768869 TTTTAAGTCCATAACTCTATGGCACCT
1 TTTTAAGTCCACAACTCCATGGCACCT
2768896 TTTTAAGTCCACAACTCCATGGCATCTTTCT
1 TTTTAAGTCCACAACTCCATGGCA-C---CT
* *
2768927 CCTTTTAAGTCTACAACTCCGTGGCACCTTGTTCT
1 --TTTTAAGTCCACAACTCCATGGCA-C-----CT
*
2768962 TTTTAAAGCCCACAACTCTC-TGGCACCCTTTTT
1 TTTT-AAGTCCACAACTC-CATGGCA-CC----T
* * *
2768995 CCTTTTAAGTCCACAACTTCGTGGCACCC
1 --TTTTAAGTCCACAACTCCATGGCACCT
* *
2769024 TTTTAAGTCCACAACTTCGTGGCATCTTTTTCT
1 TTTTAAGTCCACAACTCCATGGCA-C-----CT
*
2769057 TTTTAAGTCCACAACTCCGTGGCACCTTGTT
1 TTTTAAGTCCACAACTCCATGGCACC----T
* *
2769088 CTCTTTAAAGCCCACAACTCTATGGCACTCTTTTT
1 -T-TTT-AAGTCCACAACTCCATGGCAC-C----T
*
2769123 CCTTTTAAGTCCACAACTCCGTGGCACCT
1 --TTTTAAGTCCACAACTCCATGGCACCT
* *
2769152 TTTCAAGTCCACAACTCTATGGCACCT
1 TTTTAAGTCCACAACTCCATGGCACCT
2769179 T
1 T
2769180 GTTCCTTTTA
Statistics
Matches: 229, Mismatches: 23, Indels: 64
0.72 0.07 0.20
Matches are distributed among these distances:
27 72 0.31
28 2 0.01
29 2 0.01
31 3 0.01
32 2 0.01
33 59 0.26
34 70 0.31
35 17 0.07
36 2 0.01
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCATGGCACCT
Found at i:2768953 original size:60 final size:61
Alignment explanation
Indices: 2768834--2769214 Score: 412
Period size: 60 Copynumber: 6.1 Consensus size: 61
2768824 ATCTTTTTCT
* * **
2768834 TTTTTAAG-CTCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCATAACTCTATGGCACC
1 TTTTTAAGTC-CACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* *
2768895 TTTTTAAGTCCACAACTCCATGGCA-TCTTTCTCCTTTTAAGTCTACAACTCCGTGGCACCTTGT
1 TTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-C----
2768959 TC
61 -C
* * *
2768961 TTTTTAAAGCCCACAACTCTC-TGGCACCCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACC
1 TTTTT-AAGTCCACAACTC-CATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *
2769023 CTTTTAAGTCCACAACTTCGTGGCA-TCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACC
1 TTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* *
2769083 TTGTTCTCTTTAAAGCCCACAACTCTATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
1 ----T-T-TTT-AAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
2769148 ACC
59 ACC
* * * *
2769151 TTTTCAAGTCCACAACTCTATGGCAC-CTTGTTCCTTTTAAGTTCACAACTCCGTGGCACC
1 TTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
2769211 TTTT
1 TTTT
2769215 CTTTTTAAGT
Statistics
Matches: 274, Mismatches: 27, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
60 97 0.35
61 59 0.22
62 8 0.03
63 1 0.00
64 1 0.00
65 1 0.00
66 9 0.03
67 34 0.12
68 64 0.23
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.36
Consensus pattern (61 bp):
TTTTTAAGTCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:2768976 original size:128 final size:126
Alignment explanation
Indices: 2768645--2769282 Score: 674
Period size: 128 Copynumber: 5.0 Consensus size: 126
2768635 GCACTTTTTT
* * * *
2768645 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCGCAACTCTGTGGCA-C--
1 CTTTTT-AAGTCCACAACTCCGTGGCA-TCTTTCTCCTTTTAAGTCCACAACTCCGTGGCACCTT
** * *
2768707 TT-TTTTTAAGTTCACAACTCCGTAGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGTAC
64 TTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
*
2768768 CTTTTTCTTTTAAGTCCACAACTCTGTGGCA-----C-CC-TTTAAGTCCACAACTCCGTGGCAT
1 C----T-TTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCGTGGCA-
* * * **
2768826 CTTTTTCTTTTTTAAGCTCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCATAACTCTATGG
60 CCTTTTC-TTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGG
2768891 CAC
124 CAC
* *
2768894 CTTTTTAAGTCCACAACTCCATGGCATCTTTCTCCTTTTAAGTCTACAACTCCGTGGCACCTTGT
1 CTTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCGTGGCACCTT-T
* *
2768959 TCTTTTTAAAGCCCACAACTCTC-TGGCACCCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAC
65 TCTTTTT-AAGCCCACAACTC-CGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
* * * *
2769022 CCTTTTAAGTCCACAACTTCGTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTGT
1 CTTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCGTGGCACCTT-T
* **
2769087 TCTCTTTAAAGCCCACAACTCTATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
65 TCT-TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
* ** * *
2769150 CTTTTCAAGTCCACAACTCTATGGCACCTTGT-TCCTTTTAAGTTCACAACTCCGTGGCACCTTT
1 CTTTTTAAGTCCACAACTCCGTGGCATCTT-TCTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * ** * * ** * *
2769214 TCTTTTTAAGTCTATGACTCCGTGGCACCCTTTTCCCTTTTAAACCCACACCTTCGTGGCATC
65 TCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-C
2769277 CTTTTT
1 CTTTTT
2769283 TCTTGTAAGT
Statistics
Matches: 435, Mismatches: 54, Indels: 48
0.81 0.10 0.09
Matches are distributed among these distances:
119 21 0.05
120 2 0.00
121 22 0.05
122 1 0.00
123 3 0.01
125 23 0.05
126 77 0.18
127 39 0.09
128 242 0.56
129 5 0.01
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (126 bp):
CTTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
CTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:2769152 original size:26 final size:27
Alignment explanation
Indices: 2769123--2769215 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
2769113 CACTCTTTTT
*
2769123 CCTTTT-AAGTCCACAACTCCGTGGCA
1 CCTTTTCAAGTCCACAACTCCATGGCA
*
2769149 CCTTTTCAAGTCCACAACTCTATGGCA
1 CCTTTTCAAGTCCACAACTCCATGGCA
* *
2769176 CCTTGTTCCTTTTAAGTTCACAACTCCGTGGCA
1 CCTT-TT-C----AAGTCCACAACTCCATGGCA
2769209 CCTTTTC
1 CCTTTTC
2769216 TTTTTAAGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.11
27 22 0.40
28 2 0.04
29 1 0.02
31 1 0.02
32 2 0.04
33 21 0.38
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (27 bp):
CCTTTTCAAGTCCACAACTCCATGGCA
Found at i:2769238 original size:160 final size:159
Alignment explanation
Indices: 2769022--2769320 Score: 383
Period size: 160 Copynumber: 1.9 Consensus size: 159
2769012 TTCGTGGCAC
* *
2769022 CCTTTTAAGTCCACAACTTCGTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCA-CCTTG
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCCTT-
* *
2769086 TTCTC-TTTAAAGCCCACAAC-TCTATGGCA-CTCTTTTTCCTTTTAAGTCCACAACTCCGTGGC
65 TTCCCTTTTAAA-CCCACAACTTC-ATGGCATC-CTTTTTCCTTGTAAGTCCACAACTCCGTGGC
2769148 ACCTTTTCAAGTCCACAACTCTATGGCACCTTGTT
127 ACC-TTT-AAGTCCACAACTCTATGGCACCTTGTT
* * **
2769183 CCTTTTAAGTTCACAACTCCGTGGCA-CCTTTTCTTTTTAAGTCTATGACTCCGTGGCACCCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCCTTT
* * * * * *
2769247 TCCCTTTTAAACCCACACCTTCGTGGCATCCTTTTTTCTTGTAAGTCCATAACTCTGTGGTACCT
66 TCCCTTTTAAACCCACAACTTCATGGCATCCTTTTTCCTTGTAAGTCCACAACTCCGTGGCACCT
2769312 TTAAGTCCA
131 TTAAGTCCA
2769321 ATATCGCTAG
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
158 7 0.06
159 3 0.03
160 73 0.61
161 37 0.31
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (159 bp):
CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCCTTT
TCCCTTTTAAACCCACAACTTCATGGCATCCTTTTTCCTTGTAAGTCCACAACTCCGTGGCACCT
TTAAGTCCACAACTCTATGGCACCTTGTT
Found at i:2769388 original size:48 final size:48
Alignment explanation
Indices: 2769313--2770014 Score: 368
Period size: 49 Copynumber: 14.8 Consensus size: 48
2769303 GTGGTACCTT
* * * * *
2769313 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGCCTC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* * * * *
2769361 TAAGACCAATGTCACTGGCTTTAAATCAGCACATTGGCACTTTGTCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* *
2769409 TAAGACCAATGTCGCTCGCTTTGAATCAGCACATTGGCA--------C
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* * *
2769449 -AA-CCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
*
2769495 TAAGACCAATGTCCCTGGCCTTGAATCAGCACATTGGCA--------C
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
* * * * * * * *
2769535 -AAGCCCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTTATTTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCTC
* * * * *
2769583 TAAGATCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT----GTCTC
* * ** * *
2769635 TAAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGCATTTTCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCTC
* ** * * * * *
2769684 TAAGTCTGATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCTC
* ** * * * * *
2769733 TAAGCCCAACATCGCTAGCCTTGAATCAACACATTGGCATCTTCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCTC
* * * * * * * * *
2769782 TAAGCCCGATATAGCTGGCCTTGAATCAACATATTGGCAACTTTATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC-ACCTTGTCTC
* * * *
2769831 TAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCTC
* * * *** * *
2769880 TAAGTCCGATATTATTGGCCTTGAATCAGCATATTGGCATCTT-TAACATTCC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGT--C--T-C
* * ** * *
2769932 TAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCATTCTTCT-TC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTGTCTC
* * * *
2769980 -AAGTCTAATGTCACTGGCCATGAATCAGCACATTG
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
2770015 TCATTCTTCG
Statistics
Matches: 518, Mismatches: 101, Indels: 71
0.75 0.15 0.10
Matches are distributed among these distances:
38 30 0.06
39 34 0.07
40 1 0.00
46 1 0.00
47 31 0.06
48 114 0.22
49 225 0.43
50 5 0.01
51 1 0.00
52 71 0.14
53 4 0.01
54 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (48 bp):
TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCTC
Found at i:2769519 original size:86 final size:87
Alignment explanation
Indices: 2769366--2769622 Score: 345
Period size: 86 Copynumber: 3.0 Consensus size: 87
2769356 GCCTCTAAGA
* * * * * * * *
2769366 CCAATGTCACTGGCTTTAAATCAGCACATTGGCACTTTGTCTTTAAGACCAATGTCGCTCGCTTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
2769431 GAATCAGCACATTGGCACAA-C
66 GAATCAGCACATTGGCACAAGC
* *
2769452 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCCCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
2769517 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* * * * * * *
2769539 CCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTTATTTTTAAGATCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTCGCTGGCCT
2769604 TGAATCAGCACATTGGCAC
65 TGAATCAGCACATTGGCAC
2769623 CTTAACCATC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 75 0.50
87 35 0.23
88 40 0.27
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:2769778 original size:98 final size:98
Alignment explanation
Indices: 2769535--2770014 Score: 462
Period size: 98 Copynumber: 4.9 Consensus size: 98
2769525 ACATTGGCAC
* * * * * * * *
2769535 AAGCCCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTTATTTTTAAGAT-CGATGTCGTT
1 AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAG-TCCGATATCGCT
* *
2769599 GGCCTTGAATCAGCACATTGGCACCTTAACCATCTTT
65 GGCCTTGAATCAGCATATTGGCACCTT---TATCTTT
* * * * ** *
2769636 AAGTCCAATGTCGCCGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGTCTGATATCGCTG
1 AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
*
2769701 GCCTTAAATCAGCATATTGGCACCTTTATCTTT
66 GCCTTGAATCAGCATATTGGCACCTTTATCTTT
* * * * *
2769734 AAGCCCAACATCGCTAGCCTTGAATCAACACATTGGCATCTTCATCTTTAAGCCCGATATAGCTG
1 AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
* *
2769799 GCCTTGAATCAACATATTGGCAACTTTATCTTT
66 GCCTTGAATCAGCATATTGGCACCTTTATCTTT
* * * ***
2769832 AAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATTATTG
1 AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
* *
2769897 GCCTTGAATCAGCATATTGGCATCTTTAACATTCCT
66 GCCTTGAATCAGCATATTGGCACCTTTATC-TT--T
* * ** * * * ** * *
2769933 AAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCACTG
1 AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
* *
2769996 GCCATGAATCAGCACATTG
66 GCCTTGAATCAGCATATTG
2770015 TCATTCTTCG
Statistics
Matches: 320, Mismatches: 55, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
98 173 0.54
99 37 0.12
100 1 0.00
101 109 0.34
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (98 bp):
AAGCCCAATATCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
GCCTTGAATCAGCATATTGGCACCTTTATCTTT
Found at i:2769901 original size:147 final size:148
Alignment explanation
Indices: 2769539--2769922 Score: 432
Period size: 147 Copynumber: 2.6 Consensus size: 148
2769529 TGGCACAAGC
* * * *
2769539 CCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTTATTTTTAAGAT-CGATGTCGTTGGCC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG-TCCGATATCGTTGGCC
* * * * *
2769603 TTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGCCGGCCTTGAATCAGCACA
65 TTGAATCAGCACATTGGCATCTT-A-CATCTTTAAGCCCAATATAGCCGGCCTTGAATCAACACA
* *
2769668 TTGGCATTTTCATCTTTAAGT
128 TTGGCACTTTCATCTTTAAGA
** * * * * * *
2769689 CTGATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTATCTTTAAGCCCAACATCGCTAGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCGATATCGTTGGCCT
* * * *
2769754 TGAATCAACACATTGGCATCTT-CATCTTTAAGCCCGATATAGCTGGCCTTGAATCAACATATTG
66 TGAATCAGCACATTGGCATCTTACATCTTTAAGCCCAATATAGCCGGCCTTGAATCAACACATTG
2769818 GCAACTTT-ATCTTTAAGA
131 GC-ACTTTCATCTTTAAGA
* * * * * **
2769836 CCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCGATATTATTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCGATATCGTTGGCCT
*
2769901 TGAATCAGCATATTGGCATCTT
66 TGAATCAGCACATTGGCATCTT
2769923 TAACATTCCT
Statistics
Matches: 192, Mismatches: 40, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
147 116 0.60
148 4 0.02
150 72 0.38
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (148 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCGATATCGTTGGCCT
TGAATCAGCACATTGGCATCTTACATCTTTAAGCCCAATATAGCCGGCCTTGAATCAACACATTG
GCACTTTCATCTTTAAGA
Found at i:2770842 original size:13 final size:13
Alignment explanation
Indices: 2770824--2770849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2770814 ACATAAGTGT
2770824 TGTATCGATACAA
1 TGTATCGATACAA
2770837 TGTATCGATACAA
1 TGTATCGATACAA
2770850 AATTGCCCTG
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:2771897 original size:20 final size:20
Alignment explanation
Indices: 2771860--2771897 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2771850 TAAACCTTGA
*
2771860 TCATGCATTTTTACCATGCT
1 TCATGCATTTATACCATGCT
*
2771880 TCATGCATTTATAGCATG
1 TCATGCATTTATACCATG
2771898 TCCAACACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (20 bp):
TCATGCATTTATACCATGCT
Found at i:2777177 original size:20 final size:18
Alignment explanation
Indices: 2777151--2777209 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
2777141 TTGTATCGAT
2777151 ACATTGTATCGATTACATG
1 ACATTGTATCGA-TACATG
* *
2777170 ATCATTGTATTGACACATG
1 A-CATTGTATCGATACATG
2777189 CACAATTGTATCGATACATG
1 -AC-ATTGTATCGATACATG
2777209 A
1 A
2777210 AACTTGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 8 0.24
20 25 0.76
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:2777276 original size:13 final size:13
Alignment explanation
Indices: 2777258--2777282 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2777248 CATGGCACAT
2777258 TGTATCGATACAA
1 TGTATCGATACAA
2777271 TGTATCGATACA
1 TGTATCGATACA
2777283 TGAAGAATTG
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:2777280 original size:33 final size:32
Alignment explanation
Indices: 2777238--2777302 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2777228 TATCTCTGTT
2777238 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
2777271 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATG-AGAATTGTATCGATACA
2777303 TTCTCTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:2777811 original size:61 final size:61
Alignment explanation
Indices: 2777723--2779707 Score: 2041
Period size: 61 Copynumber: 32.5 Consensus size: 61
2777713 AAAATACTAT
* * * * * *
2777723 AAAGGGAAAAGCATCCTACTCTATGAGGACTGAAAGGTGCCACCAACTTATGTGGGTTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
2777784 AAAGGGAAAGACGTCCTGCTCTTTGAGGACTGAAATGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
2777845 AAAGGGAAAGGCGACCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
*
2777906 AAAGGGAAAGGTGTCCTGCTCTTTGAGGAC-------T-CCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* ** * * *
2777959 GAAA-TGAAA-ATGTCCTACTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTAA
1 -AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * ** * * *
2778019 AAAAGGAAAGGCATCCTATTTTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * *
2778080 AAA-GGAGAAGGCGTTCTGCTCTTTTAAGACTAAAAGGTGCCACCAACTTGTATGGGCTTTCG
1 AAAGGGA-AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-A
* * * * * * *
2778142 AAAGGAAAAGACATCCTACTCTTTAAAGACTGAAAGGTGTCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * *
2778203 AAAGGGAAAAGCATCCT-CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTAT-
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * *
2778262 AAAGGGAAAGGCATCTTGCTTTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * *
2778323 AAAGGGAAAAGCGTCCTGCTTTTTGAGGACTGAAAGTTACTACCAACTTGTGTGGGCTTTAA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-A
** * * * * *
2778385 AAAGAAAAAAGCGTCCTGCTTTTTTAGGACTGAAAGGTGTCACCAACTTGAGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
** * * * *
2778446 AAAGAAAAAGGCATCCTACTCTTTGCGGACTGAAAGGTGCCACCAACTTGTGTGGGTTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * ** *
2778507 AAAGGGAAAGGCATCCTGCTCTTCGAGGACTAAAATATGGCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * *
2778568 AAAGGAAAAGGTGTCCTGCTCTTTGAGGACTGCAAGGTGCCATCAACTTGTGTGGGCTTAA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * ** * *
2778629 AAAGGGGAAGGTGTCCTATTCTTTAAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * *
2778690 AAA-GGAGAAGGTGTCCTGCTCTTTGAAGACTAAAAGGTGCCA-CAACTTGTGTGGGCTTTA
1 AAAGGGA-AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * * * *
2778750 GAAAGGAAAATGCGTCCTACTCTTGGAAGACTAAAAGGTGTCACCAACTTGTGTGGGTTTTA
1 -AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * *
2778812 AAAGGAAAAAGCGTCCTACTTTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTATA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
2778873 AAAGGGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGCCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * * * * * *
2778934 AAAAGGAAAAGCGTCCTGCTTTTTAAGGATTGAAAGGTGCCACTAACTTCTATGTGCTATA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* *
2778995 AAAGGGAAAGGCATCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * * *
2779056 AAAGGGAAAGACATCTTGCTTTTTGAGGACTGAAAAGTACCACCAACTTGTGTGGACTTTAA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-A
* * ** * * *
2779118 AAAGGAAAAGGTGTCCTATTCTTTGAGGACTGAAAGGTGTCACCATCTTGTATGGGCTTTA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * * * *
2779179 AAAGGAAAAAGGCGTCTTCCTCTTTGAGGACTAAAAAGGTGCCACCAACTCGTGTAGGCTTCGA
1 AAAGG-GAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT-TA
* * * *
2779243 AAAGGAAAATGAC-T--TGCTCTTTGAGGACTGAAAAGTACCACCAACTTGTGTGGGCTTTA
1 AAAGGGAAA-GGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * * *
2779302 AAA-GGAGAAGGTGTCATGTTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGA
1 AAAGGGA-AAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-A
** * *
2779364 AAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGGTGCCACCAACTTGTGTGGGCTTTAA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTT-A
* * *
2779427 AAAGGAAAAGGCGTCCTGCTCTTTGAGGGCTGAAAGGGTGCCACCAACTCGTGTGGGCTTTGA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTT-A
** * * * * *
2779490 AAAGAAAAAGGCATACTGGTCTTTAAGGACTAGCAGAA--TGCCACCAACTCGTGTGGGCTTTGA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACT-G-A-AAGGTGCCACCAACTTGTGTGGGCTTT-A
* ** * * * * * *
2779553 GAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGGTGCTACCAACTCGTGTAGGCTTTGA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTT-A
* * * * * *
2779616 AAAGGAAAAGACGTCCTGCTCTTTAAGGACTAAAAAGGTGCCACCAACTTATGTCGGCTTTGA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-A
** * *
2779679 AAAGAAAAATGTGTCCTGCTCTTTGAGGA
1 AAAGGGAAAGGCGTCCTGCTCTTTGAGGA
2779708 TTAAAGGATC
Statistics
Matches: 1628, Mismatches: 256, Indels: 78
0.83 0.13 0.04
Matches are distributed among these distances:
52 17 0.01
53 25 0.02
54 4 0.00
58 3 0.00
59 26 0.02
60 149 0.09
61 888 0.55
62 217 0.13
63 283 0.17
64 13 0.01
65 1 0.00
66 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (61 bp):
AAAGGGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
Found at i:2777952 original size:53 final size:52
Alignment explanation
Indices: 2777884--2777988 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 52
2777874 CTGAAAGGTG
* *
2777884 CCACCAACTTATGTGGGCTTTA-AAAGGGAAAGGTGTCCTGCTCTTTGAGGACT
1 CCACCAACTTATGTGGGCTTTAGAAA-GGAAA-ATGTCCTACTCTTTGAGGACT
* * *
2777937 CCACCAACTTGTGTGGGCTTTAGAAATGAAAATGTCCTACTTTTTGAGGACT
1 CCACCAACTTATGTGGGCTTTAGAAAGGAAAATGTCCTACTCTTTGAGGACT
2777989 GAAAGGTGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 18 0.39
53 25 0.54
54 3 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (52 bp):
CCACCAACTTATGTGGGCTTTAGAAAGGAAAATGTCCTACTCTTTGAGGACT
Found at i:2787802 original size:80 final size:80
Alignment explanation
Indices: 2787669--2787929 Score: 315
Period size: 80 Copynumber: 3.3 Consensus size: 80
2787659 TCCATTTCCT
* * * * *
2787669 TCTTCATGTGCTACATGTTTCTTCATCATTTGCACATTGCTTGTTTTTTGTTTGCTGCTCGTGAT
1 TCTTCACGTGCTGCATGTTTCTTCATCATTTGCACATTGCTTGCTTGTTGTTTGCTGCTCGTGCT
*
2787734 GTCCTCATTCCCTGC
66 GTCCTCATTCCTTGC
** * *
2787749 TCTTCACGTGCTGCATGCCTCTTCATCATTTGCATATTGCTTACTTGTTGTTTGCTGCTCGTGCT
1 TCTTCACGTGCTGCATGTTTCTTCATCATTTGCACATTGCTTGCTTGTTGTTTGCTGCTCGTGCT
* * * *
2787814 ATCCCCCTTCCTTGT
66 GTCCTCATTCCTTGC
* * * ** *
2787829 TGTTCACGTGCTGCATGTTTCTTCATCATTTGCACATTGCTTGCTTGTTGGTTGCTACTTATGCC
1 TCTTCACGTGCTGCATGTTTCTTCATCATTTGCACATTGCTTGCTTGTTGTTTGCTGCTCGTGCT
*
2787894 GTCCTCTTTCCTTGC
66 GTCCTCATTCCTTGC
* *
2787909 TGTTCACGTGCTGTATGTTTC
1 TCTTCACGTGCTGCATGTTTC
2787930 CTCTTGCTTT
Statistics
Matches: 152, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 152 1.00
ACGTcount: A:0.10, C:0.26, G:0.18, T:0.46
Consensus pattern (80 bp):
TCTTCACGTGCTGCATGTTTCTTCATCATTTGCACATTGCTTGCTTGTTGTTTGCTGCTCGTGCT
GTCCTCATTCCTTGC
Found at i:2788643 original size:32 final size:33
Alignment explanation
Indices: 2788602--2788669 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2788592 GTAGCCAAAC
*
2788602 TTGTATCGATACA-CA-AAGTATATATCGATACA
1 TTGTATCGATACACCATAA-AATATATCGATACA
*
2788634 TTGTATCGATACACCATAAAATTTATCGATACA
1 TTGTATCGATACACCATAAAATATATCGATACA
2788667 TTG
1 TTG
2788670 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 17 0.53
34 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATATATCGATACA
Found at i:2789650 original size:13 final size:13
Alignment explanation
Indices: 2789632--2789656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2789622 TTTTTTTGGA
2789632 TATTTGATTTTTT
1 TATTTGATTTTTT
2789645 TATTTGATTTTT
1 TATTTGATTTTT
2789657 ATTTGTTATC
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TATTTGATTTTTT
Found at i:2790852 original size:20 final size:21
Alignment explanation
Indices: 2790829--2790882 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
2790819 CATTTCAGGC
2790829 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
*
2790849 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
*
2790870 TTGTATCGATACA
1 ATGTATCGATACA
2790883 AATTGTAGAA
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:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:2794794 original size:31 final size:32
Alignment explanation
Indices: 2794717--2794799 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
2794707 GATTAAAATT
* *
2794717 AAATAAAATTATAATAAAA-TAATTATTTTATAA
1 AAATTAAATTA-AATAAAATTAATTA-TTAATAA
2794750 AAATTAAATTAAATAAAATTAATTA-TAATAA
1 AAATTAAATTAAATAAAATTAATTATTAATAA
* *
2794781 TAATTTAATTAAATAAAAT
1 AAATTAAATTAAATAAAAT
2794800 AACATAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 22 0.49
32 7 0.16
33 16 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATTAAATTAAATAAAATTAATTATTAATAA
Found at i:2794797 original size:47 final size:43
Alignment explanation
Indices: 2794712--2794798 Score: 111
Period size: 43 Copynumber: 1.9 Consensus size: 43
2794702 TGGTTGATTA
**
2794712 AAATTAAATAAAATTATAATAAAATAATTATTTTATAAAAATT
1 AAATTAAATAAAATTATAATAAAATAATTATTAAATAAAAATT
*
2794755 AAATTAAATAAAATTAATTATAATAATAATTTAATTAAATAAAA
1 AAATTAAATAAAATT-ATAATAA-AATAA-TT-ATTAAATAAAA
2794799 TAACATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 15 0.41
44 6 0.16
45 5 0.14
46 2 0.05
47 9 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (43 bp):
AAATTAAATAAAATTATAATAAAATAATTATTAAATAAAAATT
Found at i:2794812 original size:31 final size:30
Alignment explanation
Indices: 2794722--2794814 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 30
2794712 AAATTAAATA
** *
2794722 AAATTATAATAAAATAATTATTTTATAAAAATT
1 AAATTA-AATAAAATAA--ATAATATAATAATT
* *
2794755 AAATTAAATAAAATTAATTATAATAATAATT
1 AAATTAAATAAAATAAATAAT-ATAATAATT
*
2794786 TAATTAAATAAAATAACATAATATAATAA
1 AAATTAAATAAAATAA-ATAATATAATAA
2794815 AACTGTATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 4 0.08
31 29 0.56
32 13 0.25
33 6 0.12
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATTAAATAAAATAAATAATATAATAATT
Found at i:2796695 original size:41 final size:41
Alignment explanation
Indices: 2796602--2796695 Score: 95
Period size: 41 Copynumber: 2.3 Consensus size: 41
2796592 ATACAATTTT
* * *
2796602 TAAGATTAAATATTATTTTTTATTATAAATATAATATTAAA
1 TAAGTTTAAATTTTATTTTTTATTAAAAATATAATATTAAA
**
2796643 TAAGTAAAAATTTTAGTTTTTATATTTAAAAATATAAT-TT-AA
1 TAAGTTTAAATTTTA-TTTTT-TA-TTAAAAATATAATATTAAA
2796685 TAA-TTTAAATT
1 TAAGTTTAAATT
2796696 AAAAAGTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
41 17 0.40
42 10 0.23
43 4 0.09
44 12 0.28
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (41 bp):
TAAGTTTAAATTTTATTTTTTATTAAAAATATAATATTAAA
Found at i:2796848 original size:14 final size:14
Alignment explanation
Indices: 2796829--2796892 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
2796819 TGCTTAAAAA
*
2796829 TTTTTAAATTATAT
1 TTTTTAAATTAAAT
*
2796843 TTTTTAAA-TATACT
1 TTTTTAAATTA-AAT
* *
2796857 TTTTCAACTTAAAT
1 TTTTTAAATTAAAT
2796871 ATTTTT-AATCTAAAT
1 -TTTTTAAAT-TAAAT
2796886 TTTTTAA
1 TTTTTAA
2796893 CAATAATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 12 0.32
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAATTAAAT
Found at i:2797143 original size:19 final size:19
Alignment explanation
Indices: 2797094--2797132 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2797084 AAAACTATTA
*
2797094 ATATATTGATTTATATATTT
1 ATATATT-ATTTATAAATTT
2797114 ATATATTATTTATAAATTT
1 ATATATTATTTATAAATTT
2797133 TTAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATATTATTTATAAATTT
Found at i:2797702 original size:18 final size:18
Alignment explanation
Indices: 2797676--2797715 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2797666 TCCTTATATT
* *
2797676 ATTTTTTTATAAAAATAC
1 ATTTATTTAAAAAAATAC
*
2797694 ATTTATTTAAAAAAATAT
1 ATTTATTTAAAAAAATAC
2797712 ATTT
1 ATTT
2797716 TTCACCCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATTTAAAAAAATAC
Found at i:2799570 original size:42 final size:42
Alignment explanation
Indices: 2799519--2799626 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
2799509 GAGAAAGAAG
*
2799519 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAA
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAA
* * *
2799561 AGATAGGAGGGATGATAGGACGAGAGACAGGAGAGATAATAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAA
*
2799603 AGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGGAGGGATGATAGGAGGAG
2799627 GAGAGAAGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.42, C:0.04, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAA
Found at i:2799593 original size:24 final size:23
Alignment explanation
Indices: 2799517--2799608 Score: 79
Period size: 24 Copynumber: 4.2 Consensus size: 23
2799507 AAGAGAAAGA
*
2799517 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGA-G
*
2799541 AGAGACAGGA--GA-GATAGTA-
1 AGAGACAGGAGGGATGATAGGAG
*
2799560 A-AGATAGGAGGGATGATAGGACG
1 AGAGACAGGAGGGATGATAGGA-G
* *
2799583 AGAGACAGGAGAGATAATA-GAG
1 AGAGACAGGAGGGATGATAGGAG
2799605 AGAG
1 AGAG
2799609 GAGGGATGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
18 7 0.13
19 1 0.02
20 2 0.04
21 12 0.22
22 7 0.13
23 3 0.05
24 23 0.42
ACGTcount: A:0.43, C:0.03, G:0.43, T:0.10
Consensus pattern (23 bp):
AGAGACAGGAGGGATGATAGGAG
Found at i:2799598 original size:21 final size:20
Alignment explanation
Indices: 2799532--2799598 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
2799522 GAGGAGGGAT
2799532 GATAGGAGGAGAGACAGGAGA
1 GATAGGA-GAGAGACAGGAGA
* *
2799553 GATAGTA-A-AGATAGGAGGGA
1 GATAGGAGAGAGACAGGA--GA
2799573 TGATAGGACGAGAGACAGGAGA
1 -GATAGGA-GAGAGACAGGAGA
2799595 GATA
1 GATA
2799599 ATAGAGAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 2 0.06
21 16 0.44
22 2 0.06
23 1 0.03
24 7 0.19
ACGTcount: A:0.43, C:0.04, G:0.42, T:0.10
Consensus pattern (20 bp):
GATAGGAGAGAGACAGGAGA
Found at i:2807491 original size:13 final size:13
Alignment explanation
Indices: 2807473--2807498 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2807463 GAATTAATGT
2807473 TTGGCTGCCTTGG
1 TTGGCTGCCTTGG
2807486 TTGGCTGCCTTGG
1 TTGGCTGCCTTGG
2807499 AAGCCATGGC
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:0.00, C:0.23, G:0.38, T:0.38
Consensus pattern (13 bp):
TTGGCTGCCTTGG
Found at i:2807817 original size:52 final size:51
Alignment explanation
Indices: 2807676--2807825 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
2807666 CGAAATATGA
*
2807676 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGACACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
2807728 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
2807780 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
2807826 TTTTTGGCAG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:2807881 original size:33 final size:33
Alignment explanation
Indices: 2807844--2807910 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2807834 AGTAGCTTAA
2807844 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2807877 ATTGTATCGATACAAGACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2807910 A
1 A
2807911 AATCGTTGAA
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:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2807884 original size:13 final size:13
Alignment explanation
Indices: 2807866--2807890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2807856 CAAAAAAATA
2807866 TGTATCGATACAT
1 TGTATCGATACAT
2807879 TGTATCGATACA
1 TGTATCGATACA
2807891 AGACTTTATG
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:2808438 original size:32 final size:30
Alignment explanation
Indices: 2808381--2808451 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 30
2808371 ATATTACTGT
*
2808381 AAAAAA-ATATTTTAAGAAAATTAAAATGTTA
1 AAAAAATATATTTTAAGAAAATTAAAA--ATA
2808412 AAAAAATATATATTTAA-AATAA-TAAAAATA
1 AAAAAATATAT-TTTAAGAA-AATTAAAAATA
2808442 AAAAAATATA
1 AAAAAATATA
2808452 AAAATAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 12 0.33
31 6 0.17
32 11 0.31
33 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAAAATATATTTTAAGAAAATTAAAAATA
Found at i:2808441 original size:9 final size:9
Alignment explanation
Indices: 2808427--2808463 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
2808417 ATATATATTT
2808427 AAAATAATA
1 AAAATAATA
2808436 AAAATAA-A
1 AAAATAATA
2808444 AAAAT-ATA
1 AAAATAATA
2808452 AAAATAATA
1 AAAATAATA
2808461 AAA
1 AAA
2808464 TTATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 12 0.46
9 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAATA
Found at i:2808446 original size:16 final size:18
Alignment explanation
Indices: 2808426--2808464 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
2808416 AATATATATT
2808426 TAAAATA-ATAAAAATAA
1 TAAAATATATAAAAATAA
2808443 -AAAA-ATATAAAAATAA
1 TAAAATATATAAAAATAA
2808459 TAAAAT
1 TAAAAT
2808465 TATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.05
16 14 0.74
17 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAATATATAAAAATAA
Found at i:2808869 original size:4 final size:4
Alignment explanation
Indices: 2808855--2808886 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
2808845 TTCCAAATAC
2808855 TTAT ATTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTA
2808887 CAAATAAGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:2812367 original size:22 final size:24
Alignment explanation
Indices: 2812342--2812391 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
2812332 TAATTTAATT
2812342 TAATATT-ATAAA-TTA-AAAAATA
1 TAATATTGATAAATTTATAAAAA-A
2812364 TAAT-TTGATAAATTTATAAAAAA
1 TAATATTGATAAATTTATAAAAAA
2812387 TAATA
1 TAATA
2812392 AATTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 8 0.33
24 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATATTGATAAATTTATAAAAAA
Found at i:2812381 original size:30 final size:31
Alignment explanation
Indices: 2812325--2812383 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2812315 ATCAACCATC
*
2812325 AAAAAAATAATTTAATTTAATATTATAAATT
1 AAAAAAATAATTTAATTAAATATTATAAATT
*
2812356 AAAAAATATAATTTGA-TAAAT-TTATAAA
1 AAAAAA-ATAATTTAATTAAATATTATAAA
2812384 AAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 10 0.40
32 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAAAAATAATTTAATTAAATATTATAAATT
Found at i:2813308 original size:13 final size:13
Alignment explanation
Indices: 2813278--2813325 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2813268 ATAATTATTT
*
2813278 TAAATATAATTTAA
1 TAAATATAA-TAAA
2813292 -AAATATAATAAA
1 TAAATATAATAAA
2813304 TAAATATAA-AAA
1 TAAATATAATAAA
2813316 T-AATATAATA
1 TAAATATAATA
2813326 TTTGATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 7 0.23
12 8 0.26
13 16 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATATAATAAA
Found at i:2814195 original size:19 final size:19
Alignment explanation
Indices: 2814171--2814218 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 19
2814161 ATATATATCA
*
2814171 TATTTATATAAATTATTTT
1 TATTTATATAAATTATATT
2814190 TA-TT-TAT-AATTATATT
1 TATTTATATAAATTATATT
2814206 TATTTTATATAAA
1 TA-TTTATATAAA
2814219 ATTTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 10 0.42
17 3 0.12
18 4 0.17
19 5 0.21
20 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTATATAAATTATATT
Found at i:2814222 original size:16 final size:16
Alignment explanation
Indices: 2814203--2814253 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2814193 TTATAATTAT
2814203 ATTTATTTTATATAAA
1 ATTTATTTTATATAAA
* *
2814219 ATTTAATATAT-TAATA
1 ATTTATTTTATATAA-A
2814235 ATTTATTTTATA-AAA
1 ATTTATTTTATATAAA
2814250 ATTT
1 ATTT
2814254 TAAATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATTTTATATAAA
Found at i:2814271 original size:16 final size:17
Alignment explanation
Indices: 2814250--2814295 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2814240 TTTTATAAAA
2814250 ATTTTAAATATTTTTAT
1 ATTTTAAATATTTTTAT
* * *
2814267 A-TTTATATAATATTAT
1 ATTTTAAATATTTTTAT
2814283 ATTTTAAATATTT
1 ATTTTAAATATTT
2814296 AATTTATTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTAAATATTTTTAT
Found at i:2814271 original size:32 final size:33
Alignment explanation
Indices: 2814199--2814295 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 33
2814189 TTATTTATAA
*
2814199 TTATATTTATTTTATATAAAA-TTT-AATATAT
1 TTATATTTATTTTATATAAAATTTTAAATATTT
*
2814230 TAATAATTTATTTTATA-AAAATTTTAAATATTT
1 TTAT-ATTTATTTTATATAAAATTTTAAATATTT
* * * *
2814263 TTATATTTATATAATATTATATTTTAAATATTT
1 TTATATTTATTTTATATAAAATTTTAAATATTT
2814296 AATTTATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 7 0.13
32 25 0.45
33 23 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TTATATTTATTTTATATAAAATTTTAAATATTT
Found at i:2814625 original size:23 final size:24
Alignment explanation
Indices: 2814597--2814645 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2814587 TTTTAATACC
*
2814597 TAAAAATTTTAATTTTAATTTTTT
1 TAAAAATTTAAATTTTAATTTTTT
*
2814621 TAAAAATTTAAATTTTACTTTTTT
1 TAAAAATTTAAATTTTAATTTTTT
2814645 T
1 T
2814646 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TAAAAATTTAAATTTTAATTTTTT
Found at i:2814830 original size:30 final size:33
Alignment explanation
Indices: 2814791--2814857 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 33
2814781 TTTAATTTTT
*
2814791 ATTATAATTTT-AATTAATTTT-TT-AATAAAA
1 ATTAAAATTTTAAATTAATTTTATTAAATAAAA
*
2814821 ATTAAAATTTTAAATTAATTTTATTAAATAATA
1 ATTAAAATTTTAAATTAATTTTATTAAATAAAA
2814854 ATTA
1 ATTA
2814858 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 10 0.31
31 10 0.31
32 2 0.06
33 10 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
ATTAAAATTTTAAATTAATTTTATTAAATAAAA
Found at i:2816690 original size:18 final size:19
Alignment explanation
Indices: 2816654--2816697 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2816644 CCTTGACACA
2816654 AATTATTTTAAATAGTAATAT
1 AATT-TTTTAAATA-TAATAT
*
2816675 AATTTTTTAAAT-TAATTT
1 AATTTTTTAAATATAATAT
2816693 AATTT
1 AATTT
2816698 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTTTAAATATAATAT
Found at i:2817904 original size:23 final size:22
Alignment explanation
Indices: 2817865--2817912 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
2817855 GAGAATGAAC
2817865 TATTAAGATTTAAATTTTAAACA
1 TATTAAGATTTAAA-TTTAAACA
* *
2817888 TATTAA-ATGTTATATTTAAATA
1 TATTAAGAT-TTAAATTTAAACA
2817910 TAT
1 TAT
2817913 GTATTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
TATTAAGATTTAAATTTAAACA
Found at i:2818032 original size:79 final size:79
Alignment explanation
Indices: 2817947--2818195 Score: 313
Period size: 79 Copynumber: 3.2 Consensus size: 79
2817937 TTTTTAAGAA
* * * *
2817947 ATATTTAAAATATAGATTATTATTTACTCACTAACAGTAAAGTTTAAAGATTTCATAAATAAAAT
1 ATATTTAAAATATAGATTATTATTTATTCACTGATAGTAGAGTTTAAAGATTTCATAAATAAAAT
*
2818012 TCATATATTTTAAT
66 TCACATATTTTAAT
* * * * *
2818026 ATATTTAAAATATAAATTATTATTTATTCATTGATAATAGAGTCTAAAGACTTT-GTAAATAAAA
1 ATATTTAAAATATAGATTATTATTTATTCACTGATAGTAGAGTTTAAAGA-TTTCATAAATAAAA
*
2818090 TTCACATATCTTAAT
65 TTCACATATTTTAAT
* * * *
2818105 ATATTCAAAATATAGATTATTATCTATTCACTGATAGTAGAGTTTAAAAATTTCATAAACAAAAT
1 ATATTTAAAATATAGATTATTATTTATTCACTGATAGTAGAGTTTAAAGATTTCATAAATAAAAT
*
2818170 TTACAT-TTCTTAAT
66 TCACATATT-TTAAT
*
2818184 ACATTTAAAATA
1 ATATTTAAAATA
2818196 AAAAAATAAA
Statistics
Matches: 143, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
78 4 0.03
79 136 0.95
80 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (79 bp):
ATATTTAAAATATAGATTATTATTTATTCACTGATAGTAGAGTTTAAAGATTTCATAAATAAAAT
TCACATATTTTAAT
Found at i:2819269 original size:12 final size:12
Alignment explanation
Indices: 2819254--2819301 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
2819244 ACTTTTTTAA
*
2819254 TATATTTTTATT
1 TATATTATTATT
2819266 TATATTATTA-T
1 TATATTATTATT
2819277 TATTATTATTA-T
1 TA-TATTATTATT
2819289 TATTATTATTATT
1 TA-TATTATTATT
2819302 ATTTTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 3 0.09
12 29 0.88
13 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTATTATT
Found at i:2819276 original size:3 final size:3
Alignment explanation
Indices: 2819268--2819304 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2819258 TTTTTATTTA
2819268 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2819305 TTGTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2820552 original size:24 final size:24
Alignment explanation
Indices: 2820525--2820572 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2820515 TAAACCAAAC
2820525 ATATCAATATAATTTTATTAAGAT
1 ATATCAATATAATTTTATTAAGAT
2820549 ATATCAATATAATTTTATTAAGAT
1 ATATCAATATAATTTTATTAAGAT
2820573 TTTAATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATCAATATAATTTTATTAAGAT
Found at i:2821139 original size:36 final size:35
Alignment explanation
Indices: 2821062--2821142 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
2821052 GGTCTTTGAT
*
2821062 ATTTGATTTTAAAATTTGCTTCAAAAGTCATTAAG
1 ATTTGATCTTAAAATTTGCTTCAAAAGTCATTAAG
* * * *
2821097 -TCTTGATCTTGAAATTTGCTTTAAAGGTCTTTTAAG
1 AT-TTGATCTTAAAATTTGCTTCAAAAGTC-ATTAAG
2821133 ATTTGATCTT
1 ATTTGATCTT
2821143 TAATCAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 1 0.03
35 23 0.61
36 13 0.34
37 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (35 bp):
ATTTGATCTTAAAATTTGCTTCAAAAGTCATTAAG
Found at i:2821554 original size:20 final size:20
Alignment explanation
Indices: 2821529--2821604 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
2821519 AAAAACTCAG
2821529 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAA
* *
2821549 AATGTATCGATACGATGATA
1 AATGTATCGATACAATGAAA
* *
2821569 AATGTATTGATACAACTTTAAA
1 AATGTATCGATACAA--TGAAA
*
2821591 CATGTATCGATACA
1 AATGTATCGATACA
2821605 TTTCTTTAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 31 0.67
22 15 0.33
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:2821649 original size:13 final size:13
Alignment explanation
Indices: 2821631--2821656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2821621 CAGGGTAGTT
2821631 TTGTATCGATACA
1 TTGTATCGATACA
2821644 TTGTATCGATACA
1 TTGTATCGATACA
2821657 AAACTTATGT
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):
TTGTATCGATACA
Found at i:2822348 original size:9 final size:9
Alignment explanation
Indices: 2822334--2822368 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2822324 ACACTAGACT
2822334 TGAAGATGA
1 TGAAGATGA
2822343 TGAAGATGA
1 TGAAGATGA
2822352 T-AAGAGTGA
1 TGAAGA-TGA
2822361 TGAAGATG
1 TGAAGATG
2822369 CCAATATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.17
9 16 0.67
10 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (9 bp):
TGAAGATGA
Found at i:2822536 original size:53 final size:52
Alignment explanation
Indices: 2822367--2822984 Score: 359
Period size: 52 Copynumber: 11.8 Consensus size: 52
2822357 GTGATGAAGA
* * *
2822367 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * * * *
2822419 TGCTAATGTGCTAATTCAATGCCAGCGACATTGGACTTAAAAATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * *
2822471 CGCCAATATGCTGATTCAAGGCCAACGATATTGGACTAAAAAAAGAAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG-AAAAAGG
* * * * * * *
2822524 TACCAATGTGCTGATTCGAGGCCAGTGACATTGGACTGAAAGATGTGAGGAATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT--TA-A----A--AATGAAAAAGG
* * * * * *
2822585 TGCTAATATGCTAATTCAAGGCTAGCGATATTGGGCTTAAAGAT-ACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* ** * * ** *
2822636 TTCCAAGGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAGTATG--AGAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * * * * ** *
2822686 AATGCCAATGTGCTAATTCAAGGCTAGCAACATTGGGCTTAGGAATGAAAAAGA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * * **
2822740 TACTAGTATGCTAATTCAAGGCCAGCGATATCAGACTTAAGAAA-GAAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA-AAATGAAAAAGG
* * ** ** **
2822792 TGCCAATGA-GCTAATTCAAGGCCAGCGACATTAAACTTAAGGATGGCAAAGG
1 TGCCAAT-ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * * * * * *
2822844 CGTCAATATGTTGATTTAAGGCCAGCAATATTAGACTTAAAGATGGAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* ** * * * *
2822896 CGTTAATATGCTAATTCAAGGCCAGTGTTATTGGACTTAAGAA--AAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
* * * * * *
2822946 TGCCAATGTACTGATTTAAGGCCAACGACATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
2822985 GAAGGAGATG
Statistics
Matches: 433, Mismatches: 114, Indels: 40
0.74 0.19 0.07
Matches are distributed among these distances:
50 37 0.09
51 43 0.10
52 267 0.62
53 39 0.09
54 4 0.01
55 2 0.00
56 1 0.00
58 1 0.00
59 1 0.00
60 1 0.00
61 34 0.08
62 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAAAAGG
Found at i:2822686 original size:112 final size:112
Alignment explanation
Indices: 2822460--2822689 Score: 266
Period size: 112 Copynumber: 2.0 Consensus size: 112
2822450 TGGACTTAAA
*
2822460 AATGACAAAGGCGCCAATATGCTGATTCAAGGCCAACGATATTGGACTAAAAAAAGAAAAAAGGT
1 AATGACAAAGGCGCCAATATGCTAATTCAAGGCCAACGATATTGGACT--AAAAAGAAAAAAGGT
* * * *
2822525 ACCAATGTGCTGATTCGAGGCCAGTGACATTGGACTGAAAGATGTGAGG
64 ACCAAGGTGCTGATTCAAGGCCAGCGACATTGGACTGAAAGATGAGAGG
* * * * * * * * *
2822574 AATGATAAAGGTGCTAATATGCTAATTCAAGGCTAGCGATATTGGGCT-TAAAGATACAAAGGTT
1 AATGACAAAGGCGCCAATATGCTAATTCAAGGCCAACGATATTGGACTAAAAAGA-AAAAAGGTA
* *
2822638 CCAAGGTGCTGATTCAAGGCCAGCGACATTGGGCT-TAAGTATGAGAGG
65 CCAAGGTGCTGATTCAAGGCCAGCGACATTGGACTGAAAG-ATGAGAGG
2822686 AATG
1 AATG
2822690 CCAATGTGCT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
111 8 0.08
112 49 0.50
114 41 0.42
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (112 bp):
AATGACAAAGGCGCCAATATGCTAATTCAAGGCCAACGATATTGGACTAAAAAGAAAAAAGGTAC
CAAGGTGCTGATTCAAGGCCAGCGACATTGGACTGAAAGATGAGAGG
Found at i:2823068 original size:33 final size:33
Alignment explanation
Indices: 2823001--2823085 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
2822991 GATGCCACTA
* *
2823001 ACTTGTGTGGGCTTTTG-AGAATGTTGCCATCG
1 ACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCG
* *
2823033 ACTTGTCTGGGCTTTTGAAGCAGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCG
* *
2823066 ACTTATGTGGGCTTTAGAAG
1 ACTTGTGTGGGCTTTTGAAG
2823086 GGATGAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 16 0.36
33 29 0.64
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.34
Consensus pattern (33 bp):
ACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCG
Found at i:2823164 original size:34 final size:33
Alignment explanation
Indices: 2823107--2823565 Score: 285
Period size: 34 Copynumber: 14.4 Consensus size: 33
2823097 CACAAAATTA
*
2823107 TGGA-TTTAAAGGAAAAAAGGTGCCACAGAGTTG
1 TGGACTTTAAAAG-AAAAAGGTGCCACAGAGTTG
* *
2823140 TGGGCTTTGAAAAGAAAAATGTGCCACAGAGTTG
1 TGGACTTT-AAAAGAAAAAGGTGCCACAGAGTTG
* *
2823174 TAGG-CTTTGAAAAGAAAAATGTGCCACGGAGTTG
1 T-GGACTTT-AAAAGAAAAAGGTGCCACAGAGTTG
2823208 TGGAC-TTAAAAG-----GGTGCCACAGAGTTG
1 TGGACTTTAAAAGAAAAAGGTGCCACAGAGTTG
* *
2823235 TGGACTTTAAGAGAAAAAGATGCCAC-GAAGTTG
1 TGGACTTTAAAAGAAAAAGGTGCCACAG-AGTTG
* * *
2823268 TGGAC-TTAAATG-----GGTGCCA-TGAGTTA
1 TGGACTTTAAAAGAAAAAGGTGCCACAGAGTTG
* * *
2823294 TGGACTTTAAGAGGAAAAGTTGCCAC-GAAGTTG
1 TGGACTTTAAAAGAAAAAGGTGCCACAG-AGTTG
* * *
2823327 TGGAC-TT---A-AAAAGGGTGCTACGGAGTTG
1 TGGACTTTAAAAGAAAAAGGTGCCACAGAGTTG
** * * *
2823355 TGGGTTTTGAAAAGAAAAAGATACCATAGAGTTG
1 TGGACTTT-AAAAGAAAAAGGTGCCACAGAGTTG
*
2823389 TGGAC-TT-----AAAAAGGTGCCACAGAGTTA
1 TGGACTTTAAAAGAAAAAGGTGCCACAGAGTTG
** *
2823416 TGGAC-TTAAAAGGAAAAAAGGTTGCCATGGAATTG
1 TGGACTTTAAAA-G-AAAAAGG-TGCCACAGAGTTG
* *
2823451 TGGGCTTTGAAAAGAAAAAGGATGCCACAGAGTTA
1 TGGACTTT-AAAAGAAAAAGG-TGCCACAGAGTTG
* *
2823486 TGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTA
1 TGGACTTT-AAAAGAAAAAGGTGCCACAGAGTTG
* * **
2823520 TAGACTTTGAAAAGACAAAGGTGCCATGGAGTTG
1 TGGACTTT-AAAAGAAAAAGGTGCCACAGAGTTG
2823554 TGGAC-TTAAAAG
1 TGGACTTTAAAAG
2823566 GGTGCTATGA
Statistics
Matches: 338, Mismatches: 51, Indels: 75
0.73 0.11 0.16
Matches are distributed among these distances:
26 9 0.03
27 53 0.16
28 23 0.07
29 4 0.01
32 25 0.07
33 38 0.11
34 123 0.36
35 56 0.17
36 3 0.01
37 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.23
Consensus pattern (33 bp):
TGGACTTTAAAAGAAAAAGGTGCCACAGAGTTG
Found at i:2823226 original size:27 final size:27
Alignment explanation
Indices: 2823194--2823357 Score: 114
Period size: 33 Copynumber: 5.6 Consensus size: 27
2823184 AAAGAAAAAT
2823194 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* *
2823221 GTGCCACAGAGTTGTGGACTTTAAGAGAAAAAG
1 GTGCCACGGAGTTGTGGAC-TT-----AAAAGG
* * *
2823254 ATGCCACGAAGTTGTGGACTTAAATGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
* * *
2823281 GTGCCA-TGAGTTATGGACTTTAAGAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
*
2823308 AAAAGTTGCCACGAAGTTGTGGACTTAAAAAGG
1 ----G-TGCCACGGAGTTGTGGACTT-AAAAGG
*
2823341 GTGCTACGGAGTTGTGG
1 GTGCCACGGAGTTGTGG
2823358 GTTTTGAAAA
Statistics
Matches: 104, Mismatches: 19, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
26 9 0.09
27 33 0.32
28 16 0.15
29 1 0.01
31 1 0.01
32 9 0.09
33 35 0.34
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:2823321 original size:59 final size:60
Alignment explanation
Indices: 2823160--2823422 Score: 291
Period size: 61 Copynumber: 4.3 Consensus size: 60
2823150 AAAGAAAAAT
* * *
2823160 GTGCCACAGAGTTGTAGG-CTTTGAAAAGAAAAATG-TGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAGTTAT-GGACTTT-AAGAGAAAAA-GATGCCACGAAGTTGTGGACTTAAAAGG
* *
2823221 GTGCCACAGAGTTGTGGACTTTAAGAGAAAAAGATGCCACGAAGTTGTGGACTTAAATGG
1 GTGCCACAGAGTTATGGACTTTAAGAGAAAAAGATGCCACGAAGTTGTGGACTTAAAAGG
* * *
2823281 GTGCCA-TGAGTTATGGACTTTAAGAGGAAAAGTTGCCACGAAGTTGTGGACTTAAAAAGG
1 GTGCCACAGAGTTATGGACTTTAAGAGAAAAAGATGCCACGAAGTTGTGGACTT-AAAAGG
* * * ** * * * *
2823341 GTGCTACGGAGTTGTGGGTTTTGAAAAGAAAAAGATACCA-TAGAGTTGTGGACTTAAAAAG
1 GTGCCACAGAGTTATGGACTTT-AAGAGAAAAAGATGCCACGA-AGTTGTGGACTTAAAAGG
2823402 GTGCCACAGAGTTATGGACTT
1 GTGCCACAGAGTTATGGACTT
2823423 AAAAGGAAAA
Statistics
Matches: 172, Mismatches: 24, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
59 44 0.26
60 51 0.30
61 52 0.30
62 25 0.15
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (60 bp):
GTGCCACAGAGTTATGGACTTTAAGAGAAAAAGATGCCACGAAGTTGTGGACTTAAAAGG
Found at i:2823469 original size:35 final size:34
Alignment explanation
Indices: 2823396--2823545 Score: 178
Period size: 35 Copynumber: 4.4 Consensus size: 34
2823386 TTGTGGACTT
*
2823396 AAAAAGGTGCCACAGAGTTATGGAC-TT-AAAAGG
1 AAAAAGGTGCCACAGAGTTATGGGCTTTGAAAA-G
** * *
2823429 AAAAAAGGTTGCCATGGAATTGTGGGCTTTGAAAAG
1 -AAAAAGG-TGCCACAGAGTTATGGGCTTTGAAAAG
2823465 AAAAAGGATGCCACAGAGTTATGGGCTTTGAAAAG
1 AAAAAGG-TGCCACAGAGTTATGGGCTTTGAAAAG
* *
2823500 AAAAAGGTGCCACAGAGTTATAGACTTTGAAAAG
1 AAAAAGGTGCCACAGAGTTATGGGCTTTGAAAAG
*
2823534 ACAAAGGTGCCA
1 AAAAAGGTGCCA
2823546 TGGAGTTGTG
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
34 43 0.43
35 50 0.50
36 3 0.03
37 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (34 bp):
AAAAAGGTGCCACAGAGTTATGGGCTTTGAAAAG
Found at i:2823479 original size:70 final size:67
Alignment explanation
Indices: 2823396--2823566 Score: 191
Period size: 69 Copynumber: 2.5 Consensus size: 67
2823386 TTGTGGACTT
** * * *
2823396 AAAAAGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAAGGTTGCCATGGAATTGTGGGCTTTGA
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAGG-AAAAAGG-TGCCACAGAATTATAGACTTTGA
2823461 AAAG
64 AAAG
* *
2823465 AAAAAGGATGCCACAGAGTTATGGGCTTTGAAAA-GAAAAAGGTGCCACAGAGTTATAGACTTTG
1 AAAAAGG-TGCCACAGAGTTATGGAC-TT-AAAAGGAAAAAGGTGCCACAGAATTATAGACTTTG
2823529 AAAAG
63 AAAAG
* ** *
2823534 ACAAAGGTGCCATGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACAGAGTTATGGACTTAAAAGG
2823567 GTGCTATGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
66 4 0.05
67 3 0.03
68 14 0.16
69 34 0.40
70 24 0.28
71 3 0.03
72 4 0.05
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (67 bp):
AAAAAGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAGGTGCCACAGAATTATAGACTTTGAAA
AG
Found at i:2823630 original size:30 final size:30
Alignment explanation
Indices: 2823594--2823677 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
2823584 GCTTTTGAAA
*
2823594 GAAAAAGGATGCCATTGAGTCATGGACTTG
1 GAAAAAGGATGCCACTGAGTCATGGACTTG
2823624 GAAAAAGGATGCCACTGAGTCATGGACTTTG
1 GAAAAAGGATGCCACTGAGTCATGGAC-TTG
* **
2823655 G-GAAAGG-TGCCACAAAGTCATGG
1 GAAAAAGGATGCCACTGAGTCATGG
2823678 GGTTTTGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.29
30 31 0.63
31 4 0.08
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.20
Consensus pattern (30 bp):
GAAAAAGGATGCCACTGAGTCATGGACTTG
Found at i:2833939 original size:13 final size:13
Alignment explanation
Indices: 2833921--2833945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2833911 TAAAGATCAG
2833921 TGTATCGATACAA
1 TGTATCGATACAA
2833934 TGTATCGATACA
1 TGTATCGATACA
2833946 TTTGAGTAAT
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:2834872 original size:52 final size:52
Alignment explanation
Indices: 2834804--2835050 Score: 291
Period size: 52 Copynumber: 4.9 Consensus size: 52
2834794 GTTAAAGATG
*
2834804 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
** * *
2834856 AAGACGCCAATATGCTGA-TCTAAGGCCAGCGATATAGGACTTAAGGATGACA
1 AAGGTGCCAATATGCTGATTC-AAGGCCAGCGATATTGGACTTAAAGATGACA
2834908 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---G--G---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
* * * * * *
2834952 -AGGTGCCAATGTGCTAATTCAAGGCCAGCTACAGTGGACTTAAAGGT-ACCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-CA
2835003 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
2835051 AGACGCCACC
Statistics
Matches: 163, Mismatches: 19, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
43 36 0.22
46 1 0.01
47 1 0.01
49 1 0.01
51 2 0.01
52 117 0.72
53 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (52 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
Found at i:2834972 original size:43 final size:45
Alignment explanation
Indices: 2834908--2835046 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 45
2834898 AAGGATGACA
2834908 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-GG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGG
* * * * *
2834952 -AGGTGCCAATGTGCTAATTCAAGGCCAGCTACAGTGGACTTAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--AGG
2834998 TACCAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
1 -----AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
2835047 AAGAAGACGC
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
43 36 0.47
46 2 0.03
50 2 0.03
52 36 0.47
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (45 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGG
Found at i:2835162 original size:30 final size:28
Alignment explanation
Indices: 2835092--2835162 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
2835082 GGCTTGCATC
* *
2835092 AACTTGTGTGCTTTTGAAGGTTGCCACT
1 AACTTGTGGGCTTTTGAAGGGTGCCACT
* *
2835120 GACTTGTAGGCTTTTGAAAAGGGTGCCACT
1 AACTTGTGGGCTTTTG--AAGGGTGCCACT
2835150 AACTTGTGGGCTT
1 AACTTGTGGGCTT
2835163 GAAAGGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 13 0.37
30 22 0.63
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (28 bp):
AACTTGTGGGCTTTTGAAGGGTGCCACT
Found at i:2835191 original size:34 final size:35
Alignment explanation
Indices: 2835153--2835227 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
2835143 TGCCACTAAC
* * *
2835153 TTGTGGGCTT-GAAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
* *
2835187 TTGTGAGCTTACAAAAGAAAAAGAGTGCCATGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
2835222 TTGTGG
1 TTGTGG
2835228 ACTTTGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.33, C:0.09, G:0.35, T:0.23
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:2835254 original size:29 final size:29
Alignment explanation
Indices: 2835205--2835548 Score: 308
Period size: 29 Copynumber: 11.9 Consensus size: 29
2835195 TTACAAAAGA
* *
2835205 AAAAGAGTGCCA-TGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACT-GACTTGTGGGCTTTGG
* *
2835235 AAAAGATGCCACCGACTTGTGGG-TGTCGG
1 AAAAGATGCCACTGACTTGTGGGCT-TTGG
* *
2835264 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * * *
2835293 -AAGGTTTCCACTGACTTGTGGACTTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* * * *
2835321 AAAAGATGCCACTGCCTTGTAGGCGTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
2835350 AAAAAGGTGCCACTGATTTGTGGGCTTT-G
1 -AAAAGATGCCACTGACTTGTGGGCTTTGG
* * * *
2835379 -AAGGTTGCCACTGACTTGTGGACTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
*
2835407 AAAAGATGCCACTGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
2835436 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * * * *
2835465 -AAGGTTGCCATTGACTTGTGGACTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
2835493 AAAAGATGCTACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
2835522 AAAAGATGCCACTGACTTGTGGGCTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
2835549 TGAAGGGTGA
Statistics
Matches: 250, Mismatches: 52, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
27 60 0.24
28 6 0.02
29 119 0.48
30 64 0.26
31 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:2835367 original size:86 final size:86
Alignment explanation
Indices: 2835222--2835554 Score: 506
Period size: 86 Copynumber: 3.9 Consensus size: 86
2835212 TGCCATGGAG
* * * *
2835222 TTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGTGTCGGAAAAGGGTGCCACTGATTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
*
2835287 GCTTTGAAGGTTTCCACTGAC
66 GCTTTGAAGGTTGCCACTGAC
* * *
2835308 TTGTGGACTTTGGAAAAGATGCCACTGCCTTGTAGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
2835373 GCTTTGAAGGTTGCCACTGAC
66 GCTTTGAAGGTTGCCACTGAC
* *
2835394 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
*
2835459 GCTTTGAAGGTTGCCATTGAC
66 GCTTTGAAGGTTGCCACTGAC
* ** * *
2835480 TTGTGGACTTTGAAAAAGATGCTACTGACTTGTGGGC-TTTGAAAAAGATGCCACTGACTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
2835544 GCTTTTGAAGG
66 GC-TTTGAAGG
2835555 GTGAGGAATG
Statistics
Matches: 228, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
85 24 0.11
86 204 0.89
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (86 bp):
TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCGTCGGAAAAAGGTGCCACTGATTTGTGG
GCTTTGAAGGTTGCCACTGAC
Found at i:2837028 original size:16 final size:17
Alignment explanation
Indices: 2837007--2837038 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2836997 TTGTTGTTGT
2837007 TGTTTTTTT-TTTTTTC
1 TGTTTTTTTCTTTTTTC
2837023 TGTTTTTTTCTTTTTT
1 TGTTTTTTTCTTTTTT
2837039 TTTGCGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (17 bp):
TGTTTTTTTCTTTTTTC
Found at i:2837031 original size:19 final size:20
Alignment explanation
Indices: 2837004--2837041 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2836994 TTGTTGTTGT
2837004 TGTTGTTTT-TTTTTTTTTC
1 TGTTGTTTTCTTTTTTTTTC
*
2837023 TGTTTTTTTCTTTTTTTTT
1 TGTTGTTTTCTTTTTTTTT
2837042 GCGGAGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (20 bp):
TGTTGTTTTCTTTTTTTTTC
Found at i:2837041 original size:10 final size:10
Alignment explanation
Indices: 2837009--2837041 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2836999 GTTGTTGTTG
2837009 TTTT-TTTTT
1 TTTTCTTTTT
*
2837018 TTTTCTGTTT
1 TTTTCTTTTT
2837028 TTTTCTTTTT
1 TTTTCTTTTT
2837038 TTTT
1 TTTT
2837042 GCGGAGGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:2850931 original size:52 final size:52
Alignment explanation
Indices: 2850853--2850981 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2850843 CGAAATATGG
*
2850853 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
* *
2850905 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
2850957 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2850982 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGC
Found at i:2850994 original size:52 final size:51
Alignment explanation
Indices: 2850853--2851001 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
2850843 CGAAATATGG
2850853 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
* * *
2850905 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGC
*
2850957 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2851002 ATGTATCTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGC
Found at i:2851014 original size:33 final size:33
Alignment explanation
Indices: 2850969--2851047 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
2850959 ATTTGCCTGC
2850969 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
* *
2851002 ATGTATCTATACAAAGATCAGTGTATTGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
2851035 ATGTATCGATACA
1 ATGTATCGATACA
2851048 TTTGAGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAGTGTATCGATACA
Found at i:2851125 original size:33 final size:33
Alignment explanation
Indices: 2851088--2851154 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2851078 AGTAGCTTAA
2851088 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2851121 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2851154 A
1 A
2851155 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2851128 original size:13 final size:13
Alignment explanation
Indices: 2851110--2851134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2851100 CAAAAAAATA
2851110 TGTATCGATACAT
1 TGTATCGATACAT
2851123 TGTATCGATACA
1 TGTATCGATACA
2851135 ACACTTTATG
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:2852744 original size:22 final size:21
Alignment explanation
Indices: 2852711--2852766 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2852701 AAAAACCCAG
*
2852711 AATGTATTGATACAATTATA-A
1 AATGTATCGATACAATT-TAGA
*
2852732 ACATGTATCGATAC-ATTTAGT
1 A-ATGTATCGATACAATTTAGA
2852753 AATGTATCGATACA
1 AATGTATCGATACA
2852767 TTTCCTTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 14 0.47
21 5 0.17
22 11 0.37
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACAATTTAGA
Found at i:2855104 original size:23 final size:23
Alignment explanation
Indices: 2855076--2855119 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2855066 ATAAGTCTAG
2855076 TTTGGCAAATCTTAGTACAAGGT
1 TTTGGCAAATCTTAGTACAAGGT
2855099 TTTGGCAAATCTTAGTACAAG
1 TTTGGCAAATCTTAGTACAAG
2855120 CTGAATTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (23 bp):
TTTGGCAAATCTTAGTACAAGGT
Found at i:2856948 original size:11 final size:12
Alignment explanation
Indices: 2856932--2856960 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2856922 TGATACCCCT
2856932 AAAGGAC-ATAA
1 AAAGGACTATAA
2856943 AAAGGACTATAA
1 AAAGGACTATAA
2856955 AAAGGA
1 AAAGGA
2856961 TGAACCTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.07, G:0.21, T:0.10
Consensus pattern (12 bp):
AAAGGACTATAA
Found at i:2857429 original size:155 final size:152
Alignment explanation
Indices: 2856899--2857723 Score: 693
Period size: 155 Copynumber: 5.3 Consensus size: 152
2856889 TGCCTATCAA
* * * * * * *
2856899 GGATACCTTTGACATAGAAG--TCCTGA-TACCCCTAAAGGACATAAAAAGGACTATAAAAAGGA
1 GGATACCTTTGACATAAAAGTATCC-GAGCAACCCTAAAGGACTTAAAAA-GACTAGAGATAGGA
** * * *
2856961 TGAACCTATCCTAAAAACCCACCTTTGGCATAAAAGCAGACTCAG-TGACGACCTAGGAGTTGGT
64 TGAACCTATCCT-AAATGCCACCTTTGGCATAAAAGCGGAC-CAGATGACAACCTAGGACTTGGT
*
2857025 TCTCAAAAATTACCAAAATACCCCTAGG
127 TCT-AAAAATTACGAAAATA-CCCTAGG
* * * *
2857053 GGTATACCTTTGACATAAAAGTATCTCG-GCAACCCAAAAGAACTTAAAAAGACTCATAAGA-GG
1 GG-ATACCTTTGACATAAAAGTATC-CGAGCAACCCTAAAGGACTTAAAAAGACT-A-GAGATAG
* ** * ** *
2857116 GATGAACCTATCCCAAATGCCTACCTCCGGCATAAAAGCGGACCTGATGATGACCTAGGAGTTGG
62 GATGAACCTATCCTAAATGCC-ACCTTTGGCATAAAAGCGGACCAGATGACAACCTAGGACTTGG
* * * * *
2857181 TTTTAAAAATTTCTAAAATACTCCCAAG
126 TTCTAAAAATTACGAAAATAC-CCTAGG
* * * * * * *
2857209 AGATACCTTCGACATGAAAGTA-CCTGA-TACCCCTAAAGGACTTAGAAAGACTAGAGATGGGAT
1 GGATACCTTTGACATAAAAGTATCC-GAGCAACCCTAAAGGACTTAAAAAGACTAGAGATAGGAT
* * * *
2857272 GAACCTATCCTCAATGCCACTTTTGGCATAAAAGTGGACTCAG-TGACAACTTAGGACTTGGTTC
65 GAACCTATCCTAAATGCCACCTTTGGCATAAAAGCGGAC-CAGATGACAACCTAGGACTTGGTTC
*
2857336 TAAGAAATTATGAAAATACCCTTATGG
129 TAA-AAATTACGAAAATACCC-TA-GG
* ** *
2857363 GTATACCTTTGATGTAAAAGTATCCGAGCAACCCTAAAGGACTTAAAAAGACTGGAGATAGGATG
1 GGATACCTTTGACATAAAAGTATCCGAGCAACCCTAAAGGACTTAAAAAGACTAGAGATAGGATG
* * * * * * *
2857428 AACCTATCCTAAATGCCCACCTTCGGCATAAAAGCAGACCCGATGACAACATAGTACTCGATTCT
66 AACCTATCCTAAATG-CCACCTTTGGCATAAAAGCGGACCAGATGACAACCTAGGACTTGGTTCT
* *
2857493 AAAAAATTACAAAAACACCCCTAGG
130 -AAAAATTACGAAAATA-CCCTAGG
* * * * *
2857518 GGATACCTTTAACATAAAAGTATCCTAGCAACCCTAAAAGACTTAAAAAGGA-TAGAAATTGGAT
1 GGATACCTTTGACATAAAAGTATCCGAGCAACCCTAAAGGACTTAAAAA-GACTAGAGATAGGAT
* * * * * * *
2857582 GAACCTATCTTAAATATCGACATTTGGCATAAAAGTGGACCCGATGATAACCTAGGACTTGGTTC
65 GAACCTATCCTAAAT-GCCACCTTTGGCATAAAAGCGGACCAGATGACAACCTAGGACTTGGTTC
*
2857647 TAAAAGAATTACGAAAATGCTCCTAGG
129 T-AAA-AATTACGAAAATAC-CCTAGG
* * * *
2857674 GGATA-CTTTCGACATAAAAGTAGCCG-GTACCCCTAAAGGGCTTAAAAAGA
1 GGATACCTTT-GACATAAAAGTATCCGAGCAACCCTAAAGGACTTAAAAAGA
2857724 TTGGTAATGA
Statistics
Matches: 540, Mismatches: 103, Indels: 56
0.77 0.15 0.08
Matches are distributed among these distances:
152 41 0.08
153 38 0.07
154 45 0.08
155 220 0.41
156 116 0.21
157 77 0.14
158 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (152 bp):
GGATACCTTTGACATAAAAGTATCCGAGCAACCCTAAAGGACTTAAAAAGACTAGAGATAGGATG
AACCTATCCTAAATGCCACCTTTGGCATAAAAGCGGACCAGATGACAACCTAGGACTTGGTTCTA
AAAATTACGAAAATACCCTAGG
Found at i:2859403 original size:13 final size:13
Alignment explanation
Indices: 2859385--2859409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2859375 ATATTGCACA
2859385 GTATCGATACATT
1 GTATCGATACATT
2859398 GTATCGATACAT
1 GTATCGATACAT
2859410 GACCAAATGT
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):
GTATCGATACATT
Found at i:2859554 original size:33 final size:32
Alignment explanation
Indices: 2859491--2859554 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
2859481 CTGAACTGTT
*
2859491 TGTATCGATACACACAATATGTATCCATACAA
1 TGTATCGATACACACAAAATGTATCCATACAA
* *
2859523 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCCATACA
2859555 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCCATACAA
Found at i:2865703 original size:20 final size:20
Alignment explanation
Indices: 2865668--2865709 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2865658 CAAATTTCTT
2865668 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
2865690 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
2865709 A
1 A
2865710 ACAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:2867395 original size:21 final size:21
Alignment explanation
Indices: 2867371--2867414 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2867361 GAGAAAGAAA
2867371 TATGTGATTAAAAATTATTGT
1 TATGTGATTAAAAATTATTGT
2867392 TATGTGATTAAAAATTATTGT
1 TATGTGATTAAAAATTATTGT
2867413 TA
1 TA
2867415 AATTGCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (21 bp):
TATGTGATTAAAAATTATTGT
Found at i:2868918 original size:20 final size:20
Alignment explanation
Indices: 2868890--2868964 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2868880 TCATACCCTG
2868890 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2868910 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2868930 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
2868950 ATGTATCGATACATT
1 ATGTATCGATACATT
2868965 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2868957 original size:40 final size:39
Alignment explanation
Indices: 2868890--2868967 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2868880 TCATACCCTG
* *
2868890 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
2868930 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
2868968 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2882954 original size:1 final size:1
Alignment explanation
Indices: 2882885--2882944 Score: 75
Period size: 1 Copynumber: 60.0 Consensus size: 1
2882875 CTTTACACCC
* * * * *
2882885 AAAAAAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2882945 TAGCAAAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.92, C:0.07, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:2884213 original size:29 final size:29
Alignment explanation
Indices: 2884171--2884527 Score: 566
Period size: 29 Copynumber: 12.6 Consensus size: 29
2884161 AATGTTCATC
2884171 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884200 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884229 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
2884257 CCTTTCAAAGCCCAC-AGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884284 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884313 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884341 CCTTTCAAAGCCTACAAGT-AGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
2884369 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884397 CCTTTCAAAGCCTACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
2884426 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
2884455 CCTTTCGAAGCCCACAAATTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884484 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
2884512 CTTTTCAAAGCCCACA
1 CCTTTCAAAGCCCACA
2884528 CCCTTTCAAA
Statistics
Matches: 304, Mismatches: 19, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
27 35 0.12
28 103 0.34
29 166 0.55
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:2884271 original size:28 final size:28
Alignment explanation
Indices: 2884170--2885085 Score: 903
Period size: 28 Copynumber: 32.4 Consensus size: 28
2884160 GAATGTTCAT
2884170 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884198 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884227 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
2884256 CCCTTTCAAAGCCCAC-AGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884283 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884311 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884340 CCCTTTCAAAGCCTACAAGT-AGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
2884367 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884396 CCCTTTCAAAGCCTACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
2884424 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884453 CTCCTTTCGAAGCCCACAAATTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884482 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* ** ** ***
2884511 CCTTTTCAAAGCCCAC-ACCCTTTCAAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *** *
2884538 GCC---CACAAG---TC-AGT--GGCACT
1 CCCTTTCA-AAGCCCACAAGTCAGTGGCA
* ** ** *
2884558 CCTTTCAAAGCCCACA-AGTCAGT--G-GCAC-
1 CCCTTTCAAAGCC-CACA---AGTCAGTG-GCA
* * *
2884586 TCTTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884614 CTCTTTTCTAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884643 CCCTTCCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2884671 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884700 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884729 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884757 CCCTTTCAGAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884785 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2884813 CCATTGCGAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2884841 CTCTTTCAAAGCCCATAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884869 CCCTTTTAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* * *
2884899 CTCCTTTTAAAGCTCACGCAAGTCAGTGGTA
1 C-CCTTTCAAAGC-C-CACAAGTCAGTGGCA
* *
2884930 CCTTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884958 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884986 TCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
**
2885014 TTCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
2885044 CCCTTTTAAAGCCCATGCAAGTCAATGGCAA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGC-A
2885075 CCCTTTTCAAA
1 CCC-TTTCAAA
2885086 TCACCACTGT
Statistics
Matches: 752, Mismatches: 102, Indels: 64
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.00
22 3 0.00
23 1 0.00
24 2 0.00
25 5 0.01
27 44 0.06
28 345 0.46
29 253 0.34
30 60 0.08
31 30 0.04
32 6 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:2884321 original size:56 final size:57
Alignment explanation
Indices: 2884170--2885085 Score: 1156
Period size: 56 Copynumber: 16.2 Consensus size: 57
2884160 GAATGTTCAT
*
2884170 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884227 CTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCAC-AGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2884283 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884340 CCCTTTCAAAGCCTACAAGT-AGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884396 CCCTTTCAAAGCCTACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2884453 CTCCTTTCGAAGCCCACAAATTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
*
2884511 CCTTTTCAAAG--C-C----CA----CAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2884556 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2884614 CTCTTTTCTAAGCCCACAAGTTAGTGGCAC-CCTTCCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884671 CTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
2884729 CCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
2884785 CCCTTTCGAAGCCCACAAGTCAGTGGCAC-CATTGCGAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884841 CTCTTTCAAAGCCCATAAGTCAGTGGCAC-CCTTTTAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* * * * *
2884899 CTCCTTTTAAAGCTCACGCAAGTCAGTGGTAC-CTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGC-C-CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2884958 CTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
** * *
2885014 TTCTTTCAAAGCCCACGCAAGTCAGTGGCAC-CCTTTTAAAGCCCATGCAAGTCAATGGCAA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGC-A
2885075 CCCTTTTCAAA
1 CCC-TTTCAAA
2885086 TCACCACTGT
Statistics
Matches: 756, Mismatches: 71, Indels: 59
0.85 0.08 0.07
Matches are distributed among these distances:
45 27 0.04
46 12 0.02
48 1 0.00
49 1 0.00
50 1 0.00
53 2 0.00
54 1 0.00
55 27 0.04
56 238 0.31
57 173 0.23
58 207 0.27
59 24 0.03
60 12 0.02
61 23 0.03
62 7 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (57 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:2884534 original size:17 final size:17
Alignment explanation
Indices: 2884509--2884544 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2884499 AAGTCAGTGG
*
2884509 CACCTTTTCAAAGCCCA
1 CACCCTTTCAAAGCCCA
2884526 CACCCTTTCAAAGCCCA
1 CACCCTTTCAAAGCCCA
2884543 CA
1 CA
2884545 AGTCAGTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (17 bp):
CACCCTTTCAAAGCCCA
Found at i:2884550 original size:45 final size:46
Alignment explanation
Indices: 2884486--2884573 Score: 160
Period size: 45 Copynumber: 1.9 Consensus size: 46
2884476 GTGGCACTCT
*
2884486 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACACCC
2884531 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA
2884574 AGTCAGTGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 26 0.63
46 15 0.37
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (46 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACACCC
Found at i:2885627 original size:20 final size:20
Alignment explanation
Indices: 2885599--2885673 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
2885589 TCATACCCTG
2885599 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2885619 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
2885639 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
2885659 ATGTATCGATACATT
1 ATGTATCGATACATT
2885674 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2885666 original size:40 final size:39
Alignment explanation
Indices: 2885599--2885676 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2885589 TCATACCCTG
* *
2885599 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
2885639 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
2885677 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:2889689 original size:17 final size:17
Alignment explanation
Indices: 2889667--2889701 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2889657 ATTTGAAATT
2889667 ATAGTGATGAACAATGA
1 ATAGTGATGAACAATGA
2889684 ATAGTGATGAACAATGA
1 ATAGTGATGAACAATGA
2889701 A
1 A
2889702 AATGAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (17 bp):
ATAGTGATGAACAATGA
Found at i:2890920 original size:21 final size:21
Alignment explanation
Indices: 2890895--2890939 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2890885 CACTTGCAAC
*
2890895 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
2890916 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
2890937 TCA
1 TCA
2890940 CTTAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:2890952 original size:21 final size:21
Alignment explanation
Indices: 2890910--2890953 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2890900 TCTTTTCTCC
* * *
2890910 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTATTT
2890931 TCTAATTCACTTAATTTATTT
1 TCTAATTCACTTAATTTATTT
2890952 TC
1 TC
2890954 AAGAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTATTT
Found at i:2893140 original size:32 final size:32
Alignment explanation
Indices: 2893099--2893188 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
2893089 AATGAATAGT
* *
2893099 GATACATGAACAGTAATGAAGAGTGAGGTATC
1 GATACATGAACAGTGATGAACAGTGAGGTATC
* * *
2893131 GATACATGAATAGTGATGAACAGTAATGTATC
1 GATACATGAACAGTGATGAACAGTGAGGTATC
*
2893163 GATACATGAACAGTGATGAATAGTGA
1 GATACATGAACAGTGATGAACAGTGA
2893189 TGAACAATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (32 bp):
GATACATGAACAGTGATGAACAGTGAGGTATC
Found at i:2894156 original size:23 final size:23
Alignment explanation
Indices: 2894130--2894186 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2894120 TGTCTTGCTT
*
2894130 TGCTGTTGTTGCGTTAGAGTTGC
1 TGCTGTTGTTGCGATAGAGTTGC
* *
2894153 TGCTGGTGTT-CGATGGAGTTGC
1 TGCTGTTGTTGCGATAGAGTTGC
*
2894175 TACTGGTTGTTG
1 TGCT-GTTGTTG
2894187 GTGTTGGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.09, C:0.12, G:0.37, T:0.42
Consensus pattern (23 bp):
TGCTGTTGTTGCGATAGAGTTGC
Found at i:2894934 original size:19 final size:18
Alignment explanation
Indices: 2894910--2894961 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
2894900 ATTCATGTGT
*
2894910 AAAAAAATTAATTTACATG
1 AAAAAAATTAAATT-CATG
2894929 AAAAAAATTAAAATTCATG
1 AAAAAAATT-AAATTCATG
*
2894948 AAATAAATTAAATT
1 AAAAAAATTAAATT
2894962 TTTTCTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 21 0.70
20 4 0.13
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAAAATTAAATTCATG
Found at i:2895426 original size:166 final size:164
Alignment explanation
Indices: 2895045--2895480 Score: 531
Period size: 166 Copynumber: 2.6 Consensus size: 164
2895035 TACCCGAATT
* * ** *
2895045 AATTTTT-AAAAATGAATTAATATG-AATCAAATAATGATGCTTGATTAATTTTAAAAATTGAAA
1 AATTTTTGAAAACTGAATTAATATGAAAT-AAATAATAATATTTGATGAATTTTAAAAATTGAAA
* * * * *
2895108 ACTCAGAAAAATCCCCTAAAAAAAATTTACGAAGTAAAAAATATCTTATTTCGAAAAAAAAGAGT
65 ACTAAGAAAAATCTCCT-AAAAAAATTTACGGAGTAAAAAATAACGTATTTCGAAAAAAAAGAGT
*
2895173 TTCAAGGAAAAAATCAAAAACTCATGAAAATGAATG
129 TTCAAGGAAAAAATCAAAAACTCATGAAAATAAATG
** * * * *
2895209 AATTTTTGAAAACAAAATTAAAATAAAATAAATGATAATATTTGATGAATTTTACAAATTGAAAA
1 AATTTTTGAAAACTGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTGAAAA
* ** *
2895274 -TAGAGAAAAATCTCCTCGAAAAAATTTACGGAGTTGAAAATAACGTATTTCGGAAAAAATAGGA
66 CTA-AGAAAAATCTCCT-AAAAAAATTTACGGAGTAAAAAATAACGTATTTC-GAAAAAA-AAGA
*
2895338 GTTTCAGGGAAAAAATCAAAAACTCATGAAAATAAATG
127 GTTTCAAGGAAAAAATCAAAAACTCATGAAAATAAATG
* *
2895376 -ATTTTTGAAAACTGAATTAATATGAAATAAATTATAATATTTGATGAATTTTAAAAATTAAAAA
1 AATTTTTGAAAACTGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTGAAAA
* *
2895440 TTAAGAAAAACCCTCCTAAAAAAATTTACGGAG-AAGAAAAT
66 CTAAGAAAAA-TCTCCTAAAAAAATTTACGGAGTAA-AAAAT
2895481 TCCGTAATTT
Statistics
Matches: 230, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
164 8 0.03
165 82 0.36
166 94 0.41
167 46 0.20
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (164 bp):
AATTTTTGAAAACTGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTGAAAA
CTAAGAAAAATCTCCTAAAAAAATTTACGGAGTAAAAAATAACGTATTTCGAAAAAAAAGAGTTT
CAAGGAAAAAATCAAAAACTCATGAAAATAAATG
Found at i:2895555 original size:166 final size:163
Alignment explanation
Indices: 2895085--2895556 Score: 406
Period size: 166 Copynumber: 2.8 Consensus size: 163
2895075 ATAATGATGC
* * * * *
2895085 TTGATTAATTTTAAAAATTGAAAACTCAGA-AAAATCC-CCTAAAAAAAATTTACGAAGTAA-AA
1 TTGATGAATTTTAAAAATT-AAAAAT-AGAGAAAAACCTCCTCAAAAAAATTTACGGAG-AAGAA
* * * * * *
2895147 AATATCTTATTTCGAAAAAA-AAGAGTTTCAAGGAAAAAATCAAAAACTCATGAAAATGAATGAA
63 AATAACGTATTTCGAAAAAAGAGGAGATTCAAGG-AAAAATCAAAAACTCA-GAAAATAAAAG-A
** **
2895211 TTTTTGAAAACAAAATTAAAATAAAATAAATGATAATAT
125 TTTTCCAAAACTGAATTAAAATAAAATAAATGATAATAT
* * * * **
2895250 TTGATGAATTTTACAAATTGAAAATAGAGAAAAATCTCCTCGAAAAAATTTACGGAGTTGAAAAT
1 TTGATGAATTTTAAAAATTAAAAATAGAGAAAAACCTCCTCAAAAAAATTTACGGAGAAGAAAAT
* * * *
2895315 AACGTATTTCGGAAAAAATAGGAGTTTCAGGGAAAAAATCAAAAACTCATGAAAATAAATGATTT
66 AACGTATTTC-GAAAAAAGAGGAGATTCAAGG-AAAAATCAAAAACTCA-GAAAATAAAAGATTT
** * * *
2895380 TTGAAAACTGAATTAATATGAAATAAATTATAATAT
128 TCCAAAACTGAATTAAAATAAAATAAATGATAATAT
2895416 TTGATGAATTTTAAAAATTAAAAATTA-AGAAAAACCCTCCT-AAAAAAATTTACGGAGAAGAAA
1 TTGATGAATTTTAAAAATTAAAAA-TAGAGAAAAA-CCTCCTCAAAAAAATTTACGGAGAAGAAA
** **
2895479 ATTCCGTAATTT-GAAAATAAGAGGA-ATTCGAAAGG-AAAATCAATAATTTCA-AAAATAAAGG
64 ATAACGT-ATTTCGAAAA-AAGAGGAGATTC--AAGGAAAAATCAA-AAACTCAGAAAATAAA--
2895540 AGATTTTCCAAAACTGA
122 AGATTTTCCAAAACTGA
2895557 TTTGATGGGA
Statistics
Matches: 256, Mismatches: 37, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
163 3 0.01
164 17 0.07
165 63 0.25
166 120 0.47
167 53 0.21
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (163 bp):
TTGATGAATTTTAAAAATTAAAAATAGAGAAAAACCTCCTCAAAAAAATTTACGGAGAAGAAAAT
AACGTATTTCGAAAAAAGAGGAGATTCAAGGAAAAATCAAAAACTCAGAAAATAAAAGATTTTCC
AAAACTGAATTAAAATAAAATAAATGATAATAT
Found at i:2898117 original size:20 final size:20
Alignment explanation
Indices: 2898092--2898132 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2898082 AAATTTTAGT
2898092 ATTTTTGATGAAGAAAATTG
1 ATTTTTGATGAAGAAAATTG
2898112 ATTTTTGATGAAGAAAATTG
1 ATTTTTGATGAAGAAAATTG
2898132 A
1 A
2898133 CATGAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTTTTGATGAAGAAAATTG
Found at i:2900315 original size:20 final size:19
Alignment explanation
Indices: 2900288--2900365 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
2900278 GTAAAAAGAC
2900288 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
* * *
2900307 AGCAATGTATTGATACATTC
1 A-AAATGTATCGATACATTG
* *
2900327 ATACATGTATCAATACATTG
1 A-AAATGTATCGATACATTG
2900347 AAAAATGTATCGATACATT
1 -AAAATGTATCGATACATT
2900366 TGGGTAAAAG
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:2902205 original size:23 final size:23
Alignment explanation
Indices: 2902175--2902254 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 23
2902165 TAATTACATA
2902175 TTTT-ATTTGTACCTTCATCACT
1 TTTTCATTTGTACCTTCATCACT
** *
2902197 TTTTCATTTAAACATTCATCA--
1 TTTTCATTTGTACCTTCATCACT
* * *
2902218 TTTCCATTCGTACCCTCA-C-CT
1 TTTTCATTTGTACCTTCATCACT
*
2902239 TTTTTATTTGTACCTT
1 TTTTCATTTGTACCTT
2902255 TGACTTTGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.57
22 4 0.10
23 13 0.31
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTCATTTGTACCTTCATCACT
Found at i:2905560 original size:17 final size:17
Alignment explanation
Indices: 2905538--2905580 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2905528 TTTCATATGT
2905538 TTTTTCTTTTTTTTTCC
1 TTTTTCTTTTTTTTTCC
* *
2905555 TTTTTCCTTTTTTTTCT
1 TTTTTCTTTTTTTTTCC
2905572 TTTCTTCTT
1 TTT-TTCTT
2905581 CATCTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTCC
Found at i:2906714 original size:48 final size:48
Alignment explanation
Indices: 2906652--2906831 Score: 274
Period size: 48 Copynumber: 3.8 Consensus size: 48
2906642 AGAGGAGTGC
**
2906652 CAATGTGCCAATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTAGG-
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGT-GGA
* *
2906700 CAATGTGCTGATTCAAGGCCAGCGACATTGAGGTGAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
2906748 CAATGTGCTGATTCAAGGCCAGCGACATTGAGTTGAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
2906796 CAATGTGCTGATTCAAGGCC-GTCGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAG-CGACATTGAGCTAA
2906832 TAAAGGTGCT
Statistics
Matches: 123, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
47 3 0.02
48 120 0.98
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
Found at i:2906977 original size:25 final size:25
Alignment explanation
Indices: 2906942--2906991 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2906932 AAAAAAACGT
2906942 GCCACTAACTTATGTGGGCTTTGAA
1 GCCACTAACTTATGTGGGCTTTGAA
* *
2906967 GCCACTGACTTGTGTGGGCTTTGAA
1 GCCACTAACTTATGTGGGCTTTGAA
2906992 AGGATGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (25 bp):
GCCACTAACTTATGTGGGCTTTGAA
Found at i:2907019 original size:28 final size:28
Alignment explanation
Indices: 2906967--2907494 Score: 515
Period size: 28 Copynumber: 18.1 Consensus size: 28
2906957 GGGCTTTGAA
2906967 GCCACTGACTTGTGTGGGCTTTGAAAGGAT
1 GCCACTGAC-T-TGTGGGCTTTGAAAGGAT
*
2906997 GCCACTGACTTGTGGGCTTTGAAAAGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
*
2907025 GCCACTGACTTGTGGGATTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
*
2907053 GCCACTGATTTGTGTGGGCTTTGAGAAGGAT
1 GCCACTGA-CT-TGTGGGCTTTGA-AAGGAT
*
2907084 GCCACTGACTTGTGGGCTTTCAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGA-AAGGAT
*
2907113 GCCACTAACTTGT-GGCTTTGAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGA-AAGGAT
*
2907141 GCCACTGACTTATGGGCTTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
2907169 GCCACTGACTTGTGGGCTTTGAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGA-AAGGAT
*
2907198 GCCACTAACTTGTGGGCTTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
* *
2907226 GCCACTGACTTGTGAGCTTTGAAATAGGTT
1 GCCACTGACTTGTGGGCTTTG-AA-AGGAT
* * *
2907256 ACCACCGACTTGTGTGGGCTTTGAAAAGGGTT
1 GCCACTGAC-T-TGTGGGCTTTG-AAA-GGAT
* * * *
2907288 GCCACCGACTTGTGTGGGCTTTCAAATAAGTT
1 GCCACTGAC-T-TGTGGGCTTT-GAA-AGGAT
*
2907320 GCCA-TCGACTTGTATGGGCTTTGAAATGAT
1 GCCACT-GACTTG--TGGGCTTTGAAAGGAT
* *
2907350 GCCACTGACTTGTGGG-TTTAAAAAAGGGT
1 GCCACTGACTTGTGGGCTTT--GAAAGGAT
* * *
2907379 GCCATTGACTTGTGGGCTTTGGAAGGGT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
* **
2907407 GCCACTAACTTGTGGGCTTAAAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
* * * ** *
2907435 GCCA-TGAAGTTATGGACTTTGGGAGGGT
1 GCCACTG-ACTTGTGGGCTTTGAAAGGAT
**
2907463 GCCACTGACTTGTGGGCTTAAAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
2907491 GCCA
1 GCCA
2907495 TGAAGTTGTG
Statistics
Matches: 422, Mismatches: 55, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.01
28 198 0.47
29 91 0.22
30 50 0.12
31 20 0.05
32 58 0.14
33 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
GCCACTGACTTGTGGGCTTTGAAAGGAT
Found at i:2907144 original size:57 final size:57
Alignment explanation
Indices: 2906967--2907494 Score: 548
Period size: 57 Copynumber: 9.1 Consensus size: 57
2906957 GGGCTTTGAA
2906967 GCCACTGACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAA-GAT
1 GCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* * *
2907025 GCCACTGACTTGTGGGATTTGAAAGGATGCCACTGATTTGTGTGGGCTTTGAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGA-CT-TGTGGGCTTTGAAAAGGAT
* * *
2907084 GCCACTGACTTGTGGGCTTTCAGAAGGATGCCACTAACTTGT-GGCTTTGAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* *
2907141 GCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* * *
2907198 GCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAATAGGTT
1 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-AGGAT
* * * * * * *
2907256 ACCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTCAAATAAGTT
1 GCCACTGAC-T-TGTGGGCTTTG-AAA-GGATGCCACTGAC-T-TGTGGGCTTTGAAA-AGGAT
* * *
2907320 GCCA-TCGACTTGTATGGGCTTTGAAATGATGCCACTGACTTGTGGG-TTTAAAAAAGGGT
1 GCCACT-GACTTG--TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAAGGAT
* * * * *
2907379 GCCATTGACTTGTGGGCTTTGGAAGGGTGCCACTAACTTGTGGGC-TTAAAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* * * ** * *
2907435 GCCA-TGAAGTTATGGACTTTGGGAGGGTGCCACTGACTTGTGGGC-TTAAAAAGGAT
1 GCCACTG-ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
2907491 GCCA
1 GCCA
2907495 TGAAGTTGTG
Statistics
Matches: 410, Mismatches: 41, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
55 2 0.00
56 103 0.25
57 130 0.32
58 36 0.09
59 41 0.10
60 34 0.08
61 4 0.01
62 23 0.06
63 5 0.01
64 32 0.08
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (57 bp):
GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
Done.