Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 2 of 25
Found at i:163364 original size:61 final size:61
Alignment explanation
Indices: 163288--163425 Score: 190
Period size: 61 Copynumber: 2.3 Consensus size: 61
163278 GGTGTAACAA
**
163288 AGTTGTGGACTTAAAAGGATGCCACAAAGTTGTGGGCTTTGAAAA-GAAAAA-GGTGCCATGG
1 AGTTGTGGACTTAAAAGGATGCCACAAAGTCATGGGC-TT-AAAAGGAAAAAGGGTGCCATGG
* * *
163349 AGTTGTAGACTTAAAAGGGTGCCACAGAGTCATGGGCTTAAAAGGAAAAAGGGTGCCATGG
1 AGTTGTGGACTTAAAAGGATGCCACAAAGTCATGGGCTTAAAAGGAAAAAGGGTGCCATGG
*
163410 AGTTATGGACTTAAAA
1 AGTTGTGGACTTAAAA
163426 AGAAAAAAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 4 0.06
60 8 0.12
61 56 0.82
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (61 bp):
AGTTGTGGACTTAAAAGGATGCCACAAAGTCATGGGCTTAAAAGGAAAAAGGGTGCCATGG
Found at i:163571 original size:35 final size:34
Alignment explanation
Indices: 163498--163948 Score: 196
Period size: 34 Copynumber: 14.1 Consensus size: 34
163488 CCATAGCACC
* * *
163498 TTTTCTTTTGAAAGCCCACAACTCTATGGCACCCT
1 TTTTCTTTT-TAAGTCCACAACTCCATGGCACCCT
* **
163533 TTTCCTTTTTAAGTTTACAACTCCATGGCACCCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
* *
163567 TTTTCTTTTCAAAGCCCACAACTCCATGGCACCCT
1 TTTTCTTTT-TAAGTCCACAACTCCATGGCACCCT
* * * *
163602 TTTTCCTTTTAAGTCCATAACTCAATGGTACCCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
* * * **
163636 TTTTCTTTTTAA-CCCTAAAACTCTATGAAACCC-
1 TTTTCTTTTTAAGTCC-ACAACTCCATGGCACCCT
* ***
163669 TTTTC------AGTCCATAACTTTGTGGCA-CC-
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
* ** *
163695 TTTTCTTTTCAAAACCCACAACACCATGGCA----
1 TTTTCTTTT-TAAGTCCACAACTCCATGGCACCCT
* * **
163726 ---TCCTTTTAAGTCCATAACTCTGTGGCA-CC-
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
**
163755 ----C-TTTTAAGTCCACAACTCTGTGGCA-CCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
* **
163783 TTTTCTTTTCAAAGTCCACAACTCTGTGGCA-CC-
1 TTTTCTTTT-TAAGTCCACAACTCCATGGCACCCT
* *
163816 ----C-TTTTAAGTCCATAACTTCATGGC-CCCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
* ** *
163844 TGTTT-TTTTAAAACCCACAACTCTATGGCACCCT
1 T-TTTCTTTTTAAGTCCACAACTCCATGGCACCCT
*
163878 TTTTCTTTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
** * * *
163912 TTTTCCATTTAAGCCCACGACTCCGTGGCACCCT
1 TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
163946 TTT
1 TTT
163949 AAGTCCACAA
Statistics
Matches: 321, Mismatches: 66, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
26 7 0.02
27 66 0.21
28 11 0.03
29 1 0.00
32 1 0.00
33 42 0.13
34 156 0.49
35 37 0.12
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.36
Consensus pattern (34 bp):
TTTTCTTTTTAAGTCCACAACTCCATGGCACCCT
Found at i:163583 original size:69 final size:69
Alignment explanation
Indices: 163498--163644 Score: 215
Period size: 69 Copynumber: 2.1 Consensus size: 69
163488 CCATAGCACC
* * ** *
163498 TTTTCTTTTGAAAGCCCACAACTCTATGGCACCC-TTTTCCTTTTTAAGTTTACAACTCCATGGC
1 TTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTTCC-TTTTAAGTCCACAACTCAATGGC
163562 ACCCT
65 ACCCT
* *
163567 TTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTTCCTTTTAAGTCCATAACTCAATGGTA
1 TTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTTCCTTTTAAGTCCACAACTCAATGGCA
163632 CCCT
66 CCCT
163636 TTTTCTTTT
1 TTTTCTTTT
163645 TAACCCTAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
69 64 0.91
70 6 0.09
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (69 bp):
TTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTTCCTTTTAAGTCCACAACTCAATGGCA
CCCT
Found at i:163752 original size:27 final size:27
Alignment explanation
Indices: 163721--164142 Score: 166
Period size: 27 Copynumber: 14.2 Consensus size: 27
163711 CACAACACCA
* *
163721 TGGCATCCTTTTAAGTCCATAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCTG
163748 TGGCACCCTTTTAAGTCCACAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCTG
163775 TGGCACCTTTTTCTTTTCAAAGTCCACAACTCTG
1 TGGCACC-----CTTTT--AAGTCCACAACTCTG
* *
163809 TGGCACCCTTTTAAGTCCATAACT-TCA
1 TGGCACCCTTTTAAGTCCACAACTCT-G
** *
163836 TGGC-CCCTTGTTTTTTTAAAACCCACAACTCTA
1 TGGCACCC------TTTT-AAGTCCACAACTCTG
*
163869 TGGCACCCTTTTTCTTTTTAAGTCCACAACTCCG
1 TGGCA-CC-----C-TTTTAAGTCCACAACTCTG
* * *
163903 TGGCACCCTTTTTCCATTTAAGCCCACGACTCCG
1 TGGCACCC----T---TTTAAGTCCACAACTCTG
163937 TGGCACCCTTTTAAGTCCACAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCTG
* * **
163964 TGGCATCTTTTCTTTTCAAAGCCCATGACTCTG
1 TGGCA-C---CCTTTT--AAGTCCACAACTCTG
* * **
163997 TGGCATCTTTTTAAGTCCACAACTCCA
1 TGGCACCCTTTTAAGTCCACAACTCTG
* * * * * **
164024 TGGTATCTTTTTAATTCCATAACTCCA
1 TGGCACCCTTTTAAGTCCACAACTCTG
* *
164051 TGGCACCTTTTTTTTTCAAAGCCCACAACTCTG
1 TGGCACC----CTTTT--AAGTCCACAACTCTG
* **
164084 -GGCATCCTTTTAAGTCCACAACTCCA
1 TGGCACCCTTTTAAGTCCACAACTCTG
*
164110 TGGCACCTTTTTAAGTCCACAACTCTG
1 TGGCACCCTTTTAAGTCCACAACTCTG
164137 TGGCAC
1 TGGCAC
164143 ATTTTTCTTT
Statistics
Matches: 306, Mismatches: 47, Indels: 84
0.70 0.11 0.19
Matches are distributed among these distances:
26 16 0.05
27 134 0.44
28 6 0.02
29 9 0.03
30 1 0.00
31 12 0.04
32 14 0.05
33 43 0.14
34 63 0.21
35 7 0.02
40 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.35
Consensus pattern (27 bp):
TGGCACCCTTTTAAGTCCACAACTCTG
Found at i:163806 original size:61 final size:60
Alignment explanation
Indices: 163728--164021 Score: 283
Period size: 61 Copynumber: 4.8 Consensus size: 60
163718 CCATGGCATC
* *
163728 CTTTT-AAGTCCATAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
1 CTTTTAAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
* * * *
163787 CTTTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCATAACT-TCATGGCCCCTTGTTT
1 CTTTT-AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCT-GTGGCACCTT-TTT
* * *
163849 -TTTTAAAACCCACAACTCTATGGCACCCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCCTT
1 CTTTTAAAGCCCACAACTCTGTGGCA-CC-----C-TTTTAAGTCCACAACTCTGTGGCA-CCTT
163913 TTT
58 TTT
* * * *
163916 CCATTT-AAGCCCACGACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATC-TTTT
1 -CTTTTAAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
** * *
163975 CTTTTCAAAGCCCATGACTCTGTGGCATCTTTTTAAGTCCACAACTC
1 CTTTT-AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTC
164022 CATGGTATCT
Statistics
Matches: 195, Mismatches: 23, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
58 4 0.02
59 9 0.05
60 56 0.29
61 74 0.38
62 4 0.02
66 1 0.01
67 24 0.12
68 20 0.10
69 3 0.02
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (60 bp):
CTTTTAAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
Found at i:163806 original size:148 final size:148
Alignment explanation
Indices: 163606--163880 Score: 340
Period size: 148 Copynumber: 1.9 Consensus size: 148
163596 CACCCTTTTT
* * *
163606 CCTTTTAAGTCCATAACTCAATGGTACCCTTTTTCTTTTTAACCCTAAAACTCTATGAAACCCTT
1 CCTTTTAAGTCCACAACTCAATGGCACCCTTTTTCTTTTAAACCCTAAAACTCTATGAAACCCTT
* ** *
163671 TTCAGTCCATAACTTTGTGGCACCTT-TTCTTTTCAAAACCCACAACACCATGGCATCCTTTTAA
66 TTAAGTCCATAACTTCATGGCACCTTGTT-TTTTCAAAACCCACAACACCATGGCACCCTTTTAA
163735 GTCCATAACTCTGTGGCAC
130 GTCCATAACTCTGTGGCAC
** * * * **
163754 CCTTTTAAGTCCACAACTCTGTGGCA-CCTTTTTCTTTTCAAAGTCC-ACAACTCTGTGGCACCC
1 CCTTTTAAGTCCACAACTCAATGGCACCCTTTTTCTTTT-AAA-CCCTAAAACTCTATGAAACCC
* * * *
163817 TTTTAAGTCCATAACTTCATGGCCCCTTGTTTTTTTAAAACCCACAACTCTATGGCACCCTTTT
64 TTTTAAGTCCATAACTTCATGGCACCTTGTTTTTTCAAAACCCACAACACCATGGCACCCTTTT
163881 TCTTTTTAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
147 12 0.11
148 90 0.85
149 4 0.04
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36
Consensus pattern (148 bp):
CCTTTTAAGTCCACAACTCAATGGCACCCTTTTTCTTTTAAACCCTAAAACTCTATGAAACCCTT
TTAAGTCCATAACTTCATGGCACCTTGTTTTTTCAAAACCCACAACACCATGGCACCCTTTTAAG
TCCATAACTCTGTGGCAC
Found at i:163844 original size:87 final size:88
Alignment explanation
Indices: 163665--164167 Score: 487
Period size: 87 Copynumber: 5.6 Consensus size: 88
163655 ACTCTATGAA
* * * * * **
163665 ACCCTTTTCAGTCCATAACTTTGTGGCACC-TTTTCTTTTCAAAACCCACAACACCATGGCATCC
1 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCATCC
* **
163729 TTTTAAGTCCATAACTCTGTGGC
66 TTTTAAGTCCACAACTCCATGGC
* *
163752 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCACCC
1 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCATCC
* *
163817 TTTTAAGTCCATAACTTCATGGC
66 TTTTAAGTCCACAACTCCATGGC
** * * * *
163840 -CCCTTGTTTTTTTAAAACCCACAACTCTATGGCACCCTTTTTCTTTT-TAAGTCCACAACTCCG
1 ACCC------TTTT-AAGTCCACAACTCTGTGGCA-CCTTTTTCTTTTCAAAGCCCACAACTCTG
* * * *
163903 TGGCACCCTTTTTCCATTTAAGCCCACGACTCCGTGGC
58 TGGCA-------TCCTTTTAAGTCCACAACTCCATGGC
* ** *
163941 ACCCTTTTAAGTCCACAACTCTGTGGCATC-TTTTCTTTTCAAAGCCCATGACTCTGTGGCATCT
1 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCATCC
*
164005 TTTTAAGTCCACAACTCCATGGT
66 TTTTAAGTCCACAACTCCATGGC
* * * * **
164028 ATCTTTTTAATTCCATAACTCCATGGCACCTTTTT-TTTTCAAAGCCCACAACTCTG-GGCATCC
1 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCATCC
164091 TTTTAAGTCCACAACTCCATGGC
66 TTTTAAGTCCACAACTCCATGGC
* * *
164114 ACCTTTTTAAGTCCACAACTCTGTGGCACATTTTTCTTTTCAAGGCCCACAACT
1 ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACT
164168 TAATGGCACC
Statistics
Matches: 339, Mismatches: 57, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
86 57 0.17
87 109 0.32
88 52 0.15
93 13 0.04
94 53 0.16
95 29 0.09
96 4 0.01
101 19 0.06
102 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.35
Consensus pattern (88 bp):
ACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCATCC
TTTTAAGTCCACAACTCCATGGC
Found at i:163974 original size:60 final size:60
Alignment explanation
Indices: 163884--164035 Score: 182
Period size: 60 Copynumber: 2.5 Consensus size: 60
163874 CCCTTTTTCT
*
163884 TTTTAAGTCCACAACTCCGTGGCACCCTTTTTCCATTT-AAGCCCACGACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCA-TCTTTTT-CATTTAAAGCCCACGACTCCGTGGCACCC
* * * * * *
163945 TTTTAAGTCCACAACTCTGTGGCATC-TTTTCTTTTCAAAGCCCATGACTCTGTGGCATCT
1 TTTTAAGTCCACAACTCCGTGGCATCTTTTTCATTT-AAAGCCCACGACTCCGTGGCACCC
* *
164005 TTTTAAGTCCACAACTCCATGGTATCTTTTT
1 TTTTAAGTCCACAACTCCGTGGCATCTTTTT
164036 AATTCCATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 4 0.05
59 4 0.05
60 43 0.55
61 27 0.35
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (60 bp):
TTTTAAGTCCACAACTCCGTGGCATCTTTTTCATTTAAAGCCCACGACTCCGTGGCACCC
Found at i:164271 original size:32 final size:32
Alignment explanation
Indices: 164212--164346 Score: 96
Period size: 32 Copynumber: 4.2 Consensus size: 32
164202 GGCAACTTTT
* * * *
164212 CCTTCT-AAAGCCCACATAAATCAATGGCAAC
1 CCTTCTCAAAGCCCATACAAGTCGATGGCAAC
*
164243 CCTTCTCAAAGCCCATACAAGTTGATGGCAACC
1 CCTTCTCAAAGCCCATACAAGTCGATGGCAA-C
* * * *
164276 CCTT-TTAAAGCCCACACAGGTCGGT-GCTAAC
1 CCTTCTCAAAGCCCATACAAGTCGATGGC-AAC
** * *
164307 CCCCCTCAAAAGCCCATACAAGTCGGTGGCATC
1 CCTTCTC-AAAGCCCATACAAGTCGATGGCAAC
164340 TCCTTCT
1 -CCTTCT
164347 AAGCCTATTG
Statistics
Matches: 79, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
31 11 0.14
32 38 0.48
33 24 0.30
34 6 0.08
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (32 bp):
CCTTCTCAAAGCCCATACAAGTCGATGGCAAC
Found at i:164482 original size:52 final size:52
Alignment explanation
Indices: 164405--164871 Score: 413
Period size: 52 Copynumber: 9.0 Consensus size: 52
164395 ATCTCCTTCC
* * * *
164405 TAAGTCCAATATCGCTAGCCATGAATCAGCATATTGGCGCCTTGGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * *
164457 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACATTT-TTATTTCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT-T
* * * *
164509 TAATTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCGT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * * *
164561 TAAGTCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTTTC-TTTCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT-T
* * *
164613 TAAATCCAATAACGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * * ** *
164665 TAAGTCCAATGTCACTGGTCTCGAATCAGCACATTAGCACCTTT-TTTTC-G
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
** * * * *
164715 TAAGTCCAATATTACTAGCCTTGAATTAGCATATTGACACCTTTGTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * * * *
164767 TATGTCCAATGTCGCTAGCCTTGAATCCGCACATTGACTCCTTAGTCATC-T
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * *
164818 TACAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCACTCTT
1 TA-AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA-TCTT
164872 CTCATCTTCA
Statistics
Matches: 322, Mismatches: 84, Indels: 16
0.76 0.20 0.04
Matches are distributed among these distances:
50 35 0.11
51 15 0.05
52 264 0.82
53 7 0.02
54 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
Found at i:164543 original size:104 final size:103
Alignment explanation
Indices: 164405--164861 Score: 508
Period size: 104 Copynumber: 4.4 Consensus size: 103
164395 ATCTCCTTCC
* * * *
164405 TAAGTCCAATATCGCTAGCCATGAATCAGCATATTGGCGCCTTGGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCTTTAAGTCCAATGTC
* *
164470 GTTGGCCTTGAATCAGCACATTGGCACATTTTTATTTCT
66 GCTAGCCTTGAATCAGCACATTGGCAC-TTTTTATTTCT
* * *
164509 TAATTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCGTTAAGTCTAATGTC
1 TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCTTTAAGTCCAATGTC
* *
164574 GCTAGCCTTGAATCAACACATTGGCACCTTTTTCTTTCT
66 GCTAGCCTTGAATCAGCACATTGGCA-CTTTTTATTTCT
* * * * *
164613 TAAATCCAATAACGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCTTTAAGTCCAATGTC
* * * * * * *
164678 ACTGGTCTCGAATCAGCACATTAGCACCTTTT-TTTCG
66 GCTAGCCTTGAATCAGCACATTGGCACTTTTTATTTCT
* * * * * * *
164715 TAAGTCCAATAT-TACTAGCCTTGAATTAGCATATTGACACCTTTGTTATCTTTATGTCCAATGT
1 TAAGTCCAATATCGA-TGGCCTTGAATCAGCATATTGGCACCTTGGTCATCTTTAAGTCCAATGT
* ** *
164779 CGCTAGCCTTGAATCCGCACATT-G-ACTCCTTAGTCATCT
65 CGCTAGCCTTGAATCAGCACATTGGCACTTTTTA-T-TTCT
* *
164818 TACAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTT
1 TA-AGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTT
164862 TATCACTCTT
Statistics
Matches: 294, Mismatches: 52, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
100 4 0.01
101 1 0.00
102 76 0.26
103 9 0.03
104 203 0.69
105 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (103 bp):
TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGGTCATCTTTAAGTCCAATGTC
GCTAGCCTTGAATCAGCACATTGGCACTTTTTATTTCT
Found at i:164840 original size:206 final size:208
Alignment explanation
Indices: 164410--164871 Score: 572
Period size: 206 Copynumber: 2.2 Consensus size: 208
164400 CTTCCTAAGT
* * * **
164410 CCAATATCGCTAGCCATGAATCAGCATATTGGCGCCTTGGTCATCTTTAAGTCCAATGTCGTTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
* * * * * *
164475 CCTTGAATCAGCACATTGGCACATTTTTATTTCTTAATTCCAATATCGATGGCCTTGAATCAGCA
66 CCTCGAATCAGCACATTAGCACACTTTTATTTCGTAAGTCCAATATCGATAGCCTTGAATCAGCA
* * * *
164540 TATTGGCACCTTGGTCATCGTTAAGTCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTT
131 TATTGACACCTTGGTCATCGTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGACACCTTA
* * *
164605 TTCTTTCTTAAAT
196 GTCTATCTTAAAC
*
164618 CCAATAACGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
* * *
164683 TCTCGAATCAGCACATTAGCAC-CTTTT-TTTCGTAAGTCCAATAT-TACTAGCCTTGAATTAGC
66 CCTCGAATCAGCACATTAGCACACTTTTATTTCGTAAGTCCAATATCGA-TAGCCTTGAATCAGC
* * * * ** *
164745 ATATTGACACCTTTGTTATCTTTATGTCCAATGTCGCTAGCCTTGAATCCGCACATTGACTCCTT
130 ATATTGACACCTTGGTCATCGTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGACACCTT
*
164810 AGTC-ATCTTACAGC
195 AGTCTATCTTA-AAC
* * *
164824 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCACTCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA-TCTT
164872 CTCATCTTCA
Statistics
Matches: 217, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
205 6 0.03
206 125 0.58
207 8 0.04
208 78 0.36
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (208 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCACTGG
CCTCGAATCAGCACATTAGCACACTTTTATTTCGTAAGTCCAATATCGATAGCCTTGAATCAGCA
TATTGACACCTTGGTCATCGTTAAGTCCAATGTCGCTAGCCTTGAATCAACACATTGACACCTTA
GTCTATCTTAAAC
Found at i:168846 original size:52 final size:53
Alignment explanation
Indices: 168761--168936 Score: 149
Period size: 52 Copynumber: 3.3 Consensus size: 53
168751 AATTAAATGT
* ** * *
168761 TTAATTGAAAATTTTATGTATAAGAATTTAATTAAAAATTCTATAGCAAAAGT
1 TTAATTAAAAATTCCATGTATAAGAATCTAATTAAAAATTCTATAGCAAAAGC
* *
168814 TTGA-TAAAAATTCCATGTATGAA-AATCTAATTAAAAATTCTATAAGTAAAAGC
1 TTAATTAAAAATTCCATGTAT-AAGAATCTAATTAAAAATTCTAT-AGCAAAAGC
* * * * * * * *
168867 TTAATTAAAAATTCTATATACAAATAATCTAACTAAAAATTTTATATGTAAAAAGT
1 TTAATTAAAAATTCCATGTA-TAAGAATCTAATTAAAAATTCTATA-G-CAAAAGC
*
168923 TTAATTTAAAATTC
1 TTAATTAAAAATTC
168937 TATTTGTAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
52 32 0.32
53 15 0.15
54 16 0.16
55 19 0.19
56 18 0.18
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (53 bp):
TTAATTAAAAATTCCATGTATAAGAATCTAATTAAAAATTCTATAGCAAAAGC
Found at i:168944 original size:28 final size:27
Alignment explanation
Indices: 168754--169011 Score: 165
Period size: 27 Copynumber: 9.6 Consensus size: 27
168744 AAAGTTTAAT
* *
168754 TAAATGTTTAATTGAAAATT-T-TATG
1 TAAAAGTTTAATTAAAAATTCTATATG
*
168779 TATAAGAATTTAATTAAAAATTCTATA-G
1 TA-AA-AGTTTAATTAAAAATTCTATATG
* * *
168807 CAAAAGTTTGA-TAAAAATTCCATGTATG
1 TAAAAGTTTAATTAAAAATT-C-TATATG
* *
168835 -AAAA-TCTAATTAAAAATTCTATAAG
1 TAAAAGTTTAATTAAAAATTCTATATG
* *
168860 TAAAAGCTTAATTAAAAATTCTATATA
1 TAAAAGTTTAATTAAAAATTCTATATG
* * * * *
168887 CAAATAATCTAACTAAAAATTTTATATG
1 TAAA-AGTTTAATTAAAAATTCTATATG
* *
168915 TAAAAAGTTTAATTTAAAATTCTATTTG
1 T-AAAAGTTTAATTAAAAATTCTATATG
* *
168943 T-AAAGTTTAATTGAAAAATAC-ACATAG
1 TAAAAGTTTAATT-AAAAATTCTATAT-G
** * *
168970 -ATGAGTTTAATTAAAAATTTTATAAG
1 TAAAAGTTTAATTAAAAATTCTATATG
168996 TAAAAAGTTTAATTAA
1 T-AAAAGTTTAATTAA
169012 CAGTTCCATA
Statistics
Matches: 174, Mismatches: 41, Indels: 33
0.70 0.17 0.13
Matches are distributed among these distances:
25 14 0.08
26 36 0.21
27 68 0.39
28 51 0.29
29 5 0.03
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (27 bp):
TAAAAGTTTAATTAAAAATTCTATATG
Found at i:169072 original size:45 final size:47
Alignment explanation
Indices: 168978--169073 Score: 108
Period size: 45 Copynumber: 2.1 Consensus size: 47
168968 AGATGAGTTT
* * * **
168978 AATTAAAAATTTTATAAGTAAAAAGTTTAATTAACAGTTCCATAGAA
1 AATTAAAAATTTTACAAGTAAAAAGTTTAATTAAAAGCTAAATAGAA
*
169025 AATT-AAAATTTTACATGT-AAAAGTTTAATTAAAAGCTAAATTA-AA
1 AATTAAAAATTTTACAAGTAAAAAGTTTAATTAAAAGCTAAA-TAGAA
169070 AATT
1 AATT
169074 CTACATGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
45 24 0.57
46 14 0.33
47 4 0.10
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.35
Consensus pattern (47 bp):
AATTAAAAATTTTACAAGTAAAAAGTTTAATTAAAAGCTAAATAGAA
Found at i:169726 original size:16 final size:17
Alignment explanation
Indices: 169707--169738 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
169697 GCTAGTCTTA
169707 TCTTGAA-CTAGCTATG
1 TCTTGAACCTAGCTATG
169723 TCTTGAACCTAGCTAT
1 TCTTGAACCTAGCTAT
169739 TTTAAGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (17 bp):
TCTTGAACCTAGCTATG
Found at i:171105 original size:49 final size:48
Alignment explanation
Indices: 171052--171240 Score: 148
Period size: 49 Copynumber: 3.9 Consensus size: 48
171042 GGTTTATCTT
* * ***
171052 AACAAAATTCCATAAATACTTTGGATTCCACCATCGAAGACTTGTTTTA
1 AACAAAATTCCATAAAT-CTTTGAATTCCACCATCAAAGACTTGAACTA
* * *
171101 AACAAAATTCCATAAATGTTTCAAATTCCACCATTAAAGACTTGAACTA
1 AACAAAATTCCATAAATCTTT-GAATTCCACCATCAAAGACTTGAACTA
* * ** * * *
171150 AACAAAATTTCTTAAATGCTTTGAATTCCATTATCAAAGAATT-ATTCTG
1 AACAAAATTCCATAAAT-CTTTGAATTCCACCATCAAAGACTTGA-ACTA
* * * *
171199 AACAAAAGTCC-TAAATGCTTTAAATTCCACAACCAAAGACTT
1 AACAAAATTCCATAAAT-CTTTGAATTCCACCATCAAAGACTT
171241 ATTTCGAAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
48 30 0.27
49 79 0.71
50 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (48 bp):
AACAAAATTCCATAAATCTTTGAATTCCACCATCAAAGACTTGAACTA
Found at i:171154 original size:98 final size:97
Alignment explanation
Indices: 171052--171228 Score: 221
Period size: 98 Copynumber: 1.8 Consensus size: 97
171042 GGTTTATCTT
* * * * * *
171052 AACAAAATTCCATAAATACTTTGGATTCCACCATCGAAGACTTGTTTTAAACAAAATTCCATAAA
1 AACAAAATTCCATAAATACTTTGAATTCCACCATCAAAGAATTATTCTAAACAAAAGTCC-TAAA
171117 TG-TTTCAAATTCCACCATTAAAGACTTGAACTA
65 TGCTTT-AAATTCCACCATTAAAGACTTGAACTA
* * * ** *
171150 AACAAAATTTCTTAAATGCTTTGAATTCCATTATCAAAGAATTATTCTGAACAAAAGTCCTAAAT
1 AACAAAATTCCATAAATACTTTGAATTCCACCATCAAAGAATTATTCTAAACAAAAGTCCTAAAT
171215 GCTTTAAATTCCAC
66 GCTTTAAATTCCAC
171229 AACCAAAGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
97 15 0.23
98 51 0.77
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (97 bp):
AACAAAATTCCATAAATACTTTGAATTCCACCATCAAAGAATTATTCTAAACAAAAGTCCTAAAT
GCTTTAAATTCCACCATTAAAGACTTGAACTA
Found at i:171236 original size:48 final size:48
Alignment explanation
Indices: 171162--171276 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 48
171152 CAAAATTTCT
* ** * *
171162 TAAATGCTTTGAATTCCATTATCAAAGAATTA-TTCTGAACAAAAGTCC
1 TAAATGCTTTAAATTCCACAACCAAAGAATTATTTC-GAAAAAAAGTCC
*
171210 TAAATGCTTTAAATTCCACAACCAAAGACTTATTTCGAAAAAAAGTCC
1 TAAATGCTTTAAATTCCACAACCAAAGAATTATTTCGAAAAAAAGTCC
*
171258 CAAATG-TTTCAAATTCCAC
1 TAAATGCTTT-AAATTCCAC
171277 CATTGAAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 3 0.05
48 52 0.90
49 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (48 bp):
TAAATGCTTTAAATTCCACAACCAAAGAATTATTTCGAAAAAAAGTCC
Found at i:173192 original size:41 final size:40
Alignment explanation
Indices: 173147--173260 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 40
173137 TGGCACCTGG
*
173147 TGAAAAAAGTACTTTTAGGTAAAACCTAAAATGGTGCCCGA
1 TGAAAAAAGTACTTTTAGG-AAAACCTAAAATGGTGCCCAA
* *
173188 TGAAAAAAATACTTTTAGGAAAAACTTAAAATGGTGCCCAA
1 TGAAAAAAGTACTTTTAGG-AAAACCTAAAATGGTGCCCAA
173229 TGAAAAAAGTACTTTTAGGAAAGACCTAAAAT
1 TGAAAAAAGTACTTTTAGGAAA-ACCTAAAAT
173261 ACTTATGGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 3 0.05
41 63 0.95
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (40 bp):
TGAAAAAAGTACTTTTAGGAAAACCTAAAATGGTGCCCAA
Found at i:173517 original size:20 final size:20
Alignment explanation
Indices: 173487--173533 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
173477 ATTTGTATCA
*
173487 ATACAATAAGTTAATGTAATG
1 ATAC-ATAAGTGAATGTAATG
*
173508 ATACATAAGTGAATGTATTG
1 ATACATAAGTGAATGTAATG
173528 ATACAT
1 ATACAT
173534 GCTTGAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (20 bp):
ATACATAAGTGAATGTAATG
Found at i:173545 original size:21 final size:20
Alignment explanation
Indices: 173519--173570 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 20
173509 TACATAAGTG
173519 AATGTATTGATACATGCTTGA
1 AATGTA-TGATACATGCTTGA
173540 AATGTA--ATACATGCTTGA
1 AATGTATGATACATGCTTGA
173558 AATGTATCGATAC
1 AATGTAT-GATAC
173571 TAAACCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 18 0.64
21 10 0.36
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (20 bp):
AATGTATGATACATGCTTGA
Found at i:176238 original size:80 final size:80
Alignment explanation
Indices: 176105--176563 Score: 564
Period size: 80 Copynumber: 5.8 Consensus size: 80
176095 TCAAAAGAGG
** * * ** * *
176105 TACTCCAACCCTGTTTTTACTTCTAAAATACTGAATTTTTCATCTTTGAGGATACTCTAACCCCA
1 TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
176170 CCATCTCTAAGGGGA
66 CCATCTCTAAGGGGA
* *
176185 TACTCCAACCCCATTTTTACTTCCAAAACACCAAAATTTTCATCTCTGTGGATACTCTAACCCCA
1 TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
**
176250 CCATCTCCGAGGGGA
66 CCATCTCTAAGGGGA
** * * * *
176265 TACTCCAACCCTGTTTTTACTTCCAAAACATCGAATTTTTCATCTTTGGGGATACTCCAACCCCA
1 TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
* *
176330 CCATCTCCAAGAGGA
66 CCATCTCTAAGGGGA
* * **
176345 TACTCCAACCCCTTTTTTACTTCCAAAACATCAAATTTTTCATCTCTGGGGATACTCTAATGCCA
1 TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
176410 CCATCTCTAAGGGGA
66 CCATCTCTAAGGGGA
* * ** * * *
176425 TACTTCAACCCCATTTTTACTTCCCAAACACTGAATTTTTCATCTCTGGTGATACTCCAACCCTA
1 TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
* *
176490 CTATCT-T-CGAGGGA
66 CCATCTCTAAG-GGGA
* *
176504 TACTCCAACCCCATTTTTACTT-CATAAACACCAAAATTTTCGTCTCTGGGGATACTCTAA
1 TACTCCAACCCCATTTTTACTTCCA-AAACACCAAATTTTTCATCTCTGGGGATACTCTAA
176564 TGCCGGTTTT
Statistics
Matches: 326, Mismatches: 51, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
78 2 0.01
79 55 0.17
80 269 0.83
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (80 bp):
TACTCCAACCCCATTTTTACTTCCAAAACACCAAATTTTTCATCTCTGGGGATACTCTAACCCCA
CCATCTCTAAGGGGA
Found at i:176303 original size:160 final size:159
Alignment explanation
Indices: 176105--176563 Score: 638
Period size: 160 Copynumber: 2.9 Consensus size: 159
176095 TCAAAAGAGG
* * *
176105 TACTCCAACCCTGTTTTTACTTCTAAAATACTGAATTTTTCATCTTTGAGGATACTCTAACCCCA
1 TACTCCAACCCTGTTTTTACTTCCAAAACACTGAATTTTTCATCTTTG-GGATACTCCAACCCCA
*
176170 CCATCTCTAAGGGGATACTCCAACCCCATTTTTACTTCCAAAACACCAAAATTTTCATCTCTGTG
65 CCATCTCTAAGGGGATACTCCAACCCCATTTTTACTTCCAAAACACCAAAATTTTCATCTCTGGG
*
176235 GATACTCTAACCCCACCATCTCCGAGGGGA
130 GATACTCTAACCCCACCATCTCCAAGGGGA
176265 TACTCCAACCCTGTTTTTACTTCCAAAACA-TCGAATTTTTCATCTTTGGGGATACTCCAACCCC
1 TACTCCAACCCTGTTTTTACTTCCAAAACACT-GAATTTTTCATCTTT-GGGATACTCCAACCCC
* * * * *
176329 ACCATCTCCAAGAGGATACTCCAACCCCTTTTTTACTTCCAAAACATCAAATTTTTCATCTCTGG
64 ACCATCTCTAAGGGGATACTCCAACCCCATTTTTACTTCCAAAACACCAAAATTTTCATCTCTGG
** *
176394 GGATACTCTAATGCCACCATCTCTAAGGGGA
129 GGATACTCTAACCCCACCATCTCCAAGGGGA
* ** * * *
176425 TACTTCAACCCCATTTTTACTTCCCAAACACTGAATTTTTCATCTCTGGTGATACTCCAACCCTA
1 TACTCCAACCCTGTTTTTACTTCCAAAACACTGAATTTTTCATCTTTGG-GATACTCCAACCCCA
* * *
176490 CTATCT-T-CGAGGGATACTCCAACCCCATTTTTACTT-CATAAACACCAAAATTTTCGTCTCTG
65 CCATCTCTAAG-GGGATACTCCAACCCCATTTTTACTTCCA-AAACACCAAAATTTTCATCTCTG
176552 GGGATACTCTAA
128 GGGATACTCTAA
176564 TGCCGGTTTT
Statistics
Matches: 266, Mismatches: 27, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
158 3 0.01
159 59 0.22
160 202 0.76
161 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (159 bp):
TACTCCAACCCTGTTTTTACTTCCAAAACACTGAATTTTTCATCTTTGGGATACTCCAACCCCAC
CATCTCTAAGGGGATACTCCAACCCCATTTTTACTTCCAAAACACCAAAATTTTCATCTCTGGGG
ATACTCTAACCCCACCATCTCCAAGGGGA
Found at i:176731 original size:11 final size:12
Alignment explanation
Indices: 176694--176732 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
176684 TCCAACCTTG
176694 TTTCTTTTCAAA
1 TTTCTTTTCAAA
176706 TTTCTTTTCAAA
1 TTTCTTTTCAAA
176718 TTTCTTTT-AAA
1 TTTCTTTTCAAA
176729 TTTC
1 TTTC
176733 AAACGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTCTTTTCAAA
Found at i:177511 original size:34 final size:35
Alignment explanation
Indices: 177473--177539 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
177463 CCTTACAACA
177473 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
*
177507 CTATCTTTTTCAAAGGCTAAGATTGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
177540 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:178025 original size:13 final size:13
Alignment explanation
Indices: 178009--178034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177999 ACTATTTATG
178009 ATGTATCGATACA
1 ATGTATCGATACA
178022 ATGTATCGATACA
1 ATGTATCGATACA
178035 TGAATAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:178107 original size:10 final size:10
Alignment explanation
Indices: 178083--178131 Score: 91
Period size: 10 Copynumber: 5.0 Consensus size: 10
178073 TAGTGATACG
178083 TGAACAGTG-
1 TGAACAGTGA
178092 TGAACAGTGA
1 TGAACAGTGA
178102 TGAACAGTGA
1 TGAACAGTGA
178112 TGAACAGTGA
1 TGAACAGTGA
178122 TGAACAGTGA
1 TGAACAGTGA
178132 AAAATGAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
9 9 0.23
10 30 0.77
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:188048 original size:21 final size:20
Alignment explanation
Indices: 188018--188150 Score: 65
Period size: 20 Copynumber: 6.6 Consensus size: 20
188008 TTTGATAATT
188018 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGTAAA
* * *
188039 TGTATTGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
* ****
188059 TGTATCAATACATGTCTGAAA
1 TGTATCGATACAAAAGT-AAA
** **
188080 TGTATCGATACAAAACCACTC
1 TGTATCGATACAAAAGTA-AA
* * *
188101 TGCATTC--TA-GAAAGGAAA
1 TGTA-TCGATACAAAAGTAAA
*
188119 TGTATCGATACATAAGTAAA
1 TGTATCGATACAAAAGTAAA
188139 TGTATCGATACA
1 TGTATCGATACA
188151 TGCTTAAAAT
Statistics
Matches: 80, Mismatches: 26, Indels: 13
0.67 0.22 0.11
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 6 0.08
20 38 0.47
21 29 0.36
22 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:188062 original size:20 final size:21
Alignment explanation
Indices: 188018--188093 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
188008 TTTGATAATT
188018 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAATAGTAAA
* * *
188039 TGTATTGATACATA-AGTGAA
1 TGTATCGATACAAATAGTAAA
* ** *
188059 TGTATCAATACATGT-CTGAAA
1 TGTATCGATACAAATAGT-AAA
188080 TGTATCGATACAAA
1 TGTATCGATACAAA
188094 ACCACTCTGC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAAATAGTAAA
Found at i:188158 original size:20 final size:21
Alignment explanation
Indices: 188116--188172 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
188106 TCTAGAAAGG
188116 AAATGTATCGATACATAAGT-
1 AAATGTATCGATACATAAGTA
***
188136 AAATGTATCGATACATGCTTA
1 AAATGTATCGATACATAAGTA
*
188157 AAATTTATCGATACAT
1 AAATGTATCGATACAT
188173 TTATCATGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATAAGTA
Found at i:190660 original size:80 final size:80
Alignment explanation
Indices: 190560--190778 Score: 280
Period size: 79 Copynumber: 2.8 Consensus size: 80
190550 TCCAAAAAGG
*
190560 CCAAAATTTTCATCTTAGGGGATATTCCAGCCCCATTATTTTTGAGGGGATACTCCAACCCCGCC
1 CCAAAATTTTCATCTTAGGGGATACTCCAGCCCCATTATTTTTGAGGGGATACTCCAACCCCGCC
*
190625 TTTACTTTTAAAACA
66 TTTACTTCTAAAACA
* ** * *
190640 CCAAAATTTTCATCTTAGGGGATACTCCAG-CCCATCAATTCCT-AGAGGATACTTCAACCCCGC
1 CCAAAATTTTCATCTTAGGGGATACTCCAGCCCCAT-TATTTTTGAGGGGATACTCCAACCCCGC
190703 CTTTACTTCTAAAACA
65 CTTTACTTCTAAAACA
* ** * * * * *
190719 CTAAAATTTTCATCTTAGAAGATACTCTAACCCCATTAATTTTGAAGGGATACCCCAACC
1 CCAAAATTTTCATCTTAGGGGATACTCCAGCCCCATTATTTTTGAGGGGATACTCCAACC
190779 TCATTTTTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
79 66 0.57
80 50 0.43
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (80 bp):
CCAAAATTTTCATCTTAGGGGATACTCCAGCCCCATTATTTTTGAGGGGATACTCCAACCCCGCC
TTTACTTCTAAAACA
Found at i:192495 original size:83 final size:83
Alignment explanation
Indices: 192386--192551 Score: 323
Period size: 83 Copynumber: 2.0 Consensus size: 83
192376 ATCCTCTTTG
192386 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
1 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
192451 CTTCCTTGGTTTTCATCA
66 CTTCCTTGGTTTTCATCA
*
192469 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCTATGGAC
1 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
192534 CTTCCTTGGTTTTCATCA
66 CTTCCTTGGTTTTCATCA
192552 ATCCCTCCTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.14, C:0.30, G:0.16, T:0.40
Consensus pattern (83 bp):
CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
CTTCCTTGGTTTTCATCA
Found at i:196880 original size:42 final size:42
Alignment explanation
Indices: 196833--196951 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
196823 TTCTTCTTTC
* *
196833 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
196875 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
196917 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
196952 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:196892 original size:12 final size:11
Alignment explanation
Indices: 196866--196941 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
196856 TCTATTATCT
*
196866 CTCCTGTCTCTC
1 CTCCTATCTC-C
196878 CTCCTATCATCC
1 CTCCTATC-TCC
196890 CTCCTATCT--
1 CTCCTATCTCC
*
196899 CTACTATCT--
1 CTCCTATCTCC
*
196908 CTCCTGTCTCTC
1 CTCCTATCTC-C
196920 CTCCTATCATCC
1 CTCCTATC-TCC
*
196932 CTCCTCTCTC
1 CTCCTATCTC
196942 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:196893 original size:24 final size:24
Alignment explanation
Indices: 196857--196942 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
196847 CCTCCTCTCT
* *
196857 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
196881 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
196902 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
196923 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
196943 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:196917 original size:18 final size:18
Alignment explanation
Indices: 196848--196918 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
196838 CCTGTCATCC
* *
196848 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
196866 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
196888 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
196908 CTCCTGTCTCT
1 CTCCTGTCTCT
196919 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:198598 original size:83 final size:83
Alignment explanation
Indices: 198489--198655 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
198479 ATCCTCTTTG
198489 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
1 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
198554 CTTCCTTGGTTTTCATCA
66 CTTCCTTGGTTTTCATCA
*
198572 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCTATGGAC
1 CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
198637 CTTCCTTGGTTTTCATCA
66 CTTCCTTGGTTTTCATCA
198655 C
1 C
198656 ATTCGATCAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.14, C:0.31, G:0.16, T:0.40
Consensus pattern (83 bp):
CCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGAC
CTTCCTTGGTTTTCATCA
Found at i:202441 original size:162 final size:165
Alignment explanation
Indices: 202273--202568 Score: 411
Period size: 165 Copynumber: 1.8 Consensus size: 165
202263 TTTCATGAGT
* *
202273 TTTTCATTTTTCCTTAGAATTC-CTCTTATTTTTTAAATACGGAGTTTT-TT-TCCAT-AATTTT
1 TTTTCATTTTTCCTTAGAATTCTCTCTT-TTTTTGAAATACGGAGTTTTCTTCTCCATAAACTTT
** * *
202334 TTTGGGAGGACTTTCATCAATTTAAAATTTTTAAAATTCAACAAATATCATCGTTTAATTCATAA
65 TTCAGGAGGACTTTCACCAATTTAAAATTTTTAAAATTCAACAAATATCATCATTTAATTCATAA
202399 TAAATTAGTTTTGAAAATTTCATTCATTTTAATTTA
130 TAAATTAGTTTTGAAAATTTCATTCATTTTAATTTA
* * *
202435 TTTTCATTTTTCCTTAGAATTCTTTCTTTTTTTGAAATACGGAGTTTTCTTCTTCGTAAACTTTT
1 TTTTCATTTTTCCTTAGAATTCTCTCTTTTTTTGAAATACGGAGTTTTCTTCTCCATAAACTTTT
* * * * * * *
202500 TCAGGAGGATTTTCACCGATTTAAAATTTTTAAAATTTATCAAATATTATCATTTGATTCATATT
66 TCAGGAGGACTTTCACCAATTTAAAATTTTTAAAATTCAACAAATATCATCATTTAATTCATAAT
202565 AAAT
131 AAAT
202569 CAATTTTAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
162 41 0.36
163 6 0.05
164 3 0.03
165 64 0.56
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (165 bp):
TTTTCATTTTTCCTTAGAATTCTCTCTTTTTTTGAAATACGGAGTTTTCTTCTCCATAAACTTTT
TCAGGAGGACTTTCACCAATTTAAAATTTTTAAAATTCAACAAATATCATCATTTAATTCATAAT
AAATTAGTTTTGAAAATTTCATTCATTTTAATTTA
Found at i:204573 original size:154 final size:155
Alignment explanation
Indices: 204390--204891 Score: 509
Period size: 154 Copynumber: 3.2 Consensus size: 155
204380 GGGTACTGGG
* * * * *
204390 ATACTTTCACATCGAAGGTATACC-TAGGGGCATTTTCATAATTTTTTTAGAACCAAGTCTTAAG
1 ATACTTTTACATCGAAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAAAACCAAGT-TTAGG
204454 TTATCACTAGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATA-GTTCATCCCATCTATAATC
65 TTATCACTAGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATC
*
204518 ATCATTAAGTCCTTTAGGGGTATCGA
130 ATTATTAAGTCCTTTAGGGGTATCGA
* * * *
204544 ATACTTCTACATCGAAGGTA-CCCTTAGGGGCTTTTTCATAATTTTATTAAAACCAAGTTCTAGG
1 ATACTTTTACATCGAAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAAAACCAAGTT-TAGG
* * * *** * *
204608 TTATCA-TGGGGTTCCGCATTTATGGTGAAGGTGAGTATTTAGGATAGGTTCATCTCATCTATAA
65 TTATCACT-AGG-TCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAA
* *
204672 -CCTTTTTAAGTCCTTTAGGGGTATCGA
128 TCATTATTAAGTCCTTTAGGGGTATCGA
** * * * * * * * *
204699 GCACTTTTA-ACTCGAAAGTATCTCTAAAGGGCTTTTTCATAA-TTTTTTAAAATCGATTATTTG
1 ATACTTTTACA-TCGAAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAAAACCAAGT-TTAG
* * * *
204762 GTTGTCACCAGGTCTGCTTTTATGCCAAAAGTGGGTATTTAGGATAGGTTCGTCCCATCTATATA
64 GTTATCACTAGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATA-A
*
204827 T-ATATATTAAGTCTTTTAGGGGTATC-A
128 TCAT-TATTAAGTCCTTTAGGGGTATCGA
* * * *
204854 GATACTTTTATATCGAAAGTACCCCCTAGGGGTATTTT
1 -ATACTTTTACATCGAAAGTATCCCTTAGGGGCATTTT
204892 TTTTATGATC
Statistics
Matches: 280, Mismatches: 54, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
153 4 0.01
154 103 0.37
155 91 0.32
156 81 0.29
157 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (155 bp):
ATACTTTTACATCGAAAGTATCCCTTAGGGGCATTTTCATAATTTTTTTAAAACCAAGTTTAGGT
TATCACTAGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCA
TTATTAAGTCCTTTAGGGGTATCGA
Found at i:204848 original size:156 final size:154
Alignment explanation
Indices: 204417--204877 Score: 477
Period size: 155 Copynumber: 3.0 Consensus size: 154
204407 GTATACCTAG
* * * * *
204417 GGGCATTTTCATAATTTTTTTAGAACCAAG-TCTTAAGTTATCACTAGGTCTGCTTTTATGCCAA
1 GGGCTTTTTCATAATTTTATTAAAACCAAGTTC-TAGGTTATCACCAGGTCTGCTTTTATGCCAA
* *
204481 AGGTGGGTATTTAGGATA-GTTCATCCCATCTATAATCATCATTAAGTCCTTTAGGGGTATCGAA
65 AGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAT-ATTATTAAGTCCTTTAGGGGTATCGAG
* * * *
204545 TACTTCT-ACATCGAAGGTACCCTTAG
129 TACTTTTAAC-TCGAAAGTACCCTAAA
*** * * ***
204571 GGGCTTTTTCATAATTTTATTAAAACCAAGTTCTAGGTTATCATGGGGTTCCGCATTTATGGTGA
1 GGGCTTTTTCATAATTTTATTAAAACCAAGTTCTAGGTTATCACCAGG-TCTGCTTTTATGCCAA
* * ** * *
204636 AGGTGAGTATTTAGGATAGGTTCATCTCATCTATAACCTTTTTAAGTCCTTTAGGGGTATCGAGC
65 AGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATATTATTAAGTCCTTTAGGGGTATCGAGT
*
204701 ACTTTTAACTCGAAAGTATCTCTAAA
130 ACTTTTAACTCGAAAGTA-CCCTAAA
* * * * *
204727 GGGCTTTTTCATAATTTT-TTAAAATCGA-TTATTTGGTTGTCACCAGGTCTGCTTTTATGCCAA
1 GGGCTTTTTCATAATTTTATTAAAACCAAGTT-CTAGGTTATCACCAGGTCTGCTTTTATGCCAA
* * *
204790 AAGTGGGTATTTAGGATAGGTTCGTCCCATCTATATATATATATTAAGTCTTTTAGGGGTATC-A
65 AGGTGGGTATTTAGGATAGGTTCATCCCATCTATA-ATAT-TATTAAGTCCTTTAGGGGTATCGA
204854 GATACTTTTATA-TCGAAAGTACCC
128 G-TACTTTTA-ACTCGAAAGTACCC
204878 CCTAGGGGTA
Statistics
Matches: 249, Mismatches: 48, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
154 82 0.33
155 90 0.36
156 76 0.31
157 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (154 bp):
GGGCTTTTTCATAATTTTATTAAAACCAAGTTCTAGGTTATCACCAGGTCTGCTTTTATGCCAAA
GGTGGGTATTTAGGATAGGTTCATCCCATCTATAATATTATTAAGTCCTTTAGGGGTATCGAGTA
CTTTTAACTCGAAAGTACCCTAAA
Found at i:208052 original size:52 final size:52
Alignment explanation
Indices: 207982--208102 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
207972 GAAAATTTAT
*
207982 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
208034 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
208086 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
208103 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:208115 original size:52 final size:51
Alignment explanation
Indices: 207982--208122 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
207972 GAAAATTTAT
207982 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
208034 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
208086 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
208123 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:208129 original size:13 final size:13
Alignment explanation
Indices: 208111--208135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208101 CAAAGATCAG
208111 TGTATCGATACAA
1 TGTATCGATACAA
208124 TGTATCGATACA
1 TGTATCGATACA
208136 TGTGAGTAAT
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:208219 original size:13 final size:13
Alignment explanation
Indices: 208201--208225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208191 CAAAAAAATA
208201 TGTATCGATACAT
1 TGTATCGATACAT
208214 TGTATCGATACA
1 TGTATCGATACA
208226 ACATTTTTTG
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:208574 original size:20 final size:20
Alignment explanation
Indices: 208549--208599 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
208539 AGTGTCTACA
*
208549 GTATCGATACACATTTAAAT
1 GTATCGATACACATTGAAAT
* * *
208569 GTATCGATACAGATTGCATT
1 GTATCGATACACATTGAAAT
208589 GTATCGATACA
1 GTATCGATACA
208600 TGACCAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACACATTGAAAT
Found at i:208611 original size:20 final size:21
Alignment explanation
Indices: 208588--208640 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
208578 CAGATTGCAT
**
208588 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
208608 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
208629 TGTATCGATACA
1 TGTATCGATACA
208641 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:208729 original size:33 final size:32
Alignment explanation
Indices: 208672--208739 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
208662 GTAGCCAAAT
208672 TTGTATAGATACACACAATATGTATCGATACA
1 TTGTATAGATACACACAATATGTATCGATACA
208704 TTGTATCA-ATACACCACAA-ATTGTATCGATACA
1 TTGTAT-AGATACA-CACAATA-TGTATCGATACA
208737 TTG
1 TTG
208740 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
TTGTATAGATACACACAATATGTATCGATACA
Found at i:211810 original size:49 final size:49
Alignment explanation
Indices: 211601--212532 Score: 1229
Period size: 49 Copynumber: 19.7 Consensus size: 49
211591 AAAAGGATGT
*
211601 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
211653 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
211696 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
211744 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
211793 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
211841 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
211890 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
211939 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
211982 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
212031 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTAC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212074 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
212123 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
212166 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212215 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212258 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212307 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212350 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * * *
212399 CAATATGCTGATTCAAGGCTAGCTATATTGGACTTAATGGTGAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
212448 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
212497 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
212533 GAAGGGTTGC
Statistics
Matches: 778, Mismatches: 64, Indels: 79
0.84 0.07 0.09
Matches are distributed among these distances:
43 234 0.30
45 5 0.01
47 5 0.01
48 95 0.12
49 408 0.52
52 31 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:212032 original size:92 final size:92
Alignment explanation
Indices: 211592--212537 Score: 1374
Period size: 92 Copynumber: 10.1 Consensus size: 92
211582 AGATGATGAA
* * *
211592 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
211657 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
211688 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
211752 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
211779 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* *
211843 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
211876 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
*
211941 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
211974 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
212039 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
212066 AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
212131 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * * *
212158 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGTCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
212223 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
212250 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
212315 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
212342 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
212407 TGATTCAAGGCTAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
212434 AATGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
1 -A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* *
212499 ATATGCTGATTCAGGGCCAGCTATATTGGGCTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
212532 AGAAGG
1 A-AAGG
212538 GTTGCCACCG
Statistics
Matches: 798, Mismatches: 39, Indels: 29
0.92 0.05 0.03
Matches are distributed among these distances:
91 38 0.05
92 439 0.55
93 6 0.01
94 2 0.00
95 42 0.05
96 5 0.01
97 145 0.18
98 121 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:212346 original size:22 final size:22
Alignment explanation
Indices: 212321--212388 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
212311 GTGCTGAGTC
212321 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
* * *
212343 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTACAT-TG--GACTTA
212364 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTACATTGGACTTA
212386 AAG
1 AAG
212389 ATAAAGGTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (22 bp):
AAGGCCAGCTACATTGGACTTA
Found at i:212576 original size:33 final size:32
Alignment explanation
Indices: 212525--212665 Score: 180
Period size: 33 Copynumber: 4.4 Consensus size: 32
212515 CCAGCTATAT
*
212525 TGGGC-TTAG-AAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAAGGTTGCCACCGACTTGTG
*
212555 TGGGCTTTGGAAAATGGTTGCCACC-ACCTTGTG
1 TGGGCTTTAGAAAA-GGTTGCCACCGA-CTTGTG
* * *
212588 TGGGCTTTGGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAAGGTTGCCACCGACTTGTG
*
212620 TGGGCTTTAGAGAAGGTTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAAGG-TTGCCACCGACTTGTG
212653 TGGGCTTTAGAAA
1 TGGGCTTTAGAAA
212666 GGGTGAAAGA
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
30 5 0.05
31 3 0.03
32 31 0.32
33 57 0.59
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (32 bp):
TGGGCTTTAGAAAAGGTTGCCACCGACTTGTG
Found at i:212609 original size:65 final size:65
Alignment explanation
Indices: 212525--212669 Score: 208
Period size: 65 Copynumber: 2.3 Consensus size: 65
212515 CCAGCTATAT
*
212525 TGGGC-TTA-GAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAATGG-TTGCCACC-ACCTTG
1 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAA-GGTTTGCCACCGA-CTTG
212586 TG
64 TG
* *
212588 TGGGCTTTGGGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTTGCCACCGACTTGTG
1 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAGGTTTGCCACCGACTTGTG
*
212653 TGGGCTTTAGAAAGGGT
1 TGGGCTTTAGGAAGGGT
212670 GAAAGATGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
63 5 0.07
64 4 0.05
65 63 0.86
66 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (65 bp):
TGGGCTTTAGGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAGGTTTGCCACCGACTTGTG
Found at i:212781 original size:34 final size:32
Alignment explanation
Indices: 212671--213078 Score: 324
Period size: 34 Copynumber: 12.7 Consensus size: 32
212661 AGAAAGGGTG
* * * *
212671 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTT-AAAGGAA
*
212704 CAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAA-GG-AA
212740 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTA-AAGGAA
*
212774 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAA-GGAA
*
212809 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAGGAA
*
212843 AAAGGTGCCACGGAGTTGTGGGCTTAAACG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAGGAA
*
212873 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAG--GAA
* * * *
212904 AAAAGTGCCACAGAATTGTGGGCTT----TAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAGGAA
* *
212932 AAGGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAG--GAA
* * **
212966 AAAAGTGCCACGGAATTGTGGG-TT---TTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAGGAA
* *
212994 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTT-AAAGGAA
*
213027 CAAGGTGCCACGGAGTTGTGGGCTTTAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAGGAA
* * *
213059 AAA-ATGCCACTGAGTCGTGG
1 AAAGGTGCCACGGAGTTGTGG
213079 ACTTTGAGAC
Statistics
Matches: 308, Mismatches: 40, Indels: 56
0.76 0.10 0.14
Matches are distributed among these distances:
27 24 0.08
28 42 0.14
29 3 0.01
31 14 0.05
32 9 0.03
33 48 0.16
34 123 0.40
35 17 0.06
36 9 0.03
37 19 0.06
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (32 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAGGAA
Found at i:212942 original size:28 final size:28
Alignment explanation
Indices: 212841--213024 Score: 111
Period size: 28 Copynumber: 6.2 Consensus size: 28
212831 CTTTAAAAAG
* * *
212841 AAAAAGGTGCCACGGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
* *
212868 AAACGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** * *
212901 GAAAAAAGTGCCACAGAATTGTGGGCTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
212930 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** **
212963 GAAAAAAGTGCCACGGAATTGTGGGTTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
212992 AAAAGGGTGCCACGGAGTTGTGGAC-TT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
213019 AAAAGG
1 AAAAGG
213025 AACAAGGTGC
Statistics
Matches: 120, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
27 30 0.25
28 43 0.36
29 2 0.02
33 2 0.02
34 43 0.36
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAATTGTGGACTTT
Found at i:212942 original size:62 final size:61
Alignment explanation
Indices: 212807--213055 Score: 356
Period size: 62 Copynumber: 4.0 Consensus size: 61
212797 CTTTAAACAG
* * * * *
212807 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT
* *
212868 AAACGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTT
*
212930 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGTTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTT
* * * *
212992 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT
213053 AAA
1 AAA
213056 GAAAAAATGC
Statistics
Matches: 171, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
60 5 0.03
61 75 0.44
62 91 0.53
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT
Found at i:214069 original size:9 final size:9
Alignment explanation
Indices: 214055--214084 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
214045 TGAAAAGGGG
214055 TTTTTCTTT
1 TTTTTCTTT
214064 TTTTTCTTT
1 TTTTTCTTT
214073 TTTTT-TTT
1 TTTTTCTTT
214081 TTTT
1 TTTT
214085 GCATCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:214430 original size:21 final size:21
Alignment explanation
Indices: 214397--214436 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
214387 TTTGGTGTTC
214397 CCTTTTTGATTTTGTCTTTGCA
1 CCTTTTTGATTTTGT-TTTGCA
*
214419 CCTTTTT-TTTTTGTTTTG
1 CCTTTTTGATTTTGTTTTG
214437 TTTTTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.05, C:0.15, G:0.12, T:0.68
Consensus pattern (21 bp):
CCTTTTTGATTTTGTTTTGCA
Found at i:221405 original size:52 final size:52
Alignment explanation
Indices: 221335--221455 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
221325 GAAAATTTAT
*
221335 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
221387 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
221439 CTGCATGTATCAATACA
1 CTGCATGTATCGATACA
221456 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:221468 original size:52 final size:52
Alignment explanation
Indices: 221335--221475 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
221325 GAAAATTTAT
* *
221335 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
221387 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
221439 CTGCATGTATCAATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCAATACATAAGAT-AGTGTATCGATACA
221476 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 76 0.95
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:221482 original size:13 final size:13
Alignment explanation
Indices: 221464--221488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221454 CAAAGATCAG
221464 TGTATCGATACAA
1 TGTATCGATACAA
221477 TGTATCGATACA
1 TGTATCGATACA
221489 TGTGAGTAAT
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:221571 original size:13 final size:13
Alignment explanation
Indices: 221553--221577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221543 CAAAAAAATA
221553 TGTATCGATACAT
1 TGTATCGATACAT
221566 TGTATCGATACA
1 TGTATCGATACA
221578 ACATTTTATG
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:221573 original size:33 final size:33
Alignment explanation
Indices: 221531--221597 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
221521 AGTAGCTTAA
221531 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
221564 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
221597 A
1 A
221598 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:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:221926 original size:20 final size:20
Alignment explanation
Indices: 221901--221951 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
221891 AGTGTCTACA
*
221901 GTATCGATACACATTTAAAT
1 GTATCGATACACATTGAAAT
* * *
221921 GTATCGATACAGATTGCATT
1 GTATCGATACACATTGAAAT
221941 GTATCGATACA
1 GTATCGATACA
221952 TGACCAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACACATTGAAAT
Found at i:221963 original size:20 final size:21
Alignment explanation
Indices: 221940--221992 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
221930 CAGATTGCAT
**
221940 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
221960 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
221981 TGTATCGATACA
1 TGTATCGATACA
221993 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:222081 original size:33 final size:32
Alignment explanation
Indices: 222024--222091 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
222014 GTAGCCAAAT
222024 TTGTATAGATACACACAATATGTATCGATACA
1 TTGTATAGATACACACAATATGTATCGATACA
222056 TTGTATCA-ATACACCACAA-ATTGTATCGATACA
1 TTGTAT-AGATACA-CACAATA-TGTATCGATACA
222089 TTG
1 TTG
222092 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
TTGTATAGATACACACAATATGTATCGATACA
Found at i:230756 original size:20 final size:21
Alignment explanation
Indices: 230733--230785 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
230723 TAGATTGCAT
**
230733 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
* *
230753 TGTATCAATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
230774 TGTATCGATACA
1 TGTATCGATACA
230786 GGTCATTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:230854 original size:13 final size:13
Alignment explanation
Indices: 230836--230860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230826 ACACAAAATA
230836 TGTATCGATACAT
1 TGTATCGATACAT
230849 TGTATCGATACA
1 TGTATCGATACA
230861 CCACAAATTG
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:230878 original size:33 final size:32
Alignment explanation
Indices: 230816--230883 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
230806 ATAGCCAAAT
*
230816 TTGTATCGCTACACAAAATATGTATCGATACA
1 TTGTATCGATACACAAAATATGTATCGATACA
230848 TTGTATCGATACACCACAAAT-TGTATCGATACA
1 TTGTATCGATACA-CA-AAATATGTATCGATACA
230881 TTG
1 TTG
230884 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 12 0.36
33 17 0.52
34 4 0.12
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACAAAATATGTATCGATACA
Found at i:234854 original size:117 final size:112
Alignment explanation
Indices: 234594--234881 Score: 398
Period size: 117 Copynumber: 2.5 Consensus size: 112
234584 TGTTTGGTTT
*
234594 AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAATAGGGCATGTATCCTATG
1 AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAATGGGGCATGTATCCTATG
* *
234659 AGTTTTGAAAATTTTGAGCCCAACAACATCAAATTTCTCTGTTTTTC
66 AGTTTTAAAAATTTTGAGCCCAACAACATCAAATTTATCTGTTTTTC
* *
234706 AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAACGGGGTATGTATCCTATT
1 AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAATGGGGCATGTATCC---T
* *
234771 ATTATAGTTTTAAAAATTTTGAGCCCAATAACATCAAATTTATCTGATTTTT-
63 A-T-GAGTTTTAAAAATTTTGAGCCCAACAACATCAAATTTATCTG-TTTTTC
* * * * *
234823 GAGAAATTCATATTTTATAAATTTCAGTCCATTCGTGCCTAGGAAAATGGGGGCATGTA
1 AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAAT-GGGGCATGTA
234882 CCCAATCAAT
Statistics
Matches: 155, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
112 58 0.37
115 2 0.01
116 1 0.01
117 80 0.52
118 14 0.09
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (112 bp):
AAAAAATTCATACTTTATACATTTCAATCCATTCGTGCCTAGGAAAATGGGGCATGTATCCTATG
AGTTTTAAAAATTTTGAGCCCAACAACATCAAATTTATCTGTTTTTC
Found at i:235341 original size:77 final size:76
Alignment explanation
Indices: 235202--235346 Score: 173
Period size: 77 Copynumber: 1.9 Consensus size: 76
235192 TGCACATTTG
* * * * * * *
235202 CATGGCATTGGTATTTGCTCGTTTCATATGCATTTACAATTTTACTGATACTTGCATCTGCATCG
1 CATGGCATTGGCATTTGATCATTCCATAAGCATTTACAACTTTACTGAAACTTGCATCTGCATCG
235267 TTTACATTTTA
66 TTTACATTTTA
* * * * *
235278 CATGGCATTGGCATTTGGATCATTCCATAAGCATTTGCCACTTTATTGAAACTTGCATTTGCATT
1 CATGGCATTGGCATTT-GATCATTCCATAAGCATTTACAACTTTACTGAAACTTGCATCTGCATC
235343 GTTT
65 GTTT
235347 CACACACATC
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
76 15 0.27
77 41 0.73
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.43
Consensus pattern (76 bp):
CATGGCATTGGCATTTGATCATTCCATAAGCATTTACAACTTTACTGAAACTTGCATCTGCATCG
TTTACATTTTA
Found at i:235393 original size:81 final size:79
Alignment explanation
Indices: 235147--235418 Score: 255
Period size: 81 Copynumber: 3.4 Consensus size: 79
235137 ACATCGTTTA
** * * *
235147 ATATGCATTTATTATTTTACTGATGCTTGCATTTACATTGTTTCATGCACATTTGCATGGCATTG
1 ATATGCATTTACCATTTTACTGATACTTGCATTTGCATTGTTTCA-ACACATTTGCATGGCATTG
*
235212 GTATTTGC-TCGTTTC
65 GTATTTGCATC-ATTC
* * * * *
235227 ATATGCATTTACAATTTTACTGATACTTGCATCTGCATCGTTT--ACA-TTTTACATGGCATTGG
1 ATATGCATTTACCATTTTACTGATACTTGCATTTGCATTGTTTCAACACATTTGCATGGCATTGG
* *
235289 CATTTGGATCATTCC
66 TATTTGCATCATT-C
* * * * * * *
235304 ATAAGCATTTGCCACTTTATTGAAACTTGCATTTGCATTGTTTCACACACATCTGCATGACATTG
1 ATATGCATTTACCATTTTACTGATACTTGCATTTGCATTGTTTCA-ACACATTTGCATGGCATTG
*
235369 GTATTCGCATCATCTC
65 GTATTTGCATCAT-TC
* * *
235385 ATATGCATTTTCCATTTTAGTGATGCTTGCATTT
1 ATATGCATTTACCATTTTACTGATACTTGCATTT
235419 ACATCATTTC
Statistics
Matches: 152, Mismatches: 33, Indels: 13
0.77 0.17 0.07
Matches are distributed among these distances:
76 21 0.14
77 40 0.26
80 40 0.26
81 50 0.33
82 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (79 bp):
ATATGCATTTACCATTTTACTGATACTTGCATTTGCATTGTTTCAACACATTTGCATGGCATTGG
TATTTGCATCATTC
Found at i:235832 original size:90 final size:91
Alignment explanation
Indices: 235677--236150 Score: 485
Period size: 92 Copynumber: 5.2 Consensus size: 91
235667 TGTAGCCCAT
* * * *
235677 ACATTCCCAATCATATCCCCTTCATTTAACTACTAGATGGTATTGATGCATCACAAAA-CTTAAT
1 ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCA-AAAAGCTGAAT
* * *
235741 TTCCTTAGGGCAAGG-GTGCGGTCCAC
65 TTCCTTAGGGCAAGGAATCCGGACCAC
* * *
235767 ACATTCCCAATCATATCCCCTTCATTCAACTACTAAATGGTATTGATACATTAAAAAGCTGAATT
1 ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCAAAAAGCTGAATT
* *
235832 TCCTTTGGGCAAGGATATCCCGACCAC
66 TCCTTAGGGCAAGGA-ATCCGGACCAC
* * * *
235859 ACATTCCCAATCATATCCGCTTCATTCAACCATTAAATGGTATTGATGCATCACAAAG-TCAAAT
1 ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCAAAAAGCT-GAAT
* * *
235923 TTTCTTGGGGCAAGGATATCCTGACCAC
65 TTCCTTAGGGCAAGGA-ATCCGGACCAC
* * * * * *
235951 ACATTCCTAATCATATCCCTTTTATTCAACCACTAGATGGTATTAATGCATCATAAAGCTTG-AT
1 ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCAAAAAGC-TGAAT
* * * *
236015 TTCCTTAGGGTAAGG-GTGCGGCCCAC
65 TTCCTTAGGGCAAGGAATCCGGACCAC
* * * *
236041 ACATTCCTAATCATATCTCCTTCATTCAACCACTAAATGGTATTGATGCATCATAAAGC-CATAT
1 ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCAAAAAGCTGA-AT
* * * *
236105 TTTCTTAGGGTAAGGATATCCCGACCATT
65 TTCCTTAGGGCAAGGA-ATCCGGACCA-C
*
236134 A-ATTCCTAATCATATCC
1 ACATTCCCAATCATATCC
236151 TTTTGTTTTA
Statistics
Matches: 324, Mismatches: 49, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
89 4 0.01
90 145 0.45
91 1 0.00
92 172 0.53
93 1 0.00
94 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (91 bp):
ACATTCCCAATCATATCCCCTTCATTCAACCACTAAATGGTATTGATGCATCAAAAAGCTGAATT
TCCTTAGGGCAAGGAATCCGGACCAC
Found at i:236043 original size:182 final size:182
Alignment explanation
Indices: 235671--236176 Score: 549
Period size: 182 Copynumber: 2.8 Consensus size: 182
235661 AAAATGTGTA
* * * *
235671 GCCCATACATTCCCAATCATATCCCCTTCATTTAACTACTAGATGGTATTGATGCATCACAAA-A
1 GCCCACACATTCCCAATCATAT-CCCTTCATTCAACCACTAAATGGTATTGATGCATCACAAAGA
* * * * * * * * * *
235735 CTTAATTTCCTTAGGGCAAGG--GTGCGGTCCACACATTCCCAATCATATCCCCTTCATTCAACT
65 C-AAATTTTCTTAGGGCAAGGATATCCCGACCACACATTCCTAATCATATCCCTTTTATTCAACC
* * * *
235798 ACTAAATGGTATTGATACATTAAAAAGCTGAATTTCCTTTGGGCAAGGATATCCC
129 ACTAGATGGTATTAATACATCAAAAAGCTGAATTTCCTTAGGGCAAGGA-ATCCC
* * *
235853 GACCACACATTCCCAATCATATCCGCTTCATTCAACCATTAAATGGTATTGATGCATCACAAAGT
1 GCCCACACATTCCCAATCATATCC-CTTCATTCAACCACTAAATGGTATTGATGCATCACAAAGA
* *
235918 CAAATTTTCTTGGGGCAAGGATATCCTGACCACACATTCCTAATCATATCCCTTTTATTCAACCA
65 CAAATTTTCTTAGGGCAAGGATATCCCGACCACACATTCCTAATCATATCCCTTTTATTCAACCA
* * * * * *
235983 CTAGATGGTATTAATGCATCATAAAGCTTG-ATTTCCTTAGGGTAAGG-GTGCG
130 CTAGATGGTATTAATACATCAAAAAGC-TGAATTTCCTTAGGGCAAGGAATCCC
* * *
236035 GCCCACACATTCCTAATCATATCTCCTTCATTCAACCACTAAATGGTATTGATGCATCATAAAGC
1 GCCCACACATTCCCAATCATATC-CCTTCATTCAACCACTAAATGGTATTGATGCATCACAAAGA
* * * * * *
236100 CATATTTTCTTAGGGTAAGGATATCCCGACCATTA-ATTCCTAATCATAT-CCTTTTGTTTTAGC
65 CAAATTTTCTTAGGGCAAGGATATCCCGACCA-CACATTCCTAATCATATCCCTTTT-ATTCAAC
236163 CACTAGATGGTATT
128 CACTAGATGGTATT
236177 GGTGCATTAC
Statistics
Matches: 275, Mismatches: 41, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
181 8 0.03
182 190 0.69
183 3 0.01
184 72 0.26
185 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (182 bp):
GCCCACACATTCCCAATCATATCCCTTCATTCAACCACTAAATGGTATTGATGCATCACAAAGAC
AAATTTTCTTAGGGCAAGGATATCCCGACCACACATTCCTAATCATATCCCTTTTATTCAACCAC
TAGATGGTATTAATACATCAAAAAGCTGAATTTCCTTAGGGCAAGGAATCCC
Found at i:236411 original size:35 final size:35
Alignment explanation
Indices: 236363--236432 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
236353 TTTCTCTCAC
* *
236363 ACTCTTTCCATCATCGTTTGACTGTATCTGGTCAA
1 ACTCTTTCCATCATCATTTGACTATATCTGGTCAA
* *
236398 ACTCTTTCTATCATCATTTGGCTATATCTGGTCAA
1 ACTCTTTCCATCATCATTTGACTATATCTGGTCAA
236433 CGTCTTCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (35 bp):
ACTCTTTCCATCATCATTTGACTATATCTGGTCAA
Found at i:236741 original size:133 final size:131
Alignment explanation
Indices: 236437--236934 Score: 521
Period size: 133 Copynumber: 3.8 Consensus size: 131
236427 GGTCAACGTC
* * * *
236437 TTCTCATTTTGGTCTAACGTATGGTTACCACCCTGGTTAGATTCTTTTTATTCTGA-TTGA-ATA
1 TTCTCATTTTGGTCTGACGTATGGTTACCACACTGGTTAGATTCTTTTCATTCTGATTTGACGTA
* *** * * *
236500 TGGTTACCACCCTGGTCAAATCTGCC-CCTTTCTGTTTGATGCATGGTTGCCA-CCTTGATTAAA
66 TGGTTACCA-CCTGGTCAAATCTACCTCCTTTCTGTTTGACATATGGTTACCACCCTAG-TCAAA
236563 CTT
129 CTT
* * * * * *
236566 TTCTCATTTTGTTCTGATGTATGGTTACTACACTGGTCAGATTCTTTTCATTCTGATTTTATGTA
1 TTCTCATTTTGGTCTGACGTATGGTTACCACACTGGTTAGATTCTTTTCATTCTGATTTGACGTA
* *
236631 TGGTTACCACTCAGGTCAAATCTACCTCC-TTCTTGTTTGACATATGGTTACCACCCTAGTGAAA
66 TGGTTACCAC-CTGGTCAAATCTACCTCCTTTC-TGTTTGACATATGGTTACCACCCTAGTCAAA
*
236695 GTCT
129 CT-T
** * * *
236699 TTCTCATTTCAGTCTGACGTATGGTTGCCATACTAGTTAGATTCATTTT-ATTCTGATTTGACGT
1 TTCTCATTTTGGTCTGACGTATGGTTACCACACTGGTTAGATTC-TTTTCATTCTGATTTGACGT
* * * *
236763 ATGGTTACCACCTTGGTCAAATCTACCTTCTTTCTATTTGACATACT-GTTACCACCTTGGTCAA
65 ATGGTTACCACC-TGGTCAAATCTACCTCCTTTCTGTTTGACATA-TGGTTACCACCCTAGTCAA
236827 ACTT
128 ACTT
* *
236831 TTCTCATTTTGGTTTGACATATGGTTACCAC-CTTGGTTAGATT-TTTTCATTCTGATTTGACGT
1 TTCTCATTTTGGTCTGACGTATGGTTACCACAC-TGGTTAGATTCTTTTCATTCTGATTTGACGT
* * *
236894 ATGGTTACCACCCTGGTAAAATC-AGCCTCATTTTTGTTTGA
65 ATGGTTACCA-CCTGGTCAAATCTA-CCTCCTTTCTGTTTGA
236935 TGTATGTGTT
Statistics
Matches: 306, Mismatches: 48, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
129 49 0.16
130 9 0.03
131 74 0.24
132 61 0.20
133 105 0.34
134 8 0.03
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (131 bp):
TTCTCATTTTGGTCTGACGTATGGTTACCACACTGGTTAGATTCTTTTCATTCTGATTTGACGTA
TGGTTACCACCTGGTCAAATCTACCTCCTTTCTGTTTGACATATGGTTACCACCCTAGTCAAACT
T
Found at i:236802 original size:44 final size:43
Alignment explanation
Indices: 236456--236916 Score: 178
Period size: 44 Copynumber: 10.6 Consensus size: 43
236446 TGGTCTAACG
* * *
236456 TATGGTTACCACCCTGGTTAGATTCTTTT-TATTCTGA-TTGA-A
1 TATGGTTACCACCTTGGTCA-AATCTTTTCT-TTCTGATTTGACA
* *** **
236498 TATGGTTACCACCCTGGTCAAATCTGCCCCTTTCTG-TTTGATG
1 TATGGTTACCACCTTGGTCAAATCT-TTTCTTTCTGATTTGACA
* * * * * **
236541 CATGGTTGCCACCTTGATTAAA-CTTTTCTCATTTTG-TTCTGATG
1 TATGGTTACCACCTTGGTCAAATCTTTTCT--TTCTGATT-TGACA
* * * * **
236585 TATGGTTACTACAC-TGGTCAGATTCTTTTCATTCTGATTTTATG
1 TATGGTTACCAC-CTTGGTCA-AATCTTTTCTTTCTGATTTGACA
* ** *
236629 TATGGTTACCA-CTCAGGTCAAATCTACCTCCTTCTTG-TTTGACA
1 TATGGTTACCACCT-TGGTCAAATCT-TTTCTTTC-TGATTTGACA
* * * * * *
236673 TATGGTTACCACCCTAGTGAAAGTCTTTCTCATTTCAG-TCTGACG
1 TATGGTTACCACCTTGGTCAAA-TCTTT-TC-TTTCTGATTTGACA
* * * * * * *
236718 TATGGTTGCCATAC-TAGTTAGATTCATTTT-ATTCTGATTTGACG
1 TATGGTTACCA-CCTTGGTCA-AATC-TTTTCTTTCTGATTTGACA
*
236762 TATGGTTACCACCTTGGTCAAATCTACCTTCTTTCT-ATTTGACA
1 TATGGTTACCACCTTGGTCAAATCT--TTTCTTTCTGATTTGACA
* *
236806 TACT-GTTACCACCTTGGTCAAA-CTTTTCTCATTTTGGTTTGACA
1 TA-TGGTTACCACCTTGGTCAAATCTTTTCT--TTCTGATTTGACA
* * * * *
236850 TATGGTTACCACCTTGGTTAGATTTTTTCATTCTGATTTGACG
1 TATGGTTACCACCTTGGTCAAATCTTTTCTTTCTGATTTGACA
* *
236893 TATGGTTACCACCCTGGTAAAATC
1 TATGGTTACCACCTTGGTCAAATC
236917 AGCCTCATTT
Statistics
Matches: 314, Mismatches: 72, Indels: 65
0.70 0.16 0.14
Matches are distributed among these distances:
41 10 0.03
42 32 0.10
43 72 0.23
44 140 0.45
45 46 0.15
46 14 0.04
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (43 bp):
TATGGTTACCACCTTGGTCAAATCTTTTCTTTCTGATTTGACA
Found at i:237289 original size:32 final size:33
Alignment explanation
Indices: 237228--237292 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
237218 ACACTTTCAG
*
237228 ATGTATTGATACATTATGCTTTGTATCGATACA
1 ATGTATTGATACATTATGCATTGTATCGATACA
237261 ATGTATTGATACATGT-T-CATTGTATCGATACA
1 ATGTATTGATACAT-TATGCATTGTATCGATACA
237293 TGAACAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (33 bp):
ATGTATTGATACATTATGCATTGTATCGATACA
Found at i:237369 original size:20 final size:20
Alignment explanation
Indices: 237343--237396 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
237333 TTACCACTAT
*
237343 TTGTATCAATACATGGCACAA
1 TTGTATCAATACAT-GAACAA
* * *
237364 -TGTATCGATAAATGAAGAA
1 TTGTATCAATACATGAACAA
237383 TTGTATCAATACAT
1 TTGTATCAATACAT
237397 TGCCTTACAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TTGTATCAATACATGAACAA
Found at i:244964 original size:33 final size:32
Alignment explanation
Indices: 244901--244968 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
244891 CCTTAACTGT
*
244901 TTGTATCGATACATACAAGATGTATTGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
244933 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
244966 TTG
1 TTG
244969 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:246566 original size:3 final size:3
Alignment explanation
Indices: 246558--246582 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
246548 GGTGACGATT
246558 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
246583 CTCAGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:250621 original size:13 final size:13
Alignment explanation
Indices: 250603--250628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250593 TACACCAAGT
250603 ATGTATCGATACA
1 ATGTATCGATACA
250616 ATGTATCGATACA
1 ATGTATCGATACA
250629 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:256784 original size:13 final size:13
Alignment explanation
Indices: 256766--256791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256756 ACATTTTACT
256766 TTGTATCGATACA
1 TTGTATCGATACA
256779 TTGTATCGATACA
1 TTGTATCGATACA
256792 GGGTGATTAT
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:256955 original size:20 final size:20
Alignment explanation
Indices: 256912--256957 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
256902 AAATCTTTTG
256912 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
256933 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
256953 CAAAA
1 CAAAA
256958 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:259367 original size:20 final size:20
Alignment explanation
Indices: 259322--259373 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
259312 GTAGCCAAAC
**
259322 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
259342 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
259361 TTGTATCGATACA
1 TTGTATCGATACA
259374 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:261017 original size:20 final size:20
Alignment explanation
Indices: 260992--261054 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
260982 AAAACTCAAA
260992 TGTATCGATATAGCATTCTC
1 TGTATCGATATAGCATTCTC
261012 TGTATCG--ATA-CA---T-
1 TGTATCGATATAGCATTCTC
261025 TGTATCGATATAGCATTCTC
1 TGTATCGATATAGCATTCTC
261045 TGTATCGATA
1 TGTATCGATA
261055 GTGTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
13 7 0.19
14 1 0.03
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 1 0.03
20 17 0.47
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (20 bp):
TGTATCGATATAGCATTCTC
Found at i:261034 original size:33 final size:33
Alignment explanation
Indices: 260992--261054 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
260982 AAAACTCAAA
260992 TGTATCGATATAGCATTCTCTGTATCGATACAT
1 TGTATCGATATAGCATTCTCTGTATCGATACAT
261025 TGTATCGATATAGCATTCTCTGTATCGATA
1 TGTATCGATATAGCATTCTCTGTATCGATA
261055 GTGTATCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (33 bp):
TGTATCGATATAGCATTCTCTGTATCGATACAT
Found at i:261063 original size:31 final size:32
Alignment explanation
Indices: 260992--261065 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 32
260982 AAAACTCAAA
*
260992 TGTATCGATATAGCATTCTCTGTATCGATACAT
1 TGTATCGATATAGCATTCTCTGTATCGATA-AG
261025 TGTATCGATATAGCATTCTCTGTATCGAT-AG
1 TGTATCGATATAGCATTCTCTGTATCGATAAG
261056 TGTATCGATA
1 TGTATCGATA
261066 CAAAGGGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 11 0.28
33 29 0.73
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (32 bp):
TGTATCGATATAGCATTCTCTGTATCGATAAG
Found at i:261237 original size:19 final size:21
Alignment explanation
Indices: 261188--261239 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
261178 AAATCTTTTG
*
261188 CAAATTTC-TCATTTTTCATTT
1 CAAAATTCATCATTTTTCA-TT
261209 CAAAATTCATCATTTTTCA-T
1 CAAAATTCATCATTTTTCATT
261229 CAAAA-TCATCA
1 CAAAATTCATCA
261240 ACAAAAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 7 0.24
22 10 0.34
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (21 bp):
CAAAATTCATCATTTTTCATT
Found at i:262929 original size:17 final size:17
Alignment explanation
Indices: 262907--262941 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
262897 GGAGAAAGAT
262907 ACATGTGATTAAAGGAA
1 ACATGTGATTAAAGGAA
262924 ACATGTGATTAAAGGAA
1 ACATGTGATTAAAGGAA
262941 A
1 A
262942 TTGTTTTATT
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):
ACATGTGATTAAAGGAA
Found at i:263654 original size:13 final size:13
Alignment explanation
Indices: 263636--263661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263626 ACATACAACA
263636 TGTATCGATACAT
1 TGTATCGATACAT
263649 TGTATCGATACAT
1 TGTATCGATACAT
263662 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:263677 original size:33 final size:32
Alignment explanation
Indices: 263616--263683 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
263606 CCTTAACTGT
263616 TTGTATCGATACATACAACATGTATCGATACA
1 TTGTATCGATACATACAACATGTATCGATACA
263648 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAACATGTATCGATACA
263681 TTG
1 TTG
263684 GCTTGTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAACATGTATCGATACA
Found at i:266960 original size:44 final size:44
Alignment explanation
Indices: 266888--267185 Score: 146
Period size: 44 Copynumber: 6.8 Consensus size: 44
266878 TGAGCTTACA
* * **
266888 GTATGGTTACCACCCTAGTCAAACTCTTTTTATTTTGGTCTGAC
1 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCTGAC
* * * * *
266932 GTATGGTTACCACCCTAGTTAGATTCTTTTCATTCTAATTTGAT
1 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCTGAC
* * * *
266976 GTATGGTTACCA-CCTGGTCAAA-TCTGCCTTC-TTCCT-GTTTGAC
1 GTATGGTTACCACCCTAGTCAAACTCT--TTTCATT-CTAATCTGAC
* * * * *
267019 GTATGGTTACCAACCTGGTCAGATTCTTTTCATTCTGAT-TCGAC
1 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCT-GAC
** * * * * *
267063 ACATGGTTACTACCCTGGTCAAA-T-TTGCATCCTTCCT-ATTTGAC
1 GTATGGTTACCACCCTAGTCAAACTCTT--TTCATT-CTAATCTGAC
* * * * * *
267107 GTATGGATACCACCCTAGTCAGACTCCTTTCATTCCTACT-TTAT
1 GTATGGTTACCACCCTAGTCAAACTCTTTTCATT-CTAATCTGAC
* * * *
267151 GTGTGGTTACCACCTTAGTCAAGCTTTTTTCATTC
1 GTATGGTTACCACCCTAGTCAAACTCTTTTCATTC
267186 CTGTTTGACA
Statistics
Matches: 195, Mismatches: 44, Indels: 31
0.72 0.16 0.11
Matches are distributed among these distances:
42 5 0.03
43 34 0.17
44 147 0.75
45 8 0.04
46 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (44 bp):
GTATGGTTACCACCCTAGTCAAACTCTTTTCATTCTAATCTGAC
Found at i:267043 original size:87 final size:87
Alignment explanation
Indices: 266928--267165 Score: 289
Period size: 88 Copynumber: 2.7 Consensus size: 87
266918 TATTTTGGTC
*
266928 TGACGTATGGTTACCACCCTAGTTAGATTCTTTTCATTCTAATTTGATGTATGGTTACCACCTGG
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTAATTTGATGTATGGTTACCACCTGG
* * *
266993 TCAAATCTGCCTTCTTCCTGTT
66 TCAAATCTGCATCCTTCCTATT
* * * * *** *
267015 TGACGTATGGTTACCAACCTGGTCAGATTCTTTTCATTCTGATTCGACACATGGTTACTACCCTG
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTAATTTGATGTATGGTTACCA-CCTG
*
267080 GTCAAATTTGCATCCTTCCTATT
65 GTCAAATCTGCATCCTTCCTATT
* * * * *
267103 TGACGTATGGATACCACCCTAGTCAGACTCCTTTCATTCCTACTTT-ATGTGTGGTTACCACCT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATT-CTAATTTGATGTATGGTTACCACCT
267166 TAGTCAAGCT
Statistics
Matches: 123, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
87 54 0.44
88 65 0.53
89 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (87 bp):
TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTAATTTGATGTATGGTTACCACCTGG
TCAAATCTGCATCCTTCCTATT
Found at i:267707 original size:83 final size:83
Alignment explanation
Indices: 267456--267805 Score: 235
Period size: 84 Copynumber: 4.2 Consensus size: 83
267446 CAGTCCCTAG
* * * *
267456 AACTCCTTTACCCTTTGTTAACTTATTGGTTCAGCCTTGGTCAACCTTTTATCCCTTCTTTATCT
1 AACTCCTTTACCCTTTGTTGACTTATTGGTTCAGCCCTGGTCAACCTTTCATCCCTTGTTTATCT
* * *
267521 GTCGGCTTAATCCCTATTG
66 GTCGGCTTAGT-CCTAGTA
* * * * * ** * *
267540 AACTCTTTTATCTTTTATTGACTTATCGGTTTGGGCCTGG-CAAACTTTTCAT--CTATGTTTAT
1 AACTCCTTTACCCTTTGTTGACTTATTGGTTCAGCCCTGGTC-AACCTTTCATCCCT-TGTTTAT
* * * *
267602 GTGTCGGCTCAGTCTTTGGTA
64 CTGTCGGCTTAGTC-CTAGTA
* * * *
267623 AACTCCCTAACCCTTTGTTGACTTATTGATTCAGCCCTGGTCAACCTTTCATCCCTTGTTTACCT
1 AACTCCTTTACCCTTTGTTGACTTATTGGTTCAGCCCTGGTCAACCTTTCATCCCTTGTTTATCT
*
267688 ATCGGCTTAGTCCTAGTA
66 GTCGGCTTAGTCCTAGTA
* * * * ** * *
267706 AA-TCCTTTTATCTTTTTTTGACTTGTCAGTTCAATG-TC-GATCAACTCTTTCATCCCTTGTTT
1 AACTCC-TTTACCCTTTGTTGACTTATTGGTTC-A-GCCCTGGTCAAC-CTTTCATCCCTTGTTT
* **
267768 ACCTGTTAGCTTAGTCCTGAGTA
62 ATCTGTCGGCTTAGTCCT-AGTA
* *
267791 AATTCCTTTATCCTT
1 AACTCCTTTACCCTT
267806 AGTCCAATCC
Statistics
Matches: 201, Mismatches: 53, Indels: 23
0.73 0.19 0.08
Matches are distributed among these distances:
82 6 0.03
83 86 0.43
84 89 0.44
85 17 0.08
86 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.44
Consensus pattern (83 bp):
AACTCCTTTACCCTTTGTTGACTTATTGGTTCAGCCCTGGTCAACCTTTCATCCCTTGTTTATCT
GTCGGCTTAGTCCTAGTA
Found at i:272257 original size:28 final size:28
Alignment explanation
Indices: 272174--272746 Score: 396
Period size: 28 Copynumber: 20.4 Consensus size: 28
272164 CACTAACTTG
*
272174 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
1 TGTGGGCTTT-AAAAG-GATGCCACTGACT
*
272204 CGTGTGAGCTTTGAAAA-GAGTGCCACTGACT
1 --TGTGGGCTTT-AAAAGGA-TGCCACTGACT
*
272235 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
272263 TGTGGGCTTTGAAAA-GAGTGCTACTAACT
1 TGTGGGCTTT-AAAAGGA-TGCCACTGACT
*
272292 TGTGGGTTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
272320 TGTGGGCTTTGAAAA-GAGTGGCCATTGACT
1 TGTGGGCTTT-AAAAGGA-T-GCCACTGACT
* *
272350 CGTGTAGGCTTTGAAAAGAGTTGCCACTGACT
1 --TGTGGGCTTT-AAAAG-GATGCCACTGACT
*
272382 CGTGTGGG----AAGA-G-TGCCACTGACT
1 --TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
272406 GGTGGGCTAT-GAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
272433 TATGGGCTTTGAAAAGG-TGCCATTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
272461 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
272489 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
272517 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** *
272545 TGTGGGCTTCGAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* ** *
272573 T-T--G----AAAAGAGTTGCCACCAATTCG
1 TGTGGGCTTTAAAAG-GATGCCACTGA--CT
*
272597 TGTGGGCTTTGAAAA-TAGTGCCACTGACT
1 TGTGGGCTTT-AAAAGGA-TGCCACTGACT
* * *
272626 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
272654 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
272682 TGTGGGCTTTGAAAGG-TGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
272709 TATGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
272737 TATGGGCTTT
1 TGTGGGCTTT
272747 GAAGAGATGA
Statistics
Matches: 457, Mismatches: 51, Indels: 70
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.01
22 14 0.03
24 13 0.03
25 4 0.01
26 1 0.00
27 54 0.12
28 232 0.51
29 57 0.12
30 10 0.02
31 18 0.04
32 48 0.11
33 1 0.00
34 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:272411 original size:86 final size:82
Alignment explanation
Indices: 272219--272749 Score: 276
Period size: 83 Copynumber: 6.4 Consensus size: 82
272209 GAGCTTTGAA
*
272219 AAGAGTGCCACTGACTTGTGGGCTTT-AAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTG
1 AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTAGGCTTTGAAAAGAGTG
* *
272283 CTACTAACTTGTGGGTTTTG
66 CCACTAACTCGTGGG---TG
* * *
272303 AAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GAGTGGCCATTGACTCGTGTAGGCTTTGAAAA
1 AAGAG-TGCCACTGACTTGTGGGCTTTGAAAAGGA-T-GCCACTAACT--TGTAGGCTTTGAAAA
*
272367 GAGTTGCCACTGACTCGTGTGG-G
61 GAG-TGCCACTAACTCGTG-GGTG
* * * * * *
272390 AAGAGTGCCACTGACTGGTGGGCTATG--AAGGGTGCCACTGACTTATGGGCTTTGAAAAG-GTG
1 AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTAGGCTTTGAAAAGAGTG
* * *
272452 CCATTGACTTGTGGGCTTTG
66 CCACTAACTCGTGGG---TG
* * * *
272472 AA-AGGATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGG
1 AAGA-G-TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTAGGCTTTGAAAAGAG
* * *
272534 TGCCATTGACTTGTGGGCTTCG
64 TGCCACTAACTCGTGGG--T-G
* * * * *
272556 AA-AGGATGCCACT-A-------ACTTTGAAAAGAGTTGCCACCAATTCGTGTGGGCTTTGAAAA
1 AAGA-G-TGCCACTGACTTGTGGGCTTTGAAAAG-GATGCCACTAA--CTTGTAGGCTTTGAAAA
* * *
272612 TAGTGCCACTGACTTGTGGGCTTTG
61 GAGTGCCACTAACTCGTGGG---TG
* * * *
272637 AAAGGGTGCCACTAACTTATGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTG-AAAG-GT
1 -AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTAGGCTTTGAAAAGAGT
**
272699 GCCACTAACTTATGGGCTTTG
65 GCCACTAACTCGTGGG---TG
* * *
272720 AAAGGGTGCCACTGATTTATGGGCTTTGAA
1 -AAGAGTGCCACTGACTTGTGGGCTTTGAA
272750 GAGATGAACG
Statistics
Matches: 373, Mismatches: 39, Indels: 70
0.77 0.08 0.15
Matches are distributed among these distances:
76 5 0.01
77 4 0.01
78 10 0.03
79 13 0.03
80 13 0.03
81 43 0.12
82 10 0.03
83 83 0.22
84 69 0.18
85 36 0.10
86 25 0.07
87 22 0.06
88 4 0.01
89 22 0.06
90 12 0.03
91 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (82 bp):
AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTAGGCTTTGAAAAGAGTG
CCACTAACTCGTGGGTG
Found at i:272496 original size:56 final size:56
Alignment explanation
Indices: 272155--272749 Score: 529
Period size: 56 Copynumber: 10.5 Consensus size: 56
272145 TTTTTTTAAA
* * * *
272155 AAAAGGTGTCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGTGAGCTTTG
1 AAAAGGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTG
* *
272217 AAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
272274 AAAAGAGTGCTACTAACTTGTGGGTTTTGAAAAGATGCCACTGACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
272331 AAAAGAGTGGCCATTGACTCGTGTAGGCTTTGAAAAGAGTTGCCACTGACTCGTGTGG----G
1 AAAAG-GT-GCCACTGACT--TGTGGGCTTTG-AAAG-GATGCCACTGACTTGTG-GGCTTTG
* * * * *
272390 AAGA-GTGCCACTGACTGGTGGGCTATG-AAGGGTGCCACTGACTTATGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
*
272444 AAAAGGTGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
272500 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTCG
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * * ** *
272556 -AAAGGATGCCACTAACTT-T--G----AAAAGAGTTGCCACCAATTCGTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGA--CTTGTGGGCTTTG
* * * *
272608 AAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * *
272665 -AAAGGATGCCACTAACTTGTGGGCTTTGAAAGG-TGCCACTAACTTATGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* * *
272720 AAAGGGTGCCACTGATTTATGGGCTTTGAA
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAA
272750 GAGATGAACG
Statistics
Matches: 444, Mismatches: 61, Indels: 63
0.78 0.11 0.11
Matches are distributed among these distances:
49 4 0.01
50 9 0.02
51 14 0.03
52 14 0.03
53 15 0.03
54 14 0.03
55 69 0.16
56 130 0.29
57 82 0.18
58 7 0.02
59 24 0.05
60 17 0.04
61 13 0.03
62 21 0.05
63 11 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (56 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:272627 original size:137 final size:135
Alignment explanation
Indices: 272461--272709 Score: 408
Period size: 137 Copynumber: 1.8 Consensus size: 135
272451 GCCATTGACT
* * *
272461 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTT
* * *
272526 TGAAAGGGTGCCATTGACTTGTGGGCTTCGAAAGGATGCCACTAACTTTGAAAAGAGTTGCCACC
66 TGAAAGGATGCCACTAACTTGTGGGCTTCGAAAGG-TGCCACTAACTTTGAAAAGAGTTGCCACC
272591 AATTCG
130 AATTCG
*
272597 TGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCT
1 TGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCT
*
272662 TTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTAACTT
65 TTGAAAGGATGCCACTAACTTGTGGGCTTCGAAAGGTGCCACTAACTT
272710 ATGGGCTTTG
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
136 27 0.26
137 77 0.74
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (135 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTT
TGAAAGGATGCCACTAACTTGTGGGCTTCGAAAGGTGCCACTAACTTTGAAAAGAGTTGCCACCA
ATTCG
Found at i:272649 original size:165 final size:163
Alignment explanation
Indices: 272435--272732 Score: 470
Period size: 165 Copynumber: 1.8 Consensus size: 163
272425 CACTGACTTA
* * * *
272435 TGGGCTTTGAAAAGGTGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
1 TGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTG
* * * * *
272500 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTCGAAAGGATGC
66 AAAGGATGCCACTAACTTGTGGGCTTTGAAA-GGTGCCACTAACTTATGGGCTTCGAAAGGATGC
272565 CACTAACTTTGAAAAGAGTTGCCACCAATTCGTG
130 CACTAACTTTGAAAAGAGTTGCCACCAATTCGTG
*
272599 TGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTT
1 TGGGCTTTGAAAA-AGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTT
* *
272664 GAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTAACTTATGGGCTTTGAAAGGGTGC
65 GAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTAACTTATGGGCTTCGAAAGGATGC
272729 CACT
130 CACT
272733 GATTTATGGG
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
164 45 0.37
165 76 0.63
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (163 bp):
TGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTG
AAAGGATGCCACTAACTTGTGGGCTTTGAAAGGTGCCACTAACTTATGGGCTTCGAAAGGATGCC
ACTAACTTTGAAAAGAGTTGCCACCAATTCGTG
Found at i:272731 original size:55 final size:56
Alignment explanation
Indices: 272599--272749 Score: 232
Period size: 55 Copynumber: 2.7 Consensus size: 56
272589 CCAATTCGTG
**
272599 TGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTA
1 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTA
* *
272656 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA-GGTGCCACTAACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTA
* *
272711 TGGGCTTTGAAAGGGTGCCACTGATTTATGGGCTTTGAA
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
272750 GAGATGAACG
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 50 0.58
56 27 0.31
57 9 0.10
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (56 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTA
Found at i:274004 original size:21 final size:21
Alignment explanation
Indices: 273980--274027 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
273970 TTTCCTTTTA
273980 TTTTTT-CCTTGGTTTTTTTGT
1 TTTTTTGCCTT-GTTTTTTTGT
* *
274001 TTTTTTGTCTTTTTTTTTTGT
1 TTTTTTGCCTTGTTTTTTTGT
274022 TTTTTT
1 TTTTTT
274028 TGGTATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.83
Consensus pattern (21 bp):
TTTTTTGCCTTGTTTTTTTGT
Found at i:274016 original size:13 final size:12
Alignment explanation
Indices: 273995--274028 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
273985 TCCTTGGTTT
273995 TTTTGTTTTTTTG
1 TTTT-TTTTTTTG
274008 TCTTTTTTTTTTG
1 T-TTTTTTTTTTG
274021 TTTTTTTT
1 TTTTTTTT
274029 GGTATAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 10 0.50
14 3 0.15
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:281630 original size:13 final size:13
Alignment explanation
Indices: 281612--281636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
281602 CATAAAGTGT
281612 TGTATCGATACAA
1 TGTATCGATACAA
281625 TGTATCGATACA
1 TGTATCGATACA
281637 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:281634 original size:33 final size:33
Alignment explanation
Indices: 281592--281658 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
281582 TTCAACGATT
281592 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
281625 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
281658 T
1 T
281659 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:281717 original size:13 final size:13
Alignment explanation
Indices: 281699--281723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
281689 ATCACTTAAA
281699 TGTATCGATACAT
1 TGTATCGATACAT
281712 TGTATCGATACA
1 TGTATCGATACA
281724 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:281861 original size:52 final size:52
Alignment explanation
Indices: 281732--281862 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
281722 CACTGATCTT
* *
281732 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
281784 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
* *
281836 TGTATCGATACATGTAGGTAAATTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
281863 ATATTTTGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
Found at i:286890 original size:19 final size:18
Alignment explanation
Indices: 286857--286914 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
286847 TTGTATCGAT
**
286857 ACATTGTATTTATACATG
1 ACATTGTATCGATACATG
286875 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
286895 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
286914 A
1 A
286915 AACTGGGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 17 0.49
20 17 0.49
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:286976 original size:13 final size:13
Alignment explanation
Indices: 286958--287010 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
286948 TGATACATGG
286958 TACATTGTATCGA
1 TACATTGTATCGA
286971 TACATTGTATCGA
1 TACATTGTATCGA
286984 TACA-TG-AT-G-
1 TACATTGTATCGA
286993 -A-ATTGTATCGA
1 TACATTGTATCGA
287004 TACATTG
1 TACATTG
287011 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:286986 original size:33 final size:33
Alignment explanation
Indices: 286942--287010 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
286932 CTACCACTGT
* *
286942 TTGTATTGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
286975 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
287008 TTG
1 TTG
287011 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:289261 original size:21 final size:22
Alignment explanation
Indices: 289226--289266 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
289216 GATATTAAAA
*
289226 AATTGGCTAAAGAAAAATAATG
1 AATTAGCTAAAGAAAAATAATG
289248 AATTAGCT-AAGAAAAATAA
1 AATTAGCTAAAGAAAAATAA
289267 AAACTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.22
Consensus pattern (22 bp):
AATTAGCTAAAGAAAAATAATG
Found at i:293312 original size:20 final size:22
Alignment explanation
Indices: 293279--293318 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
293269 CAAATTTCCT
*
293279 CATTTTTACTTC-AAATCACTC
1 CATTTTTACATCAAAATCACTC
293300 CATTTTT-CATCAAAATCAC
1 CATTTTTACATCAAAATCAC
293319 CAGCAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (22 bp):
CATTTTTACATCAAAATCACTC
Found at i:295131 original size:30 final size:32
Alignment explanation
Indices: 295086--295155 Score: 117
Period size: 30 Copynumber: 2.2 Consensus size: 32
295076 CCGATTAAGG
295086 GGGAGAAATTTTTTTTAAGCATTTATTAAA-A
1 GGGAGAAATTTTTTTTAAGCATTTATTAAAGA
*
295117 GGGAGAAA-TTTTTTTAAGCATTTATTAAAGG
1 GGGAGAAATTTTTTTTAAGCATTTATTAAAGA
295148 GGGAGAAA
1 GGGAGAAA
295156 AACAAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 21 0.57
31 16 0.43
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (32 bp):
GGGAGAAATTTTTTTTAAGCATTTATTAAAGA
Found at i:295716 original size:13 final size:13
Alignment explanation
Indices: 295698--295724 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
295688 ACATTATGCT
295698 TTGTATCGATACA
1 TTGTATCGATACA
295711 TTGTATCGATACA
1 TTGTATCGATACA
295724 T
1 T
295725 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:295733 original size:19 final size:18
Alignment explanation
Indices: 295708--295765 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
295698 TTGTATCGAT
295708 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
295726 ATCATTGTATCGATACATTG
1 A-CATTGTATCGATACA-TG
295746 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
295765 A
1 A
295766 AACTGACAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:295736 original size:32 final size:33
Alignment explanation
Indices: 295680--295745 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
295670 ACACCCAGAA
* * *
295680 GTATGGATACATTATGCTTTGTATCGATACATT
1 GTATCGATACATGATGCATTGTATCGATACATT
295713 GTATCGATACATGAT-CATTGTATCGATACATT
1 GTATCGATACATGATGCATTGTATCGATACATT
295745 G
1 G
295746 ACAATTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (33 bp):
GTATCGATACATGATGCATTGTATCGATACATT
Found at i:295754 original size:20 final size:20
Alignment explanation
Indices: 295709--295763 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
295699 TGTATCGATA
295709 CATTGTATCGATACA-TGAT
1 CATTGTATCGATACATTGAT
295728 CATTGTATCGATACATTGA-
1 CATTGTATCGATACATTGAT
295747 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
295764 GAAACTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACATTGAT
Found at i:302063 original size:154 final size:155
Alignment explanation
Indices: 301717--302141 Score: 489
Period size: 155 Copynumber: 2.7 Consensus size: 155
301707 TTTCACATCA
* * * *
301717 AAGGTATACCCTATGGGCATTTTCATAATTTTTTCAGAATTGAGTCCTAGGTTGTCACTAGGGTT
1 AAGGTAT-CCCTAGGGGCATTTTCATAATTTTCT-AGAAATGAGTCCTAGGTTGTCAC-CGGGTT
* *
301782 CGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATCCCATCTACAATCATTTTTCTAGTCC
63 CGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTTCTAGTCC
*
301847 TTTAGGGGTATGGAGCTCTTTTAAATCG
128 TTTAGGGCTATGGAGCTCTTTTAAATCG
** * * ** *
301875 AAGGTATCCCTAGCTGCATTTTCATAATTTTTCTAGAACTAAGTCCTAGGTTACCACCGGGTCCG
1 AAGGTATCCCTAGGGGCATTTTCATAA-TTTTCTAGAAATGAGTCCTAGGTTGTCACCGGGTTCG
* * * * *
301940 CTTTTATGGCAAAAGTGGGCATTTAGGATAGGTTCATCTCATCTATAA-CGTTTTT-TAGTCCTT
65 CTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTTCTAGTCCTT
*
302003 TAGGGCTATGGAG-TACTTTTAAGTCG
130 TAGGGCTATGGAGCT-CTTTTAAATCG
* ** * *
302029 AAGGTATCTCTTAGGGGCATTTTTGTAATTTTCTA-AAATCGATTCTTAGGTTGTCACCAGGGTT
1 AAGGTATC-CCTAGGGGCATTTTCATAATTTTCTAGAAAT-GAGTCCTAGGTTGTCACC-GGGTT
* * * *
302093 TGCTTTTATGTCGAAGGTGGGTATGTAGGATAGGTTCATCCCATCTATA
63 CGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATA
302142 TATACATATG
Statistics
Matches: 224, Mismatches: 38, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
153 4 0.02
154 58 0.26
155 66 0.29
156 48 0.21
157 36 0.16
158 12 0.05
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (155 bp):
AAGGTATCCCTAGGGGCATTTTCATAATTTTCTAGAAATGAGTCCTAGGTTGTCACCGGGTTCGC
TTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTTCTAGTCCTTT
AGGGCTATGGAGCTCTTTTAAATCG
Found at i:304572 original size:70 final size:70
Alignment explanation
Indices: 304351--304585 Score: 251
Period size: 70 Copynumber: 3.3 Consensus size: 70
304341 CTTTTTTGGC
* * **
304351 CCTCAAAGAGCAGGACACTTTTTTCTTCTTTTTAAAG-CCACACAAGTTGGTGGCA-CCTTTGTC
1 CCTCAAAGAGCAGGAC-CTTTTTTC-T-TTTTTAAAGCCCACACAAGCTAGTGGCACCCTTTACC
304414 TTTTTCAGT
63 TTTTT-AGT
* * * * **
304423 CCTCAAAAAGCAGGATGCC-TTTTTCTTTTTTATAGCCCACATAAGCTAATGGCACTGTTTACCT
1 CCTCAAAGAGCAGGA--CCTTTTTTCTTTTTTAAAGCCCACACAAGCTAGTGGCACCCTTTACCT
304487 TTTTAGT
64 TTTTAGT
* * *
304494 CTTTAAAGAGTAGGACCTTTTTTCTTTTTTAAAGCCCACACAAGCTAGTGGCACCCTTTACCTTT
1 CCTCAAAGAGCAGGACCTTTTTTCTTTTTTAAAGCCCACACAAGCTAGTGGCACCCTTTACCTTT
*
304559 TTAAT
66 TTAGT
*
304564 CCTCAAAGAGCAAGACGCTTTT
1 CCTCAAAGAGCAGGAC-CTTTT
304586 GGTGGCACCT
Statistics
Matches: 133, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
69 2 0.02
70 66 0.50
71 34 0.26
72 29 0.22
73 1 0.01
74 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (70 bp):
CCTCAAAGAGCAGGACCTTTTTTCTTTTTTAAAGCCCACACAAGCTAGTGGCACCCTTTACCTTT
TTAGT
Found at i:304669 original size:74 final size:74
Alignment explanation
Indices: 304585--304786 Score: 314
Period size: 74 Copynumber: 2.7 Consensus size: 74
304575 AAGACGCTTT
*
304585 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCAAGATGTTTTTCCATTTTCTTTTTTCAAGGCC
1 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCAAGATGTTTTTCCATTTTCTTTTTTCAAAGCC
304650 TACACAAGC
66 TACACAAGC
* * *
304659 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCATGACGCTTTTCCATTTTCTTTTTTCAAAGCC
1 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCAAGATGTTTTTCCATTTTCTTTTTTCAAAGCC
*
304724 TACATAAGC
66 TACACAAGC
* * * * *
304733 CGGTGGCACCCTTTATTTTAGTCCTCAAAGAGCAGGATGTTTTTTCTTTTTCTT
1 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCAAGATGTTTTTCCATTTTCTT
304787 AAAAAAAAAT
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 116 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (74 bp):
TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGCAAGATGTTTTTCCATTTTCTTTTTTCAAAGCC
TACACAAGC
Done.