Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 172 of 206
Found at i:52379412 original size:40 final size:40
Alignment explanation
Indices: 52379368--52379479 Score: 143
Period size: 41 Copynumber: 2.8 Consensus size: 40
52379358 CTTTAGTGGC
* *
52379368 ATTAGAGGCGCTTTTTAAAAAACGCCGCAATAGATCGAGA
1 ATTAGCGGCGCTTTTTGAAAAACGCCGCAATAGATCGAGA
* * * * *
52379408 ATTAGCGGCGCTTTGTCGAAAAATGCCGCTATAGATCTAGC
1 ATTAGCGGCGCTTT-TTGAAAAACGCCGCAATAGATCGAGA
52379449 ATTAGCGGCGCTTTTTGGAAAAACGCCGCAA
1 ATTAGCGGCGCTTTTT-GAAAAACGCCGCAA
52379480 AAAAGTTGAG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 14 0.23
41 46 0.77
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTTGAAAAACGCCGCAATAGATCGAGA
Found at i:52379463 original size:149 final size:147
Alignment explanation
Indices: 52379070--52379637 Score: 715
Period size: 148 Copynumber: 3.9 Consensus size: 147
52379060 TATAGATTGA
* * * * * * * *
52379070 GCATTAGCGGCGCTTTTTGAAAAACGTCGCTATAGATCAAGCATTAACGACGC-TTCTCGAAAAA
1 GCATTAGCGGCGCTTTTTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCTTTGTCGAAAAA
* ** *
52379134 CGCCGCTATAGATCGAGCATTAGCGGCGC-TTTTCAAAAAGCGCCGTAAAAAAGTTGAGCAAAAC
66 CGCCGCTATAGATCGAGCATTAGCGGCACTTTTTGGAAAA-CGCCGCAAAAAAGTTGAGCAAAAC
52379198 ACGTTGTTGAGCTTTAGTG
130 A-GTTGTTGAGCTTTAGTG
* * *
52379217 GCATTAGCGACGCTTTTTTAAAACACGCCGCAATAGATCGAGCATTAGCGGCGCTATT-T-GAAA
1 GCATTAGCGGCGC-TTTTTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCT-TTGTCGAAA
* * * *
52379280 AACGCCACTATAGATCAAGCATTAGAGGCACTTTTTGGAAAACGCCGCAAAAAAGTTGAGTAAAA
64 AACGCCGCTATAGATCGAGCATTAGCGGCACTTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAA
52379345 CGATGTTGTTGAGCTTTAGTG
129 C-A-GTTGTTGAGCTTTAGTG
*
52379366 GCATTAGAGGCGCTTTTTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCTTTGTCGAAAAA
1 GCATTAGCGGCGCTTTTTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCTTTGTCGAAAAA
* * *
52379431 TGCCGCTATAGATCTAGCATTAGCGGCGCTTTTTGGAAAAACGCCGCAAAAAAGTTGAGCAAAAC
66 CGCCGCTATAGATCGAGCATTAGCGGCACTTTTTGG-AAAACGCCGCAAAAAAGTTGAGCAAAAC
52379496 ----GTTGAGCTTTAGTG
130 AGTTGTTGAGCTTTAGTG
* * *
52379510 GCATTAGCGGCACTTTTGTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCG-TTAGTTGAAAA
1 GCATTAGCGGCGCTTTT-TAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCTTTGTCGAAAA
** * * *
52379574 A-TACGCTATAGATCGAGCATTAGCGGCACTTTTCGCAAAACACCGCAAAAAAGTTGAGCAAAAC
65 ACGCCGCTATAGATCGAGCATTAGCGGCACTTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAAC
52379638 GACGTCATTT
Statistics
Matches: 374, Mismatches: 38, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
142 27 0.07
143 29 0.08
144 39 0.10
145 35 0.09
147 14 0.04
148 126 0.34
149 75 0.20
150 29 0.08
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (147 bp):
GCATTAGCGGCGCTTTTTAAAAAACGCCGCAATAGATCGAGAATTAGCGGCGCTTTGTCGAAAAA
CGCCGCTATAGATCGAGCATTAGCGGCACTTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAACA
GTTGTTGAGCTTTAGTG
Found at i:52379558 original size:41 final size:38
Alignment explanation
Indices: 52379512--52379606 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 38
52379502 CTTTAGTGGC
52379512 ATTAGCGGCACTTTTGTAAAAA-ACGCCGCAATAGATCGAGA
1 ATTAGCGGCACTTTTG-AAAAATA---CGCAATAGATCGAGA
* * *
52379553 ATTAGCGGC-GTTAGTTGAAAAATACGCTATAGATCGAGC
1 ATTAGCGGCACTT--TTGAAAAATACGCAATAGATCGAGA
52379592 ATTAGCGGCACTTTT
1 ATTAGCGGCACTTTT
52379607 CGCAAAACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
38 2 0.04
39 22 0.48
40 4 0.09
41 14 0.30
42 4 0.09
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (38 bp):
ATTAGCGGCACTTTTGAAAAATACGCAATAGATCGAGA
Found at i:52379814 original size:14 final size:14
Alignment explanation
Indices: 52379797--52379840 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
52379787 TATTTTGGGA
52379797 TTAGAGTTTTGAGT
1 TTAGAGTTTTGAGT
52379811 TTAGAGTTTATG-GT
1 TTAGAGTTT-TGAGT
* *
52379825 TTATAGTTTAGAGT
1 TTAGAGTTTTGAGT
52379839 TT
1 TT
52379841 GGGGTTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 23 0.88
15 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (14 bp):
TTAGAGTTTTGAGT
Found at i:52379846 original size:21 final size:21
Alignment explanation
Indices: 52379808--52379847 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52379798 TAGAGTTTTG
*
52379808 AGTTTAGAGTTTATGGTTTAT
1 AGTTTAGAGTTTAGGGTTTAT
*
52379829 AGTTTAGAGTTTGGGGTTT
1 AGTTTAGAGTTTAGGGTTT
52379848 GGGGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (21 bp):
AGTTTAGAGTTTAGGGTTTAT
Found at i:52380030 original size:7 final size:7
Alignment explanation
Indices: 52380020--52380231 Score: 104
Period size: 7 Copynumber: 30.1 Consensus size: 7
52380010 GTAATATATA
52380020 TTTAGGG
1 TTTAGGG
52380027 TTTAGGG
1 TTTAGGG
* *
52380034 TGTA-AG
1 TTTAGGG
**
52380040 TTTATAG
1 TTTAGGG
52380047 TTTAGGG
1 TTTAGGG
*
52380054 TTTAAGG
1 TTTAGGG
*
52380061 TTTAAGG
1 TTTAGGG
* *
52380068 TTTATGA
1 TTTAGGG
*
52380075 TTTAGTG
1 TTTAGGG
* *
52380082 TTTATGA
1 TTTAGGG
52380089 TTTAGGG
1 TTTAGGG
*
52380096 TGTA-GG
1 TTTAGGG
*
52380102 TTTATGG
1 TTTAGGG
*
52380109 TTTAGTG
1 TTTAGGG
**
52380116 TTTATAG
1 TTTAGGG
52380123 TTTAGGG
1 TTTAGGG
*
52380130 TTTAGTG
1 TTTAGGG
**
52380137 TTTATAG
1 TTTAGGG
52380144 TTTATGGG
1 TTTA-GGG
*
52380152 TTATGGGG
1 TT-TAGGG
* *
52380160 CTTAAGG
1 TTTAGGG
52380167 TTTAGGG
1 TTTAGGG
**
52380174 TTTAAAG
1 TTTAGGG
**
52380181 TTTATAG
1 TTTAGGG
*
52380188 TTTAGAG
1 TTTAGGG
*
52380195 TTTAAGAG
1 TTT-AGGG
*
52380203 TTTAGGA
1 TTTAGGG
*
52380210 TTTATGG
1 TTTAGGG
*
52380217 TTTAGTG
1 TTTAGGG
52380224 TTTAGGG
1 TTTAGGG
52380231 T
1 T
52380232 CTAATTTTAA
Statistics
Matches: 154, Mismatches: 46, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
6 9 0.06
7 130 0.84
8 14 0.09
9 1 0.01
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:52380098 original size:62 final size:62
Alignment explanation
Indices: 52380027--52380149 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
52380017 ATATTTAGGG
52380027 TTTAGGGTGTAAGTTTATAGTTTAGGGTTTA-AGGTTTAAGGTTTA-TGATTTAGT-GTTTATGA
1 TTTAGGGTGTAAGTTTATAGTTTAGGGTTTATA-GTTTAAGGTTTAGTG-TTTA-TAGTTTATGA
* * * *
52380089 TTTAGGGTGTAGGTTTATGGTTTAGTGTTTATAGTTTAGGGTTTAGTGTTTATAGTTTATG
1 TTTAGGGTGTAAGTTTATAGTTTAGGGTTTATAGTTTAAGGTTTAGTGTTTATAGTTTATG
52380150 GGTTATGGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
61 1 0.02
62 50 0.93
63 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.50
Consensus pattern (62 bp):
TTTAGGGTGTAAGTTTATAGTTTAGGGTTTATAGTTTAAGGTTTAGTGTTTATAGTTTATGA
Found at i:52380103 original size:34 final size:34
Alignment explanation
Indices: 52380065--52380141 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 34
52380055 TTAAGGTTTA
52380065 AGGTTTATGATTTAGTGTTTAT-GATTTAGGGTGT
1 AGGTTTATGATTTAGTGTTTATAG-TTTAGGGTGT
* *
52380099 AGGTTTATGGTTTAGTGTTTATAGTTTAGGGTTT
1 AGGTTTATGATTTAGTGTTTATAGTTTAGGGTGT
52380133 AGTGTTTAT
1 AG-GTTTAT
52380142 AGTTTATGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 32 0.82
35 7 0.18
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (34 bp):
AGGTTTATGATTTAGTGTTTATAGTTTAGGGTGT
Found at i:52382740 original size:9 final size:9
Alignment explanation
Indices: 52382728--52382787 Score: 66
Period size: 9 Copynumber: 6.2 Consensus size: 9
52382718 AAATATATAT
52382728 CATAACTTA
1 CATAACTTA
52382737 CATAACTTA
1 CATAACTTA
52382746 CATAACTTA
1 CATAACTTA
*
52382755 CATAAATATA
1 CATAACT-TA
*
52382765 TATAAAAACTTA
1 CAT---AACTTA
52382777 CATAACTTA
1 CATAACTTA
52382786 CA
1 CA
52382788 GAATTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 32 0.74
10 4 0.09
12 4 0.09
13 3 0.07
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:52382764 original size:40 final size:39
Alignment explanation
Indices: 52382710--52382787 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
52382700 ATGTTTTTAA
* * *
52382710 AACTTATAAAATATATATCATAACTTACATAACTTACAT
1 AACTTACAAAATATATATAAAAACTTACATAACTTACAT
52382749 AACTTACATAAATATATATAAAAACTTACATAACTTACA
1 AACTTACA-AAATATATATAAAAACTTACATAACTTACA
52382788 GAATTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (39 bp):
AACTTACAAAATATATATAAAAACTTACATAACTTACAT
Found at i:52382854 original size:21 final size:20
Alignment explanation
Indices: 52382830--52383008 Score: 86
Period size: 21 Copynumber: 9.4 Consensus size: 20
52382820 TATTAACTTA
52382830 ATAACTTATATATATCATATC
1 ATAACTTATATA-ATCATATC
*
52382851 ATAACTTACATAA-C-TCA-C
1 ATAACTTATATAATCAT-ATC
* * *
52382869 ATAACGTACATAA-C-T-TA
1 ATAACTTATATAATCATATC
52382886 ATAACTTATATATATCATATC
1 ATAACTTATATA-ATCATATC
*
52382907 ATAACTCATATAACGTACATA--
1 ATAACTTATATAA--T-CATATC
*
52382928 GTAACTTATATATATCATATC
1 ATAACTTATATA-ATCATATC
*
52382949 ATAACTTACATAA-C-TCA-C
1 ATAACTTATATAATCAT-ATC
*
52382967 ATAACTTACAT-A--ATA-C
1 ATAACTTATATAATCATATC
*
52382983 ATAA-ATATAT-ATCATATC
1 ATAACTTATATAATCATATC
52383001 ATAACTTA
1 ATAACTTA
52383009 ATTATACTTA
Statistics
Matches: 126, Mismatches: 14, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
15 5 0.04
16 6 0.05
17 15 0.12
18 35 0.28
19 11 0.09
20 5 0.04
21 43 0.34
22 2 0.02
23 4 0.03
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAACTTATATAATCATATC
Found at i:52382862 original size:9 final size:9
Alignment explanation
Indices: 52382823--52382979 Score: 84
Period size: 9 Copynumber: 16.3 Consensus size: 9
52382813 CTTTGGATAT
52382823 TAACTTA-A
1 TAACTTACA
*
52382831 TAACTTATA
1 TAACTTACA
*
52382840 TATATCATATCA
1 TA-A-CTTA-CA
52382852 TAACTTACA
1 TAACTTACA
*
52382861 TAACTCACA
1 TAACTTACA
*
52382870 TAACGTACA
1 TAACTTACA
52382879 TAACTTA-A
1 TAACTTACA
*
52382887 TAACTTATA
1 TAACTTACA
*
52382896 TATATCATATCA
1 TA-A-CTTA-CA
* *
52382908 TAACTCATA
1 TAACTTACA
*
52382917 TAACGTACATA
1 TAACTTAC--A
*
52382928 GTAACTTATA
1 -TAACTTACA
*
52382938 TATATCATATCA
1 TA-A-CTTA-CA
52382950 TAACTTACA
1 TAACTTACA
*
52382959 TAACTCACA
1 TAACTTACA
52382968 TAACTTACA
1 TAACTTACA
52382977 TAA
1 TAA
52382980 TACATAAATA
Statistics
Matches: 113, Mismatches: 22, Indels: 27
0.70 0.14 0.17
Matches are distributed among these distances:
8 15 0.13
9 58 0.51
10 12 0.11
11 13 0.12
12 15 0.13
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (9 bp):
TAACTTACA
Found at i:52382913 original size:47 final size:47
Alignment explanation
Indices: 52382859--52383006 Score: 164
Period size: 42 Copynumber: 3.1 Consensus size: 47
52382849 TCATAACTTA
52382859 CATAACTCACATAACGTACATAACTTAATAACTTATATATATCATAT
1 CATAACTCACATAACGTACATAACTTAATAACTTATATATATCATAT
* *
52382906 CATAACTCATATAACGTAC---A--TAGTAACTTATATATATCATAT
1 CATAACTCACATAACGTACATAACTTAATAACTTATATATATCATAT
* *
52382948 CATAACTTACATAAC-TCACATAACTTACATAATACATAAATATATATCATAT
1 CATAACTCACATAACGT-ACATAACTTA-AT-A-AC-T-TATATATATCATAT
52383000 CATAACT
1 CATAACT
52383007 TAATTATACT
Statistics
Matches: 84, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
41 1 0.01
42 36 0.43
44 1 0.01
45 1 0.01
47 20 0.24
48 1 0.01
49 1 0.01
50 2 0.02
51 1 0.01
52 20 0.24
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (47 bp):
CATAACTCACATAACGTACATAACTTAATAACTTATATATATCATAT
Found at i:52382946 original size:98 final size:94
Alignment explanation
Indices: 52382831--52383006 Score: 291
Period size: 98 Copynumber: 1.8 Consensus size: 94
52382821 ATTAACTTAA
52382831 TAACTTATATATATCATATCATAACTTACATAACTCACATAACGTACATAACTTA-ATAACTTAT
1 TAACTTATATATATCATATCATAACTTACATAACTCACATAACGTACATAA--TACATAA---AT
52382895 ATATATCATATCATAACTCATATAACGTACATAG
61 ATATATCATATCATAACTCATATAACGTACATAG
*
52382929 TAACTTATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAAATATATA
1 TAACTTATATATATCATATCATAACTTACATAACTCACATAACGTACATAATACATAAATATATA
52382994 TCATATCATAACT
66 TCATATCATAACT
52383007 TAATTATACT
Statistics
Matches: 76, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
94 20 0.26
96 2 0.03
97 4 0.05
98 50 0.66
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (94 bp):
TAACTTATATATATCATATCATAACTTACATAACTCACATAACGTACATAATACATAAATATATA
TCATATCATAACTCATATAACGTACATAG
Found at i:52386092 original size:71 final size:72
Alignment explanation
Indices: 52386017--52386159 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 72
52386007 TCTGATATTA
* *
52386017 TATAGTGTGATTTTTTTTCTTTAAATTTTTTACAGTTAAATTGTTCATTCTTTT-TAAAAAATAC
1 TATAGTGTGATTTTTTTTCTTTAAATTTTTTACAGTTAAAATGTTCATTCTTTTAAAAAAAATAC
52386081 TAAATTG
66 TAAATTG
52386088 TATAGTGTGATTTTTTTTCTTTAAATTTTTTACAGTTAAAATGTTCATTCTTTTAAAAAAAATAC
1 TATAGTGTGATTTTTTTTCTTTAAATTTTTTACAGTTAAAATGTTCATTCTTTTAAAAAAAATAC
52386153 TAAATTG
66 TAAATTG
52386160 ATTTATTTGA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 53 0.77
72 16 0.23
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (72 bp):
TATAGTGTGATTTTTTTTCTTTAAATTTTTTACAGTTAAAATGTTCATTCTTTTAAAAAAAATAC
TAAATTG
Found at i:52387420 original size:16 final size:17
Alignment explanation
Indices: 52387390--52387422 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52387380 TTGTATAACA
*
52387390 AATTTTTTCTTTTTGTT
1 AATTTTTTCTATTTGTT
52387407 AATTTTTT-TATTTGTT
1 AATTTTTTCTATTTGTT
52387423 TTAGAGACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
AATTTTTTCTATTTGTT
Found at i:52395434 original size:11 final size:11
Alignment explanation
Indices: 52395413--52395444 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
52395403 GCTACAAAAA
52395413 TATATTAATTAT
1 TATA-TAATTAT
52395425 TATATAATTAT
1 TATATAATTAT
52395436 TATATAATT
1 TATATAATT
52395445 TTCCCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATAATTAT
Found at i:52397313 original size:27 final size:27
Alignment explanation
Indices: 52397275--52397509 Score: 265
Period size: 27 Copynumber: 8.7 Consensus size: 27
52397265 AGATATGTTA
* * *
52397275 GAAATGAAAGCCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52397302 GAAATGAAAGCCTTTTTGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52397329 GAAGAGAGAGCATTTGTGGCGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52397356 GAAAAAAAAGCCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52397383 GAAATGAGAGCCTTGGTGGCGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
**
52397410 GAAAAGAAAGCCTTTGTGGAAAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
*
52397437 GAAAAGAAAGCCTTTATGGCGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
52397464 GAAAAGAAAGCCTTTGTGGCAAACAAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
*
52397491 -AAAATGAAAACCTTTGTGG
1 GAAAA-GAAAGCCTTTGTGG
52397510 AAAATCCTGG
Statistics
Matches: 176, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 4 0.02
27 172 0.98
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (27 bp):
GAAAAGAAAGCCTTTGTGGCGAACCAT
Found at i:52397408 original size:81 final size:81
Alignment explanation
Indices: 52397281--52397513 Score: 306
Period size: 81 Copynumber: 2.9 Consensus size: 81
52397271 GTTAGAAATG
* * * *
52397281 AAAGCCTTTATGGTGAACCATGAAATGAAAGCCTTTTTGGTGAACCATGAAGAGAGAGCATTTGT
1 AAAGCCTTTATGGTGAACCATGAAATGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCATTTGT
**
52397346 GGCGAACCATGAAAAA
66 GGAAAACCATGAAAAA
* * *
52397362 AAAGCCTTTATGGTGAACCATGAAATGAGAGCCTTGGTGGCGAACCATGAAAAGAAAGCCTTTGT
1 AAAGCCTTTATGGTGAACCATGAAATGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCATTTGT
*
52397427 GGAAAACCATGAAAAG
66 GGAAAACCATGAAAAA
* * * * * *
52397443 AAAGCCTTTATGGCGAACCATGAAAAGAAAGCCTTTGTGGCAAACAAT-AAAATGAAAACCTTTG
1 AAAGCCTTTATGGTGAACCATGAAATGAAAGCCTTTGTGGCGAACCATGAAAA-GAAAGCATTTG
52397507 TGGAAAA
65 TGGAAAA
52397514 TCCTGGAAGG
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 4 0.03
81 130 0.97
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (81 bp):
AAAGCCTTTATGGTGAACCATGAAATGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCATTTGT
GGAAAACCATGAAAAA
Found at i:52399492 original size:5 final size:5
Alignment explanation
Indices: 52399479--52399511 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52399469 ACATGAATTG
*
52399479 TATGG TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TAT
52399512 AGTGGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:52399810 original size:36 final size:37
Alignment explanation
Indices: 52399767--52399859 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 37
52399757 AACCTATTAG
*
52399767 GGCGTGTTATTGGTTGGATTGGCTCTTATAAACATTT
1 GGCGTGTTATTGGTTGGATTAGCTCTTATAAACATTT
* * * *
52399804 GG-GTGTTATCGGTTGTATTAGCTCTTATGAGCATTT
1 GGCGTGTTATTGGTTGGATTAGCTCTTATAAACATTT
52399840 GGCGTGTT-TTGGTTGGATTA
1 GGCGTGTTATTGGTTGGATTA
52399860 CTTGTGTACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 41 0.85
37 7 0.15
ACGTcount: A:0.16, C:0.10, G:0.30, T:0.44
Consensus pattern (37 bp):
GGCGTGTTATTGGTTGGATTAGCTCTTATAAACATTT
Found at i:52400988 original size:42 final size:42
Alignment explanation
Indices: 52400904--52400991 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
52400894 ACAGTCTGGC
* **
52400904 ACACGGCCTGCGACATAGCTGTGTGACCTAATTTAGTGAGTT
1 ACACGGCCTGCGACATAACTGTGTGACCTAATTTAGAAAGTT
* * * * *
52400946 ACACGGTCTGGGACATAATTGTGTGCCCTAATTTCGAAAGTT
1 ACACGGCCTGCGACATAACTGTGTGACCTAATTTAGAAAGTT
52400988 ACAC
1 ACAC
52400992 AACCTAGGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (42 bp):
ACACGGCCTGCGACATAACTGTGTGACCTAATTTAGAAAGTT
Found at i:52406028 original size:17 final size:18
Alignment explanation
Indices: 52406002--52406036 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52405992 TGTAGGGACT
52406002 AAATTGAA-GGAAAAAAG
1 AAATTGAAGGGAAAAAAG
*
52406019 AAATTTAAGGGAAAAAAG
1 AAATTGAAGGGAAAAAAG
52406037 CATGAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (18 bp):
AAATTGAAGGGAAAAAAG
Found at i:52406111 original size:50 final size:50
Alignment explanation
Indices: 52406056--52406155 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
52406046 AAAGATAAAA
52406056 CCGGTCAGCATGAGAAATAGGAAAGATGTGGTGCCAAATATACAAAGTGT
1 CCGGTCAGCATGAGAAATAGGAAAGATGTGGTGCCAAATATACAAAGTGT
* *
52406106 CCGGTCAGCATGCGAAATAGGGAAGATGTGGTGCCAAATATACAAAGTGT
1 CCGGTCAGCATGAGAAATAGGAAAGATGTGGTGCCAAATATACAAAGTGT
52406156 GGAAGACTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (50 bp):
CCGGTCAGCATGAGAAATAGGAAAGATGTGGTGCCAAATATACAAAGTGT
Found at i:52417568 original size:19 final size:18
Alignment explanation
Indices: 52417536--52417571 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52417526 GGAAAATAAT
52417536 CAAAAAATAACCAAGAAG
1 CAAAAAATAACCAAGAAG
*
52417554 CAAAACAATACCCAAGAA
1 CAAAA-AATAACCAAGAA
52417572 AGAAATCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.22, G:0.08, T:0.06
Consensus pattern (18 bp):
CAAAAAATAACCAAGAAG
Found at i:52417708 original size:17 final size:17
Alignment explanation
Indices: 52417686--52417719 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52417676 TGAGAGTAAG
*
52417686 AGCAACTGACTTTAGGT
1 AGCAACTGACATTAGGT
52417703 AGCAACTGACATTAGGT
1 AGCAACTGACATTAGGT
52417720 TTATTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
AGCAACTGACATTAGGT
Found at i:52418040 original size:22 final size:21
Alignment explanation
Indices: 52418014--52418060 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52418004 AAAAGGGTTA
52418014 AAAGGCTATATAAAGGAAAGCT
1 AAAGGCTATAT-AAGGAAAGCT
* *
52418036 AAAGGGTTTATAAGGAAAGCT
1 AAAGGCTATATAAGGAAAGCT
52418057 AAAG
1 AAAG
52418061 TTGTTAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.19
Consensus pattern (21 bp):
AAAGGCTATATAAGGAAAGCT
Found at i:52428583 original size:40 final size:40
Alignment explanation
Indices: 52428538--52428618 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
52428528 GCTGTGTGAG
52428538 TCATACGGCCTGGCGACACAGTCGTGTATCATCTGATGAT
1 TCATACGGCCTGGCGACACAGTCGTGTATCATCTGATGAT
*
52428578 TCATACGGCCTGGTGACACAGTCGTGTATCATCTGATGAT
1 TCATACGGCCTGGCGACACAGTCGTGTATCATCTGATGAT
52428618 T
1 T
52428619 TCCTTAGGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (40 bp):
TCATACGGCCTGGCGACACAGTCGTGTATCATCTGATGAT
Found at i:52431702 original size:39 final size:39
Alignment explanation
Indices: 52431637--52431787 Score: 151
Period size: 39 Copynumber: 3.7 Consensus size: 39
52431627 ACATTGTTTG
* * *
52431637 AAATTATA-TTTAAGTCTTTAAATAAATTATATTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* * *
52431675 AAATTATATTTTAAACCTCTAAGTAAATTATGTTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* *
52431714 AACAATTAAATTATGTTGAACCCTCTAATTAAATTATATTAAGTT
1 -A-AATT--A-TAT-TTTAAGCCTCTAATTAAATTATATTAAGTT
* *
52431759 ACATTATATTTTAAGTCTCTAATTAAATT
1 AAATTATATTTTAAGCCTCTAATTAAATT
52431788 TGTGTGATGA
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
38 8 0.09
39 42 0.45
40 4 0.04
41 5 0.05
43 4 0.04
44 4 0.04
45 26 0.28
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (39 bp):
AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
Found at i:52433809 original size:15 final size:15
Alignment explanation
Indices: 52433785--52433814 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52433775 GCAGATTTTT
*
52433785 CACAGTTCGTGTGAG
1 CACAGCTCGTGTGAG
52433800 CACAGCTCGTGTGAG
1 CACAGCTCGTGTGAG
52433815 TATTATCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.23
Consensus pattern (15 bp):
CACAGCTCGTGTGAG
Found at i:52436107 original size:39 final size:39
Alignment explanation
Indices: 52436053--52436132 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
52436043 TGACCGTAGA
*
52436053 AAGAATTGTTTCACTGTGAAAACTTATAGCCCTACACAT
1 AAGAATTGTTTCACTGTGAAAACTTATAACCCTACACAT
52436092 AAGAATTGTTTCACTGTGAAAACTTATAACCCTACACAT
1 AAGAATTGTTTCACTGTGAAAACTTATAACCCTACACAT
52436131 AA
1 AA
52436133 ATGCTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (39 bp):
AAGAATTGTTTCACTGTGAAAACTTATAACCCTACACAT
Found at i:52438573 original size:23 final size:23
Alignment explanation
Indices: 52438547--52438622 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
52438537 ATAAGTGCCA
52438547 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52438570 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
52438593 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52438616 CACTGAT
1 CACTGAT
52438623 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:52438722 original size:8 final size:8
Alignment explanation
Indices: 52438709--52438737 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52438699 ACCCGGGACT
52438709 CACTGTAA
1 CACTGTAA
52438717 CACTGTAA
1 CACTGTAA
52438725 CACTGTAA
1 CACTGTAA
52438733 CACTG
1 CACTG
52438738 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:52449589 original size:7 final size:7
Alignment explanation
Indices: 52449574--52449619 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
52449564 TTTGTTATAT
*
52449574 AATTTAA
1 AATTCAA
52449581 AATTCAA
1 AATTCAA
52449588 AATTCAA
1 AATTCAA
52449595 AATTCAA
1 AATTCAA
52449602 AATTCAA
1 AATTCAA
52449609 AATTCAA
1 AATTCAA
52449616 AATT
1 AATT
52449620 TTTTTGTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.33
Consensus pattern (7 bp):
AATTCAA
Found at i:52454028 original size:16 final size:16
Alignment explanation
Indices: 52454007--52454039 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52453997 TCTCATATCC
52454007 TTTAAT-TAAATTCTAT
1 TTTAATATAAATT-TAT
52454023 TTTAATATAAATTTAT
1 TTTAATATAAATTTAT
52454039 T
1 T
52454040 ACTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATATAAATTTAT
Found at i:52454054 original size:19 final size:18
Alignment explanation
Indices: 52454026--52454106 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 18
52454016 ATTCTATTTT
52454026 AATATAAATTTATTACTTTA
1 AATAT-AATTTATT-CTTTA
* *
52454046 AATATAA-TTATCCTAT-
1 AATATAATTTATTCTTTA
52454062 AAT-TAA-TTA-T-TTTA
1 AATATAATTTATTCTTTA
* *
52454076 ATTTTAATTTATTGCTTTA
1 AATATAATTTATT-CTTTA
52454095 AATATAATTTAT
1 AATATAATTTAT
52454107 CATTTAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 9 0.19
16 6 0.12
17 4 0.08
18 4 0.08
19 16 0.33
20 5 0.10
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (18 bp):
AATATAATTTATTCTTTA
Found at i:52454075 original size:49 final size:52
Alignment explanation
Indices: 52454002--52454127 Score: 168
Period size: 49 Copynumber: 2.4 Consensus size: 52
52453992 GCCCGTCTCA
52454002 TATCCTTTAATTAAATTCTATTTTAATATAAATTTATTACTTTAAATATAA-T
1 TATCCTTTAATT-AATTCTATTTTAATATAAATTTATTACTTTAAATATAATT
* * * *
52454054 TATCCTATAATTAA-T-TATTTTAATTTTAATTTATTGCTTTAAATATAATT
1 TATCCTTTAATTAATTCTATTTTAATATAAATTTATTACTTTAAATATAATT
*
52454104 TATCATTTAATTAAATTCTATTTT
1 TATCCTTTAATT-AATTCTATTTT
52454128 TTATTTTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
49 30 0.47
50 12 0.19
51 4 0.06
52 12 0.19
53 6 0.09
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (52 bp):
TATCCTTTAATTAATTCTATTTTAATATAAATTTATTACTTTAAATATAATT
Found at i:52454361 original size:52 final size:52
Alignment explanation
Indices: 52454293--52454402 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
52454283 AGCACCGTTA
** *
52454293 TTTTTTAATCTAGTACAAGAGTATTGATCATCAGTGTCCCAACATCCAATTT
1 TTTTTTAATCTAGTACAAGAGTATCAATCATCAGTGTCCCAACACCCAATTT
* * * ** *
52454345 TTTTTTAATCTGGTACAAGAGTGTCAATCATTAGTGTTTCAGCACCCAATTT
1 TTTTTTAATCTAGTACAAGAGTATCAATCATCAGTGTCCCAACACCCAATTT
52454397 TTTTTT
1 TTTTTT
52454403 TTTATTTCCG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (52 bp):
TTTTTTAATCTAGTACAAGAGTATCAATCATCAGTGTCCCAACACCCAATTT
Found at i:52454662 original size:34 final size:35
Alignment explanation
Indices: 52454618--52454684 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
52454608 CAGTAAAATA
*
52454618 TTTTCCGTAAAATGATTT-CAGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
* *
52454652 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACAGGAAAATATTTT
52454685 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACAGGAAAATATTTTAC
Found at i:52455256 original size:18 final size:19
Alignment explanation
Indices: 52455214--52455258 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
52455204 ACAGACCCTT
52455214 AAATTAATGTGGTCCAAAG
1 AAATTAATGTGGTCCAAAG
52455233 AAATTAATGTGGTCCAAA-
1 AAATTAATGTGGTCCAAAG
52455251 AAATTAAT
1 AAATTAAT
52455259 TAGTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAG
Found at i:52456518 original size:9 final size:9
Alignment explanation
Indices: 52456504--52456597 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
52456494 TTTGGTTAAA
52456504 AATTAACCG
1 AATTAACCG
52456513 AATTAACCG
1 AATTAACCG
* *
52456522 AATTATCTG
1 AATTAACCG
*
52456531 AATTATCCG
1 AATTAACCG
52456540 AATTAACCG
1 AATTAACCG
*
52456549 AATTACCCG
1 AATTAACCG
52456558 AATTAACCG
1 AATTAACCG
*
52456567 AATTACCCG
1 AATTAACCG
52456576 AATTAACCG
1 AATTAACCG
*
52456585 AATTAACCA
1 AATTAACCG
52456594 AATT
1 AATT
52456598 GAATCACTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:52457162 original size:11 final size:11
Alignment explanation
Indices: 52457146--52457197 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
52457136 CTTTCATAAT
52457146 AATAATAATAC
1 AATAATAATAC
52457157 AATAATAATAC
1 AATAATAATAC
* **
52457168 TTATAAT-ATTT
1 -AATAATAATAC
52457179 AATAATAATAC
1 AATAATAATAC
52457190 AATAATAA
1 AATAATAA
52457198 AAATATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:52460234 original size:15 final size:14
Alignment explanation
Indices: 52460185--52460234 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
52460175 CCCGGCCCAC
52460185 TAAAAATAAACCAAA
1 TAAAAA-AAACCAAA
*
52460200 CAAAAAAATACCAAA
1 TAAAAAAA-ACCAAA
* *
52460215 TAAAACAAACCCAA
1 TAAAAAAAACCAAA
52460229 TAAAAA
1 TAAAAA
52460235 GTCCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.72, C:0.18, G:0.00, T:0.10
Consensus pattern (14 bp):
TAAAAAAAACCAAA
Found at i:52468043 original size:51 final size:51
Alignment explanation
Indices: 52467985--52468175 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
52467975 CTGGTTCACA
*
52467985 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * * * * *
52468036 TAGTAGCCTGTACATAGTACTACACACATGATCGA--AGCCATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * * *
52468087 TAGTAGCCTGCACATAGTACTACACATGCGACATATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGAC-CATCACTATCCGGTACACG
** *
52468137 TAGTAGCAGGCACATAGTACTAGACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
52468176 TTCACTTTTG
Statistics
Matches: 112, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
49 4 0.04
50 38 0.34
51 67 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:52471009 original size:42 final size:42
Alignment explanation
Indices: 52470929--52471010 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
52470919 TGTTTTCTCT
* **
52470929 ATGCCATAGTCCAACTATGATCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGATCTTACACATATGCACATATTG
* *
52470971 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGATCTTACACA-TATGCACATAT
52471011 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGATCTTACACATATGCACATATTG
Found at i:52471071 original size:47 final size:47
Alignment explanation
Indices: 52470970--52471062 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
52470960 TTTACATATT
* *
52470970 GATGCCATAGCCCAGCTATGGTCTTACACAGTAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAGCACATATCACACC
* * * *
52471017 GATGCCATATCCCAGATATGGTCTTATACGGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAG-AAGCACATATCACA
52471063 TGTTGCCATG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 27 0.69
48 12 0.31
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (47 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAGCACATATCACACC
Found at i:52478750 original size:47 final size:48
Alignment explanation
Indices: 52478697--52478794 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 48
52478687 GAAGGAGAAG
* *
52478697 AGACCAAGGCGAAAACCCGCAAAGGG-TACTTTGAGTCCTAA-AAAAAA
1 AGACCAAGACGAAAACCCACAAAGGGCT-CTTTGAGTCCTAAGAAAAAA
*
52478744 AGACCAAGACGAAAACCCATAAAGGGCTCTTTGAGTCCTAAGAAAAAA
1 AGACCAAGACGAAAACCCACAAAGGGCTCTTTGAGTCCTAAGAAAAAA
52478792 AGA
1 AGA
52478795 GAGGCCAACG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 36 0.78
48 10 0.22
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (48 bp):
AGACCAAGACGAAAACCCACAAAGGGCTCTTTGAGTCCTAAGAAAAAA
Found at i:52480326 original size:143 final size:143
Alignment explanation
Indices: 52480059--52480694 Score: 842
Period size: 143 Copynumber: 4.4 Consensus size: 143
52480049 ACTACGGTGA
* * * * *
52480059 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTTAAGCCACCAGCCTTATCTTCCTGAAGTCGT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
* * ** * *
52480124 AGCAGAGCAGACTGAAGATAATGAATCTTATTTCCCTGACGTTGTAGTGAAACAGATTAAAGCTA
66 AGCAGAGAAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
52480189 CAAATTATGGCGG
131 CAAATTATGGCGG
* * *
52480202 ATCTTATCTTCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACCAGCCTTATCTCCGTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
* * * * *
52480267 AGCAGAGAAGACTAAAGATAGCGAATATTATTTCCCTGGCGTTGCAGTGGAACATATTAAAGCTA
66 AGCAGAGAAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
52480332 CAAATTATGGCGG
131 CAAATTATGGCGG
* * ** * *
52480345 ATCTTATC-TCCTTGAAGTTGCAATAGAGCAGATTGAAGTTACCAGCTTTATCTCCCTGAAATTG
1 ATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* * * * * * *
52480409 TAGCGGAGCAGACTGAAGACATCAAATCTTATTTCTCTGGCGTTGTAGTGGAATAGATTAAAGCT
65 CAGCAGAGAAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
52480474 ACAAATTATGGCGG
130 ACAAATTATGGCGG
* *
52480488 ACCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
* * ** *
52480553 AGCGGAGAAGACTGAAGACAGCGAATCTTATTTCTCTGGTATTGTATTGGAACAGATTAAAGCTA
66 AGCAGAGAAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
*
52480618 CAAATTATGGTGG
131 CAAATTATGGCGG
* * * * * *
52480631 ATCTTATCTTCCTAAAGTTGCAGTGGAGCAAATCGAAACCACAATCCTTATCTCCCTGAAGTTG
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
52480695 TAGTGGAGCA
Statistics
Matches: 432, Mismatches: 59, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
142 3 0.01
143 426 0.99
144 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (143 bp):
ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
AGCAGAGAAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
CAAATTATGGCGG
Found at i:52480781 original size:45 final size:44
Alignment explanation
Indices: 52480633--52480792 Score: 160
Period size: 45 Copynumber: 3.6 Consensus size: 44
52480623 TATGGTGGAT
* * ** * **
52480633 CTTATCTTCCTAAAGTTGCAGTGGAGCAAATCGAAACCACAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAATTACAATC
* * *
52480677 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGATAAAAATATACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TAGAAAT-TACAATC
*
52480723 CTTATC-CCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAATTAC-AATC
* * *
52480767 CTTATCTCCTTGAAGTTACAGCGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
52480793 TAGATCGAAG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
43 3 0.03
44 39 0.41
45 42 0.44
46 11 0.12
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAATTACAATC
Found at i:52487367 original size:19 final size:19
Alignment explanation
Indices: 52487315--52487367 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
52487305 TTAGGAATAA
52487315 TAATATTAAT-TTTTAATT
1 TAATATTAATATTTTAATT
52487333 TAAT-TTAGA-ATTTTTAA-T
1 TAATATTA-ATA-TTTTAATT
52487351 TAATATTAATATCTTTA
1 TAATATTAATAT-TTTA
52487368 TTGTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
17 3 0.10
18 12 0.41
19 14 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TAATATTAATATTTTAATT
Found at i:52488449 original size:90 final size:90
Alignment explanation
Indices: 52488347--52488532 Score: 345
Period size: 90 Copynumber: 2.1 Consensus size: 90
52488337 TGAAATGGAT
52488347 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
1 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
* *
52488412 TTTTGCATTTTAAAATGCAAGCCAA
66 GTTTGCATTTCAAAATGCAAGCCAA
52488437 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
1 AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
52488502 GTTTGCATTTCAAAATGCAAGCCAA
66 GTTTGCATTTCAAAATGCAAGCCAA
*
52488527 GAGAAT
1 AAGAAT
52488533 ATGATTCTTT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (90 bp):
AAGAATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAA
GTTTGCATTTCAAAATGCAAGCCAA
Found at i:52491491 original size:23 final size:23
Alignment explanation
Indices: 52491472--52491556 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
52491462 TATTTTAGTT
*
52491472 TTATCATGTATTTTTATTTAAAG
1 TTATCATGTATTATTATTTAAAG
* *
52491495 TTATCATGTATTATTATTTTGAAT
1 TTATCATGTATTATTA-TTTAAAG
* * * *
52491519 TTATCATCTATGATCATTTAAAT
1 TTATCATGTATTATTATTTAAAG
52491542 TTATCATGTATTATT
1 TTATCATGTATTATT
52491557 TTATGCATCC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 33 0.65
24 18 0.35
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (23 bp):
TTATCATGTATTATTATTTAAAG
Found at i:52491537 original size:24 final size:23
Alignment explanation
Indices: 52491487--52491548 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
52491477 ATGTATTTTT
* * * *
52491487 ATTTAAAGTTATCATGTATTATT
1 ATTTAAATTTATCATCTATGATC
*
52491510 ATTTTGAATTTATCATCTATGATC
1 A-TTTAAATTTATCATCTATGATC
52491534 ATTTAAATTTATCAT
1 ATTTAAATTTATCAT
52491549 GTATTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (23 bp):
ATTTAAATTTATCATCTATGATC
Found at i:52491549 original size:47 final size:47
Alignment explanation
Indices: 52491444--52491556 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
52491434 TATATTATTC
** * * ** *
52491444 TAAATTTATCAT-TAACATTATTTTAGTTTTATCATGTATTTTTATT
1 TAAATTTATCATGTATTATTATTTTAGATTTATCATCTATGATCATT
*
52491490 TAAAGTTATCATGTATTATTATTTT-GAATTTATCATCTATGATCATT
1 TAAATTTATCATGTATTATTATTTTAG-ATTTATCATCTATGATCATT
52491537 TAAATTTATCATGTATTATT
1 TAAATTTATCATGTATTATT
52491557 TTATGCATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
46 12 0.21
47 44 0.79
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (47 bp):
TAAATTTATCATGTATTATTATTTTAGATTTATCATCTATGATCATT
Found at i:52491743 original size:2 final size:2
Alignment explanation
Indices: 52491736--52491768 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
52491726 TTTATGATAC
*
52491736 AT AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52491769 CATTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:52495391 original size:20 final size:21
Alignment explanation
Indices: 52495351--52495402 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
52495341 CTACAACTTA
* *
52495351 AAGCAGAGGTAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCAAGGG
52495372 AAGCAGAGGCA-CAGCAAGGG
1 AAGCAGAGGCAGCAGCAAGGG
* *
52495392 CAGTAGAGGCA
1 AAGCAGAGGCA
52495403 ACAAGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.37, C:0.17, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCAAGGG
Found at i:52495777 original size:43 final size:44
Alignment explanation
Indices: 52495715--52495811 Score: 133
Period size: 43 Copynumber: 2.2 Consensus size: 44
52495705 GGCATTTTCT
* * * * *
52495715 TACAAACACTGCTATAGAACATGATCTTTAGCGGCACTTTTA-C
1 TACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGC
*
52495758 TACAAACGCCGCTAAAGAACATGATCTTTTGCGGCAATTCTAGC
1 TACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGC
52495802 TACAAACGCC
1 TACAAACGCC
52495812 ACAACATGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 36 0.77
44 11 0.23
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (44 bp):
TACAAACGCCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGC
Found at i:52499396 original size:35 final size:35
Alignment explanation
Indices: 52499357--52499428 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
52499347 GAGAGAAAGA
*
52499357 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGGTAACACAGTTTGAATTT
52499392 AAATCAACACAAGTTTGGTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGGTAACACAGTTTGAATTT
52499427 AA
1 AA
52499429 TAATCCTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (35 bp):
AAATCAACACAAGTTTGGTAACACAGTTTGAATTT
Found at i:52502105 original size:57 final size:57
Alignment explanation
Indices: 52502025--52502138 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
52502015 GATCCTATCC
* *
52502025 TGATATAGCCCTCTCGAAGAATATGTGTGAAAA-GGATCTAGCCCGAACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAATATGTG-GAAAATGGATCTAGCCCGAACGGGTAATCT
* *
52502082 TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGCCCGGACGGGTAATCT
1 TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATCTAGCCCGAACGGGTAATCT
52502139 AAATTGGGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 5 0.10
57 47 0.90
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATCTAGCCCGAACGGGTAATCT
Found at i:52502373 original size:67 final size:67
Alignment explanation
Indices: 52502261--52502391 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
52502251 TTTATATTAC
* **
52502261 AGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATAAGGTTTGCGGGAGTATGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTTCACGGGAGTATGCTCTCTT
52502326 GT
66 GT
* *
52502328 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACGGGAGTGTGCTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTTCACGGGAGTATGCTCTCT
52502392 GAATTGGGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATAAGGTTCACGGGAGTATGCTCTCTT
GT
Found at i:52510902 original size:13 final size:13
Alignment explanation
Indices: 52510870--52510907 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
52510860 CGTATTTTGG
*
52510870 TTGTTTTGTGT-T
1 TTGTTTTATGTGT
52510882 TTGATTTTATGTGT
1 TTG-TTTTATGTGT
52510896 TTGTTTTATGTG
1 TTGTTTTATGTG
52510908 CAGCGAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 16 0.70
14 4 0.17
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTGTTTTATGTGT
Found at i:52527575 original size:18 final size:18
Alignment explanation
Indices: 52527537--52527575 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52527527 GTAGCCAAAA
*
52527537 TTAGGTCTTCAATAATTT
1 TTAGGTCTTCAATAATGT
52527555 TTAGGTCTTCATATAA-GT
1 TTAGGTCTTCA-ATAATGT
52527573 TTA
1 TTA
52527576 ATTGTGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (18 bp):
TTAGGTCTTCAATAATGT
Found at i:52528970 original size:95 final size:93
Alignment explanation
Indices: 52528793--52529214 Score: 352
Period size: 95 Copynumber: 4.5 Consensus size: 93
52528783 GTTTACAAAT
* * *
52528793 TTTAGATAAGTGCCTTAAGTGGCTTAGCAGTGTATCTAG-TATTAGACTTAGCGAGCAGTTTCCT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCT-GCTATTAGACTTAGCGAGCAGTTTCCT
** **
52528857 CTCAA-CTTGTCTGTTTTATAACTTCATTGAA
65 CT-AAGAGTGTCTACTTTATAA-TT-ATTGAA
* * * *
52528888 TTTAGCTAAGTGCCCTAATAGGCTTAGCAGTATATCTGCTATTAGAATTAGCGAGTAGTTTCCTC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGCGAGCAGTTTCCTC
* *
52528953 TAAGAGTATCTACTTTATAAATATTGAA
66 TAAGAGTGTCTACTTTATAATTATTGAA
* * * * * * ** *
52528981 TTTTGGCTAAGTGCCTTAAGAGGC-TAGAAGCA-ATTCTTCTATTACACTTAGTGATTAGTTTCT
1 -TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATA-TCTGCTATTAGACTTAGCGAGCAGTTTCC
** * *
52529044 TCTCGGTGTGTCTACTTTATAATTTTGTTGAA
64 TCTAAGAGTGTCTACTTTATAA--TTATTGAA
* * * * * *
52529076 TTTAGCTACGTGCCTTAAGAGGCTTAGCAATATATTTGCTGTTAGACTTAGTGAGCAGTTCCCTC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGCGAGCAGTTTCCTC
* * * * *
52529141 T-TGAATTGTCTGCTCTATAGA-TATTGATT
66 TAAG-AGTGTCTACTTTATA-ATTATTGA-A
* *
52529170 TTTGGCTAAGTGCCTTAAAAGGCTTAGCAGTATATCTGCTATTAG
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAG
52529215 TTTTAGTGAG
Statistics
Matches: 260, Mismatches: 56, Indels: 23
0.77 0.17 0.07
Matches are distributed among these distances:
92 1 0.00
93 58 0.22
94 85 0.33
95 114 0.44
96 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (93 bp):
TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGCGAGCAGTTTCCTC
TAAGAGTGTCTACTTTATAATTATTGAA
Found at i:52529040 original size:93 final size:93
Alignment explanation
Indices: 52528882--52529099 Score: 224
Period size: 93 Copynumber: 2.3 Consensus size: 93
52528872 TTATAACTTC
* * * * *
52528882 ATTGAATTTAGCTAAGTGCCCTAATAGGCTTAGCAGTATATCTGCTATTAGAATTAGCGAGTAGT
1 ATTGAATTTAGCTAAGTGCCTTAAGAGGC-TAGAAGAATATCTGCTATTACAATTAGCGAGTAGT
52528947 TTCCTCTAAGAGTATCTACTTTATAA-AT
65 TTCCTCTAAGAGTATCTACTTTATAATAT
* * * * *
52528975 ATTGAATTTTGGCTAAGTGCCTTAAGAGGCTAGAAGCAAT-TCTTCTATTACACTTAGTGATTAG
1 ATTGAA-TTTAGCTAAGTGCCTTAAGAGGCTAGAAG-AATATCTGCTATTACAATTAGCGAGTAG
* ** * * *
52529039 TTTCTTCTCGGTGTGTCTACTTTATAATTTT
64 TTTCCTCTAAGAGTATCTACTTTATAA-TAT
* *
52529070 GTTGAATTTAGCTACGTGCCTTAAGAGGCT
1 ATTGAATTTAGCTAAGTGCCTTAAGAGGCT
52529100 TAGCAATATA
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
93 52 0.51
94 44 0.43
95 6 0.06
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (93 bp):
ATTGAATTTAGCTAAGTGCCTTAAGAGGCTAGAAGAATATCTGCTATTACAATTAGCGAGTAGTT
TCCTCTAAGAGTATCTACTTTATAATAT
Found at i:52530304 original size:21 final size:21
Alignment explanation
Indices: 52530280--52530381 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 21
52530270 GGAGATTAAT
52530280 AGTTTTCTCTAGGAGTTAAGC
1 AGTTTTCTCTAGGAGTTAAGC
* * *
52530301 AGTTTTCTTTAGGAATT-TGAC
1 AGTTTTCTCTAGGAGTTAAG-C
*
52530322 AGTCTTT-TCAAGGAGTTAAG-
1 AGT-TTTCTCTAGGAGTTAAGC
* * *
52530342 AGTTTTCCCTAGAAGTTTAGC
1 AGTTTTCTCTAGGAGTTAAGC
* *
52530363 AATCTTTC-ATAGGAGTTAA
1 AGT-TTTCTCTAGGAGTTAA
52530382 TAACATTCCC
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
19 3 0.05
20 13 0.22
21 36 0.60
22 8 0.13
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (21 bp):
AGTTTTCTCTAGGAGTTAAGC
Found at i:52530369 original size:41 final size:42
Alignment explanation
Indices: 52530289--52530381 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 42
52530279 TAGTTTTCTC
** *
52530289 TAGGAGTTAAGCAGTTTTCTTTAGGAATTTGACAGTCTTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATC-TTTCA
52530332 -AGGAGTTAAG-AGTTTTCCCTA-GAAGTTT-AGCAATCTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAA-TTTGA-CAATCTTTCA
52530372 TAGGAGTTAA
1 TAGGAGTTAA
52530382 TAACATTCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
40 9 0.20
41 25 0.57
42 10 0.23
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (42 bp):
TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATCTTTCA
Found at i:52543537 original size:137 final size:138
Alignment explanation
Indices: 52543326--52543631 Score: 461
Period size: 137 Copynumber: 2.2 Consensus size: 138
52543316 GTACAGAAAT
* * * *
52543326 AATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTTATACAAAATATTGATTG
1 AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
* * *
52543391 TATATATTTTACCAAATTTATTATTATAAACAATTGTATTAATTAATTTTGGTCAAAATATAAAA
66 TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
52543456 GACATAGA
131 GACATAGA
** **
52543464 AATTAATATTCTTACGGAAAGAATATAATTAACATATTCA-TTGATTCATACAAAATATTAACTG
1 AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
* *
52543528 TATATATTTTATCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTTAAAATATAAAA
66 TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
**
52543593 GACATTTA
131 GACATAGA
*
52543601 AATTAATATTCTTTTGGAAAGAATACAATTA
1 AATTAATATTCTTTTGGAAAGAATATAATTA
52543632 CTTTTTCCAA
Statistics
Matches: 150, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
137 115 0.77
138 35 0.23
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.41
Consensus pattern (138 bp):
AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
GACATAGA
Found at i:52543742 original size:75 final size:75
Alignment explanation
Indices: 52543606--52543752 Score: 190
Period size: 75 Copynumber: 2.0 Consensus size: 75
52543596 ATTTAAATTA
* * * **
52543606 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAATTTTCTATTTGTCTTCTTTGTTAATAAGA
1 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
52543671 GAATAATCCT
66 GAATAATCCT
* *
52543681 ATATTCTTTTGGAAAGAATATAATT-CTTTTTTCTAACTTTCCATTTGCCTTCTCCAG-TAATAA
1 ATATTCTTTTGGAAAGAATACAATTAC-TTTTTCCAACTTTCCATTTGCCTTCT-CAGTTAATAA
*
52543744 GGGAATAAT
64 GAGAATAAT
52543753 AATGGTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
74 1 0.02
75 60 0.97
76 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
GAATAATCCT
Found at i:52572161 original size:22 final size:22
Alignment explanation
Indices: 52572108--52572161 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
52572098 TTGGGCATCA
*
52572108 CGATACCCAAAACCAGATATTG
1 CGATACCCAAAACCAAATATTG
* * *
52572130 TGATGCCCAAAATCAAATATTG
1 CGATACCCAAAACCAAATATTG
*
52572152 CGATATCCAA
1 CGATACCCAA
52572162 GCCTGACGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (22 bp):
CGATACCCAAAACCAAATATTG
Found at i:52582276 original size:103 final size:104
Alignment explanation
Indices: 52581939--52582309 Score: 593
Period size: 105 Copynumber: 3.6 Consensus size: 104
52581929 TGTATATAAA
** * * *
52581939 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
52582003 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
52582043 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
52582108 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
52582148 AGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTGGTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
52582213 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
52582251 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
52582310 ATAACGGCTA
Statistics
Matches: 249, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
103 85 0.34
104 68 0.27
105 95 0.38
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:52584089 original size:15 final size:16
Alignment explanation
Indices: 52584062--52584091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52584052 AATTACAATT
52584062 AATATATATTATATAA
1 AATATATATTATATAA
52584078 AATATA-ATTATATA
1 AATATATATTATATA
52584092 TTAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:52620949 original size:27 final size:25
Alignment explanation
Indices: 52620919--52620984 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 25
52620909 CCACAATGAA
*
52620919 CATTTCTTTTGGGTACGCCACAAAAGC
1 CATTTCTTTT-AGTACGCCAC-AAAGC
* * *
52620946 CATTCCTTCATAGTACGCCACAAAGG
1 CATTTCTT-TTAGTACGCCACAAAGC
52620972 CATTTCTTTTAGT
1 CATTTCTTTTAGT
52620985 TTATTGCTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.12
26 11 0.34
27 16 0.50
28 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (25 bp):
CATTTCTTTTAGTACGCCACAAAGC
Found at i:52621063 original size:27 final size:27
Alignment explanation
Indices: 52621031--52621093 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
52621021 AAAAGGTTAT
*
52621031 TATTCTTTCATAATT-TTCCACAAAAGC
1 TATTCTTTCATAATTCAT-CACAAAAGC
52621058 TATTCTTTCATAATTCATCACAAAAGC
1 TATTCTTTCATAATTCATCACAAAAGC
52621085 TATTCTTTC
1 TATTCTTTC
52621094 CTGTCATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (27 bp):
TATTCTTTCATAATTCATCACAAAAGC
Found at i:52622688 original size:11 final size:11
Alignment explanation
Indices: 52622672--52622702 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52622662 TCTTAAACTG
52622672 AATTTATATGT
1 AATTTATATGT
52622683 AATTTATATGT
1 AATTTATATGT
*
52622694 AAATTATAT
1 AATTTATAT
52622703 TATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (11 bp):
AATTTATATGT
Found at i:52623629 original size:2 final size:2
Alignment explanation
Indices: 52623622--52623657 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52623612 ATGAAAGAGA
52623622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52623658 TGTAGTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52629299 original size:21 final size:21
Alignment explanation
Indices: 52629275--52629317 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52629265 TCTGGGTGGA
52629275 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52629296 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52629317 T
1 T
52629318 GGAATGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:52641895 original size:25 final size:24
Alignment explanation
Indices: 52641832--52641918 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
52641822 CTACATGTAT
*
52641832 GCTCATACGAGC-GATAAACGGTAA
1 GCTCATATGAGCTGA-AAACGGTAA
* * *
52641856 GCTCTTCTGATCTGAACAACGGTAA
1 GCTCATATGAGCTGAA-AACGGTAA
* *
52641881 GCTCATATGAGCTGAGTATCGGTAA
1 GCTCATATGAGCTGA-AAACGGTAA
*
52641906 GCTCATAAGAGCT
1 GCTCATATGAGCT
52641919 TGAATCAGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 9 0.18
25 41 0.82
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (24 bp):
GCTCATATGAGCTGAAAACGGTAA
Found at i:52647300 original size:111 final size:111
Alignment explanation
Indices: 52647103--52647432 Score: 608
Period size: 111 Copynumber: 3.0 Consensus size: 111
52647093 ATATAAAAAT
*
52647103 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTTTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
*
52647168 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
*
52647214 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTAATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
*
52647279 AAAATATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
52647325 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
52647390 AAAGTATTAGTTACACGA-TGTACCATTCAACCATCACATTTGA
66 AAAGTATTAGTTACAC-ACTGTACCATTCAACCATCACATTTGA
52647433 CCTATCAGTT
Statistics
Matches: 212, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
111 211 1.00
112 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (111 bp):
ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
AAAGTATTAGTTACACACTGTACCATTCAACCATCACATTTGAATC
Found at i:52649331 original size:43 final size:41
Alignment explanation
Indices: 52649264--52649500 Score: 199
Period size: 43 Copynumber: 5.6 Consensus size: 41
52649254 CGCTTTTCCC
* * *
52649264 GCGCTTTTACACAAACGCCGCTATAGTTCAAGATCTTTAGCA
1 GCGCTTTTCCACAAATGCCGCTATAGATCAAGA-CTTTAGCA
*
52649306 GCGCTTTTCCCACAAATGCCACTATAGATCAAGACTTTTAGCA
1 GCGCTTTT-CCACAAATGCCGCTATAGATCAAGAC-TTTAGCA
* * * * **
52649349 GCGCTTTTCCTCAAAGGCCGCTACAGCTCAAGACCTTTAGTG
1 GCGCTTTTCCACAAATGCCGCTATAGATCAAGA-CTTTAGCA
* * * **
52649391 GCGCTTTTCCAACAAAAGTCGCAATAGATCAAGACTTTTAGGG
1 GCGCTTTTCC-ACAAATGCCGCTATAGATCAAGAC-TTTAGCA
* *
52649434 GCTCCTTTTCCACAAATGCCGCTATAGCTCAAGACCTTTAGC-
1 GC-GCTTTTCCACAAATGCCGCTATAGATCAAGA-CTTTAGCA
*
52649476 GACGCTTTGAT-TACAAATGCCGCTA
1 G-CGCTTT--TCCACAAATGCCGCTA
52649501 AAAATACCGT
Statistics
Matches: 159, Mismatches: 26, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
42 50 0.31
43 100 0.63
44 9 0.06
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (41 bp):
GCGCTTTTCCACAAATGCCGCTATAGATCAAGACTTTAGCA
Found at i:52649381 original size:85 final size:84
Alignment explanation
Indices: 52649264--52649483 Score: 260
Period size: 85 Copynumber: 2.6 Consensus size: 84
52649254 CGCTTTTCCC
* * * * * *
52649264 GCGCTTTTACACAAACGCCGCTATAGTTCAAGATCTTTAGCAGCGCTTTTCCCACAAATGCCACT
1 GCGCTTTTCCACAAACGCCGCTATAGCTCAAGACCTTTAGC-GCGCTTTTCCAACAAAAGCCACA
52649329 ATAGATCAAGACTTTTAGCA
65 ATAGATCAAGACTTTTAGCA
* * * * * *
52649349 GCGCTTTTCCTCAAAGGCCGCTACAGCTCAAGACCTTTAGTGGCGCTTTTCCAACAAAAGTCGCA
1 GCGCTTTTCCACAAACGCCGCTATAGCTCAAGACCTTTAG-CGCGCTTTTCCAACAAAAGCCACA
**
52649414 ATAGATCAAGACTTTTAGGG
65 ATAGATCAAGACTTTTAGCA
* *
52649434 GCTCCTTTTCCACAAATGCCGCTATAGCTCAAGACCTTTAGCGACGCTTT
1 GC-GCTTTTCCACAAACGCCGCTATAGCTCAAGACCTTTAGCG-CGCTTT
52649484 GATTACAAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
85 73 0.65
86 40 0.35
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (84 bp):
GCGCTTTTCCACAAACGCCGCTATAGCTCAAGACCTTTAGCGCGCTTTTCCAACAAAAGCCACAA
TAGATCAAGACTTTTAGCA
Found at i:52652046 original size:21 final size:21
Alignment explanation
Indices: 52652020--52652063 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
52652010 GGACGGGTAA
52652020 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
52652041 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
52652062 AA
1 AA
52652064 ACTCCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
AATTAGAAACTATAAAACTAG
Found at i:52662298 original size:45 final size:45
Alignment explanation
Indices: 52662247--52662335 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
52662237 AAATCATTAC
52662247 TCTCGTAAAGCCAAAAGAGTGTGTGCAATCACACTGTCTTTTCTG
1 TCTCGTAAAGCCAAAAGAGTGTGTGCAATCACACTGTCTTTTCTG
52662292 TCTCGTAAAGCCAAAAGAGTGTGTGCAATCACACTGTCTTTTCT
1 TCTCGTAAAGCCAAAAGAGTGTGTGCAATCACACTGTCTTTTCT
52662336 ATGAATCGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
TCTCGTAAAGCCAAAAGAGTGTGTGCAATCACACTGTCTTTTCTG
Found at i:52664121 original size:23 final size:23
Alignment explanation
Indices: 52664095--52664170 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
52664085 ATAAGTGCCA
52664095 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
52664118 CACTTATATGTAGCAGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
52664141 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52664164 CACTGAT
1 CACTGAT
52664171 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:52664270 original size:8 final size:8
Alignment explanation
Indices: 52664257--52664285 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52664247 ACCCGGGACT
52664257 CACTGTAA
1 CACTGTAA
52664265 CACTGTAA
1 CACTGTAA
52664273 CACTGTAA
1 CACTGTAA
52664281 CACTG
1 CACTG
52664286 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:52665886 original size:14 final size:16
Alignment explanation
Indices: 52665856--52665887 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
52665846 TTATAAGGCC
52665856 TTTATAATTTCTGGAT
1 TTTATAATTTCTGGAT
52665872 TTTA-AATTT-TGGAT
1 TTTATAATTTCTGGAT
52665886 TT
1 TT
52665888 GCTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTATAATTTCTGGAT
Found at i:52668706 original size:18 final size:18
Alignment explanation
Indices: 52668679--52668713 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52668669 ACTTAACACA
* *
52668679 AAGCTTGCAAATCATAAG
1 AAGCTCGCAAAGCATAAG
52668697 AAGCTCGCAAAGCATAA
1 AAGCTCGCAAAGCATAA
52668714 AATCATATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (18 bp):
AAGCTCGCAAAGCATAAG
Found at i:52673914 original size:20 final size:21
Alignment explanation
Indices: 52673889--52673932 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
52673879 ATCAGTACCA
52673889 AAACATGA-AAAAATAAGGAT
1 AAACATGACAAAAATAAGGAT
*
52673909 AAACATGACAAAATTAAGGAT
1 AAACATGACAAAAATAAGGAT
52673930 AAA
1 AAA
52673933 TTAAGGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (21 bp):
AAACATGACAAAAATAAGGAT
Found at i:52673935 original size:11 final size:11
Alignment explanation
Indices: 52673919--52673943 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52673909 AAACATGACA
52673919 AAATTAAGGAT
1 AAATTAAGGAT
52673930 AAATTAAGGAT
1 AAATTAAGGAT
52673941 AAA
1 AAA
52673944 CATCACACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
AAATTAAGGAT
Found at i:52693080 original size:12 final size:11
Alignment explanation
Indices: 52693063--52693118 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 11
52693053 AACAAATCCT
52693063 CTCTCATATTTC
1 CTCTCA-ATTTC
52693075 CTCTCAA-TTC
1 CTCTCAATTTC
52693085 CTCTCAATTTC
1 CTCTCAATTTC
**
52693096 CT-TCCAAAATC
1 CTCT-CAATTTC
52693107 C-CTCAATTTC
1 CTCTCAATTTC
52693117 CT
1 CT
52693119 TCTAAAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 17 0.47
11 13 0.36
12 6 0.17
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:52693096 original size:21 final size:22
Alignment explanation
Indices: 52693063--52693135 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
52693053 AACAAATCCT
52693063 CTCTCATATTTCCTCT-CAATTC
1 CTCTCA-ATTTCCTCTACAATTC
* *
52693085 CTCTCAATTTCCT-TCCAAAATC
1 CTCTCAATTTCCTCTAC-AATTC
*
52693107 C-CTCAATTTCCTTCTAAAATT-
1 CTCTCAATTTCC-TCTACAATTC
52693128 CTCTCAAT
1 CTCTCAAT
52693136 CTATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 19 0.45
22 21 0.50
23 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTCTACAATTC
Found at i:52693168 original size:50 final size:51
Alignment explanation
Indices: 52693108--52693220 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
52693098 TCCAAAATCC
* *
52693108 CTCAATTTCCTTCTAAAATTCTCTC-AATCTATATTTAATTTCAATTTCCT
1 CTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCT
* *
52693158 CTTAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCTT
1 CTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCT
52693209 CTCAATTTCCTT
1 CTCAATTTCCTT
52693221 TTTTAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 23 0.40
51 34 0.60
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (51 bp):
CTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCT
Found at i:52694373 original size:7 final size:7
Alignment explanation
Indices: 52694361--52694385 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52694351 ATTTGATTGA
52694361 TATTTAG
1 TATTTAG
52694368 TATTTAG
1 TATTTAG
52694375 TATTTAG
1 TATTTAG
52694382 TATT
1 TATT
52694386 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:52695063 original size:18 final size:18
Alignment explanation
Indices: 52695037--52695071 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52695027 AGGTGCGTTT
*
52695037 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
52695055 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
52695072 TCCTTTTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:52698744 original size:22 final size:22
Alignment explanation
Indices: 52698719--52698763 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52698709 TATAACATCA
52698719 ACCAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
52698741 ACCAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
52698763 A
1 A
52698764 TCAACATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.13
Consensus pattern (22 bp):
ACCAAGACATGGCATAAAACAT
Found at i:52699242 original size:41 final size:41
Alignment explanation
Indices: 52699129--52699267 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
52699119 GTACAACTTA
* * * *
52699129 CCTGATACAATACACCAGTATGAAGCCTGCTAAGC-TCAAAG
1 CCTGATATAATACACCGGCATGAAGCCTGCTAGGCAT-AAAG
* * * **
52699170 CCTAATATAACACACCGACACAAAGCCTGCTAGGCATAAAG
1 CCTGATATAATACACCGGCATGAAGCCTGCTAGGCATAAAG
* *
52699211 CCTGATATAATACACCGGCGTGAAGCTTGCTAGGCATAAAG
1 CCTGATATAATACACCGGCATGAAGCCTGCTAGGCATAAAG
* *
52699252 CCCGATATAATGCACC
1 CCTGATATAATACACC
52699268 ATAACATCAC
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 78 0.99
42 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (41 bp):
CCTGATATAATACACCGGCATGAAGCCTGCTAGGCATAAAG
Found at i:52699570 original size:45 final size:45
Alignment explanation
Indices: 52699521--52699645 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 45
52699511 ATTTGATTTT
* * *
52699521 TGATGCCATAGCGTCTTTCAGCTATGGACTTAC-ACGATGGAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTA-GATAGAATCA
* * * * *
52699566 TGATGCCATATATGGCTTTCACCTATGGTCTGACTAGATAGAATCG
1 TGATGCCATA-ACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
*
52699612 TGATGCCATAACGTCTTTTAGCTATGGTCTTACT
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACT
52699646 CGTTTTTGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
45 29 0.45
46 35 0.54
47 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
Found at i:52709114 original size:41 final size:42
Alignment explanation
Indices: 52709047--52709147 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 42
52709037 CTACTAAGCT
* * * *
52709047 CAAAGCCTAATATAACAC-ACTGGCACGAAGCCTGCTAGGGA
1 CAAAGCCTGATATAATACAACTAGCACGAAGCCTGCTAGGCA
*
52709088 CAAAGCCTGATATAATACAAC-AGCACGAAGCTTGCTAGGCA
1 CAAAGCCTGATATAATACAACTAGCACGAAGCCTGCTAGGCA
* *
52709129 TAAAGCTTGATATAATACA
1 CAAAGCCTGATATAATACA
52709148 CCACAACATC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
41 50 0.96
42 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (42 bp):
CAAAGCCTGATATAATACAACTAGCACGAAGCCTGCTAGGCA
Found at i:52709465 original size:45 final size:44
Alignment explanation
Indices: 52709371--52709504 Score: 135
Period size: 45 Copynumber: 3.0 Consensus size: 44
52709361 TGTCATTGTT
* * * ***
52709371 TCTTTCAACTATAGTCTTA-TTCGTTTGATTCATGATGCAATAGTG
1 TCTTTCAACTAT-GTCTTACTT-GATTGAATCATGATGCCATAACA
52709416 TCTTTCAACTATGCTCTTACTTGATTGAATCATGATGCCATAACA
1 TCTTTCAACTATG-TCTTACTTGATTGAATCATGATGCCATAACA
* * * *
52709461 TCTTTCACCTATGGTCTTTCTAGATAGAATCATGATGCCATAAC
1 TCTTTCAACTAT-GTCTTACTTGATTGAATCATGATGCCATAAC
52709505 GTCCTTCATC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 72 0.95
46 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (44 bp):
TCTTTCAACTATGTCTTACTTGATTGAATCATGATGCCATAACA
Found at i:52709569 original size:45 final size:45
Alignment explanation
Indices: 52709519--52709621 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
52709509 TTCATCTCTT
* * * *
52709519 GTCTTACTCGTTTCT-GGTATGGTGCCATAGTGTCTTTCAACTTTG
1 GTCTTACTCATTT-TAGGTATAGTGCCATAGAGTCTTTCAACTATG
* * *
52709564 TTCTTATTTATTTTAGGTATAGTGCCATAGAGTCTTTCAACTATG
1 GTCTTACTCATTTTAGGTATAGTGCCATAGAGTCTTTCAACTATG
*
52709609 GTCTTAATCATTT
1 GTCTTACTCATTT
52709622 CCTTCAAGCC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (45 bp):
GTCTTACTCATTTTAGGTATAGTGCCATAGAGTCTTTCAACTATG
Found at i:52714037 original size:12 final size:12
Alignment explanation
Indices: 52714012--52714050 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
52714002 ACTCGTTTCT
* *
52714012 TTACTTACTCAC
1 TTACTTGCTTAC
*
52714024 TTACTTGTTTAC
1 TTACTTGCTTAC
52714036 TTACTTGCTTAC
1 TTACTTGCTTAC
52714048 TTA
1 TTA
52714051 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:52714375 original size:50 final size:50
Alignment explanation
Indices: 52714299--52714546 Score: 253
Period size: 50 Copynumber: 4.8 Consensus size: 50
52714289 TTTTCTGTAC
* * * * **
52714299 TGCCAACGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** * *
52714349 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
52714399 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
52714449 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * * *
52714505 TGCCAATGCCAAGTCCCATACATGGTCTTATATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
52714547 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 123 0.75
53 2 0.01
56 40 0.24
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:52714427 original size:100 final size:103
Alignment explanation
Indices: 52714299--52714546 Score: 286
Period size: 100 Copynumber: 2.4 Consensus size: 103
52714289 TTTTCTGTAC
* * * ** * *
52714299 TGCCAACGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAATGCCATGTC
* *
52714364 CCAAACATGGTCTTACGGGGGACCTCT-T-ATCTC-GG
66 CCAAACATGGTCTTACAGGGGACCTCTATAATCTCAGA
* *
52714399 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGATGCCAATGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAATGCCATGTC
* *
52714464 CCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
66 CCAAACATGGTCTTACAGGGGACCTCT-ATAATCTC-A-GA
* * * * *
52714505 TGCCAATGCCAAGTCCCATACATGGTCTTATATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
52714547 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 80 0.65
102 1 0.01
103 5 0.04
106 37 0.30
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (103 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAATGCCATGTC
CCAAACATGGTCTTACAGGGGACCTCTATAATCTCAGA
Found at i:52718556 original size:41 final size:41
Alignment explanation
Indices: 52718499--52718740 Score: 281
Period size: 41 Copynumber: 5.9 Consensus size: 41
52718489 ATAATTAATT
*
52718499 ATACCC-TGAACTGCACATATGTGCCCCTATTTGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * *
52718539 GTACCCTTGAATTGCACATATGTGTCCCTATTCGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
52718580 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * * * * * *
52718621 GTACCCCTGAATTCCATAAACGTGCCCCTGTTTGTACTTTG
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * *
52718662 ATA-TCTCTGAATTGCACATAAGTGCCCCTGTATGTACTTCG
1 ATACCCT-TGAATTGCACATATGTGCCCCTATTTGTACTTCG
* * * *
52718703 ATACCCCTGAATAGCACATATATGCCCCTATTTATACT
1 ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACT
52718741 CTGGTAACTT
Statistics
Matches: 167, Mismatches: 32, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
40 6 0.04
41 160 0.96
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (41 bp):
ATACCCTTGAATTGCACATATGTGCCCCTATTTGTACTTCG
Found at i:52718721 original size:123 final size:123
Alignment explanation
Indices: 52718519--52718740 Score: 313
Period size: 123 Copynumber: 1.8 Consensus size: 123
52718509 CTGCACATAT
* * *
52718519 GTGCCCCTATTTGTACTTCGGTACCCTTGAATTGCACATATGTGTCCCTATTCGTACTTCGATAC
1 GTGCCCCTATTTGTACTTCGATACCCTTGAATTGCACATAAGTGCCCCTATTCGTACTTCGATAC
* * * *
52718584 CCTTGAATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTGAATTCCATAAAC
66 CCCTGAATAGCACATATATGCCCCTATTTATACTTCGGTACCCCTGAATTCCATAAAC
* * * *
52718642 GTGCCCCTGTTTGTACTTTGATA-TCTCTGAATTGCACATAAGTGCCCCTGTAT-GTACTTCGAT
1 GTGCCCCTATTTGTACTTCGATACCCT-TGAATTGCACATAAGTGCCCCTAT-TCGTACTTCGAT
52718705 ACCCCTGAATAGCACATATATGCCCCTATTTATACT
64 ACCCCTGAATAGCACATATATGCCCCTATTTATACT
52718741 CTGGTAACTT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
122 2 0.02
123 83 0.97
124 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.35
Consensus pattern (123 bp):
GTGCCCCTATTTGTACTTCGATACCCTTGAATTGCACATAAGTGCCCCTATTCGTACTTCGATAC
CCCTGAATAGCACATATATGCCCCTATTTATACTTCGGTACCCCTGAATTCCATAAAC
Found at i:52725102 original size:6 final size:6
Alignment explanation
Indices: 52725065--52725101 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
52725055 CTTAGTTAAA
52725065 TTAGTT TTAGTT TTAGTT TTAGTT TTAGTT TTA-TT TT
1 TTAGTT TTAGTT TTAGTT TTAGTT TTAGTT TTAGTT TT
52725102 TGGATTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (6 bp):
TTAGTT
Found at i:52726566 original size:26 final size:26
Alignment explanation
Indices: 52726537--52726590 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
52726527 ATTACTTGGA
52726537 ATGTCGATGCCAATTTTTATTTTAAT
1 ATGTCGATGCCAATTTTTATTTTAAT
52726563 ATGTCGATGCCAATTTTTATTTTAAT
1 ATGTCGATGCCAATTTTTATTTTAAT
52726589 AT
1 AT
52726591 CTCCCGTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (26 bp):
ATGTCGATGCCAATTTTTATTTTAAT
Found at i:52726945 original size:14 final size:13
Alignment explanation
Indices: 52726915--52726951 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
52726905 AAACTATACT
52726915 AAAAATAAT-AAG
1 AAAAATAATAAAG
52726927 AAAAATAATAAATG
1 AAAAATAATAAA-G
52726941 AAAAATAATAA
1 AAAAATAATAA
52726952 TCAAATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (13 bp):
AAAAATAATAAAG
Found at i:52732204 original size:20 final size:20
Alignment explanation
Indices: 52732173--52732227 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
52732163 GCGTCATAGA
52732173 TGCATAACAGGGGCACCAAA-G
1 TGCA-AACAGGGGCA-CAAATG
*
52732194 TGCAGACAGGGGCACAAATG
1 TGCAAACAGGGGCACAAATG
52732214 TGCAAACAGGGGCA
1 TGCAAACAGGGGCA
52732228 TCGTAGTGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.74
21 4 0.13
ACGTcount: A:0.36, C:0.22, G:0.33, T:0.09
Consensus pattern (20 bp):
TGCAAACAGGGGCACAAATG
Found at i:52736144 original size:14 final size:14
Alignment explanation
Indices: 52736125--52736167 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
52736115 AATGTTGGCT
*
52736125 TTTATTTTATTATC
1 TTTATTTTATTAAC
52736139 TTTATTTTAACTTAAC
1 TTTATTTT-A-TTAAC
*
52736155 ATTATTTTATTAA
1 TTTATTTTATTAA
52736168 TAATAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTTTATTAAC
Found at i:52744836 original size:19 final size:18
Alignment explanation
Indices: 52744812--52744848 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52744802 ATTGAATTTG
*
52744812 AAACAAAATTAAAGGAAAA
1 AAACAAAAATAAA-GAAAA
52744831 AAACAAAAATAAAGAAAA
1 AAACAAAAATAAAGAAAA
52744849 CTAAGGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (18 bp):
AAACAAAAATAAAGAAAA
Found at i:52746261 original size:88 final size:88
Alignment explanation
Indices: 52746149--52746312 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 88
52746139 GGACCATGAG
* *
52746149 CTACTTCACTGTCGATGCAGGAAGGCAA-AACCAGCTATCTTCAACCTGCTCCACTACAACCGAG
1 CTACTTCACTATCGATGCAGGAAGG-AAGAACCAGCTATCTTCAACCTGCTCCACTACAACCAAG
52746213 GGAGGCAAGGCTTGTGTCTTTGAT
65 GGAGGCAAGGCTTGTGTCTTTGAT
* * * * * *
52746237 CTACTTCGCTATCGAT-CTAGGAAGGAAGGATCTGCTATCTTCAACCTGTTCCTCTACAACCAAG
1 CTACTTCACTATCGATGC-AGGAAGGAAGAACCAGCTATCTTCAACCTGCTCCACTACAACCAAG
*
52746301 GGAGGGAAGGCT
65 GGAGGCAAGGCT
52746313 AGGGTCTTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 3 0.05
88 62 0.95
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (88 bp):
CTACTTCACTATCGATGCAGGAAGGAAGAACCAGCTATCTTCAACCTGCTCCACTACAACCAAGG
GAGGCAAGGCTTGTGTCTTTGAT
Found at i:52746421 original size:44 final size:44
Alignment explanation
Indices: 52746384--52746633 Score: 365
Period size: 44 Copynumber: 5.7 Consensus size: 44
52746374 CCACTACTTC
* *
52746384 TCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACTGCTGG
1 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
52746428 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
1 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
* * * * *
52746472 TCAAGGAGCTAGGTTTTATAATCTTCCGCCTATTCCACTGCTGT
1 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
* * * *
52746516 TAAGGGAGCTAGGACTTATAGTCTTCCACCTATTCCACTGCTGG
1 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
* *
52746560 TCAGGGAGCTAGGATTTACAATCTTCTACCTATTCCACTGTTGG
1 TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
* *
52746604 TCAGGGAGCTAGGATTTATAGTCTTCCACC
1 TCAGGGAGCTAGGATTTACAATCTTCCACC
52746634 GGTTTGTTCT
Statistics
Matches: 183, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 183 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (44 bp):
TCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGG
Found at i:52746522 original size:132 final size:132
Alignment explanation
Indices: 52746386--52746630 Score: 418
Period size: 132 Copynumber: 1.9 Consensus size: 132
52746376 ACTACTTCTC
*
52746386 AGGGAGCTAGGACTTACAATCTTCTACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATC
1 AGGGAGCTAGGACTTACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATC
*
52746451 TTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGTTTTATAATCTTCCGCCTATTCCACTGCTGT
66 TTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGCTGT
52746516 TA
131 TA
* *
52746518 AGGGAGCTAGGACTTATAGTCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATC
1 AGGGAGCTAGGACTTACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATC
* * * *
52746583 TTCTACCTATTCCACTGTTGGTCAGGGAGCTAGGATTTATAGTCTTCC
66 TTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCC
52746631 ACCGGTTTGT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 105 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (132 bp):
AGGGAGCTAGGACTTACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATC
TTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGCTGT
TA
Found at i:52758895 original size:102 final size:102
Alignment explanation
Indices: 52758719--52759059 Score: 502
Period size: 102 Copynumber: 3.3 Consensus size: 102
52758709 CCGGAGTACA
* ** * *
52758719 TTGAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTATTAATTCCCTGA
1 TTGAATGTAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGA
*
52758784 CTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
52758821 TTGAATATAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAAGGGTTGCTAAGTGCTGATTCCCCGA
1 TTGAATGTAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGA
* * *
52758886 TTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * ** *
52758923 TTAAATGTGAGGGGGGTTGCTAAGTGCTGATTTCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGA
1 TTGAATGTAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGA
* *
52758988 ATCATTGGTGGTTCCTAAGTGCTGATTCCACCATATC
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
52759025 TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 -TTGAATGTAAAAGGGGTTGCTAAGTGCTGATTCC
52759060 TCAAATCACT
Statistics
Matches: 212, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
102 182 0.86
103 30 0.14
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (102 bp):
TTGAATGTAAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGA
ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
Found at i:52758972 original size:27 final size:26
Alignment explanation
Indices: 52758935--52758985 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
52758925 AAATGTGAGG
52758935 GGGGTTGCTAAGTGCTGATTTCCCCAA
1 GGGGTTGCTAAGTGCTGA-TTCCCCAA
52758962 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
52758986 GAATCATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:52766511 original size:102 final size:102
Alignment explanation
Indices: 52766335--52766677 Score: 508
Period size: 102 Copynumber: 3.4 Consensus size: 102
52766325 CCGGAGTACA
* * *
52766335 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTATTGGTTCCTCGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
* * *
52766400 CTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
52766437 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
* *
52766502 TTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
* * * *
52766539 TTAAATGTGAAGGGGCTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
*
52766604 ATCATTGGTGGTTGCTAAGTGTTGATTCCACCATATTT
66 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCATA-TT
* * * *
52766642 TTGAATGTGAAA-GTGGTTGCTAAATGTTGATTCCCC
1 TTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
52766678 GAATCAGTGG
Statistics
Matches: 219, Mismatches: 20, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
102 188 0.86
103 29 0.13
104 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (102 bp):
TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGA
ATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
Found at i:52766515 original size:33 final size:33
Alignment explanation
Indices: 52766478--52766632 Score: 115
Period size: 33 Copynumber: 4.6 Consensus size: 33
52766468 TCCCCCAAGG
52766478 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
* * * * *
52766511 GGTTGCTAAGTGCTGATCCCACCATATTTTAAATGTGAAGG
1 GGTTGCTAAGTGTTGATTCC-CC-GA--TT-CAT-TG--GT
* *
52766552 GGCTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GG-TTGCTAAGTGTTGATTCCCCGATTCATTGGT
*
52766580 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
52766613 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGTTGATTCC
52766633 ACCATATTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
27 19 0.20
28 2 0.02
29 1 0.01
31 3 0.03
32 2 0.02
33 39 0.40
34 2 0.02
35 1 0.01
37 2 0.02
38 2 0.02
39 2 0.02
41 5 0.05
42 17 0.18
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
Found at i:52766587 original size:27 final size:28
Alignment explanation
Indices: 52766548--52766601 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
52766538 TTTAAATGTG
52766548 AAGGGGCTTGCTAAGTGCTGATTCCCCC
1 AAGGGGCTTGCTAAGTGCTGATTCCCCC
*
52766576 AAGGGG-TTGCTAAGTGTTGATTCCCC
1 AAGGGGCTTGCTAAGTGCTGATTCCCC
52766602 GAATCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.28
Consensus pattern (28 bp):
AAGGGGCTTGCTAAGTGCTGATTCCCCC
Found at i:52770596 original size:11 final size:11
Alignment explanation
Indices: 52770580--52770604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52770570 TGTATAGCGA
52770580 ATTTTAAAAGT
1 ATTTTAAAAGT
52770591 ATTTTAAAAGT
1 ATTTTAAAAGT
52770602 ATT
1 ATT
52770605 ATATTGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTTTAAAAGT
Found at i:52774159 original size:2 final size:2
Alignment explanation
Indices: 52774152--52774177 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52774142 AAACAAGCAA
52774152 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
52774178 CTCTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.