Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_pilon, whole genome shotgun sequence
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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1651847 original size:23 final size:23
Alignment explanation
Indices: 1651795--1651847 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1651785 TTATGTGTAT
*
1651795 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
1651818 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
1651839 TATTATTTA
1 T-TTATTTA
1651848 CTATCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:1651859 original size:76 final size:74
Alignment explanation
Indices: 1651725--1651881 Score: 171
Period size: 74 Copynumber: 2.1 Consensus size: 74
1651715 TTCTAACATC
* *
1651725 TATTTATGTATATTACCTTTTATCATTATTATATATATTATATTTATTGCTTCATTTTCTTTATG
1 TATTTATATATATTACCTTTTATCATTATTATATATATTATATTTATTACTTCATTTTC--TATG
1651790 -TGTATTTTATT
64 CTGTA-TTTATT
* *
1651801 TATTTATATATATTACCTTTT-TTATT-TTATATTTA-TACTA-TTATTTACTATCATTTTTCTA
1 TATTTATATATATTACCTTTTATCATTATTATATATATTA-TATTTA-TTACT-TCA-TTTTCTA
*
1651862 TGCTTTATTTATT
62 TGCTGTATTTATT
1651875 TATTTAT
1 TATTTAT
1651882 TTTATTTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
73 5 0.07
74 31 0.44
75 10 0.14
76 25 0.35
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.63
Consensus pattern (74 bp):
TATTTATATATATTACCTTTTATCATTATTATATATATTATATTTATTACTTCATTTTCTATGCT
GTATTTATT
Found at i:1651874 original size:4 final size:4
Alignment explanation
Indices: 1651865--1651933 Score: 68
Period size: 4 Copynumber: 15.8 Consensus size: 4
1651855 TTTTCTATGC
1651865 TTTA TTTA TTTA TTTA TTTTA TTTA TTT- TGGTTGAA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA T--TT--A TTTA TTTA TTTA
1651913 TTTTA TTTA TTTTA TTTA TTT
1 -TTTA TTTA -TTTA TTTA TTT
1651934 TTTTTATATC
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
3 1 0.02
4 39 0.68
5 14 0.25
6 2 0.04
8 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1651887 original size:9 final size:9
Alignment explanation
Indices: 1651865--1651940 Score: 75
Period size: 9 Copynumber: 8.0 Consensus size: 9
1651855 TTTTCTATGC
1651865 TTTATTTA-
1 TTTATTTAT
1651873 TTTATTTAT
1 TTTATTTAT
1651882 TTTATTTATTT
1 TTTATTTA--T
1651893 TGGTTGAATTTA-
1 T--TT--ATTTAT
1651905 TTTATTTAT
1 TTTATTTAT
1651914 TTTATTTAT
1 TTTATTTAT
1651923 TTTATTTAT
1 TTTATTTAT
*
1651932 TTTTTTTAT
1 TTTATTTAT
1651941 ATCTAACATG
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
8 13 0.22
9 34 0.58
10 2 0.03
11 2 0.03
12 1 0.02
13 2 0.03
15 5 0.08
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1651887 original size:13 final size:13
Alignment explanation
Indices: 1651865--1651940 Score: 77
Period size: 13 Copynumber: 5.8 Consensus size: 13
1651855 TTTTCTATGC
1651865 TTTA-TTTATTTA
1 TTTATTTTATTTA
1651877 TTTATTTTATTTA
1 TTTATTTTATTTA
*
1651890 TTT-TGGTTGAATTTA
1 TTTAT--TT-TATTTA
1651905 TTTA-TTTATTTTA
1 TTTATTTTA-TTTA
1651918 TTTATTTTATTTA
1 TTTATTTTATTTA
*
1651931 TTTTTTTTAT
1 TTTATTTTAT
1651941 ATCTAACATG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
12 6 0.11
13 34 0.63
14 6 0.11
15 8 0.15
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1654323 original size:8 final size:8
Alignment explanation
Indices: 1654310--1654348 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1654300 GAACATTTCA
*
1654310 TGCATTCT
1 TGCATTTT
1654318 TGCA-TTT
1 TGCATTTT
1654325 TGCATTTT
1 TGCATTTT
*
1654333 TGCCTTTT
1 TGCATTTT
1654341 TGCATTTT
1 TGCATTTT
1654349 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1655487 original size:19 final size:20
Alignment explanation
Indices: 1655465--1655521 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
1655455 AACAAAAAGG
1655465 GCAAAAAAAAAGAA-AAGAA
1 GCAAAAAAAAAGAACAAGAA
*
1655484 GCAAAAAAGGAAAAAACAAGAA
1 GCAAAAAA--AAAGAACAAGAA
*
1655506 -CAAAAAAGAAGAACAA
1 GCAAAAAAAAAGAACAA
1655522 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 15 0.47
21 12 0.38
22 5 0.16
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (20 bp):
GCAAAAAAAAAGAACAAGAA
Found at i:1655497 original size:27 final size:27
Alignment explanation
Indices: 1655453--1655505 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1655443 TGATTCAATC
*
1655453 AGAACAAAAAGGGCAAAAAAAAAGAAA
1 AGAACAAAAAAGGCAAAAAAAAAGAAA
*
1655480 AGAAGCAAAAAAGG-AAAAAACAAGAA
1 AGAA-CAAAAAAGGCAAAAAAAAAGAA
1655506 CAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.74, C:0.08, G:0.19, T:0.00
Consensus pattern (27 bp):
AGAACAAAAAAGGCAAAAAAAAAGAAA
Found at i:1655512 original size:13 final size:13
Alignment explanation
Indices: 1655494--1655524 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1655484 GCAAAAAAGG
1655494 AAAAAACAAGAAC
1 AAAAAACAAGAAC
*
1655507 AAAAAAGAAGAAC
1 AAAAAACAAGAAC
1655520 AAAAA
1 AAAAA
1655525 TAAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAGAAC
Found at i:1656164 original size:22 final size:22
Alignment explanation
Indices: 1656134--1656184 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1656124 CCCCATCAAT
*
1656134 CTTTAGAGCATCCAATGTC-AAAC
1 CTTT-GAGCATCAAATG-CGAAAC
1656157 CTTTGAGCATCAAATGCGAAAC
1 CTTTGAGCATCAAATGCGAAAC
1656179 CTTTGA
1 CTTTGA
1656185 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.81
23 4 0.15
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (22 bp):
CTTTGAGCATCAAATGCGAAAC
Found at i:1657163 original size:36 final size:36
Alignment explanation
Indices: 1657113--1657495 Score: 291
Period size: 36 Copynumber: 10.9 Consensus size: 36
1657103 ACTAGAAGAG
1657113 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1657149 TTTTGTCTCC-CTTGAGACAGTTTCTCTTGAAACATAA
1 TTTTGTC-CCTCTTGAGACAGTTTCCCTTGAAACA-AA
* * * *
1657186 -------AC-ATTGAAAACA-TTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTG-AGACAGTTTCCCTTGAAACAAA
* * *
1657214 TTTTCGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
1 TTTT-GTCCCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
1657252 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
1657288 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1657324 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * * *
1657360 ----AT--AT-TT-AAATATGTTTTCTTTGAAACAAA
1 TTTTGTCCCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
1657389 TTTCGTCCCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
1657426 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
1657462 TTTTGTCTCC-CTTGAGACAGTTACTCTTGAAACA
1 TTTTGTC-CCTCTTGAGACAGTTTCCCTTGAAACA
1657496 CAAAATCTTC
Statistics
Matches: 282, Mismatches: 40, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.02
29 33 0.12
30 5 0.02
32 1 0.00
33 1 0.00
36 151 0.54
37 79 0.28
38 7 0.02
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1657304 original size:175 final size:174
Alignment explanation
Indices: 1657113--1657495 Score: 507
Period size: 174 Copynumber: 2.2 Consensus size: 174
1657103 ACTAGAAGAG
* *
1657113 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * * *
1657178 AAACATAAACATTGAAA-ACATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAATTTCCCT
66 AAACA-AAACATTGAAATACATTTCCCTTGAAACAAA-TTTCGTCCCCCTTGAGACAATTTCCCT
*
1657242 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
129 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
1657288 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * ** * * * **
1657353 AAACAAAATATTTAAATATGTTTTCTTTGAAACAAATTTCGTCCCCCTTGAGACAGTTTCTTTTG
66 AAACAAAACATTGAAATACATTTCCCTTGAAACAAATTTCGTCCCCCTTGAGACAATTTCCCTTG
* * * *
1657418 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
131 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
1657462 TTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1657496 CAAAATCTTC
Statistics
Matches: 179, Mismatches: 28, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
174 100 0.56
175 79 0.44
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (174 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
AAACAAAACATTGAAATACATTTCCCTTGAAACAAATTTCGTCCCCCTTGAGACAATTTCCCTTG
AAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1657440 original size:138 final size:138
Alignment explanation
Indices: 1657241--1657495 Score: 377
Period size: 138 Copynumber: 1.8 Consensus size: 138
1657231 ATAATTTCCC
* * *
1657241 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
1 TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
* * * *
1657306 ATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTAAATA
66 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATA
1657371 TGTTTTCT
131 TGTTTTCT
** * *
1657379 TTGAAAC-AAATTTCGTCCCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGA
* *
1657443 CAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
65 CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACA
1657496 CAAAATCTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 26 0.25
138 77 0.75
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TTGAAACAAAATTTCGTCCCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATA
TGTTTTCT
Found at i:1657585 original size:68 final size:66
Alignment explanation
Indices: 1657435--1657598 Score: 163
Period size: 68 Copynumber: 2.4 Consensus size: 66
1657425 GTTTTGTCTC
* *
1657435 TCTTGAGA-CAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAA
1 TCTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCATGAAACACAA
1657499 AA
65 AA
* * ** * *
1657501 TCTTCAAATTTATTTCCCTT-AAGACATAATTTTGTTTCCCTTGAGACCGTT-CTCATGAAACAA
1 TCTTGAGA-TCGTTTCCCTTGAA-ACA-AATTTTGTCTCCCTTGAGACAGTTACTCATGAAAC-A
*
1657564 CAGATA
62 CA-AAA
*
1657570 TCTTGAGATCGTTTCCCTTGAAACGAATT
1 TCTTGAGATCGTTTCCCTTGAAACAAATT
1657599 CTATCTCTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
66 8 0.10
67 23 0.30
68 36 0.47
69 10 0.13
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (66 bp):
TCTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCATGAAACACAAA
A
Found at i:1658563 original size:105 final size:104
Alignment explanation
Indices: 1658205--1658722 Score: 704
Period size: 106 Copynumber: 5.0 Consensus size: 104
1658195 GCACTCGAGG
* * * * * *
1658205 CAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAG
* *
1658270 AGCCAATTTTAACTTCACAACGAAGGATATTGGACTTCAGA
64 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1658311 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGA
1658376 GCCAATTTCAAACTTCACAACGAAGGATATTGGACTCCAGA
65 GCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGA
* *
1658417 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGA
1658482 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1658522 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAA-AA-TT-TC-ATTCAGAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAG
* *
1658583 TCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * **
1658622 CAACACAAGTTCAACTTCACAACGAAGGGA-TGACTGGTTGTCAACAAACAATTTCCCGGTTCCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCCCAATT-CA
* * *
1658686 GAACCAATTTCAACTTCACGACGGAGGATATTGGACT
63 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1658723 TGGAACAATG
Statistics
Matches: 375, Mismatches: 28, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
100 80 0.21
101 4 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 103 0.27
106 177 0.47
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (104 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1659314 original size:34 final size:36
Alignment explanation
Indices: 1659270--1659371 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1659260 TTTCGTCCTA
*
1659270 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
*
1659305 -TAGGATTCAAACTCCTAAAAATATGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
1659340 GCTAGGATTCAAACTCCTAAAAATATGATAGA
1 -CTAGGATTCAAACTCCTAAAAATATGATAGA
1659372 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
Found at i:1659397 original size:37 final size:37
Alignment explanation
Indices: 1659267--1659380 Score: 153
Period size: 37 Copynumber: 3.2 Consensus size: 37
1659257 ATTTTTCGTC
* *
1659267 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
1659304 -T--TAGGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
* * * *
1659338 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
1659375 CTACTA
1 CTACTA
1659381 TTATTTAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 31 0.46
35 1 0.01
36 1 0.01
37 35 0.51
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
Found at i:1659557 original size:11 final size:12
Alignment explanation
Indices: 1659541--1659571 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1659531 AGGTAGCATC
1659541 TTTTTTTTATT-
1 TTTTTTTTATTA
1659552 TTTTTTTTATTA
1 TTTTTTTTATTA
1659564 TTTTTTTT
1 TTTTTTTT
1659572 TTGCATGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTATTA
Found at i:1659564 original size:14 final size:13
Alignment explanation
Indices: 1659541--1659573 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
1659531 AGGTAGCATC
1659541 TTTTTTTTATTTT
1 TTTTTTTTATTTT
1659554 TTTTTTATTATTTT
1 TTTTTT-TTATTTT
1659568 TTTTTT
1 TTTTTT
1659574 GCATGTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTATTTT
Found at i:1660090 original size:23 final size:23
Alignment explanation
Indices: 1660038--1660090 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1660028 TTATGTGTAT
*
1660038 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
1660061 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
1660082 TATTATTTA
1 T-TTATTTA
1660091 CTATCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:1660117 original size:4 final size:4
Alignment explanation
Indices: 1660108--1660172 Score: 60
Period size: 4 Copynumber: 14.8 Consensus size: 4
1660098 TTTTCCATGC
1660108 TTTA TTTA TTTA TTTA TTTTA TTTTA TTTA TTT- TGGTTGAA TTTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA T--TT--A TTTA TTTA
1660157 TTTA TTTA TTTTA TTT
1 TTTA TTTA -TTTA TTT
1660173 TTTTTATATC
Statistics
Matches: 54, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
3 1 0.02
4 35 0.65
5 15 0.28
6 2 0.04
8 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1660141 original size:41 final size:42
Alignment explanation
Indices: 1660096--1660179 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
1660086 ATTTACTATC
*
1660096 ATTTTTCCATG-CTTTATTTATTTATTTATTTTATTTTATTT
1 ATTTTTCCATGAATTTATTTATTTATTTATTTTATTTTATTT
*** *
1660137 A-TTTTGGTTGAATTTATTTATTTATTTATTTTATTTTTTTT
1 ATTTTTCCATGAATTTATTTATTTATTTATTTTATTTTATTT
1660178 AT
1 AT
1660180 ATCTAACATG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 6 0.17
41 30 0.83
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (42 bp):
ATTTTTCCATGAATTTATTTATTTATTTATTTTATTTTATTT
Found at i:1662885 original size:207 final size:199
Alignment explanation
Indices: 1662495--1662902 Score: 478
Period size: 207 Copynumber: 2.0 Consensus size: 199
1662485 TCCCAACTGT
* *
1662495 GTATGTGTGACTTGTGTGTTTTAATATATCAAAAATTAATAAATATTAAAATAATAGTCAATATG
1 GTATGTGTGACTTGTATGTTTTAATATATCAAAAATTAATAAATAATAAAATAATAGTCAATATG
* * * * * * *
1662560 TTGGGTATGTATTAGGGATGGCAAACAAATATACTTTTGCGAATTTCTCAATATATTCGTTTCAA
66 TTGGGTATGTATTAGGGATGGCAAACAAATATAATTTTACGAATTTCGCAACATATCCATTCCAA
* *
1662625 TTGGAACGAGGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAAAAATCATAC
131 TTGGAACGAAGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGT-AAAAAAACCATAC
*
1662690 CCGCC
195 CCACC
* *
1662695 GTATGTGTGACTTGTATGTTTTGATGTATCAAAAAGTAATACATCTTAAAGTAATAAAATAATAG
1 GTATGTGTGACTTGTATGTTTTAATATATCAAAAA-T--TA-A---TAAA-TAATAAAATAATAG
* * * * * * *
1662760 TTAATATGTTGGGTATGTATTA-GGATGGTAGACGAGTATAATTTTACGAATTTCGCACCGTATC
58 TCAATATGTTGGGTATGTATTAGGGATGGCAAACAAATATAATTTTACGAATTTCGCAACATATC
* * * * *
1662824 CATTCCAATTGCG-ATGAAGATGAGTATACGTTTAATGGATAGTGGGCGAGTGTGGATGTAAAAA
123 CATTCCAATTG-GAACGAAGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAA
1662888 AACCATACCCACC
187 AACCATACCCACC
1662901 GT
1 GT
1662903 GGTGGGTAGG
Statistics
Matches: 173, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
200 32 0.18
201 1 0.01
203 2 0.01
204 1 0.01
206 18 0.10
207 84 0.49
208 35 0.20
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (199 bp):
GTATGTGTGACTTGTATGTTTTAATATATCAAAAATTAATAAATAATAAAATAATAGTCAATATG
TTGGGTATGTATTAGGGATGGCAAACAAATATAATTTTACGAATTTCGCAACATATCCATTCCAA
TTGGAACGAAGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAAAACCATACC
CACC
Found at i:1667373 original size:40 final size:41
Alignment explanation
Indices: 1667328--1667731 Score: 193
Period size: 41 Copynumber: 9.9 Consensus size: 41
1667318 GTTTACACTT
1667328 CAAACGCCACAA-A-A-TAGTAACTTTAGCGGCGTTTTTATA
1 CAAACGCCACAACAGAGTAGT-ACTTTAGCGGCGTTTTTATA
* *
1667367 CAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATA
1 C-AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATA
* * ** * *
1667409 CAAACGCCGCAATAG-GT--TCATCCATAGTGGCGTTTTTTAAA
1 CAAACGCCACAACAGAGTAGT-A-CTTTAGCGGCG-TTTTTATA
*** * *
1667450 CAAACGCCGTGACATAGTAGTACTTTAGCGGCGTTTTAATA
1 CAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATA
* * * ** * * * * *
1667491 AAAATGTCGTAATAGGGTTCA-TA-TATTA-TGGCATTTTCA-A
1 CAAACGCCACAACAGAG-T-AGTACT-TTAGCGGCGTTTTTATA
* *
1667531 TAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTTATA
1 CAAACGCCACAACAGAGTAGTACTTTAGCGGCG-TTTTTATA
* * *
1667573 CAAACACCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATA
1 CAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATA
* * * * * * * *
1667614 CAAAAGCCGCTATAGA-CACATACTTTAGTGGCGTTTTTATT
1 CAAACGCCACAACAGAGTA-GTACTTTAGCGGCGTTTTTATA
* * * * * *
1667655 CAAACGCCGCTATA-AATACGTTCTTTAGCGGCATTTTTATA
1 CAAACGCCACAACAGAGTA-GTACTTTAGCGGCGTTTTTATA
* * * * * *
1667696 CAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1 CAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTT
1667732 GTGTTTACAA
Statistics
Matches: 287, Mismatches: 57, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
38 2 0.01
39 8 0.03
40 39 0.14
41 161 0.56
42 70 0.24
43 6 0.02
44 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
CAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATA
Found at i:1667444 original size:82 final size:82
Alignment explanation
Indices: 1667351--1667731 Score: 285
Period size: 82 Copynumber: 4.6 Consensus size: 82
1667341 ATAGTAACTT
1667351 TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGC
1 TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGC
*
1667416 CGCAATAGGTTCATCCA
66 CGCAATAGGTTCATCTA
* * ** * * * * *
1667433 TAGTGGCGTTTTT-TAAACAAACGCCGTGACATAGTAGTACTTTAGCGGCGTTTTAATAAAAATG
1 TAGCGGCGTTTTTATACA-AAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACG
* * *
1667497 TCGTAATAGGGTTCATATA
65 CCGCAATA-GGTTCATCTA
* * * * *
1667516 TTA-TGGCATTTTCA-A-TAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTTATACAAAC
1 -TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCG-TTTTTATACAAAC
* * *
1667578 ACCGCAAAAGAG-T-AGTACTT
64 GCCGCAATAG-GTTCA-T-CTA
* * * * *
1667598 TAGCGGCGTTTTTATACAAAA-GCCGCTATAGA-CACATACTTTAGTGGCGTTTTTATTCAAACG
1 TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTA-GTACTTTAGTGGCGTTTTTATACAAACG
* ** * * *
1667661 CCGCTATAAATACGTTCTT
65 CCGCAATAGGTTC-ATCTA
* * * * *
1667680 TAGCGGCATTTTTATAC-AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1 TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTT
1667732 GTGTTTACAA
Statistics
Matches: 233, Mismatches: 49, Indels: 34
0.74 0.16 0.11
Matches are distributed among these distances:
80 1 0.00
81 40 0.17
82 147 0.63
83 40 0.17
84 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (82 bp):
TAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGC
CGCAATAGGTTCATCTA
Found at i:1667638 original size:41 final size:41
Alignment explanation
Indices: 1667550--1667731 Score: 197
Period size: 41 Copynumber: 4.4 Consensus size: 41
1667540 CAACAGAGTA
* * *
1667550 GTACTTTAGCGGCGTTTTTTATACAAACA-CCGCAAAAGAGTA-
1 GTACTTTAGCGGCG-TTTTTATACAAA-AGCCGCTATAGA-CAC
1667592 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
* * * * * *
1667633 ATACTTTAGTGGCGTTTTTATTCAAACGCCGCTATAAATAC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
* * * *
1667674 GTTCTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
*
1667715 GTACTTTAGTGGCGTTT
1 GTACTTTAGCGGCGTTT
1667732 GTGTTTACAA
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 2 0.02
41 102 0.86
42 14 0.12
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
Found at i:1672590 original size:43 final size:42
Alignment explanation
Indices: 1672401--1672687 Score: 332
Period size: 42 Copynumber: 6.8 Consensus size: 42
1672391 ACGATAATTA
* **
1672401 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTGAAATTTT
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1672444 ACGGCGTTTAT-TCCAAAAACGCCGCTATAAATCTGACCTTTT
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1672486 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1672528 GCGGCGTTTTCAT--AGAAAACGCCGTTATAGATCTCGACCTATT
1 GCGGCGTTTTC-TCCA-AAAACGCCGCTATAGATCT-GACCTTTT
* *
1672571 GCGTCGTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1672613 GCGGCGTTTTCTCCGAAAACGCCGCTATAGAGCTCGA-CTTATT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCT-GACCTT-TT
**
1672656 GCGGCGTTTTCTAAAAAAACGCCGCTATAGAT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGAT
1672688 TTAGACCGAT
Statistics
Matches: 208, Mismatches: 25, Indels: 22
0.82 0.10 0.09
Matches are distributed among these distances:
41 3 0.01
42 131 0.63
43 72 0.35
44 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1672689 original size:85 final size:85
Alignment explanation
Indices: 1672401--1672687 Score: 359
Period size: 85 Copynumber: 3.4 Consensus size: 85
1672391 ACGATAATTA
* * * *
1672401 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTGAAATTTTACGGCGTTTAT-TCCAAAAACG
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTT-TCTCCGAAAACG
*
1672465 CCGCTATAAATCT-GACCTT-TT
64 CCGCTATAGATCTCGA-CTTATT
* *
1672486 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTCAT-AGAAAACGC
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTC-TCCGAAAACGC
* *
1672550 CGTTATAGATCTCGACCTATT
65 CGCTATAGATCTCGACTTATT
* * *
1672571 GCGTCGTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTTGCGGCGTTTTCTCCGAAAACGC
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTCTCCGAAAACGC
*
1672635 CGCTATAGAGCTCGACTTATT
65 CGCTATAGATCTCGACTTATT
**
1672656 GCGGCGTTTTCTAAAAAAACGCCGCTATAGAT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGAT
1672688 TTAGACCGAT
Statistics
Matches: 175, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
83 1 0.01
84 59 0.34
85 114 0.65
86 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (85 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTCTCCGAAAACGCC
GCTATAGATCTCGACTTATT
Found at i:1672700 original size:43 final size:42
Alignment explanation
Indices: 1672401--1672727 Score: 320
Period size: 42 Copynumber: 7.6 Consensus size: 42
1672391 ACGATAATTA
* ** *
1672401 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTGAAATTTT
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCTGACCTATT
* * *
1672444 ACGGCGTTTAT-TCCAAAAACGCCGCTATAAATCTGACCTTTT
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTGACCTATT
* * *
1672486 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACCTATT
*
1672528 GCGGCGTTTTCAT--AGAAAACGCCGTTATAGATCTCGACCTATT
1 GCGGCGTTTTC-TCCA-AAAACGCCGCTATAGATCT-GACCTATT
* * *
1672571 GCGTCGTTTGT-TCCAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTGACCTATT
* * *
1672613 GCGGCGTTTTCTCCGAAAACGCCGCTATAGAGCTCGACTTATT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCT-GACCTATT
** * *
1672656 GCGGCGTTTTCTAAAAAAACGCCGCTATAGATTTAGACCGATT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCT-GACCTATT
* * *
1672699 GCGGCATTTTTTTTCCACAAACGCCGCTA
1 GCGGC--GTTTTCTCCAAAAACGCCGCTA
1672728 ACTTTAGCGA
Statistics
Matches: 236, Mismatches: 36, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
41 3 0.01
42 128 0.54
43 86 0.36
44 2 0.01
45 17 0.07
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACCTATT
Found at i:1682020 original size:28 final size:28
Alignment explanation
Indices: 1681987--1682052 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
1681977 TGTGTCTTTG
*
1681987 TTTCTATTTTGATCAATCAA-TTTTAAAA
1 TTTCTATTTTAATCAATCAACTTTT-AAA
* *
1682015 TTTCTAATTTAATCACTCAACTTTTAAA
1 TTTCTATTTTAATCAATCAACTTTTAAA
1682043 TTTCTATTTT
1 TTTCTATTTT
1682053 TTTTCTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTCTATTTTAATCAATCAACTTTTAAA
Found at i:1682628 original size:29 final size:28
Alignment explanation
Indices: 1682564--1682628 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1682554 TTAAGTTAGT
* *
1682564 GTGTAAATTTGAACTTATAAAATTTCAG
1 GTGTGAATTTAAACTTATAAAATTTCAG
* *
1682592 GGGATGAATTTAAACTTATAAAATTTTGAG
1 GTG-TGAATTTAAACTTATAAAA-TTTCAG
1682622 GTGTGAA
1 GTGTGAA
1682629 AATAGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (28 bp):
GTGTGAATTTAAACTTATAAAATTTCAG
Found at i:1689125 original size:23 final size:23
Alignment explanation
Indices: 1689094--1689150 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1689084 CTACGTGCTA
* *
1689094 GGTATCGATACT-CCCTTTGAATG
1 GGTACCGATACTACCC-TTGAACG
*
1689117 GGTACCGATACTATCCTTGAACG
1 GGTACCGATACTACCCTTGAACG
1689140 GGTACCGATAC
1 GGTACCGATAC
1689151 CCCCCATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
GGTACCGATACTACCCTTGAACG
Found at i:1689657 original size:13 final size:13
Alignment explanation
Indices: 1689632--1689672 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1689622 TGAAAACTAC
1689632 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
1689646 ACATTGTTTTCAA
1 ACATTGTTTTCAA
*
1689659 ACATAGTTTTCAA
1 ACATTGTTTTCAA
1689672 A
1 A
1689673 ATTTTCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:1691790 original size:22 final size:22
Alignment explanation
Indices: 1691749--1691809 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1691739 AGATTGCCCG
1691749 GATGGTACCGGTA-CCCCCTCA
1 GATGGTACCGGTACCCCCCTCA
*
1691770 GATTGTACCGGTACCCCCCTCA
1 GATGGTACCGGTACCCCCCTCA
* *
1691792 GATGGTACTGATACCCCC
1 GATGGTACCGGTACCCCC
1691810 ATGCCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 12 0.34
22 23 0.66
ACGTcount: A:0.20, C:0.38, G:0.21, T:0.21
Consensus pattern (22 bp):
GATGGTACCGGTACCCCCCTCA
Found at i:1692996 original size:124 final size:124
Alignment explanation
Indices: 1692809--1693056 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
1692799 TTTGGTTGTT
1692809 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
1 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
1692874 TTAAAAATATCATGTCAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
66 TTAAAAATATCATGTCAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
1692933 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
1 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
*
1692998 TTAAAAATATCATGTTAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
66 TTAAAAATATCATGTCAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
1693057 ATCAAAACGT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (124 bp):
GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
TTAAAAATATCATGTCAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
Found at i:1694156 original size:2 final size:2
Alignment explanation
Indices: 1694149--1694174 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1694139 TATCAACCGA
1694149 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
1694175 TTAGATTAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1694614 original size:33 final size:32
Alignment explanation
Indices: 1694559--1694632 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
1694549 ATTTATATAT
*
1694559 TTTTTAAATTATTTTACCTTAATATTTAAATTA
1 TTTTTAAATTATTTTACCTTAATA-TGAAATTA
**
1694592 CTTTTTAAATTA-TTTATTTTAATATGAAATTA
1 -TTTTTAAATTATTTTACCTTAATATGAAATTA
1694624 -TTTTAAATT
1 TTTTTAAATT
1694633 TAGTTGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.24
32 7 0.19
33 10 0.27
34 11 0.30
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (32 bp):
TTTTTAAATTATTTTACCTTAATATGAAATTA
Found at i:1694716 original size:33 final size:33
Alignment explanation
Indices: 1694679--1694751 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 33
1694669 TTTTTTTTAG
*
1694679 ATTATATAATATGAA-TTTATAAATTTTATATTT
1 ATTATATAATATAAACTTT-TAAATTTTATATTT
* * * *
1694712 ATTATGTATTATAAACTTTTAACTTTTATGTTT
1 ATTATATAATATAAACTTTTAAATTTTATATTT
*
1694745 TTTATAT
1 ATTATAT
1694752 GAATTTTACT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (33 bp):
ATTATATAATATAAACTTTTAAATTTTATATTT
Found at i:1696455 original size:19 final size:19
Alignment explanation
Indices: 1696433--1696471 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1696423 AAGATTTGCT
1696433 AAAATATAATTATA-TTTAA
1 AAAATATAATT-TAGTTTAA
1696452 AAAATATAATTTAGTTTAA
1 AAAATATAATTTAGTTTAA
1696471 A
1 A
1696472 CTATGATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAATATAATTTAGTTTAA
Found at i:1696708 original size:3 final size:3
Alignment explanation
Indices: 1696700--1696748 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1696690 AATTAATTTT
1696700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1696748 A
1 A
1696749 AAAGAAGGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1698100 original size:26 final size:26
Alignment explanation
Indices: 1698049--1698101 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1698039 CCTTTTTTAT
**
1698049 ATTAGTGATGCATTTCAATGTGTGTC
1 ATTAGTGATGCATTTCAATGAATGTC
*
1698075 ATTAGTGGTGCATTTCAATGAATGTC
1 ATTAGTGATGCATTTCAATGAATGTC
1698101 A
1 A
1698102 CTCATTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTAGTGATGCATTTCAATGAATGTC
Found at i:1699578 original size:17 final size:17
Alignment explanation
Indices: 1699556--1699592 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1699546 TCCAAGTAAC
1699556 TTAGCATAACAGTGTAT
1 TTAGCATAACAGTGTAT
1699573 TTAGCATAACAGTGTAT
1 TTAGCATAACAGTGTAT
1699590 TTA
1 TTA
1699593 TGCGTCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (17 bp):
TTAGCATAACAGTGTAT
Found at i:1702468 original size:17 final size:17
Alignment explanation
Indices: 1702424--1702473 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1702414 TTCAAAATTA
*
1702424 AATATTATTTTTA-AAT
1 AATAATATTTTTACAAT
1702440 AATTACAT-TTTTTACAAT
1 AA-TA-ATATTTTTACAAT
*
1702458 AATAATATTTTCACAA
1 AATAATATTTTTACAA
1702474 CATAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 6 0.21
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATATTTTTACAAT
Found at i:1702583 original size:38 final size:37
Alignment explanation
Indices: 1702540--1702622 Score: 125
Period size: 35 Copynumber: 2.3 Consensus size: 37
1702530 CTACTCAAAT
1702540 TTATTAATATTTTATTAAATTAAACTATTTGTATATTA
1 TTATTAATATTTTA-TAAATTAAACTATTTGTATATTA
* *
1702578 TTATT-AT-GTTTATAAATTAAACTCTTTGTATATTA
1 TTATTAATATTTTATAAATTAAACTATTTGTATATTA
1702613 TTATTAATAT
1 TTATTAATAT
1702623 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
35 27 0.68
36 6 0.15
37 2 0.05
38 5 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (37 bp):
TTATTAATATTTTATAAATTAAACTATTTGTATATTA
Found at i:1707222 original size:45 final size:45
Alignment explanation
Indices: 1707167--1707262 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
1707157 CTTAATAATT
*
1707167 AGTTTATGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
1 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
*
1707212 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCATGA
1 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
1707257 AGTTTC
1 AGTTTC
1707263 GTCCCCTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (45 bp):
AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
Found at i:1709351 original size:194 final size:192
Alignment explanation
Indices: 1709013--1709383 Score: 573
Period size: 194 Copynumber: 1.9 Consensus size: 192
1709003 ATAATTGACT
* * * * * *
1709013 GATATGGCGGAGGTTGACATATCTTTTGGTTACTACATTTCCTGTTACTGAAGCTTCTTTTCTTT
1 GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
1709078 TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
66 TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
* * * *
1709143 CTGACTTTTATGCCTTGTATATTGTAATCTTTAGCTTTTTCCCTTGATTCCTTGAGATGAGACC
131 CCGACTTTTATGCCTTG--TATTGTAATCTTGAGCATCTTCCCTTGATTCCTTGAGATGAGACC
* *
1709207 GATATCGCAGAGGTTGACATCTCCTTTGGTCACTACATTTCCGGTTAGTCAAGCTTCTTTTCTTT
1 GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
* *
1709272 TTTGTTCATATCCATAGTAGATCTTATGTTTCCAG-TTAGTGAAACTCGGTATGTTGATCTTTTG
66 TTTGTTCATATCCATAGTAGATCTTATATTTCC-GTTTAGTGAAACTCGGTATGTCGATCTTTTG
*
1709336 ACCGACTTTTATGCCTTGTATTGTTATCTTGAGCATCTTCCCTTGATT
130 ACCGACTTTTATGCCTTGTATTGTAATCTTGAGCATCTTCCCTTGATT
1709384 GCACCAGTGT
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
192 26 0.16
194 134 0.83
195 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.44
Consensus pattern (192 bp):
GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
CCGACTTTTATGCCTTGTATTGTAATCTTGAGCATCTTCCCTTGATTCCTTGAGATGAGACC
Found at i:1724636 original size:241 final size:241
Alignment explanation
Indices: 1724252--1724709 Score: 721
Period size: 246 Copynumber: 1.9 Consensus size: 241
1724242 CGAGTTCGAG
*
1724252 TTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATT
1 TTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATT
1724317 ACAATAATACCTCCTCTATATATAATTTTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAA
66 ACAATAATACCTCCTC-ATATATAA-TTTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAA
1724382 ATATTTTTTTATTA-TT-TCGGGTCGGGTTTCTAATTCATATATCCGGGTCGGGTCGA-GTGAAA
129 ATATTTTTTTATTATTTGTCGGGTCGGGTTTCTAATTCATATATCCGGGTCGGGT-GAGGTGAAA
1724444 CTTTATTTTGGTCAGGTCGGTTATTTTTAAGTGTGATATTCGGGTCGGA
193 CTTTATTTTGGTCAGGTCGGTTATTTTTAAGTGTGATATTCGGGTCGGA
1724493 TTTAGGGTGAAAAATACCCGACCCGACCAAAAAAATATATAATTTTACCTTATATATTTAGGAAT
1 TTTAGGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTACCTTATATATTTAGGAAT
*
1724558 AATTACAATAATACC-CCTC-TATATAA-TTTTTTTTCAATTAAGTCATTGTTTTTATTGAATAA
62 AATTACAATAATACCTCCTCATATATAATTTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAA
* * *
1724620 AAATAATTTTTTTATTATTTTGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTTAGG
127 AAAT-ATTTTTTTATTA-TTT--GTCGGGTCGGGTTTCTAATTCATATATCCGGGTCGGGTGAGG
*
1724685 TGAAACTTTATTTTGGTCGGGTCGG
188 TGAAACTTTATTTTGGTCAGGTCGG
1724710 GTCTCGGATG
Statistics
Matches: 200, Mismatches: 6, Indels: 17
0.90 0.03 0.08
Matches are distributed among these distances:
240 39 0.19
241 37 0.19
242 7 0.04
243 2 0.01
244 4 0.02
245 51 0.25
246 60 0.30
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (241 bp):
TTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATT
ACAATAATACCTCCTCATATATAATTTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAAT
ATTTTTTTATTATTTGTCGGGTCGGGTTTCTAATTCATATATCCGGGTCGGGTGAGGTGAAACTT
TATTTTGGTCAGGTCGGTTATTTTTAAGTGTGATATTCGGGTCGGA
Found at i:1725064 original size:17 final size:17
Alignment explanation
Indices: 1725042--1725099 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1725032 ATTCCAATCC
* *
1725042 AATTCCTGACATATTTT
1 AATTCCTGACAGATTCT
1725059 AATTCCTGACAGATTCT
1 AATTCCTGACAGATTCT
* *
1725076 AATTCCTTCACAGATTCC
1 AATTCC-TGACAGATTCT
1725094 AATTCC
1 AATTCC
1725100 AGCGAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (17 bp):
AATTCCTGACAGATTCT
Found at i:1735096 original size:13 final size:13
Alignment explanation
Indices: 1735080--1735104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1735070 TTATTACAAG
1735080 ATAATATTTGTTT
1 ATAATATTTGTTT
1735093 ATAATATTTGTT
1 ATAATATTTGTT
1735105 AGTTATTAAT
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:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATAATATTTGTTT
Found at i:1735493 original size:51 final size:52
Alignment explanation
Indices: 1735437--1735548 Score: 119
Period size: 51 Copynumber: 2.2 Consensus size: 52
1735427 TTATAAATTT
1735437 AATATTAATAAAATAT-TTTAAT-ATCATTT-TAATTAAAATATTAATTAT-TAA
1 AATATTAATAAAATATATTTAATAAT-ATTTGTAA-TAAAATATT-ATTATATAA
* *
1735488 AATATT--TAAAATATATTTATTAATATTTGTAATAATATATTATTATAATAA
1 AATATTAATAAAATATATTTAATAATATTTGTAATAAAATATTATTAT-ATAA
1735539 AATACTTAAT
1 AATA-TTAAT
1735549 TATATTATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
49 13 0.25
50 17 0.33
51 18 0.35
52 2 0.04
54 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (52 bp):
AATATTAATAAAATATATTTAATAATATTTGTAATAAAATATTATTATATAA
Found at i:1735530 original size:23 final size:22
Alignment explanation
Indices: 1735469--1735537 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
1735459 ATCATTTTAA
1735469 TTAAAATATTAATTATTAAAATAT
1 TTAAAATA-T-ATTATTAAAATAT
*
1735493 TTAAAATATATTTATTAATAT-T
1 TTAAAATATA-TTATTAAAATAT
*
1735515 TGTAATAATATATTATTATAATA
1 T-TAA-AATATATTATTAAAATA
1735538 AAATACTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.08
23 21 0.55
24 14 0.37
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
TTAAAATATATTATTAAAATAT
Found at i:1735533 original size:26 final size:25
Alignment explanation
Indices: 1735469--1735537 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
1735459 ATCATTTTAA
* *
1735469 TTAAAATAT-TAATTATTAAAATAT
1 TTAAAATATATTATTATTAATATAT
1735493 TTAAAATATA-T-TTATTAATAT-T
1 TTAAAATATATTATTATTAATATAT
1735515 TGTAATAATATATTATTA-TAATA
1 T-TAA-AATATATTATTATTAATA
1735538 AAATACTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 2 0.05
23 12 0.32
24 15 0.39
25 6 0.16
26 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
TTAAAATATATTATTATTAATATAT
Found at i:1735573 original size:23 final size:25
Alignment explanation
Indices: 1735523--1735577 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1735513 TTTGTAATAA
* *
1735523 TATATTATTATAATAAAATACTTAAT
1 TATATTATAATAATAAAAGAC-TAAT
1735549 TATATTATAATAATAAAAGA-T-AT
1 TATATTATAATAATAAAAGACTAAT
1735572 TATATT
1 TATATT
1735578 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
24 1 0.04
26 18 0.67
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TATATTATAATAATAAAAGACTAAT
Found at i:1735686 original size:27 final size:27
Alignment explanation
Indices: 1735640--1735697 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1735630 ATATCATAAA
1735640 AATAATATTATTACATTA-TTAATATT
1 AATAATATTATTACATTATTTAATATT
*
1735666 GAATAATATTATT-TATGTATTTAATATT
1 -AATAATATTATTACAT-TATTTAATATT
1735694 AATA
1 AATA
1735698 TAATAATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 18 0.64
28 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
AATAATATTATTACATTATTTAATATT
Found at i:1737371 original size:2 final size:2
Alignment explanation
Indices: 1737364--1737416 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1737354 TACGAAGATA
1737364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1737405 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1737417 CAAATGATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1739549 original size:17 final size:17
Alignment explanation
Indices: 1739527--1739559 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1739517 TTCAGGCCAC
1739527 TCTAGATATCGACGAAT
1 TCTAGATATCGACGAAT
1739544 TCTAGATATCGACGAA
1 TCTAGATATCGACGAA
1739560 CTCATCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (17 bp):
TCTAGATATCGACGAAT
Found at i:1741076 original size:12 final size:12
Alignment explanation
Indices: 1741045--1741090 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1741035 TACCCACATT
* *
1741045 ATCATCATCAAT
1 ATCATTATCAAC
1741057 ATCATTATCAAC
1 ATCATTATCAAC
* *
1741069 ATCCTTATCTAC
1 ATCATTATCAAC
1741081 ATCATTATCA
1 ATCATTATCA
1741091 TTAATCCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (12 bp):
ATCATTATCAAC
Found at i:1741349 original size:24 final size:24
Alignment explanation
Indices: 1741296--1741350 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1741286 CACCACAACT
* *
1741296 CATATAAAATGCACCGAAGTGCCG
1 CATAGAAAATGCACCGAAGTGCCA
* *
1741320 CGTAGAAAATGCATCGAAGTGCCA
1 CATAGAAAATGCACCGAAGTGCCA
1741344 CATAGAA
1 CATAGAA
1741351 TGTCCCGAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (24 bp):
CATAGAAAATGCACCGAAGTGCCA
Found at i:1741438 original size:23 final size:22
Alignment explanation
Indices: 1741341--1741439 Score: 110
Period size: 23 Copynumber: 4.5 Consensus size: 22
1741331 CATCGAAGTG
1741341 CCACATAGAATGTCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
1741363 CCACATA-CATGTCCTGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
1741384 CCACGTAGAAATGTCCAGAAGGA
1 CCACATAG-AATGTCCCGAAGGA
* *
1741407 CCACGTAGAATTATCCCGAAGGA
1 CCACATAGAA-TGTCCCGAAGGA
*
1741430 CCGCATAGAA
1 CCACATAGAA
1741440 CCCTCGACTC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
21 18 0.28
22 9 0.14
23 38 0.58
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.15
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:1742580 original size:20 final size:20
Alignment explanation
Indices: 1742538--1742584 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1742528 GATAACCCTA
* * *
1742538 GTATCGATATTATTTCTTCG
1 GTATCGATACTACTCCTTCG
*
1742558 GTATCGATACTACTCCTTTG
1 GTATCGATACTACTCCTTCG
1742578 GTATCGA
1 GTATCGA
1742585 CACTTCTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
GTATCGATACTACTCCTTCG
Found at i:1746437 original size:17 final size:18
Alignment explanation
Indices: 1746415--1746453 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1746405 CCACCTATTT
1746415 AATCTCAT-CTCTATCCA-
1 AATCTCATCCT-TATCCAG
1746432 AATCTCATCCTTATCCAG
1 AATCTCATCCTTATCCAG
1746450 AATC
1 AATC
1746454 AGAAAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (18 bp):
AATCTCATCCTTATCCAG
Found at i:1747010 original size:14 final size:14
Alignment explanation
Indices: 1746968--1747012 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1746958 TAGTTTACCT
1746968 TAAAT-TTAAACCC
1 TAAATATTAAACCC
**
1746981 TAAATATTAAGGCC
1 TAAATATTAAACCC
*
1746995 TAAATATTAAATCC
1 TAAATATTAAACCC
1747009 TAAA
1 TAAA
1747013 CCTTAAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (14 bp):
TAAATATTAAACCC
Found at i:1754015 original size:31 final size:32
Alignment explanation
Indices: 1753976--1754062 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
1753966 TACATAACGT
1753976 TTAA-TTTTTGTTTCATTTTAGTAC-TCGTCG
1 TTAACTTTTTGTTTCATTTTAGTACTTCGTCG
* * * *
1754006 TTAACTTTTTATTTCATTTTAATACTTTGTTG
1 TTAACTTTTTGTTTCATTTTAGTACTTCGTCG
*
1754038 TTAACTTTTTGATTCATTTTAGTAC
1 TTAACTTTTTGTTTCATTTTAGTAC
1754063 CTAAATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 4 0.08
31 18 0.38
32 26 0.54
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (32 bp):
TTAACTTTTTGTTTCATTTTAGTACTTCGTCG
Found at i:1756863 original size:36 final size:36
Alignment explanation
Indices: 1756814--1756882 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1756804 TATCTTACCT
*
1756814 CCCCCTTATCCCATTACATATGGGAACAAGGGACAA
1 CCCCCTTACCCCATTACATATGGGAACAAGGGACAA
*
1756850 CCCCCTTACCCCATTACATATGGGAATAAGGGA
1 CCCCCTTACCCCATTACATATGGGAACAAGGGA
1756883 TAACTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (36 bp):
CCCCCTTACCCCATTACATATGGGAACAAGGGACAA
Found at i:1757316 original size:19 final size:19
Alignment explanation
Indices: 1757292--1757330 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1757282 CATCAAACTC
1757292 ATCGTTTGAGTTGGAAGTT
1 ATCGTTTGAGTTGGAAGTT
1757311 ATCGTTTGAGTTGGAAGTT
1 ATCGTTTGAGTTGGAAGTT
1757330 A
1 A
1757331 ACGTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (19 bp):
ATCGTTTGAGTTGGAAGTT
Found at i:1758239 original size:27 final size:29
Alignment explanation
Indices: 1758185--1758239 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
1758175 TTTGTTTTCT
* *
1758185 CCCTTATAATTTTATAAGTTTAAGTTCGC
1 CCCTTATAATTTTATAAGTTCAAATTCGC
1758214 CCCTTAT-A-TTTATAAGTTCAAATTCG
1 CCCTTATAATTTTATAAGTTCAAATTCG
1758240 TCCTCCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 1 0.04
29 7 0.29
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (29 bp):
CCCTTATAATTTTATAAGTTCAAATTCGC
Found at i:1762936 original size:30 final size:30
Alignment explanation
Indices: 1762900--1762982 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
1762890 TGGCTATCAC
1762900 ATCTTAATTAAATAAAAATAAAATTACTAT
1 ATCTTAATTAAATAAAAATAAAATTACTAT
*
1762930 ATCTTAATTAAATAAAAATAAAATTATTAT
1 ATCTTAATTAAATAAAAATAAAATTACTAT
*
1762960 ATCTTAATTAAATAAAAACAAAA
1 ATCTTAATTAAATAAAAATAAAA
1762983 GTAATTATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (30 bp):
ATCTTAATTAAATAAAAATAAAATTACTAT
Found at i:1765139 original size:2 final size:2
Alignment explanation
Indices: 1765132--1765161 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1765122 TGTTATTTTC
1765132 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
1765162 GAACATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1765551 original size:36 final size:36
Alignment explanation
Indices: 1765449--1765551 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1765439 ATTTATCCAT
* * *
1765449 TATCAGCTTTGATACATTCGTTTATCAATGCTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1765485 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1765521 TATCAGCTTTGGTACATTCATGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
1765552 CCAGCATCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1766049 original size:28 final size:28
Alignment explanation
Indices: 1766007--1766067 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
1765997 ATTATCTGAT
*
1766007 ATGTTACAAATGTTAAGTACAAGATGAC
1 ATGTTACAAAGGTTAAGTACAAGATGAC
1766035 ATGTTACAAAGGTTAAGTACAAGATGAC
1 ATGTTACAAAGGTTAAGTACAAGATGAC
1766063 ATGTT
1 ATGTT
1766068 TTAAATGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGTTACAAAGGTTAAGTACAAGATGAC
Found at i:1766103 original size:18 final size:18
Alignment explanation
Indices: 1766080--1766128 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1766070 AAATGGGTTA
1766080 ATGATAATGATAGAT-ATC
1 ATGATAATGAT-GATGATC
*
1766098 ATGATAATGATGTTGATC
1 ATGATAATGATGATGATC
*
1766116 TTGATAATGATGA
1 ATGATAATGATGA
1766129 CATATGTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (18 bp):
ATGATAATGATGATGATC
Found at i:1767183 original size:124 final size:124
Alignment explanation
Indices: 1766958--1767202 Score: 391
Period size: 124 Copynumber: 2.0 Consensus size: 124
1766948 AAGGGTGAAT
1766958 TTGAAGAAGGTTATGTTGTTACAGACATTTAATTAAATGATATGAAGAAAATGTTAGAAAGTTTT
1 TTGAAGAAGGTTATGTTGTTACAGACATTTAATTAAATGATATGAAGAAAATGTTAGAAAGTTTT
* ** *
1767023 CACTGCTCTGAAGTGGAGAAGTTAGATTGAGTAGTTTCGTTACTACGTGGGCAAACTAG
66 CACTACTCCAAAGTGGAGAAGTTAGATTGAGTAGTTTCGTTACTACGTAGGCAAACTAG
* * * * * * *
1767082 TTGAGGAAGGTTCTGTTGTTACAGATATTTGATTAAATGATATGGAGATAATGTTAGAAGGTTTT
1 TTGAAGAAGGTTATGTTGTTACAGACATTTAATTAAATGATATGAAGAAAATGTTAGAAAGTTTT
1767147 CACTACTCCAAAGTGGAGAAGTTAGATTGAGTAGTTTCGTTACTACGTAGGCAAAC
66 CACTACTCCAAAGTGGAGAAGTTAGATTGAGTAGTTTCGTTACTACGTAGGCAAAC
1767203 GAGAGTATGG
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 110 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (124 bp):
TTGAAGAAGGTTATGTTGTTACAGACATTTAATTAAATGATATGAAGAAAATGTTAGAAAGTTTT
CACTACTCCAAAGTGGAGAAGTTAGATTGAGTAGTTTCGTTACTACGTAGGCAAACTAG
Found at i:1772932 original size:36 final size:36
Alignment explanation
Indices: 1772884--1772982 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
1772874 ATTTATTATA
*
1772884 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
1772920 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
* *
1772956 AGCATTGGTATATTCGTGTATCAATGT
1 AGCTTTGGTACATTCGTGTATCAATGT
1772983 CTAGCACCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (36 bp):
AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
Found at i:1773281 original size:28 final size:28
Alignment explanation
Indices: 1773245--1773310 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1773235 AATGTATTAT
* *
1773245 ATGATATGTTACAAATGTTAAGTACAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
1773273 ATGACATGTTACAAAGGTTAAGTACAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
1773301 ATGACATGTT
1 ATGACATGTT
1773311 TTAAATGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGACATGTTACAAAGGTTAAGTACAAG
Found at i:1775437 original size:23 final size:23
Alignment explanation
Indices: 1775411--1775455 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1775401 AATCTTATAT
*
1775411 GGCACTACGGTGCAATTCTATGC
1 GGCACTACAGTGCAATTCTATGC
* *
1775434 GGCACTTCAGTGTAATTCTATG
1 GGCACTACAGTGCAATTCTATG
1775456 TGGTACATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTATGC
Found at i:1780034 original size:16 final size:16
Alignment explanation
Indices: 1780013--1780047 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1780003 ATTGGCTCAC
1780013 GAAGTTAAGAAATTGA
1 GAAGTTAAGAAATTGA
*
1780029 GAAGTTAAGCAATTGA
1 GAAGTTAAGAAATTGA
1780045 GAA
1 GAA
1780048 ATAAAACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GAAGTTAAGAAATTGA
Found at i:1781074 original size:19 final size:20
Alignment explanation
Indices: 1781047--1781100 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1781037 GAATGTCATC
*
1781047 AGTGTATCGATGCA-CAAGT
1 AGTGCATCGATGCATCAAGT
* ***
1781066 AGTGCATCGATACATGGTGT
1 AGTGCATCGATGCATCAAGT
1781086 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
1781101 ACCTTCATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
AGTGCATCGATGCATCAAGT
Found at i:1781768 original size:23 final size:23
Alignment explanation
Indices: 1781703--1781760 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1781693 TTTTATATGA
*
1781703 CACTACGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
*
1781726 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGG
1781749 CACTTCGGTGCA
1 CACTTCGGTGCA
1781761 TTTATACGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:1783145 original size:74 final size:72
Alignment explanation
Indices: 1783036--1783229 Score: 264
Period size: 73 Copynumber: 2.7 Consensus size: 72
1783026 GACACCGTCC
* ** * * *
1783036 GTAAAATAAGTAACTAATTGAAGAAAACACAGATTTCAGAGTGGGCACGAAAAAGTTCAGGGTGG
1 GTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGTTCA---TGC
1783101 AT-ACCATCA
63 ATAACCATCA
* *
1783110 GTAAAATAATTAACTAATTGAAAAAAATTCGGATTTCAGGGTGGGCACGAAAAATTTCATGCATA
1 GTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGTTCATGCATA
1783175 CACCATCA
66 -ACCATCA
*
1783183 GTAAAATAATTAGCTAATTGAAGAAAATTCGGATTTCAGGGTGGGCA
1 GTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCA
1783230 TGCTCAGCCA
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 4 0.04
73 52 0.48
74 52 0.48
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (72 bp):
GTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGTTCATGCATA
ACCATCA
Found at i:1783210 original size:73 final size:74
Alignment explanation
Indices: 1783027--1783229 Score: 268
Period size: 74 Copynumber: 2.8 Consensus size: 74
1783017 ATTTCAGTGG
* * * ** * *
1783027 ACACCGTCCGTAAAATAAGTAACTAATTGAAGAAAACACAGATTTCAGAGTGGGCACGAAAAAGT
1 ACACCATCAGTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGT
*
1783092 TCAGGGTGGAT
66 TCA--GTGCAT
* *
1783103 --ACCATCAGTAAAATAATTAACTAATTGAAAAAAATTCGGATTTCAGGGTGGGCACGAAAAATT
1 ACACCATCAGTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGT
1783166 TCA-TGCAT
66 TCAGTGCAT
*
1783174 ACACCATCAGTAAAATAATTAGCTAATTGAAGAAAATTCGGATTTCAGGGTGGGCA
1 ACACCATCAGTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCA
1783230 TGCTCAGCCA
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
71 4 0.04
73 52 0.46
74 57 0.50
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (74 bp):
ACACCATCAGTAAAATAATTAACTAATTGAAGAAAATTCGGATTTCAGGGTGGGCACGAAAAAGT
TCAGTGCAT
Found at i:1794622 original size:16 final size:16
Alignment explanation
Indices: 1794601--1794633 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1794591 AATTTATGAC
1794601 AGCTTAGAATTAAGAT
1 AGCTTAGAATTAAGAT
1794617 AGCTTAGAATTAAGAT
1 AGCTTAGAATTAAGAT
1794633 A
1 A
1794634 ACGAAGTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AGCTTAGAATTAAGAT
Found at i:1795220 original size:16 final size:17
Alignment explanation
Indices: 1795180--1795226 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
1795170 GTTTATGAGT
1795180 GAATTGAAATCTGTGAAG
1 GAATTGAAATCTGT-AAG
*
1795198 AAATTGAAATCTGT-AG
1 GAATTGAAATCTGTAAG
1795214 GAATTGAAATCTG
1 GAATTGAAATCTG
1795227 AGTCTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.30
Consensus pattern (17 bp):
GAATTGAAATCTGTAAG
Found at i:1819154 original size:15 final size:15
Alignment explanation
Indices: 1819136--1819165 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1819126 CCACGGTGCT
1819136 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1819151 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1819166 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:1823162 original size:22 final size:22
Alignment explanation
Indices: 1823134--1823178 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1823124 TAGACTTATG
1823134 TGGAGTACAAAGTTTGAGAGTT
1 TGGAGTACAAAGTTTGAGAGTT
1823156 TGGAGTACAAAGTTTGAGAGTT
1 TGGAGTACAAAGTTTGAGAGTT
1823178 T
1 T
1823179 CTTGACAACA
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:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (22 bp):
TGGAGTACAAAGTTTGAGAGTT
Found at i:1827925 original size:19 final size:19
Alignment explanation
Indices: 1827887--1827926 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1827877 CGAATGATTG
* *
1827887 AATCGAATATAATATTTTA
1 AATCGAATATAAAATCTTA
1827906 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
1827925 AA
1 AA
1827927 ATTACTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:1839328 original size:17 final size:17
Alignment explanation
Indices: 1839301--1839339 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1839291 AATTTACAAT
1839301 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1839317 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1839334 TAATTA
1 TAATTA
1839340 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1840192 original size:17 final size:17
Alignment explanation
Indices: 1840163--1840211 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
1840153 ATTAAGAGTC
*
1840163 AGTTTAATAAATGAACT
1 AGTTTAATGAATGAACT
*
1840180 AGTTTGATGAATGAACT
1 AGTTTAATGAATGAACT
*
1840197 AGTTTAATTAATGAA
1 AGTTTAATGAATGAA
1840212 ATAACTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (17 bp):
AGTTTAATGAATGAACT
Found at i:1841459 original size:15 final size:15
Alignment explanation
Indices: 1841441--1841489 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
1841431 TAAATTATTC
1841441 AAATATTAAAAAATT
1 AAATATTAAAAAATT
* *
1841456 AAATATATAAAACACT
1 AAATAT-TAAAAAATT
*
1841472 AAATATTAAAATATT
1 AAATATTAAAAAATT
1841487 AAA
1 AAA
1841490 AAGAATGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTAAAAAATT
Found at i:1841483 original size:8 final size:8
Alignment explanation
Indices: 1841431--1841490 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
1841421 ATTTTAGATA
*
1841431 TAAATTAT
1 TAAAATAT
*
1841439 TCAAATAT
1 TAAAATAT
*
1841447 TAAAAAAT
1 TAAAATAT
1841455 T-AAATAT
1 TAAAATAT
* *
1841462 ATAAAACAC
1 -TAAAATAT
1841471 T-AAATAT
1 TAAAATAT
1841478 TAAAATAT
1 TAAAATAT
1841486 TAAAA
1 TAAAA
1841491 AGAATGAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 10 0.25
8 26 0.65
9 4 0.10
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATAT
Found at i:1841491 original size:24 final size:24
Alignment explanation
Indices: 1841456--1841524 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
1841446 TTAAAAAATT
1841456 AAATA-TATAAAACACTAAATATTA
1 AAATATTA-AAAACACTAAATATTA
* * *
1841480 AAATATTAAAAAGAATGAATATT-
1 AAATATTAAAAACACTAAATATTA
* *
1841503 -CATATTAAAAATACTAAA-ATTA
1 AAATATTAAAAACACTAAATATTA
1841525 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
24 17 0.47
25 2 0.06
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (24 bp):
AAATATTAAAAACACTAAATATTA
Found at i:1843876 original size:6 final size:5
Alignment explanation
Indices: 1843860--1843946 Score: 69
Period size: 5 Copynumber: 17.4 Consensus size: 5
1843850 CTAATTTTAA
1843860 AAAAT AAAAT AACAAT AATAA- AAAAT AAAACAT AAAAT AAAA- AATAA-
1 AAAAT AAAAT AA-AAT AA-AAT AAAAT -AAA-AT AAAAT AAAAT AA-AAT
*
1843907 AAAAT AAAA- AATA- AAAAT AAAA- AAAAT AAAAT AAACAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
1843947 GTACAAGGAC
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
4 16 0.23
5 35 0.50
6 17 0.24
7 2 0.03
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1843886 original size:7 final size:7
Alignment explanation
Indices: 1843857--1843941 Score: 92
Period size: 7 Copynumber: 12.6 Consensus size: 7
1843847 AACCTAATTT
1843857 TAAAAAA
1 TAAAAAA
1843864 T--AAAA
1 TAAAAAA
1843869 TAACAATAA
1 TAA-AA-AA
1843878 TAAAAAA
1 TAAAAAA
*
1843885 TAAAACA
1 TAAAAAA
1843892 T--AAAA
1 TAAAAAA
1843897 TAAAAAA
1 TAAAAAA
1843904 TAAAAAA
1 TAAAAAA
1843911 TAAAAAA
1 TAAAAAA
1843918 T-AAAAA
1 TAAAAAA
1843924 TAAAAAA
1 TAAAAAA
1843931 -AATAAAA
1 TAA-AAAA
1843938 TAAA
1 TAAA
1843942 CATAAGTACA
Statistics
Matches: 67, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
5 9 0.13
6 8 0.12
7 39 0.58
8 6 0.09
9 5 0.07
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:1843897 original size:33 final size:31
Alignment explanation
Indices: 1843860--1843940 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 31
1843850 CTAATTTTAA
1843860 AAAATAAAATAACAATAATAAAAAATAAAACAT
1 AAAATAAAATAA-AATAATAAAAAATAAAA-AT
1843893 AAAATAAAAAATAAAA-AATAAAAAATAAAAAT
1 AAAAT--AAAATAAAATAATAAAAAATAAAAAT
1843925 AAAA-AAAATAAAATAA
1 AAAATAAAATAAAATAA
1843941 ACATAAGTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 9 0.20
30 2 0.04
32 6 0.13
33 19 0.42
34 2 0.04
35 7 0.16
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (31 bp):
AAAATAAAATAAAATAATAAAAAATAAAAAT
Found at i:1843946 original size:20 final size:20
Alignment explanation
Indices: 1843860--1843946 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 20
1843850 CTAATTTTAA
1843860 AAAATAAAATAACAATAATAAA-
1 AAAA-AAAATAA-AATAA-AAAT
1843882 AAATAAAACATAAAATAAAAAAT
1 AAA-AAAA-ATAAAAT-AAAAAT
1843905 AAAAAATAA-AAAATAAAAAT
1 AAAAAA-AATAAAATAAAAAT
*
1843925 AAAAAAAATAAAATAAACAT
1 AAAAAAAATAAAATAAAAAT
1843945 AA
1 AA
1843947 GTACAAGGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
19 2 0.03
20 24 0.41
21 5 0.09
22 16 0.28
23 11 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAAATAAAATAAAAAT
Found at i:1847307 original size:27 final size:27
Alignment explanation
Indices: 1847269--1847326 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1847259 GTAAAAATAA
1847269 AAGACATGAACAAATATTATAATCGGT
1 AAGACATGAACAAATATTATAATCGGT
1847296 AAGACATGAACAAATATTATAATCGGT
1 AAGACATGAACAAATATTATAATCGGT
1847323 AAGA
1 AAGA
1847327 AAAGATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (27 bp):
AAGACATGAACAAATATTATAATCGGT
Found at i:1849414 original size:37 final size:37
Alignment explanation
Indices: 1849364--1849437 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1849354 TTCCTTCGGA
1849364 AATGTTTAGTTTCTTTCCGCTTAGCCTCTTTCCCTCT
1 AATGTTTAGTTTCTTTCCGCTTAGCCTCTTTCCCTCT
1849401 AATGTTTAGTTTCTTTCCGCTTAGCCTCTTTCCCTCT
1 AATGTTTAGTTTCTTTCCGCTTAGCCTCTTTCCCTCT
1849438 TCGGAAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.49
Consensus pattern (37 bp):
AATGTTTAGTTTCTTTCCGCTTAGCCTCTTTCCCTCT
Found at i:1854091 original size:64 final size:64
Alignment explanation
Indices: 1853990--1854125 Score: 256
Period size: 64 Copynumber: 2.1 Consensus size: 64
1853980 CCGTTTGGGA
1853990 AGACTCGTCTCCGATGGATATGGCAGTTGCCTCTCCGTCATCCACGATGGGGAAGATCGTTGGT
1 AGACTCGTCTCCGATGGATATGGCAGTTGCCTCTCCGTCATCCACGATGGGGAAGATCGTTGGT
1854054 AGACTCGTCTCCGATGGATATGGCAGTTGCCTCTCCGTCATCCACGATGGGGAAGATCGTTGGT
1 AGACTCGTCTCCGATGGATATGGCAGTTGCCTCTCCGTCATCCACGATGGGGAAGATCGTTGGT
*
1854118 -GTCTCGTC
1 AGACTCGTC
1854126 AGTTACGTCT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 7 0.10
64 64 0.90
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (64 bp):
AGACTCGTCTCCGATGGATATGGCAGTTGCCTCTCCGTCATCCACGATGGGGAAGATCGTTGGT
Found at i:1854126 original size:33 final size:33
Alignment explanation
Indices: 1854025--1854126 Score: 79
Period size: 33 Copynumber: 3.2 Consensus size: 33
1854015 GTTGCCTCTC
*
1854025 CGTCATCCACGATGGGGAAGATCGTTGGTAGACT
1 CGTCATCCACGATGGGGAAGATCGTTGGT-GTCT
** * * **
1854059 CGTC-T-C-CGATGGATATG-GCAGTT-GCCTCT
1 CGTCATCCACGATGGGGAAGATC-GTTGGTGTCT
1854088 CCGTCATCCACGATGGGGAAGATCGTTGGTGTCT
1 -CGTCATCCACGATGGGGAAGATCGTTGGTGTCT
1854122 CGTCA
1 CGTCA
1854127 GTTACGTCTT
Statistics
Matches: 48, Mismatches: 13, Indels: 15
0.63 0.17 0.20
Matches are distributed among these distances:
29 2 0.04
30 6 0.12
31 12 0.25
32 2 0.04
33 17 0.35
34 9 0.19
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (33 bp):
CGTCATCCACGATGGGGAAGATCGTTGGTGTCT
Found at i:1857825 original size:22 final size:22
Alignment explanation
Indices: 1857800--1857888 Score: 99
Period size: 22 Copynumber: 4.0 Consensus size: 22
1857790 ACATTATATA
1857800 TGCACTACGGTGCATTTCTACG
1 TGCACTACGGTGCATTTCTACG
* *
1857822 TGCACTTCGGTGCAATTCTACG
1 TGCACTACGGTGCATTTCTACG
*
1857844 TGGCACTATGG-GCATTTCTACG
1 T-GCACTACGGTGCATTTCTACG
* * *
1857866 CGGCACTTCGGTGCATTTATACG
1 -TGCACTACGGTGCATTTCTACG
1857889 AGCTGTGGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
22 38 0.69
23 17 0.31
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (22 bp):
TGCACTACGGTGCATTTCTACG
Found at i:1862428 original size:4 final size:4
Alignment explanation
Indices: 1862383--1862488 Score: 75
Period size: 4 Copynumber: 27.8 Consensus size: 4
1862373 AGCTCTCTCT
* * * *
1862383 CTCC C-CC CTCT CTCT CTCTC CTAC CTCC C-CC C-CC CTCT CTCC CTCC
1 CTCC CTCC CTCC CTCC CTC-C CTCC CTCC CTCC CTCC CTCC CTCC CTCC
*
1862429 CTCC CTCC CT-- CTCC CTCC CTCC CT-C C-CC CTCC CTCTC TCTCC CTCT
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC
*
1862475 CTCT C-CC CTCC CTC
1 CTCC CTCC CTCC CTC
1862489 TCTCTCCCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
2 2 0.02
3 15 0.18
4 60 0.71
5 4 0.05
6 3 0.04
ACGTcount: A:0.01, C:0.70, G:0.00, T:0.29
Consensus pattern (4 bp):
CTCC
Found at i:1862459 original size:32 final size:32
Alignment explanation
Indices: 1862407--1862555 Score: 119
Period size: 34 Copynumber: 4.5 Consensus size: 32
1862397 TCTCTCCTAC
1862407 CTCCCCCC-CCCTCTCTCCCTCCCTCCCTCCCT
1 CTCCCCCCTCCCTCTC-CCCTCCCTCCCTCCCT
1862439 CTCCCTCCCTCCCTC-CCCCTCCCTCTCTCTCCCT
1 CTCCC-CCCTCCCTCTCCCCTCCCTC-C-CTCCCT
* **
1862473 CTCTCTCCCCTCCCTCT-CTCTCCCTTGTCTCCCT
1 CTC-C-CCCCTCCCTCTCCCCTCCC-TCCCTCCCT
* *
1862507 CTCCCCCTTCTCTCTCTCCCCT--CTCTCTCCCT
1 CTCCCCC--CTCCCTCTCCCCTCCCTCCCTCCCT
*
1862539 CTCCCCCCCTCTCTCTC
1 CT-CCCCCCTCCCTCTC
1862556 TCTATATGAA
Statistics
Matches: 99, Mismatches: 6, Indels: 25
0.76 0.05 0.19
Matches are distributed among these distances:
31 9 0.09
32 27 0.27
33 12 0.12
34 30 0.30
35 19 0.19
36 2 0.02
ACGTcount: A:0.00, C:0.67, G:0.01, T:0.32
Consensus pattern (32 bp):
CTCCCCCCTCCCTCTCCCCTCCCTCCCTCCCT
Found at i:1862468 original size:2 final size:2
Alignment explanation
Indices: 1862461--1862558 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
1862451 CTCCCCCTCC
* * * * *
1862461 CT CT CT CT CC CT CT CT CT C- CC CT CC CT CT CT CT CC CT -T GT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * *
1862501 CT CC CT CT CC CC CT -T CT CT CT CT C- CC CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
1862541 CC CC CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
1862559 ATATGAAAGT
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
1 4 0.05
2 71 0.95
ACGTcount: A:0.00, C:0.61, G:0.01, T:0.38
Consensus pattern (2 bp):
CT
Found at i:1862535 original size:94 final size:90
Alignment explanation
Indices: 1862377--1862558 Score: 210
Period size: 94 Copynumber: 2.0 Consensus size: 90
1862367 GGCTAAAGCT
1862377 CTCTCTCTCCCCCCTCTCTCTCTCTCCTACCTCCCCCCCCCTCTCTCCCTCCCTCCCTCCCTCTC
1 CTCTCTCTCCCCCCTCTCTCTCTCTCCTACCTCCCCCCCCCTCTCTCCCTCCCTCCCTCCCTCTC
1862442 CCTCCCTCCCTCCCCCTCCCTCTCTCTCC
66 CCT--CT-CC-CCCCCTCCCTCTCTCTCC
** * * *
1862471 CTCTCTCTCCCCTCC-CTCTCTCTC-CCTTGTCTCCCTCTCCCCCT-TCTCTCTCTC-CCCTCTC
1 CTCTCTCTCCCC-CCTCTCTCTCTCTCC-TACCTCCC-C-CCCCCTCTCTCCCTCCCTCCCTCCC
*
1862532 TCTCCCTCTCCCCCCCTCTCTCTCTCT
62 TCTCCCTCTCCCCCCCTCCCTCTCTCT
1862559 ATATGAAAGT
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
90 15 0.19
91 2 0.03
92 2 0.03
93 2 0.03
94 40 0.51
95 11 0.14
96 6 0.08
ACGTcount: A:0.01, C:0.65, G:0.01, T:0.34
Consensus pattern (90 bp):
CTCTCTCTCCCCCCTCTCTCTCTCTCCTACCTCCCCCCCCCTCTCTCCCTCCCTCCCTCCCTCTC
CCTCTCCCCCCCTCCCTCTCTCTCC
Found at i:1862558 original size:26 final size:25
Alignment explanation
Indices: 1862381--1862557 Score: 127
Period size: 25 Copynumber: 6.8 Consensus size: 25
1862371 AAAGCTCTCT
*
1862381 CTCTCCCCCCTCTCTCTCTCTCCTAC
1 CTCTCCCCCC-CTCTCTCTCTCCTCC
1862407 CTC-CCCCCCC-CTCTCTC-CCT-C
1 CTCTCCCCCCCTCTCTCTCTCCTCC
* *
1862428 C-CTCCCTCCCTCTCCCTC-CCTCC
1 CTCTCCCCCCCTCTCTCTCTCCTCC
*
1862451 CTC-CCCCTCCCTCTCTCTC-CCTCT
1 CTCTCCCC-CCCTCTCTCTCTCCTCC
*
1862475 CTCTCCCCTCCCTCTCTCTCCCTTGTCTCC
1 CTCTCCCC-CCCTCTCTCT--C-T-CCTCC
1862505 CTCTCCCCCTTCTCTCTCTCCCCTCTCTCTCC
1 CTCTCCCCC--C-CTCTCT---CTCTC-CTCC
1862537 CTCTCCCCCCCTCTCTCTCTC
1 CTCTCCCCCCCTCTCTCTCTC
1862558 TATATGAAAG
Statistics
Matches: 125, Mismatches: 8, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.01
21 8 0.06
22 12 0.10
23 12 0.10
24 19 0.15
25 21 0.17
26 8 0.06
27 1 0.01
29 7 0.06
30 12 0.10
31 1 0.01
32 20 0.16
33 1 0.01
35 2 0.02
ACGTcount: A:0.01, C:0.66, G:0.01, T:0.33
Consensus pattern (25 bp):
CTCTCCCCCCCTCTCTCTCTCCTCC
Found at i:1862620 original size:2 final size:2
Alignment explanation
Indices: 1862613--1862664 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1862603 GCACATACTC
1862613 AT AT AT 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 AT AT AT
1862655 AT AT AT AT AT
1 AT AT AT AT AT
1862665 TTCAAAAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1864179 original size:2 final size:2
Alignment explanation
Indices: 1864172--1864230 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1864162 TGATCTTGTC
1864172 AT AT AT 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 AT AT AT
1864214 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1864231 CATGTAGTGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1864658 original size:29 final size:29
Alignment explanation
Indices: 1864567--1864653 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 29
1864557 AAAATATTTT
*
1864567 TTTGAAAGTTAGAGTGATTAAATTAGAAGTGA
1 TTTGAAAGTTA-AGT-ATTAAATTA-AAGTAA
*
1864599 TTTGAAAGTGAAG-ATTAAATTAAGAGTAA
1 TTTGAAAGTTAAGTATTAAATTAA-AGTAA
1864628 TTTGAAAGTTAAGTAATTAAATTAAA
1 TTTGAAAGTTAAGT-ATTAAATTAAA
1864654 AAATTAAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.02
29 25 0.51
30 1 0.02
31 12 0.24
32 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (29 bp):
TTTGAAAGTTAAGTATTAAATTAAAGTAA
Found at i:1867016 original size:21 final size:21
Alignment explanation
Indices: 1866976--1867030 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1866966 GATTCTTGAC
1866976 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
1866996 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
1867018 AATCGCAACGCGA
1 AATCGCAATGCGA
1867031 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:1867132 original size:20 final size:20
Alignment explanation
Indices: 1867018--1867266 Score: 227
Period size: 20 Copynumber: 12.4 Consensus size: 20
1867008 GATTTTACAG
* ** *
1867018 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1867038 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
1867058 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1867078 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1867098 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1867118 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1867138 AATCGCAATGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1867158 TATTGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1867178 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1867198 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1867218 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1867238 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1867258 AATCACAAC
1 AATCGCAAC
1867267 ACTGAAATTT
Statistics
Matches: 194, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 190 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1867984 original size:24 final size:24
Alignment explanation
Indices: 1867957--1868003 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1867947 AAATTTGGTC
1867957 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
* *
1867981 TTGGTTAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
1868004 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:1868195 original size:12 final size:12
Alignment explanation
Indices: 1868178--1868202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1868168 ATATAATCCT
1868178 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1868190 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1868202 G
1 G
1868203 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1870532 original size:33 final size:33
Alignment explanation
Indices: 1870482--1870731 Score: 184
Period size: 33 Copynumber: 7.2 Consensus size: 33
1870472 CGGAAATTAC
* *
1870482 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACAAGAAAATCGCAATGCGAAATGAAA
*
1870515 ATCCCAACAAGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAACAAGAAAATCGCAATGC-GAAATGAAA
* * *
1870549 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CA
1 ATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAAA
* *
1870588 ATGCGGAA-ATGAAAATCGCAATGCGAAATGAAA
1 AT-CGCAACAAGAAAATCGCAATGCGAAATGAAA
* *
1870621 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACAAGAAAATCGCAATGCGAAATGAAA
* * *
1870654 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CA
1 ATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAAA
* *
1870693 ATGCGGAA-ATGAAAATCGCAATGCGAAATGAAA
1 AT-CGCAACAAGAAAATCGCAATGCGAAATGAAA
1870726 ATCGCA
1 ATCGCA
1870732 TTGCGATTCT
Statistics
Matches: 170, Mismatches: 27, Indels: 41
0.71 0.11 0.17
Matches are distributed among these distances:
32 9 0.05
33 62 0.36
34 43 0.25
35 3 0.02
36 1 0.01
37 1 0.01
38 17 0.10
39 24 0.14
40 10 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAACAAGAAAATCGCAATGCGAAATGAAA
Found at i:1870558 original size:53 final size:53
Alignment explanation
Indices: 1870495--1870731 Score: 440
Period size: 53 Copynumber: 4.5 Consensus size: 53
1870485 GCAACGAGAG
* * *
1870495 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1870548 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1870601 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1870653 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1870706 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1870732 TTGCGATTCT
Statistics
Matches: 180, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
52 52 0.29
53 128 0.71
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:1870564 original size:19 final size:19
Alignment explanation
Indices: 1870495--1870737 Score: 274
Period size: 19 Copynumber: 13.7 Consensus size: 19
1870485 GCAACGAGAG
1870495 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1870514 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
1870528 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1870548 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1870567 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1870581 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1870601 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1870620 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1870634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1870653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1870672 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1870686 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1870706 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1870725 AATCGCATTGCGA
1 AATCGCAATGCGA
1870738 TTCTCTCGTT
Statistics
Matches: 192, Mismatches: 9, Indels: 46
0.78 0.04 0.19
Matches are distributed among these distances:
14 40 0.21
15 5 0.03
16 5 0.03
17 9 0.05
18 1 0.01
19 92 0.48
20 40 0.21
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1870638 original size:86 final size:84
Alignment explanation
Indices: 1870482--1870660 Score: 240
Period size: 86 Copynumber: 2.1 Consensus size: 84
1870472 CGGAAATTAC
1870482 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAA-GCGG-AATGA
1870547 AAATCGCAATGCGAAATGAAA
64 AAATCGCAATGCGAAATGAAA
*
1870568 ATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G-
1 ATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAAGCGGA
*
1870630 A-GAGAATCGCAATGCGAAATGAAA
60 ATGAAAATCGCAATGCGAAATGAAA
1870654 ATCGCAA
1 ATCGCAA
1870661 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
91 2 0.02
92 11 0.13
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (84 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAAGCGGAATGAAA
ATCGCAATGCGAAATGAAA
Found at i:1870671 original size:105 final size:106
Alignment explanation
Indices: 1870495--1870731 Score: 440
Period size: 105 Copynumber: 2.2 Consensus size: 106
1870485 GCAACGAGAG
*
1870495 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1870560 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* *
1870601 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1870665 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1870706 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1870732 TTGCGATTCT
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 87 0.68
106 41 0.32
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:1870771 original size:53 final size:52
Alignment explanation
Indices: 1870708--1870823 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
1870698 GAAATGAAAA
* *
1870708 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
** ** **
1870760 TCCGCATTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
1870813 TCGCATTGCGA
1 TCGCATTGCGA
1870824 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTACGATTCTCTCGTTGCGATTTTCATT
Found at i:1870786 original size:19 final size:19
Alignment explanation
Indices: 1870746--1870833 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1870736 GATTCTCTCG
1870746 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1870766 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1870785 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1870799 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1870818 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1870834 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.08
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1870943 original size:14 final size:14
Alignment explanation
Indices: 1870924--1870960 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1870914 CATCAATTAC
1870924 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1870938 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1870952 ACAAATCAA
1 ACAAATCAA
1870961 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1872915 original size:19 final size:19
Alignment explanation
Indices: 1872873--1873026 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
1872863 TAGTTTACTT
* *
1872873 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1872893 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1872912 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1872931 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1872950 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1872964 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1872983 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
1872997 TTGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1873016 TCGCAATGCGA
1 TCGCAACGCGA
1873027 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 62 0.58
20 12 0.11
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Done.