Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001478.1 Hibiscus syriacus cultivar Beakdansim tig00002868_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: 623040
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 5
Found at i:528985 original size:26 final size:27
Alignment explanation
Indices: 528922--528987 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
528912 AATAGATTGT
* *
528922 ATATATAC-GTATACTATAGGTTATAT
1 ATATATACACTATACTATAGGTTATAC
* *
528948 ATATATATACTATAC-ATAGTTTATAC
1 ATATATACACTATACTATAGGTTATAC
*
528974 ATATATGCACTATA
1 ATATATACACTATA
528988 AGTTACATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 28 0.85
27 5 0.15
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (27 bp):
ATATATACACTATACTATAGGTTATAC
Found at i:529247 original size:48 final size:48
Alignment explanation
Indices: 529192--529306 Score: 221
Period size: 48 Copynumber: 2.4 Consensus size: 48
529182 AAGGTTTAGG
529192 ATTTCTATAAACTATATACTTTATTACTTTATATAATTTATGCATAGT
1 ATTTCTATAAACTATATACTTTATTACTTTATATAATTTATGCATAGT
*
529240 ATTTCTATAAACTATATACTTTATTACTTTATATAGTTTATGCATAGT
1 ATTTCTATAAACTATATACTTTATTACTTTATATAATTTATGCATAGT
529288 ATTTCTATAAACTATATAC
1 ATTTCTATAAACTATATAC
529307 ATATATAAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (48 bp):
ATTTCTATAAACTATATACTTTATTACTTTATATAATTTATGCATAGT
Found at i:529481 original size:15 final size:14
Alignment explanation
Indices: 529436--529481 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
529426 AAAATATAAA
529436 TATTATATTATTAT
1 TATTATATTATTAT
*
529450 ATATTATATTATGAT
1 -TATTATATTATTAT
*
529465 TATTAGTATTGTTAT
1 TATTA-TATTATTAT
529480 TA
1 TA
529482 ATAATATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:530229 original size:12 final size:12
Alignment explanation
Indices: 530208--530242 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
530198 CAGCCGTACG
530208 CCGCCGTTGGAC
1 CCGCCGTTGGAC
*
530220 CCGTCGTTGGAC
1 CCGCCGTTGGAC
530232 CCGCCGTTGGA
1 CCGCCGTTGGA
530243 GCCTCCGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.37, G:0.34, T:0.20
Consensus pattern (12 bp):
CCGCCGTTGGAC
Found at i:531848 original size:2 final size:2
Alignment explanation
Indices: 531841--531874 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
531831 TTATTCATTA
531841 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
531875 TATTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535797 original size:8 final size:8
Alignment explanation
Indices: 535781--535888 Score: 101
Period size: 8 Copynumber: 12.8 Consensus size: 8
535771 TCCATCAGAA
535781 AAAAAATG
1 AAAAAATG
*
535789 AAAAGATG
1 AAAAAATG
*
535797 AAAAAAATC
1 -AAAAAATG
*
535806 AAAAAATA
1 AAAAAATG
*
535814 AAAAAATA
1 AAAAAATG
535822 AAAAAATG
1 AAAAAATG
535830 AAAAAAATG
1 -AAAAAATG
535839 AAAAAAATG
1 -AAAAAATG
*
535848 AAAAAAAATA
1 --AAAAAATG
535858 AAAAAATG
1 AAAAAATG
535866 AAAATAAATG
1 -AAA-AAATG
535876 AAAAAA-G
1 AAAAAATG
535883 AAAAAA
1 AAAAAA
535889 AAAGAAAAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.08
8 39 0.44
9 29 0.33
10 13 0.15
ACGTcount: A:0.80, C:0.01, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:535801 original size:18 final size:18
Alignment explanation
Indices: 535778--535898 Score: 144
Period size: 17 Copynumber: 6.9 Consensus size: 18
535768 TCATCCATCA
*
535778 GAAAAAAAATGAAAAGAT
1 GAAAAAAAATGAAAAAAT
*
535796 G-AAAAAAATCAAAAAAT
1 GAAAAAAAATGAAAAAAT
*
535813 --AAAAAAATAAAAAAAT
1 GAAAAAAAATGAAAAAAT
535829 G-AAAAAAATGAAAAAAAT
1 GAAAAAAAATG-AAAAAAT
*
535847 GAAAAAAAATAAAAAAAT
1 GAAAAAAAATGAAAAAAT
*
535865 GAAAATAAATGAAAAAA-
1 GAAAAAAAATGAAAAAAT
*
535882 GAAAAAAAAAGAAAAAA
1 GAAAAAAAATGAAAAAA
535899 AAAGAAAAGA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
16 15 0.16
17 37 0.41
18 31 0.34
19 8 0.09
ACGTcount: A:0.80, C:0.01, G:0.09, T:0.10
Consensus pattern (18 bp):
GAAAAAAAATGAAAAAAT
Found at i:535802 original size:10 final size:9
Alignment explanation
Indices: 535780--535899 Score: 137
Period size: 9 Copynumber: 13.8 Consensus size: 9
535770 ATCCATCAGA
535780 AAAAAAATG
1 AAAAAAATG
*
535789 -AAAAGATG
1 AAAAAAATG
535797 AAAAAAAT-
1 AAAAAAATG
*
535805 CAAAAAAT-
1 AAAAAAATG
535813 AAAAAAAT-
1 AAAAAAATG
535821 AAAAAAATG
1 AAAAAAATG
535830 AAAAAAATG
1 AAAAAAATG
535839 AAAAAAATG
1 AAAAAAATG
535848 AAAAAAAAT-
1 -AAAAAAATG
535857 AAAAAAATG
1 AAAAAAATG
535866 AAAATAAATG
1 AAAA-AAATG
535876 -AAAAAA-G
1 AAAAAAATG
*
535883 AAAAAAAAAG
1 -AAAAAAATG
535893 AAAAAAA
1 AAAAAAA
535900 AAGAAAAGAA
Statistics
Matches: 99, Mismatches: 4, Indels: 16
0.83 0.03 0.13
Matches are distributed among these distances:
7 1 0.01
8 40 0.40
9 44 0.44
10 14 0.14
ACGTcount: A:0.81, C:0.01, G:0.08, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:535889 original size:8 final size:8
Alignment explanation
Indices: 535780--535910 Score: 93
Period size: 8 Copynumber: 15.4 Consensus size: 8
535770 ATCCATCAGA
535780 AAAAAAATG
1 AAAAAAA-G
* *
535789 AAAAGATG
1 AAAAAAAG
*
535797 AAAAAAAT
1 AAAAAAAG
* *
535805 CAAAAAAT
1 AAAAAAAG
*
535813 AAAAAAAT
1 AAAAAAAG
535821 AAAAAAATG
1 AAAAAAA-G
535830 AAAAAAATG
1 AAAAAAA-G
535839 AAAAAAATG
1 AAAAAAA-G
*
535848 AAAAAAAAT
1 -AAAAAAAG
535857 AAAAAAATG
1 AAAAAAA-G
535866 AAAATAAATG
1 AAAA-AAA-G
*
535876 AAAAAAGAA
1 AAAAAA-AG
535885 AAAAAAAG
1 AAAAAAAG
535893 AAAAAAA-
1 AAAAAAAG
*
535900 AAGAAAAG
1 AAAAAAAG
535908 AAA
1 AAA
535911 TTGAATCAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
7 6 0.06
8 44 0.43
9 35 0.34
10 17 0.17
ACGTcount: A:0.81, C:0.01, G:0.09, T:0.09
Consensus pattern (8 bp):
AAAAAAAG
Found at i:535900 original size:10 final size:10
Alignment explanation
Indices: 535807--535906 Score: 69
Period size: 10 Copynumber: 9.4 Consensus size: 10
535797 AAAAAAATCA
*
535807 AAAAATAAAAA
1 AAAAA-AAAAG
535818 AATAAAAAAATG
1 AA-AAAAAAA-G
*
535830 -AAAAAAATG
1 AAAAAAAAAG
*
535839 -AAAAAAATG
1 AAAAAAAAAG
*
535848 AAAAAAAATAA
1 AAAAAAAA-AG
*
535859 AAAAATGAAAAT
1 AAAAA--AAAAG
535871 AAATGAAAAAAG
1 AAA--AAAAAAG
535883 AAAAAAAAAG
1 AAAAAAAAAG
535893 AAAAAAAAAG
1 AAAAAAAAAG
535903 AAAA
1 AAAA
535907 GAAATTGAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
9 10 0.13
10 34 0.45
11 12 0.16
12 14 0.19
13 3 0.04
14 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.09
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:537455 original size:28 final size:27
Alignment explanation
Indices: 537416--537497 Score: 119
Period size: 28 Copynumber: 3.0 Consensus size: 27
537406 TATCCATGTG
*
537416 GGGCATTTTGAAGGCTCACATCAGCAT
1 GGGCATTTTGAAGGCTCATATCAGCAT
* *
537443 GGGCCATCTTGAAGGCTCATATCACCAT
1 GGG-CATTTTGAAGGCTCATATCAGCAT
537471 GGTGCATTTTGAAGGCTCATATCAGCA
1 GG-GCATTTTGAAGGCTCATATCAGCA
537498 AGAAACAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 3 0.06
28 44 0.92
29 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (27 bp):
GGGCATTTTGAAGGCTCATATCAGCAT
Found at i:538799 original size:40 final size:40
Alignment explanation
Indices: 538747--539031 Score: 405
Period size: 40 Copynumber: 7.1 Consensus size: 40
538737 ATACTGAGGA
* * *
538747 TTTATCTCATTCAATATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
*
538787 TTTATTTCATTCAAGATTGTTTTTCCTTGAAATAAAAGAT
1 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
*
538827 TTTATTTCATTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
* *
538867 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
538907 TTTATTTCATTCAAGATTGTTTTTTCCTTGAAACAAAAGAT
1 TTTATTTCATTCAAGATTG-TTTTTCCTTGAAACAAAAGAT
* *
538948 TTTATTTCGTTCAAGATTGTTTTTCCTTGAAACAAAATAT
1 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
* * * *
538988 TTTATCTCTC-TT-GAGATAG-TTTCCCTTGAAACAAAATAT
1 TTTAT-T-TCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
539027 TTTAT
1 TTTAT
539032 CTCGCTTGAG
Statistics
Matches: 226, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 24 0.11
40 159 0.70
41 41 0.18
42 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (40 bp):
TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
Found at i:538914 original size:23 final size:23
Alignment explanation
Indices: 538762--538983 Score: 73
Period size: 17 Copynumber: 11.0 Consensus size: 23
538752 CTCATTCAAT
538762 ATTGTT-TTTCCTTGAAACAGAAG
1 ATTGTTATTTCCTTGAAACA-AAG
*
538785 ATT-TTATTTCATT----C-AAG
1 ATTGTTATTTCCTTGAAACAAAG
*
538802 ATTGTT-TTTCCTTGAAATAAAAG
1 ATTGTTATTTCCTTGAAA-CAAAG
*
538825 ATT-TTATTTCATT----C-AAG
1 ATTGTTATTTCCTTGAAACAAAG
*
538842 ATTGTT-TTTCCTTAAAACAAAAG
1 ATTGTTATTTCCTTGAAAC-AAAG
* *
538865 ATT-TTATCTCATT----C-AAG
1 ATTGTTATTTCCTTGAAACAAAG
538882 ATTGTT-TTTCCTTGAAACAGAAG
1 ATTGTTATTTCCTTGAAACA-AAG
*
538905 ATT-TTATTTCATT----C-AAG
1 ATTGTTATTTCCTTGAAACAAAG
*
538922 ATTGTTTTTTCCTTGAAACAAAAG
1 ATTGTTATTTCCTTGAAAC-AAAG
*
538946 ATT-TTATTTCGTT----C-AAG
1 ATTGTTATTTCCTTGAAACAAAG
538963 ATTGTT-TTTCCTTGAAACAAA
1 ATTGTTATTTCCTTGAAACAAA
538984 ATATTTTATC
Statistics
Matches: 145, Mismatches: 16, Indels: 77
0.61 0.07 0.32
Matches are distributed among these distances:
17 53 0.37
18 16 0.11
19 4 0.03
21 3 0.02
22 11 0.08
23 52 0.36
24 6 0.04
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (23 bp):
ATTGTTATTTCCTTGAAACAAAG
Found at i:539024 original size:39 final size:39
Alignment explanation
Indices: 538932--539096 Score: 160
Period size: 39 Copynumber: 4.3 Consensus size: 39
538922 ATTGTTTTTT
* * * *
538932 CCTTGAAACAAAAGATTTTAT-T-TCGTTCAAGATTGTTTTT
1 CCTTGAAACAAAATATTTTATCTCTC-TT-GAGATAG-TTTC
538972 CCTTGAAACAAAATATTTTATCTCTCTTGAGATAGTTTC
1 CCTTGAAACAAAATATTTTATCTCTCTTGAGATAGTTTC
*
539011 CCTTGAAACAAAATATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAACAAAATATTTTATCTCTCTTGAGATAGTTTC
* * * * **
539050 TCTCGAAAC--AA-ATTTTGTCTCCCTTGAGACGGTTTC
1 CCTTGAAACAAAATATTTTATCTCTCTTGAGATAGTTTC
*
539086 CCATGAAACAA
1 CCTTGAAACAA
539097 GTTTTGTCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
36 27 0.25
37 2 0.02
39 48 0.45
40 25 0.23
41 3 0.03
42 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (39 bp):
CCTTGAAACAAAATATTTTATCTCTCTTGAGATAGTTTC
Found at i:539076 original size:36 final size:35
Alignment explanation
Indices: 538986--539124 Score: 134
Period size: 36 Copynumber: 3.8 Consensus size: 35
538976 GAAACAAAAT
*
538986 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 ATTTTATCTCCCTTGAGATAGTTTCCC-TGAAAC--AA
* *
539024 TATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAA
1 -ATTTTATCTCCCTTGAGATAGTTTCCCT-GAAACAA
* **
539061 ATTTTGTCTCCCTTGAGACGGTTTCCCATGAAACAA
1 ATTTTATCTCCCTTGAGATAGTTTCCC-TGAAACAA
* * * *
539097 GTTTTGTCTCCCTTGAGACAATTTCCCT
1 ATTTTATCTCCCTTGAGATAGTTTCCCT
539125 TGAGACAGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.01
36 53 0.60
37 3 0.03
38 1 0.01
39 30 0.34
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (35 bp):
ATTTTATCTCCCTTGAGATAGTTTCCCTGAAACAA
Found at i:539124 original size:51 final size:51
Alignment explanation
Indices: 539067--539199 Score: 203
Period size: 51 Copynumber: 2.6 Consensus size: 51
539057 ACAAATTTTG
* * *
539067 TCTCCCTTGAGACGGTTTCCCATGAAACAAGTTTTGTCTCCCTTGAGACAA
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
* * *
539118 TTTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCCCTTGAGACAG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
*
539169 TCTCCCTTGAGATAGTTTCCCTTGAAACAAA
1 TCTCCCTTGAGACAGTTTCCCTTGAAACAAA
539200 AGATTTTATC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (51 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAA
Found at i:539125 original size:15 final size:15
Alignment explanation
Indices: 539105--539198 Score: 71
Period size: 15 Copynumber: 5.9 Consensus size: 15
539095 AAGTTTTGTC
539105 TCCCTTGAGACAATT
1 TCCCTTGAGACAATT
*
539120 TCCCTTGAGACAGTT
1 TCCCTTGAGACAATT
*
539135 TCCCTTGAAACAAATTTTTT
1 TCCCTTGAGAC-AA----TT
* *
539155 CTCCCTTGAGACAGTC
1 -TCCCTTGAGACAATT
* *
539171 TCCCTTGAGATAGTT
1 TCCCTTGAGACAATT
*
539186 TCCCTTGAAACAA
1 TCCCTTGAGACAA
539199 AAGATTTTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
15 47 0.76
16 2 0.03
20 3 0.05
21 10 0.16
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.34
Consensus pattern (15 bp):
TCCCTTGAGACAATT
Found at i:539284 original size:39 final size:39
Alignment explanation
Indices: 539169--539275 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
539159 CTTGAGACAG
* *
539169 TCTCCCTTGAGATAGTTTCCCTTGAAACAAAAGATTTTA
1 TCTCGCTTGAGATAGTTTCACTTGAAACAAAAGATTTTA
* * *
539208 TCTCGCTTGAGATTGTTTCACTTGAAAGAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTCACTTGAAACAAAAGATTTTA
* *
539247 TCTCGCTTGAGATAGTTTCGCATGAAACA
1 TCTCGCTTGAGATAGTTTCACTTGAAACA
539276 CCATATTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (39 bp):
TCTCGCTTGAGATAGTTTCACTTGAAACAAAAGATTTTA
Found at i:539433 original size:43 final size:43
Alignment explanation
Indices: 539312--539926 Score: 493
Period size: 43 Copynumber: 13.5 Consensus size: 43
539302 TTTCAGGTGT
* * *
539312 TTCTTTGATGAAAAGCTTGAGAGACCATCGTGATATGCAGGGG
1 TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* * * *
539355 TTTCTTTGAGGACAAGTTTGA-AGGACCATCATGATATGTAGGGG
1 -TTCTTTGATGACAAGCTTGAGA-AACCATCGTGATATGTAGGGG
* *
539399 TTCTTTGATGACAAGCCTGAGAAATCATCGTGATATGTAGGGG
1 TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* ** *
539442 TT-TCTTGATGAAAAGCTTGAGGGACCATCGTGATACGTAGGGG
1 TTCT-TTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* * *
539485 TTCCTTGATGACAAACTTGATGATAAGCTTGAAGGACCATCATGATATGTAGGGG
1 TTCTTTGATGACAAGC-T--TG---A----GAA--ACCATCGTGATATGTAGGGG
*
539540 TTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGG
1 TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* **
539583 TT-TCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGG
1 TTCT-TTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* *
539626 TTCCTTGATGACAAACTTGATGATAAGCTTGAAGGACCATCGTGATATGTAGGGG
1 TTCTTTGATGACAAGC-T--TG---A----GAA--ACCATCGTGATATGTAGGGG
*
539681 TTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGG
1 TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* * **
539724 TT-TCTTGATGATAATCTTGAGGGACCATCGTGATATGTAGGGG
1 TTCT-TTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* * *
539767 TTCCTTGATGACAAACTTGATGAACACTTGAGGGACCAACGTGATATGTAGGGG
1 TTCTTTGATGACAAGCTTGA-G---A----A---ACCATCGTGATATGTAGGGG
* *
539821 TTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGG
1 TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* **
539864 TT-TCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGG
1 TTCT-TTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
* *
539907 TTCCTTGATGACAAACTTGA
1 TTCTTTGATGACAAGCTTGA
539927 TGAACACTTG
Statistics
Matches: 466, Mismatches: 60, Indels: 91
0.76 0.10 0.15
Matches are distributed among these distances:
42 3 0.01
43 297 0.64
44 40 0.09
45 6 0.01
46 5 0.01
49 4 0.01
50 1 0.00
52 4 0.01
53 3 0.01
54 39 0.08
55 64 0.14
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (43 bp):
TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
Found at i:539548 original size:98 final size:96
Alignment explanation
Indices: 539424--539883 Score: 410
Period size: 98 Copynumber: 4.9 Consensus size: 96
539414 CCTGAGAAAT
*
539424 CATCGTGATATGTAGGGGTT-TCTTGATGAA-AAGCTTGAGGGACCATCGTGATACGTAGGGGTT
1 CATCGTGATATGTAGGGGTTCT-TTGATGAACAAGCTTGAGGGACCATCGTGATATGTAGGGGTT
539487 CCTTGATGACAAACTTGATGATAAGCTTGAAGGAC
65 CCTTGATGACAAACTTGATG--AA-CTTGAAGGAC
* ** *
539522 CATCATGATATGTAGGGGTTCTTTGAT-AACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTT
1 CATCGTGATATGTAGGGGTTCTTTGATGAACAAGCTTGAGGGACCATCGTGATATGTAGGGGTTC
*
539586 CTTGATGAC--A----AT---CTTGAGGGAC
66 CTTGATGACAAACTTGATGAACTTGAAGGAC
* *
539608 CATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGATAAGCTTGAAGGACCATCGTGATA
1 CATCGTGATATGTAGGGGTT-CTT--TG----A--TGA--ACAAGCTTGAGGGACCATCGTGATA
* * *
539673 TGTAGGGGTTCTTTGATAACAAGC-T--TG-A---GAA--AC
55 TGTAGGGGTTCCTTGATGACAAACTTGATGAACTTGAAGGAC
* *
539706 CATCGTGATATGTAGGGGTT-TCTTGATG-ATAATCTTGAGGGACCATCGTGATATGTAGGGGTT
1 CATCGTGATATGTAGGGGTTCT-TTGATGAACAAGCTTGAGGGACCATCGTGATATGTAGGGGTT
*
539769 CCTTGATGACAAACTTGATGAACACTTGAGGGAC
65 CCTTGATGACAAACTTGATG-A-ACTTGAAGGAC
* * ** *
539803 CAACGTGATATGTAGGGGTTCCTTGAT-AACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTT
1 CATCGTGATATGTAGGGGTTCTTTGATGAACAAGCTTGAGGGACCATCGTGATATGTAGGGGTTC
*
539867 CTTGATGACAATCTTGA
66 CTTGATGACAAACTTGA
539884 GGGACCATCG
Statistics
Matches: 298, Mismatches: 30, Indels: 69
0.75 0.08 0.17
Matches are distributed among these distances:
86 72 0.24
87 4 0.01
89 6 0.02
91 1 0.00
92 3 0.01
93 1 0.00
95 5 0.02
96 3 0.01
97 76 0.26
98 123 0.41
99 1 0.00
100 2 0.01
101 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (96 bp):
CATCGTGATATGTAGGGGTTCTTTGATGAACAAGCTTGAGGGACCATCGTGATATGTAGGGGTTC
CTTGATGACAAACTTGATGAACTTGAAGGAC
Found at i:539810 original size:54 final size:51
Alignment explanation
Indices: 539739--539974 Score: 243
Period size: 54 Copynumber: 4.8 Consensus size: 51
539729 TGATGATAAT
539739 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGAACA
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATG---A
* * *
539793 CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGA-GA
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGA
*
539843 ----A---ACCATCGTGATATGTAGGGGTTTCTTGATGAC--A----AT--
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGA
539879 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGAACA
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATG---A
* * *
539933 CTTGAGGGACCAACGTGATATGTATGGGTTCCTTGGTGACAA
1 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
539975 TTAAGAAACT
Statistics
Matches: 152, Mismatches: 11, Indels: 38
0.76 0.05 0.19
Matches are distributed among these distances:
37 1 0.01
40 1 0.01
43 60 0.39
45 1 0.01
46 1 0.01
49 2 0.01
50 1 0.01
53 1 0.01
54 84 0.55
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGA
Found at i:539828 original size:97 final size:97
Alignment explanation
Indices: 539704--539883 Score: 279
Period size: 97 Copynumber: 1.9 Consensus size: 97
539694 AGCTTGAGAA
* * * * * **
539704 ACCATCGTGATATGTAGGGGTTTCTTGATGATAATCTTGAGGGACCATCGTGATATGTAGGGGTT
1 ACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
539769 CCTTGATGACAAACTTGATGAACACTTGAGGG
66 CCTTGATGACAAACTTGATGAACACTTGAGGG
539801 ACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
1 ACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
* *
539866 TCTTGATGACAATCTTGA
66 CCTTGATGACAAACTTGA
539884 GGGACCATCG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 74 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (97 bp):
ACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
CCTTGATGACAAACTTGATGAACACTTGAGGG
Found at i:539967 original size:140 final size:141
Alignment explanation
Indices: 539372--539963 Score: 1003
Period size: 141 Copynumber: 4.2 Consensus size: 141
539362 GAGGACAAGT
* * * *
539372 TTGAAGGACCATCATGATATGTAGGGGTTCTTTGATGACAAGCCTGAGAAATCATCGTGATATGT
1 TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
* * *
539437 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATACGTAGGGGTTCCTTGATGACAAACT
66 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
539502 TGATGATAAGC
131 TGATGATAAGC
*
539513 TTGAAGGACCATCATGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
1 TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
539578 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
66 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
539643 TGATGATAAGC
131 TGATGATAAGC
539654 TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
1 TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
*
539719 AGGGGTTTCTTGATGATAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
66 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
539784 TGATGA-ACA-C
131 TGATGATA-AGC
* * *
539794 TTGAGGGACCAACGTGATATGTAGGGGTTCCTTGATAACAAGCTTGAGAAACCATCGTGATATGT
1 TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
539859 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
66 AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
539924 TGATGA-ACA-C
131 TGATGATA-AGC
* * *
539934 TTGAGGGACCAACGTGATATGTATGGGTTC
1 TTGAAGGACCATCGTGATATGTAGGGGTTC
539964 CTTGGTGACA
Statistics
Matches: 437, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
140 167 0.38
141 270 0.62
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (141 bp):
TTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATAACAAGCTTGAGAAACCATCGTGATATGT
AGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACT
TGATGATAAGC
Found at i:540124 original size:20 final size:21
Alignment explanation
Indices: 540099--540159 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
540089 TTCTTGATTT
540099 GTAAGTCCTCCGGGCCATCA-
1 GTAAGTCCTCCGGGCCATCAC
* * *
540119 GTAAGTCTTCCGAG-CATGATGC
1 GTAAGTCCTCCGGGCCATCA--C
540141 GTAAGTCCTCCGGGCCATC
1 GTAAGTCCTCCGGGCCATC
540160 CATAAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
22 12 0.39
23 3 0.10
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (21 bp):
GTAAGTCCTCCGGGCCATCAC
Found at i:540251 original size:132 final size:131
Alignment explanation
Indices: 540010--540452 Score: 663
Period size: 132 Copynumber: 3.4 Consensus size: 131
540000 TCTTAATTTT
* * *
540010 TAAGTCTTTCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGATATTTTAGAAACT
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
*
540075 AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATG
66 AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCTATCAGTAAGTCTTCCGAGCATGATG
540140 CG
131 -G
540142 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
* * *
540207 AACCCTTCGAGGGTTTCTTGATTTGTAAATCCTCTGGGCTATCAGTAAGTCTTCCGAGCATGATG
66 AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCTATCAGTAAGTCTTCCGAGCATGATG
540272 TG
131 -G
540274 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
** * * * *
540339 AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGG-TCATGTGTAAGCCTTTCGATCAAGAT
66 AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCT-ATCAGTAAGTCTTCCGAGCATGAT
*
540403 GA
130 GG
* * **** *
540405 TAAGTCTTACAAAACATCCATAAGACCTTTAGTGCAGGATGTTTTCAA
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAA
540453 CATTTTCGTT
Statistics
Matches: 285, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
131 42 0.15
132 243 0.85
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (131 bp):
TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAGAAACT
AACCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCTATCAGTAAGTCTTCCGAGCATGATG
G
Found at i:540712 original size:136 final size:136
Alignment explanation
Indices: 540468--540816 Score: 540
Period size: 136 Copynumber: 2.6 Consensus size: 136
540458 TCGTTGCTCA
540468 ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCAT
1 ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCAT
** * *
540533 AATGAGAAGAACTCATCCGATGGAGGGAGAAGAAGTTCATAATGAAAAGAGCTTGTTCGACCTAT
66 AATGAGAAGAACTCATCCGACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAACCTAT
*
540598 CACTTG
131 CACTCG
* * * * *
540604 ATTCATGACATTTTGAATCAGTGACGCCTCGTTTGAGGAATTGACATTTCCAATGGAGAGATCAT
1 ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCAT
*
540669 AATGAGAAGAACTCATCCGACAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTAT
66 AATGAGAAGAACTCATCCGACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAACCTAT
540734 CACTCG
131 CACTCG
* * ** *
540740 ATTCACGGCATTTCGAATCAGTGACGCCTCACTTGAGGGATCAACATTTCC-A-GAAGAGTTCAT
1 ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCAT
540803 AATGAGAAGAACTC
66 AATGAGAAGAACTC
540817 GTCCTAAAGT
Statistics
Matches: 192, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
134 23 0.12
135 1 0.01
136 168 0.88
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (136 bp):
ATTCACGACATTTCGAATCAGTGACGCCTCGCTTGAGGGATTGACATTTCCAATGGAGAGTTCAT
AATGAGAAGAACTCATCCGACAGAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAACCTAT
CACTCG
Found at i:541789 original size:2 final size:2
Alignment explanation
Indices: 541782--541838 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
541772 TCTTTAGTCT
541782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
541824 TA TA TG TA TT TA TA T
1 TA TA TA TA TA TA TA T
541839 GTATTTATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:542272 original size:2 final size:2
Alignment explanation
Indices: 542265--542315 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
542255 TTATTCATTA
542265 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
*
542307 AT AT TT AT A
1 AT AT AT AT A
542316 ATTTTGTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:554661 original size:8 final size:8
Alignment explanation
Indices: 554617--554714 Score: 71
Period size: 8 Copynumber: 12.1 Consensus size: 8
554607 ATGTTTGAAG
554617 AAAAATGA
1 AAAAATGA
*
554625 ACAAAT-A
1 AAAAATGA
*
554632 AAAAGGTGA
1 AAAA-ATGA
*
554641 AAAAAGGAAA
1 AAAAATG--A
554651 AAAAATGA
1 AAAAATGA
554659 AAAAATGAAAA
1 AAAAATG---A
554670 AAAAATGA
1 AAAAATGA
554678 AAAAATGA
1 AAAAATGA
554686 AAAAA-G-
1 AAAAATGA
*
554692 --AAATAA
1 AAAAATGA
554698 AAAAATGA
1 AAAAATGA
554706 AAAAATGA
1 AAAAATGA
554714 A
1 A
554715 GAGAGAAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
4 3 0.04
7 5 0.07
8 43 0.61
9 5 0.07
10 7 0.10
11 8 0.11
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAAATGA
Found at i:554662 original size:19 final size:19
Alignment explanation
Indices: 554640--554710 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
554630 TAAAAAGGTG
*
554640 AAAAAAGGAAAAAAAATGA
1 AAAAAAGAAAAAAAAATGA
*
554659 AAAAATGAAAAAAAAATGA
1 AAAAAAGAAAAAAAAATGA
*
554678 AAAAATGAAAAAAGAAAT-A
1 AAAAAAGAAAAAA-AAATGA
554697 AAAAAATGAAAAAA
1 AAAAAA-GAAAAAA
554711 TGAAGAGAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 36 0.77
20 11 0.23
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAATGA
Found at i:554670 original size:27 final size:25
Alignment explanation
Indices: 554650--554724 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 25
554640 AAAAAAGGAA
554650 AAAAAATGAAAAAATGAAAAAAAAATG
1 AAAAAATGAAAAAA-GAAAAAAAAA-G
554677 AAAAAATGAAAAAAGAAATAAAAAAATG
1 AAAAAATGAAAAAAG-AA-AAAAAAA-G
* *
554705 AAAAAATGAAGAGAGAAAAA
1 AAAAAATGAAAAAAGAAAAA
554725 TGAGGGTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 4 0.09
27 18 0.41
28 22 0.50
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (25 bp):
AAAAAATGAAAAAAGAAAAAAAAAG
Found at i:554689 original size:20 final size:20
Alignment explanation
Indices: 554617--554710 Score: 104
Period size: 20 Copynumber: 4.7 Consensus size: 20
554607 ATGTTTGAAG
554617 AAAAATGAACAAATAAAAAGGTGA
1 AAAAATGAA-AAA-AAAAA--TGA
*
554641 AAAAA-G-GAAAAAAAATGA
1 AAAAATGAAAAAAAAAATGA
554659 AAAAATG-AAAAAAAAATGA
1 AAAAATGAAAAAAAAAATGA
* *
554678 AAAAATGAAAAAAGAAATAA
1 AAAAATGAAAAAAAAAATGA
554698 AAAAATGAAAAAA
1 AAAAATGAAAAAA
554711 TGAAGAGAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.12
19 19 0.30
20 28 0.44
21 3 0.05
23 1 0.02
24 5 0.08
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAAATGAAAAAAAAAATGA
Found at i:554701 original size:28 final size:27
Alignment explanation
Indices: 554617--554714 Score: 105
Period size: 27 Copynumber: 3.6 Consensus size: 27
554607 ATGTTTGAAG
* *
554617 AAAAATGAACAAAT-AAAAAGGTGAAAA
1 AAAAATGAAAAAATGAAAAA-ATGAAAA
*
554644 AAGGAA--AAAAAATGAAAAAATGAAAA
1 AA-AAATGAAAAAATGAAAAAATGAAAA
554670 AAAAATGAAAAAATGAAAAAA-GAAATAA
1 AAAAATGAAAAAATGAAAAAATG-AA-AA
554698 AAAAATGAAAAAATGAA
1 AAAAATGAAAAAATGAA
554715 GAGAGAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
25 2 0.03
26 15 0.25
27 23 0.38
28 21 0.34
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (27 bp):
AAAAATGAAAAAATGAAAAAATGAAAA
Found at i:554722 original size:28 final size:28
Alignment explanation
Indices: 554650--554714 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
554640 AAAAAAGGAA
554650 AAAAAATGAAAAAATG-AA-AAAAAAATG
1 AAAAAATGAAAAAA-GAAATAAAAAAATG
554677 AAAAAATGAAAAAAGAAATAAAAAAATG
1 AAAAAATGAAAAAAGAAATAAAAAAATG
554705 AAAAAATGAA
1 AAAAAATGAA
554715 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.03
27 16 0.44
28 19 0.53
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (28 bp):
AAAAAATGAAAAAAGAAATAAAAAAATG
Found at i:555766 original size:111 final size:111
Alignment explanation
Indices: 555597--555894 Score: 497
Period size: 111 Copynumber: 2.7 Consensus size: 111
555587 GTGAACCGAT
* * * ** * *
555597 ATTTCCAATAAAGAGTTCATAATGAGAAGAATTCATCCAACGATGAAGAAGAAGTTCATAATGAG
1 ATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAG
*
555662 AAGAACTTGTTCCTTTTGATTCCATCACATAAGGAGATGGATCAAC
66 AAGAACTTGTTCCTTTTGATTCCATCACAGAAGGAGATGGATCAAC
* * *
555708 ATTTGTAATGAAGAGTTCATAATGAGAAGAACTCGTCCAATAAGGAAGAAAAAATTCATAATGAG
1 ATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAG
555773 AAGAACTTGTTCCTTTTGATTCCATCACAGAAGGAGATGGATCAAC
66 AAGAACTTGTTCCTTTTGATTCCATCACAGAAGGAGATGGATCAAC
555819 ATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAG
1 ATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAG
555884 AAGAACTTGTT
66 AAGAACTTGTT
555895 TAACCTTGCA
Statistics
Matches: 173, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 173 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (111 bp):
ATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAG
AAGAACTTGTTCCTTTTGATTCCATCACAGAAGGAGATGGATCAAC
Found at i:555925 original size:91 final size:91
Alignment explanation
Indices: 555830--556349 Score: 821
Period size: 91 Copynumber: 5.7 Consensus size: 91
555820 TTTCTAATGA
*
555830 AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
555895 TAACCTTGCATCAGTGTTCCCAATAG
66 CAACCTTGCATCAGTGTTTCCAATAG
*
555921 AGAGTTCATAATGAGAAGAACTCATCCAATGAA-GAAAAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCAAT-AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
555985 TCAACCTTGCATCAGTGTTTCCAAT-G
65 TCAACCTTGCATCAGTGTTTCCAATAG
556011 AAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 -AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
556076 TCAACCTTGCATCAGTGTTCCCAATGG
65 TCAACCTTGCATCAGTGTTTCCAATAG
* * *
556103 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAATTCATAATGAGAATAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
556168 CAACCTTGCATCAGTGTTTCCAATGG
66 CAACCTTGCATCAGTGTTTCCAATAG
* *
556194 AGAGATCATAATGAGAAGAACTCATTCAA-AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCAATA-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
556258 TCAACCTTACATCAATGTTTCTAATAG
65 TCAACCTTGCATCAGTGTTTCCAATAG
* * * *
556285 AGAGTTCATAATGAGAAGAACTCATCCAACAAGAAAGAACAAGTTCATAATGAGAAAAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
556350 TAATCCAACG
Statistics
Matches: 399, Mismatches: 24, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
90 3 0.01
91 392 0.98
92 4 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (91 bp):
AGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTGCATCAGTGTTTCCAATAG
Found at i:556077 original size:20 final size:19
Alignment explanation
Indices: 556015--556078 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
556005 CCAATGAAGA
556015 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
556034 CATCCAATAAGGAAGAAGAA--
1 -GTTC-ATAATG-AGAAGAACT
556054 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
556074 GTTCA
1 GTTCA
556079 ACCTTGCATC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 2 0.06
20 7 0.21
21 5 0.15
22 7 0.21
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:556259 original size:20 final size:20
Alignment explanation
Indices: 556199--556260 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
556189 AATGGAGAGA
556199 TCATAATGAGAAGAACTCA-T
1 TCATAATGAGAAGAACT-AGT
**
556219 TCA-AA-GAGGAAGAAGAAGT
1 TCATAATGA-GAAGAACTAGT
*
556238 TCATAATGAGAAGAACTTGT
1 TCATAATGAGAAGAACTAGT
556258 TCA
1 TCA
556261 ACCTTACATC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.09
19 12 0.36
20 16 0.48
21 2 0.06
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (20 bp):
TCATAATGAGAAGAACTAGT
Found at i:556548 original size:15 final size:14
Alignment explanation
Indices: 556503--556548 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
556493 AAAATATAAA
556503 TATTATATTATTAT
1 TATTATATTATTAT
*
556517 ATATTATATTATGAT
1 -TATTATATTATTAT
*
556532 TATTAGTATTGTTAT
1 TATTA-TATTATTAT
556547 TA
1 TA
556549 ATAATATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:558058 original size:22 final size:22
Alignment explanation
Indices: 558033--558086 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
558023 TATATATTTT
558033 ACTATTTTAACTTTTAACAAAC
1 ACTATTTTAACTTTTAACAAAC
558055 ACTATTTTAACTTTTAACAAAC
1 ACTATTTTAACTTTTAACAAAC
558077 ACTATTTTAA
1 ACTATTTTAA
558087 TTGGTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.43
Consensus pattern (22 bp):
ACTATTTTAACTTTTAACAAAC
Found at i:558519 original size:19 final size:19
Alignment explanation
Indices: 558495--558532 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
558485 GCTAATGTCG
558495 AGATTTCTTTTCAAATTAA
1 AGATTTCTTTTCAAATTAA
* *
558514 AGATTTTTTTTCTAATTAA
1 AGATTTCTTTTCAAATTAA
558533 TTAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (19 bp):
AGATTTCTTTTCAAATTAA
Found at i:558952 original size:2 final size:2
Alignment explanation
Indices: 558938--559012 Score: 73
Period size: 2 Copynumber: 37.5 Consensus size: 2
558928 TTATGACAAC
* * * * *
558938 TA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA TA -A TT TT TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
558979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
559013 TAATATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
1 2 0.03
2 57 0.92
3 3 0.05
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:559068 original size:15 final size:14
Alignment explanation
Indices: 559048--559150 Score: 88
Period size: 13 Copynumber: 7.1 Consensus size: 14
559038 ATATATTTTT
559048 TATAGTTTATACATA
1 TATAGTTTATA-ATA
559063 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
559076 CATAGTTTAT-ATA
1 TATAGTTTATAATA
559089 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
559104 CATAATTTAT-ATA
1 TATAGTTTATAATA
559117 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
559135 TATAGTTTATAATA
1 TATAGTTTATAATA
559149 TA
1 TA
559151 AATATAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 19
0.74 0.06 0.19
Matches are distributed among these distances:
12 1 0.01
13 28 0.38
14 6 0.08
15 24 0.33
16 4 0.05
17 3 0.04
18 7 0.10
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.47
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:559083 original size:28 final size:26
Alignment explanation
Indices: 559049--559128 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 26
559039 TATATTTTTT
*
559049 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTAT--ATATATAGTTTATAAAC
559077 ATAGTTTATATATATAGTTCATATAAAC
1 ATAGTTTATATATATAGTT--TATAAAC
* *
559105 ATAATTTATATATATAGCTTATAA
1 ATAGTTTATATATATAGTTTATAA
559129 TAATTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 15 0.32
28 32 0.68
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTTATAAAC
Found at i:559155 original size:18 final size:18
Alignment explanation
Indices: 559111--559169 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
559101 AAACATAATT
* *
559111 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
559129 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
*
559147 TATAAATATAATTTAT-A
1 TATAAATATAGTTTATAA
559164 TATAAA
1 TATAAA
559170 CTCATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.22
18 27 0.75
19 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:560471 original size:34 final size:35
Alignment explanation
Indices: 560430--560497 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
560420 AAATTCGAAC
*
560430 TTAAAATTTTATTTAAAAT-AAAAAACAT-TTAAAT
1 TTAAAA-TTAATTTAAAATCAAAAAACATATTAAAT
* *
560464 TTAAAATTAATTTAAACTCAATAAACATATTAAA
1 TTAAAATTAATTTAAAATCAAAAAACATATTAAA
560498 ATAGTTTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.34
34 14 0.48
35 5 0.17
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (35 bp):
TTAAAATTAATTTAAAATCAAAAAACATATTAAAT
Found at i:561504 original size:8 final size:8
Alignment explanation
Indices: 561481--561515 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
561471 TGATCACCAC
*
561481 TGTATGTA
1 TGTATGTG
561489 TGTATGTG
1 TGTATGTG
561497 TGTATGTG
1 TGTATGTG
*
561505 TGTGTGTG
1 TGTATGTG
561513 TGT
1 TGT
561516 GAAGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.51
Consensus pattern (8 bp):
TGTATGTG
Found at i:561583 original size:96 final size:96
Alignment explanation
Indices: 561419--561612 Score: 370
Period size: 96 Copynumber: 2.0 Consensus size: 96
561409 AAAACTAATA
*
561419 TGAAGAAATTCAGATTTCAGGACGAGCATGTGCCCACTCTAGGCAAGCCCTGTGATCACCACTGT
1 TGAAGAAATTCAGATTTCAAGACGAGCATGTGCCCACTCTAGGCAAGCCCTGTGATCACCACTGT
561484 ATGTATGTATGTGTGTATGTGTGTGTGTGTG
66 ATGTATGTATGTGTGTATGTGTGTGTGTGTG
561515 TGAAGAAATTCAGATTTCAAGACGAGCATGTGCCCACTCTAGGCAAGCCCTGTGATCACCACTGT
1 TGAAGAAATTCAGATTTCAAGACGAGCATGTGCCCACTCTAGGCAAGCCCTGTGATCACCACTGT
*
561580 ATGTATGTATGTGTGTGTGTGTGTGTGTGTG
66 ATGTATGTATGTGTGTATGTGTGTGTGTGTG
561611 TG
1 TG
561613 TGTGGTGTGT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (96 bp):
TGAAGAAATTCAGATTTCAAGACGAGCATGTGCCCACTCTAGGCAAGCCCTGTGATCACCACTGT
ATGTATGTATGTGTGTATGTGTGTGTGTGTG
Found at i:561596 original size:2 final size:2
Alignment explanation
Indices: 561589--561676 Score: 153
Period size: 2 Copynumber: 45.0 Consensus size: 2
561579 TATGTATGTA
561589 TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG T-
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
561629 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
561671 CG TG TG
1 TG TG TG
561677 CGCGTGCGCG
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.02
2 80 0.98
ACGTcount: A:0.00, C:0.01, G:0.50, T:0.49
Consensus pattern (2 bp):
TG
Found at i:561693 original size:20 final size:20
Alignment explanation
Indices: 561670--562096 Score: 243
Period size: 20 Copynumber: 20.4 Consensus size: 20
561660 GTGTGTGTGT
561670 GCGTGTGCGCGTGCGCGTGC
1 GCGTGTGCGCGTGCGCGTGC
561690 GCGTGTGCGCGTGCGCGTGTGC
1 GCGTGTGCGCGTGCGC--GTGC
* *
561712 GCGTGCGCGTGTGCGCGTGC
1 GCGTGTGCGCGTGCGCGTGC
*
561732 GCGTGTGCGCGTGCGCGTGT
1 GCGTGTGCGCGTGCGCGTGC
* *
561752 GCGCGTGCGCGTGTGGCGTGC
1 GCGTGTGCGCGTG-CGCGTGC
561773 GCGTGTGCGC--GCGCGTG-
1 GCGTGTGCGCGTGCGCGTGC
561790 GCGTGTGCGCGTGCGCGTGC
1 GCGTGTGCGCGTGCGCGTGC
* *
561810 GTGCGTGCGTGCGTGCGCGCGTGC
1 --GCGT--GTGCGCGTGCGCGTGC
*
561834 GTGCGTGTGCGCGTGCGTGCGTGT
1 --GCGTGTGCGCGTGC--GCGTGC
* * *
561858 GTGCGTGCGTGTGCGCGTGC
1 GCGTGTGCGCGTGCGCGTGC
*
561878 GTGCGTGTGTGCGTGCGTGCGTGC
1 --GCGTGTGCGCGTGC--GCGTGC
*
561902 GTGCGTGTGTGCGTGCGTGCGTGC
1 --GCGTGTGCGCGTGC--GCGTGC
* * * *
561926 GTGCGTGCGTGTGCGTGTGCGC
1 GCGTGTGCGCGTGCGCGT--GC
* * *
561948 GCGTGTGCGTGTGTGCGTGT
1 GCGTGTGCGCGTGCGCGTGC
*
561968 GCGTGTGCGC--GCGTGTGC
1 GCGTGTGCGCGTGCGCGTGC
* * * * *
561986 GTGTGTGTGCGTGTGTGTGT
1 GCGTGTGCGCGTGCGCGTGC
* * * *
562006 GTGTGTGCGCGCGCACGTGT
1 GCGTGTGCGCGTGCGCGTGC
*
562026 GCGTGTGCGTGCGTGTGCGTGC
1 GCGTGTGC--GCGTGCGCGTGC
* * * * *
562048 GTGTGTGTGTGCGCGCGTGT
1 GCGTGTGCGCGTGCGCGTGC
* * * * *
562068 GTGTGTGTGCGCGCACGTGT
1 GCGTGTGCGCGTGCGCGTGC
562088 GCGTGTGCG
1 GCGTGTGCG
562097 TGCGTGTGCG
Statistics
Matches: 324, Mismatches: 61, Indels: 44
0.76 0.14 0.10
Matches are distributed among these distances:
17 10 0.03
18 18 0.06
19 8 0.02
20 128 0.40
21 14 0.04
22 91 0.28
24 55 0.17
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.26
Consensus pattern (20 bp):
GCGTGTGCGCGTGCGCGTGC
Found at i:562001 original size:8 final size:8
Alignment explanation
Indices: 561589--562130 Score: 258
Period size: 8 Copynumber: 66.5 Consensus size: 8
561579 TATGTATGTA
*
561589 TGTGTGTG
1 TGTGCGTG
*
561597 TGTGTGTG
1 TGTGCGTG
*
561605 TGTGTGTG
1 TGTGCGTG
561613 TGTG-GTG
1 TGTGCGTG
*
561620 TGTGTGTG
1 TGTGCGTG
*
561628 T-TGTGTG
1 TGTGCGTG
*
561635 TGTGTGTG
1 TGTGCGTG
*
561643 TGTGTGTG
1 TGTGCGTG
*
561651 TGTGTGTG
1 TGTGCGTG
*
561659 TGTGTGTG
1 TGTGCGTG
561667 TGTGCGTG
1 TGTGCGTG
*
561675 TGCGCGTGCG
1 TGTGCGT--G
* *
561685 CGTGCGCG
1 TGTGCGTG
561693 TGTGC--G
1 TGTGCGTG
* *
561699 CGTGCGCG
1 TGTGCGTG
*
561707 TGTGCGCG
1 TGTGCGTG
*
561715 TGCGCGTG
1 TGTGCGTG
*
561723 TGCGCGTGCG
1 TGTGCGT--G
* * *
561733 CGTGTGCG
1 TGTGCGTG
* *
561741 CGTGCGCG
1 TGTGCGTG
*
561749 TGTGCGCG
1 TGTGCGTG
*
561757 TGCGCGTG
1 TGTGCGTG
561765 TG-GC--G
1 TGTGCGTG
*
561770 TGCGCGTG
1 TGTGCGTG
* *
561778 TGCGCGCG
1 TGTGCGTG
* *
561786 CGTG-GCG
1 TGTGCGTG
*
561793 TGTGCGCG
1 TGTGCGTG
*
561801 TGCGCGTG
1 TGTGCGTG
*
561809 CGTGCGTG
1 TGTGCGTG
*
561817 CGTGCGTG
1 TGTGCGTG
* *
561825 CGCGCGTG
1 TGTGCGTG
*
561833 CGTGCGTG
1 TGTGCGTG
*
561841 TGCGCGTG
1 TGTGCGTG
*
561849 CGTGCGTG
1 TGTGCGTG
561857 TGTGCGTGCG
1 TGTGCGT--G
561867 TGTGCGCGTG
1 TGT--GCGTG
*
561877 CGTGCGTG
1 TGTGCGTG
561885 TGTGCGTG
1 TGTGCGTG
*
561893 CGTGCGTG
1 TGTGCGTG
*
561901 CGTGCGTG
1 TGTGCGTG
561909 TGTGCGTG
1 TGTGCGTG
*
561917 CGTGCGTG
1 TGTGCGTG
*
561925 CGTGCGTGCG
1 TGTGCGT--G
561935 TGTGCGTG
1 TGTGCGTG
* *
561943 TGCGCGCG
1 TGTGCGTG
561951 TGTGCGTG
1 TGTGCGTG
561959 TGTGC--G
1 TGTGCGTG
561965 TGTGCGTG
1 TGTGCGTG
* *
561973 TGCGCGCG
1 TGTGCGTG
561981 TGTGCGTGTG
1 TGTGC--GTG
561991 TGTGCGTG
1 TGTGCGTG
*
561999 TGTGTGTG
1 TGTGCGTG
* *
562007 TGTGTGCG
1 TGTGCGTG
* * **
562015 CGCGCACG
1 TGTGCGTG
562023 TGTGCGTG
1 TGTGCGTG
562031 TGCGTGCGTG
1 T--GTGCGTG
562041 TGCGTGCGTG
1 T--GTGCGTG
*
562051 TGTGTGTG
1 TGTGCGTG
* *
562059 CGCGCGTG
1 TGTGCGTG
*
562067 TGTGTGTG
1 TGTGCGTG
* *
562075 TGCGCGCACG
1 TGTGCG--TG
562085 TGTGCGTG
1 TGTGCGTG
* * *
562093 TGCGTGCG
1 TGTGCGTG
562101 TGTGCGTG
1 TGTGCGTG
*
562109 CATGTGTGTG
1 --TGTGCGTG
562119 TGTGCGTG
1 TGTGCGTG
562127 TGTG
1 TGTG
562131 TATTTGGTTA
Statistics
Matches: 429, Mismatches: 77, Indels: 56
0.76 0.14 0.10
Matches are distributed among these distances:
5 3 0.01
6 13 0.03
7 22 0.05
8 326 0.76
10 61 0.14
12 4 0.01
ACGTcount: A:0.01, C:0.19, G:0.50, T:0.31
Consensus pattern (8 bp):
TGTGCGTG
Found at i:562003 original size:4 final size:4
Alignment explanation
Indices: 561854--562131 Score: 61
Period size: 4 Copynumber: 69.5 Consensus size: 4
561844 GCGTGCGTGC
* * * * * * * * * *
561854 GTGT GTGC GTGC GTGT GCGC GTGC GTGC GTGT GTGC GTGC GTGC GTGC
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * * * * * *
561902 GTGC GTGT GTGC GTGC GTGC GTGC GTGC GTGC GTGT GCGT GTGC GCGC
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * * *
561950 GTGT GCGT GTGT GCGT GTGC GTGT GCGC GCGT GTGC GTGT GTGT GCGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * *** * * * *
561998 GTGT GTGT GTGT GTGC GCGC GCAC GTGT GCGT GTGC GTGC GTGT GCGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * * ** *
562046 GCGT GTGT GTGT GCGC GCGT GTGT GTGT GTGC GCGC ACGT GTGC GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * *
562094 GCGT GCGT GTGC GTGC ATGT GTGT GTGT GCGT GTGT GT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GT
562132 ATTTGGTTAG
Statistics
Matches: 212, Mismatches: 62, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 212 1.00
ACGTcount: A:0.01, C:0.19, G:0.49, T:0.31
Consensus pattern (4 bp):
GTGT
Found at i:562038 original size:62 final size:62
Alignment explanation
Indices: 561596--562078 Score: 86
Period size: 62 Copynumber: 7.7 Consensus size: 62
561586 GTATGTGTGT
* * * * * * * * *
561596 GTGTGTGTGTGTGTGTGTGTG-GTGTGTGTGTGTTGTGTGTGTGTGTGTGTGTGTGTGTG--T
1 GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTG-TGTGTGCGTGTGTGTGTGTGCGCGCGCAC
* * * * * * * * * *
561656 GTGTGTGTGTGTGTGCGTGTGCGCGTGCGCGTGCGCGTGTGCGCGTGCGCGTGTGCGCGTGCGC
1 GTGTGCGTGTGCGTGCGTGT--GCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGCGCGCGCAC
* * * * * * * * * *
561720 GTGTGCGCGTGCGCGTGTGCGCGTGCGCGTGTGCGCGTGCGCGTGTG-GCGTGCGCGTGTGCGCG
1 GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGCGC----GCGCA
561784 C
62 C
* * * * * * * * * **
561785 GCGTGGCGTGTGCGCGTGCGCGTGCGTGCGTGCGTGCGTGCGCGCGTGCGTGCGTGTGCGCGTGC
1 GTGT-GCGTGT--GCGTGCGTGTGCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGCGCGCGCAC
* * * * * * *
561850 GTGCGTGTGTGCGTGCGTGTGCGCGTGCGTGCGTGTGTGCGTGCGTGCGTGCGTGCGTGTGTGCG
1 GTGTGCGTGTGCGTGCGTGT--GCGTGCGT--GTGTGTGTGTGCGT--GTGTGTGTGTGCGCGCG
**
561915 TGC
60 CAC
* * * * * * * * *
561918 GTGCGTGCGTGCGTGCGTGTGCGT--GTGCGCGCGTGTGCGTGTGTGCGTGTGCGTGTGCGCGC
1 GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGC--GCGCGCAC
* * * * *** * * *
561980 GTGTGCGTGTGTGTGCGTGT--GTGTGTGTGTGTGCGCGCGCACGTGTGCGTGTGCGTG--C
1 GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGCGCGCGCAC
* * * *
562038 GTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCG
1 GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGTGCG
562079 CGCACGTGTG
Statistics
Matches: 319, Mismatches: 79, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
58 19 0.06
60 47 0.15
61 7 0.02
62 103 0.32
63 8 0.03
64 29 0.09
65 15 0.05
66 18 0.06
68 66 0.21
69 7 0.02
ACGTcount: A:0.00, C:0.20, G:0.50, T:0.30
Consensus pattern (62 bp):
GTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGTGCGTGTGTGTGTGTGCGCGCGCAC
Found at i:562080 original size:62 final size:62
Alignment explanation
Indices: 561898--562131 Score: 247
Period size: 62 Copynumber: 3.6 Consensus size: 62
561888 GCGTGCGTGC
* * * * * * *
561898 GTGCGTGCGTGT--GTGCGTGCGTGCGTGCGTGCGTGCGTGTGCGTGTGCGCGCGTGTGCGTGT
1 GTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCGCGCACGTGTGC--GT
* * *
561960 GTGCGTGTGCGTGTGCGCGCGTGTGCGTGTGTGTGCGTGTGTGTGTGTGTGTGCGCGCGCACGTG
1 GTGC--GTGCGTGTGCGTGC--GT--GTGTGTGTGCGCGCGTGTGTGTGTGT--GCGCGCACGTG
562025 TGCGT
58 TGCGT
562030 GTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCGCGCACGTGTGCGT
1 GTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCGCGCACGTGTGCGT
* * *
562092 GTGCGTGCGTGTGCGTGCATGTGTGTGTGTGCGTGTGTGT
1 GTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGT
562132 ATTTGGTTAG
Statistics
Matches: 148, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
62 57 0.39
64 32 0.22
66 5 0.03
68 15 0.10
70 27 0.18
72 12 0.08
ACGTcount: A:0.01, C:0.18, G:0.49, T:0.32
Consensus pattern (62 bp):
GTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCGCGCACGTGTGCGT
Found at i:562093 original size:68 final size:68
Alignment explanation
Indices: 561606--562128 Score: 330
Period size: 68 Copynumber: 7.6 Consensus size: 68
561596 GTGTGTGTGT
* * * * * * * * * *
561606 GTGTGTGTGTG-GTGTGTGTGTGT-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
1 GTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGCGCG
*
561669 TGC
66 CGC
* * * * * * *
561672 GTGTGCGCGTGC--GCGTGCGCGTGTGC--GCGTGCGCGTGTGC--GCGTGCGCGTGTGCGCGTG
1 GTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGCGCG
561731 CGC
66 CGC
* * * * * * * * *
561734 GTGTGCGCGTGCGCGTGTGCGCGTGCGCGTGTGGCGTGCGCGTGTGCGCGCGCGTG-GCGTGTGC
1 GTGTGCGTGTGCGTGCGTGTGCGTGTGC--GT-GCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGC
*
561798 GCGTGC
63 GCGCGC
* * * *
561804 GCGTGCGTGCGTGCGTGCGTGCGCGCGTGCGTGCGTGTGCGCGTGCGTGCGTGTGTGCGTGCGTG
1 GTGTGCGT--GTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGT--GT--GTG
*
561869 TGCGCGTGC
60 TGCGCGCGC
* * * * * * * *
561878 GTGCGTGTGTGCGTGCGTGCGTGCGTGCGTGTGTGCGTGCGTGCGTGCGTGCGTGCGTGTGCGTG
1 GTGTGCGTGTGCGTGCGT--GTGCGT--GTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTG
*
561943 TGCGCGC
62 CGCGCGC
* * * *
561950 GTGTGCGTGT--GTGCGTGTGCGTGTGCGCGCGTGTGCGTGTGTGTGCGTGTGTGTGTGTGTGTG
1 GTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGCGCG
562013 CGC
66 CGC
* ** * * * *
562016 GCGCACGTGTGCGTGTGCGTGCGTGTGCGTGCGTGTGTGTGTGCGCGCGTGTGTGTGTGTGCGCG
1 GTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGCGCG
*
562081 CAC
66 CGC
* *
562084 GTGTGCGTGTGCGTGCGTGTGCGTGCATGTGTGTGTGTGCGTGTG
1 GTGTGCGTGTGCGTGCGTGTGCGTG--TGCGTGCGTGTGCGTGTG
562129 TGTATTTGGT
Statistics
Matches: 353, Mismatches: 78, Indels: 48
0.74 0.16 0.10
Matches are distributed among these distances:
62 28 0.08
64 22 0.06
65 7 0.02
66 53 0.15
68 73 0.21
69 33 0.09
70 39 0.11
71 5 0.01
72 44 0.12
74 23 0.07
76 26 0.07
ACGTcount: A:0.01, C:0.20, G:0.50, T:0.30
Consensus pattern (68 bp):
GTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGCGTGTGCGTGCGTGTGTGTGTGTGCGCG
CGC
Found at i:562114 original size:10 final size:10
Alignment explanation
Indices: 561592--562131 Score: 195
Period size: 10 Copynumber: 54.4 Consensus size: 10
561582 GTATGTATGT
* *
561592 GTGTGTGTGT
1 GTGTGCGTGC
* *
561602 GTGTGTGTGT
1 GTGTGCGTGC
*
561612 GTGTG-GTGT
1 GTGTGCGTGC
* *
561621 GTGTGTGTTGT
1 GTGTGCG-TGC
* *
561632 GTGTGTGTGT
1 GTGTGCGTGC
* *
561642 GTGTGTGTGT
1 GTGTGCGTGC
* *
561652 GTGTGTGTGT
1 GTGTGCGTGC
*
561662 GTGTGTGTGC
1 GTGTGCGTGC
561672 GTGTGC--GC
1 GTGTGCGTGC
*
561680 GTGCGCGTGC
1 GTGTGCGTGC
*
561690 GCGT--GTGC
1 GTGTGCGTGC
* * *
561698 GCGTGCGCGT
1 GTGTGCGTGC
*
561708 GTGCGCGTGC
1 GTGTGCGTGC
*
561718 GCGT--GTGC
1 GTGTGCGTGC
* * *
561726 GCGTGCGCGT
1 GTGTGCGTGC
*
561736 GTGCGCGTGC
1 GTGTGCGTGC
*
561746 GCGT--GTGC
1 GTGTGCGTGC
*
561754 GCGTGC--GC
1 GTGTGCGTGC
561762 GTGTGGCGTGC
1 GTGT-GCGTGC
*
561773 GCGT--GTGC
1 GTGTGCGTGC
* *
561781 GCGCGCGTGGC
1 GTGTGCGT-GC
561792 GTGTGC--GC
1 GTGTGCGTGC
*
561800 GTGCGCGTGC
1 GTGTGCGTGC
561810 GTGCGTGCGTGC
1 GT--GTGCGTGC
*
561822 GTGCGCGCGTGC
1 GT--GTGCGTGC
* *
561834 GTGCGTGTGC
1 GTGTGCGTGC
*
561844 GCGTGCGTGC
1 GTGTGCGTGC
561854 GTGT--GTGC
1 GTGTGCGTGC
* *
561862 GTGCGTGTGC
1 GTGTGCGTGC
*
561872 GCGTGCGTGC
1 GTGTGCGTGC
561882 GTGTGTGCGTGC
1 --GTGTGCGTGC
561894 GTGCGTGCGTGC
1 GT--GTGCGTGC
561906 GTGTGTGCGTGC
1 --GTGTGCGTGC
561918 GTGCGTGCGTGC
1 GT--GTGCGTGC
* *
561930 GTGCGTGTGC
1 GTGTGCGTGC
*
561940 GTGTGCGCGC
1 GTGTGCGTGC
*
561950 GTGTGCGTGT
1 GTGTGCGTGC
* *
561960 GTGCGTGTGC
1 GTGTGCGTGC
*
561970 GTGTGCGCGC
1 GTGTGCGTGC
*
561980 GTGTGCGTGT
1 GTGTGCGTGC
561990 GTGTGCGT--
1 GTGTGCGTGC
* *
561998 GTGTGTGTGT
1 GTGTGCGTGC
*
562008 GTGTGCGCGC
1 GTGTGCGTGC
*** *
562018 GCACGTGTGC
1 GTGTGCGTGC
562028 GTGTGCGTGC
1 GTGTGCGTGC
562038 GTGTGCGTGC
1 GTGTGCGTGC
* *
562048 GTGTGTGTGT
1 GTGTGCGTGC
* * *
562058 GCGCGCGTGT
1 GTGTGCGTGC
*
562068 GTGTGTGTGC
1 GTGTGCGTGC
* * *
562078 GCGCACGTGTGC
1 GTG--TGCGTGC
562090 GTGTGCGTGC
1 GTGTGCGTGC
562100 GTGTGCGTGC
1 GTGTGCGTGC
* *
562110 ATGT--GTGT
1 GTGTGCGTGC
*
562118 GTGTGCGTGT
1 GTGTGCGTGC
562128 GTGT
1 GTGT
562132 ATTTGGTTAG
Statistics
Matches: 410, Mismatches: 84, Indels: 72
0.72 0.15 0.13
Matches are distributed among these distances:
8 70 0.17
9 11 0.03
10 243 0.59
11 21 0.05
12 63 0.15
14 2 0.00
ACGTcount: A:0.01, C:0.19, G:0.50, T:0.31
Consensus pattern (10 bp):
GTGTGCGTGC
Found at i:562131 original size:28 final size:28
Alignment explanation
Indices: 561594--562131 Score: 274
Period size: 28 Copynumber: 18.8 Consensus size: 28
561584 ATGTATGTGT
* * *
561594 GTGTGTGTGTGTGTGTGTGTGTG-GTGT
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * * *
561621 GTGTGTGT-TGTGTGTGTGTGTGTGTGT
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * *
561648 GTGTGTGTGTGTGTGTGTGTGTGCGTGT
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * * * *
561676 GCGCGTGCGCGTGCGCGTGTGCGCGTGC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * * *
561704 GCGTGTGCGCGTGCGCGTGTGCGCGTGC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * * *
561732 GCGTGTGCGCGTGCGCGTGTGCGCGTGC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * * *
561760 GCGTGTG-GCGTGCGCGTGTGCGCGCGC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * *
561787 GTGGCGTGTGCGCGTGCGCGTGCGTGCGTGC
1 GT---GTGTGTGCGTGCGTGTGTGTGCGTGC
* * *
561818 GTGCGTGCGCGCGTGCGTGCGTGTGCGCGTGC
1 GT--GTGTGTGCGTGCGT--GTGTGTGCGTGC
*
561850 GTGCGTGTGTGCGTGC--GTGTGCGCGTGC
1 GT--GTGTGTGCGTGCGTGTGTGTGCGTGC
*
561878 GTGCGTGTGTGCGTGC--GTGCGTGCGTGC
1 GT--GTGTGTGCGTGCGTGTGTGTGCGTGC
*
561906 --GTGTGTGCGTGCGTGCGTGCGTGCGTGC
1 GTGTGTGTGCGTGCGT--GTGTGTGCGTGC
* * *
561934 GTGTGCGTGTGCGCGCGTGTGCGTGTGTGC
1 GTGT--GTGTGCGTGCGTGTGTGTGCGTGC
* *
561964 GTGTGCGTGTGCGCGCGTGTGCGTGTGTGTGC
1 GTGT--GTGTGCGTGCGTGT--GTGTGCGTGC
* * * **
561996 GTGTGTGT--GTGTGTGTGCGCGCGCAC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
*
562022 GTGTGCGTGTGCGTGCGTGTGCGTGCGT--
1 GTGT--GTGTGCGTGCGTGTGTGTGCGTGC
* *
562050 GTGTGTGTGCGCGCGTGTGTGTGTGTGC
1 GTGTGTGTGCGTGCGTGTGTGTGCGTGC
* * *
562078 GCGCACGTGTGCGTGTGCGTGCGTGTGCGTGC
1 GTG--TGTGTGC--GTGCGTGTGTGTGCGTGC
* *
562110 ATGTGTGTGTGTGCGTGTGTGT
1 GTGTGTGTGCGTGCGTGTGTGT
562132 ATTTGGTTAG
Statistics
Matches: 434, Mismatches: 49, Indels: 55
0.81 0.09 0.10
Matches are distributed among these distances:
24 12 0.03
26 42 0.10
27 40 0.09
28 177 0.41
30 80 0.18
31 19 0.04
32 64 0.15
ACGTcount: A:0.01, C:0.19, G:0.50, T:0.30
Consensus pattern (28 bp):
GTGTGTGTGCGTGCGTGTGTGTGCGTGC
Found at i:564066 original size:27 final size:28
Alignment explanation
Indices: 564036--564103 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
564026 TAAATGAATC
*
564036 GAAAAAAATAATAA-TAACAAGT-CAAAA
1 GAAAAAAATAA-AATTAACAAGTGAAAAA
*
564063 GAAAGAAAA-AAAATTAATAAGTGAAAAA
1 GAAA-AAAATAAAATTAACAAGTGAAAAA
*
564091 GAAATAAATAAAA
1 GAAAAAAATAAAA
564104 AGAAATAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 16 0.47
28 16 0.47
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (28 bp):
GAAAAAAATAAAATTAACAAGTGAAAAA
Found at i:564103 original size:14 final size:14
Alignment explanation
Indices: 564059--564111 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
564049 ATAACAAGTC
*
564059 AAAAGAAAGAAA-A
1 AAAAGAAATAAATA
** *
564072 AAAATTAATAAGTGA
1 AAAAGAAATAAAT-A
564087 AAAAGAAATAAATA
1 AAAAGAAATAAATA
564101 AAAAGAAATAA
1 AAAAGAAATAA
564112 GTCAAAGGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 8 0.26
14 12 0.39
15 11 0.35
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.13
Consensus pattern (14 bp):
AAAAGAAATAAATA
Found at i:564113 original size:29 final size:28
Alignment explanation
Indices: 564059--564113 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
564049 ATAACAAGTC
**
564059 AAAAGAAAGAAAAAAAATTAATAAGTGA
1 AAAAGAAAGAAAAAAAAGAAATAAGTGA
*
564087 AAAAGAAATAAATAAAAAGAAATAAGT
1 AAAAGAAAGAAA-AAAAAGAAATAAGT
564114 CAAAGGGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (28 bp):
AAAAGAAAGAAAAAAAAGAAATAAGTGA
Found at i:564200 original size:10 final size:9
Alignment explanation
Indices: 564147--564200 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
564137 AGATAAATAT
*
564147 AAAATTAAA
1 AAAAGTAAA
564156 AAAAG-AAA
1 AAAAGTAAA
*
564164 AAAAGAAAA
1 AAAAGTAAA
*
564173 AAAATTAAA
1 AAAAGTAAA
*
564182 AAAAATAAA
1 AAAAGTAAA
564191 AAAAGGTAAA
1 AAAA-GTAAA
564201 GTTTTAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
8 8 0.21
9 26 0.68
10 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (9 bp):
AAAAGTAAA
Found at i:564200 original size:19 final size:19
Alignment explanation
Indices: 564153--564200 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
564143 ATATAAAATT
564153 AAAAAAAG--AAAAAAAGA
1 AAAAAAAGTAAAAAAAAGA
* *
564170 AAAAAAATTAAAAAAAATA
1 AAAAAAAGTAAAAAAAAGA
*
564189 AAAAAAGGTAAA
1 AAAAAAAGTAAA
564201 GTTTTAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 7 0.28
19 18 0.72
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAAAAAGTAAAAAAAAGA
Found at i:565886 original size:39 final size:38
Alignment explanation
Indices: 565779--565914 Score: 134
Period size: 39 Copynumber: 3.5 Consensus size: 38
565769 GTAAAAATTA
*
565779 TATATTATATATTTTCCTAAAATGTTTTTAAAAAAC-TATA-
1 TATA-TATATATTTT--TAAAAT-TTTTTAAAAACCATATAT
* *
565819 TAT-TATACAGTTTTCAAAATTGTTTTAAAAACCATATAT
1 TATATATATA-TTTTTAAAATT-TTTTAAAAACCATATAT
*
565858 TATATATATATTTTTAAAATATTTTTAAAAACTATATAT
1 TATATATATATTTTTAAAAT-TTTTTAAAAACCATATAT
**
565897 TATATACGTATTTTTAAA
1 TATATATATATTTTTAAA
565915 CCGTTTGTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
36 1 0.01
37 15 0.18
38 9 0.11
39 48 0.59
40 9 0.11
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (38 bp):
TATATATATATTTTTAAAATTTTTTAAAAACCATATAT
Found at i:565938 original size:76 final size:75
Alignment explanation
Indices: 565777--565953 Score: 182
Period size: 76 Copynumber: 2.3 Consensus size: 75
565767 TTGTAAAAAT
* **
565777 TATATAT-TATATATTTTCCTAAAATGTTTTTAAAAAACTATATATTATACAGTTTTCAAAATTG
1 TATATATATATATATTTT-CTAAAATATTTTTAAAAAACTATATATTATACAGTTTTCAAAACCG
565841 TTTTAAAAACCA
65 TTTT-AAAACCA
* **
565853 TATATTATATATATATTTT-TAAAATATTTTT-AAAAACTATATATTATATACGTATTTTTAAAC
1 TATA-TATATATATATTTTCTAAAATATTTTTAAAAAACTATATATTATACA-GT-TTTCAAAAC
*
565916 CGTTTGT-AAACTA
63 CGTTT-TAAAACCA
*
565929 TAATATATATATATATATATCTAAA
1 T-ATATATATATATAT-TTTCTAAA
565954 TAAAAAAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
75 18 0.21
76 34 0.40
77 18 0.21
78 15 0.18
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (75 bp):
TATATATATATATATTTTCTAAAATATTTTTAAAAAACTATATATTATACAGTTTTCAAAACCGT
TTTAAAACCA
Found at i:568643 original size:41 final size:41
Alignment explanation
Indices: 568589--568904 Score: 355
Period size: 41 Copynumber: 7.6 Consensus size: 41
568579 GGTTCATCGA
*
568589 TAGTGGCGTTTTT-TCAACAAACGCCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTCGTACTT
* *
568631 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * * * *
568672 TAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
568713 TAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCATAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
*
568756 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
568797 TATTGACATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * *
568838 TAGTGGCGTTTTTATTCAAACGCCGCTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
*
568879 TAGTGGCGTTTGTGTTTACAAACGCC
1 TAGTGGCGTTT-T-TATACAAACGCC
568905 TCAAGTTTAC
Statistics
Matches: 229, Mismatches: 40, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
41 173 0.76
42 16 0.07
43 40 0.17
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:568899 original size:125 final size:122
Alignment explanation
Indices: 568588--568904 Score: 382
Period size: 125 Copynumber: 2.5 Consensus size: 122
568578 AGGTTCATCG
* *
568588 ATAGTGGCGTTTTTTCAACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACT
1 ATAGTGGCGTTTTTT--TCAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACG
* * * * *
568653 CCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACT
64 CCGCTAAAGACGCGTACTTTAGTGACATTTTTATACAAACGCCGCTAAACACTCGTACT
* * *
568712 ATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAAC
1 ATAGTGGCGTTT-T-TTT-CAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAAC
* * *
568777 GCCGCTAAAGACTCGTACTTTATTGACATTTTTATACAAACGCCGCTAAAGACTCGTACT
63 GCCGCTAAAGACGCGTACTTTAGTGACATTTTTATACAAACGCCGCTAAACACTCGTACT
* * * ** * *
568837 TTAGTGGCGTTTTTATTCAAACGCCGCTATACACTTGTACTATAGTGGCGTTTGTGTTTACAAAC
1 ATAGTGGCGTTTTT-TTCAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTT-T-TATACAAAC
568902 GCC
63 GCC
568905 TCAAGTTTAC
Statistics
Matches: 164, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
123 29 0.18
124 16 0.10
125 117 0.71
126 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (122 bp):
ATAGTGGCGTTTTTTTCAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCC
GCTAAAGACGCGTACTTTAGTGACATTTTTATACAAACGCCGCTAAACACTCGTACT
Found at i:572403 original size:85 final size:85
Alignment explanation
Indices: 572215--572536 Score: 355
Period size: 85 Copynumber: 3.8 Consensus size: 85
572205 GGTAATTAGT
* * * * *
572215 GGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGT-TCAAAAACGC
1 GGCGTTTATATCCAAAAACGCCACTATAGATATGACCTTTTGCGGCGTTTGT-TCT-AAAAACGC
* *
572279 CGTTATAGGTCTGACATTTTGC
64 CGCTATAGGTCTTACATTTTGC
* * * *
572301 GGCGTTTATGTCCAAAAACGCCACTATAGGTATGACTTTTTACGGCGTTTGTTCTAAAAACGCCA
1 GGCGTTTATATCCAAAAACGCCACTATAGATATGACCTTTTGCGGCGTTTGTTCTAAAAACGCC-
572366 G-TATAGGTCTTATC-TTTTGC
65 GCTATAGGTCTTA-CATTTTGC
* * * *
572386 GGCGTTTGTATCCAAAAACGCCACTATAGATCTGACCTTTTGCGGCGTTTTTTCTAGAAACGCCG
1 GGCGTTTATATCCAAAAACGCCACTATAGATATGACCTTTTGCGGCGTTTGTTCTAAAAACGCCG
** * * *
572451 CTATATATCATAACTTTTTGT
66 CTATAGGTC-TTACATTTTGC
* * *
572472 GGCGTTTAT-TCCAAAAATGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACGCC
1 GGCGTTTATATCCAAAAACGCCACTATAGATAT-GACCTTTTGCGGCGTTTGTTCTAAAAACGCC
572536 G
65 G
572537 TAATAGATAT
Statistics
Matches: 204, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
84 1 0.00
85 109 0.53
86 94 0.46
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (85 bp):
GGCGTTTATATCCAAAAACGCCACTATAGATATGACCTTTTGCGGCGTTTGTTCTAAAAACGCCG
CTATAGGTCTTACATTTTGC
Found at i:572467 original size:128 final size:124
Alignment explanation
Indices: 572215--572567 Score: 366
Period size: 128 Copynumber: 2.7 Consensus size: 124
572205 GGTAATTAGT
*
572215 GGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTCAAAAACGCC
1 GGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGAC-TTTTGCGGCGTTTGT-TCCAAAAACGCC
* * * * * *
572280 GTTATAGGTCTGACATTTTGCGGCGTTTATGTCCAAAAACGCCACTATAGGTATGACTTTTTAC
63 -CTATAGATCTGACCTTTTGCGGCGTTT-TTTCCAAAAACGCCACTATAGATATAACTTTTTAC
* *
572344 GGCGTTTGTTCTAAAAACGCCAG-TATAGGTCTTATCTTTTGCGGCGTTTGTATCCAAAAACGCC
1 GGCGTTTGTTCCAAAAACGCC-GCTATAGGTCTGA-CTTTTGCGGCGTTTGT-TCCAAAAACGCC
* * * * **
572408 ACTATAGATCTGACCTTTTGCGGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGT
63 -CTATAGATCTGACCTTTTGCGGCGTTTTTTCCAAAAACGCCACTATAGAT-ATAACTTTTTAC
* * * * * *
572472 GGCGTTTATTCCAAAAATGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCG
1 GGCGTTTGTTCCAAAAACGCCGCTATAGGTCT-GA-CTTTTGCGGCGTTTGTTCCAAAAACGCCC
* *
572537 TAATAGATATTGACCTATTGCGGCGTTTTTT
64 T-ATAGAT-CTGACCTTTTGCGGCGTTTTTT
572568 GTTCTCAAAC
Statistics
Matches: 189, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
127 19 0.10
128 122 0.65
129 48 0.25
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (124 bp):
GGCGTTTGTTCCAAAAACGCCGCTATAGGTCTGACTTTTGCGGCGTTTGTTCCAAAAACGCCCTA
TAGATCTGACCTTTTGCGGCGTTTTTTCCAAAAACGCCACTATAGATATAACTTTTTAC
Found at i:572543 original size:43 final size:41
Alignment explanation
Indices: 572215--572564 Score: 295
Period size: 43 Copynumber: 8.2 Consensus size: 41
572205 GGTAATTAGT
* * *
572215 GGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTGC
1 GGCGTTTGT-TCCAAAAACGCCG-TATAGATATGACCTTTTGC
* * * *
572258 GGCGTTTGTGTTCAAAAACGCCGTTATAGGTCTGACATTTTGC
1 GGCGTTTGT-TCCAAAAACGCCG-TATAGATATGACCTTTTGC
* * * * *
572301 GGCGTTTATGTCCAAAAACGCCACTATAGGTATGACTTTTTAC
1 GGCGTTTGT-TCCAAAAACGCC-GTATAGATATGACCTTTTGC
* * * * *
572344 GGCGTTTGTTCTAAAAACGCCAGTATAGGTCTTATCTTTTGC
1 GGCGTTTGTTCCAAAAACGCC-GTATAGATATGACCTTTTGC
* *
572386 GGCGTTTGTATCCAAAAACGCCACTATAGATCTGACCTTTTGC
1 GGCGTTTGT-TCCAAAAACGCC-GTATAGATATGACCTTTTGC
* * * * * * *
572429 GGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGT
1 GGCGTTTGTTCCAAAAACGCCG-TATAGAT-ATGACCTTTTGC
* *
572472 GGCGTTTATTCCAAAAATGCCGCTATAGATATCGACCTTTTGC
1 GGCGTTTGTTCCAAAAACGCCG-TATAGATAT-GACCTTTTGC
* *
572515 GGCGTTTGTTCAAAAAACGCCGTAATAGATATTGACCTATTGC
1 GGCGTTTGTTCCAAAAACGCCGT-ATAGATA-TGACCTTTTGC
572558 GGCGTTT
1 GGCGTTT
572565 TTTGTTCTCA
Statistics
Matches: 256, Mismatches: 44, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
42 54 0.21
43 201 0.79
44 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (41 bp):
GGCGTTTGTTCCAAAAACGCCGTATAGATATGACCTTTTGC
Found at i:573577 original size:20 final size:20
Alignment explanation
Indices: 573552--573623 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
573542 TAGTTGAAAA
573552 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
573572 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
573593 TCGCG-TGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
573612 TCGCGTTGCGAT
1 TCGCGTTGCGAT
573624 AGTCTACAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 8 0.20
20 24 0.60
21 8 0.20
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:573613 original size:40 final size:41
Alignment explanation
Indices: 573527--573667 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
573517 ATTCGCGTTG
573527 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
573568 CATTTCGCGTTGCGATAGTTGAAAATCGCG-TGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
573608 CATTTCGCGTTGCGATAGTCT-ACAGTCGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
*
573650 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
573668 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
40 34 0.37
41 45 0.48
42 11 0.12
43 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:573642 original size:22 final size:21
Alignment explanation
Indices: 573615--573686 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
573605 TTCCATTTCG
573615 CGTTGCGATAGTCTACAGTCGT
1 CGTTGCGATAGTCTACAGT-GT
** * *
573637 CGTTGCGATTTTCCA-AAT-T
1 CGTTGCGATAGTCTACAGTGT
573656 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAG-TGT
573678 CGTTGCGAT
1 CGTTGCGAT
573687 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 1 0.03
21 3 0.08
22 22 0.56
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:573660 original size:19 final size:19
Alignment explanation
Indices: 573636--573701 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
573626 TCTACAGTCG
573636 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
573655 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
573676 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
573696 TCGTTG
1 TCGTTG
573702 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:573668 original size:41 final size:40
Alignment explanation
Indices: 573534--573714 Score: 174
Period size: 41 Copynumber: 4.5 Consensus size: 40
573524 TTGCATTTCG
*
573534 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
*
573574 GCGTTGCGATAGTTGAAAATCGCG-TGCGATTTTCCATTTC
1 -CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
* *
573614 GCGTTGCGATAGTCT-ACAGTCGTCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTC
* * *
573656 CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-
1 CGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTC
* *
573697 CGTTGTGATAGTTAAAAA
1 CGTTGCGATAGTTGAAAA
573715 AAAAGATTTT
Statistics
Matches: 128, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
40 35 0.27
41 79 0.62
42 11 0.09
43 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
Found at i:573797 original size:6 final size:6
Alignment explanation
Indices: 573786--573852 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
573776 GACACGTATT
573786 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
573834 ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
573853 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.16
6 51 0.84
ACGTcount: A:0.31, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:574381 original size:6 final size:6
Alignment explanation
Indices: 574355--574432 Score: 135
Period size: 6 Copynumber: 13.5 Consensus size: 6
574345 TCTCGTCTCG
574355 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
574400 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
574433 AATACGTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.21
6 57 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:574559 original size:22 final size:21
Alignment explanation
Indices: 574532--574688 Score: 78
Period size: 21 Copynumber: 7.6 Consensus size: 21
574522 AATTTGGAAA
574532 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAGACT
* **
574554 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGC-AACTGTAGACT
* *
574574 ATCGCAATGCGACTGTAGACT
1 ATCGCAACGCAACTGTAGACT
* **
574595 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGC-AACTGTAGACT
* *
574615 ATCGTAACGCGAA-TTTCA-ACT
1 ATCGCAACGC-AACTGT-AGACT
* **
574636 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGC-AACTGTAGACT
*
574656 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCAACTGTAGACT
574677 ATCGCAACGCAA
1 ATCGCAACGCAA
574689 AATGGAAAAC
Statistics
Matches: 98, Mismatches: 26, Indels: 23
0.67 0.18 0.16
Matches are distributed among these distances:
19 7 0.07
20 36 0.37
21 38 0.39
22 17 0.17
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCAACTGTAGACT
Found at i:574589 original size:41 final size:41
Alignment explanation
Indices: 574526--574733 Score: 285
Period size: 41 Copynumber: 5.0 Consensus size: 41
574516 ACAACGAATT
*
574526 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAA
*
574568 TGGAAAATCGCAATGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
* * *
574609 TGGAAAATCGTAACGCGAATTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
*
574650 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCAAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
* * * *
574691 TGGAAAACCACAACGCGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
574732 TG
1 TG
574734 CAACGCGAAT
Statistics
Matches: 148, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.01
41 131 0.89
42 16 0.11
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
Found at i:574600 original size:21 final size:21
Alignment explanation
Indices: 574532--574686 Score: 90
Period size: 20 Copynumber: 7.5 Consensus size: 21
574522 AATTTGGAAA
*
574532 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CGACTGTAGACT
* **
574554 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGCG-ACTGTAGACT
*
574574 ATCGCAATGCGACTGTAGACT
1 ATCGCAACGCGACTGTAGACT
* **
574595 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGCG-ACTGTAGACT
* * *
574615 ATCGTAACGCGAATTTCA-ACT
1 ATCGCAACGCGACTGT-AGACT
* **
574636 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGCG-ACTGTAGACT
574656 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCGACTGTAGACT
574677 ATCGCAACGC
1 ATCGCAACGC
574687 AAAATGGAAA
Statistics
Matches: 99, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
19 9 0.09
20 36 0.36
21 36 0.36
22 18 0.18
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGACTGTAGACT
Found at i:574821 original size:41 final size:41
Alignment explanation
Indices: 574766--574998 Score: 334
Period size: 41 Copynumber: 5.7 Consensus size: 41
574756 AGATCGCGTT
574766 GCGAT-TTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
574806 GCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
* *
574847 GCGA-CTGT-AGACTATCGCAATGCGAAATGGAAAATCACAAC
1 GCGATCT-TCA-ACTATCGCAACGCGAAATGGAAAATCGCAAC
574888 GCGAAT-TTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCG-ATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
* *
574929 GCGA-CTGT-AGACTATCGCAACGCGAAATGGAAAACCACAAC
1 GCGATCT-TCA-ACTATCGCAACGCGAAATGGAAAATCGCAAC
*
574970 GCGATTTTCAACTATCGCAACGCGAAATG
1 GCGATCTTCAACTATCGCAACGCGAAATG
574999 CAACGCGAAT
Statistics
Matches: 175, Mismatches: 7, Indels: 21
0.86 0.03 0.10
Matches are distributed among these distances:
40 11 0.06
41 159 0.91
42 5 0.03
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
GCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
Found at i:574874 original size:82 final size:81
Alignment explanation
Indices: 574775--574998 Score: 394
Period size: 82 Copynumber: 2.7 Consensus size: 81
574765 TGCGATTTCA
*
574775 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGAT-TTCAACTATCGCAACGCGAAATGGAAAA
574840 TCGCAACGCGACTGTAG
65 TCGCAACGCGACTGTAG
*
574857 ACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCG-ATTTCAACTATCGCAACGCGAAATGGAAAA
574922 TCGCAACGCGACTGTAG
65 TCGCAACGCGACTGTAG
*
574939 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGA-TTTCAACTATCGCAACGCGAAATG
574999 CAACGCGAAT
Statistics
Matches: 136, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
81 1 0.01
82 133 0.98
83 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (81 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTCAACTATCGCAACGCGAAATGGAAAAT
CGCAACGCGACTGTAG
Found at i:574945 original size:224 final size:224
Alignment explanation
Indices: 574551--574957 Score: 617
Period size: 224 Copynumber: 1.8 Consensus size: 224
574541 ACAACTGTAG
*
574551 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
* * * *
574616 TCGTAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCG
66 TCGCAACGCGAATGTCAACTATCGCAACGCGAAATGGAAAATCACAACGCGAATGTAGACTATCG
* *
574681 CAACGCAAAATGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTT
131 CAACGCAAAATGGAAAACCACAACGCGACTGTCAACTATCGCAACGCGAAATGCAACGCGAATTT
574746 GCAATGATGGAGATCGCGTTGCGATTTCA
196 GCAATGATGGAGATCGCGTTGCGATTTCA
574775 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCT-TCA-ACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA-CTGT-AGACTATCGCAACGCGAAATGGAA
* * *
574838 AATCGCAACGCGACTGT-AGACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCA-ACT
64 AATCGCAACGCGAATGTCA-ACTATCGCAACGCGAAATGGAAAATCACAACGCGAATGT-AGACT
* * *
574901 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATG
127 ATCGCAACGCAAAATGGAAAACCACAACGCGACTGTCA-ACTATCGCAACGCGAAATG
574958 GAAAACCACA
Statistics
Matches: 165, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
223 2 0.01
224 159 0.96
225 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (224 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
TCGCAACGCGAATGTCAACTATCGCAACGCGAAATGGAAAATCACAACGCGAATGTAGACTATCG
CAACGCAAAATGGAAAACCACAACGCGACTGTCAACTATCGCAACGCGAAATGCAACGCGAATTT
GCAATGATGGAGATCGCGTTGCGATTTCA
Found at i:575024 original size:265 final size:265
Alignment explanation
Indices: 574526--575140 Score: 1074
Period size: 265 Copynumber: 2.3 Consensus size: 265
574516 ACAACGAATT
* *
574526 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAATGCGACTG
1 TGGAAAATCGCAACG-CGATCT-TCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTG
* **
574589 TAGACTATCGCAACGCGAAATGGAAAATCGTAACGCGAATTTCAACTATCGCAACGCGAAATGGA
63 TAGACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCAACTATCGCAACGCGAAATGGA
574654 AAATCGCAACGCGACTGTAGACTATCGCAACGCAAAATGGAAAACCACAACGCGATTTTCAACTA
128 AAATCGCAACGCGACTGTAGACTATCGCAACGCAAAATGGAAAACCACAACGCGATTTTCAACTA
574719 TCGCAACGCGAAATGCAACGCGAATTTGCAATGATGGAGATCGCGTTGCGATTTCAACTATCGCA
193 TCGCAACGCGAAATGCAACGCGAATTTGCAATGATGGAGATCGCGTTGCGATTTCAACTATCGCA
574784 ACGCGAAA
258 ACGCGAAA
574792 TGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
1 TGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
574857 ACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
66 ACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
*
574922 TCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCAACTATCG
131 TCGCAACGCGACTGTAGACTATCGCAACGCAAAATGGAAAACCACAACGCGATTTTCAACTATCG
*
574987 CAACGCGAAATGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACG
196 CAACGCGAAATGCAACGCGAATTTGCAATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACG
575052 CGAAA
261 CGAAA
* * * *
575057 TGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCA
1 TGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
575122 -ACTATCGCAATGCGAAATG
65 GACTATCGCAATGCGAAATG
575141 CAACGTGAAT
Statistics
Matches: 335, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
265 315 0.94
266 20 0.06
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (265 bp):
TGGAAAATCGCAACGCGATCTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
ACTATCGCAATGCGAAATGGAAAATCACAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
TCGCAACGCGACTGTAGACTATCGCAACGCAAAATGGAAAACCACAACGCGATTTTCAACTATCG
CAACGCGAAATGCAACGCGAATTTGCAATGATGGAGATCGCGTTGCGATTTCAACTATCGCAACG
CGAAA
Found at i:575054 original size:20 final size:20
Alignment explanation
Indices: 575031--575136 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
575021 AGATCGCGTT
*
575031 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
575051 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
575071 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
575092 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
575112 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
575133 GCGA
1 GCGA
575137 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:575062 original size:142 final size:142
Alignment explanation
Indices: 574892--575169 Score: 470
Period size: 142 Copynumber: 2.0 Consensus size: 142
574882 CACAACGCGA
**
574892 ATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA-CTGTAGACTATCGCAACGCGAAA
1 ATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCA-ACTATCGCAACGCGAAA
*
574956 TGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGAT-GATG
65 TGGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TG
575020 GAGATCGCGTTGCG
129 GAGATCGCGTTGCG
575034 ATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAAT
1 ATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAAT
* * *
575099 GGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGA
66 GGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGA
575164 GATCGC
131 GATCGC
575170 AATGCGAATT
Statistics
Matches: 128, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
142 124 0.97
143 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (142 bp):
ATTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAAT
GGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGA
GATCGCGTTGCG
Found at i:575088 original size:41 final size:41
Alignment explanation
Indices: 575038--575140 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
575028 GTTGCGATTT
*
575038 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
575079 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
575120 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
575141 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:575984 original size:46 final size:46
Alignment explanation
Indices: 575930--576030 Score: 175
Period size: 46 Copynumber: 2.2 Consensus size: 46
575920 GTTACTCGGA
*
575930 ACGGATCTGGTGCAGCCGCAGTTATTATGCGGCTGTGCTATCTACG
1 ACGGATCTGGTGCAGCCGCAGTTAATATGCGGCTGTGCTATCTACG
* *
575976 ACGGATCTGGTGCAGCCGCAGTTAATATGCTGCTGTGCTATCTGCG
1 ACGGATCTGGTGCAGCCGCAGTTAATATGCGGCTGTGCTATCTACG
576022 ACGGATCTG
1 ACGGATCTG
576031 AATCTGTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.28
Consensus pattern (46 bp):
ACGGATCTGGTGCAGCCGCAGTTAATATGCGGCTGTGCTATCTACG
Found at i:578853 original size:26 final size:26
Alignment explanation
Indices: 578814--578870 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
578804 CATCATACCA
578814 GGGCC-TTTTCATTTTTAATT-TATTT
1 GGGCCTTTTTCATTTTTAATTAT-TTT
578839 GGGCCTTTTTCATTTTTAATTATTTT
1 GGGCCTTTTTCATTTTTAATTATTTT
578865 GGGCCT
1 GGGCCT
578871 CTTTAGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 5 0.17
26 24 0.80
27 1 0.03
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (26 bp):
GGGCCTTTTTCATTTTTAATTATTTT
Found at i:600391 original size:30 final size:30
Alignment explanation
Indices: 600356--600425 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
600346 ATGATTTTTT
* *
600356 AATTTAGTCCTTTAACTTTAGATTTTACTC
1 AATTTAGTACTTTAACTTTACATTTTACTC
600386 AATTTAGTACTTTAACTTTACATTTTACTC
1 AATTTAGTACTTTAACTTTACATTTTACTC
600416 AATTTAGTAC
1 AATTTAGTAC
600426 AGTTATCTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.49
Consensus pattern (30 bp):
AATTTAGTACTTTAACTTTACATTTTACTC
Found at i:602507 original size:39 final size:39
Alignment explanation
Indices: 602448--602554 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 39
602438 CCATCTTACG
* *
602448 AGTATAAGTCTCCTCCACCACCACCCAAGCACCCTCACA
1 AGTACAAGTCTCCACCACCACCACCCAAGCACCCTCACA
*
602487 AGTACAAGTCTCCACCACCACCATCACCACCCAAGCACCCTTACA
1 AGTACAAGTCT---CCACCA-C--CACCACCCAAGCACCCTCACA
*
602532 AGTACAAGTCTCCACCTCCACCA
1 AGTACAAGTCTCCACCACCACCA
602555 TCACCACCCA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
39 15 0.26
41 1 0.02
42 10 0.17
43 1 0.02
45 31 0.53
ACGTcount: A:0.32, C:0.46, G:0.07, T:0.15
Consensus pattern (39 bp):
AGTACAAGTCTCCACCACCACCACCCAAGCACCCTCACA
Found at i:602523 original size:45 final size:45
Alignment explanation
Indices: 602466--602605 Score: 199
Period size: 45 Copynumber: 3.1 Consensus size: 45
602456 TCTCCTCCAC
*
602466 CACCACCCAAGCACCCTCACAAGTACAAGTCTCCACCACCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
*
602511 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCTCCACCAT
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
* * * * * * *
602556 CACCACCCAATCACCATTATAAATACAAGTCCCCACCCCCACCAC
1 CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
602601 CACCA
1 CACCA
602606 GTTTACAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.34, C:0.49, G:0.05, T:0.13
Consensus pattern (45 bp):
CACCACCCAAGCACCCTTACAAGTACAAGTCTCCACCACCACCAT
Found at i:602842 original size:29 final size:29
Alignment explanation
Indices: 602802--602857 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
602792 TAACCTACAT
602802 TTTTTTTTTGCATCTCTTCAAGGAGCACA
1 TTTTTTTTTGCATCTCTTCAAGGAGCACA
602831 TTTTTTTTTGCATCTCTTCAAGGAGCA
1 TTTTTTTTTGCATCTCTTCAAGGAGCA
602858 TTATTTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (29 bp):
TTTTTTTTTGCATCTCTTCAAGGAGCACA
Found at i:604017 original size:20 final size:20
Alignment explanation
Indices: 603992--604032 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
603982 ATGTTGGAGG
* *
603992 AAATATTATATTTTACGTTT
1 AAATATTATATATTAAGTTT
604012 AAATATTATATATTAAGTTT
1 AAATATTATATATTAAGTTT
604032 A
1 A
604033 TTACATCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATATTATATATTAAGTTT
Found at i:606901 original size:16 final size:19
Alignment explanation
Indices: 606880--606918 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
606870 ATTCAAAGTT
606880 TTCA-TTCCTTTG-A-TCC
1 TTCATTTCCTTTGTACTCC
606896 TTCATTTCCTTTGTACTCC
1 TTCATTTCCTTTGTACTCC
606915 TTCA
1 TTCA
606919 AGGATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 8 0.40
18 1 0.05
19 7 0.35
ACGTcount: A:0.13, C:0.31, G:0.05, T:0.51
Consensus pattern (19 bp):
TTCATTTCCTTTGTACTCC
Found at i:610056 original size:16 final size:16
Alignment explanation
Indices: 610037--610068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
610027 ATTAACATGT
610037 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
610053 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
610069 ATTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:616293 original size:19 final size:20
Alignment explanation
Indices: 616255--616299 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
616245 ATTTGTTTTT
616255 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATGAA
* *
616275 ATTAAATTTTTAT-TTTGAA
1 AATAAATTTTTATCTATGAA
616294 AATAAA
1 AATAAA
616300 ATATTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATGAA
Found at i:621495 original size:20 final size:20
Alignment explanation
Indices: 621467--621506 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
621457 ACACCAAATC
621467 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
* *
621487 CTCTTAAATCCTCTTAACTT
1 CTCTCAAATCCTCTCAACTT
621507 AAGGTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (20 bp):
CTCTCAAATCCTCTCAACTT
Found at i:621503 original size:10 final size:10
Alignment explanation
Indices: 621461--621500 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
621451 TTCATCACAC
621461 CAAATCCTCT
1 CAAATCCTCT
621471 CAAATCCTCT
1 CAAATCCTCT
* *
621481 CAACTTCTCT
1 CAAATCCTCT
*
621491 TAAATCCTCT
1 CAAATCCTCT
621501 TAACTTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:621529 original size:12 final size:12
Alignment explanation
Indices: 621512--621565 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
621502 AACTTAAGGT
621512 ATATTTTATTTA
1 ATATTTTATTTA
621524 ATATTTTA-TTA
1 ATATTTTATTTA
*
621535 GTA-TTTATTT-
1 ATATTTTATTTA
621545 A-A--TTATTTA
1 ATATTTTATTTA
621554 ATATTTTATTTA
1 ATATTTTATTTA
621566 TTTAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 6 0.17
9 2 0.06
10 5 0.14
11 7 0.20
12 15 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATATTTTATTTA
Found at i:621575 original size:15 final size:16
Alignment explanation
Indices: 621516--621575 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 16
621506 TAAGGTATAT
621516 TTTATTTAATATTTTA
1 TTTATTTAATATTTTA
621532 -TTAGTATT--TA-TTTA
1 TTTA-T-TTAATATTTTA
*
621546 ATTATTTAATATTTTA
1 TTTATTTAATATTTTA
621562 TTTATTTAAT-TTTT
1 TTTATTTAATATTTT
621576 TTTGCATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 2 0.05
14 5 0.14
15 14 0.38
16 14 0.38
17 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTATTTAATATTTTA
Done.