Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 109 of 770
Found at i:31098786 original size:21 final size:20
Alignment explanation
Indices: 31098762--31098801 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
31098752 TATTATCTTT
31098762 ATTATT-TACCATATTATTTAC
1 ATTATTATA-CAT-TTATTTAC
31098783 ATTATTATACATTTATTTA
1 ATTATTATACATTTATTTA
31098802 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 9 0.50
22 2 0.11
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTATACATTTATTTAC
Found at i:31098841 original size:22 final size:19
Alignment explanation
Indices: 31098799--31098868 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 19
31098789 ATACATTTAT
31098799 TTATATATTTTATAATATA
1 TTATATATTTTATAATATA
31098818 TTATATCATTTTACTATATATA
1 TTATAT-ATTTTA-TA-ATATA
*
31098840 TTATATTATTTT-TATTATA
1 TTATA-TATTTTATAATATA
*
31098859 TTTTATATTT
1 TTATATATTT
31098869 ATTATTATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 5 0.11
19 14 0.31
20 8 0.18
21 2 0.04
22 15 0.33
23 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATATATTTTATAATATA
Found at i:31098873 original size:19 final size:18
Alignment explanation
Indices: 31098795--31098876 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 18
31098785 TATTATACAT
31098795 TTAT-TTATATATTTTATA
1 TTATATTATATATTTT-TA
*
31098813 ATATATTATATCATTTTACTA
1 TTATATTATAT-ATTTT--TA
31098834 TATATATTATATTATTTTTA
1 T-TATATTATA-TATTTTTA
*
31098854 TTATATTTTATATTTATTA
1 TTATATTATATATTT-TTA
31098873 TTAT
1 TTAT
31098877 GTATAATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.15
19 21 0.39
20 8 0.15
21 2 0.04
22 14 0.26
23 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTATATATTTTTA
Found at i:31098881 original size:16 final size:14
Alignment explanation
Indices: 31098793--31098873 Score: 51
Period size: 14 Copynumber: 5.6 Consensus size: 14
31098783 ATTATTATAC
31098793 ATTTATT-TA-TAT
1 ATTTATTATATTAT
31098805 ATTTTATAATATATTAT
1 A-TTTAT--TATATTAT
* * *
31098822 A-TCATTTTACTAT
1 ATTTATTATATTAT
*
31098835 ATATATTATATTAT
1 ATTTATTATATTAT
*
31098849 TTTTATTATATTTTAT
1 ATTTATTATA--TTAT
31098865 ATTTATTAT
1 ATTTATTAT
31098874 TATGTATAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
12 1 0.02
13 12 0.24
14 16 0.31
15 4 0.08
16 14 0.27
17 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATTATATTAT
Found at i:31099133 original size:12 final size:13
Alignment explanation
Indices: 31099111--31099147 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
31099101 TTTTTACCTG
*
31099111 ATTTATTTTTTAA
1 ATTTGTTTTTTAA
31099124 A-TTGTTTTTTAA
1 ATTTGTTTTTTAA
31099136 ATTTGTTTTTTA
1 ATTTGTTTTTTA
31099148 TCCTTTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (13 bp):
ATTTGTTTTTTAA
Found at i:31099420 original size:23 final size:23
Alignment explanation
Indices: 31099354--31099421 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
31099344 TTTTGTATTT
* *
31099354 TGCATGAAATGATAATGTGTATA
1 TGCATGAAATGTTAATGTATATA
* ** * *
31099377 TTCATGTTATTTGTGAT-TATATA
1 TGCATGAAATGT-TAATGTATATA
31099400 TGCATGAAATGTTAATGTATAT
1 TGCATGAAATGTTAATGTATAT
31099422 TGTGTGATTT
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
22 3 0.10
23 25 0.81
24 3 0.10
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (23 bp):
TGCATGAAATGTTAATGTATATA
Found at i:31100215 original size:30 final size:30
Alignment explanation
Indices: 31100181--31100242 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31100171 GCTGCATATG
31100181 TTTGTTATCTTGTTTCCACAAACATTGCAT
1 TTTGTTATCTTGTTTCCACAAACATTGCAT
31100211 TTTGTTATCTTGTTTCCACAAACATTGCAT
1 TTTGTTATCTTGTTTCCACAAACATTGCAT
31100241 TT
1 TT
31100243 ACATGACCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTGTTATCTTGTTTCCACAAACATTGCAT
Found at i:31105588 original size:40 final size:40
Alignment explanation
Indices: 31105438--31105605 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
31105428 CGGAATACAA
* * *
31105438 CCGGATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGC
* ** *
31105478 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
31105518 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
** * * *
31105558 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
31105598 CCGGATAT
1 CCGGATAT
31105606 CATTCAATTG
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 102 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31106850 original size:20 final size:20
Alignment explanation
Indices: 31106825--31106862 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31106815 GGATGAACAC
31106825 TTTTCTTCCTTTCTTTTTTT
1 TTTTCTTCCTTTCTTTTTTT
* *
31106845 TTTTCTTTCTTTGTTTTT
1 TTTTCTTCCTTTCTTTTT
31106863 GTTTCTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTCCTTTCTTTTTTT
Found at i:31106852 original size:16 final size:18
Alignment explanation
Indices: 31106833--31106868 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
31106823 ACTTTTCTTC
31106833 CTTTCTTT-TTTTT-TTT
1 CTTTCTTTGTTTTTGTTT
31106849 CTTTCTTTGTTTTTGTTT
1 CTTTCTTTGTTTTTGTTT
31106867 CT
1 CT
31106869 CTCATGTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (18 bp):
CTTTCTTTGTTTTTGTTT
Found at i:31113608 original size:40 final size:40
Alignment explanation
Indices: 31113458--31113625 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
31113448 CGGAATACAA
* * *
31113458 CCGGATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGC
* ** *
31113498 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
31113538 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
** * * *
31113578 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
31113618 CCGGATAT
1 CCGGATAT
31113626 CATTCAATTG
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 102 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31114885 original size:18 final size:18
Alignment explanation
Indices: 31114864--31114901 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31114854 ACTTTTCTTC
* *
31114864 CTTTCTTTTTTTTTTTTT
1 CTTTCTTTGTTTTTGTTT
31114882 CTTTCTTTGTTTTTGTTT
1 CTTTCTTTGTTTTTGTTT
31114900 CT
1 CT
31114902 CTCATGTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (18 bp):
CTTTCTTTGTTTTTGTTT
Found at i:31118632 original size:13 final size:13
Alignment explanation
Indices: 31118610--31118642 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31118600 AAGGGTTTGT
31118610 TTAT-TAAACTAA
1 TTATCTAAACTAA
31118622 TTATCTAAACTAA
1 TTATCTAAACTAA
*
31118635 TTAACTAA
1 TTATCTAA
31118643 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:31121567 original size:7 final size:6
Alignment explanation
Indices: 31121547--31121608 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
31121537 AAGAAAATTG
* * * * *
31121547 AAATGA AAATAA AAATCA AAAGAA AAATAA GAAT-A AAATAA ATAAAAGA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATA-A
31121596 AAATAA AAATAA A
1 AAATAA AAATAA A
31121609 TAGGAGGATT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 4 0.09
6 32 0.73
7 6 0.14
8 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:31124288 original size:39 final size:40
Alignment explanation
Indices: 31124241--31124384 Score: 193
Period size: 39 Copynumber: 3.6 Consensus size: 40
31124231 AATATTCGAG
31124241 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* *
31124280 TGATATCCGGGCTAAG-CTCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
* * *
31124319 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
** * *
31124359 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAGTCCCGAAGGC
31124385 GTTTGAATGA
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 52 0.57
40 40 0.43
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (40 bp):
TGATATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA
Found at i:31126965 original size:13 final size:13
Alignment explanation
Indices: 31126928--31126965 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
31126918 GTTTGTTTAT
*
31126928 TAAATTAATTATC
1 TAAATTAATTAAC
*
31126941 TAAACTAATTAAC
1 TAAATTAATTAAC
31126954 TAAATTAATTAA
1 TAAATTAATTAA
31126966 AGTGAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATTAATTAAC
Found at i:31129951 original size:59 final size:57
Alignment explanation
Indices: 31129867--31129997 Score: 210
Period size: 59 Copynumber: 2.3 Consensus size: 57
31129857 AAAATTGTAC
* *
31129867 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
31129924 AGCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTG---ATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
31129983 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
31129998 GATTCACTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 2 0.03
57 17 0.25
59 50 0.72
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
AGCACTAAGTGTGCGAGTCTGATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:31129955 original size:30 final size:30
Alignment explanation
Indices: 31129837--31129997 Score: 206
Period size: 29 Copynumber: 5.5 Consensus size: 30
31129827 GACAAGATTG
* * * * *
31129837 GCACTAAGTGTGCGGGTTTTAAAATTGTACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
* *
31129868 GCACTAAGTGTGCGAGTTTG---ATTATGTA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
31129896 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31129925 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31129955 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31129984 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31129998 GATTCACTAT
Statistics
Matches: 119, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.02
28 21 0.18
29 48 0.40
30 30 0.25
31 18 0.15
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:31134322 original size:40 final size:40
Alignment explanation
Indices: 31134264--31134488 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
31134254 GGATATAACA
* * *
31134264 ACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTC
* * *
31134303 ACTAGCATAAATGCCTTCGGGTCTTAGCCCGG-ATATAG-C
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTC
*
31134342 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 -ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
* *
31134383 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
* *
31134423 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGAATTAATC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
* *
31134463 ACTAGCACAAATGTCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
31134489 ACCCCGTTAG
Statistics
Matches: 167, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 7 0.04
40 158 0.95
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
Found at i:31134396 original size:80 final size:80
Alignment explanation
Indices: 31134239--31134488 Score: 328
Period size: 80 Copynumber: 3.1 Consensus size: 80
31134229 ACCCAAGTAT
* * * * *
31134239 CTTCGGGATTTAG-CCGGATATAACAACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGG-ATATGG
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAG
*
31134301 TCACTAGCATAAATGC
65 TCACTAGCACAAATGC
*
31134317 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* * *
31134382 AACTCGCACCAATGC
66 CACTAGCACAAATGC
* * *
31134397 CTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGAATTAA
1 CTTCGGGACTTAGCCCGGATA-TAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
*
31134461 TCACTAGCACAAATGT
65 TCACTAGCACAAATGC
31134477 CTTCGGGACTTA
1 CTTCGGGACTTA
31134489 ACCCCGTTAG
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
78 11 0.07
79 20 0.13
80 117 0.78
81 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
CACTAGCACAAATGC
Found at i:31152880 original size:20 final size:20
Alignment explanation
Indices: 31152855--31152899 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
31152845 ATGGACTAAA
* *
31152855 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
31152875 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
31152895 ATGAA
1 ATGAA
31152900 TACATGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:31158935 original size:48 final size:48
Alignment explanation
Indices: 31158860--31159181 Score: 332
Period size: 48 Copynumber: 6.7 Consensus size: 48
31158850 TAACATGTGT
*
31158860 GCCAGTGTAAAACCATGTCTGGGACATGGCATCAGCCA-TGATATGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCCATTGATATGAGA
* * * *
31158908 GCCAGTGTAAGACCATGTCTGGTACATGGCATCGGCATTGATATGTGC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATTGATATGAGA
** * * * *
31158956 GATAGTGTAAGACCATGTCTGAGACATGGCATAGACCA--CACTATAAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG-CCATTGA-TATGAGA
* *
31159004 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACT-AGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATTGATA-TGAGA
* * * *
31159052 GCTAGTGTAAGACCGTGTCTGGGACATGGCATCGACATTGAGACT-AGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATTGATA-TGAGA
* * * * *
31159100 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCC-TCGACATGTGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCCATTGATATGAGA
* *
31159148 GCCAGTGTAAGACCATGTTTGGAACATGGCATCG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCG
31159182 ACAATTCACC
Statistics
Matches: 234, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
47 8 0.03
48 220 0.94
49 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATTGATATGAGA
Found at i:31159035 original size:144 final size:144
Alignment explanation
Indices: 31158860--31159184 Score: 408
Period size: 144 Copynumber: 2.3 Consensus size: 144
31158850 TAACATGTGT
* * *
31158860 GCCAGTGTAAAACCATGTCTGGGACATGGCATCAGCCA-TGATA-TGAGAGCCAGTGTAAGACCA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACATTGAGACT-AGAGCCAGTGTAAGACCA
* * * *
31158923 TGTCTGGTACATGGCATCGGCATTGATA-T-GTGCGATAGTGTAAGACCATGTCTGAGACATGGC
64 TGTCTGGGACATGGCATCGACATTGAGACTAGAGC--TAGTGTAAGACCATGTCTGAGACATGGC
31158986 ATAGACCAC-ACTATAAGA
127 ATAGACCACGAC-ATAAGA
* *
31159004 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACTAGAGCTAGTGTAAGACCGTG
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACTAGAGCCAGTGTAAGACCATG
* * *
31159069 TCTGGGACATGGCATCGACATTGAGACTAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCG
66 TCTGGGACATGGCATCGACATTGAGACTAGAGCTAGTGTAAGACCATGTCTGAGACATGGCATAG
* * **
31159134 GCCTCGACATGTGA
131 ACCACGACATAAGA
* *
31159148 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGACA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACA
31159185 ATTCACCCTT
Statistics
Matches: 158, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
143 3 0.02
144 148 0.94
145 4 0.03
146 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (144 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACTAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGACATTGAGACTAGAGCTAGTGTAAGACCATGTCTGAGACATGGCATAG
ACCACGACATAAGA
Found at i:31162570 original size:46 final size:46
Alignment explanation
Indices: 31162517--31162692 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31162507 TATTTGGGCA
31162517 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
31162563 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
31162610 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
31162656 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31162693 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:31162672 original size:93 final size:93
Alignment explanation
Indices: 31162513--31162684 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31162503 GGGATATTTG
* *
31162513 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31162578 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
31162606 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31162671 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31162685 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:31166775 original size:31 final size:31
Alignment explanation
Indices: 31166697--31166775 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
31166687 TTTTGAGGGT
*
31166697 CATACGCCCGTGTAGGTAGGCCATGTGGTCA
1 CATACGCCCGTGTGGGTAGGCCATGTGGTCA
* * * *
31166728 CACACACTCGTGTGGGTAGGCCGTGTGGTCA
1 CATACGCCCGTGTGGGTAGGCCATGTGGTCA
*
31166759 CATACGCCCGTATGGGT
1 CATACGCCCGTGTGGGT
31166776 TGGGATACGC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.23
Consensus pattern (31 bp):
CATACGCCCGTGTGGGTAGGCCATGTGGTCA
Found at i:31170639 original size:68 final size:70
Alignment explanation
Indices: 31170567--31170764 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
31170557 ACACCCTGTA
* * * *
31170567 GTAGCTAGGTCACATGTGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCACATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
31170629 ATAAAT
65 ATAAAT
* * *
31170635 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTATGTGAAAG
1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
31170700 ATAAAT
65 ATAAAT
*
31170706 GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
31170765 AGACAAATCG
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
68 23 0.20
69 3 0.03
70 1 0.01
71 90 0.77
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (70 bp):
GTAGCTAGGTCACATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:31170689 original size:71 final size:71
Alignment explanation
Indices: 31170601--31170764 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
31170591 GAGATGTATC
*
31170601 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
31170666 AGGACA
66 AGGACA
*
31170672 CCATGTAGACAAGAGAGCTATGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
31170737 AGGACA
66 AGGACA
31170743 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
31170765 AGACAAATCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 90 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA
AGGACA
Found at i:31172968 original size:2 final size:2
Alignment explanation
Indices: 31172961--31172987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31172951 GAGACTAGTC
31172961 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 A
31172988 CATGTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31175023 original size:30 final size:30
Alignment explanation
Indices: 31174989--31175049 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
31174979 TCCTTAACTC
31174989 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
31175019 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
31175049 A
1 A
31175050 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:31177417 original size:2 final size:2
Alignment explanation
Indices: 31177410--31177434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31177400 GAGACTAGTC
31177410 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 A
31177435 CATGTCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31181627 original size:20 final size:20
Alignment explanation
Indices: 31181589--31181627 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31181579 ATAGCCATAG
*
31181589 ATAATATTCTTTCATTCAAC
1 ATAATATTCTTTCAATCAAC
31181609 ATAAT-TTCTTATCAATCAA
1 ATAATATTCTT-TCAATCAA
31181628 GCAAAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATATTCTTTCAATCAAC
Found at i:31188448 original size:29 final size:28
Alignment explanation
Indices: 31188381--31188452 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
31188371 AAAATTGTAC
* * *
31188381 AGCACTAAGTGTGCGAGTTTGATTCTAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
31188409 AGCACTAAGTGTGCGAG-CTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTG--AATATAT
31188438 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
31188453 GATTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 17 0.44
29 20 0.51
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:31193430 original size:41 final size:41
Alignment explanation
Indices: 31193373--31193458 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
31193363 TACTGGGAGT
31193373 AAATCGATAATCCGATCTATGCTCATAAACACCTGGAAAGA
1 AAATCGATAATCCGATCTATGCTCATAAACACCTGGAAAGA
31193414 AAATCGATAATCCGATCTATGCTCATAAACACCTGGAAAGA
1 AAATCGATAATCCGATCTATGCTCATAAACACCTGGAAAGA
31193455 AAAT
1 AAAT
31193459 TACAAAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (41 bp):
AAATCGATAATCCGATCTATGCTCATAAACACCTGGAAAGA
Found at i:31196643 original size:12 final size:12
Alignment explanation
Indices: 31196626--31196651 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31196616 GGCTTAAACC
31196626 TAGAATTTTTCT
1 TAGAATTTTTCT
31196638 TAGAATTTTTCT
1 TAGAATTTTTCT
31196650 TA
1 TA
31196652 AGTTCTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (12 bp):
TAGAATTTTTCT
Found at i:31203022 original size:43 final size:44
Alignment explanation
Indices: 31202973--31203107 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 44
31202963 TGAGATAATG
31202973 GCATCTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGTG-A
1 GCATCTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGTGCA
* * * *
31203016 GCATCTGAGCTTGTTGAAAGGTCTGAGTTCATAATGGATGCGATTCATGCA
1 GCATCTGAGCTCGTTGAGAGGTCCGAGTTCAT--T--ATG-GA-T-GTGCA
* * *
31203067 ACATCCGAGCTCGTTGAGAGGTTCGAGTTCATTATGGATGT
1 GCATCTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGT
31203108 ATTACATGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
43 29 0.40
44 1 0.01
45 2 0.03
46 2 0.03
47 6 0.08
48 2 0.03
49 2 0.03
50 2 0.03
51 27 0.37
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (44 bp):
GCATCTGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGTGCA
Found at i:31204654 original size:48 final size:48
Alignment explanation
Indices: 31204580--31204759 Score: 183
Period size: 48 Copynumber: 3.9 Consensus size: 48
31204570 CACATGGTAG
* * * *
31204580 GATGCCAATGCCATAT-CTCGGGTATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCT-AGATATGGTCTTACATGGGATCACATATT
31204628 GATGCCAATGCCATGTCCTAGATATGGTCTTACATGGGATCACATATT
1 GATGCCAATGCCATGTCCTAGATATGGTCTTACATGGGATCACATATT
* * * ** *
31204676 GATGCCGAT---A-GTCC-AGCTATGGTCTTACACGAAATTACATATT
1 GATGCCAATGCCATGTCCTAGATATGGTCTTACATGGGATCACATATT
* * * *
31204719 GATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC
1 GATGCCAATGCCATGTCCTAGATATGGTCTTACATGGGATC
31204760 GCACATAACC
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
43 31 0.29
44 4 0.04
45 1 0.01
46 1 0.01
47 4 0.04
48 64 0.60
49 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCTAGATATGGTCTTACATGGGATCACATATT
Found at i:31206820 original size:28 final size:28
Alignment explanation
Indices: 31206780--31206841 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
31206770 GTTACCAATC
31206780 TAGTATTAAAATGGCATTGTATGAAGCA
1 TAGTATTAAAATGGCATTGTATGAAGCA
*
31206808 TAGTATTAAAATGGCATTGTATGAAGCC
1 TAGTATTAAAATGGCATTGTATGAAGCA
31206836 TAGTAT
1 TAGTAT
31206842 GGATGCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (28 bp):
TAGTATTAAAATGGCATTGTATGAAGCA
Found at i:31206829 original size:16 final size:16
Alignment explanation
Indices: 31206782--31206829 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
31206772 TACCAATCTA
31206782 GTATTAAAATGGCATT
1 GTATTAAAATGGCATT
* *
31206798 GTA-T-GAA--GCATA
1 GTATTAAAATGGCATT
31206810 GTATTAAAATGGCATT
1 GTATTAAAATGGCATT
31206826 GTAT
1 GTAT
31206830 GAAGCCTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 8
0.67 0.11 0.22
Matches are distributed among these distances:
12 7 0.29
13 1 0.04
14 4 0.17
15 1 0.04
16 11 0.46
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (16 bp):
GTATTAAAATGGCATT
Found at i:31211526 original size:49 final size:50
Alignment explanation
Indices: 31211289--31211531 Score: 228
Period size: 49 Copynumber: 4.9 Consensus size: 50
31211279 ATCTATTGTG
* * *
31211289 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* *
31211339 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-ATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTA-CCAGATAA-TT
* * * * * * **
31211389 CGATCACGTGTGTAGTGCTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
** * * *
31211439 AGGTCATGTGTGCAGTACT-A--GCAGGCTACTACGAGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
** * *
31211486 -GGTCGTATGTGTAGTACTAAGTGCAGGATACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
31211532 GCTTTGGCTA
Statistics
Matches: 155, Mismatches: 31, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
46 15 0.10
47 23 0.15
49 60 0.39
50 22 0.14
51 35 0.23
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:31215450 original size:16 final size:15
Alignment explanation
Indices: 31215429--31215480 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
31215419 AGGGTGGAAA
31215429 GAAAATTGGAAGGATG
1 GAAAATT-GAAGGATG
*
31215445 GAAAATTGAAGGGGTG
1 GAAAATTGAA-GGATG
*
31215461 GAAAACTAGAAGGAT-
1 GAAAA-TTGAAGGATG
31215476 GAAAA
1 GAAAA
31215481 ACATAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 19 0.61
17 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.35, T:0.15
Consensus pattern (15 bp):
GAAAATTGAAGGATG
Found at i:31227694 original size:18 final size:19
Alignment explanation
Indices: 31227671--31227708 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
31227661 CAATTTTAAA
*
31227671 TTTGAATCCCA-ATTCATT
1 TTTGAAGCCCAGATTCATT
*
31227689 TTTGAAGCTCAGATTCATT
1 TTTGAAGCCCAGATTCATT
31227708 T
1 T
31227709 CAGGTCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGAAGCCCAGATTCATT
Found at i:31228143 original size:21 final size:21
Alignment explanation
Indices: 31228097--31228149 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31228087 GAGGTGATCA
31228097 TGGGCCGGGCCGGGCCGAGTT
1 TGGGCCGGGCCGGGCCGAGTT
* * *
31228118 CGGGCCGGGCCGGGCTGGGTT
1 TGGGCCGGGCCGGGCCGAGTT
*
31228139 TGGGCCTGGCC
1 TGGGCCGGGCC
31228150 CAAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.30, G:0.53, T:0.15
Consensus pattern (21 bp):
TGGGCCGGGCCGGGCCGAGTT
Found at i:31228346 original size:26 final size:25
Alignment explanation
Indices: 31228302--31228362 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
31228292 TTATTTCATT
* * *
31228302 AAATAAAAAAATTTAAAAAATATAA
1 AAATAAATATATTTAAAAAACATAA
31228327 TAAATCAAATATATTT-AAAAACATAA
1 -AAAT-AAATATATTTAAAAAACATAA
31228353 AAATAAATAT
1 AAATAAATAT
31228363 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 6 0.19
25 4 0.13
26 13 0.42
27 8 0.26
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (25 bp):
AAATAAATATATTTAAAAAACATAA
Found at i:31228374 original size:22 final size:22
Alignment explanation
Indices: 31228333--31228391 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
31228323 ATAATAAATC
* *
31228333 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
31228353 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
31228375 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
31228392 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:31228468 original size:15 final size:16
Alignment explanation
Indices: 31228438--31228470 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31228428 AAATAGTTAT
31228438 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
31228455 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
31228470 A
1 A
31228471 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:31230075 original size:74 final size:74
Alignment explanation
Indices: 31229983--31230127 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 74
31229973 AATTAAAACT
*
31229983 AAATCATCATATGTATCATGTTAGTCTAAAAAAAGTAGATAATAATAAGATTACTAATAAAAATA
1 AAATCATCATATGCATCATGTTAGTCTAAAAAAAGTAGATAATAATAAGATTACTAATAAAAATA
31230048 GTAAGAATC
66 GTAAGAATC
* * * *
31230057 AAATCATCGTATGCATCATGTTAGTCTAAGAAAAGTAGATGATAATATGATTACTAATAAAAATA
1 AAATCATCATATGCATCATGTTAGTCTAAAAAAAGTAGATAATAATAAGATTACTAATAAAAATA
31230122 GTAAGA
66 GTAAGA
31230128 CAAATAAACA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (74 bp):
AAATCATCATATGCATCATGTTAGTCTAAAAAAAGTAGATAATAATAAGATTACTAATAAAAATA
GTAAGAATC
Found at i:31230731 original size:14 final size:14
Alignment explanation
Indices: 31230712--31230762 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
31230702 ATATCTCTTT
31230712 TTTATAATATAATA
1 TTTATAATATAATA
*
31230726 TTTATAATATTTAACA
1 TTTATAATA--TAATA
*
31230742 TTTATAA-AAAATA
1 TTTATAATATAATA
31230755 TTTTATAA
1 -TTTATAA
31230763 ATTGCCCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 1 0.03
16 11 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTATAATATAATA
Found at i:31240407 original size:28 final size:28
Alignment explanation
Indices: 31240342--31240442 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
31240332 ATAGTGAATC
*
31240342 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
31240371 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31240399 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
31240429 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31240443 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31248326 original size:28 final size:28
Alignment explanation
Indices: 31248261--31248361 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
31248251 ATAGTGAATC
*
31248261 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
31248290 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31248318 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
31248348 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31248362 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31249875 original size:37 final size:37
Alignment explanation
Indices: 31249797--31249878 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
31249787 ACCTTTAGTT
* * * *
31249797 CGGGGCTTACCCGGACAAAATCTCCACCCGTGGTCAT
1 CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAG
*
31249834 CGGGTCTTACCCGGACATAATCTCCACACGTAGTCAG
1 CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAG
31249871 CGGGTCTT
1 CGGGTCTT
31249879 TAGAGCTCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.22
Consensus pattern (37 bp):
CGGGTCTTACCCGGACAAAATCTCCACACGTAGTCAG
Found at i:31250065 original size:47 final size:47
Alignment explanation
Indices: 31249996--31250104 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
31249986 CCCTTCGGGA
*
31249996 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
* *
31250043 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
31250090 CTTATCACATATATA
1 CTTATCACATATATA
31250105 TATCTCATAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
Found at i:31253165 original size:28 final size:28
Alignment explanation
Indices: 31253134--31253233 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
31253124 CTGACTGATT
*
31253134 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * ** *
31253162 TCGCACACATAGTGCTTCAACTACTGATC
1 TCGCACACATAGTGC-TCGATTAAAGAAC
* * *
31253191 TGGCACACATAGTGCTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* *
31253219 TTGCACACACAGTGC
1 TCGCACACATAGTGC
31253234 CTCATAATTC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 33 0.60
29 22 0.40
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGATTAAAGAAC
Found at i:31253298 original size:40 final size:40
Alignment explanation
Indices: 31253243--31253603 Score: 555
Period size: 40 Copynumber: 9.1 Consensus size: 40
31253233 CCTCATAATT
** * * *
31253243 CTAGCACGAATGCTCTTC-GAGGTTTCGCCCGAATATATCA
1 CTAGCACGAATGCTCTTCGGA-ACTTAGTCCGGATATATCA
* * *
31253283 CTAGCATGAATGCTCTTCGAAACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
31253323 CTAGCACGAATGCTCTTCGGAACTTAG-CCGGATATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
* *
31253362 CTAGCACGAATGCTCTTCGGAAGTTAGTCCGGTTATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
* *
31253402 CTAGCACGAATGCTCTTCGGAAATTGGTCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
*
31253442 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGTTATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
*
31253482 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGTTATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
*
31253522 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGTTATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
*
31253562 CTAGCACGAATGCTCTTCAGAACTTAGTCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
31253602 CT
1 CT
31253604 CTCAATTCTT
Statistics
Matches: 301, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.13
40 262 0.87
41 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
CTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATATCA
Found at i:31255590 original size:37 final size:37
Alignment explanation
Indices: 31255511--31255593 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
31255501 AACCTTTAGT
* * *
31255511 TCGGGGCTTACCCGGACAAAATCTCCACCCGTGGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
*
31255548 TCGGGTCTTACCCGGACATAATCTCCACACGTAGTCA
1 TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
31255585 TCGGGTCTT
1 TCGGGTCTT
31255594 TAGAGCTCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.24
Consensus pattern (37 bp):
TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA
Found at i:31255780 original size:47 final size:47
Alignment explanation
Indices: 31255711--31255819 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
31255701 CCCTTCGGGA
*
31255711 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
* *
31255758 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
31255805 CTTATCACATATATA
1 CTTATCACATATATA
31255820 TATCTCATAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCACTCGGC
Found at i:31261066 original size:66 final size:69
Alignment explanation
Indices: 31260980--31261109 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 69
31260970 ACATGTTGAA
* * *
31260980 CACTTAGTACCACTCATGCGACCTAGC-CGA-TT-TGTCT-CGTAGCTCTCTTGTCTACATGGTG
1 CACTTAGAACCACGCATGCGACCTAGCAC-ATTTATCTCTCCGTAGCTCTCTTGTCTACATGGTG
31261041 TCCTT
65 TCCTT
*
31261046 CACTTAGAATCACGCATGCGACCTAGCTACATTTATCTCTCCCGTAGCTCTCTTGTCTACATGG
1 CACTTAGAACCACGCATGCGACCTAGC-ACATTTATCTCT-CCGTAGCTCTCTTGTCTACATGG
31261110 GATACATCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
66 24 0.44
67 1 0.02
68 3 0.06
69 4 0.07
71 22 0.41
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (69 bp):
CACTTAGAACCACGCATGCGACCTAGCACATTTATCTCTCCGTAGCTCTCTTGTCTACATGGTGT
CCTT
Found at i:31267199 original size:24 final size:24
Alignment explanation
Indices: 31267167--31267214 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
31267157 GTCTAGACAC
31267167 GCCCGTGTGTTTAGGCTATGGCAA
1 GCCCGTGTGTTTAGGCTATGGCAA
*
31267191 GCCCGTGTGTTTAGGCTGTGGCAA
1 GCCCGTGTGTTTAGGCTATGGCAA
31267215 AACAGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (24 bp):
GCCCGTGTGTTTAGGCTATGGCAA
Found at i:31267666 original size:39 final size:39
Alignment explanation
Indices: 31267623--31267699 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
31267613 GATTATACCA
31267623 TACATACATACATACCATAAAACATACTTTCCAAAAATG
1 TACATACATACATACCATAAAACATACTTTCCAAAAATG
31267662 TACATACATACATACCATAAAACATACTTTCCAAAAAT
1 TACATACATACATACCATAAAACATACTTTCCAAAAAT
31267700 AGACTCATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.26
Consensus pattern (39 bp):
TACATACATACATACCATAAAACATACTTTCCAAAAATG
Found at i:31268792 original size:43 final size:43
Alignment explanation
Indices: 31268717--31268821 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
31268707 TTCAATAAAC
*
31268717 TCGCACACTTAGTGCTAATTAATTAACCGAAGCTATAATTGTA
1 TCGCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTA
* * * *
31268760 TCTCACGCTTAGTGCCAATTAATTAGCTGAAGCTATAATTGTA
1 TCGCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTA
*
31268803 TCGCACACTTAGTTCCAAT
1 TCGCACACTTAGTGCCAAT
31268822 AGATTAAACC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (43 bp):
TCGCACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTA
Found at i:31273991 original size:40 final size:40
Alignment explanation
Indices: 31273883--31274132 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
31273873 CGGGATTTAA
* * * * *
31273883 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
31273923 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31273963 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31274003 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31274043 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31274083 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31274123 CCGGATATAT
1 CCGGATATAT
31274133 TCCAATGTTC
Statistics
Matches: 193, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 192 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:31282165 original size:40 final size:40
Alignment explanation
Indices: 31282057--31282306 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
31282047 CGGGATTTAA
* * * * *
31282057 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
31282097 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31282137 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31282177 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31282217 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31282257 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
31282297 CCGGATATAT
1 CCGGATATAT
31282307 TTCCAATGTT
Statistics
Matches: 193, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 192 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:31295258 original size:15 final size:15
Alignment explanation
Indices: 31295238--31295268 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31295228 ACTCTGAGGT
*
31295238 ACTGGATCTTTTCTA
1 ACTGGATCATTTCTA
31295253 ACTGGATCATTTCTA
1 ACTGGATCATTTCTA
31295268 A
1 A
31295269 TTCTTTCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
ACTGGATCATTTCTA
Found at i:31300802 original size:24 final size:24
Alignment explanation
Indices: 31300770--31300881 Score: 113
Period size: 24 Copynumber: 4.7 Consensus size: 24
31300760 GGCTATCTCA
*
31300770 AATGCACTATGTGTGCAATTTATT
1 AATGCACTATGTGTGCAATTTACT
*
31300794 AATGCACTATGTGTGCGATTTACT
1 AATGCACTATGTGTGCAATTTACT
* *
31300818 -ATGGCACTATGTGTGCGATTTGCT
1 AAT-GCACTATGTGTGCAATTTACT
** *
31300842 -ATGGCACTATGTGTGCGAACATAAT
1 AAT-GCACTATGTGTGC-AATTTACT
31300867 AA-GCACTATGTGTGC
1 AATGCACTATGTGTGC
31300882 CACATTCGGT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
23 2 0.03
24 71 0.92
25 3 0.04
26 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (24 bp):
AATGCACTATGTGTGCAATTTACT
Found at i:31309174 original size:16 final size:15
Alignment explanation
Indices: 31309153--31309191 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31309143 TATTAGGGGT
*
31309153 AAAAGTGTAAATTTTC
1 AAAAGTGT-AATTTAC
*
31309169 AAAAGTATAATTTAC
1 AAAAGTGTAATTTAC
31309184 AAAAGTGT
1 AAAAGTGT
31309192 GTATTTTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (15 bp):
AAAAGTGTAATTTAC
Found at i:31313818 original size:86 final size:86
Alignment explanation
Indices: 31313631--31313832 Score: 248
Period size: 86 Copynumber: 2.3 Consensus size: 86
31313621 GGTTACCGAG
*
31313631 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACGTATAAGACAAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATAGTATTGTGATTACGTATAAGACAAT
*
31313696 GTCTGGGACATTGGCATCATT
66 GTCTGGGACAATGGCATCATT
** * * *
31313717 AT-TCGATTATGTGTAAGACCATGTCTGGGACATTGGCATAGTTATT-TGATTTCGTGTAAGACT
1 ATGT-GATTACATGTAAGACCATGTCTGGGACATTGGCATAG-TATTGTGATTACGTATAAGACA
* * *
31313780 CTGTTTGGGATAATGGCATCGA-T
64 ATGTCTGGGACAATGGCATC-ATT
* *
31313803 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACATGTAAGACCATGTCTGGGA
31313833 TATGTCATTG
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
85 1 0.01
86 91 0.93
87 6 0.06
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (86 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATAGTATTGTGATTACGTATAAGACAAT
GTCTGGGACAATGGCATCATT
Found at i:31313834 original size:43 final size:43
Alignment explanation
Indices: 31313631--31313832 Score: 205
Period size: 43 Copynumber: 4.7 Consensus size: 43
31313621 GGTTACCGAG
* *
31313631 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* *
31313673 ATTGTGATTACGTATAAGACAATGTCTGGGACATTGGCATC-ATT
1 A-TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGA-T
* * *
31313717 AT-TCGATTATGTGTAAGACCATGTCTGGGACATTGGCATAGTT
1 ATGT-GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* * * * *
31313760 ATTTGATTTCGTGTAAGACTC-TGTTTGGGATAATGGCATCGAT
1 ATGTGATTACGTGTAAGAC-CATGTCTGGGACATTGGCATCGAT
* * *
31313803 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACGTGTAAGACCATGTCTGGGA
31313833 TATGTCATTG
Statistics
Matches: 130, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
42 3 0.02
43 123 0.95
44 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:31321864 original size:29 final size:29
Alignment explanation
Indices: 31321819--31321874 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
31321809 CAGAGAAGTT
*
31321819 AGATTTTTGGGGCACATTATTTTAGCGGA
1 AGATTTTTGGGGAACATTATTTTAGCGGA
*
31321848 AGATTTTTGGGGAACATTGTTTTAGCG
1 AGATTTTTGGGGAACATTATTTTAGCG
31321875 AAAGGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.39
Consensus pattern (29 bp):
AGATTTTTGGGGAACATTATTTTAGCGGA
Found at i:31325477 original size:27 final size:27
Alignment explanation
Indices: 31325356--31325484 Score: 195
Period size: 27 Copynumber: 4.8 Consensus size: 27
31325346 ATTACCAAAG
* *
31325356 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
31325383 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31325410 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31325437 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
31325464 TACCCTCGATTTACAAAATTA
1 TACCCTCGATTTACAGAATTA
31325485 GTAAAATACC
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:31325494 original size:27 final size:28
Alignment explanation
Indices: 31325464--31325684 Score: 99
Period size: 27 Copynumber: 8.2 Consensus size: 28
31325454 ATTACTGTTT
**
31325464 TACCCTCGA-TTTACAAAATTAGTAAAA
1 TACCCTCGAGTTTACAAAATTACCAAAA
*
31325491 TACCCT-TAGTTTACAAAATTACCAAAA
1 TACCCTCGAGTTTACAAAATTACCAAAA
* * *
31325518 TACCCTC-A-ATCAGTAAAATTACCAAAA
1 TACCCTCGAGTTTA-CAAAATTACCAAAA
* * ** * *
31325545 CACCCT--AGTCTGTAAAATTGCTAAAA
1 TACCCTCGAGTTTACAAAATTACCAAAA
* **
31325571 TATCACT-G-GTTTGTAAAATTACCAAAA
1 TA-CCCTCGAGTTTACAAAATTACCAAAA
*** *
31325598 TACCACT-G-GTTTGTGAAATTACCGAAA
1 TACC-CTCGAGTTTACAAAATTACCAAAA
* **
31325625 TACCCTC-AATTTGTAAAATTACCAAAA
1 TACCCTCGAGTTTACAAAATTACCAAAA
* *
31325652 TACCC-CTGA-TTTACAAAGTTACAAAAA
1 TACCCTC-GAGTTTACAAAATTACCAAAA
31325679 TACCCT
1 TACCCT
31325685 TGACTTTCTA
Statistics
Matches: 154, Mismatches: 28, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
26 21 0.14
27 132 0.86
28 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (28 bp):
TACCCTCGAGTTTACAAAATTACCAAAA
Found at i:31325495 original size:54 final size:54
Alignment explanation
Indices: 31325356--31325513 Score: 156
Period size: 54 Copynumber: 2.9 Consensus size: 54
31325346 ATTACCAAAG
* * * *** *
31325356 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
* * **** *
31325410 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
* *
31325464 TACCCTCGATTTACAAAATTAGTAAAATACCCTT-AGTTTACAAAATTACC
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGA-TTTACAGAATTACC
31325514 AAAATACCCT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 89 0.99
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAGAATTACCGTTT
Found at i:31325511 original size:81 final size:80
Alignment explanation
Indices: 31325356--31325512 Score: 174
Period size: 81 Copynumber: 1.9 Consensus size: 80
31325346 ATTACCAAAG
* * ** *
31325356 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTA-CGTAATACCCTAGATT
* *
31325421 TATAGAATTACTGTTT
65 TACAAAATTACTGTTT
* **
31325437 TACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTA-GTAAAATACCCTTAG-
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACGT--AATACCC-TAGA
31325500 TTTACAAAATTAC
63 TTTACAAAATTAC
31325513 CAAAATACCC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
79 2 0.03
81 59 0.94
82 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (80 bp):
TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACGTAATACCCTAGATTT
ACAAAATTACTGTTT
Found at i:31325550 original size:54 final size:53
Alignment explanation
Indices: 31325464--31325767 Score: 180
Period size: 54 Copynumber: 5.6 Consensus size: 53
31325454 ATTACTGTTT
* ** **
31325464 TACCCTCGATTTACAAAATTAGTAAAATACCCTTAGTTTACAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCC-TAGTTTACAAAATTACCAAAA
** * * ** * *
31325518 TACCCTCAATCAGTAAAATTACCAAAACACCCTAGTCTGTAAAATTGCTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTAGTTTACAAAATTACCAAAA
* ** * *** *
31325571 TATCACT-GGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TA-CCCTCAATTTGTAAAATTACCAAAATACC-CTAGTTTACAAAATTACCAAAA
* *
31325625 TACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAGTTACAAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATA-CCCTAG-TTTACAAAATTACCAAAA
* * * *** * **
31325679 TACCCTTGACTTTCTAAAAATTATGGAAATACCATTAGTTTACAAAATTACTGAAA
1 TACCC-TCAATTTGT-AAAATTACCAAAATACC-CTAGTTTACAAAATTACCAAAA
*** * * *
31325735 TACCCTTGGTTTGTAGATTTACCAAAACACCCT
1 TACCCTCAATTTGTAAAATTACCAAAATACCCT
31325768 TGTAGGATGA
Statistics
Matches: 186, Mismatches: 55, Indels: 19
0.72 0.21 0.07
Matches are distributed among these distances:
53 42 0.23
54 95 0.51
55 15 0.08
56 33 0.18
57 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (53 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTAGTTTACAAAATTACCAAAA
Found at i:31325746 original size:27 final size:27
Alignment explanation
Indices: 31325437--31325746 Score: 92
Period size: 27 Copynumber: 11.4 Consensus size: 27
31325427 ATTACTGTTT
* * ****
31325437 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGGTTTACAAAATTACTAAAA
* * *
31325464 TACCCTCGATTTACAAAATTAGTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* *
31325491 TACCCTTAGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*** * * *
31325518 TACCC-TCAATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTA-CAAAATTACTAAAA
* * * ** *
31325545 CACCC-TAGTCTGTAAAATTGCTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* ** *
31325571 TATCAC-TGGTTTGTAAAATTACCAAAA
1 TA-CCCTTGGTTTACAAAATTACTAAAA
*** **
31325598 TACCAC-TGGTTTGTGAAATTACCGAAA
1 TACC-CTTGGTTTACAAAATTACTAAAA
*** ** *
31325625 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * * *
31325652 TACCCCTGATTTACAAAGTTACAAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* *
31325679 TACCCTTGACTTT-CTAAAAATTA-TGGAAA
1 TACCCTTG-GTTTAC--AAAATTACT-AAAA
* * *
31325708 TACCATTAGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
31325735 TACCCTTGGTTT
1 TACCCTTGGTTT
31325747 GTAGATTTAC
Statistics
Matches: 216, Mismatches: 57, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
26 18 0.08
27 175 0.81
28 7 0.03
29 16 0.07
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACTAAAA
Found at i:31325830 original size:27 final size:27
Alignment explanation
Indices: 31325800--31325891 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
31325790 ACCCCTATTA
*
31325800 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
*
31325827 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
31325854 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
31325881 GGTAAAATGAC
1 GGTAAAATGAC
31325892 GAATATGCCC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 59 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:31326955 original size:31 final size:31
Alignment explanation
Indices: 31326901--31326964 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
31326891 CGTTTACAGT
* *
31326901 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
* **
31326932 AAAGGCTTCGGCCTAATGTTATGAAATATGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
31326963 AA
1 AA
31326965 TATCAAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATAATATGAAATATGA
Found at i:31335457 original size:46 final size:46
Alignment explanation
Indices: 31335402--31335659 Score: 167
Period size: 46 Copynumber: 5.5 Consensus size: 46
31335392 ATTGTGGACT
*
31335402 AGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATATGA-GACGAGCC
* * *
31335448 ATTGTAAGACTATTTCTGGGACATTGCATC-G--ATATCGAGACGAGTGCT
1 AGTGTAAGAC-ATGTCTGGGACA-TGCATCAGCCATAT-GAGACGA--GCC
* * *
31335496 AGTGTAAGACATGTCTGGGACATGCATCGGCC-T-CGAGACGTAAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATATGAGACG--AGCC
* * *
31335542 AGTGTAAGACATGTCTGGGACATGCATCAG-C-TACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATATGAGACG--AGCC
* * * * * * *
31335588 GGGGTAAGACCATGTCTAGGACATGGCATC-GGCATGA-GATATGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCAT-ATGAGACGAGCC
31335635 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
31335660 GCATTGGTTC
Statistics
Matches: 173, Mismatches: 22, Indels: 34
0.76 0.10 0.15
Matches are distributed among these distances:
45 8 0.05
46 72 0.42
47 61 0.35
48 25 0.14
49 6 0.03
50 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATATGAGACGAGCC
Found at i:31337903 original size:48 final size:48
Alignment explanation
Indices: 31337807--31337942 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 48
31337797 CACCATGATT
* ****
31337807 TATGAGAGCCAGTGTAAGACCATGTCTTGGACATGGCATCGGTGTTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGA
*
31337855 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGA
* * * * *
31337903 TACGTA-TGCCAGTCTAAGACCATATCTGGGATATGGCATC
1 TATG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
31337943 GGCCTCGGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
48 74 0.99
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGA
Found at i:31349456 original size:31 final size:31
Alignment explanation
Indices: 31349421--31349483 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
31349411 AATTTGGGTA
31349421 TTTGTTATGTAATAAGGCCTCTTTAAATTTT
1 TTTGTTATGTAATAAGGCCTCTTTAAATTTT
*
31349452 TTTGTTATGTAATAAGGCCTTTTTAAATTTT
1 TTTGTTATGTAATAAGGCCTCTTTAAATTTT
31349483 T
1 T
31349484 ACTTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (31 bp):
TTTGTTATGTAATAAGGCCTCTTTAAATTTT
Found at i:31353789 original size:46 final size:46
Alignment explanation
Indices: 31353722--31353895 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
31353712 TGTAACCCGC
*
31353722 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
31353768 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
31353818 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
31353860 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
31353896 ATGCTCAACC
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 1 0.01
44 3 0.03
45 28 0.25
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:31353888 original size:92 final size:93
Alignment explanation
Indices: 31353730--31353899 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 93
31353720 GCCCATAAGT
* *
31353730 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
31353795 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
31353823 GAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
31353887 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31353900 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 46 0.62
93 28 0.38
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31356327 original size:30 final size:30
Alignment explanation
Indices: 31356283--31356371 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
31356273 CAAAGATAAC
31356283 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
31356312 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
31356342 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
31356372 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:31356331 original size:15 final size:15
Alignment explanation
Indices: 31356283--31356362 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
31356273 CAAAGATAAC
*
31356283 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
31356297 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31356312 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
31356327 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
31356342 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
31356357 AAGAAA
1 AAGAAA
31356363 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31356371 original size:15 final size:15
Alignment explanation
Indices: 31356294--31356371 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
31356284 AGAAAACCGA
31356294 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
31356309 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
31356323 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
31356338 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
31356354 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
31356369 ATA
1 ATA
31356372 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31359430 original size:93 final size:93
Alignment explanation
Indices: 31359318--31359488 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
31359308 GCCCATAAGT
* *
31359318 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31359383 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
31359411 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31359476 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31359489 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:31359485 original size:46 final size:46
Alignment explanation
Indices: 31359310--31359485 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
31359300 TGTAACCCGC
* * *
31359310 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
31359356 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
31359406 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
31359449 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
31359486 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:31368399 original size:44 final size:44
Alignment explanation
Indices: 31368342--31368426 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
31368332 GTGTAAGACC
* * *
31368342 ATATCTGGGATATGGCATCTATATGAGACTTCGTGTAAGACAAT
1 ATATCTGGGATATGGCATCGATAAGAGACTTAGTGTAAGACAAT
31368386 ATATCTGGGATATGGCATCGATAAGAGACTTAGTGTAAGAC
1 ATATCTGGGATATGGCATCGATAAGAGACTTAGTGTAAGAC
31368427 CATAGTTGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (44 bp):
ATATCTGGGATATGGCATCGATAAGAGACTTAGTGTAAGACAAT
Found at i:31374092 original size:40 final size:40
Alignment explanation
Indices: 31374032--31374276 Score: 195
Period size: 40 Copynumber: 6.2 Consensus size: 40
31374022 GATGATAACT
*
31374032 GGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-TCC
1 GGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-GCTAATATCC
* * *
31374072 GGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATATCC
* * *
31374112 GGGCTAAGTCCCGAAGGCGTTTGTAC--GAGCTATTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTA--ATATCC
** * *
31374152 AAGCTAAGTCCCGAAGGCATTTGTGCAAGT--TATTATACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT-CC
* * * *
31374191 AGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATATCC
* *
31374231 GGGTTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GCTAATATCC
31374271 -GGCTAA
1 GGGCTAA
31374277 ACTCCGAAGG
Statistics
Matches: 167, Mismatches: 25, Indels: 27
0.76 0.11 0.12
Matches are distributed among these distances:
37 2 0.01
38 4 0.02
39 38 0.23
40 116 0.69
41 5 0.03
42 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATATCC
Found at i:31374275 original size:79 final size:79
Alignment explanation
Indices: 31374070--31374276 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 79
31374060 GTGGCTAATT
* * * *
31374070 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATATCCAGGCTAAGTCCCGAAGGCATTTG
* * *
31374135 TACGAGCTATTATAT
65 TACAAGCTACTATAA
** *
31374150 CCAAGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATA-CCAGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATATCCAGGCTAAGTCCCGAAGGCATTTG
* *
31374214 TGCAAGTTACTATAA
65 TACAAGCTACTATAA
* * * *
31374229 CCGGGTTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ACTATATCCAGGCTAA
31374277 ACTCCGAAGG
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
78 1 0.01
79 69 0.66
80 35 0.33
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTATATCCAGGCTAAGTCCCGAAGGCATTTGT
ACAAGCTACTATAA
Found at i:31380629 original size:43 final size:42
Alignment explanation
Indices: 31380582--31380681 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
31380572 TGCCAACTTT
* *
31380582 CCAGACGTGGTCTTACATGCAA-TCAAACATCGTTGCC-ACTGTC
1 CCAGACGTGGTCTTACACG-AAGTCAAACA-CGATGCCGA-TGTC
* *
31380625 CCAGACAG-GGTGTTACACGAAGTCAAATACGATGCCGATGTC
1 CCAGAC-GTGGTCTTACACGAAGTCAAACACGATGCCGATGTC
*
31380667 CCAGACATGGTCTTA
1 CCAGACGTGGTCTTA
31380682 TATGAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
42 24 0.51
43 22 0.47
44 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (42 bp):
CCAGACGTGGTCTTACACGAAGTCAAACACGATGCCGATGTC
Found at i:31389349 original size:43 final size:42
Alignment explanation
Indices: 31389301--31389399 Score: 101
Period size: 44 Copynumber: 2.3 Consensus size: 42
31389291 ATCCGATATG
* *
31389301 TGTTTTCATGTAAGGCCACCTCTGGGACATTGGCATCG-ACTTC
1 TGTTTTCATGTAAGACCACCTCTGGGACATCGGCATCGTA--TC
* ** *
31389344 TGTTTTACGTGTAAGACCATGTTTGGGACATCGGCATCGTATC
1 TGTTTT-CATGTAAGACCACCTCTGGGACATCGGCATCGTATC
*
31389387 TGATTTCATGTAA
1 TGTTTTCATGTAA
31389400 AACCCTATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
42 6 0.13
43 13 0.28
44 26 0.57
45 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TGTTTTCATGTAAGACCACCTCTGGGACATCGGCATCGTATC
Found at i:31390002 original size:20 final size:18
Alignment explanation
Indices: 31389979--31390014 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31389969 ATGTTTTGAA
31389979 GTGTGTATATATCTAGCC
1 GTGTGTATATATCTAGCC
31389997 GTGTGTATATATCTAGCC
1 GTGTGTATATATCTAGCC
31390015 ATATAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (18 bp):
GTGTGTATATATCTAGCC
Found at i:31396045 original size:22 final size:23
Alignment explanation
Indices: 31396013--31396055 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
31396003 GCCAAATGAA
*
31396013 TTGGTATTGTAAATATTTATATT
1 TTGGTATTGTAAATATATATATT
*
31396036 TTGGT-TTGTATATATATATA
1 TTGGTATTGTAAATATATATA
31396056 GCCATGAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (23 bp):
TTGGTATTGTAAATATATATATT
Found at i:31398459 original size:18 final size:18
Alignment explanation
Indices: 31398436--31398478 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
31398426 ACTTGAATGA
31398436 CAAATTTTATTCTAGCCT
1 CAAATTTTATTCTAGCCT
31398454 CAAATTTTATTCTAGCCT
1 CAAATTTTATTCTAGCCT
31398472 CAAATTT
1 CAAATTT
31398479 AATATATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
CAAATTTTATTCTAGCCT
Found at i:31408753 original size:30 final size:30
Alignment explanation
Indices: 31408709--31408766 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31408699 CCTGAGCCTC
* *
31408709 GGGGCAAAAGTGTAATTATGCAAAAGTTTA
1 GGGGAAAAAATGTAATTATGCAAAAGTTTA
* *
31408739 GGGGAAAAAATGTAATTTTGCCAAAGTT
1 GGGGAAAAAATGTAATTATGCAAAAGTT
31408767 CGTATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGCAAAAGTTTA
Found at i:31423920 original size:28 final size:27
Alignment explanation
Indices: 31423888--31423963 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 27
31423878 AATGAGATTG
31423888 GCACTAAGTGTGCGAGTTTAAT-TGTATA
1 GCACTAAGTGTGCGAGTTTAATAT-TA-A
*
31423916 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTT-AATATTAA
*
31423944 GCACTAAGTGTGCGACTTTA
1 GCACTAAGTGTGCGAGTTTA
31423964 TCGAGTAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 1 0.02
28 38 0.86
29 4 0.09
30 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTTAATATTAA
Found at i:31428398 original size:45 final size:45
Alignment explanation
Indices: 31428327--31428416 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
31428317 TTTTGGCAAC
* *
31428327 ACATCAAAAATTGAATGTGATCGTCTAAACCATTCTACTAAAATT
1 ACATCAAAAACTGAAGGTGATCGTCTAAACCATTCTACTAAAATT
* *
31428372 ACATCGAAAACTGAAGGTGATTGTCTAAACCATTCTACTAAAATT
1 ACATCAAAAACTGAAGGTGATCGTCTAAACCATTCTACTAAAATT
31428417 GACAATATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (45 bp):
ACATCAAAAACTGAAGGTGATCGTCTAAACCATTCTACTAAAATT
Found at i:31441243 original size:21 final size:21
Alignment explanation
Indices: 31441219--31441290 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
31441209 TAGCTCCCAA
31441219 ACATATTCATATTCGGCAACC
1 ACATATTCATATTCGGCAACC
* * * * **
31441240 ACATATTTAAACAT-AGCTCCC
1 ACATATTCATA-TTCGGCAACC
31441261 AAGCATATTCATATTCGGCAACC
1 -A-CATATTCATATTCGGCAACC
31441284 ACATATT
1 ACATATT
31441291 TACTTCCATG
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 19 0.54
22 4 0.11
23 12 0.34
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.29
Consensus pattern (21 bp):
ACATATTCATATTCGGCAACC
Found at i:31441268 original size:44 final size:44
Alignment explanation
Indices: 31441203--31441292 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
31441193 ATCAAATTCG
31441203 TAAACATAGCTCCCAAACATATTCATATTCGGCAACCACATATT
1 TAAACATAGCTCCCAAACATATTCATATTCGGCAACCACATATT
*
31441247 TAAACATAGCTCCCAAGCATATTCATATTCGGCAACCACATATT
1 TAAACATAGCTCCCAAACATATTCATATTCGGCAACCACATATT
31441291 TA
1 TA
31441293 CTTCCATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.28
Consensus pattern (44 bp):
TAAACATAGCTCCCAAACATATTCATATTCGGCAACCACATATT
Found at i:31442694 original size:41 final size:41
Alignment explanation
Indices: 31442649--31442766 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
31442639 TGAAAGATAA
31442649 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
31442690 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31442720 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
31442761 ATGTAG
1 ATGTAG
31442767 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:31442705 original size:71 final size:71
Alignment explanation
Indices: 31442617--31442780 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
31442607 GAGATGTATC
31442617 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31442682 AGGACA
66 AGGACA
31442688 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
31442753 AGGACA
66 AGGACA
31442759 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
31442781 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:31450203 original size:68 final size:67
Alignment explanation
Indices: 31450165--31450318 Score: 245
Period size: 68 Copynumber: 2.2 Consensus size: 67
31450155 GAGATGTATC
*
31450165 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGAC-A-AGAGCTACGTGAAAGAT-AATGTAGCTAGGTCGCATGCGTGATACCAAGTGA
31450230 AGGACA
63 A-GACA
*
31450236 CCATGTAGACAAGAGCTACGTGAAAGATAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGG
1 CCATGTAGACAAGAGCTACGTGAAAGATAATGTAGCTAGGTCGCATGCGTGATACCAAGTGAA-G
31450301 ACA
65 ACA
31450304 CCATGTAGACAAGAG
1 CCATGTAGACAAGAG
31450319 AGCTACGAGA
Statistics
Matches: 83, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
68 55 0.66
69 17 0.20
70 1 0.01
71 10 0.12
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (67 bp):
CCATGTAGACAAGAGCTACGTGAAAGATAATGTAGCTAGGTCGCATGCGTGATACCAAGTGAAGA
CA
Found at i:31459215 original size:30 final size:30
Alignment explanation
Indices: 31459179--31459279 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
31459169 GACAAGATTG
* * *
31459179 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
31459209 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
31459237 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
31459266 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31459280 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:31459291 original size:29 final size:28
Alignment explanation
Indices: 31459208--31459283 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
31459198 AAAATTGTAC
* *
31459208 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
31459236 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
31459265 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
31459284 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:31461042 original size:18 final size:18
Alignment explanation
Indices: 31461000--31461034 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31460990 AAAAAGATAC
31461000 TCAAATTTGGCCGTAAAG
1 TCAAATTTGGCCGTAAAG
31461018 TCAAATTTGGCCGTAAA
1 TCAAATTTGGCCGTAAA
31461035 TGCAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (18 bp):
TCAAATTTGGCCGTAAAG
Found at i:31463135 original size:29 final size:29
Alignment explanation
Indices: 31463073--31463175 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
31463063 GTGACGAGAT
* * *
31463073 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
31463102 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * **
31463131 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
31463160 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31463176 TGATTGAGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:31466669 original size:29 final size:28
Alignment explanation
Indices: 31466614--31466728 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
31466604 GTGAGCATGA
* * *
31466614 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
31466642 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * **
31466671 ATATACAGGTGGTTTGATCCTAATGGGCC
1 ATATAAATGT-GATTGGGCCTAATGGGCC
* * *
31466700 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
31466728 A
1 A
31466729 GATACAGGTA
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
28 26 0.38
29 42 0.61
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:31471031 original size:40 final size:39
Alignment explanation
Indices: 31470986--31471115 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
31470976 CGGAATATAA
31470986 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
31471026 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
31471066 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
31471106 CCGGATATAA
1 CCGGATATAA
31471116 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:31471130 original size:40 final size:40
Alignment explanation
Indices: 31471002--31471153 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
31470992 ATAACCATGT
* * *
31471002 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
31471042 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
31471082 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
31471122 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
31471154 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:31471136 original size:80 final size:80
Alignment explanation
Indices: 31471002--31471151 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
31470992 ATAACCATGT
*
31471002 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
31471066 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
31471082 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
31471145 CCCGGAT
64 CCCGGAT
31471152 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:31477822 original size:24 final size:24
Alignment explanation
Indices: 31477790--31477840 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
31477780 AAACATAAAG
31477790 TTAATTAAAATCTATACTAAATAA
1 TTAATTAAAATCTATACTAAATAA
31477814 TTAATTAAAATCTATACTAAATAA
1 TTAATTAAAATCTATACTAAATAA
31477838 TTA
1 TTA
31477841 GTTAGGTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAATTAAAATCTATACTAAATAA
Found at i:31489390 original size:40 final size:40
Alignment explanation
Indices: 31489325--31489588 Score: 302
Period size: 40 Copynumber: 6.7 Consensus size: 40
31489315 GGATATAACC
* * * * *
31489325 ACTCGCAC-AAGGCCTTCGGGCCTTAGTCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * *
31489364 ACTAGCACAGATGCCTTCGGGACTTAGCCCGG-ATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * * *
31489404 ACTTGCGCAAATGCCTTCGGGGCTTAGCCCGGAATTTGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31489444 ACTCGCACAAAAGCCTTCGGGACTTAGCCCAGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31489484 ACTCGCACAGATGCCTTCGGGACTTAGCCCGGAATTTGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31489524 ACTCGCACAAATGCCTTCGGGACTTA-CCCGGAATTAATC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31489563 ACTAGCACAAATGTCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
31489589 ACCCCGTTAG
Statistics
Matches: 193, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 41 0.21
40 150 0.78
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:31494634 original size:40 final size:40
Alignment explanation
Indices: 31494575--31494660 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
31494565 CGGAATACAA
*
31494575 CCGGATATAACCACATGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATAGAACCACATGCACGAATGCCCTCGGGTCTTAGC
* * *
31494615 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACCACATGCACGAATGCCCTCGGGTCTTAGC
31494655 CCGGAT
1 CCGGAT
31494661 GTAGTCACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (40 bp):
CCGGATAGAACCACATGCACGAATGCCCTCGGGTCTTAGC
Found at i:31494682 original size:40 final size:41
Alignment explanation
Indices: 31494591--31494700 Score: 138
Period size: 40 Copynumber: 2.7 Consensus size: 41
31494581 ATAACCACAT
* *
31494591 GCACGAATGCCCTCGGGTCTTAGCCCGGA-TAGAACGACTT
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTA
*
31494631 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTA
*
31494671 GCAC-AATTGCCTTCGGGTCTTAACCCGGAT
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGAT
31494701 ATAATTTCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
39 2 0.03
40 57 0.90
41 1 0.02
42 3 0.05
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (41 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTA
Found at i:31494725 original size:40 final size:40
Alignment explanation
Indices: 31494575--31494741 Score: 124
Period size: 40 Copynumber: 4.2 Consensus size: 40
31494565 CGGAATACAA
* * * *
31494575 CCGGATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAAC
* ** * *
31494615 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAAC
* * * *
31494655 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAAC
** * * * *
31494695 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTT-AG
1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAAC
31494734 CCGGATAT
1 CCGGATAT
31494742 CATTCAATTG
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
39 10 0.10
40 92 0.89
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAAC
Found at i:31496000 original size:18 final size:18
Alignment explanation
Indices: 31495972--31496012 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31495962 GGATGAACAC
*
31495972 TTTTC-TTCTTTTTTTTT
1 TTTTCTTTCTTTGTTTTT
31495989 TTTTCTTTCTTTGTTTTT
1 TTTTCTTTCTTTGTTTTT
*
31496007 GTTTCT
1 TTTTCT
31496013 CTCATGTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (18 bp):
TTTTCTTTCTTTGTTTTT
Found at i:31500889 original size:40 final size:40
Alignment explanation
Indices: 31500824--31501088 Score: 284
Period size: 40 Copynumber: 6.7 Consensus size: 40
31500814 GGATATAACC
* * * * *
31500824 ACTCGCAC-AAGGCCTTCGGGTCTTAGTCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * *
31500863 ACTAGCACAGATGCCTTCGGGACTTAGCCCGG-ATATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * * *
31500903 ACTTGCACAAATGCCTTTGGGGCTTAGCCCGGAATTTGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31500943 ACTCGCACAAAAGCCTTCGGGACTTAGCCTGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
** * *
31500983 ACTCGCACAGCTCCCTTCGGGACTTAGCCCGGAATTTGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* * *
31501023 ACTCGGACAAATGCCTTCGGGACTTAGCCCGGAATTAATC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
31501063 ACTCGCACAAATGTCTTCAGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
31501089 ACCCCGTTAG
Statistics
Matches: 188, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
39 7 0.04
40 179 0.95
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:31507577 original size:43 final size:43
Alignment explanation
Indices: 31507529--31507664 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 43
31507519 AGCTCTGAGC
*
31507529 CTAGCAGGCATAATGCTGGTGAAATGATAACGGACTTAAAGGT
1 CTAGCAGGCATAATGCTGGTGAAATGATATCGGACTTAAAGGT
** * ** * *** *
31507572 CTAGCAAACTTTAA-GCTGGTG-AATTTTATCGGGCTCCGA-GC
1 CTAGCAGGC-ATAATGCTGGTGAAATGATATCGGACTTAAAGGT
* * *
31507613 CTAGCAGGCGTAATGCCGGTGAAATGATATCAGACTTAAAGGT
1 CTAGCAGGCATAATGCTGGTGAAATGATATCGGACTTAAAGGT
*
31507656 CTAGTAGGC
1 CTAGCAGGC
31507665 TTATTGCCGG
Statistics
Matches: 65, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
40 3 0.05
41 14 0.22
42 22 0.34
43 23 0.35
44 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (43 bp):
CTAGCAGGCATAATGCTGGTGAAATGATATCGGACTTAAAGGT
Found at i:31507677 original size:84 final size:83
Alignment explanation
Indices: 31507432--31507659 Score: 321
Period size: 84 Copynumber: 2.7 Consensus size: 83
31507422 GTGATGAATT
* * *
31507432 TCGGGCTTTGAGCCTAGCAGGCGTAATGGCGATGAAATGATATCGAACTTAAAGGTCTAGCAAGC
1 TCGGGCTCTGAGCCTAGCAGGCGTAATGCCGGTGAAATGATATCG-ACTTAAAGGTCTAGCAAGC
*
31507497 TTTAAGCTAGTGAATATTA
65 TTTAAGCTGGTGAATATTA
* * * * * *
31507516 TAGAGCTCTGAGCCTAGCAGGCATAATGCTGGTGAAATGATAACGGACTTAAAGGTCTAGCAAAC
1 TCGGGCTCTGAGCCTAGCAGGCGTAATGCCGGTGAAATGATATC-GACTTAAAGGTCTAGCAAGC
*
31507581 TTTAAGCTGGTGAATTTTA
65 TTTAAGCTGGTGAATATTA
*
31507600 TCGGGCTCCGAGCCTAGCAGGCGTAATGCCGGTGAAATGATATCAGACTTAAAGGTCTAG
1 TCGGGCTCTGAGCCTAGCAGGCGTAATGCCGGTGAAATGATATC-GACTTAAAGGTCTAG
31507660 TAGGCTTATT
Statistics
Matches: 125, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
84 124 0.99
85 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (83 bp):
TCGGGCTCTGAGCCTAGCAGGCGTAATGCCGGTGAAATGATATCGACTTAAAGGTCTAGCAAGCT
TTAAGCTGGTGAATATTA
Found at i:31518448 original size:48 final size:48
Alignment explanation
Indices: 31518384--31518721 Score: 604
Period size: 48 Copynumber: 7.0 Consensus size: 48
31518374 ATAAATATAT
* *
31518384 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
31518432 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
31518480 ATATGTATATGTGGTAAAGCCGACTGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
31518528 ATATGTATATGTGGTAAAGCAGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
31518576 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
31518624 ATATGTATATGTCGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
31518672 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
31518720 AT
1 AT
31518722 GTGTGTATAT
Statistics
Matches: 277, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 277 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Done.