Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 85 of 128
Found at i:28082869 original size:21 final size:21
Alignment explanation
Indices: 28082809--28082871 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
28082799 GAAGCCCGAA
28082809 GGCTGAACGGAAGCACATAAG
1 GGCTGAACGGAAGCACATAAG
* * * * *
28082830 TGCTAAACAGAAACCCATAAG
1 GGCTGAACGGAAGCACATAAG
* *
28082851 GGTTGAACGGAAGCTCATAAG
1 GGCTGAACGGAAGCACATAAG
28082872 AGCTTAATGA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (21 bp):
GGCTGAACGGAAGCACATAAG
Found at i:28082924 original size:21 final size:21
Alignment explanation
Indices: 28082898--28082950 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28082888 ATAAGGGTTA
28082898 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
* * * * *
28082919 AACAGAAACTCATATGAGTTT
1 AACAGAAGCTCAAAAGAGCTG
28082940 AACAGAAGCTC
1 AACAGAAGCTC
28082951 GTGAGAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCAAAAGAGCTG
Found at i:28091089 original size:24 final size:24
Alignment explanation
Indices: 28091024--28091094 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 24
28091014 GGATGCTCCA
* *
28091024 AAGAGCTATTAATGAGAAGCTCAT
1 AAGAGCTAATAATGGGAAGCTCAT
* *
28091048 AAGAACCATATAATGGGAAGCTCAT
1 AAGAGCTA-ATAATGGGAAGCTCAT
* * *
28091073 GAGAGCTAATAACGGGACGCTC
1 AAGAGCTAATAATGGGAAGCTC
28091095 TTTCGAGCTG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 18 0.49
25 19 0.51
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (24 bp):
AAGAGCTAATAATGGGAAGCTCAT
Found at i:28092510 original size:18 final size:17
Alignment explanation
Indices: 28092487--28092529 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28092477 TTCCCAACCC
28092487 TACAATTAACTCTCTAAT
1 TACAATTAACTCT-TAAT
* *
28092505 TACAATTTAATTCTTCAT
1 TACAA-TTAACTCTTAAT
28092523 TACAATT
1 TACAATT
28092530 TGGTTCCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
TACAATTAACTCTTAAT
Found at i:28092974 original size:16 final size:16
Alignment explanation
Indices: 28092950--28093010 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
28092940 TAAACAGTGC
28092950 TAAACATAACATACAT
1 TAAACATAACATACAT
*
28092966 TAAATATAACATACA-
1 TAAACATAACATACAT
* *
28092981 T-AATAT-ACATGCAT
1 TAAACATAACATACAT
28092995 TAAACATAACATACAT
1 TAAACATAACATACAT
28093011 AATATACTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 6 0.16
14 6 0.16
15 5 0.13
16 21 0.55
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAACATAACATACAT
Found at i:28093003 original size:29 final size:29
Alignment explanation
Indices: 28092958--28093028 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
28092948 GCTAAACATA
*
28092958 ACATACATTAAATATAACATACATAATAT
1 ACATACATTAAACATAACATACATAATAT
*
28092987 ACATGCATTAAACATAACATACATAATAT
1 ACATACATTAAACATAACATACATAATAT
*
28093016 ACTTACA-TAAACA
1 ACATACATTAAACA
28093029 GTAATATTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 6 0.16
29 32 0.84
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (29 bp):
ACATACATTAAACATAACATACATAATAT
Found at i:28095167 original size:19 final size:20
Alignment explanation
Indices: 28095129--28095170 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28095119 ATTTAACTAC
*
28095129 AAAACTTACAAAACTATCAT
1 AAAACTTACAAAAATATCAT
*
28095149 AAAACTTA-AAAAATCTCAT
1 AAAACTTACAAAAATATCAT
28095168 AAA
1 AAA
28095171 TTAAATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAACTTACAAAAATATCAT
Found at i:28095774 original size:13 final size:13
Alignment explanation
Indices: 28095756--28095809 Score: 65
Period size: 13 Copynumber: 4.0 Consensus size: 13
28095746 CAAATATATC
28095756 ACATAACATACAT
1 ACATAACATACAT
*
28095769 ACATAACAGTAATAT
1 ACATAACA-T-ACAT
28095784 ACATAACATACAT
1 ACATAACATACAT
28095797 A-ATATACATACAT
1 ACATA-ACATACAT
28095810 GAAGCATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 3 0.08
13 20 0.56
14 2 0.06
15 11 0.31
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.26
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:28095796 original size:9 final size:9
Alignment explanation
Indices: 28095756--28095806 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
28095746 CAAATATATC
28095756 ACATAACAT
1 ACATAACAT
28095765 ACAT-ACAT
1 ACATAACAT
*
28095773 AACAGTAATAT
1 -ACA-TAACAT
28095784 ACATAACAT
1 ACATAACAT
*
28095793 ACATAATAT
1 ACATAACAT
28095802 ACATA
1 ACATA
28095807 CATGAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.11
9 25 0.69
10 4 0.11
11 3 0.08
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (9 bp):
ACATAACAT
Found at i:28095872 original size:24 final size:24
Alignment explanation
Indices: 28095843--28095928 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
28095833 ATAATAGTCT
28095843 CATACATAACAATAATATACATAA
1 CATACATAACAATAATATACATAA
* *
28095867 CATACATTATAGACATACATTAAACATAATAGA
1 CATACA-TA-ACA-ATA-A-TATAC---ATA-A
*
28095900 CATACATAACAGTAATATACATAA
1 CATACATAACAATAATATACATAA
28095924 CATAC
1 CATAC
28095929 TTTGGTAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
24 12 0.25
25 5 0.10
26 2 0.04
27 3 0.06
28 5 0.10
29 5 0.10
30 2 0.04
31 2 0.04
32 5 0.10
33 7 0.15
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.26
Consensus pattern (24 bp):
CATACATAACAATAATATACATAA
Found at i:28095926 original size:33 final size:33
Alignment explanation
Indices: 28095756--28095927 Score: 99
Period size: 33 Copynumber: 5.2 Consensus size: 33
28095746 CAAATATATC
*
28095756 ACATAACATACATACATAACAGTAATATACATA
1 ACATAATATACATACATAACAGTAATATACATA
* * *
28095789 ACATACATA-ATATACAT-ACA-TGA-A-GCATA
1 ACATA-ATATACATACATAACAGTAATATACATA
* * * *
28095818 AAAGTAATATAC-CACATAATAGT-CTCATACATA
1 ACA-TAATATACATACATAACAGTAAT-ATACATA
* *
28095851 ACAATAATATACATAACAT-ACATTATAGACATACATTAA
1 AC-ATAATATACAT-ACATAACA--GTA-ATATACA-T-A
*
28095890 ACATAATAGACATACATAACAGTAATATACATA
1 ACATAATATACATACATAACAGTAATATACATA
28095923 ACATA
1 ACATA
28095928 CTTTGGTAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 36
0.65 0.12 0.23
Matches are distributed among these distances:
29 13 0.13
30 6 0.06
31 3 0.03
32 4 0.04
33 31 0.30
34 6 0.06
35 10 0.10
36 3 0.03
37 9 0.09
38 14 0.14
39 3 0.03
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.26
Consensus pattern (33 bp):
ACATAATATACATACATAACAGTAATATACATA
Found at i:28095927 original size:77 final size:75
Alignment explanation
Indices: 28095756--28095927 Score: 193
Period size: 77 Copynumber: 2.2 Consensus size: 75
28095746 CAAATATATC
* * * *
28095756 ACATAACATACATACATAACAGTAATATACATAACATACATAATATACATACATGAAGCATAAAA
1 ACATAATATACATACATAACAATAATATACATAACATACATAATAGACATACATGAAACATAAAA
* *
28095821 GTAATATACC
66 GTAATACACA
* * *
28095831 ACATAATAGTCTCATACATAACAATAATATACATAACATACATTATAGACATACATTAAACATAA
1 ACATAATA-T-ACATACATAACAATAATATACATAACATACATAATAGACATACATGAAACATAA
* *
28095896 TAG-ACATACATA
64 AAGTA-ATACACA
28095908 ACAGTAATATACATAACATA
1 ACA-TAATATACAT-ACATA
28095928 CTTTGGTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
75 7 0.09
76 5 0.06
77 63 0.79
78 5 0.06
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.26
Consensus pattern (75 bp):
ACATAATATACATACATAACAATAATATACATAACATACATAATAGACATACATGAAACATAAAA
GTAATACACA
Found at i:28097171 original size:18 final size:19
Alignment explanation
Indices: 28097148--28097184 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28097138 TTAGAAACAT
28097148 ATTTTTTA-ACAATTTTTA
1 ATTTTTTACACAATTTTTA
*
28097166 ATTTTTTACCCAATTTTTA
1 ATTTTTTACACAATTTTTA
28097185 TAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTTACACAATTTTTA
Found at i:28097192 original size:10 final size:9
Alignment explanation
Indices: 28097177--28097206 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
28097167 TTTTTTACCC
28097177 AATTTTTAT
1 AATTTTTAT
28097186 AATTTTTAT
1 AATTTTTAT
28097195 AATTTCTTAT
1 AATTT-TTAT
28097205 AA
1 AA
28097207 CTAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (9 bp):
AATTTTTAT
Found at i:28099580 original size:31 final size:31
Alignment explanation
Indices: 28099511--28099580 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
28099501 TTATAAAATT
* *
28099511 ATTATTGAATTATTCGAAAGTTTTCATTTAA
1 ATTATTGAAATATTCAAAAGTTTTCATTTAA
* * * * *
28099542 GTCATTGAAATATTTAAAATTTTTTATTTAA
1 ATTATTGAAATATTCAAAAGTTTTCATTTAA
28099573 ATTATTGA
1 ATTATTGA
28099581 GTTATTAAGT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (31 bp):
ATTATTGAAATATTCAAAAGTTTTCATTTAA
Found at i:28100662 original size:13 final size:14
Alignment explanation
Indices: 28100644--28100672 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28100634 TTCTCTCCGC
28100644 AAAAAGAGAAA-AA
1 AAAAAGAGAAAGAA
28100657 AAAAAGAGAAAGAA
1 AAAAAGAGAAAGAA
28100671 AA
1 AA
28100673 GCCTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAAGAA
Found at i:28104797 original size:14 final size:14
Alignment explanation
Indices: 28104778--28104816 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
28104768 GAATCTTTAA
28104778 AGTTAAG-CTCTTAG
1 AGTTAAGTC-CTTAG
28104792 AGTTAAGTCCTTAG
1 AGTTAAGTCCTTAG
*
28104806 TGTTAAGTCCT
1 AGTTAAGTCCT
28104817 CAGTTTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (14 bp):
AGTTAAGTCCTTAG
Found at i:28112588 original size:25 final size:25
Alignment explanation
Indices: 28112515--28112573 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
28112505 GTTCAAGCGA
28112515 GCCTATATCAGGAAACCCATAAAGG
1 GCCTATATCAGGAAACCCATAAAGG
28112540 GCCTATATCAGGAAACCCATAAAGG
1 GCCTATATCAGGAAACCCATAAAGG
28112565 GCCTATATC
1 GCCTATATC
28112574 GGGACGCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (25 bp):
GCCTATATCAGGAAACCCATAAAGG
Found at i:28115169 original size:26 final size:26
Alignment explanation
Indices: 28115140--28115269 Score: 102
Period size: 26 Copynumber: 4.9 Consensus size: 26
28115130 CTTTTATGGT
*
28115140 TATCTCTGAATAGACA-CTTTTGTGGC
1 TATCTCTGAATAGA-AGCCTTTGTGGC
*
28115166 TATCTCT-AAAAGGAAGCCTTTGTGGC
1 TATCTCTGAATA-GAAGCCTTTGTGGC
* * * *
28115192 TATCTCTAAATGGAAGCCTTTGTAGT
1 TATCTCTGAATAGAAGCCTTTGTGGC
* * *
28115218 TATCTCTGAATGGAAACCTTTGTGTC
1 TATCTCTGAATAGAAGCCTTTGTGGC
* *
28115244 GATCTCTGTTATAAGAAAGCCTTTGT
1 TATCTCTG-AAT-AG-AAGCCTTTGT
28115270 AGCCATCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.05
26 65 0.78
27 4 0.05
28 1 0.01
29 9 0.11
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (26 bp):
TATCTCTGAATAGAAGCCTTTGTGGC
Found at i:28115437 original size:29 final size:29
Alignment explanation
Indices: 28115158--28115438 Score: 117
Period size: 29 Copynumber: 10.0 Consensus size: 29
28115148 AATAGACACT
*
28115158 TTTGTGGCTATCTC--TAAAAGGAA-GCC
1 TTTGTGGCTATCTCTGTTAAAGGAATGCC
28115184 TTTGTGGCTATCTC---TAAATGGAA-GCC
1 TTTGTGGCTATCTCTGTTAAA-GGAATGCC
* * * *
28115210 TTTGTAGTTATCTCTG--AATGGAA-ACC
1 TTTGTGGCTATCTCTGTTAAAGGAATGCC
* * *
28115236 TTTGTGTCGATCTCTGTTATAA-GAAAGCC
1 TTTGTGGCTATCTCTGTTA-AAGGAATGCC
* * * * *
28115265 TTTGTAGCCATCTTTGTTAAAAGG-CTGCA
1 TTTGTGGCTATCTCTGTT-AAAGGAATGCC
* * * **
28115294 TTTGTGGCTATCTTTTTTAAACGAATATC
1 TTTGTGGCTATCTCTGTTAAAGGAATGCC
* * * *
28115323 TTTGTGGCTTTCTCAGTTAAATGAAT-CA
1 TTTGTGGCTATCTCTGTTAAAGGAATGCC
* * * *
28115351 TTT-TAGGGCAACCTCTGTCAAAAGG-ATGTC
1 TTTGT--GGCTATCTCTGT-TAAAGGAATGCC
* * *
28115381 TTTATGGCTATCTCAGTCAAAAGG-ATGCC
1 TTTGTGGCTATCTCTGT-TAAAGGAATGCC
*
28115410 TTTGTGGCCATCTCTGTTAAAGGAATGCC
1 TTTGTGGCTATCTCTGTTAAAGGAATGCC
28115439 ATAGGCAGAC
Statistics
Matches: 190, Mismatches: 49, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
25 3 0.02
26 51 0.27
27 3 0.02
28 16 0.08
29 107 0.56
30 9 0.05
31 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (29 bp):
TTTGTGGCTATCTCTGTTAAAGGAATGCC
Found at i:28124209 original size:22 final size:20
Alignment explanation
Indices: 28124176--28124218 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
28124166 TTTATATGTT
* *
28124176 TGAATTTAAAATTGTATATG
1 TGAATTTAAAATGGCATATG
28124196 TGAATTGTATAAATGGCATATG
1 TGAATT-TA-AAATGGCATATG
28124218 T
1 T
28124219 ATGAAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (20 bp):
TGAATTTAAAATGGCATATG
Found at i:28126382 original size:18 final size:17
Alignment explanation
Indices: 28126351--28126395 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
28126341 GAAAAAAAGG
28126351 GGTTACAAGGAGATGAAA
1 GGTTA-AAGGAGATGAAA
*
28126369 GGTTTAAGGAAGATGAAA
1 GGTTAAAGG-AGATGAAA
28126387 GGTTAAAGG
1 GGTTAAAGG
28126396 TTAAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.42, C:0.02, G:0.36, T:0.20
Consensus pattern (17 bp):
GGTTAAAGGAGATGAAA
Found at i:28133398 original size:29 final size:31
Alignment explanation
Indices: 28133364--28133423 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
28133354 TATTTTTTTT
28133364 ATAA-TTTTAATGATTTTT-AATTTTTAAAA
1 ATAATTTTTAATGATTTTTGAATTTTTAAAA
* **
28133393 ATAATTTTTTATTTTTTTTGAATTTTTAAAA
1 ATAATTTTTAATGATTTTTGAATTTTTAAAA
28133424 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 11 0.42
31 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
ATAATTTTTAATGATTTTTGAATTTTTAAAA
Found at i:28133426 original size:40 final size:41
Alignment explanation
Indices: 28133327--28133439 Score: 128
Period size: 40 Copynumber: 2.8 Consensus size: 41
28133317 GATGTTAATA
* *
28133327 TTTAATTAATTTTTAAAA-TTTTAAAAATATTTTTTTTATAAT
1 TTTAATGAATTTTTAAAATTTTTAAAAATA-ATTTTTTAT-AT
28133369 TTTAATG-ATTTTT--AATTTTTAAAAATAATTTTTTAT-T
1 TTTAATGAATTTTTAAAATTTTTAAAAATAATTTTTTATAT
**
28133406 TTTTTTGAATTTTTAAAATTTTTAAAAATTAATT
1 TTTAATGAATTTTTAAAATTTTTAAAAA-TAATT
28133440 AAATGTTGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
37 6 0.10
38 6 0.10
39 10 0.16
40 23 0.37
41 11 0.18
42 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (41 bp):
TTTAATGAATTTTTAAAATTTTTAAAAATAATTTTTTATAT
Found at i:28138768 original size:23 final size:23
Alignment explanation
Indices: 28138738--28138788 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
28138728 CCCCCCCCAC
28138738 AAAAAAAAAAAGAAAAAACAAAA
1 AAAAAAAAAAAGAAAAAACAAAA
* * * *
28138761 AAAAAAAAAGAGAGAGAACCAAA
1 AAAAAAAAAAAGAAAAAACAAAA
28138784 AAAAA
1 AAAAA
28138789 GAGTCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAGAAAAAACAAAA
Found at i:28139649 original size:27 final size:27
Alignment explanation
Indices: 28139619--28139671 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28139609 AAATTATCGT
*
28139619 TGTTAAT-GTGATTTTTTACATATTGTG
1 TGTTAATCGTG-TGTTTTACATATTGTG
* *
28139646 TGTTCATCTTGTGTTTTACATATTGT
1 TGTTAATCGTGTGTTTTACATATTGT
28139672 ATTATGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.57
Consensus pattern (27 bp):
TGTTAATCGTGTGTTTTACATATTGTG
Found at i:28143795 original size:27 final size:27
Alignment explanation
Indices: 28143765--28143844 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
28143755 ATTGCAAGAT
*
28143765 GTCTCTACAAGTGACGAGCTGCGAGAA
1 GTCTCTACAAGTGACAAGCTGCGAGAA
* *
28143792 GTCT-TCACAAGTGGCAAGCTGTGAGAA
1 GTCTCT-ACAAGTGACAAGCTGCGAGAA
* * *
28143819 GTCTCCACAAGTGGCAAGCTGTGAGA
1 GTCTCTACAAGTGACAAGCTGCGAGA
28143845 TGAACTGCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (27 bp):
GTCTCTACAAGTGACAAGCTGCGAGAA
Found at i:28143924 original size:28 final size:28
Alignment explanation
Indices: 28143856--28143942 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
28143846 GAACTGCAAA
* * *
28143856 ATGACACCAAGAAGGGGTG-AGCTGTGAG
1 ATGACACCACGAAGTGGTGAAG-TGCGAG
***
28143884 ATGACATTGCGAAGTGGTGAAGTGCGAG
1 ATGACACCACGAAGTGGTGAAGTGCGAG
*
28143912 ATGACACCACGAAATGGTGAAGTGCGAG
1 ATGACACCACGAAGTGGTGAAGTGCGAG
28143940 ATG
1 ATG
28143943 TCTTTGCAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 46 0.96
29 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.37, T:0.17
Consensus pattern (28 bp):
ATGACACCACGAAGTGGTGAAGTGCGAG
Found at i:28157947 original size:25 final size:24
Alignment explanation
Indices: 28157902--28157953 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
28157892 ACATACTACA
28157902 GCTCTTTATGAGTGTCCTGATATAG
1 GCTCTTTATGAGTGTCCTGATAT-G
* *
28157927 GCTCTTTGTGAGCT-TCTTGATATG
1 GCTCTTTATGAG-TGTCCTGATATG
28157951 GCT
1 GCT
28157954 AGCTTGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 19 0.79
26 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (24 bp):
GCTCTTTATGAGTGTCCTGATATG
Found at i:28166110 original size:30 final size:30
Alignment explanation
Indices: 28166068--28166180 Score: 172
Period size: 30 Copynumber: 3.8 Consensus size: 30
28166058 AGAATCAGTC
* * * **
28166068 TGGGCCTGAGCCCTATACAGTAGCACTGTG
1 TGGGCCTTAGCCCAATACAGTAACAGAGTG
*
28166098 TGGGCCATAGCCCAATACAGTAACAGAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGAGTG
28166128 TGGGCCTTAGCCCAATACAGTAACAGAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGAGTG
28166158 TGGGCCTTAGCCCAATACAGTAA
1 TGGGCCTTAGCCCAATACAGTAA
28166181 TAGTGCAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (30 bp):
TGGGCCTTAGCCCAATACAGTAACAGAGTG
Found at i:28166322 original size:26 final size:26
Alignment explanation
Indices: 28166291--28166388 Score: 108
Period size: 26 Copynumber: 3.8 Consensus size: 26
28166281 ACACCAATAT
*
28166291 CGCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAACAAAGCTGCCAGTAATAGTAA
* * * *
28166317 CACAGCAAAGCTGCCAATAACAGTAA
1 CGCAACAAAGCTGCCAGTAATAGTAA
* * *
28166343 TGCAACAGAGTTGCCAGT-ATCAGTAA
1 CGCAACAAAGCTGCCAGTAAT-AGTAA
28166369 CGCAACAAAGCTGCCAGTAA
1 CGCAACAAAGCTGCCAGTAA
28166389 CAATATTTGT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
25 1 0.02
26 55 0.96
27 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.15
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAGTAATAGTAA
Found at i:28166636 original size:27 final size:27
Alignment explanation
Indices: 28166587--28167216 Score: 695
Period size: 27 Copynumber: 23.3 Consensus size: 27
28166577 GGTATAACGG
* * * * *
28166587 TCATTTTACCATACAAGGATATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
28166614 TAATTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * **
28166640 GTCATTTTACCTTTCGGGGGTATTTTAA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* * *
28166668 TAATTTTACCCATCGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * * * *
28166695 TAAATTTACCCATCAAAGGGTATTTCGT
1 TCATTTTACCCTTC-GAGGGTATTTCGA
* *
28166723 TCAGTTTA-CCTATCGAGGGTATTTCGG
1 TCATTTTACCCT-TCGAGGGTATTTCGA
28166750 TCATTTTACCCTTCG-GGAGTATTTCGA
1 TCATTTTACCCTTCGAGG-GTATTTCGA
* *
28166777 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
28166804 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
28166831 TCATTTTACCCTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
28166857 GTCATTTTACCCTTC-AGGAGTATTTC-A
1 -TCATTTTACCCTTCGAGG-GTATTTCGA
*
28166884 GTTATTTTACCCTTCGAGGGTATTTCGA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
** * * *
28166912 TCATTTTACATTTTGAGAGTATTTCGT
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
28166939 TCATTTTACCCTTCAAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
28166966 TCATTTTACCCTTTGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
28166993 TCATTTTACCCTTCGAGGGTATTTTCG-
1 TCATTTTACCCTTCGAGGGTA-TTTCGA
* *
28167020 TCATTTTATCCTTCGAGGGTCTTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
28167047 TCATTTTACCCTAC-AGGGGTATTTCGA
1 TCATTTTACCCTTCGA-GGGTATTTCGA
*
28167074 TCATTTTACCCTTCAAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
28167101 TCATTTTACCCTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
28167127 GTCATTTTACCCTTTGATGGTATTTCGA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
28167155 TCATTTTACCCATCAAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
28167182 TAATTTTATCCATCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
28167208 GTCATTTTA
1 -TCATTTTA
28167217 GAGGCCGATT
Statistics
Matches: 519, Mismatches: 66, Indels: 36
0.84 0.11 0.06
Matches are distributed among these distances:
26 15 0.03
27 469 0.90
28 35 0.07
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:28168362 original size:14 final size:14
Alignment explanation
Indices: 28168343--28168371 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28168333 TTGGAATGGC
28168343 TAGTGATGGTATGT
1 TAGTGATGGTATGT
28168357 TAGTGATGGTATGT
1 TAGTGATGGTATGT
28168371 T
1 T
28168372 TTGATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (14 bp):
TAGTGATGGTATGT
Found at i:28170572 original size:26 final size:26
Alignment explanation
Indices: 28170543--28170602 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
28170533 GAAAACTCTG
28170543 AAGAGCCATTAATCAGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAGCTCACA
* * *
28170569 AAGAGCCTTTAATCGGGAAGCTCACG
1 AAGAGCCATTAATCAGGAAGCTCACA
28170595 AAGAGCCA
1 AAGAGCCA
28170603 AATAACGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (26 bp):
AAGAGCCATTAATCAGGAAGCTCACA
Found at i:28170611 original size:26 final size:26
Alignment explanation
Indices: 28170543--28170612 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
28170533 GAAAACTCTG
* *
28170543 AAGAGCCATTAATCAGGAAGCTCACA
1 AAGAGCCAATAATCGGGAAGCTCACA
** *
28170569 AAGAGCCTTTAATCGGGAAGCTCACG
1 AAGAGCCAATAATCGGGAAGCTCACA
28170595 AAGAGCCAAATAA-CGGGA
1 AAGAGCC-AATAATCGGGA
28170613 CACTCATAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 35 0.92
27 3 0.08
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.14
Consensus pattern (26 bp):
AAGAGCCAATAATCGGGAAGCTCACA
Found at i:28172384 original size:24 final size:24
Alignment explanation
Indices: 28172357--28172404 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28172347 AAGCTCATGC
* * *
28172357 GAGCCAATGATGGGTAGCTCCGAA
1 GAGCCAATAACGGGAAGCTCCGAA
*
28172381 GAGCCATTAACGGGAAGCTCCGAA
1 GAGCCAATAACGGGAAGCTCCGAA
28172405 TAGACATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (24 bp):
GAGCCAATAACGGGAAGCTCCGAA
Found at i:28172488 original size:26 final size:26
Alignment explanation
Indices: 28172379--28172510 Score: 80
Period size: 26 Copynumber: 5.3 Consensus size: 26
28172369 GGTAGCTCCG
* *
28172379 AAGAGCCATTAA-CGGGAAGCTC-CG
1 AAGAGCCATTAATCAGGAAGCTCACA
* * *
28172403 AATAGACA-TATATCAGGAAGTTCA-A
1 AAGAGCCATTA-ATCAGGAAGCTCACA
** * *
28172428 GCGAGCCA-T-ATCAGGAAACTC-CG
1 AAGAGCCATTAATCAGGAAGCTCACA
*
28172451 AAGAGACATTAATCAGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAGCTCACA
* * * *
28172477 AAGAGCCTTTAATTAGGAAGCTTAGA
1 AAGAGCCATTAATCAGGAAGCTCACA
28172503 AAGAGCCA
1 AAGAGCCA
28172511 AATAACGTGA
Statistics
Matches: 78, Mismatches: 23, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
23 17 0.22
24 8 0.10
25 24 0.31
26 29 0.37
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (26 bp):
AAGAGCCATTAATCAGGAAGCTCACA
Found at i:28174154 original size:33 final size:33
Alignment explanation
Indices: 28174112--28174341 Score: 166
Period size: 33 Copynumber: 6.6 Consensus size: 33
28174102 AATATAAAGG
28174112 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
28174145 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
28174187 GGTTGCTAAGTGCCGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
28174214 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
28174247 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAT
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG--GT
**
28174288 GGGTTGCTAAGTGCTGATTCCCCGATTCGCTGGT
1 -GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
28174322 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
28174342 ACCGTATTTT
Statistics
Matches: 156, Mismatches: 17, Indels: 48
0.71 0.08 0.22
Matches are distributed among these distances:
27 20 0.13
28 2 0.01
31 2 0.01
32 2 0.01
33 59 0.38
34 7 0.04
35 2 0.01
36 2 0.01
37 4 0.03
38 6 0.04
39 3 0.02
40 1 0.01
41 6 0.04
42 40 0.26
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:28174284 original size:102 final size:102
Alignment explanation
Indices: 28174108--28174310 Score: 352
Period size: 102 Copynumber: 2.0 Consensus size: 102
28174098 ATTGAATATA
* *
28174108 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
*
28174173 TTAAATGTGAAGGGGGTTGCTAAGTGCCGATTCCCCC
66 TTAAATGTGAAAGGGGTTGCTAAGTGCCGATTCCCCC
*
28174210 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
* *
28174275 TTAAATGTGAAATGGGTTGCTAAGTGCTGATTCCCC
66 TTAAATGTGAAAGGGGTTGCTAAGTGCCGATTCCCC
28174311 GATTCGCTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
TTAAATGTGAAAGGGGTTGCTAAGTGCCGATTCCCCC
Found at i:28174336 original size:75 final size:76
Alignment explanation
Indices: 28174210--28174390 Score: 274
Period size: 75 Copynumber: 2.4 Consensus size: 76
28174200 CGATTCCCCC
* *
28174210 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTA-T
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
28174274 CTTAAATGTGA
66 CTTAAATGTGA
* * *
28174285 AATGGGTTGCTAAGTGCTGATTCCCCGATTCGCTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
* *
28174350 TTTGAATGTGA
66 CTTAAATGTGA
*
28174361 AAGGGGTTGCTAAGTGCTGAATCCACCGAT
1 AAGGGGTTGCTAAGTGCTGATTCC-CCGAT
28174391 AATGGATAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 58 0.61
76 32 0.34
77 5 0.05
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCACTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
CTTAAATGTGA
Found at i:28176257 original size:16 final size:13
Alignment explanation
Indices: 28176223--28176250 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28176213 CTTTATTTTA
28176223 TTATTTATCATCT
1 TTATTTATCATCT
28176236 TTATTTATCATCT
1 TTATTTATCATCT
28176249 TT
1 TT
28176251 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:28202764 original size:230 final size:230
Alignment explanation
Indices: 28202359--28202821 Score: 917
Period size: 230 Copynumber: 2.0 Consensus size: 230
28202349 AAACATTCAA
28202359 AAGAGTAGAAGAGAGATTTGGATCCAGAGATATTAATTGTGCGCAGAAACATAAAATCTCATCAC
1 AAGAGTAGAAGAGAGATTTGGATCCAGAGATATTAATTGTGCGCAGAAACATAAAATCTCATCAC
28202424 AGATGTTGAACGATTGGTGATCGAATGCAAGGAACACTAATGATTGAAGAAATAAACTAAAACTA
66 AGATGTTGAACGATTGGTGATCGAATGCAAGGAACACTAATGATTGAAGAAATAAACTAAAACTA
28202489 GAATTGAAATTGAAAGTAAGAAAGTTTAAATAGAAAAAACCCTAAATAACAAACCCTAATCTAAG
131 GAATTGAAATTGAAAGTAAGAAAGTTTAAATAGAAAAAACCCTAAATAACAAACCCTAATCTAAG
28202554 AATAGAAATTCAAACTAAGAAAAAGCTCCCTAATT
196 AATAGAAATTCAAACTAAGAAAAAGCTCCCTAATT
28202589 AAGAGTAGAAGAGAGATTTGGATCCAGAGATATTAATTGTGCGCAGAAACATAAAATCTCATCAC
1 AAGAGTAGAAGAGAGATTTGGATCCAGAGATATTAATTGTGCGCAGAAACATAAAATCTCATCAC
28202654 AGATGTTGAACGATTGGTGATCGAATGCAAGGAACACTAATGATTGAAGAAATAAACTAAAACTA
66 AGATGTTGAACGATTGGTGATCGAATGCAAGGAACACTAATGATTGAAGAAATAAACTAAAACTA
*
28202719 GAATTGAAATTGAAAGTAAGAAAGTTTAAATAGAAAAACCCCTAAATAACAAACCCTAATCTAAG
131 GAATTGAAATTGAAAGTAAGAAAGTTTAAATAGAAAAAACCCTAAATAACAAACCCTAATCTAAG
28202784 AATAGAAATTCAAACTAAGAAAAAGCTCCCTAATT
196 AATAGAAATTCAAACTAAGAAAAAGCTCCCTAATT
28202819 AAG
1 AAG
28202822 CCCTGAGCAA
Statistics
Matches: 232, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 232 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (230 bp):
AAGAGTAGAAGAGAGATTTGGATCCAGAGATATTAATTGTGCGCAGAAACATAAAATCTCATCAC
AGATGTTGAACGATTGGTGATCGAATGCAAGGAACACTAATGATTGAAGAAATAAACTAAAACTA
GAATTGAAATTGAAAGTAAGAAAGTTTAAATAGAAAAAACCCTAAATAACAAACCCTAATCTAAG
AATAGAAATTCAAACTAAGAAAAAGCTCCCTAATT
Found at i:28204366 original size:25 final size:23
Alignment explanation
Indices: 28204338--28204417 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 23
28204328 CATAAACATA
28204338 AAGCTCCTTCGAGCCATATAACGGG
1 AAGCTCCTT-GAGCCAT-TAACGGG
* ** *
28204363 AAGCTCATGTGAGTTATGTAACAGG
1 AAGCTCCT-TGAGCCAT-TAACGGG
**
28204388 AAGCTCCGGAGAGCCATTAACGGG
1 AAGCTCC-TTGAGCCATTAACGGG
28204412 AAGCTC
1 AAGCTC
28204418 ATAAGAGCCA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
24 12 0.29
25 29 0.69
26 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
AAGCTCCTTGAGCCATTAACGGG
Found at i:28204413 original size:24 final size:25
Alignment explanation
Indices: 28204348--28204427 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
28204338 AAGCTCCTTC
* *
28204348 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCAGGA
** * * *
28204373 GAGTTATGTAACAGGAAGCTCCGGA
1 GAGCCATATAACGGGAAGCTCAGGA
**
28204398 GAGCCAT-TAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCAGGA
28204422 GAGCCA
1 GAGCCA
28204428 ATATCATAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCAGGA
Found at i:28205014 original size:10 final size:11
Alignment explanation
Indices: 28204990--28205021 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
28204980 GAATTTAACA
28204990 TCAATTCATAT
1 TCAATTCATAT
28205001 TCAATTCA-AT
1 TCAATTCATAT
28205011 TCAATTCATAT
1 TCAATTCATAT
28205022 CTTATGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (11 bp):
TCAATTCATAT
Found at i:28208293 original size:46 final size:46
Alignment explanation
Indices: 28208202--28208348 Score: 161
Period size: 46 Copynumber: 3.2 Consensus size: 46
28208192 TCCTGTGCAC
* * * ** * *
28208202 GTTCAATCCTAACAGGTGA-CAATGTACTATTATTCGATTCATGTAG
1 GTTCAACCCTAACAGGTGACCAA-GCACAATTACCCAATTCGTGTAG
*
28208248 GTTCAACCCTAACAGGTGACCAAGCACAATTACCCAATTTGTGTAG
1 GTTCAACCCTAACAGGTGACCAAGCACAATTACCCAATTCGTGTAG
** * *
28208294 GTTCAACCCTAATGGGTGACCAGGCACAATTATCCAATTCGTGTAG
1 GTTCAACCCTAACAGGTGACCAAGCACAATTACCCAATTCGTGTAG
*
28208340 GTTTAACCC
1 GTTCAACCC
28208349 AAACGGGTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 83 0.97
47 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (46 bp):
GTTCAACCCTAACAGGTGACCAAGCACAATTACCCAATTCGTGTAG
Found at i:28210113 original size:27 final size:27
Alignment explanation
Indices: 28210074--28210277 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
28210064 CTTGGGTAGG
* *
28210074 AAAATTATCGAAATACCCTCGAAAGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
** *
28210101 AAAATTATTGAAATACCCACGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
28210128 TAAATTACTGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
**
28210155 AAAATTAATGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
28210182 AAAATTACCGAAAT-CTCTTGAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
*
28210208 AAAATTACCGAAATACCCTCAAAGGGT
1 AAAATTACCGAAATACCCTCGAAGGGT
* *
28210235 AAAATTACCCTAAATACCC-CAAAGGGT
1 AAAATTA-CCGAAATACCCTCGAAGGGT
*
28210262 AAAATGACCGAAATAC
1 AAAATTACCGAAATAC
28210278 ATCTGTAGGT
Statistics
Matches: 157, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
26 32 0.20
27 115 0.73
28 10 0.06
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCGAAGGGT
Found at i:28210239 original size:80 final size:81
Alignment explanation
Indices: 28210074--28210277 Score: 245
Period size: 80 Copynumber: 2.5 Consensus size: 81
28210064 CTTGGGTAGG
* ** * *
28210074 AAAATT-ATCGAAATACCCTCGAAAGGTAAAATTATTGAAATACCCACGAAGGGTTAAATTACTG
1 AAAATTAAT-GAAATACCCTCGAAGGGTAAAATTACCGAAATACCCACGAAGGGTAAAATTACCG
*
28210138 AAATACCCTCGAAGGGT
65 AAATACCCTCAAAGGGT
* **
28210155 AAAATTAATGAAATACCCTCGAAGGGTAAAATTACCGAAAT-CTCTTGAAGGGTAAAATTACCGA
1 AAAATTAATGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCACGAAGGGTAAAATTACCGA
28210219 AATACCCTCAAAGGGT
66 AATACCCTCAAAGGGT
* * *
28210235 AAAATTACCCT-AAATACCC-CAAAGGGTAAAATGACCGAAATAC
1 AAAATTA--ATGAAATACCCTCGAAGGGTAAAATTACCGAAATAC
28210278 ATCTGTAGGT
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
80 60 0.56
81 44 0.41
82 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (81 bp):
AAAATTAATGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCACGAAGGGTAAAATTACCGA
AATACCCTCAAAGGGT
Found at i:28210668 original size:28 final size:27
Alignment explanation
Indices: 28210631--28210688 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
28210621 GTACTGATTT
*
28210631 CTGTATTGGGCTAAGGCCCACACTGTTA
1 CTGTAATGGGCTAAGGCCCACACTG-TA
28210659 CTGTAATGGGCTAAGGCCCACACTGTA
1 CTGTAATGGGCTAAGGCCCACACTGTA
28210686 CTG
1 CTG
28210689 ATACTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (27 bp):
CTGTAATGGGCTAAGGCCCACACTGTA
Found at i:28210694 original size:33 final size:33
Alignment explanation
Indices: 28210620--28210709 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 33
28210610 ATCACTGCAT
* *
28210620 TGTACTGATTTCTGTATTGGGCTAAGGCCCACAC
1 TGTACTGA-TACTGTAATGGGCTAAGGCCCACAC
28210654 TG---T--TACTGTAATGGGCTAAGGCCCACAC
1 TGTACTGATACTGTAATGGGCTAAGGCCCACAC
*
28210682 TGTACTGATACTGT-ATAGGGCTCAGGCC
1 TGTACTGATACTGTAAT-GGGCTAAGGCC
28210710 TAGACTGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
28 25 0.53
31 2 0.04
32 2 0.04
33 16 0.34
34 2 0.04
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (33 bp):
TGTACTGATACTGTAATGGGCTAAGGCCCACAC
Found at i:28217305 original size:27 final size:27
Alignment explanation
Indices: 28217267--28217487 Score: 232
Period size: 27 Copynumber: 8.2 Consensus size: 27
28217257 CTTAGGCTAG
* *
28217267 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTCAAAGGGT
* *
28217294 AAAATTACCGAAATACCTTCGAAGGGT
1 AAAATTACCGAAATACCCTCAAAGGGT
* * *
28217321 AAAATTACTGAAATATCCTCAAAAGGT
1 AAAATTACCGAAATACCCTCAAAGGGT
* *
28217348 AAAATTACTGAAATACCCGCAAAGGGT
1 AAAATTACCGAAATACCCTCAAAGGGT
* ** * *
28217375 AAAATTATCGAAATATTCTCGAAGGTT
1 AAAATTACCGAAATACCCTCAAAGGGT
*
28217402 AAAATTACCAAAATACCCTCAAAGGGT
1 AAAATTACCGAAATACCCTCAAAGGGT
*
28217429 AAAATTACCCAAAATAACCC-CAAA-GGT
1 AAAATTA-CCGAAAT-ACCCTCAAAGGGT
* *
28217456 AAAATAACCGAAATACCC-CTAAAGGTT
1 AAAATTACCGAAATACCCTC-AAAGGGT
28217483 AAAAT
1 AAAAT
28217488 AACTGTTATA
Statistics
Matches: 164, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
25 5 0.03
26 9 0.05
27 135 0.82
28 11 0.07
29 4 0.02
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCAAAGGGT
Found at i:28217833 original size:27 final size:27
Alignment explanation
Indices: 28217793--28218000 Score: 172
Period size: 27 Copynumber: 7.7 Consensus size: 27
28217783 GCTTAAGCCG
* *
28217793 AAAATTATCGAAATGCCCTCAAAGGGT
1 AAAATTATCAAAATACCCTCAAAGGGT
* * *
28217820 AAAATCATCAAAATACCCTCGAAGGTT
1 AAAATTATCAAAATACCCTCAAAGGGT
** *
28217847 AAAATTATTGAAATACCCT-AGAAGAGT
1 AAAATTATCAAAATACCCTCA-AAGGGT
*
28217874 AAAATTA-CTGAAATACCCTCAAAGGGT
1 AAAATTATC-AAAATACCCTCAAAGGGT
* * *
28217901 AAAATTA-CAGAAATATCCTCGAAGGTT
1 AAAATTATCA-AAATACCCTCAAAGGGT
**
28217928 AAAATTCCCAAAATACCCTCAAAGGGT
1 AAAATTATCAAAATACCCTCAAAGGGT
* * *
28217955 AAAATTACCCAAAATAACCC-AAAAAGGT
1 AAAATTA-TCAAAAT-ACCCTCAAAGGGT
* *
28217983 AAAATGATCGAAATACCC
1 AAAATTATCAAAATACCC
28218001 CCGTAAGGTA
Statistics
Matches: 147, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.03
27 117 0.80
28 22 0.15
29 4 0.03
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (27 bp):
AAAATTATCAAAATACCCTCAAAGGGT
Found at i:28217942 original size:81 final size:82
Alignment explanation
Indices: 28217793--28218014 Score: 231
Period size: 81 Copynumber: 2.7 Consensus size: 82
28217783 GCTTAAGCCG
* ***
28217793 AAAATTA-TCGAAATGCCCTCAAAGGGTAAAATCATCAAAATACCCTCGAAGGTTAAAATTATTG
1 AAAATTACTCGAAATACCCTCAAAGGGTAAAATCATCAAAATACCCTCGAAGGTTAAAATTACCA
28217857 AAATACCCT-AGAAGAGT
66 AAATACCCTCA-AAGAGT
* * *
28217874 AAAATTACT-GAAATACCCTCAAAGGGTAAAATTA-CAGAAATATCCTCGAAGGTTAAAATTCCC
1 AAAATTACTCGAAATACCCTCAAAGGGTAAAATCATCA-AAATACCCTCGAAGGTTAAAATTACC
*
28217937 AAAATACCCTCAAAGGGT
65 AAAATACCCTCAAAGAGT
* * * * * * *
28217955 AAAATTACCCAAAATAACCC-AAAAAGGTAAAATGATCGAAATACCCCCGTAAGG-TAAAAT
1 AAAATTACTCGAAAT-ACCCTCAAAGGGTAAAATCATCAAAATACCCTCG-AAGGTTAAAAT
28218015 GACTGTTATA
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
80 2 0.02
81 74 0.63
82 33 0.28
83 9 0.08
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (82 bp):
AAAATTACTCGAAATACCCTCAAAGGGTAAAATCATCAAAATACCCTCGAAGGTTAAAATTACCA
AAATACCCTCAAAGAGT
Found at i:28218401 original size:28 final size:27
Alignment explanation
Indices: 28218359--28218415 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
28218349 GTACTAATTT
*
28218359 CTGTATTGGGCTAAGGCCCACACTGATA
1 CTGTAATGGGCTAAGGCCCACACTG-TA
*
28218387 CTGTAATGGGTTAAGGCCCACACTGTA
1 CTGTAATGGGCTAAGGCCCACACTGTA
28218414 CT
1 CT
28218416 AATACTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (27 bp):
CTGTAATGGGCTAAGGCCCACACTGTA
Found at i:28221257 original size:16 final size:17
Alignment explanation
Indices: 28221236--28221277 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
28221226 TTTTCGCTAT
28221236 ATACCA-CAAATAATGC
1 ATACCATCAAATAATGC
*
28221252 ATACCATATCAAATAATGG
1 ATACC--ATCAAATAATGC
28221271 ATACCAT
1 ATACCAT
28221278 ATGATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 5 0.23
17 2 0.09
18 1 0.05
19 14 0.64
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (17 bp):
ATACCATCAAATAATGC
Found at i:28221266 original size:19 final size:19
Alignment explanation
Indices: 28221242--28221279 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28221232 CTATATACCA
28221242 CAAATAATGCATACCATAT
1 CAAATAATGCATACCATAT
*
28221261 CAAATAATGGATACCATAT
1 CAAATAATGCATACCATAT
28221280 GATAACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (19 bp):
CAAATAATGCATACCATAT
Found at i:28221388 original size:3 final size:3
Alignment explanation
Indices: 28221374--28221419 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
28221364 AATCTACCTT
*
28221374 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28221420 AAGATTTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28226752 original size:25 final size:25
Alignment explanation
Indices: 28226724--28226775 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
28226714 TAAATTTGAT
28226724 TTTGTAAACAATTATTAAAGATGAG
1 TTTGTAAACAATTATTAAAGATGAG
*
28226749 TTTGTAAACAATTATTAAAGATTAG
1 TTTGTAAACAATTATTAAAGATGAG
28226774 TT
1 TT
28226776 ATTTGAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (25 bp):
TTTGTAAACAATTATTAAAGATGAG
Found at i:28229419 original size:40 final size:40
Alignment explanation
Indices: 28229346--28229465 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 40
28229336 AAACTGTTCA
* *
28229346 TCCACGTCAGCAAATCGCGTCCT--CGTAGG-CGCGATTTGTG
1 TCCACGTAAGCAAATCGCG--CTGACGT-GGACGCGATTTCTG
28229386 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATGTTCTG
1 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGAT-TTCTG
* * ** *
28229427 -ACATGTACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 TCCACGTAAGC--AAATCGCGCTGACGTGGACGCGATTTC
28229466 GCGGAAAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 33 0.49
41 7 0.10
42 23 0.34
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCTG
Found at i:28230950 original size:15 final size:16
Alignment explanation
Indices: 28230927--28230960 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28230917 TGTATCAACT
28230927 TATAAA-TTTTTTAAA
1 TATAAATTTTTTTAAA
*
28230942 TATATATTTTTTTAAA
1 TATAAATTTTTTTAAA
28230958 TAT
1 TAT
28230961 TCAAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAAATTTTTTTAAA
Found at i:28235613 original size:42 final size:42
Alignment explanation
Indices: 28235557--28235677 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 42
28235547 AGCACATGTA
* * ** * **
28235557 AGCTAAACAGAAACCCATAAGGGTTGGACGGAAGCTCGTAAG
1 AGCTGAACAAAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
*
28235599 AGCTGAACAAAAACCTATAAGGGTTAAACAGAAGCTCAAAAG
1 AGCTGAACAAAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
* * * * *
28235641 AGCTGAACGAAAACTCATATGAGTTAAACAGTAGCTC
1 AGCTGAACAAAAACCCATAAGGGTTAAACAGAAGCTC
28235678 GTGAGAGCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (42 bp):
AGCTGAACAAAAACCCATAAGGGTTAAACAGAAGCTCAAAAG
Found at i:28250320 original size:17 final size:16
Alignment explanation
Indices: 28250275--28250309 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28250265 ACAAAGTTTG
* *
28250275 AATTCCATAACTATTT
1 AATTTCATAGCTATTT
28250291 AATTTCATAGCTATTT
1 AATTTCATAGCTATTT
28250307 AAT
1 AAT
28250310 CCTTCTAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTTCATAGCTATTT
Found at i:28251231 original size:13 final size:13
Alignment explanation
Indices: 28251203--28251238 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
28251193 GCAGATGCAG
*
28251203 ATACAGATACAGAT
1 ATACAGA-ATAGAT
28251217 ATACAGAATAGAT
1 ATACAGAATAGAT
28251230 ATACAGAAT
1 ATACAGAAT
28251239 CCTACGCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (13 bp):
ATACAGAATAGAT
Found at i:28254887 original size:49 final size:49
Alignment explanation
Indices: 28254810--28254906 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
28254800 TTATGCTATG
* * *
28254810 CATTTCTAAACTTGGTCTTCCATTGTCTACACACTTATCACTATTTATA
1 CATTGCTAAACTTAGTCTTACATTGTCTACACACTTATCACTATTTATA
*
28254859 CATTGCTAAACTTAGTCTTACATTGTCTACACTCTTATCACTATTTAT
1 CATTGCTAAACTTAGTCTTACATTGTCTACACACTTATCACTATTTAT
28254907 CCCTTCTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTACATTGTCTACACACTTATCACTATTTATA
Found at i:28256269 original size:43 final size:43
Alignment explanation
Indices: 28256213--28256298 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
28256203 TCATATTTCA
* *
28256213 TTTCTCATTTCATAATCATTTCTCATATTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
* * *
28256256 TTTCTCATCTCATATTCATTTATCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
28256299 CAATAACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:28257014 original size:19 final size:18
Alignment explanation
Indices: 28256974--28257014 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
28256964 AATATTACAC
*
28256974 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
28256992 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
28257011 ATTT
1 ATTT
28257015 TGCTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:28257806 original size:371 final size:370
Alignment explanation
Indices: 28257103--28257819 Score: 1174
Period size: 371 Copynumber: 1.9 Consensus size: 370
28257093 CACTCTAGAC
28257103 TACATTTAGCTTCCTCTTTTCCAATTCAAACCCTTAATTTCAAAATTTTCATAATTTAGTCCCCA
1 TACATTTAGCTTCCTCTTTTCCAATTCAAACCCTTAATTTCAAAATTTTCATAATTTAGTCCCCA
28257168 TTACACAAAATCAACAATAAATTCCACAATTTAGTCCTTTTCCATTTCTAACTTAAAAATCTATC
66 TTACACAAAATCAACAATAAATTCCACAATTTAGTCCTTTTCCATTTCTAACTTAAAAATCTATC
*
28257233 TATTTAATCTCTAATACTTAAACTATTCAACAATGTCAACATCTAAAATCTTGAATAATACTAAA
131 TATTTAATCTCTAATACTTAAACTATTCAACAATGTCAACATCTAAAATCTTGAACAATACTAAA
* * * *
28257298 AATTACAATATAGGTCAAGTAGCCTTCAGTACCAGGATTCCAAAAACGTAAAAATTACAAGTGTA
196 AATTACAATATAGATCAAGTAGCCCTAAGTACCAGGATTCCAAAAACGTAAAAATTACAAGTATA
* * ** *
28257363 GAGACTAAATTGCACTAACCAATTTGAGCTTGAACTTCCAAACCCCTAGTGCTGTGCGTTCTCTT
261 GAGACTAAATTGCACTAACCAATTTGAGCTTGAACTACCAAACCCCAAGTGCCATGCGTTCCCTT
28257428 CTCTTTTTTCTTTCTTTCTTTTGTTTAATTTGCATGTCTCCACTTT
326 CTC-TTTTTCTTTCTTTCTTTTGTTTAATTTGCATGTCTCCACTTT
28257474 TACATTTAGCTTCCTCTTTTCCAATTCAAACCCTTAATTTCAAAATTTTCATAATTTAGTCCCCA
1 TACATTTAGCTTCCTCTTTTCCAATTCAAACCCTTAATTTCAAAATTTTCATAATTTAGTCCCCA
28257539 TTACACAAAATCAACAATAAATTCCACAATTTAGTCCTTTTCCATTTCTAACTTAAAAATCTATC
66 TTACACAAAATCAACAATAAATTCCACAATTTAGTCCTTTTCCATTTCTAACTTAAAAATCTATC
28257604 TATTTAATCTCTAATACTTAAACTATTCAACAATGTCAACATCTAAAATCTTGAACAATACTAAA
131 TATTTAATCTCTAATACTTAAACTATTCAACAATGTCAACATCTAAAATCTTGAACAATACTAAA
* * *
28257669 AATTACACTA-AGTATCAAGTAGCCCTAAGTACCGAGG-TTCTAAAAACGTAAAAGTTACAAGTA
196 AATTACAATATAG-ATCAAGTAGCCCTAAGTACC-AGGATTCCAAAAACGTAAAAATTACAAGTA
* * * * * *
28257732 TAGGGACTAAATTGCA-TAACCAGTTTG-GATTTGAAC-ACCAAGCCCCCAAGTTCCATGTGTTC
259 TAGAGACTAAATTGCACTAACCAATTTGAG-CTTGAACTACCAA-ACCCCAAGTGCCATGCGTTC
28257794 CCTTCTTCTTTTTCTTTCTTTCTTTT
322 CCTTC-TCTTTTTCTTTCTTTCTTTT
28257820 CTCTTTTCTC
Statistics
Matches: 322, Mismatches: 19, Indels: 11
0.91 0.05 0.03
Matches are distributed among these distances:
369 5 0.02
370 54 0.17
371 260 0.81
372 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (370 bp):
TACATTTAGCTTCCTCTTTTCCAATTCAAACCCTTAATTTCAAAATTTTCATAATTTAGTCCCCA
TTACACAAAATCAACAATAAATTCCACAATTTAGTCCTTTTCCATTTCTAACTTAAAAATCTATC
TATTTAATCTCTAATACTTAAACTATTCAACAATGTCAACATCTAAAATCTTGAACAATACTAAA
AATTACAATATAGATCAAGTAGCCCTAAGTACCAGGATTCCAAAAACGTAAAAATTACAAGTATA
GAGACTAAATTGCACTAACCAATTTGAGCTTGAACTACCAAACCCCAAGTGCCATGCGTTCCCTT
CTCTTTTTCTTTCTTTCTTTTGTTTAATTTGCATGTCTCCACTTT
Found at i:28260289 original size:28 final size:30
Alignment explanation
Indices: 28260246--28260315 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 30
28260236 GATTTTGAAA
*
28260246 AGTTGAGTGACTAAAACA-AAA-AAATTAAT
1 AGTTG-GTGACCAAAACAGAAAGAAATTAAT
*
28260275 AGTTGGTGACCAAAACAGAAAGAACTTAAT
1 AGTTGGTGACCAAAACAGAAAGAAATTAAT
28260305 AGTTTGGTGAC
1 AG-TTGGTGAC
28260316 TAATTATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 11 0.31
29 8 0.22
30 9 0.25
31 8 0.22
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (30 bp):
AGTTGGTGACCAAAACAGAAAGAAATTAAT
Found at i:28260786 original size:43 final size:43
Alignment explanation
Indices: 28260693--28260832 Score: 201
Period size: 43 Copynumber: 3.3 Consensus size: 43
28260683 TTGGAAACAT
* * *
28260693 ACGCCGCTAAAGAGCCGGAACTTTAACGGCGC-TTTCCCAGAA
1 ACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCACAA
* * *
28260735 ACGCCGCTAAAGAGACTGACCTTTAGCGGCGCTTTTCCCCCAA
1 ACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCACAA
*
28260778 ACGCCGCTAAAGAGCCGGACCTTTAGCGACGCTTTTCCCACAA
1 ACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCACAA
*
28260821 ACACCGCTAAAG
1 ACGCCGCTAAAG
28260833 GTCATGAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 28 0.33
43 58 0.67
ACGTcount: A:0.27, C:0.34, G:0.21, T:0.18
Consensus pattern (43 bp):
ACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCACAA
Found at i:28262620 original size:16 final size:17
Alignment explanation
Indices: 28262599--28262631 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28262589 AAAGAATTTC
28262599 GAATTT-AAAAAAAAAA
1 GAATTTCAAAAAAAAAA
28262615 GAATTTCGAAAAAAAAA
1 GAATTTC-AAAAAAAAA
28262632 TTGCAAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (17 bp):
GAATTTCAAAAAAAAAA
Found at i:28262631 original size:23 final size:23
Alignment explanation
Indices: 28262583--28262631 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28262573 AAATTCATTC
***
28262583 AAAAAAAAAGAATTTCGAATTTA
1 AAAAAAAAAGAATTTCGAAAAAA
28262606 AAAAAAAAAGAATTTCGAAAAAA
1 AAAAAAAAAGAATTTCGAAAAAA
28262629 AAA
1 AAA
28262632 TTGCAAGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAGAATTTCGAAAAAA
Found at i:28264767 original size:48 final size:47
Alignment explanation
Indices: 28264715--28264821 Score: 105
Period size: 48 Copynumber: 2.2 Consensus size: 47
28264705 GCGAGAGCAA
* *
28264715 AAAAATGAAAAGAGTG-TTGAAAAGAAGAAAAGCAAAAAG-ACGAGTGAT
1 AAAAATGAAAAGAGTGATTCAAAAG-AG-AAA-CAAAAAGAACGAGTGAC
28264763 AAAAA--AAGAGAGAGTGATTCAAAAGAGAAACAAAAAGAAACGAGTGAC
1 AAAAATGAA-A-AGAGTGATTCAAAAGAGAAACAAAAAG-AACGAGTGAC
*
28264811 GAAAATGAAAA
1 AAAAATGAAAA
28264822 AAAGAGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
46 9 0.18
47 4 0.08
48 26 0.53
49 8 0.16
50 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.23, T:0.10
Consensus pattern (47 bp):
AAAAATGAAAAGAGTGATTCAAAAGAGAAACAAAAAGAACGAGTGAC
Found at i:28269353 original size:111 final size:109
Alignment explanation
Indices: 28268982--28269380 Score: 573
Period size: 109 Copynumber: 3.6 Consensus size: 109
28268972 TGGTCAAATG
* * ** * *
28268982 GAAAAATCGAAACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACGCAAAATATTATCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACCTT
* * * * *
28269047 ACTTCGAAATTTTTAAAAAGATATTTAGCCATTTGGTTGAATGA
66 ATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
* * * * *
28269091 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCTAAACGCAAAACATTGCCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACCTT
*
28269156 ATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
66 ATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
* * *
28269200 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTACCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACCTT
28269265 ATTTTGAAATTTTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
66 ATTTTGAAA--TTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
* * *
28269311 GAAAAATCGACACCCAGCATATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAATATTACATT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACCTT
28269376 ATTTT
66 ATTTT
28269381 AAAAAAATTC
Statistics
Matches: 262, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
109 163 0.62
111 99 0.38
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACCTT
ATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
Found at i:28269363 original size:220 final size:218
Alignment explanation
Indices: 28268982--28269384 Score: 590
Period size: 220 Copynumber: 1.8 Consensus size: 218
28268972 TGGTCAAATG
* * * *
28268982 GAAAAATCGAAACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACGCAAAATATTATCTT
1 GAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAACATTACCTT
* * *
28269047 ACTTCGAAATTTTTAAAAAGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACC
66 ACTTCGAAATTTTTAAAAAGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACA
* * * * *
28269112 TTAGGGCATGTTTTCTCGAATTTCTAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGA
131 TTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACATTATTTTAAAATTTTTAAAAGGA
28269177 TATTAAGCCATTTGGTTGAACGA
196 TATTAAGCCATTTGGTTGAACGA
* * * * *
28269200 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTACCTT
1 GAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAACATTACCTT
* * *
28269265 ATTTTGAAATTTTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCA
66 ACTTCGAAA--TTTTTAAAAAGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCA
* *
28269330 TATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAATATTACATTATTTTAAAA
129 CATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACATTATTTTAAAA
28269385 AAATTCTTTT
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
218 63 0.39
220 98 0.61
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (218 bp):
GAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAACATTACCTT
ACTTCGAAATTTTTAAAAAGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACA
TTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAACATTACATTATTTTAAAATTTTTAAAAGGA
TATTAAGCCATTTGGTTGAACGA
Found at i:28269752 original size:30 final size:30
Alignment explanation
Indices: 28269718--28269789 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
28269708 TGTATTACAT
*
28269718 TAAAAATATATAAGTATGTATAT-TATAAAA
1 TAAAAATATATAAGTATGTACATATAT-AAA
**
28269748 TAAAACA-ATATAAGTATGTACATATATATT
1 TAAAA-ATATATAAGTATGTACATATATAAA
28269778 TAAAAATATATA
1 TAAAAATATATA
28269790 TAAATATGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 31 0.86
31 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (30 bp):
TAAAAATATATAAGTATGTACATATATAAA
Found at i:28270045 original size:3 final size:3
Alignment explanation
Indices: 28270037--28270089 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
28270027 NNNNNNNNNN
28270037 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28270085 TAA TA
1 TAA TA
28270090 TCAAAATTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28270735 original size:10 final size:10
Alignment explanation
Indices: 28270707--28270739 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
28270697 ACACAAAAAC
28270707 AAAATAAAT-
1 AAAATAAATA
28270716 AAAATAAATA
1 AAAATAAATA
*
28270726 AAAATGAATA
1 AAAATAAATA
28270736 AAAA
1 AAAA
28270740 AAGGATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAATAAATA
Found at i:28274699 original size:121 final size:125
Alignment explanation
Indices: 28274556--28274928 Score: 592
Period size: 121 Copynumber: 3.0 Consensus size: 125
28274546 ATTGATTATC
28274556 TATTGCGGCATTTATCATAAAAACGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
1 TATTGCGGCATTTATCATAAAAACGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
28274621 TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTTGC-A-G-
66 TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTTGCTATGT
* *
28274678 T-TTGCGGCATTTATAATAAAAACGCCACAAAAAAATTATTTTATTTTAAACAAAATGACGTCGT
1 TATTGCGGCATTTATCATAAAAACGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
*
28274742 TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTGCGGCTATTGATT
66 TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTT--TGCTA-TG---
28274807 ATT
125 --T
* *
28274810 TATTGCGGCGTTTATCATAAAAATGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
1 TATTGCGGCATTTATCATAAAAACGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
*
28274875 TTTACTATGCACAAATTTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTTG
66 TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTTG
28274929 TGGTGTTTTT
Statistics
Matches: 230, Mismatches: 9, Indels: 15
0.91 0.04 0.06
Matches are distributed among these distances:
121 113 0.49
122 1 0.00
123 2 0.01
124 1 0.00
126 1 0.00
131 1 0.00
132 1 0.00
133 110 0.48
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (125 bp):
TATTGCGGCATTTATCATAAAAACGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGT
TTTACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTTGCTATGT
Found at i:28274803 original size:20 final size:20
Alignment explanation
Indices: 28274780--28274818 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28274770 TTTTTTATAA
28274780 ATTGATTTATTT-TTGCGGCT
1 ATTGA-TTATTTATTGCGGCT
28274800 ATTGATTATTTATTGCGGC
1 ATTGATTATTTATTGCGGC
28274819 GTTTATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTGATTATTTATTGCGGCT
Found at i:28274816 original size:133 final size:133
Alignment explanation
Indices: 28274679--28274926 Score: 451
Period size: 133 Copynumber: 1.9 Consensus size: 133
28274669 TTTTTGCAGT
28274679 TTGCGGCATTTATAATAAAAACGCCACAAAAAAATTATTTTATTTTAAACAAAATGACGTCGTTT
1 TTGCGGCATTTATAATAAAAACGCCACAAAAAAATTATTTTATTTTAAACAAAATGACGTCGTTT
28274744 TACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTGCGGCTATTGATTAT
66 TACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTGCGGCTATTGATTAT
28274809 TTA
131 TTA
* * * *
28274812 TTGCGGCGTTTATCATAAAAATGCCACAAAAAATTTATTTTATTTTAAACAAAATGACGTCGTTT
1 TTGCGGCATTTATAATAAAAACGCCACAAAAAAATTATTTTATTTTAAACAAAATGACGTCGTTT
*
28274877 TACTATGCACAAATTTTTTTAATTTGTTTTTTATAAATTGATTTATTTTT
66 TACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTT
28274927 TGTGGTGTTT
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 110 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (133 bp):
TTGCGGCATTTATAATAAAAACGCCACAAAAAAATTATTTTATTTTAAACAAAATGACGTCGTTT
TACTATGCACAAAATTTTTTAATTTGTTTTTTATAAATTGATTTATTTTTGCGGCTATTGATTAT
TTA
Found at i:28274973 original size:159 final size:153
Alignment explanation
Indices: 28274797--28275080 Score: 480
Period size: 154 Copynumber: 1.8 Consensus size: 153
28274787 TATTTTTGCG
* *
28274797 GCTATTGATTATTTATTGCGGCGTTTATCATAAAAATGCCACAAAAAATTTATTTTATTTTAAAC
1 GCTATTGATTATCTATTGCGGCGTTTATCATAAAAACGCCAC-AAAAA---A-TTTATTTTAAAC
28274862 AAAATGACGTCGTTTTACTATGCAC-AAATTTTTTTAATTTGTTTTTTATAAATTGATTTATTTT
61 AAAATGACGTCGTTTTACTATGCACTAAA-TTTTTTAATTTG-TTTTTATAAATTGATTTATTTT
28274926 TTGTGGTGTTTTTTTATAAAAAAAAACGCC
124 TTGTGGTGTTTTTTTATAAAAAAAAACGCC
28274956 GCTATTGATTATCTATTGCGGCGTTTATCATAAAAACGCCACAAAAAATTTATTTTAAACAAAAT
1 GCTATTGATTATCTATTGCGGCGTTTATCATAAAAACGCCACAAAAAATTTATTTTAAACAAAAT
28275021 GACGTCGTTTTACTATGCACTAAATTTTTTAATTTGTTTTTATAAATTGATTTATTTTTT
66 GACGTCGTTTTACTATGCACTAAATTTTTTAATTTGTTTTTATAAATTGATTTATTTTTT
28275081 ACGGCGTTTT
Statistics
Matches: 122, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
153 24 0.20
154 49 0.40
155 4 0.03
158 5 0.04
159 40 0.33
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (153 bp):
GCTATTGATTATCTATTGCGGCGTTTATCATAAAAACGCCACAAAAAATTTATTTTAAACAAAAT
GACGTCGTTTTACTATGCACTAAATTTTTTAATTTGTTTTTATAAATTGATTTATTTTTTGTGGT
GTTTTTTTATAAAAAAAAACGCC
Found at i:28275635 original size:17 final size:17
Alignment explanation
Indices: 28275607--28275649 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
28275597 TGAAACCTTA
28275607 AACCCC-AAATCCCCCT
1 AACCCCTAAATCCCCCT
28275623 AACCCCTAAATCCCCCT
1 AACCCCTAAATCCCCCT
28275640 AACCCCTAAA
1 AACCCCTAAA
28275650 GCATAACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.35, C:0.51, G:0.00, T:0.14
Consensus pattern (17 bp):
AACCCCTAAATCCCCCT
Found at i:28276039 original size:72 final size:73
Alignment explanation
Indices: 28275935--28276098 Score: 267
Period size: 72 Copynumber: 2.3 Consensus size: 73
28275925 GGCGCTTCTT
* * * *
28275935 AAAAATGCCGCTAAATCTCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAG-TTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCGAC
28275999 GCTTTCCC
66 GCTTTCCC
*
28276007 AAAAACGCCGCTAGATCCCCAAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCGAC
1 AAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCGAC
28276072 GCTTTCCC
66 GCTTTCCC
*
28276080 AAAAGCGCCGCTAAATCCC
1 AAAAACGCCGCTAAATCCC
28276099 TGAGCATTAG
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 48 0.57
73 36 0.43
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCGAC
GCTTTCCC
Found at i:28276153 original size:41 final size:41
Alignment explanation
Indices: 28276087--28276176 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
28276077 CCCAAAAGCG
*
28276087 CCGCTAAATCCCTGAGCATTAGCGGCGCATTCTTAAAAACA
1 CCGCTAAAGCCCTGAGCATTAGCGGCGCATTCTTAAAAACA
* *
28276128 CCGTTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACA
1 CCGCTAAAGCCCTGAGCATTAGCGGCGCATTCTTAAAAACA
28276169 CCGCTAAA
1 CCGCTAAA
28276177 TCCACGAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (41 bp):
CCGCTAAAGCCCTGAGCATTAGCGGCGCATTCTTAAAAACA
Found at i:28276276 original size:155 final size:155
Alignment explanation
Indices: 28275994--28276280 Score: 432
Period size: 155 Copynumber: 1.9 Consensus size: 155
28275984 TAGTTTTTTT
* * * *
28275994 GCGGCGCTTTCCCAAAAACGCCGCTAGATCCCCAAAAGCTCAGAAAACGGCGCCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACACCGCTAAATCCACAAAAGCACAGAAAACGGCGCCGTTGGGCTTAG
* * * *
28276059 TTTTTTTTGCGACGCTTTCCCAAAAGCGCCGCTAAATCCCTGAGCATTAGCGGCGCATTCTTAAA
66 TTTTTTTTGCGACGCTTTCCCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCACATTCTTAAA
28276124 AACACCGTTAAAGCCCTGAGCATTA
131 AACACCGTTAAAGCCCTGAGCATTA
** *
28276149 GCGGCGCTTTCTTAAAAACACCGCTAAATCCACGAAAGCACAGAAAACGGCGCCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACACCGCTAAATCCACAAAAGCACAGAAAACGGCGCCGTTGGGCTTAG
* * *
28276214 TTTTTTTAT-CGGCGCTTTCCCAAAAATGCCACTAAAGCCCTGAGCATTAGCGGCACTTTCTTAA
66 TTTTTTT-TGCGACGCTTTCCCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCACATTCTTAA
28276278 AAA
130 AAA
28276281 TGCCACTAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
155 116 0.99
156 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (155 bp):
GCGGCGCTTTCCCAAAAACACCGCTAAATCCACAAAAGCACAGAAAACGGCGCCGTTGGGCTTAG
TTTTTTTTGCGACGCTTTCCCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCACATTCTTAAA
AACACCGTTAAAGCCCTGAGCATTA
Found at i:28276290 original size:114 final size:113
Alignment explanation
Indices: 28276132--28276459 Score: 453
Period size: 114 Copynumber: 2.9 Consensus size: 113
28276122 AAAACACCGT
*
28276132 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCACGAAAGCACAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCC-CGAAAGCACAGAAAAC
*
28276197 GGCGCCGTTGGGCTTAGTTTTTTTAT-CGGCGCTTTCCCAAAAATGCCAC
65 GGCGCCGTTGGGCTTAGTTTTTTT-TGCGGCGCTTTCCCAAAAACGCCAC
* * * *
28276246 TAAAGCCCTGAGCATTAGCGGCACTTTCTTAAAAATGCCACTAAATCCCCGAAAGCACAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT-CCCGAAAGCACAGAAAAC
* *
28276311 GGCGCCGTTGTGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
65 GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCAC
* * * * * *
28276360 TAAAGCCCCGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCAAAAGCTCGGTAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC-CCGAAAGCACAGAAAAC
* * *
28276425 GGCGTCGTTGGGCTTAG-GTTTTTTGCGGCACTTTC
65 GGCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTC
28276460 TGGAAAACGC
Statistics
Matches: 189, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
113 18 0.10
114 169 0.89
115 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (113 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCGAAAGCACAGAAAACG
GCGCCGTTGGGCTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCCAC
Found at i:28277026 original size:15 final size:16
Alignment explanation
Indices: 28276990--28277027 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28276980 CATAATAATA
* *
28276990 AAATTTAATTATAACG
1 AAATTTAATAAGAACG
28277006 AAATTTAATAAGAAC-
1 AAATTTAATAAGAACG
28277021 AAATTTA
1 AAATTTA
28277028 TCATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (16 bp):
AAATTTAATAAGAACG
Found at i:28280435 original size:55 final size:55
Alignment explanation
Indices: 28280333--28280440 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 55
28280323 AATATATATA
* *
28280333 TTTTTCGTATATTTATATCTGAGTCTAACACGAAAAAAAATAATTTTTTTAAATT
1 TTTTTCGTATATTTATATCTGAGTCTAACACAAAAAAAAATAATTTTTGTAAATT
* * * **
28280388 TTTTTCGTATATTTATATCTGATTTTGACA-AAAAAAAGAATTTTTTTTGTAAA
1 TTTTTCGTATATTTATATCTGAGTCTAACACAAAAAAA-AATAATTTTTGTAAA
28280441 ATTTATACTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 6 0.13
55 39 0.87
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (55 bp):
TTTTTCGTATATTTATATCTGAGTCTAACACAAAAAAAAATAATTTTTGTAAATT
Found at i:28282933 original size:2 final size:2
Alignment explanation
Indices: 28282926--28282954 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28282916 TAACTTGAAT
28282926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28282955 TATTGCAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28284819 original size:9 final size:9
Alignment explanation
Indices: 28284805--28284875 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
28284795 TATTTTCTCT
28284805 TAAAAATAA
1 TAAAAATAA
*
28284814 TAAAAA-AT
1 TAAAAATAA
* *
28284822 TAAAATTAT
1 TAAAAATAA
*
28284831 TAAAAATTA
1 TAAAAATAA
* *
28284840 TAAAATTAT
1 TAAAAATAA
*
28284849 TAAAAACTTA
1 TAAAAA-TAA
28284859 TAAAAATAA
1 TAAAAATAA
*
28284868 AAAAAATA
1 TAAAAATA
28284876 TATTAAAATT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
8 6 0.13
9 34 0.72
10 7 0.15
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAAATAA
Found at i:28284836 original size:10 final size:9
Alignment explanation
Indices: 28284805--28284942 Score: 93
Period size: 10 Copynumber: 14.7 Consensus size: 9
28284795 TATTTTCTCT
*
28284805 TAAAAATAA
1 TAAAAATTA
28284814 TAAAAA--A
1 TAAAAATTA
*
28284821 TTAAAATTA
1 TAAAAATTA
28284830 TTAAAAATTA
1 -TAAAAATTA
28284840 T-AAAATTA
1 TAAAAATTA
28284848 TTAAAAACTTA
1 -TAAAAA-TTA
*
28284859 TAAAAATAA
1 TAAAAATTA
*
28284868 AAAAAATATA
1 TAAAAAT-TA
*
28284878 TTAAAATTGA
1 TAAAAATT-A
**
28284888 TATAACCTTA
1 TA-AAAATTA
*
28284898 TAAAAGTTA
1 TAAAAATTA
28284907 TAAAAGATTA
1 TAAAA-ATTA
*
28284917 TTAAATATTA
1 -TAAAAATTA
28284927 TAAAAATTTA
1 TAAAAA-TTA
28284937 TAAAAA
1 TAAAAA
28284943 AATCTAATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
7 6 0.06
8 7 0.07
9 33 0.32
10 45 0.44
11 11 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:28284859 original size:19 final size:17
Alignment explanation
Indices: 28284807--28284941 Score: 92
Period size: 19 Copynumber: 7.2 Consensus size: 17
28284797 TTTTCTCTTA
* *
28284807 AAAATAATAAAAAAT-T
1 AAAATTATAAAAATTAT
28284823 AAAATTATTAAAAATTAT
1 AAAATTA-TAAAAATTAT
28284841 AAAATTATTAAAAACTTAT
1 AAAATTA-TAAAAA-TTAT
* *
28284860 AAAAATAAAAAAAATATATT
1 -AAAATTATAAAAAT-TA-T
**
28284880 AAAATTGATATAACCTTAT
1 AAAATT-ATA-AAAATTAT
28284899 AAAAGTTATAAAAGATTATT
1 AAAA-TTATAAAA-ATTA-T
28284919 AAATATTATAAAAATTTAT
1 AAA-ATTATAAAAA-TTAT
28284938 AAAA
1 AAAA
28284942 AAATCTAATA
Statistics
Matches: 96, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.06
17 7 0.07
18 19 0.20
19 32 0.33
20 28 0.29
21 4 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATTAT
Found at i:28284919 original size:39 final size:37
Alignment explanation
Indices: 28284822--28284941 Score: 111
Period size: 39 Copynumber: 3.1 Consensus size: 37
28284812 AATAAAAAAT
28284822 TAAAATTATTAAAAATTA-TAAAATTATTAAAAACTTA
1 TAAAATTA-TAAAAATTATTAAAATTATTAAAAACTTA
* * * *
28284859 TAAAAATAAAAAAAATATATTAAAATTGA-TATAACCTTA
1 T-AAAATTATAAAAAT-TATTAAAATT-ATTAAAAACTTA
*
28284898 TAAAAGTTATAAAAGATTATTAAATATTA-TAAAAATTTA
1 TAAAA-TTATAAAA-ATTATTAAA-ATTATTAAAAACTTA
28284937 TAAAA
1 TAAAA
28284942 AAATCTAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
37 7 0.10
38 12 0.18
39 42 0.63
40 6 0.09
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (37 bp):
TAAAATTATAAAAATTATTAAAATTATTAAAAACTTA
Found at i:28295037 original size:20 final size:20
Alignment explanation
Indices: 28295019--28295093 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
28295009 AATAGAAAAG
28295019 AAAAAAAGAAAAATCAAAATC
1 AAAAAAA-AAAAATCAAAATC
*
28295040 AAAATAAAAAAATCAAAATC
1 AAAAAAAAAAAATCAAAATC
* * *
28295060 AAAATAAAAAAATAAAAATG
1 AAAAAAAAAAAATCAAAATC
28295080 ATAAAAAAAGAAAA
1 A-AAAAAAA-AAAA
28295094 AGGAAAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 32 0.67
21 12 0.25
22 4 0.08
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAAATCAAAATC
Found at i:28295050 original size:26 final size:25
Alignment explanation
Indices: 28295007--28295077 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 25
28294997 AAAAAAATAA
28295007 AAAATAGAAAAGAAAAAAAGAAAAATC
1 AAAATA-AAAA-AAAAAAAGAAAAATC
* **
28295034 AAAATCAAAATAAAAAAATCAAAATC
1 AAAAT-AAAAAAAAAAAAGAAAAATC
28295060 AAAATAAAAAAATAAAAA
1 AAAATAAAAAAA-AAAAA
28295078 TGATAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 6 0.16
26 23 0.61
27 8 0.21
28 1 0.03
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (25 bp):
AAAATAAAAAAAAAAAAGAAAAATC
Found at i:28295085 original size:14 final size:14
Alignment explanation
Indices: 28294999--28295085 Score: 52
Period size: 14 Copynumber: 5.9 Consensus size: 14
28294989 ATTCAATCAA
28294999 AAAAATAA-AAAAT
1 AAAAATAATAAAAT
* * *
28295012 AGAAAAGAAAAAAAG
1 A-AAAATAATAAAAT
28295027 AAAAATCAAAATCAAAAT
1 AAAAAT---AAT-AAAAT
28295045 AAAAA-AATCAAAAT
1 AAAAATAAT-AAAAT
* *
28295059 CAAAATAAAAAAAT
1 AAAAATAATAAAAT
*
28295073 AAAAATGATAAAA
1 AAAAATAATAAAA
28295086 AAAGAAAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
13 1 0.02
14 38 0.67
15 7 0.12
17 2 0.04
18 9 0.16
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:28295093 original size:24 final size:25
Alignment explanation
Indices: 28295066--28295123 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
28295056 AATCAAAATA
* *
28295066 AAAAAATAAAAATGATAAA-AAAAG
1 AAAAAAGAAAAATGAAAAAGAAAAG
*
28295090 -AAAAAGGAAAATGAAAAAGAAAAG
1 AAAAAAGAAAAATGAAAAAGAAAAG
*
28295114 AAAAATGAAA
1 AAAAAAGAAA
28295124 GGCCAAGGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 15 0.56
24 5 0.19
25 7 0.26
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (25 bp):
AAAAAAGAAAAATGAAAAAGAAAAG
Found at i:28295106 original size:18 final size:18
Alignment explanation
Indices: 28295084--28295123 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28295074 AAAATGATAA
*
28295084 AAAAAGAAAAAGGAAAATG
1 AAAAAG-AAAAGAAAAATG
28295103 AAAAAGAAAAGAAAAATG
1 AAAAAGAAAAGAAAAATG
28295121 AAA
1 AAA
28295124 GGCCAAGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATG
Found at i:28297671 original size:89 final size:89
Alignment explanation
Indices: 28297473--28298407 Score: 899
Period size: 89 Copynumber: 10.6 Consensus size: 89
28297463 TGGAGTAGGT
* * * * * * * *
28297473 TGAAAATAGTAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATA-CCAGCCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
** * * **
28297537 TCCCTGAGCAGCAGTGGAGTAGGT
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * * * *
28297561 TAAAAATAGCAGATCTTGTCTTCTTATATTGGTAGCAAAGTAGATCGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
* * *
28297626 TCTCTGAGTTGCAACGGACCAGAC
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * * * * *
28297650 TGAGGATGGCAGGTCTTGTCTT-TCTGTACTGCCAGCGAAGTAGATCAAAGATAGAAAATCTTAT
1 TGAAGATAGCAGATCTTGTCTTCT-TGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTAT
* *
28297714 CTCCCTAAGTTGCAGCAGAGCAGAC
65 CTCCCTGAGTTGCAGCGGAGCAGAC
* * * * * * *
28297739 TGAAGATAGCAGATATTATCTTCTTGTACTGGCAGCAAAACAGATCGAAGACATC-AGCCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
* ** * * * **
28297803 TCCATGAGCAGCAGTGAAGTAGGT
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * *
28297827 TAAAAATAGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTATTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
* * *
28297892 TCCCTAAGTTGCAGCGAAGTAGAC
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * * * * *
28297916 TGAGGATAGCAGATCTTGTCTTCCTATACTGGCAGCAAAGTAGATCAAAGATAACACGTCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
*
28297981 TCCCTAAGTTGCAGCGGAGCAGAC
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * * *
28298005 TGAAGATAGCAGATCTTATGTTCTTGTACTGGCAGTGAAGCAGATCGAAGACATC-AGCCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
* * * **
28298069 TCCCTGAGTAGCAGTGGAGTAGGT
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * *
28298093 TGAAAATAGCAGATCTTGGCTTCTTGTACTGGCAGCGAAACAGATTGAAGATAACAAGTCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
*
28298158 TCCCTGAGTTGCAGCAGAGCAGAC
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * *
28298182 TGAGGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
28298247 TCCCTGAGTTGCAGCGGAGCAGAC
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * * * *
28298271 TGAAGATAGCAGATTTTGTCTTCCTATACTGGCAGCGAAGCAGATCGAAGACA-CCAGCCTTATC
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
** ** * **
28298335 TCCCTGAGCAGCAATGGAGTAGGT
66 TCCCTGAGTTGCAGCGGAGCAGAC
* * * *
28298359 TGAAAATAGCAGATCTTGCCTTCCTGTACTGGCGGCGAAGCAGATCGAA
1 TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAA
28298408 AACACCGGTC
Statistics
Matches: 686, Mismatches: 156, Indels: 10
0.81 0.18 0.01
Matches are distributed among these distances:
88 254 0.37
89 431 0.63
90 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGTCTTCTTGTACTGGCAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
TCCCTGAGTTGCAGCGGAGCAGAC
Found at i:28297865 original size:177 final size:177
Alignment explanation
Indices: 28297277--28298407 Score: 893
Period size: 177 Copynumber: 6.4 Consensus size: 177
28297267 CTTTTCTCTT
* * ** * * * * *
28297277 TGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTTCCTATATTGGCAACGAAGTAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * * ** * * ** * * *
28297342 TGAAGATA-CTAGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGTCT
66 CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
* * * * * ** * * * * * *
28297406 TTCTGTATTGGTAGCGAAGTAGATCAAAAACACCAGCTTTATCTTCT
131 TCCTATACTGGCAGCAAAACAGATCGAAGACAACAGCCTTATCTCCC
* * ** * * * *
28297453 TGAGCAGCAGTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * ** * * ** * *
28297518 CGAAGATA-CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCT
66 CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
* * * ** * * * *
28297582 TCTTATATTGGTAGCAAAGTAGATCGAAGATAGCAAGTCTTATCTCTC
131 TCCTATACTGGCAGCAAAACAGATCGAAGACAAC-AGCCTTATCTCCC
** ** * * ** * * * * *
28297630 TGAGTTGCAACGGACCAGACTGAGGATGGCAGGTCTTGTCTTTCTGTACTGCCAGCGAAGTAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * * * *
28297695 CAAAGATAGAAAATCTTATCTCCCTAAGTTGCAGCAGAGCAGACTGAAGATAGCAGATATTATCT
66 CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
* * * *
28297760 TCTTGTACTGGCAGCAAAACAGATCGAAGACATCAGCCTTATCTCCA
131 TCCTATACTGGCAGCAAAACAGATCGAAGACAACAGCCTTATCTCCC
* ** * *
28297807 TGAGCAGCAGTGAAGTAGGTTAAAAATAGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * *
28297872 CGAAGATAGCAAGTATTATCTCCCTAAGTTGCAGCGAAGTAGACTGAGGATAGCAGATCTTGTCT
66 CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
** * * *
28297937 TCCTATACTGGCAGCAAAGTAGATCAAAGATAACACGTCTTATCTCCC
131 TCCTATACTGGCAGCAAAACAGATCGAAGACAACA-GCCTTATCTCCC
* ** * * * * * * *
28297985 TAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTATGTTCTTGTACTGGCAGTGAAGCAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * * * * * ** * *
28298050 CGAAGACATC-AGCCTTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGGCT
66 CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
* * * * * *
28298114 TCTTGTACTGGCAGCGAAACAGATTGAAGATAACAAGTCTTATCTCCC
131 TCCTATACTGGCAGCAAAACAGATCGAAGACAAC-AGCCTTATCTCCC
** * ** *
28298162 TGAGTTGCAG-CAGAGCAGACTGAGGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGA
1 TGAGCAGCAGTGA-AGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGA
* *
28298226 TCGAAGATAGCAAGTCTTATCTCCCTGAGTTGCAGCGGAGCAGACTGAAGATAGCAGATTTTGTC
65 TCGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTC
* * *
28298291 TTCCTATACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTATCTCCC
130 TTCCTATACTGGCAGCAAAACAGATCGAAGACAACAGCCTTATCTCCC
* * * ** * *
28298339 TGAGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCGGCGAAGCAGAT
1 TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
28298404 CGAA
66 CGAA
28298408 AACACCGGTC
Statistics
Matches: 769, Mismatches: 179, Indels: 13
0.80 0.19 0.01
Matches are distributed among these distances:
176 145 0.19
177 415 0.54
178 209 0.27
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (177 bp):
TGAGCAGCAGTGAAGCAGACTGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
CGAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCT
TCCTATACTGGCAGCAAAACAGATCGAAGACAACAGCCTTATCTCCC
Found at i:28297957 original size:45 final size:45
Alignment explanation
Indices: 28297478--28298321 Score: 252
Period size: 45 Copynumber: 19.0 Consensus size: 45
28297468 TAGGTTGAAA
* * * *
28297478 ATAGTAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * * * * ** *
28297523 ATACCAG-CCTTATCTCCCTGA-GC-AGCAGTGGAGTAGGTTAAAA
1 ATAGCAGATCTTGTCTTCCT-ATACTGGCAGCGAAGTAGATCGAAG
* * * *
28297566 ATAGCAGATCTTGTCTTCTTATATTGGTAGCAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * ** *
28297611 ATAGCA-AGTCTTATC-TCTCT-GAGTTGCAACGGACCAGA-CTGAGG
1 ATAGCAGA-TCTTGTCTTC-CTATACTGGCAGCGAAGTAGATC-GAAG
* * * * * *
28297655 ATGGCAGGTCTTGTCTTTCTGTACTGCCAGCGAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * *
28297700 ATAGAAAATCTTATCTCCCTA-AGTTGCAGC-AGAGCAGA-CTGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGA-AGTAGATC-GAAG
* * * * * **
28297744 ATAGCAGATATTATCTTCTTGTACTGGCAGCAAAACAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * * ** *
28297789 ACATCAG-CCTTATC-TCC-ATGAGC-AGCAGTGAAGTAGGTTAAAA
1 ATAGCAGATCTTGTCTTCCTAT-A-CTGGCAGCGAAGTAGATCGAAG
* * *
28297832 ATAGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * *
28297877 ATAGCA-AGTATTATCTCCCTA-AGTTGCAGCGAAGTAGA-CTGAGG
1 ATAGCAGA-TCTTGTCTTCCTATACTGGCAGCGAAGTAGATC-GAAG
* *
28297921 ATAGCAGATCTTGTCTTCCTATACTGGCAGCAAAGTAGATCAAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * *
28297966 ATAACACG-TCTTATCTCCCTA-AGTTGCAGCGGAGCAGA-CTGAAG
1 ATAGCA-GATCTTGTCTTCCTATACTGGCAGCGAAGTAGATC-GAAG
* * * * * *
28298010 ATAGCAGATCTTATGTTCTTGTACTGGCAGTGAAGCAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * * * * * * * *
28298055 ACATCAG-CCTTATCTCCCT-GAGTAGCAGTGGAGTAGGTTGAAA
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * ** *
28298098 ATAGCAGATCTTGGCTTCTTGTACTGGCAGCGAAACAGATTGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * * *
28298143 ATAACA-AGTCTTATCTCCCT-GAGTTGCAGC-AGAGCAGA-CTGAGG
1 ATAGCAGA-TCTTGTCTTCCTATACTGGCAGCGA-AGTAGATC-GAAG
*
28298187 ATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
* * * * * * *
28298232 ATAGCA-AGTCTTATCTCCCT-GAGTTGCAGCGGAGCAGA-CTGAAG
1 ATAGCAGA-TCTTGTCTTCCTATACTGGCAGCGAAGTAGATC-GAAG
* *
28298276 ATAGCAGATTTTGTCTTCCTATACTGGCAGCGAAGCAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
28298321 A
1 A
28298322 CACCAGCCTT
Statistics
Matches: 549, Mismatches: 204, Indels: 92
0.65 0.24 0.11
Matches are distributed among these distances:
42 1 0.00
43 68 0.12
44 228 0.42
45 242 0.44
46 10 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTATACTGGCAGCGAAGTAGATCGAAG
Found at i:28298437 original size:266 final size:265
Alignment explanation
Indices: 28297277--28298409 Score: 1318
Period size: 266 Copynumber: 4.3 Consensus size: 265
28297267 CTTTTCTCTT
* * * * * *
28297277 TGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTTCCTATATTGGCAACGAAGTAGAT
1 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * * * * ** * * ** * ** *
28297342 TGAAGATA-CTAGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGTCT
66 CGAAAATAGCAAGTCTTATCTCCCTGAGTTGCAG-CGAGCAGACTGAGGATAGCAGATCTTGTCT
* * * * * * * * * ** * *
28297406 TTCTGTATTGGTAGCGAAGTAGATCAAAAACA-CCAG-CTTTATCTTCTTGAGCAGCAGTGGAGT
130 TCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAAGTC-TTATCTCCCTAAGTTGCAGCGGAGC
** * * * * * * *
28297469 AGGTTGAAAATAGTAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAGATACCAGCCTT
194 AGACTGAAGATAGCAGATCTTATCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTT
28297534 ATCTCCC
259 ATCTCCC
* * * * * *
28297541 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCTTATATTGGTAGCAAAGTAGAT
1 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * * * *
28297606 CGAAGATAGCAAGTCTTATCTCTCTGAGTTGCAACGGACCAGACTGAGGATGGCAGGTCTTGTCT
66 CGAAAATAGCAAGTCTTATCTCCCTGAGTTGCAGC-GAGCAGACTGAGGATAGCAGATCTTGTCT
* * * * *
28297671 TTCTGTACTGCCAGCGAAGTAGATCAAAGATAGAAAATCTTATCTCCCTAAGTTGCAGCAGAGCA
130 TCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCA
* * * * *
28297736 GACTGAAGATAGCAGATATTATCTTCTTGTACTGGCAGCAAAACAGATCGAAGACATCAGCCTTA
195 GACTGAAGATAGCAGATCTTATCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTA
*
28297801 TCTCCA
260 TCTCCC
* *
28297807 TGAGCAGCAGTGAAGTAGGTTAAAAATAGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
1 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * * *
28297872 CGAAGATAGCAAGTATTATCTCCCTAAGTTGCAGCGAAGTAGACTGAGGATAGCAGATCTTGTCT
66 CGAAAATAGCAAGTCTTATCTCCCTGAGTTGCAGCG-AGCAGACTGAGGATAGCAGATCTTGTCT
* * * *
28297937 TCCTATACTGGCAGCAAAGTAGATCAAAGATAACACGTCTTATCTCCCTAAGTTGCAGCGGAGCA
130 TCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCA
* * * *
28298002 GACTGAAGATAGCAGATCTTATGTTCTTGTACTGGCAGTGAAGCAGATCGAAGACATCAGCCTTA
195 GACTGAAGATAGCAGATCTTATCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTA
28298067 TCTCCC
260 TCTCCC
* * * * *
28298073 TGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGGCTTCTTGTACTGGCAGCGAAACAGAT
1 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
* * *
28298138 TGAAGATAACAAGTCTTATCTCCCTGAGTTGCAGCAGAGCAGACTGAGGATAGCAGATCTTGTCT
66 CGAAAATAGCAAGTCTTATCTCCCTGAGTTGCAGC-GAGCAGACTGAGGATAGCAGATCTTGTCT
* *
28298203 TCCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTATCTCCCTGAGTTGCAGCGGAGCA
130 TCCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCA
* * *
28298268 GACTGAAGATAGCAGATTTTGTCTTCCTATACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTA
195 GACTGAAGATAGCAGATCTTATCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTA
28298333 TCTCCC
260 TCTCCC
* * * *
28298339 TGAGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCGGCGAAGCAGAT
1 TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
28298404 CGAAAA
66 CGAAAA
28298410 CACCGGTCTT
Statistics
Matches: 742, Mismatches: 121, Indels: 10
0.85 0.14 0.01
Matches are distributed among these distances:
264 66 0.09
265 64 0.09
266 610 0.82
267 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (265 bp):
TGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGAT
CGAAAATAGCAAGTCTTATCTCCCTGAGTTGCAGCGAGCAGACTGAGGATAGCAGATCTTGTCTT
CCTGTACTGGCAGCGAAGTAGATCAAAGATAGCAAGTCTTATCTCCCTAAGTTGCAGCGGAGCAG
ACTGAAGATAGCAGATCTTATCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTAT
CTCCC
Found at i:28298533 original size:51 final size:51
Alignment explanation
Indices: 28298416--28298536 Score: 118
Period size: 51 Copynumber: 2.3 Consensus size: 51
28298406 AAAACACCGG
**
28298416 TCTTATTGCCTTGGCGTTGCAGTGGAACAGATTAAAAGCTAAAGATAGCGAA
1 TCTTATT-CCTTGGCGTTGCAACGGAACAGATTAAAAGCTAAAGATAGCGAA
* * * ** * * *
28298468 TTTTGTGTCTTTGGCGTTGCAACGGGGCAGATT-AAAGCTGAGGGTAGCGAA
1 TCTTAT-TCCTTGGCGTTGCAACGGAACAGATTAAAAGCTAAAGATAGCGAA
28298519 TCTTATCTCCTTGGCGTT
1 TCTTAT-TCCTTGGCGTT
28298537 AAGACTTGGA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
51 29 0.54
52 24 0.44
53 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCTTATTCCTTGGCGTTGCAACGGAACAGATTAAAAGCTAAAGATAGCGAA
Found at i:28298662 original size:50 final size:50
Alignment explanation
Indices: 28298605--28298797 Score: 181
Period size: 50 Copynumber: 3.9 Consensus size: 50
28298595 TTTGGCATTA
* *
28298605 CAGTGGAATAGATTGAAGCTACAACAACGAATCTTACTACCCTGGCGATG
1 CAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGATG
* * * * * * * *
28298655 CAGTGGAACATATTTAAGCTATAATAGCGAATCTTGCTTCCCCGAC-ATTG
1 CAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGA-TG
* ** * * * *
28298705 TAGTTAAATAGATTGAAGCAACAACAACGAATCTTACTTCCCTGGAGGTG
1 CAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGATG
* ** *
28298755 CAGTGGAACAGATTAAAGCTACAACAGTGAATCTTATTTCCCT
1 CAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCT
28298798 AGCGCCACAG
Statistics
Matches: 107, Mismatches: 34, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
49 1 0.01
50 106 0.99
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCTGGCGATG
Found at i:28298796 original size:100 final size:100
Alignment explanation
Indices: 28298611--28298796 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 100
28298601 ATTACAGTGG
* * * *
28298611 AATAGATTGAAGCTACAACAACGAATCTTACTACCCTGGCGATGCAGTGGAACATATTTAAGCTA
1 AATAGATTGAAGCAACAACAACGAATCTTACTACCCTGGAGATGCAGTGGAACAGATTAAAGCTA
* * *
28298676 TAATAGCGAATCTTGCTTCCCCGACATTGTAGTTA
66 CAACAGCGAATCTTACTTCCCCGACATTGTAGTTA
* *
28298711 AATAGATTGAAGCAACAACAACGAATCTTACTTCCCTGGAGGTGCAGTGGAACAGATTAAAGCTA
1 AATAGATTGAAGCAACAACAACGAATCTTACTACCCTGGAGATGCAGTGGAACAGATTAAAGCTA
* *
28298776 CAACAGTGAATCTTATTTCCC
66 CAACAGCGAATCTTACTTCCC
28298797 TAGCGCCACA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (100 bp):
AATAGATTGAAGCAACAACAACGAATCTTACTACCCTGGAGATGCAGTGGAACAGATTAAAGCTA
CAACAGCGAATCTTACTTCCCCGACATTGTAGTTA
Found at i:28300169 original size:12 final size:12
Alignment explanation
Indices: 28300152--28300192 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
28300142 TTTTTATTTT
28300152 TTTAATTTAGTA
1 TTTAATTTAGTA
28300164 TTTAATTTAGT-
1 TTTAATTTAGTA
28300175 TTT--TTTAGTA
1 TTTAATTTAGTA
*
28300185 CTTAATTT
1 TTTAATTT
28300193 TAATTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 3 0.12
12 14 0.56
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTAATTTAGTA
Found at i:28302839 original size:15 final size:15
Alignment explanation
Indices: 28302819--28302849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28302809 TGCTATTCAA
*
28302819 TTCTTCAACTTTTGG
1 TTCTTCAACTCTTGG
28302834 TTCTTCAACTCTTGG
1 TTCTTCAACTCTTGG
28302849 T
1 T
28302850 CAGCATCCTG
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:0.13, C:0.23, G:0.13, T:0.52
Consensus pattern (15 bp):
TTCTTCAACTCTTGG
Found at i:28303961 original size:29 final size:29
Alignment explanation
Indices: 28303900--28303962 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
28303890 ATCTATGTTT
**
28303900 AGATAATTATACATAGAATGTATAAGTTT
1 AGATAATTATACATAGAATGTATAAGTAA
* *
28303929 AGATTATTATACATAGAATGTCCTAA-TAA
1 AGATAATTATACATAGAATGT-ATAAGTAA
28303958 AGATA
1 AGATA
28303963 TCAAGAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (29 bp):
AGATAATTATACATAGAATGTATAAGTAA
Found at i:28305400 original size:46 final size:44
Alignment explanation
Indices: 28305312--28305400 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
28305302 ATTACACCTC
28305312 TATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTG
1 TATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTG
* *
28305356 TATTTCATTCAACCAAACA-ATTGAACTACCTATTACGCCTCTATT
1 TATTCCATTCAACCAAACACA-AGAA-TACC-ATTACGCCTCTATT
28305401 CCATTACGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 21 0.52
45 4 0.10
46 14 0.35
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTG
Found at i:28305408 original size:16 final size:16
Alignment explanation
Indices: 28305387--28305439 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
28305377 TGAACTACCT
*
28305387 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
* *
28305403 ATTACGCATATATTTC
1 ATTACGCATCTATTCC
*
28305419 ATTACACATCTATTCC
1 ATTACGCATCTATTCC
28305435 ATTAC
1 ATTAC
28305440 AGCGAACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:28306246 original size:190 final size:191
Alignment explanation
Indices: 28305908--28306258 Score: 444
Period size: 190 Copynumber: 1.8 Consensus size: 191
28305898 GTTGTTTATT
** *
28305908 AGGTTCCCTCCTCCAGCCTTTAAAAATTAATTTTTCTTAACCCGTATTATAATCGGTATAAACTA
1 AGGTTCCCTCCTCCAGCCTTTAAAAATTAATTTTTCTTAACCCACATTATAACCGGTATAAACTA
* * *
28305973 CGTACAGATGTCGCATCTCTTACTCCCTCCATCATTTAAATATATATATTTTTAACACATATTAT
66 CGTACAGATGTCGCATCTCCTACTCCCTCCATCATTTAAATATACATATTTTTAACACAAATTAT
* *
28306038 ATACTTGATAGGGTTATGATTTCCAGCAAAACAAACACTGCCTCCACTGATGTTGCCTTTC
131 ATACTTGATAGAGTTATGATTGCCAGCAAAACAAACACTGCCTCCACTGATGTTGCCTTTC
* * * * *
28306099 AGGTTCCTTTCTCCAGCCTTTAAAAATT-ATTTTT-TTCAACCTACATTTTAACCGGTGTAAACT
1 AGGTTCCCTCCTCCAGCCTTTAAAAATTAATTTTTCTT-AACCCACATTATAACCGGTATAAACT
* * * *
28306162 A-GATACAGGTGTTGCCTGTCCTACTCCCTCCATCATTT-AA-ATACAT-TTTTTAACACAAATT
65 ACG-TACAGATGTCGCATCTCCTACTCCCTCCATCATTTAAATATACATATTTTTAACACAAATT
* *
28306223 ATATACTTAACGATTGAGTTATGATTGCCGGCAAAA
129 ATATACTT---GATAGAGTTATGATTGCCAGCAAAA
28306259 TAATGGTGGA
Statistics
Matches: 136, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
187 22 0.16
188 5 0.04
189 5 0.04
190 78 0.57
191 26 0.19
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (191 bp):
AGGTTCCCTCCTCCAGCCTTTAAAAATTAATTTTTCTTAACCCACATTATAACCGGTATAAACTA
CGTACAGATGTCGCATCTCCTACTCCCTCCATCATTTAAATATACATATTTTTAACACAAATTAT
ATACTTGATAGAGTTATGATTGCCAGCAAAACAAACACTGCCTCCACTGATGTTGCCTTTC
Found at i:28306415 original size:43 final size:43
Alignment explanation
Indices: 28306352--28306557 Score: 268
Period size: 43 Copynumber: 4.8 Consensus size: 43
28306342 GCGTTGCTAA
28306352 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
* * * * *
28306395 TTTTAGCAGCGCTTTCCCCACAAACGCTGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
**
28306438 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCACGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
* * * *
28306481 TTTTAACGGCGCTTTTCCCACAAACGCCGCTATAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
* * ** *
28306524 CTTTAGCGACGCTTCTAGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
28306558 AACATAAACT
Statistics
Matches: 137, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 137 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGAC
Found at i:28306449 original size:86 final size:86
Alignment explanation
Indices: 28306352--28306557 Score: 304
Period size: 86 Copynumber: 2.4 Consensus size: 86
28306342 GCGTTGCTAA
* *
28306352 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACTTTTAGCAGCGCTTTCCCCACA
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCACGACTTTTAACAGCGCTTTCCCCACA
*
28306417 AACGCTGCTAAAGACCAAGAC
66 AACGCCGCTAAAGACCAAGAC
* * *
28306438 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCACGACTTTTAACGGCGCTTTTCCCACA
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCACGACTTTTAACAGCGCTTTCCCCACA
* *
28306503 AACGCCGCTATAGACCATGAC
66 AACGCCGCTAAAGACCAAGAC
* * * *
28306524 CTTTAGCGACGCTTCTAGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAA
28306558 AACATAAACT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 108 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCACGACTTTTAACAGCGCTTTCCCCACA
AACGCCGCTAAAGACCAAGAC
Found at i:28308774 original size:15 final size:16
Alignment explanation
Indices: 28308725--28308777 Score: 106
Period size: 16 Copynumber: 3.3 Consensus size: 16
28308715 TTTTTTGTAT
28308725 AAAGTGCATGCCTTAA
1 AAAGTGCATGCCTTAA
28308741 AAAGTGCATGCCTTAA
1 AAAGTGCATGCCTTAA
28308757 AAAGTGCATGCCTTAA
1 AAAGTGCATGCCTTAA
28308773 AAAGT
1 AAAGT
28308778 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAGTGCATGCCTTAA
Found at i:28308999 original size:8 final size:8
Alignment explanation
Indices: 28308986--28309012 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28308976 ATTAGACAAA
28308986 AAAAAAAC
1 AAAAAAAC
28308994 AAAAAAAC
1 AAAAAAAC
28309002 AAAAAAAC
1 AAAAAAAC
28309010 AAA
1 AAA
28309013 TACAATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:28310856 original size:19 final size:20
Alignment explanation
Indices: 28310828--28310870 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28310818 AAATTATAAA
*
28310828 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
28310848 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
28310867 TTTT
1 TTTT
28310871 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:28311185 original size:21 final size:20
Alignment explanation
Indices: 28311161--28311201 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28311151 TCTAACCCCT
*
28311161 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
28311182 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
28311202 TAGTCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:28311657 original size:41 final size:41
Alignment explanation
Indices: 28311612--28311708 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
28311602 TAAAATGTTT
* *
28311612 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGAGTA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
*
28311653 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
*
28311694 TTAGTGGCGCTTTTT
1 TTAGCGGCGCTTTTT
28311709 TGAAAACACT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:28317109 original size:20 final size:20
Alignment explanation
Indices: 28317084--28317121 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28317074 CTGCTCGAGA
28317084 ACCAATCAAGCTTATCCCGC
1 ACCAATCAAGCTTATCCCGC
28317104 ACCAATCAAGCTTATCCC
1 ACCAATCAAGCTTATCCC
28317122 TTCTAACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.39, G:0.08, T:0.21
Consensus pattern (20 bp):
ACCAATCAAGCTTATCCCGC
Found at i:28318518 original size:50 final size:49
Alignment explanation
Indices: 28318406--28318842 Score: 377
Period size: 49 Copynumber: 8.9 Consensus size: 49
28318396 TTGATAAATT
* * * *
28318406 TGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTTTTTTTCATCTAC
1 TGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTCGTATAC
** * *
28318455 TGGTGCCAACCATTGACAGGCCAGCACCTAAATTTTTTTTTTCGTACTGC
1 TGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTCGTA-TAC
* * **
28318505 TGGTGTCGTCCATTGACAGGCCAGCACTCAAAAAAGTTTTTTTT-GTATAC
1 TGGTGCCGGCCATTGACAGGCCAGCAC-C-AAAATTTTTTTTTTCGTATAC
* * *****
28318555 TGGTGCAGGCCATTGTCAGGCCAGCA-CAAAA-AAAAATTTTCGTATAC
1 TGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTCGTATAC
* * ****** * *
28318602 TGGTGCCGGCCATTGACAAGCCAACACCCAAAAAAAAAAATTTCCGTACTGC
1 TGGTGCCGGCCATTGACAGGCCAGCA-CC-AAAATTTTTTTTTTCGTA-TAC
* * *
28318654 TGGTGCCGGCCATTAACAGGCCAGCACC-AAA-TTTTTTTTTCATATTGC
1 TGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTCGTA-TAC
* **
28318702 TTGTGCCGGCCATTGACAGGCCAGCACCATAAA--TTTTTTTTCGTATTG
1 TGGTGCCGGCCATTGACAGGCCAGCACCA-AAATTTTTTTTTTCGTATAC
* *
28318750 TGGTGCCGGCCATTGACAGTCCAGCACCCAAAAATTTTTTTTTTCGTATAT
1 TGGTGCCGGCCATTGACAGGCCAGCA-CC-AAAATTTTTTTTTTCGTATAC
*
28318801 TGGTGCCGGCCATTGACAAGG-CAGCACCCAAATTTTTTTTTT
1 TGGTGCCGGCCATTGAC-AGGCCAGCACCAAAATTTTTTTTTT
28318843 GTTTTTTTTA
Statistics
Matches: 322, Mismatches: 50, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
46 4 0.01
47 32 0.10
48 61 0.19
49 74 0.23
50 60 0.19
51 53 0.16
52 38 0.12
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (49 bp):
TGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTCGTATAC
Done.