Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 78 of 82
Found at i:29353985 original size:27 final size:27
Alignment explanation
Indices: 29353938--29353993 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29353928 ATAATTAATT
*
29353938 ATATAAAAATATATAAAAATTAAAAAA
1 ATATAAAAATATAAAAAAATTAAAAAA
* *
29353965 ATATAAAAGTA-AAAAATAATTAATAAA
1 ATATAAAAATATAAAAA-AATTAAAAAA
29353992 AT
1 AT
29353994 TATTTATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
ATATAAAAATATAAAAAAATTAAAAAA
Found at i:29354050 original size:56 final size:55
Alignment explanation
Indices: 29353980--29354096 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 55
29353970 AAAGTAAAAA
29353980 ATAATTAATAAAATTATTTATTCTTTCACTTTTTTAATTATGTGCCTAATAAATC
1 ATAATTAATAAAATTATTTATTCTTTCACTTTTTTAATTATGTGCCTAATAAATC
*
29354035 NATAATTAATAAAATTATTTTTTCTTTCACTTTTTTAATTATGTGCCTAATAAATC
1 -ATAATTAATAAAATTATTTATTCTTTCACTTTTTTAATTATGTGCCTAATAAATC
*
29354091 TTAATT
1 ATAATT
29354097 TTTTATTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 5 0.08
56 54 0.92
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.50
Consensus pattern (55 bp):
ATAATTAATAAAATTATTTATTCTTTCACTTTTTTAATTATGTGCCTAATAAATC
Found at i:29354301 original size:25 final size:24
Alignment explanation
Indices: 29354254--29354313 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
29354244 GATTTCCAAC
*
29354254 AACTATTTTTTTTCCTATATATAA
1 AACTATTTTTTTTCCAATATATAA
* *
29354278 AACTAATTTTTTTTTCAATGTATAA
1 AACT-ATTTTTTTTCCAATATATAA
*
29354303 TATCTATTTTT
1 -AACTATTTTT
29354314 GAAATCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.57
Consensus pattern (24 bp):
AACTATTTTTTTTCCAATATATAA
Found at i:29370252 original size:12 final size:12
Alignment explanation
Indices: 29370235--29370275 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
29370225 GTTTATATAT
29370235 AGAGAAAAAGAG
1 AGAGAAAAAGAG
29370247 AGAGAAAAAGAG
1 AGAGAAAAAGAG
* *
29370259 AAAGAAAGAGAG
1 AGAGAAAAAGAG
29370271 AGAGA
1 AGAGA
29370276 CGTGTGGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAGAG
Found at i:29381956 original size:4 final size:4
Alignment explanation
Indices: 29381940--29381977 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
29381930 CAGGCATGCA
*
29381940 AAAG AAAG GAAG AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
29381978 AAAATAGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:29397303 original size:13 final size:13
Alignment explanation
Indices: 29397285--29397309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29397275 GGTAAATTTC
29397285 TTTTTATAAGTTT
1 TTTTTATAAGTTT
29397298 TTTTTATAAGTT
1 TTTTTATAAGTT
29397310 ATAATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTATAAGTTT
Found at i:29397329 original size:18 final size:20
Alignment explanation
Indices: 29397288--29397329 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
29397278 AAATTTCTTT
* *
29397288 TTATAAGTTTTTTTTATAAG
1 TTATAAGTTTTTGTTATAAA
29397308 TTATAA-TTTTTGTTA-AAA
1 TTATAAGTTTTTGTTATAAA
29397326 TTAT
1 TTAT
29397330 CATAGAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTTTGTTATAAA
Found at i:29402096 original size:24 final size:24
Alignment explanation
Indices: 29402060--29402159 Score: 60
Period size: 24 Copynumber: 4.0 Consensus size: 24
29402050 GGGAGGTGGC
**
29402060 TTTGGTGCCGGAGGTGG-GTCTGGT
1 TTTGGTGGTGGAGGTGGTG-CTGGT
*
29402084 TTTGGTGGTGGAGCTGGTGGAGGTGGTGGT
1 TTTGGTGGTGGA---GGT---GGTGCTGGT
* * *
29402114 TTTGGTGGAGGAGGTGGTGGTGGG
1 TTTGGTGGTGGAGGTGGTGCTGGT
*
29402138 TTTGGAGGTGGAGGTGGT-CTGG
1 TTTGGTGGTGGAGGTGGTGCTGG
29402160 GTGGCGGCGG
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
23 3 0.05
24 34 0.56
27 6 0.10
30 17 0.28
31 1 0.02
ACGTcount: A:0.07, C:0.05, G:0.56, T:0.32
Consensus pattern (24 bp):
TTTGGTGGTGGAGGTGGTGCTGGT
Found at i:29402250 original size:30 final size:29
Alignment explanation
Indices: 29402194--29402309 Score: 97
Period size: 30 Copynumber: 3.9 Consensus size: 29
29402184 GTGGTGGAAT
* * * **
29402194 TGGTGGTGGAGGTGGGAAAGGAGGAGGATT
1 TGGTGGTGG-GATTGGAAAGGTGGAGGAGG
* *
29402224 TGGTGGTGGGATTGGTAAGGGTGGAGGCGG
1 TGGTGGTGGGATTGG-AAAGGTGGAGGAGG
* * * *
29402254 TGGTGGTGGAATAGAAAAAGGTGGTGGAGG
1 TGGTGGTGGGATTG-GAAAGGTGGAGGAGG
*
29402284 TGGTGGTGGGATTGGCAAGGTGGAGG
1 TGGTGGTGGGATTGGAAAGGTGGAGG
29402310 TGGTCTGGGT
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
29 13 0.20
30 53 0.80
ACGTcount: A:0.21, C:0.02, G:0.56, T:0.22
Consensus pattern (29 bp):
TGGTGGTGGGATTGGAAAGGTGGAGGAGG
Found at i:29402337 original size:158 final size:158
Alignment explanation
Indices: 29402117--29402468 Score: 663
Period size: 158 Copynumber: 2.2 Consensus size: 158
29402107 TGGTGGTTTT
* *
29402117 GGTGGAGGAGGTGGTGGTGGGTTTGG--AGGTGGAGGTGGTCTGGGTGGCGGCGGGGGTGTAGGT
1 GGTGGTGGAGGTGGTGGTGGGATTGGCAAGGTGGAGGTGGTCTGGGTGGCGGCGGGGGTGTAGGT
29402180 GTCGGTGGTGGAATTGGTGGTGGAGGTGGGAAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGG
66 GTCGGTGGTGGAATTGGTGGTGGAGGTGGGAAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGG
29402245 TGGAGGCGGTGGTGGTGGAATAGAAAAA
131 TGGAGGCGGTGGTGGTGGAATAGAAAAA
29402273 GGTGGTGGAGGTGGTGGTGGGATTGGCAAGGTGGAGGTGGTCTGGGTGGCGGCGGGGGTGTAGGT
1 GGTGGTGGAGGTGGTGGTGGGATTGGCAAGGTGGAGGTGGTCTGGGTGGCGGCGGGGGTGTAGGT
29402338 GTCGGTGGTGGAATTGGTGGTGGAGGTGGGAAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGG
66 GTCGGTGGTGGAATTGGTGGTGGAGGTGGGAAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGG
29402403 TGGAGGCGGTGGTGGTGGAATAGAAAAA
131 TGGAGGCGGTGGTGGTGGAATAGAAAAA
29402431 GGTGGTGGAGGTGGTGGTGGGATTGGCAAGGGTGGAGG
1 GGTGGTGGAGGTGGTGGTGGGATTGGCAA-GGTGGAGG
29402469 CGGTGGTGGT
Statistics
Matches: 191, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
156 24 0.13
158 159 0.83
159 8 0.04
ACGTcount: A:0.16, C:0.03, G:0.57, T:0.23
Consensus pattern (158 bp):
GGTGGTGGAGGTGGTGGTGGGATTGGCAAGGTGGAGGTGGTCTGGGTGGCGGCGGGGGTGTAGGT
GTCGGTGGTGGAATTGGTGGTGGAGGTGGGAAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGG
TGGAGGCGGTGGTGGTGGAATAGAAAAA
Found at i:29402405 original size:60 final size:60
Alignment explanation
Indices: 29402368--29402585 Score: 301
Period size: 60 Copynumber: 3.6 Consensus size: 60
29402358 TGGAGGTGGG
* * *
29402368 AAAGGAGGAGGATTTGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATAGAA
1 AAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATAGGA
** *
29402428 AAAGGTGGTGGAGGTGGTGGTGGGATTGGCAAGGGTGGAGGCGGTGGTGGTGGAATAGGA
1 AAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATAGGA
* * *
29402488 AAAGGTGGTGGATTGGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATTGGC
1 AAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATAGGA
* * * * * *
29402548 AAGGGCGGTGGGTTTGGAGGTGGCATTGGAAAGGGTGG
1 AAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTGG
29402586 TGGAATTGGC
Statistics
Matches: 139, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 139 1.00
ACGTcount: A:0.20, C:0.03, G:0.55, T:0.22
Consensus pattern (60 bp):
AAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTGGAGGCGGTGGTGGTGGAATAGGA
Found at i:29402408 original size:30 final size:30
Alignment explanation
Indices: 29402382--29402585 Score: 169
Period size: 30 Copynumber: 6.8 Consensus size: 30
29402372 GAGGAGGATT
* * *
29402382 TGGTGGTGGGATTGGTAAGGGTGGAGGCGG
1 TGGTGGTGGAATTGGAAAGGGTGGAGGAGG
* * * *
29402412 TGGTGGTGGAATAGAAAAAGGTGGTGGAGG
1 TGGTGGTGGAATTGGAAAGGGTGGAGGAGG
* * *
29402442 TGGTGGTGGGATTGGCAAGGGTGGAGGCGG
1 TGGTGGTGGAATTGGAAAGGGTGGAGGAGG
* * * *
29402472 TGGTGGTGGAATAGGAAAAGGTGGTGGA-T
1 TGGTGGTGGAATTGGAAAGGGTGGAGGAGG
* * *
29402501 TGGGTGGTGGGATTGGTAAGGGTGGAGGCGG
1 T-GGTGGTGGAATTGGAAAGGGTGGAGGAGG
* * * *
29402532 TGGTGGTGGAATTGGCAAGGGCGGTGG-GTT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGAG-G
* *
29402562 TGGAGGTGGCATTGGAAAGGGTGG
1 TGGTGGTGGAATTGGAAAGGGTGG
29402586 TGGAATTGGC
Statistics
Matches: 134, Mismatches: 37, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
29 2 0.01
30 131 0.98
31 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.55, T:0.23
Consensus pattern (30 bp):
TGGTGGTGGAATTGGAAAGGGTGGAGGAGG
Found at i:29402585 original size:48 final size:48
Alignment explanation
Indices: 29402533--29402630 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
29402523 TGGAGGCGGT
29402533 GGTGGTGGAATTGGCAAGGGCGGTGGGTTTGGAGGTGGCATTGGAAAG
1 GGTGGTGGAATTGGCAAGGGCGGTGGGTTTGGAGGTGGCATTGGAAAG
*
29402581 GGTGGTGGAATTGGCAAGGGTGGTGGGTTTGGAGGTGGCATTGGAAAG
1 GGTGGTGGAATTGGCAAGGGCGGTGGGTTTGGAGGTGGCATTGGAAAG
29402629 GG
1 GG
29402631 CGGCGGCGGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.18, C:0.05, G:0.53, T:0.23
Consensus pattern (48 bp):
GGTGGTGGAATTGGCAAGGGCGGTGGGTTTGGAGGTGGCATTGGAAAG
Found at i:29402612 original size:18 final size:18
Alignment explanation
Indices: 29402566--29402606 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
29402556 TGGGTTTGGA
*
29402566 GGTGGCATTGGAAAGGGT
1 GGTGGAATTGGAAAGGGT
*
29402584 GGTGGAATTGGCAAGGGT
1 GGTGGAATTGGAAAGGGT
29402602 GGTGG
1 GGTGG
29402607 GTTTGGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.54, T:0.22
Consensus pattern (18 bp):
GGTGGAATTGGAAAGGGT
Found at i:29402722 original size:60 final size:60
Alignment explanation
Indices: 29402650--29402774 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 60
29402640 CGGTGGTGGC
* * * *
29402650 AAAGGGGGAGGCATTGGTGGTGGTATTGGTAAGGGAGGAGGAATTGGTGGTGGGATTGGT
1 AAAGGGGGAGGCATTGGTGGTGGAATTGGAAAGGGAGGAGGAATTGGTGGTGGGATAGGA
* *
29402710 AAAGGGGGAGGCATTGGTGGTGGAATTGGAAAGGGTGGCGGAATTGGTGGTGGGATAGGA
1 AAAGGGGGAGGCATTGGTGGTGGAATTGGAAAGGGAGGAGGAATTGGTGGTGGGATAGGA
29402770 AAAGG
1 AAAGG
29402775 TGGTGGTGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.25, C:0.02, G:0.51, T:0.22
Consensus pattern (60 bp):
AAAGGGGGAGGCATTGGTGGTGGAATTGGAAAGGGAGGAGGAATTGGTGGTGGGATAGGA
Found at i:29402771 original size:30 final size:30
Alignment explanation
Indices: 29402650--29402777 Score: 152
Period size: 30 Copynumber: 4.3 Consensus size: 30
29402640 CGGTGGTGGC
* *
29402650 AAAGGG-GGAGGCATTGGTGGTGGTATTGG
1 AAAGGGTGGAGGAATTGGTGGTGGGATTGG
* *
29402679 TAAGGGAGGAGGAATTGGTGGTGGGATTGG
1 AAAGGGTGGAGGAATTGGTGGTGGGATTGG
* *
29402709 TAAAGGG-GGAGGCATTGGTGGTGGAATTGG
1 -AAAGGGTGGAGGAATTGGTGGTGGGATTGG
* *
29402739 AAAGGGTGGCGGAATTGGTGGTGGGATAGG
1 AAAGGGTGGAGGAATTGGTGGTGGGATTGG
*
29402769 AAAAGGTGG
1 AAAGGGTGG
29402778 TGGTGGTGGT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.13
30 69 0.81
31 5 0.06
ACGTcount: A:0.24, C:0.02, G:0.52, T:0.22
Consensus pattern (30 bp):
AAAGGGTGGAGGAATTGGTGGTGGGATTGG
Found at i:29402786 original size:24 final size:24
Alignment explanation
Indices: 29402754--29402804 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
29402744 GTGGCGGAAT
29402754 TGGTGGTGGGATAGGAAAAGGTGG
1 TGGTGGTGGGATAGGAAAAGGTGG
** * *
29402778 TGGTGGTGGTTTTGGTAAAGGTGG
1 TGGTGGTGGGATAGGAAAAGGTGG
29402802 TGG
1 TGG
29402805 CATTGGAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.53, T:0.29
Consensus pattern (24 bp):
TGGTGGTGGGATAGGAAAAGGTGG
Found at i:29402801 original size:54 final size:54
Alignment explanation
Indices: 29402664--29402834 Score: 173
Period size: 54 Copynumber: 3.1 Consensus size: 54
29402654 GGGGAGGCAT
* * * *
29402664 TGGTGGTGGTATTGGTAAGGGAGGAGGAATTGGTGGTGGGATTGGTAAAGGGGGAGG
1 TGGTGGTGGTATTGGTAAAGGTGGAGGAATTGGTGGTGGGATTGG-AAA--AGGTGG
* * *
29402721 CATTGGTGGTGGAATTGG-AAAGGGTGGCGGAATTGGTGGTGGGATAGGAAAAGGTGG
1 ---TGGTGGTGGTATTGGTAAA-GGTGGAGGAATTGGTGGTGGGATTGGAAAAGGTGG
* * * *
29402778 TGGTGGTGGTTTTGGTAAAGGTGGTGGCATTGGAGGTGGGATTGGAAAAGGTGG
1 TGGTGGTGGTATTGGTAAAGGTGGAGGAATTGGTGGTGGGATTGGAAAAGGTGG
29402832 TGG
1 TGG
29402835 ATTCGGTGGC
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
54 47 0.49
55 3 0.03
57 4 0.04
59 5 0.05
60 37 0.39
ACGTcount: A:0.21, C:0.02, G:0.51, T:0.26
Consensus pattern (54 bp):
TGGTGGTGGTATTGGTAAAGGTGGAGGAATTGGTGGTGGGATTGGAAAAGGTGG
Found at i:29402869 original size:12 final size:12
Alignment explanation
Indices: 29402845--29402882 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
29402835 ATTCGGTGGC
*
29402845 GGTGCTGGTGGT
1 GGTGCTGGAGGT
29402857 GGTGCTGGAGGT
1 GGTGCTGGAGGT
*
29402869 GGTGCAGGAGGT
1 GGTGCTGGAGGT
29402881 GG
1 GG
29402883 ATTTGGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.61, T:0.24
Consensus pattern (12 bp):
GGTGCTGGAGGT
Found at i:29402913 original size:12 final size:12
Alignment explanation
Indices: 29402896--29402925 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29402886 TGGCAAAGGT
*
29402896 GGTGGAGTTGGA
1 GGTGGAGTAGGA
29402908 GGTGGAGTAGGA
1 GGTGGAGTAGGA
29402920 GGTGGA
1 GGTGGA
29402926 AGTGGTGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (12 bp):
GGTGGAGTAGGA
Found at i:29402948 original size:18 final size:18
Alignment explanation
Indices: 29402927--29402969 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
29402917 GGAGGTGGAA
29402927 GTGGTGGCGGTTTTGGTG
1 GTGGTGGCGGTTTTGGTG
*
29402945 GTGGTGGTGGTTTTGGTG
1 GTGGTGGCGGTTTTGGTG
*
29402963 GAGGTGG
1 GTGGTGG
29402970 AGGTGGAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.02, G:0.58, T:0.37
Consensus pattern (18 bp):
GTGGTGGCGGTTTTGGTG
Found at i:29402955 original size:12 final size:12
Alignment explanation
Indices: 29402941--29402996 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
29402931 TGGCGGTTTT
*
29402941 GGTGGTGGTGGT
1 GGTGGTGGTGGA
**
29402953 GGTTTTGGTGGA
1 GGTGGTGGTGGA
*
29402965 GGTGGAGGTGGA
1 GGTGGTGGTGGA
**
29402977 GGTGCAGGTGGA
1 GGTGGTGGTGGA
29402989 GGTGGTGG
1 GGTGGTGG
29402997 ATTTGGAGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.09, C:0.02, G:0.62, T:0.27
Consensus pattern (12 bp):
GGTGGTGGTGGA
Found at i:29402968 original size:6 final size:6
Alignment explanation
Indices: 29402959--29402993 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
29402949 TGGTGGTTTT
*
29402959 GGTGGA GGTGGA GGTGGA GGTGCA GGTGGA GGTGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
29402994 TGGATTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.03, G:0.66, T:0.17
Consensus pattern (6 bp):
GGTGGA
Found at i:29403019 original size:18 final size:18
Alignment explanation
Indices: 29402992--29403029 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29402982 AGGTGGAGGT
29402992 GGTGGATTTGGAGGTGGC
1 GGTGGATTTGGAGGTGGC
*
29403010 GGTGGTTTTGGAGGTGGC
1 GGTGGATTTGGAGGTGGC
29403028 GG
1 GG
29403030 AGGTGGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.05, G:0.58, T:0.29
Consensus pattern (18 bp):
GGTGGATTTGGAGGTGGC
Found at i:29419829 original size:202 final size:202
Alignment explanation
Indices: 29419472--29419955 Score: 693
Period size: 202 Copynumber: 2.4 Consensus size: 202
29419462 ATGCCATGAA
* * * *
29419472 AGAGGCATTTCATGTAAGTCCATTAGCATTCAAAACGAAACATTGCCTATAAGATGTTTTAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCCTATAAGACGTTTTAGCTT
* * * * *
29419537 CGCCAAGATGGACTACATGCCTAAGTAAAACACTCCAAGCAAGAACTTGGCCCACTTTTATTGGT
66 TGCCAAGATGGACTAAATGCCCAAGTAAAACACTCCAAACAAGAACTTGGCCAACTTTTATTGGT
*
29419602 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCT-CGTAGAAGAAGAAGCACAAA
131 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTAC-TACAAGAAGAAGCACAAA
* *
29419666 GCTGTGAG
195 GCCGTAAG
* * *
29419674 ATAGACATTTGATGTAAGTCCGTTAGCATTCAAAACTAAACATTGCCTAAAAGACGTTTTAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCCTATAAGACGTTTTAGCTT
* * * * *
29419739 TGCCAAGATGGACTAAATGCCCAAGTAAGATACTGCAAACAATAACTTGGCCAACTTTTTTTGGT
66 TGCCAAGATGGACTAAATGCCCAAGTAAAACACTCCAAACAAGAACTTGGCCAACTTTTATTGGT
* * *
29419804 GCAAGCCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTACTACAATAAGAAGCCCAAAG
131 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTACTACAAGAAGAAGCACAAAG
29419869 CCGTAAG
196 CCGTAAG
* * * *
29419876 AGAGAAATTTGATATAAGTCCATTAGCATTCAAAACTAAACATTGCGTATAAGGC-TTTCTAGCT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCCTATAAGACGTTT-TAGCT
29419940 TTGCCAAGATGGACTA
65 TTGCCAAGATGGACTA
29419956 GCATGTTCTC
Statistics
Matches: 250, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
201 3 0.01
202 246 0.98
203 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (202 bp):
AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCCTATAAGACGTTTTAGCTT
TGCCAAGATGGACTAAATGCCCAAGTAAAACACTCCAAACAAGAACTTGGCCAACTTTTATTGGT
GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTACTACAAGAAGAAGCACAAAG
CCGTAAG
Found at i:29431287 original size:2 final size:2
Alignment explanation
Indices: 29431277--29431310 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29431267 CACATTAATG
29431277 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29431311 GACTTGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29433858 original size:2 final size:2
Alignment explanation
Indices: 29433851--29433906 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
29433841 GAAAATTACC
29433851 AT AT AT AT AT AT AT AT AT AT -T AT -T AT -T AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29433888 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
29433907 ATTAAATAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:29435156 original size:2 final size:2
Alignment explanation
Indices: 29435151--29435180 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29435141 CCCCTCCCTC
29435151 CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
29435181 CAGATAGTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29444364 original size:23 final size:25
Alignment explanation
Indices: 29444324--29444370 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
29444314 AATAATTTAC
29444324 TTAAACAAATTAATTAGT-ACAATT
1 TTAAACAAATTAATTAGTGACAATT
* *
29444348 TTAAATAATTTAA-TAGTGACAAT
1 TTAAACAAATTAATTAGTGACAAT
29444371 AATTCCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (25 bp):
TTAAACAAATTAATTAGTGACAATT
Found at i:29444991 original size:14 final size:14
Alignment explanation
Indices: 29444974--29445004 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29444964 AACGATTGAA
29444974 AATAATTTTATTAT
1 AATAATTTTATTAT
29444988 AATAATTTTATTAT
1 AATAATTTTATTAT
29445002 AAT
1 AAT
29445005 TTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATAATTTTATTAT
Found at i:29445107 original size:20 final size:21
Alignment explanation
Indices: 29445066--29445113 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29445056 AAAATTACTA
*
29445066 TAAAAGTAAAATTATAAAA-TT
1 TAAAA-TAAAATTAAAAAATTT
29445087 TAAAATAAAA-TAAAAATATTT
1 TAAAATAAAATTAAAAA-ATTT
29445108 TAAAAT
1 TAAAAT
29445114 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAATAAAATTAAAAAATTT
Found at i:29453076 original size:21 final size:22
Alignment explanation
Indices: 29453034--29453076 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
29453024 GAATGATACA
* *
29453034 TTATTATGTCAAACAATGTAAG
1 TTATTATGACAAAAAATGTAAG
*
29453056 TTATTAT-ACAAAAAATTTAAG
1 TTATTATGACAAAAAATGTAAG
29453077 GACATGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TTATTATGACAAAAAATGTAAG
Found at i:29456410 original size:2 final size:2
Alignment explanation
Indices: 29456403--29456448 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
29456393 TGTCATTGGC
29456403 AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29456443 AT AT AT
1 AT AT AT
29456449 TTTGTCAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29456645 original size:139 final size:140
Alignment explanation
Indices: 29456437--29456724 Score: 560
Period size: 139 Copynumber: 2.1 Consensus size: 140
29456427 ATATATATAT
29456437 ATATATATATATTTTGTCAAGGCATTGCCTGATATCTTTTACACTTGGCCTATATATTTTTTGGG
1 ATATATATATATTTTGTCAAGGCATTGCCTGATATCTTTTACACTTGGCCTATATATTTTTTGGG
29456502 GTGGTGGGGGGCATGCTTTAGGATAATTAACCTCATTATCTGCTTCAGACATATTTTGAAGAGTT
66 GTGGTGGGGGGCATGCTTTAGGATAATTAACCTCATTATCTGCTTCAGACATATTTTGAAGAGTT
29456567 ATTAAAAAAC
131 ATTAAAAAAC
*
29456577 ATANATATATA-TTTGTCAAGGCATTGCCTGATATCTTTTACACTTGGCCTATATATTTTTTGGG
1 ATATATATATATTTTGTCAAGGCATTGCCTGATATCTTTTACACTTGGCCTATATATTTTTTGGG
29456641 GTGGTGGGGGGCATGCTTTAGGATAATTAACCTCATTATCTGCTTCAGACATATTTTGAAGAGTT
66 GTGGTGGGGGGCATGCTTTAGGATAATTAACCTCATTATCTGCTTCAGACATATTTTGAAGAGTT
29456706 ATTAAAAAAC
131 ATTAAAAAAC
29456716 ATATATATA
1 ATATATATA
29456725 ATAAAATAAA
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
139 136 0.93
140 10 0.07
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (140 bp):
ATATATATATATTTTGTCAAGGCATTGCCTGATATCTTTTACACTTGGCCTATATATTTTTTGGG
GTGGTGGGGGGCATGCTTTAGGATAATTAACCTCATTATCTGCTTCAGACATATTTTGAAGAGTT
ATTAAAAAAC
Found at i:29457971 original size:107 final size:107
Alignment explanation
Indices: 29457785--29458099 Score: 585
Period size: 107 Copynumber: 2.9 Consensus size: 107
29457775 ATAATTGCAG
* * * *
29457785 CTGCAAATGTCATTAAAAATCAAAAAGATATATGTTAATTATTAATTAATGGAATAATGTTGCAA
1 CTGCAAAAGTCATTAAAAATGAAAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
29457850 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAATTATTA
66 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAATTATTA
*
29457892 CTGCAAAAGTCATTAAAAATGACAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
1 CTGCAAAAGTCATTAAAAATGAAAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
29457957 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAATTATTA
66 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAATTATTA
29457999 CTGCAAAAGTCATTAAAAATGAAAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
1 CTGCAAAAGTCATTAAAAATGAAAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
29458064 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAA
66 TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAA
29458100 CATGTTTAGA
Statistics
Matches: 202, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 202 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (107 bp):
CTGCAAAAGTCATTAAAAATGAAAAAGATATATGTTAAATATTAATTAATGGAATAATATTGCAA
TTAAAAAAACATGTGCAGAAACTATTCATGTTTCAATTATTA
Found at i:29459522 original size:29 final size:29
Alignment explanation
Indices: 29459486--29459543 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29459476 TTATTTTAAA
29459486 ATATTTAAATAAATTTTTAT-TTTTATATT
1 ATATTTAAATAAATTTTTATATTTT-TATT
*
29459515 ATATTTAATTAAATTTTTATATTTTTATT
1 ATATTTAAATAAATTTTTATATTTTTATT
29459544 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
ATATTTAAATAAATTTTTATATTTTTATT
Found at i:29459754 original size:59 final size:59
Alignment explanation
Indices: 29459683--29459797 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
29459673 CTATATCAAC
* *** *
29459683 ATGTTATGTTTTTCATCTATTATGACATGTTCGTAACATATGATATAAAATGATTAGAA
1 ATGTTATATTTTTCATCTATTATGACATGTTAACAACATATGATATAAAATAATTAGAA
* *
29459742 ATGTTATATTTTTTATCTATTATGATATGTTAACAACATATGATATAAAATAATTA
1 ATGTTATATTTTTCATCTATTATGACATGTTAACAACATATGATATAAAATAATTA
29459798 AGGATGTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (59 bp):
ATGTTATATTTTTCATCTATTATGACATGTTAACAACATATGATATAAAATAATTAGAA
Found at i:29473423 original size:413 final size:411
Alignment explanation
Indices: 29472331--29473975 Score: 3076
Period size: 411 Copynumber: 4.0 Consensus size: 411
29472321 TGAAATCAAT
29472331 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
1 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
*
29472396 TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTTATCTTGGATTTTCACG
66 TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCACG
29472461 CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
131 CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
29472526 TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
196 TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
29472591 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
261 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
29472656 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
326 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
29472721 TTATTACATGTATAAATTGAA
391 TTATTACATGTATAAATTGAA
29472742 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
1 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
* *
29472807 TATTAAATATTTGTAAAGTTAGGATACATTCAACGAATGATGAGACGTCATCTTGGATTTTCACG
66 TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCACG
29472872 CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
131 CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
*
29472937 TTAATTCCTGAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
196 TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
29473002 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
261 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
29473067 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
326 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
29473132 TTATTACATGTATAAATTGAA
391 TTATTACATGTATAAATTGAA
*
29473153 GTGCTGAAATACAAATAGTGCATTAAATTGGAATAATTATTTTTTAAAATAAACATATAACTAAT
1 GTGCTGAAATACAAATAGTGCATTAAA-T-GAAAAATTATTTTTTAAAATAAACATATAACTAAT
*
29473218 TTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAATGATGAGACGTCATCTTGGATTTTCA
64 TTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCA
*
29473283 CGCCTTGAAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGA
129 CGCCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGA
29473348 GATTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCAT
194 GATTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCAT
29473413 TTATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAA
259 TTATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAA
*
29473478 TTTGAACATATTAATATGTTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAA
324 TTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAA
29473543 TATTATTACATGTATAAATTGAA
389 TATTATTACATGTATAAATTGAA
*
29473566 GTGCTGAAATACAAATAGTGCATTAAATTACAAAAATTATTTTTTAAAAATAAACATATAACTAA
1 GTGCTGAAATACAAATAGTGCATTAAA-T-GAAAAATTATTTTTT-AAAATAAACATATAACTAA
29473631 TTTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTC
63 TTTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTC
* *
29473696 ACGCCTTGGAAATGTAACTGTCCTTGGCGCTCCATGCCAAGGTTGTTCTTCATCATACATTAAGG
128 ACGCCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGG
* **
29473761 AGATTAATTCTTGGAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCA
193 AGATTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCA
* *
29473826 TTTATTTCTTTGTAAT-TCTTTTTGTTTTCTCCACCGAACAAATCAGGTCCAGTTGAACTATTGG
258 TTTATTTCTTTGTAATCT-TTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGG
*
29473890 AATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGGTT
322 AATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTT
29473955 AATATTATTACATGTATAAAT
387 AATATTATTACATGTATAAAT
29473976 AAGACAAAAT
Statistics
Matches: 1207, Mismatches: 23, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
411 434 0.36
412 1 0.00
413 421 0.35
414 351 0.29
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (411 bp):
GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCACG
CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
TTATTACATGTATAAATTGAA
Found at i:29473443 original size:824 final size:825
Alignment explanation
Indices: 29472331--29473975 Score: 3100
Period size: 824 Copynumber: 2.0 Consensus size: 825
29472321 TGAAATCAAT
29472331 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
1 GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
*
29472396 TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTTATCTTGGATTTTCACG
66 TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCACG
*
29472461 CCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
131 CCTTGAAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
29472526 TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
196 TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
29472591 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
261 ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
29472656 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
326 TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
*
29472721 TTATTACATGTATAAATTGAAGTGCTGAAATACAAATAGTGCATTAAA-T-GAAAAATTATTTTT
391 TTATTACATGTATAAATTGAAGTGCTGAAATACAAATAGTGCATTAAATTACAAAAATTATTTTT
*
29472784 T-AAAATAAACATATAACTAATTTTATTAAATATTTGTAAAGTTAGGATACATTCAACGAATGAT
456 TAAAAATAAACATATAACTAATTTTATTAAATATTTGTAAAGTTAGGATACATTCAACGAAGGAT
*
29472848 GAGACGTCATCTTGGATTTTCACGCCTTGGAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTT
521 GAGACGTCATCTTGGATTTTCACGCCTTGGAAATGTAACTGTCCTTGGCGCTCCATGCCAAGGTT
*
29472913 TTTCTTCATCATACATTAAGGAGATTAATTCCTGAAGATTACTATTTTTGTAATGAAATTGCCAT
586 GTTCTTCATCATACATTAAGGAGATTAATTCCTGAAGATTACTATTTTTGTAATGAAATTGCCAT
*
29472978 GTCAAACATGTGGGGAAGTCATTTATTTCTTTGTAA-TCTTTTTTGTTTTCTCCACCTAACAAAT
651 GTCAAACATGTGGGGAAGTCATTTATTTCTTTGTAATTC-TTTTTGTTTTCTCCACCGAACAAAT
29473042 CAAGTCCAGTTGAACTATTGGAATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATT
715 CAAGTCCAGTTGAACTATTGGAATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATT
*
29473107 TATTTAAATTTTGATTTGTTTAATATTATTACATGTATAAATTGAA
780 TATTTAAATTTTGATTTGGTTAATATTATTACATGTATAAATTGAA
*
29473153 GTGCTGAAATACAAATAGTGCATTAAATTGGAATAATTATTTTTTAAAATAAACATATAACTAAT
1 GTGCTGAAATACAAATAGTGCATTAAA-T-GAAAAATTATTTTTTAAAATAAACATATAACTAAT
*
29473218 TTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAATGATGAGACGTCATCTTGGATTTTCA
64 TTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCA
29473283 CGCCTTGAAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGA
129 CGCCTTGAAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGA
29473348 GATTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCAT
194 GATTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCAT
29473413 TTATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAA
259 TTATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAA
*
29473478 TTTGAACATATTAATATGTTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAA
324 TTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAA
29473543 TATTATTACATGTATAAATTGAAGTGCTGAAATACAAATAGTGCATTAAATTACAAAAATTATTT
389 TATTATTACATGTATAAATTGAAGTGCTGAAATACAAATAGTGCATTAAATTACAAAAATTATTT
*
29473608 TTTAAAAATAAACATATAACTAATTTTATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGG
454 TTTAAAAATAAACATATAACTAATTTTATTAAATATTTGTAAAGTTAGGATACATTCAACGAAGG
29473673 ATGAGACGTCATCTTGGATTTTCACGCCTTGGAAATGTAACTGTCCTTGGCGCTCCATGCCAAGG
519 ATGAGACGTCATCTTGGATTTTCACGCCTTGGAAATGTAACTGTCCTTGGCGCTCCATGCCAAGG
* *
29473738 TTGTTCTTCATCATACATTAAGGAGATTAATTCTTGGAGATTACTATTTTTGTAATGAAATTGCC
584 TTGTTCTTCATCATACATTAAGGAGATTAATTCCTGAAGATTACTATTTTTGTAATGAAATTGCC
29473803 ATGTCAAACATGTGGGGAAGTCATTTATTTCTTTGTAATTCTTTTTGTTTTCTCCACCGAACAAA
649 ATGTCAAACATGTGGGGAAGTCATTTATTTCTTTGTAATTCTTTTTGTTTTCTCCACCGAACAAA
*
29473868 TCAGGTCCAGTTGAACTATTGGAATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAAT
714 TCAAGTCCAGTTGAACTATTGGAATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAAT
29473933 TTATTTAAATTTTGATTTGGTTAATATTATTACATGTATAAAT
779 TTATTTAAATTTTGATTTGGTTAATATTATTACATGTATAAAT
29473976 AAGACAAAAT
Statistics
Matches: 802, Mismatches: 15, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
822 27 0.03
823 1 0.00
824 405 0.50
825 1 0.00
826 14 0.02
827 352 0.44
828 2 0.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (825 bp):
GTGCTGAAATACAAATAGTGCATTAAATGAAAAATTATTTTTTAAAATAAACATATAACTAATTT
TATTAAATGTTTGTAAAGTTAGGATACATTCAACGAAGGATGAGACGTCATCTTGGATTTTCACG
CCTTGAAAATGTCACTGTCCTTGGCGCTCCATGCCAAGGTTTTTCTTCATCATACATTAAGGAGA
TTAATTCCTAAAGATTACTATTTTTGTAATGAAATTGCCATGTCAAACATGTGGGGAAGTCATTT
ATTTCTTTGTAATCTTTTTTGTTTTCTCCACCTAACAAATCAAGTCCAGTTGAACTATTGGAATT
TGAACATATTAATATATTTGATTTAAATGATTTTTGAATTTATTTAAATTTTGATTTGTTTAATA
TTATTACATGTATAAATTGAAGTGCTGAAATACAAATAGTGCATTAAATTACAAAAATTATTTTT
TAAAAATAAACATATAACTAATTTTATTAAATATTTGTAAAGTTAGGATACATTCAACGAAGGAT
GAGACGTCATCTTGGATTTTCACGCCTTGGAAATGTAACTGTCCTTGGCGCTCCATGCCAAGGTT
GTTCTTCATCATACATTAAGGAGATTAATTCCTGAAGATTACTATTTTTGTAATGAAATTGCCAT
GTCAAACATGTGGGGAAGTCATTTATTTCTTTGTAATTCTTTTTGTTTTCTCCACCGAACAAATC
AAGTCCAGTTGAACTATTGGAATTTGAACATATTAATATATTTGATTTAAATGATTTTTGAATTT
ATTTAAATTTTGATTTGGTTAATATTATTACATGTATAAATTGAA
Found at i:29475224 original size:18 final size:19
Alignment explanation
Indices: 29475201--29475244 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
29475191 TTTCGATTTC
*
29475201 TCTCTCTCA-TTATTGAGT
1 TCTCTCTAATTTATTGAGT
*
29475219 TCTCTCTAATTTTATTGATT
1 TCTCTCTAA-TTTATTGAGT
29475239 TCTCTC
1 TCTCTC
29475245 ATCAACATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.55
Consensus pattern (19 bp):
TCTCTCTAATTTATTGAGT
Found at i:29475717 original size:29 final size:29
Alignment explanation
Indices: 29475685--29475803 Score: 95
Period size: 29 Copynumber: 4.2 Consensus size: 29
29475675 ATATAACAAA
*
29475685 ATTTTTTAAACATGATGTGTAATAATAAT
1 ATTTTTTAAACATGACGTGTAATAATAAT
* * * * *
29475714 ATTTTTTTAACATGGCATGTAATAACAAC
1 ATTTTTTAAACATGACGTGTAATAATAAT
* *
29475743 ATTTTTTTCAACATG--GTGT-GTAAT-AT
1 A-TTTTTTAAACATGACGTGTAATAATAAT
* * *
29475769 -GTTTTTATACATGACGTGTATTAATAAT
1 ATTTTTTAAACATGACGTGTAATAATAAT
29475797 ATTTTTT
1 ATTTTTT
29475804 GTCAACATGG
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
24 10 0.15
26 5 0.07
27 7 0.10
28 5 0.07
29 29 0.43
30 12 0.18
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.47
Consensus pattern (29 bp):
ATTTTTTAAACATGACGTGTAATAATAAT
Found at i:29475722 original size:30 final size:29
Alignment explanation
Indices: 29475677--29475767 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
29475667 GTATTAAAAT
* * *
29475677 ATAACAAAATTTTTTAAACATGATGTGTA
1 ATAACAACATTTTTTTAACATGGTGTGTA
* * **
29475706 ATAATAATATTTTTTTAACATGGCATGTA
1 ATAACAACATTTTTTTAACATGGTGTGTA
29475735 ATAACAACATTTTTTTCAACATGGTGTGTA
1 ATAACAACATTTTTTT-AACATGGTGTGTA
29475765 ATA
1 ATA
29475768 TGTTTTTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 37 0.73
30 14 0.27
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
ATAACAACATTTTTTTAACATGGTGTGTA
Found at i:29475811 original size:55 final size:53
Alignment explanation
Indices: 29475710--29475822 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 53
29475700 TGTGTAATAA
* * *
29475710 TAATATTTTTTTAACATGGCATGTAATAACAACATTTTTTTCAACATGGTGTG
1 TAATATGTTTTTAACATGACATGTAATAACAACATTTTTTTCAACATGGTATG
* * * *
29475763 TAATATGTTTTTATACATGACGTGTATTAATAATATTTTTTGTCAACATGGTATG
1 TAATATGTTTTTA-ACATGACATGTAATAACAACATTTTTT-TCAACATGGTATG
29475818 TAATA
1 TAATA
29475823 ACATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 12 0.24
54 22 0.43
55 17 0.33
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (53 bp):
TAATATGTTTTTAACATGACATGTAATAACAACATTTTTTTCAACATGGTATG
Found at i:29475900 original size:81 final size:81
Alignment explanation
Indices: 29475688--29475901 Score: 209
Period size: 82 Copynumber: 2.6 Consensus size: 81
29475678 TAACAAAATT
* *
29475688 TTTTAAACATGATGTGTAATAATAATATTTTTTTAACATGGCATGTAATAACAACATTTTTTTCA
1 TTTTAAACATGATGTGTAATAATAATTTTTTTTTAACATGGCATGTAAT-A-AACATTTTTATCA
* ** * * *
29475753 ACATGGTGTGTAATATGT
64 ACACGACGTATAACATGC
* * * * *
29475771 TTTTATACATGACGTGTATTAATAATATTTTTTGTCAACATGGTATGTAAT-AACATTTTTAT-A
1 TTTTAAACATGATGTGTAATAATAAT-TTTTTT-TTAACATGGCATGTAATAAACATTTTTATCA
29475834 ACTACGACGTATAACATGC
64 AC-ACGACGTATAACATGC
* *
29475853 TTTTAAACATG-TGTGTAACAATAAATTTTTTTTTGAACATGACATGTAA
1 TTTTAAACATGATGTGTAATAAT-AATTTTTTTTT-AACATGGCATGTAA
29475902 CAATCTTTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
80 1 0.01
81 29 0.27
82 33 0.31
83 23 0.22
84 5 0.05
85 15 0.14
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (81 bp):
TTTTAAACATGATGTGTAATAATAATTTTTTTTTAACATGGCATGTAATAAACATTTTTATCAAC
ACGACGTATAACATGC
Found at i:29476155 original size:14 final size:13
Alignment explanation
Indices: 29476130--29476161 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
29476120 AAATTATAAA
29476130 AAAAATTATTTTT
1 AAAAATTATTTTT
29476143 AAAAATTATTTTT
1 AAAAATTATTTTT
*
29476156 TAAAAT
1 AAAAAT
29476162 GTCCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:29486992 original size:16 final size:16
Alignment explanation
Indices: 29486971--29487006 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29486961 CACAGTTAAA
* *
29486971 TAAAATTTTAATATTT
1 TAAAATCTTAATATAT
29486987 TAAAATCTTAATATAT
1 TAAAATCTTAATATAT
29487003 TAAA
1 TAAA
29487007 TTCAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATCTTAATATAT
Found at i:29487503 original size:15 final size:15
Alignment explanation
Indices: 29487475--29487543 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
29487465 AAGAATATTT
** *
29487475 ATAAAAATTTATAAC
1 ATAAAAATAAATAAA
29487490 ATAAAAATAAATAAA
1 ATAAAAATAAATAAA
29487505 ATAATAAAT-AATAATA
1 ATAA-AAATAAATAA-A
*
29487521 ATAATAATAATATAAA
1 ATAAAAATAA-ATAAA
*
29487537 TTAAAAA
1 ATAAAAA
29487544 AATTTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 24 0.55
16 16 0.36
17 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAATAAATAAA
Found at i:29487512 original size:12 final size:13
Alignment explanation
Indices: 29487490--29487537 Score: 66
Period size: 12 Copynumber: 3.9 Consensus size: 13
29487480 AATTTATAAC
*
29487490 ATAAAAATAAATA
1 ATAATAATAAATA
29487503 A-AATAATAAATA
1 ATAATAATAAATA
29487515 ATAATAAT-AATA
1 ATAATAATAAATA
29487527 ATAAT-ATAAAT
1 ATAATAATAAAT
29487538 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.06
12 23 0.72
13 7 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:29487517 original size:3 final size:3
Alignment explanation
Indices: 29487499--29487532 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
29487489 CATAAAAATA
29487499 AAT AA- AAT AAT AAAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
29487533 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29487700 original size:196 final size:196
Alignment explanation
Indices: 29487490--29487882 Score: 720
Period size: 196 Copynumber: 2.0 Consensus size: 196
29487480 AATTTATAAC
29487490 ATAAAAATAAATAAAATAATAAATAATAATAATAATAATAATATAAATTAAAAAAATTTAAAATT
1 ATAAAAATAAATAAAATAATAAATAATAATAATAATAATAATATAAATTAAAAAAATTTAAAATT
29487555 AAGTAAGATAAGTGAAATCATTTTATTATTTTTATTTATATTAATTATTAAATAAAATCTTATTT
66 AAGTAAGATAAGTGAAATCA--TTATTATTTTTATTTATATTAATTATTAAATAAAATCTTATTT
29487620 TTAGGGAGTTAGTAATAGAATATATAAAAAAATTAAAAA-TTTTT-AT-ATGTTATGAAAAAAAT
129 TTAGGGAGTTAGTAATAGAATATATAAAAAAATTAAAAATTTTTTAATAATGTTATGAAAAAAAT
29487682 TTT
194 TTT
29487685 NATAAAAATAAATAAAATAATAAATAATAATAATAATAATAATATAAATTAAAAAAATTTAAAAT
1 -ATAAAAATAAATAAAATAATAAATAATAATAATAATAATAATATAAATTAAAAAAATTTAAAAT
29487750 TAAGTAAGATAAGTGAAATCATTATTATTTTTATTTATATTAATTATTAAATAAAATCTTATTTT
65 TAAGTAAGATAAGTGAAATCATTATTATTTTTATTTATATTAATTATTAAATAAAATCTTATTTT
* *
29487815 TAGGGAGTTAGTAATAGAATATATAAAAAATTTAAAAATTTTTTAATAATGTTATGGAAAAAATT
130 TAGGGAGTTAGTAATAGAATATATAAAAAAATTAAAAATTTTTTAATAATGTTATGAAAAAAATT
29487880 TT
195 TT
29487882 A
1 A
29487883 AAACCCCCCA
Statistics
Matches: 192, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
194 81 0.42
195 5 0.03
196 88 0.46
197 18 0.09
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.39
Consensus pattern (196 bp):
ATAAAAATAAATAAAATAATAAATAATAATAATAATAATAATATAAATTAAAAAAATTTAAAATT
AAGTAAGATAAGTGAAATCATTATTATTTTTATTTATATTAATTATTAAATAAAATCTTATTTTT
AGGGAGTTAGTAATAGAATATATAAAAAAATTAAAAATTTTTTAATAATGTTATGAAAAAAATTT
T
Found at i:29487706 original size:12 final size:13
Alignment explanation
Indices: 29487686--29487733 Score: 66
Period size: 12 Copynumber: 3.9 Consensus size: 13
29487676 AAAAATTTTN
*
29487686 ATAAAAATAAATA
1 ATAATAATAAATA
29487699 A-AATAATAAATA
1 ATAATAATAAATA
29487711 ATAATAAT-AATA
1 ATAATAATAAATA
29487723 ATAAT-ATAAAT
1 ATAATAATAAAT
29487734 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.06
12 23 0.72
13 7 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:29487713 original size:3 final size:3
Alignment explanation
Indices: 29487695--29487728 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
29487685 NATAAAAATA
29487695 AAT AA- AAT AAT AAAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
29487729 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29488328 original size:20 final size:20
Alignment explanation
Indices: 29488303--29488344 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29488293 CCATGAAGAA
* *
29488303 AAATTATCGAATATATTATC
1 AAATTATCAAAAATATTATC
*
29488323 AAATTATCAAAAATATTCTC
1 AAATTATCAAAAATATTATC
29488343 AA
1 AA
29488345 GACAATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATTATCAAAAATATTATC
Found at i:29490390 original size:17 final size:17
Alignment explanation
Indices: 29490366--29490408 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
29490356 TTTATTATAT
29490366 TAAAAAATATATAAAAA
1 TAAAAAATATATAAAAA
*
29490383 TTAAAAATATATAAAAA
1 TAAAAAATATATAAAAA
29490400 TAAAAAATA
1 TAAAAAATA
29490409 ATTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAATATATAAAAA
Found at i:29492483 original size:28 final size:28
Alignment explanation
Indices: 29492427--29492484 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
29492417 ATAATCAATT
* *
29492427 AAGAAACACACGCAACTTCCTACTCATC
1 AAGAAACAAACGCAACTTCCTACTAATC
*
29492455 AAGAAACAAATGCAACTTCCTTA-TAATC
1 AAGAAACAAACGCAACTTCC-TACTAATC
29492483 AA
1 AA
29492485 TTAATTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (28 bp):
AAGAAACAAACGCAACTTCCTACTAATC
Found at i:29512931 original size:17 final size:17
Alignment explanation
Indices: 29512907--29512953 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 17
29512897 ATATTAAAAG
29512907 TATAAAAATTAAAAAATA
1 TATAAAAA-TAAAAAATA
29512925 TATAAAAATAAAAAATA
1 TATAAAAATAAAAAATA
29512942 -ATAATAAATAAA
1 TATAA-AAATAAA
29512954 TAAACATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 8 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TATAAAAATAAAAAATA
Found at i:29512947 original size:13 final size:14
Alignment explanation
Indices: 29512920--29512957 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
29512910 AAAAATTAAA
*
29512920 AAATATATAAAAAT
1 AAATAAATAAAAAT
*
29512934 AAA-AAATAATAAT
1 AAATAAATAAAAAT
29512947 AAATAAATAAA
1 AAATAAATAAA
29512958 CATTGGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:29519320 original size:63 final size:63
Alignment explanation
Indices: 29519216--29519411 Score: 252
Period size: 63 Copynumber: 3.1 Consensus size: 63
29519206 CTTCTGACAA
* * * **
29519216 TTTTTAAATTTTTATAATTTTTTTGTATTTTTTAAAAATTTTATAATTTCACCTTTTTAATAAT
1 TTTTTAAATTTTTATAAATATTTT-TATTTTTTAAAAATTTTATAATTTCACCTCTACAATAAT
* * * *
29519280 TTTTTAAATTTTTATAACTGTTTTTACTTTTTAAAAATTTTATAATTTCACCTCTACAA-AAG
1 TTTTTAAATTTTTATAAATATTTTTATTTTTTAAAAATTTTATAATTTCACCTCTACAATAAT
* *
29519342 TTTTAAAATTTTT-TGAATATATTTTTATTTTTTAAAAATTTTATAATTTTACCTCTACAATAAT
1 TTTTTAAATTTTTAT-AA-ATATTTTTATTTTTTAAAAATTTTATAATTTCACCTCTACAATAAT
29519406 TTTTTA
1 TTTTTA
29519412 TTTAGTGAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
61 1 0.01
62 16 0.14
63 69 0.60
64 29 0.25
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (63 bp):
TTTTTAAATTTTTATAAATATTTTTATTTTTTAAAAATTTTATAATTTCACCTCTACAATAAT
Found at i:29520226 original size:22 final size:22
Alignment explanation
Indices: 29520201--29520243 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29520191 TATTAAAATT
29520201 GATTCATTTAAATAATTTTCAC
1 GATTCATTTAAATAATTTTCAC
* **
29520223 GATTTATTTGTATAATTTTCA
1 GATTCATTTAAATAATTTTCA
29520244 TATGAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (22 bp):
GATTCATTTAAATAATTTTCAC
Found at i:29524284 original size:45 final size:45
Alignment explanation
Indices: 29524194--29524287 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
29524184 ATTAAATTTA
** *
29524194 AATAATACTAAATAATATTATTTATTACATTTATTATATTCAAAT
1 AATAATACTAAATAATATTATTTAAAACATTTATTATAATCAAAT
* * *
29524239 AATAATATTAAATAATATTCTTTAAAATATTTATTATAGAT-AAAT
1 AATAATACTAAATAATATTATTTAAAACATTTATTATA-ATCAAAT
29524284 AATA
1 AATA
29524288 TTAATATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (45 bp):
AATAATACTAAATAATATTATTTAAAACATTTATTATAATCAAAT
Found at i:29529934 original size:12 final size:12
Alignment explanation
Indices: 29529917--29529941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29529907 ATTGATTGTG
29529917 CTATCTTGGGTA
1 CTATCTTGGGTA
29529929 CTATCTTGGGTA
1 CTATCTTGGGTA
29529941 C
1 C
29529942 GGTTAGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CTATCTTGGGTA
Found at i:29531143 original size:24 final size:25
Alignment explanation
Indices: 29531116--29531196 Score: 96
Period size: 24 Copynumber: 3.2 Consensus size: 25
29531106 TTAAATGTAA
29531116 TATTATCATATATATATATAA-A-AG
1 TATTAT-ATATATATATATAATATAG
29531140 TATTAGTATATATATATATAATATAG
1 TATTA-TATATATATATATAATATAG
29531166 TATATATATATATAATATATATATATA-
1 TAT-TATATATAT-ATATATA-ATATAG
29531193 TATT
1 TATT
29531197 GTCATTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
24 19 0.37
25 2 0.04
26 13 0.25
27 12 0.24
28 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (25 bp):
TATTATATATATATATATAATATAG
Found at i:29531151 original size:20 final size:20
Alignment explanation
Indices: 29531124--29531195 Score: 110
Period size: 20 Copynumber: 3.5 Consensus size: 20
29531114 AATATTATCA
*
29531124 TATATATATATAAAAGTATTAG
1 TATATATATATATAA-TA-TAG
29531146 TATATATATATATAATATAG
1 TATATATATATATAATATAG
29531166 TATATATATATATAATATA-
1 TATATATATATATAATATAG
29531185 TATATATATAT
1 TATATATATAT
29531196 TGTCATTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 11 0.22
20 22 0.45
21 2 0.04
22 14 0.29
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATATATATATAATATAG
Found at i:29531215 original size:2 final size:2
Alignment explanation
Indices: 29531123--29531195 Score: 82
Period size: 2 Copynumber: 37.0 Consensus size: 2
29531113 TAATATTATC
*
29531123 AT AT AT AT AT AT A- AA AGT AT -T AGT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
29531164 AGT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29531196 TGTCATTAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
1 4 0.06
2 54 0.86
3 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:29544737 original size:19 final size:20
Alignment explanation
Indices: 29544713--29544751 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29544703 ATAAAAACTT
29544713 ATTT-AAATTTTATTAAATA
1 ATTTAAAATTTTATTAAATA
*
29544732 ATTTAAAATTTTTTTAAATA
1 ATTTAAAATTTTATTAAATA
29544752 TTACATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAAATTTTATTAAATA
Found at i:29545239 original size:74 final size:74
Alignment explanation
Indices: 29545118--29545340 Score: 290
Period size: 74 Copynumber: 3.0 Consensus size: 74
29545108 TCTTACTCTA
* * *
29545118 GTACAACCT-GAAAAATCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCAT
1 GTACAA-CTGGAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTCTGTGCAC
*
29545182 TGTTTGAAAT
65 TGTCTGAAAT
* *
29545192 GTACAACTGGAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGATTAAGTTTCTGTGCCCT
1 GTACAACTGGAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTCTGTGCACT
*
29545257 GTCTGGAAT
66 GTCTGAAAT
* * * * *
29545266 GTACAGCAGGAAAAACCAAGCAGTCAAGGTTAATCTCAGCTTGGTAGAGTAAGTATTC-GTGC-C
1 GTACAACTGGAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGT-TTCTGTGCAC
29545329 ATGTCTGAAAT
65 -TGTCTGAAAT
29545340 G
1 G
29545341 GAACATACAA
Statistics
Matches: 132, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
73 3 0.02
74 126 0.95
75 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (74 bp):
GTACAACTGGAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTCTGTGCACT
GTCTGAAAT
Found at i:29545615 original size:7 final size:7
Alignment explanation
Indices: 29545605--29545629 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29545595 GTTTCTCTTT
29545605 CTTTGAG
1 CTTTGAG
29545612 CTTTGAG
1 CTTTGAG
29545619 CTTTGAG
1 CTTTGAG
29545626 CTTT
1 CTTT
29545630 TTGTAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (7 bp):
CTTTGAG
Found at i:29547155 original size:3 final size:3
Alignment explanation
Indices: 29547147--29547179 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29547137 AGAGTGTTAT
29547147 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
29547180 CAAAGGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29557427 original size:16 final size:16
Alignment explanation
Indices: 29557406--29557436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29557396 TCTTTTGATC
29557406 TCTCTGTTTGTTGGTG
1 TCTCTGTTTGTTGGTG
*
29557422 TCTCTGTTTTTTGGT
1 TCTCTGTTTGTTGGT
29557437 CTTCGACGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.26, T:0.61
Consensus pattern (16 bp):
TCTCTGTTTGTTGGTG
Found at i:29566738 original size:29 final size:29
Alignment explanation
Indices: 29566696--29566753 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29566686 TATTGCAGTG
29566696 GGCAATGGAGAAAATATAAAATTTTCACA
1 GGCAATGGAGAAAATATAAAATTTTCACA
29566725 GGCAATGGAGAAAATATAAAATTTTCACA
1 GGCAATGGAGAAAATATAAAATTTTCACA
29566754 TGATGAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.24
Consensus pattern (29 bp):
GGCAATGGAGAAAATATAAAATTTTCACA
Found at i:29568405 original size:16 final size:16
Alignment explanation
Indices: 29568381--29568425 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
29568371 CAACTTTTAA
* *
29568381 TAAAATATTGATATTT
1 TAAATTATTAATATTT
29568397 TAAATTATTAATATTT
1 TAAATTATTAATATTT
*
29568413 TAAATTATAAATA
1 TAAATTATTAATA
29568426 AATATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TAAATTATTAATATTT
Found at i:29568977 original size:15 final size:15
Alignment explanation
Indices: 29568936--29568979 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29568926 NNNNNNTATT
*
29568936 AATTATTAATATTTT
1 AATTATTAATATTTA
29568951 AATTA--AAT-TTTA
1 AATTATTAATATTTA
29568963 AATTATTAATATTTA
1 AATTATTAATATTTA
29568978 AA
1 AA
29568980 AAATCTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
14 3 0.12
15 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATTAATATTTA
Found at i:29568997 original size:18 final size:19
Alignment explanation
Indices: 29568976--29569017 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29568966 TATTAATATT
29568976 TAAAAAATC-TAATAAA-AA
1 TAAAAAATCAT-ATAAATAA
*
29568994 TAAAATATCATATAAATAA
1 TAAAAAATCATATAAATAA
29569013 TAAAA
1 TAAAA
29569018 GATATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAATCATATAAATAA
Found at i:29569036 original size:8 final size:7
Alignment explanation
Indices: 29569020--29569049 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
29569010 TAATAAAAGA
29569020 TATTTTT
1 TATTTTT
29569027 TATCTTTT
1 TAT-TTTT
29569035 TATTTTT
1 TATTTTT
29569042 TATTTTT
1 TATTTTT
29569049 T
1 T
29569050 TCTTATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (7 bp):
TATTTTT
Found at i:29569050 original size:15 final size:15
Alignment explanation
Indices: 29569020--29569049 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29569010 TAATAAAAGA
29569020 TATTTTTTATCTTTT
1 TATTTTTTATCTTTT
29569035 TATTTTTTAT-TTTT
1 TATTTTTTATCTTTT
29569049 T
1 T
29569050 TCTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TATTTTTTATCTTTT
Found at i:29571584 original size:117 final size:117
Alignment explanation
Indices: 29571378--29571610 Score: 439
Period size: 117 Copynumber: 2.0 Consensus size: 117
29571368 TTTCTGTTGT
29571378 TTCAATTTTTTCTGCTATTTAGCTTTTTCAGTCAAGCAACGTGTTTGCTTTTGCACAATTGCAGC
1 TTCAATTTTTTCTGCTATTTAGCTTTTTCAGTCAAGCAACGTGTTTGCTTTTGCACAATTGCAGC
* *
29571443 AAAGGACAGCTGACGATTTTAGTGGCTGCACCTTGTGTTAAACAGCTTTTCC
66 AAAGGACAACTGACAATTTTAGTGGCTGCACCTTGTGTTAAACAGCTTTTCC
29571495 TTCAATTTTTTCTGCTATTTAGCTTTTTCAGTCAAGCAACGTGTTTGCTTTTGCACAATTGCAGC
1 TTCAATTTTTTCTGCTATTTAGCTTTTTCAGTCAAGCAACGTGTTTGCTTTTGCACAATTGCAGC
*
29571560 AAAGGACAACTGACAATTTTAGTGGCTGCACCTTGTGTTAAGCAGCTTTTC
66 AAAGGACAACTGACAATTTTAGTGGCTGCACCTTGTGTTAAACAGCTTTTC
29571611 TTTATTTTAA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 113 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (117 bp):
TTCAATTTTTTCTGCTATTTAGCTTTTTCAGTCAAGCAACGTGTTTGCTTTTGCACAATTGCAGC
AAAGGACAACTGACAATTTTAGTGGCTGCACCTTGTGTTAAACAGCTTTTCC
Found at i:29577930 original size:2 final size:2
Alignment explanation
Indices: 29577923--29577966 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29577913 AGGTAGGATA
29577923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29577965 AT
1 AT
29577967 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29579377 original size:33 final size:34
Alignment explanation
Indices: 29579320--29579387 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
29579310 CGTTAGCAGG
*
29579320 ATATTTGATGTTAAAGTCTATAATGTTAGCAGACT
1 ATATTTGATATTAAAGTC-ATAATGTTAGCAGACT
*
29579355 ATATTTTATATTAAAGTC-TAATGTTAGCAGACT
1 ATATTTGATATTAAAGTCATAATGTTAGCAGACT
29579388 CTAGTTTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 15 0.48
35 16 0.52
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (34 bp):
ATATTTGATATTAAAGTCATAATGTTAGCAGACT
Found at i:29579424 original size:44 final size:42
Alignment explanation
Indices: 29579365--29579527 Score: 159
Period size: 44 Copynumber: 3.5 Consensus size: 42
29579355 ATATTTTATA
29579365 TTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
1 TTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
*
29579407 TTAAAGTCAGTAATGTTAGCAGACTACATGGATGTTAGCAGACTA-TATTTTATA-
1 TTAAAGTC--TAATGTTAGCAGACT-C-T--A-GTT-TC---CTACTA--TTA-AG
29579461 TTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
1 TTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
29579503 TTAAAGTCAGTAATGTTAGCAGACT
1 TTAAAGTC--TAATGTTAGCAGACT
29579528 ACATGGATGT
Statistics
Matches: 101, Mismatches: 2, Indels: 34
0.74 0.01 0.25
Matches are distributed among these distances:
41 1 0.01
42 19 0.19
43 3 0.03
44 32 0.32
45 1 0.01
46 2 0.02
47 3 0.03
48 2 0.02
49 3 0.03
50 2 0.02
51 1 0.01
52 17 0.17
53 3 0.03
54 11 0.11
55 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (42 bp):
TTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
Found at i:29579506 original size:96 final size:96
Alignment explanation
Indices: 29579342--29579546 Score: 410
Period size: 96 Copynumber: 2.1 Consensus size: 96
29579332 AAAGTCTATA
29579342 ATGTTAGCAGACTATATTTTATATTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
1 ATGTTAGCAGACTATATTTTATATTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
29579407 TTAAAGTCAGTAATGTTAGCAGACTACATGG
66 TTAAAGTCAGTAATGTTAGCAGACTACATGG
29579438 ATGTTAGCAGACTATATTTTATATTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
1 ATGTTAGCAGACTATATTTTATATTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
29579503 TTAAAGTCAGTAATGTTAGCAGACTACATGG
66 TTAAAGTCAGTAATGTTAGCAGACTACATGG
29579534 ATGTTAGCAGACT
1 ATGTTAGCAGACT
29579547 GGAATCGGAT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 109 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (96 bp):
ATGTTAGCAGACTATATTTTATATTAAAGTCTAATGTTAGCAGACTCTAGTTTCCTACTATTAAG
TTAAAGTCAGTAATGTTAGCAGACTACATGG
Found at i:29580750 original size:21 final size:20
Alignment explanation
Indices: 29580703--29580751 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
29580693 AAGAATTTAT
29580703 TTAATTTAAAAATAAAAATA
1 TTAATTTAAAAATAAAAATA
*
29580723 TAAAATTTAACATAATAAAAA-A
1 T-TAATTTAA-A-AATAAAAATA
29580745 TTAATTT
1 TTAATTT
29580752 TTAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 3 0.12
23 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAATTTAAAAATAAAAATA
Found at i:29580758 original size:21 final size:22
Alignment explanation
Indices: 29580707--29580759 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
29580697 ATTTATTTAA
*
29580707 TTTAAAAATAAAAATATAAAAT
1 TTTAATAATAAAAATATAAAAT
* * *
29580729 TTAACATAATAAAAA-ATTAATT
1 TTTA-ATAATAAAAATATAAAAT
29580751 TTTAATAAT
1 TTTAATAAT
29580760 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.20
22 11 0.44
23 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAATAATAAAAATATAAAAT
Found at i:29583667 original size:2 final size:2
Alignment explanation
Indices: 29583660--29583717 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
29583650 TTCTTCAGTA
29583660 AT AT AT AT AT AT NAT AT -T AT A- AT AT AT -T AT AT -T AT AT -T
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29583698 AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
29583718 TACCCCACCA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
1 5 0.10
2 41 0.85
3 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29595526 original size:44 final size:44
Alignment explanation
Indices: 29595477--29595579 Score: 206
Period size: 44 Copynumber: 2.3 Consensus size: 44
29595467 TTGAAAGCAA
29595477 AAGGAAAGTAAATCACATTTCTAAATGTATTTTATGGGGAATTT
1 AAGGAAAGTAAATCACATTTCTAAATGTATTTTATGGGGAATTT
29595521 AAGGAAAGTAAATCACATTTCTAAATGTATTTTATGGGGAATTT
1 AAGGAAAGTAAATCACATTTCTAAATGTATTTTATGGGGAATTT
29595565 AAGGAAAGTAAATCA
1 AAGGAAAGTAAATCA
29595580 ACTATGTAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
AAGGAAAGTAAATCACATTTCTAAATGTATTTTATGGGGAATTT
Found at i:29599920 original size:41 final size:41
Alignment explanation
Indices: 29599863--29599944 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
29599853 TCAACTTGTA
29599863 GTCAATCATTATGAGGACAAAAACTAGTTGAGTGAAAAACT
1 GTCAATCATTATGAGGACAAAAACTAGTTGAGTGAAAAACT
29599904 GTCAATCATTATGAGGACAAAAACTAGTTGAGTGAAAAACT
1 GTCAATCATTATGAGGACAAAAACTAGTTGAGTGAAAAACT
29599945 ATGGACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (41 bp):
GTCAATCATTATGAGGACAAAAACTAGTTGAGTGAAAAACT
Found at i:29612089 original size:2 final size:2
Alignment explanation
Indices: 29612082--29612112 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29612072 TCCTAATCCA
*
29612082 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29612113 GATCTGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:29615497 original size:30 final size:31
Alignment explanation
Indices: 29615454--29615520 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
29615444 ATTGCATGGA
*
29615454 AAAT-CAT-TCAACATCATCTAAAGCAAAAT
1 AAATCCATGTCAACATCAGCTAAAGCAAAAT
* *
29615483 AAA-CCATGTCAACATCAGCTCAAGCAAACT
1 AAATCCATGTCAACATCAGCTAAAGCAAAAT
29615513 AAATCCAT
1 AAATCCAT
29615521 ATCTTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.19
30 22 0.69
31 4 0.12
ACGTcount: A:0.48, C:0.25, G:0.06, T:0.21
Consensus pattern (31 bp):
AAATCCATGTCAACATCAGCTAAAGCAAAAT
Found at i:29643014 original size:10 final size:10
Alignment explanation
Indices: 29642989--29643020 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
29642979 TCAGACACGA
29642989 TAAACACGTT
1 TAAACACGTT
29642999 TAAAACACGTT
1 T-AAACACGTT
29643010 TAAACACGTT
1 TAAACACGTT
29643020 T
1 T
29643021 TCTTAATCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (10 bp):
TAAACACGTT
Found at i:29643050 original size:18 final size:19
Alignment explanation
Indices: 29643023--29643072 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
29643013 ACACGTTTTC
*
29643023 TTAATCGTGTTAT-CGTGT
1 TTAAACGTGTTATACGTGT
*
29643041 TTAAATGTG-TATACGTGT
1 TTAAACGTGTTATACGTGT
29643059 TTAAACGTG-TATAC
1 TTAAACGTGTTATAC
29643073 ATGACACGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (19 bp):
TTAAACGTGTTATACGTGT
Found at i:29643259 original size:23 final size:24
Alignment explanation
Indices: 29643197--29643266 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
29643187 TTTATGTATG
*
29643197 TTATTTATATTA-AATT-TTATTA
1 TTATTTATGTTATAATTATTATTA
*
29643219 -TATTTGATGTTATTATTATTATTA
1 TTATTT-ATGTTATAATTATTATTA
*
29643243 TTATTT-TGTTATAATTATTTTTA
1 TTATTTATGTTATAATTATTATTA
29643266 T
1 T
29643267 AATTATAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 19 0.47
24 6 0.15
25 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTATTTATGTTATAATTATTATTA
Found at i:29663474 original size:19 final size:19
Alignment explanation
Indices: 29663446--29663498 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
29663436 AGCTTAAAAT
* *
29663446 TTTTAAAAAAATTTTCATA
1 TTTTATAAAAATTTTAATA
* *
29663465 TTTTATAAAATTTTTAATT
1 TTTTATAAAAATTTTAATA
* *
29663484 TTTTTTATAAATTTT
1 TTTTATAAAAATTTT
29663499 TTTAGTTTCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATAAAAATTTTAATA
Found at i:29664121 original size:16 final size:19
Alignment explanation
Indices: 29664079--29664122 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
29664069 CCTCATTGTT
*
29664079 ACATCATCATGTTTGTGCC
1 ACATCATCATGTTGGTGCC
29664098 ACATCATCATGTTGGTGCC
1 ACATCATCATGTTGGTGCC
29664117 ACATCA
1 ACATCA
29664123 ACTCCACGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
ACATCATCATGTTGGTGCC
Found at i:29664457 original size:2 final size:2
Alignment explanation
Indices: 29664450--29664474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29664440 TCCATCCTTT
29664450 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 T
29664475 TAGAAGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29667705 original size:43 final size:43
Alignment explanation
Indices: 29667657--29667743 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
29667647 CATATGGAAA
29667657 AATTATTCAAGTTTGATTGGAACAGGAAGCTACTTGGAAATTC
1 AATTATTCAAGTTTGATTGGAACAGGAAGCTACTTGGAAATTC
* * *
29667700 AATTATTCAAGTTTGATTGGAGCAGGAAGTTACTTGGCAATTC
1 AATTATTCAAGTTTGATTGGAACAGGAAGCTACTTGGAAATTC
29667743 A
1 A
29667744 GTACTAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (43 bp):
AATTATTCAAGTTTGATTGGAACAGGAAGCTACTTGGAAATTC
Found at i:29673450 original size:74 final size:74
Alignment explanation
Indices: 29673361--29673502 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 74
29673351 GACAAATTTG
* * * ** *
29673361 TTTCATATTTGTTCCTTAATTTATTCTCTTTAT-AGAAATATCAAATTTTATGTAATTGTTGATT
1 TTTCATATCTGTTCCTGAATTTATTCCCTCAATAAG-AATATCAAATTTTATGTAAGTGTTGATT
29673425 TTTTCCCATA
65 TTTTCCCATA
* *
29673435 TTTCATATCTGTTCCTGAATTTATTCCCTCAATAAGAATTTCAAATTTTATGTAAGTGTTGTTTT
1 TTTCATATCTGTTCCTGAATTTATTCCCTCAATAAGAATATCAAATTTTATGTAAGTGTTGATTT
29673500 TTT
66 TTT
29673503 TTTCATATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
74 57 0.97
75 2 0.03
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (74 bp):
TTTCATATCTGTTCCTGAATTTATTCCCTCAATAAGAATATCAAATTTTATGTAAGTGTTGATTT
TTTCCCATA
Found at i:29678614 original size:17 final size:18
Alignment explanation
Indices: 29678592--29678631 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
29678582 ATATAAATTT
29678592 AATTAAATATAA-TTAAA
1 AATTAAATATAAGTTAAA
29678609 AATTAAATATAATGTTAAA
1 AATTAAATATAA-GTTAAA
29678628 AATT
1 AATT
29678632 TTACAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAAATATAAGTTAAA
Found at i:29679695 original size:9 final size:9
Alignment explanation
Indices: 29679683--29679707 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29679673 CTGTTTCTTT
29679683 AGTTTATCA
1 AGTTTATCA
29679692 AGTTTATCA
1 AGTTTATCA
29679701 AGTTTAT
1 AGTTTAT
29679708 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (9 bp):
AGTTTATCA
Found at i:29680785 original size:28 final size:28
Alignment explanation
Indices: 29680754--29680811 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
29680744 GATTCTGAAG
**
29680754 TATGTATATGTGTTAGTTTTGCTCTTGA
1 TATGTATATGCATTAGTTTTGCTCTTGA
29680782 TATGTATATGCATTAGTTTTGCTCTTGA
1 TATGTATATGCATTAGTTTTGCTCTTGA
29680810 TA
1 TA
29680812 ATAAATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.52
Consensus pattern (28 bp):
TATGTATATGCATTAGTTTTGCTCTTGA
Found at i:29684276 original size:2 final size:2
Alignment explanation
Indices: 29684269--29684349 Score: 130
Period size: 2 Copynumber: 41.0 Consensus size: 2
29684259 ATATACATGT
29684269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
29684310 GTN TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29684350 ATAGGCTGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 71 0.96
3 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29689542 original size:18 final size:18
Alignment explanation
Indices: 29689514--29689563 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
29689504 CATTAAAGGC
*
29689514 GGGTCAGTGGTTAATGG-
1 GGGTCAATGGTTAATGGT
29689531 GGGCTCAATGGTTAATGGT
1 GGG-TCAATGGTTAATGGT
*
29689550 GGGTCAATCGTTAA
1 GGGTCAATGGTTAA
29689564 CGGGTCAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 23 0.79
19 3 0.10
ACGTcount: A:0.22, C:0.10, G:0.38, T:0.30
Consensus pattern (18 bp):
GGGTCAATGGTTAATGGT
Found at i:29695617 original size:19 final size:19
Alignment explanation
Indices: 29695582--29695619 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29695572 AAGGATTTAA
*
29695582 TCGAGAAAAATTGTTAAAT
1 TCGAGAAAAATTATTAAAT
29695601 TCGAGTAAAAA-TATTAAAT
1 TCGAG-AAAAATTATTAAAT
29695620 AACTATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (19 bp):
TCGAGAAAAATTATTAAAT
Found at i:29696355 original size:3 final size:3
Alignment explanation
Indices: 29696347--29696386 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
29696337 TAGTTTTACT
* **
29696347 TGG TGG TGG TGG TGG TGG TGG TAG TGG CAG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
29696387 TCTTCTGGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.03, G:0.60, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:29697181 original size:16 final size:18
Alignment explanation
Indices: 29697145--29697182 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
29697135 TCTGAGATCT
29697145 TATATCACTCATTTGTGG
1 TATATCACTCATTTGTGG
*
29697163 TATATC-CTC-TTTGTTG
1 TATATCACTCATTTGTGG
29697179 TATA
1 TATA
29697183 CAAACTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 3 0.16
18 6 0.32
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (18 bp):
TATATCACTCATTTGTGG
Found at i:29699738 original size:34 final size:35
Alignment explanation
Indices: 29699700--29699767 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
29699690 ATGAAAATCC
*
29699700 TTTTTTGA-GGTCTAATCAGTGATTTGAAGCCATG
1 TTTTTTCAGGGTCTAATCAGTGATTTGAAGCCATG
29699734 TTTTTTCAGGGTCTAATCAGTGATTTGAAGCCAT
1 TTTTTTCAGGGTCTAATCAGTGATTTGAAGCCAT
29699768 AAAACCTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (35 bp):
TTTTTTCAGGGTCTAATCAGTGATTTGAAGCCATG
Found at i:29715866 original size:5 final size:5
Alignment explanation
Indices: 29715856--29715889 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
29715846 TCCTTTTTTT
29715856 AAAA- AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
29715890 GATTGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:29725362 original size:6 final size:6
Alignment explanation
Indices: 29725361--29725499 Score: 93
Period size: 6 Copynumber: 22.8 Consensus size: 6
29725351 TATATATGTA
*
29725361 TATATG TATATG TATATATG TATATG TATATG TATATG TATA-- TATATA
1 TATATG TATATG --TATATG TATATG TATATG TATATG TATATG TATATG
** * * * * *
29725409 TATATG TATACA CATATA CATATG TATCTATA TATATG TATATA TATATG
1 TATATG TATATG TATATG TATATG TA--TATG TATATG TATATG TATATG
* * * * * * *
29725459 TGTATA CATATG TATATA TATATG TGTATA CATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
29725500 ATCTCTATCC
Statistics
Matches: 102, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
4 4 0.04
6 87 0.85
8 11 0.11
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:29725457 original size:12 final size:12
Alignment explanation
Indices: 29725340--29725501 Score: 148
Period size: 12 Copynumber: 13.2 Consensus size: 12
29725330 AAATCTCCAA
* *
29725340 ATATATATAAAT
1 ATATATGTATAT
29725352 ATATATGTATAT
1 ATATATGTATAT
29725364 ATGTATATGTATAT
1 A--TATATGTATAT
29725378 ATGTATATGTATAT
1 A--TATATGTATAT
*
29725392 GTATATGTATAT
1 ATATATGTATAT
29725404 ATATA--TATAT
1 ATATATGTATAT
* ***
29725414 GTATACACATAT
1 ATATATGTATAT
*
29725426 ACATATGTATCTAT
1 ATATATGTA--TAT
29725440 ATATATGTATAT
1 ATATATGTATAT
*
29725452 ATATATGTGTAT
1 ATATATGTATAT
*
29725464 ACATATGTATAT
1 ATATATGTATAT
*
29725476 ATATATGTGTAT
1 ATATATGTATAT
*
29725488 ACATATGTATAT
1 ATATATGTATAT
29725500 AT
1 AT
29725502 CTCTATCCAG
Statistics
Matches: 124, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
10 9 0.07
12 79 0.64
14 36 0.29
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:29725493 original size:14 final size:14
Alignment explanation
Indices: 29725340--29725481 Score: 131
Period size: 14 Copynumber: 9.9 Consensus size: 14
29725330 AAATCTCCAA
* *
29725340 ATATATATAAATAT
1 ATATGTATATATAT
*
29725354 ATATGTATATATGT
1 ATATGTATATATAT
*
29725368 ATATGTATATATGT
1 ATATGTATATATAT
*
29725382 ATATGTATATGTAT
1 ATATGTATATATAT
* *
29725396 ATGTATATATATAT
1 ATATGTATATATAT
*
29725410 ATATGTATACACATATAC
1 ATATGTAT----ATATAT
*
29725428 ATATGTATCTATAT
1 ATATGTATATATAT
29725442 ATATGTATATATAT
1 ATATGTATATATAT
* *
29725456 ATGTGTATACATAT
1 ATATGTATATATAT
* *
29725470 GTATATATATAT
1 ATATGTATATAT
29725482 GTGTATACAT
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
14 91 0.88
18 13 0.12
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:29725655 original size:19 final size:18
Alignment explanation
Indices: 29725617--29725655 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29725607 CGTCTGATTT
*
29725617 TTGTAAATCTTATTTAAA
1 TTGTAAATCTTATATAAA
*
29725635 TTGTAAATTTTAATATAAA
1 TTGTAAATCTT-ATATAAA
29725654 TT
1 TT
29725656 AATTGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTGTAAATCTTATATAAA
Found at i:29745043 original size:31 final size:30
Alignment explanation
Indices: 29744971--29745063 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 30
29744961 AATCAAATCT
* *
29744971 TTATA-TTTT-TTTTGAATCACATAAATTC
1 TTATACTTTTATTTTAAATCAAATAAATTC
* *
29744999 TTGTACTTTTATTTTAAATCGAATAAATTC
1 TTATACTTTTATTTTAAATCAAATAAATTC
** *
29745029 TTATACTTTTTATTTTGGATCAAATAAATTT
1 TTATAC-TTTTATTTTAAATCAAATAAATTC
29745060 TTAT
1 TTAT
29745064 TATTAATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
28 4 0.08
29 4 0.08
30 21 0.40
31 24 0.45
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (30 bp):
TTATACTTTTATTTTAAATCAAATAAATTC
Found at i:29746199 original size:2 final size:2
Alignment explanation
Indices: 29746186--29746215 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29746176 ACAAATTCAC
*
29746186 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29746216 TCCTTTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29747770 original size:38 final size:38
Alignment explanation
Indices: 29747719--29747796 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
29747709 TCCAAGTGCC
29747719 AAATTTTGAGCTATGATTAAAAAGTAATCTAATTGACT
1 AAATTTTGAGCTATGATTAAAAAGTAATCTAATTGACT
29747757 AAATTTTGAGCTATGATTAAAAAGTAATCTAATTGACT
1 AAATTTTGAGCTATGATTAAAAAGTAATCTAATTGACT
29747795 AA
1 AA
29747797 CTCTAATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (38 bp):
AAATTTTGAGCTATGATTAAAAAGTAATCTAATTGACT
Found at i:29752347 original size:27 final size:25
Alignment explanation
Indices: 29752277--29752347 Score: 63
Period size: 30 Copynumber: 2.6 Consensus size: 25
29752267 ATGAGATCTT
29752277 TTTTATTGA-AATTAAAAAAAATTA
1 TTTTATTGAGAATTAAAAAAAATTA
*
29752301 TTATTAGTTGGAGATCATTAAAAATATATTA
1 TT-TTA-TT-GAGA--ATTAAAAA-AAATTA
29752332 TATTTATTGAGAATTA
1 T-TTTATTGAGAATTA
29752348 TTAGTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
26 2 0.05
27 6 0.16
28 1 0.03
29 4 0.11
30 10 0.26
31 9 0.24
32 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (25 bp):
TTTTATTGAGAATTAAAAAAAATTA
Found at i:29753000 original size:22 final size:24
Alignment explanation
Indices: 29752975--29753018 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
29752965 CTTGAATCAA
29752975 GGATCA-AAT-ATATAAAATTTTT
1 GGATCATAATGATATAAAATTTTT
* *
29752997 GGATTATTATGATATAAAATTT
1 GGATCATAATGATATAAAATTT
29753019 GGTGATTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (24 bp):
GGATCATAATGATATAAAATTTTT
Found at i:29753415 original size:27 final size:29
Alignment explanation
Indices: 29753360--29753418 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
29753350 CTTTTATCTC
* *
29753360 TTATGATTTTAATTTTTTTTATATGACACT
1 TTATGATTTT-ATTTTTTCTATATAACACT
29753390 TTATGATTTT-TTTTTTCTAT-TAACACT
1 TTATGATTTTATTTTTTCTATATAACACT
29753417 TT
1 TT
29753419 GTGAATACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 8 0.30
28 9 0.33
30 10 0.37
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (29 bp):
TTATGATTTTATTTTTTCTATATAACACT
Found at i:29756908 original size:33 final size:33
Alignment explanation
Indices: 29756871--29756937 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29756861 GGTTGTAGAT
29756871 ACTAGATTTTGGTTAATACTGTTACTCTAAAGA
1 ACTAGATTTTGGTTAATACTGTTACTCTAAAGA
29756904 ACTAGATTTTGGTTAATACTGTTACTCTAAAGA
1 ACTAGATTTTGGTTAATACTGTTACTCTAAAGA
29756937 A
1 A
29756938 TTATGTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
ACTAGATTTTGGTTAATACTGTTACTCTAAAGA
Found at i:29757001 original size:26 final size:26
Alignment explanation
Indices: 29756972--29757118 Score: 123
Period size: 26 Copynumber: 5.3 Consensus size: 26
29756962 AGAGAACAAC
29756972 CAGAACAAGTGAAGTGTTACTTCACG
1 CAGAACAAGTGAAGTGTTACTTCACG
* *
29756998 CAGAATAACTAGAACAAGTGAAGCGTTACTTCACG
1 CAGAACAAGT-G---AAGT-----GTTACTTCACG
* *
29757033 CAGAACAAGTGAAGCGCTACTTCACG
1 CAGAACAAGTGAAGTGTTACTTCACG
* *
29757059 CAGAACAAGTGAAGCGCTACTTCACG
1 CAGAACAAGTGAAGTGTTACTTCACG
* * * *
29757085 CAGAATAAGTGAAGTATTACTTAAAG
1 CAGAACAAGTGAAGTGTTACTTCACG
29757111 CAGAACAA
1 CAGAACAA
29757119 TTAGAAAAAG
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
26 71 0.72
27 1 0.01
30 4 0.04
31 3 0.03
34 1 0.01
35 19 0.19
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (26 bp):
CAGAACAAGTGAAGTGTTACTTCACG
Found at i:29757019 original size:35 final size:35
Alignment explanation
Indices: 29756964--29757040 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
29756954 TATTATATAG
*
29756964 AGAACAACCAGAACAAGTGAAGTGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
* *
29756999 AGAATAACTAGAACAAGTGAAGCGTTACTTCACGC
1 AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
29757034 AGAACAA
1 AGAACAA
29757041 GTGAAGCGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (35 bp):
AGAACAACCAGAACAAGTGAAGCGTTACTTCACGC
Found at i:29757106 original size:52 final size:52
Alignment explanation
Indices: 29757008--29757118 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
29756998 CAGAATAACT
* * * *
29757008 AGAACAAGTGAAGCGTTACTTCACGCAGAACAAGTGAAGCGCTACTTCACGC
1 AGAACAAGTGAAGCGCTACTTCACGCAGAACAAGTGAAGCACTACTTAAAGC
* * *
29757060 AGAACAAGTGAAGCGCTACTTCACGCAGAATAAGTGAAGTATTACTTAAAGC
1 AGAACAAGTGAAGCGCTACTTCACGCAGAACAAGTGAAGCACTACTTAAAGC
29757112 AGAACAA
1 AGAACAA
29757119 TTAGAAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.18
Consensus pattern (52 bp):
AGAACAAGTGAAGCGCTACTTCACGCAGAACAAGTGAAGCACTACTTAAAGC
Found at i:29757406 original size:29 final size:28
Alignment explanation
Indices: 29757372--29757455 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
29757362 TGTTCTCGTA
*
29757372 TACCTATTCATGTACAGCTTTTTCTCTTG
1 TACCTATTC-TGTACAGCTTTTTCTCTCG
* * *
29757401 TACCTATTCTCATATAGCTTCTTCTCTCG
1 TACCTATTCT-GTACAGCTTTTTCTCTCG
*
29757430 TACCTATTCTTGTACACCTCTTTTCT
1 TACCTATTC-TGTACAGCT-TTTTCT
29757456 ATTACCATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.02
29 37 0.84
30 6 0.14
ACGTcount: A:0.17, C:0.29, G:0.07, T:0.48
Consensus pattern (28 bp):
TACCTATTCTGTACAGCTTTTTCTCTCG
Done.