Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 60 of 153
Found at i:19357707 original size:30 final size:29
Alignment explanation
Indices: 19357667--19357786 Score: 104
Period size: 30 Copynumber: 4.1 Consensus size: 29
19357657 TTAAAAATAA
*
19357667 AAATTGCATTTTGACCCCTAAATTTTTCCT
1 AAATTTCATTTTGACCCCTAAATTTTT-CT
*
19357697 AAATTTCATTTTGACCCTTAAACTTTCTT-T
1 AAATTTCATTTTGACCCCTAAA-TTT-TTCT
* * *
19357727 AAATTTCACTTAGACCCCTAAA-CTTTCATT
1 AAATTTCATTTTGACCCCTAAATTTTTC--T
**
19357757 AAATTTCATTTT-AATCCTAAA-TTTTCT
1 AAATTTCATTTTGACCCCTAAATTTTTCT
19357784 AAA
1 AAA
19357787 AATTACATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.08
28 1 0.01
29 11 0.15
30 51 0.69
31 3 0.04
32 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCCTAAATTTTTCT
Found at i:19358051 original size:10 final size:10
Alignment explanation
Indices: 19358032--19358081 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
19358022 TTTTTCGAAG
*
19358032 GAAAAAAGAA
1 GAAAAGAGAA
19358042 GAAAAGAGAA
1 GAAAAGAGAA
19358052 GAAAAGAGAA
1 GAAAAGAGAA
* *
19358062 -AGAGGAGAA
1 GAAAAGAGAA
19358071 GAAAAGA-AA
1 GAAAAGAGAA
19358080 GA
1 GA
19358082 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:19358082 original size:17 final size:19
Alignment explanation
Indices: 19358035--19358077 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
19358025 TTCGAAGGAA
19358035 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
19358053 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
19358072 AAAAGA
1 AAAAGA
19358078 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:19358143 original size:3 final size:3
Alignment explanation
Indices: 19358137--19358182 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
19358127 GCTAGACTTT
*
19358137 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
19358183 AGAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19358155 original size:10 final size:10
Alignment explanation
Indices: 19358140--19358168 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19358130 AGACTTTGAA
19358140 GAAGAAGAAG
1 GAAGAAGAAG
19358150 GAAGAAGAAG
1 GAAGAAGAAG
19358160 GAAGAAGAA
1 GAAGAAGAA
19358169 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:19358155 original size:13 final size:13
Alignment explanation
Indices: 19358137--19358182 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
19358127 GCTAGACTTT
19358137 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
19358150 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
19358163 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
19358174 GAAGAAGAA
1 GAAGAAGAA
19358183 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:19358564 original size:16 final size:17
Alignment explanation
Indices: 19358538--19358575 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19358528 TTATATTTAT
19358538 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
19358555 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
19358571 ATTTT
1 ATTTT
19358576 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:19358790 original size:16 final size:16
Alignment explanation
Indices: 19358739--19358792 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
19358729 CGTGCTTTTA
19358739 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
19358755 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
19358773 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
19358789 AAAA
1 AAAA
19358793 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:19358803 original size:17 final size:18
Alignment explanation
Indices: 19358728--19358884 Score: 121
Period size: 17 Copynumber: 8.8 Consensus size: 18
19358718 TCAATAATCC
*
19358728 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
19358746 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
19358763 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
19358780 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
19358797 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
* *
19358818 TCGTGTTTT-ATAAATCT
1 TCGTGTTTTCAAAAATTT
19358835 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
** *
19358852 TCG-GTGTTTCTTAGATTT
1 TCGTGT-TTTCAAAAATTT
19358870 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
19358885 CTCCGGTGAT
Statistics
Matches: 107, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
16 9 0.08
17 53 0.50
18 27 0.25
19 2 0.02
21 16 0.15
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:19358859 original size:35 final size:34
Alignment explanation
Indices: 19358716--19358937 Score: 146
Period size: 35 Copynumber: 6.3 Consensus size: 34
19358706 AAAATTGTAA
* * *
19358716 TTTCAATAATCCTCGTGCTTTT-AAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAAAATT-TCGTG
*
19358751 TTTCAAAAATCTTCGTGTTTTC-AAAATTCTAGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAAATT-TCGTG
* *
19358785 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTG
1 TTTCAAAAATCTTCGTGTTTTC---AAAAA-TTTCGTG
* *
19358823 TTTTATAAATCTTCGTGTTTTCAAAAATTTCGGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAAATTTC-GTG
** * * * *
19358858 TTTCTTAGATTTTCGTGTTTTCAAAAACTCCGGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAAATTTC-GTG
*** *
19358893 ATTT-AAAAAAAATCGT-TTTCTAAAAAATTTCCGTG
1 -TTTCAAAAATCTTCGTGTTT-TCAAAAATTT-CGTG
19358928 TTTCAAAAAT
1 TTTCAAAAAT
19358938 TTTTAAAAAT
Statistics
Matches: 149, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
34 44 0.30
35 73 0.49
36 4 0.03
38 26 0.17
39 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAAATTTCGTG
Found at i:19358935 original size:17 final size:17
Alignment explanation
Indices: 19358749--19358939 Score: 72
Period size: 17 Copynumber: 10.8 Consensus size: 17
19358739 AAAATTCTCA
19358749 TGTTTCAAAAATCTT-CG
1 TGTTTCAAAAAT-TTCCG
*
19358766 TGTTTTC-AAAA-TTCTAG
1 TG-TTTCAAAAATTTC-CG
* *
19358783 TGTTTCAAAAATTTTCT
1 TGTTTCAAAAATTTCCG
*
19358800 TGTTTTCAGAAAAAATTTTCG
1 TG-TTTC---AAAAATTTCCG
* *
19358821 TGTTTTATAAATCTT-CG
1 TGTTTCAAAAAT-TTCCG
*
19358838 TGTTTTCAAAAATTTCGG
1 TG-TTTCAAAAATTTCCG
** * *
19358856 TGTTTCTTAGATTTTCG
1 TGTTTCAAAAATTTCCG
*
19358873 TGTTTTCAAAAA-CTCCGG
1 TG-TTTCAAAAATTTCC-G
* **
19358891 TGATTTAAAAAAAAT-CG
1 TG-TTTCAAAAATTTCCG
19358908 T-TTTCTAAAAAATTTCCG
1 TGTTTC--AAAAATTTCCG
19358926 TGTTTCAAAAATTT
1 TGTTTCAAAAATTT
19358940 TTAAAAATTC
Statistics
Matches: 129, Mismatches: 26, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
15 5 0.04
16 4 0.03
17 56 0.43
18 44 0.34
19 5 0.04
20 3 0.02
21 12 0.09
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTCAAAAATTTCCG
Found at i:19358978 original size:20 final size:19
Alignment explanation
Indices: 19358955--19358992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19358945 AATTCTCGTG
19358955 TTTTAAAAAAAAAACTTTCA
1 TTTTAAAAAAAAAA-TTTCA
*
19358975 TTTTTAAAAAAAAATTTC
1 TTTTAAAAAAAAAATTTC
19358993 GTGCTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTTAAAAAAAAAATTTCA
Found at i:19359003 original size:16 final size:17
Alignment explanation
Indices: 19358984--19359020 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19358974 ATTTTTAAAA
19358984 AAAAATT-TCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
19358999 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
19359016 AAAAA
1 AAAAA
19359021 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:19372460 original size:17 final size:17
Alignment explanation
Indices: 19372431--19372552 Score: 90
Period size: 17 Copynumber: 7.4 Consensus size: 17
19372421 TTTTTTAAGA
19372431 AAAAAAT-T-GTGTTTC
1 AAAAAATGTCGTGTTTC
* *
19372446 AAAAAATGTCTTGTTTT
1 AAAAAATGTCGTGTTTC
* *
19372463 AAAAATTCTCGTGTTTC
1 AAAAAATGTCGTGTTTC
*
19372480 AAAAAATGTCGTGTTTT
1 AAAAAATGTCGTGTTTC
* *
19372497 AAAAATTTTCGTGTTTC
1 AAAAAATGTCGTGTTTC
** *
19372514 -TGAAATTTCCGTGTTT-
1 AAAAAATGT-CGTGTTTC
* * *
19372530 AAAAATTCTCGTGTTTT
1 AAAAAATGTCGTGTTTC
19372547 AAAAAA
1 AAAAAA
19372553 AAAAACTTTC
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
15 7 0.09
16 13 0.16
17 62 0.76
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (17 bp):
AAAAAATGTCGTGTTTC
Found at i:19372479 original size:34 final size:33
Alignment explanation
Indices: 19372439--19372552 Score: 140
Period size: 34 Copynumber: 3.4 Consensus size: 33
19372429 GAAAAAAATT
19372439 GTGTTTCAAAAAATGTCTTGTTTTAAAAATTCTC
1 GTGTTTCAAAAAATGTC-TGTTTTAAAAATTCTC
*
19372473 GTGTTTCAAAAAATGTCGTGTTTTAAAAATTTTC
1 GTGTTTCAAAAAATGTC-TGTTTTAAAAATTCTC
** * *
19372507 GTGTTTC-TGAAATTTCCGTGTTTAAAAATTCTC
1 GTGTTTCAAAAAATGTCTGT-TTTAAAAATTCTC
*
19372540 GTGTTTTAAAAAA
1 GTGTTTCAAAAAA
19372553 AAAAACTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 24 0.35
34 42 0.62
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (33 bp):
GTGTTTCAAAAAATGTCTGTTTTAAAAATTCTC
Found at i:19372592 original size:17 final size:17
Alignment explanation
Indices: 19372572--19372609 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19372562 CATTTTTTAA
*
19372572 AAAAATTTTCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
19372588 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
19372605 AAAAA
1 AAAAA
19372610 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:19381847 original size:22 final size:22
Alignment explanation
Indices: 19381806--19381851 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
19381796 AAAACTATTA
*
19381806 AAAACATAATTTTTATATTTTT
1 AAAACATAATTTTTAAATTTTT
*
19381828 AAAA-ATAATTTTTAAA-ATTT
1 AAAACATAATTTTTAAATTTTT
19381848 AAAA
1 AAAA
19381852 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAACATAATTTTTAAATTTTT
Found at i:19381881 original size:26 final size:27
Alignment explanation
Indices: 19381825--19381883 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
19381815 TTTTTATATT
19381825 TTTAAAA-ATAATTTTTAAAATTTAAA
1 TTTAAAATATAATTTTTAAAATTTAAA
* *
19381851 -ATAAAATATAA-TTTTAAATTTTAAA
1 TTTAAAATATAATTTTTAAAATTTAAA
19381876 TTTAAAAT
1 TTTAAAAT
19381884 GTTTATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAAAATATAATTTTTAAAATTTAAA
Found at i:19382988 original size:15 final size:14
Alignment explanation
Indices: 19382964--19383017 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
19382954 TCAAACACCG
*
19382964 GAAAATATTTTCCA
1 GAAAACATTTTCCA
19382978 GTAAAACATTTTCCA
1 G-AAAACATTTTCCA
* * *
19382993 GAAATCATTTTACG
1 GAAAACATTTTCCA
*
19383007 GAAAATATTTT
1 GAAAACATTTT
19383018 ACTCTCAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (14 bp):
GAAAACATTTTCCA
Found at i:19394834 original size:138 final size:139
Alignment explanation
Indices: 19394558--19394933 Score: 385
Period size: 138 Copynumber: 2.7 Consensus size: 139
19394548 ATGGAACTTC
* * * ** *
19394558 GATGTAATCGTAATTATCTAACCATCTAACGAAAGTAGCTAATATGTT-AAAAATATTAATT---
1 GATGTAATTGCAACTATCTAACCATCTAAC-AAAAAAACTAATATGTTAAAAAAT-TTAATTAAA
** * * * *
19394619 AA---AAAAAGTTTGAAGCAACATGAAATAAAAAAAATACAAATGCGAGTAATAGAAGAATCGAC
64 AATTTAAAAAACTTGAAGCAACATGAAAT--AAAAAATACAAATGCGAATAAGAAAAGAATCAAC
* *
19394681 CTCGAGATTTAAG
127 CTCGAGACTCAAG
* *
19394694 GATGTAATTGCAACTATCTAACGATCTAATAAAAATAACTAATATG-TAAAAAA-TTAATTAAAA
1 GATGTAATTGCAACTATCTAACCATCTAACAAAAA-AACTAATATGTTAAAAAATTTAATTAAAA
* * * *
19394757 TTTTAAAAAACTTGAAGCATCATGAAATAAAAAATACAAATGTGAATAGGAAAAGAATCTAACC-
65 ATTTAAAAAACTTGAAGCAACATGAAATAAAAAATACAAATGCGAATAAGAAAAGAATC-AACCT
19394821 CGAGACTCAAG
129 CGAGACTCAAG
* * * *
19394832 GATGTATTTGCAACTATCTAACCATCTAACCAAAAACCTAATATGTTAAAAAATTTAGTTAAAAA
1 GATGTAATTGCAACTATCTAACCATCTAACAAAAAAACTAATATGTTAAAAAATTTAATTAAAAA
* * *
19394897 TTTAAAAAGCTTTAAGCAACATTAAATAAAAAATACA
66 TTTAAAAAACTTGAAGCAACATGAAATAAAAAATACA
19394934 TGTCACACCC
Statistics
Matches: 198, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
134 6 0.03
135 4 0.02
136 39 0.20
137 10 0.05
138 73 0.37
139 45 0.23
140 21 0.11
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (139 bp):
GATGTAATTGCAACTATCTAACCATCTAACAAAAAAACTAATATGTTAAAAAATTTAATTAAAAA
TTTAAAAAACTTGAAGCAACATGAAATAAAAAATACAAATGCGAATAAGAAAAGAATCAACCTCG
AGACTCAAG
Found at i:19399869 original size:9 final size:9
Alignment explanation
Indices: 19399853--19399886 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19399843 AAGAAAAACC
19399853 TGGAAAAAGA
1 TGGAAAAA-A
*
19399863 AGGAAAAAA
1 TGGAAAAAA
19399872 TGGAAAAAA
1 TGGAAAAAA
19399881 TGGAAA
1 TGGAAA
19399887 TAGGTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (9 bp):
TGGAAAAAA
Found at i:19399916 original size:22 final size:22
Alignment explanation
Indices: 19399891--19399934 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19399881 TGGAAATAGG
*
19399891 TTTTAAAATATTATTTATTTAT
1 TTTTAAAATATTATTTAATTAT
* *
19399913 TTTTAATATATTTTTTAATTAT
1 TTTTAAAATATTATTTAATTAT
19399935 GACATCATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTAAAATATTATTTAATTAT
Found at i:19408013 original size:33 final size:33
Alignment explanation
Indices: 19407971--19408173 Score: 145
Period size: 33 Copynumber: 5.6 Consensus size: 33
19407961 AAGATATGGT
*
19407971 GGAATCAGCACTTAGCAACCACTAATGATTTGG
1 GGAATCAGCACTTAGCAACCACTAATGATTCGG
* * *
19408004 GGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--TA-A--T--GATTCGG
* *
19408045 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACTAATGATTCGG
* * *
19408079 GGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--TA-A--T--GATTCGG
* *
19408120 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACTAATGATTCGG
19408154 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
19408174 CCCTTCACAT
Statistics
Matches: 133, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
33 56 0.42
34 14 0.11
36 5 0.04
37 2 0.02
38 2 0.02
39 4 0.03
41 14 0.11
42 36 0.27
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACTAATGATTCGG
Found at i:19408063 original size:42 final size:40
Alignment explanation
Indices: 19408002--19408192 Score: 203
Period size: 33 Copynumber: 5.0 Consensus size: 40
19407992 CTAATGATTT
19408002 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCC-TTACATTTAAAATAC
* *
19408043 GGTGGAATCAGCACTTAGCAACCACC--A-A--T-GAAT-C
1 GG-GGAATCAGCACTTAGCAACCCCCTTACATTTAAAATAC
19408077 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCC-TTACATTTAAAATAC
* *
19408118 GGTGGAATCAGCACTTAGCAACCACC--A-A--T-GAAT-C
1 GG-GGAATCAGCACTTAGCAACCCCCTTACATTTAAAATAC
19408152 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCCTT-ACATTTAAAATAC
19408193 TTCGGCTTAT
Statistics
Matches: 124, Mismatches: 8, Indels: 36
0.74 0.05 0.21
Matches are distributed among these distances:
33 44 0.35
34 6 0.05
35 6 0.05
36 4 0.03
37 2 0.02
38 2 0.02
39 4 0.03
40 6 0.05
41 6 0.05
42 44 0.35
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (40 bp):
GGGGAATCAGCACTTAGCAACCCCCTTACATTTAAAATAC
Found at i:19408073 original size:75 final size:75
Alignment explanation
Indices: 19407890--19408192 Score: 457
Period size: 75 Copynumber: 4.0 Consensus size: 75
19407880 TAACCGTTAT
* * ** *
19407890 CGGTGGATTCAGCACTTAGCAACCACTAGTAT-TTTCGGGGAATCAACACTTAGCAA-CCCCTTT
1 CGGTGGAATCAGCACTTAGCAACCACCA--ATGAATCGGGGAATCAGCACTTAGCAACCCCCTTT
*
19407953 CACATTCAAAGATA
64 -ACATTTAAA-ATA
* * * *
19407967 TGGTGGAATCAGCACTTAGCAACCACTAATGATTTGGGGAATCAGCACTTAGCAACCCCCTTTAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
19408032 ATTTAAAATA
66 ATTTAAAATA
19408042 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
19408107 ATTTAAAATA
66 ATTTAAAATA
*
19408117 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
19408182 ATTTAAAATA
66 ATTTAAAATA
19408192 C
1 C
19408193 TTCGGCTTAT
Statistics
Matches: 213, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
75 151 0.71
76 29 0.14
77 33 0.15
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
ATTTAAAATA
Found at i:19415530 original size:69 final size:69
Alignment explanation
Indices: 19415419--19415560 Score: 266
Period size: 69 Copynumber: 2.1 Consensus size: 69
19415409 TTTAGCACTT
19415419 AGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGG
1 AGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGG
19415484 AATC
66 AATC
* *
19415488 AGCAACCACCATTGATTCGGGGAATCAGTACTTAGCAACCCCTTTCACATTCAAAGATATGGTGG
1 AGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGG
19415553 AATC
66 AATC
19415557 AGCA
1 AGCA
19415561 CTTAGCAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (69 bp):
AGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGG
AATC
Found at i:19415569 original size:43 final size:43
Alignment explanation
Indices: 19415508--19415613 Score: 203
Period size: 43 Copynumber: 2.5 Consensus size: 43
19415498 ATTGATTCGG
*
19415508 GGAATCAGTACTTAGCAACCCCTTTCACATTCAAAGATATGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGT
19415551 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGT
19415594 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
19415614 GCCAATGATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGT
Found at i:19415701 original size:42 final size:41
Alignment explanation
Indices: 19415652--19415767 Score: 149
Period size: 33 Copynumber: 3.0 Consensus size: 41
19415642 CAACCCCTTG
19415652 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
* *
19415693 GGTGGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-C
1 GG-GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
19415727 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
19415768 TTCGGCTTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
33 18 0.29
34 6 0.10
35 3 0.05
36 3 0.05
37 1 0.02
38 1 0.02
39 3 0.05
40 3 0.05
41 6 0.10
42 18 0.29
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (41 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
Found at i:19415753 original size:103 final size:103
Alignment explanation
Indices: 19415551--19415750 Score: 330
Period size: 102 Copynumber: 2.0 Consensus size: 103
19415541 AAGATATGGT
* * *
19415551 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACCGC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACCAC
*
19415616 CAATGATTCGGGAAATCAGCACATAGCAACCCCTTGGG
66 CAATGAATCGGGAAATCAGCACATAGCAACCCCTTGGG
*
19415654 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAA-ATACGGTGGAATCAGCACTTAGCAACCAC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACCAC
* *
19415718 CAATGAATCGGGGAATCAGCACTTAGCAACCCC
66 CAATGAATCGGGAAATCAGCACATAGCAACCCC
19415751 CTTCACATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 57 0.63
103 33 0.37
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (103 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACCAC
CAATGAATCGGGAAATCAGCACATAGCAACCCCTTGGG
Found at i:19415856 original size:196 final size:196
Alignment explanation
Indices: 19415615--19416002 Score: 677
Period size: 196 Copynumber: 2.0 Consensus size: 196
19415605 TTAGCAACCG
*
19415615 CCAATGATTCGGGAAATCAGCACATAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTC
1 CCAATGAATCGGGAAATCAGCACATAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTC
*
19415680 ACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGC
66 ACATTCAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGC
19415745 AACCCCCTTCACATTTAAAATACTTCGGCTTATTCCGAGTGTTCAACCGGAACCCATATTTTACC
131 AACCCCCTTCACATTTAAAATACTTCGGCTTATTCCGAGTGTTCAACCGGAACCCATATTTTACC
19415810 A
196 A
* * * ** *
19415811 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGTGGGAATCAGCACTTAGCAACCTTCTTT
1 CCAATGAATCGGGAAATCAGCACATAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTC
* * *
19415876 ATATTCAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGC
66 ACATTCAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGC
19415941 AACCCCCTTCACATTTAAAATACTTCGGCTTATTCCGAGTGTTCAACCGGAACCCATATTTT
131 AACCCCCTTCACATTTAAAATACTTCGGCTTATTCCGAGTGTTCAACCGGAACCCATATTTT
19416003 CAACATTTTA
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 181 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (196 bp):
CCAATGAATCGGGAAATCAGCACATAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTC
ACATTCAAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGC
AACCCCCTTCACATTTAAAATACTTCGGCTTATTCCGAGTGTTCAACCGGAACCCATATTTTACC
A
Found at i:19427549 original size:28 final size:28
Alignment explanation
Indices: 19427509--19427573 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
19427499 ATTGGAAGCC
* *
19427509 GAGCATGAATGAACCGAAGAGAAAAGGA
1 GAGCATGGATGAACCGAAGAGAAAAAGA
*
19427537 GAGCTTGGATGAACCGAAGAGAAAAAGA
1 GAGCATGGATGAACCGAAGAGAAAAAGA
19427565 GAGCATGGA
1 GAGCATGGA
19427574 ACCAAACTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.34, T:0.09
Consensus pattern (28 bp):
GAGCATGGATGAACCGAAGAGAAAAAGA
Found at i:19431870 original size:51 final size:51
Alignment explanation
Indices: 19431752--19431930 Score: 288
Period size: 51 Copynumber: 3.5 Consensus size: 51
19431742 TTTCAGTACT
* * * *
19431752 TCTGATCAGTAACAAGTGATAAGTGATAAGTGGTAGCCT-AGTTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTA
*
19431802 TCTGATCAGTGATAAGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTA
* *
19431853 TCTGATTAGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTA
19431904 TCTGATCAGTGACAAGTGACAAGTGAT
1 TCTGATCAGTGACAAGTGACAAGTGAT
19431931 GTAACACCCC
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 35 0.29
51 84 0.71
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTA
Found at i:19432177 original size:46 final size:46
Alignment explanation
Indices: 19432110--19432386 Score: 374
Period size: 46 Copynumber: 6.0 Consensus size: 46
19432100 ACATTGCTAT
* * * * *
19432110 AACTCAATATGGTTATCTTCACGGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
19432156 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
19432202 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
19432248 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACCTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * * * **
19432294 AGCTCAGTATGGTTTTCTTTACCAAAATACCATACCTACTTTTTGC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * * *
19432340 AATTCAGTATGGTTTACTTCACTGAAACACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
19432386 A
1 A
19432387 CTTTGCCATG
Statistics
Matches: 200, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 200 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:19432267 original size:92 final size:92
Alignment explanation
Indices: 19432110--19432386 Score: 428
Period size: 92 Copynumber: 3.0 Consensus size: 92
19432100 ACATTGCTAT
* * * * * *
19432110 AACTCAATATGGTTATCTTCACGGAAATACCATACATACTTTTCACAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGCAACTCAGTATGGTTTTCTT
* *
19432175 CACCGAAACACCATACCTACTTTTCAC
66 CACTGAAACACCATACCTACCTTTCAC
19432202 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGCAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGCAACTCAGTATGGTTTTCTT
19432267 CACTGAAACACCATACCTACCTTTCAC
66 CACTGAAACACCATACCTACCTTTCAC
* * * * *
19432294 AGCTCAGTATGGTTTTCTTTACCAAAATACCATACCTACTTTTTGCAATTCAGTATGGTTTACTT
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGCAACTCAGTATGGTTTTCTT
*
19432359 CACTGAAACACCATACCTACGTTTCAC
66 CACTGAAACACCATACCTACCTTTCAC
19432386 A
1 A
19432387 CTTTGCCATG
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 171 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (92 bp):
AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCGCAACTCAGTATGGTTTTCTT
CACTGAAACACCATACCTACCTTTCAC
Found at i:19434899 original size:51 final size:51
Alignment explanation
Indices: 19434822--19434982 Score: 245
Period size: 51 Copynumber: 3.2 Consensus size: 51
19434812 TCTGGCTATT
*
19434822 ACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTG
1 ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTG
*
19434873 ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGAGAAGTG
1 ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTG
* * *
19434924 GCAAGCGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GACAAGTG
1 ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGTGACAAGTG
*
19434974 ATAAGTGAT
1 ACAAGTGAT
19434983 CATACGTAAG
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
50 33 0.33
51 67 0.67
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTG
Found at i:19437359 original size:15 final size:16
Alignment explanation
Indices: 19437336--19437374 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
19437326 TTTGGTTTAA
19437336 ATTTATATATATTATT
1 ATTTATATATATTATT
19437352 ATTT-TATATATTATT
1 ATTTATATATATTATT
*
19437367 ATCTATAT
1 ATTTATAT
19437375 TAAATCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATATATATTATT
Found at i:19437690 original size:16 final size:16
Alignment explanation
Indices: 19437669--19437700 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19437659 AAATATACAT
*
19437669 GCCTCTATTCTATTAC
1 GCCTCTATTCCATTAC
19437685 GCCTCTATTCCATTAC
1 GCCTCTATTCCATTAC
19437701 AGCGAACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.34, G:0.06, T:0.41
Consensus pattern (16 bp):
GCCTCTATTCCATTAC
Found at i:19437955 original size:24 final size:24
Alignment explanation
Indices: 19437897--19437945 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19437887 TATATATGCG
19437897 TACTTAAATATATATATCTTATAA
1 TACTTAAATATATATATCTTATAA
19437921 TACTTAAATATATATATCTTATAA
1 TACTTAAATATATATATCTTATAA
19437945 T
1 T
19437946 TTTTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (24 bp):
TACTTAAATATATATATCTTATAA
Found at i:19441741 original size:21 final size:21
Alignment explanation
Indices: 19441713--19441778 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
19441703 CCTTCTCAAA
*
19441713 TTCTGCTTTTAGTTCCTTCAT
1 TTCTGCTTTTCGTTCCTTCAT
*
19441734 TTTTGCTTTTCGTTCCTTCAT
1 TTCTGCTTTTCGTTCCTTCAT
* *
19441755 TTCAGCTTTTCCTTCCTTCAT
1 TTCTGCTTTTCGTTCCTTCAT
19441776 TTC
1 TTC
19441779 CCCTTCTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (21 bp):
TTCTGCTTTTCGTTCCTTCAT
Found at i:19441925 original size:33 final size:33
Alignment explanation
Indices: 19441888--19441958 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
19441878 ACATCCTCCT
*
19441888 TTGAAATTTCTTCTTCATGTTGTTCTTCTTCAC
1 TTGAAAATTCTTCTTCATGTTGTTCTTCTTCAC
* *
19441921 TTGAAAATTCTTCTTCATTTTGTTCTTCTTCAT
1 TTGAAAATTCTTCTTCATGTTGTTCTTCTTCAC
19441954 TTGAA
1 TTGAA
19441959 CAAATCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (33 bp):
TTGAAAATTCTTCTTCATGTTGTTCTTCTTCAC
Found at i:19441954 original size:15 final size:15
Alignment explanation
Indices: 19441895--19441955 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
19441885 CCTTTGAAAT
*
19441895 TTCTTCTTCATGTTG
1 TTCTTCTTCATTTTG
*
19441910 TTCTTCTTCA-CTTG
1 TTCTTCTTCATTTTG
19441924 AAAATTCTTCTTCATTTTG
1 ----TTCTTCTTCATTTTG
19441943 TTCTTCTTCATTT
1 TTCTTCTTCATTT
19441956 GAACAAATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.08
15 23 0.59
18 10 0.26
19 3 0.08
ACGTcount: A:0.13, C:0.21, G:0.07, T:0.59
Consensus pattern (15 bp):
TTCTTCTTCATTTTG
Found at i:19444179 original size:20 final size:20
Alignment explanation
Indices: 19444156--19444198 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19444146 TATAAATAAT
19444156 TATTATAAATT-TTATATTAA
1 TATT-TAAATTATTATATTAA
**
19444176 TATTTGTATTATTATATTAA
1 TATTTAAATTATTATATTAA
19444196 TAT
1 TAT
19444199 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTAAATTATTATATTAA
Found at i:19444251 original size:13 final size:13
Alignment explanation
Indices: 19444233--19444266 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19444223 ACCCAACCCA
*
19444233 TCCCTCTCCCGTC
1 TCCCTCTCCCCTC
19444246 TCCCTCTCCCCTC
1 TCCCTCTCCCCTC
19444259 T-CCTCTCC
1 TCCCTCTCC
19444267 TCCACCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.00, C:0.65, G:0.03, T:0.32
Consensus pattern (13 bp):
TCCCTCTCCCCTC
Found at i:19444434 original size:17 final size:16
Alignment explanation
Indices: 19444391--19444444 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
19444381 TGGGGAAAGT
*
19444391 TTTATTTTTTTTAATA
1 TTTATTTTATTTAATA
19444407 TAATTATTTTATTTAATA
1 T--TTATTTTATTTAATA
*
19444425 TTTATATTTATATAATA
1 TTTAT-TTTATTTAATA
19444442 TTT
1 TTT
19444445 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 5 0.15
17 13 0.39
18 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTTATTTAATA
Found at i:19446676 original size:12 final size:11
Alignment explanation
Indices: 19446659--19446697 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
19446649 GATAAGTAGC
19446659 AATAATATAAGT
1 AATAATA-AAGT
19446671 AATAATAATAGT
1 AATAATAA-AGT
19446683 AATAATAAA-T
1 AATAATAAAGT
19446693 AATAA
1 AATAA
19446698 AAGATGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 2 0.08
12 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
AATAATAAAGT
Found at i:19446677 original size:15 final size:16
Alignment explanation
Indices: 19446659--19446696 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
19446649 GATAAGTAGC
19446659 AATAATA-TAAGTAAT-
1 AATAATAGTAA-TAATA
19446674 AATAATAGTAATAATA
1 AATAATAGTAATAATA
19446690 AATAATA
1 AATAATA
19446697 AAAGATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
AATAATAGTAATAATA
Found at i:19448278 original size:44 final size:42
Alignment explanation
Indices: 19448054--19448537 Score: 496
Period size: 44 Copynumber: 11.5 Consensus size: 42
19448044 CTTCTGTCTA
* * * *
19448054 CTCCTCTACTGCTTAGGTAGATAAGA-CT-TGATGCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTGTTTCGATCTG
** *
19448094 CTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT-GTTTCGATCTG
* * ** * *
19448137 CTCCGCTGCCACTTCAGGGAGATAGGAT-TGGTGTCTTTC-CTCTG
1 CTCCACTACTGCTT-AGGGAGATAAGATCT-GTG--TTTCGATCTG
* * * *
19448181 CTCCACTACTACTTAGGGGGATAA-AACT-TGATGT-GATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTG-TTTCGATCTG
19448221 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT-GT-TTCGATCTG
* *
19448265 CTCCACTACTGCTTAGGGAGATAA-AACT-TGATAT-GATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTG-TTTCGATCTG
19448305 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT-GT-TTCGATCTG
* *
19448349 CTCCACTACTGCTTAGGGAGATAA-AACT-TGATAT-GATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTG-TTTCGATCTG
19448389 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT-GT-TTCGATCTG
* *
19448433 CTCCACTACTGCTTAGGGAGATAA-AACT-TGATAT-GATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTG-TTTCGATCTG
19448473 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGT-GT-TTCGATCTG
19448517 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
19448538 GCATATCTGA
Statistics
Matches: 372, Mismatches: 40, Indels: 60
0.79 0.08 0.13
Matches are distributed among these distances:
40 142 0.38
41 22 0.06
42 16 0.04
43 44 0.12
44 145 0.39
45 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (42 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTGTTTCGATCTG
Found at i:19448280 original size:84 final size:84
Alignment explanation
Indices: 19448054--19448537 Score: 703
Period size: 84 Copynumber: 5.8 Consensus size: 84
19448044 CTTCTGTCTA
* * * *
19448054 CTCCTCTACTGCTTAGGTAGATAAGA-CT-T-G-ATGCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
* * * * *
19448115 TAAGATCTGTGGTTTTAATCCG
66 TAA-AACT-T-GATATGATCTG
* * ** * * *
19448137 CTCCGCTGCCACTTCAGGGAGATAGGAT-TGGT-GTCTTTC-CTCTGCTCCACTACTACTTAGGG
1 CTCCACTACTGCTT-AGGGAGATAAGATCT-GTCGTC-TTCGATCTGCTCCACTACTGCTTAGGG
* *
19448199 GGATAAAACTTGATGTGATCTG
63 AGATAAAACTTGATATGATCTG
19448221 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19448286 TAAAACTTGATATGATCTG
66 TAAAACTTGATATGATCTG
19448305 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19448370 TAAAACTTGATATGATCTG
66 TAAAACTTGATATGATCTG
19448389 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19448454 TAAAACTTGATATGATCTG
66 TAAAACTTGATATGATCTG
19448473 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19448538 GCATATCTGA
Statistics
Matches: 367, Mismatches: 25, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
83 27 0.07
84 306 0.83
85 1 0.00
86 5 0.01
87 26 0.07
88 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (84 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
TAAAACTTGATATGATCTG
Found at i:19448607 original size:168 final size:168
Alignment explanation
Indices: 19448177--19448608 Score: 521
Period size: 168 Copynumber: 2.6 Consensus size: 168
19448167 GTGTCTTTCC
* * * *** ** * *
19448177 TCTGCTCCACTACTACTTAGGGGGATAAAACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGACAAAACTTGACACGATCCACTCCACTACTACTTAGAGAGA
* * **
19448242 TAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCT
66 TAAGATCTGTCATCTTCAATCCACTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCT
19448307 CCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGA
131 CCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGA
* * * ** * *
19448345 TCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCTCCACTACTGCTTAGGGAGA
1 TCTGCTCCACTACTGCTTAGGGAGACAAAACTTGACACGATCCACTCCACTACTACTTAGAGAGA
* * **
19448410 TAAGATCTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCT
66 TAAGATCTGTCATCTTCAATCCACTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCT
19448475 CCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGA
131 CCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGA
* * * *
19448513 TCTGCTCCACTACTGCTTAGGGAGAGCATATC-TGACACGATCCACTCTACT-GTAACTTCAGAG
1 TCTGCTCCACTACTGCTTAGGGAGA-CAAAACTTGACACGATCCACTCCACTACT-ACTT-AGAG
* *
19448576 AGATAAGATCCT-TTAT-TTTAATCCACTCCACTA
63 AGATAAGAT-CTGTCATCTTCAATCCACTCCACTA
19448609 AAATCTCAGG
Statistics
Matches: 240, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
167 1 0.00
168 220 0.92
169 17 0.07
170 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (168 bp):
TCTGCTCCACTACTGCTTAGGGAGACAAAACTTGACACGATCCACTCCACTACTACTTAGAGAGA
TAAGATCTGTCATCTTCAATCCACTCCACTACTGCTTAGGGAGATAAAACTTGATATGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTGTCGTCTTCGA
Found at i:19448710 original size:44 final size:43
Alignment explanation
Indices: 19448552--19448715 Score: 120
Period size: 44 Copynumber: 3.8 Consensus size: 43
19448542 ATCTGACACG
*
19448552 ATCCACTCTACTGTAACT-TCAGAGAGATAAGATCCTTTATTTTA
1 ATCCACTCTACTGTAACTCTCAGAGAGATAGGATCC--TATTTTA
* * * * * ** * *
19448596 ATCCACTCCACT-AAAATCTCAGGGGGATAGGATAGTGTCTTCA
1 ATCCACTCTACTGTAACTCTCAGAGAGATAGGATCCTAT-TTTA
** *
19448639 ATCTGCTCTGCTGTAA-TCTCAGAGAGATAGGATCCTAAATTTTA
1 ATCCACTCTACTGTAACTCTCAGAGAGATAGGATCCT--ATTTTA
* *
19448683 ATCCGCTCTACTGTAACT-TCAGGGAGATAGGAT
1 ATCCACTCTACTGTAACTCTCAGAGAGATAGGAT
19448716 TATCGGCTTC
Statistics
Matches: 90, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
42 2 0.02
43 30 0.33
44 56 0.62
45 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
ATCCACTCTACTGTAACTCTCAGAGAGATAGGATCCTATTTTA
Found at i:19448712 original size:87 final size:87
Alignment explanation
Indices: 19448557--19448715 Score: 205
Period size: 87 Copynumber: 1.8 Consensus size: 87
19448547 ACACGATCCA
** *
19448557 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTAAAATCTCAGGGGG
1 CTCTACTGTAACTTCAGAGAGATAAGATCCTAAATTTTAATCCACTCCACTAAAATCTCAGGGAG
19448622 ATAGGATAGTGTCTTCAATCTG
66 ATAGGATAGTGTCTTCAATCTG
* * * * **
19448644 CTCTGCTGTAA-TCTCAGAGAGATAGGATCCTAAATTTTAATCCGCTCTACTGTAA-CTTCAGGG
1 CTCTACTGTAACT-TCAGAGAGATAAGATCCTAAATTTTAATCCACTCCACTAAAATC-TCAGGG
19448707 AGATAGGAT
64 AGATAGGAT
19448716 TATCGGCTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
86 2 0.03
87 59 0.97
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (87 bp):
CTCTACTGTAACTTCAGAGAGATAAGATCCTAAATTTTAATCCACTCCACTAAAATCTCAGGGAG
ATAGGATAGTGTCTTCAATCTG
Found at i:19464723 original size:3 final size:3
Alignment explanation
Indices: 19464715--19464767 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
19464705 AAGCTGTTAT
* *
19464715 ATA ATA AT- ATA AGTA ATA ATA ATA ATA ATA ATA GTA GTA ATA ATAA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
19464761 ATA ATA A
1 ATA ATA A
19464768 AAGATGATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19466261 original size:19 final size:18
Alignment explanation
Indices: 19466219--19466278 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
19466209 AATTTACAAA
* *
19466219 AAAAATCAAAATAATTTTC
1 AAAATTCAAAAT-ATTTTT
19466238 AAAATTCAAAATATTTTT
1 AAAATTCAAAATATTTTT
*
19466256 ATAAATT-ATAAATTTTTTT
1 A-AAATTCA-AAATATTTTT
19466275 AAAA
1 AAAA
19466279 AAATATGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.28
19 26 0.72
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTCAAAATATTTTT
Found at i:19472902 original size:12 final size:12
Alignment explanation
Indices: 19472881--19472911 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19472871 ATGAAGAATT
19472881 ATAA-TTTCTTC
1 ATAATTTTCTTC
19472892 ATAATTTTCTTC
1 ATAATTTTCTTC
19472904 ATAATTTT
1 ATAATTTT
19472912 TTAATAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAATTTTCTTC
Found at i:19473283 original size:64 final size:66
Alignment explanation
Indices: 19473203--19473331 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 66
19473193 AATGTCAAAC
* *** * *
19473203 TATTTCTTTGATATAAAAA-TTTCAATTGTTAAATATATATTAAC-ACAATAATATCATAAATTG
1 TATTTCTTTGACATAAAAATTTTCAACCATTAAACATATATTAACAAAAATAATATCATAAATTG
19473266 A
66 A
* *
19473267 TATTTTTTTGACATAAAAATTTTCGACCATTAAACATATATTAACAAAAATAATATCATAAATTG
1 TATTTCTTTGACATAAAAATTTTCAACCATTAAACATATATTAACAAAAATAATATCATAAATTG
19473332 TTATGTTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 17 0.31
65 20 0.36
66 18 0.33
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (66 bp):
TATTTCTTTGACATAAAAATTTTCAACCATTAAACATATATTAACAAAAATAATATCATAAATTG
A
Found at i:19475970 original size:26 final size:25
Alignment explanation
Indices: 19475923--19475971 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
19475913 AAATCTATAT
* *
19475923 AATTAAAATATATTAAATATAAAAG
1 AATTAAAATATATAAAAAATAAAAG
*
19475948 AATTAAAAATTTATAAAAAATAAA
1 AATT-AAAATATATAAAAAATAAA
19475972 TATATAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AATTAAAATATATAAAAAATAAAAG
Found at i:19482822 original size:12 final size:13
Alignment explanation
Indices: 19482797--19482826 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
19482787 AGATATCAGT
19482797 CTGATATAAAGAA
1 CTGATATAAAGAA
19482810 CTGATAT-AAGAA
1 CTGATATAAAGAA
19482822 CTGAT
1 CTGAT
19482827 CCTTGAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (13 bp):
CTGATATAAAGAA
Found at i:19487819 original size:525 final size:525
Alignment explanation
Indices: 19486820--19487877 Score: 2093
Period size: 525 Copynumber: 2.0 Consensus size: 525
19486810 TCTATTGTTG
19486820 CATGTTC--CGTGATTGTTGCTTGGTTGCAGGTCTAAAACCGAGAACAGCTGTGGCTGAGAGACT
1 CATGTTCTGCGTGATTGTTGCTTGGTTGCAGGTCTAAAACCGAGAACAGCTGTGGCTGAGAGACT
19486883 TGCTGTTCTAGGTATCCTGCCACTTCTCTTAGCGGGTGTTCTTGGATCTCCTGGTAAGCGTGAAC
66 TGCTGTTCTAGGTATCCTGCCACTTCTCTTAGCGGGTGTTCTTGGATCTCCTGGTAAGCGTGAAC
19486948 AGTTAGCAGACTACTTGAGAAAGCTATTAGTTGAAGGTGCCATGAAAGAGAATCAGTCTATAACA
131 AGTTAGCAGACTACTTGAGAAAGCTATTAGTTGAAGGTGCCATGAAAGAGAATCAGTCTATAACA
19487013 CACAACAATGATATTGTTAATGCTGTCCGCTTCCTTTGGTTTGTAATTAAAAACTTCAGTCCTAA
196 CACAACAATGATATTGTTAATGCTGTCCGCTTCCTTTGGTTTGTAATTAAAAACTTCAGTCCTAA
19487078 CCATTTGTTATTTATTTCTGAATATTCACATAGAATCTACTTTAATAATGCAGTACATTCGAAGA
261 CCATTTGTTATTTATTTCTGAATATTCACATAGAATCTACTTTAATAATGCAGTACATTCGAAGA
19487143 ACATCATAGCTTGATATTTGATATCTTGTGGGAAATGGTTGTTAGCTCAAATATAGAATTGAAGA
326 ACATCATAGCTTGATATTTGATATCTTGTGGGAAATGGTTGTTAGCTCAAATATAGAATTGAAGA
19487208 TTGGTGCTGCCAATATACTGAAAGTCATTGTATGTTCTCTTTCCTTTGAAACAAAATTTATCTTG
391 TTGGTGCTGCCAATATACTGAAAGTCATTGTATGTTCTCTTTCCTTTGAAACAAAATTTATCTTG
19487273 CTACACCCGACAATAAGATATTTATACATTTTAACAGGTGACATACGTTGATGCAAAAGTTGCCT
456 CTACACCCGACAATAAGATATTTATACATTTTAACAGGTGACATACGTTGATGCAAAAGTTGCCT
19487338 CTACA
521 CTACA
19487343 CATGTTCTGCGTGATTGTTGCTTGGTTGCAGGTCTAAAACCGAGAACAGCTGTGGCTGAGAGACT
1 CATGTTCTGCGTGATTGTTGCTTGGTTGCAGGTCTAAAACCGAGAACAGCTGTGGCTGAGAGACT
19487408 TGCTGTTCTAGGTATCCTGCCACTTCTCTTAGCGGGTGTTCTTGGATCTCCTGGTAAGCGTGAAC
66 TGCTGTTCTAGGTATCCTGCCACTTCTCTTAGCGGGTGTTCTTGGATCTCCTGGTAAGCGTGAAC
19487473 AGTTAGCAGACTACTTGAGAAAGCTATTAGTTGAAGGTGCCATGAAAGAGAATCAGTCTATAACA
131 AGTTAGCAGACTACTTGAGAAAGCTATTAGTTGAAGGTGCCATGAAAGAGAATCAGTCTATAACA
19487538 CACAACAATGATATTGTTAATGCTGTCCGCTTCCTTTGGTTTGTAATTAAAAACTTCAGTCCTAA
196 CACAACAATGATATTGTTAATGCTGTCCGCTTCCTTTGGTTTGTAATTAAAAACTTCAGTCCTAA
19487603 CCATTTGTTATTTATTTCTGAATATTCACATAGAATCTACTTTAATAATGCAGTACATTCGAAGA
261 CCATTTGTTATTTATTTCTGAATATTCACATAGAATCTACTTTAATAATGCAGTACATTCGAAGA
19487668 ACATCATAGCTTGATATTTGATATCTTGTGGGAAATGGTTGTTAGCTCAAATATAGAATTGAAGA
326 ACATCATAGCTTGATATTTGATATCTTGTGGGAAATGGTTGTTAGCTCAAATATAGAATTGAAGA
19487733 TTGGTGCTGCCAATATACTGAAAGTCATTGTATGTTCTCTTTCCTTTGAAACAAAATTTATCTTG
391 TTGGTGCTGCCAATATACTGAAAGTCATTGTATGTTCTCTTTCCTTTGAAACAAAATTTATCTTG
*
19487798 CTACACCCGACAATCAGATATTTATACATTTTAACAGGTGACATACGTTGATGCAAAAGTTGCCT
456 CTACACCCGACAATAAGATATTTATACATTTTAACAGGTGACATACGTTGATGCAAAAGTTGCCT
19487863 CTACA
521 CTACA
19487868 CATGTTCTGC
1 CATGTTCTGC
19487878 CTGCCTTGAT
Statistics
Matches: 532, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
523 7 0.01
525 525 0.99
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (525 bp):
CATGTTCTGCGTGATTGTTGCTTGGTTGCAGGTCTAAAACCGAGAACAGCTGTGGCTGAGAGACT
TGCTGTTCTAGGTATCCTGCCACTTCTCTTAGCGGGTGTTCTTGGATCTCCTGGTAAGCGTGAAC
AGTTAGCAGACTACTTGAGAAAGCTATTAGTTGAAGGTGCCATGAAAGAGAATCAGTCTATAACA
CACAACAATGATATTGTTAATGCTGTCCGCTTCCTTTGGTTTGTAATTAAAAACTTCAGTCCTAA
CCATTTGTTATTTATTTCTGAATATTCACATAGAATCTACTTTAATAATGCAGTACATTCGAAGA
ACATCATAGCTTGATATTTGATATCTTGTGGGAAATGGTTGTTAGCTCAAATATAGAATTGAAGA
TTGGTGCTGCCAATATACTGAAAGTCATTGTATGTTCTCTTTCCTTTGAAACAAAATTTATCTTG
CTACACCCGACAATAAGATATTTATACATTTTAACAGGTGACATACGTTGATGCAAAAGTTGCCT
CTACA
Found at i:19494653 original size:19 final size:20
Alignment explanation
Indices: 19494616--19494659 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
19494606 TATTCGTTAG
* *
19494616 ATTTTTTAAAATGTTTAT-A
1 ATTTTTTAAAATATATATAA
*
19494635 ATTTTTTAATATATATATAA
1 ATTTTTTAAAATATATATAA
19494655 ATTTT
1 ATTTT
19494660 GGGATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTTTAAAATATATATAA
Found at i:19494687 original size:20 final size:20
Alignment explanation
Indices: 19494664--19494709 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
19494654 AATTTTGGGA
19494664 TTTTTATAAA-TATTTTAAAT
1 TTTTTA-AAATTATTTTAAAT
*
19494684 TTTTTAAAATTATTTTGAAT
1 TTTTTAAAATTATTTTAAAT
19494704 TATTTT
1 T-TTTT
19494710 GGAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTAAAATTATTTTAAAT
Found at i:19495554 original size:32 final size:32
Alignment explanation
Indices: 19495518--19495597 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
19495508 CGCGTGGTTC
*
19495518 TGTGAAATGATAATAAA-TATCAACTTTC-ATTT
1 TGTGAAATGATAACAAATTA-CAAC-TTCAATTT
*
19495550 TGTGAAATGGTAACAAATTACAACTTCAATTT
1 TGTGAAATGATAACAAATTACAACTTCAATTT
*
19495582 TGTTAAATGATAACAA
1 TGTGAAATGATAACAA
19495598 TATTCCTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.07
32 37 0.88
33 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (32 bp):
TGTGAAATGATAACAAATTACAACTTCAATTT
Found at i:19498801 original size:22 final size:22
Alignment explanation
Indices: 19498773--19498816 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19498763 ATTTCCTAAA
*
19498773 AATATTTTCCGCAAAAGCTGTT
1 AATATTTTCCGCAAAAACTGTT
19498795 AATATTTTCCGCAAAAACTGTT
1 AATATTTTCCGCAAAAACTGTT
19498817 TTTACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
AATATTTTCCGCAAAAACTGTT
Found at i:19498846 original size:15 final size:15
Alignment explanation
Indices: 19498826--19498855 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19498816 TTTTACATAT
19498826 ATTAATAAATTTATA
1 ATTAATAAATTTATA
19498841 ATTAATAAATTTATA
1 ATTAATAAATTTATA
19498856 TTTTAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATAAATTTATA
Found at i:19502197 original size:20 final size:20
Alignment explanation
Indices: 19502160--19502198 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19502150 ATTAATGAAA
**
19502160 AAAACTTTCGTATGGAAATT
1 AAAACTTTCGTAAAGAAATT
*
19502180 AAAACTTTTGTAAAGAAAT
1 AAAACTTTCGTAAAGAAAT
19502199 AATTTAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (20 bp):
AAAACTTTCGTAAAGAAATT
Found at i:19507586 original size:5 final size:5
Alignment explanation
Indices: 19507576--19507601 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19507566 TGAGCATTCG
19507576 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
19507602 ACTTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:19517455 original size:28 final size:27
Alignment explanation
Indices: 19517415--19517467 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
19517405 AAGTAGAAAA
*
19517415 GGGTATTGCCATTTAGGTTTTTTTTTTT
1 GGGTATTGCCATTTA-GTTTATTTTTTT
19517443 GGGTATTGCCATTTAGTTTATTTTT
1 GGGTATTGCCATTTAGTTTATTTTT
19517468 CCTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.13, C:0.08, G:0.21, T:0.58
Consensus pattern (27 bp):
GGGTATTGCCATTTAGTTTATTTTTTT
Found at i:19520909 original size:20 final size:20
Alignment explanation
Indices: 19520881--19520918 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19520871 GTGAGATCGC
*
19520881 TTACTCTTAATTTTTAAAGG
1 TTACACTTAATTTTTAAAGG
19520901 TTACACTTAATTTTTAAA
1 TTACACTTAATTTTTAAA
19520919 AATTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (20 bp):
TTACACTTAATTTTTAAAGG
Found at i:19521093 original size:53 final size:52
Alignment explanation
Indices: 19521036--19521159 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 52
19521026 CATTATAAAC
* ** *
19521036 TCTTATACAAATATTATTGTTATAAAAAAAGTCTAATAGAAAAAGAAAGACAA
1 TCTTATACAAATA-TACTGACACAAAAAAAGTCTAATAGAAAAAGAAAGACAA
* *
19521089 TC-T-TACACATATACTGACACATAAAAAGTCTAATAGAAAAAGAAAGACAA
1 TCTTATACAAATATACTGACACAAAAAAAGTCTAATAGAAAAAGAAAGACAA
*
19521139 TC-T-TACACATATACTGACACA
1 TCTTATACAAATATACTGACACA
19521160 TAATATAACA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 55 0.85
51 7 0.11
52 1 0.02
53 2 0.03
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.25
Consensus pattern (52 bp):
TCTTATACAAATATACTGACACAAAAAAAGTCTAATAGAAAAAGAAAGACAA
Found at i:19521117 original size:50 final size:50
Alignment explanation
Indices: 19521061--19521162 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
19521051 ATTGTTATAA
19521061 AAAAAGTCTAATAGAAAAAGAAAGACAATCTTACACATATACTGACACAT
1 AAAAAGTCTAATAGAAAAAGAAAGACAATCTTACACATATACTGACACAT
19521111 AAAAAGTCTAATAGAAAAAGAAAGACAATCTTACACATATACTGACACAT
1 AAAAAGTCTAATAGAAAAAGAAAGACAATCTTACACATATACTGACACAT
19521161 AA
1 AA
19521163 TATAACAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.20
Consensus pattern (50 bp):
AAAAAGTCTAATAGAAAAAGAAAGACAATCTTACACATATACTGACACAT
Found at i:19522132 original size:14 final size:14
Alignment explanation
Indices: 19522104--19522141 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
19522094 TGCCAAAAAT
19522104 AATAAAAG-A-AAG
1 AATAAAAGAACAAG
19522116 AATAAAAGAACAAG
1 AATAAAAGAACAAG
19522130 AATAAAAGAACA
1 AATAAAAGAACA
19522142 CAAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.33
13 1 0.04
14 15 0.62
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (14 bp):
AATAAAAGAACAAG
Found at i:19522241 original size:4 final size:4
Alignment explanation
Indices: 19522232--19522257 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19522222 ATAAAGAAGT
19522232 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
19522258 CAATTGGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:19524241 original size:6 final size:6
Alignment explanation
Indices: 19524227--19524272 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
19524217 TTCTCATCAT
*
19524227 CTCTTC CTCTGC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCT
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCT
19524273 GTTTTGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (6 bp):
CTCTTC
Found at i:19525680 original size:15 final size:16
Alignment explanation
Indices: 19525657--19525691 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19525647 AATTCTTTAA
*
19525657 ATTTATAAAAAAATAT
1 ATTTATAAAAAAAAAT
19525673 ATTT-TAAAAAAAAAT
1 ATTTATAAAAAAAAAT
19525688 ATTT
1 ATTT
19525692 CATTGAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTATAAAAAAAAAT
Found at i:19531655 original size:27 final size:27
Alignment explanation
Indices: 19531615--19531675 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
19531605 TAAGGGTGTA
* *
19531615 AGATCGGGATCTGATGTGGTGGATATT
1 AGATCGGGAACTGAAGTGGTGGATATT
19531642 AGATCGGGAACTGAAGTGGTGGATATT
1 AGATCGGGAACTGAAGTGGTGGATATT
*
19531669 AAATCGG
1 AGATCGG
19531676 ACGATGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (27 bp):
AGATCGGGAACTGAAGTGGTGGATATT
Found at i:19532120 original size:10 final size:12
Alignment explanation
Indices: 19532089--19532118 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19532079 TGATTAATAT
19532089 AAAAAAAATTAG
1 AAAAAAAATTAG
19532101 AAAAAAAATT-G
1 AAAAAAAATTAG
19532112 AAAAAAA
1 AAAAAAA
19532119 TTACCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTAG
Found at i:19532994 original size:11 final size:10
Alignment explanation
Indices: 19532969--19533033 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 10
19532959 TTAATCCTAG
19532969 TTTTA-ATAA
1 TTTTATATAA
19532978 TTTTATATAA
1 TTTTATATAA
*
19532988 CTTT-TATAA
1 TTTTATATAA
19532997 TTTT-TAATAA
1 TTTTAT-ATAA
*
19533007 TTTTTATTTAA
1 -TTTTATATAA
*
19533018 TTTTA-AAAA
1 TTTTATATAA
19533027 TTTTATA
1 TTTTATA
19533034 ATGTTTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 21 0.46
10 17 0.37
11 7 0.15
12 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTATATAA
Found at i:19532995 original size:9 final size:9
Alignment explanation
Indices: 19532969--19533040 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
19532959 TTAATCCTAG
*
19532969 TTTTAATAA
1 TTTTTATAA
19532978 TTTTATATAA
1 TTTT-TATAA
*
19532988 CTTTTATAA
1 TTTTTATAA
19532997 TTTTTAATAA
1 TTTTT-ATAA
19533007 TTTTTATTTAA
1 TTTTTA--TAA
*
19533018 -TTTTAAAA
1 TTTTTATAA
*
19533026 ATTTTATAA
1 TTTTTATAA
19533035 TGTTTT
1 T-TTTT
19533041 TATAGTCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 2 0.04
9 21 0.41
10 25 0.49
11 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:19533001 original size:29 final size:28
Alignment explanation
Indices: 19532969--19533044 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
19532959 TTAATCCTAG
* *
19532969 TTTTAATAATTTTATATAACTTTTATAAT
1 TTTTAATAATTTTATATAA-TTTTAAAAA
*
19532998 TTTTAATAATTTTTATTTAATTTTAAAAA
1 TTTTAATAA-TTTTATATAATTTTAAAAA
*
19533027 TTTT-ATAATGTTTTTATA
1 TTTTAATAAT-TTTATATA
19533045 GTCCTTTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 10 0.25
29 20 0.50
30 9 0.22
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTTAATAATTTTATATAATTTTAAAAA
Found at i:19533040 original size:19 final size:19
Alignment explanation
Indices: 19532969--19533040 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
19532959 TTAATCCTAG
*
19532969 TTTTAATAA-TTTTATATAAC
1 TTTT-ATAATTTTTA-ATAAA
*
19532989 TTTTATAATTTTTAATAAT
1 TTTTATAATTTTTAATAAA
19533008 TTTTATTTAA-TTTTAA-AAA
1 TTTTA--TAATTTTTAATAAA
19533027 TTTTATAATGTTTT
1 TTTTATAAT-TTTT
19533041 TATAGTCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.07
19 24 0.53
20 15 0.33
21 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAA
Found at i:19533116 original size:9 final size:10
Alignment explanation
Indices: 19533105--19533156 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
19533095 TTTTATTCTT
19533105 TTTTATAAT-
1 TTTTATAATA
*
19533114 TTTTATAATC
1 TTTTATAATA
19533124 TTTTCATAATA
1 TTTT-ATAATA
*
19533135 TATTAATAATA
1 T-TTTATAATA
19533146 TTTTATAATA
1 TTTTATAATA
19533156 T
1 T
19533157 ACAACAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 9 0.24
10 13 0.35
11 13 0.35
12 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTATAATA
Found at i:19533155 original size:21 final size:21
Alignment explanation
Indices: 19533105--19533157 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
19533095 TTTTATTCTT
* *
19533105 TTTTATAAT-T-TTTATAATC
1 TTTTATAATATATTAATAATA
19533124 TTTTCATAATATATTAATAATA
1 TTTT-ATAATATATTAATAATA
19533146 TTTTATAATATA
1 TTTTATAATATA
19533158 CAACAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 5 0.17
21 9 0.31
22 11 0.38
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAATATATTAATAATA
Found at i:19535566 original size:3 final size:3
Alignment explanation
Indices: 19535558--19535602 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19535548 TAGTCCTCAT
19535558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19535603 CTACTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19537629 original size:27 final size:27
Alignment explanation
Indices: 19537599--19537652 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19537589 TATCACTTTC
19537599 ATATAACATACTTGATATATCACACAT
1 ATATAACATACTTGATATATCACACAT
19537626 ATATAACATACTTGATATATCACACAT
1 ATATAACATACTTGATATATCACACAT
19537653 TCACTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (27 bp):
ATATAACATACTTGATATATCACACAT
Found at i:19537645 original size:16 final size:16
Alignment explanation
Indices: 19537599--19537645 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
19537589 TATCACTTTC
19537599 ATATAACATACTTGAT
1 ATATAACATACTTGAT
*
19537615 ATAT--CACAC---AT
1 ATATAACATACTTGAT
19537626 ATATAACATACTTGAT
1 ATATAACATACTTGAT
19537642 ATAT
1 ATAT
19537646 CACACATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
11 6 0.25
13 4 0.17
14 4 0.17
16 10 0.42
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (16 bp):
ATATAACATACTTGAT
Found at i:19538468 original size:22 final size:21
Alignment explanation
Indices: 19538440--19538486 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
19538430 TTTTCCTCTT
19538440 TTTTC-CCCTTT-TTTCTTTCC
1 TTTTCTCCCTTTATTT-TTTCC
19538460 TTTTCTCCCTTTATTTTTTCC
1 TTTTCTCCCTTTATTTTTTCC
*
19538481 CTTTCT
1 TTTTCT
19538487 TTCCAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTCTCCCTTTATTTTTTCC
Found at i:19539389 original size:15 final size:15
Alignment explanation
Indices: 19539370--19539399 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19539360 AAACAACACT
19539370 AAAAAGCAAACTAAAC
1 AAAAAG-AAACTAAAC
19539386 AAAAAGAAACTAAA
1 AAAAAGAAACTAAA
19539400 GTAGAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.13, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAGAAACTAAAC
Found at i:19539837 original size:23 final size:22
Alignment explanation
Indices: 19539797--19539840 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
19539787 TTTATGTGTC
**
19539797 TAAATTATTATTTGTTTATTTA
1 TAAATTATTATTAATTTATTTA
19539819 TAAATTACTTATTAATTTATTT
1 TAAATTA-TTATTAATTTATTT
19539841 TATGTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TAAATTATTATTAATTTATTTA
Found at i:19540988 original size:31 final size:31
Alignment explanation
Indices: 19540895--19540990 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
19540885 GGCAAATTAC
*
19540895 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
*
19540926 AAGAGTAATTGAATCTTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
19540958 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
19540989 AA
1 AA
19540991 ATTATCTAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:19546841 original size:31 final size:31
Alignment explanation
Indices: 19546748--19546843 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
19546738 GGCAAATTAC
*
19546748 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
19546779 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
19546811 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
19546842 AA
1 AA
19546844 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:19547265 original size:3 final size:3
Alignment explanation
Indices: 19547257--19547281 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19547247 GCATGTATTG
19547257 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
19547282 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19548806 original size:17 final size:16
Alignment explanation
Indices: 19548786--19548861 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 16
19548776 CTTTTGAACT
*
19548786 AAATTTTTATTTGAAAA
1 AAATATTTATTT-AAAA
19548803 AAATATTTATCTTTAAAA
1 AAATATTTA--TTTAAAA
*
19548821 AAGTAATTTATTTAAAA
1 AAAT-ATTTATTTAAAA
* *
19548838 ATATTTTTTATTCTAAAA
1 A-AATATTTATT-TAAAA
19548856 ATAATA
1 A-AATA
19548862 CTAAACAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
17 22 0.46
18 18 0.38
19 8 0.17
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
AAATATTTATTTAAAA
Found at i:19551107 original size:21 final size:20
Alignment explanation
Indices: 19551064--19551108 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19551054 ATGTGCCAAG
* *
19551064 ATGCACCTCGTGTGCTAGAT
1 ATGCACCTCGTGCGCCAGAT
*
19551084 ATGCACTTCGTGCGCCAGGAT
1 ATGCACCTCGTGCGCCA-GAT
19551105 ATGC
1 ATGC
19551109 TTTGTGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGCACCTCGTGCGCCAGAT
Found at i:19552566 original size:5 final size:5
Alignment explanation
Indices: 19552550--19552580 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
19552540 TTGGGAAATT
19552550 ATTTA A-TTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
19552581 ATGTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:19560955 original size:9 final size:9
Alignment explanation
Indices: 19560941--19560980 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
19560931 TTTGGTTAAA
19560941 AATTAACCG
1 AATTAACCG
*
19560950 AATTAACCT
1 AATTAACCG
*
19560959 AATTACCCG
1 AATTAACCG
19560968 AATTAACCG
1 AATTAACCG
19560977 AATT
1 AATT
19560981 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:19561134 original size:18 final size:18
Alignment explanation
Indices: 19561111--19561145 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19561101 GATTGAGTTA
* *
19561111 GGTTGGGTATTTGGGTTG
1 GGTTGGATACTTGGGTTG
19561129 GGTTGGATACTTGGGTT
1 GGTTGGATACTTGGGTT
19561146 TGGATCGGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.46, T:0.43
Consensus pattern (18 bp):
GGTTGGATACTTGGGTTG
Found at i:19569020 original size:15 final size:16
Alignment explanation
Indices: 19569000--19569034 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19568990 AGTTTCAATG
*
19569000 AAATATTTTTTTTTA-
1 AAATATATTTTTTTAT
19569015 AAATATATTTTTTTAT
1 AAATATATTTTTTTAT
19569031 AAAT
1 AAAT
19569035 TTAAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AAATATATTTTTTTAT
Found at i:19577281 original size:23 final size:23
Alignment explanation
Indices: 19577255--19577350 Score: 138
Period size: 23 Copynumber: 4.2 Consensus size: 23
19577245 AGTGCCACAT
19577255 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
19577278 TGATATGTAGCCGTAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
*
19577301 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
* * * *
19577324 TAAAACGTAGCAGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
19577347 TGAT
1 TGAT
19577351 CAATAACACT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:19577674 original size:17 final size:18
Alignment explanation
Indices: 19577652--19577692 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
19577642 TAATTTTCCT
19577652 TTCACAT-TC-AATATTAA
1 TTCACATATCAAATA-TAA
19577669 TTCACATATCAAATATAA
1 TTCACATATCAAATATAA
19577687 TTCACA
1 TTCACA
19577693 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
TTCACATATCAAATATAA
Found at i:19581031 original size:21 final size:20
Alignment explanation
Indices: 19580989--19581033 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
19580979 AATACATACA
*
19580989 TTTATGGGCCTTAAATCAAG
1 TTTATGGGCCTTAAATAAAG
19581009 TTTATGTGGCCTTAAA-AATAG
1 TTTATG-GGCCTTAAATAA-AG
19581030 TTTA
1 TTTA
19581034 GGAACAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (20 bp):
TTTATGGGCCTTAAATAAAG
Found at i:19587501 original size:47 final size:47
Alignment explanation
Indices: 19587421--19587816 Score: 595
Period size: 47 Copynumber: 8.4 Consensus size: 47
19587411 TCCTTTGGGA
*
19587421 CTTATCACAGT-TATACA-TTTC-CACTTCCATCACATTGACCATTCGGC
1 CTTATCACA-TATATACACTTTCACA-TT-CATCACATTGGCCATTCGGC
* *
19587468 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
** *
19587515 CTTATCACACGTACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
19587562 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
19587611 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
19587658 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
19587705 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
19587752 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
19587799 CTTATCACATATACACAC
1 CTTATCACATATATACAC
19587817 CTTGTACATC
Statistics
Matches: 325, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 275 0.85
48 5 0.02
49 43 0.13
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:19587667 original size:22 final size:22
Alignment explanation
Indices: 19587639--19587761 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
19587629 TTTCACATTC
19587639 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
19587661 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
19587685 CATCACATTGGCCACTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
** * * *
19587708 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
19587732 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
19587755 ATCACAT
1 ATCACAT
19587762 ATATACACTT
Statistics
Matches: 69, Mismatches: 22, Indels: 20
0.62 0.20 0.18
Matches are distributed among these distances:
22 28 0.41
23 10 0.14
24 10 0.14
25 21 0.30
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:19587690 original size:143 final size:142
Alignment explanation
Indices: 19587421--19587816 Score: 606
Period size: 143 Copynumber: 2.8 Consensus size: 142
19587411 TCCTTTGGGA
* * *
19587421 CTTATCACAGT-TATACA-TTTC-CACTTCCATCACATTGACCATTCGGCCTTATCTCATATATG
1 CTTATCACA-TATATACACTTTCACA-TT-CATCACATTGGCCATTCGGCCTTATCACATATATA
**
19587483 CA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACGTACACA-TGTTCACATTCATC
63 CACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTGTTCACATTCATC
*
19587546 ACATTGGCCATTCGGC
127 ACATTGGCCACTCGGC
*
19587562 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
19587627 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCAC
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTGTTCACATTCATCAC
19587691 ATTGGCCACTCGGC
129 ATTGGCCACTCGGC
19587705 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* *
19587770 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACAC
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACAC
19587817 CTTGTACATC
Statistics
Matches: 236, Mismatches: 12, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
141 108 0.46
142 1 0.00
143 117 0.50
144 8 0.03
145 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (142 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTGTTCACATTCATCACAT
TGGCCACTCGGC
Found at i:19587744 original size:190 final size:189
Alignment explanation
Indices: 19587421--19587816 Score: 615
Period size: 190 Copynumber: 2.1 Consensus size: 189
19587411 TCCTTTGGGA
* *
19587421 CTTATCACAGT-TATACA-TTTCCACTTCCATCACATTGACCATTCGGCCTTATCTCATATATGC
1 CTTATCACA-TATATACACTTTCCACTTCCATCACATTGACCATTCGGCCTTATCACATATATAC
* *
19587484 ATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACGTACACATGTTCACATTCATCACA
65 ATGTTCACATTCATCACATTGGCCACTCGGCCTTATCACACATACACATGTTCACATTCATCACA
*
19587549 TTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
130 TTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19587611 CTTATCACATATATACACTTT-CACATT-CATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATACACTTTCCAC-TTCCATCACATTGACCATTCGGCCTTATCACATATATAC
* *
19587674 ACT-TTCACATTCATCACATTGGCCACTCGGCCTTATCACATATATACACT-TTCACATTCATCA
65 A-TGTTCACATTCATCACATTGGCCACTCGGCCTTATCACACATACACA-TGTTCACATTCATCA
19587737 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
128 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19587799 CTTATCACATATACACAC
1 CTTATCACATATATACAC
19587817 CTTGTACATC
Statistics
Matches: 192, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
188 55 0.29
189 1 0.01
190 129 0.67
191 7 0.04
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (189 bp):
CTTATCACATATATACACTTTCCACTTCCATCACATTGACCATTCGGCCTTATCACATATATACA
TGTTCACATTCATCACATTGGCCACTCGGCCTTATCACACATACACATGTTCACATTCATCACAT
TGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19598804 original size:17 final size:16
Alignment explanation
Indices: 19598778--19598811 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19598768 TTCTCTGCTA
19598778 TAATTATAAAAACACC
1 TAATTATAAAAACACC
*
19598794 TAATATATAAACACACC
1 TAAT-TATAAAAACACC
19598811 T
1 T
19598812 TTCTTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (16 bp):
TAATTATAAAAACACC
Found at i:19599721 original size:29 final size:29
Alignment explanation
Indices: 19599677--19599754 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
19599667 TTAAGTTTTA
19599677 ATAAAAAAATATTAAAAAATTA-TAAAAGTC
1 ATAAAAAAATA-TAAAAAATTATTAAAA-TC
* **
19599707 ATAAAAGAATATAAAATTTTATTAAAATC
1 ATAAAAAAATATAAAAAATTATTAAAATC
19599736 ATAAAAAAAT-TAATAAAAT
1 ATAAAAAAATATAA-AAAAT
19599755 ACATAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.08
29 22 0.55
30 15 0.38
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (29 bp):
ATAAAAAAATATAAAAAATTATTAAAATC
Found at i:19599979 original size:19 final size:20
Alignment explanation
Indices: 19599943--19600000 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
19599933 ATACGATAAT
19599943 TTTTATAATTCTTTTACAAA
1 TTTTATAATTCTTTTACAAA
**
19599963 TTTTATAATTC-TTTACATC
1 TTTTATAATTCTTTTACAAA
19599982 TTTTATAATT-TTCTTACAA
1 TTTTATAATTCTT-TTACAA
19600001 CGTTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAATTCTTTTACAAA
Found at i:19606179 original size:16 final size:15
Alignment explanation
Indices: 19606154--19606197 Score: 65
Period size: 13 Copynumber: 3.0 Consensus size: 15
19606144 AATACTTAAG
19606154 TATATAATATAATAA
1 TATATAATATAATAA
19606169 TATATTAATATAAT-A
1 TATA-TAATATAATAA
19606184 -ATATAATATAATAA
1 TATATAATATAATAA
19606198 AACATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 5 0.19
16 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAATATAATAA
Found at i:19606197 original size:8 final size:8
Alignment explanation
Indices: 19606157--19606191 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
19606147 ACTTAAGTAT
19606157 ATAATATA
1 ATAATATA
19606165 ATAATATA
1 ATAATATA
*
19606173 TTAATATA
1 ATAATATA
19606181 ATAATATA
1 ATAATATA
19606189 ATA
1 ATA
19606192 TAATAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATATA
Found at i:19606212 original size:21 final size:22
Alignment explanation
Indices: 19606178--19606231 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
19606168 ATATATTAAT
* *
19606178 ATAATAATATAATATAATAAAAC
1 ATAAGAATA-AATAAAATAAAAC
19606201 ATAA-AATAAATAAAATAAAAC
1 ATAAGAATAAATAAAATAAAAC
*
19606222 AAAAGAATAA
1 ATAAGAATAA
19606232 GAATAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 9 0.32
23 4 0.14
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAAGAATAAATAAAATAAAAC
Found at i:19606212 original size:29 final size:29
Alignment explanation
Indices: 19606155--19606218 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
19606145 ATACTTAAGT
* * *
19606155 ATATAATATAATAATATATTAATATAATA
1 ATATAATATAATAAAACATAAATATAATA
19606184 ATATAATATAATAAAACATAAA-ATAAATA
1 ATATAATATAATAAAACATAAATAT-AATA
*
19606213 AAATAA
1 ATATAA
19606219 AACAAAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (29 bp):
ATATAATATAATAAAACATAAATATAATA
Found at i:19606254 original size:11 final size:11
Alignment explanation
Indices: 19606217--19606285 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
19606207 TAAATAAAAT
*
19606217 AAAACAAAAGA
1 AAAAGAAAAGA
* *
19606228 ATAAGAATAGA
1 AAAAGAAAAGA
* *
19606239 GAAAGAAATGAA
1 AAAAGAAAAG-A
19606251 AAAGAGAGAAAGA
1 AAA-AGA-AAAGA
19606264 AAGAAGAAAAGA
1 AA-AAGAAAAGA
19606276 AAAAGAAAAG
1 AAAAGAAAAG
19606286 GGAAATTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 22 0.49
12 10 0.22
13 9 0.20
14 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:19610541 original size:25 final size:25
Alignment explanation
Indices: 19610453--19610540 Score: 149
Period size: 25 Copynumber: 3.5 Consensus size: 25
19610443 GAAGCTCATA
*
19610453 CGAGCCAATGTCGAGAAGGTTCAAG
1 CGAGCCAATATCGAGAAGGTTCAAG
19610478 CGAGCCAATATCGAGAAGGTTCAAG
1 CGAGCCAATATCGAGAAGGTTCAAG
*
19610503 CGAGCCAATATCGGGAAGGTTCAAG
1 CGAGCCAATATCGAGAAGGTTCAAG
*
19610528 CGAGCTAATATCG
1 CGAGCCAATATCG
19610541 GAAAGCTCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (25 bp):
CGAGCCAATATCGAGAAGGTTCAAG
Found at i:19610558 original size:50 final size:50
Alignment explanation
Indices: 19610444--19610558 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 50
19610434 CATTAATAGG
* * *
19610444 AAGCTCATACGAGCCAATGTCGAGAAGGTTCAAGCGAGCCAATATCGAGA
1 AAGCTCAAAAGAGCCAATATCGAGAAGGTTCAAGCGAGCCAATATCGAGA
* * ** * *
19610494 AGGTTCAAGCGAGCCAATATCGGGAAGGTTCAAGCGAGCTAATATCG-GA
1 AAGCTCAAAAGAGCCAATATCGAGAAGGTTCAAGCGAGCCAATATCGAGA
19610543 AAGCTCACAAAGAGCC
1 AAGCTCA-AAAGAGCC
19610559 TTTAATTGAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 7 0.13
50 46 0.87
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.16
Consensus pattern (50 bp):
AAGCTCAAAAGAGCCAATATCGAGAAGGTTCAAGCGAGCCAATATCGAGA
Found at i:19610703 original size:25 final size:25
Alignment explanation
Indices: 19610660--19610730 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 25
19610650 GGATGCTCCA
19610660 AAGAACTAT-TAACGGGAAGCTCAC
1 AAGAACTATATAACGGGAAGCTCAC
* *
19610684 AAGAACCATATAACGGGAAGCTCAT
1 AAGAACTATATAACGGGAAGCTCAC
* *
19610709 AAGAGCTA-ATAACGGGACGCTC
1 AAGAACTATATAACGGGAAGCTC
19610731 TTTCGAGCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCAC
Found at i:19620330 original size:62 final size:62
Alignment explanation
Indices: 19620253--19620435 Score: 314
Period size: 62 Copynumber: 3.0 Consensus size: 62
19620243 GTACCTAATC
* *
19620253 TATATTACAAAGTTTGTTTCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAAAATT
1 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAAATT
*
19620315 TATATTATAAAGTTTGTTCCAA-TTTTAATTATTGTAATGTATTTAATTTATATAACAAAATT
1 TATATTACAAAGTTTGTTCCAATTTTTAA-TATTGTAATGTATTTAATTTATATAACAAAATT
*
19620377 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAAA
1 TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAA
19620436 GTTTGTTCCA
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
61 6 0.05
62 102 0.89
63 6 0.05
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (62 bp):
TATATTACAAAGTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATAACAAAATT
Found at i:19620400 original size:24 final size:25
Alignment explanation
Indices: 19620375--19620451 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 25
19620365 TATAACAAAA
19620375 TTTATATTACAAAGTTTGTTCCAATT
1 TTTATATTACAAAGTTTGTTCCAA-T
** * *
19620401 TTTAATATTGTAATGTAT-TT--AA-
1 TTT-ATATTACAAAGTTTGTTCCAAT
*
19620423 TTTATATTACAAAGTTTGTTCCAAG
1 TTTATATTACAAAGTTTGTTCCAAT
19620448 TTTA
1 TTTA
19620452 GTGTTGTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
24 4 0.11
25 4 0.11
26 5 0.13
27 10 0.26
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TTTATATTACAAAGTTTGTTCCAAT
Found at i:19621263 original size:12 final size:13
Alignment explanation
Indices: 19621227--19621264 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
19621217 AAATATTTGA
19621227 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
19621240 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
19621254 CTTG-TCTTAAT
1 CTTGTTCTTAAT
19621265 ATTCTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:19626524 original size:46 final size:46
Alignment explanation
Indices: 19626459--19626608 Score: 158
Period size: 46 Copynumber: 3.1 Consensus size: 46
19626449 ACACACTGTA
**
19626459 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGATATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
19626505 GCCATATCCCAGATGTGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGATATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
19626558 GCCATAGCCCAGATATGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCACATTGAT
19626604 GCCAT
1 GCCAT
19626609 GGTCCAACCA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
46 30 0.36
47 8 0.10
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 27 0.32
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (46 bp):
GCCATAGCCCAGATATGGTCTTACACGAATCACATATCACATTGAT
Found at i:19632251 original size:14 final size:14
Alignment explanation
Indices: 19632232--19632266 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
19632222 CAAATTACAT
19632232 GTTAGAATAGTATC
1 GTTAGAATAGTATC
19632246 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
19632260 ATTAGAA
1 GTTAGAA
19632267 AAAAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:19633747 original size:31 final size:31
Alignment explanation
Indices: 19633688--19633747 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
19633678 ATTAAATTCG
*
19633688 AATTAAATCAACAATAATAAATACAAAAACA
1 AATTAAATCAACAATAATAAATAAAAAAACA
* * **
19633719 AATTAAATTAACATTAATTTATAAAAAAA
1 AATTAAATCAACAATAATAAATAAAAAAA
19633748 TACATTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (31 bp):
AATTAAATCAACAATAATAAATAAAAAAACA
Done.