Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 132 of 175
Found at i:41070540 original size:12 final size:12
Alignment explanation
Indices: 41070523--41070548 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41070513 TCTCACACCA
41070523 CTCAATCTCATC
1 CTCAATCTCATC
41070535 CTCAATCTCATC
1 CTCAATCTCATC
41070547 CT
1 CT
41070549 GCCGTGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
CTCAATCTCATC
Found at i:41070618 original size:53 final size:52
Alignment explanation
Indices: 41070516--41070640 Score: 202
Period size: 53 Copynumber: 2.4 Consensus size: 52
41070506 AGACTCTTCT
*
41070516 CACACCACTCAATCTCAT-C-CTCAATCTCATCCTGCCGTGAAGTTGTTTCC
1 CACACCACTCAATCTCATCCTCTCAACCTCATCCTGCCGTGAAGTTGTTTCC
41070566 CACACCACTCAATCTCATCCTTCTCACACCTC-TCCTGCCGTGAAGTTGTTTCC
1 CACACCACTCAATCTCATCC-TCTCA-ACCTCATCCTGCCGTGAAGTTGTTTCC
41070619 CACACCACTCAATCTCATCCTC
1 CACACCACTCAATCTCATCCTC
41070641 GTGTCTGAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
50 18 0.26
51 1 0.01
52 2 0.03
53 45 0.64
54 4 0.06
ACGTcount: A:0.22, C:0.42, G:0.08, T:0.29
Consensus pattern (52 bp):
CACACCACTCAATCTCATCCTCTCAACCTCATCCTGCCGTGAAGTTGTTTCC
Found at i:41075381 original size:19 final size:20
Alignment explanation
Indices: 41075357--41075394 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41075347 ATGTGAATAG
41075357 TAAAATATACATA-AAAAAT
1 TAAAATATACATATAAAAAT
*
41075376 TAAAATATATATATAAAAA
1 TAAAATATACATATAAAAA
41075395 ACCGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAATATACATATAAAAAT
Found at i:41079829 original size:9 final size:9
Alignment explanation
Indices: 41079815--41079851 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41079805 TATAGTTTGG
41079815 TATTCGAAT
1 TATTCGAAT
41079824 TATTCGAAT
1 TATTCGAAT
*
41079833 TATTCGAGT
1 TATTCGAAT
41079842 TATTCGAAT
1 TATTCGAAT
41079851 T
1 T
41079852 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41079922 original size:9 final size:9
Alignment explanation
Indices: 41079905--41079935 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41079895 TCGAGTTTAT
41079905 TCGAATAAC
1 TCGAATAAC
*
41079914 TCGATTAAC
1 TCGAATAAC
41079923 TCGAATAAC
1 TCGAATAAC
41079932 TCGA
1 TCGA
41079936 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:41102232 original size:12 final size:12
Alignment explanation
Indices: 41102207--41102245 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41102197 ACTCGCTTCT
* *
41102207 TTACTTACTCAC
1 TTACTTGCTTAC
*
41102219 TTACTTGTTTAC
1 TTACTTGCTTAC
41102231 TTACTTGCTTAC
1 TTACTTGCTTAC
41102243 TTA
1 TTA
41102246 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:41102569 original size:50 final size:49
Alignment explanation
Indices: 41102445--41102630 Score: 180
Period size: 50 Copynumber: 3.8 Consensus size: 49
41102435 TAATAATACA
* * * * * *
41102445 TGCCAAAGCTATGTCCCAGACATAGTCTTATATGGGATGTTTTCTGTA-C-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTC-ATACCG
* * *
41102494 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATACCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATACC-G
* ** **
41102544 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT-CTTCG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATAC--CG
41102594 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41102631 TCTCTTTACC
Statistics
Matches: 112, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
47 2 0.02
48 6 0.05
49 31 0.28
50 72 0.64
51 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATACCG
Found at i:41111517 original size:24 final size:24
Alignment explanation
Indices: 41111486--41111547 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
41111476 AAAAGGAGAG
*
41111486 GGAAAGGAGAGGAAAGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAAA
41111510 GGAAAGGAGAAGAAAGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAGAAAA
*
41111534 AGAAAGGAGAAGAA
1 GGAAAGGAGAAGAA
41111548 GAAGAGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
GGAAAGGAGAAGAAAGAAAGAAAA
Found at i:41111558 original size:13 final size:13
Alignment explanation
Indices: 41111511--41111550 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
41111501 GAAAGAAAAG
41111511 GAAAGGAGAAGAAA
1 GAAAGGAGAAG-AA
41111525 GAAA-GA-AA-AA
1 GAAAGGAGAAGAA
41111535 GAAAGGAGAAGAA
1 GAAAGGAGAAGAA
41111548 GAA
1 GAA
41111551 GAGGGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.26
11 2 0.09
12 4 0.17
13 7 0.30
14 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAAGGAGAAGAA
Found at i:41111907 original size:39 final size:40
Alignment explanation
Indices: 41111786--41111921 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
41111776 GTTTGGACAA
* **
41111786 AAAATGCCGCTAAAAATCAAGCATTAGCGGCGC-TTTACAC
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTA-GG
* * *
41111826 AAAACGCCGCTAAAGATCAAGAATTAGCGGCACTTTTAGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAGG
* * *
41111866 AAAGCGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAGG
*
41111905 AAAAACGCCGCAAAAAA
1 -AAAACGCCGCTAAAAA
41111922 ACCTAAGCCC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 18 0.22
40 58 0.73
41 4 0.05
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTAGG
Found at i:41112013 original size:41 final size:41
Alignment explanation
Indices: 41111951--41112149 Score: 290
Period size: 41 Copynumber: 4.9 Consensus size: 41
41111941 TTTTGACCTA
* *
41111951 TCAGGTCTTTAGCGGCGTTTTTAAAAAAGCACCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
* * *
41111992 TCAGATCTTTAGCGTCGTTTTTCAAAAAGTGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
* *
41112033 TCAGATCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
* *
41112074 TTAGATCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
* * *
41112115 TCAAATCTTTAGCGGCGTTTTTGAGAAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGC
41112150 AAAAATATTT
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 142 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC
Found at i:41112299 original size:26 final size:26
Alignment explanation
Indices: 41112242--41112300 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
41112232 TTAAATGGAT
* *
41112242 AAATTTGAAATAATGATACATAGAAA
1 AAATTTGAAATAATAAAACATAGAAA
*
41112268 TAATTTGAAATAA-AAAACATAGAAA
1 AAATTTGAAATAATAAAACATAGAAA
41112293 AATATTTG
1 AA-ATTTG
41112301 TTAAAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (26 bp):
AAATTTGAAATAATAAAACATAGAAA
Found at i:41112703 original size:62 final size:62
Alignment explanation
Indices: 41112651--41112767 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
41112641 AGGCTTTAGG
* *
41112651 GTTTAGATTAATTAGTGTGTTTT-AATTT-TTTATGAAATAAGGTTTAGGGGTTAGGGATTCAA
1 GTTTAGATTAATTAATGT-TTTTGAATTTATATATGAAATAAGGTTTAGGGGTTA-GGATTCAA
* *
41112713 GTTTAGATTAATTAATGTTTTTGAATTTATATATTAGATAAGGTTTAGGGGTTAG
1 GTTTAGATTAATTAATGTTTTTGAATTTATATATGAAATAAGGTTTAGGGGTTAG
41112768 TAGTTAGGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 4 0.08
62 23 0.47
63 22 0.45
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (62 bp):
GTTTAGATTAATTAATGTTTTTGAATTTATATATGAAATAAGGTTTAGGGGTTAGGATTCAA
Found at i:41112795 original size:20 final size:20
Alignment explanation
Indices: 41112757--41112800 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
41112747 TAGATAAGGT
41112757 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAG-AGTTAGGGG
41112778 TTAGGGGTTTAG-GTTAGGGG
1 TTAGGGG-TTAGAGTTAGGGG
41112798 TTA
1 TTA
41112801 AAAGTTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.36
Consensus pattern (20 bp):
TTAGGGGTTAGAGTTAGGGG
Found at i:41112815 original size:34 final size:34
Alignment explanation
Indices: 41112757--41112824 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
41112747 TAGATAAGGT
** * * *
41112757 TTAGGGGTTAGTAGTTAGGGGTTAGGGGTTTAGG
1 TTAGGGGTTAAAAGTTAAGAGTTAGGGATTTAGG
*
41112791 TTAGGGGTTAAAAGTTAAGAGTTAGTGATTTAGG
1 TTAGGGGTTAAAAGTTAAGAGTTAGGGATTTAGG
41112825 GTTTAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (34 bp):
TTAGGGGTTAAAAGTTAAGAGTTAGGGATTTAGG
Found at i:41112942 original size:14 final size:14
Alignment explanation
Indices: 41112923--41112969 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
41112913 GTAAAAGAGG
41112923 GGTTAGGGGTTAGA
1 GGTTAGGGGTTAGA
**
41112937 GGTTAGGAATTA-A
1 GGTTAGGGGTTAGA
*
41112950 GGGTTAGAGGTTAGA
1 -GGTTAGGGGTTAGA
41112965 GGTTA
1 GGTTA
41112970 AAGGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.30
Consensus pattern (14 bp):
GGTTAGGGGTTAGA
Found at i:41112970 original size:21 final size:20
Alignment explanation
Indices: 41112922--41112976 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
41112912 TGTAAAAGAG
*
41112922 GGGTTAGGGGTTAGAGGTTA
1 GGGTTAAGGGTTAGAGGTTA
*
41112942 GGAATTAAGGGTTAGAGGTTA
1 GG-GTTAAGGGTTAGAGGTTA
*
41112963 GAGGTTAAAGGTTA
1 G-GGTTAAGGGTTA
41112977 ATTGCTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (20 bp):
GGGTTAAGGGTTAGAGGTTA
Found at i:41116897 original size:9 final size:9
Alignment explanation
Indices: 41116865--41116907 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
41116855 GTGTCTGTCT
41116865 TTTTATTGC
1 TTTTATTGC
* *
41116874 TTTCA-CGC
1 TTTTATTGC
41116882 TTTTTATTGC
1 -TTTTATTGC
41116892 TTTTATTGC
1 TTTTATTGC
41116901 TTTTATT
1 TTTTATT
41116908 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.86
10 2 0.07
ACGTcount: A:0.12, C:0.14, G:0.09, T:0.65
Consensus pattern (9 bp):
TTTTATTGC
Found at i:41118764 original size:43 final size:43
Alignment explanation
Indices: 41118716--41118921 Score: 238
Period size: 43 Copynumber: 4.8 Consensus size: 43
41118706 AGGTTATGTT
* *
41118716 TTTAGCGGCGTTTGT-ATCTAAAGCGCCGCTAAAGATCACGATA
1 TTTAGCGGCGTTTGTGA-CTAAAGCGCCGCTAAAGGTCACGATC
*
41118759 TTTAGCGGCGTTTGTGGCTAAAGCGCCGCTAAAGGTCACGATC
1 TTTAGCGGCGTTTGTGACTAAAGCGCCGCTAAAGGTCACGATC
* ** *
41118802 TTTAGCGGTGTTTGTGA-TAAAAATGCCGCTAAAGGTCAAGATC
1 TTTAGCGGCGTTTGTGACT-AAAGCGCCGCTAAAGGTCACGATC
* ** * *
41118845 TTTAGCGGCGTTTGTGACAAAAGCGTTGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGACTAAAGCGCCGCTAAAGGTCACGATC
* *
41118888 TTTAGCGGCGTTTTTCACATAAA-CGCCGCTAAAG
1 TTTAGCGGCGTTTGTGAC-TAAAGCGCCGCTAAAG
41118922 TTAGCGGCGT
Statistics
Matches: 138, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 134 0.97
44 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGACTAAAGCGCCGCTAAAGGTCACGATC
Found at i:41118931 original size:33 final size:33
Alignment explanation
Indices: 41118889--41118965 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
41118879 GTCATGTTCT
41118889 TTAGCGGCGTTTTTCACATAAACGCCGCTAAAG
1 TTAGCGGCGTTTTTCACATAAACGCCGCTAAAG
41118922 TTAGCGGCGTTTTTCACATAAACGCCGCTAAAG
1 TTAGCGGCGTTTTTCACATAAACGCCGCTAAAG
41118955 TTAGCGGCGTT
1 TTAGCGGCGTT
41118966 GTCAATAGCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
TTAGCGGCGTTTTTCACATAAACGCCGCTAAAG
Found at i:41119656 original size:152 final size:152
Alignment explanation
Indices: 41119252--41119980 Score: 843
Period size: 152 Copynumber: 4.8 Consensus size: 152
41119242 AAAAATTATA
* *
41119252 TATTT-AAAAACACACTAAA-TTA-ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* * * *
41119314 TAAAATTCA-AAAATATGATTTTTTTTAAAGTAAT-AAAATGAGGAGAAAAAATACGAACAAATG
66 TAAAATT-AGAAAATAT-ATATTTTTTAAAGTAATAAAAAT-CGG-GAAAAAATACGAGCAAAGG
*
41119377 GCCGAAGTAAGGGTTTTTTACTAAATT
127 GCCGAAATAAGGGTTTTTTA-TAAATT
* *
41119404 TA---AAAAAA-ACA--AAATTAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA-
1 TATTTAAAAAACACACTAAATTTATT--TAAATTTCAAACATAATGTACTAAAATAATGTAAAAT
*
41119462 AATAAAA-TAGGAAAATAATATATTTTTATTGAAAGTAGTAAAAATCGGGAAAAAATACGAGCAA
64 AATAAAATTA-GAAAAT-ATATA-TTTT-TT-AAAGTAATAAAAATCGGGAAAAAATACGAGCAA
*
41119526 AGGGCCGAAATGAGGGTTTTTT-TAAATT
124 AGGGCCGAAATAAGGGTTTTTTATAAATT
*
41119554 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTACAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* *
41119619 TAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATTCGGGAAAAAATACGAACAAAGGGCC
66 TAAAATTAGAAAATA-TATATTTTTTAAAGTAATAAAAATCGGGAAAAAATACGAGCAAAGGGCC
41119684 GAAATAAGGGTTTTTTACTAAA-T
130 GAAATAAGGGTTTTTTA-TAAATT
* * * * * * * **
41119707 T-TTAAAAAAATAGAATTAA-TTA-ATAAATTTCAAACATAATGTACTAAGATAAAATAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
41119769 TAAAA-TATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATACGAGCAAAG
66 TAAAATTA-GAAAAT-ATATA-TTTT-TT-AAAGTAATAAAAATCGGGAAAAAATACGAGCAAAG
* * *
41119833 TGCCGAAAAAAGAGTTTTTT-T-AATT
126 GGCCGAAATAAGGGTTTTTTATAAATT
*
41119858 TATTTAAAAAACACACTAAATTTATTTAAATTTCGAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
**
41119923 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAAGGCGGAGAAAAAAATACGAG
66 TAAAATTAGAAAATAT-ATATTTTTTAAAGTAATAAAAATCGG-G-AAAAAATACGAG
41119981 AATAAGTTCA
Statistics
Matches: 497, Mismatches: 44, Indels: 71
0.81 0.07 0.12
Matches are distributed among these distances:
147 3 0.01
148 3 0.01
149 6 0.01
150 79 0.16
151 66 0.13
152 120 0.24
153 91 0.18
154 100 0.20
155 19 0.04
156 10 0.02
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (152 bp):
TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAGAAAATATATATTTTTTAAAGTAATAAAAATCGGGAAAAAATACGAGCAAAGGGCCG
AAATAAGGGTTTTTTATAAATT
Found at i:41119914 original size:304 final size:305
Alignment explanation
Indices: 41119252--41119979 Score: 1155
Period size: 304 Copynumber: 2.4 Consensus size: 305
41119242 AAAAATTATA
* *
41119252 TATTT-AAAAACACACTAAA-TTA-ATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* * *
41119314 TAAAATTCA-AAAATATGATTTTTTTTAAAGTAATAAAATGAGGAGAAAAAATACGAACAAATGG
66 TAAAATT-AGAAAATATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGGG
* *
41119378 CCGAAGTAAGGGTTTTTTACTAAATTTAAAAAAAACAAAATTAATTAATACATTTCAAACATAAT
130 CCGAAATAAGGGTTTTTTACTAAATTTAAAAAAAACAAAATTAATTAATAAATTTCAAACATAAT
** *
41119443 GTACTAAAATAATGTAAAAAATAAAATAGGAAAATAATATATTTTTATTGAAAGTAGTAAAAATC
195 GTACTAAAATAAAATAAAAAATAAAATAGGAAAATAATATATTTTTATTGAAAGTAATAAAAATC
** *
41119508 GGGAAAAAATACGAGCAAAGGGCCGAAATGAGGGTTTTTTTAAATT
260 GGGAAAAAATACGAGCAAAGGGCCGAAAAAAGAGTTTTTTTAAATT
*
41119554 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTACAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
41119619 TAAAATTAGAAAATA-GTATATTTTTTAAAGTAATAAAATTCGG-GAAAAAATACGAACAAAGGG
66 TAAAATTAGAAAATATG-ATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGGG
* * *
41119682 CCGAAATAAGGGTTTTTTACTAAATTTTAAAAAAATAGAATTAATTAATAAATTTCAAACATAAT
130 CCGAAATAAGGGTTTTTTACTAAATTTAAAAAAAACAAAATTAATTAATAAATTTCAAACATAAT
* * *
41119747 GTACTAAGATAAAATAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATT
195 GTACTAAAATAAAATAAAA-AATAAAATAGGAAAATAATATATTTTTATTGAAAGTAATAAAAAT
*
41119812 CGGGAAAAAATACGAGCAAAGTGCCGAAAAAAGAGTTTTTTT-AATT
259 CGGGAAAAAATACGAGCAAAGGGCCGAAAAAAGAGTTTTTTTAAATT
*
41119858 TATTTAAAAAACACACTAAATTTATTTAAATTTCGAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
41119923 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAAGGCGGAGAAAAAAATACGA
66 TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGA
41119980 GAATAAGTTC
Statistics
Matches: 391, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
302 5 0.01
303 14 0.04
304 206 0.53
305 155 0.40
306 11 0.03
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (305 bp):
TATTTAAAAAACACACTAAATTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAGAAAATATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAGGGC
CGAAATAAGGGTTTTTTACTAAATTTAAAAAAAACAAAATTAATTAATAAATTTCAAACATAATG
TACTAAAATAAAATAAAAAATAAAATAGGAAAATAATATATTTTTATTGAAAGTAATAAAAATCG
GGAAAAAATACGAGCAAAGGGCCGAAAAAAGAGTTTTTTTAAATT
Found at i:41121110 original size:259 final size:259
Alignment explanation
Indices: 41120646--41121171 Score: 998
Period size: 259 Copynumber: 2.0 Consensus size: 259
41120636 CTCACACCGT
* *
41120646 GTTAAATTATAATCATGTTATTAATCATGCAGTTTATATGGATGCCATATCGTCGCCCAGAAATT
1 GTTAGATTATAACCATGTTATTAATCATGCAGTTTATATGGATGCCATATCGTCGCCCAGAAATT
*
41120711 ATAGTTGTGATACCCTCGTCTGCATGCGTTCATTTTGAAATGTGGTGCACTAGCACACCAATTAT
66 ATAGTTGTGATACCCTCGTCTGCATACGTTCATTTTGAAATGTGGTGCACTAGCACACCAATTAT
* *
41120776 AAATTTCAATGTAGTCGAGTGGTATCACGGGGATTGAATGCTACGATAGTTTGGTTGCATCCAAT
131 AAATTTCAATGTAGTCGAGTGGTATCACAGGGATCGAATGCTACGATAGTTTGGTTGCATCCAAT
41120841 ATATCCCGGATCAGCCATGCGATGTGGGGGCGGTTCACGGCATCAATAAGAGAGGAAAACTGCA
196 ATATCCCGGATCAGCCATGCGATGTGGGGGCGGTTCACGGCATCAATAAGAGAGGAAAACTGCA
*
41120905 GTTAGATTATAACCATGTTATTAATCATGCAGTTTATATGGATGCCATATCGTCTCCCAGAAATT
1 GTTAGATTATAACCATGTTATTAATCATGCAGTTTATATGGATGCCATATCGTCGCCCAGAAATT
41120970 ATAGTTGTGATACCCTCGTCTGCATACGTTCATTTTGAAATGTGGTGCACTAGCACACCAATTAT
66 ATAGTTGTGATACCCTCGTCTGCATACGTTCATTTTGAAATGTGGTGCACTAGCACACCAATTAT
41121035 AAATTTCAATGTAGTCGAGTGGTATCACAGGGATCGAATGCTACGATAGTTTGGTTGCATCCAAT
131 AAATTTCAATGTAGTCGAGTGGTATCACAGGGATCGAATGCTACGATAGTTTGGTTGCATCCAAT
41121100 ATATCCCGGATCAGCCATGCGATGTGGGGGCGGTTCACGGCATCAATAAGAGAGGAAAACTGCA
196 ATATCCCGGATCAGCCATGCGATGTGGGGGCGGTTCACGGCATCAATAAGAGAGGAAAACTGCA
41121164 GTTAGATT
1 GTTAGATT
41121172 CGAGGGTTAA
Statistics
Matches: 261, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 261 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (259 bp):
GTTAGATTATAACCATGTTATTAATCATGCAGTTTATATGGATGCCATATCGTCGCCCAGAAATT
ATAGTTGTGATACCCTCGTCTGCATACGTTCATTTTGAAATGTGGTGCACTAGCACACCAATTAT
AAATTTCAATGTAGTCGAGTGGTATCACAGGGATCGAATGCTACGATAGTTTGGTTGCATCCAAT
ATATCCCGGATCAGCCATGCGATGTGGGGGCGGTTCACGGCATCAATAAGAGAGGAAAACTGCA
Found at i:41122015 original size:77 final size:77
Alignment explanation
Indices: 41121931--41122502 Score: 1009
Period size: 77 Copynumber: 7.4 Consensus size: 77
41121921 TTTCGATATC
41121931 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
41121996 ATAAGCTGAATA
66 ATAAGCTGAATA
41122008 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
41122073 ATAAACTGAATA
66 ATAAGCTGAATA
*
41122085 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAAC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
41122150 ATAAGCTGAATA
66 ATAAGCTGAATA
* * * *
41122162 GTTTTAATTTTTCCAAATGAATTATATTTTTTATAACTTAATTTAGATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
41122227 ATAAACTGAATA
66 ATAAGCTGAATA
*
41122239 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATAAAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
41122304 ATAAGCTGAATA
66 ATAAGCTGAATA
* *
41122316 ATTTTAATTATTCCAAATGAATTATACTTTTCATAACTTAATTTGGATACAATTTAAGCATAAGT
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
41122381 ATAAACTGAATA
66 ATAAGCTGAATA
* * *
41122393 ATTTTAATTATTCCAAATAAATTATATTTTTTATAACTTAATTTGAATACAATTTAAGCATAAGC
1 ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
*
41122458 ATAAGCTTAATA
66 ATAAGCTGAATA
41122470 ATTTTAATTATTCCAAATGAATTATACTTTTTA
1 ATTTTAATTATTCCAAATGAATTATACTTTTTA
41122503 CAACATTACA
Statistics
Matches: 467, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 467 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (77 bp):
ATTTTAATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGC
ATAAGCTGAATA
Found at i:41125527 original size:23 final size:23
Alignment explanation
Indices: 41125482--41125528 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41125472 TAAAAATAAT
*
41125482 AACTATCAATAATATAATGTAAA
1 AACTATCAATAATATAATCTAAA
*
41125505 AACTATCAATCATACTAA-CTAAA
1 AACTATCAATAATA-TAATCTAAA
41125528 A
1 A
41125529 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
AACTATCAATAATATAATCTAAA
Found at i:41125846 original size:3 final size:3
Alignment explanation
Indices: 41125840--41125873 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
41125830 CCTCCTCCTC
*
41125840 CTT CTT CTT CTT CTT CTT CATT TTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT
41125874 TTCCTTCAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:41126811 original size:30 final size:29
Alignment explanation
Indices: 41126749--41126813 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
41126739 AATTTTAAAA
*
41126749 AAAAATTATAAAAATTATTTTTAAAAAATT
1 AAAAATTATAAAAAATATTTTT-AAAAATT
*
41126779 AAAAATTATAAAAAAAATATTTTT-AAATTT
1 AAAAATTAT--AAAAAATATTTTTAAAAATT
41126809 AAAAA
1 AAAAA
41126814 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 19 0.61
32 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAATTATAAAAAATATTTTTAAAAATT
Found at i:41130183 original size:21 final size:22
Alignment explanation
Indices: 41130157--41130199 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
41130147 AAGTTGAATT
41130157 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
41130178 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
41130200 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:41130195 original size:60 final size:61
Alignment explanation
Indices: 41130121--41130239 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
41130111 ATGGATATGT
* * * **
41130121 AGTTAGAATGTATGATTTAATTTC-TTAAGTTGAATTTAA-AGTTATGAATTATATATATAA
1 AGTTAGAATGTATGATATAAGTTCTTTAAGCTGAACATAATA-TTATGAATTATATATATAA
* *
41130181 AGTTTGAATGTATGATATAAGTTCTTTGAGCTGAACATAATATTATGAATTATATATAT
1 AGTTAGAATGTATGATATAAGTTCTTTAAGCTGAACATAATATTATGAATTATATATAT
41130240 GCACATATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 21 0.42
61 28 0.56
62 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (61 bp):
AGTTAGAATGTATGATATAAGTTCTTTAAGCTGAACATAATATTATGAATTATATATATAA
Found at i:41130198 original size:20 final size:21
Alignment explanation
Indices: 41130157--41130200 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
41130147 AAGTTGAATT
*
41130157 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
41130178 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
41130198 TAA
1 TAA
41130201 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:41130355 original size:64 final size:65
Alignment explanation
Indices: 41130284--41130443 Score: 224
Period size: 64 Copynumber: 2.5 Consensus size: 65
41130274 TTGAGTTGTT
*
41130284 TTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTACAAAGTT-TTTGAGC-GGA
1 TTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTACAAA-TTCTTTGAGCTGAA
41130347 A
65 A
* * *
41130348 TTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTACAAATTCTTTGAGCTGAAA
1 TTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTACAAATTCTTTGAGCTGAAA
41130413 TTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 TTTAATGTATG-AATTATATATACATATGTGGTTC
41130444 GAATTTTTGT
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
62 15 0.17
63 3 0.03
64 56 0.64
65 13 0.15
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (65 bp):
TTTAATGTATGAATTATATATACATATGTGGTTCAAATATAGGTTACAAATTCTTTGAGCTGAAA
Found at i:41130666 original size:41 final size:41
Alignment explanation
Indices: 41130563--41130669 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
41130553 ATCTGAGATT
* * * *
41130563 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
* *
41130604 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGTTGAATTTC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
41130645 TTCAGACTTTATGTCTAGCAGGCTT
1 TTCAGACTTTATGTCTAGCAGGCTT
41130670 TGTGCCGGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
Found at i:41137754 original size:22 final size:22
Alignment explanation
Indices: 41137728--41137771 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41137718 TTACAATTCT
*
41137728 TGAATATATCTTAATAATCAAC
1 TGAATATATCTTAACAATCAAC
*
41137750 TGAATATATTTTAACAATCAAC
1 TGAATATATCTTAACAATCAAC
41137772 AGATCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
TGAATATATCTTAACAATCAAC
Found at i:41154818 original size:27 final size:27
Alignment explanation
Indices: 41154780--41154923 Score: 159
Period size: 27 Copynumber: 5.3 Consensus size: 27
41154770 AATCATGGAC
*
41154780 AAATGACCGAATTACCCTCGAAGGGTA
1 AAATGACTGAATTACCCTCGAAGGGTA
*
41154807 AAATGACTGAATTACCCTCAAAGGGTA
1 AAATGACTGAATTACCCTCGAAGGGTA
* *
41154834 AAATGA-TCGAATTACCCCCGAAAGGTA
1 AAATGACT-GAATTACCCTCGAAGGGTA
* *
41154861 AAATGA-TCAAATTACCCCCGAAGGGTA
1 AAATGACT-GAATTACCCTCGAAGGGTA
* * *
41154888 AAATGACCGAAATACCCTC-ATAAGGTA
1 AAATGACTGAATTACCCTCGA-AGGGTA
41154915 AAATGACTG
1 AAATGACTG
41154924 TCATACCCCT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.02
27 99 0.98
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTGAATTACCCTCGAAGGGTA
Found at i:41154932 original size:54 final size:54
Alignment explanation
Indices: 41154780--41154923 Score: 193
Period size: 54 Copynumber: 2.7 Consensus size: 54
41154770 AATCATGGAC
* *
41154780 AAATGACCGAATTACCCTCGAAGGGTAAAATGACTGAATTACCCTCAAAGGGTA
1 AAATGACCGAATTACCCTCGAAAGGTAAAATGACTGAATTACCCCCAAAGGGTA
* * * *
41154834 AAATGATCGAATTACCCCCGAAAGGTAAAATGA-TCAAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAAGGTAAAATGACT-GAATTACCCCCAAAGGGTA
*
41154888 AAATGACCGAAATACCCTC-ATAAGGTAAAATGACTG
1 AAATGACCGAATTACCCTCGA-AAGGTAAAATGACTG
41154924 TCATACCCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
53 2 0.03
54 74 0.96
55 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (54 bp):
AAATGACCGAATTACCCTCGAAAGGTAAAATGACTGAATTACCCCCAAAGGGTA
Found at i:41155105 original size:27 final size:26
Alignment explanation
Indices: 41155074--41155131 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
41155064 TGTACCGGTG
* *
41155074 GCTTTACCACATATACTGTTACTGGCA
1 GCTTTACCACAT-TACTATTAATGGCA
* *
41155101 GCTTTGCTACATTACTATTAATGGCA
1 GCTTTACCACATTACTATTAATGGCA
*
41155127 ACTTT
1 GCTTT
41155132 GTTGCATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (26 bp):
GCTTTACCACATTACTATTAATGGCA
Found at i:41155116 original size:26 final size:26
Alignment explanation
Indices: 41155082--41155160 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
41155072 TGGCTTTACC
*
41155082 ACATATACTGTTACTGGCAGCTTTGCT
1 ACAT-TACTATTACTGGCAGCTTTGCT
* * *
41155109 ACATTACTATTAATGGCAACTTTGTT
1 ACATTACTATTACTGGCAGCTTTGCT
* * *
41155135 GCATCACTATTACTAGCAGCTTTGCT
1 ACATTACTATTACTGGCAGCTTTGCT
41155161 GCAATATTGG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (26 bp):
ACATTACTATTACTGGCAGCTTTGCT
Found at i:41155163 original size:26 final size:26
Alignment explanation
Indices: 41155092--41155163 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
41155082 ACATATACTG
* *
41155092 TTACTGGCAGCTTTGCTACATTACTA
1 TTACTGGCAGCTTTGCTGCATCACTA
* * *
41155118 TTAATGGCAACTTTGTTGCATCACTA
1 TTACTGGCAGCTTTGCTGCATCACTA
*
41155144 TTACTAGCAGCTTTGCTGCA
1 TTACTGGCAGCTTTGCTGCA
41155164 ATATTGGTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCATCACTA
Found at i:41155314 original size:28 final size:29
Alignment explanation
Indices: 41155269--41155328 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
41155259 ACTGCATTGT
* *
41155269 ACTGATTATTGTATTGGGCTAAGGCCCAC
1 ACTGATTACTGTAATGGGCTAAGGCCCAC
41155298 ACTG-TTACTGTAATGGGCTAAGGCCCAC
1 ACTGATTACTGTAATGGGCTAAGGCCCAC
41155326 ACT
1 ACT
41155329 ATACTGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (29 bp):
ACTGATTACTGTAATGGGCTAAGGCCCAC
Found at i:41157172 original size:26 final size:27
Alignment explanation
Indices: 41157132--41157205 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
41157122 ATATTTTCTC
41157132 AAAATTTTACTAGGGGTAAAATCACCA
1 AAAATTTTACTAGGGGTAAAATCACCA
*
41157159 AAAATTTTAC-AGGGGTAAAATCATC-
1 AAAATTTTACTAGGGGTAAAATCACCA
* * *
41157184 AAAACTTTATTGGGGGTAAAAT
1 AAAATTTTACTAGGGGTAAAAT
41157206 AGGGATGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 8 0.19
26 24 0.57
27 10 0.24
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (27 bp):
AAAATTTTACTAGGGGTAAAATCACCA
Found at i:41158866 original size:19 final size:20
Alignment explanation
Indices: 41158842--41158887 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
41158832 GTTGAAAAAG
41158842 TTTCAAT-TGTGTTAAACAT
1 TTTCAATGTGTGTTAAACAT
* *
41158861 TTTCAAATGTGTTTTAACCAT
1 TTTC-AATGTGTGTTAAACAT
41158882 TTTCAA
1 TTTCAA
41158888 ATAAGTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 14 0.61
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (20 bp):
TTTCAATGTGTGTTAAACAT
Found at i:41159065 original size:20 final size:19
Alignment explanation
Indices: 41159030--41159081 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
41159020 GTATCGATCT
*
41159030 AGTATCAATACTTTTCTTAA
1 AGTATCAATA-TTTTCCTAA
41159050 AGTATCAATATATTTCCTAA
1 AGTATCAATAT-TTTCCTAA
* *
41159070 GGTATCGATATT
1 AGTATCAATATT
41159082 CTTGATCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (19 bp):
AGTATCAATATTTTCCTAA
Found at i:41160314 original size:35 final size:35
Alignment explanation
Indices: 41160252--41160337 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
41160242 ATTTTATTTG
*
41160252 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
41160285 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
41160321 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
41160338 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:41160323 original size:25 final size:23
Alignment explanation
Indices: 41160279--41160339 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
41160269 TGATATTTAA
*
41160279 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
41160303 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
41160328 ATATTATTAAAT
1 ATATAATTAAAT
41160340 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:41161644 original size:3 final size:3
Alignment explanation
Indices: 41161636--41161706 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
41161626 GTGAGGTAAG
41161636 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41161684 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
41161707 AGATGAATGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41161894 original size:24 final size:27
Alignment explanation
Indices: 41161857--41161920 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
41161847 AATTGCAGAT
*
41161857 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
41161881 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
41161907 TTGTGATTGAATTG
1 TAATGATTGAATTG
41161921 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:41168286 original size:27 final size:27
Alignment explanation
Indices: 41168246--41168374 Score: 154
Period size: 27 Copynumber: 4.8 Consensus size: 27
41168236 TCCAAAATTT
*
41168246 GTAAAATGATCGTAATGCCCCTGTAGA
1 GTAAAATGACCGTAATGCCCCTGTAGA
* *
41168273 GTAAAATGACCGTAATGCCCATGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGA
*
41168300 GTAAAATGACCGTAATGCCCCTGCA-A
1 GTAAAATGACCGTAATGCCCCTGTAGA
* * *
41168326 GGTAAAATGACTGTGATGCCCTTGTAG-
1 -GTAAAATGACCGTAATGCCCCTGTAGA
* *
41168353 GTAAAATGACTGTAATACCCCT
1 GTAAAATGACCGTAATGCCCCT
41168375 ATTAGGTGAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
26 19 0.22
27 68 0.78
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCCTGTAGA
Found at i:41168331 original size:54 final size:53
Alignment explanation
Indices: 41168246--41168374 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 53
41168236 TCCAAAATTT
* *
41168246 GTAAAATGATCGTAATGCCCCTGTAGAGTAAAATGACCGTAATGCCCATGTAGG
1 GTAAAATGACCGTAATGCCCCTGAAGAGTAAAATGACCGTAATGCCCATGTA-G
* * *
41168300 GTAAAATGACCGTAATGCCCCTGCAAG-GTAAAATGACTGTGATGCCCTTGTAG
1 GTAAAATGACCGTAATGCCCCTG-AAGAGTAAAATGACCGTAATGCCCATGTAG
* *
41168353 GTAAAATGACTGTAATACCCCT
1 GTAAAATGACCGTAATGCCCCT
41168375 ATTAGGTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
53 21 0.31
54 44 0.66
55 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (53 bp):
GTAAAATGACCGTAATGCCCCTGAAGAGTAAAATGACCGTAATGCCCATGTAG
Found at i:41175849 original size:17 final size:16
Alignment explanation
Indices: 41175829--41175863 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
41175819 GTTTAATATA
41175829 TAATTTTATATAAATTT
1 TAATTTTATAT-AATTT
*
41175846 TAATTTTATGTAATTT
1 TAATTTTATATAATTT
41175862 TA
1 TA
41175864 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TAATTTTATATAATTT
Found at i:41189481 original size:24 final size:24
Alignment explanation
Indices: 41189426--41189481 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
41189416 GCTCACATTT
*
41189426 ATATTTTTTATTTCATGTTATTTA
1 ATATTTTTTATTTCATGTTAATTA
* * *
41189450 AAACTTTTT-TTTCATTTTTAATTA
1 ATATTTTTTATTTCA-TGTTAATTA
41189474 ATATTTTT
1 ATATTTTT
41189482 AACTAATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (24 bp):
ATATTTTTTATTTCATGTTAATTA
Found at i:41190130 original size:17 final size:17
Alignment explanation
Indices: 41190080--41190130 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
41190070 ATACTTAACC
*
41190080 TATACATCACTTGGGCA
1 TATACATCACTTGGGTA
41190097 TATACATCACTTGGGTA
1 TATACATCACTTGGGTA
*
41190114 TATACATCACTTAGGTA
1 TATACATCACTTGGGTA
41190131 CATGCCACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (17 bp):
TATACATCACTTGGGTA
Found at i:41191330 original size:45 final size:46
Alignment explanation
Indices: 41191238--41191340 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 46
41191228 GATAGCAGTG
* *
41191238 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCTGAATCTGTA
1 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
*
41191284 ACAGTAACAGTAACAGTA-TTCGACACACAAAGTGCCGAATCGGTA
1 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
*
41191329 ACAATAACAGTA
1 ACAGTAACAGTA
41191341 GTCGATACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 35 0.66
46 18 0.34
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (46 bp):
ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
Found at i:41192511 original size:17 final size:17
Alignment explanation
Indices: 41192489--41192521 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41192479 TGTTTCTCTC
41192489 TTTCTTTCTTTTATTTA
1 TTTCTTTCTTTTATTTA
41192506 TTTCTTTCTTTTATTT
1 TTTCTTTCTTTTATTT
41192522 CTTGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTCTTTTATTTA
Found at i:41192671 original size:5 final size:5
Alignment explanation
Indices: 41192663--41192697 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
41192653 ATTTTACCTA
41192663 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
41192698 TTCTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:41199317 original size:44 final size:44
Alignment explanation
Indices: 41199268--41199363 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
41199258 CAGTTGTTCG
* * *
41199268 GTTGAATGGAATGGAATAGATATATAATAGCATTTTTGTGTTTA
1 GTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTTA
* * * * *
41199312 GTTGAATGCAATTGAATAGATCTGTAATAGTATTATTGTATTTG
1 GTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTTA
41199356 GTTGAATG
1 GTTGAATG
41199364 AAATAGATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (44 bp):
GTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTTA
Found at i:41199675 original size:13 final size:14
Alignment explanation
Indices: 41199634--41199675 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
41199624 AATCCAAGTC
* *
41199634 AAATAAAACAATTA
1 AAATAAAATAACTA
41199648 AAAT-AAATAACTA
1 AAATAAAATAACTA
41199661 AAATAAAATAA-TA
1 AAATAAAATAACTA
41199674 AA
1 AA
41199676 TCAAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:41200133 original size:25 final size:22
Alignment explanation
Indices: 41200100--41200151 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
41200090 ATAAAATTCC
*
41200100 TAAATAAATTAAAATACTTAATAA
1 TAAAAAAATTAAAATA--TAATAA
*
41200124 TTAAAAAAATTAGAATATAATAA
1 -TAAAAAAATTAAAATATAATAA
41200147 TAAAA
1 TAAAA
41200152 TAATAAGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 6 0.24
25 14 0.56
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAAAATTAAAATATAATAA
Found at i:41206024 original size:43 final size:43
Alignment explanation
Indices: 41205971--41206062 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
41205961 GAAGCGAATA
41205971 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
**
41206014 AAGAAGATAAATGGAAAGATAGAACGTGGCGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
41206057 AAGAAG
1 AAGAAG
41206063 CCTTGGAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.17
Consensus pattern (43 bp):
AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
Found at i:41210646 original size:54 final size:54
Alignment explanation
Indices: 41210551--41210839 Score: 289
Period size: 54 Copynumber: 5.4 Consensus size: 54
41210541 GATTCGTGGG
* * * * * * *
41210551 AAAATAACTGAAATACCCCTGAAGGGTAGAATAACCGAAATACCCCCGAATGGT
1 AAAATGACTGAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
* * *
41210605 AGAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
* * *
41210659 AAAATGA-TCGAAATACCCTCGAAGGGTAAAATGA-CTGAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCCCCGAAGGGTAAAATGATC-AAAATACCCCCGAAGGGT
* * * *
41210713 AAAATGACTAAAATACCCCCAAAGGGTAAAATGATCAGAATACCCCTGAAGGGT
1 AAAATGACTGAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
* ** * ** * *
41210767 AAAATGACCGAAATACCCCTAAAGTGTAAAAT-AAAAAAATA-CCCCTATATGGT
1 AAAATGACTGAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGA-AGGGT
*
41210820 AAAATAACTGAAATACCCCC
1 AAAATGACTGAAATACCCCC
41210840 ATAGGATAGA
Statistics
Matches: 196, Mismatches: 34, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.02
53 29 0.15
54 161 0.82
55 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (54 bp):
AAAATGACTGAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
Found at i:41210692 original size:81 final size:79
Alignment explanation
Indices: 41210551--41210865 Score: 287
Period size: 81 Copynumber: 3.9 Consensus size: 79
41210541 GATTCGTGGG
* * * * * * * *
41210551 AAAATAACTGAAATACCCCTGAAGGGTAGAATAACCGAAATACCCCCGAATGGTAGAATGACTAA
1 AAAATGACTAAAATACCCC-GAAGGGTAAAATGATCGAAATA-CCCCGAAGGGTAAAATGACTGA
41210616 AATACCCCCGAAGGGT
64 AATACCCCCGAAGGGT
41210632 AAAATGA-TCAAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTG
1 AAAATGACT-AAAATACCC-CGAAGGGTAAAATGATCGAAATACCC-CGAAGGGTAAAATGACTG
*
41210696 AAATACCCTCGAAGGGT
63 AAATACCCCCGAAGGGT
* *
41210713 AAAATGACTAAAATACCCCCAAAGGGTAAAATGATC-AGAATACCCCTGAAGGGTAAAATGACCG
1 AAAATGACTAAAATA-CCCCGAAGGGTAAAATGATCGA-AATACCCC-GAAGGGTAAAATGACTG
** *
41210777 AAATACCCCTAAAGTGT
63 AAATACCCCCGAAGGGT
** * * * * * *
41210794 AAAAT-AAAAAAATACCCCTATATGGTAAAAT-AACTGAAATACCCCCATAGGATAGAATGACTG
1 AAAATGACTAAAATACCCCGA-AGGGTAAAATGATC-GAAATACCCCGA-AGGGTAAAATGACTG
**
41210857 TTATACCCC
63 AAATACCCC
41210866 AAGATGATGA
Statistics
Matches: 197, Mismatches: 26, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
79 8 0.04
80 49 0.25
81 135 0.69
82 5 0.03
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (79 bp):
AAAATGACTAAAATACCCCGAAGGGTAAAATGATCGAAATACCCCGAAGGGTAAAATGACTGAAA
TACCCCCGAAGGGT
Found at i:41210856 original size:27 final size:26
Alignment explanation
Indices: 41210551--41210865 Score: 251
Period size: 27 Copynumber: 11.7 Consensus size: 26
41210541 GATTCGTGGG
*
41210551 AAAATAACTGAAATACCCCTGAAGGGT
1 AAAATGACTGAAATACCCC-GAAGGGT
* * * *
41210578 AGAATAACCGAAATACCCCCGAATGGT
1 AAAATGACTGAAATA-CCCCGAAGGGT
* *
41210605 AGAATGACTAAAATACCCCCGAAGGGT
1 AAAATGACTGAAATA-CCCCGAAGGGT
*
41210632 AAAATGA-TCAAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCC-CGAAGGGT
41210659 AAAATGA-TCGAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCC-CGAAGGGT
41210686 AAAATGACTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCC-CGAAGGGT
* *
41210713 AAAATGACTAAAATACCCCCAAAGGGT
1 AAAATGACTGAAATA-CCCCGAAGGGT
*
41210740 AAAATGA-TCAGAATACCCCTGAAGGGT
1 AAAATGACTGA-AATACCCC-GAAGGGT
* * *
41210767 AAAATGACCGAAATACCCCTAAAGTGT
1 AAAATGACTGAAATACCCC-GAAGGGT
*** * *
41210794 AAAAT-AAAAAAATACCCCTATATGGT
1 AAAATGACTGAAATACCCCGA-AGGGT
* * *
41210820 AAAATAACTGAAATACCCCCATAGGAT
1 AAAATGACTGAAATACCCCGA-AGGGT
* **
41210847 AGAATGACTGTTATACCCC
1 AAAATGACTGAAATACCCC
41210866 AAGATGATGA
Statistics
Matches: 245, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.00
26 28 0.11
27 207 0.84
28 9 0.04
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (26 bp):
AAAATGACTGAAATACCCCGAAGGGT
Found at i:41211103 original size:26 final size:26
Alignment explanation
Indices: 41211042--41211107 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
41211032 TGATACTGGT
* * *
41211042 AGCTTTGCTGCAATACTGTTACTGCC
1 AGCTTTGCTGCGATACTATTACAGCC
41211068 AG-TTTCGCTGCGATACTATTACCAG-C
1 AGCTTT-GCTGCGATACTATTA-CAGCC
41211094 AGCTTTGCTGCGAT
1 AGCTTTGCTGCGAT
41211108 GTTGGTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 26 0.76
27 5 0.15
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (26 bp):
AGCTTTGCTGCGATACTATTACAGCC
Found at i:41211262 original size:33 final size:33
Alignment explanation
Indices: 41211205--41211270 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
41211195 TGTATTACTG
* *
41211205 CATTGTACTAATACTGTATTGGGCTAAGGCCCA
1 CATTGTACTAATACTATATAGGGCTAAGGCCCA
** *
41211238 CATTGTACTGTTACTATATAGGGCTCAGGCCCA
1 CATTGTACTAATACTATATAGGGCTAAGGCCCA
41211271 AACTAATACT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (33 bp):
CATTGTACTAATACTATATAGGGCTAAGGCCCA
Found at i:41218377 original size:15 final size:16
Alignment explanation
Indices: 41218357--41218396 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
41218347 AAAATAATTT
41218357 AAAACTT-AAATTTTG
1 AAAACTTAAAATTTTG
41218372 AAAACTTAAAAATTTTG
1 AAAACTT-AAAATTTTG
41218389 AGAAACTT
1 A-AAACTT
41218397 TGGAACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:41218670 original size:57 final size:57
Alignment explanation
Indices: 41218609--41218777 Score: 275
Period size: 57 Copynumber: 3.0 Consensus size: 57
41218599 AAACTACAGA
* *
41218609 GAATATTTACTGTTTTCACCAGAGAATATTTCCTATTCACTTGTCTTTTCTTGCAGG
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
* * *
41218666 GAATATTTACTTTTTTCGCTAGAGAATATTTCCTGTTCACTTATCTTTTCTTGCAGG
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
* *
41218723 GAATATTTACTGTTTTCGCCAAAGAATATTTCCTGTTCACTCGTCTTTTCTTGCA
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCA
41218778 TCATTTTTTC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (57 bp):
GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
Found at i:41224324 original size:22 final size:22
Alignment explanation
Indices: 41224299--41224343 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
41224289 TATCGCCACA
*
41224299 TGGAGTGTTG-GGCTGGACTGAG
1 TGGAGTGTAGAGGCTGGA-TGAG
41224321 TGGAGTGTAGAGGCTGGATGAG
1 TGGAGTGTAGAGGCTGGATGAG
41224343 T
1 T
41224344 AGGATTTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.18, C:0.07, G:0.49, T:0.27
Consensus pattern (22 bp):
TGGAGTGTAGAGGCTGGATGAG
Found at i:41231427 original size:57 final size:57
Alignment explanation
Indices: 41231360--41231540 Score: 281
Period size: 57 Copynumber: 3.2 Consensus size: 57
41231350 CTATTCATGC
*
41231360 ATCTTTTCTTGCAGGGAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTT
1 ATCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTT
* * *
41231417 ATCTTTTCTTGTAGGGAATATTTACTATTTTTGCCAGAGAATATTTCCTGTTCATTT
1 ATCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTT
* * * *
41231474 ATCTTTTCTTGCAGAGAATATTTACTATTTTCGCCAGAGAATATTTCTTATTCACTC
1 ATCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTT
*
41231531 GTCTTTTCTT
1 ATCTTTTCTT
41231541 ACATCATTTT
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 112 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (57 bp):
ATCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTT
Found at i:41232643 original size:30 final size:30
Alignment explanation
Indices: 41232602--41232683 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
41232592 CATATTTATG
* *
41232602 GAAAATCAAAGACATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
41232632 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
41232662 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
41232684 TAGATATTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:41232655 original size:15 final size:15
Alignment explanation
Indices: 41232606--41232696 Score: 53
Period size: 15 Copynumber: 6.1 Consensus size: 15
41232596 TTTATGGAAA
*
41232606 ATCAAAGACATGGGT
1 ATCAAAGATATGGGT
* * **
41232621 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
41232635 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41232651 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41232665 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* *
41232681 ATC-TAGATATTGGT
1 ATCAAAGATATGGGT
41232695 AT
1 AT
41232697 AATAAAATCT
Statistics
Matches: 56, Mismatches: 16, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
14 19 0.34
15 29 0.52
16 8 0.14
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41237307 original size:15 final size:15
Alignment explanation
Indices: 41237287--41237364 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
41237277 TTTATGGAAA
41237287 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
41237302 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
41237316 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41237332 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41237346 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41237362 ATC
1 ATC
41237365 TAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41237324 original size:30 final size:30
Alignment explanation
Indices: 41237283--41237364 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
41237273 CATATTTATG
*
41237283 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
41237313 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
41237343 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
41237365 TAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:41240569 original size:20 final size:20
Alignment explanation
Indices: 41240507--41240570 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
41240497 AAAAAACTAA
*
41240507 ATTTTTAACGTAATACAAAT
1 ATTTTTAATGTAATACAAAT
41240527 ATTTTTAATGTAATACCAAAT
1 ATTTTTAATGTAATA-CAAAT
* * *
41240548 -TTTCTAATG-GATACTAAT
1 ATTTTTAATGTAATACAAAT
41240566 ATTTT
1 ATTTT
41240571 AAAGGCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 22 0.59
21 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTTTAATGTAATACAAAT
Found at i:41249497 original size:28 final size:28
Alignment explanation
Indices: 41249441--41249500 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
41249431 ACCACCCTAT
*
41249441 TTTATTTTATATTTGAATTATGTTTGAA
1 TTTATTTTATATTTGAATTATGTTAGAA
*
41249469 TTTA-TTTATATGTTAGAATTGTG-TAGAA
1 TTTATTTTATAT-TT-GAATTATGTTAGAA
41249497 TTTA
1 TTTA
41249501 GTGATTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 14 0.50
29 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TTTATTTTATATTTGAATTATGTTAGAA
Found at i:41249862 original size:30 final size:30
Alignment explanation
Indices: 41249828--41249884 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
41249818 GAGTAACCTC
* *
41249828 GATATACTGTTAGCTTGTGTGAGCAACCCT
1 GATATACTGTCAGCTTGTGTGAACAACCCT
*
41249858 GATATATTGTCAGCTTGTGTGAACAAC
1 GATATACTGTCAGCTTGTGTGAACAAC
41249885 TTTTTCCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
GATATACTGTCAGCTTGTGTGAACAACCCT
Found at i:41249987 original size:10 final size:11
Alignment explanation
Indices: 41249968--41249996 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
41249958 TAAATGCAAA
41249968 TTTGATATATG
1 TTTGATATATG
41249979 TTT-ATATATG
1 TTTGATATATG
41249989 TTTGATAT
1 TTTGATAT
41249997 TTGATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (11 bp):
TTTGATATATG
Found at i:41251301 original size:30 final size:30
Alignment explanation
Indices: 41251267--41251340 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
41251257 ACTTAACAAG
*
41251267 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
41251297 CAAATGCCTTTGAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
41251327 CAAATGCCTTTAAA
1 CAAATGCCTTTAAA
41251341 TTAACAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:41251402 original size:22 final size:22
Alignment explanation
Indices: 41251376--41251424 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41251366 ATATCCAAAC
41251376 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * * *
41251398 CATAATAGTAAAATGGTAGCAA
1 AATAACAATAAAATAGTAGCAA
41251420 AATAA
1 AATAA
41251425 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:41254283 original size:13 final size:13
Alignment explanation
Indices: 41254265--41254297 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41254255 ACAAACAAAC
41254265 AAATAAATAAGAT
1 AAATAAATAAGAT
*
41254278 AAATAAATAGGAT
1 AAATAAATAAGAT
41254291 -AATAAAT
1 AAATAAAT
41254298 TAAATATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
AAATAAATAAGAT
Found at i:41255268 original size:23 final size:23
Alignment explanation
Indices: 41255238--41255294 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
41255228 ACAATAGCAT
*
41255238 ATCAACATCATCTTTTTTAAAAA
1 ATCAACATCATCTTTCTTAAAAA
41255261 ATCAACATCATCTTTCTTAAAAA
1 ATCAACATCATCTTTCTTAAAAA
41255284 ATCAACATCAT
1 ATCAACATCAT
41255295 TTCTCCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (23 bp):
ATCAACATCATCTTTCTTAAAAA
Found at i:41259879 original size:19 final size:20
Alignment explanation
Indices: 41259800--41259905 Score: 115
Period size: 20 Copynumber: 5.3 Consensus size: 20
41259790 TGAAGAACAT
**
41259800 GAAATTTTGGTATCACATTA
1 GAAATTTTGGTATCATGTTA
* * * * *
41259820 CATATATTGGTATCGTGTCA
1 GAAATTTTGGTATCATGTTA
**
41259840 GAAATTTTGGTATTTTGTTA
1 GAAATTTTGGTATCATGTTA
41259860 GAAATTTTGGTATC-TGTTA
1 GAAATTTTGGTATCATGTTA
*
41259879 GAAATTTTAGTATCATGTTA
1 GAAATTTTGGTATCATGTTA
41259899 GAAATTT
1 GAAATTT
41259906 AGTACATGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
19 18 0.26
20 52 0.74
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (20 bp):
GAAATTTTGGTATCATGTTA
Found at i:41259898 original size:39 final size:40
Alignment explanation
Indices: 41259826--41259905 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
41259816 ATTACATATA
* **
41259826 TTGGTATCGTGTCAGAAATTTTGGTATTTTGTTAGAAATT
1 TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
*
41259866 TTGGTATC-TGTTAGAAATTTTAGTATCATGTTAGAAATT
1 TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
41259905 T
1 T
41259906 AGTACATGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (40 bp):
TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
Found at i:41260029 original size:18 final size:18
Alignment explanation
Indices: 41260006--41260050 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
41259996 TCACATTAAA
41260006 AATTTTGGTATTCCA-TAG
1 AATTTTGGTATT-CATTAG
41260024 AATTTTTGGTATTCATTAG
1 AA-TTTTGGTATTCATTAG
*
41260043 AAATTTGG
1 AATTTTGG
41260051 ATATACTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (18 bp):
AATTTTGGTATTCATTAG
Found at i:41260228 original size:20 final size:20
Alignment explanation
Indices: 41260190--41260228 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41260180 TAATGGTTTC
*
41260190 CATTAGAAATATTTTTATTG
1 CATTAGAAATATTTGTATTG
41260210 CATTAGAAAT-TTTGGTATT
1 CATTAGAAATATTT-GTATT
41260229 AACTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
CATTAGAAATATTTGTATTG
Found at i:41276494 original size:22 final size:22
Alignment explanation
Indices: 41276467--41276509 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41276457 ATATCAAAGT
41276467 AACAACCATCAAGAAGGCCAAC
1 AACAACCATCAAGAAGGCCAAC
41276489 AACAACCATCAAGAAGGCCAA
1 AACAACCATCAAGAAGGCCAA
41276510 GGATATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.30, G:0.14, T:0.05
Consensus pattern (22 bp):
AACAACCATCAAGAAGGCCAAC
Found at i:41292482 original size:50 final size:50
Alignment explanation
Indices: 41292363--41292504 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
41292353 GATAATAACA
* * **
41292363 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * * *
41292414 TGCCTATGCCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
41292464 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTC
41292505 ATTCCCTTAA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 47 0.59
51 32 0.41
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:41294278 original size:13 final size:13
Alignment explanation
Indices: 41294262--41294286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41294252 ATATTTTATT
41294262 CTTAATTTTTGTA
1 CTTAATTTTTGTA
41294275 CTTAATTTTTGT
1 CTTAATTTTTGT
41294287 TTGTTTGTTT
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:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
CTTAATTTTTGTA
Found at i:41309394 original size:7 final size:7
Alignment explanation
Indices: 41309382--41309413 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
41309372 TAGTTGATTC
41309382 GTATTTA
1 GTATTTA
41309389 GTATTTA
1 GTATTTA
41309396 -TATTTA
1 GTATTTA
41309402 GTATTTA
1 GTATTTA
41309409 GTATT
1 GTATT
41309414 ATGTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
GTATTTA
Found at i:41309401 original size:13 final size:14
Alignment explanation
Indices: 41309382--41309413 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
41309372 TAGTTGATTC
41309382 GTATTTAGTATTTA
1 GTATTTAGTATTTA
41309396 -TATTTAGTATTTA
1 GTATTTAGTATTTA
41309409 GTATT
1 GTATT
41309414 ATGTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
GTATTTAGTATTTA
Found at i:41313754 original size:126 final size:126
Alignment explanation
Indices: 41313529--41313816 Score: 459
Period size: 126 Copynumber: 2.3 Consensus size: 126
41313519 GCCAAATAGG
* *
41313529 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCTGTACTTTTGCTGACATTGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* *
41313594 TACTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* * *
41313655 AACTACTGTAGCAAAAGAACGTCCATGTGGGAGCTTCTTTCAGTACTTTTGTTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* * * *
41313720 TGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTAGG
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* *
41313781 AACTACTGTAGTAAAATAGCGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
41313817 TTTTAAATTA
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 147 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (126 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
Found at i:41313960 original size:95 final size:96
Alignment explanation
Indices: 41313849--41314179 Score: 487
Period size: 97 Copynumber: 3.5 Consensus size: 96
41313839 ATTAACCCTA
* * * *
41313849 AACCCCAAACCCTAATTTATTTGATTTTTTCTT-AAAACCCTAAATACTAAACCCTAATCTAATT
1 AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAATT
41313913 TTTTTAAAATTTATAATTAATTTACTCAAGT
66 TTTTTAAAATTTATAATTAATTTACTCAAGT
*
41313944 AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAAACC-TAAACCCTAAACCCTAATCTAAT
1 AACCCTAAACCTTAATTTATTTGATTTTTTCTT-AAAAACCATAAACACTAAACCCTAATCTAAT
41314008 TTTTTTAAAAATTTATAATTAATTTACTCAAGT
65 TTTTTT-AAAATTTATAATTAATTTACTCAAGT
41314041 AACCCTAAACAC-TAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA-
1 AACCCTAAAC-CTTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAAT
* * * *
41314104 TTTTTTAAAATTTATAATTAATTGAATTAAGA
65 TTTTTTAAAATTTATAATTAATTTACTCAAGT
41314136 AACCCTAAACCCTT-ATTTATTT-ATTTTTTCCTT-AAAACCATAAA
1 AACCCTAAA-CCTTAATTTATTTGATTTTTT-CTTAAAAACCATAAA
41314180 ATCTAAAAAC
Statistics
Matches: 219, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
94 18 0.08
95 74 0.34
96 42 0.19
97 84 0.38
98 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (96 bp):
AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAATT
TTTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:41314043 original size:97 final size:95
Alignment explanation
Indices: 41313849--41314172 Score: 485
Period size: 95 Copynumber: 3.4 Consensus size: 95
41313839 ATTAACCCTA
* * * *
41313849 AACCCCAAACCCTAATTTATTTGATTTTTTCTTAAAACCCTAAATACTAAACCCTAATCTAATTT
1 AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAACCTAAACACTAAACCCTAATCTAATTT
41313914 TTTTAAAATTTATAATTAATTTACTCAAGT
66 TTTTAAAATTTATAATTAATTTACTCAAGT
*
41313944 AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAAACCTAAACCCTAAACCCTAATCTAATT
1 AACCCTAAACCTTAATTTATTTGATTTTTTCTT-AAAAACCTAAACACTAAACCCTAATCTAATT
41314009 TTTTTAAAAATTTATAATTAATTTACTCAAGT
65 TTTTT-AAAATTTATAATTAATTTACTCAAGT
41314041 AACCCTAAACAC-TAATTTATTTGATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA-
1 AACCCTAAAC-CTTAATTTATTTGATTTTTTCTTAAAAACC-TAAACACTAAACCCTAATCTAAT
* * * *
41314104 TTTTTTAAAATTTATAATTAATTGAATTAAGA
64 TTTTTTAAAATTTATAATTAATTTACTCAAGT
41314136 AACCCTAAACCCTT-ATTTATTT-ATTTTTTCCTTAAAA
1 AACCCTAAA-CCTTAATTTATTTGATTTTTT-CTTAAAA
41314173 CCATAAAATC
Statistics
Matches: 212, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
94 7 0.03
95 78 0.37
96 48 0.23
97 78 0.37
98 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (95 bp):
AACCCTAAACCTTAATTTATTTGATTTTTTCTTAAAAACCTAAACACTAAACCCTAATCTAATTT
TTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:41315373 original size:41 final size:42
Alignment explanation
Indices: 41315311--41315402 Score: 161
Period size: 41 Copynumber: 2.2 Consensus size: 42
41315301 TGAATATCAA
*
41315311 TCATGCAGTGAAGGCTTTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
41315353 T-ATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
41315394 TCATG-AGTG
1 TCATGCAGTG
41315403 TACATCATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (42 bp):
TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
Found at i:41315837 original size:17 final size:17
Alignment explanation
Indices: 41315807--41315839 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41315797 ATTGTTACCC
41315807 TTGTTGATGATGATGAT
1 TTGTTGATGATGATGAT
41315824 TTGTGTGATG-TGATGA
1 TTGT-TGATGATGATGA
41315840 GGCAACGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (17 bp):
TTGTTGATGATGATGAT
Found at i:41318805 original size:6 final size:6
Alignment explanation
Indices: 41318794--41318820 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41318784 TAGGCTTTGA
41318794 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
41318821 CATGAATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:41321459 original size:19 final size:19
Alignment explanation
Indices: 41321432--41321474 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
41321422 ATTTAATAAA
41321432 TAAAATAAAAATCTAAAAC
1 TAAAATAAAAATCTAAAAC
* *
41321451 TAAACTAAAAGTCTAAAAC
1 TAAAATAAAAATCTAAAAC
41321470 TAAAA
1 TAAAA
41321475 CATAGACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAATAAAAATCTAAAAC
Found at i:41325426 original size:9 final size:9
Alignment explanation
Indices: 41325412--41325444 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
41325402 ATTCAATGCT
41325412 TTAATTCGG
1 TTAATTCGG
*
41325421 TTAATTTGG
1 TTAATTCGG
41325430 TTAATTCGG
1 TTAATTCGG
41325439 TTAATT
1 TTAATT
41325445 TTATACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (9 bp):
TTAATTCGG
Found at i:41326046 original size:23 final size:23
Alignment explanation
Indices: 41326008--41326051 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41325998 ATTTTACATC
* *
41326008 AATAAAATTAATACAACTTTTAA
1 AATAAAATTAACACAAATTTTAA
*
41326031 AATAAAATTAGCACAAATTTT
1 AATAAAATTAACACAAATTTT
41326052 TACATCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAAAATTAACACAAATTTTAA
Found at i:41330405 original size:25 final size:25
Alignment explanation
Indices: 41330370--41330447 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
41330360 GTACATGTAT
*
41330370 GCTCATACGAGCATGTAAACAGGAA
1 GCTCATCCGAGCATGTAAACAGGAA
* *
41330395 GCTCTTCCGAGCCATAT-AACAGGAA
1 GCTCATCCGAG-CATGTAAACAGGAA
* *
41330420 GCTCATCTGAG-TTGTATAACAGGAA
1 GCTCATCCGAGCATGTA-AACAGGAA
41330445 GCT
1 GCT
41330448 TATACGAGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 2 0.05
25 37 0.86
26 4 0.09
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (25 bp):
GCTCATCCGAGCATGTAAACAGGAA
Found at i:41330515 original size:25 final size:25
Alignment explanation
Indices: 41330487--41330631 Score: 143
Period size: 25 Copynumber: 5.8 Consensus size: 25
41330477 AGAGCCGTTA
*
41330487 ATCGAGAAGCTCATGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
*
41330512 ATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
* * *
41330537 ATCGGGATGCTCATAAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
**
41330562 AAT-GGGAAGCTTGTGAGAGCCAAAT
1 -ATCGGGAAGCTCATGAGAGCCAAAT
*
41330587 ATCGGGATGCTCAT-A-AGCTCTAAAT
1 ATCGGGAAGCTCATGAGAGC-C-AAAT
* * *
41330612 AACGGAAAGCTCGTGAGAGC
1 ATCGGGAAGCTCATGAGAGC
41330632 TATGGTATGT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.03
24 4 0.04
25 83 0.86
26 3 0.03
27 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCAAAT
Found at i:41330549 original size:75 final size:75
Alignment explanation
Indices: 41330461--41330600 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
41330451 ACGAGTCAAT
* ***
41330461 TATCTGGAAGCTCAAAAGAGC-CGTTAATCGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCA
1 TATCGGGAAGCTCAAAAGAGCTAAATAAT-GAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCA
41330525 TGAAAGCCAAA
65 TGAAAGCCAAA
* * * ** *
41330536 TATCGGGATGCTCATAAGAGCTAAATAATGGGAAGCTTGTGAGAGCCAAATATCGGGATGCTCAT
1 TATCGGGAAGCTCAAAAGAGCTAAATAATGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCAT
41330601 AAGCTCTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 50 0.93
76 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (75 bp):
TATCGGGAAGCTCAAAAGAGCTAAATAATGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCAT
GAAAGCCAAA
Found at i:41330610 original size:50 final size:50
Alignment explanation
Indices: 41330495--41330631 Score: 184
Period size: 50 Copynumber: 2.7 Consensus size: 50
41330485 TAATCGAGAA
* * * * *
41330495 GCTCATGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATATCGGGAT
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
* *
41330545 GCTCATAAGAGCTAAATAATGGGAAGCTTGTGAGAGCCAAATATCGGGAT
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
** *
41330595 GCTCATAAGCTCTAAATAACGGAAAGCTCGTGAGAGC
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGC
41330632 TATGGTATGT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (50 bp):
GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
Found at i:41336674 original size:75 final size:75
Alignment explanation
Indices: 41336610--41336756 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
41336600 AGCTTATACG
* *** *
41336610 AGCCAATTATCTAGAA-GCTCAAAAGAGC-CGTTAATCGGGAAGCTCATGAGAGCCAAATATCGG
1 AGCCAAATATC-AGAATGCTCAAAAGAGCTAAATAAT-GGAAAGCTCATGAGAGCCAAATATCGG
41336673 GAAGCTCATGAA
64 GAAGCTCATGAA
* * *
41336685 AGCCAAATATCGGAATGCTCATAAGAGCTAAATAATGGAAAGCTCGTGAGAGCCAAATATCGGGA
1 AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
*
41336750 TGCTCAT
66 AGCTCAT
41336757 AAGAGCTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.05
75 54 0.89
76 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (75 bp):
AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
AGCTCATGAA
Found at i:41336697 original size:50 final size:50
Alignment explanation
Indices: 41336643--41336814 Score: 195
Period size: 50 Copynumber: 3.4 Consensus size: 50
41336633 AGAGCCGTTA
* * * *
41336643 ATCGGGAAGCTCATGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATAAGAGCTAAATATCGGGAAGCTCGTGAGAGCCAAAT
*
41336693 ATC-GGAATGCTCATAAGAGCTAAATAAT-GGAAAGCTCGTGAGAGCCAAAT
1 ATCGGGAA-GCTCATAAGAGCTAAAT-ATCGGGAAGCTCGTGAGAGCCAAAT
* * * *
41336743 ATCGGGATGCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGTGCTAAAT
1 ATCGGGAAGCTCATAAGAGCTAAATATCGGGAAGCTCGTGAGAGCCAAAT
** * *
41336793 ATCAAGAAGCTCGTGAGAGCTA
1 ATCGGGAAGCTCATAAGAGCTA
41336815 TGGTGTGTTC
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
49 5 0.05
50 93 0.90
51 5 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (50 bp):
ATCGGGAAGCTCATAAGAGCTAAATATCGGGAAGCTCGTGAGAGCCAAAT
Found at i:41336768 original size:75 final size:75
Alignment explanation
Indices: 41336648--41336812 Score: 201
Period size: 75 Copynumber: 2.2 Consensus size: 75
41336638 CGTTAATCGG
* *
41336648 GAAGCTCATGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATATC-GGAATGCTCATAAGAG
1 GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATAACGGGAA-GCTCATAAGAG
**
41336712 CTAAATAATGGA
65 CTAAAT-ATCAA
* * * * *
41336724 -AAGCTCGTGAGAGCCAAATATCGGGATGCTCAT-AAGAGCTAAATAACGGGAAGCTCGTGAGTG
1 GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAA-AGCCAAATAACGGGAAGCTCATAAGAG
41336787 CTAAATATCAA
65 CTAAATATCAA
41336798 GAAGCTCGTGAGAGC
1 GAAGCTCGTGAGAGC
41336813 TATGGTGTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
74 5 0.06
75 68 0.88
76 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (75 bp):
GAAGCTCGTGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATAACGGGAAGCTCATAAGAGC
TAAATATCAA
Found at i:41336814 original size:25 final size:25
Alignment explanation
Indices: 41336643--41336814 Score: 177
Period size: 25 Copynumber: 6.9 Consensus size: 25
41336633 AGAGCCGTTA
*
41336643 ATCGGGAAGCTCATGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
41336668 ATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
*
41336693 ATC-GGAATGCTCATAAGAGCTAAAT
1 ATCGGGAA-GCTCATGAGAGCTAAAT
* * *
41336718 AAT-GGAAAGCTCGTGAGAGCCAAAT
1 -ATCGGGAAGCTCATGAGAGCTAAAT
* *
41336743 ATCGGGATGCTCATAAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* * *
41336768 AACGGGAAGCTCGTGAGTGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
** *
41336793 ATCAAGAAGCTCGTGAGAGCTA
1 ATCGGGAAGCTCATGAGAGCTA
41336815 TGGTGTGTTC
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
24 6 0.05
25 110 0.91
26 5 0.04
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCTAAAT
Found at i:41343617 original size:23 final size:21
Alignment explanation
Indices: 41343590--41343639 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
41343580 TATGCGTATT
41343590 TTTCTATATAGTATATAGACATA
1 TTTCTATATA-TA-ATAGACATA
* *
41343613 TTTCTTTATATAATATACATA
1 TTTCTATATATAATAGACATA
41343634 TATTCT
1 T-TTCT
41343640 TAAACCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 6 0.25
23 9 0.38
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (21 bp):
TTTCTATATATAATAGACATA
Found at i:41348309 original size:23 final size:21
Alignment explanation
Indices: 41348247--41348310 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
41348237 TTAGAAAAAT
*
41348247 AAATAAATAAAAAAATAATACA
1 AAAT-AATAAATAAATAATACA
* *
41348269 AAACTAATTAATATAATAATATA
1 AAA-TAATAAATA-AATAATACA
41348292 ATAATAAGTAAATAAATAA
1 A-AATAA-TAAATAAATAA
41348311 AAGGAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 9 0.26
23 18 0.53
24 7 0.21
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAATAAATAAATAATACA
Found at i:41353335 original size:24 final size:24
Alignment explanation
Indices: 41353308--41353359 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41353298 TTAGTAAGTC
*
41353308 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41353332 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41353356 AAAT
1 AAAT
41353360 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41361739 original size:39 final size:38
Alignment explanation
Indices: 41361689--41361774 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 38
41361679 ATGCATTTTT
*
41361689 TTATAT-A-AAATAATAGAACATAAATATTAATAATTACA
1 TTATATAATAAATAAAAGAACATAAATATTAAT-ATTA-A
** * *
41361727 TTATA-AATAAATAAAAGATTATTAATTTTAATATTAA
1 TTATATAATAAATAAAAGAACATAAATATTAATATTAA
41361764 TTATATAATAA
1 TTATATAATAA
41361775 TTGAAAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
37 6 0.15
38 15 0.38
39 19 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATATAATAAATAAAAGAACATAAATATTAATATTAA
Found at i:41372135 original size:15 final size:15
Alignment explanation
Indices: 41372115--41372146 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41372105 TGATCTTAAA
*
41372115 TTAAATTATAAATAT
1 TTAAATTATAAACAT
41372130 TTAAATTATAAACAT
1 TTAAATTATAAACAT
41372145 TT
1 TT
41372147 TCTTGAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATTATAAACAT
Found at i:41373632 original size:18 final size:18
Alignment explanation
Indices: 41373609--41373650 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
41373599 CAACAAAAAA
41373609 ACAAAAAAAATATTTTTT
1 ACAAAAAAAATATTTTTT
41373627 ACAAAAAAAATATTTTTT
1 ACAAAAAAAATATTTTTT
41373645 A-AAAAA
1 ACAAAAA
41373651 TAATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
ACAAAAAAAATATTTTTT
Found at i:41378830 original size:19 final size:19
Alignment explanation
Indices: 41378806--41378847 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
41378796 TGAAATTTGG
41378806 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
41378825 AATAAAACATAATAAATAT
1 AATAAAAAATAATAAATAT
41378844 AATA
1 AATA
41378848 TTGGACTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:41380938 original size:19 final size:19
Alignment explanation
Indices: 41380905--41380957 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
41380895 TTCAGAATAG
41380905 TAATTCATCAA-CATTTAAC
1 TAATT-ATCAATCATTTAAC
* *
41380924 TAA-TATCATATCATTTCAG
1 TAATTATCA-ATCATTTAAC
41380943 TAATTATCAATCATT
1 TAATTATCAATCATT
41380958 CATATTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 18 0.62
20 5 0.17
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATTATCAATCATTTAAC
Found at i:41381019 original size:5 final size:5
Alignment explanation
Indices: 41381009--41381033 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41380999 AAACATCATA
41381009 CACAT CACAT CACAT CACAT CACAT
1 CACAT CACAT CACAT CACAT CACAT
41381034 ACTATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CACAT
Found at i:41381715 original size:14 final size:14
Alignment explanation
Indices: 41381696--41381731 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
41381686 CGGCACCAAC
41381696 CCACCTCCATCGAT
1 CCACCTCCATCGAT
41381710 CCACCTCCATCGAT
1 CCACCTCCATCGAT
41381724 CCACCTCC
1 CCACCTCC
41381732 GGTCCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.56, G:0.06, T:0.19
Consensus pattern (14 bp):
CCACCTCCATCGAT
Found at i:41397183 original size:15 final size:15
Alignment explanation
Indices: 41397141--41397183 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
41397131 GAAGGCTTCA
*
41397141 CACATACAGGGTTCT
1 CACATATAGGGTTCT
41397156 CACATAT-GGGTTCT
1 CACATATAGGGTTCT
*
41397170 CACATGTAGGGTTC
1 CACATATAGGGTTC
41397184 ACTGTAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (15 bp):
CACATATAGGGTTCT
Found at i:41398283 original size:12 final size:12
Alignment explanation
Indices: 41398266--41398293 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41398256 GTGTCTTGCG
41398266 CACGGCCAAGCA
1 CACGGCCAAGCA
41398278 CACGGCCAAGCA
1 CACGGCCAAGCA
41398290 CACG
1 CACG
41398294 CTCGTGTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.43, G:0.25, T:0.00
Consensus pattern (12 bp):
CACGGCCAAGCA
Found at i:41399073 original size:23 final size:23
Alignment explanation
Indices: 41399047--41399092 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41399037 TAGAGTTATC
* *
41399047 ACATATAGGGTTCGAATATTAAA
1 ACATACAGGGTTCGAATACTAAA
*
41399070 ACATACAGGGTTCGCATACTAAA
1 ACATACAGGGTTCGAATACTAAA
41399093 TCCATAAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (23 bp):
ACATACAGGGTTCGAATACTAAA
Found at i:41399145 original size:16 final size:16
Alignment explanation
Indices: 41399126--41399208 Score: 64
Period size: 16 Copynumber: 5.4 Consensus size: 16
41399116 TCGCATTCAT
*
41399126 GGGTTCGCATGTAAGA
1 GGGTTCGCATGCAAGA
* * *
41399142 GGGTTCACAT--ATGG
1 GGGTTCGCATGCAAGA
*
41399156 GGGTCCGCATGCAAGA
1 GGGTTCGCATGCAAGA
* * *
41399172 GGGTTCACTTGCAAGG
1 GGGTTCGCATGCAAGA
*
41399188 GGGTTCGC-TACAAGA
1 GGGTTCGCATGCAAGA
41399203 GGGTTC
1 GGGTTC
41399209 ACATATGGGA
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
14 10 0.20
15 11 0.22
16 30 0.59
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (16 bp):
GGGTTCGCATGCAAGA
Found at i:41399165 original size:30 final size:30
Alignment explanation
Indices: 41399126--41399230 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
41399116 TCGCATTCAT
*
41399126 GGGTTCGCATGTAAGAGGGTTCACATATGG
1 GGGTTCGCATGCAAGAGGGTTCACATATGG
* * *
41399156 GGGTCCGCATGCAAGAGGGTTCACTTGCAAGG
1 GGGTTCGCATGCAAGAGGGTTCACAT--ATGG
*
41399188 GGGTTCGC-TACAAGAGGGTTCACATATGG
1 GGGTTCGCATGCAAGAGGGTTCACATATGG
* *
41399217 GAGTTTGCATGCAA
1 GGGTTCGCATGCAA
41399231 TGGGATTTGC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 9 0.15
30 27 0.44
31 15 0.25
32 10 0.16
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (30 bp):
GGGTTCGCATGCAAGAGGGTTCACATATGG
Done.