Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 6 of 29
Found at i:1853635 original size:30 final size:30
Alignment explanation
Indices: 1853580--1853648 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1853570 CTTTATTTTT
1853580 TATTTAA-TTAATTATTAAGAAATTTTTAA
1 TATTTAATTTAATTATTAAGAAATTTTTAA
*
1853609 TATTTAATTTAAGTTTTTAA-AAATTTTTAA
1 TATTTAATTTAA-TTATTAAGAAATTTTTAA
*
1853639 T-TTTATTTTA
1 TATTTAATTTA
1853649 TTAATAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 15 0.42
30 15 0.42
31 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TATTTAATTTAATTATTAAGAAATTTTTAA
Found at i:1857449 original size:14 final size:14
Alignment explanation
Indices: 1857411--1857450 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1857401 TATATTATTT
*
1857411 TTTTATTAATAATAA
1 TTTT-TTAATATTAA
1857426 TTTTTT-ATATTAA
1 TTTTTTAATATTAA
1857439 TTTTTTAATATT
1 TTTTTTAATATT
1857451 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 7 0.30
15 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTAATATTAA
Found at i:1858032 original size:25 final size:25
Alignment explanation
Indices: 1857982--1858030 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1857972 GCAAAACAAA
*
1857982 TTTTA-ATTCTTTCATGTTTTTCCC
1 TTTTACATTCTTCCATGTTTTTCCC
*
1858006 TTTTACATTGCTTCCATTTTTTTCC
1 TTTTACATT-CTTCCATGTTTTTCC
1858031 TTCTTACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 13 0.62
ACGTcount: A:0.12, C:0.22, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTACATTCTTCCATGTTTTTCCC
Found at i:1879380 original size:2 final size:2
Alignment explanation
Indices: 1879373--1879402 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1879363 TTAAAGCTAA
1879373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1879403 TACACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1879971 original size:13 final size:14
Alignment explanation
Indices: 1879948--1879978 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1879938 CGGAAGATAC
1879948 TACATGATACAAAA
1 TACATGATACAAAA
1879962 TACA-GATACAAAA
1 TACATGATACAAAA
1879975 TACA
1 TACA
1879979 AATGTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (14 bp):
TACATGATACAAAA
Found at i:1902937 original size:18 final size:18
Alignment explanation
Indices: 1902914--1902948 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1902904 AATATGGGAA
1902914 TTTTTA-GATTGTTTTGAC
1 TTTTTATGATT-TTTTGAC
1902932 TTTTTATGATTTTTTGA
1 TTTTTATGATTTTTTGA
1902949 ATATTATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.66
Consensus pattern (18 bp):
TTTTTATGATTTTTTGAC
Found at i:1903869 original size:82 final size:82
Alignment explanation
Indices: 1903732--1903889 Score: 212
Period size: 82 Copynumber: 1.9 Consensus size: 82
1903722 TATTTATTAA
* * * *
1903732 GATAAACTCCACCTGTACCTATTAGGATTTTAACTTTTTTCATATTGCGATTTGTAATTTTTTTT
1 GATAAACTCCACCTATACCTATTAGGATTTTAACTCTTTTCATATTGCGACTTGTAATTTCTTTT
*
1903797 TTTTGCAATTAACACAG
66 GTTTGCAATTAACACAG
* *
1903814 GATAAACTCCACCTATACCTATT-GTGGTTTTAGCTCTTTTCATA-TGCTGACTTGTAATTTCTT
1 GATAAACTCCACCTATACCTATTAG-GATTTTAACTCTTTTCATATTGC-GACTTGTAATTTCTT
*
1903877 TTGTTTGTAATTA
64 TTGTTTGCAATTA
1903890 GCACTCTATG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 4 0.06
82 62 0.94
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (82 bp):
GATAAACTCCACCTATACCTATTAGGATTTTAACTCTTTTCATATTGCGACTTGTAATTTCTTTT
GTTTGCAATTAACACAG
Found at i:1910498 original size:17 final size:18
Alignment explanation
Indices: 1910476--1910514 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1910466 TCAAACATAA
*
1910476 TTTTTAAAAAATTA-ATT
1 TTTTTAAAAAATAACATT
*
1910493 TTTTTAAATAATAACATT
1 TTTTTAAAAAATAACATT
1910511 TTTT
1 TTTT
1910515 AGAAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAAAAAATAACATT
Found at i:1912153 original size:14 final size:14
Alignment explanation
Indices: 1912119--1912159 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1912109 GGAGAGTAGG
1912119 AGCAAAAAGAG-AAA
1 AGCAAAAA-AGCAAA
1912133 AGC--AAAAGCAAA
1 AGCAAAAAAGCAAA
1912145 AGCAAAAAAGCAAA
1 AGCAAAAAAGCAAA
1912159 A
1 A
1912160 AAAAAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.08
12 9 0.38
14 13 0.54
ACGTcount: A:0.71, C:0.12, G:0.17, T:0.00
Consensus pattern (14 bp):
AGCAAAAAAGCAAA
Found at i:1912163 original size:18 final size:17
Alignment explanation
Indices: 1912122--1912189 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 17
1912112 GAGTAGGAGC
*
1912122 AAAAAGAGAAAAGCAAA
1 AAAAAGAAAAAAGCAAA
1912139 AGCAAAAGCAAAAAAGCAAAA
1 A--AAAAG-AAAAAAGC-AAA
1912160 AAAAAGAAATAAA-CAAA
1 AAAAAGAAA-AAAGCAAA
1912177 TAAAAAGAAAAAA
1 -AAAAAGAAAAAA
1912190 TACTTTTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
17 7 0.16
18 13 0.30
19 13 0.30
20 7 0.16
21 4 0.09
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAAGCAAA
Found at i:1913775 original size:97 final size:98
Alignment explanation
Indices: 1913588--1913779 Score: 278
Period size: 97 Copynumber: 2.0 Consensus size: 98
1913578 AAGTGCATAC
* * * * *
1913588 AAGGTCCATGCTTCTATTGCATATGTTCTAGTATTTTGAGCATAACTCTCATTCTAGAAGTTCAA
1 AAGGTCCATGATTATATTGCATATGTTCCAGTATTTTGAACATAAC-CTCATTCTAGAAGTCCAA
*
1913653 TTGAGCTGATTCTTAAGCCAGTGGAAAGTTAAGA
65 TTGAGCTAATTCTTAAGCCAGTGGAAAGTTAAGA
* *
1913687 AAGGTCCATGATTATATTGCATATGTTCCATTATTTTTAACATAA-CTCATTCTAGAAGTCCAAT
1 AAGGTCCATGATTATATTGCATATGTTCCAGTATTTTGAACATAACCTCATTCTAGAAGTCCAAT
* *
1913751 TGAGGTAATTCTTAAGCCATTGGAAAGTT
66 TGAGCTAATTCTTAAGCCAGTGGAAAGTT
1913780 GATAGTGTGG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 44 0.53
99 39 0.47
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (98 bp):
AAGGTCCATGATTATATTGCATATGTTCCAGTATTTTGAACATAACCTCATTCTAGAAGTCCAAT
TGAGCTAATTCTTAAGCCAGTGGAAAGTTAAGA
Found at i:1915777 original size:12 final size:12
Alignment explanation
Indices: 1915760--1915802 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1915750 CTAATCTTAG
1915760 TTAATTTTATGC
1 TTAATTTTATGC
*
1915772 TTAA-TTTA-GAG
1 TTAATTTTATG-C
1915783 TTAATTTTATGC
1 TTAATTTTATGC
1915795 TTAATTTT
1 TTAATTTT
1915803 GTGTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 1 0.04
11 8 0.31
12 16 0.62
13 1 0.04
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (12 bp):
TTAATTTTATGC
Found at i:1915784 original size:23 final size:23
Alignment explanation
Indices: 1915758--1915810 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1915748 GTCTAATCTT
1915758 AGTTAATTTTATGCTTAATTTAG
1 AGTTAATTTTATGCTTAATTTAG
*
1915781 AGTTAATTTTATGCTTAATTTTG
1 AGTTAATTTTATGCTTAATTTAG
*
1915804 TGTTAAT
1 AGTTAAT
1915811 GTGGTTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (23 bp):
AGTTAATTTTATGCTTAATTTAG
Found at i:1917663 original size:6 final size:6
Alignment explanation
Indices: 1917652--1917686 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1917642 TTCTCTGTAG
*
1917652 CTCATA CTCATA CTCATA CTCATA CTTAT- CTCATA
1 CTCATA CTCATA CTCATA CTCATA CTCATA CTCATA
1917687 ATATATGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCATA
Found at i:1927932 original size:11 final size:11
Alignment explanation
Indices: 1927916--1927940 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1927906 AGTGCTTAAG
1927916 AATTATAAGAC
1 AATTATAAGAC
1927927 AATTATAAGAC
1 AATTATAAGAC
1927938 AAT
1 AAT
1927941 GTCGACGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (11 bp):
AATTATAAGAC
Found at i:1928854 original size:71 final size:70
Alignment explanation
Indices: 1928779--1928954 Score: 214
Period size: 71 Copynumber: 2.5 Consensus size: 70
1928769 ATTGTTTAAC
* * *
1928779 TTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCTAATAACTTGATTAA
1 TTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCAATAACATAATTAA
1928844 ACAAAT
66 AC-AAT
* * * * *
1928850 TTAATCAATTAGGCCCAATAACTTGATTAAATAAATTTAATCAATTAGGCCCAATAGCATAATTA
1 TTAATCAATTAAGCCCAATAACTTAATTAAA-CAATTTAATCAATTAAGCCCAATAACATAATTA
1928915 AACAAT
65 AACAAT
* * *
1928921 TTAATGAATT-AG-GC-ACAACTTAATTAAACAATTT
1 TTAATCAATTAAGCCCAATAACTTAATTAAACAATTT
1928955 TAATTAAGTG
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
67 5 0.06
68 12 0.13
69 1 0.01
70 1 0.01
71 41 0.46
72 30 0.33
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (70 bp):
TTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCAATAACATAATTAA
ACAAT
Found at i:1928932 original size:35 final size:35
Alignment explanation
Indices: 1928779--1928954 Score: 223
Period size: 36 Copynumber: 5.1 Consensus size: 35
1928769 ATTGTTTAAC
*
1928779 TTAATCAATTAAGCCCAATAACTTAATTAAACAAT
1 TTAATCAATTAGGCCCAATAACTTAATTAAACAAT
* * *
1928814 TTAATCAATTAAGCCTAATAACTTGATTAAACAAAT
1 TTAATCAATTAGGCCCAATAACTTAATTAAAC-AAT
* *
1928850 TTAATCAATTAGGCCCAATAACTTGATTAAATAAAT
1 TTAATCAATTAGGCCCAATAACTTAATTAAA-CAAT
* *
1928886 TTAATCAATTAGGCCCAATAGCATAATTAAACAAT
1 TTAATCAATTAGGCCCAATAACTTAATTAAACAAT
* *
1928921 TTAATGAATTAGG--C-ACAACTTAATTAAACAAT
1 TTAATCAATTAGGCCCAATAACTTAATTAAACAAT
1928953 TT
1 TT
1928955 TAATTAAGTG
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
32 17 0.13
33 1 0.01
35 45 0.36
36 63 0.50
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (35 bp):
TTAATCAATTAGGCCCAATAACTTAATTAAACAAT
Found at i:1945005 original size:15 final size:16
Alignment explanation
Indices: 1944985--1945017 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1944975 CCTTTCAACC
1944985 TGTTTTTT-TTTTTTT
1 TGTTTTTTATTTTTTT
1945000 TGTTTTTTAGTTTTTTT
1 TGTTTTTTA-TTTTTTT
1945017 T
1 T
1945018 CAATCCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (16 bp):
TGTTTTTTATTTTTTT
Found at i:1947765 original size:18 final size:18
Alignment explanation
Indices: 1947733--1947767 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1947723 TTCACTAGAA
*
1947733 TTTTCAACCACAATTTCT
1 TTTTCAACAACAATTTCT
*
1947751 TTTTCAACAATAATTTC
1 TTTTCAACAACAATTTC
1947768 AACTTCTTTT
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTCAACAACAATTTCT
Found at i:1949900 original size:24 final size:25
Alignment explanation
Indices: 1949835--1949900 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
1949825 TGCTAGTCCT
1949835 CAATTAAGCAAAATCAATTTTCACA
1 CAATTAAGCAAAATCAATTTTCACA
* * * **
1949860 CCATAAAACTCAA-CAATTTTC-CA
1 CAATTAAGCAAAATCAATTTTCACA
1949883 CAATTAAGCAAAATCAAT
1 CAATTAAGCAAAATCAAT
1949901 AAAACAAACA
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
23 10 0.33
24 12 0.40
25 8 0.27
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (25 bp):
CAATTAAGCAAAATCAATTTTCACA
Found at i:1954068 original size:29 final size:31
Alignment explanation
Indices: 1954027--1954099 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
1954017 AAATATTTAT
* *
1954027 AATATCGATAATAGCTAAACAAGATATA-C-
1 AATATCCACAATAGCTAAACAAGATATATCA
* *
1954056 AATATTCACAATAGCTAAGCAAGATATATCA
1 AATATCCACAATAGCTAAACAAGATATATCA
1954087 AATATCCACAATA
1 AATATCCACAATA
1954100 ACTAGTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.65
30 1 0.03
31 12 0.32
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (31 bp):
AATATCCACAATAGCTAAACAAGATATATCA
Found at i:1958569 original size:6 final size:6
Alignment explanation
Indices: 1958558--1958583 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1958548 ATTTTCACAT
1958558 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
1958584 GAGCAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:1960147 original size:2 final size:2
Alignment explanation
Indices: 1960140--1960174 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1960130 GTATGGGTTT
1960140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1960175 TCATTCTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1964298 original size:28 final size:25
Alignment explanation
Indices: 1964245--1964298 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
1964235 TAATATTTTT
* *
1964245 TTATTATGAAATAAATTTAAAGAAA
1 TTATTATGAAAAAAATTTAAAAAAA
1964270 TTATTATGAAAAAGAATATATAAAAAAA
1 TTATTATGAAAAA-AAT-T-TAAAAAAA
1964298 T
1 T
1964299 ATTTAAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 1 0.04
28 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (25 bp):
TTATTATGAAAAAAATTTAAAAAAA
Found at i:1968727 original size:28 final size:28
Alignment explanation
Indices: 1968691--1968764 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
1968681 GTGGGTTAAG
* *
1968691 GTATCCATCTACTTTTGGTACGTTGA-AA
1 GTATACATCTACTTTTGGTAAGTT-ACAA
*
1968719 GTATTCATCTA-TTTGTGGTAAGTTACAA
1 GTATACATCTACTTT-TGGTAAGTTACAA
*
1968747 GTATACATCCACTTTTGG
1 GTATACATCTACTTTTGG
1968765 GTGGTGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.10
28 32 0.82
29 3 0.08
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (28 bp):
GTATACATCTACTTTTGGTAAGTTACAA
Found at i:1969120 original size:13 final size:13
Alignment explanation
Indices: 1969102--1969126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1969092 TTCAGGGAAT
1969102 GAACATTCATAAC
1 GAACATTCATAAC
1969115 GAACATTCATAA
1 GAACATTCATAA
1969127 GTTTTTATTA
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
GAACATTCATAAC
Found at i:1971013 original size:33 final size:33
Alignment explanation
Indices: 1970966--1971043 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1970956 AAATTGTAAG
1970966 ATTATA-AAGGTTATGCTTGCTCCTTGAAAAGGC
1 ATTATAGAA-GTTATGCTTGCTCCTTGAAAAGGC
**
1970999 ATTGA-AGAAGTTATGCTTGCTTTTTGAAAAGGC
1 ATT-ATAGAAGTTATGCTTGCTCCTTGAAAAGGC
1971032 ATTATAGAAGTT
1 ATTATAGAAGTT
1971044 CTACTTGATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 1 0.03
33 36 0.90
34 3 0.08
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (33 bp):
ATTATAGAAGTTATGCTTGCTCCTTGAAAAGGC
Found at i:1971064 original size:34 final size:33
Alignment explanation
Indices: 1970989--1971085 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
1970979 TGCTTGCTCC
* * *
1970989 TTGAAAAGGCATTGAAGAAGTTATGCTTGCTTT
1 TTGAAAAGGCATTGAAGAAGTTATACTTGATAT
*
1971022 TTGAAAAGGCATT-ATAGAAGTTCTACTTGATCAT
1 TTGAAAAGGCATTGA-AGAAGTTATACTTGAT-AT
* *
1971056 TTGAAAAGGTATTG-TGAAGGTTATACTTGA
1 TTGAAAAGGCATTGAAGAA-GTTATACTTGA
1971086 GCCTTGAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 29 0.55
34 23 0.43
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (33 bp):
TTGAAAAGGCATTGAAGAAGTTATACTTGATAT
Found at i:1972547 original size:36 final size:36
Alignment explanation
Indices: 1972490--1972586 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
1972480 TATCAGCTTG
* *
1972490 CTTTTCAATAGGATCAGGTGTAACCTTTACAATATAC
1 CTTTT-AATAGGATCAAGTGTAACCTTCACAATATAC
* *
1972527 CTTTTAATAGAATCAAGTGTAACCTTCACAATATGC
1 CTTTTAATAGGATCAAGTGTAACCTTCACAATATAC
* *
1972563 CTTTT-ACAGGACCAAGTGTAACCT
1 CTTTTAATAGGATCAAGTGTAACCT
1972587 CTACTAAGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
35 16 0.30
36 32 0.60
37 5 0.09
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (36 bp):
CTTTTAATAGGATCAAGTGTAACCTTCACAATATAC
Found at i:1986765 original size:27 final size:30
Alignment explanation
Indices: 1986724--1986784 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 30
1986714 TAGTTTTTAA
1986724 TTATAATTTAGTTATTTT-T-AA-TTATTT
1 TTATAATTTAGTTATTTTATGAAGTTATTT
1986751 TTATAA-TTAGTTTATTTTATGAAGTTATTT
1 TTATAATTTAG-TTATTTTATGAAGTTATTT
1986781 TTAT
1 TTAT
1986785 TTTATATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.13
27 13 0.43
28 1 0.03
29 2 0.07
30 10 0.33
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (30 bp):
TTATAATTTAGTTATTTTATGAAGTTATTT
Found at i:1989367 original size:21 final size:22
Alignment explanation
Indices: 1989337--1989382 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1989327 AAACTCATAT
*
1989337 TTTTTCATTTCAGTTATTTTTA
1 TTTTTCATTTCAGTTATTTATA
* *
1989359 TTTTT-ATTTTATTTATTTATA
1 TTTTTCATTTCAGTTATTTATA
1989380 TTT
1 TTT
1989383 CTACTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTCATTTCAGTTATTTATA
Found at i:1989390 original size:21 final size:21
Alignment explanation
Indices: 1989350--1989390 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1989340 TTCATTTCAG
* * *
1989350 TTATTTTTATTTTTATTTTAT
1 TTATTTATATTTCTACTTTAT
1989371 TTATTTATATTTCTACTTTA
1 TTATTTATATTTCTACTTTA
1989391 ATCTTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTATATTTCTACTTTAT
Found at i:1995957 original size:53 final size:55
Alignment explanation
Indices: 1995862--1996020 Score: 171
Period size: 53 Copynumber: 2.9 Consensus size: 55
1995852 CTATTATATA
* * * *
1995862 ACTATTAATGAAAAACCATGAATATCCATTCCCTAAAATGAATGTGACAAATGA-G
1 ACTACTAAT-AAAAACTATGAATATCCATTCCCTAAAGTGAATGTGACAAACGAGG
**
1995917 -CTACTAATAAAAACTATGAATATCCATTCCCTAAAGTGAATACGACAAACGAGG
1 ACTACTAATAAAAACTATGAATATCCATTCCCTAAAGTGAATGTGACAAACGAGG
* * * *
1995971 TACTACTAA-AAAAATTATAAATCCATGCATTCCCTGAAGTGAATGTGACA
1 -ACTACTAATAAAAACTATGAAT--ATCCATTCCCTAAAGTGAATGTGACA
1996021 TCATTATGGT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
53 39 0.45
54 8 0.09
55 11 0.13
56 7 0.08
57 22 0.25
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (55 bp):
ACTACTAATAAAAACTATGAATATCCATTCCCTAAAGTGAATGTGACAAACGAGG
Found at i:1996300 original size:28 final size:29
Alignment explanation
Indices: 1996268--1996346 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
1996258 TGTGTGAATC
* *
1996268 ACCTACCAAAAGTGGATGTATACTTGT-A
1 ACCTACCAAAAGTAGATGAATACTTGTCA
*
1996296 ACCTACCAGAAA-TAGATGAATA-TTTTCA
1 ACCTACCA-AAAGTAGATGAATACTTGTCA
*
1996324 ACGTACCAAAAGTAGATGAATAC
1 ACCTACCAAAAGTAGATGAATAC
1996347 CTTAACCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 6 0.14
28 34 0.79
29 3 0.07
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (29 bp):
ACCTACCAAAAGTAGATGAATACTTGTCA
Found at i:2005165 original size:21 final size:20
Alignment explanation
Indices: 2005141--2005182 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2005131 AATACCATTT
* *
2005141 ATTATAATATTTCATTTTTAA
1 ATTAAAATATTT-ATTGTTAA
2005162 ATTAAAATATTTATTGTTAA
1 ATTAAAATATTTATTGTTAA
2005182 A
1 A
2005183 ACATTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAAAATATTTATTGTTAA
Found at i:2007091 original size:15 final size:15
Alignment explanation
Indices: 2007071--2007102 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2007061 CGGGGCAGGG
2007071 GATTTGGATTCCCTT
1 GATTTGGATTCCCTT
2007086 GATTTGGATTCCCTT
1 GATTTGGATTCCCTT
2007101 GA
1 GA
2007103 ATCATCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (15 bp):
GATTTGGATTCCCTT
Found at i:2015404 original size:22 final size:22
Alignment explanation
Indices: 2015378--2015439 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
2015368 TTATTTGCTT
2015378 GATTTGATTTATTGCTTGTAGG
1 GATTTGATTTATTGCTTGTAGG
* *
2015400 GATTTGATTTATTGCTTCTATG
1 GATTTGATTTATTGCTTGTAGG
* *
2015422 GTTTTGATTTGTTG-TTGT
1 GATTTGATTTATTGCTTGT
2015440 TTTGGTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 3 0.09
22 32 0.91
ACGTcount: A:0.15, C:0.05, G:0.24, T:0.56
Consensus pattern (22 bp):
GATTTGATTTATTGCTTGTAGG
Found at i:2022093 original size:27 final size:27
Alignment explanation
Indices: 2022055--2022113 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
2022045 GTGCATAAAC
* *
2022055 CCCTTGCTTAAAGAGCAGGGTTCGAAT
1 CCCTTGCCTAAAGAGCAGAGTTCGAAT
2022082 CCCTTGCCTAAAGAGCAGAGTTCGAAT
1 CCCTTGCCTAAAGAGCAGAGTTCGAAT
2022109 CCCTT
1 CCCTT
2022114 TTCCCCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (27 bp):
CCCTTGCCTAAAGAGCAGAGTTCGAAT
Found at i:2023425 original size:19 final size:19
Alignment explanation
Indices: 2023393--2023430 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
2023383 TTAAAAATAC
2023393 AAATATATGAAATAGATAAAT
1 AAATATAT-AAATAG-TAAAT
2023414 AAATATAT-AATAGTAAA
1 AAATATATAAATAGTAAA
2023431 AATATAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
21 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (19 bp):
AAATATATAAATAGTAAAT
Found at i:2026954 original size:12 final size:12
Alignment explanation
Indices: 2026920--2026957 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2026910 TAGCTTATAT
* *
2026920 ATTTTCGAAGCC
1 ATTTTCAAAGTC
2026932 ATTTTCAAAGTC
1 ATTTTCAAAGTC
2026944 ATTTTCAAAGTC
1 ATTTTCAAAGTC
2026956 AT
1 AT
2026958 AACACCCACN
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (12 bp):
ATTTTCAAAGTC
Found at i:2055407 original size:32 final size:32
Alignment explanation
Indices: 2055348--2055409 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2055338 TAAGGTTTGC
* **
2055348 TGAAGAAATAATGAAAAAAATTTACATAAATT
1 TGAAAAAATAATGAAAAAAATCAACATAAATT
* *
2055380 TGAAAAAATAATGAAGAAAGTCAACATAAA
1 TGAAAAAATAATGAAAAAAATCAACATAAA
2055410 ATTAAAAGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.23
Consensus pattern (32 bp):
TGAAAAAATAATGAAAAAAATCAACATAAATT
Found at i:2058135 original size:21 final size:17
Alignment explanation
Indices: 2058088--2058124 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2058078 GATTAAAAAG
2058088 TTTCAAGTATTGATACC
1 TTTCAAGTATTGATACC
2058105 TTTCAAGTATTGATACC
1 TTTCAAGTATTGATACC
2058122 TTT
1 TTT
2058125 GTCAAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (17 bp):
TTTCAAGTATTGATACC
Found at i:2074030 original size:15 final size:15
Alignment explanation
Indices: 2074010--2074039 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2074000 ATGTTGATTG
2074010 TTAGGAGTTGTTGAA
1 TTAGGAGTTGTTGAA
2074025 TTAGGAGTTGTTGAA
1 TTAGGAGTTGTTGAA
2074040 CTAAGTATTT
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:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (15 bp):
TTAGGAGTTGTTGAA
Found at i:2077529 original size:29 final size:27
Alignment explanation
Indices: 2077464--2077535 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 27
2077454 AAGTATGCTT
* *
2077464 ATGGGCTTATATTTACGTGTCAAGACC
1 ATGGGATTATATTTACGTGTAAAGACC
2077491 ATGGGATTATACTTTCACGTGGTAAAGACC
1 ATGGGATTATA-TTT-ACGT-GTAAAGACC
*
2077521 ATGGG-TTATAATTAC
1 ATGGGATTATATTTAC
2077536 ATTCGCGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 12 0.31
28 5 0.13
29 9 0.23
30 13 0.33
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
ATGGGATTATATTTACGTGTAAAGACC
Found at i:2082392 original size:46 final size:47
Alignment explanation
Indices: 2082281--2082418 Score: 138
Period size: 46 Copynumber: 3.0 Consensus size: 47
2082271 GATACATATT
* * * *
2082281 TGATTATGGATAACATGTGCCAA-GTGAAAGGTGCAAGTATATTGTCT
1 TGATTATGGATAACATGTG-TAAGGTGAAGGGTACAAGTATATTGTCA
* * * * *
2082328 TGATTGTGGATAGCATGTGTAAGGTGAAGGGTATATGTCTATTGT-A
1 TGATTATGGATAACATGTGTAAGGTGAAGGGTACAAGTATATTGTCA
* *
2082374 TGATTATGGATAACATGTGTGAGGTGAAGGGAACAAG-ATCATTGT
1 TGATTATGGATAACATGTGTAAGGTGAAGGGTACAAGTAT-ATTGT
2082419 TTTGCTAGTG
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
45 1 0.01
46 38 0.52
47 34 0.47
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (47 bp):
TGATTATGGATAACATGTGTAAGGTGAAGGGTACAAGTATATTGTCA
Found at i:2084361 original size:39 final size:39
Alignment explanation
Indices: 2084268--2084351 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
2084258 CATCCCATTC
* *
2084268 ATTTAAAGTGGTAGTTGCAAGAAACTCTAATCATCCTTT
1 ATTTAAAGTGGCAGTTGCAAGAAACTCTAATCACCCTTT
*
2084307 ATTTAAAGTGGCAGTTGTAAGAAACTCTAATCACCCCTTT
1 ATTTAAAGTGGCAGTTGCAAGAAACTCTAATCA-CCCTTT
*
2084347 GTTTA
1 ATTTA
2084352 GAATTCAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (39 bp):
ATTTAAAGTGGCAGTTGCAAGAAACTCTAATCACCCTTT
Found at i:2092096 original size:44 final size:44
Alignment explanation
Indices: 2092033--2092121 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
2092023 AGAGATAGAA
2092033 ATTACTTCTAAAAAACTAAATGATATATTTTTCTCTTTTACAAT
1 ATTACTTCTAAAAAACTAAATGATATATTTTTCTCTTTTACAAT
*
2092077 ATTACTTCTAAAAAGCTAAATGATATATTTTTCTCTTTTACAAT
1 ATTACTTCTAAAAAACTAAATGATATATTTTTCTCTTTTACAAT
2092121 A
1 A
2092122 AATTATGACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.45
Consensus pattern (44 bp):
ATTACTTCTAAAAAACTAAATGATATATTTTTCTCTTTTACAAT
Found at i:2092402 original size:21 final size:21
Alignment explanation
Indices: 2092376--2092440 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 21
2092366 CATGTTTACA
2092376 TTAAAATTGAAAAAATATTTT
1 TTAAAATTGAAAAAATATTTT
2092397 TTAAAATT--AAAAAT-TTTAT
1 TTAAAATTGAAAAAATATTT-T
* *
2092416 TTAATTGATTGAAATAATATTTT
1 TTAA--AATTGAAAAAATATTTT
2092439 TT
1 TT
2092441 GTGAAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.08
19 11 0.31
21 11 0.31
23 8 0.22
24 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAAAATTGAAAAAATATTTT
Found at i:2110306 original size:65 final size:65
Alignment explanation
Indices: 2110202--2110332 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
2110192 TAGTGGATCC
* *
2110202 TAAGAAGGAAATATATGAAAAAATTTGAACTTTCTAGTCCAAGATCGACTACAAACCCTCCATAG
1 TAAGAAGGAAATATACGAAAAAATGTGAACTTTCTAGTCCAAGATCGACTACAAACCCTCCATAG
*
2110267 TAAGAAGGAAATATACGAGAAAATGTGAACTTTCTAGTCCAAGATCGACTACAAACCCTCCATAG
1 TAAGAAGGAAATATACGAAAAAATGTGAACTTTCTAGTCCAAGATCGACTACAAACCCTCCATAG
2110332 T
1 T
2110333 TAATCATTGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (65 bp):
TAAGAAGGAAATATACGAAAAAATGTGAACTTTCTAGTCCAAGATCGACTACAAACCCTCCATAG
Found at i:2113037 original size:44 final size:46
Alignment explanation
Indices: 2112987--2113098 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 46
2112977 TCTTCTAGGA
* * *
2112987 AATTCTTTTCAAAACCTCTAAGT-ATACT-TTTAAATGCTTTGAGT
1 AATTCTTTTCAAAACCTCTAAGTAATACTCTTGAAATCCTTTAAGT
* * * * *
2113031 AATTCTTTTTAAATCCTTTAGGTAATCCTCTTGAAATCCTTTAAGT
1 AATTCTTTTCAAAACCTCTAAGTAATACTCTTGAAATCCTTTAAGT
2113077 AA-TCTTTCCTCAAAACCTCTAA
1 AATTCTTT--TCAAAACCTCTAA
2113099 CCATTTGCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
44 19 0.37
45 9 0.17
46 15 0.29
47 9 0.17
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (46 bp):
AATTCTTTTCAAAACCTCTAAGTAATACTCTTGAAATCCTTTAAGT
Found at i:2113142 original size:23 final size:23
Alignment explanation
Indices: 2112878--2113411 Score: 89
Period size: 23 Copynumber: 23.5 Consensus size: 23
2112868 CCAAGTGCAT
* *
2112878 TTTTCAAATCCTCTAAGTAAGCAA
1 TTTTCAAATCCTCTAGGTAATC-A
** * * *
2112902 TGCTCAAAACCTTTAGGTAATCC
1 TTTTCAAATCCTCTAGGTAATCA
* *
2112925 TTTTCAAAT-CTTTCAGG-CA-CA
1 TTTTCAAATCCTCT-AGGTAATCA
* * *
2112946 TCTTT-AAATCCTCCATGTAATCC
1 T-TTTCAAATCCTCTAGGTAATCA
* * *
2112969 TCTTCAAATCTTCTAGGAAATTC-
1 TTTTCAAATCCTCTAGGTAA-TCA
* *
2112992 TTTTCAAAACCTCTAAGT-AT-A
1 TTTTCAAATCCTCTAGGTAATCA
* *
2113013 CTTTT-AAATGCT-TTGAGTAATTC-
1 -TTTTCAAATCCTCTAG-GTAA-TCA
* * *
2113036 TTTTTAAATCCTTTAGGTAATCC
1 TTTTCAAATCCTCTAGGTAATCA
* * * *
2113059 TCTTGAAATCCTTTAAGTAATC-
1 TTTTCAAATCCTCTAGGTAATCA
* *
2113081 TTTCCTCAAAACCTC----TAACCA
1 TTT--TCAAATCCTCTAGGTAATCA
* *
2113102 TTTGCAATAT-CTCCAGGTAATCA
1 TTTTCAA-ATCCTCTAGGTAATCA
2113125 TTTTCAAATCCTCTAGGT-A-CA
1 TTTTCAAATCCTCTAGGTAATCA
* *
2113146 TCTTTCAAATCCTCTA-GAAAACTA
1 T-TTTCAAATCCTCTAGGTAATC-A
* * * **
2113170 TTTTTCAAAACCT-TCGAATAGCCA
1 -TTTTCAAATCCTCTAG-GTAATCA
* *
2113194 TTTTCAAAACCTTTAGGTAATCA
1 TTTTCAAATCCTCTAGGTAATCA
* *
2113217 TTTTCAAATACT-TCAAGT-A-CA
1 TTTTCAAATCCTCT-AGGTAATCA
** * * *
2113238 ACTTCAAATCCTCCAAGTAACCA
1 TTTTCAAATCCTCTAGGTAATCA
* * **
2113261 TTTTTCAAAACCT-TTGAGTAGCCA
1 -TTTTCAAATCCTCTAG-GTAATCA
* * *
2113285 TTTTCAAATCTTTTAAGT-AT-A
1 TTTTCAAATCCTCTAGGTAATCA
*
2113306 TCTTTCAAATCCTCTAAGTAA-CTA
1 T-TTTCAAATCCTCTAGGTAATC-A
* * * **
2113330 TTTTTCAAAACCTTTGGGTAGCCA
1 -TTTTCAAATCCTCTAGGTAATCA
* * **
2113354 TTTTCAAAACCT-TTGAGTAGCCA
1 TTTTCAAATCCTCTAG-GTAATCA
* *
2113377 TTTTCAAAACCTTTAGGTAATCA
1 TTTTCAAATCCTCTAGGTAATCA
*
2113400 ATTTCAAATCCT
1 TTTTCAAATCCT
2113412 TTGATTACTA
Statistics
Matches: 372, Mismatches: 90, Indels: 97
0.67 0.16 0.17
Matches are distributed among these distances:
19 6 0.02
20 6 0.02
21 40 0.11
22 65 0.17
23 175 0.47
24 75 0.20
25 5 0.01
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (23 bp):
TTTTCAAATCCTCTAGGTAATCA
Found at i:2113221 original size:46 final size:46
Alignment explanation
Indices: 2113171--2113429 Score: 174
Period size: 46 Copynumber: 5.7 Consensus size: 46
2113161 AGAAAACTAT
2113171 TTTTCAAAACCTTCGAATAGCCATTTTCAAAACCTTTAGGTAATCA
1 TTTTCAAAACCTTCGAATAGCCATTTTCAAAACCTTTAGGTAATCA
** * ** * *
2113217 TTTTCAAATA-CTTC-AAGTA--CAACTTCAAATCCTCCAAGTAACCA
1 TTTTCAAA-ACCTTCGAA-TAGCCATTTTCAAAACCTTTAGGTAATCA
* * * * *
2113261 TTTTTCAAAACCTTTGAGTAGCCATTTTCAAATCTTTTAAGT-AT-A
1 -TTTTCAAAACCTTCGAATAGCCATTTTCAAAACCTTTAGGTAATCA
* * * * * **
2113306 TCTTTCAAATCC-TCTAAGTAACTATTTTTCAAAACCTTTGGGTAGCCA
1 T-TTTCAAAACCTTCGAA-TAGCCA-TTTTCAAAACCTTTAGGTAATCA
* *
2113354 TTTTCAAAACCTTTGAGTAGCCATTTTCAAAACCTTTAGGTAATCA
1 TTTTCAAAACCTTCGAATAGCCATTTTCAAAACCTTTAGGTAATCA
* * * * *
2113400 ATTTCAAATCCTTTGATTA-CTATTTTCAAA
1 TTTTCAAAACCTTCGAATAGCCATTTTCAAA
2113430 GACTATTTAA
Statistics
Matches: 160, Mismatches: 40, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
44 22 0.14
45 39 0.24
46 66 0.41
47 29 0.18
48 4 0.03
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (46 bp):
TTTTCAAAACCTTCGAATAGCCATTTTCAAAACCTTTAGGTAATCA
Found at i:2113340 original size:69 final size:68
Alignment explanation
Indices: 2113194--2113361 Score: 223
Period size: 69 Copynumber: 2.5 Consensus size: 68
2113184 CGAATAGCCA
**
2113194 TTTTCAAAACCTTT-AGGTAATCATTTTCAAATACTTCAAGTACAACTTCAAATCCTCCAAGTAA
1 TTTTCAAAACCTTTGA-GTAGCCATTTTCAAATACTTCAAGTACAACTTCAAATCCTCCAAGTAA
2113258 CCAT
65 CCAT
* * * *
2113262 TTTTCAAAACCTTTGAGTAGCCATTTTCAAAT-CTTTTAAGTATATCTTTCAAATCCTCTAAGTA
1 TTTTCAAAACCTTTGAGTAGCCATTTTCAAATAC-TTCAAGTACAAC-TTCAAATCCTCCAAGTA
*
2113326 ACTAT
64 ACCAT
*
2113331 TTTTCAAAACCTTTGGGTAGCCATTTTCAAA
1 TTTTCAAAACCTTTGAGTAGCCATTTTCAAA
2113362 ACCTTTGAGT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
67 1 0.01
68 37 0.42
69 51 0.57
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (68 bp):
TTTTCAAAACCTTTGAGTAGCCATTTTCAAATACTTCAAGTACAACTTCAAATCCTCCAAGTAAC
CAT
Found at i:2113405 original size:69 final size:69
Alignment explanation
Indices: 2113195--2113429 Score: 196
Period size: 69 Copynumber: 3.4 Consensus size: 69
2113185 GAATAGCCAT
** * * * *
2113195 TTTCAAAACCTTT-AGGTAATCATTTTCAAATA-CTTCAAGTACAAC-TTCAAATCCTCCAAGTA
1 TTTCAAAACCTTTGA-GTAGCCATTTTCAAA-ACCTTTAAGTACATCTTTCAAAACCTCTAAGTA
* *
2113257 ACCATT
64 ACTATA
* * * *
2113263 TTTCAAAACCTTTGAGTAGCCATTTTCAAATCTTTTAAGTATATCTTTCAAATCCTCTAAGTAAC
1 TTTCAAAACCTTTGAGTAGCCATTTTCAAAACCTTTAAGTACATCTTTCAAAACCTCTAAGTAAC
*
2113328 TATT
66 TATA
* * * *
2113332 TTTCAAAACCTTTGGGTAGCCATTTTCAAAACCTTTGAGTAGCCAT-TTTCAAAACCTTTAGGTA
1 TTTCAAAACCTTTGAGTAGCCATTTTCAAAACCTTTAAGTA--CATCTTTCAAAACCTCTAAGTA
2113396 A-TCA-A
64 ACT-ATA
* * *
2113401 TTTCAAATCCTTTGATTA-CTATTTTCAAA
1 TTTCAAAACCTTTGAGTAGCCATTTTCAAA
2113430 GACTATTTAA
Statistics
Matches: 139, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
68 45 0.32
69 75 0.54
70 17 0.12
71 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (69 bp):
TTTCAAAACCTTTGAGTAGCCATTTTCAAAACCTTTAAGTACATCTTTCAAAACCTCTAAGTAAC
TATA
Found at i:2113412 original size:23 final size:23
Alignment explanation
Indices: 2113116--2113413 Score: 130
Period size: 23 Copynumber: 13.0 Consensus size: 23
2113106 CAATATCTCC
* * *
2113116 AGGTAATCATTTTCAAATCCTCT
1 AGGTAACCATTTTCAAAACCTTT
* *
2113139 AGGT-A-CATCTTTCAAATCCTCT
1 AGGTAACCAT-TTTCAAAACCTTT
** *
2113161 AGAAAACTATTTTTCAAAACC-TT
1 AGGTAACCA-TTTTCAAAACCTTT
* * *
2113184 CGAATAGCCATTTTCAAAACCTTT
1 AG-GTAACCATTTTCAAAACCTTT
* *
2113208 AGGTAATCATTTTCAAATA-CTTC
1 AGGTAACCATTTTCAAA-ACCTTT
* ** * **
2113231 AAGT-A-CAACTTCAAATCCTCC
1 AGGTAACCATTTTCAAAACCTTT
*
2113252 AAGTAACCATTTTTCAAAACCTTT
1 AGGTAACCA-TTTTCAAAACCTTT
* * *
2113276 -GAGTAGCCATTTTCAAATCTTTT
1 AG-GTAACCATTTTCAAAACCTTT
* * * *
2113299 AAGT-A-TATCTTTCAAATCCTCT
1 AGGTAACCAT-TTTCAAAACCTTT
* *
2113321 AAGTAACTATTTTTCAAAACCTTT
1 AGGTAACCA-TTTTCAAAACCTTT
* *
2113345 GGGTAGCCATTTTCAAAACCTTT
1 AGGTAACCATTTTCAAAACCTTT
*
2113368 -GAGTAGCCATTTTCAAAACCTTT
1 AG-GTAACCATTTTCAAAACCTTT
* * *
2113391 AGGTAATCAATTTCAAATCCTTT
1 AGGTAACCATTTTCAAAACCTTT
2113414 GATTACTATT
Statistics
Matches: 213, Mismatches: 43, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
21 20 0.09
22 34 0.16
23 105 0.49
24 52 0.24
25 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (23 bp):
AGGTAACCATTTTCAAAACCTTT
Found at i:2114610 original size:16 final size:17
Alignment explanation
Indices: 2114581--2114613 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2114571 GAGAACAGTG
2114581 TATATAGATCTGTACATT
1 TATATAGA-CTGTACATT
2114599 TATATAGA-TGTACAT
1 TATATAGACTGTACAT
2114614 GTTAACATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
TATATAGACTGTACATT
Found at i:2120924 original size:33 final size:35
Alignment explanation
Indices: 2120849--2120926 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 35
2120839 ATAAAATTTA
* *
2120849 AATTTAATTAATCAAAAACAAATATCTCAAATATC
1 AATTTAAATAATCAAAAACAAATATCTCAAATAAC
** *
2120884 ACCTTAAATAATTAAAAA-AAATAT-TCAAATAAC
1 AATTTAAATAATCAAAAACAAATATCTCAAATAAC
2120917 AATTTAAATA
1 AATTTAAATA
2120927 TTACAAGTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 16 0.44
34 6 0.17
35 14 0.39
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (35 bp):
AATTTAAATAATCAAAAACAAATATCTCAAATAAC
Found at i:2136376 original size:16 final size:16
Alignment explanation
Indices: 2136355--2136395 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
2136345 AAAATAAACT
2136355 AAAAGCAATAATCTTA
1 AAAAGCAATAATCTTA
*
2136371 AAAAGC--TAGTCTTA
1 AAAAGCAATAATCTTA
*
2136385 AAAGGCAATAA
1 AAAAGCAATAA
2136396 CCCTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
14 12 0.60
16 8 0.40
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (16 bp):
AAAAGCAATAATCTTA
Found at i:2136501 original size:622 final size:627
Alignment explanation
Indices: 2135773--2136915 Score: 1504
Period size: 622 Copynumber: 1.8 Consensus size: 627
2135763 AAAAGCAACT
* ** *
2135773 ACCCTCAAATTTGTGTAACTAGTAGCTTTCAACATTCTTGTTAAATCTTGATTTATTGAACCTGA
1 ACCCTAAAATTTGTAAAACTAGTAACTTTCAACATTCTTGTTAAATCTTGATTTATTGAACCTGA
** * * * * *
2135838 AATTCTGATACTAGTTTGTTATGAAAATCACATACGAAACAACAAAGATAAAACCTAAAGAAATC
66 AACGCTGATACCAATTTATTATGAAAATCACACAAGAAACAACAAAGAT-AAACCTAAAGAAATC
* * *
2135903 AAGAAAATAG-AAAGCACAAGAATTTA-CAAGGCGTACCTACATCCACGGAGTGAAA-TCATTCT
130 AAGAAAATAGAAAAACACAAGAATTTATCAACGCGTACCTACATCCACGAAGTGAAACT-ATTCT
* * *
2135965 TTTATTATTGAGAAATTAAAGTACAATAAATTAACCTCT-A-TGGTT-TCTCAAACTAACCCAAG
194 TCTATTATTAAGAAATTAAAGTACAATAAACTAACCTCTAACTGGTTCTC-CAAACTAACCCAAG
* * *
2136027 ATCCCTTGCACATCTTTTCTCAATAACATCTC-AAGAACACTCA-CTCAAACCACTCTAGCTTCA
258 ATCCCTTGCACACCTTCTCTCAATAA-ATCTCTAAGAACACTCACCT-AAACCACTCTAACTTCA
* * * ** *
2136090 CCTAGAGCAAAAGACAGAGTTACAAGGTATTCTTCTATAAAGCTTTC-AAG-TTACTCACTCTTT
321 CCTAGAACAAAAAACAAAGTTACAAGGTATTCTTCTATAAAGCTCCCAAAGATTACTCACTCTTC
* * *
2136153 TAAAGCCTAG-AGATCAACTTTTGTAATATAAAAATCCAAAGTAAAAAGGGGATTAGGACCTAAT
386 CAAAGCCT-GCAGATCAACTTTTATAATATAAAAATCCAAAGT-AAAAGGAGATTAGGACCTAAT
2136217 GTGGAACAAAAACTTT-AAACCATATAACTATTCAAAT-TTGTACACAAACAAGAATCCTAGTCA
449 GTGGAACAAAAACTTTAAAACCATATAACTATTC-AATGTTGTACACAAACAAGAATCCTAGTCA
2136280 ACCTAAAACTCAATAGCCATCAACTACCTAATCTACTGATCACATCCTTGTCAAGCCTCCAATGA
513 ACCTAAAACTCAATAGCCATCAACTACCTAATCTACTGATCACATCCTTGTCAAGCCTCCAATGA
2136345 AAAATAAACTAAAAGCAATAATCTTAAAAAGCTAGTCTTAAAAGGCAATA
578 AAAATAAACTAAAAGCAATAATCTTAAAAAGCTAGTCTTAAAAGGCAATA
*
2136395 ACCCTAAAATTTGTAAAACTAGTAACTTTCAACATTCTTG-TAGAATCTTGATTTATTGAACTTG
1 ACCCTAAAATTTGTAAAACTAGTAACTTTCAACATTCTTGTTA-AATCTTGATTTATTGAACCTG
*
2136459 AAACGCTGATACCAATTTATTATGAAAATCACCCAAGAAACAACAAAGATAAACCTAAAGAAATC
65 AAACGCTGATACCAATTTATTATGAAAATCACACAAGAAACAACAAAGATAAACCTAAAGAAATC
* *** *
2136524 AAGCAAATAGAAAAACACAAGAATTTATGTGGTTCAACTTTTACCTACATCCATGAAGTGAAACT
130 AAGAAAATAGAAAAACACAAGAATTTA------TCAACGCGTACCTACATCCACGAAGTGAAACT
* ** *
2136589 GTTCTTCTATTATTAAGAAATTAAAGTACAATAAACTGGCCTCTAAACTGGTTCTCCAAACTAAT
189 ATTCTTCTATTATTAAGAAATTAAAGTACAATAAACTAACCTCT-AACTGGTTCTCCAAACTAAC
* * *
2136654 CTAAGATCCCTTGCACACCTTCTCTCAATAAATTTCTAAGAGCACTCACCTAAACCACTCTAACT
253 CCAAGATCCCTTGCACACCTTCTCTCAATAAATCTCTAAGAACACTCACCTAAACCACTCTAACT
* * * * * * *
2136719 TTACCTAGAATAAAAAACAAAGTTACAAGGTGTTCTTCTCTAGAGCTCCCAAAGCATTACTTATT
318 TCACCTAGAACAAAAAACAAAGTTACAAGGTATTCTTCTATAAAGCTCCCAAAG-ATTACTCACT
* * * * * * *
2136784 CTTCCAAAGCCTGCAGATCAACTTTTATAATGTAAAAGTTCAAAGTAGAATGAGATTAGGACTTG
382 CTTCCAAAGCCTGCAGATCAACTTTTATAATATAAAAATCCAAAGTAAAAGGAGATTAGGACCTA
* *
2136849 ATGTGGAACAAAAACTTTAAAACCATATAACTATTCAATGTTGTACATAAATAAGAATCCTAGTC
447 ATGTGGAACAAAAACTTTAAAACCATATAACTATTCAATGTTGTACACAAACAAGAATCCTAGTC
2136914 AA
512 AA
2136916 ATAAGATTTA
Statistics
Matches: 440, Mismatches: 59, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
621 26 0.06
622 113 0.26
629 61 0.14
630 1 0.00
631 5 0.01
632 104 0.24
633 7 0.02
634 36 0.08
635 87 0.20
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (627 bp):
ACCCTAAAATTTGTAAAACTAGTAACTTTCAACATTCTTGTTAAATCTTGATTTATTGAACCTGA
AACGCTGATACCAATTTATTATGAAAATCACACAAGAAACAACAAAGATAAACCTAAAGAAATCA
AGAAAATAGAAAAACACAAGAATTTATCAACGCGTACCTACATCCACGAAGTGAAACTATTCTTC
TATTATTAAGAAATTAAAGTACAATAAACTAACCTCTAACTGGTTCTCCAAACTAACCCAAGATC
CCTTGCACACCTTCTCTCAATAAATCTCTAAGAACACTCACCTAAACCACTCTAACTTCACCTAG
AACAAAAAACAAAGTTACAAGGTATTCTTCTATAAAGCTCCCAAAGATTACTCACTCTTCCAAAG
CCTGCAGATCAACTTTTATAATATAAAAATCCAAAGTAAAAGGAGATTAGGACCTAATGTGGAAC
AAAAACTTTAAAACCATATAACTATTCAATGTTGTACACAAACAAGAATCCTAGTCAACCTAAAA
CTCAATAGCCATCAACTACCTAATCTACTGATCACATCCTTGTCAAGCCTCCAATGAAAAATAAA
CTAAAAGCAATAATCTTAAAAAGCTAGTCTTAAAAGGCAATA
Found at i:2143081 original size:12 final size:12
Alignment explanation
Indices: 2143064--2143090 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2143054 TTTTCTAGTG
2143064 ACACTATGAACA
1 ACACTATGAACA
2143076 ACACTATGAACA
1 ACACTATGAACA
2143088 ACA
1 ACA
2143091 TTATTATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
ACACTATGAACA
Found at i:2163183 original size:18 final size:19
Alignment explanation
Indices: 2163162--2163200 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2163152 GAAAAATTAA
*
2163162 AATGAAAACAA-CTTAAAT
1 AATGAAAACAATCATAAAT
*
2163180 AATGACAACAATCATAAAT
1 AATGAAAACAATCATAAAT
2163199 AA
1 AA
2163201 ACAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.62, C:0.13, G:0.05, T:0.21
Consensus pattern (19 bp):
AATGAAAACAATCATAAAT
Found at i:2181662 original size:112 final size:112
Alignment explanation
Indices: 2181464--2181719 Score: 372
Period size: 112 Copynumber: 2.3 Consensus size: 112
2181454 ACAAAAGATA
* * *
2181464 GGAGAATTGGTTAAAAGTTGTATTTGCTCATCAATTTACAGAAAGCAAAGTTTTAAATGCAAAAG
1 GGAGAATTAGTTAAAATTTGTATTTGCTCATCAATTTACAAAAAGCAAAGTTTTAAATGCAAAAG
*
2181529 GTGTTAGATTTAAAGAAACAAAAACAAATTTTTAAATGAAA-CTAGG
66 GTGTTAGATTTAAAGAAACAAAAACAAATTTTTAAATGAAATCTAAG
* ** *
2181575 GAGAGAATTAGTTAAAATTTGTATTTGCTCGT-AACTTTACAAAAAGCAAAGTTTTAAATGTGAG
1 G-GAGAATTAGTTAAAATTTGTATTTGCTCATCAA-TTTACAAAAAGCAAAGTTTTAAATGCAAA
* *
2181639 AGGTGTTAGATTTGAAGAAACAAAAATAAATTTTTAAATGAAATCTAAG
64 AGGTGTTAGATTTAAAGAAACAAAAACAAATTTTTAAATGAAATCTAAG
* *
2181688 GGAGAATGAGTTAAAATTTGTATTTACTCATC
1 GGAGAATTAGTTAAAATTTGTATTTGCTCATC
2181720 CTTGAAAAAG
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
111 3 0.02
112 120 0.94
113 5 0.04
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (112 bp):
GGAGAATTAGTTAAAATTTGTATTTGCTCATCAATTTACAAAAAGCAAAGTTTTAAATGCAAAAG
GTGTTAGATTTAAAGAAACAAAAACAAATTTTTAAATGAAATCTAAG
Found at i:2186023 original size:73 final size:73
Alignment explanation
Indices: 2185870--2186032 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
2185860 AACCAAAAGA
* * *
2185870 CAATGTTAGTCGACTAAGAGCTTACTGCCAAAAACTAAGTTCAGAGATAGAAATGACTTAATCAA
1 CAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAAGTTCAGAGACAGAAACGACTTAATCAA
*
2185935 TTAAGAAG
66 CTAAGAAG
***
2185943 TTTTGTTAGTCGACTAAGAGCTTACTACCAAAAACT-AGTTTCAGAGACA-AAGACGACTTAATC
1 CAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAAG-TTCAGAGACAGAA-ACGACTTAATC
** **
2186006 GGCTAAGTGG
64 AACTAAGAAG
2186016 CAATGTTAGTCGACTAA
1 CAATGTTAGTCGACTAA
2186033 TAGCATCCTG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
72 4 0.05
73 70 0.95
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (73 bp):
CAATGTTAGTCGACTAAGAGCTTACTACCAAAAACTAAGTTCAGAGACAGAAACGACTTAATCAA
CTAAGAAG
Found at i:2188443 original size:21 final size:21
Alignment explanation
Indices: 2188417--2188457 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2188407 GTGACTGTGA
*
2188417 AGAAA-TAGAGAGTAAAGAAAC
1 AGAAATTAGAGA-AAAAGAAAC
2188438 AGAAATTAGAGAAAAAGAAA
1 AGAAATTAGAGAAAAAGAAA
2188458 GATAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.66, C:0.02, G:0.22, T:0.10
Consensus pattern (21 bp):
AGAAATTAGAGAAAAAGAAAC
Found at i:2189050 original size:15 final size:16
Alignment explanation
Indices: 2189024--2189056 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2189014 TTTTTGAATG
*
2189024 ATGCAGTTTGCTTTTA
1 ATGCAGTTTGCTCTTA
2189040 ATGCA-TTTGCTCTTA
1 ATGCAGTTTGCTCTTA
2189055 AT
1 AT
2189057 TTAAGGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (16 bp):
ATGCAGTTTGCTCTTA
Found at i:2193647 original size:73 final size:73
Alignment explanation
Indices: 2193544--2193681 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
2193534 AGAGACAGTG
* * * * * * *
2193544 TTAGTCGACTTAGAGCTTACTGCCAAAAACTGGGTTTAGAGATAAAAATGACTTAATCGACTAAG
1 TTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTAAG
2193609 AAGTTTTA
66 AAGTTTTA
* *
2193617 TTAGTCGACTAAAAGCTTACTACCAGAAACTGGGTTCAGAGACAAAGACGACTTAATCAACTAAG
1 TTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTAAG
2193682 TGGCAATGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (73 bp):
TTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTAAG
AAGTTTTA
Found at i:2193694 original size:73 final size:73
Alignment explanation
Indices: 2193542--2193701 Score: 185
Period size: 73 Copynumber: 2.2 Consensus size: 73
2193532 CAAGAGACAG
* * * * * * *
2193542 TGTTAGTCGACTTAGAGCTTACTGCCAAAAACTGGGTTTAGAGATAAAAATGACTTAATCGACTA
1 TGTTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTA
***
2193607 AGAAGTTT
66 AGAAGCAA
* * *
2193615 TATTAGTCGACTAAAAGCTTACTACCAGAAACTGGGTTCAGAGACAAAGACGACTTAATCAACTA
1 TGTTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTA
**
2193680 AGTGGCAA
66 AGAAGCAA
2193688 TGTTAGTCGACTAA
1 TGTTAGTCGACTAA
2193702 GAGCATTCTA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (73 bp):
TGTTAGTCGACTAAAAGCTTACTACCAAAAACTGGGTTCAGAGACAAAAACGACTTAATCAACTA
AGAAGCAA
Found at i:2194589 original size:40 final size:40
Alignment explanation
Indices: 2194534--2194614 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2194524 ATATGATTCT
2194534 TATTTAATGTCTATGGTCTCACCTAAAGCTAATTATTTGC
1 TATTTAATGTCTATGGTCTCACCTAAAGCTAATTATTTGC
*
2194574 TATTTAATGTCTATGGTCTCACCTGAAGCTAATTATTTGC
1 TATTTAATGTCTATGGTCTCACCTAAAGCTAATTATTTGC
2194614 T
1 T
2194615 TCCTTGCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (40 bp):
TATTTAATGTCTATGGTCTCACCTAAAGCTAATTATTTGC
Found at i:2194756 original size:19 final size:19
Alignment explanation
Indices: 2194732--2194780 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2194722 TTCTTACTCT
2194732 AAAAAAAAACTAATTT-TCA
1 AAAAAAAAACTAATTTCT-A
*
2194751 AAAAAAAACCCTAATTTCTA
1 AAAAAAAA-ACTAATTTCTA
*
2194771 GAAAAAAAAC
1 AAAAAAAAAC
2194781 CCTAATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.63, C:0.14, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAAAAAAACTAATTTCTA
Found at i:2194757 original size:20 final size:19
Alignment explanation
Indices: 2194732--2194780 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2194722 TTCTTACTCT
2194732 AAAAAAAAACTAATTTTCAA
1 AAAAAAAAACTAA-TTTCAA
** *
2194752 AAAAAAACCCTAATTTCTA
1 AAAAAAAAACTAATTTCAA
*
2194771 GAAAAAAAAC
1 AAAAAAAAAC
2194781 CCTAATATGA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.63, C:0.14, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAAAAAAACTAATTTCAA
Found at i:2194775 original size:21 final size:20
Alignment explanation
Indices: 2194729--2194786 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
2194719 TGCTTCTTAC
2194729 TCTAAAAAAAAA--CTAATT
1 TCTAAAAAAAAACCCTAATT
2194747 T-TCAAAAAAAAACCCTAATT
1 TCT-AAAAAAAAACCCTAATT
2194767 TCTAGAAAAAAAACCCTAAT
1 TCTA-AAAAAAAACCCTAAT
2194787 ATGAATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
20 8 0.23
21 16 0.46
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (20 bp):
TCTAAAAAAAAACCCTAATT
Found at i:2196956 original size:2 final size:2
Alignment explanation
Indices: 2196949--2197037 Score: 118
Period size: 2 Copynumber: 46.5 Consensus size: 2
2196939 ATGATGTTAG
2196949 TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC GTC TC -C TC -C T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC
2196988 TC TC TC TC TC TC -C TC TC ATC TC T- TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC
2197029 TC TC TC TC T
1 TC TC TC TC T
2197038 TCCCCTCTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
1 6 0.08
2 69 0.87
3 4 0.05
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2196991 original size:25 final size:25
Alignment explanation
Indices: 2196949--2197039 Score: 109
Period size: 25 Copynumber: 3.6 Consensus size: 25
2196939 ATGATGTTAG
2196949 TCTCTCT-CTCTCTCTCTCTCTCTCT
1 TCTCTCTCCTCTCT-TCTCTCTCTCT
2196974 TCTCGTCTCCTC-CTTCTCTCTCTC-
1 TCTC-TCTCCTCTCTTCTCTCTCTCT
*
2196998 TC-CTCTCATCTCTTCTCTCTCTCT
1 TCTCTCTCCTCTCTTCTCTCTCTCT
2197022 CTCTCTCTCTCTCTCTTC
1 -TCTCTCTC-CTCTCTTC
2197040 CCCTCTATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.11
23 13 0.23
24 2 0.04
25 16 0.28
26 10 0.18
27 10 0.18
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.49
Consensus pattern (25 bp):
TCTCTCTCCTCTCTTCTCTCTCTCT
Found at i:2196999 original size:27 final size:29
Alignment explanation
Indices: 2196949--2197034 Score: 113
Period size: 27 Copynumber: 3.0 Consensus size: 29
2196939 ATGATGTTAG
*
2196949 TCTCTCTCTCTCTCTCTCTCTCTCTTCTCG
1 TCTC-CTCTCTCTCTCTCTCTCTCTTCTCA
*
2196979 TCTCCTC-CT-TCTCTCTCTCTCCTCTCA
1 TCTCCTCTCTCTCTCTCTCTCTCTTCTCA
*
2197006 TCTCTTCTCTCTCTCTCTCTCTCTCTCTC
1 TCTCCTCTCTCTCTCTCTCTCTCT-TCTC
2197035 TCTTCCCCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 4 0.08
29 15 0.31
30 8 0.16
ACGTcount: A:0.01, C:0.49, G:0.01, T:0.49
Consensus pattern (29 bp):
TCTCCTCTCTCTCTCTCTCTCTCTTCTCA
Found at i:2198182 original size:67 final size:67
Alignment explanation
Indices: 2198042--2198187 Score: 184
Period size: 67 Copynumber: 2.2 Consensus size: 67
2198032 TCATGTCTTA
* * * * **
2198042 GTGTGTAACATCAATAAGAAGAAGAAAGTTTTGGCGTATACTATCTGGTGCTAAAGCTTTGATTT
1 GTGTGTAACATCAATAAGAAGAAGAAAGCTTTGGCGTACAATATCTGGTGCTAAAGCTTTAACCT
2198107 TG
66 TG
* * * * *
2198109 GAGTGTAACATCAATAGGAAGAAGGAAGCTTTGGCGTGCAATATCTGGTGCTCAAGCTTTAACCT
1 GTGTGTAACATCAATAAGAAGAAGAAAGCTTTGGCGTACAATATCTGGTGCTAAAGCTTTAACCT
2198174 TG
66 TG
*
2198176 GTGTGTACCATC
1 GTGTGTAACATC
2198188 CGGTGCTGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (67 bp):
GTGTGTAACATCAATAAGAAGAAGAAAGCTTTGGCGTACAATATCTGGTGCTAAAGCTTTAACCT
TG
Found at i:2198209 original size:34 final size:34
Alignment explanation
Indices: 2198155--2198238 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
2198145 TGCAATATCT
* ** *
2198155 GGTGCTCAAGCTTTAACCTTGGTGTGT-ACCATCC
1 GGTGCTGAAGCTTTGGCCTTGGCGTGTGA-CATCC
*
2198189 GGTGCTGAAGCTTTGGCCTTGGCGTGTGACATCT
1 GGTGCTGAAGCTTTGGCCTTGGCGTGTGACATCC
**
2198223 ATTGCTGAAGCTTTGG
1 GGTGCTGAAGCTTTGG
2198239 TGTGTAACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 41 0.98
35 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (34 bp):
GGTGCTGAAGCTTTGGCCTTGGCGTGTGACATCC
Found at i:2198814 original size:27 final size:27
Alignment explanation
Indices: 2198784--2198841 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
2198774 ATCATAAAAA
**
2198784 AACATGACGTGTAATAATTTTTTTTTC
1 AACATGACGTGTAATAACATTTTTTTC
* *
2198811 AACATGAGGTGTAATAGCATTTTTTTC
1 AACATGACGTGTAATAACATTTTTTTC
2198838 AACA
1 AACA
2198842 CGTACGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (27 bp):
AACATGACGTGTAATAACATTTTTTTC
Found at i:2205650 original size:29 final size:28
Alignment explanation
Indices: 2205600--2205655 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2205590 TATCTTCTTT
* *
2205600 TAAAATTTTTGAAAAAATAAAATAAAAA
1 TAAAAATTTTGAAAAAATAAAACAAAAA
2205628 TAAAAATTTTGACAACAAA-AAAACAAAA
1 TAAAAATTTTGA-AA-AAATAAAACAAAA
2205656 TTAGGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 10 0.42
30 3 0.12
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (28 bp):
TAAAAATTTTGAAAAAATAAAACAAAAA
Found at i:2207234 original size:35 final size:35
Alignment explanation
Indices: 2207188--2207257 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
2207178 GTCAACAAAT
*
2207188 GGATGCTTAGCATTATATACATCAAATATAACCTA
1 GGATGCATAGCATTATATACATCAAATATAACCTA
*
2207223 GGATGCATAGCATTGTATACATCAAATATAACCTA
1 GGATGCATAGCATTATATACATCAAATATAACCTA
2207258 TCTACCACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (35 bp):
GGATGCATAGCATTATATACATCAAATATAACCTA
Found at i:2214823 original size:22 final size:22
Alignment explanation
Indices: 2214780--2214823 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2214770 TCACCTTAGC
**
2214780 TGTCTATATGCTGTAATGAAGG
1 TGTCTATATGCTGTAACAAAGG
2214802 TGTCTATATGCTGTAACAAAGG
1 TGTCTATATGCTGTAACAAAGG
2214824 CGAGCAAAAA
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:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (22 bp):
TGTCTATATGCTGTAACAAAGG
Found at i:2217150 original size:40 final size:41
Alignment explanation
Indices: 2217074--2217153 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
2217064 TAGGCTATTA
* * * *
2217074 TTCACCTTAGTGGGGTTTTTTAACCTTGTCAAGATTGGTGG
1 TTCACCTTAGTGGGGCTTTCTAACCTCGCCAAGATTGGTGG
*
2217115 TTCACCTTAGT-GGGCTTTCTAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGCTTTCTAACCTCGCCAAGATTGGTG
2217154 TCTTTCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 23 0.68
41 11 0.32
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (41 bp):
TTCACCTTAGTGGGGCTTTCTAACCTCGCCAAGATTGGTGG
Found at i:2218937 original size:6 final size:6
Alignment explanation
Indices: 2218926--2218957 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2218916 AAAATAGTAA
*
2218926 GGCAAT GGCAAT GGCAAT GGCAAT GGCTAT GG
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GG
2218958 ATGAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.38, T:0.19
Consensus pattern (6 bp):
GGCAAT
Found at i:2219433 original size:18 final size:18
Alignment explanation
Indices: 2219410--2219474 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
2219400 TTTCTTGCAT
2219410 TTTTTTCATTTTTCTGTA
1 TTTTTTCATTTTTCTGTA
*
2219428 TTTTTT-A-TTTTCAGTA
1 TTTTTTCATTTTTCTGTA
*
2219444 TTTTTATTATTTTT-TGTA
1 TTTTT-TCATTTTTCTGTA
2219462 TTTTTTTCATTTT
1 -TTTTTTCATTTT
2219475 CCTGCACGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.32
17 2 0.05
18 16 0.40
19 9 0.22
ACGTcount: A:0.14, C:0.06, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTCATTTTTCTGTA
Found at i:2219449 original size:15 final size:16
Alignment explanation
Indices: 2219419--2219467 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2219409 TTTTTTTCAT
*
2219419 TTTTCTGTATTTTTTA
1 TTTTCAGTATTTTTTA
2219435 TTTTCAGTATTTTTATTA
1 TTTTCAGTA-TTTT-TTA
**
2219453 TTTTTTGTATTTTTT
1 TTTTCAGTATTTTTT
2219468 TCATTTTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.36
17 8 0.29
18 10 0.36
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTCAGTATTTTTTA
Found at i:2219506 original size:16 final size:16
Alignment explanation
Indices: 2219487--2219532 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
2219477 TGCACGCTTA
*
2219487 ATTTCTTTGTATTTTT
1 ATTTCTGTGTATTTTT
*
2219503 ATTTCTGT-TATTTCT
1 ATTTCTGTGTATTTTT
2219518 ATTT-TGTGTATTTTT
1 ATTTCTGTGTATTTTT
2219533 TTAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 3 0.12
15 16 0.62
16 7 0.27
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.72
Consensus pattern (16 bp):
ATTTCTGTGTATTTTT
Found at i:2222610 original size:940 final size:907
Alignment explanation
Indices: 2220843--2223515 Score: 2925
Period size: 909 Copynumber: 2.9 Consensus size: 907
2220833 GCACATTTAT
* * * * *
2220843 AACTTACCTCATG-ATTGTTAAAATTTCTACATGATTGGAATAAATAGCAACTATAATTTATTTT
1 AACTT-CCTCATGAATTGTTAAAATTTCTACATGATTAGAAAAAATAACAACTATAGTTTGTTTT
* *
2220907 CTAAAACACTATGAAATAGTTGTACCTCTT--TATCTGAATAAGTAATCTATTTA-AGATTAAGC
65 C-AAAACACTATGAAATAGTTGTA--TCTTCATATGTGAATAAGTAATCTATCTAGA-ATTAAGC
* * *
2220969 TTTATGTGGATCAAATAAATATTCTACGTATACATAACCAATGCATTTGAATAATATAAGCCCAT
126 TTTATGTAGATCAAATAAATATTCTACGTATGCATAACCAATGCATTTGAATACTATAAGCCCAT
* * * * * * * *
2221034 GTCTATTGTTCTTCAGAGATA-TCAAA-GTATGTTAATTCTATTCTAATTTCTTTGAGTTTGAGA
191 ATCCATTATTCTTCAGAGATATTGAAATATATGTTAATTCCATTCCAATTTCTTTGAGTTAGAGA
* * *
2221097 AAAACTATATCTTATTAATAAAATTATAACAAATGATATATTAGGTCATGTATTGCAAACAAGAT
256 AAAACTATATCTTATTAATAAATTTATAACAAATGATATATTAGGTCGTGTATTGCTAACAAGAT
* * * * ** *
2221162 ATATCAGTGCTCCAATTATATTAAGATATAGTACTTCA-GACCAAGAAGTTTTTTATCATTCTCA
321 ATATTAGT-CTCCAATTATACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTTATCATTCTCA
* * * * * *
2221226 CGAGGTCAAAAATGATACTTTGTCACATTTAATAACCTTAATACCATTGGTGAACTCAATGGATA
385 AGAGGTCGAAAATGGTACTTTCTCACATCTAATGACCTTAA-A-CATTGGTGAACTCAATGGATA
* * * *
2221291 TGCTTTGTCTATATAGAATTGTTTTAGCACGTTTGTTATATAATTTGATTGATGGAC-GAA--AA
448 TGCTTTGTCTATATAGAATTGTTTTAACACTTTTGTTATATAATTTGATTGATAGACAAAATTAA
* * * * *
2221353 TTTGTCAAGTACTCAATCTAAAGA-CTCAAACAAAATTTTTTTTTTC-AAAGATCTTTCATCTTA
513 TTTGTCAAGTGCTCAATCTGAAGACCT-AAAAAAAATTTTGTTTTTCAAAAG-TCTTTCATCTCA
* * * * * * **
2221416 AATTCTTTCTTTATGTAATTCATGGCTTTTGCTAACTTTTTAAGAGTTTTAATAATGTTTATGTC
576 AATTCTTTTTTTATGTAATTCACGACTTTTGATAACTCTTCAAGAGTTCAAATAATGTTTATGTC
* * * *
2221481 ATCAACATAAATAGCAATTATGACAAATTCATATCCAAATCTTTTTACAAAAACATATAAGCATA
641 ATCAACATAAAAAACAATTATGACAAATTCATATCCAAATCTTTTTATAAAAACACATAAGCATA
* * * *
2221546 TGGGATCATTTTTATAGTCTTCTTTTAACAAATATTCATTGAGATGATTATACCATATGCATCTA
706 TAGGATCATTTTTATAG--TTCTTTTAACAAATATTCATTAAGATGATTATACCACATGCATCCA
* * * ** *
2221611 GATTGCTTTAATTTATATACATATTTGTTTAATTTGATTGAATAAATTTCTTGAGAATTGTGTAC
769 AATTGCTTTAATTTATATACATATTTATTTAACTTGATTGAATAAATTTCTAAAGAATTGTGTAA
* * *
2221676 ATATAATGTTATTGAAATTTCTTTCTTGATTGACAAGCCACACGTTTCTGAAATATGTTGAATTA
834 ATATAATGTTATTGAAATTTCCTTCTTGATTGACAAGCCACACATTTCTCAAATATGTTGAA-T-
2221741 CATATCTTAACAAGACATATTCAG
897 --TA-C---A-AA-AC---TT--G
* * *
2221765 ACATACTCACAACTTGCCTCATGAATTGTTAAAATTTCTATATGATTAAAAAAAATTAACAACAA
1 ----------AACTT-CCTCATGAATTGTTAAAATTTCTACATGATTAGAAAAAA-TAACAACTA
*
2221830 TAGTTTGTTTTGCAAAACATTATGAAATAGTTGTATCTTCATATGTGAATAAGTAATCTATCTAG
54 TAGTTTGTTTT-CAAAACACTATGAAATAGTTGTATCTTCATATGTGAATAAGTAATCTATCTAG
* * * *
2221895 AATTGAGCTTTATGTAGATCAAATAAATATTCTACATATGCATAA-CAATGTATTTAAATACTAT
118 AATTAAGCTTTATGTAGATCAAATAAATATTCTACGTATGCATAACCAATGCATTTGAATACTAT
* * * * * *
2221959 AAGCACATATCCATTTTTATTTAGAGATATTGAAATATATGTTAATTCCATTCCAATTTATTTAA
183 AAGCCCATATCCATTATTCTTCAGAGATATTGAAATATATGTTAATTCCATTCCAATTTCTTTGA
* * * * *
2222024 GTCAGA-AGAAAACTATATCTTACTAATAAATTTATAGCAAATGGTATATTAGGTCGTGTATCGC
248 GTTAGAGA-AAAACTATATCTTATTAATAAATTTATAACAAATGATATATTAGGTCGTGTATTGC
* * ** *
2222088 TAGCAATATATATTAGTACTCCAATTGCACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTCA
312 TAACAAGATATATTAGT-CTCCAATTATACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTTA
* * * * * * *
2222153 TTATCCTCAAAAGGTTGGAAATGGTACTTT-TCATATCTAATGATCTTATAATCATTGGTGAACT
376 TCATTCTCAAGAGGTCGAAAATGGTACTTTCTCACATCTAATGACCTTA-AA-CATTGGTGAACT
* * * *
2222217 CAATGGATATGCTTTATCTATATAAAATTATTTTAACATTTTTGTTATATAATTTGATTGATAGA
439 CAATGGATATGCTTTGTCTATATAGAATTGTTTTAACACTTTTGTTATATAATTTGATTGATAGA
* * * * *
2222282 CAAAATTCAATTTGTCAAATGCTTAATATGAAGACCTAAAAAGAAACTTTGTTTTTCAAAAGTTT
504 CAAAATT-AATTTGTCAAGTGCTCAATCTGAAGACCTAAAAA-AAATTTTGTTTTTCAAAAGTCT
* * * *
2222347 TTTATCTCAGATTCTTTTTTTATGTAATTCACGACTTTTAATAACTCTTCAAGAGTTCCAATAAT
567 TTCATCTCAAATTCTTTTTTTATGTAATTCACGACTTTTGATAACTCTTCAAGAGTTCAAATAAT
* * *
2222412 GTTTATATCATTAACATAAAAAACAAGTATGACAAATTCATATCCAAATCTTTTTATAAAAACAC
632 GTTTATGTCATCAACATAAAAAACAATTATGACAAATTCATATCCAAATCTTTTTATAAAAACAC
* * *
2222477 ATGAGCATATAGGATCATTTTTATAG-TC-TTTAACAAATATTCATTAAGGTGATTATACTACAT
697 ATAAGCATATAGGATCATTTTTATAGTTCTTTTAACAAATATTCATTAAGATGATTATACCACAT
** *
2222540 GTGTCCAAATTGCTTTAATCCATATATATATATATTTATTTAACTTGATTGAATAAATTTCTAAA
762 GCATCCAAATTGCTTTAAT---T-TATATACATATTTATTTAACTTGATTGAATAAATTTCTAAA
* * *
2222605 GAATTGTGTAAATATAATGTTGTTGGAATTTCCTTCTTGATTGACAAGCCACATATTTCTCAAAT
823 GAATTGTGTAAATATAATGTTATTGAAATTTCCTTCTTGATTGACAAGCCACACATTTCTCAAAT
2222670 ATGTTGAATTACAAAACTTG
888 ATGTTGAATTACAAAACTTG
* ***
2222690 --C-T--TCATGAATTGTTGAAATTTCTACATGATTAGAAGAACGCAACAACTAT-GTTTTGTTT
1 AACTTCCTCATGAATTGTTAAAATTTCTACATGATTAGAA-AAAATAACAACTATAG-TTTGTTT
* * * * *
2222749 TATAAAACACTATGAAATAGTTGTATCTCCATATGTGAATAAGTAATCTGTCTAGGATCAAG-TT
64 T-CAAAACACTATGAAATAGTTGTATCTTCATATGTGAATAAGTAATCTATCTAGAATTAAGCTT
* *
2222813 GTATGTAGATCAAATAAATATTTTACGTATGCATAACCAAAGCATTTGAATAAC-ATAAGCCCAT
128 -TATGTAGATCAAATAAATATTCTACGTATGCATAACCAATGCATTTGAAT-ACTATAAGCCCAT
* * * * *
2222877 TTCCATTATTCTTCAAAGATATTGAAGTACATGTTAATTCC-TTCCAATTGCTTTGAGTTAGAGA
191 ATCCATTATTCTTCAGAGATATTGAAATATATGTTAATTCCATTCCAATTTCTTTGAGTTAGAGA
* * * *
2222941 AAAATTATATCTTATTAATAAATTTATAACAAATGATATATCAAGTCGTATATTGCTAACAAGAT
256 AAAACTATATCTTATTAATAAATTTATAACAAATGATATATTAGGTCGTGTATTGCTAACAAGAT
* * * *
2223006 ACATTAGTGTGCTAATTATACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTTATCATTCTTA
321 ATATTAGTCT-CCAATTATACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTTATCATTCTCA
* * * * *
2223071 TGAGGTCGAAAAT-GTACTTTCTCACAACTAATGACCTTACAACTATTGGTAAACTCAATGAATG
385 AGAGGTCGAAAATGGTACTTTCTCACATCTAATGACCTTA-AAC-ATTGGTGAACTCAATGGATA
* * *
2223135 TTCTTTGTCTATATAGAATTGTTTTAACGCTTTTGTTATATAATTTGATTGATAGATAAAAATAT
448 TGCTTTGTCTATATAGAATTGTTTTAACACTTTTGTTATATAATTTGATTGATAGA-CAAAAT-T
* * * *
2223200 AATTTGTCAAGTGCTCAATCTGAAGACCCAAATAAAATTTTGGTTTGCAAAAGTCTTTCATCTCA
511 AATTTGTCAAGTGCTCAATCTGAAGACCTAAAAAAAATTTTGTTTTTCAAAAGTCTTTCATCTCA
* * * *
2223265 AATGCTTTTTTTATGTAATTCACAACTTTTGATAAATCTTCAAGAGTTCAAATAATATTTATGTC
576 AATTCTTTTTTTATGTAATTCACGACTTTTGATAACTCTTCAAGAGTTCAAATAATGTTTATGTC
* * *
2223330 ACCAACATAAACAACAATTATAACAAATTCATATCCAAATCTTTTTATAAAAACACATAAGCATA
641 ATCAACATAAAAAACAATTATGACAAATTCATATCCAAATCTTTTTATAAAAACACATAAGC--A
** * * * ** * *
2223395 TTATAAAATCATTTTATTATAATCTTTTTTTAACAAATATTCACTAAGACAATTATATCACATAC
704 -TATAGGATCA-TTT-TTAT-A-GTTCTTTTAACAAATATTCATTAAGATGATTATACCACATGC
* * ** *
2223460 ATCCAGATTACTTTAATCCATATACATATTTATTTAATTTGATTGAATAAATTTCT
764 ATCCAAATTGCTTTAATTTATATACATATTTATTTAACTTGATTGAATAAATTTCT
2223516 CGAGAATTAT
Statistics
Matches: 1463, Mismatches: 236, Indels: 102
0.81 0.13 0.06
Matches are distributed among these distances:
908 12 0.01
909 490 0.33
910 91 0.06
911 4 0.00
912 9 0.01
913 4 0.00
914 39 0.03
915 1 0.00
917 1 0.00
918 43 0.03
925 1 0.00
927 2 0.00
930 2 0.00
931 2 0.00
932 17 0.01
933 66 0.05
934 103 0.07
935 204 0.14
936 86 0.06
937 2 0.00
939 27 0.02
940 253 0.17
941 4 0.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (907 bp):
AACTTCCTCATGAATTGTTAAAATTTCTACATGATTAGAAAAAATAACAACTATAGTTTGTTTTC
AAAACACTATGAAATAGTTGTATCTTCATATGTGAATAAGTAATCTATCTAGAATTAAGCTTTAT
GTAGATCAAATAAATATTCTACGTATGCATAACCAATGCATTTGAATACTATAAGCCCATATCCA
TTATTCTTCAGAGATATTGAAATATATGTTAATTCCATTCCAATTTCTTTGAGTTAGAGAAAAAC
TATATCTTATTAATAAATTTATAACAAATGATATATTAGGTCGTGTATTGCTAACAAGATATATT
AGTCTCCAATTATACTAAGATATGGTACTTTAGGATTAAGAAGTTCTTTATCATTCTCAAGAGGT
CGAAAATGGTACTTTCTCACATCTAATGACCTTAAACATTGGTGAACTCAATGGATATGCTTTGT
CTATATAGAATTGTTTTAACACTTTTGTTATATAATTTGATTGATAGACAAAATTAATTTGTCAA
GTGCTCAATCTGAAGACCTAAAAAAAATTTTGTTTTTCAAAAGTCTTTCATCTCAAATTCTTTTT
TTATGTAATTCACGACTTTTGATAACTCTTCAAGAGTTCAAATAATGTTTATGTCATCAACATAA
AAAACAATTATGACAAATTCATATCCAAATCTTTTTATAAAAACACATAAGCATATAGGATCATT
TTTATAGTTCTTTTAACAAATATTCATTAAGATGATTATACCACATGCATCCAAATTGCTTTAAT
TTATATACATATTTATTTAACTTGATTGAATAAATTTCTAAAGAATTGTGTAAATATAATGTTAT
TGAAATTTCCTTCTTGATTGACAAGCCACACATTTCTCAAATATGTTGAATTACAAAACTTG
Found at i:2224961 original size:8 final size:8
Alignment explanation
Indices: 2224944--2225049 Score: 52
Period size: 9 Copynumber: 12.2 Consensus size: 8
2224934 ATGAATAGTT
*
2224944 TTTTTTTA
1 TTTTTGTA
2224952 TTTTTGTA
1 TTTTTGTA
*
2224960 TTGTTGTA
1 TTTTTGTA
*
2224968 TTTTCTATA
1 TTTT-TGTA
*
2224977 TTTTTATTA
1 TTTTT-GTA
2224986 TTTTTTGTA
1 -TTTTTGTA
*
2224995 TTTTTTTTCA
1 -TTTTTGT-A
*
2225005 TTTTTCTA
1 TTTTTGTA
* *
2225013 TACTTTTAATT
1 T--TTTT-GTA
2225024 TTTTTGTA
1 TTTTTGTA
2225032 -TTTTGTA
1 TTTTTGTA
2225039 TTTTTTGTA
1 -TTTTTGTA
2225048 TT
1 TT
2225050 ATTAATTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
7 7 0.09
8 23 0.30
9 35 0.45
10 10 0.13
11 2 0.03
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.75
Consensus pattern (8 bp):
TTTTTGTA
Found at i:2225035 original size:16 final size:15
Alignment explanation
Indices: 2225016--2225076 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
2225006 TTTTCTATAC
2225016 TTTTAATTTTTTTGTA
1 TTTT-ATTTTTTTGTA
*
2225032 TTTTGTATTTTTTGTA
1 TTTTAT-TTTTTTGTA
*
2225048 TTATTAATTTTTGTGT-
1 TT-TT-ATTTTTTTGTA
2225064 TTTCTATTTTTTT
1 TTT-TATTTTTTT
2225077 AATTATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 9 0.24
16 18 0.49
17 9 0.24
18 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTTTGTA
Found at i:2225041 original size:17 final size:16
Alignment explanation
Indices: 2224952--2225076 Score: 67
Period size: 17 Copynumber: 7.3 Consensus size: 16
2224942 TTTTTTTTTA
2224952 TTTTTGTATTGTTGTA-T
1 TTTTTGTATT-TT-TATT
* *
2224969 TTTCTATATTTTTATTAT
1 TTTTTGTATTTTTA-T-T
*
2224987 TTTTTGTATTTTTTTT
1 TTTTTGTATTTTTATT
*
2225003 CATTTTTCTATACTTTTAATT
1 --TTTTTGTAT--TTTT-ATT
2225024 TTTTTGTATTTTGTA-T
1 TTTTTGTATTTT-TATT
*
2225040 TTTTTGTATTATTAATT
1 TTTTTGTATT-TTTATT
* *
2225057 TTTGTGT-TTTCTATT
1 TTTTTGTATTTTTATT
2225072 TTTTT
1 TTTTT
2225077 AATTATAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
15 10 0.12
16 17 0.20
17 22 0.26
18 21 0.25
19 8 0.10
20 4 0.05
21 2 0.02
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTTTGTATTTTTATT
Found at i:2225043 original size:18 final size:17
Alignment explanation
Indices: 2224942--2225076 Score: 71
Period size: 18 Copynumber: 7.8 Consensus size: 17
2224932 AGATGAATAG
*
2224942 TTTTTTTTTATTTTTGTA
1 TTTTTATTT-TTTTTGTA
* * * * *
2224960 TTGTTGTATTTTCTATA
1 TTTTTATTTTTTTTGTA
2224977 TTTTTATTATTTTTTGTA
1 TTTTTATT-TTTTTTGTA
*
2224995 TTTTT-TTTCATTTTTCTA
1 TTTTTATTT--TTTTTGTA
*
2225013 TACTTTTAATTTTTTTGTA
1 T--TTTTATTTTTTTTGTA
2225032 TTTTGTA--TTTTTTGTA
1 TTTT-TATTTTTTTTGTA
* * *
2225048 TTATTAATTTTTGTGT-
1 TTTTTATTTTTTTTGTA
*
2225064 TTTCTATTTTTTT
1 TTTTTATTTTTTT
2225077 AATTATAAAA
Statistics
Matches: 89, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
15 2 0.02
16 22 0.25
17 23 0.26
18 28 0.31
19 8 0.09
20 4 0.04
21 2 0.02
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTTTGTA
Found at i:2229822 original size:2 final size:2
Alignment explanation
Indices: 2229815--2229842 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2229805 ATTTATTTTG
2229815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2229843 TTAGCTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2230061 original size:28 final size:28
Alignment explanation
Indices: 2230002--2230096 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
2229992 ATCTCTTCAC
* *
2230002 TATTCATCCACTCCTAACG-GTTAAAAA
1 TATTCATCCACTCTTAATGAGTTAAAAA
*
2230029 TATTCATCCACTCTTGATGAGTTAAAAA
1 TATTCATCCACTCTTAATGAGTTAAAAA
* * *
2230057 TATTCATCCACTTTTTATGAGTTAAAAG
1 TATTCATCCACTCTTAATGAGTTAAAAA
*
2230085 TATTTATCCACT
1 TATTCATCCACT
2230097 TGTGGTGGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 16 0.27
28 44 0.73
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (28 bp):
TATTCATCCACTCTTAATGAGTTAAAAA
Found at i:2230097 original size:28 final size:28
Alignment explanation
Indices: 2230021--2230181 Score: 125
Period size: 28 Copynumber: 5.8 Consensus size: 28
2230011 ACTCCTAACG
*
2230021 GTTAAAAATATTCATCCACTCTTGATGA
1 GTTAAAAATATTCATCCACTTTTGATGA
*
2230049 GTTAAAAATATTCATCCACTTTTTATGA
1 GTTAAAAATATTCATCCACTTTTGATGA
* * * *
2230077 GTTAAAAGTATTTATCCACTTGTGGTG-
1 GTTAAAAATATTCATCCACTTTTGATGA
* * * *
2230104 GATT-AAAGTATTCATCCAATTCT-ATTGG
1 G-TTAAAAATATTCATCCACTTTTGA-TGA
* * *
2230132 GTT-AAAATATTCATCTACTTCTGGT-A
1 GTTAAAAATATTCATCCACTTTTGATGA
* *
2230158 GGTTAAAAGTATTCATCTACTTTT
1 -GTTAAAAATATTCATCCACTTTT
2230182 AAAAATAGTG
Statistics
Matches: 109, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
27 41 0.38
28 68 0.62
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (28 bp):
GTTAAAAATATTCATCCACTTTTGATGA
Found at i:2230116 original size:55 final size:56
Alignment explanation
Indices: 2230025--2230181 Score: 155
Period size: 55 Copynumber: 2.8 Consensus size: 56
2230015 CTAACGGTTA
* *
2230025 AAAATATTCATCCAC-TCTTG-ATGAGTTAAAAATATTCATCCACTTTTTA-TGAGTT
1 AAAATATTCATCCACTTCTGGTA-G-GTTAAAAGTATTCATCCACTTTTTATTGAGTT
* * * * *
2230080 AAAAGTATTTATCCACTTGTGGT-GGATT-AAAGTATTCATCCA-ATTCTATTGGGTT
1 AAAA-TATTCATCCACTTCTGGTAGG-TTAAAAGTATTCATCCACTTTTTATTGAGTT
* *
2230135 AAAATATTCATCTACTTCTGGTAGGTTAAAAGTATTCATCTACTTTT
1 AAAATATTCATCCACTTCTGGTAGGTTAAAAGTATTCATCCACTTTT
2230182 AAAAATAGTG
Statistics
Matches: 81, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
54 21 0.26
55 42 0.52
56 15 0.19
57 3 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (56 bp):
AAAATATTCATCCACTTCTGGTAGGTTAAAAGTATTCATCCACTTTTTATTGAGTT
Found at i:2230120 original size:27 final size:26
Alignment explanation
Indices: 2230002--2230179 Score: 97
Period size: 28 Copynumber: 6.5 Consensus size: 26
2229992 ATCTCTTCAC
* *** *
2230002 TATTCATCCACTCCTAACGGTTAAAAA
1 TATTCATCCACTTCTGGTGGTT-AAAG
* *
2230029 TATTCATCCAC-TCTTGATGAGTTAAAAA
1 TATTCATCCACTTC-TGGTG-GTT-AAAG
* **
2230057 TATTCATCCACTTTTTATGAGTTAAAAG
1 TATTCATCCACTTCTGGTG-GTT-AAAG
* *
2230085 TATTTATCCACTTGTGGTGGATTAAAG
1 TATTCATCCACTTCTGGTGG-TTAAAG
* ** *
2230112 TATTCATCCAATTCTATTGGGTTAAAA
1 TATTCATCCACTTCTGGT-GGTTAAAG
*
2230139 TATTCATCTACTTCTGGTAGGTTAAAAG
1 TATTCATCCACTTCTGGT-GGTT-AAAG
*
2230167 TATTCATCTACTT
1 TATTCATCCACTT
2230180 TTAAAAATAG
Statistics
Matches: 123, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.01
27 55 0.45
28 66 0.54
29 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (26 bp):
TATTCATCCACTTCTGGTGGTTAAAG
Found at i:2239869 original size:86 final size:86
Alignment explanation
Indices: 2239724--2240595 Score: 1230
Period size: 86 Copynumber: 10.2 Consensus size: 86
2239714 ATTATTGACA
* * *
2239724 GTAAAATAAATTTATATTACTTGAACTATGCTGAAAACTTAAATATATAAAATTTTTATATTAGC
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* *
2239789 TGAACTTGTAAATTGATAAAT
66 TGAACTTGTAAACTAATAAAT
* * * * *
2239810 GTAAAATAAATTCATATTACTTGAGCTATTATGAAAACTTAAATATATCAAATTTTTATATTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
*
2239875 TGAACTTGTAAACTGATAAAT
66 TGAACTTGTAAACTAATAAAT
* *
2239896 GTAAAATAAATTTATATTACTTGAACTATAATGCAAACTTTAATATATAAAATTTTTATATTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* *
2239961 TGAACTTGTAAACTGATAATT
66 TGAACTTGTAAACTAATAAAT
* * *
2239982 CTAAAATAAATTTATATTACTTAAACTATGATGCAAACTT-AA-ATATAAAATTTTTATATTAAT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* * * *
2240045 GGAATTTGTAGATTAATAAAT
66 TGAACTTGTAAACTAATAAAT
* *
2240066 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAGATATATAAAATTTTTATAGTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* * * *
2240131 TAAACTTATAAACTAACAAAC
66 TGAACTTGTAAACTAATAAAT
*
2240152 GTAAAATTAATTTATATTACTTGAACTATGATGCAAACTT-AATATATAAAATTTTTATATTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
2240216 TGAACTTGTAAACTAATAAAT
66 TGAACTTGTAAACTAATAAAT
* * *
2240237 GTAAAATAAATTTATATTACTTGAACTATGGTGCAAACTTAAATATATAAAACTTTTATATTAAT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* *
2240302 TGAACTTGAAAACTAATTAAT
66 TGAACTTGTAAACTAATAAAT
* * * *
2240323 GTAAAATGAATTTATATTACTTGAACTATGATGCAAACTTAAATATGTAAAATCTTTATAGTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* * *
2240388 TGACCATGTAAACTAACAAAT
66 TGAACTTGTAAACTAATAAAT
* * * * *
2240409 GTAAAATTAATTTATATTATTTGAACGATGATGTAAACTT-AATATATAAAATTTTTATACTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* * *
2240473 TGAATTTGGAAACTAACAAAT
66 TGAACTTGTAAACTAATAAAT
*
2240494 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATAATAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
* * *
2240559 TAAACTTATAAACTAACAAAT
66 TGAACTTGTAAACTAATAAAT
*
2240580 GTAAAATTAATTTATA
1 GTAAAATAAATTTATA
2240596 GGAAAAATAT
Statistics
Matches: 699, Mismatches: 83, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
84 73 0.10
85 154 0.22
86 472 0.68
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (86 bp):
GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAGT
TGAACTTGTAAACTAATAAAT
Found at i:2240274 original size:171 final size:171
Alignment explanation
Indices: 2239724--2240595 Score: 1219
Period size: 171 Copynumber: 5.1 Consensus size: 171
2239714 ATTATTGACA
* * *
2239724 GTAAAATAAATTTATATTACTTGAACTATGCTGAAAACTTAAATATATAAAATTTTTATATTAGC
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTT-AATATATAAAATTTTTATATTAGT
* * * * * *
2239789 TGAACTTGTAAATTGATAAATGTAAAATAAATTCATATTACTTGAGCTATTATGAAAACTTAAAT
65 TGAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* *
2239854 ATATCAAATTTTTATATTAGTTGAACTTGTAAACTGATAAAT
130 ATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
*
2239896 GTAAAATAAATTTATATTACTTGAACTATAATGCAAACTTTAATATATAAAATTTTTATATTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAAC-TTAATATATAAAATTTTTATATTAGT
* * * *
2239961 TGAACTTGTAAACTGATAATTCTAAAATAAATTTATATTACTTAAACTATGATGCAAACTT-AA-
65 TGAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* * * * *
2240024 ATATAAAATTTTTATATTAATGGAATTTGTAGATTAATAAAT
130 ATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
*
2240066 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAGATATATAAAATTTTTATAGTAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTA-ATATATAAAATTTTTATATTAGT
* * * * *
2240131 TAAACTTATAAACTAACAAACGTAAAATTAATTTATATTACTTGAACTATGATGCAAACTT-AAT
65 TGAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
2240195 ATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
130 ATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
* * *
2240237 GTAAAATAAATTTATATTACTTGAACTATGGTGCAAACTTAAATATATAAAACTTTTATATTAAT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTT-AATATATAAAATTTTTATATTAGT
* * *
2240302 TGAACTTGAAAACTAATTAATGTAAAATGAATTTATATTACTTGAACTATGATGCAAACTTAAAT
65 TGAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* * * * * *
2240367 ATGTAAAATCTTTATAGTAGTTGACCATGTAAACTAACAAAT
130 ATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
* * * * *
2240409 GTAAAATTAATTTATATTATTTGAACGATGATGTAAACTTAATATATAAAATTTTTATACTAGTT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTT
* * *
2240474 GAATTTGGAAACTAACAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATA
66 GAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATA
* * * *
2240539 TATAAAATTTTTATAATAGTTAAACTTATAAACTAACAAAT
131 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
*
2240580 GTAAAATTAATTTATA
1 GTAAAATAAATTTATA
2240596 GGAAAAATAT
Statistics
Matches: 623, Mismatches: 72, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
169 3 0.00
170 148 0.24
171 284 0.46
172 186 0.30
173 2 0.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (171 bp):
GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTT
GAACTTGTAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATA
TATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
Found at i:2240404 original size:257 final size:257
Alignment explanation
Indices: 2239724--2240595 Score: 1255
Period size: 257 Copynumber: 3.4 Consensus size: 257
2239714 ATTATTGACA
* * **
2239724 GTAAAATAAATTTATATTACTTGAACTATGCTGAAAACTTAAATATATAAAATTTTTATATTAGC
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAAT
* * * * * * *
2239789 TGAACTTGTAAATTGATAAATGTAAAATAAATTCATATTACTTGAGCTATTATGAAAACTTAAAT
66 TGAACTTGAAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* * * * *
2239854 ATATCAAATTTTTATATTAGTTGAACTTGTAAACTGATAAATGTAAAATAAATTTATATTACTTG
131 ATATAAAATTTTTATAGTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTG
* * *
2239919 AACTATAATGCAAACTTTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTGATAATT
196 AACTATGATGCAAAC-TTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
* *
2239982 CTAAAATAAATTTATATTACTTAAACTATGATGCAAACTT-AA-ATATAAAATTTTTATATTAAT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAAT
* * * * * *
2240045 GGAATTTGTAGATTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAGAT
66 TGAACTTGAAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* * *
2240110 ATATAAAATTTTTATAGTAGTTAAACTTATAAACTAACAAACGTAAAATTAATTTATATTACTTG
131 ATATAAAATTTTTATAGTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTG
2240175 AACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
196 AACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
* *
2240237 GTAAAATAAATTTATATTACTTGAACTATGGTGCAAACTTAAATATATAAAACTTTTATATTAAT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAAT
* *
2240302 TGAACTTGAAAACTAATTAATGTAAAATGAATTTATATTACTTGAACTATGATGCAAACTTAAAT
66 TGAACTTGAAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
* * * * *
2240367 ATGTAAAATCTTTATAGTAGTTGACCATGTAAACTAACAAATGTAAAATTAATTTATATTATTTG
131 ATATAAAATTTTTATAGTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTG
* * * * * *
2240432 AACGATGATGTAAACTTAATATATAAAATTTTTATACTAGTTGAATTTGGAAACTAACAAAT
196 AACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
* *
2240494 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATAATAGT
1 GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAAT
* * *
2240559 TAAACTT-ATAAACTAACAAATGTAAAATTAATTTATA
66 TGAACTTGA-AAACTAATAAATGTAAAATAAATTTATA
2240596 GGAAAAATAT
Statistics
Matches: 551, Mismatches: 60, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
255 82 0.15
256 149 0.27
257 284 0.52
258 36 0.07
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (257 bp):
GTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAATATATAAAATTTTTATATTAAT
TGAACTTGAAAACTAATAAATGTAAAATAAATTTATATTACTTGAACTATGATGCAAACTTAAAT
ATATAAAATTTTTATAGTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTG
AACTATGATGCAAACTTAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAAT
Found at i:2241293 original size:79 final size:78
Alignment explanation
Indices: 2241177--2241333 Score: 269
Period size: 79 Copynumber: 2.0 Consensus size: 78
2241167 TATTTGAACT
*
2241177 ATGATGCAAACTTAATACATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAATGTAAAAT
1 ATGATGCAAACTTAATACATAAAATTTTTATAGTAGTTGAACTTGTAAACTAATAAATGTAAAAT
2241242 TAATTTATATTAC
66 TAATTTATATTAC
* * *
2241255 ATGATGCAAACTTAAATATATATAATTTTTATAGTAGTTGAATTTGTAAACTAATAAATGTAAAA
1 ATGATGCAAACTT-AATACATAAAATTTTTATAGTAGTTGAACTTGTAAACTAATAAATGTAAAA
2241320 TTAATTTATATTAC
65 TTAATTTATATTAC
2241334 TTGAACTATG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 13 0.18
79 61 0.82
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (78 bp):
ATGATGCAAACTTAATACATAAAATTTTTATAGTAGTTGAACTTGTAAACTAATAAATGTAAAAT
TAATTTATATTAC
Found at i:2241328 original size:42 final size:39
Alignment explanation
Indices: 2241196--2241338 Score: 132
Period size: 42 Copynumber: 3.6 Consensus size: 39
2241186 ACTTAATACA
*
2241196 TAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAATG
1 TAAAATTTTTATATTACTTGAA-TTGTAAACTAATAAATG
* * *
2241236 TAAAATTAATTTATATTACATG-A-TGCAAACT--TAAATA
1 TAAAATT--TTTATATTACTTGAATTGTAAACTAATAAATG
* *
2241273 TATATAATTTTTATAGTAGTTGAATTTGTAAACTAATAAATG
1 TA-A-AATTTTTATATTACTTGAA-TTGTAAACTAATAAATG
2241315 TAAAATTAATTTATATTACTTGAA
1 TAAAATT--TTTATATTACTTGAA
2241339 CTATGATGCA
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
37 17 0.21
38 2 0.02
39 11 0.14
40 18 0.22
41 2 0.02
42 31 0.38
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (39 bp):
TAAAATTTTTATATTACTTGAATTGTAAACTAATAAATG
Found at i:2257131 original size:17 final size:17
Alignment explanation
Indices: 2257111--2257143 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2257101 TTTTTTTCTT
2257111 TTTTGATTCTT-TTGTTC
1 TTTTG-TTCTTCTTGTTC
2257128 TTTTGTTCTTCTTGTT
1 TTTTGTTCTTCTTGTT
2257144 TTGTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.73
Consensus pattern (17 bp):
TTTTGTTCTTCTTGTTC
Found at i:2261766 original size:2 final size:2
Alignment explanation
Indices: 2261759--2261784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2261749 TCAAGTGTTT
2261759 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2261785 CGTACACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2261830 original size:2 final size:2
Alignment explanation
Indices: 2261823--2261856 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2261813 TGTATGTATG
2261823 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2261857 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2261861 original size:2 final size:2
Alignment explanation
Indices: 2261856--2261880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2261846 ACACACACAC
2261856 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2261881 GACACAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2261891 original size:2 final size:2
Alignment explanation
Indices: 2261886--2261918 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2261876 ATATAGACAC
2261886 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2261919 TAAAAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2272666 original size:24 final size:24
Alignment explanation
Indices: 2272619--2272673 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2272609 AAAAACTTTT
*
2272619 CTGCAACTGTCATGCATGACATTC
1 CTGCTACTGTCATGCATGACATTC
***
2272643 CTGCTACTGTCATGCATTTTATTC
1 CTGCTACTGTCATGCATGACATTC
2272667 CTGCTAC
1 CTGCTAC
2272674 CTAATGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (24 bp):
CTGCTACTGTCATGCATGACATTC
Found at i:2282338 original size:24 final size:23
Alignment explanation
Indices: 2282310--2282356 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2282300 AAAATACTTT
* *
2282310 TTATTTTTTTATTAATTTAAAAAA
1 TTATTATTATATT-ATTTAAAAAA
*
2282334 TTATTATTATATTTTTTAAAAAA
1 TTATTATTATATTATTTAAAAAA
2282357 AATAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTATTATATTATTTAAAAAA
Found at i:2292254 original size:14 final size:14
Alignment explanation
Indices: 2292229--2292263 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2292219 AGTTGTTTGG
2292229 TAAATT-TTTTTTA
1 TAAATTATTTTTTA
*
2292242 TAAGTTATTTTTTA
1 TAAATTATTTTTTA
2292256 TAAATTAT
1 TAAATTAT
2292264 AATTTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TAAATTATTTTTTA
Found at i:2293037 original size:19 final size:18
Alignment explanation
Indices: 2293004--2293039 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2292994 CTATTATGGT
*
2293004 AATTAAAATATATATTTC
1 AATTAAAAAATATATTTC
2293022 AATTAAGAAAATATATTT
1 AATTAA-AAAATATATTT
2293040 TCAACATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTAAAAAATATATTTC
Found at i:2296758 original size:29 final size:29
Alignment explanation
Indices: 2296681--2296749 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
2296671 GACATTTTTG
* * *
2296681 TCAATTTAGTCCCTTCACTCCAAAATTGA
1 TCAATTTAGTCCCTTTACTTCAAAACTGA
*
2296710 TCAATTTAGTCCCTTTACTTCAAAACTGG
1 TCAATTTAGTCCCTTTACTTCAAAACTGA
2296739 TCAATTTAGTC
1 TCAATTTAGTC
2296750 TTTATACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (29 bp):
TCAATTTAGTCCCTTTACTTCAAAACTGA
Found at i:2297794 original size:23 final size:23
Alignment explanation
Indices: 2297768--2297813 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2297758 TTATAACATA
*
2297768 ATAAA-AATAAATAATTAAATATT
1 ATAAAGAACAAATAATT-AATATT
*
2297791 ATAAAGTACAAATAATTAATATT
1 ATAAAGAACAAATAATTAATATT
2297814 TGTGATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
ATAAAGAACAAATAATTAATATT
Found at i:2301369 original size:2 final size:2
Alignment explanation
Indices: 2301362--2301386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2301352 CGTGCGCGTG
2301362 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
2301387 GCATACGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2309827 original size:192 final size:189
Alignment explanation
Indices: 2309496--2309883 Score: 480
Period size: 192 Copynumber: 2.0 Consensus size: 189
2309486 TCTATCCATA
* *
2309496 TCTAGAGTAAAACTATATATTTAACAATGTAATTTTAAACTCTGGCATTTTAACTTAGTACTCAA
1 TCTAGAGTAAAACTACATATTTAACAATGTAATTTTAAACTCTAGCA-TTTAACTTAGTACTCAA
* * *
2309561 CCCTCTCACCCCCCACAGTCCCTCCACTAACTCAAACATGCCTTTGACAACATGAGTTTACATAA
65 CCCTCTCA-CCCCCACAGTCCCCCCACTAACTCAAACATGCCTTTGACAACATCAGTTAACATAA
* *
2309626 ATATTAAATAGGTAGAGCTGCATTAACACCACCAGTTTCTTAACAACACTTTGCTATTTTAC
129 ATATTAAATAGGTAGAGCTGCATTAACACCACCAGCTTCATAACAACACTTTGC-ATTTTAC
* *
2309688 TCTAGAGTAAAACTACATA-TTAACAAATGTAATTTTAAACT-TCAGCA-TTAACTTGGTATTCA
1 TCTAGAGTAAAACTACATATTTAAC-AATGTAATTTTAAACTCT-AGCATTTAACTTAGTACTCA
* * * * *
2309750 TCCTTCTCA-CCCCACATTCCCCCCTGCTAACTCAAACA-GCCTTTGAGTAACATAACAGTTAAC
64 ACCCTCTCACCCCCACAGTCCCCCC-ACTAACTCAAACATGCCTTTGA-CAACAT--CAGTTAAC
* * * * *
2309813 ATAAATTCTTAAATAGGTTGAGCTGCATTAACATCGCCAGCTTCATAACAACACTTTGCCTTTTA
125 ATAAA-TATTAAATAGGTAGAGCTGCATTAACACCACCAGCTTCATAACAACACTTTGCATTTTA
2309878 C
189 C
2309879 TCTAG
1 TCTAG
2309884 TTTAAAATTT
Statistics
Matches: 170, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
188 21 0.12
189 17 0.10
190 20 0.12
191 28 0.16
192 84 0.49
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (189 bp):
TCTAGAGTAAAACTACATATTTAACAATGTAATTTTAAACTCTAGCATTTAACTTAGTACTCAAC
CCTCTCACCCCCACAGTCCCCCCACTAACTCAAACATGCCTTTGACAACATCAGTTAACATAAAT
ATTAAATAGGTAGAGCTGCATTAACACCACCAGCTTCATAACAACACTTTGCATTTTAC
Found at i:2318380 original size:90 final size:89
Alignment explanation
Indices: 2318196--2318369 Score: 233
Period size: 90 Copynumber: 1.9 Consensus size: 89
2318186 GATATCGAGT
* * * * **
2318196 CACTTACTTGATTTGTTACAACTAGAAATTAAAACCAATCATTGAAATCCTTTTAAAGTTTGGAG
1 CACTTACTTGATTTGCTACAACTAGAAATCAAAACCAATAATTGAAATCCTTTTAAAGCTTAAAG
* *
2318261 ATGATGAAAATAAAATAATACTAA
66 ATGATAAAAACAAAATAATACTAA
* *
2318285 CACTTACTTGATTTGCT-CTAACTAGATATCAAAACCCAATAATTGAAATCCTTTTGAAGCTTAA
1 CACTTACTTGATTTGCTAC-AACTAGAAATCAAAA-CCAATAATTGAAATCCTTTTAAAGCTTAA
2318349 AGATGATAAAAACAAAATAAT
64 AGATGATAAAAACAAAATAAT
2318370 TCTCAAACTT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 1 0.01
89 29 0.40
90 43 0.59
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (89 bp):
CACTTACTTGATTTGCTACAACTAGAAATCAAAACCAATAATTGAAATCCTTTTAAAGCTTAAAG
ATGATAAAAACAAAATAATACTAA
Found at i:2318898 original size:21 final size:21
Alignment explanation
Indices: 2318857--2318903 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2318847 TATTATATTT
* * *
2318857 TTATTAAAATTTTATTTTAAA
1 TTATTAAAATGTTAATATAAA
2318878 TTATTAAAATGTTAATATAAA
1 TTATTAAAATGTTAATATAAA
2318899 -TATTA
1 TTATTA
2318904 TTTTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTATTAAAATGTTAATATAAA
Found at i:2320513 original size:10 final size:10
Alignment explanation
Indices: 2320488--2320533 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
2320478 GAGAGGAGAG
2320488 AGAAAGAAACAA
1 AGAAAG-AA-AA
2320500 AGAAAGAAAA
1 AGAAAGAAAA
*
2320510 AGAAAGAACA
1 AGAAAGAAAA
2320520 AG-AAGAAAA
1 AGAAAGAAAA
2320529 AGAAA
1 AGAAA
2320534 CAATTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.26
10 15 0.48
11 2 0.06
12 6 0.19
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:2320528 original size:19 final size:22
Alignment explanation
Indices: 2320488--2320533 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
2320478 GAGAGGAGAG
2320488 AGAAAGAAACAAAGAAAGAAAA
1 AGAAAGAAACAAAGAAAGAAAA
2320510 AGAAAG-AAC-AAG-AAGAAAA
1 AGAAAGAAACAAAGAAAGAAAA
2320529 AGAAA
1 AGAAA
2320534 CAATTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
20 3 0.12
21 3 0.12
22 6 0.25
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (22 bp):
AGAAAGAAACAAAGAAAGAAAA
Found at i:2324611 original size:2 final size:2
Alignment explanation
Indices: 2324604--2324628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2324594 CAACTCCCAC
2324604 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2324629 GATTCGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2327715 original size:16 final size:16
Alignment explanation
Indices: 2327694--2327724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2327684 AATAAAAATT
*
2327694 AAAATAATTTTTTATA
1 AAAATAATATTTTATA
2327710 AAAATAATATTTTAT
1 AAAATAATATTTTAT
2327725 TTTATTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATAATATTTTATA
Found at i:2331698 original size:20 final size:20
Alignment explanation
Indices: 2331658--2331698 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2331648 TTGGGGGCAT
*
2331658 AGTTAAATTCAATGATGGGA
1 AGTTAAATTCAATGATAGGA
2331678 AGTTAAATTCAA-GATAAGGA
1 AGTTAAATTCAATGAT-AGGA
2331698 A
1 A
2331699 TAATCTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (20 bp):
AGTTAAATTCAATGATAGGA
Done.