Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 11 of 129
Found at i:1399578 original size:3 final size:3
Alignment explanation
Indices: 1399570--1399616 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1399560 CACTCTTATC
* * *
1399570 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATG ATA ATA GTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1399617 GTAAGTTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1402922 original size:88 final size:88
Alignment explanation
Indices: 1402762--1402921 Score: 227
Period size: 88 Copynumber: 1.8 Consensus size: 88
1402752 TTACTGTTGT
*
1402762 TTGTTTTACTGGAATGAACCTTGTGATCCAAAAATGGTCCTAAACATGTATTTCAGCATTTTTTA
1 TTGTTTTACTGGAATGAACCTTGTGATCCAAAAATGGTCCTAAACATGTATTTCAGCATTTTTCA
1402827 TGGAAAAATTGTCATTGATGCTG
66 TGGAAAAATTGTCATTGATGCTG
* * * * *
1402850 TTGTTTTACTCTG-ATGAA-CTCTGTGATTCAAAAGTGGTTCTAAACATGTATTTTAGCA-TTTT
1 TTGTTTTACT-GGAATGAACCT-TGTGATCCAAAAATGGTCCTAAACATGTATTTCAGCATTTTT
1402912 CATGGAAAAA
64 CATGGAAAAA
1402922 AAATGCTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
87 15 0.23
88 48 0.75
89 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (88 bp):
TTGTTTTACTGGAATGAACCTTGTGATCCAAAAATGGTCCTAAACATGTATTTCAGCATTTTTCA
TGGAAAAATTGTCATTGATGCTG
Found at i:1404933 original size:13 final size:14
Alignment explanation
Indices: 1404910--1404943 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1404900 CTGAATGATC
*
1404910 ACCATATTATTGGG
1 ACCATAATATTGGG
1404924 A-CATAATATTGGG
1 ACCATAATATTGGG
1404937 ACCATAA
1 ACCATAA
1404944 CATTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (14 bp):
ACCATAATATTGGG
Found at i:1408031 original size:6 final size:6
Alignment explanation
Indices: 1408020--1408044 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1408010 AGTGTATACT
1408020 GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA G
1408045 GAAGCACGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:1408815 original size:2 final size:2
Alignment explanation
Indices: 1408808--1408837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1408798 TACCCAATTC
1408808 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1408838 GTAATATATA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1410941 original size:33 final size:33
Alignment explanation
Indices: 1410894--1410959 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1410884 CAGCTGATGA
*
1410894 GAATGTATTCTTTATAGACTTTATCAACAACCC
1 GAATATATTCTTTATAGACTTTATCAACAACCC
* * *
1410927 GAATATATTTTTTATAGACTTTATTAGCAACCC
1 GAATATATTCTTTATAGACTTTATCAACAACCC
1410960 TATTACCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (33 bp):
GAATATATTCTTTATAGACTTTATCAACAACCC
Found at i:1414142 original size:6 final size:7
Alignment explanation
Indices: 1414125--1414151 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1414115 TAAATTTTGA
1414125 AAAAAAT
1 AAAAAAT
1414132 AAAAAAT
1 AAAAAAT
1414139 AAAAAAT
1 AAAAAAT
1414146 AAAAAA
1 AAAAAA
1414152 ATATTTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1418788 original size:20 final size:19
Alignment explanation
Indices: 1418763--1418825 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 19
1418753 ATGAAAAAAT
1418763 AAAAAAATAAAAAAATAAAG
1 AAAAAAAT-AAAAAATAAAG
*
1418783 AAAAAAATGAAAAAAT-GAG
1 AAAAAAAT-AAAAAATAAAG
1418802 AAAAAAATAAAAAATGAAAG
1 AAAAAAATAAAAAAT-AAAG
1418822 AAAA
1 AAAA
1418826 GAAAGAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 21 0.55
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAAAAATAAAG
Found at i:1418806 original size:46 final size:46
Alignment explanation
Indices: 1418756--1418850 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
1418746 ATGGTGGATG
*
1418756 AAAAAATAAAAAAAT-AAA-AAAATAAAGAAAAAAATGAAAAAATGAGA
1 AAAAAAT-AAAAAATGAAAGAAAAGAAAG-AAAAAA-GAAAAAATGAGA
*
1418803 AAAAAATAAAAAATGAAAGAAAAGAAAGAAAAGAGAAAAAATGA-A
1 AAAAAATAAAAAATGAAAGAAAAGAAAGAAAAAAGAAAAAATGAGA
1418848 AAA
1 AAA
1418851 TGAAAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
45 4 0.09
46 17 0.39
47 15 0.34
48 8 0.18
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (46 bp):
AAAAAATAAAAAATGAAAGAAAAGAAAGAAAAAAGAAAAAATGAGA
Found at i:1418829 original size:9 final size:8
Alignment explanation
Indices: 1418755--1418859 Score: 68
Period size: 9 Copynumber: 12.0 Consensus size: 8
1418745 AATGGTGGAT
1418755 GAAAAAATA
1 GAAAAAA-A
*
1418764 AAAAAATAA
1 GAAAAA-AA
*
1418773 AAAAATAAA
1 GAAAA-AAA
1418782 GAAAAAAA
1 GAAAAAAA
1418790 TGAAAAAATGA
1 -GAAAAAA--A
1418801 GAAAAAAA
1 GAAAAAAA
* *
1418809 TAAAAAAT
1 GAAAAAAA
1418817 GAAAGAAAA
1 GAAA-AAAA
1418826 GAAAGAAAA
1 GAAA-AAAA
1418835 GAGAAAAAA
1 GA-AAAAAA
*
1418844 TG-AAAAAT
1 -GAAAAAAA
1418852 GAAAAAAA
1 GAAAAAAA
1418860 TGTAAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
7 1 0.01
8 23 0.29
9 42 0.53
10 12 0.15
11 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1418848 original size:19 final size:17
Alignment explanation
Indices: 1418774--1418876 Score: 88
Period size: 18 Copynumber: 5.9 Consensus size: 17
1418764 AAAAAATAAA
1418774 AAAATAAAGAAAAAAATG
1 AAAA-AAAGAAAAAAATG
1418792 AAAAAATGAGAAAAAAAT-
1 AAAAAA--AGAAAAAAATG
*
1418810 AAAAAATGAAAGAAAA-G
1 AAAAAAAGAAA-AAAATG
1418827 AAAGAAAAGAGAAAAAATG
1 AAA-AAAAGA-AAAAAATG
*
1418846 -AAAAATGAAAAAAATG
1 AAAAAAAGAAAAAAATG
*
1418862 -TAAAAAGAAATAAAA
1 AAAAAAAGAAA-AAAA
1418877 AGAATACTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
16 20 0.28
17 18 0.25
18 21 0.29
19 13 0.18
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAGAAAAAAATG
Found at i:1418850 original size:35 final size:35
Alignment explanation
Indices: 1418763--1418867 Score: 115
Period size: 35 Copynumber: 2.9 Consensus size: 35
1418753 ATGAAAAAAT
*
1418763 AAAAAAATAAAAAAATAAAGAAAAAAATGAAAAAATGAG
1 AAAAAAAT-AAAAAAT---GAAAAAAATGAAAAAAAGAG
1418802 AAAAAAATAAAAAATGAAAGAAAA-GAAAGAAAAGAG
1 AAAAAAATAAAAAATGAAA-AAAATGAAA-AAAAGAG
* *
1418838 -AAAAAATGAAAAATGAAAAAAATGTAAAAA
1 AAAAAAATAAAAAATGAAAAAAATGAAAAAA
1418868 GAAATAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
34 7 0.12
35 28 0.47
36 10 0.17
38 7 0.12
39 8 0.13
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (35 bp):
AAAAAAATAAAAAATGAAAAAAATGAAAAAAAGAG
Found at i:1418860 original size:9 final size:9
Alignment explanation
Indices: 1418756--1418867 Score: 80
Period size: 8 Copynumber: 12.4 Consensus size: 9
1418746 ATGGTGGATG
1418756 AAAAAAT-A
1 AAAAAATGA
1418764 AAAAAAT-A
1 AAAAAATGA
1418772 AAAAAATAAAGA
1 AAAAAAT---GA
1418784 AAAAAATG-
1 AAAAAATGA
1418792 AAAAAATGA
1 AAAAAATGA
1418801 GAAAAAA--A
1 -AAAAAATGA
1418809 TAAAAAATGA
1 -AAAAAATGA
1418819 AAGAAAA-GA
1 AA-AAAATGA
1418828 AAGAAAA-GA
1 AA-AAAATGA
1418837 GAAAAAATG-
1 -AAAAAATGA
1418846 -AAAAATGA
1 AAAAAATGA
1418854 AAAAAATGTA
1 AAAAAATG-A
1418864 AAAA
1 AAAA
1418868 GAAATAAAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 26
0.77 0.01 0.22
Matches are distributed among these distances:
7 7 0.08
8 30 0.34
9 25 0.28
10 19 0.21
12 8 0.09
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:1419460 original size:117 final size:115
Alignment explanation
Indices: 1419283--1419509 Score: 377
Period size: 117 Copynumber: 2.0 Consensus size: 115
1419273 ATTTTTCAAG
* *
1419283 AATTGAAAAGATAATGAATGAATGATGATGTTCATAAGAGATTATTGCATTCTTTTGAAAAGAAA
1 AATTGAAAAGATAATGAATGAATGATGATGTTCATAAAAGATTATTGCATTCCTTTGAAAAGAAA
1419348 TCCAAGACAATGTGGGCAAAAAAAAATGAAA-AAATGACAAAAACTTGGCAAA
66 TCCAAGACAATGTGGGC--AAAAAAAT-AAAGAAATGACAAAAACTTGGCAAA
1419400 AATTGAAATA-ATAATGAATGAATGATGATGTTCATAAAAGATTATTGCATTCCTTTGAAAAGAA
1 AATTGAAA-AGATAATGAATGAATGATGATGTTCATAAAAGATTATTGCATTCCTTTGAAAAGAA
*
1419464 ATCCAAGACAATGTGGGCAAAAAAATAAAGAAATGATAAAAACTTG
65 ATCCAAGACAATGTGGGCAAAAAAATAAAGAAATGACAAAAACTTG
1419510 AAAAGGTGAT
Statistics
Matches: 105, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
114 3 0.03
115 23 0.22
117 78 0.74
118 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (115 bp):
AATTGAAAAGATAATGAATGAATGATGATGTTCATAAAAGATTATTGCATTCCTTTGAAAAGAAA
TCCAAGACAATGTGGGCAAAAAAATAAAGAAATGACAAAAACTTGGCAAA
Found at i:1420193 original size:33 final size:33
Alignment explanation
Indices: 1420156--1420225 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1420146 GCTTGACGTT
* * **
1420156 TGCATAACAGGCATTGTATTTTTGAATGTTTAG
1 TGCATAACAGGCATTGCATGTGAGAATGTTTAG
* *
1420189 TGCATAGCATGCATTGCATGTGAGAATGTTTAG
1 TGCATAACAGGCATTGCATGTGAGAATGTTTAG
1420222 TGCA
1 TGCA
1420226 AGAATTCCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (33 bp):
TGCATAACAGGCATTGCATGTGAGAATGTTTAG
Found at i:1420479 original size:41 final size:43
Alignment explanation
Indices: 1420421--1420706 Score: 179
Period size: 45 Copynumber: 6.5 Consensus size: 43
1420411 ATTCCTCTGT
*
1420421 TTAGAGGAGCCTTATTTATTTTTTCAAAGTTATTAAGCCTCTTA
1 TTAGAGGA-CTTTATTTATTTTTTCAAAGTTATTAAGCCTCTTA
* * * *
1420465 TTATA-G-CTTTATTTATTTTTTAAAAGTTGTTAAGCTTCTTA
1 TTAGAGGACTTTATTTATTTTTTCAAAGTTATTAAGCCTCTTA
* * * * *
1420506 TTAGAGGAACTTTATTTAATTTTTCAAAAGGTGA-TGAG-CTTTTCT
1 TTAGAGG-ACTTTATTTATTTTTTC-AAA-GTTATTAAGCCTCTT-A
* * ** * *
1420551 TTAGAGGAGCCTTATTTATTTTTTTGAAAGTCGTTAAACCTCTAA
1 TTAGAGGA-CTTTATTTA-TTTTTTCAAAGTTATTAAGCCTCTTA
* *
1420596 TTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAGCCTC-TA
1 TTAGAGGA-CTTTATTTATTTTTTCAAAGTTATTAAGCCTCTTA
** * * **
1420639 TTTAGAATAGCCTTATTTATGTTGCCAAAAGTTATTAAGCCTC-TA
1 -TTAGAGGA-CTTTATTTATTTTTTC-AAAGTTATTAAGCCTCTTA
* *
1420684 TTTAGATGACCCTTATTTATTTT
1 -TTAGAGGA-CTTTATTTATTTT
1420707 CTAAAAGTCG
Statistics
Matches: 187, Mismatches: 43, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
41 35 0.19
42 1 0.01
43 2 0.01
44 60 0.32
45 79 0.42
46 10 0.05
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (43 bp):
TTAGAGGACTTTATTTATTTTTTCAAAGTTATTAAGCCTCTTA
Found at i:1420656 original size:134 final size:130
Alignment explanation
Indices: 1420420--1420657 Score: 307
Period size: 134 Copynumber: 1.8 Consensus size: 130
1420410 CATTCCTCTG
* * * *
1420420 TTTAGAGGAGCCTTATTTATTTTTTCAAAGTTATTAAGCCTCTTATTATAGCTTTATTTATTTTT
1 TTTAGAGGAGCCTTATTTATTTTTTCAAAGTCATTAAACCTCTAATTAGAGCTTTATTTATTTTT
* * * *
1420485 TAAAAGTTGTTAAGCTTCTTATTAGAGGAACTTTATTTAATTTTTCAAAAGGTGATGAGCTTTTC
66 TAAAAGTTATTAAGCCTCTTATTAGAAGAACCTTATTTAATTTTTCAAAAGGTGATGAGCTTTTC
* *
1420550 TTTAGAGGAGCCTTATTTATTTTTTTGAAAGTCGTTAAACCTCTAATTAGAGGAGCTTTATTTAT
1 TTTAGAGGAGCCTTATTTA-TTTTTTCAAAGTCATTAAACCTCTAATT--A-GAGCTTTATTTAT
* * *
1420615 TTTTTAAAAGTTATTGAGCCTC-TATTTAGAATAGCCTTATTTA
62 TTTTTAAAAGTTATTAAGCCTCTTA-TTAGAAGAACCTTATTTA
1420658 TGTTGCCAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
130 19 0.21
131 23 0.26
133 3 0.03
134 45 0.50
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (130 bp):
TTTAGAGGAGCCTTATTTATTTTTTCAAAGTCATTAAACCTCTAATTAGAGCTTTATTTATTTTT
TAAAAGTTATTAAGCCTCTTATTAGAAGAACCTTATTTAATTTTTCAAAAGGTGATGAGCTTTTC
Found at i:1420670 original size:89 final size:87
Alignment explanation
Indices: 1420421--1420862 Score: 286
Period size: 89 Copynumber: 5.0 Consensus size: 87
1420411 ATTCCTCTGT
* * *
1420421 TTAGAGGAGCCTTATTTATTTTTTCAAAGTTATTAAGCCTCTTATT---ATAGCTTTATTTATTT
1 TTAGAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCTCTT-TTAGAATAGCCTTATTTATTT
* *
1420483 TTTAAAAGTTGTTAAGCTTCTTA
65 TTTAAAAGTTGTTAAGCCTCTAA
* * * * * * **
1420506 TTAGAGGAACTTTATTTAATTTTTCAAAAGGTGA-TGAGCTTTTCTTTAGAGGAGCCTTATTTAT
1 TTAGAGGAGCCTTATTT-ATTTTTTAAAA-GTTATTGAGCCTCT-TTTAGAATAGCCTTATTTA-
* * *
1420570 TTTTTTGAAAGTCGTTAAACCTCTAA
62 TTTTTTAAAAGTTGTTAAGCCTCTAA
*
1420596 TTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAGCCTCTATTTAGAATAGCCTTATTTATGT
1 TTAGAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCTCT-TTTAGAATAGCCTTATTTAT-T
*** * *
1420661 TGCCAAAAGTTATTAAGCCTCTAT
64 TTTTAAAAGTTGTTAAGCCTCTAA
* * * * * * * *
1420685 TTAGATGACCCTTATTTATTTTCTAAAAGTCGAAGTTGTTGAACCTTTGTTTAGAAGAGACTTAT
1 TTAGAGGAGCCTTATTTATTTT-T-TAA----AAGTTATTGAGCCTCT-TTTAGAATAGCCTTAT
* ** * * *
1420750 TTA-TTTTTAGAAGCCGTTGAGCCTTTGA
59 TTATTTTTTAAAAGTTGTTAAGCCTCTAA
* * * * * * *
1420778 TTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGGGCCTCCGTTTA-AATGAGCCTTATCTATT
1 TTAGAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCT-CTTTTAGAAT-AGCCTTATTTATT
* *
1420842 TTTTAAAAATTG-TGAGCCTCT
64 TTTTAAAAGTTGTTAAGCCTCT
1420863 GCTTAGAAGA
Statistics
Matches: 269, Mismatches: 70, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
85 15 0.06
86 19 0.07
87 35 0.13
88 13 0.05
89 80 0.30
90 38 0.14
91 4 0.01
92 1 0.00
93 34 0.13
95 30 0.11
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (87 bp):
TTAGAGGAGCCTTATTTATTTTTTAAAAGTTATTGAGCCTCTTTTAGAATAGCCTTATTTATTTT
TTAAAAGTTGTTAAGCCTCTAA
Found at i:1420688 original size:134 final size:131
Alignment explanation
Indices: 1420414--1420706 Score: 297
Period size: 134 Copynumber: 2.2 Consensus size: 131
1420404 ATTTATCATT
* * * * *
1420414 CCTCTGTTTAGAGGAGCCTTATTTA-TTTTTTCAAAGTTATTAAGCCTCTTATTATAGCTTTATT
1 CCTCTATTTAGAGGAGCCTTATTTATTTTTTTCAAAGTCATTAAACCTCTAATTAGAGCTTTATT
* * * * ** *
1420478 TATTTTTTAAAAGTTGTTAAGCTTCTTATTAGAGGAACTTTATTTAATTTTTCAAAAGGTGATGA
66 TATTTTTTAAAAGTTATTAAGCCTCTTATTAGAAGAACCTTATTTAATTTGCCAAAAGGTGATAA
1420543 G
131 G
* * * * *
1420544 CTTTTCTTTAGAGGAGCCTTATTTATTTTTTTGAAAGTCGTTAAACCTCTAATTAGAGGAGCTTT
1 CCTCTATTTAGAGGAGCCTTATTTATTTTTTTCAAAGTCATTAAACCTCTAATT--A-GAGCTTT
* * *
1420609 ATTTATTTTTTAAAAGTTATTGAGCCTC-TATTTAGAATAGCCTTATTT-ATGTTGCCAAAA-GT
63 ATTTATTTTTTAAAAGTTATTAAGCCTCTTA-TTAGAAGAACCTTATTTAAT-TTGCCAAAAGGT
*
1420671 TATTAAG
126 GA-TAAG
* *
1420678 CCTCTATTTAGATGACCCTTATTTATTTT
1 CCTCTATTTAGAGGAGCCTTATTTATTTT
1420707 CTAAAAGTCG
Statistics
Matches: 131, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
130 22 0.17
131 23 0.18
133 8 0.06
134 78 0.60
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46
Consensus pattern (131 bp):
CCTCTATTTAGAGGAGCCTTATTTATTTTTTTCAAAGTCATTAAACCTCTAATTAGAGCTTTATT
TATTTTTTAAAAGTTATTAAGCCTCTTATTAGAAGAACCTTATTTAATTTGCCAAAAGGTGATAA
G
Found at i:1420834 original size:44 final size:44
Alignment explanation
Indices: 1420414--1420849 Score: 183
Period size: 44 Copynumber: 9.8 Consensus size: 44
1420404 ATTTATCATT
* * * *
1420414 CCTCTGTTTAGAGGAGCCTTATTTATTTTTTC-AAAGTTATTAAG
1 CCTCTGTTTAAATGAGCCTTATTTA-TTTTTCAAAAGTCATTGAG
* * ** *
1420458 CCTCT-TATT--AT-AGCTTTATTTATTTTTTAAAAGTTGTTAAG
1 CCTCTGT-TTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGAG
* * * * * *
1420499 CTTCT-TATTAGAGGAACTTTATTTAATTTTTCAAAAGGTGA-TGAG
1 CCTCTGT-TTAAATGAGCCTTATTT-ATTTTTCAAAA-GTCATTGAG
* * * * * ** * * *
1420544 CTTTTCTTTAGAGGAGCCTTATTTATTTTTTTGAAAGTCGTTAAA
1 CCTCTGTTTAAATGAGCCTTATTTA-TTTTTCAAAAGTCATTGAG
** * * * * *
1420589 CCTCTAATTAGAGGAGCTTTATTTATTTTTTAAAAGTTATTGAG
1 CCTCTGTTTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGAG
* ** * *
1420633 CCTCTATTTAGAAT-AGCCTTATTTATGTTGCCAAAAGTTATTAAG
1 CCTCTGTTTA-AATGAGCCTTATTTAT-TTTTCAAAAGTCATTGAG
* * * *
1420678 CCTCTATTTAGATGACCCTTATTTA-TTTTCTAAAAGTCGAAGTTGTTGAA
1 CCTCTGTTTAAATGAGCCTTATTTATTTTTC-AAAAGTC--A----TTGAG
* * * * *
1420728 CCTTTGTTTAGAA-GAGACTTATTTATTTTT-AGAAGCCGTTGAG
1 CCTCTGTTTA-AATGAGCCTTATTTATTTTTCAAAAGTCATTGAG
* * *
1420771 CCTTTGATTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGGG
1 CCTCTGTTTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGAG
* * *
1420815 CCTCCGTTTAAATGAGCCTTATCTATTTTTTAAAA
1 CCTCTGTTTAAATGAGCCTTATTTATTTTTCAAAA
1420850 ATTGTGAGCC
Statistics
Matches: 303, Mismatches: 65, Indels: 48
0.73 0.16 0.12
Matches are distributed among these distances:
40 5 0.02
41 29 0.10
42 3 0.01
43 34 0.11
44 100 0.33
45 97 0.32
46 4 0.01
49 5 0.02
50 21 0.07
51 5 0.02
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (44 bp):
CCTCTGTTTAAATGAGCCTTATTTATTTTTCAAAAGTCATTGAG
Found at i:1421128 original size:4 final size:4
Alignment explanation
Indices: 1421121--1421166 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
1421111 TATTTTATAT
* *
1421121 TTTA TTTA TTTA -TTA TTTA TCTA TTTA CTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1421167 TTGGTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1421605 original size:20 final size:20
Alignment explanation
Indices: 1421580--1421618 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1421570 GGAAAATTCT
1421580 CAAATTTCGATGAATTTTTC
1 CAAATTTCGATGAATTTTTC
* *
1421600 CAAATTTTGGTGAATTTTT
1 CAAATTTCGATGAATTTTT
1421619 TTGGCTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
CAAATTTCGATGAATTTTTC
Found at i:1422067 original size:17 final size:17
Alignment explanation
Indices: 1422042--1422088 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1422032 AGCTGAGCCG
*
1422042 TTTTATTATTTTGG-TAT
1 TTTTTTTATTTTGGAT-T
*
1422059 TTTTTTTATTTTTGATT
1 TTTTTTTATTTTGGATT
1422076 TTATTTTTATTTT
1 TT-TTTTTATTTT
1422089 TAAGTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTTATTTTGGATT
Found at i:1422883 original size:20 final size:19
Alignment explanation
Indices: 1422830--1422883 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1422820 TCCAGTGAAT
*
1422830 TTTTCAGTGAAAATTCAAG
1 TTTTCAGTGAAAAATCAAG
** *
1422849 TTTTCCAACGAAAAATCCAG
1 TTTT-CAGTGAAAAATCAAG
1422869 TTTTCAGTGATAAAA
1 TTTTCAGTGA-AAAA
1422884 CCCAAAAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (19 bp):
TTTTCAGTGAAAAATCAAG
Found at i:1423527 original size:59 final size:59
Alignment explanation
Indices: 1423294--1424035 Score: 753
Period size: 60 Copynumber: 12.3 Consensus size: 59
1423284 ATTTTCAATG
* * * * *
1423294 ATTTTT-TT-AAAATAAAAACTTTAAAAAACATATATTTTAAAAGAAAAAATTG-AAGTATCA
1 ATTTTTCTTGAAAAT-AAAATTTTAAAAAA-A-ACATTTT-TAAGGAAAAGTTGAAAGTATCA
* * * * *
1423354 ATTTTTCTTAAAAATAAAATTTTCAAAAAAAGCATTTTTGAGAAAAAGTTTAAAGTATCA
1 ATTTTTCTTGAAAATAAAATTTT-AAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * * *
1423414 ATTTTTCCTGAAAATAAAATATTCTGAAAAAAAACATTTTTAAGGAAAAGTTAAAAATGTCA
1 ATTTTTCTTGAAAATAAAAT-TT-T-AAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * * *
1423476 ATTTTTCTTGAAAATAAAACTGTT-GAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCA
1 ATTTTTCTTGAAAATAAAA-TTTTAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * * *
1423535 ATTTTTCTTAAAAATAAAATTTTCAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATTA
1 ATTTTTCTTGAAAATAAAATTTT-AAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* *
1423595 ATTTTTCTTGAAAATAAAATTTAAAAAAAAAAACATTTTTAAGGAAAAGTTGATAA-TGTCA
1 ATTTTTCTTGAAAATAAAATTT--TAAAAAAAACATTTTTAAGGAAAAGTTGA-AAGTATCA
* * * *
1423656 ATTTTTCTTGAAAATAAAAATTGT-CAAAAAACATTTTTAAAGAAAAGTTAAAAGTATCA
1 ATTTTTCTTGAAAAT-AAAATTTTAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * *
1423715 ATTTTTCTTAAAAATAAAATTTTAAAAAAAAGCATTTTTGAGAAAAAGTTGAAAGTATCA
1 ATTTTTCTTGAAAATAAAATTTTAAAAAAAA-CATTTTTAAGGAAAAGTTGAAAGTATCA
* * * * *
1423775 ATTTTTCTTGAAAATTAAATTTTAAAAAAAAGTATTTTTAAGAAAAAGTTGAAAATGTCA
1 ATTTTTCTTGAAAATAAAATTTTAAAAAAAA-CATTTTTAAGGAAAAGTTGAAAGTATCA
* * * *
1423835 ATTTTTCTTGAAAATAACATTGTT-GAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
1 ATTTTTCTTGAAAATAAAATT-TTAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * *** * *
1423894 ATTCTCCTTGAAAATAAAGATTTT-AAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATTA
1 ATTTTTCTTGAAAATAAA-ATTTTAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
* * * * *
1423953 ATTTTTCATGAAAATAAAATTTTTAAAAAAGAAGTATTTTTAAGGAAAAATTAAAAGTATTA
1 ATTTTTCTTGAAAATAAAA-TTTTAAAAAA-AA-CATTTTTAAGGAAAAGTTGAAAGTATCA
*
1424015 ATTTTTCTTGATAATAGAAAT
1 ATTTTTCTTGAAAATA-AAAT
1424036 ATCAAAATGC
Statistics
Matches: 580, Mismatches: 79, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
58 13 0.02
59 196 0.34
60 200 0.34
61 59 0.10
62 108 0.19
63 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (59 bp):
ATTTTTCTTGAAAATAAAATTTTAAAAAAAACATTTTTAAGGAAAAGTTGAAAGTATCA
Found at i:1423719 original size:180 final size:178
Alignment explanation
Indices: 1423346--1424035 Score: 902
Period size: 180 Copynumber: 3.8 Consensus size: 178
1423336 GAAAAAATTG
* *
1423346 AAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAAGCATTTTTGAGAAAAAGTTTAAAGTA
1 AAGTATCAATTTTTCTTAAAAATAAAATTTT-AAAAAAAACATTTTTGAGAAAAAGTTGAAAGTA
* ** *
1423411 TCAATTTTTCCTGAAAATAAAATATTCTGAAAAAAAACATTTTTAAGGAAAAGTTAAAAATGTCA
65 TCAATTTTTCTTGAAAATAAAAT-TT-AAAAAAAAAACATTTTTAAGGAAAAGTTGAAAATGTCA
* *
1423476 ATTTTTCTTGAAAATAAAACTGTTGAAAAAATATTTTTAAGGAAAAGTTAA
128 ATTTTTCTTGAAAATAAAATTGTTGAAAAAATATTTTTAAAGAAAAGTTAA
* *
1423527 AAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTA
1 AAGTATCAATTTTTCTTAAAAATAAAATTTT-AAAAAAAACATTTTTGAGAAAAAGTTGAAAGTA
* *
1423592 TTAATTTTTCTTGAAAATAAAATTTAAAAAAAAAAACATTTTTAAGGAAAAGTTGATAATGTCAA
65 TCAATTTTTCTTGAAAATAAAATTT-AAAAAAAAAACATTTTTAAGGAAAAGTTGAAAATGTCAA
* *
1423657 TTTTTCTTGAAAATAAAAATTG-TCAAAAAACATTTTTAAAGAAAAGTTAA
129 TTTTTCTTGAAAAT-AAAATTGTTGAAAAAATATTTTTAAAGAAAAGTTAA
1423707 AAGTATCAATTTTTCTTAAAAATAAAATTTTAAAAAAAAGCATTTTTGAGAAAAAGTTGAAAGTA
1 AAGTATCAATTTTTCTTAAAAATAAAATTTTAAAAAAAA-CATTTTTGAGAAAAAGTTGAAAGTA
* * ** *
1423772 TCAATTTTTCTTGAAAATTAAATTTTAAAAAAAAGTATTTTTAAGAAAAAGTTGAAAATGTCAAT
65 TCAATTTTTCTTGAAAATAAAATTTAAAAAAAAAACATTTTTAAGGAAAAGTTGAAAATGTCAAT
* *
1423837 TTTTCTTGAAAATAACATTGTTGAAAAAATATTTTT-AAGAAAAAGTTGA
130 TTTTCTTGAAAATAAAATTGTTGAAAAAATATTTTTAAAG-AAAAGTTAA
* * * *** *
1423886 AAGTATCAATTCTCCTTGAAAATAAAGATTTT-AAAAAGGGATTTTTGAGGAAAAGTTGAAAGTA
1 AAGTATCAATTTTTCTTAAAAATAAA-ATTTTAAAAAAAACATTTTTGAGAAAAAGTTGAAAGTA
* * * ** * * *
1423950 TTAATTTTTCATGAAAATAAAATTTTTAAAAAAGAAGTATTTTTAAGGAAAAATT-AAAAGTATT
65 TCAATTTTTCTTGAAAATAAAA--TTTAAAAAAAAAACATTTTTAAGGAAAAGTTGAAAA-TGTC
*
1424014 AATTTTTCTTGATAATAGAAAT
127 AATTTTTCTTGAAAATA-AAAT
1424036 ATCAAAATGC
Statistics
Matches: 454, Mismatches: 46, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
178 51 0.11
179 109 0.24
180 203 0.45
181 91 0.20
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (178 bp):
AAGTATCAATTTTTCTTAAAAATAAAATTTTAAAAAAAACATTTTTGAGAAAAAGTTGAAAGTAT
CAATTTTTCTTGAAAATAAAATTTAAAAAAAAAACATTTTTAAGGAAAAGTTGAAAATGTCAATT
TTTCTTGAAAATAAAATTGTTGAAAAAATATTTTTAAAGAAAAGTTAA
Found at i:1427331 original size:15 final size:15
Alignment explanation
Indices: 1427311--1427347 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1427301 CATGCATGTA
1427311 TGCATTTTCATTAAT
1 TGCATTTTCATTAAT
*
1427326 TGCATTTTCATTCAT
1 TGCATTTTCATTAAT
*
1427341 TACATTT
1 TGCATTT
1427348 AACAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (15 bp):
TGCATTTTCATTAAT
Found at i:1433900 original size:21 final size:20
Alignment explanation
Indices: 1433855--1433901 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1433845 GGTATGAAAT
*
1433855 TTTTAAAAAAGAAAATTTTG
1 TTTTGAAAAAGAAAATTTTG
*
1433875 ATTTGAAAAAG-AAATTTGGTG
1 TTTTGAAAAAGAAAATTT--TG
1433896 TTTTGA
1 TTTTGA
1433902 TGAATGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 9 0.41
21 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTTGAAAAAGAAAATTTTG
Found at i:1451467 original size:8 final size:8
Alignment explanation
Indices: 1451454--1451490 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1451444 GACAAGTGGA
1451454 TATATATT
1 TATATATT
1451462 TATATATT
1 TATATATT
*
1451470 TATTTATT
1 TATATATT
*
1451478 TATTTATT
1 TATATATT
1451486 TATAT
1 TATAT
1451491 GCTAGCTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TATATATT
Found at i:1451473 original size:4 final size:4
Alignment explanation
Indices: 1451458--1451488 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1451448 AGTGGATATA
*
1451458 TATT TATA TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
1451489 ATGCTAGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1451473 original size:12 final size:12
Alignment explanation
Indices: 1451453--1451490 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1451443 TGACAAGTGG
*
1451453 ATATATATTTAT
1 ATATTTATTTAT
1451465 ATATTTATTTAT
1 ATATTTATTTAT
*
1451477 TTATTTATTTAT
1 ATATTTATTTAT
1451489 AT
1 AT
1451491 GCTAGCTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTTATTTAT
Found at i:1453551 original size:2 final size:2
Alignment explanation
Indices: 1453544--1453573 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1453534 TGTTTATGTG
1453544 TA TA 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 TA TA
1453574 AACTCTAAAA
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):
TA
Found at i:1453753 original size:2 final size:2
Alignment explanation
Indices: 1453746--1453793 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
1453736 ATTACCTAAG
* * *
1453746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TG TA AA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
1453789 TA TA T
1 TA TA T
1453794 CACATATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1453963 original size:15 final size:16
Alignment explanation
Indices: 1453936--1453966 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1453926 TAAAGTAACA
1453936 TCTCTTCTTTCTTTTT
1 TCTCTTCTTTCTTTTT
1453952 TCTCTT-TTTCTTTTT
1 TCTCTTCTTTCTTTTT
1453967 GTGGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTCTTCTTTCTTTTT
Found at i:1457914 original size:2 final size:2
Alignment explanation
Indices: 1457907--1457961 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
1457897 ATTTCATTCC
* *
1457907 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1457949 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
1457962 CACGAGCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1458876 original size:21 final size:21
Alignment explanation
Indices: 1458851--1458892 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1458841 TATTACTTAA
1458851 TCTGGATATGAACTTTTAATT
1 TCTGGATATGAACTTTTAATT
1458872 TCTGGATATGAACTTTTAATT
1 TCTGGATATGAACTTTTAATT
1458893 ATATGACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
TCTGGATATGAACTTTTAATT
Found at i:1463490 original size:61 final size:61
Alignment explanation
Indices: 1463392--1463509 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
1463382 TCATATCTTT
* * * * *
1463392 GCCAAGAACAGAATCAAAACAGAAGCTGCAACGGGCAACAGCAACACAATCTCCAAAGGCA
1 GCCAAGAACAGAATCAAAACACAACCAGCAACAGGCAACAGCAACACAAGCTCCAAAGGCA
1463453 GCCAAGAACAGAATCAAAACACAACCAGCAACAGGCAACAGCAACACAAGCTCCAAA
1 GCCAAGAACAGAATCAAAACACAACCAGCAACAGGCAACAGCAACACAAGCTCCAAA
1463510 AGTAGCCTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.48, C:0.30, G:0.17, T:0.05
Consensus pattern (61 bp):
GCCAAGAACAGAATCAAAACACAACCAGCAACAGGCAACAGCAACACAAGCTCCAAAGGCA
Found at i:1476195 original size:22 final size:24
Alignment explanation
Indices: 1476154--1476201 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
1476144 ATTAATAATT
*
1476154 TTTTTAAATATTGATTTTTATATA
1 TTTTTAAATATTGATATTTATATA
*
1476178 TTTTT-AA-ATTGATATTTATTTA
1 TTTTTAAATATTGATATTTATATA
1476200 TT
1 TT
1476202 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 2 0.09
24 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTAAATATTGATATTTATATA
Found at i:1476207 original size:22 final size:22
Alignment explanation
Indices: 1476163--1476207 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1476153 TTTTTTAAAT
* **
1476163 ATTGATTTTTATATATTTTTAA
1 ATTGATATTTATATATTAATAA
*
1476185 ATTGATATTTATTTATTAATAA
1 ATTGATATTTATATATTAATAA
1476207 A
1 A
1476208 AAATATTATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTGATATTTATATATTAATAA
Found at i:1476243 original size:21 final size:20
Alignment explanation
Indices: 1476191--1476244 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
1476181 TTAAATTGAT
1476191 ATTTATTTATT-A-ATAAAAA
1 ATTTA-TTATTAATATAAAAA
*
1476210 ATATTATGA-TAATATAAAAA
1 AT-TTATTATTAATATAAAAA
1476230 ATTTATATATTAATA
1 ATTTAT-TATTAATA
1476245 ATGTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.04
19 9 0.32
20 13 0.46
21 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTATTATTAATATAAAAA
Found at i:1492369 original size:6 final size:7
Alignment explanation
Indices: 1492351--1492376 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1492341 GGCTCGTCTG
1492351 CAAAAAA
1 CAAAAAA
1492358 CAAAAAA
1 CAAAAAA
1492365 CAAAAAA
1 CAAAAAA
1492372 CAAAA
1 CAAAA
1492377 TATAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:1499182 original size:13 final size:12
Alignment explanation
Indices: 1499166--1499209 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
1499156 AATAAAATCT
1499166 TTTAATTTATTAA
1 TTTAATTT-TTAA
1499179 TTTAGATTTTTAA
1 TTTA-ATTTTTAA
1499192 TTTTAATTTTT-A
1 -TTTAATTTTTAA
1499204 TTTAAT
1 TTTAAT
1499210 CATTTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.21
12 1 0.03
13 14 0.48
14 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTAATTTTTAA
Found at i:1501796 original size:5 final size:5
Alignment explanation
Indices: 1501788--1501815 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1501778 AATGGGTTAG
1501788 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
1501816 ATGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1501825 original size:15 final size:15
Alignment explanation
Indices: 1501787--1501825 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1501777 AAATGGGTTA
1501787 GAAATAAAATAAAAT
1 GAAATAAAATAAAAT
*
1501802 AAAATAAAATAAAAAT
1 GAAATAAAAT-AAAAT
1501818 GAAA-AAAA
1 GAAATAAAA
1501826 AAACTTGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (15 bp):
GAAATAAAATAAAAT
Found at i:1502168 original size:14 final size:13
Alignment explanation
Indices: 1502149--1502178 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1502139 TAGGAAACCC
*
1502149 AAAAAAATTCAAA
1 AAAAAAAATCAAA
1502162 AAAAAAAATCAAA
1 AAAAAAAATCAAA
1502175 AAAA
1 AAAA
1502179 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:1502595 original size:3 final size:3
Alignment explanation
Indices: 1502589--1502654 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1502579 GAAGAAACAG
1502589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1502637 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
1502655 CTAATTGGAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1502695 original size:26 final size:25
Alignment explanation
Indices: 1502659--1502729 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 25
1502649 AATAATCTAA
* *
1502659 TTGGACCAAAATGGGCCCAGTTAGGT
1 TTGGA-CAAAATAGGCCCAATTAGGT
*
1502685 TTGGACAAAAATAGGCCCAATTGGGT
1 TTGGAC-AAAATAGGCCCAATTAGGT
*
1502711 TAGGATCAAAATAGGCCCA
1 TTGGA-CAAAATAGGCCCA
1502730 TTTGAGCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.95
27 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (25 bp):
TTGGACAAAATAGGCCCAATTAGGT
Found at i:1503295 original size:119 final size:117
Alignment explanation
Indices: 1503115--1503516 Score: 360
Period size: 119 Copynumber: 3.4 Consensus size: 117
1503105 GGGACGGGAC
* * * * * **
1503115 GAAATCACGAACCATAATAAATGATTTGGACTGAGCCAAAATCAGGTGATTGTGATAAAATCACA
1 GAAATCACGAATCA-AAAAAATGATTTGGACTGAGCCAAGATCAAGTGATAG-GACGAAATCACA
* * * *
1503180 AGTCAAAATGAAGCGATTAAGACCAAGTCGAGGTTGAAAATGAATGATCGAGAT
64 AGTCAAAATAAAGCGATTAAGATCGAGTCGAGGTAGAAAATGAATGATCGAGAT
* * *
1503234 GAAATCACGAATCATAAAAAATGATTTGGATTGAGTCAAGATCAAGTGACTAGGACGAAATCATA
1 GAAATCACGAATCA-AAAAAATGATTTGGACTGAGCCAAGATCAAGTGA-TAGGACGAAATCACA
* * * * * * *
1503299 AATCTAAATAAAGCGATCAATATCGAGTTGAGGTAAAAAATGATTGATCGAGAT
64 AGTCAAAATAAAGCGATTAAGATCGAGTCGAGGTAGAAAATGAATGATCGAGAT
* * * * * * * * *
1503353 GAAATCATG-A-CAATAGAGATAATTTGGATTGAACCAAGATCAAGTGATCAGAACGAAACCACG
1 GAAATCACGAATCAA-AAAAATGATTTGGACTGAGCCAAGATCAAGTGAT-AGGACGAAATCACA
* * * * *
1503416 AGTCACAATAAAGCGATTAGGATCGAGTCGAGGTCGAAAATAAATAATC-ATGAT
64 AGTCAAAATAAAGCGATTAAGATCGAGTCGAGGTAGAAAATGAATGATCGA-GAT
* * * * *
1503470 GGAATCCCAAATCACAAAAATGATCTGGACTGAGCCAAGATCAAGTG
1 GAAATCACGAATCAAAAAAATGATTTGGACTGAGCCAAGATCAAGTG
1503517 GGTGAATAAT
Statistics
Matches: 223, Mismatches: 54, Indels: 13
0.77 0.19 0.04
Matches are distributed among these distances:
116 3 0.01
117 85 0.38
118 28 0.13
119 105 0.47
120 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (117 bp):
GAAATCACGAATCAAAAAAATGATTTGGACTGAGCCAAGATCAAGTGATAGGACGAAATCACAAG
TCAAAATAAAGCGATTAAGATCGAGTCGAGGTAGAAAATGAATGATCGAGAT
Found at i:1503427 original size:117 final size:118
Alignment explanation
Indices: 1503216--1503432 Score: 262
Period size: 117 Copynumber: 1.8 Consensus size: 118
1503206 GTCGAGGTTG
* **
1503216 AAAATGAATGATCGAGATGAAATCACGAATCATAAAAAATGATTTGGATTGAGTCAAGATCAAGT
1 AAAATGAATGATCGAGATGAAATCACGAA-CATAAAAAATAATTTGGATTGAACCAAGATCAAGT
* * *
1503281 GACTAGGACGAAATCATAAATCTAAATAAAGCGATCAATATCGAGTTGAGGTAA
65 GACTAGAACGAAACCACAAATCTAAATAAAGCGATCAATATCGAGTTGAGGTAA
* * * *
1503335 AAAATGATTGATCGAGATGAAATCATG-ACA-ATAGAGATAATTTGGATTGAACCAAGATCAAGT
1 AAAATGAATGATCGAGATGAAATCACGAACATA-AAAAATAATTTGGATTGAACCAAGATCAAGT
* *
1503398 GA-TCAGAACGAAACCACGAGTC-ACAATAAAGCGAT
65 GACT-AGAACGAAACCACAAATCTA-AATAAAGCGAT
1503433 TAGGATCGAG
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
116 3 0.04
117 54 0.65
118 1 0.01
119 25 0.30
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (118 bp):
AAAATGAATGATCGAGATGAAATCACGAACATAAAAAATAATTTGGATTGAACCAAGATCAAGTG
ACTAGAACGAAACCACAAATCTAAATAAAGCGATCAATATCGAGTTGAGGTAA
Found at i:1504429 original size:12 final size:12
Alignment explanation
Indices: 1504412--1504445 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
1504402 CGATTTGAAC
1504412 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1504424 TTTC--TTTTTT
1 TTTCTTTTTTTT
1504434 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1504446 AATCAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:1504433 original size:10 final size:10
Alignment explanation
Indices: 1504418--1504445 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1504408 GAACTTTCTT
1504418 TTTTTTTTTC
1 TTTTTTTTTC
1504428 TTTTTTTTTC
1 TTTTTTTTTC
1504438 TTTTTTTT
1 TTTTTTTT
1504446 AATCAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1504961 original size:22 final size:22
Alignment explanation
Indices: 1504936--1505001 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
1504926 TATATATTTA
1504936 TATTTGTATATCTAGAATTAAG
1 TATTTGTATATCTAGAATTAAG
* *
1504958 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATATCTAGAATTAAG
1504980 TATTTGTATATCTAGAATTAAG
1 TATTTGTATATCTAGAATTAAG
1505002 GATAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (22 bp):
TATTTGTATATCTAGAATTAAG
Found at i:1509014 original size:22 final size:22
Alignment explanation
Indices: 1508989--1509031 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1508979 TGTATATTTA
*
1508989 TATTTGTATATCTAGAATTAAG
1 TATTTGTATATCTAAAATTAAG
1509011 TATTTGTATATCTAAAATTAA
1 TATTTGTATATCTAAAATTAA
1509032 TGATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTTGTATATCTAAAATTAAG
Found at i:1515000 original size:16 final size:16
Alignment explanation
Indices: 1514979--1515015 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1514969 TATGTCGGTA
1514979 TTGGTTAATAAAAGAT
1 TTGGTTAATAAAAGAT
1514995 TTGGTTAATAAAAGAT
1 TTGGTTAATAAAAGAT
1515011 TTGGT
1 TTGGT
1515016 CAAATCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (16 bp):
TTGGTTAATAAAAGAT
Found at i:1519657 original size:5 final size:5
Alignment explanation
Indices: 1519649--1519680 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1519639 AAATGGGTTA
1519649 AAAAT AAAAT AAAAT AAAAT --AAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1519681 ACCTACAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1519680 original size:28 final size:28
Alignment explanation
Indices: 1519623--1519681 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1519613 TTAAGAAAAT
****
1519623 AATAAAATAAAATAAAAAATGGGTTAAA
1 AATAAAATAAAATAAAAAATAAAATAAA
1519651 AATAAAATAAAATAAAATAATAAAATAAA
1 AATAAAATAAAATAAAA-AATAAAATAAA
1519680 AA
1 AA
1519682 CCTACAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (28 bp):
AATAAAATAAAATAAAAAATAAAATAAA
Found at i:1519983 original size:11 final size:11
Alignment explanation
Indices: 1519967--1520008 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1519957 CAGGAAATCC
1519967 AAAAAAATTCA
1 AAAAAAATTCA
* *
1519978 AAAAAAA-ACC
1 AAAAAAATTCA
1519988 AAAAAAATTCA
1 AAAAAAATTCA
1519999 AAAAAAATTC
1 AAAAAAATTC
1520009 CTAAATCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:1519989 original size:21 final size:21
Alignment explanation
Indices: 1519965--1520005 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1519955 TTCAGGAAAT
1519965 CCAAAAAAATTCAAAAAAAAA
1 CCAAAAAAATTCAAAAAAAAA
1519986 CCAAAAAAATTCAAAAAAAA
1 CCAAAAAAATTCAAAAAAAA
1520006 TTCCTAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.10
Consensus pattern (21 bp):
CCAAAAAAATTCAAAAAAAAA
Found at i:1519991 original size:9 final size:10
Alignment explanation
Indices: 1519961--1520004 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1519951 GTTCTTCAGG
1519961 AAATCCAAAA
1 AAATCCAAAA
*
1519971 AAATTCAAAAA
1 AAA-TCCAAAA
*
1519982 AAAACCAAAA
1 AAATCCAAAA
*
1519992 AAATTCAAAA
1 AAATCCAAAA
1520002 AAA
1 AAA
1520005 ATTCCTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATCCAAAA
Found at i:1520504 original size:25 final size:25
Alignment explanation
Indices: 1520467--1520576 Score: 85
Period size: 26 Copynumber: 4.3 Consensus size: 25
1520457 AATGGACTAT
* *
1520467 AATGGGCTTAGTTGGGCTTGACCAA
1 AATGGGCTCAGTTGGGCTGGACCAA
* ** *
1520492 AATGGGCTCAGTTGGGTTCAAACAAA
1 AATGGGCTCAGTTGGGCT-GGACCAA
* * *
1520518 AATGGGCTCAATTGGGTCAGGATCAA
1 AATGGGCTCAGTTGGG-CTGGACCAA
* * *
1520544 AATGGACTCACTTGGGCTAGGACCAG
1 AATGGGCTCAGTTGGGCT-GGACCAA
1520570 AATGGGC
1 AATGGGC
1520577 CCAACTAGGC
Statistics
Matches: 64, Mismatches: 18, Indels: 5
0.74 0.21 0.06
Matches are distributed among these distances:
25 17 0.27
26 47 0.73
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (25 bp):
AATGGGCTCAGTTGGGCTGGACCAA
Found at i:1522041 original size:14 final size:14
Alignment explanation
Indices: 1522004--1522042 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1521994 TAATAAAATC
*
1522004 TTTTAATTTATAAA
1 TTTTAATTTTTAAA
*
1522018 TTTTGATTTTT-AA
1 TTTTAATTTTTAAA
1522031 TTTTAATTTTTA
1 TTTTAATTTTTA
1522043 TTTAATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTTAATTTTTAAA
Found at i:1522270 original size:3 final size:3
Alignment explanation
Indices: 1522262--1522310 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1522252 CTTCAACTCG
1522262 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1522310 T
1 T
1522311 TCAGTAACTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1526942 original size:23 final size:23
Alignment explanation
Indices: 1526916--1526967 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1526906 AATAAAAATA
* * *
1526916 AAAATAGATAGTTAAATTTATTC
1 AAAATAGAAAGATAAATCTATTC
* *
1526939 AAAACAGAAAGATAAATCTATTT
1 AAAATAGAAAGATAAATCTATTC
1526962 AAAATA
1 AAAATA
1526968 AACTGTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAATAGAAAGATAAATCTATTC
Found at i:1534791 original size:8 final size:8
Alignment explanation
Indices: 1534760--1534793 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
1534750 GATCTCTCTC
*
1534760 TTTCTTTC
1 TTTCTTTT
1534768 TTTCTTTT
1 TTTCTTTT
1534776 TTTCTTTT
1 TTTCTTTT
1534784 TTTCTTTT
1 TTTCTTTT
1534792 TT
1 TT
1534794 AGTGTATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1541406 original size:12 final size:12
Alignment explanation
Indices: 1541366--1541407 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1541356 ATCACATAGT
*
1541366 TATCTTTTTCCA
1 TATCTTTATCCA
1541378 TATCTGTTAT-CA
1 TATCT-TTATCCA
1541390 TTATCTTTATCCA
1 -TATCTTTATCCA
1541403 TATCT
1 TATCT
1541408 GTCAACTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.55
Consensus pattern (12 bp):
TATCTTTATCCA
Found at i:1545801 original size:3 final size:3
Alignment explanation
Indices: 1545788--1545823 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1545778 ATTTATTTAT
1545788 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1545824 CATCATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1547875 original size:2 final size:2
Alignment explanation
Indices: 1547868--1547901 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1547858 AGTTTCCGTT
1547868 TA TA TA TA 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 TA TA TA TA
1547902 GGCTGATTTA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1549410 original size:3 final size:3
Alignment explanation
Indices: 1549402--1549430 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1549392 AAGCTCCAGA
1549402 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1549431 AAAAAAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1556612 original size:14 final size:14
Alignment explanation
Indices: 1556593--1556621 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1556583 TCAATAAATC
1556593 AGTTAATAATTTGG
1 AGTTAATAATTTGG
1556607 AGTTAATAATTTGG
1 AGTTAATAATTTGG
1556621 A
1 A
1556622 AATCATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
AGTTAATAATTTGG
Found at i:1558415 original size:2 final size:2
Alignment explanation
Indices: 1558408--1558434 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1558398 ATGAGGTTAT
1558408 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 T
1558435 TTGAGTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1571011 original size:2 final size:2
Alignment explanation
Indices: 1570970--1570994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1570960 ATTTTTAGTC
1570970 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1570995 GTTAGATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1572263 original size:3 final size:3
Alignment explanation
Indices: 1572255--1572288 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1572245 AAGACAAAGG
1572255 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1572289 TTGTTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1578531 original size:2 final size:2
Alignment explanation
Indices: 1578524--1578554 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1578514 ATTCTAGTAC
1578524 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 T
1578555 GTAGTTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1581565 original size:23 final size:23
Alignment explanation
Indices: 1581538--1581583 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1581528 GTGGGGATCT
1581538 GAGAAAGAGAAAGTTATAAAAGG
1 GAGAAAGAGAAAGTTATAAAAGG
1581561 GAGAAAGAGAAAGTTATAAAAGG
1 GAGAAAGAGAAAGTTATAAAAGG
1581584 AAGAGGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.13
Consensus pattern (23 bp):
GAGAAAGAGAAAGTTATAAAAGG
Found at i:1584603 original size:2 final size:2
Alignment explanation
Indices: 1584596--1584632 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1584586 GAAACAATTC
1584596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1584633 GGAAAAGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1584648 original size:68 final size:68
Alignment explanation
Indices: 1584564--1584695 Score: 264
Period size: 68 Copynumber: 1.9 Consensus size: 68
1584554 AATAAAAGAA
1584564 AGGAAAAGTAGCAAACGATGGTGAAACAATTCATATATATATATATATATATATATATATATATA
1 AGGAAAAGTAGCAAACGATGGTGAAACAATTCATATATATATATATATATATATATATATATATA
1584629 TAT
66 TAT
1584632 AGGAAAAGTAGCAAACGATGGTGAAACAATTCATATATATATATATATATATATATATATATAT
1 AGGAAAAGTAGCAAACGATGGTGAAACAATTCATATATATATATATATATATATATATATATAT
1584696 GAATTGAGGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (68 bp):
AGGAAAAGTAGCAAACGATGGTGAAACAATTCATATATATATATATATATATATATATATATATA
TAT
Found at i:1584671 original size:2 final size:2
Alignment explanation
Indices: 1584664--1584695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1584654 GAAACAATTC
1584664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1584696 GAATTGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1587485 original size:2 final size:2
Alignment explanation
Indices: 1587478--1587505 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1587468 TACAACCTTC
1587478 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
1587506 GTCAGCAAAG
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:1594718 original size:14 final size:14
Alignment explanation
Indices: 1594699--1594725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1594689 ATCTAATCTT
1594699 TAAAAAAATTTAAA
1 TAAAAAAATTTAAA
1594713 TAAAAAAATTTAA
1 TAAAAAAATTTAA
1594726 GTTCGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAAATTTAAA
Found at i:1594865 original size:11 final size:11
Alignment explanation
Indices: 1594849--1594890 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1594839 TTTTTATTTA
1594849 TATATATAAAT
1 TATATATAAAT
1594860 TATATATAAAT
1 TATATATAAAT
* *
1594871 TAAAAATAAAAT
1 TATATAT-AAAT
1594883 TATATATA
1 TATATATA
1594891 TTTATCATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATATATAAAT
Found at i:1599288 original size:39 final size:39
Alignment explanation
Indices: 1599235--1599311 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1599225 AACACCTTTT
**
1599235 TTTTTTTTTTAATATAAAATTATATAATAATATATGAAC
1 TTTTTTTTAAAATATAAAATTATATAATAATATATGAAC
1599274 TTTTTTTTAAAATATAAAATTATATAATAATATATGAA
1 TTTTTTTTAAAATATAAAATTATATAATAATATATGAA
1599312 TTAATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (39 bp):
TTTTTTTTAAAATATAAAATTATATAATAATATATGAAC
Found at i:1619357 original size:2 final size:2
Alignment explanation
Indices: 1619350--1619394 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1619340 TTGGTGGCGT
1619350 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1619392 TG T
1 TG T
1619395 ATATATATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1630225 original size:20 final size:20
Alignment explanation
Indices: 1630200--1630253 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1630190 AATTTATTAA
*
1630200 TAAATAAATATTAATTTTTT
1 TAAATAAATATTAATTTTAT
* *
1630220 TAAATAATTTATTTATTTTAT
1 TAAATAA-ATATTAATTTTAT
1630241 T-AATAAAATATTA
1 TAAAT-AAATATTA
1630254 TTCAATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAATAAATATTAATTTTAT
Found at i:1630262 original size:23 final size:22
Alignment explanation
Indices: 1630189--1630266 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
1630179 TCGATGGTAA
*
1630189 TAATTTATTAAT-AAATAAATAT
1 TAATTTATTAATAAAAT-ATTAT
* *
1630211 TAATTTTTTTAA-ATAAT-TTATT
1 TAA-TTTATTAATAAAATATTA-T
*
1630233 TATTTTATTAATAAAATATTAT
1 TAATTTATTAATAAAATATTAT
1630255 TCAATTTATTAA
1 T-AATTTATTAA
1630267 CATTATATAC
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
21 9 0.21
22 12 0.28
23 22 0.51
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATTTATTAATAAAATATTAT
Found at i:1630932 original size:21 final size:20
Alignment explanation
Indices: 1630893--1630937 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1630883 CTAAAAAAAT
**
1630893 ATATAAAAAATAATTTTTAA
1 ATATAAAAAATAAAGTTTAA
*
1630913 ATATAAAAAATAAGAGTTTAG
1 ATATAAAAAATAA-AGTTTAA
1630934 ATAT
1 ATAT
1630938 TTCAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (20 bp):
ATATAAAAAATAAAGTTTAA
Found at i:1644285 original size:28 final size:27
Alignment explanation
Indices: 1644235--1644290 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1644225 ATTAATTTTT
* *
1644235 AAAATTAAAAAATTAATTCAATTAAAA
1 AAAATAAAAAAAATAATTCAATTAAAA
* *
1644262 AAAATAAAATAAAATAATTTAATTTAAA
1 AAAATAAAA-AAAATAATTCAATTAAAA
1644290 A
1 A
1644291 TAATTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATAAAAAAAATAATTCAATTAAAA
Found at i:1644291 original size:15 final size:15
Alignment explanation
Indices: 1644271--1644306 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1644261 AAAAATAAAA
1644271 TAAAATAATTTAATT
1 TAAAATAATTTAATT
1644286 TAAAATAATTTAATT
1 TAAAATAATTTAATT
1644301 TAAAAT
1 TAAAAT
1644307 TAATCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATAATTTAATT
Found at i:1644291 original size:20 final size:20
Alignment explanation
Indices: 1644266--1644303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1644256 TTAAAAAAAA
1644266 TAAAATAAAATAATTTAATT
1 TAAAATAAAATAATTTAATT
**
1644286 TAAAATAATTTAATTTAA
1 TAAAATAAAATAATTTAA
1644304 AATTAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATAAAATAATTTAATT
Found at i:1644853 original size:17 final size:17
Alignment explanation
Indices: 1644833--1644888 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
1644823 AAAGTGAGTT
1644833 ATTTTATATTTAATAAA
1 ATTTTATATTTAATAAA
** *
1644850 ATTTTA-ATTTTTTATA
1 ATTTTATATTTAATAAA
*
1644866 ATTTTATATTTAAATTAA
1 ATTTTATATTT-AATAAA
1644884 ATTTT
1 ATTTT
1644889 TTTATTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 13 0.43
17 10 0.33
18 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATTTAATAAA
Found at i:1644897 original size:34 final size:36
Alignment explanation
Indices: 1644833--1644919 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 36
1644823 AAAGTGAGTT
*
1644833 ATTTTATATTT-AATAAAATTTTAATTTTTT-A-TA
1 ATTTTATATTTAAATTAAATTTTAATTTTTTAATTA
*
1644866 ATTTTATATTTAAATTAAATTTT-TTTATTTTAATTA
1 ATTTTATATTTAAATTAAATTTTAATT-TTTTAATTA
*
1644902 A-TTAAT-TTTAAATTAAAT
1 ATTTTATATTTAAATTAAAT
1644920 ACTAAACATT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
33 13 0.28
34 26 0.55
35 5 0.11
36 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
ATTTTATATTTAAATTAAATTTTAATTTTTTAATTA
Found at i:1644910 original size:19 final size:22
Alignment explanation
Indices: 1644864--1644919 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 22
1644854 TAATTTTTTA
1644864 TAATTTTATATTTAAATTAAAT
1 TAATTTTATATTTAAATTAAAT
*
1644886 T--TTTT-TATTTTAATT-AAT
1 TAATTTTATATTTAAATTAAAT
*
1644904 TAATTTTA-AATTAAAT
1 TAATTTTATATTTAAAT
1644920 ACTAAACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 14 0.50
22 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTTTATATTTAAATTAAAT
Found at i:1644912 original size:143 final size:143
Alignment explanation
Indices: 1644640--1644909 Score: 353
Period size: 143 Copynumber: 1.9 Consensus size: 143
1644630 TAAAATTAGT
** * *
1644640 AATTTTTTTTATTTTTATTTACACATGATGTAGATTTATTAAAATAAATTATCATATATCTAATA
1 AATTTTTTTTATTTTTATTTACACATGATAAAAATTTAATAAAATAAATTATCATATATCTAATA
* * * *
1644705 AATTTTTAATTTTTTATAATATTATATTTAAGTTGAATCTTTCAATTTTTAATCAATTGATTTAA
66 AAATTTTAATTTTTTATAATATTATATTTAAATTAAATCTTTCAATTTTTAATCAATTAATTTAA
1644770 TTTATCACAAGTA
131 TTTATCACAAGTA
* * * * ** *
1644783 AATTTTTTTTATTTTTATTTATACATGATAAAAATTTAATAAAGTGAGTTATTTTATATTTAATA
1 AATTTTTTTTATTTTTATTTACACATGATAAAAATTTAATAAAATAAATTATCATATATCTAATA
* * ** *
1644848 AAATTTTAATTTTTTATAATTTTATATTTAAATTAAATTTTTTTA-TTTTAATTAATTAATTT
66 AAATTTTAATTTTTTATAATATTATATTTAAATTAAATCTTTCAATTTTTAATCAATTAATTT
1644910 TAAATTAAAT
Statistics
Matches: 107, Mismatches: 20, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
142 15 0.14
143 92 0.86
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (143 bp):
AATTTTTTTTATTTTTATTTACACATGATAAAAATTTAATAAAATAAATTATCATATATCTAATA
AAATTTTAATTTTTTATAATATTATATTTAAATTAAATCTTTCAATTTTTAATCAATTAATTTAA
TTTATCACAAGTA
Found at i:1645843 original size:15 final size:12
Alignment explanation
Indices: 1645808--1645834 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1645798 ATATAAATTA
1645808 TAAATTATTTTT
1 TAAATTATTTTT
1645820 TAAATTATTTTT
1 TAAATTATTTTT
1645832 TAA
1 TAA
1645835 CATATTATTG
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAAATTATTTTT
Found at i:1650654 original size:2 final size:2
Alignment explanation
Indices: 1650647--1650675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1650637 TGAGGTCAAC
1650647 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 A
1650676 ACAATTCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1664792 original size:20 final size:20
Alignment explanation
Indices: 1664761--1664831 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1664751 ATATAAATAA
*
1664761 AATTTT-TAATTATTTATTT
1 AATTTTATAATTATTTATAT
1664780 AATTTTATAATTATTTATAT
1 AATTTTATAATTATTTATAT
*
1664800 -ATATTTAT-A-TATATATAT
1 AAT-TTTATAATTATTTATAT
*
1664818 AATTTTATATTTAT
1 AATTTTATAATTAT
1664832 ATTAAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 13 0.30
19 11 0.25
20 20 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTTATAATTATTTATAT
Found at i:1664796 original size:10 final size:9
Alignment explanation
Indices: 1664765--1664835 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 9
1664755 AAATAAAATT
1664765 TTTA-ATTA
1 TTTATATTA
1664773 TTTAT-TTAA
1 TTTATATT-A
1664782 TTTTATAATTA
1 -TTTAT-ATTA
1664793 TTTATATATA
1 TTTATAT-TA
1664803 TTTATA-TA
1 TTTATATTA
* *
1664811 TATATATAA
1 TTTATATTA
1664820 TTT-TA-TA
1 TTTATATTA
1664827 TTTATATTA
1 TTTATATTA
1664836 AAAATAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
7 4 0.08
8 17 0.34
9 8 0.16
10 18 0.36
11 1 0.02
12 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTATATTA
Found at i:1664814 original size:16 final size:16
Alignment explanation
Indices: 1664790--1664833 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1664780 AATTTTATAA
*
1664790 TTATTTATATAT-ATT
1 TTATATATATATAATT
1664805 TATATATATATATAATT
1 T-TATATATATATAATT
*
1664822 TTATATTTATAT
1 TTATATATATAT
1664834 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 20 0.80
17 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATATATATAATT
Found at i:1664826 original size:14 final size:15
Alignment explanation
Indices: 1664785--1664832 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
1664775 TATTTAATTT
1664785 TATAATTATT-TATA
1 TATAATTATTATATA
*
1664799 TATATTTATATATATA
1 TATAATTAT-TATATA
*
1664815 TATAATT-TTATATT
1 TATAATTATTATATA
1664829 TATA
1 TATA
1664833 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.59
15 2 0.07
16 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATAATTATTATATA
Found at i:1672544 original size:21 final size:21
Alignment explanation
Indices: 1672489--1672546 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1672479 CTTGATGCAA
*
1672489 CAACTGCT-TCAATTGATTCTT
1 CAACTGCTCT-AATTGAATCTT
* * * *
1672510 CCACGGTTCCAATTGAATCTT
1 CAACTGCTCTAATTGAATCTT
1672531 CAACTGCTCTAATTGA
1 CAACTGCTCTAATTGA
1672547 TCCTTCCGTT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
CAACTGCTCTAATTGAATCTT
Found at i:1687711 original size:29 final size:28
Alignment explanation
Indices: 1687678--1687741 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1687668 TTTATATTTA
1687678 AAAAAAT-TTTAAAATACAAATTAAAAATT
1 AAAAAATATTTAAAATAC--ATTAAAAATT
* *
1687707 AAAAAGTTATTTAATATACATTAAAAATT
1 AAAAA-ATATTTAAAATACATTAAAAATT
1687736 AAAAAA
1 AAAAAA
1687742 AAAAATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 20 0.67
30 1 0.03
31 9 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAAAATATTTAAAATACATTAAAAATT
Found at i:1691314 original size:2 final size:2
Alignment explanation
Indices: 1691307--1691335 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1691297 TATACTAGGG
1691307 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1691336 AAAGGCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1694129 original size:16 final size:16
Alignment explanation
Indices: 1694108--1694139 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1694098 TTAGGAAGTT
1694108 TTACTTCATATTAGAC
1 TTACTTCATATTAGAC
1694124 TTACTTCATATTAGAC
1 TTACTTCATATTAGAC
1694140 AGACAGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
TTACTTCATATTAGAC
Found at i:1695475 original size:12 final size:13
Alignment explanation
Indices: 1695456--1695490 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1695446 ATTTGAATTA
1695456 TAAATAATATTTT
1 TAAATAATATTTT
1695469 T-AATAAT-TTTT
1 TAAATAATATTTT
1695480 TAAATAATATT
1 TAAATAATATT
1695491 GATCTCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.25
12 12 0.60
13 3 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATAATATTTT
Found at i:1696373 original size:23 final size:21
Alignment explanation
Indices: 1696346--1696388 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1696336 TAAAAAAGGA
1696346 ATAAAAAGAAAAAAGCAAGAAAT
1 ATAAAAA-AAAAAA-CAAGAAAT
1696369 ATAAAAAAAAAAACAAGAAA
1 ATAAAAAAAAAAACAAGAAA
1696389 GTTGAAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 6 0.30
23 7 0.35
ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07
Consensus pattern (21 bp):
ATAAAAAAAAAAACAAGAAAT
Found at i:1696378 original size:21 final size:21
Alignment explanation
Indices: 1696337--1696388 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1696327 TAATCAATCT
*
1696337 AAAA-AAGGAATAAAAAGAAA
1 AAAACAAGAAATAAAAAGAAA
*
1696357 AAAGCAAGAAATATAAAA-AAA
1 AAAACAAGAAATA-AAAAGAAA
1696378 AAAACAAGAAA
1 AAAACAAGAAA
1696389 GTTGAAAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.06
Consensus pattern (21 bp):
AAAACAAGAAATAAAAAGAAA
Found at i:1703888 original size:32 final size:32
Alignment explanation
Indices: 1703847--1703910 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1703837 CCTTTAGCAG
* *
1703847 ACAAGCAGGAATACTTTTGACATTTGTACTAA
1 ACAAGCAGGAATACTTCTAACATTTGTACTAA
1703879 ACAAGCAGGAATACTTCTAACATTTGTACTAA
1 ACAAGCAGGAATACTTCTAACATTTGTACTAA
1703911 TCTGACATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (32 bp):
ACAAGCAGGAATACTTCTAACATTTGTACTAA
Found at i:1707747 original size:21 final size:21
Alignment explanation
Indices: 1707723--1707763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1707713 AATTTTTGAA
1707723 TTATGATT-TTTTAATAAAAAT
1 TTATGATTATTTT-ATAAAAAT
*
1707744 TTATTATTATTTTATAAAAA
1 TTATGATTATTTTATAAAAA
1707764 ATGAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATGATTATTTTATAAAAAT
Found at i:1709236 original size:18 final size:18
Alignment explanation
Indices: 1709193--1709236 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
1709183 AATATTTTTT
*
1709193 AATATTATTTTTAATATA
1 AATATTATTTTTAAAATA
1709211 AATGATTATTTTTAAAATA
1 AAT-ATTATTTTTAAAATA
1709230 AATATTA
1 AATATTA
1709237 AAAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATTATTTTTAAAATA
Found at i:1710085 original size:3 final size:3
Alignment explanation
Indices: 1710077--1710120 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1710067 CCAAAATTCC
1710077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1710121 AATAGTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1711710 original size:18 final size:18
Alignment explanation
Indices: 1711664--1711723 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
1711654 AAGCTTGATA
1711664 TATATATAATTTTTAATTATT
1 TATATATAA-TTTT-A-TATT
1711685 TAT-T-TAATTTTATATT
1 TATATATAATTTTATATT
1711701 TATATATAATTTTATATT
1 TATATATAATTTTATATT
1711719 TATAT
1 TATAT
1711724 TAAAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.19
17 2 0.05
18 21 0.57
19 3 0.08
20 1 0.03
21 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATAATTTTATATT
Found at i:1711732 original size:23 final size:22
Alignment explanation
Indices: 1711706--1711749 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1711696 ATATTTATAT
*
1711706 ATAAT-TTTATATTTATATTAAAA
1 ATAATATTT-TATTAAT-TTAAAA
1711729 ATAATATTTTATTAATTTAAA
1 ATAATATTTTATTAATTTAAA
1711750 TTATGATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATTTTATTAATTTAAAA
Found at i:1716681 original size:182 final size:180
Alignment explanation
Indices: 1716369--1716723 Score: 602
Period size: 182 Copynumber: 2.0 Consensus size: 180
1716359 AAACAGCATG
*
1716369 CAAAATATAAGAAACATGGAACAAGCTTAACCTTAGATGGTCTCAAAAGGTAGCTAATAATTAGT
1 CAAAATATAAGAAACATGGAACAAGCTTAACCTTAGACGGTCTCAAAAGGTAGCTAATAATTAGT
* * * *
1716434 CTAATTTAAAACCCTTATTACATTGATATATGTCAAAACTACTAACCTGAAAATCTAACACCTTG
66 CAAATTTAAAACCCTCATTACATTGATATATGTCAAAACCACTAACCTGAAAATCAAACACCTTG
1716499 GTTCACCTTAATACAGTAATGAAATTGAAAAAACTACATATTCCCTCACA
131 GTTCACCTTAATACAGTAATGAAATTGAAAAAACTACATATTCCCTCACA
* * *
1716549 CAAAATATAAGAAACATGTAACAAGCTTAACCTTAGACGGTCTCTAAAGGTAGCTAATAATTATT
1 CAAAATATAAGAAACATGGAACAAGCTTAACCTTAGACGGTCTCAAAAGGTAGCTAATAATTAGT
*
1716614 CAAAAATTTAAAACCCTCATTACATTGATATATGTCAAAACCACTAACCTGAAAATCAAATACCT
66 C--AAATTTAAAACCCTCATTACATTGATATATGTCAAAACCACTAACCTGAAAATCAAACACCT
*
1716679 TGGTTCATCTTAATACAGTAATGAAATTGAAAAAACTACATATTC
129 TGGTTCACCTTAATACAGTAATGAAATTGAAAAAACTACATATTC
1716724 GTTCCCCAAA
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
180 62 0.38
182 101 0.62
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (180 bp):
CAAAATATAAGAAACATGGAACAAGCTTAACCTTAGACGGTCTCAAAAGGTAGCTAATAATTAGT
CAAATTTAAAACCCTCATTACATTGATATATGTCAAAACCACTAACCTGAAAATCAAACACCTTG
GTTCACCTTAATACAGTAATGAAATTGAAAAAACTACATATTCCCTCACA
Found at i:1726990 original size:41 final size:41
Alignment explanation
Indices: 1726932--1727014 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1726922 TCTTAGTTTA
*
1726932 TCCTCATTTATCTGTGAATGCAATTTAACAATTCATCTTGT
1 TCCTCATTTATCAGTGAATGCAATTTAACAATTCATCTTGT
* *
1726973 TCCTCATTTGTCAGTGAATGCAATTTAACAATTCATTTTGT
1 TCCTCATTTATCAGTGAATGCAATTTAACAATTCATCTTGT
1727014 T
1 T
1727015 GTTACATAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (41 bp):
TCCTCATTTATCAGTGAATGCAATTTAACAATTCATCTTGT
Found at i:1728211 original size:12 final size:12
Alignment explanation
Indices: 1728194--1728221 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1728184 CATAGCCAGA
1728194 CCCAGCAATTAG
1 CCCAGCAATTAG
1728206 CCCAGCAATTAG
1 CCCAGCAATTAG
1728218 CCCA
1 CCCA
1728222 ATGTAGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.39, G:0.14, T:0.14
Consensus pattern (12 bp):
CCCAGCAATTAG
Found at i:1729704 original size:16 final size:16
Alignment explanation
Indices: 1729685--1729715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1729675 TAATTAATTA
*
1729685 TTAAATTAATTTTAAT
1 TTAAAATAATTTTAAT
1729701 TTAAAATAATTTTAA
1 TTAAAATAATTTTAA
1729716 AAAAATTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATAATTTTAAT
Found at i:1729950 original size:18 final size:18
Alignment explanation
Indices: 1729927--1729962 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1729917 AACTAATCGA
*
1729927 TTTAAAATCGATAAAATT
1 TTTAAAATCAATAAAATT
*
1729945 TTTAAAATTAATAAAATT
1 TTTAAAATCAATAAAATT
1729963 AAAATAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTAAAATCAATAAAATT
Found at i:1734470 original size:35 final size:35
Alignment explanation
Indices: 1734424--1734504 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
1734414 ATGATAAGTA
1734424 GGATGCTCACCATTGCTTGCTTCCTACTCTGTGGC
1 GGATGCTCACCATTGCTTGCTTCCTACTCTGTGGC
1734459 GGATGCTCACCATTGCTTGCTTCCTACTCTGTGGC
1 GGATGCTCACCATTGCTTGCTTCCTACTCTGTGGC
1734494 GGATGCTCACC
1 GGATGCTCACC
1734505 TAGTTGTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.32
Consensus pattern (35 bp):
GGATGCTCACCATTGCTTGCTTCCTACTCTGTGGC
Found at i:1736401 original size:13 final size:13
Alignment explanation
Indices: 1736383--1736409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1736373 GTGGAGCTCA
1736383 TAAAAATTGTTCT
1 TAAAAATTGTTCT
1736396 TAAAAATTGTTCT
1 TAAAAATTGTTCT
1736409 T
1 T
1736410 TTTCATCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TAAAAATTGTTCT
Found at i:1751912 original size:6 final size:6
Alignment explanation
Indices: 1751877--1751911 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1751867 AGATAATAAT
* *
1751877 TATTAG TATTAG TATTAG TAGTAG TATTAT TATTA
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTA
1751912 TAATTACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:1752452 original size:27 final size:27
Alignment explanation
Indices: 1752422--1752475 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1752412 AAATTTTCAG
1752422 AGTAACCAAACAGTGGAATATATAGGA
1 AGTAACCAAACAGTGGAATATATAGGA
1752449 AGTAACCAAACAGTGGAATATATAGGA
1 AGTAACCAAACAGTGGAATATATAGGA
1752476 CAGACACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (27 bp):
AGTAACCAAACAGTGGAATATATAGGA
Done.