Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1748865 original size:17 final size:17
Alignment explanation
Indices: 1748845--1748897 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1748835 TTTTAATTTA
*
1748845 ATAATAATTCATATTAT
1 ATAATAATTTATATTAT
*
1748862 ATAA-ATTTTA-ATT-T
1 ATAATAATTTATATTAT
1748876 AATAATAATTTATATTAT
1 -ATAATAATTTATATTAT
1748894 ATAA
1 ATAA
1748898 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 9 0.31
17 11 0.38
18 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATAATTTATATTAT
Found at i:1748923 original size:32 final size:32
Alignment explanation
Indices: 1748826--1748923 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
1748816 ATTTTATTTT
* **
1748826 TTATATAAATTTTAATTTAATAATAATTCATA
1 TTATATAAATATTAAAATAATAATAATTCATA
* ** *
1748858 TTATATAAATTTTAATTTAATAATAATTTATA
1 TTATATAAATATTAAAATAATAATAATTCATA
*
1748890 TTATATAAATATTAAAAT-ATTATATATTCATA
1 TTATATAAATATTAAAATAATAATA-ATTCATA
1748922 TT
1 TT
1748924 TCCATTCATA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 5 0.08
32 54 0.92
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TTATATAAATATTAAAATAATAATAATTCATA
Found at i:1751807 original size:67 final size:68
Alignment explanation
Indices: 1751735--1752035 Score: 283
Period size: 67 Copynumber: 4.5 Consensus size: 68
1751725 TCACATTGTG
* * * ** *
1751735 GAGAAGTCAACCGTTGTGATCTTATACGTCATTTTCGTCAC-TTTTCCTAATGCAAGTGTTTTTA
1 GAGAAGTCAATCGTTGTGATCTTATGCGTCACTTTCGTCACTTTTTCCTAATGCAAGTACTCTTA
1751799 ATA
66 ATA
** * * * * * *
1751802 GAGAAGTTGATCGTTGT-AGTCATATGCGCCGCTTCCGTCACTTTTTCC-AATGCAAGTATTTTT
1 GAGAAGTCAATCGTTGTGA-TCTTATGCGTCACTTTCGTCACTTTTTCCTAATGCAAGTACTCTT
1751865 AATA
65 AATA
** *
1751869 GAGAAGTTGATCGTTATGAT-TATATGCGTCACTTTCGTCACTTTTTCCT-ATGCAAGTACTCTT
1 GAGAAGTCAATCGTTGTGATCT-TATGCGTCACTTTCGTCACTTTTTCCTAATGCAAGTACTCTT
*
1751932 GATA
65 AATA
* * * * *
1751936 GAAAAGTCAATCGTTGTGGTCATATGCGTTAC-TTCGATCAC-TTTTCCCAATGCAAGTACTCTT
1 GAGAAGTCAATCGTTGTGATCTTATGCGTCACTTTCG-TCACTTTTTCCTAATGCAAGTACTCTT
1751999 AATA
65 AATA
* * * *
1752003 GAAAAGTCAATCATTGTGGTCTTATGCTTCACT
1 GAGAAGTCAATCGTTGTGATCTTATGCGTCACT
1752036 CCCGTTACTC
Statistics
Matches: 194, Mismatches: 31, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
66 11 0.06
67 176 0.91
68 7 0.04
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (68 bp):
GAGAAGTCAATCGTTGTGATCTTATGCGTCACTTTCGTCACTTTTTCCTAATGCAAGTACTCTTA
ATA
Found at i:1752029 original size:134 final size:134
Alignment explanation
Indices: 1751738--1752078 Score: 337
Period size: 134 Copynumber: 2.5 Consensus size: 134
1751728 CATTGTGGAG
* * * ** * *
1751738 AAGTCAACCGTTGTGATCTTATACGTCATTTTCGTCAC-TTTTCCTAATGCAAGTGTTTTTAATA
1 AAGTCAATCGTTGTGATCTTATGCGTCACTTTCGTCACTTTTTCCT-ATGCAAGTACTCTTGATA
* ** * * * *
1751802 GAGAAGTTGATCGTTGTAGTCATATGCGCCGCTTCCGTCACTTTTTCCAATGCAAGTATTTTTAA
65 GAAAAGTCAATCGTTGTAGTCATATGCGCCACTTCCGTCACTTTTCCCAATGCAAGTACTCTTAA
*
1751867 TAGAG
130 TAGAA
** *
1751872 AAGTTGATCGTTATGAT-TATATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTGATA
1 AAGTCAATCGTTGTGATCT-TATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTGATA
* **
1751936 GAAAAGTCAATCGTTGTGGTCATATGCGTTACTT-CGATCACTTTTCCCAATGCAAGTACTCTTA
65 GAAAAGTCAATCGTTGTAGTCATATGCGCCACTTCCG-TCACTTTTCCCAATGCAAGTACTCTTA
1752000 ATAGAA
129 ATAGAA
* * * ** * * * * * * *
1752006 AAGTCAATCATTGTGGTCTTATGCTTCACTCCCGTTACTCTCTCATTTACAAGTACTCTTGATGG
1 AAGTCAATCGTTGTGATCTTATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTGATAG
1752071 AAAAGTCA
66 AAAAGTCA
1752079 TCTATTGTGG
Statistics
Matches: 167, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
133 3 0.02
134 156 0.93
135 8 0.05
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (134 bp):
AAGTCAATCGTTGTGATCTTATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTGATAG
AAAAGTCAATCGTTGTAGTCATATGCGCCACTTCCGTCACTTTTCCCAATGCAAGTACTCTTAAT
AGAA
Found at i:1752059 original size:67 final size:67
Alignment explanation
Indices: 1751921--1752096 Score: 189
Period size: 67 Copynumber: 2.6 Consensus size: 67
1751911 TTTTCCTATG
* * * *
1751921 CAAGTACTCTTGATAGAAAAGTCAATCGTTGTGGTCATATGCGTTACTTCGATCACTTTTCCCAA
1 CAAGTACTCTTGATAGAAAAGTCAATCATTGTGGTCTTATGCGTTACTCCGATCACTTCTCCCAA
*
1751986 TG
66 TA
* * *
1751988 CAAGTACTCTTAATAGAAAAGTCAATCATTGTGGTCTTATGC-TTCACTCCCG-TTAC-TCTCTC
1 CAAGTACTCTTGATAGAAAAGTCAATCATTGTGGTCTTATGCGTT-ACT-CCGATCACTTCTCCC
*
1752050 ATTTA
64 A-ATA
* *
1752055 CAAGTACTCTTGATGGAAAAGTC-ATCTATTGTGGTCTCATGC
1 CAAGTACTCTTGATAGAAAAGTCAATC-ATTGTGGTCTTATGC
1752097 ACCATTTTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
66 10 0.11
67 81 0.87
68 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (67 bp):
CAAGTACTCTTGATAGAAAAGTCAATCATTGTGGTCTTATGCGTTACTCCGATCACTTCTCCCAA
TA
Found at i:1752534 original size:20 final size:19
Alignment explanation
Indices: 1752505--1752567 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
1752495 TATTTATTCT
1752505 TAAAAAA-TAT-TATTTTA
1 TAAAAAACTATATATTTTA
1752522 TAAAAAACTATAT-TTTTA
1 TAAAAAACTATATATTTTA
*
1752540 TAAAAAA-TA-ATATCTTA
1 TAAAAAACTATATATTTTA
1752557 TTAAAAAACTA
1 -TAAAAAACTA
1752568 CTTTAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 2 0.05
17 13 0.32
18 22 0.55
19 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAAACTATATATTTTA
Found at i:1752660 original size:16 final size:16
Alignment explanation
Indices: 1752639--1752669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1752629 CAGTTACAGG
*
1752639 CAGCACTTGTTGCTGC
1 CAGCACTTGCTGCTGC
1752655 CAGCACTTGCTGCTG
1 CAGCACTTGCTGCTG
1752670 GCTGCAATTG
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:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (16 bp):
CAGCACTTGCTGCTGC
Found at i:1753418 original size:2 final size:2
Alignment explanation
Indices: 1753411--1753435 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1753401 ATTCACTCTT
1753411 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
1753436 TACCATTATA
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:1753706 original size:13 final size:14
Alignment explanation
Indices: 1753676--1753731 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1753666 ATATTTTTTT
*
1753676 GCACAAATACTTTG
1 GCACAAATACTTTA
*
1753690 GCACAGATAC-TTA
1 GCACAAATACTTTA
*
1753703 GCACACAAGTGCTTTA
1 GCACA-AA-TACTTTA
*
1753719 GCACAAACACTTT
1 GCACAAATACTTT
1753732 GATAGAGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.21
14 14 0.42
15 4 0.12
16 8 0.24
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (14 bp):
GCACAAATACTTTA
Found at i:1753753 original size:15 final size:14
Alignment explanation
Indices: 1753729--1753785 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
1753719 GCACAAACAC
*
1753729 TTTGATAGAGATAT
1 TTTGACAGAGATAT
1753743 GTTTGACAGAGATACT
1 -TTTGACAGAGATA-T
*
1753759 TTTGACATAGATAT
1 TTTGACAGAGATAT
*
1753773 TTTGACATAGATA
1 TTTGACAGAGATA
1753786 CTTAGCATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
14 14 0.36
15 24 0.62
16 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (14 bp):
TTTGACAGAGATAT
Found at i:1753777 original size:14 final size:14
Alignment explanation
Indices: 1753737--1753785 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 14
1753727 ACTTTGATAG
*
1753737 AGATATGTTTGACAG
1 AGATAT-TTTGACAT
1753752 AGATACTTTTGACAT
1 AGATA-TTTTGACAT
1753767 AGATATTTTGACAT
1 AGATATTTTGACAT
1753781 AGATA
1 AGATA
1753786 CTTAGCATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 14 0.44
15 17 0.53
16 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (14 bp):
AGATATTTTGACAT
Found at i:1754839 original size:14 final size:14
Alignment explanation
Indices: 1754820--1754857 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1754810 TTTCTACCCT
1754820 TTATAA-TTATTATA
1 TTATAATTTATT-TA
1754834 TTATAATTTATTTA
1 TTATAATTTATTTA
*
1754848 TTATTATTTA
1 TTATAATTTA
1754858 AAATTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATAATTTATTTA
Found at i:1754927 original size:16 final size:15
Alignment explanation
Indices: 1754895--1754932 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1754885 TGAAACTCTT
1754895 ATTTATAAATATTAA
1 ATTTATAAATATTAA
*
1754910 ATTTATATAATTTTAA
1 ATTTATA-AATATTAA
1754926 A-TTATAA
1 ATTTATAA
1754933 TTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATAAATATTAA
Found at i:1754941 original size:10 final size:11
Alignment explanation
Indices: 1754922--1754966 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1754912 TTATATAATT
1754922 TTAAAT-TATAA
1 TTAAATATAT-A
1754933 TTAAATATATA
1 TTAAATATATA
*
1754944 TAAAAT-TATA
1 TTAAATATATA
1754954 TTAAATATA-A
1 TTAAATATATA
1754964 TTA
1 TTA
1754967 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 13 0.43
11 14 0.47
12 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATATATA
Found at i:1754947 original size:21 final size:22
Alignment explanation
Indices: 1754914--1754971 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
1754904 TATTAAATTT
*
1754914 ATATAATTTTAAATTATAATTAA
1 ATATAATTATAAATTAT-ATTAA
1754937 ATAT-A-TATAAAATTATATTAA
1 ATATAATTAT-AAATTATATTAA
1754958 ATATAATTATAAAT
1 ATATAATTATAAAT
1754972 AAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 11 0.35
22 13 0.42
23 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTATAAATTATATTAA
Found at i:1754956 original size:27 final size:26
Alignment explanation
Indices: 1754905--1754976 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
1754895 ATTTATAAAT
* **
1754905 ATTAAATTTATATAATTTTAAATTATA
1 ATTAAATATATATAAAATTAAATTA-A
*
1754932 ATTAAATATATATAAAATTATATTAA
1 ATTAAATATATATAAAATTAAATTAA
* *
1754958 ATATAATTATAAATAAAAT
1 AT-TAAATATATATAAAAT
1754977 ATTTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAAATATATATAAAATTAAATTAA
Found at i:1756935 original size:28 final size:28
Alignment explanation
Indices: 1756896--1756951 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1756886 CATCAAATAA
*
1756896 ATTTTAATTTTAATATTTA-TAAATTTTT
1 ATTTTAAATTTAA-ATTTATTAAATTTTT
*
1756924 ATTTTAAATTTAAATTTATTATATTTTT
1 ATTTTAAATTTAAATTTATTAAATTTTT
1756952 TATATATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTTAAATTTAAATTTATTAAATTTTT
Found at i:1756950 original size:22 final size:22
Alignment explanation
Indices: 1756892--1756935 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1756882 ATAACATCAA
*
1756892 ATAAATTTTAATTTTAATATTT
1 ATAAATTTTTATTTTAATATTT
1756914 ATAAATTTTTATTTTAA-ATTT
1 ATAAATTTTTATTTTAATATTT
1756935 A
1 A
1756936 AATTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATAAATTTTTATTTTAATATTT
Found at i:1758822 original size:42 final size:42
Alignment explanation
Indices: 1758762--1758841 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
1758752 AGAACTTTAG
*
1758762 AAAAATATACAATTTTTATAAATAATCAGATCTTTTAGTTAT
1 AAAAAAATACAATTTTTATAAATAATCAGATCTTTTAGTTAT
*
1758804 AAAAAAATACTAA-TTTTATAGATAATCAGATCTTTTAG
1 AAAAAAATAC-AATTTTTATAAATAATCAGATCTTTTAG
1758842 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (42 bp):
AAAAAAATACAATTTTTATAAATAATCAGATCTTTTAGTTAT
Found at i:1758850 original size:42 final size:42
Alignment explanation
Indices: 1758762--1758852 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
1758752 AGAACTTTAG
* ** *
1758762 AAAAATATACAATTTTTATAAATAATCAGATCTTTTAGTTAT
1 AAAAAAATACAATTTTTATAAATAATCAGATCTTTTAGAAAA
*
1758804 AAAAAAATACTAA-TTTTATAGATAATCAGATCTTTTAGAAAA
1 AAAAAAATAC-AATTTTTATAAATAATCAGATCTTTTAGAAAA
1758846 AAAAAAA
1 AAAAAAA
1758853 ACTTTAACGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (42 bp):
AAAAAAATACAATTTTTATAAATAATCAGATCTTTTAGAAAA
Found at i:1767788 original size:13 final size:13
Alignment explanation
Indices: 1767770--1767795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1767760 AGTATCACTG
1767770 ATATTTTATCAAA
1 ATATTTTATCAAA
1767783 ATATTTTATCAAA
1 ATATTTTATCAAA
1767796 CCATTTTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTTATCAAA
Found at i:1770992 original size:159 final size:159
Alignment explanation
Indices: 1770774--1771242 Score: 794
Period size: 159 Copynumber: 2.9 Consensus size: 159
1770764 AGAGAAGAAC
* * *
1770774 GAAAATGCTATATTGGATTCAATGGGTAGCTTGAGAGAGGAAATTGGTGCAGTCAAAAACAAAGA
1 GAAAATGCTATATTGGATTCAATGGGTAGCTTGAAAGAGGAAATTGGTGGAGTCGAAAACAAAGA
* * * *
1770839 AAATAGTTCAACTGCTCTGATGGAAAATAACACTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
66 AAATAGGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
*
1770904 AAAAACTTGAAGCTGGTGGTGGTGAGGAT
131 AAGAACTTGAAGCTGGTGGTGGTGAGGAT
* * * *
1770933 GAAAATGCTATTTTGGATTCAATGGGTAGCTTTAAAGAGGAAATTGGTGGACTCGAAAACAAGGA
1 GAAAATGCTATATTGGATTCAATGGGTAGCTTGAAAGAGGAAATTGGTGGAGTCGAAAACAAAGA
1770998 AAATAGGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
66 AAATAGGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
1771063 AAGAACTTGAAGCTGGTGGTGGTGAGGAT
131 AAGAACTTGAAGCTGGTGGTGGTGAGGAT
*
1771092 GAAAATGCTATATTGGATTCAATGGGTAGCTTGAAAGAGGAAATTGGTGGAGTCGAAAACAGAGA
1 GAAAATGCTATATTGGATTCAATGGGTAGCTTGAAAGAGGAAATTGGTGGAGTCGAAAACAAAGA
*
1771157 AAATAGGTCTACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
66 AAATAGGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
* *
1771222 AAGAACTTGAGGCCGGTGGTG
131 AAGAACTTGAAGCTGGTGGTG
1771243 ATGGGATTCA
Statistics
Matches: 290, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
159 290 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (159 bp):
GAAAATGCTATATTGGATTCAATGGGTAGCTTGAAAGAGGAAATTGGTGGAGTCGAAAACAAAGA
AAATAGGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGTGGTGTCTGAGAGAGTGGAAGAAC
AAGAACTTGAAGCTGGTGGTGGTGAGGAT
Found at i:1773242 original size:120 final size:120
Alignment explanation
Indices: 1773029--1773259 Score: 381
Period size: 120 Copynumber: 1.9 Consensus size: 120
1773019 TTTCAGAAAG
* * *
1773029 TGATCCATTGTGGTTGTGATAGTTATAGTAGTGTTCAGACATCTTTAGAAACTATAATCTAGAAA
1 TGATCCATTGTGGCTGTGATAGTTATAGTAGTGTTCAGACAGCTTTAGAAACTACAATCTAGAAA
* *
1773094 GATAATTTTTGATTGAGAGGTACGTCTTGTATCCAAAAGACGTTTTTAGTAACCA
66 GACAATTTTTGATTGAGAGGTACGTCTTGTATCCAAAACACGTTTTTAGTAACCA
* * * *
1773149 TGATCCATTGTGGCTGTGATAGTTATAGTGGTGTTCAGACAGCTTTGGCAACTACGATCTAGAAA
1 TGATCCATTGTGGCTGTGATAGTTATAGTAGTGTTCAGACAGCTTTAGAAACTACAATCTAGAAA
1773214 GACAATTTTTGATTGAGAGGTACGTCTTGTATCCAAAACACGTTTT
66 GACAATTTTTGATTGAGAGGTACGTCTTGTATCCAAAACACGTTTT
1773260 GATTGAGTTA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 102 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (120 bp):
TGATCCATTGTGGCTGTGATAGTTATAGTAGTGTTCAGACAGCTTTAGAAACTACAATCTAGAAA
GACAATTTTTGATTGAGAGGTACGTCTTGTATCCAAAACACGTTTTTAGTAACCA
Found at i:1777830 original size:21 final size:21
Alignment explanation
Indices: 1777805--1777872 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1777795 TTAATCTATT
1777805 ATTTTAGTAACTTTTAATATA
1 ATTTTAGTAACTTTTAATATA
* *
1777826 ATTTTA-AAAGCTTATAATATA
1 ATTTTAGTAA-CTTTTAATATA
* *
1777847 ATTTTTGGTAAC-TTTGATATA
1 A-TTTTAGTAACTTTTAATATA
1777868 ATTTT
1 ATTTT
1777873 GATAGCTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 6 0.16
21 25 0.66
22 5 0.13
23 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTTTAGTAACTTTTAATATA
Found at i:1777881 original size:20 final size:20
Alignment explanation
Indices: 1777821--1777882 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1777811 GTAACTTTTA
* * *
1777821 ATATAATTTTAAAAGCTTATA
1 ATATAATTTTGATAGCTT-TG
* *
1777842 ATATAATTTTTGGTAACTTTG
1 ATATAA-TTTTGATAGCTTTG
1777863 ATATAATTTTGATAGCTTTG
1 ATATAATTTTGATAGCTTTG
1777883 GAGATTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 12 0.36
21 13 0.39
22 8 0.24
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.48
Consensus pattern (20 bp):
ATATAATTTTGATAGCTTTG
Found at i:1777924 original size:22 final size:22
Alignment explanation
Indices: 1777896--1777978 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 22
1777886 ATTATTTTGG
1777896 TAATTTTGATATATTTATATAA
1 TAATTTTGATATATTTATATAA
* *
1777918 TAATTTTGA-AAATTTTTATAA
1 TAATTTTGATATATTTATATAA
*
1777939 TAATTTT-AGTA-ATTTTTGAT-A
1 TAATTTTGA-TATATTTAT-ATAA
*
1777960 TAATTTTAATATA-TTATAT
1 TAATTTTGATATATTTATAT
1777979 CACCCAGCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
20 3 0.06
21 36 0.68
22 14 0.26
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATTTTGATATATTTATATAA
Found at i:1781760 original size:20 final size:20
Alignment explanation
Indices: 1781724--1781763 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1781714 CAACTCAAAC
*
1781724 TTAAATTTTAATATAAATAA
1 TTAAATTTAAATATAAATAA
1781744 TTAAATTTAAA-ATTAAATAA
1 TTAAATTTAAATA-TAAATAA
1781764 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATTTAAATATAAATAA
Found at i:1781770 original size:25 final size:26
Alignment explanation
Indices: 1781724--1781773 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1781714 CAACTCAAAC
* * *
1781724 TTAAATTTTAATATAAATAATTAAAT
1 TTAAAATTAAATATAAAAAATTAAAT
1781750 TTAAAATTAAATA-AAAAAATTAAA
1 TTAAAATTAAATATAAAAAATTAAA
1781774 CTCATTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TTAAAATTAAATATAAAAAATTAAAT
Found at i:1789874 original size:16 final size:16
Alignment explanation
Indices: 1789850--1789880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1789840 AAATTCAGAT
*
1789850 TCACGATTAATTAATG
1 TCACAATTAATTAATG
1789866 TCACAATTAATTAAT
1 TCACAATTAATTAAT
1789881 TGAAAATAGA
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:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (16 bp):
TCACAATTAATTAATG
Found at i:1789999 original size:10 final size:10
Alignment explanation
Indices: 1789972--1790003 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1789962 GATATACTCA
1789972 TATATATTTT
1 TATATATTTT
1789982 T-T-TATTTT
1 TATATATTTT
1789990 TATATATTTT
1 TATATATTTT
1790000 TATA
1 TATA
1790004 ATTATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATATATTTT
Found at i:1790101 original size:23 final size:23
Alignment explanation
Indices: 1790067--1790117 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1790057 AATTTTAATA
*
1790067 TATTTA-CATATT-TATTATATTT
1 TATTTATCATATTATAAT-TATTT
1790089 TATTTATCATATTATAATTATTT
1 TATTTATCATATTATAATTATTT
1790112 T-TTTAT
1 TATTTAT
1790118 TATACTCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
23 12 0.46
24 3 0.12
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTATCATATTATAATTATTT
Found at i:1790103 original size:22 final size:24
Alignment explanation
Indices: 1790067--1790117 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
1790057 AATTTTAATA
*
1790067 TATTTA-CATATTTATTA-TATTT
1 TATTTATCATATTTATAATTATTT
1790089 TATTTATCATA-TTATAATTATTT
1 TATTTATCATATTTATAATTATTT
1790112 T-TTTAT
1 TATTTAT
1790118 TATACTCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATCATATTTATAATTATTT
Found at i:1792356 original size:38 final size:37
Alignment explanation
Indices: 1792303--1792378 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 37
1792293 AGGAAATATT
*
1792303 CTTTCACTAGATCCCTATGGGTATTTTATATTCTCTTA
1 CTTTCACTAGATCCCTATGGGTACTTTATATTCT-TTA
*
1792341 CTTTCACTAGGTCCCTATGGGTACTTTATATTCTTTA
1 CTTTCACTAGATCCCTATGGGTACTTTATATTCTTTA
1792378 C
1 C
1792379 GCGTAGAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (37 bp):
CTTTCACTAGATCCCTATGGGTACTTTATATTCTTTA
Found at i:1797300 original size:27 final size:28
Alignment explanation
Indices: 1797270--1797330 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
1797260 TTATAATTAT
*
1797270 TTTTAAAATTGATTGATATTTTAATAA-
1 TTTTAAAATTGATTAATATTTTAATAAG
* *
1797297 TTTTAATATTTATTAATATTTTAATAAG
1 TTTTAAAATTGATTAATATTTTAATAAG
1797325 TTTTAA
1 TTTTAA
1797331 GATTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
TTTTAAAATTGATTAATATTTTAATAAG
Found at i:1797330 original size:18 final size:18
Alignment explanation
Indices: 1797288--1797330 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1797278 TTGATTGATA
*
1797288 TTTTAATAATTTTAATAT
1 TTTTAATAATTTTAATAG
1797306 TTATTAAT-ATTTTAATAAG
1 TT-TTAATAATTTTAAT-AG
1797325 TTTTAA
1 TTTTAA
1797331 GATTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTAATAATTTTAATAG
Found at i:1799354 original size:19 final size:17
Alignment explanation
Indices: 1799322--1799370 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
1799312 TTTTTTTATT
1799322 TAGATAATATAATTAAA
1 TAGATAATATAATTAAA
1799339 TAGATTAATAATAATTAAA
1 TAGA-TAAT-ATAATTAAA
1799358 TA-A-AAT-TAATTAA
1 TAGATAATATAATTAA
1799371 TGATATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.23
16 3 0.10
17 4 0.13
18 5 0.17
19 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
TAGATAATATAATTAAA
Found at i:1799541 original size:17 final size:17
Alignment explanation
Indices: 1799521--1799554 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1799511 TTTTGAGATT
*
1799521 TTAAATTATAAATTTTA
1 TTAAATTATAAAATTTA
*
1799538 TTAAATTTTAAAATTTA
1 TTAAATTATAAAATTTA
1799555 AATTAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATAAAATTTA
Found at i:1800060 original size:25 final size:25
Alignment explanation
Indices: 1800024--1800071 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1800014 AATTGAATCT
*
1800024 TAAAAAATTCAAACTCA-AATAATA
1 TAAAAAACTCAAACTCATAATAATA
*
1800048 TAAATAAACTCAAATTCATAATAA
1 TAAA-AAACTCAAACTCATAATAA
1800072 CATTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 11 0.55
26 5 0.25
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAAAAACTCAAACTCATAATAATA
Found at i:1809091 original size:13 final size:13
Alignment explanation
Indices: 1809073--1809109 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1809063 CGTTAATATG
1809073 TTTTATTTTTAAT
1 TTTTATTTTTAAT
*
1809086 TTTTATATTTAAT
1 TTTTATTTTTAAT
1809099 TATTTATTTTT
1 T-TTTATTTTT
1809110 TATGTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTAAT
Found at i:1810846 original size:7 final size:7
Alignment explanation
Indices: 1810834--1810858 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1810824 TACTTGCAAA
1810834 AAAAAAT
1 AAAAAAT
1810841 AAAAAAT
1 AAAAAAT
1810848 AAAAAAT
1 AAAAAAT
1810855 AAAA
1 AAAA
1810859 GATTTTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1811347 original size:10 final size:9
Alignment explanation
Indices: 1811319--1811393 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
1811309 AATAATTAAA
1811319 ATATAAAAT
1 ATATAAAAT
1811328 ATAT-AAAT
1 ATATAAAAT
1811336 ATAATAAAAT
1 AT-ATAAAAT
1811346 ATATAAAA-
1 ATATAAAAT
* *
1811354 ATA-ATATT
1 ATATAAAAT
1811362 AATATAAAAT
1 -ATATAAAAT
*
1811372 AAATTAAAAT
1 ATA-TAAAAT
* *
1811382 TTATATAAT
1 ATATAAAAT
1811391 ATA
1 ATA
1811394 ATTTATTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
7 2 0.04
8 9 0.18
9 24 0.47
10 16 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1811368 original size:17 final size:15
Alignment explanation
Indices: 1811318--1811378 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
1811308 AAATAATTAA
*
1811318 AATATAAAATATA-T
1 AATATAAAATAAATT
* *
1811332 AA-ATATAATAAAAT
1 AATATAAAATAAATT
1811346 -ATATAAAAATAATATT
1 AATAT-AAAATAA-ATT
1811362 AATATAAAATAAATT
1 AATATAAAATAAATT
1811377 AA
1 AA
1811379 AATTTATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 9 0.24
14 5 0.13
15 11 0.29
16 9 0.24
17 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAAATAAATT
Found at i:1811380 original size:26 final size:26
Alignment explanation
Indices: 1811317--1811394 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
1811307 TAAATAATTA
*
1811317 AAATATAAAATATATAAATATAATAAAAT
1 AAATA-AAAATATATATA-AT-ATAAAAT
*
1811346 ATATAAAAATA-ATATTAATATAAAAT
1 AAATAAAAATATATA-TAATATAAAAT
* *
1811372 AAATTAAAATTTATATAATATAA
1 AAATAAAAATATATATAATATAA
1811395 TTTATTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 23 0.55
27 8 0.19
28 7 0.17
29 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATAAAAATATATATAATATAAAAT
Found at i:1811451 original size:38 final size:35
Alignment explanation
Indices: 1811318--1811451 Score: 88
Period size: 35 Copynumber: 3.8 Consensus size: 35
1811308 AAATAATTAA
*
1811318 AATATAA-AATATATAAATATAA-TAAAA-TATATA-
1 AATATAATAA-AT-TAAATATAATTAAAATTTTATAT
*
1811351 AAAATAATATTAATATAAA-ATAAATTAAAA-TTTATAT
1 AATATAATA--AAT-TAAATAT-AATTAAAATTTTATAT
**
1811388 AATATAATTTATT-AATAT-ATT-AAATTTTATAT
1 AATATAATAAATTAAATATAATTAAAATTTTATAT
1811420 ACATATATCATAAATTAAATATAATTAAAATT
1 A-ATATA--ATAAATTAAATATAATTAAAATT
1811452 AAAAAATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
31 3 0.04
32 11 0.14
33 13 0.16
34 6 0.08
35 16 0.20
36 16 0.20
37 10 0.12
38 5 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATAATAAATTAAATATAATTAAAATTTTATAT
Found at i:1811809 original size:18 final size:17
Alignment explanation
Indices: 1811774--1811814 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1811764 TGGGTTGAAT
**
1811774 TTAAATATTTTATTAAA
1 TTAAATATTTTAAAAAA
1811791 TATAAATATTTTAAAAAA
1 T-TAAATATTTTAAAAAA
1811809 TTAAAT
1 TTAAAT
1811815 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATATTTTAAAAAA
Found at i:1811843 original size:33 final size:33
Alignment explanation
Indices: 1811780--1811843 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1811770 GAATTTAAAT
* * *
1811780 ATTTTATTAAATATAAATATTTTAAAAAATTAA
1 ATTTAATTAAATATAAATATATAAAAAAATTAA
*
1811813 ATTTAATTAAATTTAAAT-TATAAAATAAATT
1 ATTTAATTAAATATAAATATATAAAA-AAATT
1811844 TAGTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATTTAATTAAATATAAATATATAAAAAAATTAA
Found at i:1813882 original size:23 final size:25
Alignment explanation
Indices: 1813851--1813901 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1813841 ATATTTTATT
1813851 AAATATAATT-ATTTTAAAAAATAA
1 AAATATAATTAATTTTAAAAAATAA
*
1813875 AAAT-TAATTAATTTTAAATAATAA
1 AAATATAATTAATTTTAAAAAATAA
1813899 AAA
1 AAA
1813902 AATATGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATATAATTAATTTTAAAAAATAA
Found at i:1814728 original size:30 final size:30
Alignment explanation
Indices: 1814693--1814750 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1814683 ACGCAACTAA
1814693 ATTATTATACA-TATATATTAAACAAAAAAT
1 ATTATTATACATTATATATT-AACAAAAAAT
*
1814723 ATTATTATATATTATATATTAACAAAAA
1 ATTATTATACATTATATATTAACAAAAA
1814751 TCTTAATTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTATTATACATTATATATTAACAAAAAAT
Found at i:1822167 original size:2 final size:2
Alignment explanation
Indices: 1822162--1822202 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1822152 TTTCGTAATT
1822162 TA TA TA 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 TA TA TA T
1822203 GCATCAAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1824870 original size:3 final size:3
Alignment explanation
Indices: 1824862--1824895 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1824852 ACATAACATC
1824862 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1824896 AAAGATCTTG
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:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1825220 original size:42 final size:42
Alignment explanation
Indices: 1825174--1825269 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 42
1825164 TTTTAATATT
* *
1825174 TTTAAATTTAAATTTAAGAT-AATTTAATTTAAATAAA-TAATA
1 TTTAAATTTAAA-TTAA-ATAAATTCAAATTAAATAAATTAATA
* *
1825216 TTTAAAATTTAAATTAATTAAATTCAAATTAATTAAATTTAATA
1 TTT-AAATTTAAATTAAATAAATTCAAATTAAATAAA-TTAATA
1825260 TTTAAATTTA
1 TTTAAATTTA
1825270 TCAAATTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 1 0.02
42 21 0.46
43 16 0.35
44 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TTTAAATTTAAATTAAATAAATTCAAATTAAATAAATTAATA
Found at i:1825234 original size:37 final size:37
Alignment explanation
Indices: 1825176--1825276 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
1825166 TTAATATTTT
* *
1825176 TAAATTT-AAATTTAAGA-TAATTTAATTTAAA-TAAA
1 TAAATTTAAAATTTAA-ATTAATTAAATTCAAATTAAA
*
1825211 TAATATTTAAAATTTAAATTAATTAAATTCAAATTAAT
1 TAA-ATTTAAAATTTAAATTAATTAAATTCAAATTAAA
* * *
1825249 TAAATTTAATATTTAAATTTATCAAATT
1 TAAATTTAAAATTTAAATTAATTAAATT
1825277 TACTCATTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 3 0.05
36 5 0.09
37 42 0.75
38 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (37 bp):
TAAATTTAAAATTTAAATTAATTAAATTCAAATTAAA
Found at i:1825238 original size:15 final size:15
Alignment explanation
Indices: 1825220--1825269 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1825210 ATAATATTTA
1825220 AAATTTAAATTAATT
1 AAATTTAAATTAATT
*
1825235 AAATTCAAATTAATT
1 AAATTTAAATTAATT
*
1825250 AAATTT-AA-TATTT
1 AAATTTAAATTAATT
1825263 AAATTTA
1 AAATTTA
1825270 TCAAATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 19 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATTTAAATTAATT
Found at i:1825264 original size:7 final size:6
Alignment explanation
Indices: 1825174--1825269 Score: 51
Period size: 6 Copynumber: 15.7 Consensus size: 6
1825164 TTTTAATATT
* *
1825174 TTTAAA TTTAAA TTTAAGA TAATTTAA TTTAAA TAAATAATA TTTAAAA
1 TTTAAA TTTAAA TTTAA-A T--TTAAA TTTAAA T--TTAA-A TTT-AAA
*
1825223 TTTAAA -TT-AA -TTAAA TTCAAA -TT-AA -TTAAA TTTAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
1825266 TTTA
1 TTTA
1825270 TCAAATTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
4 8 0.11
5 7 0.10
6 32 0.44
7 13 0.18
8 7 0.10
9 5 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:1825275 original size:22 final size:21
Alignment explanation
Indices: 1825233--1825278 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1825223 TTTAAATTAA
*
1825233 TTAAATTCAAATTAATTAAAT
1 TTAAATTCAAATTAATCAAAT
* *
1825254 TTAATATTTAAATTTATCAAAT
1 TTAA-ATTCAAATTAATCAAAT
1825276 TTA
1 TTA
1825279 CTCATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATTCAAATTAATCAAAT
Found at i:1825348 original size:23 final size:26
Alignment explanation
Indices: 1825295--1825350 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 26
1825285 AATTTTTTGA
*
1825295 TCAAATCAAATTGAGTTAAACTTGAAT
1 TCAAATCAAATTGAGTTAAAC-TAAAT
1825322 TCAAAT-AAATTGA-TTAAA-TAAAT
1 TCAAATCAAATTGAGTTAAACTAAAT
1825345 TCAAAT
1 TCAAAT
1825351 TAAAATTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
25 5 0.18
26 7 0.25
27 6 0.21
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (26 bp):
TCAAATCAAATTGAGTTAAACTAAAT
Found at i:1825738 original size:20 final size:20
Alignment explanation
Indices: 1825702--1825744 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1825692 AGTTTGTAGG
*
1825702 AAAAATAAATTACAAATGTT
1 AAAAATAAATTACAAATATT
*
1825722 AAAAATAAAATT-TAAATATT
1 AAAAAT-AAATTACAAATATT
1825742 AAA
1 AAA
1825745 TATGTTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATAAATTACAAATATT
Found at i:1826220 original size:3 final size:3
Alignment explanation
Indices: 1826212--1826252 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1826202 AAGCGTATGA
1826212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1826253 AACAATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1828391 original size:20 final size:19
Alignment explanation
Indices: 1828358--1828395 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1828348 TTAAATTAAA
1828358 TTGTAATTTGTATTATTAC
1 TTGTAATTTGTATTATTAC
*
1828377 TTGTTATTTGTTATTATTA
1 TTGTAATTTG-TATTATTA
1828396 TATCACTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (19 bp):
TTGTAATTTGTATTATTAC
Found at i:1830188 original size:16 final size:15
Alignment explanation
Indices: 1830167--1830205 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1830157 AAAATAATAT
*
1830167 ATAAAATATATTTAAA
1 ATAAAATATAATT-AA
*
1830183 ATAAAAAATAATTAA
1 ATAAAATATAATTAA
1830198 ATAAAATA
1 ATAAAATA
1830206 AGATATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAATATAATTAA
Found at i:1830193 original size:23 final size:21
Alignment explanation
Indices: 1830144--1830206 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1830134 TATATTTTGT
*
1830144 AAATAAAATTAATAAAATAAT
1 AAATAAAATTAATAAAATAAA
* *
1830165 ATATAAAATATATTTAAAATAAA
1 AAATAAAAT-TA-ATAAAATAAA
1830188 AAAT--AATTAAATAAAATAA
1 AAATAAAATT-AATAAAATAA
1830207 GATATATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 9 0.26
21 12 0.35
22 2 0.06
23 11 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAAATTAATAAAATAAA
Found at i:1830379 original size:25 final size:26
Alignment explanation
Indices: 1830329--1830384 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1830319 GAACTTGATA
*
1830329 ATTTTTATATAAATTAAATTTATTTT
1 ATTTTTATATAAATTAAATATATTTT
*
1830355 ATTTTTA-ATTAAGTTAAATAT-TTTT
1 ATTTTTATA-TAAATTAAATATATTTT
1830380 ATTTT
1 ATTTT
1830385 ATTAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTTATATAAATTAAATATATTTT
Found at i:1832627 original size:2 final size:2
Alignment explanation
Indices: 1832620--1832672 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1832610 GACTTATAAC
1832620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1832662 AT AT -T AT AT AT
1 AT AT AT AT AT AT
1832673 TCGAAGTGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1834321 original size:363 final size:363
Alignment explanation
Indices: 1833656--1834386 Score: 1462
Period size: 363 Copynumber: 2.0 Consensus size: 363
1833646 TAGGTTATGT
1833656 GTTTCTGAAATCATCAACGCTTGTAGCCCAAAAAAGTTTGTTAGATTGGGCCTTGGGTTAGTGTC
1 GTTTCTGAAATCATCAACGCTTGTAGCCCAAAAAAGTTTGTTAGATTGGGCCTTGGGTTAGTGTC
1833721 TAATATATTTGAGTGAAGAAGACCTTGTTTTAGACTTAGATACTGTAACAACTTACAGTATAAGC
66 TAATATATTTGAGTGAAGAAGACCTTGTTTTAGACTTAGATACTGTAACAACTTACAGTATAAGC
1833786 ACAAAAATGGGCTTTGCCTGCAGAGCTATATACTGTAAGTTGAGCTTTTAAAATTTGGGTTTACC
131 ACAAAAATGGGCTTTGCCTGCAGAGCTATATACTGTAAGTTGAGCTTTTAAAATTTGGGTTTACC
1833851 ACTCTTTTTCCATTTAATGAAAAAAGCCCAACTTTTATCTTCTTTAAACCCTAATTCCATATGCC
196 ACTCTTTTTCCATTTAATGAAAAAAGCCCAACTTTTATCTTCTTTAAACCCTAATTCCATATGCC
1833916 TCGGCCCTAGCCTATGTAAATCCCCCAAAAATTTTCCTCTTTCAGCTTGGAGAAATGTTGTCATG
261 TCGGCCCTAGCCTATGTAAATCCCCCAAAAATTTTCCTCTTTCAGCTTGGAGAAATGTTGTCATG
1833981 TTTCATTAAATTGATATCTGAAAAGAATTATAACTGGC
326 TTTCATTAAATTGATATCTGAAAAGAATTATAACTGGC
1834019 GTTTCTGAAATCATCAACGCTTGTAGCCCAAAAAAGTTTGTTAGATTGGGCCTTGGGTTAGTGTC
1 GTTTCTGAAATCATCAACGCTTGTAGCCCAAAAAAGTTTGTTAGATTGGGCCTTGGGTTAGTGTC
1834084 TAATATATTTGAGTGAAGAAGACCTTGTTTTAGACTTAGATACTGTAACAACTTACAGTATAAGC
66 TAATATATTTGAGTGAAGAAGACCTTGTTTTAGACTTAGATACTGTAACAACTTACAGTATAAGC
1834149 ACAAAAATGGGCTTTGCCTGCAGAGCTATATACTGTAAGTTGAGCTTTTAAAATTTGGGTTTACC
131 ACAAAAATGGGCTTTGCCTGCAGAGCTATATACTGTAAGTTGAGCTTTTAAAATTTGGGTTTACC
1834214 ACTCTTTTTCCATTTAATGAAAAAAGCCCAACTTTTATCTTCTTTAAACCCTAATTCCATATGCC
196 ACTCTTTTTCCATTTAATGAAAAAAGCCCAACTTTTATCTTCTTTAAACCCTAATTCCATATGCC
1834279 TCGGCCCTAGCCTATGTAAATCCCCCAAAAATTTTCCTCTTTCAGCTTGGAGAAATGTTGTCATG
261 TCGGCCCTAGCCTATGTAAATCCCCCAAAAATTTTCCTCTTTCAGCTTGGAGAAATGTTGTCATG
1834344 TTTCATTAAATTGATATCTGAAAAGAATTATAACTGGC
326 TTTCATTAAATTGATATCTGAAAAGAATTATAACTGGC
1834382 GTTTC
1 GTTTC
1834387 ACTTTTTCTA
Statistics
Matches: 368, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
363 368 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (363 bp):
GTTTCTGAAATCATCAACGCTTGTAGCCCAAAAAAGTTTGTTAGATTGGGCCTTGGGTTAGTGTC
TAATATATTTGAGTGAAGAAGACCTTGTTTTAGACTTAGATACTGTAACAACTTACAGTATAAGC
ACAAAAATGGGCTTTGCCTGCAGAGCTATATACTGTAAGTTGAGCTTTTAAAATTTGGGTTTACC
ACTCTTTTTCCATTTAATGAAAAAAGCCCAACTTTTATCTTCTTTAAACCCTAATTCCATATGCC
TCGGCCCTAGCCTATGTAAATCCCCCAAAAATTTTCCTCTTTCAGCTTGGAGAAATGTTGTCATG
TTTCATTAAATTGATATCTGAAAAGAATTATAACTGGC
Found at i:1837529 original size:33 final size:33
Alignment explanation
Indices: 1837492--1837568 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
1837482 AATATTTATA
* *
1837492 AATATTTTAATTTTTTTATTA-ATATAAAATGTT
1 AATATTATAATTTTTTTATAATATATAAAAT-TT
*
1837525 AATA-TATGATTTTTTTATAATATATAAAATTT
1 AATATTATAATTTTTTTATAATATATAAAATTT
1837557 ATATATTGATAA
1 A-ATATT-ATAA
1837569 ATATAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
32 16 0.44
33 16 0.44
34 1 0.03
35 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (33 bp):
AATATTATAATTTTTTTATAATATATAAAATTT
Found at i:1837561 original size:31 final size:32
Alignment explanation
Indices: 1837501--1837562 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1837491 AAATATTTTA
*
1837501 ATTTTTTTATTAATATAAAATGTTAATATATG
1 ATTTTTTTATAAATATAAAATGTTAATATATG
1837533 ATTTTTTTATAATATATAAAAT-TT-ATATAT
1 ATTTTTTTATAA-ATATAAAATGTTAATATAT
1837563 TGATAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.21
32 13 0.46
33 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTTTTTTATAAATATAAAATGTTAATATATG
Found at i:1838034 original size:3 final size:3
Alignment explanation
Indices: 1838026--1838064 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1838016 TTTAATACAA
1838026 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
1838065 ATTAACTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1838745 original size:2 final size:2
Alignment explanation
Indices: 1838738--1838769 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1838728 TAAATGTTAC
1838738 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
1838770 TTGTTCCAAA
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:1839578 original size:11 final size:11
Alignment explanation
Indices: 1839562--1839587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1839552 ATAAATAAAA
1839562 TAATAAAATTT
1 TAATAAAATTT
1839573 TAATAAAATTT
1 TAATAAAATTT
1839584 TAAT
1 TAAT
1839588 TTGTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATAAAATTT
Found at i:1840545 original size:2 final size:2
Alignment explanation
Indices: 1840538--1840565 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1840528 ATCATTTTTA
1840538 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
1840566 TTAAGGGCTA
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:1843686 original size:21 final size:23
Alignment explanation
Indices: 1843662--1843709 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
1843652 TTATTAAAAT
*
1843662 TAATTAATTT-AT-TATATATAA
1 TAATTAATTTAATATAAATATAA
1843683 TAA-T-ATTTAATATAAATATAA
1 TAATTAATTTAATATAAATATAA
1843704 TAATTA
1 TAATTA
1843710 GTATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.18
20 3 0.14
21 14 0.64
22 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTAATTTAATATAAATATAA
Found at i:1844181 original size:29 final size:29
Alignment explanation
Indices: 1844112--1844192 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 29
1844102 TATCATGAGT
* * *
1844112 TAATAA-AATATCAACTTAATTATAAGAA
1 TAATAATAATATAAACTTAATAATAATAA
1844140 TAA-AACT--TA-AAACTTAATAATAATAA
1 TAATAA-TAATATAAACTTAATAATAATAA
1844166 TAATAATAATATAAACTTTAA-AATAAT
1 TAATAATAATATAAAC-TTAATAATAAT
1844193 TATGTTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
26 18 0.42
27 6 0.14
28 5 0.12
29 10 0.23
30 4 0.09
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.33
Consensus pattern (29 bp):
TAATAATAATATAAACTTAATAATAATAA
Found at i:1844560 original size:28 final size:26
Alignment explanation
Indices: 1844528--1844590 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
1844518 TATAATTTTA
*
1844528 TATTTTAAACAAATTATATATTTAAAAT
1 TATTTTAAA-AAA-TATAAATTTAAAAT
* * *
1844556 TATTTCAAATAATATAAATTTAAATT
1 TATTTTAAAAAATATAAATTTAAAAT
1844582 TACTTTTAA
1 TA-TTTTAA
1844591 TTAAAAATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 14 0.48
27 7 0.24
28 8 0.28
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTTTAAAAAATATAAATTTAAAAT
Found at i:1846616 original size:3 final size:3
Alignment explanation
Indices: 1846610--1846634 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1846600 AACTTGTGTG
1846610 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1846635 CAATAGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1851729 original size:3 final size:3
Alignment explanation
Indices: 1851721--1851760 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1851711 TTTGGTCAAT
1851721 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1851761 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1853600 original size:2 final size:2
Alignment explanation
Indices: 1853593--1853619 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1853583 ACAGAAAAAG
1853593 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 A
1853620 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1855453 original size:2 final size:2
Alignment explanation
Indices: 1855446--1855477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1855436 AGTAACATAC
1855446 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
1855478 CCCGAATTTC
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:1860911 original size:28 final size:29
Alignment explanation
Indices: 1860836--1860918 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 29
1860826 AAATTATATT
* *
1860836 ATATAAAAAATAAATATAAATATATT-ATTAA
1 ATATAATAAAT-AAT-TAAA-ATTTTAATTAA
* *
1860867 ATTTAATAATTAATTAAAATTTTAATTAA
1 ATATAATAAATAATTAAAATTTTAATTAA
*
1860896 ATAT-ATAAATAATTAAATTTTTA
1 ATATAATAAATAATTAAAATTTTA
1860919 GTGATATACT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 21 0.48
29 12 0.27
30 3 0.07
31 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATAATAAATAATTAAAATTTTAATTAA
Found at i:1864710 original size:14 final size:15
Alignment explanation
Indices: 1864691--1864719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1864681 TGTATGAGCA
1864691 TTATA-TTTTATATT
1 TTATATTTTTATATT
1864705 TTATATTTTTATATT
1 TTATATTTTTATATT
1864720 AATTATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATTTTTATATT
Found at i:1864817 original size:13 final size:13
Alignment explanation
Indices: 1864801--1864842 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1864791 TTAAATATAT
1864801 TTTTAATATATTA
1 TTTTAATATATTA
1864814 TTTT--TATATTA
1 TTTTAATATATTA
1864825 TATTTAA-ATATTA
1 T-TTTAATATATTA
1864838 TTTTA
1 TTTTA
1864843 CTTAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.31
12 7 0.27
13 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATATATTA
Found at i:1864821 original size:11 final size:12
Alignment explanation
Indices: 1864795--1864842 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
1864785 AATATATTAA
*
1864795 ATATATT-TTTA
1 ATATATTATTTT
1864806 ATATATTATTTT
1 ATATATTATTTT
1864818 -TATATTATATTT
1 ATATATTAT-TTT
*
1864830 AAATATTATTTT
1 ATATATTATTTT
1864842 A
1 A
1864843 CTTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 15 0.47
12 10 0.31
13 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATATTATTTT
Found at i:1866328 original size:13 final size:13
Alignment explanation
Indices: 1866310--1866339 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1866300 TTTCACTAGA
1866310 GAAAGACATCGAC
1 GAAAGACATCGAC
1866323 GAAAGACATCGAC
1 GAAAGACATCGAC
1866336 -AAAG
1 GAAAG
1866340 TTCATACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (13 bp):
GAAAGACATCGAC
Found at i:1868408 original size:3 final size:3
Alignment explanation
Indices: 1868400--1868433 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1868390 CCATTAAGTT
1868400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1868434 GTTTATTTAA
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:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1871400 original size:2 final size:2
Alignment explanation
Indices: 1871393--1871434 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1871383 ACATGCATAC
1871393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1871435 GAAAAAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1874627 original size:20 final size:20
Alignment explanation
Indices: 1874602--1874641 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1874592 CTACGGCATT
1874602 TTCTTTTAGCCTCAAACTAA
1 TTCTTTTAGCCTCAAACTAA
1874622 TTCTTTTAGCCTCAAACTAA
1 TTCTTTTAGCCTCAAACTAA
1874642 AGCCTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (20 bp):
TTCTTTTAGCCTCAAACTAA
Found at i:1878758 original size:13 final size:13
Alignment explanation
Indices: 1878742--1878784 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1878732 TTTTTAAAAT
*
1878742 TATTTATATTTGA
1 TATTTATATTTAA
1878755 TATTTATATTTAA
1 TATTTATATTTAA
*
1878768 TATGTA-ATTTAA
1 TATTTATATTTAA
1878780 -ATTTA
1 TATTTA
1878785 AATATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:1882273 original size:25 final size:25
Alignment explanation
Indices: 1882245--1882319 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
1882235 TTATAATTAT
1882245 AATTAAAATATTATATATTTATATA
1 AATTAAAATATTATATATTTATATA
**
1882270 AATTTTAATATTA-ATAATTTATA-A
1 AATTAAAATATTATAT-ATTTATATA
* * *
1882294 TATATAAAATATTATATGTTTTTATA
1 AAT-TAAAATATTATATATTTATATA
1882320 TTCTTATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 5 0.13
25 31 0.79
26 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
AATTAAAATATTATATATTTATATA
Found at i:1883174 original size:23 final size:23
Alignment explanation
Indices: 1883148--1883191 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1883138 AGGATTGAAA
1883148 TATTAAA-ATTAAAATTTTAAATT
1 TATTAAATATT-AAATTTTAAATT
*
1883171 TATTAAATATTATATTTTAAA
1 TATTAAATATTAAATTTTAAA
1883192 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAAATATTAAATTTTAAATT
Found at i:1885492 original size:9 final size:10
Alignment explanation
Indices: 1885468--1885507 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1885458 ATTAACATAT
1885468 AAAATTTTTA
1 AAAATTTTTA
1885478 AAAATTTTTA
1 AAAATTTTTA
* *
1885488 TAATTTTTTCA
1 AAAATTTTT-A
1885499 AAAATTTTT
1 AAAATTTTT
1885508 TTAATTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:1885512 original size:21 final size:20
Alignment explanation
Indices: 1885472--1885514 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1885462 ACATATAAAA
1885472 TTTTTAAAAATTTTTATAAT
1 TTTTTAAAAATTTTTATAAT
*
1885492 TTTTTCAAAAATTTTTTTAAT
1 TTTTT-AAAAATTTTTATAAT
1885513 TT
1 TT
1885515 ATCTGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAATTTTTATAAT
Found at i:1886955 original size:24 final size:22
Alignment explanation
Indices: 1886928--1886976 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1886918 GCTAGCAAGA
*
1886928 AAATAGAAAAATGTCTAGAATTAT
1 AAATAGAAAAATGAC--GAATTAT
*
1886952 AAATAGATAAATGACGAATTAT
1 AAATAGAAAAATGACGAATTAT
1886974 AAA
1 AAA
1886977 ATTATGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (22 bp):
AAATAGAAAAATGACGAATTAT
Found at i:1889760 original size:2 final size:2
Alignment explanation
Indices: 1889753--1889790 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1889743 AAAATTTTCA
1889753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1889791 CTTATGTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1892681 original size:3 final size:3
Alignment explanation
Indices: 1892673--1892716 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1892663 TTTAAATAAC
*
1892673 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1892717 TTCATTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1893019 original size:30 final size:29
Alignment explanation
Indices: 1892975--1893047 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
1892965 GAATGACTTG
1892975 AATATATATGATAAAAAAAATAATTAAAAGAT
1 AATATA-AT-ATAAAAAAAATAA-TAAAAGAT
* *
1893007 GATATAATATAAAAAAAATAATAAAATAT
1 AATATAATATAAAAAAAATAATAAAAGAT
1893036 AATATTAATATA
1 AATA-TAATATA
1893048 TGAATATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 10 0.27
30 20 0.54
31 2 0.05
32 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (29 bp):
AATATAATATAAAAAAAATAATAAAAGAT
Found at i:1894219 original size:6 final size:6
Alignment explanation
Indices: 1894208--1894322 Score: 63
Period size: 6 Copynumber: 18.0 Consensus size: 6
1894198 GTGTTTCAAG
* * * *
1894208 TTTATA TTTATA TTTATA TATATATA TATATA TGTTATAA TTAATA TATAAAA
1 TTTATA TTTATA TTTATA T-T-TATA TTTATA T-TTAT-A TTTATA T-TTATA
** *
1894261 TATTATA TTTATA TAAAT- TTTAATA TATTCATA TATATA TTTATA -TTATA
1 T-TTATA TTTATA TTTATA TTT-ATA T-TT-ATA TTTATA TTTATA TTTATA
*
1894311 TTTAAA TTTATA
1 TTTATA TTTATA
1894323 AATTCATGCA
Statistics
Matches: 85, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
5 6 0.07
6 47 0.55
7 19 0.22
8 13 0.15
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTATA
Found at i:1894225 original size:12 final size:12
Alignment explanation
Indices: 1894208--1894322 Score: 63
Period size: 14 Copynumber: 9.0 Consensus size: 12
1894198 GTGTTTCAAG
1894208 TTTATATTTATA
1 TTTATATTTATA
1894220 TTTATATATATATA
1 TTTATAT-T-TATA
*
1894234 TATATATGTTATAA
1 TTTATAT-TTAT-A
* * *
1894248 TTAATATATAAAA
1 TTTATAT-TTATA
1894261 TATTATATTTATA
1 T-TTATATTTATA
**
1894274 TAAAT-TTTAATA
1 TTTATATTT-ATA
*
1894286 TATTCATATATATA
1 T-TT-ATATTTATA
1894300 TTTATA-TTATA
1 TTTATATTTATA
*
1894311 TTTAAATTTATA
1 TTTATATTTATA
1894323 AATTCATGCA
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
11 12 0.16
12 21 0.27
13 12 0.16
14 30 0.39
15 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:1894229 original size:2 final size:2
Alignment explanation
Indices: 1894210--1894311 Score: 53
Period size: 2 Copynumber: 55.5 Consensus size: 2
1894200 GTTTCAAGTT
* * *
1894210 TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TG T- TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1894249 TA -A TA TA TA -A AA TA T- TA TA TT TA TA TA AA T- TT TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1894286 TA T- TCA TA TA TA TA TT TA TA T- TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA T
1894312 TTAAATTTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
1 10 0.13
2 65 0.86
3 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1894239 original size:20 final size:20
Alignment explanation
Indices: 1894210--1894311 Score: 74
Period size: 20 Copynumber: 5.2 Consensus size: 20
1894200 GTTTCAAGTT
*
1894210 TATATTTATATTTATATATA
1 TATATATATATTTATATATA
1894230 TATATATATATGTTATA-AT-
1 TATATATATAT-TTATATATA
*
1894249 TAATATATAAAATATTATAT-T-
1 T-ATATAT-ATAT-TTATATATA
*
1894270 TATATAAAT-TTTA-ATATA
1 TATATATATATTTATATATA
1894288 TTCATATATATATTTATAT-TA
1 -T-ATATATATATTTATATATA
1894309 TAT
1 TAT
1894312 TTAAATTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
16 2 0.03
17 4 0.06
18 1 0.02
19 5 0.08
20 31 0.47
21 21 0.32
22 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TATATATATATTTATATATA
Found at i:1894284 original size:32 final size:34
Alignment explanation
Indices: 1894227--1894324 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 34
1894217 ATATTTATAT
* *
1894227 ATATATATATATATGTTATAA--TTAATATATAAA
1 ATATATATATTTATATTA-AATTTTAATATATAAA
**
1894260 ATAT-TATATTTATA-TAAATTTTAATATAT-TC
1 ATATATATATTTATATTAAATTTTAATATATAAA
* * *
1894291 ATATATATATTTATATTATATTTAAATTTATAAA
1 ATATATATATTTATATTAAATTTTAATATATAAA
1894325 TTCATGCACA
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 2 0.04
31 6 0.12
32 27 0.53
33 16 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
ATATATATATTTATATTAAATTTTAATATATAAA
Found at i:1894795 original size:2 final size:2
Alignment explanation
Indices: 1894780--1894820 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
1894770 GGAGGTTAAT
1894780 TC TC TC T- TC ATC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1894821 TTGTGAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1895200 original size:11 final size:11
Alignment explanation
Indices: 1895167--1895193 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1895157 AAGGCTGTAC
1895167 TTTTTCATTTT
1 TTTTTCATTTT
1895178 TTTTTCATTTT
1 TTTTTCATTTT
1895189 TTTTT
1 TTTTT
1895194 TGTTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:1895256 original size:3 final size:3
Alignment explanation
Indices: 1895248--1895282 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1895238 GTTTTATTTG
1895248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1895283 TTCTTCTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1896609 original size:2 final size:2
Alignment explanation
Indices: 1896602--1896628 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1896592 GACTAAGGTG
1896602 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
1896629 TAAAGTCTGT
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:1898240 original size:2 final size:2
Alignment explanation
Indices: 1898229--1898275 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1898219 TTCCATATTC
1898229 TA TA -A TA 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 TA TA TA TA
1898270 TA TA TA
1 TA TA TA
1898276 ATGGACATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1902115 original size:19 final size:18
Alignment explanation
Indices: 1902091--1902126 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1902081 ATTAAAAAAT
*
1902091 ATTATTTTTTATAATCATG
1 ATTATTTATTAT-ATCATG
1902110 ATTATTTATTATATCAT
1 ATTATTTATTATATCAT
1902127 TAACGAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTATTTATTATATCATG
Found at i:1908956 original size:20 final size:20
Alignment explanation
Indices: 1908931--1908976 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1908921 AAATAGAGGC
*
1908931 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
1908951 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
1908971 TCCCTC
1 TCCCTC
1908977 TTTAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:1914946 original size:2 final size:2
Alignment explanation
Indices: 1914939--1914965 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1914929 ATGTAATTGA
1914939 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 A
1914966 TGGGAAGTAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1925713 original size:22 final size:23
Alignment explanation
Indices: 1925674--1925718 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1925664 TTTTATTTTT
1925674 ATTTTTTAAAAATAAAAT-TTAA
1 ATTTTTTAAAAATAAAATCTTAA
* *
1925696 ATTTTTTAAAATTTAAATCTTAA
1 ATTTTTTAAAAATAAAATCTTAA
1925719 TATGTGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTTTAAAAATAAAATCTTAA
Found at i:1929680 original size:54 final size:54
Alignment explanation
Indices: 1929588--1929695 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1929578 AGGTAGAGTT
**
1929588 AGGTGAGGGAAGTAATCCATCACTGCTGTTTGCCGAGTGCTGATCTCTTCCTTC
1 AGGTGAGGGAAGTAATCCATCACTGCTGCCTGCCGAGTGCTGATCTCTTCCTTC
* **
1929642 AGGTGAGGGAAGTACTCCATCACTGCTGCCTGTTGAGTGCTGATCTCTTCCTTC
1 AGGTGAGGGAAGTAATCCATCACTGCTGCCTGCCGAGTGCTGATCTCTTCCTTC
1929696 CTACTGCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (54 bp):
AGGTGAGGGAAGTAATCCATCACTGCTGCCTGCCGAGTGCTGATCTCTTCCTTC
Found at i:1931796 original size:2 final size:2
Alignment explanation
Indices: 1931789--1931824 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1931779 AAACGGGATT
1931789 TA 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 TA
1931825 CATCAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1931869 original size:17 final size:19
Alignment explanation
Indices: 1931843--1931880 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1931833 TTTTTTATTA
*
1931843 ATAATTTAAA-TA-TAAAT
1 ATAATATAAATTATTAAAT
1931860 ATAATATAAATTATTAAAT
1 ATAATATAAATTATTAAAT
1931879 AT
1 AT
1931881 GTTAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATATAAATTATTAAAT
Found at i:1931981 original size:18 final size:19
Alignment explanation
Indices: 1931958--1931998 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1931948 TGATACTAAG
1931958 TTTATATT-TATTAAATAT
1 TTTATATTATATTAAATAT
*
1931976 TTTATATTCATATTATATAT
1 TTTATATT-ATATTAAATAT
1931996 TTT
1 TTT
1931999 TTAATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATATTATATTAAATAT
Found at i:1932085 original size:2 final size:2
Alignment explanation
Indices: 1932078--1932103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1932068 CGATATACAT
1932078 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
1932104 GATAAGAGGA
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:1933257 original size:2 final size:2
Alignment explanation
Indices: 1933216--1933242 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1933206 TGAAGGCACC
1933216 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
1933243 TGATAAAACT
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:1937100 original size:5 final size:5
Alignment explanation
Indices: 1937090--1937115 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1937080 ACATTACAAA
1937090 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
1937116 CATGTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1938622 original size:3 final size:3
Alignment explanation
Indices: 1938614--1938651 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1938604 TTGCAAGTCT
1938614 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1938652 TATAATGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1939280 original size:26 final size:27
Alignment explanation
Indices: 1939229--1939281 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1939219 TGAAGTGACA
* **
1939229 TTTTATAAAGCAGTTTATAATTTATTT
1 TTTTATAAAGCAGTTAATAAAATATTT
1939256 TTTTATAAAGCAG-TAATAAAATATTT
1 TTTTATAAAGCAGTTAATAAAATATTT
1939282 ATATGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (27 bp):
TTTTATAAAGCAGTTAATAAAATATTT
Found at i:1940619 original size:20 final size:19
Alignment explanation
Indices: 1940594--1940657 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
1940584 CCTCAATAAA
*
1940594 TTTTATTATAAAATTCATAT
1 TTTTATAATAAAATT-ATAT
*
1940614 TTTTATAATATAATTATA-
1 TTTTATAATAAAATTATAT
* * *
1940632 TATTATAAAAATAATTATAA
1 TTTTATAATAA-AATTATAT
1940652 TTTTAT
1 TTTTAT
1940658 TTTTTAACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 8 0.22
19 10 0.28
20 18 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATAATAAAATTATAT
Found at i:1940775 original size:19 final size:20
Alignment explanation
Indices: 1940731--1940783 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1940721 AAATAAAAGT
**
1940731 ATAATAAAATATATTT-AATT
1 ATAA-AAAATATATTTAAAAA
*
1940751 ATTAAAAATATATTTAAAAA
1 ATAAAAAATATATTTAAAAA
1940771 ATAAAAAATATAT
1 ATAAAAAATATAT
1940784 AATCTTATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAAATATATTTAAAAA
Found at i:1941741 original size:21 final size:19
Alignment explanation
Indices: 1941706--1941751 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1941696 ATTAGTGCGA
*
1941706 AATTTTTATTTTAAAATATT
1 AATTTTAATTTTAAAAT-TT
1941726 AATTTTAATATTTAAAATTT
1 AATTTTAAT-TTTAAAATTT
*
1941746 TATTTT
1 AATTTT
1941752 GTATATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTAATTTTAAAATTT
Done.