Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 125 of 208
Found at i:41060614 original size:17 final size:17
Alignment explanation
Indices: 41060592--41060658 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
41060582 GTTTAACTAT
41060592 TTTTTTATAATTTTAAA
1 TTTTTTATAATTTTAAA
* *
41060609 TTTTTTAGAATTTAACTAA
1 TTTTTTATAATTTTA--AA
* *
41060628 TCTTTTAT-ATTTTTAA
1 TTTTTTATAATTTTAAA
*
41060644 TTTTTCTATACTTTT
1 TTTTT-TATAATTTT
41060659 TTTGGATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 6 0.16
17 16 0.42
18 8 0.21
19 8 0.21
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTTTAAA
Found at i:41060623 original size:36 final size:37
Alignment explanation
Indices: 41060571--41060651 Score: 112
Period size: 36 Copynumber: 2.2 Consensus size: 37
41060561 CCCTAAATGC
* *
41060571 TTTTTCTAGAAGTTTAACTATTTTTTTATAATTTTAAA
1 TTTTTCTAGAAGTTTAACTAATCTTTTAT-ATTTTAAA
*
41060609 TTTTT-TAGAA-TTTAACTAATCTTTTATATTTTTAA
1 TTTTTCTAGAAGTTTAACTAATCTTTTATATTTTAAA
41060644 TTTTTCTA
1 TTTTTCTA
41060652 TACTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 12 0.31
36 17 0.44
37 5 0.13
38 5 0.13
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (37 bp):
TTTTTCTAGAAGTTTAACTAATCTTTTATATTTTAAA
Found at i:41060669 original size:30 final size:27
Alignment explanation
Indices: 41060630--41060713 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 27
41060620 TTAACTAATC
41060630 TTTTATATTTTTAATTTTTCTATACTTT
1 TTTTATATTTTTAATTTTTCTATAC-TT
* *
41060658 TTTTGGATATTTTT-ATGTTTCTA-A-TC
1 TTTT--ATATTTTTAATTTTTCTATACTT
*
41060684 TTTTATATTTTTAATTTTTCTATACAT
1 TTTTATATTTTTAATTTTTCTATACTT
41060711 TTT
1 TTT
41060714 CTTAACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
24 8 0.17
25 8 0.17
26 6 0.13
27 3 0.07
28 5 0.11
29 8 0.17
30 8 0.17
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (27 bp):
TTTTATATTTTTAATTTTTCTATACTT
Found at i:41060789 original size:27 final size:27
Alignment explanation
Indices: 41060743--41060797 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
41060733 TAAATATTTT
*
41060743 TATTTTTATAAATTTTGAATTTTTATA
1 TATTTTTATAAATTTTGAATTTATATA
*
41060770 TATTTTTA-GAATTTTAGAATTTATATA
1 TATTTTTATAAATTTT-GAATTTATATA
41060797 T
1 T
41060798 CTCTACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (27 bp):
TATTTTTATAAATTTTGAATTTATATA
Found at i:41064396 original size:16 final size:16
Alignment explanation
Indices: 41064354--41064399 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 16
41064344 AATTAAAAAA
41064354 ATTTAAATTTTGAGTT
1 ATTTAAATTTTGAGTT
* *
41064370 AATTGAA--TTGAGTT
1 ATTTAAATTTTGAGTT
41064384 ATTTAAATTTTGAGTT
1 ATTTAAATTTTGAGTT
41064400 TTGTAATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
ATTTAAATTTTGAGTT
Found at i:41064475 original size:9 final size:9
Alignment explanation
Indices: 41064446--41064475 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41064436 TGGATTTCAC
41064446 AATTCGAAT
1 AATTCGAAT
*
41064455 AACTCGAAT
1 AATTCGAAT
41064464 AATTCGAAT
1 AATTCGAAT
41064473 AAT
1 AAT
41064476 AGATTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41064636 original size:24 final size:25
Alignment explanation
Indices: 41064607--41064659 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
41064597 AAAATTCAAA
* *
41064607 ATATTTATAAAAATTTC-AAAATTT
1 ATATTTATAAAAAATTCTAAAAATT
*
41064631 ATATTTTTAAAAAATTCTAAAAATT
1 ATATTTATAAAAAATTCTAAAAATT
41064656 ATAT
1 ATAT
41064660 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTATAAAAAATTCTAAAAATT
Found at i:41064653 original size:26 final size:27
Alignment explanation
Indices: 41064610--41064660 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
41064600 ATTCAAAATA
*
41064610 TTTATAAAAATTTCAAAATT-TATATT
1 TTTATAAAAATTTAAAAATTATATATT
41064636 TTTA-AAAAATTCTAAAAATTATATA
1 TTTATAAAAATT-TAAAAATTATATA
41064661 AAAAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTATAAAAATTTAAAAATTATATATT
Found at i:41064683 original size:45 final size:44
Alignment explanation
Indices: 41064590--41064682 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
41064580 ATTTTTTAAT
*
41064590 AATTTTT--AAAATTCAAAATATTTATAAAAATTTCAAAATTTA
1 AATTTTTAAAAAATTCAAAATATTTATAAAAAGTTCAAAATTTA
*
41064632 TATTTTTAAAAAATTCTAAAA-ATTATATAAAAAGTT-AAAATTTA
1 AATTTTTAAAAAATTC-AAAATATT-TATAAAAAGTTCAAAATTTA
41064676 AATTTTT
1 AATTTTT
41064683 TTCTAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 6 0.14
44 24 0.55
45 14 0.32
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (44 bp):
AATTTTTAAAAAATTCAAAATATTTATAAAAAGTTCAAAATTTA
Found at i:41065887 original size:43 final size:43
Alignment explanation
Indices: 41065834--41065929 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
41065824 ACCACCACTA
* * * *
41065834 ATTTACAGATATAAACTGTCACTAGGTTGTGA-ATGTACAACAT
1 ATTTGCAGATAAAAACTGCCACTAGGTTG-GAGATGCACAACAT
* *
41065877 ATTTGCAGATAAAAACTGCCACTGGGTTGGAGATGCGCAACAT
1 ATTTGCAGATAAAAACTGCCACTAGGTTGGAGATGCACAACAT
*
41065920 ATTTGTAGAT
1 ATTTGCAGAT
41065930 GAACTGCCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.04
43 43 0.96
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (43 bp):
ATTTGCAGATAAAAACTGCCACTAGGTTGGAGATGCACAACAT
Found at i:41067843 original size:42 final size:42
Alignment explanation
Indices: 41067792--41067890 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
41067782 CTCTTGGTAC
* *
41067792 CGCACACTTAGTGCCCGTTATTCAGCATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
* *
41067834 CGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
*
41067876 TGCACACTTAGTGCC
1 CGCACACTTAGTGCC
41067891 GTTCATATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
Found at i:41072032 original size:132 final size:132
Alignment explanation
Indices: 41071790--41072887 Score: 1736
Period size: 132 Copynumber: 8.3 Consensus size: 132
41071780 ACATTAGTTT
* *
41071790 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTACTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
*
41071855 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCACGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41071920 GC
131 GC
* * * * *
41071922 TTCAATATGCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGGTCAGCTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
*
41071987 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072052 GC
131 GC
* *
41072054 TTCAATGTACTCCACTGTAACCTCAGGGAGATAAAATCCGCCATCCTTGATCTGCTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
* * *
41072119 CTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCATTGCTACCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072184 GC
131 GC
* *
41072186 TTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCGTCAT-CTTCGATCTGCTCCACTACT
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACT
* * * *
41072250 GCTTA-GG-GATAAGATCTGGAATCTTTAATCTATTCCACTACTGCCCAGGGAGATAGAATTACT
65 ACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACT
41072313 GGC
130 GGC
* *
41072316 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
*
41072381 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTACACTGCTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072446 GC
131 GC
* *
41072448 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
* * *
41072513 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGGGATATAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072578 GC
131 GC
* * * * * * *
41072580 TTTAACGTATTCCACTATAACCTCAGGGAGGTATAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
*
41072645 CTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072710 GC
131 GC
* * * *
41072712 TTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCTACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
** * * *
41072777 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCTAGGGGGATAGAATTATTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
41072842 GC
131 GC
* *
41072844 CTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA-CTGCCATC
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATC
41072888 AACCTGCTCC
Statistics
Matches: 900, Mismatches: 62, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
130 114 0.13
131 15 0.02
132 771 0.86
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (132 bp):
TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTGCTCCACTACTA
CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
GC
Found at i:41072670 original size:44 final size:44
Alignment explanation
Indices: 41072622--41072817 Score: 121
Period size: 44 Copynumber: 4.5 Consensus size: 44
41072612 ATAATCCACC
* * *
41072622 ATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* * * * *
41072666 ATCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* * * * * ****
41072707 CTGGCTTCAATGTACTCCACTA-TAACCTCAGGGAGGTAAAATCCACC
1 AT--CTTTAATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTA
* * * *
41072754 ATCTTTGATCTGCTCTACTACTACTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* *
41072798 ATCTTCAATCTATTCCACTA
1 ATCTTTAATCTACTCCACTA
41072818 TTGCCTAGGG
Statistics
Matches: 105, Mismatches: 39, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 17 0.16
44 65 0.62
45 16 0.15
46 1 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (44 bp):
ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
Found at i:41072783 original size:526 final size:528
Alignment explanation
Indices: 41071790--41072879 Score: 1788
Period size: 526 Copynumber: 2.1 Consensus size: 528
41071780 ACATTAGTTT
* *
41071790 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTACTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCTACTCCACTACTA
*
41071855 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCACGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTACACTGCTGCCCACGGAGATAGAATTACTG
* * *
41071920 GCTTCAATATGCTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGGTCAGCTCCACTAC
131 GCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCAGCTCCACTAC
*
41071985 TGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTAC
196 TACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTAC
* * *
41072050 TGGCTTCAATGTACTCCACTGTAACCTCAGGGAGATAAAATCCGCCATCCTTGATCTGCTCCACT
261 TGGCTTCAACGTACTCCACTATAACCTCAGGGAGATAAAATCCACCATCCTTGATCTGCTCCACT
* *
41072115 ACTGCTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCATTGCTACCCAGGGAGATAGAATT
326 ACTACTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATT
**
41072180 ACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCGTCATCTTCGATCTGCTCCA
391 ACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCA
* *
41072245 CTACTGCTTA-GG-GATAAGATCTGGAATCTTTAATCTATTCCACTACTGCCCAGGGAGATAGAA
456 CTACTACTTAGGGAGATAAGATCTGGAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAA
41072308 TTACTGGC
521 TTACTGGC
* *
41072316 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCTACTCCACTACTA
*
41072381 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTACACTGCTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTACACTGCTGCCCACGGAGATAGAATTACTG
* * *
41072446 GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTAC
131 GCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCAGCTCCACTAC
** * *
41072511 TACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGGGATATAATTAC
196 TACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTAC
* * * * *
41072576 TGGCTTTAACGTATTCCACTATAACCTCAGGGAGGTATAATCCACCATCTTTGATCTGCTCCACT
261 TGGCTTCAACGTACTCCACTATAACCTCAGGGAGATAAAATCCACCATCCTTGATCTGCTCCACT
* * *
41072641 ACTACTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATT
326 ACTACTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATT
* *
41072706 ACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCTA
391 ACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCA
* * * *
41072771 CTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTGCCTAGGGGGATAGAA
456 CTACTACTTAGGGAGATAAGATCTGGAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAA
*
41072836 TTATTGGC
521 TTACTGGC
*
41072844 CTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA
41072880 CTGCCATCAA
Statistics
Matches: 520, Mismatches: 42, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
526 430 0.83
527 2 0.00
528 88 0.17
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (528 bp):
TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCTACTCCACTACTA
CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTACACTGCTGCCCACGGAGATAGAATTACTG
GCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCCTTGATCAGCTCCACTAC
TACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAATTAC
TGGCTTCAACGTACTCCACTATAACCTCAGGGAGATAAAATCCACCATCCTTGATCTGCTCCACT
ACTACTTAGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATT
ACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCA
CTACTACTTAGGGAGATAAGATCTGGAATCTTCAATCTATTCCACTACTGCCCAGGGAGATAGAA
TTACTGGC
Found at i:41073703 original size:13 final size:13
Alignment explanation
Indices: 41073685--41073709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41073675 AAATTGTCGA
41073685 GGATAACAAAGAT
1 GGATAACAAAGAT
41073698 GGATAACAAAGA
1 GGATAACAAAGA
41073710 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:41080732 original size:17 final size:17
Alignment explanation
Indices: 41080702--41080735 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41080692 AATAATTTCT
* *
41080702 AAAAACATGTATATGTA
1 AAAAAAATGCATATGTA
41080719 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
41080736 TTATAAAATA
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:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
AAAAAAATGCATATGTA
Found at i:41084013 original size:30 final size:30
Alignment explanation
Indices: 41083979--41084067 Score: 135
Period size: 29 Copynumber: 3.0 Consensus size: 30
41083969 CTAAATTAAA
* *
41083979 GCATGCATGTGTTTAGGGAGCTAAATGGGG
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
*
41084009 GCATGCATGTATTTAGGGAGCTGAAT-GGA
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
*
41084038 GCATGCATGAATTTAGGGAGCTGAATGGGG
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
41084068 ATGCTAGATT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 27 0.51
30 26 0.49
ACGTcount: A:0.26, C:0.10, G:0.38, T:0.26
Consensus pattern (30 bp):
GCATGCATGTATTTAGGGAGCTGAATGGGG
Found at i:41086140 original size:2 final size:2
Alignment explanation
Indices: 41086133--41086182 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
41086123 ATATGGTAAA
41086133 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41086175 AG AG AG AG
1 AG AG AG AG
41086183 CTAAAAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41097764 original size:7 final size:7
Alignment explanation
Indices: 41097752--41097780 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41097742 AAAGTGAATA
41097752 ATATGTG
1 ATATGTG
41097759 ATATGTG
1 ATATGTG
41097766 ATATGTG
1 ATATGTG
41097773 ATATGTG
1 ATATGTG
41097780 A
1 A
41097781 GCATGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
ATATGTG
Found at i:41098021 original size:48 final size:48
Alignment explanation
Indices: 41097943--41098038 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
41097933 GCAATTTATT
41097943 TGTGATTATGTGGCCATTATCGACAATTATGTGGTGGCTTGTCCACAA
1 TGTGATTATGTGGCCATTATCGACAATTATGTGGTGGCTTGTCCACAA
* * *
41097991 TGTG-TTATGTGGTCGTTCATCGACATTTATGTGGTGGCTTGTCCACAA
1 TGTGATTATGTGGCCATT-ATCGACAATTATGTGGTGGCTTGTCCACAA
41098039 ATGGTGTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 11 0.25
48 33 0.75
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (48 bp):
TGTGATTATGTGGCCATTATCGACAATTATGTGGTGGCTTGTCCACAA
Found at i:41100540 original size:16 final size:15
Alignment explanation
Indices: 41100515--41100544 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41100505 GTAAGCACTA
41100515 ATTTGATAGGTGAAC
1 ATTTGATAGGTGAAC
41100530 ATTTAGATAGGTGAA
1 ATTT-GATAGGTGAA
41100545 ACTGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (15 bp):
ATTTGATAGGTGAAC
Found at i:41101426 original size:22 final size:24
Alignment explanation
Indices: 41101384--41101428 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
41101374 AAAATTTAAA
*
41101384 ATATTTATAAAAATTCCAAAATTT
1 ATATTTATAAAAATTCAAAAATTT
41101408 ATATTT-TAAAAATT-AAAAATT
1 ATATTTATAAAAATTCAAAAATT
41101429 CTAAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTTATAAAAATTCAAAAATTT
Found at i:41106570 original size:17 final size:18
Alignment explanation
Indices: 41106550--41106584 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
41106540 CGAATTACCT
41106550 GAATTAAAGTATT-AATC
1 GAATTAAAGTATTGAATC
41106567 GAATTAAAGTATTGAATC
1 GAATTAAAGTATTGAATC
41106585 ACTACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
GAATTAAAGTATTGAATC
Found at i:41108279 original size:239 final size:239
Alignment explanation
Indices: 41107807--41108278 Score: 811
Period size: 238 Copynumber: 2.0 Consensus size: 239
41107797 AAATACAAAC
41107807 ATTAAGACACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTCTA
1 ATTAAGACACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTCTA
* *
41107872 ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCTAATACGTTCAACAGATTTATTCATTT
66 ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
* * *
41107937 CCTTTAAGTCTTCAACAACAATTAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
41108002 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
* *
41108046 ATTAAGAGACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
1 ATTAAGACACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTCTA
* * *
41108111 ATCTAACTGGAGATTGTCTTACATATGTAATAG-CCCCCAACACTTTCAACAGATTTATTCATTT
66 ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
* *
41108175 CCTTTAAGTCTTTAACAACAATCAAATCCACAATGCGTGTCATTCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
* *
41108240 CCATTTTGAACTAAACCCCCTCGAGGGTTAATTTTTTTT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTT
41108279 TAAATAACCA
Statistics
Matches: 219, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
238 125 0.57
239 94 0.43
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.36
Consensus pattern (239 bp):
ATTAAGACACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTCTA
ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
Found at i:41110787 original size:25 final size:25
Alignment explanation
Indices: 41110751--41110837 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
41110741 ATTCAGGAAT
*
41110751 GCTCATATGAGCATGTAAACGAGAA
1 GCTCATGTGAGCATGTAAACGAGAA
* *
41110776 GCTC-TTTCGAGCCATAT-AACGAGAA
1 GCTCATGT-GAG-CATGTAAACGAGAA
*
41110801 GCTCATGTGAG-TTGTATAACGAGAA
1 GCTCATGTGAGCATGTA-AACGAGAA
*
41110826 GCTCATGCGAGC
1 GCTCATGTGAGC
41110838 CAAATATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 40 0.80
26 6 0.12
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
GCTCATGTGAGCATGTAAACGAGAA
Found at i:41110910 original size:24 final size:24
Alignment explanation
Indices: 41110823--41110913 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
41110813 TGTATAACGA
**
41110823 GAAGCTCATGCGAGCCAAATATCAA
1 GAAGCTCATGCGAGCCAAAT-TCGG
* *
41110848 TAAGCTCATGCGAGCCATAA-ACGG
1 GAAGCTCATGCGAGCCA-AATTCGG
***
41110872 GAAGCTCAAAAGAGCCAAATTCGG
1 GAAGCTCATGCGAGCCAAATTCGG
*
41110896 GAGGCTCATGCGAGCCAA
1 GAAGCTCATGCGAGCCAA
41110914 TATCAGGAAG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
23 2 0.04
24 31 0.61
25 16 0.31
26 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAGCTCATGCGAGCCAAATTCGG
Found at i:41111007 original size:25 final size:25
Alignment explanation
Indices: 41110938--41111007 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
41110928 GGAGAGCCAT
*
41110938 ATATC-GGATGCTCATAAGAGTTAA
1 ATATCGGGATGCTCATAAGAGTCAA
* ** * * *
41110962 ATAACGAAAAGCTCGTGAGAGTCAA
1 ATATCGGGATGCTCATAAGAGTCAA
*
41110987 GTATCGGGATGCTCATAAGAG
1 ATATCGGGATGCTCATAAGAG
41111008 CTGTTGTGTG
Statistics
Matches: 31, Mismatches: 14, Indels: 1
0.67 0.30 0.02
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (25 bp):
ATATCGGGATGCTCATAAGAGTCAA
Found at i:41121232 original size:20 final size:20
Alignment explanation
Indices: 41121195--41121234 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41121185 CCTATTTCGT
*
41121195 ACACACGGGCAGAGACATGG
1 ACACACGGCCAGAGACATGG
41121215 ACACACGGCCA-AGCACATGG
1 ACACACGGCCAGAG-ACATGG
41121235 GCGTGTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.30, G:0.30, T:0.05
Consensus pattern (20 bp):
ACACACGGCCAGAGACATGG
Found at i:41125372 original size:25 final size:25
Alignment explanation
Indices: 41125318--41125364 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
41125308 AAATCTACTC
41125318 TAAAAAGAAAAGAGAAAGCCTAAAT
1 TAAAAAGAAAAGAGAAAGCCTAAAT
41125343 TAAAAATGAAAAGA-AAA-CCTAA
1 TAAAAA-GAAAAGAGAAAGCCTAA
41125365 CCTTAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (25 bp):
TAAAAAGAAAAGAGAAAGCCTAAAT
Found at i:41126765 original size:26 final size:26
Alignment explanation
Indices: 41126736--41126814 Score: 106
Period size: 26 Copynumber: 3.1 Consensus size: 26
41126726 GCCAACACAC
* *
41126736 CAATATCGCAGCAAAGCTGCCAGTAT
1 CAATATCGCAGCAAAGCTGCCAGCAA
*
41126762 CAATAACGCAGCAAAGCTGCCAGCAA
1 CAATATCGCAGCAAAGCTGCCAGCAA
* *
41126788 CAGTATCGCAGCAGAGCTGCCAG-AA
1 CAATATCGCAGCAAAGCTGCCAGCAA
41126813 CA
1 CA
41126815 GTACACTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 4 0.09
26 43 0.91
ACGTcount: A:0.37, C:0.29, G:0.22, T:0.13
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGCAA
Found at i:41127015 original size:27 final size:27
Alignment explanation
Indices: 41126985--41127345 Score: 349
Period size: 27 Copynumber: 13.4 Consensus size: 27
41126975 GATATAGTGG
* *
41126985 TAATTTTACCCTTCGGGGGCATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTTGA
* * * *
41127012 TAATTTTACCCATCAAGGGTATTTCGG
1 TAATTTTACCCTTCGAGGGTATTTTGA
* * *
41127039 TAATTTTATCCTTC-AGGGGCATTTCGA
1 TAATTTTACCCTTCGA-GGGTATTTTGA
* * *
41127066 TAATTTTACCTTTTGGGGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTTGA
41127093 TAATTTTACCCTTCGAGGGTATTTT-A
1 TAATTTTACCCTTCGAGGGTATTTTGA
* *
41127119 GTAATTTTACCCATCGAGGGTATTTTAA
1 -TAATTTTACCCTTCGAGGGTATTTTGA
* *
41127147 TAATTTTACTCTT-TAGGGGTATTTT-A
1 TAATTTTACCCTTCGA-GGGTATTTTGA
* * * *
41127173 GTAATTTTATCCATTAG-GGGTATTTCGG
1 -TAATTTTA-CCCTTCGAGGGTATTTTGA
41127201 TAATTTTACCCTTCGAGGGTATTTT-A
1 TAATTTTACCCTTCGAGGGTATTTTGA
* * *
41127227 GTAATTTTACCCTTCGAGAGTATTTCGG
1 -TAATTTTACCCTTCGAGGGTATTTTGA
* * *
41127255 TAATTTTACTCATCGAGGGTATTTTGG
1 TAATTTTACCCTTCGAGGGTATTTTGA
* *
41127282 TAATTTTACCCATCGAAGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTTGA
**
41127309 TAATTTTACCCTTCGAGGGTATTTCAA
1 TAATTTTACCCTTCGAGGGTATTTTGA
41127336 TAA-TTTACCC
1 TAATTTTACCC
41127346 ACGAATCGAA
Statistics
Matches: 276, Mismatches: 46, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
26 16 0.06
27 256 0.93
28 4 0.01
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (27 bp):
TAATTTTACCCTTCGAGGGTATTTTGA
Found at i:41127095 original size:81 final size:81
Alignment explanation
Indices: 41126985--41127346 Score: 399
Period size: 81 Copynumber: 4.5 Consensus size: 81
41126975 GATATAGTGG
* *
41126985 TAATTTTACCCTTCGGGGGCATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTATCC
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCC
* * *
41127050 TTC-AGGGGCATTTCGA
66 ATCGA-GGGTATTTTGA
* * * * **
41127066 TAATTTTACCTTTTGGGGGTATTTTGATAATTTTACCCTTCGAGGGTATTTTAGTAATTTTACCC
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCC
*
41127131 ATCGAGGGTATTTTAA
66 ATCGAGGGTATTTTGA
* ** * * *
41127147 TAATTTTACTCTTTAGGGGTATTTT-AGTAATTTTATCCATTAGGGGTATTTCGGTAATTTTACC
1 TAATTTTACCCTTCGGGGGTATTTTGA-TAATTTTACCCATCAAGGGTATTTCGGTAATTTTACC
*
41127211 CTTCGAGGGTATTTT-A
65 CATCGAGGGTATTTTGA
* * * * * * *
41127227 GTAATTTTACCCTTCGAGAGTATTTCGGTAATTTTACTCATCGAGGGTATTTTGGTAATTTTACC
1 -TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACC
*
41127292 CATCGAAGGTATTTTGA
65 CATCGAGGGTATTTTGA
* **
41127309 TAATTTTACCCTTCGAGGGTATTTCAATAA-TTTACCCA
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCA
41127347 CGAATCGAAA
Statistics
Matches: 234, Mismatches: 42, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
80 9 0.04
81 223 0.95
82 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (81 bp):
TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCC
ATCGAGGGTATTTTGA
Found at i:41130022 original size:90 final size:90
Alignment explanation
Indices: 41129860--41130106 Score: 225
Period size: 90 Copynumber: 2.7 Consensus size: 90
41129850 CTCAGTTTAA
* * * * *** *
41129860 AAATTCGGTGAATGT-ATCAAGTCTACCTCACTAGGACCACCCAAAGC-CTGATATATGAATTCA
1 AAATTTGGTGAAT-TCATCAAGTCTATCTCAATAAGACCACCCAAA-CTCTGGGCTATGAACTCA
* * **
41129923 TTAAGAACATTTAGTGGCTCATCCTAT
64 TTAAAAACATCTAGAAGCTCATCCTAT
* * * *
41129950 AAATTTGGT-AAGTTCATCAAGTTTGTCTCAATAGGAACC-CCCGAAA-TCTGGGTTATGAACTC
1 AAATTTGGTGAA-TTCATCAAGTCTATCTCAATAAG-ACCACCC-AAACTCTGGGCTATGAACTC
*
41130012 ATTAAAAACATCTAGAAGTTCATCCTAT
63 ATTAAAAACATCTAGAAGCTCATCCTAT
* * * *
41130040 GAATTTGGTGAATTTATCAAGTCTATCTTAATAAGACCATCCAAACTCTGGGCTATGAACTCATT
1 AAATTTGGTGAATTCATCAAGTCTATCTCAATAAGACCACCCAAACTCTGGGCTATGAACTCATT
41130105 AA
66 AA
41130107 GAGCACAGAG
Statistics
Matches: 127, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
89 9 0.07
90 110 0.87
91 8 0.06
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (90 bp):
AAATTTGGTGAATTCATCAAGTCTATCTCAATAAGACCACCCAAACTCTGGGCTATGAACTCATT
AAAAACATCTAGAAGCTCATCCTAT
Found at i:41133805 original size:18 final size:18
Alignment explanation
Indices: 41133763--41133806 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
41133753 TATGAGTTAT
41133763 AAATTAC-ATAATATATA
1 AAATTACAATAATATATA
*
41133780 AAAATACAATAATATA-A
1 AAATTACAATAATATATA
41133797 AACATTACAA
1 AA-ATTACAA
41133807 ACTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTACAATAATATATA
Found at i:41134397 original size:58 final size:58
Alignment explanation
Indices: 41134326--41134439 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
41134316 TTTTCTTTTT
* *
41134326 CTTTACAATCAGTC-ACACTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTTGATTGGC
1 CTTTACAACCAGTCGAC-CTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTGGC
* * **
41134384 CTTTTCAACCAGTCGACCTTTTTCTTTTCTTTTTCTCTCTGTCACTCTTTCGATTG
1 CTTTACAACCAGTCGACCTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTG
41134440 CTCTCAATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 47 0.96
59 2 0.04
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (58 bp):
CTTTACAACCAGTCGACCTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTGGC
Found at i:41136676 original size:23 final size:24
Alignment explanation
Indices: 41136648--41136710 Score: 96
Period size: 23 Copynumber: 2.7 Consensus size: 24
41136638 TTGTTTTGAT
41136648 ATTGTTCTTGATTTGTT-CTGGAA
1 ATTGTTCTTGATTTGTTGCTGGAA
41136671 ATTGTT-TTGA-TTGTCTGCTGGAA
1 ATTGTTCTTGATTTGT-TGCTGGAA
41136694 ATTGTTCTTGATTTGTT
1 ATTGTTCTTGATTTGTT
41136711 AGTCAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 18 0.50
24 5 0.14
25 4 0.11
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.54
Consensus pattern (24 bp):
ATTGTTCTTGATTTGTTGCTGGAA
Found at i:41139521 original size:11 final size:11
Alignment explanation
Indices: 41139505--41139531 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41139495 TAGAAATTAG
41139505 TTTGTGAAACT
1 TTTGTGAAACT
41139516 TTTGTGAAACT
1 TTTGTGAAACT
41139527 TTTGT
1 TTTGT
41139532 ATTGATTTTT
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:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:41139596 original size:7 final size:7
Alignment explanation
Indices: 41139584--41139634 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
41139574 ATTTCTTGTC
41139584 ATTTTAA
1 ATTTTAA
41139591 ATTTTAA
1 ATTTTAA
41139598 ATTTT--
1 ATTTTAA
* *
41139603 GTGTTATA
1 ATTTTA-A
41139611 ATTTTAA
1 ATTTTAA
41139618 ATTTTAA
1 ATTTTAA
*
41139625 ATTTGAA
1 ATTTTAA
41139632 ATT
1 ATT
41139635 ATAGTTTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
5 3 0.08
7 29 0.81
8 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:41139615 original size:20 final size:20
Alignment explanation
Indices: 41139590--41139661 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
41139580 TGTCATTTTA
41139590 AATTTTAAATTTTGTGTTAT
1 AATTTTAAATTTTGTGTTAT
***
41139610 AATTTTAAATTTTAAATT-T
1 AATTTTAAATTTTGTGTTAT
* * *
41139629 GAA-ATTATAGTTTGTGTTAT
1 -AATTTTAAATTTTGTGTTAT
41139649 AATTTTAAATTTT
1 AATTTTAAATTTT
41139662 TTGTGGTATA
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
19 12 0.32
20 25 0.68
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
AATTTTAAATTTTGTGTTAT
Found at i:41139636 original size:27 final size:27
Alignment explanation
Indices: 41139584--41139637 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41139574 ATTTCTTGTC
**
41139584 ATTTTAAATTTTAAATTTTGTGTTATA
1 ATTTTAAATTTTAAATTTTGAATTATA
41139611 ATTTTAAATTTTAAA-TTTGAAATTATA
1 ATTTTAAATTTTAAATTTTG-AATTATA
41139638 GTTTGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (27 bp):
ATTTTAAATTTTAAATTTTGAATTATA
Found at i:41141376 original size:120 final size:120
Alignment explanation
Indices: 41141117--41141893 Score: 1351
Period size: 120 Copynumber: 6.5 Consensus size: 120
41141107 AATTATTTTA
* * * *
41141117 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
41141181 TATAGTAT-ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
41141236 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
41141301 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
41141356 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
41141421 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41141476 AATTTTATTAAATTATGTATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* * *
41141541 ATAGTATCATATATTATGAGTTGAATAAATTCATATAAGAATATTAATTATTAAT
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
41141596 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATATTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
41141661 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41141716 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
41141781 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
41141836 AATTTTATTAAATTGTATATTTTAATTATAATATATTTAATAATATTTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
41141894 ATAATTAAAT
Statistics
Matches: 636, Mismatches: 19, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
119 68 0.11
120 562 0.88
121 6 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41141630 original size:18 final size:18
Alignment explanation
Indices: 41141584--41141631 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
41141574 TATAAGAATA
*
41141584 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
41141600 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
41141617 TTAATTATAATATAT
1 TTAATTATAATATAT
41141632 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:41141639 original size:18 final size:16
Alignment explanation
Indices: 41141584--41141647 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
41141574 TATAAGAATA
41141584 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
41141600 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
41141617 TTAATTATAATATATT
1 TTAATTATAATATATT
*
41141633 TAATAATTATTATAT
1 T--TAATTATAATAT
41141648 TAAATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.08
16 16 0.41
17 6 0.15
18 14 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:41141751 original size:16 final size:16
Alignment explanation
Indices: 41141730--41141776 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
41141720 TTATTAAATT
41141730 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
41141746 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
41141761 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
41141777 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:41142130 original size:16 final size:16
Alignment explanation
Indices: 41142105--41142142 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41142095 TTGATTTGCT
41142105 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
41142121 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
41142137 AATACA
1 ATTACA
41142143 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:41147485 original size:23 final size:23
Alignment explanation
Indices: 41147459--41147507 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
41147449 TTAACTTGAT
41147459 ACTATTTTAGTATTCTGACTATA
1 ACTATTTTAGTATTCTGACTATA
41147482 ACTATTTTAGTATTCTGACTATA
1 ACTATTTTAGTATTCTGACTATA
41147505 ACT
1 ACT
41147508 TAAGTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (23 bp):
ACTATTTTAGTATTCTGACTATA
Found at i:41148757 original size:161 final size:161
Alignment explanation
Indices: 41148576--41148879 Score: 599
Period size: 161 Copynumber: 1.9 Consensus size: 161
41148566 GACTAAACTA
41148576 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
1 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
41148641 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
66 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
41148706 GATTAAGGTTTTAATTAATATATATAATAGT
131 GATTAAGGTTTTAATTAATATATATAATAGT
*
41148737 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAATAAGGAAAATAAA
1 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
41148802 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
66 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
41148867 GATTAAGGTTTTA
131 GATTAAGGTTTTA
41148880 GGGTAGATTA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 142 1.00
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (161 bp):
AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
GATTAAGGTTTTAATTAATATATATAATAGT
Found at i:41152630 original size:21 final size:21
Alignment explanation
Indices: 41152606--41152657 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
41152596 TTAATCACTT
*
41152606 TAATATTAAACTA-ATATAATA
1 TAATATTAAACAAGATA-AATA
* *
41152627 TAATATTTATCAAGATAAATA
1 TAATATTAAACAAGATAAATA
41152648 TAATATTAAA
1 TAATATTAAA
41152658 TATAATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATTAAACAAGATAAATA
Found at i:41152659 original size:12 final size:12
Alignment explanation
Indices: 41152642--41152670 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41152632 TTTATCAAGA
41152642 TAAATATAATAT
1 TAAATATAATAT
41152654 TAAATATAATAT
1 TAAATATAATAT
41152666 TAAAT
1 TAAAT
41152671 CTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATAATAT
Found at i:41152769 original size:25 final size:27
Alignment explanation
Indices: 41152714--41152769 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
41152704 TAAGCATTAA
*
41152714 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
41152741 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
41152765 ATTAA
1 ATTAA
41152770 GATAACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:41154089 original size:12 final size:12
Alignment explanation
Indices: 41154068--41154126 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
41154058 ACGTCACAAG
41154068 TGAATTAATTCA
1 TGAATTAATTCA
*
41154080 TGAATGAATTCA
1 TGAATTAATTCA
41154092 -GAATTAATTCA
1 TGAATTAATTCA
* ** *
41154103 CGAACGAATTTA
1 TGAATTAATTCA
41154115 -GAATTAATTCA
1 TGAATTAATTCA
41154126 T
1 T
41154127 CTTGGATCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (12 bp):
TGAATTAATTCA
Found at i:41154098 original size:23 final size:23
Alignment explanation
Indices: 41154069--41154126 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
41154059 CGTCACAAGT
*
41154069 GAATTAATTCATGAATGAATTCA
1 GAATTAATTCATGAACGAATTCA
* *
41154092 GAATTAATTCACGAACGAATTTA
1 GAATTAATTCATGAACGAATTCA
41154115 GAATTAATTCAT
1 GAATTAATTCAT
41154127 CTTGGATCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (23 bp):
GAATTAATTCATGAACGAATTCA
Found at i:41155230 original size:20 final size:20
Alignment explanation
Indices: 41155206--41155257 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
41155196 TCGAAATGCT
*
41155206 AACAGAGGCATTAAAGCGCA
1 AACAGAGGCATCAAAGCGCA
* *
41155226 TACAGAGGCATCAAAGTGCA
1 AACAGAGGCATCAAAGCGCA
*
41155246 AACAAAGGCATC
1 AACAGAGGCATC
41155258 GTGTAACAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
AACAGAGGCATCAAAGCGCA
Found at i:41155967 original size:24 final size:24
Alignment explanation
Indices: 41155895--41156020 Score: 118
Period size: 22 Copynumber: 5.3 Consensus size: 24
41155885 CACTAATGAA
* *
41155895 CAGAGAGCACTAAAGTGCT-ATA-
1 CAGAGAGCACTAACGTGCTAAAAT
*
41155917 CAGAGAGCAC-ATATGTGCT-AAAT
1 CAGAGAGCACTA-ACGTGCTAAAAT
*
41155940 -AGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACTAACGTGCTAAAAT
* * * *
41155963 CAGAGAGCACCAACGTACTAGTAGT
1 CAGAGAGCACTAACGTGCTA-AAAT
41155988 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAA-AAT
41156013 CAGAGAGC
1 CAGAGAGC
41156021 GCGCTAAAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.39
23 4 0.05
24 16 0.19
25 30 0.36
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTAAAAT
Found at i:41155996 original size:25 final size:25
Alignment explanation
Indices: 41155940--41156020 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
41155930 TGTGCTAAAT
** *
41155940 AGAGAGCACTGACGTGCTAA-AATC
1 AGAGAGCACCAACGTACTAATAATC
* *
41155964 AGAGAGCACCAACGTACTAGTAGTC
1 AGAGAGCACCAACGTACTAATAATC
* *
41155989 AGAGAGCACTAACGTGCTAATAATC
1 AGAGAGCACCAACGTACTAATAATC
41156014 AGAGAGC
1 AGAGAGC
41156021 GCGCTAAAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 16 0.34
25 31 0.66
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (25 bp):
AGAGAGCACCAACGTACTAATAATC
Found at i:41157157 original size:13 final size:13
Alignment explanation
Indices: 41157118--41157157 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
41157108 TGTTTTATGT
41157118 ATATAATAATAAT-
1 ATATAAT-ATAATA
*
41157131 ATATATTATAATA
1 ATATAATATAATA
41157144 ATATAATATAATA
1 ATATAATATAATA
41157157 A
1 A
41157158 CTTACTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:41158374 original size:9 final size:9
Alignment explanation
Indices: 41158317--41158374 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
41158307 TTTGGTTAAA
*
41158317 AATTAACTG
1 AATTAACCG
41158326 AATTAACCG
1 AATTAACCG
* *
41158335 AATTCACTG
1 AATTAACCG
*
41158344 AATTACCCG
1 AATTAACCG
*
41158353 AATTAATCG
1 AATTAACCG
*
41158362 AATTAACCA
1 AATTAACCG
41158371 AATT
1 AATT
41158375 GAATCACTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:41158531 original size:13 final size:13
Alignment explanation
Indices: 41158515--41158539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41158505 AATTTTTATG
41158515 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
41158528 ATTGGGTTGGGT
1 ATTGGGTTGGGT
41158540 TGGATACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:41158539 original size:18 final size:19
Alignment explanation
Indices: 41158516--41158563 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
41158506 ATTTTTATGA
41158516 TTGGGTTGGGTAATTGGG-
1 TTGGGTTGGGTAATTGGGT
* *
41158534 TTGGGTTGGATACTTGGGT
1 TTGGGTTGGGTAATTGGGT
*
41158553 TTGGATTGGGT
1 TTGGGTTGGGT
41158564 TTAGGTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.10, C:0.02, G:0.46, T:0.42
Consensus pattern (19 bp):
TTGGGTTGGGTAATTGGGT
Found at i:41170233 original size:11 final size:12
Alignment explanation
Indices: 41170212--41170260 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
41170202 TAGTAGTTTC
41170212 TTTGAAAAAAAA
1 TTTGAAAAAAAA
41170224 TTTGAAAAAAAA
1 TTTGAAAAAAAA
* *
41170236 ATTAAAAAAAAA
1 TTTGAAAAAAAA
* *
41170248 ATTCAAAAAAAA
1 TTTGAAAAAAAA
41170260 T
1 T
41170261 AGTTTCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (12 bp):
TTTGAAAAAAAA
Found at i:41170234 original size:13 final size:13
Alignment explanation
Indices: 41170212--41170259 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
41170202 TAGTAGTTTC
41170212 TTTG-AAAAAAAA
1 TTTGAAAAAAAAA
41170224 TTTGAAAAAAAAA
1 TTTGAAAAAAAAA
41170237 -TT-AAAAAAAAA
1 TTTGAAAAAAAAA
* *
41170248 ATTCAAAAAAAA
1 TTTGAAAAAAAA
41170260 TAGTTTCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.27
12 8 0.24
13 16 0.48
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
TTTGAAAAAAAAA
Found at i:41170318 original size:13 final size:13
Alignment explanation
Indices: 41170300--41170332 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
41170290 ATCAAGTTGA
41170300 AAAAAAAATCGTG
1 AAAAAAAATCGTG
*
41170313 AAAAAAAATTGTG
1 AAAAAAAATCGTG
41170326 AAAAAAA
1 AAAAAAA
41170333 GAAAAGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (13 bp):
AAAAAAAATCGTG
Found at i:41176194 original size:19 final size:18
Alignment explanation
Indices: 41176158--41176197 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41176148 TTTCCACTCG
*
41176158 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
41176176 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
41176195 TTT
1 TTT
41176198 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:41183126 original size:9 final size:9
Alignment explanation
Indices: 41183108--41183141 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
41183098 TATCCCGTAA
41183108 AAAAATAGTC
1 AAAAA-AGTC
41183118 AAAAAAGTC
1 AAAAAAGTC
*
41183127 AAAAAAATC
1 AAAAAAGTC
41183136 AAAAAA
1 AAAAAA
41183142 TACGAAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:41184472 original size:18 final size:18
Alignment explanation
Indices: 41184451--41184490 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41184441 GATTGAGAGT
* * *
41184451 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
41184469 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
41184487 GAAA
1 GAAA
41184491 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:41197789 original size:41 final size:41
Alignment explanation
Indices: 41197724--41197809 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
41197714 TTTAATTAGG
* *
41197724 TGTTTTAAATATGTCTGGAGGAATTTAATGCTGCCACTACA
1 TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
*
41197765 TGTTATAAATATGTCTGGACGAATTTAATGCTGCTACTACA
1 TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
41197806 TGTT
1 TGTT
41197810 TGGCCGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
Found at i:41201842 original size:13 final size:13
Alignment explanation
Indices: 41201821--41201855 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
41201811 ATAAGTTGCT
* *
41201821 GTTAGTTAAATTA
1 GTTAATTAAATAA
41201834 GTTAATTAAATAA
1 GTTAATTAAATAA
41201847 GTTAATTAA
1 GTTAATTAA
41201856 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:41204580 original size:12 final size:12
Alignment explanation
Indices: 41204563--41204589 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41204553 GACGTCAAGC
41204563 CAAGGTGAGTAT
1 CAAGGTGAGTAT
41204575 CAAGGTGAGTAT
1 CAAGGTGAGTAT
41204587 CAA
1 CAA
41204590 ATTGAAATGA
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:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:41216998 original size:27 final size:29
Alignment explanation
Indices: 41216967--41217021 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
41216957 TTAGGACTTA
41216967 TCTTTT-AATT-T-CTTGCTGTCAATTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTT
41216994 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
41217022 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 4 0.16
29 11 0.44
30 4 0.16
ACGTcount: A:0.16, C:0.15, G:0.09, T:0.60
Consensus pattern (29 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTT
Found at i:41221499 original size:52 final size:52
Alignment explanation
Indices: 41221416--41221516 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
41221406 TAAGGAAAAG
* * *
41221416 TAATGGACAGTAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAACAA
41221468 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAA
41221517 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAACAA
Found at i:41222873 original size:24 final size:23
Alignment explanation
Indices: 41222807--41222876 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
41222797 AATTCCATCA
*
41222807 TTTCCCTTTGTTTATTTTATTTTC
1 TTTCCCTTTGTTTA-TTTATTTCC
* * *
41222831 TTATCCTTTTACTCT-TTTATTATCC
1 TT-TCCCTTT-GTTTATTTATT-TCC
41222856 TTTCCCTTTGTTTATTTATTT
1 TTTCCCTTTGTTTATTTATTT
41222877 ATTTTTTCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
23 3 0.09
24 20 0.57
25 10 0.29
26 2 0.06
ACGTcount: A:0.11, C:0.19, G:0.03, T:0.67
Consensus pattern (23 bp):
TTTCCCTTTGTTTATTTATTTCC
Found at i:41227769 original size:46 final size:46
Alignment explanation
Indices: 41227716--41227809 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
41227706 CAAAGAAAAG
**
41227716 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAAAACCTTGGTATATGATGA
41227762 ACCTCGACCCACTATCAATGATGATAAAAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAAAACCTTGGTATATGATGA
41227808 AC
1 AC
41227810 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAAAACCTTGGTATATGATGA
Found at i:41231160 original size:19 final size:19
Alignment explanation
Indices: 41231136--41231173 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
41231126 TTGAAGGCAA
41231136 AGCCCAAT-AAGCAAATTCC
1 AGCCCAATCAAG-AAATTCC
41231155 AGCCCAATCAAGAAATTCC
1 AGCCCAATCAAGAAATTCC
41231174 TACATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (19 bp):
AGCCCAATCAAGAAATTCC
Found at i:41234881 original size:23 final size:22
Alignment explanation
Indices: 41234830--41234881 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41234820 CTTCGTCTTT
*
41234830 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41234852 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41234875 TTCTTTT
1 TTCTTTT
41234882 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41243841 original size:18 final size:18
Alignment explanation
Indices: 41243820--41243859 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41243810 GATTGAGAGT
* * *
41243820 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
41243838 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
41243856 GAAA
1 GAAA
41243860 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:41262387 original size:19 final size:19
Alignment explanation
Indices: 41262363--41262399 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41262353 TAAGTATGTA
41262363 GGAATTT-CTTGATTGGGCT
1 GGAATTTGCTT-ATTGGGCT
41262382 GGAATTTGCTTATTGGGC
1 GGAATTTGCTTATTGGGC
41262400 ATTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (19 bp):
GGAATTTGCTTATTGGGCT
Found at i:41262515 original size:58 final size:59
Alignment explanation
Indices: 41262424--41262542 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 59
41262414 TTTGGGCCTG
41262424 TGATCTATCTCCTACCGAAATTGGGTCGTTGATGCTCGTGACGGAGATCCAATGCGCTT
1 TGATCTATCTCCTACCGAAATTGGGTCGTTGATGCTCGTGACGGAGATCCAATGCGCTT
*
41262483 TGATCTATCTCCTACC-AAATTGGGTCGTTGATGCTCGTGGCGGAGATCCAATGCGCTT
1 TGATCTATCTCCTACCGAAATTGGGTCGTTGATGCTCGTGACGGAGATCCAATGCGCTT
41262541 TG
1 TG
41262543 GCTGCAAGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 43 0.73
59 16 0.27
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (59 bp):
TGATCTATCTCCTACCGAAATTGGGTCGTTGATGCTCGTGACGGAGATCCAATGCGCTT
Found at i:41263278 original size:22 final size:21
Alignment explanation
Indices: 41263246--41263309 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
41263236 TTGGTATTTA
41263246 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
41263267 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
41263289 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
41263310 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:41269720 original size:19 final size:18
Alignment explanation
Indices: 41269696--41269749 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
41269686 GTATACAATT
*
41269696 TTTTTTTCTTTTTTTTCAG
1 TTTTTTT-TTTTTTTTCAA
*
41269715 TTTTTTTGATTTTTTTCAA
1 TTTTTTT-TTTTTTTTCAA
41269734 TTTTTTTTTATTTTTT
1 TTTTTTTTT-TTTTTT
41269750 TTCACAAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 1 0.03
19 29 0.97
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTCAA
Found at i:41270094 original size:22 final size:23
Alignment explanation
Indices: 41270058--41270100 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41270048 TATTTAGGAA
*
41270058 TTGGTAGGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
41270080 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
41270101 TCAAAAAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.35, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:41272462 original size:23 final size:22
Alignment explanation
Indices: 41272410--41272462 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
41272400 TCCTTGTCTT
*
41272410 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
41272432 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
41272455 TTTCTTTT
1 TTTCTTTT
41272463 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41272492 original size:18 final size:18
Alignment explanation
Indices: 41272455--41272493 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41272445 CTTTCTTCAA
* * *
41272455 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
41272473 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
41272491 TTT
1 TTT
41272494 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:41287424 original size:16 final size:17
Alignment explanation
Indices: 41287386--41287427 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
41287376 AAGCTTATGC
41287386 TAAGTAAATGGAATGAAAAG
1 TAAGTAAATGGAATG---AG
41287406 TAAGTAAATGGAATG-G
1 TAAGTAAATGGAATGAG
41287422 TAAGTA
1 TAAGTA
41287428 TGTAAGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
20 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (17 bp):
TAAGTAAATGGAATGAG
Found at i:41292671 original size:50 final size:50
Alignment explanation
Indices: 41292439--41292681 Score: 308
Period size: 50 Copynumber: 4.8 Consensus size: 50
41292429 GATCATAACA
* ** ** *
41292439 TGCCAAAGCCATGTCTGAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
41292490 TGCCCATGCCATGTCCCAGACTTGGTCTTAC-GGGGAACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATCTCGG
* * * **
41292540 TGCCAACTCCATGTCTCAGACATGGTCTTACATGAGACCTCTCATCTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
41292590 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
41292640 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41292682 TTACCCAACT
Statistics
Matches: 164, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
50 135 0.82
51 29 0.18
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:41293209 original size:43 final size:43
Alignment explanation
Indices: 41293148--41293232 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
41293138 GTCTACCAAC
41293148 TTAACCAATGGTCTAATTACCATATAAGGACCTCCAATGAAAT
1 TTAACCAATGGTCTAATTACCATATAAGGACCTCCAATGAAAT
41293191 TTAACCAATGGTCTAATTACCATATAAGGACCTCCAATGAAA
1 TTAACCAATGGTCTAATTACCATATAAGGACCTCCAATGAAA
41293233 AGTTTCATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (43 bp):
TTAACCAATGGTCTAATTACCATATAAGGACCTCCAATGAAAT
Found at i:41298002 original size:41 final size:41
Alignment explanation
Indices: 41297953--41298056 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
41297943 GACTATAAGT
*
41297953 CTAGCAGGCTAAGTGCCGGTGATCA-AAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-ATAAATCAGGCTATAAAC
* * * * *
41297994 TTGGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATATAAATCAGGCTATAAAC
41298035 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
41298057 ATATGTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATATAAATCAGGCTATAAAC
Found at i:41305130 original size:74 final size:72
Alignment explanation
Indices: 41305052--41305188 Score: 170
Period size: 74 Copynumber: 1.9 Consensus size: 72
41305042 ATGAATGTTA
* *
41305052 TATATATGCATAAATGAAG-TTCGAACATG-TATATATATGTATATGATCTTAAATTTAGTTAAA
1 TATATAT--ATAAAT-AAGATTCGAAAATGATATATATATGTATA-GATCTTAAATTTAATTAAA
41305115 GGTAAGAATGT
62 GGTAAGAATGT
* * *
41305126 TATATATATATATAAGATTCGAAAATGTATATATATATGTATAGATTTTGAATTTAATTAAAG
1 TATATATATAAATAAGATTCGAAAATG-ATATATATATGTATAGATCTTAAATTTAATTAAAG
41305189 CTATGGACAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
71 3 0.05
72 14 0.25
73 17 0.31
74 21 0.38
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (72 bp):
TATATATATAAATAAGATTCGAAAATGATATATATATGTATAGATCTTAAATTTAATTAAAGGTA
AGAATGT
Found at i:41305157 original size:72 final size:75
Alignment explanation
Indices: 41305031--41305188 Score: 184
Period size: 76 Copynumber: 2.1 Consensus size: 75
41305021 TGGATCGAAA
* * *
41305031 TTAGTT-AATGTATGAATGTTATATATATGCATAAATGAAGTTCGAACATG-TATATATATGTAT
1 TTAGTTAAAGGTAAGAATGTTATATATAT-CATAAATGAAGTTCGAAAATGATATATATATGTAT
41305094 ATGATCTTAAAT
65 A-GATCTTAAAT
41305106 TTAGTTAAAGGTAAGAATGTTATATATAT-AT--AT-AAGATTCGAAAATGTATATATATATGTA
1 TTAGTTAAAGGTAAGAATGTTATATATATCATAAATGAAG-TTCGAAAATG-ATATATATATGTA
* *
41305167 TAGATTTTGAAT
64 TAGATCTTAAAT
*
41305179 TTAATTAAAG
1 TTAGTTAAAG
41305189 CTATGGACAA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
71 3 0.04
72 11 0.15
73 17 0.23
74 16 0.22
75 6 0.08
76 20 0.27
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (75 bp):
TTAGTTAAAGGTAAGAATGTTATATATATCATAAATGAAGTTCGAAAATGATATATATATGTATA
GATCTTAAAT
Found at i:41305689 original size:41 final size:41
Alignment explanation
Indices: 41305640--41305743 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
41305630 GACTATAAGT
*
41305640 CTAGCAGGCTAAGTGCCGGTGATCA-AAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-ATAAATCAGGCTATAAAC
* * * *
41305681 CTGGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATATAAATCAGGCTATAAAC
41305722 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
41305744 ATATGTTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 54 0.98
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATATAAATCAGGCTATAAAC
Found at i:41310631 original size:27 final size:30
Alignment explanation
Indices: 41310567--41310633 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
41310557 AAGCGATGGT
41310567 GATCTTATTTTACTAGAAGTTGATGTGATAA
1 GATCTTATTTTACTAGAAG-TGATGTGATAA
41310598 GATCTTATTTTACTAGAAG-G-TG-GATAA
1 GATCTTATTTTACTAGAAGTGATGTGATAA
41310625 GATCTTATT
1 GATCTTATT
41310634 CTGGCAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 14 0.39
28 2 0.06
29 1 0.03
31 19 0.53
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.42
Consensus pattern (30 bp):
GATCTTATTTTACTAGAAGTGATGTGATAA
Found at i:41332535 original size:19 final size:19
Alignment explanation
Indices: 41332508--41332545 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41332498 GAAGTCTTCA
*
41332508 AGATTAGTATTAATCAGAC
1 AGATCAGTATTAATCAGAC
41332527 AGATCAGTATTAATCAGAC
1 AGATCAGTATTAATCAGAC
41332546 GCATTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
AGATCAGTATTAATCAGAC
Found at i:41335117 original size:16 final size:17
Alignment explanation
Indices: 41335096--41335128 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41335086 TTATATTTTT
*
41335096 TAAAAA-TATTTTTAAA
1 TAAAAATTAATTTTAAA
41335112 TAAAAATTAATTTTAAA
1 TAAAAATTAATTTTAAA
41335129 AAACCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATTAATTTTAAA
Found at i:41335876 original size:13 final size:13
Alignment explanation
Indices: 41335853--41335889 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
41335843 TTTAAATATA
41335853 TATAA-TTTATTT
1 TATAATTTTATTT
*
41335865 TATATTTTTATTT
1 TATAATTTTATTT
41335878 TATAATTTTATT
1 TATAATTTTATT
41335890 AACTGAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATAATTTTATTT
Found at i:41336160 original size:23 final size:24
Alignment explanation
Indices: 41336134--41336182 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
41336124 CACAAATAAC
*
41336134 AAATATGATTAAA-ATCTATA-ATG
1 AAAT-TGATTAAATATATATATATG
*
41336157 AAATTGTTTAAATATATATATATG
1 AAATTGATTAAATATATATATATG
41336181 AA
1 AA
41336183 TATTATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 10 0.45
24 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (24 bp):
AAATTGATTAAATATATATATATG
Found at i:41336255 original size:3 final size:3
Alignment explanation
Indices: 41336247--41336291 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
41336237 TAATCGATTG
41336247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41336292 GATGATGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41341294 original size:15 final size:15
Alignment explanation
Indices: 41341274--41341303 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41341264 CATTTAATTC
*
41341274 ACAAAATCAATCAAT
1 ACAAAACCAATCAAT
41341289 ACAAAACCAATCAAT
1 ACAAAACCAATCAAT
41341304 GACATACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (15 bp):
ACAAAACCAATCAAT
Found at i:41342185 original size:15 final size:16
Alignment explanation
Indices: 41342156--41342185 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41342146 CAAACATGCT
41342156 TTAACACATTATCAAA
1 TTAACACATTATCAAA
41342172 TTAACACA-TATCAA
1 TTAACACATTATCAA
41342186 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:41345271 original size:11 final size:11
Alignment explanation
Indices: 41345255--41345279 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41345245 TTAGAACCTC
41345255 TTAAGGAAAGT
1 TTAAGGAAAGT
41345266 TTAAGGAAAGT
1 TTAAGGAAAGT
41345277 TTA
1 TTA
41345280 GAAACCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (11 bp):
TTAAGGAAAGT
Found at i:41348817 original size:34 final size:33
Alignment explanation
Indices: 41348714--41348823 Score: 130
Period size: 34 Copynumber: 3.3 Consensus size: 33
41348704 TTTAGTGTTA
* *
41348714 TTTTTTAAAAATTAATTAAATTAGGGTTTAAGG
1 TTTTTAAAAAATTAATTAAATTAGGGTTTAATG
* * * *
41348747 GTTTTAAATAAATTAAATAAATTCGGGTTTAGTG
1 TTTTTAAA-AAATTAATTAAATTAGGGTTTAATG
* *
41348781 TTTTTAAGAAAATTAATTAAATTAAGGTTTATTG
1 TTTTTAA-AAAATTAATTAAATTAGGGTTTAATG
41348815 TTTTTAAAA
1 TTTTTAAAA
41348824 TAATATTGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 8 0.12
34 55 0.86
35 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (33 bp):
TTTTTAAAAAATTAATTAAATTAGGGTTTAATG
Found at i:41349043 original size:125 final size:126
Alignment explanation
Indices: 41348884--41349151 Score: 353
Period size: 125 Copynumber: 2.1 Consensus size: 126
41348874 GATTTTGTTT
* * *
41348884 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAATATGATTT-TGAACAAATAGTGTGAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACG-TTTCTGAACAAATAGTGTCAAA
* * *
41348948 AATGCTTCAAGCAGGATGCACTGTTAGC-AAATT-ACTGAAAAAAGCTCCCATGTAGATACTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTAGATACTC
* * *
41349009 TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* * * * *
41349074 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGTTCTCACGTTGACACTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGATACTC
**
41349135 GATTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
41349152 ATGTTTTGCC
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
124 3 0.02
125 79 0.64
126 40 0.33
127 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGATACTC
Found at i:41352269 original size:24 final size:23
Alignment explanation
Indices: 41352213--41352269 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
41352203 AAGAACTTAT
*
41352213 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
41352236 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
41352261 ACTTTTATT
1 A-TTTTATT
41352270 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:41352439 original size:21 final size:21
Alignment explanation
Indices: 41352414--41352453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41352404 TCAGCTTCTG
*
41352414 GCAAGGGCTGTGGTTGCTCTA
1 GCAAGGGCTGTGATTGCTCTA
*
41352435 GCAAGGGTTGTGATTGCTC
1 GCAAGGGCTGTGATTGCTC
41352454 CGGTTGTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.38, T:0.30
Consensus pattern (21 bp):
GCAAGGGCTGTGATTGCTCTA
Found at i:41352728 original size:18 final size:18
Alignment explanation
Indices: 41352707--41352742 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41352697 AAAAGGAAAT
*
41352707 ATATAAGGGTTAGGATAC
1 ATATAAGGGCTAGGATAC
41352725 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
41352743 GCACCTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:41354526 original size:30 final size:30
Alignment explanation
Indices: 41354492--41354556 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
41354482 ATTAATTAAA
*
41354492 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGCTTTAAGAAATTTAAGGAGAAATTT
*
41354522 GAGAGCTTTAAGAAATTTAGGGAGAAATTT
1 GAGAGCTTTAAGAAATTTAAGGAGAAATTT
41354552 GAGAG
1 GAGAG
41354557 TTTTTTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.28
Consensus pattern (30 bp):
GAGAGCTTTAAGAAATTTAAGGAGAAATTT
Found at i:41361937 original size:51 final size:51
Alignment explanation
Indices: 41361814--41361949 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 51
41361804 AGTGAAAATG
* *
41361814 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACTAGAATGAT
* * * * * * *
41361865 A-GATCGCATGTGTAGTACTATGTATAGGTTACTACGTGTA-TCGGATGGT
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACTAGAATGAT
41361914 AATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
41361950 TGTGAACCGA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 6 0.09
50 34 0.49
51 30 0.43
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACTAGAATGAT
Found at i:41371187 original size:16 final size:16
Alignment explanation
Indices: 41371166--41371198 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41371156 GAGATCGTGA
*
41371166 AACTTCATGGGGTTCC
1 AACTTCATAGGGTTCC
41371182 AACTTCATAGGGTTCC
1 AACTTCATAGGGTTCC
41371198 A
1 A
41371199 GTCTCGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (16 bp):
AACTTCATAGGGTTCC
Found at i:41377521 original size:22 final size:20
Alignment explanation
Indices: 41377471--41377523 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
41377461 CCAACATGTT
*
41377471 CATATTTCATCACATCATAAT
1 CATATTT-ATCACATCATAAA
* *
41377492 CCTCTTTATCACCATTCATAAA
1 CATATTTATCA-CA-TCATAAA
41377514 CATATTTATC
1 CATATTTATC
41377524 TCATATTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 7 0.28
22 14 0.56
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (20 bp):
CATATTTATCACATCATAAA
Found at i:41381332 original size:19 final size:17
Alignment explanation
Indices: 41381305--41381348 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
41381295 ATAAAAGGTT
*
41381305 AAAAGTTAAATTTAACTAA
1 AAAAATTAAA-TTAAC-AA
*
41381324 AAAAATTAAATTGACAA
1 AAAAATTAAATTAACAA
41381341 AAAAATTA
1 AAAAATTA
41381349 TAACATTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
19 9 0.39
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAAATTAAATTAACAA
Found at i:41383956 original size:28 final size:28
Alignment explanation
Indices: 41383920--41383979 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
41383910 GGGGGGAAGT
* *
41383920 AAAAGTTTTGCGTGAAAGCAAAAGGAAA
1 AAAACTTTTGCGAGAAAGCAAAAGGAAA
* *
41383948 AAAACTTTTGGGAGAAAGTAAAAGGAAA
1 AAAACTTTTGCGAGAAAGCAAAAGGAAA
41383976 AAAA
1 AAAA
41383980 AATTTGTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (28 bp):
AAAACTTTTGCGAGAAAGCAAAAGGAAA
Found at i:41384033 original size:83 final size:85
Alignment explanation
Indices: 41383887--41384042 Score: 201
Period size: 83 Copynumber: 1.8 Consensus size: 85
41383877 ACATAAATTC
* * * *
41383887 AAAAAAAAATGTTTTTGGAGTTTGGGGGGAAGTAAAAGTTTTGCGTGAAAGCAAAAGGAAAAAAA
1 AAAAAAAAA-GTTTGTGGAGTTTGGAGGGAAGTAAAAGTTTTGCGAGAAAACAAAAGGAAAAAAA
41383952 CTTTTGGGAGAAAGTAAAAGG
65 CTTTTGGGAGAAAGTAAAAGG
* * *
41383973 AAAAAAAAA-TTTGTGG-GTTTGGAGGGAAGTAACAGTTTTGGGGAGAAAATAAAAGG-AAAAAA
1 AAAAAAAAAGTTTGTGGAGTTTGGAGGGAAGTAAAAGTTTT-GCGAGAAAACAAAAGGAAAAAAA
*
41384035 GTTTTGGG
65 CTTTTGGG
41384043 GGAACTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
83 34 0.56
84 18 0.30
86 9 0.15
ACGTcount: A:0.44, C:0.03, G:0.30, T:0.24
Consensus pattern (85 bp):
AAAAAAAAAGTTTGTGGAGTTTGGAGGGAAGTAAAAGTTTTGCGAGAAAACAAAAGGAAAAAAAC
TTTTGGGAGAAAGTAAAAGG
Found at i:41385746 original size:20 final size:21
Alignment explanation
Indices: 41385723--41385773 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
41385713 ACGGGTTTAC
* *
41385723 ACTTCGGTGCCATTGTTTG-T
1 ACTTCGGTGCCACTATTTGCT
*
41385743 ACTTCAGTGCCACTATTTGCT
1 ACTTCGGTGCCACTATTTGCT
41385764 -CTTCGGTGCC
1 ACTTCGGTGCC
41385774 TTGGAGTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (21 bp):
ACTTCGGTGCCACTATTTGCT
Found at i:41389524 original size:40 final size:39
Alignment explanation
Indices: 41389487--41389664 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 39
41389477 ATATCCGGAC
41389487 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* * *
41389527 TAAGCCTCGAAGGCCTTTGTGTGAGATACTAAATCCGGGT
1 TAAGTC-CGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
41389567 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * * *
41389607 TATGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
41389646 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
41389665 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:41389577 original size:80 final size:79
Alignment explanation
Indices: 41389440--41389664 Score: 224
Period size: 80 Copynumber: 2.8 Consensus size: 79
41389430 TTGAATGCTG
* * * * * * *
41389440 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAG-TGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTG-TGAGAT-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
41389503 TTGTGCGAGATA-CAAA
63 TTGTGCGAGATATCAAA
* * *
41389519 TTCCGGGTTAAG-CCTCGAAGGCCTTTGTGTGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 -TCCGGGTTAAGTCC-CGAAGG-CATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCAT
* * *
41389583 TCGTGCGAGTTATTAAA
63 TTGTGCGAGATATCAAA
* * *
41389600 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
41389665 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
79 42 0.34
80 68 0.55
81 13 0.11
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:41389661 original size:79 final size:80
Alignment explanation
Indices: 41389493--41389662 Score: 220
Period size: 79 Copynumber: 2.1 Consensus size: 80
41389483 GGACTAAGAT
* *
41389493 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCTCGAAGGCCTTTGTGTGAGATACTA
1 CCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCTCGAAGGCCATTGTGTGAGATACTA
* *
41389558 AATCCGGGTTAAGTC
66 AAACCGGGCTAAGTC
* * * *
41389573 CCGAAGGCATTCGTGCGAGTTATTAAA-TCCGGGTTATGTCC-CGAAGG-CATTGTGTGAGTTAC
1 CCGAAGGCATTCGTGCGAGATA-CAAATTCCGGGTTAAG-CCTCGAAGGCCATTGTGTGAGATAC
*
41389635 TAAAACCGGGCTATGTC
64 TAAAACCGGGCTAAGTC
41389652 CCGAAGGCATT
1 CCGAAGGCATT
41389663 TGAACGAGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
79 38 0.48
80 36 0.46
81 5 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCTCGAAGGCCATTGTGTGAGATACTA
AAACCGGGCTAAGTC
Found at i:41389682 original size:79 final size:80
Alignment explanation
Indices: 41389520--41389697 Score: 193
Period size: 79 Copynumber: 2.2 Consensus size: 80
41389510 AGATACAAAT
* * *
41389520 TCCGGGTTAAG-CCTCGAAGGCCTTTGTGTGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCC-CGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
** * *
41389584 CGTGCGAGTTATTAAA
65 CGAACGAGTGACTAAA
* * * *
41389600 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
41389664 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
41389679 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41389698 TACGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 15 0.18
79 49 0.60
80 16 0.20
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGTGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:41397450 original size:39 final size:39
Alignment explanation
Indices: 41397277--41397498 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
41397267 TTGAATGCTG
* * * * * *
41397277 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** *
41397317 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
* * *
41397356 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
41397397 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-TTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * *
41397436 TCTGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
41397475 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41397499 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 22, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
38 5 0.03
39 61 0.40
40 75 0.49
41 11 0.07
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:41412380 original size:39 final size:39
Alignment explanation
Indices: 41412286--41412442 Score: 130
Period size: 38 Copynumber: 4.1 Consensus size: 39
41412276 TGATCTAAAC
* * *
41412286 TAAAGACATGTATTAAAGATGTCTAAACTAGGACAT-AT
1 TAAAAACATATATTAAAGATGTCTAAACTATGACATAAT
*
41412324 TTAAAACATATATTTAAA-ATGTCCTAAACTATGACATAAT
1 TAAAAACATATA-TTAAAGATGT-CTAAACTATGACATAAT
* *
41412364 TAAAAACCCT-TATTAAAGATGT-TCAAATTATGACATAAT
1 TAAAAA-CATATATTAAAGATGTCT-AAACTATGACATAAT
* * *
41412403 T-AAAAC-TCATATTAATGATGT-TCAAATTGTGACATAAT
1 TAAAAACAT-ATATTAAAGATGTCT-AAACTATGACATAAT
41412441 TA
1 TA
41412443 TAGACTTAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 46 0.46
39 38 0.38
40 13 0.13
41 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (39 bp):
TAAAAACATATATTAAAGATGTCTAAACTATGACATAAT
Found at i:41412417 original size:38 final size:39
Alignment explanation
Indices: 41412296--41412442 Score: 151
Period size: 39 Copynumber: 3.8 Consensus size: 39
41412286 TAAAGACATG
* *
41412296 TATTAAAGATG-TCTAAACTAGGACATATTTAAAACAT-A
1 TATTAAAGATGTTCTAAACTATGACATAATTAAAAC-TCA
* * *
41412334 TATTTAAA-ATGTCCTAAACTATGACATAATTAAAAACCCT
1 TA-TTAAAGATGTTCTAAACTATGACATAATT-AAAACTCA
*
41412374 TATTAAAGATGTTC-AAATTATGACATAATTAAAACTCA
1 TATTAAAGATGTTCTAAACTATGACATAATTAAAACTCA
* * *
41412412 TATTAATGATGTTC-AAATTGTGACATAATTA
1 TATTAAAGATGTTCTAAACTATGACATAATTA
41412443 TAGACTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
38 40 0.43
39 41 0.44
40 12 0.13
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (39 bp):
TATTAAAGATGTTCTAAACTATGACATAATTAAAACTCA
Found at i:41418164 original size:42 final size:43
Alignment explanation
Indices: 41418110--41418332 Score: 297
Period size: 42 Copynumber: 5.2 Consensus size: 43
41418100 GTGAAAAAGT
* * *
41418110 GCCGCTATAGAACATGACCTTTAGCGGCGCTTCTAT-AAAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* *
41418152 GCCGCTAAAGAACATAACCTTTAGCGGTGCTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* *
41418195 GCCGCTAAAGAGCATGACC-TTAGCGGTGCTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
*
41418237 GCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* * * * * *
41418280 ACCTCTAAAGAACATGATCTTTAGTGGCTCTTTTTATCACAAAT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTTATCACAAAC
41418324 GCCGCTAAA
1 GCCGCTAAA
41418333 AATGTCGTTC
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
42 74 0.46
43 68 0.42
44 19 0.12
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
Found at i:41418211 original size:85 final size:86
Alignment explanation
Indices: 41418110--41418332 Score: 279
Period size: 85 Copynumber: 2.6 Consensus size: 86
41418100 GTGAAAAAGT
*
41418110 GCCGCTATAGAACATGACCTTTAGCGGCGCTTCTAT-AAAAACGCCGCTAAAGAACATAACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTATCAAAAACGCCGCTAAAGAACATAACCTTT
*
41418174 AGCGGTGCTTTTATCACAAAC
66 AGCGGCGCTTTTATCACAAAC
* * * * * *
41418195 GCCGCTAAAGAGCATGACC-TTAGCGGTGCTTTTATCACAAACGCCGCTAAAGAGCATGACCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTATCAAAAACGCCGCTAAAGAACATAACCTTT
41418259 AGCGGCGCTTTTATCACAAAC
66 AGCGGCGCTTTTATCACAAAC
* * * * * * * *
41418280 ACCTCTAAAGAACATGATCTTTAGTGGCTCTTTTTATCACAAATGCCGCTAAA
1 GCCGCTAAAGAACATGACCTTTAGCGGCGC-TTCTATCAAAAACGCCGCTAAA
41418333 AATGTCGTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
84 14 0.12
85 77 0.65
86 7 0.06
87 21 0.18
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (86 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTCTATCAAAAACGCCGCTAAAGAACATAACCTTT
AGCGGCGCTTTTATCACAAAC
Done.