Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 57 of 335
Found at i:20139430 original size:23 final size:23
Alignment explanation
Indices: 20139411--20139473 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
20139401 TAAAAAATGC
20139411 TAATACAATTACATATAAAATTT
1 TAATACAATTACATATAAAATTT
*
20139434 TAATA-AATATAAAT-TAAAAATTT
1 TAATACAAT-TACATAT-AAAATTT
20139457 TAATACAATTACATATA
1 TAATACAATTACATATA
20139474 TAGGATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATACAATTACATATAAAATTT
Found at i:20139493 original size:46 final size:46
Alignment explanation
Indices: 20139411--20139500 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
20139401 TAAAAAATGC
*
20139411 TAATACAATTACATATAAAATTTTAATAAATATAAATTAAAAATTT
1 TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
* *
20139457 TAATACAATTACATATATAGGATATTAA-ATAT-TAAATTAAAAAT
1 TAATACAATTACATATA-A-AATATTAATAAATATAAATTAAAAAT
20139501 AATATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 29 0.74
47 4 0.10
48 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (46 bp):
TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
Found at i:20140740 original size:7 final size:7
Alignment explanation
Indices: 20140673--20140757 Score: 64
Period size: 7 Copynumber: 12.1 Consensus size: 7
20140663 CCCATAAATA
*
20140673 CTAAACT
1 CTAAACC
20140680 CTAAACC
1 CTAAACC
*
20140687 CTTAACC
1 CTAAACC
*
20140694 CCAAACC
1 CTAAACC
*
20140701 CTTACACC
1 C-TAAACC
* *
20140709 TTAAACT
1 CTAAACC
20140716 CT-AACC
1 CTAAACC
*
20140722 CTAACCC
1 CTAAACC
20140729 CTAAACC
1 CTAAACC
*
20140736 CTAAATC
1 CTAAACC
* *
20140743 ATAATCC
1 CTAAACC
20140750 CTAAACC
1 CTAAACC
20140757 C
1 C
20140758 ATAATTCATC
Statistics
Matches: 57, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
6 5 0.09
7 48 0.84
8 4 0.07
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:20140826 original size:21 final size:21
Alignment explanation
Indices: 20140800--20140884 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
20140790 ACTCCTAAAC
*
20140800 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
** * *
20140821 CTTAAAATATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
20140846 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
20140867 CTTAAATCATAAACCATA
1 CTTAAACCATAAACCATA
20140885 AACTATAATG
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
21 29 0.60
22 3 0.06
24 3 0.06
25 13 0.27
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:20140837 original size:46 final size:47
Alignment explanation
Indices: 20140778--20140872 Score: 174
Period size: 46 Copynumber: 2.0 Consensus size: 47
20140768 ATAAACCTTC
*
20140778 AAATACTAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTA
1 AAATACTAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTA
20140825 AAATA-TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTA
1 AAATACTAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTA
20140871 AA
1 AA
20140873 TCATAAACCA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 42 0.89
47 5 0.11
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.29
Consensus pattern (47 bp):
AAATACTAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTA
Found at i:20141095 original size:41 final size:41
Alignment explanation
Indices: 20141049--20141330 Score: 406
Period size: 41 Copynumber: 6.9 Consensus size: 41
20141039 TTATATGACT
*
20141049 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
* * *
20141090 TTTAGC-G-GTTTTTACAAAAGCGCTGCTAATGCTCCGGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
* *
20141129 TTTAGCGGCGTTTTTACAAAAGCGCCGCTAATGCTCTTGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
* * * *
20141170 TTTAGCGGCGTTTTGCCATAAGTGCCGCTAATGCTCTTGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
* *
20141211 TTTAGTGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
*
20141252 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
* * *
20141293 ATTAGCGGCGCTTTTCCAAAAGCGTCGCTAATGCTCTG
1 TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTG
20141331 TGTTTTACAA
Statistics
Matches: 218, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
39 34 0.16
40 2 0.01
41 182 0.83
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:20151815 original size:15 final size:15
Alignment explanation
Indices: 20151797--20151835 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20151787 TTATATAATC
*
20151797 AATATATTTATATTA
1 AATATATTTAAATTA
*
20151812 AATATATTAAAATTA
1 AATATATTTAAATTA
*
20151827 AATAAATTT
1 AATATATTT
20151836 TTAGTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTTAAATTA
Found at i:20158572 original size:13 final size:12
Alignment explanation
Indices: 20158550--20158585 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
20158540 GTTCAGCCCG
20158550 TATTAATTTTTTA
1 TATT-ATTTTTTA
20158563 TATTATTTTTTA
1 TATTATTTTTTA
*
20158575 TATAATTTTTT
1 TATTATTTTTT
20158586 TAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:20160095 original size:52 final size:50
Alignment explanation
Indices: 20159997--20160095 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 50
20159987 TGAAGTAAAC
* * * * *
20159997 AAGAAAACAAGAAAGCTTTGAGTAAATTTTCTAAGGTCGCATGGTTAATT
1 AAGAAAACAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTAATT
*
20160047 AAGAAAACTCAAGAAATCTTTGAGTAAACTCTCTAAGGCCACACGGTTA
1 AAGAAAA--CAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTA
20160096 GTTCGACTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.17
52 34 0.83
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (50 bp):
AAGAAAACAAGAAAGCTTTGAGTAAACTCTCTAAGGCCACACGGTTAATT
Found at i:20161060 original size:10 final size:9
Alignment explanation
Indices: 20161031--20161249 Score: 58
Period size: 10 Copynumber: 23.2 Consensus size: 9
20161021 TAAATTTTTT
*
20161031 TATTAACAA
1 TATTAAAAA
*
20161040 TCATAAAAAA
1 T-ATTAAAAA
20161050 TACTTAAAAA
1 TA-TTAAAAA
20161060 TATATAAAAA
1 TAT-TAAAAA
20161070 TTATTAAAAA
1 -TATTAAAAA
* *
20161080 -ATT-AGAT
1 TATTAAAAA
*
20161087 TAATAAAAA
1 TATTAAAAA
*
20161096 -ATTAAATA
1 TATTAAAAA
20161104 T-TGTAAAAA
1 TAT-TAAAAA
* *
20161113 AATTAAATA
1 TATTAAAAA
* *
20161122 TTTTAAATAT
1 TATTAAA-AA
*
20161132 TATTAAATAT
1 TATTAAA-AA
*
20161142 TGTTAAAAA
1 TATTAAAAA
*
20161151 TATTTTAAAAG
1 TA--TTAAAAA
*
20161162 T-GTAAAAA
1 TATTAAAAA
20161170 GTTATTAAAAA
1 --TATTAAAAA
20161181 T-TATAAAACA
1 TAT-TAAAA-A
*
20161191 TTATTTAAAAG
1 -TA-TTAAAAA
*
20161202 TTTTAAAAAA
1 TATT-AAAAA
20161212 TATTAAAAA
1 TATTAAAAA
*
20161221 T-TGTGAAAAT
1 TAT-T-AAAAA
20161231 TATTAAAAA
1 TATTAAAAA
*
20161240 -ATTATAAA
1 TATTAAAAA
20161248 TA
1 TA
20161250 ATTATTCAAG
Statistics
Matches: 153, Mismatches: 32, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
7 2 0.01
8 26 0.17
9 42 0.27
10 59 0.39
11 18 0.12
12 5 0.03
13 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (9 bp):
TATTAAAAA
Found at i:20161093 original size:16 final size:16
Alignment explanation
Indices: 20161069--20161099 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20161059 ATATATAAAA
*
20161069 ATTATTAAAAAATTAG
1 ATTAATAAAAAATTAG
20161085 ATTAATAAAAAATTA
1 ATTAATAAAAAATTA
20161100 AATATTGTAA
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:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTAATAAAAAATTAG
Found at i:20161112 original size:18 final size:18
Alignment explanation
Indices: 20161091--20161150 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
20161081 TTAGATTAAT
20161091 AAAAAATTAAATATTGTA
1 AAAAAATTAAATATTGTA
*
20161109 AAAAAATTAAATATTTTA
1 AAAAAATTAAATATTGTA
** *
20161127 AATATTATTAAATATTGTT
1 AA-AAAATTAAATATTGTA
20161146 AAAAA
1 AAAAA
20161151 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAAATTAAATATTGTA
Found at i:20161154 original size:19 final size:19
Alignment explanation
Indices: 20161090--20161154 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
20161080 ATTAGATTAA
20161090 TAAAAA-ATTAAATATTG-
1 TAAAAATATTAAATATTGT
*
20161107 TAAAAAAATTAAATATT-T
1 TAAAAATATTAAATATTGT
*
20161125 TAAATATTATTAAATATTGT
1 TAAA-AATATTAAATATTGT
20161145 TAAAAATATT
1 TAAAAATATT
20161155 TTAAAAGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.15
18 14 0.34
19 16 0.39
20 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAAATATTAAATATTGT
Found at i:20161200 original size:21 final size:20
Alignment explanation
Indices: 20161042--20161273 Score: 102
Period size: 20 Copynumber: 11.6 Consensus size: 20
20161032 ATTAACAATC
* *
20161042 ATAAAAAATACTTAAAAATAT
1 ATAAAAATTATTTAAAAAT-T
*
20161063 ATAAAAATTATTAAAAAATT
1 ATAAAAATTATTTAAAAATT
* * *
20161083 AGATTAATAAA-AAATTAAATATT
1 --A-TAA-AAATTATTTAAAAATT
* * *
20161106 GTAAAAA--AATTAAATATT
1 ATAAAAATTATTTAAAAATT
* * *
20161124 TTAAATATTA-TTAAATATT
1 ATAAAAATTATTTAAAAATT
* * *
20161143 GTTAAAAA-TATTTTAAAAGT
1 -ATAAAAATTATTTAAAAATT
*
20161163 GTAAAAAGTTA-TTAAAAATT
1 ATAAAAA-TTATTTAAAAATT
*
20161183 ATAAAACATTATTTAAAAGTT
1 ATAAAA-ATTATTTAAAAATT
* *
20161204 TTAAAAAATA-TTAAAAATT
1 ATAAAAATTATTTAAAAATT
* * *
20161223 GTGAAAATTATTAAAAAATT
1 ATAAAAATTATTTAAAAATT
* *
20161243 ATAAATAATTA-TTCAAGATT
1 ATAAA-AATTATTTAAAAATT
*
20161263 GTAAAAATTAT
1 ATAAAAATTAT
20161274 GAACCAGTGG
Statistics
Matches: 164, Mismatches: 32, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
18 16 0.10
19 40 0.24
20 56 0.34
21 37 0.23
22 1 0.01
23 11 0.07
24 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (20 bp):
ATAAAAATTATTTAAAAATT
Found at i:20161208 original size:30 final size:29
Alignment explanation
Indices: 20161166--20161273 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 29
20161156 TAAAAGTGTA
*
20161166 AAAAGTTATTAAAAATTATAAAACATTATTT
1 AAAA-TTATTAAAAATTATAAAA-ATTATTC
* * *
20161197 AAAAGTT-TTAAAAAATATTAAAAATT-GTG
1 AAAA-TTATTAAAAATTA-TAAAAATTATTC
20161226 AAAATTATTAAAAAATTATAAATAATTATTC
1 AAAATTATT-AAAAATTATAAA-AATTATTC
* *
20161257 AAGATT-GTAAAAATTAT
1 AAAATTATTAAAAATTAT
20161274 GAACCAGTGG
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.03
29 20 0.31
30 24 0.38
31 18 0.28
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATTATTAAAAATTATAAAAATTATTC
Found at i:20161252 original size:10 final size:10
Alignment explanation
Indices: 20161164--20161254 Score: 60
Period size: 10 Copynumber: 9.1 Consensus size: 10
20161154 TTTAAAAGTG
*
20161164 TAAAAAGTTA
1 TAAAAAATTA
*
20161174 TTAAAAATTA
1 TAAAAAATTA
*
20161184 TAAAACATTA
1 TAAAAAATTA
* * *
20161194 TTTAAAAGTTT
1 -TAAAAAATTA
20161205 TAAAAAA-TA
1 TAAAAAATTA
* *
20161214 TTAAAAATTG
1 TAAAAAATTA
*
20161224 T-GAAAATTA
1 TAAAAAATTA
20161233 TTAAAAAATTA
1 -TAAAAAATTA
*
20161244 TAAATAATTA
1 TAAAAAATTA
20161254 T
1 T
20161255 TCAAGATTGT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
9 13 0.22
10 34 0.57
11 13 0.22
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:20161271 original size:40 final size:40
Alignment explanation
Indices: 20161053--20161273 Score: 148
Period size: 40 Copynumber: 5.5 Consensus size: 40
20161043 TAAAAAATAC
* * **
20161053 TTAAAAATATATAAAAATTATTAAAAAATTAGATTAATAAAAAA
1 TTAAAAAT-TGTAAAAATTATTAAAAAATT--ATAAAT-AATTA
* * * *
20161097 TTAAATATTGTAAAAA-AATT-AAATATTTTAAAT-ATTA
1 TTAAAAATTGTAAAAATTATTAAAAAATTATAAATAATTA
* ** * *
20161134 TTAAATATTGTTAAAAA-TATTTTAAAAGTGTAAA-AAGTTA
1 TTAAAAATTG-TAAAAATTATTAAAAAATTATAAATAA-TTA
* * * * *
20161174 TTAAAAATTATAAAACATTATTTAAAAGTTTTAAA-AAATA
1 TTAAAAATTGTAAAA-ATTATTAAAAAATTATAAATAATTA
*
20161214 TTAAAAATTGTGAAAATTATTAAAAAATTATAAATAATTA
1 TTAAAAATTGTAAAAATTATTAAAAAATTATAAATAATTA
* *
20161254 TTCAAGATTGTAAAAATTAT
1 TTAAAAATTGTAAAAATTAT
20161274 GAACCAGTGG
Statistics
Matches: 141, Mismatches: 29, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
37 12 0.09
38 9 0.06
39 34 0.24
40 48 0.34
41 21 0.15
42 3 0.02
43 7 0.05
44 7 0.05
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (40 bp):
TTAAAAATTGTAAAAATTATTAAAAAATTATAAATAATTA
Found at i:20161494 original size:22 final size:21
Alignment explanation
Indices: 20161468--20161565 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
20161458 TTGTTAACTA
20161468 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
20161490 TTTACGATTTTTAATAA-T-T
1 TTTACAATTTTTAATAATTAT
* ** * *
20161509 TTTAAAAAATTAAATAA-TGT
1 TTTACAATTTTTAATAATTAT
* * *
20161529 TTTATAACTTTTAATAATTTT
1 TTTACAATTTTTAATAATTAT
* *
20161550 TTTAAAATTTTAAATA
1 TTTACAATTTTTAATA
20161566 TTTTAAAAAG
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
19 14 0.23
20 15 0.25
21 25 0.42
22 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:20161511 original size:10 final size:10
Alignment explanation
Indices: 20161476--20161550 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
20161466 TATTTACAAT
20161476 TTTTTAATAA
1 TTTTTAATAA
* **
20161486 TTATTTTACGA
1 TT-TTTAATAA
20161497 TTTTTAATAA
1 TTTTTAATAA
20161507 TTTTTAA-AA
1 TTTTTAATAA
** *
20161516 AATTAAATAA
1 TTTTTAATAA
20161526 TGTTTT-ATAA
1 T-TTTTAATAA
*
20161536 CTTTTAATAA
1 TTTTTAATAA
20161546 TTTTT
1 TTTTT
20161551 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
9 10 0.21
10 28 0.60
11 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:20161544 original size:20 final size:19
Alignment explanation
Indices: 20161498--20161588 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
20161488 ATTTTACGAT
20161498 TTTTAATAATTTTTAAAAA
1 TTTTAATAATTTTTAAAAA
* * * *
20161517 ATTAAATAATGTTTTATAAC
1 TTTTAATAAT-TTTTAAAAA
*
20161537 TTTTAATAATTTTTTTAAAA
1 TTTTAATAA-TTTTTAAAAA
*
20161557 TTTTAA-ATATTTTAAAAAGA
1 TTTTAATA-ATTTTTAAAA-A
20161577 TATTTAATAATT
1 T-TTTAATAATT
20161589 ATTACAATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
19 16 0.29
20 29 0.53
21 9 0.16
22 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTTAAAAA
Found at i:20174770 original size:2 final size:2
Alignment explanation
Indices: 20174763--20174799 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20174753 TAAATGTGTA
20174763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20174800 AACTATAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20177247 original size:16 final size:15
Alignment explanation
Indices: 20177221--20177280 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
20177211 GAGCAAAGGT
20177221 AAATATAATATTATAAA
1 AAAT-TAATATTA-AAA
20177238 AAATTAATA-TAAATA
1 AAATTAATATTAAA-A
*
20177253 AAATTAACATTAAAA
1 AAATTAATATTAAAA
20177268 TAAATTAAT-TTAA
1 -AAATTAATATTAA
20177281 CAATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 16 0.42
16 16 0.42
17 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTAATATTAAAA
Found at i:20177264 original size:21 final size:21
Alignment explanation
Indices: 20177240--20177297 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
20177230 ATTATAAAAA
20177240 ATTAATATAAATAAAATTAAC
1 ATTAATATAAATAAAATTAAC
* * *
20177261 ATTAAAATAAATTAATTTAAC
1 ATTAATATAAATAAAATTAAC
*
20177282 AATATATAATAAATAA
1 ATTA-AT-ATAAATAA
20177298 CTTATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 21 0.72
22 1 0.03
23 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTAATATAAATAAAATTAAC
Found at i:20177314 original size:23 final size:23
Alignment explanation
Indices: 20177266--20177327 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
20177256 TTAACATTAA
*
20177266 AATAAATTAATTTAACAATATAT
1 AATAAATTAATTTAAAAATATAT
20177289 AATAAA-TAACTTATAAAAATAT-T
1 AATAAATTAA-TT-TAAAAATATAT
20177312 AATAACATT-ATTTAAA
1 AATAA-ATTAATTTAAA
20177328 TTACAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 7 0.21
23 16 0.47
24 10 0.29
25 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAATTAATTTAAAAATATAT
Found at i:20183628 original size:11 final size:11
Alignment explanation
Indices: 20183614--20183647 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20183604 TGAAAAGTTC
20183614 AAAAAAA-AAA
1 AAAAAAAGAAA
20183624 AAAAAAAGAAA
1 AAAAAAAGAAA
*
20183635 AGAAAAAGAAA
1 AAAAAAAGAAA
20183646 AA
1 AA
20183648 GGAACATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:20184860 original size:19 final size:20
Alignment explanation
Indices: 20184824--20184862 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20184814 ACGATTAATA
*
20184824 ATAATTTTTTTCGGTACAATC
1 ATAATTTTTTTC-ATACAATC
20184845 ATAATTTTTTT-ATACAAT
1 ATAATTTTTTTCATACAAT
20184863 TATCAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
ATAATTTTTTTCATACAATC
Found at i:20194440 original size:13 final size:13
Alignment explanation
Indices: 20194422--20194448 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20194412 ACAAATATCA
20194422 TACTTGTTTTGAG
1 TACTTGTTTTGAG
20194435 TACTTGTTTTGAG
1 TACTTGTTTTGAG
20194448 T
1 T
20194449 GTCTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TACTTGTTTTGAG
Found at i:20206738 original size:10 final size:11
Alignment explanation
Indices: 20206705--20206738 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20206695 TGATTAATCA
*
20206705 TTTTTAAATAC
1 TTTTTAAATAT
20206716 TTTTTAAATAT
1 TTTTTAAATAT
20206727 TTTTTAAA-AT
1 TTTTTAAATAT
20206737 TT
1 TT
20206739 AATAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:20216644 original size:20 final size:20
Alignment explanation
Indices: 20216616--20216654 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20216606 CGACCACGAG
20216616 CCTACCCACACGGGCGTGTC
1 CCTACCCACACGGGCGTGTC
*
20216636 CCTATCCACACGGGCGTGT
1 CCTACCCACACGGGCGTGT
20216655 GGCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACACGGGCGTGTC
Found at i:20218552 original size:42 final size:42
Alignment explanation
Indices: 20218486--20218612 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
20218476 CTTCGTTTTC
* * *
20218486 TCGATGCCATAGTCCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* *
20218529 T-GATGTCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
20218570 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
20218611 TC
1 TC
20218613 TCACTGATGT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:20218681 original size:47 final size:47
Alignment explanation
Indices: 20218571--20218697 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 47
20218561 ATTCATATAT
* * * * *
20218571 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC
* * * *
20218617 TGATGTCATATCCCAGATATGGTCTTATACAGCAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC
*
20218664 CGATGCCATATCTCAGATATGGTCTTATACAGAA
1 CGATGCCATATCCCAGATATGGTCTTATACAGAA
20218698 ATCACTTGTC
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
46 25 0.37
47 42 0.63
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC
Found at i:20218747 original size:31 final size:31
Alignment explanation
Indices: 20218712--20218860 Score: 190
Period size: 31 Copynumber: 4.8 Consensus size: 31
20218702 CTTGTCACTT
* *
20218712 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * * *
20218743 GTAGCCGGAGTTATCATTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
20218774 GTAGCCGGAGCTACCACTTTTCACTGATCTG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
20218805 GTAGCAGAAGTTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
20218836 GTAGCCGAAGCTATCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
20218861 TGTCATTTGT
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:20218942 original size:50 final size:50
Alignment explanation
Indices: 20218836--20219012 Score: 300
Period size: 50 Copynumber: 3.5 Consensus size: 50
20218826 CACTGATCAG
*
20218836 GTAGCCGAAGCTATCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
20218887 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTTATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
20218937 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
20218987 GTAGCCGAAGCTATTACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
20219013 GTTGCCATGG
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 95 0.79
51 25 0.21
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:20219515 original size:21 final size:22
Alignment explanation
Indices: 20219488--20219544 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
20219478 ATATATTAAA
20219488 TTATTATTATTATTTATTATAG
1 TTATTATTATTATTTATTATAG
* *
20219510 TT-TTA-TATTTAATTATTATTG
1 TTATTATTA-TTATTTATTATAG
*
20219531 TTATTGTTATTATT
1 TTATTATTATTATT
20219545 ATTTAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 8 0.29
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTTATTATAG
Found at i:20219740 original size:15 final size:15
Alignment explanation
Indices: 20219720--20219748 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20219710 GAAATAAAGG
20219720 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
20219735 AAAGAAACAGAATG
1 AAAGAAACAGAATG
20219749 TGGAAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:20219759 original size:18 final size:15
Alignment explanation
Indices: 20219718--20219763 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
20219708 AGGAAATAAA
20219718 GGAAAGAAACAGAAT
1 GGAAAGAAACAGAAT
*
20219733 GAAAAGAAACAGAATGT
1 GGAAAGAAACAGAA--T
20219750 GGAAACGAAACAGA
1 GGAAA-GAAACAGA
20219764 GAAGAAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.59, C:0.09, G:0.26, T:0.07
Consensus pattern (15 bp):
GGAAAGAAACAGAAT
Found at i:20220183 original size:23 final size:21
Alignment explanation
Indices: 20220136--20220176 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
20220126 TTTGGTTAAA
20220136 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
20220158 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
20220177 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:20220554 original size:15 final size:15
Alignment explanation
Indices: 20220506--20220555 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
20220496 TTTATTAAAT
20220506 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
20220521 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
20220536 TTATATTGATTGAAA
1 TTATATTGATTGAAA
20220551 TTATA
1 TTATA
20220556 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:20220570 original size:13 final size:13
Alignment explanation
Indices: 20220552--20220578 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20220542 TGATTGAAAT
20220552 TATAATATATATA
1 TATAATATATATA
20220565 TATAATATATATA
1 TATAATATATATA
20220578 T
1 T
20220579 GATTTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATATATATA
Found at i:20221091 original size:23 final size:23
Alignment explanation
Indices: 20221063--20221172 Score: 157
Period size: 23 Copynumber: 4.5 Consensus size: 23
20221053 TAATATTCCG
20221063 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
20221086 GGTGTGTTTGGGTTGAATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
20221109 GGTGTGTTTGGGTTTGGGTTGGATATTCT
1 -G-GTG--T--GTTTGGGTTGGATATTCT
20221138 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
20221161 GGTGTGTTTGGG
1 GGTGTGTTTGGG
20221173 AGGAATTGTC
Statistics
Matches: 79, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
23 52 0.66
24 1 0.01
25 4 0.05
27 4 0.05
28 1 0.01
29 17 0.22
ACGTcount: A:0.08, C:0.04, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:20221134 original size:52 final size:52
Alignment explanation
Indices: 20221068--20221172 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
20221058 TTCCGGGTGT
20221068 GTTTGGGTTGGATATTCTGGTGTGTTTGGGTTGAATATTCTGGTGTGTTTGG
1 GTTTGGGTTGGATATTCTGGTGTGTTTGGGTTGAATATTCTGGTGTGTTTGG
*
20221120 GTTTGGGTTGGATATTCTGGTGTGTTTGGGTTGGATATTCTGGTGTGTTTGG
1 GTTTGGGTTGGATATTCTGGTGTGTTTGGGTTGAATATTCTGGTGTGTTTGG
20221172 G
1 G
20221173 AGGAATTGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.09, C:0.04, G:0.40, T:0.48
Consensus pattern (52 bp):
GTTTGGGTTGGATATTCTGGTGTGTTTGGGTTGAATATTCTGGTGTGTTTGG
Found at i:20221298 original size:18 final size:19
Alignment explanation
Indices: 20221277--20221317 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20221267 AATGAAATGA
20221277 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
20221295 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
20221314 GAAA
1 GAAA
20221318 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:20221426 original size:17 final size:17
Alignment explanation
Indices: 20221404--20221436 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20221394 TATTGTTAAG
20221404 AAGTAAAGTGTGAATAC
1 AAGTAAAGTGTGAATAC
*
20221421 AAGTAAATTGTGAATA
1 AAGTAAAGTGTGAATA
20221437 TATTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (17 bp):
AAGTAAAGTGTGAATAC
Found at i:20222962 original size:31 final size:31
Alignment explanation
Indices: 20222925--20223004 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
20222915 CTTGTCACTT
*
20222925 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAG
* * * *
20222956 GTAGCCGGAGCTACCATTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAG
20222987 GTAGCCGAAGCTACCACT
1 GTAGCCGAAGCTACCACT
20223005 TTTTACTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAG
Found at i:20223080 original size:50 final size:50
Alignment explanation
Indices: 20222987--20223263 Score: 473
Period size: 50 Copynumber: 5.5 Consensus size: 50
20222977 CATTGATCAG
* * *
20222987 GTAGCCGAAGCTACCACTTTTTACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
20223038 GTAGCTGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
20223088 GTAGTCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
20223138 GTTGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
20223188 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
20223238 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
20223264 GTTGCCATGG
Statistics
Matches: 215, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
50 193 0.90
51 22 0.10
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:20227498 original size:17 final size:17
Alignment explanation
Indices: 20227476--20227509 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20227466 ATTTTATATA
20227476 TATTAAATATTA-ATTAT
1 TATT-AATATTATATTAT
20227493 TATTAATATTATATTAT
1 TATTAATATTATATTAT
20227510 GAAATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAATATTATATTAT
Found at i:20227507 original size:14 final size:15
Alignment explanation
Indices: 20227469--20227515 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
20227459 TTCTTAGATT
20227469 TTATATATATTAAATA
1 TTATAT-TATTAAATA
20227485 TTA-ATTATTATTAATA
1 TTATATTATTA--AATA
*
20227501 TTATATTATGAAATA
1 TTATATTATTAAATA
20227516 AATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 10 0.37
17 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTATATTATTAAATA
Found at i:20233124 original size:40 final size:40
Alignment explanation
Indices: 20233078--20233163 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
20233068 AATTCATTAC
* * *
20233078 TTCAGTAATTTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
* **
20233118 TTCAGTAACTTCACAATTCAATTCAGTATTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
20233158 TTCAGT
1 TTCAGT
20233164 TCAGTATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.33
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:20233143 original size:21 final size:21
Alignment explanation
Indices: 20233078--20233145 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
20233068 AATTCATTAC
* *
20233078 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
20233099 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
20233118 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
20233139 TTCAGTA
1 TTCAGTA
20233146 TTCAAAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
21 15 0.43
22 5 0.14
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Found at i:20233963 original size:14 final size:13
Alignment explanation
Indices: 20233926--20233977 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
20233916 TTCTTCTTTA
* *
20233926 CTTTGTTTTGTTT
1 CTTTATTTTATTT
20233939 CTTTATTTTATTT
1 CTTTATTTTATTT
*
20233952 CATTTCTTTTATTAT
1 C-TTTATTTTATT-T
20233967 -TTTATTTTATT
1 CTTTATTTTATT
20233978 AACTTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:20234035 original size:2 final size:2
Alignment explanation
Indices: 20234028--20234053 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20234018 TTAATAACAA
20234028 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
20234054 TACAATAGGA
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):
AT
Found at i:20234269 original size:3 final size:3
Alignment explanation
Indices: 20234261--20234336 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
20234251 ATTTTATTTT
* * *
20234261 TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA T-A TAAA TTA TAA T-T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* *
20234304 TAA T-A GAA TAA TAA TAA TAA TGA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
20234337 ATATCTATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 5 0.09
3 48 0.84
4 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:20234289 original size:20 final size:20
Alignment explanation
Indices: 20234264--20234324 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20234254 TTATTTTTAA
20234264 TAATAATAATAATAATAATT
1 TAATAATAATAATAATAATT
*
20234284 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATAATAATT
20234304 TAATAGAATAATAATAATAAT
1 TAAT--AATAATAATAATAAT
20234325 GATAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 20 0.57
22 11 0.31
23 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATAATAATT
Found at i:20234477 original size:25 final size:27
Alignment explanation
Indices: 20234443--20234504 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
20234433 TGGCTTTAAT
*
20234443 TTAATTTAATTCATAATATGATATTTATAA
1 TTAA-TTAATTAATAATAT-AT-TTTATAA
20234473 TTAATTAATTTAATAATATATTTTATAA
1 TTAATTAA-TTAATAATATATTTTATAA
20234501 TTAA
1 TTAA
20234505 ATTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 6 0.20
30 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATTAATTAATAATATATTTTATAA
Found at i:20234515 original size:24 final size:23
Alignment explanation
Indices: 20234474--20234528 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
20234464 TATTTATAAT
* **
20234474 TAATTAATTTAATAATATATTTTA
1 TAATTAAATTAATAATAT-TTACA
20234498 TAATTAAATT-ATATATATTTACA
1 TAATTAAATTAATA-ATATTTACA
20234521 TAATTAAA
1 TAATTAAA
20234529 ATCTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAAATTAATAATATTTACA
Found at i:20235093 original size:20 final size:20
Alignment explanation
Indices: 20235055--20235095 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20235045 AACATTTTTT
* * *
20235055 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
20235075 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
20235095 A
1 A
20235096 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:20235142 original size:71 final size:71
Alignment explanation
Indices: 20234994--20235141 Score: 271
Period size: 71 Copynumber: 2.1 Consensus size: 71
20234984 TTTAAAATAT
* *
20234994 ATTTTTAAAAAATATATTGAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
20235059 TATTTA
66 TATTTA
20235065 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACA-TTTTTAATA
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
20235129 TATTTA
66 TATTTA
20235135 ATTTTTT
1 ATTTTTT
20235142 TTAAGTTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 22 0.29
71 53 0.71
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (71 bp):
ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
TATTTA
Found at i:20256564 original size:4 final size:4
Alignment explanation
Indices: 20256555--20256579 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20256545 GAAGAAGAAG
20256555 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
20256580 CAAATCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:20259851 original size:15 final size:15
Alignment explanation
Indices: 20259831--20259859 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20259821 GACTTCCCCC
20259831 GTTTACCCGAAACGA
1 GTTTACCCGAAACGA
20259846 GTTTACCCGAAACG
1 GTTTACCCGAAACG
20259860 CTTCATTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (15 bp):
GTTTACCCGAAACGA
Found at i:20262642 original size:18 final size:18
Alignment explanation
Indices: 20262612--20262650 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20262602 TTAAAACTTG
20262612 AAAAATGAATAATTA-AA
1 AAAAATGAATAATTATAA
*
20262629 AAAAATTAATTAATTATAA
1 AAAAATGAA-TAATTATAA
20262648 AAA
1 AAA
20262651 GTGTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATGAATAATTATAA
Found at i:20272622 original size:20 final size:20
Alignment explanation
Indices: 20272593--20272660 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
20272583 AAAAATATAT
*
20272593 CAAATTTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
*
20272613 CAAATCTTCATTATCCG-ATTGCA
1 CAAATCTTCATAATCCGCA----A
*
20272636 CCAATCTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
20272656 CAAAT
1 CAAAT
20272661 TGATGCCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 20 0.53
23 16 0.42
24 1 0.03
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (20 bp):
CAAATCTTCATAATCCGCAA
Found at i:20277626 original size:21 final size:22
Alignment explanation
Indices: 20277600--20277641 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20277590 ATCCTAGTCA
20277600 AGATTTAC-TCTT-AACTTTTAC
1 AGATTT-CTTCTTAAACTTTTAC
20277621 AGATTTCTTCTTAAACTTTTA
1 AGATTTCTTCTTAAACTTTTA
20277642 TTCGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (22 bp):
AGATTTCTTCTTAAACTTTTAC
Found at i:20278518 original size:43 final size:43
Alignment explanation
Indices: 20278457--20278543 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
20278447 TTCTGTTCAC
20278457 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
20278500 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
20278543 A
1 A
20278544 ATTACATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.41
Consensus pattern (43 bp):
ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
Found at i:20289344 original size:2 final size:2
Alignment explanation
Indices: 20289337--20289371 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20289327 TACTATACTA
20289337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20289372 AGACATCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20290373 original size:27 final size:25
Alignment explanation
Indices: 20290308--20290374 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
20290298 AATTTATTTT
*
20290308 TATTTATAATGTTAATCATTTAAATA
1 TATTTATAAT-TTAATAATTTAAATA
20290334 TGATTTATTAATTTAATAATTTAAAACTA
1 T-ATTTA-TAATTTAATAATTT-AAA-TA
*
20290363 TATTTACAATTT
1 TATTTATAATTT
20290375 TAACAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 12 0.34
29 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTTATAATTTAATAATTTAAATA
Found at i:20292113 original size:9 final size:11
Alignment explanation
Indices: 20292087--20292115 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20292077 TAATAATTAA
20292087 AATATTTTTTT
1 AATATTTTTTT
20292098 AATATTTTTTT
1 AATATTTTTTT
20292109 AAT-TTTT
1 AATATTTT
20292116 AAGAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:20293734 original size:65 final size:65
Alignment explanation
Indices: 20293625--20293747 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
20293615 TGTATTCTCC
* * * *
20293625 AACTGATCTAGTAGTCCCTCTACTGTTTCTAGGCAATTCTCAGCAATTTCGAGTTCTGCACTCTT
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
* *
20293690 AACTAATCTAATAGTCTCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGGGTTCTG
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTG
20293748 TGCCTTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (65 bp):
AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
Found at i:20302622 original size:31 final size:31
Alignment explanation
Indices: 20302584--20302646 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20302574 TACAGATTGT
20302584 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
20302615 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
20302646 A
1 A
20302647 TAATAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (31 bp):
AAATGGCAAAAGAATTGACCTTCCCTTGAGA
Found at i:20317822 original size:22 final size:23
Alignment explanation
Indices: 20317797--20317842 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20317787 CAACCAATCC
20317797 AATTCA-ACATATTT-TCAAGATA
1 AATTCACACATATTTAT-AAGATA
*
20317819 AATTCACGCATATTTATAAGATA
1 AATTCACACATATTTATAAGATA
20317842 A
1 A
20317843 CCTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (23 bp):
AATTCACACATATTTATAAGATA
Found at i:20321379 original size:18 final size:18
Alignment explanation
Indices: 20321352--20321415 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
20321342 GAACAATTAT
* *
20321352 TTATTTAGTAATAGTCAG
1 TTATTCAGTAATAATCAG
*
20321370 TTATTCAGT-ATCAATCAA
1 TTATTCAGTAAT-AATCAG
* *
20321388 TTATTCAATAACAATCAG
1 TTATTCAGTAATAATCAG
20321406 TTATTCAGTA
1 TTATTCAGTA
20321416 TCAATCAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 2 0.05
18 34 0.92
19 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (18 bp):
TTATTCAGTAATAATCAG
Found at i:20321420 original size:18 final size:18
Alignment explanation
Indices: 20321366--20321422 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
20321356 TTAGTAATAG
20321366 TCAGTTATTCAGTATCAA
1 TCAGTTATTCAGTATCAA
* * *
20321384 TCAATTATTCAATAACAA
1 TCAGTTATTCAGTATCAA
20321402 TCAGTTATTCAGTATCAA
1 TCAGTTATTCAGTATCAA
20321420 TCA
1 TCA
20321423 ATTGATCGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (18 bp):
TCAGTTATTCAGTATCAA
Found at i:20321458 original size:18 final size:18
Alignment explanation
Indices: 20321431--20321505 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
20321421 CAATTGATCG
*
20321431 ATTATCCAGTAACAGTCA
1 ATTATTCAGTAACAGTCA
* *
20321449 ATTATTCAGTAAAAATCA
1 ATTATTCAGTAACAGTCA
* * * * *
20321467 AATATACAATAACAATTAA
1 ATTATTCAGTAAC-AGTCA
20321486 ATTATTCAGTAACAGTCA
1 ATTATTCAGTAACAGTCA
20321504 AT
1 AT
20321506 ATTTCCAGTT
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
18 29 0.69
19 13 0.31
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.31
Consensus pattern (18 bp):
ATTATTCAGTAACAGTCA
Found at i:20323013 original size:47 final size:46
Alignment explanation
Indices: 20322907--20323034 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 46
20322897 TGTAACCCGC
**
20322907 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAAATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAAATGCCTACAT
* * * *
20322953 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCC-ACAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCA-A-ATGCCTACAT
20323001 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
20323035 GGATGCTCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
46 4 0.06
47 53 0.78
48 7 0.10
49 4 0.06
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAAATGCCTACAT
Found at i:20330372 original size:47 final size:49
Alignment explanation
Indices: 20330254--20330433 Score: 209
Period size: 47 Copynumber: 3.8 Consensus size: 49
20330244 TGTAACCCGC
* * * *
20330254 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--A-GGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
20330300 CCATAAGTGAACGCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
*
20330350 -C-TCA-TGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-CACAT
20330394 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
20330434 TCAACCATCC
Statistics
Matches: 113, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.04
45 1 0.01
46 34 0.30
47 59 0.52
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:20330421 original size:94 final size:93
Alignment explanation
Indices: 20330261--20330433 Score: 285
Period size: 94 Copynumber: 1.8 Consensus size: 93
20330251 CGCCCATAAG
* *
20330261 TGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACGCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACGCGGACTCAACTCA
20330326 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
20330354 TGAACTCGGACTCAACTCAACGAGTTC-GGACATTCCACATCCATAAGTGAACTCGGACTCAACT
1 TGAACTCGGACTCAACTCAACGAGCTCAGG-CATT-CACATCCATAAGTGAACGCGGACTCAACT
20330418 CAACGAGTTCGGATGC
64 CAACGAGTTCGGATGC
20330434 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
92 2 0.03
93 29 0.39
94 43 0.58
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACGCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:20331688 original size:6 final size:6
Alignment explanation
Indices: 20331677--20331707 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20331667 ATATTACAAG
20331677 AACAGT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
20331708 CGGTACACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:20331768 original size:47 final size:47
Alignment explanation
Indices: 20331695--20331807 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 47
20331685 CAGTAACAGT
*
20331695 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCTAG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAG
* * *
20331742 AACAGTAACAGTACGGTACACGGAGTACCTCATTGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAG
20331789 AACAGTAACAGTAACGGTA
1 AACAGTAACAGT-ACGGTA
20331808 GCAGTAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 55 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAG
Found at i:20331879 original size:51 final size:50
Alignment explanation
Indices: 20331791--20331886 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
20331781 AAATCCGGAA
* *
20331791 CAGTAACAGTAACGGTAGCAGTAACAACATCCTACACACAAAGTGCCGAAT
1 CAGTAACAGTAACGGTAACAGTAACAACATCCGACACAC-AAGTGCCGAAT
* **
20331842 CAGTAACAGTAATGGTAACAGTAACAGTAGT-CGACACACAAGTGC
1 CAGTAACAGTAACGGTAACAGTAACAACA-TCCGACACACAAGTGC
20331887 TTGATTAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 6 0.15
51 32 0.82
52 1 0.03
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (50 bp):
CAGTAACAGTAACGGTAACAGTAACAACATCCGACACACAAGTGCCGAAT
Found at i:20332279 original size:2 final size:2
Alignment explanation
Indices: 20332272--20332299 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20332262 CACCTACTAC
20332272 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
20332300 TAAATAATAA
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:20332933 original size:19 final size:17
Alignment explanation
Indices: 20332905--20332944 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
20332895 AAACCTTGAA
20332905 TTTT-TCCTTTCTTCTTT
1 TTTTCTCCTTTCTT-TTT
20332922 CTTTTCTCCTTTCTTTTT
1 -TTTTCTCCTTTCTTTTT
20332940 TTTTC
1 TTTTC
20332945 CCTGCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTCCTTTCTTTTT
Found at i:20333020 original size:2 final size:2
Alignment explanation
Indices: 20333013--20333045 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20333003 ATTAAACCAT
20333013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20333046 ATAACTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20341474 original size:28 final size:26
Alignment explanation
Indices: 20341411--20341464 Score: 72
Period size: 30 Copynumber: 1.9 Consensus size: 26
20341401 AATAGTAATA
20341411 TAAAATTTATTTTTTTATATTTTTTT
1 TAAAATTTATTTTTTTATATTTTTTT
20341437 TAAAATATTTATGTATTTTTATATTTTT
1 T-AAA-ATTTAT-T-TTTTTATATTTTT
20341465 ATTTGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 3 0.12
28 6 0.25
29 1 0.04
30 13 0.54
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TAAAATTTATTTTTTTATATTTTTTT
Found at i:20345847 original size:499 final size:499
Alignment explanation
Indices: 20344909--20346406 Score: 2951
Period size: 499 Copynumber: 3.0 Consensus size: 499
20344899 GCAAGGCAAG
20344909 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
1 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
20344974 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
66 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
20345039 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
131 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
20345104 ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
196 ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
20345169 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
261 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
20345234 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
326 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
20345299 CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
391 CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
20345364 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
456 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
20345408 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
1 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
20345473 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
66 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
20345538 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
131 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
20345603 ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
196 ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
20345668 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
261 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
20345733 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
326 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
20345798 CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
391 CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
20345863 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
456 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
20345907 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
1 ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
20345972 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
66 CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
20346037 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
131 TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
* * * *
20346102 ATTGAAACTCCACTTTAACTGAGGAAGTAAAATAGCCAGAAGAGTCGAACACTGCAATTCTGCTG
196 ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
20346167 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
261 TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
20346232 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
326 TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
*
20346297 CTGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
391 CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
20346362 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
456 TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
20346406 A
1 A
20346407 CCATTGACCA
Statistics
Matches: 994, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
499 994 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (499 bp):
ATCACTTTGGGCCTGAACTTGGATCATAGCTGCATATACTTTTTGGTCCACAGATTCCATGAATT
CTACAGGAGTTAGACATAGCTTGCCATGTGACTGACCAAATTCCCTTTTGCTCTTCGAGACTGTA
TAACCTAAGGTTACCATCAAAATCAAGTGTTAATCTCCTCCAAGGTCCCCTACCAAAATCAGCAG
ATTGAAACTCCACTTTATCCGAGGAAGTAAAATAGCCAGAAGAGTCAAACACTGCAATTCTACTG
TCATTGAATCTTGTTCTTCCTTGTAGGTAGTCCAAAACCGTAGAATCCGGCCAGTAGATGCTGGA
TGTCTCAGGACTATCCAAGACAAGACGAAGAACGTTATCATAGTCATACATCAGCTTATAGTTAC
CCGAGGAGTAGTCACTTTGGCTTCGAGCTGATACAAGTCTATTATGTTGAGTGAGCGGTTGTTCA
TGGAGAAGCGTATCAGTTGGCGAATCAAAGCTTTGCCTAAGCGT
Found at i:20353837 original size:74 final size:74
Alignment explanation
Indices: 20353716--20353860 Score: 290
Period size: 74 Copynumber: 2.0 Consensus size: 74
20353706 CTTCAGTCAA
20353716 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
20353781 GTCATTCAG
66 GTCATTCAG
20353790 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
20353855 GTCATT
66 GTCATT
20353861 ATAAGGGTAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (74 bp):
AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
GTCATTCAG
Found at i:20355101 original size:2 final size:2
Alignment explanation
Indices: 20355094--20355147 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
20355084 TTGCGTGCGC
20355094 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
*
20355136 AT AT AT CT AT AT
1 AT AT AT AT AT AT
20355148 GAAATTCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20356999 original size:18 final size:18
Alignment explanation
Indices: 20356976--20357010 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20356966 TGTAATATCA
* *
20356976 ATTAATTTTTTTATTTTT
1 ATTAATTATTATATTTTT
20356994 ATTAATTATTATATTTT
1 ATTAATTATTATATTTT
20357011 AATTCCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTAATTATTATATTTTT
Found at i:20357640 original size:3 final size:3
Alignment explanation
Indices: 20357632--20357671 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20357622 CAATAAAGTA
20357632 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20357672 GAATTAATGA
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):
AAT
Found at i:20363824 original size:53 final size:53
Alignment explanation
Indices: 20363683--20363833 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
20363673 ATAAGTGCAC
* **
20363683 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTAACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTAACT
* *
20363736 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTAACT
* *
20363789 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
20363834 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTAACT
Found at i:20371267 original size:53 final size:53
Alignment explanation
Indices: 20371126--20371276 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
20371116 ATAAGTGCGC
* **
20371126 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
20371179 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
20371232 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
20371277 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:20373224 original size:2 final size:2
Alignment explanation
Indices: 20373217--20373241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20373207 TCTCCTAAAG
20373217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20373242 GGTTACCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20374113 original size:17 final size:16
Alignment explanation
Indices: 20374088--20374134 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
20374078 GTTTTATATG
20374088 AAAAT-TTAAAATTTA
1 AAAATATTAAAATTTA
20374103 TAAAATATTAAAAAATTTA
1 -AAAATATT--AAAATTTA
20374122 AAAA-ATTAAAATT
1 AAAATATTAAAATT
20374135 AAGTATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.21
16 5 0.18
17 5 0.18
18 4 0.14
19 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTAAAATTTA
Found at i:20374125 original size:10 final size:9
Alignment explanation
Indices: 20374095--20374132 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
20374085 ATGAAAATTT
*
20374095 AAAATTTAT
1 AAAATTTAA
20374104 AAAATATTAA
1 AAAAT-TTAA
20374114 AAAATTTAA
1 AAAATTTAA
20374123 AAAA-TTAA
1 AAAATTTAA
20374131 AA
1 AA
20374133 TTAAGTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 6 0.22
9 13 0.48
10 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:20374459 original size:14 final size:16
Alignment explanation
Indices: 20374431--20374463 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
20374421 TTACGGTAAT
20374431 AAAAATATAATATTTA
1 AAAAATATAATATTTA
20374447 AAAAAT-TAA-ATTTA
1 AAAAATATAATATTTA
20374461 AAA
1 AAA
20374464 TTTTATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATAATATTTA
Found at i:20378058 original size:15 final size:15
Alignment explanation
Indices: 20378034--20378066 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20378024 TTTATATTGA
*
20378034 CTTGATATTATTTGT
1 CTTGACATTATTTGT
20378049 CTTGACATTATTTGT
1 CTTGACATTATTTGT
20378064 CTT
1 CTT
20378067 ATATTCCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (15 bp):
CTTGACATTATTTGT
Found at i:20382845 original size:18 final size:19
Alignment explanation
Indices: 20382824--20382862 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20382814 ATTTTGGATT
*
20382824 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
20382842 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
20382861 TT
1 TT
20382863 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:20391349 original size:11 final size:11
Alignment explanation
Indices: 20391335--20391379 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
20391325 AGATAAATAT
20391335 TATTTTATTAA
1 TATTTTATTAA
*
20391346 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
20391359 TATTTTATTAT
1 TATTTTATTAA
20391370 TATTTTATTA
1 TATTTTATTA
20391380 GTTTATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20393139 original size:46 final size:46
Alignment explanation
Indices: 20393069--20393473 Score: 528
Period size: 46 Copynumber: 8.8 Consensus size: 46
20393059 GCTCTCTGAA
* * *
20393069 ATGAAATGTGCAAGACCATTGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
20393115 ATGAAATGTGTAAGACCATGGTTGAAAGATGCCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
20393161 ATGAAA--TGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
20393205 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
20393251 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGCCAATATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** * * *
20393297 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
20393343 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** * *
20393389 ATGAAAAGAATAAGACCCTAGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
20393435 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20393474 TCAATGTCAA
Statistics
Matches: 327, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
44 43 0.13
45 1 0.00
46 283 0.87
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:20396063 original size:7 final size:7
Alignment explanation
Indices: 20396051--20396079 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
20396041 TATACAGAAA
20396051 TCACTTG
1 TCACTTG
20396058 TCACTTG
1 TCACTTG
20396065 TCACTTG
1 TCACTTG
20396072 TCACTTG
1 TCACTTG
20396079 T
1 T
20396080 AGCCAAAGCT
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:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:20396122 original size:31 final size:31
Alignment explanation
Indices: 20396085--20396255 Score: 252
Period size: 31 Copynumber: 5.5 Consensus size: 31
20396075 CTTGTAGCCA
* *
20396085 AAGCTACCACTATTCATTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** * *
20396116 GTGCTACCATTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
* *
20396147 GAGCTACCACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
*
20396178 AAGCTACCACTTTTCACTGATTAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
*
20396209 AAACTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
20396240 AAGCTACCACTTTTCA
1 AAGCTACCACTTTTCA
20396256 GTTGTCATTT
Statistics
Matches: 126, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 126 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:20396339 original size:50 final size:50
Alignment explanation
Indices: 20396233--20396409 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
20396223 CACTGATCAG
* * * *
20396233 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
20396284 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
20396334 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
20396384 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
20396410 GTTTCCATGG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:20399707 original size:11 final size:11
Alignment explanation
Indices: 20399693--20399737 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
20399683 AGATAAATAT
20399693 TATTTTATTAA
1 TATTTTATTAA
*
20399704 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
20399717 TATTTTATTAT
1 TATTTTATTAA
20399728 TATTTTATTA
1 TATTTTATTA
20399738 GTATATGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20401451 original size:21 final size:21
Alignment explanation
Indices: 20401427--20401498 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
20401417 CTCTCTGAAA
20401427 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
20401448 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
20401472 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
20401494 TGAAA
1 TGAAA
20401499 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:20401478 original size:46 final size:46
Alignment explanation
Indices: 20401426--20401785 Score: 481
Period size: 46 Copynumber: 7.8 Consensus size: 46
20401416 GCTCTCTGAA
** * *
20401426 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** **
20401472 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
20401518 ATGAAA-AAATAAGACCATGGTTGAGAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
20401563 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
20401609 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
20401655 ATGAAATGAATAAGATCATGGTTGAAAGAGACCATGACAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
20401701 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
20401747 A-GAAAATGAGTAAGATCATAGTTGAAAGAAACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
20401786 TCAATGTCAA
Statistics
Matches: 279, Mismatches: 33, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
45 38 0.14
46 241 0.86
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:20403409 original size:44 final size:45
Alignment explanation
Indices: 20403319--20403451 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
20403309 ACAGGACAGA
* *
20403319 ACAGAAATGAGCCATGTAAGT-CATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
20403364 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
20403408 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20403452 CAGGATATTG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 36 0.49
45 20 0.27
46 17 0.23
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:20408640 original size:39 final size:39
Alignment explanation
Indices: 20408584--20408718 Score: 107
Period size: 39 Copynumber: 3.4 Consensus size: 39
20408574 ACCAATATGG
* *
20408584 CACCCAGTGCCTTATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
20408623 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
20408661 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
20408702 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
20408719 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
38 19 0.26
39 35 0.47
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:20410300 original size:5 final size:5
Alignment explanation
Indices: 20410282--20410316 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
20410272 TTTCTTTTAT
20410282 ATATA ATAATA ATATA ATATA ATATA A-ATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
20410317 CTTAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:20410303 original size:16 final size:14
Alignment explanation
Indices: 20410282--20410316 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20410272 TTTCTTTTAT
20410282 ATATAATAATAATATA
1 ATATAAT-ATAA-ATA
20410298 ATATAATATAAATA
1 ATATAATATAAATA
20410312 ATATA
1 ATATA
20410317 CTTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 4 0.21
16 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:20415828 original size:3 final size:3
Alignment explanation
Indices: 20415815--20415893 Score: 60
Period size: 3 Copynumber: 26.3 Consensus size: 3
20415805 GAGGGCATAT
20415815 ATA AT- ATA ATA ATA AT- ATA ATA ATA TATA CATGA GA-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA ATA ATA
* *
20415861 AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20415894 AACAAAGCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 9 0.15
3 44 0.71
4 7 0.11
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20416242 original size:26 final size:25
Alignment explanation
Indices: 20416193--20416242 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
20416183 AAAAACTAGC
* *
20416193 CTTTCCAAGAAACAAAAATAACCTT
1 CTTTCCAAAAAACAAAAAAAACCTT
20416218 CTTTCCAAAAAACAAAAAAACACCT
1 CTTTCCAAAAAACAAAAAAA-ACCT
20416243 CCAAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (25 bp):
CTTTCCAAAAAACAAAAAAAACCTT
Found at i:20416247 original size:21 final size:21
Alignment explanation
Indices: 20416221--20416269 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
20416211 TAACCTTCTT
20416221 TCCAAAAAACAAAAAAACACC
1 TCCAAAAAACAAAAAAACACC
*
20416242 TCCAAAAAACAAAAAAACTCC
1 TCCAAAAAACAAAAAAACACC
20416263 TCCAAAA
1 TCCAAAA
20416270 CAAAGAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (21 bp):
TCCAAAAAACAAAAAAACACC
Found at i:20416455 original size:4 final size:4
Alignment explanation
Indices: 20416446--20416472 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20416436 TGGCCAAGGT
20416446 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
20416473 TTTGTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:20416863 original size:44 final size:44
Alignment explanation
Indices: 20416800--20417264 Score: 374
Period size: 44 Copynumber: 10.6 Consensus size: 44
20416790 TCAGATTTGC
*
20416800 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20416844 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTT-GATTT
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* * * * * * * *
20416887 GCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTT-GATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATAT-TTTCAACTT
* *
20416932 GTTCCCTATAAGCACAGGGATGCTAAATCTGATGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20416976 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-T
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* ** * * * * * * *
20417019 GCTTCACTGCAAGCACAGGAATGTCAGATCTGCTATCTTCGATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* *
20417064 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* * *
20417108 GTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-T
1 GTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACTT
* * * ** * * * * *
20417151 GCTTCACTGTAAGCACAGGAATGTTAGATCTGTTATCTTCGATTT
1 G-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
* *
20417196 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
20417240 GTTCCCTATAAGCACAGGGATGCCA
1 GTTCCCTATAAGCACAGGGATGCCA
20417265 TGCTGAAATC
Statistics
Matches: 328, Mismatches: 75, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
42 6 0.02
43 25 0.08
44 262 0.80
45 29 0.09
46 6 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
GTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACTT
Found at i:20417037 original size:132 final size:132
Alignment explanation
Indices: 20416800--20417299 Score: 919
Period size: 132 Copynumber: 3.8 Consensus size: 132
20416790 TCAGATTTGC
20416800 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
* *
20416865 GCCATGCTGAAATCTTTGATTTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTTGAT
66 GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGAT
20416930 TT
131 TT
*
20416932 GTTCCCTATAAGCACAGGGATGCTAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
* *
20416997 GCCATGCTGAAATCTTTGATCTGCTTCACTGCAAGCACAGGAATGTCAGATCTGCTATCTTCGAT
66 GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGAT
20417062 TT
131 TT
*
20417064 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
*
20417129 GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTTAGATCTGTTATCTTCGAT
66 GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGAT
20417194 TT
131 TT
*
20417196 GTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
1 GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
*
20417261 GCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACA
66 GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACA
20417300 TCTTCGATCT
Statistics
Matches: 357, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 357 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (132 bp):
GTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGAT
GCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGAT
TT
Found at i:20417310 original size:27 final size:26
Alignment explanation
Indices: 20417272--20417325 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
20417262 CCATGCTGAA
*
20417272 ATCTTCGATCTGCTTCACTGTAAGCAC
1 ATCTTCGATCTG-TTCACTATAAGCAC
*
20417299 ATCTTCGATCTGTTCCCTATAAGCAC
1 ATCTTCGATCTGTTCACTATAAGCAC
20417325 A
1 A
20417326 GGGATGCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (26 bp):
ATCTTCGATCTGTTCACTATAAGCAC
Found at i:20417352 original size:70 final size:70
Alignment explanation
Indices: 20417239--20417369 Score: 244
Period size: 70 Copynumber: 1.9 Consensus size: 70
20417229 GTTTTCAACT
* *
20417239 TGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACATCTT
1 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACATCTT
20417304 CGATC
66 CGATC
20417309 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACA
1 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACA
20417370 GGGATGCCAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (70 bp):
TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACATCTT
CGATC
Found at i:20417373 original size:44 final size:43
Alignment explanation
Indices: 20417299--20417503 Score: 193
Period size: 44 Copynumber: 4.7 Consensus size: 43
20417289 CTGTAAGCAC
*
20417299 ATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCATGCTAAA
1 ATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
* **
20417342 ATCTTCGATCTGCTTCACC-GTAAGCACAGGGATGCCA-GATCTGCT
1 ATCTTCGATCTG-TTC-CCTATAAGCACAGGGATGCCATG--CTGAA
* **
20417387 ATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGCT
1 ATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAA
* * * *
20417431 GTTTTC-AACTTGTTCCCTATAAGCACAAGGATGCCATGCTGAA
1 ATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCTGAA
* *
20417474 ATCTTCGATCTGCTTCACTGTAAGCACAGG
1 ATCTTCGATCTG-TTCCCTATAAGCACAGG
20417504 AATGTCAGAT
Statistics
Matches: 131, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 25 0.19
44 88 0.67
45 15 0.11
46 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
ATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
Found at i:20417453 original size:202 final size:202
Alignment explanation
Indices: 20417107--20417501 Score: 718
Period size: 202 Copynumber: 2.0 Consensus size: 202
20417097 GTTTTCAACT
* * *
20417107 TGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAA
1 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACAGGAA
** *
20417172 TGTTAGATCTGTTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAA
66 TGCCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAA
*
20417237 CTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACATC
131 CTTGTTCCCTATAAGCACAAGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACATC
20417302 TTCGATC
196 TTCGATC
*
20417309 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACAGGGA
1 TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACAGGAA
20417374 TGCCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAA
66 TGCCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAA
20417439 CTTGTTCCCTATAAGCACAAGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACA
131 CTTGTTCCCTATAAGCACAAGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACA
20417502 GGAATGTCAG
Statistics
Matches: 185, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
202 185 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (202 bp):
TGTTCCCTATAAGCACAGGGATGCCATGCTAAAATCTTCGATCTGCTTCACCGTAAGCACAGGAA
TGCCAGATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAA
CTTGTTCCCTATAAGCACAAGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACATC
TTCGATC
Found at i:20417660 original size:68 final size:69
Alignment explanation
Indices: 20417578--20417765 Score: 274
Period size: 68 Copynumber: 2.8 Consensus size: 69
20417568 TCTTCTTCCA
* * * * *
20417578 CTGAAACTTCAAGGAGGTCTGCTGTGGCTTTTAGCCTCTCCAATGCCATTTCT-GGAAGAAGAGG
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCTAAGAAGAAAAGA
*
20417642 T-TT
66 TCCT
* *
20417645 GCTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATTT-TAAGAAGAAAAG
1 -CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCTAAGAAGAAAAG
20417709 ATCCT
65 ATCCT
20417714 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTC
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTC
20417766 AGGGAAAAAG
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
67 1 0.01
68 105 0.98
69 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (69 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCTAAGAAGAAAAGA
TCCT
Found at i:20417943 original size:43 final size:43
Alignment explanation
Indices: 20417856--20418253 Score: 308
Period size: 44 Copynumber: 9.2 Consensus size: 43
20417846 CAACTTCTTA
* * *
20417856 AGGGGTTAAGATCTGTAAA-TTCAACCTGTTACCCTACTGGTT
1 AGGGGTTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
*
20417898 AGGGGTTAAGATTTGTAAATTTTAGCCTGTTACCCTACTGCTT
1 AGGGGTTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
* * * *
20417941 AGGGTTTAAGGTTTGTAAA-TTCGGCTTGTTACCCTACTGCTT
1 AGGGGTTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
*** * ** * * *
20417983 AGGGGGTTAAAGCCCAT-CATTTTTTA-TCTGTTTCCCTACTGCTT
1 A-GGGGTT-AAG-ATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
* *
20418027 AGGGGTTAAGATCTGTAAATCTTCAGCCAGTTACCCTACTGCTT
1 AGGGGTTAAGATTTGTAAAT-TTCAGCCTGTTACCCTACTGCTT
** * *
20418071 AGGGGTTTAAGGCTTGTAAA-TTCGGCTTGTTACCCTACTGCTT
1 AGGGG-TTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
*** * ** * * *
20418114 AGGGGGTTAAAGCCCAT-CATCTTTGA-TCTGTTTCCCTACTGCTT
1 A-GGGGTT-AAG-ATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
* *
20418158 AGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTACTT
1 AGGGGTTAAGATTTGTAAAT-TTCAGCCTGTTACCCTACTGCTT
** * *
20418202 AGGGGTTAAGGCTTGTAAATTT-GGCTTGTTACCCTACTGCTT
1 AGGGGTTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
20418244 AAGGGGTTAA
1 -AGGGGTTAA
20418254 AGCCCATCAT
Statistics
Matches: 276, Mismatches: 63, Indels: 33
0.74 0.17 0.09
Matches are distributed among these distances:
41 2 0.01
42 66 0.24
43 94 0.34
44 96 0.35
45 18 0.07
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (43 bp):
AGGGGTTAAGATTTGTAAATTTCAGCCTGTTACCCTACTGCTT
Found at i:20418022 original size:44 final size:44
Alignment explanation
Indices: 20417881--20418297 Score: 214
Period size: 43 Copynumber: 9.6 Consensus size: 44
20417871 TAAATTCAAC
* *** *
20417881 CTGTTACCCTACTGGTTA-GGGGTT-AAGATTTGTAAATTTT-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAAG-CCCGTAAATTTTGA-T
* * *** ** *
20417924 CTGTTACCCTACTGCTTA-GGGTTTAAGGTTTGTAAATTCGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAATTTTGAT
* * * *
20417967 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCATTTTTTAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAATTTTGAT
* * * * * *
20418010 CTGTTTCCCTACTGCTTA-GGGGTT-AAGATCTGTAAATCTTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAAG-CCCGTAAATTTTGA-T
* * * ** ** *
20418054 CAGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAATTCGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAATTTTGAT
* *
20418098 -TGTTACCCTACTGCTTAGGGGGTTAAAGCCCAT-CATCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAAT-TTTGAT
* * * * * *
20418141 CTGTTTCCCTACTGCTTA-GGGGTT-AAGATCTGTAAATCTTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAAG-CCCGTAAATTTTGA-T
* * ** * *
20418185 CTGTTACCCTACTACTTA-GGGGTTAAGGCTTGTAAATTTGGCT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAATTTTGAT
* * * *
20418228 -TGTTACCCTACTGCTTAAGGGGTTAAAGCCCAT-CATCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAAT-TTTGAT
*
20418271 CTGTTTCCCTACTGCTTAGGGGGTTAA
1 CTGTTACCCTACTGCTTAGGGGGTTAA
20418298 GATCTTCATC
Statistics
Matches: 279, Mismatches: 78, Indels: 33
0.72 0.20 0.08
Matches are distributed among these distances:
42 43 0.15
43 114 0.41
44 106 0.38
45 14 0.05
46 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAAGCCCGTAAATTTTGAT
Done.