Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 123 of 295
Found at i:42155323 original size:15 final size:15
Alignment explanation
Indices: 42155303--42155334 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42155293 AAAGAAAGAA
42155303 ATCAATAAAGTGGCC
1 ATCAATAAAGTGGCC
42155318 ATCAATAAAGTGGCC
1 ATCAATAAAGTGGCC
42155333 AT
1 AT
42155335 TAAACCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (15 bp):
ATCAATAAAGTGGCC
Found at i:42165533 original size:43 final size:43
Alignment explanation
Indices: 42165480--42165562 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
42165470 AGGTTATCAA
* *
42165480 ATTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT
1 ATTGAGATTACATGTAAGACCATGTCCGGGACATTGGCATTGT
*
42165523 ATTGAGATTACGTGTAAGACCATGTCCGGGACATTGGCAT
1 ATTGAGATTACATGTAAGACCATGTCCGGGACATTGGCAT
42165563 CGTTAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
ATTGAGATTACATGTAAGACCATGTCCGGGACATTGGCATTGT
Found at i:42170650 original size:17 final size:17
Alignment explanation
Indices: 42170628--42170660 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42170618 TTCATGTGTT
*
42170628 TTTTTTTTAAATATTTA
1 TTTTTTTAAAATATTTA
42170645 TTTTTTTAAAATATTT
1 TTTTTTTAAAATATTT
42170661 TACTATAACT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTTAAAATATTTA
Found at i:42171494 original size:17 final size:17
Alignment explanation
Indices: 42171472--42171514 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
42171462 CTTGAATTTT
*
42171472 TATAAATTATTTTTAAA
1 TATAAAGTATTTTTAAA
42171489 TATAAAGTATTTTTAAA
1 TATAAAGTATTTTTAAA
42171506 TATAAAGTA
1 TATAAAGTA
42171515 AATTCAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
TATAAAGTATTTTTAAA
Found at i:42172528 original size:7 final size:7
Alignment explanation
Indices: 42172516--42172570 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
42172506 TACAGCCTTT
42172516 GGGTTTA
1 GGGTTTA
42172523 GGGTTTTA
1 GGG-TTTA
42172531 GGGTTTA
1 GGGTTTA
*
42172538 AGGTTTAA
1 GGGTTT-A
**
42172546 GATTTTA
1 GGGTTTA
42172553 GGGTTTA
1 GGGTTTA
42172560 GGGTTTA
1 GGGTTTA
42172567 GGGT
1 GGGT
42172571 AAGTTTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 29 0.73
8 11 0.28
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:42172536 original size:15 final size:15
Alignment explanation
Indices: 42172516--42172570 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
42172506 TACAGCCTTT
42172516 GGGTTTAGGGTTTTA
1 GGGTTTAGGGTTTTA
* *
42172531 GGGTTTAAGGTTTAA
1 GGGTTTAGGGTTTTA
**
42172546 GATTTTAGGG-TTTA
1 GGGTTTAGGGTTTTA
42172560 GGGTTTAGGGT
1 GGGTTTAGGGT
42172571 AAGTTTATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (15 bp):
GGGTTTAGGGTTTTA
Found at i:42172551 original size:22 final size:22
Alignment explanation
Indices: 42172517--42172566 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
42172507 ACAGCCTTTG
* *
42172517 GGTTTAGGGTTTTAGGGTTTAA
1 GGTTTAAGATTTTAGGGTTTAA
*
42172539 GGTTTAAGATTTTAGGGTTTAG
1 GGTTTAAGATTTTAGGGTTTAA
42172561 GGTTTA
1 GGTTTA
42172567 GGGTAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (22 bp):
GGTTTAAGATTTTAGGGTTTAA
Found at i:42173323 original size:26 final size:24
Alignment explanation
Indices: 42173286--42173333 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
42173276 TTATTTTAAT
*
42173286 ATTTGTTTTTATGTTTTTAAATAC
1 ATTTGTTTTTATATTTTTAAATAC
42173310 ATTTGATTTATTATATTTTTAAAT
1 ATTTG-TTT-TTATATTTTTAAAT
42173334 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (24 bp):
ATTTGTTTTTATATTTTTAAATAC
Found at i:42179729 original size:43 final size:43
Alignment explanation
Indices: 42179677--42179928 Score: 333
Period size: 43 Copynumber: 6.0 Consensus size: 43
42179667 ATATCATACA
* * * *
42179677 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCATATATCA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
42179720 ATGCTAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
42179763 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* *
42179806 ATGCCAACATCCCAGATGTGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
42179849 ATGCCAACGTCCCAGAC----TCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
42179888 ATGCC-ACTGTCCCAAAGA-G-GGTCTTACACGTAATCACATAT
1 ATGCCAAC-GTCCC--AGACGTGGTCTTACACGTAATCACATAT
42179929 AAAAAATCCT
Statistics
Matches: 189, Mismatches: 10, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 32 0.17
41 3 0.02
42 3 0.02
43 146 0.77
44 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:42179916 original size:125 final size:126
Alignment explanation
Indices: 42179677--42179928 Score: 389
Period size: 125 Copynumber: 2.0 Consensus size: 126
42179667 ATATCATACA
* * * *
42179677 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCATATATCAATGCTAACGTCCCAGACGTGGT
1 ATGCCAACATCCCAAACGTGGTCTTACACGTAATCACATATCAATGCCAACGTCCCAGAC---GT
*
42179742 CTTACACGTAATCACATATCGATGCCACTGTCCCAGACAGGGTCTTACACGTAATCACATATCG
63 CTTACACGTAATCACATATCGATGCCACTGTCCCAAACAGGGTCTTACACGTAATCACATATCG
* * *
42179806 ATGCCAACATCCCAGATGTGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAC-TCTT
1 ATGCCAACATCCCAAACGTGGTCTTACACGTAATCACATATCAATGCCAACGTCCCAGACGTCTT
*
42179870 ACACGTAATCACATATCGATGCCACTGTCCCAAAGAGGGTCTTACACGTAATCACATAT
66 ACACGTAATCACATATCGATGCCACTGTCCCAAACAGGGTCTTACACGTAATCACATAT
42179929 AAAAAATCCT
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 61 0.54
129 53 0.46
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (126 bp):
ATGCCAACATCCCAAACGTGGTCTTACACGTAATCACATATCAATGCCAACGTCCCAGACGTCTT
ACACGTAATCACATATCGATGCCACTGTCCCAAACAGGGTCTTACACGTAATCACATATCG
Found at i:42183386 original size:18 final size:19
Alignment explanation
Indices: 42183340--42183388 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
42183330 CTTGGCCCAT
*
42183340 TGTAGTAACAATAAACAGC
1 TGTAGTAACAGTAAACAGC
*
42183359 T-TAGTAACAGTAATCAG-
1 TGTAGTAACAGTAAACAGC
42183376 TGTAGTAACAGTA
1 TGTAGTAACAGTA
42183389 TACAAGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (19 bp):
TGTAGTAACAGTAAACAGC
Found at i:42184262 original size:27 final size:27
Alignment explanation
Indices: 42183700--42184251 Score: 660
Period size: 27 Copynumber: 20.6 Consensus size: 27
42183690 AAATATACAT
*
42183700 CACAT-AGGGCAAATCAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * * *
42183726 CATATAAGGACAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * * *
42183753 CACACAAGAGAAAAATAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * * * *
42183780 CATATAAGGGCAAAATAGTTATTTTAT
1 CACATAAGGGCAAAACAGTCATCTTAC
42183807 CACATAAGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
42183834 CAAATAAGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
42183861 CACATAAGGGAAAAACAGTTATCTTA-
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
42183887 -ACATAAGGGAAAAATAGTTATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * * *
42183913 CACATAGGGGAAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
42183940 CACATAAGGGCAAAACAATCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
42183967 CACATAAGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
42183994 CATATAAGGGCAAAAGAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
42184021 CACATAAAGGCAAAAGAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
42184048 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
42184075 TACATAAGGGCAAAACAGTTATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
42184102 CACATAAGGGCAAAATAGTTATCTTAA
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
42184129 CACATAAGGGCAAAACAATCGTCTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
42184156 CACATAAGGTCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
*
42184183 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* * *
42184210 CACATAAGGACAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATCTTAC
* *
42184237 CATATAAGGGAAAAA
1 CACATAAGGGCAAAA
42184252 TATTCATTTT
Statistics
Matches: 456, Mismatches: 67, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
25 24 0.05
26 4 0.01
27 428 0.94
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATCTTAC
Found at i:42188625 original size:23 final size:22
Alignment explanation
Indices: 42188540--42188662 Score: 90
Period size: 23 Copynumber: 5.2 Consensus size: 22
42188530 GACTCACCAT
42188540 AGCTCGTATGAGCTTATCGATATATC
1 AGCTCGTATGAGCTTA-CG-T-T-TC
* * *
42188566 AACTCGTAAGAGCTTACTGTTTTT
1 AGCTCGTATGAGCTTAC-G-TTTC
*
42188590 AGCTCAT-TAGAGCTTAGCGTTTC
1 AGCTCGTAT-GAGCTTA-CGTTTC
42188613 AGCTCGTATGAGCTTACTGTTT-
1 AGCTCGTATGAGCTTAC-GTTTC
42188635 AGCTCG-ATAGAGCTTACCGTTTC
1 AGCTCGTAT-GAGCTTA-CGTTTC
42188658 AGCTC
1 AGCTC
42188663 AATAGAGCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.03
22 18 0.22
23 26 0.32
24 15 0.19
25 3 0.04
26 16 0.20
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (22 bp):
AGCTCGTATGAGCTTACGTTTC
Found at i:42188647 original size:22 final size:23
Alignment explanation
Indices: 42188574--42188678 Score: 110
Period size: 23 Copynumber: 4.6 Consensus size: 23
42188564 TCAACTCGTA
*
42188574 AGAGCTTACTGTTTTTAGCTC-ATT
1 AGAGCTTACTG-TTTCAGCTCGA-T
42188598 AGAGCTTAGC-GTTTCAGCTCG-T
1 AGAGCTTA-CTGTTTCAGCTCGAT
42188620 ATGAGCTTACTGTTT-AGCTCGAT
1 A-GAGCTTACTGTTTCAGCTCGAT
* *
42188643 AGAGCTTACCGTTTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCGAT
*
42188666 AGAGCTTATTGTT
1 AGAGCTTACTGTT
42188679 CATCAGCTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
22 21 0.30
23 39 0.56
24 9 0.13
25 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCGAT
Found at i:42188656 original size:45 final size:46
Alignment explanation
Indices: 42188568--42188662 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 46
42188558 GATATATCAA
*
42188568 CTCGTAAGAGCTTACTGTTTTTAGCTCATTAGAGCTTAGCGTTTCAG
1 CTCGTAAGAGCTTACTG-TTTTAGCTCATTAGAGCTTACCGTTTCAG
*
42188615 CTCGTATGAGCTTACTG-TTTAGCTCGA-TAGAGCTTACCGTTTCAG
1 CTCGTAAGAGCTTACTGTTTTAGCTC-ATTAGAGCTTACCGTTTCAG
42188660 CTC
1 CTC
42188663 AATAGAGCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 28 0.62
46 1 0.02
47 16 0.36
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (46 bp):
CTCGTAAGAGCTTACTGTTTTAGCTCATTAGAGCTTACCGTTTCAG
Found at i:42188671 original size:45 final size:44
Alignment explanation
Indices: 42188574--42188678 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
42188564 TCAACTCGTA
* *
42188574 AGAGCTTACTGTTTTTAGCTCATTAGAGCTTAGCGTTTCAGCTCGT
1 AGAGCTTACTG--TTTAGCTCATTAGAGCTTACCGTTTCAGCTCAT
42188620 ATGAGCTTACTGTTTAGCTCGA-TAGAGCTTACCGTTTCAGCTCAAT
1 A-GAGCTTACTGTTTAGCTC-ATTAGAGCTTACCGTTTCAGCTC-AT
*
42188666 AGAGCTTATTGTT
1 AGAGCTTACTGTT
42188679 CATCAGCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 39 0.74
46 4 0.08
47 10 0.19
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (44 bp):
AGAGCTTACTGTTTAGCTCATTAGAGCTTACCGTTTCAGCTCAT
Found at i:42188880 original size:20 final size:19
Alignment explanation
Indices: 42188849--42188926 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
42188839 AGATATGTGT
* *
42188849 TTATATGGATGAATTACTA
1 TTATACGGATGAACTACTA
* *
42188868 TTGATACGGATGAATTACTG
1 TT-ATACGGATGAACTACTA
*
42188888 TTATTACTGATGAACTACTA
1 TTA-TACGGATGAACTACTA
42188908 TTTATACGGATGAACTACT
1 -TTATACGGATGAACTACT
42188927 GGTTATATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.06
20 44 0.88
21 3 0.06
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
TTATACGGATGAACTACTA
Found at i:42188940 original size:20 final size:20
Alignment explanation
Indices: 42188857--42188941 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
42188847 GTTTATATGG
* *
42188857 ATGAATTACTA-TTGATACGG
1 ATGAACTACTAGTT-ATACGA
*
42188877 ATGAATTACT-GTTATTACTG-
1 ATGAACTACTAGTTA-TAC-GA
* *
42188897 ATGAACTACTATTTATACGG
1 ATGAACTACTAGTTATACGA
* *
42188917 ATGAACTACTGGTTATATGA
1 ATGAACTACTAGTTATACGA
42188937 ATGAA
1 ATGAA
42188942 TTACAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.04
20 48 0.89
21 4 0.07
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
ATGAACTACTAGTTATACGA
Found at i:42188941 original size:40 final size:38
Alignment explanation
Indices: 42188849--42188953 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 38
42188839 AGATATGTGT
* *
42188849 TTATATGGATGAATTACTATTGATACGGATGAATTACTG
1 TTATAT-GATGAATTACTATTTATACGGATGAACTACTG
*
42188888 TTATTACTGATGAACTACTATTTATACGGATGAACTACTGG
1 TTA-TA-TGATGAATTACTATTTATACGGATGAACTACT-G
*
42188929 TTATATGAATGAATTACAATTTATA
1 TTATATG-ATGAATTACTATTTATA
42188954 TGAATAGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.09
40 47 0.82
41 5 0.09
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (38 bp):
TTATATGATGAATTACTATTTATACGGATGAACTACTG
Found at i:42193526 original size:43 final size:42
Alignment explanation
Indices: 42193478--42193587 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 42
42193468 TTTGAGGTGT
42193478 GATTTCGTGTAAGACCATGTCTGGGACATTGGCAACGATATGA-
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCAACG-TAT-AC
* *
42193521 GATTTCGTGTAAGACCATGTTTGGGACATTGGCATCGTATAC
1 GATTTCGTGTAAGACCATGTCTGGGACATTGGCAACGTATAC
* * *
42193563 GA-TTCGTATAAGACCCTTTCTGGGA
1 GATTTCGTGTAAGACCATGTCTGGGA
42193588 TAGTGACATC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
41 20 0.33
42 5 0.08
43 35 0.58
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTGGGACATTGGCAACGTATAC
Found at i:42198481 original size:27 final size:26
Alignment explanation
Indices: 42198409--42198503 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
42198399 TTGTACATGT
* *
42198409 ATGCTCCCACGAGCTGTG-AATCAAA
1 ATGCTCACACGAGCTGTGAAATCAGA
* * * *
42198434 ATACTCATATGAGTTGT-AAATCAGA
1 ATGCTCACACGAGCTGTGAAATCAGA
* *
42198459 ATGCTCACACGAGCTGTGAAAATGAGC
1 ATGCTCACACGAGCTGTG-AAATCAGA
* *
42198486 CTGCTCACATGAGCTGTG
1 ATGCTCACACGAGCTGTG
42198504 GAGTATCTGC
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
25 31 0.58
27 22 0.42
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (26 bp):
ATGCTCACACGAGCTGTGAAATCAGA
Found at i:42210600 original size:25 final size:25
Alignment explanation
Indices: 42210546--42210601 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
42210536 TTAATTAGTA
42210546 TAAAATATTAATAATTCAAT-AAAT
1 TAAAATATTAATAATTCAATAAAAT
42210570 TGAAAA-ATTAAATAATT-ATATAAAAT
1 T-AAAATATT-AATAATTCA-ATAAAAT
42210596 TAAAAT
1 TAAAAT
42210602 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
24 5 0.19
25 17 0.63
26 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAAATATTAATAATTCAATAAAAT
Found at i:42211467 original size:16 final size:15
Alignment explanation
Indices: 42211442--42211475 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
42211432 AAAGCTGGTA
*
42211442 ATAATTAATATATATT
1 ATAATAAATATA-ATT
42211458 ATAATAAATATAATT
1 ATAATAAATATAATT
42211473 ATA
1 ATA
42211476 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:42212797 original size:23 final size:23
Alignment explanation
Indices: 42212765--42212816 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
42212755 ATAATTCTAC
*
42212765 CTCATTGATGTTTGTTTGGGGCAT
1 CTCA-TGATGTTTGTTCGGGGCAT
42212789 CTCATGATGTTTGTTCGGGGCAT
1 CTCATGATGTTTGTTCGGGGCAT
42212812 CTCAT
1 CTCAT
42212817 TTCTATTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.42
Consensus pattern (23 bp):
CTCATGATGTTTGTTCGGGGCAT
Found at i:42216739 original size:48 final size:48
Alignment explanation
Indices: 42216553--42216725 Score: 265
Period size: 48 Copynumber: 3.6 Consensus size: 48
42216543 ATAAGATCCT
*
42216553 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGAGAGCCA
*
42216601 GTGTAAGACCATGTCTGGGACATGGCATCGACGTTGATATGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGAGAGCCA
** * *
42216649 GTGTAAGACCATGTCTAAGACATGGCATCGACATTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGAGAGCCA
* * *
42216697 GTGTAAGACCATATCTAGGATATGGCATC
1 GTGTAAGACCATGTCTGGGACATGGCATC
42216726 AACCTCGATA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 115 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACATTGATATGAGAGCCA
Found at i:42216750 original size:48 final size:48
Alignment explanation
Indices: 42216553--42216766 Score: 187
Period size: 48 Copynumber: 4.5 Consensus size: 48
42216543 ATAAGATCCT
* * * ** * * *
42216553 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCCA
1 GTGTAAGACCATATCTAGGATATGGCATCAACATCGATATGTGTGCCA
* * * * * * * *
42216601 GTGTAAGACCATGTCTGGGACATGGCATCGACGTTGATATGAGAGCCA
1 GTGTAAGACCATATCTAGGATATGGCATCAACATCGATATGTGTGCCA
* * * * *
42216649 GTGTAAGACCATGTCTAAGACATGGCATCGACATTGATATGTGTGCCA
1 GTGTAAGACCATATCTAGGATATGGCATCAACATCGATATGTGTGCCA
* **
42216697 GTGTAAGACCATATCTAGGATATGGCATCAACCTCGATATGTGATTTCA
1 GTGTAAGACCATATCTAGGATATGGCATCAACATCGATATGTG-TGCCA
*
42216746 -TGTAAGACCATATCTGGGATA
1 GTGTAAGACCATATCTAGGATA
42216767 CGACGTTAAT
Statistics
Matches: 149, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 146 0.98
49 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
GTGTAAGACCATATCTAGGATATGGCATCAACATCGATATGTGTGCCA
Found at i:42216821 original size:42 final size:42
Alignment explanation
Indices: 42216730--42216848 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 42
42216720 GGCATCAACC
* * * *
42216730 TCGATATGTGATTTCATGTAAGACCATATCTGGGATACGACG
1 TCGATATGAGATTTCATGTAAGACCATATATGGGACACGACA
** * ** *
42216772 TTAATATGAGATTTCATGTAAGACCATGTATGGGACGTGGCA
1 TCGATATGAGATTTCATGTAAGACCATATATGGGACACGACA
* * * * *
42216814 TCGATATGAGACTTCGTATAAGACCACATCTGGGA
1 TCGATATGAGATTTCATGTAAGACCATATATGGGA
42216849 TATGGCATTG
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (42 bp):
TCGATATGAGATTTCATGTAAGACCATATATGGGACACGACA
Found at i:42225305 original size:20 final size:20
Alignment explanation
Indices: 42225268--42225310 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
42225258 GCAACCAAAA
*
42225268 CATGCCAATTTATACACATAT
1 CATGCCAATCTATACACA-AT
*
42225289 CATG-CAATCTATTCACAAT
1 CATGCCAATCTATACACAAT
42225308 CAT
1 CAT
42225311 TTCAACTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.33
Consensus pattern (20 bp):
CATGCCAATCTATACACAAT
Found at i:42227786 original size:26 final size:26
Alignment explanation
Indices: 42227753--42227804 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42227743 TGATATTTGG
42227753 CTATGTAAATTGGCTTATTTTGGCTA
1 CTATGTAAATTGGCTTATTTTGGCTA
*
42227779 CTATGTAAATTGGCTTGTTTTGGCTA
1 CTATGTAAATTGGCTTATTTTGGCTA
42227805 ACATGGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (26 bp):
CTATGTAAATTGGCTTATTTTGGCTA
Found at i:42238269 original size:27 final size:27
Alignment explanation
Indices: 42238212--42238272 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42238202 ACCCCAGTTT
* * * *
42238212 GTAAGATTACCGAAATACCCTTGTAAT
1 GTAAAATTACCGAAATACCCCTATAAG
*
42238239 GTAAAATTACCGAAATACCCCTATAGG
1 GTAAAATTACCGAAATACCCCTATAAG
42238266 GTAAAAT
1 GTAAAAT
42238273 GACTATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCCTATAAG
Found at i:42242816 original size:46 final size:46
Alignment explanation
Indices: 42242764--42242936 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
42242754 AACCCGCCCC
* *
42242764 TAAGTGAACTCGAACTCAAATCAACGAGCTCGGACGTTCGCATCCA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
42242810 TAAGTGAACTC-AGACTCAACTCAACGAGTTCGGATGCTTAGTTACAT-C-
1 TAAGTGAACTCGA-ACTCAACTCAACGAGTTCGGACG-TTCG---CATCCA
* * * *
42242858 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* *
42242903 TAAGTGAACTCGGACTCAACTTAACGAGTTCGGA
1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
42242937 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 3 0.03
46 62 0.59
47 30 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:42242881 original size:93 final size:93
Alignment explanation
Indices: 42242769--42242940 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
42242759 GCCCCTAAGT
*
42242769 GAACTCGAACTCAAATCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGAACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
42242834 CGAGTTCGGATGCTTAGTTACATCTCAC
66 CGAGTTCGGATGCTTAGTTACATCTCAC
* * * * *
42242862 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCGAACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
42242927 CGAGTTCGGATGCT
66 CGAGTTCGGATGCT
42242941 CAACCATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGAACTCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCTTAGTTACATCTCAC
Found at i:42243393 original size:30 final size:30
Alignment explanation
Indices: 42243359--42243418 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42243349 ATTTAATACG
42243359 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
42243389 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
42243419 GGCTAGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:42251468 original size:203 final size:203
Alignment explanation
Indices: 42251119--42251534 Score: 697
Period size: 203 Copynumber: 2.0 Consensus size: 203
42251109 CTCCAACATG
* *
42251119 TTGGACGAAATTGGGCAAACGAAGAGTTTTAGGCCCTAAGTTAGTAACAGATACTGAGGGCAAGG
1 TTGGACGGAATTGGGCAAACGAAAAGTTTTAGGCCCTAAGTTAGTAACAGATACTGAGGGCAAGG
* * * *
42251184 TAAGATTGATTTGGGATCGGTTGAAGGAGGCCTCGGATAGGCAGAAGTCGTATTCTGACCTTAAG
66 TAAAATTGATTCGGGATCGGTTGAAGGAGGCCTCAGATAGGCAGAAGTCGTATGCTGACCTTAAG
* *
42251249 CATTGAGAGATAGAGTATGTAGTGGGGGACTTAGTTTTTCTTAAGGTCTCTCCGTGGAAGAAGGT
131 CATCGAGAGATAGAGTATGCAGTGGGGGACTTAGTTTTTCTTAAGGTCTCTCCGTGGAAGAAGGT
42251314 ATTAAGGT
196 ATTAAGGT
* * * * *
42251322 TTGGACGGAATTGGGCGAACGAAAAGTTTTGGGCCCTGATTTAGTAACAGATACTGAGGGTAAGG
1 TTGGACGGAATTGGGCAAACGAAAAGTTTTAGGCCCTAAGTTAGTAACAGATACTGAGGGCAAGG
*
42251387 TAAAATTGATTCGGGATCGTTTGAAGGAGGCCTCAGATAGGCAGAAGTCGTATGCTGACCTTAAG
66 TAAAATTGATTCGGGATCGGTTGAAGGAGGCCTCAGATAGGCAGAAGTCGTATGCTGACCTTAAG
*
42251452 CATCGAGAGATAGAGTATGCAGTGGGGGACTTAGTTTTTCTTAAGGTCTCTCTGTGGAAGAAGGT
131 CATCGAGAGATAGAGTATGCAGTGGGGGACTTAGTTTTTCTTAAGGTCTCTCCGTGGAAGAAGGT
42251517 ATTAAGGT
196 ATTAAGGT
42251525 TTGGACGGAA
1 TTGGACGGAA
42251535 GGGGAAGCTA
Statistics
Matches: 198, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
203 198 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.27
Consensus pattern (203 bp):
TTGGACGGAATTGGGCAAACGAAAAGTTTTAGGCCCTAAGTTAGTAACAGATACTGAGGGCAAGG
TAAAATTGATTCGGGATCGGTTGAAGGAGGCCTCAGATAGGCAGAAGTCGTATGCTGACCTTAAG
CATCGAGAGATAGAGTATGCAGTGGGGGACTTAGTTTTTCTTAAGGTCTCTCCGTGGAAGAAGGT
ATTAAGGT
Found at i:42253276 original size:17 final size:18
Alignment explanation
Indices: 42253243--42253276 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42253233 TCGGGCCAAA
42253243 ATGGGCTAAATGGGCCCG
1 ATGGGCTAAATGGGCCCG
*
42253261 ATGGGCTGAA-GGGCCC
1 ATGGGCTAAATGGGCCC
42253277 ATAATAGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.24, G:0.41, T:0.15
Consensus pattern (18 bp):
ATGGGCTAAATGGGCCCG
Found at i:42260805 original size:25 final size:25
Alignment explanation
Indices: 42260777--42260870 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
42260767 CATGCCAATC
*
42260777 TACAGCTCGTGTGAGCATACTGATT
1 TACAGCTCGTGTGAGCATACCGATT
* * * * *
42260802 TACAGCTTGTGAGAGTATACCAATC
1 TACAGCTCGTGTGAGCATACCGATT
*
42260827 TAGAGCTC-TAGTGAGCATACCGATT
1 TACAGCTCGT-GTGAGCATACCGATT
* *
42260852 CACAGCTCGTATGAGCATA
1 TACAGCTCGTGTGAGCATA
42260871 AATGTACATG
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.96
26 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
TACAGCTCGTGTGAGCATACCGATT
Found at i:42260834 original size:50 final size:50
Alignment explanation
Indices: 42260752--42260858 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
42260742 CATTCCGACC
* * *
42260752 CACAACTTGTGAGAGCATGCCAATCTACAGCTCGT-GTGAGCATACTGATT
1 CACAGCTTGTGAGAGCATACCAATCTACAGCTC-TAGTGAGCATACCGATT
* * *
42260802 TACAGCTTGTGAGAGTATACCAATCTAGAGCTCTAGTGAGCATACCGATT
1 CACAGCTTGTGAGAGCATACCAATCTACAGCTCTAGTGAGCATACCGATT
42260852 CACAGCT
1 CACAGCT
42260859 CGTATGAGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (50 bp):
CACAGCTTGTGAGAGCATACCAATCTACAGCTCTAGTGAGCATACCGATT
Found at i:42263413 original size:93 final size:93
Alignment explanation
Indices: 42263305--42263475 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
42263295 GCCCCTAAGT
* *
42263305 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42263370 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
42263398 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42263463 CGAGTTCGGATGC
66 CGAGTTCGGATGC
42263476 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:42263472 original size:46 final size:46
Alignment explanation
Indices: 42263300--42263472 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
42263290 AACCCGCCCC
* * * *
42263300 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
42263346 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
42263394 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
42263439 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42263473 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:42277062 original size:51 final size:47
Alignment explanation
Indices: 42276970--42277355 Score: 522
Period size: 47 Copynumber: 8.1 Consensus size: 47
42276960 TTAGGATTTT
* * *
42276970 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
42277017 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
*
42277068 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
** *
42277115 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C---ATGCATATGTGTGATAAGGCCGAATGGCCA
* *
42277166 ATGTGATGAGTGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
*
42277213 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCG-ATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
42277259 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * * *
42277306 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCTGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
42277353 ATG
1 ATG
42277356 CGAAACGTGT
Statistics
Matches: 304, Mismatches: 26, Indels: 18
0.87 0.07 0.05
Matches are distributed among these distances:
46 43 0.14
47 174 0.57
48 1 0.00
49 2 0.01
50 1 0.00
51 83 0.27
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:42277072 original size:24 final size:24
Alignment explanation
Indices: 42277044--42277119 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
42277034 CCGTATATAT
42277044 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
42277068 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
42277091 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
42277115 ATGTG
1 ATGTG
42277120 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:42277081 original size:98 final size:97
Alignment explanation
Indices: 42276970--42277355 Score: 570
Period size: 98 Copynumber: 4.0 Consensus size: 97
42276960 TTAGGATTTT
* *
42276970 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
42277035 CGTATATATATGTGTGATAAGGCCGAATGGCCA
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCA
42277068 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* *
42277133 TGTATATATATGCGTGATAAGGCCGAATGGCCA
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCA
*
42277166 ATGTGATGAGTGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
***
42277229 C-ATGCGTATGTGTGATAAGGCCG-ATGGCCA
66 CGATATATATGTGTGATAAGGCCGAATGGCCA
* * * *
42277259 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* * *
42277324 TGA-ATATATGTG-G-TAAGGCTGAATGGCTA
66 CGATATATATGTGTGATAAGGCCGAATGGCCA
42277353 ATG
1 ATG
42277356 CGAAACGTGT
Statistics
Matches: 264, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
93 73 0.28
94 28 0.11
95 6 0.02
96 1 0.00
98 156 0.59
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (97 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
CGATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:42277418 original size:46 final size:46
Alignment explanation
Indices: 42277329--42277419 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
42277319 GAACATGAAT
* ** * *
42277329 ATATGTGGTAAGGCTGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
42277375 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
42277420 TGTATATATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:42277672 original size:37 final size:37
Alignment explanation
Indices: 42277564--42277672 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
42277554 GGAAATATAT
* *
42277564 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
42277601 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
42277638 TCCGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
42277673 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:42279491 original size:40 final size:40
Alignment explanation
Indices: 42278928--42279479 Score: 843
Period size: 40 Copynumber: 13.8 Consensus size: 40
42278918 GAGAATTGAG
*
42278928 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
42278968 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* *
42279008 AGTGGTATATCCGGGCTAAGTCTCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * *
42279048 AGTGATATATCTGGGCTAAGTCTCGAGGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
42279088 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
42279128 AGTGATATATCTGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * *
42279168 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* ** *
42279208 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* *
42279248 GGTGTTATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
42279288 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
42279328 AGTGATATATCTGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * *
42279368 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* ** *
42279408 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * * *
42279448 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCA
42279480 ATCATGCTGG
Statistics
Matches: 467, Mismatches: 45, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 467 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
Found at i:42279763 original size:58 final size:57
Alignment explanation
Indices: 42279691--42279799 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
42279681 CGAATGATTA
* *
42279691 GAGGCACTGTGTGTGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* * *
42279749 GAGGCACTGTGTGTGCGAGTTCTTCAACCAAGCACTATGTGTGCGAGATCG
1 GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCG
42279800 ATCAGTGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 26 0.57
58 20 0.43
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:42294666 original size:43 final size:43
Alignment explanation
Indices: 42294552--42294659 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
42294542 GATTAACGAG
42294552 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGACATCATT
1 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGACATCATT
* * *
42294595 ATGTGATTATATGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGACATCATT
*
42294638 ATTTGATT-TCGTGTAAGACCAT
1 ATGTGATTAT-GTGTAAGACCAT
42294660 AGCTGGGCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (43 bp):
ATGTGATTATGTGTAAGACCATGTCTGGGACATTGACATCATT
Found at i:42297924 original size:24 final size:24
Alignment explanation
Indices: 42297897--42297970 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
42297887 ACTAAGTGCT
42297897 AATATCATGGCTCGAAGCCAAATC
1 AATATCATGGCTCGAAGCCAAATC
* * *
42297921 AATAT-A--ACTCGCACCCAAAGTGC
1 AATATCATGGCTCGAAGCCAAA-T-C
*
42297944 TAATATCATGGCTTGAAGCCAAATC
1 -AATATCATGGCTCGAAGCCAAATC
42297969 AA
1 AA
42297971 AGTAATTTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
21 10 0.27
22 1 0.03
23 2 0.05
24 12 0.32
25 2 0.05
26 1 0.03
27 9 0.24
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (24 bp):
AATATCATGGCTCGAAGCCAAATC
Found at i:42297951 original size:48 final size:49
Alignment explanation
Indices: 42297880--42298019 Score: 185
Period size: 48 Copynumber: 2.9 Consensus size: 49
42297870 ACTTAGGAGT
* *
42297880 CTCGCACACTAAGTGCTAATATCATGGCTCGAAGCCAAATCAATA-TAA
1 CTCGCACCCAAAGTGCTAATATCATGGCTCGAAGCCAAATCAATAGTAA
*
42297928 CTCGCACCCAAAGTGCTAATATCATGGCTTGAAGCCAAATCAA-AGTAA
1 CTCGCACCCAAAGTGCTAATATCATGGCTCGAAGCCAAATCAATAGTAA
* * ** * *
42297976 TTTGCACCTGAAGTGCTGATATCATGGCCCGAAGCCAAATCAAT
1 CTCGCACCCAAAGTGCTAATATCATGGCTCGAAGCCAAATCAAT
42298020 GTATTCCCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.01
48 79 0.99
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (49 bp):
CTCGCACCCAAAGTGCTAATATCATGGCTCGAAGCCAAATCAATAGTAA
Found at i:42297966 original size:27 final size:27
Alignment explanation
Indices: 42297890--42297966 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
42297880 CTCGCACACT
42297890 AAGTGCTAATATCATGGCTCGAAGCCA
1 AAGTGCTAATATCATGGCTCGAAGCCA
* * *
42297917 AA-T-C-AATAT-A--ACTCGCACCCA
1 AAGTGCTAATATCATGGCTCGAAGCCA
*
42297938 AAGTGCTAATATCATGGCTTGAAGCCA
1 AAGTGCTAATATCATGGCTCGAAGCCA
42297965 AA
1 AA
42297967 TCAAAGTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
21 10 0.27
22 1 0.03
23 2 0.05
24 10 0.27
25 2 0.05
26 1 0.03
27 11 0.30
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (27 bp):
AAGTGCTAATATCATGGCTCGAAGCCA
Found at i:42302646 original size:51 final size:50
Alignment explanation
Indices: 42302569--42302680 Score: 188
Period size: 51 Copynumber: 2.2 Consensus size: 50
42302559 CTGATCAATA
42302569 ACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTAACAAGTG
1 ACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTAAC-AGTG
* * *
42302620 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAGTG
1 ACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTAACAGTG
42302670 ACAAGTGATAA
1 ACAAGTGATAA
42302681 ATGTGATCAG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
50 15 0.26
51 43 0.74
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (50 bp):
ACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTAACAGTG
Found at i:42321750 original size:27 final size:26
Alignment explanation
Indices: 42321708--42321861 Score: 105
Period size: 27 Copynumber: 5.8 Consensus size: 26
42321698 GCTCGAGTTG
* * *
42321708 AAAATTACTGAATACCCCTGATTTTT
1 AAAATTACAGAATACCCCTAATTTGT
* *
42321734 GAAATTACAGAAGTACCTCTAATTTGT
1 AAAATTACAGAA-TACCCCTAATTTGT
* ** *
42321761 AAAATTACCAAAATACCCC-AGGTTAT
1 AAAATTA-CAGAATACCCCTAATTTGT
* *
42321787 AAAATTACCGAAATACCCCCAATTTGT
1 AAAATTACAG-AATACCCCTAATTTGT
* *
42321814 AAAATTACCGAAATACTCCC-AGTTTGT
1 AAAATTACAG-AATAC-CCCTAATTTGT
* *
42321841 AAAATGACCATAATACCCCTA
1 AAAATTA-CAGAATACCCCTA
42321862 TAGGGTAAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
25 1 0.01
26 32 0.32
27 60 0.59
28 8 0.08
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (26 bp):
AAAATTACAGAATACCCCTAATTTGT
Found at i:42321767 original size:53 final size:52
Alignment explanation
Indices: 42321735--42321845 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 52
42321725 CTGATTTTTG
* * *
42321735 AAATTACAGAAGTACCTCTAATTTGTAAAATTACCAAAATACCCCAGGTTATA
1 AAATTACAGAAATACCCCCAATTTGTAAAATTA-CAAAATACCCCAGGTTATA
* * * *
42321788 AAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACTCCCAGTTTGTA
1 AAATTACAGAAATACCCCCAATTTGTAAAATTA-CAAAATAC-CCCAGGTTATA
42321842 AAAT
1 AAAT
42321846 GACCATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 37 0.74
54 13 0.26
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (52 bp):
AAATTACAGAAATACCCCCAATTTGTAAAATTACAAAATACCCCAGGTTATA
Found at i:42321869 original size:27 final size:27
Alignment explanation
Indices: 42321839--42321953 Score: 146
Period size: 27 Copynumber: 4.4 Consensus size: 27
42321829 CTCCCAGTTT
* *
42321839 GTAAAATGACCATAATACCCCTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
**
42321866 GTAAAATGA-CGT--GGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
42321890 GTAAATTGACCGTAATACCTCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
42321917 GTAAAATGACCGTAATACCCCTGTATG
1 GTAAAATGACCGTAATACCCCTGTAGG
42321944 GTAAAATGAC
1 GTAAAATGAC
42321954 GATTATGCCC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
24 17 0.23
25 3 0.04
26 2 0.03
27 52 0.70
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:42321870 original size:54 final size:53
Alignment explanation
Indices: 42321759--42321872 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 53
42321749 CCTCTAATTT
* **
42321759 GTAAAATTACCAAAATACCCCAGGTTATAAAATTACCGAAATACCCCCAATTT
1 GTAAAATTACCAAAATACCCCAGGTTATAAAATGACCGAAATACCCCCAATGG
* * * *
42321812 GTAAAATTACCGAAATACTCCCAGTTTGTAAAATGACC-ATAATA-CCCCTATAGG
1 GTAAAATTACCAAAATAC-CCCAGGTTATAAAATGACCGA-AATACCCCCAAT-GG
42321866 GTAAAAT
1 GTAAAAT
42321873 GACGTGGCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
53 24 0.47
54 27 0.53
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (53 bp):
GTAAAATTACCAAAATACCCCAGGTTATAAAATGACCGAAATACCCCCAATGG
Found at i:42322179 original size:26 final size:27
Alignment explanation
Indices: 42322089--42322179 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
42322079 AAGGAGGAAG
* *
42322089 TACTG-TATTGGTGACTATGTCACATT
1 TACTGTTACTGGTGACTATGCCACATT
* *
42322115 CACTGTTACTGGTGACTATGCCACAAT
1 TACTGTTACTGGTGACTATGCCACATT
* *
42322142 TACTGATACTGGTGGCT-TGCCACATT
1 TACTGTTACTGGTGACTATGCCACATT
*
42322168 TACTGTTTCTGG
1 TACTGTTACTGG
42322180 CAACTACGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 22 0.41
27 32 0.59
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (27 bp):
TACTGTTACTGGTGACTATGCCACATT
Found at i:42322383 original size:28 final size:28
Alignment explanation
Indices: 42322329--42322395 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
42322319 CATTACACTG
* * * * *
42322329 TACTGATATTGTATTGGGCTTAGGCCCA
1 TACTGTTACTGTATAGGGCTAAAGCCCA
42322357 TACTGTTACTGTATAGGGCTAAAGCCCA
1 TACTGTTACTGTATAGGGCTAAAGCCCA
*
42322385 GACTGTT-CTGT
1 TACTGTTACTGT
42322396 TACTATGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (28 bp):
TACTGTTACTGTATAGGGCTAAAGCCCA
Found at i:42322396 original size:33 final size:33
Alignment explanation
Indices: 42322363--42322490 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 33
42322353 CCCATACTGT
* * *
42322363 TACTGTATAGGGCTAAAGCCCAGACTGTTCTGT
1 TACTGGATAGGGCTAAGGCCCAGACTGTTCTGA
* * * *
42322396 TACTATG-TAGGGCTAAGGCCCAGATTGTACTAA
1 TACT-GGATAGGGCTAAGGCCCAGACTGTTCTGA
* *
42322429 TACTGGATAGGGCTAAGGCTCAGA-TTTTACTGA
1 TACTGGATAGGGCTAAGGCCCAGACTGTT-CTGA
* *
42322462 TACTGGATATGGCTCAGGCCCAGACTGTT
1 TACTGGATAGGGCTAAGGCCCAGACTGTT
42322491 ACTGCATGCA
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
32 3 0.04
33 69 0.92
34 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (33 bp):
TACTGGATAGGGCTAAGGCCCAGACTGTTCTGA
Found at i:42331781 original size:16 final size:16
Alignment explanation
Indices: 42331756--42331793 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42331746 TATGTACGTA
42331756 AAACTC-ATAAGTAAT
1 AAACTCGATAAGTAAT
*
42331771 AAACTCGATAAGTGAT
1 AAACTCGATAAGTAAT
*
42331787 GAACTCG
1 AAACTCG
42331794 TGGTAAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (16 bp):
AAACTCGATAAGTAAT
Found at i:42333955 original size:46 final size:46
Alignment explanation
Indices: 42333905--42334077 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
42333895 TGGTTGAGCA
42333905 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
42333951 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
42333996 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
42334044 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
42334078 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.58
47 27 0.26
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42334061 original size:93 final size:93
Alignment explanation
Indices: 42333902--42334072 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
42333892 GGATGGTTGA
***
42333902 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
*
42333967 TGAGTTCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
42333995 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
42334060 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42334073 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:42338183 original size:25 final size:25
Alignment explanation
Indices: 42338153--42338209 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
42338143 CTATAAACAG
*
42338153 TAAGCTCCTCCAAGCTAAATAACGA
1 TAAGCTCCTCCAAGATAAATAACGA
* * *
42338178 TAAGCTCCTCCGAGATAAATAATGG
1 TAAGCTCCTCCAAGATAAATAACGA
42338203 TAAGCTC
1 TAAGCTC
42338210 ATATGAGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (25 bp):
TAAGCTCCTCCAAGATAAATAACGA
Found at i:42350624 original size:47 final size:47
Alignment explanation
Indices: 42350526--42350794 Score: 169
Period size: 47 Copynumber: 5.7 Consensus size: 47
42350516 AGATGTAAGC
* * *
42350526 CAGTGTAAGA-CATGTCTGGGGCAT-GCATCAGCTGCGA--GATG-TGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGATTGA-GATGT
* * *
42350570 CAATGTAAGACCATGTCTAGGACATGGCATCGGCACGATAGAGATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATTGAGATGT
* * *
42350617 CAGTGTAAAACCATGTCTGGGACATGGCCTCGGCATGGAAATGTGAGA-G-
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CG--AT-TGAGATGT
* * * * **
42350666 CTAGTCTAAGACCATGTCTGTGACATGGCGTCGGCCTCGATTTCGATAGT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATTGAGAT-GT
* ** ** *
42350716 CAGTGTAAGACTATGTCTGGGACATGGCATCAACTTGA-TG-GATGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATTGAGATG-T
* *
42350762 CTAGTGTAAGTCCATGTCTGGGACAAGGCATCG
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCG
42350795 ATAGACCCCA
Statistics
Matches: 177, Mismatches: 32, Indels: 29
0.74 0.13 0.12
Matches are distributed among these distances:
44 9 0.05
45 16 0.09
46 12 0.07
47 67 0.38
48 7 0.04
49 28 0.16
50 33 0.19
51 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATTGAGATGT
Found at i:42352380 original size:43 final size:44
Alignment explanation
Indices: 42352319--42352456 Score: 165
Period size: 43 Copynumber: 3.2 Consensus size: 44
42352309 GGTGTGATTA
*
42352319 CATGTCTGGGACAATGGCATTGTAT-TGTGATTTCGTGTAAGAT
1 CATGTCTGGGACAATGGCATTGTATATGTGATTTCGTGTAAGAC
* * * *
42352362 CATGTTTGGGACATTGGCATCGT-TATATGATTTCGTGTAAGAC
1 CATGTCTGGGACAATGGCATTGTATATGTGATTTCGTGTAAGAC
* ** *
42352405 CCTGTCTGGGACAATGGCATTG-ATATGTGATAACATGTAAGAC
1 CATGTCTGGGACAATGGCATTGTATATGTGATTTCGTGTAAGAC
*
42352448 CATATCTGG
1 CATGTCTGG
42352457 ATATGGTGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 77 0.99
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (44 bp):
CATGTCTGGGACAATGGCATTGTATATGTGATTTCGTGTAAGAC
Found at i:42354728 original size:50 final size:50
Alignment explanation
Indices: 42354648--42354751 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
42354638 CTGTAAACTG
* * *
42354648 TAAGCTCCTCCGAGCTAAATAATGATAAGCT-CTCTTGATCAGAATAACAA
1 TAAGATCCTCCGAGCTAAATAATGATAAGCTCCTC-CGAGCAGAATAACAA
* * *
42354698 TAAGATCCTCTGAGCTGAATAAT-AGTAAGCTCCTCCGAGCTGAATAACAA
1 TAAGATCCTCCGAGCTAAATAATGA-TAAGCTCCTCCGAGCAGAATAACAA
42354748 TAAG
1 TAAG
42354752 CTCATACGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.02
50 42 0.91
51 3 0.07
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (50 bp):
TAAGATCCTCCGAGCTAAATAATGATAAGCTCCTCCGAGCAGAATAACAA
Found at i:42354764 original size:25 final size:24
Alignment explanation
Indices: 42354648--42354765 Score: 101
Period size: 25 Copynumber: 4.7 Consensus size: 24
42354638 CTGTAAACTG
* **
42354648 TAAGCTCCTCCGAGCTAAATAATGA
1 TAAGCTCCT-CGAGCTGAATAACAA
* * *
42354673 TAAGCTCTCTTGATCAGAATAACAA
1 TAAGCTC-CTCGAGCTGAATAACAA
* * *
42354698 TAAGATCCTCTGAGCTGAATAATAG
1 TAAGCTCCTC-GAGCTGAATAACAA
42354723 TAAGCTCCTCCGAGCTGAATAACAA
1 TAAGCTCCT-CGAGCTGAATAACAA
*
42354748 TAAGCTCATACGAGCTGA
1 TAAGCTCCT-CGAGCTGA
42354766 GTTTCGGTAA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
24 2 0.03
25 68 0.93
26 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (24 bp):
TAAGCTCCTCGAGCTGAATAACAA
Found at i:42380051 original size:13 final size:13
Alignment explanation
Indices: 42380029--42380061 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42380019 AAAGGGCTTT
42380029 TTAT-TAAACTAA
1 TTATCTAAACTAA
42380041 TTATCTAAACTAA
1 TTATCTAAACTAA
*
42380054 TTAACTAA
1 TTATCTAA
42380062 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:42382793 original size:5 final size:5
Alignment explanation
Indices: 42382783--42382874 Score: 59
Period size: 5 Copynumber: 17.8 Consensus size: 5
42382773 TATGTCTTTC
* *
42382783 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
42382831 AAAA- ATAAA- AAAAT AAAAT AAAAT AAAAAT AAGAAT -AAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
42382875 AATAGGAGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
3 3 0.04
4 7 0.10
5 32 0.45
6 29 0.41
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:42382829 original size:6 final size:6
Alignment explanation
Indices: 42382803--42382878 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
42382793 AATAAAATTG
* * * *
42382803 AAATGA AAATAA AAATCA AAAGAA AAATAA AAATAA AAAAATA AAAT-A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATA-A AAATAA
* *
42382851 AAATAA AAATAA GAATAA ATA-AA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATA
42382879 GGAGCATTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
5 9 0.16
6 43 0.77
7 4 0.07
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:42382876 original size:17 final size:16
Alignment explanation
Indices: 42382784--42382878 Score: 65
Period size: 17 Copynumber: 5.8 Consensus size: 16
42382774 ATGTCTTTCA
42382784 AAATAAAATAATAAAATT
1 AAATAAAA-AATAAAA-T
*
42382802 GAAAT-GAAAATAAAAAT
1 -AAATAAAAAAT-AAAAT
42382819 CAAA-AGAAAAATAAAA-
1 -AAATA-AAAAATAAAAT
*
42382835 ATA-AAAAAATAAAAT
1 AAATAAAAAATAAAAT
42382850 AAA-ATAAAAATAAGAAT
1 AAATA-AAAAATAA-AAT
42382867 AAATAAAAAATA
1 AAATAAAAAATA
42382879 GGAGCATTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.16
15 6 0.09
16 8 0.12
17 24 0.38
18 12 0.19
19 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (16 bp):
AAATAAAAAATAAAAT
Found at i:42388253 original size:13 final size:13
Alignment explanation
Indices: 42388231--42388263 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42388221 AAGGGTTTGT
42388231 TTAT-TAAACTAA
1 TTATCTAAACTAA
42388243 TTATCTAAACTAA
1 TTATCTAAACTAA
*
42388256 TTAACTAA
1 TTATCTAA
42388264 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:42391815 original size:40 final size:40
Alignment explanation
Indices: 42391741--42391874 Score: 180
Period size: 40 Copynumber: 3.4 Consensus size: 40
42391731 TCTGAATTCT
* * *
42391741 TGAAAAGGTT-AAAAAGGTATATCCGAAATAGATATCAAA
1 TGAAAAGGTTGAAAAGGGTATATCTGAAATGGATATCAAA
42391780 TGAAAAGGTTGAAAAGGGTATATCTGAAATGGATATCAAA
1 TGAAAAGGTTGAAAAGGGTATATCTGAAATGGATATCAAA
* * * *
42391820 TGAAAAGGTTGAAAAGGATATATGTGAAACGGATATCCAA
1 TGAAAAGGTTGAAAAGGGTATATCTGAAATGGATATCAAA
* *
42391860 TTAAAAGGTTAAAAA
1 TGAAAAGGTTGAAAA
42391875 AGCTTGTTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 10 0.12
40 75 0.88
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.24
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGGTATATCTGAAATGGATATCAAA
Found at i:42402844 original size:18 final size:17
Alignment explanation
Indices: 42402812--42402845 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42402802 ATCTGATGAG
*
42402812 AAATTTTTTATTTTATT
1 AAATTTTTAATTTTATT
42402829 AAATTTTTAATGTTTAT
1 AAATTTTTAAT-TTTAT
42402846 GGGATCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
AAATTTTTAATTTTATT
Found at i:42414129 original size:16 final size:16
Alignment explanation
Indices: 42414110--42414140 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42414100 CTTCTTCACT
42414110 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
42414126 TACTTACTTACTTAA
1 TACTCACTTACTTAA
42414141 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:42414146 original size:20 final size:20
Alignment explanation
Indices: 42414107--42414146 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42414097 AAACTTCTTC
* *
42414107 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
42414127 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
42414147 TTATTAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:42414521 original size:55 final size:53
Alignment explanation
Indices: 42414390--42414578 Score: 170
Period size: 55 Copynumber: 3.5 Consensus size: 53
42414380 ACTTACCATT
* *
42414390 GCCATGTCTTGACGTGGTCTTACATGATATCCTTGCCTTATGAACTCACCAAA
1 GCCATGTCTTGACATGGTCTTACATGAGATCCTTGCCTTATGAACTCACCAAA
* * * *
42414443 GCCAT-TCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATA
1 GCCATGT-CTTGACATGGTCTTACATGAGATCC-TTGCCTTAT-G-AACTCACCAA-A
** * *
42414499 -CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAACCTTACCAATT
1 GCCATGTCTTGACATGGTCTTACATGAGATCCTTGCCTTATG-AA-CTCACCAA-A
* *
42414553 GCCATGCCTTGGCATGGTCTTACATG
1 GCCATGTCTTGACATGGTCTTACATG
42414579 GTATTCTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
52 3 0.03
53 35 0.31
54 9 0.08
55 61 0.54
56 4 0.04
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
GCCATGTCTTGACATGGTCTTACATGAGATCCTTGCCTTATGAACTCACCAAA
Found at i:42415979 original size:4 final size:4
Alignment explanation
Indices: 42415970--42416001 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
42415960 GAATTAATCT
42415970 TGAA TGAA TG-A TGAA TGAA TG-A TGAA TGAA TG
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TG
42416002 GTTAGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.23
4 20 0.77
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (4 bp):
TGAA
Found at i:42415984 original size:11 final size:11
Alignment explanation
Indices: 42415970--42416001 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
42415960 GAATTAATCT
42415970 TGAATGAATGA
1 TGAATGAATGA
42415981 TGAATGAATGA
1 TGAATGAATGA
42415992 TGAATGAATG
1 TGAATGAATG
42416002 GTTAGTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
TGAATGAATGA
Found at i:42415984 original size:22 final size:22
Alignment explanation
Indices: 42415959--42416001 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42415949 GTTTTATTAT
* *
42415959 TGAATTAATCTTGAATGAATGA
1 TGAATGAATCATGAATGAATGA
*
42415981 TGAATGAATGATGAATGAATG
1 TGAATGAATCATGAATGAATG
42416002 GTTAGTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (22 bp):
TGAATGAATCATGAATGAATGA
Found at i:42415985 original size:7 final size:8
Alignment explanation
Indices: 42415970--42416001 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
42415960 GAATTAATCT
42415970 TGAATGAA
1 TGAATGAA
42415978 TG-ATGAA
1 TGAATGAA
42415985 TGAATG-A
1 TGAATGAA
42415992 TGAATGAA
1 TGAATGAA
42416000 TG
1 TG
42416002 GTTAGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (8 bp):
TGAATGAA
Found at i:42417971 original size:25 final size:26
Alignment explanation
Indices: 42417921--42417981 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
42417911 ACATATTTTC
42417921 TCAAAATTTTACCAAAGGAAATATTG
1 TCAAAATTTTACCAAAGGAAATATTG
*
42417947 TCAAAATTTTTCC-AAGGTAAA-ATTG
1 TCAAAATTTTACCAAAGG-AAATATTG
*
42417972 TCTAAATTTT
1 TCAAAATTTT
42417982 GTTGAGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (26 bp):
TCAAAATTTTACCAAAGGAAATATTG
Found at i:42422400 original size:49 final size:49
Alignment explanation
Indices: 42422338--42422443 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
42422328 CTGTGACCGC
* * * *
42422338 ATAACCACTATCAACTAGGA-TCCTGAGTTATACTCCAAC-CTGTGATTGT
1 ATAACCACTATCAACTAAGAGCCCT-AGTTATACTCCAACTC-ATGATCGT
*
42422387 ATAACCA-TCATCAACTAAGAGCCCTAGTTATACTTCAACTCATGATCGT
1 ATAACCACT-ATCAACTAAGAGCCCTAGTTATACTCCAACTCATGATCGT
42422436 ATAACCAC
1 ATAACCAC
42422444 CGTGAACAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
48 1 0.02
49 43 0.90
50 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (49 bp):
ATAACCACTATCAACTAAGAGCCCTAGTTATACTCCAACTCATGATCGT
Found at i:42422839 original size:13 final size:13
Alignment explanation
Indices: 42422821--42422846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42422811 TTCTAATGTC
42422821 TTATAATTACAAT
1 TTATAATTACAAT
42422834 TTATAATTACAAT
1 TTATAATTACAAT
42422847 GAATCCACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTATAATTACAAT
Found at i:42425891 original size:48 final size:48
Alignment explanation
Indices: 42425834--42426017 Score: 183
Period size: 48 Copynumber: 3.8 Consensus size: 48
42425824 ACGACATGTG
* *
42425834 AGTATTGAGATCCTGTATAAGACCATACCTGGGATATGGCATCGGCATC
1 AGTA-TGAGATCCAGTATAAGACCATATCTGGGATATGGCATCGGCATC
* * *
42425883 AGTATGAGATCCAATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 AGTATGAGATCCAGTATAAGACCATATCTGGGATATGGCATCGGCATC
* * * * * *
42425931 AATATGAGGTCCCGTATAAGACCATGTTTGGGACATGGCATCGGCA-C
1 AGTATGAGATCCAGTATAAGACCATATCTGGGATATGGCATCGGCATC
* * * * *
42425978 CGTTATGAGACTTCA-TGTAAGACCATGTCTGGGACATGGC
1 AG-TATGAGA-TCCAGTATAAGACCATATCTGGGATATGGC
42426018 TTTGATATGA
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
47 1 0.01
48 105 0.94
49 6 0.05
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (48 bp):
AGTATGAGATCCAGTATAAGACCATATCTGGGATATGGCATCGGCATC
Found at i:42425971 original size:96 final size:96
Alignment explanation
Indices: 42425839--42426017 Score: 236
Period size: 96 Copynumber: 1.9 Consensus size: 96
42425829 ATGTGAGTAT
* *
42425839 TGAGATCCTGTATAAGACCATACCTGGGATATGGCATCGGCATCAG-TATGAGA-TCCAATGTAA
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATCGGCA-CAGTTATGAGACTCC-ATGTAA
*
42425902 GACCATATCTGGGATATGGCATTGGCATCAATA
64 GACCATATCTGGGACATGGCATTGGCATCAATA
* *** * *
42425935 TGAGGTCCCGTATAAGACCATGTTTGGGACATGGCATCGGCACCGTTATGAGACTTCATGTAAGA
1 TGAGATCCCGTATAAGACCATACCTGGGACATGGCATCGGCACAGTTATGAGACTCCATGTAAGA
*
42426000 CCATGTCTGGGACATGGC
66 CCATATCTGGGACATGGC
42426018 TTTGATATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
95 2 0.03
96 67 0.94
97 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (96 bp):
TGAGATCCCGTATAAGACCATACCTGGGACATGGCATCGGCACAGTTATGAGACTCCATGTAAGA
CCATATCTGGGACATGGCATTGGCATCAATA
Found at i:42426040 original size:42 final size:42
Alignment explanation
Indices: 42425924--42426215 Score: 182
Period size: 42 Copynumber: 6.8 Consensus size: 42
42425914 GATATGGCAT
* * ** * *
42425924 TGGCATCAATATGAGGTCCCGTATAAGACCATGTTTGGGACA
1 TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGACA
* *
42425966 TGGCATCGGCACCGTTATGAGACTTCATGTAAGACCATGTCTGGGACA
1 TGGCATC-G-A----TATGAGATTTCGTGTAAGACCATGTCTGGGACA
* * * * *
42426014 TGGCTTTGATATGATATTTTGTGTAAGACCATGTCTTGGACA
1 TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGACA
* *
42426056 TGG-AGCCGATACGAGA-TTCTGTGTAAGACCATAGT-TGGG-CTA
1 TGGCA-TCGATATGAGATTTC-GTGTAAGACCAT-GTCTGGGAC-A
* * * *
42426098 TTGGCATCGGTATGATATTACGTGTAAGACCATGTCTGAGACA
1 -TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGACA
* *
42426141 TGGCATCGTTATGAGATTTCGCGTAAGACCATAG-CTGGG-CTA
1 TGGCATCGATATGAGATTTCGTGTAAGACCAT-GTCTGGGAC-A
* * * * *
42426183 TTGTCTTCAATATGAGATTACATGTAAGACCAT
1 -TGGCATCGATATGAGATTTCGTGTAAGACCAT
42426216 ATCCAGGATA
Statistics
Matches: 192, Mismatches: 40, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
41 4 0.02
42 96 0.50
43 54 0.28
44 5 0.03
46 1 0.01
47 1 0.01
48 31 0.16
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (42 bp):
TGGCATCGATATGAGATTTCGTGTAAGACCATGTCTGGGACA
Found at i:42426134 original size:85 final size:85
Alignment explanation
Indices: 42426022--42426215 Score: 223
Period size: 85 Copynumber: 2.3 Consensus size: 85
42426012 CATGGCTTTG
** *
42426022 ATATGATATTTTGTGTAAGACCATGTCTTG-GACATGG-AGCCGATACGAGA-TTCTGTGTAAGA
1 ATATGATATTACGTGTAAGACCATGTC-TGAGACATGGCA-CCGATACGAGATTTC-GCGTAAGA
* *
42426084 CCATAGTTGGGCTATTGGCATCG
63 CCATAGCTGGGCTATTGGCATCA
* * * *
42426107 GTATGATATTACGTGTAAGACCATGTCTGAGACATGGCATCGTTATGAGATTTCGCGTAAGACCA
1 ATATGATATTACGTGTAAGACCATGTCTGAGACATGGCACCGATACGAGATTTCGCGTAAGACCA
* *
42426172 TAGCTGGGCTATTGTCTTCA
66 TAGCTGGGCTATTGGCATCA
* *
42426192 ATATGAGATTACATGTAAGACCAT
1 ATATGATATTACGTGTAAGACCAT
42426216 ATCCAGGATA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
84 2 0.02
85 86 0.93
86 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (85 bp):
ATATGATATTACGTGTAAGACCATGTCTGAGACATGGCACCGATACGAGATTTCGCGTAAGACCA
TAGCTGGGCTATTGGCATCA
Found at i:42434918 original size:17 final size:17
Alignment explanation
Indices: 42434896--42434932 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42434886 AGTGAATGAA
42434896 TGAATATTTGTTAAGTT
1 TGAATATTTGTTAAGTT
42434913 TGAATATTTGTTAAGTT
1 TGAATATTTGTTAAGTT
42434930 TGA
1 TGA
42434933 CTGGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (17 bp):
TGAATATTTGTTAAGTT
Found at i:42440987 original size:28 final size:28
Alignment explanation
Indices: 42440934--42440988 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
42440924 GAACTTTAGA
* **
42440934 ATAAAAATATACATAAAAGAGTTTTGAC
1 ATAAAAATATAAATAAAAGAAATTTGAC
42440962 ATAAATAATATAAATAAAA-AAATTTGA
1 ATAAA-AATATAAATAAAAGAAATTTGA
42440989 AGTTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAAAAATATAAATAAAAGAAATTTGAC
Found at i:42441221 original size:3 final size:3
Alignment explanation
Indices: 42441195--42441291 Score: 90
Period size: 3 Copynumber: 32.7 Consensus size: 3
42441185 GAATATAAAT
* * * * * *
42441195 ATA ATA CTA ATA GTA ATA AT- ATA ATA AT- ATA ATA ATG ACA ATA GTG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
42441241 ACA AAA AGTA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42441287 ATA AT
1 ATA AT
42441292 GATGATGATG
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
2 4 0.05
3 68 0.92
4 2 0.03
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:42444159 original size:40 final size:40
Alignment explanation
Indices: 42444082--42444299 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
42444072 AAACCAAGTA
* *
42444082 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
42444121 CCTTCGGGACTTAGCTCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42444161 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
42444201 CCTTCGAGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
42444241 CCTTCGGGGCTTAGCCCAGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
42444281 CCTTCGGGACTTAACCCGG
1 CCTTCGGGACTTAGCCCGG
42444300 TTATCATCCG
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 144 0.91
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42447343 original size:4 final size:4
Alignment explanation
Indices: 42447329--42447364 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
42447319 AATTTATTGA
*
42447329 AATT GATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT
42447365 GTGTAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:42447461 original size:21 final size:20
Alignment explanation
Indices: 42447420--42447472 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
42447410 AATTTATATG
* *
42447420 AAAATATGATAGTAAATAAAT
1 AAAATAT-ATAGAAAAAAAAT
42447441 ATAAATATATAGAAAAAAAAT
1 A-AAATATATAGAAAAAAAAT
42447462 AAAATGATATA
1 AAAAT-ATATA
42447473 TCAATTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.14
21 18 0.64
22 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAATATATAGAAAAAAAAT
Found at i:42447837 original size:13 final size:13
Alignment explanation
Indices: 42447819--42447843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42447809 AATAAGTAAA
42447819 ATATTAAAATTAT
1 ATATTAAAATTAT
42447832 ATATTAAAATTA
1 ATATTAAAATTA
42447844 AACTAAAATT
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:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTAAAATTAT
Found at i:42450070 original size:24 final size:24
Alignment explanation
Indices: 42450037--42450083 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42450027 TTCATATTTT
42450037 TAAAAAAGATAACAAAAAAAAAAG
1 TAAAAAAGATAACAAAAAAAAAAG
* * *
42450061 TAAAAGAGATCACAAAAATAAAA
1 TAAAAAAGATAACAAAAAAAAAA
42450084 TATAATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (24 bp):
TAAAAAAGATAACAAAAAAAAAAG
Found at i:42451109 original size:17 final size:17
Alignment explanation
Indices: 42451069--42451118 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
42451059 CACTTATAAA
* *
42451069 AATAATATACATAATTAT
1 AATAATATA-TTATTTAT
42451087 AA-AATATATTATTTAT
1 AATAATATATTATTTAT
*
42451103 AATAATATATTGTTTA
1 AATAATATATTATTTA
42451119 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.29
17 18 0.64
18 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
AATAATATATTATTTAT
Found at i:42455863 original size:20 final size:18
Alignment explanation
Indices: 42455830--42455871 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
42455820 TCCTTTTTTT
42455830 TTTTTTTTCTTTTTTAAC
1 TTTTTTTTCTTTTTTAAC
*
42455848 TTTTTTTTCTGCTTTTTCAC
1 TTTTTTTTCT--TTTTTAAC
42455868 TTTT
1 TTTT
42455872 ATATTTGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTAAC
Found at i:42456264 original size:12 final size:13
Alignment explanation
Indices: 42456247--42456283 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
42456237 CAAAAGACCA
42456247 TCATCATCTTC-T
1 TCATCATCTTCAT
*
42456259 TCATCACCTTCAT
1 TCATCATCTTCAT
42456272 T-ATCATCTTCAT
1 TCATCATCTTCAT
42456284 CAAAAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (13 bp):
TCATCATCTTCAT
Found at i:42463423 original size:21 final size:21
Alignment explanation
Indices: 42463397--42463436 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42463387 GGGGTTTATA
42463397 TTAAAAAACTATAAAAATGTT
1 TTAAAAAACTATAAAAATGTT
* *
42463418 TTAAAAAATTATTAAAATG
1 TTAAAAAACTATAAAAATG
42463437 ATAAAAAAAT
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:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAAAAAACTATAAAAATGTT
Found at i:42464787 original size:23 final size:23
Alignment explanation
Indices: 42464736--42464781 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
42464726 TAGATTTTTC
42464736 CTAAATATGATCACAAAATAATT
1 CTAAATATGATCACAAAATAATT
* *
42464759 CTAAATATTATCACTAAATAATT
1 CTAAATATGATCACAAAATAATT
42464782 TGAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (23 bp):
CTAAATATGATCACAAAATAATT
Found at i:42469326 original size:29 final size:29
Alignment explanation
Indices: 42469293--42469347 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42469283 TTTCTTCATA
42469293 ATTTTTATATTT-T-AAAATAATTTTAACG
1 ATTTTTA-ATTTCTAAAAATAATTTTAACG
*
42469321 ATTTTTAATTTCTAAAAATAGTTTTAA
1 ATTTTTAATTTCTAAAAATAATTTTAA
42469348 TTATTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.33
29 12 0.50
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTTTTAATTTCTAAAAATAATTTTAACG
Found at i:42469488 original size:17 final size:17
Alignment explanation
Indices: 42469468--42469500 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42469458 AAAATTAAAT
42469468 TAAAAAAATTTAAAAAG
1 TAAAAAAATTTAAAAAG
*
42469485 TAAAAAATTTTAAAAA
1 TAAAAAAATTTAAAAA
42469501 AAAAGCTAAA
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:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAAAATTTAAAAAG
Found at i:42473387 original size:21 final size:21
Alignment explanation
Indices: 42473319--42473392 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
42473309 TACAAATATA
*
42473319 AAAATATTTATAATTTAA--T
1 AAAATAATTATAATTTAATTT
* *
42473338 AGAAGTTATTATAATTGTACATTT
1 A-AAATAATTATAATT-TA-ATTT
*
42473362 CAAATAATTATAATTTAATTT
1 AAAATAATTATAATTTAATTT
*
42473383 AAAATTATTA
1 AAAATAATTA
42473393 GTTAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 14 0.33
22 3 0.07
23 12 0.29
24 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (21 bp):
AAAATAATTATAATTTAATTT
Found at i:42473592 original size:22 final size:21
Alignment explanation
Indices: 42473566--42473607 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
42473556 TTGAAATATT
42473566 AAAAATACTTTAATTATAATTA
1 AAAAAT-CTTTAATTATAATTA
*
42473588 TAAAAATTTTTAATTATAAT
1 -AAAAATCTTTAATTATAAT
42473608 ATTTAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATCTTTAATTATAATTA
Found at i:42480849 original size:19 final size:19
Alignment explanation
Indices: 42480825--42480873 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
42480815 AAAGTTTATT
**
42480825 CAATTTAGTTTAATTTTTA
1 CAATTTAGTCCAATTTTTA
42480844 CAATTTAGTCCAATTTTTA
1 CAATTTAGTCCAATTTTTA
42480863 CAATTTAGTCC
1 CAATTTAGTCC
42480874 TTGTACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (19 bp):
CAATTTAGTCCAATTTTTA
Found at i:42488666 original size:27 final size:25
Alignment explanation
Indices: 42488633--42488710 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 25
42488623 TGTAATAATG
42488633 ATATATACACAATATGGTATTAAGAA
1 ATATATACACAATATGGTATTAA-AA
* *
42488659 TATATATATACAATATAGTATTTAAAA
1 -ATATATACACAATATGGTA-TTAAAA
* *
42488686 ATATATACATAAGATGGTA-TAAAA
1 ATATATACACAATATGGTATTAAAA
42488710 A
1 A
42488711 CATGTACATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 6 0.14
26 15 0.34
27 19 0.43
28 4 0.09
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (25 bp):
ATATATACACAATATGGTATTAAAA
Found at i:42488708 original size:24 final size:24
Alignment explanation
Indices: 42488681--42488741 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
42488671 ATATAGTATT
*
42488681 TAAAAATATATACAT-AAGATGGTA
1 TAAAAATATATACATGAAAAT-GTA
* *
42488705 TAAAAACATGTACATGAAAATGTA
1 TAAAAATATATACATGAAAATGTA
42488729 TAAGAAATATATA
1 TAA-AAATATATA
42488742 TAATTAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.28
Consensus pattern (24 bp):
TAAAAATATATACATGAAAATGTA
Found at i:42488909 original size:44 final size:43
Alignment explanation
Indices: 42488861--42488975 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 43
42488851 ACACACATAT
*
42488861 ATATATAAATAATAGTATTAGAAATATACAA-T-ATAATATTAGAA
1 ATATATAAATAATA-TA-TAAAAATATACAACTAATAATATTA-AA
* * * *
42488905 ATATACATATAACAATATAAAAATATATAACTAATAATATTAAA
1 ATATATAAATAA-TATATAAAAATATACAACTAATAATATTAAA
42488949 ATATATATAATAATATATAAAAATATA
1 ATATATA-AATAATATATAAAAATATA
42488976 ATATTGAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
43 11 0.19
44 34 0.58
45 14 0.24
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (43 bp):
ATATATAAATAATATATAAAAATATACAACTAATAATATTAAA
Found at i:42488931 original size:22 final size:22
Alignment explanation
Indices: 42488882--42488979 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
42488872 ATAGTATTAG
*
42488882 AAATATACA-AT-ATAATATTAG
1 AAATATACATATAATAATA-TAA
*
42488903 AAATATACATATAACAATATAA
1 AAATATACATATAATAATATAA
* *
42488925 AAATATATA-ACTAATAATATTA
1 AAATATACATA-TAATAATATAA
*
42488947 AAATATATATAATAAT-ATATAA
1 AAATATACAT-ATAATAATATAA
42488969 AAATATA-ATAT
1 AAATATACATAT
42488980 TGAAAACATA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.03
21 12 0.18
22 42 0.64
23 9 0.14
24 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (22 bp):
AAATATACATATAATAATATAA
Found at i:42488934 original size:10 final size:10
Alignment explanation
Indices: 42488919--42488975 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
42488909 ACATATAACA
42488919 ATATAAAAAT
1 ATATAAAAAT
*
42488929 ATATAACTAAT
1 ATATAA-AAAT
42488940 AATATTAAAATAT
1 -ATA-TAAAA-AT
*
42488953 ATATAATAAT
1 ATATAAAAAT
42488963 ATATAAAAAT
1 ATATAAAAAT
42488973 ATA
1 ATA
42488976 ATATTGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 20 0.51
11 7 0.18
12 7 0.18
13 5 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:42488976 original size:42 final size:44
Alignment explanation
Indices: 42488859--42488976 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 44
42488849 ACACACACAT
*
42488859 ATATATATAAATAATAGTATTAGAAATAT-ACAATATAATATTAGAA
1 ATATATAT-AATAATA-TA-TAAAAATATAACAATATAATATTAGAA
* *
42488905 ATATACATATAACAATATA-AAAATATATAACTA-ATAATATTA-AA
1 ATAT--ATATAATAATATATAAAA-ATATAACAATATAATATTAGAA
42488949 ATATATATAATAATATATAAAAATATAA
1 ATATATATAATAATATATAAAAATATAA
42488977 TATTGAAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
42 18 0.29
43 4 0.06
44 9 0.14
45 13 0.21
46 9 0.14
47 6 0.10
48 4 0.06
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (44 bp):
ATATATATAATAATATATAAAAATATAACAATATAATATTAGAA
Found at i:42489203 original size:17 final size:16
Alignment explanation
Indices: 42489177--42489208 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42489167 CTATATGTAA
42489177 ATATATATACATACAT
1 ATATATATACATACAT
42489193 ATATAATATACATACA
1 ATAT-ATATACATACA
42489209 CTAATGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:42489224 original size:3 final size:3
Alignment explanation
Indices: 42489216--42489373 Score: 62
Period size: 3 Copynumber: 52.7 Consensus size: 3
42489206 ACACTAATGT
*
42489216 TAA TAA TAA TAA TAA -AA CTAGA -AA TAA TAA TAA TTAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA -TAA TAA TAA TAA
* * * ** * *
42489262 TACG TTA GAA -AA TAA TTAA T-A TGT TAA TAA AAA TAA TAG TAA TGAA
1 TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * *
42489308 -AA TAA TAC TAA CAG TAA TAA TAA -AGA TAA TAA TAGA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA
* **
42489351 TAA TAG TAA TAA TGT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
42489374 TGTAAAAAAA
Statistics
Matches: 113, Mismatches: 26, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
2 13 0.12
3 88 0.78
4 11 0.10
5 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:42489370 original size:32 final size:33
Alignment explanation
Indices: 42489325--42489386 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
42489315 CTAACAGTAA
42489325 TAATAAAGATAATAATA-G-AAATAAAATAATAG
1 TAATAAAGATAATAATATGTAAA-AAAATAATAG
* *
42489357 TAATAATGTTAATAATATGTAAAAAAATAA
1 TAATAAAGATAATAATATGTAAAAAAATAA
42489387 AAATAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 15 0.58
33 8 0.31
34 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (33 bp):
TAATAAAGATAATAATATGTAAAAAAATAATAG
Found at i:42495187 original size:21 final size:21
Alignment explanation
Indices: 42495163--42495206 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42495153 CCTTTATGTC
* *
42495163 TTATTCTGAGTAAATATTCTT
1 TTATTCTAAGCAAATATTCTT
*
42495184 TTATTTTAAGCAAATATTCTT
1 TTATTCTAAGCAAATATTCTT
42495205 TT
1 TT
42495207 CTTGCATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (21 bp):
TTATTCTAAGCAAATATTCTT
Found at i:42499860 original size:64 final size:64
Alignment explanation
Indices: 42499786--42499913 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
42499776 TCATTCATAA
**
42499786 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGTATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
* *
42499850 CACATCTAGTTAGGAGTATTTGATTCATTTCGATCATAACATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
42499914 AAATATATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAGCAT
Found at i:42500151 original size:45 final size:44
Alignment explanation
Indices: 42499980--42500151 Score: 154
Period size: 45 Copynumber: 3.9 Consensus size: 44
42499970 GTGAAGTCAG
** **
42499980 ATCTTATCTCCCTGAAGTTGCAGCAGAATAGATCAAAGATTA-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGA-TAGC-A
* * * *
42500025 ACCTTATCTTCCTGAAGTTGCAGTGGAGTAGGTTGAAG-T-GACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGATAG-CA
** *
42500068 AGTCTTATCTCCCTGAAGTTGC-GATGGAGCAGACTGAAGATAGCGA
1 A-TCTTATCTCCCTGAAGTTGCAG-TGGAATAGATTGAAGATAGC-A
*
42500114 ATCTTATTTCCCTGAAGTTGCAGTGGAATAGATTGAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAG
42500152 CTATAAATAA
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
43 4 0.04
44 31 0.30
45 63 0.62
46 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGATAGCA
Found at i:42503810 original size:11 final size:10
Alignment explanation
Indices: 42503774--42503825 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
42503764 TTTAGGAAAA
*
42503774 TTTTAAATTT
1 TTTTATATTT
42503784 TTTTAT-TTT
1 TTTTATATTT
*
42503793 CTTTATATATT
1 TTTTATAT-TT
42503804 TTTTATA-TT
1 TTTTATATTT
*
42503813 TTTTAGATTT
1 TTTTATATTT
42503823 TTT
1 TTT
42503826 AAATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 16 0.46
10 11 0.31
11 8 0.23
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTATATTT
Found at i:42504378 original size:3 final size:3
Alignment explanation
Indices: 42504370--42504395 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42504360 CACTCTGCTC
42504370 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
42504396 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42515388 original size:4 final size:4
Alignment explanation
Indices: 42515379--42515413 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
42515369 AATCACCACC
*
42515379 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CATT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
42515414 ATGTTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Done.