Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 35 of 226
Found at i:15313736 original size:17 final size:18
Alignment explanation
Indices: 15313706--15313744 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
15313696 GTTGAACTGA
*
15313706 AATTTTTAAAAA-TTTTT
1 AATTTGTAAAAATTTTTT
*
15313723 AATTTGTAATAATTTTTT
1 AATTTGTAAAAATTTTTT
15313741 AATT
1 AATT
15313745 AGATTGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTGTAAAAATTTTTT
Found at i:15315652 original size:16 final size:16
Alignment explanation
Indices: 15315630--15315668 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
15315620 TACACCATAA
15315630 AAAATTAAAT-TAATT
1 AAAATTAAATATAATT
15315645 ATAAATTAAATAATAATT
1 A-AAATTAAAT-ATAATT
15315663 AAAATT
1 AAAATT
15315669 CGATTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 9 0.43
17 5 0.24
18 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAAATATAATT
Found at i:15319947 original size:13 final size:13
Alignment explanation
Indices: 15319926--15319959 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
15319916 TCTTTGATTT
15319926 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
15319940 GTTATTTATTTTA
1 ATTATTTATTTTA
15319953 ATTATTT
1 ATTATTT
15319960 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:15321621 original size:22 final size:22
Alignment explanation
Indices: 15321594--15321649 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
15321584 TGGGCACGGT
15321594 AAAGAAAAAAAAAAGAGAGAAAG
1 AAAGAAAAAAAAAAGA-AGAAAG
* * *
15321617 -GAGAAAAGAAGAAGAAGAAAG
1 AAAGAAAAAAAAAAGAAGAAAG
15321638 AAAGAAAAAAAA
1 AAAGAAAAAAAA
15321650 GGTAATGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAAAGAAGAAAG
Found at i:15321730 original size:12 final size:12
Alignment explanation
Indices: 15321713--15321738 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15321703 TTTGTGAATT
15321713 TTTTAGAAGATA
1 TTTTAGAAGATA
15321725 TTTTAGAAGATA
1 TTTTAGAAGATA
15321737 TT
1 TT
15321739 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:15321829 original size:19 final size:19
Alignment explanation
Indices: 15321805--15322067 Score: 132
Period size: 19 Copynumber: 14.2 Consensus size: 19
15321795 TTTGGATTAG
*
15321805 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
15321824 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
* *
15321846 AATTTTTTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
15321865 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * * *
15321888 -ATTTATAATTTTGCAT-TAGT
1 AATTT-T--GTATGAATATTGT
15321908 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
15321926 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
15321947 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
15321966 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
15321980 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
15321996 AATTTTATATGAATATTGC
1 AATTTTGTATGAATATTGT
* *
15322015 AATTTTTTTTG--TA-TG-
1 AATTTTGTATGAATATTGT
*
15322030 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
15322046 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
15322065 AAT
1 AAT
15322068 GTCGAGATAT
Statistics
Matches: 190, Mismatches: 23, Indels: 62
0.69 0.08 0.23
Matches are distributed among these distances:
13 2 0.01
14 9 0.05
15 10 0.05
16 15 0.08
17 7 0.04
18 8 0.04
19 74 0.39
20 14 0.07
21 20 0.11
22 23 0.12
23 3 0.02
24 4 0.02
25 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:15321834 original size:22 final size:22
Alignment explanation
Indices: 15321807--15321873 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
15321797 TGGATTAGAA
*
15321807 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTATAATTT
*
15321829 TTTTGTATGAATATTGTAA--T
1 TTTTGTATGAATATTATAATTT
*
15321849 TTTT-TATGAATATTATAATTA
1 TTTTGTATGAATATTATAATTT
15321870 TTTT
1 TTTT
15321874 ATAATTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 13 0.32
20 5 0.12
21 4 0.10
22 18 0.45
ACGTcount: A:0.30, C:0.01, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTTGTATGAATATTATAATTT
Found at i:15321894 original size:101 final size:101
Alignment explanation
Indices: 15321788--15321974 Score: 295
Period size: 101 Copynumber: 1.9 Consensus size: 101
15321778 ATATTTAGTG
*
15321788 TTTAT-AGTTTGGATTAGAATTTTGTATGAATATTCTAATTTTTTTGTATGAATATTGTAATTTT
1 TTTATAAGTTTGCATTAGAATTTTGTATGAATATTCTAA-TTTTTTGTATGAATATTGTAATTTT
*
15321852 TTATGAATATTATAATTATTTTATAATTAAATTTGTA
65 GTATGAATATTATAATTATTTTATAATTAAATTTGTA
* * *
15321889 TTTATAATTTTGCATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTG
1 TTTATAAGTTTGCATTAGAATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTG
* *
15321954 TATGAATATTGTAATTTTTTT
66 TATGAATATTATAATTATTTT
15321975 GTATGAATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 49 0.63
102 29 0.37
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (101 bp):
TTTATAAGTTTGCATTAGAATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAATTTTG
TATGAATATTATAATTATTTTATAATTAAATTTGTA
Found at i:15322009 original size:27 final size:26
Alignment explanation
Indices: 15321939--15322067 Score: 164
Period size: 27 Copynumber: 5.1 Consensus size: 26
15321929 TTTTTGTATG
15321939 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-TAATTTTGTATGAATATTGT
15321966 -A-ATTT--TTTTGTATGAATATTGT
1 AATATTTAATTTTGTATGAATATTGT
* *
15321988 AATATTATAATTTTATATGAATATTGC
1 AATATT-TAATTTTGTATGAATATTGT
15322015 AAT-TTT--TTTTGTATGAATATTGT
1 AATATTTAATTTTGTATGAATATTGT
15322038 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-TAATTTTGTATGAATATTGT
15322065 AAT
1 AAT
15322068 GTCGAGATAT
Statistics
Matches: 89, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.19
23 19 0.21
24 6 0.07
25 6 0.07
26 3 0.03
27 38 0.43
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
AATATTTAATTTTGTATGAATATTGT
Found at i:15322027 original size:101 final size:99
Alignment explanation
Indices: 15321800--15322067 Score: 235
Period size: 101 Copynumber: 2.7 Consensus size: 99
15321790 TATAGTTTGG
* * * * *
15321800 ATTAGAATTTTGTATGAATATTCTAATTTTTTTGTATGAATATTGTAATTTTTTATGAATATTAT
1 ATTAGAATATTGAATGAATATTGT-A-TTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
*
15321865 AATTATTTTATAATTAAATTTGTATTTATAATTTTGC
64 AATTATTTTATAATGAAATTTGTATTTATAATTTT-C
* * *
15321902 ATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGTA
1 ATTAGAATATTGAATGAATATTGT-ATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGTA
* *
15321967 ATTTTTTTGT-ATG-AATATTGTAATATTATAATTTT-
65 ATTATTTTATAATGAAAT-TTGT-AT-TTATAATTTTC
*** * * *
15322002 A-TATGAATATTGCAATTTTTTTTGTATGAATATTG--T-AATATTGTAATTTTGTATGAATATT
1 ATTA-GAATATTG-AATGAATATTGTAT--TTTTTGTATGAATATTGTAATTTTGTATGAATATT
15322063 GTAAT
62 GTAAT
15322068 GTCGAGATAT
Statistics
Matches: 143, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
99 35 0.24
100 16 0.11
101 54 0.38
102 38 0.27
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (99 bp):
ATTAGAATATTGAATGAATATTGTATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGTAA
TTATTTTATAATGAAATTTGTATTTATAATTTTC
Found at i:15322043 original size:50 final size:49
Alignment explanation
Indices: 15321939--15322063 Score: 214
Period size: 50 Copynumber: 2.5 Consensus size: 49
15321929 TTTTTGTATG
*
15321939 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
* *
15321988 AATATTATAATTTTATATGAATATTGCAATTTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGCAA-TTTTTTTGTATGAATATTGT
15322038 AATATTGTAATTTTGTATGAATATTG
1 AATATTGTAATTTTGTATGAATATTG
15322064 TAATGTCGAG
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 26 0.37
50 44 0.63
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
Found at i:15322189 original size:60 final size:60
Alignment explanation
Indices: 15322108--15322220 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
15322098 TGTATGAATA
* * * *
15322108 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTTTTGTGT
15322168 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATT
15322221 GTGTTTAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 6 0.12
60 42 0.88
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTTTTGTGT
Found at i:15322311 original size:37 final size:37
Alignment explanation
Indices: 15322260--15322340 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
15322250 CATATAAAGT
15322260 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGTTTAA
15322298 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
15322335 TTATAA
1 TTATAA
15322341 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 39 0.91
38 4 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
Found at i:15322403 original size:16 final size:15
Alignment explanation
Indices: 15322382--15322418 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
15322372 CTCATTTAAT
15322382 TTTTATATAATGTAA
1 TTTTATATAATGTAA
*
15322397 CTTTTATATAATTTAA
1 -TTTTATATAATGTAA
15322413 TTTTAT
1 TTTTAT
15322419 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:15323378 original size:16 final size:15
Alignment explanation
Indices: 15323347--15323390 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
15323337 ACAAAATCAA
15323347 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
15323362 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
15323378 ATAAAAATTAAAT
1 AT-AAAATTAAAT
15323391 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:15323688 original size:19 final size:19
Alignment explanation
Indices: 15323685--15323952 Score: 160
Period size: 19 Copynumber: 14.5 Consensus size: 19
15323675 CATACAAAAT
15323685 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
15323704 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
* *
15323720 TACAATATT-C-AT-TACA
1 TACAAAATTACAATATTCA
* *
15323736 -AAAAAATTGCAATATTCA
1 TACAAAATTACAATATTCA
* *
15323754 TATAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
15323770 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
*
15323785 -AAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
15323803 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
15323822 TACAAAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCA
* *
15323843 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
*
15323861 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
15323884 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
*
15323904 TAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
15323923 TACAAAAAATTAGAATATTCA
1 TAC--AAAATTACAATATTCA
15323944 TACAAAATT
1 TACAAAATT
15323953 CTAATCCAAA
Statistics
Matches: 195, Mismatches: 25, Indels: 58
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.05
15 8 0.04
16 19 0.10
17 5 0.03
18 15 0.08
19 74 0.38
20 13 0.07
21 39 0.20
22 5 0.03
23 5 0.03
25 2 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:15323700 original size:27 final size:27
Alignment explanation
Indices: 15323664--15323815 Score: 189
Period size: 27 Copynumber: 6.0 Consensus size: 27
15323654 ATATCCCGAC
15323664 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAA
15323691 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAA
15323718 ATTACAATATTCATTAC--AA--A-AAA
1 ATTACAATATTCA-TACAAAATTACAAA
* * * *
15323741 ATTGCAATATTCATATAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAA
15323768 ATTACAATATTCATAC--AA--A-AAA
1 ATTACAATATTCATACAAAATTACAAA
15323790 ATTACAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAATTACAA
15323816 TATTCATACA
Statistics
Matches: 108, Mismatches: 6, Indels: 22
0.79 0.04 0.16
Matches are distributed among these distances:
22 20 0.19
23 16 0.15
24 5 0.05
25 2 0.02
26 4 0.04
27 58 0.54
28 3 0.03
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAA
Found at i:15323752 original size:50 final size:49
Alignment explanation
Indices: 15323616--15323850 Score: 235
Period size: 50 Copynumber: 4.9 Consensus size: 49
15323606 ATTATAAAAT
** *
15323616 AATTACAATATTCATAC-AAAAAATTACAATA-T--TACAATATATCCCGA
1 AATTACAATATTCATACAAAAAAATTACAATATTCATACAA-A-ATTACAA
*
15323663 CATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATAC--AA--A-AAAATTACAATATTCATACAAAATTACAA
* * *
15323717 AATTACAATATTCATTACAAAAAAATTGCAATATTCATATAAAATTATAA
1 AATTACAATATTCA-TACAAAAAAATTACAATATTCATACAAAATTACAA
*
15323767 TATTACAATATTCATACAAAAAAATTACAATA-T--T-C---A-TACAA
1 AATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTACAA
15323808 AATTACAATATTCATAC-AAAAAATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAAAATTACAATATTCATACAAAAT
15323851 ACTAATCCAA
Statistics
Matches: 157, Mismatches: 13, Indels: 35
0.77 0.06 0.17
Matches are distributed among these distances:
40 14 0.09
41 21 0.13
42 1 0.01
43 1 0.01
44 1 0.01
46 1 0.01
47 17 0.11
48 1 0.01
49 17 0.11
50 40 0.25
51 1 0.01
52 1 0.01
53 14 0.09
54 18 0.11
55 4 0.03
56 5 0.03
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (49 bp):
AATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTACAA
Found at i:15323840 original size:40 final size:40
Alignment explanation
Indices: 15323768--15323950 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 40
15323758 AAATTATAAT
15323768 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
1 ATTACAATATTCATAC-AAAAAATTACAATATTCATACAAA
15323809 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
1 ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
* * * * * *
15323849 A-TACTA-ATCCAAAACTATAAA-TACAAATTTAATT-ATAAAATA
1 ATTACAATATTC-ATACAAAAAATTAC-AA--T-ATTCATACAA-A
15323891 ATTACAATATTCAT--AAAAAATTACAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAAATTACAATATTCATAC--AAA
*
15323931 ATTAGAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
15323951 TTCTAATCCA
Statistics
Matches: 115, Mismatches: 13, Indels: 27
0.74 0.08 0.17
Matches are distributed among these distances:
38 9 0.08
39 17 0.15
40 39 0.34
41 30 0.26
42 12 0.10
43 5 0.04
44 3 0.03
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (40 bp):
ATTACAATATTCATACAAAAAATTACAATATTCATACAAA
Found at i:15323914 original size:101 final size:100
Alignment explanation
Indices: 15323784--15323969 Score: 327
Period size: 101 Copynumber: 1.9 Consensus size: 100
15323774 ATATTCATAC
*
15323784 AAAAAAATTACAATATTCATACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
1 AAAAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
15323849 ATACTAATCCAAAACTATAAATACAAATTTAATTAT
66 ATACTAATCC-AAACTATAAATACAAATTTAATTAT
* *
15323885 AAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTAGAATATTCATACAAA
1 AAAAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
*
15323950 ATTCTAATCCAAACTATAAA
66 ATACTAATCCAAACTATAAA
15323970 CACTAAATAT
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 10 0.12
101 71 0.88
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (100 bp):
AAAAAAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
ATACTAATCCAAACTATAAATACAAATTTAATTAT
Found at i:15323951 original size:40 final size:40
Alignment explanation
Indices: 15323685--15323952 Score: 156
Period size: 40 Copynumber: 6.2 Consensus size: 40
15323675 CATACAAAAT
15323685 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATTCA
1 TACAAAATTACAATATTCATAC---A--A-AAAATTACAATATTCA
* *
15323731 TTACAAAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCA
1 -TAC---AAAATTACAATATTC--ATACAA--A-AA-ATTACAATATTCA
15323781 TACAAAAAAATTACAATATTCATAC--AAAATTACAATATTCA
1 TAC---AAAATTACAATATTCATACAAAAAATTACAATATTCA
* *
15323822 TACAAAAAATTACAATATTCATAC--AAAA-TACTA-ATCCAA
1 TAC--AAAATTACAATATTCATACAAAAAATTACAATATTC-A
* * *
15323861 AACTATAAA-TACAA-ATTTAATTATAAAATAATTACAATATTCA
1 TAC-A-AAATTACAATA-TTCA-TACAAAA-AATTACAATATTCA
* *
15323904 TAAAAAATTACAATATTCATACAAAAAATTAGAATATTCA
1 TACAAAATTACAATATTCATACAAAAAATTACAATATTCA
15323944 TACAAAATT
1 TACAAAATT
15323953 CTAATCCAAA
Statistics
Matches: 183, Mismatches: 19, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
37 1 0.01
38 12 0.07
39 12 0.07
40 46 0.25
41 27 0.15
42 13 0.07
43 8 0.04
44 3 0.02
47 7 0.04
48 1 0.01
49 23 0.13
50 27 0.15
52 3 0.02
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (40 bp):
TACAAAATTACAATATTCATACAAAAAATTACAATATTCA
Found at i:15324033 original size:101 final size:101
Alignment explanation
Indices: 15323784--15324023 Score: 295
Period size: 101 Copynumber: 2.3 Consensus size: 101
15323774 ATATTCATAC
* * * *
15323784 AAAAAAATTACAATATTCATACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
1 AAAATAATTACAATAATAATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
* * *
15323849 ATACTAATCCAAAACTATAAATACAAATTTAATTAT
66 ATACTAATCCAAAACTATAAACACAAATATAATAAT
* * *
15323885 AAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAAAATTAGAATATTCATACAAA
1 AAAATAATTACAATAATAATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
*
15323950 ATTCTAATCC-AAACTATAAACACTAAATATAGATAAT
66 ATACTAATCCAAAACTATAAACAC-AAATATA-ATAAT
** *
15323987 -TTATAATTAGTAATTAATAATAAAAAATTCACAATAT
1 AAAATAATTA-CAA-TAATAATAAAAAATT-ACAATAT
15324024 CTTCTAAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
100 12 0.10
101 84 0.69
102 6 0.05
103 13 0.11
104 7 0.06
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (101 bp):
AAAATAATTACAATAATAATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAA
ATACTAATCCAAAACTATAAACACAAATATAATAAT
Found at i:15324036 original size:12 final size:12
Alignment explanation
Indices: 15324019--15324044 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15324009 AAAAATTCAC
15324019 AATATCTTCTAA
1 AATATCTTCTAA
15324031 AATATCTTCTAA
1 AATATCTTCTAA
15324043 AA
1 AA
15324045 AATTCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATCTTCTAA
Found at i:15324129 original size:3 final size:3
Alignment explanation
Indices: 15324111--15324150 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
15324101 CATTACCTTT
*
15324111 TTC TTT TTC TTTC TTC TTC TTC TTC TTC TTC -TC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
15324151 CCTTTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:15339481 original size:29 final size:30
Alignment explanation
Indices: 15339445--15339502 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
15339435 GTAAATACCC
* *
15339445 AAAATTTG-AGGGTTAAT-GTGTAAATATG
1 AAAATTTGAAGGATCAATAGTGTAAATATG
15339473 AAAATTTTGAAGGATCAATAGTGTAAATAT
1 AAAA-TTTGAAGGATCAATAGTGTAAATAT
15339503 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 7 0.28
31 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATTTGAAGGATCAATAGTGTAAATATG
Found at i:15341564 original size:57 final size:60
Alignment explanation
Indices: 15341450--15341589 Score: 180
Period size: 57 Copynumber: 2.4 Consensus size: 60
15341440 AATTGACAGT
*
15341450 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAACCCTCCCGAAGAATATGTGTG
1 AAAAAGGATCTAGCCCGGACGGGTGATCC-AT-CTGATATAACCCTCCCGAAAAATATGTG-G
*
15341513 AAAAA-GATCTAGCCCGGACGGGTGAT-C-T-TGATATATCCCTCCCGAAAAATATGTGG
1 AAAAAGGATCTAGCCCGGACGGGTGATCCATCTGATATAACCCTCCCGAAAAATATGTGG
* * *
15341569 AAAATGGATTTAGCTCGGACG
1 AAAAAGGATCTAGCCCGGACG
15341590 AGTAATCCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
56 5 0.07
57 38 0.54
59 1 0.01
61 1 0.01
62 21 0.30
63 5 0.07
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (60 bp):
AAAAAGGATCTAGCCCGGACGGGTGATCCATCTGATATAACCCTCCCGAAAAATATGTGG
Found at i:15342695 original size:16 final size:17
Alignment explanation
Indices: 15342674--15342707 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15342664 ACATAATTAT
*
15342674 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
15342690 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
15342707 T
1 T
15342708 TAAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:15343635 original size:42 final size:42
Alignment explanation
Indices: 15343575--15343674 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
15343565 CTATATGAAC
* **
15343575 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
* * *
15343617 GGCACTAAGTGTGTGAAATTAAAATGATGATGTTGAATTACA
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
15343659 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
15343675 TACCAAGAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
Found at i:15348329 original size:2 final size:2
Alignment explanation
Indices: 15348322--15348347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15348312 AGTAAATTGG
15348322 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
15348348 GCGTGGGTAA
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:15367212 original size:12 final size:12
Alignment explanation
Indices: 15367181--15367216 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
15367171 ACTGTGTAAA
* *
15367181 CTCTCTCTCTCT
1 CTCTCTCGCTCG
15367193 CTCTCTCGCTCG
1 CTCTCTCGCTCG
15367205 CTCTCTCGCTCG
1 CTCTCTCGCTCG
15367217 TTCACACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.11, T:0.39
Consensus pattern (12 bp):
CTCTCTCGCTCG
Found at i:15369459 original size:13 final size:13
Alignment explanation
Indices: 15369441--15369517 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
15369431 AGTTCTTCAT
15369441 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
15369454 TGCTTTTGGAAAG
1 TGCTTTTGAAAAG
* * *
15369467 TGCTGTGGAGAAG
1 TGCTTTTGAAAAG
* *
15369480 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
*
15369493 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
15369506 TGCTTTTGAAAA
1 TGCTTTTGAAAA
15369518 TTTTGAGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:15372495 original size:64 final size:64
Alignment explanation
Indices: 15372378--15372497 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 64
15372368 GATCAGTATT
* * * * * * *
15372378 GATCCTGCATGTGTTGCGGACATACCGCAGCTCTTTGTAAGTGTTCTATTATATGATCGGTGTG
1 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGTCCGATTATATGATCGGTGTG
*
15372442 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATGAGCGTCCCGA-TATATGA
1 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGT-CCGATTATATGA
15372498 CTCTTAATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
64 45 0.96
65 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (64 bp):
GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGTCCGATTATATGATCGGTGTG
Found at i:15379432 original size:12 final size:11
Alignment explanation
Indices: 15379413--15379443 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
15379403 AATTGAAAGC
15379413 TTTTTTTCTCT
1 TTTTTTTCTCT
15379424 TTCTTTTTCTCT
1 TT-TTTTTCTCT
15379436 TTTTTTTC
1 TTTTTTTC
15379444 AGTTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:15379641 original size:31 final size:32
Alignment explanation
Indices: 15379575--15379641 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
15379565 AAAAATTGTT
**
15379575 AATAGTCTAGTAACTTAAATGAAAAACTTTTG
1 AATAGTCTAGTAACTTAAATGAAAAACTTCCG
* *
15379607 AATAGTTTAGTGACTTAAATG-AAAACTTCCG
1 AATAGTCTAGTAACTTAAATGAAAAACTTCCG
15379638 AATA
1 AATA
15379642 ACTCAATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (32 bp):
AATAGTCTAGTAACTTAAATGAAAAACTTCCG
Found at i:15385907 original size:20 final size:21
Alignment explanation
Indices: 15385869--15385908 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15385859 CCCATTTTTC
*
15385869 ATTCTTTTTTACGTTTAAATTT
1 ATTCTTTTATACG-TTAAATTT
15385891 ATTCTTTTATACG-TAAAT
1 ATTCTTTTATACGTTAAAT
15385909 CTAGAGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTCTTTTATACGTTAAATTT
Found at i:15390478 original size:65 final size:64
Alignment explanation
Indices: 15390350--15390481 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 64
15390340 AATTTTCAAC
15390350 CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
1 CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
*
15390414 CCTTAGTAAACTATCAGCTGTGTGGATACTTGGAAGTGAATTCAGATACTGAATATTTTATGCAT
1 CCTTAGTAAACTATCAGCTGTGTGGATACTT-GAAGTGAATTAAGATACTGAATATTTTATGCAT
15390479 CCT
1 CCT
15390482 AGTTCACTAG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 31 0.47
65 35 0.53
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (64 bp):
CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
Found at i:15394283 original size:45 final size:45
Alignment explanation
Indices: 15394232--15394322 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
15394222 AGTTTTTATT
15394232 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
1 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
* *
15394277 TCAAACAAAAGATTACTAGCTTTAGATTCTAATAAAAATTAAAGC
1 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
15394322 T
1 T
15394323 TTATCTAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (45 bp):
TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
Found at i:15405952 original size:13 final size:13
Alignment explanation
Indices: 15405925--15405992 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
15405915 GTATAAGCAC
15405925 TTCATATAACCAT
1 TTCATATAACCAT
* *
15405938 TTCATATATCTAT
1 TTCATATAACCAT
*
15405951 TTCCATATAAACAT
1 TT-CATATAACCAT
** *
15405965 TTTGTATATCCAT
1 TTCATATAACCAT
15405978 TTCATA-ATACCAT
1 TTCATATA-ACCAT
15405991 TT
1 TT
15405993 TCGTTTACTC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 1 0.02
13 30 0.73
14 10 0.24
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:15405965 original size:27 final size:27
Alignment explanation
Indices: 15405927--15405980 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
15405917 ATAAGCACTT
* *
15405927 CATATAACCATTTCATATATCTATTTC
1 CATATAAACATTTCATATATCCATTTC
**
15405954 CATATAAACATTTTGTATATCCATTTC
1 CATATAAACATTTCATATATCCATTTC
15405981 ATAATACCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (27 bp):
CATATAAACATTTCATATATCCATTTC
Found at i:15405982 original size:53 final size:53
Alignment explanation
Indices: 15405884--15405992 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 53
15405874 AAATGTCCCT
* *
15405884 TTTCACATATCTATATTCATATAAATATTTTGTATAAGCACTTCAT-ATAACCA
1 TTTCACATATCTATATTCATATAAACATTTTGTATAACCACTTCATAAT-ACCA
* * *
15405937 TTTCATATATCTAT-TTCCATATAAACATTTTGTATATCCATTTCATAATACCA
1 TTTCACATATCTATATT-CATATAAACATTTTGTATAACCACTTCATAATACCA
15405990 TTT
1 TTT
15405993 TCGTTTACTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 2 0.04
53 45 0.92
54 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (53 bp):
TTTCACATATCTATATTCATATAAACATTTTGTATAACCACTTCATAATACCA
Found at i:15411208 original size:82 final size:81
Alignment explanation
Indices: 15411125--15411813 Score: 893
Period size: 82 Copynumber: 8.4 Consensus size: 81
15411115 TTTTTTTTTG
* * * *
15411125 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATACGATCTGCTCCACTATTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGTTTCG-TCTGCTCCACTACTGCTTAGGGA
* **
15411188 GATAAGATCTGTGGTTTTG-
65 GATAAGA-CT-T-GATGCGA
* * * * * * *
15411207 TCCGCTCCGCTACTGCTTAGGAAGATAAGA-CT-TGATGCGATCTGCTCCACTATTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGTTTCG-TCTGCTCCACTACTGCTTAGGGA
15411270 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * * *
15411287 TCTGCTCCACTATTGCTTAGGGAGATGAGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT-GTTTCGTCTGCTCCACTACTGCTTAGGGA
15411352 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * * *
15411369 TTTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT-GTTTCGTCTGCTCCACTACTGCTTAGGGA
15411434 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * *
15411451 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTATGGTTCTGTCTGCTCCACTATTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGTTTC-GTCTGCTCCACTACTGCTTAGGGA
15411516 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* * * *
15411533 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTATGGTTTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT-GTTTCGTCTGCTCCACTACTGCTTAGGGA
15411598 GATAAGACTTGATGCGA
65 GATAAGACTTGATGCGA
* *
15411615 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGTTTC-GTCTGCTCCACTACTGCTTAGGGA
**
15411680 GATAAGACTTGACACGA
65 GATAAGACTTGATGCGA
* *
15411697 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCT-G--TGTTTCGTCTGCTCCACTACTGCTTAGG
*
15411762 GAGATAAGACTTGATGTGA
63 GAGATAAGACTTGATGCGA
*
15411781 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCT
15411814 AGTTTTCTTC
Statistics
Matches: 550, Mismatches: 47, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
79 3 0.01
80 26 0.05
81 10 0.02
82 430 0.78
83 7 0.01
84 70 0.13
85 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (81 bp):
TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGTTTCGTCTGCTCCACTACTGCTTAGGGAG
ATAAGACTTGATGCGA
Found at i:15411573 original size:246 final size:245
Alignment explanation
Indices: 15411125--15411814 Score: 1016
Period size: 246 Copynumber: 2.8 Consensus size: 245
15411115 TTTTTTTTTG
* * *
15411125 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATACGATCTGCTCCACTATTGCTTAGGG
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTATG-TCTGCTCCACTATTGCTTAGGG
* ** * * * * *
15411187 AGATAAGATCTGTGGTTTTG-TCCGCTCCGCTACTGCTTAGGAAGATAAGA-CTTGATGC-GATC
65 AGATAAGA-CT-T-GATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTGGTTCTG-TC
*
15411249 TGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATG
126 TGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATA
*
15411314 AGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGA
191 AGATCTATGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * *
15411369 TTTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTATGTCTGCTCCACTATTGCTTAGGGA
* *
15411434 GATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTATGGTTCTGTCTGCT
66 GATAAGACTTGATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-TGGTTCTGTCTGCT
15411499 CCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGAT
130 CCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGAT
15411564 CTATGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGA
195 CTATGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGA
*
15411615 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTAGGGA
1 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTATGTCTGCTCCACTATTGCTTAGGGA
*
15411680 GATAAGACTTGACACGATCTGCTCCACTACTGCTTAGGGAGATAAGATC-TGGTTTCTTTCGTCT
66 GATAAGACTTGATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTGG-TTC--T-GTCT
* * *
15411744 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATAA
127 GCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
15411809 GATCTA
192 GATCTA
15411815 GTTTTCTTCA
Statistics
Matches: 405, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
243 3 0.01
244 58 0.14
245 9 0.02
246 258 0.64
247 5 0.01
248 72 0.18
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (245 bp):
TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTATGTCTGCTCCACTATTGCTTAGGGA
GATAAGACTTGATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTGGTTCTGTCTGCTC
CACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATC
TATGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:15411973 original size:46 final size:46
Alignment explanation
Indices: 15411923--15412255 Score: 194
Period size: 46 Copynumber: 7.4 Consensus size: 46
15411913 ATCTGCTTCG
*
15411923 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCA
* ** * *
15411969 CTGCC-AA-CCAGGGA-G-ATAGAGT-TGTCGGT-TTCAATGTACTCCA
1 CTGCCAAATACAGGGAGGCA-AGA-TCTG-CAATCTTCAATCTATTCCA
* * * * * * * * *
15412012 CTG--TAGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTT-CG
1 CTGCCAAAT-ACAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCA
*
15412057 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCA
** * *
15412103 CTGCCAAATACAGGGA-G-ATAGAGT-TGTCGGT-TTCAATGTACTCCA
1 CTGCCAAATACAGGGAGGCA-AGA-TCTG-CAATCTTCAATCTATTCCA
* * * * * ** * *
15412148 CTG--TAGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CG
1 CTGCCAAAT-ACAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCA
*
15412193 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCA
15412239 CTGCCAAATACAGGGAG
1 CTGCCAAATACAGGGAG
15412256 ATAGAATTAT
Statistics
Matches: 207, Mismatches: 54, Indels: 52
0.66 0.17 0.17
Matches are distributed among these distances:
42 2 0.01
43 23 0.11
44 28 0.14
45 55 0.27
46 95 0.46
47 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (46 bp):
CTGCCAAATACAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:15412178 original size:136 final size:136
Alignment explanation
Indices: 15411819--15412322 Score: 863
Period size: 136 Copynumber: 3.7 Consensus size: 136
15411809 GATCTAGTTT
* *
15411819 TCTTCACTCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
15411884 AGT--CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
66 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
15411947 CTGCAA
131 CTGCAA
* * *
15411953 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTGTCGGTTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
* *
15412016 AGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
66 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
15412081 CTGCAA
131 CTGCAA
* *
15412087 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTGTCGGTTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
15412152 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
66 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
15412217 CTGCAA
131 CTGCAA
*
15412223 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
* * *
15412288 AGTCACAGGGAGGTAAAATCTACCATTTTTTATCT
66 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCT
15412323 TCAATCTATT
Statistics
Matches: 350, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
132 40 0.11
133 2 0.01
134 104 0.30
135 2 0.01
136 202 0.58
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (136 bp):
TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGAT
CTGCAA
Found at i:15412387 original size:95 final size:97
Alignment explanation
Indices: 15412222--15412402 Score: 321
Period size: 95 Copynumber: 1.9 Consensus size: 97
15412212 AAGATCTGCA
*
15412222 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATAGGCTTCAATGTACTCCACTG
15412287 TAGTCACAGGGAGGTAAAATCTACCATTTTTT
66 TAGTCACAGGGAGGTAAAATCTACCATTTTTT
* *
15412319 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATAGGCTTCAATGTACTCCACTG
15412382 TAGTCACAGGGAGGTAAAATC
66 TAGTCACAGGGAGGTAAAATC
15412403 CGCCATCTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
95 57 0.70
96 2 0.02
97 22 0.27
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (97 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATAGGCTTCAATGTACTCCACTG
TAGTCACAGGGAGGTAAAATCTACCATTTTTT
Found at i:15412491 original size:231 final size:233
Alignment explanation
Indices: 15412086--15412544 Score: 814
Period size: 231 Copynumber: 2.0 Consensus size: 233
15412076 AAGATCTGCA
* * *
15412086 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTGTCGGTTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTG
* *
15412151 TAGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
*
15412216 TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTACT
131 TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACT
*
15412281 CCACTGTAGTCACAGGGAGGTAAAATCTACCATTTTTT
196 CCACTGTAGTCACAAGGAGGTAAAATCTACCATTTTTT
*
15412319 ATCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTG
15412382 TAGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
66 TAGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
*
15412447 TCTGCAATTTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACT
131 TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACT
*
15412512 CCACTGTAGTCACAAGGAGGTAAAATCTGCCAT
196 CCACTGTAGTCACAAGGAGGTAAAATCTACCAT
15412545 CTTCGATCTG
Statistics
Matches: 216, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
231 192 0.89
232 2 0.01
233 22 0.10
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (233 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTG
TAGTCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGA
TCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACT
CCACTGTAGTCACAAGGAGGTAAAATCTACCATTTTTT
Found at i:15412508 original size:136 final size:134
Alignment explanation
Indices: 15412322--15412585 Score: 429
Period size: 136 Copynumber: 2.0 Consensus size: 134
15412312 ATTTTTTATC
* * *
15412322 TTCAATCTATTCCACTGCCAACCAGGGAGATAGAGTTATAGGCTTCAATGTACTCCACTGTAGTC
1 TTCAATCTATTCCACTGCCAAACAGGGAGATAGAATTATAGACTTCAATGTACTCCACTGTAGTC
* *
15412387 ACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGC
66 ACAAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAGGCAAGATCTGC
15412452 AATT
131 AATT
*
15412456 TTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGACTTCAATGTACTCCACTGTAG
1 TTCAATCTATTCCACTGCC-AA-ACAGGGAGATAGAATTATAGACTTCAATGTACTCCACTGTAG
* * *
15412521 TCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTACCAAATACTGGAAGGTAAGATCT
64 TCACAAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAGGCAAGATCT
15412586 ATTAACTTCA
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
134 19 0.16
135 2 0.02
136 98 0.82
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (134 bp):
TTCAATCTATTCCACTGCCAAACAGGGAGATAGAATTATAGACTTCAATGTACTCCACTGTAGTC
ACAAGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTACCAAATACAGGAAGGCAAGATCTGC
AATT
Found at i:15413572 original size:9 final size:8
Alignment explanation
Indices: 15413555--15413597 Score: 54
Period size: 7 Copynumber: 5.5 Consensus size: 8
15413545 TGGCCTCTCC
15413555 TTTTTCTT
1 TTTTTCTT
15413563 TTTGTTCTT
1 TTT-TTCTT
15413572 TTTTTC-T
1 TTTTTCTT
15413579 TTTTT-TT
1 TTTTTCTT
*
15413586 TGTTTCTT
1 TTTTTCTT
15413594 TTTT
1 TTTT
15413598 CGAGTGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 11 0.37
8 11 0.37
9 8 0.27
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:15413587 original size:21 final size:23
Alignment explanation
Indices: 15413556--15413597 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
15413546 GGCCTCTCCT
15413556 TTTTCTTTTTG-TTCTTTTTTTC
1 TTTTCTTTTTGTTTCTTTTTTTC
15413578 TTTT-TTTTTGTTTCTTTTTT
1 TTTTCTTTTTGTTTCTTTTTT
15413598 CGAGTGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (23 bp):
TTTTCTTTTTGTTTCTTTTTTTC
Found at i:15414072 original size:22 final size:20
Alignment explanation
Indices: 15414046--15414133 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 20
15414036 TTTTTTTGTT
15414046 TTTTTTTTGCTTTTGTTTT-C
1 TTTTTTTTGCTTTT-TTTTAC
15414066 TCGTTTTTTTGCTTCCTTTTTTAC
1 T--TTTTTTTGCTT--TTTTTTAC
*
15414090 TTTTTTTTGC--TTTTTTGC
1 TTTTTTTTGCTTTTTTTTAC
*
15414108 TTTTTTGCT-CTTTTTTTTA-
1 TTTTTT-TTGCTTTTTTTTAC
15414127 TTTTTTT
1 TTTTTTT
15414134 GTTTTTGCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
18 14 0.25
19 7 0.12
20 7 0.12
22 20 0.36
23 4 0.07
24 4 0.07
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTTTTTGCTTTTTTTTAC
Found at i:15414087 original size:12 final size:10
Alignment explanation
Indices: 15414036--15414113 Score: 63
Period size: 10 Copynumber: 7.5 Consensus size: 10
15414026 TTATTTTTTA
*
15414036 TTTTTTTGTTT
1 TTTTTTTG-CT
15414047 TTTTTTTGCT
1 TTTTTTTGCT
15414057 TTTGTTTT-CT
1 TTT-TTTTGCT
15414067 CGTTTTTTTGCT
1 --TTTTTTTGCT
*
15414079 TCCTTTTTTACT
1 T--TTTTTTGCT
15414091 TTTTTTTGC-
1 TTTTTTTGCT
15414100 -TTTTTTGCT
1 TTTTTTTGCT
15414109 TTTTT
1 TTTTT
15414114 GCTCTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
8 8 0.14
10 18 0.32
11 16 0.29
12 14 0.25
ACGTcount: A:0.01, C:0.12, G:0.09, T:0.78
Consensus pattern (10 bp):
TTTTTTTGCT
Found at i:15414098 original size:38 final size:35
Alignment explanation
Indices: 15414056--15414139 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
15414046 TTTTTTTTGC
*
15414056 TTTTGTTTTCTCGTTTTTTTGCTTCCTTTTTTACT-TTT
1 TTTTGTTTT-TCGCTTTTTTGC-T-CTTTTTT-CTATTT
* *
15414094 TTTTGCTTTTTTGCTTTTTTGCTCTTTTTTTTATTT
1 TTTTG-TTTTTCGCTTTTTTGCTCTTTTTTCTATTT
15414130 TTTTGTTTTT
1 TTTTGTTTTT
15414140 GCCTCCACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
35 6 0.15
36 15 0.37
37 1 0.02
38 15 0.37
39 4 0.10
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.77
Consensus pattern (35 bp):
TTTTGTTTTTCGCTTTTTTGCTCTTTTTTCTATTT
Found at i:15414103 original size:8 final size:8
Alignment explanation
Indices: 15414092--15414122 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
15414082 TTTTTTACTT
15414092 TTTTTTGC
1 TTTTTTGC
15414100 TTTTTTGC
1 TTTTTTGC
15414108 TTTTTTGC
1 TTTTTTGC
15414116 TCTTTTT
1 T-TTTTT
15414123 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (8 bp):
TTTTTTGC
Found at i:15421678 original size:8 final size:8
Alignment explanation
Indices: 15421665--15421717 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
15421655 ATTTTATCTT
15421665 TAATTACC
1 TAATTACC
15421673 TAATTACC
1 TAATTACC
*
15421681 AAATTACC
1 TAATTACC
*
15421689 ---CTACC
1 TAATTACC
15421694 TAATTACC
1 TAATTACC
15421702 TAATTACC
1 TAATTACC
*
15421710 AAATTACC
1 TAATTACC
15421718 CTTACTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
8 34 0.89
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (8 bp):
TAATTACC
Found at i:15421695 original size:21 final size:21
Alignment explanation
Indices: 15421669--15421709 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15421659 TATCTTTAAT
15421669 TACCTAATTACCAAATTACCC
1 TACCTAATTACCAAATTACCC
*
15421690 TACCTAATTACCTAATTACC
1 TACCTAATTACCAAATTACC
15421710 AAATTACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (21 bp):
TACCTAATTACCAAATTACCC
Found at i:15441782 original size:2 final size:2
Alignment explanation
Indices: 15441775--15441803 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15441765 AAAATCGCAA
15441775 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
15441804 TATTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15443511 original size:10 final size:10
Alignment explanation
Indices: 15443479--15443512 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
15443469 AATCAAAGTT
15443479 TTATTATATA
1 TTATTATATA
*
15443489 TTTTTATAT-
1 TTATTATATA
15443498 TTATTATATA
1 TTATTATATA
15443508 TTATT
1 TTATT
15443513 TTCAAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATATA
Found at i:15444409 original size:113 final size:114
Alignment explanation
Indices: 15444045--15444532 Score: 554
Period size: 114 Copynumber: 4.3 Consensus size: 114
15444035 TAAAGAAAGT
* * ** *
15444045 ATTAGTGGCGCTTAT-TTAAAATCGCCGCTAAAGCATAGAATTAGCGGCGAGTCGCAAAAAGAAC
1 ATTAGTGGCGCTTATATTAAAA-CGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCAC
*
15444109 CGCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGC
65 CGCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
** * *
15444159 ATTAGTGGCGCTTATACAAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCC
1 ATTAGTGGCGCTTATATTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCACC
** * *
15444224 GCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGG
66 GCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
*** ** * * *
15444273 ATTAGTGGCGCTTATCGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTATTGTAAAGCACT
1 ATTAGTGGCGCTTATATTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCACC
* * *
15444338 GCAA-A-ATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGC
66 GCAATACATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGC
* * * *
15444386 AGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTAGTGAAAAACGCC
1 ATTAGTGGCGCTTATATTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCACC
* ** * * * * *
15444451 GCAAGATTTTTTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGGC
66 GCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTA-GC
* *
15444501 -TTAGTGGCGCTTAT-TGGAAAACGCCGCAAAAG
1 ATTAGTGGCGCTTATAT-TAAAACGCCGCTAAAG
15444533 ATTAACCAAA
Statistics
Matches: 314, Mismatches: 54, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
112 17 0.05
113 78 0.25
114 198 0.63
115 21 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (114 bp):
ATTAGTGGCGCTTATATTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTAGTGAAAAGCACC
GCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGC
Found at i:15444441 original size:227 final size:226
Alignment explanation
Indices: 15444120--15444532 Score: 664
Period size: 227 Copynumber: 1.8 Consensus size: 226
15444110 GCAATACATC
*
15444120 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCGCTTATACAAAAACGCC
1 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGCC
* * *
15444185 GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGA
66 GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAA
*
15444250 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCTAAAGCATAGTATT
131 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAGCATAGTATT
15444315 AGCGGCGCTTATTGTAAAGCACTGCAAAATA
196 AGCGGCGCTTATTGTAAAGCACTGCAAAATA
* * * **
15444346 TTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTAGTGGCGCTTATATTAAAACGC
1 TTAACCAAAACGCAGAG-TTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGC
** * *
15444411 CGCTAAATCATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTTTTAACCAAAATGCAA
65 CGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAA
* * *
15444476 AGTTTGGTCTTGCGGTATATTAGGCTTAGTGGCGCTTATTGGAAAACGCCGCAAAAG
130 AGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAG
15444533 ATTAACCAAA
Statistics
Matches: 169, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
226 16 0.09
227 153 0.91
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (226 bp):
TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGCC
GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAA
GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAGCATAGTATT
AGCGGCGCTTATTGTAAAGCACTGCAAAATA
Found at i:15444568 original size:74 final size:73
Alignment explanation
Indices: 15444461--15444606 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 73
15444451 GCAAGATTTT
* * *
15444461 TTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGGC-TTAGTGGCGCTTAT-TGGAAAACG
1 TTAACCAAAACGCAAAGTTTGGTCTTGAGGTATAGTA-GCATTAGTGGCGCTTATAT-GAAAACG
15444524 CCGCAAAAGA
64 CCGCAAAAGA
** * *
15444534 TTAACCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTATATTAAAACGC
1 TTAACCAAAACGCAAAG-TTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATATGAAAACGC
*
15444599 CGCTAAAG
65 CGCAAAAG
15444607 TATAGTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
73 16 0.26
74 45 0.73
75 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (73 bp):
TTAACCAAAACGCAAAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATATGAAAACGCC
GCAAAAGA
Found at i:15444641 original size:188 final size:188
Alignment explanation
Indices: 15444312--15444709 Score: 609
Period size: 188 Copynumber: 2.1 Consensus size: 188
15444302 AAAGCATAGT
* * * * *
15444312 ATTAGCGGCGCTTATTGTAAAGCACTGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
*
15444377 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTAGTG
66 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTACTG
* * * * *
15444442 AAAAACGCCGCAAGATTTTTTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGG
131 AAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
* *
15444500 CTTAGTGGCGCTTATTGGAAAACGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* *
15444565 TATAGTAGCATTAGTGGCGCTTATATTAAAACGCCGCTAAAGT-ATAGTATTAGCGGCGAGTACT
66 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAA-TCATAGTATTAGCGGCGAGTACT
* * *
15444629 GAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAAG
130 GAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
*
15444688 ATTAGTGGCGCTTATTTGAAAA
1 ATTAGTGGCGCTTATTGGAAAA
15444710 TGCCACTAAA
Statistics
Matches: 189, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 188 0.99
189 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (188 bp):
ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTACTG
AAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
Found at i:15444843 original size:113 final size:112
Alignment explanation
Indices: 15444501--15444850 Score: 395
Period size: 114 Copynumber: 3.1 Consensus size: 112
15444491 TATATTAGGC
* *
15444501 TTAGTGGCGCTTATTGGAAAA-CGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 TTAGCGGCGCTTATT-GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATG
* *
15444565 TATAGTAGCA-TTAGTGGCGCTTATATTAAAACGCCGCTAAAGTATAGTA
64 TATACTAGCAGTTAGTGGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTA
** * * * * *
15444614 TTAGCGGCGAGTACTGAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGG
1 TTAGCGGCGCTTATTGAAAAGCGCCGCAA-A-ATATTAACCAAAACGCAGCGTTTGGTCTTGATG
* * * *
15444679 TACATTA--AGATTAGTGGCGCTTATTTGAAAATGCCACTAAAGCATAGTA
64 TATACTAGCAG-TTAGTGGCGCTTATTT-AAAACGCCGCTAAAGCATAGTA
* * *
15444728 TTAGCGGCGCTTATTGTAAAGCGCCGCAAAATATTAACTAAAATGCAGCGTTTTGGTCTTGATGT
1 TTAGCGGCGCTTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGT
* * *
15444793 ATACTAGCAGTT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATTA
65 ATACTAGCAGTTAGTGGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTA
15444841 TTAGCGGCGC
1 TTAGCGGCGC
15444851 GTTGTGGGAA
Statistics
Matches: 196, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
112 21 0.11
113 78 0.40
114 79 0.40
115 18 0.09
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (112 bp):
TTAGCGGCGCTTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGTTTGGTCTTGATGTA
TACTAGCAGTTAGTGGCGCTTATTTAAAACGCCGCTAAAGCATAGTA
Found at i:15444864 original size:113 final size:112
Alignment explanation
Indices: 15444517--15444867 Score: 372
Period size: 113 Copynumber: 3.1 Consensus size: 112
15444507 GCGCTTATTG
* *
15444517 GAAAA-CGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCA-TTAGT
1 GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCAGTTAGT
* * *
15444580 GGCGCTTATATTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACT
65 GGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
* * * * * *
15444629 GAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTA--AGATTA
1 GAAAAGCGCCGCAA-A-ATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCAG-TTA
* * *
15444692 GTGGCGCTTATTTGAAAATGCCACTAAAGCATAGTATTAGCGGCGC-TTATT
63 GTGGCGCTTATTT-AAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTT-CT
* * *
15444743 GTAAAGCGCCGCAAAATATTAACTAAAATGCAGCGTTTTGGTCTTGATGTATACTAGCAGTT-GT
1 GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCAGTTAGT
* * * *
15444807 GGCGCTTATGGTAAAACGCCGCTAAAACATATTATTAGCGGCGCGTTGT
65 GGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
**
15444856 GGGAAGCGCCGC
1 GAAAAGCGCCGC
15444868 TAGATTATCA
Statistics
Matches: 197, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
112 21 0.11
113 79 0.40
114 79 0.40
115 18 0.09
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (112 bp):
GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCAGTTAGTG
GCGCTTATTTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
Found at i:15449858 original size:21 final size:20
Alignment explanation
Indices: 15449833--15449898 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
15449823 CAACTTAAAA
*
15449833 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCA-CAGCGAGAGAAG
15449854 CAGAGGCTACAGCGAGAGAAG
1 CAGAGGC-ACAGCGAGAGAAG
* *
15449875 TAGAGGCCACAGTGAGAGAAG
1 CAGAGG-CACAGCGAGAGAAG
15449896 CAG
1 CAG
15449899 CGAGAGAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.41, T:0.05
Consensus pattern (20 bp):
CAGAGGCACAGCGAGAGAAG
Found at i:15450450 original size:42 final size:42
Alignment explanation
Indices: 15450348--15450599 Score: 276
Period size: 43 Copynumber: 5.9 Consensus size: 42
15450338 TTTGTGAAAT
* * ** **
15450348 AAGCGCTGCGAAAGAACACT-ACTTTTAGCGGCGTTTGTAGATG
1 AAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTT-TTTACC
* *
15450391 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
* * *
15450433 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
*
15450475 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTCCC
1 -AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTACC
* *
15450518 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTCCC
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTACC
* * *
15450560 TAAGCGCCGCTAAAGAATATGACCTTTAGCAGCGTTTTTT
1 -AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTT
15450600 CTGTAAGCGC
Statistics
Matches: 187, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
42 84 0.45
43 103 0.55
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACC
Found at i:15450459 original size:85 final size:85
Alignment explanation
Indices: 15450348--15450597 Score: 299
Period size: 85 Copynumber: 2.9 Consensus size: 85
15450338 TTTGTGAAAT
* * * * ** *
15450348 AAGCGCTGCGAAAGAACACTACTTTTAGCGGCG-TTTGTAGATGAAGCGCCGCTAAAGAACATTA
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACCT-AAGCGCCGCTAAAGAACATGA
15450412 CTTTTAGCGGCGTTTTCTACC
65 CTTTTAGCGGCGTTTTCTACC
* *
15450433 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA-
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGAC
* *
15450497 TCTTTAGCGGCGTTTTTTCCC
66 T-TTTAGCGGCGTTTTCTACC
* * * *
15450518 AAGCGCCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTCCCTAAGCGCCGCTAAAGAATATGA
1 AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGA
* *
15450582 CCTTTAGCAGCGTTTT
65 CTTTTAGCGGCGTTTT
15450598 TTCTGTAAGC
Statistics
Matches: 143, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
84 2 0.01
85 136 0.95
86 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACCTAAGCGCCGCTAAAGAACATGAC
TTTTAGCGGCGTTTTCTACC
Found at i:15450597 original size:43 final size:43
Alignment explanation
Indices: 15450391--15450617 Score: 296
Period size: 43 Copynumber: 5.3 Consensus size: 43
15450381 TTTGTAGATG
* * * *
15450391 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACC-
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
* * * *
15450433 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
*
15450476 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCC-
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
* *
15450518 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCCT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
* * **
15450561 AAGCGCCGCTAAAGAATATGACCTTTAGCAGCGTTTTTTCTGT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
*
15450604 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
15450618 TTAGCGACGT
Statistics
Matches: 167, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
42 80 0.48
43 87 0.52
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCT
Found at i:15450598 original size:85 final size:85
Alignment explanation
Indices: 15450391--15450600 Score: 305
Period size: 85 Copynumber: 2.5 Consensus size: 85
15450381 TTTGTAGATG
* * * * * *
15450391 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTCTACCAAGCGCCGCTATAGAACATTACT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGACT
* *
15450456 TTTAGCGGCGTTTTTTTCCT
66 ATTAGCGGCGTTTTTTCCCT
*
15450476 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGA-T
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGACT
15450540 CATTAGCGGCGTTTTTTCCCT
66 -ATTAGCGGCGTTTTTTCCCT
* *
15450561 AAGCGCCGCTAAAGAATATGACCTTTAGCAGCGTTTTTTC
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTC
15450601 TGTAAGCGCC
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 111 0.99
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGACT
ATTAGCGGCGTTTTTTCCCT
Found at i:15451094 original size:34 final size:33
Alignment explanation
Indices: 15451054--15451159 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 33
15451044 AAATATAAAA
15451054 ATAAAATATTTGAAATATTTTAATATAATTTAAT
1 ATAAAATATTT-AAATATTTTAATATAATTTAAT
** *
15451088 ATAAAATATTT-AAT-TTCAAAGTATAATTTAAA
1 ATAAAATATTTAAATATTTTAA-TATAATTTAAT
* *
15451120 ATAAAGTATTTTAAAAATTTTAATATAATTTAAT
1 ATAAAATA-TTTAAATATTTTAATATAATTTAAT
15451154 ATAAAA
1 ATAAAA
15451160 ATAATTATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
31 4 0.07
32 20 0.34
33 3 0.05
34 28 0.47
35 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (33 bp):
ATAAAATATTTAAATATTTTAATATAATTTAAT
Found at i:15460258 original size:2 final size:2
Alignment explanation
Indices: 15460251--15460275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15460241 TTGATAGACT
15460251 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15460276 TAAAACTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15460683 original size:12 final size:12
Alignment explanation
Indices: 15460666--15460703 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
15460656 AAAAAAGTGA
15460666 GGCATTGGCAAT
1 GGCATTGGCAAT
*
15460678 GGCATTGGCAAA
1 GGCATTGGCAAT
15460690 GGCATTGGGCAAT
1 GGCATT-GGCAAT
15460703 G
1 G
15460704 CATGATGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (12 bp):
GGCATTGGCAAT
Found at i:15466528 original size:2 final size:2
Alignment explanation
Indices: 15466521--15466545 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15466511 GTCGAGGTAC
15466521 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15466546 CAATATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15467445 original size:2 final size:2
Alignment explanation
Indices: 15467438--15467471 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
15467428 AAATCTTGGG
* *
15467438 AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15467472 TATGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:15473169 original size:3 final size:3
Alignment explanation
Indices: 15473161--15473198 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
15473151 ATTGGTAACA
15473161 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
15473199 ATGTTAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:15482359 original size:15 final size:12
Alignment explanation
Indices: 15482326--15482361 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
15482316 CTTTCCGGCA
15482326 ATCCTTCTTCTC
1 ATCCTTCTTCTC
15482338 ATCCTTCTTCTC
1 ATCCTTCTTCTC
15482350 ATCCTTCTTCTC
1 ATCCTTCTTCTC
15482362 CTCTTTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.42, G:0.00, T:0.50
Consensus pattern (12 bp):
ATCCTTCTTCTC
Found at i:15487415 original size:3 final size:3
Alignment explanation
Indices: 15487404--15487444 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
15487394 AAAATCCAAA
15487404 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
15487445 CAAGCAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15492890 original size:13 final size:13
Alignment explanation
Indices: 15492872--15492899 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15492862 AGTTTATCGG
15492872 AATTATTATAATT
1 AATTATTATAATT
15492885 AATTATTATAATT
1 AATTATTATAATT
15492898 AA
1 AA
15492900 GATTTTGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATTATAATT
Found at i:15503699 original size:24 final size:25
Alignment explanation
Indices: 15503666--15503726 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
15503656 ATGAAACAAC
*
15503666 AAAAAGAAAATA-TATTCTAAAAAG
1 AAAAAGAAAATACTAATCTAAAAAG
* *
15503690 GAAAAGAAAA-ACCTAATCTAAAAAT
1 AAAAAGAAAATA-CTAATCTAAAAAG
15503715 AAAAAGAAAATA
1 AAAAAGAAAATA
15503727 AACAAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 19 0.63
26 1 0.03
ACGTcount: A:0.69, C:0.07, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAAGAAAATACTAATCTAAAAAG
Found at i:15503736 original size:16 final size:16
Alignment explanation
Indices: 15503715--15503745 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15503705 ATCTAAAAAT
*
15503715 AAAAAGAAAATAAACA
1 AAAAAGAAAAGAAACA
15503731 AAAAAGAAAAGAAAC
1 AAAAAGAAAAGAAAC
15503746 TTAACGTAAA
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:0.81, C:0.06, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAACA
Found at i:15506300 original size:2 final size:2
Alignment explanation
Indices: 15506293--15506326 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15506283 ATGAAGACAA
15506293 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
15506327 TACTGCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15507620 original size:69 final size:69
Alignment explanation
Indices: 15507509--15507638 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
15507499 TGGGATGCTA
* *
15507509 AAACTATGCTATGATCATGTAGAATAATGATTTCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
1 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
15507574 ATAG
66 ATAG
15507578 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGC
1 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGC
15507639 ATATCTGAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (69 bp):
AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
ATAG
Found at i:15512816 original size:15 final size:15
Alignment explanation
Indices: 15512796--15512825 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15512786 CATATTTCAC
*
15512796 TTAATATTATATAAA
1 TTAATATAATATAAA
15512811 TTAATATAATATAAA
1 TTAATATAATATAAA
15512826 AATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATATAATATAAA
Found at i:15514092 original size:3 final size:3
Alignment explanation
Indices: 15514086--15514114 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15514076 AAAAAAAAAT
15514086 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
15514115 GCATGTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15520773 original size:25 final size:24
Alignment explanation
Indices: 15520738--15520794 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
15520728 TATATTACAT
* *
15520738 ATAC-AAATAATTTTATTTATTTA
1 ATACAAAATAATTTGATGTATTTA
15520761 ATACAAAAGTAATTTGATGTATTTA
1 ATACAAAA-TAATTTGATGTATTTA
*
15520786 ATAAAAAAT
1 ATACAAAAT
15520795 TCTCGGCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 21 0.72
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (24 bp):
ATACAAAATAATTTGATGTATTTA
Found at i:15530087 original size:15 final size:15
Alignment explanation
Indices: 15530069--15530133 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
15530059 AACTAAAATT
15530069 TATTTTTCAAAAAAA
1 TATTTTTCAAAAAAA
*
15530084 TATTTGTTC-AAATAA
1 TATTT-TTCAAAAAAA
* *** *
15530099 TCTTTTTTGTAAAAT
1 TATTTTTCAAAAAAA
*
15530114 TATTTTTCAAAAAAT
1 TATTTTTCAAAAAAA
15530129 TATTT
1 TATTT
15530134 GAACGGGAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 2 0.05
15 33 0.87
16 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (15 bp):
TATTTTTCAAAAAAA
Found at i:15534909 original size:24 final size:24
Alignment explanation
Indices: 15534872--15534933 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
15534862 TGATCCCCAT
15534872 ATTTTTTTCGTTTTAAGTAATTTAA
1 ATTTTTTTC-TTTTAAGTAATTTAA
* **
15534897 ATTTTTTTCTTTTATGTTCTTTAA
1 ATTTTTTTCTTTTAAGTAATTTAA
* *
15534921 ACTTTCTTCTTTT
1 ATTTTTTTCTTTT
15534934 TTTCCATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.66
Consensus pattern (24 bp):
ATTTTTTTCTTTTAAGTAATTTAA
Found at i:15535066 original size:14 final size:14
Alignment explanation
Indices: 15535049--15535082 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
15535039 TCATCATTTG
15535049 CCTATAACCAAAAC
1 CCTATAACCAAAAC
15535063 CCTATAACCAAAAC
1 CCTATAACCAAAAC
15535077 CC-ATAA
1 CCTATAA
15535083 ACTCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:15538370 original size:17 final size:16
Alignment explanation
Indices: 15538350--15538383 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15538340 ATGAATATAG
15538350 AGAAAAAGAAGGAAATA
1 AGAAAAA-AAGGAAATA
*
15538367 AGAAAAAATGGAAATA
1 AGAAAAAAAGGAAATA
15538383 A
1 A
15538384 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (16 bp):
AGAAAAAAAGGAAATA
Found at i:15554051 original size:29 final size:30
Alignment explanation
Indices: 15553992--15554049 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
15553982 TCCGAGCCTT
*
15553992 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
15554022 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
15554050 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:15554279 original size:13 final size:13
Alignment explanation
Indices: 15554261--15554292 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
15554251 TTTCCAGCAA
15554261 TTATGAATTTATT
1 TTATGAATTTATT
15554274 TTATGAATTTATT
1 TTATGAATTTATT
*
15554287 TGATGA
1 TTATGA
15554293 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:15554499 original size:50 final size:50
Alignment explanation
Indices: 15554387--15554628 Score: 313
Period size: 50 Copynumber: 4.7 Consensus size: 50
15554377 ATTTGGGTAA
* *
15554387 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC----GA-CATG
* *
15554443 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
* * *
15554493 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
* * *
15554543 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
**
15554593 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
15554629 TTTGGCATGT
Statistics
Matches: 168, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 96 0.57
51 31 0.18
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
Found at i:15554576 original size:100 final size:103
Alignment explanation
Indices: 15554387--15554636 Score: 371
Period size: 100 Copynumber: 2.4 Consensus size: 103
15554377 ATTTGGGTAA
15554387 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
15554452 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
* * *
15554493 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
15554555 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
* *
15554593 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
15554637 GTTATTATCA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
100 52 0.39
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
Found at i:15565482 original size:24 final size:23
Alignment explanation
Indices: 15565453--15565501 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
15565443 TTTTTTGTAT
*
15565453 TTTTAATTTGTTGAAAAATATTTA
1 TTTTAATAT-TTGAAAAATATTTA
* *
15565477 TTTTAATATTTGTAATATATTTA
1 TTTTAATATTTGAAAAATATTTA
15565500 TT
1 TT
15565502 GTATTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTTAATATTTGAAAAATATTTA
Found at i:15565499 original size:23 final size:22
Alignment explanation
Indices: 15565468--15565531 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
15565458 ATTTGTTGAA
*
15565468 AAATATTTATTTTAATATTTGT
1 AAATATTTATTTTTATATTTGT
*
15565490 AATATATTTATTGTATTATATTTTT
1 AA-ATATTTATT-T-TTATATTTGT
15565515 AAA-ATTTATTTTTATAT
1 AAATATTTATTTTTATAT
15565532 AAAAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 16 0.43
24 2 0.05
25 10 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (22 bp):
AAATATTTATTTTTATATTTGT
Found at i:15572336 original size:3 final size:3
Alignment explanation
Indices: 15572328--15572380 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
15572318 GGCGGCAATC
15572328 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
15572376 TCT TC
1 TCT TC
15572381 CTAGCTACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:15577259 original size:81 final size:81
Alignment explanation
Indices: 15577148--15577322 Score: 305
Period size: 81 Copynumber: 2.1 Consensus size: 81
15577138 GAAATGAATG
* *
15577148 ACTATGTGAAAGTATATCTGATTCAGGTACGTACGAAGTGTATATGATATTCAAGAATGAAAGGT
1 ACTATGTGAAAGTATATCCGATTCAGGTACGTACGAAGTGTATACGATATTCAAGAATGAAAGGT
15577213 GAGTATGTTTCAAATA
66 GAGTATGTTTCAAATA
15577229 ACTATGTGAAAGTATATCCGATTCAGGTACGTACGAAGTGTATACGATATTCAAGAATGAAAGGT
1 ACTATGTGAAAGTATATCCGATTCAGGTACGTACGAAGTGTATACGATATTCAAGAATGAAAGGT
*
15577294 GAGTATGTTTCAAATG
66 GAGTATGTTTCAAATA
15577310 ACGATATGTGAAA
1 AC--TATGTGAAA
15577323 TACATGAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
81 80 0.90
83 9 0.10
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (81 bp):
ACTATGTGAAAGTATATCCGATTCAGGTACGTACGAAGTGTATACGATATTCAAGAATGAAAGGT
GAGTATGTTTCAAATA
Found at i:15581524 original size:14 final size:14
Alignment explanation
Indices: 15581513--15581556 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
15581503 GTTTTATTTC
15581513 ATATTATATATTAT
1 ATATTATATATTAT
15581527 ATATTATATTATTATT
1 ATATTATA-TATTA-T
15581543 ATATTAT-TATTAT
1 ATATTATATATTAT
15581556 A
1 A
15581557 GTAAAGTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.07
14 13 0.46
15 5 0.18
16 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTATATATTAT
Found at i:15581541 original size:3 final size:3
Alignment explanation
Indices: 15581514--15581555 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
15581504 TTTTATTTCA
15581514 TAT TAT ATAT TAT ATAT TA- TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15581556 AGTAAAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.11
3 25 0.71
4 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:15581544 original size:11 final size:11
Alignment explanation
Indices: 15581514--15581556 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
15581504 TTTTATTTCA
15581514 TATTA-TATAT
1 TATTATTATAT
15581524 TATATATTATAT
1 TAT-TATTATAT
15581536 TATTATTATAT
1 TATTATTATAT
15581547 TATTATTATA
1 TATTATTATA
15581557 GTAAAGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.10
11 20 0.65
12 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATAT
Found at i:15581947 original size:21 final size:21
Alignment explanation
Indices: 15581922--15581989 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
15581912 TGTTTTTGAG
15581922 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
15581943 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* * *
15581961 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
15581983 TACTGAA
1 TACTGAA
15581990 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 13 0.37
22 6 0.17
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:15581965 original size:40 final size:40
Alignment explanation
Indices: 15581882--15581989 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
15581872 TTGAGACTGA
* * * * *
15581882 TACTGAATTGCATTATGAAATATTGAATATTGTTTTTGAG
1 TACTGAATTGAATTGTGAATTACTGAATATTGTTTATGAG
*
15581922 TACTGAATTGAATTGTGAAGTTACTGAATATTG-TTATGTG
1 TACTGAATTGAATTGTGAA-TTACTGAATATTGTTTATGAG
* *
15581962 TACTGCATTGAACTGTGAAATTACTGAA
1 TACTGAATTGAATTGTG-AATTACTGAA
15581990 GTAATGAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 45 0.78
41 13 0.22
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.41
Consensus pattern (40 bp):
TACTGAATTGAATTGTGAATTACTGAATATTGTTTATGAG
Found at i:15582260 original size:45 final size:45
Alignment explanation
Indices: 15582193--15582288 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
15582183 CCGACTACTA
* *
15582193 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
1 TTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACCG
* *
15582238 TTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATACTATTACTG
1 TTACTGTTACAGATTCGA-CACTTTGTGTGTCGAATACTATTACCG
15582283 TTACTG
1 TTACTG
15582289 CTACCGTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACCG
Found at i:15584963 original size:22 final size:22
Alignment explanation
Indices: 15584904--15584965 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
15584894 GATAACATTG
** *
15584904 AATTTTAAAG-GTTTTTCCTAT
1 AATTTTAAAGAGTTTTTTTTAA
*
15584925 ATTTTTAAA-A-TTATTTTTTAA
1 AATTTTAAAGAGTT-TTTTTTAA
15584946 AATTTTAAAGAGTTTTTTTT
1 AATTTTAAAGAGTTTTTTTT
15584966 CATATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.06
21 21 0.66
22 7 0.22
23 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (22 bp):
AATTTTAAAGAGTTTTTTTTAA
Found at i:15584972 original size:22 final size:21
Alignment explanation
Indices: 15584905--15584973 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
15584895 ATAACATTGA
**
15584905 ATTTTAAAG-GTTTTTCCTAT
1 ATTTTAAAGAGTTTTTTTTAT
*
15584925 ATTTTTAAA-A-TTATTTTTTAAA
1 A-TTTTAAAGAGTT-TTTTTT-AT
15584947 ATTTTAAAGAGTTTTTTTTCAT
1 ATTTTAAAGAGTTTTTTTT-AT
15584969 ATTTT
1 ATTTT
15584974 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.08
21 18 0.47
22 15 0.39
23 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.59
Consensus pattern (21 bp):
ATTTTAAAGAGTTTTTTTTAT
Found at i:15586170 original size:43 final size:42
Alignment explanation
Indices: 15586121--15586347 Score: 226
Period size: 43 Copynumber: 5.2 Consensus size: 42
15586111 TTATTTTTAA
* *
15586121 AAACGCCGCTAAAAGTCATATTCTTTAGTGGCGCTTTATACAC
1 AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTT-TACAC
* *
15586164 AAACGCCGCTAAAGGTCGTGTTCCGACCTTTAGCGGCGCTTTTAACAC
1 AAACGCCGCTAAAAGTCATGTT-----CTTTAGCGGCGCTTTT-ACAC
* * * *
15586212 AAACGCCGCTAAAGGTCATATTTTTTGGCGGCGCTTTTA-AC
1 AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTTTACAC
* *
15586253 ATTAAAGCCGCT-AAAGTTCATGTTCTTTAGCGGCGCTTCTAACAC
1 A--AACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGCTT-TTACAC
15586298 AAACGCCGCT-AAAGCTCATGTTCTTTAGCGGCGCTTTTTACAC
1 AAACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGC-TTTTACAC
15586341 AAACGCC
1 AAACGCC
15586348 ACTATTTATT
Statistics
Matches: 155, Mismatches: 17, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.02
42 4 0.03
43 102 0.66
44 4 0.03
45 3 0.02
47 1 0.01
48 38 0.25
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTTTACAC
Found at i:15586329 original size:86 final size:85
Alignment explanation
Indices: 15586121--15586343 Score: 261
Period size: 86 Copynumber: 2.5 Consensus size: 85
15586111 TTATTTTTAA
* * *
15586121 AAACGCCGCTAAAAGTCATATTCTTTAGTGGCGCTTTATACACAAACGCCGCTAAAGGTCGTGTT
1 AAACGCCGCT-AAAGTCATATTCTTTAGCGGCGCTTT-TACACAAAAGCCGCTAAAGGTCATGTT
*
15586186 CCGACCTTTAGCGGCGCTTTTAACAC
64 ----CCTTTAGCGGCGCTTCTAACAC
* * *
15586212 AAACGCCGCTAAAGGTCATATTTTTTGGCGGCGCTTTTA-ACATTAAAGCCGCTAAAGTTCATGT
1 AAACGCCGCTAAA-GTCATATTCTTTAGCGGCGCTTTTACACA--AAAGCCGCTAAAGGTCATGT
15586276 T-CTTTAGCGGCGCTTCTAACAC
63 TCCTTTAGCGGCGCTTCTAACAC
*
15586298 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTTACACAAA
1 AAACGCCGCTAAAG-TCATATTCTTTAGCGGCGC-TTTTACACAAA
15586344 CGCCACTATT
Statistics
Matches: 116, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
85 1 0.01
86 51 0.44
87 5 0.04
88 3 0.03
89 3 0.03
90 5 0.04
91 48 0.41
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (85 bp):
AAACGCCGCTAAAGTCATATTCTTTAGCGGCGCTTTTACACAAAAGCCGCTAAAGGTCATGTTCC
TTTAGCGGCGCTTCTAACAC
Found at i:15586704 original size:21 final size:21
Alignment explanation
Indices: 15586680--15586747 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
15586670 TGCTCTACTT
15586680 TGCTTCTCTCGCTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
15586701 TGCTTCTCTCGCTGCAACCTC
1 TGCTTCTCTCGCTGCAGCCTC
* * *
15586722 TGTTTCCCTCGCTGCCGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
15586743 TGCTT
1 TGCTT
15586748 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:15587380 original size:16 final size:16
Alignment explanation
Indices: 15587359--15587428 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
15587349 CCCTAAACCA
15587359 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
* * **
15587375 TAAACTA-CATACTAT
1 TAAACTATAAAACCCT
*
15587390 AGTAAAC-ATTAAA-CCT
1 --TAAACTATAAAACCCT
15587406 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
15587422 TAAACTA
1 TAAACTA
15587429 CATACTATAG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 19 0.47
17 7 0.17
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.27
Consensus pattern (16 bp):
TAAACTATAAAACCCT
Found at i:15587388 original size:23 final size:23
Alignment explanation
Indices: 15587362--15587437 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
15587352 TAAACCATAA
15587362 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
*
15587385 ACTATAGTAAA-CATTAAACCTTA-A-
1 ACTATA--AAACCCTTAAA-C-TACAT
15587409 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
15587432 ACTATA
1 ACTATA
15587438 GCCCTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
21 2 0.05
22 5 0.11
23 18 0.41
24 12 0.27
25 5 0.11
26 2 0.05
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (23 bp):
ACTATAAAACCCTTAAACTACAT
Found at i:15587894 original size:41 final size:41
Alignment explanation
Indices: 15587843--15588190 Score: 517
Period size: 41 Copynumber: 8.5 Consensus size: 41
15587833 GCGTTTTTTA
* *
15587843 AAAAAGCGCCGCTAAAGGCCTGAGAA-A-TAGCGGCGCAT-CAAT
1 AAAAA-CGCCGCTAAA-GCC-CAGAACATTAGCGGCGCTTAC-AT
*
15587885 AAAAACGCCGCTAAAGTCCAGAACATTAGCGGCGCTTAC-T
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
*
15587925 AAAAAACGCCGCTAAATCCCAGAACATTAGCGGCGCTTACAT
1 -AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
15587967 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTGA-AT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTT-ACAT
15588008 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
15588049 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGTTTAGAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
15588090 AAAAATGCCGCTAAAGCCTAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
15588131 AAAAACACCGCTAAAGCTCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
15588172 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
15588191 CCGAAAAGTC
Statistics
Matches: 281, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
39 4 0.01
40 5 0.02
41 264 0.94
42 8 0.03
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:15587940 original size:123 final size:120
Alignment explanation
Indices: 15587791--15588186 Score: 480
Period size: 123 Copynumber: 3.2 Consensus size: 120
15587781 TAATTTTTTT
* * * * * * **
15587791 GCGGCGCTTTC-TAAAAATGCCACTAAATGAAGAGCATTAGTGGCGTTT-TTTAAAAAAGCGCCG
1 GCGGCGCTTACATAAAAACGCCGCTAAATGCAGAACATTAGCGGCGTTTACAT-AAAAA-CGCCG
15587854 CTAAAGGCCTGAGAA-A-TAGCGGCGCATCAATAAAAACGCCGCTAAAGTCCAGAACATTA
64 CTAAA-GCCT-AGAACATTAGCGGCGC-TCAATAAAAACGCCGCTAAAG-CCAGAACATTA
* *
15587913 GCGGCGCTTAC-TAAAAAACGCCGCTAAATCCCAGAACATTAGCGGCGCTTACATAAAAACGCCG
1 GCGGCGCTTACAT-AAAAACGCCGCTAAAT-GCAGAACATTAGCGGCGTTTACATAAAAACGCCG
* *
15587977 CTAAAGCCCAGAACATTAGCGGCGCTTGAATAAAAACGCCGCTAAAGCCCAGAACATTA
64 CTAAAGCCTAGAACATTAGCGGCGC-TCAATAAAAACGCCGCTAAAG-CCAGAACATTA
* *
15588036 GCGGCGCTTACATAAAAACGCCGCTAAA-GCCCAGAACATTAGCGGCGTTTAGATAAAAATGCCG
1 GCGGCGCTTACATAAAAACGCCGCTAAATG--CAGAACATTAGCGGCGTTTACATAAAAACGCCG
* *
15588100 CTAAAGCCTAGAACATTAGCGGCGCTTACATAAAAACACCGCTAAAGCTCAGAACATTA
64 CTAAAGCCTAGAACATTAGCGGCGCTCA-ATAAAAACGCCGCTAAAGC-CAGAACATTA
15588159 GCGGCGCTTACATAAAAACGCCGCTAAA
1 GCGGCGCTTACATAAAAACGCCGCTAAA
15588187 GCCCCCGAAA
Statistics
Matches: 243, Mismatches: 21, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
121 4 0.02
122 18 0.07
123 199 0.82
124 21 0.09
125 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (120 bp):
GCGGCGCTTACATAAAAACGCCGCTAAATGCAGAACATTAGCGGCGTTTACATAAAAACGCCGCT
AAAGCCTAGAACATTAGCGGCGCTCAATAAAAACGCCGCTAAAGCCAGAACATTA
Found at i:15608180 original size:6 final size:6
Alignment explanation
Indices: 15608147--15608177 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
15608137 GAATGAAAGC
*
15608147 GGCGTT GGCGTT GGCGTT GGCGTT GACGTT G
1 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT G
15608178 ACGATGGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.48, T:0.32
Consensus pattern (6 bp):
GGCGTT
Found at i:15613155 original size:18 final size:18
Alignment explanation
Indices: 15613134--15613170 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15613124 TCATTAATTT
* *
15613134 TAAATTTTATTATTAAAA
1 TAAATTATACTATTAAAA
15613152 TAAATTATACTATTAAAA
1 TAAATTATACTATTAAAA
15613170 T
1 T
15613171 TTTATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTATACTATTAAAA
Found at i:15614259 original size:30 final size:29
Alignment explanation
Indices: 15614223--15614289 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
15614213 ATAATTTGTG
* *
15614223 AAAATTAAACCAAATCAAAATTTCATATAT
1 AAAATTAAACAAAATCAAAA-CTCATATAT
* *
15614253 AAAATTACACAAAATTAAAACTCATATAT
1 AAAATTAAACAAAATCAAAACTCATATAT
*
15614282 AATATTAA
1 AAAATTAA
15614290 CATTACATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAATTAAACAAAATCAAAACTCATATAT
Found at i:15615121 original size:3 final size:3
Alignment explanation
Indices: 15615113--15615138 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15615103 AAATATAAAT
15615113 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
15615139 TTAAGTTGAC
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:15618316 original size:40 final size:40
Alignment explanation
Indices: 15618271--15618352 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
15618261 CGTTTCTTTT
15618271 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
1 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
*
15618311 ATGTAATAATAGACTCAATAATCTTTCATTTACTATCTCA
1 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
15618351 AT
1 AT
15618353 CACCCTCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (40 bp):
ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
Found at i:15618684 original size:48 final size:48
Alignment explanation
Indices: 15618612--15618819 Score: 236
Period size: 48 Copynumber: 4.3 Consensus size: 48
15618602 TCGGAATAAA
* * * * * *
15618612 AACAGATTTCTCGGTGGCTTGCACACAGTCCGTACCACCTTTGTGTAAT
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * * *
15618661 AACAGATTCTCGGTGGCCGGCACATAGTCCGTGCCACCCTTGTATCTT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * *
15618709 AACCGGTTATTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * * **
15618757 TACAGAATATCAGTGGCCTGCACACAGTCCGTGCCACCCTTGTGCCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
*
15618805 AACAGAATATCGGTG
1 AACAGATTATCGGTG
15618820 CGCATAGTAG
Statistics
Matches: 134, Mismatches: 25, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
48 128 0.96
49 6 0.04
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (48 bp):
AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
Found at i:15619190 original size:16 final size:16
Alignment explanation
Indices: 15619169--15619202 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
15619159 ATAATAATAA
15619169 TAATTTAT-TTAAATTG
1 TAATTTATATT-AATTG
15619185 TAATTTATATTAATTG
1 TAATTTATATTAATTG
15619201 TA
1 TA
15619203 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATTTATATTAATTG
Found at i:15619345 original size:12 final size:13
Alignment explanation
Indices: 15619326--15619356 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
15619316 TAAGTAAAAG
15619326 ATATTAATTAATT
1 ATATTAATTAATT
15619339 A-ATTAATTAATT
1 ATATTAATTAATT
15619351 ATATTA
1 ATATTA
15619357 TGAGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAATTAATT
Found at i:15619540 original size:15 final size:17
Alignment explanation
Indices: 15619522--15619553 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15619512 CAGAATAGAA
15619522 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
15619537 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
15619554 GGGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Done.