Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 83 of 313
Found at i:27893648 original size:21 final size:21
Alignment explanation
Indices: 27893618--27893690 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
27893608 ACCAAATGTG
*
27893618 TAAAAAAATTTATAATTATAA
1 TAAAATAATTTATAATTATAA
27893639 TAAAATAATTATATAA-TATATA
1 TAAAATAATT-TATAATTATA-A
* *
27893661 TAAATATAAATTTAGAATAAT-A
1 TAAA-AT-AATTTATAATTATAA
27893683 TAAAATAA
1 TAAAATAA
27893691 GTAATTAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
20 2 0.05
21 15 0.34
22 15 0.34
23 6 0.14
24 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
TAAAATAATTTATAATTATAA
Found at i:27893847 original size:7 final size:7
Alignment explanation
Indices: 27893835--27894051 Score: 116
Period size: 7 Copynumber: 31.1 Consensus size: 7
27893825 TTTAATGATA
27893835 ATAATAT
1 ATAATAT
*
27893842 ATAATAAA
1 ATAAT-AT
27893850 ATAAT-T
1 ATAATAT
27893856 ATAATAT
1 ATAATAT
27893863 ATAATAT
1 ATAATAT
27893870 A-AA-AGT
1 ATAATA-T
*
27893876 AT-ATTT
1 ATAATAT
* * *
27893882 GTAAAAA
1 ATAATAT
27893889 ATAATAT
1 ATAATAT
27893896 ATAATAT
1 ATAATAT
*
27893903 AT-ATAA
1 ATAATAT
27893909 ATAA-AT
1 ATAATAT
27893915 AATAAATAT
1 -AT-AATAT
27893924 ATAATAT
1 ATAATAT
*
27893931 AAGTAAAAAT
1 -A-T-AATAT
27893941 ATAATA-
1 ATAATAT
27893947 ATAATAT
1 ATAATAT
27893954 ATAA-AT
1 ATAATAT
*
27893960 AATAATGT
1 -ATAATAT
*
27893968 AAAATA-
1 ATAATAT
*
27893974 ATAATTT
1 ATAATAT
* *
27893981 GTGAA-AA
1 AT-AATAT
27893988 ATAATAT
1 ATAATAT
*
27893995 ATAATAA
1 ATAATAT
27894002 ATAATA-
1 ATAATAT
*
27894008 AT-ATAA
1 ATAATAT
27894014 ATAATAT
1 ATAATAT
*
27894021 ATAATAAA
1 ATAAT-AT
27894029 ATAATTAT
1 ATAA-TAT
27894037 ATAATAT
1 ATAATAT
27894044 ATAATAT
1 ATAATAT
27894051 A
1 A
27894052 AAAATAAGGT
Statistics
Matches: 159, Mismatches: 28, Indels: 46
0.68 0.12 0.20
Matches are distributed among these distances:
5 4 0.03
6 36 0.23
7 85 0.53
8 25 0.16
9 5 0.03
10 4 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:27893892 original size:44 final size:44
Alignment explanation
Indices: 27893844--27894058 Score: 155
Period size: 51 Copynumber: 4.8 Consensus size: 44
27893834 AATAATATAT
27893844 AATAA-AATAATTATAATATATAATATAAAAGTAT-ATTTGTAAAA
1 AATAATAATAA-TATAATATATAATATAAAA-TATAATTTGTAAAA
* *
27893888 AATAATATATAATATATATAAATAAATAATAAATATATAATATAAGTAAAA
1 AATAATA-ATAATATA-ATATAT-AAT-ATAAA-ATATAAT-T-TGTAAAA
* * *
27893939 ATATAATAATAATATATAAATAATAATGTAAAATAATAATTTGTGAAA
1 A-ATAATAATAATATA-ATAT-ATAATATAAAAT-ATAATTTGTAAAA
* *
27893987 AATAATATATAATA-AATA-ATAATAT--AA-ATAATATATAATAA
1 AATAATA-ATAATATAATATATAATATAAAATATAATTTGTAA-AA
27894028 AATAAT--T-ATATAATATATAATATAAAA-ATAA
1 AATAATAATAATATAATATATAATATAAAATATAA
27894059 GGTTAAAAAT
Statistics
Matches: 141, Mismatches: 12, Indels: 39
0.73 0.06 0.20
Matches are distributed among these distances:
37 3 0.02
38 5 0.04
39 7 0.05
40 8 0.06
41 14 0.10
42 2 0.01
44 11 0.08
45 5 0.04
46 11 0.08
47 10 0.07
48 20 0.14
49 6 0.04
50 10 0.07
51 21 0.15
52 8 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (44 bp):
AATAATAATAATATAATATATAATATAAAATATAATTTGTAAAA
Found at i:27893916 original size:17 final size:17
Alignment explanation
Indices: 27893883--27894046 Score: 68
Period size: 17 Copynumber: 10.0 Consensus size: 17
27893873 AGTATATTTG
27893883 TAAA-AAATAATATATAA
1 TAAATAAATAATATAT-A
27893900 TATATATAAATAA-ATA-A
1 TA-A-ATAAATAATATATA
*
27893917 TAAATATATAATATA-A
1 TAAATAAATAATATATA
27893933 GTAAA-AATATAATA-ATAA
1 -TAAATAA-ATAATATAT-A
* *
27893951 TATATAAATAATA-ATG
1 TAAATAAATAATATATA
*
27893967 TAAA-ATAATAAT-T-TG
1 TAAATA-AATAATATATA
*
27893982 TGAA-AAATAATATATAA
1 TAAATAAATAATATAT-A
*
27893999 TAAAT-AATAATATAAA
1 TAAATAAATAATATATA
* *
27894015 T-AATATATAATA-AAA
1 TAAATAAATAATATATA
* *
27894030 TAATTATATAATATATA
1 TAAATAAATAATATATA
27894047 ATATAAAAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 36
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.05
15 22 0.19
16 35 0.30
17 40 0.34
18 4 0.03
19 4 0.03
20 6 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAATAAATAATATATA
Found at i:27893941 original size:30 final size:29
Alignment explanation
Indices: 27893883--27894052 Score: 104
Period size: 30 Copynumber: 5.8 Consensus size: 29
27893873 AGTATATTTG
* *
27893883 TAAAAAAT-AATATATAATAT-ATATAAA
1 TAAATAATAAATATATAATATAATAAAAA
27893910 TAAATAATAAATATATAATATAAGTAAAAA
1 TAAATAATAAATATATAATATAA-TAAAAA
**
27893940 TATAATAAT-AATATATAA-ATAAT-AATG
1 TA-AATAATAAATATATAATATAATAAAAA
* * * *
27893967 TAAAATAAT-AATTTGTGAAAAATAATATATAA
1 T-AAATAATAAATATAT--AATATAATA-AAAA
*
27893999 TAAATAATAATATAAATAATAT-ATAATAAA
1 TAAATAATAA-ATATATAATATAATAA-AAA
*
27894029 -ATAATTATATAATATATAATATAA
1 TA-AATAATA-AATATATAATATAA
27894053 AAATAAGGTT
Statistics
Matches: 111, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
27 21 0.19
28 14 0.13
29 9 0.08
30 42 0.38
31 19 0.17
32 3 0.03
33 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
TAAATAATAAATATATAATATAATAAAAA
Found at i:27893943 original size:99 final size:100
Alignment explanation
Indices: 27893845--27894049 Score: 255
Period size: 99 Copynumber: 2.1 Consensus size: 100
27893835 ATAATATATA
*
27893845 ATAA-AATAAT-TAT-AATATATAATATAAAAGT-AT-ATTTGTAAAAAATAATATATAATATAT
1 ATAATAATAATATATAAATA-ATAATATAAAA-TAATAATTTGTAAAAAATAATATATAATAAAT
*
27893905 -ATAA-ATAAATAATAAATATATAATATAAGTAAAAAT
64 AATAATATAAATAATAAATA-ATAAAATAAGTAAAAAT
* *
27893941 ATAATAATAATATATAAATAATAATGTAAAATAATAATTTGTGAAAAATAATATATAATAAATAA
1 ATAATAATAATATATAAATAATAATATAAAATAATAATTTGTAAAAAATAATATATAATAAATAA
* * *
27894006 TAATATAAATAATATATAATAAAATAATTATATAAT
66 TAATATAAATAATAAATAATAAAATAAGTA-AAAAT
27894042 AT-ATAATA
1 ATAATAATA
27894050 TAAAAATAAG
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
96 4 0.04
97 7 0.07
98 15 0.16
99 29 0.31
100 20 0.21
101 19 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (100 bp):
ATAATAATAATATATAAATAATAATATAAAATAATAATTTGTAAAAAATAATATATAATAAATAA
TAATATAAATAATAAATAATAAAATAAGTAAAAAT
Found at i:27893962 original size:34 final size:35
Alignment explanation
Indices: 27893903--27893971 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
27893893 TATATAATAT
*
27893903 ATATAAATAAATAATAAATATATAATATAAGTAAAA
1 ATATAAATAAATAATAAATAAATAATA-AAGTAAAA
* *
27893939 ATAT-AAT-AATAATATATAAATAATAATGTAAAA
1 ATATAAATAAATAATAAATAAATAATAAAGTAAAA
27893972 TAATAATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 7 0.23
34 16 0.53
35 3 0.10
36 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (35 bp):
ATATAAATAAATAATAAATAAATAATAAAGTAAAA
Found at i:27893973 original size:58 final size:57
Alignment explanation
Indices: 27893834--27894108 Score: 152
Period size: 56 Copynumber: 4.8 Consensus size: 57
27893824 CTTTAATGAT
* *
27893834 AATAATATATAATAAAATAATTATAATATATAATATAA-AAGTATATTTGTAAAAAATAATATAT
1 AATAATA-AT-ATAAAATAA-TA-AATATATAATATAATAA--A-A--TATAATAAATAATATAT
27893898 A
57 A
27893899 ATATATATAA-AT-AAATAATAAATATATAATATAAGTAAAAATATAAT-AATAATATATA
1 A-ATA-ATAATATAAAATAATAAATATATAATATAA-T-AAAATATAATAAATAATATATA
* * * *
27893957 AATAATAATGTAAAATAAT-AATTTGTGAA-A-AATAATATATAATAAATAATAATATA
1 AATAATAATATAAAATAATAAATATAT-AATATAATAAAATATAATAAATAAT-ATATA
* *
27894013 AATAAT-ATATAATAA-AATAATTATATAATAT-AT--AATATAA-AAATAAGGT-TAAA
1 AATAATAATATAA-AATAATAAATATATAATATAATAAAATATAATAAATAA--TATATA
* * *
27894066 AATAAAACAAATAACAATAAAAAATATAT-ATAT-ATAAAA-ATAA
1 AATAATA-ATATAA-AATAATAAATATATAATATAATAAAATATAA
27894109 ATATATAGGG
Statistics
Matches: 172, Mismatches: 17, Indels: 51
0.72 0.07 0.21
Matches are distributed among these distances:
53 14 0.08
54 15 0.09
55 31 0.18
56 39 0.23
57 12 0.07
58 21 0.12
59 4 0.02
61 15 0.09
62 3 0.02
63 6 0.03
64 4 0.02
65 1 0.01
66 4 0.02
67 3 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (57 bp):
AATAATAATATAAAATAATAAATATATAATATAATAAAATATAATAAATAATATATA
Found at i:27894104 original size:16 final size:16
Alignment explanation
Indices: 27894085--27894115 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27894075 AATAACAATA
*
27894085 AAAAATATATATATAT
1 AAAAATAAATATATAT
27894101 AAAAATAAATATATA
1 AAAAATAAATATATA
27894116 GGGTTAGATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATAAATATATAT
Found at i:27895708 original size:82 final size:82
Alignment explanation
Indices: 27895602--27895980 Score: 605
Period size: 82 Copynumber: 4.6 Consensus size: 82
27895592 GTCATCTTGG
* * * * *
27895602 ATCTACTCCCCGTCCATTACAGAGAGATAAGATCTGTCATCTTGGATCTACCCCAATGAAGGTCA
1 ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
*
27895667 GATCTACTATGTCTTCA
66 GATCTGCTATGTCTTCA
* *
27895684 ATCTGCTCCCCTTCGAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
1 ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
*
27895749 GATCTGCTATGTCTTCG
66 GATCTGCTATGTCTTCA
* * *
27895766 ATCTACTCCCCATCAAATACAGAGAGATAAAATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
1 ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
27895831 GATCTGCTATGTCTTCA
66 GATCTGCTATGTCTTCA
* *
27895848 ATCTGCTTCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCTGATGAAGGTCA
1 ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
*
27895913 GATCTGCTATGTCTTCG
66 GATCTGCTATGTCTTCA
* *
27895930 ATCTGCTCCCCGTCGAATACAGAGAGATAAGATCTGTCATCTTAGATCTGC
1 ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGC
27895981 TCCCCGTCTA
Statistics
Matches: 275, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 275 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (82 bp):
ATCTGCTCCCCGTCAAATACAGAGAGATAAGATCTGTCATCTTGGATCTGCCCCGATGAAGGTCA
GATCTGCTATGTCTTCA
Found at i:27903412 original size:32 final size:32
Alignment explanation
Indices: 27903342--27903416 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
27903332 AAAATTTAAC
* *
27903342 TTATAATAAAAAATATATTTATAAGAATAACAA
1 TTAT-ATAAAAAATATATTGATAAGAAAAACAA
* *
27903375 TTATATAAAAAATATATTGATTTAGAAAAATAA
1 TTATATAAAAAATATATTGA-TAAGAAAAACAA
27903408 -TATATAAAA
1 TTATATAAAA
27903417 TATCAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 24 0.65
33 13 0.35
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (32 bp):
TTATATAAAAAATATATTGATAAGAAAAACAA
Found at i:27903779 original size:19 final size:19
Alignment explanation
Indices: 27903755--27903805 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
27903745 AATATATAAT
*
27903755 ATATATAA-ATAATTAAGAA
1 ATATATAATATAAGTAA-AA
27903774 ATATATAATATAAGTAAAA
1 ATATATAATATAAGTAAAA
27903793 ATATAATAATATA
1 ATAT-ATAATATA
27903806 TAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
ATATATAATATAAGTAAAA
Found at i:27903796 original size:17 final size:16
Alignment explanation
Indices: 27903763--27903800 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
27903753 ATATATATAA
*
27903763 ATAAT-TAAGAAATAT
1 ATAATATAAGAAAAAT
27903778 ATAATATAAGTAAAAAT
1 ATAATATAAG-AAAAAT
27903795 ATAATA
1 ATAATA
27903801 ATATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 4 0.20
17 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
ATAATATAAGAAAAAT
Found at i:27903813 original size:59 final size:60
Alignment explanation
Indices: 27903688--27903906 Score: 188
Period size: 59 Copynumber: 3.6 Consensus size: 60
27903678 CAAATGACAT
* * * *
27903688 AATAATATATAATAAAATAATT-ATAATATATAATATAAAAGTATATATGTAA-AAAATAATA
1 AATAATATATAATAAAATAATTAATAATATATAATAT--AAGTAAAAATATAATAATAT-ATA
* *
27903749 TATAATATAT-AT-AAATAATTAAGAAATATATAATATAAGTAAAAATATAATAATATATA
1 AATAATATATAATAAAATAATTAA-TAATATATAATATAAGTAAAAATATAATAATATATA
* * * *
27903808 AATAATA-AT-GTAAAATAA-TAATAATTTGTGAA-A-AATGATATATAATA-AATAATAATATA
1 AATAATATATAATAAAATAATTAATAATATAT-AATATAA-G-TA-AAAATATAATAAT-ATATA
27903867 AATAATATATAATAAAATAATTATATAATATATAATATAA
1 AATAATATATAATAAAATAATTA-ATAATATATAATATAA
27903907 AAATAAGGTT
Statistics
Matches: 128, Mismatches: 15, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
56 2 0.02
57 7 0.05
58 16 0.12
59 51 0.40
60 9 0.07
61 29 0.23
62 4 0.03
63 8 0.06
64 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (60 bp):
AATAATATATAATAAAATAATTAATAATATATAATATAAGTAAAAATATAATAATATATA
Found at i:27903894 original size:23 final size:25
Alignment explanation
Indices: 27903688--27903911 Score: 116
Period size: 26 Copynumber: 8.9 Consensus size: 25
27903678 CAAATGACAT
27903688 AATAATATATAATAA-AATAAT-T-
1 AATAATATATAATAATAATAATATA
27903710 -ATAATATATAAT-ATAA-AAGTATA
1 AATAATATATAATAATAATAA-TATA
* * *
27903733 TATGTAAAAAATAATATATAATATATATA
1 -A-ATAATATATAATA-ATAATA-ATATA
27903762 AATAAT-TA-AGA-AATATATAATATA
1 AATAATATATA-ATAATA-ATAATATA
* *
27903786 AGTAAAAATATAATAATATATAA-AT-
1 AAT-AATATATAATAATA-ATAATATA
* * *
27903811 AATAATGTAAAATAATAATAATTTGTGAAA
1 AATAATATATAATAATAATAA----T-ATA
*
27903841 AATGATATATAATAAATAATAATATA
1 AATAATATATAAT-AATAATAATATA
27903867 AATAATATATAATAA-AATAAT-TA
1 AATAATATATAATAATAATAATATA
* *
27903890 TATAATATATAAT-ATAAAAATA
1 AATAATATATAATAATAATAATA
27903912 AGGTTAAAAA
Statistics
Matches: 155, Mismatches: 20, Indels: 52
0.68 0.09 0.23
Matches are distributed among these distances:
20 3 0.02
21 15 0.10
22 2 0.01
23 23 0.15
24 27 0.17
25 11 0.07
26 30 0.19
27 14 0.09
28 5 0.03
29 6 0.04
30 11 0.07
31 8 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AATAATATATAATAATAATAATATA
Found at i:27903898 original size:47 final size:45
Alignment explanation
Indices: 27903644--27903911 Score: 158
Period size: 47 Copynumber: 6.0 Consensus size: 45
27903634 CTTTAATGAT
* * *
27903644 AATAATATATAGAT-AAA-AATGTATAATAATATAACA-AATGACAT-
1 AATAATATATA-ATAAAATAATATATAAT-ATATAA-ATAATAATATA
27903688 AATAATATATAATAAAATAAT-TATAATATAT-AAT-AT-A-A-A
1 AATAATATATAATAAAATAATATATAATATATAAATAATAATATA
* * *
27903727 AGTATATATGTAA-AAAATAATATATAATATATATA-AATAAT-TA
1 AATA-ATATATAATAAAATAATATATAATATATAAATAATAATATA
* *
27903770 AGA-AATATATAATATAAGTAAAAATATAATAATATATAAATAATAATGTAA
1 A-ATAATATAT-A-ATAA--AATAATAT-ATAATATATAAATAATAATAT-A
*
27903821 AATAATA-ATAATTTGTGAAA-AATGATAT-ATA-ATAAATAATAATATA
1 AATAATATATAA----TAAAATAAT-ATATAATATATAAATAATAATATA
*
27903867 AATAATATATAATAAAATAATTATATAATATATAATATAAAAATA
1 AATAATATATAATAAAATAA-TATATAATATATAA-ATAATAATA
27903912 AGGTTAAAAA
Statistics
Matches: 180, Mismatches: 11, Indels: 63
0.71 0.04 0.25
Matches are distributed among these distances:
39 12 0.07
40 18 0.10
41 6 0.03
42 7 0.04
43 14 0.08
44 27 0.15
45 9 0.05
46 12 0.07
47 32 0.18
48 15 0.08
49 12 0.07
50 8 0.04
51 6 0.03
52 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (45 bp):
AATAATATATAATAAAATAATATATAATATATAAATAATAATATA
Found at i:27905507 original size:31 final size:31
Alignment explanation
Indices: 27905461--27905525 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
27905451 AATAAAATAT
* * *
27905461 TTAAAAATAATTTTTATATTAATATTTTTAA
1 TTAAAAATAAATTTTAAAATAATATTTTTAA
* * *
27905492 TTAAAATTAAATTTTAAAATATTATTTTTTA
1 TTAAAAATAAATTTTAAAATAATATTTTTAA
27905523 TTA
1 TTA
27905526 TTTAAATCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAAAAATAAATTTTAAAATAATATTTTTAA
Found at i:27912435 original size:16 final size:16
Alignment explanation
Indices: 27912414--27912446 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27912404 TAATGTGTTC
27912414 AATATTTAACTATCAA
1 AATATTTAACTATCAA
27912430 AATATTTAACTATCAA
1 AATATTTAACTATCAA
27912446 A
1 A
27912447 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATTTAACTATCAA
Found at i:27919974 original size:24 final size:24
Alignment explanation
Indices: 27919947--27920002 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
27919937 AGCTTATGAA
27919947 ATAGATATGTACAAAGGGATGATG
1 ATAGATATGTACAAAGGGATGATG
27919971 ATAGATATGTACAAAGGGATGATG
1 ATAGATATGTACAAAGGGATGATG
*
27919995 ATATATAT
1 ATAGATAT
27920003 ACGCATGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.25, T:0.29
Consensus pattern (24 bp):
ATAGATATGTACAAAGGGATGATG
Found at i:27920546 original size:21 final size:22
Alignment explanation
Indices: 27920522--27920565 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
27920512 AAAGGGACTT
*
27920522 TATGATGATGTTTGAC-TATGA
1 TATGATGATGTATGACTTATGA
27920543 TATGATGATGTATGACTTATGA
1 TATGATGATGTATGACTTATGA
27920565 T
1 T
27920566 TGTGAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (22 bp):
TATGATGATGTATGACTTATGA
Found at i:27930097 original size:50 final size:50
Alignment explanation
Indices: 27929986--27930224 Score: 295
Period size: 50 Copynumber: 4.8 Consensus size: 50
27929976 AGGTGCCGAC
* * * * ** **
27929986 GCCATGTCCTAAACATGGTCTTACACTGGCTCACATATC-AAATTC-GAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCTGAT
* * * *
27930034 GCCATGTCCCAGACATGGTCTTACATTTGCTCTCATCTATCG-GTGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAG-GCTGAT
* * *
27930084 GCCATGTCTCAGACATGGTCTTACACTAGCTCTCATATCTTGAGGCTAAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCTGAT
* *
27930134 GCCATGTCCCAGACATGGTATTACACTAGCTCTCATATCTCGAGGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCTGAT
27930184 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTC
27930225 CCTAGCATCA
Statistics
Matches: 163, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
48 32 0.20
49 1 0.01
50 129 0.79
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCTCGAGGCTGAT
Found at i:27940278 original size:27 final size:27
Alignment explanation
Indices: 27940122--27940267 Score: 193
Period size: 27 Copynumber: 5.4 Consensus size: 27
27940112 AGGGGCATTT
*
27940122 TAGTCATTTTACCACATAAGGTAAAAA
1 TAGTCATTTTACCACATAAGGGAAAAA
*
27940149 TAATCATTTTACCACATAAGGGAAAAA
1 TAGTCATTTTACCACATAAGGGAAAAA
* * *
27940176 TAGTCATTTTAACACATAAAGGCAAAA
1 TAGTCATTTTACCACATAAGGGAAAAA
* ** *
27940203 CAGTCATTTTACCACATAACTGTAAAA
1 TAGTCATTTTACCACATAAGGGAAAAA
* *
27940230 CAGTCATTTTACCACATAAGGGCAAAA
1 TAGTCATTTTACCACATAAGGGAAAAA
27940257 TAGTCATTTTA
1 TAGTCATTTTA
27940268 TCAATTAAGG
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 104 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
TAGTCATTTTACCACATAAGGGAAAAA
Found at i:27950440 original size:40 final size:40
Alignment explanation
Indices: 27950418--27950728 Score: 406
Period size: 40 Copynumber: 7.8 Consensus size: 40
27950408 TGGGGTTTCA
27950418 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
27950458 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * * *
27950498 AAGTACAAATAGGGGCACGTATGTGCATTTAAGGGCACCA
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * *
27950538 AAGTACAAACAGGGGCACGTATGTGCATTCAGGGGCACCA
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * * **
27950578 AAGTACAAACAGGGGCATGTATGTGCATTCAGGCGTATTG
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * * *
27950618 AAGTACAAACAGGGGCACATATGTGCATTCAGGGGCACTG
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * ** *
27950658 AAGTATAAATAGGGGCACGTATGTGCATTTAGGCATACTG
1 AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
* * *
27950698 AAGTAAAAACAGGGGCACGTATGTGCTTTCA
1 AAGTACAAATAGGGGCACGTATGTGCATTCA
27950729 TGGAAATTTC
Statistics
Matches: 242, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 242 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (40 bp):
AAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTACCG
Found at i:27966440 original size:13 final size:13
Alignment explanation
Indices: 27966422--27966451 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27966412 GCTCAGCAGG
27966422 GACACGCCCGTGT
1 GACACGCCCGTGT
*
27966435 GACACGGCCGTGT
1 GACACGCCCGTGT
27966448 GACA
1 GACA
27966452 TGATTGCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.13
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:27968013 original size:13 final size:13
Alignment explanation
Indices: 27967995--27968021 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27967985 ATGGTCTAAT
27967995 ATCATAGCAATTA
1 ATCATAGCAATTA
27968008 ATCATAGCAATTA
1 ATCATAGCAATTA
27968021 A
1 A
27968022 GCACTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATCATAGCAATTA
Found at i:27970033 original size:17 final size:17
Alignment explanation
Indices: 27970011--27970049 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
27970001 TTCAATTTAT
27970011 TAAATTAAATTTAA-TAA
1 TAAATTAAA-TTAATTAA
*
27970028 TAAATTATATTAATTAA
1 TAAATTAAATTAATTAA
27970045 TAAAT
1 TAAAT
27970050 ACAATAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAAATTAATTAA
Found at i:27972730 original size:17 final size:18
Alignment explanation
Indices: 27972708--27972742 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27972698 ATAATTGTAA
*
27972708 TTTAAAT-TTTAATTATT
1 TTTAAATATGTAATTATT
27972725 TTTAAATATGTAATTATT
1 TTTAAATATGTAATTATT
27972743 ATAACTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTAAATATGTAATTATT
Found at i:27972766 original size:26 final size:26
Alignment explanation
Indices: 27972726--27972807 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
27972716 TTAATTATTT
*
27972726 TTAAATATGTAATTATTATAACTTCTA
1 TTAAAT-TATAATTATTATAACTTCTA
* *
27972753 TTAAATTATAATTATTTTTAAATT-T-
1 TTAAATTATAATTA-TTATAACTTCTA
* *
27972778 TTAAATTTATAATTATGACAAACTTCTA
1 TTAAA-TTATAATTATTA-TAACTTCTA
27972806 TT
1 TT
27972808 TTCTAACTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
25 6 0.14
26 21 0.49
27 14 0.33
28 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAAATTATAATTATTATAACTTCTA
Found at i:27978067 original size:29 final size:29
Alignment explanation
Indices: 27978025--27978087 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
27978015 AAAAAGATGG
* *
27978025 GGGAAGGGGAAGGGGAAGGGGAAGGGGAA
1 GGGAAGGGAAAGGGGAAGGGGAAGGGAAA
27978054 GGGAAGGGAAAGGGGAAGGGGAAGGGAAA
1 GGGAAGGGAAAGGGGAAGGGGAAGGGAAA
27978083 GGGAA
1 GGGAA
27978088 AATCGTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (29 bp):
GGGAAGGGAAAGGGGAAGGGGAAGGGAAA
Found at i:27978088 original size:6 final size:6
Alignment explanation
Indices: 27978024--27978085 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
27978014 GAAAAAGATG
*
27978024 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA -GGGAA GGGAAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
*
27978071 GGGGAA GGGAAA GGG
1 GGGGAA GGGGAA GGG
27978086 AAAATCGTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
5 5 0.10
6 47 0.90
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:27979209 original size:10 final size:9
Alignment explanation
Indices: 27979150--27979235 Score: 63
Period size: 9 Copynumber: 9.6 Consensus size: 9
27979140 ATTTACAATT
*
27979150 TTTTTCTAA
1 TTTTTATAA
27979159 TTTTTAATAA
1 TTTTT-ATAA
*
27979169 ATTTTA-AA
1 TTTTTATAA
*
27979177 TTTTTTTAA
1 TTTTTATAA
27979186 CTTTTT-TAAA
1 -TTTTTAT-AA
*
27979196 TTTTAATAA
1 TTTTTATAA
*
27979205 TTTTTATTGA
1 TTTTTA-TAA
27979215 TTTTTAT--
1 TTTTTATAA
27979222 TTTTTATAA
1 TTTTTATAA
27979231 TTTTT
1 TTTTT
27979236 TCCACATGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
7 7 0.11
8 6 0.10
9 26 0.42
10 23 0.37
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:27979209 original size:19 final size:19
Alignment explanation
Indices: 27979149--27979209 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
27979139 TATTTACAAT
*
27979149 TTTTTTCTAATTTTTAATAA
1 TTTTTT-TAAATTTTAATAA
* **
27979169 --ATTTTAAATTTTTTTAA
1 TTTTTTTAAATTTTAATAA
*
27979186 CTTTTTTAAATTTTAATAA
1 TTTTTTTAAATTTTAATAA
27979205 TTTTT
1 TTTTT
27979210 ATTGATTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 18 0.58
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTTAAATTTTAATAA
Found at i:27984015 original size:27 final size:27
Alignment explanation
Indices: 27983985--27984162 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27983975 ATATTGAGTC
* * * *
27983985 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27984012 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27984039 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27984067 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27984094 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27984121 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27984148 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27984163 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:27984124 original size:82 final size:81
Alignment explanation
Indices: 27984006--27984161 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27983996 TGCTATATAA
* *
27984006 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27984071 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27984088 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27984152 CACTTAGTGC
65 CACTTAGTGC
27984162 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:27996408 original size:5 final size:6
Alignment explanation
Indices: 27996394--27996418 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27996384 TCTCTTCGTT
27996394 CCCCTC CCCCTC CCCCTC CCCCTC C
1 CCCCTC CCCCTC CCCCTC CCCCTC C
27996419 TCTTCCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCCTC
Found at i:28009429 original size:132 final size:132
Alignment explanation
Indices: 28009191--28009442 Score: 407
Period size: 132 Copynumber: 1.9 Consensus size: 132
28009181 TTGCTTGAGC
* * *
28009191 TTGCAGAGATACAAGTGATTGGTTAGGAGCATGTTAATAGGATTTTGTGAATAAATTATAATTTT
1 TTGCAGAAATACAAGTAATTGGTTAGGAGCATGTTAATAGGATTTTGTGAATAAATTATAAATTT
* * *
28009256 AGTTTGATAATAATTTATTCTAAATTTCTAGTTTTGGACTACTTAGTTCAATTTAGTTTGATAAT
66 AGTTTGATAATAAATTATTCTAAATTTCTAATTTTAGACTACTTAGTTCAATTTAGTTTGATAAT
28009321 AA
131 AA
28009323 TTGCAGAAATACAAGTAATTGGGTT-GGAGCATGTTAATAGGATTTTGTGAATAAATTATAAATT
1 TTGCAGAAATACAAGTAATT-GGTTAGGAGCATGTTAATAGGATTTTGTGAATAAATTATAAATT
* * *
28009387 TAGTTTGATAATAAATTATTTTAAATTTTTAATTTTATACTACTTAGTTCAATTTA
65 TAGTTTGATAATAAATTATTCTAAATTTCTAATTTTAGACTACTTAGTTCAATTTA
28009443 TTACATTGTA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
132 106 0.96
133 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.44
Consensus pattern (132 bp):
TTGCAGAAATACAAGTAATTGGTTAGGAGCATGTTAATAGGATTTTGTGAATAAATTATAAATTT
AGTTTGATAATAAATTATTCTAAATTTCTAATTTTAGACTACTTAGTTCAATTTAGTTTGATAAT
AA
Found at i:28013666 original size:17 final size:17
Alignment explanation
Indices: 28013646--28013682 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28013636 TTAATTTTTA
28013646 TTTTAGTTTAAT-TTAAT
1 TTTTA-TTTAATATTAAT
28013663 TTTTATTTAATATTAAT
1 TTTTATTTAATATTAAT
28013680 TTT
1 TTT
28013683 AAATGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATTTAATATTAAT
Found at i:28013670 original size:11 final size:11
Alignment explanation
Indices: 28013634--28013673 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
28013624 AGAGGGAGAG
28013634 ATTTAATTTTT
1 ATTTAATTTTT
* * *
28013645 ATTTTAGTTTA
1 ATTTAATTTTT
28013656 ATTTAATTTTT
1 ATTTAATTTTT
28013667 ATTTAAT
1 ATTTAAT
28013674 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:28013678 original size:22 final size:22
Alignment explanation
Indices: 28013634--28013681 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28013624 AGAGGGAGAG
*
28013634 ATTTAATTTTTATTTTAGTTTA
1 ATTTAATTTTTATTTTAATTTA
28013656 ATTTAATTTTTA-TTTAATATTA
1 ATTTAATTTTTATTTTAAT-TTA
28013678 ATTT
1 ATTT
28013682 TAAATGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTAATTTTTATTTTAATTTA
Found at i:28013941 original size:20 final size:20
Alignment explanation
Indices: 28013912--28013953 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28013902 TATATTTTTA
*
28013912 AAATTTAAAAAATAAATATC
1 AAATTAAAAAAATAAATATC
* *
28013932 AAATTAAAAATATATATATC
1 AAATTAAAAAAATAAATATC
28013952 AA
1 AA
28013954 TGATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAAAAAAATAAATATC
Found at i:28015694 original size:14 final size:14
Alignment explanation
Indices: 28015677--28015703 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28015667 GTTAATACAT
28015677 TATAAAAAATAAAA
1 TATAAAAAATAAAA
28015691 TATAAAAAATAAA
1 TATAAAAAATAAA
28015704 TCTCAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TATAAAAAATAAAA
Found at i:28019724 original size:25 final size:26
Alignment explanation
Indices: 28019696--28019750 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
28019686 TGAGAAGTTT
**
28019696 TGTCTTGC-AATGACTTCTTGTTTGA
1 TGTCTTGCAAATGACTTAATGTTTGA
28019721 TGTCTTGCAAAATGACTTAATGTTTGA
1 TGTCTTGC-AAATGACTTAATGTTTGA
28019748 TGT
1 TGT
28019751 TATAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 8 0.31
27 18 0.69
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (26 bp):
TGTCTTGCAAATGACTTAATGTTTGA
Found at i:28022925 original size:17 final size:17
Alignment explanation
Indices: 28022903--28022936 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28022893 ATCCACTAAT
*
28022903 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
28022920 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
28022937 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:28027564 original size:17 final size:17
Alignment explanation
Indices: 28027542--28027575 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28027532 ATCCACTAAT
*
28027542 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
28027559 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
28027576 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:28032203 original size:17 final size:17
Alignment explanation
Indices: 28032181--28032214 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28032171 ATCCACTAAT
*
28032181 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
28032198 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
28032215 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:28037833 original size:13 final size:14
Alignment explanation
Indices: 28037809--28037837 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28037799 TAAAAATATA
28037809 ATATTAAATAATTT
1 ATATTAAATAATTT
28037823 ATATT-AATAATTT
1 ATATTAAATAATTT
28037836 AT
1 AT
28037838 TATGTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTAAATAATTT
Found at i:28037916 original size:21 final size:21
Alignment explanation
Indices: 28037892--28037932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28037882 TTCAACATTA
* *
28037892 TAATATTTAATTTTAGTATTC
1 TAATATATAATTTTAATATTC
*
28037913 TAATATATATTTTTAATATT
1 TAATATATAATTTTAATATT
28037933 TTTAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATATATAATTTTAATATTC
Found at i:28038326 original size:39 final size:39
Alignment explanation
Indices: 28038282--28038360 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
28038272 ATATCCAATA
*
28038282 AATAAATATGAATTTTAAATCAAAATAAATAACAACTAT
1 AATAAAAATGAATTTTAAATCAAAATAAATAACAACTAT
*
28038321 AATAAAAATGAATTTTAAATCAAAATAAATAATAACTAT
1 AATAAAAATGAATTTTAAATCAAAATAAATAACAACTAT
28038360 A
1 A
28038361 CTTAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (39 bp):
AATAAAAATGAATTTTAAATCAAAATAAATAACAACTAT
Found at i:28039894 original size:34 final size:34
Alignment explanation
Indices: 28039856--28039928 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
28039846 GCAATATGCC
28039856 ATGCTCAAAACAAATT-AATACAGTAGC-AATCAAT
1 ATGCTCAAAAC-AATTCAATACAGTAGCAAAT-AAT
* ** *
28039890 ATGCTTATGACAGTTCAATACAGTAGCAAATAAT
1 ATGCTCAAAACAATTCAATACAGTAGCAAATAAT
28039924 ATGCT
1 ATGCT
28039929 TATAACAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 27 0.82
35 3 0.09
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.27
Consensus pattern (34 bp):
ATGCTCAAAACAATTCAATACAGTAGCAAATAAT
Found at i:28039953 original size:34 final size:35
Alignment explanation
Indices: 28039872--28039941 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 35
28039862 AAAACAAATT
* *
28039872 AATACAGTAGC-AATCAATATGCTTATGACAGTTC
1 AATACAGTAGCAAATCAATATGCTTATAACAGATC
28039906 AATACAGTAGCAAAT-AATATGCTTATAACAGATC
1 AATACAGTAGCAAATCAATATGCTTATAACAGATC
28039940 AA
1 AA
28039942 CTTAGTAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 30 0.91
35 3 0.09
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (35 bp):
AATACAGTAGCAAATCAATATGCTTATAACAGATC
Found at i:28043705 original size:28 final size:29
Alignment explanation
Indices: 28043622--28043732 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
28043612 AGAAGAGCGG
* * *
28043622 CAAAACTGTAAAATCTGGAAAACTAGTGG
1 CAAAACTATAAAATCTGGAAAACCAGTGA
** * *
28043651 CAAATTTGTAAAATTTGGAAAACCAGTGA
1 CAAAACTATAAAATCTGGAAAACCAGTGA
* *
28043680 CAGAACTA-AAAATCTGGAATAA-CAGTGG
1 CAAAACTATAAAATCTGGAA-AACCAGTGA
28043708 CAAAACTATAAAATCTGGAAAACCA
1 CAAAACTATAAAATCTGGAAAACCA
28043733 ACGGCCCAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
28 24 0.36
29 43 0.64
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (29 bp):
CAAAACTATAAAATCTGGAAAACCAGTGA
Found at i:28044387 original size:16 final size:16
Alignment explanation
Indices: 28044375--28044408 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28044365 TCATATTCTT
28044375 TTTCTACCATATTTAA
1 TTTCTACCATATTTAA
28044391 TTTCTACCATATTTAA
1 TTTCTACCATATTTAA
28044407 TT
1 TT
28044409 CTTACACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTCTACCATATTTAA
Found at i:28047682 original size:28 final size:28
Alignment explanation
Indices: 28047629--28047684 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28047619 TTTTTAATTT
*
28047629 TTTATAAATTTGTAAAAAATTATTAAAA
1 TTTATAAATTTGTAAAAAAATATTAAAA
28047657 TTTATAAAATTT-TAAATAAAAT-TTAAAA
1 TTTAT-AAATTTGTAAA-AAAATATTAAAA
28047685 ATTAAGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTATAAATTTGTAAAAAAATATTAAAA
Found at i:28056010 original size:18 final size:17
Alignment explanation
Indices: 28055987--28056025 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
28055977 ATAAAACAAC
*
28055987 TAAAAACAAAAATAAAGA
1 TAAAAACAAAAAGAAA-A
*
28056005 TAAAAAGAAAAAGAAAA
1 TAAAAACAAAAAGAAAA
28056022 TAAA
1 TAAA
28056026 TAAAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (17 bp):
TAAAAACAAAAAGAAAA
Found at i:28057483 original size:27 final size:26
Alignment explanation
Indices: 28057426--28057483 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28057416 AAACAAGACT
** *
28057426 TAATACTAAAAAGAACCAATAATGAA
1 TAATACTAAAAAGAAAAAATAATCAA
* *
28057452 CAATACTAAAAATAATAAAATAATCAA
1 TAATACTAAAAAGAA-AAAATAATCAA
28057479 TAATA
1 TAATA
28057484 GGAATTGTAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.22
Consensus pattern (26 bp):
TAATACTAAAAAGAAAAAATAATCAA
Found at i:28057522 original size:9 final size:9
Alignment explanation
Indices: 28057508--28057568 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
28057498 AATAATGATA
28057508 AAAAATAAT
1 AAAAATAAT
28057517 AAAAATTATCAT
1 AAAAA-TA--AT
* *
28057529 AACAAGAAT
1 AAAAATAAT
*
28057538 AAACATAAT
1 AAAAATAAT
28057547 AATAAA-AAT
1 AA-AAATAAT
28057556 AAAAATAAT
1 AAAAATAAT
28057565 AAAA
1 AAAA
28057569 CTAGTAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
8 3 0.07
9 27 0.66
10 4 0.10
11 1 0.02
12 6 0.15
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:28059327 original size:30 final size:30
Alignment explanation
Indices: 28059263--28059331 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
28059253 AGAACTTATC
*
28059263 AAAATCAAACAAACAAAAAATTAAAATGTG
1 AAAATCAAACAAACAAAAAATTAAAATATG
28059293 AAAATCAAACTAAA-ACAAAAA-TATAAATAT-
1 AAAATCAAAC-AAACA-AAAAATTA-AAATATG
28059323 AAAATCAAA
1 AAAATCAAA
28059332 ATGACTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (30 bp):
AAAATCAAACAAACAAAAAATTAAAATATG
Found at i:28061687 original size:39 final size:41
Alignment explanation
Indices: 28061633--28061716 Score: 127
Period size: 42 Copynumber: 2.1 Consensus size: 41
28061623 GGAAAAAGCG
28061633 ACCTACTTTGCCA-TTTTTTTCGAC-TTTTTTCCCTAATTT
1 ACCTACTTTGCCATTTTTTTTCGACTTTTTTTCCCTAATTT
**
28061672 ACCTACTTTGCCATTTTTTTTTTACTTTTTTTTCCCTAATTT
1 ACCTACTTTGCCATTTTTTTTCGAC-TTTTTTTCCCTAATTT
28061714 ACC
1 ACC
28061717 CTATCTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 13 0.32
40 9 0.22
42 18 0.45
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (41 bp):
ACCTACTTTGCCATTTTTTTTCGACTTTTTTTCCCTAATTT
Found at i:28061737 original size:4 final size:4
Alignment explanation
Indices: 28061728--28061780 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
28061718 TATCTTTTTC
*
28061728 TCTA TCTA TCTA TTTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
28061776 TCTA T
1 TCTA T
28061781 AACTAGTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (4 bp):
TCTA
Found at i:28061738 original size:16 final size:16
Alignment explanation
Indices: 28061717--28061780 Score: 92
Period size: 16 Copynumber: 4.0 Consensus size: 16
28061707 CTAATTTACC
* *
28061717 CTATCTTTTTCTCTAT
1 CTATCTATTTATCTAT
28061733 CTATCTATTTATCTAT
1 CTATCTATTTATCTAT
*
28061749 CTATCTATCTATCTAT
1 CTATCTATTTATCTAT
*
28061765 CTATCTATCTATCTAT
1 CTATCTATTTATCTAT
28061781 AACTAGTTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.22, C:0.23, G:0.00, T:0.55
Consensus pattern (16 bp):
CTATCTATTTATCTAT
Found at i:28061856 original size:27 final size:28
Alignment explanation
Indices: 28061821--28061876 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
28061811 ATTTTAGGTA
* *
28061821 ATATTAAAAATCAATAGGG-TATTTTAG
1 ATATAAAAAATCAATAGGGATAATTTAG
* *
28061848 ATATAAAAAATTACTAGGGATAATTTAG
1 ATATAAAAAATCAATAGGGATAATTTAG
28061876 A
1 A
28061877 CACTAAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.34
Consensus pattern (28 bp):
ATATAAAAAATCAATAGGGATAATTTAG
Found at i:28063265 original size:3 final size:3
Alignment explanation
Indices: 28063254--28063283 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
28063244 TACAAAAAAA
28063254 AAG AGAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AA
28063284 ATTTCAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28065523 original size:18 final size:18
Alignment explanation
Indices: 28065489--28065523 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28065479 AAAAATTCAA
*
28065489 ACCAAACAGTCCAAAAAG
1 ACCAAACAGTCAAAAAAG
*
28065507 ACCAAAGAGTCAAAAAA
1 ACCAAACAGTCAAAAAA
28065524 TCACAAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.23, G:0.11, T:0.06
Consensus pattern (18 bp):
ACCAAACAGTCAAAAAAG
Found at i:28070252 original size:13 final size:13
Alignment explanation
Indices: 28070236--28070261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28070226 ATATGTTTCA
28070236 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28070249 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28070262 ATGGATGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:28072570 original size:13 final size:13
Alignment explanation
Indices: 28072554--28072579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28072544 ATATGTTTCA
28072554 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28072567 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28072580 ATGGATGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:28074543 original size:13 final size:13
Alignment explanation
Indices: 28074527--28074552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28074517 ATATGTTTCA
28074527 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28074540 TGATTGTTTTGGT
1 TGATTGTTTTGGT
28074553 ATGGATGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:28083802 original size:22 final size:22
Alignment explanation
Indices: 28083776--28083830 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28083766 TACAATAATA
*
28083776 AAACCCTAATTTAATTAACCAT
1 AAACCCTAATTTAATAAACCAT
* * *
28083798 AAACCATACTTTAATAAACCTT
1 AAACCCTAATTTAATAAACCAT
28083820 AAACCCTAATT
1 AAACCCTAATT
28083831 AAACAATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (22 bp):
AAACCCTAATTTAATAAACCAT
Found at i:28085385 original size:21 final size:21
Alignment explanation
Indices: 28085359--28085401 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28085349 GGTTCGCTGT
*
28085359 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
28085380 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
28085401 A
1 A
28085402 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:28085401 original size:16 final size:16
Alignment explanation
Indices: 28085382--28085414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28085372 TGTATTGGAT
*
28085382 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
28085398 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
28085414 T
1 T
28085415 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:28085459 original size:45 final size:44
Alignment explanation
Indices: 28085393--28085487 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
28085383 GGATTAGAGG
* *
28085393 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
28085438 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
28085482 TGTAAT
1 TGTAAT
28085488 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:28085670 original size:18 final size:17
Alignment explanation
Indices: 28085649--28085683 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28085639 TTATTATTTA
*
28085649 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28085667 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28085684 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28085677 original size:28 final size:27
Alignment explanation
Indices: 28085607--28085679 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
28085597 TTTATTATCA
*
28085607 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
28085635 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
28085662 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
28085680 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:28085796 original size:144 final size:147
Alignment explanation
Indices: 28085568--28085839 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
28085558 ATGATTATTG
28085568 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
28085633 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
28085698 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
28085717 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
28085779 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
28085840 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:28085814 original size:18 final size:17
Alignment explanation
Indices: 28085793--28085827 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28085783 TTATTATTAA
*
28085793 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28085811 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28085828 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28085890 original size:17 final size:16
Alignment explanation
Indices: 28085868--28085914 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
28085858 ACTCAAATCA
28085868 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
28085885 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
28085899 TAAATATATGATTTAA
1 T-AATATATGATTTAA
28085915 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:28085904 original size:144 final size:143
Alignment explanation
Indices: 28085610--28085883 Score: 352
Period size: 144 Copynumber: 1.9 Consensus size: 143
28085600 ATTATCAAAA
*
28085610 ATAAATAATTTAATCATATTTAAACATAATTATTATTTAATATATTTTAATTAAAATATATAATT
1 ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATT
* * * * ** * ** * *
28085675 TAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATAA
66 TAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATCATAATATATAAATTATAATAA
28085740 GATTAATATCAAT
131 GATTAATATCAAT
28085753 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
1 -ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
* ** *
28085818 TTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATAT-GATTAT
65 TTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-AAATCATAATATATAAATTAT
28085882 AA
126 AA
28085884 CTAATATGAT
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
144 86 0.78
146 4 0.04
147 10 0.09
148 10 0.09
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (143 bp):
ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATT
TAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATCATAATATATAAATTATAATAA
GATTAATATCAAT
Found at i:28085915 original size:17 final size:17
Alignment explanation
Indices: 28085887--28085920 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28085877 ATTATAACTA
*
28085887 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
28085904 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
28085921 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:28086063 original size:93 final size:92
Alignment explanation
Indices: 28085953--28086147 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
28085943 GATTATAGTT
* * *
28085953 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
28086016 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
28086046 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
28086111 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
28086138 TATGAATTTA
1 TATGAATTTA
28086148 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:28087562 original size:11 final size:11
Alignment explanation
Indices: 28087548--28087574 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28087538 AAAAATCAAT
28087548 ACAAAAGTTTC
1 ACAAAAGTTTC
28087559 ACAAAAGTTTC
1 ACAAAAGTTTC
28087570 ACAAA
1 ACAAA
28087575 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:28094893 original size:19 final size:19
Alignment explanation
Indices: 28094848--28094895 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
28094838 AACATTGAAA
28094848 TTTGAA-TTTTTTTATATT
1 TTTGAATTTTTTTTATATT
*
28094866 TTTAAAATTTATTTTTATA-T
1 TTT-GAATTT-TTTTTATATT
28094886 TTTGAATTTT
1 TTTGAATTTT
28094896 AAAGAGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 4 0.16
19 7 0.28
20 6 0.24
21 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTGAATTTTTTTTATATT
Found at i:28094894 original size:28 final size:30
Alignment explanation
Indices: 28094865--28094918 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
28094855 TTTTTTATAT
28094865 TTTTAAA-A-TTTATTTTT-ATATTTTGAA
1 TTTTAAAGAGTTTATTTTTCATATTTTGAA
*
28094892 TTTTAAAGAGTTTGTTTTTCATATTTT
1 TTTTAAAGAGTTTATTTTTCATATTTT
28094919 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 1 0.04
29 8 0.35
30 7 0.30
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTAAAGAGTTTATTTTTCATATTTTGAA
Found at i:28097043 original size:23 final size:23
Alignment explanation
Indices: 28097017--28097067 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
28097007 ATAATATAAA
* *
28097017 AAAATAAGAAAAT-AGTATATTTT
1 AAAA-AAGAAAATCAGAAAATTTT
*
28097040 AAAAAATAAAATCAGAAAATTTT
1 AAAAAAGAAAATCAGAAAATTTT
28097063 AAAAA
1 AAAAA
28097068 TACAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (23 bp):
AAAAAAGAAAATCAGAAAATTTT
Found at i:28097598 original size:152 final size:151
Alignment explanation
Indices: 28097000--28098005 Score: 1469
Period size: 151 Copynumber: 6.6 Consensus size: 151
28096990 GAGTTTTTTT
* *
28097000 TACTAAAATAATAT---AAA-AAAATAAGAAAATAGTATATTTTAAAAAATAAAATCAGAAAATT
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATT
* * * *
28097061 TTAAAAATACAAACAAAGGCCCAAAAT-ATGTTTATTTACTAAATTAATATAAAAAATACGAAAA
66 TTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAAAA
*
28097125 CAATACATTTGAAACATTATG
131 TAATACATTTGAAACATTATG
28097146 TACTAAAATAATATAAAAAATAAAATACG-AAATAGTATATTTTAAAAAATAAAATCCGAAAATT
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATT
* *
28097210 TTAAAAGTACAAACAAAGGGCCAAAATCACGGTTATTTACTAAA--AATATATAAAACCCCACGA
66 TTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATA-AAAA--ACACGA
28097273 AAATAATACATTTGAAACA-T-TG
128 AAATAATACATTTGAAACATTATG
*
28097295 TACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAGTAAAATCC-AAAAT
1 TACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAA-
* * *
28097359 TTTTAAAAATACAACCAAATGGCCAAAATCACGTTTATTTACTAAATTAATATAAAAAACACGAA
64 TTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAA
*
28097424 AATAATACATTAGAAACATTATG
129 AATAATACATTTGAAACATTATG
* *
28097447 TACTAAAGTAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATT
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATT
* *
28097512 TTAAAGATACAAACAAAGGGCTAAAATCACGGTTATTTACTAAATTAATATAAAGAAACACGAAA
66 TTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAA-AAACACGAAA
28097577 ATAATACATTTGAAACATTATG
130 ATAATACATTTGAAACATTATG
* * * *
28097599 TACAAAAATAGTATAAAAAATAAAATATGAAAATAGTATACTTTAAAAAATAAATAAAATCC-AG
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATA-TTT--TAAA-AAATAAAATCCGA-
*
28097663 AAATTTTAAAAATACAAACAAAGGGCTAAAATCACGGTTATTTACTAAATTAATATAAAAAAACA
61 AAATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATAT-AAAAAACA
* * *
28097728 CGAAAATAATACATTTTAAAAATTATA
125 CGAAAATAATACATTTGAAACATTATG
* *
28097755 TACTAAAATAGTATTAAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATCCGAAAAT
1 TACTAAAATAATA-TAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAAT
*
28097820 TTTAAAAATACAAACAAATGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAAACACGAA
65 TTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATAT-AAAAAACACGAA
*
28097885 AATAATACATTTGAAACATTATT
129 AATAATACATTTGAAACATTATG
* * * * *
28097908 TACTAAATTAATATAAAAAATAAAATATGAAAACAGTATATTTTAAAAAATAAAAATCCAAAAAA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAAT-AAAATCCGAAAAT
*
28097973 TTTAAAAATACAAACAAAAGGCCAAAATCACGG
65 TTTAAAAATACAAACAAAGGGCCAAAATCACGG
28098006 AATAAAAAAA
Statistics
Matches: 786, Mismatches: 48, Indels: 45
0.89 0.05 0.05
Matches are distributed among these distances:
146 14 0.02
148 6 0.01
149 82 0.10
150 64 0.08
151 185 0.24
152 127 0.16
153 161 0.20
154 4 0.01
155 4 0.01
156 109 0.14
157 30 0.04
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (151 bp):
TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATT
TTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAAAA
TAATACATTTGAAACATTATG
Found at i:28097834 original size:309 final size:302
Alignment explanation
Indices: 28097000--28098005 Score: 1469
Period size: 309 Copynumber: 3.3 Consensus size: 302
28096990 GAGTTTTTTT
* *
28097000 TACTAAAATAATAT---AAA-AAAATAAGAAAATAGTATATTTTAAAAAATAAAAT-CAGAAAAT
1 TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTAAAAAAATAAAATCCAG-AAAT
* * * *
28097060 TTTAAAAATACAAACAAAGGCCCAAAAT-ATGTTTATTTACTAAATTAATATAAAAAATACGAAA
65 TTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAAA
*
28097124 ACAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACG-AAATAGTATATTT
130 ATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTT
*
28097188 TAAAAAATAAAATCCGAAAATTTTAAAAGTACAAACAAAGGGCCAAAATCACGGTTATTTACTAA
195 TAAAAAATAAAATCCGAAAATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAA
*
28097253 A--AATATATAAAACCCCACGAAAATAATACATTTGAAACA-T-TG
260 ATTAATATA-AAAA--ACACGAAAATAATACATTTGAAACATTATG
* * *
28097295 TACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAGTAAAATCCA-AAAT
1 TACTAAAATAATAT-AAAAAATAAAATATGAAAATAGTATATTTAAAAAAATAAAATCCAGAAA-
* * *
28097359 TTTTAAAAATACAACCAAATGGCCAAAATCACGTTTATTTACTAAATTAATATAAAAAACACGAA
64 TTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAA
* *
28097424 AATAATACATTAGAAACATTATGTACTAAAGTAATATAAAAAATAAAATACGAAAATAGTATATT
129 AATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATT
* * *
28097489 TTAAAAAATAAAATCTGAAAATTTTAAAGATACAAACAAAGGGCTAAAATCACGGTTATTTACTA
194 TTAAAAAATAAAATCCGAAAATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTA
28097554 AATTAATATAAAGAAACACGAAAATAATACATTTGAAACATTATG
259 AATTAATATAAA-AAACACGAAAATAATACATTTGAAACATTATG
* *
28097599 TACAAAAATAGTATAAAAAATAAAATATGAAAATAGTATACTTTAAAAAATAAATAAAATCCAGA
1 TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATA-TTT--AAAA-AAATAAAATCCAGA
*
28097664 AATTTTAAAAATACAAACAAAGGGCTAAAATCACGGTTATTTACTAAATTAATATAAAAAAACAC
62 AATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATAT-AAAAAACAC
* * * * *
28097729 GAAAATAATACATTTTAAAAATTATATACTAAAATAGTATTAAAAAATAAAATATGAAAATAGTA
126 GAAAATAATACATTTGAAACATTATGTACTAAAATAATA-TAAAAAATAAAATACGAAAATAGTA
*
28097794 TATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAACAAATGGCCAAAATCACGGTTATTT
190 TATTTTAAAAAATAAAATCCGAAAATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTT
*
28097859 ACTAAATTAATATAAAAAAACACGAAAATAATACATTTGAAACATTATT
255 ACTAAATTAATAT-AAAAAACACGAAAATAATACATTTGAAACATTATG
* * * * *
28097908 TACTAAATTAATATAAAAAATAAAATATGAAAACAGTATATTTTAAAAAATAAAAATCCAAAAAA
1 TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTAAAAAAAT-AAAATCCAGAAAT
*
28097973 TTTAAAAATACAAACAAAAGGCCAAAATCACGG
65 TTTAAAAATACAAACAAAGGGCCAAAATCACGG
28098006 AATAAAAAAA
Statistics
Matches: 643, Mismatches: 45, Indels: 35
0.89 0.06 0.05
Matches are distributed among these distances:
295 14 0.02
299 6 0.01
300 59 0.09
301 84 0.13
302 99 0.15
303 28 0.04
304 25 0.04
305 4 0.01
306 48 0.07
307 60 0.09
308 48 0.07
309 165 0.26
310 3 0.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (302 bp):
TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTAAAAAAATAAAATCCAGAAATT
TTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAATTAATATAAAAAACACGAAAA
TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTT
AAAAAATAAAATCCGAAAATTTTAAAAATACAAACAAAGGGCCAAAATCACGGTTATTTACTAAA
TTAATATAAAAAACACGAAAATAATACATTTGAAACATTATG
Found at i:28100190 original size:72 final size:72
Alignment explanation
Indices: 28100103--28100242 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 72
28100093 GAGCGATCAT
* * *
28100103 ATTCACATTCGGCTGATACTTCTTATCATCCGGATTTACAGAGCAATGAAAATTTCTCGGGCTCG
1 ATTCACATTCAGCTGATACTTATTATCATCCAGATTTACAGAGCAATGAAAATTTCTCGGGCTCG
28100168 TCATCGC
66 TCATCGC
** * * * **
28100175 ATTCACATTCAGCTGATACTTATTATCATTTAGATTTGCCGGGCAATGACTATTTCTCGGGCTCG
1 ATTCACATTCAGCTGATACTTATTATCATCCAGATTTACAGAGCAATGAAAATTTCTCGGGCTCG
28100240 TCA
66 TCA
28100243 GGGGGCGGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (72 bp):
ATTCACATTCAGCTGATACTTATTATCATCCAGATTTACAGAGCAATGAAAATTTCTCGGGCTCG
TCATCGC
Found at i:28100813 original size:63 final size:63
Alignment explanation
Indices: 28100738--28100893 Score: 303
Period size: 63 Copynumber: 2.5 Consensus size: 63
28100728 AAATTTAGTC
*
28100738 TTTTAATATAAATTAAATACATTACAACATTAATCTAATTGGAACAAACTTTGCAATATAATT
1 TTTTTATATAAATTAAATACATTACAACATTAATCTAATTGGAACAAACTTTGCAATATAATT
28100801 TTTTTATATAAATTAAATACATTACAACATTAATCTAATTGGAACAAACTTTGCAATATAATT
1 TTTTTATATAAATTAAATACATTACAACATTAATCTAATTGGAACAAACTTTGCAATATAATT
28100864 TTTTTATATAAATTAAATACATTACAACAT
1 TTTTTATATAAATTAAATACATTACAACAT
28100894 AAGCTCAATT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 92 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (63 bp):
TTTTTATATAAATTAAATACATTACAACATTAATCTAATTGGAACAAACTTTGCAATATAATT
Found at i:28104159 original size:19 final size:20
Alignment explanation
Indices: 28104118--28104169 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
28104108 TTTTAATTTT
28104118 TTTTCAA-TTTTTTTTCAGA
1 TTTTCAATTTTTTTTTCAGA
28104137 --TTCAATTTTTTTTTCA-A
1 TTTTCAATTTTTTTTTCAGA
*
28104154 TTTTCAGTTTTTTTTT
1 TTTTCAATTTTTTTTT
28104170 ACTGTAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 10 0.34
19 13 0.45
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTCAATTTTTTTTTCAGA
Found at i:28104810 original size:10 final size:9
Alignment explanation
Indices: 28104797--28104908 Score: 54
Period size: 9 Copynumber: 12.4 Consensus size: 9
28104787 GAATTTAAAC
28104797 TTTTATATAT
1 TTTTATA-AT
*
28104807 TTTTATACT
1 TTTTATAAT
28104816 TTTTATAAT
1 TTTTATAAT
* *
28104825 TTTTACACT
1 TTTTATAAT
*
28104834 TTTCCAT-A-
1 TTT-TATAAT
28104842 TTTT-TAAT
1 TTTTATAAT
*
28104850 TTTTAATAAA
1 TTTT-ATAAT
*
28104860 TTATAT-AT
1 TTTTATAAT
* *
28104868 ATTTGTAAT
1 TTTTATAAT
*
28104877 TTTTATGAT
1 TTTTATAAT
28104886 TTTCTATCAA-
1 TTT-TAT-AAT
*
28104896 TTCTATAAT
1 TTTTATAAT
28104905 TTTT
1 TTTT
28104909 TTAACCTTTT
Statistics
Matches: 73, Mismatches: 20, Indels: 19
0.65 0.18 0.17
Matches are distributed among these distances:
6 1 0.01
7 1 0.01
8 13 0.18
9 38 0.52
10 19 0.26
11 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:28104816 original size:18 final size:17
Alignment explanation
Indices: 28104790--28104848 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
28104780 TTAAAAAGAA
28104790 TTTAAACTTTTATATATT
1 TTTAAACTTTT-TATATT
*
28104808 TTTATACTTTTTATAATT
1 TTTAAACTTTTTAT-ATT
* *
28104826 TTTACACTTTTCCATATT
1 TTTAAACTTTT-TATATT
28104844 TTTAA
1 TTTAA
28104849 TTTTTAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.09
18 30 0.86
19 2 0.06
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAACTTTTTATATT
Found at i:28104818 original size:9 final size:9
Alignment explanation
Indices: 28104790--28104836 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
28104780 TTAAAAAGAA
*
28104790 TTTAAACTT
1 TTTATACTT
28104799 TTATATA-TT
1 TT-TATACTT
28104808 TTTATACTT
1 TTTATACTT
*
28104817 TTTATAATT
1 TTTATACTT
*
28104826 TTTACACTT
1 TTTATACTT
28104835 TT
1 TT
28104837 CCATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 4 0.12
9 25 0.78
10 3 0.09
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTATACTT
Found at i:28108397 original size:19 final size:20
Alignment explanation
Indices: 28108373--28108410 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28108363 GGCTCCCTTG
28108373 AATAAGT-TGTAAAATAGTT
1 AATAAGTATGTAAAATAGTT
*
28108392 AATAAGTATGTGAAATAGT
1 AATAAGTATGTAAAATAGT
28108411 GATAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (20 bp):
AATAAGTATGTAAAATAGTT
Found at i:28108530 original size:30 final size:30
Alignment explanation
Indices: 28108496--28108553 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28108486 TTTTCGGGCA
* *
28108496 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
*
28108526 TAGGGGCAAAATGGTTATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
28108554 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:28108964 original size:47 final size:46
Alignment explanation
Indices: 28108896--28109197 Score: 256
Period size: 47 Copynumber: 6.5 Consensus size: 46
28108886 TTTGTGCGCC
* * *
28108896 AGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAGAGCT
* *** *
28108942 AGTGTAAGACCATGTCTGGGACATGCATCATCCATGCTATGATAGCT
1 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCACAATATGAGAGCT
* * * *
28108989 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCACAGAGATGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACA-ATATGAGAGCT
* ** *
28109037 AGTGTAAGACATGTCTGAGACATGCATCAGCCTTAATA-GAGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAG--AGCT
* * * *
28109084 AGTGTAAGACGTGTCTGGGACATGCATCGGCTA-AGAGT-T--GTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACA-A-TATGAGAGCT
* *
28109128 AGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTATATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGC-CAC-AATATGAGAGCT
*
28109176 AGTGTAAGACCATGTCTAGGAC
1 AGTGTAAGA-CATGTCTGGGAC
28109198 TTGGCATGGT
Statistics
Matches: 204, Mismatches: 36, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
44 31 0.15
45 4 0.02
46 20 0.10
47 104 0.51
48 34 0.17
49 11 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAGAGCT
Found at i:28109059 original size:94 final size:91
Alignment explanation
Indices: 28108896--28109197 Score: 315
Period size: 94 Copynumber: 3.2 Consensus size: 91
28108886 TTTGTGCGCC
* ** *
28108896 AGTGTAAGACATGTCTGGGACATGCTTCGGCCACA-TTATGAGAGCTAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CACAGAGATGAGTGCTAGTGTAAGA-CATGTCTG
28108960 GGACATGCATCATCCATGCTATGATAGCT
64 GGACATGCATCA-CCATGCTATGATAGCT
*
28108989 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGAGTGCCAGTGTAAGACATGTCTG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGAGATGAGTGCTAGTGTAAGACATGTCTG
* * ** * *
28109054 AGACATGCATCAGCCTTAATAGAGATAGCC
64 GGACATGCATCA-CCATGCTA-TGATAGCT
* *
28109084 AGTGTAAGACGTGTCTGGGACATGCATCGGCTA-AGAG-T-TGTGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-ACAGAGATGAGTGCTAGTGTAAGACATGTCTGG
* * *
28109146 GACATGCATCAGCACGCGTATATGAGAGCT
65 GACATGCATCACCATGC---TATGATAGCT
*
28109176 AGTGTAAGACCATGTCTAGGAC
1 AGTGTAAGA-CATGTCTGGGAC
28109198 TTGGCATGGT
Statistics
Matches: 174, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
90 1 0.01
91 32 0.18
92 15 0.09
93 33 0.19
94 56 0.32
95 37 0.21
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (91 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGATGAGTGCTAGTGTAAGACATGTCTGGG
ACATGCATCACCATGCTATGATAGCT
Found at i:28116212 original size:27 final size:27
Alignment explanation
Indices: 28116173--28116226 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28116163 CCTTTAAATT
* *
28116173 TTGTAAAAATAAAAGCTTTCAAGTTTG
1 TTGTAAAAATAAAAACTCTCAAGTTTG
* *
28116200 TTGTGAAATTAAAAACTCTCAAGTTTG
1 TTGTAAAAATAAAAACTCTCAAGTTTG
28116227 CAAATATTTA
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:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (27 bp):
TTGTAAAAATAAAAACTCTCAAGTTTG
Found at i:28116468 original size:24 final size:24
Alignment explanation
Indices: 28116411--28116462 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
28116401 TATATATATG
28116411 TTAAAAATATTAATCCATATTAAA
1 TTAAAAATATTAATCCATATTAAA
28116435 TTAAAAATATTAATCCATATTAAA
1 TTAAAAATATTAATCCATATTAAA
28116459 TTAA
1 TTAA
28116463 TTATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAAATATTAATCCATATTAAA
Found at i:28120628 original size:48 final size:48
Alignment explanation
Indices: 28120572--28120742 Score: 236
Period size: 48 Copynumber: 3.6 Consensus size: 48
28120562 TGTGAGCCAA
*
28120572 TGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGAGAGCTAG
* * * * * * *
28120620 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGAGCCAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGAGAGCTAG
* *
28120668 TGTAAGACCATGTTTGGAACATGGCATCGGCTTTATTACGAGAGCTAG
1 TGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGAGAGCTAG
28120716 TGTAAGACCATGTTTAGG-ACATGGCAT
1 TGTAAGACCATGTTT-GGAACATGGCAT
28120743 GAGCATCTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 104 0.98
49 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGAGAGCTAG
Found at i:28120725 original size:96 final size:96
Alignment explanation
Indices: 28120561--28120742 Score: 310
Period size: 96 Copynumber: 1.9 Consensus size: 96
28120551 GTTAGGGTAC
* *
28120561 ATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAG
1 ATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCGGCATTATTACGAGAGCTAGTGTAAG
*
28120626 ACCATGTCTGGGACATGGCATCGGCCTCAAT
66 ACCATGTCTAGGACATGGCATCGGCCTCAAT
* *
28120657 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCTTTATTACGAGAGCTAGTGTAAG
1 ATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCGGCATTATTACGAGAGCTAGTGTAAG
*
28120722 ACCATGTTTAGGACATGGCAT
66 ACCATGTCTAGGACATGGCAT
28120743 GAGCATCTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (96 bp):
ATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCGGCATTATTACGAGAGCTAGTGTAAG
ACCATGTCTAGGACATGGCATCGGCCTCAAT
Found at i:28126284 original size:48 final size:48
Alignment explanation
Indices: 28126227--28126451 Score: 270
Period size: 48 Copynumber: 4.7 Consensus size: 48
28126217 TCATGTCAGT
* * * *
28126227 GCCGTTGCCATCTCCCAGACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAAC
** * *
28126275 GCCGATGCCATGTGTCAGACATGATCTTACACTGGCTCACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAAC
*
28126323 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAAC
* * * * * * * *
28126371 GACGACGCCATGTCTCAAACATGGTCTTACACTGGTTCTCATCTCGAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-AAC
* *
28126420 GTCGATGCCATGTCCTAGACATGGTCTTACAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACAC
28126452 GGGAGCTCAT
Statistics
Matches: 149, Mismatches: 27, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 120 0.81
49 29 0.19
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAAC
Found at i:28126343 original size:96 final size:97
Alignment explanation
Indices: 28126226--28126451 Score: 319
Period size: 96 Copynumber: 2.3 Consensus size: 97
28126216 CTCATGTCAG
* * * * * *
28126226 TGCCGTTGCCATCTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTGTC
1 TGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAACGACGACGCCATGTCTC
*
28126291 AGACATGATCTTACACTGGCTCACATATC-AA
66 AAACATGATCTTACACTGGCTCACATATCGAA
* *
28126322 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCACATATCAACGACGACGCCATGTCTC
1 TGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAACGACGACGCCATGTCTC
* * * *
28126387 AAACATGGTCTTACACTGGTTCTCATCTCGAA
66 AAACATGATCTTACACTGGCTCACATATCGAA
*
28126419 TGTCGATGCCATGTCCTAGACATGGTCTTACAC
1 TGCCGATGCCATGTCCTAGACATGGTCTTACAC
28126452 GGGAGCTCAT
Statistics
Matches: 115, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 81 0.70
97 34 0.30
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (97 bp):
TGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAACGACGACGCCATGTCTC
AAACATGATCTTACACTGGCTCACATATCGAA
Found at i:28126944 original size:10 final size:10
Alignment explanation
Indices: 28126931--28126969 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
28126921 GTTATTTTCG
28126931 TTTATCTTTA
1 TTTATCTTTA
28126941 TTTATCTTTA
1 TTTATCTTTA
28126951 TTTAT-TTGTA
1 TTTATCTT-TA
28126961 TTTATCTTT
1 TTTATCTTT
28126970 TAAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:28130689 original size:4 final size:4
Alignment explanation
Indices: 28130680--28130757 Score: 51
Period size: 4 Copynumber: 19.8 Consensus size: 4
28130670 TTATTTTATT
* *
28130680 TTTA TTTA TTTA TTTA -TTA TTT- TTTG TTT- TCTTT TTTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
28130725 CTTTA TTTTA TTT- TATTA TTTA -TTA CTTTA TTT
1 -TTTA -TTTA TTTA T-TTA TTTA TTTA -TTTA TTT
28130758 GGATATTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
3 14 0.23
4 36 0.58
5 12 0.19
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:28130749 original size:25 final size:25
Alignment explanation
Indices: 28130666--28130757 Score: 98
Period size: 26 Copynumber: 3.6 Consensus size: 25
28130656 AGGCAACCCA
*
28130666 ATTT-TTATTTTATTTTTATTTATTT
1 ATTTATTACTTTATTTTTATTTA-TT
* * * *
28130691 ATTTATTATTTTTTGTTTTCTTTTTT
1 ATTTATTACTTTAT-TTTTATTTATT
28130717 ATTTATTACTTTA-TTTTATTTTATT
1 ATTTATTACTTTATTTTTA-TTTATT
28130742 ATTTATTACTTTATTT
1 ATTTATTACTTTATTT
28130758 GGATATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.07
25 22 0.39
26 23 0.41
27 7 0.12
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (25 bp):
ATTTATTACTTTATTTTTATTTATT
Found at i:28131981 original size:96 final size:98
Alignment explanation
Indices: 28131811--28131999 Score: 292
Period size: 96 Copynumber: 1.9 Consensus size: 98
28131801 TTTTTAAGAA
* ** * *
28131811 TATGTTGGGCTGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGTGTCAAAATGTTCG
1 TATGTTAGGCTGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCA
*
28131876 ATATGTTCTTAAG-AAAAATAAA-AATTAGGAG
66 ATATATTCTTAAGTAAAAATAAATAATTAGGAG
* *
28131907 TATGTTAGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCA
1 TATGTTAGGCTGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCA
28131972 ATATATTCTTAAGTAAAAATAAATAATT
66 ATATATTCTTAAGTAAAAATAAATAATT
28132000 TAAATTAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 70 0.84
97 9 0.11
98 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (98 bp):
TATGTTAGGCTGAGTAACCAGGGTGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCA
ATATATTCTTAAGTAAAAATAAATAATTAGGAG
Found at i:28132046 original size:8 final size:9
Alignment explanation
Indices: 28132032--28132059 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28132022 TTAGAAAATT
28132032 AGAAAAAAG
1 AGAAAAAAG
28132041 AGAAAAAAG
1 AGAAAAAAG
28132050 AGAAAAAAG
1 AGAAAAAAG
28132059 A
1 A
28132060 CATATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:28132703 original size:10 final size:10
Alignment explanation
Indices: 28132690--28132737 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
28132680 TTATTTTCAC
28132690 TTATCTTTAT
1 TTATCTTTAT
*
28132700 TTATCTTTAA
1 TTATCTTTAT
28132710 TTATCTTTAT
1 TTATCTTTAT
*
28132720 TTAT-TCGTAT
1 TTATCT-TTAT
28132730 TTATCTTT
1 TTATCTTT
28132738 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 1 0.03
10 30 0.94
11 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATCTTTAT
Found at i:28132703 original size:20 final size:19
Alignment explanation
Indices: 28132678--28132724 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
28132668 TAAATTTAGG
*
28132678 ATTTATTTTCACTTATCTTT
1 ATTTATTTT-AATTATCTTT
28132698 ATTTATCTTTAATTATCTTT
1 ATTTAT-TTTAATTATCTTT
28132718 ATTTATT
1 ATTTATT
28132725 CGTATTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTATTTTAATTATCTTT
Found at i:28133489 original size:17 final size:18
Alignment explanation
Indices: 28133461--28133494 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28133451 TATTCTCCAT
28133461 TTTAATTTTCGCAATTTA
1 TTTAATTTTCGCAATTTA
28133479 TTTAA-TTTCGCAATTT
1 TTTAATTTTCGCAATTT
28133495 CAATTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCGCAATTTA
Found at i:28144513 original size:16 final size:18
Alignment explanation
Indices: 28144494--28144530 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
28144484 TCTTAGATTA
*
28144494 CCCCATTAAT-GAA-AAT
1 CCCCATGAATCGAATAAT
28144510 CCCCATGAATCGAATAAT
1 CCCCATGAATCGAATAAT
28144528 CCC
1 CCC
28144531 AAACAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.22
Consensus pattern (18 bp):
CCCCATGAATCGAATAAT
Found at i:28145035 original size:2 final size:2
Alignment explanation
Indices: 28145028--28145052 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28145018 CCCAAGACCT
28145028 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
28145053 CCCTAGAACA
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28148508 original size:58 final size:58
Alignment explanation
Indices: 28148418--28148537 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
28148408 GCAAATTTCC
28148418 CTAATCATATTTTAAACATTCAATTGAAACATAAAATAAGATAAGGGAAAAGTGAAAT
1 CTAATCATATTTTAAACATTCAATTGAAACATAAAATAAGATAAGGGAAAAGTGAAAT
28148476 CTAATCATATTTTAAACATTCAATTGAAACATAAAATAAGATAAGGGAAAAGTGAAAT
1 CTAATCATATTTTAAACATTCAATTGAAACATAAAATAAGATAAGGGAAAAGTGAAAT
28148534 CTAA
1 CTAA
28148538 GTCTGATGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.28
Consensus pattern (58 bp):
CTAATCATATTTTAAACATTCAATTGAAACATAAAATAAGATAAGGGAAAAGTGAAAT
Found at i:28168296 original size:36 final size:37
Alignment explanation
Indices: 28168234--28168340 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 37
28168224 ATTCAAAAAA
*
28168234 TAATATTATTTTAATAGTTTAATATT-ATATT-ATATT
1 TAATATTATCTTAATAGTTTAATATTAAT-TTAATATT
*
28168270 TAATATTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATATTATCTTAATAGT-TTAATATTAATTTAATATT
* *
28168307 AAAGTTATTATCTTAATA-TTAAAT-TTAATTTAAT
1 TAA--TATTATCTTAATAGTTTAATATTAATTTAAT
28168341 GATTATACAT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
36 23 0.38
37 22 0.37
38 2 0.03
39 13 0.22
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATATT
Found at i:28168303 original size:47 final size:50
Alignment explanation
Indices: 28168234--28168327 Score: 131
Period size: 47 Copynumber: 1.9 Consensus size: 50
28168224 ATTCAAAAAA
* * *
28168234 TAATATTATTTTAATAGTTTAATATTATA-TTA-TAT-TTAATATTATCT
1 TAATAGTATTTTAATAATTTAATATTAAAGTTATTATCTTAATATTATCT
*
28168281 TAATAGTATTTTATTAATTTAATATTAAAGTTATTATCTTAATATTA
1 TAATAGTATTTTAATAATTTAATATTAAAGTTATTATCTTAATATTA
28168328 AATTTAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 25 0.62
48 3 0.08
49 3 0.08
50 9 0.22
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (50 bp):
TAATAGTATTTTAATAATTTAATATTAAAGTTATTATCTTAATATTATCT
Found at i:28168308 original size:11 final size:11
Alignment explanation
Indices: 28168234--28168308 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
28168224 ATTCAAAAAA
*
28168234 TAATATTATTT
1 TAATATTAATT
28168245 TAATAGTTTAATAT
1 TAATA--TTAAT-T
28168259 T-ATATTATATT
1 TAATATTA-ATT
28168270 TAATATT-ATCT
1 TAATATTAAT-T
*
28168281 TAATAGT-ATT
1 TAATATTAATT
28168291 T--TATTAATT
1 TAATATTAATT
28168300 TAATATTAA
1 TAATATTAA
28168309 AGTTATTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 4 0.08
11 25 0.48
12 7 0.13
13 7 0.13
14 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (11 bp):
TAATATTAATT
Found at i:28168316 original size:20 final size:19
Alignment explanation
Indices: 28168291--28168345 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
28168281 TAATAGTATT
28168291 TTATTAATTTAATATTAAA
1 TTATTAATTTAATATTAAA
28168310 GTTATT-ATCTTAATATTAAA
1 -TTATTAAT-TTAATATTAAA
28168330 -T-TTAATTTAATGATTA
1 TTATTAATTTAAT-ATTA
28168346 TACATTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.22
18 7 0.22
19 2 0.06
20 16 0.50
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:28173610 original size:14 final size:15
Alignment explanation
Indices: 28173591--28173619 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28173581 CAAACAAACA
28173591 AAAAATC-AACAGTT
1 AAAAATCAAACAGTT
28173605 AAAAATCAAACAGTT
1 AAAAATCAAACAGTT
28173620 TAGAGAGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAAATCAAACAGTT
Found at i:28179923 original size:26 final size:25
Alignment explanation
Indices: 28179866--28179927 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
28179856 ACATATTTTC
*
28179866 TCAAAATTTTATCGAGGCAAAATCA
1 TCAAAATTTTAACGAGGCAAAATCA
* * *
28179891 TCAAAAATTTTAACAGGGGTAAAATTA
1 TC-AAAATTTTAAC-GAGGCAAAATCA
28179918 TCAAAATTTT
1 TCAAAATTTT
28179928 GTTGGGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 18 0.58
27 11 0.35
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTAACGAGGCAAAATCA
Found at i:28182894 original size:28 final size:28
Alignment explanation
Indices: 28182853--28182906 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28182843 GCAAAAGGGA
*
28182853 AAGTGAAAATACATAAAGTTAGACTTGT
1 AAGTGAAAACACATAAAGTTAGACTTGT
28182881 AAGTGAAAACACATAAAGTTAGACTT
1 AAGTGAAAACACATAAAGTTAGACTT
28182907 CTAGGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (28 bp):
AAGTGAAAACACATAAAGTTAGACTTGT
Found at i:28187899 original size:291 final size:291
Alignment explanation
Indices: 28187375--28187952 Score: 865
Period size: 291 Copynumber: 2.0 Consensus size: 291
28187365 GAATGATGCT
* * * *
28187375 ACATATTACAGAAGTCGTATACCCGACGCACCAACTTTCGGTTCCTTATCTATTTGAACTCATGC
1 ACATATTACAGAAGTCGTATACCCAACGCACCAACTTTCAGTTCCTTATCTATTTAAACTCAAGC
* * *
28187440 TTTTACTTGTATCAAAGTATATGAGTCACACATACATAGTCTATCATTTACTCAGGATTGAAGTA
66 TTTTACTTATATCAAAGTATACGAGTCACACATACATAGTCTATCATCTACTCAGGATTGAAGTA
* * *
28187505 TGTCACACTATGAACGTCACAAGTGAATAAATCCATAAGCGCATTCAGGATCTATTCTACTTGGG
131 TGTCACACTATGAACGTCACAAGTAAATAAATCCATAAGCACATTCAGGATATATTCTACTTGGG
* * * * *
28187570 TTTTGTTCGATGTACTGCCAGTCAAGTCAGTCACATCTATTTCTATCTTCTGGGAGTCATTCACT
196 TCTTGTTCGATGTACTACCAGTCAAGTCAGCCACATCTATGTCTATCTTCTGGGAGTCATCCACT
* * *
28187635 TTGATACTCAAGACAAATCATTTCCTCTGTC
261 TCGATACTCAAGAAAAATCATCTCCTCTGTC
* *
28187666 ACATATTGCAGAAGTCGTATACCCAACGCACCAACTTGT-AGTT-CTATATTTATTTAAACTCAA
1 ACATATTACAGAAGTCGTATACCCAACGCACCAACTT-TCAGTTCCT-TATCTATTTAAACTCAA
* *
28187729 GCTTTTACTTATATCAAAGTATACGAGTCACACATTCATAAT-TCATCATCTACTCAGGATTGAA
64 GCTTTTACTTATATCAAAGTATACGAGTCACACATACATAGTCT-ATCATCTACTCAGGATTGAA
*
28187793 GTATGTCACACTATGAACGTCGCAAGTAAATAAATCCATAAGCACATTCAGGATATATTCTACTT
128 GTATGTCACACTATGAACGTCACAAGTAAATAAATCCATAAGCACATTCAGGATATATTCTACTT
* *
28187858 GGGTCTTGTTCGATGTACTATCGGTCAAGTCAGCCACATCTATGTCTATCTTCTGGGAGTCATCC
193 GGGTCTTGTTCGATGTACTACCAGTCAAGTCAGCCACATCTATGTCTATCTTCTGGGAGTCATCC
* *
28187923 GCTTCGATACTCAAGAAAAATTATCTCCTC
258 ACTTCGATACTCAAGAAAAATCATCTCCTC
28187953 AATTAGACTT
Statistics
Matches: 257, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
290 3 0.01
291 253 0.98
292 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (291 bp):
ACATATTACAGAAGTCGTATACCCAACGCACCAACTTTCAGTTCCTTATCTATTTAAACTCAAGC
TTTTACTTATATCAAAGTATACGAGTCACACATACATAGTCTATCATCTACTCAGGATTGAAGTA
TGTCACACTATGAACGTCACAAGTAAATAAATCCATAAGCACATTCAGGATATATTCTACTTGGG
TCTTGTTCGATGTACTACCAGTCAAGTCAGCCACATCTATGTCTATCTTCTGGGAGTCATCCACT
TCGATACTCAAGAAAAATCATCTCCTCTGTC
Found at i:28189847 original size:40 final size:40
Alignment explanation
Indices: 28189792--28189998 Score: 315
Period size: 40 Copynumber: 5.2 Consensus size: 40
28189782 AGGGTTCAAT
* *
28189792 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28189832 CCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28189872 CCTTCGGGAGTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28189912 CCTTCGGGACTTAACCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
28189952 CCTTCGGGACTTAACCCGAATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28189992 CCTTCGG
1 CCTTCGG
28189999 ATCTTAGTCC
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 155 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.