Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 17 of 27
Found at i:2489745 original size:26 final size:26
Alignment explanation
Indices: 2489712--2489781 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
2489702 ATTAATATAT
2489712 TAAATTTTTAATTAAATTGATATCGA
1 TAAATTTTTAATTAAATTGATATCGA
* ** *
2489738 TAATTTTTTATATT-AATTTTTATCTA
1 TAAATTTTTA-ATTAAATTGATATCGA
2489764 TAAATTTTTAATTAAATT
1 TAAATTTTTAATTAAATT
2489782 AATTAGACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.08
26 31 0.84
27 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
TAAATTTTTAATTAAATTGATATCGA
Found at i:2489768 original size:52 final size:53
Alignment explanation
Indices: 2489712--2489812 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
2489702 ATTAATATAT
* * **
2489712 TAAATTTTTAATTAAATTGATATCGA-TAAT-TTTTTATATTAATTTTTATCTA
1 TAAATTTTTAATTAAATTAAT-TAGACTAATATTAATATATTAATTTTTATCTA
2489764 TAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTTTA
1 TAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTTTA
2489813 ATTAAATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 3 0.07
52 24 0.56
53 16 0.37
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (53 bp):
TAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTTTATCTA
Found at i:2489796 original size:92 final size:91
Alignment explanation
Indices: 2489654--2489853 Score: 348
Period size: 92 Copynumber: 2.2 Consensus size: 91
2489644 TTAATAGATA
* * *
2489654 TATATCAATTTTTATATATAAATTTTTAATTAAATTAATTAGATTAATATTAATATATTAAATTT
1 TATATTAATTTTTATCTATAAATTTTTAATTAAATTAATTAGACTAATATTAATATATT-AATTT
2489719 TTAATTAAATTGATATCGATAATTTTT
65 TTAATTAAATTGATATCGATAATTTTT
2489746 TATATTAATTTTTATCTATAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTT
1 TATATTAATTTTTATCTATAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTT
*
2489811 TAATTAAATTGATATTGATAATTTTT
66 TAATTAAATTGATATCGATAATTTTT
2489837 T-TATTAATTTTTATCTA
1 TATATTAATTTTTATCTA
2489854 AATTGATTGT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
90 16 0.15
91 32 0.31
92 56 0.54
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (91 bp):
TATATTAATTTTTATCTATAAATTTTTAATTAAATTAATTAGACTAATATTAATATATTAATTTT
TAATTAAATTGATATCGATAATTTTT
Found at i:2489872 original size:37 final size:37
Alignment explanation
Indices: 2489751--2489860 Score: 109
Period size: 39 Copynumber: 2.9 Consensus size: 37
2489741 TTTTTTATAT
*
2489751 TAATTTTTATCTATAAATTTTTAATTAAATT-A-ATTAGA
1 TAATTTTT-T-TATTAATTTTTAATTAAATTGATATT-GA
* *
2489789 CTAATATTAATATATTAATTTTTAATTAAATTGATATTGA
1 -TAAT-TT-TTTTATTAATTTTTAATTAAATTGATATTGA
2489829 TAATTTTTTTATTAATTTTT-ATCTAAATTGAT
1 TAATTTTTTTATTAATTTTTAAT-TAAATTGAT
2489861 TGTTTCAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
36 2 0.03
37 21 0.34
38 2 0.03
39 27 0.44
40 5 0.08
41 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (37 bp):
TAATTTTTTTATTAATTTTTAATTAAATTGATATTGA
Found at i:2490031 original size:22 final size:22
Alignment explanation
Indices: 2489987--2490031 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2489977 TTAATTATAA
*
2489987 ATTTAATAAATTAAATATAATT
1 ATTTAATAAATTAAATAAAATT
*
2490009 ATTT-ATAAATTTAATAAATATT
1 ATTTAATAAATTAAATAAA-ATT
2490031 A
1 A
2490032 ATCGAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATAAATTAAATAAAATT
Found at i:2497769 original size:15 final size:15
Alignment explanation
Indices: 2497738--2497766 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2497728 AACTTCCATC
2497738 CCTTTCTCTCTTTTT
1 CCTTTCTCTCTTTTT
2497753 CCTTTCTC-CTTTTT
1 CCTTTCTCTCTTTTT
2497767 TCCCATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CCTTTCTCTCTTTTT
Found at i:2498366 original size:28 final size:26
Alignment explanation
Indices: 2498306--2498374 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
2498296 GATTAACTTA
2498306 TTATAA-T-AAATTTAATTTTTATTT
1 TTATAATTAAAATTTAATTTTTATTT
* *
2498330 TAAAAAATTAAAATATTAATTTTATATTT
1 T-TATAATTAAAAT-TTAATTTT-TATTT
2498359 TTATAATT-AAATTTAA
1 TTATAATTAAAATTTAA
2498375 ATAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
26 5 0.14
27 8 0.22
28 13 0.36
29 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATAATTAAAATTTAATTTTTATTT
Found at i:2498377 original size:33 final size:28
Alignment explanation
Indices: 2498312--2498377 Score: 71
Period size: 33 Copynumber: 2.2 Consensus size: 28
2498302 CTTATTATAA
2498312 TAAAT-TTAATTTTTATTTTAAAAAATT
1 TAAATATTAATTTTTATTTTAAAAAATT
*
2498339 AAAATATTAATTTTATATTTTTATAATTAAATT
1 TAAATATTAATTTT-TA-TTTTA-AA--AAATT
2498372 TAAATA
1 TAAATA
2498378 AAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 4 0.13
28 8 0.26
29 2 0.06
30 5 0.16
31 2 0.06
33 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAATATTAATTTTTATTTTAAAAAATT
Found at i:2498393 original size:15 final size:15
Alignment explanation
Indices: 2498353--2498399 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2498343 TATTAATTTT
*
2498353 ATATTTTTATAATTA
1 ATATTTTTATAAATA
** *
2498368 A-ATTTAAATAAAAA
1 ATATTTTTATAAATA
2498382 ATATTTTTATAAATA
1 ATATTTTTATAAATA
2498397 ATA
1 ATA
2498400 AATTAAATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTTTATAAATA
Found at i:2504387 original size:34 final size:34
Alignment explanation
Indices: 2504324--2504391 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
2504314 ATATAAAAAA
* *
2504324 TATTTTTATAATAAAATTTAAATTAAATTTTATT
1 TATTATTATAATAAAATTCAAATTAAATTTTATT
2504358 TATTATTA-AATAAGAATTCAAA-TAGAATTTTATT
1 TATTATTATAATAA-AATTCAAATTA-AATTTTATT
2504392 AACTTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (34 bp):
TATTATTATAATAAAATTCAAATTAAATTTTATT
Found at i:2504628 original size:24 final size:24
Alignment explanation
Indices: 2504601--2504660 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2504591 AGTAATATTT
*
2504601 TTAATTTAAATTTAATTATAAATA
1 TTAATTTAAATATAATTATAAATA
* * * *
2504625 TTAATATAAAAATAATTTTTAATA
1 TTAATTTAAATATAATTATAAATA
*
2504649 TTATTTTAAATA
1 TTAATTTAAATA
2504661 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAATTTAAATATAATTATAAATA
Found at i:2509162 original size:4 final size:4
Alignment explanation
Indices: 2509153--2509188 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2509143 TGGGTATTTC
* *
2509153 TCTT TCTT TCTC TCCT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
2509189 ATTCTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:2512692 original size:2 final size:2
Alignment explanation
Indices: 2512685--2512740 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
2512675 TGTAAGCAAA
*
2512685 AT AT AT AT AT AT AT AT AT AT AT GA- AT AT -T A- AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
2512724 AT AT -T AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
2512741 ATTAAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
1 6 0.13
2 39 0.85
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2518668 original size:22 final size:22
Alignment explanation
Indices: 2518643--2518689 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2518633 TTAATTTGCT
2518643 TATTCTCATGTTGTTTTCATCA
1 TATTCTCATGTTGTTTTCATCA
2518665 TATTCTCATGTTGTTTTCATCA
1 TATTCTCATGTTGTTTTCATCA
2518687 TAT
1 TAT
2518690 ACATTACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (22 bp):
TATTCTCATGTTGTTTTCATCA
Found at i:2518988 original size:28 final size:30
Alignment explanation
Indices: 2518957--2519016 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2518947 TTTAAAAAAT
2518957 AATTATT-AAA-TATATTTTTTATTT-TTAA
1 AATTATTAAAAGTA-ATTTTTTATTTATTAA
*
2518985 AATTTTTAAAAGTAATTTTTTATTTATTAA
1 AATTATTAAAAGTAATTTTTTATTTATTAA
2519015 AA
1 AA
2519017 ATAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
29 14 0.50
30 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
AATTATTAAAAGTAATTTTTTATTTATTAA
Found at i:2520070 original size:19 final size:17
Alignment explanation
Indices: 2520046--2520100 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
2520036 TAATTAATAA
2520046 AAATATTTTTAAATGTTT
1 AAATATTTTTAAAT-TTT
*
2520064 -AATATATTTTAAATAATT
1 AAATAT-TTTTAAAT-TTT
2520082 AAATATATTTTAAATTTT
1 AAATAT-TTTTAAATTTT
2520100 A
1 A
2520101 TAAAATCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.16
18 13 0.41
19 14 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATATTTTTAAATTTT
Found at i:2520886 original size:2 final size:2
Alignment explanation
Indices: 2520879--2520911 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2520869 ACTTTTGGCA
*
2520879 AT AT AT AT AT AT AT AT AT AT A- AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2520912 TACCAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2525828 original size:15 final size:15
Alignment explanation
Indices: 2525805--2525842 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2525795 CATAGTTGAT
*
2525805 ATTTGATAATTTTAA
1 ATTTAATAATTTTAA
2525820 ATTTAATAATTTTAA
1 ATTTAATAATTTTAA
*
2525835 ATATAATA
1 ATTTAATA
2525843 TAAAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTAATAATTTTAA
Found at i:2525850 original size:23 final size:24
Alignment explanation
Indices: 2525824--2525893 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
2525814 TTTTAAATTT
*
2525824 AATAATTTTAAATATAATATA-AA
1 AATAATTTAAAATATAATATATAA
*
2525847 AATAA-TTAAAATATATTATATAA
1 AATAATTTAAAATATAATATATAA
* * * *
2525870 TATAA-TTAATATAAAAAATATAA
1 AATAATTTAAAATATAATATATAA
2525893 A
1 A
2525894 TATATATCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 13 0.34
23 25 0.66
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATAATTTAAAATATAATATATAA
Found at i:2525896 original size:29 final size:27
Alignment explanation
Indices: 2525832--2525897 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
2525822 TTAATAATTT
2525832 TAAATATAATATAAAAATAATTAAAATA
1 TAAATATAATATAAAAATAA-TAAAATA
*
2525860 TATTATATAATATAATTAATATAA-AAAATA
1 TA-AATATAATATAA--AA-ATAATAAAATA
2525890 TAAATATA
1 TAAATATA
2525898 TATCTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 16 0.50
30 8 0.25
31 2 0.06
32 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATATAATATAAAAATAATAAAATA
Found at i:2525917 original size:38 final size:36
Alignment explanation
Indices: 2525833--2525918 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 36
2525823 TAATAATTTT
*
2525833 AAATATAATATAAAAATAATTAAAATATATTATATA
1 AAATTTAATATAAAAATAATTAAAATATATTATATA
*
2525869 ATATAATTAATAT-AAAA-AATATAAATATATATCTATATTA
1 A-A-ATTTAATATAAAAATAAT-TAAA-ATATAT-TATA-TA
2525909 AAATTTAATA
1 AAATTTAATA
2525919 ATAATTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
36 4 0.10
37 9 0.22
38 20 0.49
39 5 0.12
40 3 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (36 bp):
AAATTTAATATAAAAATAATTAAAATATATTATATA
Found at i:2525970 original size:15 final size:14
Alignment explanation
Indices: 2525938--2525966 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2525928 ATTAATATTT
2525938 TAAAAAAATTATAA
1 TAAAAAAATTATAA
2525952 TAAAAAAATT-TAA
1 TAAAAAAATTATAA
2525965 TA
1 TA
2525967 TAAATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAAATTATAA
Found at i:2532068 original size:24 final size:24
Alignment explanation
Indices: 2532035--2532098 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
2532025 AATAAATTCA
*
2532035 ATTTAAATTTGATT-TTTTTATAAAT
1 ATTTTAATTT-ATTATTTTTA-AAAT
2532060 -TTTTAATTTATTATTTTTAAAAT
1 ATTTTAATTTATTATTTTTAAAAT
2532083 AATTTTAA-TTATTATT
1 -ATTTTAATTTATTATT
2532099 AACAAATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 7 0.20
24 22 0.63
25 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTTAATTTATTATTTTTAAAAT
Found at i:2533195 original size:21 final size:21
Alignment explanation
Indices: 2533170--2533209 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2533160 ATTTGAATAT
2533170 TTAAAA-ATTCATTTTATATGA
1 TTAAAATATT-ATTTTATATGA
2533191 TTAAAATATTATTTTATAT
1 TTAAAATATTATTTTATAT
2533210 TAATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAAATATTATTTTATATGA
Found at i:2533221 original size:17 final size:17
Alignment explanation
Indices: 2533195--2533234 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2533185 ATATGATTAA
2533195 AATA-TTATTT-TATATT
1 AATATTTATTTATA-ATT
2533211 AATATTTATTTATAATT
1 AATATTTATTTATAATT
2533228 AA-ATTTA
1 AATATTTA
2533235 AATAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 11 0.50
18 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTATTTATAATT
Found at i:2533253 original size:39 final size:38
Alignment explanation
Indices: 2533204--2533305 Score: 98
Period size: 39 Copynumber: 2.7 Consensus size: 38
2533194 AAATATTATT
* * **
2533204 TTATATTAATATTTATTTATAATTAAATTTAAATAAAAA
1 TTATTTTAATATTTATTAATAATTAAAAATAAAT-AAAA
* * *
2533243 TTATTTTAATATTAAATAATAATTAAAAATAAATTAAA
1 TTATTTTAATATTTATTAATAATTAAAAATAAATAAAA
* * *
2533281 TTAATTTAA-ATTTATAAAAAATTAA
1 TTATTTTAATATTTATTAATAATTAA
2533306 CATATATATC
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
37 12 0.24
38 11 0.22
39 28 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
TTATTTTAATATTTATTAATAATTAAAAATAAATAAAA
Found at i:2533276 original size:45 final size:44
Alignment explanation
Indices: 2533192--2533281 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 44
2533182 TTTATATGAT
* * * *
2533192 TAAAATATTATTTTATATTAATATTTATTTATAATTAAATTTAAA
1 TAAAATATTATTTTATATTAATATATAATTAAAAATAAA-TTAAA
2533237 TAAAA-ATTATTTTAATATTAA-ATAATAATTAAAAATAAATTAAA
1 TAAAATATTATTTT-ATATTAATAT-ATAATTAAAAATAAATTAAA
2533281 T
1 T
2533282 TAATTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (44 bp):
TAAAATATTATTTTATATTAATATATAATTAAAAATAAATTAAA
Found at i:2533912 original size:27 final size:26
Alignment explanation
Indices: 2533881--2533941 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2533871 ATTAAAAAAA
2533881 TAAA-TAAATAAATTTA-TATATTAATAT
1 TAAATTAAA-AAATTTATTA-ATTAA-AT
*
2533908 TAAATTAAACAATTTATTAATTAAAT
1 TAAATTAAAAAATTTATTAATTAAAT
*
2533934 TAATTTAA
1 TAAATTAA
2533942 TCTGATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 9 0.30
27 15 0.50
28 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATTAAAAAATTTATTAATTAAAT
Found at i:2535293 original size:22 final size:20
Alignment explanation
Indices: 2535260--2535305 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2535250 AATTATTTTT
2535260 TATTAAATTTAATTATAAAATA
1 TATTAAATTTAA-TATAAAA-A
2535282 TATT-AATATTAATATAAAAA
1 TATTAAAT-TTAATATAAAAA
2535302 TATT
1 TATT
2535306 TCTACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAAATTTAATATAAAAA
Found at i:2536219 original size:20 final size:20
Alignment explanation
Indices: 2536179--2536219 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2536169 ATTTTAAAAA
*
2536179 ATATTTTTATATTAATTTTT
1 ATATTTTTATATTAATATTT
2536199 ATATTTTTATAATTAA-ATTT
1 ATATTTTTAT-ATTAATATTT
2536219 A
1 A
2536220 AATAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTTATATTAATATTT
Found at i:2536707 original size:17 final size:19
Alignment explanation
Indices: 2536676--2536723 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
2536666 AATAATTTAA
2536676 AAAATATA-AATATATAAT
1 AAAATATATAATATATAAT
**
2536694 -AAATATATAA-ATATTTT
1 AAAATATATAATATATAAT
2536711 AAAATATATAATA
1 AAAATATATAATA
2536724 AAAAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.48
18 12 0.48
19 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATATAATATATAAT
Found at i:2537876 original size:43 final size:41
Alignment explanation
Indices: 2537806--2537936 Score: 117
Period size: 44 Copynumber: 3.1 Consensus size: 41
2537796 ACTCAACATA
* *
2537806 AATATAAAATGATAAAAATATTTAAAATATTATATAATATAT
1 AATATAAAATAAT-AATATATTTAAAATATTATATAATATAT
* *
2537848 AATATAAAATAGAT-ATATATTATAAAAATATCTAAAT-ATATTAA
1 AATATAAAATA-ATAATATATT-T-AAAATAT-TATATAATA-TAT
* *
2537892 AATATAAATTATTAATATATTT-AAAT-TTATATAAATATAT
1 AATATAAAATAATAATATATTTAAAATATTATAT-AATATAT
2537932 AATAT
1 AATAT
2537937 TTTAATTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
39 4 0.05
40 8 0.11
41 13 0.18
42 11 0.15
43 14 0.19
44 23 0.32
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (41 bp):
AATATAAAATAATAATATATTTAAAATATTATATAATATAT
Found at i:2537888 original size:25 final size:24
Alignment explanation
Indices: 2537829--2537911 Score: 54
Period size: 23 Copynumber: 3.7 Consensus size: 24
2537819 AAAAATATTT
*
2537829 AAAATATTATATA-ATATATAATA
1 AAAATATTAAATATATATATAATA
* *
2537852 TAAA-A-TAGATATATAT-T-ATA
1 AAAATATTAAATATATATATAATA
*
2537872 AAAATATCTAAATATAT-TAAAATA
1 AAAATAT-TAAATATATATATAATA
*
2537896 TAAATTATT-AATATAT
1 -AAAATATTAAATATAT
2537912 TTAAATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 6 0.13
21 7 0.15
22 6 0.13
23 18 0.38
24 4 0.09
25 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
AAAATATTAAATATATATATAATA
Found at i:2537927 original size:27 final size:26
Alignment explanation
Indices: 2537893--2537974 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 26
2537883 ATATATTAAA
2537893 ATATAAATTATTAATATATTTAAATTT
1 ATATAAA-TATTAATATATTTAAATTT
2537920 ATATAAATATATAATAT-TTT-AA--T
1 ATATAAATAT-TAATATATTTAAATTT
2537943 -TATAAATA-TAATATA--TAAATTT
1 ATATAAATATTAATATATTTAAATTT
2537965 ATATAAATAT
1 ATATAAATAT
2537975 AACTGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
19 1 0.02
20 8 0.17
22 9 0.19
23 9 0.19
25 2 0.04
26 6 0.12
27 13 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATAAATATTAATATATTTAAATTT
Found at i:2537930 original size:20 final size:20
Alignment explanation
Indices: 2537905--2537975 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 20
2537895 ATAAATTATT
2537905 AATATATTTAAATTTATATA
1 AATATATTTAAATTTATATA
2537925 AATATA--TAATATTTTAATTATA
1 AATATATTTAA-A-TTT-A-TATA
2537947 AATATAATATATAAATTTATATA
1 AATAT-AT-T-TAAATTTATATA
2537970 AATATA
1 AATATA
2537976 ACTGAAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 9 0.21
21 1 0.02
22 10 0.24
23 10 0.24
24 1 0.02
25 3 0.07
26 1 0.02
27 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTTAAATTTATATA
Found at i:2537957 original size:33 final size:33
Alignment explanation
Indices: 2537860--2537962 Score: 88
Period size: 33 Copynumber: 3.1 Consensus size: 33
2537850 TATAAAATAG
* * *
2537860 ATATATATTATAAAAATATCTAAATATAT-TAAA
1 ATATAAATTATTAATATAT-TAAATATATATAAA
*
2537893 ATATAAATTATTAATATATTTAAATTTATATAAA
1 ATATAAATTATTAATATA-TTAAATATATATAAA
2537927 TATATAATATT-TTAAT-TA-TAAATATAATATATAA
1 -ATATAA-ATTATTAATATATTAAATAT-ATATA-AA
2537961 AT
1 AT
2537963 TTATATAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
32 6 0.10
33 30 0.51
34 9 0.15
35 11 0.19
36 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATAAATTATTAATATATTAAATATATATAAA
Found at i:2537958 original size:22 final size:23
Alignment explanation
Indices: 2537882--2537976 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 23
2537872 AAAATATCTA
*
2537882 AATATA-TTAAA-ATATAAATTATT
1 AATATATTTAAATTTATAAA-TA-T
2537905 AATATATTTAAATTTATATAA-AT
1 AATATATTTAAATTTATA-AATAT
*
2537928 ATATAATATTTTAA-TTATAAATAT
1 A-AT-ATATTTAAATTTATAAATAT
2537952 AATATA--TAAATTTATATAAATAT
1 AATATATTTAAA-TT-TATAAATAT
2537975 AA
1 AA
2537977 CTGAAATACA
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
20 3 0.05
22 4 0.07
23 23 0.38
24 16 0.27
25 12 0.20
26 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATATATTTAAATTTATAAATAT
Found at i:2539635 original size:29 final size:25
Alignment explanation
Indices: 2539589--2539644 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 25
2539579 TTAAATTTAA
2539589 TTAAAAATATTAATATAAAATAATT
1 TTAAAAATATTAATATAAAATAATT
2539614 TTAAAAATATTTTAAATAATAAAATAATT
1 TTAAAAATA--TT-AAT-ATAAAATAATT
2539643 TT
1 TT
2539645 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.33
27 2 0.07
28 3 0.11
29 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAATATTAATATAAAATAATT
Found at i:2543584 original size:20 final size:19
Alignment explanation
Indices: 2543546--2543584 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2543536 ATTCATATTT
* *
2543546 ATTTTAATTTTTTTTTTAA
1 ATTTTAATTTATTTATTAA
2543565 ATTTTATATTTATTTATTAA
1 ATTTTA-ATTTATTTATTAA
2543585 TAAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTAATTTATTTATTAA
Found at i:2544197 original size:20 final size:19
Alignment explanation
Indices: 2544172--2544210 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2544162 TAAAATATTA
*
2544172 TATAAAAATTAAATTAAAAT
1 TATAAAAA-TAAAATAAAAT
*
2544192 TATAAATATAAAATAAAAT
1 TATAAAAATAAAATAAAAT
2544211 AAATTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATAAAATAAAAT
Found at i:2544208 original size:24 final size:24
Alignment explanation
Indices: 2544154--2544204 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2544144 AGGTAATATT
* *
2544154 AATTTAATTAAAATATTATATAAA
1 AATTAAATTAAAATATAATATAAA
2544178 AATTAAATTAAAATTATAAATATAAA
1 AATTAAATTAAAA-TAT-AATATAAA
2544204 A
1 A
2544205 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTAAATTAAAATATAATATAAA
Found at i:2544519 original size:19 final size:19
Alignment explanation
Indices: 2544495--2544532 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2544485 TATTTTAATT
2544495 TTTTTAAAAATATTTTTAA
1 TTTTTAAAAATATTTTTAA
**
2544514 TTTTTAAATTTATTTTTAA
1 TTTTTAAAAATATTTTTAA
2544533 CAACTTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAAAAATATTTTTAA
Found at i:2545284 original size:27 final size:29
Alignment explanation
Indices: 2545234--2545326 Score: 99
Period size: 27 Copynumber: 3.4 Consensus size: 29
2545224 ACATTAATTA
* *
2545234 AATTAAAT-TAAAT-TAACACATAAAAAT
1 AATTAAATATTAATATAAAACATAAAAAT
2545261 -ATTAAATATT-ATATAAAACATAAAAAT
1 AATTAAATATTAATATAAAACATAAAAAT
* *
2545288 AATTTAAT-TTAATATAAAA-TTAAAAAT
1 AATTAAATATTAATATAAAACATAAAAAT
2545315 AATATAAATATT
1 AAT-TAAATATT
2545327 TAAAAATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 9 0.16
27 26 0.47
28 18 0.33
29 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATTAAATATTAATATAAAACATAAAAAT
Found at i:2545317 original size:17 final size:19
Alignment explanation
Indices: 2545297--2545333 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2545287 TAATTTAATT
2545297 TAATATAAA-A-TTAAAAA
1 TAATATAAATATTTAAAAA
2545314 TAATATAAATATTTAAAAA
1 TAATATAAATATTTAAAAA
2545333 T
1 T
2545334 TATAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATATAAATATTTAAAAA
Found at i:2545427 original size:15 final size:16
Alignment explanation
Indices: 2545396--2545433 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2545386 GTAAAATTTT
*
2545396 AAATAATAATTTAATA
1 AAATATTAATTTAATA
2545412 AAATATTAATTT-ATA
1 AAATATTAATTTAATA
2545427 AAATATT
1 AAATATT
2545434 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAATTTAATA
Found at i:2545427 original size:23 final size:24
Alignment explanation
Indices: 2545365--2545420 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2545355 TTAAATATTT
*
2545365 ATATTAATATAAATATTTTAAGTAAA
1 ATATTAA-AT-AATAATTTAAGTAAA
*
2545391 ATTTTAAATAATAATTTAA-TAAA
1 ATATTAAATAATAATTTAAGTAAA
2545414 ATATTAA
1 ATATTAA
2545421 TTTATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 9 0.33
25 2 0.07
26 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATTAAATAATAATTTAAGTAAA
Found at i:2546238 original size:14 final size:14
Alignment explanation
Indices: 2546216--2546252 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2546206 ATTAATATTT
2546216 TTTAT-ATATATAA
1 TTTATAATATATAA
2546229 TTTATAATATA-AA
1 TTTATAATATATAA
2546242 TTT-TAATATAT
1 TTTATAATATAT
2546253 TGATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 10 0.45
14 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATAATATATAA
Found at i:2546240 original size:12 final size:12
Alignment explanation
Indices: 2546216--2546261 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2546206 ATTAATATTT
2546216 TTTATATATATAA
1 TTTATA-ATATAA
2546229 TTTATAATATAAA
1 TTTATAATAT-AA
2546242 TTT-TAATAT-A
1 TTTATAATATAA
*
2546252 TTGATAATAT
1 TTTATAATAT
2546262 TATATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 3 0.10
11 6 0.20
12 10 0.33
13 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTATAATATAA
Found at i:2546251 original size:28 final size:31
Alignment explanation
Indices: 2546225--2546300 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
2546215 TTTTATATAT
2546225 ATAAT-TTATAATATAAATTTTAATATATTG
1 ATAATATTATAATATAAATTTTAATATATTG
* * * *
2546255 ATAATATTAT-AT-TATATTTAAATTATTTTT
1 ATAATATTATAATATAAATTTTAA-TATATTG
*
2546285 ATAATATTATATTATA
1 ATAATATTATAATATA
2546301 TATAAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 8 0.22
30 22 0.59
31 5 0.14
32 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
ATAATATTATAATATAAATTTTAATATATTG
Found at i:2551135 original size:29 final size:29
Alignment explanation
Indices: 2551090--2551157 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
2551080 AAAATTCTTT
* **
2551090 ATATATTA-CTTTAAAAATTTAT-ATTTA
1 ATATATTATTTTTAAAAATTTATAAAATA
2551117 ATATATTATTTTTATAAAATTTATAAAATA
1 ATATATTATTTTTA-AAAATTTATAAAATA
2551147 ATATATTATTT
1 ATATATTATTT
2551158 ATATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.23
28 4 0.11
29 9 0.26
30 14 0.40
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATATTATTTTTAAAAATTTATAAAATA
Found at i:2552516 original size:29 final size:26
Alignment explanation
Indices: 2552475--2552528 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
2552465 TACCTAAATG
*
2552475 ATTTTAAACATAATTATATAAATATAAT
1 ATTTTAAACATAA-AATATAAA-ATAAT
*
2552503 ATTTATAAATATAAAATATAAAATAA
1 ATTT-TAAACATAAAATATAAAATAA
2552529 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 11 0.48
29 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTTAAACATAAAATATAAAATAAT
Found at i:2552538 original size:33 final size:34
Alignment explanation
Indices: 2552490--2552595 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 34
2552480 AAACATAATT
*
2552490 ATATAAATATAATATTTATAAATATAAAATATAAA
1 ATATAAAAAT-ATATTTATAAATATAAAATATAAA
* * *
2552525 ATA-AAAAATATATTT-TATAATTTAAATTAT-TA
1 ATATAAAAATATATTTATA-AATATAAAATATAAA
* *
2552557 ATATTAAAATATA--TAAAAATATAAAAATATAAA
1 ATATAAAAATATATTTATAAATAT-AAAATATAAA
2552590 ATATAA
1 ATATAA
2552596 TTATAATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
31 5 0.09
32 13 0.23
33 30 0.54
34 5 0.09
35 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
ATATAAAAATATATTTATAAATATAAAATATAAA
Found at i:2552575 original size:10 final size:9
Alignment explanation
Indices: 2552556--2552634 Score: 60
Period size: 8 Copynumber: 8.8 Consensus size: 9
2552546 TTAAATTATT
2552556 AATAT-TAA
1 AATATATAA
2552564 AATATATAA
1 AATATATAA
2552573 AA-ATATAA
1 AATATATAA
2552581 AA-ATATAA
1 AATATATAA
*
2552589 AATATAATTAT
1 AATAT-A-TAA
2552600 AATATA-ATA
1 AATATATA-A
*
2552609 AAT-TATTA
1 AATATATAA
2552617 AATATAATATA
1 AATAT-ATA-A
2552628 AATATAT
1 AATATAT
2552635 GAATTATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 28 0.48
9 11 0.19
10 6 0.10
11 13 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATATATAA
Found at i:2552605 original size:11 final size:11
Alignment explanation
Indices: 2552490--2552633 Score: 70
Period size: 11 Copynumber: 13.0 Consensus size: 11
2552480 AAACATAATT
2552490 ATATAAATATA
1 ATATAAATATA
**
2552501 ATATTTATA-A
1 ATATAAATATA
2552511 ATATAAAATATA
1 ATAT-AAATATA
*
2552523 AAATAAA-A-A
1 ATATAAATATA
**
2552532 ATATATTTTATA
1 ATATA-AATATA
*
2552544 ATTTAAATTATTA
1 ATATAAA-TA-TA
2552557 ATATTAAA-ATA
1 ATA-TAAATATA
*
2552568 TATAAAAATATA
1 -ATATAAATATA
*
2552580 A-A-AATATAAA
1 ATATAA-ATATA
*
2552590 ATATAATTATA
1 ATATAAATATA
2552601 ATAT-AATA-A
1 ATATAAATATA
2552610 ATTATTAAATATA
1 A-TA-TAAATATA
2552623 ATATAAATATA
1 ATATAAATATA
2552634 TGAATTATTA
Statistics
Matches: 99, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
9 9 0.09
10 17 0.17
11 37 0.37
12 26 0.26
13 6 0.06
14 4 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:2552634 original size:8 final size:8
Alignment explanation
Indices: 2552484--2552622 Score: 66
Period size: 8 Copynumber: 18.1 Consensus size: 8
2552474 GATTTTAAAC
*
2552484 ATAATTAT
1 ATAAATAT
2552492 ATAAATAT
1 ATAAATAT
* *
2552500 A-ATATTT
1 ATAAATAT
2552507 ATAAATAT
1 ATAAATAT
2552515 A-AAATAT
1 ATAAATAT
2552522 A-AAATA-
1 ATAAATAT
*
2552528 AAAAATAT
1 ATAAATAT
**
2552536 ATTTTATAAT
1 A-TAAAT-AT
*
2552546 TTAAAT-T
1 ATAAATAT
*
2552553 ATTAATAT
1 ATAAATAT
2552561 -TAAAATAT
1 AT-AAATAT
*
2552569 ATAAAAAT
1 ATAAATAT
*
2552577 ATAAAAAT
1 ATAAATAT
2552585 ATAAA-AT
1 ATAAATAT
2552592 AT-AAT-T
1 ATAAATAT
2552598 AT-AATAT
1 ATAAATAT
2552605 AATAAAT-T
1 -ATAAATAT
2552613 ATTAAATAT
1 A-TAAATAT
2552622 A
1 A
2552623 ATATAAATAT
Statistics
Matches: 102, Mismatches: 15, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
6 9 0.09
7 34 0.33
8 46 0.45
9 11 0.11
10 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAAATAT
Found at i:2552963 original size:15 final size:13
Alignment explanation
Indices: 2552952--2553055 Score: 55
Period size: 12 Copynumber: 8.3 Consensus size: 13
2552942 GTAATATTAA
2552952 TTAAAATAATATT
1 TTAAAATAATATT
*
2552965 TTAAAAAAATATAT
1 TTAAAATAATAT-T
2552979 TT--AAT--T-TT
1 TTAAAATAATATT
**
2552987 TTAAAATTTTA-T
1 TTAAAATAATATT
* *
2552999 TAAAAATAATATA
1 TTAAAATAATATT
2553012 TT-AAATATATATT
1 TTAAAATA-ATATT
2553025 TTAAAAATAATAATT
1 TT-AAAATAAT-ATT
2553040 ATT-AAATAAT-TT
1 -TTAAAATAATATT
2553052 TTAA
1 TTAA
2553056 TCAATATCTA
Statistics
Matches: 70, Mismatches: 8, Indels: 27
0.67 0.08 0.26
Matches are distributed among these distances:
8 3 0.04
9 1 0.01
10 4 0.06
11 2 0.03
12 20 0.29
13 18 0.26
14 12 0.17
15 8 0.11
16 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAAAATAATATT
Found at i:2553015 original size:14 final size:14
Alignment explanation
Indices: 2552996--2553040 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
2552986 TTTAAAATTT
2552996 TATTAAAAATAATA
1 TATTAAAAATAATA
*
2553010 TATTAAATAT-ATA
1 TATTAAAAATAATA
*
2553023 TTTTAAAAATAATA
1 TATTAAAAATAATA
2553037 -ATTA
1 TATTA
2553041 TTAAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATTAAAAATAATA
Found at i:2553033 original size:27 final size:27
Alignment explanation
Indices: 2552998--2553055 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
2552988 TAAAATTTTA
2552998 TTAAAAATAAT-A-TATTAAATATATATT
1 TTAAAAATAATAATTATTAAATA-AT-TT
2553025 TTAAAAATAATAATTATTAAATAATTT
1 TTAAAAATAATAATTATTAAATAATTT
2553052 TTAA
1 TTAA
2553056 TCAATATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.59
28 3 0.10
29 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAAAATAATAATTATTAAATAATTT
Found at i:2553048 original size:14 final size:14
Alignment explanation
Indices: 2552995--2553049 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
2552985 TTTTAAAATT
2552995 TTATTAAA-AATAA
1 TTATTAAATAATAA
2553008 TATATTAAAT-ATATA
1 T-TATTAAATAATA-A
2553023 TT-TTAAAAATAATAA
1 TTATT--AAATAATAA
2553038 TTATTAAATAAT
1 TTATTAAATAAT
2553050 TTTTAATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.09
14 18 0.51
15 9 0.26
16 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATTAAATAATAA
Found at i:2554904 original size:29 final size:29
Alignment explanation
Indices: 2554845--2554906 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2554835 AATATATTTT
* *
2554845 TATTTTTATGTATTTATAATTTTATATAA
1 TATTTTTATGTATTTATAATATTATAAAA
2554874 TATTTTTAT-TAGTTTTATAATATTA-AAAA
1 TATTTTTATGTA--TTTATAATATTATAAAA
2554903 TATT
1 TATT
2554907 AAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 16 0.55
30 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TATTTTTATGTATTTATAATATTATAAAA
Found at i:2555612 original size:13 final size:13
Alignment explanation
Indices: 2555594--2555638 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
2555584 ATATTTTATT
2555594 TATTTTTAAAATA
1 TATTTTTAAAATA
2555607 -ATTTTTAAAATA
1 TATTTTTAAAATA
*
2555619 TA-TTTAAAAATA
1 TATTTTTAAAATA
2555631 TATATTTT
1 TAT-TTTT
2555639 TGTGATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 23 0.85
13 1 0.04
14 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTTTAAAATA
Found at i:2563977 original size:6 final size:6
Alignment explanation
Indices: 2563966--2563990 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2563956 AAAAATTATA
2563966 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
2563991 GTTTGATCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:2564110 original size:19 final size:20
Alignment explanation
Indices: 2564086--2564124 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2564076 TAATTTTTTT
2564086 AAAATACTATTTT-AATTAA
1 AAAATACTATTTTAAATTAA
*
2564105 AAAATATTATTTTAAATTAA
1 AAAATACTATTTTAAATTAA
2564125 GTCGAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATACTATTTTAAATTAA
Found at i:2569551 original size:7 final size:7
Alignment explanation
Indices: 2569539--2569602 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
2569529 TATAGAATTC
2569539 TTATATA
1 TTATATA
2569546 TTATATA
1 TTATATA
*
2569553 ATATATA
1 TTATATA
*
2569560 ATATAT-
1 TTATATA
*
2569566 TTAT-TT
1 TTATATA
2569572 TTATATA
1 TTATATA
2569579 TTATATA
1 TTATATA
*
2569586 ATATATA
1 TTATATA
*
2569593 ATAT-TA
1 TTATATA
2569599 TTAT
1 TTAT
2569603 GTAAATAGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
5 1 0.02
6 12 0.24
7 37 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATATA
Found at i:2569936 original size:24 final size:25
Alignment explanation
Indices: 2569909--2569964 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
2569899 GCATCATTTT
* *
2569909 ATTTCAAAA-TTATTGTCAATTAAA
1 ATTTAAAAAGTTATTATCAATTAAA
* *
2569933 ATTTAAAAAGTTTTTATTAATTAAA
1 ATTTAAAAAGTTATTATCAATTAAA
2569958 ATATTAA
1 AT-TTAA
2569965 TATAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
ATTTAAAAAGTTATTATCAATTAAA
Found at i:2572306 original size:10 final size:10
Alignment explanation
Indices: 2572262--2572310 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
2572252 AGAAAATTTT
2572262 AATTAATAAA
1 AATTAATAAA
2572272 AATCTTAATAAA
1 AA--TTAATAAA
* *
2572284 ATTTAAATCAA
1 AATT-AATAAA
2572295 AATTAATAAA
1 AATTAATAAA
2572305 AATTAA
1 AATTAA
2572311 ATTTATTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 15 0.47
11 8 0.25
12 9 0.28
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AATTAATAAA
Found at i:2572512 original size:20 final size:20
Alignment explanation
Indices: 2572489--2572527 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2572479 AAACTATATT
*
2572489 AAATTAATATAAATTTTAAA
1 AAATTAATATAAAATTTAAA
* *
2572509 AAATTTATTTAAAATTTAA
1 AAATTAATATAAAATTTAA
2572528 TTCATATGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTAATATAAAATTTAAA
Found at i:2573316 original size:22 final size:18
Alignment explanation
Indices: 2573275--2573314 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2573265 ATTTAATATG
2573275 ATATTATTATTAGAAATA
1 ATATTATTATTAGAAATA
*
2573293 ATATATATTATTAGATATA
1 ATAT-TATTATTAGAAATA
2573312 ATA
1 ATA
2573315 ATGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATTATTATTAGAAATA
Found at i:2574061 original size:2 final size:2
Alignment explanation
Indices: 2574054--2574083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2574044 TTTCGAATCT
2574054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2574084 AACCTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2574201 original size:13 final size:14
Alignment explanation
Indices: 2574183--2574211 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2574173 GATTGAAAAA
2574183 TAAAAAATT-TTAT
1 TAAAAAATTATTAT
2574196 TAAAAAATTATTAT
1 TAAAAAATTATTAT
2574210 TA
1 TA
2574212 TTATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAAAATTATTAT
Found at i:2576840 original size:2 final size:2
Alignment explanation
Indices: 2576833--2576867 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2576823 CTGAGTAATA
*
2576833 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2576868 CACATATACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2576856 original size:18 final size:18
Alignment explanation
Indices: 2576833--2576875 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2576823 CTGAGTAATA
2576833 ATATATATATATATATAC
1 ATATATATATATATATAC
2576851 ATATATATATATATATAC
1 ATATATATATATATATAC
*
2576869 ACATATA
1 ATATATA
2576876 CGCACACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATATATATATATAC
Found at i:2576874 original size:10 final size:10
Alignment explanation
Indices: 2576833--2576875 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
2576823 CTGAGTAATA
*
2576833 ATATATATAT
1 ATATATACAT
2576843 ATATATACAT
1 ATATATACAT
*
2576853 ATATATATAT
1 ATATATACAT
*
2576863 ATATACACAT
1 ATATATACAT
2576873 ATA
1 ATA
2576876 CGCACACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATACAT
Found at i:2577275 original size:24 final size:24
Alignment explanation
Indices: 2577226--2577269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2577216 AATTTGATAA
*
2577226 TTTATATATTATATTATAATTATT
1 TTTATATATTATATTATAATAATT
2577250 TTTATATATTAT-TTA-AATAA
1 TTTATATATTATATTATAATAA
2577270 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATATATTATATTATAATAATT
Found at i:2577334 original size:18 final size:18
Alignment explanation
Indices: 2577305--2577395 Score: 60
Period size: 16 Copynumber: 5.6 Consensus size: 18
2577295 TATATTAGTG
2577305 TATTAT-TT-TAATATTT
1 TATTATATTATAATATTT
2577321 TATTATATTAT-A-ATTT
1 TATTATATTATAATATTT
2577337 TATT-TA--A-AATATTT
1 TATTATATTATAATATTT
*
2577351 TA-TAT-TTATAAAAATTT
1 TATTATATTAT-AATATTT
**
2577368 TATTATATTAATAAT-TAA
1 TATTATATT-ATAATATTT
2577386 TATTATATTA
1 TATTATATTA
2577396 ATTTTAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 23
0.69 0.05 0.27
Matches are distributed among these distances:
13 3 0.05
14 7 0.12
15 3 0.05
16 14 0.24
17 12 0.20
18 14 0.24
19 4 0.07
20 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATATTATAATATTT
Found at i:2577369 original size:17 final size:16
Alignment explanation
Indices: 2577337--2577370 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2577327 ATTATAATTT
*
2577337 TATTTAAAATATTTTA
1 TATTTAAAAAATTTTA
2577353 TATTTATAAAAATTTTA
1 TATTTA-AAAAATTTTA
2577370 T
1 T
2577371 TATATTAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAAAAAATTTTA
Found at i:2577399 original size:32 final size:33
Alignment explanation
Indices: 2577363--2577443 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
2577353 TATTTATAAA
*
2577363 AATTTTATTATATTAATA-ATTAATATTATATT
1 AATTTTAATATATTAATATATTAATATTATATT
* * * *
2577395 AATTTTAAAATATTTATATATTTATATTATTTT
1 AATTTTAATATATTAATATATTAATATTATATT
*
2577428 TA-TTTAATATATTAAT
1 AATTTTAATATATTAAT
2577444 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 27 0.68
33 13 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
AATTTTAATATATTAATATATTAATATTATATT
Found at i:2577445 original size:28 final size:28
Alignment explanation
Indices: 2577370--2577455 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
2577360 AAAAATTTTA
*
2577370 TTATATTAATA-ATTAATATTATATTAATT
1 TTAT-TTAATATATTAAT-TTATATTATTT
* *
2577399 TTA--AAATATTTATATATTTATATTATTT
1 TTATTTAATATAT-TA-ATTTATATTATTT
*
2577427 TTATTTAATATATTAATTT-TTTTATTT
1 TTATTTAATATATTAATTTATATTATTT
2577454 TT
1 TT
2577456 TATAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
26 4 0.09
27 10 0.22
28 19 0.41
29 7 0.15
30 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATTTAATATATTAATTTATATTATTT
Found at i:2578049 original size:23 final size:23
Alignment explanation
Indices: 2578003--2578058 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2577993 TAATTTATTG
* **
2578003 ATAATAATTCTTATTATATTTAAT
1 ATAATAA-TATTATTATAAATAAT
2578027 ATAATAATATTATTATAAATAAT
1 ATAATAATATTATTATAAATAAT
* *
2578050 TTATTAATA
1 ATAATAATA
2578059 ACTAACTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATAATATTATTATAAATAAT
Found at i:2578053 original size:14 final size:13
Alignment explanation
Indices: 2577993--2578055 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
2577983 ATTTTACTTT
2577993 TAATTTATTGATAA
1 TAATTTATT-ATAA
* *
2578007 TAA-TTCTTATTA
1 TAATTTATTATAA
*
2578019 T-ATTTAATATAA
1 TAATTTATTATAA
2578031 TAATATTATTATAAA
1 TAAT-TTATTAT-AA
2578046 TAATTTATTA
1 TAATTTATTA
2578056 ATAACTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 1 0.03
12 11 0.28
13 6 0.15
14 15 0.38
15 6 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (13 bp):
TAATTTATTATAA
Found at i:2578223 original size:35 final size:33
Alignment explanation
Indices: 2578176--2578245 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 33
2578166 TATTTACTAA
2578176 AATTAATTTTAAAAAATTTAAAATAATATTTAT-TT
1 AATTAATTTTAAAAAA---AAAATAATATTTATCTT
*
2578211 AATT-ATTATTAAATAAAAAATAATATTTATCTT
1 AATTAATT-TTAAAAAAAAAATAATATTTATCTT
2578244 AA
1 AA
2578246 CACTGTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 14 0.44
33 4 0.12
34 3 0.09
35 11 0.34
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTAATTTTAAAAAAAAAATAATATTTATCTT
Found at i:2582399 original size:12 final size:12
Alignment explanation
Indices: 2582379--2582411 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
2582369 AAGTTGTCAA
2582379 TAAAGTTAAAAAT
1 TAAA-TTAAAAAT
2582392 TAAATTAAAAAT
1 TAAATTAAAAAT
2582404 TAAATTAA
1 TAAATTAA
2582412 TATAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TAAATTAAAAAT
Found at i:2582615 original size:22 final size:21
Alignment explanation
Indices: 2582567--2582623 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2582557 TCTAATCTTT
* *
2582567 AATTTAATTTTAAAGGTTTAG
1 AATTTAATTTTAAAAGATTAG
**
2582588 GGTTTAATTTTAAAAGATTATG
1 AATTTAATTTTAAAAGATTA-G
2582610 AATTTAAATTTTAA
1 AATTT-AATTTTAA
2582624 TAAATATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 16 0.57
22 4 0.14
23 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (21 bp):
AATTTAATTTTAAAAGATTAG
Found at i:2584076 original size:24 final size:24
Alignment explanation
Indices: 2584046--2584091 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2584036 TTGATTTGGT
2584046 GGTTTGTCATTATTGATTAAATAA
1 GGTTTGTCATTATTGATTAAATAA
*
2584070 GGTTTGTCATTTTTGATTAAAT
1 GGTTTGTCATTATTGATTAAAT
2584092 GAGAGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (24 bp):
GGTTTGTCATTATTGATTAAATAA
Found at i:2584120 original size:34 final size:33
Alignment explanation
Indices: 2584082--2584263 Score: 161
Period size: 34 Copynumber: 5.4 Consensus size: 33
2584072 TTTGTCATTT
2584082 TTGATTAAATGAGAGATTTGATAGTTTGCTATTG
1 TTGATTAAATGAGAGATTTGATAGTTT-CTATTG
* * * *
2584116 TTGATTAAATGGGTGATTTGGTGAATTATC-ATTG
1 TTGATTAAATGAGAGATTTGAT-AGTT-TCTATTG
* *
2584150 TTGACTAAATGAGA-ATTTTGATAGTTTGTCATTG
1 TTGATTAAATGAGAGA-TTTGATAGTTTCT-ATTG
* * *
2584184 TTGATTAAATGAGTGATTTGATGGTTTACCATTG
1 TTGATTAAATGAGAGATTTGATAGTTT-CTATTG
* * * * *
2584218 TTGACTAAATGGGAGATTTGATAATTTATCATTA
1 TTGATTAAATGAGAGATTTGATAGTTTCT-ATTG
2584252 TTGATTAAATGA
1 TTGATTAAATGA
2584264 TGATTTGGTG
Statistics
Matches: 115, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
32 1 0.01
33 4 0.03
34 104 0.90
35 5 0.04
36 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGATTAAATGAGAGATTTGATAGTTTCTATTG
Found at i:2584160 original size:68 final size:68
Alignment explanation
Indices: 2584076--2584273 Score: 249
Period size: 68 Copynumber: 2.9 Consensus size: 68
2584066 ATAAGGTTTG
* *
2584076 TCATTTTTGATTAAATGAGAGATTTGATAGTTTG-CTATTGTTGATTAAATGGGTGATTTGGTGA
1 TCATTGTTGACTAAATGAGAGATTTGATAGTTTGTC-ATTGTTGATTAAATGGGTGATTTGGTGA
2584140 ATTA
65 ATTA
* * *
2584144 TCATTGTTGACTAAATGAGA-ATTTTGATAGTTTGTCATTGTTGATTAAATGAGTGATTTGATGG
1 TCATTGTTGACTAAATGAGAGA-TTTGATAGTTTGTCATTGTTGATTAAATGGGTGATTTGGTGA
*
2584208 TTTA
65 ATTA
* * * * * *
2584212 CCATTGTTGACTAAATGGGAGATTTGATAATTTATCATTATTGATTAAAT-GATGATTTGGTG
1 TCATTGTTGACTAAATGAGAGATTTGATAGTTTGTCATTGTTGATTAAATGGGTGATTTGGTG
2584274 GTTTTTACCA
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
67 10 0.09
68 101 0.89
69 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (68 bp):
TCATTGTTGACTAAATGAGAGATTTGATAGTTTGTCATTGTTGATTAAATGGGTGATTTGGTGAA
TTA
Found at i:2584193 original size:102 final size:102
Alignment explanation
Indices: 2584071--2584263 Score: 280
Period size: 102 Copynumber: 1.9 Consensus size: 102
2584061 ATTAAATAAG
* * * * *
2584071 GTTTGTCATTTTTGATTAAATGAGAGATTTGATAGTTTGCTATTGTTGATTAAATGGGTGATTTG
1 GTTTGTCATTGTTGATTAAATGAGAGATTTGATAGTTTACCATTGTTGACTAAATGGGAGATTTG
* *
2584136 GTGAA-TTATCATTGTTGACTAAATGAGAATTTTGATA
66 AT-AATTTATCATTATTGACTAAATGAGAATTTTGATA
* *
2584173 GTTTGTCATTGTTGATTAAATGAGTGATTTGATGGTTTACCATTGTTGACTAAATGGGAGATTTG
1 GTTTGTCATTGTTGATTAAATGAGAGATTTGATAGTTTACCATTGTTGACTAAATGGGAGATTTG
*
2584238 ATAATTTATCATTATTGATTAAATGA
66 ATAATTTATCATTATTGACTAAATGA
2584264 TGATTTGGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 2 0.03
102 78 0.98
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.45
Consensus pattern (102 bp):
GTTTGTCATTGTTGATTAAATGAGAGATTTGATAGTTTACCATTGTTGACTAAATGGGAGATTTG
ATAATTTATCATTATTGACTAAATGAGAATTTTGATA
Found at i:2586436 original size:32 final size:33
Alignment explanation
Indices: 2586386--2586460 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
2586376 ATATATAAAT
* *
2586386 ATTAATATAAAAATAATATTTTAAT-AATAT-A
1 ATTAATTTTAAAATAATATTTTAATCAATATGA
*
2586417 ATTAATTTTAAAATAAATATTTTAATCAATTTGA
1 ATTAATTTTAAAAT-AATATTTTAATCAATATGA
*
2586451 TTTAATTTTA
1 ATTAATTTTA
2586461 GTAAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 12 0.32
32 11 0.30
33 4 0.11
34 10 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
ATTAATTTTAAAATAATATTTTAATCAATATGA
Found at i:2587003 original size:21 final size:20
Alignment explanation
Indices: 2586979--2587044 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 20
2586969 AAATATTAAA
*
2586979 TTATATAAAATTTATTTATAT
1 TTATATAAAA-TAATTTATAT
*
2587000 TTATAAATAAATAATTTAAATAT
1 TTATATA-AAATAATTT--ATAT
*
2587023 TTATTTAAAATAATTTATAT
1 TTATATAAAATAATTTATAT
2587043 TT
1 TT
2587045 TTTAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.16
21 11 0.29
22 12 0.32
23 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATAAAATAATTTATAT
Found at i:2587050 original size:19 final size:21
Alignment explanation
Indices: 2587008--2587056 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2586998 ATTTATAAAT
2587008 AAATAATTTAAATATTTATTTA
1 AAATAATTT-AATATTTATTTA
2587030 AAATAATTT-ATATTT-TTTA
1 AAATAATTTAATATTTATTTA
*
2587049 AAAAAATT
1 AAATAATT
2587057 AAAAACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
22 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATTTAATATTTATTTA
Found at i:2590474 original size:23 final size:22
Alignment explanation
Indices: 2590431--2590474 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2590421 AATCAATTTA
*
2590431 TTTAAAAAAATATTTCAAATAT
1 TTTAAAAAAATATTTAAAATAT
2590453 TTTAAAAAGAAT-TTTAATAATA
1 TTTAAAAA-AATATTTAA-AATA
2590475 AATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTAAAAAAATATTTAAAATAT
Found at i:2590609 original size:21 final size:23
Alignment explanation
Indices: 2590578--2590619 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2590568 TAGATTCAAA
2590578 TTTTAATAAAT-ATAAAAATATT
1 TTTTAATAAATAATAAAAATATT
*
2590600 TTTTAA-AAATAATTAAAATA
1 TTTTAATAAATAATAAAAATA
2590620 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTTAATAAATAATAAAAATATT
Found at i:2590899 original size:20 final size:19
Alignment explanation
Indices: 2590871--2590908 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2590861 TAATAGTTTA
*
2590871 AAATTTTAATTATAAAATAT
1 AAATATTAA-TATAAAATAT
2590891 AAATATTAATATAAAATA
1 AAATATTAATATAAAATA
2590909 ATATTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATTAATATAAAATAT
Found at i:2591100 original size:24 final size:24
Alignment explanation
Indices: 2591046--2591100 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2591036 TTAAATTATA
*
2591046 TTGATATTTTAATTAATAAAATTT
1 TTGAAATTTTAATTAATAAAATTT
* *
2591070 TTTAAATTTTAATTGATAATAA-TT
1 TTGAAATTTTAATTAATAA-AATTT
2591094 TTGAAAT
1 TTGAAAT
2591101 AAAATGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (24 bp):
TTGAAATTTTAATTAATAAAATTT
Found at i:2591468 original size:26 final size:26
Alignment explanation
Indices: 2591414--2591467 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 26
2591404 TTTATATAAT
2591414 AATATTATATATAATATAATATAAAA
1 AATATTATATATAATATAATATAAAA
2591440 AATATTATATATATTATATAAT-TAAAA
1 AATATTATATATA--ATATAATATAAAA
2591467 A
1 A
2591468 TTAGATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 13 0.50
27 6 0.23
28 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATTATATATAATATAATATAAAA
Found at i:2591685 original size:27 final size:30
Alignment explanation
Indices: 2591655--2591717 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2591645 AATTTAACAC
2591655 ATAT-TTTAATGTTTATAT-TATAATATTAT
1 ATATATTTAATGTTTATATATATAA-ATTAT
*
2591684 ATATATTTAATTTTTATATAATATAAATTAT
1 ATATATTTAATGTTTATAT-ATATAAATTAT
2591715 ATA
1 ATA
2591718 ATATATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 13 0.43
31 8 0.27
32 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATATTTAATGTTTATATATATAAATTAT
Found at i:2591690 original size:17 final size:17
Alignment explanation
Indices: 2591668--2591717 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
2591658 TTTTAATGTT
2591668 TATATTATAATATTATA
1 TATATTATAATATTATA
*
2591685 TATATT-TAAT-TTTTA
1 TATATTATAATATTATA
*
2591700 TATAATATAA-ATTATA
1 TATATTATAATATTATA
2591716 TA
1 TA
2591718 ATATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.32
16 13 0.46
17 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTATAATATTATA
Found at i:2591723 original size:16 final size:15
Alignment explanation
Indices: 2591668--2591726 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
2591658 TTTTAATGTT
2591668 TATAT-TATAATATTA
1 TATATATATAA-ATTA
* * *
2591683 TATATATTTAATTTT
1 TATATATATAAATTA
2591698 TATATAATATAAATTA
1 TATAT-ATATAAATTA
2591714 TATAATATATAAA
1 TAT-ATATATAAA
2591727 AAAATGTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.34
16 21 0.60
17 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATAAATTA
Found at i:2592181 original size:12 final size:12
Alignment explanation
Indices: 2592164--2592194 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2592154 CAAACAGTTT
2592164 ATATATACATAG
1 ATATATACATAG
2592176 ATATATACATAG
1 ATATATACATAG
2592188 ATATATA
1 ATATATA
2592195 TATAAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (12 bp):
ATATATACATAG
Found at i:2592407 original size:3 final size:3
Alignment explanation
Indices: 2592401--2592426 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2592391 TTATTATGAT
2592401 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2592427 AACAAAGTAG
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2592630 original size:21 final size:20
Alignment explanation
Indices: 2592606--2592671 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 20
2592596 AAATATTAAA
*
2592606 TTATATAAAATTTATTTATAT
1 TTATATAAAA-TAATTTATAT
*
2592627 TTATAAATAAATAATTTAAATAT
1 TTATATA-AAATAATTT--ATAT
*
2592650 TTATTTAAAATAATTTATAT
1 TTATATAAAATAATTTATAT
2592670 TT
1 TT
2592672 TTTAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.16
21 11 0.29
22 12 0.32
23 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATAAAATAATTTATAT
Found at i:2592677 original size:19 final size:21
Alignment explanation
Indices: 2592635--2592683 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2592625 ATTTATAAAT
2592635 AAATAATTTAAATATTTATTTA
1 AAATAATTT-AATATTTATTTA
2592657 AAATAATTT-ATATTT-TTTA
1 AAATAATTTAATATTTATTTA
*
2592676 AAAAAATT
1 AAATAATT
2592684 AAAAACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
22 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATTTAATATTTATTTA
Found at i:2592891 original size:2 final size:2
Alignment explanation
Indices: 2592886--2592930 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
2592876 TAATTCTTTG
*
2592886 AT AT AT AT A- AT AT -T CAT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
2592927 AT AT
1 AT AT
2592931 TAAAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2592891 original size:19 final size:20
Alignment explanation
Indices: 2592867--2592930 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
2592857 ACATAATTTA
*
2592867 ATATATATATA-ATTC-TTT
1 ATATATATATATATTCATAT
2592885 GATATATATA-ATATTCATAT
1 -ATATATATATATATTCATAT
2592905 ATATATATATATA-T-ATAT
1 ATATATATATATATTCATAT
*
2592923 AGATATAT
1 ATATATAT
2592931 TAAAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.30
19 23 0.57
20 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (20 bp):
ATATATATATATATTCATAT
Found at i:2593195 original size:2 final size:2
Alignment explanation
Indices: 2593188--2593216 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2593178 TAATAAGTCC
2593188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2593217 AGCTAAACAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2594778 original size:3 final size:3
Alignment explanation
Indices: 2594770--2594802 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2594760 TTTATTAAAA
2594770 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2594803 GATTCTAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2595922 original size:21 final size:21
Alignment explanation
Indices: 2595850--2595942 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 21
2595840 TAATTTAATT
* *
2595850 TATATTAATTTAAATTA-AAA
1 TATATTATTTTTAATTATAAA
* *
2595870 TATAATATTTTTAATTTAATTTAA
1 TATATTATTTTTAA-TT-A-TAAA
*
2595894 TTTATTA-TTTTAATTAATAAA
1 TATATTATTTTTAATT-ATAAA
2595915 TATATTATTATTTAATTATAAAA
1 TATATTATT-TTTAATTAT-AAA
2595938 TATAT
1 TATAT
2595943 AAATATATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
20 11 0.19
21 11 0.19
22 8 0.14
23 21 0.36
24 7 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATTATTTTTAATTATAAA
Found at i:2595928 original size:41 final size:46
Alignment explanation
Indices: 2595840--2595931 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 46
2595830 TCTCGTTGGA
*
2595840 TAATTTAATTTATATTAATTTAAATTAAAATATAATATTTTTAATT
1 TAATTTAATTTATATTAATTTAAATTAAAATATAATATTATTAATT
*
2595886 TAATTTAA-TT-TATT-ATTTTAATTAATAA-AT-ATATTATT-ATT
1 TAATTTAATTTATATTAATTTAAATTAA-AATATAATATTATTAATT
2595927 TAATT
1 TAATT
2595932 ATAAAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
41 8 0.19
42 7 0.16
43 12 0.28
44 6 0.14
45 2 0.05
46 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (46 bp):
TAATTTAATTTATATTAATTTAAATTAAAATATAATATTATTAATT
Found at i:2595945 original size:31 final size:29
Alignment explanation
Indices: 2595908--2595974 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
2595898 TTATTTTAAT
*
2595908 TAATAAATATATTATTATTTAAT-TATAAAA
1 TAATAAATATA-TAATATTTAATAT-TAAAA
*
2595938 TATATAAATATATAATATTTTATATTAAAA
1 TA-ATAAATATATAATATTTAATATTAAAA
2595968 TAATAAA
1 TAATAAA
2595975 ATAAGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATAAATATATAATATTTAATATTAAAA
Found at i:2595953 original size:23 final size:23
Alignment explanation
Indices: 2595904--2595953 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2595894 TTTATTATTT
* * *
2595904 TAATTAATAAATATATTATTATT
1 TAATTAATAAATATATAAATATA
2595927 TAATT-ATAAAATATATAAATATA
1 TAATTAAT-AAATATATAAATATA
2595950 TAAT
1 TAAT
2595954 ATTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTAATAAATATATAAATATA
Found at i:2596574 original size:20 final size:20
Alignment explanation
Indices: 2596537--2596574 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2596527 TTTTATATAA
*
2596537 ATTATATTTTTTAATTTAAT
1 ATTATATTTTATAATTTAAT
*
2596557 ATTATATTTTATATTTTA
1 ATTATATTTTATAATTTA
2596575 TTCATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATATTTTATAATTTAAT
Found at i:2596585 original size:27 final size:27
Alignment explanation
Indices: 2596538--2596589 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2596528 TTTATATAAA
*
2596538 TTATATTTTTTAATTTAATATTATATT
1 TTATATTTTTTAATATAATATTATATT
*
2596565 TTATATTTTATTCATAT-ATATTATA
1 TTATATTTT-TTAATATAATATTATA
2596590 GATGTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATATTTTTTAATATAATATTATATT
Found at i:2605366 original size:39 final size:40
Alignment explanation
Indices: 2605267--2605366 Score: 93
Period size: 39 Copynumber: 2.6 Consensus size: 40
2605257 TTTCTCTTTT
2605267 ATTTTATTATTTAAAGTAAT-ATTAAAAATTAAAAAATTA
1 ATTTTATTATTTAAAGTAATAATTAAAAATTAAAAAATTA
* * * **
2605306 AGTTTA-TA-TTAATATTTATAATTATAATTTTAAAAAA-TA
1 ATTTTATTATTTAA-AGTAATAATTA-AAAATTAAAAAATTA
*
2605345 TTTTTATTATTTAAA-TAATAAT
1 ATTTTATTATTTAAAGTAATAAT
2605367 AATTGAAGCT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
37 4 0.08
38 6 0.12
39 21 0.44
40 13 0.27
41 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (40 bp):
ATTTTATTATTTAAAGTAATAATTAAAAATTAAAAAATTA
Found at i:2606012 original size:2 final size:2
Alignment explanation
Indices: 2606005--2606030 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2605995 ATTAATCAAC
2606005 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
2606031 TCACTTGCTT
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:2606629 original size:2 final size:2
Alignment explanation
Indices: 2606622--2606656 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2606612 ATAACTCTAA
*
2606622 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2606657 TATCCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2606660 original size:8 final size:9
Alignment explanation
Indices: 2606622--2606660 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
2606612 ATAACTCTAA
2606622 ATATAT-AT
1 ATATATCAT
2606630 ATATA-CAT
1 ATATATCAT
2606638 ATATAT-AT
1 ATATATCAT
2606646 ATATATCAT
1 ATATATCAT
2606655 AT-TATC
1 ATATATC
2606661 CTAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 24 0.86
9 4 0.14
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATATCAT
Found at i:2606750 original size:31 final size:31
Alignment explanation
Indices: 2606709--2606770 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 31
2606699 AAACTTTCAA
*
2606709 TAGATGATTTTG-AAAATATTTTTCTATTATT
1 TAGATAATTTTGTAAAATATTTTTC-ATTATT
2606740 TAGATAATTTTGTTTAAAATATTTTTCATTA
1 TAGATAATTTTG--TAAAATATTTTTCATTA
2606771 CTTGACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 11 0.41
33 4 0.15
34 12 0.44
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
TAGATAATTTTGTAAAATATTTTTCATTATT
Found at i:2607167 original size:21 final size:22
Alignment explanation
Indices: 2607125--2607168 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2607115 ATTTTTAAAA
* *
2607125 TATATATATATATATAATATTT
1 TATATATACATATATAAAATTT
*
2607147 TATAT-TACATATTTAAAATTT
1 TATATATACATATATAAAATTT
2607168 T
1 T
2607169 TTATGACAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATATACATATATAAAATTT
Found at i:2607572 original size:26 final size:27
Alignment explanation
Indices: 2607535--2607586 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2607525 TAGAAATGAA
2607535 ATAAAAATATAAT-TAAAATATAATATT
1 ATAAAAATATAATAT-AAATATAATATT
*
2607562 ATAAAAA-ATAATATAAATATCATAT
1 ATAAAAATATAATATAAATATAATAT
2607587 AAATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAAAAATATAATATAAATATAATATT
Found at i:2607624 original size:27 final size:27
Alignment explanation
Indices: 2607583--2607682 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 27
2607573 TATAAATATC
2607583 ATATAAATATATAAATTATTTTAAAATTT
1 ATAT-AATATATAAA-TATTTTAAAATTT
*
2607612 ATATAATAT-TAAATATATTAAAATTT
1 ATATAATATATAAATATTTTAAAATTT
*
2607638 ATAT-ATATAAAAAATATTTT-AAATTT
1 ATATAATAT-ATAAATATTTTAAAATTT
*
2607664 AAATATAATACATAAATAT
1 --ATATAATATATAAATAT
2607683 AATATAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
25 4 0.07
26 22 0.36
27 12 0.20
28 16 0.26
29 7 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAATATATAAATATTTTAAAATTT
Done.