Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 5 of 20
Found at i:769515 original size:2 final size:2
Alignment explanation
Indices: 769508--769533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
769498 TTTATAATTA
769508 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
769534 TTCCTTCATT
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:770186 original size:22 final size:24
Alignment explanation
Indices: 770141--770191 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
770131 CATATATAAA
* *
770141 TATATATTTTATATGAATATTTTT
1 TATATATTTAAAATGAATATTTTT
770165 TATATATTTAAAAT-AATA-TTTT
1 TATATATTTAAAATGAATATTTTT
770187 TATAT
1 TATAT
770192 TTATATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATATATTTAAAATGAATATTTTT
Found at i:770207 original size:24 final size:24
Alignment explanation
Indices: 770156--770211 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
770146 ATTTTATATG
*
770156 AATATTTTT-TATATATTTAAAAT
1 AATATTTTTATATATATTCAAAAT
*
770179 AATATTTTTATATTTATATCAAAAT
1 AATATTTTTATATATAT-TCAAAAT
770204 ATATATTT
1 A-ATATTT
770212 AATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 6 0.21
25 7 0.25
26 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATTTTTATATATATTCAAAAT
Found at i:770581 original size:2 final size:2
Alignment explanation
Indices: 770576--770603 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
770566 TCTCTTAGTT
770576 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
770604 CACACCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:773954 original size:2 final size:2
Alignment explanation
Indices: 773947--773989 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
773937 ACTCTATTAA
* * *
773947 AT AT AT AT AT AT AT AT AT GT AT AT AT TT AT AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
773988 AT
1 AT
773990 TGATACTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:791207 original size:2 final size:2
Alignment explanation
Indices: 791190--791226 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
791180 ATCGAAAACA
791190 CT CT C- CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
791227 GCGTTTGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:794849 original size:24 final size:23
Alignment explanation
Indices: 794808--794862 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 23
794798 AGTTTGAGTC
794808 TTTTATTATATAAAATTT-AAAA
1 TTTTATTATATAAAATTTAAAAA
794830 -TTTATTACTATAAGATATTTAAAAA
1 TTTTATTA-TATAA-A-ATTTAAAAA
794855 TTTTATTA
1 TTTTATTA
794863 ACATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 7 0.25
22 5 0.18
23 1 0.04
24 4 0.14
25 4 0.14
26 7 0.25
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTATTATATAAAATTTAAAAA
Found at i:794870 original size:19 final size:19
Alignment explanation
Indices: 794846--794900 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
794836 ACTATAAGAT
794846 ATTTAAAAATTTTATTAAC-
1 ATTTAAAAATTTT-TTAACA
*
794865 ATTTAAATATTTTTTAACA
1 ATTTAAAAATTTTTTAACA
*
794884 ACTTTCAAAATTTTTTA
1 A-TTTAAAAATTTTTTA
794901 TTTGTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAAAAATTTTTTAACA
Found at i:794896 original size:20 final size:17
Alignment explanation
Indices: 794846--794900 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 17
794836 ACTATAAGAT
794846 ATTTAAAAATTTTATTAAC
1 ATTT-AAAATTTT-TTAAC
794865 ATTTAAATATTTTTTAAC
1 ATTTAAA-ATTTTTTAAC
794883 AACTTTCAAAATTTTTTA
1 -A-TTT-AAAATTTTTTA
794901 TTTGTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.25
19 10 0.31
20 11 0.34
21 3 0.09
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAAATTTTTTAAC
Found at i:796267 original size:29 final size:30
Alignment explanation
Indices: 796211--796267 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
796201 GCTAAGGTTT
796211 ATTTAATTATAAATTAATTAAAAATTAAAA
1 ATTTAATTATAAATTAATTAAAAATTAAAA
*
796241 ATTT-ATT-TAAATTAAATTAAAAGTTAA
1 ATTTAATTATAAATT-AATTAAAAATTAA
796268 TGATTGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 15 0.60
30 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
ATTTAATTATAAATTAATTAAAAATTAAAA
Found at i:796277 original size:29 final size:28
Alignment explanation
Indices: 796220--796277 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
796210 TATTTAATTA
*
796220 TAAATTAATTAAAAATTAAAAATTTATT
1 TAAATTAATTAAAAATTAAAAATTGATT
* **
796248 TAAATTAAATTAAAAGTTAATGATTGATT
1 TAAATT-AATTAAAAATTAAAAATTGATT
796277 T
1 T
796278 TCATTCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
TAAATTAATTAAAAATTAAAAATTGATT
Found at i:796852 original size:19 final size:20
Alignment explanation
Indices: 796811--796859 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
796801 TGAACATAAA
*
796811 TTAAATTTT--TAATTATTT
1 TTAAATTTTAATAATTATAT
796829 TTAAATTTTAATAATTA-AT
1 TTAAATTTTAATAATTATAT
796848 TTAAATTTTAAT
1 TTAAATTTTAAT
796860 TAAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAAATTTTAATAATTATAT
Found at i:796861 original size:16 final size:17
Alignment explanation
Indices: 796811--796872 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
796801 TGAACATAAA
*
796811 TTAAATTTTTAATTATTT
1 TTAAATTTTTAATTA-AT
796829 TTAAATTTTAATAATTAAT
1 TTAAATTTT--TAATTAAT
*
796848 TTAAA-TTTTAATTAAA
1 TTAAATTTTTAATTAAT
*
796864 TAAAATTTT
1 TTAAATTTT
796873 ATTACTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 11 0.29
17 3 0.08
18 12 0.32
19 6 0.16
20 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTTTAATTAAT
Found at i:796873 original size:16 final size:16
Alignment explanation
Indices: 796840--796873 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
796830 TAAATTTTAA
* *
796840 TAATTAATTTAAATTT
1 TAATTAAATAAAATTT
796856 TAATTAAATAAAATTT
1 TAATTAAATAAAATTT
796872 TA
1 TA
796874 TTACTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAAATAAAATTT
Found at i:797323 original size:17 final size:17
Alignment explanation
Indices: 797301--797351 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
797291 ACATTTTAAA
797301 ATATAAAAAAATAAATT
1 ATATAAAAAAATAAATT
797318 ATATAAAATATAA-AAA-T
1 ATATAAAA-A-AATAAATT
*
797335 A-ATTAAAAAATAAATT
1 ATATAAAAAAATAAATT
797351 A
1 A
797352 AAAAAATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.07
15 4 0.14
16 7 0.24
17 10 0.34
18 4 0.14
19 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATAAAAAAATAAATT
Found at i:797347 original size:24 final size:24
Alignment explanation
Indices: 797297--797358 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
797287 TATTACATTT
*
797297 TAAAATATAAAAA-AATAAATTATA
1 TAAAATATAAAAATAATAAA-TAAA
797321 TAAAATATAAAAATAATTAAA-AAA
1 TAAAATATAAAAATAA-TAAATAAA
* *
797345 TAAATTAAAAAAAT
1 TAAAATATAAAAAT
797359 TGAGTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 27 0.82
25 2 0.06
26 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAATATAAAAATAATAAATAAA
Found at i:797689 original size:19 final size:20
Alignment explanation
Indices: 797660--797697 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
797650 GATTTAATTT
797660 ATTTAAATTAAATTTAAATA
1 ATTTAAATTAAATTTAAATA
797680 ATTT-AATTAAATTTAAAT
1 ATTTAAATTAAATTTAAAT
797698 TATTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAAATTAAATTTAAATA
Found at i:797765 original size:37 final size:40
Alignment explanation
Indices: 797686--797766 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 40
797676 AATAATTTAA
* *
797686 TTAAATTTAAATTATTATTTAATAATAAAATTTATTTTTAT
1 TTAAATTTAAATTATTA-TAAATAATAAAATTTATTTATAT
797727 TTAAATTT-AATTATTA-AAAT-ATAAAATATTA-TTATAT
1 TTAAATTTAAATTATTATAAATAATAAAAT-TTATTTATAT
797764 TTA
1 TTA
797767 TTATAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 15 0.41
38 6 0.16
40 8 0.22
41 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (40 bp):
TTAAATTTAAATTATTATAAATAATAAAATTTATTTATAT
Found at i:797768 original size:41 final size:40
Alignment explanation
Indices: 797680--797761 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 40
797670 AATTTAAATA
* *
797680 ATTTAATTAAATTTAAATTATTATTTAATAATAAAATTTATT
1 ATTTATTTAAATTT-AATTATTA-TAAATAATAAAATTTATT
797722 -TTTATTTAAATTTAATTATTA-AAAT-ATAAAATATTATT
1 ATTTATTTAAATTTAATTATTATAAATAATAAAAT-TTATT
797760 AT
1 AT
797762 ATTTATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
37 7 0.19
38 8 0.22
39 1 0.03
40 8 0.22
41 12 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
ATTTATTTAAATTTAATTATTATAAATAATAAAATTTATT
Found at i:804772 original size:2 final size:2
Alignment explanation
Indices: 804765--804791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
804755 CACCACGCAT
804765 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
804792 AAAACGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:806952 original size:36 final size:37
Alignment explanation
Indices: 806905--806976 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
806895 CATGATGATT
* *
806905 TTTTTTAATGTTTAAA-TTTTGGAATT-AATAATAATG
1 TTTTTTAATG-TTAAAGTTTTGAAATTCAAAAATAATG
*
806941 TTTTTTCATGTTAAAGTTTTGAAATTCAAAAATAAT
1 TTTTTTAATGTTAAAGTTTTGAAATTCAAAAATAAT
806977 TTTACAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.16
36 18 0.58
37 8 0.26
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (37 bp):
TTTTTTAATGTTAAAGTTTTGAAATTCAAAAATAATG
Found at i:814171 original size:33 final size:33
Alignment explanation
Indices: 814134--814200 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
814124 TTCAATGATT
814134 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
814167 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
814200 T
1 T
814201 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:814172 original size:13 final size:13
Alignment explanation
Indices: 814154--814178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
814144 CATAAAATGT
814154 TGTATCGATACAA
1 TGTATCGATACAA
814167 TGTATCGATACA
1 TGTATCGATACA
814179 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:814259 original size:13 final size:13
Alignment explanation
Indices: 814241--814265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
814231 ATTACTCAAA
814241 TGTATCGATACAT
1 TGTATCGATACAT
814254 TGTATCGATACA
1 TGTATCGATACA
814266 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:814330 original size:52 final size:52
Alignment explanation
Indices: 814274--814393 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
814264 CACTGATCTT
*
814274 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
814326 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
814378 TGTATCGATACATGCA
1 TGTATCGATACATGCA
814394 AACAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:819466 original size:2 final size:2
Alignment explanation
Indices: 819461--819493 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
819451 AACACCAATA
*
819461 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
819494 AACTGTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:820939 original size:31 final size:30
Alignment explanation
Indices: 820897--820982 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 30
820887 AATAAGTAAT
* **
820897 TTAAATTTATTTATATTATATTTTTAATTT
1 TTAAATATATTTATATTATATTTTTAATAA
*
820927 TTAAAATATATTTTAAATT-TAATTTTTAATAA
1 TT-AAATATA-TTTATATTAT-ATTTTTAATAA
*
820959 TTAAATATATTTTTATTA-ATTTTT
1 TTAAATATATTTATATTATATTTTT
820983 TTTGTTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
29 6 0.13
30 8 0.17
31 14 0.30
32 18 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTAAATATATTTATATTATATTTTTAATAA
Found at i:820984 original size:31 final size:30
Alignment explanation
Indices: 820897--820983 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
820887 AATAAGTAAT
* * **
820897 TTAAATTTATTTATATT-ATATTTTTAATTT
1 TTAAATATATTTTTATTAAT-TTTTTAATAA
*
820927 TTAAAATATATTTTAAATTTAA-TTTTTAATAA
1 TT-AAATATATTTT-TA-TTAATTTTTTAATAA
820959 TTAAATATATTTTTATTAATTTTTT
1 TTAAATATATTTTTATTAATTTTTT
820984 TTGTTAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
29 4 0.09
30 8 0.17
31 20 0.43
32 11 0.24
33 2 0.04
34 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTAAATATATTTTTATTAATTTTTTAATAA
Found at i:821665 original size:3 final size:3
Alignment explanation
Indices: 821659--821700 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
821649 TTTTAATTAT
*
821659 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
821701 CAACAATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:822753 original size:20 final size:21
Alignment explanation
Indices: 822730--822779 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
822720 TTTTTATTTT
822730 TATTTAAATTTAATTATA-AA
1 TATTTAAATTTAATTATATAA
* * *
822750 TATTAAAAGTTAATTTTATAA
1 TATTTAAATTTAATTATATAA
*
822771 TTTTTAAAT
1 TATTTAAAT
822780 AATAAAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTAAATTTAATTATATAA
Found at i:823108 original size:20 final size:19
Alignment explanation
Indices: 823068--823108 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
823058 TATTTTTATT
*
823068 ATATTTTATTATATTTAAA
1 ATATTTTATTATATATAAA
*
823087 ATATTTTATATTTATATAAA
1 ATATTTTAT-TATATATAAA
823107 AT
1 AT
823109 TTATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTATTATATATAAA
Found at i:824861 original size:2 final size:2
Alignment explanation
Indices: 824856--824889 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
824846 ATATATATAT
824856 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
824890 TGAGCAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:827087 original size:15 final size:16
Alignment explanation
Indices: 827049--827089 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
827039 TTTATGGTTA
827049 AAAATTTTA-AATATT
1 AAAATTTTATAATATT
827064 AATAA-TTTATAAT-TT
1 AA-AATTTTATAATATT
827079 AAAATTTTATA
1 AAAATTTTATA
827090 TTTGCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTTATAATATT
Found at i:827306 original size:25 final size:25
Alignment explanation
Indices: 827270--827350 Score: 119
Period size: 25 Copynumber: 3.2 Consensus size: 25
827260 TATATTTATC
*
827270 AACATATGTATTAATATAAAAAA-A
1 AACATTTGTATTAATATAAAAAATA
827294 AAGCATTTGTATTAATATAAAAAATA
1 AA-CATTTGTATTAATATAAAAAATA
**
827320 AACATACGTATTAATATAAAAAATA
1 AACATTTGTATTAATATAAAAAATA
827345 AACATT
1 AACATT
827351 GACAACAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
24 2 0.04
25 46 0.90
26 3 0.06
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (25 bp):
AACATTTGTATTAATATAAAAAATA
Found at i:827770 original size:29 final size:26
Alignment explanation
Indices: 827722--827774 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
827712 TAAGAAATTA
*
827722 AATATTATATAAATATAAAATATATT
1 AATATTATATAAATACAAAATATATT
827748 AATATTATTATAATATAACAAAATATA
1 AATATTA-TATAA-AT-ACAAAATATA
827775 CCAACATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 5 0.22
28 2 0.09
29 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATTATATAAATACAAAATATATT
Found at i:833315 original size:15 final size:16
Alignment explanation
Indices: 833295--833327 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
833285 TATTATAAAA
833295 AATTATG-ACAAAATT
1 AATTATGTACAAAATT
*
833310 AATTATGTATAAAATT
1 AATTATGTACAAAATT
833326 AA
1 AA
833328 CACTTACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (16 bp):
AATTATGTACAAAATT
Found at i:840106 original size:2 final size:2
Alignment explanation
Indices: 840099--840145 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
840089 AATATGAGTA
840099 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
840141 AG AG A
1 AG AG A
840146 TTGAAAGACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:841750 original size:3 final size:3
Alignment explanation
Indices: 841742--841767 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
841732 CATAAAGTGC
841742 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
841768 ACATATCTTT
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:843577 original size:28 final size:29
Alignment explanation
Indices: 843536--843600 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
843526 TTTACGTGAT
*
843536 AAAATAAAAGTA-TTTAGATAAATTATTT-
1 AAAATTAAAGTATTTTA-ATAAATTATTTA
* * *
843564 TAAATTAAATTATTTTAATAATTTATTTA
1 AAAATTAAAGTATTTTAATAAATTATTTA
843593 AAAATTAA
1 AAAATTAA
843601 GGGTAGGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
AAAATTAAAGTATTTTAATAAATTATTTA
Found at i:845202 original size:18 final size:19
Alignment explanation
Indices: 845179--845216 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
845169 ATGATTATAA
*
845179 AATAATAAAT-TTTATTAT
1 AATAATAAATATTAATTAT
845197 AATAATAAATATTAATTAT
1 AATAATAAATATTAATTAT
845216 A
1 A
845217 TACATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAATAAATATTAATTAT
Found at i:845234 original size:29 final size:27
Alignment explanation
Indices: 845201--845270 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
845191 TATTATAATA
*
845201 ATAAATATTAATTATATACATAAAAAATT
1 ATAAATATTAATTATA-AAAT-AAAAATT
* *
845230 ATAAAAATTATTTATAAAATAAAAATT
1 ATAAATATTAATTATAAAATAAAAATT
845257 AT-AATATTATATTA
1 ATAAATATTA-ATTA
845271 CCATCATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.17
27 12 0.34
28 3 0.09
29 14 0.40
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAAATATTAATTATAAAATAAAAATT
Found at i:852382 original size:2 final size:2
Alignment explanation
Indices: 852375--852401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
852365 TTAAACAAAG
852375 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
852402 GTACTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:854423 original size:26 final size:26
Alignment explanation
Indices: 854392--854479 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 26
854382 TTATAATTAT
*
854392 ATTTAAAATATTATATTTTTTTATAA
1 ATTTAATATATTATATTTTTTTATAA
854418 ATTTAATATATTAATAATTTATATTATATAA
1 ATTTAATATATT-AT-ATTT-T-TT-TATAA
* * *
854449 ATTTTAATATATT-TATATATTTATAT
1 A-TTTAATATATTATATTTTTTTATAA
854475 ATTTA
1 ATTTA
854480 TTTTTATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.08
26 16 0.31
27 4 0.08
28 4 0.08
29 4 0.08
30 3 0.06
31 6 0.12
32 11 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTAATATATTATATTTTTTTATAA
Found at i:854459 original size:32 final size:32
Alignment explanation
Indices: 854413--854474 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
854403 TATATTTTTT
854413 TATAAATTTAATATATTAATA-ATTTATATTA
1 TATAAATTTAATATATTAATATATTTATATTA
*
854444 TATAAATTTTAATATATTTATATATTTATAT
1 TATAAA-TTTAATATATTAATATATTTATAT
854475 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 6 0.21
32 14 0.50
33 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATAAATTTAATATATTAATATATTTATATTA
Found at i:854478 original size:8 final size:8
Alignment explanation
Indices: 854411--854497 Score: 65
Period size: 8 Copynumber: 10.8 Consensus size: 8
854401 ATTATATTTT
*
854411 TTTATAAA
1 TTTATATA
854419 TTTAATATA
1 TTT-ATATA
*
854428 TTAATA-A
1 TTTATATA
854435 TTTATAT-
1 TTTATATA
* *
854442 TATATAAA
1 TTTATATA
854450 TTTTAATATA
1 -TTT-ATATA
854460 TTTATATA
1 TTTATATA
854468 TTTATATA
1 TTTATATA
854476 TTTAT-T-
1 TTTATATA
854482 TTTATTATTA
1 TTTA-TA-TA
854492 TTTATA
1 TTTATA
854498 ACATATTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
6 4 0.06
7 13 0.21
8 24 0.38
9 14 0.22
10 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTATATA
Found at i:854478 original size:16 final size:16
Alignment explanation
Indices: 854389--854480 Score: 73
Period size: 16 Copynumber: 5.6 Consensus size: 16
854379 AAATTATAAT
854389 TATATTTA-AAATATTA
1 TATATTTATAAAT-TTA
*
854405 TATTTTTTTATAAATTTAA
1 TA--TATTTATAAATTT-A
*
854424 TATATTAAT-AATTTA
1 TATATTTATAAATTTA
*
854439 TAT-TATATAAATTTTAA
1 TATATTTATAAA-TTT-A
*
854456 TATATTTATATATTTA
1 TATATTTATAAATTTA
854472 TATATTTAT
1 TATATTTAT
854481 TTTTATTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 20 0.33
17 12 0.20
18 13 0.21
19 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTATAAATTTA
Found at i:854773 original size:3 final size:3
Alignment explanation
Indices: 854765--854800 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
854755 TGAATAAACT
854765 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
854801 TTTGTCACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:862002 original size:17 final size:16
Alignment explanation
Indices: 861971--862001 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
861961 TAAATGATTT
*
861971 TTTTTAATAATTTTTC
1 TTTTTAACAATTTTTC
861987 TTTTTAACAATTTTT
1 TTTTTAACAATTTTT
862002 TACGAATTGA
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:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAACAATTTTTC
Found at i:864417 original size:20 final size:20
Alignment explanation
Indices: 864339--864419 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 20
864329 AGATCAAACA
* *
864339 ATTTATAT-AGTTTTTATAT
1 ATTTATATAAATTTTAATAT
*
864358 ATTT-TATAATATTATAAT-T
1 ATTTATATAA-ATTTTAATAT
* *
864377 ATTTATTTAAAAAATTT--TAT
1 ATTTA--TATAAATTTTAATAT
864397 ATTTATATAAATTTTAATAT
1 ATTTATATAAATTTTAATAT
864417 ATT
1 ATT
864420 AATAATTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
18 11 0.24
19 11 0.24
20 17 0.37
21 3 0.07
22 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
ATTTATATAAATTTTAATAT
Found at i:864424 original size:18 final size:16
Alignment explanation
Indices: 864380--864424 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
864370 TATAATTATT
*
864380 TATTTAAAAAATTTTA
1 TATTTAATAAATTTTA
864396 TATTTATATAAATTTTAA
1 TATTTA-ATAAATTTT-A
864414 TATATTAATAA
1 TAT-TTAATAA
864425 TTTATACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 8 0.32
19 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTAATAAATTTTA
Found at i:866389 original size:24 final size:24
Alignment explanation
Indices: 866337--866390 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
866327 ATTTAATTTG
*
866337 AATTATTATTTAAATAATAAAAAA
1 AATTTTTATTTAAATAATAAAAAA
* *
866361 TATTTTTATTTAAAT-TTAAATAAA
1 AATTTTTATTTAAATAATAAA-AAA
866385 AATTTT
1 AATTTT
866391 GATATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTTTTATTTAAATAATAAAAAA
Found at i:867116 original size:15 final size:16
Alignment explanation
Indices: 867096--867129 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
867086 TTAATAGAAT
*
867096 AATATTATTAT-ATAA
1 AATATTAATATGATAA
867111 AATATTAATATGATAA
1 AATATTAATATGATAA
867127 AAT
1 AAT
867130 TGATCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATTAATATGATAA
Found at i:873507 original size:82 final size:82
Alignment explanation
Indices: 873375--873529 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 82
873365 TTCCTATTTA
** *
873375 AAATGAAAAGAAATTCTTGATTTTCACTGTCAAGCCTTTATGAACAGCCCTTCAGCATACATCAC
1 AAATGAAAAGAAATTCTTGATTTTCACAATCAAACCTTTATGAACAGCCCTTCAGCATACATCAC
873440 AAAGCAAATCCTACTAT
66 AAAGCAAATCCTACTAT
* * * ** *
873457 AAATGAAAGGAAATTCTTGATTTTTACAATCAAACCTTTATGGAA-GGCCCTTGGGCATCCATCA
1 AAATGAAAAGAAATTCTTGATTTTCACAATCAAACCTTTAT-GAACAGCCCTTCAGCATACATCA
873521 CAAAGCAAA
65 CAAAGCAAA
873530 AGATCTCCGC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
82 60 0.95
83 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (82 bp):
AAATGAAAAGAAATTCTTGATTTTCACAATCAAACCTTTATGAACAGCCCTTCAGCATACATCAC
AAAGCAAATCCTACTAT
Found at i:874685 original size:21 final size:21
Alignment explanation
Indices: 874661--874707 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
874651 AACTATAGGG
874661 CTTCCAAATAGAACTAATTTA
1 CTTCCAAATAGAACTAATTTA
*
874682 CTTCCAAATAGATCTAATTTA
1 CTTCCAAATAGAACTAATTTA
874703 CTTCC
1 CTTCC
874708 CATGAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (21 bp):
CTTCCAAATAGAACTAATTTA
Found at i:878215 original size:25 final size:24
Alignment explanation
Indices: 878183--878245 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
878173 TATATTTCGG
*
878183 TTAATTTTTTAT-A-TTTATTTTAA
1 TTAATTTTTTTTAATTTTA-TTTAA
878206 TTAATTTTTTTTAATTTTATTTAA
1 TTAATTTTTTTTAATTTTATTTAA
*
878230 TTTATTTAATTTTTAA
1 TTAATTT--TTTTTAA
878246 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 11 0.32
24 12 0.35
25 4 0.12
26 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTAATTTTTTTTAATTTTATTTAA
Found at i:878218 original size:19 final size:19
Alignment explanation
Indices: 878190--878242 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
878180 CGGTTAATTT
878190 TTTATATTTATTTTAATTAA
1 TTTAT-TTTATTTTAATTAA
* *
878210 TTTTTTTTAATTTTATTTAA
1 TTTATTTT-ATTTTAATTAA
*
878230 TTTATTTAATTTT
1 TTTATTTTATTTT
878243 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTATTTTAATTAA
Found at i:878219 original size:10 final size:10
Alignment explanation
Indices: 878183--878243 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
878173 TATATTTCGG
878183 TTAATTTTTT
1 TTAATTTTTT
* *
878193 ATATTTATTTT
1 TTAATT-TTTT
878204 AATTAATTTTTT
1 --TTAATTTTTT
*
878216 TTAATTTTAT
1 TTAATTTTTT
*
878226 TTAA-TTTAT
1 TTAATTTTTT
878235 TTAATTTTT
1 TTAATTTTT
878244 AAAATTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
9 9 0.22
10 20 0.49
11 4 0.10
12 4 0.10
13 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTAATTTTTT
Found at i:878233 original size:9 final size:9
Alignment explanation
Indices: 878194--878241 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
878184 TAATTTTTTA
*
878194 TATTTATTT
1 TATTTAATT
*
878203 TAATTAATTT
1 TATTTAA-TT
*
878213 TTTTTAATTT
1 TATTTAA-TT
878223 TATTTAATT
1 TATTTAATT
878232 TATTTAATT
1 TATTTAATT
878241 T
1 T
878242 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TATTTAATT
Found at i:878244 original size:20 final size:20
Alignment explanation
Indices: 878194--878242 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
878184 TAATTTTTTA
878194 TATTT-ATTTTAATTAATTT
1 TATTTAATTTTAATTAATTT
* *
878213 TTTTTAATTTTATTTAA-TT
1 TATTTAATTTTAATTAATTT
878232 TATTTAATTTT
1 TATTTAATTTT
878243 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTAATTTTAATTAATTT
Found at i:878729 original size:11 final size:11
Alignment explanation
Indices: 878710--878766 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
878700 CTCCTTTTCA
878710 TTTTT-TTTAT
1 TTTTTATTTAT
878720 TTTTTATTTAT
1 TTTTTATTTAT
* *
878731 TTTTAATGTA-
1 TTTTTATTTAT
*
878741 TTTATATTTAT
1 TTTTTATTTAT
*
878752 ATTTTATTTAT
1 TTTTTATTTAT
878763 TTTT
1 TTTT
878767 AATATAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
10 12 0.32
11 25 0.68
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:878763 original size:21 final size:21
Alignment explanation
Indices: 878709--878764 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
878699 ACTCCTTTTC
* *
878709 ATTTTTTTTATTTTTTATTTAT
1 ATTTTATTTA-TTTATATTTAT
*
878731 -TTTTAATGTATTTATATTTAT
1 ATTTT-ATTTATTTATATTTAT
878752 ATTTTATTTATTT
1 ATTTTATTTATTT
878765 TTAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
ATTTTATTTATTTATATTTAT
Found at i:878914 original size:24 final size:24
Alignment explanation
Indices: 878853--878920 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
878843 TTTAATTTTA
*
878853 ATAACTTAT-TTTTATT-ATAAAT
1 ATAATTTATATTTTATTAATAAAT
*
878875 ATATTTTTTAATTATTTTATTAATAAAT
1 ATA--ATTT-A-TATTTTATTAATAAAT
878903 ATAATTTATATTTTATTA
1 ATAATTTATATTTTATTA
878921 TCTAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
22 3 0.08
24 12 0.32
25 2 0.05
26 4 0.11
27 7 0.19
28 9 0.24
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
ATAATTTATATTTTATTAATAAAT
Found at i:878926 original size:28 final size:30
Alignment explanation
Indices: 878833--878936 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 30
878823 ATTTCATTAT
* *
878833 TTAATACAAATTTAATTTTAATAACTTA-TTT-
1 TTAATATAAATATAA-TTT-ATAA-TTATTTTA
* * *
878864 TTATTATAAATATATTTTTTAATTATTTTA
1 TTAATATAAATATAATTTATAATTATTTTA
878894 TT-A-ATAAATATAATTTAT-ATT-TTATTA
1 TTAATATAAATATAATTTATAATTATT-TTA
878921 TCTAATATAAATATAA
1 T-TAATATAAATATAA
878937 GTTTTAGTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
26 2 0.03
27 7 0.12
28 17 0.29
29 7 0.12
30 15 0.25
31 11 0.19
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAATATAAATATAATTTATAATTATTTTA
Found at i:879613 original size:14 final size:14
Alignment explanation
Indices: 879574--879616 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
879564 TATGTTTTAT
879574 ATATAGTTAAATATA
1 ATATA-TTAAATATA
**
879589 ATATAAAAAATATA
1 ATATATTAAATATA
*
879603 ATATTTTAAATATA
1 ATATATTAAATATA
879617 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATATTAAATATA
Found at i:879648 original size:21 final size:22
Alignment explanation
Indices: 879622--879662 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
879612 ATATATAAAA
879622 ATTTTATAAAA-AA-TTAAATAT
1 ATTTTA-AAAAGAAGTTAAATAT
879643 ATTTTAAAAAGAAGTTAAAT
1 ATTTTAAAAAGAAGTTAAAT
879663 TTGATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
ATTTTAAAAAGAAGTTAAATAT
Found at i:880848 original size:32 final size:33
Alignment explanation
Indices: 880803--880878 Score: 111
Period size: 32 Copynumber: 2.3 Consensus size: 33
880793 TATAAGAATG
880803 ATATAAATATATTAATAT-GTAATAATTTATATA
1 ATATAAATATATTAATATAGTAA-AATTTATATA
*
880836 ATATAAAT-TATTAATATATTAAAATTTATATA
1 ATATAAATATATTAATATAGTAAAATTTATATA
880868 ATATATAATAT
1 ATATA-AATAT
880879 TTTTAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 24 0.62
33 14 0.36
34 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATATAAATATATTAATATAGTAAAATTTATATA
Found at i:880891 original size:30 final size:31
Alignment explanation
Indices: 880803--880891 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 31
880793 TATAAGAATG
*
880803 ATATAAATATATTA-ATATGTAATAATTTATATA
1 ATATAAAT-TATTATATA-ATAA-AATTTATATA
*
880836 ATATAAATTATTAATATATTAAAATTTATATA
1 ATATAAATTATT-ATATAATAAAATTTATATA
*
880868 ATATATAA-TATT-TTTAATAAAATT
1 ATATA-AATTATTATATAATAAAATT
880892 ATCTATATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
30 10 0.20
32 23 0.46
33 14 0.28
34 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
ATATAAATTATTATATAATAAAATTTATATA
Found at i:880931 original size:21 final size:21
Alignment explanation
Indices: 880862--880931 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 21
880852 TATTAAAATT
880862 TATATAATATATAATATTTTTAA
1 TATA-AATATATAA-ATTTTTAA
* ** *
880885 TAAAATTATCTATATAAAAATATAA
1 TATAA--A--TATATAAATTTTTAA
880910 TATAAATATATAAATTTTTAA
1 TATAAATATATAAATTTTTAA
880931 T
1 T
880932 TATCAAGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
21 13 0.37
22 1 0.03
23 4 0.11
24 1 0.03
25 9 0.26
26 7 0.20
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAAATATATAAATTTTTAA
Found at i:881389 original size:7 final size:7
Alignment explanation
Indices: 881374--881408 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
881364 AATAATAAAA
881374 AAATTTT
1 AAATTTT
*
881381 AAATATT
1 AAATTTT
881388 AAATTTT
1 AAATTTT
881395 AAATTTT
1 AAATTTT
881402 -AATTTT
1 AAATTTT
881408 A
1 A
881409 CTGAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:882732 original size:24 final size:24
Alignment explanation
Indices: 882705--882792 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
882695 AAAAATTAGT
* *
882705 CACCAATTTTGACAAATAACAAAT
1 CACCAATTTTGACAAACAACAAAC
*
882729 CACCAATTTTGACAAACAACAAGC
1 CACCAATTTTGACAAACAACAAAC
* *
882753 CACCATTTTTGACAAACAACAAGC
1 CACCAATTTTGACAAACAACAAAC
*
882777 CACCATTTTTGACAAA
1 CACCAATTTTGACAAA
882793 TACAAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (24 bp):
CACCAATTTTGACAAACAACAAAC
Found at i:887343 original size:27 final size:27
Alignment explanation
Indices: 887299--887398 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
887289 ATAAATCATC
* *
887299 ATTTTTTACAAATA-AAAAAAATTACT
1 ATTTTTTACAAATACAAAATAATCACT
*
887325 ATTTTTTACAAACACAAAATAATCACT
1 ATTTTTTACAAATACAAAATAATCACT
* *
887352 ATTTTTAACAATTACAAAATAATCACT
1 ATTTTTTACAAATACAAAATAATCACT
* * *
887379 ATTTTTAATAAATAAAAAAT
1 ATTTTTTACAAATACAAAAT
887399 GTAACTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
26 13 0.20
27 51 0.80
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTTTTTACAAATACAAAATAATCACT
Found at i:888649 original size:45 final size:46
Alignment explanation
Indices: 888599--888698 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
888589 AATTTTCGTC
* *
888599 GATGAAAATAAA-TTTGACGAAATATTGCATCAAAATTAAAGTTTT
1 GATGAAAATAAATTTTAACGAAACATTGCATCAAAATTAAAGTTTT
* *
888644 GATGAAAATAAATTTTAACGAAACATTGCATCAACATTAAATTTTT
1 GATGAAAATAAATTTTAACGAAACATTGCATCAAAATTAAAGTTTT
888690 GATGAAAAT
1 GATGAAAAT
888699 TTTTTTATGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 12 0.24
46 38 0.76
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (46 bp):
GATGAAAATAAATTTTAACGAAACATTGCATCAAAATTAAAGTTTT
Found at i:894155 original size:81 final size:81
Alignment explanation
Indices: 894069--894689 Score: 927
Period size: 81 Copynumber: 7.7 Consensus size: 81
894059 CCACATCAGA
894069 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
*
894134 TGATCGCCACATTGGC
66 TGATCGCCACCTTGGC
* *
894150 ATCAATATTACCAGTGACACCAAGTCACTCTGATCCTGCTCGCTACCATGGCTTCACCCTGATCC
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
* *
894215 TCATCGCCATCTTGGC
66 TGATCGCCACCTTGGC
** * *
894231 ATCAATATTATCAGTGACACCAAGTCACTCTGATTTTACTCGCCACCATGGCTTCACCCTGATCT
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
894296 TGATCGCCACCTTGGC
66 TGATCGCCACCTTGGC
* * *
894312 ATCAATATTATCAATGTCACCAAGTCACTCTGATCTTGCTCGCCACCATGGCTTCACCCTGATCC
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
894377 TGATCGCCACCTTGGC
66 TGATCGCCACCTTGGC
* * * * ** * * ** *
894393 ATCAATATTATCAATGACACCAAGTCACTTTGATCTTGCTGGCCACTTTGGATTCGCTGTAATCC
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
*
894458 TGATCGCCACATTGGC
66 TGATCGCCACCTTGGC
* * *
894474 ATCAATATTATCAGTGACACTAAGTCACTCTGATCCAGCTCACCACCATGGCTTCACCCTGATCC
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
* *
894539 GGATTGCCACCTTGGC
66 TGATCGCCACCTTGGC
** * * *
894555 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCAACTCACCACCATGGCTTCGCCCTGATCT
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
894620 TGATCGCCACCTTGGC
66 TGATCGCCACCTTGGC
*
894636 ATCAATATTATCAGTGACACTAAGTCACTCTGATCCTGCTCGCCACCATGGCTT
1 ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTT
894690 AGCATTAATA
Statistics
Matches: 484, Mismatches: 56, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 484 1.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (81 bp):
ATCAATATTATCAGTGACACCAAGTCACTCTGATCCTGCTCGCCACCATGGCTTCACCCTGATCC
TGATCGCCACCTTGGC
Found at i:894292 original size:29 final size:29
Alignment explanation
Indices: 894270--894392 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 29
894260 CTGATTTTAC
894270 TCGCCACCATGGCTTCACCCTGATCTTGA
1 TCGCCACCATGGCTTCACCCTGATCTTGA
* * *** * *
894299 TCGCCACCTTGGCATCAATATTATC--AA
1 TCGCCACCATGGCTTCACCCTGATCTTGA
* * * *
894326 T-GTCACCA-AG--TCACTCTGATCTTGC
1 TCGCCACCATGGCTTCACCCTGATCTTGA
*
894351 TCGCCACCATGGCTTCACCCTGATCCTGA
1 TCGCCACCATGGCTTCACCCTGATCTTGA
*
894380 TCGCCACCTTGGC
1 TCGCCACCATGGC
894393 ATCAATATTA
Statistics
Matches: 67, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
23 8 0.12
25 2 0.03
26 11 0.16
27 3 0.04
29 43 0.64
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.28
Consensus pattern (29 bp):
TCGCCACCATGGCTTCACCCTGATCTTGA
Found at i:894709 original size:57 final size:57
Alignment explanation
Indices: 894634--894746 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
894624 CGCCACCTTG
* *
894634 GCATCAATATTATCAGTGACACTAAGTCACTCTGATCCTGCTCGCCACCATGGCTTA
1 GCATCAATATTATCAGTGACACCAAGTCACTATGATCCTGCTCGCCACCATGGCTTA
*
894691 GCATTAATATTATCAGTGACACCAAGTCACTATGATCCTGCTCGCCACCATGGCTT
1 GCATCAATATTATCAGTGACACCAAGTCACTATGATCCTGCTCGCCACCATGGCTT
894747 CACCCCAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (57 bp):
GCATCAATATTATCAGTGACACCAAGTCACTATGATCCTGCTCGCCACCATGGCTTA
Found at i:894833 original size:51 final size:53
Alignment explanation
Indices: 894757--894872 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 53
894747 CACCCCAATC
* *
894757 CTGATCGCCA-CATTGGCATCAATATTATCAATGACGTCAAGTCACTC-CGA-T
1 CTGATCGCCACCATTGGCACCAATATTATCAATGACGCCAAGTCAC-CGCGATT
* * * *
894808 CTGATCGCCACCA-TGGCACCAATATTATTAGTGACGCCGAGTCACCGTGATT
1 CTGATCGCCACCATTGGCACCAATATTATCAATGACGCCAAGTCACCGCGATT
894860 CTGATCGCCACCA
1 CTGATCGCCACCA
894873 AGTCACTCCG
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 39 0.70
52 16 0.29
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (53 bp):
CTGATCGCCACCATTGGCACCAATATTATCAATGACGCCAAGTCACCGCGATT
Found at i:894865 original size:138 final size:138
Alignment explanation
Indices: 894557--894852 Score: 358
Period size: 138 Copynumber: 2.2 Consensus size: 138
894547 ACCTTGGCAT
* ** *
894557 CAATATTATCAGTGACACCAAGTCAC--TCTGATCCAACTCACCACCATGGCTTCGCCCTGATCT
1 CAATATTATCAGTGACACCAAGTCACTATCTGATCCAACTCACCACCATGGCTTCACCCCAATCC
* * * *
894620 TGATCGCCACCTTGGCATCAATATTATCAGTGACACTAAGTCACTCTGATCCTGCTCGCCACCAT
66 TGATCGCCACATTGGCATCAATATTATCAATGACACTAAGTCACTCCGATCCTGATCGCCACCAT
894685 GGCTTAGCA
131 GGC-TAGCA
* ** *
894694 TTAATATTATCAGTGACACCAAGTCACTA--TGATCCTGCTCGCCACCATGGCTTCACCCCAATC
1 -CAATATTATCAGTGACACCAAGTCACTATCTGATCCAACTCACCACCATGGCTTCACCCCAATC
*
894757 CTGATCGCCACATTGGCATCAATATTATCAATGAC-GTCAAGTCACTCCGAT-CTGATCGCCACC
65 CTGATCGCCACATTGGCATCAATATTATCAATGACACT-AAGTCACTCCGATCCTGATCGCCACC
894820 ATGGC-A-C-
129 ATGGCTAGCA
* * *
894827 CAATATTATTAGTGACGCCGAGTCAC
1 CAATATTATCAGTGACACCAAGTCAC
894853 CGTGATTCTG
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
132 22 0.16
134 1 0.01
135 1 0.01
137 17 0.12
138 97 0.70
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.26
Consensus pattern (138 bp):
CAATATTATCAGTGACACCAAGTCACTATCTGATCCAACTCACCACCATGGCTTCACCCCAATCC
TGATCGCCACATTGGCATCAATATTATCAATGACACTAAGTCACTCCGATCCTGATCGCCACCAT
GGCTAGCA
Found at i:894991 original size:22 final size:22
Alignment explanation
Indices: 894966--895007 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
894956 CTATCATTAC
*
894966 AGTGACACCTAGTCACTCCAGT
1 AGTGACACCGAGTCACTCCAGT
* *
894988 AGTGACGCCGAGTCATTCCA
1 AGTGACACCGAGTCACTCCA
895008 ATTCTGCCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTGACACCGAGTCACTCCAGT
Found at i:898017 original size:15 final size:15
Alignment explanation
Indices: 897999--898041 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
897989 ATTTTTGAAT
897999 TTTAAATTAATTTAA
1 TTTAAATTAATTTAA
*
898014 TTTAAATTATTTTTAA
1 TTTAAATTA-ATTTAA
898030 -TTAAATTTAATT
1 TTTAAA-TTAATT
898042 AAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATTAATTTAA
Found at i:898026 original size:25 final size:25
Alignment explanation
Indices: 897997--898084 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 25
897987 AAATTTTTGA
897997 ATTTTAAATTAATTTAATTTAAATT
1 ATTTTAAATTAATTTAATTTAAATT
* * *
898022 ATTTTTAATTAAATTTAATTAAAAAT
1 ATTTTAAATT-AATTTAATTTAAATT
*
898048 ATTAATATATAAATAATTT--TTTAATATT
1 ATT--T-TA-AATTAATTTAATTTAA-ATT
898076 ATTTTAAAT
1 ATTTTAAAT
898085 AGTATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
24 2 0.04
25 11 0.22
26 17 0.35
27 4 0.08
28 6 0.12
29 6 0.12
30 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTTAAATTAATTTAATTTAAATT
Found at i:898028 original size:26 final size:26
Alignment explanation
Indices: 897997--898050 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
897987 AAATTTTTGA
* * *
897997 ATTTTAAATT-AATTTAATTTAAATT
1 ATTTTTAATTAAATTTAATTAAAAAT
898022 ATTTTTAATTAAATTTAATTAAAAAT
1 ATTTTTAATTAAATTTAATTAAAAAT
898048 ATT
1 ATT
898051 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTTAATTAAATTTAATTAAAAAT
Found at i:899143 original size:12 final size:12
Alignment explanation
Indices: 899126--899162 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
899116 TTGAATATTC
899126 ATATTTTATTAT
1 ATATTTTATTAT
899138 ATATTTTATTAT
1 ATATTTTATTAT
*
899150 AT-TTTAATTAT
1 ATATTTTATTAT
899161 AT
1 AT
899163 TTAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:899280 original size:26 final size:27
Alignment explanation
Indices: 899229--899290 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
899219 TAATTTAAAA
* *
899229 TATATTTATAATACTTTTTATTTTTAT
1 TATATTTATAATACTTTTCATATTTAT
*
899256 TATATTT-TAATTCTTTTCATATTTAT
1 TATATTTATAATACTTTTCATATTTAT
*
899282 ATTTATTTA
1 -TATATTTA
899291 ATATTATCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (27 bp):
TATATTTATAATACTTTTCATATTTAT
Found at i:899936 original size:29 final size:28
Alignment explanation
Indices: 899904--899964 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
899894 AAAAATATAA
*
899904 ATATATATATATA-ATATTATATTATTTTT
1 ATATATATAT-TAGATATAATA-TATTTTT
* *
899933 ATATTTTTATTAGATATAATATATTTTT
1 ATATATATATTAGATATAATATATTTTT
899961 ATAT
1 ATAT
899965 CGTATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATATATATATTAGATATAATATATTTTT
Found at i:900351 original size:33 final size:35
Alignment explanation
Indices: 900314--900433 Score: 113
Period size: 33 Copynumber: 3.5 Consensus size: 35
900304 TTAATGTGAA
900314 ATATT-TATTTAAATTTTAATATATTAATA-ATTT
1 ATATTATATTTAAATTTTAATATATTAATATATTT
* * * *
900347 ATATTATA--AAAATTTAAATACATTTATATATTT
1 ATATTATATTTAAATTTTAATATATTAATATATTT
* **
900380 ATATTATATTTTAATTTTTTTATATTACATCATATTT
1 ATATTATATTTAAATTTTAATATATTA-AT-ATATTT
*
900417 ATTATTATATTTTAATT
1 A-TATTATATTTAAATT
900434 ATTTTTTATA
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.23
33 17 0.25
34 2 0.03
35 10 0.14
36 2 0.03
37 7 0.10
38 15 0.22
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (35 bp):
ATATTATATTTAAATTTTAATATATTAATATATTT
Found at i:900423 original size:38 final size:37
Alignment explanation
Indices: 900374--900459 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 37
900364 ATACATTTAT
*
900374 ATATTTATATTATATTTTAATT-TTTTTATATTACATC
1 ATATTTATATTATATTTTAATTATTTTT-TATAACATC
900411 ATATTTATTATTATATTTTAATTATTTTTTATAACAT-
1 ATATTTA-TATTATATTTTAATTATTTTTTATAACATC
*
900448 ATAATTA-ATTAT
1 ATATTTATATTAT
900460 GTAATTGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 5 0.11
37 13 0.29
38 22 0.49
39 5 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (37 bp):
ATATTTATATTATATTTTAATTATTTTTTATAACATC
Found at i:900442 original size:21 final size:21
Alignment explanation
Indices: 900381--900442 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
900371 TATATATTTA
900381 TATTATATTTTAATT-TTTTT
1 TATTATATTTTAATTATTTTT
* * *
900401 ATATTACA---TCA-TATTTAT
1 -TATTATATTTTAATTATTTTT
900419 TATTATATTTTAATTATTTTT
1 TATTATATTTTAATTATTTTT
900440 TAT
1 TAT
900443 AACATATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 7 0.23
18 6 0.20
20 2 0.07
21 15 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATATTTTAATTATTTTT
Found at i:900734 original size:11 final size:12
Alignment explanation
Indices: 900716--900752 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
900706 ATAATTTAAT
*
900716 TTATTTTTACAA
1 TTATTTTTAAAA
900728 TTATTTTTAAAA
1 TTATTTTTAAAA
900740 TTATTTTTAAAA
1 TTATTTTTAAAA
900752 T
1 T
900753 ATAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:900772 original size:23 final size:23
Alignment explanation
Indices: 900745--900788 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
900735 TAAAATTATT
900745 TTTAAAATAT-AATATTTAATAAA
1 TTTAAAATATAAAT-TTTAATAAA
*
900768 TTTAAAATTTAAATTTTAATA
1 TTTAAAATATAAATTTTAATA
900789 TATGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAAATATAAATTTTAATAAA
Found at i:903136 original size:21 final size:20
Alignment explanation
Indices: 903107--903151 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
903097 AAATTTTAAT
* *
903107 AAATTAATTTAATTAATGAA
1 AAATTAATTAAATTAATAAA
903127 AAATTGAATTAAATTAATAAA
1 AAATT-AATTAAATTAATAAA
903148 AAAT
1 AAAT
903152 AATATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AAATTAATTAAATTAATAAA
Found at i:903445 original size:43 final size:43
Alignment explanation
Indices: 903380--903465 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
903370 GATACAATAG
* *
903380 GATCTGAAATGTGCTGTCATCATATCTTCAAATAGAGTCAGCC
1 GATCTGAAATGTGATGTCATCATATCTTCAAATAGAGGCAGCC
*
903423 GATCTGAAATGTGATGTTATCATATCTTCAAATAGAGGCAGCC
1 GATCTGAAATGTGATGTCATCATATCTTCAAATAGAGGCAGCC
903466 TCCACAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (43 bp):
GATCTGAAATGTGATGTCATCATATCTTCAAATAGAGGCAGCC
Found at i:904252 original size:16 final size:17
Alignment explanation
Indices: 904233--904270 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
904223 TTTAATGATT
*
904233 TTAATATTTT-TTATTA
1 TTAATATTTTATTATAA
904249 TTAATATTTTATTATAA
1 TTAATATTTTATTATAA
904266 TTAAT
1 TTAAT
904271 TATAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTAATATTTTATTATAA
Found at i:904288 original size:25 final size:26
Alignment explanation
Indices: 904250--904299 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
904240 TTTTTATTAT
904250 TAATATTTTATTATA-ATTAATTATAG
1 TAATATTTTATTATATA-TAATTATAG
904276 TAATA-TTTATTATATATAATTATA
1 TAATATTTTATTATATATAATTATA
904300 ATAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TAATATTTTATTATATATAATTATAG
Found at i:906572 original size:2 final size:2
Alignment explanation
Indices: 906565--906593 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
906555 AAACAATTAA
906565 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
906594 AGTTTGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:907549 original size:3 final size:3
Alignment explanation
Indices: 907543--907578 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
907533 TGATGATGAT
907543 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
907579 AACATGTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:908240 original size:6 final size:6
Alignment explanation
Indices: 908231--908255 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
908221 AGAAAAAAGT
908231 AATGGC AATGGC AATGGC AATGGC A
1 AATGGC AATGGC AATGGC AATGGC A
908256 TTAATTACCA
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AATGGC
Found at i:909115 original size:19 final size:19
Alignment explanation
Indices: 909091--909128 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
909081 AAAAAATATA
909091 TAAAATATTAAT-TTTATTT
1 TAAAAT-TTAATATTTATTT
*
909110 TAAAATTTTATATTTATTT
1 TAAAATTTAATATTTATTT
909129 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAAAATTTAATATTTATTT
Found at i:909417 original size:34 final size:34
Alignment explanation
Indices: 909372--909439 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
909362 TTACATCTAA
*
909372 TTCTTTCACTTGTATTAAAGAACAGTTAAAATCT
1 TTCTTTAACTTGTATTAAAGAACAGTTAAAATCT
909406 TTCTTTAACTTGTATTAAAGAACAGTTAAAATCT
1 TTCTTTAACTTGTATTAAAGAACAGTTAAAATCT
909440 AGTGTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (34 bp):
TTCTTTAACTTGTATTAAAGAACAGTTAAAATCT
Found at i:910456 original size:6 final size:6
Alignment explanation
Indices: 910445--910488 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
910435 AATGAGACTT
* * * *
910445 AATTTA AATTTA GATTTA GATTTA GATCTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
910489 GAAAGAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:910467 original size:12 final size:12
Alignment explanation
Indices: 910446--910488 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
910436 ATGAGACTTA
910446 ATTTAAATTTAG
1 ATTTAAATTTAG
*
910458 ATTTAGATTTAG
1 ATTTAAATTTAG
* *
910470 ATCTAAATTTAA
1 ATTTAAATTTAG
910482 ATTTAAA
1 ATTTAAA
910489 GAAAGAGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (12 bp):
ATTTAAATTTAG
Found at i:910532 original size:30 final size:30
Alignment explanation
Indices: 910497--910557 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
910487 AAGAAAGAGT
910497 AAAAGCTTAATATATAATTTTTTTAGTGTA
1 AAAAGCTTAATATATAATTTTTTTAGTGTA
* *
910527 AAAAGCTTATTGTATAATTTTTTTAGTGTA
1 AAAAGCTTAATATATAATTTTTTTAGTGTA
910557 A
1 A
910558 TATAAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (30 bp):
AAAAGCTTAATATATAATTTTTTTAGTGTA
Found at i:910712 original size:22 final size:21
Alignment explanation
Indices: 910678--910718 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
910668 ATTAAAAAAT
910678 TATTTGTATATTAATATTTATA
1 TATTTGTATATTAA-ATTTATA
910700 TATTT-TATAATTAAATTTA
1 TATTTGTAT-ATTAAATTTA
910719 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTGTATATTAAATTTATA
Found at i:912075 original size:15 final size:16
Alignment explanation
Indices: 912051--912083 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
912041 CAAAAAAATT
*
912051 ATAATTTAAAT-ATAA
1 ATAATATAAATAATAA
912066 ATAATATAAATAATAA
1 ATAATATAAATAATAA
912082 AT
1 AT
912084 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATATAAATAATAA
Found at i:913578 original size:34 final size:34
Alignment explanation
Indices: 913532--913749 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
913522 GTAAAAACCA
*
913532 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
913566 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * *
913600 CCATTTAATCAACAATGATAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
913634 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
913667 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
913701 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
913734 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
913750 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
33 45 0.28
34 113 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:913646 original size:68 final size:67
Alignment explanation
Indices: 913530--913749 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
913520 TGGTAAAAAC
* * *
913530 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
913595 AT
66 AT
** * *
913597 CACCCATTTAATCAACAATGATAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
913662 AAT
65 AAT
* * * * * *
913665 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
913730 AT
66 AT
913732 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
913750 TCTCCCACTT
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:917845 original size:19 final size:19
Alignment explanation
Indices: 917815--917877 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
917805 TCACGTGTAC
* *
917815 AGTAACCATATACTTGAAT
1 AGTACCCATATACGTGAAT
*
917834 AGTACCCGTATACGTGAAT
1 AGTACCCATATACGTGAAT
*
917853 AGTACCTATATACGTGAAT
1 AGTACCCATATACGTGAAT
917872 AGTACC
1 AGTACC
917878 TCGACAACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (19 bp):
AGTACCCATATACGTGAAT
Found at i:918230 original size:34 final size:34
Alignment explanation
Indices: 918184--918399 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
918174 GTAAAAACCA
*
918184 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
918218 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
918252 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
918286 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
918319 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
918353 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
918386 CCATTTAATCAACA
1 CCATTTAATCAACA
918400 GAAAATAAAA
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:918298 original size:68 final size:67
Alignment explanation
Indices: 918182--918399 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
918172 TGGTAAAAAC
* * *
918182 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
918247 AT
66 AT
* * *
918249 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
918314 AAT
65 AAT
* * * * * *
918317 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
918382 AT
66 AT
918384 CACCATTTAATCAACA
1 CACCATTTAATCAACA
918400 GAAAATAAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:918711 original size:2 final size:2
Alignment explanation
Indices: 918693--918730 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
918683 AATGCCCCGC
* *
918693 AT AT AA AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
918731 CCAAGTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:920026 original size:2 final size:2
Alignment explanation
Indices: 920019--920049 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
920009 ACAATATAAG
*
920019 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
920050 ACTGCACCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:920161 original size:18 final size:19
Alignment explanation
Indices: 920117--920167 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
920107 AACTCAAAAA
920117 AATAAT-TAAAATATGATAT
1 AATAATATAAAATA-GATAT
920136 AA-AA-ATAAAATA-ATAT
1 AATAATATAAAATAGATAT
920152 AATAATATAAAA-AGAT
1 AATAATATAAAATAGAT
920168 GAATGTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 17 0.61
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAATATAAAATAGATAT
Found at i:920232 original size:20 final size:19
Alignment explanation
Indices: 920195--920247 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
920185 CGTATTAAAA
920195 TTTAAATAATAAATAATAT
1 TTTAAATAATAAATAATAT
920214 TTTAAAT-ATAATTATAATA-
1 TTTAAATAATAA--ATAATAT
* *
920233 TATAAAAAATAAATA
1 TTTAAATAATAAATA
920248 CAATATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 7 0.24
19 12 0.41
20 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAAATAATAAATAATAT
Found at i:920886 original size:27 final size:29
Alignment explanation
Indices: 920849--920903 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
920839 TAAAATTTTG
*
920849 TTTCAATTAATTAT-ATTTAGAAAAAAAC
1 TTTCAATTAATAATGATTTAGAAAAAAAC
*
920877 TTTCAA-TAATAATGATTTATAAAAAAA
1 TTTCAATTAATAATGATTTAGAAAAAAA
920904 TTAAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTCAATTAATAATGATTTAGAAAAAAAC
Found at i:928142 original size:22 final size:23
Alignment explanation
Indices: 928112--928158 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
928102 TGAATTAATT
* *
928112 AAATTTTAA-TTATTATATTTTA
1 AAATCTTAATTTATTATAATTTA
*
928134 AAATCTTAATTTTTTATAATTTA
1 AAATCTTAATTTATTATAATTTA
928157 AA
1 AA
928159 TAAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATCTTAATTTATTATAATTTA
Found at i:928159 original size:22 final size:21
Alignment explanation
Indices: 928110--928159 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
928100 ATTGAATTAA
* *
928110 TTAAATTTTAATTATTATATT
1 TTAAATCTTAATTATTATAAT
*
928131 TTAAAATCTTAATTTTTTATAAT
1 TT-AAATCTTAA-TTATTATAAT
928154 TTAAAT
1 TTAAAT
928160 AAATATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.50
23 10 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATCTTAATTATTATAAT
Found at i:928392 original size:19 final size:18
Alignment explanation
Indices: 928365--928400 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
928355 ATTCTTTAAC
928365 TGATGAACAAATTGAATTT
1 TGATGAACAAATT-AATTT
*
928384 TGATTAACAAATTAATT
1 TGATGAACAAATTAATT
928401 AAACTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TGATGAACAAATTAATTT
Found at i:928510 original size:13 final size:13
Alignment explanation
Indices: 928492--928516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
928482 TTATTATTAA
928492 ATCAATTCAATTC
1 ATCAATTCAATTC
928505 ATCAATTCAATT
1 ATCAATTCAATT
928517 ATTTTTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
ATCAATTCAATTC
Found at i:928628 original size:2 final size:2
Alignment explanation
Indices: 928621--928658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
928611 TTTCAGTTCA
928621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
928659 CAAGGATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:935253 original size:26 final size:26
Alignment explanation
Indices: 935218--935286 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
935208 TAATATTAAT
935218 ATATTTTATAATTAAATTTAAATAAA
1 ATATTTTATAATTAAATTTAAATAAA
935244 ATATTTTATAATTAAATTTAAATAAA
1 ATATTTTATAATTAAATTTAAATAAA
935270 ATATTTTATAATTAAAT
1 ATATTTTATAATTAAAT
935287 AATAAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTTTATAATTAAATTTAAATAAA
Found at i:935319 original size:26 final size:25
Alignment explanation
Indices: 935218--935320 Score: 131
Period size: 26 Copynumber: 4.1 Consensus size: 25
935208 TAATATTAAT
935218 ATATTTTATAATTAAATTTAAATAAA
1 ATATTTTATAATTAAATTT-AATAAA
935244 ATATTTTATAATTAAATTTAAATAAA
1 ATATTTTATAATTAAATTT-AATAAA
935270 ATATTTTATAATTAAA--TAATAAA
1 ATATTTTATAATTAAATTTAATAAA
* *
935293 ATATCTAATTAATTTAAATTT-ATAAA
1 ATATTTTA-TAA-TTAAATTTAATAAA
935319 AT
1 AT
935321 TTTATACAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
23 12 0.17
24 4 0.06
25 5 0.07
26 49 0.69
27 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTTTATAATTAAATTTAATAAA
Done.