Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 23 of 27
Found at i:3949885 original size:8 final size:8
Alignment explanation
Indices: 3949822--3949899 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
3949812 AAGAAAAAAT
*
3949822 TTTATGTA
1 TTTATATA
*
3949830 TTTATATT
1 TTTATATA
*
3949838 TTTATTTA
1 TTTATATA
3949846 TATTAT-TA
1 T-TTATATA
*
3949854 TTTTTATTA
1 TTTATA-TA
*
3949863 TTTAAAGTA
1 TTTATA-TA
3949872 -TTATATA
1 TTTATATA
3949879 TTTATATAAA
1 TTTATAT--A
3949889 TTTATATA
1 TTTATATA
3949897 TTT
1 TTT
3949900 TATGTTTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
7 5 0.09
8 30 0.55
9 12 0.22
10 8 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:3949947 original size:11 final size:11
Alignment explanation
Indices: 3949923--3949972 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
3949913 CGTATCATGT
3949923 TTATTTTTATA
1 TTATTTTTATA
3949934 TTATATTTTA-A
1 TTAT-TTTTATA
3949945 TTATTTTTATA
1 TTATTTTTATA
* *
3949956 TCATATTTATA
1 TTATTTTTATA
3949967 TTATTT
1 TTATTT
3949973 ATTGTATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:3949948 original size:22 final size:22
Alignment explanation
Indices: 3949923--3949972 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3949913 CGTATCATGT
*
3949923 TTATTTTTATATTATATTT-TAA
1 TTATTTTTATATCATATTTAT-A
3949945 TTATTTTTATATCATATTTATA
1 TTATTTTTATATCATATTTATA
3949967 TTATTT
1 TTATTT
3949973 ATTGTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTTTATATCATATTTATA
Found at i:3951594 original size:17 final size:17
Alignment explanation
Indices: 3951569--3951601 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3951559 ATAAATATTA
3951569 TTTAATAAAATTAATTT
1 TTTAATAAAATTAATTT
*
3951586 TTTATTAAAATTAATT
1 TTTAATAAAATTAATT
3951602 AAAAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATAAAATTAATTT
Found at i:3951914 original size:72 final size:72
Alignment explanation
Indices: 3951833--3951975 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
3951823 GAAGCGAAAG
* *
3951833 CATAACTCTAATATATAATTTTTTTAATTTGTTTATAAAATTAAATAAATCATCTATCTATTCCA
1 CATAACTCTAATATATAATTTTTTTAATCTATTTATAAAATTAAATAAATCATCTATCTATTCCA
3951898 TTAATAT
66 TTAATAT
**
3951905 CATAACTCTAATATATAATTTTTTTAATCTATTTATAAAATTAAATAAATCATCTATCTATTTTA
1 CATAACTCTAATATATAATTTTTTTAATCTATTTATAAAATTAAATAAATCATCTATCTATTCCA
3951970 TTAATA
66 TTAATA
3951976 CCTTAAAACT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (72 bp):
CATAACTCTAATATATAATTTTTTTAATCTATTTATAAAATTAAATAAATCATCTATCTATTCCA
TTAATAT
Found at i:3952013 original size:2 final size:2
Alignment explanation
Indices: 3952006--3952039 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3951996 AACTTTTTAA
3952006 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
3952040 CTGCGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3960539 original size:28 final size:28
Alignment explanation
Indices: 3960489--3960590 Score: 72
Period size: 28 Copynumber: 3.7 Consensus size: 28
3960479 TTGGCATAAT
3960489 ATTTTTTA-A-AAATTTTAATAAATTACTA
1 ATTTTTTATATAAATTTT-A-AAATTACTA
* *
3960517 ATTTTTTATATAAATTTTAAAA-TAATT
1 ATTTTTTATATAAATTTTAAAATTACTA
* * * *
3960544 ATATTATAT-TATATTTT-ATATTACATA
1 ATTTTTTATATAAATTTTAAAATTAC-TA
3960571 A-TTTTTATATAATATTTTAA
1 ATTTTTTATATAA-ATTTTAA
3960591 TTATTTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
25 2 0.04
26 14 0.25
27 14 0.25
28 16 0.29
29 3 0.05
30 7 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTTTTTATATAAATTTTAAAATTACTA
Found at i:3960572 original size:30 final size:27
Alignment explanation
Indices: 3960509--3960593 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
3960499 AATTTTAATA
3960509 AATTAC-TAATTTTTTATATAA-ATTTT
1 AATTACATAA-TTTTTATATAATATTTT
*
3960535 AA--A-ATAATTATATTATATTATATTTT
1 AATTACATAATT-T-TTATATAATATTTT
3960561 ATATTACATAATTTTTATATAATATTTT
1 A-ATTACATAATTTTTATATAATATTTT
3960589 AATTA
1 AATTA
3960594 TTTTTTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
23 2 0.04
24 5 0.10
25 7 0.14
26 8 0.16
27 5 0.10
28 14 0.29
29 2 0.04
30 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTACATAATTTTTATATAATATTTT
Found at i:3960597 original size:21 final size:21
Alignment explanation
Indices: 3960573--3960619 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3960563 ATTACATAAT
3960573 TTTTATATAA-TATTTTAATTA
1 TTTTATA-AATTATTTTAATTA
* * *
3960594 TTTTTTAAATTTTTTTTATTA
1 TTTTATAAATTATTTTAATTA
3960615 TTTTA
1 TTTTA
3960620 ATATTTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATAAATTATTTTAATTA
Found at i:3960612 original size:18 final size:20
Alignment explanation
Indices: 3960580--3960627 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
3960570 AATTTTTATA
**
3960580 TAATATTTTAATTATT-TTT
1 TAATATTTTTTTTATTATTT
3960599 TAA-ATTTTTTTTATTATTT
1 TAATATTTTTTTTATTATTT
3960618 TAATATTTTT
1 TAATATTTTT
3960628 AGACTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 9 0.36
20 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TAATATTTTTTTTATTATTT
Found at i:3962801 original size:16 final size:16
Alignment explanation
Indices: 3962782--3962838 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
3962772 TTTAAGAAAC
*
3962782 TATTTAATTAAATATA
1 TATTTAATTAAATATT
*
3962798 TATTTTTATTAAATATT
1 TA-TTTAATTAAATATT
*
3962815 TA-TTACATTTAATATT
1 TATTTA-ATTAAATATT
3962831 TATTTAAT
1 TATTTAAT
3962839 ATTTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.06
16 15 0.44
17 17 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTAATTAAATATT
Found at i:3963225 original size:2 final size:2
Alignment explanation
Indices: 3963218--3963246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3963208 TGAGTACCAC
3963218 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
3963247 AGCTAAACTA
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:3965089 original size:18 final size:19
Alignment explanation
Indices: 3965056--3965098 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3965046 ACGTGGGATA
*
3965056 AAAATATTATAAAATTTAAT
1 AAAA-ATTATAAAATTAAAT
3965076 AAAAATTA-AAAATTAAAT
1 AAAAATTATAAAATTAAAT
3965094 AAAAA
1 AAAAA
3965099 ATTTATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATTATAAAATTAAAT
Found at i:3968227 original size:17 final size:17
Alignment explanation
Indices: 3968202--3968240 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3968192 TAATTGAGTG
3968202 TATTAAATATAAATATA
1 TATTAAATATAAATATA
* *
3968219 TATTTAATATGAATATA
1 TATTAAATATAAATATA
3968236 T-TTAA
1 TATTAA
3968241 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTAAATATAAATATA
Found at i:3972539 original size:2 final size:2
Alignment explanation
Indices: 3972532--3972559 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3972522 TGTTGAGATT
3972532 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
3972560 AAATGAAAAC
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:3972728 original size:158 final size:160
Alignment explanation
Indices: 3972545--3973028 Score: 713
Period size: 158 Copynumber: 2.9 Consensus size: 160
3972535 ATATATATAT
*
3972545 ATATATATATATATAAAATGAAAACCATAAGATTATCCCTATAAATTTTTTTAATTAATGGTTAC
1 ATATATATATATATAAAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAATGGTTAC
3972610 CAAATTCATTGAAAAAACCAAGGAAAG-AAAAAAATTAATTTTTCTTTTATTGTGTTTGGTATTA
66 CAAATTCATTGAAAAAACCAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTTTGGTATTA
*
3972674 AATATAAAAAAAAAAAAGAGATTAAAGAC-
131 AATATAAAAAAAAAAAAAAGATTAAAGACA
* *
3972703 ATATATAGATATATAAAATGAAAACCATAAGATTATCCCTAGAAAATTTTTTAATTAATGGTTAC
1 ATATATATATATATAAAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAATGGTTAC
*
3972768 CAAATTCATTGCAAAAAA-CAAGGAAAGAAAAAAAAATTAATTTTTCTTTTATTTTGTTTGGTAT
66 CAAATTCATTG-AAAAAACCAAGGAAAG-AAAAAAAATTAATTTTTCTTTTATTGTGTTTGGTAT
3972832 TAAATATAAAAATAAAAACAAAAAAAAAGATTAAAGACATATA
129 T-AA-AT----ATAAAAA-AAAAAAAAAGATTAAAGAC----A
*
3972875 TATATATATATATATATATAATGAAAACCATAAGATTATCCTTAGAAATTTTTTTAATTAATGGT
1 -ATATATATATATATA-A-AATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAATGGT
* *
3972940 TACCAAATTCATTGCAAAAACCAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTTTAGTA
63 TACCAAATTCATTGAAAAAACCAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTTTGGTA
3973005 TTAAATATAAAAATAAAAACAAAA
128 TTAAATATAAAAA-AAAAA-AAAA
3973029 AAAAGAGATT
Statistics
Matches: 294, Mismatches: 12, Indels: 29
0.88 0.04 0.09
Matches are distributed among these distances:
158 82 0.28
159 6 0.02
160 35 0.12
161 2 0.01
162 2 0.01
166 7 0.02
167 18 0.06
168 12 0.04
169 4 0.01
172 2 0.01
173 16 0.05
174 41 0.14
175 67 0.23
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.34
Consensus pattern (160 bp):
ATATATATATATATAAAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAATGGTTAC
CAAATTCATTGAAAAAACCAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTTTGGTATTA
AATATAAAAAAAAAAAAAAGATTAAAGACA
Found at i:3972875 original size:2 final size:2
Alignment explanation
Indices: 3972870--3972894 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3972860 GATTAAAGAC
3972870 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 A
3972895 ATGAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3972911 original size:175 final size:173
Alignment explanation
Indices: 3972537--3973045 Score: 789
Period size: 175 Copynumber: 3.0 Consensus size: 173
3972527 AGATTTATAT
*
3972537 ATATATATATATATATATATATAAAATGAAAACCATAAGATTATCCCTATAAATTTTTTTAATTA
1 ATATATATATATATATATATAT-AAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTA
3972602 ATGGTTACCAAATTCATTG-AAAAAACCAAGGAAAG-AAAAAAATTAATTTTTCTTTTATTGTGT
65 ATGGTTACCAAATTCATTGCAAAAAA-CAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGT
*
3972665 TTGGTATT-AA-AT----ATAAAAA-AAAAAAAGAGATTAAAGAC
129 TTGGTATTAAATATAAAAATAAAAACAAAAAAAAAGATTAAAGAC
* *
3972703 ------ATATATAGATATATA-AAATGAAAACCATAAGATTATCCCTAGAAAATTTTTTAATTAA
1 ATATATATATATATATATATATAAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAA
*
3972761 TGGTTACCAAATTCATTGCAAAAAACAAGGAAAGAAAAAAAAATTAATTTTTCTTTTATTTTGTT
66 TGGTTACCAAATTCATTGCAAAAAACAAGGAAAG-AAAAAAAATTAATTTTTCTTTTATTGTGTT
3972826 TGGTATTAAATATAAAAATAAAAACAAAAAAAAAGATTAAAGAC
130 TGGTATTAAATATAAAAATAAAAACAAAAAAAAAGATTAAAGAC
*
3972870 ATATATATATATATATATATATATAATGAAAACCATAAGATTATCCTTAGAAATTTTTTTAATTA
1 ATATATATATATATATATATATA-AATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTA
*
3972935 ATGGTTACCAAATTCATTGCAAAAACCAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTT
65 ATGGTTACCAAATTCATTGCAAAAAACAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTT
*
3973000 TAGTATTAAATATAAAAATAAAAACAAAAAAAAGAGATTAAAGAC
130 TGGTATTAAATATAAAAATAAAAACAAAAAAAA-AGATTAAAGAC
3973045 A
1 A
3973046 AAATTATGAA
Statistics
Matches: 313, Mismatches: 11, Indels: 29
0.89 0.03 0.08
Matches are distributed among these distances:
158 68 0.22
159 6 0.02
160 49 0.16
161 2 0.01
162 2 0.01
166 7 0.02
167 18 0.06
173 14 0.04
174 62 0.20
175 85 0.27
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (173 bp):
ATATATATATATATATATATATAAATGAAAACCATAAGATTATCCCTAGAAATTTTTTTAATTAA
TGGTTACCAAATTCATTGCAAAAAACAAGGAAAGAAAAAAAATTAATTTTTCTTTTATTGTGTTT
GGTATTAAATATAAAAATAAAAACAAAAAAAAAGATTAAAGAC
Found at i:3973988 original size:10 final size:10
Alignment explanation
Indices: 3973973--3974007 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3973963 ACAAAAAGTA
3973973 AAAATTAAAT
1 AAAATTAAAT
3973983 AAAATTAAAT
1 AAAATTAAAT
*
3973993 AAAATAAAAT
1 AAAATTAAAT
3974003 GAAAA
1 -AAAA
3974008 CACTTGCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAAATTAAAT
Found at i:3974639 original size:34 final size:34
Alignment explanation
Indices: 3974575--3974641 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3974565 TTTATTTTAT
** * *
3974575 AATTAAATTTAAATAAAAAATATTATTTAAATCG
1 AATTAAATCAAAATAAAAAATATAACTTAAATCG
3974609 AATTAAATCAAAAT-AAAAATATAAACTTAAATC
1 AATTAAATCAAAATAAAAAATAT-AACTTAAATC
3974642 TAATAGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (34 bp):
AATTAAATCAAAATAAAAAATATAACTTAAATCG
Found at i:3974872 original size:2 final size:2
Alignment explanation
Indices: 3974865--3974890 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3974855 ATGCATGCAA
3974865 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
3974891 GTAAATAAGG
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:3978293 original size:29 final size:28
Alignment explanation
Indices: 3978257--3978311 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
3978247 ATTTAAATTT
* *
3978257 AATTAA-TTTAATTTTTAATAATTTTTAA
1 AATTAATTTTAATATAT-ATAATTTTTAA
3978285 AATTAAATTTTAATATATATAATTTTT
1 AATT-AATTTTAATATATATAATTTTT
3978312 TTATTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 11 0.48
30 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTAATTTTAATATATATAATTTTTAA
Found at i:3981044 original size:27 final size:27
Alignment explanation
Indices: 3981007--3981060 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3980997 CAACGCTAGG
3981007 TTTTATAAGATTCAACTGTTAGGAACT
1 TTTTATAAGATTCAACTGTTAGGAACT
3981034 TTTTATAAGATTCAACTGTTAGGAACT
1 TTTTATAAGATTCAACTGTTAGGAACT
3981061 AAGTTACTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (27 bp):
TTTTATAAGATTCAACTGTTAGGAACT
Found at i:3992962 original size:4 final size:4
Alignment explanation
Indices: 3992953--3992995 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
3992943 CTTCAGTCTG
3992953 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3992996 GAGAACATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3997841 original size:18 final size:19
Alignment explanation
Indices: 3997818--3997863 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
3997808 TTGCAGATCT
3997818 GGAAATCTG-AAGAAATCA
1 GGAAATCTGCAAGAAATCA
* *
3997836 GGAAATCTGCTAGAATTCA
1 GGAAATCTGCAAGAAATCA
3997855 GGAAATCTG
1 GGAAATCTG
3997864 GAAATCTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (19 bp):
GGAAATCTGCAAGAAATCA
Found at i:4002036 original size:20 final size:20
Alignment explanation
Indices: 4001977--4002037 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
4001967 TTATTTATAA
* *
4001977 TATTATTTTAATATTAAATTT
1 TATTA-TTTAATAATAATTTT
4001998 TATATATCATT-ATAA-AATTTT
1 TAT-TAT--TTAATAATAATTTT
4002019 TATTATTTAATAATAATTT
1 TATTATTTAATAATAATTT
4002038 AAATTGAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 8 0.24
21 12 0.36
22 5 0.15
23 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTAATAATAATTTT
Found at i:4006331 original size:9 final size:9
Alignment explanation
Indices: 4006317--4006349 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4006307 AGAAGGCTCA
4006317 AGCAGAGAC
1 AGCAGAGAC
4006326 AGCAGAGAC
1 AGCAGAGAC
*
4006335 AGCAGAGAT
1 AGCAGAGAC
4006344 AGCAGA
1 AGCAGA
4006350 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:4009636 original size:12 final size:12
Alignment explanation
Indices: 4009619--4009650 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4009609 GCCAACAAAG
4009619 GCTGCCAACTGT
1 GCTGCCAACTGT
4009631 GCTGCCAACTGT
1 GCTGCCAACTGT
*
4009643 GCCGCCAA
1 GCTGCCAA
4009651 TTTTGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:4009688 original size:27 final size:27
Alignment explanation
Indices: 4009649--4009701 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
4009639 CTGTGCCGCC
* * *
4009649 AATTTTGACATTCAATTTGAAATAGTA
1 AATTATGAAATTCAATTTAAAATAGTA
4009676 AATTATGAAATTCAATTTAAAATAGT
1 AATTATGAAATTCAATTTAAAATAGT
4009702 GAAGGCTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (27 bp):
AATTATGAAATTCAATTTAAAATAGTA
Found at i:4009774 original size:9 final size:9
Alignment explanation
Indices: 4009760--4009792 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4009750 AGAAGGCTCA
4009760 AGCAGAGAC
1 AGCAGAGAC
4009769 AGCAGAGAC
1 AGCAGAGAC
*
4009778 AGCAGAGAT
1 AGCAGAGAC
4009787 AGCAGA
1 AGCAGA
4009793 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:4011246 original size:21 final size:25
Alignment explanation
Indices: 4011222--4011271 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 25
4011212 AATAATATTT
4011222 TAATAAAT-AAGTA-A-TATATA-A
1 TAATAAATAAAGTATATTATATAGA
*
4011243 TAATGAATAAAGTATATTATATAGA
1 TAATAAATAAAGTATATTATATAGA
4011268 TAAT
1 TAAT
4011272 TATTACATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 1 0.04
24 6 0.25
25 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (25 bp):
TAATAAATAAAGTATATTATATAGA
Found at i:4011848 original size:3 final size:3
Alignment explanation
Indices: 4011840--4011868 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4011830 TACAGTTGAT
4011840 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4011869 GATAGTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4012152 original size:2 final size:2
Alignment explanation
Indices: 4012145--4012177 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4012135 ACAGCAAAGA
4012145 AT AT 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 AT AT A
4012178 GTTATTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4013150 original size:24 final size:25
Alignment explanation
Indices: 4013083--4013155 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 25
4013073 AAAAGGCACC
*
4013083 CTTTGTGTTTGTCAAAAATAGTGGTTT
1 CTTTGTGTTTGTCAAAAATGGTGG--T
* *
4013110 CTTTGTGTTTATAAAAAATGGTGG-
1 CTTTGTGTTTGTCAAAAATGGTGGT
*
4013134 CTTAT-TGTTTGTCAAAATTGGT
1 CTT-TGTGTTTGTCAAAAATGGT
4013156 AGCTAATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 17 0.44
25 1 0.03
27 21 0.54
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47
Consensus pattern (25 bp):
CTTTGTGTTTGTCAAAAATGGTGGT
Found at i:4020268 original size:17 final size:18
Alignment explanation
Indices: 4020246--4020283 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4020236 ATATAAATAC
4020246 TATCTTCT-ATGAAAAGA
1 TATCTTCTAATGAAAAGA
* *
4020263 TATCTTTTAATGAAATGA
1 TATCTTCTAATGAAAAGA
4020281 TAT
1 TAT
4020284 ATTGATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
TATCTTCTAATGAAAAGA
Found at i:4024597 original size:12 final size:12
Alignment explanation
Indices: 4024538--4024604 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
4024528 ATTTATATAA
4024538 TAAATATTATTTTT
1 TAAATATTA--TTT
4024552 TAAAT-TTATTT
1 TAAATATTATTT
* *
4024563 ATAAATATTAATA
1 -TAAATATTATTT
*
4024576 TAAA-AATATTT
1 TAAATATTATTT
*
4024587 TTAATATTATTT
1 TAAATATTATTT
4024599 TAAATA
1 TAAATA
4024605 ATAAAATAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 10 0.24
12 20 0.48
13 7 0.17
14 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TAAATATTATTT
Found at i:4025009 original size:3 final size:3
Alignment explanation
Indices: 4025001--4025034 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4024991 TATAAATTTG
4025001 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4025035 AATTAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4026117 original size:120 final size:120
Alignment explanation
Indices: 4025904--4026143 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 120
4025894 AGATGTTGTC
* * * *
4025904 TCACAAATTTAAAATTGAGAAATTCAATAAATCAAATGATTTCACTTTATGGAAGGTAAAGATGA
1 TCACAAATTCAAAATTAAGAAATTCAATAAATCAAATGATTTCACTTTATGGAAGGTAAAAATAA
4025969 AAGCTATTCTTGCTCAGTAAAGATGTATGAAAACGCTAGAAGGAAAAGAAATATT
66 AAGCTATTCTTGCTCAGTAAAGATGTATGAAAACGCTAGAAGGAAAAGAAATATT
** *
4026024 TCACAAATTCAAAATTAAGAAATTCAATGGATCGAATGATTTCACTTTATGGAAGGTAAAAATAA
1 TCACAAATTCAAAATTAAGAAATTCAATAAATCAAATGATTTCACTTTATGGAAGGTAAAAATAA
*
4026089 AAGCTATTCTTGTTCAGTAAAGATGTATGAAAACGCTAGAAGGAAAAGAAATATT
66 AAGCTATTCTTGCTCAGTAAAGATGTATGAAAACGCTAGAAGGAAAAGAAATATT
4026144 GCCTATGAAT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (120 bp):
TCACAAATTCAAAATTAAGAAATTCAATAAATCAAATGATTTCACTTTATGGAAGGTAAAAATAA
AAGCTATTCTTGCTCAGTAAAGATGTATGAAAACGCTAGAAGGAAAAGAAATATT
Found at i:4026846 original size:16 final size:16
Alignment explanation
Indices: 4026818--4026850 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4026808 AACTGTAATT
4026818 AAAAATAATTTTGATAA
1 AAAAATAATTTTG-TAA
4026835 AAAAATAA-TTTGTAA
1 AAAAATAATTTTGTAA
4026850 A
1 A
4026851 CACTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAAAATAATTTTGTAA
Found at i:4028166 original size:34 final size:33
Alignment explanation
Indices: 4028118--4028339 Score: 259
Period size: 34 Copynumber: 6.5 Consensus size: 33
4028108 TGGTAAAAGC
*
4028118 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
4028151 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
4028185 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
4028219 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
4028253 CTCCCATTTAGTCAATCAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAA-CAATGG-TAACCTACCAAAT
*
4028288 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
4028322 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
4028340 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
33 23 0.14
34 108 0.67
35 28 0.17
36 3 0.02
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:4028262 original size:102 final size:102
Alignment explanation
Indices: 4028118--4028339 Score: 347
Period size: 102 Copynumber: 2.2 Consensus size: 102
4028108 TGGTAAAAGC
* *
4028118 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAA-CAATGGTAAGCCACCA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATCAATGGCAAACCACCA
* *
4028182 AATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
4028219 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATCAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATCAATGGCAAACCACC
4028284 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
4028322 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
4028340 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 57 0.53
103 50 0.46
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (102 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATCAATGGCAAACCACCA
AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:4032797 original size:34 final size:34
Alignment explanation
Indices: 4032750--4032968 Score: 252
Period size: 34 Copynumber: 6.5 Consensus size: 34
4032740 GGTAAAAGCC
*
4032750 ACCATTTAATCAACAATGGCAACCTACCAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
*
4032784 ACCATTTAGTCAACAATGGTAAGCC-ACCAAAT-T
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* *
4032817 ACCCATTTAATCAATAATGGTAAGCTACCAAAT-T
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
* *
4032851 TCTCATTTAATCAACAATGGTAAGCTACCAAATCT
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* * * *
4032886 CCCATTTAGTCATCAATGGCAAACC-ACCAAATC-
1 ACCATTTAATCAACAATGG-TAACCTACCAAATCT
*
4032919 ACCCATTTAATCAACAATGGTAAACTACCAAATC-
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
4032953 ACCATTTAATCAACAA
1 ACCATTTAATCAACAA
4032969 ATTTGAGGAA
Statistics
Matches: 160, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
33 22 0.14
34 131 0.82
35 7 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:4032893 original size:102 final size:101
Alignment explanation
Indices: 4032749--4032968 Score: 332
Period size: 102 Copynumber: 2.2 Consensus size: 101
4032739 TGGTAAAAGC
* *
4032749 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
4032814 ATTACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
4032850 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCATCAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
4032915 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
4032952 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
4032969 ATTTGAGGAA
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:4035491 original size:34 final size:38
Alignment explanation
Indices: 4035441--4035509 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
4035431 ATATTAGATA
4035441 TGACATGTATATAAAATAA-AAAAATA-AAATATATTG
1 TGACATGTATATAAAATAATAAAAATACAAATATATTG
*
4035477 TGACATG-A-ATAAAATAATATAAATACAAATATA
1 TGACATGTATATAAAATAATAAAAATACAAATATA
4035510 AAAATATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.30
35 7 0.23
36 14 0.47
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.29
Consensus pattern (38 bp):
TGACATGTATATAAAATAATAAAAATACAAATATATTG
Found at i:4039440 original size:20 final size:19
Alignment explanation
Indices: 4039412--4039529 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 19
4039402 AATGATGTCA
4039412 AAATTATATAAAATTTTATT
1 AAATTATATAAAATTTT-TT
* *
4039432 AACTTATATAAAAGGTTTTT
1 AAATTATATAAAA-TTTTTT
* * *
4039452 AAATTATATCAAATTTATC
1 AAATTATATAAAATTTTTT
* * *
4039471 AAATTATTTCAAAAGTTATTC
1 AAATTATAT-AAAA-TTTTTT
* *
4039492 AAATTATCAGTAAAAGTTATTA
1 AAATTAT-A-TAAAA-TTTTTT
4039514 AAATTATATCAAAATT
1 AAATTATAT-AAAATT
4039530 AACCAAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
19 11 0.14
20 31 0.39
21 19 0.24
22 17 0.22
23 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (19 bp):
AAATTATATAAAATTTTTT
Found at i:4039472 original size:9 final size:10
Alignment explanation
Indices: 4039452--4039526 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 10
4039442 AAAGGTTTTT
4039452 AAATTATATC
1 AAATTATATC
4039462 AAATT-TATC
1 AAATTATATC
*
4039471 AAATTATTTC
1 AAATTATATC
4039481 AAAAGTTAT-TC
1 -AAA-TTATATC
*
4039492 AAATTATCAGTA
1 AAATTAT-A-TC
*
4039504 AAAGTTAT-TA
1 AAA-TTATATC
4039514 AAATTATATC
1 AAATTATATC
4039524 AAA
1 AAA
4039527 ATTAACCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 17 0.31
10 20 0.37
11 5 0.09
12 8 0.15
13 4 0.07
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (10 bp):
AAATTATATC
Found at i:4039485 original size:40 final size:40
Alignment explanation
Indices: 4039412--4039498 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
4039402 AATGATGTCA
* * *
4039412 AAATTATATAAAATTTTATTAACTTATATAAAAGGTT-TTT
1 AAATTATATAAAATTTTATCAAATTATATAAAA-GTTATTC
* *
4039452 AAATTATATCAAA-TTTATCAAATTATTTCAAAAGTTATTC
1 AAATTATATAAAATTTTATCAAATTATAT-AAAAGTTATTC
4039492 AAATTAT
1 AAATTAT
4039499 CAGTAAAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 15 0.38
40 25 0.62
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (40 bp):
AAATTATATAAAATTTTATCAAATTATATAAAAGTTATTC
Found at i:4039529 original size:11 final size:11
Alignment explanation
Indices: 4039452--4039530 Score: 57
Period size: 9 Copynumber: 7.5 Consensus size: 11
4039442 AAAGGTTTTT
4039452 AAATTATATC-
1 AAATTATATCA
4039462 AAATT-TATC-
1 AAATTATATCA
*
4039471 AAATTATTTCA
1 AAATTATATCA
4039482 AAAGTTAT-TC-
1 AAA-TTATATCA
4039492 AAATTATCAGT-A
1 AAATTAT-A-TCA
4039504 AAAGTTAT-T-A
1 AAA-TTATATCA
4039514 AAATTATATCA
1 AAATTATATCA
4039525 AAATTA
1 AAATTA
4039531 ACCAAAATAA
Statistics
Matches: 58, Mismatches: 1, Indels: 19
0.74 0.01 0.24
Matches are distributed among these distances:
9 17 0.29
10 17 0.29
11 12 0.21
12 8 0.14
13 4 0.07
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (11 bp):
AAATTATATCA
Found at i:4039565 original size:28 final size:27
Alignment explanation
Indices: 4039513--4039568 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
4039503 AAAAGTTATT
*
4039513 AAAATTATATCAAAATTAACCAAAATA
1 AAAATTATATAAAAATTAACCAAAATA
*
4039540 AAAATATATATAAAACATTAA-GAAAATA
1 AAAAT-TATATAAAA-ATTAACCAAAATA
4039568 A
1 A
4039569 TATCATAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 15 0.60
29 5 0.20
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAATTATATAAAAATTAACCAAAATA
Found at i:4039670 original size:20 final size:19
Alignment explanation
Indices: 4039645--4039701 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
4039635 AAAGATTATC
4039645 AAAATTATTTTAAAAATATA
1 AAAATTA-TTTAAAAATATA
* * *
4039665 AAAATTACATCAAAAATTATC
1 AAAATTA-TTTAAAAA-TATA
4039686 AAAATTATTTAAAAAT
1 AAAATTATTTAAAAAT
4039702 TTACCAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.63
21 10 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTATTTAAAAATATA
Found at i:4039677 original size:41 final size:41
Alignment explanation
Indices: 4039623--4039701 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
4039613 AAAGATTACT
* *
4039623 AAAATATATATCAAAGATTATCAAAATTATTTTAAAAATATA
1 AAAATATACATCAAAAATTATCAAAATTA-TTTAAAAATATA
4039665 AAAAT-TACATCAAAAATTATCAAAATTATTTAAAAAT
1 AAAATATACATCAAAAATTATCAAAATTATTTAAAAAT
4039702 TTACCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 9 0.26
41 21 0.60
42 5 0.14
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (41 bp):
AAAATATACATCAAAAATTATCAAAATTATTTAAAAATATA
Found at i:4039689 original size:21 final size:21
Alignment explanation
Indices: 4039607--4039750 Score: 100
Period size: 21 Copynumber: 6.9 Consensus size: 21
4039597 CTTACCAGAA
4039607 TATAT-AAAAGATTA-CTAAAAT
1 TATATCAAAA-ATTATC-AAAAT
*
4039628 ATATATCAAAGATTATCAAAAT
1 -TATATCAAAAATTATCAAAAT
* * *
4039650 TATTTTAAAAA-TATAAAAAT
1 TATATCAAAAATTATCAAAAT
*
4039670 TACATCAAAAATTATCAAAAT
1 TATATCAAAAATTATCAAAAT
* *
4039691 TAT-TTAAAAATTTACCAAAAT
1 TATATCAAAAA-TTATCAAAAT
* * * *
4039712 TTTGTCAAAAGTTATCAAATT
1 TATATCAAAAATTATCAAAAT
*
4039733 TACAT-AAAATATTATCAA
1 TATATCAAAA-ATTATCAA
4039751 GCTTTATTAA
Statistics
Matches: 95, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
20 26 0.27
21 46 0.48
22 19 0.20
23 4 0.04
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (21 bp):
TATATCAAAAATTATCAAAAT
Found at i:4039732 original size:41 final size:41
Alignment explanation
Indices: 4039635--4039730 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
4039625 AATATATATC
4039635 AAAGATTATCAAAATTATTTTAAAAATATAAAAATTACATCA
1 AAAG-TTATCAAAATTATTTTAAAAATATAAAAATTACATCA
* * ***
4039677 AAAATTATCAAAATTA-TTTAAAAATTTACCAAAATTTTGTCA
1 AAAGTTATCAAAATTATTTTAAAAATATA--AAAATTACATCA
4039719 AAAGTTATCAAA
1 AAAGTTATCAAA
4039731 TTTACATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 11 0.24
41 12 0.26
42 23 0.50
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (41 bp):
AAAGTTATCAAAATTATTTTAAAAATATAAAAATTACATCA
Found at i:4039840 original size:42 final size:42
Alignment explanation
Indices: 4039793--4039897 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
4039783 AAAGGTTATT
4039793 AAATTATATTAAACATT-AT-TAAAATCAAAT-TAAAAGATAATA
1 AAATTATATTAAA-ATTGATAT-AAATCAAATAT-AAAGATAATA
* * * *
4039835 AAATTATGTTAAAATTGATATAAATCATATATAAAGTTATTA
1 AAATTATATTAAAATTGATATAAATCAAATATAAAGATAATA
*
4039877 AAATTATATTAAAATTTATAT
1 AAATTATATTAAAATTGATAT
4039898 TTTATATTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 3 0.06
42 49 0.91
43 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (42 bp):
AAATTATATTAAAATTGATATAAATCAAATATAAAGATAATA
Found at i:4039895 original size:21 final size:21
Alignment explanation
Indices: 4039787--4039895 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
4039777 TATACCAAAG
4039787 GTTATT-AAATTATATTAAACA
1 GTTATTAAAATTATATTAAA-A
* *
4039808 -TTATTAAAATCAAATTAAAA
1 GTTATTAAAATTATATTAAAA
* * *
4039828 GATAATAAAATTATGTTAAAA
1 GTTATTAAAATTATATTAAAA
*
4039849 -TTGA-TATAAATCATA-TATAAA
1 GTT-ATTA-AAATTATATTA-AAA
4039870 GTTATTAAAATTATATTAAAA
1 GTTATTAAAATTATATTAAAA
*
4039891 TTTAT
1 GTTAT
4039896 ATTTTATATT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 11 0.16
21 51 0.75
22 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
GTTATTAAAATTATATTAAAA
Found at i:4039897 original size:12 final size:11
Alignment explanation
Indices: 4039789--4039898 Score: 65
Period size: 11 Copynumber: 10.4 Consensus size: 11
4039779 TACCAAAGGT
4039789 TATT-AAATTA
1 TATTAAAATTA
4039799 TATTAAACA-T-
1 TATTAAA-ATTA
*
4039809 TATTAAAATCA
1 TATTAAAATTA
* *
4039820 AATTAAAA-GA
1 TATTAAAATTA
*
4039830 TAATAAAATTA
1 TATTAAAATTA
*
4039841 TGTTAAAATTGA
1 TATTAAAATT-A
*
4039853 TA-T-AAATCA
1 TATTAAAATTA
*
4039862 TA-TATAAAGT-
1 TATTA-AAATTA
4039872 TATTAAAATTA
1 TATTAAAATTA
4039883 TATTAAAATTTA
1 TATTAAAA-TTA
4039895 TATT
1 TATT
4039899 TTATATTGTA
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
9 5 0.07
10 28 0.37
11 33 0.43
12 10 0.13
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:4040406 original size:19 final size:18
Alignment explanation
Indices: 4040378--4040424 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
4040368 TGTTATTAAT
4040378 TTAATAATAAAATCAATAA
1 TTAATAATAAAAT-AATAA
*
4040397 TTAATCATAAAATAATATA
1 TTAATAATAAAATAATA-A
4040416 TTTAATAAT
1 -TTAATAAT
4040425 GACATATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAATAATAAAATAATAA
Found at i:4040765 original size:2 final size:2
Alignment explanation
Indices: 4040758--4040809 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
4040748 ACAGCAAAGA
* *
4040758 AT AT AT AT AT AA AA 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 AT AT
4040800 AT AT AT AT AT
1 AT AT AT AT AT
4040810 GTTGAGGAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4041365 original size:22 final size:23
Alignment explanation
Indices: 4041325--4041391 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
4041315 ACCAAATTTG
4041325 ATAATATTAAATATAATATAAAA
1 ATAATATTAAATATAATATAAAA
* *
4041348 ATAAT-TTATATATGATATAAATA
1 ATAATATTAAATATAATATAAA-A
4041371 A-AATAATATAAATAT-ATATAA
1 ATAAT-AT-TAAATATAATATAA
4041392 TAGATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 17 0.46
23 7 0.19
24 7 0.19
25 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAATATTAAATATAATATAAAA
Found at i:4041365 original size:27 final size:25
Alignment explanation
Indices: 4041335--4041393 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
4041325 ATAATATTAA
* *
4041335 ATATAATATAAAAATAATTTATATAT
1 ATATAATAT-AAAATAATATAAATAT
4041361 GATATAA-ATAAAATAATATAAATAT
1 -ATATAATATAAAATAATATAAATAT
4041386 ATATAATA
1 ATATAATA
4041394 GATGAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.21
25 15 0.52
26 2 0.07
27 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATAATATAAAATAATATAAATAT
Found at i:4041385 original size:20 final size:20
Alignment explanation
Indices: 4041325--4041391 Score: 53
Period size: 25 Copynumber: 3.0 Consensus size: 20
4041315 ACCAAATTTG
4041325 ATAATATTAAATATAATATAAAA
1 ATAATA-TAAATATAA-AT-AAA
4041348 ATAATTTATATATGATATAAATAAA
1 ATAA--TATA-A--ATATAAATAAA
*
4041373 ATAATATAAATATATATAA
1 ATAATATAAATATAAATAA
4041392 TAGATGAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
20 9 0.24
22 1 0.03
23 8 0.21
24 2 0.05
25 10 0.26
26 2 0.05
27 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (20 bp):
ATAATATAAATATAAATAAA
Found at i:4042183 original size:3 final size:3
Alignment explanation
Indices: 4042175--4042209 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4042165 TATAAATTTG
4042175 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4042210 ATACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4043279 original size:120 final size:120
Alignment explanation
Indices: 4043061--4043300 Score: 356
Period size: 120 Copynumber: 2.0 Consensus size: 120
4043051 AGATGTTCTC
* * * * *
4043061 TCACAAATTTAAAATTGAGAAATTCAATGGATCGAATGATTTCACTTTATGAAAAGTAAAGATGA
1 TCACAAATTCAAAATTAAAAAATTCAATGAATCGAATGATTTCACTTTATGAAAAGTAAAAATGA
* * * **
4043126 GAGCTATTCTTGTTCAGTAAAGATGTATAAAAACGCTAAAAGGAAAGGAAATATT
66 AAGCTATTCTTGTTCAATAAAGATATATAAAAACGCTAAAAGGAAAAAAAATATT
*
4043181 TCACAAATTCAAAATTAAAAAATTCAATGAATCGAATGATTTTC-CTTTATGAAAGGTAAAAATG
1 TCACAAATTCAAAATTAAAAAATTCAATGAATCGAATGA-TTTCACTTTATGAAAAGTAAAAATG
*
4043245 AAAGCTATTCTTGTTCAATAAAGATATATGAAAACGCTAAAAGGAAAAAAAATATT
65 AAAGCTATTCTTGTTCAATAAAGATATATAAAAACGCTAAAAGGAAAAAAAATATT
4043301 GCTTGTGAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 103 0.96
121 4 0.04
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (120 bp):
TCACAAATTCAAAATTAAAAAATTCAATGAATCGAATGATTTCACTTTATGAAAAGTAAAAATGA
AAGCTATTCTTGTTCAATAAAGATATATAAAAACGCTAAAAGGAAAAAAAATATT
Found at i:4044730 original size:13 final size:13
Alignment explanation
Indices: 4044712--4044736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4044702 ATTTAATAAA
4044712 TAAAAAAATTATT
1 TAAAAAAATTATT
4044725 TAAAAAAATTAT
1 TAAAAAAATTAT
4044737 GAAAATAATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATTATT
Found at i:4046051 original size:19 final size:19
Alignment explanation
Indices: 4046024--4046066 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4046014 ATATAATTTA
4046024 AAATA-AATA-AAATAATAC
1 AAATATAATATAAAT-ATAC
*
4046042 AAATATAATATAAATATAT
1 AAATATAATATAAATATAC
4046061 AAATAT
1 AAATAT
4046067 TTAAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATAATATAAATATAC
Found at i:4046056 original size:29 final size:29
Alignment explanation
Indices: 4046003--4046063 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4045993 TATGAAGTAA
* *
4046003 AAAATATTAAAATATAATTTAAAATAAAT
1 AAAATAATAAAATATAATATAAAATAAAT
*
4046032 AAAATAATACAAATATAATAT-AAATATAT
1 AAAATAATA-AAATATAATATAAAATAAAT
4046061 AAA
1 AAA
4046064 TATTTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (29 bp):
AAAATAATAAAATATAATATAAAATAAAT
Found at i:4046080 original size:63 final size:62
Alignment explanation
Indices: 4046013--4046130 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 62
4046003 AAAATATTAA
*
4046013 AATATAAT-TTAA-AATAAATAAAATAATACAAATATAATATAAATATATAAATATTTAAAAGTT
1 AATATAATATGAATAATAAATAAAATAATA-AAAT-TAATATAAATATA-AAATATTTAAAAGTT
* * * * *
4046076 AATATTATATGAATAATTATTAACATATTAAAATTAATATAAATATAAAATATTT
1 AATATAATATGAATAATAAATAAAATAATAAAATTAATATAAATATAAAATATTT
4046131 TAAATACGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
62 8 0.17
63 20 0.43
64 7 0.15
65 12 0.26
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (62 bp):
AATATAATATGAATAATAAATAAAATAATAAAATTAATATAAATATAAAATATTTAAAAGTT
Found at i:4050610 original size:21 final size:22
Alignment explanation
Indices: 4050572--4050625 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
4050562 GTATCTTTTT
4050572 ATATAATTATTAATTATATATG
1 ATATAATTATTAATTATATATG
*
4050594 ATATAA-TATTTAA-TATATATT
1 ATATAATTA-TTAATTATATATG
*
4050615 ATATAGTTATT
1 ATATAATTATT
4050626 TATTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATATAATTATTAATTATATATG
Found at i:4050638 original size:22 final size:21
Alignment explanation
Indices: 4050570--4050639 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
4050560 TAGTATCTTT
*
4050570 TTATATAATTATTAATTATATA
1 TTATAT-ATTATTTATTATATA
* * *
4050592 TGATATAATATTTAATATATA
1 TTATATATTATTTATTATATA
* *
4050613 TTATATAGTTATTTATTTTATT
1 TTATATA-TTATTTATTATATA
4050635 TTATA
1 TTATA
4050640 ATTTTAACAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATATATTATTTATTATATA
Found at i:4052596 original size:18 final size:18
Alignment explanation
Indices: 4052582--4052645 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 18
4052572 TATAAATATC
4052582 ATATAAAAAATAAATAAA
1 ATATAAAAAATAAATAAA
*
4052600 ATATAAAATTATATGAATAAA
1 ATATAAAA--A-ATAAATAAA
4052621 ATAATAATACAAATAAAT-AA
1 AT-ATAA-A-AAATAAATAAA
4052641 ATATA
1 ATATA
4052646 TCTCGAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
18 8 0.21
19 3 0.08
20 5 0.13
21 15 0.39
22 5 0.13
23 1 0.03
24 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
ATATAAAAAATAAATAAA
Found at i:4052646 original size:33 final size:32
Alignment explanation
Indices: 4052584--4052646 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
4052574 TAAATATCAT
*
4052584 ATAAAAAATAAATAAAATATAAAATTATATGA
1 ATAAAAAATAAATAAAATATAAAAATATATGA
4052616 ATAAAATAAT-AATACAAATA-AATAAATATAT
1 ATAAAA-AATAAATA-AAATATAA-AAATATAT
4052647 CTCGAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (32 bp):
ATAAAAAATAAATAAAATATAAAAATATATGA
Found at i:4058375 original size:27 final size:27
Alignment explanation
Indices: 4058305--4058378 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
4058295 ACAAGCCAGA
*
4058305 ATTTTTTACAAATAAAAAGGAACCACC
1 ATTTTTTACAAATACAAAGGAACCACC
* *
4058332 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTTACAAATACAAAGGAACCACC
*
4058359 ATTTTTTACAAACACAAAGG
1 ATTTTTTACAAATACAAAGG
4058379 GTGGCTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (27 bp):
ATTTTTTACAAATACAAAGGAACCACC
Found at i:4059779 original size:21 final size:21
Alignment explanation
Indices: 4059738--4059827 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
4059728 CACAGATAAT
4059738 AAAATTATATCTAATAA--TATA
1 AAAATTATATC-AA-AAGTTATA
4059759 AAAATTATATCAAAAGTTATA
1 AAAATTATATCAAAAGTTATA
* * * *
4059780 AAAAGTATATTAAAAGTTCTT
1 AAAATTATATCAAAAGTTATA
* * * *
4059801 AATATTATATTAAAAATTATC
1 AAAATTATATCAAAAGTTATA
4059822 AAAATT
1 AAAATT
4059828 TTTAAAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 53 0.93
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATTATATCAAAAGTTATA
Found at i:4059941 original size:20 final size:20
Alignment explanation
Indices: 4059912--4059970 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
4059902 GATAAAAAGT
*
4059912 ATATCAAAAGTTATTAAATC
1 ATATCAAAAGCTATTAAATC
4059932 ATATTC-AAAGCTATTAGAATC
1 ATA-TCAAAAGCTATTA-AATC
4059953 ATATCAAAAGCTATTAAA
1 ATATCAAAAGCTATTAAA
4059971 ATCGTGTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
ATATCAAAAGCTATTAAATC
Found at i:4060939 original size:50 final size:50
Alignment explanation
Indices: 4060863--4061048 Score: 216
Period size: 50 Copynumber: 3.7 Consensus size: 50
4060853 TTTATTAATT
* * *
4060863 TTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTGTTCTTTACTAACT
1 TTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTGTTCTTCACTAACC
*
4060913 TTTGACAATCGAGAGAGGT-AGCCGTAATTGTTGA-TGATTCTTCACCAACC
1 TTTGACAATCGAGAGAGGTGA-CCGTAATTGTTGACTG-TTCTTCACTAACC
* * *** * *
4060963 TTTGATAATTGAGAGAGGTGGTTGTAATTGTTGATTATTCTTCA-TCAACC
1 TTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTGTTCTTCACT-AACC
*
4061013 TTTGACAATAGAGAGAGGTGACCGTAATTGTTGACT
1 TTTGACAATCGAGAGAGGTGACCGTAATTGTTGACT
4061049 CTAAGTAACT
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 3 0.03
50 110 0.96
51 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (50 bp):
TTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTGTTCTTCACTAACC
Found at i:4061038 original size:100 final size:100
Alignment explanation
Indices: 4060863--4061046 Score: 255
Period size: 100 Copynumber: 1.8 Consensus size: 100
4060853 TTTATTAATT
* * * *
4060863 TTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTGTTCTTTACTAACTTTTGACAATCGAGAG
1 TTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTATTCTTCACTAACCTTTGACAATAGAGAG
4060928 AGGTAGCCGTAATTGTTGATGATTCTTCACCAACC
66 AGGTAGCCGTAATTGTTGATGATTCTTCACCAACC
* * * * *
4060963 TTTGATAATTGAGAGAGGTGGTTGTAATTGTTGATTATTCTTCA-TCAACCTTTGACAATAGAGA
1 TTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTATTCTTCACT-AACCTTTGACAATAGAGA
4061027 GAGGT-GACCGTAATTGTTGA
65 GAGGTAG-CCGTAATTGTTGA
4061047 CTCTAAGTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 2 0.03
100 71 0.97
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (100 bp):
TTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTATTCTTCACTAACCTTTGACAATAGAGAG
AGGTAGCCGTAATTGTTGATGATTCTTCACCAACC
Found at i:4064472 original size:22 final size:22
Alignment explanation
Indices: 4064447--4064513 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
4064437 GAAGGACTTC
4064447 GGATCGACAAACAAGATTCTAG
1 GGATCGACAAACAAGATTCTAG
** *
4064469 GGAT-G-CAATGAAGGA--CTTG
1 GGATCGACAAACAA-GATTCTAG
4064488 GGATCGACAAACAAGATTCTAG
1 GGATCGACAAACAAGATTCTAG
4064510 GGAT
1 GGAT
4064514 GCAAATTCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 8 0.24
22 11 0.32
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.19
Consensus pattern (22 bp):
GGATCGACAAACAAGATTCTAG
Found at i:4064492 original size:41 final size:41
Alignment explanation
Indices: 4064435--4064517 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
4064425 AGAGTTTGAC
4064435 ATGAAGGACTTCGGATCGACAAACAAGATTCTAGGGATGCA
1 ATGAAGGACTTCGGATCGACAAACAAGATTCTAGGGATGCA
*
4064476 ATGAAGGACTTGGGATCGACAAACAAGATTCTAGGGATGCA
1 ATGAAGGACTTCGGATCGACAAACAAGATTCTAGGGATGCA
4064517 A
1 A
4064518 ATTCACCGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (41 bp):
ATGAAGGACTTCGGATCGACAAACAAGATTCTAGGGATGCA
Found at i:4065711 original size:50 final size:50
Alignment explanation
Indices: 4065462--4065721 Score: 369
Period size: 50 Copynumber: 5.2 Consensus size: 50
4065452 AAGTGTTGCC
* * *
4065462 ATTGTTGACTATTTTTCACTAACCTTTGACAATCGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
4065512 ATTGTTGACTATTCTTCACTAACATTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * * * *
4065562 ATTATTAACTATTCTTCACCAACCTTTAACAATCGAGAGAGATGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
4065612 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
4065662 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGATGT-AGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGA-CCGTA
4065712 ATTGTTGACT
1 ATTGTTGACT
4065722 CTAAGCAACT
Statistics
Matches: 189, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 1 0.01
50 188 0.99
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:4066406 original size:8 final size:8
Alignment explanation
Indices: 4066385--4066424 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
4066375 TATTATATAT
4066385 TATAAAAA
1 TATAAAAA
4066393 TAATAAAAA
1 T-ATAAAAA
4066402 TATAAAAAA
1 TAT-AAAAA
4066411 TATAAAAA
1 TATAAAAA
4066419 T-TAAAA
1 TATAAAA
4066425 TACATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 5 0.17
8 9 0.30
9 16 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TATAAAAA
Found at i:4066407 original size:17 final size:17
Alignment explanation
Indices: 4066388--4066424 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4066378 TATATATTAT
4066388 AAAAATAATAAAAATATA
1 AAAAAT-ATAAAAATATA
4066406 AAAAATATAAAAAT-TA
1 AAAAATATAAAAATATA
4066422 AAA
1 AAA
4066425 TACATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATATAAAAATATA
Found at i:4066788 original size:32 final size:31
Alignment explanation
Indices: 4066752--4066820 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
4066742 ATTATTTTTA
* *
4066752 TTTAAAT-TTAATTATAAATATTAATATAAAAT
1 TTTAAATATT-ATTATAAATAATAAAAT-AAAT
*
4066784 TTTAAATATTATTTTAAATAATAAAATAAAT
1 TTTAAATATTATTATAAATAATAAAATAAAT
4066815 TTTAAA
1 TTTAAA
4066821 ATCTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 10 0.30
32 21 0.64
33 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAAATATTATTATAAATAATAAAATAAAT
Found at i:4070568 original size:10 final size:10
Alignment explanation
Indices: 4070545--4070612 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
4070535 ATCAAAAGTA
*
4070545 ATTAAAATTAT
1 ATTAAAAAT-T
4070556 ATTAAAAATT
1 ATTAAAAATT
*
4070566 ATTAACGTAA-T
1 ATTAA--AAATT
**
4070577 ATTAAATGTT
1 ATTAAAAATT
4070587 A-TAAAAATT
1 ATTAAAAATT
*
4070596 ATTACAAATT
1 ATTAAAAATT
4070606 ATTAAAA
1 ATTAAAA
4070613 TTAAATAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
9 7 0.16
10 21 0.48
11 14 0.32
12 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:4070569 original size:21 final size:21
Alignment explanation
Indices: 4070545--4070723 Score: 108
Period size: 21 Copynumber: 8.9 Consensus size: 21
4070535 ATCAAAAGTA
4070545 ATTAAAATTATATTAAAAATT
1 ATTAAAATTATATTAAAAATT
** * **
4070566 ATTAACGTAATATTAAATGTT
1 ATTAAAATTATATTAAAAATT
* *
4070587 A-TAAAAAT-TATTACAAATT
1 ATTAAAATTATATTAAAAATT
*
4070606 ATTAAAATTA-AATAAAAAGTT
1 ATTAAAATTATATTAAAAA-TT
* * *
4070627 ATCAAATTTGTATCT-AAAATT
1 ATTAAAATTATAT-TAAAAATT
*
4070648 A-T-AAATTATA-T-CAAATT
1 ATTAAAATTATATTAAAAATT
* *
4070665 ATT-AAATT-TTTTAAATATT
1 ATTAAAATTATATTAAAAATT
* * *
4070684 ATCAAAATTAAATAAAAAATT
1 ATTAAAATTATATTAAAAATT
4070705 ATTAAAATTATATCTAAAA
1 ATTAAAATTATAT-TAAAA
4070724 TTTACCAAAA
Statistics
Matches: 113, Mismatches: 34, Indels: 21
0.67 0.20 0.12
Matches are distributed among these distances:
17 8 0.07
18 7 0.06
19 21 0.19
20 20 0.18
21 47 0.42
22 9 0.08
23 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTAAAATTATATTAAAAATT
Found at i:4070577 original size:42 final size:40
Alignment explanation
Indices: 4070531--4070610 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
4070521 TTATATTCAA
*
4070531 TAATATCAAAAGTAATTAAAATTATATTAAAAATTATTAACG
1 TAATATCAAAAGTAA-TAAAAAT-TATTAAAAATTATTAACG
* * * *
4070573 TAATATTAAATGTTATAAAAATTATTACAAATTATTAA
1 TAATATCAAAAGTAATAAAAATTATTAAAAATTATTAA
4070611 AATTAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 15 0.45
41 6 0.18
42 12 0.36
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (40 bp):
TAATATCAAAAGTAATAAAAATTATTAAAAATTATTAACG
Found at i:4070968 original size:21 final size:21
Alignment explanation
Indices: 4070916--4070971 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
4070906 ACAAAAAAAA
*
4070916 TTATTAAAATTTTATTAAAGG
1 TTATTAAAATTATATTAAAGG
*
4070937 TTATT-AAATTATATTAAATG
1 TTATTAAAATTATATTAAAGG
4070957 TTATTAAAATTATAT
1 TTATTAAAATTATAT
4070972 CAAAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTATTAAAATTATATTAAAGG
Found at i:4072468 original size:11 final size:11
Alignment explanation
Indices: 4072442--4072521 Score: 65
Period size: 11 Copynumber: 6.9 Consensus size: 11
4072432 TCTAGATTTG
*
4072442 ATAATATTAAAC
1 ATAATA-TAAAA
*
4072454 ATAATATAAAT
1 ATAATATAAAA
4072465 ATAATATAAAA
1 ATAATATAAAA
4072476 ATAAT-T-AAA
1 ATAATATAAAA
4072485 ATACGATACGTATAAA
1 ATA--ATA--TA-AAA
*
4072501 ATAATATAAAC
1 ATAATATAAAA
4072512 ATAATATAAA
1 ATAATATAAA
4072522 TATATAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
9 6 0.10
10 1 0.02
11 33 0.57
12 8 0.14
14 4 0.07
16 6 0.10
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:4073297 original size:3 final size:3
Alignment explanation
Indices: 4073289--4073323 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4073279 TATAAATTTG
4073289 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4073324 ACACCCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4076652 original size:2 final size:2
Alignment explanation
Indices: 4076645--4076673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4076635 CTAATGATTA
4076645 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
4076674 ATGGGTTAAA
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:4078379 original size:142 final size:142
Alignment explanation
Indices: 4078123--4078403 Score: 562
Period size: 142 Copynumber: 2.0 Consensus size: 142
4078113 CTTACTGAAT
4078123 TTCCCGAAGTTAAAAATCTTTCTCCTTGATGCTGTGGGACTCATAAATCTCTAGCTGAATTCTTG
1 TTCCCGAAGTTAAAAATCTTTCTCCTTGATGCTGTGGGACTCATAAATCTCTAGCTGAATTCTTG
4078188 TTTTCTGATAATGAAACTCCAGATTTTTCTTCTTTTTCATTTAAGTTTAGTACATGAATTTATGG
66 TTTTCTGATAATGAAACTCCAGATTTTTCTTCTTTTTCATTTAAGTTTAGTACATGAATTTATGG
4078253 GATGTAAATTTA
131 GATGTAAATTTA
4078265 TTCCCGAAGTTAAAAATCTTTCTCCTTGATGCTGTGGGACTCATAAATCTCTAGCTGAATTCTTG
1 TTCCCGAAGTTAAAAATCTTTCTCCTTGATGCTGTGGGACTCATAAATCTCTAGCTGAATTCTTG
4078330 TTTTCTGATAATGAAACTCCAGATTTTTCTTCTTTTTCATTTAAGTTTAGTACATGAATTTATGG
66 TTTTCTGATAATGAAACTCCAGATTTTTCTTCTTTTTCATTTAAGTTTAGTACATGAATTTATGG
4078395 GATGTAAAT
131 GATGTAAAT
4078404 ATTTTATACA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (142 bp):
TTCCCGAAGTTAAAAATCTTTCTCCTTGATGCTGTGGGACTCATAAATCTCTAGCTGAATTCTTG
TTTTCTGATAATGAAACTCCAGATTTTTCTTCTTTTTCATTTAAGTTTAGTACATGAATTTATGG
GATGTAAATTTA
Found at i:4079191 original size:58 final size:58
Alignment explanation
Indices: 4079121--4079236 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
4079111 GTCCCTTGGC
4079121 TGCAAACACATCGTCTTCGGGATCCTTCTCTAACAAGTTGGTGAGAATTGTAGAGCAA
1 TGCAAACACATCGTCTTCGGGATCCTTCTCTAACAAGTTGGTGAGAATTGTAGAGCAA
4079179 TGCAAACACATCGTCTTCGGGATCCTTCTCTAACAAGTTGGTGAGAATTGTAGAGCAA
1 TGCAAACACATCGTCTTCGGGATCCTTCTCTAACAAGTTGGTGAGAATTGTAGAGCAA
4079237 AGAACAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (58 bp):
TGCAAACACATCGTCTTCGGGATCCTTCTCTAACAAGTTGGTGAGAATTGTAGAGCAA
Found at i:4079538 original size:34 final size:34
Alignment explanation
Indices: 4079490--4079706 Score: 335
Period size: 34 Copynumber: 6.4 Consensus size: 34
4079480 AAATATTTTA
* * *
4079490 CTCACCTAACACATTACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
* * *
4079524 TTCACCAAATACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
* *
4079558 CTCACCAAATACAGCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
* *
4079592 CTCACCAAATACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
*
4079626 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
4079660 CTCACCAAATACATCACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
4079694 CTCACCAAATACA
1 CTCACCAAATACA
4079707 CTTAACAAAG
Statistics
Matches: 166, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 166 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAATATT
Found at i:4079678 original size:25 final size:25
Alignment explanation
Indices: 4079581--4079682 Score: 69
Period size: 25 Copynumber: 4.4 Consensus size: 25
4079571 GCACCTAACA
4079581 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
* * * *
4079606 TACCTAACACATCT-A--ATATTC-T
1 CACCTAACA-TTCTCACCAAATACAT
* *
4079628 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
4079649 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
4079674 CACCTAACA
1 CACCTAACA
4079683 CACCTAATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 22
0.64 0.11 0.25
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 8 0.14
22 13 0.23
23 8 0.14
24 3 0.05
25 18 0.32
26 3 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:4084463 original size:34 final size:34
Alignment explanation
Indices: 4084415--4084631 Score: 335
Period size: 34 Copynumber: 6.4 Consensus size: 34
4084405 AAATATTTTA
* * * *
4084415 CTCACCTAACACATTACCTAGCACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
* * *
4084449 TTCACCAAATACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
*
4084483 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
* *
4084517 CTCACCAAATACATTACCTAACACATCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
*
4084551 CTCACCAAATACATCACCTAACACACCTAACATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
4084585 CTCACCAAATACATCACCTAACACACCTAATATT
1 CTCACCAAATACATCACCTAACACACCTAATATT
4084619 CTCACCAAATACA
1 CTCACCAAATACA
4084632 CTTAACAAAG
Statistics
Matches: 167, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 167 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (34 bp):
CTCACCAAATACATCACCTAACACACCTAATATT
Found at i:4084603 original size:25 final size:25
Alignment explanation
Indices: 4084506--4084607 Score: 69
Period size: 25 Copynumber: 4.4 Consensus size: 25
4084496 TCACCTAACA
4084506 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
* * * *
4084531 TACCTAACACATCT-A--ATATTC-T
1 CACCTAACA-TTCTCACCAAATACAT
* *
4084553 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
4084574 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
4084599 CACCTAACA
1 CACCTAACA
4084608 CACCTAATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 22
0.64 0.11 0.25
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 8 0.14
22 13 0.23
23 8 0.14
24 3 0.05
25 18 0.32
26 3 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:4088858 original size:28 final size:28
Alignment explanation
Indices: 4088820--4088889 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
4088810 AAACAAGCCT
*
4088820 CCATATTTGACAAATC-CAAAGGA-AACCA
1 CCATTTTTGACAAATCACAAA--ATAACCA
4088848 CCATTTTTGACAAA-CACAAAATAACCA
1 CCATTTTTGACAAATCACAAAATAACCA
*
4088875 TCATTTTTGACAAAT
1 CCATTTTTGACAAAT
4088890 AAATAAGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (28 bp):
CCATTTTTGACAAATCACAAAATAACCA
Found at i:4089558 original size:22 final size:24
Alignment explanation
Indices: 4089527--4089581 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
4089517 AATCTAATTT
*
4089527 AAATTATTATTTAAA-TAA-TA-A
1 AAATTTTTATTTAAATTAATTATA
4089548 AAATATTTTATTTAAATTAATTATA
1 AAAT-TTTTATTTAAATTAATTATA
4089573 AAATTTTTA
1 AAATTTTTA
4089582 ATATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.14
22 10 0.34
23 3 0.10
24 7 0.24
25 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATTTTTATTTAAATTAATTATA
Found at i:4089599 original size:26 final size:25
Alignment explanation
Indices: 4089535--4089603 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
4089525 TTAAATTATT
*
4089535 ATTTAAATAATAAAAATATTTTATTTA
1 ATTTAAATAAT-AAAAT-TTTTATATA
* *
4089562 AATT-AATTATAAAATTTTTAATATA
1 ATTTAAATAATAAAATTTTT-ATATA
*
4089587 TTTTAAATAATAAAATT
1 ATTTAAATAATAAAATT
4089604 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 4 0.12
25 11 0.32
26 16 0.47
27 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTAAATAATAAAATTTTTATATA
Found at i:4090649 original size:5 final size:5
Alignment explanation
Indices: 4090639--4090697 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
4090629 CAACATATAA
* * *
4090639 AATAT AATAT AATAT AAATTT AATAT AA-AT -ATAT ATATAT ATTAA AAT-T
1 AATAT AATAT AATAT -AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT
4090688 AATAT AATAT
1 AATAT AATAT
4090698 TAATTATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
3 1 0.02
4 7 0.16
5 26 0.60
6 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:4090664 original size:11 final size:11
Alignment explanation
Indices: 4090633--4090697 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
4090623 TTAAATCAAC
*
4090633 ATATAAAATATA
1 ATATAATATA-A
4090645 ATATAATATAA
1 ATATAATATAA
*
4090656 ATTTAATATAA
1 ATATAATATAA
*
4090667 ATAT-ATATAT
1 ATATAATATAA
* *
4090677 ATATTAAAATTA
1 ATA-TAATATAA
4090689 ATATAATAT
1 ATATAATAT
4090698 TAATTATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
10 8 0.19
11 20 0.47
12 15 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAATATAA
Found at i:4090665 original size:28 final size:29
Alignment explanation
Indices: 4090633--4090694 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
4090623 TTAAATCAAC
*
4090633 ATATAAAATATA-ATATA-ATATAAATTTA
1 ATATAAAATATATATATATAT-TAAAATTA
4090661 ATAT-AAATATATATATATATTAAAATTA
1 ATATAAAATATATATATATATTAAAATTA
4090689 ATATAA
1 ATATAA
4090695 TATTAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 20 0.67
29 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATAAAATATATATATATATTAAAATTA
Found at i:4090725 original size:15 final size:15
Alignment explanation
Indices: 4090672--4090731 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
4090662 TATAAATATA
*
4090672 TATATATATTAAAAT
1 TATATAAATTAAAAT
*
4090687 TAATATAATATTAATTAT
1 T-ATATAA-ATTAA-AAT
4090705 TA-ATAAATTAAAAT
1 TATATAAATTAAAAT
4090719 TATATAAA-TAAAA
1 TATATAAATTAAAA
4090732 AATATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 11 0.29
16 9 0.24
17 6 0.16
18 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATAAATTAAAAT
Found at i:4091480 original size:21 final size:21
Alignment explanation
Indices: 4091446--4091496 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
4091436 CGTTTAATTC
4091446 AATTTAAA-TTAAATAAAAAT
1 AATTTAAATTTAAATAAAAAT
* * *
4091466 ATTTTAAATTTAAATTAATAT
1 AATTTAAATTTAAATAAAAAT
4091487 AATTTAAATT
1 AATTTAAATT
4091497 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTAAATTTAAATAAAAAT
Found at i:4092372 original size:30 final size:30
Alignment explanation
Indices: 4092328--4092402 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
4092318 TATTTTATCG
*
4092328 TATTATAATTATATT-TA-ATAATTTTAATA
1 TATTATAATTATATTATATA-AATTTTAAAA
*
4092357 TATTAATATTTATATTATATAAATTTTAAAA
1 TATT-ATAATTATATTATATAAATTTTAAAA
4092388 TA-TAT-ATTAATATTA
1 TATTATAATT-ATATTA
4092403 CATCATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 2 0.05
29 12 0.31
30 11 0.28
31 13 0.33
32 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTATAATTATATTATATAAATTTTAAAA
Found at i:4096568 original size:22 final size:22
Alignment explanation
Indices: 4096540--4096582 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4096530 GGGCGGTTGA
4096540 TAATATAATAAAGATTTATATT
1 TAATATAATAAAGATTTATATT
* *
4096562 TAATATATTAATGATTTATAT
1 TAATATAATAAAGATTTATAT
4096583 ACCATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAATATAATAAAGATTTATATT
Found at i:4097084 original size:15 final size:14
Alignment explanation
Indices: 4097060--4097094 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4097050 GTCATCCATT
4097060 AAATTTAATATTTA
1 AAATTTAATATTTA
4097074 AAATATTAATATTTA
1 AAAT-TTAATATTTA
*
4097089 TAATTT
1 AAATTT
4097095 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTTAATATTTA
Found at i:4098123 original size:14 final size:13
Alignment explanation
Indices: 4098097--4098126 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
4098087 TATGTTTAAA
4098097 ATATTTTATATTT
1 ATATTTTATATTT
4098110 ATATTTTAATATTT
1 ATATTTT-ATATTT
4098124 ATA
1 ATA
4098127 AATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATTTTATATTT
Found at i:4099388 original size:2 final size:2
Alignment explanation
Indices: 4099383--4099418 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4099373 CTAAAAAAAA
*
4099383 AC AC AC AC CC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4099419 CAAGATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4100162 original size:27 final size:28
Alignment explanation
Indices: 4100112--4100175 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
4100102 TTTTTAAATA
* *
4100112 TTTTTATCA-ATTAAATTAATATC-ACT
1 TTTTTATAATATTAAATTAATATCAACC
*
4100138 TATTTTATAATATTAAATTTA-ATCAACC
1 T-TTTTATAATATTAAATTAATATCAACC
4100166 TTTTTATAAT
1 TTTTTATAAT
4100176 TACCACAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 1 0.03
27 19 0.59
28 12 0.38
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTATAATATTAAATTAATATCAACC
Found at i:4101827 original size:21 final size:21
Alignment explanation
Indices: 4101801--4101852 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
4101791 CCACCAGTGT
* *
4101801 CACCACCACCGCCGCCGCCGC
1 CACCACCACCGCCACCACCGC
*
4101822 CACCACCACCTCCACCACCGC
1 CACCACCACCGCCACCACCGC
*
4101843 CGCCACCACC
1 CACCACCACC
4101853 AGTGTCATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.67, G:0.12, T:0.02
Consensus pattern (21 bp):
CACCACCACCGCCACCACCGC
Found at i:4101838 original size:12 final size:12
Alignment explanation
Indices: 4101818--4101853 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4101808 ACCGCCGCCG
4101818 CCGCCACCACCA
1 CCGCCACCACCA
* *
4101830 CCTCCACCACCG
1 CCGCCACCACCA
4101842 CCGCCACCACCA
1 CCGCCACCACCA
4101854 GTGTCATCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.22, C:0.67, G:0.08, T:0.03
Consensus pattern (12 bp):
CCGCCACCACCA
Found at i:4101842 original size:24 final size:24
Alignment explanation
Indices: 4101801--4101853 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
4101791 CCACCAGTGT
* *
4101801 CACCACCACCGCCGCCGCCGCCAC
1 CACCACCACCACCACCGCCGCCAC
*
4101825 CACCACCTCCACCACCGCCGCCAC
1 CACCACCACCACCACCGCCGCCAC
4101849 CACCA
1 CACCA
4101854 GTGTCATCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.66, G:0.11, T:0.02
Consensus pattern (24 bp):
CACCACCACCACCACCGCCGCCAC
Found at i:4103053 original size:14 final size:14
Alignment explanation
Indices: 4103034--4103071 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4103024 AAAATTAAAA
*
4103034 AATATTTTTATATT
1 AATATTTATATATT
4103048 AATATTTATA-ATT
1 AATATTTATATATT
4103061 AA-ATTTATATA
1 AATATTTATATA
4103072 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:4109073 original size:33 final size:35
Alignment explanation
Indices: 4109011--4109080 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
4109001 TTTTTATTTT
*
4109011 AATTTATATTTTTTAATTAAATTATATAAAATATA
1 AATTTATATTTTTAAATTAAATTATATAAAATATA
*
4109046 AATTT-TATTTTTAAA-TATAATTA-ATAAATTATA
1 AATTTATATTTTTAAATTA-AATTATATAAAATATA
4109079 AA
1 AA
4109081 AAAAAAAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 13 0.41
34 14 0.44
35 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
AATTTATATTTTTAAATTAAATTATATAAAATATA
Found at i:4109720 original size:19 final size:21
Alignment explanation
Indices: 4109678--4109725 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
4109668 TATGAATCAG
*
4109678 AAAATATAATTTTAAAAATAT
1 AAAATATAATTTAAAAAATAT
4109699 AAAATA-AATTTAAAAAAT-T
1 AAAATATAATTTAAAAAATAT
4109718 AAATATAT
1 AAA-ATAT
4109726 TCTATTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATAATTTAAAAAATAT
Found at i:4115572 original size:2 final size:2
Alignment explanation
Indices: 4115565--4115591 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4115555 ATACTAAATT
4115565 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
4115592 TGCAAAGGCA
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:4115942 original size:19 final size:18
Alignment explanation
Indices: 4115920--4115999 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
4115910 ATTTGTATAA
4115920 TTATATTATATTTTTATT
1 TTATATTATATTTTTATT
*
4115938 TT-TATTATAATTAATTATT
1 TTATATTAT-ATT-TTTATT
* * * *
4115957 TTTTAATAAATTTATATT
1 TTATATTATATTTTTATT
* *
4115975 TAATATCATA-TTTTATTT
1 TTATATTATATTTTTA-TT
4115993 TTATATT
1 TTATATT
4116000 TTATGTATCA
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
17 10 0.22
18 21 0.47
19 10 0.22
20 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTATATTTTTATT
Found at i:4116262 original size:12 final size:12
Alignment explanation
Indices: 4116245--4116277 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4116235 CACATTTTGT
4116245 TTAATAATATTA
1 TTAATAATATTA
4116257 TTAATAATTATTA
1 TTAATAA-TATTA
4116270 TT-ATAATA
1 TTAATAATA
4116278 ATACAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 11 0.55
13 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:4119205 original size:15 final size:14
Alignment explanation
Indices: 4119184--4119227 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4119174 AAAAGTAATA
4119184 AAAATAATATATTT
1 AAAATAATATATTT
*
4119198 AAATATAAAATATTT
1 AAA-ATAATATATTT
*
4119213 TAAATAATA-ATTT
1 AAAATAATATATTT
4119226 AA
1 AA
4119228 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATAATATATTT
Found at i:4119273 original size:25 final size:24
Alignment explanation
Indices: 4119244--4119297 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
4119234 TTAATTAATA
* **
4119244 TTTATAAATATTCGTTAATCCAATC
1 TTTATAAATACTAATTAA-CCAATC
*
4119269 TTTATATATACTAATTAACCAATC
1 TTTATAAATACTAATTAACCAATC
4119293 TTTAT
1 TTTAT
4119298 TCAGACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTATAAATACTAATTAACCAATC
Done.