Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 31
Found at i:3460900 original size:19 final size:19
Alignment explanation
Indices: 3460876--3460924 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3460866 ATAAAATAAT
3460876 AATAAAATAAAAAATAAAA
1 AATAAAATAAAAAATAAAA
*
3460895 AATAAACAGT--AAAATATAA
1 AATAAA-A-TAAAAAATAAAA
3460914 AATAAAATAAA
1 AATAAAATAAA
3460925 CATGCATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 21 0.84
20 1 0.04
21 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AATAAAATAAAAAATAAAA
Found at i:3460917 original size:7 final size:7
Alignment explanation
Indices: 3460865--3460915 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
3460855 TAATTAAGCT
3460865 AATAAAA
1 AATAAAA
3460872 TAATAATAA
1 -AATAA-AA
3460881 AATAAAA
1 AATAAAA
3460888 AATAAAA
1 AATAAAA
*
3460895 AATAAAC
1 AATAAAA
*
3460902 AGTAAAA
1 AATAAAA
*
3460909 TATAAAA
1 AATAAAA
3460916 TAAAATAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 25 0.68
8 10 0.27
9 2 0.05
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (7 bp):
AATAAAA
Found at i:3462553 original size:66 final size:65
Alignment explanation
Indices: 3462447--3462626 Score: 245
Period size: 66 Copynumber: 2.7 Consensus size: 65
3462437 AGGGTGATGG
* * *
3462447 TTTCAAGAGAAACCATCTCAAGAGAGACAAAACATGTTTCAAGGGAAACA-ATCTCAAAGGTTGG
1 TTTCAAGGGAAACCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACATAT-TCAAAGATT-G
3462511 TA
64 TA
* * *
3462513 TTTCAAGGGAAACCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACATATTCAAATATTTTG
1 TTTCAAGGGAAACCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACATATTCAAAGATTGTA
* * *
3462578 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAA
1 TTTCAAGGGAAACCGTCTCAAGAGAGACAAAAC-ATGTTTCAAGGGAAA
3462627 TTGTCTCAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
65 33 0.32
66 68 0.66
67 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (65 bp):
TTTCAAGGGAAACCGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACATATTCAAAGATTGTA
Found at i:3462632 original size:37 final size:37
Alignment explanation
Indices: 3462574--3462869 Score: 339
Period size: 37 Copynumber: 8.3 Consensus size: 37
3462564 ATTCAAATAT
*
3462574 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
*
3462611 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* *
3462648 TTTGTTTTAAGAGAAATTGTCTCAAGAGAGAC-AAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * *
3462684 TTTGTTTCAAGGGAAAATGTCTCAAG-GAAGAC-AAAT
1 TTTGTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAAC
* ** *
3462720 TTTGTTTCAAGGGAAA------C-A-A-ATTCAACAAT
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AAC
*
3462749 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
*
3462786 ATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* *
3462823 TTTGTTTCAAGAGAAATTGTCTCAAGAGAAAC-AAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
*
3462859 TTTGTCTCAAG
1 TTTGTTTCAAG
3462870 GGAGACAAAT
Statistics
Matches: 228, Mismatches: 18, Indels: 27
0.84 0.07 0.10
Matches are distributed among these distances:
27 2 0.01
28 1 0.00
29 20 0.09
30 1 0.00
35 2 0.01
36 65 0.29
37 133 0.58
38 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (37 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
Found at i:3462730 original size:175 final size:173
Alignment explanation
Indices: 3462513--3463034 Score: 666
Period size: 175 Copynumber: 3.1 Consensus size: 173
3462503 AAGGTTGGTA
* ***
3462513 TTTCAAGGGAAACCGTCTCAA-GAGAGACAAAACATGTTTCAAGGGAAACATATTCAAATATTTT
1 TTTCAAGGGAAA-TGTCTCAAGGA-AGACAAATTTTGTTTCAAGGGAAACATATTCAAA-ATTTT
*
3462577 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
63 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
3462642 CAAAACTTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAACTTTG
128 CAAAACTTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAACTTTG
*
3462688 TTTCAAGGGAAAATGTCTCAAGGAAGACAAATTTTGTTTCAAGGGAAACAAATTCAACAATTTTG
1 TTTCAAGGG-AAATGTCTCAAGGAAGACAAATTTTGTTTCAAGGGAAACATATTCAA-AATTTTG
*
3462753 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
64 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
* *
3462818 AAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAAACAAAC----
129 AAAACTTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAACTTTG
* * *
3462859 -TT---------TGTCTCAAGGGAGACAAATTTTGTTTAAAGGGAAACATATTCAACGATTTTGT
1 TTTCAAGGGAAATGTCTCAAGGAAGACAAATTTTGTTTCAAGGGAAACATATTCAA-AATTTTGT
* * * *
3462914 TTCAAGGGAAACTATCCCAAGAGAGACAAAACTTTGTTTCAGGAGAAACTGTCTCAAGGGAGAC-
65 TTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
* * *
3462978 AAATTTTGTTTTAAGAGAAACTGTCTCAAG-GATGACGGAA-TTTG
130 AAACTTTGTTTTAAGAGAAATTGTCTCAAGAGA-GAC-AAACTTTG
*
3463022 TTTCAAGAGAAAT
1 TTTCAAGGGAAAT
3463035 AGATTCAAAG
Statistics
Matches: 305, Mismatches: 23, Indels: 40
0.83 0.06 0.11
Matches are distributed among these distances:
158 2 0.01
159 29 0.10
160 110 0.36
164 2 0.01
170 2 0.01
173 1 0.00
175 153 0.50
176 6 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (173 bp):
TTTCAAGGGAAATGTCTCAAGGAAGACAAATTTTGTTTCAAGGGAAACATATTCAAAATTTTGTT
TCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAACTTTG
Found at i:3462785 original size:138 final size:139
Alignment explanation
Indices: 3462611--3462880 Score: 427
Period size: 138 Copynumber: 1.9 Consensus size: 139
3462601 GAGACAAAAC
* * * *
3462611 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTTAAGAGAAATTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAG
* * *
3462676 AGAC-AAACTTTGTTTCAAGGGAAAATGTCTCAAG-GAAGACAAATTTTGTTTCAAGGGAAACAA
66 AGACAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAA-ACAAACTTTGTCTCAAGGGAAACAA
3462739 ATTCAACAAT
130 ATTCAACAAT
*
3462749 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAG
* *
3462814 AGACAAAACTTTGTTTCAAGAGAAATTGTCTCAAGAGAAACAAACTTTGTCTCAAGGGAGACAAA
66 AGACAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAAACAAACTTTGTCTCAAGGGAAACAAA
3462879 TT
131 TT
3462881 TTGTTTAAAG
Statistics
Matches: 120, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
138 64 0.53
139 53 0.44
140 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (139 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAG
AGACAAAACTTTGTTTCAAGAGAAAATGTCTCAAGAGAAACAAACTTTGTCTCAAGGGAAACAAA
TTCAACAAT
Found at i:3462795 original size:22 final size:21
Alignment explanation
Indices: 3462762--3462836 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
3462752 GTTTCAAGGG
*
3462762 AAAC-TGTCTCAAGAGAGACA
1 AAACTTGTTTCAAGAGAGACA
3462782 AAACATTGTTTC-A-AGAG---
1 AAAC-TTGTTTCAAGAGAGACA
*
3462799 AAAC-TGTCTCAAGAGAGACA
1 AAACTTGTTTCAAGAGAGACA
3462819 AAACTTTGTTTCAAGAGA
1 AAAC-TTGTTTCAAGAGA
3462837 AATTGTCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
15 5 0.12
16 1 0.02
17 8 0.19
20 12 0.28
21 1 0.02
22 16 0.37
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (21 bp):
AAACTTGTTTCAAGAGAGACA
Found at i:3462798 original size:20 final size:19
Alignment explanation
Indices: 3462775--3462836 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
3462765 CTGTCTCAAG
3462775 AGAGACAAAACATTGTTTCA
1 AGAGACAAAAC-TTGTTTCA
*
3462795 AGAG---AAAC-TGTCTCAA
1 AGAGACAAAACTTGTTTC-A
3462811 GAGAGACAAAACTTTGTTTCA
1 -AGAGACAAAAC-TTGTTTCA
3462832 AGAGA
1 AGAGA
3462837 AATTGTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 5 0.15
16 1 0.03
17 8 0.24
20 13 0.39
21 1 0.03
22 5 0.15
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (19 bp):
AGAGACAAAACTTGTTTCA
Found at i:3462847 original size:15 final size:15
Alignment explanation
Indices: 3462824--3462853 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3462814 AGACAAAACT
*
3462824 TTGTTTCAAGAGAAA
1 TTGTCTCAAGAGAAA
3462839 TTGTCTCAAGAGAAA
1 TTGTCTCAAGAGAAA
3462854 CAAACTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (15 bp):
TTGTCTCAAGAGAAA
Found at i:3462865 original size:21 final size:21
Alignment explanation
Indices: 3462766--3462884 Score: 82
Period size: 21 Copynumber: 6.1 Consensus size: 21
3462756 CAAGGGAAAC
*
3462766 TGTCTCAAGAGAGACAAAACAT
1 TGTCTCAAGAGAGAC-AAACTT
*
3462788 TGTTTC-A-AGAG--AAAC--
1 TGTCTCAAGAGAGACAAACTT
3462803 TGTCTCAAGAGAGACAAAACTT
1 TGTCTCAAGAGAGAC-AAACTT
*
3462825 TGTTTC-A-AGAG--AAA--T
1 TGTCTCAAGAGAGACAAACTT
*
3462840 TGTCTCAAGAGAAACAAACTT
1 TGTCTCAAGAGAGACAAACTT
* *
3462861 TGTCTCAAGGGAGACAAATTT
1 TGTCTCAAGAGAGACAAACTT
3462882 TGT
1 TGT
3462885 TTAAAGGGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 27
0.68 0.07 0.24
Matches are distributed among these distances:
15 11 0.14
16 2 0.03
17 14 0.18
19 3 0.04
20 12 0.16
21 24 0.32
22 10 0.13
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (21 bp):
TGTCTCAAGAGAGACAAACTT
Found at i:3462867 original size:160 final size:159
Alignment explanation
Indices: 3462701--3463007 Score: 497
Period size: 160 Copynumber: 1.9 Consensus size: 159
3462691 CAAGGGAAAA
*
3462701 TGTCTCAAGGAAGACAAATTTTGTTTCAAGGGAAACAAATTCAACAATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGAAGACAAATTTTGTTTAAAGGGAAACAAATTCAACAATTTTGTTTCAAGGGAAAC
* *
3462766 TGTCTCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTC
66 TATCCCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAACTTTGTTTC
*
3462831 AAGAGAAATTGTCTCAAGAGAAACAAACTT
130 AAGAGAAACTGTCTCAAGAGAAACAAACTT
* * *
3462861 TGTCTCAAGGGAGACAAATTTTGTTTAAAGGGAAACATATTCAACGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGAAGACAAATTTTGTTTAAAGGGAAACAAATTCAACAATTTTGTTTCAAGGGAAAC
* * * * *
3462926 TATCCCAAGAGAGACAAAACTTTGTTTCAGGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTTA
66 TATCCCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACTTTGTTTCA
3462991 AGAGAAACTGTCTCAAG
131 AGAGAAACTGTCTCAAG
3463008 GATGACGGAA
Statistics
Matches: 135, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
159 27 0.20
160 108 0.80
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (159 bp):
TGTCTCAAGGAAGACAAATTTTGTTTAAAGGGAAACAAATTCAACAATTTTGTTTCAAGGGAAAC
TATCCCAAGAGAGACAAAACATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAACTTTGTTTCA
AGAGAAACTGTCTCAAGAGAAACAAACTT
Found at i:3462891 original size:21 final size:21
Alignment explanation
Indices: 3462839--3462893 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3462829 TCAAGAGAAA
* * *
3462839 TTGTCTCAAGAGAAACAAACT
1 TTGTCTAAAGGGAGACAAACT
* *
3462860 TTGTCTCAAGGGAGACAAATT
1 TTGTCTAAAGGGAGACAAACT
*
3462881 TTGTTTAAAGGGA
1 TTGTCTAAAGGGA
3462894 AACATATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGTCTAAAGGGAGACAAACT
Found at i:3462996 original size:36 final size:37
Alignment explanation
Indices: 3462907--3463033 Score: 143
Period size: 36 Copynumber: 3.5 Consensus size: 37
3462897 ATATTCAACG
* * * *
3462907 ATTTTGTTTCAAGGGAAACTATCCCAAGAGAGACAAA
1 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
* *
3462944 ACTTTGTTTCAGGAGAAACTGTCTCAAGGGAGAC-AA
1 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
* **
3462980 ATTTTGTTTTAAGAGAAACTGTCTCAA-GGATGACGGA
1 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGA-GACAAA
3463017 A-TTTGTTTCAAGAGAAA
1 ATTTTGTTTCAAGAGAAA
3463034 TAGATTCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
35 3 0.04
36 44 0.57
37 30 0.39
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
Found at i:3463608 original size:20 final size:22
Alignment explanation
Indices: 3463583--3463622 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3463573 AGTCGTATAT
3463583 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3463603 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3463623 TATACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3463674 original size:21 final size:21
Alignment explanation
Indices: 3463650--3463692 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3463640 CCCAGAATAG
*
3463650 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3463671 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3463692 A
1 A
3463693 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:3463765 original size:19 final size:20
Alignment explanation
Indices: 3463728--3463769 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3463718 CTGTTGAACA
3463728 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3463748 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3463768 GG
1 GG
3463770 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:3463846 original size:15 final size:15
Alignment explanation
Indices: 3463826--3463870 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
3463816 CCCCCTGGGG
3463826 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3463841 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3463856 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3463871 CCTGGGGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:3463884 original size:20 final size:20
Alignment explanation
Indices: 3463856--3463896 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3463846 ATCTGTACCC
* *
3463856 GGGGTATCTGTACCCCCTGG
1 GGGGAATCTATACCCCCTGG
3463876 GGGGAATCTATACCCCCTGG
1 GGGGAATCTATACCCCCTGG
3463896 G
1 G
3463897 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (20 bp):
GGGGAATCTATACCCCCTGG
Found at i:3464017 original size:28 final size:31
Alignment explanation
Indices: 3463986--3464042 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
3463976 AACTTTGAAT
*
3463986 AATTCAATT-ACGTCC-AAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
3464014 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
3464043 CCTTAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 5 0.20
30 4 0.16
31 7 0.28
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:3465256 original size:19 final size:20
Alignment explanation
Indices: 3465213--3465260 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3465203 TTTAAATCCT
*
3465213 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3465233 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3465252 TTTTCAAAA
1 TTTTCAAAA
3465261 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3466182 original size:34 final size:32
Alignment explanation
Indices: 3466120--3466189 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3466110 ACCTTACAAC
* *
3466120 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGACTAAACTAGAACCTT
*
3466152 TCCCTAGCTTTTACACGGACTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGACTAAACTAGAACCTT
3466186 TCCC
1 TCCC
3466190 CTTTATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGACTAAACTAGAACCTT
Found at i:3466429 original size:20 final size:22
Alignment explanation
Indices: 3466404--3466443 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3466394 AGTCGTATAT
3466404 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3466424 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3466444 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3466495 original size:21 final size:21
Alignment explanation
Indices: 3466471--3466513 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3466461 CCCAGAATAG
*
3466471 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3466492 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3466513 A
1 A
3466514 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:3466576 original size:22 final size:22
Alignment explanation
Indices: 3466549--3466592 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3466539 CTGTTGAACA
3466549 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCGGTACCCCCTGG
3466571 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCGGTACCCCCTGG
3466593 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCCTGG
Found at i:3466651 original size:21 final size:21
Alignment explanation
Indices: 3466626--3466704 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
3466616 AAAACCTGCA
*
3466626 GGGGGTATCTGTACCCGCTGG
1 GGGGGTATCTGTACCCCCTGG
3466647 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
3466663 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
3466683 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
3466704 G
1 G
3466705 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 2 0.04
21 32 0.65
ACGTcount: A:0.13, C:0.27, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:3466667 original size:36 final size:36
Alignment explanation
Indices: 3466627--3466698 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3466617 AAACCTGCAG
* * *
3466627 GGGGTATCTGTACCCGCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
3466663 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
3466699 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.26, G:0.36, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:3466668 original size:15 final size:15
Alignment explanation
Indices: 3466648--3466677 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3466638 ACCCGCTGGG
3466648 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3466663 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3466678 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:3466826 original size:29 final size:31
Alignment explanation
Indices: 3466794--3466853 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3466784 AAACTTTGAA
*
3466794 TAAATTCAATT-ACGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3466823 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
3466854 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:3467061 original size:36 final size:36
Alignment explanation
Indices: 3466893--3467075 Score: 129
Period size: 36 Copynumber: 5.0 Consensus size: 36
3466883 AACAGGAAAC
* **
3466893 TGTCTCAAGAGAGACAAAACTTTGTTTCAA-GAGAAGC
1 TGTCTCAAGAGAGACAAAA-TTTGTTTTAAGGA-AAAT
* * *
3466930 TGTCTCAAGAGAGAC-AAACTTGTTTTGAGTAAAAAT
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAG-GAAAAT
* **
3466966 TGTCTCAAGTGAGACAAAATTCAT-TTTTTTGGAGAAAT
1 TGTCTCAAGAGAGACAAAATT--TGTTTTAAGGA-AAAT
* * **
3467004 TAATCTCAAGTGAGATTAAATTTGTTTTAAGGAAAAT
1 T-GTCTCAAGAGAGACAAAATTTGTTTTAAGGAAAAT
* * * *
3467041 TGTCTCCAGCGAGACAAAATTTGTTCTCAGGAAAA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGAAAA
3467076 CTATCTCATG
Statistics
Matches: 115, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
35 7 0.06
36 46 0.40
37 27 0.23
38 17 0.15
39 18 0.16
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGAGAGACAAAATTTGTTTTAAGGAAAAT
Found at i:3467551 original size:20 final size:20
Alignment explanation
Indices: 3467494--3467555 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3467484 AAGACTTGTA
*
3467494 GATGGCCCGAAGGACTTACA
1 GATGGCCCGAAGGACTTACT
* * * *
3467514 CATCACGCTCGAAAGACTTACT
1 GAT--GGCCCGAAGGACTTACT
3467536 GATGGCCCGAAGGACTTACT
1 GATGGCCCGAAGGACTTACT
3467556 TATCAAGAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 16 0.52
22 15 0.48
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.19
Consensus pattern (20 bp):
GATGGCCCGAAGGACTTACT
Found at i:3467901 original size:280 final size:272
Alignment explanation
Indices: 3467161--3467905 Score: 963
Period size: 264 Copynumber: 2.7 Consensus size: 272
3467151 AAAGGAAATA
* * * * * *
3467161 TTGAAAAAACCCTACCCGAAGGTCTTATGGATGACCAAAGGACTTATCATCTTGCTCGAAAGACT
1 TTGAAAACATCCTGCCCGAGGGTCTTATGGATGGCCGAAGGACTTATCATCTTG-T-GAAAGACT
** *
3467226 TATAGATGGCCCGAAA-GACTTACGCATCACGCTTAAAAGACTTACTAATGGCCCGAAGAACTTA
64 TATAGATGGCCC-AAAGGACTTACGCATCACGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
*
3467290 CTTATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCTTAACAATTAG
128 CTTATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCTTAAAAATTAG
* *
3467355 GCTTAGCTTTATTTTTTATAAAAATTATTTGGAGATAATCGTAAACCCCTGAAAACCAGGCTTAG
193 GCTTAGCTTCATCTTTTATAAAAATTATTTGGAGATAATCGTAAACCCCTGAAAACCAGGCTTAG
*
3467420 TTTCTAAAAACTCAT
258 TTTATAAAAACTCAT
* *
3467435 TTGAAAACATCCTGCCCTAGGGTCTTATAGATGGCCCGAAGGAC---T--TC----GAAAGACTT
1 TTGAAAACATCCTGCCCGAGGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGTGAAAGACTT
* * * *
3467491 GTAGATGGCCCGAAGGACTTACACATCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACT
65 ATAGATGGCCCAAAGGACTTACGCATCACGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACT
* * *
3467556 TATCAAGAAACCATTGAAAAGCAAGCTTAGTTTCTTGGTTGCCAAGGAACCCTTAAAAATTAGGC
130 TATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCTTAAAAATTAGGC
* * * *
3467621 TTATCTTCCATCTTTTA-AAAAATTCTTTGGAGATAATCTTCAAAAAACCCCTTGAAAATCAGGC
195 TTAGCTT-CATCTTTTATAAAAATTATTTGGAGATAATCGT----AAACCCC-TGAAAACCAGGC
3467685 TTAGTTTATAAAAACTCAT
254 TTAGTTTATAAAAACTCAT
* *
3467704 TTGAAAACATCCTGCTCGAGGGTCTTATGGATGGCTGGAAGGACTTATCATCTTGTTTGAAAGAC
1 TTGAAAACATCCTGCCCGAGGGTCTTATGGATGGC-CGAAGGACTTATCATCTTG--TGAAAGAC
* * *
3467769 TTATAGATGGCCCAAAGGACTTACGCGTCATGCTCGAGAGACTTACTAATGGCCCGAAGGACTTA
63 TTATAGATGGCCCAAAGGACTTACGCATCACGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * * * *
3467834 CTCATCAATAAACCCTTGAAAATCAAGCTTTGTTTCTTTGTTGTCAAAGAACCCCTAAAAATTAG
128 CTTATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCTTAAAAATTAG
3467899 GCTTAGC
193 GCTTAGC
3467906 ATCCTTTTAA
Statistics
Matches: 404, Mismatches: 47, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
263 2 0.00
264 152 0.38
265 7 0.02
268 8 0.02
269 67 0.17
270 2 0.00
272 2 0.00
274 29 0.07
275 8 0.02
280 127 0.31
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (272 bp):
TTGAAAACATCCTGCCCGAGGGTCTTATGGATGGCCGAAGGACTTATCATCTTGTGAAAGACTTA
TAGATGGCCCAAAGGACTTACGCATCACGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTT
ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCTTAAAAATTAGGCT
TAGCTTCATCTTTTATAAAAATTATTTGGAGATAATCGTAAACCCCTGAAAACCAGGCTTAGTTT
ATAAAAACTCAT
Found at i:3468097 original size:98 final size:98
Alignment explanation
Indices: 3467835--3468543 Score: 754
Period size: 98 Copynumber: 7.4 Consensus size: 98
3467825 AAGGACTTAC
* * * **
3467835 TCATCAATAAACCCTTGAAAATCAAGCTTTGTTTCTTTGTTGTCAAAGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
*
3467900 CTTAGCATCCTTTTAAAAACTCATTGAAAATCA
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * * * * *
3467933 TCATCAAG-AA-CCTAGAAAATTAGGCTTAGTTTTTTAAATGTCAAGGAATCCCTAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
* *
3467996 CTTAGCTTCCTTTAAAAAATTCATTGAAAATCA
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * * *
3468029 TCATCGAGAAACCCTTGAACATCAGGCTTAGTTTCTTAATTGTCAAGGAACCCATAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
* * * *
3468094 CTTAGCTTCCTTTAAAAAATTCACTCAAAATCA
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * * * *
3468127 TTATCAAGAAACCCCTGAAAATCAGGCTTAGCTTATTAATTGTCAATGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
* * * *
3468192 CTTAGCTTCATTTTTTTAAAACTCATTGAAACTCT
66 CTTAGCTTC--CTTTTAAAAACTCATTGAAAATCA
* * * * *
3468227 TCATCAAGAAATACC-TGAAAATCAGGCTTAGCTTCTTAGTTGTTAAAGAA-CCTTAAAAATTAG
1 TCATCAAGAAA-CCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAG
*
3468290 GCTTAGTTTCC-TTT------T-A---AAAA-C-
65 GCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * *
3468311 TC-TCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
* * * *
3468375 CTTAACTTCC-TTTAAAAAATTATTGAAAATCT
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * * *
3468407 TCATCAAGAAACCCCTGAAAATCTGGCTTAGTTTCTTACTTGTCAAGGAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
* * * ** *
3468472 CTCAACTTTCTTTTAAAATTTCATTGAAAATCT
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* *
3468505 TCATCAAGAAACCCCTGAAAACCAGGCTTAGTTTCTTAA
1 TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAA
3468544 AATATTTTAT
Statistics
Matches: 521, Mismatches: 69, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
82 2 0.00
83 40 0.08
84 26 0.05
85 1 0.00
86 3 0.01
89 1 0.00
90 2 0.00
91 1 0.00
94 4 0.01
95 1 0.00
96 85 0.16
97 70 0.13
98 205 0.39
99 21 0.04
100 57 0.11
101 2 0.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (98 bp):
TCATCAAGAAACCCTTGAAAATCAGGCTTAGTTTCTTAATTGTCAAAGAACCCCTAAAAATTAGG
CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
Found at i:3468378 original size:39 final size:39
Alignment explanation
Indices: 3468244--3468378 Score: 103
Period size: 39 Copynumber: 3.3 Consensus size: 39
3468234 GAAATACCTG
* * *
3468244 AAAATCAGGCTTAGCTTCTTAGTTGTTAAAGAA-CCTTA
1 AAAATCAGGCTTAGTTTCTTAGTTGTCAAAGAACCCCTA
* ** * *
3468282 AAAATTAGGCTTAGTTTCCTTTTAAAAACTCTC-AAGAAACCCCTG
1 AAAATCAGGCTTAGTTT-C--TT---AGTTGTCAAAG-AACCCCTA
*
3468327 AAAATCAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTA
1 AAAATCAGGCTTAGTTTCTTAGTTGTCAAAGAACCCCTA
*
3468366 AAAATTAGGCTTA
1 AAAATCAGGCTTA
3468379 ACTTCCTTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
38 15 0.21
39 23 0.32
40 3 0.04
41 2 0.03
42 2 0.03
43 3 0.04
44 6 0.08
45 18 0.25
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (39 bp):
AAAATCAGGCTTAGTTTCTTAGTTGTCAAAGAACCCCTA
Found at i:3468389 original size:83 final size:83
Alignment explanation
Indices: 3468230--3468393 Score: 238
Period size: 83 Copynumber: 2.0 Consensus size: 83
3468220 AAACTCTTCA
* * * *
3468230 TCAAGAAATACCTGAAAATCAGGCTTAGCTTCTTAGTTGTTAAAGAACCTTAAAAATTAGGCTTA
1 TCAAGAAACACCTGAAAATCAAGCTTAGCTTCTTAGTTGTCAAAGAACCCTAAAAATTAGGCTTA
**
3468295 GTTTCCTTTTAAAAACTC
66 ACTTCCTTTTAAAAACTC
* *
3468313 TCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTAAAAATTAGGCTT
1 TCAAGAAACACCTGAAAATCAAGCTTAGCTTCTTAGTTGTCAAAGAA-CCCTAAAAATTAGGCTT
*
3468378 AACTTCCTTTAAAAAA
65 AACTTCCTTTTAAAAA
3468394 TTATTGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 42 0.59
84 29 0.41
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (83 bp):
TCAAGAAACACCTGAAAATCAAGCTTAGCTTCTTAGTTGTCAAAGAACCCTAAAAATTAGGCTTA
ACTTCCTTTTAAAAACTC
Found at i:3468444 original size:97 final size:98
Alignment explanation
Indices: 3468313--3468542 Score: 372
Period size: 97 Copynumber: 2.4 Consensus size: 98
3468303 TTAAAAACTC
* * *
3468313 TCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAAGAACCCCTAAAAATTAGGCTT
1 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTACTTGTCAAAGAACCCCTAAAAATTAGGCTC
3468378 AACTTCCTTTAAAAAATT-ATTGAAAATCTTCA
66 AACTTCCTTTAAAAAATTCATTGAAAATCTTCA
* *
3468410 TCAAGAAACCCCTGAAAATCTGGCTTAGTTTCTTACTTGTCAAGGAACCCCTAAAAATTAGGCTC
1 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTACTTGTCAAAGAACCCCTAAAAATTAGGCTC
* * *
3468475 AACTTTCTTTTAAAATTTCATTGAAAATCTTCA
66 AACTTCCTTTAAAAAATTCATTGAAAATCTTCA
*
3468508 TCAAGAAACCCCTGAAAACCAGGCTTAGTTTCTTA
1 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTA
3468543 AAATATTTTA
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
97 75 0.61
98 47 0.39
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (98 bp):
TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTACTTGTCAAAGAACCCCTAAAAATTAGGCTC
AACTTCCTTTAAAAAATTCATTGAAAATCTTCA
Found at i:3469949 original size:14 final size:15
Alignment explanation
Indices: 3469898--3469958 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
3469888 TTTCTTTTTC
3469898 TTTTTCT-TGTTGCT
1 TTTTTCTCTGTTGCT
*
3469912 TTTTTCTATGTT--T
1 TTTTTCTCTGTTGCT
*
3469925 TTTTCTTTCT-TTGCT
1 TTTT-TCTCTGTTGCT
*
3469940 TTTTTCTCT-TTGAT
1 TTTTTCTCTGTTGCT
3469954 TTTTT
1 TTTTT
3469959 TGCTTTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.18
14 23 0.59
15 9 0.23
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.75
Consensus pattern (15 bp):
TTTTTCTCTGTTGCT
Found at i:3469956 original size:28 final size:28
Alignment explanation
Indices: 3469907--3469965 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3469897 CTTTTTCTTG
*
3469907 TTGCTTTTTTCTATGTT-TTTTTCTTTCT
1 TTGCTTTTTTCTATGTTATTTTT-TTGCT
*
3469935 TTGCTTTTTTCTCT-TTGATTTTTTTGCT
1 TTGCTTTTTTCTATGTT-ATTTTTTTGCT
3469963 TTG
1 TTG
3469966 ATTTGATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 20 0.74
29 5 0.19
ACGTcount: A:0.03, C:0.14, G:0.10, T:0.73
Consensus pattern (28 bp):
TTGCTTTTTTCTATGTTATTTTTTTGCT
Found at i:3469964 original size:14 final size:14
Alignment explanation
Indices: 3469932--3469969 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3469922 TTTTTTTCTT
*
3469932 TCTTTGCTTTTTTC
1 TCTTTGATTTTTTC
3469946 TCTTTGATTTTTT-
1 TCTTTGATTTTTTC
3469959 TGCTTTGATTT
1 T-CTTTGATTT
3469970 GATCTTTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (14 bp):
TCTTTGATTTTTTC
Found at i:3473665 original size:3 final size:3
Alignment explanation
Indices: 3473659--3473702 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
3473649 AATTTTTTTC
3473659 ATT ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3473703 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3475264 original size:119 final size:120
Alignment explanation
Indices: 3475148--3475384 Score: 281
Period size: 120 Copynumber: 2.0 Consensus size: 120
3475138 ATTTTAATGA
* *
3475148 TGTTTTAA-TATTTATTTA-TTTTTCAATAT-TAAG-AAAGGGCAGACTTAAAACAACT-GAATG
1 TGTTTTAATTATTTATTTAGTTTTT-AATATCGAAGAAAAGAGCAGACTTAAAACAACTAGAA-G
* *
3475208 TCCATTTTCTGATATTT-TTAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
64 TCC-TTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAAT
* * ** *
3475265 TGTTTTAATTATTTATTTAGTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAATTATTTATTTAGTTTTTAATATCGAAGAAAAGAGCAGACTTAAAACAACTAGAAGTC
* **
3475330 CTTTTCTGGTATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
66 CTTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
3475385 ATTTTTTTCA
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
117 8 0.08
118 15 0.15
119 29 0.29
120 46 0.46
121 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (120 bp):
TGTTTTAATTATTTATTTAGTTTTTAATATCGAAGAAAAGAGCAGACTTAAAACAACTAGAAGTC
CTTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:3475378 original size:27 final size:27
Alignment explanation
Indices: 3475348--3475402 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3475338 GTATTTCTAA
3475348 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATATTTT-TTTCATAAATAT
* *
3475375 ATAAATTAATATTTTTTTCATAATTAT
1 ATAAATAAATATTTTTTTCATAAATAT
3475402 A
1 A
3475403 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAATAAATATTTTTTTCATAAATAT
Found at i:3475461 original size:47 final size:47
Alignment explanation
Indices: 3475374--3475464 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
3475364 TTTATAAATA
* * * *
3475374 TATAAATTAATATTTTTTTCATAATTATAATTTTGAAATAATAGGAT
1 TATAAATTAATATATTTTTCAAAATTATAAATTTCAAATAATAGGAT
* *
3475421 TATAAATTAAATATATTTTTGAAAATT-TAAATTTCTAATAATAG
1 TATAAATT-AATATATTTTTCAAAATTATAAATTTCAAATAATAG
3475465 AGACAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 22 0.59
48 15 0.41
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (47 bp):
TATAAATTAATATATTTTTCAAAATTATAAATTTCAAATAATAGGAT
Found at i:3482676 original size:114 final size:114
Alignment explanation
Indices: 3482476--3482695 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
3482466 CACATTCTCG
*
3482476 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
* * *
3482541 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCAATAGAATTAAAAGATGAATTTGCTCA
* *
3482590 TAGTAGAAATAA-AGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGTAGAAATAAGA-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTT
* * *
3482654 CGGTAGGAACCCCAGAACCAATCAATGGAATTGAAAGATGAA
65 CGGTAGGAACCCCAAAACCAATCAATAGAATTAAAAGATGAA
3482696 CTGCATGATC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 95 0.99
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
GGTAGGAACCCCAAAACCAATCAATAGAATTAAAAGATGAATTTGCTCA
Found at i:3483889 original size:76 final size:75
Alignment explanation
Indices: 3483754--3483932 Score: 207
Period size: 76 Copynumber: 2.3 Consensus size: 75
3483744 TTAGCATCTG
* * * *
3483754 TATCAGCAAATATTGGGGTATGCTGAAAACCTTTTTTCAATCAGAATCAGGAATGTTGATGTATC
1 TATCAGCAAA-ATTGGGGCATGCTGAAAACCTTTTTTCAATCAAAATCAAGAAGGTTGATGTATC
* *
3483819 CTGAATGTTTA
65 CTGAACGTTCA
* *
3483830 TATCAGCAAAATGCTGGGGCATGCTGAAAGCC-TTTTTCAATCAAAATGAAGAAGGTTGATGTAT
1 TATCAGCAAAAT--TGGGGCATGCTGAAAACCTTTTTTCAATCAAAATCAAGAAGGTTGATGTAT
** *
3483894 TTTGAACGTTCG
64 CCTGAACGTTCA
*
3483906 TATCAGCAATTATTGGGGCATGCTGAA
1 TATCAGCAA-AATTGGGGCATGCTGAA
3483933 GGCCCACATC
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
75 16 0.18
76 54 0.61
77 18 0.20
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (75 bp):
TATCAGCAAAATTGGGGCATGCTGAAAACCTTTTTTCAATCAAAATCAAGAAGGTTGATGTATCC
TGAACGTTCA
Found at i:3484859 original size:54 final size:53
Alignment explanation
Indices: 3484777--3484934 Score: 189
Period size: 54 Copynumber: 3.0 Consensus size: 53
3484767 TGATTGAGAA
*
3484777 ATTTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATG-TTTACGAAC
* *
3484831 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTT---TAC
1 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTACGAAC
* * * * *
3484881 ATCTGAGCAGAAACCACATG-AGATGATGCATGTGTTATCAAATGTTTTACGAAC
1 ATTTGAGCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATG-TTTACGAAC
3484935 CAGTTATTCT
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
50 38 0.43
51 4 0.04
53 3 0.03
54 44 0.49
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (53 bp):
ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTACGAAC
Found at i:3484914 original size:50 final size:50
Alignment explanation
Indices: 3484780--3484930 Score: 169
Period size: 50 Copynumber: 2.9 Consensus size: 50
3484770 TTGAGAAATT
* * * *
3484780 TGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATT
1 TGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATG-TTT---TACATC
* *
3484834 TGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 TGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATGTTTTACATC
* * *
3484884 TGAGCAGAAACCACATG-AGATGATGCATGTGTTATCAAATGTTTTAC
1 TGAGCAGAAACCACA-GAAAAGGATGAATGTGTTATCAAATGTTTTAC
3484931 GAACCAGTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
50 44 0.51
51 1 0.01
53 3 0.03
54 39 0.45
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (50 bp):
TGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAATGTTTTACATC
Found at i:3485327 original size:22 final size:22
Alignment explanation
Indices: 3485301--3485377 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
3485291 ATTTACACTC
3485301 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3485323 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
3485345 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3485367 TTCAAAGATGA
1 TTCAAAGATGA
3485378 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3486180 original size:76 final size:76
Alignment explanation
Indices: 3486054--3486858 Score: 1283
Period size: 76 Copynumber: 10.6 Consensus size: 76
3486044 CTATTTCCCA
* *
3486054 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTCTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3486119 AGCCTTAGGGT
66 AGCCTTAGGGT
3486130 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3486195 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3486206 CATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3486271 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3486282 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAACCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3486347 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3486358 CATCTGTAAGTCCTACCGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3486423 AGCCATAGGGT
66 AGCCTTAGGGT
* * * *
3486434 CATCTATAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3486499 AGCCTTAGGGC
66 AGCCTTAGGGT
*
3486510 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
*
3486575 AAGTCTTAGGGT
65 AAGCCTTAGGGT
* * * *
3486587 CATCTGTAAGTCCTGCAGTGGATGATGTTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
3486652 AGTCTTAGGGA
66 AGCCTTAGGGT
*
3486663 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3486728 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3486739 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3486804 AACCTTCA-GGT
66 AGCCTT-AGGGT
* * * * * * *
3486815 CGTCTATAAGCCCTTCAATGCATGATATTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
3486859 TCATCTATAA
Statistics
Matches: 683, Mismatches: 44, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
74 7 0.01
75 4 0.01
76 599 0.88
77 73 0.11
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3486866 original size:45 final size:45
Alignment explanation
Indices: 3486792--3486894 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
3486782 GGGAGCTTTT
*
3486792 TGATGTTTTCAAAACCTTCAGGTCGTCTATAAGCCCTTCAATGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
* * *
3486837 TGATATTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
*
3486882 TGATGTTTACAAA
1 TGATGTTTTCAAA
3486895 CATTTACATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
Found at i:3487019 original size:3 final size:3
Alignment explanation
Indices: 3487013--3487056 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
3487003 CATTTTTTTC
3487013 ATT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3487057 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3488626 original size:119 final size:120
Alignment explanation
Indices: 3488510--3488746 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 120
3488500 ATTTTAATCC
* * * *
3488510 TGTTTTAA-TATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* *
3488572 CATTTTCTGATATTT-TTAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
66 C-TTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATAAATTAAT
* * ** * *
3488627 TGTTTTAATTATTTATTTATTTTTTAATGTCGAAGAAAAGAGTTGTCTTAAGACACCTAGAAGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
3488692 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
66 CTTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
3488747 ATTTTTTCAT
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
117 8 0.08
118 19 0.19
119 25 0.25
120 49 0.49
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (120 bp):
TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
CTTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:3488638 original size:20 final size:19
Alignment explanation
Indices: 3488613--3488654 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3488603 CTATTTTATA
3488613 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
3488633 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
3488652 AAT
1 AAT
3488655 GTCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:3488768 original size:119 final size:120
Alignment explanation
Indices: 3488551--3488768 Score: 273
Period size: 120 Copynumber: 1.8 Consensus size: 120
3488541 AGAAAGGGCA
* * *
3488551 GTCTTAAAACAACTGGATGTCCATTTTCTGATATTTTTAATAAATAAATATCCTATTTTATAAAT
1 GTCTTAAAACAACTAGAAGTCCATTTTCTGATATTTTAAATAAATAAATATCCTATTTTATAAAT
* * *
3488616 TATATATTAATTGTTTTAATTATTTATTTATTTTTTAATGTCGAAGAAAAGAGTT
66 TATAAATTAATTGTTTTAATTAATTATTAATTTTTTAATGTCGAAGAAAAGAGTT
* * **
3488671 GTCTTAAGACACCTAGAAGTCC-TTTTCTGATATTTCTAAATAAATAAATATTTTA-TTTATAAA
1 GTCTTAAAACAACTAGAAGTCCATTTTCTGATATTT-TAAATAAATAAATATCCTATTTTATAAA
* *
3488734 TATATAAATTAATATTTTTTCA-TAATTA-TAATTTT
65 T-TATAAATTAAT-TGTTTTAATTAATTATTAATTTT
3488769 GAAATAATAG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 28 0.34
120 49 0.59
121 6 0.07
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.47
Consensus pattern (120 bp):
GTCTTAAAACAACTAGAAGTCCATTTTCTGATATTTTAAATAAATAAATATCCTATTTTATAAAT
TATAAATTAATTGTTTTAATTAATTATTAATTTTTTAATGTCGAAGAAAAGAGTT
Found at i:3488822 original size:47 final size:46
Alignment explanation
Indices: 3488736--3488825 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 46
3488726 TTTATAAATA
* * *
3488736 TATAAATTAATATTTTTTCATAATTATAATTTTGAAATAATAGGAT
1 TATAAATTAATATTTTTTCAAAATTATAAATTTCAAATAATAGGAT
* *
3488782 TATAAATTAAATATATTTTTGAAAATT-TAAATTTCTAATAATAG
1 TATAAATT-AATAT-TTTTTCAAAATTATAAATTTCAAATAATAG
3488826 AGACAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 8 0.22
47 19 0.51
48 10 0.27
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.47
Consensus pattern (46 bp):
TATAAATTAATATTTTTTCAAAATTATAAATTTCAAATAATAGGAT
Found at i:3489231 original size:21 final size:21
Alignment explanation
Indices: 3489205--3489244 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3489195 ATTAACAAGC
3489205 TAAAAGAGGATAAATTAAACA
1 TAAAAGAGGATAAATTAAACA
* *
3489226 TAAAAGGGGCTAAATTAAA
1 TAAAAGAGGATAAATTAAA
3489245 AGATAAAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (21 bp):
TAAAAGAGGATAAATTAAACA
Found at i:3490596 original size:3 final size:3
Alignment explanation
Indices: 3490577--3490639 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
3490567 GCATAATGTA
3490577 AAT AA- AAT AATT AAT AAT AAT AAT AATT AAT AAT AAT AAT -AT AA-
1 AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
3490621 AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT -AAT AAT
3490640 TTTCGAGACC
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.11
3 39 0.72
4 9 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3490600 original size:13 final size:12
Alignment explanation
Indices: 3490577--3490639 Score: 78
Period size: 13 Copynumber: 5.2 Consensus size: 12
3490567 GCATAATGTA
3490577 AATAA-AATAATT
1 AATAATAATAA-T
3490589 AATAATAATAAT
1 AATAATAATAAT
3490601 AATTAATAATAAT
1 AA-TAATAATAAT
3490614 AAT-ATAA-AAT
1 AATAATAATAAT
3490624 AATAATAATAAAT
1 AATAATAAT-AAT
3490637 AAT
1 AAT
3490640 TTTCGAGACC
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.13
11 8 0.17
12 9 0.20
13 23 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:3490603 original size:16 final size:16
Alignment explanation
Indices: 3490577--3490639 Score: 89
Period size: 16 Copynumber: 4.2 Consensus size: 16
3490567 GCATAATGTA
3490577 AATAA-AATAATTAAT
1 AATAATAATAATTAAT
3490592 AATAATAATAATTAAT
1 AATAATAATAATTAAT
3490608 AATAATAAT-A-TAA-
1 AATAATAATAATTAAT
*
3490621 AATAATAATAATAAAT
1 AATAATAATAATTAAT
3490637 AAT
1 AAT
3490640 TTTCGAGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
13 9 0.21
14 4 0.09
15 8 0.19
16 22 0.51
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATTAAT
Found at i:3501322 original size:24 final size:24
Alignment explanation
Indices: 3501294--3501342 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
3501284 ATAAAGAACC
3501294 AAATAAA-CTTAAATATACCATTAA
1 AAATAAAGCTTAAATAT-CCATTAA
*
3501318 AAATAAAGTTTAAATATCCATTAA
1 AAATAAAGCTTAAATATCCATTAA
3501342 A
1 A
3501343 CCAACCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAAGCTTAAATATCCATTAA
Found at i:3506943 original size:24 final size:24
Alignment explanation
Indices: 3506898--3506947 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3506888 ATAAAGAACC
*
3506898 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3506922 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
3506946 AA
1 AA
3506948 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3515162 original size:190 final size:190
Alignment explanation
Indices: 3514791--3515163 Score: 554
Period size: 190 Copynumber: 2.0 Consensus size: 190
3514781 AATAATATCT
* *
3514791 TTTAATTTGAAATATTCAAAAGATAAAACTTCTTTTACCTTTCAAACTTAAATAGATATTATTTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCTTTCAAACTTAAATAGATATTATTTT
* * *
3514856 AATTTGAAATATACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAGGTAACAAATATC
66 AATTTGAAATATACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATATC
* * * *
3514921 TTTTTAAGTTGACATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATAAA
131 TTTTAAAATTGACATATTAAAAGAGTAATTATCCTACAAATATTCAAATTAAATAATAAA
* * * *
3514981 TTTAATTTGCAATGGTCAAAAGGT-AAACTCCTTTTA-CTATTCAAACTTAAATATATATTATTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCT-TTCAAACTTAAATAGATATTATTT
*
3515044 TAATTTGAAATATACAAAAATATATAATTATCTTTCAATATTCAAAATTAAAAAGATATCAAATA
65 TAATTTGAAATATACAAAAATATATAATTATCTTT-AATATTCAAAATTAAAAAGATAACAAATA
* *
3515109 -CATTTTAAAATTGACTTATTAAAAGAGTAATTATCCTACAAATATTTAAATTAAA
129 TC-TTTTAAAATTGACATATTAAAAGAGTAATTATCCTACAAATATTCAAATTAAA
3515164 AGTTATCTTT
Statistics
Matches: 164, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
188 2 0.01
189 69 0.42
190 93 0.57
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (190 bp):
TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCTTTCAAACTTAAATAGATATTATTTT
AATTTGAAATATACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAGATAACAAATATC
TTTTAAAATTGACATATTAAAAGAGTAATTATCCTACAAATATTCAAATTAAATAATAAA
Found at i:3518645 original size:31 final size:31
Alignment explanation
Indices: 3518610--3518670 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3518600 CTCCGGATGA
3518610 CCATATCTTAACTAAATAAAAACGAAAGTGG
1 CCATATCTTAACTAAATAAAAACGAAAGTGG
*
3518641 CCATATCTTAATTAAATAAAAACGAAAGTG
1 CCATATCTTAACTAAATAAAAACGAAAGTG
3518671 ACAATACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (31 bp):
CCATATCTTAACTAAATAAAAACGAAAGTGG
Found at i:3519427 original size:35 final size:35
Alignment explanation
Indices: 3519388--3519457 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3519378 GAGCTGCGAC
3519388 GACAATAGATGATTTACTCCTTTTGATTTAGATGA
1 GACAATAGATGATTTACTCCTTTTGATTTAGATGA
3519423 GACAATAGATGATTTACTCCTTTTGATTTAGATGA
1 GACAATAGATGATTTACTCCTTTTGATTTAGATGA
3519458 AAAGTCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (35 bp):
GACAATAGATGATTTACTCCTTTTGATTTAGATGA
Found at i:3528237 original size:42 final size:42
Alignment explanation
Indices: 3528178--3528345 Score: 155
Period size: 41 Copynumber: 4.0 Consensus size: 42
3528168 TGGGTTGGGT
* * *
3528178 ATTTCACCCTTCAAGATGAATTTCACTTCAGATTATCAGTGG
1 ATTTCACCCTTCGAGATGAATTTCACTTCAGAATATCAATGG
* *
3528220 ATTTCACCCTTCGAGATGAATTTCACTTCACAATATCAAT-A
1 ATTTCACCCTTCGAGATGAATTTCACTTCAGAATATCAATGG
* * * * * *
3528261 AATTCACCTTTTGATATGAATTTCTCTTC-GAAATATTAGA-GG
1 ATTTCACCCTTCGAGATGAATTTCACTTCAG-AATATCA-ATGG
* * * *
3528303 A-TTCATCATTCGGGATGAATTTCACTTCAGATTATCAATGG
1 ATTTCACCCTTCGAGATGAATTTCACTTCAGAATATCAATGG
3528344 AT
1 AT
3528346 CCTCTCTTCG
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 59 0.60
42 39 0.39
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (42 bp):
ATTTCACCCTTCGAGATGAATTTCACTTCAGAATATCAATGG
Found at i:3529798 original size:86 final size:86
Alignment explanation
Indices: 3529652--3529817 Score: 187
Period size: 86 Copynumber: 1.9 Consensus size: 86
3529642 AGTATTGATA
* * * **
3529652 CTCCTCATAGGGGTATCGATACTAAGGTATTTTTCAAAACATCGAAGTCATTTTTAGTATCGGTA
1 CTCCTCATAGGGGTATCGATACTAAGGTATTTTCCAAAACATCGAACTCATTTTCAGTATCAATA
*
3529717 CTCAGGGT-AGTATCGATACC
66 CTCACGGTGAGTATCGATACC
* * *
3529737 CTCC-CATAGGAGAGTATCGATACTCTAGGT-TTTTCCAAAACATTGAAACT-ATTTTCGGTATC
1 CTCCTCATAGG-G-GTATCGATACT-AAGGTATTTTCCAAAACATCG-AACTCATTTTCAGTATC
3529799 AATACTCACGGTGAGTATC
62 AATACTCACGGTGAGTATC
3529818 AATAACTAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
84 6 0.09
85 5 0.07
86 43 0.64
87 13 0.19
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (86 bp):
CTCCTCATAGGGGTATCGATACTAAGGTATTTTCCAAAACATCGAACTCATTTTCAGTATCAATA
CTCACGGTGAGTATCGATACC
Found at i:3535302 original size:3 final size:3
Alignment explanation
Indices: 3535296--3535391 Score: 104
Period size: 3 Copynumber: 31.3 Consensus size: 3
3535286 TTATCATTTC
3535296 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * ** * *
3535344 A-T ATT TTT ACT AGTT AGC ACT ATT ATT AATT ACT ATT ATT ATTT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT A-TT ATT
3535391 A
1 A
3535392 GTTTCATATG
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 68 0.87
4 8 0.10
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:3540719 original size:50 final size:49
Alignment explanation
Indices: 3540593--3540726 Score: 128
Period size: 51 Copynumber: 2.7 Consensus size: 49
3540583 GAGTTTCTAT
* * * *
3540593 AAAAAATATTTTTATTCAAACTCATCACGTCGATATAACGAGTTCTAATA
1 AAAAAATATTTTTATT-AAACTTATCACATCGAGATAACAAGTTCTAATA
* * *
3540643 AAACATAATA-TTTTATTAAATTTTATCACATCGGGATAATAAGTT-TGAATA
1 AAA-A-AATATTTTTATTAAA-CTTATCACATCGAGATAACAAGTTCT-AATA
*
3540694 AAAAAATATTTTTATTGAAACTTATCACCTCGA
1 AAAAAATATTTTTATT-AAACTTATCACATCGA
3540727 CGTGATGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
49 4 0.06
50 25 0.37
51 35 0.51
52 4 0.06
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37
Consensus pattern (49 bp):
AAAAAATATTTTTATTAAACTTATCACATCGAGATAACAAGTTCTAATA
Found at i:3541682 original size:49 final size:48
Alignment explanation
Indices: 3541582--3541689 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
3541572 ATTTAATTTT
3541582 ATTAGATTTTACATGTTCATCCTAATTTTTTAGATCAATTTACGTAAG
1 ATTAGATTTTACATGTTCATCCTAATTTTTTAGATCAATTTACGTAAG
* ** ** *
3541630 ATTAAATTTTA-ATAGTTCATCCTAATTTTTTATTTCTAATTTATTTAGG
1 ATTAGATTTTACAT-GTTCATCCTAATTTTTTAGATC-AATTTACGTAAG
3541679 ATTAGATTTTA
1 ATTAGATTTTA
3541690 TCTATTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 2 0.04
48 30 0.59
49 19 0.37
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.51
Consensus pattern (48 bp):
ATTAGATTTTACATGTTCATCCTAATTTTTTAGATCAATTTACGTAAG
Found at i:3544512 original size:60 final size:60
Alignment explanation
Indices: 3544386--3544533 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
3544376 GAAATTTTTG
* * ** *
3544386 GGACAAATTTAAAA--AGAGTCATAGTTTAGGGATGAAATTAGAATATTAAAATGTTCTA
1 GGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTCAA
* *
3544444 GGATTAATTTAAAATGAGAGTCATAGTTTAGTGATGAAATTAAAATATTAAAAAAATT-AA
1 GGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATT-AAAAAATTCAA
** **
3544504 GGACTAATTTAATGTGAGAGTTGTAGTTTA
1 GGACTAATTTAAAATGAGAGTCATAGTTTA
3544534 AGAACAAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
58 12 0.16
60 57 0.76
61 6 0.08
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (60 bp):
GGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATTAAAAAATTCAA
Found at i:3547680 original size:24 final size:24
Alignment explanation
Indices: 3547653--3547702 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3547643 TGGTGGTTGA
*
3547653 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
3547677 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
3547701 TT
1 TT
3547703 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:3554534 original size:21 final size:22
Alignment explanation
Indices: 3554480--3554534 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3554470 CCTCTTAAAT
* *
3554480 TTTTAACTTTTTCTTCTCTTTCT
1 TTTTAAC-TTTTCTTATCTTTCA
3554503 TTATTAA-TTTT-TTATCTTTCA
1 TT-TTAACTTTTCTTATCTTTCA
3554524 TTTTAACTTTT
1 TTTTAACTTTT
3554535 ACTTTTTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 4 0.14
21 14 0.50
22 4 0.14
23 2 0.07
24 4 0.14
ACGTcount: A:0.16, C:0.15, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTAACTTTTCTTATCTTTCA
Found at i:3557873 original size:24 final size:24
Alignment explanation
Indices: 3557846--3557895 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3557836 TGGTGGTTGA
*
3557846 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
3557870 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
3557894 TT
1 TT
3557896 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:3559802 original size:6 final size:6
Alignment explanation
Indices: 3559783--3559825 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
3559773 CCGTTAACCT
* * *
3559783 TCCTCC TCCATC TCCTTC TCCTTC TCCTTC TCTTTC TCCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
3559826 TACCCTCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTTC
Found at i:3562094 original size:16 final size:16
Alignment explanation
Indices: 3562073--3562108 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3562063 TGTCATGACG
3562073 CATGTCACCGATAACA
1 CATGTCACCGATAACA
**
3562089 CATGTCATTGATAACA
1 CATGTCACCGATAACA
3562105 CATG
1 CATG
3562109 ACATATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (16 bp):
CATGTCACCGATAACA
Found at i:3573074 original size:19 final size:19
Alignment explanation
Indices: 3573050--3573095 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3573040 AAATTTAGTT
3573050 TTTATATTAATTACAATTC
1 TTTATATTAATTACAATTC
** *
3573069 TTTATATTTTTTATAATTC
1 TTTATATTAATTACAATTC
3573088 -TTATATTA
1 TTTATATTA
3573096 TAAATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:3573733 original size:23 final size:23
Alignment explanation
Indices: 3573707--3573761 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3573697 AATCGGCAAG
*
3573707 CATCAATGTACCAATTCAACAAA
1 CATCAATGCACCAATTCAACAAA
* * * *
3573730 CATCATTGCATCAATTCAGCAAG
1 CATCAATGCACCAATTCAACAAA
3573753 CATC-ATGCA
1 CATCAATGCA
3573762 TTAAGGAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24
Consensus pattern (23 bp):
CATCAATGCACCAATTCAACAAA
Found at i:3575600 original size:22 final size:22
Alignment explanation
Indices: 3575555--3575630 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 22
3575545 TATAAAATTT
* *
3575555 ATATTAATAAATTATTTATAATTA
1 ATATTAAT-AATAACTTAT-ATTA
*
3575579 ATATTAA-AATAATTGTATATT-
1 ATATTAATAATAACT-TATATTA
*
3575600 ATAATTAATATTAACTTATATTA
1 AT-ATTAATAATAACTTATATTA
3575623 ATA-TAATA
1 ATATTAATA
3575631 TAGTTTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
21 7 0.16
22 21 0.47
23 10 0.22
24 7 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
ATATTAATAATAACTTATATTA
Found at i:3575689 original size:21 final size:22
Alignment explanation
Indices: 3575665--3575711 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3575655 TAATATAAAC
*
3575665 TATATG-TTATAAATTATATAA
1 TATATGTTTATAAACTATATAA
*
3575686 TATA-GTTTATAAACTATATAC
1 TATATGTTTATAAACTATATAA
3575707 TATAT
1 TATAT
3575712 ATAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATGTTTATAAACTATATAA
Found at i:3575724 original size:6 final size:6
Alignment explanation
Indices: 3575715--3575923 Score: 186
Period size: 6 Copynumber: 34.7 Consensus size: 6
3575705 ACTATATATA
* * *
3575715 AATATG AATATG AATACG AATACG AATATG AATACG AATACG AATACG
1 AATACG AATACG AATACG AATACG AATACG AATACG AATACG AATACG
* * * * * *
3575763 AATACG AATACA AATATG AATATG AATATG AATACA AATACA AATACG
1 AATACG AATACG AATACG AATACG AATACG AATACG AATACG AATACG
** * * * * *
3575811 AATATA AATATG AATATG AATATG AATACG AATATG AATACG AATACA
1 AATACG AATACG AATACG AATACG AATACG AATACG AATACG AATACG
* * * * *
3575859 AATACG AATACG AATACA AATACA AATACAA AATATC- AATACA AATACA
1 AATACG AATACG AATACG AATACG AATAC-G AATA-CG AATACG AATACG
* *
3575908 AATACA AATACA AATA
1 AATACG AATACG AATA
3575924 TCAATATCAA
Statistics
Matches: 182, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
5 1 0.01
6 175 0.96
7 5 0.03
8 1 0.01
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.22
Consensus pattern (6 bp):
AATACG
Found at i:3575935 original size:12 final size:12
Alignment explanation
Indices: 3575920--3576055 Score: 130
Period size: 12 Copynumber: 11.4 Consensus size: 12
3575910 TACAAATACA
*
3575920 AATATCAATATC
1 AATATCGATATC
* *
3575932 AATATCAATATT
1 AATATCGATATC
* ** *
3575944 GATATTTATATT
1 AATATCGATATC
*
3575956 AATATAGATATC
1 AATATCGATATC
*
3575968 GATATCGATATC
1 AATATCGATATC
3575980 AATATCGATATC
1 AATATCGATATC
* **
3575992 GATATAAATATC
1 AATATCGATATC
*
3576004 CATATCGATATC
1 AATATCGATATC
*
3576016 GATATCGATATC
1 AATATCGATATC
3576028 -ATATCGATATC
1 AATATCGATATC
*
3576039 GATATCGATATC
1 AATATCGATATC
3576051 AATAT
1 AATAT
3576056 AAACCCTAAA
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
11 11 0.11
12 93 0.89
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (12 bp):
AATATCGATATC
Found at i:3575935 original size:18 final size:17
Alignment explanation
Indices: 3575859--3575935 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 17
3575849 TACGAATACA
*
3575859 AATACGAATACGAATA-C
1 AATACAAATAC-AATATC
3575876 AAATACAAATACAAAATATC
1 -AATACAAATAC--AATATC
3575896 AATACAAATACAA-ATAC
1 AATACAAATACAATAT-C
3575913 AAATACAAATATCAATATC
1 -AATACAAATA-CAATATC
3575932 AATA
1 AATA
3575936 TCAATATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
16 2 0.04
17 3 0.06
18 24 0.47
19 19 0.37
20 3 0.06
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (17 bp):
AATACAAATACAATATC
Found at i:3575941 original size:18 final size:18
Alignment explanation
Indices: 3575920--3576055 Score: 121
Period size: 18 Copynumber: 7.6 Consensus size: 18
3575910 TACAAATACA
* *
3575920 AATATCAATATCAATATC
1 AATATCGATATCGATATC
* ** *
3575938 AATATTGATATTTATATT
1 AATATCGATATCGATATC
*
3575956 AATATAGATATCGATATC
1 AATATCGATATCGATATC
* *
3575974 GATATCAATATCGATATC
1 AATATCGATATCGATATC
* ** *
3575992 GATATAAATATCCATATC
1 AATATCGATATCGATATC
*
3576010 GATATCGATATCGATATC
1 AATATCGATATCGATATC
3576028 -ATATCGATATCGATATC
1 AATATCGATATCGATATC
* *
3576045 GATATCAATAT
1 AATATCGATAT
3576056 AAACCCTAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
17 17 0.17
18 82 0.83
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (18 bp):
AATATCGATATCGATATC
Found at i:3575979 original size:6 final size:6
Alignment explanation
Indices: 3575957--3576055 Score: 137
Period size: 6 Copynumber: 16.7 Consensus size: 6
3575947 ATTTATATTA
* * ** *
3575957 ATATAG ATATCG ATATCG ATATCA ATATCG ATATCG ATATAA ATATCC
1 ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG
*
3576005 ATATCG ATATCG ATATCG ATATC- ATATCG ATATCG ATATCG ATATCA
1 ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG
3576052 ATAT
1 ATAT
3576056 AAACCCTAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
5 5 0.06
6 78 0.94
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (6 bp):
ATATCG
Found at i:3576082 original size:2 final size:2
Alignment explanation
Indices: 3576075--3576330 Score: 90
Period size: 2 Copynumber: 127.0 Consensus size: 2
3576065 ACCATATTAC
* * *
3576075 TA TA TA TA TA TA TA TA TA TA AA CTA TA TA -A TT TA TA CA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
3576116 TA TA T- TA TT TA TA -A T- TA TA CA TA -A TA TA TA AA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3576154 T- TG TA TA GTT TA TA TA TA -A T- TCA TA TA TA -A TT TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* * * * *
3576194 AA CTA TG TA GTT TC TA TA TA GTA TA TA TA GTT TA TA TA TA TA -A
1 TA -TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
* *
3576237 TA TA TA GTA TA TA AA TA TA AA CTA TA -A TA TA TA TA TA TA -A GTCA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -T-A
* * *
3576281 TA TG TA AA CTA TA TA GTA TA TA AA TA TCA -A CTA TA GTA TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA TA
3576325 TA TA TA
1 TA TA TA
3576331 GGTCATATGT
Statistics
Matches: 187, Mismatches: 37, Indels: 60
0.66 0.13 0.21
Matches are distributed among these distances:
1 14 0.07
2 153 0.82
3 19 0.10
4 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3576110 original size:9 final size:9
Alignment explanation
Indices: 3576076--3576330 Score: 65
Period size: 9 Copynumber: 27.8 Consensus size: 9
3576066 CCATATTACT
3576076 ATATATATA
1 ATATATATA
3576085 TATATATATA
1 -ATATATATA
3576095 A-ACTATATA
1 ATA-TATATA
* *
3576104 ATTTATACA
1 ATATATATA
3576113 ATATATAT-
1 ATATATATA
*
3576121 -TATTTATA
1 ATATATATA
*
3576129 ATTATACATA
1 A-TATATATA
3576139 ATATATA-A
1 ATATATATA
3576147 ATATA-A-A
1 ATATATATA
* *
3576154 TTGTATAGT-
1 ATATATA-TA
*
3576163 TTATATATA
1 ATATATATA
3576172 ATTCATATATA
1 A-T-ATATATA
3576183 ATTTATATATA
1 A--TATATATA
*
3576194 A-ACTATGTA
1 ATA-TATATA
* *
3576203 GTTTCTATATA
1 --ATATATATA
*
3576214 GTATATATA
1 ATATATATA
* *
3576223 GTTTATAT-
1 ATATATATA
3576231 ATATA-ATA
1 ATATATATA
3576239 TATAGTATATA
1 -ATA-TATATA
3576250 A-ATATA-A
1 ATATATATA
3576257 ACTATA-ATA
1 A-TATATATA
3576266 TATATATATA
1 -ATATATATA
*
3576276 AGTCATATGTA
1 A-T-ATATATA
3576287 A-ACTATATA
1 ATA-TATATA
*
3576296 GTATATA-A
1 ATATATATA
3576304 ATATCAACTATA
1 ATAT--A-TATA
*
3576316 GTATATAT-
1 ATATATATA
3576324 ATATATA
1 ATATATA
3576331 GGTCATATGT
Statistics
Matches: 185, Mismatches: 27, Indels: 68
0.66 0.10 0.24
Matches are distributed among these distances:
7 15 0.08
8 29 0.16
9 74 0.40
10 28 0.15
11 33 0.18
12 6 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (9 bp):
ATATATATA
Found at i:3576116 original size:23 final size:23
Alignment explanation
Indices: 3576073--3576117 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3576063 AAACCATATT
*
3576073 ACTATATATATATATATATATAA
1 ACTATATATATATATAAATATAA
*
3576096 ACTATATA-ATTTATACAATATA
1 ACTATATATATATATA-AATATA
3576118 TATTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (23 bp):
ACTATATATATATATAAATATAA
Found at i:3576192 original size:13 final size:11
Alignment explanation
Indices: 3576157--3576194 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3576147 ATATAAATTG
*
3576157 TATAGTTTATA
1 TATAATTTATA
*
3576168 TATAATTCATA
1 TATAATTTATA
3576179 TATAATTTATA
1 TATAATTTATA
3576190 TATAA
1 TATAA
3576195 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:3576270 original size:40 final size:40
Alignment explanation
Indices: 3576076--3576276 Score: 114
Period size: 40 Copynumber: 5.0 Consensus size: 40
3576066 CCATATTACT
* * * *
3576076 ATATATA-TATATATATATAAACTAT-ATA-ATTTATACA
1 ATATATAGTATATAAATATATACTATAATATATATATATA
* * *
3576113 ATATATATTATTTATAAT-TATAC-ATAATATATAAATATAA
1 ATATATAGTATATA-AATATATACTATAATATATATATAT-A
* *
3576153 ATTGTATAGTTTATATATAAT-TCATA-TATAATTTATATATA-A
1 A-TATATAG--TATATA-AATAT-ATACTATAATATATATATATA
* * * * * *
3576195 ACTATGTAGTTTCTATATAGTATA-TATAGTTTATATATATA
1 A-TATATAGTATATAAATA-TATACTATAATATATATATATA
*
3576236 ATATATAGTATATAAATATAAACTATAATATATATATATA
1 ATATATAGTATATAAATATATACTATAATATATATATATA
3576276 A
1 A
3576277 GTCATATGTA
Statistics
Matches: 125, Mismatches: 25, Indels: 25
0.71 0.14 0.14
Matches are distributed among these distances:
37 9 0.07
38 12 0.10
39 12 0.10
40 52 0.42
41 8 0.06
42 7 0.06
43 10 0.08
44 15 0.12
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (40 bp):
ATATATAGTATATAAATATATACTATAATATATATATATA
Found at i:3576301 original size:33 final size:31
Alignment explanation
Indices: 3576226--3576377 Score: 112
Period size: 33 Copynumber: 5.0 Consensus size: 31
3576216 ATATATAGTT
* *
3576226 TATATATATA-ATATATAGTATATAAATATAAAC
1 TATATATATATATATATAGT-CAT--ATGTAAAC
3576259 TATA-ATATATATATATAAGTCATATGTAAAC
1 TATATATATATATATAT-AGTCATATGTAAAC
3576290 TATATAGTATATA-A-ATA-TC-------AAC
1 TATATA-TATATATATATAGTCATATGTAAAC
3576312 TATAGTATATATATATATAGGTCATATGTAAAC
1 TATA-TATATATATATATA-GTCATATGTAAAC
*
3576345 TATATAGTTTATATATATAGTTCATATGTAAAC
1 TATATA-TATATATATATAG-TCATATGTAAAC
3576378 AATAGTTCAT
Statistics
Matches: 98, Mismatches: 3, Indels: 36
0.72 0.02 0.26
Matches are distributed among these distances:
22 13 0.13
23 3 0.03
24 3 0.03
26 2 0.02
29 2 0.02
30 1 0.01
31 13 0.13
32 10 0.10
33 48 0.49
34 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (31 bp):
TATATATATATATATATAGTCATATGTAAAC
Found at i:3576323 original size:55 final size:53
Alignment explanation
Indices: 3576237--3576363 Score: 200
Period size: 55 Copynumber: 2.4 Consensus size: 53
3576227 ATATATATAA
3576237 TATATAGTATATAAATATAAACTATAATATATATATATAAGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAATATATATATATAAGTCATATGTAAAC
* *
3576290 TATATAGTATATAAATATCAACTATAGTATATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATA--ATATATATATATAAGTCATATGTAAAC
* *
3576345 TATATAGTTTATATATATA
1 TATATAGTATATAAATATA
3576364 GTTCATATGT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
53 25 0.37
55 42 0.63
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (53 bp):
TATATAGTATATAAATATAAACTATAATATATATATATAAGTCATATGTAAAC
Found at i:3576350 original size:20 final size:19
Alignment explanation
Indices: 3576324--3576550 Score: 162
Period size: 18 Copynumber: 12.4 Consensus size: 19
3576314 TAGTATATAT
*
3576324 ATATATAGGTCATATGTAA
1 ATATATAGTTCATATGTAA
3576343 ACTATATAGTT--TA--T--
1 A-TATATAGTTCATATGTAA
3576357 ATATATAGTTCATATGTAA
1 ATATATAGTTCATATGTAA
*
3576376 ACA-ATAGTTCATATGTAA
1 ATATATAGTTCATATGTAA
* *
3576394 A-CTATAGTT-AGTATATAA
1 ATATATAGTTCA-TATGTAA
*
3576412 ATTATATAGTTTATATGTAA
1 A-TATATAGTTCATATGTAA
*
3576432 A-ATATAGTTCATATATAA
1 ATATATAGTTCATATGTAA
* *
3576450 ATATCA-ACTT--TA-GTAT
1 ATAT-ATAGTTCATATGTAA
3576466 ATATATAGTTCATATGTAA
1 ATATATAGTTCATATGTAA
*
3576485 ACTATATAGTTCATATAGTTTAT
1 A-TATATAGTTCATAT-G--TAA
*
3576508 ATATATAGTTCATATGCAA
1 ATATATAGTTCATATGTAA
* *
3576527 A-CTATAGTTCATATAT-A
1 ATATATAGTTCATATGTAA
3576544 ATATATA
1 ATATATA
3576551 AATATAAATT
Statistics
Matches: 165, Mismatches: 20, Indels: 47
0.71 0.09 0.20
Matches are distributed among these distances:
13 9 0.05
14 1 0.01
15 3 0.02
16 10 0.06
17 6 0.04
18 65 0.39
19 14 0.08
20 37 0.22
21 3 0.02
22 14 0.08
23 3 0.02
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATATAGTTCATATGTAA
Found at i:3576383 original size:31 final size:33
Alignment explanation
Indices: 3576312--3576389 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
3576302 AAATATCAAC
3576312 TATAGTATATATATATATAGGTCATATGTAAACTA
1 TATAGT-T-TATATATATAGGTCATATGTAAACTA
*
3576347 TATAGTTTATATATATAGTTCATATGTAAAC-A
1 TATAGTTTATATATATAGGTCATATGTAAACTA
*
3576379 -ATAGTTCATAT
1 TATAGTTTATAT
3576390 GTAAACTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 10 0.24
32 1 0.02
33 23 0.56
34 1 0.02
35 6 0.15
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (33 bp):
TATAGTTTATATATATAGGTCATATGTAAACTA
Found at i:3576428 original size:38 final size:38
Alignment explanation
Indices: 3576359--3576500 Score: 129
Period size: 38 Copynumber: 3.9 Consensus size: 38
3576349 TAGTTTATAT
* *
3576359 ATATAGTTCATATGTAAA-CA-ATAGTTCATATGTAAA
1 ATATAGTTCATATATAAATTATATAGTTCATATGTAAA
* *
3576395 CTATAGTT-AGTATATAAATTATATAGTTTATATGTAAA
1 ATATAGTTCA-TATATAAATTATATAGTTCATATGTAAA
* *
3576433 ATATAGTTCATATATAAA-TATCA-ACTT--TA-GTATAT
1 ATATAGTTCATATATAAATTAT-ATAGTTCATATGTA-AA
* *
3576468 ATATAGTTCATATGTAAACTATATAGTTCATAT
1 ATATAGTTCATATATAAATTATATAGTTCATAT
3576501 AGTTTATATA
Statistics
Matches: 86, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
34 3 0.03
35 22 0.26
36 20 0.23
37 7 0.08
38 33 0.38
39 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (38 bp):
ATATAGTTCATATATAAATTATATAGTTCATATGTAAA
Found at i:3576490 original size:22 final size:22
Alignment explanation
Indices: 3576465--3576532 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3576455 AACTTTAGTA
3576465 TATATATAGTTCATATGTAAAC
1 TATATATAGTTCATATGTAAAC
**
3576487 --TATATAGTTCATATAGTTTA-
1 TATATATAGTTCATAT-GTAAAC
*
3576507 TATATATAGTTCATATGCAAAC
1 TATATATAGTTCATATGTAAAC
3576529 TATA
1 TATA
3576533 GTTCATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 14 0.38
21 5 0.14
22 18 0.49
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TATATATAGTTCATATGTAAAC
Found at i:3576549 original size:40 final size:41
Alignment explanation
Indices: 3576463--3576550 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
3576453 TCAACTTTAG
* *
3576463 TATATATATAGTTCATATGTAAACTATATAGTTCATATAGTT
1 TATATATATAGTTCATATGCAAAC-ATATAGTTCATATAGTA
3576505 TATATATATAGTTCATATGCAAAC-TATAGTTCATATA-TA
1 TATATATATAGTTCATATGCAAACATATAGTTCATATAGTA
3576544 -ATATATA
1 TATATATA
3576551 AATATAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 7 0.16
39 1 0.02
40 13 0.30
42 23 0.52
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (41 bp):
TATATATATAGTTCATATGCAAACATATAGTTCATATAGTA
Found at i:3576556 original size:42 final size:41
Alignment explanation
Indices: 3576463--3576541 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
3576453 TCAACTTTAG
*
3576463 TATATATATAGTTCATATGTAAACTATATAGTTCATATAGTT
1 TATATATATAGTTCATATGCAAAC-ATATAGTTCATATAGTT
3576505 TATATATATAGTTCATATGCAAAC-TATAGTTCATATA
1 TATATATATAGTTCATATGCAAACATATAGTTCATATA
3576542 TAATATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 13 0.36
42 23 0.64
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (41 bp):
TATATATATAGTTCATATGCAAACATATAGTTCATATAGTT
Found at i:3576582 original size:40 final size:40
Alignment explanation
Indices: 3576538--3576616 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
3576528 CTATAGTTCA
3576538 TATATAATATATAAA-TATAA-ATTATAGTTTATATAAATAG
1 TATATAA-ATATAAATTATAATA-TATAGTTTATATAAATAG
* *
3576578 TATATAAATATAAATTATAGTATGTAGTTTATATAAATA
1 TATATAAATATAAATTATAATATATAGTTTATATAAATA
3576617 TACACCCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.20
40 27 0.77
41 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (40 bp):
TATATAAATATAAATTATAATATATAGTTTATATAAATAG
Found at i:3576587 original size:33 final size:31
Alignment explanation
Indices: 3576529--3576598 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 31
3576519 ATATGCAAAC
3576529 TATAGTTCATATATAATATATAAATATAAAT
1 TATAGTTCATATATAATATATAAATATAAAT
* *
3576560 TATAGTTTATATAAATAGTATATAAATATAAAT
1 TATAGTTCATAT--ATAATATATAAATATAAAT
3576593 TATAGT
1 TATAGT
3576599 ATGTAGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 11 0.31
33 24 0.69
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (31 bp):
TATAGTTCATATATAATATATAAATATAAAT
Found at i:3576694 original size:17 final size:17
Alignment explanation
Indices: 3576672--3576765 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 17
3576662 ACCCTAAATC
3576672 ATATATACTATATATAT
1 ATATATACTATATATAT
3576689 ATATATAAACTATATAGTTAT
1 ATATAT--ACTATATA--TAT
*
3576710 ATTAATAAACTATATA-AT
1 A-T-ATATACTATATATAT
*
3576728 -T-TATACAATATAT-T
1 ATATATACTATATATAT
* *
3576742 ATTTATAAT-TATATAT
1 ATATATACTATATATAT
3576758 AATATATA
1 -ATATATA
3576766 AATATAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
14 10 0.17
15 6 0.10
16 6 0.10
17 12 0.20
18 2 0.03
19 8 0.13
21 12 0.20
22 1 0.02
23 3 0.05
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
ATATATACTATATATAT
Found at i:3576710 original size:21 final size:19
Alignment explanation
Indices: 3576672--3577001 Score: 116
Period size: 20 Copynumber: 16.9 Consensus size: 19
3576662 ACCCTAAATC
*
3576672 ATATATACTATATATATAT
1 ATATAAACTATATATATAT
3576691 ATATAAACTATATAGT-TAT
1 ATATAAACTATATA-TATAT
3576710 ATTAATAAACTATATA-AT-T
1 A-T-ATAAACTATATATATAT
*
3576729 -TATACAA-TATAT-TATTT
1 ATATA-AACTATATATATAT
* *
3576746 ATAATTATA-TATAATATATAA
1 AT-A-TAAACTAT-ATATATAT
* * *
3576767 ATATAAATTGTATAGTTTAT
1 ATATAAACTATATA-TATAT
* *
3576787 ATATAATTCATATATAATTTAT
1 ATATAA-AC-TATAT-ATATAT
* *
3576809 ATATAAACTATGTAGGT-TCT
1 ATATAAACTATATA--TATAT
** * *
3576829 ATATAGTTCAATAGT-TCT-T
1 ATATA-AACTATA-TATATAT
3576848 ATATAAACTATATAGTATTAT
1 ATATAAACTATATA-TA-TAT
* * *
3576869 AGTTTATAC-ATGGTATATAT
1 A-TATAAACTAT-ATATATAT
* *
3576889 AGTTTATAC-ATA-ATATAT
1 A-TATAAACTATATATATAT
3576907 ATATAAACTATATAGTTTATAT
1 ATATAAACTATATA---TATAT
*
3576929 ATATAATAC-ATATACTTTAT
1 ATATAA-ACTATATA-TATAT
3576949 ATATAAACTATATATATAT
1 ATATAAACTATATATATAT
*
3576968 ATATATA-TATATATATAT
1 ATATAAACTATATATATAT
*
3576986 ATATATA-TATATATAT
1 ATATAAACTATATATAT
3577002 TAGTTGTTTT
Statistics
Matches: 244, Mismatches: 32, Indels: 71
0.70 0.09 0.20
Matches are distributed among these distances:
16 10 0.04
17 10 0.04
18 42 0.17
19 51 0.21
20 61 0.25
21 28 0.11
22 39 0.16
23 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATAAACTATATATATAT
Found at i:3576762 original size:22 final size:21
Alignment explanation
Indices: 3576740--3576814 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
3576730 ATACAATATA
*
3576740 TTATTTATAATTATATATAAT
1 TTATATATAATTATATATAAT
* * * *
3576761 ATATAAATATAAAT-TGTATAGT
1 -T-TATATATAATTATATATAAT
3576783 TTATATATAATTCATATATAAT
1 TTATATATAATT-ATATATAAT
3576805 TTATATATAA
1 TTATATATAA
3576815 ACTATGTAGG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 9 0.22
21 1 0.02
22 23 0.56
23 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (21 bp):
TTATATATAATTATATATAAT
Found at i:3576787 original size:33 final size:33
Alignment explanation
Indices: 3576680--3576809 Score: 94
Period size: 37 Copynumber: 3.9 Consensus size: 33
3576670 TCATATATAC
*
3576680 TATATATATATATATA-AACTATATAGTTATATTAAT
1 TATATATA-ATATATACAA-TATATAATT-TA-TAAT
* * *
3576716 AAACTATATAATTTATACAATATATTATTTATAAT
1 -TA-TATATAATATATACAATATATAATTTATAAT
*
3576751 TATATATAATATATA-AATATA-AATTGTATAGT
1 TATATATAATATATACAATATATAATT-TATAAT
*
3576783 T-TATAT-ATA-ATTC-ATATATAATTTATA
1 TATATATAATATATACAATATATAATTTATA
3576810 TATAAACTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
29 11 0.14
30 7 0.09
31 8 0.10
32 12 0.15
33 12 0.15
34 1 0.01
35 4 0.05
36 2 0.03
37 14 0.18
38 8 0.10
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (33 bp):
TATATATAATATATACAATATATAATTTATAAT
Found at i:3576812 original size:13 final size:11
Alignment explanation
Indices: 3576720--3576814 Score: 63
Period size: 11 Copynumber: 8.6 Consensus size: 11
3576710 ATTAATAAAC
3576720 TATATAATTTA
1 TATATAATTTA
*
3576731 TACA-ATATATTA
1 TATATA-AT-TTA
*
3576743 TTTATAA-TTA
1 TATATAATTTA
3576753 TATATAATATATA
1 TATATAAT-T-TA
* *
3576766 AATATAA-AT-
1 TATATAATTTA
* *
3576775 TGTATAGTTTA
1 TATATAATTTA
*
3576786 TATATAATTCA
1 TATATAATTTA
3576797 TATATAATTTA
1 TATATAATTTA
3576808 TATATAA
1 TATATAA
3576815 ACTATGTAGG
Statistics
Matches: 62, Mismatches: 14, Indels: 16
0.67 0.15 0.17
Matches are distributed among these distances:
9 4 0.06
10 12 0.19
11 30 0.48
12 7 0.11
13 9 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATAATTTA
Found at i:3576832 original size:42 final size:44
Alignment explanation
Indices: 3576740--3576838 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 44
3576730 ATACAATATA
* * * *
3576740 TTATTTATAATT-ATATATAATATATAAATATAAATTGTATAGT
1 TTATATATAATTCATATATAATATATAAATATAAACTATATAGG
* *
3576783 TTATATATAATTCATATATAAT-T-TATATATAAACTATGTAGG
1 TTATATATAATTCATATATAATATATAAATATAAACTATATAGG
* *
3576825 TTCTATATAGTTCA
1 TTATATATAATTCA
3576839 ATAGTTCTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 26 0.55
43 12 0.26
44 9 0.19
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (44 bp):
TTATATATAATTCATATATAATATATAAATATAAACTATATAGG
Found at i:3576889 original size:2 final size:2
Alignment explanation
Indices: 3576882--3577001 Score: 118
Period size: 2 Copynumber: 58.5 Consensus size: 2
3576872 TTATACATGG
* * * *
3576882 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA AA CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
3576924 TA TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
3576967 TA TA TA TA 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 TA TA TA TA T
3577002 TAGTTGTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.02
2 90 0.93
3 5 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3577778 original size:216 final size:215
Alignment explanation
Indices: 3577084--3577779 Score: 1034
Period size: 210 Copynumber: 3.3 Consensus size: 215
3577074 TGATCCCTTT
* * **
3577084 TGTGTTGTTTAATTTATTTTAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCACT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * *
3577149 TTTTATTTGCATATGAAATTAACCCATACTTATTACTT-ATT-TATATTTATTAATTGACCCATA
66 TTTTATTTGCATATGAAATTGA-CCATACTTATTACTTAATTCTAT-TTTTTTAATTGGCCCATA
* * * * * *
3577212 ACTTTTTAAATGAGTATAATTTAGTACATTTGTGTATTAATTTCAACCTTAAAATTTAAAATTAT
129 ACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTAT
*
3577277 TTCGATTTGATCC-C-T---TT
194 TTCGATTTGATCCTCATCAATG
* *
3577294 TGTGTTGTTTAGTTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * *
3577359 TTTTATTTGCATCTGAAATTGACACATACTTATTACTTATTTCTA-TTTTTAAATTGG-CCATAA
66 TTTTATTTGCATATGAAATTGAC-CATACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAA
*
3577422 CTTTTTAAATTGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
130 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
3577487 TCGATTTGATCCCTCATCAATG
195 TCGATTTGAT-CCTCATCAATG
* *
3577509 TGTGTTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTTTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
3577574 TTTTATTTGCATATGAAATTGATCCAGACTTTTTACTTAATTCTATTTTTTTAATTGGCCCATAA
66 TTTTATTTGCATATGAAATTGA-CCATACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAA
3577639 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTA-T
130 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
3577703 TCGATTTGATCCATCATCAATG
195 TCGATTTGATCC-TCATCAATG
* *
3577725 TGTGTTGTTTAATTTATTTAAATTTTTATTTGCAATCTCATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
3577780 ATTCTTAAAT
Statistics
Matches: 439, Mismatches: 34, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
209 75 0.17
210 104 0.24
211 3 0.01
212 3 0.01
215 103 0.23
216 83 0.19
217 68 0.15
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (215 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATATGAAATTGACCATACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
CGATTTGATCCTCATCAATG
Found at i:3578509 original size:30 final size:30
Alignment explanation
Indices: 3578474--3578539 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3578464 TAATATTATT
*
3578474 TATTTTGA-TCTTATCATAACTCATAAAATA
1 TATTTTGATTCTTACCATAACTCA-AAAATA
* *
3578504 TATTTT-ATTCTTACCTTAACTTAAAAATA
1 TATTTTGATTCTTACCATAACTCAAAAATA
3578533 TATTTTG
1 TATTTTG
3578540 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (30 bp):
TATTTTGATTCTTACCATAACTCAAAAATA
Found at i:3578551 original size:29 final size:29
Alignment explanation
Indices: 3578498--3578747 Score: 116
Period size: 29 Copynumber: 8.4 Consensus size: 29
3578488 CATAACTCAT
3578498 AAAATATATTTTATTCTTACCTTAACTTA
1 AAAATATATTTTATTCTTACCTTAACTTA
* * ** *
3578527 AAAATATATTTTGTTTTTATTTTAACTTGT
1 AAAATATATTTTATTCTTACCTTAACTT-A
* * ** *
3578557 TACATATA-TTTATTCTTAATTTAAATTA
1 AAAATATATTTTATTCTTACCTTAACTTA
* * *
3578585 TATATATATATATTATATTCTTACCTTAAATGA
1 -A-A-A-ATATATTTTATTCTTACCTTAACTTA
* * *
3578618 TTAAATAT-TATTTATTCTTATCTTAATTTA
1 -AAAATATAT-TTTATTCTTACCTTAACTTA
* * *
3578648 AAAATATATATT-TTATT--C-TAATTTCA
1 AAAATATATTTTATTCTTACCTTAACTT-A
* ** *
3578674 AAATGTATATTTTATTCTTATTTTAATTTA
1 AAA-ATATATTTTATTCTTACCTTAACTTA
* *
3578704 AGAAATATATTTTATTTTTTATCTTAACTATA
1 A-AAATATATTTTA-TTCTTACCTTAACT-TA
*
3578736 AAAATATTTTTT
1 AAAATATATTTT
3578748 TATCTTAATT
Statistics
Matches: 169, Mismatches: 35, Indels: 32
0.72 0.15 0.14
Matches are distributed among these distances:
25 6 0.04
26 5 0.03
27 7 0.04
28 8 0.05
29 48 0.28
30 39 0.23
31 30 0.18
32 9 0.05
33 17 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (29 bp):
AAAATATATTTTATTCTTACCTTAACTTA
Found at i:3578669 original size:25 final size:25
Alignment explanation
Indices: 3578641--3578696 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3578631 ATTCTTATCT
3578641 TAATTTAAAAATATATATTTTATTC
1 TAATTTAAAAATATATATTTTATTC
* *
3578666 TAATTTCAAAATGTATATTTTATTC
1 TAATTTAAAAATATATATTTTATTC
*
3578691 TTATTT
1 TAATTT
3578697 TAATTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (25 bp):
TAATTTAAAAATATATATTTTATTC
Found at i:3578715 original size:30 final size:29
Alignment explanation
Indices: 3578498--3578760 Score: 139
Period size: 30 Copynumber: 8.9 Consensus size: 29
3578488 CATAACTCAT
** *
3578498 AAAATATATTTTATTCTTACCTTAACTTA
1 AAAATATATTTTATTCTTATTTTAATTTA
* *
3578527 AAAATATATTTTGTTTTTATTTTAACTTGT-
1 AAAATATATTTTATTCTTATTTTAA-TT-TA
* * *
3578557 TACATATA-TTTATTCTTAATTTAAATTATA
1 AAAATATATTTTATTCTT-ATTTTAATT-TA
* * * *
3578587 TATATATATATTATATTCTTACCTTAAATGATTA
1 -A-AAATATATTTTATTCTTA-TTTTAAT--TTA
* *
3578621 AATAT-TA-TTTATTCTTATCTTAATTTA
1 AAAATATATTTTATTCTTATTTTAATTTA
*
3578648 AAAATATA---TATT-TTATTCTAATTTCA
1 AAAATATATTTTATTCTTATTTTAATTT-A
*
3578674 AAATGTATATTTTATTCTTATTTTAATTTA
1 AAA-ATATATTTTATTCTTATTTTAATTTA
* * *
3578704 AGAAATATATTTTATTTTTTATCTTAACTATA
1 A-AAATATATTTTA-TTCTTATTTTAA-TTTA
* *
3578736 AAAATAT-TTTTTTATCTTAATTTAA
1 AAAATATATTTTAT-TCTTATTTTAA
3578761 AATACTATAA
Statistics
Matches: 181, Mismatches: 32, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
25 10 0.06
26 8 0.04
27 11 0.06
28 2 0.01
29 36 0.20
30 49 0.27
31 32 0.18
32 15 0.08
33 15 0.08
34 2 0.01
35 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (29 bp):
AAAATATATTTTATTCTTATTTTAATTTA
Found at i:3581743 original size:7 final size:7
Alignment explanation
Indices: 3581731--3581761 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3581721 GTAAAAGAAA
3581731 GTCAACG
1 GTCAACG
3581738 GTCAACG
1 GTCAACG
3581745 GTCAACG
1 GTCAACG
3581752 GTCAACG
1 GTCAACG
3581759 GTC
1 GTC
3581762 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3581792 original size:19 final size:18
Alignment explanation
Indices: 3581768--3581817 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
3581758 GGTCGGGTCG
3581768 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
3581786 GGTTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
3581805 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
3581818 TTCCAGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3581798 original size:10 final size:9
Alignment explanation
Indices: 3581768--3581817 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
3581758 GGTCGGGTCG
3581768 GGTCAGACC
1 GGTCAGACC
*
3581777 GGTCAAACC
1 GGTCAGACC
3581786 GGTTCAGACC
1 GG-TCAGACC
*
3581796 GGTCAAACC
1 GGTCAGACC
3581805 GGTCAGAACC
1 GGTCAG-ACC
3581815 GGT
1 GGT
3581818 TTCCAGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 21 0.60
10 14 0.40
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (9 bp):
GGTCAGACC
Found at i:3584945 original size:5 final size:5
Alignment explanation
Indices: 3584935--3584960 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3584925 CAACATGCAA
3584935 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
3584961 GGACTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3586470 original size:22 final size:24
Alignment explanation
Indices: 3586426--3586470 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3586416 AAGGAAAACA
*
3586426 AATAATAAATATTATAATTAAAAAT
1 AATAATAAATAATATAA-TAAAAAT
3586451 AATAAT-AATAATATAA-AAAA
1 AATAATAAATAATATAATAAAA
3586471 GGATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
24 9 0.47
25 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
AATAATAAATAATATAATAAAAAT
Found at i:3586844 original size:134 final size:134
Alignment explanation
Indices: 3586676--3587343 Score: 774
Period size: 134 Copynumber: 5.0 Consensus size: 134
3586666 TATTAAAACG
* * * *
3586676 AGGCATACTTGTTTCACTGTTACTCAGAGAATATCAAATCTTGAAATAGTGGGATCTGTTTCGCT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGGATCTGTTCCGCT
* * * * * *
3586741 TTTTCTTGAGGGAAAATCAGATTTGGGGACGATGATTCATTCCATTATTACTCAGAGAAGATTGA
66 TTTTCTTGAGGGAAAATCATATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
3586806 ATCA
131 ATCA
* * *
3586810 AGGCATACTTGTTCCACTGTTACTCAGGGCATATCAAATCTTGAAAGAGAGGGAAT-TGTTCCAC
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGG-ATCTGTTCCGC
* * * * *
3586874 TTCTTGCAT-AGGGAAAATCATATATGGGGACGTTGATCCATTCCACTGTTACTCAGGGAAGATT
65 TT-TTTCTTGAGGGAAAATCATATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
**
3586938 G-ATTG
129 GAATCA
* * * * * *
3586943 AGACATACTTGTTCCACTGTTACTTAGGGAATATCAAATATTGAAATATAGAGATCTATTCCGCT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGGATCTGTTCCGCT
* *
3587008 TCTTT-TTGTGGGAAAATCATATCTAGGGGA-GTTGATTCATTCCACTGTCACTCAGGGAAGATT
66 T-TTTCTTGAGGGAAAATCATAT-TTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
3587071 GAATCA
129 GAATCA
* * * *
3587077 AGGCAGACTTGTTCCACTGTTACTCAGGGAATATTAAATCTTGAAAGT-GAGGGATATTTTCCGC
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAA-TAGAGGGATCTGTTCCGC
* * * *
3587141 TTCTTCTTGAGGGAAAATCATATCTAGGGGA-GTTGATTTATTCCACCGTCACTCAGGGAAGATT
65 TTTTTCTTGAGGGAAAATCATAT-TTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
*
3587205 GAATCG
129 GAATCA
* * * * * *
3587211 AGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGAGATCTGTTCCACT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGGATCTGTTCCGCT
* * * * * * **
3587276 TTTTCTTGAGGAAAAATTAGATATGGGGACATTGATTCATTCCACTATCACTCAGAAAAGATTGA
66 TTTTCTTGAGGGAAAATCATATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
3587341 ATC
131 ATC
3587344 GAGTTCGATT
Statistics
Matches: 454, Mismatches: 70, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
132 3 0.01
133 111 0.24
134 333 0.73
135 7 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (134 bp):
AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATAGAGGGATCTGTTCCGCT
TTTTCTTGAGGGAAAATCATATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
ATCA
Found at i:3587156 original size:267 final size:268
Alignment explanation
Indices: 3586674--3587343 Score: 874
Period size: 267 Copynumber: 2.5 Consensus size: 268
3586664 AATATTAAAA
* * * *
3586674 CGAGG-CATACTTGTTTCACTGTTACTCAGAGAATATCAAATCTTGAAATAGT-GGGATCTGTTT
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATA-TAGAGATCTGTTC
* * *
3586737 CGCTTTTTCTTGAGGGAAAATCAGATTTGGGGACGATGATTCATTCCATTATTACTCAGAGAAGA
65 CGCTTTTTCTTGAGGGAAAATCAGA-TTGGGGACGTTGATTCATTCCACTATCACTCAGAGAAGA
* *
3586802 TTGAATCAAGGCATACTTGTTCCACTGTTACTCAGGGCATATCAAATCTTGAAAGAGAGGGAATT
129 TTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGAATT
* *
3586867 GTTCCACTTCTTGCATAGGGAAAATCATATAT-GGGGACGTTGATCCATTCCACTGTTACTCAGG
194 GTTCCACTTCTTGCATAGGGAAAATCATATATAGGGGA-GTTGATCCATTCCACCGTCACTCAGG
3586931 GAAGATTG-AT
258 GAAGATTGAAT
* * * *
3586941 TGA-GACATACTTGTTCCACTGTTACTTAGGGAATATCAAATATTGAAATATAGAGATCTATTCC
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATATAGAGATCTGTTCC
* * * *
3587005 GCTTCTTT-TTGTGGGAAAATCATATCTAGGGGA-GTTGATTCATTCCACTGTCACTCAGGGAAG
66 GCTT-TTTCTTGAGGGAAAATCAGAT-T-GGGGACGTTGATTCATTCCACTATCACTCAGAGAAG
* *
3587068 ATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATTAAATCTTGAAAGTGAGGGATA
128 ATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGA-A
* * * **
3587133 TT-TTCCGCTTCTT-CTTGAGGGAAAATCATATCTAGGGGAGTTGATTTATTCCACCGTCACTCA
192 TTGTTCCACTTCTTGCAT-AGGGAAAATCATATATAGGGGAGTTGATCCATTCCACCGTCACTCA
3587196 GGGAAGATTGAAT
256 GGGAAGATTGAAT
* * * *
3587209 CGAGGA-AGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGAGATCTGTTCC
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATATAGAGATCTGTTCC
* * * * *
3587273 ACTTTTTCTTGAGGAAAAATTAGATATGGGGACATTGATTCATTCCACTATCACTCAGAAAAGAT
66 GCTTTTTCTTGAGGGAAAATCAGAT-TGGGGACGTTGATTCATTCCACTATCACTCAGAGAAGAT
3587338 TGAATC
130 TGAATC
3587344 GAGTTCGATT
Statistics
Matches: 347, Mismatches: 44, Indels: 23
0.84 0.11 0.06
Matches are distributed among these distances:
266 5 0.01
267 218 0.63
268 122 0.35
269 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (268 bp):
CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAATATAGAGATCTGTTCC
GCTTTTTCTTGAGGGAAAATCAGATTGGGGACGTTGATTCATTCCACTATCACTCAGAGAAGATT
GAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGAATTGT
TCCACTTCTTGCATAGGGAAAATCATATATAGGGGAGTTGATCCATTCCACCGTCACTCAGGGAA
GATTGAAT
Found at i:3591799 original size:22 final size:22
Alignment explanation
Indices: 3591765--3591825 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
3591755 AGCGCTAGAA
* * *
3591765 ATCGATACCCCCTTGCATGGGT
1 ATCGATTCCCCCTTGAATAGGT
*
3591787 ATCGATTCGCCCTTTGAATAGGT
1 ATCGATTC-CCCCTTGAATAGGT
*
3591810 ACCGATTCCCCCTTGA
1 ATCGATTCCCCCTTGA
3591826 GGGAACTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.30
Consensus pattern (22 bp):
ATCGATTCCCCCTTGAATAGGT
Found at i:3594063 original size:21 final size:21
Alignment explanation
Indices: 3594037--3594087 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3594027 ATTTAACAAA
3594037 AAGGGGGAGAAGTGTTATAGT
1 AAGGGGGAGAAGTGTTATAGT
*
3594058 AAGGGGAAGAAGTGTTATAGT
1 AAGGGGGAGAAGTGTTATAGT
3594079 AAGGGGGAG
1 AAGGGGGAG
3594088 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.45, T:0.20
Consensus pattern (21 bp):
AAGGGGGAGAAGTGTTATAGT
Found at i:3596064 original size:15 final size:16
Alignment explanation
Indices: 3596040--3596073 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3596030 AGCGTCATTT
*
3596040 AAATT-TTTTTAAGAA
1 AAATTGTTTTCAAGAA
3596055 AAATTGTTTTCAAGAA
1 AAATTGTTTTCAAGAA
3596071 AAA
1 AAA
3596074 AGTTGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (16 bp):
AAATTGTTTTCAAGAA
Done.