Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 69 of 105
Found at i:12297612 original size:58 final size:58
Alignment explanation
Indices: 12297542--12297697 Score: 231
Period size: 58 Copynumber: 2.7 Consensus size: 58
12297532 TTTTAAAAAA
* * *
12297542 TAAAAAAAATTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTC
1 TAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAATTTC
* * * *
12297600 TAAAAAATATTTTGAGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTTT
1 TAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAATTTC
* *
12297658 TAAAAAGTATTTTGAGGAAAAGTTAAAAGTATCAATTTTC
1 TAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTC
12297698 TTTATATAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 86 1.00
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (58 bp):
TAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAATTTC
Found at i:12301220 original size:18 final size:18
Alignment explanation
Indices: 12301197--12301235 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12301187 TTTTTTGAAA
*
12301197 AAAAAAG-GCAAAACAAAG
1 AAAAAAGAG-AAAAAAAAG
12301215 AAAAAAGAGAAAAAAAAG
1 AAAAAAGAGAAAAAAAAG
12301233 AAA
1 AAA
12301236 TGAATGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:12301658 original size:9 final size:9
Alignment explanation
Indices: 12301646--12301699 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
12301636 ACAAAAAAAG
12301646 AAAAAGAAA
1 AAAAAGAAA
*
12301655 AAAATG-AA
1 AAAAAGAAA
*
12301663 AAAATGAAA
1 AAAAAGAAA
12301672 AAATAAGAGAA
1 AAA-AAGA-AA
12301683 AAAAATGAAA
1 AAAAA-GAAA
12301693 AAAAAGA
1 AAAAAGA
12301700 TGAAAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 8 0.21
9 12 0.31
10 12 0.31
11 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:12301685 original size:21 final size:21
Alignment explanation
Indices: 12301652--12301705 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
12301642 AAAGAAAAAG
12301652 AAAAAA-ATG-AAAAAATGAA
1 AAAAAAGATGAAAAAAATGAA
12301671 AAAATAAGA-GAAAAAAATGAA
1 AAAA-AAGATGAAAAAAATGAA
12301692 AAAAAAGATGAAAA
1 AAAAAAGATGAAAA
12301706 GAAAAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 20 0.65
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (21 bp):
AAAAAAGATGAAAAAAATGAA
Found at i:12302398 original size:61 final size:63
Alignment explanation
Indices: 12302323--12302449 Score: 161
Period size: 63 Copynumber: 2.0 Consensus size: 63
12302313 TAACTTGTGT
*
12302323 ATTGTGATCAAATGATG-AGGA-TAAATTCATTCTGGAATGGCTAATGCTGAAAA-GCCTCTGA
1 ATTGTGATCAAATGATGAAGGACAAAATTCATTCTGGAATGGCTAATGCT-AAAAGGCCTCTGA
* * * * * *
12302384 ATTGTGATTAAATGATGAAGGACAAAATTTATTTTGGAATGGTTAGTGCTAAAAGGCCTGTGA
1 ATTGTGATCAAATGATGAAGGACAAAATTCATTCTGGAATGGCTAATGCTAAAAGGCCTCTGA
12302447 ATT
1 ATT
12302450 ACGGTTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 16 0.29
62 8 0.14
63 32 0.57
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (63 bp):
ATTGTGATCAAATGATGAAGGACAAAATTCATTCTGGAATGGCTAATGCTAAAAGGCCTCTGA
Found at i:12302806 original size:14 final size:14
Alignment explanation
Indices: 12302787--12302828 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
12302777 CCTGATTTTT
12302787 TTTAAATGAGAATC
1 TTTAAATGAGAATC
12302801 TTTAAA--A-AATC
1 TTTAAATGAGAATC
12302812 TTTAAATGAGAATC
1 TTTAAATGAGAATC
12302826 TTT
1 TTT
12302829 GAGTGTCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.40
12 1 0.04
13 1 0.04
14 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (14 bp):
TTTAAATGAGAATC
Found at i:12302907 original size:21 final size:21
Alignment explanation
Indices: 12302854--12302935 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
12302844 ATCTTCGAAC
12302854 TCAAATGAGAATATTTGAATCT
1 TCAAATGAGAATATTTGAAT-T
*
12302876 TCAAATGAGAATCTTTGAATGT
1 TCAAATGAGAATATTTGAAT-T
*
12302898 T-AAATAAGAATATTTGAATT
1 TCAAATGAGAATATTTGAATT
*
12302918 TCAAATGAGAATCTTTGA
1 TCAAATGAGAATATTTGA
12302936 GGTGTGAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.04
21 30 0.57
22 21 0.40
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
TCAAATGAGAATATTTGAATT
Found at i:12302960 original size:35 final size:36
Alignment explanation
Indices: 12302914--12303008 Score: 129
Period size: 35 Copynumber: 2.6 Consensus size: 36
12302904 AGAATATTTG
*
12302914 AATTTCAAATGAGAATCTTTGAGGTGTGAAACC-CA
1 AATTTCAAATGAGAATCTTTGAGGTGTGAAACCTAA
*
12302949 AATTTCAAATGAGAATCTTTAAGGTGTGAAACCTAA
1 AATTTCAAATGAGAATCTTTGAGGTGTGAAACCTAA
* *
12302985 AATTTGTCAAATGTGAATATTTGA
1 AA-TT-TCAAATGAGAATCTTTGA
12303009 ATTTCAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.62
36 3 0.06
37 2 0.04
38 15 0.29
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
AATTTCAAATGAGAATCTTTGAGGTGTGAAACCTAA
Found at i:12303015 original size:59 final size:59
Alignment explanation
Indices: 12302949--12303085 Score: 179
Period size: 59 Copynumber: 2.3 Consensus size: 59
12302939 GTGAAACCCA
* * *
12302949 AATTTCAAATGAGAATCTTTAAGGTGTG-AAACCTAAAATTTGTCAAATGTGAATATTTG
1 AATTTCAAATGAGAATCTTTAAGGTGTGAAAATC-AAAATTTATCAAATGTGAATATTCG
* * * * *
12303008 AATTTCAAATGGGAATATTTGAGGTGTGAAAATCAAAATTTATCGAATGTGAATCTTCG
1 AATTTCAAATGAGAATCTTTAAGGTGTGAAAATCAAAATTTATCAAATGTGAATATTCG
12303067 AA-TTCAAATGAGAATCTTT
1 AATTTCAAATGAGAATCTTT
12303086 GAATTTCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 15 0.22
59 48 0.72
60 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (59 bp):
AATTTCAAATGAGAATCTTTAAGGTGTGAAAATCAAAATTTATCAAATGTGAATATTCG
Found at i:12303081 original size:20 final size:21
Alignment explanation
Indices: 12303053--12303105 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
12303043 AAATTTATCG
*
12303053 AATGTGAATCTTCGAA-TTCA
1 AATGAGAATCTTCGAATTTCA
*
12303073 AATGAGAATCTTTGAATTTCA
1 AATGAGAATCTTCGAATTTCA
* *
12303094 AATAAAAATCTT
1 AATGAGAATCTT
12303106 TGAGATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (21 bp):
AATGAGAATCTTCGAATTTCA
Found at i:12303095 original size:21 final size:20
Alignment explanation
Indices: 12303053--12303108 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
12303043 AAATTTATCG
* *
12303053 AATGTGAATCTTCGAATTCA
1 AATGAGAATCTTTGAATTCA
12303073 AATGAGAATCTTTGAATTTCA
1 AATGAGAATCTTTGAA-TTCA
* *
12303094 AATAAAAATCTTTGA
1 AATGAGAATCTTTGA
12303109 GATGTGAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGAGAATCTTTGAATTCA
Found at i:12303733 original size:43 final size:43
Alignment explanation
Indices: 12303686--12303779 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 43
12303676 AGAAGCCTTG
* * *
12303686 TTTATTTTTTTTAAAGTCATTGAGCCTCTGTTTAAAGGAGCAA
1 TTTATTTTTTTCAAAATCATGGAGCCTCTGTTTAAAGGAGCAA
* * *
12303729 TTTA-TTTTTTCAAAATTATGGAGCCTCTGTTTAGAGGAGCAT
1 TTTATTTTTTTCAAAATCATGGAGCCTCTGTTTAAAGGAGCAA
12303771 TTTATTTTT
1 TTTATTTTT
12303780 CAAAGTTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 36 0.82
43 8 0.18
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.48
Consensus pattern (43 bp):
TTTATTTTTTTCAAAATCATGGAGCCTCTGTTTAAAGGAGCAA
Found at i:12303798 original size:41 final size:41
Alignment explanation
Indices: 12303707--12303864 Score: 147
Period size: 42 Copynumber: 3.8 Consensus size: 41
12303697 TAAAGTCATT
* *
12303707 GAGCCTCTGTTTAAAGGAGCAATTTATTTTTTCAAAATTATG
1 GAGCCTCTGTTTAGAGGAGCATTTTA-TTTTTCAAAATTATG
* * *
12303749 GAGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGTTGTT
1 GAGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAATTATG
* * * * *
12303790 GTGTCTCTGTTTAGAGGAGTTATGTTTA-TTTTCAAAAGTCATC
1 GAGCCTCTGTTTAGAGGAG-CAT-TTTATTTTTCAAAA-TTATG
* * *
12303833 AAGCATCTGTTTAGAGGAGCTTTGTTATTTTT
1 GAGCCTCTGTTTAGAGGAGCATT-TTATTTTT
12303865 TTTTTTAAAA
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
41 30 0.32
42 38 0.41
43 25 0.27
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (41 bp):
GAGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAATTATG
Found at i:12304016 original size:9 final size:9
Alignment explanation
Indices: 12304002--12304034 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12303992 TCTGGCAGTT
12304002 AAAAAAGTA
1 AAAAAAGTA
*
12304011 AAAAAAATA
1 AAAAAAGTA
12304020 AAAAAA-TA
1 AAAAAAGTA
12304028 AAAAAAG
1 AAAAAAG
12304035 ATGTTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAAAGTA
Found at i:12304023 original size:17 final size:17
Alignment explanation
Indices: 12304001--12304033 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12303991 CTCTGGCAGT
*
12304001 TAAAAAAGTAAAAAAAA
1 TAAAAAAATAAAAAAAA
12304018 TAAAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
12304034 GATGTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
TAAAAAAATAAAAAAAA
Found at i:12304705 original size:20 final size:22
Alignment explanation
Indices: 12304682--12304734 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
12304672 CGTTTTGATT
12304682 TTTTTTATTTATT-TTTG-GTA
1 TTTTTTATTTATTATTTGTGTA
* *
12304702 TTTTTTATTTTTTATTTGTGTG
1 TTTTTTATTTATTATTTGTGTA
12304724 TTTGTTTATTT
1 TTT-TTTATTT
12304735 TTTAAGAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 5 0.18
23 7 0.25
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (22 bp):
TTTTTTATTTATTATTTGTGTA
Found at i:12304715 original size:23 final size:24
Alignment explanation
Indices: 12304679--12304738 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
12304669 AGTCGTTTTG
* *
12304679 ATTTTTT-TTATTTATTTTTG-GT
1 ATTTTTTATTTTTTATTTGTGTGT
12304701 ATTTTTTATTTTTTATTTGTGTGT
1 ATTTTTTATTTTTTATTTGTGTGT
*
12304725 -TTGTTTATTTTTTA
1 ATTTTTTATTTTTTA
12304739 AGAGTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 24 0.73
24 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (24 bp):
ATTTTTTATTTTTTATTTGTGTGT
Found at i:12304898 original size:19 final size:19
Alignment explanation
Indices: 12304857--12304900 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12304847 GATGAAAAGT
** * *
12304857 TAAAAATACCAATTTTTAT
1 TAAAAATAAAAATTTTCAA
12304876 TAAAAATAAAAATTTTCAA
1 TAAAAATAAAAATTTTCAA
12304895 TAAAAA
1 TAAAAA
12304901 AACATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAATAAAAATTTTCAA
Found at i:12304932 original size:62 final size:58
Alignment explanation
Indices: 12304819--12304959 Score: 167
Period size: 62 Copynumber: 2.4 Consensus size: 58
12304809 AAAATAATCA
* *
12304819 AAAAATAAAAATTTCTAAAACACATTTTGATGAAAAGTTAAAAATACCAATTTTTATT
1 AAAAATAAAAATTTCTAAAAAACATTTTGAAGAAAAGTTAAAAATACCAATTTTTATT
* * * * * *
12304877 AAAAATAAAAATTTTCAATAAAAAAACATTTTTAAGAAAATTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAAA-TTTC--T-AAAAAACATTTTGAAGAAAAGTTAAAAATACCAATTTTTATT
12304939 AAAAAT-AAAATTTCTAAAAAA
1 AAAAATAAAAATTTCTAAAAAA
12304960 TAAAAAAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 6 0.08
58 12 0.17
59 4 0.06
60 4 0.06
61 5 0.07
62 40 0.56
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATAAAAATTTCTAAAAAACATTTTGAAGAAAAGTTAAAAATACCAATTTTTATT
Found at i:12304957 original size:77 final size:77
Alignment explanation
Indices: 12304877--12305176 Score: 412
Period size: 77 Copynumber: 3.9 Consensus size: 77
12304867 AATTTTTATT
12304877 AAAAATAAAAATTTTCAATAAAAAAACATTTTTAAG-AAAATTTGAAAGTATCAATTTTTCTTAA
1 AAAAATAAAAATTTT-AA-AAAAAAACATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAA
12304941 AAATAAAATTTCTA
64 AAATAAAATTTCTA
** * *
12304955 AAAAATAAAAAAATTAAAAAAATATATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAAAA
1 AAAAATAAAAATTTTAAAAAAAAACATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAAAA
12305020 ATAAAATTTCTA
66 ATAAAATTTCTA
* * * * * * *
12305032 AAAGATAAAAATTTTAAAAATATATATTTTTGAGAAAAATTTGAATGTATCAATTTTCCTTAAAA
1 AAAAATAAAAATTTTAAAAAAAAACATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAAAA
12305097 ATAAAATTTCTA
66 ATAAAATTTCTA
* * *
12305109 AAAAATAAAAATTTCT---AAAAAACA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAA
1 AAAAATAAAAATTT-TAAAAAAAAACATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAAA
12305170 AATAAAA
65 AATAAAA
12305177 ATTTTCAAAA
Statistics
Matches: 201, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
74 40 0.20
75 5 0.02
76 15 0.07
77 127 0.63
78 14 0.07
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (77 bp):
AAAAATAAAAATTTTAAAAAAAAACATTTTTAAGAAAAATTTGAAAGTATCAATTTTTCTTAAAA
ATAAAATTTCTA
Found at i:12304958 original size:16 final size:16
Alignment explanation
Indices: 12304933--12304964 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12304923 AGTATCAATT
*
12304933 TTTCTTAAAAATAAAA
1 TTTCTAAAAAATAAAA
12304949 TTTCTAAAAAATAAAA
1 TTTCTAAAAAATAAAA
12304965 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTCTAAAAAATAAAA
Found at i:12305039 original size:16 final size:16
Alignment explanation
Indices: 12305010--12305053 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12305000 AGTATCAATT
12305010 TTTCTTAAAAAT-AAAA
1 TTTC-TAAAAATAAAAA
12305026 TTTCTAAAAGATAAAAA
1 TTTCTAAAA-ATAAAAA
12305043 TTT-TAAAAATA
1 TTTCTAAAAATA
12305054 TATATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.31
16 11 0.42
17 7 0.27
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTCTAAAAATAAAAA
Found at i:12305114 original size:16 final size:17
Alignment explanation
Indices: 12305093--12305130 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12305083 AATTTTCCTT
12305093 AAAAAT-AAAATTTCTA
1 AAAAATAAAAATTTCTA
12305109 AAAAATAAAAATTTCTA
1 AAAAATAAAAATTTCTA
12305126 AAAAA
1 AAAAA
12305131 CATTTTGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAAAATTTCTA
Found at i:12305171 original size:58 final size:58
Alignment explanation
Indices: 12305103--12305339 Score: 282
Period size: 58 Copynumber: 4.0 Consensus size: 58
12305093 AAAAATAAAA
*
12305103 TTTCTAAAAAATAAAAATTTCTAAAAAACATTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATTTCTAAAAAACATTTTGAGGAAAAGTTGAAAGTATCAATT
**
12305161 TTTCTTAAAAATAAAAATTT-TCAAAAAGTATTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATTTCT-AAAAAACATTTTGAGGAAAAGTTGAAAGTATCAATT
* * * * ** *
12305219 TTCCTTGAAATTAAAATTTTAGAAAAAAGCATTTTGAGGAAAAGTTGAAAGTACCAATT
1 TTTCTTAAAAATAAAAATTTCTAAAAAA-CATTTTGAGGAAAAGTTGAAAGTATCAATT
* * *
12305278 TTTTTTAAAAAT-AAAATTATC-AAGAAAACTATTTTTAAAGAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATT-TCTAA-AAAAC-A-TTTTGAGGAAAAGTTGAAAGTATCAATT
12305338 TT
1 TT
12305340 CCTTGTATAA
Statistics
Matches: 152, Mismatches: 20, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 82 0.54
59 42 0.28
60 27 0.18
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (58 bp):
TTTCTTAAAAATAAAAATTTCTAAAAAACATTTTGAGGAAAAGTTGAAAGTATCAATT
Found at i:12305254 original size:117 final size:118
Alignment explanation
Indices: 12305125--12305344 Score: 347
Period size: 117 Copynumber: 1.9 Consensus size: 118
12305115 AAAAATTTCT
* *
12305125 AAAAAACATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTTC-A-AAAA
1 AAAAAACATTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTTAAAAAT-AAAATTATCAAGAAAA
* * *
12305188 GTA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTAG
65 CTATTTTTAAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTAG
*
12305241 AAAAAAGCATTTTGAGGAAAAGTTGAAAGTACCAATTTTTTTTAAAAATAAAATTATCAAGAAAA
1 AAAAAA-CATTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAATTATCAAGAAAA
12305306 CTATTTTTAAAGAAAAGTTGAAAGTATCAATTTTCCTTG
65 CTATTTTTAAAGAAAAGTTGAAAGTATCAATTTTCCTTG
12305345 TATAAAAGCA
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
116 14 0.15
117 41 0.44
118 6 0.06
119 33 0.35
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (118 bp):
AAAAAACATTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAATTATCAAGAAAAC
TATTTTTAAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAATTTTAG
Found at i:12305433 original size:5 final size:5
Alignment explanation
Indices: 12305423--12305459 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
12305413 TCATTATTCC
12305423 TTTTA TTTTA TTTTA TTTTA TTTTA -TTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12305460 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.20
5 24 0.80
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:12308179 original size:127 final size:127
Alignment explanation
Indices: 12307912--12308269 Score: 303
Period size: 127 Copynumber: 2.8 Consensus size: 127
12307902 ATTCAAGACA
* * * *
12307912 TTTTTTGAT-CAAAAATACCTTGAATAATC-CAC-TAAAAAAATT-AAAAGGAATTATTCAAGGC
1 TTTTTTGATAAAAAAACACCTTGAATAATCTCTCAAAAAAAAATTGAAAAGG-ATTATTCAAGGC
* *
12307973 GTTTTT-TTGCTAGAAAC-TCCTTGAATAACC-CTATTTAA-TTTTTTGTAAGAAATTAATCAAT
65 GTTTTTGGT-C-A-AAACGT-CTTGAATAACCTC-ATTTAATTTTTTTGTAAGAAATTAATCAAG
12308034 GTG
125 GTG
* ** *
12308037 TTTTTTGATAAAAAAA-ATGTCTTGAATAATCAT-T-TTATAAAAATTGAAAAGGATTATTCAAG
1 TTTTTTGATAAAAAAACA--CCTTGAATAATC-TCTCAAAAAAAAATTGAAAAGGATTATTCAAG
* *
12308099 GCGTTTTTGGTCAATAACGTCTTGAATAACCTCATTTAATTTTTTTG-ATGAAATTATTCAAGGT
63 GCGTTTTTGGTCAA-AACGTCTTGAATAACCTCATTTAATTTTTTTGTAAGAAATTAATCAAGGT
*
12308163 AT
127 -G
* * *
12308165 TTTTTTGGT-CAAAAACACCTTGAATAATCTCTCAAAAAAAAAATGAAAGAGGATTAATT-AAGG
1 TTTTTTGATAAAAAAACACCTTGAATAATCTCTCAAAAAAAAATTGAAA-AGGATT-ATTCAAGG
* * *
12308228 CGTTTTTTTGAGTAAAAACGTCTTGAATAATCTCATTCAATT
64 CG--TTTTTG-GTCAAAACGTCTTGAATAACCTCATTTAATT
12308270 AAAAATTAAA
Statistics
Matches: 193, Mismatches: 19, Indels: 37
0.78 0.08 0.15
Matches are distributed among these distances:
125 11 0.06
126 18 0.09
127 62 0.32
128 58 0.30
129 10 0.05
130 30 0.16
131 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (127 bp):
TTTTTTGATAAAAAAACACCTTGAATAATCTCTCAAAAAAAAATTGAAAAGGATTATTCAAGGCG
TTTTTGGTCAAAACGTCTTGAATAACCTCATTTAATTTTTTTGTAAGAAATTAATCAAGGTG
Found at i:12318739 original size:39 final size:39
Alignment explanation
Indices: 12318694--12318777 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
12318684 CCAAACACTT
12318694 CTCCAACTCCCTTTCAAGTCCAAAACATCCAAACAAATC
1 CTCCAACTCCCTTTCAAGTCCAAAACATCCAAACAAATC
*
12318733 CTCCAACTCCCTTTCAAGTCCAAAACATCCAACCAAATC
1 CTCCAACTCCCTTTCAAGTCCAAAACATCCAAACAAATC
12318772 CTCCAA
1 CTCCAA
12318778 GCTCGAAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.20
Consensus pattern (39 bp):
CTCCAACTCCCTTTCAAGTCCAAAACATCCAAACAAATC
Found at i:12326717 original size:22 final size:22
Alignment explanation
Indices: 12326689--12326732 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12326679 TGTATATTTA
12326689 TATTTGTAC-CTCTAGAATTAAG
1 TATTTGTACTC-CTAGAATTAAG
*
12326711 TATTTGTATTCCTAGAATTAAG
1 TATTTGTACTCCTAGAATTAAG
12326733 GATAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTACTCCTAGAATTAAG
Found at i:12330779 original size:22 final size:22
Alignment explanation
Indices: 12330753--12330796 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12330743 TGTATATTTA
*
12330753 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12330775 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12330797 GACAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:12330978 original size:25 final size:25
Alignment explanation
Indices: 12330939--12330987 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
12330929 ATATACATTT
12330939 AGTTTTACTCTTAG-TTTTCCACAC
1 AGTTTTACTCTTAGTTTTTCCACAC
*
12330963 AGTTTTATTTCTTAGTTTTTCCACA
1 AGTTTTA-CTCTTAGTTTTTCCACA
12330988 TAAAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.51
Consensus pattern (25 bp):
AGTTTTACTCTTAGTTTTTCCACAC
Found at i:12333976 original size:5 final size:5
Alignment explanation
Indices: 12333966--12334016 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
12333956 TTTAAAATAG
* **
12333966 ATTAA ATTAA ATTAA ATTAA ATT-A TTTTT ATT-A ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
12334014 ATT
1 ATT
12334017 TTTTAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
4 6 0.15
5 34 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (5 bp):
ATTAA
Found at i:12334007 original size:28 final size:27
Alignment explanation
Indices: 12333970--12334037 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
12333960 AAATAGATTA
*
12333970 AATTAAATTAAATTAAATTATTTTTATT
1 AATTAAATTAAATTAAATT-TTTTAATT
12333998 AATTAAATTAAATTAAATTTTTTAATT
1 AATTAAATTAAATTAAATTTTTTAATT
* *
12334025 TA-TAAAATAAATT
1 AATTAAATTAAATT
12334038 GATTCTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.27
27 8 0.22
28 19 0.51
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTAAATTAAATTAAATTTTTTAATT
Found at i:12334022 original size:23 final size:23
Alignment explanation
Indices: 12333975--12334024 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
12333965 GATTAAATTA
*
12333975 AATTAAATTAAATTATTTTTATT
1 AATTAAATTAAATTAATTTTATT
12333998 AATTAAATTAAATTAAATTTT-TT
1 AATTAAATTAAATT-AATTTTATT
12334021 AATT
1 AATT
12334025 TATAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTAAATTAAATTAATTTTATT
Found at i:12334133 original size:13 final size:12
Alignment explanation
Indices: 12334120--12334191 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
12334110 AAATAAATTA
*
12334120 AATAAATTATTT
1 AATAAAATATTT
12334132 AATAAAATATTT
1 AATAAAATATTT
*
12334144 GAATATCAAATATTA
1 -AATA--AAATATTT
12334159 AATTAAAAT-TTT
1 AA-TAAAATATTT
* **
12334171 AATAATATATAA
1 AATAAAATATTT
12334183 AATAAAATA
1 AATAAAATA
12334192 ACTTATTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.10
12 24 0.50
13 8 0.17
14 2 0.04
15 9 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (12 bp):
AATAAAATATTT
Found at i:12334226 original size:16 final size:16
Alignment explanation
Indices: 12334196--12334225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12334186 AAAATAACTT
12334196 ATTTTATATATTTTTA
1 ATTTTATATATTTTTA
12334212 ATTTTATAT-TTTTT
1 ATTTTATATATTTTT
12334226 TTTACATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATATATTTTTA
Found at i:12335679 original size:20 final size:20
Alignment explanation
Indices: 12335654--12335691 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12335644 TACAAATTAT
12335654 AATATT-TTTATTTATTTTAA
1 AATATTATTT-TTTATTTTAA
12335674 AATATTATTTTTTATTTT
1 AATATTATTTTTTATTTT
12335692 TATCTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATATTATTTTTTATTTTAA
Found at i:12337187 original size:11 final size:11
Alignment explanation
Indices: 12337157--12337189 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12337147 CATAAAACAC
12337157 AAAAAAAAAGA
1 AAAAAAAAAGA
*
12337168 AAAGAAAAAGA
1 AAAAAAAAAGA
12337179 AAAAAAAAAGA
1 AAAAAAAAAGA
12337190 GGATCCAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:12337844 original size:24 final size:23
Alignment explanation
Indices: 12337815--12337865 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
12337805 AATGATGATG
*
12337815 ATGATGAATGATAATTGATGA-AAA
1 ATGATGAATGA-AA-GGATGAGAAA
12337839 ATGATGAATGAAAGGATGAGAAA
1 ATGATGAATGAAAGGATGAGAAA
12337862 ATGA
1 ATGA
12337866 ATGGAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 9 0.36
24 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (23 bp):
ATGATGAATGAAAGGATGAGAAA
Found at i:12338045 original size:15 final size:15
Alignment explanation
Indices: 12338001--12338044 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
12337991 AAATGATGAA
*
12338001 AAATGAATGGATGAAT
1 AAATGAATGGA-AAAT
12338017 AAATGAATGGAAAAT
1 AAATGAATGGAAAAT
12338032 AAATGAA-GGAAAA
1 AAATGAATGGAAAA
12338045 AAAAGGGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.22
15 10 0.37
16 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (15 bp):
AAATGAATGGAAAAT
Found at i:12338388 original size:19 final size:19
Alignment explanation
Indices: 12338360--12338396 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12338350 AAAACCCAAA
12338360 GAGAAGAGACGATTTTAAG
1 GAGAAGAGACGATTTTAAG
* *
12338379 GAGAATAGACGGTTTTAA
1 GAGAAGAGACGATTTTAA
12338397 AGAAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.24
Consensus pattern (19 bp):
GAGAAGAGACGATTTTAAG
Found at i:12338528 original size:48 final size:48
Alignment explanation
Indices: 12338452--12338723 Score: 179
Period size: 48 Copynumber: 5.7 Consensus size: 48
12338442 TTAAGATTGG
* *
12338452 GATTTTTAAAGTCTTCTGGCCAT-TTTTTAGAGAGGCTTTCAAAATTAA
1 GATTTTTAAAGTTTTCTAGCC-TCTTTTTAGAGAGGCTTTCAAAATTAA
* * * * *
12338500 GATTCTTAAAGTTTTCTTGCCTCTTTTTAGA-ATAGCTTTTAAAATTGA
1 GATTTTTAAAGTTTTCTAGCCTCTTTTTAGAGA-GGCTTTCAAAATTAA
12338548 GATTTTTAAAAGTTCTT-TAG-C-CTTTTTAGAG-GAG-TTTCAAAATTGAA
1 GATTTTT-AAAGTT-TTCTAGCCTCTTTTTAGAGAG-GCTTTCAAAATT-AA
* * * * * * *
12338595 -ATATTTAAAGTTTCCAAGACTCTTGTTCGAG-GAGCTTTCAAAATTGA
1 GATTTTTAAAGTTTTCTAGCCTCTTTTTAGAGAG-GCTTTCAAAATTAA
* * * * *
12338642 GATTTTGTAAAATTTTCTAACCTTTTTTTA-AAATAGCTTTTCAAAATTAA
1 GATTTT-TAAAGTTTTCTAGCCTCTTTTTAGAGA-GGC-TTTCAAAATTAA
* *
12338692 GATTTTTAAAG-TTACATAGCCCCTTTTTAGAG
1 GATTTTTAAAGTTTTC-TAGCCTCTTTTTAGAG
12338724 GATTTTTTTT
Statistics
Matches: 171, Mismatches: 35, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
44 1 0.01
45 8 0.05
46 15 0.09
47 25 0.15
48 63 0.37
49 39 0.23
50 20 0.12
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (48 bp):
GATTTTTAAAGTTTTCTAGCCTCTTTTTAGAGAGGCTTTCAAAATTAA
Found at i:12339661 original size:144 final size:142
Alignment explanation
Indices: 12339395--12339803 Score: 350
Period size: 144 Copynumber: 2.9 Consensus size: 142
12339385 TCAAATCATG
* * * * * * * * *
12339395 TTTAAATATTATTTGATGGTTATTGGTGCATTAAAAACCTTAATCATATCTCAAGAGCTATGAAA
1 TTTAAA-ATTATTTTATGATTTTTAGTGCATTAAAAACCTT-ATCACACCTCAAAAGGTATAAAA
* * * ** * *
12339460 TTACTAAAATGTCTTTTAAAGGTATTTTTGTAATTTGATCTTTATGGGGTTAGTTTTTCATG-AA
64 TTACTAAAATGCCATTT-AAGGTATTTTTGTAATTTGA-CTTTTTAAGGTCAATTTTTCATGCAA
*
12339524 AAGC-TCTTGATCATAA
127 AAGCTTC-AGATCATAA
* * *
12339540 TTTAATATTATTTTATGATTTTTTA-TGTATTAAAAACCTTGATCACACCTTAAAAGGTATAAAA
1 TTTAAAATTATTTTATGA-TTTTTAGTGCATTAAAAACCTT-ATCACACCTCAAAAGGTATAAAA
* * * *
12339604 TTACTAAAATGCCCTTTAGAGGTTTTTTTATAATTTGACCTTTTTTAGGTCAATTTTT--TGCTA
64 TTACTAAAATGCCATTTA-AGGTATTTTTGTAATTTGA-CTTTTTAAGGTCAATTTTTCATGC-A
* **
12339667 AATGCTTCAGATCATGT
126 AAAGCTTCAGATCATAA
* * *
12339684 TTTAAAATTATTTTATGATTTTTAGTGCATTAAGAAACC---TC-GACCTCGAAAGGTGTAAAAT
1 TTTAAAATTATTTTATGATTTTTAGTGCATTAA-AAACCTTATCACACCTCAAAAGGTATAAAAT
* * *
12339745 TACTAAAATACCATTTAAGATATTTTTGTAATTTGACTTTTCTAAGGTCATTTTTTCAT
65 TACTAAAATGCCATTTAAGGTATTTTTGTAATTTGACTTTT-TAAGGTCAATTTTTCAT
12339804 TTTTTCCCAA
Statistics
Matches: 214, Mismatches: 40, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
138 5 0.02
139 28 0.13
140 31 0.14
141 3 0.01
142 2 0.01
143 7 0.03
144 122 0.57
145 16 0.07
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (142 bp):
TTTAAAATTATTTTATGATTTTTAGTGCATTAAAAACCTTATCACACCTCAAAAGGTATAAAATT
ACTAAAATGCCATTTAAGGTATTTTTGTAATTTGACTTTTTAAGGTCAATTTTTCATGCAAAAGC
TTCAGATCATAA
Found at i:12341430 original size:19 final size:18
Alignment explanation
Indices: 12341382--12341441 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
12341372 AACTTTAAAG
12341382 CTAAATAAACCCTGAACC
1 CTAAATAAACCCTGAACC
12341400 CTAAATAAACCCTGAACC
1 CTAAATAAACCCTGAACC
* *
12341418 CTAAGTAAAACCCTAAACC
1 CTAAAT-AAACCCTGAACC
*
12341437 TTAAA
1 CTAAA
12341442 CCCTAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 23 0.62
19 14 0.38
ACGTcount: A:0.47, C:0.30, G:0.05, T:0.18
Consensus pattern (18 bp):
CTAAATAAACCCTGAACC
Found at i:12341435 original size:7 final size:7
Alignment explanation
Indices: 12341425--12341524 Score: 61
Period size: 7 Copynumber: 14.9 Consensus size: 7
12341415 ACCCTAAGTA
12341425 AAACCCT
1 AAACCCT
*
12341432 AAACCTT
1 AAACCCT
12341439 AAACCCT
1 AAACCCT
12341446 AAA-CC-
1 AAACCCT
**
12341451 AAACATT
1 AAACCCT
12341458 AAATCCC-
1 AAA-CCCT
12341465 AAA-CCT
1 AAACCCT
*
12341471 AAAACC-
1 AAACCCT
12341477 AAAGCCCT
1 AAA-CCCT
*
12341485 AAATCCT
1 AAACCCT
**
12341492 AAACTTT
1 AAACCCT
12341499 AAACCCT
1 AAACCCT
12341506 AAA--CT
1 AAACCCT
12341511 AAAACCCT
1 -AAACCCT
12341519 AAACCC
1 AAACCC
12341525 CAAATAAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
5 7 0.10
6 11 0.16
7 46 0.66
8 6 0.09
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:12341517 original size:13 final size:14
Alignment explanation
Indices: 12341489--12341522 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
12341479 AGCCCTAAAT
*
12341489 CCTAAACTTTAAAC
1 CCTAAACTTAAAAC
12341503 CCTAAAC-TAAAAC
1 CCTAAACTTAAAAC
12341516 CCTAAAC
1 CCTAAAC
12341523 CCCAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTAAACTTAAAAC
Found at i:12341545 original size:60 final size:58
Alignment explanation
Indices: 12341429--12341562 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 58
12341419 TAAGTAAAAC
* * * *
12341429 CCTAAACCTTAAACCCTAAACCAAACATTAAATCCCAAACCTAAAACCAAAGCCCTAAA
1 CCTAAACTTTAAACCCTAAACAAAACACTAAACCCCAAA-CTAAAACCAAAGCCCTAAA
* *
12341488 TCCTAAACTTTAAACCCTAAACTAAAACCCTAAACCCCAAA-TAAAATCTTAAA-CCCTAAA
1 -CCTAAACTTTAAACCCTAAAC-AAAACACTAAACCCCAAACTAAAA-C-CAAAGCCCTAAA
12341548 CTCTAAACTTTAAAC
1 C-CTAAACTTTAAAC
12341563 TAACTCTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
59 6 0.09
60 41 0.64
61 17 0.27
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (58 bp):
CCTAAACTTTAAACCCTAAACAAAACACTAAACCCCAAACTAAAACCAAAGCCCTAAA
Found at i:12341569 original size:18 final size:18
Alignment explanation
Indices: 12341546--12341580 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12341536 TTAAACCCTA
*
12341546 AACTCTAAACTTTAAACT
1 AACTCTAAACCTTAAACT
12341564 AACTCTAAACCTTAAAC
1 AACTCTAAACCTTAAAC
12341581 AGAAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (18 bp):
AACTCTAAACCTTAAACT
Found at i:12341630 original size:22 final size:22
Alignment explanation
Indices: 12341605--12341647 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12341595 CTCCAAAACT
12341605 AAATCGAACCAACCTTAAACCC
1 AAATCGAACCAACCTTAAACCC
* *
12341627 AAATCGAATCTACCTTAAACC
1 AAATCGAACCAACCTTAAACC
12341648 TTAAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.19
Consensus pattern (22 bp):
AAATCGAACCAACCTTAAACCC
Found at i:12349587 original size:14 final size:15
Alignment explanation
Indices: 12349553--12349588 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12349543 GCAATATACT
12349553 AATTTCACAAGCCAC
1 AATTTCACAAGCCAC
*
12349568 AATTTCACAAGCTA-
1 AATTTCACAAGCCAC
12349582 AATTTCA
1 AATTTCA
12349589 AAATGATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (15 bp):
AATTTCACAAGCCAC
Found at i:12351490 original size:73 final size:72
Alignment explanation
Indices: 12351399--12351661 Score: 222
Period size: 73 Copynumber: 3.6 Consensus size: 72
12351389 GTCCATAAAG
* * * *
12351399 GGGATTGATTGGTTCCTCACATTTTCCACATAATTTGACTACTGAATGGAAAGTTGATCAATTGA
1 GGGATCGATCGGTTCCTCACATTTTCC-CATAATTTGGCTACTGAATGGAAAGTTGATCAATTCA
*
12351464 GTCTAAGG
65 GTCTAAGA
* ** ** * * * ** * *
12351472 GGGATCAAAGGGTTCCTCA-ATGTTTTCCTTTAATTTGGTTACTGGATGAAAAACTAATCGATTC
1 GGGATCGATCGGTTCCTCACA--TTTTCCCATAATTTGGCTACTGAATGGAAAGTTGATCAATTC
* *
12351536 AATCTAAAA
64 AGTCTAAGA
* * * * * *
12351545 TGGATTGATTGGTTCCTCACATTTTTCACACAATTTGGCTACTGAATGGAAAGTTGATCAATCCA
1 GGGATCGATCGGTTCCTCACA-TTTTCCCATAATTTGGCTACTGAATGGAAAGTTGATCAATTCA
*
12351610 GTCCAAGA
65 GTCTAAGA
* *
12351618 GGGATCGATCGGTTCCTCAATATTTTCCCTTAATTTGGCTACTG
1 GGGATCGATCGGTTCCTC-ACATTTTCCCATAATTTGGCTACTG
12351662 GATGCAAAAC
Statistics
Matches: 140, Mismatches: 46, Indels: 8
0.72 0.24 0.04
Matches are distributed among these distances:
72 1 0.01
73 130 0.93
74 9 0.06
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (72 bp):
GGGATCGATCGGTTCCTCACATTTTCCCATAATTTGGCTACTGAATGGAAAGTTGATCAATTCAG
TCTAAGA
Found at i:12351580 original size:146 final size:146
Alignment explanation
Indices: 12351390--12351704 Score: 432
Period size: 146 Copynumber: 2.1 Consensus size: 146
12351380 ATCGATTAGG
*
12351390 TCCATAAAGGGGATTGATTGGTTCCTCACATTTTCCACATAATTTGACTACTGAATGGAAAGTTG
1 TCCA-AAA-GGGATTGATTGGTTCCTCACATTTTCCACACAATTTGACTACTGAATGGAAAGTTG
** * * * * * *
12351455 ATCAATTGAGTCTAAGGGGGATCAAAGGGTTCCTCAATGTTTTCCTTTAATTTGGTTACTGGATG
64 ATCAATCCAGTCCAAGAGGGATCAAACGGTTCCTCAATATTTTCCCTTAATTTGGCTACTGGATG
* *
12351520 AAAAACTAATCGATTCAA
129 AAAAACTAATCAATCCAA
* * * *
12351538 TCTAAAATGGATTGATTGGTTCCTCACATTTTTCACACAATTTGGCTACTGAATGGAAAGTTGAT
1 TCCAAAAGGGATTGATTGGTTCCTCACATTTTCCACACAATTTGACTACTGAATGGAAAGTTGAT
* * *
12351603 CAATCCAGTCCAAGAGGGATCGATCGGTTCCTCAATATTTTCCCTTAATTTGGCTACTGGATGCA
66 CAATCCAGTCCAAGAGGGATCAAACGGTTCCTCAATATTTTCCCTTAATTTGGCTACTGGATGAA
*
12351668 AAACTAATCAATCCGA
131 AAACTAATCAATCCAA
*
12351684 TCCAAAGGGGATTGATTGGTT
1 TCCAAAAGGGATTGATTGGTT
12351705 TTTCTTATAG
Statistics
Matches: 145, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
146 139 0.96
147 3 0.02
148 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (146 bp):
TCCAAAAGGGATTGATTGGTTCCTCACATTTTCCACACAATTTGACTACTGAATGGAAAGTTGAT
CAATCCAGTCCAAGAGGGATCAAACGGTTCCTCAATATTTTCCCTTAATTTGGCTACTGGATGAA
AAACTAATCAATCCAA
Found at i:12351678 original size:73 final size:72
Alignment explanation
Indices: 12351482--12351704 Score: 212
Period size: 73 Copynumber: 3.1 Consensus size: 72
12351472 GGGATCAAAG
* * * * * *
12351482 GGTTCCTCAATGTTTTCCTTTAATTTGGTTACTGGATGAAAAACTAATCGATTCAATCTAAAATG
1 GGTTCCTCAAT-TTTTCCCTTAATTTGGCTACTGGATGAAAAACTAATCAATCCAATCCAAAAGG
* *
12351547 GATTGATT
65 GATCGATC
* ** * * ** * * *
12351555 GGTTCCTCACATTTTTCACACAATTTGGCTACTGAATGGAAAGTTGATCAATCCAGTCCAAGAGG
1 GGTTCCTCA-ATTTTTCCCTTAATTTGGCTACTGGATGAAAAACTAATCAATCCAATCCAAAAGG
12351620 GATCGATC
65 GATCGATC
* * *
12351628 GGTTCCTCAATATTTTCCCTTAATTTGGCTACTGGATGCAAAACTAATCAATCCGATCCAAAGGG
1 GGTTCCTCAAT-TTTTCCCTTAATTTGGCTACTGGATGAAAAACTAATCAATCCAATCCAAAAGG
* *
12351693 GATTGATT
65 GATCGATC
12351701 GGTT
1 GGTT
12351705 TTTCTTATAG
Statistics
Matches: 116, Mismatches: 32, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
72 2 0.02
73 112 0.97
74 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (72 bp):
GGTTCCTCAATTTTTCCCTTAATTTGGCTACTGGATGAAAAACTAATCAATCCAATCCAAAAGGG
ATCGATC
Found at i:12358427 original size:23 final size:23
Alignment explanation
Indices: 12358396--12358440 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12358386 TTTGACTTGG
* *
12358396 TGAAAGGTAGCAACTTCGAATTA
1 TGAAAGGTAACAACTTCAAATTA
*
12358419 TGAAGGGTAACAACTTCAAATT
1 TGAAAGGTAACAACTTCAAATT
12358441 TAGGGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (23 bp):
TGAAAGGTAACAACTTCAAATTA
Found at i:12360193 original size:19 final size:19
Alignment explanation
Indices: 12360171--12360209 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12360161 CTATAATAAG
*
12360171 TATTAAGGGTGAGAATACT
1 TATTAAAGGTGAGAATACT
*
12360190 TATTAAAGGTGAGACTACT
1 TATTAAAGGTGAGAATACT
12360209 T
1 T
12360210 TGATCATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (19 bp):
TATTAAAGGTGAGAATACT
Found at i:12363903 original size:27 final size:26
Alignment explanation
Indices: 12363845--12363904 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
12363835 TGCGTTTATT
*
12363845 AAAAATTTTGATATAAAAATTCAAAA
1 AAAAATTGTGATATAAAAATTCAAAA
* *
12363871 ATAAAATTGTGATATGAGAAATTTGAAAA
1 A-AAAATTGTGATAT-A-AAAATTCAAAA
12363900 AAAAA
1 AAAAA
12363905 ATACATGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 12 0.43
28 5 0.18
29 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (26 bp):
AAAAATTGTGATATAAAAATTCAAAA
Found at i:12365153 original size:22 final size:24
Alignment explanation
Indices: 12365127--12365186 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
12365117 TTTTTACATA
* *
12365127 TTATTGATTTTTTAA-TT-AAATT
1 TTATTAATTTATTAATTTAAAATT
12365149 TTATTAATTTATTAATTTAAAATTT
1 TTATTAATTTATTAATTTAAAA-TT
*
12365174 TTATTAAATTATT
1 TTATTAATTTATT
12365187 TTTAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.41
23 2 0.06
24 3 0.09
25 14 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTAATTTATTAATTTAAAATT
Found at i:12365161 original size:30 final size:31
Alignment explanation
Indices: 12365104--12365166 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12365094 ATAAATGACA
*
12365104 TTTTTAATAATATTTTTTACATATTATTGAT
1 TTTTTAATAATATTTTTTACATATTATTAAT
12365135 TTTTTAATTAA-ATTTTATTA-AT-TTATTAAT
1 TTTTTAA-TAATATTTT-TTACATATTATTAAT
12365165 TT
1 TT
12365167 AAAATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 9 0.31
31 14 0.48
32 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTTAATAATATTTTTTACATATTATTAAT
Found at i:12365218 original size:27 final size:26
Alignment explanation
Indices: 12365167--12365222 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
12365157 TTATTAATTT
*
12365167 AAAATTTTTATTAAATTATTTTTAATA
1 AAAAATTTTATTAAATTATTTTTAA-A
12365194 AAAAATTTTA-TAAATT-TTTACTTAAA
1 AAAAATTTTATTAAATTATTT--TTAAA
12365220 AAA
1 AAA
12365223 CTTCATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.12
26 10 0.38
27 13 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAAATTTTATTAAATTATTTTTAAA
Found at i:12372928 original size:85 final size:84
Alignment explanation
Indices: 12372781--12372946 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 84
12372771 AGTCGGGAGA
* * *
12372781 GGTGTGCTACAACTGGGGTAGTCCACCCAAGCCCCCTTACGGGATTAGCATGATGGTTGGTGTCA
1 GGTGTGCTACAACTGGGGCAGTCCACCCAAGCCCCCTTACAGGACTAGCATGATGGTTGGTGTCA
12372846 ACCATGCGTACGGGCGATT
66 ACCATGCGTACGGGCGATT
* * * *
12372865 GGTGTGCTGCAGCTGGGGGCAGTCCACCCAAGTCCCCTTGCAGGACTAGCATGAT-GTTGGGTGT
1 GGTGTGCTACAACT-GGGGCAGTCCACCCAAGCCCCCTTACAGGACTAGCATGATGGTT-GGTGT
* *
12372929 CAATCATGCGTGCGGGCG
64 CAACCATGCGTACGGGCG
12372947 GCCGATACTA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 15 0.21
85 56 0.79
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (84 bp):
GGTGTGCTACAACTGGGGCAGTCCACCCAAGCCCCCTTACAGGACTAGCATGATGGTTGGTGTCA
ACCATGCGTACGGGCGATT
Found at i:12379659 original size:84 final size:84
Alignment explanation
Indices: 12379513--12379671 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 84
12379503 AATCAGGAGA
*
12379513 GGTGTGCTACAGCTGGAGCAGTCCACCCAAGCCCTCTTACGAGATTAGCATGATGGTTGGTGTCA
1 GGTGTGCTACAGCTGGAGCAGTCCACCCAAGCCCTCTTACGAGACTAGCATGATGGTTGGTGTCA
12379578 ACCATGCGTGCAGGCGACT
66 ACCATGCGTGCAGGCGACT
* * * *
12379597 GGTGTGCTGCAGCT-GAGGTAGTCCACCCAAGTCCC-CTTGC-AGGACTAGTATGAT-GTTGGGT
1 GGTGTGCTACAGCTGGA-GCAGTCCACCCAAG-CCCTCTTACGA-GACTAGCATGATGGTT-GGT
*
12379658 GTCAATCATGCGTG
62 GTCAACCATGCGTG
12379672 TGGGCGGCCG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
83 6 0.09
84 56 0.86
85 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (84 bp):
GGTGTGCTACAGCTGGAGCAGTCCACCCAAGCCCTCTTACGAGACTAGCATGATGGTTGGTGTCA
ACCATGCGTGCAGGCGACT
Found at i:12391270 original size:33 final size:33
Alignment explanation
Indices: 12391233--12391302 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
12391223 ACTTCTCAAA
* *
12391233 CTCCCTTTCACGTCCAAAACATCCAACTAGATC
1 CTCCCTTTCAAGTCCAAAACATACAACTAGATC
*
12391266 CTCCCTTTCAAGTCCAAAACATACAACTGGATC
1 CTCCCTTTCAAGTCCAAAACATACAACTAGATC
12391299 CTCC
1 CTCC
12391303 AAGCCCAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.24
Consensus pattern (33 bp):
CTCCCTTTCAAGTCCAAAACATACAACTAGATC
Found at i:12395220 original size:2 final size:2
Alignment explanation
Indices: 12395213--12395252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12395203 AGTTACACAA
12395213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12395253 AAGTATACGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12396319 original size:5 final size:5
Alignment explanation
Indices: 12396309--12396333 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12396299 GTGCGATCAG
12396309 GACGA GACGA GACGA GACGA GACGA
1 GACGA GACGA GACGA GACGA GACGA
12396334 TGCAACAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GACGA
Found at i:12396351 original size:2 final size:2
Alignment explanation
Indices: 12396344--12396375 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12396334 TGCAACAGGC
*
12396344 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12396376 CTGCTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12399164 original size:101 final size:101
Alignment explanation
Indices: 12399040--12399228 Score: 263
Period size: 101 Copynumber: 1.9 Consensus size: 101
12399030 TTATTTTAAG
* * *
12399040 AAAATTCATTAACCCCTCTAATATTTTAG-CAAGATTTAATTCAAGATTTTGATCCTCCAATAGT
1 AAAATTCATTAACCCCTCCAATATTTT-GTCAAGACTTAATTCAAGATTTTAATCCTCCAATAGT
12399104 TTAATAGAATTAAAAATTTTATTAATATGTTTTACAT
65 TTAATAGAATTAAAAATTTTATTAATATGTTTTACAT
*** * **
12399141 AAAATTCATTAAGTTCTCCAATATTTTGTTAAGACTTAATTCAAGATTTTAATCCTTTAATAGTT
1 AAAATTCATTAACCCCTCCAATATTTTGTCAAGACTTAATTCAAGATTTTAATCCTCCAATAGTT
* *
12399206 TGATAGGATTAAAAATTTTATTA
66 TAATAGAATTAAAAATTTTATTA
12399229 TTATTAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 75 0.99
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (101 bp):
AAAATTCATTAACCCCTCCAATATTTTGTCAAGACTTAATTCAAGATTTTAATCCTCCAATAGTT
TAATAGAATTAAAAATTTTATTAATATGTTTTACAT
Found at i:12400875 original size:17 final size:17
Alignment explanation
Indices: 12400815--12400887 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 17
12400805 GGAATATTCA
12400815 CAAGATTTT-AAGATTTG
1 CAAGATTTTCAA-ATTTG
* * * *
12400832 TAAAAATTTCAAATTCG
1 CAAGATTTTCAAATTTG
* *
12400849 CTAGAGTTTCAAATTTG
1 CAAGATTTTCAAATTTG
*
12400866 CAAGATTTTCATATTTG
1 CAAGATTTTCAAATTTG
12400883 CAAGA
1 CAAGA
12400888 ACTTCAAGTC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 41 0.95
18 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (17 bp):
CAAGATTTTCAAATTTG
Found at i:12400893 original size:17 final size:17
Alignment explanation
Indices: 12400856--12400894 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12400846 TCGCTAGAGT
**
12400856 TTCAAATTTGCAAGATT
1 TTCAAATTTGCAAGAAC
*
12400873 TTCATATTTGCAAGAAC
1 TTCAAATTTGCAAGAAC
12400890 TTCAA
1 TTCAA
12400895 GTCTGTGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (17 bp):
TTCAAATTTGCAAGAAC
Found at i:12400944 original size:17 final size:17
Alignment explanation
Indices: 12400924--12400985 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
12400914 TTAACAAGAC
12400924 TTTCAGATTCGTAAAAA
1 TTTCAGATTCGTAAAAA
* * *
12400941 TTTCAAATTCATAAGAA
1 TTTCAGATTCGTAAAAA
* *
12400958 CTTCAGATTCGTAAAAG
1 TTTCAGATTCGTAAAAA
*
12400975 TTTTAGATTCG
1 TTTCAGATTCG
12400986 CAAGTGATTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (17 bp):
TTTCAGATTCGTAAAAA
Found at i:12401068 original size:17 final size:18
Alignment explanation
Indices: 12401032--12401078 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
12401022 AGATTTCAGG
*
12401032 TTTGCAAGAA-TTTTAGA
1 TTTGCAAGAACTTTGAGA
12401049 TTTGCAAGAACTTTGA-A
1 TTTGCAAGAACTTTGAGA
*
12401066 TTTACAAGAACTT
1 TTTGCAAGAACTT
12401079 CATGTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGCAAGAACTTTGAGA
Found at i:12401264 original size:44 final size:44
Alignment explanation
Indices: 12401216--12401321 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
12401206 GAATTCACAT
* * *
12401216 AAAAAATTTAAAGGTTCAC-CTCTAGAA-TTAAAAAATTTTCATTC
1 AAAAAATTTAAAGATTCACACTC-AAAAGTT-AAAAATTTCCATTC
*
12401260 AAAAATTTTAAAGATTCACACTCAAAAGTTAAAAATTTCCATTC
1 AAAAAATTTAAAGATTCACACTCAAAAGTTAAAAATTTCCATTC
* *
12401304 GAAAAATTTAAGGATTCA
1 AAAAAATTTAAAGATTCA
12401322 TAGCCAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 48 0.91
45 5 0.09
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (44 bp):
AAAAAATTTAAAGATTCACACTCAAAAGTTAAAAATTTCCATTC
Found at i:12401314 original size:23 final size:22
Alignment explanation
Indices: 12401241--12401314 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
12401231 TCACCTCTAG
* *
12401241 AATTAAAAAATTTTCATTCAAA
1 AATTTAAAAATTTCCATTCAAA
* *
12401263 AATTTTAAAGA-TTCACACTC-AA
1 AA-TTTAAAAATTTC-CATTCAAA
*
12401285 AAGTTAAAAATTTCCATTCGAAA
1 AATTTAAAAATTTCCATTC-AAA
12401308 AATTTAA
1 AATTTAA
12401315 GGATTCATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 10 0.26
22 11 0.28
23 18 0.46
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (22 bp):
AATTTAAAAATTTCCATTCAAA
Found at i:12401412 original size:81 final size:81
Alignment explanation
Indices: 12401260--12401414 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
12401250 ATTTTCATTC
* * *
12401260 AAAAATTTTAAAGATTCACACTCAAAAGTTAAAAATTTCCATTCGAAAAATTTAAGGATTCATAG
1 AAAAATTTTAAAGATTCACACTCAAAACTTAAAAATTTCCATTCGAAAAACTTAAGGATTCACAG
12401325 CCAAAATTTATATTTG
66 CCAAAATTTATATTTG
* * ** **
12401341 AAAAATTTTAAAGATTCACATTCAAAACTTAAAGATTTTTATTTTAAAAACTT-AGAGATTCACA
1 AAAAATTTTAAAGATTCACACTCAAAACTTAAAAATTTCCATTCGAAAAACTTAAG-GATTCACA
* *
12401405 TCGAAAATTT
65 GCCAAAATTT
12401415 TTAAAATTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
80 2 0.03
81 60 0.97
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (81 bp):
AAAAATTTTAAAGATTCACACTCAAAACTTAAAAATTTCCATTCGAAAAACTTAAGGATTCACAG
CCAAAATTTATATTTG
Found at i:12401423 original size:22 final size:23
Alignment explanation
Indices: 12401398--12401459 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
12401388 AAACTTAGAG
*
12401398 ATTCACATCGAAAATTTTTAA-A
1 ATTCACATCCAAAATTTTTAACA
** *
12401420 ATTCACATTTAAAAATTTTAACA
1 ATTCACATCCAAAATTTTTAACA
* *
12401443 TTTCACAACCAAAATTT
1 ATTCACATCCAAAATTT
12401460 CAAAGATTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTCACATCCAAAATTTTTAACA
Found at i:12401639 original size:44 final size:44
Alignment explanation
Indices: 12401574--12401690 Score: 164
Period size: 44 Copynumber: 2.7 Consensus size: 44
12401564 TTCATAAATT
12401574 TTTAGAGATTCACA-TCTAAAGTTTCAAAGACTCACATTCAAAAA
1 TTTAGAGATTCACATTC-AAAGTTTCAAAGACTCACATTCAAAAA
* * *
12401618 TTTAAAGATTCACATTCAAAGTTTCAAATATTCACATTCAAAAA
1 TTTAGAGATTCACATTCAAAGTTTCAAAGACTCACATTCAAAAA
* * *
12401662 ATTAGATATTCATATTCAAAGTTTCAAAG
1 TTTAGAGATTCACATTCAAAGTTTCAAAG
12401691 GTTCTTTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 62 0.97
45 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (44 bp):
TTTAGAGATTCACATTCAAAGTTTCAAAGACTCACATTCAAAAA
Found at i:12401655 original size:22 final size:23
Alignment explanation
Indices: 12401544--12401690 Score: 117
Period size: 22 Copynumber: 6.6 Consensus size: 23
12401534 AATTCCGATC
**
12401544 CAAAA-TTTCAAAGATTCATTTT
1 CAAAAGTTTCAAAGATTCACATT
* * *
12401566 CATAAATTTTTAGAGATTCACA-T
1 CA-AAAGTTTCAAAGATTCACATT
* *
12401589 CTAAAGTTTCAAAGACTCACATT
1 CAAAAGTTTCAAAGATTCACATT
*
12401612 CAAAAATTT-AAAGATTCACATT
1 CAAAAGTTTCAAAGATTCACATT
*
12401634 C-AAAGTTTCAAATATTCACATT
1 CAAAAGTTTCAAAGATTCACATT
** * * *
12401656 CAAAAAATT-AGATATTCATATT
1 CAAAAGTTTCAAAGATTCACATT
12401678 C-AAAGTTTCAAAG
1 CAAAAGTTTCAAAG
12401691 GTTCTTTTTC
Statistics
Matches: 97, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
21 11 0.11
22 57 0.59
23 18 0.19
24 11 0.11
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.35
Consensus pattern (23 bp):
CAAAAGTTTCAAAGATTCACATT
Found at i:12403281 original size:14 final size:14
Alignment explanation
Indices: 12403231--12403281 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
12403221 AGAACATACA
12403231 TTTTCATTTTTTTT
1 TTTTCATTTTTTTT
* *
12403245 CTTACATTTTTTTT
1 TTTTCATTTTTTTT
*
12403259 TTTT--GTTTTTTT
1 TTTTCATTTTTTTT
12403271 TTTTCATTTTT
1 TTTTCATTTTT
12403282 CCACATCTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 11 0.38
14 18 0.62
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTCATTTTTTTT
Found at i:12404659 original size:133 final size:132
Alignment explanation
Indices: 12404478--12404725 Score: 356
Period size: 133 Copynumber: 1.9 Consensus size: 132
12404468 TATACGAATC
* * * ** ** *
12404478 CATGTATGCAATATATAATAACAATAAAAATTCATATTCAAAACTATGTACAAAATTGGAAAGGC
1 CATGTATACAATACATAATAACAACAAAAATTCATACCCAAAACTATGTACAAAATTAAAAAGAC
* * *
12404543 AAAGATATTT-CCAAACAAATGAAATAACATACATACAAAGATGTTTACATAGATTTATATGCAA
66 AAAAAT-TTTCCCAAACAAATGAAATAACAAACATACAAAAATGTTTACATAGATTTATATGCAA
12404607 ATA
130 ATA
12404610 CATGTATACAATACATAAATGAA-AACAAAAATTCATACCCAAAACTATGTACAAAATTAAAAAG
1 CATGTATACAATACAT-AAT-AACAACAAAAATTCATACCCAAAACTATGTACAAAATTAAAAAG
12404674 ACAAAAATTTTCCCAAACAAATGAAATAACAAACATACAAAAATGTTTACAT
64 ACAAAAATTTTCCCAAACAAATGAAATAACAAACATACAAAAATGTTTACAT
12404726 GCATGTATGC
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
132 17 0.17
133 83 0.81
134 2 0.02
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (132 bp):
CATGTATACAATACATAATAACAACAAAAATTCATACCCAAAACTATGTACAAAATTAAAAAGAC
AAAAATTTTCCCAAACAAATGAAATAACAAACATACAAAAATGTTTACATAGATTTATATGCAAA
TA
Found at i:12404961 original size:19 final size:19
Alignment explanation
Indices: 12404939--12404977 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12404929 TAAACATGAT
*
12404939 ATATACAAATAACAACATA
1 ATATACAAAGAACAACATA
*
12404958 ATATATAAAGAACAACATA
1 ATATACAAAGAACAACATA
12404977 A
1 A
12404978 AGGGTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.21
Consensus pattern (19 bp):
ATATACAAAGAACAACATA
Found at i:12405633 original size:24 final size:24
Alignment explanation
Indices: 12405606--12405653 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12405596 GTATGATTGG
*
12405606 CTATCTAACTGAATCTGTCACATT
1 CTATCTAACTAAATCTGTCACATT
12405630 CTATCTAACTAAATCTGTCACATT
1 CTATCTAACTAAATCTGTCACATT
12405654 TTAAAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (24 bp):
CTATCTAACTAAATCTGTCACATT
Found at i:12406235 original size:104 final size:101
Alignment explanation
Indices: 12406051--12406248 Score: 272
Period size: 104 Copynumber: 1.9 Consensus size: 101
12406041 TAGATCTCCT
* * *
12406051 AATAGTTTGATAGGATTGAAAATTTTATTAATATTTTTTACAAAAAATTCATTAAGTCATCTAAT
1 AATAATTTGATAGGATTAAAAATTTTATTAATATTTTTTACAAAAAATTCATTAAGTCATATAAT
* *
12406116 ATTTTGTTAAAACTTAATTCAAGATTTAACTCATTC
66 AATTTGGTAAAACTTAATTCAAGATTTAACTCATTC
* * *
12406152 AATAATTTGATAGGATTAAAAATTTTATTATTATTATTATTTT-TAAAAAATTCTTTAAGTCCTA
1 AATAATTTGATAGGATTAAAAATTTTATTA--A-TATT-TTTTACAAAAAATTCATTAAGTCATA
*
12406216 TAATAATTTGGTAATACTTAATTCAAGATTTAA
62 TAATAATTTGGTAAAACTTAATTCAAGATTTAA
12406249 ATCCTCCAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
101 28 0.33
103 1 0.01
104 51 0.61
105 4 0.05
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (101 bp):
AATAATTTGATAGGATTAAAAATTTTATTAATATTTTTTACAAAAAATTCATTAAGTCATATAAT
AATTTGGTAAAACTTAATTCAAGATTTAACTCATTC
Found at i:12406278 original size:104 final size:104
Alignment explanation
Indices: 12406067--12406291 Score: 253
Period size: 104 Copynumber: 2.2 Consensus size: 104
12406057 TTGATAGGAT
* * *
12406067 TGAAAATTTTATTA--A-TATTTTTTACAAAAAATTCATTAAGTCATCTAATATTTTGTTAAAAC
1 TGAAAATTTTATTATTATTATTTTTTACAAAAAATTCATTAAGTCATATAATAATTTGGTAAAAC
* * * * *
12406129 TTAATTCAAGATTTAACTCATTCAATAATTTGATAGGAT
66 TTAATTCAAGATTTAAATCATCCAATAATTAGATAAGAC
* * * * *
12406168 TAAAAATTTTATTATTATTATTATTTT-TAAAAAATTCTTTAAGTCCTATAATAATTTGGTAATA
1 TGAAAATTTTATTATTATTATT-TTTTACAAAAAATTCATTAAGTCATATAATAATTTGGTAAAA
* *
12406232 CTTAATTCAAGATTTAAATCCTCCAATAATATAG-TAATAC
65 CTTAATTCAAGATTTAAATCATCCAATAAT-TAGATAAGAC
*
12406272 TGAAAATTTTGTTATTATTA
1 TGAAAATTTTATTATTATTA
12406292 AAAAAAATTA
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
101 13 0.13
103 1 0.01
104 82 0.80
105 6 0.06
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (104 bp):
TGAAAATTTTATTATTATTATTTTTTACAAAAAATTCATTAAGTCATATAATAATTTGGTAAAAC
TTAATTCAAGATTTAAATCATCCAATAATTAGATAAGAC
Found at i:12409222 original size:24 final size:23
Alignment explanation
Indices: 12409195--12409254 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
12409185 TTAAATAGAG
*
12409195 GTACAACAAATAATGAAAATA-AAA
1 GTACAA-AAATAAT-AAAACAGAAA
12409219 GTACAAAAAAATAATAAAACAGAAA
1 GTAC--AAAAATAATAAAACAGAAA
*
12409244 ATACAAAAATA
1 GTACAAAAATA
12409255 TAGTCGCGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 7 0.23
24 9 0.29
25 13 0.42
26 2 0.06
ACGTcount: A:0.70, C:0.08, G:0.07, T:0.15
Consensus pattern (23 bp):
GTACAAAAATAATAAAACAGAAA
Found at i:12409248 original size:25 final size:25
Alignment explanation
Indices: 12409202--12409252 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
12409192 GAGGTACAAC
* *
12409202 AAATAATGAAAATAAAAGTACAAAA
1 AAATAATGAAAACAAAAATACAAAA
12409227 AAATAAT-AAAACAGAAAATACAAAA
1 AAATAATGAAAACA-AAAATACAAAA
12409252 A
1 A
12409253 TATAGTCGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (25 bp):
AAATAATGAAAACAAAAATACAAAA
Found at i:12415409 original size:39 final size:39
Alignment explanation
Indices: 12415352--12415431 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
12415342 ACACTTCTCA
*
12415352 AACTCCCTTTCACATCCAAAACATCCAACCAGATCCTCC
1 AACTCCCTTTCACATCCAAAACATCCAACCAAATCCTCC
*
12415391 AACTCCCTTTCA-ACTCCAAAACATTCAACCAAATCCTCC
1 AACTCCCTTTCACA-TCCAAAACATCCAACCAAATCCTCC
12415430 AA
1 AA
12415432 GCTTGTAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.36, C:0.41, G:0.01, T:0.21
Consensus pattern (39 bp):
AACTCCCTTTCACATCCAAAACATCCAACCAAATCCTCC
Found at i:12427717 original size:22 final size:22
Alignment explanation
Indices: 12427692--12427735 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12427682 GTTTTCTGTC
12427692 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12427714 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
12427736 TAAATATACA
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:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:12433690 original size:22 final size:22
Alignment explanation
Indices: 12433664--12433705 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12433654 TGTATATTTA
* *
12433664 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
12433686 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
12433706 GGATAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:12433946 original size:25 final size:26
Alignment explanation
Indices: 12433892--12433956 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
12433882 AAATTTTCAA
* * *
12433892 CCTTCATTGCCGACTTCTATTTTAGG
1 CCTTCATTGCCGAATCCTAGTTTAGG
12433918 CCTTCATTGCCGAATCCT-GTTTAGG
1 CCTTCATTGCCGAATCCTAGTTTAGG
12433943 CCTTCATTGCCGAA
1 CCTTCATTGCCGAA
12433957 CCCTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 20 0.56
26 16 0.44
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (26 bp):
CCTTCATTGCCGAATCCTAGTTTAGG
Found at i:12437625 original size:22 final size:22
Alignment explanation
Indices: 12437599--12437640 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12437589 TGTATATTTA
* *
12437599 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
12437621 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
12437641 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:12441473 original size:30 final size:30
Alignment explanation
Indices: 12441439--12441497 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12441429 ACTTCCTCAA
12441439 TTTCTT-CCATTGCTCCCTCTGATTGCTTTG
1 TTTCTTCCCATT-CTCCCTCTGATTGCTTTG
* *
12441469 TTTCTTCCCCTTCTCCCTCTGATTTCTTT
1 TTTCTTCCCATTCTCCCTCTGATTGCTTT
12441498 ATTTGGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.05, C:0.34, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTCTTCCCATTCTCCCTCTGATTGCTTTG
Found at i:12443111 original size:15 final size:15
Alignment explanation
Indices: 12443091--12443150 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
12443081 TATATATATA
*
12443091 TTATTTTTTAATTAT
1 TTATTTTTTATTTAT
12443106 TTATTTTATT-TTTAT
1 TTATTTT-TTATTTAT
12443121 TT-TTTTTATATTTAT
1 TTATTTTT-TATTTAT
*
12443136 TTAATTTTATATTTA
1 TT-ATTTTTTATTTA
12443151 CATTAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 5 0.13
15 20 0.53
16 8 0.21
17 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTTTTTATTTAT
Found at i:12443122 original size:26 final size:26
Alignment explanation
Indices: 12443091--12443149 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
12443081 TATATATATA
*
12443091 TTATTTTTTA-ATTATTTATTTTATTT
1 TTATTTTTTATA-TATTTATTTAATTT
*
12443117 TTATTTTTTTTATATTTATTTAATTT
1 TTATTTTTTATATATTTATTTAATTT
12443143 TATATTT
1 T-TATTT
12443150 ACATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (26 bp):
TTATTTTTTATATATTTATTTAATTT
Found at i:12448145 original size:243 final size:248
Alignment explanation
Indices: 12447691--12448183 Score: 701
Period size: 243 Copynumber: 2.0 Consensus size: 248
12447681 GCATTGTTGA
*
12447691 CTGATCAGAAATTAATAAAAGCTTTTAATGTCTTATCTATTCCAATTTCCAAGAGAAGCTGTTTT
1 CTGATCAGAAATTAATAAAAGCTTTTAATGTCTTATCTATT-C-ATTTCCAAGAGAAGCTGTTTC
* * * * *
12447756 TTATTTGCTACCGACATAGTTTCTGAAATTTTATTTTAATGGAGTGACAGGAAGTAAGATTTTAC
64 TGATTTGCTACCAACATAGTTTCTGAAATTCTATTTTAATGCAGTGA-A-GAAGCAAGATTTTAC
* *
12447821 CACAATCTTGTCCAACCCTAATATTCAAAATGGCAACTTGACATCATACAGAAAATCAAAAACCA
127 CACAATCTTGTCCAACCCTAATATTCAAAATAGCAACTTGACATCATACAGAAAATCAAAAACAA
* * * *** *
12447886 CTTTCCAGTCACAAGTTTCCTCTGGCCATTTGCGGTTCAAACAGGATTGACATTTGG
192 CATTCCAATCACAAGTTTCCTCTAGCCATTTGCAACTCAAACAAGATTGACATTTGG
*
12447943 CTGATCAGAGATTAATAAAAG-TTTGTAATGTCTTATCTA-T-ATTT-CAAGAGAAGCTGTTTCT
1 CTGATCAGAAATTAATAAAAGCTTT-TAATGTCTTATCTATTCATTTCCAAGAGAAGCTGTTTCT
*
12448004 GATTTGCTACCAACATGGTTTCTGAAATTCTATTTTAATGCAGTG-A-AAGCAAGATTTTACCAC
65 GATTTGCTACCAACATAGTTTCTGAAATTCTATTTTAATGCAGTGAAGAAGCAAGATTTTACCAC
* *
12448067 AATCTTGTCCAACCTTAATGTTCAAAATAGCAACTTGACATCATACAGAAAATCAAAAACAACAT
130 AATCTTGTCCAACCCTAATATTCAAAATAGCAACTTGACATCATACAGAAAATCAAAAACAACAT
* * *
12448132 TCCAATTACAAGTTTCCTTTAGCTATTTGCAACTCAAACAAGATTGACATTT
195 TCCAATCACAAGTTTCCTCTAGCCATTTGCAACTCAAACAAGATTGACATTT
12448184 CTTGGACCAT
Statistics
Matches: 218, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
243 119 0.55
245 1 0.00
247 56 0.26
248 4 0.02
251 4 0.02
252 34 0.16
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (248 bp):
CTGATCAGAAATTAATAAAAGCTTTTAATGTCTTATCTATTCATTTCCAAGAGAAGCTGTTTCTG
ATTTGCTACCAACATAGTTTCTGAAATTCTATTTTAATGCAGTGAAGAAGCAAGATTTTACCACA
ATCTTGTCCAACCCTAATATTCAAAATAGCAACTTGACATCATACAGAAAATCAAAAACAACATT
CCAATCACAAGTTTCCTCTAGCCATTTGCAACTCAAACAAGATTGACATTTGG
Found at i:12449853 original size:56 final size:56
Alignment explanation
Indices: 12449767--12449878 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
12449757 TGTTACATAA
12449767 ACATTTACAATATTGCATGTCTATTCCTGTATATCCACCTCACTTGACAGATGCCC
1 ACATTTACAATATTGCATGTCTATTCCTGTATATCCACCTCACTTGACAGATGCCC
12449823 ACATTTACAATATTGCATGTCTATTCCTGTATATCCACCTCACTTGACAGATGCCC
1 ACATTTACAATATTGCATGTCTATTCCTGTATATCCACCTCACTTGACAGATGCCC
12449879 TCTCCAGAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (56 bp):
ACATTTACAATATTGCATGTCTATTCCTGTATATCCACCTCACTTGACAGATGCCC
Found at i:12459273 original size:20 final size:21
Alignment explanation
Indices: 12459248--12459337 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 21
12459238 CCAAGCATGA
12459248 ATTAATAA-CCTACAACATAT
1 ATTAATAATCCTACAACATAT
* ** *
12459268 ATTAATAATCATGTAATA-AT
1 ATTAATAATCCTACAACATAT
12459288 A-TAATATATCCTACAACATAT
1 ATTAATA-ATCCTACAACATAT
*
12459309 ATTAATAATCATACAA-ATA-
1 ATTAATAATCCTACAACATAT
*
12459328 ATAAATAATC
1 ATTAATAATC
12459338 ATGCAATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
19 14 0.25
20 21 0.38
21 16 0.29
22 5 0.09
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.33
Consensus pattern (21 bp):
ATTAATAATCCTACAACATAT
Found at i:12459336 original size:19 final size:19
Alignment explanation
Indices: 12459282--12459367 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 19
12459272 ATAATCATGT
*
12459282 AATAATATAATATATCCTACA
1 AATAATA-AATA-ATCATACA
*
12459303 ACATATATTAATAATCATACA
1 A-ATA-ATAAATAATCATACA
*
12459324 AATAATAAATAATCATGC-
1 AATAATAAATAATCATACA
* *
12459342 AATATATTAATGAATCACACA
1 AATA-ATAAAT-AATCATACA
12459363 AATAA
1 AATAA
12459368 AATATTAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.08
19 17 0.32
20 10 0.19
21 13 0.25
22 7 0.13
23 2 0.04
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAATAAATAATCATACA
Found at i:12459678 original size:16 final size:15
Alignment explanation
Indices: 12459647--12459680 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12459637 CAATCACAAT
*
12459647 TAAATAGAAAAATAA
1 TAAAAAGAAAAATAA
12459662 TAAAAAGAAAGAATAA
1 TAAAAAGAAA-AATAA
12459678 TAA
1 TAA
12459681 TCAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAAAAGAAAAATAA
Found at i:12462431 original size:111 final size:112
Alignment explanation
Indices: 12462316--12462516 Score: 253
Period size: 112 Copynumber: 1.8 Consensus size: 112
12462306 TAAAAATATT
* * *** * *
12462316 AAAAAATTAATTTT-CAAAATTTAACAAAGGTGACATTTTTAAGATA-AAAATGCAATCATTGCT
1 AAAAAAAT-ATTTTCCAAAATTCAACAAAAACGACATTTCTAAGATAGAAAATGCAATCATTACT
*
12462379 AGAAAGATAATATTTTTAAGATAAAACACAGTTTTTATTATTAACATG
65 AAAAAGATAATATTTTTAAGATAAAACACAGTTTTTATTATTAACATG
* * * ** *
12462427 AAAAAAATATTTTCCAAAATTCAATAAAAACGATATTTCTAATATAGAAAATGCAATTTTTATTA
1 AAAAAAATATTTTCCAAAATTCAACAAAAACGACATTTCTAAGATAGAAAATGCAATCATTACTA
12462492 AAAAGATAATATTTTTAAGATAAAA
66 AAAAGATAATATTTTTAAGATAAAA
12462517 ATATAGTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
110 5 0.07
111 31 0.42
112 38 0.51
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (112 bp):
AAAAAAATATTTTCCAAAATTCAACAAAAACGACATTTCTAAGATAGAAAATGCAATCATTACTA
AAAAGATAATATTTTTAAGATAAAACACAGTTTTTATTATTAACATG
Found at i:12463056 original size:17 final size:18
Alignment explanation
Indices: 12463036--12463085 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
12463026 TTGTCACGTG
12463036 TTATTCACATATTA-ATA-
1 TTATTCA-ATATTATATAT
*
12463053 TTA-TGAATATTATATAT
1 TTATTCAATATTATATAT
12463070 TTATTCATATATTATA
1 TTATTCA-ATATTATA
12463086 AAAGATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.22
16 5 0.19
17 6 0.22
18 2 0.07
19 8 0.30
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTCAATATTATATAT
Found at i:12466023 original size:16 final size:15
Alignment explanation
Indices: 12466002--12466049 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
12465992 AGTTATAACA
12466002 ATTTAAAATTTGAATC
1 ATTTAAAATTT-AATC
12466018 ATTTAAAATTTAATC
1 ATTTAAAATTTAATC
*
12466033 TATTTCAAATTTAATC
1 -ATTTAAAATTTAATC
12466049 A
1 A
12466050 ATCTTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTTAAAATTTAATC
Found at i:12468914 original size:12 final size:13
Alignment explanation
Indices: 12468882--12468937 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
12468872 TATCATTTAC
12468882 CTATATCTATCCAT
1 CTATATCTAT-CAT
12468896 CTATATCTAT-AT
1 CTATATCTATCAT
*
12468908 TTATATCTA-CAT
1 CTATATCTATCAT
12468920 C--TATCTATCTAT
1 CTATATCTATC-AT
12468932 CTATAT
1 CTATAT
12468938 ATGTAAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
10 6 0.17
11 1 0.03
12 15 0.43
14 13 0.37
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (13 bp):
CTATATCTATCAT
Found at i:12469645 original size:16 final size:16
Alignment explanation
Indices: 12469605--12469647 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12469595 ATATATGTAT
* *
12469605 GTTAATGATTTTATTA
1 GTTAATTATTTTATGA
* *
12469621 TTTATTTATTTTATGA
1 GTTAATTATTTTATGA
12469637 GTTAATTATTT
1 GTTAATTATTT
12469648 GATCATTGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (16 bp):
GTTAATTATTTTATGA
Found at i:12472159 original size:12 final size:12
Alignment explanation
Indices: 12472142--12472166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12472132 ATTTTGAATG
12472142 ATGGTAATAAGA
1 ATGGTAATAAGA
12472154 ATGGTAATAAGA
1 ATGGTAATAAGA
12472166 A
1 A
12472167 GTTAATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGGTAATAAGA
Found at i:12472750 original size:22 final size:22
Alignment explanation
Indices: 12472710--12472814 Score: 74
Period size: 21 Copynumber: 5.0 Consensus size: 22
12472700 GTTATAAGAT
*
12472710 ATCAAAAGATTACTAAAATTAC
1 ATCAAAAGATTACCAAAATTAC
* * **
12472732 ATCAAAAGATTTCCCAAATTTT
1 ATCAAAAGATTACCAAAATTAC
**
12472754 ATC-AAA-ATTACCAAAATTGT
1 ATCAAAAGATTACCAAAATTAC
* * * *
12472774 ATC-AATGCTTATCAAAATTAT
1 ATCAAAAGATTACCAAAATTAC
*
12472795 ATCATAAG-TTACCAAAATTA
1 ATCAAAAGATTACCAAAATTA
12472815 TATAAATGGT
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.24
21 28 0.42
22 22 0.33
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (22 bp):
ATCAAAAGATTACCAAAATTAC
Found at i:12472791 original size:21 final size:21
Alignment explanation
Indices: 12472747--12472854 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
12472737 AAGATTTCCC
* * *
12472747 AAATTTTATCAAA-ATTACCA
1 AAATTATATCAAAGGTTATCA
* * *
12472767 AAATTGTATCAATGCTTATCA
1 AAATTATATCAAAGGTTATCA
*
12472788 AAATTATATCATAA-GTTACCA
1 AAATTATATCA-AAGGTTATCA
12472809 AAATTATAT-AAATGGTTA-CAA
1 AAATTATATCAAA-GGTTATC-A
*
12472830 AAATTTTATCAAAGGTTATCA
1 AAATTATATCAAAGGTTATCA
12472851 AAAT
1 AAAT
12472855 CAAAATTGTG
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
19 2 0.03
20 13 0.18
21 52 0.72
22 5 0.07
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (21 bp):
AAATTATATCAAAGGTTATCA
Found at i:12472807 original size:42 final size:41
Alignment explanation
Indices: 12472747--12472854 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
12472737 AAGATTTCCC
* * *
12472747 AAATTTTATCAAAATTACCAAAATTGTATCAATGCTTATC-A
1 AAATTTTATCAAAGTTACCAAAATTATATAAATGCTTA-CAA
* *
12472788 AAATTATATCATAAGTTACCAAAATTATATAAATGGTTACAA
1 AAATTTTATCA-AAGTTACCAAAATTATATAAATGCTTACAA
*
12472830 AAATTTTATCAAAGGTTATCAAAAT
1 AAATTTTATCAAA-GTTACCAAAAT
12472855 CAAAATTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 13 0.23
42 44 0.77
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (41 bp):
AAATTTTATCAAAGTTACCAAAATTATATAAATGCTTACAA
Found at i:12473292 original size:42 final size:42
Alignment explanation
Indices: 12473235--12473358 Score: 121
Period size: 42 Copynumber: 3.0 Consensus size: 42
12473225 ATAAGTTATC
* * *
12473235 AAAAGATTACTAAAATTACATCAAAATGTTACCAAAATTTTT
1 AAAAAATTACCAAAATTATATCAAAATGTTACCAAAATTTTT
*
12473277 AAAAAATTACCAAAATTATATC--ATTGGTTACCAAAATTATATT
1 AAAAAATTACCAAAATTATATCAAAAT-GTTACCAAAATT-T-TT
* * * *
12473320 -ACAAGTTACCAAAATTATAT-AAAAGGTTGCCAAAATTTT
1 AAAAAATTACCAAAATTATATCAAAATGTTACCAAAATTTT
12473359 ATCGAAGGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
40 3 0.04
41 13 0.19
42 49 0.72
43 3 0.04
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (42 bp):
AAAAAATTACCAAAATTATATCAAAATGTTACCAAAATTTTT
Found at i:12473309 original size:21 final size:21
Alignment explanation
Indices: 12473231--12473361 Score: 86
Period size: 21 Copynumber: 6.2 Consensus size: 21
12473221 TATCATAAGT
* *
12473231 TATCAAAAGATTACTAAAATTA
1 TATCACAAG-TTACCAAAATTA
* *
12473253 CATCAAAATGTTACCAAAATT-
1 TATCACAA-GTTACCAAAATTA
* * * *
12473274 TTTAAAAAATTACCAAAATTA
1 TATCACAAGTTACCAAAATTA
***
12473295 TATCATTGGTTACCAAAATTA
1 TATCACAAGTTACCAAAATTA
*
12473316 TATTACAAGTTACCAAAATTA
1 TATCACAAGTTACCAAAATTA
* * *
12473337 TAT-AAAAGGTTGCCAAAATTT
1 TATCACAA-GTTACCAAAATTA
12473358 TATC
1 TATC
12473362 GAAGGTTATC
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.16
21 54 0.63
22 17 0.20
23 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (21 bp):
TATCACAAGTTACCAAAATTA
Found at i:12473818 original size:21 final size:21
Alignment explanation
Indices: 12473760--12473874 Score: 124
Period size: 21 Copynumber: 5.4 Consensus size: 21
12473750 ATATAATAAG
*
12473760 TTATCAAAATATTACTAAAATT
1 TTATCAAAA-ATTACCAAAATT
**
12473782 ACATCAAAAGATTACCAAAATT
1 TTATCAAAA-ATTACCAAAATT
*
12473804 TTATTAAAAATTACCAAAATT
1 TTATCAAAAATTACCAAAATT
* *
12473825 GTATTC-ATAATTACCAAAATT
1 TTA-TCAAAAATTACCAAAATT
* *
12473846 ATATCATAAATTACCAAAATT
1 TTATCAAAAATTACCAAAATT
12473867 TTATCAAA
1 TTATCAAA
12473875 GGTTATCAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.03
21 49 0.64
22 25 0.33
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (21 bp):
TTATCAAAAATTACCAAAATT
Found at i:12474175 original size:516 final size:509
Alignment explanation
Indices: 12473304--12476024 Score: 2495
Period size: 516 Copynumber: 5.3 Consensus size: 509
12473294 ATATCATTGG
* * * * ** * *
12473304 TTACCAAAATTATATTACAAGTTACCAAAATTATAT-AAAAGGTTGCCAAAATTTTATCGAAGGT
1 TTACCAAAATTGTATCATAA-TTACCAAAATTATATCATAATATTACCAAAATTTTATCAAAGGT
* *
12473368 TATCAAAATCAAAATTATATAAAAA-TATTCAAAATTTACTTATATTAGATCAAAATCAAAATTA
65 TATCAAAATCAAAATTATATAAAAATTA-TCAAATTTTACTTATATTATATCAAAATCAAAATTA
* * *
12473432 AATTA-TATGTATTTATCATTATTGTCATAGCATAAAAAATTATTTGTTGGAATGAATTTTTAAA
129 AATTATTA-GTATTTATCATTATTATCATAGTATAAAAAATTATTTATTGGAATGAATTTTTAAA
* * * * * *
12473496 AATAAGAAATACACAATTGAATCTTAGTTACTAGTAAAAATATAGTTAGAAATTTTGTCTTGAAA
193 GATAAGAATTACACAATTGAATCTT-GTTACTAGCAAAAATAGAGTTAGAAATTTTATCTTG-GA
* * * * *
12473561 TATTAGGATAAACTTACTATAAAGCTATTTAATAAAAAAATTTTGTGAACAAAAATTCTAAATTT
256 GACTAGGATAAACTTACCATAAACCTATTTAATAAAAAAATTTAGTGAACAAAAATTCTAAATTT
* * * * *
12473626 AAATAAAACAATAATGTTATTGTAT-AAAAAAATTATTTTATATTAGAACTGGACTTATGCTTTT
321 AAATGAAACAATAATGTTATTGTATAAAAAAAATTATCTTATACTAGAACTGAACCTATGCTTTT
* * * *
12473690 C-TATAAAAATCTATTGTTAAATATATGATAACATAAATTTTATTAATAATTACAAAAAGTATAT
386 CTTATAAGAATCTATTATTAAATATATGATGACATAAATTTTATCAATAATTACAAAAAGTATAT
* *
12473754 AATAAGTTATCAAAATATTACTAAAATTACATCAAAA-GATTACCAAAATTTTATTAAAAA
451 CATAAGTTATCAAAA-ATTACTAAAATTACATCAAAATG-TTACCAAAATTTTATAAAAAA
12473814 TTACCAAAATTGTATTCATAATTACCAAAATTATATCATAA-ATTACCAAAATTTTATCAAAGGT
1 TTACCAAAATTGTA-TCATAATTACCAAAATTATATCATAATATTACCAAAATTTTATCAAAGGT
* *
12473878 TATCAAAATCAAAATTATATAAAAATTATCAAATTTTAATTATATTGTATCAAAATCAAAATTAA
65 TATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATATTATATCAAAATCAAAATTAA
* *
12473943 ATTATTAGTATTTATTATTATTATTATTATCATAGTATAAAAAATTATTTATTAGAATGAATTTT
130 ATTATTAG----TA-T-TTATCATTATTATCATAGTATAAAAAATTATTTATTGGAATGAATTTT
* *
12474008 TAAAGATAAGAATTACACAATTAAATCTTAGTTAATAGCAAAAATAGAGTTAGAAATTTTATCTT
189 TAAAGATAAGAATTACACAATTGAATCTT-GTTACTAGCAAAAATAGAGTTAGAAATTTTATCTT
** * * * * *
12474073 AAAAGACTAAGATAAACTTACCATAAACCTATTGAATAAAAACAAATTAGTG-A-AAAAATTTTT
253 -GGAGACTAGGATAAACTTACCATAAACCTATTTAATAAAAA-AATTTAGTGAACAAAAATTCTA
* * * * *
12474136 AATTTAAAAGAAAAAATAATGTTATTGTATATAAAAAATTATCTTATACTAGAATTGAACCCATG
316 AATTTAAATGAAACAATAATGTTATTGTATAAAAAAAATTATCTTATACTAGAACTGAACCTATG
* * * * ** * * ***
12474201 C-TTTCGTAGATGAATCTATTATGAAATATATGATGAGGTAGATTTTATTAATAATTTTTAAAAG
381 CTTTTCTTATAAGAATCTATTATTAAATATATGATGACATAAATTTTATCAATAATTACAAAAAG
* * * * * *
12474265 TATATAATTAGTTATCAAAAAGTTACTGAAATTGCATTAAAATGTTACTAAAATTTTATAAAAAA
446 TATATCATAAGTTATCAAAAA-TTACTAAAATTACATCAAAATGTTACCAAAATTTTATAAAAAA
* *
12474330 TTACCAAAATTGTATCAACAATTACTAAAACTATATCATAAATTACCAAATTATATAGAAGGTTA
1 TTACCAAAATTGTATC-ATAATTAC-CAAA--AT-T-AT--A-T--C--A-TA-AT---A--TTA
* * * * * *
12474395 ACAAAATTTTATCAAAAGTTATCAAAATAAAAACTATATAAAAATAATCAAAATTTTATTTATAT
46 CCAAAATTTTATCAAAGGTTATCAAAATCAAAATTATATAAAAATTATC-AAATTTTACTTATAT
* *
12474460 TATATTAAAATCAAAATTAAATTA-TACGTATTTATCATTATTATCATAGCATAAAAAATTATTT
110 TATATCAAAATCAAAATTAAATTATTA-GTATTTATCATTATTATCATAGTATAAAAAATTATTT
* * * * *
12474524 ATTGGAATGAATTTTTAAAGTTAAGAATTTCACAATTGAATTTTGGCTACTAAGTAAAAATAGAG
174 ATTGGAATGAATTTTTAAAGATAAGAATTACACAATTGAATCTT-GTTACT-AGCAAAAATAGAG
* * * *
12474589 -TAGAAATTTTATTTTAGGAGACTAGTATAAAATTACCATAAACCTATTTAGT-AAAAAATATTA
237 TTAGAAATTTTATCTT-GGAGACTAGGATAAACTTACCATAAACCTATTTAATAAAAAAAT-TTA
* * *
12474652 ATGAACAAAAATTCTAAATTTAAATGAAACAATATTGTTATTGTATAAAAAGAAAATTATCATAT
300 GTGAACAAAAATTCTAAATTTAAATGAAACAATAATGTTATTGTAT-AAAA-AAAATTATCTTAT
* * *
12474717 ACTAGAATTGAA-CT-CGCGTTTTCTTATAAGAATCTATTGTTAAATATATGATGACATAAATTT
363 ACTAGAACTGAACCTATGC-TTTTCTTATAAGAATCTATTATTAAATATATGATGACATAAATTT
* * * * *
12474780 TATCAATAATTA-AAAAAATATATCACAAGTTATTAAAAATTTACTAAAGTTACATAAAAATGTT
427 TATCAATAATTACAAAAAGTATATCATAAGTTATCAAAAA-TTACTAAAATTACATCAAAATGTT
* *
12474844 ACCAAAATTTTATCATAAA
491 ACCAAAATTTTATAAAAAA
*** * ** * * *
12474863 TTTTGAAAATTATATCAATGGTTACCAAAATTTTATCATAA-GTTACTAAAATTTTATCAAAGGT
1 TTACCAAAATTGTATC-ATAATTACCAAAATTATATCATAATATTACCAAAATTTTATCAAAGGT
*
12474927 TATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATATTATATCAAAATCAAACTTAA
65 TATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATATTATATCAAAATCAAAATTAA
*
12474992 ATTATTAGTATTTATCATTATTATCATTGTATAAAAAATTATTTATTGGAATGAATTTTTAAAGA
130 ATTATTAGTATTTATCATTATTATCATAGTATAAAAAATTATTTATTGGAATGAATTTTTAAAGA
* * * * *
12475057 TAAGAATT--AC----G---GTTG-T--TAGCAAATATAGAGATAGAAATTTTATCTGTGGGGAT
195 TAAGAATTACACAATTGAATCTTGTTACTAGCAAAAATAGAGTTAGAAATTTTATCT-TGGAGAC
** * *
12475110 TAGGATAAACTTATTATAAACCTATTTAATAAAAAACTTTAGTGAACAAAAATTCCAAATTTAAA
259 TAGGATAAACTTACCATAAACCTATTTAATAAAAAAATTTAGTGAACAAAAATTCTAAATTTAAA
* * * *
12475175 TGAAACAATAATATTATTGTATAAAAAAAAATTATCTTATACTACAACTGAACCCACGCTTTTC-
324 TGAAACAATAATGTTATTGTAT-AAAAAAAATTATCTTATACTAGAACTGAACCTATGCTTTTCT
* * * * * * * * *
12475239 --GAAGAATTTATTGTTAAATATATGATGACACATAGTTTATTAATAATTATGAAAAA-TATATT
388 TATAAGAATCTATTATTAAATATATGATGACATAAATTTTATCAATAATTA-CAAAAAGTATATC
* * * * *
12475301 ATAAATGATCAAAATATTACTAAAATTACA-CAAAAAAGGTACCAAAATTTTATCAAAAA
452 ATAAGTTATCAAAA-ATTACTAAAATTACATC-AAAATGTTACCAAAATTTTATAAAAAA
* *
12475360 TTACCTAAATTGTATCAATGGTTATCAAAATTATATCAAAAGTGACCAAAATTATAT-AGAATGT
1 TTACC-AAA----AT---T-G-TATC---A-TA-AT------T-ACCAAAATTATATCATAATAT
* * *
12475424 TATCAAAATTTTATCAAAGATTATTAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATA
44 TACCAAAATTTTATCAAAGGTTATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATA
* * * * *
12475489 TTATATCAAAATTAAAATTAAATTATTAGCATTTATCATTATTATCATAATAT-AAAATTTTTTT
109 TTATATCAAAATCAAAATTAAATTATTAGTATTTATCATTATTATCATAGTATAAAAAATTATTT
* * * * *
12475553 ATTAGAATAAATTTTTAAAGATAAGAATTATACAATTGAATATTGTTTACTAGCAAAAATAGTGT
174 ATTGGAATGAATTTTTAAAGATAAGAATTACACAATTGAATCTTG-TTACTAGCAAAAATAGAGT
* * *
12475618 TAAAAATTTTA---T-----CT--G-T-AA---A-C-T-----TATTTATTAAAAATATTTAGTG
238 TAGAAATTTTATCTTGGAGACTAGGATAAACTTACCATAAACCTATTTAATAAAAAAATTTAGTG
* * *
12475661 AACAAAATTTATAAATTTAAATGAAACAATAATGTTATTATATAAAAAAAATTATCTTATACTAG
303 AACAAAAATTCTAAATTTAAATGAAACAATAATGTTATTGTATAAAAAAAATTATCTTATACTAG
* * *
12475726 AACTAAACCTATGC-TTTCTTATAAGAATCTATTATTAAAAATATGATGATATAAATTTTATCAA
368 AACTGAACCTATGCTTTTCTTATAAGAATCTATTATTAAATATATGATGACATAAATTTTATCAA
* * * ***
12475790 TAATTACCAAAAA-CATATCATAAGTTATTAAAAGATTACTAAAATTACATTAAAA-GATTGTTA
433 TAATTA-CAAAAAGTATATCATAAGTTATCAAAA-ATTACTAAAATTACATCAAAATG-TTACCA
*
12475853 AAATTTTGTAAAAAAA
495 AAATTTTAT-AAAAAA
* * **
12475869 TTACCAAAATTGTATTAATAATTACCAAACTTATATCATAAGTTTTTAAAATTATATAGAATGTT
1 TTACCAAAATTGTA-TCATAATTACCAAAATTATATC---A-----T--AA-TAT-T---A--CC
* *
12475934 ATCAAATTTTATCAAAGATTATCAAAATCAGAATTATATAAAAATTATCAAATTTTACTTATATT
48 A--AAATTTTATCAAAGGTTATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATATT
* *
12475999 ATATAAAAATTAAAATTAAATTATTA
111 ATATCAAAATCAAAATTAAATTATTA
12476025 AAATTTATTT
Statistics
Matches: 1836, Mismatches: 256, Indels: 240
0.79 0.11 0.10
Matches are distributed among these distances:
488 12 0.01
489 1 0.00
492 1 0.00
495 2 0.00
496 45 0.02
497 55 0.03
498 42 0.02
499 103 0.06
500 14 0.01
501 3 0.00
502 3 0.00
503 2 0.00
504 3 0.00
505 5 0.00
506 35 0.02
507 62 0.03
508 177 0.10
509 12 0.01
510 114 0.06
511 12 0.01
512 100 0.05
513 48 0.03
514 3 0.00
515 43 0.02
516 286 0.16
517 53 0.03
518 124 0.07
519 6 0.00
520 3 0.00
521 4 0.00
523 3 0.00
524 1 0.00
525 1 0.00
526 6 0.00
528 3 0.00
529 5 0.00
530 34 0.02
531 119 0.06
532 53 0.03
533 81 0.04
534 71 0.04
536 49 0.03
537 37 0.02
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (509 bp):
TTACCAAAATTGTATCATAATTACCAAAATTATATCATAATATTACCAAAATTTTATCAAAGGTT
ATCAAAATCAAAATTATATAAAAATTATCAAATTTTACTTATATTATATCAAAATCAAAATTAAA
TTATTAGTATTTATCATTATTATCATAGTATAAAAAATTATTTATTGGAATGAATTTTTAAAGAT
AAGAATTACACAATTGAATCTTGTTACTAGCAAAAATAGAGTTAGAAATTTTATCTTGGAGACTA
GGATAAACTTACCATAAACCTATTTAATAAAAAAATTTAGTGAACAAAAATTCTAAATTTAAATG
AAACAATAATGTTATTGTATAAAAAAAATTATCTTATACTAGAACTGAACCTATGCTTTTCTTAT
AAGAATCTATTATTAAATATATGATGACATAAATTTTATCAATAATTACAAAAAGTATATCATAA
GTTATCAAAAATTACTAAAATTACATCAAAATGTTACCAAAATTTTATAAAAAA
Found at i:12474328 original size:22 final size:21
Alignment explanation
Indices: 12474276--12474415 Score: 63
Period size: 21 Copynumber: 6.6 Consensus size: 21
12474266 ATATAATTAG
*
12474276 TTATCAAAAAGTTACTGAAATT
1 TTAT-AAAAAGTTACTAAAATT
** *
12474298 GCATTAAAATGTTACTAAAATT
1 TTA-TAAAAAGTTACTAAAATT
* *
12474320 TTATAAAAAATTACCAAAATT
1 TTATAAAAAGTTACTAAAATT
* * *
12474341 GTATCAACAA-TTACTAAAACT
1 TTAT-AAAAAGTTACTAAAATT
* * *
12474362 ATATCATAAA-TTAC-CAAATT
1 TTAT-AAAAAGTTACTAAAATT
* * *
12474382 ATATAGAAGGTTAAC-AAAATT
1 TTATAAAAAGTT-ACTAAAATT
*
12474403 TTATCAAAAGTTA
1 TTATAAAAAGTTA
12474416 TCAAAATAAA
Statistics
Matches: 89, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 11 0.12
21 53 0.60
22 21 0.24
23 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (21 bp):
TTATAAAAAGTTACTAAAATT
Found at i:12474333 original size:21 final size:21
Alignment explanation
Indices: 12474281--12474359 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
12474271 ATTAGTTATC
* * *
12474281 AAAAAGTTACTGAAATTGCATT
1 AAAAAATTACTAAAATTGTA-T
** *
12474303 AAAATGTTACTAAAATTTTAT
1 AAAAAATTACTAAAATTGTAT
*
12474324 AAAAAATTACCAAAATTGTAT
1 AAAAAATTACTAAAATTGTAT
* *
12474345 CAACAATTACTAAAA
1 AAAAAATTACTAAAA
12474360 CTATATCATA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 30 0.65
22 16 0.35
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAAAATTACTAAAATTGTAT
Found at i:12474366 original size:21 final size:20
Alignment explanation
Indices: 12474309--12474385 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 20
12474299 CATTAAAATG
* *
12474309 TTACTAAAATTTTATAAAAAA
1 TTACTAAAATTATAT-CAAAA
* *
12474330 TTACCAAAATTGTATCAACAA
1 TTACTAAAATTATATCAA-AA
*
12474351 TTACTAAAACTATATCATAAA
1 TTACTAAAATTATATCA-AAA
*
12474372 TTAC-CAAATTATAT
1 TTACTAAAATTATAT
12474386 AGAAGGTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.22
21 35 0.76
22 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (20 bp):
TTACTAAAATTATATCAAAA
Found at i:12474888 original size:42 final size:42
Alignment explanation
Indices: 12474841--12474935 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
12474831 ACATAAAAAT
* *
12474841 GTTACCAAAATTTTATCATAAATT-TTGAAAATTATATCAATG
1 GTTACCAAAATTTTATCATAAATTACT-AAAATTATATCAAAG
* *
12474883 GTTACCAAAATTTTATCATAAGTTACTAAAATTTTATCAAAG
1 GTTACCAAAATTTTATCATAAATTACTAAAATTATATCAAAG
*
12474925 GTTATCAAAAT
1 GTTACCAAAAT
12474936 CAAAATTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (42 bp):
GTTACCAAAATTTTATCATAAATTACTAAAATTATATCAAAG
Found at i:12474892 original size:21 final size:21
Alignment explanation
Indices: 12474868--12474935 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
12474858 ATAAATTTTG
*
12474868 AAAATTATATCAATGGTTACC
1 AAAATTTTATCAATGGTTACC
* *
12474889 AAAATTTTATC-ATAAGTTACT
1 AAAATTTTATCAAT-GGTTACC
* *
12474910 AAAATTTTATCAAAGGTTATC
1 AAAATTTTATCAATGGTTACC
12474931 AAAAT
1 AAAAT
12474936 CAAAATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAATTTTATCAATGGTTACC
Found at i:12475364 original size:21 final size:21
Alignment explanation
Indices: 12475334--12475441 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
12475324 AATTACACAA
* *
12475334 AAAAGGTACCAAAATTTTATC
1 AAAAGTTACCAAAATTATATC
* * *
12475355 AAAAATTACCTAAATTGTATC
1 AAAAGTTACCAAAATTATATC
** *
12475376 AATGGTTATCAAAATTATATC
1 AAAAGTTACCAAAATTATATC
*
12475397 AAAAGTGACCAAAATTATAT-
1 AAAAGTTACCAAAATTATATC
* * *
12475417 AGAATGTTATCAAAATTTTATC
1 A-AAAGTTACCAAAATTATATC
12475439 AAA
1 AAA
12475442 GATTATTAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (21 bp):
AAAAGTTACCAAAATTATATC
Found at i:12475397 original size:42 final size:42
Alignment explanation
Indices: 12475343--12475446 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
12475333 AAAAAGGTAC
* *
12475343 CAAAATTTTATCAAAAATTACCTAAATTGTAT-CAATGGTTAT
1 CAAAATTTTATCAAAAATTACCAAAATTATATACAAT-GTTAT
* * * *
12475385 CAAAATTATATCAAAAGTGACCAAAATTATATAGAATGTTAT
1 CAAAATTTTATCAAAAATTACCAAAATTATATACAATGTTAT
*
12475427 CAAAATTTTATCAAAGATTA
1 CAAAATTTTATCAAAAATTA
12475447 TTAAAATCAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (42 bp):
CAAAATTTTATCAAAAATTACCAAAATTATATACAATGTTAT
Found at i:12475447 original size:21 final size:21
Alignment explanation
Indices: 12475343--12475453 Score: 75
Period size: 21 Copynumber: 5.3 Consensus size: 21
12475333 AAAAAGGTAC
* * *
12475343 CAAAATTTTATCAAAAATTAC
1 CAAAATTATATCAAAGATTAT
* * * *
12475364 CTAAATTGTATCAATGGTTAT
1 CAAAATTATATCAAAGATTAT
* *
12475385 CAAAATTATATCAAA-AGTGAC
1 CAAAATTATATCAAAGA-TTAT
12475406 CAAAATTATAT-AGAATG-TTAT
1 CAAAATTATATCA-AA-GATTAT
*
12475427 CAAAATTTTATCAAAGATTAT
1 CAAAATTATATCAAAGATTAT
*
12475448 TAAAAT
1 CAAAAT
12475454 CAAAATTATA
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.03
21 65 0.96
22 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (21 bp):
CAAAATTATATCAAAGATTAT
Found at i:12475457 original size:16 final size:16
Alignment explanation
Indices: 12475436--12475468 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12475426 TCAAAATTTT
12475436 ATCAAAGATTAT-TAAA
1 ATCAAA-ATTATATAAA
12475452 ATCAAAATTATATAAA
1 ATCAAAATTATATAAA
12475468 A
1 A
12475469 ATTATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (16 bp):
ATCAAAATTATATAAA
Found at i:12475841 original size:22 final size:22
Alignment explanation
Indices: 12475816--12475857 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12475806 ATCATAAGTT
12475816 ATTAAAAGATTACTAAAATTAC
1 ATTAAAAGATTACTAAAATTAC
**
12475838 ATTAAAAGATTGTTAAAATT
1 ATTAAAAGATTACTAAAATT
12475858 TTGTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (22 bp):
ATTAAAAGATTACTAAAATTAC
Done.