Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 17 of 100
Found at i:4786051 original size:47 final size:47
Alignment explanation
Indices: 4785977--4786071 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
4785967 TGGTAACATC
*
4785977 TTGCTGTTGGTGGAAGTGATGAAGACAGACTAGAAAATGGGGCCTGG
1 TTGCCGTTGGTGGAAGTGATGAAGACAGACTAGAAAATGGGGCCTGG
4786024 TTGCCGTTGGTGGAAGT-AGTGAAGACAGACTAGAAAATGGGGCCTGG
1 TTGCCGTTGGTGGAAGTGA-TGAAGACAGACTAGAAAATGGGGCCTGG
4786071 T
1 T
4786072 GAATGCAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.27, C:0.12, G:0.38, T:0.23
Consensus pattern (47 bp):
TTGCCGTTGGTGGAAGTGATGAAGACAGACTAGAAAATGGGGCCTGG
Found at i:4788996 original size:29 final size:29
Alignment explanation
Indices: 4788964--4789021 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
4788954 TTTGATCTGT
4788964 TAAAGCAAA-TCAAGCTAAGTTTAGATTTC
1 TAAAG-AAAGTCAAGCTAAGTTTAGATTTC
*
4788993 TAAAGAAAGTCAAGTTAAGTTTAGATTTC
1 TAAAGAAAGTCAAGCTAAGTTTAGATTTC
4789022 CAAAATGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAAGAAAGTCAAGCTAAGTTTAGATTTC
Found at i:4795817 original size:12 final size:12
Alignment explanation
Indices: 4795797--4795836 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4795787 TACGCAAAAT
*
4795797 ACATGCACACAC
1 ACATACACACAC
*
4795809 ACATACACACAT
1 ACATACACACAC
*
4795821 ACATACACAGAC
1 ACATACACACAC
4795833 ACAT
1 ACAT
4795837 GCTTTTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.35, G:0.05, T:0.12
Consensus pattern (12 bp):
ACATACACACAC
Found at i:4798124 original size:14 final size:14
Alignment explanation
Indices: 4798107--4798137 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4798097 CTGTTTATAA
4798107 TTTTCTTCTTTCTC
1 TTTTCTTCTTTCTC
*
4798121 TTTTCTTTTTTCTC
1 TTTTCTTCTTTCTC
4798135 TTT
1 TTT
4798138 AGTTACCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTCTTTCTC
Found at i:4800953 original size:34 final size:33
Alignment explanation
Indices: 4800915--4800984 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
4800905 ATTTTATAAA
* *
4800915 AAAAT-ATTTAATACTTATTAAATAAATAATTTAT
1 AAAATAATTAAATA-TTATTAAATAAA-AAATTAT
**
4800949 AAAATAATTAAATATTATTTTATAAAAAATTAT
1 AAAATAATTAAATATTATTAAATAAAAAATTAT
4800982 AAA
1 AAA
4800985 GTATAAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 9 0.29
34 15 0.48
35 7 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAATAATTAAATATTATTAAATAAAAAATTAT
Found at i:4800959 original size:24 final size:22
Alignment explanation
Indices: 4800931--4800980 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
4800921 TTTAATACTT
4800931 ATTAAATAAATAATTTATAAAATA
1 ATTAAAT-AATAATTTATAAAA-A
* *
4800955 ATTAAATATTATTTTATAAAAA
1 ATTAAATAATAATTTATAAAAA
4800977 ATTA
1 ATTA
4800981 TAAAGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATAATAATTTATAAAAA
Found at i:4804950 original size:21 final size:20
Alignment explanation
Indices: 4804894--4804951 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
4804884 TGCTGAATCT
* *
4804894 GAAGTTGAGGACCCTGAACAT
1 GAAGTTGAGGA-CCTGAGCAA
*
4804915 GAAGTTGA--ACCTGAGGAA
1 GAAGTTGAGGACCTGAGCAA
4804933 GAAGTTGAGGATCCTGAGC
1 GAAGTTGAGGA-CCTGAGC
4804952 CGGAAGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 14 0.47
19 1 0.03
20 1 0.03
21 14 0.47
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.19
Consensus pattern (20 bp):
GAAGTTGAGGACCTGAGCAA
Found at i:4810705 original size:21 final size:22
Alignment explanation
Indices: 4810667--4810719 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
4810657 TCTAAAATTA
*
4810667 ATAAAGTATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
*
4810689 ATAAAATATTA-TTTTTAATAT
1 ATAAAATATTATTTTTTAAAAT
4810710 ATAAATATAT
1 ATAAA-ATAT
4810720 AAATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:4816259 original size:13 final size:13
Alignment explanation
Indices: 4816241--4816266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4816231 AAGAGGTAAC
4816241 TAAATAAATAAAA
1 TAAATAAATAAAA
4816254 TAAATAAATAAAA
1 TAAATAAATAAAA
4816267 GAGAATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:4824410 original size:18 final size:16
Alignment explanation
Indices: 4824384--4824431 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4824374 TATTTTTTAA
*
4824384 TTATTTATTTATATATTT
1 TTATATATTTATATA--T
*
4824402 TTATATATTTATGTAT
1 TTATATATTTATATAT
*
4824418 TTAAATATTTATAT
1 TTATATATTTATAT
4824432 TTAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATATATTTATATAT
Found at i:4825764 original size:11 final size:11
Alignment explanation
Indices: 4825748--4825780 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4825738 ATAATAAAAG
4825748 AAAAAATTATA
1 AAAAAATTATA
4825759 AAAAAATT-TA
1 AAAAAATTATA
*
4825769 CAAAAATTATA
1 AAAAAATTATA
4825780 A
1 A
4825781 GAAATGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:4825923 original size:22 final size:21
Alignment explanation
Indices: 4825896--4825937 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
4825886 AAGATAATCA
4825896 AAATATACTATAAAATGTTATC
1 AAATATACTATAAAA-GTTATC
*
4825918 AAATATATTATAAAAGTTAT
1 AAATATACTATAAAAGTTAT
4825938 AAAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATATACTATAAAAGTTATC
Found at i:4825990 original size:21 final size:21
Alignment explanation
Indices: 4825950--4826000 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4825940 AAAAATTTCA
*
4825950 AAAAATGTTATAAATGTTATC
1 AAAAATATTATAAATGTTATC
* *
4825971 AGAAATATTATAAA-GATTATT
1 AAAAATATTATAAATG-TTATC
4825992 AAAAATATT
1 AAAAATATT
4826001 GCAGAGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
AAAAATATTATAAATGTTATC
Found at i:4826142 original size:63 final size:64
Alignment explanation
Indices: 4826028--4826164 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 64
4826018 TACTACACAT
* * *
4826028 ATTA-AAAAATACTTAATATGTTATTAAAAATTAAAAAAATTATATTAAAAAAACGTTAC-AAAG
1 ATTATAAAAATAATTAATATGTTATTAAAAATTAAAAAAATTATA-TAAAAAAACGCTACAAAAA
* * * *
4826091 ATTATAAAAATAATTGA-ATGTTATTAAAAATATAACAAAAGTTATA-GAAAAAATGCTACAAAA
1 ATTATAAAAATAATTAATATGTTATTAAAAAT-TAA-AAAAATTATATAAAAAAACGCTACAAAA
4826154 A
64 A
4826155 ATTATAAAAA
1 ATTATAAAAA
4826165 AAAATTACAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 28 0.44
64 26 0.41
65 9 0.14
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (64 bp):
ATTATAAAAATAATTAATATGTTATTAAAAATTAAAAAAATTATATAAAAAAACGCTACAAAAA
Found at i:4828742 original size:21 final size:21
Alignment explanation
Indices: 4828700--4828742 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4828690 ATATATATTA
* *
4828700 AAATAAATTTTTATTCATTTT
1 AAATAAATGTTTATTAATTTT
4828721 AAATAAATGTTT-TTAATGTTT
1 AAATAAATGTTTATTAAT-TTT
4828742 A
1 A
4828743 TTTTTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
AAATAAATGTTTATTAATTTT
Found at i:4844928 original size:13 final size:13
Alignment explanation
Indices: 4844869--4844948 Score: 53
Period size: 13 Copynumber: 6.2 Consensus size: 13
4844859 TTATTTAATA
4844869 TAAATT-ATATTT
1 TAAATTAATATTT
*
4844881 T-AATT-ATA-TA
1 TAAATTAATATTT
4844891 TAAATATAATATTT
1 TAAAT-TAATATTT
4844905 TATTAAGTTAATATTT
1 TA--AA-TTAATATTT
* *
4844921 TAAATTAAAATAT
1 TAAATTAATATTT
4844934 TAAA-TAATAATTT
1 TAAATTAAT-ATTT
4844947 TA
1 TA
4844949 TTAAAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.04
11 10 0.19
12 5 0.09
13 19 0.35
14 5 0.09
16 12 0.22
17 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (13 bp):
TAAATTAATATTT
Found at i:4844977 original size:29 final size:31
Alignment explanation
Indices: 4844920--4844997 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
4844910 AGTTAATATT
* *
4844920 TTAAATTAAAATAT-TAAATAAT-AATTTTA
1 TTAAAATAAAATATATAAATAATAAATTTAA
*
4844949 TTAAAATAAAATATATAAA-ATTAAATTTAAA
1 TTAAAATAAAATATATAAATAATAAATTT-AA
*
4844980 TAAATAATAAAATATATA
1 TTAA-AATAAAATATATA
4844998 TTTTATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.37
30 9 0.22
31 4 0.10
32 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
TTAAAATAAAATATATAAATAATAAATTTAA
Found at i:4850206 original size:17 final size:18
Alignment explanation
Indices: 4850184--4850217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4850174 TCTCAATTAT
*
4850184 AAGA-TTAGTTTTTTAGG
1 AAGATTTAGTTTCTTAGG
4850201 AAGATTTAGTTTCTTAG
1 AAGATTTAGTTTCTTAG
4850218 TTTAACCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (18 bp):
AAGATTTAGTTTCTTAGG
Found at i:4873415 original size:5 final size:5
Alignment explanation
Indices: 4873405--4873433 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4873395 ATCTTGTTGA
4873405 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
4873434 AAAATAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:4880539 original size:22 final size:21
Alignment explanation
Indices: 4880497--4880540 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
4880487 ATTAAATTTC
*
4880497 AAATATAAATTATAAATTAAT
1 AAATATAAATCATAAATTAAT
4880518 AAATAATAAATCA-AAATATAAT
1 AAAT-ATAAATCATAAAT-TAAT
4880540 A
1 A
4880541 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATATAAATCATAAATTAAT
Found at i:4884682 original size:152 final size:153
Alignment explanation
Indices: 4884401--4884705 Score: 522
Period size: 152 Copynumber: 2.0 Consensus size: 153
4884391 ACCCCCTTAG
* *
4884401 CTGTTAATATATCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGTGAGTTAGGTGTGA
1 CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
* * *
4884466 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATTATGTGGGAAGCATAATTTTGAAACT
66 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
4884531 GAGTATTT-CCTAATGGTGTATA
131 GAGTATTTCCCTAATGGTGTATA
* * *
4884553 CTGTTAATATACCTTTTGGTCTGTTGATCAGGACTGTGTCCAGAATTGCAGCGAGTTAGTTGTGA
1 CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
*
4884618 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAATCAAAATTTTCAAACT
66 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
4884683 GAGTATTTCCCTAATGGTGTATA
131 GAGTATTTCCCTAATGGTGTATA
4884706 TTTGTCAATC
Statistics
Matches: 143, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
152 129 0.90
153 14 0.10
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.38
Consensus pattern (153 bp):
CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
GAGTATTTCCCTAATGGTGTATA
Found at i:4893489 original size:5 final size:5
Alignment explanation
Indices: 4893479--4893507 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4893469 ATCTTGTTGA
4893479 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
4893508 AAAATAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:4893850 original size:2 final size:2
Alignment explanation
Indices: 4893843--4893870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4893833 TAGTTGTCTA
4893843 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4893871 TTCTGCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4904789 original size:153 final size:153
Alignment explanation
Indices: 4904507--4904812 Score: 522
Period size: 153 Copynumber: 2.0 Consensus size: 153
4904497 ACCCCCTTAG
* *
4904507 CTGTTAATATATCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGTGAGTTAGGTGTGA
1 CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
* * *
4904572 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATTATGTGGGAAGCATAATTTTGAAACT
66 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
*
4904637 GAGTATTTTCCTAATGGTGTATA
131 GAGTATTTCCCTAATGGTGTATA
* * *
4904660 CTGTTAATATACCTTTTGGTCTGTTGATCAGGACTGTGTCCAGAATTGCAGCGAGTTAGTTGTGA
1 CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
*
4904725 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAATCAAAATTTTCAAACT
66 AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
4904790 GAGTATTTCCCTAATGGTGTATA
131 GAGTATTTCCCTAATGGTGTATA
4904813 TTTGTCAATC
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 143 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (153 bp):
CTGTTAATATACCTTTTGGTCTGTTGATCAGAACTGTGACCAGAATTGCAGCGAGTTAGGTGTGA
AGTTTATAGCATTGGTTGTGTGGATATGATGATTCTCATCATGTGGGAAGCAAAATTTTCAAACT
GAGTATTTCCCTAATGGTGTATA
Found at i:4913032 original size:2 final size:2
Alignment explanation
Indices: 4913025--4913058 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4913015 CTTTTTAGGA
4913025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4913059 CATCCCCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4914102 original size:25 final size:24
Alignment explanation
Indices: 4914022--4914165 Score: 114
Period size: 24 Copynumber: 6.0 Consensus size: 24
4914012 AATACCATGC
* **
4914022 AAATATATTACTAAGTCACACAAAT
1 AAATATATTAATAA-TCATGCAAAT
4914047 -AATATATTAATAATCATGCAAAT
1 AAATATATTAATAATCATGCAAAT
*
4914070 AAGTATATTAATAA-CATGCAATCAT
1 AAATATATTAATAATCATGCAA--AT
* *
4914095 AAATATATTAAGTAATTATTCAAAT
1 AAATATATTAA-TAATCATGCAAAT
* * * *
4914120 AAATATA-AAATAACCATACAAGT
1 AAATATATTAATAATCATGCAAAT
* **
4914143 AAATATAATAATTTTCATGCAAA
1 AAATATATTAATAATCATGCAAA
4914166 CATGCAATTA
Statistics
Matches: 95, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
23 31 0.33
24 35 0.37
25 21 0.22
26 3 0.03
27 5 0.05
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATATATTAATAATCATGCAAAT
Found at i:4914246 original size:85 final size:85
Alignment explanation
Indices: 4914157--4914334 Score: 259
Period size: 85 Copynumber: 2.1 Consensus size: 85
4914147 ATAATAATTT
** * *
4914157 TCATGCAAACATGCAATTAAATATATTATTATGCAAATAATAATATAAATCATGCAAATAAACAT
1 TCATGCAAACATGCAATTAAATATATTAACATGCAAATAATAATATAAATCATACAAACAAACAT
*
4914222 GTAATTAAA-TATATAAATAA
66 GCAATTAAATTA-ATAAATAA
* * *
4914242 TCATGCAAACATGTAATTAAATATATTAACATGCAAATAATAATATAAATTATACAAACAAACTT
1 TCATGCAAACATGCAATTAAATATATTAACATGCAAATAATAATATAAATCATACAAACAAACAT
*
4914307 GCAATTAAATTAATCAATAA
66 GCAATTAAATTAATAAATAA
4914327 TCATGCAA
1 TCATGCAA
4914335 TAATAAATAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 81 0.98
86 2 0.02
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (85 bp):
TCATGCAAACATGCAATTAAATATATTAACATGCAAATAATAATATAAATCATACAAACAAACAT
GCAATTAAATTAATAAATAA
Found at i:4914275 original size:28 final size:30
Alignment explanation
Indices: 4914216--4914278 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
4914206 TCATGCAAAT
4914216 AAACATGTAATTAAATATATAAATAATCATGC
1 AAACATGTAATTAAATATAT--ATAATCATGC
4914248 AAACATGTAATTAAATATAT-TAA-CATGC
1 AAACATGTAATTAAATATATATAATCATGC
4914276 AAA
1 AAA
4914279 TAATAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 8 0.26
29 3 0.10
32 20 0.65
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (30 bp):
AAACATGTAATTAAATATATATAATCATGC
Found at i:4915530 original size:12 final size:12
Alignment explanation
Indices: 4915515--4915580 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 12
4915505 TTTTTTTCAG
*
4915515 AAAACTAAAAGTA
1 AAAACTAAAA-TC
4915528 AAAAC-AAAATC
1 AAAACTAAAATC
*
4915539 AAAATTGAAAATC
1 AAAACT-AAAATC
*
4915552 AAAACTAAAATT
1 AAAACTAAAATC
*
4915564 AAAATTAAAAATC
1 AAAACT-AAAATC
4915577 AAAA
1 AAAA
4915581 TCAAAACTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 5 0.11
12 14 0.32
13 25 0.57
ACGTcount: A:0.70, C:0.09, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAACTAAAATC
Found at i:4915543 original size:6 final size:6
Alignment explanation
Indices: 4915527--4915591 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
4915517 AACTAAAAGT
* * * *
4915527 AAAAAC AAAATC AAAATTG AAAATC AAAA-C TAAAATT AAAATTA AAAATC
1 AAAATC AAAATC AAAA-TC AAAATC AAAATC -AAAATC AAAA-TC AAAATC
4915577 AAAATC AAAACTC AA
1 AAAATC AAAA-TC AA
4915592 TTAATAATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
5 1 0.02
6 33 0.69
7 14 0.29
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:4915549 original size:7 final size:6
Alignment explanation
Indices: 4915533--4915610 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
4915523 AAGTAAAAAC
* * * * *
4915533 AAAATC AAAATT GAAAATC AAAACT AAAATT AAAATT AAAAATC AAAATC
1 AAAATT AAAATT -AAAATT AAAATT AAAATT AAAATT -AAAATT AAAATT
* * *
4915583 AAAACT -CAATT AATAATC AAAATT AAAA
1 AAAATT AAAATT AA-AATT AAAATT AAAA
4915611 ATCAAGGTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
5 3 0.05
6 37 0.67
7 15 0.27
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.23
Consensus pattern (6 bp):
AAAATT
Found at i:4915549 original size:13 final size:12
Alignment explanation
Indices: 4915533--4915615 Score: 80
Period size: 13 Copynumber: 6.7 Consensus size: 12
4915523 AAGTAAAAAC
4915533 AAAATCAAAATT
1 AAAATCAAAATT
*
4915545 GAAAATCAAAACT
1 -AAAATCAAAATT
*
4915558 AAAATTAAAATT
1 AAAATCAAAATT
*
4915570 AAAAATCAAAATC
1 -AAAATCAAAATT
4915583 AAAACTC--AATT
1 AAAA-TCAAAATT
4915594 AATAATCAAAATT
1 AA-AATCAAAATT
4915607 AAAAATCAA
1 -AAAATCAA
4915616 GGTTCAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.12
12 16 0.28
13 33 0.57
14 2 0.03
ACGTcount: A:0.65, C:0.11, G:0.01, T:0.23
Consensus pattern (12 bp):
AAAATCAAAATT
Found at i:4915549 original size:25 final size:23
Alignment explanation
Indices: 4915515--4915591 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
4915505 TTTTTTTCAG
*
4915515 AAAACTAAAAGTAAAAACAAAATC
1 AAAATTAAAA-TAAAAACAAAATC
* *
4915539 AAAATTGAAAATCAAAACTAAAATT
1 AAAATT-AAAATAAAAAC-AAAATC
*
4915564 AAAATTAAAAATCAAAATCAAAACTC
1 AAAATT-AAAAT-AAAAACAAAA-TC
4915590 AA
1 AA
4915592 TTAATAATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 11 0.26
25 24 0.57
26 7 0.17
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.18
Consensus pattern (23 bp):
AAAATTAAAATAAAAACAAAATC
Found at i:4915561 original size:31 final size:30
Alignment explanation
Indices: 4915521--4915615 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
4915511 TCAGAAAACT
* *
4915521 AAAAGTAAAAACAAAATCAAAATTGAAAATC
1 AAAACTAAAAA-AAAATCAAAATTAAAAATC
* * * *
4915552 AAAACTAAAATTAAAATTAAAAATCAAAATC
1 AAAACTAAAA-AAAAATCAAAATTAAAAATC
** *
4915583 AAAACTCAATTAATAATCAAAATTAAAAATC
1 AAAACT-AAAAAAAAATCAAAATTAAAAATC
4915614 AA
1 AA
4915616 GGTTCAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.21
Consensus pattern (30 bp):
AAAACTAAAAAAAAATCAAAATTAAAAATC
Found at i:4915593 original size:24 final size:24
Alignment explanation
Indices: 4915566--4915615 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
4915556 CTAAAATTAA
*
4915566 AATTAAAAATCAAAATCAAAACTC
1 AATTAAAAATCAAAATCAAAAATC
* *
4915590 AATTAATAATCAAAATTAAAAATC
1 AATTAAAAATCAAAATCAAAAATC
4915614 AA
1 AA
4915616 GGTTCAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (24 bp):
AATTAAAAATCAAAATCAAAAATC
Found at i:4916575 original size:2 final size:2
Alignment explanation
Indices: 4916568--4916593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4916558 GTTTTTGGAG
4916568 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4916594 GCATTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4919004 original size:29 final size:29
Alignment explanation
Indices: 4918955--4919021 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
4918945 AAGTTTTTGA
4918955 ATTATTTT-ACTTTTAAATTAAATTAAATT
1 ATTATTTTAACTTTTAAATTAAA-TAAATT
*
4918984 ATTATTTTAACTTTT-ATTTAAATAAATT
1 ATTATTTTAACTTTTAAATTAAATAAATT
* *
4919012 TTTACTTTAA
1 ATTATTTTAA
4919022 AAAATTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 14 0.41
29 14 0.41
30 6 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTATTTTAACTTTTAAATTAAATAAATT
Found at i:4919026 original size:16 final size:16
Alignment explanation
Indices: 4918995--4919028 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4918985 TTATTTTAAC
4918995 TTTTATTTAAATAAAT
1 TTTTATTTAAATAAAT
4919011 TTTTACTTTAAA-AAAT
1 TTTTA-TTTAAATAAAT
4919027 TT
1 TT
4919029 ATTTGTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTATTTAAATAAAT
Found at i:4920867 original size:27 final size:27
Alignment explanation
Indices: 4920837--4920889 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4920827 AAGAGTTATT
4920837 TTTAATTTATAAAATT-AAATTTATATG
1 TTTAA-TTATAAAATTAAAATTTATATG
**
4920864 TTTAATTATAATTTTAAAATTTATAT
1 TTTAATTATAAAATTAAAATTTATAT
4920890 TAATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTAATTATAAAATTAAAATTTATATG
Found at i:4920899 original size:20 final size:17
Alignment explanation
Indices: 4920870--4920912 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4920860 TATGTTTAAT
*
4920870 TATAATT-TTAAAATTTA
1 TATAATTATTTAAA-TTA
4920887 TATTAATTATTTAAATTA
1 TA-TAATTATTTAAATTA
4920905 TATAATTA
1 TATAATTA
4920913 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATTATTTAAATTA
Found at i:4924016 original size:2 final size:2
Alignment explanation
Indices: 4924009--4924033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4923999 TTTAACGCAG
4924009 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4924034 GCTTTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4934653 original size:17 final size:18
Alignment explanation
Indices: 4934623--4934658 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4934613 GTTATTAAAC
*
4934623 TATTTTTATGATAAATAA
1 TATTTTTATAATAAATAA
4934641 TATTTTT-TAATAAATAA
1 TATTTTTATAATAAATAA
4934658 T
1 T
4934659 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTTTTATAATAAATAA
Found at i:4934746 original size:31 final size:34
Alignment explanation
Indices: 4934707--4934803 Score: 114
Period size: 33 Copynumber: 2.9 Consensus size: 34
4934697 TACAATTTTG
*
4934707 TTTATTTATTAATTTGTAATATAAAT-ATAAATT
1 TTTATTTATTAATTTATAATATAAATAATAAATT
*
4934740 TTT-TTATATTAATTTATTATATAAATAATAAA-T
1 TTTATT-TATTAATTTATAATATAAATAATAAATT
*
4934773 TTTATTTATT-ATTATATAATA-AATTAATAAA
1 TTTATTTATTAATT-TATAATATAAATAATAAA
4934804 ATTATTTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
32 14 0.25
33 35 0.62
34 7 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTATTTATTAATTTATAATATAAATAATAAATT
Found at i:4934751 original size:33 final size:36
Alignment explanation
Indices: 4934693--4934786 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 36
4934683 TTATTATTTT
* *
4934693 ATAATACAATTTTGTTTATTTATTAATTTGTAATATAA
1 ATAATA-AATTTTATTTA-TTATTAATTTATAATATAA
*
4934731 AT-ATAAATTTT-TTTA-TATTAATTTATTATATAA
1 ATAATAAATTTTATTTATTATTAATTTATAATATAA
4934764 ATAATAAATTTTATTTATTATTA
1 ATAATAAATTTTATTTATTATTA
4934787 TATAATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
33 18 0.35
34 9 0.18
35 8 0.16
36 11 0.22
37 3 0.06
38 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (36 bp):
ATAATAAATTTTATTTATTATTAATTTATAATATAA
Found at i:4935045 original size:13 final size:13
Alignment explanation
Indices: 4935027--4935056 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4935017 CAATATTGAT
4935027 ATTATTGTAAAAA
1 ATTATTGTAAAAA
*
4935040 ATTATTGTAATAA
1 ATTATTGTAAAAA
4935053 ATTA
1 ATTA
4935057 AAATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
ATTATTGTAAAAA
Found at i:4935101 original size:28 final size:30
Alignment explanation
Indices: 4935055--4935115 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
4935045 TGTAATAAAT
4935055 TAAAATATTTAAAAAATATGCATA-AAATAA
1 TAAAATATTTAAAAAATATG-ATATAAATAA
* *
4935085 TAAAA-ATTT-AAAGATATGATATTAATAA
1 TAAAATATTTAAAAAATATGATATAAATAA
4935113 TAA
1 TAA
4935116 CATTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 16 0.57
29 4 0.14
30 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAAATATTTAAAAAATATGATATAAATAA
Found at i:4937809 original size:32 final size:32
Alignment explanation
Indices: 4937768--4937829 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
4937758 TGCATTTCAA
4937768 GCACTAAATGGATTAAAATCGTCCCACTTTGT
1 GCACTAAATGGATTAAAATCGTCCCACTTTGT
*
4937800 GCACTAAATGGATTAAAATCTTCCCACTTT
1 GCACTAAATGGATTAAAATCGTCCCACTTT
4937830 ATGTCACCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (32 bp):
GCACTAAATGGATTAAAATCGTCCCACTTTGT
Found at i:4943196 original size:2 final size:2
Alignment explanation
Indices: 4943189--4943220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4943179 CTGTTGAGAA
4943189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4943221 TGAGCAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4946512 original size:2 final size:2
Alignment explanation
Indices: 4946507--4946531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4946497 AAAGAGAGAG
4946507 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4946532 AAGAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4947227 original size:16 final size:16
Alignment explanation
Indices: 4947206--4947238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4947196 TCAAATTTTT
4947206 TATTTAAAAATAAATA
1 TATTTAAAAATAAATA
*
4947222 TATTTAAAAATATATA
1 TATTTAAAAATAAATA
4947238 T
1 T
4947239 TGAATTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTTAAAAATAAATA
Found at i:4947319 original size:23 final size:21
Alignment explanation
Indices: 4947273--4947324 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
4947263 AATCATGTAC
**
4947273 AAAATAAATATCCAATATTTA
1 AAAATAAATATCCAATATCCA
4947294 AAAATATAATTATCCAATATCC-
1 AAAATA-AA-TATCCAATATCCA
4947316 AAAATAAAT
1 AAAATAAAT
4947325 CAAACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 8 0.30
23 10 0.37
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAAATATCCAATATCCA
Found at i:4950594 original size:13 final size:13
Alignment explanation
Indices: 4950576--4950602 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4950566 AGTTCTGCAG
4950576 GCAAAGGCAAGCT
1 GCAAAGGCAAGCT
4950589 GCAAAGGCAAGCT
1 GCAAAGGCAAGCT
4950602 G
1 G
4950603 AACTGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.33, T:0.07
Consensus pattern (13 bp):
GCAAAGGCAAGCT
Found at i:4955060 original size:22 final size:23
Alignment explanation
Indices: 4955034--4955081 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
4955024 CTGTATATTT
*
4955034 ATATTTGTATCTCTAAAATTA-A
1 ATATTTGTATCCCTAAAATTAGA
4955056 ATATTTGTATCCCTAAAATTAGA
1 ATATTTGTATCCCTAAAATTAGA
4955079 ATA
1 ATA
4955082 GACAATTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATTTGTATCCCTAAAATTAGA
Found at i:4957164 original size:21 final size:21
Alignment explanation
Indices: 4957138--4957179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4957128 AATTCTTTCT
4957138 TTAAAATCCAAA-AAAGGGAAG
1 TTAAAAT-CAAAGAAAGGGAAG
*
4957159 TTAAAATCAAAGAAAGTGAAG
1 TTAAAATCAAAGAAAGGGAAG
4957180 AAAGGAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (21 bp):
TTAAAATCAAAGAAAGGGAAG
Found at i:4957912 original size:25 final size:25
Alignment explanation
Indices: 4957884--4957939 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
4957874 CTGATAAAAA
*
4957884 TCAAACATTACTACTTGTTTTTATT
1 TCAAACATTACAACTTGTTTTTATT
*
4957909 TCAAAATATTACAACTTGTTTTTATT
1 TC-AAACATTACAACTTGTTTTTATT
4957935 TCAAA
1 TCAAA
4957940 ATATTAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (25 bp):
TCAAACATTACAACTTGTTTTTATT
Found at i:4957920 original size:26 final size:26
Alignment explanation
Indices: 4957890--4957945 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
4957880 AAAATCAAAC
*
4957890 ATTACTACTTGTTTTTATTTCAAAAT
1 ATTACAACTTGTTTTTATTTCAAAAT
4957916 ATTACAACTTGTTTTTATTTCAAAAT
1 ATTACAACTTGTTTTTATTTCAAAAT
4957942 ATTA
1 ATTA
4957946 AGGAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTACAACTTGTTTTTATTTCAAAAT
Found at i:4962136 original size:61 final size:60
Alignment explanation
Indices: 4962024--4962183 Score: 216
Period size: 61 Copynumber: 2.6 Consensus size: 60
4962014 TTTTGTACAA
* * *
4962024 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTGATAATTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTGATAATTTTTAATTTCAAG
* *
4962084 AAAAATTGGTACTTCCAACTTTTTCTTAAAATGATTTTTTTGGTGA-AA-TTTTAATTTCAAG
1 AAAAATTGATACTTTCAACTTTTTCTTAAAAT-ATTTTTTT--TGATAATTTTTAATTTCAAG
* *
4962145 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTT
1 AAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTT
4962184 GACAAAAATT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
60 35 0.40
61 48 0.55
62 2 0.02
63 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.49
Consensus pattern (60 bp):
AAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTGATAATTTTTAATTTCAAG
Found at i:4962222 original size:72 final size:74
Alignment explanation
Indices: 4962129--4962320 Score: 291
Period size: 72 Copynumber: 2.6 Consensus size: 74
4962119 TTTTTTGGTG
* *
4962129 AAATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTG-ACAAAAA-
1 AAATTTTACTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAAAAAAT
4962192 TTATTTTAA
66 TTATTTTAA
4962201 AAATTTTACTTTCAAGAAAAATTGATACTTTCAAC-TTTTCTCTAAAATACTTTTTGAAAAAAAA
1 AAATTTTACTTTCAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATACTTTTTG-AAAAAAA
* *
4962265 ATTTGTTTTAG
64 ATTTATTTTAA
* *
4962276 AAATTTTACTTTTAAAAAAAATTGATACTTTCAACTTTTTCTCAA
1 AAATTTTACTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAA
4962321 TTTTTTTTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
71 7 0.06
72 47 0.43
74 6 0.06
75 42 0.39
76 7 0.06
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (74 bp):
AAATTTTACTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAAAAAAT
TTATTTTAA
Found at i:4962390 original size:58 final size:58
Alignment explanation
Indices: 4962260--4962537 Score: 204
Period size: 58 Copynumber: 4.7 Consensus size: 58
4962250 CTTTTTGAAA
* * * * * *
4962260 AAAAAATTTGTTTTAGAAATTTTACTTTTAAAAAAAATTGATACTTTCAACTTTTTCT
1 AAAAAATATATTTTTGAAATTTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCT
* *** * *
4962318 CAATTTTTTTTTTTTGAAATTTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCCT
1 AAAAAATATATTTTTGAAATTTTAATTTTAAGAAAAATTGATACTTTCAACTTTT-CCT
* * * **
4962377 -AAAAATATATTTTTTAAACCTTTTTATTTTCAAGAGAAATTGATACTTTCAACTTTTTGT
1 AAAAAATATATTTTTGAAA--TTTTAATTTT-AAGAAAAATTGATACTTTCAACTTTTCCT
* * * * *
4962437 -AAAAATAT-TTTTTAAAACTTTTTTTATTTTCAA-AAAAATTGATATTTTTAACTTTCCCTT
1 AAAAAATATATTTTTGAAA---TTTTAATTTT-AAGAAAAATTGATACTTTCAACTTTTCC-T
* *
4962497 AAAAATATATATATTTTTGAAACTTTAATTTTAAGGAAAAT
1 -AAAA-A-ATATATTTTTGAAATTTTAATTTTAAGAAAAAT
4962538 AAAAAAAATA
Statistics
Matches: 176, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
58 59 0.34
59 29 0.16
60 32 0.18
61 27 0.15
62 16 0.09
63 1 0.01
64 4 0.02
65 8 0.05
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (58 bp):
AAAAAATATATTTTTGAAATTTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCT
Found at i:4962500 original size:60 final size:61
Alignment explanation
Indices: 4962337--4962506 Score: 208
Period size: 60 Copynumber: 2.8 Consensus size: 61
4962327 TTTTTTGAAA
* *
4962337 TTTTAATTTT-AAGAAAAATTGATACTTTCAACTTTTCCC-TAAAAATATATTTTTTAAACC
1 TTTTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTCCCTTAAAAATATATTTTTAAAACC
* * *
4962397 TTTTTATTTTCAAGAGAAATTGATACTTTCAACTTT--TTGTAAAAATAT-TTTTTAAAACTT
1 TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCT-TAAAAATATATTTTTAAAAC-C
* *
4962457 TTTTTATTTTCAA-AAAAATTGATATTTTTAACTTTCCCTTAAAAATATAT
1 TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATAT
4962507 ATATTTTTGA
Statistics
Matches: 94, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
59 28 0.30
60 43 0.46
61 23 0.24
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (61 bp):
TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATATTTTTAAAACC
Found at i:4963410 original size:3 final size:3
Alignment explanation
Indices: 4963402--4963558 Score: 214
Period size: 3 Copynumber: 53.7 Consensus size: 3
4963392 AATCAATCAA
4963402 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * *
4963450 AAT AA- ACG AA- AAA AAC AAT AAT AAT AA- AAT AAT GAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
4963495 AA- AAT AAA AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4963542 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
4963559 AATGGGCCCA
Statistics
Matches: 139, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
2 7 0.05
3 132 0.95
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:4963761 original size:29 final size:29
Alignment explanation
Indices: 4963716--4963772 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4963706 TTAACTCGAC
4963716 TTTTTTTTTTACCTTTT-TTTATTTTGTTG
1 TTTTTTTTTTACCTTTTATTT-TTTTGTTG
*
4963745 TTTTTGTTTTTA-TTTTTATTTTTTTGTT
1 TTTTT-TTTTTACCTTTTATTTTTTTGTT
4963773 AAGATTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.82
Consensus pattern (29 bp):
TTTTTTTTTTACCTTTTATTTTTTTGTTG
Found at i:4963860 original size:44 final size:44
Alignment explanation
Indices: 4963814--4963962 Score: 172
Period size: 46 Copynumber: 3.3 Consensus size: 44
4963804 GCTTAATAAC
*
4963814 TTTGAAAAAATAAACAAAGTTCCTCTAATAAGAGGCTCAACGACT
1 TTTGAAAAAATAAACAAAGCTCCTCTAA-AAGAGGCTCAACGACT
* * * * *
4963859 TTTGAGAAAAATAAATAAAGCTCCTATAAACAGAAGCTCCACAACT
1 TTTGA-AAAAATAAACAAAGCTCCTCTAAA-AGAGGCTCAACGACT
* ** *
4963905 TTTAAAAAAATAAACAAAGCTCCTCTAGCAGAGACTCAACGACT
1 TTTGAAAAAATAAACAAAGCTCCTCTAAAAGAGGCTCAACGACT
*
4963949 TTTGAAGAAATAAA
1 TTTGAAAAAATAAA
4963963 TGCTATTTTA
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
44 23 0.27
45 26 0.31
46 36 0.42
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (44 bp):
TTTGAAAAAATAAACAAAGCTCCTCTAAAAGAGGCTCAACGACT
Found at i:4964004 original size:86 final size:88
Alignment explanation
Indices: 4963811--4964004 Score: 232
Period size: 86 Copynumber: 2.2 Consensus size: 88
4963801 GAGGCTTAAT
* * * *
4963811 AACTTTGAAAAAATAAACAAAGTTCCTCTAATAAGAGGCTCAACGACTTTTGAGAAAAATAAATA
1 AACTTTTAAAAAATAAACAAAGCTCCTCTAAGAAGAGACTCAACGACTTTTGAGAAAAATAAAT-
*
4963876 AAGCTCCTATAAACAGAAGCTCCAC
65 -AGCTACTATAAACAGAAGCTCCAC
* *
4963901 AACTTTTAAAAAAATAAACAAAGCTCCTCT-AGCAGAGACTCAACGACTTTTGA-AGAAATAAAT
1 AACTTTT-AAAAAATAAACAAAGCTCCTCTAAGAAGAGACTCAACGACTTTTGAGAAAAATAAAT
* * * *
4963964 -GCTATTTTAAACAGAGGCTCTAC
65 AGCTACTATAAACAGAAGCTCCAC
4963987 AACTTTTAAGAAAATAAA
1 AACTTTTAA-AAAATAAA
4964005 TGTTCCTCTA
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 2 0.02
86 33 0.36
89 9 0.10
90 26 0.29
91 21 0.23
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (88 bp):
AACTTTTAAAAAATAAACAAAGCTCCTCTAAGAAGAGACTCAACGACTTTTGAGAAAAATAAATA
GCTACTATAAACAGAAGCTCCAC
Found at i:4964017 original size:42 final size:42
Alignment explanation
Indices: 4963834--4964023 Score: 143
Period size: 42 Copynumber: 4.4 Consensus size: 42
4963824 TAAACAAAGT
* *
4963834 TCCTCTAATA-AGAGGCTCAACGACTTTTGAGAAAAATAAATAAAGC
1 TCCTCTAA-ACAGAGGCTCAACAACTTTTAAG-AAAATAAAT---GC
* * * * *
4963880 TCCTATAAACAGAAGCTCCACAACTTTTAAAAAAATAAACAAAGC
1 TCCTCTAAACAGAGGCTCAACAACTTTTAAGAAAAT--A-AATGC
* * *
4963925 TCCTCT-AGCAGAGACTCAACGACTTTTGAAG-AAATAAATGC
1 TCCTCTAAACAGAGGCTCAACAACTTTT-AAGAAAATAAATGC
** * * *
4963966 TATTTTAAACAGAGGCTCTACAACTTTTAAGAAAATAAATGT
1 TCCTCTAAACAGAGGCTCAACAACTTTTAAGAAAATAAATGC
4964008 TCCTCTAAACAGAGGC
1 TCCTCTAAACAGAGGC
4964024 AACCACGACT
Statistics
Matches: 111, Mismatches: 26, Indels: 18
0.72 0.17 0.12
Matches are distributed among these distances:
41 10 0.09
42 40 0.36
44 20 0.18
45 15 0.14
46 23 0.21
47 1 0.01
48 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (42 bp):
TCCTCTAAACAGAGGCTCAACAACTTTTAAGAAAATAAATGC
Found at i:4964056 original size:42 final size:42
Alignment explanation
Indices: 4963997--4964217 Score: 229
Period size: 42 Copynumber: 5.2 Consensus size: 42
4963987 AACTTTTAAG
4963997 AAAATAAA-TG-TTCCTCTAAACAGAGGCAACCACGACTTTGA
1 AAAATAAATTGCTT-CTCTAAACAGAGGCAACCACGACTTTGA
* *
4964038 AAAATAAATTGCTTCTCTAAACATAGGCAACTACGACTTTGA
1 AAAATAAATTGCTTCTCTAAACAGAGGCAACCACGACTTTGA
* *
4964080 AAAATAAATTAC-TCATCTAAACAG-GGACAACCATGACTTTAGA
1 AAAATAAATTGCTTC-TCTAAACAGAGG-CAACCACGACTTT-GA
* * * *
4964123 AAAATAAATTGC-TCTTTTAAATAGAGGTAACTACGACTTTTGGA
1 AAAATAAATTGCTTC-TCTAAACAGAGGCAACCACGAC-TTT-GA
* * *
4964167 AAAATAAATTGCTCCTCTAAA-TGAAGGTAACCACGACTTTGA
1 AAAATAAATTGCTTCTCTAAACAG-AGGCAACCACGACTTTGA
4964209 AAAATAAAT
1 AAAATAAAT
4964218 GACTCATTGA
Statistics
Matches: 153, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
41 12 0.08
42 69 0.45
43 35 0.23
44 36 0.24
45 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (42 bp):
AAAATAAATTGCTTCTCTAAACAGAGGCAACCACGACTTTGA
Found at i:4964872 original size:22 final size:22
Alignment explanation
Indices: 4964847--4964902 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
4964837 TTCACACCTT
*
4964847 AAAGATTCTTATTTTAA-AACTC
1 AAAGATTCTCA-TTTAAGAACTC
4964869 AAAGATTCTCATTTAAGAACTC
1 AAAGATTCTCATTTAAGAACTC
*
4964891 AAAAATTCTCAT
1 AAAGATTCTCAT
4964903 CAAAATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAGATTCTCATTTAAGAACTC
Found at i:4966440 original size:9 final size:9
Alignment explanation
Indices: 4966428--4966457 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
4966418 ATGTATGTCA
4966428 TTTATTTTT
1 TTTATTTTT
4966437 TTTATTTTT
1 TTTATTTTT
4966446 TTTCATTTTT
1 TTT-ATTTTT
4966456 TT
1 TT
4966458 AAAGCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:4966789 original size:351 final size:351
Alignment explanation
Indices: 4966103--4966798 Score: 1214
Period size: 351 Copynumber: 2.0 Consensus size: 351
4966093 CCACATCAAA
*
4966103 TTTTAAAGCAATAAAGCATGATTCTGTCATTCCATTATAAGGATGCCTTAGCCCAACATATGATT
1 TTTTAAAGCAACAAAGCATGATTCTGTCATTCCATTATAAGGATGCCTTAGCCCAACATATGATT
* **
4966168 ATTCAATTTGAGCATTCACATTTGATCCAAATGGACTTTAAAAGTTGTAATGTAGACCATAGTAA
66 ATTCAATTCGAGCATTCACATTTGATCCAAATAAACTTTAAAAGTTGTAATGTAGACCATAGTAA
* *
4966233 GGGGTCATAAAAGAAATAGATAAAATAAGCTCAAAACCTATGTTTAAAGGGTTTAAAACCAAAAG
131 AGGGTCATAAAAGAAACAGATAAAATAAGCTCAAAACCTATGTTTAAAGGGTTTAAAACCAAAAG
*
4966298 ATCACTTGTTATCATTTGAAACAACTTAGCATTTTACCCCTTTCCACTTCATTTCACTTTATTTT
196 ATCACTTGTTATCATTTGAAACAACTTAGCATTTTACCCCTTTCCACTTCATTTCACTTCATTTT
* *
4966363 CCCTTTTTTCATCTCATTCCTTATAAAAAAAACTCTCATTACTTTACCCCAAATCATGTATGTCA
261 CCCTTTTTTCATCTCATTCCTCATAAAAAAAACTCTCATTACTTTACCCCAAATCATGTACGTCA
* *
4966428 TTTATTTTTTTTATTTTTTTTCATTT
326 TTTATTTTTTTCATATTTTTTCATTT
*
4966454 TTTTAAAGCAACAAAGCATGATTCTGTCGTTCCATTATAAGGATGCCTTAGCCCAACATATGATT
1 TTTTAAAGCAACAAAGCATGATTCTGTCATTCCATTATAAGGATGCCTTAGCCCAACATATGATT
*
4966519 ATTCAATTCGAGCATTCACATTTGATCCAAATAAACTTTAAAGGTTGTAATGTAGACCATAGTAA
66 ATTCAATTCGAGCATTCACATTTGATCCAAATAAACTTTAAAAGTTGTAATGTAGACCATAGTAA
*
4966584 AGGGTCATAAAAGAAACAGATAAAATAAGCTCAAAACCTATGTTTAAAGGGTTTAAAACCAAAGG
131 AGGGTCATAAAAGAAACAGATAAAATAAGCTCAAAACCTATGTTTAAAGGGTTTAAAACCAAAAG
* *
4966649 ATCACTTGTTATCATTTGAAACAACTTGGCATTTTACCCCTTTCCATTTCATTTCACTTCATTTT
196 ATCACTTGTTATCATTTGAAACAACTTAGCATTTTACCCCTTTCCACTTCATTTCACTTCATTTT
* *
4966714 CCCTTTTTTCATCTCATTCCTCA-CAAAAAGACTCTCATTACTTTACCCCAAATCATGTACGTCA
261 CCCTTTTTTCATCTCATTCCTCATAAAAAAAACTCTCATTACTTTACCCCAAATCATGTACGTCA
4966778 TTTATTTTTTTTCATATTTTT
326 TTTA-TTTTTTTCATATTTTT
4966799 AAAGAATTTT
Statistics
Matches: 326, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
350 42 0.13
351 284 0.87
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (351 bp):
TTTTAAAGCAACAAAGCATGATTCTGTCATTCCATTATAAGGATGCCTTAGCCCAACATATGATT
ATTCAATTCGAGCATTCACATTTGATCCAAATAAACTTTAAAAGTTGTAATGTAGACCATAGTAA
AGGGTCATAAAAGAAACAGATAAAATAAGCTCAAAACCTATGTTTAAAGGGTTTAAAACCAAAAG
ATCACTTGTTATCATTTGAAACAACTTAGCATTTTACCCCTTTCCACTTCATTTCACTTCATTTT
CCCTTTTTTCATCTCATTCCTCATAAAAAAAACTCTCATTACTTTACCCCAAATCATGTACGTCA
TTTATTTTTTTCATATTTTTTCATTT
Found at i:4969737 original size:19 final size:19
Alignment explanation
Indices: 4969715--4969751 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4969705 CTACGAAGGC
4969715 ATTAAAACCTCACGAAAGT
1 ATTAAAACCTCACGAAAGT
*
4969734 ATTAAAACCTCATGAAAG
1 ATTAAAACCTCACGAAAG
4969752 CAATAGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.22
Consensus pattern (19 bp):
ATTAAAACCTCACGAAAGT
Found at i:4970744 original size:59 final size:56
Alignment explanation
Indices: 4970488--4970761 Score: 280
Period size: 60 Copynumber: 4.7 Consensus size: 56
4970478 ACTTTTGTAC
* * * *
4970488 AAGAAAAATTGATACTTTCAAATTTTTCTTAAAATATTTTTCTTGATAATTTTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTAAAAATA-TTTT-TT-AAAATTTTTA-TTTT
* * * *
4970548 AATAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTTAAAA-TTTTAATTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTAAAAATA-TTTTTTAAAATTTTTATTTT
* *
4970604 AAAAAAAATTGATACTTTCAACTTTTTCCTAAAAATATATTTTTTAAACTTTTTTATTTT
1 AAGAAAAATTGATACTTTCAAC-TTTTCCT-AAAA-ATATTTTTTAAA-ATTTTTATTTT
** *
4970664 CAAGGGATATTGATACTTTCAACTTTTCCTAAAAATATTTTTTAAAACCTCTTTTATTTT
1 -AAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTAAAA--T-TTTTATTTT
* *
4970724 CAGAAAAATTGATACTTTCAACTTCTCCTTAAAAATAT
1 AAGAAAAATTGATACTTTCAACTTTTCC-TAAAAATAT
4970762 ATATTTTTTG
Statistics
Matches: 184, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
56 24 0.13
57 11 0.06
58 27 0.15
59 33 0.18
60 71 0.39
61 18 0.10
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (56 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTAAAATTTTTATTTT
Found at i:4970880 original size:4 final size:4
Alignment explanation
Indices: 4970871--4970912 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
4970861 TAATAATAAT
4970871 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
4970913 ACCTTAAGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:4971696 original size:17 final size:16
Alignment explanation
Indices: 4971679--4971783 Score: 76
Period size: 17 Copynumber: 6.4 Consensus size: 16
4971669 TAAAATCAAT
4971679 AAAAATAATAATATAA
1 AAAAATAATAATATAA
*
4971695 TAGCAAATAAT-A-AT-A
1 -A-AAAATAATAATATAA
4971710 AAAAATAATAA-ATGAA
1 AAAAATAATAATAT-AA
*
4971726 AAAAA-ACAGTAATAAAA
1 AAAAATA-A-TAATATAA
*
4971743 AAATAATGATAATATAA
1 AAA-AATAATAATATAA
4971760 ATAAAATAATAATAATAA
1 A-AAAATAATAAT-ATAA
4971778 AAAAAT
1 AAAAAT
4971784 GGACTAATCT
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
13 7 0.10
14 4 0.06
15 2 0.03
16 9 0.13
17 31 0.44
18 18 0.25
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (16 bp):
AAAAATAATAATATAA
Found at i:4971709 original size:13 final size:13
Alignment explanation
Indices: 4971699--4971781 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
4971689 ATATAATAGC
4971699 AAATAATAATAAA
1 AAATAATAATAAA
4971712 AAATAATAAATGAAA
1 AAATAAT-AAT-AAA
*
4971727 AAAAACAGTAAT-AA
1 AAATA-A-TAATAAA
*
4971741 AAA-AATAAT-GA
1 AAATAATAATAAA
*
4971752 TAAT-ATAAATAAA
1 AAATAAT-AATAAA
4971765 ATAATAATAATAAA
1 A-AATAATAATAAA
4971779 AAA
1 AAA
4971782 ATGGACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
11 9 0.16
12 4 0.07
13 11 0.20
14 18 0.32
15 9 0.16
16 4 0.07
17 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (13 bp):
AAATAATAATAAA
Found at i:4971768 original size:14 final size:14
Alignment explanation
Indices: 4971668--4971777 Score: 61
Period size: 15 Copynumber: 7.6 Consensus size: 14
4971658 TCAAGAAAAG
4971668 ATAAAATCAATAA-A
1 ATAAAAT-AATAATA
*
4971682 A-ATAATAAT-ATA
1 ATAAAATAATAATA
4971694 ATAGCAAATAATAATA
1 ATA--AAATAATAATA
4971710 A-AAAATAATAAATGA
1 ATAAAATAAT-AAT-A
*
4971725 A-AAAAAACAGTAATA
1 ATAAAATA-A-TAATA
* *
4971740 AAAAAATAATGATA
1 ATAAAATAATAATA
4971754 ATATAAATAA-AATA
1 ATA-AAATAATAATA
4971768 ATAATAATAA
1 ATAA-AATAA
4971778 AAAAATGGAC
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
11 1 0.01
12 5 0.06
13 13 0.17
14 21 0.27
15 23 0.30
16 13 0.17
17 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.24
Consensus pattern (14 bp):
ATAAAATAATAATA
Found at i:4971887 original size:18 final size:18
Alignment explanation
Indices: 4971864--4971909 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
4971854 GGATTGACTT
4971864 TTGCAGGAAGGCAGGGAA
1 TTGCAGGAAGGCAGGGAA
4971882 TTGCAGGAAGGCAGGGAA
1 TTGCAGGAAGGCAGGGAA
4971900 TTGCAGGAAG
1 TTGCAGGAAG
4971910 ACACTGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.43, T:0.13
Consensus pattern (18 bp):
TTGCAGGAAGGCAGGGAA
Found at i:4973623 original size:2 final size:2
Alignment explanation
Indices: 4973616--4973643 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4973606 AGATAGAAGA
4973616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4973644 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4977328 original size:3 final size:3
Alignment explanation
Indices: 4977320--4977345 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4977310 AGAAAACAAG
4977320 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
4977346 CAAAGACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4985770 original size:22 final size:22
Alignment explanation
Indices: 4985745--4985792 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4985735 AAAATTTTTT
4985745 ATTAAAAATAATTAAA-TAAAAA
1 ATTAAAAATAA-TAAATTAAAAA
* *
4985767 ATTAAAATTAATAAATTAAAAG
1 ATTAAAAATAATAAATTAAAAA
4985789 ATTA
1 ATTA
4985793 TATTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
ATTAAAAATAATAAATTAAAAA
Found at i:5004222 original size:30 final size:31
Alignment explanation
Indices: 5004181--5004244 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5004171 AAAAATTAAA
*
5004181 TTAAATATAAATTAAAATTTTAA-AAC-TTAT
1 TTAAATATAAATTAAAA-GTTAATAACTTTAT
*
5004211 TTAAATGTAAATTAAAAGTTAATAACTTTAT
1 TTAAATATAAATTAAAAGTTAATAACTTTAT
5004242 TTA
1 TTA
5004245 GGTGTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 4 0.13
30 19 0.63
31 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
TTAAATATAAATTAAAAGTTAATAACTTTAT
Found at i:5004981 original size:16 final size:16
Alignment explanation
Indices: 5004947--5005016 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
5004937 ATTAAATAAG
5004947 TTCATGAAT-ACTATAAA
1 TTCATGAATAAC--TAAA
5004964 TTCATGAATAACTAAA
1 TTCATGAATAACTAAA
* * *
5004980 TTAATTAATAATTAAA
1 TTCATGAATAACTAAA
* * *
5004996 TTCATAAATAATTATA
1 TTCATGAATAACTAAA
5005012 TTCAT
1 TTCAT
5005017 ATAATTTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 35 0.76
17 9 0.20
18 2 0.04
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (16 bp):
TTCATGAATAACTAAA
Found at i:5005017 original size:16 final size:16
Alignment explanation
Indices: 5004960--5005017 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
5004950 ATGAATACTA
* *
5004960 TAAATTCATGAATAAC
1 TAAATTCATAAATAAT
* *
5004976 TAAATTAATTAATAAT
1 TAAATTCATAAATAAT
5004992 TAAATTCATAAATAAT
1 TAAATTCATAAATAAT
*
5005008 TATATTCATA
1 TAAATTCATA
5005018 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATTCATAAATAAT
Found at i:5035644 original size:10 final size:11
Alignment explanation
Indices: 5035619--5035646 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5035609 CCTACAACCA
5035619 TTTTTCTTCTC
1 TTTTTCTTCTC
5035630 TTTTTCTTCTC
1 TTTTTCTTCTC
5035641 TTTTTC
1 TTTTTC
5035647 ACTGAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:5045703 original size:2 final size:2
Alignment explanation
Indices: 5045696--5045722 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5045686 AAAATGAAAG
5045696 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5045723 CACGAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5052266 original size:20 final size:21
Alignment explanation
Indices: 5052198--5052269 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
5052188 CCCGAAATTA
5052198 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
5052219 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
5052240 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
5052261 AT-AAATATT
1 ATAAAATATT
5052270 TAAAAATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 7 0.14
21 44 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:5052278 original size:30 final size:30
Alignment explanation
Indices: 5052242--5052298 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5052232 TTTTAAATAT
* *
5052242 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATATTTA
*
5052272 AAAATATTATTATATAAATATATATAT
1 AAAATATTATTATATAAATATAAATAT
5052299 ATAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATATTTA
Found at i:5052323 original size:13 final size:13
Alignment explanation
Indices: 5052307--5052331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5052297 ATATAATAAA
5052307 AAATTAAAAAATT
1 AAATTAAAAAATT
5052320 AAATTAAAAAAT
1 AAATTAAAAAAT
5052332 ATATTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:5073724 original size:106 final size:109
Alignment explanation
Indices: 5073578--5073775 Score: 267
Period size: 106 Copynumber: 1.8 Consensus size: 109
5073568 GCAGTAATTC
* * * * **
5073578 CATAATAAATACTCGTTAAATCAAAAGCCATCAAGTCAAACGGAT-AAAAAAAATTAA-A-TGTC
1 CATAATAAATACTCATTAAATCAAAAGCCATAAAGGCAAACAGATGAAAAAAAAAAAAGAGTGTC
* *
5073640 AAATATTGTGCTTCTGTTCAAAGAAACACAATAATTGTTATAAT
66 AAATACTGCGCTTCTGTTCAAAGAAACACAATAATTGTTATAAT
* *
5073684 CATAATAAATGCTCATTAAATCAAAAGCTATAAAGGCAAACAGATGAAAAAAAAAAAAGAGTTGT
1 CATAATAAATACTCATTAAATCAAAAGCCATAAAGGCAAACAGATGAAAAAAAAAAAAGAG-TGT
*
5073749 CAAATACTGCGCTTTTGTTCAAAGAAA
65 CAAATACTGCGCTTCTGTTCAAAGAAA
5073776 TGCAATACGT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 39 0.51
107 10 0.13
108 1 0.01
110 27 0.35
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (109 bp):
CATAATAAATACTCATTAAATCAAAAGCCATAAAGGCAAACAGATGAAAAAAAAAAAAGAGTGTC
AAATACTGCGCTTCTGTTCAAAGAAACACAATAATTGTTATAAT
Found at i:5079059 original size:25 final size:26
Alignment explanation
Indices: 5079025--5079076 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
5079015 CCCGTTTTGG
5079025 AATTCTATTAAGACTGGTAG-GTATT
1 AATTCTATTAAGACTGGTAGTGTATT
*
5079050 AATTCTATTAAGACTTGTAGTGTATT
1 AATTCTATTAAGACTGGTAGTGTATT
5079076 A
1 A
5079077 TAGTGAAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (26 bp):
AATTCTATTAAGACTGGTAGTGTATT
Found at i:5085085 original size:49 final size:49
Alignment explanation
Indices: 5085010--5085107 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
5085000 GATAGACGAC
*
5085010 TAAAAGAAGTTGATTGGAAGCCTGATGAGGATGTAGAAGTAATGTGGGA
1 TAAAAGAAATTGATTGGAAGCCTGATGAGGATGTAGAAGTAATGTGGGA
*
5085059 TAAAAGAAATTGATTGGAAGCTTGATGAGGATGTAGAAGTAATGTGGGA
1 TAAAAGAAATTGATTGGAAGCCTGATGAGGATGTAGAAGTAATGTGGGA
5085108 AAATATTACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.03, G:0.34, T:0.26
Consensus pattern (49 bp):
TAAAAGAAATTGATTGGAAGCCTGATGAGGATGTAGAAGTAATGTGGGA
Found at i:5090885 original size:2 final size:2
Alignment explanation
Indices: 5090878--5090909 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5090868 TATGAAGTGG
5090878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5090910 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5096133 original size:16 final size:16
Alignment explanation
Indices: 5096095--5096134 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5096085 ATGTGCGGAA
5096095 TTTTTAA-TTAAATTT
1 TTTTTAATTTAAATTT
**
5096110 TTCATAATTTAAATTT
1 TTTTTAATTTAAATTT
5096126 TTTTTAATT
1 TTTTTAATT
5096135 ATTGATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAATTTAAATTT
Found at i:5097734 original size:2 final size:2
Alignment explanation
Indices: 5097729--5097756 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5097719 TGTTGTAATA
5097729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5097757 GATTACGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5109088 original size:12 final size:12
Alignment explanation
Indices: 5109071--5109095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5109061 ACGAATTGAA
5109071 TATTTCTTAGTT
1 TATTTCTTAGTT
5109083 TATTTCTTAGTT
1 TATTTCTTAGTT
5109095 T
1 T
5109096 TCAGGCAAGA
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTCTTAGTT
Found at i:5114095 original size:18 final size:17
Alignment explanation
Indices: 5114067--5114100 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5114057 CTTGCATCCA
*
5114067 GAAAGCATGATTTTGCT
1 GAAAGCATGATGTTGCT
5114084 GAAAGACATGATGTTGC
1 GAAAG-CATGATGTTGC
5114101 ATTATCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (17 bp):
GAAAGCATGATGTTGCT
Found at i:5116695 original size:20 final size:19
Alignment explanation
Indices: 5116660--5116702 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5116650 TGATTATATA
* *
5116660 TATTTAATAAATAAATTTT
1 TATTAAATAAATAAATTAT
5116679 TATTAAATAATATAAATTAT
1 TATTAAATAA-ATAAATTAT
5116699 TATT
1 TATT
5116703 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAAATAAATAAATTAT
Found at i:5116706 original size:22 final size:22
Alignment explanation
Indices: 5116652--5116716 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
5116642 TACATATATG
5116652 ATTATATATATTT-AATAA-ATAA
1 ATTAT-TAT-TTTAAATAATATAA
*
5116674 ATT-TT-TATTAAATAATATAA
1 ATTATTATTTTAAATAATATAA
5116694 ATTATTATTTTAAATTAAT-TAA
1 ATTATTATTTTAAA-TAATATAA
5116716 A
1 A
5116717 ATTAATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 8 0.22
21 3 0.08
22 13 0.36
23 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATTATTTTAAATAATATAA
Found at i:5121172 original size:17 final size:17
Alignment explanation
Indices: 5121143--5121176 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5121133 ATAATATTTT
5121143 TTTAGTTAAAATTAAAA
1 TTTAGTTAAAATTAAAA
5121160 TTTA-TTAATAATTAAAA
1 TTTAGTTAA-AATTAAAA
5121177 ATCTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAGTTAAAATTAAAA
Found at i:5125755 original size:2 final size:2
Alignment explanation
Indices: 5125748--5125777 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5125738 CACTTTTATG
*
5125748 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5125778 ATCACTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5140439 original size:2 final size:2
Alignment explanation
Indices: 5140434--5140458 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5140424 TAAATAGGGG
5140434 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5140459 TTTATTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5140961 original size:2 final size:2
Alignment explanation
Indices: 5140954--5140989 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5140944 AATGGAGATC
5140954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5140990 GATTCCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5145796 original size:18 final size:18
Alignment explanation
Indices: 5145775--5145813 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5145765 CGATGATGAT
*
5145775 GAAGATGATGAAGAAGAA
1 GAAGAAGATGAAGAAGAA
* *
5145793 GAAGAAGATGACGGAGAA
1 GAAGAAGATGAAGAAGAA
5145811 GAA
1 GAA
5145814 CCCGAATCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGATGAAGAAGAA
Found at i:5146254 original size:13 final size:13
Alignment explanation
Indices: 5146236--5146260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5146226 GGCCGATAAT
5146236 AAATTGGTTTCCC
1 AAATTGGTTTCCC
5146249 AAATTGGTTTCC
1 AAATTGGTTTCC
5146261 ACGTTGGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
AAATTGGTTTCCC
Found at i:5152782 original size:15 final size:14
Alignment explanation
Indices: 5152755--5152788 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
5152745 AAATATATAA
5152755 TAATTTTATTAATT
1 TAATTTTATTAATT
5152769 TAATTTTAATTAATT
1 TAATTTT-ATTAATT
5152784 TAATT
1 TAATT
5152789 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTTTATTAATT
Found at i:5159395 original size:52 final size:52
Alignment explanation
Indices: 5159317--5159469 Score: 220
Period size: 52 Copynumber: 2.9 Consensus size: 52
5159307 ATAACCATAC
* * *
5159317 AAACTTGCCTATTAAAAATCCA-TTTTCTCTTAGAATTCTTTTTCTGTAAATT
1 AAACTTACCTATTAAGAAT-CATTTTTCTCTTAAAATTCTTTTTCTGTAAATT
* *
5159369 AAACTTACCTATTAAGAATCATTTTTCTCTTAAAATTCTTTTCCTGCAAATT
1 AAACTTACCTATTAAGAATCATTTTTCTCTTAAAATTCTTTTTCTGTAAATT
*
5159421 AAACTTACCTATTAAGAATCATCTTTCTCTTAAAATTCTTCTTT-TGTAA
1 AAACTTACCTATTAAGAATCATTTTTCTCTTAAAATTCTT-TTTCTGTAA
5159470 GTCTTTTTGT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.96
53 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (52 bp):
AAACTTACCTATTAAGAATCATTTTTCTCTTAAAATTCTTTTTCTGTAAATT
Found at i:5159509 original size:21 final size:21
Alignment explanation
Indices: 5159483--5159533 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
5159473 TTTTTGTCCA
*
5159483 TCAAACAATGT-TAGGCAAATC
1 TCAAACAATGTCTA-ACAAATC
5159504 TCAAACAAATGTCTAACAAATC
1 TCAAAC-AATGTCTAACAAATC
*
5159526 CCAAACAA
1 TCAAACAA
5159534 ATCTCCTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.49, C:0.24, G:0.08, T:0.20
Consensus pattern (21 bp):
TCAAACAATGTCTAACAAATC
Found at i:5159532 original size:11 final size:11
Alignment explanation
Indices: 5159498--5159538 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5159488 CAATGTTAGG
5159498 CAAATCTCAAA
1 CAAATCTCAAA
* *
5159509 CAAATGTCTAA
1 CAAATCTCAAA
*
5159520 CAAATCCCAAA
1 CAAATCTCAAA
5159531 CAAATCTC
1 CAAATCTC
5159539 CTATGGGATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (11 bp):
CAAATCTCAAA
Found at i:5159964 original size:73 final size:73
Alignment explanation
Indices: 5159845--5159992 Score: 233
Period size: 73 Copynumber: 2.0 Consensus size: 73
5159835 TAAGGATCAC
* * * * *
5159845 CACAGCTCTGATATCATTTATTAGGCTAAAAGGCCTTAATCCAATCATACTAGCGGAAGCATAAT
1 CACAGCTCTGATATCACTTATTAGGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
5159910 CAAATAAT
66 CAAATAAT
* *
5159918 CACAGCTCTGATATCACTTGTTAGGCCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAAT
1 CACAGCTCTGATATCACTTATTAGGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
5159983 CAAATAAT
66 CAAATAAT
5159991 CA
1 CA
5159993 ATGAATCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (73 bp):
CACAGCTCTGATATCACTTATTAGGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
CAAATAAT
Found at i:5160710 original size:73 final size:73
Alignment explanation
Indices: 5160591--5160738 Score: 224
Period size: 73 Copynumber: 2.0 Consensus size: 73
5160581 TAAGGATCAC
* * * * *
5160591 CACAGCTCTGATATCATTTATTAAGCTAAAAGGCCTTAATCCAATCATACTAGCGGAAGCATAAT
1 CACAGCTCTGATATCACTTATTAAGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
5160656 CAAATAAT
66 CAAATAAT
* * *
5160664 CACAGCTCTGATATCACTTGTTAGGCCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAAT
1 CACAGCTCTGATATCACTTATTAAGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
5160729 CAAATAAT
66 CAAATAAT
5160737 CA
1 CA
5160739 ATGAATCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (73 bp):
CACAGCTCTGATATCACTTATTAAGCCAAAAGGCCCTAATCCAATCATACTAACAGAAGCATAAT
CAAATAAT
Found at i:5160919 original size:746 final size:746
Alignment explanation
Indices: 5159488--5160979 Score: 2795
Period size: 746 Copynumber: 2.0 Consensus size: 746
5159478 GTCCATCAAA
5159488 CAATGTTAGGCAAATCTCAAACAAATGTCTAACAAATCCCAAACAAATCTCCTATGGGATTTGAG
1 CAATGTTAGGCAAATCTCAAACAAATGTCTAACAAATCCCAAACAAATCTCCTATGGGATTTGAG
* *
5159553 TCATTATTCCTAATAATATCGACCTTGACTCAAATTCCATCAATCATTTATTTTTATGCTACACA
66 TCATTATTCCTAATAATATCGACCTTGACTCAAATTCCATCAATCATTTATCTTCATGCTACACA
* *
5159618 TGCTTGGCTCCACTTGCAATGGAAGTCTCACAATTATCTTTTCTTCTCTTATGTGTCTTCACGTT
131 TGCTTGGCTCCACTTGCAATGAAAGTCTCACAATTATCTTCTCTTCTCTTATGTGTCTTCACGTT
*
5159683 TTAAGCAAATCGATCCTCAATCCTCAAAACATGAACTCAAACTCTTCTATTGAATCATGCTCCTC
196 TTAAGCAAATCGATCCTCAATCCTCAAAACATGAACTCAAACTCTTCTATTGAATCACGCTCCTC
5159748 TAAGCTTGCATCTTCTCATGTCTCGAACCATGCTTTTCCCATCTCTTGAACCTTCGGCCCTTCTC
261 TAAGCTTGCATCTTCTCATGTCTCGAACCATGCTTTTCCCATCTCTTGAACCTTCGGCCCTTCTC
*
5159813 ACATAACTCTGATACAACTTGTTAAGGATCACCACAGCTCTGATATCATTTATTAGGCTAAAAGG
326 ACATAACTCTGATACAACTTGTTAAGGATCACCACAGCTCTGATATCATTTATTAAGCTAAAAGG
5159878 CCTTAATCCAATCATACTAGCGGAAGCATAATCAAATAATCACAGCTCTGATATCACTTGTTAGG
391 CCTTAATCCAATCATACTAGCGGAAGCATAATCAAATAATCACAGCTCTGATATCACTTGTTAGG
*
5159943 CCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAATCAAATAATCAATGAATCAAACACAT
456 CCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAATCAAATAATCAATGAATCAAACACAC
* * *
5160008 AAAAGATAATAATTTAACGTGGTTCGGTCCAACTGACCTACATCCACGGATAAGAAATAATATCC
521 AAAAGATAATAATTTAACGTGATTCGATCCAACTGACCTACATCCACGGATAAGAAACAATATCC
5160073 ACTAGTTGTAGAGAATTATAAACATACATCAAAATAATCTCACCCAACAACCCCGCCCCGTTATG
586 ACTAGTTGTAGAGAATTATAAACATACATCAAAATAATCTCACCCAACAACCCCGCCCCGTTATG
*
5160138 TTATGGAAGAATTGAACTTATTGCTGGGCTGGTTATTCAGAGCCAGCAATTGGCTGTCGGATTTC
651 TTATGGAAGAATTGAACTTATTGCTGGGCTGGTTATTCAGAGCCAGCAATTGGCTGCCGGATTTC
* *
5160203 ATCCCGTAAATAGAAGAAGATCGCTTTGGGG
716 ATCCCGCAAATAGAAGAAGATCGCTTCGGGG
* *
5160234 CAATGTTAGGCAAATCTCAAACAAATGTCTAACAAATCCCAAACAAATTTCTTATGGGATTTGAG
1 CAATGTTAGGCAAATCTCAAACAAATGTCTAACAAATCCCAAACAAATCTCCTATGGGATTTGAG
5160299 TCATTATTCCTAATAATATCGACCTTGACTCAAATTCCATCAATCATTTATCTTCATGCTACACA
66 TCATTATTCCTAATAATATCGACCTTGACTCAAATTCCATCAATCATTTATCTTCATGCTACACA
*
5160364 TGCTTGGCTCCACTTGCAATGAAAGTCTTACAATTATCTTCTCTTCTCTTATGTGTCTTCACGTT
131 TGCTTGGCTCCACTTGCAATGAAAGTCTCACAATTATCTTCTCTTCTCTTATGTGTCTTCACGTT
*
5160429 TTAAGCAAATCGATCCTCAATCCTCAAAACATGAACTCAAACTCTTCTCTTGAATCACGCTCCTC
196 TTAAGCAAATCGATCCTCAATCCTCAAAACATGAACTCAAACTCTTCTATTGAATCACGCTCCTC
5160494 TAAGCTTGCATCTTCTCATGTCTCGAACCATGCTTTTCCCATCTCTTGAACCTTCGGCCCTTCTC
261 TAAGCTTGCATCTTCTCATGTCTCGAACCATGCTTTTCCCATCTCTTGAACCTTCGGCCCTTCTC
5160559 ACATAACTCTGATACAACTTGTTAAGGATCACCACAGCTCTGATATCATTTATTAAGCTAAAAGG
326 ACATAACTCTGATACAACTTGTTAAGGATCACCACAGCTCTGATATCATTTATTAAGCTAAAAGG
5160624 CCTTAATCCAATCATACTAGCGGAAGCATAATCAAATAATCACAGCTCTGATATCACTTGTTAGG
391 CCTTAATCCAATCATACTAGCGGAAGCATAATCAAATAATCACAGCTCTGATATCACTTGTTAGG
*
5160689 CCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAATCAAATAATCAATGAATCAAATACAC
456 CCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAATCAAATAATCAATGAATCAAACACAC
* *
5160754 AAAAGATAATAATTTAACGTGATTCGATCTAACTGACTTACATCCACGGATAAGAAACAATATCC
521 AAAAGATAATAATTTAACGTGATTCGATCCAACTGACCTACATCCACGGATAAGAAACAATATCC
5160819 ACTAGTTGTAGAGAATTATAAACATACATCAAAATAATCTCACCCAACAACCCCGCCCCGTTATG
586 ACTAGTTGTAGAGAATTATAAACATACATCAAAATAATCTCACCCAACAACCCCGCCCCGTTATG
5160884 TTATGGAAGAATTGAACTTATTGCTGGGCTGGTTATTCAGAGCCAGCAATTGGCTGCCGGATTTC
651 TTATGGAAGAATTGAACTTATTGCTGGGCTGGTTATTCAGAGCCAGCAATTGGCTGCCGGATTTC
*
5160949 GTCCCGCAAATAGAAGAAGATCGCTTCGGGG
716 ATCCCGCAAATAGAAGAAGATCGCTTCGGGG
5160980 GTCACTGTGG
Statistics
Matches: 725, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
746 725 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (746 bp):
CAATGTTAGGCAAATCTCAAACAAATGTCTAACAAATCCCAAACAAATCTCCTATGGGATTTGAG
TCATTATTCCTAATAATATCGACCTTGACTCAAATTCCATCAATCATTTATCTTCATGCTACACA
TGCTTGGCTCCACTTGCAATGAAAGTCTCACAATTATCTTCTCTTCTCTTATGTGTCTTCACGTT
TTAAGCAAATCGATCCTCAATCCTCAAAACATGAACTCAAACTCTTCTATTGAATCACGCTCCTC
TAAGCTTGCATCTTCTCATGTCTCGAACCATGCTTTTCCCATCTCTTGAACCTTCGGCCCTTCTC
ACATAACTCTGATACAACTTGTTAAGGATCACCACAGCTCTGATATCATTTATTAAGCTAAAAGG
CCTTAATCCAATCATACTAGCGGAAGCATAATCAAATAATCACAGCTCTGATATCACTTGTTAGG
CCAAAATGCCCTAATCCAATCATACTAACAGAAGCATAATCAAATAATCAATGAATCAAACACAC
AAAAGATAATAATTTAACGTGATTCGATCCAACTGACCTACATCCACGGATAAGAAACAATATCC
ACTAGTTGTAGAGAATTATAAACATACATCAAAATAATCTCACCCAACAACCCCGCCCCGTTATG
TTATGGAAGAATTGAACTTATTGCTGGGCTGGTTATTCAGAGCCAGCAATTGGCTGCCGGATTTC
ATCCCGCAAATAGAAGAAGATCGCTTCGGGG
Found at i:5161435 original size:52 final size:49
Alignment explanation
Indices: 5161370--5161510 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 49
5161360 ACCATACAAT
* * *
5161370 CTTACCTAATAAGAATATCTTTCTTCTTAGAATTTTTCTTATGTAAATCAAA
1 CTTACCTATTAAGAAT-TCTTTCTTCTTAGAATTTTTCCTA--CAAATCAAA
*
5161422 CTTACCTATTAAGAATTCCTTTCCTCTTAGAATTCTTTTCCTACAAATCAAA
1 CTTACCTATTAAGAATT-CTTTCTTCTTAGAA-T-TTTTCCTACAAATCAAA
*
5161474 CTTACCTATTAAGAATTTTCTTTCTT-TTAAAATTTTT
1 CTTACCTATTAAGAA--TTCTTTCTTCTTAGAATTTTT
5161511 ATTTTACAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
50 4 0.05
51 2 0.03
52 56 0.72
53 7 0.09
54 9 0.12
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.46
Consensus pattern (49 bp):
CTTACCTATTAAGAATTCTTTCTTCTTAGAATTTTTCCTACAAATCAAA
Found at i:5161563 original size:11 final size:11
Alignment explanation
Indices: 5161547--5161585 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5161537 ATAATATATG
5161547 ATAAATTTCAA
1 ATAAATTTCAA
**
5161558 ATAAATTTTTA
1 ATAAATTTCAA
*
5161569 ATAAATATCAA
1 ATAAATTTCAA
5161580 ATAAAT
1 ATAAAT
5161586 CTTTTATGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAAATTTCAA
Found at i:5161574 original size:22 final size:23
Alignment explanation
Indices: 5161547--5161591 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5161537 ATAATATATG
*
5161547 ATAAATTTCAAATAAAT-TTTTA
1 ATAAATATCAAATAAATCTTTTA
5161569 ATAAATATCAAATAAATCTTTTA
1 ATAAATATCAAATAAATCTTTTA
5161592 TGAGATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAATATCAAATAAATCTTTTA
Found at i:5162504 original size:2 final size:2
Alignment explanation
Indices: 5162499--5162529 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5162489 AATTCTTTTT
5162499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5162530 GAATGTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5163104 original size:30 final size:29
Alignment explanation
Indices: 5163070--5163178 Score: 80
Period size: 30 Copynumber: 3.7 Consensus size: 29
5163060 TTTTGTTTGA
* *
5163070 AATAAAAATTTATTTTGATACAAATCAAAG
1 AATAAAAATTTATTTTAATA-AAATAAAAG
** * * *
5163100 AATAATGAGTTATTTTAATATAATAAAAT
1 AATAAAAATTTATTTTAATAAAATAAAAG
*
5163129 ATATAAAAATTTATTTT-A-AAAATAAAAT
1 A-ATAAAAATTTATTTTAATAAAATAAAAG
5163157 AATTCAAAAACTTT-TTTTAATA
1 AA-T-AAAAA-TTTATTTTAATA
5163179 TTTTAGTCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.02
28 11 0.18
29 17 0.27
30 32 0.52
31 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (29 bp):
AATAAAAATTTATTTTAATAAAATAAAAG
Found at i:5163175 original size:29 final size:30
Alignment explanation
Indices: 5163109--5163179 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
5163099 GAATAATGAG
5163109 TTATTTTAATATAATAAAATATATAAAAAT
1 TTATTTTAATATAATAAAATATATAAAAAT
5163139 TTATTTTAA-A-AATAAAATA-ATTCAAAAACT
1 TTATTTTAATATAATAAAATATA-T-AAAAA-T
5163169 TT-TTTTAATAT
1 TTATTTTAATAT
5163180 TTTAGTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 1 0.03
28 10 0.28
29 12 0.33
30 13 0.36
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATTTTAATATAATAAAATATATAAAAAT
Found at i:5164620 original size:17 final size:16
Alignment explanation
Indices: 5164579--5164622 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
5164569 AATAAATTCA
5164579 AAAAATAAAA-CATTT
1 AAAAATAAAATCATTT
*
5164594 AAAATTTAAAATCATTAT
1 AAAA-ATAAAATCATT-T
5164612 AAAAATAAAAT
1 AAAAATAAAAT
5164623 TATAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 10 0.42
18 5 0.21
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATAAAATCATTT
Found at i:5169465 original size:3 final size:3
Alignment explanation
Indices: 5169457--5169509 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
5169447 AACCATACAG
5169457 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5169505 AAT AA
1 AAT AA
5169510 AATGCTTATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5169630 original size:17 final size:19
Alignment explanation
Indices: 5169605--5169642 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
5169595 GATGTTGGAG
5169605 AATTATAAAAA-A-ATAAA
1 AATTATAAAAATATATAAA
*
5169622 AATTTTAAAAATATATAAA
1 AATTATAAAAATATATAAA
5169641 AA
1 AA
5169643 AGATACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTATAAAAATATATAAA
Found at i:5169655 original size:14 final size:16
Alignment explanation
Indices: 5169636--5169667 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5169626 TTAAAAATAT
5169636 ATAAAAAA-GAT-ACA
1 ATAAAAAATGATAACA
5169650 ATAAAAAATGATAACA
1 ATAAAAAATGATAACA
5169666 AT
1 AT
5169668 TAATAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
ATAAAAAATGATAACA
Done.