Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 68 of 204
Found at i:21551289 original size:29 final size:30
Alignment explanation
Indices: 21551230--21551287 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
21551220 TTCGAGCCTT
*
21551230 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
*
21551260 GGGGC-AAAATGGTAATTTTGAAAAAGTT
1 GGGGCAAAAAT-GTAATTATGAAAAAGTT
21551288 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:21551517 original size:13 final size:13
Alignment explanation
Indices: 21551499--21551530 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21551489 TTTCCAGCAA
21551499 TTATGAATTTATT
1 TTATGAATTTATT
21551512 TTATGAATTTATT
1 TTATGAATTTATT
*
21551525 TGATGA
1 TTATGA
21551531 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:21551705 original size:50 final size:50
Alignment explanation
Indices: 21551625--21551867 Score: 387
Period size: 50 Copynumber: 4.8 Consensus size: 50
21551615 ATTTGGGTAA
*
21551625 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
21551675 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
21551725 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * **
21551775 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGTCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
21551825 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21551868 TGTTATTATC
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 144 0.81
51 34 0.19
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:21557026 original size:2 final size:2
Alignment explanation
Indices: 21557019--21557049 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21557009 ATAAAGTAAA
21557019 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21557050 GTATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21557113 original size:3 final size:3
Alignment explanation
Indices: 21557092--21557147 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
21557082 TACATAAGCG
21557092 TAA TAA -AA TAA TAA CTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21557137 TAA TAA TAA TA
1 TAA TAA TAA TA
21557148 CAAAAAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:21557588 original size:22 final size:22
Alignment explanation
Indices: 21557560--21557712 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
21557550 TTTATTGTTC
*
21557560 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
21557582 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
21557604 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
21557626 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
21557648 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
21557670 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
21557692 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
21557713 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:21558256 original size:12 final size:12
Alignment explanation
Indices: 21558239--21558266 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21558229 TTGAAAATTG
21558239 GCTATTGGGCCT
1 GCTATTGGGCCT
21558251 GCTATTGGGCCT
1 GCTATTGGGCCT
21558263 GCTA
1 GCTA
21558267 GTGTTGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.32
Consensus pattern (12 bp):
GCTATTGGGCCT
Found at i:21558564 original size:13 final size:13
Alignment explanation
Indices: 21558546--21558570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21558536 GCTTGATTCG
21558546 ACTTAAAATATTA
1 ACTTAAAATATTA
21558559 ACTTAAAATATT
1 ACTTAAAATATT
21558571 GCTCAAGTCT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ACTTAAAATATTA
Found at i:21559193 original size:28 final size:29
Alignment explanation
Indices: 21559162--21559216 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
21559152 TTTTTTCTTT
*
21559162 TAAAAAAACATAAATT-TCAAAAAAAATG
1 TAAAAAAACAAAAATTGTCAAAAAAAATG
*
21559190 TAAAAATACAAAAATTGTCAAAAAAAA
1 TAAAAAAACAAAAATTGTCAAAAAAAA
21559217 ACCTCTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (29 bp):
TAAAAAAACAAAAATTGTCAAAAAAAATG
Found at i:21564236 original size:29 final size:29
Alignment explanation
Indices: 21564188--21564243 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
21564178 GTCGTACATA
** *
21564188 GTCTGGCACACGACTGTGTGTCACACACG
1 GTCTGGCACACGACCATGTGCCACACACG
21564217 GTCTGGCACACGACCATGTGCCACACA
1 GTCTGGCACACGACCATGTGCCACACA
21564244 TGGCCTACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (29 bp):
GTCTGGCACACGACCATGTGCCACACACG
Found at i:21569259 original size:23 final size:23
Alignment explanation
Indices: 21569233--21569277 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21569223 TGATTTTGAA
21569233 TATTATTTAACAAA-ATTTCTAAG
1 TATT-TTTAACAAATATTTCTAAG
* *
21569256 TATTTTTCATAAATATTTCTAA
1 TATTTTTAACAAATATTTCTAA
21569278 AAAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTTTAACAAATATTTCTAAG
Found at i:21573977 original size:12 final size:11
Alignment explanation
Indices: 21573960--21574008 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
21573950 CTTATTCTTT
21573960 AAAAAAACAGC
1 AAAAAAACAGC
21573971 AAAAAAA-AGC
1 AAAAAAACAGC
*
21573981 -AAAAAGC-GC
1 AAAAAAACAGC
*
21573990 AAAAAAAACTGC
1 -AAAAAAACAGC
21574002 AAAAAAA
1 AAAAAAA
21574009 AGTTGCCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.22
10 3 0.09
11 20 0.62
12 2 0.06
ACGTcount: A:0.73, C:0.14, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAACAGC
Found at i:21574009 original size:12 final size:11
Alignment explanation
Indices: 21573960--21574009 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
21573950 CTTATTCTTT
21573960 AAAAAAACAGCA
1 AAAAAAAC-GCA
21573972 AAAAAAA-GC-
1 AAAAAAACGCA
*
21573981 -AAAAAGCGCA
1 AAAAAAACGCA
21573991 AAAAAAACTGCA
1 AAAAAAAC-GCA
21574003 AAAAAAA
1 AAAAAAA
21574010 GTTGCCTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 2 0.06
11 6 0.19
12 17 0.53
ACGTcount: A:0.74, C:0.14, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAACGCA
Found at i:21587201 original size:15 final size:15
Alignment explanation
Indices: 21587181--21587218 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
21587171 TTAATTGGTG
21587181 ATTAAATCTTAAG-TA
1 ATTAAA-CTTAAGTTA
*
21587196 ATTAAAGTTAAGTTA
1 ATTAAACTTAAGTTA
21587211 ATTAAACT
1 ATTAAACT
21587219 AGTTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (15 bp):
ATTAAACTTAAGTTA
Found at i:21591962 original size:232 final size:232
Alignment explanation
Indices: 21591556--21592019 Score: 829
Period size: 232 Copynumber: 2.0 Consensus size: 232
21591546 GCAAGCTGCC
* * *
21591556 CATCGAGAAAGACTCAGCTTGAGCCCACAAAACCCACGTCCAGAACTACCATGTGAACTCATTTT
1 CATCGAGAAAGACTCAGCTTGAGCCCACAAAACCCACATCCACAACTACCATGTGAACTCATTTC
* * *
21591621 AATAAATTATCTACAATGTCAGAAACGCACAGATCAGTTTAGCGTCTTTACCACAGTTCTCATGT
66 AACAAATTATCTACAATGTCAGAAACGCACAGATCAGTTCAGAGTCTTTACCACAGTTCTCATGT
*
21591686 CAATTCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCATA
131 CAATTCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACA
21591751 ATAACTAAACAGGAATACTTACAGGTTTAGTGTCAGA
196 ATAACTAAACAGGAATACTTACAGGTTTAGTGTCAGA
*
21591788 CATCGAGAAAGACTCAGCTTGAGCCCACAAAACTCACATCCACAACTACCATGTGAACTCATTTC
1 CATCGAGAAAGACTCAGCTTGAGCCCACAAAACCCACATCCACAACTACCATGTGAACTCATTTC
* *
21591853 AACAAATTATCTACAATGTCAGAAATGCATAGATCAGTTCAGAGTCTTTACCACAGTTCTCATGT
66 AACAAATTATCTACAATGTCAGAAACGCACAGATCAGTTCAGAGTCTTTACCACAGTTCTCATGT
21591918 CAATTCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACA
131 CAATTCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACA
*
21591983 ATAACTGAACAGGAATACTTACAGGTTTAGTGTCAGA
196 ATAACTAAACAGGAATACTTACAGGTTTAGTGTCAGA
21592020 AACTCGATCC
Statistics
Matches: 221, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 221 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (232 bp):
CATCGAGAAAGACTCAGCTTGAGCCCACAAAACCCACATCCACAACTACCATGTGAACTCATTTC
AACAAATTATCTACAATGTCAGAAACGCACAGATCAGTTCAGAGTCTTTACCACAGTTCTCATGT
CAATTCATATTAGAATGTTTGACCAAACCACAGTTTCAATCACTACTATGTCTCAACAAATCACA
ATAACTAAACAGGAATACTTACAGGTTTAGTGTCAGA
Found at i:21593334 original size:22 final size:22
Alignment explanation
Indices: 21593309--21593361 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21593299 TGTCAGATAC
*
21593309 ATATGCAGAACATATCAGATTT
1 ATATGCAGAACAAATCAGATTT
* *
21593331 ATATGTAGAATAAATCAGATTT
1 ATATGCAGAACAAATCAGATTT
*
21593353 AGATGCAGA
1 ATATGCAGA
21593362 TTTCTAACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (22 bp):
ATATGCAGAACAAATCAGATTT
Found at i:21593553 original size:312 final size:312
Alignment explanation
Indices: 21592981--21593718 Score: 1332
Period size: 312 Copynumber: 2.4 Consensus size: 312
21592971 CTACTGTTCA
21592981 ATGGTATGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
1 ATGGTATGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
* *
21593046 CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCTCAACACACCATATAGGGCATCA
66 CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACACACCATATAAGGCATCA
* *
21593111 AGTACTCGTATATCCCTACACTACGTAATGACTATATGTCACGTTTCAGAATAATCGCAGCGTAG
131 AGTACTCGTACATCCCTACACTACGTAATGACTATATCTCACGTTTCAGAATAATCGCAGCGTAG
*
21593176 CTGCCAGATCAAAATGCAATAAATTGGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCC
196 CTGCCAGATCAAAATGCAATAAATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCC
*
21593241 GTTACTTAGAATTAGATACAGAATAGAAACAAAAAAAGTCGGATACAGTTAC
261 GTTACTCAGAATTAGATACAGAATAGAAACAAAAAAAGTCGGATACAGTTAC
* *
21593293 ATGGTATGTCAGATACATATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTTAGATG
1 ATGGTATGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
*
21593358 CAGATTTCTAACCCCGTCCATTACACACCATCTCCATCCATCCCAACACACCATATAAGGCATCA
66 CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACACACCATATAAGGCATCA
* * *
21593423 AGTACTCGTCCATCCCTACACTGCGTAATGACTATATCTCACGTTTCAGAATAATCGTAGCGTAG
131 AGTACTCGTACATCCCTACACTACGTAATGACTATATCTCACGTTTCAGAATAATCGCAGCGTAG
* *
21593488 CTGCCAGATCAGAATGCAATAAATTAGTAAACTACAATTGTAATCTCATTTACCGTAGGTCATCC
196 CTGCCAGATCAAAATGCAATAAATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCC
*
21593553 GTTACTCAGAATTAGATACAGAATAGAAACAAAGAAAGTCGGATACAGTTAC
261 GTTACTCAGAATTAGATACAGAATAGAAACAAAAAAAGTCGGATACAGTTAC
*
21593605 ATGGTCTGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
1 ATGGTATGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
21593670 CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACAC
66 CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACAC
21593719 TGCGTAATGA
Statistics
Matches: 407, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
312 407 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (312 bp):
ATGGTATGTCAGATACAGATGCAGAACATATCAGATTTATATGTAGAATAAATCAGATTCAGATG
CAGATTTCTAACCCCATCCATTACACACCATCTCCATCCATCCCAACACACCATATAAGGCATCA
AGTACTCGTACATCCCTACACTACGTAATGACTATATCTCACGTTTCAGAATAATCGCAGCGTAG
CTGCCAGATCAAAATGCAATAAATTAGTAAACTACAATTGTAATCTCATTTACCGTAGATCATCC
GTTACTCAGAATTAGATACAGAATAGAAACAAAAAAAGTCGGATACAGTTAC
Found at i:21593638 original size:22 final size:22
Alignment explanation
Indices: 21593613--21593673 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
21593603 ACATGGTCTG
* *
21593613 TCAGATACAGATGCAGAACATA
1 TCAGATTCAGATGCAGAACAAA
* * * *
21593635 TCAGATTTATATGTAGAATAAA
1 TCAGATTCAGATGCAGAACAAA
21593657 TCAGATTCAGATGCAGA
1 TCAGATTCAGATGCAGA
21593674 TTTCTAACCC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (22 bp):
TCAGATTCAGATGCAGAACAAA
Found at i:21594848 original size:25 final size:24
Alignment explanation
Indices: 21594818--21594877 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
21594808 AGCAAAAAGA
*
21594818 AAGAAAATGAAAGAGCAAAGAAAAT
1 AAGAAAATGAAAGA-AAAAGAAAAT
*
21594843 AAGAAAAATGAAGGAAAAAGAAAAT
1 AAG-AAAATGAAAGAAAAAGAAAAT
21594868 -AGAAAA-GAAA
1 AAGAAAATGAAA
21594878 AACGTTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.10
23 4 0.13
24 2 0.06
25 12 0.39
26 10 0.32
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.07
Consensus pattern (24 bp):
AAGAAAATGAAAGAAAAAGAAAAT
Found at i:21594850 original size:26 final size:24
Alignment explanation
Indices: 21594821--21594873 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
21594811 AAAAAGAAAG
*
21594821 AAAATGAAAGAGCAAAGAAAATAAGA
1 AAAATGAAAGA-AAAAGAAAAT-AGA
*
21594847 AAAATGAAGGAAAAAGAAAATAGA
1 AAAATGAAAGAAAAAGAAAATAGA
21594871 AAA
1 AAA
21594874 GAAAAACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 9 0.36
26 10 0.40
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08
Consensus pattern (24 bp):
AAAATGAAAGAAAAAGAAAATAGA
Found at i:21597117 original size:68 final size:68
Alignment explanation
Indices: 21597035--21597189 Score: 229
Period size: 68 Copynumber: 2.3 Consensus size: 68
21597025 CAGTTATGAT
* * * * * *
21597035 CTTACACAAATTAAACCCATGTTTACTGTCCTAACGGACTCTATATGTTGCCGTAGTCTAGCTAT
1 CTTACACATATTAAACCCATGTTCACTGTCCTAACGAACTCCATATGTTGCCATAGACTAGCTAT
21597100 GGA
66 GGA
**
21597103 CTTACACATATTAAACCCATGTTCACTGTCCTGGCGAACTCCATATGTTGCCATAGACTAGCTAT
1 CTTACACATATTAAACCCATGTTCACTGTCCTAACGAACTCCATATGTTGCCATAGACTAGCTAT
*
21597168 GGT
66 GGA
21597171 CTTACACATATTAAACCCA
1 CTTACACATATTAAACCCA
21597190 CATTTAACTG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 78 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (68 bp):
CTTACACATATTAAACCCATGTTCACTGTCCTAACGAACTCCATATGTTGCCATAGACTAGCTAT
GGA
Found at i:21599055 original size:25 final size:24
Alignment explanation
Indices: 21599020--21599100 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 24
21599010 ACTAAATATT
21599020 AGGCTTTGTGCC-GATGTTTATCTATC
1 AGGC-TTGTGCCAG-TG-TTATCTATC
*
21599046 AGGCTTGTGCCAGTGTTATCTATT
1 AGGCTTGTGCCAGTGTTATCTATC
*
21599070 AGGCCTTGTGCCAGTGTCATCTATC
1 AGG-CTTGTGCCAGTGTTATCTATC
21599095 AGGCTT
1 AGGCTT
21599101 TGAGCCGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.28
25 31 0.62
26 5 0.10
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (24 bp):
AGGCTTGTGCCAGTGTTATCTATC
Found at i:21603274 original size:14 final size:16
Alignment explanation
Indices: 21603257--21603288 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
21603247 CATTATTTAA
21603257 ATTTCA-AACTT-TGC
1 ATTTCATAACTTCTGC
21603271 ATTTCATAACTTCTGC
1 ATTTCATAACTTCTGC
21603287 AT
1 AT
21603289 GCGTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTCATAACTTCTGC
Found at i:21604285 original size:2 final size:2
Alignment explanation
Indices: 21604275--21604308 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
21604265 CATATCACAC
21604275 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21604309 ACACATAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21605039 original size:16 final size:17
Alignment explanation
Indices: 21605018--21605049 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21605008 AAATATGCAA
21605018 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
21605034 TCACATAACTTCATAT
1 TCACATAACTTCATAT
21605050 CATCAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:21605332 original size:41 final size:43
Alignment explanation
Indices: 21605274--21605388 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
21605264 CCAGACAGGG
*
21605274 TGTCCCAGACA-GAGTCTTAGACAAAT-CA-AA-TACGATGCCAA
1 TGTCCCAGACATG-GTCTTACACAAATACACAAGT-CGATGCCAA
**
21605315 TGTCCCAGACATGGTCTTACACGTATACACAAGTCGATGCCAA
1 TGTCCCAGACATGGTCTTACACAAATACACAAGTCGATGCCAA
* *
21605358 CGTCCCAGACGTGGTCTTACACGAAAATACA
1 TGTCCCAGACATGGTCTTACAC--AAATACA
21605389 TATCGAAATC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
41 21 0.34
42 3 0.05
43 31 0.51
44 1 0.02
45 5 0.08
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (43 bp):
TGTCCCAGACATGGTCTTACACAAATACACAAGTCGATGCCAA
Found at i:21611929 original size:2 final size:2
Alignment explanation
Indices: 21611919--21611948 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
21611909 CATATCACAC
21611919 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
21611949 ACACATAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21612972 original size:41 final size:43
Alignment explanation
Indices: 21612913--21613027 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
21612903 CCAGACAGGG
* *
21612913 TGTCCCAGACA-GAATCTTAGACAAAT-CA-AA-TACGATGCCAA
1 TGTCCCAGACATG-GTCTTACACAAATACACAAGT-CGATGCCAA
**
21612954 TGTCCCAGACATGGTCTTACACGTATACACAAGTCGATGCCAA
1 TGTCCCAGACATGGTCTTACACAAATACACAAGTCGATGCCAA
* *
21612997 CGTCCCAGACGTGGTCTTACACGAAAATACA
1 TGTCCCAGACATGGTCTTACAC--AAATACA
21613028 TATCGAAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
41 20 0.33
42 3 0.05
43 31 0.52
44 1 0.02
45 5 0.08
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (43 bp):
TGTCCCAGACATGGTCTTACACAAATACACAAGTCGATGCCAA
Found at i:21615708 original size:22 final size:20
Alignment explanation
Indices: 21615657--21615708 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
21615647 AATTGATCCT
21615657 AATTTTAAAAAAATTAAAGA
1 AATTTTAAAAAAATTAAAGA
*
21615677 AATATATAAAAATACA-TAAAGAA
1 AAT-TTTAAAAA-A-ATTAAAG-A
21615700 AATTTTAAA
1 AATTTTAAA
21615709 TTTTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 11 0.42
23 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AATTTTAAAAAAATTAAAGA
Found at i:21615740 original size:19 final size:20
Alignment explanation
Indices: 21615699--21615740 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
21615689 TACATAAAGA
*
21615699 AAAT-TTTAAATTTTATATT
1 AAATATTTAAATTTCATATT
21615718 -AATATTTAAA-TTCATATT
1 AAATATTTAAATTTCATATT
21615736 AAATA
1 AAATA
21615741 AATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTAAATTTCATATT
Found at i:21621991 original size:20 final size:21
Alignment explanation
Indices: 21621950--21621990 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21621940 TTTGTCCGGG
* *
21621950 CTCAAAATTAAATAAATAAAA
1 CTCAAAATAAAAAAAATAAAA
21621971 CTCAAAATAAAAAAAATAAA
1 CTCAAAATAAAAAAAATAAA
21621991 CAGTCCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
CTCAAAATAAAAAAAATAAAA
Found at i:21623379 original size:15 final size:15
Alignment explanation
Indices: 21623361--21623394 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21623351 ATTCCTTTAT
21623361 TTATACATT-TCATTA
1 TTAT-CATTATCATTA
21623376 TTATCATTATCATTA
1 TTATCATTATCATTA
21623391 TTAT
1 TTAT
21623395 TAGTGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATCATTATCATTA
Found at i:21630289 original size:13 final size:13
Alignment explanation
Indices: 21630269--21630304 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
21630259 TCAAAGTTAT
21630269 CCTAGCCCAAATA
1 CCTAGCCCAAATA
*
21630282 CTTAGCCCAAATA
1 CCTAGCCCAAATA
21630295 CCTAGCCCAA
1 CCTAGCCCAA
21630305 TTGCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (13 bp):
CCTAGCCCAAATA
Found at i:21630705 original size:23 final size:22
Alignment explanation
Indices: 21630675--21630717 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
21630665 AATTTTACGA
21630675 TTTCTTTT-TTTCTTCTTCTTTGT
1 TTTCTTTTGTTT-TTC-TCTTTGT
21630698 TTTCTTTTGTTTTTCTCTTT
1 TTTCTTTTGTTTTTCTCTTT
21630718 CCAAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTCTTTTGTTTTTCTCTTTGT
Found at i:21631531 original size:45 final size:46
Alignment explanation
Indices: 21631462--21631582 Score: 138
Period size: 45 Copynumber: 2.6 Consensus size: 46
21631452 CTTAACATTG
* *
21631462 TTTTAAATTTATCATTAGTATTATTTTAATATATAATATA-CTATTA
1 TTTTAAATTTATCATTAATATTATTTTAATATATAATATATC-ATAA
* * *
21631508 TTTTAAA-TTATCATTAATATTATTTAAATTTATCATATATCATAA
1 TTTTAAATTTATCATTAATATTATTTTAATATATAATATATCATAA
* * *
21631553 TTTGAAATTTATCATGTACTATAATTTTAA
1 TTTTAAATTTATCAT-TAATATTATTTTAA
21631583 ACTTATCATA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 37 0.59
46 15 0.24
47 11 0.17
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (46 bp):
TTTTAAATTTATCATTAATATTATTTTAATATATAATATATCATAA
Found at i:21631563 original size:24 final size:23
Alignment explanation
Indices: 21631463--21631619 Score: 119
Period size: 24 Copynumber: 6.9 Consensus size: 23
21631453 TTAACATTGT
* *
21631463 TTTAAATTTATCAT-TAGTATTA
1 TTTAAATTTATCATATACTATAA
* * * *
21631485 TTTTAATATATAATATACTATTAT
1 TTTAAATTTATCATATACTA-TAA
* *
21631509 TTTAAA-TTATCAT-TAATATTA
1 TTTAAATTTATCATATACTATAA
21631530 TTTAAATTTATCATATA-TCATAA
1 TTTAAATTTATCATATACT-ATAA
*
21631553 TTTGAAATTTATCATGTACTATAA
1 TTT-AAATTTATCATATACTATAA
* *
21631577 TTTTAAACTTATCATAT-C-ATTA
1 -TTTAAATTTATCATATACTATAA
* *
21631599 TTTATATCTATCATATACTAT
1 TTTAAATTTATCATATACTAT
21631620 TTTTATGTAT
Statistics
Matches: 105, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
21 20 0.19
22 27 0.26
23 20 0.19
24 34 0.32
25 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAATTTATCATATACTATAA
Found at i:21636489 original size:9 final size:9
Alignment explanation
Indices: 21636472--21636502 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21636462 TCGAGTTGAT
21636472 TCGAATAAC
1 TCGAATAAC
*
21636481 TCGATTAAC
1 TCGAATAAC
21636490 TCGAATAAC
1 TCGAATAAC
21636499 TCGA
1 TCGA
21636503 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:21639556 original size:89 final size:91
Alignment explanation
Indices: 21639432--21639779 Score: 239
Period size: 89 Copynumber: 3.8 Consensus size: 91
21639422 CATCATGGTA
* *
21639432 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGC-CATT-AG-TCTTATCTCTCTGAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAA-CAAATTCAGATCTTATCTCTCTGAAG
*
21639494 TTGCAGTGGAGCAGACTGAAGATAGCG
65 TTGCAGTAGAGCAGACTGAAGATAGCG
* * *
21639521 AATCTTATTTCCTTGAAGTTGCAGTGGAATGGATTAAACTATAAATTGCAGATCTTATCTCTCTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAC---AAATT-CAGATCTTATCTCTCTG
* * *
21639586 AAGTTGCAGTAGAGCAGA-TCATG--A-CA
62 AAGTTGCAGTAGAGCAGACTGAAGATAGCG
* * ** * * *** *
21639612 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTA-CCA-AGTCTTATCTC-CTTGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAACAAATTCAGA-TCTTATCTCTC-TGAA
* * * *
21639674 GTCGCAGTAGAGAAGACTGAAGATCATATCA
64 GTTGCAGTAGAGCAGACTGAAG---ATAGCG
* * * * *
21639705 AATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGAAGCTATAAATTGTAGATCTTATCTCTCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT-AA---ACAAATT-CAGATCTTATCTCTCT
21639770 GAAGTTGCAG
61 GAAGTTGCAG
21639780 CAGATCATAG
Statistics
Matches: 196, Mismatches: 39, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
85 2 0.01
86 29 0.15
87 3 0.02
88 2 0.01
89 34 0.17
91 30 0.15
92 5 0.03
93 31 0.16
94 6 0.03
95 30 0.15
97 2 0.01
99 20 0.10
100 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (91 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAACAAATTCAGATCTTATCTCTCTGAAGT
TGCAGTAGAGCAGACTGAAGATAGCG
Found at i:21639743 original size:48 final size:47
Alignment explanation
Indices: 21639601--21639743 Score: 123
Period size: 48 Copynumber: 3.0 Consensus size: 47
21639591 GCAGTAGAGC
* * * *
21639601 AGATCATGACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGA
1 AGATCAT-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* * * * *
21639649 AG-T--TACCAAGTCTTATCTCCTTGAAGTCGCAGTAGAGA-AGACTGA
1 AGATCATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGA-ACAGATTGA
* *
21639694 AGATCATATCAAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGA
1 AGATCATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
21639742 AG
1 AG
21639744 CTATAAATTG
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
44 1 0.01
45 32 0.44
46 1 0.01
47 2 0.03
48 36 0.50
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (47 bp):
AGATCATACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
Found at i:21639787 original size:180 final size:175
Alignment explanation
Indices: 21639435--21639823 Score: 462
Period size: 180 Copynumber: 2.2 Consensus size: 175
21639425 CATGGTAAAT
* *
21639435 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCATTAGTCTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-TAGTCTTATCTCTCTGAAGTCGCAG
* * * * **
21639500 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTGAAGTTGCAGTGGAATGGATTAAACTATAA
65 TAGAGAAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAACTATAA
21639565 ATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAT-GACAAAC
130 ATTGCAGATCTTATCTCTCTGAAGTTGC---A-AGCAGATCATAG-CAAAC
* * *
21639615 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACCA-AGTCTTATCTC-CTTGAAGTCG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG---CCATAGTCTTATCTCTC-TGAAGTCG
* *
21639678 CAGTAGAGAAGACTGAAGATCATATCAAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGAA
62 CAGTAGAGAAGACTGAAG---ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT-AA
* *
21639743 GCTATAAATTGTAGATCTTATCTCTCTGAAGTTGC-AGCAGATCATAGCAAAC
123 ACTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAAGCAGATCATAGCAAAC
* * *
21639795 ATTATCGCCCTGAAGTTACAGTGGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
21639824 TTGTAGTAGA
Statistics
Matches: 181, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
180 73 0.40
181 35 0.19
183 3 0.02
184 35 0.19
185 35 0.19
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (175 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAGTCTTATCTCTCTGAAGTCGCAGT
AGAGAAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAACTATAAA
TTGCAGATCTTATCTCTCTGAAGTTGCAAGCAGATCATAGCAAAC
Found at i:21640058 original size:21 final size:19
Alignment explanation
Indices: 21640032--21640070 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
21640022 TTTTCCCAGG
21640032 CCCAAAACTAAATAAATAAAA
1 CCCAAAA-TAAA-AAATAAAA
21640053 CCCAAAATAAAAAATAAA
1 CCCAAAATAAAAAATAAA
21640071 CAATCCATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.69, C:0.18, G:0.00, T:0.13
Consensus pattern (19 bp):
CCCAAAATAAAAAATAAAA
Found at i:21643145 original size:31 final size:31
Alignment explanation
Indices: 21643110--21643169 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
21643100 TTTTTAGTTA
* * *
21643110 AATTTAACTCTCAATATTTCAAAATGAGTCC
1 AATTTAACTATCAACATTTCAAAAAGAGTCC
* *
21643141 AATTTAGCTATCACCATTTCAAAAAGAGT
1 AATTTAACTATCAACATTTCAAAAAGAGT
21643170 TGACTTGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (31 bp):
AATTTAACTATCAACATTTCAAAAAGAGTCC
Found at i:21648181 original size:11 final size:10
Alignment explanation
Indices: 21648156--21648197 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
21648146 TTTTTACAAG
21648156 TATATAAAAA
1 TATATAAAAA
21648166 T-TATAAAATA
1 TATATAAAA-A
21648176 TATATAAAAA
1 TATATAAAAA
*
21648186 CATGATAAAAA
1 TAT-ATAAAAA
21648197 T
1 T
21648198 CCTAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 6 0.22
11 14 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TATATAAAAA
Found at i:21648610 original size:20 final size:21
Alignment explanation
Indices: 21648567--21648612 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
21648557 CCTTTTTTTT
*
21648567 TTTTTTTTAAAGAATTTTGAA
1 TTTTTTTTAAAGAATTATGAA
21648588 TTTTTTTTAAA-AATTAT-ATA
1 TTTTTTTTAAAGAATTATGA-A
21648608 TTTTT
1 TTTTT
21648613 AAAATTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTTTTAAAGAATTATGAA
Found at i:21652110 original size:40 final size:40
Alignment explanation
Indices: 21652037--21652156 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 40
21652027 AAACTGTTCA
* *
21652037 TCCACGTCAGCAAATCGCGTCCT--CGTAGG-CGCGATTTGTG
1 TCCACGTAAGCAAATCGCG--CTGACGT-GGACGCGATTTCTG
21652077 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATGTTCTG
1 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGAT-TTCTG
* ** * *
21652118 -ACACGTACCCTGACATCGCGCTGACGTGGACGTGATTTC
1 TCCACGTAAGC--AAATCGCGCTGACGTGGACGCGATTTC
21652157 GCGGAAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 34 0.51
41 7 0.10
42 22 0.33
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCTG
Found at i:21656783 original size:17 final size:18
Alignment explanation
Indices: 21656751--21656785 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21656741 TAGGGCCAAA
21656751 ACCCGCATGTGTGACCCG
1 ACCCGCATGTGTGACCCG
*
21656769 ACCCGCTTG-GTGACCCG
1 ACCCGCATGTGTGACCCG
21656786 CGTGTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (18 bp):
ACCCGCATGTGTGACCCG
Found at i:21658621 original size:10 final size:10
Alignment explanation
Indices: 21658592--21658622 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21658582 AGTATGAATG
*
21658592 GTGAGAATTG
1 GTGAGAATTA
21658602 GTGAGAATTA
1 GTGAGAATTA
21658612 GTGAGAATTA
1 GTGAGAATTA
21658622 G
1 G
21658623 ACTAAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (10 bp):
GTGAGAATTA
Found at i:21659027 original size:51 final size:51
Alignment explanation
Indices: 21658950--21659050 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
21658940 AGATACTTGA
** * *
21658950 GTATCCGAGTTCGTTTAATAACGTTCATCGGGTGAAATAAATTACATGAAG
1 GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAAG
* *
21659001 GTATCCGAGCCCGTTTACTAAGGTTCATCGGGCGAAACAAATTACATGAA
1 GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAA
21659051 TTGAGAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (51 bp):
GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAAG
Found at i:21659945 original size:11 final size:11
Alignment explanation
Indices: 21659929--21660063 Score: 73
Period size: 11 Copynumber: 13.1 Consensus size: 11
21659919 TATTTTTTTA
21659929 ATTTTTAAAAT
1 ATTTTTAAAAT
* *
21659940 ATTTTTTTACAT
1 A-TTTTTAAAAT
21659952 ACTTTTT-AAAT
1 A-TTTTTAAAAT
*
21659963 -TTTTT--TA-
1 ATTTTTAAAAT
21659970 ATT-TTAAAAT
1 ATTTTTAAAAT
21659980 ATTTTTAAAAT
1 ATTTTTAAAAT
*
21659991 ACTTTTTTTAAAT
1 A--TTTTTAAAAT
21660004 ATTTTT----T
1 ATTTTTAAAAT
*
21660011 AATTTTAAAAT
1 ATTTTTAAAAT
21660022 ATTTTTAAAAT
1 ATTTTTAAAAT
*
21660033 ACTTTTT--TA-
1 A-TTTTTAAAAT
21660042 ATTTTTAAAA-
1 ATTTTTAAAAT
21660052 ATTTTTAAAAT
1 ATTTTTAAAAT
21660063 A
1 A
21660064 AAAATGGGCC
Statistics
Matches: 97, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
7 8 0.08
8 8 0.08
9 7 0.07
10 15 0.15
11 30 0.31
12 19 0.20
13 10 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:21659999 original size:41 final size:40
Alignment explanation
Indices: 21659920--21660047 Score: 188
Period size: 42 Copynumber: 3.1 Consensus size: 40
21659910 AAATATATTT
* *
21659920 ATTTTTTTAATTTTTAAAATATTTTTTTACATAC-TTTTTAA
1 ATTTTTTTAA-TTTTAAAATA-TTTTTAAAATACTTTTTTAA
21659961 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAA
21660002 ATATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT-A
1 AT-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
21660042 ATTTTT
1 ATTTTT
21660048 AAAAATTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
39 14 0.17
40 13 0.16
41 25 0.30
42 30 0.37
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:21660017 original size:31 final size:31
Alignment explanation
Indices: 21659980--21660063 Score: 120
Period size: 30 Copynumber: 2.7 Consensus size: 31
21659970 ATTTTAAAAT
*
21659980 ATTTTTAAAATACTTTTTTTAAATA-TTTTTTA
1 ATTTTTAAAATA--TTTTTAAAATACTTTTTTA
21660012 A-TTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTA
21660042 ATTTTTAAAA-ATTTTTAAAATA
1 ATTTTTAAAATATTTTTAAAATA
21660064 AAAATGGGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
29 10 0.20
30 20 0.41
31 18 0.37
32 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:21663632 original size:8 final size:8
Alignment explanation
Indices: 21663615--21663676 Score: 115
Period size: 8 Copynumber: 7.8 Consensus size: 8
21663605 TACTTGGGAA
21663615 AAATGATT
1 AAATGATT
*
21663623 AAATGGTT
1 AAATGATT
21663631 AAATGATT
1 AAATGATT
21663639 AAATGATT
1 AAATGATT
21663647 AAATGATT
1 AAATGATT
21663655 AAATGATT
1 AAATGATT
21663663 AAATGATT
1 AAATGATT
21663671 AAATGA
1 AAATGA
21663677 ACTTGAACAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (8 bp):
AAATGATT
Found at i:21667461 original size:17 final size:17
Alignment explanation
Indices: 21667434--21667467 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21667424 CCATTTTTAA
21667434 TTTTAATTTTAATATATT
1 TTTTAATTTTAAT-TATT
21667452 TTTTAA-TTTAATTATT
1 TTTTAATTTTAATTATT
21667468 ACGTTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTAATTATT
Found at i:21673054 original size:20 final size:20
Alignment explanation
Indices: 21673029--21673068 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21673019 AATGGTAAGT
*
21673029 AAAATGGTAAATATGCATGA
1 AAAATGGTAAATATACATGA
21673049 AAAATGGTAAATATACATGA
1 AAAATGGTAAATATACATGA
21673069 TTTTTGCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (20 bp):
AAAATGGTAAATATACATGA
Found at i:21674970 original size:12 final size:12
Alignment explanation
Indices: 21674953--21674982 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21674943 ACAAAGTCCG
21674953 AATTTAATTTCC
1 AATTTAATTTCC
*
21674965 AATTTAATTTCT
1 AATTTAATTTCC
21674977 AATTTA
1 AATTTA
21674983 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:21674987 original size:4 final size:4
Alignment explanation
Indices: 21674978--21675003 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21674968 TTAATTTCTA
21674978 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
21675004 GCTATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:21680498 original size:3 final size:3
Alignment explanation
Indices: 21680490--21680530 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
21680480 GTTATTAGGC
* * *
21680490 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TCA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
21680531 TTCGTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:21680689 original size:9 final size:9
Alignment explanation
Indices: 21680666--21680715 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
21680656 ACATAGATTT
*
21680666 TTATTTTTA
1 TTATTTTCA
*
21680675 TAATTTT-A
1 TTATTTTCA
21680683 TTTATTTTCA
1 -TTATTTTCA
21680693 TTATTTTCA
1 TTATTTTCA
*
21680702 TTATTGTC-
1 TTATTTTCA
21680710 TTATTT
1 TTATTT
21680716 GATATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 28 0.80
10 1 0.03
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (9 bp):
TTATTTTCA
Found at i:21680698 original size:18 final size:18
Alignment explanation
Indices: 21680665--21680726 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
21680655 TACATAGATT
* *
21680665 TTTATTTTTATAATTTTA
1 TTTATTTTCATTATTTTA
21680683 TTTATTTTCATTATTTTCA
1 TTTATTTTCATTATTTT-A
*
21680702 -TTATTGTC-TTATTTGATA
1 TTTATTTTCATTATTT--TA
21680720 TTTATTT
1 TTTATTT
21680727 ATGTGTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 6 0.17
18 23 0.64
19 7 0.19
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTATTTTCATTATTTTA
Found at i:21681938 original size:11 final size:11
Alignment explanation
Indices: 21681918--21681955 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
21681908 TTAAAAATTA
21681918 AAAAAGTATTTT
1 AAAAA-TATTTT
21681930 AAAAATATTTT
1 AAAAATATTTT
*
21681941 TAAAATATTTT
1 AAAAATATTTT
21681952 AAAA
1 AAAA
21681956 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:21681953 original size:10 final size:10
Alignment explanation
Indices: 21681904--21681991 Score: 60
Period size: 10 Copynumber: 8.9 Consensus size: 10
21681894 ACCAAAAATT
21681904 TATTTTAAAA
1 TATTTTAAAA
**
21681914 -ATTAAAAAA
1 TATTTTAAAA
21681923 GTATTTTAAAAA
1 -TATTTT-AAAA
21681935 TATTTTTAAAA
1 TA-TTTTAAAA
21681946 TATTTT-AAA
1 TATTTTAAAA
*
21681955 -A-TTAAAAA
1 TATTTTAAAA
* *
21681963 AAATTTAAAA
1 TATTTTAAAA
21681973 GTA-TTTAAAA
1 -TATTTTAAAA
21681983 TATTTTAAA
1 TATTTTAAA
21681992 TTAAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 13 0.21
10 23 0.37
11 12 0.19
12 8 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:21681972 original size:9 final size:9
Alignment explanation
Indices: 21681939--21682042 Score: 65
Period size: 9 Copynumber: 11.8 Consensus size: 9
21681929 TAAAAATATT
21681939 TTTAAAATA
1 TTTAAAATA
21681948 TTTTAAAAT-
1 -TTTAAAATA
** *
21681957 TAAAAAAAA
1 TTTAAAATA
21681966 TTTAAAAGTA
1 TTTAAAA-TA
21681976 TTTAAAATA
1 TTTAAAATA
*
21681985 TTT-TAA-A
1 TTTAAAATA
*
21681992 TTAAAAATA
1 TTTAAAATA
* *
21682001 ATAAAAAGTA
1 TTTAAAA-TA
21682011 TTTAAAATA
1 TTTAAAATA
*
21682020 TTTTAAA-A
1 TTTAAAATA
*
21682028 -TTAAAAAA
1 TTTAAAATA
21682036 TTTAAAA
1 TTTAAAA
21682043 ATAAATATAT
Statistics
Matches: 73, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
7 8 0.11
8 11 0.15
9 31 0.42
10 23 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
TTTAAAATA
Found at i:21682029 original size:36 final size:37
Alignment explanation
Indices: 21681904--21682043 Score: 162
Period size: 35 Copynumber: 3.7 Consensus size: 37
21681894 ACCAAAAATT
*
21681904 TATTTTAAAAATTAAAAAAGTATTTTAAAAA-TATTTTTAAAA
1 TATTTT-AAAATTAAAAAA--A-ATTAAAAAGTA--TTTAAAA
*
21681946 TATTTTAAAATTAAAAAAAATTTAAAAGTATTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAGTATTTAAAA
*
21681983 TATTTT-AAATTAAAAATAA-TAAAAAGTATTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAGTATTTAAAA
*
21682018 TATTTTAAAATT-AAAAAATTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAA
21682044 TAAATATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
35 26 0.29
36 23 0.26
37 13 0.15
38 6 0.07
39 3 0.03
41 12 0.13
42 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (37 bp):
TATTTTAAAATTAAAAAAAATTAAAAAGTATTTAAAA
Found at i:21682055 original size:16 final size:16
Alignment explanation
Indices: 21682015--21682055 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
21682005 AAAGTATTTA
*
21682015 AAATAT-TTTAAAATT
1 AAATATATTTAAAAAT
*
21682030 AAA-AAATTTAAAAAT
1 AAATATATTTAAAAAT
21682045 AAATATATTTA
1 AAATATATTTA
21682056 TTATATCGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 14 0.67
16 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATATTTAAAAAT
Found at i:21682602 original size:15 final size:15
Alignment explanation
Indices: 21682567--21682595 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21682557 ATTTAATTAG
21682567 AAATAATATAATTTT
1 AAATAATATAATTTT
21682582 AAATAATAT-ATTTT
1 AAATAATATAATTTT
21682596 TTTATAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATAATATAATTTT
Found at i:21682746 original size:3 final size:3
Alignment explanation
Indices: 21682738--21682800 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
21682728 TTTTAAAGCA
21682738 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21682786 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
21682801 AGGGAGTGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21683168 original size:3 final size:3
Alignment explanation
Indices: 21683162--21683196 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21683152 CTCCTCCTCC
21683162 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
21683197 TACTTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:21688704 original size:2 final size:2
Alignment explanation
Indices: 21688697--21688725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21688687 GCTCAATTAA
21688697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21688726 GCAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21688753 original size:22 final size:21
Alignment explanation
Indices: 21688723--21688766 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
21688713 ATATATATAT
* *
21688723 ATAGCAAAAGTAAAAAGTAAAA
1 ATAGAAAAAG-AAAAAGAAAAA
21688745 ATAGAAAAAGAAAAAGAAAAA
1 ATAGAAAAAGAAAAAGAAAAA
21688766 A
1 A
21688767 GTAAGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (21 bp):
ATAGAAAAAGAAAAAGAAAAA
Found at i:21690731 original size:3 final size:3
Alignment explanation
Indices: 21690723--21690863 Score: 135
Period size: 3 Copynumber: 45.3 Consensus size: 3
21690713 ATATGCAAGT
*
21690723 ATA ATA ATA ATAA ATA AT- ATA ATA ATTA TTA AT- ATGA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA
*
21690769 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
21690817 ACAA ATA ATGCA ATA ATA ATG ATGCA ATA ACA ATA TTA ATA A-A ATA
1 A-TA ATA AT--A ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA ATA
21690863 A
1 A
21690864 ACTAAAAAAG
Statistics
Matches: 116, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
2 6 0.05
3 96 0.83
4 9 0.08
5 5 0.04
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:21692232 original size:50 final size:50
Alignment explanation
Indices: 21692178--21692688 Score: 230
Period size: 50 Copynumber: 10.2 Consensus size: 50
21692168 ACCGTCGTGA
* * * * *
21692178 CTTCAATCTATTTCACTACACCGCTAGGGAAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * * ** * *
21692228 CTTCAATCTTTTTAATTGTAATG-TCGGGGAAACT-AGATCCGCCGCTGTAG
1 CTTCAATCTGTTTCACTGCACCGCT-AGGGAAA-TAAGATCCGCCGTTGTAG
* * * * * * * *
21692278 CTTCAATTTGCTCCACTGCACCGCCAGAGAAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * ** * ** * * *
21692328 CTTCAATCT-TTTAATTACAATG-TCGAGGAAACCAGATCCACCATCGTAG
1 CTTCAATCTGTTTCACTGCACCGCTAG-GGAAATAAGATCCGCCGTTGTAG
* * * *
21692377 CTTCAATCT-TCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGT-TTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * ** * ** * *
21692427 CTTCAATCAT-TTTAATTGCAATG-TCGGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATC-TGTTTCACTGCACCGCT-AGGGAAATAAGATCCGCCGTTGTAG
* * * *
21692477 CTTCAATCTGTTCCACTACACCGCAAGGGAAATAAGATCCGCCATTGTAG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * * ** * * *
21692527 CTTCAATCTTTTTAATTGTAATG-TCGGGGAAACAAGATCCGCCGTCGTAG
1 CTTCAATCTGTTTCACTGCACCGCT-AGGGAAATAAGATCCGCCGTTGTAG
* * * * *
21692577 CTTCAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * ** * * * *
21692627 CTTCAATCTTTTTAATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-G
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
*
21692676 ATTTCAATCTGTT
1 -CTTCAATCTGTT
21692689 CCTCTACACC
Statistics
Matches: 317, Mismatches: 130, Indels: 28
0.67 0.27 0.06
Matches are distributed among these distances:
48 1 0.00
49 34 0.11
50 278 0.88
51 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
Found at i:21692310 original size:100 final size:100
Alignment explanation
Indices: 21692144--21692732 Score: 729
Period size: 100 Copynumber: 5.9 Consensus size: 100
21692134 TCTGCTCAAC
* * * * ** * * *
21692144 TGCAATGTCGGGAAAACAAGATTCACCGTCGT-GACTTCAATCTATTTCACTACACCGCTAGGGA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGA
*
21692208 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
21692244 TGTAATGTCGGGGAAACTAGATCCGCCG-CTGTAGCTTCAATTTGCTCCACTGCACCGCCAGAGA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTC-GTAGCTTCAATCTGCTCCACTGCACCGCCAGGGA
*
21692308 AGTAAGATCTGCCGTTGTGGCTTCAATC-TTTTAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * *
21692343 TACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
*
21692408 GTAAGATCCGCCGTTGTGGCTTCAATCATTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
21692443 TGCAATGTCGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCAAGGGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* * *
21692508 ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
21692543 TGTAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGAGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
21692608 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * * * *
21692643 TGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGTTCCTCTACACCACC-GGGA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGA
* * **
21692706 AGTAAGATTCACCGTTGTCACTTCAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAAT
21692733 AATTTCCACT
Statistics
Matches: 427, Mismatches: 57, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
99 115 0.27
100 311 0.73
101 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:21692708 original size:299 final size:299
Alignment explanation
Indices: 21692144--21692737 Score: 831
Period size: 299 Copynumber: 2.0 Consensus size: 299
21692134 TCTGCTCAAC
* *
21692144 TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTTCACTACACCGCTAGGGAA
1 TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTCCACTACACCGCAAGGGAA
* * * * *
21692209 GTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACTAGATCCGCCGCT
66 ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGCT
* *
21692274 GTAGCTTCAATTTGCTCCACTGCACCGCCAGAGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTT
131 GTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
* *
21692339 TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTGCACCGCCAG
196 TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTACACCACCAG
* ** *
21692404 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAAT
261 GGAAGTAAGATCCACCGTTGTCACTTCAATAATTTTAAT
* * * *
21692443 TGCAATGTCGGGGAAACCAGA-TCTGCCGTCGT-AGCTTCAATCTGTTCCACTACACCGCAAGGG
1 TGCAATGTCGGGAAAACAAGATTC-ACCGTCGTGA-CTTCAATCTATTCCACTACACCGCAAGGG
21692506 AAATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCG
64 AAATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCG
*
21692571 -TCGTAGCTTCAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATC
129 CT-GTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATC
* * * * * * * *
21692635 TTTTTAATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGT-TCCTCTACAC
193 -TTTTAATTACAATGTCGAGGAAACCAGATCCACCATCGTAG-CTTCAATCT-TCTCCACTACAC
*
21692698 CACC-GGGAAGTAAGATTCACCGTTGTCACTTCAATAATTT
255 CACCAGGGAAGTAAGATCCACCGTTGTCACTTCAATAATTT
21692738 CCACTGTAAT
Statistics
Matches: 260, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
298 4 0.02
299 203 0.78
300 52 0.20
301 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (299 bp):
TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTCCACTACACCGCAAGGGAA
ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGCT
GTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTACACCACCAG
GGAAGTAAGATCCACCGTTGTCACTTCAATAATTTTAAT
Found at i:21692781 original size:200 final size:200
Alignment explanation
Indices: 21692178--21692793 Score: 562
Period size: 199 Copynumber: 3.1 Consensus size: 200
21692168 ACCGTCGTGA
* * * * * *
21692178 CTTCAATCTAT-TTCACTACACCGCTAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTA
1 CTTCAATCT-TCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTA
* * * * * * * *
21692242 ATTGTAATGTCGGGGAAACTAGATCCGCCG-CTGTAGCTTCAATTTGCTCCACTGCACCGCCAGA
65 ATTGCAATGTCGGGGAAACCAGATCCGCCGTC-GTAGCTTCAATCTGTTCCACTACACCACAAGG
* ** * * * * * ** * * * * *
21692306 GAAGTAAGATCTGCCGTTGTGGCTTCAAT-CTTTTAATTACAATGTCGAGGAAACCAGATCCACC
129 GAAATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCC
* **
21692370 ATCGTAG
194 GTCACAG
*
21692377 CTTCAATCTTCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
1 CTTCAATCTTCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
* *
21692442 TTGCAATGTCGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCAAGGGA
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCACAAGGGA
* ** * * * ***
21692507 AATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGT
131 AATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCCGT
**
21692572 CGTAG
196 CACAG
*
21692577 CTTCAATCTGT-TCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
1 CTTCAATCT-TCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTA
* * * * *
21692641 ATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGTTCCTCTACACCAC-CGG
65 ATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTACACCACAAGG
* * * * *** * *
21692704 GAAGTAAGATTCACCGTTGTCA-CTTCAATAATTTCCACTGTAATGCCAAAGAGGTAGGATTCGC
129 GAAATAAGATCCACCATTGT-AGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGC
21692768 CGTTCACAG
193 CG-TCACAG
**
21692777 CTTCAATCCACTCCACT
1 CTTCAATCTTCTCCACT
21692794 TCAGCTAATC
Statistics
Matches: 354, Mismatches: 55, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
198 1 0.00
199 185 0.52
200 167 0.47
201 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (200 bp):
CTTCAATCTTCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCACAAGGGA
AATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCCGT
CACAG
Found at i:21693713 original size:23 final size:23
Alignment explanation
Indices: 21693683--21693726 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
21693673 TCCAAAGAGA
21693683 AAGTCTTAATTTAGACTCTTTTT
1 AAGTCTTAATTTAGACTCTTTTT
*
21693706 AAGTCTTAATTTATACTCTTT
1 AAGTCTTAATTTAGACTCTTT
21693727 CTTATCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (23 bp):
AAGTCTTAATTTAGACTCTTTTT
Found at i:21694385 original size:15 final size:15
Alignment explanation
Indices: 21694367--21694424 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
21694357 TTTTTTCATC
21694367 ATTTTTATTTTTTCG
1 ATTTTTATTTTTTCG
* *
21694382 ATTTTAATTTTTT-T
1 ATTTTTATTTTTTCG
*
21694396 ATTTTGA-TTTTTCTG
1 ATTTTTATTTTTTC-G
21694411 ATTTTTGATTTTTT
1 ATTTTT-ATTTTTT
21694425 TTATTTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 17 0.50
16 1 0.03
17 5 0.15
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.74
Consensus pattern (15 bp):
ATTTTTATTTTTTCG
Found at i:21694392 original size:20 final size:20
Alignment explanation
Indices: 21694367--21694406 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21694357 TTTTTTCATC
*
21694367 ATTTTTATTTTTTCGATTTTA
1 ATTTTT-TTATTTCGATTTTA
*
21694388 ATTTTTTTATTTTGATTTT
1 ATTTTTTTATTTCGATTTT
21694407 TCTGATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (20 bp):
ATTTTTTTATTTCGATTTTA
Found at i:21694431 original size:15 final size:15
Alignment explanation
Indices: 21694367--21694440 Score: 71
Period size: 14 Copynumber: 5.0 Consensus size: 15
21694357 TTTTTTCATC
* **
21694367 ATTTTTATTTTTTCG
1 ATTTTGATTTTTTTT
*
21694382 ATTTT-AATTTTTTT
1 ATTTTGATTTTTTTT
* *
21694396 ATTTTGATTTTTCTG
1 ATTTTGATTTTTTTT
21694411 ATTTTTGATTTTTTTT
1 A-TTTTGATTTTTTTT
21694427 ATTTTG-TTTTTTTT
1 ATTTTGATTTTTTTT
21694441 TTCAGATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 19 0.39
15 17 0.35
16 13 0.27
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
ATTTTGATTTTTTTT
Found at i:21694442 original size:16 final size:16
Alignment explanation
Indices: 21694389--21694441 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
21694379 TCGATTTTAA
21694389 TTTTTTTATTTTG-AT
1 TTTTTTTATTTTGTAT
* *
21694404 TTTTCTGATTTT-TGAT
1 TTTTTTTATTTTGT-AT
21694420 TTTTTTTATTTTGT-T
1 TTTTTTTATTTTGTAT
21694435 TTTTTTT
1 TTTTTTT
21694442 TCAGATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 18 0.58
16 12 0.39
17 1 0.03
ACGTcount: A:0.09, C:0.02, G:0.08, T:0.81
Consensus pattern (16 bp):
TTTTTTTATTTTGTAT
Found at i:21695284 original size:25 final size:25
Alignment explanation
Indices: 21695231--21695290 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
21695221 TAGAAAATCC
* *
21695231 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
21695256 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
21695281 AAAA-AATGAA
1 AAAAGAATGAA
21695291 TGCAAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:21698875 original size:27 final size:28
Alignment explanation
Indices: 21698804--21698883 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 28
21698794 ATAGTGTAAG
*
21698804 AATATATATATATTATAAAGA-ATGTATAA
1 AATATATATATATTATAAA-ATATG-AGAA
*
21698833 ACATATATATAGATTATAAAATATG-GAA
1 A-ATATATATATATTATAAAATATGAGAA
*
21698861 AATATATAAATATTATAAAATAT
1 AATATATATATATTATAAAATAT
21698884 AAATGTATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 20 0.44
28 3 0.07
29 2 0.04
30 20 0.44
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (28 bp):
AATATATATATATTATAAAATATGAGAA
Found at i:21699037 original size:3 final size:3
Alignment explanation
Indices: 21699029--21699145 Score: 112
Period size: 3 Copynumber: 37.3 Consensus size: 3
21699019 ATATACAAGT
*
21699029 ATA ATA ATAA ATA AT- ATA ATA ATTA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
* *
21699075 ATA ATA ATA ATA ATA ATA ATA ATA ACAA ATA ATGCA ATA ATA ATG ATGCA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT--A ATA ATA ATA AT--A
* *
21699125 ATA ACA ATA TTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
21699146 ACTAAAAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.04
3 79 0.83
4 7 0.07
5 5 0.05
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:21700604 original size:24 final size:24
Alignment explanation
Indices: 21700564--21700610 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21700554 AAAGGGAAAT
*
21700564 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
21700588 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
21700611 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:21701484 original size:22 final size:24
Alignment explanation
Indices: 21701459--21701505 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
21701449 TATCTAAATT
21701459 ACAAAATTGAAT-GAAATTT-AGA
1 ACAAAATTGAATGGAAATTTGAGA
* *
21701481 ACAATATTGAGTGGAAATTTGAGA
1 ACAAAATTGAATGGAAATTTGAGA
21701505 A
1 A
21701506 AAATAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 7 0.33
24 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (24 bp):
ACAAAATTGAATGGAAATTTGAGA
Found at i:21703609 original size:18 final size:18
Alignment explanation
Indices: 21703586--21703621 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21703576 TTAGAATGCT
21703586 ATTTTGGTATCAATATTA
1 ATTTTGGTATCAATATTA
*
21703604 ATTTTGGTATCGATATTA
1 ATTTTGGTATCAATATTA
21703622 GATGTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
ATTTTGGTATCAATATTA
Found at i:21708323 original size:15 final size:16
Alignment explanation
Indices: 21708303--21708336 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21708293 TCTTCACCTG
21708303 CAAGGAAACAAA-AAA
1 CAAGGAAACAAATAAA
*
21708318 CAAGGAAAGAAATAAA
1 CAAGGAAACAAATAAA
21708334 CAA
1 CAA
21708337 CAAATGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.12, G:0.15, T:0.03
Consensus pattern (16 bp):
CAAGGAAACAAATAAA
Found at i:21710132 original size:98 final size:98
Alignment explanation
Indices: 21710012--21710205 Score: 352
Period size: 98 Copynumber: 2.0 Consensus size: 98
21710002 AAAAAAATAA
*
21710012 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21710077 TTAAATCTTGGATAAGTGGATGTTCTTTTAAGG
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAAGG
* *
21710110 TAAAGGAAATATTCTGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
21710175 TTAAATCTAGGATAAGTGGATGTTCTTTTAA
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAA
21710206 AGTTTTATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTAGGATAAGTGGATGTTCTTTTAAGG
Found at i:21722455 original size:98 final size:98
Alignment explanation
Indices: 21722334--21722530 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
21722324 AAAAAAAAAA
* *
21722334 TAAAGGAAATATTTTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21722399 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
*
21722432 TAAAGGAAATATTCTGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
21722497 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
21722530 T
1 T
21722531 TTTATTACTC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (98 bp):
TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
Found at i:21725138 original size:204 final size:204
Alignment explanation
Indices: 21724783--21725190 Score: 690
Period size: 204 Copynumber: 2.0 Consensus size: 204
21724773 TACATGCTGG
* * * *
21724783 ATCCTGATATAACCTGTAATAATCTTTGTACAATCACATATCTCATATAAGCGCACATATAACCT
1 ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
* * *
21724848 TATTAGCATGTCAATTGTATTCTAACCTTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
66 TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
*
21724913 CTTTATCATACTTGTAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
131 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
21724978 TCATACCCT
196 TCATACCCT
* *
21724987 ATCCCGATATAACATGTAATAATCTTCGTGCAATCACATATCTCATATAAGCGGACATATAACCC
1 ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
* * *
21725052 TATTAGCATGTCAATCGTATCCTAGCATTTTACTAAGTTCATATGGGCATAAATATTCATATTTT
66 TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
*
21725117 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATGTCCTATAATCATTTACATTTATTTG
131 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
21725182 TCATACCCT
196 TCATACCCT
21725191 GTGTTCGGTC
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
204 190 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (204 bp):
ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
TCATACCCT
Found at i:21725926 original size:22 final size:21
Alignment explanation
Indices: 21725892--21725941 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
21725882 TTAGTCCTTT
* *
21725892 TCAAAATCTAAGCTTAATATCTA
1 TCAAATTCTAAGCCTAAT-TC-A
21725915 TCAAATTC-AAGCCTAATTCA
1 TCAAATTCTAAGCCTAATTCA
21725935 TCAAATT
1 TCAAATT
21725942 ATCGATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 8 0.32
23 7 0.28
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (21 bp):
TCAAATTCTAAGCCTAATTCA
Found at i:21732249 original size:3 final size:3
Alignment explanation
Indices: 21732241--21732278 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21732231 AATAGGTTTA
21732241 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21732279 CGCTGGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21733009 original size:9 final size:9
Alignment explanation
Indices: 21732973--21733026 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
21732963 TTTAATTATT
21732973 TTTTAA-AA
1 TTTTAATAA
21732981 -TTT-ATAA
1 TTTTAATAA
21732988 TTTT-ATAA
1 TTTTAATAA
21732996 CTTTTAATAA
1 -TTTTAATAA
*
21733006 TTTTAATGA
1 TTTTAATAA
21733015 TTTTAA-AA
1 TTTTAATAA
21733023 TTTT
1 TTTT
21733027 TAAAATAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.03
7 5 0.12
8 12 0.30
9 18 0.45
10 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:21739093 original size:2 final size:2
Alignment explanation
Indices: 21739086--21739123 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
21739076 TACCCTTTTA
21739086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21739124 GAAAAGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21740254 original size:19 final size:18
Alignment explanation
Indices: 21740204--21740254 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
21740194 GTATATTTTA
21740204 ATATTTCAAATTTTAAAT
1 ATATTTCAAATTTTAAAT
* *
21740222 ATGGTTGC-AATTTTAAAT
1 AT-ATTTCAAATTTTAAAT
21740240 ATATATTCAAATTTT
1 ATAT-TTCAAATTTT
21740255 TAACAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 1 0.04
18 16 0.62
19 9 0.35
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATTTCAAATTTTAAAT
Found at i:21740888 original size:17 final size:16
Alignment explanation
Indices: 21740852--21740891 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
21740842 TATTTTTATG
21740852 TTATTAAATTACATTA
1 TTATTAAATTACATTA
21740868 TTATTAATATATACA-TA
1 TTATTAA-AT-TACATTA
21740885 TTATTAA
1 TTATTAA
21740892 CCTGAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTAAATTACATTA
Found at i:21745060 original size:54 final size:54
Alignment explanation
Indices: 21744995--21745376 Score: 414
Period size: 54 Copynumber: 7.1 Consensus size: 54
21744985 ATTCGTCGGC
**
21744995 AAATGACCGAAATAATCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * *
21745049 AAATGATCGAAACACCCCCATAGGAT-AAATGATTGAAATA-CCCCGAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * * *
21745101 AAATGACCGAAATACACCCATAAGGTAAAATGA-CTGCAATGCCCCCGAAGGGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCAAAGGGTA
* * * * *
21745155 AAATGACCAAAACACCCCCATAGGGTAAAATGATCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* *
21745209 AAATGACCGAAATACCCCCATAGGGTAAAAT-AACTGAAATACCCCTAAAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCAAAGGGTA
** * * ** * *
21745263 AAATGAATGAAATACCCCCATAGGGTAGAATAATTAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
* * * * *
21745317 AAATGACTGGAACA-CCCCATAGGGTAAAATGATCGAAATACCCCGATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
21745370 AAATGAC
1 AAATGAC
21745377 TGTTATACCC
Statistics
Matches: 272, Mismatches: 50, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
52 32 0.12
53 65 0.24
54 173 0.64
55 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (54 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCAAAGGGTA
Found at i:21745384 original size:27 final size:27
Alignment explanation
Indices: 21744995--21745387 Score: 324
Period size: 27 Copynumber: 14.7 Consensus size: 27
21744985 ATTCGTCGGC
* *
21744995 AAATGACCGAAATAATCCC-ATAGGGTA
1 AAATGACTGAAAT-ACCCCGATAGGGTA
* *
21745022 AAATGA-TCGAAATACCCCCAAAGGGTA
1 AAATGACT-GAAATACCCCGATAGGGTA
* * *
21745049 AAATGA-TCGAAACACCCCCATAGGAT-
1 AAATGACT-GAAATACCCCGATAGGGTA
*
21745075 AAATGATTGAAATACCCCGA-AGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* *
21745101 AAATGACCGAAATACACCC-ATAAGGTA
1 AAATGACTGAAATAC-CCCGATAGGGTA
* * *
21745128 AAATGACTGCAATGCCCCCGA-AGGGAA
1 AAATGACTGAAAT-ACCCCGATAGGGTA
** * *
21745155 AAATGACCAAAACACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
*
21745182 AAATGA-TCAAAATACCCTCGA-AGGGTA
1 AAATGACT-GAAATACCC-CGATAGGGTA
* *
21745209 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* * *
21745236 AAATAACTGAAATACCCCTAAAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* *
21745263 AAATGAATGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
* * * *
21745290 GAATAATTAAAATACCCTC-ATAGGGTA
1 AAATGACTGAAATACCC-CGATAGGGTA
* *
21745317 AAATGACTGGAACACCCC-ATAGGGTA
1 AAATGACTGAAATACCCCGATAGGGTA
21745343 AAATGA-TCGAAATACCCCGATAGGGTA
1 AAATGACT-GAAATACCCCGATAGGGTA
**
21745370 AAATGACTGTTATACCCC
1 AAATGACTGAAATACCCC
21745388 TAGGAGATGA
Statistics
Matches: 297, Mismatches: 52, Indels: 34
0.78 0.14 0.09
Matches are distributed among these distances:
25 5 0.02
26 64 0.22
27 222 0.75
28 6 0.02
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACTGAAATACCCCGATAGGGTA
Found at i:21745558 original size:26 final size:26
Alignment explanation
Indices: 21745529--21745591 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
21745519 TGATACTAGT
*
21745529 AGCTTTGCTGCGATACTATTACTGGC
1 AGCTTTGCTGCGATACTACTACTGGC
* * *
21745555 AGCTTTGTTGCGATGCTACTACTGGT
1 AGCTTTGCTGCGATACTACTACTGGC
21745581 AGCTTTGCTGC
1 AGCTTTGCTGC
21745592 AACATTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (26 bp):
AGCTTTGCTGCGATACTACTACTGGC
Found at i:21745741 original size:28 final size:28
Alignment explanation
Indices: 21745698--21745791 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
21745688 ATTACATTGT
* * *
21745698 ACTGATACTGTGTTGGGCTAAGGCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
21745726 ACTGTTACTGTATTGGGTTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
21745754 ATTGTTTCTGTATCGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
21745782 AATG-TACTGT
1 ACTGTTACTGT
21745792 TACTGAATAG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 5 0.09
28 51 0.91
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:21755151 original size:4 final size:4
Alignment explanation
Indices: 21755137--21755170 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
21755127 TTCAAAAAAG
*
21755137 GAAA TAAA GAAA GAAA GAAA GAAA GAAA -AAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
21755171 CAAAGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:21758434 original size:11 final size:12
Alignment explanation
Indices: 21758403--21758427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21758393 TAAACTTTCG
21758403 AAATATTTGAAA
1 AAATATTTGAAA
21758415 AAATATTTGAAA
1 AAATATTTGAAA
21758427 A
1 A
21758428 CTATTTGCTT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATATTTGAAA
Found at i:21772367 original size:20 final size:20
Alignment explanation
Indices: 21772341--21772437 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
21772331 CTTGTATGAG
21772341 TTTGCACTTTGGTGCCTCTGA
1 TTTGCACTTTGGTGCCTCT-A
* *** *
21772362 -TTGCACATCAATTCCTCTA
1 TTTGCACTTTGGTGCCTCTA
* *
21772381 TTTGGACTTCGGTGCCTCTA
1 TTTGCACTTTGGTGCCTCTA
*
21772401 TTTGCACTTTGGTGCTTCTGA
1 TTTGCACTTTGGTGCCTCT-A
21772422 -TTGCACATTT-GTGCCT
1 TTTGCAC-TTTGGTGCCT
21772438 TTATCTAAAC
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.02
20 54 0.92
21 4 0.07
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTGCACTTTGGTGCCTCTA
Found at i:21772457 original size:60 final size:60
Alignment explanation
Indices: 21772341--21772457 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
21772331 CTTGTATGAG
* * ** **
21772341 TTTGCACTTTGGTGCCTCTGATTGCACATCAATTCCTCTATTTGGACTTCGGTGCCTCTA
1 TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCTCTA
* *** *
21772401 TTTGCACTTTGGTGCTTCTGATTGCACATTTGTGCCTTTATCTAAACTTCAATGCCT
1 TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCT
21772458 TTGTTACGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (60 bp):
TTTGCACTTTGGTGCCTCTGATTGCACATCAATGCCTCTATCTAAACTTCAATGCCTCTA
Found at i:21776959 original size:2 final size:2
Alignment explanation
Indices: 21776952--21776981 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21776942 TTCAAGAAAC
*
21776952 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21776982 CATGCCAAAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21777791 original size:15 final size:15
Alignment explanation
Indices: 21777771--21777824 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
21777761 ATACTAAAAA
21777771 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
21777786 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
21777803 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
21777820 ATATT
1 ATATT
21777825 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:21783381 original size:2 final size:2
Alignment explanation
Indices: 21783374--21783398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21783364 GAAAGACACC
21783374 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
21783399 ATGGGCATAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:21785809 original size:30 final size:32
Alignment explanation
Indices: 21785757--21785815 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
21785747 AATTAGACAC
21785757 TTTTAAGAAGTTAATGATCAAATTCAACTATT
1 TTTTAAGAAGTTAATGATCAAATTCAACTATT
* *
21785789 TTTTAA-AAGTTTATG-TCAAATTTAACT
1 TTTTAAGAAGTTAATGATCAAATTCAACT
21785816 CTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 8 0.32
32 6 0.24
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTAAGAAGTTAATGATCAAATTCAACTATT
Found at i:21786868 original size:22 final size:22
Alignment explanation
Indices: 21786789--21786860 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
21786779 GTTGTTGCTG
* **
21786789 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
21786811 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
21786833 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
21786855 CATGAG
1 CATGAG
21786861 GGTTTAGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:21787985 original size:50 final size:50
Alignment explanation
Indices: 21787895--21788005 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
21787885 AATTGTATGT
* * * *
21787895 TTTTTTGTAATTGAGCCTATCTCAGAAGCGCTAATGAATATTTTATAATAA
1 TTTTTT-TAATGGAGCCTATCTAAGAAGCGCCAATAAATATTTTATAATAA
* * * *
21787946 TTTTTTTAATGGCGCCTATCTAATAGGCGCCAATAAATATTTTATATTAA
1 TTTTTTTAATGGAGCCTATCTAAGAAGCGCCAATAAATATTTTATAATAA
*
21787996 ATTTTTTAAT
1 TTTTTTTAAT
21788006 AAAATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
50 45 0.88
51 6 0.12
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (50 bp):
TTTTTTTAATGGAGCCTATCTAAGAAGCGCCAATAAATATTTTATAATAA
Found at i:21788108 original size:27 final size:27
Alignment explanation
Indices: 21788078--21788144 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
21788068 CCTATCTTAG
*
21788078 AGGCGCCAATGGTGGTGCC-TTTCTGAC
1 AGGCGCCAATGGTGGTGCCATGT-TGAC
* * * *
21788105 AGGCGCCACTAGTTGTGCCATGTTGAG
1 AGGCGCCAATGGTGGTGCCATGTTGAC
21788132 AGGCGCCAATGGT
1 AGGCGCCAATGGT
21788145 CTTATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.24
Consensus pattern (27 bp):
AGGCGCCAATGGTGGTGCCATGTTGAC
Found at i:21791002 original size:18 final size:18
Alignment explanation
Indices: 21790981--21791034 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
21790971 AAGGCAACAT
21790981 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
*
21790999 AAATTAAA---AGAAA-A
1 AAATTAAATTGATAAATA
*
21791013 AATTTAAATTGATAAATA
1 AAATTAAATTGATAAATA
21791031 AAAT
1 AAAT
21791035 GCCAACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
17 4 0.14
18 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
AAATTAAATTGATAAATA
Found at i:21791033 original size:19 final size:19
Alignment explanation
Indices: 21790984--21791034 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 19
21790974 GCAACATAAA
21790984 TTAAATTGATAAATAAAA-
1 TTAAATTGATAAATAAAAT
*
21791002 TTAAA---A-GAA-AAAAT
1 TTAAATTGATAAATAAAAT
21791016 TTAAATTGATAAATAAAAT
1 TTAAATTGATAAATAAAAT
21791035 GCCAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 11
0.66 0.05 0.29
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
15 1 0.04
17 1 0.04
18 7 0.28
19 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
TTAAATTGATAAATAAAAT
Found at i:21793037 original size:15 final size:16
Alignment explanation
Indices: 21793017--21793055 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
21793007 ATAAAAAATC
21793017 ATATAAAAA-TACATT
1 ATATAAAAATTACATT
21793032 ATATAAAAATTACATT
1 ATATAAAAATTACATT
21793048 ATATAAAA
1 ATATAAAA
21793056 TTTAAATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:21793323 original size:22 final size:21
Alignment explanation
Indices: 21793262--21793326 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
21793252 ATATATATTT
*
21793262 AAATATTTTTAATATAAATAA
1 AAATATTTTTAATATAAAAAA
* *
21793283 AAATCAATATTT-ATTTAAACAAA
1 AAAT--ATTTTTAATATAAA-AAA
21793306 AAATATTTTTAATATAAAAAA
1 AAATATTTTTAATATAAAAAA
21793327 TTGATTTGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 12 0.34
22 12 0.34
23 11 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATTTTTAATATAAAAAA
Found at i:21793404 original size:57 final size:58
Alignment explanation
Indices: 21793297--21793408 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
21793287 CAATATTTAT
* *
21793297 TTAAACAAAAAATATTTTTAATATAAAAAATTGATTTGCGCCTGTTAGATAGGCGGGA
1 TTAAACAAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCGGGA
* * * *
21793355 TTAAA-AAAATATATTTTTCAGTAT-AAAAATTTATTCGCGTCTGTCAGATAGGCG
1 TTAAACAAAAAATATTTTT-AATATAAAAAATTGATTCGCGCCTGTCAGATAGGCG
21793409 CTATTAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 38 0.81
58 9 0.19
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (58 bp):
TTAAACAAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTCAGATAGGCGGGA
Found at i:21794223 original size:14 final size:14
Alignment explanation
Indices: 21794206--21794232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21794196 TGGGTTTATG
21794206 GGTTTTGGTTATAA
1 GGTTTTGGTTATAA
21794220 GGTTTTGGTTATA
1 GGTTTTGGTTATA
21794233 GGCAAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (14 bp):
GGTTTTGGTTATAA
Found at i:21794866 original size:17 final size:17
Alignment explanation
Indices: 21794841--21794875 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21794831 ATTAATAATT
21794841 AATAACAAAAAAATCAC
1 AATAACAAAAAAATCAC
*
21794858 AATATCAAAAAAATCAC
1 AATAACAAAAAAATCAC
21794875 A
1 A
21794876 TTACCTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAACAAAAAAATCAC
Found at i:21805465 original size:44 final size:44
Alignment explanation
Indices: 21805402--21805489 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
21805392 ATTTAAGAAC
21805402 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
21805446 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
1 CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
21805490 TAGATCCGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (44 bp):
CAGTTGAAAGATTTAAATTTTATACTTATATTTATTCTTTTCTT
Found at i:21816941 original size:29 final size:30
Alignment explanation
Indices: 21816860--21816930 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
21816850 GATTAAATCA
*
21816860 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATATATTTGAACC
* * *
21816890 ACAACTAAAGTTTCACGTATATATTTGCACC
1 A-AATTAAAGTTTCAAGTATATATTTGAACC
21816921 AAATTAAAGT
1 AAATTAAAGT
21816931 CCATGTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 9 0.26
31 26 0.74
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATATTTGAACC
Found at i:21818502 original size:26 final size:25
Alignment explanation
Indices: 21818469--21818540 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
21818459 TTAGCTCTTA
21818469 TAAGCTTCCCGATTATAGGCTCTTCG
1 TAAGCTTCCCGATTAT-GGCTCTTCG
* * *
21818495 TGAGCTT-CCTATTAATTGGCTCTTTG
1 TAAGCTTCCCGATT-A-TGGCTCTTCG
21818521 TAAGCTTCCCGA-TATGGCTC
1 TAAGCTTCCCGATTATGGCTC
21818541 GTTTGAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 6 0.16
25 6 0.16
26 22 0.58
27 4 0.11
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
TAAGCTTCCCGATTATGGCTCTTCG
Done.