Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 132 of 199
Found at i:39911084 original size:14 final size:14
Alignment explanation
Indices: 39911053--39911105 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 14
39911043 ACCCTTGAAC
39911053 CTTAAACCC-AAAT
1 CTTAAACCCTAAAT
*
39911066 ATTAAACCCTAAAT
1 CTTAAACCCTAAAT
39911080 CTTAAACCCTAAA-
1 CTTAAACCCTAAAT
* *
39911093 CCTAAACCTTAAA
1 CTTAAACCCTAAA
39911106 CCAAGAGCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 19 0.54
14 16 0.46
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
CTTAAACCCTAAAT
Found at i:39911096 original size:20 final size:21
Alignment explanation
Indices: 39911068--39911126 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
39911058 ACCCAAATAT
*
39911068 TAAACCCTAAATCTTAAACCC
1 TAAACCCTAAACCTTAAACCC
39911089 TAAA-CCTAAACCTTAAA-CC
1 TAAACCCTAAACCTTAAACCC
39911108 -AAGAGCCCTAAACCTTAAA
1 TAA-A-CCCTAAACCTTAAA
39911127 TCTCAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 12 0.35
21 17 0.50
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCTTAAACCC
Found at i:39911486 original size:2 final size:2
Alignment explanation
Indices: 39911479--39911543 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
39911469 NNNNNNNNNN
39911479 TA TA TA 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 TA TA TA
39911521 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
39911544 CGGGAGGGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39918024 original size:15 final size:16
Alignment explanation
Indices: 39917992--39918025 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39917982 ATTGTATCTC
*
39917992 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
39918008 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
39918023 ATT
1 ATT
39918026 ATTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:39918288 original size:7 final size:7
Alignment explanation
Indices: 39918271--39918303 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
39918261 GCAATTTGGT
39918271 TTTTTTA
1 TTTTTTA
39918278 -TTTTTA
1 TTTTTTA
39918284 TTTTTTA
1 TTTTTTA
39918291 TTTTTTA
1 TTTTTTA
39918298 TTTTTT
1 TTTTTT
39918304 GTGATTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:39918289 original size:14 final size:15
Alignment explanation
Indices: 39918270--39918303 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
39918260 TGCAATTTGG
39918270 TTTTTTTA-TTTTTA
1 TTTTTTTATTTTTTA
39918284 -TTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
39918298 TTTTTT
1 TTTTTT
39918304 GTGATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:39922083 original size:18 final size:18
Alignment explanation
Indices: 39922069--39922105 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39922059 TTCACTTAGT
39922069 TTGAGAGCCCAACTTAAA
1 TTGAGAGCCCAACTTAAA
*
39922087 TTGAGAGCCCAATTTAAA
1 TTGAGAGCCCAACTTAAA
39922105 T
1 T
39922106 CAAAAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (18 bp):
TTGAGAGCCCAACTTAAA
Found at i:39932615 original size:12 final size:13
Alignment explanation
Indices: 39932594--39932632 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
39932584 TCAAAGATTG
39932594 GAATAATAAAGAA
1 GAATAATAAAGAA
39932607 GAA-AATAAAGAA
1 GAATAATAAAGAA
*
39932619 -AATAATAAGGAA
1 GAATAATAAAGAA
39932631 GA
1 GA
39932633 TAGATGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.09
12 17 0.74
13 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (13 bp):
GAATAATAAAGAA
Found at i:39932824 original size:27 final size:27
Alignment explanation
Indices: 39932784--39932838 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
39932774 GTTAAAACCT
39932784 AAAAGAAAACTC-AAGAAAATTTATTA
1 AAAAGAAAACTCAAAGAAAATTTATTA
*
39932810 AAAAGAACAACTCAAAGAGAATTTATTA
1 AAAAGAA-AACTCAAAGAAAATTTATTA
39932838 A
1 A
39932839 CTCAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.27
27 5 0.19
28 14 0.54
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (27 bp):
AAAAGAAAACTCAAAGAAAATTTATTA
Found at i:39935493 original size:32 final size:32
Alignment explanation
Indices: 39935452--39935524 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
39935442 TTTATAGTTA
39935452 GTATCGATATTCAATTACTAGGCATCAATACT
1 GTATCGATATTCAATTACTAGGCATCAATACT
* *
39935484 GTATCGATATTTAATTACTAGGCATCGATACT
1 GTATCGATATTCAATTACTAGGCATCAATACT
*
39935516 ATATCGATA
1 GTATCGATA
39935525 CCATATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (32 bp):
GTATCGATATTCAATTACTAGGCATCAATACT
Found at i:39937708 original size:20 final size:20
Alignment explanation
Indices: 39937685--39937729 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39937675 TAATGTGTCT
*
39937685 AATTAAGTTTTAAT-TAGATA
1 AATTAA-TTTTAATAAAGATA
*
39937705 AATTTATTTTAATAAAGATA
1 AATTAATTTTAATAAAGATA
39937725 AATTA
1 AATTA
39937730 GGAAAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AATTAATTTTAATAAAGATA
Found at i:39938139 original size:19 final size:18
Alignment explanation
Indices: 39938105--39938140 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39938095 ACTAGATAAA
*
39938105 TAAAAGAAAGAAAAGAAG
1 TAAAAGAAAAAAAAGAAG
39938123 TAAAAGAAACAAAAAGAA
1 TAAAAGAAA-AAAAAGAA
39938141 CAGCAGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
TAAAAGAAAAAAAAGAAG
Found at i:39939092 original size:23 final size:20
Alignment explanation
Indices: 39939065--39939125 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
39939055 GCCTTGCCAA
39939065 TCAGGCACTTTATGTGTCTTATT
1 TCAGGCAC-TTATGTGTC-T-TT
**
39939088 TCAGGCACCTCGTGTGTCTTT
1 TCAGGCA-CTTATGTGTCTTT
*
39939109 TAAGGCACTTATGTGTC
1 TCAGGCACTTATGTGTC
39939126 GTATACTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 1 0.03
23 14 0.44
24 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TCAGGCACTTATGTGTCTTT
Found at i:39941200 original size:41 final size:41
Alignment explanation
Indices: 39941131--39941235 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
39941121 ACCAGAGCGT
* * *
39941131 AAACAGGGGCACAAAAGTGC-ATTTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATTTAGGGGCACCGAAGTAC
* * * *
39941171 AAACAGGGGTACGTATGTGTAATTTAGGGGCATCGAAGTAC
1 AAACAGGGGCACGAATGTGCAATTTAGGGGCACCGAAGTAC
*
39941212 AAACATGGGCACGAATGTGCAATT
1 AAACAGGGGCACGAATGTGCAATT
39941236 CAACAATATT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (41 bp):
AAACAGGGGCACGAATGTGCAATTTAGGGGCACCGAAGTAC
Found at i:39948992 original size:26 final size:27
Alignment explanation
Indices: 39948960--39949011 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39948950 AAAAATTATA
*
39948960 TTTTTTATC-CTTCTATTTTTTTTCAT
1 TTTTTTATCTCTTCAATTTTTTTTCAT
*
39948986 TTTTTTATCTTTTCAATTTTTTTTCA
1 TTTTTTATCTCTTCAATTTTTTTTCA
39949012 CTTTACTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTTTATCTCTTCAATTTTTTTTCAT
Found at i:39959175 original size:19 final size:21
Alignment explanation
Indices: 39959147--39959195 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39959137 GGTTTTTTAC
*
39959147 TAAAATAATA-CAAAAGAA-A
1 TAAAAAAATACCAAAAGAATA
*
39959166 TAAAAAAATACCAAAATAATA
1 TAAAAAAATACCAAAAGAATA
39959187 TAAAAAAAT
1 TAAAAAAAT
39959196 TATTTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 7 0.27
21 10 0.38
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAAATACCAAAAGAATA
Found at i:39959281 original size:27 final size:27
Alignment explanation
Indices: 39959243--39959305 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
39959233 GGTAATGGAA
*
39959243 TGGCGGCACCGGTGGTGCCATTCTCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
39959270 TGGCGGCACCGGTGGTGCCATTCCCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
39959297 TGGCGGCAC
1 TGGCGGCAC
39959306 AGGACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.11, C:0.32, G:0.35, T:0.22
Consensus pattern (27 bp):
TGGCGGCACCGGTGGTGCCATTCCCAT
Found at i:39961107 original size:19 final size:21
Alignment explanation
Indices: 39961065--39961113 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39961055 TTGGTAAATA
39961065 ATTTTTTTATATTATTTTGAT
1 ATTTTTTTATATTATTTTGAT
*
39961086 ATTTTTTTAT-TTCTTTTG-T
1 ATTTTTTTATATTATTTTGAT
*
39961105 ATTATTTTA
1 ATTTTTTTA
39961114 GTAAAAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 7 0.27
21 10 0.38
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTTTATATTATTTTGAT
Found at i:39965863 original size:17 final size:17
Alignment explanation
Indices: 39965815--39965865 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
39965805 ATATGAGACA
* *
39965815 TAATCTTCGAAGATATG
1 TAATCTTAGAAGATTTG
* **
39965832 CAATCTTAGGGGATTTG
1 TAATCTTAGAAGATTTG
39965849 TAATCTTAGAAGATTTG
1 TAATCTTAGAAGATTTG
39965866 ATTCTGTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (17 bp):
TAATCTTAGAAGATTTG
Found at i:39967938 original size:24 final size:24
Alignment explanation
Indices: 39967911--39967965 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
39967901 GATATTGACT
* *
39967911 TTTTCATTGATATTATTTTCGACC
1 TTTTCATTGATATCATTTTCAACC
*
39967935 TTTTCATTTATATCATTTTCAACC
1 TTTTCATTGATATCATTTTCAACC
39967959 TTCTTCA
1 TT-TTCA
39967966 ATGGATCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTCATTGATATCATTTTCAACC
Found at i:39968138 original size:36 final size:36
Alignment explanation
Indices: 39968091--39968297 Score: 119
Period size: 36 Copynumber: 5.6 Consensus size: 36
39968081 GTGCCCTGCA
*
39968091 CTAGTCGGATAAACCGACAATGTTTTGCGCCCAACG
1 CTAGTCGGATAAACCGACAATGTTTTGCGCCCAGCG
* ** * * * *
39968127 CTAGTTGGATAAATTGACAATATCAAATGTGTG-CCAGCA
1 CTAGTCGGATAAACCGACAATGT----TTTGCGCCCAGCG
** *
39968166 CTAGTCGGATAAATTGACAATGTTTTGCTCCCAGCG
1 CTAGTCGGATAAACCGACAATGTTTTGCGCCCAGCG
* * * ** **
39968202 CTAGTTGGATAAACCGACAATATCAAATGTGTACCCAGTA
1 CTAGTCGGATAAACCGACAATGT----TTTGCGCCCAGCG
* * * * *
39968242 CTAATTGGATAAATCGACAATGATTTGCGCCCAGCA
1 CTAGTCGGATAAACCGACAATGTTTTGCGCCCAGCG
*
39968278 CTAGTCGGATAAACTGACAA
1 CTAGTCGGATAAACCGACAA
39968298 ATACATATGT
Statistics
Matches: 127, Mismatches: 35, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
35 3 0.02
36 68 0.54
39 25 0.20
40 31 0.24
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (36 bp):
CTAGTCGGATAAACCGACAATGTTTTGCGCCCAGCG
Found at i:39968185 original size:75 final size:75
Alignment explanation
Indices: 39968079--39968297 Score: 294
Period size: 75 Copynumber: 2.9 Consensus size: 75
39968069 ACCGACGAAG
* * * *
39968079 GTGTGCCCTGCACTAGTCGGATAAACCGACAATGTTTTGCGCCCAACGCTAGTTGGATAAATTGA
1 GTGTG-CCAGCACTAGTCGGATAAATCGACAATGTTTTGCGCCCAGCGCTAGTTGGATAAACTGA
39968144 CAATATCAAAT
65 CAATATCAAAT
* * *
39968155 GTGTGCCAGCACTAGTCGGATAAATTGACAATGTTTTGCTCCCAGCGCTAGTTGGATAAACCGAC
1 GTGTGCCAGCACTAGTCGGATAAATCGACAATGTTTTGCGCCCAGCGCTAGTTGGATAAACTGAC
39968220 AATATCAAAT
66 AATATCAAAT
* * * * * * *
39968230 GTGTACCCAGTACTAATTGGATAAATCGACAATGATTTGCGCCCAGCACTAGTCGGATAAACTGA
1 GTGT-GCCAGCACTAGTCGGATAAATCGACAATGTTTTGCGCCCAGCGCTAGTTGGATAAACTGA
39968295 CAA
65 CAA
39968298 ATACATATGT
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
75 67 0.54
76 58 0.46
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (75 bp):
GTGTGCCAGCACTAGTCGGATAAATCGACAATGTTTTGCGCCCAGCGCTAGTTGGATAAACTGAC
AATATCAAAT
Found at i:39968410 original size:2 final size:2
Alignment explanation
Indices: 39968403--39968434 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39968393 AACCATTTTC
*
39968403 AT AT AT AT AT GT 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
39968435 TTCCATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39972523 original size:18 final size:19
Alignment explanation
Indices: 39972483--39972524 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39972473 GCAAATGAAT
*
39972483 CATTTCTCATTTTCAATTC
1 CATTTCTCATTTTCAATTA
*
39972502 CATTTCT-ATTTTCATTTA
1 CATTTCTCATTTTCAATTA
39972520 CATTT
1 CATTT
39972525 TGAGAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (19 bp):
CATTTCTCATTTTCAATTA
Found at i:39972606 original size:19 final size:18
Alignment explanation
Indices: 39972564--39972608 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
39972554 TATGCCCAGG
** *
39972564 CCCAAACCAACACTCAGG
1 CCCAAACCAACAAACAGA
39972582 CCCAAACCAACAAACAAGA
1 CCCAAACCAACAAAC-AGA
39972601 CCCAAACC
1 CCCAAACC
39972609 CTAAACCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.47, C:0.44, G:0.07, T:0.02
Consensus pattern (18 bp):
CCCAAACCAACAAACAGA
Found at i:39973634 original size:3 final size:3
Alignment explanation
Indices: 39973626--39973691 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
39973616 TAATATTGCA
39973626 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
39973674 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
39973692 GCCTACATAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39975451 original size:17 final size:17
Alignment explanation
Indices: 39975425--39975460 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39975415 GTGTGTTTTG
*
39975425 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
*
39975442 TTTTGACTGCATGGCAT
1 TTTTGACTGCATGACAT
39975459 TT
1 TT
39975461 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:39975903 original size:19 final size:18
Alignment explanation
Indices: 39975879--39975924 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
39975869 ACGTCTCTTT
*
39975879 TTTGCATTCATTCCATGCA
1 TTTGCATTCATTACAT-CA
39975898 TTTGCATTTCATTACATCA
1 TTTGCA-TTCATTACATCA
*
39975917 TATGCATT
1 TTTGCATT
39975925 AGACTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (18 bp):
TTTGCATTCATTACATCA
Found at i:39983455 original size:34 final size:34
Alignment explanation
Indices: 39983417--39983483 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
39983407 AATATATGAA
*
39983417 TGTTTTATTTTCAGTTTGAAAATGGCACCAACTT
1 TGTTTTATTTTCACTTTGAAAATGGCACCAACTT
*
39983451 TGTTTTATTTTTACTTTGAAAATGGCACCAACT
1 TGTTTTATTTTCACTTTGAAAATGGCACCAACT
39983484 CTTTTATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (34 bp):
TGTTTTATTTTCACTTTGAAAATGGCACCAACTT
Found at i:39986772 original size:20 final size:20
Alignment explanation
Indices: 39986747--39986799 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
39986737 TACAGGATTG
* *
39986747 CACTTCGGTGCCTCTATTTA
1 CACTTCAGTGCCTCTAATTA
* *
39986767 CACTTCAGTGTCTCTAATTG
1 CACTTCAGTGCCTCTAATTA
39986787 CACTTCAGTGCCT
1 CACTTCAGTGCCT
39986800 TTGTTTAGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (20 bp):
CACTTCAGTGCCTCTAATTA
Found at i:39989620 original size:2 final size:2
Alignment explanation
Indices: 39989613--39989649 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39989603 TATGTTTTAT
39989613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39989650 TCAAAATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39989728 original size:12 final size:12
Alignment explanation
Indices: 39989711--39989743 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39989701 TCTTAGTTTT
39989711 TACATACATACG
1 TACATACATACG
*
39989723 TACATACATAGG
1 TACATACATACG
39989735 TACATACAT
1 TACATACAT
39989744 TATTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (12 bp):
TACATACATACG
Found at i:39993488 original size:20 final size:20
Alignment explanation
Indices: 39993463--39993568 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
39993453 TTAAGTGTTC
39993463 ATGGTTTTGGGTTTGAGTTT
1 ATGGTTTTGGGTTTGAGTTT
* *
39993483 ATGGTTTAGGG-TTCA----
1 ATGGTTTTGGGTTTGAGTTT
*
39993498 AT-GTTTAGGGTTTGAGATTCT
1 ATGGTTTTGGGTTTGAG-TT-T
* * *
39993519 A-GATTTATGGTTTTGGGTTT
1 ATGGTTT-TGGGTTTGAGTTT
* *
39993539 ATGGTTATGGTTTTGAGTTT
1 ATGGTTTTGGGTTTGAGTTT
39993559 ATGGTTTTGG
1 ATGGTTTTGG
39993569 CTTCTAGGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.12
15 5 0.08
19 3 0.05
20 33 0.51
21 9 0.14
22 7 0.11
ACGTcount: A:0.15, C:0.02, G:0.32, T:0.51
Consensus pattern (20 bp):
ATGGTTTTGGGTTTGAGTTT
Found at i:39993556 original size:76 final size:75
Alignment explanation
Indices: 39993463--39993619 Score: 188
Period size: 76 Copynumber: 2.1 Consensus size: 75
39993453 TTAAGTGTTC
* * * *
39993463 ATGGTTTTGGGTTTGAGTTTATGGTTTAGGGTTCAATGTTTAGGGTTTGAGATTCTAGATTTATG
1 ATGGTTATGGGTTTGAGTTTATGGTTTAGGCTTCAAGGTTTAGGGTTTAAGATTCTAGATTTATG
*
39993528 GTTTTGGGTTT
66 GTTTAGGG-TT
* * * ** * * *
39993539 ATGGTTATGGTTTTGAGTTTATGGTTTTGGCTTCTAGGTTTTTGGTTTAAGATTTTATATTTGTG
1 ATGGTTATGGGTTTGAGTTTATGGTTTAGGCTTCAAGGTTTAGGGTTTAAGATTCTAGATTTATG
39993604 GTTTAGGGTT
66 GTTTAGGGTT
39993614 ATGGTT
1 ATGGTT
39993620 TTGATTTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
75 8 0.12
76 60 0.88
ACGTcount: A:0.15, C:0.03, G:0.30, T:0.52
Consensus pattern (75 bp):
ATGGTTATGGGTTTGAGTTTATGGTTTAGGCTTCAAGGTTTAGGGTTTAAGATTCTAGATTTATG
GTTTAGGGTT
Found at i:39993560 original size:34 final size:33
Alignment explanation
Indices: 39993522--39993628 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 33
39993512 AGATTCTAGA
*
39993522 TTTATGGTTTTGGGTTTATGGTTATGGTTTTGAG
1 TTTATGGTTTTGGGTTTA-GGTTATGGTTTTGAT
* * *
39993556 TTTATGGTTTTGGCTTCTAGGTTTTTGGTTTAAGAT
1 TTTATGGTTTTGGGTT-TAGG-TTATGGTTT-TGAT
*
39993592 TTTAT--ATTTGTGGTTTAGGGTTATGGTTTTGAT
1 TTTATGGTTTTG-GGTTTA-GGTTATGGTTTTGAT
39993625 TTTA
1 TTTA
39993629 AGATTTAGGG
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
33 7 0.12
34 31 0.52
35 15 0.25
36 7 0.12
ACGTcount: A:0.14, C:0.02, G:0.27, T:0.57
Consensus pattern (33 bp):
TTTATGGTTTTGGGTTTAGGTTATGGTTTTGAT
Found at i:39993662 original size:27 final size:27
Alignment explanation
Indices: 39993603--39993663 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39993593 TTATATTTGT
* *
39993603 GGTTTAGGGTTATGGTTTTGATTTTAA
1 GGTTTAGGGTTATGGTTCTAATTTTAA
* *
39993630 GATTTAGGGTTAT-GTGTCTAATTTTAG
1 GGTTTAGGGTTATGGT-TCTAATTTTAA
39993657 GGTTTAG
1 GGTTTAG
39993664 TGTTCAAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.49
Consensus pattern (27 bp):
GGTTTAGGGTTATGGTTCTAATTTTAA
Found at i:39993780 original size:22 final size:22
Alignment explanation
Indices: 39993745--39993786 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39993735 ATTCGAGGTT
*
39993745 AGGTTTTGGAGTTTAAGGTTTA
1 AGGTTTTAGAGTTTAAGGTTTA
* *
39993767 AGGTTTTAGTGTTTATGGTT
1 AGGTTTTAGAGTTTAAGGTT
39993787 CTATGTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (22 bp):
AGGTTTTAGAGTTTAAGGTTTA
Found at i:39993795 original size:14 final size:13
Alignment explanation
Indices: 39993771--39993821 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
39993761 GGTTTAAGGT
39993771 TTTAGTGTTTATGG
1 TTTA-TGTTTATGG
39993785 TTCTATGTTTATGG
1 TT-TATGTTTATGG
*
39993799 TTTATGGTTTAGGG
1 TTTAT-GTTTATGG
*
39993813 TTTGTGTTT
1 TTTATGTTT
39993822 TGGGTTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 7 0.21
14 24 0.73
15 2 0.06
ACGTcount: A:0.12, C:0.02, G:0.27, T:0.59
Consensus pattern (13 bp):
TTTATGTTTATGG
Found at i:39993815 original size:21 final size:21
Alignment explanation
Indices: 39993743--39993838 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 21
39993733 GGATTCGAGG
* * *
39993743 TTAGGTTTTGGAGTTTAAGGT
1 TTAGGTTTTAGTGTTTATGGT
39993764 TTAAGGTTTTAGTGTTTATGGT
1 TT-AGGTTTTAGTGTTTATGGT
*
39993786 TCTATG-TTTA-TGGTTTATGGT
1 T-TAGGTTTTAGT-GTTTATGGT
*
39993807 TTAGGGTTT-GTGTTT-TGGGT
1 TTAGGTTTTAGTGTTTAT-GGT
*
39993827 TTAAGTGTTTAG
1 TTAGGT-TTTAG
39993839 GGTTACGTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.02
20 15 0.25
21 23 0.38
22 20 0.33
23 1 0.02
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.53
Consensus pattern (21 bp):
TTAGGTTTTAGTGTTTATGGT
Found at i:39993851 original size:28 final size:27
Alignment explanation
Indices: 39993797--39993889 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
39993787 CTATGTTTAT
* *
39993797 GGTTTATGGTTTAGGGTTTGTGTTTTG
1 GGTTTAAGGTTTAGGGTTCGTGTTTTG
39993824 GGTTTAAGTGTTTAGGGTTACGTG-TTTG
1 GGTTTAAG-GTTTAGGGTT-CGTGTTTTG
* * * * * *
39993852 AGATTATGATTTAGGGTTTGTGTTTAG
1 GGTTTAAGGTTTAGGGTTCGTGTTTTG
*
39993879 GATTTAAGGTT
1 GGTTTAAGGTT
39993890 ACGTGTTTGA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
26 3 0.06
27 25 0.50
28 19 0.38
29 3 0.06
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.49
Consensus pattern (27 bp):
GGTTTAAGGTTTAGGGTTCGTGTTTTG
Found at i:39993987 original size:27 final size:26
Alignment explanation
Indices: 39993933--39994031 Score: 74
Period size: 27 Copynumber: 3.6 Consensus size: 26
39993923 AATTTAGGGG
*
39993933 TTGTGTTTAGTGTTTAAGGGTT-TAGTGT
1 TTGTGTTT-GAGTTT-AGGGTTAT-GTGT
39993961 TATGTGTTTGAGTTTAGGGTTATGTGT
1 T-TGTGTTTGAGTTTAGGGTTATGTGT
* * * *
39993988 TTGAGTTTAAGGTTTAGTGTAATGTGT
1 TTGTGTTTGA-GTTTAGGGTTATGTGT
* *
39994015 TTGGGTTTAGGGTTTAG
1 TTGTGTTT-GAGTTTAG
39994032 ATTTCTAGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
26 7 0.12
27 38 0.64
28 7 0.12
29 7 0.12
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (26 bp):
TTGTGTTTGAGTTTAGGGTTATGTGT
Found at i:39994005 original size:47 final size:48
Alignment explanation
Indices: 39993925--39994029 Score: 151
Period size: 47 Copynumber: 2.2 Consensus size: 48
39993915 GGTTATTAAA
* * *
39993925 TTTAGGGGTTGTGTTTAGTGTTTAAGGGTTTAGTGTTATGTGTTTGAG
1 TTTAGGGTTTGTGTTTAGAGTTTAAGGGTTTAGTGTAATGTGTTTGAG
*
39993973 TTTAGGGTTATGTGTTT-GAGTTTAA-GGTTTAGTGTAATGTGTTTGGG
1 TTTAGGGTT-TGTGTTTAGAGTTTAAGGGTTTAGTGTAATGTGTTTGAG
39994020 TTTAGGGTTT
1 TTTAGGGTTT
39994030 AGATTTCTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 29 0.56
48 15 0.29
49 7 0.13
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.50
Consensus pattern (48 bp):
TTTAGGGTTTGTGTTTAGAGTTTAAGGGTTTAGTGTAATGTGTTTGAG
Found at i:39994007 original size:20 final size:20
Alignment explanation
Indices: 39993952--39994001 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
39993942 GTGTTTAAGG
*
39993952 GTTTAGTGTTATGTGTTTGA
1 GTTTAGGGTTATGTGTTTGA
39993972 GTTTAGGGTTATGTGTTTGA
1 GTTTAGGGTTATGTGTTTGA
*
39993992 GTTTAAGGTT
1 GTTTAGGGTT
39994002 TAGTGTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (20 bp):
GTTTAGGGTTATGTGTTTGA
Found at i:39994017 original size:119 final size:117
Alignment explanation
Indices: 39993806--39994024 Score: 255
Period size: 119 Copynumber: 1.9 Consensus size: 117
39993796 TGGTTTATGG
* * * *
39993806 TTTAGGGTTTGTGTTTTGGGTTTAAGTGTTTAGGGTTACGTGTTTGAGATTATGATTTAGGGTTT
1 TTTAGGGGTTGTGTTTAGGGTTTAAGGGTTTAGGGTTACGTGTTTGAGATTAGGATTTAGGGTTT
* *
39993871 GTGTTTAGGATTTAAGGTTACGTGTTTGAGGGTTTAGCATTTATGGTTATTAAA
66 GAGTTTAGGATTTAAGGTAACGTGTTT--GGGTTTAGCATTTATGGTTATTAAA
* * * * * *
39993925 TTTAGGGGTTGTGTTTAGTGTTTAAGGGTTTAGTGTTATGTGTTTGAGTTTAGG-GTTATGTGTT
1 TTTAGGGGTTGTGTTTAGGGTTTAAGGGTTTAGGGTTACGTGTTTGAGATTAGGATTTA-GGGTT
*
39993989 TGAGTTTAAGG-TTT-AGTGTAATGTGTTTGGGTTTAG
65 TGAGTTT-AGGATTTAAG-GTAACGTGTTTGGGTTTAG
39994025 GGTTTAGATT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
117 8 0.10
118 5 0.06
119 68 0.81
120 3 0.04
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (117 bp):
TTTAGGGGTTGTGTTTAGGGTTTAAGGGTTTAGGGTTACGTGTTTGAGATTAGGATTTAGGGTTT
GAGTTTAGGATTTAAGGTAACGTGTTTGGGTTTAGCATTTATGGTTATTAAA
Found at i:40000917 original size:95 final size:95
Alignment explanation
Indices: 40000749--40000940 Score: 339
Period size: 95 Copynumber: 2.0 Consensus size: 95
40000739 CTATTTGATT
* *
40000749 TATTAGTTGATTTGCTTATAAATGTATGAGATGCCAAAGGGATTTCATGCTTAATTCCAATGTAT
1 TATTAGTTGATTTGCATATAAATGTATAAGATGCCAAAGGGATTTCATGCTTAATTCCAATGTAT
*
40000814 TTTAATTGCTTAATTGTTGGTATGTTAAGG
66 TTTAATTGCCTAATTGTTGGTATGTTAAGG
* *
40000844 TATTTGTTGATTTGCATATAAATGTATAAGATGCCAAAGGGATTTCTTGCTTAATTCCAATGTAT
1 TATTAGTTGATTTGCATATAAATGTATAAGATGCCAAAGGGATTTCATGCTTAATTCCAATGTAT
40000909 TTTAATTGCCTAATTGTTGGTATGTTAAGG
66 TTTAATTGCCTAATTGTTGGTATGTTAAGG
40000939 TA
1 TA
40000941 AGTTAAGTAA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (95 bp):
TATTAGTTGATTTGCATATAAATGTATAAGATGCCAAAGGGATTTCATGCTTAATTCCAATGTAT
TTTAATTGCCTAATTGTTGGTATGTTAAGG
Found at i:40006661 original size:21 final size:21
Alignment explanation
Indices: 40006619--40006661 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40006609 CAAAAACAAA
**
40006619 ACATTAAAATATACATTTCAT
1 ACATTAAAATATACATAACAT
*
40006640 ACATTAATATATACATAACAT
1 ACATTAAAATATACATAACAT
40006661 A
1 A
40006662 AACCATTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
ACATTAAAATATACATAACAT
Found at i:40008274 original size:22 final size:22
Alignment explanation
Indices: 40008231--40008275 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40008221 CACTACCATT
* *
40008231 TTAAATACACATTAACCTATAA
1 TTAAATACACATAAACATATAA
40008253 TTAAATA-ACATAAACATAATAA
1 TTAAATACACATAAACAT-ATAA
40008275 T
1 T
40008276 CAGTACATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (22 bp):
TTAAATACACATAAACATATAA
Found at i:40017310 original size:16 final size:16
Alignment explanation
Indices: 40017289--40017322 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40017279 TACAATCCTT
40017289 ATAGAGTATCATTTGA
1 ATAGAGTATCATTTGA
40017305 ATAGAGTATCATTTGA
1 ATAGAGTATCATTTGA
40017321 AT
1 AT
40017323 TGAGCGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (16 bp):
ATAGAGTATCATTTGA
Found at i:40023861 original size:76 final size:76
Alignment explanation
Indices: 40023674--40024030 Score: 330
Period size: 76 Copynumber: 4.7 Consensus size: 76
40023664 TCTGTTTATC
* * ** * *
40023674 CGACTAGCGCTGGGTGCAACTCATTGTTGGTACATTGAACTAGTACTAGGCACACA-TTGATAT-
1 CGACTAGCACTGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACACATTTGATATC
40023737 GTCGATTTACT
66 GTCGATTTACT
* ** * * *
40023748 TGACTAGCTTTGGGCGCAACTTATTGTTGGTACATCCAACTAGTGCTGGGCACACATTTGATATC
1 CGACTAGCACTGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACACATTTGATATC
*
40023813 GTCGGTTTACT
66 GTCGATTTACT
* *
40023824 CGACTAGCACTGGGTGCAACTCATTGTTGGTATATCCAGCTAGTGTTGGGCACACATTTGATATC
1 CGACTAGCACTGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACACATTTGATATC
*
40023889 ATCGATTTAC-
66 GTCGATTTACT
* * * ** * * * *
40023899 CGGACTAGCACTTTGCT-CAACTCATTATCAGTTTTTCCAACTAGTGCTGGGCACACATATGGTA
1 C-GACTAGCAC-TGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACACATTTGATA
*
40023963 TCGTC-AGTTTATT
64 TCGTCGA-TTTACT
* ** ** * * *
40023976 CGACTTA-CACCGGGCACAAAACATTGTTGGTGTATCCGACTAGTGCAGGGCACAC
1 CGAC-TAGCACTGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACAC
40024031 CTATCATCAG
Statistics
Matches: 229, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
74 47 0.21
75 10 0.04
76 166 0.72
77 6 0.03
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (76 bp):
CGACTAGCACTGGGTGCAACTCATTGTTGGTATATCCAACTAGTGCTGGGCACACATTTGATATC
GTCGATTTACT
Found at i:40026875 original size:3 final size:3
Alignment explanation
Indices: 40026867--40026896 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40026857 AATGATCTTA
*
40026867 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
40026897 TACTATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:40032660 original size:36 final size:36
Alignment explanation
Indices: 40032620--40032695 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
40032610 TGAAACATAG
*
40032620 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
40032656 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
40032693 AAA
1 AAA
40032696 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:40033251 original size:23 final size:22
Alignment explanation
Indices: 40033208--40033265 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40033198 AAAGGATATC
* *
40033208 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40033229 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40033252 TGCATATCATATCT
1 TACAAATCATATCT
40033266 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40033788 original size:41 final size:43
Alignment explanation
Indices: 40033740--40033849 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 43
40033730 GATCTACTCT
*
40033740 ACTGCAACTTCAGAGAGATAAGATCTA-T-TTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCTACTGTTCAATCCGCTCC
* *
40033781 ACTGCAACTTCA-AGGAGATAGGAT-TACTGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGA-GAGATAAGATCTACT-G-TTCAATCCGCTCC
* *
40033825 ACTGCAACTT-AGGGAGATAAAATCT
1 ACTGCAACTTCAGAGAGATAAGATCT
40033850 GTAATTTTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
40 3 0.05
41 22 0.39
43 9 0.16
44 22 0.39
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
ACTGCAACTTCAGAGAGATAAGATCTACTGTTCAATCCGCTCC
Found at i:40034001 original size:44 final size:44
Alignment explanation
Indices: 40033953--40034071 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 44
40033943 CTTCGATTTG
* ** *
40033953 CTCCACTACTGCTTAGGGAGATAAGA-TCTGTAATTTTCAACCTA
1 CTCCACTACTGCTCAGGGAGATAAGATTCACT-ATCTTCAACCTA
* *
40033997 CTCCACTGCTGCTCAGGGAGATAGGATTCACTATCTTCAACCTA
1 CTCCACTACTGCTCAGGGAGATAAGATTCACTATCTTCAACCTA
* *
40034041 TTCCACTACTGAC-CAGGGAGATAGGATTCAC
1 CTCCACTACTG-CTCAGGGAGATAAGATTCAC
40034072 CTATTCCACT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
44 61 0.94
45 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
CTCCACTACTGCTCAGGGAGATAAGATTCACTATCTTCAACCTA
Found at i:40034079 original size:34 final size:34
Alignment explanation
Indices: 40034036--40034221 Score: 138
Period size: 34 Copynumber: 4.9 Consensus size: 34
40034026 ACTATCTTCA
*
40034036 ACCTATTCCACTACTGACCAGGGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
* *
40034070 ACCTATTCCACTACTGACTAGGGAGATAGGACTTAC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TT-C
* *
40034106 AATTTTCAATCTCTTCCACTGCTGACCAGGGAGATAGGACTC
1 -A----C---CTATTCCACTGCTGACCAGGGAGATAGGATTC
*
40034148 ACAATCTTCAACCATTCCACTGCTGACCAGGGAGATCGGATTC
1 AC---C-T-----ATTCCACTGCTGACCAGGGAGATAGGATTC
*
40034191 ACCTATTCCACTGCTGACTAGGGAGATAGGA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA
40034222 CTTACAATTT
Statistics
Matches: 126, Mismatches: 10, Indels: 32
0.75 0.06 0.19
Matches are distributed among these distances:
34 55 0.44
35 2 0.02
36 1 0.01
37 6 0.05
38 1 0.01
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 30 0.24
44 26 0.21
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:40034123 original size:78 final size:78
Alignment explanation
Indices: 40033992--40034149 Score: 212
Period size: 78 Copynumber: 2.0 Consensus size: 78
40033982 GTAATTTTCA
* *
40033992 ACCTACTCCACTGCTGCTCAGGGAGATAGGATTCACTATCTTCAACCTATTCCACTACTGACCAG
1 ACCTACTCCACTACTGCTCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTACTGACCAG
*
40034057 GGAGATAGGATTC
66 GGAGATAGGACTC
* * * * *
40034070 ACCTATTCCACTACTGACT-AGGGAGATAGGACTT-ACAATTTTCAATCTCTTCCACTGCTGACC
1 ACCTACTCCACTACTG-CTCAGGGAGATAGGA-TTCACAATCTTCAACCTATTCCACTACTGACC
40034133 AGGGAGATAGGACTC
64 AGGGAGATAGGACTC
40034148 AC
1 AC
40034150 AATCTTCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 66 0.94
79 4 0.06
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (78 bp):
ACCTACTCCACTACTGCTCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTACTGACCAG
GGAGATAGGACTC
Found at i:40034138 original size:44 final size:43
Alignment explanation
Indices: 40034067--40034350 Score: 329
Period size: 44 Copynumber: 6.7 Consensus size: 43
40034057 GGAGATAGGA
* * * *
40034067 TTCACCTATTCCACTACTGACTAGGGAGATAGGACTTACAATT
1 TTCAACTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* *
40034110 TTCAATCTCTTCCACTGCTGACCAGGGAGATAGGACTCACAATC
1 TTCAA-CTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* *
40034154 TTCAACCATTCCACTGCTGACCAGGGAGATCGGA-TT-C-A--
1 TTCAACTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
* *
40034192 --C--CTATTCCACTGCTGACTAGGGAGATAGGACTTACAATT
1 TTCAACTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
*
40034231 TTCAATCTCTTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
1 TTCAA-CTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
40034275 TTCAACCTATTCCACTGCTGACCAGGGA-AGTAGGACTTACAATC
1 TTCAA-CTATTCCACTGCTGACCAGGGAGA-TAGGACTTACAATC
*
40034319 TTCAACCTATTCCACTACTGACCAGGGAGATA
1 TTCAA-CTATTCCACTGCTGACCAGGGAGATA
40034351 AAGCTTTGTG
Statistics
Matches: 207, Mismatches: 19, Indels: 29
0.81 0.07 0.11
Matches are distributed among these distances:
34 26 0.13
35 2 0.01
36 2 0.01
37 1 0.00
40 1 0.00
41 2 0.01
42 1 0.00
43 33 0.16
44 136 0.66
45 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
TTCAACTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
Found at i:40034215 original size:121 final size:122
Alignment explanation
Indices: 40033954--40034302 Score: 548
Period size: 121 Copynumber: 2.9 Consensus size: 122
40033944 TTCGATTTGC
* *
40033954 TCCACTACTG-CTTAGGGAGATAAGATCTGT--AATTTTCAACCTAC-TCCACTGCTG-CTCAGG
1 TCCACTACTGAC-TAGGGAGATAGGA-CT-TACAATTTTCAATCT-CTTCCACTGCTGAC-CAGG
* *
40034014 GAGATAGGATTCACTATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGATTCACCTAT
61 GAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTAT
40034076 TCCACTACTGACTAGGGAGATAGGACTTACAATTTTCAATCTCTTCCACTGCTGACCAGGGAGAT
1 TCCACTACTGACTAGGGAGATAGGACTTACAATTTTCAATCTCTTCCACTGCTGACCAGGGAGAT
* *
40034141 AGGACTCACAATCTTCAACC-ATTCCACTGCTGACCAGGGAGATCGGATTCACCTAT
66 AGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTAT
*
40034197 TCCACTGCTGACTAGGGAGATAGGACTTACAATTTTCAATCTCTTCCACTGCTGACCAGGGAGAT
1 TCCACTACTGACTAGGGAGATAGGACTTACAATTTTCAATCTCTTCCACTGCTGACCAGGGAGAT
40034262 AGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGA
66 AGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGA
40034303 AGTAGGACTT
Statistics
Matches: 213, Mismatches: 8, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
120 1 0.00
121 120 0.56
122 90 0.42
123 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (122 bp):
TCCACTACTGACTAGGGAGATAGGACTTACAATTTTCAATCTCTTCCACTGCTGACCAGGGAGAT
AGGATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTAT
Found at i:40035651 original size:16 final size:16
Alignment explanation
Indices: 40035616--40035660 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
40035606 GCCTCTCCTG
* **
40035616 TTTCTTTTTTTTTCTT
1 TTTCTTTTTTTATCAC
40035632 TTTCTTTTTTTATCAC
1 TTTCTTTTTTTATCAC
*
40035648 TTTCATTTTTTAT
1 TTTCTTTTTTTAT
40035661 TTTGATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTTTATCAC
Found at i:40036512 original size:25 final size:25
Alignment explanation
Indices: 40036459--40036524 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
40036449 AAGAAAATCC
* *
40036459 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
40036484 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
40036509 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
40036525 TGTATTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:40040719 original size:36 final size:36
Alignment explanation
Indices: 40040679--40040754 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
40040669 TGAAACATAG
*
40040679 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
40040715 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
40040752 AAA
1 AAA
40040755 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:40041305 original size:22 final size:23
Alignment explanation
Indices: 40041280--40041382 Score: 114
Period size: 21 Copynumber: 4.8 Consensus size: 23
40041270 TACAAATTAA
* *
40041280 ATCTCTAAGATTACA-AAATCAT
1 ATCTCTAAGATTGCATATATCAT
40041302 ATCTTCTAAGATTGC--ATATCAT
1 ATC-TCTAAGATTGCATATATCAT
*
40041324 ATCT-AAAGATTGCATATATCAT
1 ATCTCTAAGATTGCATATATCAT
40041346 A--TCTAAGATTGCATATATCAT
1 ATCTCTAAGATTGCATATATCAT
40041367 A--TCTAAGATTGCATAT
1 ATCTCTAAGATTGCATAT
40041383 CCTTGACGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.12
21 34 0.47
22 20 0.27
23 10 0.14
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (23 bp):
ATCTCTAAGATTGCATATATCAT
Found at i:40041313 original size:23 final size:22
Alignment explanation
Indices: 40041270--40041327 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40041260 AAAGGGTATC
* *
40041270 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40041291 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40041314 TGCATATCATATCT
1 TACAAATCATATCT
40041328 AAAGATTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40041355 original size:21 final size:21
Alignment explanation
Indices: 40041306--40041382 Score: 131
Period size: 21 Copynumber: 3.7 Consensus size: 21
40041296 AATCATATCT
40041306 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
40041325 TCTAAAGATTGCATATATCATA
1 TCT-AAGATTGCATATATCATA
40041347 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
40041368 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
40041383 CCTTGACGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 3 0.05
20 8 0.15
21 33 0.60
22 11 0.20
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:40042460 original size:157 final size:156
Alignment explanation
Indices: 40042076--40042535 Score: 531
Period size: 157 Copynumber: 3.0 Consensus size: 156
40042066 AAATCAAAGC
* * * * *
40042076 TTTCTTTTAAAAAATCACTACTTTTATTAAAGAT-AAAAGATTTTATTCCGAAATAATTTTAAAA
1 TTTCTTTTAAAAAATCACTACTTTTCTTAAAGATCAAAA-CTTTTATTTCGAAAT-AGTTGAAAA
* *
40042140 AAATCAAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTCAAAAAAATGGGTTTTCT
64 AAATCAAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACT-AAAAAAAT-AG-----A
*
40042205 TTTTTTTTTTTAAAAATCTAAAC-TT-TC----TT
122 TTTTTATTTTTAAAAATCTAAACTTTCTCTTTTTT
* * *
40042234 TTT-TTTTAAAAAATCACTAATTTTCTTAAAGATCAAAGCTTTTATTTCAAAATAGTTGAAAAAA
1 TTTCTTTTAAAAAATCACTACTTTTCTTAAAGATCAAAACTTTTATTTCGAAATAGTTGAAAAAA
* *
40042298 ATCAAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAATAGATTTTTATTT
66 ATCAAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAATAGATTTTTATTT
*
40042363 TTAAACATCTAAACTTTCTCCTTTTTT
131 TTAAAAATCTAAACTTTCT-CTTTTTT
* * * *
40042390 TTTCTTTTGAAAAATCACTACTTTTCTTAAAGATCAAAACTTTTATTTTGAAGTAGTAGAAAAAA
1 TTTCTTTTAAAAAATCACTACTTTTCTTAAAGATCAAAACTTTTATTTCGAAATAGTTGAAAAAA
*
40042455 ATCAAAAATTTGTTTT-AAAA--T----TTTCCTTTAAAATGACT--AAAAATAGGTTTTTATTT
66 ATCAAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAATAGATTTTTATTT
*
40042511 TTAAAAATCTAAATTTTCTCTTTTT
131 TTAAAAATCTAAACTTTCTCTTTTT
40042536 AAAAAAAATC
Statistics
Matches: 267, Mismatches: 26, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
147 6 0.02
148 34 0.13
149 21 0.08
150 19 0.07
151 1 0.00
152 1 0.00
154 2 0.01
155 8 0.03
156 61 0.23
157 108 0.40
158 6 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (156 bp):
TTTCTTTTAAAAAATCACTACTTTTCTTAAAGATCAAAACTTTTATTTCGAAATAGTTGAAAAAA
ATCAAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAATAGATTTTTATTT
TTAAAAATCTAAACTTTCTCTTTTTT
Found at i:40043600 original size:13 final size:13
Alignment explanation
Indices: 40043584--40043621 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40043574 TCAGATACAA
40043584 ATAACAGAATCAG
1 ATAACAGAATCAG
40043597 ATAAGCAGAA-CAG
1 ATAA-CAGAATCAG
40043610 ATATACAGAATC
1 ATA-ACAGAATC
40043622 CTACCCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
ATAACAGAATCAG
Found at i:40049738 original size:6 final size:6
Alignment explanation
Indices: 40049727--40049753 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40049717 CAATACATCC
40049727 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
40049754 CTATACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:40058435 original size:45 final size:44
Alignment explanation
Indices: 40058386--40058558 Score: 190
Period size: 45 Copynumber: 3.9 Consensus size: 44
40058376 GTGCCGATTT
*
40058386 TCATGCCATATAAATA-AAGCAGATACTATGTACCGGTATTGGCTA
1 TCATGCCATATAAATACAA-CAG-TACTATGTACCGGTGTTGGCTA
* * * * * *
40058431 TCATGCTATATACATACAATATGTACTATTTATCGGTGTTGGCTT
1 TCATGCCATATAAATACAACA-GTACTATGTACCGGTGTTGGCTA
*
40058476 TCATGCCATGTAAATACAACAGGTACTATGTACCGGTGTTGGCTA
1 TCATGCCATATAAATACAACA-GTACTATGTACCGGTGTTGGCTA
* * *
40058521 TCATGCCATATACATAC-A-TGTACTATGTACTGGTGTTG
1 TCATGCCATATAAATACAACAGTACTATGTACCGGTGTTG
40058559 ATTTTCTTAC
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
42 18 0.17
44 1 0.01
45 85 0.79
46 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (44 bp):
TCATGCCATATAAATACAACAGTACTATGTACCGGTGTTGGCTA
Found at i:40058503 original size:90 final size:90
Alignment explanation
Indices: 40058348--40058549 Score: 268
Period size: 90 Copynumber: 2.3 Consensus size: 90
40058338 AACAATTAGA
*
40058348 ATATACATACAATAAGTACTATGTATAGGTGCCGATTTTCATGCCATATAAATAAAGCAGATACT
1 ATATACATACAATAAGTACTATGTATAGGTGCCGACTTTCATGCCATATAAATAAAGCAGATACT
*
40058413 ATGTACCGGTATTGGCTATCATGCT
66 ATGTACCGGTATTGGCTATCATGCC
* * * ** * * *
40058438 ATATACATACAATATGTACTATTTATCGGTGTTGGCTTTCATGCCATGTAAATACAA-CAGGTAC
1 ATATACATACAATAAGTACTATGTATAGGTGCCGACTTTCATGCCATATAAATA-AAGCAGATAC
*
40058502 TATGTACCGGTGTTGGCTATCATGCC
65 TATGTACCGGTATTGGCTATCATGCC
40058528 ATATACATAC-AT--GTACTATGTA
1 ATATACATACAATAAGTACTATGTA
40058550 CTGGTGTTGA
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
87 9 0.09
89 2 0.02
90 86 0.87
91 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (90 bp):
ATATACATACAATAAGTACTATGTATAGGTGCCGACTTTCATGCCATATAAATAAAGCAGATACT
ATGTACCGGTATTGGCTATCATGCC
Found at i:40060169 original size:28 final size:28
Alignment explanation
Indices: 40060102--40060169 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
40060092 ATACAAAAGT
*
40060102 GCACTGAGGTGCATTCACGTAGCAGTGA
1 GCACTGTGGTGCATTCACGTAGCAGTGA
* * * *
40060130 GCACCGTAGTGCATTTACGTAGTAGTGA
1 GCACTGTGGTGCATTCACGTAGCAGTGA
40060158 GCACTGTGGTGC
1 GCACTGTGGTGC
40060170 TTAACAGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (28 bp):
GCACTGTGGTGCATTCACGTAGCAGTGA
Found at i:40071929 original size:28 final size:28
Alignment explanation
Indices: 40071892--40071948 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40071882 AATTATTTAG
40071892 TTAGTTATAATTTTAATTCAACATACTT
1 TTAGTTATAATTTTAATTCAACATACTT
40071920 TTAGTTATAATTTTAATTCAACATACTT
1 TTAGTTATAATTTTAATTCAACATACTT
40071948 T
1 T
40071949 GTATAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (28 bp):
TTAGTTATAATTTTAATTCAACATACTT
Found at i:40072169 original size:37 final size:39
Alignment explanation
Indices: 40072128--40072218 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 39
40072118 TATATAGGAA
*
40072128 CTATACTGACAAAAATA-ATCTGTCAGTATAAATTT-AT
1 CTATACTGACAAAAATACATCTGTCAGTATAAATTTGAG
* * * * *
40072165 CTATATTGACAGTAATTACATGTGTCAGTATAAGTTTGAG
1 CTATACTGACA-AAAATACATCTGTCAGTATAAATTTGAG
*
40072205 ATATACTGACAAAA
1 CTATACTGACAAAA
40072219 TGGTTATCTG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
37 10 0.24
38 4 0.10
39 18 0.43
40 10 0.24
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (39 bp):
CTATACTGACAAAAATACATCTGTCAGTATAAATTTGAG
Found at i:40090627 original size:17 final size:17
Alignment explanation
Indices: 40090602--40090644 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
40090592 TAAGCGAAAT
40090602 AAAAATAAATAAATAAC
1 AAAAATAAATAAATAAC
* *
40090619 AAAAGTAAATAAATAAAG
1 AAAAATAAATAAAT-AAC
40090637 AAAAATAA
1 AAAAATAA
40090645 GCAAATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAAATAAATAAC
Found at i:40098415 original size:21 final size:21
Alignment explanation
Indices: 40098358--40098415 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
40098348 GCGAAAGTGT
* *
40098358 AATTTTACCATTACTAATTTAA
1 AATTTTACCATT-TTAAATTAA
*
40098380 AATTTTATACA--TTAAATTAA
1 AATTTTA-CCATTTTAAATTAA
40098400 AATTTTACCATTTTAA
1 AATTTTACCATTTTAA
40098416 GGGGCTATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.07
20 14 0.48
21 4 0.14
22 7 0.24
23 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTACCATTTTAAATTAA
Found at i:40099829 original size:29 final size:29
Alignment explanation
Indices: 40099767--40099831 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
40099757 GTGTGGTAGG
* *
40099767 CCATATGAGTCACATGGTCGTGTGTCAGA
1 CCATGTGAGTCACATGGCCGTGTGTCAGA
40099796 CCATGTGAGTCACATGGCCGTGTGTCAGA
1 CCATGTGAGTCACATGGCCGTGTGTCAGA
40099825 CCATGTG
1 CCATGTG
40099832 GTAGGCCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (29 bp):
CCATGTGAGTCACATGGCCGTGTGTCAGA
Found at i:40103906 original size:2 final size:2
Alignment explanation
Indices: 40103899--40103925 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40103889 ACATGCATGA
40103899 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
40103926 CACAGTAGTA
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:40104789 original size:5 final size:5
Alignment explanation
Indices: 40104779--40104806 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40104769 ATAATACTAT
40104779 ATACC ATACC ATACC ATACC ATACC ATA
1 ATACC ATACC ATACC ATACC ATACC ATA
40104807 TACCATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (5 bp):
ATACC
Found at i:40105311 original size:25 final size:26
Alignment explanation
Indices: 40105263--40105311 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40105253 CCAACCATGT
**
40105263 TTAATAGTACATACATGAGTCATTAA
1 TTAATAGTACATACATGACCCATTAA
*
40105289 TTAA-AGTCCATACATGACCCATT
1 TTAATAGTACATACATGACCCATT
40105312 TTGTTGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (26 bp):
TTAATAGTACATACATGACCCATTAA
Found at i:40113838 original size:19 final size:19
Alignment explanation
Indices: 40113816--40113853 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40113806 ACGATAAATA
*
40113816 AAATAAATAAAACTATATG
1 AAATAAATAAAAATATATG
*
40113835 AAATATATAAAAATATATG
1 AAATAAATAAAAATATATG
40113854 TATGTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATAAATAAAAATATATG
Found at i:40113997 original size:20 final size:20
Alignment explanation
Indices: 40113958--40114012 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
40113948 TTTAATAAAA
* * *
40113958 TAAAAAATATGTATATATAT
1 TAAAAAATATATGTACATAT
* *
40113978 TATAGAATATATGTACATAT
1 TAAAAAATATATGTACATAT
40113998 TAAAAAATATATGTA
1 TAAAAAATATATGTA
40114013 TGCGTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
TAAAAAATATATGTACATAT
Found at i:40114672 original size:14 final size:15
Alignment explanation
Indices: 40114648--40114676 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40114638 TCCCCTAAAA
40114648 AAAACAAAACCTCTC
1 AAAACAAAACCTCTC
40114663 AAAA-AAAACCTCTC
1 AAAACAAAACCTCTC
40114677 CCCTCAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAACAAAACCTCTC
Found at i:40117750 original size:17 final size:17
Alignment explanation
Indices: 40117730--40117762 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40117720 GTTTATGAAA
*
40117730 AAATAAAATACGAAAAG
1 AAATAAAAAACGAAAAG
40117747 AAATAAAAAACGAAAA
1 AAATAAAAAACGAAAA
40117763 TAGTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (17 bp):
AAATAAAAAACGAAAAG
Found at i:40117937 original size:162 final size:160
Alignment explanation
Indices: 40117748--40118118 Score: 557
Period size: 160 Copynumber: 2.3 Consensus size: 160
40117738 TACGAAAAGA
*
40117748 AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCTGAAAA-AAAAAAGAAAAATAC
1 AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCAGAAAAGAAAAAAGAAAAATAC
* *
40117812 GAACAAAGGGCCAAAATAAGGATTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACA
66 GAACAAAAGGCCAAAAT-AGGATTTTTCACTAAATTTATAT-AAAAAA-ACACTAAAATAATACA
* *
40117877 TTTCAAACGTTATGTACTAAAATAATATAAAAT
128 TTTCAAACATTATGTACTAAAATAACATAAAAT
*
40117910 AATAAAAAATGAAAATAGTATATTTACTGAAAGTAATAAAATCCA-AAAAGAAAAAAGAAAAATA
1 AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAAT-CAGAAAAGAAAAAAGAAAAATA
* * *
40117974 CGGACAAAAGGCCAAAATAGGGTTTTTCACTAAATTTATATAAAAAAACACTAAAATAATATATT
65 CGAACAAAAGGCCAAAATAGGATTTTTCACTAAATTTATATAAAAAAACACTAAAATAATACATT
*
40118039 TCAAATATTATGTACTAAAATAACATAAAAT
130 TCAAACATTATGTACTAAAATAACATAAAAT
* ** * *
40118070 AATAAAATACGAAAATAGTATATTTTTTTACAGTAATAAAATCAGAAAA
1 AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCAGAAAA
40118119 TAAGAAATGT
Statistics
Matches: 190, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
159 2 0.01
160 85 0.45
161 6 0.03
162 66 0.35
163 31 0.16
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (160 bp):
AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCAGAAAAGAAAAAAGAAAAATAC
GAACAAAAGGCCAAAATAGGATTTTTCACTAAATTTATATAAAAAAACACTAAAATAATACATTT
CAAACATTATGTACTAAAATAACATAAAAT
Found at i:40118163 original size:10 final size:10
Alignment explanation
Indices: 40118148--40118175 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40118138 GTGTATTAAT
40118148 TTTTATATTA
1 TTTTATATTA
40118158 TTTTATATTA
1 TTTTATATTA
40118168 TTTTATAT
1 TTTTATAT
40118176 AGGCGGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATATTA
Found at i:40118362 original size:157 final size:157
Alignment explanation
Indices: 40118189--40118575 Score: 573
Period size: 157 Copynumber: 2.4 Consensus size: 157
40118179 CGGCACCCCC
40118189 TTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTTTTAT
1 TTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTTTTAT
*
40118254 TATTTTATATTATTTTATTAAATAAAGTTTGAAATGTATTAATTTA-GTG-TATTTTTATATAAA
66 TATTTTATATTATTTTAGTAAATAAAGTTTGAAATGTATTAATTTAGGTGTTATTTTTATATAAA
* *
40118317 TTTAGTAAAAAAAACTCTCATTTTGGCCA
131 TTTAGT--AAAAAACCCTCATTTTGGCAA
* *
40118346 TTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAAATATGCTATTTTCGTATTTT
1 TTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCG--TTTT
* * * *
40118411 ATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTTATAT
64 ATTATTTTATATTATTTTAGTAAATAAAGTTTGAAATGTATTAATTTAG-GTGTTATTTTTATAT
* *
40118476 AAATTTAGTGAAAAACCCTTATTTTGGCAA
128 AAATTTAGTAAAAAACCCTCATTTTGGCAA
* **
40118506 TTTGTTCGTATTTTTCATTTTTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTCGTTTT-
1 TTTGTTCGTATTTTTC-TTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTTTTA
40118570 TTATTT
65 TTATTT
40118576 CTTTTTGTAT
Statistics
Matches: 208, Mismatches: 16, Indels: 11
0.89 0.07 0.05
Matches are distributed among these distances:
157 57 0.27
158 6 0.03
159 52 0.25
160 33 0.16
161 41 0.20
162 19 0.09
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (157 bp):
TTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTTTTAT
TATTTTATATTATTTTAGTAAATAAAGTTTGAAATGTATTAATTTAGGTGTTATTTTTATATAAA
TTTAGTAAAAAACCCTCATTTTGGCAA
Found at i:40118697 original size:27 final size:27
Alignment explanation
Indices: 40118648--40118711 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
40118638 ATAAATGGGG
* * * *
40118648 GGTGCCGCCTGTGGCAGTGGCACCTTT
1 GGTGCCGCCTCTGCCACTGGCACCATT
*
40118675 GGTGCCGCCTCTGCCACTTGCACCATT
1 GGTGCCGCCTCTGCCACTGGCACCATT
*
40118702 GGTGCTGCCT
1 GGTGCCGCCT
40118712 GTGGCAGTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.08, C:0.34, G:0.31, T:0.27
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCACTGGCACCATT
Found at i:40122626 original size:29 final size:28
Alignment explanation
Indices: 40122586--40122640 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
40122576 ATTTAATTTT
*
40122586 TTTTTCTTTTATGTTCTTTTAACTTTAC
1 TTTTTCTTTTATGTTCTATTAACTTTAC
* *
40122614 TTTTTCTCTTTATTTTCTATTATCTTT
1 TTTTTCT-TTTATGTTCTATTAACTTT
40122641 TGCTTCTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTTTCTTTTATGTTCTATTAACTTTAC
Found at i:40126641 original size:117 final size:115
Alignment explanation
Indices: 40126520--40126764 Score: 287
Period size: 115 Copynumber: 2.1 Consensus size: 115
40126510 CAAATTTCAT
* * *
40126520 TTTTTTTACTTA-GAAATACACATATTTTTGCAATTT-AATTCATTATAAAATTCATTACAATAG
1 TTTTTTTACTTATG-AATACAC--ATTTATGAAATTTCAATT-ATTACAAAATTCATTACAATAG
** * *
40126583 TAATAAAATAAAAATTATTACACCAAATTAAGAGACTTCATTGTCAGATTCTAA
62 TAATAAAATAAAAATTATTACACCAAACCAAGAGACTTCATTGTCAAAATCTAA
* * * ** *
40126637 TTTTTATATTTATGAATACACATTTATGAAATTTCACTTATTACAAAATTCATTGTAATATTAAT
1 TTTTTTTACTTATGAATACACATTTATGAAATTTCAATTATTACAAAATTCATTACAATAGTAAT
* * *
40126702 AGAATAAAAATTATTAGACCAAGCCAAGAGACTTCATTGTCAAAATCTAA
66 AAAATAAAAATTATTACACCAAACCAAGAGACTTCATTGTCAAAATCTAA
*
40126752 TATTTTTACTTAT
1 TTTTTTTACTTAT
40126765 CAACTCAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
115 86 0.80
116 3 0.03
117 17 0.16
118 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (115 bp):
TTTTTTTACTTATGAATACACATTTATGAAATTTCAATTATTACAAAATTCATTACAATAGTAAT
AAAATAAAAATTATTACACCAAACCAAGAGACTTCATTGTCAAAATCTAA
Found at i:40136758 original size:18 final size:19
Alignment explanation
Indices: 40136732--40136770 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40136722 ATATTTATTT
* *
40136732 ATTTTTATATAGTA-TATA
1 ATTTATATATAATACTATA
40136750 ATTTATATATAATACTATA
1 ATTTATATATAATACTATA
40136769 AT
1 AT
40136771 GTAACCATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTTATATATAATACTATA
Found at i:40140431 original size:5 final size:5
Alignment explanation
Indices: 40140421--40140449 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40140411 TTGTGTACGT
40140421 GTGGG GTGGG GTGGG GTGGG GTGGG GTGG
1 GTGGG GTGGG GTGGG GTGGG GTGGG GTGG
40140450 ACAGAGACTG
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:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (5 bp):
GTGGG
Found at i:40144191 original size:20 final size:20
Alignment explanation
Indices: 40144163--40144201 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40144153 ACACCACGGA
*
40144163 CCTAGAGTTAGTTTGCAAAC
1 CCTAAAGTTAGTTTGCAAAC
40144183 CCTAAAGTTAGTTTGCAAA
1 CCTAAAGTTAGTTTGCAAA
40144202 ACTTAGCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (20 bp):
CCTAAAGTTAGTTTGCAAAC
Found at i:40157842 original size:13 final size:13
Alignment explanation
Indices: 40157824--40157855 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40157814 AAATGCCTCT
*
40157824 TTAATATTTTTCA
1 TTAATATTTGTCA
40157837 TTAATATTTGTCA
1 TTAATATTTGTCA
40157850 TTAATA
1 TTAATA
40157856 CATTCATGTT
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:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (13 bp):
TTAATATTTGTCA
Found at i:40159964 original size:29 final size:29
Alignment explanation
Indices: 40159915--40160013 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 29
40159905 ATTTAGGCCA
*
40159915 TTCAAT-A-TTTAATTATTTTTTATACTTT
1 TTCAATAATTTTAATTA-TTTTTATAATTT
*
40159943 TTCAATAATTTTAATGATTTTTA-AATTT
1 TTCAATAATTTTAATTATTTTTATAATTT
** * * **
40159971 TAAAAATAATTTTGATTTTTTTTATTTTTT
1 T-TCAATAATTTTAATTATTTTTATAATTT
40160001 TTCAA-AATTTTAA
1 TTCAATAATTTTAA
40160014 AAATTAATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 18 0.33
29 26 0.47
30 11 0.20
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (29 bp):
TTCAATAATTTTAATTATTTTTATAATTT
Found at i:40159971 original size:28 final size:28
Alignment explanation
Indices: 40159915--40159971 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
40159905 ATTTAGGCCA
* *
40159915 TTCAATATTTAATTATTTTTTATACTTT
1 TTCAATATTTAATGATTTTTTATAATTT
40159943 TTCAATAATTTTAATGA-TTTTTA-AATTT
1 TTCAAT-A-TTTAATGATTTTTTATAATTT
40159971 T
1 T
40159972 AAAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 11 0.44
29 7 0.28
30 7 0.28
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTCAATATTTAATGATTTTTTATAATTT
Found at i:40163465 original size:104 final size:104
Alignment explanation
Indices: 40162929--40163468 Score: 599
Period size: 104 Copynumber: 5.2 Consensus size: 104
40162919 AAAAATTGCA
* * * *
40162929 AACCTTAATAATATCAGCTGTGAATGTAGGTC-T-GCAGATTGTTAGAAGTTGCGATCTTAAATC
1 AACCTTAATAACATCAACTGTGAATGTAGGTCATCG-AG-CTGTTAGGAGTTGCGATCTTAAATC
** * *
40162992 AATGAACTCAAATAATTGGAGGTTGCGATCTTAAAT-AAGCT
64 AGCGAACTCAAATAATTGAAGGCTGCGATCTTAAATCAA-CT
* * *
40163033 AACCTTAATAACATCATA-TGTAAATTTAGGTCAGT-GAGCTGTTAGGAGTTGCGATCTTAAATT
1 AACCTTAATAACATCA-ACTGTGAATGTAGGTCA-TCGAGCTGTTAGGAGTTGCGATCTTAAATC
* * * *
40163096 AGCAAACTTAAATAATTGGAGGCTGCGATCTTAAATCAGCT
64 AGCGAACTCAAATAATTGAAGGCTGCGATCTTAAATCAACT
* * * * * * * *
40163137 AGCCTTAATAACATTAACTATGAATGGAGGTTAGCGAGCTGTTAGAAGTTGCAATCTTAAATCAG
1 AACCTTAATAACATCAACTGTGAATGTAGGTCATCGAGCTGTTAGGAGTTGCGATCTTAAATCAG
* * *
40163202 CAAACTCAAATAATTAGAA-GCTGGGATCTTAAATCAGCT
66 CGAACTCAAATAATT-GAAGGCTGCGATCTTAAATCAACT
* * * * *
40163241 AGCCTTAATAACATTAGCTGTGAACGTAGGTCATCGAGCTGTTAGGAGTTGCGATCTTAAATCAA
1 AACCTTAATAACATCAACTGTGAATGTAGGTCATCGAGCTGTTAGGAGTTGCGATCTTAAATCAG
* *
40163306 CGAACTCAAATAATT-AGAGGTTGCGATTTTAAATCAACT
66 CGAACTCAAATAATTGA-AGGCTGCGATCTTAAATCAACT
* * * *
40163345 AGCCTTGATAATATCAACTGTGAATGTAGGTCATCGAGCCGTTAGGAGTTGCGATCTTAAATCAG
1 AACCTTAATAACATCAACTGTGAATGTAGGTCATCGAGCTGTTAGGAGTTGCGATCTTAAATCAG
* * * *
40163410 CGAATTAAAATAATTGAAGGCTGTGATCTTAGATCAACT
66 CGAACTCAAATAATTGAAGGCTGCGATCTTAAATCAACT
40163449 AACCTTAATAACATCAACTG
1 AACCTTAATAACATCAACTG
40163469 CAAGGTCAGA
Statistics
Matches: 369, Mismatches: 57, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
102 1 0.00
103 2 0.01
104 358 0.97
105 6 0.02
106 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (104 bp):
AACCTTAATAACATCAACTGTGAATGTAGGTCATCGAGCTGTTAGGAGTTGCGATCTTAAATCAG
CGAACTCAAATAATTGAAGGCTGCGATCTTAAATCAACT
Found at i:40175363 original size:6 final size:7
Alignment explanation
Indices: 40175338--40175362 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40175328 CCAAAAGAGA
40175338 TTTTTAT
1 TTTTTAT
40175345 TTTTTAT
1 TTTTTAT
40175352 TTTTTAT
1 TTTTTAT
40175359 TTTT
1 TTTT
40175363 AACTTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:40178346 original size:55 final size:54
Alignment explanation
Indices: 40178187--40178381 Score: 255
Period size: 56 Copynumber: 3.5 Consensus size: 54
40178177 AAATTTAGTA
*
40178187 CTGGCCTGTCAATGGCCACCACCAAGTACAAAAATAAATCAAAATTTTTTTGTG
1 CTGGCCTGTCAATGGCCACCACCAAGTACAAAAAAAAATCAAAATTTTTTTGTG
* * ****
40178241 CTGGCCTATCAATGGCCACCACCAAGTACCAAAAAATAATCTTTTTTTTTTTGTTG
1 CTGGCCTGTCAATGGCCACCACCAAGTA-CAAAAAAAAATCAAAATTTTTTTG-TG
* *
40178297 TTGGCCTGTTAATGGCCACCACCAAGTACAAAAAAAAAATCAAAATTTTTTTGTG
1 CTGGCCTGTCAATGGCCACCACCAAGTAC-AAAAAAAAATCAAAATTTTTTTGTG
* *
40178352 CTCGCCTGTCAATGGCCAGCACCAAAGTAC
1 CTGGCCTGTCAATGGCCACCACC-AAGTAC
40178382 GAGTTTTAGA
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
54 27 0.23
55 40 0.34
56 51 0.43
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (54 bp):
CTGGCCTGTCAATGGCCACCACCAAGTACAAAAAAAAATCAAAATTTTTTTGTG
Found at i:40178405 original size:55 final size:54
Alignment explanation
Indices: 40178346--40178451 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 54
40178336 TCAAAATTTT
40178346 TTTGTGCTCGCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTAGAAAAAAAAAA
1 TTTGTGCTCGCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTA-AAAAAAAAAA
* * * *
40178401 TTTGTGCTGGCCTGTCAATGGCTAGCACCAGAGTACGCGTTTTAAAAAAAA
1 TTTGTGCTCGCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTAAAAAAAA
40178452 TTGGTACTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 7 0.15
55 40 0.85
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (54 bp):
TTTGTGCTCGCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTAAAAAAAAAAA
Found at i:40178413 original size:110 final size:102
Alignment explanation
Indices: 40178172--40178436 Score: 242
Period size: 110 Copynumber: 2.4 Consensus size: 102
40178162 ATCAGTATTT
* *
40178172 AAAAAAAATTTAGTACTGGCCTGTCAATGGCCACCACCAAGTACAAAAATAAATCAAAATTTTTT
1 AAAAAAAATTT-GTGCTGGCCTGTCAATGGCCACCACCAAGTACAAAAAAAAATCAAAATTTTTT
*
40178237 TGTGCTGGCCTATCAATGGCCACCACCAAGTACCAAAA
65 TGTGCTCGCCTATCAATGGCCACCACCAAGTACCAAAA
**** * *
40178275 AATAATCTTTTTTTTTTTGTTGTTGGCCTGTTAATGGCCACCACCAAGTACAAAAAAAAAATCAA
1 AA-AA------AAAATTTG-TGCTGGCCTGTCAATGGCCACCACCAAGTAC-AAAAAAAAATCAA
* * *
40178340 AATTTTTTTGTGCTCGCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTAGAA
57 AATTTTTTTGTGCTCGCCTATCAATGGCCACCACC-AAGTACCA-----A-AA
* *
40178393 AAAAAAAATTTGTGCTGGCCTGTCAATGGCTAGCACCAGAGTAC
1 AAAAAAAATTTGTGCTGGCCTGTCAATGGCCACCACCA-AGTAC
40178437 GCGTTTTAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
103 2 0.02
104 2 0.02
109 1 0.01
110 53 0.42
111 53 0.42
112 7 0.06
117 3 0.02
118 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (102 bp):
AAAAAAAATTTGTGCTGGCCTGTCAATGGCCACCACCAAGTACAAAAAAAAATCAAAATTTTTTT
GTGCTCGCCTATCAATGGCCACCACCAAGTACCAAAA
Found at i:40178470 original size:51 final size:52
Alignment explanation
Indices: 40178355--40178499 Score: 161
Period size: 51 Copynumber: 2.8 Consensus size: 52
40178345 TTTTGTGCTC
* * *
40178355 GCCTGTCAATGGCCAGCACCAAAGTACGAGTTTTAGAAAAAAAAAATTTGTGCTG
1 GCCTGTCAATGGCCAGCACCAGAGTACGAGTTTT---AAAAAAAAATTGGTACTG
* *
40178410 GCCTGTCAATGGCTAGCACCAGAGTACGCGTTTT-AAAAAAAATTGGTACTG
1 GCCTGTCAATGGCCAGCACCAGAGTACGAGTTTTAAAAAAAAATTGGTACTG
* * * *
40178461 GCCTATCAATGGCCGGCACCAGACT-C-AGTATTAAAAAAA
1 GCCTGTCAATGGCCAGCACCAGAGTACGAGTTTTAAAAAAA
40178500 TTTTGTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
49 4 0.05
50 7 0.09
51 36 0.46
55 31 0.40
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (52 bp):
GCCTGTCAATGGCCAGCACCAGAGTACGAGTTTTAAAAAAAAATTGGTACTG
Found at i:40179477 original size:31 final size:31
Alignment explanation
Indices: 40179425--40179504 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
40179415 AATATTAAAA
* ** *
40179425 AACAGAATAATTTCATTATAAAAG-AAATATT
1 AACAGAATAATTTAAAAAT-AAAGTAAAAATT
*
40179456 TACAGAATAATTTAAAAATAAAGTAAAAATT
1 AACAGAATAATTTAAAAATAAAGTAAAAATT
*
40179487 AACAGAAAAAATTTAAAA
1 AACAG-AATAATTTAAAA
40179505 TTGTCGCGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 4 0.10
31 25 0.62
32 11 0.28
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (31 bp):
AACAGAATAATTTAAAAATAAAGTAAAAATT
Found at i:40181566 original size:53 final size:53
Alignment explanation
Indices: 40181489--40181643 Score: 202
Period size: 53 Copynumber: 2.9 Consensus size: 53
40181479 CTGGCGCCGA
* * *
40181489 CCATTGACAAGCTAGTCCCAAAAAATTTTAATTTTTTTTTGTACTTGGTGGTGG
1 CCATTGACAAGCCAG-CACAAAAAATTTTGATTTTTTTTTGTACTTGGTGGTGG
* * * *
40181543 TCATTGATAAGCCAGCACAAAAAAATTTGATTTTTTTTTGTACTTAGTGGTGG
1 CCATTGACAAGCCAGCACAAAAAATTTTGATTTTTTTTTGTACTTGGTGGTGG
* *
40181596 CCATTGACAGGCCAGCACAAAAAAAATTTTGATTTATTTTTGTACTTG
1 CCATTGACAAGCCAGCAC--AAAAAATTTTGATTTTTTTTTGTACTTG
40181644 TATAATGGAA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
53 49 0.57
54 12 0.14
55 25 0.29
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (53 bp):
CCATTGACAAGCCAGCACAAAAAATTTTGATTTTTTTTTGTACTTGGTGGTGG
Found at i:40183459 original size:22 final size:22
Alignment explanation
Indices: 40183407--40183483 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
40183397 ATCCTAATTC
40183407 TAAAAAATAT-ATAA-ATATTT
1 TAAAAAATATAATAATATATTT
*
40183427 TCAAAGAATATAATAATATATTT
1 T-AAAAAATATAATAATATATTT
* *
40183450 TAAAATATATAAAAATGA-ATGTT
1 TAAAAAATATAATAAT-ATAT-TT
40183473 TAAAAAATATA
1 TAAAAAATATA
40183484 TAACAAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 8 0.17
22 18 0.38
23 20 0.43
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAAAAATATAATAATATATTT
Found at i:40183532 original size:25 final size:24
Alignment explanation
Indices: 40183499--40183547 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
40183489 AATTAAAATT
*
40183499 TTATATTAATATTAAATAAATATAA
1 TTATATTAATATGAAATAAA-ATAA
40183524 TTATATTAATATGAAATAAAATAA
1 TTATATTAATATGAAATAAAATAA
40183548 AATCTGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TTATATTAATATGAAATAAAATAA
Found at i:40184410 original size:88 final size:88
Alignment explanation
Indices: 40184252--40184512 Score: 373
Period size: 86 Copynumber: 3.0 Consensus size: 88
40184242 CATCATCTCC
* *
40184252 AATAAAATTTCAAATTAATAGTTTTATTTGAAAACTTATTTTTTCTCATAGAAAGTTTGCTAATA
1 AATAAAATTTCAAATTAATAGTTTTATTTAAAAAGTTA-TTTTTCTCATAGAAAGTTTGCTAATA
*
40184317 AGTTAAAACAGTAAGGTAAAAAAA
65 AGTTAAAACAATAAGGTAAAAAAA
* * *
40184341 AATAAAATTTCAAATTAATAGTTTTAGTTAAAAAGTTGTTTTTCTCATAGAAAATTTGCTAATAA
1 AATAAAATTTCAAATTAATAGTTTTATTTAAAAAGTTATTTTTCTCATAGAAAGTTTGCTAATAA
40184406 GTTAAAACAATAAGGT--AAAAA
66 GTTAAAACAATAAGGTAAAAAAA
* * * * **
40184427 TATAAATTTTCAAATTAATAGTTTTATTTCAAAAGTTATTTTTCTTATAGAAAGTTTGCTAAGGA
1 AATAAAATTTCAAATTAATAGTTTTATTTAAAAAGTTATTTTTCTCATAGAAAGTTTGCTAATAA
* *
40184492 GCTAAAACAATAAGCTAAAAA
66 GTTAAAACAATAAGGTAAAAA
40184513 GAACGTTAAT
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
86 75 0.49
88 44 0.29
89 34 0.22
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (88 bp):
AATAAAATTTCAAATTAATAGTTTTATTTAAAAAGTTATTTTTCTCATAGAAAGTTTGCTAATAA
GTTAAAACAATAAGGTAAAAAAA
Found at i:40188872 original size:25 final size:25
Alignment explanation
Indices: 40188838--40188886 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40188828 CAACATGCTA
*
40188838 GTTTACTTGGCGATTATCTTTGATT
1 GTTTACTTGGCGATTATCCTTGATT
40188863 GTTTACTTGGCGATTATCCTTGAT
1 GTTTACTTGGCGATTATCCTTGAT
40188887 CCACAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (25 bp):
GTTTACTTGGCGATTATCCTTGATT
Found at i:40191803 original size:26 final size:26
Alignment explanation
Indices: 40191766--40191829 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
40191756 AATAACATTA
* *
40191766 AAAAAATAAAAATATAAA-ATTATGAT
1 AAAAAATTAAAATATAAAGATTA-AAT
40191792 AAAAAATTAAAATATAAAGATTAAAT
1 AAAAAATTAAAATATAAAGATTAAAT
40191818 AAAAAATTAAAA
1 AAAAAATTAAAA
40191830 AAATGGACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (26 bp):
AAAAAATTAAAATATAAAGATTAAAT
Found at i:40191817 original size:13 final size:12
Alignment explanation
Indices: 40191775--40191832 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
40191765 AAAAAAATAA
*
40191775 AAATATAAAATT
1 AAATAAAAAATT
*
40191787 ATGATAAAAAATT
1 A-AATAAAAAATT
*
40191800 AAAATATAAAGATT
1 -AAATA-AAAAATT
40191814 AAATAAAAAATT
1 AAATAAAAAATT
40191826 AAA-AAAA
1 AAATAAAA
40191833 TGGACCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 4 0.11
12 10 0.26
13 17 0.45
14 7 0.18
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AAATAAAAAATT
Found at i:40197698 original size:38 final size:37
Alignment explanation
Indices: 40197635--40197729 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
40197625 ATTGAGATTT
** *
40197635 GATT-GCATGTTAAACACACCCTACATGATATTATCC
1 GATTCGCATGTTAAACATGCCTTACATGATATTATCC
* *
40197671 GATTTGTATGTTAAAACATGCCTTACATGATATTATCC
1 GATTCGCATGTT-AAACATGCCTTACATGATATTATCC
*
40197709 GATTCGCATGTTCAACATGCC
1 GATTCGCATGTTAAACATGCC
40197730 CAATGTGACA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 4 0.08
37 14 0.28
38 32 0.64
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (37 bp):
GATTCGCATGTTAAACATGCCTTACATGATATTATCC
Found at i:40197870 original size:24 final size:24
Alignment explanation
Indices: 40197829--40197885 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
40197819 GAGAAAGAAT
* * *
40197829 TGGTGGTTTCATCTACAACTTACA
1 TGGTGGCTTCATCAACAACCTACA
* *
40197853 TGGTGGCTTCGTCAACAACCTATA
1 TGGTGGCTTCATCAACAACCTACA
40197877 TGGTGGCTT
1 TGGTGGCTT
40197886 GTTTGCAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (24 bp):
TGGTGGCTTCATCAACAACCTACA
Found at i:40203556 original size:42 final size:43
Alignment explanation
Indices: 40203458--40203548 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
40203448 TCTCGGACGT
* * *
40203458 GGTCTTACATGTAATTACATATCGATGCCATTGTCTCAGACAG
1 GGTCTTACACGTAATTACATATCGATGCCAATGTCCCAGACAG
* *
40203501 GGTCTTACACGTAATTATATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATTACATATCGATGCCAATGTCCCAGACAG
40203543 GGTCTT
1 GGTCTT
40203549 TTACGTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 24 0.56
43 19 0.44
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
GGTCTTACACGTAATTACATATCGATGCCAATGTCCCAGACAG
Found at i:40208166 original size:2 final size:2
Alignment explanation
Indices: 40208161--40208186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40208151 TATTTTTTAG
40208161 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
40208187 TTACAGTCTC
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:40210285 original size:19 final size:21
Alignment explanation
Indices: 40210256--40210313 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
40210246 CTTGGTCGTC
40210256 GTACCAATACAAGTCCCTTAG
1 GTACCAATACAAGTCCCTTAG
* *
40210277 G-A-TAATACAATTCCCCTTAG
1 GTACCAATACAAGT-CCCTTAG
40210297 GTACCAATACAAGTCCC
1 GTACCAATACAAGTCCC
40210314 AAACTTGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.27
20 9 0.30
21 5 0.17
22 8 0.27
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
GTACCAATACAAGTCCCTTAG
Found at i:40210295 original size:20 final size:19
Alignment explanation
Indices: 40210261--40210313 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
40210251 TCGTCGTACC
40210261 AATACAAGTCCCTTAGGAT
1 AATACAAGTCCCTTAGGAT
* *
40210280 AATACAATTCCCCTTAGGTACC
1 AATACAAGT-CCCTTAGG-A-T
40210302 AATACAAGTCCC
1 AATACAAGTCCC
40210314 AAACTTGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.29
20 8 0.29
21 4 0.14
22 8 0.29
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (19 bp):
AATACAAGTCCCTTAGGAT
Found at i:40210308 original size:22 final size:22
Alignment explanation
Indices: 40210256--40210313 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
40210246 CTTGGTCGTC
40210256 GTACCAATACAAGT-CCCTTAG
1 GTACCAATACAAGTCCCCTTAG
* *
40210277 G-A-TAATACAATTCCCCTTAG
1 GTACCAATACAAGTCCCCTTAG
40210297 GTACCAATACAAGTCCC
1 GTACCAATACAAGTCCC
40210314 AAACTTGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.27
20 9 0.30
21 2 0.07
22 11 0.37
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
GTACCAATACAAGTCCCCTTAG
Found at i:40214166 original size:27 final size:27
Alignment explanation
Indices: 40214067--40214171 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 27
40214057 TGGCATTTTG
* * * *
40214067 ATAACCTTTGTGCCGAAA-TCTGAAAGG
1 ATAACCTTTATGGC-AAACTCTAAAAGA
* * *
40214094 ATAGCCTTTATGGCGAAC-CTTGAAAGA
1 ATAACCTTTATGGCAAACTC-TAAAAGA
* **
40214121 ATAAGCTTTATGGTGAACTCTAAAAGA
1 ATAACCTTTATGGCAAACTCTAAAAGA
*
40214148 ATAACCTTTGTGGCAAACTCTAAA
1 ATAACCTTTATGGCAAACTCTAAA
40214172 TGAACTGTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 3 0.05
27 58 0.94
28 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (27 bp):
ATAACCTTTATGGCAAACTCTAAAAGA
Found at i:40219087 original size:43 final size:42
Alignment explanation
Indices: 40219003--40219090 Score: 113
Period size: 43 Copynumber: 2.1 Consensus size: 42
40218993 CCATGTTTAA
* *
40219003 CTTCTCCTCTTTTTAAATTCTTTTTCAAAAACCCAATATTAT
1 CTTCTCCTCTTTTTAAATTCTTTTTCAAAAACACAAGATTAT
* * **
40219045 CTTCTCCTTTTTTTAAATTATTTTTTCAAAAACATGAGATTAT
1 CTTCTCCTCTTTTTAAATT-CTTTTTCAAAAACACAAGATTAT
40219088 CTT
1 CTT
40219091 TTTTTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 18 0.46
43 21 0.54
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.50
Consensus pattern (42 bp):
CTTCTCCTCTTTTTAAATTCTTTTTCAAAAACACAAGATTAT
Found at i:40219797 original size:21 final size:21
Alignment explanation
Indices: 40219771--40219829 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
40219761 ATGTAAAAGT
40219771 AGGGTTCGCGTACCATATCTA
1 AGGGTTCGCGTACCATATCTA
* * *
40219792 AGGGTTCGCGTATC-TAATGTG
1 AGGGTTCGCGTACCAT-ATCTA
*
40219813 ATGGTTCGCGTACCATA
1 AGGGTTCGCGTACCATA
40219830 CCTTGCGAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (21 bp):
AGGGTTCGCGTACCATATCTA
Found at i:40220055 original size:9 final size:9
Alignment explanation
Indices: 40220041--40220071 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40220031 GTTAAACGAA
40220041 TCGAGTTAT
1 TCGAGTTAT
*
40220050 TCGAGTTAA
1 TCGAGTTAT
40220059 TCGAGTTAT
1 TCGAGTTAT
40220068 TCGA
1 TCGA
40220072 ATCAACTCAA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40220139 original size:9 final size:9
Alignment explanation
Indices: 40220122--40220158 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40220112 TTGAGTTTCG
40220122 AATTCGAAT
1 AATTCGAAT
*
40220131 AACTCGAAT
1 AATTCGAAT
40220140 AATTCGAAT
1 AATTCGAAT
40220149 AATTCGAAT
1 AATTCGAAT
40220158 A
1 A
40220159 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.