Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:202176 original size:29 final size:29
Alignment explanation
Indices: 202134--202192 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
202124 ATTTTCACCT
*
202134 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
202163 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
202192 A
1 A
202193 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:204037 original size:23 final size:23
Alignment explanation
Indices: 204001--204073 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
203991 CACCACAGCT
*
204001 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
204022 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
204045 CGCGTAGAATTGTACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
204068 CATATA
1 CATATA
204074 AATCCCATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 34 0.81
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:204315 original size:18 final size:18
Alignment explanation
Indices: 204292--204327 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
204282 GAATACATAT
204292 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
204310 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
204328 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:204391 original size:118 final size:118
Alignment explanation
Indices: 204082--204427 Score: 583
Period size: 118 Copynumber: 2.9 Consensus size: 118
204072 TAAATCCCAT
*
204082 AAGGACCACATATCATTCCTTAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAAATCATATACATATACTAGGGATCAAGTAT--GTCTCACCAG
204147 ACTTCACACATGTTCCAAAGAATACATAT-TGTCCCGAAGGACCACAATGTCCCG
64 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
* * * *
204201 AAGGA-CACATATCATTCCTTAAGA--ATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAAATCATATACATATACTAGGGATCAAGTA--TGTCTCACCAG
204263 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
64 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
204318 AAGGACCACATATCATTCCTTAAAATCATATACATATACTAGGGATCAAGTATGTCTCACCAGAC
1 AAGGACCACATATCATTCCTTAAAATCATATACATATACTAGGGATCAAGTATGTCTCACCAGAC
204383 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
204428 TAGACCCTCG
Statistics
Matches: 212, Mismatches: 9, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
116 61 0.29
117 30 0.14
118 94 0.44
119 5 0.02
120 22 0.10
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (118 bp):
AAGGACCACATATCATTCCTTAAAATCATATACATATACTAGGGATCAAGTATGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
Found at i:209410 original size:22 final size:23
Alignment explanation
Indices: 209385--209434 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
209375 CATATAAATG
209385 CACCGAAGAGCC-CATAGAATTA
1 CACCGAAGAGCCGCATAGAATTA
* * * *
209407 CACCGTAGTGCCGCGTAGAATTG
1 CACCGAAGAGCCGCATAGAATTA
209430 CACCG
1 CACCG
209435 TAGTGCCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (23 bp):
CACCGAAGAGCCGCATAGAATTA
Found at i:209667 original size:62 final size:63
Alignment explanation
Indices: 209601--209796 Score: 155
Period size: 62 Copynumber: 3.2 Consensus size: 63
209591 ATCATTCCTT
*
209601 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCTA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCTA
* * * * * *
209663 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATATACC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
209718 CCTT
61 -CTA
* * *
209722 AAGAAT-CATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCTA
209784 AAGAATACATATA
1 AAGAATACATATA
209797 TGTCCCGAAG
Statistics
Matches: 99, Mismatches: 17, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
57 7 0.07
58 10 0.10
59 21 0.21
60 5 0.05
61 6 0.06
62 27 0.27
63 16 0.16
64 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (63 bp):
AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCTA
Found at i:209678 original size:121 final size:119
Alignment explanation
Indices: 209449--209813 Score: 559
Period size: 121 Copynumber: 3.0 Consensus size: 119
209439 GCCATATAAT
** * * * *
209449 AATGTCCATAAGGACCCACATATAATTCCATAAGAATCATATACATATACTAGGTATCAAGTATG
1 AATGTCCCGAAGGA-CCACATATCATTCCTTAAGAATCATATACATATCCAAGG-ATCAAGTATG
** * *
209514 CATCTCACCAGACTTCACACATGTTGCAAAGAATACATATATGTCCTGAAGGACTAC
64 TGTCTCACCAGACTTCACACATGTT-CAAAGAATACATATATGTCCCGAAGGACCAC
209571 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATAT-CCAAGGATCAAGTATGT
209636 GTCTCACCAGACTTCACACATGTTCTAAAGAATACATATATGTCCCGAAGGACCAC
65 GTCTCACCAGACTTCACACATGTTC-AAAGAATACATATATGTCCCGAAGGACCAC
* *
209692 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATAT-CCAAGGATCAAGTATGT
209757 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
65 GTCTCACCAGACTTCACACATGTT-CAAAGAATACATATATGTCCCGAAGGACCAC
209813 A
1 A
209814 TAGACCCTCG
Statistics
Matches: 227, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
120 1 0.00
121 209 0.92
122 17 0.07
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (119 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATCCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:209698 original size:18 final size:18
Alignment explanation
Indices: 209675--209710 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
209665 GAATACATAT
209675 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
209693 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
209711 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:211115 original size:21 final size:21
Alignment explanation
Indices: 211089--211132 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
211079 ATTTTATTCG
* *
211089 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
211110 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
211131 CT
1 CT
211133 AGCCCATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:214666 original size:30 final size:30
Alignment explanation
Indices: 214631--214693 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
214621 AACATTCTTC
214631 TTTAATTGTGGTCTTTAAAGCAAACATTGT
1 TTTAATTGTGGTCTTTAAAGCAAACATTGT
214661 TTTAATTGTGGTCTTTAAAGCAAACATTGT
1 TTTAATTGTGGTCTTTAAAGCAAACATTGT
214691 TTT
1 TTT
214694 GCCTGATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (30 bp):
TTTAATTGTGGTCTTTAAAGCAAACATTGT
Found at i:215405 original size:29 final size:29
Alignment explanation
Indices: 215363--215421 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
215353 ATTTTCACCT
215363 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
215392 AACTAAATTGATGTAAGCGATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
215421 A
1 A
215422 TTAAAACTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:220821 original size:16 final size:16
Alignment explanation
Indices: 220775--220827 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
220765 AAAGTACATG
*
220775 AATGAAGTGATATATC
1 AATGAAGTGATTTATC
* **
220791 ATTGAAAAG-TTTATC
1 AATGAAGTGATTTATC
220806 AATGAAGTGATTTATC
1 AATGAAGTGATTTATC
*
220822 ACTGAA
1 AATGAA
220828 AAGTTTCTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (16 bp):
AATGAAGTGATTTATC
Found at i:220894 original size:62 final size:62
Alignment explanation
Indices: 220732--220898 Score: 219
Period size: 62 Copynumber: 2.7 Consensus size: 62
220722 CTCGCTTTTT
* * * * * * *
220732 AAAAGTTTCTGAAATGAATTGATATATGATTGAAAAG-TACATGAATGAAGTGATATATCATTG
1 AAAAGTTTCT-AAATGAAGTGATATATCACTGAAAAGTTTC-TGAATGAAGTGATATAACACTA
* * *
220795 AAAAGTTTATCAATGAAGTGATTTATCACTGAAAAGTTTCTGAATGAAGTGATATAACACTA
1 AAAAGTTTCTAAATGAAGTGATATATCACTGAAAAGTTTCTGAATGAAGTGATATAACACTA
220857 AAAAGTTTCTAAATGAAGTGATATATCACTGAAAAGTTTCTG
1 AAAAGTTTCTAAATGAAGTGATATATCACTGAAAAGTTTCTG
220899 TCACCGAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
62 79 0.88
63 11 0.12
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (62 bp):
AAAAGTTTCTAAATGAAGTGATATATCACTGAAAAGTTTCTGAATGAAGTGATATAACACTA
Found at i:220895 original size:31 final size:31
Alignment explanation
Indices: 220732--220897 Score: 199
Period size: 31 Copynumber: 5.3 Consensus size: 31
220722 CTCGCTTTTT
* * *
220732 AAAAGTTTCTGAAATGAATTGATATATGATTG
1 AAAAGTTTCT-AAATGAAGTGATATATCACTG
* * *
220764 AAAAG-TACATGAATGAAGTGATATATCATTG
1 AAAAGTTTC-TAAATGAAGTGATATATCACTG
* * *
220795 AAAAGTTTATCAATGAAGTGATTTATCACTG
1 AAAAGTTTCTAAATGAAGTGATATATCACTG
* * *
220826 AAAAGTTTCTGAATGAAGTGATATAACACTA
1 AAAAGTTTCTAAATGAAGTGATATATCACTG
220857 AAAAGTTTCTAAATGAAGTGATATATCACTG
1 AAAAGTTTCTAAATGAAGTGATATATCACTG
220888 AAAAGTTTCT
1 AAAAGTTTCT
220898 GTCACCGAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
31 108 0.94
32 7 0.06
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (31 bp):
AAAAGTTTCTAAATGAAGTGATATATCACTG
Found at i:221108 original size:22 final size:22
Alignment explanation
Indices: 221083--221149 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
221073 CATTTATAGG
*
221083 AAGGGATCAATCCATTTGGTGA
1 AAGGGATCAATCCTTTTGGTGA
* **
221105 AA-GGATCGATCCTTTTCATCG-
1 AAGGGATCAATCCTTTTGGT-GA
221126 -AGGGATCAATCCTTTTGGTGA
1 AAGGGATCAATCCTTTTGGTGA
221147 AAG
1 AAG
221150 AATCGATCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
21 27 0.79
22 5 0.15
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (22 bp):
AAGGGATCAATCCTTTTGGTGA
Found at i:221116 original size:21 final size:21
Alignment explanation
Indices: 221086--221158 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
221076 TTATAGGAAG
*
221086 GGATCAATCCATTTGGTGAAA
1 GGATCAATCCTTTTGGTGAAA
* ** *
221107 GGATCGATCCTTTTCATCG-AG
1 GGATCAATCCTTTTGGT-GAAA
221128 GGATCAATCCTTTTGGTGAAA
1 GGATCAATCCTTTTGGTGAAA
* *
221149 GAATCGATCC
1 GGATCAATCC
221159 CAAACATACT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
GGATCAATCCTTTTGGTGAAA
Found at i:225966 original size:23 final size:22
Alignment explanation
Indices: 225933--225998 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
225923 TTGATTCCCC
225933 TCAAGGAGGGAATCGGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
* *
225956 TCAAAGGGGGAATCAGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
* *
225979 TCAAGGGGGTATCGATTCCC
1 TCAAGGGGGAATCGGTTCCC
225999 TCTGCACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.41
23 18 0.49
24 4 0.11
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:225987 original size:22 final size:22
Alignment explanation
Indices: 225927--225987 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
225917 GGGGTATTGA
*
225927 TTCCCC-TCAAGGAGGGAATCGG
1 TTCCCCTTCAAGG-GGGAATCAG
*
225949 TTCCCATTCAAAGGGGGAATCAG
1 TTCCCCTTC-AAGGGGGAATCAG
225972 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
225988 TATCGATTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.35
23 18 0.53
24 4 0.12
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCAG
Found at i:225997 original size:22 final size:22
Alignment explanation
Indices: 225916--225998 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
225906 CAGAACCCGT
* *
225916 GGGGGTATTGATTCCCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
225937 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
225961 GGGGGAATC-AGTTCCCCTTCAA
1 GGGGGAATCGA-TTCCCCTTCAA
*
225983 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
225999 TCTGCACTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
21 2 0.04
22 26 0.52
23 18 0.36
24 4 0.08
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:235039 original size:2 final size:2
Alignment explanation
Indices: 235034--235075 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
235024 ATTTTTTATG
235034 AT AT 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 AT AT
235076 TAAAATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244321 original size:3 final size:3
Alignment explanation
Indices: 244313--244347 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
244303 ATTAATTAAT
244313 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
244348 TTTTTGAACT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:244993 original size:2 final size:2
Alignment explanation
Indices: 244986--245010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
244976 TCATGGCATT
244986 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
245011 AAAATTATGC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:251247 original size:22 final size:21
Alignment explanation
Indices: 251213--251253 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
251203 ATAATTATTT
251213 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
251234 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
251254 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:252813 original size:6 final size:6
Alignment explanation
Indices: 252797--252836 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
252787 TTAAAAAGTA
252797 ATTTAAT ATTTAT ATTTAT ATTTAT ATTT-T ATTTAT ATTT
1 ATTT-AT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
252837 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 23 0.72
7 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:262514 original size:18 final size:18
Alignment explanation
Indices: 262491--262531 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
262481 GTAACTTATG
262491 TTGTGTTGTGTCTTTGAA
1 TTGTGTTGTGTCTTTGAA
262509 TTGTGTTGTGTCTTTGAA
1 TTGTGTTGTGTCTTTGAA
262527 TTGTG
1 TTGTG
262532 CCTCAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.05, G:0.29, T:0.56
Consensus pattern (18 bp):
TTGTGTTGTGTCTTTGAA
Found at i:266147 original size:18 final size:18
Alignment explanation
Indices: 266094--266147 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
266084 TAAAAGACTA
266094 AAAATTAATAATAATAATT
1 AAAA-TAATAATAATAATT
* * *
266113 AAAATAATTACATTAATT
1 AAAATAATAATAATAATT
266131 AAAA-AATAGATAATAAT
1 AAAATAATA-ATAATAAT
266148 AATAATACTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.11
18 21 0.75
19 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATAATAATAATAATT
Found at i:267469 original size:42 final size:43
Alignment explanation
Indices: 267386--267470 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
267376 TCATGTTCGA
* *
267386 TATTGATACTACTATACATAGTGGTATCGATACTCACTGGACAG
1 TATTGATACTAC-ATACAAAGTAGTATCGATACTCACTGGACAG
267430 TATTGATACTAC-TACAAAGTAGTATCGATACTC-CTTGGACA
1 TATTGATACTACATACAAAGTAGTATCGATACTCAC-TGGACA
267471 TCGATATCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.03
42 25 0.66
44 12 0.32
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (43 bp):
TATTGATACTACATACAAAGTAGTATCGATACTCACTGGACAG
Found at i:270043 original size:18 final size:19
Alignment explanation
Indices: 270022--270063 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
270012 ATCTAAAATT
270022 ATAATAT-CAAATAAAAAA
1 ATAATATGCAAATAAAAAA
*
270040 ATAA-ATGCATATAAAAAA
1 ATAATATGCAAATAAAAAA
*
270058 AAAATA
1 ATAATA
270064 AAGGATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.85
19 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (19 bp):
ATAATATGCAAATAAAAAA
Found at i:271224 original size:33 final size:35
Alignment explanation
Indices: 271153--271250 Score: 159
Period size: 33 Copynumber: 2.9 Consensus size: 35
271143 TAAAATCTAA
271153 GTCCATTCACCAAGTGACATAACTTATTATAATAG
1 GTCCATTCACCAAGTGACATAACTTATTATAATAG
271188 GTCCATTCACCAAGTGACATAACTTA-T-TAATAG
1 GTCCATTCACCAAGTGACATAACTTATTATAATAG
*
271221 GTCCATTCACCAAGTGAC-TGA-TTATTATAA
1 GTCCATTCACCAAGTGACATAACTTATTATAA
271251 GTAGCACAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
31 3 0.05
32 3 0.05
33 27 0.45
34 1 0.02
35 26 0.43
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (35 bp):
GTCCATTCACCAAGTGACATAACTTATTATAATAG
Found at i:273793 original size:28 final size:30
Alignment explanation
Indices: 273756--273837 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 30
273746 CCCGAACCCG
273756 AAAATATTATATATATA-AT-AAAAAATAT
1 AAAATATTATATATATATATAAAAAAATAT
273784 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATA-T-TATATAT-A-T-ATATAAAAAAATAT
273819 AAAATATTATATATATATA
1 AAAATATTATATATATATA
273838 ATCGTGGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
28 6 0.13
29 1 0.02
30 10 0.21
31 2 0.04
32 2 0.04
33 8 0.17
34 3 0.06
35 15 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATATTATATATATATATAAAAAAATAT
Found at i:273819 original size:25 final size:26
Alignment explanation
Indices: 273764--273819 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
273754 CGAAAATATT
*
273764 ATATATATAATAAAAAATATAAAATA
1 ATATATATAATAAAAAATATAAAAAA
* **
273790 TTATATAT-ATAATTAATATAAAAAA
1 ATATATATAATAAAAAATATAAAAAA
273815 ATATA
1 ATATA
273820 AAATATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATATAATAAAAAATATAAAAAA
Found at i:274437 original size:21 final size:21
Alignment explanation
Indices: 274413--274458 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
274403 TACAAGTTAT
*
274413 AAATAAGTCACT-TATTATTA
1 AAATAAGTCACTCTATCATTA
274433 CAAATAAGTCACTCTATCATTA
1 -AAATAAGTCACTCTATCATTA
274455 AAAT
1 AAAT
274459 TGAAAAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATAAGTCACTCTATCATTA
Found at i:275931 original size:25 final size:24
Alignment explanation
Indices: 275903--275965 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
275893 TTATTTAAAC
*
275903 TTAAAATATAAAATACAAATAACTA
1 TTAAAATATAAAATAC-AATAAATA
* **
275928 TTAAGATATTCAATACAATAAATA
1 TTAAAATATAAAATACAATAAATA
275952 TATACAAATATAAA
1 T-TA-AAATATAAA
275966 TTATTAAAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 8 0.28
25 15 0.52
26 6 0.21
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAAAATATAAAATACAATAAATA
Found at i:276732 original size:35 final size:34
Alignment explanation
Indices: 276656--276778 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
276646 TTGTGCATAC
*
276656 TCTAAATGCGACACATGACATTGTTGTAT--ATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
* * **
276689 TATGAATGCGACACATGACACACTTCTATGCATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
*
276724 TCTAAATGCGACACATGGCATTCTGTT-TGCATTA
1 TCTAAATGCGACACATGACATTCT-TTATGCATTA
* *
276758 TCTAAATGTGACACATTACAT
1 TCTAAATGCGACACATGACAT
276779 ACTGCTAGCA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
33 23 0.32
34 25 0.34
35 24 0.33
36 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (34 bp):
TCTAAATGCGACACATGACATTCTTTATGCATTA
Found at i:281965 original size:23 final size:22
Alignment explanation
Indices: 281935--282016 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
281925 GCATGACCTT
281935 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
281957 AGTGCATCGGTACACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
281979 GTGTATCGATGCATATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
282002 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
282017 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 18 0.41
24 11 0.25
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:287831 original size:19 final size:19
Alignment explanation
Indices: 287782--287831 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
287772 GGACCCTTAT
**
287782 TGCATCGATATACTAAGAG
1 TGCATCGATGCACTAAGAG
*
287801 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCACTAAGAG
287820 TGCATCGATGCA
1 TGCATCGATGCA
287832 TGAAATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAG
Found at i:287902 original size:64 final size:62
Alignment explanation
Indices: 287819--288025 Score: 222
Period size: 64 Copynumber: 3.2 Consensus size: 62
287809 TGCACTAAGA
287819 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-CCATAGTGCATCGATGCATGG-TG
* *
287883 GTGCATCGATGCATTAAATGCATTCGATGTTTCATAAA-ACTC-TGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCA-AAATAC-CAT-AGTGCATCGATGCATGGT-
*
287946 T
62 G
* * * * *
287947 GTGCATCAATGCATGGAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA--AATACCATAGTGCATCGATGCATGG--T
288011 G
62 G
*
288012 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
288026 CACTTTGAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 94 0.78
65 17 0.14
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATACCATAGTGCATCGATGCATGGTG
Found at i:289966 original size:18 final size:18
Alignment explanation
Indices: 289901--289957 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
289891 AGTTTTCATA
*
289901 ATTTATTTTAATTAT-TT
1 ATTTATTATAATTATATT
*
289918 A-TTA-TATAA-AATATT
1 ATTTATTATAATTATATT
289933 ATTTATTATAATTATATT
1 ATTTATTATAATTATATT
289951 ATTTATT
1 ATTTATT
289958 TTTATTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 6 0.18
17 6 0.18
18 12 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTATTATAATTATATT
Found at i:290169 original size:13 final size:13
Alignment explanation
Indices: 290151--290183 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
290141 AACAATTAAA
290151 TTTTAAACAACAC
1 TTTTAAACAACAC
*
290164 TTTTAAACAATAC
1 TTTTAAACAACAC
290177 TTTTAAA
1 TTTTAAA
290184 AATTCGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTTAAACAACAC
Found at i:291160 original size:2 final size:2
Alignment explanation
Indices: 291153--291186 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
291143 AACACCTATC
291153 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
291187 CTCACACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294317 original size:128 final size:128
Alignment explanation
Indices: 294081--294331 Score: 351
Period size: 128 Copynumber: 2.0 Consensus size: 128
294071 GGCCAAGCGC
* * * * *
294081 TTCATTGTTGGAGTAGGCAGGGGGACAGGATTCATGCCAAGCATTTTCAAGAGGGGAATAGACAT
1 TTCATTATTGGAGTAGGCAGGGGGACAGGATTCATGCCAAGCACTTCCAAGAGGAGAATAGACAA
* *
294146 GATGACTTGGTCTTGCACCAAGCTCTCTTACGTGTAGAGTAGGCAGAGTGTCCCTATTATCAG
66 GATGACTTGGTCTTGCACCAAGCGCTCTTACGTGTAGAATAGGCAGAGTGTCCCTATTATCAG
* * * * *
294209 TTCATTATTGGAGTAGGCAGGGGGACATGATTCATTCCAAGCACTTCCAAGAGGAGAGTGGGCAA
1 TTCATTATTGGAGTAGGCAGGGGGACAGGATTCATGCCAAGCACTTCCAAGAGGAGAATAGACAA
* * *
294274 GATGACCTT-GTTTTGCACCAAGCGCTCTTACGTGTGGAATAGGCAGGGTGTCCCTATT
66 GATGA-CTTGGTCTTGCACCAAGCGCTCTTACGTGTAGAATAGGCAGAGTGTCCCTATT
294332 TCACGCCAAG
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 104 0.97
129 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (128 bp):
TTCATTATTGGAGTAGGCAGGGGGACAGGATTCATGCCAAGCACTTCCAAGAGGAGAATAGACAA
GATGACTTGGTCTTGCACCAAGCGCTCTTACGTGTAGAATAGGCAGAGTGTCCCTATTATCAG
Found at i:303573 original size:30 final size:30
Alignment explanation
Indices: 303516--303590 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
303506 TTAAAGAACC
*
303516 AAAATAGCAAAAACAAAAATTTAAAGGACT
1 AAAATAGCAAAAACAAAAATTCAAAGGACT
* * * * *
303546 AAAATAGCAAACATAGAAATTCGAAGGATT
1 AAAATAGCAAAAACAAAAATTCAAAGGACT
303576 AAAATAG-AAAGAACA
1 AAAATAGCAAA-AACA
303591 GAATTTTGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 3 0.08
30 33 0.92
ACGTcount: A:0.61, C:0.09, G:0.13, T:0.16
Consensus pattern (30 bp):
AAAATAGCAAAAACAAAAATTCAAAGGACT
Found at i:303860 original size:29 final size:28
Alignment explanation
Indices: 303810--303876 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
303800 CTCATGACCA
303810 AAGTAAAACATTGACAATAATAACAGAAT
1 AAGTAAAACATTGACAATAAT-ACAGAAT
303839 AAGTAAGAACA-TGACTAA-AATACAG-AT
1 AAGTAA-AACATTGAC-AATAATACAGAAT
*
303866 AA-TGAAACATT
1 AAGTAAAACATT
303877 AGTGCTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 4 0.12
28 4 0.12
29 13 0.38
30 6 0.18
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (28 bp):
AAGTAAAACATTGACAATAATACAGAAT
Found at i:305033 original size:3 final size:3
Alignment explanation
Indices: 305025--305058 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
305015 ATAATTTTGT
305025 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
305059 CAACAACAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:305686 original size:21 final size:20
Alignment explanation
Indices: 305658--305700 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
305648 GTGTTTCAAG
*
305658 AAAATTGTCTCAAGGGAGAC
1 AAAATTGTCTCAAGGGAAAC
*
305678 AAAACTTGTTTCAAGGGAAAC
1 AAAA-TTGTCTCAAGGGAAAC
305699 AA
1 AA
305701 TCTCAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAATTGTCTCAAGGGAAAC
Found at i:305976 original size:66 final size:66
Alignment explanation
Indices: 305564--305975 Score: 508
Period size: 66 Copynumber: 6.3 Consensus size: 66
305554 TATTTAAAGA
* * * * * * * *
305564 GAAATAGACTCAAAGA-TGATGCTTCAAGAGAAATTGTCTCAAGAGAGGCAAAATTCGTTTCAAG
1 GAAACAGACTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
*
305628 T
66 G
* * * * *
305629 GAAACA-ATCTCAAAAATGGGTGTTTCAAGA-AAATTGTCTCAAGGGAGACAAAACTTGTTTCAA
1 GAAACAGA-CTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
305692 GG
65 GG
* *
305694 GAAACA-ATCTCAAAGGTTGGTGCTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
1 GAAACAGA-CTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
305758 GG
65 GG
* * * * *
305760 GAAACAAACTCAAAGGTTGGTGTTTTATAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
1 GAAACAGACTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
305825 G
66 G
* * * * *
305826 GAAACAAACTCAAAGGTTGGTGTTTTATGAGAAACTGTCACAAGGGAGACAAAATTTGTTCCAAG
1 GAAACAGACTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
305891 G
66 G
* * *
305892 GAAACAGACTCAAAGATTAGTGTTTCATGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAA
1 GAAACAGACTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
305957 G
66 G
*
305958 TAAACAGACTCAAAGATT
1 GAAACAGACTCAAAGATT
305976 ATAAATTTTG
Statistics
Matches: 309, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
64 1 0.00
65 67 0.22
66 240 0.78
67 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (66 bp):
GAAACAGACTCAAAGATTGGTGTTTCATGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
G
Found at i:306100 original size:37 final size:37
Alignment explanation
Indices: 306024--306100 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
306014 GTTTAAAAGA
* * * *
306024 AAATATGTCTCAAGCGAGACACAATTTGTTTTGATAG
1 AAATATGTCTCAAACGAAACAAAATTTGTTTTCATAG
306061 AAAT-TGTCTCAAACGAAACAAAATTTTGTTTTTCA-AG
1 AAATATGTCTCAAACGAAACAAAA-TTTG-TTTTCATAG
306098 AAA
1 AAA
306101 AGCTATCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 16 0.47
37 13 0.38
38 5 0.15
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
AAATATGTCTCAAACGAAACAAAATTTGTTTTCATAG
Found at i:307360 original size:20 final size:22
Alignment explanation
Indices: 307337--307388 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
307327 TCTTTCTTTG
307337 TTTTTTCT-TTTGTTTTTT-TA
1 TTTTTTCTCTTTGTTTTTTCTA
* *
307357 TTTTTGCTCTTTGTTTTTTCTT
1 TTTTTTCTCTTTGTTTTTTCTA
307379 TTTTTTCTCT
1 TTTTTTCTCT
307389 GCTTTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 10 0.37
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTTTTCTCTTTGTTTTTTCTA
Found at i:307382 original size:22 final size:20
Alignment explanation
Indices: 307337--307388 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
307327 TCTTTCTTTG
307337 TTTTTTCT-TTTGTTTTTTT
1 TTTTTTCTCTTTGTTTTTTT
*
307356 ATTTTTGCTCTTTGTTTTTTCTT
1 -TTTTTTCTCTTTG-TTTTT-TT
307379 TTTTTTCTCT
1 TTTTTTCTCT
307389 GCTTTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 14 0.52
23 2 0.07
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTTCTCTTTGTTTTTTT
Found at i:311120 original size:30 final size:28
Alignment explanation
Indices: 311058--311139 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 28
311048 ATCATATTCG
* *
311058 ATTTAAAGAACCAAAATAGCAAAAACAAAA
1 ATTTAAAGGACTAAAATAG--AAAACAAAA
311088 ATTTAAAGGACTAAAATAGAAAACATAGAA
1 ATTTAAAGGACTAAAATAGAAAACA-A-AA
* *
311118 ATTCAAAGGATTAAAATAGAAA
1 ATTTAAAGGACTAAAATAGAAA
311140 TAACAGAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 6 0.13
29 1 0.02
30 39 0.85
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (28 bp):
ATTTAAAGGACTAAAATAGAAAACAAAA
Found at i:312580 original size:3 final size:3
Alignment explanation
Indices: 312572--312605 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
312562 ATAATTTTGT
*
312572 TAA TAA TAA -AA TAA TAA TAA TAC TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
312606 TTTTTCGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:313545 original size:30 final size:31
Alignment explanation
Indices: 313469--313562 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 31
313459 AATTCCAATT
* * * *
313469 CAAACGAGATAAAGTATAATTAACCATGAAAA
1 CAAAGGAG-TAAAATATAATTAACTATAAAAA
313501 CAAAGGAAGTAAAATATAATTAACTATAAAAA
1 CAAAGG-AGTAAAATATAATTAACTATAAAAA
* *
313533 CAAAGG-GTAAAATATAATTAAATAGAAAAA
1 CAAAGGAGTAAAATATAATTAACTATAAAAA
313563 ATAAGAGGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 22 0.40
32 31 0.56
33 2 0.04
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (31 bp):
CAAAGGAGTAAAATATAATTAACTATAAAAA
Found at i:314029 original size:29 final size:29
Alignment explanation
Indices: 313987--314044 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
313977 GTCAGTTTGT
313987 GTCGATACTTTATAAAAATGTATCGATCC
1 GTCGATACTTTATAAAAATGTATCGATCC
314016 GTCGATACTTTATAAAAATGTATCGATCC
1 GTCGATACTTTATAAAAATGTATCGATCC
314045 ATAACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (29 bp):
GTCGATACTTTATAAAAATGTATCGATCC
Found at i:314138 original size:112 final size:112
Alignment explanation
Indices: 314016--314588 Score: 959
Period size: 112 Copynumber: 5.1 Consensus size: 112
314006 GTATCGATCC
* *
314016 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGA
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
* *
314081 TCTATAAATGACAAAATAGATAAAGCGCTACCGGATATATTGAAAGT
66 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
* *
314128 GTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAAAATGACAAAACCGA
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
*
314193 TCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGT
66 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
*
314240 GTCGATACTTTATAAGAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
314305 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
66 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
* * *
314352 GTCGATACTTTATAAAAATGTATCGATCCATAACAATAGAACATGTAAAAAAAATGATAAAACCG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCG
* *
314417 GTCTATAAATGATAAAACAGGTAAAGCGCTACCAGATATATTGAAAGT
65 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
* * *
314465 GTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACATGT-AAAAAATGATAAAACCGG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
* * *
314529 TCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATGTTGATAGT
66 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
314576 GTCGATACTTTAT
1 GTCGATACTTTAT
314589 TATAAGTATC
Statistics
Matches: 438, Mismatches: 22, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
111 73 0.17
112 258 0.59
113 107 0.24
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGT
Found at i:314773 original size:182 final size:182
Alignment explanation
Indices: 314460--314914 Score: 705
Period size: 182 Copynumber: 2.5 Consensus size: 182
314450 AGATATATTG
* * *
314460 AAAGTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACATGTAAAAA-ATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** ** * * *
314524 ACCGGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
* * *
314589 TATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
*
314641 AAATTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
314706 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCATATATGTTGAAAGTGTCGATAGTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
*
314771 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
131 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
* *
314823 AAAGTGTCGATACTTTATAAAAATGTTTCGATCCATAATAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** *
314888 ATGGGTCTCGAATTGACAAAACCGGTA
66 ACCGGTCTCGAAATGACAAAACCGGTA
314915 GTAAAAATGT
Statistics
Matches: 250, Mismatches: 23, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
181 53 0.21
182 197 0.79
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Found at i:315392 original size:23 final size:23
Alignment explanation
Indices: 315346--315393 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
315336 AAATAGGTTA
* *
315346 ATATAAGCGCTACTTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
315369 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
315392 AT
1 AT
315394 TATACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:315890 original size:13 final size:13
Alignment explanation
Indices: 315856--315922 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 13
315846 TCGTTTTTAT
315856 TTTATTATATATAA
1 TTTATTATATAT-A
*
315870 TATAATTATATATA
1 T-TTATTATATATA
315884 TTTATTAT-TAT-
1 TTTATTATATATA
*
315895 TATATTATAT-TA
1 TTTATTATATATA
* *
315907 -TTATTACAAATA
1 TTTATTATATATA
315919 TTTA
1 TTTA
315923 CAAATCAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
11 14 0.33
12 6 0.14
13 9 0.21
14 3 0.07
15 10 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATTATATATA
Found at i:315896 original size:19 final size:19
Alignment explanation
Indices: 315852--315912 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
315842 TCGTTCGTTT
*
315852 TTATT-TTAT-TATATATA
1 TTATTATTATATATATTTA
* *
315869 ATATAATTATATATATTTA
1 TTATTATTATATATATTTA
315888 TTATTATTATAT-TATATTA
1 TTATTATTATATATAT-TTA
315907 TTATTA
1 TTATTA
315913 CAAATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.08
18 7 0.19
19 26 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATTATATATATTTA
Found at i:315902 original size:5 final size:5
Alignment explanation
Indices: 315853--315912 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
315843 CGTTCGTTTT
* *
315853 TATTT TATTA TA-TA TAATA TAATTA TA-TA TATT- TATTA TTATTA TATTA
1 TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA -TATTA TATTA
315902 TATTA TTATTA
1 TATTA -TATTA
315913 CAAATATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
4 12 0.26
5 21 0.45
6 14 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:318157 original size:33 final size:32
Alignment explanation
Indices: 318109--318179 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
318099 AATTTTAATT
*
318109 AATATAAACACTAATTTATAT-T-TTAATAGTAAA
1 AATAAAAACACTAATTTA-ATGTATTAAT--TAAA
*
318142 AATAAAAACTCTAATTTAATGTATTAATTAAA
1 AATAAAAACACTAATTTAATGTATTAATTAAA
318174 AATAAA
1 AATAAA
318180 GAAGATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 12 0.35
33 17 0.50
34 5 0.15
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (32 bp):
AATAAAAACACTAATTTAATGTATTAATTAAA
Found at i:318972 original size:73 final size:73
Alignment explanation
Indices: 318853--319001 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
318843 GTTGGGTTTT
318853 GATCCTTAGATAATAAATAAGCTTAAGGAAAGCTTAATTTGTCTTAAAATAAAAAGATGACGAAG
1 GATCCTTAGATAATAAATAAGCTTAAGGAAAGCTTAATTTGTCTTAAAATAAAAAGATGACGAAG
318918 TTATGAAA
66 TTATGAAA
318926 GATCCTTAGATAATAAATAAGCTTAAGGAAAGCTTAATTTGTCTTAAAATAAAAAGATGACGAAG
1 GATCCTTAGATAATAAATAAGCTTAAGGAAAGCTTAATTTGTCTTAAAATAAAAAGATGACGAAG
318991 TTATGAAA
66 TTATGAAA
318999 GAT
1 GAT
319002 TAAAGAAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (73 bp):
GATCCTTAGATAATAAATAAGCTTAAGGAAAGCTTAATTTGTCTTAAAATAAAAAGATGACGAAG
TTATGAAA
Found at i:320141 original size:23 final size:23
Alignment explanation
Indices: 320108--320151 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
320098 GAGTCGAGGG
320108 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
320131 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
320152 TATATGTAAT
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:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:320305 original size:98 final size:98
Alignment explanation
Indices: 320136--320349 Score: 401
Period size: 98 Copynumber: 2.2 Consensus size: 98
320126 ACAATTCTAC
320136 GTGGTCCTTCGGGACATATATGTAATTTAGTGGAACATGCATGTGGTACTTCGGTACACTTATTT
1 GTGGTCCTTCGGGACATATATGTAATTTAGTGGAACATGCATGTGGTACTTCGGTACACTTATTT
*
320201 GGTCCATTGTATTATGTATATAATTCTTAAGTA
66 GGTCCATTGTATTATGTATATAATTCTTAAGGA
*
320234 GTGGTCCTTCGGGACATATATGTAATTTCGTGGAACATGCATGTGGTACTTCGGTACACTTATTT
1 GTGGTCCTTCGGGACATATATGTAATTTAGTGGAACATGCATGTGGTACTTCGGTACACTTATTT
*
320299 GGTCCATTGTATTATGTATATGATTCTTAAGGA
66 GGTCCATTGTATTATGTATATAATTCTTAAGGA
320332 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
320350 GTGGTCATTC
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 113 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (98 bp):
GTGGTCCTTCGGGACATATATGTAATTTAGTGGAACATGCATGTGGTACTTCGGTACACTTATTT
GGTCCATTGTATTATGTATATAATTCTTAAGGA
Found at i:320354 original size:18 final size:18
Alignment explanation
Indices: 320331--320405 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
320321 ATTCTTAAGG
320331 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
320349 AGTGGTCATTCAGGATATAT
1 AGTGGTCCTTC-GG-GACAT
** *
320369 ACAGTGGTTTTTAGGGACAT
1 --AGTGGTCCTTCGGGACAT
*
320389 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
320406 AATATACAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
18 24 0.57
19 2 0.05
20 6 0.14
21 2 0.05
22 8 0.19
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:322139 original size:21 final size:21
Alignment explanation
Indices: 322069--322154 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 21
322059 TATATTATCG
322069 TTATATGTATTAT-TCATTAAGTA
1 TTATAT-TATTATCT-ATTAA-TA
* *
322092 TTATTTTATTATACTTATTAGTCA
1 TTATATTATTAT-C-TATTAAT-A
322116 TTATATTATTATCTATTAATA
1 TTATATTATTATCTATTAATA
*
322137 TTATGTTATTATCTATTA
1 TTATATTATTATCTATTA
322155 TTTATTACGT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
21 18 0.33
22 12 0.22
23 7 0.13
24 16 0.30
25 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATATTATTATCTATTAATA
Found at i:322199 original size:14 final size:14
Alignment explanation
Indices: 322098--322200 Score: 50
Period size: 16 Copynumber: 6.9 Consensus size: 14
322088 AGTATTATTT
322098 TATTATACTTATTAG
1 TATTATA-TTATTAG
*
322113 TCATTATATTATTATC
1 T-ATTATATTATTA-G
*
322129 TATTAATATTATGTTAT
1 TATT-ATATTA--TTAG
322146 TATCTATTATTTATTACG
1 TAT-TA-TA-TTATTA-G
*
322164 TATTAT-TT-TTAC
1 TATTATATTATTAG
* *
322176 CACT-TATTATTAG
1 TATTATATTATTAG
322189 TATTATATTATT
1 TATTATATTATT
322201 TATATAAGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 25
0.66 0.09 0.25
Matches are distributed among these distances:
11 1 0.01
12 4 0.06
13 8 0.12
14 9 0.13
15 10 0.15
16 14 0.21
17 9 0.13
18 9 0.13
19 3 0.04
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (14 bp):
TATTATATTATTAG
Found at i:322243 original size:3 final size:3
Alignment explanation
Indices: 321963--322200 Score: 59
Period size: 3 Copynumber: 76.7 Consensus size: 3
321953 CATCTTTATC
*
321963 TTA TTA TT- TTA TTTA TTA TTTA TTA TTA ATA TTA TT- TTA TATA GTTAA
1 TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA -TT-A
* * * *
322011 TCTA ATA -TA TTA TTA -TA TTTA CTA TTT TGTA GTTA CTA TATA TTA
1 T-TA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA -TTA TTA T-TA TTA
* ** *
322056 GT- TTA -TA TTA TCG TTA -TA TGTA TTA TTCA TTAA GTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT-A TT-A TTA TTA TTA TTA
* * *
322100 TTA -TA CTTA TTA GTCA TTA -TA TTA TTA TCTA TTA ATA TTA -TG TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * ** *
322145 TTA TCTA TTA TTTA TTA CGTA TTA TTT TTA CCA CTTA TTA TTA GTA TTA
1 TTA T-TA TTA -TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
322194 -TA TTA TT
1 TTA TTA TT
322201 TATATAAGTA
Statistics
Matches: 170, Mismatches: 34, Indels: 62
0.64 0.13 0.23
Matches are distributed among these distances:
2 22 0.13
3 101 0.59
4 43 0.25
5 4 0.02
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:324277 original size:3 final size:3
Alignment explanation
Indices: 324269--324308 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
324259 TCATCTCGTT
**
324269 TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
324309 ATATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:324313 original size:2 final size:2
Alignment explanation
Indices: 324306--324334 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
324296 TTATTATTAT
324306 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 T
324335 TTAATAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:325768 original size:23 final size:23
Alignment explanation
Indices: 325731--325801 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
325721 ATTTATTTGC
*
325731 AATATTATTTCATTATTACTTTT
1 AATATTATTTTATTATTACTTTT
* *
325754 GATA-TATTTTAATTATTACTTTC
1 AATATTATTTT-ATTATTACTTTT
*
325777 AATATTATTTTATTATTATTTTT
1 AATATTATTTTATTATTACTTTT
325800 AA
1 AA
325802 CTTAGTCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 5 0.12
23 29 0.73
24 6 0.15
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (23 bp):
AATATTATTTTATTATTACTTTT
Found at i:325795 original size:11 final size:11
Alignment explanation
Indices: 325733--325798 Score: 55
Period size: 11 Copynumber: 5.8 Consensus size: 11
325723 TTATTTGCAA
*
325733 TATTATTTCAT
1 TATTATTTTAT
325744 TATTACTTTTGA-
1 TATTA-TTTT-AT
325756 TA-TATTTTAAT
1 TATTATTTT-AT
* *
325767 TATTACTTTCAA
1 TATTA-TTTTAT
325779 TATTATTTTAT
1 TATTATTTTAT
325790 TATTATTTT
1 TATTATTTT
325799 TAACTTAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.11
11 22 0.50
12 13 0.30
13 4 0.09
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:328720 original size:46 final size:46
Alignment explanation
Indices: 328654--328741 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
328644 TTATTTCATT
* * *
328654 TTTTTCTAAACAAAGCATGGAACTAGAAATCATGTGGTTAGGTTAA
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGTTAA
*
328700 TTTTTCCAAACAAAGCATGGAATTAGAAAGCATGAGGTTAGG
1 TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGG
328742 ATTTATACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (46 bp):
TTTTTCCAAACAAAGCATGGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:330437 original size:27 final size:26
Alignment explanation
Indices: 330406--330471 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
330396 CATTCACATA
*
330406 TTTACATTTGCATTTGCATTCTGCATT
1 TTTACATTTGCATTTACATT-TGCATT
* * *
330433 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTACATTTGCATT
*
330459 TTTGCATTTGCAT
1 TTTACATTTGCAT
330472 CTTTGCATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTGCATT
Found at i:332796 original size:10 final size:10
Alignment explanation
Indices: 332795--332841 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
332785 AAAAGAAGAA
332795 AAGAAAAAAG
1 AAGAAAAAAG
332805 AAGAAAAAA-
1 AAGAAAAAAG
332814 AGAGAAAAAAAG
1 A-AG-AAAAAAG
*
332826 AAAAAGAAAAG
1 AAGAA-AAAAG
332837 AAGAA
1 AAGAA
332842 TTTTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 1 0.03
10 13 0.42
11 16 0.52
12 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:332798 original size:8 final size:8
Alignment explanation
Indices: 332781--332841 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
332771 CTCATTCATT
332781 AGAA-AAA
1 AGAAGAAA
332788 AGAAGAAA
1 AGAAGAAA
332796 AGAA-AAA
1 AGAAGAAA
332803 AGAAGAAA
1 AGAAGAAA
*
332811 AAAAGAGAA
1 AGAAGA-AA
332820 A-AA-AAGA
1 AGAAGAA-A
*
332827 AAAAGAAA
1 AGAAGAAA
332835 AGAAGAA
1 AGAAGAA
332842 TTTTTTTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
6 1 0.02
7 14 0.30
8 26 0.57
9 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AGAAGAAA
Found at i:332801 original size:15 final size:15
Alignment explanation
Indices: 332781--332830 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
332771 CTCATTCATT
332781 AGAAAAAAGAAGAAA
1 AGAAAAAAGAAGAAA
332796 AGAAAAAAGAAG-AA
1 AGAAAAAAGAAGAAA
* *
332810 A-AAAAGAGAAAAAA
1 AGAAAAAAGAAGAAA
332824 AGAAAAA
1 AGAAAAA
332831 GAAAAGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 16 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAGAAA
Found at i:332814 original size:18 final size:18
Alignment explanation
Indices: 332783--332830 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
332773 CATTCATTAG
*
332783 AAAAAAGAAGAAAAGA-A
1 AAAAAAGAAAAAAAGAGA
332800 AAAAGAAGAAAAAAAGAGA
1 AAAA-AAGAAAAAAAGAGA
332819 AAAAAAGAAAAA
1 AAAAAAGAAAAA
332831 GAAAAGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAGAGA
Found at i:332824 original size:21 final size:21
Alignment explanation
Indices: 332784--332837 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
332774 ATTCATTAGA
*
332784 AAAAAGAAGAAAAG-AAAAAAG
1 AAAAAGAA-AAGAGAAAAAAAG
332805 AAGAAA-AAAAGAGAAAAAAAG
1 AA-AAAGAAAAGAGAAAAAAAG
332826 AAAAAGAAAAGA
1 AAAAAGAAAAGA
332838 AGAATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 7 0.24
21 19 0.66
22 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGAGAAAAAAAG
Found at i:336239 original size:75 final size:74
Alignment explanation
Indices: 336155--336684 Score: 279
Period size: 74 Copynumber: 7.1 Consensus size: 74
336145 AACAAGAAGA
* * *
336155 AAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAGTTGGAATATTAATGCATTTTGAACGT
1 AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAA-TTAGAATATTAATGCATTTTGAACAT
*
336220 TTGTATCAGT
65 TTGTATCAGC
* * *
336230 AAATACTGGGGCAGGCTGAAAGCCCATTTCAATCAAAATCAAGAATATTAACT-CATTTTGAACA
1 AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAAT-TAGAATATTAA-TGCATTTTGAACA
336294 TTTG---CAGC
64 TTTGTATCAGC
** * *** ***
336302 AAATGTTGGGGCATGCTGAAAGCCC-TTTTAATCAGAA-TAGAATATTGGGGCATCTCAAAAGCC
1 AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAATATTAATGCAT-TTTGAA--C
*
336365 TATTT-CA-CA-C
63 -ATTTGTATCAGC
* * * * ***
336375 AAAAATGATCCATGTGGGGCATTCTGAAGGCCCA---C-GTCAGTA-T-GAATATTTGGGCATTT
1 --AAAT-A--C---TGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAATATTAATGCATTT
*** ** *
336434 TGAAAACTCACATCAATAAGAAGA
58 TG---A---ACATTTGT-ATCAGC
** * *
336458 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAGTTGGAATATTAATGCATTTTGAACGT
1 AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAA-TTAGAATATTAATGCATTTTGAACAT
336523 TTGTATCAGC
65 TTGTATCAGC
* *
336533 AAATACTGGGGCA-GACTGAAAG-CCATTTCAATCAGAATCAAGAATATTGACT-CATTTTGAAC
1 AAATACTGGGGCATG-CTGAAAGCCCATTTCAATCAGAAT-TAGAATATT-AATGCATTTTGAAC
*
336595 ATTTGTATCAAC
63 ATTTGTATCAGC
* * * * * ** *
336607 AAATGCTAGGGCATGCTGAAAGCCC-TTTTAATCAGAATCAGGAATGTTGGTGCATTTTGAACGT
1 AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTA-GAATATTAATGCATTTTGAACAT
336671 TTGTATCAGC
65 TTGTATCAGC
336681 AAAT
1 AAAT
336685 GTTAGGGCAT
Statistics
Matches: 346, Mismatches: 67, Indels: 85
0.69 0.13 0.17
Matches are distributed among these distances:
69 11 0.03
70 3 0.01
71 10 0.03
72 26 0.08
73 8 0.02
74 106 0.31
75 106 0.31
76 6 0.02
77 13 0.04
78 7 0.02
79 9 0.03
80 1 0.00
81 23 0.07
82 17 0.05
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (74 bp):
AAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAATATTAATGCATTTTGAACATT
TGTATCAGC
Found at i:336685 original size:74 final size:74
Alignment explanation
Indices: 336466--336700 Score: 296
Period size: 74 Copynumber: 3.2 Consensus size: 74
336456 GAAAATGTTG
* *
336466 GGGCATGCTGAAAGCCCATTTCAATCAGAAGT-TGGAATATTAATGCATTTTGAACGTTTGTATC
1 GGGCATGCTGAAAGCCC-TTTCAATCAGAA-TCAGGAATATTGATGCATTTTGAACGTTTGTATC
* *
336530 AGCAAATACTG
64 AGCAAATGCTA
* * *
336541 GGGCA-GACTGAAAGCCATTTCAATCAGAATCAAGAATATTGACT-CATTTTGAACATTTGTATC
1 GGGCATG-CTGAAAGCCCTTTCAATCAGAATCAGGAATATTGA-TGCATTTTGAACGTTTGTATC
*
336604 AACAAATGCTA
64 AGCAAATGCTA
* * *
336615 GGGCATGCTGAAAGCCCTTTTAATCAGAATCAGGAATGTTGGTGCATTTTGAACGTTTGTATCAG
1 GGGCATGCTGAAAGCCCTTTCAATCAGAATCAGGAATATTGATGCATTTTGAACGTTTGTATCAG
*
336680 CAAATGTTA
66 CAAATGCTA
*
336689 GGGCATGTTGAA
1 GGGCATGCTGAA
336701 GACCCATATC
Statistics
Matches: 138, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
73 2 0.01
74 120 0.87
75 16 0.12
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (74 bp):
GGGCATGCTGAAAGCCCTTTCAATCAGAATCAGGAATATTGATGCATTTTGAACGTTTGTATCAG
CAAATGCTA
Found at i:338020 original size:22 final size:22
Alignment explanation
Indices: 337986--338065 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
337976 ACATCTACAT
337986 TCTTCAAAAGATGATAGATTCTC
1 TCTTC-AAAGATGATAGATTCTC
338009 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
338031 TTTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
338053 TTTTCAAAGATGA
1 TCTTCAAAGATGA
338066 AAGCTTTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 51 0.91
23 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:338882 original size:45 final size:45
Alignment explanation
Indices: 338784--338886 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
338774 GGAGCTTTTT
* ** * * *
338784 GATATTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCAT
1 GATATTTTCAAAACCTTTGGGTCATCCATAAGACCTTCAGTACAG
338829 GATATTTTCAAAACCTTTGGGTCATCCATAAGACCTGT-AGTACAG
1 GATATTTTCAAAACCTTTGGGTCATCCATAAGACCT-TCAGTACAG
*
338874 GATGTTTTCAAAA
1 GATATTTTCAAAA
338887 AGCCTTCGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (45 bp):
GATATTTTCAAAACCTTTGGGTCATCCATAAGACCTTCAGTACAG
Found at i:339060 original size:89 final size:89
Alignment explanation
Indices: 338904--339570 Score: 1050
Period size: 89 Copynumber: 7.5 Consensus size: 89
338894 GGGAGCTTTT
* * * *
338904 TGATATTTCAAAATCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAACCTTTGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
338968 GTCATCTGTAAGCCCTTCAGTGCA
66 GTCATCTGTAAGCCCTTCAGTGCA
* * * *
338992 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATG-TTTAAAAATCTTCG
1 TGATG-TTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
339056 GGTCATCTGTAAGCCGTTCAGTGCA
65 GGTCATCTGTAAGCCCTTCAGTGCA
* * * *
339081 TGATGTTTTCAAAACCTTTGGGCCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
1 TGATG-TTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
339146 GGTCATCTTTAAGCCCTTCAGTGCA
65 GGTCATCTGTAAGCCCTTCAGTGCA
339171 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
*
339236 GTCATCTGTAAGCCCTTCAGCGCA
66 GTCATCTGTAAGCCCTTCAGTGCA
* *
339260 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGATTTCAAAACCTTCGA
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* *
339325 GTCATCTGTATGCACTTCAGTGCA
66 GTCATCTGTAAGCCCTTCAGTGCA
* *
339349 TGATGTTTAAAAATCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* *
339414 GTTATCTGTAAGCCCTTCAGTACA
66 GTCATCTGTAAGCCCTTCAGTGCA
339438 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* *
339503 GCCATCTGTAAGCCCTTCAGAGCA
66 GTCATCTGTAAGCCCTTCAGTGCA
* * *
339527 TGATGTTTAAAAACCTTCGGGTCATTTGTAAGACCTACAGTGCA
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
339571 AAATGATAGG
Statistics
Matches: 534, Mismatches: 43, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
88 4 0.01
89 491 0.92
90 39 0.07
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (89 bp):
TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GTCATCTGTAAGCCCTTCAGTGCA
Found at i:339152 original size:134 final size:134
Alignment explanation
Indices: 338904--339570 Score: 1045
Period size: 134 Copynumber: 5.0 Consensus size: 134
338894 GGGAGCTTTT
* * * *
338904 TGATATTTCAAAATCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCAAAACCTTTGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
*
338968 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
339033 TGCA
131 TGCA
* * *
339037 TGATGTTTAAAAATCTTCGGGTCATCTGTAAGCCGTTCAGTGCATGATGTTTTCAAAACCTTTGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* * *
339102 GCCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTTTAAGCCCTTCAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
339167 TGCA
131 TGCA
339171 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* *
339236 GTCATCTGTAAGCCCTTCAGCGCATGATG-TTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
339300 TGCA
131 TGCA
* * * * * *
339304 TGATGATTTCAAAACCTTCGAGTCATCTGTATGCACTTCAGTGCATGATG-TTTAAAAATCTTCG
1 TGATG-TTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
339368 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTTATCTGTAAGCCCTTCA
65 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
*
339433 GTACA
130 GTGCA
339438 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
1 TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* * * * * *
339503 GCCATCTGTAAGCCCTTCAGAGCATGATG-TTTAAAAACCTTCGGGTCATTTGTAAGACCTACAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
339567 TGCA
131 TGCA
339571 AAATGATAGG
Statistics
Matches: 489, Mismatches: 41, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
133 200 0.41
134 289 0.59
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (134 bp):
TGATGTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
TGCA
Found at i:339736 original size:3 final size:3
Alignment explanation
Indices: 339728--339787 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
339718 TCATTTCGTT
** *
339728 TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
339772 TATA TATA TTA TTA TT
1 T-TA T-TA TTA TTA TT
339788 TAATAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 33 0.69
4 11 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:341663 original size:2 final size:2
Alignment explanation
Indices: 341651--341695 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
341641 ATATCTTATT
*
341651 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
341691 TA TA T
1 TA TA T
341696 TTTCTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:355198 original size:17 final size:16
Alignment explanation
Indices: 355167--355200 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
355157 AAACAAAGGA
*
355167 AAAATATTAATTTAAT
1 AAAATAATAATTTAAT
355183 AAAATAATAATATTAAT
1 AAAATAATAAT-TTAAT
355200 A
1 A
355201 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATAATAATTTAAT
Found at i:355205 original size:2 final size:2
Alignment explanation
Indices: 355198--355265 Score: 79
Period size: 2 Copynumber: 34.5 Consensus size: 2
355188 AATAATATTA
*
355198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT GT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
355239 A- AT AA AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT A
355266 CCATAAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
1 3 0.05
2 50 0.88
3 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:360463 original size:22 final size:22
Alignment explanation
Indices: 360399--360474 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
360389 CACACATAAT
360399 GAAAGAAAATTAAATTCAAAAG
1 GAAAGAAAATTAAATTCAAAAG
* * *
360421 GATATGAAACA--AAAGTACAAAAT
1 GA-AAGAAA-ATTAAA-TTCAAAAG
360444 GAAAGAAAATTAAATTCAAAAG
1 GAAAGAAAATTAAATTCAAAAG
360466 GAAATGAAA
1 GAAA-GAAA
360475 TGAAGTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 1 0.02
22 20 0.48
23 20 0.48
24 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.14, T:0.17
Consensus pattern (22 bp):
GAAAGAAAATTAAATTCAAAAG
Found at i:369501 original size:16 final size:17
Alignment explanation
Indices: 369480--369512 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
369470 AAACAAAGGA
*
369480 AAAATATTAAT-TTAAT
1 AAAATAATAATATTAAT
369496 AAAATAATAATATTAAT
1 AAAATAATAATATTAAT
369513 TCGTTGCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATAATAATATTAAT
Found at i:370437 original size:15 final size:15
Alignment explanation
Indices: 370413--370444 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
370403 AATCTGAGAA
*
370413 CAGTGGAATTGGAGG
1 CAGTGCAATTGGAGG
370428 CAGTGCAATTGGAGG
1 CAGTGCAATTGGAGG
370443 CA
1 CA
370445 ATGAGATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.41, T:0.19
Consensus pattern (15 bp):
CAGTGCAATTGGAGG
Found at i:372948 original size:14 final size:14
Alignment explanation
Indices: 372929--372961 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
372919 CTAAAAACCT
372929 CAAGAGCATATTAC
1 CAAGAGCATATTAC
372943 CAAGAGCATATTAC
1 CAAGAGCATATTAC
372957 CAAGA
1 CAAGA
372962 AGTTTATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.18
Consensus pattern (14 bp):
CAAGAGCATATTAC
Found at i:375154 original size:2 final size:2
Alignment explanation
Indices: 375139--375179 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
375129 ATACTTAACT
*
375139 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375179 T
1 T
375180 TAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:375219 original size:27 final size:29
Alignment explanation
Indices: 375179--375287 Score: 84
Period size: 31 Copynumber: 3.7 Consensus size: 29
375169 TATATTTATA
*
375179 TTAATTTATTAAATATATTTTA-T-TAAAC
1 TTAATTTA-AAAATATATTTTATTCTAAAC
**
375207 TTAATTT-AAAA-ATATTTTATTCTAATT
1 TTAATTTAAAAATATATTTTATTCTAAAC
*
375234 TTAATTTAAAAATATATATTTTATTCCT-ATC
1 TTAATTT-AAAA-ATATATTTTATT-CTAAAC
*
375265 TAAATTTAAAAAAATATATTTTA
1 TTAATTT--AAAAATATATTTTA
375288 CTATTATTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
25 8 0.12
26 4 0.06
27 10 0.15
28 7 0.10
29 3 0.04
30 1 0.01
31 28 0.41
32 7 0.10
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAATTTAAAAATATATTTTATTCTAAAC
Found at i:375256 original size:31 final size:31
Alignment explanation
Indices: 375214--375287 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
375204 AACTTAATTT
* *
375214 AAAA-ATATTTTATT-CTAATTTTAATTTAAA
1 AAAATATATTTTATTCCT-ATCTAAATTTAAA
*
375244 AATATATATTTTATTCCTATCTAAATTTAAA
1 AAAATATATTTTATTCCTATCTAAATTTAAA
375275 AAAATATATTTTA
1 AAAATATATTTTA
375288 CTATTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 33 0.87
32 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAATATATTTTATTCCTATCTAAATTTAAA
Found at i:375372 original size:18 final size:21
Alignment explanation
Indices: 375323--375384 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 21
375313 TTATTTTATC
375323 TTAATTTACTAAATATATTATAATA
1 TTAATTT--TAAAT-TATTA-AATA
375348 TTAA-TTTAAATTATTAAAT-
1 TTAATTTTAAATTATTAAATA
*
375367 TT-ATTTTAATTTATTAAA
1 TTAATTTTAAATTATTAAA
375385 AGTATAACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 15 0.43
20 3 0.09
21 5 0.14
22 5 0.14
24 2 0.06
25 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATTTTAAATTATTAAATA
Found at i:375380 original size:19 final size:20
Alignment explanation
Indices: 375332--375384 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
375322 CTTAATTTAC
375332 TAAATATATTATAATATTAATT
1 TAAAT-TATTA-AATATTAATT
*
375354 TAAATTATTAAAT-TTATTT
1 TAAATTATTAAATATTAATT
*
375373 TAATTTATTAAA
1 TAAATTATTAAA
375385 AGTATAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 3 0.10
21 5 0.17
22 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTATTAAATATTAATT
Found at i:375758 original size:9 final size:9
Alignment explanation
Indices: 375744--375772 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
375734 TCAAATAAAC
375744 TATTTAATT
1 TATTTAATT
375753 TATTTAATT
1 TATTTAATT
375762 TATTTAATT
1 TATTTAATT
375771 TA
1 TA
375773 ATGACTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:375851 original size:2 final size:2
Alignment explanation
Indices: 375844--375875 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
375834 TGTATGTATG
*
375844 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375876 ATCTATAATC
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:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:376828 original size:29 final size:29
Alignment explanation
Indices: 376766--376828 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
376756 ATTGTATACC
*
376766 TGCGAGGAAGAAGGTCGCCATGTACTCCG
1 TGCGAGGAAGAAGGTCGCCATGCACTCCG
* * *
376795 GGCGAGGAAGGAGGTTGCCATGGCA-TCCG
1 TGCGAGGAAGAAGGTCGCCAT-GCACTCCG
376824 TGCGA
1 TGCGA
376829 CATGTGGTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.16
Consensus pattern (29 bp):
TGCGAGGAAGAAGGTCGCCATGCACTCCG
Found at i:377370 original size:21 final size:20
Alignment explanation
Indices: 377285--377370 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
377275 TTATATGAAA
377285 TTATTAGTTTGTTAGTTTATG
1 TTATTAGTTTGTTAGTTTA-G
* ** *
377306 GT-TTAGGGT-TTAATTTAG
1 TTATTAGTTTGTTAGTTTAG
*
377324 TTAATTAGTTTGTTAGTATAG
1 TT-ATTAGTTTGTTAGTTTAG
377345 ATTATTAGTTTGTTAGTTTAAG
1 -TTATTAGTTTGTTAGTTT-AG
377367 TTAT
1 TTAT
377371 ATTATATTAG
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
18 2 0.04
19 7 0.14
20 10 0.20
21 27 0.54
22 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (20 bp):
TTATTAGTTTGTTAGTTTAG
Found at i:377380 original size:28 final size:28
Alignment explanation
Indices: 377347--377437 Score: 164
Period size: 28 Copynumber: 3.2 Consensus size: 28
377337 TAGTATAGAT
377347 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
377375 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
377403 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAG-T-TATATTA
377433 TATTA
1 TATTA
377438 TATAAAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 48 0.79
29 1 0.02
30 12 0.20
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:377453 original size:56 final size:55
Alignment explanation
Indices: 377347--377457 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 55
377337 TAGTATAGAT
* *** **
377347 TATTAGTTTGTTAGTTTAAGTTATATTATATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTA-ATTA
377403 TATTAGTTTGTTAGTTTAAGTTATATATTATATTA-TATAAAAAATT-AGTTAATTA
1 TATTAGTTTGTTAGTTTAAG-T-TATATTATATTAGTATAAAAAATTAAGTTAATTA
377458 GTTTCTTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
55 4 0.09
56 25 0.53
57 6 0.13
58 12 0.26
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (55 bp):
TATTAGTTTGTTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTAATTA
Found at i:378431 original size:14 final size:14
Alignment explanation
Indices: 378398--378440 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
378388 TAATAATGAT
*
378398 ATGATTTGATTTAGTA
1 ATGATTTGA--TAATA
378414 ATGATTTGATAATA
1 ATGATTTGATAATA
*
378428 ATGATTTAATAAT
1 ATGATTTGATAAT
378441 GAATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.64
16 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (14 bp):
ATGATTTGATAATA
Found at i:378492 original size:13 final size:12
Alignment explanation
Indices: 378369--378548 Score: 67
Period size: 11 Copynumber: 14.8 Consensus size: 12
378359 TTGAAGTTGA
*
378369 ATTATAATAATA
1 ATTATAATAATG
378381 ATTTATGTAATAATG
1 A-TTA--TAATAATG
* *
378396 A-TATGAT-TTG
1 ATTATAATAATG
*
378406 ATT-TAGTAATG
1 ATTATAATAATG
378417 ATTTGATAATAATG
1 A-TT-ATAATAATG
378431 ATT-TAATAATG
1 ATTATAATAATG
* *
378442 AATTTATATTTAA-A
1 -A-TTATA-ATAATG
378456 ATTATAATAATG
1 ATTATAATAATG
*
378468 ATT-TAGTAATG
1 ATTATAATAATG
378479 ATTACTAATAATG
1 ATTA-TAATAATG
*
378492 ATTTATTATTAAT-
1 A-TTA-TAATAATG
*
378505 ATT-TAATGAT-
1 ATTATAATAATG
*
378515 -TTGATATTAATG
1 ATT-ATAATAATG
*
378527 ATT-TAGTAATG
1 ATTATAATAATG
378538 ATTGATAATAA
1 ATT-ATAATAA
378549 AGAAATTATT
Statistics
Matches: 125, Mismatches: 21, Indels: 43
0.66 0.11 0.23
Matches are distributed among these distances:
9 2 0.02
10 10 0.08
11 43 0.34
12 14 0.11
13 26 0.21
14 19 0.15
15 11 0.09
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.46
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:378513 original size:21 final size:22
Alignment explanation
Indices: 378487--378531 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
378477 TGATTACTAA
378487 TAATGATTT-ATTATTAAT-ATT
1 TAATGATTTGA-TATTAATGATT
378508 TAATGATTTGATATTAATGATT
1 TAATGATTTGATATTAATGATT
378530 TA
1 TA
378532 GTAATGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TAATGATTTGATATTAATGATT
Found at i:378547 original size:59 final size:59
Alignment explanation
Indices: 378404--378667 Score: 274
Period size: 59 Copynumber: 4.5 Consensus size: 59
378394 TGATATGATT
* * * *
378404 TGATTTAGTAATGATTTGATAATAATGATTTAATAATGAATTTATATTTAA--AATT-ATAATAA
1 TGATTTAGTAATGATTAG-TAATAATGATTT-AT--T--ATTAATATTTAATGATTTGATATTAA
*
378466 TGATTTAGTAATGATTACTAATAATGATTTATTATTAATATTTAATGATTTGATATTAA
1 TGATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATATTAA
* * *
378525 TGATTTAGTAATGATT-GATAATAAAGAAATTATTATTAATATTTAATGATTTGATAGTAA
1 TGATTTAGTAATGATTAG-TAATAATG-ATTTATTATTAATATTTAATGATTTGATATTAA
* * *
378585 T-ATTTAGTAATAATTAGTAATAATGA--AATTATTAATATTTAATGTTTTGAT-TGTAA
1 TGATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATAT-TAA
* *
378641 TTATTTAGTAATTATTAGTAATAATGA
1 TGATTTAGTAATGATTAGTAATAATGA
378668 AATTATAATA
Statistics
Matches: 179, Mismatches: 15, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
56 38 0.21
57 24 0.13
58 5 0.03
59 49 0.27
60 35 0.20
61 12 0.07
62 16 0.09
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (59 bp):
TGATTTAGTAATGATTAGTAATAATGATTTATTATTAATATTTAATGATTTGATATTAA
Found at i:378578 original size:60 final size:59
Alignment explanation
Indices: 378463--378687 Score: 282
Period size: 59 Copynumber: 3.8 Consensus size: 59
378453 AAAATTATAA
* *
378463 TAATGATTTAGTAATGATTACTAATAATGATTTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATATTTAATGATTTGATAT
* *
378522 TAATGATTTAGTAATGATT-GATAATAAAGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAG-TAATAATG-AATTATTATTAATATTTAATGATTTGATAT
* *
378582 TAAT-ATTTAGTAATAATTAGTAATAATGAA--ATTATTAATATTTAATGTTTTGAT-T
1 TAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATATTTAATGATTTGATAT
* * *
378637 GTAATTATTTAGTAATTATTAGTAATAATGAAATTA-TAATAATGATTTAAT
1 -TAATGATTTAGTAATGATTAGTAATAATG-AATTATTATTAAT-ATTTAAT
378688 AATTATTACT
Statistics
Matches: 147, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
56 27 0.18
57 23 0.16
58 4 0.03
59 52 0.35
60 41 0.28
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (59 bp):
TAATGATTTAGTAATGATTAGTAATAATGAATTATTATTAATATTTAATGATTTGATAT
Found at i:378594 original size:10 final size:10
Alignment explanation
Indices: 378579--378608 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
378569 AATGATTTGA
*
378579 TAGTAATATT
1 TAGTAATAAT
378589 TAGTAATAAT
1 TAGTAATAAT
378599 TAGTAATAAT
1 TAGTAATAAT
378609 GAAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (10 bp):
TAGTAATAAT
Found at i:378622 original size:116 final size:118
Alignment explanation
Indices: 378463--378687 Score: 307
Period size: 116 Copynumber: 1.9 Consensus size: 118
378453 AAAATTATAA
* *
378463 TAATGATTTAGTAATGATTACTAATAATGATTTATTATTAATATTTAATGATTTGATAT-TAATG
1 TAATGATTTAGTAATAATTACTAATAATGA-TAATTATTAATATTTAATGATTTGAT-TGTAATG
*
378527 ATTTAGTAATGATT-GATAATAAAGAAATTATTATTAAT-ATTTAATGATTTGATAG
64 ATTTAGTAATGATTAG-TAATAAAGAAATTA-TAATAATGATTTAATGATTTGATAG
* * *
378582 TAAT-ATTTAGTAATAATTAGTAATAATGA-AATTATTAATATTTAATGTTTTGATTGTAATTAT
1 TAATGATTTAGTAATAATTACTAATAATGATAATTATTAATATTTAATGATTTGATTGTAATGAT
* *
378645 TTAGTAATTATTAGTAATAATGAAATTATAATAATGATTTAAT
66 TTAGTAATGATTAGTAATAAAGAAATTATAATAATGATTTAAT
378688 AATTATTACT
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
115 7 0.07
116 60 0.63
117 1 0.01
118 23 0.24
119 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (118 bp):
TAATGATTTAGTAATAATTACTAATAATGATAATTATTAATATTTAATGATTTGATTGTAATGAT
TTAGTAATGATTAGTAATAAAGAAATTATAATAATGATTTAATGATTTGATAG
Found at i:378702 original size:13 final size:12
Alignment explanation
Indices: 378638--378706 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 12
378628 GTTTTGATTG
*
378638 TAATTATT-TAG
1 TAATTATTATAA
378649 TAATTATTAGTAA
1 TAATTATTA-TAA
*
378662 TAATGAAATTATAA
1 TAAT--TATTATAA
*
378676 TAATGATT-TAA
1 TAATTATTATAA
378687 TAATTATTACTAA
1 TAATTATTA-TAA
378700 TAATTAT
1 TAATTAT
378707 GGAATAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
11 18 0.38
12 3 0.06
13 16 0.33
14 7 0.15
15 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (12 bp):
TAATTATTATAA
Found at i:378713 original size:116 final size:115
Alignment explanation
Indices: 378404--378714 Score: 283
Period size: 116 Copynumber: 2.6 Consensus size: 115
378394 TGATATGATT
* * * * *
378404 TGATTTAGTAATGATTTGATAATAATGATTTAATAATGAATTTATATTTAA-AA-TTATAATAAT
1 TGATTTAGTAATGA-TTGATAATAAAGA---AATTATTAA-TAATATTTAATAATTTATACTAAT
* * * * *
378467 GATTTAGTAATGATTACTAATAATGATTTATTATTAATATTTAATGATTTGATATTAA
61 -AATTAGGAATAATTAGTAATAATGA--AATTATTAATATTTAATGATTTGATATTAA
* * * *
378525 TGATTTAGTAATGATTGATAATAAAGAAATTATTATTAATATTTAATGATTTGATAGTAATATTT
1 TGATTTAGTAATGATTGATAATAAAGAAATTATTAATAATATTTAATAATTT-ATACTAATAATT
* *
378590 AGTAATAATTAGTAATAATGAAATTATTAATATTTAATGTTTTGAT-TGTAA
65 AGGAATAATTAGTAATAATGAAATTATTAATATTTAATGATTTGATAT-TAA
* * *
378641 TTATTTAGTAATTATT-AGTAATAATGAAATTA-TAATAATGATTTAATAA-TTATTACTAATAA
1 TGATTTAGTAATGATTGA-TAATAAAGAAATTATTAATAAT-ATTTAATAATTTA-TACTAATAA
378703 TTATGGAATAAT
63 TTA-GGAATAAT
378715 AATATTTCAT
Statistics
Matches: 163, Mismatches: 19, Indels: 21
0.80 0.09 0.10
Matches are distributed among these distances:
114 1 0.01
115 20 0.12
116 77 0.47
117 7 0.04
118 25 0.15
119 7 0.04
120 12 0.07
121 14 0.09
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (115 bp):
TGATTTAGTAATGATTGATAATAAAGAAATTATTAATAATATTTAATAATTTATACTAATAATTA
GGAATAATTAGTAATAATGAAATTATTAATATTTAATGATTTGATATTAA
Found at i:380419 original size:20 final size:20
Alignment explanation
Indices: 380394--380431 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
380384 ATCAGATTGT
*
380394 CCAGGGGGTACAGATTCCTC
1 CCAGGGGATACAGATTCCTC
380414 CCAGGGGATACAGATTCC
1 CCAGGGGATACAGATTCC
380432 CCCTTCAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (20 bp):
CCAGGGGATACAGATTCCTC
Found at i:380442 original size:42 final size:43
Alignment explanation
Indices: 380395--380477 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
380385 TCAGATTGTC
* *
380395 CAGGGGGTACAGATT-CCTCC-CAGGGGATACAGATTCCCCCTT
1 CAGGGGGAACAGATTCCCCCCTCAGGGG-TACAGATTCCCCCTT
* *
380437 CAGGGGGAATAGATTCCCCCCTCAGGGGTACCGATTCCCCC
1 CAGGGGGAACAGATTCCCCCCTCAGGGGTACAGATTCCCCC
380478 CTGTCTAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 13 0.37
43 16 0.46
44 6 0.17
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (43 bp):
CAGGGGGAACAGATTCCCCCCTCAGGGGTACAGATTCCCCCTT
Found at i:380464 original size:21 final size:21
Alignment explanation
Indices: 380398--380479 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
380388 GATTGTCCAG
* *
380398 GGGGTACAGATT-CCTCC-CA
1 GGGGAACAGATTCCCCCCTCA
*
380417 GGGGATACAGATTCCCCCTTCA
1 GGGGA-ACAGATTCCCCCCTCA
*
380439 GGGGGAATAGATTCCCCCCTCA
1 -GGGGAACAGATTCCCCCCTCA
* *
380461 GGGGTACCGATTCCCCCCT
1 GGGGAACAGATTCCCCCCT
380480 GTCTAACGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
21 19 0.37
22 16 0.31
23 5 0.10
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.21
Consensus pattern (21 bp):
GGGGAACAGATTCCCCCCTCA
Found at i:381781 original size:19 final size:20
Alignment explanation
Indices: 381757--381804 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
381747 AATGATTTTC
*
381757 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
381776 TTTTGAAAGCTAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
381796 TTTTGAAAA
1 TTTTGAAAA
381805 TGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:383283 original size:20 final size:20
Alignment explanation
Indices: 383256--383317 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
383246 ATCAGATTGT
383256 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* * *
383276 CTAGGGGGAATAGATTCCCCCC
1 CCAGGGGGTACAGATT--CCCC
*
383298 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
383318 TTATCTAACG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:385328 original size:21 final size:23
Alignment explanation
Indices: 385304--385359 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
385294 TTTATGTATG
385304 ATATAACTTAAATTAAC-AA-TA
1 ATATAACTTAAATTAACAAACTA
* *
385325 ATATAATTTAAACTAACAAACTA
1 ATATAACTTAAATTAACAAACTA
385348 AT-TAAC-TAAATT
1 ATATAACTTAAATT
385360 TTTGTTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 20 0.69
22 5 0.17
23 4 0.14
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATAACTTAAATTAACAAACTA
Found at i:385403 original size:21 final size:22
Alignment explanation
Indices: 385374--385416 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
385364 TTTTACCCTA
*
385374 AATTCTAAACTAACAAACTAAT
1 AATTCTAAAATAACAAACTAAT
*
385396 AATT-TAAAATAATAAACTAAT
1 AATTCTAAAATAACAAACTAAT
385417 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTCTAAAATAACAAACTAAT
Found at i:385654 original size:22 final size:23
Alignment explanation
Indices: 385629--385674 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
385619 CAATAATTAA
385629 TGCATGAAGCAGC-AAATGATGC
1 TGCATGAAGCAGCAAAATGATGC
385651 TGCATGAAGCAGCGAAAATGATGC
1 TGCATGAAGCAGC-AAAATGATGC
385675 AGCGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (23 bp):
TGCATGAAGCAGCAAAATGATGC
Done.