Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008240.1 Hibiscus syriacus cultivar Beakdansim tig00110888_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: 893855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:184490 original size:21 final size:21
Alignment explanation
Indices: 184464--184547 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
184454 CCATTAGACA
*
184464 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
184485 GGGGGGAATCTGTTCCCCCT-
1 GGGGGGAATCTGTACCCCCTG
*
184505 GGGGGGAATCAGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
184526 GGGGGAAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
184547 G
1 G
184548 ACAATATGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.32
21 38 0.68
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:184521 original size:41 final size:41
Alignment explanation
Indices: 184464--184547 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
184454 CCATTAGACA
* * *
184464 GGGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGGGAATCAGTACCCCCTGGGGGGAAATCTGTACCCCCT
184505 GGGGGGAATCAGTACCCCCTGGGGGGAAATCTGTACCCCCT
1 GGGGGGAATCAGTACCCCCTGGGGGGAAATCTGTACCCCCT
184546 GG
1 GG
184548 ACAATATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (41 bp):
GGGGGGAATCAGTACCCCCTGGGGGGAAATCTGTACCCCCT
Found at i:187968 original size:21 final size:20
Alignment explanation
Indices: 187937--188018 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 20
187927 CCATTAGACA
**
187937 GGGGG-ATCGGTACCTACTG
1 GGGGGAATCGGTACCCCCTG
187956 GGGGAGAATCGGTACCCCCTGG
1 GGGG-GAATCGGTACCCCCT-G
*
187978 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
187998 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
188018 G
1 G
188019 ACAATCTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
19 4 0.07
20 23 0.40
21 25 0.44
22 5 0.09
ACGTcount: A:0.16, C:0.27, G:0.39, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:187994 original size:20 final size:21
Alignment explanation
Indices: 187953--188018 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
187943 TCGGTACCTA
* *
187953 CTGGGGGAGAATCGGTACCCC
1 CTGGGGGGGAATCTGTACCCC
187974 CTGGGGGGGAATCTGTACCCC
1 CTGGGGGGGAATCTGTACCCC
187995 CT-GGGGGGAATCTGTACCCC
1 CTGGGGGGGAATCTGTACCCC
188015 CTGG
1 CTGG
188019 ACAATCTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 20 0.48
21 22 0.52
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (21 bp):
CTGGGGGGGAATCTGTACCCC
Found at i:190437 original size:13 final size:13
Alignment explanation
Indices: 190419--190445 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
190409 ACTGAAATTA
190419 ACGATTCACGACG
1 ACGATTCACGACG
190432 ACGATTCACGACG
1 ACGATTCACGACG
190445 A
1 A
190446 AAGATTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (13 bp):
ACGATTCACGACG
Found at i:192073 original size:32 final size:31
Alignment explanation
Indices: 192037--192109 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
192027 GCCACGGGGA
*
192037 CTACCTAAGAACACATCTTAGGGCCGCA-AGGC
1 CTACCTAAGAA-ACATCTCAGGGCCGCAGA-GC
** *
192069 CTACCCGAGAAATATCTCAGGGCCGCAGAGC
1 CTACCTAAGAAACATCTCAGGGCCGCAGAGC
192100 CTACCTAAGA
1 CTACCTAAGA
192110 GATACAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.15
Consensus pattern (31 bp):
CTACCTAAGAAACATCTCAGGGCCGCAGAGC
Found at i:193123 original size:34 final size:32
Alignment explanation
Indices: 193056--193125 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
193046 ACCTTACAGC
* * *
193056 TCCCTAGTTTTTCCGGGCTAAACTAGAATCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
193088 TCCCTAGATTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
193122 TCCC
1 TCCC
193126 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:193555 original size:34 final size:33
Alignment explanation
Indices: 193511--193622 Score: 95
Period size: 34 Copynumber: 3.4 Consensus size: 33
193501 CATGGAAGGA
193511 TGCATCGATGCACTAAGTGTATTCGATGTTTGAG
1 TGCATCGATGCACTAAGTG-ATTCGATGTTTGAG
* * * * ***
193545 TGCATGGATGCATTGCA-TGATGC-ATGGAAG-G
1 TGCATCGATGCACT-AAGTGATTCGATGTTTGAG
193576 ATGCATCGATGCACTAAGTGCATTCGATGTTTGAG
1 -TGCATCGATGCACTAAGTG-ATTCGATGTTTGAG
*
193611 TGCATGGATGCA
1 TGCATCGATGCA
193623 TTGCATGATG
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
31 2 0.04
32 18 0.32
33 6 0.11
34 29 0.51
35 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.30
Consensus pattern (33 bp):
TGCATCGATGCACTAAGTGATTCGATGTTTGAG
Found at i:193591 original size:66 final size:66
Alignment explanation
Indices: 193491--193635 Score: 272
Period size: 66 Copynumber: 2.2 Consensus size: 66
193481 ACAGCCTTGA
*
193491 TGCATGGATGCATGGAAGGATGCATCGATGCACTAAGTGTATTCGATGTTTGAGTGCATGGATGC
1 TGCAT-GATGCATGGAAGGATGCATCGATGCACTAAGTGCATTCGATGTTTGAGTGCATGGATGC
193556 AT
65 AT
193558 TGCATGATGCATGGAAGGATGCATCGATGCACTAAGTGCATTCGATGTTTGAGTGCATGGATGCA
1 TGCATGATGCATGGAAGGATGCATCGATGCACTAAGTGCATTCGATGTTTGAGTGCATGGATGCA
193623 T
66 T
193624 TGCATGATGCAT
1 TGCATGATGCAT
193636 CGATGCATTA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 72 0.94
67 5 0.06
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (66 bp):
TGCATGATGCATGGAAGGATGCATCGATGCACTAAGTGCATTCGATGTTTGAGTGCATGGATGCA
T
Found at i:193679 original size:21 final size:20
Alignment explanation
Indices: 193611--193708 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 20
193601 GATGTTTGAG
* *
193611 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
193631 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
193653 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
193674 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
193695 TGCATGGATGCACT
1 TGCATGGATGCACT
193709 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.07
20 12 0.18
21 35 0.51
22 10 0.15
23 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:193809 original size:29 final size:28
Alignment explanation
Indices: 193777--193868 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 28
193767 GAAACCTTTT
193777 AAAACTTTGAATAAATTCAATTAAGTCCAA
1 AAAACTTTG--TAAATTCAATTAAGTCCAA
*
193807 AAATATTTTGTAAATTCAATTAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTAAGTCCAA
* * *
193836 AAATATTTTGGAAATTCAATTCAAGTCTAA
1 AAA-ACTTTGTAAATTCAATT-AAGTCCAA
193866 AAA
1 AAA
193869 CATTTTTGCC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 39 0.68
30 13 0.23
31 5 0.09
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.34
Consensus pattern (28 bp):
AAAACTTTGTAAATTCAATTAAGTCCAA
Found at i:193868 original size:30 final size:29
Alignment explanation
Indices: 193789--193874 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
193779 AACTTTGAAT
*
193789 AAATTCAATTAAGTCCAAAAATATTTTGT
1 AAATTCAATTAAGTCCAAAAATATTTTGG
193818 AAATTCAATTAAGTCCAAAAATATTTTGG
1 AAATTCAATTAAGTCCAAAAATATTTTGG
* *
193847 AAATTCAATTCAAGTCTAAAAACATTTT
1 AAATTCAATT-AAGTCCAAAAATATTTT
193875 TGCCTTAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 38 0.72
30 15 0.28
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATTCAATTAAGTCCAAAAATATTTTGG
Found at i:197607 original size:22 final size:22
Alignment explanation
Indices: 197582--197657 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
197572 TTAAATCACA
*
197582 AAAGTGCCTTAGCACTAATACT
1 AAAGTGCCTTAGCACTGATACT
*
197604 AAAGTGCCTCAGCACTGATAC-
1 AAAGTGCCTTAGCACTGATACT
*
197625 AGAAGTG-CATATGCACTGATACT
1 A-AAGTGCCTTA-GCACTGATACT
197648 AAAGTGCCTT
1 AAAGTGCCTT
197658 TAGGGATGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.07
22 39 0.87
23 3 0.07
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (22 bp):
AAAGTGCCTTAGCACTGATACT
Found at i:197879 original size:24 final size:22
Alignment explanation
Indices: 197852--197896 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
197842 TAGGAGTTTT
197852 TATT-TTTATATTATT-AAAATA
1 TATTATTTA-ATTATTAAAAATA
197873 TATTATTTAATTATTAAAAATA
1 TATTATTTAATTATTAAAAATA
197895 TA
1 TA
197897 AAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTTAATTATTAAAAATA
Found at i:197885 original size:21 final size:21
Alignment explanation
Indices: 197852--197999 Score: 71
Period size: 21 Copynumber: 7.3 Consensus size: 21
197842 TAGGAGTTTT
197852 TATT-TTTATATTATTAAAATA
1 TATTATTTA-ATTATTAAAATA
197873 TATTATTTAATTATTAAAA-A
1 TATTATTTAATTATTAAAATA
* *** *
197893 TATAAAAAATATTA-TAAAAAA
1 TATTATTTA-ATTATTAAAATA
* *
197914 TATTATTTAA-CAGTTTAAATA
1 TATTATTTAATTA-TTAAAATA
* *
197935 TA-AATAT-ATTA-TAAAATA
1 TATTATTTAATTATTAAAATA
** *
197953 TATTATTTAACAATTTAAATA
1 TATTATTTAATTATTAAAATA
* **
197974 TAATAAATAATTA-T-AAATA
1 TATTATTTAATTATTAAAATA
197993 TATTATT
1 TATTATT
198000 CTAAAATATT
Statistics
Matches: 90, Mismatches: 28, Indels: 20
0.65 0.20 0.14
Matches are distributed among these distances:
18 8 0.09
19 14 0.16
20 19 0.21
21 45 0.50
22 4 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
TATTATTTAATTATTAAAATA
Found at i:197906 original size:39 final size:39
Alignment explanation
Indices: 197859--198006 Score: 165
Period size: 39 Copynumber: 3.7 Consensus size: 39
197849 TTTTATTTTT
* *
197859 ATATTATTAAAATATATTATTTAATTATTAAAAATATAAAAA
1 ATATTA-TAAAATATATTATTTAA-AATT-TAAATATAAAAA
* * *
197901 ATATTATAAAAAATATTATTTAACAGTTTAAATAT-AAAT
1 ATATTATAAAATATATTATTTAA-AATTTAAATATAAAAA
*
197940 ATATTATAAAATATATTATTTAACAATTTAAATATAATAA
1 ATATTATAAAATATATTATTTAA-AATTTAAATATAAAAA
197980 ATAATTAT-AAATATATTATTCTAAAAT
1 AT-ATTATAAAATATATTATT-TAAAAT
198007 ATTTTATTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 36 0.39
40 25 0.27
41 26 0.28
42 6 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (39 bp):
ATATTATAAAATATATTATTTAAAATTTAAATATAAAAA
Found at i:197910 original size:12 final size:12
Alignment explanation
Indices: 197893--197919 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
197883 TTATTAAAAA
197893 TATAAAAAATAT
1 TATAAAAAATAT
197905 TATAAAAAATAT
1 TATAAAAAATAT
197917 TAT
1 TAT
197920 TTAACAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAAAATAT
Found at i:198030 original size:80 final size:78
Alignment explanation
Indices: 197849--198033 Score: 185
Period size: 80 Copynumber: 2.3 Consensus size: 78
197839 TTTTAGGAGT
* * **
197849 TTTTATTTTTATATTATTAAAATATATTATTTAATTATTAAAAATATAAAAAATATTATAAAAAA
1 TTTTATTTTAATATTTTTAAAATATATTATTTAACAATTAAAAATATAAAAAATATTATAAAAAA
* *
197914 TATTATTTAACAG
66 TATTATTTAAAAA
* * * * * *
197927 TTTAAATATAAATATATTATAAAATATATTATTTAACAATT-TAAATATAATAAATAATTAT-AA
1 TTT-TATTTTAATAT-TTTTAAAATATATTATTTAACAATTAAAAATATAAAAAAT-ATTATAAA
*
197990 ATATATTATTCTAAAATA
63 AAATATTATT-TAAAA-A
198008 TTTTATTTTAATTATTTTTAAAATAT
1 TTTTATTTTAA-TATTTTTAAAATAT
198034 TAATATATTC
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
78 3 0.04
79 30 0.36
80 45 0.54
81 6 0.07
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (78 bp):
TTTTATTTTAATATTTTTAAAATATATTATTTAACAATTAAAAATATAAAAAATATTATAAAAAA
TATTATTTAAAAA
Found at i:200218 original size:22 final size:24
Alignment explanation
Indices: 200189--200249 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
200179 TCAACTATTC
200189 AAAAAAATTAAATATAAAAATA-T
1 AAAAAAATTAAATATAAAAATACT
*
200212 -AAAAAATATAAAT-T-AAATTACT
1 AAAAAAAT-TAAATATAAAAATACT
200234 AAAAAAATTAAATATA
1 AAAAAAATTAAATATA
200250 CATATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 5 0.16
22 14 0.44
23 13 0.41
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAAATTAAATATAAAAATACT
Found at i:200258 original size:22 final size:21
Alignment explanation
Indices: 200184--200260 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 21
200174 ACTATTCAAC
200184 TATTCAAAAAAATTAAATATAA
1 TATT-AAAAAAATTAAATATAA
* *
200206 AAATATAAAAAATATAAAT-TAAA
1 TATTA-AAAAAAT-TAAATAT-AA
*
200229 TTACTAAAAAAATTAAATATACA
1 -TATTAAAAAAATTAAATATA-A
200252 TATTAAAAA
1 TATTAAAAA
200261 TACTAAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.02
22 24 0.55
23 16 0.36
24 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
TATTAAAAAAATTAAATATAA
Found at i:200260 original size:23 final size:22
Alignment explanation
Indices: 200184--200260 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
200174 ACTATTCAAC
*
200184 TATTCAAAAAAATTAAATATAA
1 TATTAAAAAAAATTAAATATAA
* * *
200206 AAATATAAAAAATATAAAT-TAA
1 TATTAAAAAAAAT-TAAATATAA
200228 -ATTACTAAAAAAATTAAATATACA
1 TATTA--AAAAAAATTAAATATA-A
200252 TATTAAAAA
1 TATTAAAAA
200261 TACTAAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
21 3 0.07
22 17 0.40
23 18 0.42
24 1 0.02
25 4 0.09
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
TATTAAAAAAAATTAAATATAA
Found at i:200267 original size:22 final size:20
Alignment explanation
Indices: 200206--200267 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
200196 TTAAATATAA
*
200206 AAATATAAAAAATATAAATT
1 AAATATTAAAAATATAAATT
* *
200226 AAATTACTAAAAAAATTAAATAT
1 AAA-TATTAAAAATA-TAAAT-T
*
200249 ACATATTAAAAATACTAAA
1 AAATATTAAAAATA-TAAA
200268 ACTATTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 3 0.09
21 8 0.25
22 18 0.56
23 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATTAAAAATATAAATT
Found at i:200627 original size:25 final size:25
Alignment explanation
Indices: 200599--200655 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
200589 ATGAGTTTTT
200599 ACTAATCTAAATATTATAAGTCTCG
1 ACTAATCTAAATATTATAAGTCTCG
* * **
200624 ACTAATTTAAATTTTATATTTCTCG
1 ACTAATCTAAATATTATAAGTCTCG
*
200649 ATTAATC
1 ACTAATC
200656 CAGTAAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (25 bp):
ACTAATCTAAATATTATAAGTCTCG
Found at i:205912 original size:31 final size:30
Alignment explanation
Indices: 205877--205954 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
205867 TAAAAAAACA
*
205877 TAAGTTTTAGTCACTTACGTTATCGTTTTAT
1 TAAGTTTT-GTCACTTACGTTATCGTTTTAC
205908 TAAGTTTTGGTCACTTACGTTATCGTTTTAC
1 TAAGTTTT-GTCACTTACGTTATCGTTTTAC
*
205939 TAAATTTTGATCACTT
1 TAAGTTTTG-TCACTT
205955 GGAAGTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (30 bp):
TAAGTTTTGTCACTTACGTTATCGTTTTAC
Found at i:208693 original size:59 final size:59
Alignment explanation
Indices: 208562--208674 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
208552 CACCGTAATG
* * * **
208562 CAATCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTA
1 CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTA
*
208621 CAATCCCGAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTT
1 CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
208675 TAGTGTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (59 bp):
CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTA
Found at i:213378 original size:27 final size:27
Alignment explanation
Indices: 213323--213378 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
213313 ACCAAAATTC
*
213323 AAAGTCCAATGTACAAAATAAATGTTA
1 AAAGTCCAATGTACAAAATAAATGATA
*
213350 AAAGTCCAATGTCCAAAAATAAAT-ATA
1 AAAGTCCAATGTAC-AAAATAAATGATA
213377 AA
1 AA
213379 TAATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAGTCCAATGTACAAAATAAATGATA
Found at i:216085 original size:3 final size:3
Alignment explanation
Indices: 216070--216118 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
216060 ATTTTTTATT
* *
216070 TAA TAA TAT TAA TAA T-A TATA GAA TAA TAA TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA -TAA TAA TAA
216116 TAA
1 TAA
216119 AAACAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:216326 original size:45 final size:45
Alignment explanation
Indices: 216275--216435 Score: 196
Period size: 45 Copynumber: 3.6 Consensus size: 45
216265 GGTCTTATGA
* * * * *
216275 ATGACCCGAAGGTTTTGATAATATCATGCATTGTAGGGATTACAG
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
* * * * * **
216320 ATGACCCAAAGGGTTTGAAAACATCATGCACTGCATGTCTTATGG
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
*
216365 ATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTTACAG
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
*
216410 ATGACCCGAAGGTTTTGAAAATATCA
1 ATGACCCGAAGGTTTTGAAAACATCA
216436 AAAAGCTCCC
Statistics
Matches: 95, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (45 bp):
ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAG
Found at i:216427 original size:90 final size:90
Alignment explanation
Indices: 216266--216435 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
216256 ATGCCCAAAG
* * *
216266 GTCTTATGAATGACCCGAAGGTTTTGATAATATCATGCATTGTAGGGATTACAGATGACCCAAAG
1 GTCTTATGAATGACCCGAAGGTTTTGATAACATCATGCACTGAAGGGATTACAGATGACCCAAAG
216331 GGTTTGAAAACATCATGCACTGCAT
66 GGTTTGAAAACATCATGCACTGCAT
* * *
216356 GTCTTATGGATGACCCGAAGGTTTTGA-AAGCATCATGCACTGAAGGGCTTACAGATGACCCGAA
1 GTCTTATGAATGACCCGAAGGTTTTGATAA-CATCATGCACTGAAGGGATTACAGATGACCCAAA
* *
216420 GGTTTTGAAAATATCA
65 GGGTTTGAAAACATCA
216436 AAAAGCTCCC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 2 0.03
90 69 0.97
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (90 bp):
GTCTTATGAATGACCCGAAGGTTTTGATAACATCATGCACTGAAGGGATTACAGATGACCCAAAG
GGTTTGAAAACATCATGCACTGCAT
Found at i:216516 original size:45 final size:45
Alignment explanation
Indices: 216443--216551 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
216433 TCAAAAAGCT
* * **
216443 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
**
216490 CCCGAAGGTTTTGAAAGGATCATGCACTGAAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
216535 CCCGAAGGTTTTGAAAA
1 CCCGAAGGTTTTGAAAA
216552 TATAAAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 47 0.85
47 8 0.15
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
Found at i:216547 original size:121 final size:121
Alignment explanation
Indices: 216333--216654 Score: 545
Period size: 121 Copynumber: 2.7 Consensus size: 121
216323 ACCCAAAGGG
*
216333 TTTGAAAACATCATGCACTGCATGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTG
1 TTTGAAAACATCATGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTG
* *
216398 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATAAAAAAACTCCCGAAGGCTT
* *
216454 TTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGGATCATGCACTG
1 TTTGAAAACATCATGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTG
* *
216519 AAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATAAAAAAACTCCTGAAGGCTT
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATAAAAAAACTCCCGAAGGCTT
* * * *
216575 CTTGAAAACATCATGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCACTG
1 TTTGAAAACATCATGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTG
216640 AAGGGCTTACAGATG
66 AAGGGCTTACAGATG
216655 GTGAGAAATA
Statistics
Matches: 187, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 187 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (121 bp):
TTTGAAAACATCATGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAGCATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATAAAAAAACTCCCGAAGGCTT
Found at i:217904 original size:54 final size:54
Alignment explanation
Indices: 217691--217904 Score: 229
Period size: 54 Copynumber: 4.0 Consensus size: 54
217681 AGAATAACTA
* * *** *
217691 GTTCGTAAAACCTTTGACAACACATTCATCC--AGATGTGGCTTCTGTACAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAGAT
* * * * **
217743 GTTCGTAAAACATTTGATAATACATCCATCCTTTCTTGTGGCTTCTGGTCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAGAT
*
217797 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTTTGGC-CAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCT-GCACAGAT
** * *
217851 GTTTATAAAGCATTTGACAACACATTCATCATTT-TCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCT-TGTGGCTTCTGCACAGAT
217905 TTTTGATCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
52 27 0.20
53 3 0.02
54 106 0.77
55 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAGAT
Found at i:218841 original size:63 final size:63
Alignment explanation
Indices: 218762--218886 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
218752 TCAACATTTC
* * * * *
218762 TGATTCTGATTGAAATGGGCTTTCAACATGCCCCAACATTGGCTATTACAAACGTTCAAAATG
1 TGATTCTGATTAAAATGAGATTTCAACATGCCCCAACATTGGCTAATACAAACATTCAAAATG
* ** * *
218825 TGATTCTGATTAAAATGAGATTTTAGTATGCCCTAACATTGGCTAATACAAATATTCAAAAT
1 TGATTCTGATTAAAATGAGATTTCAACATGCCCCAACATTGGCTAATACAAACATTCAAAAT
218887 ACATCAACAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (63 bp):
TGATTCTGATTAAAATGAGATTTCAACATGCCCCAACATTGGCTAATACAAACATTCAAAATG
Found at i:221699 original size:32 final size:32
Alignment explanation
Indices: 221658--221719 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
221648 GAAGAAATGA
* *
221658 TTGTTATGCTTATCTGGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
221690 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
221720 TGTTTCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:227167 original size:15 final size:17
Alignment explanation
Indices: 227147--227185 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
227137 TTGAAAATAA
227147 AATAAAAAA-ATTA-AT
1 AATAAAAAATATTATAT
227162 AATAAAAAATATTATAT
1 AATAAAAAATATTATAT
227179 ATATAAA
1 A-ATAAA
227186 TATTATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 3 0.14
18 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAAAAATATTATAT
Found at i:229638 original size:3 final size:3
Alignment explanation
Indices: 229623--229674 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
229613 ATTTTTTATT
*
229623 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA
229669 TAA TAA
1 TAA TAA
229675 AAACAATATG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:240995 original size:18 final size:18
Alignment explanation
Indices: 240960--240998 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
240950 GGAGCAGCAC
*
240960 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
240978 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
240996 GAG
1 GAG
240999 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:241465 original size:34 final size:34
Alignment explanation
Indices: 241422--241489 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
241412 CCATGTCACA
241422 TTGTTTATGAATATTGATTATGAAACTAATGGCT
1 TTGTTTATGAATATTGATTATGAAACTAATGGCT
241456 TTGTTTATGAATATTGATTATGAAACTAATGGCT
1 TTGTTTATGAATATTGATTATGAAACTAATGGCT
241490 AACGTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (34 bp):
TTGTTTATGAATATTGATTATGAAACTAATGGCT
Found at i:250574 original size:48 final size:48
Alignment explanation
Indices: 250481--250571 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
250471 AGATTTTACT
*
250481 ATTATGTCTTCAAGATATAAAAGAACAAAAGGGTTTATCTGAAATTCA
1 ATTATGTCTTCAAGATATAAAAGAACAAAAGCGTTTATCTGAAATTCA
* * *
250529 ATTATGTCTTGAAGGTATAAAAG-ACAAAAGCGTTTTTCTGAAA
1 ATTATGTCTTCAAGATATAAAAGAACAAAAGCGTTTATCTGAAA
250572 ATTTTGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 18 0.46
48 21 0.54
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (48 bp):
ATTATGTCTTCAAGATATAAAAGAACAAAAGCGTTTATCTGAAATTCA
Found at i:251455 original size:13 final size:14
Alignment explanation
Indices: 251437--251467 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
251427 TTTTTAAAAT
251437 AAAATA-TTTTTTA
1 AAAATATTTTTTTA
251450 AAAATATTTTTTTA
1 AAAATATTTTTTTA
251464 AAAA
1 AAAA
251468 ATATGGACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTTTTA
Found at i:251461 original size:15 final size:15
Alignment explanation
Indices: 251424--251471 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
251414 CAAGTCTAGA
*
251424 ATTTTTTTAAAATAAA
1 ATTTTTTTAAAA-AAT
251440 ATATTTTTT-AAAAAT
1 AT-TTTTTTAAAAAAT
251455 ATTTTTTTAAAAAAT
1 ATTTTTTTAAAAAAT
251470 AT
1 AT
251472 GGACGTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.21
15 12 0.41
16 5 0.17
17 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTTTTAAAAAAT
Found at i:258017 original size:2 final size:2
Alignment explanation
Indices: 258010--258043 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
258000 ATGAAAAATA
258010 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
258044 TAAAGTTTTA
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:258312 original size:2 final size:2
Alignment explanation
Indices: 258305--258329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
258295 ATTGAAAATA
258305 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
258330 AAAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:267762 original size:26 final size:26
Alignment explanation
Indices: 267696--267762 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 26
267686 AGTTCGAGTA
*
267696 TCGCTGAGCTTGACTCGACTCGAAAAC
1 TCGC-GAGCTCGACTCGACTCGAAAAC
*
267723 TCTGAAATGCAGCTCGACTCGACTCGAAAAC
1 TC-G---CG-AGCTCGACTCGACTCGAAAAC
267754 TCGCGAGCT
1 TCGCGAGCT
267763 TAAAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
26 4 0.12
27 3 0.09
28 1 0.03
30 2 0.06
31 22 0.69
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (26 bp):
TCGCGAGCTCGACTCGACTCGAAAAC
Found at i:268079 original size:11 final size:10
Alignment explanation
Indices: 268063--268102 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
268053 CGTTAGGAAT
268063 TCGAGTCGAG
1 TCGAGTCGAG
268073 CTCGAGTCGAG
1 -TCGAGTCGAG
268084 TTCGAGCTCGAG
1 -TCGAG-TCGAG
268096 TCGAGTC
1 TCGAGTC
268103 CATTCGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 2 0.07
11 20 0.74
12 5 0.19
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (10 bp):
TCGAGTCGAG
Found at i:268082 original size:5 final size:5
Alignment explanation
Indices: 268063--268102 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
268053 CGTTAGGAAT
268063 TCGAG TCGAG CTCGAG TCGAG TTCGAG CTCGAG TCGAG TC
1 TCGAG TCGAG -TCGAG TCGAG -TCGAG -TCGAG TCGAG TC
268103 CATTCGATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 17 0.53
6 15 0.47
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (5 bp):
TCGAG
Found at i:268090 original size:17 final size:17
Alignment explanation
Indices: 268063--268101 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
268053 CGTTAGGAAT
268063 TCGAG-TCGAGCTCGAG
1 TCGAGTTCGAGCTCGAG
268079 TCGAGTTCGAGCTCGAG
1 TCGAGTTCGAGCTCGAG
268096 TCGAGT
1 TCGAGT
268102 CCATTCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (17 bp):
TCGAGTTCGAGCTCGAG
Found at i:274944 original size:12 final size:13
Alignment explanation
Indices: 274915--274946 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
274905 GAAGTCATAA
274915 TTTTTCTTGTTGC
1 TTTTTCTTGTTGC
274928 TTTTTCTTGTTGC
1 TTTTTCTTGTTGC
274941 TTTTTC
1 TTTTTC
274947 AGCCATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (13 bp):
TTTTTCTTGTTGC
Found at i:279219 original size:2 final size:2
Alignment explanation
Indices: 279212--279236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
279202 ACAAAGAGTT
279212 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
279237 GCAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:281295 original size:40 final size:40
Alignment explanation
Indices: 281251--281360 Score: 97
Period size: 40 Copynumber: 2.9 Consensus size: 40
281241 ATAAAACATT
*
281251 AAATAATA-AAATAATAA-TAATATATTATATATATTTTCAA
1 AAATAATATAAATAA-AACT-ATATAATATATATATTTTCAA
* ***
281291 AAATATTATTTTTAAAACTATATAATATATATATTTTCAA
1 AAATAATATAAATAAAACTATATAATATATATATTTTCAA
* *
281331 AAAT-AT-T--TTAAAACTATATATTATATATAT
1 AAATAATATAAATAAAACTATATAATATATATAT
281361 AATTTTAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
36 22 0.36
38 1 0.02
39 1 0.02
40 33 0.54
41 4 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (40 bp):
AAATAATATAAATAAAACTATATAATATATATATTTTCAA
Found at i:281302 original size:15 final size:16
Alignment explanation
Indices: 281277--281314 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
281267 ATAATATATT
281277 ATATATATTTTCAAAA
1 ATATATATTTTCAAAA
*
281293 ATAT-TATTTTTAAAA
1 ATATATATTTTCAAAA
*
281308 CTATATA
1 ATATATA
281315 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATTTTCAAAA
Found at i:281326 original size:25 final size:25
Alignment explanation
Indices: 281293--281432 Score: 90
Period size: 25 Copynumber: 5.6 Consensus size: 25
281283 ATTTTCAAAA
*
281293 ATAT-TATTTTTAAAACTATATAAT
1 ATATATATTTTCAAAACTATATAAT
* * *
281317 ATATATATTTTCAAAAATATTTTAAA
1 ATATATATTTTCAAAACTA-TATAAT
* * **
281343 ACTATATATTAT--ATA-TATAATTTT
1 A-TATATATTTTCAAAACTAT-ATAAT
* * * *
281367 AAAAATGTTTTCAAAACTATATATT
1 ATATATATTTTCAAAACTATATAAT
* *
281392 ATATATGTTTTCAAAACTATATATT
1 ATATATATTTTCAAAACTATATAAT
*
281417 ATATATGTTTTCAAAA
1 ATATATATTTTCAAAA
281433 ATGTTTTCAA
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
23 7 0.08
24 8 0.09
25 59 0.65
26 8 0.09
27 9 0.10
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATATATTTTCAAAACTATATAAT
Found at i:281340 original size:36 final size:36
Alignment explanation
Indices: 281270--281407 Score: 161
Period size: 39 Copynumber: 3.6 Consensus size: 36
281260 AATAATAATA
*
281270 ATATATTATATATATTTTCAAAAATATTATTTTTAAAACT
1 ATATAATATATATATTTTC-AAAA-A-TA-TTTTAAAACT
281310 ATATAATATATATATTTTCAAAAATATTTTAAAACT
1 ATATAATATATATATTTTCAAAAATATTTTAAAACT
*
281346 ATATATTATATATATAATTTT-AAAAATGTTTTCAAAACT
1 ATATA--ATATATAT-ATTTTCAAAAATATTTT-AAAACT
* *
281385 ATATATTATATATGTTTTCAAAA
1 ATATAATATATATATTTTCAAAA
281408 CTATATATTA
Statistics
Matches: 89, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
36 19 0.21
37 13 0.15
38 19 0.21
39 20 0.22
40 18 0.20
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (36 bp):
ATATAATATATATATTTTCAAAAATATTTTAAAACT
Found at i:281397 original size:37 final size:36
Alignment explanation
Indices: 281270--281598 Score: 225
Period size: 37 Copynumber: 9.6 Consensus size: 36
281260 AATAATAATA
* *
281270 ATATATTATATATATTTTCAAAAATATTATTTTTAAAACT
1 ATATATTATATATATTTT--AAAA-A-TGTTTTCAAAACT
* *
281310 ATATAATATATATATTTTCAAAAATATTTT-AAAACT
1 ATATATTATATATATTTT-AAAAATGTTTTCAAAACT
281346 ATATATTATATATATAATTTTAAAAATGTTTTCAAAAC-
1 ATATA-T-TATATAT-ATTTTAAAAATGTTTTCAAAACT
281384 -TATA-TAT-TATA---T----ATGTTTTCAAAACT
1 ATATATTATATATATTTTAAAAATGTTTTCAAAACT
*
281410 ATATATTATATATGTTTTCAAAAATGTTTTCAAAAC-
1 ATATATTATATATATTTT-AAAAATGTTTTCAAAACT
281446 -TATA-TAT-TATA---T---AA-GTTTTCAAAAACT
1 ATATATTATATATATTTTAAAAATGTTTTC-AAAACT
*
281473 ATATATTATATATATATTTTCAAAATGTTTTCAAAAACT
1 ATATA-T-TATATATATTTTAAAAATGTTTTC-AAAACT
* *
281512 ATATCTTATATATATTTTCAAAATGTTTTC--AA--
1 ATATATTATATATATTTTAAAAATGTTTTCAAAACT
* *
281544 A-A-A--CTATATATTTTCAAAATGTTTTCAAAACT
1 ATATATTATATATATTTTAAAAATGTTTTCAAAACT
*
281576 ATTTATTATATATATTTTAAAAA
1 ATATATTATATATATTTTAAAAA
281599 ACTATTTATT
Statistics
Matches: 239, Mismatches: 12, Indels: 80
0.72 0.04 0.24
Matches are distributed among these distances:
25 19 0.08
26 7 0.03
27 4 0.02
28 29 0.12
29 4 0.02
30 3 0.01
31 4 0.02
32 8 0.03
33 6 0.03
34 9 0.04
35 5 0.02
36 25 0.10
37 47 0.20
38 21 0.09
39 31 0.13
40 17 0.07
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (36 bp):
ATATATTATATATATTTTAAAAATGTTTTCAAAACT
Found at i:281477 original size:28 final size:27
Alignment explanation
Indices: 281435--281497 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
281425 TTTCAAAAAT
281435 GTTTTC-AAAACTATA-TAT-TATATAA
1 GTTTTCAAAAACTATATTATATATAT-A
281460 GTTTTCAAAAACTATATATTATATATATA
1 GTTTTCAAAAAC--TATATTATATATATA
281489 -TTTTCAAAA
1 GTTTTCAAAA
281498 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
28 13 0.39
29 4 0.12
30 5 0.15
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (27 bp):
GTTTTCAAAAACTATATTATATATATA
Found at i:281482 original size:24 final size:25
Alignment explanation
Indices: 281435--281484 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
281425 TTTCAAAAAT
281435 GTTTTCAAAACTATATATTATATAA
1 GTTTTCAAAACTATATATTATATAA
281460 GTTTTCAAAAACTATATATTATATA
1 GTTTTC-AAAACTATATATTATATA
281485 TATATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (25 bp):
GTTTTCAAAACTATATATTATATAA
Found at i:281582 original size:27 final size:28
Alignment explanation
Indices: 281520--281582 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
281510 CTATATCTTA
281520 TATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATTTTCAAAATGTTTTCAAAAAC
281548 TATATATTTTCAAAATGTTTTC-AAAAC
1 TATATATTTTCAAAATGTTTTCAAAAAC
*
281575 TATTTATT
1 TATATATT
281583 ATATATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (28 bp):
TATATATTTTCAAAATGTTTTCAAAAAC
Found at i:281620 original size:64 final size:63
Alignment explanation
Indices: 281333--281625 Score: 332
Period size: 65 Copynumber: 4.6 Consensus size: 63
281323 ATTTTCAAAA
*
281333 ATATTTT-AAAACTATATATTATATATATAATTTTAAAAATGTTTTCAAAACTATATATTATAT
1 ATATTTTAAAAACTATATATTATATATAT-ATTTTCAAAATGTTTTCAAAACTATATATTATAT
* * *
281396 ATGTTTTCAAAACTATATA-T-TATATATGTTTTCAAAAATGTTTTCAAAACTATATATTATAT
1 ATATTTTAAAAACTATATATTATATATATATTTTC-AAAATGTTTTCAAAACTATATATTATAT
*
281458 A-AGTTTTCAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATCTTATA
1 ATA-TTTT-AAAAACTATATATTATATATATATTTTCAAAATGTTTTC-AAAACTATATATTATA
281522 T
63 T
* * * *
281523 ATATTTTCAAAA-TGT-T-TTCAAAAACTATATATTTTCAAAATGTTTTCAAAACTATTTATTAT
1 ATATTTTAAAAACTATATATT---ATA-TATATATTTTCAAAATGTTTTCAAAACTATATATTAT
281585 AT
62 AT
* * *
281587 ATATTTTAAAAAACTATTTATTATATGTGTA-TTTCAAAA
1 ATATTTT-AAAAACTATATATTATATATATATTTTCAAAA
281626 ACCATTTTTC
Statistics
Matches: 197, Mismatches: 17, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
61 6 0.03
62 41 0.21
63 28 0.14
64 55 0.28
65 61 0.31
66 3 0.02
67 1 0.01
68 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (63 bp):
ATATTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAACTATATATTATAT
Found at i:282156 original size:47 final size:47
Alignment explanation
Indices: 282087--282181 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
282077 CAGAGGCAGC
282087 TTTAAGTTTGGAAATGGAGGTGGCAACGTAAAAGCTGGTGAAAAGGG
1 TTTAAGTTTGGAAATGGAGGTGGCAACGTAAAAGCTGGTGAAAAGGG
282134 TTTAAGTTTGGAAATGGAGGTGGCAACGTAAAAGCTGGTGAAAAGGG
1 TTTAAGTTTGGAAATGGAGGTGGCAACGTAAAAGCTGGTGAAAAGGG
282181 T
1 T
282182 GTCGGACATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.06, G:0.36, T:0.24
Consensus pattern (47 bp):
TTTAAGTTTGGAAATGGAGGTGGCAACGTAAAAGCTGGTGAAAAGGG
Found at i:283421 original size:27 final size:26
Alignment explanation
Indices: 283391--283453 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
283381 GTATCTATTT
283391 TTAAAAAAAATGATGAACAA-ATAATTA
1 TTAAAAAAAAT-ATGAA-AATATAATTA
* *
283418 TTAAATAAATATATTAAAATATAATTA
1 TTAAA-AAAAATATGAAAATATAATTA
283445 TTAAAAAAA
1 TTAAAAAAA
283454 TCATTACACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 5 0.16
27 21 0.68
28 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAAAAAATATGAAAATATAATTA
Found at i:283446 original size:14 final size:14
Alignment explanation
Indices: 283411--283450 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
283401 TGATGAACAA
283411 ATAATTATT-AAAT
1 ATAATTATTAAAAT
283424 A-AATATATTAAAAT
1 ATAAT-TATTAAAAT
283438 ATAATTATTAAAA
1 ATAATTATTAAAA
283451 AAATCATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 5 0.21
14 13 0.54
15 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATTATTAAAAT
Found at i:283459 original size:15 final size:15
Alignment explanation
Indices: 283409--283459 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
283399 AATGATGAAC
*
283409 AAATAATTATTAAAT
1 AAATAATTATTAAAA
283424 AAAT-A-TATT-AAA
1 AAATAATTATTAAAA
*
283436 ATATAATTATTAAAA
1 AAATAATTATTAAAA
*
283451 AAATCATTA
1 AAATAATTA
283460 CACAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 5 0.17
15 14 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATTATTAAAA
Found at i:284686 original size:20 final size:18
Alignment explanation
Indices: 284644--284678 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
284634 AAAAATGATT
284644 TTCCCTCTCATTCTTCTC
1 TTCCCTCTCATTCTTCTC
284662 TTCCCTCTCA-TCTTCTC
1 TTCCCTCTCATTCTTCTC
284679 ATCTTCCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.06, C:0.46, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCCCTCTCATTCTTCTC
Found at i:284959 original size:22 final size:22
Alignment explanation
Indices: 284934--284981 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
284924 CTAAAGAGGC
284934 ACTAAAGTTCATCAATGGAGAA
1 ACTAAAGTTCATCAATGGAGAA
** *
284956 ACTATGGTTCATCACTGGAGAA
1 ACTAAAGTTCATCAATGGAGAA
284978 ACTA
1 ACTA
284982 TGGGTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (22 bp):
ACTAAAGTTCATCAATGGAGAA
Found at i:284982 original size:22 final size:21
Alignment explanation
Indices: 284940--285000 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
284930 AGGCACTAAA
284940 GTTCATCAATGGAGAAACTATG
1 GTTCATC-ATGGAGAAACTATG
284962 GTTCATCACTGGAGAAACTATG
1 GTTCATCA-TGGAGAAACTATG
* *
284984 GGTCATCATGGTGAAAC
1 GTTCATCATGGAGAAAC
285001 CATTATTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 9 0.25
22 27 0.75
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (21 bp):
GTTCATCATGGAGAAACTATG
Found at i:285021 original size:25 final size:24
Alignment explanation
Indices: 284988--285036 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
284978 ACTATGGGTC
284988 ATCATGGTGAAACCATTATTCTTT
1 ATCATGGTGAAACCATTATTCTTT
285012 ATCACTGGTGAAACCATTATTCTTT
1 ATCA-TGGTGAAACCATTATTCTTT
285037 CTTTGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (24 bp):
ATCATGGTGAAACCATTATTCTTT
Found at i:285684 original size:15 final size:15
Alignment explanation
Indices: 285664--285695 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
285654 GGAATGTTGC
*
285664 AGAGTGACGAGGAAG
1 AGAGTGAAGAGGAAG
285679 AGAGTGAAGAGGAAG
1 AGAGTGAAGAGGAAG
285694 AG
1 AG
285696 GAAGAGGGGG
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:0.44, C:0.03, G:0.47, T:0.06
Consensus pattern (15 bp):
AGAGTGAAGAGGAAG
Found at i:285888 original size:29 final size:29
Alignment explanation
Indices: 285831--285888 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
285821 TTACGAAATG
* * * *
285831 AAATGTTAGGCATCAAATTAAAACGAAAA
1 AAATGCTAGACATCAAACTAAAACAAAAA
*
285860 AAATGCTAGACATCAAACTAAAATAAAAA
1 AAATGCTAGACATCAAACTAAAACAAAAA
285889 GGCATACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (29 bp):
AAATGCTAGACATCAAACTAAAACAAAAA
Found at i:287705 original size:130 final size:130
Alignment explanation
Indices: 287472--287738 Score: 473
Period size: 130 Copynumber: 2.1 Consensus size: 130
287462 AATATGATTA
*
287472 GGTGCTCATATGCGAGTCACTCTAATCCTTTGAGGCTCTTGTACGAGTAATTCTAATCCTCCAAT
1 GGTGCTCATATGCGAGTCACTCTAATCCTTTGAGACTCTTGTACGAGTAATTCTAATCCTCCAAT
*
287537 ACTCCCATATGAATCACCTAGAATAAATATGATTAGGTGTTCCCATGCGAGTCATCTAATCCTTT
66 ACTCCCATATGAATCACCCAGAATAAATATGATTAGGTGTTCCCATGCGAGTCATCTAATCCTTT
*
287602 GGTGCTCATATGCGAGTCACTCTAAT-CTTTCGAGACTCTTGTATGAGTAATTCTAATCCTCCAA
1 GGTGCTCATATGCGAGTCACTCTAATCCTTT-GAGACTCTTGTACGAGTAATTCTAATCCTCCAA
*
287666 TACTCCCATATGAATCACCCAGAATAAATATGATTAGGTGTTCCCATGCGAGTTATCTAATCCTT
65 TACTCCCATATGAATCACCCAGAATAAATATGATTAGGTGTTCCCATGCGAGTCATCTAATCCTT
287731 T
130 T
*
287732 GGGGCTC
1 GGTGCTC
287739 CTACACCAGT
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
129 4 0.03
130 127 0.97
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (130 bp):
GGTGCTCATATGCGAGTCACTCTAATCCTTTGAGACTCTTGTACGAGTAATTCTAATCCTCCAAT
ACTCCCATATGAATCACCCAGAATAAATATGATTAGGTGTTCCCATGCGAGTCATCTAATCCTTT
Found at i:288132 original size:13 final size:12
Alignment explanation
Indices: 288101--288134 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
288091 TTTTAATATT
*
288101 TATCGGGTCGGG
1 TATCGGGGCGGG
288113 TATCGGGGCGGG
1 TATCGGGGCGGG
288125 TAATCGGGGC
1 T-ATCGGGGC
288135 AGGGATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.12, C:0.18, G:0.50, T:0.21
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:288399 original size:69 final size:69
Alignment explanation
Indices: 288288--288417 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 69
288278 TCCTTAGTCC
* ** * *
288288 CGTGCGAGTCACTCTAATACTTCGGGACTTCTGTGCGAGTCACCCTAAATAAATATGATTAGGTG
1 CGTGCGAGTCACTCTAATACTTCGGGACTCCCATGAGAGTCACCCAAAATAAATATGATTAGGTG
288353 CTCT
66 CTCT
* * * *
288357 CGTGCGATTCACTCTAATCCTTTGGGGCTCCCATGAGAGTCACCCAAAATAAATATGATTA
1 CGTGCGAGTCACTCTAATACTTCGGGACTCCCATGAGAGTCACCCAAAATAAATATGATTA
288418 TATATCTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (69 bp):
CGTGCGAGTCACTCTAATACTTCGGGACTCCCATGAGAGTCACCCAAAATAAATATGATTAGGTG
CTCT
Found at i:288548 original size:26 final size:25
Alignment explanation
Indices: 288516--288700 Score: 90
Period size: 26 Copynumber: 7.3 Consensus size: 25
288506 TAGCACATGT
288516 CATAACACATATTTCCAGCAGTGAAA
1 CATAACACATA-TTCCAGCAGTGAAA
* * * ** * *
288542 CTTAACATAGACTTATACCAATGAAA
1 CATAACACATA-TTCCAGCAGTGAAA
* *
288568 -TTAACACTTGATTCCAGCAGTGAAA
1 CATAACACAT-ATTCCAGCAGTGAAA
* * * *
288593 CATAACATAGAATTACACCAGTGAAA
1 CATAACACA-TATTCCAGCAGTGAAA
*
288619 -ATAACACTTAGTTCCAGCAGTGAAA
1 CATAACACATA-TTCCAGCAGTGAAA
* * * *
288644 CATAACATAGACTTACA-CGGTGAAA
1 CATAACACATA-TTCCAGCAGTGAAA
* *
288669 -ATAACACTTAATTCCAACAGTGAAA
1 CATAACACAT-ATTCCAGCAGTGAAA
*
288694 TATAACA
1 CATAACA
288701 TAGACTTACA
Statistics
Matches: 114, Mismatches: 37, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
24 11 0.10
25 49 0.43
26 54 0.47
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (25 bp):
CATAACACATATTCCAGCAGTGAAA
Found at i:288583 original size:51 final size:51
Alignment explanation
Indices: 288517--289018 Score: 587
Period size: 51 Copynumber: 9.9 Consensus size: 51
288507 AGCACATGTC
* * * * *
288517 ATAACACATATTTCCAGCAGTGAAACTTAACATAGACTTATACCAATGAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * *
288568 TTAACACTTGATTCCAGCAGTGAAACATAACATAGAATTACACCAGTGAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* *
288619 ATAACACTTAGTTCCAGCAGTGAAACATAACATAGACTTACA-CGGTGAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * *
288669 ATAACACTTAATTCCAACAGTGAAATATAACATAGACTTACACCAGGGAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * * * * *
288720 ATAGCACTCAGTTCCATCAGTGAAATAGAACATAGACTTACACC-GAT-AAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAG-TGAAA
* ** * * ** *
288770 AGTAACACATAATTCCAATAGTGAAACATAACATATACTTATACGGGCGAAA
1 A-TAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
*
288822 ATAACACTTAATTCCAGCTGTGAAACATAACATAGACTTACACCAGTGAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * *** *
288873 ATAACACTTAATTCCAGTATTGAAACATAACATAGACTTACAATGGTTAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * * *
288924 ATAACATTTAATTCCAGTAGTGAAACATAACATAGACTTACACCGGTAAAA
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
* * * *
288975 ATAATACTTAATTCTAGTAGTGAGACATAACATAGACTTACACC
1 ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACC
289019 TATCAAATGG
Statistics
Matches: 385, Mismatches: 61, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
50 51 0.13
51 329 0.85
52 5 0.01
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (51 bp):
ATAACACTTAATTCCAGCAGTGAAACATAACATAGACTTACACCAGTGAAA
Found at i:288591 original size:25 final size:25
Alignment explanation
Indices: 288528--288962 Score: 153
Period size: 25 Copynumber: 17.1 Consensus size: 25
288518 TAACACATAT
*
288528 TTCCAGCAGTGAAACTTAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
** * * * *
288554 TTATACCAATGAAATTAACACTTGA-
1 TTCCAGCAGTGAAAATAACA-TAGAC
*
288579 TTCCAGCAGTGAAACATAACATAGAA
1 TTCCAGCAGTGAAA-ATAACATAGAC
* *
288605 TTACACCAGTGAAAATAACACTTAG--
1 TTCCAGCAGTGAAAATAACA--TAGAC
288630 TTCCAGCAGTGAAACATAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
* *
288656 TTACA-CGGTGAAAATAACACTTA-A-
1 TTCCAGCAGTGAAAATAACA--TAGAC
*
288680 TTCCAACAGTGAAATATAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
* * * *
288706 TTACACCAGGGAAAATAGCACTCAG--
1 TTCCAGCAGTGAAAATAACA-T-AGAC
* *
288731 TTCCATCAGTGAAATAGAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
* * * * *
288757 TTACA-CCGAT-AAAAGTAACACATAA
1 TTCCAGCAG-TGAAAA-TAACATAGAC
** *
288782 TTCCAATAGTGAAACATAACATATAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
** * *
288808 TTATA-CGGGCGAAAATAACACTTA-A-
1 TTCCAGC-AGTGAAAATAACA--TAGAC
*
288833 TTCCAGCTGTGAAACATAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
* *
288859 TTACACCAGTGAAAATAACACTTA-A-
1 TTCCAGCAGTGAAAATAACA--TAGAC
* *
288884 TTCCAGTATTGAAACATAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
* *** * ** *
288910 TTACAATGGTTAAAATAACATTTAA
1 TTCCAGCAGTGAAAATAACATAGAC
*
288935 TTCCAGTAGTGAAACATAACATAGAC
1 TTCCAGCAGTGAAA-ATAACATAGAC
288961 TT
1 TT
288963 ACACCGGTAA
Statistics
Matches: 302, Mismatches: 70, Indels: 74
0.68 0.16 0.17
Matches are distributed among these distances:
24 22 0.07
25 136 0.45
26 134 0.44
27 10 0.03
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (25 bp):
TTCCAGCAGTGAAAATAACATAGAC
Found at i:288802 original size:26 final size:26
Alignment explanation
Indices: 288772--288957 Score: 105
Period size: 26 Copynumber: 7.3 Consensus size: 26
288762 CCGATAAAAG
* *
288772 TAACACATAATTCCAATAGTGAAACA
1 TAACATATAATTCCACTAGTGAAACA
* ** ** *
288798 TAACATATACTTATACGGGCGAAA-A
1 TAACATATAATTCCACTAGTGAAACA
288823 TAACACT-TAATTCCAGCT-GTGAAACA
1 TAACA-TATAATTCCA-CTAGTGAAACA
* * * *
288849 TAACATAGACTTACACCAGTGAAA-A
1 TAACATATAATTCCACTAGTGAAACA
* *
288874 TAACACT-TAATTCCAGTATTGAAACA
1 TAACA-TATAATTCCACTAGTGAAACA
* * * * * *
288900 TAACATAGACTTACAATGGTTAAA-A
1 TAACATATAATTCCACTAGTGAAACA
* *
288925 TAACATTTAATTCCAGTAGTGAAACA
1 TAACATATAATTCCACTAGTGAAACA
288951 TAACATA
1 TAACATA
288958 GACTTACACC
Statistics
Matches: 113, Mismatches: 38, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
25 54 0.48
26 59 0.52
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (26 bp):
TAACATATAATTCCACTAGTGAAACA
Found at i:289457 original size:3 final size:3
Alignment explanation
Indices: 289449--289486 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
289439 TTTTCATTTG
289449 ATT ATT ATT -TAT ATT ATAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT A
289487 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:289465 original size:9 final size:10
Alignment explanation
Indices: 289444--289485 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
289434 ACTCTTTTTC
289444 ATTTGATTATT
1 ATTT-ATTATT
289455 ATTTA-TATT
1 ATTTATTATT
*
289464 ATATATTATT
1 ATTTATTATT
289474 A-TTATTATT
1 ATTTATTATT
289483 ATT
1 ATT
289486 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 16 0.59
10 7 0.26
11 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTATTATT
Found at i:291047 original size:16 final size:16
Alignment explanation
Indices: 291008--291054 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
290998 CAATTTTCTG
*
291008 ATAT-TTTTAAATAAAT
1 ATATATTTTAAAT-TAT
*
291024 AAATATTTTAAATTAT
1 ATATATTTTAAATTAT
291040 ATATATTTT-AATTAT
1 ATATATTTTAAATTAT
291055 TTTTAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTAAATTAT
Found at i:300600 original size:18 final size:18
Alignment explanation
Indices: 300579--300613 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
300569 AAAACCCCAG
*
300579 GGGGTATCGATTCCCCTA
1 GGGGAATCGATTCCCCTA
*
300597 GGGGAATCGGTTCCCCT
1 GGGGAATCGATTCCCCT
300614 TCAAAGGGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.26
Consensus pattern (18 bp):
GGGGAATCGATTCCCCTA
Found at i:300642 original size:22 final size:23
Alignment explanation
Indices: 300597--300655 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
300587 GATTCCCCTA
300597 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTCAAAG
300620 GGGGAATCGGTTCCCCTTC-AAG
1 GGGGAATCGGTTCCCCTTCAAAG
* *
300642 GGGGTATCGATTCC
1 GGGGAATCGGTTCC
300656 TTCAGCCCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAG
Found at i:304509 original size:22 final size:21
Alignment explanation
Indices: 304467--304506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
304457 GAGTTTATTT
*
304467 TCATTTTTAAATTTTGAAATA
1 TCATTTTTAAATTTTAAAATA
*
304488 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
304507 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAATA
Found at i:304513 original size:20 final size:21
Alignment explanation
Indices: 304469--304513 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
304459 GTTTATTTTC
* *
304469 ATTTTTAAATTTTGAAATATC
1 ATTTTTAAATTTTGAAAAATA
*
304490 ATTTTTATATTTT-AAAAATA
1 ATTTTTAAATTTTGAAAAATA
304510 ATTT
1 ATTT
304514 CTCATAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAAATTTTGAAAAATA
Found at i:311323 original size:7 final size:7
Alignment explanation
Indices: 311297--311343 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
311287 TGCTTGAAGA
311297 AAAAAAT
1 AAAAAAT
*
311304 GAAAAAT
1 AAAAAAT
*
311311 GAAAAAT
1 AAAAAAT
311318 AAAAAA-
1 AAAAAAT
311324 AAAAAA-
1 AAAAAAT
*
311330 AAAAAAA
1 AAAAAAT
311337 AAAAAAT
1 AAAAAAT
311344 GAAATGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 12 0.33
7 24 0.67
ACGTcount: A:0.87, C:0.00, G:0.04, T:0.09
Consensus pattern (7 bp):
AAAAAAT
Found at i:311359 original size:1 final size:1
Alignment explanation
Indices: 311312--311342 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
311302 ATGAAAAATG
*
311312 AAAAATAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
311343 TGAAATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:311751 original size:18 final size:18
Alignment explanation
Indices: 311725--311762 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
311715 CAAGATTATC
*
311725 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
311743 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
311761 TT
1 TT
311763 CTTTCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:313149 original size:112 final size:112
Alignment explanation
Indices: 312954--313605 Score: 544
Period size: 112 Copynumber: 5.7 Consensus size: 112
312944 ATTCCCAAAG
* * * * *
312954 AAGTTCGTAATGCGAAGAACTCATCTGAAGA--AGGAAGAAG--CATAATGAGAAGAATTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
313015 AACCTTTTGTTCA--AAT-TCATCACTAGATGAATCAACTTTTCCAGAGA
66 AACCTTTTG--CATGAATCT-ATCACTAGATGAATCAAATTTTCCAGAGA
* * *
313062 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAGCATGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
313127 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCATCATCAACTTTTCCAGAGA
66 AACCTTTTGCATGAATCTATCAC-----TAGAT-GA--ATCA--AA-TTTTCCAGAGA
* * * * *
313185 AAGTTCATAATGAGAATAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTG-AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * *
313250 CAAACCTTTTGTTTGAAT-TCATCACTCGATGGATCAAAATTTT-CAGAGG
65 C-AACCTTTTGCATGAATCT-ATCACTAGATGAATC-AAATTTTCCAGAGA
313299 AAGTTCATAATGAGAAGAA-TTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGTTCATAATGAGAAGAACTT-ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* ** * * *
313363 TTAACCTTTTGTTTGAATTTATCATTCGATTG-ATCAAATTTTCCAGAGA
64 TCAACCTTTTGCATGAATCTATCACTAGA-TGAATCAAATTTTCCAGAGA
*
313412 AAGTTCGTAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
** * *
313477 AACC-TTTGTTTGATTCTATCACAGAAGGAGATAGATCAGTATCAACA-TTTCCAGA-A
66 AACCTTTTGCATGAATCTATCAC---------TAGAT--GAATCAA-ATTTTCCAGAGA
* * * *
313533 GTA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AATAAGTTCATAATGAGAAGAATTTGT
1 -AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
313596 TCAACTTTTT
64 TCAACCTTTT
313606 CTTAATTCAT
Statistics
Matches: 454, Mismatches: 46, Indels: 74
0.79 0.08 0.13
Matches are distributed among these distances:
108 28 0.06
110 9 0.02
111 15 0.03
112 79 0.17
113 62 0.14
114 65 0.14
115 4 0.01
116 2 0.00
117 7 0.02
118 3 0.01
119 2 0.00
120 10 0.02
121 57 0.13
122 23 0.05
123 37 0.08
124 33 0.07
125 18 0.04
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCATGAATCTATCACTAGATGAATCAAATTTTCCAGAGA
Found at i:313354 original size:24 final size:23
Alignment explanation
Indices: 313311--313355 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
313301 GTTCATAATG
*
313311 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
313334 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
313356 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:313428 original size:113 final size:113
Alignment explanation
Indices: 313168--313498 Score: 474
Period size: 114 Copynumber: 2.9 Consensus size: 113
313158 ATAGATCATC
* * * * *
313168 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAAAAGGAAGAAGAAATTCAT
1 ATCAAATTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
313233 AATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCACTCGATGG
66 AATGAGAAGAACTTGTT-AAACCTTTTGTTTGAATTTATCACTCGATGG
*
313282 ATCAAAATTTT-CAGAGGAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATC-AAATTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
313346 TAATGAGAAGAACTTGTTTAACCTTTTGTTTGAATTTATCATTCGATTG
65 TAATGAGAAGAACTTGTTAAACCTTTTGTTTGAATTTATCACTCGATGG
*
313395 ATCAAATTTTCCAGAGAAAGTTCGTAATGAGAAGAACTT-ATCTGAAG-AGGAAGAAGAAGTTCA
1 ATCAAATTTTCCAGAGAAAGTTCATAATGAGAAGAA-TTCATCTGAAGAAGGAAGAAGAAGTTCA
*
313458 TAATGAGAAGAACTTGTTCAACC-TTTGTTTG-ATTCTATCAC
65 TAATGAGAAGAACTTGTTAAACCTTTTGTTTGAATT-TATCAC
313499 AGAAGGAGAT
Statistics
Matches: 198, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
110 3 0.02
111 13 0.07
112 45 0.23
113 61 0.31
114 70 0.35
115 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (113 bp):
ATCAAATTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTAAACCTTTTGTTTGAATTTATCACTCGATGG
Found at i:313959 original size:9 final size:10
Alignment explanation
Indices: 313940--313981 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
313930 CATTTTTTTC
313940 ATTTGATTATT
1 ATTT-ATTATT
313951 ATTTA-TATT
1 ATTTATTATT
*
313960 ATATATTATT
1 ATTTATTATT
313970 A-TTATTATT
1 ATTTATTATT
313979 ATT
1 ATT
313982 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 16 0.59
10 7 0.26
11 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTATTATT
Found at i:313995 original size:3 final size:3
Alignment explanation
Indices: 313945--313982 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
313935 TTTTCATTTG
313945 ATT ATT ATT -TAT ATT ATAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT A
313983 AAAAATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:315348 original size:16 final size:16
Alignment explanation
Indices: 315309--315355 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
315299 CTATTTTTTG
*
315309 ATAT-TTTTAAATAAAT
1 ATATATTTTAAAT-TAT
*
315325 AAATATTTTAAATTAT
1 ATATATTTTAAATTAT
315341 ATATATTTT-AATTAT
1 ATATATTTTAAATTAT
315356 TTTTAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTAAATTAT
Found at i:316786 original size:17 final size:15
Alignment explanation
Indices: 316730--316791 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 15
316720 TTACCCATTT
*
316730 TTATTATTATT--TT
1 TTATTATTATTAATA
*
316743 TTATAATTA-TAATA
1 TTATTATTATTAATA
316757 TTATTATTATTAATA
1 TTATTATTATTAATA
316772 TATATTATTTATTAATA
1 T-TATTA-TTATTAATA
316789 TTA
1 TTA
316792 CAAAACCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.02
13 8 0.20
14 9 0.22
15 6 0.15
16 7 0.17
17 10 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:331035 original size:83 final size:83
Alignment explanation
Indices: 330760--331141 Score: 662
Period size: 83 Copynumber: 4.6 Consensus size: 83
330750 AACAAATGCC
* * * *
330760 ATGTGCACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
* *
330825 ATT-AGTTTTGAAGAGGA
66 ATTGAATTTGGAAGAGGA
330842 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGT-AAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
330905 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
330923 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
330988 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
331006 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
331071 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* * *
331089 ATGTGCTCATAGAATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
331142 ATATAAAACC
Statistics
Matches: 288, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
80 9 0.03
81 66 0.23
82 53 0.18
83 160 0.56
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGA
Found at i:331512 original size:25 final size:25
Alignment explanation
Indices: 331477--331526 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
331467 CATCAGAATC
331477 AGAATTCAAGATTTCTCGGTATTAAA
1 AGAATTCAAGATTTCTC-GTATTAAA
331503 AGAA-TCAAGATTTCTCGTATTAAA
1 AGAATTCAAGATTTCTCGTATTAAA
331527 GAACTATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.33
25 12 0.50
26 4 0.17
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (25 bp):
AGAATTCAAGATTTCTCGTATTAAA
Found at i:332269 original size:218 final size:216
Alignment explanation
Indices: 331885--332521 Score: 696
Period size: 218 Copynumber: 2.9 Consensus size: 216
331875 TAGCAAAGAT
* * *
331885 TCAAATCC-TCATTTGATGGATCA---TTTCCAGGTAGAGTCATAATGAGAAGAACTCGTCA-TC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGT--TCAT-A-AAGAACTCATTACTC
* **
331945 TGAAAGAGAAGAAGAAATTCATATGAGAAGAATTTT-TTCAACTTTTTGCTTGAATCCATCACTT
62 TG-AAGAGAAGAAGAAATTCATAT--G-AGAATTTTGTTCAACCTTTTGCTCAAATCC-TCACTT
*
332009 GATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAT
122 GATGGATT-ACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCAT-TGAAGAAGGAAGAAGAAT
*
332074 TCATAATGA-AAGAATTTGTTCAACCTTTTGC
185 TCATAATGAGAAGAATTTGTTCAACCTTATGC
332105 TCAAATCCATCATTTGATGGATCAGCTTTTTCCAGGTAGAGTTCATAAAGAACTCATTACT-TGA
1 TCAAATCCATCATTTGATGGATCAGC-TTTTCCAGGTAGAGTTCATAAAGAACTCATTACTCTGA
332169 ATGAGAAGAAGAAATTCATAATGAGAATTTTGTTCAACCTTTTGCTCAAATCCTCACTTGATGGA
65 A-GAGAAGAAGAAATTCAT-ATGAGAATTTTGTTCAACCTTTTGCTCAAATCCTCACTTGATGGA
332234 TTACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCA-TGAA-AA-GAAGAAGAATTCATAATG
128 TTACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATTGAAGAAGGAAGAAGAATTCATAATG
332296 AAAGAAGAATTTGTTCAACCTTATGC
193 --AGAAGAATTTGTTCAACCTTATGC
* * * **
332322 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAA-GAATT-CATCT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAA--AGAACTCATTAC-TCT
* * ** * * *
332385 GAAGA-AGGAAAAAAGTTCATATGAGAAGAACTTGTTTAACCTTTTGTTCAAATTCATCACTTGA
63 GAAGAGAAGAAGAAA-TTCATATGAG-A-ATTTTGTTCAACCTTTTGCTCAAA-TCCTCACTTGA
* * *
332449 TGGATCAACATTT-CCAGAGAAAGTTCATAAT-AAAAGAACTTATTTGAAG-AGGAAGAAGAAGT
124 TGGAT-TAC-TTTGCCAGAGAAAGTTCATAATGAGAAGAACTCA-TTGAAGAAGGAAGAAGAA-T
*
332511 TCACAATGAGA
185 TCATAATGAGA
332522 GCTTGTTCAC
Statistics
Matches: 366, Mismatches: 24, Indels: 53
0.83 0.05 0.12
Matches are distributed among these distances:
214 17 0.05
215 2 0.01
216 37 0.10
217 58 0.16
218 64 0.17
219 46 0.13
220 49 0.13
221 55 0.15
222 13 0.04
223 11 0.03
225 14 0.04
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (216 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAAAGAACTCATTACTCTGAA
GAGAAGAAGAAATTCATATGAGAATTTTGTTCAACCTTTTGCTCAAATCCTCACTTGATGGATTA
CTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATTGAAGAAGGAAGAAGAATTCATAATGAGA
AGAATTTGTTCAACCTTATGC
Found at i:332511 original size:110 final size:110
Alignment explanation
Indices: 331885--332521 Score: 597
Period size: 110 Copynumber: 5.8 Consensus size: 110
331875 TAGCAAAGAT
* *
331885 TCAAATCC-TCATTTGATGGATC-A-TTTCCAG-GTAGAG-TCATAATGAGAAGAACTCGTCATC
1 TCAAATCCATCACTTGATGGATCAACTTTCCAGAG-AAAGTTCATAATGAGAAGAACT--T-ATC
* *
331945 TGAA-AGAGAAGAAGAAATTCAT-ATGAGAAGAATTTTTTCAACTTTTTGC
62 TGAAGAG-GAAGAAG-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * *
331994 TTGAATCCATCACTTGATGGATTAACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTT-CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
*
332059 AGAAGGAATAAGAATTCATAATGA-AAGAATTTGTTCAACCTTTTGC
65 AG-AGGAAGAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * **
332105 TCAAATCCATCATTTGATGGATCAGCTTTTTCCAG-GTAGAGTTCATAA--AGAA-CTCATTA-C
1 TCAAATCCATCACTTGATGGATCAAC--TTTCCAGAG-AAAGTTCATAATGAGAAGAAC-TTATC
*
332165 TTGAATGA-GAAGAAGAAATTCATAATGAG-A-ATTTTGTTCAACCTTTTGC
62 -TGAA-GAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
332214 TCAAATCC-TCACTTGATGGAT-TACTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCA--TGA
1 TCAAATCCATCACTTGATGGATCAACTTT-CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
* *
332275 A-AAGAAGAAGAATTCATAATGAAAGAAGAATTTGTTCAACCTTATGC
65 AGAGGAAGAAGAATTCATAATG--AGAAGAATTTGTTCAACCTTTTGC
* ****
332322 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAAC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTT-ATCTG
* * *
332386 AAGAAGGAA-AA-AAGTTCAT-ATGAGAAGAACTTGTTTAACCTTTTGT
64 AAG-AGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
332432 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAAT-AAAAGAACTTATTTGA
1 TCAAATCCATCACTTGATGGATCAAC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
*
332496 AGAGGAAGAAGAAGTTCACAATGAGA
65 AGAGGAAGAAGAA-TTCATAATGAGA
332522 GCTTGTTCAC
Statistics
Matches: 437, Mismatches: 51, Indels: 78
0.77 0.09 0.14
Matches are distributed among these distances:
104 12 0.03
105 10 0.02
106 20 0.05
107 3 0.01
108 48 0.11
109 70 0.16
110 130 0.30
111 67 0.15
112 36 0.08
113 19 0.04
114 22 0.05
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (110 bp):
TCAAATCCATCACTTGATGGATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA
GAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:332763 original size:3 final size:3
Alignment explanation
Indices: 332757--332813 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
332747 TACCCATTTT
*
332757 TTA TTA TT- TT- TTA TAA TTA TTA -TA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
332800 TT- TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA
332814 CAAAACCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 8 0.17
3 35 0.76
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:332782 original size:21 final size:24
Alignment explanation
Indices: 332758--332813 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
332748 ACCCATTTTT
332758 TATTATT-TT-TTATA-ATTATTA
1 TATTATTATTATTATATATTATTA
*
332779 TATTATTATTATTATATATTATTT
1 TATTATTATTATTATATATTATTA
*
332803 TATTAATATTA
1 TATTATTATTA
332814 CAAAACCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 7 0.23
22 2 0.07
23 5 0.17
24 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATTATTATTATATATTATTA
Found at i:335134 original size:2 final size:2
Alignment explanation
Indices: 335122--335154 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
335112 ATTTTCGTCC
*
335122 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
335155 GTTTACAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:335223 original size:37 final size:35
Alignment explanation
Indices: 335182--335477 Score: 203
Period size: 36 Copynumber: 8.5 Consensus size: 35
335172 TAAAAATACG
335182 TATATAATATATAGTTTTTAAAAAATATTTTTGAAAATA
1 TATATAATATATAGTTTTT--AAAATATTTTTG-AAA-A
*
335221 TATATAATATATAGTTTTTAAAACATTTTTGAAAA
1 TATATAATATATAGTTTTTAAAATATTTTTGAAAA
* *
335256 CTATATAATATAAAGTTTTTAAAACA-TTTT----A
1 -TATATAATATATAGTTTTTAAAATATTTTTGAAAA
* *
335287 GA-A-AATATATAGTTTTTAAAATCA--TTTGATAACT
1 TATATAATATATAGTTTTTAAAAT-ATTTTTGA-AA-A
* *
335321 TATATAATATATAGTTTTGAAAACATTTTTTGAAAA
1 TATATAATATATAGTTTTTAAAATA-TTTTTGAAAA
335357 CTTATATAATAT-T--TTTTT-AAATCATTTTTGAAAA
1 --TATATAATATATAGTTTTTAAAAT-ATTTTTGAAAA
* ** **
335391 CTATATACTATATAG-TTTTGGAAT-TTTTTTTAAA
1 -TATATAATATATAGTTTTTAAAATATTTTTGAAAA
* *
335425 -ATATAATATATAATTTTAAAAAATATTTTTGAAATA
1 TATATAATATATAGTTTT-TAAAATATTTTTGAAA-A
*
335461 TATATATTATATA-TTTT
1 TATATAATATATAGTTTT
335478 AGAATATATA
Statistics
Matches: 207, Mismatches: 25, Indels: 53
0.73 0.09 0.19
Matches are distributed among these distances:
28 20 0.10
29 2 0.01
30 1 0.00
31 1 0.00
32 11 0.05
33 12 0.06
34 26 0.13
35 23 0.11
36 52 0.25
37 25 0.12
38 15 0.07
39 19 0.09
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAATATTTTTGAAAA
Found at i:335273 original size:36 final size:36
Alignment explanation
Indices: 335182--335409 Score: 230
Period size: 36 Copynumber: 6.5 Consensus size: 36
335172 TAAAAATACG
* *
335182 TATATAATATATAGTTTTTAAAAAATATTTTTGAAAATA
1 TATATAATATATAGTTTTT--AAAACATTTTTGAAAA-C
335221 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
*
335257 TATATAATATAAAGTTTTTAAAACA-TTTT----A-
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
* *
335287 GA-A-AATATATAGTTTTTAAAATCA--TTTGATAAC
1 TATATAATATATAGTTTTTAAAA-CATTTTTGAAAAC
*
335320 TTATATAATATATAGTTTTGAAAACATTTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAACA-TTTTTGAAAAC
*
335358 TTATATAATAT-T--TTTTTAAATCATTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
*
335392 TATATACTATATAGTTTT
1 TATATAATATATAGTTTT
335410 GGAATTTTTT
Statistics
Matches: 163, Mismatches: 11, Indels: 33
0.79 0.05 0.16
Matches are distributed among these distances:
28 20 0.12
29 3 0.02
30 1 0.01
31 1 0.01
32 1 0.01
33 9 0.06
34 13 0.08
35 16 0.10
36 45 0.28
37 16 0.10
38 19 0.12
39 19 0.12
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAC
Found at i:335299 original size:64 final size:66
Alignment explanation
Indices: 335226--335477 Score: 219
Period size: 64 Copynumber: 3.7 Consensus size: 66
335216 AAATATATAT
* *
335226 AATATATAGTTTTTAAAACATTTTTGAAAACTATATAATATAAAGTTTTTAAAACA-TTTTAG-A
1 AATATATAGTTTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTTTAGAA
335289 A
66 A
* *
335290 AATATATAGTTTTTAAAATCA--TTTGATAACTTATATAATATATAGTTTTGAAAACATTTTTTG
1 AATATATAGTTTTTAAAA-CATTTTTGAAAAC-TATATAATATATAGTTTTGAAAACATTTTTAG
335353 AAA
64 AAA
* * * * ***
335356 ACTTATATAATATTTTTTTAAATCATTTTTGAAAACTATATACTATATAGTTTTGGAATTTTTTT
1 A---ATAT-ATA-GTTTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTT
*
335421 TAAAATA
61 TAGAA-A
* * * *
335428 TAATATATAATTTTAAAAAATATTTTTGAAATA-TATATATTATATA-TTTT
1 -AATATATAGTTTT-TAAAACATTTTTGAAA-ACTATATAATATATAGTTTT
335478 AGAATATATA
Statistics
Matches: 154, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
63 8 0.05
64 41 0.27
65 7 0.05
66 3 0.02
68 8 0.05
69 32 0.21
70 10 0.06
71 35 0.23
72 9 0.06
73 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (66 bp):
AATATATAGTTTTTAAAACATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTTTAGAA
A
Found at i:335344 original size:100 final size:100
Alignment explanation
Indices: 335187--335397 Score: 270
Period size: 100 Copynumber: 2.1 Consensus size: 100
335177 ATACGTATAT
*
335187 AATATATAGTTTTTAAAAAATATTTTTGAAAATATATATAATATATAGTTTTTAAAACA-TTTTT
1 AATATATAGTTTTT-AAAAATA-TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTT
335251 GAAAAC-TATATAATATAAAGTTTTTAAAACATTTTAGAA
64 GAAAACTTATATAATAT---GTTTTTAAAACATTTTAGAA
*
335290 AATATATAGTTTTT-AAAATCA-TTTGATAACT-TATATAATATATAGTTTTGAAAACATTTTTT
1 AATATATAGTTTTTAAAAAT-ATTTTGA-AAATATATATAATATATAGTTTTGAAAACATTTTTT
* * *
335352 GAAAACTTATATAATATTTTTTTAAATCATTTTTGAA
64 GAAAACTTATATAATATGTTTTTAAAACATTTTAGAA
335389 AACTATATA
1 AA-TATATA
335398 CTATATAGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
99 19 0.19
100 35 0.36
101 19 0.19
102 11 0.11
103 14 0.14
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (100 bp):
AATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTTGA
AAACTTATATAATATGTTTTTAAAACATTTTAGAA
Found at i:335421 original size:71 final size:69
Alignment explanation
Indices: 335182--335410 Score: 213
Period size: 64 Copynumber: 3.3 Consensus size: 69
335172 TAAAAATACG
* * *
335182 TATATAATATATAGTTTTTAAAAAATATTTTTGAAAATATATATAATATATAGTTTTTAAAA-CA
1 TATATAATATATAGTTTTGAAAACAT-TTTTTG-AAA-A-CT-T-ATATATAGTTTTTAAAATCA
335246 TTTTTGAAAAC-
60 --TTTGAAAACT
* * * *
335257 TATATAATATAAAGTTTTTAAAACA-TTTTAG-AAA---ATATATAGTTTTTAAAATCATTTGAT
1 TATATAATATATAGTTTTGAAAACATTTTTTGAAAACTTATATATAGTTTTTAAAATCATTTGAA
335317 AACT
66 AACT
* *
335321 TATATAATATATAGTTTTGAAAACATTTTTTGAAAACTTATATAATATTTTTTTAAATCATTTTT
1 TATATAATATATAGTTTTGAAAACATTTTTTGAAAACTTATAT-ATAGTTTTTAAAATCA--TTT
335386 GAAAAC-
63 GAAAACT
*
335392 TATATACTATATAGTTTTG
1 TATATAATATATAGTTTTG
335411 GAATTTTTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
63 8 0.06
64 40 0.30
65 7 0.05
66 3 0.02
69 4 0.03
70 15 0.11
71 20 0.15
72 8 0.06
73 5 0.04
75 23 0.17
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (69 bp):
TATATAATATATAGTTTTGAAAACATTTTTTGAAAACTTATATATAGTTTTTAAAATCATTTGAA
AACT
Found at i:335484 original size:34 final size:32
Alignment explanation
Indices: 335347--335484 Score: 102
Period size: 34 Copynumber: 4.0 Consensus size: 32
335337 TTGAAAACAT
*
335347 TTTTTGAAAACT-TATATAATATTTTTTTA-AATCA
1 TTTTTGAAAA-TATATAT-ATA-TATTTTAGAAT-A
* *
335381 TTTTTGAAAACTATATACTATATAGTTTTGGAATT
1 TTTTTGAAAA-TATATA-TATATA-TTTTAGAATA
* *
335416 TTTTTTAAAATATA-ATATATAATTTTAAAAAATA
1 TTTTTGAAAATATATATATAT-ATTTT--AGAATA
335450 TTTTTGAAATATATATATTATATATTTTAGAATA
1 TTTTTGAAA-ATATATA-TATATATTTTAGAATA
335484 T
1 T
335485 ATATATTATT
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
32 9 0.11
33 2 0.02
34 34 0.40
35 25 0.29
36 10 0.12
37 5 0.06
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTTTGAAAATATATATATATATTTTAGAATA
Found at i:335496 original size:3 final size:3
Alignment explanation
Indices: 335488--335537 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
335478 AGAATATATA
* *
335488 TAT TAT TAT TAT TAT TAT TACT TTT TAT TAT CTTT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT
335536 TA
1 TA
335538 ATTCCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 33 0.82
4 7 0.17
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:335500 original size:25 final size:24
Alignment explanation
Indices: 335447--335497 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
335437 ATTTTAAAAA
*
335447 ATATTTTTGAAATATATATATTAT
1 ATATTTTAGAAATATATATATTAT
335471 ATATTTTAG-AATATATATATTAT
1 ATATTTTAGAAATATATATATTAT
335494 -TATT
1 ATATT
335498 ATTATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 4 0.15
23 14 0.54
24 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
ATATTTTAGAAATATATATATTAT
Found at i:335517 original size:10 final size:9
Alignment explanation
Indices: 335488--335537 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
335478 AGAATATATA
*
335488 TATTATTAT
1 TATTTTTAT
*
335497 TATTATTAT
1 TATTTTTAT
335506 TACTTTTTAT
1 TA-TTTTTAT
335516 TATCTTTTAT
1 TAT-TTTTAT
335526 TATTTATTAT
1 TATTT-TTAT
335536 TA
1 TA
335538 ATTCCTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 14 0.38
10 23 0.62
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTTTAT
Found at i:335555 original size:32 final size:32
Alignment explanation
Indices: 335490--335555 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
335480 AATATATATA
* *
335490 TTATTATTATTATTATTACTTTTTATTATCTT
1 TTATTATTATTATTATTACCTTTTATTAACTT
335522 TTATTATTTATTATTAATT-CCTTTT-TTAACTT
1 TTATTA-TTATTATT-ATTACCTTTTATTAACTT
335554 TT
1 TT
335556 GTTTCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 14 0.47
33 13 0.43
34 3 0.10
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (32 bp):
TTATTATTATTATTATTACCTTTTATTAACTT
Found at i:336656 original size:13 final size:13
Alignment explanation
Indices: 336608--336688 Score: 60
Period size: 13 Copynumber: 6.1 Consensus size: 13
336598 ATTATCATGA
*
336608 TATTTA-TTTATT
1 TATTTATTTTTTT
336620 TATTTTATTTTTTAT
1 TA-TTTATTTTTT-T
336635 T-TTTATTTTTTT
1 TATTTATTTTTTT
336647 TATTTATTTTCTTT
1 TATTTATTTT-TTT
*
336661 TGACTTT-TTTATTT
1 T-A-TTTATTTTTTT
**
336675 TCCTTATTTTTTT
1 TATTTATTTTTTT
336688 T
1 T
336689 TTTTCCATTC
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
12 6 0.11
13 29 0.52
14 12 0.21
15 6 0.11
16 3 0.05
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (13 bp):
TATTTATTTTTTT
Found at i:336687 original size:17 final size:16
Alignment explanation
Indices: 336665--336713 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
336655 TTCTTTTGAC
*
336665 TTTTTTATTTTCCTTA
1 TTTTTTTTTTTCCTTA
*
336681 TTTTTTTTTTTTCCATTC
1 -TTTTTTTTTTTCC-TTA
*
336699 TTTCTTTTTTTCCTT
1 TTTTTTTTTTTCCTT
336714 TTTCTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTTTTTCCTTA
Found at i:336687 original size:19 final size:17
Alignment explanation
Indices: 336622--336693 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 17
336612 TATTTATTTA
* *
336622 TTTTATTTTTTATTTTTA
1 TTTTTTTTTTTA-TTTTC
336640 TTTTTTTTATTTATTTTC
1 TTTTTTTT-TTTATTTTC
*
336658 TTTTGACTTTTTTATTTTCC
1 TTTT--TTTTTTTATTTT-C
*
336678 TTATTTTTTTT-TTTTC
1 TTTTTTTTTTTATTTTC
336694 CATTCTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 4 0.09
18 21 0.47
19 12 0.27
20 7 0.16
ACGTcount: A:0.11, C:0.07, G:0.01, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTTTATTTTC
Found at i:336717 original size:15 final size:16
Alignment explanation
Indices: 336680--336721 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
336670 TATTTTCCTT
336680 ATTTTT-TTTTTTTCC
1 ATTTTTCTTTTTTTCC
336695 ATTCTTTCTTTTTTTCC
1 ATT-TTTCTTTTTTTCC
336712 -TTTTTCTTTT
1 ATTTTTCTTTT
336722 GACTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.44
16 5 0.20
17 9 0.36
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTCTTTTTTTCC
Found at i:336742 original size:60 final size:54
Alignment explanation
Indices: 336611--336743 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 54
336601 ATCATGATAT
336611 TTATTTATTTATTTTATTTTTTATTTTTATTTTTTTTATTTATTTTCTTTTGAC
1 TTATTTATTTATTTTATTTTTTATTTTTATTTTTTTTATTTATTTTCTTTTGAC
* * * * *
336665 TTTTTTATTT-TCCTTATTTTTTTTTTTTCCATTCTTTCTTTTTTTCCTTTTTCTTTTGAC
1 TTATTTATTTAT-TTTATTTTTTATTTTT--ATT-TTT-TTTATTT--ATTTTCTTTTGAC
336725 TTATTTATTTATTTTATTT
1 TTATTTATTTATTTTATTT
336744 CTATTTATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
53 1 0.02
54 23 0.36
56 3 0.05
57 3 0.05
58 6 0.09
60 27 0.42
61 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.77
Consensus pattern (54 bp):
TTATTTATTTATTTTATTTTTTATTTTTATTTTTTTTATTTATTTTCTTTTGAC
Found at i:340597 original size:96 final size:94
Alignment explanation
Indices: 340431--340689 Score: 304
Period size: 96 Copynumber: 2.7 Consensus size: 94
340421 AATATTACAT
* * *
340431 ATATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACACCACGGCTTTATGGATAA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC-CGGCTTTATGGATAA
*
340496 GATTTAGCTAAGCCAGATAAAGG-TGATTATA
65 GATTTAGCT-AGCCAGATAAAGGCAG-TTATA
* * *
340527 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTATTGTTAA
1 ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCC-GGCTTTATGGATAA
* *
340592 TATTTAGCTAGCCTGATAAAGGCAGTTATA
65 GATTTAGCTAGCCAGATAAAGGCAGTTATA
* * * *
340622 ATATATATATACAATGATATTGAGCTGTCCCTATAGAGCAATTGCTTAAACGCCCCGGCTTTATG
1 ATATACA-ATA-AA-G--CTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACG-CCCGGCTTTATG
340687 GAT
60 GAT
340690 CCAGCTAGCC
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
95 24 0.17
96 69 0.50
97 2 0.01
98 1 0.01
100 40 0.29
101 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (94 bp):
ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATGGATAAG
ATTTAGCTAGCCAGATAAAGGCAGTTATA
Found at i:341959 original size:84 final size:83
Alignment explanation
Indices: 341809--342572 Score: 919
Period size: 84 Copynumber: 9.2 Consensus size: 83
341799 AACAATTGGT
* *
341809 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC
341874 TCCAAGGCACATCATTTGC
65 TCCAAGGCACATCATTTGC
** * * * * *
341893 AATATAGCCCAAGGCAAGAAGGGTTATTTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACACTCAGC
341958 TCCAAGGCACATCATTTGC
65 TCCAAGGCACATCATTTGC
* * * * *
341977 AGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAAGACCTTCAAGTTTGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC
*
342042 TCTAAGGCACATCATTTGC
65 TCCAAGGCACATCATTTGC
* * * * * *
342061 AGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC
*
342126 TCCAAGGTACATCATTTGC
65 TCCAAGGCACATCATTTGC
* * *
342145 AGCATAACTCAAGGCTAGAAGGGTTATATGCTAACAAAAGACCTTCGAGTTCGACTACACTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGC-CACCAAAGACCTTCGAGTTCGACTACACTCAGC
*
342210 TCCAAGGCACATCATTTGT
65 TCCAAGGCACATCATTTGC
* * * * * * * *
342229 AGCATAACTTAAGTCGAGAAGGGATATCTGCCAACCAAAAACCTTCAAGTTCAATTACACTCAGC
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC
*
342294 TCCAAGGCACATCATTTAC
65 TCCAAGGCACATCATTTGC
* * * *
342313 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAATCAGCT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCT
*
342378 CAAAGGCACCATCATTTGC
66 CCAAGGCA-CATCATTTGC
* * * * *
342397 AGCATAACTCAAGGCGAGAAGGGTTATCTG---CCAAATACCTTTGAGTTCGATTACACTCAACT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCT
*
342459 CAAAGGCACCATCATTTGC
66 CCAAGGCA-CATCATTTGC
* * * * *
342478 AGTATAGCTCAAGGCAAGAAGGGTTATCTG---CCAAAGACCTCCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCT
* *
342540 CAAAGGCGCCATCATTTGC
66 CCAAGGC-ACATCATTTGC
*
342559 AGCATAGCTCAAGG
1 AGCATAACTCAAGG
342573 TAAGAGGGGC
Statistics
Matches: 595, Mismatches: 79, Indels: 15
0.86 0.11 0.02
Matches are distributed among these distances:
81 131 0.22
83 38 0.06
84 424 0.71
85 2 0.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (83 bp):
AGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCT
CCAAGGCACATCATTTGC
Found at i:343249 original size:37 final size:36
Alignment explanation
Indices: 343187--343421 Score: 279
Period size: 37 Copynumber: 6.5 Consensus size: 36
343177 TGAAAAAACG
*
343187 TATATAATATATAGGTTTTAAAAAACATTTTTGAAAAT
1 TATATAATATATA-GTTTT-TAAAACATTTTTGAAAAT
*
343225 GTATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
* *
343262 TACATAATATATAGTTTTTAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
343298 ATATATAATATATAGTTTTTAAAATC-TTTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAA-CATTTTTGAAAA-T
*
343336 TATATAATATATAGTTTTGAAAACATTTTTTTGAAAACT
1 TATATAATATATAGTTTTTAAAACA--TTTTTGAAAA-T
*
343375 TATAT-A-ATAT--TTTTTAAATCATTTTTG-AAA-
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
343405 -ATATAATATATAGTTTT
1 TATATAATATATAGTTTT
343422 GGAATTTTTT
Statistics
Matches: 176, Mismatches: 10, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
29 4 0.02
30 1 0.01
31 4 0.02
32 3 0.02
33 10 0.06
35 9 0.05
36 34 0.19
37 73 0.41
38 8 0.05
39 30 0.17
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:343296 original size:73 final size:73
Alignment explanation
Indices: 343181--343421 Score: 286
Period size: 73 Copynumber: 3.3 Consensus size: 73
343171 GTTTTTTGAA
343181 AAAACGTATATAATATATAGGTTTTAAAAAACATTTTTGAAAATGTATATAATATATAGTTTTTA
1 AAAACGTATATAATATATA-GTTTT-AAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTA
343246 AAACATTTTTG
63 AAACATTTTTG
* * *
343257 AAAAC-TACATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAA
1 AAAACGTATATAATATATAGTTTTAAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTAAA
343321 ATC-TTTTTG
65 A-CATTTTTG
* *
343330 AAAACTTATATAATATATAGTTTTGAAAACATTTTTTTGAAAACTTATAT-A-ATAT--TTTTTA
1 AAAACGTATATAATATATAGTTTTAAAAACA--TTTTTGAAAA-TTATATAATATATAGTTTTTA
*
343391 AATCATTTTTG
63 AAACATTTTTG
343402 -AAA---ATATAATATATAGTTTT
1 AAAACGTATATAATATATAGTTTT
343422 GGAATTTTTT
Statistics
Matches: 151, Mismatches: 8, Indels: 20
0.84 0.04 0.11
Matches are distributed among these distances:
68 17 0.11
71 4 0.03
72 14 0.09
73 50 0.33
74 33 0.22
75 13 0.09
76 19 0.13
77 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (73 bp):
AAAACGTATATAATATATAGTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTTAAAA
CATTTTTG
Found at i:343496 original size:25 final size:25
Alignment explanation
Indices: 343463--343510 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
343453 AAAAAATATT
343463 TTTGAAATATATA-TATATATTATAA
1 TTTGAAATATATATTAT-TATTATAA
*
343488 TTTGGAATATATATTATTATTAT
1 TTTGAAATATATATTATTATTAT
343511 TATTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTGAAATATATATTATTATTATAA
Found at i:343542 original size:14 final size:13
Alignment explanation
Indices: 343510--343539 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
343500 ATTATTATTA
343510 TTATTA-CTTTTT
1 TTATTATCTTTTT
343522 TTATTATCTTTTT
1 TTATTATCTTTTT
343535 TTATT
1 TTATT
343540 TATTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTATCTTTTT
Done.