Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 38 of 113
Found at i:11001284 original size:9 final size:8
Alignment explanation
Indices: 11001239--11001283 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
11001229 AATTTTCAGA
11001239 TTTAAAAT
1 TTTAAAAT
11001247 TTTAAAAAT
1 TTT-AAAAT
11001256 TTTAAAAT
1 TTTAAAAT
* *
11001264 CTGAAAATT
1 TTTAAAA-T
11001273 TTTAAAAT
1 TTTAAAAT
11001281 TTT
1 TTT
11001284 TTAATTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 17 0.55
9 14 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (8 bp):
TTTAAAAT
Found at i:11001287 original size:10 final size:9
Alignment explanation
Indices: 11001239--11001284 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
11001229 AATTTTCAGA
11001239 TTTAAAA-T
1 TTTAAAATT
*
11001247 TTTAAAAAT
1 TTTAAAATT
11001256 TTTAAAA-T
1 TTTAAAATT
* *
11001264 CTGAAAATT
1 TTTAAAATT
11001273 TTTAAAATT
1 TTTAAAATT
11001282 TTT
1 TTT
11001285 TAATTTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 13 0.41
9 19 0.59
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (9 bp):
TTTAAAATT
Found at i:11001619 original size:34 final size:34
Alignment explanation
Indices: 11001580--11001646 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
11001570 ATATTTTTTA
*
11001580 AACTTACTAGATATAAATATTT-GATAAATTATAT
1 AACTTAATAGATATAAATATTTAG-TAAATTATAT
11001614 AACTTAATAGATATAAATATTTAGTAAATTATA
1 AACTTAATAGATATAAATATTTAGTAAATTATA
11001647 AAATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (34 bp):
AACTTAATAGATATAAATATTTAGTAAATTATAT
Found at i:11001658 original size:17 final size:18
Alignment explanation
Indices: 11001591--11001658 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 18
11001581 ACTTACTAGA
11001591 TATAAATATTT-GATAAAT
1 TATAAATATTTAG-TAAAT
* * * *
11001609 TATATA-ACTTAATAGA-
1 TATAAATATTTAGTAAAT
11001625 TATAAATATTTAGTAAAT
1 TATAAATATTTAGTAAAT
*
11001643 TATAAA-ATTTATTAAA
1 TATAAATATTTAGTAAA
11001659 CATGCATACC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.13
17 22 0.58
18 11 0.29
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (18 bp):
TATAAATATTTAGTAAAT
Found at i:11009802 original size:9 final size:9
Alignment explanation
Indices: 11009787--11009839 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
11009777 GATTTTGTTA
11009787 ATAAAAAGAT
1 ATAAAAA-AT
11009797 -TAAAAAAT
1 ATAAAAAAT
11009805 AT-AAAAAT
1 ATAAAAAAT
11009813 AT--AAAAT
1 ATAAAAAAT
*
11009820 ATAAAAAAA
1 ATAAAAAAT
11009829 ATGAAAAAAT
1 AT-AAAAAAT
11009839 A
1 A
11009840 GGAAAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.19
8 10 0.27
9 13 0.35
10 7 0.19
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:11011076 original size:54 final size:52
Alignment explanation
Indices: 11011017--11011276 Score: 152
Period size: 53 Copynumber: 5.1 Consensus size: 52
11011007 AATAAAAAGA
11011017 ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAATTTCGAAAAAAAAAAT
1 ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAA-TTC-AAAAAAAAAAT
* * * * * * *
11011071 ATTTCTAAAT-TGACCTAAATGATGAGAAATTTAGAAA-TAAAAAACTAAAAAGA
1 ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAATTCAAAAA--AAAAA-T
* * *
11011124 ATTTCTAAAATAGGCCC-AAATGGTAGAGAATTTAAAAATTCAAAACAAGAAAAT
1 ATTTCT-AAATAGGCCCTAAATGGTAAAAAATTTAGAAATTCAAAA-AA-AAAAT
* * ** * *
11011178 ATTTTTAAATTGATCC--AGTGG---AAAATTTAGAAA-T---AAAAAGAAT
1 ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAATTCAAAAAAAAAAT
* ** *
11011221 -TTTCTAAATAGG-CTTAAATGGTGGAGAATTTAGAAATTCAAAATAAGAAAAT
1 ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAATTCAAAA-AA-AAAAT
11011273 ATTT
1 ATTT
11011277 TTAATTTGAC
Statistics
Matches: 154, Mismatches: 32, Indels: 41
0.68 0.14 0.18
Matches are distributed among these distances:
41 1 0.01
42 9 0.06
43 8 0.05
44 2 0.01
45 2 0.01
46 11 0.07
47 1 0.01
48 1 0.01
49 10 0.06
50 7 0.05
51 3 0.02
52 13 0.08
53 38 0.25
54 35 0.23
55 12 0.08
56 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (52 bp):
ATTTCTAAATAGGCCCTAAATGGTAAAAAATTTAGAAATTCAAAAAAAAAAT
Found at i:11011121 original size:53 final size:52
Alignment explanation
Indices: 11011060--11011190 Score: 124
Period size: 54 Copynumber: 2.5 Consensus size: 52
11011050 AGAAATTTCG
* *
11011060 AAAA-AAAAAATATTTCTAAATTGACCTAAATGAT-GAGAAATTTAGAAATAA
1 AAAACAAAAAATATTTCTAAATTGACCCAAATGATAGAG-AATTTAAAAATAA
* * * **
11011111 AAAACTAAAAAGA-ATTTCTAAAATAGGCCCAAATGGTAGAGAATTTAAAAATTC
1 AAAAC-AAAAA-ATATTTCT-AAATTGACCCAAATGATAGAGAATTTAAAAATAA
*
11011165 AAAACAAGAAAATATTTTTAAATTGA
1 AAAACAA-AAAATATTTCTAAATTGA
11011191 TCCAGTGGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
51 4 0.06
53 19 0.30
54 37 0.59
55 3 0.05
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.27
Consensus pattern (52 bp):
AAAACAAAAAATATTTCTAAATTGACCCAAATGATAGAGAATTTAAAAATAA
Found at i:11011128 original size:107 final size:105
Alignment explanation
Indices: 11011000--11011291 Score: 290
Period size: 95 Copynumber: 2.9 Consensus size: 105
11010990 TCTTTCCAAA
*
11011000 AAATAAAAATAAAAAGAATTTCT-AAATAGGCCCTAAATGGTAAAAAATTTAGAAATTTCGAAAA
1 AAATAAAAATAAAAAGAATTTCTAAAATAGGCCC-AAATGGTAAAAAATTTA-AAAATTC-AAAA
11011064 -AA-AAAATATTTCTAAATTGACCTAAATGATGAGAAATTTAG
63 CAAGAAAATATTTCTAAATTGACCTAAATGATGAGAAATTTAG
* *
11011105 AAATAAAAAACTAAAAAGAATTTCTAAAATAGGCCCAAATGGTAGAGAATTTAAAAATTCAAAAC
1 AAAT-AAAAA-TAAAAAGAATTTCTAAAATAGGCCCAAATGGTAAAAAATTTAAAAATTCAAAAC
* *
11011170 AAGAAAATATTTTTAAATTGATCC--AGTG--GA-AAATTTAG
64 AAGAAAATATTTCTAAATTGA-CCTAAATGATGAGAAATTTAG
** ** * * *
11011208 ------AAATAAAAAGAATTTTCT-AAATAGGCTTAAATGGTGGAGAATTTAGAAATTCAAAATA
1 AAATAAAAATAAAAAGAA-TTTCTAAAATAGGCCCAAATGGTAAAAAATTTAAAAATTCAAAACA
* *
11011266 AGAAAATATTTTTAATTTGACCTAAA
65 AGAAAATATTTCTAAATTGACCTAAA
11011292 AGATAAAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
94 2 0.01
95 63 0.38
96 9 0.05
103 8 0.05
104 2 0.01
105 8 0.05
106 16 0.10
107 46 0.28
108 12 0.07
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (105 bp):
AAATAAAAATAAAAAGAATTTCTAAAATAGGCCCAAATGGTAAAAAATTTAAAAATTCAAAACAA
GAAAATATTTCTAAATTGACCTAAATGATGAGAAATTTAG
Found at i:11020888 original size:28 final size:28
Alignment explanation
Indices: 11020848--11020904 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
11020838 TCACCTATGC
11020848 ACATTTTGTTATTTTTCATTGCAAAGCA
1 ACATTTTGTTATTTTTCATTGCAAAGCA
11020876 ACATTTTGTTATTTTTCATTGCAAAGCA
1 ACATTTTGTTATTTTTCATTGCAAAGCA
11020904 A
1 A
11020905 GATCAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (28 bp):
ACATTTTGTTATTTTTCATTGCAAAGCA
Found at i:11028099 original size:27 final size:27
Alignment explanation
Indices: 11028061--11028115 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
11028051 TTCTCAAATT
11028061 ATAAATCCTCTGCAGATGATAAGCATC
1 ATAAATCCTCTGCAGATGATAAGCATC
11028088 ATAAATCCTCTGCAGATGATAAGCATC
1 ATAAATCCTCTGCAGATGATAAGCATC
11028115 A
1 A
11028116 GGGTCATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (27 bp):
ATAAATCCTCTGCAGATGATAAGCATC
Found at i:11035915 original size:12 final size:12
Alignment explanation
Indices: 11035898--11035923 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11035888 AGCCTTGACT
11035898 TAGATTACCTAA
1 TAGATTACCTAA
11035910 TAGATTACCTAA
1 TAGATTACCTAA
11035922 TA
1 TA
11035924 ACATGGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
TAGATTACCTAA
Found at i:11039983 original size:624 final size:624
Alignment explanation
Indices: 11038782--11040657 Score: 3243
Period size: 624 Copynumber: 3.0 Consensus size: 624
11038772 ACATCAGTAA
* * *
11038782 CAGAGTCTCGGATTCTCTGTAATTCTTGATCATCTGGATCGGGCTCATCAATTTTCATATCGTAT
1 CAGAGTCTTGGATTCTCTGTAATTCTTGATCATCCGGATCGGGCTCATCAATTTTCATATCATAT
* * *
11038847 ATTCCCAGCTG-AGGCAATAACTTATCATCTGGATGAGGTTCTGCTTGTTCTATTTCATCTGCTT
66 ATTCCCAGCTGTA-GCAATAACTTATCATCTCGATGAGGATCTGCTTGTGCTATTTCATCTGCTT
* *
11038911 TAGTTTGATCAGGATCAGGTTCTTTATGACCTTGGTTGAAATGGGCTTGATCTACCAGGGTTTCA
130 TAGTTTCATCAGGATCAGGTTCTTTATGACCTTGGTTGAAATGGGCTTGATCTACCAAGGTTTCA
* * * *
11038976 GTTGTTATTTGATGACGAGGATCATGTCTTGCCATACTTGTGCATCCCAAAATGTTCAATCGTGC
195 GTTGTTATGTGATGACGAGGATCATGTCTTGCCATGCTTGTGCATCCCAAAATGTTCGATTGTGC
* *
11039041 TTCTCCATCATCAGGATCTGGTTCACCTATGGTCTCTCTTGTTAGAATCTTGGTGTCCAGAATCT
260 TTCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCT
*
11039106 CCATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAACCATCAGGATCAGGCTCT
325 CCATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCAGGCTCT
11039171 TCACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAATCGTTTTTAGTAGATTCAGA
390 TCACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAATCGTTTTTAGTAGATTCAGA
*
11039236 ATGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCTGGTTCAAACTTGTTCT
455 ATGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCAGGTTCAAACTTGTTCT
* * *
11039301 GATTTCTAGAAAGGTCATCAGGATCTGGTTCATAAGCAAGTTTCCCCACAGGCCTAATTGGACTT
520 GATTGCTAGAAAGGTCATCAGGATCTGGTTCATAAGCAAGTTTCCCCAAAGACCTAATTGGACTT
* *
11039366 TGAATATCTAGATTTTCATTTCCATCATGAATGGTCAACC
585 TGAATATCTAGATTTTCATTTCCATCGTGAATAGTCAACC
* *
11039406 CAGAGTCTTGGATTCTCTGTAATTTTTGATCATCCGGATCAGGCTCATCAATTTTCATATCATAT
1 CAGAGTCTTGGATTCTCTGTAATTCTTGATCATCCGGATCGGGCTCATCAATTTTCATATCATAT
* *
11039471 ATTCCCAGCTGTAGCAATAACTTATCATCTCGATGAGGCTCTGCTCGTGCTATTTCATCTGCTTT
66 ATTCCCAGCTGTAGCAATAACTTATCATCTCGATGAGGATCTGCTTGTGCTATTTCATCTGCTTT
**
11039536 AGTTTCATCAGGATCAGGTTCTTTATGACCTTGGTTGAAACAGGCTTGATCTACCAAGGTTTCAG
131 AGTTTCATCAGGATCAGGTTCTTTATGACCTTGGTTGAAATGGGCTTGATCTACCAAGGTTTCAG
* * *
11039601 TTGTTATGTGATGTCCAGGATCATGTCTTGCCATGCTTGGGCATCCCAAAATGTTCGATTGTGCT
196 TTGTTATGTGATGACGAGGATCATGTCTTGCCATGCTTGTGCATCCCAAAATGTTCGATTGTGCT
11039666 TCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCTC
261 TCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCTC
*
11039731 CATCACCACAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCAGGCTCTT
326 CATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCAGGCTCTT
* * * *
11039796 CACTTGAACATATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAATCATTTTTAGTAGATGCAGAC
391 CACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAATCGTTTTTAGTAGATTCAGAA
*
11039861 TGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCAGGTTCAAACTTGTTATG
456 TGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCAGGTTCAAACTTGTTCTG
* *
11039926 ATTGCTAGAAAGGTCATCAGGATATGGTTCATAAGCAAGTTTCCTCAAAGACCTAATTGGACTTT
521 ATTGCTAGAAAGGTCATCAGGATCTGGTTCATAAGCAAGTTTCCCCAAAGACCTAATTGGACTTT
* *
11039991 GAATATCTAGATTTTCATTTCCATTGTGAATAGTCAAAC
586 GAATATCTAGATTTTCATTTCCATCGTGAATAGTCAACC
11040030 CAGAGTCTTGGATTCTCTGTAATTCTTGATCATCCGGATCGGGCTCATCAATTTTCATATCATAT
1 CAGAGTCTTGGATTCTCTGTAATTCTTGATCATCCGGATCGGGCTCATCAATTTTCATATCATAT
*
11040095 ATTCCCAGCTGTGGCAATAACTTATCATCTCGATGAGGATCTGCTTGTGCTATTTCATCTGCTTT
66 ATTCCCAGCTGTAGCAATAACTTATCATCTCGATGAGGATCTGCTTGTGCTATTTCATCTGCTTT
* *
11040160 AGTTTCATCAGGATCAGGTTCTTTATGGCCTTGATTGAAATGGGCTTGATCTACCAAGGTTTCAG
131 AGTTTCATCAGGATCAGGTTCTTTATGACCTTGGTTGAAATGGGCTTGATCTACCAAGGTTTCAG
*
11040225 TTGTTATGTGATGACGAGGATCATGTCTTGCCAAGCTTGTGCATCCCAAAATGTTCGATTGTGCT
196 TTGTTATGTGATGACGAGGATCATGTCTTGCCATGCTTGTGCATCCCAAAATGTTCGATTGTGCT
11040290 TCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCTC
261 TCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCTC
*
11040355 CATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCGGGCTCTT
326 CATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCAGGCTCTT
11040420 CACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAAAT-GTTTTTAGTAGATTCAGA
391 CACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAG-AATCGTTTTTAGTAGATTCAGA
** ***
11040484 ATGATGTTTCAGTAGCAGAGTTTCACCGGGCAGCGTGTCATCTGGATCAGGTTCAAACTTGTTCT
455 ATGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCAGGTTCAAACTTGTTCT
* * *
11040549 GATTGCTAGAAAGATCATCAGGATCTGGTTCATAAGCAAGTTTCCCCAGAGCCCTAATTGGACTT
520 GATTGCTAGAAAGGTCATCAGGATCTGGTTCATAAGCAAGTTTCCCCAAAGACCTAATTGGACTT
11040614 TGAATATCTAGATTTTCATTTCCATCGTGAATAGTCAACC
585 TGAATATCTAGATTTTCATTTCCATCGTGAATAGTCAACC
11040654 CAGA
1 CAGA
11040658 ATCATCAGGG
Statistics
Matches: 1179, Mismatches: 71, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
624 1175 1.00
625 4 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (624 bp):
CAGAGTCTTGGATTCTCTGTAATTCTTGATCATCCGGATCGGGCTCATCAATTTTCATATCATAT
ATTCCCAGCTGTAGCAATAACTTATCATCTCGATGAGGATCTGCTTGTGCTATTTCATCTGCTTT
AGTTTCATCAGGATCAGGTTCTTTATGACCTTGGTTGAAATGGGCTTGATCTACCAAGGTTTCAG
TTGTTATGTGATGACGAGGATCATGTCTTGCCATGCTTGTGCATCCCAAAATGTTCGATTGTGCT
TCTCCATCATCAGGATCTGGTTCATCTATGGTCTCTCTTGTCAGAATCTTGGTGTCCAGAATCTC
CATCACCATAGGTTCAACTACATTTCCAAAACTTGAAGCACCTGAATCATCAGGATCAGGCTCTT
CACTTGAACACATGGCTGCTGATTTCCCAAGAGTCTTCTGAGAATCGTTTTTAGTAGATTCAGAA
TGATGTTTCAGTAGCAGAGTTTCACCATGCAGCAAATCATCTGGATCAGGTTCAAACTTGTTCTG
ATTGCTAGAAAGGTCATCAGGATCTGGTTCATAAGCAAGTTTCCCCAAAGACCTAATTGGACTTT
GAATATCTAGATTTTCATTTCCATCGTGAATAGTCAACC
Found at i:11043748 original size:22 final size:23
Alignment explanation
Indices: 11043723--11043768 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
11043713 ATATTTTTTA
*
11043723 TTTTTTAAT-AAA-TTATTAATT
1 TTTTTTTATGAAATTTATTAATT
11043744 TTTTTTTATGAAATTTTATTAATT
1 TTTTTTTATGAAA-TTTATTAATT
11043768 T
1 T
11043769 ATCAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTTATGAAATTTATTAATT
Found at i:11045470 original size:12 final size:12
Alignment explanation
Indices: 11045453--11045481 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11045443 CAAAAACTAG
11045453 ATTTATAATCAA
1 ATTTATAATCAA
11045465 ATTTATAATCAA
1 ATTTATAATCAA
11045477 ATTTA
1 ATTTA
11045482 GAAAAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTATAATCAA
Found at i:11053470 original size:14 final size:13
Alignment explanation
Indices: 11053430--11053459 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11053420 GATTTTAAGA
11053430 TTTTT-AAGATTT
1 TTTTTAAAGATTT
11053442 TTTTTAAAGATTT
1 TTTTTAAAGATTT
11053455 TTTTT
1 TTTTT
11053460 GGAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTAAAGATTT
Found at i:11054204 original size:56 final size:55
Alignment explanation
Indices: 11054133--11054302 Score: 214
Period size: 57 Copynumber: 3.0 Consensus size: 55
11054123 AAATTTTCAA
11054133 AAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTTTAAAAATAAAATT
1 AAAAAAAATATTTTTGAAGAAAAGTT-AAAGTATCAATTTTTTTAAAAATAAAATT
** * * * * *
11054189 AAAAAATTTTTTTTTGAAGAAAAGTTAAATGTATCAATTTCCTTTGAACATAAAAAT
1 AAAAAAAATATTTTTGAAGAAAAGTTAAA-GTATCAATTT-TTTTAAAAATAAAATT
* *
11054246 AAAAAAAATATTTTTGAGGAAAAGTTACAAATATCAATTTTTCTTAAAAATAAAATT
1 AAAAAAAATATTTTTGAAGAAAAGTTA-AAGTATCAATTTTT-TTAAAAATAAAATT
11054303 TCTTAAATAA
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
55 3 0.03
56 34 0.36
57 55 0.59
58 2 0.02
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (55 bp):
AAAAAAAATATTTTTGAAGAAAAGTTAAAGTATCAATTTTTTTAAAAATAAAATT
Found at i:11054317 original size:15 final size:16
Alignment explanation
Indices: 11054285--11054318 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11054275 AATATCAATT
11054285 TTTCTTAAAAATAAAA
1 TTTCTTAAAAATAAAA
*
11054301 TTTCTTAAATA-AAAA
1 TTTCTTAAAAATAAAA
11054316 TTT
1 TTT
11054319 TCAAAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCTTAAAAATAAAA
Found at i:11054325 original size:130 final size:129
Alignment explanation
Indices: 11054199--11054691 Score: 538
Period size: 129 Copynumber: 3.8 Consensus size: 129
11054189 AAAAAATTTT
* * *
11054199 TTTTTGAAGAAAAGTT-AAATGTATCAATTTCCTTTGAACATAAAA-ATAAAAAAAATATTTTTG
1 TTTTTGGAGAAAAGTTGAAA-GTATCAATTTCCTTTGAAAATAAAAGAT-TAAAAAATATTTTTG
*
11054262 AGGAAAAGTTACAAA-TATCAATTTTTCTTAAAAATAAAATTTCTTAAATAAAAATTTTC-AAAA
64 AGGAAAAGTTA-AAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTTTCAAAAA
11054325 TCA
128 T-A
* * * * *
11054328 TTTTGGGAG-AAAGTTGAAAGTATAAATTTTCTTTGAAAATAAAAAGGTTAAAAAATACTTTT-A
1 TTTTTGGAGAAAAGTTGAAAGTATCAATTTCCTTTGAAAAT-AAAAGATTAAAAAATATTTTTGA
* *
11054391 GGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTCTAAAATAAAAATTTTCAAAAAG
65 GG-AAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTTTCAAAAA-
11054456 T-
128 TA
* * * *
11054457 GTTTTGGGGAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAGGTTCTAAAAATATTTTTGA
1 TTTTTGGAGAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAGATT-AAAAAATATTTTTGA
* * * *
11054522 GGAAAAGTGAAAAGTATAAATTTTTCTTAAAAATAAAATTTCTAAAAAAGAAAAATTTCTAAAAA
65 GGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTCT--AAAATAAAAATTT-TCAAAA
11054587 ATA
127 ATA
* * * ** *
11054590 TTTTT-GAGAAAAAGTTGAAAGTGTCAATTT-TTCTTAAAAATAAAATTTCTAAAAAGTATTTTT
1 TTTTTGGAG-AAAAGTTGAAAGTATCAATTTCCT-TTGAAAATAAAAGAT-TAAAAAATATTTTT
* * *
11054653 AAGAAAAAGTTAAAAGTATCAATTTTCCTT-AAAATAAAA
63 GAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAA
11054692 ATCTTTAAAT
Statistics
Matches: 309, Mismatches: 38, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
128 30 0.10
129 89 0.29
130 82 0.27
131 4 0.01
132 25 0.08
133 78 0.25
134 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (129 bp):
TTTTTGGAGAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAGATTAAAAAATATTTTTGAG
GAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTTTCAAAAATA
Found at i:11054454 original size:72 final size:73
Alignment explanation
Indices: 11054363--11054511 Score: 187
Period size: 72 Copynumber: 2.1 Consensus size: 73
11054353 ATTTTCTTTG
*
11054363 AAAATAAAAAGGTTAAAAAA-TACTTTTAGGAAAAAGTTGAAAGTATCAATTT-TTCTTGAAAAT
1 AAAATAAAAAGGTTAAAAAAGT-CTTTTAGGAAAAAGTTGAAAGTATCAATTTCCT-TTGAAAAT
*
11054426 AAAA-TTTCT
64 AAAAGGTTCT
** * * * *
11054435 AAAATAAAAATTTTCAAAAAGTGTTTTGGGGAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAA
1 AAAATAAAAAGGTTAAAAAAGTCTTTTAGGAAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAA
11054500 AAGGTTCT
66 AAGGTTCT
11054508 AAAA
1 AAAA
11054512 ATATTTTTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 56 0.85
73 10 0.15
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (73 bp):
AAAATAAAAAGGTTAAAAAAGTCTTTTAGGAAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAA
AAGGTTCT
Found at i:11054512 original size:58 final size:57
Alignment explanation
Indices: 11054435--11054569 Score: 132
Period size: 58 Copynumber: 2.3 Consensus size: 57
11054425 TAAAATTTCT
* * * * *
11054435 AAAATAAAAATTTTCAAAAAGT-GTTTTGGGGAAAAGTTG-AAAGTATCAATTTC-CTTTG
1 AAAATAAAAGTTCT-AAAAA-TAGTTTTGAGGAAAAG-TGAAAAGTATAAATTTCTC-TTA
* *
11054493 AAAATAAAAGGTTCTAAAAATATTTTTGAGGAAAAGTGAAAAGTATAAATTTTTCTTA
1 AAAATAAAA-GTTCTAAAAATAGTTTTGAGGAAAAGTGAAAAGTATAAATTTCTCTTA
*
11054551 AAAATAAAATTTCTAAAAA
1 AAAATAAAAGTTCTAAAAA
11054570 AGAAAAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
57 12 0.18
58 49 0.75
59 4 0.06
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.33
Consensus pattern (57 bp):
AAAATAAAAGTTCTAAAAATAGTTTTGAGGAAAAGTGAAAAGTATAAATTTCTCTTA
Found at i:11054569 original size:16 final size:16
Alignment explanation
Indices: 11054544--11054589 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
11054534 AGTATAAATT
*
11054544 TTTCTTAAAAATAAAA
1 TTTCTAAAAAATAAAA
*
11054560 TTTCTAAAAAAGAAAAA
1 TTTCTAAAAAA-TAAAA
11054577 TTTCTAAAAAATA
1 TTTCTAAAAAATA
11054590 TTTTTGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (16 bp):
TTTCTAAAAAATAAAA
Found at i:11054570 original size:58 final size:58
Alignment explanation
Indices: 11054458--11054569 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 58
11054448 TCAAAAAGTG
* * *
11054458 TTTTGGGGAAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAGGTTCTAAAAATAT
1 TTTTGAGGAAAAGTTGAAAGTATAAATTTCCTTTAAAAATAAAAGGTTCTAAAAATAT
* *
11054516 TTTTGAGGAAAAG-TGAAAAGTATAAATTT-TTCTTAAAAATAAAA-TTTCTAAAAA
1 TTTTGAGGAAAAGTTG-AAAGTATAAATTTCCT-TTAAAAATAAAAGGTTCTAAAAA
11054570 AGAAAAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 12 0.26
58 35 0.74
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (58 bp):
TTTTGAGGAAAAGTTGAAAGTATAAATTTCCTTTAAAAATAAAAGGTTCTAAAAATAT
Found at i:11054593 original size:75 final size:74
Alignment explanation
Indices: 11054504--11054644 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 74
11054494 AAATAAAAGG
*
11054504 TTCTAAAAATATTTTTGAGGAAAAG-TGAAAAGTATAAATTTTTCTTAAAAATAAAATTTCTAAA
1 TTCTAAAAATATTTTTGAGAAAAAGTTG-AAAGTATAAATTTTTCTTAAAAATAAAATTTCTAAA
11054568 AAAGAAAAAT
65 AAAGAAAAAT
* *
11054578 TTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTGTCAATTTTTCTTAAAAATAAAATTTCTAAA
1 TTCT-AAAAATATTTTTGAGAAAAAGTTGAAAGTATAAATTTTTCTTAAAAATAAAATTTCTAAA
11054643 AA
65 AA
11054645 GTATTTTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
74 4 0.06
75 56 0.90
76 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.35
Consensus pattern (74 bp):
TTCTAAAAATATTTTTGAGAAAAAGTTGAAAGTATAAATTTTTCTTAAAAATAAAATTTCTAAAA
AAGAAAAAT
Found at i:11054629 original size:59 final size:58
Alignment explanation
Indices: 11054560--11054693 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
11054550 AAAAATAAAA
* * * *
11054560 TTTCTAAAAAAGAAAAATTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTGTCAATT
1 TTTCTTAAAAA-AAAAATTTCTAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATT
* *
11054619 TTTCTTAAAAATAAAATTTCTAAAAAGTATTTTTAAGAAAAAGTTAAAAGTATCAATT
1 TTTCTTAAAAAAAAAATTTCTAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATT
* *
11054677 TTCCTTAAAATAAAAAT
1 TTTCTTAAAAAAAAAAT
11054694 CTTTAAATGC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 56 0.85
59 10 0.15
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (58 bp):
TTTCTTAAAAAAAAAATTTCTAAAAAATATTTTTAAGAAAAAGTTAAAAGTATCAATT
Found at i:11054832 original size:10 final size:9
Alignment explanation
Indices: 11054802--11054839 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
11054792 AGTTGAATCA
11054802 TTATTTCTT
1 TTATTTCTT
*
11054811 TT-TTTGTT
1 TTATTTCTT
11054819 TTATTTCATT
1 TTATTTC-TT
11054829 TTATTTCTT
1 TTATTTCTT
11054838 TT
1 TT
11054840 TTCTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 9 0.36
10 9 0.36
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTCTT
Found at i:11055778 original size:4 final size:4
Alignment explanation
Indices: 11055771--11055796 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
11055761 GTGTGACGTT
11055771 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
11055797 TCTCTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:11060073 original size:20 final size:20
Alignment explanation
Indices: 11060048--11060087 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11060038 AAAAGAGTGT
11060048 TGAAATATCCATGACTGACA
1 TGAAATATCCATGACTGACA
11060068 TGAAATATCCATGACTGACA
1 TGAAATATCCATGACTGACA
11060088 AGCCTACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
TGAAATATCCATGACTGACA
Found at i:11061758 original size:8 final size:8
Alignment explanation
Indices: 11061745--11061775 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
11061735 TTCATTATTG
11061745 CCATTTTT
1 CCATTTTT
11061753 CCATTTTT
1 CCATTTTT
11061761 CCATTTTT
1 CCATTTTT
*
11061769 TCATTTT
1 CCATTTT
11061776 CCAAACACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.65
Consensus pattern (8 bp):
CCATTTTT
Found at i:11065274 original size:15 final size:16
Alignment explanation
Indices: 11065254--11065313 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
11065244 AGTACTAACT
*
11065254 TAAAAAAAT-GAAAAA
1 TAAAAAAATAAAAAAA
11065269 T-AAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
* *
11065284 TAAAAAAA-CAAATAA
1 TAAAAAAATAAAAAAA
**
11065299 GGAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
11065314 GAAAGACTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 7 0.20
15 18 0.51
16 10 0.29
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (16 bp):
TAAAAAAATAAAAAAA
Found at i:11065313 original size:7 final size:7
Alignment explanation
Indices: 11065256--11065313 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
11065246 TACTAACTTA
11065256 AAAAAAT
1 AAAAAAT
*
11065263 GAAAAAT
1 AAAAAAT
11065270 AAAAAAT
1 AAAAAAT
11065277 AAAAAAAT
1 -AAAAAAT
11065285 AAAAAA-
1 AAAAAAT
*
11065291 ACAAATAAGG
1 A-AAA-AA-T
11065301 AAAAAAT
1 AAAAAAT
11065308 AAAAAA
1 AAAAAA
11065314 GAAAGACTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 27 0.63
8 11 0.26
9 3 0.07
10 1 0.02
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:11066048 original size:21 final size:20
Alignment explanation
Indices: 11066020--11066058 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11066010 ATTAGCAAGT
11066020 ATTTGCATAGCA-TGCATTGA
1 ATTTGCAT-GCATTGCATTGA
11066040 ATTTCGCATGCATTGCATT
1 ATTT-GCATGCATTGCATT
11066059 TTGTATAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTTGCATGCATTGCATTGA
Found at i:11066050 original size:16 final size:16
Alignment explanation
Indices: 11066029--11066059 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11066019 TATTTGCATA
11066029 GCATGCATTGAATTTC
1 GCATGCATTGAATTTC
*
11066045 GCATGCATTGCATTT
1 GCATGCATTGAATTT
11066060 TGTATAGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (16 bp):
GCATGCATTGAATTTC
Found at i:11066436 original size:44 final size:43
Alignment explanation
Indices: 11066370--11066569 Score: 186
Period size: 44 Copynumber: 4.5 Consensus size: 43
11066360 AGTTGAGCAA
* *
11066370 TTTATTTTTTCAAAGTTATTGAGCCTTTAATTAAAGGAGCTTTG
1 TTTA-TTTTTCAAAATTGTTGAGCCTTTAATTAAAGGAGCTTTG
* * *
11066414 TTTATTCTTCAAAAATTGTTGAGCCTCTT-ATTAGAGGAGCCTTG
1 TTTATTTTTC-AAAATTGTTGAGCCT-TTAATTAAAGGAGCTTTG
* **
11066458 TTTATTTTTCAAAATTCGTTGAGCCTCTAATTAAAAAAGCTTTG
1 TTTATTTTTCAAAATT-GTTGAGCCTTTAATTAAAGGAGCTTTG
* * * * * * *
11066502 TTTATTTTTCCAAAGTCGTTAAGCTTTTGATTAGAGGAGCTTTA
1 TTTATTTTT-CAAAATTGTTGAGCCTTTAATTAAAGGAGCTTTG
* *
11066546 TTTATTTTTTCAAGATCGTTGAGC
1 TTTA-TTTTTCAAAATTGTTGAGC
11066570 TTATGCTTAA
Statistics
Matches: 126, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
43 12 0.10
44 102 0.81
45 12 0.10
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (43 bp):
TTTATTTTTCAAAATTGTTGAGCCTTTAATTAAAGGAGCTTTG
Found at i:11066482 original size:88 final size:89
Alignment explanation
Indices: 11066369--11066569 Score: 239
Period size: 88 Copynumber: 2.3 Consensus size: 89
11066359 TAGTTGAGCA
* * * ** *
11066369 ATTTATTTTTTCAAAGTT-ATTGAGCCTTTAATTAAAGGAGCTTTGTTTATTCTTCAAAAATTGT
1 ATTTATTTTTTCAAAATTCGTTGAGCCTCTAATTAAAAAAGCTTTGTTTATTCTTCAAAAATCGT
*
11066433 TGAGCCTCTT-ATTAGAGGAGCCTT
66 TAAG-CTCTTGATTAGAGGAGCCTT
* * * *
11066457 GTTTA-TTTTTCAAAATTCGTTGAGCCTCTAATTAAAAAAGCTTTGTTTATTTTTCCAAAGTCGT
1 ATTTATTTTTTCAAAATTCGTTGAGCCTCTAATTAAAAAAGCTTTGTTTATTCTTCAAAAATCGT
* *
11066521 TAAGCTTTTGATTAGAGGAGCTTT
66 TAAGCTCTTGATTAGAGGAGCCTT
*
11066545 ATTTATTTTTTCAAGA-TCGTTGAGC
1 ATTTATTTTTTCAAAATTCGTTGAGC
11066570 TTATGCTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
87 15 0.16
88 71 0.75
89 9 0.09
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (89 bp):
ATTTATTTTTTCAAAATTCGTTGAGCCTCTAATTAAAAAAGCTTTGTTTATTCTTCAAAAATCGT
TAAGCTCTTGATTAGAGGAGCCTT
Found at i:11067605 original size:3 final size:3
Alignment explanation
Indices: 11067599--11067645 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
11067589 AATTATTTAT
* * *
11067599 TTA TTA TTA TTG TTA TTA TTA TTA TTA CTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11067646 TATAAATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11067614 original size:12 final size:12
Alignment explanation
Indices: 11067599--11067645 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
11067589 AATTATTTAT
11067599 TTATTATTATTG
1 TTATTATTATTG
*
11067611 TTATTATTATTA
1 TTATTATTATTG
*
11067623 TTACTATTATTG
1 TTATTATTATTG
11067635 TTATTATTATT
1 TTATTATTATT
11067646 TATAAATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:11067920 original size:57 final size:56
Alignment explanation
Indices: 11067748--11068033 Score: 211
Period size: 57 Copynumber: 4.9 Consensus size: 56
11067738 AAATTTTCAA
* ***
11067748 AAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGTAAACAA-AATTTTTTTT
1 AAAAAATAATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCT--TAAA-AATAA---AAATT
** * * * * * * *
11067809 AAAAAATTTTCTTTGAAGG-AAAGTTGAACGTATCAA-TTTCCTTTGAACACAAAAATAG
1 AAAAAATAAT-TTTG-AGGAAAAGTTAAAAGTATCAATTTTTC-TTAAAAATAAAAAT-T
* *
11067867 AAAAAATAATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTT
1 AAAAAATAATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAA-TT
* * * * * **
11067924 TAAAAATCATTTTGGGGGAATGTTAAAAGTATCAATTTTTCTTGAAAGAA-AAAGGTT
1 AAAAAATAATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTT-AAA-AATAAAAATT
* *
11067981 AAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAA
1 AAAAAATAATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAA
11068034 TTTCTAAAAT
Statistics
Matches: 178, Mismatches: 36, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
55 2 0.01
56 8 0.04
57 105 0.59
58 19 0.11
59 3 0.02
60 5 0.03
61 13 0.07
62 20 0.11
63 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (56 bp):
AAAAAATAATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATT
Found at i:11068050 original size:128 final size:129
Alignment explanation
Indices: 11067911--11068152 Score: 323
Period size: 128 Copynumber: 1.9 Consensus size: 129
11067901 ATTTTTCTTA
* * *
11067911 AAAATAAAAATTTT-AAAAATCATTTTGGGGGAATGTTAAAAGTATCAATTTTTC-TTGAAAGA-
1 AAAATAAAAATTTTCAAAAAT-ATTTTGGAGGAAAGTTAAAAGTATCAA-TTTCCATTGAAA-AT
* *
11067973 AAAAGGTT-AAAAAATATTTTT-AAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATT
63 AAAAAGTTCAAAAAATATTTTTGAA-AAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATT
11068036 TCT
127 TCT
* * *
11068039 AAAATAAAAATTTTCAAAAGTATTTTGGAGGAAAGTTGAAAGTATTAATTTCCATTGAAAATAAA
1 AAAATAAAAATTTTCAAAAATATTTTGGAGGAAAGTTAAAAGTATCAATTTCCATTGAAAATAAA
* *
11068104 AAGTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTT
66 AAGTTCAAAAAATATTTTTGAAAAAAAGTTAAAAGTATCAATTTTTCTT
11068153 GTACAAAAGT
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
127 5 0.05
128 50 0.51
129 42 0.42
130 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (129 bp):
AAAATAAAAATTTTCAAAAATATTTTGGAGGAAAGTTAAAAGTATCAATTTCCATTGAAAATAAA
AAGTTCAAAAAATATTTTTGAAAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTCT
Found at i:11071529 original size:18 final size:17
Alignment explanation
Indices: 11071502--11071536 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11071492 GATAATTCTT
*
11071502 AAAAAATCTTTTTTTTG
1 AAAAAATCTTCTTTTTG
11071519 AAAAAAGTCTTCTTTTTG
1 AAAAAA-TCTTCTTTTTG
11071537 CGTAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (17 bp):
AAAAAATCTTCTTTTTG
Found at i:11076755 original size:4 final size:4
Alignment explanation
Indices: 11076746--11076796 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
11076736 TTTAACAAGT
* * *
11076746 TAAA TAAA TAAA TAAA TAATT TACA T-AT TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA
11076794 TAA
1 TAA
11076797 TTCATAGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 36 0.92
5 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:11076818 original size:32 final size:32
Alignment explanation
Indices: 11076682--11076798 Score: 117
Period size: 32 Copynumber: 3.5 Consensus size: 32
11076672 TTTTACTTAT
* *
11076682 TAAATAAATAAATAATTTGCATGTTAAATAAA
1 TAAATAAATAAATAATTTACATATTAAATAAA
* *** ** *
11076714 TAAATAAATAACCATTAAGTTGTTTAACAAGTTAAA
1 TAAATAAATAA--A-TAATTTACATATTAA-ATAAA
11076750 TAAATAAATAAATAATTTACATATTAAATAAA
1 TAAATAAATAAATAATTTACATATTAAATAAA
11076782 TAAATAAATAAATAATT
1 TAAATAAATAAATAATT
11076799 CATAGGTTAC
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
32 32 0.48
33 9 0.13
34 2 0.03
35 9 0.13
36 15 0.22
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (32 bp):
TAAATAAATAAATAATTTACATATTAAATAAA
Found at i:11077198 original size:45 final size:45
Alignment explanation
Indices: 11077142--11077244 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
11077132 CTATTTATAT
*
11077142 TTTTTTAATTTTTTACATGAATCAATA-TTTTCAATCTAGGTTTTTC
1 TTTTTT-ATTTTTTACAT-AATCAATATTTTTCAATCTAGGTTCTTC
* ** *
11077188 TTTTTTATTTTCTGGATAATCAGTATTTTTCAATCTAGGTTCTTC
1 TTTTTTATTTTTTACATAATCAATATTTTTCAATCTAGGTTCTTC
*
11077233 TCTTTTATTTTT
1 TTTTTTATTTTT
11077245 GGGATAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 7 0.14
45 36 0.73
46 6 0.12
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.59
Consensus pattern (45 bp):
TTTTTTATTTTTTACATAATCAATATTTTTCAATCTAGGTTCTTC
Found at i:11077250 original size:45 final size:44
Alignment explanation
Indices: 11077161--11077252 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
11077151 TTTTTACATG
* *
11077161 AATCAATATTTTCAATCTAGGTTTTTCTTTTTTATTTTCTGGAT
1 AATCAATATTTTCAATCTAGGTTCTTCTCTTTTATTTTCTGGAT
*
11077205 AATCAGTATTTTTCAATCTAGGTTCTTCTCTTTTATTTT-TGGGAT
1 AATCAATA-TTTTCAATCTAGGTTCTTCTCTTTTATTTTCT-GGAT
11077250 AAT
1 AAT
11077253 ATCCTATATG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 8 0.19
45 35 0.81
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (44 bp):
AATCAATATTTTCAATCTAGGTTCTTCTCTTTTATTTTCTGGAT
Found at i:11080344 original size:30 final size:30
Alignment explanation
Indices: 11080311--11080480 Score: 112
Period size: 30 Copynumber: 5.7 Consensus size: 30
11080301 CTAGAGTAGT
*
11080311 AGCCACACCACCTAGAGTGACCAGAACAGT
1 AGCCACACCACCTAGAGTGACCAGAACAGC
* * *
11080341 AGCCACTCCACTTAGAGTGACCA-AAGTAGC
1 AGCCACACCACCTAGAGTGACCAGAA-CAGC
* * * * * *
11080371 AACCACACTACCTAAAGTAACCAGAATAAC
1 AGCCACACCACCTAGAGTGACCAGAACAGC
* * * * *
11080401 AGCTACATCA-GTAAGAGTGACTAGAGCAGC
1 AGCCACACCACCT-AGAGTGACCAGAACAGC
* * **
11080431 AGCCACACCATCC-AGAGTGACTACAACAAT
1 AGCCACACCA-CCTAGAGTGACCAGAACAGC
*
11080461 AGCCACACCATCTAGAGTGA
1 AGCCACACCACCTAGAGTGA
11080481 GTAAAGCAAT
Statistics
Matches: 104, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
29 4 0.04
30 98 0.94
31 2 0.02
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (30 bp):
AGCCACACCACCTAGAGTGACCAGAACAGC
Found at i:11080491 original size:30 final size:30
Alignment explanation
Indices: 11080431--11080493 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
11080421 CTAGAGCAGC
11080431 AGCCACACCATCCAGAGTGACTACAACAAT
1 AGCCACACCATCCAGAGTGACTACAACAAT
* *
11080461 AGCCACACCATCTAGAGTGAGTA-AAGCAAT
1 AGCCACACCATCCAGAGTGACTACAA-CAAT
11080491 AGC
1 AGC
11080494 AGTAGCCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.40, C:0.29, G:0.17, T:0.14
Consensus pattern (30 bp):
AGCCACACCATCCAGAGTGACTACAACAAT
Found at i:11080512 original size:36 final size:35
Alignment explanation
Indices: 11080457--11080555 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 35
11080447 GTGACTACAA
*
11080457 CAATAGCCACACCATCTAGAGTGAGT-AAAGCAATAG
1 CAATAGCCACACCA-CTAGAGTGA-TCAAAGCAAGAG
* * * *
11080493 CAGTAGCCATACCACCTAGAATGATCAAAGCCAGAG
1 CAATAGCCACACCA-CTAGAGTGATCAAAGCAAGAG
11080529 CAATAGCCACACCACTCAGAGTGATCA
1 CAATAGCCACACCACT-AGAGTGATCA
11080556 CAGTAGCATC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 3 0.06
36 49 0.94
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.15
Consensus pattern (35 bp):
CAATAGCCACACCACTAGAGTGATCAAAGCAAGAG
Found at i:11080671 original size:30 final size:29
Alignment explanation
Indices: 11080622--11080698 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
11080612 ATCATAACCA
** * * *
11080622 AAACAGCAGTCACACCATCTAGAGTGTCC
1 AAACAGCAACCACACCATCTACAATGACC
*
11080651 ACAACAGCAACCACATCATCTACAATGACC
1 A-AACAGCAACCACACCATCTACAATGACC
11080681 AAAGCAGCAACCACACCA
1 AAA-CAGCAACCACACCA
11080699 CCCAACCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.12
Consensus pattern (29 bp):
AAACAGCAACCACACCATCTACAATGACC
Found at i:11083627 original size:24 final size:24
Alignment explanation
Indices: 11083561--11083614 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
11083551 AATTTTTTAT
* * *
11083561 TTATTTAATAATTTAATATGTAAA
1 TTATTTATTCATTTAACATGTAAA
*
11083585 TTATTTATTCATTTAACATGTAAT
1 TTATTTATTCATTTAACATGTAAA
11083609 TTATTT
1 TTATTT
11083615 TTATGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (24 bp):
TTATTTATTCATTTAACATGTAAA
Found at i:11088926 original size:8 final size:8
Alignment explanation
Indices: 11088894--11088953 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
11088884 AAAATTTTAA
*
11088894 TTATTTAT
1 TTATATAT
*
11088902 TTA-ATTT
1 TTATATAT
*
11088909 TTA-ATTT
1 TTATATAT
11088916 TTATATAT
1 TTATATAT
* *
11088924 TTATGTAA
1 TTATATAT
11088932 TTATATAT
1 TTATATAT
*
11088940 TTAAATAT
1 TTATATAT
11088948 TTATAT
1 TTATAT
11088954 TTAAAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 12 0.29
8 30 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
TTATATAT
Found at i:11088941 original size:26 final size:25
Alignment explanation
Indices: 11088886--11088951 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
11088876 TAAAAATTAA
* *
11088886 AATTTTAATTATTTATTTAATTTTT
1 AATTTTAATTATTTATGTAATTTAT
*
11088911 AATTTTTATATATTTATGTAA-TTAT
1 AATTTTAAT-TATTTATGTAATTTAT
*
11088936 -ATATTTAAATATTTAT
1 AAT-TTTAATTATTTAT
11088952 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 9 0.26
25 15 0.44
26 10 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
AATTTTAATTATTTATGTAATTTAT
Found at i:11096063 original size:13 final size:13
Alignment explanation
Indices: 11096045--11096091 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
11096035 TATTATATAA
11096045 AAATTAAAAATAT
1 AAATTAAAAATAT
* *
11096058 AAATTATATATAT
1 AAATTAAAAATAT
*
11096071 AAATTAAAAATAA
1 AAATTAAAAATAT
11096084 AAATTAAA
1 AAATTAAA
11096092 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTAAAAATAT
Found at i:11096074 original size:26 final size:26
Alignment explanation
Indices: 11096038--11096089 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
11096028 TAATTCATAT
*
11096038 TATATAAAAATTAAAAATATAAATTA
1 TATATAAAAATTAAAAATAAAAATTA
*
11096064 TATATATAAATTAAAAATAAAAATTA
1 TATATAAAAATTAAAAATAAAAATTA
11096090 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TATATAAAAATTAAAAATAAAAATTA
Found at i:11096647 original size:30 final size:30
Alignment explanation
Indices: 11096610--11096676 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
11096600 TATTGCATTT
11096610 AAATAAATTTTTAACATTTAATTTGTA-CC
1 AAATAAATTTTTAACATTTAATTTGTATCC
* *
11096639 ATAATAAATTTTTAATATTTAATTTTTATCC
1 A-AATAAATTTTTAACATTTAATTTGTATCC
11096670 AAATAAA
1 AAATAAA
11096677 ATCTTTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (30 bp):
AAATAAATTTTTAACATTTAATTTGTATCC
Found at i:11096664 original size:14 final size:14
Alignment explanation
Indices: 11096615--11096666 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
11096605 CATTTAAATA
*
11096615 AATTTTTAACATTT
1 AATTTTTAATATTT
* * *
11096629 AATTTGTACCATAATA
1 AATTTTTA--ATATTT
11096645 AATTTTTAATATTT
1 AATTTTTAATATTT
11096659 AATTTTTA
1 AATTTTTA
11096667 TCCAAATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 19 0.66
16 10 0.34
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (14 bp):
AATTTTTAATATTT
Found at i:11096700 original size:17 final size:17
Alignment explanation
Indices: 11096657--11096707 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
11096647 TTTTTAATAT
*
11096657 TTAATTTTT-ATCCAAA
1 TTAATTTTTAATCTAAA
* *
11096673 TAAAATCTTTAATCTAAA
1 T-TAATTTTTAATCTAAA
*
11096691 TTAATTTTTAATTTAAA
1 TTAATTTTTAATCTAAA
11096708 ATAAGGGCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 1 0.04
17 19 0.70
18 7 0.26
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATTTTTAATCTAAA
Found at i:11098276 original size:2 final size:2
Alignment explanation
Indices: 11098269--11098306 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11098259 ACGATAAAGC
11098269 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
11098307 TAGATAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11098560 original size:26 final size:26
Alignment explanation
Indices: 11098531--11098581 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
11098521 CATAACAAAT
11098531 ATTATGGATAATTAATAGATTCCAAC
1 ATTATGGATAATTAATAGATTCCAAC
11098557 ATTATGGATAATTAATAGATTCCAA
1 ATTATGGATAATTAATAGATTCCAA
11098582 GTCATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (26 bp):
ATTATGGATAATTAATAGATTCCAAC
Found at i:11104010 original size:2 final size:2
Alignment explanation
Indices: 11104003--11104028 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11103993 AATTCGTTTC
11104003 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
11104029 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11108841 original size:93 final size:92
Alignment explanation
Indices: 11108659--11108845 Score: 311
Period size: 93 Copynumber: 2.0 Consensus size: 92
11108649 ACAAAGCCAT
* *
11108659 TTGTTTTTAAGTACCATTCGTTTCTTTGGACTAGTCGAAAAGAATAACAAGTTAAATCAACAAAG
1 TTGTTTTTAAGTACCATTCGTTTCTTTGGACCAGTCGAAAAGAATAACAAGCTAAATCAACAAAG
*
11108724 ATATTTGTATATTGCTCATATGCATGG
66 ATATTTGTATATTGCTCACATGCATGG
* *
11108751 TTGTTTTTAAGTACCATTCGTTTCTTTGGACCAGTCGAAAAGACTTAACAAGCTAAATCAACAAG
1 TTGTTTTTAAGTACCATTCGTTTCTTTGGACCAGTCGAAAAGA-ATAACAAGCTAAATCAACAAA
*
11108816 GATATTTGTATATTGCTCACGTGCATGG
65 GATATTTGTATATTGCTCACATGCATGG
11108844 TT
1 TT
11108846 TCCATTGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 42 0.48
93 46 0.52
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (92 bp):
TTGTTTTTAAGTACCATTCGTTTCTTTGGACCAGTCGAAAAGAATAACAAGCTAAATCAACAAAG
ATATTTGTATATTGCTCACATGCATGG
Found at i:11112848 original size:52 final size:52
Alignment explanation
Indices: 11112812--11112968 Score: 305
Period size: 52 Copynumber: 3.0 Consensus size: 52
11112802 ATCAAACACT
11112812 TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
1 TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
11112864 TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
1 TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
*
11112916 TAATTTGTTGTTATTAATAAATTATTAATGTATTAAATACTAAGTTATTCTA
1 TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
11112968 T
1 T
11112969 CTCAGGTCCA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (52 bp):
TAATTTGTTGTTATTAATAAATTATCAATGTATTAAATACTAAGTTATTCTA
Found at i:11116479 original size:13 final size:13
Alignment explanation
Indices: 11116439--11116483 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
11116429 TATATACATT
**
11116439 TATATTAAATGCA
1 TATATTAAATATA
*
11116452 TATATTAAAAAATA
1 TATATT-AAATATA
11116466 TATATTAAATATA
1 TATATTAAATATA
11116479 TATAT
1 TATAT
11116484 ATTAGTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
TATATTAAATATA
Found at i:11116500 original size:17 final size:15
Alignment explanation
Indices: 11116451--11116487 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11116441 TATTAAATGC
*
11116451 ATATATTAAA-AAAT
1 ATATATTAAATATAT
11116465 ATATATTAAATATAT
1 ATATATTAAATATAT
11116480 ATATATTA
1 ATATATTA
11116488 GTAATGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATTAAATATAT
Found at i:11116831 original size:22 final size:23
Alignment explanation
Indices: 11116796--11116838 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11116786 ATGAATATAC
*
11116796 AATAATATATTATAATGATAATA
1 AATAACATATTATAATGATAATA
11116819 AATAACAT-TTATAATGATAA
1 AATAACATATTATAATGATAA
11116839 GAAACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (23 bp):
AATAACATATTATAATGATAATA
Found at i:11117470 original size:24 final size:24
Alignment explanation
Indices: 11117414--11117471 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
11117404 AGTAACATAA
*
11117414 ATATATTAATTTAACTTTTTAAAT
1 ATATATTAATTTAAATTTTTAAAT
*
11117438 ATATATTAATTTAATATTTTTTAAT
1 ATATATTAATTTAA-ATTTTTAAAT
*
11117463 A-ATTTTAAT
1 ATATATTAAT
11117472 AAGTCATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATATTAATTTAAATTTTTAAAT
Found at i:11117605 original size:16 final size:17
Alignment explanation
Indices: 11117584--11117618 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11117574 TAATATTAAG
11117584 TATAAAAA-ACAAAAAA
1 TATAAAAATACAAAAAA
*
11117600 TATAAAAATATAAAAAA
1 TATAAAAATACAAAAAA
11117617 TA
1 TA
11117619 GCTTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
TATAAAAATACAAAAAA
Found at i:11124782 original size:22 final size:23
Alignment explanation
Indices: 11124757--11124799 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11124747 ATATAGTTTC
*
11124757 TTATCATTATAA-ATATTATTTA
1 TTATCACTATAATATATTATTTA
11124779 TTATCACTATAATATATTATT
1 TTATCACTATAATATATTATT
11124800 ATGTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATCACTATAATATATTATTTA
Found at i:11125468 original size:38 final size:38
Alignment explanation
Indices: 11125381--11125453 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
11125371 GCTAATTAAG
11125381 TATCATAATTAAAAGATTAAAAATTAAAATAAATTTAT
1 TATCATAATTAAAAGATTAAAAATTAAAATAAATTTAT
11125419 TATCATAATTAAAAGATTAAAAATTAAAATAAATT
1 TATCATAATTAAAAGATTAAAAATTAAAATAAATT
11125454 ATATGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (38 bp):
TATCATAATTAAAAGATTAAAAATTAAAATAAATTTAT
Found at i:11143006 original size:2 final size:2
Alignment explanation
Indices: 11142999--11143036 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11142989 CAAACACATC
11142999 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11143037 ATTAACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11161511 original size:15 final size:17
Alignment explanation
Indices: 11161460--11161524 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
11161450 ATATAAATTA
*
11161460 AAAATAAAAAATATATAT
1 AAAATATAAAAT-TATAT
*
11161478 TAAATATAAAATTATAT
1 AAAATATAAAATTATAT
* *
11161495 AAAAT-TAAATTTAATAA
1 AAAATATAAAATT-ATAT
*
11161512 AAAATATATAATT
1 AAAATATAAAATT
11161525 TTTATTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 6 0.16
17 17 0.45
18 15 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATAAAATTATAT
Found at i:11162251 original size:23 final size:20
Alignment explanation
Indices: 11162221--11162274 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
11162211 CCTTAATTTA
11162221 TTATTATTTTATCATTTTATTCC
1 TTATTATTTTAT-ATTTT-TT-C
11162244 TTATTATTTTTATATTTTTTC
1 TTATTA-TTTTATATTTTTTC
*
11162265 ATATTATTTT
1 TTATTATTTT
11162275 CGCATATGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 2 0.07
23 11 0.38
24 6 0.21
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTATTTTATATTTTTTC
Found at i:11169330 original size:10 final size:11
Alignment explanation
Indices: 11169299--11169332 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
11169289 TCACTTATAA
11169299 ATATAAATTTT
1 ATATAAATTTT
11169310 ATATAAAATTTT
1 ATAT-AAATTTT
11169322 A-ATAAATTTT
1 ATATAAATTTT
11169332 A
1 A
11169333 CATATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 6 0.27
12 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATAAATTTT
Found at i:11169834 original size:17 final size:18
Alignment explanation
Indices: 11169812--11169845 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11169802 GATTTTATTT
11169812 TATTTAATT-TTTGTTTA
1 TATTTAATTATTTGTTTA
*
11169829 TATTTATTTATTTGTTT
1 TATTTAATTATTTGTTT
11169846 CATGTGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TATTTAATTATTTGTTTA
Found at i:11171302 original size:3 final size:3
Alignment explanation
Indices: 11171294--11171323 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11171284 ATGAAAAAAC
*
11171294 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11171324 GAAAATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11179209 original size:25 final size:25
Alignment explanation
Indices: 11179181--11179240 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
11179171 GGTTTGAAAC
11179181 GTGAGAAGAGTTAAAGATTCAAGAT
1 GTGAGAAGAGTTAAAGATTCAAGAT
* *
11179206 GTGAGAAGAGTTGAAGATTTAAGAT
1 GTGAGAAGAGTTAAAGATTCAAGAT
*
11179231 GTGGGAAGAG
1 GTGAGAAGAG
11179241 CCGATGGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.35, T:0.23
Consensus pattern (25 bp):
GTGAGAAGAGTTAAAGATTCAAGAT
Found at i:11179264 original size:50 final size:48
Alignment explanation
Indices: 11179210--11179312 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 48
11179200 CAAGATGTGA
* *
11179210 GAAGAGTTGA-AGATTTAAGATGTGGGAAGAGCCGATGGTTCGAAACATGG
1 GAAGAGTTGACAG-TTCAAGATATGGGAAGAG-C-ATGGTTCGAAACATGG
* * * *
11179260 GAAGAGTTGACAGTTCGAGATATGGGAAGAGCTTGGTTTGAGACATGG
1 GAAGAGTTGACAGTTCAAGATATGGGAAGAGCATGGTTCGAAACATGG
11179308 GAAGA
1 GAAGA
11179313 AGTAAGCTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 18 0.39
49 1 0.02
50 25 0.54
51 2 0.04
ACGTcount: A:0.33, C:0.08, G:0.37, T:0.22
Consensus pattern (48 bp):
GAAGAGTTGACAGTTCAAGATATGGGAAGAGCATGGTTCGAAACATGG
Found at i:11179307 original size:23 final size:22
Alignment explanation
Indices: 11179245--11179312 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
11179235 GAAGAGCCGA
*
11179245 TGGTTCGAAACATGGGAAGAGT
1 TGGTTCGAGACATGGGAAGAGT
*
11179267 TGACAGTTCGAGATATGGGAAGAGCT
1 TG---GTTCGAGACATGGGAAGAG-T
*
11179293 TGGTTTGAGACATGGGAAGA
1 TGGTTCGAGACATGGGAAGA
11179313 AGTAAGCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.05
23 16 0.42
25 17 0.45
26 3 0.08
ACGTcount: A:0.31, C:0.09, G:0.37, T:0.24
Consensus pattern (22 bp):
TGGTTCGAGACATGGGAAGAGT
Found at i:11179549 original size:11 final size:11
Alignment explanation
Indices: 11179533--11179571 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
11179523 ATCATAAGAA
11179533 ATTTGTTTGAG
1 ATTTGTTTGAG
*
11179544 ATTTGTTGGAG
1 ATTTGTTTGAG
11179555 ATTTGTTTGAG
1 ATTTGTTTGAG
11179566 ATTTGT
1 ATTTGT
11179572 CAGATATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (11 bp):
ATTTGTTTGAG
Found at i:11179686 original size:52 final size:52
Alignment explanation
Indices: 11179596--11179752 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
11179586 TGGACAAGAA
* * *
11179596 GACTTACAAAAGAAGAATTCCAAGA-GAAAGAGGGTTCTTAATAGGTAAGTTT
1 GACTTACAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGTAAGTTT
* * *
11179648 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAATTT
1 GACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * * *
11179700 GACTTACAGGAGAAGAATTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTT
1 GACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
11179752 G
1 G
11179753 TATGGTTATA
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 85 0.94
53 5 0.06
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (52 bp):
GACTTACAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:11180422 original size:31 final size:31
Alignment explanation
Indices: 11180349--11180425 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
11180339 TTAGCCCAAT
* *
11180349 AAATGGTATCAAAGCTGTGGTGTTCCCCAAC
1 AAATGGTATCAGAGCTGTGGTGTTCCCAAAC
**
11180380 AAATGGTATCAGAGCTGTGGTGTTTTCAAAC
1 AAATGGTATCAGAGCTGTGGTGTTCCCAAAC
*
11180411 AAGTGGTATCAGAGC
1 AAATGGTATCAGAGC
11180426 GAGGTTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (31 bp):
AAATGGTATCAGAGCTGTGGTGTTCCCAAAC
Found at i:11180444 original size:14 final size:14
Alignment explanation
Indices: 11180425--11180454 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11180415 GGTATCAGAG
11180425 CGAGGTTCAAGGTT
1 CGAGGTTCAAGGTT
*
11180439 CGAGGTTTAAGGTT
1 CGAGGTTCAAGGTT
11180453 CG
1 CG
11180455 TGGGCCCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.37, T:0.30
Consensus pattern (14 bp):
CGAGGTTCAAGGTT
Found at i:11181820 original size:43 final size:43
Alignment explanation
Indices: 11181759--11181844 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
11181749 CTGGAATGCC
* *
11181759 TGTGATGAAAGAAAAAAAGAAAGGTAAGCATGTTAGCTTTGCA
1 TGTGATGAAAGAAAAAAAGAAAGGTAAACATGTTAACTTTGCA
11181802 TGTGATGAAAGAAAAAAAGAAAGGTAAACATGTTAACTTTGCA
1 TGTGATGAAAGAAAAAAAGAAAGGTAAACATGTTAACTTTGCA
11181845 GATATTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (43 bp):
TGTGATGAAAGAAAAAAAGAAAGGTAAACATGTTAACTTTGCA
Found at i:11181944 original size:20 final size:20
Alignment explanation
Indices: 11181919--11181958 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11181909 CATAATCCCA
11181919 CATCGAAAGTTAAGTAAGTT
1 CATCGAAAGTTAAGTAAGTT
11181939 CATCGAAAGTTAAGTAAGTT
1 CATCGAAAGTTAAGTAAGTT
11181959 TGAATTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
CATCGAAAGTTAAGTAAGTT
Found at i:11182134 original size:39 final size:39
Alignment explanation
Indices: 11182080--11182156 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
11182070 AGAGAATAGC
11182080 TAAGTGAGTAGGCTATTAAAGGGTGTAATTGGGTTTTGA
1 TAAGTGAGTAGGCTATTAAAGGGTGTAATTGGGTTTTGA
11182119 TAAGTGAGTAGGCTATTAAAGGGTGTAATTGGGTTTTG
1 TAAGTGAGTAGGCTATTAAAGGGTGTAATTGGGTTTTG
11182157 GGTTAAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.03, G:0.34, T:0.36
Consensus pattern (39 bp):
TAAGTGAGTAGGCTATTAAAGGGTGTAATTGGGTTTTGA
Found at i:11188116 original size:13 final size:13
Alignment explanation
Indices: 11188097--11188137 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
11188087 TTTTAAAATC
11188097 TATT-TTTT-ATA
1 TATTATTTTAATA
11188108 TATTATTTTAATA
1 TATTATTTTAATA
**
11188121 TAAAATTTTAATA
1 TATTATTTTAATA
11188134 TATT
1 TATT
11188138 TAAATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 4 0.17
12 4 0.17
13 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTATTTTAATA
Found at i:11191265 original size:22 final size:22
Alignment explanation
Indices: 11191204--11191292 Score: 83
Period size: 22 Copynumber: 3.9 Consensus size: 22
11191194 GTTTCAAAGC
*
11191204 TTTAGGGTTTT-AGTTTCGGGA
1 TTTAGGGTTTTGAGTTTAGGGA
* *
11191225 TTTCAAGGTTTTAGAGTTTAGGGT
1 TTT-AGGGTTTT-GAGTTTAGGGA
*
11191249 TTTTGGGTTTTGAGTTTTA-GGA
1 TTTAGGGTTTTGAG-TTTAGGGA
11191271 TTTAGGGTTTTGAAAGTTTAGG
1 TTTAGGGTTTTG--AGTTTAGG
11191293 CCTTAGGGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.06
22 23 0.43
23 14 0.26
24 14 0.26
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.48
Consensus pattern (22 bp):
TTTAGGGTTTTGAGTTTAGGGA
Found at i:11191290 original size:23 final size:22
Alignment explanation
Indices: 11191261--11191304 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
11191251 TTGGGTTTTG
11191261 AGTTTTAGGATTTAGGGTTTTGAA
1 AGTTT-AGGATTTAGGGTTTTG-A
**
11191285 AGTTTAGGCCTTAGGGTTTT
1 AGTTTAGGATTTAGGGTTTT
11191305 AAGGGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (22 bp):
AGTTTAGGATTTAGGGTTTTGA
Found at i:11191327 original size:25 final size:26
Alignment explanation
Indices: 11191295--11191355 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
11191285 AGTTTAGGCC
*
11191295 TTAGGGTTTTAAGGGTTTTGA-AGTT
1 TTAGGGTTTTAAGGATTTTGAGAGTT
* * *
11191320 TTAGGGTTTTGAGTATTTTGAGGGTT
1 TTAGGGTTTTAAGGATTTTGAGAGTT
11191346 TTAGGGTTTT
1 TTAGGGTTTT
11191356 TGGGCTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 18 0.58
26 13 0.42
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (26 bp):
TTAGGGTTTTAAGGATTTTGAGAGTT
Found at i:11191328 original size:8 final size:8
Alignment explanation
Indices: 11191231--11191371 Score: 78
Period size: 8 Copynumber: 17.8 Consensus size: 8
11191221 GGGATTTCAA
11191231 GGTTTTAG
1 GGTTTTAG
*
11191239 AG-TTTAG
1 GGTTTTAG
*
11191246 GGTTTTTG
1 GGTTTTAG
11191254 GGTTTT-G
1 GGTTTTAG
*
11191261 AGTTTTA-
1 GGTTTTAG
*
11191268 GGATTTAG
1 GGTTTTAG
*
11191276 GGTTTTGAA
1 GGTTTT-AG
*
11191285 AG-TTTA-
1 GGTTTTAG
**
11191291 GGCCTTAG
1 GGTTTTAG
11191299 GGTTTTAAG
1 GGTTTT-AG
11191308 GGTTTT-G
1 GGTTTTAG
*
11191315 AAGTTTTAG
1 -GGTTTTAG
11191324 GGTTTTGAG
1 GGTTTT-AG
**
11191333 TATTTTGAG
1 GGTTTT-AG
11191342 GGTTTTAG
1 GGTTTTAG
*
11191350 GGTTTTTG
1 GGTTTTAG
*
11191358 GGCTTTAG
1 GGTTTTAG
11191366 GGTTTT
1 GGTTTT
11191372 GAGATTTTAA
Statistics
Matches: 100, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
6 1 0.01
7 22 0.22
8 53 0.53
9 24 0.24
ACGTcount: A:0.16, C:0.02, G:0.33, T:0.49
Consensus pattern (8 bp):
GGTTTTAG
Found at i:11191455 original size:8 final size:8
Alignment explanation
Indices: 11191299--11191456 Score: 56
Period size: 8 Copynumber: 19.8 Consensus size: 8
11191289 TAGGCCTTAG
11191299 GGTTTTAA
1 GGTTTTAA
11191307 GGGTTTTGAA
1 -GGTTTT-AA
*
11191317 -GTTTTAG
1 GGTTTTAA
*
11191324 GGTTTTGA
1 GGTTTTAA
* *
11191332 GTATTTTGAG
1 G-GTTTT-AA
*
11191342 GGTTTTAG
1 GGTTTTAA
**
11191350 GGTTTTTG
1 GGTTTTAA
* *
11191358 GGCTTTAG
1 GGTTTTAA
*
11191366 GGTTTTGA
1 GGTTTTAA
*
11191374 GATTTTAA
1 GGTTTTAA
* *
11191382 -GATTTAG
1 GGTTTTAA
11191389 GGTTTTAAA
1 GGTTTT-AA
*
11191398 GG-CTTAA
1 GGTTTTAA
11191405 GGTTTT--
1 GGTTTTAA
*
11191411 GATTTTAA
1 GGTTTTAA
* *
11191419 AGTTTTAT
1 GGTTTTAA
*
11191427 GATTTTAA
1 GGTTTTAA
*
11191435 GGTTTCAA
1 GGTTTTAA
*
11191443 AGTTTTAA
1 GGTTTTAA
11191451 GGTTTT
1 GGTTTT
11191457 GACTTTTTTT
Statistics
Matches: 106, Mismatches: 34, Indels: 19
0.67 0.21 0.12
Matches are distributed among these distances:
6 5 0.05
7 9 0.08
8 72 0.68
9 17 0.16
10 3 0.03
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (8 bp):
GGTTTTAA
Found at i:11191456 original size:24 final size:22
Alignment explanation
Indices: 11191401--11191458 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
11191391 TTTTAAAGGC
*
11191401 TTAAGGTTTTGATTTTAAAGTT
1 TTAAGGTTTTGATTTCAAAGTT
* * *
11191423 TTATGATTTTAAGGTTTCAAAGTT
1 TTAAGGTTTT--GATTTCAAAGTT
11191447 TTAAGGTTTTGA
1 TTAAGGTTTTGA
11191459 CTTTTTTTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
22 9 0.33
24 18 0.67
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.52
Consensus pattern (22 bp):
TTAAGGTTTTGATTTCAAAGTT
Found at i:11191855 original size:21 final size:22
Alignment explanation
Indices: 11191831--11191873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11191821 AACGTTTAAG
11191831 CAAAATTAAATT-TTTTAAACA
1 CAAAATTAAATTCTTTTAAACA
* *
11191852 CAAATTTAAATTCTTTTCAACA
1 CAAAATTAAATTCTTTTAAACA
11191874 TTTAGGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (22 bp):
CAAAATTAAATTCTTTTAAACA
Found at i:11192106 original size:2 final size:2
Alignment explanation
Indices: 11192058--11192097 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
11192048 CACCACACTC
* * *
11192058 AT AT AT AT AT AT AT AT AT AT AC AT AT AA AA 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
11192098 GCATATATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:11200734 original size:23 final size:23
Alignment explanation
Indices: 11200704--11200751 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
11200694 TCCTTTCTTA
11200704 TTTTTCTT-TCTATTTTTCTTGGT
1 TTTTTCTTATCTATTTTT-TTGGT
* *
11200727 TTTTTCTTATTTCTTTTTTTGGT
1 TTTTTCTTATCTATTTTTTTGGT
11200750 TT
1 TT
11200752 GCGACACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.04, C:0.10, G:0.08, T:0.77
Consensus pattern (23 bp):
TTTTTCTTATCTATTTTTTTGGT
Found at i:11211219 original size:18 final size:18
Alignment explanation
Indices: 11211172--11211219 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11211162 AAAATGTGAT
*
11211172 TTTTAAAAAAAATAAAAA
1 TTTTAAAAAAAAGAAAAA
*
11211190 -TTCATAAAAAAAGAAAAA
1 TTTTA-AAAAAAAGAAAAA
11211208 TTTTAAAAAAAA
1 TTTTAAAAAAAA
11211220 TGATAAGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
TTTTAAAAAAAAGAAAAA
Found at i:11214057 original size:27 final size:27
Alignment explanation
Indices: 11214027--11214078 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
11214017 ATACAACATA
* *
11214027 ATTAATCTATTTAAATATGATTAACTT
1 ATTAACCTATTTAAATAGGATTAACTT
*
11214054 ATTAACCTGTTTAAATAGGATTAAC
1 ATTAACCTATTTAAATAGGATTAAC
11214079 ATGTTATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (27 bp):
ATTAACCTATTTAAATAGGATTAACTT
Found at i:11217338 original size:25 final size:25
Alignment explanation
Indices: 11217310--11217361 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
11217300 GATTTTAAGA
11217310 GATGAAAGAGAAAATTAATGGCGAT
1 GATGAAAGAGAAAATTAATGGCGAT
11217335 GATGAAAGAGAAAATTAATGGCGAT
1 GATGAAAGAGAAAATTAATGGCGAT
11217360 GA
1 GA
11217362 ATCGGTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.29, T:0.19
Consensus pattern (25 bp):
GATGAAAGAGAAAATTAATGGCGAT
Found at i:11219424 original size:41 final size:41
Alignment explanation
Indices: 11219352--11219431 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
11219342 TTATAAAATT
* ***
11219352 TAAAAAATTGGAAAAATCATAAATTGGAATTAGTTAGTGTA
1 TAAAAAATTGGAAAAATAATAAATAAAAATTAGTTAGTGTA
11219393 TAAAAAAGTTGGAAAAATAATAAA-AAAAATTAGTTAGTG
1 TAAAAAA-TTGGAAAAATAATAAATAAAAATTAGTTAGTG
11219432 AATCATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.54, C:0.01, G:0.16, T:0.29
Consensus pattern (41 bp):
TAAAAAATTGGAAAAATAATAAATAAAAATTAGTTAGTGTA
Found at i:11224422 original size:3 final size:3
Alignment explanation
Indices: 11224416--11224448 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
11224406 GATGATAGTG
11224416 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11224449 CTTAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11225626 original size:22 final size:23
Alignment explanation
Indices: 11225590--11225644 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
11225580 ATAATTATTT
* *
11225590 TATATATAAATTTATTTAAATA-
1 TATATAAAAATTTATTAAAATAG
11225612 TATA-AAAAATCTTATTAAAATAG
1 TATATAAAAAT-TTATTAAAATAG
11225635 TATATAAAAA
1 TATATAAAAA
11225645 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 4 0.14
24 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TATATAAAAATTTATTAAAATAG
Found at i:11227313 original size:2 final size:2
Alignment explanation
Indices: 11227298--11227331 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11227288 TATTGGCTAA
* *
11227298 AT AT AT AG AC 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
11227332 GGTATTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:11236745 original size:27 final size:26
Alignment explanation
Indices: 11236705--11236759 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
11236695 AGATAGAATG
11236705 ATATTATTTAATTTAATCATATTTATA
1 ATATTATTTAATTTAATCATA-TTATA
* *
11236732 ATATTATCTT-ATTTTATCCTATTATA
1 ATATTAT-TTAATTTAATCATATTATA
11236758 AT
1 AT
11236760 TTTGTATCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 16 0.64
28 2 0.08
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATTATTTAATTTAATCATATTATA
Found at i:11242664 original size:110 final size:110
Alignment explanation
Indices: 11242466--11242669 Score: 381
Period size: 110 Copynumber: 1.9 Consensus size: 110
11242456 GCAAATGAAA
11242466 CAAAAATCATAAAAGACTTCCTAAAGTCCCTTTGCCTTGTTGAAGTGGCTATCCACTCTTTGGCC
1 CAAAAATCATAAAAGACTTCCTAAAGTCCCTTTGCCTTGTTGAAGTGGCTATCCACTCTTTGGCC
*
11242531 TGGGTTGGATTCTTTGAGTGGGATTAGACCAACTTTTTGATGACC
66 TGGGTTGGATTCTTTGAGGGGGATTAGACCAACTTTTTGATGACC
*
11242576 CAAAAATCATAAAAGACTTCCTAAAGTGCCTTTGCCTTGTTGAAGTGGCTATCCACTCTTTGGCC
1 CAAAAATCATAAAAGACTTCCTAAAGTCCCTTTGCCTTGTTGAAGTGGCTATCCACTCTTTGGCC
*
11242641 TTGGTTGGATTCTTTGAGGGGGATTAGAC
66 TGGGTTGGATTCTTTGAGGGGGATTAGAC
11242670 TAAGTGATAT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 91 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (110 bp):
CAAAAATCATAAAAGACTTCCTAAAGTCCCTTTGCCTTGTTGAAGTGGCTATCCACTCTTTGGCC
TGGGTTGGATTCTTTGAGGGGGATTAGACCAACTTTTTGATGACC
Found at i:11243487 original size:13 final size:13
Alignment explanation
Indices: 11243464--11243497 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
11243454 ATAATTTTTT
11243464 TTTATTTTATCATA
1 TTTA-TTTATCATA
11243478 TTTATTTATCATA
1 TTTATTTATCATA
11243491 TTT-TTTA
1 TTTATTTA
11243498 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 12 0.60
14 4 0.20
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTTATCATA
Found at i:11243621 original size:8 final size:7
Alignment explanation
Indices: 11243604--11243637 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
11243594 TCAATCAATC
11243604 AAAATTA
1 AAAATTA
11243611 AAAATTAA
1 AAAATT-A
11243619 AAAATTA
1 AAAATTA
11243626 AAAATTA
1 AAAATTA
11243633 GAAAA
1 -AAAA
11243638 AAACAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:11243624 original size:15 final size:16
Alignment explanation
Indices: 11243604--11243638 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
11243594 TCAATCAATC
11243604 AAAATTAAAAATTA-A
1 AAAATTAAAAATTAGA
11243619 AAAATTAAAAATTAGA
1 AAAATTAAAAATTAGA
11243635 AAAA
1 AAAA
11243639 AACAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAATTAAAAATTAGA
Found at i:11245702 original size:22 final size:22
Alignment explanation
Indices: 11245640--11245706 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
11245630 ACTTGTTTGG
11245640 TTTTAGAGAGAGAGGGAATGAA-T
1 TTTTAGAGAGAGA-GG-ATGAATT
* * *
11245663 TTTTAGAGGGAAATGATGAATT
1 TTTTAGAGAGAGAGGATGAATT
*
11245685 TTTTAAAGAGAGAGGATGAATT
1 TTTTAGAGAGAGAGGATGAATT
11245707 GAAATGAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.14
22 20 0.56
23 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.31
Consensus pattern (22 bp):
TTTTAGAGAGAGAGGATGAATT
Found at i:11246301 original size:85 final size:86
Alignment explanation
Indices: 11246187--11246347 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 86
11246177 TTATTTTGTT
* * * *
11246187 TAATTATGATTAGAAGGTATTATAGTAATTTTAGAC-AATTATAATATGATG-GGCATTTTCGTA
1 TAATTATGAGTAGAAGGTATTATAGTAATTTT-GACAAATCATAATAT-AAGAGGCATTTTCATA
11246250 ATTATGATAATAGAGCATTTTTG
64 ATTATGATAATAGAGCATTTTTG
*
11246273 TAATTAT-AGTAG-AGGATATTATAGTAATTTTGACAAATCATAATATAAGAGGTATTTTCATAA
1 TAATTATGAGTAGAAGG-TATTATAGTAATTTTGACAAATCATAATATAAGAGGCATTTTCATAA
*
11246336 TTATGGTAATAG
65 TTATGATAATAG
11246348 GGACATTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
84 8 0.12
85 51 0.77
86 7 0.11
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (86 bp):
TAATTATGAGTAGAAGGTATTATAGTAATTTTGACAAATCATAATATAAGAGGCATTTTCATAAT
TATGATAATAGAGCATTTTTG
Found at i:11246365 original size:35 final size:35
Alignment explanation
Indices: 11246326--11246400 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
11246316 TATAAGAGGT
* *
11246326 ATTTT-CATAATTATGGTAATAGGGACATTATAGTA
1 ATTTTGCATAATAATGGTAAGAGGG-CATTATAGTA
* *
11246361 ATTTTGGATAATAATGGTAAGAGGGCATTGTAGTA
1 ATTTTGCATAATAATGGTAAGAGGGCATTATAGTA
11246396 ATTTT
1 ATTTT
11246401 AGTCAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (35 bp):
ATTTTGCATAATAATGGTAAGAGGGCATTATAGTA
Found at i:11246372 original size:36 final size:35
Alignment explanation
Indices: 11246332--11246400 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
11246322 AGGTATTTTC
* *
11246332 ATAATTATGGTAATAGGGACATTATAGTAATTTTGG
1 ATAATAATGGTAAGAGGG-CATTATAGTAATTTTGG
*
11246368 ATAATAATGGTAAGAGGGCATTGTAGTAATTTT
1 ATAATAATGGTAAGAGGGCATTATAGTAATTTT
11246401 AGTCAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (35 bp):
ATAATAATGGTAAGAGGGCATTATAGTAATTTTGG
Found at i:11246986 original size:8 final size:8
Alignment explanation
Indices: 11246960--11246998 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
11246950 TAAATAATTT
11246960 TAAAGAAAA
1 TAAA-AAAA
*
11246969 GTAAAGAAA
1 -TAAAAAAA
11246978 TAAAAAAA
1 TAAAAAAA
11246986 TAAAAAAA
1 TAAAAAAA
11246994 TAAAA
1 TAAAA
11246999 TCCAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 3 0.11
10 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:11247272 original size:12 final size:11
Alignment explanation
Indices: 11247237--11247272 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
11247227 TTATTTAAAA
11247237 AATTATTTTTT
1 AATTATTTTTT
11247248 AATTAATTTTTT
1 AATT-ATTTTTT
11247260 AATTATTTATTT
1 AATTATTT-TTT
11247272 A
1 A
11247273 TATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTATTTTTT
Found at i:11247300 original size:16 final size:16
Alignment explanation
Indices: 11247276--11247330 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
11247266 TTATTTATAT
*
11247276 ATATATTTATATAATA
1 ATATATTTAAATAATA
*
11247292 ATATTTTTAAAT-AT-
1 ATATATTTAAATAATA
* *
11247306 TTATATTTAAAAAATA
1 ATATATTTAAATAATA
*
11247322 ATATTTTTA
1 ATATATTTA
11247331 TTAATTTCGG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 9 0.30
15 4 0.13
16 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTAAATAATA
Found at i:11247311 original size:30 final size:30
Alignment explanation
Indices: 11247272--11247330 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
11247262 TTATTTATTT
* *
11247272 ATATATATATTTATATAATAATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
11247302 ATATTTATATTTAAAAAATAATATTTTTA
1 ATATATATATTTAAAAAATAATATTTTTA
11247331 TTAATTTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:11247647 original size:17 final size:16
Alignment explanation
Indices: 11247625--11247662 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
11247615 AAGTTTCACA
11247625 TATAAAAATATAATTTT
1 TATAAAAATAT-ATTTT
*
11247642 TATAAATATATATTTT
1 TATAAAAATATATTTT
11247658 TATAA
1 TATAA
11247663 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAAAAATATATTTT
Found at i:11247650 original size:15 final size:16
Alignment explanation
Indices: 11247630--11247662 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11247620 TCACATATAA
11247630 AAATATA-ATTTTTAT
1 AAATATATATTTTTAT
11247645 AAATATATATTTTTAT
1 AAATATATATTTTTAT
11247661 AA
1 AA
11247663 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:11249754 original size:9 final size:8
Alignment explanation
Indices: 11249720--11249987 Score: 104
Period size: 8 Copynumber: 34.4 Consensus size: 8
11249710 TGGGATCTCA
11249720 TTTTAGGG
1 TTTTAGGG
11249728 TTTT--GG
1 TTTTAGGG
*
11249734 TTTT-GAG
1 TTTTAGGG
11249741 TTTTAAGGG
1 TTTT-AGGG
11249750 TTTTAGGG
1 TTTTAGGG
11249758 ---T-GGAG
1 TTTTAGG-G
*
11249763 TTTTGGGG
1 TTTTAGGG
*
11249771 TTTTA-GA
1 TTTTAGGG
*
11249778 TTTTAAGG
1 TTTTAGGG
11249786 TTTTAGGG
1 TTTTAGGG
*
11249794 CTTT-GGAG
1 TTTTAGG-G
*
11249802 TTTTGGGG
1 TTTTAGGG
11249810 TTTTAAGGG
1 TTTT-AGGG
*
11249819 TTTTAGGA
1 TTTTAGGG
*
11249827 TTTTA-GA
1 TTTTAGGG
11249834 TTTTAGGG
1 TTTTAGGG
**
11249842 TTTTAAAG
1 TTTTAGGG
*
11249850 -TTTAAGG
1 TTTTAGGG
*
11249857 TTTGGAGGG
1 TTT-TAGGG
11249866 -TTTAGGG
1 TTTTAGGG
11249873 -TTTAGTGG
1 TTTTAG-GG
11249881 ATTTTA-GG
1 -TTTTAGGG
**
11249889 TTTTCAAAG
1 TTTT-AGGG
11249898 -TTTAGGG
1 TTTTAGGG
**
11249905 TTTT-GAAA
1 TTTTAG-GG
*
11249913 TTTTAAGG
1 TTTTAGGG
11249921 TTTTAAGGG
1 TTTT-AGGG
*
11249930 TTTTAAGG
1 TTTTAGGG
*
11249938 TTTTATGG
1 TTTTAGGG
11249946 TTTTGAGGG
1 TTTT-AGGG
*
11249955 TTTT-GAG
1 TTTTAGGG
* *
11249962 TGTTATGG
1 TTTTAGGG
*
11249970 TTTT-GGA
1 TTTTAGGG
11249977 TTTTAGGG
1 TTTTAGGG
11249985 TTT
1 TTT
11249988 CAAAATTTAA
Statistics
Matches: 196, Mismatches: 37, Indels: 54
0.68 0.13 0.19
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 6 0.03
7 52 0.27
8 95 0.48
9 35 0.18
10 4 0.02
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (8 bp):
TTTTAGGG
Found at i:11249933 original size:25 final size:26
Alignment explanation
Indices: 11249901--11249960 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
11249891 TTCAAAGTTT
11249901 AGGGTTTTGAA-ATTTTAAGGTTTTA
1 AGGGTTTTGAAGATTTTAAGGTTTTA
* * *
11249926 AGGGTTTT-AAGGTTTTATGGTTTTG
1 AGGGTTTTGAAGATTTTAAGGTTTTA
11249951 AGGGTTTTGA
1 AGGGTTTTGA
11249961 GTGTTATGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.07
25 27 0.90
26 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (26 bp):
AGGGTTTTGAAGATTTTAAGGTTTTA
Found at i:11249949 original size:16 final size:16
Alignment explanation
Indices: 11249913--11250044 Score: 58
Period size: 16 Copynumber: 8.2 Consensus size: 16
11249903 GGTTTTGAAA
*
11249913 TTTTAAGGTTTTAAGGG
1 TTTTAAGGTTTT-ATGG
11249930 TTTTAAGGTTTTATGG
1 TTTTAAGGTTTTATGG
* *
11249946 TTTTGAGGGTTT-TGAG
1 TTTTAAGGTTTTATG-G
* *
11249962 TGTTATGG-TTT-TGG
1 TTTTAAGGTTTTATGG
* * **
11249976 ATTTTAGGGTTTCA-AA
1 -TTTTAAGGTTTTATGG
* *
11249992 ATTTAAGATTTTGA-GG
1 TTTTAAGGTTTT-ATGG
* **
11250008 ATTTAAGGTTTTGATTT
1 TTTTAAGGTTTT-ATGG
11250025 TTTTAAGGTTTTATGG
1 TTTTAAGGTTTTATGG
11250041 TTTT
1 TTTT
11250045 TTATTTTAGA
Statistics
Matches: 86, Mismatches: 23, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
14 1 0.01
15 21 0.24
16 41 0.48
17 23 0.27
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.53
Consensus pattern (16 bp):
TTTTAAGGTTTTATGG
Found at i:11250044 original size:71 final size:73
Alignment explanation
Indices: 11249964--11250110 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 73
11249954 GTTTTGAGTG
* * *
11249964 TTATGGTTTTGGATTTTAGGGTTTCA-AAATTTAAGATTTTGAGGATTT-AAGGTTTTGATTTTT
1 TTATGGTTTTGGATTTTAGAGTTT-AGAAATTTAAGAGTTTCAGGATTTGAAGGTTTTGATTTTT
*
11250027 TT-AAGGTT
65 TTGAAAGTT
** * * *
11250035 TTATGGTTTTTTATTTTAGAGTTTAGAAATTTTAGGGTTTCAGGTTTTGAAGGTTTTGATTTTTT
1 TTATGGTTTTGGATTTTAGAGTTTAGAAATTTAAGAGTTTCAGGATTTGAAGGTTTTGATTTTTT
11250100 TGAAAGTT
66 TGAAAGTT
11250108 TTA
1 TTA
11250111 AAAAAATATG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 38 0.59
72 17 0.27
73 8 0.12
ACGTcount: A:0.23, C:0.01, G:0.22, T:0.54
Consensus pattern (73 bp):
TTATGGTTTTGGATTTTAGAGTTTAGAAATTTAAGAGTTTCAGGATTTGAAGGTTTTGATTTTTT
TGAAAGTT
Found at i:11250228 original size:3 final size:3
Alignment explanation
Indices: 11250220--11250249 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11250210 TATTTTATAT
11250220 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11250250 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.