Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 138 of 208
Found at i:42126351 original size:71 final size:71
Alignment explanation
Indices: 42126270--42126412 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
42126260 TTGTTACCTT
42126270 ATTTAACCTCTTGAATTTGACATGGCAAAACCTAACATAACCTGCATACTAACCATTTAAATACT
1 ATTTAACCTCTTGAATTTGACATGGCAAAACCTAACATAACCTGCATACTAACCATTTAAATACT
42126335 GTACAA
66 GTACAA
42126341 ATTTAACCTCTTGAATTTGACATGGCAAAACCTAACATAACCTGCATACTAACCATTTAAATACT
1 ATTTAACCTCTTGAATTTGACATGGCAAAACCTAACATAACCTGCATACTAACCATTTAAATACT
42126406 GTACAA
66 GTACAA
42126412 A
1 A
42126413 CAAGACAAGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (71 bp):
ATTTAACCTCTTGAATTTGACATGGCAAAACCTAACATAACCTGCATACTAACCATTTAAATACT
GTACAA
Found at i:42129746 original size:11 final size:11
Alignment explanation
Indices: 42129732--42129770 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42129722 GTTTTCTTCT
42129732 TATTTTACTAC
1 TATTTTACTAC
*
42129743 TATTTTACTAT
1 TATTTTACTAC
* *
42129754 TATATTGCTAC
1 TATTTTACTAC
42129765 TATTTT
1 TATTTT
42129771 TTTGTTATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.59
Consensus pattern (11 bp):
TATTTTACTAC
Found at i:42129748 original size:22 final size:22
Alignment explanation
Indices: 42129723--42129779 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
42129713 TTTCTTGTTG
*
42129723 TTTTCTTCTTATTTTACTACTA
1 TTTTCTTATTATTTTACTACTA
* *
42129745 TTTTAC-TATTATATTGCTACTA
1 TTTT-CTTATTATTTTACTACTA
* *
42129767 TTTTTTTGTTATT
1 TTTTCTTATTATT
42129780 GTTTGGATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTCTTATTATTTTACTACTA
Found at i:42129842 original size:30 final size:30
Alignment explanation
Indices: 42129808--42129872 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
42129798 AATTATTTTA
42129808 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
42129838 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
42129868 TTGTT
1 TTGTT
42129873 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:42131936 original size:47 final size:46
Alignment explanation
Indices: 42131817--42131942 Score: 153
Period size: 47 Copynumber: 2.7 Consensus size: 46
42131807 AATGTATATA
* * *
42131817 TATAAATATTTGTTATGCATGAAAATGAATTAATCTATAGCTGAATG
1 TATATATATTTGTTATGCATG-AAATGAATTAAACTATAGCCGAATG
* * * *
42131864 TATATGTAATTGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG
1 TATATATATTTGTTATGCA-TGAAATGAATTAAACTATAGCCGAATG
*
42131911 TATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATTTGTTATGCA-TGAAATGAATTA
42131943 TTTGAAATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 65 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (46 bp):
TATATATATTTGTTATGCATGAAATGAATTAAACTATAGCCGAATG
Found at i:42132010 original size:163 final size:164
Alignment explanation
Indices: 42131809--42132107 Score: 521
Period size: 163 Copynumber: 1.8 Consensus size: 164
42131799 TAACTACGAA
*
42131809 TGTATATATATAAATATTTGTTATGCATGAAAATGAATTAATCTATAGCTGAATGTATATGTAAT
1 TGTATATATATAAATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATATGTAAT
* *
42131874 TGTTATGCAGAGAAATGAATTAAACTATGGCCGAATG-TATATATATTTGTTATGCATTGAAATA
66 TGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATTGAAATA
42131938 AATTATTTGAAATTACATAGGTTATGGCCGAATG
131 AATTATTTGAAATTACATAGGTTATGGCCGAATG
*
42131972 TGTATATATATATATATTTGTTATACATTG-AAATGAATTAATCTATAGCTGAATGTATATGTAA
1 TGTATATATATAAATATTTGTTATACA-TGAAAATGAATTAATCTATAGCTGAATGTATATGTAA
42132036 TTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGTATATATATATTTGTTATACATTGAAA
65 TTGTTATGCAGAGAAATAAATTAAACTATGGCCGAATG-ATATATATATTTGTTATACATTGAAA
*
42132101 TGAATTA
129 TAAATTA
42132108 ATCTATAGCT
Statistics
Matches: 128, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
163 96 0.75
164 2 0.02
165 30 0.23
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (164 bp):
TGTATATATATAAATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATATGTAAT
TGTTATGCAGAGAAATAAATTAAACTATGGCCGAATGATATATATATTTGTTATACATTGAAATA
AATTATTTGAAATTACATAGGTTATGGCCGAATG
Found at i:42132116 original size:96 final size:96
Alignment explanation
Indices: 42131978--42132280 Score: 543
Period size: 96 Copynumber: 3.1 Consensus size: 96
42131968 AATGTGTATA
42131978 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
42132043 GCAGAGAAATAAATTAAACTATGGCCGAATG
66 GCAGAGAAATAAATTAAACTATGGCCGAATG
*
42132074 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTATTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
42132139 GCAGAGAAATAAATTAAACTATGGCCGAATGTG
66 GCAGAGAAATAAATTAAACTATGGCCGAA--TG
42132172 TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
1 --TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTT
* *
42132237 ATGCAGAGAAATGAATTAAACTATGGTCGAATG
64 ATGCAGAGAAATAAATTAAACTATGGCCGAATG
42132270 TATATATATAT
1 TATATATATAT
42132281 ATATATATTT
Statistics
Matches: 199, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
96 104 0.52
98 4 0.02
100 91 0.46
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (96 bp):
TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
GCAGAGAAATAAATTAAACTATGGCCGAATG
Found at i:42132229 original size:100 final size:100
Alignment explanation
Indices: 42131960--42132284 Score: 568
Period size: 100 Copynumber: 3.3 Consensus size: 100
42131950 TTACATAGGT
42131960 TATGGCCGAATGTGTATATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAA
1 TATGGCCGAATGTG--TATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAA
42132025 TGTATATGTAATTGTTATGCAGAGAAATAAATTAAAC
64 TGTATATGTAATTGTTATGCAGAGAAATAAATTAAAC
42132062 TATGGCCGAA--TG--TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 TATGGCCGAATGTGTATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
*
42132123 TATATGTAATTATTATGCAGAGAAATAAATTAAAC
66 TATATGTAATTGTTATGCAGAGAAATAAATTAAAC
42132158 TATGGCCGAATGTGTATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
1 TATGGCCGAATGTGTATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
*
42132223 TATATGTAATTGTTATGCAGAGAAATGAATTAAAC
66 TATATGTAATTGTTATGCAGAGAAATAAATTAAAC
* *
42132258 TATGGTCGAATGTATATATATATATAT
1 TATGGCCGAATGTGTATATATATATAT
42132285 ATATTTGTTG
Statistics
Matches: 214, Mismatches: 5, Indels: 10
0.93 0.02 0.04
Matches are distributed among these distances:
96 93 0.43
98 2 0.01
100 109 0.51
102 10 0.05
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (100 bp):
TATGGCCGAATGTGTATATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATG
TATATGTAATTGTTATGCAGAGAAATAAATTAAAC
Found at i:42132475 original size:41 final size:41
Alignment explanation
Indices: 42132419--42132572 Score: 218
Period size: 41 Copynumber: 3.8 Consensus size: 41
42132409 TGTAAGTTCG
* **
42132419 GGCTTTATACCTAGCAGGCTCTGTGCCGGTGAAATGTATTG
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
42132460 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
* *
42132501 GGCTTTATGCCTAGCAGGCTCTGTGCTGGTGAAATTTATCA
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
* * * * *
42132542 GGCTTTGTGTCTAGCAGACTTTATGCCGGTG
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTG
42132573 TTTTATATAA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 102 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.32
Consensus pattern (41 bp):
GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
Found at i:42132586 original size:82 final size:82
Alignment explanation
Indices: 42132419--42132591 Score: 202
Period size: 82 Copynumber: 2.1 Consensus size: 82
42132409 TGTAAGTTCG
* ** * *
42132419 GGCTTTATACCTAGCAGGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTGT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCAGGCTTTATGCCTAGCAGACTCTAT
* *
42132484 GCCGGTGAAATGTATCA
66 GCCGGTGAAATATATAA
* * * * *
42132501 GGCTTTATGCCTAGCAGGCTCTGTGCTGGTGAAATTTATCAGGCTTTGTGTCTAGCAGACTTTAT
1 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCAGGCTTTATGCCTAGCAGACTCTAT
***
42132566 GCCGGTGTTTTATATAA
66 GCCGGTGAAATATATAA
*
42132583 GGCTCTATG
1 GGCTTTATG
42132592 TTTAACAAGT
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCAGGCTTTATGCCTAGCAGACTCTAT
GCCGGTGAAATATATAA
Found at i:42135317 original size:21 final size:21
Alignment explanation
Indices: 42135291--42135332 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42135281 AAACCTGGTA
42135291 AAAGGTATCAATACTTTTTGT
1 AAAGGTATCAATACTTTTTGT
*
42135312 AAAGGTATCGATACTTTTTGT
1 AAAGGTATCAATACTTTTTGT
42135333 GTAATTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (21 bp):
AAAGGTATCAATACTTTTTGT
Found at i:42137711 original size:22 final size:21
Alignment explanation
Indices: 42137669--42137708 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42137659 AAACTTGGTA
42137669 AAAGGTATCAATACTTTTTGT
1 AAAGGTATCAATACTTTTTGT
*
42137690 AAAGGTATCGATACTTTTT
1 AAAGGTATCAATACTTTTT
42137709 TGTGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
AAAGGTATCAATACTTTTTGT
Found at i:42140223 original size:45 final size:45
Alignment explanation
Indices: 42140159--42140275 Score: 162
Period size: 45 Copynumber: 2.6 Consensus size: 45
42140149 AAACAAGTTG
* *
42140159 CTAGTACGATGTGGATAAACCACTCATTGGTGCAGATAAAAATTA
1 CTAGTACGGTGTGGATAAACCACTCATTGATGCAGATAAAAATTA
* ** *
42140204 CTAGTACGGTGTGGATAAACCACTCATTGATGTAGATAAATGTTG
1 CTAGTACGGTGTGGATAAACCACTCATTGATGCAGATAAAAATTA
* *
42140249 CTAATACGGTGTGGATAAACCATTCAT
1 CTAGTACGGTGTGGATAAACCACTCAT
42140276 CCGTACAGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
CTAGTACGGTGTGGATAAACCACTCATTGATGCAGATAAAAATTA
Found at i:42140286 original size:45 final size:43
Alignment explanation
Indices: 42140153--42140310 Score: 147
Period size: 45 Copynumber: 3.6 Consensus size: 43
42140143 TTTTACAAAC
* * *
42140153 AAGTTGCTAGTACGATGTGGATAAACCACTCATTGGTGCAGATAA
1 AAGTTGCTAATACGGTGTGGATAAACCACTCA-TCGTGCAGAT-A
* * * * *
42140198 AAATTACTAGTACGGTGTGGATAAACCACTCATTGATGTAGATA
1 AAGTTGCTAATACGGTGTGGATAAACCACTCATCG-TGCAGATA
* *
42140242 AATGTTGCTAATACGGTGTGGATAAACCATTCATCCGTACAGATA
1 AA-GTTGCTAATACGGTGTGGATAAACCACTCAT-CGTGCAGATA
* * *
42140287 AA-CTGCTTATACGGTGTGCATAAA
1 AAGTTGCTAATACGGTGTGGATAAA
42140311 GCATTAACGG
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
43 19 0.20
44 5 0.05
45 70 0.74
46 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (43 bp):
AAGTTGCTAATACGGTGTGGATAAACCACTCATCGTGCAGATA
Found at i:42140425 original size:34 final size:34
Alignment explanation
Indices: 42140382--42140464 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
42140372 ATGCAATATG
** *
42140382 ACATGCTTATAGTAAATCAATAC-GATAGTAATAA
1 ACATGCTTATAACAAATCAATACAG-TAGCAATAA
*
42140416 ACATGCTTATAACATATCAATACAGTAGCAATAA
1 ACATGCTTATAACAAATCAATACAGTAGCAATAA
42140450 ACATGCTTATAACAA
1 ACATGCTTATAACAA
42140465 GTCCGTATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 42 0.98
35 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.28
Consensus pattern (34 bp):
ACATGCTTATAACAAATCAATACAGTAGCAATAA
Found at i:42148017 original size:23 final size:22
Alignment explanation
Indices: 42147931--42148017 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
42147921 GCTGGTAAAT
*
42147931 GGTAAGCTCTATTGAGCTG-AAC
1 GGTAAGCTC-ATAGAGCTGAAAC
* * *
42147953 GGTAAGCTCCGTAAAGCTAAAAC
1 GGTAAGCT-CATAGAGCTGAAAC
* *
42147976 GGTAAGCTCAAAAGGGCTGAAAC
1 GGTAAGCTC-ATAGAGCTGAAAC
42147999 GGTAAGCTCATACGAGCTG
1 GGTAAGCTCATA-GAGCTG
42148018 TGGTGAGTCC
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
22 16 0.32
23 34 0.68
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
GGTAAGCTCATAGAGCTGAAAC
Found at i:42153758 original size:32 final size:31
Alignment explanation
Indices: 42153722--42153782 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
42153712 CTGACGCTGG
*
42153722 TTTTCCGTTCTCTGCGT-TTTTCTGGCAATTAT
1 TTTTCCGTTCTCT-C-TAATTTCTGGCAATTAT
*
42153754 TTTTCCTTTCTCTCTAATTTCTGGCAATT
1 TTTTCCGTTCTCTCTAATTTCTGGCAATT
42153783 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 13 0.50
32 12 0.46
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.54
Consensus pattern (31 bp):
TTTTCCGTTCTCTCTAATTTCTGGCAATTAT
Found at i:42154431 original size:50 final size:50
Alignment explanation
Indices: 42154329--42154431 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 50
42154319 GCCGTGTAGG
* * *
42154329 CCACACGGGCAAGGCTAATCCGGGCCTGTGGGCCACATGAGCGTGTGTGC
1 CCACACGGGCAAGGCCAATCCGGGCCTGTGGGCCACATGAGCATGTGAGC
* **
42154379 CCACACTGGCAAGGCCAATCCGGGTGTGTGGGTCACACA-G-GCATGTGAGC
1 CCACACGGGCAAGGCCAATCCGGGCCTGTGGG-C-CACATGAGCATGTGAGC
42154429 CCA
1 CCA
42154432 TAATTCTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 39 0.87
51 2 0.04
52 4 0.09
ACGTcount: A:0.20, C:0.30, G:0.34, T:0.16
Consensus pattern (50 bp):
CCACACGGGCAAGGCCAATCCGGGCCTGTGGGCCACATGAGCATGTGAGC
Found at i:42160306 original size:14 final size:14
Alignment explanation
Indices: 42160283--42160312 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42160273 CATCCCTCAT
*
42160283 TCACATCTCTTCTC
1 TCACAACTCTTCTC
42160297 TCACAACTCTTCTC
1 TCACAACTCTTCTC
42160311 TC
1 TC
42160313 CTCTTTCACT
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:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:42165340 original size:11 final size:11
Alignment explanation
Indices: 42165324--42165359 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
42165314 TATAGTGAGA
42165324 TTTTATTTTAT
1 TTTTATTTTAT
*
42165335 TTTTATTTTAC
1 TTTTATTTTAT
*
42165346 TTTTATTTTGT
1 TTTTATTTTAT
42165357 TTT
1 TTT
42165360 CAAAAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:42190152 original size:20 final size:20
Alignment explanation
Indices: 42190114--42190152 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42190104 TAATTTTTCC
**
42190114 AAATATAATATTATTTTAAT
1 AAATATAATATTAAATTAAT
*
42190134 AAATTTAATATTAAATTAA
1 AAATATAATATTAAATTAA
42190153 ATTAAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATAATATTAAATTAAT
Found at i:42190175 original size:32 final size:30
Alignment explanation
Indices: 42190139--42190254 Score: 90
Period size: 31 Copynumber: 3.8 Consensus size: 30
42190129 TTAATAAATT
*
42190139 TAATATTAAATTAAATTAAATATTTATTTAGA
1 TAATATTAAATTAAATT-AATATTTATAT-GA
** *
42190171 TAATATTTTATTAAATTAATATTAATATGA
1 TAATATTAAATTAAATTAATATTTATATGA
* * * *
42190201 -GATATTAAATTTAATTTAATATTTATCTTGT
1 TAATATTAAA-TTAAATTAATATTTAT-ATGA
** *
42190232 TAATATTTTATTAATTTAATATT
1 TAATATTAAATTAAATTAATATT
42190255 AATGTGATTA
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 6 0.09
30 16 0.24
31 24 0.36
32 21 0.31
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATATTAAATTAAATTAATATTTATATGA
Found at i:42190190 original size:16 final size:16
Alignment explanation
Indices: 42190125--42190193 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
42190115 AATATAATAT
*
42190125 TATTTTAATAAATTTAA
1 TATTTTATTAAA-TTAA
**
42190142 TATTAAATTAAATTAA
1 TATTTTATTAAATTAA
*
42190158 -ATATTTATTTAGA-TAA
1 TAT-TTTA-TTAAATTAA
42190174 TATTTTATTAAATTAA
1 TATTTTATTAAATTAA
42190190 TATT
1 TATT
42190194 AATATGAGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
15 6 0.15
16 20 0.49
17 15 0.37
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TATTTTATTAAATTAA
Found at i:42190223 original size:61 final size:61
Alignment explanation
Indices: 42190141--42190257 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
42190131 AATAAATTTA
42190141 ATATTAAATTAAATTAAATATTTAT-TTAGATAATATTTTATTAAATTAATATTAATATGAG
1 ATATTAAATTAAATTAAATATTTATCTT-GATAATATTTTATTAAATTAATATTAATATGAG
* * * *
42190202 ATATTAAATTTAATTTAATATTTATCTTGTTAATATTTTATTAATTTAATATTAAT
1 ATATTAAATTAAATTAAATATTTATCTTGATAATATTTTATTAAATTAATATTAAT
42190258 GTGATTAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 49 0.96
62 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (61 bp):
ATATTAAATTAAATTAAATATTTATCTTGATAATATTTTATTAAATTAATATTAATATGAG
Found at i:42190278 original size:21 final size:20
Alignment explanation
Indices: 42190241--42190279 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
42190231 TTAATATTTT
*
42190241 ATTAATTTAATATTAATGTG
1 ATTAATTTAATACTAATGTG
*
42190261 ATTAATTCTAATCCTAATG
1 ATTAATT-TAATACTAATG
42190280 GAACTCTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTAATTTAATACTAATGTG
Found at i:42192937 original size:16 final size:16
Alignment explanation
Indices: 42192910--42192968 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
42192900 TGGTAAAGTA
42192910 AATAAA-AAAGTAAAT
1 AATAAATAAAGTAAAT
42192925 AATAAATAAAGTAAAAT
1 AATAAATAAAGT-AAAT
*
42192942 ATATATATAAA-TATAAT
1 A-ATAAATAAAGTA-AAT
*
42192959 AATAATTAAA
1 AATAAATAAA
42192969 TCGCACTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.16
16 13 0.35
17 10 0.27
18 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAATAAAGTAAAT
Found at i:42195359 original size:9 final size:9
Alignment explanation
Indices: 42195342--42195378 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42195332 TGAGATTTCG
42195342 AATTCGAAT
1 AATTCGAAT
*
42195351 AACTCGAAT
1 AATTCGAAT
42195360 AATTCGAAT
1 AATTCGAAT
42195369 AATTCGAAT
1 AATTCGAAT
42195378 A
1 A
42195379 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42196416 original size:5 final size:5
Alignment explanation
Indices: 42196406--42196431 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42196396 CTCGAAAATT
42196406 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
42196432 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:42213020 original size:14 final size:16
Alignment explanation
Indices: 42213001--42213044 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
42212991 AGCAGCCCAT
42213001 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
42213015 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
*
42213031 ATTAAGTTTAATTT
1 ATTTA-TTTAATTT
42213045 ATGTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:42218248 original size:22 final size:25
Alignment explanation
Indices: 42218220--42218275 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
42218210 TATAAATAAG
42218220 TTATAATAA-AAA-ATAAAATATTT
1 TTATAATAATAAATATAAAATATTT
* *
42218243 TT-TAATGAATAAATATATATTATTT
1 TTATAAT-AATAAATATAAAATATTT
42218268 TTATAATA
1 TTATAATA
42218276 TATATCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 3 0.11
25 12 0.44
26 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTATAATAATAAATATAAAATATTT
Found at i:42221714 original size:13 final size:13
Alignment explanation
Indices: 42221696--42221721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42221686 GTGGAATTCG
42221696 AATAAGGACACAA
1 AATAAGGACACAA
42221709 AATAAGGACACAA
1 AATAAGGACACAA
42221722 GGCCCCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
AATAAGGACACAA
Found at i:42226010 original size:5 final size:4
Alignment explanation
Indices: 42225982--42226046 Score: 55
Period size: 4 Copynumber: 15.8 Consensus size: 4
42225972 TAGACGCTTT
*
42225982 TTTA TTTA -TTA TTTTA TTTA TTTA CTTTAA CTTA TTTA TTTTCA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA -TTT-A TTTA TTTA -TTT-A TTTA
42226030 -TTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTT
42226047 CAACTTTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
3 9 0.18
4 26 0.51
5 14 0.27
6 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:42226030 original size:14 final size:12
Alignment explanation
Indices: 42225981--42226046 Score: 71
Period size: 14 Copynumber: 5.2 Consensus size: 12
42225971 TTAGACGCTT
42225981 TTTTATTTATTA
1 TTTTATTTATTA
42225993 TTTTATTTATTTA
1 TTTTATTTA-TTA
* *
42226006 CTTTAACTTATTTA
1 -TTTTATTTA-TTA
42226020 TTTTCATTTATTA
1 TTTT-ATTTATTA
42226033 -TTTATTTATTA
1 TTTTATTTATTA
42226044 TTT
1 TTT
42226047 CAACTTTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 8 0.17
12 14 0.30
13 9 0.20
14 15 0.33
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:42238070 original size:14 final size:14
Alignment explanation
Indices: 42238051--42238085 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
42238041 CCCAATAAAG
*
42238051 ACCCAAACTTAACA
1 ACCCAAACATAACA
42238065 ACCCAAA-ATAACA
1 ACCCAAACATAACA
42238078 ACCCAAAC
1 ACCCAAAC
42238086 CCAACAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.54, C:0.37, G:0.00, T:0.09
Consensus pattern (14 bp):
ACCCAAACATAACA
Found at i:42238651 original size:22 final size:22
Alignment explanation
Indices: 42238620--42238669 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
42238610 CACCGTGGAC
*
42238620 GGCGGTGCCGTCGTCAGTGATT
1 GGCGGCGCCGTCGTCAGTGATT
*
42238642 GGCGGCGCCGTCGTCGGTGATT
1 GGCGGCGCCGTCGTCAGTGATT
42238664 GGCGGC
1 GGCGGC
42238670 CTACACGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.06, C:0.26, G:0.46, T:0.22
Consensus pattern (22 bp):
GGCGGCGCCGTCGTCAGTGATT
Found at i:42239213 original size:8 final size:9
Alignment explanation
Indices: 42239192--42239263 Score: 53
Period size: 10 Copynumber: 7.9 Consensus size: 9
42239182 ATTTAGACTC
42239192 TTTT-TTTA
1 TTTTATTTA
42239200 -TTTA-TTA
1 TTTTATTTA
42239207 TTTTATTTA
1 TTTTATTTA
42239216 -TTTACTTTA
1 TTTTA-TTTA
**
42239225 ACTTATTTA
1 TTTTATTTA
42239234 TTTTCATTTA
1 TTTT-ATTTA
42239244 TTATTTATTTA
1 -T-TTTATTTA
42239255 TTATTATTT
1 TT-TTATTT
42239264 CAACTTTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
7 6 0.12
8 8 0.15
9 14 0.27
10 15 0.29
11 6 0.12
12 3 0.06
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTTA
Found at i:42239224 original size:5 final size:4
Alignment explanation
Indices: 42239196--42239256 Score: 54
Period size: 4 Copynumber: 14.5 Consensus size: 4
42239186 AGACTCTTTT
*
42239196 TTTA TTTA -TTA TTTTA TTTA TTTA CTTTAA CTTA TTTA TTTTCA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA -TTT-A TTTA TTTA -TTT-A TTTA
42239244 -TTA TTTA TTTA TT
1 TTTA TTTA TTTA TT
42239257 ATTATTTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 6 0.12
4 26 0.54
5 14 0.29
6 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:42239258 original size:14 final size:15
Alignment explanation
Indices: 42239196--42239263 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 15
42239186 AGACTCTTTT
*
42239196 TTTATTTATTATTTTA
1 TTTATTTATT-TATTA
42239212 TTTATTTACTTTAACTTA
1 TTTATTTA-TTT-A-TTA
42239230 TTTATTTTCATTTATTA
1 TTTA-TTT-ATTTATTA
42239247 TTTATTTA-TTATTA
1 TTTATTTATTTATTA
42239261 TTT
1 TTT
42239264 CAACTTTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 12 0.26
17 9 0.20
18 8 0.17
19 6 0.13
20 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:42239441 original size:10 final size:9
Alignment explanation
Indices: 42239426--42239459 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
42239416 TCCTATTTTC
42239426 ATTTTATTCT
1 ATTTTATT-T
42239436 ATTTTATGTT
1 ATTTTAT-TT
42239446 ATTTTATTT
1 ATTTTATTT
42239455 ATTTT
1 ATTTT
42239460 GTTGTTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 15 0.65
11 1 0.04
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:42240879 original size:31 final size:31
Alignment explanation
Indices: 42240836--42240898 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
42240826 TAATAGTGCT
42240836 TGGTTACCCATTTGGGTTAAACCTACACGAA
1 TGGTTACCCATTTGGGTTAAACCTACACGAA
*
42240867 TGGTTACTCATTTGGGTTAAACCTACACGAA
1 TGGTTACCCATTTGGGTTAAACCTACACGAA
42240898 T
1 T
42240899 AATGAATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (31 bp):
TGGTTACCCATTTGGGTTAAACCTACACGAA
Found at i:42242988 original size:19 final size:18
Alignment explanation
Indices: 42242944--42242989 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
42242934 GAGTTAAACG
* * *
42242944 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAATC
42242962 AATCGAATTATTCGAATC
1 AATCGAATTATTCGAATC
42242980 AACTCGAATT
1 AA-TCGAATT
42242990 TTTTTTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCGAATC
Found at i:42243047 original size:9 final size:9
Alignment explanation
Indices: 42243030--42243066 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42243020 TGAGATTTCG
42243030 AATTCGAAT
1 AATTCGAAT
*
42243039 AACTCGAAT
1 AATTCGAAT
42243048 AATTCGAAT
1 AATTCGAAT
42243057 AATTCGAAT
1 AATTCGAAT
42243066 A
1 A
42243067 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42244044 original size:5 final size:5
Alignment explanation
Indices: 42244034--42244079 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
42244024 CTCGAAAATT
42244034 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
42244080 CGAATGCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (5 bp):
TTCGA
Found at i:42247763 original size:12 final size:12
Alignment explanation
Indices: 42247746--42247783 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
42247736 CGACCCGCCC
42247746 ATATTAATTTTT
1 ATATTAATTTTT
42247758 ATATT-ATTTTT
1 ATATTAATTTTT
*
42247769 ATA-TAATTTTA
1 ATATTAATTTTT
42247780 ATAT
1 ATAT
42247784 ATATAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 1 0.04
11 17 0.74
12 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:42247926 original size:30 final size:30
Alignment explanation
Indices: 42247882--42247944 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
42247872 ACTTAATAAG
42247882 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
42247912 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
42247942 CAA
1 CAA
42247945 TAAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:42263662 original size:6 final size:6
Alignment explanation
Indices: 42263638--42263681 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
42263628 CGCCTTCTTC
* * *
42263638 TCCCCTT TCCCCT TTCCCT TCCCCT TCCCTT TTCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
42263682 GGGTTGCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCCCT
Found at i:42263665 original size:18 final size:18
Alignment explanation
Indices: 42263638--42263681 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
42263628 CGCCTTCTTC
42263638 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCCCTTTCCCT
*
42263657 TCCCCTTCCCTTTTCCCT
1 TCCCCTTCCCCTTTCCCT
42263675 TCCCCTT
1 TCCCCTT
42263682 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCCCTTTCCCT
Found at i:42263763 original size:14 final size:13
Alignment explanation
Indices: 42263743--42263800 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
42263733 GGTAAGGCTC
42263743 CTTCTTCTTCTTT
1 CTTCTTCTTCTTT
42263756 CGTTCTTCATTCCTTT
1 C-TTCTTC-TT-CTTT
42263772 -TTCTTCTTCTGTT
1 CTTCTTCTTCT-TT
*
42263785 CTTCATCTTCTCTT
1 CTTCTTCTTCT-TT
42263799 CT
1 CT
42263801 CAGCATATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 2 0.05
13 5 0.13
14 25 0.66
15 2 0.05
16 4 0.11
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.62
Consensus pattern (13 bp):
CTTCTTCTTCTTT
Found at i:42263775 original size:25 final size:25
Alignment explanation
Indices: 42263741--42263790 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
42263731 CAGGTAAGGC
42263741 TCCTTCTTCTTCTT-TCGTTCTTCAT
1 TCCTTCTTCTTCTTCT-GTTCTTCAT
*
42263766 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCTGTTCTTCAT
42263791 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCTGTTCTTCAT
Found at i:42263994 original size:11 final size:11
Alignment explanation
Indices: 42263978--42264003 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42263968 TTGCTGGATG
42263978 ATATTTTGGTT
1 ATATTTTGGTT
42263989 ATATTTTGGTT
1 ATATTTTGGTT
42264000 ATAT
1 ATAT
42264004 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:42270493 original size:22 final size:22
Alignment explanation
Indices: 42270468--42270542 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
42270458 TAATGAGGGT
*
42270468 TTAGTTCGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
42270490 TTAGTACGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
*
42270512 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
42270534 TTAGTACGT
1 TTAGTACGT
42270543 GAGTCTGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (22 bp):
TTAGTACGTTAAACATGAGAGC
Found at i:42271199 original size:44 final size:43
Alignment explanation
Indices: 42271101--42271436 Score: 278
Period size: 44 Copynumber: 7.8 Consensus size: 43
42271091 ATCTGTTATT
* * *
42271101 TTCAACCTACTCCACTGCTG-CTCCGGGAGATA-GA-TTCATGATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGACTACA--ATC
*
42271144 TTCAACCTATTCCACCGCTGACCAGGGAGATAGGACCTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-CTACAATC
* * * *
42271188 TTCAATCTATTCCACTACTG-CACAGGGAGATAGAATTATCAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGACTA-CAATC
* *
42271232 TTCAACCTATTCCACTGCTGACAAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT-ACAATC
* * **
42271276 TTTAACCTATTCTACTGCTTTCCAGGGAGATAGGA-T----TC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTACAATC
* * * * * * *
42271314 TTTAATCTATTCCACTACTGCCCAGGAAGATAGAATTCT-CAATT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA--CTACAATC
*
42271358 TTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT-ACAATC
* * * *
42271402 TTTAACCTATTCCACTGTTGTCTAGGGAGATAGGA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA
42271437 TTCANNNNNN
Statistics
Matches: 240, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
38 30 0.12
41 1 0.00
42 2 0.01
43 31 0.13
44 171 0.71
45 2 0.01
46 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTACAATC
Found at i:42271325 original size:38 final size:38
Alignment explanation
Indices: 42271274--42271390 Score: 99
Period size: 38 Copynumber: 2.9 Consensus size: 38
42271264 GGATTCACAA
* * ** * *
42271274 TCTTTAACCTATTCTACTGCTTTCCAGGGAGATAGGAT
1 TCTTTAACCTATTCCACTACTGCCCAGGAAGATAGAAT
*
42271312 TCTTTAATCTATTCCACTACTGCCCAGGAAGATAGAATT
1 TCTTTAACCTATTCCACTACTGCCCAGGAAGATAGAA-T
* *
42271351 CTCAATTTTCAACCTATTCCACTACTGACCAGGGAGATAG
1 -TC---TTT-AACCTATTCCACTACTGCCCAGGAAGATAG
42271391 GACTCACAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
38 30 0.48
39 1 0.02
40 2 0.03
43 3 0.05
44 27 0.43
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTACTGCCCAGGAAGATAGAAT
Found at i:42271362 original size:126 final size:126
Alignment explanation
Indices: 42271098--42271439 Score: 429
Period size: 126 Copynumber: 2.7 Consensus size: 126
42271088 GAGATCTGTT
* * ** * *
42271098 ATTTTCAACCTACTCCACTGCTG-CTCCGGGAGATA-GATTCATGATCTTCAACCTATTCCACCG
1 ATTTTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTG
** *
42271161 CTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTACTGCACAGGGAGATAGAATTA
65 CTTTCCAGGGAGATAGGA--T----TCTTCAATCTATTCCACTACTGCACAGGAAGATAGAATTA
42271226 TCA
124 TCA
* * *
42271229 ATCTTCAACCTATTCCACTGCTGACAAGGGAGATAGGATTCACAATCTTTAACCTATTCTACTGC
1 ATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGC
* * *
42271294 TTTCCAGGGAGATAGGATTCTTTAATCTATTCCACTACTGCCCAGGAAGATAGAATTCTCA
66 TTTCCAGGGAGATAGGATTCTTCAATCTATTCCACTACTGCACAGGAAGATAGAATTATCA
* *
42271355 ATTTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTTAACCTATTCCACTG-
1 ATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGC
*
42271419 TTGTCTAGGGAGATAGGATTC
66 TT-TCCAGGGAGATAGGATTC
42271440 ANNNNNNNNN
Statistics
Matches: 187, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
125 2 0.01
126 115 0.61
130 1 0.01
131 29 0.16
132 40 0.21
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (126 bp):
ATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGC
TTTCCAGGGAGATAGGATTCTTCAATCTATTCCACTACTGCACAGGAAGATAGAATTATCA
Found at i:42271365 original size:82 final size:82
Alignment explanation
Indices: 42271182--42271392 Score: 210
Period size: 82 Copynumber: 2.5 Consensus size: 82
42271172 GATAGGACCT
* * * *
42271182 ACAATCTTCAATCTATTCCACTACTG-CACAGGGAGATAGAATTATCAATCTTCAACCTATTCCA
1 ACAATCTTTAACCTATTCCACTACTGAC-CAGGGAGATAGGA-T-TC--T-TT-AATCTATTCCA
* * *
42271246 CTGCTGACAAGGGAGATAGGATTC
59 CTACTGACAAGGAAGATAGAATTC
* * ** *
42271270 ACAATCTTTAACCTATTCTACTGCTTTCCAGGGAGATAGGATTCTTTAATCTATTCCACTACTGC
1 ACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGGATTCTTTAATCTATTCCACTACTGA
*
42271335 CCAGGAAGATAGAATTC
66 CAAGGAAGATAGAATTC
*
42271352 TCAAT-TTTCAACCTATTCCACTACTGACCAGGGAGATAGGA
1 ACAATCTTT-AACCTATTCCACTACTGACCAGGGAGATAGGA
42271393 CTCACAATCT
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
81 3 0.03
82 61 0.59
83 2 0.02
84 1 0.01
86 2 0.02
87 1 0.01
88 33 0.32
89 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (82 bp):
ACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGGATTCTTTAATCTATTCCACTACTGA
CAAGGAAGATAGAATTC
Found at i:42271588 original size:22 final size:22
Alignment explanation
Indices: 42271560--42271712 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
42271550 TGTTGATAGT
*
42271560 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
42271582 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
42271604 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
42271626 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
42271648 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
42271670 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
42271692 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
42271713 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:42271876 original size:38 final size:38
Alignment explanation
Indices: 42271817--42272014 Score: 128
Period size: 38 Copynumber: 4.9 Consensus size: 38
42271807 TTAAGGTTTC
* *
42271817 ACCTATTCCACTACTGTCCAGGGAGATAAGATTCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAAGATTCTTTA
* *
42271855 ATCTATTCCACTGCTGCCCAGGGAGAT-AGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAAG-A-T-TC--T-TT-A
* * *
42271899 ACCTATTACACTGCTGACTAGGGAGATAGGATTCATAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATA--A--GAT--TCTTTA
* **
42271943 ACCTATTCCACTGCTGACCAGGGAGATAGGGCTCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAAGATTCTTTA
* * * ** *
42271981 ATCTATTCCACAGCTGCCCAATGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAAGATTC
42272015 ACAATCTTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
37 2 0.02
38 58 0.46
39 1 0.01
40 2 0.02
42 1 0.01
43 2 0.02
44 51 0.41
45 2 0.02
46 1 0.01
47 2 0.02
48 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (38 bp):
ACCTATTCCACTGCTGACCAGGGAGATAAGATTCTTTA
Found at i:42271972 original size:44 final size:43
Alignment explanation
Indices: 42271817--42272054 Score: 208
Period size: 44 Copynumber: 5.7 Consensus size: 43
42271807 TTAAGGTTTC
* * *
42271817 ACCTATTCCACTACTGTCCAGGGAGATAAGA---T--TCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCTAATCTTTA
* * * *
42271855 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCT-AATCTTTA
* *
42271899 ACCTATTACACTGCTGACTAGGGAGATAGGATTCATAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-TAATCTTTA
*
42271943 ACCTATTCCACTGCTGACCAGGGAGATAGG--GC---TCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCTAATCTTTA
* * * ** *
42271981 ATCTATTCCACAGCTGCCCAATGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-TAATCTTTA
* * *
42272025 ACCTATTCCTCTACTGACCAGGAAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
42272055 GCTGGGGTCA
Statistics
Matches: 158, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
38 57 0.36
40 1 0.01
41 1 0.01
42 1 0.01
44 97 0.61
45 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCTAATCTTTA
Found at i:42272042 original size:126 final size:126
Alignment explanation
Indices: 42271817--42272054 Score: 332
Period size: 126 Copynumber: 1.9 Consensus size: 126
42271807 TTAAGGTTTC
* * * *
42271817 ACCTATTCCACTACTGTCCAGGGAGATAAGATTCTTTAATCTATTCCACTGCTGCCCAGGGAGAT
1 ACCTATTCCACTACTGACCAGGGAGATAAGACTCTTTAATCTATTCCACAGCTGCCCAAGGAGAT
* * * *
42271882 AGAATTCTCAATCTTCAACCTATTACACTGCTGACTAGGGAGATAGGATTCATAATCTTTA
66 AGAATTCACAATCTTCAACCTATTACACTACTGACCAGGAAGATAGGATTCATAATCTTTA
* * * *
42271943 ACCTATTCCACTGCTGACCAGGGAGATAGGGCTCTTTAATCTATTCCACAGCTGCCCAATGAGAT
1 ACCTATTCCACTACTGACCAGGGAGATAAGACTCTTTAATCTATTCCACAGCTGCCCAAGGAGAT
* * * *
42272008 AGGATTCACAATCTTTAACCTATTCCTCTACTGACCAGGAAGATAGG
66 AGAATTCACAATCTTCAACCTATTACACTACTGACCAGGAAGATAGG
42272055 GCTGGGGTCA
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
126 96 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (126 bp):
ACCTATTCCACTACTGACCAGGGAGATAAGACTCTTTAATCTATTCCACAGCTGCCCAAGGAGAT
AGAATTCACAATCTTCAACCTATTACACTACTGACCAGGAAGATAGGATTCATAATCTTTA
Found at i:42272170 original size:88 final size:87
Alignment explanation
Indices: 42272054--42272371 Score: 465
Period size: 88 Copynumber: 3.6 Consensus size: 87
42272044 AGGAAGATAG
* * * * *
42272054 GGCTGGGGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATTTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
42272119 TCCGCTGCAATCCAGGGAGGCAA
66 TCCGCTGCAA-CCAGGGAGGCAA
* * * *
42272142 GGCTGGTGCCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATTTACTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
*
42272207 TCCGCTGTAACCCAGGGAGGCAA
66 TCCGCTGCAA-CCAGGGAGGCAA
*
42272230 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
* *
42272295 TTCACTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACC-AGGGAGGCAA
* * *
42272318 GGCTAGTGTCTTCGATCTGCTTCGCTATCGGTACAGGAAGGCAAGATCTGCTAT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
42272372 CTTCGATCTA
Statistics
Matches: 208, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
87 2 0.01
88 206 0.99
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (87 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCAGGGAGGCAA
Found at i:42272272 original size:44 final size:45
Alignment explanation
Indices: 42272219--42272431 Score: 120
Period size: 44 Copynumber: 4.8 Consensus size: 45
42272209 CGCTGTAACC
* * * *
42272219 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGAGCTGCTATCTTCGATCTGCTTCACTGTCGGTA
* ** * *
42272263 CAGGAAGGCAAGATCTGCTAT-TTTTAGCCTGCTTCACTG-C--AA
1 CAGGAAGGCAAGAGCTGCTATCTTCGA-TCTGCTTCACTGTCGGTA
* * * *
42272305 CCTAGGGAGGCAAG-GCTAG-TGTCTTCGATCTGCTTCGCTATCGGTA
1 -C-AGGAAGGCAAGAGCT-GCTATCTTCGATCTGCTTCACTGTCGGTA
* * **
42272351 CAGGAAGGCAAGATCTGCTATCTTCGATCTACTTCAC-G-CTAATA
1 CAGGAAGGCAAGAGCTGCTATCTTCGATCTGCTTCACTGTC-GGTA
* * * * *
42272395 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCAC
1 CAGGAAGGCAAGAGCTGCTATCTTCGATCTGCTTCAC
42272432 CACCAGTATG
Statistics
Matches: 128, Mismatches: 29, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
43 15 0.12
44 77 0.60
45 35 0.27
46 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (45 bp):
CAGGAAGGCAAGAGCTGCTATCTTCGATCTGCTTCACTGTCGGTA
Found at i:42272463 original size:44 final size:45
Alignment explanation
Indices: 42272352--42272508 Score: 192
Period size: 44 Copynumber: 3.5 Consensus size: 45
42272342 CTATCGGTAC
* * * *
42272352 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCA-CGCTAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * *
42272396 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * *
42272441 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
*
42272485 AGGAAGACAGGATCTGCTATCTTC
1 AGGAAGACAAGATCTGCTATCTTC
42272509 ACTGATCTGC
Statistics
Matches: 95, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 69 0.73
45 26 0.27
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
Found at i:42277140 original size:15 final size:15
Alignment explanation
Indices: 42277102--42277153 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
42277092 GAACATTTCG
42277102 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
*
42277119 ATTTTTATTAATAAAA
1 A-ATTTATTAATAAAA
*
42277135 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
42277151 AAT
1 AAT
42277154 CATTGCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 11 0.37
16 11 0.37
17 5 0.17
18 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:42277227 original size:22 final size:20
Alignment explanation
Indices: 42277184--42277222 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42277174 TAATTTAAAA
42277184 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
42277204 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
42277223 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:42277366 original size:34 final size:35
Alignment explanation
Indices: 42277309--42277374 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
42277299 CAAACACCAG
*
42277309 AAAATATTTTCCAATAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAATAAATCATTTTACAGAAAAGT
*
42277344 AAAACATTTTCCAA-AAATCATTTTACGGAAA
1 AAAACATTTTCCAATAAATCATTTTACAGAAA
42277375 TTATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (35 bp):
AAAACATTTTCCAATAAATCATTTTACAGAAAAGT
Found at i:42282600 original size:3 final size:3
Alignment explanation
Indices: 42282592--42282644 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
42282582 GACTTTTTAT
*
42282592 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42282640 TAA TA
1 TAA TA
42282645 CTTTAAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:42283681 original size:19 final size:19
Alignment explanation
Indices: 42283635--42283682 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
42283625 GTATATATTT
*
42283635 TAAA-TTTATTTAGTTAGA
1 TAAATTTTATTTAGGTAGA
*
42283653 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
42283672 TAAGTTTTATT
1 TAAATTTTATT
42283683 CATATCCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:42285295 original size:42 final size:42
Alignment explanation
Indices: 42285214--42285297 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
42285204 ATATTTTATT
42285214 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCCC
* *
42285256 TTATGTTTTAGTAGTTTATTAGAATAAGAGAATTTTTTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCCC
42285298 AATTAGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (42 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCCC
Found at i:42286969 original size:31 final size:31
Alignment explanation
Indices: 42286931--42286990 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
42286921 TTGCATGGTC
42286931 AATTTTGTTTTTGAGATTTCAATATCAATGG
1 AATTTTGTTTTTGAGATTTCAATATCAATGG
*
42286962 AATTTTGTTTTTGAGATTTTAATATCAAT
1 AATTTTGTTTTTGAGATTTCAATATCAAT
42286991 TACAGGTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (31 bp):
AATTTTGTTTTTGAGATTTCAATATCAATGG
Found at i:42290250 original size:59 final size:60
Alignment explanation
Indices: 42290154--42290280 Score: 204
Period size: 59 Copynumber: 2.1 Consensus size: 60
42290144 AATAAAATTT
*
42290154 TTCAAGCACAAATACTTAAACAAGACATAAACATATTGAATTTCAACAAGAG-ATGACAA
1 TTCAAGCACAAATACTTAAACAAGACATAAACATATTGAATTGCAACAAGAGAATGACAA
* *
42290213 TTCAAGCACAAATACTTAAACAAGACATAAACGTATTGAATTGCAAGAAGAGATATGACAA
1 TTCAAGCACAAATACTTAAACAAGACATAAACATATTGAATTGCAACAAGAGA-ATGACAA
42290274 TT-AAGCA
1 TTCAAGCA
42290281 TTGGAGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
59 49 0.78
60 5 0.08
61 9 0.14
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.22
Consensus pattern (60 bp):
TTCAAGCACAAATACTTAAACAAGACATAAACATATTGAATTGCAACAAGAGAATGACAA
Found at i:42291367 original size:13 final size:13
Alignment explanation
Indices: 42291333--42291371 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
42291323 CTAACCTATT
42291333 AACTTAAGTT-TA
1 AACTTAAGTTCTA
* *
42291345 ATCCTAAGTTCTA
1 AACTTAAGTTCTA
42291358 AACTTAAGTTCTA
1 AACTTAAGTTCTA
42291371 A
1 A
42291372 GTTTTTAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTTAAGTTCTA
Found at i:42298727 original size:9 final size:9
Alignment explanation
Indices: 42298713--42298738 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42298703 TAACTTCTGG
42298713 TACATAATA
1 TACATAATA
42298722 TACATAATA
1 TACATAATA
42298731 TACATAAT
1 TACATAAT
42298739 TTAAGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (9 bp):
TACATAATA
Found at i:42300265 original size:18 final size:16
Alignment explanation
Indices: 42300234--42300267 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
42300224 ATAATTATTC
42300234 ATTTAATATTATAATT
1 ATTTAATATTATAATT
42300250 ATTTAAATAGTTATAATT
1 ATTT-AATA-TTATAATT
42300268 TTTTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTAATATTATAATT
Found at i:42302171 original size:23 final size:24
Alignment explanation
Indices: 42302141--42302190 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
42302131 CTTTATTGTG
*
42302141 TTTTGATTTATTTTGAACT-ATTA
1 TTTTGATTTATTGTGAACTGATTA
* *
42302164 TTTTGATTTCTTGTGAGCTGATTA
1 TTTTGATTTATTGTGAACTGATTA
42302188 TTT
1 TTT
42302191 CTCTATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTTGATTTATTGTGAACTGATTA
Found at i:42302803 original size:2 final size:2
Alignment explanation
Indices: 42302796--42302833 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
42302786 ATCTTAGTCT
*
42302796 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42302834 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:42315099 original size:20 final size:20
Alignment explanation
Indices: 42315071--42315110 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42315061 CTCTAACCAG
*
42315071 AATCTCTAAAAATTAGCTAT
1 AATCCCTAAAAATTAGCTAT
*
42315091 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATTAGCTAT
42315111 TTGGTACTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCCCTAAAAATTAGCTAT
Found at i:42320313 original size:27 final size:27
Alignment explanation
Indices: 42320282--42320349 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
42320272 TAAAGTTCAA
*
42320282 TTTGAATTAAAGACTTGATTTTATAAT
1 TTTGAAATAAAGACTTGATTTTATAAT
* *
42320309 TTTGAAACAAAGATTTGATTTTATAAT
1 TTTGAAATAAAGACTTGATTTTATAAT
42320336 TTTGAAATAAAGAC
1 TTTGAAATAAAGAC
42320350 ATGAGTGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (27 bp):
TTTGAAATAAAGACTTGATTTTATAAT
Found at i:42321793 original size:12 final size:13
Alignment explanation
Indices: 42321775--42321802 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42321765 TTTAGAAAAA
42321775 CATTTTTAACATT
1 CATTTTTAACATT
42321788 CATTTTTAACATT
1 CATTTTTAACATT
42321801 CA
1 CA
42321803 ATTGATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (13 bp):
CATTTTTAACATT
Found at i:42324565 original size:184 final size:185
Alignment explanation
Indices: 42324330--42324704 Score: 590
Period size: 184 Copynumber: 2.0 Consensus size: 185
42324320 TCGATACTTT
*
42324330 TTGTGATTGTTTAAAAATCATTAAGTCAGAACGCAAAAACGGTATCGATATCAAAGATGGTATTG
1 TTGTGATTGTTTAAAAATC--TAAGTCAGAACGCAAAAACGGTATCGATATCAAAGATGGTATCG
* * ** *
42324395 ATAAAAATACAATAGGTATCCATATTTTTTGAAAAGTATTGATACTTTTTGTTTTTGTTCAGTTT
64 ATAAAAATACAATAGGTATACATATTTTTTGAAAAGTATCGATACTTTTTACTTTTGTTCAATTT
* * *
42324460 TTGTTTCAAGTCAGTAAGCAAGTTTGGTATCGATCTTTAAATAGGTATCAATAAAAA
129 TTATTTCAAGTCAGTAAGCAAGTTTGGTATCAATCTTGAAATAGGTATCAATAAAAA
* * *
42324517 TTGTGATTGTTTAAAAATC-AAGTTATAATGCAAAAACGGTATCGATATCAAAGATGGTATCGAT
1 TTGTGATTGTTTAAAAATCTAAGTCAGAACGCAAAAACGGTATCGATATCAAAGATGGTATCGAT
* * *
42324581 AAAAATACAATAGGTATAGATATTTTTTGATAGGTATCGATACTTTTTACTTTTGTTCAATTTTT
66 AAAAATACAATAGGTATACATATTTTTTGAAAAGTATCGATACTTTTTACTTTTGTTCAATTTTT
42324646 ATTTCAAGTCAGTAAGCAAGTTTGGTATCAATCTTGAAATAGGTATCAATAAAAA
131 ATTTCAAGTCAGTAAGCAAGTTTGGTATCAATCTTGAAATAGGTATCAATAAAAA
42324701 TTGT
1 TTGT
42324705 ATGGGTATTG
Statistics
Matches: 173, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
184 154 0.89
187 19 0.11
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (185 bp):
TTGTGATTGTTTAAAAATCTAAGTCAGAACGCAAAAACGGTATCGATATCAAAGATGGTATCGAT
AAAAATACAATAGGTATACATATTTTTTGAAAAGTATCGATACTTTTTACTTTTGTTCAATTTTT
ATTTCAAGTCAGTAAGCAAGTTTGGTATCAATCTTGAAATAGGTATCAATAAAAA
Found at i:42324568 original size:18 final size:18
Alignment explanation
Indices: 42324547--42324581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42324537 AGTTATAATG
42324547 CAAAAACGGTATCGATAT
1 CAAAAACGGTATCGATAT
* *
42324565 CAAAGATGGTATCGATA
1 CAAAAACGGTATCGATA
42324582 AAAATACAAT
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:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (18 bp):
CAAAAACGGTATCGATAT
Found at i:42324615 original size:20 final size:21
Alignment explanation
Indices: 42324590--42324628 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42324580 TAAAAATACA
42324590 ATAGGTATAGATA-TTTTTTG
1 ATAGGTATAGATACTTTTTTG
*
42324610 ATAGGTATCGATACTTTTT
1 ATAGGTATAGATACTTTTT
42324629 ACTTTTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (21 bp):
ATAGGTATAGATACTTTTTTG
Found at i:42333817 original size:5 final size:5
Alignment explanation
Indices: 42333797--42333831 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
42333787 ACGTGAGTAT
*
42333797 TCGA- TCGAG TCAAG TCGAG TCGAG TCGAG TCGAG T
1 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG T
42333832 TGAATTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (5 bp):
TCGAG
Found at i:42334160 original size:70 final size:70
Alignment explanation
Indices: 42334074--42334255 Score: 274
Period size: 76 Copynumber: 2.5 Consensus size: 70
42334064 AACTTAATGA
*
42334074 GTAAACATTTATCAAAACAATGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGA
1 GTAAATATTTATCAAAACAATGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGA
42334139 AAAAG
66 AAAAG
*
42334144 GTAAATATTTATCAAAACGATAACAAAGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAA
1 GTAAATATTTATC---A--A-AACAATGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAA
42334209 CTTTGAAAAAG
60 CTTTGAAAAAG
* *
42334220 GTAAATATTTATCAAAACGATGTACTTTTGCCTTTT
1 GTAAATATTTATCAAAACAATGTAGTTTTGCCTTTT
42334256 CTTATTCAGA
Statistics
Matches: 101, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
70 30 0.30
71 1 0.01
73 2 0.02
75 1 0.01
76 67 0.66
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (70 bp):
GTAAATATTTATCAAAACAATGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGA
AAAAG
Found at i:42334182 original size:76 final size:76
Alignment explanation
Indices: 42334089--42334240 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
42334079 CATTTATCAA
*
42334089 AACAATGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGAAAAAGGTAAATATTT
1 AACAAAGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGAAAAAGGTAAATATTT
42334154 ATCAAAACGAT
66 ATCAAAACGAT
42334165 AACAAAGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGAAAAAGGTAAATATTT
1 AACAAAGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGAAAAAGGTAAATATTT
42334230 ATCAAAACGAT
66 ATCAAAACGAT
42334241 GTACTTTTGC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (76 bp):
AACAAAGTAGTTTTGCCTTTTAACTTAATGGTTTTGGCTTTTAACTTTGAAAAAGGTAAATATTT
ATCAAAACGAT
Found at i:42335022 original size:21 final size:23
Alignment explanation
Indices: 42334984--42335029 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
42334974 CAATTAAGTT
42334984 TAATTTTTTTAATATTTTA-AAA
1 TAATTTTTTTAATATTTTATAAA
* *
42335006 TAATTTTTTT-GTCTTTTATAAA
1 TAATTTTTTTAATATTTTATAAA
42335028 TA
1 TA
42335030 GGTGAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TAATTTTTTTAATATTTTATAAA
Found at i:42344548 original size:15 final size:15
Alignment explanation
Indices: 42344523--42344557 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42344513 GACTCTATTT
*
42344523 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
42344537 TAATTAATATTAAGA
1 TAATTAATATTAAGA
42344552 TAATTA
1 TAATTA
42344558 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:42357039 original size:13 final size:13
Alignment explanation
Indices: 42357021--42357047 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42357011 TCCAAAAAAT
42357021 AAGAAAAATCAAA
1 AAGAAAAATCAAA
42357034 AAGAAAAATCAAA
1 AAGAAAAATCAAA
42357047 A
1 A
42357048 TCAAAATAAA
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:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAGAAAAATCAAA
Found at i:42357054 original size:34 final size:35
Alignment explanation
Indices: 42357015--42357161 Score: 136
Period size: 34 Copynumber: 4.1 Consensus size: 35
42357005 ATCCAATCCA
*
42357015 AAAAATAAGAAAAATCAAAAAGAAAAATCAAAATC
1 AAAAATAAGAAAAATCAAAAAGAAAAATCAAAGTC
* **
42357050 AAAATAAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAGTC
1 AAAA-ATAAG---AAAA-ATCAAAAAGAAAAATCAAAGTC
* **
42357090 AAAAAGAAGAAAAATC-AAAATCAAAATCAAAGTC
1 AAAAATAAGAAAAATCAAAAAGAAAAATCAAAGTC
* * **
42357124 AAAAAGAAGAAAAA-GAAAAATCAAAATCAAAGTC
1 AAAAATAAGAAAAATCAAAAAGAAAAATCAAAGTC
42357158 AAAA
1 AAAA
42357162 TGAAAATGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
34 52 0.54
35 5 0.05
36 8 0.08
39 8 0.08
40 23 0.24
ACGTcount: A:0.71, C:0.09, G:0.10, T:0.10
Consensus pattern (35 bp):
AAAAATAAGAAAAATCAAAAAGAAAAATCAAAGTC
Found at i:42357099 original size:22 final size:22
Alignment explanation
Indices: 42357034--42357115 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
42357024 AAAAATCAAA
42357034 AAGAAAAATCAAAATC---AA-
1 AAGAAAAATCAAAATCAAAAAG
* * **
42357052 AATAAAAGTCAAAAAGAAGAAA-
1 AAGAAAAATCAAAATCAA-AAAG
*
42357074 AAGAAAAATCAAAGTCAAAAAG
1 AAGAAAAATCAAAATCAAAAAG
42357096 AAGAAAAATCAAAATCAAAA
1 AAGAAAAATCAAAATCAAAA
42357116 TCAAAGTCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
18 12 0.24
21 3 0.06
22 34 0.69
ACGTcount: A:0.72, C:0.09, G:0.10, T:0.10
Consensus pattern (22 bp):
AAGAAAAATCAAAATCAAAAAG
Found at i:42357106 original size:62 final size:62
Alignment explanation
Indices: 42357034--42357154 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
42357024 AAAAATCAAA
*
42357034 AAGAAAAATCAAAATCAAAATAAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAGTCAAAAAG
1 AAGAAAAATCAAAATCAAAATAAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAATCAAAAAG
*
42357096 AAGAAAAATCAAAATCAAAATCAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAATCAAA
1 AAGAAAAATCAAAATCAAAATAAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAATCAAA
42357155 GTCAAAATGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.71, C:0.09, G:0.10, T:0.10
Consensus pattern (62 bp):
AAGAAAAATCAAAATCAAAATAAAAGTCAAAAAGAAGAAAAAGAAAAATCAAAATCAAAAAG
Found at i:42357109 original size:6 final size:6
Alignment explanation
Indices: 42357100--42357173 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
42357090 AAAAAGAAGA
* * ** **
42357100 AAAATC AAAATC AAAATC AAAGTC AAAA-- AGAAGA AAAAGA AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * *
42357146 AAAATC AAAGTC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
42357174 AGAGAAAAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
4 3 0.05
6 54 0.95
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:42357143 original size:28 final size:28
Alignment explanation
Indices: 42357050--42357154 Score: 129
Period size: 28 Copynumber: 3.5 Consensus size: 28
42357040 AATCAAAATC
*
42357050 AAAATAAAAGTCAAAAAGAAGAAAAAGA
1 AAAATCAAAGTCAAAAAGAAGAAAAAGA
*
42357078 AAAATCAAAGTCAAAAAGAAGAAAAATCAAAA
1 AAAATCAAAGTCAAAAAGAAG--AAA--AAGA
42357110 TCAAAATCAAAGTCAAAAAGAAGAAAAAGA
1 --AAAATCAAAGTCAAAAAGAAGAAAAAGA
*
42357140 AAAATCAAAATCAAA
1 AAAATCAAAGTCAAA
42357155 GTCAAAATGA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
28 34 0.51
30 6 0.09
32 6 0.09
34 21 0.31
ACGTcount: A:0.71, C:0.09, G:0.10, T:0.10
Consensus pattern (28 bp):
AAAATCAAAGTCAAAAAGAAGAAAAAGA
Found at i:42357187 original size:6 final size:6
Alignment explanation
Indices: 42357158--42357206 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
42357148 AATCAAAGTC
* *
42357158 AAAATG AAAATG AAAAAG AGAAAAG AAAAAAG AAAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG -AAAAAG -AAAAAG AAAAAG AAAA
42357207 GGAGAGGCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 22 0.55
7 17 0.43
8 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:42357187 original size:14 final size:14
Alignment explanation
Indices: 42357170--42357206 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42357160 AATGAAAATG
*
42357170 AAAAAGAGAAAAGA
1 AAAAAGAAAAAAGA
42357184 AAAAAGAAAAAAG-
1 AAAAAGAAAAAAGA
42357197 AAAAAGAAAA
1 AAAAAGAAAA
42357207 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:42358937 original size:87 final size:87
Alignment explanation
Indices: 42358786--42359031 Score: 348
Period size: 87 Copynumber: 2.8 Consensus size: 87
42358776 AGATCGGTGA
* * *
42358786 AGATTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTAGAGCTGGTTAAATATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* ***
42358851 CTTCCTGCATTAACAGCGAAGC
66 CTTCCTACATTAACAAAAAAGC
* **
42358873 AGATCGAAAACAAAACCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
42358938 CTTCCTACATTAACAAAAAATC
66 CTTCCTACATTAACAAAAAAGC
* * * * *
42358960 AGATCGAAAACGAAGTCTTGCCTCTATCGATTGTAGCGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
42359025 CTTCCTA
66 CTTCCTA
42359032 AGCACTAGTG
Statistics
Matches: 140, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 140 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTACATTAACAAAAAAGC
Found at i:42361187 original size:27 final size:26
Alignment explanation
Indices: 42361155--42361209 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
42361145 TTACTGTTTC
* *
42361155 AAGTTATTTTATATGTCATTTTATTTT
1 AAGTTATTTTACATATCA-TTTATTTT
*
42361182 AAGTTATTTTACATATTATTTATTTT
1 AAGTTATTTTACATATCATTTATTTT
42361208 AA
1 AA
42361210 AATTAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (26 bp):
AAGTTATTTTACATATCATTTATTTT
Found at i:42361366 original size:2 final size:2
Alignment explanation
Indices: 42361359--42361399 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42361349 TTCAACTCTT
42361359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42361400 TATTTACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42365378 original size:29 final size:29
Alignment explanation
Indices: 42365345--42365408 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
42365335 ACGAACGCAT
* ** *
42365345 CTTTTGATAGAGATTTCCACAAAGGCTTC
1 CTTTTAATAGAGATCACCACAAAAGCTTC
42365374 CTTTTAATAGAGATCACCACAAAAGCTTC
1 CTTTTAATAGAGATCACCACAAAAGCTTC
*
42365403 CATTTA
1 CTTTTA
42365409 GAAATAGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (29 bp):
CTTTTAATAGAGATCACCACAAAAGCTTC
Found at i:42366061 original size:27 final size:27
Alignment explanation
Indices: 42366031--42366090 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
42366021 TAACATACTA
42366031 ACCATTTAGATTAAT-ATTAAGACCAGG
1 ACCATTTAGATT-ATCATTAAGACCAGG
* *
42366058 ACCATTTGGATTATCATTGAGACCAGG
1 ACCATTTAGATTATCATTAAGACCAGG
*
42366085 ATCATT
1 ACCATT
42366091 CCCGTTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (27 bp):
ACCATTTAGATTATCATTAAGACCAGG
Found at i:42366997 original size:25 final size:25
Alignment explanation
Indices: 42366967--42367016 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
42366957 TTAAGGGCAT
* *
42366967 GTTGCAGAGTCGTCTATGTCTAGGG
1 GTTGCACAGTCATCTATGTCTAGGG
42366992 GTTGCACAGTCATCTATGTCTAGGG
1 GTTGCACAGTCATCTATGTCTAGGG
42367017 ACTGCACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (25 bp):
GTTGCACAGTCATCTATGTCTAGGG
Found at i:42367022 original size:25 final size:25
Alignment explanation
Indices: 42366969--42367023 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
42366959 AAGGGCATGT
* * **
42366969 TGCAGAGTCGTCTATGTCTAGGGGT
1 TGCACAGTCATCTATGTCTAGGGAC
42366994 TGCACAGTCATCTATGTCTAGGGAC
1 TGCACAGTCATCTATGTCTAGGGAC
42367019 TGCAC
1 TGCAC
42367024 TCATACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (25 bp):
TGCACAGTCATCTATGTCTAGGGAC
Found at i:42369814 original size:23 final size:23
Alignment explanation
Indices: 42369788--42369843 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
42369778 TATGACATCA
*
42369788 TTTATGTCACGTGTCATAATCTT
1 TTTATGCCACGTGTCATAATCTT
*
42369811 TTTATGCCATGTGTCATAATCTT
1 TTTATGCCACGTGTCATAATCTT
* *
42369834 ATTCTGCCAC
1 TTTATGCCAC
42369844 TAGTCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (23 bp):
TTTATGCCACGTGTCATAATCTT
Found at i:42374242 original size:17 final size:17
Alignment explanation
Indices: 42374220--42374252 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42374210 AATTCACATG
*
42374220 CTTTTTTTTTCCTTTTT
1 CTTTTTTTGTCCTTTTT
42374237 CTTTTTTTGTCCTTTT
1 CTTTTTTTGTCCTTTT
42374253 GCACACTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTTTTTGTCCTTTTT
Found at i:42387560 original size:42 final size:42
Alignment explanation
Indices: 42387405--42387561 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 42
42387395 ATGTGATTTT
*
42387405 GTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGA-GATTTAC
1 GTGTAAGACCACGTCTAGGACGTTGGCATCG-TTT-ATGA-TTAC
* * *
42387449 GTGTAAGACCATGTCTAGGACATTGGCATCGTATATGATTAC
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGTTTATGATTAC
** *
42387491 GTGTAAGACC-CTGTCCGGGAC-TGTGGCATCGTTGTTTG-TTAC
1 GTGTAAGACCAC-GTCTAGGACGT-TGGCATCGTT-TATGATTAC
*
42387533 ATGTAAGACCACGTCTAGGACGTTGGCAT
1 GTGTAAGACCACGTCTAGGACGTTGGCAT
42387562 TGTACGAGCT
Statistics
Matches: 95, Mismatches: 12, Indels: 14
0.79 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 57 0.60
43 9 0.09
44 28 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCACGTCTAGGACGTTGGCATCGTTTATGATTAC
Found at i:42392219 original size:13 final size:12
Alignment explanation
Indices: 42392199--42392260 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
42392189 TTTTTATAAT
42392199 TTTTATTATTTA
1 TTTTATTATTTA
42392211 TTATTATTATTT-
1 TT-TTATTATTTA
*
42392223 TTCT-TTACTTTA
1 TTTTATTA-TTTA
42392235 -TTTATTACTTTA
1 TTTTATTA-TTTA
42392247 TTTTATTATTTA
1 TTTTATTATTTA
42392259 TT
1 TT
42392261 ACTTATTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 18 0.42
13 16 0.37
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:42399448 original size:98 final size:99
Alignment explanation
Indices: 42399335--42399542 Score: 364
Period size: 98 Copynumber: 2.1 Consensus size: 99
42399325 ACAAGAGATC
*
42399335 CTTATAAATATAAATATATATTAATAATTTCATTACAAGTTTTGATTATATCTA-TTTTTTTGAC
1 CTTATAAATATAAATATATATTAATAATTTCATTACAAGTTTCGATTATATCTATTTTTTTTGAC
*
42399399 ATAATATTTAGTACTACCTATAGTTCATCTCAAA
66 ATAATATTTAGTACTACCTATAGTTCATCCCAAA
*
42399433 CTTATAAATATAAATATATATTAATAATTTCATTACAAGTTTCGATTATATCTATTTTTTTTTTA
1 CTTATAAATATAAATATATATTAATAATTTCATTACAAGTTTCGATTATATCTA-TTTTTTTTGA
42399498 CATAATATTTAGTACTACCTATAGTTCATCCCAAA
65 CATAATATTTAGTACTACCTATAGTTCATCCCAAA
*
42399533 CCTATAAATA
1 CTTATAAATA
42399543 GGTGGATAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
98 53 0.51
100 51 0.49
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.45
Consensus pattern (99 bp):
CTTATAAATATAAATATATATTAATAATTTCATTACAAGTTTCGATTATATCTATTTTTTTTGAC
ATAATATTTAGTACTACCTATAGTTCATCCCAAA
Found at i:42406960 original size:23 final size:23
Alignment explanation
Indices: 42406932--42406977 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
42406922 TTGATACTAT
*
42406932 TTAAAAATGT-AAAATTAAAATA
1 TTAAAAATCTAAAAATTAAAATA
*
42406954 TTAAAAATCTAAAAATTATAATA
1 TTAAAAATCTAAAAATTAAAATA
42406977 T
1 T
42406978 CATCCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TTAAAAATCTAAAAATTAAAATA
Found at i:42410736 original size:23 final size:22
Alignment explanation
Indices: 42410689--42410736 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
42410679 CGATTATGAA
*
42410689 AAACATTAAAAAATTTAATTTT
1 AAACATTAAAAAATTTAATTAT
*
42410711 AAACGATTAATAAATATT-ATTAT
1 AAAC-ATTAAAAAAT-TTAATTAT
42410734 AAA
1 AAA
42410737 ATGTTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 16 0.73
24 2 0.09
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AAACATTAAAAAATTTAATTAT
Found at i:42411097 original size:31 final size:31
Alignment explanation
Indices: 42411062--42411162 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 31
42411052 AATTGAAATG
42411062 TATTTAATATTCTTACACCAATGTATTTACA
1 TATTTAATATTCTTACACCAATGTATTTACA
* **
42411093 TATTTAAATTTATAT-TTACTCACAAT-T-TAAAC-
1 TATTT-AA--TAT-TCTTACAC-CAATGTATTTACA
*
42411125 TATTTAATATTCTTACACCGATGTATTTACA
1 TATTTAATATTCTTACACCAATGTATTTACA
42411156 TATTTAA
1 TATTTAA
42411163 ATTTATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
28 4 0.07
29 9 0.17
30 3 0.06
31 14 0.26
32 7 0.13
33 3 0.06
34 9 0.17
35 5 0.09
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.47
Consensus pattern (31 bp):
TATTTAATATTCTTACACCAATGTATTTACA
Found at i:42411161 original size:63 final size:63
Alignment explanation
Indices: 42411062--42411189 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
42411052 AATTGAAATG
42411062 TATTTAATATTCTTACACCAATGTATTTACATATTTAAATTTATATTTACTCACAATTTAAAC
1 TATTTAATATTCTTACACCAATGTATTTACATATTTAAATTTATATTTACTCACAATTTAAAC
*
42411125 TATTTAATATTCTTACACCGATGTATTTACATATTTAAATTTATATTTACTCACAATTTAAAC
1 TATTTAATATTCTTACACCAATGTATTTACATATTTAAATTTATATTTACTCACAATTTAAAC
42411188 TA
1 TA
42411190 ACTTATTTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (63 bp):
TATTTAATATTCTTACACCAATGTATTTACATATTTAAATTTATATTTACTCACAATTTAAAC
Found at i:42411986 original size:20 final size:20
Alignment explanation
Indices: 42411945--42411986 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42411935 TTTACATGTA
*
42411945 TTTATAATATTTAAATTATT
1 TTTATAATATTTAAAATATT
*
42411965 TTTATAATTTTTAAAA-ATT
1 TTTATAATATTTAAAATATT
42411984 TTT
1 TTT
42411987 GCATATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATAATATTTAAAATATT
Found at i:42421612 original size:53 final size:53
Alignment explanation
Indices: 42421510--42421662 Score: 173
Period size: 53 Copynumber: 2.9 Consensus size: 53
42421500 GGCGCTAAAG
* * **
42421510 ACCATATCGTGTAAGA-TGTAACTGGTGAGTTATGACATCATATAAAAAGAAA
1 ACCATATCGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAA
** *
42421562 ATGATATCGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAT
1 ACCATATCGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAA
* * * ** * *
42421615 ACCATATTGTATAAGACCATAGTTGGTGGGTTATGGCATTATATGGAA
1 ACCATATCGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGGAA
42421663 GAATTTAATG
Statistics
Matches: 84, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
52 14 0.17
53 70 0.83
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (53 bp):
ACCATATCGTGTAAGACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAA
Found at i:42423936 original size:34 final size:34
Alignment explanation
Indices: 42423898--42423963 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
42423888 AGTAACAAAC
42423898 AATATGCTCATAAC-GATTCAATTTAGTAGCAATT
1 AATATGCTCATAACAGA-TCAATTTAGTAGCAATT
** *
42423932 AATATGCTTGTGACAGATCAATTTAGTAGCAA
1 AATATGCTCATAACAGATCAATTTAGTAGCAA
42423964 AAATCATGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (34 bp):
AATATGCTCATAACAGATCAATTTAGTAGCAATT
Found at i:42426731 original size:119 final size:122
Alignment explanation
Indices: 42426601--42426833 Score: 355
Period size: 119 Copynumber: 1.9 Consensus size: 122
42426591 TTTACTAAGT
* * *
42426601 TAAAATTAGAATAATCTAGAGTTTTCATCTTTGAATAGTTTTAAAATCTAAAAAAAAAATAATGA
1 TAAAATTAGAATAATCTAAAGTTTTCATCTTTAAATAGTTTTAAAATCTAAAAAAAAAATAATAA
*
42426666 TAATTTTATAAAATCTAAAA-TT-TT-TTATTATTATTTTTTTAGAAAATATAATTG
66 GAATTTTATAAAATCTAAAAGTTGTTATTATTATTATTTTTTTAGAAAATATAATTG
* ****
42426720 TAAAATTAGAATAATCTAAAGTTTTCATCTTTAAATAGTTTTAAAATCTAAACAACTTTTAATAA
1 TAAAATTAGAATAATCTAAAGTTTTCATCTTTAAATAGTTTTAAAATCTAAAAAAAAAATAATAA
*
42426785 GAATTTTATAATATCTAAAAGTTGTTATTATTATTATTTTTTTAGAAAA
66 GAATTTTATAAAATCTAAAAGTTGTTATTATTATTATTTTTTTAGAAAA
42426834 ATGGAATTCT
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
119 75 0.74
120 2 0.02
121 2 0.02
122 22 0.22
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (122 bp):
TAAAATTAGAATAATCTAAAGTTTTCATCTTTAAATAGTTTTAAAATCTAAAAAAAAAATAATAA
GAATTTTATAAAATCTAAAAGTTGTTATTATTATTATTTTTTTAGAAAATATAATTG
Found at i:42427595 original size:49 final size:50
Alignment explanation
Indices: 42427494--42427598 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 50
42427484 TATGGGTAGT
* ** *
42427494 GTTTTAGTGTTTAGGGTTAGGATGTTTGAAAAAATAAATTTGGGTTTAGG
1 GTTTTAGGGTTTAGCATTAGGATGTTTGAAAAAATAAATTAGGGTTTAGG
* *
42427544 GTTTTAGGGTTTAGCATTAGGGTTTTTG-AAAAATAAATTAGGGTTTAGG
1 GTTTTAGGGTTTAGCATTAGGATGTTTGAAAAAATAAATTAGGGTTTAGG
42427593 GTTTTA
1 GTTTTA
42427599 AAAAAATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 26 0.53
50 23 0.47
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.43
Consensus pattern (50 bp):
GTTTTAGGGTTTAGCATTAGGATGTTTGAAAAAATAAATTAGGGTTTAGG
Found at i:42427958 original size:126 final size:126
Alignment explanation
Indices: 42427696--42428354 Score: 795
Period size: 126 Copynumber: 5.3 Consensus size: 126
42427686 TTGTACAGTT
* * * * * *
42427696 AGCAAAAGCACTGAAAAAAGCTCTCAACTGGACACTTTTTTTGTATAGTTGTTTCT-GAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
* * * * * * *
42427760 ATTTTGAGAAGATGGATAT-AAAAAATATGTTGAAAAATGATTCAAGCAAGATGCATTGCC
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATGCACTGTC
* * * * * ** *
42427820 AGCAAAATTACTGAAAGAAGCTCTCAGTTGGACGCTCTTTTTGTATGGTTGCTTCTAAAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
* * *
42427885 ATTTTGAGAAGATGGTTTTGAAAAAATAGGTTGAAAAACGCTTCAAGCAGGATGCACTATC
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATGCACTGTC
* * * * * * * * *
42427946 AGAAAAAATACTGAAAAAAGTTCCCAGCTAGACATTTTTTTTGTACAATTGTTTCTGAAAGAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
* * * *
42428011 ATTTTAAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGTTTCAAGTAGGATGCACTGTT
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATGCACTGTC
* * * * *
42428072 AGCAAATGTACTGAAAAAAGCTCCTAGCAGGACGCTCTTTTTGTACAGTTGTTTCTGAAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
* * * * *
42428137 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTAAAAAACGCTTCAAACAAGATGCACTATC
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATGCACTGTC
* * *
42428198 AGCAAAAGTACT-AAAAAAGATCCCAACTAGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
* *
42428262 ATTTCGAGAAGATGGTTTTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATTG-ACTGTC
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGA-TGCACTGTC
* *
42428323 AGCAGAAGTACTGAAAAAAGCTCCCAACTGGA
1 AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGA
42428355 TGCTTTTTTC
Statistics
Matches: 450, Mismatches: 81, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
124 47 0.10
125 131 0.29
126 272 0.60
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (126 bp):
AGCAAAAGTACTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGTACAGTTGTTTCTAAAAAAATA
ATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAATGCTTCAAGCAGGATGCACTGTC
Found at i:42450093 original size:84 final size:84
Alignment explanation
Indices: 42449952--42450116 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
42449942 TGTTTCGAAG
* * *
42449952 CATTATAGGGAAGAAGGTGCAGATCACCTACCTGTTGGTTGGAACTCGGTGAGAGAAAGATAATT
1 CATTATAGGGAAGAAGGTGCAGATCACATACCTATTGGTTGGAACTCAGTGAGAGAAAGATAATT
42450017 GGTCTTGACTTCGTACAAA
66 GGTCTTGACTTCGTACAAA
* ** * *
42450036 CATTATAGGGAAGAAGGTGCAGATCATATACCTATTGGTTTTAACTCAGTGATAGAAAGTTAATT
1 CATTATAGGGAAGAAGGTGCAGATCACATACCTATTGGTTGGAACTCAGTGAGAGAAAGATAATT
42450101 GGTCTTGACTTCGTAC
66 GGTCTTGACTTCGTAC
42450117 GAGAAACAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (84 bp):
CATTATAGGGAAGAAGGTGCAGATCACATACCTATTGGTTGGAACTCAGTGAGAGAAAGATAATT
GGTCTTGACTTCGTACAAA
Found at i:42454852 original size:11 final size:10
Alignment explanation
Indices: 42454821--42454859 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
42454811 GAAAATGATC
*
42454821 AAAATTAATC
1 AAAATTAATT
*
42454831 AAAATTTATT
1 AAAATTAATT
42454841 ATAAATTAATT
1 A-AAATTAATT
42454852 AAAATTAA
1 AAAATTAA
42454860 ACATGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTAATT
Found at i:42455144 original size:37 final size:37
Alignment explanation
Indices: 42455094--42455223 Score: 104
Period size: 37 Copynumber: 3.4 Consensus size: 37
42455084 ATTCTTCCCA
42455094 AAATTATGAATTTAGTATACTTATGCCCAAGAACAAG
1 AAATTATGAATTTAGTATACTTATGCCCAAGAACAAG
* ** ** * *
42455131 AAATT-TGATATTTATGCTACTTAATTATAG-ATATCATTCAAA
1 AAATTATGA-ATTTA-G-TA--TACTTAT-GCCCAAGA-ACAAG
42455173 AAATTATGAATTTAGTATACTTATGCCCAAGAACAAG
1 AAATTATGAATTTAGTATACTTATGCCCAAGAACAAG
42455210 AAATT-TGATATTTA
1 AAATTATGA-ATTTA
42455224 TGCTACTTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
36 6 0.09
37 24 0.35
38 9 0.13
39 2 0.03
40 2 0.03
41 9 0.13
42 14 0.20
43 3 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (37 bp):
AAATTATGAATTTAGTATACTTATGCCCAAGAACAAG
Found at i:42455224 original size:79 final size:79
Alignment explanation
Indices: 42455093--42455251 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
42455083 AATTCTTCCC
42455093 AAAATTATGAATTTAGTATACTTATGCCCAAGAACAAGAAATTTGATATTTATGCTACTTAATTA
1 AAAATTATGAATTTAGTATACTTATGCCCAAGAACAAGAAATTTGATATTTATGCTACTTAATTA
*
42455158 TAGATATCATTCAA
66 TACATATCATTCAA
42455172 AAAATTATGAATTTAGTATACTTATGCCCAAGAACAAGAAATTTGATATTTATGCTACTTAATTA
1 AAAATTATGAATTTAGTATACTTATGCCCAAGAACAAGAAATTTGATATTTATGCTACTTAATTA
42455237 TACATATCATTCAA
66 TACATATCATTCAA
42455251 A
1 A
42455252 TTAATCTCAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (79 bp):
AAAATTATGAATTTAGTATACTTATGCCCAAGAACAAGAAATTTGATATTTATGCTACTTAATTA
TACATATCATTCAA
Done.