Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:297805 original size:21 final size:21
Alignment explanation
Indices: 297759--297805 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
297749 TTTTCTTCTT
* *
297759 ATTTTATTTATTTTATTTATC
1 ATTTTATTTATGTTATTTACC
*
297780 TTTTTATTTACTGTT-TTTACC
1 ATTTTATTTA-TGTTATTTACC
297801 ATTTT
1 ATTTT
297806 TCATTGCCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATGTTATTTACC
Found at i:300784 original size:116 final size:113
Alignment explanation
Indices: 300582--300807 Score: 425
Period size: 116 Copynumber: 2.0 Consensus size: 113
300572 TGAAATGCCA
300582 AGGCATTTCTGAATTGAACTCAGTGATTGAAGAAGACTGAACATCTTTTCCAGAACACTTCATTC
1 AGGCATTTCTGAATTGAACTCAGTGATTGAAGAAGACTGAACATCTTTTCCAGAACACTTCATTC
300647 AGCTAGCAGAAAATGAATATTGGGTGGATGATGAAAGCTTAGTGGTCC
66 AGCTAGCAGAAAATGAATATTGGGTGGATGATGAAAGCTTAGTGGTCC
300695 AGGCATTTCTGAATTGAACTCAGTGATTGAAGAAGAGACTGAACATCTTTTCCAGAACAACTTCA
1 AGGCATTTCTGAATTGAACTCAGTGATTGAAG-A-AGACTGAACATCTTTTCCAGAAC-ACTTCA
300760 TTCAGCTAGCAGAAAATGAATATTGGGTGGATGATGAAAGCTTAGTGG
63 TTCAGCTAGCAGAAAATGAATATTGGGTGGATGATGAAAGCTTAGTGG
300808 AGTCCGACGA
Statistics
Matches: 110, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
113 32 0.29
114 1 0.01
115 23 0.21
116 54 0.49
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (113 bp):
AGGCATTTCTGAATTGAACTCAGTGATTGAAGAAGACTGAACATCTTTTCCAGAACACTTCATTC
AGCTAGCAGAAAATGAATATTGGGTGGATGATGAAAGCTTAGTGGTCC
Found at i:315170 original size:6 final size:7
Alignment explanation
Indices: 315143--315173 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
315133 TTAAAATTTT
315143 ATTTAAA
1 ATTTAAA
315150 ATTTAAA
1 ATTTAAA
315157 ATTTAAA
1 ATTTAAA
315164 A-TTAAA
1 ATTTAAA
315170 ATTT
1 ATTT
315174 TAGAGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTTAAA
Found at i:315175 original size:14 final size:14
Alignment explanation
Indices: 315143--315173 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
315133 TTAAAATTTT
315143 ATTTAAAATTTAAA
1 ATTTAAAATTTAAA
315157 ATTTAAAA-TTAAA
1 ATTTAAAATTTAAA
315170 ATTT
1 ATTT
315174 TAGAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAAAATTTAAA
Found at i:315303 original size:2 final size:2
Alignment explanation
Indices: 315298--315332 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
315288 ATTTTGTGTG
315298 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 T
315333 TTGTAACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:317959 original size:40 final size:40
Alignment explanation
Indices: 317880--317959 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
317870 ATATGAGTCA
* *
317880 AATATTGCACCGCAGTACTGAGGTCGAGCTTTGCTCACCT
1 AATATTGCACCGCAGTACTGAGGTCGAGCTTTACCCACCT
* * * *
317920 AATATTGCACCGTAGTGCTGAGGTTGGGCTTTACCCACCT
1 AATATTGCACCGCAGTACTGAGGTCGAGCTTTACCCACCT
317960 TGTACACCGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (40 bp):
AATATTGCACCGCAGTACTGAGGTCGAGCTTTACCCACCT
Found at i:318635 original size:18 final size:18
Alignment explanation
Indices: 318612--318651 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
318602 CTCAAATATG
318612 AATCTATCCATATAAAGA
1 AATCTATCCATATAAAGA
318630 AATCTATCCATATAAAGA
1 AATCTATCCATATAAAGA
318648 AATC
1 AATC
318652 CTTCTAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (18 bp):
AATCTATCCATATAAAGA
Found at i:320679 original size:4 final size:4
Alignment explanation
Indices: 320670--320873 Score: 121
Period size: 4 Copynumber: 50.0 Consensus size: 4
320660 ATATCCCTTC
* * * * **
320670 AAAT AAAT AAAT AAAT AAAT AATTTT GAAAC AAAC AAAC AAAT AAAT TCA-
1 AAAT AAAT AAAT AAAT AAAT AA--AT -AAAT AAAT AAAT AAAT AAAT AAAT
* * * **
320720 AAAT AACT AAAT AAAT AAATT CAAGT GGAAT AAAT AAAT AAAT CCA- AAAT
1 AAAT AAAT AAAT AAAT AAA-T -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * *
320770 AAAT AAAT AAAC AAAT AAAT -TAG AAAT AAAT GAAT ACAT AAAT TAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
**
320816 AAAT AAAT AAAT AAATT CAAATT AAAT AAAT AAAT CCA- AAAT AAAT AAAT
1 AAAT AAAT AAAT AAA-T -AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
320866 AAAT AAAT
1 AAAT AAAT
320874 TACCGTCAGA
Statistics
Matches: 153, Mismatches: 35, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
3 6 0.04
4 129 0.84
5 8 0.05
6 8 0.05
7 2 0.01
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:320735 original size:23 final size:23
Alignment explanation
Indices: 320674--320873 Score: 146
Period size: 23 Copynumber: 8.7 Consensus size: 23
320664 CCCTTCAAAT
* **
320674 AAATAAATAAATAAATAATTTTG
1 AAATAAATAAATAAATAAATTCA
* * *
320697 AAACAAACAAACAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
320720 AAATAACTAAATAAATAAATTC-
1 AAATAAATAAATAAATAAATTCA
* * *
320742 AAGTGGAATAAATAAATAAATCCA
1 AAAT-AAATAAATAAATAAATTCA
320766 AAATAAATAAATAAACAAATAAATT-A
1 AAATAAATAAAT----AAATAAATTCA
* *
320792 GAAATAAATGAATACATAAATT--
1 -AAATAAATAAATAAATAAATTCA
320814 -AA-AAATAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
* *
320835 AATTAAATAAATAAATCCAAAAT--
1 AAATAAATAAATAAAT--AAATTCA
320858 AAATAAATAAATAAAT
1 AAATAAATAAATAAAT
320874 TACCGTCAGA
Statistics
Matches: 140, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
19 15 0.11
20 2 0.01
22 4 0.03
23 92 0.66
24 3 0.02
25 4 0.03
26 1 0.01
27 19 0.14
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATTCA
Found at i:320770 original size:19 final size:18
Alignment explanation
Indices: 320748--320869 Score: 119
Period size: 19 Copynumber: 6.8 Consensus size: 18
320738 ATTCAAGTGG
320748 AATAAATAAATAAATCCAA
1 AATAAATAAATAAAT-CAA
320767 AATAAATAAATAAA-C-A
1 AATAAATAAATAAATCAA
* *
320783 AATAAAT-TAGAAAT--A
1 AATAAATAAATAAATCAA
* * *
320798 AATGAATACATAAATTAAA
1 AATAAATAAATAAA-TCAA
320817 AATAAATAAATAAATTCAA
1 AATAAATAAATAAA-TCAA
*
320836 ATTAAATAAATAAATCCAA
1 AATAAATAAATAAAT-CAA
320855 AATAAATAAATAAAT
1 AATAAATAAATAAAT
320870 AAATTACCGT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
15 11 0.13
16 12 0.14
17 2 0.02
18 1 0.01
19 61 0.70
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.25
Consensus pattern (18 bp):
AATAAATAAATAAATCAA
Found at i:329169 original size:36 final size:37
Alignment explanation
Indices: 329110--329185 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
329100 TTTTTATATT
*
329110 TTTAATTTTGTAAAAAATTTATATAAATATTAT-CAA
1 TTTAATTTTGTAAAAAATATATATAAATATTATACAA
* *
329146 TTTAATTTTTTAAAGAAA-ATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATATATATAAATATTATACAA
329183 TTT
1 TTT
329186 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATATATAAATATTATACAA
Found at i:336202 original size:19 final size:20
Alignment explanation
Indices: 336175--336212 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
336165 ATAGCACATA
*
336175 AATCTATGCAAGT-ATACAC
1 AATCGATGCAAGTAATACAC
336194 AATCGATGCAAGTAATACA
1 AATCGATGCAAGTAATACA
336213 GTAGTGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AATCGATGCAAGTAATACAC
Found at i:340141 original size:2 final size:2
Alignment explanation
Indices: 340134--340163 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
340124 ACATACTCGA
340134 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
340164 GTGAATTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:340232 original size:15 final size:15
Alignment explanation
Indices: 340212--340243 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
340202 TGATTCCAGA
340212 ATCTAAACACAAAAC
1 ATCTAAACACAAAAC
340227 ATCTAAACACAAAAC
1 ATCTAAACACAAAAC
340242 AT
1 AT
340244 AATCCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.25, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCTAAACACAAAAC
Found at i:343632 original size:30 final size:30
Alignment explanation
Indices: 343598--343679 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
343588 GGAAGAACCT
*
343598 AAATAGCAAAAATAGAAATTTAATGGACTA
1 AAATAGCAAAAATAGAAATTTAAAGGACTA
* * *
343628 AAATAGCAAATATAGAAACTTAAAGGATTA
1 AAATAGCAAAAATAGAAATTTAAAGGACTA
* * *
343658 AAATAGCTAAAACATAAATTTA
1 AAATAGCAAAAATAGAAATTTA
343680 GAGGGTTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.24
Consensus pattern (30 bp):
AAATAGCAAAAATAGAAATTTAAAGGACTA
Found at i:345186 original size:31 final size:31
Alignment explanation
Indices: 345150--345208 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
345140 AACTTAAAAG
*
345150 AGTTTTGCAATACT-AAGATTTAAATAATTTT
1 AGTTTTACAATACTGAA-ATTTAAATAATTTT
345181 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
345209 CCATACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:345284 original size:22 final size:22
Alignment explanation
Indices: 345235--345283 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
345225 ATAAATTATT
**
345235 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
345257 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
345280 TAAA
1 TAAA
345284 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:345287 original size:54 final size:54
Alignment explanation
Indices: 345223--345617 Score: 447
Period size: 54 Copynumber: 7.4 Consensus size: 54
345213 ACAACTACAA
*
345223 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * *
345277 TAATAAATTA-TTAAAATAAATCAATCCATACAACTACAATAAAAATCAATCTATA-
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTA-AA-ATAAATCAATCCATAC
** * ** ** ** *
345332 TTTTAAAATAAAT-AAATCTATACAAATAAAT-TATTTAAAATAAATCAGTCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
345387 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
345441 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
345495 TAATAAATTATTTAAAA-AAACCAATCCATA-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
345547 TAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAAATCAATTCATAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
345594 TTATAACATTTATTTAAAATAAAT
1 TAATAA-A-TTATTTAAAATAAAT
345618 TATTTTATAA
Statistics
Matches: 292, Mismatches: 32, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
46 2 0.01
47 25 0.09
48 1 0.00
49 14 0.05
51 2 0.01
52 39 0.13
53 32 0.11
54 121 0.41
55 27 0.09
56 24 0.08
57 5 0.02
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:345370 original size:32 final size:32
Alignment explanation
Indices: 345333--345524 Score: 174
Period size: 32 Copynumber: 6.7 Consensus size: 32
345323 CAATCTATAT
* *
345333 TTTAAAATAAATAAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
345365 TTTAAAATAAATCAGTCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
345397 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
345419 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
345451 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
345473 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
345505 TTTAAAA-AAACCAATCCATA
1 TTTAAAATAAATCAATCCATA
345525 TTTAAAATAA
Statistics
Matches: 134, Mismatches: 6, Indels: 41
0.74 0.03 0.23
Matches are distributed among these distances:
22 32 0.24
23 4 0.03
24 2 0.01
26 6 0.04
28 6 0.04
30 2 0.01
31 16 0.12
32 66 0.49
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:345423 original size:22 final size:22
Alignment explanation
Indices: 345397--345439 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
345387 TAATAAATTA
345397 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
345419 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
345440 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:345448 original size:22 final size:22
Alignment explanation
Indices: 345399--345447 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
345389 ATAAATTATT
**
345399 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
345421 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
345444 TAAA
1 TAAA
345448 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:345477 original size:22 final size:22
Alignment explanation
Indices: 345451--345493 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
345441 TAATAAATTA
345451 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
345473 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
345494 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:345502 original size:22 final size:22
Alignment explanation
Indices: 345453--345501 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
345443 ATAAATTATT
**
345453 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
345475 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
345498 TAAA
1 TAAA
345502 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:345528 original size:20 final size:21
Alignment explanation
Indices: 345503--345545 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
345493 ACTAATAAAT
345503 TATTTAAAA-AAACCAATCCA
1 TATTTAAAATAAACCAATCCA
*
345523 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAACCAATCCA
345544 TA
1 TA
345546 CTAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.30
Consensus pattern (21 bp):
TATTTAAAATAAACCAATCCA
Found at i:345577 original size:15 final size:15
Alignment explanation
Indices: 345548--345689 Score: 141
Period size: 15 Copynumber: 9.5 Consensus size: 15
345538 AATCCATACT
345548 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
345562 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* * *
345577 AATAAATCAATTCATATT
1 AATAAAT-TATT-TTA-A
*
345595 TATAACATT-TATTTAA
1 AATAA-ATTAT-TTTAA
*
345611 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
345626 AAT-AATTA-TTTAT
1 AATAAATTATTTTAA
345639 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
345653 AATAAATTATTTTAT
1 AATAAATTATTTTAA
345668 AATAAATTATTTTAA
1 AATAAATTATTTTAA
345683 AATAAAT
1 AATAAAT
345690 AACCTTATTA
Statistics
Matches: 107, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
13 8 0.07
14 32 0.30
15 47 0.44
16 8 0.07
17 5 0.05
18 5 0.05
19 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:345625 original size:28 final size:26
Alignment explanation
Indices: 345593--345685 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 26
345583 TCAATTCATA
*
345593 TTTATAACATTTATTTAAAATAAATTAT
1 TTTATAA-A-TTATTTATAATAAATTAT
345621 TTTATAATAATTATTTATAATAAATTAT
1 TTTAT-A-AATTATTTATAATAAATTAT
*
345649 TTAAAATAAATTATTTTATAATAAATTAT
1 TT--TATAAATTA-TTTATAATAAATTAT
345678 TTTA-AAAT
1 TTTATAAAT
345686 AAATAACCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 29 0.51
29 20 0.35
30 3 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTATAAATTATTTATAATAAATTAT
Found at i:345653 original size:42 final size:44
Alignment explanation
Indices: 345548--345689 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 44
345538 AATCCATACT
* * * *
345548 AATAAATTATTTAAAATAAATTATTTTAAAATAAATCAATTCATATT
1 AATAAATTATTTAAAATAAATTATTTTATAATAAAT-TATT-TTA-A
* *
345595 TATAACATTTATTTAAAATAAATTATTTTATAAT-AATTA-TTTAT
1 AATAA-A-TTATTTAAAATAAATTATTTTATAATAAATTATTTTAA
345639 AATAAATTATTTAAAATAAATTATTTTATAATAAATTATTTTAA
1 AATAAATTATTTAAAATAAATTATTTTATAATAAATTATTTTAA
345683 AATAAAT
1 AATAAAT
345690 AACCTTATTA
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
42 26 0.31
43 6 0.07
44 16 0.19
45 2 0.02
46 1 0.01
47 5 0.06
48 4 0.05
49 25 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (44 bp):
AATAAATTATTTAAAATAAATTATTTTATAATAAATTATTTTAA
Found at i:346186 original size:42 final size:41
Alignment explanation
Indices: 346072--346188 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 41
346062 TTCCGAATTC
* *
346072 CCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
346113 CCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
1 CC-GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
* *
346155 CTCGTGTTTGCTTCACGTAATTGGTTTTCCGGAA
1 C-CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
346189 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.03
42 67 0.96
43 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
Found at i:346661 original size:27 final size:28
Alignment explanation
Indices: 346611--346668 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
346601 TTGATTTCAC
*
346611 TAAAATATACAAAAATATATTTTATTAA
1 TAAAATATACAAAAATATATTTTAATAA
*
346639 TAAAAT-TATAAAAATA-ATATTTAATAA
1 TAAAATATACAAAAATATAT-TTTAATAA
346666 TAA
1 TAA
346669 TAAATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 19 0.70
28 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATATACAAAAATATATTTTAATAA
Found at i:347008 original size:3 final size:3
Alignment explanation
Indices: 347000--347037 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
346990 AAACATACCT
*
347000 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
347038 TTTTGTAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:347952 original size:37 final size:36
Alignment explanation
Indices: 347911--347984 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 36
347901 CACTATTATA
347911 TTTACTTATGA-TGTCATG-ATTATTGAATACTTGTTGT
1 TTTACTTATGATTGTCATGAATTA--GAATA-TTGTTGT
347948 TTTACTTATGATTGTCATGAATTAGAATATTGTTGT
1 TTTACTTATGATTGTCATGAATTAGAATATTGTTGT
347984 T
1 T
347985 GTTGTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
36 8 0.23
37 16 0.46
38 7 0.20
39 4 0.11
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (36 bp):
TTTACTTATGATTGTCATGAATTAGAATATTGTTGT
Found at i:349172 original size:13 final size:14
Alignment explanation
Indices: 349149--349189 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
349139 GTAGATGTTA
349149 TTTATATTGGTATT
1 TTTATATTGGTATT
*
349163 TTTA-ATTGGT-TA
1 TTTATATTGGTATT
349175 TTTATATTGGTATT
1 TTTATATTGGTATT
349189 T
1 T
349190 AACTATCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 6 0.26
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (14 bp):
TTTATATTGGTATT
Found at i:351405 original size:22 final size:20
Alignment explanation
Indices: 351380--351455 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
351370 CATGACGCAT
351380 TTTTCTATATTTTATGACATG
1 TTTT-TATATTTTATGACATG
*
351401 ATTTTTATATCTTTATGGCATG
1 -TTTTTATAT-TTTATGACATG
*
351423 TTTCTCTACA-TTT-TGACATG
1 TTT-T-TATATTTTATGACATG
351443 TTTTTAATATTTT
1 TTTTT-ATATTTT
351456 CTATCGGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 12 0.27
21 11 0.24
22 15 0.33
23 3 0.07
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTTTATATTTTATGACATG
Found at i:351436 original size:44 final size:40
Alignment explanation
Indices: 351362--351448 Score: 95
Period size: 44 Copynumber: 2.0 Consensus size: 40
351352 TTTCTAATAA
*
351362 TATATCTTCATGACGCATTTTTCTATATTTTATGACATGATTTT
1 TATATCTTCATGA-GCATTTTTCTACA-TTT-TGACATG-TTTT
*
351406 TATATCTTTATG-GCATGTTTCTCTACATTTTGACATGTTTT
1 TATATCTTCATGAGCAT-TTT-TCTACATTTTGACATGTTTT
351447 TA
1 TA
351449 ATATTTTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
41 6 0.15
42 11 0.28
43 6 0.15
44 16 0.41
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (40 bp):
TATATCTTCATGAGCATTTTTCTACATTTTGACATGTTTT
Found at i:355394 original size:23 final size:23
Alignment explanation
Indices: 355368--355412 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
355358 CACCACAGCT
*
355368 CGTATAAATGCACCGA-AGTGCCC
1 CGTAGAAATGCACC-ATAGTGCCC
*
355391 CGTAGAATTGCACCATAGTGCC
1 CGTAGAAATGCACCATAGTGCC
355413 ATATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCATAGTGCCC
Found at i:355661 original size:149 final size:149
Alignment explanation
Indices: 355391--355694 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
355381 CGAAGTGCCC
355391 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
355456 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
355521 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
* *
355540 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCTATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
355605 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
355670 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
355689 CGTAGA
1 CGTAGA
355695 CCCTCTATCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:356197 original size:18 final size:19
Alignment explanation
Indices: 356161--356197 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
356151 TTTTTTCTCA
*
356161 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
356180 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
356198 ACTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:356273 original size:65 final size:67
Alignment explanation
Indices: 356163--356308 Score: 228
Period size: 65 Copynumber: 2.2 Consensus size: 67
356153 TTTTCTCATG
*
356163 GGGGAATCGGTT-CCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGG-AATTCATA-TCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTG
356225 AA
66 AA
* *
356227 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTG
*
356292 AG
66 AA
356294 GGGGTATC-GTTCCCC
1 GGGGTATCGGTTCCCC
356309 TTGAATGGTA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
64 11 0.15
65 34 0.45
66 15 0.20
67 15 0.20
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTG
AA
Found at i:359073 original size:200 final size:197
Alignment explanation
Indices: 358715--359111 Score: 758
Period size: 200 Copynumber: 2.0 Consensus size: 197
358705 CAGGTACTTC
358715 AGGCTCTTATGATCCGTATATAAGTAACAACGCTCCCCATAAAGATAATGGCGCCAAATCCTGAG
1 AGGCTCTTATGATCCGTATATAAGTAACAACGCTCCCCATAAAGATAATGGCGCCAAATCCTGAG
358780 GGCGATACTACAGCAGCCATTTCAAATCATGAGGGGGTAATTCCTTTCATGTGGTTTCAACTGTC
66 GGCGATACTACAGCAGCCATTTCAAATCATGAGGGGGTAATTCCTTTCATGTGGTTTCAACTGTC
358845 TCGATGCGTACGCTACCACTTTTCCTTCTTGCATTAATACACACCCCAACCCGTTATGGGATGCG
131 TCGATGCGTACGCTACCACTTTTCCTTCTTGCATTAATACACACCCCAA-CCGTTATGGGATGCG
358910 TCA
195 TCA
358913 AGGCTCTTATGATCCGTATATAAGTAACAACGCTCCCCATAAAGATAATGGCGCCAAATCCTGAG
1 AGGCTCTTATGATCCGTATATAAGTAACAACGCTCCCCATAAAGATAATGGCGCCAAATCCTGAG
*
358978 GGCGAATACTACAGCAGCCATTTCTAAATCATGAGTGGGTAATTCCTTTCATGTGGTTTCAACTG
66 GGCG-ATACTACAGCAGCCATTTC-AAATCATGAGGGGGTAATTCCTTTCATGTGGTTTCAACTG
359043 TCTCGATGCGTACGCTACCACTTTTCCTTCTTGCATTAATACACACCCCAACCGTTATGGGATGC
129 TCTCGATGCGTACGCTACCACTTTTCCTTCTTGCATTAATACACACCCCAACCGTTATGGGATGC
359108 GTCA
194 GTCA
359112 CTGTATAACA
Statistics
Matches: 196, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
198 69 0.35
199 37 0.19
200 90 0.46
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (197 bp):
AGGCTCTTATGATCCGTATATAAGTAACAACGCTCCCCATAAAGATAATGGCGCCAAATCCTGAG
GGCGATACTACAGCAGCCATTTCAAATCATGAGGGGGTAATTCCTTTCATGTGGTTTCAACTGTC
TCGATGCGTACGCTACCACTTTTCCTTCTTGCATTAATACACACCCCAACCGTTATGGGATGCGT
CA
Found at i:359128 original size:33 final size:33
Alignment explanation
Indices: 359089--359151 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
359079 TAATACACAC
359089 CCCAA-CCGTTATGGGATGCGTCACTGTATAACA
1 CCCAACCCGTTAT-GGATGCGTCACTGTATAACA
359122 CCCAACCCGTTATGGATGCGTCACTGTATA
1 CCCAACCCGTTATGGATGCGTCACTGTATA
359152 CTACAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (33 bp):
CCCAACCCGTTATGGATGCGTCACTGTATAACA
Found at i:362463 original size:23 final size:23
Alignment explanation
Indices: 362437--362481 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
362427 CACCACAGCT
*
362437 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
362460 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
362482 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:362730 original size:149 final size:147
Alignment explanation
Indices: 362460--362761 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 147
362450 CGAAGTGCCC
362460 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
362525 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
362590 CATATGTCCTAAAGAACCG
131 C--ATGTCCTAAAGAACCG
*
362609 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
362674 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
362739 CATGTCCTAAAGAACCG
131 CATGTCCTAAAGAACCG
362756 CGTAGA
1 CGTAGA
362762 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 22 0.15
149 129 0.85
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
CATGTCCTAAAGAACCG
Found at i:363343 original size:65 final size:66
Alignment explanation
Indices: 363231--363379 Score: 246
Period size: 65 Copynumber: 2.2 Consensus size: 66
363221 TTTTTCTCAT
*
363231 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGG-AATTCATATTCGTT
1 GGGGTATCGGTT--CCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTT
363295 GAG
64 GAG
* *
363298 GGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTTGA
1 GGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTGA
363363 G
66 G
363364 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
363380 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
65 34 0.44
66 33 0.42
67 11 0.14
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATTCATATTCGTTGA
G
Found at i:369442 original size:22 final size:20
Alignment explanation
Indices: 369414--369456 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
369404 TTGATGATGA
369414 AAAATAAAAAATAAAAAATATT
1 AAAAT-AAAAATAAAAAA-ATT
*
369436 AAAATAAAATTAAAAAAATT
1 AAAATAAAAATAAAAAAATT
369456 A
1 A
369457 TAAACCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAAAAATAAAAAAATT
Found at i:369466 original size:21 final size:21
Alignment explanation
Indices: 369420--369468 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
369410 ATGAAAAATA
* *
369420 AAAAATAAAAAATATTAAAAT
1 AAAATTAAAAAATATTAAAAC
369441 AAAATTAAAAAA-ATTATAAAC
1 AAAATTAAAAAATATTA-AAAC
*
369462 CAAATTA
1 AAAATTA
369469 TCTCAGTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATTAAAAAATATTAAAAC
Found at i:369784 original size:33 final size:33
Alignment explanation
Indices: 369747--369829 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
369737 AAACAAGAAG
369747 GAAATGATAGTGCAATGTGACCAAACATAGAGA
1 GAAATGATAGTGCAATGTGACCAAACATAGAGA
*
369780 GAAATGATAGTGCAATGTGACCAAACGTAGAGA
1 GAAATGATAGTGCAATGTGACCAAACATAGAGA
369813 GAAATGATAGTGCAATG
1 GAAATGATAGTGCAATG
369830 GTCATATCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (33 bp):
GAAATGATAGTGCAATGTGACCAAACATAGAGA
Found at i:378881 original size:185 final size:185
Alignment explanation
Indices: 378292--378956 Score: 683
Period size: 186 Copynumber: 3.5 Consensus size: 185
378282 CCAAATTTAC
* * ** * * * * *
378292 TATACATATTCCTAACAATTTTAGATTTTAACGTATTTTGTTATCGTGAG-ATTGTCGAAGGCC-
1 TATAGATATTCATAAC-ATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAAT-TCAAAAGCCT
* * * *
378355 CTGTCAACTTAAAATCTAGTAACATTTTAGGCACAACTGATTTTATTAAACATAAAATTAACATT
64 C-GTCAACTTAAAATTTGGTAACATTTTAGGCGCAATTGATTTTATTAAACATAAAATTAACATT
* ** * * * *
378420 TCAAATCGCAACCTACTAAGATTTCTTAGCGACCCCTAATATTCTTAGACGCAATATGATTTAT
128 TCAAATCGCAA-C-A-T-A-CTTT-TTAGCGACCTATAACATTCTTAGGCGCAACATGATTTCT
* *
378484 TATAGATATTCATAACATTTTTTATATTTTAACTTATTTTGTTATCGTGGGAAGTTCAAAAGCCA
1 TATAGATATTCATAACA-TTTTT-TATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCT
* * * *
378549 CGCCAACTTAAACTTTGGTAACATTTTAGGCGCAATCGATATTATTAAACATAAAATTAACATTT
64 CGTCAACTTAAAATTTGGTAACATTTTAGGCGCAATTGATTTTATTAAACATAAAATTAACATTT
* * * * * *
378614 CAGATCACAAAATACCTTATTT-GCGA-CTCATAACATTTTTGGGCGCAACTTGATTTCT
129 CAAATCGCAACATA-CTT-TTTAGCGACCT-ATAACATTCTTAGGCGCAACATGATTTCT
* * *
378672 TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTGTAGTGAGAAATTCAAAAGCCTCG
1 TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTCG
* * *
378737 TCAACTTAAAATTTGGTAACATTTTAGGTGCAATTGATTTTATT-GACATAAAATTAGCATTTCA
66 TCAACTTAAAATTTGGTAACATTTTAGGCGCAATTGATTTTATTAAACATAAAATTAACATTTCA
* * ** * * * *
378801 AATCGTAACTTACTTTTTAAATGACCTATAACATTCTTCGGTGCAACCTGGTTTCT
131 AATCGCAACATACTTTTT-AGCGACCTATAACATTCTTAGGCGCAACATGATTTCT
* * *
378857 TATAGATATTCATTACATTTTTTATTTTAAACTTATTTTGTTATCGTGGGAAATTCAAAATCTTC
1 TATAGATATTCATAACATTTTTTATTTT-AACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTC
* * *
378922 ATCACCTTAAACTTTGGTAACATTTTAGGCGCAAT
65 GTCAACTTAAAATTTGGTAACATTTTAGGCGCAAT
378957 ATAATATGTT
Statistics
Matches: 398, Mismatches: 65, Indels: 26
0.81 0.13 0.05
Matches are distributed among these distances:
183 3 0.01
184 3 0.01
185 78 0.20
186 141 0.35
187 6 0.02
188 42 0.11
189 5 0.01
190 2 0.01
191 2 0.01
192 18 0.05
193 95 0.24
194 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (185 bp):
TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTCG
TCAACTTAAAATTTGGTAACATTTTAGGCGCAATTGATTTTATTAAACATAAAATTAACATTTCA
AATCGCAACATACTTTTTAGCGACCTATAACATTCTTAGGCGCAACATGATTTCT
Found at i:383500 original size:21 final size:21
Alignment explanation
Indices: 383476--383519 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
383466 GAGGTACCAC
383476 GAACCTCACCTTGAACCATGT
1 GAACCTCACCTTGAACCATGT
383497 GAACCTCACCTTGAACCATGT
1 GAACCTCACCTTGAACCATGT
383518 GA
1 GA
383520 GCACTCATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (21 bp):
GAACCTCACCTTGAACCATGT
Found at i:387121 original size:35 final size:34
Alignment explanation
Indices: 387082--387155 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 34
387072 TTCATGTTCA
387082 AAATTCCAAAATACTTT--TTAATAATTCTAAACCCT
1 AAATTCCAAAATACTTTAATT-AT-ATTCTAAA-CCT
387117 AAATTCCAAAATACTTTAATTATATTCTAAACCT
1 AAATTCCAAAATACTTTAATTATATTCTAAACCT
387151 AAATT
1 AAATT
387156 AAAGTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.22
35 25 0.68
36 2 0.05
37 2 0.05
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATTCCAAAATACTTTAATTATATTCTAAACCT
Found at i:393948 original size:16 final size:16
Alignment explanation
Indices: 393927--393957 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
393917 AATATATCAA
393927 TTTAAATATAAAATAT
1 TTTAAATATAAAATAT
*
393943 TTTAAATATATAATA
1 TTTAAATATAAAATA
393958 AAAATATATC
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATATAAAATAT
Found at i:393971 original size:22 final size:22
Alignment explanation
Indices: 393916--393971 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
393906 AGAATAATGT
*
393916 AAATATATC-AATTTAAATATA
1 AAATATATCAAATATAAATATA
* *
393937 AAATATTTTAAATATATAATA-A
1 AAATATATCAAATATA-AATATA
393959 AAATATATCAAAT
1 AAATATATCAAAT
393972 TACATAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 17 0.61
23 4 0.14
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATATCAAATATAAATATA
Found at i:395050 original size:32 final size:32
Alignment explanation
Indices: 395009--395081 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
394999 TCATCTTTGG
*
395009 TCCCTAAAATATTAGGTTATTTATAAGTTTAA
1 TCCCTAAAATATTAGATTATTTATAAGTTTAA
*
395041 TCCCTAAAATATTAGATTATTTATAAGTTTAG
1 TCCCTAAAATATTAGATTATTTATAAGTTTAA
395073 TCCCTAAAA
1 TCCCTAAAA
395082 CTCAACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (32 bp):
TCCCTAAAATATTAGATTATTTATAAGTTTAA
Found at i:399559 original size:38 final size:39
Alignment explanation
Indices: 399485--399559 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
399475 CAAGTTGATT
399485 GGTGGCCAACATGTACACATGAGAAAATTCATCTTTGGTA
1 GGTGGCCAACATGTA-ACATGAGAAAATTCATCTTTGGTA
*
399525 GGTGGCCAACTATGT-ACATG-GAAATTTCATCTTTG
1 GGTGGCCAAC-ATGTAACATGAGAAAATTCATCTTTG
399560 ATCCCTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 14 0.42
39 5 0.15
40 10 0.30
41 4 0.12
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (39 bp):
GGTGGCCAACATGTAACATGAGAAAATTCATCTTTGGTA
Found at i:402949 original size:14 final size:14
Alignment explanation
Indices: 402930--402957 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
402920 ATTTTAAAAG
402930 AAAAGTAAAAACTT
1 AAAAGTAAAAACTT
402944 AAAAGTAAAAACTT
1 AAAAGTAAAAACTT
402958 TATTAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAAGTAAAAACTT
Found at i:404495 original size:5 final size:5
Alignment explanation
Indices: 404487--404512 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
404477 TTTATTATTT
404487 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
404513 TTCTAAGTCA
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:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:405440 original size:18 final size:19
Alignment explanation
Indices: 405417--405455 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
405407 TTCCTAGTAA
*
405417 TTTTATTCC-CTGGTAATC
1 TTTTATCCCACTGGTAATC
405435 TTTTATCCCACTGGTAATC
1 TTTTATCCCACTGGTAATC
405454 TT
1 TT
405456 ACATTCTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (19 bp):
TTTTATCCCACTGGTAATC
Found at i:405720 original size:20 final size:21
Alignment explanation
Indices: 405679--405724 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
405669 TTAGATATTT
*
405679 ATTTTGTATTTTTTTATTAAA
1 ATTTTGTATTTTTTTATAAAA
405700 ATTTTGT-TTTTATTT-TAAAA
1 ATTTTGTATTTT-TTTATAAAA
405720 ATTTT
1 ATTTT
405725 ATAAGTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTTTGTATTTTTTTATAAAA
Found at i:412338 original size:6 final size:6
Alignment explanation
Indices: 412327--412381 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
412317 GACACGTATT
412327 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
412375 ACCACG A
1 ACCACG A
412382 GCCGAGCCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:412389 original size:5 final size:5
Alignment explanation
Indices: 412379--412422 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
412369 ACCACGACCA
*
412379 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
412423 ACGGACGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.18, C:0.39, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:418297 original size:6 final size:6
Alignment explanation
Indices: 418286--418364 Score: 149
Period size: 6 Copynumber: 13.2 Consensus size: 6
418276 GACACGTATT
418286 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
418334 ACCTCG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
418365 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:418372 original size:5 final size:5
Alignment explanation
Indices: 418362--418410 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
418352 ACCACGACCA
* * *
418362 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
418411 ACGGACGGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:422201 original size:7 final size:7
Alignment explanation
Indices: 422189--422223 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
422179 ATGCAAAGAT
422189 TTTTTTA
1 TTTTTTA
*
422196 TTTTTTT
1 TTTTTTA
422203 TATTTTTA
1 T-TTTTTA
422211 TTTTTTA
1 TTTTTTA
422218 TTTTTT
1 TTTTTT
422224 CAATCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:422216 original size:13 final size:13
Alignment explanation
Indices: 422198--422222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422188 TTTTTTTATT
422198 TTTTTTATTTTTA
1 TTTTTTATTTTTA
422211 TTTTTTATTTTT
1 TTTTTTATTTTT
422223 TCAATCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:422577 original size:29 final size:26
Alignment explanation
Indices: 422517--422586 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
422507 GGTTGGTATC
*
422517 AACGGTGGTGGCCTGGGAGTGGATGA
1 AACGGTGGTGGCCTGGGAGTGGACGA
422543 AACGGTGGTGGCCTGGGAGTGGACGA
1 AACGGTGGTGGCCTGGGAGTGGACGA
*
422569 AACGGCGGTGGCCTGGGA
1 AACGGTGGTGGCCTGGGA
422587 TTGGTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.19, C:0.16, G:0.50, T:0.16
Consensus pattern (26 bp):
AACGGTGGTGGCCTGGGAGTGGACGA
Found at i:422799 original size:3 final size:3
Alignment explanation
Indices: 422791--422840 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
422781 ACAAAAACAA
422791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
422839 AA
1 AA
422841 ATAAATATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:425815 original size:13 final size:12
Alignment explanation
Indices: 425797--425830 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
425787 TGAATAAATG
425797 AAAAAATGAAGAA
1 AAAAAAT-AAGAA
425810 AAAAAATAAGAA
1 AAAAAATAAGAA
425822 AAAAAATAA
1 AAAAAATAA
425831 AAGGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAATAAGAA
Found at i:426167 original size:19 final size:19
Alignment explanation
Indices: 426145--426235 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
426135 AAAAAAAAGT
426145 ATATATATATAAATAATAA
1 ATATATATATAAATAATAA
* *
426164 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-T-ATAAATAA-TAA
* *
426187 ATGAATATAAATAAATAAAAA
1 AT--ATATATATAAATAATAA
* *
426208 ATATATGTATAGATAAT-A
1 ATATATATATAAATAATAA
426226 ATA-ATATATA
1 ATATATATATA
426236 GTGCAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 16 0.29
20 2 0.04
21 5 0.09
22 14 0.25
23 4 0.07
24 2 0.04
25 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
ATATATATATAAATAATAA
Found at i:426749 original size:37 final size:37
Alignment explanation
Indices: 426708--426812 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 37
426698 GTGCTTGTGG
* * *
426708 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTT-T
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAAATTCT
*
426745 ATCCTATTTTAAGGAGTTTGAATCCTAGCA-AAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAAATTCT
426782 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
426813 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.12
37 48 0.81
38 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAAATTCT
Found at i:427861 original size:106 final size:106
Alignment explanation
Indices: 427543--429236 Score: 2585
Period size: 106 Copynumber: 16.0 Consensus size: 106
427533 GCATTGTTCT
* * * * *
427543 GAGTCCAATATCC-TCAG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTGAC
1 GAGTCCAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
* * * * *
427606 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
427649 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
427708 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
427749 GGGTCCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
427814 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
427855 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
427920 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
427961 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428026 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
428067 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428132 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
428173 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
428238 CCAGCGGTCCCTTCGTCGTGATGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
428279 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428344 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
428385 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
428450 CCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
428491 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
428556 CCAGCTGTCCCTTCGTCGTGAAGTTGAACTTGCGTTCTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
428597 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428662 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
428703 GAGTCCAATATCCTTCGCTGTGAAGTTGTAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
428768 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
428809 GAGTCCAATATCCTTCGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428874 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
428915 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
428980 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
429021 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
429086 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
429127 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
429192 CCAGTGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
429233 GAGT
1 GAGT
429237 GGCACGATAT
Statistics
Matches: 1458, Mismatches: 122, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
100 81 0.06
101 3 0.00
102 4 0.00
104 4 0.00
105 3 0.00
106 1360 0.93
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:430069 original size:22 final size:21
Alignment explanation
Indices: 430043--430094 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
430033 TGTTTGGTCA
*
430043 AAGGTTTGGTATTTGATGCTC
1 AAGGTTTGGCATTTGATGCTC
430064 ATAGGTTTGGCATTTGATGCTC
1 A-AGGTTTGGCATTTGATGCTC
430086 AACGGTTTG
1 AA-GGTTTG
430095 ATGGGGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (21 bp):
AAGGTTTGGCATTTGATGCTC
Found at i:430786 original size:172 final size:173
Alignment explanation
Indices: 430489--430835 Score: 601
Period size: 172 Copynumber: 2.0 Consensus size: 173
430479 TAAATAGGCC
*
430489 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
430554 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCAAGTGAAGTGATTAAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCAAGTGAAGTGATTAAGTGATTCGGGAATG
430619 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
430664 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
* *
430726 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCAAGTGAAGTGATTAAGTGATTCGGGAATG
430791 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
430836 TTTTAGGGAA
Statistics
Matches: 166, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
170 14 0.08
172 100 0.60
174 1 0.01
175 51 0.31
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCAAGTGAAGTGATTAAGTGATTCGGGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:430926 original size:8 final size:7
Alignment explanation
Indices: 430869--430942 Score: 53
Period size: 7 Copynumber: 9.7 Consensus size: 7
430859 TTTTTGTCCC
430869 TTTTTCT
1 TTTTTCT
430876 TTTTGAT-T
1 TTTT--TCT
430884 TTTGTTCT
1 TTT-TTCT
430892 TGTTTCTCT
1 T-TTT-TCT
430901 TTTTTCT
1 TTTTTCT
430908 TTGTTT-T
1 TT-TTTCT
*
430915 TTTTACT
1 TTTTTCT
430922 TTTTTGCT
1 TTTTT-CT
430930 TCTTTTCT
1 T-TTTTCT
430938 TTTTT
1 TTTTT
430943 GTTCTTGATT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
6 2 0.04
7 22 0.40
8 19 0.35
9 12 0.22
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:430941 original size:16 final size:16
Alignment explanation
Indices: 430915--430948 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
430905 TCTTTGTTTT
430915 TTTTACTTTTTTGCTTC
1 TTTTACTTTTTTG-TTC
430932 TTTT-CTTTTTTGTTC
1 TTTTACTTTTTTGTTC
430947 TT
1 TT
430949 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTACTTTTTTGTTC
Found at i:435517 original size:12 final size:12
Alignment explanation
Indices: 435494--435527 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
435484 TGAATAAATG
435494 AAAAAATGAAGAA
1 AAAAAAT-AAGAA
*
435507 TAAAAATAAGAA
1 AAAAAATAAGAA
435519 AAAAAATAA
1 AAAAAATAA
435528 AAGGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAATAAGAA
Found at i:435646 original size:18 final size:18
Alignment explanation
Indices: 435597--435650 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
435587 AAAATAGAAA
*
435597 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
435618 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
435637 AATA-TAATATAAAA
1 AATAGTAATATAAAA
435651 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:435651 original size:18 final size:19
Alignment explanation
Indices: 435601--435651 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
435591 TAGAAAAATA
*
435601 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
435621 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
435640 ATAATATAAAAA
1 ATAATATAAAAA
435652 AACCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:435681 original size:27 final size:27
Alignment explanation
Indices: 435651--435703 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
435641 TAATATAAAA
435651 AAACCAAAAACAAAAAAATAAATATAT
1 AAACCAAAAACAAAAAAATAAATATAT
* * * *
435678 AAACCAAATATAAAAATATACATATA
1 AAACCAAAAACAAAAAAATAAATATA
435704 ATGATAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.19
Consensus pattern (27 bp):
AAACCAAAAACAAAAAAATAAATATAT
Found at i:435871 original size:19 final size:19
Alignment explanation
Indices: 435849--435939 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
435839 TAAAAAAAGT
435849 ATATATATATAAATAATAA
1 ATATATATATAAATAATAA
* *
435868 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-T-ATAAATAA-TAA
* *
435891 ATGAATATAAATAAATAAAAA
1 AT--ATATATATAAATAATAA
* *
435912 ATATATGTATAGATAAT-A
1 ATATATATATAAATAATAA
435930 ATA-ATATATA
1 ATATATATATA
435940 GTGCAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 16 0.29
20 2 0.04
21 5 0.09
22 14 0.25
23 4 0.07
24 2 0.04
25 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
ATATATATATAAATAATAA
Found at i:436452 original size:37 final size:37
Alignment explanation
Indices: 436411--436515 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 37
436401 GTGCTTGTGG
* * *
436411 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTT-T
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAAATTCT
*
436448 ATCCTATTTTAAGGAGTTTGAATCCTAGCA-AAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAAATTCT
436485 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
436516 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.12
37 48 0.81
38 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAAATTCT
Found at i:436686 original size:3 final size:3
Alignment explanation
Indices: 436678--436706 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
436668 TATGTTATCT
436678 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
436707 TATGATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:437873 original size:23 final size:23
Alignment explanation
Indices: 437824--437896 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
437814 TAAGCTACCA
437824 AAAGACAGAGAAAAACATGTCAC
1 AAAGACAGAGAAAAACATGTCAC
* * *
437847 AAAGATAGAGATAAACATG-CTAT
1 AAAGACAGAGAAAAACATGTC-AC
*
437870 AAAGGC--AG-AAAACATGTCAC
1 AAAGACAGAGAAAAACATGTCAC
437890 AAAGACA
1 AAAGACA
437897 TAATTATTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 13 0.33
21 3 0.08
22 1 0.03
23 22 0.56
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAGACAGAGAAAAACATGTCAC
Found at i:438350 original size:18 final size:19
Alignment explanation
Indices: 438321--438372 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
438311 TTTTATAGCT
438321 CAAATATAACAACTTAA-AA
1 CAAAT-TAACAACTTAACAA
438340 CAAATTAACAAAC-TAACAA
1 CAAATTAAC-AACTTAACAA
*
438359 CTAATT-ACAACTTA
1 CAAATTAACAACTTA
438373 TTTCTAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 15 0.52
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (19 bp):
CAAATTAACAACTTAACAA
Found at i:439817 original size:25 final size:26
Alignment explanation
Indices: 439789--439838 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
439779 ATAAGACACT
439789 AAAAGTGAC-ATCTT-ATTATTGTCAC
1 AAAAGTGACAAT-TTAATTATTGTCAC
439814 AAAAGTGACAATTTAATTATTGTCA
1 AAAAGTGACAATTTAATTATTGTCA
439839 TATTTGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (26 bp):
AAAAGTGACAATTTAATTATTGTCAC
Found at i:439980 original size:25 final size:24
Alignment explanation
Indices: 439927--439980 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
439917 TTTTAATAAT
* *
439927 AAAAAAATTCTTTAATATTCATTCT
1 AAAAAAATTCTTTAAAATTCATT-A
*
439952 AAAACAATTCTTTAAAATAT-ATTA
1 AAAAAAATTCTTTAAAAT-TCATTA
439976 AAAAA
1 AAAAA
439981 TTATTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 4 0.17
25 19 0.79
26 1 0.04
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAAAATTCTTTAAAATTCATTA
Found at i:439987 original size:22 final size:23
Alignment explanation
Indices: 439951--440017 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
439941 ATATTCATTC
*
439951 TAAAACAATTCTTTAAAATATAT
1 TAAAACAATTATTTAAAATATAT
* *
439974 TAAAA-AATTATTTAATATATGT
1 TAAAACAATTATTTAAAATATAT
* *
439996 TAACAGACATTTTTTTAAAATA
1 TAA-A-ACAATTATTTAAAATA
440018 CATAGAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 17 0.49
23 6 0.17
24 1 0.03
25 11 0.31
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAAACAATTATTTAAAATATAT
Found at i:440115 original size:19 final size:20
Alignment explanation
Indices: 440091--440130 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
440081 TTTTAATAAC
440091 TATTTTAAATTAAT-TAAAT
1 TATTTTAAATTAATCTAAAT
* *
440110 TATTTTTAATTTATCTAAAT
1 TATTTTAAATTAATCTAAAT
440130 T
1 T
440131 TTCTTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTAAATTAATCTAAAT
Found at i:440443 original size:82 final size:85
Alignment explanation
Indices: 440304--440701 Score: 369
Period size: 82 Copynumber: 4.8 Consensus size: 85
440294 CAAAATGGCA
* * *
440304 ACTTTAGCGGCGTTTCTT-TACAAACGCCGCAATAGGGTTCATCTGTAGTGGTG-TTTTTCGATA
1 ACTTTAGCGGCGTTT-TTATACAAACGCCGCAATAGGGTTCACCTATAGTGGTGTTTTTTCAATA
*
440367 AACACCGCATCAA-AGACT-T
65 AACACCGCATCAACAGATTAT
* * * * *
440386 ACTTTAGCGGCATTTTTATACAAACGCCGTAATA-GGTCCATCTATAGTGGCGTTTTTTTTCAAT
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTTCACCTATAGT-G-GTGTTTTTTCAAT
**
440450 AAACGTCG--T-AACAGATTAGT
64 AAACACCGCATCAACAGATTA-T
* * * * * *
440470 ACTTTAGTGGGGTTTTTATACAAATGACGTAATAGGGTTCACCTATAGTGGCG-TTTTTCAATAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTTCACCTATAGTGGTGTTTTTTCAATAA
* *
440534 ACGCCGCA--ATA-A-ATTAGA
66 ACACCGCATCA-ACAGATTA-T
* * *
440552 ACTTTAGCGGCGTTTTTATACAAATGTCGCAATAGGGTTAACCTATAGTGGTGTTTTTTCAATAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTTCACCTATAGTGGTGTTTTTTCAATAA
440617 ACA-C-CA-CAACAGATTAT
66 ACACCGCATCAACAGATTAT
* * * * * *
440634 AACTTTAGCTGCATTTTTATACAAACACCGCAATAGTGTTTACCTATAGTGGTGTTTTTTAAATA
1 -ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTTCACCTATAGTGGTGTTTTTTCAATA
440699 AAC
65 AAC
440702 GTCGCAATTG
Statistics
Matches: 264, Mismatches: 36, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
81 19 0.07
82 106 0.40
83 81 0.31
84 46 0.17
85 12 0.05
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (85 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTTCACCTATAGTGGTGTTTTTTCAATAA
ACACCGCATCAACAGATTAT
Found at i:440608 original size:41 final size:41
Alignment explanation
Indices: 440474--440609 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
440464 ATTAGTACTT
* * *
440474 TAGTGGGGTTTTTATACAAATGACGTAATAGGGTTCACCTA
1 TAGTGGCGTTTTTATACAAATGACGCAATAGGGTTAACCTA
* * * ** * *
440515 TAGTGGCGTTTTTCA-ATAAACGCCGCAATA-AATTAGAACTT
1 TAGTGGCGTTTTT-ATACAAATGACGCAATAGGGTTA-ACCTA
* *
440556 TAGCGGCGTTTTTATACAAATGTCGCAATAGGGTTAACCTA
1 TAGTGGCGTTTTTATACAAATGACGCAATAGGGTTAACCTA
*
440597 TAGTGGTGTTTTT
1 TAGTGGCGTTTTT
440610 TCAATAAACA
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
40 3 0.04
41 64 0.90
42 4 0.06
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAATGACGCAATAGGGTTAACCTA
Found at i:441738 original size:15 final size:16
Alignment explanation
Indices: 441714--441756 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
441704 TAAAATCGTC
441714 TTTTAA-AAAAA-CAA
1 TTTTAAGAAAAATCAA
*
441728 TTTTAAGAAAAATCAT
1 TTTTAAGAAAAATCAA
441744 TTTTAAGACAAAA
1 TTTTAAGA-AAAA
441757 GCTGGCCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (16 bp):
TTTTAAGAAAAATCAA
Found at i:442194 original size:2 final size:2
Alignment explanation
Indices: 442187--442222 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
442177 TGAATCATAA
442187 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
442223 CAAATAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:444210 original size:3 final size:3
Alignment explanation
Indices: 444202--444238 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
444192 AAATTTGTAT
*
444202 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
444239 TTTTTTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:444843 original size:91 final size:91
Alignment explanation
Indices: 444735--444906 Score: 274
Period size: 91 Copynumber: 1.9 Consensus size: 91
444725 GATAGGTCGA
* *
444735 ACAAGCTCTTCTCATTATGAACTTCTTCT-TCCTCATTGGATGAGTTCTTCTCATTATGAGCTCT
1 ACAAGCTCTTCTCATTATGAACTTATTCTCT-CTCATTGGATGAGTTCTTCTCATTATGAACTCT
444799 CCATTGAAAATGTTGATGCAAAGTTTG
65 CCATTGAAAATGTTGATGCAAAGTTTG
* * *
444826 ACAAGTTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTTATTATGAACTTTC
1 ACAAGCTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTCATTATGAACTCTC
*
444891 CATTGGAAATGTTGAT
66 CATTGAAAATGTTGAT
444907 CCATCTCTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 73 0.99
92 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (91 bp):
ACAAGCTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTCATTATGAACTCTC
CATTGAAAATGTTGATGCAAAGTTTG
Found at i:445039 original size:331 final size:331
Alignment explanation
Indices: 444402--445145 Score: 1043
Period size: 331 Copynumber: 2.2 Consensus size: 331
444392 GCATTGGATT
* * *
444402 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGATGAGTTCTTCTTATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
444467 TTCCCTGGAAAA-ACTGATGCAAGGTTGAACATGTTCTTCTCATTATGAACTTCTTCTTCCTCGT
66 -TCCATTGAAAATGCTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCAT
*
444531 TGGATGAGTTCTTCTCATTATGAACTCTCAACTAAAAATGTTGAGTCACCTATTTCTGTGGTGGA
130 TGGATGAGTTCTTCTCATTATGAACTCTCAACTAAAAATGTTGAGTCACCTATTTCTGTGATGGA
*
444596 CTTAAAAGGAACAAGTTCTTTTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGA
195 CTTAAAAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGA
* * * *
444661 ACTCTTTTGGAAATGTCAATCCTTCTAACGAGGCGTCACTGATTCGAAATG-TCGTGAATCGAGT
260 ACTCTTCTGAAAATGTCAATCCTTCTAACGAGGCGTCACTAATTCGAAATGCT-GTAAATCGAGT
444725 GATAGGTC
324 GATAGGTC
* *
444733 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAGCTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* *
444798 TCCATTGAAAATGTTGATGCAAAGTTTG-ACAAGTTCTTCTCATTATGAACTTATTC-TCTCTCA
66 TCCATTGAAAATGCTGATGC-AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTC-CTCA
* * * * ** * *
444861 TTGGATGAGTTCTTCTTATTATGAACTTTCCATTGGAAATGTTGA-TCCATCTCTTTCTGTGATG
129 TTGGATGAGTTCTTCTCATTATGAACTCTCAACTAAAAATGTTGAGT-CACCTATTTCTGTGATG
* *
444925 GACTTGAAAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTAT
193 GACTTAAAAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTAT
* * *
444990 GAACTCTTCTGAAAATTTCAATTCC-TC-AAGCGAGGTGTCACTAATTCGAAATGCTGTAAATCT
258 GAACTCTTCTGAAAATGTCAA-TCCTTCTAA-CGAGGCGTCACTAATTCGAAATGCTGTAAATCG
445053 AGTGATAGGTC
321 AGTGATAGGTC
* * *
445064 GAATAGGCTCTTCTCATTATGAACTTCTTCTACCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
*
445129 CTCCATTGGAAATGCTG
65 CTCCATTGAAAATGCTG
445146 GTTCACCTCC
Statistics
Matches: 366, Mismatches: 39, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
330 14 0.04
331 303 0.83
332 49 0.13
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (331 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGCTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCATT
GGATGAGTTCTTCTCATTATGAACTCTCAACTAAAAATGTTGAGTCACCTATTTCTGTGATGGAC
TTAAAAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAA
CTCTTCTGAAAATGTCAATCCTTCTAACGAGGCGTCACTAATTCGAAATGCTGTAAATCGAGTGA
TAGGTC
Found at i:446045 original size:14 final size:14
Alignment explanation
Indices: 446028--446078 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
446018 TCTCTTTTCA
446028 TTTTTTTATTTCTT
1 TTTTTTTATTTCTT
*
446042 TTTTCATTTTTTTCTT
1 TTTT--TTTATTTCTT
* *
446058 TTTATTTGTTTCTT
1 TTTTTTTATTTCTT
446072 TTTTTTT
1 TTTTTTT
446079 TCTTCAAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 19 0.61
16 12 0.39
ACGTcount: A:0.06, C:0.08, G:0.02, T:0.84
Consensus pattern (14 bp):
TTTTTTTATTTCTT
Found at i:446045 original size:20 final size:20
Alignment explanation
Indices: 446016--446054 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
446006 AACCCTCATT
446016 TTTCTCTTTTCATTTTTTTA
1 TTTCTCTTTTCATTTTTTTA
*
446036 TTTCTTTTTTCATTTTTTT
1 TTTCTCTTTTCATTTTTTT
446055 CTTTTTATTT
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:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCTTTTCATTTTTTTA
Found at i:446049 original size:34 final size:34
Alignment explanation
Indices: 446011--446080 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
446001 TCTCAAACCC
*
446011 TCATTTTTCTCTTTTCATTTTTTTATTTCTTTTT
1 TCATTTTTCTCTTTTCATTTGTTTATTTCTTTTT
* * * *
446045 TCATTTTTTTCTTTTTATTTGTTTCTTTTTTTTT
1 TCATTTTTCTCTTTTCATTTGTTTATTTCTTTTT
446079 TC
1 TC
446081 TTCAAGCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (34 bp):
TCATTTTTCTCTTTTCATTTGTTTATTTCTTTTT
Found at i:446051 original size:26 final size:26
Alignment explanation
Indices: 446014--446064 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
446004 CAAACCCTCA
446014 TTTTTCTCTTTTCATT-TTTTTATTTC
1 TTTTTCTCTTTT-ATTCTTTTTATTTC
*
446040 TTTTT-TCATTTTTTTCTTTTTATTT
1 TTTTTCTC-TTTTATTCTTTTTATTT
446065 GTTTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTCTCTTTTATTCTTTTTATTTC
Found at i:446077 original size:26 final size:26
Alignment explanation
Indices: 446030--446082 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
446020 TCTTTTCATT
446030 TTTTTATTTCTTTTTTCATTTTTTTC
1 TTTTTATTTCTTTTTTCATTTTTTTC
*
446056 TTTTTATTTGTTTCTTT--TTTTTTTC
1 TTTTTATTTCTTT-TTTCATTTTTTTC
446081 TT
1 TT
446083 CAAGCATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 12 0.48
27 3 0.12
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (26 bp):
TTTTTATTTCTTTTTTCATTTTTTTC
Found at i:457066 original size:15 final size:16
Alignment explanation
Indices: 457048--457091 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
457038 TAAAATTGTC
457048 TTTTTAA-AAAAATAA
1 TTTTTAAGAAAAATAA
*
457063 -TTTTAAGAAAAATCA
1 TTTTTAAGAAAAATAA
457078 TTTTTAAGACAAAA
1 TTTTTAAGA-AAAA
457092 GCTGCTATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 8 0.32
17 4 0.16
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
TTTTTAAGAAAAATAA
Found at i:457447 original size:29 final size:30
Alignment explanation
Indices: 457385--457499 Score: 78
Period size: 30 Copynumber: 3.9 Consensus size: 30
457375 AAGTATAAAT
* *
457385 TTAAAATATCAAAAT-ATCACAAACAAAAAC
1 TTAAAATATTAAAATAAT-AAAAACAAAAAC
* * *
457415 TT-AAGTATTAAAATAATAAAAACAAATAT
1 TTAAAATATTAAAATAATAAAAACAAAAAC
* * *
457444 TTAAAATATTGAAATAGTAAAAATAGAAAA-
1 TTAAAATATTAAAATAATAAAAACA-AAAAC
* *
457474 TT-AAATAACTAAAATAA-AATAACAAA
1 TTAAAAT-ATTAAAATAATAAAAACAAA
457500 CATTTTAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.03
29 30 0.45
30 31 0.47
31 3 0.05
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.25
Consensus pattern (30 bp):
TTAAAATATTAAAATAATAAAAACAAAAAC
Found at i:459421 original size:3 final size:3
Alignment explanation
Indices: 459413--459452 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
459403 AAATTTGTAT
*
459413 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
459453 TTTTTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:459597 original size:42 final size:42
Alignment explanation
Indices: 459549--459807 Score: 231
Period size: 42 Copynumber: 6.1 Consensus size: 42
459539 TTTAAAATTA
459549 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTATACAAACG
1 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTATACAAACG
* * * * *
459591 CCGCAAAAGGTCAGATATGTAGCGGTG-TTTTCAGTACAAACG
1 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTA-TACAAACG
*
459633 CCGC-AAAAGATCGAGATCTATAGCGGTGTTTTTTGGA-ACAAACG
1 CCGCAAAAAG-TC-AGATCTATAGCGGCGTTTTTT--ATACAAACG
* * * *
459677 CCGCAAAATGTCAGA-CTATAGCAGTGTTTTTGGATACAAACG
1 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTT-TATACAAACG
* * * *
459719 CCGCAAAAGGTCAGATCTGTAGCAGCG-TTTTTAGAACAAACG
1 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTA-TACAAACG
* * * * * *
459761 CCGTAAAACGTCAGAACTATAGCGGCATTTTTGGAAACAAACG
1 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTT-TATACAAACG
459804 CCGC
1 CCGC
459808 TAATTACCAT
Statistics
Matches: 179, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
41 11 0.06
42 105 0.59
43 40 0.22
44 18 0.10
45 4 0.02
46 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTATACAAACG
Found at i:459731 original size:128 final size:127
Alignment explanation
Indices: 459549--459807 Score: 344
Period size: 128 Copynumber: 2.0 Consensus size: 127
459539 TTTAAAATTA
* *
459549 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTATACAAACGCCGCAAAAGGTCAGATATGTAGC
1 CCGCAAAAAGTCAGATCTATAGCAGCGTTTTTGATACAAACGCCGCAAAAGGTCAGATATGTAGC
* * * * **
459614 GGTGTTTTCAGTACAAACGCCGCAAAA-GATCGAGATCTATAGCGGTGTTTTTTGG-AACAAACG
66 AGCGTTTTCAGAACAAACGCCGCAAAACG-TC-AGAACTATAGCGG-CATTTTTGGAAACAAACG
* * *
459677 CCGCAAAATGTCAGA-CTATAGCAGTGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTGTAG
1 CCGCAAAAAGTCAGATCTATAGCAGCGTTTTT-GATACAAACGCCGCAAAAGGTCAGATATGTAG
* *
459741 CAGCGTTTTTAGAACAAACGCCGTAAAACGTCAGAACTATAGCGGCATTTTTGGAAACAAACG
65 CAGCGTTTTCAGAACAAACGCCGCAAAACGTCAGAACTATAGCGGCATTTTTGGAAACAAACG
459804 CCGC
1 CCGC
459808 TAATTACCAT
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
126 7 0.06
127 38 0.33
128 69 0.60
129 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (127 bp):
CCGCAAAAAGTCAGATCTATAGCAGCGTTTTTGATACAAACGCCGCAAAAGGTCAGATATGTAGC
AGCGTTTTCAGAACAAACGCCGCAAAACGTCAGAACTATAGCGGCATTTTTGGAAACAAACG
Found at i:459792 original size:85 final size:86
Alignment explanation
Indices: 459549--459807 Score: 312
Period size: 85 Copynumber: 3.0 Consensus size: 86
459539 TTTAAAATTA
* * * *
459549 CCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTA-TACAAACGCCGCAAAAGGTCAGATA-TGTA
1 CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTAGAACAAACGCCGCAAAACGTCAGA-ACTATA
**
459612 GCGGTGTTTTCAG-TACAAACG
65 GCGGTGTTTTTGGATACAAACG
* * * *
459633 CCGCAAAAGATCGAGATCTATAGCGGTGTTTTTTGGAACAAACGCCGCAAAATGTCAG-ACTATA
1 CCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTTAGAACAAACGCCGCAAAACGTCAGAACTATA
*
459697 GCAGTGTTTTTGGATACAAACG
65 GCGGTGTTTTTGGATACAAACG
* * *
459719 CCGCAAAAGGTCAGATCTGTAGCAGCG-TTTTTAGAACAAACGCCGTAAAACGTCAGAACTATAG
1 CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTAGAACAAACGCCGCAAAACGTCAGAACTATAG
** *
459783 CGGCATTTTTGGAAACAAACG
66 CGGTGTTTTTGGATACAAACG
459804 CCGC
1 CCGC
459808 TAATTACCAT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
84 37 0.25
85 73 0.49
86 39 0.26
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (86 bp):
CCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTAGAACAAACGCCGCAAAACGTCAGAACTATAG
CGGTGTTTTTGGATACAAACG
Found at i:459937 original size:18 final size:19
Alignment explanation
Indices: 459903--459938 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
459893 TTTATATAAA
*
459903 TAACAACAACCATAAATTT
1 TAACAACAACAATAAATTT
459922 TAACAACAA-AATAAATT
1 TAACAACAACAATAAATT
459939 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (19 bp):
TAACAACAACAATAAATTT
Found at i:466509 original size:192 final size:193
Alignment explanation
Indices: 466154--466562 Score: 437
Period size: 192 Copynumber: 2.1 Consensus size: 193
466144 GTGTTTTGCT
** * *
466154 ACAATATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAATTATCA
1 ACAATATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGACAATATAAATCACCA
* ** *
466219 ATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCACAGAATATAAATTATAAAGTGAC
66 ATAAAGAAATCTTAGATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTGAC
* * * * * * *
466284 GTTATGCATAAACATCATTCATAATATTATTAGGTAAC-ATTTA-TATTGCCACTAAAAATGTG
131 ATTATACATAAACAGCATCCATAATACTATTAGGTAACGATATACTA-CGCCACTAAAAATGTG
* * *
466346 ACAATATCTTTTTCGTCACATATAGGTTGATTTTAATGTATTATCCGTGACGATATAAATCACCA
1 ACAATATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGACAATATAAATCACCA
* ** ** ** ** *
466411 ATAAAGAAATTTTAGATAATTTAGTGACATAATTAGTTGTCATTGAATATTCATTATATAGTGAC
66 ATAAAGAAATCTTAGATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTGAC
* ** ** * ** *
466476 ATTATATATAAATGGCATCCATGCTACTATTAGGTGACGATATACTACGTTACTAACAATGTG
131 ATTATACATAAACAGCATCCATAATACTATTAGGTAACGATATACTACGCCACTAAAAATGTG
*
466539 ACAAT-TTTCTTTTCGTCACATATA
1 ACAATATCT-TTTTCGTCACATATA
466563 CAATGACATT
Statistics
Matches: 176, Mismatches: 38, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
192 138 0.78
193 36 0.20
194 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (193 bp):
ACAATATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGACAATATAAATCACCA
ATAAAGAAATCTTAGATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTGAC
ATTATACATAAACAGCATCCATAATACTATTAGGTAACGATATACTACGCCACTAAAAATGTG
Found at i:469817 original size:23 final size:22
Alignment explanation
Indices: 469784--469827 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
469774 ATAATCACAT
*
469784 AAAATTTAATAATTGAAATTTA
1 AAAATTTAATAATTAAAATTTA
*
469806 AAAATATTAATATTTAAAATTT
1 AAAAT-TTAATAATTAAAATTT
469828 TATTAGGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATTTAATAATTAAAATTTA
Found at i:471516 original size:60 final size:59
Alignment explanation
Indices: 471452--471617 Score: 165
Period size: 60 Copynumber: 2.8 Consensus size: 59
471442 ATTGGAAGAT
* * *
471452 TCAAAA-TTTTAGGAACTAATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGGAATGC
1 TCAAAAGTTTAAGG-ACTAATTTAGAATGAGAGTCATA-TTTGAGGATGAAATTGAAATAC
* * * * *
471512 TCAAAAGTTTAACGAGTAATTTAGAATGAGAATCATATCTT-ATGGATGGAATTGAAATAT
1 TCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAT-TTGA-GGATGAAATTGAAATAC
* * * *
471572 TTAAAAGTTTAAGGACTAATTTAAAATAAGGGTCATAATTTGAGGA
1 TCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCAT-ATTTGAGGA
471618 CATATAATGC
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
59 2 0.02
60 76 0.88
61 8 0.09
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (59 bp):
TCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATATTTGAGGATGAAATTGAAATAC
Found at i:476380 original size:29 final size:28
Alignment explanation
Indices: 476363--476431 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
476353 AAATAGGATT
476363 AACAGAAACTTGATGACCAACATAGCAAA
1 AACAGAAACTTGATGACCAA-ATAGCAAA
* *
476392 AATAGAAAGTTGATGACCAAAATAGCAAA
1 AACAGAAACTTGATGACC-AAATAGCAAA
476421 AACTA-AAACTT
1 AAC-AGAAACTT
476432 AAGGGACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (28 bp):
AACAGAAACTTGATGACCAAATAGCAAA
Found at i:476533 original size:59 final size:58
Alignment explanation
Indices: 476410--476560 Score: 189
Period size: 59 Copynumber: 2.6 Consensus size: 58
476400 GTTGATGACC
* *
476410 AAAATAGCAAAAACTAAAACTTAAGGGACTAAAATAACAAAAATATACATTTAAAGGACT
1 AAAATAGCAAAAA-TAAAACTTAAAGGACT-AAATAACAAAAACATACATTTAAAGGACT
* *
476470 AAAATATCAAAAATAGAAACTTAAAGGACTAAATAGA-AAATACATACATTTAAAGGACT
1 AAAATAGCAAAAATA-AAACTTAAAGGACTAAATA-ACAAAAACATACATTTAAAGGACT
* *
476529 AAAATAGCAAAAACAAAAACTT-AAGGATTAAA
1 AAAATAGCAAAAA-TAAAACTTAAAGGACTAAA
476561 ATGGTATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
58 9 0.11
59 45 0.56
60 27 0.33
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.20
Consensus pattern (58 bp):
AAAATAGCAAAAATAAAACTTAAAGGACTAAATAACAAAAACATACATTTAAAGGACT
Found at i:476561 original size:29 final size:30
Alignment explanation
Indices: 476410--476562 Score: 150
Period size: 30 Copynumber: 5.2 Consensus size: 30
476400 GTTGATGACC
* *
476410 AAAATAGCAAAAACTAAAACTTAAGGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* * * * *
476440 AAAATAACAAAAATATACATTTAAAGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* * *
476470 AAAATATCAAAAATAGAAACTTAAAGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* * *
476500 -AAATAG-AAAATACATACATTTAAAGGACT
1 AAAATAGCAAAA-ACAAAAACTTAAAGGACT
*
476529 AAAATAGCAAAAACAAAAACTT-AAGGATT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
476558 AAAAT
1 AAAAT
476563 GGTATTAACA
Statistics
Matches: 100, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
28 4 0.04
29 30 0.30
30 62 0.62
31 4 0.04
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
AAAATAGCAAAAACAAAAACTTAAAGGACT
Found at i:477840 original size:20 final size:20
Alignment explanation
Indices: 477815--477858 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
477805 TGGGTTTAAT
477815 TGTTGGGCTAGTGTATTGGG
1 TGTTGGGCTAGTGTATTGGG
* *
477835 TGTTGGGTTGGTGTATTGGG
1 TGTTGGGCTAGTGTATTGGG
477855 -GTTG
1 TGTTG
477859 ATTGGTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.07, C:0.02, G:0.48, T:0.43
Consensus pattern (20 bp):
TGTTGGGCTAGTGTATTGGG
Found at i:479967 original size:31 final size:31
Alignment explanation
Indices: 479929--479995 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
479919 TTTTGCCTAT
*
479929 ATAATTTGTTGTCTTGTCCGCTGTTACTTTC
1 ATAATTTGTTGTCTTGTACGCTGTTACTTTC
479960 ATAATTTGTTGTCTTGTACGCTGTTACTTTC
1 ATAATTTGTTGTCTTGTACGCTGTTACTTTC
479991 ATAAT
1 ATAAT
479996 AAATACATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.15, T:0.51
Consensus pattern (31 bp):
ATAATTTGTTGTCTTGTACGCTGTTACTTTC
Found at i:482204 original size:29 final size:29
Alignment explanation
Indices: 482170--482228 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
482160 CCTAAATTAA
*
482170 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
482199 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
482228 T
1 T
482229 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:486874 original size:29 final size:29
Alignment explanation
Indices: 486840--486898 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
486830 CCTAAATTAA
486840 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
486869 TTTGATGTCATTGCTTACATTAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
486898 T
1 T
486899 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:487583 original size:6 final size:6
Alignment explanation
Indices: 487561--487585 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
487551 GTCGTCCGTC
487561 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
487586 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:487791 original size:22 final size:23
Alignment explanation
Indices: 487740--487791 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
487730 GATAACAGCT
** *
487740 GGGAGTTATTTGATTTAATTTCA
1 GGGAGTTACATGATATAATTTCA
*
487763 TGG-GTTACATGATATAATTTC-
1 GGGAGTTACATGATATAATTTCA
487784 GGGAGTTA
1 GGGAGTTA
487792 TAACAGCTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (23 bp):
GGGAGTTACATGATATAATTTCA
Found at i:488351 original size:2 final size:2
Alignment explanation
Indices: 488344--488428 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
488334 TTTCAGAGTA
488344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
488386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
488428 A
1 A
488429 CACACACAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:495394 original size:7 final size:7
Alignment explanation
Indices: 495384--495414 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
495374 AAATTAAATT
495384 TTTAAAA
1 TTTAAAA
495391 TTTAAAA
1 TTTAAAA
495398 TTTAAAA
1 TTTAAAA
495405 TTTAAAA
1 TTTAAAA
495412 TTT
1 TTT
495415 TCTGATAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:498844 original size:21 final size:21
Alignment explanation
Indices: 498800--498844 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
498790 GATTTCTGGG
* * *
498800 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
498821 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
498842 CAA
1 CAA
498845 ATGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Done.