Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009622.1 Hibiscus syriacus cultivar Beakdansim tig00117011_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: 790348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 4
Found at i:428382 original size:22 final size:22
Alignment explanation
Indices: 428333--428382 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
428323 GGTCGAGTCG
**
428333 GGTCAACGGGTCGGGTCGGGTC
1 GGTCAACGGGTCGGGTCGGACC
* *
428355 GATCAACGGTTCGGGTCGGACC
1 GGTCAACGGGTCGGGTCGGACC
428377 GGTCAA
1 GGTCAA
428383 ACCGGTCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (22 bp):
GGTCAACGGGTCGGGTCGGACC
Found at i:435438 original size:31 final size:31
Alignment explanation
Indices: 435314--435438 Score: 139
Period size: 31 Copynumber: 4.0 Consensus size: 31
435304 GTCGAGGGTA
435314 TACCTATGTTCTACGGAACATATGGACA-TAAT
1 TACCTATGTTCTACGGAACATATGGACAGT--T
* *
435346 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
435377 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
435408 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
435439 GCCAAGGATC
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
31 53 0.67
32 25 0.32
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:435533 original size:83 final size:83
Alignment explanation
Indices: 435394--435600 Score: 378
Period size: 83 Copynumber: 2.5 Consensus size: 83
435384 GTTCTAAGGA
435394 ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCT
1 ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCT
435459 CTGGATAGGTCATTCGGG
66 CTGGATAGGTCATTCGGG
*
435477 ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTTCCAAGGATCTTTATGACCT
1 ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCT
*
435542 CTGGATAGGTCCTTCGGG
66 CTGGATAGGTCATTCGGG
* *
435560 ACATATGGACTGTTTACCTAGGTTCTTCGGAATCTATGGAC
1 ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGAC
435601 TGGTCCTTCG
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 120 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (83 bp):
ACATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCT
CTGGATAGGTCATTCGGG
Found at i:439740 original size:31 final size:31
Alignment explanation
Indices: 439651--439777 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
439641 AGAGTCGATG
439651 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
439682 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
439714 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
439745 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
439776 GT
1 GT
439778 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:439778 original size:31 final size:31
Alignment explanation
Indices: 439654--439861 Score: 125
Period size: 31 Copynumber: 7.0 Consensus size: 31
439644 GTCGATGGTA
* * *
439654 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTAGGTTCTTCGGAACATATGGACAG-TT
* *
439686 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTAGGTTC-TTCGGA-ACATATGGACAGTT
* ** *
439717 TACCTATGTTCTAAGGAATATATGGACAGTT
1 TACCTAGGTTCTTCGGAACATATGGACAGTT
*
439748 TACCTAGGTTCTTCGGAACCTATGGACAG-T
1 TACCTAGGTTCTTCGGAACATATGGACAGTT
* * * *
439778 TGCCAAGGATCTT-------TAT-GAC-CTT
1 TACCTAGGTTCTTCGGAACATATGGACAGTT
*** * *
439800 TGGATAGGTCCTTCGGGACATATGGACAGTT
1 TACCTAGGTTCTTCGGAACATATGGACAGTT
*
439831 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTAGGTTCTTCGGAACATATGGACAGTT
439862 GCCAAGGTCT
Statistics
Matches: 134, Mismatches: 28, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
22 12 0.09
23 3 0.02
29 3 0.02
30 14 0.10
31 76 0.57
32 26 0.19
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (31 bp):
TACCTAGGTTCTTCGGAACATATGGACAGTT
Found at i:439920 original size:82 final size:83
Alignment explanation
Indices: 439736--439939 Score: 365
Period size: 82 Copynumber: 2.5 Consensus size: 83
439726 TCTAAGGAAT
*
439736 ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCTTT
1 ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCTCT
439801 GGATAGGTCCTTCGGGAC
66 GGATAGGTCCTTCGGGAC
439819 ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGG-TCTTTATGACCTCT
1 ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCTCT
439883 GGATAGGTCCTTCGGGAC
66 GGATAGGTCCTTCGGGAC
* * *
439901 ATATGGACTGTTTACCTAGGTTCTTCGAAATCTATGGAC
1 ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGAC
439940 TGGTCATTCG
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 67 0.57
83 50 0.43
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (83 bp):
ATATGGACAGTTTACCTAGGTTCTTCGGAACCTATGGACAGTTGCCAAGGATCTTTATGACCTCT
GGATAGGTCCTTCGGGAC
Found at i:441256 original size:45 final size:44
Alignment explanation
Indices: 441207--441335 Score: 143
Period size: 45 Copynumber: 2.8 Consensus size: 44
441197 AAAATAGCCA
* *
441207 GAGTGCATCAATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATCCA-T
* **
441252 GAGTGCATCGATGCATGGTATGTGCATCGATGTTCAATTTAATCCAT
1 GAGTGCATCGATGCATGGTTTGTGCATCGATG--C-ATCAAATCCAT
* *
441299 G-GTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 GAGTGCATCGATGCATGG-TTTGTGCATCGATGCATCA
441336 CTTTGAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
44 2 0.03
45 31 0.44
46 16 0.23
47 14 0.20
48 7 0.10
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATCCAT
Found at i:441695 original size:16 final size:16
Alignment explanation
Indices: 441674--441726 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
441664 CCCCTTACTA
441674 TAACACTTCTCCCCTT
1 TAACACTTCTCCCCTT
** *
441690 TAACAC--CT-TACTA
1 TAACACTTCTCCCCTT
441703 TAACACTTCTCCCCTT
1 TAACACTTCTCCCCTT
441719 TAACACTT
1 TAACACTT
441727 AATATTTCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
13 8 0.29
14 2 0.07
15 2 0.07
16 16 0.57
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (16 bp):
TAACACTTCTCCCCTT
Found at i:441708 original size:29 final size:29
Alignment explanation
Indices: 441666--441724 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
441656 AATTACTCCC
441666 CCTTACTATAACACTTCTCCCCTTTAACA
1 CCTTACTATAACACTTCTCCCCTTTAACA
441695 CCTTACTATAACACTTCTCCCCTTTAACA
1 CCTTACTATAACACTTCTCCCCTTTAACA
441724 C
1 C
441725 TTAATATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.39, G:0.00, T:0.34
Consensus pattern (29 bp):
CCTTACTATAACACTTCTCCCCTTTAACA
Found at i:442034 original size:14 final size:15
Alignment explanation
Indices: 442015--442043 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
442005 TCAAGCATTT
442015 AACAATCCA-AAACA
1 AACAATCCAGAAACA
442029 AACAATCCAGAAACA
1 AACAATCCAGAAACA
442044 TCAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:444028 original size:21 final size:19
Alignment explanation
Indices: 443998--444064 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 19
443988 CGTGCATTGG
443998 TGCACCTTCATGGTGTATCGA
1 TGCA-CTTCA-GGTGTATCGA
*
444019 TGCACATTCAAGGATGCATCGA
1 TGCAC-TTC-AGG-TGTATCGA
*
444041 TGCACTGTTAGGTGTATCGA
1 TGCACT-TCAGGTGTATCGA
444061 TGCA
1 TGCA
444065 TTAAGCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 12 0.31
21 13 0.33
22 14 0.36
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (19 bp):
TGCACTTCAGGTGTATCGA
Found at i:444061 original size:20 final size:21
Alignment explanation
Indices: 443998--444064 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
443988 CGTGCATTGG
* *
443998 TGCACCTTCATGGTGTATCGA
1 TGCACATTCAAGGTGTATCGA
*
444019 TGCACATTCAAGGATGCATCGA
1 TGCACATTCAAGG-TGTATCGA
*
444041 TGCAC-TGT-TAGGTGTATCGA
1 TGCACAT-TCAAGGTGTATCGA
444061 TGCA
1 TGCA
444065 TTAAGCACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.28
21 15 0.38
22 13 0.33
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
TGCACATTCAAGGTGTATCGA
Found at i:453547 original size:14 final size:15
Alignment explanation
Indices: 453528--453556 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
453518 TCAAGCATTT
453528 AACAATCCA-AAACA
1 AACAATCCAGAAACA
453542 AACAATCCAGAAACA
1 AACAATCCAGAAACA
453557 TAAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:455509 original size:44 final size:42
Alignment explanation
Indices: 455458--455552 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
455448 GGCCTTGTGC
* *
455458 ATCGATGCAAATTCAAGGCATGCATCGTTTCACCT-TCATGGTGT
1 ATCGATGCAAATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
* *
455502 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCAAATTCAAGGATGCATCGATGCACTGTCAGGTGT
455544 ATCGATGCA
1 ATCGATGCA
455553 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 13 0.28
44 17 0.37
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (42 bp):
ATCGATGCAAATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:455549 original size:20 final size:21
Alignment explanation
Indices: 455458--455552 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 21
455448 GGCCTTGTGC
* *
455458 ATCGATGCAAATTCAAGGCATGC
1 ATCGATGCACATTCAAGG--TGT
* * * *
455481 ATCGTTTCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
455502 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
455524 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
455544 ATCGATGCA
1 ATCGATGCA
455553 TTAAGCACAA
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 11 0.19
21 20 0.35
22 13 0.23
23 13 0.23
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:456411 original size:164 final size:164
Alignment explanation
Indices: 456133--456460 Score: 599
Period size: 164 Copynumber: 2.0 Consensus size: 164
456123 GGCATGATTG
456133 AAATGTAGCACATAAGCAAACACTAAACATAATGTACGGTCTATTGCAGTTAGATAAAGCAAAGA
1 AAATGTAGCACATAAGCAAACACTAAACATAATGTACGGTCTATTGCAGTTAGATAAAGCAAAGA
456198 ACCATCATGATCTATATAATTTAACATCCACACATTTACCTTCTTCATCTATGCCAAGC-TTGGC
66 ACCATCATGATCTATATAATTTAACATCCACACATTTACCTTCTTCATCTATGCCAAGCTTTGGC
456262 GATGAGCTCATTGGAGTG-TATGTGG-TTCCCAT
131 GATGAGCTCATTGGAGTGTTATGTGGCTTCCCAT
456294 AAATGTAGCACATAAGCAAACACTAAACATAATGTACGGTCTACTTGCAGTTAGATAAAGCAAAG
1 AAATGTAGCACATAAGCAAACACTAAACATAATGTACGGTCTA-TTGCAGTTAGATAAAGCAAAG
456359 AACCAATCATTGATCTATATAATTTAACATCCACACATTTACCTTCTTCATCTATGCCAAGCTTT
65 AACC-ATCA-TGATCTATATAATTTAACATCCACACATTTACCTTCTTCATCTATGCCAAGCTTT
*
456424 GTCGATGAGCTCATTGGAGTGTTATGTGGCTTCCCAT
128 GGCGATGAGCTCATTGGAGTGTTATGTGGCTTCCCAT
456461 TTTCCAGTCC
Statistics
Matches: 160, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
161 43 0.27
162 25 0.16
163 4 0.03
164 52 0.32
165 22 0.14
166 7 0.04
167 7 0.04
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (164 bp):
AAATGTAGCACATAAGCAAACACTAAACATAATGTACGGTCTATTGCAGTTAGATAAAGCAAAGA
ACCATCATGATCTATATAATTTAACATCCACACATTTACCTTCTTCATCTATGCCAAGCTTTGGC
GATGAGCTCATTGGAGTGTTATGTGGCTTCCCAT
Found at i:460578 original size:18 final size:18
Alignment explanation
Indices: 460533--460587 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
460523 CCGTTGGACC
*
460533 CTTAGTGCATCGGTGCA-
1 CTTAGTGCATCGATGCAT
*
460550 CTAAGAGTGCATCGATGCAT
1 CT--TAGTGCATCGATGCAT
*
460570 CTTAGTGCACCGATGCAT
1 CTTAGTGCATCGATGCAT
460588 AAAATACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 14 0.45
19 13 0.42
20 2 0.06
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (18 bp):
CTTAGTGCATCGATGCAT
Found at i:461373 original size:36 final size:35
Alignment explanation
Indices: 461308--461377 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
461298 CCTTATGTCC
* *
461308 ATAAGGAATTACCAGTTGATCGATGCTGAACCTAT
1 ATAAGAAATTACCAGTTGATCGATACTGAACCTAT
*
461343 ATAAGAAATTATCAGCTTGATCAGA-ACTGAACCTA
1 ATAAGAAATTACCAG-TTGATC-GATACTGAACCTA
461378 CAGAGACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 13 0.43
36 15 0.50
37 2 0.07
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (35 bp):
ATAAGAAATTACCAGTTGATCGATACTGAACCTAT
Found at i:466410 original size:2 final size:2
Alignment explanation
Indices: 466405--466447 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
466395 TTTTTTAAAT
466405 TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA
466447 T
1 T
466448 TGTAATGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:470025 original size:2 final size:2
Alignment explanation
Indices: 470013--470052 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
470003 TTTTATATTT
470013 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
470053 ATTTTCAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:470090 original size:38 final size:37
Alignment explanation
Indices: 470039--470128 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
470029 ATATATATAT
* *
470039 ATATATATAATATAATTTTCAGAAAACGGTTTTCAA-AA
1 ATATATATTATATAATTTTCA-AAAACGCTTTT-AATAA
* * *
470077 ATATATATTATATAGTTTTTAAAAACGCTTTTAATAT
1 ATATATATTATATAATTTTCAAAAACGCTTTTAATAA
470114 ATATATATATATATA
1 ATATATAT-TATATA
470129 TAATATAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
36 2 0.04
37 19 0.42
38 24 0.53
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (37 bp):
ATATATATTATATAATTTTCAAAAACGCTTTTAATAA
Found at i:470151 original size:11 final size:11
Alignment explanation
Indices: 470137--470161 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
470127 TATAATATAG
470137 TTTTGAAAACA
1 TTTTGAAAACA
470148 TTTTGAAAACA
1 TTTTGAAAACA
470159 TTT
1 TTT
470162 ATATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:470179 original size:83 final size:82
Alignment explanation
Indices: 470027--470177 Score: 234
Period size: 83 Copynumber: 1.8 Consensus size: 82
470017 TTATATATAT
*
470027 ATATATATATATATATATATAATATAATTTTCAGAAAACGGTTTTCAAAAATATATATTATATAG
1 ATATATATATATATATATATAATATAATTTT-AGAAAACGATTTTCAAAAATATATATTATATAG
470092 TTTTTAAAAACGCTTTTA
65 TTTTTAAAAACGCTTTTA
* * *
470110 ATATATATATATATATATATAATATAGTTTT-GAAAAC-ATTTTGAAAACATTTATATTATATAG
1 ATATATATATATATATATATAATATAATTTTAGAAAACGATTTTCAAAA-ATATATATTATATAG
470173 TTTTT
65 TTTTT
470178 TTGAAAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 8 0.13
81 25 0.40
83 30 0.48
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (82 bp):
ATATATATATATATATATATAATATAATTTTAGAAAACGATTTTCAAAAATATATATTATATAGT
TTTTAAAAACGCTTTTA
Found at i:470192 original size:28 final size:28
Alignment explanation
Indices: 470148--470204 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
470138 TTTGAAAACA
**
470148 TTTTGAAAACATTTATATTATATAGTTT
1 TTTTGAAAACATTTATAACATATAGTTT
*
470176 TTTTGAAAA-TTTATATAACATATAGTTT
1 TTTTGAAAACATT-TATAACATATAGTTT
470204 T
1 T
470205 GAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (28 bp):
TTTTGAAAACATTTATAACATATAGTTT
Found at i:470230 original size:38 final size:37
Alignment explanation
Indices: 470175--470404 Score: 175
Period size: 38 Copynumber: 6.0 Consensus size: 37
470165 TTATATAGTT
* *
470175 TTTTTG-AAAATTTATATAACATATAG-TTTTGAAAA
1 TTTTTGAAAAATTTATATAATATATAGTTTTTAAAAA
* *
470210 TGTTTTGAAAACATTTATATATTATATGGTTTTTATAAAA
1 T-TTTTGAAAA-ATTTATATAATATATAGTTTTTA-AAAA
* *
470250 TATTTTGAAGATTTATATATAATATATAGTTTTTTTAAAACA
1 T-TTTTGAAAAATT-TATATAATATATAG--TTTTTAAAA-A
* * *
470292 TTTTTGAAAACATTTATATATTAAATGGTTTTTCAAAAA
1 TTTTTGAAAA-ATTTATATAATATATAGTTTTT-AAAAA
* *
470331 TATTTTG-AAGATATATATAATATATAGTTTTTTAAAACA
1 T-TTTTGAAAAATTTATATAATATATAG-TTTTTAAAA-A
* *
470370 TTTTT-AAAAA--TATATATTGTATAGTTTTTTAAAAA
1 TTTTTGAAAAATTTATATAATATATAG-TTTTTAAAAA
470405 AATCATTTTG
Statistics
Matches: 158, Mismatches: 22, Indels: 30
0.75 0.10 0.14
Matches are distributed among these distances:
35 2 0.01
36 27 0.17
37 3 0.02
38 38 0.24
39 22 0.14
40 34 0.22
41 22 0.14
42 10 0.06
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (37 bp):
TTTTTGAAAAATTTATATAATATATAGTTTTTAAAAA
Found at i:470250 original size:40 final size:40
Alignment explanation
Indices: 470206--470420 Score: 169
Period size: 40 Copynumber: 5.4 Consensus size: 40
470196 TATAGTTTTG
*
470206 AAAATGTTTTGAAAACATTTATATATTATATGGTTTTTAT
1 AAAATATTTTGAAAACATTTATATATTATATGGTTTTTAT
* * *
470246 AAAATATTTTG--AAGATTTATATATAATATATAGTTTTTTT
1 AAAATATTTTGAAAACATTTATATAT--TATATGGTTTTTAT
* *
470286 AAAACATTTTTGAAAACATTTATATATTAAATGGTTTTTCA-
1 AAAATA-TTTTGAAAACATTTATATATTATATGGTTTTT-AT
* * * *
470327 AAAATATTTTG--AAGATATATATAATATATAGTTTTT-T
1 AAAATATTTTGAAAACATTTATATATTATATGGTTTTTAT
* * * * *
470364 AAAACATTTTTAAAA-A--TATATATTGTATAGTTTTTTAAA
1 AAAATATTTTGAAAACATTTATATATTATAT-GGTTTTT-AT
470403 AAAATCATTTTGAAAACA
1 AAAAT-ATTTTGAAAACA
470421 CGTATAATAT
Statistics
Matches: 137, Mismatches: 24, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
36 10 0.07
37 14 0.10
38 33 0.24
39 6 0.04
40 41 0.30
41 21 0.15
43 12 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (40 bp):
AAAATATTTTGAAAACATTTATATATTATATGGTTTTTAT
Found at i:470320 original size:81 final size:78
Alignment explanation
Indices: 470176--470440 Score: 285
Period size: 81 Copynumber: 3.4 Consensus size: 78
470166 TATATAGTTT
* * * * *
470176 TTTTGAAAATTTATATAACATATAG--TTTTGAAA-ATGTTTTGAAAACATTTATATATTATATG
1 TTTTGAAGATATATATAATATATAGTTTTTTAAAACAT-TTTTGAAAACATTTATATATTAAATG
470238 GTTTTT-ATAAAATA
65 GTTTTTCA-AAAATA
470252 TTTTGAAGATTTATATATAATATATAGTTTTTTTAAAACATTTTTGAAAACATTTATATATTAAA
1 TTTTGAAGA--TATATATAATATATAG-TTTTTTAAAACATTTTTGAAAACATTTATATATTAAA
470317 TGGTTTTTCAAAAATA
63 TGGTTTTTCAAAAATA
**
470333 TTTTGAAGATATATATAATATATAGTTTTTTAAAACATTTTT-AAAA-A--TATATATTGTATAG
1 TTTTGAAGATATATATAATATATAGTTTTTTAAAACATTTTTGAAAACATTTATATATTAAAT-G
* *
470394 TTTTTTAAAAAAATCA
65 GTTTTT-CAAAAAT-A
* * **
470410 TTTTGAAAACACGTATAATATATAGTTTTTT
1 TTTTGAAGATATATATAATATATAGTTTTTT
470441 GAAATTTATA
Statistics
Matches: 166, Mismatches: 13, Indels: 19
0.84 0.07 0.10
Matches are distributed among these distances:
74 10 0.06
75 6 0.04
76 15 0.09
77 32 0.19
78 31 0.19
79 16 0.10
81 53 0.32
82 3 0.02
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (78 bp):
TTTTGAAGATATATATAATATATAGTTTTTTAAAACATTTTTGAAAACATTTATATATTAAATGG
TTTTTCAAAAATA
Found at i:471656 original size:23 final size:24
Alignment explanation
Indices: 471613--471666 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
471603 TTTATATTTT
*
471613 TTTATTCATTTCTTTGATTTA-CC
1 TTTATTTATTTCTTTGATTTAGCC
* *
471636 TTTATTTATTTACTTT-TTTTAGTC
1 TTTATTTATTT-CTTTGATTTAGCC
471660 TTTATTT
1 TTTATTT
471667 CCTTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTATTTATTTCTTTGATTTAGCC
Found at i:471717 original size:2 final size:2
Alignment explanation
Indices: 471710--471738 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
471700 TTATTACTAT
471710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
471739 TATTTTATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:471852 original size:13 final size:13
Alignment explanation
Indices: 471834--471863 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
471824 GAATTTAATG
471834 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
471847 TTTTAATTTTTAA
1 TTTTAAATTTTAA
471860 TTTT
1 TTTT
471864 CGCAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:476458 original size:39 final size:39
Alignment explanation
Indices: 476404--476499 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
476394 AAGAGTACGA
* * * *
476404 TGAAGAAAAACCTCAGCCGGTGATGCCAA-TAGAA-GTTGC
1 TGAAGAAAAATCTCAGCCGCTGATACCAATTA-AATGCT-C
**
476443 TGAAGAAAAATCTCAGTTGCTGATACCAATTAAATGCTC
1 TGAAGAAAAATCTCAGCCGCTGATACCAATTAAATGCTC
476482 TGAAGAAAAATCTCAGCC
1 TGAAGAAAAATCTCAGCC
476500 ATTGACTCCA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
39 43 0.91
40 4 0.09
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (39 bp):
TGAAGAAAAATCTCAGCCGCTGATACCAATTAAATGCTC
Found at i:479572 original size:18 final size:18
Alignment explanation
Indices: 479549--479584 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
479539 TGTCCAGAGC
479549 TTTTAGAAAGGTCTTTTG
1 TTTTAGAAAGGTCTTTTG
479567 TTTTAGAAAGGTCTTTTG
1 TTTTAGAAAGGTCTTTTG
479585 ATCAGTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (18 bp):
TTTTAGAAAGGTCTTTTG
Found at i:482457 original size:24 final size:24
Alignment explanation
Indices: 482425--482481 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
482415 GAAAGGACAG
482425 CAGGCAACACCAAATGATCAATAT
1 CAGGCAACACCAAATGATCAATAT
482449 CAGGCAACACCAAATGATCAATAT
1 CAGGCAACACCAAATGATCAATAT
482473 CAGGCAACA
1 CAGGCAACA
482482 ACAGTTTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (24 bp):
CAGGCAACACCAAATGATCAATAT
Found at i:490235 original size:2 final size:2
Alignment explanation
Indices: 490228--490260 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
490218 AGTTTACAAC
490228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
490261 ATTACCTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:492449 original size:21 final size:22
Alignment explanation
Indices: 492412--492452 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
492402 TTAAAAATTA
*
492412 TAAAGGTAGTACTGATACTCAT
1 TAAAGGTAGTACCGATACTCAT
492434 TAAAGG-AGTACCGATACTC
1 TAAAGGTAGTACCGATACTC
492453 TCTTTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCAT
Found at i:495441 original size:32 final size:32
Alignment explanation
Indices: 495367--495441 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
495357 TACACCTTAA
* * *
495367 GAGGATAAAGTATAATTAATCATAAAAATGAG
1 GAGGACAAAATATAATTAACCATAAAAATGAG
*
495399 GAGAACAAAATATAATTAACCATAAAAATGAAG
1 GAGGACAAAATATAATTAACCATAAAAATG-AG
495432 GAGGA-AAAAT
1 GAGGACAAAAT
495442 CAAAACAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 31 0.84
33 6 0.16
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (32 bp):
GAGGACAAAATATAATTAACCATAAAAATGAG
Found at i:496951 original size:37 final size:37
Alignment explanation
Indices: 496875--496951 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
496865 TTTTTATATT
*
496875 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
496912 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
496949 TTT
1 TTT
496952 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:501079 original size:2 final size:2
Alignment explanation
Indices: 501068--501114 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
501058 ATAAACATTG
501068 TA TA -A TA TA TA TA TA TA TA TA TA TA 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 TA TA
501109 TA TA TA
1 TA TA TA
501115 AGTTTTTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:503427 original size:30 final size:28
Alignment explanation
Indices: 503387--503484 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 28
503377 TAAAGGCTGG
503387 AAAA-TAAAAGGATTGAAATTAAAAGTAA-A
1 AAAATTAAAAGGA-T-AAATTAAAA-TAACA
503416 AAAATTAAAAGGCATAAATTAAAATAACA
1 AAAATTAAAAGG-ATAAATTAAAATAACA
*
503445 GAAATTTAAAAGGAATAAATGT-AAATAACA
1 -AAAATTAAAAGG-ATAAAT-TAAAATAACA
503475 AAAATTAAAA
1 AAAATTAAAA
503485 TCAAATAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
28 3 0.05
29 23 0.38
30 33 0.54
31 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.21
Consensus pattern (28 bp):
AAAATTAAAAGGATAAATTAAAATAACA
Found at i:503464 original size:15 final size:14
Alignment explanation
Indices: 503391--503469 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 14
503381 GGCTGGAAAA
*
503391 TAAAAGGATTGAAAT
1 TAAAAGGAAT-AAAT
* *
503406 TAAAAGTAAAAAAAT
1 TAAAAG-GAATAAAT
*
503421 TAAAAGGCATAAAT
1 TAAAAGGAATAAAT
** *
503435 TAAAATAACAGAAATT
1 TAAAAGGA-ATAAA-T
503451 TAAAAGGAATAAAT
1 TAAAAGGAATAAAT
503465 GTAAA
1 -TAAA
503470 TAACAAAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 11 0.23
15 28 0.60
16 8 0.17
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (14 bp):
TAAAAGGAATAAAT
Found at i:503485 original size:15 final size:14
Alignment explanation
Indices: 503402--503499 Score: 54
Period size: 15 Copynumber: 6.6 Consensus size: 14
503392 AAAAGGATTG
503402 AAATTAAAAGTAAAA
1 AAATTAAAA-TAAAA
*** *
503417 AAATTAAAAGGCAT
1 AAATTAAAATAAAA
503431 AAATTAAAATAACAGA
1 AAATTAAAATAA-A-A
* ** *
503447 AATTTAAAAGGAAT
1 AAATTAAAATAAAA
503461 AAATGT-AAATAACAA
1 AAAT-TAAAATAA-AA
503476 AAATTAAAATCAAATA
1 AAATTAAAAT-AAA-A
503492 AAATTAAA
1 AAATTAAA
503500 TGTTAGTAAC
Statistics
Matches: 60, Mismatches: 16, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
14 18 0.30
15 22 0.37
16 20 0.33
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAATTAAAATAAAA
Found at i:503500 original size:30 final size:29
Alignment explanation
Indices: 503429--503500 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
503419 ATTAAAAGGC
* **
503429 ATAAATTAAAATAACAGAAATTTAAAAGGA
1 ATAAATT-AAATAACAGAAAATTAAAACAA
503459 ATAAATGTAAATAACA-AAAATTAAAATCAA
1 ATAAAT-TAAATAACAGAAAATTAAAA-CAA
503489 ATAAAATTAAAT
1 AT-AAATTAAAT
503501 GTTAGTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 9 0.25
30 22 0.61
31 5 0.14
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (29 bp):
ATAAATTAAATAACAGAAAATTAAAACAA
Found at i:505308 original size:24 final size:24
Alignment explanation
Indices: 505281--505371 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
505271 CATAATTCAA
*
505281 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
505305 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
505329 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * * *
505352 GTTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
505372 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:505351 original size:47 final size:48
Alignment explanation
Indices: 505281--505371 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
505271 CATAATTCAA
* * *
505281 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
* *
505329 GTCAA-TATCAGATCAGAATCCAGGTTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
505372 TCAAATTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:507872 original size:15 final size:16
Alignment explanation
Indices: 507842--507875 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
507832 GGTCAATAGT
507842 GGTCAATGTCGGTCAAC
1 GGTCAATG-CGGTCAAC
507859 GGTCAATG-GGTCAAC
1 GGTCAATGCGGTCAAC
507874 GG
1 GG
507876 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (16 bp):
GGTCAATGCGGTCAAC
Found at i:507884 original size:13 final size:13
Alignment explanation
Indices: 507866--507896 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
507856 AACGGTCAAT
507866 GGGTCAACGGGTC
1 GGGTCAACGGGTC
507879 GGGTCAACGGGTC
1 GGGTCAACGGGTC
507892 GGGTC
1 GGGTC
507897 GGGTCGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (13 bp):
GGGTCAACGGGTC
Found at i:509759 original size:32 final size:32
Alignment explanation
Indices: 509718--509784 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
509708 AATGAAAAAA
509718 TACTTTGAGGATTTGTACTTAACTCGATTAAG
1 TACTTTGAGGATTTGTACTTAACTCGATTAAG
509750 TACTTTGAGGATTTGTACTTAACTCGATTAAG
1 TACTTTGAGGATTTGTACTTAACTCGATTAAG
509782 TAC
1 TAC
509785 GAATTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (32 bp):
TACTTTGAGGATTTGTACTTAACTCGATTAAG
Found at i:511129 original size:12 final size:12
Alignment explanation
Indices: 511108--511176 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
511098 TTTACCTAAA
*
511108 TTCTGTTATGAT
1 TTCTGATATGAT
511120 TTCTGATATGGA-
1 TTCTGATAT-GAT
*
511132 TTCTGTTATGAT
1 TTCTGATATGAT
* * *
511144 ATCTGATCTGAA
1 TTCTGATATGAT
* *
511156 TTCTGTTTTGAT
1 TTCTGATATGAT
511168 TTCTGATAT
1 TTCTGATAT
511177 CTCTGTTTAC
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.52
Consensus pattern (12 bp):
TTCTGATATGAT
Found at i:511134 original size:24 final size:24
Alignment explanation
Indices: 511106--511176 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
511096 TTTTTACCTA
511106 AATTCTGTTATGATTTCTGATATG
1 AATTCTGTTATGATTTCTGATATG
* * *
511130 GATTCTGTTATGATATCTGATCTG
1 AATTCTGTTATGATTTCTGATATG
*
511154 AATTCTGTTTTGATTTCTGATAT
1 AATTCTGTTATGATTTCTGATAT
511177 CTCTGTTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.51
Consensus pattern (24 bp):
AATTCTGTTATGATTTCTGATATG
Found at i:512288 original size:14 final size:14
Alignment explanation
Indices: 512269--512295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
512259 ATTAACACTA
512269 ACTTAAGGAGGATC
1 ACTTAAGGAGGATC
512283 ACTTAAGGAGGAT
1 ACTTAAGGAGGAT
512296 GGAGGCCGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (14 bp):
ACTTAAGGAGGATC
Found at i:513867 original size:9 final size:9
Alignment explanation
Indices: 513853--513882 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
513843 CCAATTACAT
513853 TTCGAAAAA
1 TTCGAAAAA
513862 TTCGAAAAA
1 TTCGAAAAA
513871 TTCGAAAAA
1 TTCGAAAAA
513880 TTC
1 TTC
513883 AATCAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (9 bp):
TTCGAAAAA
Found at i:521948 original size:30 final size:30
Alignment explanation
Indices: 521912--521973 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
521902 GAATAAAATG
521912 AAAGTTT-GGTAACTAAAATA-TAAATTTAAA
1 AAAGTTTAGG-AACTAAAATAGT-AATTTAAA
* *
521942 AAAGTTTAGGGACTAGAATAGTAATTTAAA
1 AAAGTTTAGGAACTAAAATAGTAATTTAAA
521972 AA
1 AA
521974 GTATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.31
Consensus pattern (30 bp):
AAAGTTTAGGAACTAAAATAGTAATTTAAA
Found at i:524738 original size:520 final size:519
Alignment explanation
Indices: 523721--524758 Score: 1483
Period size: 520 Copynumber: 2.0 Consensus size: 519
523711 ACATTCCTCA
* ** * *
523721 TCTATAAAATGCTTCGTGGTTATTACTAGCTTTGCATCTTTCTTTAAAAAATTTCTTGGTTTGAG
1 TCTATAAAATGCTTCGTGATTATTACTAGCTTTGCATCTTTCTTTAAAAAAAATCTTGATTTAAG
* * *
523786 TCCACGGAATGACGTTGATATTCTTCATTGAAACATTTTCAAAGATGTAATTGTGCTTCGAGGCT
66 TCCACGGAATGACATTGATATTCTTCATTGAAACATTTTCAAAGATATAATTGTGCTTCGAAGCT
* *
523851 TCATGAAAAGTCTTACAACTCAACCGTGTATTGAGAAAATTGACGATAGAATTAGACGTCACATG
131 TCATGAAAAGTCTTACAACTCAACCGTGGATTGAGAAAATTAACGATAGAATTAGACGTCACATG
*
523916 CACAAGAATTTTAAATAACACTTCTCTTGGGAATAACTCCACAATATTACTACATATTTTCCCAT
196 CACAAGAATTTTAAATAACACTTCTCTTAGGAATAACTCCACAATATTACTACATATTTTCCCAT
* *
523981 TTTTTTGAAACATGTATGGAAATCCCCCGGAAATGGGCTCCTATTTATAAAAGTCCACGCACTCT
261 TTTTTTAAAACA-GTATGGAAATCCCCCAGAAATGGGCTCCTATTTATAAAAGTCCACGCACTCT
* * ****
524046 TTCTGAAGCGAGGAATCGATGGACCTTACGTTATACAGGACAGTTGTGGTCATGACTAAAATTGA
325 TTCTGAAGCGAGGAATCAATGGACCTTACGTTATACAAGACAGTTGCAACCATGACTAAAATTGA
* * * *
524111 TGCAAAAATACATATTGGGAACAGTTGTGGAATTGAAAATTATAATGACAAAAAAAATGATAGCA
390 TGCAAAAACACATATTGGGAACAGTTGTGAAACTGAAAATTATAACGACAAAAAAAATGATAGCA
* * *
524176 TCATACAAGGTATGTGCCAATTCTACAAGTTATTTTGACATATCTGTAGTGTGTTAATGCATTCC
455 TCATACAAGGTATGTGCCAATTCTACAAGCTATTTTGACATATCTATAGTGCGTTAATGCATTCC
*
524241 TCTATATAATGCTTCGTGATTATTACTAGCTTTGCATCTTTCTTTAAAAAAAATCTTGATTTAAG
1 TCTATAAAATGCTTCGTGATTATTACTAGCTTTGCATCTTTCTTTAAAAAAAATCTTGATTTAAG
* * * * * *
524306 TCCATGGAATTATATTGATATTCTTGATTGAAACATTTTTAAAGATATAATTGTGCTTTGAAGCT
66 TCCACGGAATGACATTGATATTCTTCATTGAAACATTTTCAAAGATATAATTGTGCTTCGAAGCT
*
524371 TCATGAAAAGTCTTGCAACTCAACCGTGGATTGAGAAAATTAACGATAGAATTAGACGTCACATG
131 TCATGAAAAGTCTTACAACTCAACCGTGGATTGAGAAAATTAACGATAGAATTAGACGTCACATG
*
524436 CACAAGAATTTTAGATAACACTTCTCTTAGGAATAACTCCACAATATTACTACATATTTTCCCAT
196 CACAAGAATTTTAAATAACACTTCTCTTAGGAATAACTCCACAATATTACTACATATTTTCCCAT
* *
524501 TTTTTTAAATACA-TATGGAAATCCCCTAGAAATTGGC-CCATATTTATAAAAGT-CATCGCACT
261 TTTTTTAAA-ACAGTATGGAAATCCCCCAGAAATGGGCTCC-TATTTATAAAAGTCCA-CGCACT
* * * *
524563 TTTTCTGAAGTGAGGAATCAATGGACCTTGCGTTATACAAGACTGTTGCAACCAT-AGCTAAAAT
323 CTTTCTGAAGCGAGGAATCAATGGACCTTACGTTATACAAGACAGTTGCAACCATGA-CTAAAAT
* * * * ** *
524627 TGATGTAAAAACACATA-TGAGGAGCAGTTGTGAAACTGAAAATTGTACCGACGTAAAAATTGAT
387 TGATGCAAAAACACATATTG-GGAACAGTTGTGAAACTGAAAATTATAACGACAAAAAAAATGAT
*** * * * *
524691 ATTGTCGTAGAAGGTATGTTCCAATTCTGCAAGCTATTTTGGACATATCTATAGTGCGTTAATGC
451 AGCATCATACAAGGTATGTGCCAATTCTACAAGCTATTTT-GACATATCTATAGTGCGTTAATGC
524756 ATT
515 ATT
524759 TCGCCACTAC
Statistics
Matches: 457, Mismatches: 55, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
518 7 0.02
519 174 0.38
520 273 0.60
521 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (519 bp):
TCTATAAAATGCTTCGTGATTATTACTAGCTTTGCATCTTTCTTTAAAAAAAATCTTGATTTAAG
TCCACGGAATGACATTGATATTCTTCATTGAAACATTTTCAAAGATATAATTGTGCTTCGAAGCT
TCATGAAAAGTCTTACAACTCAACCGTGGATTGAGAAAATTAACGATAGAATTAGACGTCACATG
CACAAGAATTTTAAATAACACTTCTCTTAGGAATAACTCCACAATATTACTACATATTTTCCCAT
TTTTTTAAAACAGTATGGAAATCCCCCAGAAATGGGCTCCTATTTATAAAAGTCCACGCACTCTT
TCTGAAGCGAGGAATCAATGGACCTTACGTTATACAAGACAGTTGCAACCATGACTAAAATTGAT
GCAAAAACACATATTGGGAACAGTTGTGAAACTGAAAATTATAACGACAAAAAAAATGATAGCAT
CATACAAGGTATGTGCCAATTCTACAAGCTATTTTGACATATCTATAGTGCGTTAATGCATTCC
Found at i:537026 original size:20 final size:20
Alignment explanation
Indices: 537001--537042 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
536991 AACCCGGTTA
537001 AAAAGAAACCACGAACAAAG
1 AAAAGAAACCACGAACAAAG
537021 AAAAGAAACCACGAACAAAG
1 AAAAGAAACCACGAACAAAG
537041 AA
1 AA
537043 GATCTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.19, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAGAAACCACGAACAAAG
Found at i:542254 original size:12 final size:12
Alignment explanation
Indices: 542239--542263 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
542229 ACCATATACA
542239 ATTAAAAATAAT
1 ATTAAAAATAAT
542251 ATTAAAAATAAT
1 ATTAAAAATAAT
542263 A
1 A
542264 AAGAAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAAAATAAT
Found at i:542553 original size:26 final size:27
Alignment explanation
Indices: 542513--542581 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
542503 AAATAATTAT
* *
542513 TAAATTTATTAAATTAG-TATAAATTGA
1 TAAATTT-TTTAATTAGTTATAAAATGA
*
542540 TCAATTTTTTAATT-GTTATAAAATGA
1 TAAATTTTTTAATTAGTTATAAAATGA
*
542566 TAAATATTTTTTATTA
1 TAAAT-TTTTTAATTA
542582 AACTATTGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
25 1 0.03
26 19 0.56
27 14 0.41
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (27 bp):
TAAATTTTTTAATTAGTTATAAAATGA
Found at i:546205 original size:21 final size:21
Alignment explanation
Indices: 546174--546286 Score: 83
Period size: 21 Copynumber: 5.3 Consensus size: 21
546164 AGATTTTTAT
546174 TTTATATTATTAAAATATATTA
1 TTTA-ATTATTAAAATATATTA
546196 TTTAATTATTAAAA-ATA-TA
1 TTTAATTATTAAAATATATTA
**
546215 -ACAATTATTATGAAATATATTA
1 TTTAATTATTA--AAATATATTA
* *
546237 TTTTAATCATTTAAAATATAATA
1 -TTTAATTA-TTAAAATATATTA
**
546260 AATAATTA-T-AAATATATTA
1 TTTAATTATTAAAATATATTA
546279 TTATAATT
1 TT-TAATT
546287 TTTTATATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
18 8 0.11
19 11 0.15
20 12 0.17
21 13 0.18
22 11 0.15
23 9 0.13
24 4 0.06
25 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (21 bp):
TTTAATTATTAAAATATATTA
Found at i:546242 original size:42 final size:42
Alignment explanation
Indices: 546179--546286 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
546169 TTTATTTTAT
*
546179 ATTATTA-AAATATATTA-TTTAATTATTAAAAATATAA-CA
1 ATTATTATAAATATATTATTTTAATTATTAAAAATATAATAA
* *
546218 ATTATTATGAAATATATTATTTTAATCATTTAAAATATAATAA
1 ATTATTAT-AAATATATTATTTTAATTATTAAAAATATAATAA
* *
546261 ATAATTATAAATATATTATTATAATT
1 ATTATTATAAATATATTATTTTAATT
546287 TTTTATATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.12
41 10 0.17
42 34 0.58
43 8 0.14
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (42 bp):
ATTATTATAAATATATTATTTTAATTATTAAAAATATAATAA
Found at i:549688 original size:20 final size:20
Alignment explanation
Indices: 549659--549813 Score: 91
Period size: 20 Copynumber: 7.7 Consensus size: 20
549649 AAATGACCAA
*
549659 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACACGAATTC
* *
549679 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACACGA-ATTC
549699 CAAATTCGC-A-ACGTAATTTTC
1 CAAATTCGCAACACG-AA--TTC
*
549720 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTC
* *
549741 CAAATTCGCAACTCGATTTC
1 CAAATTCGCAACACGAATTC
** * * *
549761 TGAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTC
* * * *
549781 CGAATTCGTAACACAAATTT
1 CAAATTCGCAACACGAATTC
* *
549801 TAATTTCGCAACA
1 CAAATTCGCAACA
549814 GGTTTTATTT
Statistics
Matches: 106, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 69 0.65
21 27 0.25
22 1 0.01
23 4 0.04
24 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTC
Found at i:549719 original size:21 final size:22
Alignment explanation
Indices: 549659--549752 Score: 94
Period size: 21 Copynumber: 4.5 Consensus size: 22
549649 AAATGACCAA
*
549659 CAAATTCGCAACGC-GAA-TTC
1 CAAATTCGCAACACTGAATTTC
* *
549679 CAATTTCGCAACAC--AGTTTC
1 CAAATTCGCAACACTGAATTTC
*
549699 CAAATTCGCAAC-GT-AATTTTC
1 CAAATTCGCAACACTGAA-TTTC
549720 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAACACTGAATTTC
549741 CAAATTCGCAAC
1 CAAATTCGCAAC
549753 TCGATTTCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 27 0.44
21 28 0.45
22 4 0.06
23 2 0.03
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.27
Consensus pattern (22 bp):
CAAATTCGCAACACTGAATTTC
Found at i:549730 original size:41 final size:40
Alignment explanation
Indices: 549659--549788 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 40
549649 AAATGACCAA
* *
549659 CAAATTCGCAACGCGAATTCCAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACGCGAATTCCAAATTCGCAACACGAATTT
*
549698 CCAAATTCGCAACG-TAATTTTCCAAATTCGCAACACTGAATTT
1 -CAAATTCGCAACGCGAA--TTCCAAATTCGCAACAC-GAATTT
* * ** * *
549741 CAAATTCGCAACTCGATTTCTGAATTCGCAACTCGATTTT
1 CAAATTCGCAACGCGAATTCCAAATTCGCAACACGAATTT
*
549781 CGAATTCG
1 CAAATTCG
549789 TAACACAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
39 2 0.03
40 25 0.34
41 30 0.41
42 12 0.16
43 5 0.07
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATTCCAAATTCGCAACACGAATTT
Found at i:550758 original size:24 final size:24
Alignment explanation
Indices: 550741--550787 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
550731 AGTCAGTATT
550741 CGAAATTTGATCTTAGTCAATACC
1 CGAAATTTGATCTTAGTCAATACC
* *
550765 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTAGTCAATAC
550788 TCAGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTAGTCAATACC
Found at i:550799 original size:24 final size:24
Alignment explanation
Indices: 550746--550792 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
550736 GTATTCGAAA
*
550746 TTTGATCTTAGTCAATACCCGAAC
1 TTTGATCTTAGTCAATACCAGAAC
*
550770 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTAGTCAATAC-CAGA
550793 TTTTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCAGAAC
Found at i:553081 original size:18 final size:18
Alignment explanation
Indices: 553060--553099 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
553050 TCAAGCAAAA
*
553060 AAAATCAAAATCGCAATC
1 AAAATCAAAATCCCAATC
553078 AAAATCAAAATCCCAATC
1 AAAATCAAAATCCCAATC
553096 AAAA
1 AAAA
553100 CCGGCTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.23, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATCAAAATCCCAATC
Found at i:553370 original size:42 final size:42
Alignment explanation
Indices: 553308--553403 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
553298 AATTCGCAAC
**
553308 GCGAAAGTCAAATTCACGTTGTGATTTCTT-GTTGCGATTGTT
1 GCGAAAGTCAAATTCACGTTGCAATTT-TTCGTTGCGATTGTT
* *
553350 GCGAAAGTCAAATTCGCGTTGCAATTTTTGCGTTGTGATTGTT
1 GCGAAAGTCAAATTCACGTTGCAATTTTT-CGTTGCGATTGTT
553393 GCGAAAGTCAA
1 GCGAAAGTCAA
553404 CGCGAAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
41 2 0.04
42 24 0.50
43 22 0.46
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (42 bp):
GCGAAAGTCAAATTCACGTTGCAATTTTTCGTTGCGATTGTT
Found at i:556174 original size:20 final size:20
Alignment explanation
Indices: 556151--556233 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
556141 AAACTTAAAT
556151 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
556171 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
556191 TCGCAACTCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
556211 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
556230 TCGC
1 TCGC
556234 GTTGCGATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
19 8 0.13
20 52 0.87
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:556658 original size:22 final size:22
Alignment explanation
Indices: 556597--556669 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
556587 GATGGAAATA
*
556597 GACGGATTTCGTCGGAGATGGA
1 GACGGATTTCGTCGGAGATGGG
* * *
556619 GAAGGATTTTGTCAGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
** *
556641 GACGGATTTCACCGGAGATAGG
1 GACGGATTTCGTCGGAGATGGG
556663 GACGGAT
1 GACGGAT
556670 GTCGCCGTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.40, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:556802 original size:19 final size:20
Alignment explanation
Indices: 556780--556817 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
556770 AATATTGTGT
556780 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
556799 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
556818 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:556875 original size:20 final size:20
Alignment explanation
Indices: 556839--556876 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
556829 AATTTGACTT
* *
556839 CTGTGTTGCGAATTTGGAAA
1 CTGTGTTGCAAAATTGGAAA
556859 CTGTGTTGCAAAATTGGA
1 CTGTGTTGCAAAATTGGA
556877 GTTCGCGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (20 bp):
CTGTGTTGCAAAATTGGAAA
Found at i:557856 original size:21 final size:21
Alignment explanation
Indices: 557813--557856 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
557803 CTTTATTCTA
* *
557813 GTGTATAATTTTAAAATTTAT
1 GTGTATAATTTTAAAAATGAT
557834 GTGT-TAATTTTAAAAGATGAT
1 GTGTATAATTTTAAAA-ATGAT
557855 GT
1 GT
557857 CTATCTTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
GTGTATAATTTTAAAAATGAT
Found at i:561365 original size:14 final size:14
Alignment explanation
Indices: 561346--561374 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
561336 ATGGAGAAAC
561346 CTTGCTGTGTTGTT
1 CTTGCTGTGTTGTT
561360 CTTGCTGTGTTGTT
1 CTTGCTGTGTTGTT
561374 C
1 C
561375 CATCCGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.28, T:0.55
Consensus pattern (14 bp):
CTTGCTGTGTTGTT
Found at i:564437 original size:13 final size:14
Alignment explanation
Indices: 564377--564447 Score: 67
Period size: 14 Copynumber: 4.9 Consensus size: 14
564367 TAATAATAAT
*
564377 TATTATTATTTTTAA
1 TATTATTACTTTT-A
564392 TATTATTAC-TTTA
1 TATTATTACTTTTA
564405 TA-TATATACGTATTTCA
1 TATTAT-TAC-T-TTT-A
564422 TATT-TTACTTTTA
1 TATTATTACTTTTA
564435 TATTATTACTTTT
1 TATTATTACTTTT
564448 TGTTTTGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
12 3 0.06
13 11 0.23
14 14 0.29
15 9 0.19
16 6 0.12
17 4 0.08
18 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (14 bp):
TATTATTACTTTTA
Found at i:564538 original size:2 final size:2
Alignment explanation
Indices: 564531--564555 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
564521 TTTACTAATT
564531 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
564556 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:564633 original size:2 final size:2
Alignment explanation
Indices: 564626--564660 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
564616 CTATATTCTA
564626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
564661 CTCTTAATAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:564789 original size:17 final size:17
Alignment explanation
Indices: 564764--564796 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
564754 TTTGATGATC
*
564764 ATTTTTTTATTCATTGT
1 ATTTATTTATTCATTGT
564781 ATTTATTTATTCATTG
1 ATTTATTTATTCATTG
564797 GTTGTATATA
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:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTATTTATTCATTGT
Found at i:575292 original size:45 final size:46
Alignment explanation
Indices: 575225--575312 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
575215 AATATTTCGC
*
575225 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAA-AAAATGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAGAAAATGT
*
575270 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAGAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAGAAAA
575313 AAAAAATAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (46 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAGAAAATGT
Found at i:576353 original size:98 final size:98
Alignment explanation
Indices: 576096--576753 Score: 874
Period size: 98 Copynumber: 6.5 Consensus size: 98
576086 AGGTTTTACC
*
576096 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
576161 GCGAAGGGACCGCTGGTTGTCAACAGACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAATA-A-A-----CAATTT
*
576201 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
576266 ACGAAGGGATCGCTGGTTGTTAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* *
576299 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
576364 ATGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
576397 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
576462 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
576495 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCTCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
576556 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATTT
* * * * * *
576597 CAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGAAAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* **
576662 ACGAAGGGACCGCTGGTTGTCAACAAGTAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
* * * *
576695 CCCGGTTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACGCA
1 --C------AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
576754 TCTTGCATTG
Statistics
Matches: 499, Mismatches: 34, Indels: 39
0.87 0.06 0.07
Matches are distributed among these distances:
94 83 0.17
96 1 0.00
97 2 0.00
98 199 0.40
100 1 0.00
102 7 0.01
103 2 0.00
104 2 0.00
105 84 0.17
106 118 0.24
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:576468 original size:43 final size:43
Alignment explanation
Indices: 576407--576562 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
576397 CAGAGCCAAT
576407 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
576450 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
576501 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
576544 TTCAACTTCTCGACGAAGG
1 TTCAACTTCACAACGAAGG
576563 GACCGCTGGT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
43 37 0.45
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:576681 original size:106 final size:106
Alignment explanation
Indices: 576496--576738 Score: 351
Period size: 106 Copynumber: 2.3 Consensus size: 106
576486 AAACAATTTC
* * * * *
576496 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCTCGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGAAAACACAAGTTCAACTTCACAACGAA
*
576561 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
* *
576602 CCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGAAAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGAAAACACAAGTTCAACTTCACAACGAA
** * ** *
576667 GGGACCGCTGGTTGTCAACAAGTAATTTCCCGGTTTTAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
*
576708 CCAATTTCAACTTCACAGCGAAGGATATTGG
1 CCAATTTCAACTTCACAACGAAGGATATTGG
576739 CCTCGAAACA
Statistics
Matches: 121, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 121 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGAAAACACAAGTTCAACTTCACAACGAA
GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
Found at i:578532 original size:21 final size:23
Alignment explanation
Indices: 578481--578535 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
578471 CAAATTAATA
578481 TATTATTTATTATTATATTACTAT
1 TATTATTT-TTATTATATTACTAT
* * *
578505 TACTATTTTTTTTATTTTA-T-T
1 TATTATTTTTATTATATTACTAT
578526 TATTATTTTT
1 TATTATTTTT
578536 CTAACTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.37
22 1 0.04
23 9 0.33
24 7 0.26
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTATTTTTATTATATTACTAT
Found at i:578587 original size:21 final size:21
Alignment explanation
Indices: 578555--578599 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
578545 TAATTATATA
578555 TATATATATATATGTATATT-T
1 TATATATATATATGT-TATTAT
578576 TATAGTAT-TATATGTTATTAT
1 TATA-TATATATATGTTATTAT
578597 TAT
1 TAT
578600 TATGTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
TATATATATATATGTTATTAT
Found at i:578846 original size:219 final size:212
Alignment explanation
Indices: 578545--578966 Score: 717
Period size: 220 Copynumber: 2.0 Consensus size: 212
578535 TCTAACTATA
578545 TAATTATATATATATATATATATGTATATTTTATAGTATTATATGTTATTATTATTATGTACATT
1 TAATTATATATATATATATATATGTATATTTTATAGTATTATATGTTATTATTATTATGTACATT
578610 TCATCATTTTTATTCGA-TACC-TTTTCTTTGCTTTGTTTTTATTTCTTTGATGATCATTTTTTT
66 TCATCATTTTTATTCGATTACCTTTTTCTTTGCTTTGTTTTTA-TTCTTTGATGATCATTTTTTT
578673 ATTCATTGTATTTATTTATCATTGGTTGTATATAGATTATTAATATTT-ATTTATTTATTTATTT
130 ATTCATTGTATTTATTT-TCATTGGTTGTATATAGATTATTAATATTTCATTTATTTATTTATTT
578737 ACTCTGCTTAGCTATATTC
194 ACTCTGCTTAGCTATATTC
578756 TAATATATATATATATATATATATGTATACTTTTAATAGTAATTTATATGTCTATTATTATTATG
1 TAAT-TATATATATATATATATATGTATA-TTTT-ATAGT-A-TTATATGT-TATTATTATTA--
578821 TGTACATTTCAATCA-TTTTATTCGATTACCTTTTTCTTTGCTTTGTTTTTATTCTTTGATGATC
58 TGTACATTTC-ATCATTTTTATTCGATTACCTTTTTCTTTGCTTTGTTTTTATTCTTTGATGATC
578885 ATTTTTTTATTCATTGTATTTATTTTCATTGGTTGTATATAGATTATTAATATTTCATTTATTTA
122 ATTTTTTTATTCATTGTATTTATTTTCATTGGTTGTATATAGATTATTAATATTTCATTTATTTA
578950 TTTATTTACTCTGCTTA
187 TTTATTTACTCTGCTTA
578967 TTAACTTTTT
Statistics
Matches: 199, Mismatches: 0, Indels: 15
0.93 0.00 0.07
Matches are distributed among these distances:
211 4 0.02
212 24 0.12
213 4 0.02
214 5 0.03
215 1 0.01
216 8 0.04
217 11 0.06
219 50 0.25
220 72 0.36
221 20 0.10
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (212 bp):
TAATTATATATATATATATATATGTATATTTTATAGTATTATATGTTATTATTATTATGTACATT
TCATCATTTTTATTCGATTACCTTTTTCTTTGCTTTGTTTTTATTCTTTGATGATCATTTTTTTA
TTCATTGTATTTATTTTCATTGGTTGTATATAGATTATTAATATTTCATTTATTTATTTATTTAC
TCTGCTTAGCTATATTC
Found at i:579989 original size:2 final size:2
Alignment explanation
Indices: 579982--580006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
579972 ATTTTTCTTT
579982 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
580007 TGATATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:580886 original size:50 final size:51
Alignment explanation
Indices: 580755--580888 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 51
580745 GATGAATTTT
* * * * * **** *
580755 AATAAAAAAATATTTTTTATTTAAATTTGTCACGTCGGAGTGGCGAGTTCG
1 AATAAAAAAATATTTTTTATTAAAATTTATCACATCGAAATAAAAAGTTAG
*
580806 AATAAAATAAATTTTTTTTATTAAAATTTATCACATCGAAATAAAAAGTTAG
1 AATAAAA-AAATATTTTTTATTAAAATTTATCACATCGAAATAAAAAGTTAG
580858 AAT-AAAAAATATTTTTTATTAAAATTTATCA
1 AATAAAAAAATATTTTTTATTAAAATTTATCA
580889 TCTCAACGTA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 24 0.34
51 10 0.14
52 36 0.51
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (51 bp):
AATAAAAAAATATTTTTTATTAAAATTTATCACATCGAAATAAAAAGTTAG
Found at i:583524 original size:17 final size:17
Alignment explanation
Indices: 583502--583537 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
583492 CAGTGATAAT
* *
583502 CACGAATCGATCATGAC
1 CACGAACCGAGCATGAC
583519 CACGAACCGAGCATGAC
1 CACGAACCGAGCATGAC
583536 CA
1 CA
583538 ATTGACAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.11
Consensus pattern (17 bp):
CACGAACCGAGCATGAC
Found at i:595293 original size:27 final size:27
Alignment explanation
Indices: 595262--595313 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
595252 ATATTTACAC
595262 TTAGAAAATATACCTCAAAAATTTTAA
1 TTAGAAAATATACCTCAAAAATTTTAA
595289 TTAGAAAATATACCTCAAAAATTTT
1 TTAGAAAATATACCTCAAAAATTTT
595314 GATTTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (27 bp):
TTAGAAAATATACCTCAAAAATTTTAA
Found at i:595858 original size:28 final size:28
Alignment explanation
Indices: 595827--595882 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
595817 CAGACACAGG
*
595827 ATTTATATTTAAAATAAAAGCTGCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
* *
595855 ATTTGCATTTAAAATAAAAGTTGCTTTT
1 ATTTACATTTAAAATAAAAGCTGCTTTT
595883 GCTTCGGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (28 bp):
ATTTACATTTAAAATAAAAGCTGCTTTT
Found at i:596601 original size:123 final size:124
Alignment explanation
Indices: 596467--596702 Score: 323
Period size: 123 Copynumber: 1.9 Consensus size: 124
596457 AATGAAGGGA
* * * * * * * *
596467 CATCTTCTTCCTCATCTTCTTTTACACCCTTTTCGTTTTCAAGCTCGTCATCCAAGGCTACAAAT
1 CATCTTCTTCCTCATCATCTTTCACACCCTCTTCGTCTTCAAGCTCATCACCCAAGACAACAAAT
** *
596532 GCAACTACGTTTTTCTT-TTAAGATGAC-TTCTTCTTACCTGAAAATCCAAATGAATGAG
66 AAAACAACGTTTTTCTTCTT-AGATGACTTTCTTCTTACCTGAAAATCCAAATGAATGAG
596590 CATCTTCTTCCTCATCATCTTTCACACCCTCTTCGTCTTCAAGCTCATCACCCAAGACAACAAAT
1 CATCTTCTTCCTCATCATCTTTCACACCCTCTTCGTCTTCAAGCTCATCACCCAAGACAACAAAT
*
596655 AAAACAATGTTTTTCTTCTTAGATGACTTTTTCTTCTTACCTGAAAAT
66 AAAACAACGTTTTTCTTCTTAGATGAC--TTTCTTCTTACCTGAAAAT
596703 GCAACCATAG
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
123 77 0.79
124 2 0.02
126 18 0.19
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (124 bp):
CATCTTCTTCCTCATCATCTTTCACACCCTCTTCGTCTTCAAGCTCATCACCCAAGACAACAAAT
AAAACAACGTTTTTCTTCTTAGATGACTTTCTTCTTACCTGAAAATCCAAATGAATGAG
Found at i:600750 original size:24 final size:25
Alignment explanation
Indices: 600723--600773 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
600713 TTTATATTTG
*
600723 ATTTACAAAATTAT-TTCAT-TTAAA
1 ATTTA-AAAATTATGTCCATATTAAA
*
600747 ATTTAAAATTTATGTCCATATTAAA
1 ATTTAAAAATTATGTCCATATTAAA
600772 AT
1 AT
600774 GATCTACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 9 0.39
25 7 0.30
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTAAAAATTATGTCCATATTAAA
Found at i:600918 original size:31 final size:31
Alignment explanation
Indices: 600880--600943 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
600870 TAAGATTTTG
*
600880 ATATTTTATAATTTCTTGTATTTTATCAATA
1 ATATTTTATAATTTCTTATATTTTATCAATA
600911 ATATTTTATAATTTCTTATATTTTATCAATA
1 ATATTTTATAATTTCTTATATTTTATCAATA
600942 AT
1 AT
600944 TTTGTTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (31 bp):
ATATTTTATAATTTCTTATATTTTATCAATA
Found at i:600933 original size:17 final size:17
Alignment explanation
Indices: 600880--600936 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
600870 TAAGATTTTG
600880 ATATTTTATAATTTCTT
1 ATATTTTATAATTTCTT
* *
600897 GTATTTTATCAA----TA
1 ATATTTTAT-AATTTCTT
600911 ATATTTTATAATTTCTT
1 ATATTTTATAATTTCTT
600928 ATATTTTAT
1 ATATTTTAT
600937 CAATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.29
17 18 0.58
18 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
ATATTTTATAATTTCTT
Found at i:607793 original size:21 final size:21
Alignment explanation
Indices: 607763--607814 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
607753 ACCTGTTTCT
*
607763 GAAGAGATTCTTCTAGATGAG
1 GAAGATATTCTTCTAGATGAG
607784 GAAGATATTCTTCTAGATGAG
1 GAAGATATTCTTCTAGATGAG
607805 GAAGATATTC
1 GAAGATATTC
607815 AGCCATGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (21 bp):
GAAGATATTCTTCTAGATGAG
Found at i:612441 original size:13 final size:13
Alignment explanation
Indices: 612425--612450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
612415 ATTTTGATAA
612425 ATAATTTTATTCT
1 ATAATTTTATTCT
612438 ATAATTTTATTCT
1 ATAATTTTATTCT
612451 TTAAGTCTAC
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:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAATTTTATTCT
Found at i:613854 original size:20 final size:20
Alignment explanation
Indices: 613826--613863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
613816 TGAATTTTTA
* *
613826 AAATTTATTTTTGAAATTAT
1 AAATATATTTTTAAAATTAT
613846 AAATATATTTTTAAAATT
1 AAATATATTTTTAAAATT
613864 GTATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATATTTTTAAAATTAT
Found at i:613880 original size:32 final size:32
Alignment explanation
Indices: 613819--613880 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
613809 AAATATATGA
*
613819 ATTTTTAAAATTTATTTTTGAAATTATAAATAT
1 ATTTTTAAAATTTA-TTTTAAAATTATAAATAT
613852 ATTTTTAAAATTGTA-TTTAAAATTATAAA
1 ATTTTTAAAATT-TATTTTAAAATTATAAA
613881 ACAAAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 12 0.44
34 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTTTTAAAATTTATTTTAAAATTATAAATAT
Found at i:614074 original size:26 final size:26
Alignment explanation
Indices: 614023--614078 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
614013 ATATTTTCTA
* **
614023 AAAATATAATTATTATTTTATGATTT
1 AAAATATAATTATAAAGTTATGATTT
614049 AAAATATTAATTATAAAGTTAT-ATTT
1 AAAATA-TAATTATAAAGTTATGATTT
614075 AAAA
1 AAAA
614079 AAATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AAAATATAATTATAAAGTTATGATTT
Found at i:614079 original size:27 final size:27
Alignment explanation
Indices: 614021--614079 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
614011 TCATATTTTC
* **
614021 TAAAAATATAATTATTATTTTATGATT
1 TAAAAATATAATTATAAAGTTATGATT
614048 T-AAAATATTAATTATAAAGTTAT-ATT
1 TAAAAATA-TAATTATAAAGTTATGATT
614074 TAAAAA
1 TAAAAA
614080 AATATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
TAAAAATATAATTATAAAGTTATGATT
Found at i:614107 original size:22 final size:24
Alignment explanation
Indices: 614067--614112 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
614057 AATTATAAAG
614067 TTATATTTAAAAAAATATT-TTTA
1 TTATATTTAAAAAAATATTGTTTA
**
614090 TTAT-TTTAAAAATTTATTGTTTA
1 TTATATTTAAAAAAATATTGTTTA
614113 ATGACCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATTTAAAAAAATATTGTTTA
Found at i:617939 original size:60 final size:60
Alignment explanation
Indices: 617866--617983 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
617856 AGGCATTATA
*
617866 AAATCTCAGAGGACCAAACTCTCTGAAGAAGAAAACTTATTAAATGAGACAACCGCGATG
1 AAATCTCAGAGGACCAAACTCTCTGAAGAAGAAAACTTATTAAAAGAGACAACCGCGATG
*** * *
617926 AAATCTCAGAGGACCAAACTCTCTGAAGAAGTTTACTTATTAAAAGGGACAATCGCGA
1 AAATCTCAGAGGACCAAACTCTCTGAAGAAGAAAACTTATTAAAAGAGACAACCGCGA
617984 CTTATTAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCTCAGAGGACCAAACTCTCTGAAGAAGAAAACTTATTAAAAGAGACAACCGCGATG
Found at i:617990 original size:23 final size:23
Alignment explanation
Indices: 617960--618006 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
617950 GAAGAAGTTT
*
617960 ACTTATTAAAAGGGACAATCGCG
1 ACTTATTAAAAGAGACAATCGCG
*
617983 ACTTATTAAACGAGACAATCGCG
1 ACTTATTAAAAGAGACAATCGCG
618006 A
1 A
618007 GGAAATCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (23 bp):
ACTTATTAAAAGAGACAATCGCG
Found at i:621407 original size:629 final size:624
Alignment explanation
Indices: 619822--621707 Score: 1596
Period size: 627 Copynumber: 3.0 Consensus size: 624
619812 TTTTGACGAG
* * * * * * * *
619822 TCTTAAATATTTGAAAAAAATTGATGAGAGTGGTTTGGTGAGAACATC-TGGAACTTGATCAATA
1 TCTTAAGTATTT-AAAAAAAATGATGAAAGTAGTTTGATGAGAACATCGT-CAACTTGATAAATG
* * * *
619886 ACAGGCACATAATTGATTTGAATGGAGTCATTCATCATTTTTTCCTCGAACAAAACACAAATCTA
64 ACA--CACATAATTGACTTGAATGAAGT-ATTCATGATTTTTTTCTCGAACAAAACACAAATCTA
* * * * * * ** * * ** * * *
619951 GTTTAGCATAT-TTC-ATTTTTGCATCATGTACTGGATTGGCTAACTG-AGCGAAGACATTAGTT
126 ATTCA--ATGTATTCTATTTTTACATGATATACT--A--AACTGATTGCAATGATGACACTAATT
* * * * * * *
620013 TCATCACATCAAATAATTTG-AGAAGAA-ATAAGATTTTGTTCCAAGTGCAATGAATAGAA-AAT
185 T-ATCGCACCAAATAA-CTGAAGAAGAAGA-AAGA-TTTATTCCAAATTCAATGAGTA-AAGAAT
* *
620075 ATGTTGCAAATGACTCTGATACCATGACAGAATCTAAGATATGAGAAGTAAAAT-CTTAATACTA
245 AAGTTGTAAATGACTCTGATACCATGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTA
** * * * * * * * *
620139 CAAAAACATTTCCTTACAAATTCAATCACACCTCTTTATACAAAGAGTTGACAAGTAAAAACCAC
310 CAAAAATGTGTCTTTATAAATCCAATCACACCTCTTTATACAAAGAGTTGATAGGTTAAAACCAT
* * * * * *
620204 CTAACTAATAACAAATTAGTTATATAATATTAACGGTTTAATACATTTCCTATTACATCTCTCTT
375 CTAATTAATAACAAATTAGTTATA-AATATTAAAGATCTAATACACTTCCTACTACAT-TCTCTT
* * * * * * *
620269 CTAAAATTTAGTTTAACTAACATTTTT-TATCTGGTTCATTAATATTACAACCTAGTATGTTTCT
438 CTAGAATTTAGTTTGATTAACATTTTTCTTTCTGATTCATTAATATTACAACCTAATATGTTTCC
* * * * * *
620333 TGCTACTTACCTCTTTTAGAATTTAATCTGATTAATATTTTCCTTTGTCTGTTGCATTAAGTAGT
503 TACCACTTACATCTTTAAGAATTTAATCTAATTAATATTTTCCTTTGTCTGTTGCATTAAGTAAT
*
620398 TTGCAACTTTCAAGCGTTGTCCTTAATTTCTTCAAGAGAGAAGACTCTCAACTTATA
568 TTGCAACTTTCAAGCGTTGTCCTTAACTTCTTCAAGAGAGAAGACTCTCAACTTATA
* * * * *
620455 TCTTAAGTATTTAAAAATACTGATGAAAGTAGTTTGGTGAGAACATCTTCAACTTGATCAATGAC
1 TCTTAAGTATTTAAAAAAAATGATGAAAGTAGTTTGATGAGAACATCGTCAACTTGATAAATGAC
* * * * *
620520 ATACATAATTGACTTGAATGAAGTTTTCATGATTTTTTTCTCGAATAAAAGACAAATCTAGTTCA
66 ACACATAATTGACTTGAATGAAGTATTCATGATTTTTTTCTCGAACAAAACACAAATCTAATTCA
* * * * *
620585 GTGTGTTCTATTTTTACATGGTGTACTAGACTGATTGCATGAATGATGACACTAATTTATCGCAC
131 ATGTATTCTATTTTTACATGATATACTAAACTGATTGC---AATGATGACACTAATTTATCGCAC
* * * * * * *
620650 CAAATAACTGAAGAAGAAGGAAGATTTATTTCAAGTTCAGTGAGTTAATAATAGGTTGTAAATGA
193 CAAATAACTGAAGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAAATGA
* * * * * *
620715 CTCTGATACCAT-ATAGAATTTAATATATGAGAAGTAAAAAAATTAATATTACAAAAATGTGTCT
258 CTCTGATACCATGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTACAAAAATGTGTCT
* * *
620779 TTATAAATCCAATCACACCTCTTTATACAAAGAGTTGGTAGGTTATAATCATCTAATTAATAACA
323 TTATAAATCCAATCACACCTCTTTATACAAAGAGTTGATAGGTTAAAACCATCTAATTAATAACA
** *
620844 AATTAGTTATACAATATTAAAGATCTAATACAGATCCTACTACATGTCTCCTCTAGAATTTAGTT
388 AATTAGTTATA-AATATTAAAGATCTAATACACTTCCTACTACAT-TCTCTTCTAGAATTTAGTT
* * * * **
620909 TGATTAACATTTTTCTTTGTTTATTACATTAGTATTACGACCTAATATGTTTCCTACCACTTTTA
451 TGATTAACATTTTTCTTT-CTGATT-CATTAATATTACAACCTAATATGTTTCCTACCACTTACA
* * * *
620974 TCTTCTAAG-ATTTAGTTTAATTAATATTTTCC-TTGTTTGTTGCATTAGGTAATTCT-CAACTT
514 TCTT-TAAGAATTTAATCTAATTAATATTTTCCTTTGTCTGTTGCATTAAGTAATT-TGCAACTT
* * * * *
621036 TCAAGCGTTGTCCTTAACTTCTTCAGGAGAGAATACTATCTCAATTTTTG
577 TCAAGCGTTGTCCTTAACTTCTTCAAGAGAGAAGAC--TCTCAACTTATA
* * *
621086 TCTTAAGTGTTTGAAAAAAAATCGATGAGAGTGGTTTGATGAGAACATACGT-AACTTGATAAAT
1 TCTTAAGTATTT-AAAAAAAAT-GATGAAAGTAGTTTGATGAGAACAT-CGTCAACTTGATAAAT
* *
621150 GATAGACACATAATT-A-TTGAATGAAGTCATTCATGA-TTTTTTCTCGAACAAAACACAAATTT
63 G--ACACACATAATTGACTTGAATGAAGT-ATTCATGATTTTTTTCTCGAACAAAACACAAATCT
* * *
621212 AATTCAATAG-ATTCTATTTTTGCATGATATATTAAATTGATTGC-AT-ATGACACT-ATGGTTG
125 AATTCAAT-GTATTCTATTTTTACATGATATACTAAACTGATTGCAATGATGACACTAAT--TT-
* * *
621273 TTC-CACCAAATAACTAGAA-ATGAAGAAATATTTATTCCAAATTCAATGAGTAAAGAATAAGTT
186 ATCGCACCAAATAACT-GAAGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTT
* * *
621336 GTAGATG-CTCTCATACCATGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTAGAAAA
250 GTAAATGACTCTGATACCATGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTACAAAA
* * * * * *
621400 GTGTGTCTTTGCAT-AA-CCAATCACACCTTTTTTATACAGAGAATTGATAGGTTAGAACCATAT
315 ATGTGTCTTT--ATAAATCCAATCACACC-TCTTTATACAAAGAGTTGATAGGTTAAAACCATCT
* * * * * *
621463 AATT-ATACCAAGTTAGTTATAGATATTAACA-ACCTAATACACTTCTTACTACCCTTCTCTTCT
377 AATTAATAACAAATTAGTTATAAATATTAA-AGATCTAATACACTTCCTACTA-CATTCTCTTCT
* * * * * *
621526 AGAATTTAATTTGATTAACATTTTTCTTTATCGATTGCATTAGT-TTACAACATAATATGCTTCA
440 AGAATTTAGTTTGATTAACATTTTTCTTTCT-GATT-CATTAATATTACAACCTAATATGTTTCC
* * * * * ** *
621590 TGCTACCTGT-C-TCTTTTAAG-ATTTAATTTGAA-TAACACTTTCC-TTGTCTACTGCATTAGG
503 TACCA-CT-TACATC-TTTAAGAATTTAATCT-AATTAATATTTTCCTTTGTCTGTTGCATTAAG
* * **
621650 CAATTTAG-AA-TTTCCAAGCGTTGTGCTTGCCTTCTTCACA-AGAGAAGACTCTCAACTT
564 TAATTT-GCAACTTT-CAAGCGTTGTCCTTAACTTCTTCA-AGAGAGAAGACTCTCAACTT
621708 CTACCTCAAG
Statistics
Matches: 1027, Mismatches: 182, Indels: 96
0.79 0.14 0.07
Matches are distributed among these distances:
625 14 0.01
626 30 0.03
627 280 0.27
628 121 0.12
629 256 0.25
630 114 0.11
631 25 0.02
632 53 0.05
633 113 0.11
634 11 0.01
635 10 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (624 bp):
TCTTAAGTATTTAAAAAAAATGATGAAAGTAGTTTGATGAGAACATCGTCAACTTGATAAATGAC
ACACATAATTGACTTGAATGAAGTATTCATGATTTTTTTCTCGAACAAAACACAAATCTAATTCA
ATGTATTCTATTTTTACATGATATACTAAACTGATTGCAATGATGACACTAATTTATCGCACCAA
ATAACTGAAGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAAATGACTC
TGATACCATGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTACAAAAATGTGTCTTTA
TAAATCCAATCACACCTCTTTATACAAAGAGTTGATAGGTTAAAACCATCTAATTAATAACAAAT
TAGTTATAAATATTAAAGATCTAATACACTTCCTACTACATTCTCTTCTAGAATTTAGTTTGATT
AACATTTTTCTTTCTGATTCATTAATATTACAACCTAATATGTTTCCTACCACTTACATCTTTAA
GAATTTAATCTAATTAATATTTTCCTTTGTCTGTTGCATTAAGTAATTTGCAACTTTCAAGCGTT
GTCCTTAACTTCTTCAAGAGAGAAGACTCTCAACTTATA
Found at i:621800 original size:628 final size:631
Alignment explanation
Indices: 620033--622155 Score: 1454
Period size: 627 Copynumber: 3.4 Consensus size: 631
620023 AAATAATTTG
* * * * * * *
620033 AGAAGAA-ATAAGATTTTGTTCCAAGTGCAATGAATAGAA-AATATGTTGCAAATGACTCTGATA
1 AGAAGAAGA-AAGA-TTTATTCCAAATTCAATGAGTA-AAGAATAAGTTGTAAATGACTCTCATA
** ** * * *
620096 CCATGACAGAATCTAAGATATGAGAAGT-AAAATCTTAATACTACAAAAACATTTCCTTACAAAT
63 CCAT-ACAGAATCTAAGATATGAGAAGTAAAAAAATTAATACTACAAAAATGTGTCTTTATAAAT
* * * * * * ** *
620160 TCAATCACACCTCTTTATACAAAGAGTTGACAAGTAAAAACCACCTAACTAATAACAAATTAGTT
127 CCAATCACACCTCTTTATACAAAGAATTGATAGGTTAGAACCATATAATTAATAACAAATTAGTT
* * *** ** * * * * * * *
620225 ATATAATATTAACGGTTTAATACATTTCCTATTACATCTCTCTTCTAAAATTTAGTTTAACTAAC
192 ATACAATATTAAAGACCTAATACACATCCTACTACATGTCTCCTCTAGAATTTAATTTGATTAAC
* * * * * * * *
620290 A--TTT-TTTATCTGGTT-CATTAATATTACAACCTAGTATGTTTCTTGCTA-CT-TACCTCTT-
257 ATTTTTCTTTATC-GATTACATTAGTATTACAACATAATATGCTTCATACCACCTGTA--TCTTC
* * * * * ** * * * *
620348 TTAGAATTTAATCTGATTAATATTTTCCTTTGTCTGTTGCATTAAGTAGTT-TGCAACTTTCAAG
319 TAAG-ATTTAATTTAATTAACACTTTCC-TTGTCTACTGCATTAGGCAATTCT-CAAATTTCAAG
* * * * * *
620412 CGTTGTCCTTAATTTCTTCA-AGAGAGAAGAC-TCTCAACTTATATCTTAAGTATTT-AAAAATA
381 CGTTGTCCTTAACTTCTTCACA-AGAGAAGACATCTCAACTTCTACCTCAAGTGTTTGAAAAAAA
* * * * ** * * * *
620474 CT-GATGAAAGT-AGTTTGGTGAGAACAT-CTTCAACTTGATCAATG--ACATACATAATTGACT
445 ATCCATGAGAGTGA-TTTGATGAGAACATAC-GGAACTTAATAAATGATAGACACATAATTGACT
* * * * * *
620534 TGAATGAAGTTTTCATGATTTTTTTCTCGAATAAAAGACAAATCTAGTTCAGTGTGTTCTATTTT
508 TGAATGAAGTATTCATGATTTTTTTCTCGAACAAAACACAAATCTAATTCAATGTATTCTATTTT
* * *
620599 TACATGGTGTACTAGACTGATTGCATGAATGATGACACTAATTTATCGCACCAAATAACTGA
573 TACATGATATACTAAACTGATTGC---AATGATGACACTAATTTATCGCACCAAATAACTGA
* * * * * * * *
620661 AGAAGAAGGAAGATTTATTTCAAGTTCAGTGAGTTAATAATAGGTTGTAAATGACTCTGATACCA
1 AGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAAATGACTCTCATACCA
* * * *
620726 TATAGAATTTAATATATGAGAAGTAAAAAAATTAATATTACAAAAATGTGTCTTTATAAATCCAA
66 TACAGAATCTAAGATATGAGAAGTAAAAAAATTAATACTACAAAAATGTGTCTTTATAAATCCAA
* * * * *
620791 TCACACCTCTTTATACAAAGAGTTGGTAGGTTATAATCATCTAATTAATAACAAATTAGTTATAC
131 TCACACCTCTTTATACAAAGAATTGATAGGTTAGAACCATATAATTAATAACAAATTAGTTATAC
* * *
620856 AATATTAAAGATCTAATACAGATCCTACTACATGTCTCCTCTAGAATTTAGTTTGATTAACATTT
196 AATATTAAAGACCTAATACACATCCTACTACATGTCTCCTCTAGAATTTAATTTGATTAACATTT
* ** * * * * * *
620921 TTCTTTGTTTATTACATTAGTATTACGACCTAATATGTTTCCTACCACTTTTATCTTCTAAGATT
261 TTCTTTATCGATTACATTAGTATTACAACATAATATGCTTCATACCACCTGTATCTTCTAAGATT
* * * * ** * *
620986 TAGTTTAATTAATATTTTCCTTGTTTGTTGCATTAGGTAATTCTCAACTTTCAAGCGTTGTCCTT
326 TAATTTAATTAACACTTTCCTTGTCTACTGCATTAGGCAATTCTCAAATTTCAAGCGTTGTCCTT
** * * * ** * *
621051 AACTTCTTCAGGAGAGAATACTATCTCAATTTTTGTCTTAAGTGTTTGAAAAAAAATCGATGAGA
391 AACTTCTTCACAAGAGAAGAC-ATCTCAACTTCTACCTCAAGTGTTTGAAAAAAAATCCATGAGA
* * *
621116 GTGGTTTGATGAGAACATACGTAACTTGATAAATGATAGACACATAATT-A-TTGAATGAAGTCA
455 GTGATTTGATGAGAACATACGGAACTTAATAAATGATAGACACATAATTGACTTGAATGAAGT-A
* *
621179 TTCATGA-TTTTTTCTCGAACAAAACACAAATTTAATTCAATAG-ATTCTATTTTTGCATGATAT
519 TTCATGATTTTTTTCTCGAACAAAACACAAATCTAATTCAAT-GTATTCTATTTTTACATGATAT
* * *
621242 ATTAAATTGATTGC-AT-ATGACACT-ATGGTTGTTC-CACCAAATAACTAGA
583 ACTAAACTGATTGCAATGATGACACTAAT--TT-ATCGCACCAAATAACT-GA
* * *
621291 A-ATGAAGAAATATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAGATG-CTCTCATACCA
1 AGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAAATGACTCTCATACCA
* * * *
621354 TGACAGAATCTAAGATATGAGAAGTAAAATACTTAATACTAGAAAAGTGTGTCTTTGCAT-AA-C
66 T-ACAGAATCTAAGATATGAGAAGTAAAAAAATTAATACTACAAAAATGTGTCTTT--ATAAATC
* * * *
621417 CAATCACACCTTTTTTATACAGAGAATTGATAGGTTAGAACCATATAATT-ATACCAAGTTAGTT
128 CAATCACACC-TCTTTATACAAAGAATTGATAGGTTAGAACCATATAATTAATAACAAATTAGTT
* * * * *
621481 ATA-GATATTAACA-ACCTAATACACTTCTTACTACCCT-TCTCTTCTAGAATTTAATTTGATTA
192 ATACAATATTAA-AGACCTAATACACATCCTACTA-CATGTCTCCTCTAGAATTTAATTTGATTA
* * * * *
621543 ACATTTTTCTTTATCGATTGCATTAGT-TTACAACATAATATGCTTCATGCTACCTGTCTCTTTT
255 ACATTTTTCTTTATCGATTACATTAGTATTACAACATAATATGCTTCATACCACCTGTATCTTCT
621607 AAGATTTAATTTGAA-TAACACTTTCCTTGTCTACTGCATTAGGCAATT-T-AGAATTTCCAAGC
320 AAGATTTAATTT-AATTAACACTTTCCTTGTCTACTGCATTAGGCAATTCTCA-AATTT-CAAGC
* **
621669 GTTGTGCTTGCCTTCTTCACAAGAGAAGAC-TCTCAACTTCTACCTCAAGTGTTTGAAAAAATAA
382 GTTGTCCTTAACTTCTTCACAAGAGAAGACATCTCAACTTCTACCTCAAGTGTTTGAAAAAA-AA
* *
621733 -CCACTGAGAGTGATTT-AGTGAGAACAT-CTGGAACTTAATCAAT-AGTAGGCACATAATTGAC
446 TCCA-TGAGAGTGATTTGA-TGAGAACATAC-GGAACTTAATAAATGA-TAGACACATAATTGAC
* * * ** * * * *
621794 TTGAATG-GGTTCATTCGTCA--TTTCCCCCCAA-AACACCACAAATC-AAGTTTAGCATGT-TT
507 TTGAATGAAG-T-ATTCATGATTTTTTTCTCGAACAA-AACACAAATCTAA-TTCA--ATGTATT
* * * ** * * * *
621853 -AATTTTTTGCATGATGTACTGGACTGGTTGCATGAGTGATGATACTAGCTTTATCGCATCAAAT
566 CTA-TTTTTACATGATATACTAAACTGATTGCA--A-TGATGACACTA-ATTTATCGCACCAAAT
*
621917 AATTGA
626 AACTGA
* * * * * * **** * * * *
621923 AGAAAAAGGAAGACTTATT-TAATGTTCAGTGAACGGAGAATAGGTTGCAAATGAATCTGATACC
1 AGAAGAAGAAAGATTTATTCCAA-ATTCAATGAGTAAAGAATAAGTTGTAAATGACTCTCATACC
* * * * *
621987 ATGACAGAATCTAAGATATGAGAGGTAAAAAAAATTAATATTACAAAAAAAGTTTCTTTACAAAT
65 AT-ACAGAATCTAAGATATGAGAAGT-AAAAAAATTAATACTAC-AAAAATGTGTCTTTATAAAT
* ** * * * * ** * * *
622052 TCAATCACACCTCTTTATACAAA-AAGTTGGCATGCTATAACTACCTAACTAATACCAAAATTAA
127 CCAATCACACCTCTTTATACAAAGAA-TTGATAGGTTAGAACCATATAATTAATAAC-AAATTAG
* ** *
622116 TTATACAATATTAACGACCTAATACATTTCCTGCTACATG
190 TTATACAATATTAAAGACCTAATACACATCCTACTACATG
622156 GTTGGTTGTC
Statistics
Matches: 1192, Mismatches: 233, Indels: 130
0.77 0.15 0.08
Matches are distributed among these distances:
625 32 0.03
626 76 0.06
627 297 0.25
628 141 0.12
629 196 0.16
630 95 0.08
631 27 0.02
632 17 0.01
633 152 0.13
634 46 0.04
635 51 0.04
636 26 0.02
637 12 0.01
638 24 0.02
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (631 bp):
AGAAGAAGAAAGATTTATTCCAAATTCAATGAGTAAAGAATAAGTTGTAAATGACTCTCATACCA
TACAGAATCTAAGATATGAGAAGTAAAAAAATTAATACTACAAAAATGTGTCTTTATAAATCCAA
TCACACCTCTTTATACAAAGAATTGATAGGTTAGAACCATATAATTAATAACAAATTAGTTATAC
AATATTAAAGACCTAATACACATCCTACTACATGTCTCCTCTAGAATTTAATTTGATTAACATTT
TTCTTTATCGATTACATTAGTATTACAACATAATATGCTTCATACCACCTGTATCTTCTAAGATT
TAATTTAATTAACACTTTCCTTGTCTACTGCATTAGGCAATTCTCAAATTTCAAGCGTTGTCCTT
AACTTCTTCACAAGAGAAGACATCTCAACTTCTACCTCAAGTGTTTGAAAAAAAATCCATGAGAG
TGATTTGATGAGAACATACGGAACTTAATAAATGATAGACACATAATTGACTTGAATGAAGTATT
CATGATTTTTTTCTCGAACAAAACACAAATCTAATTCAATGTATTCTATTTTTACATGATATACT
AAACTGATTGCAATGATGACACTAATTTATCGCACCAAATAACTGA
Found at i:627300 original size:32 final size:32
Alignment explanation
Indices: 627197--627356 Score: 159
Period size: 32 Copynumber: 5.1 Consensus size: 32
627187 ACCTCGGCAA
* * *
627197 CTGTCCATAGGTCCCG-AAGAACCTAGGTAA-A
1 CTGTCCATATGTCCCGAAAG-ACATAGGTAATT
* ** *
627228 CTGTCTATATGATCCTTAGA-ACATAGGT-ATAT
1 CTGTCCATATG-TCCCGAAAGACATAGGTAAT-T
*
627260 -TGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACATAGGTAATT
* *
627291 CTGTCCATATGTCCCGAAAAACATAAGTAATT
1 CTGTCCATATGTCCCGAAAGACATAGGTAATT
*
627323 ATGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACATAGGTAATT
627355 CT
1 CT
627357 CGACTCTTGG
Statistics
Matches: 103, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
30 5 0.05
31 34 0.33
32 63 0.61
33 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAAGACATAGGTAATT
Found at i:631971 original size:23 final size:23
Alignment explanation
Indices: 631941--631986 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
631931 TTGTTTTAAT
631941 TGACGTGGCGTAGCGCATGTCCA
1 TGACGTGGCGTAGCGCATGTCCA
* * *
631964 TGACGTGGTGTGGTGCATGTCCA
1 TGACGTGGCGTAGCGCATGTCCA
631987 ACCTGGAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.22, G:0.37, T:0.26
Consensus pattern (23 bp):
TGACGTGGCGTAGCGCATGTCCA
Found at i:643011 original size:14 final size:14
Alignment explanation
Indices: 642992--643019 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
642982 AGGAAATATG
642992 AGCAATAAACATTT
1 AGCAATAAACATTT
643006 AGCAATAAACATTT
1 AGCAATAAACATTT
643020 TGGAGTCCTA
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:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
AGCAATAAACATTT
Found at i:649150 original size:2 final size:2
Alignment explanation
Indices: 649138--649167 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
649128 ACATCCCTGT
*
649138 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
649168 GCTAAAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:659756 original size:81 final size:80
Alignment explanation
Indices: 659615--659845 Score: 324
Period size: 81 Copynumber: 2.9 Consensus size: 80
659605 TAGAATAAGT
* *
659615 GGGACCTTGATCCTTCCTTGCAACAACTTGCCACAGTTTCTGTTCAGACACTAGCGCAACAGAAC
1 GGGACCTTGCTCCTTCCTTGCAA-AACATGCCACAGTTTCTGTTCAGACACTAGCGCAACAGAAC
*
659680 AATATGGATCAGGAGA
65 AATATGGAACAGGAGA
* *
659696 GGGACCTTGCTCGTTCCTTGCAAAACAATGCCACAGTTTCTGTTCAGACACTA-CAACAACAGAA
1 GGGACCTTGCTCCTTCCTTGCAAAAC-ATGCCACAGTTTCTGTTCAGACACTAGC-GCAACAGAA
*
659760 CAATATGGAACTGGAGA
64 CAATATGGAACAGGAGA
* * *
659777 GGGACCTTGCTCCTTTCTTGCAACACCATG-C-CGGTTTCTGTTCAGACACTAGCGCAACAGAAC
1 GGGACCTTGCTCCTTCCTTGCAA-AACATGCCACAGTTTCTGTTCAGACACTAGCGCAACAGAAC
659840 AATATG
65 AATATG
659846 AAAGGGACCT
Statistics
Matches: 135, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
79 34 0.25
80 6 0.04
81 93 0.69
82 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (80 bp):
GGGACCTTGCTCCTTCCTTGCAAAACATGCCACAGTTTCTGTTCAGACACTAGCGCAACAGAACA
ATATGGAACAGGAGA
Found at i:666735 original size:20 final size:19
Alignment explanation
Indices: 666710--666763 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
666700 GCGAAATAAA
666710 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
666730 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
666750 AATCGCAACGCGAT
1 AATCGCAACGCGAT
666764 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:666838 original size:20 final size:20
Alignment explanation
Indices: 666813--667104 Score: 227
Period size: 20 Copynumber: 14.5 Consensus size: 20
666803 AATTTTCCAG
* *
666813 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
666833 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
666853 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * *
666872 CTATCGCAACGAGTAT-CTGTAA
1 -AATCGCAACGCGAATAC-GT-A
* *
666894 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
666914 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * * *
666935 AATCGCAATGGGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
666955 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
666975 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
* *
666995 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * * *
667015 AATCGCAATGCGTATCCATA
1 AATCGCAACGCGAATACGTA
*
667035 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
667055 AATCACAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
667075 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
667095 AATCGCAACG
1 AATCGCAACG
667105 AGATTCTGAC
Statistics
Matches: 222, Mismatches: 38, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 180 0.81
21 34 0.15
22 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:666990 original size:40 final size:40
Alignment explanation
Indices: 666813--667104 Score: 268
Period size: 40 Copynumber: 7.2 Consensus size: 40
666803 AATTTTCCAG
* ** * * * **
666813 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
666853 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTAT-CTGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATAC-GT-A
*
666894 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
* *
666935 AATCGCAATGGGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
666975 AATCGCAACGCGTATCTGTAAATCACAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
667015 AATCGCAATGCGTATCCATAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * * *
667055 AATCACAATGCGAATACGTAAATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATAC-GTA
667095 AATCGCAACG
1 AATCGCAACG
667105 AGATTCTGAC
Statistics
Matches: 212, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.02
40 137 0.65
41 65 0.31
42 5 0.02
43 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:667991 original size:24 final size:24
Alignment explanation
Indices: 667964--668017 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
667954 GTATTCGAAA
667964 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
667988 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
668012 TTTGAT
1 TTTGAT
668018 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:670591 original size:19 final size:19
Alignment explanation
Indices: 670567--670704 Score: 116
Period size: 19 Copynumber: 7.7 Consensus size: 19
670557 GCAACGAGAG
670567 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
670586 AATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
670606 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
670625 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
* *
670639 AATCGTAATGAGAAATGAA
1 AATCGCAATGCGAAATGAA
* **
670658 AATCGCAAT----TA-GGG
1 AATCGCAATGCGAAATGAA
670672 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
670691 AATCGCAACGCGAA
1 AATCGCAATGCGAA
670705 TTTAGTTTCG
Statistics
Matches: 92, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 5 0.05
17 6 0.07
18 1 0.01
19 46 0.50
20 16 0.17
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:670591 original size:33 final size:33
Alignment explanation
Indices: 670554--670700 Score: 177
Period size: 33 Copynumber: 4.3 Consensus size: 33
670544 GGAAATTACT
*
670554 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAATGAAA
670587 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAAA-GA--ATCGCAATGCGAAATGAAA
* *
670626 ATCGCAACGAAAGAATCGTAATGAGAAATGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAATGAAA
** **
670659 ATCGCAATTAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAATGAAA
670692 ATCGCAACG
1 ATCGCAACG
670701 CGAATTTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
33 58 0.60
35 3 0.03
36 7 0.07
37 3 0.03
39 26 0.27
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAACGAAAGAATCGCAATGCGAAATGAAA
Found at i:670633 original size:72 final size:66
Alignment explanation
Indices: 670554--670700 Score: 186
Period size: 72 Copynumber: 2.1 Consensus size: 66
670544 GGAAATTACT
* * *
670554 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGGAAATGACTATCGCAATGCGA
1 ATCGCAACGAAAGAATCGCAATGAGAAATGAAAATCGCAACGAGG----GA--ATCGCAATGCGA
670619 AATGAAA
60 AATGAAA
* **
670626 ATCGCAACGAAAGAATCGTAATGAGAAATGAAAATCGCAATTAGGGAATCGCAATGCGAAATGAA
1 ATCGCAACGAAAGAATCGCAATGAGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAA
670691 A
66 A
670692 ATCGCAACG
1 ATCGCAACG
670701 CGAATTTAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
66 28 0.41
68 2 0.03
72 39 0.57
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (66 bp):
ATCGCAACGAAAGAATCGCAATGAGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAA
A
Found at i:670742 original size:19 final size:19
Alignment explanation
Indices: 670700--670775 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 19
670690 AAATCGCAAC
* * *
670700 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAATTTCGCATT
670719 GCGATTTTAATTTCGCATT
1 GCGATTTTAATTTCGCATT
* *
670738 GCGA--TT-CTCTCG--TT
1 GCGATTTTAATTTCGCATT
*
670752 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCATT
670771 GCGAT
1 GCGAT
670776 AGTCATTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.13
16 6 0.13
17 6 0.13
19 27 0.60
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGATTTTAATTTCGCATT
Found at i:670901 original size:14 final size:14
Alignment explanation
Indices: 670882--670918 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
670872 CATCAATTAA
670882 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
670896 ACAAATCATCTTTT
1 ACAAATCAACTTTT
670910 ACAAATCAA
1 ACAAATCAA
670919 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:672853 original size:33 final size:33
Alignment explanation
Indices: 672811--672904 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
672801 AAAAATGACT
672811 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
672844 ATCGCAACGCGAAATGAAAATCGCAAAGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
672877 ATCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
672905 CGATTATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:672867 original size:19 final size:19
Alignment explanation
Indices: 672787--672907 Score: 82
Period size: 19 Copynumber: 6.8 Consensus size: 19
672777 TCTGGAACTT
*
672787 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
672808 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
672827 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
672841 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
672860 AAAATCGCAA----AGA-G
1 AAAATCGCAACGCGAAATG
* *
672874 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
672893 AAAATTGCAACGCGA
1 AAAATCGCAACGCGA
672908 TTATAGTTTC
Statistics
Matches: 77, Mismatches: 13, Indels: 22
0.69 0.12 0.20
Matches are distributed among these distances:
14 20 0.26
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 36 0.47
21 11 0.14
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:672946 original size:38 final size:38
Alignment explanation
Indices: 672904--673057 Score: 124
Period size: 38 Copynumber: 4.1 Consensus size: 38
672894 AAATTGCAAC
**
672904 GCGATTAT-AGTTTCGCGTTGCGATTTTGGTTTCGCGTT
1 GCGATTATCA-TTTCGCGTTGCGATTTTCATTTCGCGTT
* *
672942 GCGATTTTCATTTCGTGTTGCGATTTTCATTTCGCGTT
1 GCGATTATCATTTCGCGTTGCGATTTTCATTTCGCGTT
* *
672980 GCGA-T-TC---TCTCGTTGCGAATTTCATTTCGCGTT
1 GCGATTATCATTTCGCGTTGCGATTTTCATTTCGCGTT
* * * *
673013 GCGA-TAGTCATTTTTCACGTTGTGATTTTAAGTTTCGTGTT
1 GCGATTA-TCA--TTTCGCGTTGCGATTTTCA-TTTCGCGTT
673054 GCGA
1 GCGA
673058 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
33 28 0.29
35 2 0.02
36 2 0.02
37 1 0.01
38 36 0.38
39 1 0.01
40 13 0.14
41 12 0.13
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (38 bp):
GCGATTATCATTTCGCGTTGCGATTTTCATTTCGCGTT
Found at i:673025 original size:19 final size:19
Alignment explanation
Indices: 672914--673017 Score: 128
Period size: 19 Copynumber: 5.7 Consensus size: 19
672904 GCGATTATAG
**
672914 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
672933 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
672952 TTTCGTGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
672971 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
672987 --TCTCGTTGCGAATTTCA
1 TTTCGCGTTGCGATTTTCA
673004 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
673018 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 57 0.78
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Done.