Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008506.1 Hibiscus syriacus cultivar Beakdansim tig00111358_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: 1253200
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 3 of 6
Found at i:448323 original size:142 final size:143
Alignment explanation
Indices: 448013--448345 Score: 362
Period size: 142 Copynumber: 2.4 Consensus size: 143
448003 ATGCGATCTC
* * *
448013 TAAATCGCAACACGAT-CT--CTAAATCGCATCGCGATCTCCAGTATCGCAAATCAGTTTCCAGA
1 TAAATCGCAACACGATAATGACT-AATCGCAACGCGATCTCGAGTATCGCAAATCAGTTTCCAGA
* ** * *
448075 TTCGCAACGCGATTTTGACTATCGCATTACGATTTTCCAAATGCGCGTTGCGATTTTAGAAAATC
65 TTCGCAACGCGATTTTGACTATCGCATTACGATTTTCAAAATGCGCAATGCGAATATAGAAAATC
*
448140 GCAATGAGAATATG
130 GCAATCAGAATATG
* ** *
448154 TAAATCGCAACGCGATTCTGACT-ATCGCAACGCAATCTCGAGTATCGCAAATCAGTTTCCAGAT
1 TAAATCGCAACACGATAATGACTAATCGCAACGCGATCTCGAGTATCGCAAATCAGTTTCCAGAT
* * *
448218 TCGCAACGCGATTTTGACTATCGCATTGCGATTTTAGAAAAT-CGCAATGCGAATAT-GTAAATC
66 TCGCAACGCGATTTTGACTATCGCATTACGATTTT-CAAAATGCGCAATGCGAATATAGAAAATC
* *
448281 GCAA-CACGATTCTG
130 GCAATCA-GAATATG
* *
448295 -ACTATCGCAACACGATAAT-ACATAATCGCAACGCGAT-TCTGACTATCGCAA
1 TA-AATCGCAACACGATAATGAC-TAATCGCAACGCGATCTC-GAGTATCGCAA
448346 CACGATAATA
Statistics
Matches: 162, Mismatches: 21, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
140 4 0.02
141 46 0.28
142 106 0.65
143 4 0.02
144 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (143 bp):
TAAATCGCAACACGATAATGACTAATCGCAACGCGATCTCGAGTATCGCAAATCAGTTTCCAGAT
TCGCAACGCGATTTTGACTATCGCATTACGATTTTCAAAATGCGCAATGCGAATATAGAAAATCG
CAATCAGAATATG
Found at i:448789 original size:19 final size:19
Alignment explanation
Indices: 448762--448803 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
448752 TATTTTGGAT
*
448762 TTTTCACTATCGCAACACA
1 TTTTAACTATCGCAACACA
448781 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
448800 TTTT
1 TTTT
448804 TCCAAATCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:448856 original size:21 final size:21
Alignment explanation
Indices: 448808--448868 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
448798 CATTTTTCCA
*
448808 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
*
448828 AATCGCGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* * *
448849 ATTCGCGTTGCAAATTTGGA
1 AATCGCGTTGCGAATCTGGA
448869 AACTGAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:456999 original size:21 final size:21
Alignment explanation
Indices: 456946--457024 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
456936 AACAATTCTC
* * * *
456946 TTCATAAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCAT
*
456967 TTCATGAAAAGGTTAAGTCAT
1 TTCATCAAAAGGTTAAGTCAT
**
456988 TTCATCAAAAGGAGAAGTCA-
1 TTCATCAAAAGGTTAAGTCAT
457008 TTCAATCAAAAGGTTAA
1 TTC-ATCAAAAGGTTAA
457025 ATCTTTTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCAT
Found at i:460667 original size:19 final size:18
Alignment explanation
Indices: 460629--460672 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
460619 ATTTTTTTAA
*
460629 AAATAAAAAATAAGAATT
1 AAATAAAAAAAAAGAATT
*
460647 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAAGAATT
460666 AAATAAA
1 AAATAAA
460673 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAATAAAAAAAAAGAATT
Found at i:461369 original size:24 final size:24
Alignment explanation
Indices: 461342--461449 Score: 85
Period size: 24 Copynumber: 4.3 Consensus size: 24
461332 AAATCCTAAT
461342 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** * *
461366 TAAAATACCTAAAACAAATATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * *
461391 TATAAA-AATAATATCCTAAAAATT-AAC
1 TA-AAATACTAA-AACCT---ATTTAAAC
461418 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
461442 TAAAATAC
1 TAAAATAC
461450 AAAGATAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 16
0.67 0.15 0.17
Matches are distributed among these distances:
23 3 0.05
24 21 0.34
25 18 0.29
26 10 0.16
27 8 0.13
28 2 0.03
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:461370 original size:64 final size:68
Alignment explanation
Indices: 461267--461465 Score: 162
Period size: 76 Copynumber: 2.9 Consensus size: 68
461257 TAAAACATCT
* * * *
461267 TAAATCCTAATT-AAATCACTTAAAA-TTGTCTAAAATAAAATACCAAA-AAAATAATATAAT-A
1 TAAATCCTAATTAAAAT-AC-TAAAACCTATTTAAACTAAAATACCAAACAAAATAATATAATAA
461328 T-T-C
64 TATCC
461331 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACC--AAACAAA-AT--AATAT--
461396 AAATAATATCC
59 -AATAATATCC
*** * * *
461407 TAAAAATTAACTAAAATACTAAAACCTATTTAAACTAAAATA-CAAAGATAA-AATATAAT
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAACAAAATAATATAAT
461466 GTTTAAAATA
Statistics
Matches: 111, Mismatches: 10, Indels: 26
0.76 0.07 0.18
Matches are distributed among these distances:
63 5 0.05
64 29 0.26
65 4 0.04
66 6 0.05
67 3 0.03
68 2 0.02
69 5 0.05
70 5 0.05
72 1 0.01
73 8 0.07
74 2 0.02
75 2 0.02
76 39 0.35
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.29
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAACAAAATAATATAATAATA
TCC
Found at i:461473 original size:76 final size:75
Alignment explanation
Indices: 461342--461485 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 75
461332 AAATCCTAAT
*
461342 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAATAATATCC
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATAT-AAAATAATATCC
461407 TAAAAATTAAC
65 TAAAAATTAAC
** * *
461418 TAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAGATAAAATATAATGTTTAAAATATTATC
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAA-A-AAAATATAAAATATAAAATAATATC
461481 CTAAA
64 CTAAA
461486 CTTGAGTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
74 3 0.05
75 17 0.28
76 41 0.67
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.28
Consensus pattern (75 bp):
TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATATAAAATAATATCCT
AAAAATTAAC
Found at i:462683 original size:14 final size:13
Alignment explanation
Indices: 462664--462693 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
462654 AATGGGAAGT
462664 AATCCCTGCAAATA
1 AATCCCTGCAAA-A
462678 AATCCCTGCAAAA
1 AATCCCTGCAAAA
462691 AAT
1 AAT
462694 GAGGCGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (13 bp):
AATCCCTGCAAAA
Found at i:463407 original size:5 final size:5
Alignment explanation
Indices: 463399--463448 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
463389 TAAGCATCTG
**
463399 ATAAA ATAAA ATAAA AT-AA ATGGA ATAAA AT-AA ATAAA ATGAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
463448 A
1 A
463449 CGAAATGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 8 0.21
5 26 0.67
6 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:463425 original size:14 final size:14
Alignment explanation
Indices: 463402--463447 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
463392 GCATCTGATA
463402 AAATAAAATAAAAT
1 AAATAAAATAAAAT
**
463416 AAATGGAATAAAAT
1 AAATAAAATAAAAT
463430 AAATAAAATGAAAAT
1 AAATAAAAT-AAAAT
463445 AAA
1 AAA
463448 ACGAAATGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:466441 original size:18 final size:18
Alignment explanation
Indices: 466420--466470 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
466410 AAAAGTTTTT
466420 TTAAATAAAAAATAAGAA
1 TTAAATAAAAAATAAGAA
* *
466438 TTAAATAAAAGAAAAATAA
1 TTAAATAAAA-AATAAGAA
466457 TTAAATAAACAAAT
1 TTAAATAAA-AAAT
466471 TTAAGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 17 0.61
20 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
TTAAATAAAAAATAAGAA
Found at i:467205 original size:33 final size:33
Alignment explanation
Indices: 467164--467226 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
467154 TTTAAACTAA
467164 AATACCTAAAAC-AAATATAAAATA-TAAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAAT
*
467196 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
467227 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 15 0.56
34 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.25
Consensus pattern (33 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAAT
Found at i:467269 original size:77 final size:75
Alignment explanation
Indices: 467107--467281 Score: 201
Period size: 77 Copynumber: 2.3 Consensus size: 75
467097 AAAATACCTA
* * * *
467107 AAAAAATAATATAATATTCTAAATCCTAATTAAAATACAAAAACCTATTTAAACTAAAATACCTA
1 AAAATATAAAATAATATCCTAAAACCTAATTAAAATACAAAAACCTATTTAAACTAAAATACCTA
*
467172 AAACAAATAT
66 AAAAAAATAT
* *
467182 AAAATATAAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C
1 AAAATAT--AAAATAATATCCTAAAACCTAATTAAAATACAAAAACCTATTTAAACTAAAATACC
467246 -AAAGATAAAATAT
64 TAAA-A-AAAATAT
** * *
467259 AATGTTTAAAATATTATCCTAAA
1 AAAATATAAAATAATATCCTAAA
467282 CTTGAGTTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
75 24 0.28
76 2 0.02
77 59 0.69
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.29
Consensus pattern (75 bp):
AAAATATAAAATAATATCCTAAAACCTAATTAAAATACAAAAACCTATTTAAACTAAAATACCTA
AAAAAAATAT
Found at i:467903 original size:21 final size:21
Alignment explanation
Indices: 467827--467903 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
467817 GATTAAATCC
* * *
467827 TTTCATGAAAAGGTTAAGCCA
1 TTTCATCAAAAGGTTAAGTCT
**
467848 TTTCATCAAAAGGAGAAGTCT
1 TTTCATCAAAAGGTTAAGTCT
*
467869 TTTAATCAAAAGGTTAAGTCT
1 TTTCATCAAAAGGTTAAGTCT
*
467890 TTTCATCGAAAGGT
1 TTTCATCAAAAGGT
467904 CTTAACCTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (21 bp):
TTTCATCAAAAGGTTAAGTCT
Found at i:471683 original size:20 final size:21
Alignment explanation
Indices: 471658--471727 Score: 90
Period size: 20 Copynumber: 3.3 Consensus size: 21
471648 AATAGAAGCC
471658 AAATAATAAAAAATAA-AATA
1 AAATAATAAAAAATAATAATA
471678 AAATAATAAAAAATAATAA-A
1 AAATAATAAAAAATAATAATA
*
471698 AGACTAATCTAAAAAATAATAATA
1 A-AATAA--TAAAAAATAATAATA
471722 AAATAA
1 AAATAA
471728 AACACAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
20 18 0.42
21 6 0.14
23 17 0.40
24 2 0.05
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.21
Consensus pattern (21 bp):
AAATAATAAAAAATAATAATA
Found at i:471695 original size:23 final size:23
Alignment explanation
Indices: 471659--471729 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 23
471649 ATAGAAGCCA
471659 AATAATAAAA-AATAAAATAAAAT
1 AATAA-AAAATAATAAAATAAAAT
**
471682 AATAAAAAATAATAAAAGACTAATCT
1 AATAAAAAATAAT-AAA-A-TAAAAT
471708 AA-AAAATAATAATAAAATAAAA
1 AATAAAA-AATAATAAAATAAAA
471730 CACAATAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
22 4 0.10
23 11 0.28
24 4 0.10
25 8 0.21
26 12 0.31
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (23 bp):
AATAAAAAATAATAAAATAAAAT
Found at i:471761 original size:24 final size:24
Alignment explanation
Indices: 471723--471782 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
471713 ATAATAATAA
*
471723 AATAAAACACAATAAAGA-AAAAAAG
1 AATAAAATA-AATAAA-ACAAAAAAG
* *
471748 AGTAAAATAAATAAAACAAAATAG
1 AATAAAATAAATAAAACAAAAAAG
471772 AATAAAATAAA
1 AATAAAATAAA
471783 AAATAAGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 22 0.73
25 7 0.23
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (24 bp):
AATAAAATAAATAAAACAAAAAAG
Found at i:471909 original size:17 final size:16
Alignment explanation
Indices: 471856--471910 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
471846 AAAAGAATAG
* * *
471856 AATAAAAAATATAAAA
1 AATAAAATATATATAT
*
471872 AATAAAATGTATATAT
1 AATAAAATATATATAT
*
471888 AATAAAATATAGTATTT
1 AATAAAATATA-TATAT
471905 AATAAA
1 AATAAA
471911 TAAAAAAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 22 0.69
17 10 0.31
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAAAATATATATAT
Found at i:472390 original size:23 final size:22
Alignment explanation
Indices: 472346--472394 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
472336 AAACTAAAAC
472346 TAAAACAAAAGAAATATGTAAA
1 TAAAACAAAAGAAATATGTAAA
*
472368 TAAAACAAATGAAA-ATGAATAAA
1 TAAAACAAAAGAAATATG--TAAA
472391 TAAA
1 TAAA
472395 TAAATAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 3 0.12
22 13 0.54
23 8 0.33
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (22 bp):
TAAAACAAAAGAAATATGTAAA
Found at i:472471 original size:21 final size:22
Alignment explanation
Indices: 472447--472490 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
472437 TAATAGTAAT
*
472447 AATAATAATAA-TAAGGAAAAA
1 AATAAAAATAATTAAGGAAAAA
*
472468 AATAAAAATAATTAAGTAAAAA
1 AATAAAAATAATTAAGGAAAAA
472490 A
1 A
472491 TGAATTAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAAAAATAATTAAGGAAAAA
Found at i:473548 original size:23 final size:23
Alignment explanation
Indices: 473522--473566 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
473512 CCGTTTGTAT
* *
473522 TGGGCTTTTGAGTTTGTAAACGC
1 TGGGCTTCTGAGTCTGTAAACGC
*
473545 TGGGCTTCTGGGTCTGTAAACG
1 TGGGCTTCTGAGTCTGTAAACG
473567 AAAAAAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.36
Consensus pattern (23 bp):
TGGGCTTCTGAGTCTGTAAACGC
Found at i:474616 original size:87 final size:85
Alignment explanation
Indices: 474461--474696 Score: 235
Period size: 87 Copynumber: 2.8 Consensus size: 85
474451 GTTATCGAGC
* ** * * * *
474461 TGAATGGAATCGAACTCGACCGTTTT--TTTACAGATAACCCTTATCGTCTTGAGTTGTAATGTA
1 TGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATACTGTA
* *
474524 AATTTGATATTCATTTAAGT
66 AATTTGATATGCACTTAAGT
* * * * * *
474544 TGAATGTAATCGAACTTGAAGGTCTTT-TTACTGATAGATAGCCCTTCTCGCCTTGAGCTATACT
1 TGAATGTAATCGAACTCGAAGGT-TTTGGT--TGACAGATAACCCTTATCGCCTTGAGTTATACT
* * *
474608 GTAAATTTGGTATGCCCTTGAGT
63 GTAAATTTGATATGCACTTAAGT
* * *
474631 TGAATTTAATTGAACTCGAAGGTTTTGGTTGACAAATAACCCTTATCGCCTTGAGTTATACTGTA
1 TGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATACTGTA
474696 A
66 A
474697 TAACCCCCTA
Statistics
Matches: 122, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
83 19 0.16
84 3 0.02
85 33 0.27
86 3 0.02
87 64 0.52
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (85 bp):
TGAATGTAATCGAACTCGAAGGTTTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATACTGTA
AATTTGATATGCACTTAAGT
Found at i:480427 original size:15 final size:15
Alignment explanation
Indices: 480407--480442 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
480397 CATGCTGATG
* *
480407 AATAAAAAGAAATAA
1 AATAAAAACAAAGAA
480422 AATAAAAACAAAGAA
1 AATAAAAACAAAGAA
480437 AATAAA
1 AATAAA
480443 TGGTCAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.11
Consensus pattern (15 bp):
AATAAAAACAAAGAA
Found at i:480618 original size:11 final size:11
Alignment explanation
Indices: 480591--480691 Score: 51
Period size: 11 Copynumber: 8.6 Consensus size: 11
480581 AATAATAATA
480591 AATAAAACAACAT
1 AATAAAA-AA-AT
480604 AATAAAAAAAT
1 AATAAAAAAAT
* *
480615 AATAAAAGACT
1 AATAAAAAAAT
*
480626 AATCTAAAAAAAC
1 AA--TAAAAAAAT
480639 AATAAAGAAAA-
1 AATAAA-AAAAT
* **
480650 AAGAGTAAAAT
1 AATAAAAAAAT
* *
480661 AAATAAAAATAG
1 -AATAAAAAAAT
*
480673 AATAAAATAAAA
1 AATAAAA-AAAT
480685 AATAAAA
1 AATAAAA
480692 TAAGGGAAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
10 4 0.06
11 27 0.40
12 21 0.31
13 15 0.22
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:480663 original size:19 final size:20
Alignment explanation
Indices: 480639--480683 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
480629 CTAAAAAAAC
*
480639 AATAAAGAAAAA-AGAGTAA
1 AATAAAGAAAAATAGAATAA
*
480658 AATAAATAAAAATAGAATAA
1 AATAAAGAAAAATAGAATAA
480678 AATAAA
1 AATAAA
480684 AAATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
AATAAAGAAAAATAGAATAA
Found at i:480668 original size:17 final size:15
Alignment explanation
Indices: 480655--480694 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
480645 GAAAAAAGAG
480655 TAAAATAAATAAAAA
1 TAAAATAAATAAAAA
*
480670 TAGAATAAAATAAAAAA
1 TAAAAT-AAAT-AAAAA
480687 TAAAATAA
1 TAAAATAA
480695 GGGAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
TAAAATAAATAAAAA
Found at i:480682 original size:16 final size:16
Alignment explanation
Indices: 480661--480708 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
480651 AGAGTAAAAT
480661 AAATAAAAATAGAATA
1 AAATAAAAATAGAATA
*
480677 AAATAAAAAATAAAATA
1 AAAT-AAAAATAGAATA
***
480694 AGGGAAAAATAGAAT
1 AAATAAAAATAGAAT
480709 TGAATAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAGAATA
Found at i:481219 original size:3 final size:3
Alignment explanation
Indices: 481213--481292 Score: 144
Period size: 3 Copynumber: 26.7 Consensus size: 3
481203 AAAAATATAT
481213 AAG AAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
481260 AAG AAG AAAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AA
481293 AAAAAAATAA
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 70 0.93
4 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:481312 original size:16 final size:16
Alignment explanation
Indices: 481291--481341 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
481281 GAAGAAGAAG
481291 AAAAAAAAATAAACAA
1 AAAAAAAAATAAACAA
481307 AAAAAAAACA-AAACAA
1 AAAAAAAA-ATAAACAA
* *
481323 AACAAAGAAATAAATAA
1 AA-AAAAAAATAAACAA
481340 AA
1 AA
481342 CAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.84, C:0.08, G:0.02, T:0.06
Consensus pattern (16 bp):
AAAAAAAAATAAACAA
Found at i:481367 original size:19 final size:19
Alignment explanation
Indices: 481321--481360 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
481311 AAAACAAAAC
481321 AAAACAAA-G-AAATAAAT
1 AAAACAAATGAAAATAAAT
481338 AAAACAAATGAAAATGAAAT
1 AAAACAAATGAAAAT-AAAT
481358 AAA
1 AAA
481361 TAAATGAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 4 0.20
20 7 0.35
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACAAATGAAAATAAAT
Found at i:481438 original size:20 final size:21
Alignment explanation
Indices: 481409--481452 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
481399 TAGTACTAGT
* *
481409 AATAATAATAA-TAAGGAAAA
1 AATAAAAATAATTAAGAAAAA
481429 AATAAAAATAATTAAGAAAAA
1 AATAAAAATAATTAAGAAAAA
481450 AAT
1 AAT
481453 GAATTAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AATAAAAATAATTAAGAAAAA
Found at i:481851 original size:4 final size:4
Alignment explanation
Indices: 481812--481907 Score: 64
Period size: 4 Copynumber: 26.0 Consensus size: 4
481802 TCGGGCCGGG
* * * *
481812 TATA TATA TTTA AAT- TAAA TATA TAAA TAT- TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
481858 T-TA -ATT TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
481900 TATA TATA
1 TATA TATA
481908 ATAGTTATTT
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
3 15 0.22
4 54 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:481851 original size:6 final size:6
Alignment explanation
Indices: 481812--481907 Score: 64
Period size: 6 Copynumber: 17.3 Consensus size: 6
481802 TCGGGCCGGG
* * * *
481812 TATATA TATTTA AAT-TA AATATA TAAATA T-TATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
481858 T-TA-A TTTAAA T-TAAA TTTAT- TA-ATA T-TATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
481900 TATATA TA
1 TATATA TA
481908 ATAGTTATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
4 4 0.05
5 24 0.32
6 47 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:481867 original size:42 final size:41
Alignment explanation
Indices: 481812--481900 Score: 144
Period size: 42 Copynumber: 2.2 Consensus size: 41
481802 TCGGGCCGGG
481812 TATATA-TATTTAAATTAAATATATAAATATTATATATATA
1 TATATATTATTTAAATTAAATATATAAATATTATATATATA
* *
481852 TATATATTAATTTAAATTAAATTTATTAATATTATATATATA
1 TATATATT-ATTTAAATTAAATATATAAATATTATATATATA
481894 TATATAT
1 TATATAT
481901 ATATATAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 6 0.13
41 1 0.02
42 38 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (41 bp):
TATATATTATTTAAATTAAATATATAAATATTATATATATA
Found at i:487312 original size:3 final size:3
Alignment explanation
Indices: 487304--487329 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
487294 GAATTGGGTT
487304 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
487330 TTTGCCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:487449 original size:2 final size:2
Alignment explanation
Indices: 487442--487498 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
487432 TAAAAGAATT
487442 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
487484 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
487499 TGATCACTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:489135 original size:80 final size:80
Alignment explanation
Indices: 488997--489156 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
488987 ATTGACACCA
488997 GCATAAAAAGCCATGGGTAAGAAACTGGAAAACAATCTCATTGAAAACATCCTCATCTATCTGGA
1 GCATAAAAAGCCATGGGTAAGAAACTGGAAAACAATCTCATTGAAAACATCCTCATCTATCTGGA
489062 AAAAATAGAACATAG
66 AAAAATAGAACATAG
*
489077 GCATAAAAAGCCATGGGTAAGAAACTGGAAAACAATCTCATTGAAAACATCCTTATCTATCTGGA
1 GCATAAAAAGCCATGGGTAAGAAACTGGAAAACAATCTCATTGAAAACATCCTCATCTATCTGGA
489142 AAAAATAGAACATAG
66 AAAAATAGAACATAG
489157 TTGAGCAATT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (80 bp):
GCATAAAAAGCCATGGGTAAGAAACTGGAAAACAATCTCATTGAAAACATCCTCATCTATCTGGA
AAAAATAGAACATAG
Found at i:494376 original size:20 final size:19
Alignment explanation
Indices: 494343--494383 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
494333 TTTTATCACA
*
494343 CTAAATTCTATCAAATTCT
1 CTAAATTCTATCAAATACT
*
494362 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTATCAAATACT
494382 CT
1 CT
494384 CTCTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (19 bp):
CTAAATTCTATCAAATACT
Found at i:494461 original size:17 final size:18
Alignment explanation
Indices: 494431--494466 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
494421 ATGTATATAA
494431 TTTATTTAAGTATTTTAC
1 TTTATTTAAGTATTTTAC
494449 TTTATTTAA-TATTTTAC
1 TTTATTTAAGTATTTTAC
494466 T
1 T
494467 AATATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATTTAAGTATTTTAC
Found at i:494722 original size:111 final size:111
Alignment explanation
Indices: 494528--494860 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
494518 TGAAAATCAT
*
494528 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCCACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
494593 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
494639 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCCACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
494704 TAATTAGTTGATGTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
494750 ATATCTCCACACTTTGCCGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTTTTAGTAA
1 ATATCTCCACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
494815 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
494861 TTTTTGTAAT
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCCACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:496730 original size:9 final size:9
Alignment explanation
Indices: 496718--496755 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
496708 ACCTGCTCAG
496718 GACGACGAT
1 GACGACGAT
*
496727 GACGATGAT
1 GACGACGAT
*
496736 GACGACGAC
1 GACGACGAT
496745 GACGACGAT
1 GACGACGAT
496754 GA
1 GA
496756 TGACAGTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:499827 original size:51 final size:51
Alignment explanation
Indices: 499724--499858 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
499714 CCCGTACGTG
* * * * *
499724 GCGTATAGCGCGGA-GCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGC-GATACAGGGGGCGCGCTATACTCCACGTGGAACCAAATCA
* **
499775 GCGTATAGCGCGATACAGGGGGGGCGCTATACTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGATACAGGGGGCGCGCTATACTCCACGTGGAACCAAATCA
* * * * *
499826 GCATATAACGCGGTTCAGGGGGCGCGCTTTACT
1 GCGTATAGCGCGATACAGGGGGCGCGCTATACT
499859 GCTACGGGTG
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
50 2 0.03
51 67 0.97
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.17
Consensus pattern (51 bp):
GCGTATAGCGCGATACAGGGGGCGCGCTATACTCCACGTGGAACCAAATCA
Found at i:500140 original size:23 final size:22
Alignment explanation
Indices: 500110--500152 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
500100 TATTTTCGTT
500110 AAAAAAATAACATTTTAGGTAGA
1 AAAAAAATAACA-TTTAGGTAGA
500133 AAAAAAATAACATTTAGGTA
1 AAAAAAATAACATTTAGGTA
500153 TTACCCGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.26
Consensus pattern (22 bp):
AAAAAAATAACATTTAGGTAGA
Found at i:513737 original size:21 final size:22
Alignment explanation
Indices: 513701--513742 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
513691 TGCTGAAAGT
513701 TACTGTAACAAGGGTATCTGTG
1 TACTGTAACAAGGGTATCTGTG
*
513723 TACTGTAGC-AGGGTATCTGT
1 TACTGTAACAAGGGTATCTGT
513743 ATCATTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (22 bp):
TACTGTAACAAGGGTATCTGTG
Found at i:517633 original size:22 final size:19
Alignment explanation
Indices: 517608--517650 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 19
517598 GATGTATTGA
517608 ATGAGTATTAATGAGTTCAAGT
1 ATGAGTA-T-ATGAGTT-AAGT
517630 ATGAGTATATGAGTTAAGT
1 ATGAGTATATGAGTTAAGT
517649 AT
1 AT
517651 ATGTAAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 1 0.05
22 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (19 bp):
ATGAGTATATGAGTTAAGT
Found at i:517801 original size:67 final size:65
Alignment explanation
Indices: 517727--517892 Score: 160
Period size: 65 Copynumber: 2.5 Consensus size: 65
517717 TTCTGGACAG
* * **
517727 AGGGTATCTGTACCCTATTAAGGTGTAAT-TATACCCCCTTTTTA-ATGAAAAATTACAGAATAT
1 AGGGTATCTGTACCCTA-TAAGGGGT-ATCGATACCCCC-TTGAAGATGAAAAATT-CAGAATAT
517790 CAGT
62 CAGT
* * *
517794 AGGGTATC-GATACCCTATAGGGGGTATCGATACCCCCTTGAAGATGAAAAATTCAGAATGTCAT
1 AGGGTATCTG-TACCCTATAAGGGGTATCGATACCCCCTTGAAGATGAAAAATTCAGAATATCAG
517858 T
65 T
* * *
517859 AGGGTATCTATACCCTAGACA-GGGTATCAATACC
1 AGGGTATCTGTACCCTATA-AGGGGTATCGATACC
517893 TCAGTTAGGG
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
65 43 0.52
66 25 0.30
67 15 0.18
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (65 bp):
AGGGTATCTGTACCCTATAAGGGGTATCGATACCCCCTTGAAGATGAAAAATTCAGAATATCAGT
Found at i:519447 original size:18 final size:19
Alignment explanation
Indices: 519398--519450 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
519388 TAAGGGTTAC
*
519398 AGTGGTCCTACGAGACAGT
1 AGTGGTCCTACGGGACAGT
519417 -GTGGTCCTACGGGAC-GT
1 AGTGGTCCTACGGGACAGT
*
519434 AGTGGTCCTTCGGGACA
1 AGTGGTCCTACGGGACA
519451 AATTTCAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.23
Consensus pattern (19 bp):
AGTGGTCCTACGGGACAGT
Found at i:528180 original size:25 final size:25
Alignment explanation
Indices: 528145--528250 Score: 185
Period size: 25 Copynumber: 4.2 Consensus size: 25
528135 AAGGTCAATG
*
528145 GGTCAGACCGATTCGGGTTGACTCA
1 GGTCAGGCCGATTCGGGTTGACTCA
528170 GGTCAGGCCGATTCGGGTTGACTCA
1 GGTCAGGCCGATTCGGGTTGACTCA
528195 GGTCAGGCCGATTCGGGTTGACTCA
1 GGTCAGGCCGATTCGGGTTGACTCA
*
528220 GGTCAGGCCGATTCGGGTTGATTCA
1 GGTCAGGCCGATTCGGGTTGACTCA
*
528245 TGTCAG
1 GGTCAG
528251 TTCGGGTAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 78 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (25 bp):
GGTCAGGCCGATTCGGGTTGACTCA
Found at i:540845 original size:21 final size:21
Alignment explanation
Indices: 540819--540860 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
540809 CCAGAATGGG
*
540819 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
540840 GGGAATCGATACGCCTTCATA
1 GGGAATCGATACCCCTTCATA
540861 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:541027 original size:33 final size:34
Alignment explanation
Indices: 540973--541058 Score: 122
Period size: 37 Copynumber: 2.5 Consensus size: 34
540963 AAACCATGCA
540973 GGGGGGAATCTGTACCCGGGAATCG-ATA-CCCT
1 GGGGGGAATCTGTACCCGGGAATCGAATACCCCT
*
541005 GGGGGGAATCTGTTCCCAGGGAATCGATATACCCCCT
1 GGGGGGAATCTGTACCC-GGGAATCGA-ATA-CCCCT
541042 GGGGGGAATCTGTACCC
1 GGGGGGAATCTGTACCC
541059 CCTGGACAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
32 16 0.34
33 8 0.17
35 3 0.06
37 20 0.43
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.20
Consensus pattern (34 bp):
GGGGGGAATCTGTACCCGGGAATCGAATACCCCT
Found at i:544528 original size:15 final size:15
Alignment explanation
Indices: 544508--544562 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 15
544498 AACCATGCAG
544508 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
544523 GGGGAAT-TGATACCCC
1 GGGGAATCTG-TA-CCC
*
544539 TGGGGGAATC-GTTCCC
1 --GGGGAATCTGTACCC
544555 GGGGAATC
1 GGGGAATC
544563 GATACCCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 6 0.18
17 1 0.03
18 8 0.24
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:544560 original size:32 final size:35
Alignment explanation
Indices: 544507--544589 Score: 127
Period size: 32 Copynumber: 2.5 Consensus size: 35
544497 AAACCATGCA
*
544507 GGGGGAATCTGTACCCGGGGAATTGATA-CCCCT-
1 GGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
*
544540 GGGGGAATC-GTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
544574 GGGGGAATCTGTACCC
1 GGGGGAATCTGTACCC
544590 CCTGGACAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 16 0.36
33 14 0.32
34 9 0.20
35 5 0.11
ACGTcount: A:0.19, C:0.27, G:0.35, T:0.19
Consensus pattern (35 bp):
GGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
Found at i:544580 original size:20 final size:20
Alignment explanation
Indices: 544555--544594 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
544545 AATCGTTCCC
544555 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
544575 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
544595 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:545059 original size:8 final size:8
Alignment explanation
Indices: 545048--545081 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
545038 TTCAAGTTGA
545048 TTTGAAAT
1 TTTGAAAT
545056 TTTGAAAT
1 TTTGAAAT
545064 TTTGAAAT
1 TTTGAAAT
545072 TTTG-AAT
1 TTTGAAAT
545079 TTT
1 TTT
545082 CGAGTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (8 bp):
TTTGAAAT
Found at i:545488 original size:157 final size:158
Alignment explanation
Indices: 545188--545525 Score: 489
Period size: 157 Copynumber: 2.1 Consensus size: 158
545178 AATTTCATCA
* * * ** * * *
545188 TTTTACCAAATTTGAACCGCAAACTCCTAAACCATATTAGAATACATGTTTACTTTCAATTTCTC
1 TTTTACCAAATTTAAATCACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCTA
* * * *
545253 TTTTTGATAACAAATGTTTTATTTTTCAATTTAGTCCTTAAATTTTTCATAATCTCCTTATTTCT
66 TTTTTGATAACAAATATTTAATTTTTCAATTTAGTCCTTAAATTTTTCATAATCTCCTTATTCCA
545318 TCAATTTGTCATTTATTGTAAGTCTATT
131 TCAATTTGTCATTTATTGTAAGTCTATT
* * *
545346 TTTTATCAAATTTGAGTCACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCTA
1 TTTTACCAAATTTAAATCACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCTA
* * *
545411 TTTTT-ATAACAATTATTTAATTTTTTAATTTAGTCCTTTAATTTTTCATAATCTCCTTATTCCA
66 TTTTTGATAACAAATATTTAATTTTTCAATTTAGTCCTTAAATTTTTCATAATCTCCTTATTCCA
* *
545475 TCAATTTGTCATTTATTTTAAGTTTATT
131 TCAATTTGTCATTTATTGTAAGTCTATT
545503 TTTTACCAAATTTAAATCACATG
1 TTTTACCAAATTTAAATCACATG
545526 ATCATATACC
Statistics
Matches: 159, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
157 98 0.62
158 61 0.38
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (158 bp):
TTTTACCAAATTTAAATCACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCTA
TTTTTGATAACAAATATTTAATTTTTCAATTTAGTCCTTAAATTTTTCATAATCTCCTTATTCCA
TCAATTTGTCATTTATTGTAAGTCTATT
Found at i:546479 original size:24 final size:26
Alignment explanation
Indices: 546435--546484 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
546425 CTCATAAAAT
546435 GATTTATCAATATGCAAAATAAAACA
1 GATTTATCAATATGCAAAATAAAACA
*
546461 GATTT-TCAA-ATGCATAATAAAACA
1 GATTTATCAATATGCAAAATAAAACA
546485 AAATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.61
25 4 0.17
26 5 0.22
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (26 bp):
GATTTATCAATATGCAAAATAAAACA
Found at i:547050 original size:24 final size:24
Alignment explanation
Indices: 547019--547127 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
547009 GTAACGAGAT
*
547019 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
547043 ATCTGAAATCATAGCAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
547067 ATCAGAAATCAGAACATAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
* * *
547091 ATAAGAAATCAGAACATAATTCAT
1 ATCAGAAATCAGAACAGAATTCAG
547115 ATCAGAAATCAGA
1 ATCAGAAATCAGA
547128 TAAAACAATC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:549556 original size:24 final size:24
Alignment explanation
Indices: 549517--549588 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
549507 GATACATTAC
* *
549517 CTGAATTTTGTCCTGATTTCTGAT
1 CTGAATTATGTTCTGATTTCTGAT
* * *
549541 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTATGTTCTGATTTCTGAT
* *
549565 CTGAATTATGTTTTGATTTTTGAT
1 CTGAATTATGTTCTGATTTCTGAT
549589 ATCTTCATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
CTGAATTATGTTCTGATTTCTGAT
Found at i:551771 original size:18 final size:19
Alignment explanation
Indices: 551748--551804 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
551738 TCAATGACTC
*
551748 GATGGCTCAGCTCGG-TTA
1 GATGGCTCAGCTCGGCTCA
**
551766 GATGGCTTGGCTCGGCTCA
1 GATGGCTCAGCTCGGCTCA
*
551785 G-TGGCTCAGCTTGGCTCA
1 GATGGCTCAGCTCGGCTCA
551803 GA
1 GA
551805 CCGGTCCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.14, C:0.25, G:0.35, T:0.26
Consensus pattern (19 bp):
GATGGCTCAGCTCGGCTCA
Found at i:560177 original size:21 final size:21
Alignment explanation
Indices: 560151--560194 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
560141 ACCCAATCTT
560151 CATTTTACTGCAATTTCAGTC
1 CATTTTACTGCAATTTCAGTC
560172 CATTTTACTGCAATTTCAGTC
1 CATTTTACTGCAATTTCAGTC
560193 CA
1 CA
560195 ATTCATGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (21 bp):
CATTTTACTGCAATTTCAGTC
Found at i:562779 original size:182 final size:182
Alignment explanation
Indices: 562452--562867 Score: 615
Period size: 182 Copynumber: 2.3 Consensus size: 182
562442 GAAAAAATAT
* * * *
562452 GACAAAACCGATAAAGCGCTACCGGATATATTGCAAGTGTCGCTACTTTAATATAAGTATCGACA
1 GACAAAACCGATAAAGAGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
562517 CATAGTGAATTTAAAGGAGAAGAAGTTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATATA
66 CATAGTGAATTTAAAGGAGAAGAAATTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATATA
* * *
562582 TCGATCCACAACGATATAACATGTAAAAATATGATAAAACCAATCTGGAAAA
131 TCGATCCACAACGATATAAAAGGTAAAAATATGATAAAACCAATCTCGAAAA
*
562634 GAGAAAACC-AGTAAAGAGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
1 GACAAAACCGA-TAAAGAGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
*
562698 ACATTGTGAATTTAAAGGAGAA-ACAATTTTAGCGCCTATAAAGTGTCGATTCTTTATATAA-AT
65 ACATAGTGAATTTAAAGGAGAAGA-AATTTTAGCGCCTATAAAGTGTCGATTCTTTATA-AATAT
* ** * * *
562761 ATATCGATCCATAACGATATAAAAGGTAAAAATATGATAAAACCGGTTTCTAAAT
128 ATATCGATCCACAACGATATAAAAGGTAAAAATATGATAAAACCAATCTCGAAAA
* *
562816 GACAAAACCGATAAAGCGCTACCGG-TATATTGAAAGTGTCGATACTTTAATA
1 GACAAAACCGATAAAGAGATACCGGATATATTGAAAGTGTCGATACTTTAATA
562868 AGTATGCGTA
Statistics
Matches: 211, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
181 29 0.14
182 179 0.85
183 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
GACAAAACCGATAAAGAGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CATAGTGAATTTAAAGGAGAAGAAATTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATATA
TCGATCCACAACGATATAAAAGGTAAAAATATGATAAAACCAATCTCGAAAA
Found at i:564837 original size:19 final size:20
Alignment explanation
Indices: 564792--564843 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
564782 CGTTTTTGTG
*
564792 TTTTATATAAAATGATATAG
1 TTTTATATAAAATGATATAA
*
564812 TTATTATATAAAATTATA-AA
1 TT-TTATATAAAATGATATAA
564832 TTTTATTATAAA
1 TTTTA-TATAAA
564844 TGCAGGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 11 0.39
21 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTATATAAAATGATATAA
Found at i:565243 original size:21 final size:21
Alignment explanation
Indices: 565219--565279 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
565209 ACAATCAGAG
565219 TCGAAGAGAAACTTGAGAGAA
1 TCGAAGAGAAACTTGAGAGAA
*
565240 TCGAAGAGAAACTTGAGAGAG
1 TCGAAGAGAAACTTGAGAGAA
*
565261 TCGAAGAGACACTTGAGAG
1 TCGAAGAGAAACTTGAGAG
565280 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.15
Consensus pattern (21 bp):
TCGAAGAGAAACTTGAGAGAA
Found at i:565349 original size:32 final size:33
Alignment explanation
Indices: 565313--565377 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
565303 AAATAGATGG
565313 GTGGTGAAAGAAGTTAAGATGTTGA-GGGTGAA
1 GTGGTGAAAGAAGTTAAGATGTTGAGGGGTGAA
* *
565345 GTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
1 GTGGTGAAAGAAGTTAAGATGTTGAGGGGTGAA
565378 CTTAAGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.25
Consensus pattern (33 bp):
GTGGTGAAAGAAGTTAAGATGTTGAGGGGTGAA
Found at i:566986 original size:19 final size:19
Alignment explanation
Indices: 566962--567010 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
566952 AATGTAGAGT
566962 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
566981 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
567000 TAATGTTGTAT
1 TAATTTTGTAT
567011 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:567997 original size:200 final size:199
Alignment explanation
Indices: 567728--568853 Score: 1361
Period size: 200 Copynumber: 5.7 Consensus size: 199
567718 CTGTTTCTCC
** * *
567728 AAAAGGGTGCACGCAAAAAGTGTCGATACATTTATAAATA-AGT--AT--CAGAAACATCGAAAC
1 AAAAGGGTGCAC-CACTAAGTGTCGATACATTTATAAA-AGTGTCGATCCCAGAAACATCGAAAA
* *
567788 CCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATACATATACCGATTTTATGAGA
64 CCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGA
567853 GAATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAA
129 GAATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAA
567918 TGCCCA
194 TGCCCA
* * *
567924 AAAAAGGTGCACCACTAAGTGTCGATACATTTATAAGAAGTATCGATCCCAGAAACATCAAAAAC
1 AAAAGGGTGCACCACTAAGTGTCGATACATTTATAA-AAGTGTCGATCCCAGAAACATCGAAAAC
* **
567989 CATAATTATAATGTAATAGGTAATTTTTCAATGTAACTGGTATACTTATACCGGTTTTATGA-AG
65 CATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAG
* * * * *
568053 AATAGGTGTACAATATGTATCGACACTTTTGTAATTTGTGTTGATGCTTTTCGTCCAGAAGGAAT
130 AATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAAT
568118 GCCCA
195 GCCCA
* * *
568123 AAAAGGGTGCACCACTAGGGGTCGATACATTTATACAAAGTGTCGATCCCAGAAACATCAAAAAC
1 AAAAGGGTGCACCACTAAGTGTCGATACATTTATA-AAAGTGTCGATCCCAGAAACATCGAAAAC
* **
568188 CATAATTATAATGTAATAGGTAATTTTTCAATGTAACTGGTATATTTATACCGGTTTTATGAGAG
65 CATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAG
*
568253 AATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGCCGATACTTTTGGTCCAGAATGAAT
130 AATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAAT
568318 GCCCA
195 GCCCA
* ** * * * *
568323 AAGAGGGTATACCACTAAGTGTCGATACATTTATACAATGTGTCGATCCTAAAAACATCGAAACC
1 AAAAGGGTGCACCACTAAGTGTCGATACATTTATA-AAAGTGTCGATCCCAGAAACATCGAAAAC
* * * * * *
568388 CCTAATTATAATATAATAGGTAATTTTGT-AATATAACAGGTATAAATATATCGGTTTTATGTGA
65 CATAATTATAATGTAATAGGTAATTTT-TCAATGTAACCGGTATAAATATACCGGTTTTATGAGA
* * * *
568452 GAATAGGTCTAC-ATAATGTATCGACACTTTTTTACTTTGTGTCGATACGTTTT-GTCCAGAATG
129 GAATAGGTGTACAAT-ATGTATCGACACTTGTGTAATTTGTGTCGATAC-TTTTGGTCCAGAATG
568515 AATGCCC-
192 AATGCCCA
* * * * * *
568522 AAAATGATGAACGCA-TAAAGTGTCGATA-TTTTATAAAAGTGTCGATACCAAAAACATCG-AAA
1 AAAAGGGTGCAC-CACT-AAGTGTCGATACATTTATAAAAGTGTCGATCCCAGAAACATCGAAAA
* * * * * *
568584 CTCATAAATATAATGTAATAGGTAAATTTACAATGTAACCGATATAACTATACCTGTTTTATGAG
64 C-CATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAG
* * * * * * *
568649 AGAATATGTCTACAACATGTATCGACACTTGTGGAATTGGTGTCAATACTTTTTGTCCAGAATGA
128 AGAATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGA
568714 ATG-CC-
193 ATGCCCA
* * * *
568719 -AAAGGGTTGCATGCA-TAAAGTGTCGATGCGTTTTTAAAAAGTGTCGATCCCA-AGAACATCGA
1 AAAAGGG-TGCA-CCACT-AAGTGTCGATACATTTAT-AAAAGTGTCGATCCCAGA-AACATCGA
* * * *
568781 AATCGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGGTTTTATG
61 AAACCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATG
*
568846 AGAAAATA
126 AGAGAATA
568854 AGTCATCATA
Statistics
Matches: 812, Mismatches: 95, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
195 23 0.03
196 17 0.02
197 26 0.03
198 131 0.16
199 288 0.35
200 322 0.40
201 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (199 bp):
AAAAGGGTGCACCACTAAGTGTCGATACATTTATAAAAGTGTCGATCCCAGAAACATCGAAAACC
ATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGA
ATAGGTGTACAATATGTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATG
CCCA
Found at i:568874 original size:199 final size:198
Alignment explanation
Indices: 567805--568853 Score: 1249
Period size: 199 Copynumber: 5.3 Consensus size: 198
567795 TATAATGTAA
* *
567805 TAGGTAATTTTTCAATGTAACCGGTATACATATACCGATTTTATGAGAGAATAGGTGTACAATAT
1 TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAATAT
*
567870 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAAAAAAGGTGCA
66 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCC--AAAGGGTGCA
* * *
567935 CCACTAAGTGTCGATACATTTATAAGAAGTATCGATCCC-AGAAACATCAAAAACCATAATTATA
129 CCACTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAG-AACATCGAAAACCATAATTATA
567999 ATGTAA
193 ATGTAA
* **
568005 TAGGTAATTTTTCAATGTAACTGGTATACTTATACCGGTTTTATGA-AGAATAGGTGTACAATAT
1 TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAATAT
* * * * *
568069 GTATCGACACTTTTGTAATTTGTGTTGATGCTTTTCGTCCAGAAGGAATGCCCAAAAAGGGTGCA
66 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCC--AAAGGGTGCA
* * * *
568134 CCACTAGGGGTCGATACATTTATACAAAGTGTCGATCCC-AGAAACATCAAAAACCATAATTATA
129 CCACTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAG-AACATCGAAAACCATAATTATA
568198 ATGTAA
193 ATGTAA
* **
568204 TAGGTAATTTTTCAATGTAACTGGTATATTTATACCGGTTTTATGAGAGAATAGGTGTACAATAT
1 TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAATAT
* **
568269 GTATCGACACTTGTGTAATTTGTGCCGATACTTTTGGTCCAGAATGAATGCCCAAAGAGGGTATA
66 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCC-AA-AGGGTGCA
* * * * * *
568334 CCACTAAGTGTCGATACATTTATACAATGTGTCGATCCTAAAAACATCGAAACCCCTAATTATAA
129 CCACTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAGAACATCGAAAACCATAATTATAA
*
568399 TATAA
194 TGTAA
* * * * *
568404 TAGGTAATTTTGT-AATATAACAGGTATAAATATATCGGTTTTATGTGAGAATAGGTCTAC-ATA
1 TAGGTAATTTT-TCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAAT-
* * * * *
568467 ATGTATCGACACTTTTTTACTTTGTGTCGATACGTTTT-GTCCAGAATGAATGCCCAAAATGATG
64 ATGTATCGACACTTGTGTAATTTGTGTCGATAC-TTTTGGTCCAGAATGAATGCCC-AAAGGGTG
* * * * *
568531 AACGCA-TAAAGTGTCGATA-TTTTAT-AAAAGTGTCGATACCAAAAACATCG-AAACTCATAAA
127 CAC-CACT-AAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAGAACATCGAAAAC-CATAAT
568592 TATAATGTAA
189 TATAATGTAA
* * * * * * * *
568602 TAGGTAAATTTACAATGTAACCGATATAACTATACCTGTTTTATGAGAGAATATGTCTACAACAT
1 TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAATAT
* * * *
568667 GTATCGACACTTGTGGAATTGGTGTCAATACTTTTTGTCCAGAATGAATG-CCAAAGGGTTGCAT
66 GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAAAGGG-TGCA-
* * * * * *
568731 GCA-TAAAGTGTCGATGCGTTTTTAAAAAGTGTCGATCCCAAGAACATCGAAATCGATAATTATA
129 CCACT-AAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAGAACATCGAAAACCATAATTATA
568795 ATGTAA
193 ATGTAA
* * *
568801 TAGGTAAATTTCCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATA
1 TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATA
568854 AGTCATCATA
Statistics
Matches: 742, Mismatches: 90, Indels: 35
0.86 0.10 0.04
Matches are distributed among these distances:
196 4 0.01
197 26 0.04
198 128 0.17
199 289 0.39
200 289 0.39
201 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (198 bp):
TAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTACAATAT
GTATCGACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAAAGGGTGCACC
ACTAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAGAACATCGAAAACCATAATTATAATG
TAA
Found at i:570403 original size:12 final size:12
Alignment explanation
Indices: 570377--570416 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
570367 CAAGAGGTCA
* *
570377 ATGAAGATGACG
1 ATGAAGATTATG
570389 ATGAAGATTATG
1 ATGAAGATTATG
*
570401 ATGATGATTATG
1 ATGAAGATTATG
570413 ATGA
1 ATGA
570417 TCCAAACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.30
Consensus pattern (12 bp):
ATGAAGATTATG
Found at i:571421 original size:25 final size:25
Alignment explanation
Indices: 571393--571444 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
571383 TCGTTGTGGG
571393 TACATTATTTGAACATTGTTATGTA
1 TACATTATTTGAACATTGTTATGTA
571418 TACATTATTTGAACATTGTTATGTA
1 TACATTATTTGAACATTGTTATGTA
571443 TA
1 TA
571445 AATTTCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (25 bp):
TACATTATTTGAACATTGTTATGTA
Found at i:571422 original size:14 final size:14
Alignment explanation
Indices: 571405--571444 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
571395 CATTATTTGA
571405 ACATTGTTATGTAT
1 ACATTGTTATGTAT
*
571419 ACATTATT-TG-A-
1 ACATTGTTATGTAT
571430 ACATTGTTATGTAT
1 ACATTGTTATGTAT
571444 A
1 A
571445 AATTTCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.33
12 3 0.14
13 3 0.14
14 8 0.38
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (14 bp):
ACATTGTTATGTAT
Found at i:571726 original size:15 final size:15
Alignment explanation
Indices: 571706--571744 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
571696 TCTCCACAAC
* *
571706 AAAGTTTTCATACAT
1 AAAGTTTCCAAACAT
*
571721 AAAGTTTCCAAACTT
1 AAAGTTTCCAAACAT
571736 AAAGTTTCC
1 AAAGTTTCC
571745 CATAAAGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (15 bp):
AAAGTTTCCAAACAT
Found at i:572220 original size:200 final size:199
Alignment explanation
Indices: 571745--572512 Score: 932
Period size: 200 Copynumber: 3.8 Consensus size: 199
571735 TAAAGTTTCC
* * * * *
571745 CATAAAGTGTCGATATAATTTTAAAAAGTATTGATCCCATAAACATCGAAATCCATAAATATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAA-CCATAATTATAAT
* * * * * * *
571810 GTAGTAGGTAAATTTACAATGTAACCAATATAACTAAACTAGTTTTATGAGAGAATAGGTCTACA
65 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACA
* * * *
571875 TAATTTATCGACACTTCTAGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCATAAAGGG
130 TAATGTATCGACACTTTTA-AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCA-AAAGGG
* *
571940 TTCACT-
193 TTGAATG
* * *
571946 CATAAAGTGTCGAAACATTTTTAAAATGTATCGATCCCAAAAACATCGAAACATATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAAC-CATAATTATAAT
* ** * * * * * *
572011 GTAATAGGTAATTTTGTAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACA
65 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACA
* * * *
572076 TAATATGTCGACACTTTTTAAAGTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAAAAGGG-
130 TAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGT
572140 TGAATG
194 TGAATG
* *
572146 CATAAAGTGTCGATGCATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACC-ATAATTATAAT
** ** *
572211 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACTGGTTTTATGTTAAAATAGGTGAACA
65 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACA
*
572276 TAATGTATCGACACGTTTT-AATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAAAGGGT
130 TAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGT
* *
572339 TGCACG
194 TGAATG
* * *
572345 CATAAAGTATCGATACATGTTTTAAAAAGTATCGATCCAAAAAACATTGAAACCAATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACC-ATAATTATAA
* * * * *
572410 TGTAATAGGTAAATTTACAATGTAAACGGTATAAATGTACCGGTTTTATGAGAAAATAGGTGAAC
64 TGTAATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAAC
* *
572475 ATAATGTATCAACACCTTTTAGATTTGTGTCGATACTT
129 ATAATGTATCGACA-CTTTTAAATTTGTGTCGATACTT
572513 ATAAATAACG
Statistics
Matches: 491, Mismatches: 68, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
198 9 0.02
199 54 0.11
200 253 0.52
201 171 0.35
202 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCATAATTATAATG
TAATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACAT
AATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTTG
AATG
Found at i:572505 original size:400 final size:401
Alignment explanation
Indices: 571745--572512 Score: 1039
Period size: 400 Copynumber: 1.9 Consensus size: 401
571735 TAAAGTTTCC
* * *
571745 CATAAAGTGTCGATATAATTTTAAAAAGTATTGATCCCATAAACATCGAAATCCATAAATATAAT
1 CATAAAGTGTCGATAGAATTTTAAAAAGTATCGATCCCAAAAACATCGAAATCCATAAATATAAT
* * * *
571810 GTAGTAGGTAAATTTACAATGTAACCAATATAACTAAACTAGTTTTATGAGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCAATATAAATAAACTAGTTTTATGAGAAAATAGGTCAACA
* *
571875 TAATTTATCGACACTTCTAGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCATAAAGGG
131 TAATGTATCGACACTTCTAGAATTTGTGTCGATACTGTTTGTCCAAAAGGAATGCCCATAAAGGG
* * * *
571940 TTCACTCATAAAGTGTCGAAACATTTTTAAAATGTATCGATCCCAAAAACATCGAAACATATAAT
196 TTCACGCATAAAGTATCGAAACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACATATAAT
* ** * *
572005 TATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAATATACCAGTTTTATGTGAGAATAGG
261 TATAATGTAATAGGTAAATTTACAATATAACTGGTATAAATATACCAGTTTTATGAGAAAATAGG
* * * *
572070 TCTACATAATATGTCGACACTTTTTAAAGTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAA
326 TCAACATAATATATCAACACCTTTTAAAGTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAA
572135 AAGGGTGAATG
391 AAGGGTGAATG
* *
572146 CATAAAGTGTCGAT-GCATTTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAATTATA
1 CATAAAGTGTCGATAGAATTT-TAAAAAGTATCGATCCCAAAAACATCGAAATCC-ATAAATATA
* * * ** *
572209 ATGTAATAGGTAAATTTACAATGTAACCGATATAAATATACTGGTTTTATGTTAAAATAGGTGAA
64 ATGTAATAGGTAAATTTACAATGTAACCAATATAAATAAACTAGTTTTATGAGAAAATAGGTCAA
* * *
572274 CATAATGTATCGACACGTT-T-TAATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCA-AAA
129 CATAATGTATCGACAC-TTCTAGAATTTGTGTCGATACTGTTTGTCCAAAAGGAATGCCCATAAA
* *
572335 GGGTTGCACGCATAAAGTATCGATACATGTTTTAAAAAGTATCGATCCAAAAAACATTGAAACCA
193 GGGTT-CACGCATAAAGTATCGAAACAT-TTTTAAAAAGTATCGATCCAAAAAACATCGAAA-CA
* * *
572400 -ATAATTATAATGTAATAGGTAAATTTACAATGTAAAC-GGTATAAATGTACCGGTTTTATGAGA
255 TATAATTATAATGTAATAGGTAAATTTACAATAT-AACTGGTATAAATATACCAGTTTTATGAGA
* * * *
572463 AAATAGGTGAACATAATGTATCAACACCTTTTAGATTTGTGTCGATACTT
319 AAATAGGTCAACATAATATATCAACACCTTTTAAAGTTGTGTCGATACTT
572513 ATAAATAACG
Statistics
Matches: 318, Mismatches: 42, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
398 8 0.03
399 22 0.07
400 160 0.50
401 126 0.40
402 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (401 bp):
CATAAAGTGTCGATAGAATTTTAAAAAGTATCGATCCCAAAAACATCGAAATCCATAAATATAAT
GTAATAGGTAAATTTACAATGTAACCAATATAAATAAACTAGTTTTATGAGAAAATAGGTCAACA
TAATGTATCGACACTTCTAGAATTTGTGTCGATACTGTTTGTCCAAAAGGAATGCCCATAAAGGG
TTCACGCATAAAGTATCGAAACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACATATAAT
TATAATGTAATAGGTAAATTTACAATATAACTGGTATAAATATACCAGTTTTATGAGAAAATAGG
TCAACATAATATATCAACACCTTTTAAAGTTGTGTCGATACTTTTTGTACAGAATGAATGCCCAA
AAGGGTGAATG
Found at i:575047 original size:23 final size:24
Alignment explanation
Indices: 575003--575058 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
574993 TGTTTGTTTG
* ** *
575003 TTTATTTTTTATTTGTTTTATTTC
1 TTTATTTTTAATTTGTAATATTAC
575027 TTTATTTTTAATTT-TAATATTAC
1 TTTATTTTTAATTTGTAATATTAC
575050 TTT-TTTTTA
1 TTTATTTTTA
575059 GGACAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.21
23 9 0.32
24 13 0.46
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTATTTTTAATTTGTAATATTAC
Found at i:577359 original size:22 final size:23
Alignment explanation
Indices: 577331--577378 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
577321 TGGTGGTTGG
*
577331 TTTAATGG-ATGTTTAACTTTAT
1 TTTAATGGTATATTTAACTTTAT
*
577353 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
577376 TTT
1 TTT
577379 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:578631 original size:21 final size:21
Alignment explanation
Indices: 578607--578650 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
578597 AAGACAATCA
578607 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
578628 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
578649 AG
1 AG
578651 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:578721 original size:33 final size:33
Alignment explanation
Indices: 578684--578768 Score: 161
Period size: 33 Copynumber: 2.6 Consensus size: 33
578674 AAATAGATGG
578684 AGTGGTGAAAGAAGTTGAGATGCTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGATGCTGAGGGGTGA
*
578717 AGTGGTGAAAGAAGTTGAGATGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGATGCTGAGGGGTGA
578750 AGTGGTGAAAGAAGTTGAG
1 AGTGGTGAAAGAAGTTGAG
578769 GTGTTTAAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.32, C:0.01, G:0.45, T:0.22
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGATGCTGAGGGGTGA
Found at i:579006 original size:18 final size:19
Alignment explanation
Indices: 578952--579006 Score: 96
Period size: 18 Copynumber: 3.0 Consensus size: 19
578942 TGAAAAAATA
578952 TGAAGAAGAAAAGAGGGA-
1 TGAAGAAGAAAAGAGGGAG
578970 TGAAGAAGAAAAGAGGGAG
1 TGAAGAAGAAAAGAGGGAG
578989 T-AAGAAGAAAAGAGGGAG
1 TGAAGAAGAAAAGAGGGAG
579007 GAAATGAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (19 bp):
TGAAGAAGAAAAGAGGGAG
Found at i:584003 original size:200 final size:195
Alignment explanation
Indices: 583653--584575 Score: 974
Period size: 199 Copynumber: 4.6 Consensus size: 195
583643 ACCTAAATAT
* * * *
583653 GTGTCGATACATTTTCTAAAAGTATCGA-CCCAAAAAATATCGAGACCAATAATTATAATCTAAT
1 GTGTCGATACAATTT-TAAAAGTATCGATCCC-AAAAACATCGAAACCAATAATTATAATGTAAT
* * * *
583717 AGGTAAATTAACAATGTAACCGGTATAAATATGCTGGTTAATTA-G-AAAACAGGTCAACATAAT
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTT--TTATGAAAAATAGGTCAACATAAT
* *
583780 GTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAAAATGAATGCCCAAATGAGGTGCA
127 GTATCGACACTTAT-TAATTTGTGTCGATACTT-TTGTCCAAAATGAATG-CCAAACG-GGTGCA
583845 CGCATAAA
188 CGCATAAA
* * *
583853 GTGTCGATACAATTATTAAAAGTATCGATCCCAATAAA-AT-AAAAACTATAATTATAATGTAAT
1 GTGTCGATACAATT-TTAAAAGTATCGATCCCAA-AAACATCGAAACCAATAATTATAATGTAAT
* * * *
583916 AGGTAAATCTACCATGTAACCGGTATAAATATACCGGTTTTATGTTAAAATAGGTGAACATAATG
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATG-AAAAATAGGTCAACATAATG
* *
583981 TATCGACACGTT-TTATATTTGTGTCGATACTTTTTTTCCAAAATGAATGCCAAAAGGGTTGCAC
128 TATCGACAC-TTATTA-ATTTGTGTCGATAC-TTTTGTCCAAAATGAATGCCAAACGGG-TGCAC
584045 GCATAAA
189 GCATAAA
* * * *
584052 GTGTCGATACACGTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTGTAAGGTAAT
1 GTGTCGATACA-ATTTT-AAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAT
* * * *
584117 ATGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCATCATAAAG
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAATAGGTCAACATAATG
* *
584182 TATCGACACTTATTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACGGGTGTACGC
128 TATCGACACTTATT-AATTTGTGTCGATAC-TTTTGTCCAAAATGAATGCCAAACGGGTGCACGC
584247 ATAAA
191 ATAAA
* * * * *
584252 GTGTCGATACATTTATTAAAACTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTGATA
1 GTGTCGATACAATT-TTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * * *
584317 GATAAATTTACAATGTACCCGATAGAAATATACCGATTTTATAAAAAAATAGGTCTAA-ATAATG
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTAT-GAAAAATAGGTC-AACATAATG
* * * *
584381 TATCGACACTCT-TTAAGTTTATGTCGATACTTGTT-TCTAGAATGAATGTCC-AACGAAGTGCA
128 TATCGACACT-TATTAA-TTTGTGTCGATACTT-TTGTCCAAAATGAATG-CCAAACG-GGTGCA
584443 CGCATAAA
188 CGCATAAA
* *
584451 GTGTCGATAC-A-TTTAAAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACAATTTTAAAA--GTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAT
* * * ** * * *
584514 ATGTAAATTTGCAATGTTA-CTATATAAATATACCTG-TTTACTTATAAAATAGGTCAATATAA
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTA-TGA-AAAATAGGTCAACATAA
584576 GCTCTATCTA
Statistics
Matches: 620, Mismatches: 73, Indels: 63
0.82 0.10 0.08
Matches are distributed among these distances:
196 13 0.02
197 32 0.05
198 75 0.12
199 231 0.37
200 134 0.22
201 134 0.22
202 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (195 bp):
GTGTCGATACAATTTTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATAGGTCAACATAATGTAT
CGACACTTATTAATTTGTGTCGATACTTTTGTCCAAAATGAATGCCAAACGGGTGCACGCATAAA
Found at i:584408 original size:400 final size:396
Alignment explanation
Indices: 583653--584575 Score: 1134
Period size: 400 Copynumber: 2.3 Consensus size: 396
583643 ACCTAAATAT
* * * * *
583653 GTGTCGATACATTTTCTAAAAGTATCGACCCAAAAAATATCGAGACCAATAATTATAATCTAATA
1 GTGTCGATACATTTT-AAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * * *
583718 GGTAAATTAACAATGTAACCGGTATAAATAT-GCTGGTTAATTAGAAAACAGGTCAACATAATGT
65 TGTAAATTTACAATGTAACCGGTATAAATATACCT-GTTTATTAGAAAATAGGTCAACATAAAGT
* *
583782 ATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAAAATGAATGCCCAAATGAGGTGCACG
129 ATCGACACTTATGTAATTTGTGTCGATACTTATTGTCCAAAATGAATGCCCAAACGAGGTGCACG
* * *
583847 CATAAAGTGTCGATACAATTATTAAAAGTATCGATCCCAATAAAATAAAAACTATAATTATAATG
194 CATAAAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAAATAAAAACGATAATTACAATG
* * * * * ***
583912 TAATAGGTAAATCTACCATGTAACCGGTATAAATATACCGGTTTTATGTTAAAATAGGTGAACAT
259 TAATAGATAAATCTACAATGTAACCGATAGAAATATACCGATTTTATAAAAAAATAGGTGAACAT
* *
583977 AATGTATCGACACGTTTTATATTTGTGTCGATACTTTTTTTCCAAAATGAATG-CCAA-AAGGGT
324 AATGTATCGACACGTTTTATATTTATGTCGATAC-TTGTTTCCAAAATGAATGTCCAACAA--G-
584040 TGCACGCATAAA
385 TGCACGCATAAA
* *
584052 GTGTCGATACACGTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTGTAAGGTAAT
1 GTGTCGATACA--TTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAAT
* * *
584117 ATGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATGAGAAAATAGGTCATCATAAAG
64 ATGTAAATTTACAATGTAACCGGTATAAATATACCTG-TTTATTAGAAAATAGGTCAACATAAAG
* *
584182 TATCGACACTTAT-TAAATTTGTGTCGATACATT-TTGTCCATAATGAATG-CCAAACG-GGTGT
128 TATCGACACTTATGT-AATTTGTGTCGATAC-TTATTGTCCAAAATGAATGCCCAAACGAGGTGC
* * *
584243 ACGCATAAAGTGTCGATACATTTATTAAAACTATCGATCCCAA-AAACATCGAAACCGATAATTA
191 ACGCATAAAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAA-AT-AAAAACGATAATTA
* * *
584307 CAATGTGATAGATAAATTTACAATGTACCCGATAGAAATATACCGATTTTATAAAAAAATAGGTC
254 CAATGTAATAGATAAATCTACAATGTAACCGATAGAAATATACCGATTTTATAAAAAAATAGGT-
* * *
584372 TAA-ATAATGTATCGACAC-TCTTTA-AGTTTATGTCGATACTTGTTTCTAGAATGAATGTCCAA
318 GAACATAATGTATCGACACGT-TTTATA-TTTATGTCGATACTTGTTTCCAAAATGAATGTCCAA
584434 CGAAGTGCACGCATAAA
381 C-AAGTGCACGCATAAA
* *
584451 GTGTCGATACA-TTTAAAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTTAAAA-AGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * ** * *
584515 TGTAAATTTGCAATGTTA-CTATATAAATATACCTGTTTACTTATAAAATAGGTCAATATAA
65 TGTAAATTTACAATGTAACCGGTATAAATATACCTGTTTA-TTAGAAAATAGGTCAACATAA
584576 GCTCTATCTA
Statistics
Matches: 453, Mismatches: 55, Indels: 35
0.83 0.10 0.06
Matches are distributed among these distances:
395 4 0.01
396 38 0.08
397 57 0.13
398 3 0.01
399 98 0.22
400 178 0.39
401 71 0.16
402 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (396 bp):
GTGTCGATACATTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAT
GTAAATTTACAATGTAACCGGTATAAATATACCTGTTTATTAGAAAATAGGTCAACATAAAGTAT
CGACACTTATGTAATTTGTGTCGATACTTATTGTCCAAAATGAATGCCCAAACGAGGTGCACGCA
TAAAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAAATAAAAACGATAATTACAATGTA
ATAGATAAATCTACAATGTAACCGATAGAAATATACCGATTTTATAAAAAAATAGGTGAACATAA
TGTATCGACACGTTTTATATTTATGTCGATACTTGTTTCCAAAATGAATGTCCAACAAGTGCACG
CATAAA
Found at i:584681 original size:86 final size:86
Alignment explanation
Indices: 584570--584730 Score: 272
Period size: 86 Copynumber: 1.9 Consensus size: 86
584560 AAATAGGTCA
*
584570 ATATAAGCTCTATCTATTACATATATAAGCG-CTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATATATAAGCGTC-ACCTAATATGTTATTGTACTTGATAATATTT
584634 CCGGTTAAATGCCTATTTTATT
65 CCGGTTAAATGCCTATTTTATT
584656 ATATAAGCGCTA-CTATTACATTATATAAGCGTCACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACA-TATATAAGCGTCACCTAATATGTTATTGTACTTGATAATATTT
*
584720 TCGGTTAAATG
65 CCGGTTAAATG
584731 ATATAACATA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
85 8 0.11
86 62 0.87
87 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (86 bp):
ATATAAGCGCTATCTATTACATATATAAGCGTCACCTAATATGTTATTGTACTTGATAATATTTC
CGGTTAAATGCCTATTTTATT
Found at i:587560 original size:60 final size:61
Alignment explanation
Indices: 587487--587623 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 61
587477 TTTTTAGGGT
* * * * * *
587487 AAAGTATAC-AAATGGTCCCCT-GACTATATAATTTTGCTTTGTTGAGTTCCTCGACTATTA
1 AAAGT-TACAAAATGGTCCACTCGACTATAGAATGTTGCTTTATTGAGTCCCTCGACTACTA
*
587547 AAAGTTACAAAATGGT-CACTCGACTATAGGATGTTGCTTTATTGAGTCCCTCGACTACTA
1 AAAGTTACAAAATGGTCCACTCGACTATAGAATGTTGCTTTATTGAGTCCCTCGACTACTA
587607 AAAGTTACAAAATGGTC
1 AAAGTTACAAAATGGTC
587624 ACCCAACTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 6 0.09
60 61 0.91
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (61 bp):
AAAGTTACAAAATGGTCCACTCGACTATAGAATGTTGCTTTATTGAGTCCCTCGACTACTA
Found at i:587633 original size:60 final size:60
Alignment explanation
Indices: 587520--587633 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
587510 CTATATAATT
* * * * *
587520 TTGCTTTGTTGAGTTCCTCGACTATTAAAAGTTACAAAATGGTCACTCGACTATAGGATG
1 TTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGGTCACCCAACTATAGGATG
587580 TTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGGTCACCCAACTAT
1 TTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGGTCACCCAACTAT
587634 TCATTATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (60 bp):
TTGCTTTATTGAGTCCCTCGACTACTAAAAGTTACAAAATGGTCACCCAACTATAGGATG
Found at i:603047 original size:18 final size:18
Alignment explanation
Indices: 603024--603085 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
603014 AGGGATTATC
603024 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTTGGGACAT
*
603042 AGTGGTCCTTTGGGACAC
1 AGTGGTCCTTTGGGACAT
*
603060 AGTGGT-CTTGGGGACAT
1 AGTGGTCCTTTGGGACAT
603077 AGTGGTCCT
1 AGTGGTCCT
603086 ACGGGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:606426 original size:17 final size:17
Alignment explanation
Indices: 606390--606436 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
606380 GGATTATCAA
*
606390 TGGTCCTTCGGGACATAG
1 TGGTCCTTC-GGACACAG
606408 TGGTCCTTCGGACACAG
1 TGGTCCTTCGGACACAG
606425 TGGTCCTTCGGA
1 TGGTCCTTCGGA
606437 AAAATTCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.28
Consensus pattern (17 bp):
TGGTCCTTCGGACACAG
Found at i:609123 original size:2 final size:2
Alignment explanation
Indices: 609116--609146 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
609106 TTTCATTTTC
609116 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 A
609147 CAATTTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:609305 original size:16 final size:16
Alignment explanation
Indices: 609279--609323 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
609269 GTTACAATTG
609279 AAACAATTAAATAAAAA
1 AAAC-ATTAAATAAAAA
*
609296 AAACATT-AA-AAAAG
1 AAACATTAAATAAAAA
609310 AAA-ATTAAATAAAA
1 AAACATTAAATAAAA
609324 GCAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 6 0.24
16 3 0.12
17 4 0.16
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (16 bp):
AAACATTAAATAAAAA
Found at i:609345 original size:13 final size:13
Alignment explanation
Indices: 609279--609352 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 13
609269 GTTACAATTG
609279 AAACAATTAAATAAA
1 AAACAATTAAAT--A
*
609294 AAAAACATTAAA-A
1 AAACA-ATTAAATA
*
609307 AAGAAAATTAAATA
1 AA-ACAATTAAATA
609321 AAAGCAATTAAATA
1 AAA-CAATTAAATA
609335 TAAAC-ATTAAATA
1 -AAACAATTAAATA
609348 CAAAC
1 -AAAC
609353 GTTACAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
13 22 0.43
14 16 0.31
15 7 0.14
16 6 0.12
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.20
Consensus pattern (13 bp):
AAACAATTAAATA
Found at i:609382 original size:25 final size:25
Alignment explanation
Indices: 609290--609385 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
609280 AACAATTAAA
*
609290 TAAA-AAAAACATTAAAAAAGAAAAT
1 TAAATAAAAACATT-ACAAAGAAAAT
* *
609315 TAAATAAAAGCAATTA-AATATAAACAT
1 TAAATAAAAAC-ATTACAA-AGAAA-AT
* * *
609342 TAAATACAAACGTTACAAAGAAAAC
1 TAAATAAAAACATTACAAAGAAAAT
609367 TAAATAAAAACATTACAAA
1 TAAATAAAAACATTACAAA
609386 CTAAACAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
25 24 0.42
26 17 0.30
27 16 0.28
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAATAAAAACATTACAAAGAAAAT
Found at i:610455 original size:2 final size:2
Alignment explanation
Indices: 610448--610489 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
610438 ACTAAAACAA
610448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610490 CTTATCAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611624 original size:19 final size:18
Alignment explanation
Indices: 611600--611669 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
611590 CAACTGTAAA
611600 AAAATAAAAAATCATTAGT
1 AAAATAAAAAAT-ATTAGT
611619 AAAAT--AAAATATTA-T
1 AAAATAAAAAATATTAGT
611634 AAAATAATAAAAATATTAAGT
1 AAAAT-A-AAAAATATT-AGT
611655 AAATATAATAAAATA
1 AAA-ATAA-AAAATA
611670 AAAAATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
15 6 0.14
16 4 0.09
17 5 0.12
19 13 0.30
20 2 0.05
21 11 0.26
22 2 0.05
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATAAAAAATATTAGT
Found at i:611671 original size:35 final size:35
Alignment explanation
Indices: 611598--611676 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
611588 TACAACTGTA
**
611598 AAAAAATAAAAAATCATTAGTAAAATAAAATATTAT
1 AAAAAAT-AAAAATCATTAGTAAAATAAAATAAAAT
*
611634 AAAATAATAAAAAT-ATTAAGT-AAATATAATAAAAT
1 AAAA-AATAAAAATCATT-AGTAAAATAAAATAAAAT
611669 AAAAAATA
1 AAAAAATA
611677 TTTTTACCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
34 4 0.11
35 18 0.47
36 13 0.34
37 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (35 bp):
AAAAAATAAAAATCATTAGTAAAATAAAATAAAAT
Found at i:611675 original size:37 final size:37
Alignment explanation
Indices: 611597--611676 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
611587 TTACAACTGT
*
611597 AAAAA-AATAAAAAATCATTAGTAAAATAAAATATTA
1 AAAAATAATAAAAAATCATTAGTAAAATAAAATAATA
*
611633 TAAAATAAT-AAAAAT-ATTAAGTAAATATAATAA-AATA
1 AAAAATAATAAAAAATCATT-AGTAAA-ATAA-AATAATA
611670 AAAAATA
1 AAAAATA
611677 TTTTTACCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
35 3 0.08
36 16 0.43
37 16 0.43
38 2 0.05
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (37 bp):
AAAAATAATAAAAAATCATTAGTAAAATAAAATAATA
Found at i:622400 original size:148 final size:143
Alignment explanation
Indices: 622213--622475 Score: 382
Period size: 148 Copynumber: 1.8 Consensus size: 143
622203 AAAAACTATT
* * * *
622213 TAAATTAGAATCAAATTATATTATAGTATTATAAGTATTTATAATTAAATTTAAACAGAAACTCA
1 TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAA-T-A
* *
622278 AAAATTTAATTCACTTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAATTTTTGAGTCAA
64 AAAA---AATTCAATTCGACTTGATTTAAATTTTATAAAATCAAATCGAAAAATTTTTGAGTCAA
622343 CTATTTTATAAACTGAAC
126 CTATTTTATAAACTGAAC
* * ***
622361 TAAATTAGAGTCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAATTTG
1 TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAATAAA
622426 AAAATTCAATTCGACTTGATTTAAATTTTATAAAATCAAATCGAAAAATT
66 AAAATTCAATTCGACTTGATTTAAATTTTATAAAATCAAATCGAAAAATT
622476 CACTAGAACA
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
143 46 0.44
146 2 0.02
147 1 0.01
148 55 0.53
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (143 bp):
TAAATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAATAAA
AAAATTCAATTCGACTTGATTTAAATTTTATAAAATCAAATCGAAAAATTTTTGAGTCAACTATT
TTATAAACTGAAC
Found at i:623203 original size:2 final size:2
Alignment explanation
Indices: 623135--623184 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
623125 TTGTGTTCTC
*
623135 TA TA AA 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
623177 TA TA TA TA
1 TA TA TA TA
623185 AGAATTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:623794 original size:18 final size:16
Alignment explanation
Indices: 623745--623801 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 16
623735 CAATATTATT
623745 TTAAAATATT-AAAAA
1 TTAAAATATTAAAAAA
*
623760 TTAAAATATGTAGAAAA
1 TTAAAATAT-TAAAAAA
623777 TATAAAATTATTAAAAAA
1 T-TAAAA-TATTAAAAAA
623795 TCTAAAA
1 T-TAAAA
623802 AAAACTCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 5 0.14
18 17 0.49
19 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (16 bp):
TTAAAATATTAAAAAA
Found at i:623803 original size:27 final size:26
Alignment explanation
Indices: 623747--623803 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
623737 ATATTATTTT
* * *
623747 AAAATATTAAAAATTAAAATATGTAG
1 AAAATATTAAAAATTAAAAAATCTAA
623773 AAAATA-TAAAATTATTAAAAAATCTAA
1 AAAATATTAAAA--ATTAAAAAATCTAA
623800 AAAA
1 AAAA
623804 AACTCTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 6 0.23
27 15 0.58
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (26 bp):
AAAATATTAAAAATTAAAAAATCTAA
Found at i:623962 original size:16 final size:17
Alignment explanation
Indices: 623941--623975 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
623931 AATATTTTTT
*
623941 AAATAT-AAATTATTAA
1 AAATATAAAAATATTAA
623957 AAATATAAAAATATTAA
1 AAATATAAAAATATTAA
623974 AA
1 AA
623976 CTTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATAAAAATATTAA
Found at i:624123 original size:40 final size:40
Alignment explanation
Indices: 624068--624146 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
624058 CAAAGGTTCC
624068 CTTGGTGAATAAGCACTAAACATAGTGTTGTAGATCTCCA
1 CTTGGTGAATAAGCACTAAACATAGTGTTGTAGATCTCCA
624108 CTTGGTGAATAAGCACTAAACATAGTGTTGTAGATCTCC
1 CTTGGTGAATAAGCACTAAACATAGTGTTGTAGATCTCC
624147 CGTTCGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (40 bp):
CTTGGTGAATAAGCACTAAACATAGTGTTGTAGATCTCCA
Found at i:624323 original size:20 final size:20
Alignment explanation
Indices: 624271--624327 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
624261 ATATTTCTTT
*
624271 TTAATTTTATAA-TTTT-AA
1 TTAATTTTAAAATTTTTAAA
*
624289 -TAATATTTAATATTTTTAAA
1 TTAAT-TTTAAAATTTTTAAA
624309 TTAATTTTAAAATTTTTAA
1 TTAATTTTAAAATTTTTAA
624328 GAAAACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 4 0.12
20 15 0.47
21 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATTTTAAAATTTTTAAA
Found at i:624338 original size:39 final size:37
Alignment explanation
Indices: 624222--624338 Score: 96
Period size: 39 Copynumber: 3.1 Consensus size: 37
624212 AATAAAATAC
*
624222 AATATTTTTATATT--TTTTCAAATTTTATAGAAATAATT
1 AATATTTTTA-ATTAATTTTAAAATTTTA-AGAAA-AATT
* * * * *
624260 AATATTTCTT-TTTAATTTTATAATTTTAATAATATTT
1 AATATTT-TTAATTAATTTTAAAATTTTAAGAAAAATT
*
624297 AATATTTTTAAATTAATTTTAAAATTTTTAAGAAAACTT
1 AATATTTTT-AATTAATTTTAAAA-TTTTAAGAAAAATT
624336 AAT
1 AAT
624339 TGGGCTGAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
36 2 0.03
37 12 0.19
38 21 0.34
39 27 0.44
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (37 bp):
AATATTTTTAATTAATTTTAAAATTTTAAGAAAAATT
Found at i:624377 original size:3 final size:3
Alignment explanation
Indices: 624369--624394 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
624359 GAGGCTTGAG
624369 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
624395 TCCATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:625620 original size:63 final size:63
Alignment explanation
Indices: 625504--625623 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
625494 CTAAACCCGA
* * *
625504 ACCCGACCCGACCCGAATATCACACTTAAAAAAACTGACCCGACCTGAACAAAATAAAGCTTC
1 ACCCGACCCGACCCGAATATCACAATTAAAAAAACCGACCCGACCCGAACAAAATAAAGCTTC
* * * *
625567 ACCCGACCCGACCCGAATAT-ATGAATT-AGAAATCCGACCCGACCCGACCCAAAATAA
1 ACCCGACCCGACCCGAATATCA-CAATTAAAAAAACCGACCCGACCCGA-ACAAAATAA
625624 TAAAAAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
62 17 0.35
63 31 0.65
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.13
Consensus pattern (63 bp):
ACCCGACCCGACCCGAATATCACAATTAAAAAAACCGACCCGACCCGAACAAAATAAAGCTTC
Found at i:627881 original size:29 final size:29
Alignment explanation
Indices: 627849--627984 Score: 166
Period size: 29 Copynumber: 4.7 Consensus size: 29
627839 TTTTCCTTTG
* * *
627849 ATTGTAATATATAAAAAGTTTTGGTGTTT
1 ATTGTAATTTATAAAAAGTTTTGATATTT
* *
627878 ATTGTAATTTTTAGAAAA-TTTTGGTATTT
1 ATTGTAATTTATA-AAAAGTTTTGATATTT
* *
627907 ATTGTAATTTACATAAAGTTTTGATATTT
1 ATTGTAATTTATAAAAAGTTTTGATATTT
* *
627936 ATTGTAATTTACATAAAGTTTTGATATTT
1 ATTGTAATTTATAAAAAGTTTTGATATTT
*
627965 ATTATAATTTATAAAAAGTT
1 ATTGTAATTTATAAAAAGTT
627985 CAGTCTTGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.03
29 88 0.93
30 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (29 bp):
ATTGTAATTTATAAAAAGTTTTGATATTT
Found at i:628665 original size:35 final size:35
Alignment explanation
Indices: 628626--628700 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
628616 GTTGGGCATA
*
628626 TAATTGAAGTGTTTTGGAATTTGAGGTTTAAAATG
1 TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATG
* * *
628661 TAATTGAAGTATTTTGGATTTTGGGGTTTAGAATG
1 TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATG
628696 TAATT
1 TAATT
628701 AATGATTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.45
Consensus pattern (35 bp):
TAATTGAAGTATTTTGGAATTTGAGGTTTAAAATG
Found at i:630170 original size:20 final size:20
Alignment explanation
Indices: 630145--630185 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
630135 AGGCAGATTG
630145 CCCAGAGGGTACCGATACCC
1 CCCAGAGGGTACCGATACCC
*
630165 CCCAGAGGGTACTGATACCC
1 CCCAGAGGGTACCGATACCC
630185 C
1 C
630186 TATGTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.39, G:0.24, T:0.12
Consensus pattern (20 bp):
CCCAGAGGGTACCGATACCC
Found at i:636056 original size:23 final size:22
Alignment explanation
Indices: 636021--636074 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
636011 AGGAGGTATT
*
636021 GATACCCCTTTGAATGGCTACC
1 GATACCCCCTTGAATGGCTACC
*
636043 GATACCCTCCTTGAATGGGTACC
1 GATACCC-CCTTGAATGGCTACC
636066 GATACCCCC
1 GATACCCCC
636075 ACGTGAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (22 bp):
GATACCCCCTTGAATGGCTACC
Found at i:638071 original size:19 final size:19
Alignment explanation
Indices: 638028--638077 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 19
638018 TGTTTTAACA
638028 TTTTGGATGTTTGAATTTG
1 TTTTGGATGTTTGAATTTG
*
638047 ---TGGATGGTTGAATTTG
1 TTTTGGATGTTTGAATTTG
638063 TTTTGGATGTTTGAA
1 TTTTGGATGTTTGAA
638078 CTTAAATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 15 0.58
19 11 0.42
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (19 bp):
TTTTGGATGTTTGAATTTG
Found at i:638352 original size:19 final size:19
Alignment explanation
Indices: 638330--638387 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
638320 GGGAGAAGTG
638330 TTATAGTAAGGGGGAGTAA
1 TTATAGTAAGGGGGAGTAA
*
638349 TTATAGTAAGGGGAAGTAA
1 TTATAGTAAGGGGGAGTAA
638368 TTATAGTAAGGGGGAGTAA
1 TTATAGTAAGGGGGAGTAA
638387 T
1 T
638388 AATTTTCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (19 bp):
TTATAGTAAGGGGGAGTAA
Found at i:638408 original size:28 final size:28
Alignment explanation
Indices: 638376--638432 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
638366 AATTATAGTA
*
638376 AGGGGGAGTAATAATTTTCTCAAAATTG
1 AGGGGGACTAATAATTTTCTCAAAATTG
638404 AGGGGGACTAATAATTTTCTCAAAATTG
1 AGGGGGACTAATAATTTTCTCAAAATTG
638432 A
1 A
638433 ATTGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (28 bp):
AGGGGGACTAATAATTTTCTCAAAATTG
Found at i:656261 original size:17 final size:17
Alignment explanation
Indices: 656236--656271 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
656226 GTTACTAGTT
656236 ATTTCTAGCCATTGGGG
1 ATTTCTAGCCATTGGGG
* *
656253 ATTTTTAGCCGTTGGGG
1 ATTTCTAGCCATTGGGG
656270 AT
1 AT
656272 CAAAATAACC
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:0.17, C:0.14, G:0.31, T:0.39
Consensus pattern (17 bp):
ATTTCTAGCCATTGGGG
Found at i:656400 original size:21 final size:20
Alignment explanation
Indices: 656348--656406 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
656338 AAACTCACTA
*
656348 TTGTCCAAGGGATAGATCCT
1 TTGTCAAAGGGATAGATCCT
* *
656368 TTTTCAAGGGGATCA-ATCCT
1 TTGTCAAAGGGAT-AGATCCT
*
656388 TTGGTCAAAGGGATTGATC
1 TT-GTCAAAGGGATAGATC
656407 TATGAGGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (20 bp):
TTGTCAAAGGGATAGATCCT
Found at i:657863 original size:15 final size:15
Alignment explanation
Indices: 657842--657876 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
657832 AAATATATTA
657842 ATATTTTAAAATAAT
1 ATATTTTAAAATAAT
* *
657857 TTATTTTATAATAAT
1 ATATTTTAAAATAAT
657872 ATATT
1 ATATT
657877 ATAAGATCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTTAAAATAAT
Found at i:662450 original size:14 final size:14
Alignment explanation
Indices: 662431--662469 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
662421 AATGGGAAGT
662431 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
662445 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
662459 AATCTCTGCAT
1 AATCCCTGCAT
662470 GTAGACAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:664840 original size:58 final size:61
Alignment explanation
Indices: 664756--664872 Score: 204
Period size: 62 Copynumber: 2.0 Consensus size: 61
664746 AAAACTAAAA
664756 ATTAGTAAGATTCAACAACTT--TAT-ATAATGTTCCTTATATAGAATACTACAAAAAACC
1 ATTAGTAAGATTCAACAACTTAATATAATAATGTTCCTTATATAGAATACTACAAAAAACC
664814 ATTAGTAAGATTCAACAACTTAATATACATAATGTTCCTTATATAGAATACTACAAAAA
1 ATTAGTAAGATTCAACAACTTAATATA-ATAATGTTCCTTATATAGAATACTACAAAAA
664873 CCCACTCAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
58 21 0.38
60 3 0.05
62 31 0.56
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (61 bp):
ATTAGTAAGATTCAACAACTTAATATAATAATGTTCCTTATATAGAATACTACAAAAAACC
Found at i:669059 original size:35 final size:34
Alignment explanation
Indices: 668974--669060 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
668964 AATGTAATTT
*
668974 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
669008 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
669046 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
669061 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:669687 original size:9 final size:9
Alignment explanation
Indices: 669673--669697 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
669663 ACATCATAAA
669673 TGGCTGCGG
1 TGGCTGCGG
669682 TGGCTGCGG
1 TGGCTGCGG
669691 TGGCTGC
1 TGGCTGC
669698 TGTGAAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (9 bp):
TGGCTGCGG
Found at i:671387 original size:17 final size:18
Alignment explanation
Indices: 671367--671407 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
671357 AAATTATATT
671367 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
671384 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
671402 ATTAAA
1 AGTAAA
671408 TACATAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:673449 original size:74 final size:75
Alignment explanation
Indices: 673341--673506 Score: 219
Period size: 74 Copynumber: 2.2 Consensus size: 75
673331 TCGTTTTTAT
* * * *
673341 ACTTAATATTATGATTTGAGTCTT-AAGATTTGACACTTTAATATTATGATTTGATTATGAATTT
1 ACTTAATATTGTGGTTTAAATCTTGAA-ATTTGACACTTTAATATTATGATTTGATTATGAATTT
*
673405 T-TTATTCTAG
65 TATTATTCTAA
* * * * *
673415 AGTTAATATTGTGGTTTAAATCTTGAAATTTGACATTTTAATATTATGGTTTGTTTATGGATTTT
1 ACTTAATATTGTGGTTTAAATCTTGAAATTTGACACTTTAATATTATGATTTGATTATGAATTTT
673480 ATTATTCTAA
66 ATTATTCTAA
673490 ACTTAATATTGTGGTTT
1 ACTTAATATTGTGGTTT
673507 GAGTATTGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 53 0.67
75 26 0.33
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (75 bp):
ACTTAATATTGTGGTTTAAATCTTGAAATTTGACACTTTAATATTATGATTTGATTATGAATTTT
ATTATTCTAA
Done.