Multiple sequence alignment - TraesCS1B01G077300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G077300 chr1B 100.000 4169 0 0 1 4169 59834988 59830820 0.000000e+00 7699.0
1 TraesCS1B01G077300 chr1B 88.158 76 7 2 581 656 252023449 252023522 5.740000e-14 89.8
2 TraesCS1B01G077300 chr1D 91.308 2531 156 36 804 3316 40168904 40166420 0.000000e+00 3397.0
3 TraesCS1B01G077300 chr1D 90.728 151 11 3 336 486 419478111 419477964 9.140000e-47 198.0
4 TraesCS1B01G077300 chr1D 80.851 94 14 2 671 760 40168994 40168901 2.080000e-08 71.3
5 TraesCS1B01G077300 chr1A 88.803 1938 142 40 1398 3308 39651362 39649473 0.000000e+00 2307.0
6 TraesCS1B01G077300 chr1A 98.472 851 13 0 3319 4169 557912284 557911434 0.000000e+00 1500.0
7 TraesCS1B01G077300 chr1A 90.629 747 45 17 669 1396 39652208 39651468 0.000000e+00 968.0
8 TraesCS1B01G077300 chr1A 87.097 434 25 11 177 595 39652687 39652270 2.940000e-126 462.0
9 TraesCS1B01G077300 chr1A 93.056 144 9 1 336 478 84012523 84012380 4.220000e-50 209.0
10 TraesCS1B01G077300 chr2B 98.824 850 9 1 3320 4169 314669853 314670701 0.000000e+00 1513.0
11 TraesCS1B01G077300 chr2B 98.476 853 13 0 3317 4169 335201778 335200926 0.000000e+00 1504.0
12 TraesCS1B01G077300 chr2B 98.471 850 12 1 3320 4169 334695462 334696310 0.000000e+00 1496.0
13 TraesCS1B01G077300 chr2B 83.140 172 26 1 641 809 342253512 342253341 2.010000e-33 154.0
14 TraesCS1B01G077300 chr3B 98.472 851 13 0 3319 4169 775344250 775345100 0.000000e+00 1500.0
15 TraesCS1B01G077300 chr3B 90.000 70 5 2 587 656 763045010 763044943 5.740000e-14 89.8
16 TraesCS1B01G077300 chr4B 98.471 850 13 0 3320 4169 404406851 404406002 0.000000e+00 1498.0
17 TraesCS1B01G077300 chr7B 98.469 849 13 0 3321 4169 732693083 732692235 0.000000e+00 1496.0
18 TraesCS1B01G077300 chr5B 98.355 851 13 1 3319 4169 370090074 370089225 0.000000e+00 1493.0
19 TraesCS1B01G077300 chr4A 98.239 852 15 0 3318 4169 32658251 32659102 0.000000e+00 1491.0
20 TraesCS1B01G077300 chr4A 93.525 139 9 0 336 474 252243876 252243738 1.520000e-49 207.0
21 TraesCS1B01G077300 chr4A 93.525 139 9 0 336 474 384826237 384826099 1.520000e-49 207.0
22 TraesCS1B01G077300 chr4A 94.915 59 3 0 583 641 352496877 352496819 4.440000e-15 93.5
23 TraesCS1B01G077300 chr7A 93.525 139 9 0 336 474 526516530 526516668 1.520000e-49 207.0
24 TraesCS1B01G077300 chr7A 96.364 55 2 0 581 635 28406874 28406820 1.600000e-14 91.6
25 TraesCS1B01G077300 chr5D 93.525 139 9 0 336 474 198954931 198955069 1.520000e-49 207.0
26 TraesCS1B01G077300 chr4D 93.525 139 9 0 336 474 408572650 408572512 1.520000e-49 207.0
27 TraesCS1B01G077300 chr2A 93.525 139 9 0 336 474 614723536 614723398 1.520000e-49 207.0
28 TraesCS1B01G077300 chr2A 81.977 172 28 1 641 809 350701517 350701346 4.340000e-30 143.0
29 TraesCS1B01G077300 chr2A 88.462 78 6 3 581 656 81144555 81144479 1.600000e-14 91.6
30 TraesCS1B01G077300 chr2D 82.558 172 27 1 641 809 271540305 271540476 9.340000e-32 148.0
31 TraesCS1B01G077300 chr7D 96.610 59 0 2 581 638 423302213 423302270 3.430000e-16 97.1
32 TraesCS1B01G077300 chr7D 88.571 70 6 2 587 656 550641998 550642065 2.670000e-12 84.2
33 TraesCS1B01G077300 chr5A 93.443 61 4 0 581 641 14028420 14028360 1.600000e-14 91.6
34 TraesCS1B01G077300 chr6B 88.571 70 6 2 587 656 401107658 401107725 2.670000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G077300 chr1B 59830820 59834988 4168 True 7699.000000 7699 100.0000 1 4169 1 chr1B.!!$R1 4168
1 TraesCS1B01G077300 chr1D 40166420 40168994 2574 True 1734.150000 3397 86.0795 671 3316 2 chr1D.!!$R2 2645
2 TraesCS1B01G077300 chr1A 557911434 557912284 850 True 1500.000000 1500 98.4720 3319 4169 1 chr1A.!!$R2 850
3 TraesCS1B01G077300 chr1A 39649473 39652687 3214 True 1245.666667 2307 88.8430 177 3308 3 chr1A.!!$R3 3131
4 TraesCS1B01G077300 chr2B 314669853 314670701 848 False 1513.000000 1513 98.8240 3320 4169 1 chr2B.!!$F1 849
5 TraesCS1B01G077300 chr2B 335200926 335201778 852 True 1504.000000 1504 98.4760 3317 4169 1 chr2B.!!$R1 852
6 TraesCS1B01G077300 chr2B 334695462 334696310 848 False 1496.000000 1496 98.4710 3320 4169 1 chr2B.!!$F2 849
7 TraesCS1B01G077300 chr3B 775344250 775345100 850 False 1500.000000 1500 98.4720 3319 4169 1 chr3B.!!$F1 850
8 TraesCS1B01G077300 chr4B 404406002 404406851 849 True 1498.000000 1498 98.4710 3320 4169 1 chr4B.!!$R1 849
9 TraesCS1B01G077300 chr7B 732692235 732693083 848 True 1496.000000 1496 98.4690 3321 4169 1 chr7B.!!$R1 848
10 TraesCS1B01G077300 chr5B 370089225 370090074 849 True 1493.000000 1493 98.3550 3319 4169 1 chr5B.!!$R1 850
11 TraesCS1B01G077300 chr4A 32658251 32659102 851 False 1491.000000 1491 98.2390 3318 4169 1 chr4A.!!$F1 851

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
41 42 0.107459 CAGCTCCTTGGTAGGCCTTC 60.107 60.0 12.58 5.39 41.69 3.46 F
1364 1424 0.252513 TACCCAGCTGCTGTAAGGGA 60.253 55.0 26.41 15.62 42.25 4.20 F
1761 1928 0.809385 TCTACAACGAGAGCTTCCCG 59.191 55.0 0.00 0.00 0.00 5.14 F
2383 2563 0.322456 CCACCGATCCAGGAAAAGCA 60.322 55.0 0.00 0.00 34.73 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1852 0.031178 CAGCTTGCACAAAGTGGGAC 59.969 55.0 0.00 0.0 38.25 4.46 R
2175 2346 0.319900 TTGTGAGCGCACCTCTTCTC 60.320 55.0 18.33 0.0 44.51 2.87 R
2927 3117 0.668401 GCAACATTTCAGTGCCCAGC 60.668 55.0 0.00 0.0 0.00 4.85 R
3258 3454 0.937304 CAATTACCGGTCGAGCCATG 59.063 55.0 12.40 0.0 36.97 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.474570 CCTCCGGGCTCCTTCCAG 61.475 72.222 0.00 0.00 0.00 3.86
18 19 4.168291 CTCCGGGCTCCTTCCAGC 62.168 72.222 0.00 0.00 38.84 4.85
34 35 4.096003 GCCGCCAGCTCCTTGGTA 62.096 66.667 0.00 0.00 40.49 3.25
35 36 2.187946 CCGCCAGCTCCTTGGTAG 59.812 66.667 0.00 0.00 40.49 3.18
36 37 2.187946 CGCCAGCTCCTTGGTAGG 59.812 66.667 0.00 0.00 43.46 3.18
37 38 2.124529 GCCAGCTCCTTGGTAGGC 60.125 66.667 0.00 0.00 41.69 3.93
38 39 2.592308 CCAGCTCCTTGGTAGGCC 59.408 66.667 0.00 0.00 41.69 5.19
39 40 1.997874 CCAGCTCCTTGGTAGGCCT 60.998 63.158 11.78 11.78 41.69 5.19
40 41 1.566298 CCAGCTCCTTGGTAGGCCTT 61.566 60.000 12.58 0.00 41.69 4.35
41 42 0.107459 CAGCTCCTTGGTAGGCCTTC 60.107 60.000 12.58 5.39 41.69 3.46
42 43 1.224870 GCTCCTTGGTAGGCCTTCC 59.775 63.158 21.15 21.15 41.69 3.46
43 44 1.562672 GCTCCTTGGTAGGCCTTCCA 61.563 60.000 26.14 26.14 41.69 3.53
44 45 0.543749 CTCCTTGGTAGGCCTTCCAG 59.456 60.000 27.82 21.21 41.69 3.86
45 46 0.914417 TCCTTGGTAGGCCTTCCAGG 60.914 60.000 27.73 27.73 41.69 4.45
79 80 2.912542 CGCCGGGCTCCTCTCATA 60.913 66.667 18.34 0.00 0.00 2.15
80 81 2.279069 CGCCGGGCTCCTCTCATAT 61.279 63.158 18.34 0.00 0.00 1.78
81 82 0.965866 CGCCGGGCTCCTCTCATATA 60.966 60.000 18.34 0.00 0.00 0.86
82 83 1.267121 GCCGGGCTCCTCTCATATAA 58.733 55.000 12.87 0.00 0.00 0.98
83 84 1.834263 GCCGGGCTCCTCTCATATAAT 59.166 52.381 12.87 0.00 0.00 1.28
84 85 2.237392 GCCGGGCTCCTCTCATATAATT 59.763 50.000 12.87 0.00 0.00 1.40
85 86 3.307762 GCCGGGCTCCTCTCATATAATTT 60.308 47.826 12.87 0.00 0.00 1.82
86 87 4.807643 GCCGGGCTCCTCTCATATAATTTT 60.808 45.833 12.87 0.00 0.00 1.82
87 88 4.938226 CCGGGCTCCTCTCATATAATTTTC 59.062 45.833 0.00 0.00 0.00 2.29
88 89 4.938226 CGGGCTCCTCTCATATAATTTTCC 59.062 45.833 0.00 0.00 0.00 3.13
89 90 5.257262 GGGCTCCTCTCATATAATTTTCCC 58.743 45.833 0.00 0.00 0.00 3.97
90 91 5.257262 GGCTCCTCTCATATAATTTTCCCC 58.743 45.833 0.00 0.00 0.00 4.81
91 92 5.257262 GCTCCTCTCATATAATTTTCCCCC 58.743 45.833 0.00 0.00 0.00 5.40
128 129 4.037858 GTGTATTACACCGGTACAGAGG 57.962 50.000 6.87 0.00 43.05 3.69
129 130 2.428171 TGTATTACACCGGTACAGAGGC 59.572 50.000 6.87 0.00 0.00 4.70
130 131 1.563924 ATTACACCGGTACAGAGGCA 58.436 50.000 6.87 0.00 0.00 4.75
131 132 1.340088 TTACACCGGTACAGAGGCAA 58.660 50.000 6.87 0.00 0.00 4.52
132 133 0.892755 TACACCGGTACAGAGGCAAG 59.107 55.000 6.87 0.00 0.00 4.01
133 134 0.830444 ACACCGGTACAGAGGCAAGA 60.830 55.000 6.87 0.00 0.00 3.02
134 135 0.320374 CACCGGTACAGAGGCAAGAA 59.680 55.000 6.87 0.00 0.00 2.52
135 136 1.053424 ACCGGTACAGAGGCAAGAAA 58.947 50.000 4.49 0.00 0.00 2.52
136 137 1.418637 ACCGGTACAGAGGCAAGAAAA 59.581 47.619 4.49 0.00 0.00 2.29
137 138 2.076863 CCGGTACAGAGGCAAGAAAAG 58.923 52.381 0.00 0.00 0.00 2.27
138 139 2.550208 CCGGTACAGAGGCAAGAAAAGT 60.550 50.000 0.00 0.00 0.00 2.66
139 140 3.139077 CGGTACAGAGGCAAGAAAAGTT 58.861 45.455 0.00 0.00 0.00 2.66
140 141 3.564225 CGGTACAGAGGCAAGAAAAGTTT 59.436 43.478 0.00 0.00 0.00 2.66
141 142 4.753107 CGGTACAGAGGCAAGAAAAGTTTA 59.247 41.667 0.00 0.00 0.00 2.01
142 143 5.333875 CGGTACAGAGGCAAGAAAAGTTTAC 60.334 44.000 0.00 0.00 0.00 2.01
143 144 4.813296 ACAGAGGCAAGAAAAGTTTACG 57.187 40.909 0.00 0.00 0.00 3.18
144 145 4.196971 ACAGAGGCAAGAAAAGTTTACGT 58.803 39.130 0.00 0.00 0.00 3.57
145 146 5.362263 ACAGAGGCAAGAAAAGTTTACGTA 58.638 37.500 0.00 0.00 0.00 3.57
146 147 5.995897 ACAGAGGCAAGAAAAGTTTACGTAT 59.004 36.000 0.00 0.00 0.00 3.06
147 148 6.073222 ACAGAGGCAAGAAAAGTTTACGTATG 60.073 38.462 0.00 0.00 0.00 2.39
148 149 6.147164 CAGAGGCAAGAAAAGTTTACGTATGA 59.853 38.462 0.00 0.00 0.00 2.15
149 150 6.879458 AGAGGCAAGAAAAGTTTACGTATGAT 59.121 34.615 0.00 0.00 0.00 2.45
150 151 7.390718 AGAGGCAAGAAAAGTTTACGTATGATT 59.609 33.333 0.00 0.00 0.00 2.57
151 152 7.527457 AGGCAAGAAAAGTTTACGTATGATTC 58.473 34.615 0.00 0.00 0.00 2.52
152 153 7.174253 AGGCAAGAAAAGTTTACGTATGATTCA 59.826 33.333 0.00 0.00 0.00 2.57
153 154 7.806014 GGCAAGAAAAGTTTACGTATGATTCAA 59.194 33.333 0.00 0.00 0.00 2.69
154 155 9.176181 GCAAGAAAAGTTTACGTATGATTCAAA 57.824 29.630 0.00 0.00 0.00 2.69
172 173 9.529325 TGATTCAAATTCTACTACGTATTGAGG 57.471 33.333 0.00 0.00 0.00 3.86
173 174 8.888579 ATTCAAATTCTACTACGTATTGAGGG 57.111 34.615 0.00 0.00 0.00 4.30
174 175 6.812998 TCAAATTCTACTACGTATTGAGGGG 58.187 40.000 0.00 0.00 0.00 4.79
175 176 6.608405 TCAAATTCTACTACGTATTGAGGGGA 59.392 38.462 0.00 0.00 0.00 4.81
179 180 5.068636 TCTACTACGTATTGAGGGGATGAC 58.931 45.833 0.00 0.00 0.00 3.06
195 196 3.503227 GGATGACCCCCTAGCTCTATTCT 60.503 52.174 0.00 0.00 0.00 2.40
198 199 4.481072 TGACCCCCTAGCTCTATTCTTAC 58.519 47.826 0.00 0.00 0.00 2.34
246 247 0.394216 TGGATTGATGAAGTGCCCCG 60.394 55.000 0.00 0.00 0.00 5.73
248 249 1.303309 GATTGATGAAGTGCCCCGAG 58.697 55.000 0.00 0.00 0.00 4.63
270 271 6.267496 AGTGGCTTTCGCTAACAAAAATAT 57.733 33.333 0.00 0.00 33.87 1.28
333 334 0.979665 ATCCATGCATACTCCCTCCG 59.020 55.000 0.00 0.00 0.00 4.63
334 335 0.398522 TCCATGCATACTCCCTCCGT 60.399 55.000 0.00 0.00 0.00 4.69
353 369 5.235516 TCCGTGACCTTTTAGAGATTTCAC 58.764 41.667 0.00 0.00 0.00 3.18
591 607 1.933853 CCGACAGTGCTTGCCTAATAC 59.066 52.381 0.00 0.00 0.00 1.89
595 611 2.092914 ACAGTGCTTGCCTAATACTCCC 60.093 50.000 0.00 0.00 0.00 4.30
596 612 2.171448 CAGTGCTTGCCTAATACTCCCT 59.829 50.000 0.00 0.00 0.00 4.20
597 613 2.436173 AGTGCTTGCCTAATACTCCCTC 59.564 50.000 0.00 0.00 0.00 4.30
598 614 1.768870 TGCTTGCCTAATACTCCCTCC 59.231 52.381 0.00 0.00 0.00 4.30
599 615 1.270358 GCTTGCCTAATACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63
600 616 2.040178 CTTGCCTAATACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
602 618 0.967662 GCCTAATACTCCCTCCGTCC 59.032 60.000 0.00 0.00 0.00 4.79
603 619 1.630223 CCTAATACTCCCTCCGTCCC 58.370 60.000 0.00 0.00 0.00 4.46
604 620 1.133262 CCTAATACTCCCTCCGTCCCA 60.133 57.143 0.00 0.00 0.00 4.37
605 621 2.674420 CTAATACTCCCTCCGTCCCAA 58.326 52.381 0.00 0.00 0.00 4.12
606 622 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
607 623 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
608 624 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
609 625 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
610 626 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
611 627 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
612 628 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
613 629 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
614 630 1.202348 CCTCCGTCCCAAAATTCTTGC 59.798 52.381 0.00 0.00 0.00 4.01
615 631 1.202348 CTCCGTCCCAAAATTCTTGCC 59.798 52.381 0.00 0.00 0.00 4.52
616 632 1.203001 TCCGTCCCAAAATTCTTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
617 633 1.618343 CCGTCCCAAAATTCTTGCCTT 59.382 47.619 0.00 0.00 0.00 4.35
618 634 2.823154 CCGTCCCAAAATTCTTGCCTTA 59.177 45.455 0.00 0.00 0.00 2.69
619 635 3.119495 CCGTCCCAAAATTCTTGCCTTAG 60.119 47.826 0.00 0.00 0.00 2.18
620 636 3.756434 CGTCCCAAAATTCTTGCCTTAGA 59.244 43.478 0.00 0.00 0.00 2.10
621 637 4.399303 CGTCCCAAAATTCTTGCCTTAGAT 59.601 41.667 0.00 0.00 0.00 1.98
622 638 5.105756 CGTCCCAAAATTCTTGCCTTAGATT 60.106 40.000 0.00 0.00 0.00 2.40
623 639 6.572314 CGTCCCAAAATTCTTGCCTTAGATTT 60.572 38.462 0.00 0.00 0.00 2.17
624 640 6.591448 GTCCCAAAATTCTTGCCTTAGATTTG 59.409 38.462 0.00 0.00 29.84 2.32
625 641 6.269769 TCCCAAAATTCTTGCCTTAGATTTGT 59.730 34.615 0.00 0.00 28.79 2.83
626 642 6.591448 CCCAAAATTCTTGCCTTAGATTTGTC 59.409 38.462 0.00 0.00 28.79 3.18
627 643 7.381323 CCAAAATTCTTGCCTTAGATTTGTCT 58.619 34.615 0.00 0.00 28.79 3.41
628 644 8.522830 CCAAAATTCTTGCCTTAGATTTGTCTA 58.477 33.333 0.00 0.00 28.79 2.59
629 645 9.912634 CAAAATTCTTGCCTTAGATTTGTCTAA 57.087 29.630 0.00 0.00 0.00 2.10
634 650 8.420374 TCTTGCCTTAGATTTGTCTAAATACG 57.580 34.615 0.26 0.00 36.66 3.06
635 651 7.494625 TCTTGCCTTAGATTTGTCTAAATACGG 59.505 37.037 0.26 0.00 36.66 4.02
636 652 6.880484 TGCCTTAGATTTGTCTAAATACGGA 58.120 36.000 5.76 0.00 36.66 4.69
637 653 7.506114 TGCCTTAGATTTGTCTAAATACGGAT 58.494 34.615 5.76 0.00 36.66 4.18
638 654 7.990886 TGCCTTAGATTTGTCTAAATACGGATT 59.009 33.333 0.00 0.00 36.66 3.01
669 685 6.278363 TGATAGTAAAAGAATGCGGGTCTAC 58.722 40.000 0.00 0.00 0.00 2.59
679 717 5.128171 AGAATGCGGGTCTACACAGTAAATA 59.872 40.000 0.00 0.00 0.00 1.40
799 841 1.836166 AGCAATAGAGCAGAGGAAGCA 59.164 47.619 0.00 0.00 36.85 3.91
820 862 2.264794 GGAGGACAACGGACGCAT 59.735 61.111 0.00 0.00 0.00 4.73
899 941 3.279434 CAAAGGTTCCTTATCCTTCCCG 58.721 50.000 4.43 0.00 42.38 5.14
932 975 1.978580 TCCTCTTCTTCACAAGGTCCC 59.021 52.381 0.00 0.00 0.00 4.46
1065 1109 5.357032 CCCTGCAAAACGAGGTAATTAATCT 59.643 40.000 0.00 0.00 0.00 2.40
1085 1130 4.295870 TCTAGTCAACACTTTGTACGCAG 58.704 43.478 0.00 0.00 33.62 5.18
1092 1137 4.141855 ACACTTTGTACGCAGCAATTAC 57.858 40.909 0.00 0.00 0.00 1.89
1167 1224 1.009829 CAATGTCGAGGTTAGGCAGC 58.990 55.000 0.00 0.00 0.00 5.25
1206 1266 2.933573 ACGTCGAGGATAAGGATCACT 58.066 47.619 12.85 0.00 33.27 3.41
1230 1290 2.751259 GCTCAAGCAACAAGATCATCCA 59.249 45.455 0.00 0.00 41.59 3.41
1284 1344 2.426024 CGGGATAGACTTCGGAACTTCA 59.574 50.000 0.00 0.00 0.00 3.02
1362 1422 1.279271 ACTTACCCAGCTGCTGTAAGG 59.721 52.381 34.03 24.17 43.55 2.69
1364 1424 0.252513 TACCCAGCTGCTGTAAGGGA 60.253 55.000 26.41 15.62 42.25 4.20
1390 1450 7.027874 TGGTCACTTCTCTACCCATTTTTAT 57.972 36.000 0.00 0.00 31.97 1.40
1430 1595 5.105513 TCCTTATGAGCTTGTTCGTACATCA 60.106 40.000 0.00 0.00 33.44 3.07
1467 1632 1.156736 CTAGGCAGGTTGGACAAACG 58.843 55.000 0.00 0.00 39.91 3.60
1478 1643 1.170290 GGACAAACGACCAACTGGGG 61.170 60.000 0.00 0.00 42.91 4.96
1512 1677 2.470983 AAGCACTCTTCCAGCTTCTC 57.529 50.000 0.00 0.00 44.67 2.87
1527 1692 3.518998 CTCGGCGACATCCCGTCT 61.519 66.667 4.99 0.00 45.71 4.18
1611 1776 3.686016 TGATAGGTTTGCAGACTTTCCC 58.314 45.455 7.38 0.00 0.00 3.97
1619 1784 1.339055 TGCAGACTTTCCCCGAATCAG 60.339 52.381 0.00 0.00 0.00 2.90
1628 1793 2.047061 TCCCCGAATCAGGAATACAGG 58.953 52.381 0.00 0.00 0.00 4.00
1629 1794 2.047061 CCCCGAATCAGGAATACAGGA 58.953 52.381 0.00 0.00 0.00 3.86
1630 1795 2.037772 CCCCGAATCAGGAATACAGGAG 59.962 54.545 0.00 0.00 0.00 3.69
1632 1797 2.366916 CCGAATCAGGAATACAGGAGCT 59.633 50.000 0.00 0.00 0.00 4.09
1633 1798 3.574396 CCGAATCAGGAATACAGGAGCTA 59.426 47.826 0.00 0.00 0.00 3.32
1634 1799 4.321601 CCGAATCAGGAATACAGGAGCTAG 60.322 50.000 0.00 0.00 0.00 3.42
1635 1800 4.279671 CGAATCAGGAATACAGGAGCTAGT 59.720 45.833 0.00 0.00 0.00 2.57
1636 1801 5.221342 CGAATCAGGAATACAGGAGCTAGTT 60.221 44.000 0.00 0.00 0.00 2.24
1638 1803 6.658188 ATCAGGAATACAGGAGCTAGTTAC 57.342 41.667 0.00 0.00 0.00 2.50
1639 1804 4.579340 TCAGGAATACAGGAGCTAGTTACG 59.421 45.833 0.00 0.00 0.00 3.18
1642 1807 6.430308 CAGGAATACAGGAGCTAGTTACGATA 59.570 42.308 0.00 0.00 0.00 2.92
1643 1808 7.002879 AGGAATACAGGAGCTAGTTACGATAA 58.997 38.462 0.00 0.00 0.00 1.75
1644 1809 7.040548 AGGAATACAGGAGCTAGTTACGATAAC 60.041 40.741 0.00 0.00 0.00 1.89
1645 1810 7.040548 GGAATACAGGAGCTAGTTACGATAACT 60.041 40.741 12.76 12.76 0.00 2.24
1646 1811 5.754543 ACAGGAGCTAGTTACGATAACTC 57.245 43.478 11.88 0.00 0.00 3.01
1651 1816 8.404000 CAGGAGCTAGTTACGATAACTCTTTTA 58.596 37.037 11.88 0.00 0.00 1.52
1665 1830 5.344743 ACTCTTTTAGATGATGAAGCCGA 57.655 39.130 0.00 0.00 0.00 5.54
1666 1831 5.923204 ACTCTTTTAGATGATGAAGCCGAT 58.077 37.500 0.00 0.00 0.00 4.18
1667 1832 5.988561 ACTCTTTTAGATGATGAAGCCGATC 59.011 40.000 0.00 0.00 0.00 3.69
1668 1833 5.917462 TCTTTTAGATGATGAAGCCGATCA 58.083 37.500 0.00 0.00 34.37 2.92
1669 1834 6.348498 TCTTTTAGATGATGAAGCCGATCAA 58.652 36.000 0.00 0.00 33.59 2.57
1687 1852 5.684184 CGATCAAATGACCAATGCAATGTAG 59.316 40.000 0.21 0.00 0.00 2.74
1688 1853 5.981088 TCAAATGACCAATGCAATGTAGT 57.019 34.783 0.21 0.00 0.00 2.73
1689 1854 5.953183 TCAAATGACCAATGCAATGTAGTC 58.047 37.500 0.21 2.84 0.00 2.59
1690 1855 4.989279 AATGACCAATGCAATGTAGTCC 57.011 40.909 0.21 0.00 0.00 3.85
1692 1857 2.040947 TGACCAATGCAATGTAGTCCCA 59.959 45.455 0.21 0.00 0.00 4.37
1693 1858 2.423538 GACCAATGCAATGTAGTCCCAC 59.576 50.000 0.21 0.00 0.00 4.61
1761 1928 0.809385 TCTACAACGAGAGCTTCCCG 59.191 55.000 0.00 0.00 0.00 5.14
1788 1955 1.663074 GCCGATGGTCAGCTCGATC 60.663 63.158 0.00 0.00 37.05 3.69
1806 1973 3.084579 GCTCCTGCGAATCACACG 58.915 61.111 0.00 0.00 0.00 4.49
1875 2042 0.960364 AGCATTGTTCGAATGGCGGT 60.960 50.000 0.00 0.00 41.33 5.68
1941 2108 2.682856 GCTTTTGCATGGAGAATACGGA 59.317 45.455 0.00 0.00 46.58 4.69
1944 2111 2.890808 TGCATGGAGAATACGGAGTC 57.109 50.000 0.00 0.00 43.93 3.36
1974 2141 4.833390 ACAACAATACTCTCAAGGTAGCC 58.167 43.478 0.00 0.00 0.00 3.93
2002 2173 7.138736 AGTACATTGTTGCAAATAGTTCACAC 58.861 34.615 0.00 0.00 0.00 3.82
2058 2229 3.297134 TTTCCTGCAATGGATCCTACC 57.703 47.619 14.23 0.00 35.83 3.18
2143 2314 3.814842 CACACATGTTGCCTTCTTCTGTA 59.185 43.478 0.00 0.00 0.00 2.74
2175 2346 0.826062 GTTCCCATTGGCCCAATCAG 59.174 55.000 5.84 0.68 31.05 2.90
2182 2353 2.795231 TTGGCCCAATCAGAGAAGAG 57.205 50.000 0.00 0.00 0.00 2.85
2197 2368 1.661112 GAAGAGGTGCGCTCACAATAC 59.339 52.381 9.73 0.00 44.87 1.89
2368 2548 0.823356 TTCTTGCAGCAGGAACCACC 60.823 55.000 15.67 0.00 39.35 4.61
2383 2563 0.322456 CCACCGATCCAGGAAAAGCA 60.322 55.000 0.00 0.00 34.73 3.91
2397 2577 3.381590 GGAAAAGCAGTGAGTTCCAGTTT 59.618 43.478 12.57 0.00 39.51 2.66
2405 2585 1.154197 GAGTTCCAGTTTGGCCGTAC 58.846 55.000 0.00 0.00 37.47 3.67
2500 2688 5.201713 TCTAATTGATCGATCAGGTGACC 57.798 43.478 25.95 0.00 38.19 4.02
2533 2721 2.161486 GCTCGCGATCAAGCTCGTT 61.161 57.895 10.36 0.00 40.73 3.85
2587 2775 2.687200 TACAGCCACCGCCTGGAT 60.687 61.111 0.00 0.00 43.95 3.41
2662 2850 1.373497 CTTCAGCGACGACCAGCTT 60.373 57.895 0.00 0.00 42.52 3.74
2827 3015 3.220110 CTTGCATGGCATATTGGAGTCT 58.780 45.455 0.00 0.00 38.76 3.24
2873 3063 2.732412 ACTCATGCGCGCTAGATAAT 57.268 45.000 33.29 13.53 0.00 1.28
2874 3064 2.600731 ACTCATGCGCGCTAGATAATC 58.399 47.619 33.29 0.00 0.00 1.75
2875 3065 2.029918 ACTCATGCGCGCTAGATAATCA 60.030 45.455 33.29 8.79 0.00 2.57
2876 3066 2.597748 CTCATGCGCGCTAGATAATCAG 59.402 50.000 33.29 8.11 0.00 2.90
2877 3067 2.029918 TCATGCGCGCTAGATAATCAGT 60.030 45.455 33.29 0.54 0.00 3.41
2880 3070 2.552743 TGCGCGCTAGATAATCAGTAGT 59.447 45.455 33.29 0.00 0.00 2.73
2884 3074 4.093703 CGCGCTAGATAATCAGTAGTAGCT 59.906 45.833 5.56 0.00 30.71 3.32
2885 3075 5.291371 CGCGCTAGATAATCAGTAGTAGCTA 59.709 44.000 5.56 0.00 30.71 3.32
2888 3078 7.642194 GCGCTAGATAATCAGTAGTAGCTATTG 59.358 40.741 0.00 0.00 30.71 1.90
2927 3117 5.066117 TCAGGAGTAGCATGTACGAACTTAG 59.934 44.000 0.00 0.00 0.00 2.18
2954 3144 5.039333 GGCACTGAAATGTTGCTGAATATC 58.961 41.667 0.00 0.00 0.00 1.63
3099 3289 2.114411 GGGGTGCCTGTTCGGAAA 59.886 61.111 0.00 0.00 33.16 3.13
3207 3397 4.592351 TGCCATTTTCTTTTGAATCCCAGA 59.408 37.500 0.00 0.00 38.37 3.86
3217 3407 8.059798 TCTTTTGAATCCCAGAAGAATCATTC 57.940 34.615 0.00 0.00 41.35 2.67
3219 3409 7.779754 TTTGAATCCCAGAAGAATCATTCAA 57.220 32.000 0.00 0.00 38.08 2.69
3221 3411 9.478238 TTTGAATCCCAGAAGAATCATTCAATA 57.522 29.630 0.00 0.00 39.04 1.90
3222 3412 8.687292 TGAATCCCAGAAGAATCATTCAATAG 57.313 34.615 0.00 0.00 29.46 1.73
3224 3418 8.688747 AATCCCAGAAGAATCATTCAATAGTC 57.311 34.615 0.00 0.00 0.00 2.59
3233 3429 7.882755 AGAATCATTCAATAGTCCCCCTTTTA 58.117 34.615 0.00 0.00 0.00 1.52
3241 3437 7.704727 TCAATAGTCCCCCTTTTAAAATGAGA 58.295 34.615 0.09 0.00 0.00 3.27
3243 3439 8.470002 CAATAGTCCCCCTTTTAAAATGAGAAG 58.530 37.037 0.09 0.00 0.00 2.85
3244 3440 5.333581 AGTCCCCCTTTTAAAATGAGAAGG 58.666 41.667 0.09 0.00 38.67 3.46
3252 3448 9.219603 CCCTTTTAAAATGAGAAGGAAAAATCC 57.780 33.333 0.09 0.00 40.86 3.01
3256 3452 9.762933 TTTAAAATGAGAAGGAAAAATCCACAG 57.237 29.630 0.00 0.00 0.00 3.66
3258 3454 3.157087 TGAGAAGGAAAAATCCACAGGC 58.843 45.455 0.00 0.00 0.00 4.85
3261 3457 3.512724 AGAAGGAAAAATCCACAGGCATG 59.487 43.478 0.00 0.00 0.00 4.06
3273 3469 3.845259 GGCATGGCTCGACCGGTA 61.845 66.667 7.34 0.00 43.94 4.02
3293 3489 6.816140 CCGGTAATTGCAATCCTTGTAAATTT 59.184 34.615 13.38 0.00 38.71 1.82
3477 3673 1.337167 GCAAGCCAGCCTAAACCAAAG 60.337 52.381 0.00 0.00 0.00 2.77
3526 3722 1.608590 CAAAGAAAGCCGAAGAAGCCA 59.391 47.619 0.00 0.00 0.00 4.75
3598 3794 6.062749 GGTCCCCTTCTTTAGTCAATAATCC 58.937 44.000 0.00 0.00 0.00 3.01
3716 3912 3.818787 CAGCCAATCGCAGCCCAC 61.819 66.667 0.00 0.00 41.38 4.61
3781 3977 5.121380 ACATAATGCCTCAGGTCTTCAAT 57.879 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.168291 GCTGGAAGGAGCCCGGAG 62.168 72.222 0.73 0.00 32.35 4.63
17 18 4.096003 TACCAAGGAGCTGGCGGC 62.096 66.667 11.19 11.19 40.45 6.53
18 19 2.187946 CTACCAAGGAGCTGGCGG 59.812 66.667 0.00 0.00 40.45 6.13
46 47 4.137872 CGCATGCTTGCCAAGGGG 62.138 66.667 17.13 0.12 46.57 4.79
47 48 4.807039 GCGCATGCTTGCCAAGGG 62.807 66.667 17.13 5.63 46.57 3.95
62 63 0.965866 TATATGAGAGGAGCCCGGCG 60.966 60.000 3.05 0.00 0.00 6.46
63 64 1.267121 TTATATGAGAGGAGCCCGGC 58.733 55.000 0.00 0.00 0.00 6.13
64 65 4.559862 AAATTATATGAGAGGAGCCCGG 57.440 45.455 0.00 0.00 0.00 5.73
65 66 4.938226 GGAAAATTATATGAGAGGAGCCCG 59.062 45.833 0.00 0.00 0.00 6.13
66 67 5.257262 GGGAAAATTATATGAGAGGAGCCC 58.743 45.833 0.00 0.00 0.00 5.19
67 68 5.257262 GGGGAAAATTATATGAGAGGAGCC 58.743 45.833 0.00 0.00 0.00 4.70
68 69 5.257262 GGGGGAAAATTATATGAGAGGAGC 58.743 45.833 0.00 0.00 0.00 4.70
108 109 2.428171 GCCTCTGTACCGGTGTAATACA 59.572 50.000 19.93 12.47 0.00 2.29
109 110 2.428171 TGCCTCTGTACCGGTGTAATAC 59.572 50.000 19.93 7.54 0.00 1.89
110 111 2.737544 TGCCTCTGTACCGGTGTAATA 58.262 47.619 19.93 0.00 0.00 0.98
111 112 1.563924 TGCCTCTGTACCGGTGTAAT 58.436 50.000 19.93 0.00 0.00 1.89
112 113 1.274167 CTTGCCTCTGTACCGGTGTAA 59.726 52.381 19.93 3.87 0.00 2.41
113 114 0.892755 CTTGCCTCTGTACCGGTGTA 59.107 55.000 19.93 4.71 0.00 2.90
114 115 0.830444 TCTTGCCTCTGTACCGGTGT 60.830 55.000 19.93 0.00 0.00 4.16
115 116 0.320374 TTCTTGCCTCTGTACCGGTG 59.680 55.000 19.93 0.00 0.00 4.94
116 117 1.053424 TTTCTTGCCTCTGTACCGGT 58.947 50.000 13.98 13.98 0.00 5.28
117 118 2.076863 CTTTTCTTGCCTCTGTACCGG 58.923 52.381 0.00 0.00 0.00 5.28
118 119 2.767505 ACTTTTCTTGCCTCTGTACCG 58.232 47.619 0.00 0.00 0.00 4.02
119 120 5.333875 CGTAAACTTTTCTTGCCTCTGTACC 60.334 44.000 0.00 0.00 0.00 3.34
120 121 5.235831 ACGTAAACTTTTCTTGCCTCTGTAC 59.764 40.000 0.00 0.00 0.00 2.90
121 122 5.362263 ACGTAAACTTTTCTTGCCTCTGTA 58.638 37.500 0.00 0.00 0.00 2.74
122 123 4.196971 ACGTAAACTTTTCTTGCCTCTGT 58.803 39.130 0.00 0.00 0.00 3.41
123 124 4.813296 ACGTAAACTTTTCTTGCCTCTG 57.187 40.909 0.00 0.00 0.00 3.35
124 125 6.228258 TCATACGTAAACTTTTCTTGCCTCT 58.772 36.000 0.00 0.00 0.00 3.69
125 126 6.476243 TCATACGTAAACTTTTCTTGCCTC 57.524 37.500 0.00 0.00 0.00 4.70
126 127 7.174253 TGAATCATACGTAAACTTTTCTTGCCT 59.826 33.333 0.00 0.00 0.00 4.75
127 128 7.302524 TGAATCATACGTAAACTTTTCTTGCC 58.697 34.615 0.00 0.00 0.00 4.52
128 129 8.722342 TTGAATCATACGTAAACTTTTCTTGC 57.278 30.769 0.00 0.00 0.00 4.01
160 161 3.662247 GGTCATCCCCTCAATACGTAG 57.338 52.381 0.08 0.00 0.00 3.51
173 174 2.632763 ATAGAGCTAGGGGGTCATCC 57.367 55.000 0.00 0.00 44.16 3.51
174 175 3.785364 AGAATAGAGCTAGGGGGTCATC 58.215 50.000 0.00 0.00 44.16 2.92
175 176 3.933239 AGAATAGAGCTAGGGGGTCAT 57.067 47.619 0.00 0.00 44.16 3.06
179 180 5.888982 TTTGTAAGAATAGAGCTAGGGGG 57.111 43.478 0.00 0.00 0.00 5.40
224 225 2.094026 GGGGCACTTCATCAATCCAAAC 60.094 50.000 0.00 0.00 0.00 2.93
289 290 1.024579 CCGGCCGAAAGTATTGTGCT 61.025 55.000 30.73 0.00 0.00 4.40
296 297 3.469739 GGATAAAATCCGGCCGAAAGTA 58.530 45.455 30.73 12.29 40.13 2.24
324 325 1.900486 CTAAAAGGTCACGGAGGGAGT 59.100 52.381 0.00 0.00 0.00 3.85
327 328 2.176889 TCTCTAAAAGGTCACGGAGGG 58.823 52.381 0.00 0.00 0.00 4.30
329 330 5.348997 GTGAAATCTCTAAAAGGTCACGGAG 59.651 44.000 0.00 0.00 0.00 4.63
330 331 5.011738 AGTGAAATCTCTAAAAGGTCACGGA 59.988 40.000 0.00 0.00 37.06 4.69
368 384 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
459 475 9.901172 AATCTAAACTTTATACTCCATCCGTTT 57.099 29.630 0.00 0.00 0.00 3.60
517 533 9.681062 ATGCAGTTATTTACAAATGTAGTACCT 57.319 29.630 0.00 0.00 0.00 3.08
579 595 1.270358 CGGAGGGAGTATTAGGCAAGC 60.270 57.143 0.00 0.00 0.00 4.01
585 601 2.376695 TGGGACGGAGGGAGTATTAG 57.623 55.000 0.00 0.00 0.00 1.73
591 607 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
595 611 1.202348 GGCAAGAATTTTGGGACGGAG 59.798 52.381 0.00 0.00 0.00 4.63
596 612 1.203001 AGGCAAGAATTTTGGGACGGA 60.203 47.619 0.00 0.00 0.00 4.69
597 613 1.256812 AGGCAAGAATTTTGGGACGG 58.743 50.000 0.00 0.00 0.00 4.79
598 614 3.756434 TCTAAGGCAAGAATTTTGGGACG 59.244 43.478 0.00 0.00 0.00 4.79
599 615 5.921962 ATCTAAGGCAAGAATTTTGGGAC 57.078 39.130 0.00 0.00 0.00 4.46
600 616 6.269769 ACAAATCTAAGGCAAGAATTTTGGGA 59.730 34.615 14.87 0.00 33.04 4.37
602 618 7.381323 AGACAAATCTAAGGCAAGAATTTTGG 58.619 34.615 14.87 0.57 33.04 3.28
603 619 9.912634 TTAGACAAATCTAAGGCAAGAATTTTG 57.087 29.630 11.38 11.38 41.58 2.44
608 624 8.879759 CGTATTTAGACAAATCTAAGGCAAGAA 58.120 33.333 0.00 0.00 45.93 2.52
609 625 7.494625 CCGTATTTAGACAAATCTAAGGCAAGA 59.505 37.037 0.00 0.00 45.93 3.02
610 626 7.494625 TCCGTATTTAGACAAATCTAAGGCAAG 59.505 37.037 0.00 0.00 45.93 4.01
611 627 7.332557 TCCGTATTTAGACAAATCTAAGGCAA 58.667 34.615 0.00 0.00 45.93 4.52
612 628 6.880484 TCCGTATTTAGACAAATCTAAGGCA 58.120 36.000 0.00 0.00 45.93 4.75
613 629 7.964604 ATCCGTATTTAGACAAATCTAAGGC 57.035 36.000 0.00 0.00 45.93 4.35
632 648 9.661563 TTCTTTTACTATCATGTGTAAATCCGT 57.338 29.630 15.98 0.00 38.10 4.69
636 652 9.935682 CGCATTCTTTTACTATCATGTGTAAAT 57.064 29.630 15.98 5.33 38.10 1.40
637 653 8.394877 CCGCATTCTTTTACTATCATGTGTAAA 58.605 33.333 13.25 13.25 37.01 2.01
638 654 7.011950 CCCGCATTCTTTTACTATCATGTGTAA 59.988 37.037 0.00 0.00 0.00 2.41
679 717 9.179909 TGTTATATCCGTTATTTTGTCCACAAT 57.820 29.630 0.00 0.00 35.55 2.71
710 748 8.757982 ATGGATGATACATAAGCTGAAGTTTT 57.242 30.769 0.00 0.00 0.00 2.43
799 841 2.932234 CGTCCGTTGTCCTCCAGCT 61.932 63.158 0.00 0.00 0.00 4.24
820 862 3.057033 GCTGGTCTAACTGAACCGAGTAA 60.057 47.826 0.00 0.00 0.00 2.24
932 975 1.835494 TGGTGGTAGGAAGAGACGAG 58.165 55.000 0.00 0.00 0.00 4.18
997 1040 2.496291 GGCTGAGGATTGGCATGGC 61.496 63.158 13.29 13.29 0.00 4.40
1065 1109 2.798283 GCTGCGTACAAAGTGTTGACTA 59.202 45.455 0.00 0.00 38.20 2.59
1085 1130 9.556030 GATACTGTTTAGAAACCAAGTAATTGC 57.444 33.333 0.00 0.00 38.11 3.56
1092 1137 7.848128 TCCCTAGATACTGTTTAGAAACCAAG 58.152 38.462 2.80 0.00 38.11 3.61
1167 1224 4.072088 GACGCAAGGTTCCGCACG 62.072 66.667 0.00 0.00 46.39 5.34
1230 1290 1.678970 GCTGCCGGTTTCATTCCCT 60.679 57.895 1.90 0.00 0.00 4.20
1330 1390 3.552890 GCTGGGTAAGTTCTTTTGCCTTG 60.553 47.826 0.00 0.00 33.80 3.61
1362 1422 1.826096 GGGTAGAGAAGTGACCAGTCC 59.174 57.143 0.00 0.00 34.73 3.85
1364 1424 2.696526 TGGGTAGAGAAGTGACCAGT 57.303 50.000 0.00 0.00 34.73 4.00
1430 1595 4.082125 CCTAGCAAGTCTCCAACCAAAAT 58.918 43.478 0.00 0.00 0.00 1.82
1467 1632 1.002011 GGAGCTTCCCCAGTTGGTC 60.002 63.158 0.00 0.00 0.00 4.02
1478 1643 0.901124 TGCTTCTCTCCAGGAGCTTC 59.099 55.000 12.26 0.00 41.60 3.86
1527 1692 0.327924 AGATTGATGGCCGGTGAACA 59.672 50.000 1.90 0.00 0.00 3.18
1566 1731 5.233083 TGATGAGAGTGGTTGATGAAGTT 57.767 39.130 0.00 0.00 0.00 2.66
1611 1776 2.366916 AGCTCCTGTATTCCTGATTCGG 59.633 50.000 0.00 0.00 0.00 4.30
1619 1784 5.708877 ATCGTAACTAGCTCCTGTATTCC 57.291 43.478 0.00 0.00 0.00 3.01
1629 1794 9.953697 CATCTAAAAGAGTTATCGTAACTAGCT 57.046 33.333 9.44 0.00 0.00 3.32
1630 1795 9.947669 TCATCTAAAAGAGTTATCGTAACTAGC 57.052 33.333 9.44 1.51 0.00 3.42
1636 1801 9.464714 GCTTCATCATCTAAAAGAGTTATCGTA 57.535 33.333 0.00 0.00 0.00 3.43
1638 1803 7.358765 CGGCTTCATCATCTAAAAGAGTTATCG 60.359 40.741 0.00 0.00 0.00 2.92
1639 1804 7.653713 TCGGCTTCATCATCTAAAAGAGTTATC 59.346 37.037 0.00 0.00 0.00 1.75
1642 1807 5.734720 TCGGCTTCATCATCTAAAAGAGTT 58.265 37.500 0.00 0.00 0.00 3.01
1643 1808 5.344743 TCGGCTTCATCATCTAAAAGAGT 57.655 39.130 0.00 0.00 0.00 3.24
1644 1809 5.987953 TGATCGGCTTCATCATCTAAAAGAG 59.012 40.000 0.00 0.00 0.00 2.85
1645 1810 5.917462 TGATCGGCTTCATCATCTAAAAGA 58.083 37.500 0.00 0.00 0.00 2.52
1646 1811 6.609237 TTGATCGGCTTCATCATCTAAAAG 57.391 37.500 0.00 0.00 30.26 2.27
1651 1816 4.514441 GTCATTTGATCGGCTTCATCATCT 59.486 41.667 0.00 0.00 30.26 2.90
1658 1823 3.699067 CATTGGTCATTTGATCGGCTTC 58.301 45.455 0.00 0.00 0.00 3.86
1661 1826 1.134753 TGCATTGGTCATTTGATCGGC 59.865 47.619 0.00 0.00 0.00 5.54
1665 1830 6.406177 GGACTACATTGCATTGGTCATTTGAT 60.406 38.462 12.87 0.00 0.00 2.57
1666 1831 5.105797 GGACTACATTGCATTGGTCATTTGA 60.106 40.000 12.87 0.00 0.00 2.69
1667 1832 5.104374 GGACTACATTGCATTGGTCATTTG 58.896 41.667 12.87 0.00 0.00 2.32
1668 1833 4.160252 GGGACTACATTGCATTGGTCATTT 59.840 41.667 12.87 0.00 0.00 2.32
1669 1834 3.701040 GGGACTACATTGCATTGGTCATT 59.299 43.478 12.87 0.00 0.00 2.57
1687 1852 0.031178 CAGCTTGCACAAAGTGGGAC 59.969 55.000 0.00 0.00 38.25 4.46
1688 1853 1.737355 GCAGCTTGCACAAAGTGGGA 61.737 55.000 0.00 0.00 44.26 4.37
1689 1854 1.300388 GCAGCTTGCACAAAGTGGG 60.300 57.895 0.00 0.00 44.26 4.61
1690 1855 4.331356 GCAGCTTGCACAAAGTGG 57.669 55.556 0.00 0.00 44.26 4.00
1773 1940 3.929389 GCGATCGAGCTGACCATC 58.071 61.111 21.57 0.00 0.00 3.51
1806 1973 2.737376 GACGAACCGGAGCACACC 60.737 66.667 9.46 0.00 0.00 4.16
1875 2042 3.578688 CATCAGTATCGCCGAATCATCA 58.421 45.455 0.00 0.00 0.00 3.07
1941 2108 7.896811 TGAGAGTATTGTTGTAATCACAGACT 58.103 34.615 0.00 0.00 35.67 3.24
1944 2111 7.604164 ACCTTGAGAGTATTGTTGTAATCACAG 59.396 37.037 0.00 0.00 35.67 3.66
1974 2141 5.545658 ACTATTTGCAACAATGTACTCCG 57.454 39.130 0.00 0.00 0.00 4.63
2002 2173 2.167693 TGCCTTCCGTACATAGAACCTG 59.832 50.000 0.00 0.00 0.00 4.00
2058 2229 1.273606 CTGGATCATACCCTACCTGCG 59.726 57.143 0.00 0.00 0.00 5.18
2143 2314 2.593956 GGGAACTCCGGGTGCTCTT 61.594 63.158 0.00 0.00 36.71 2.85
2175 2346 0.319900 TTGTGAGCGCACCTCTTCTC 60.320 55.000 18.33 0.00 44.51 2.87
2182 2353 0.458889 TACCGTATTGTGAGCGCACC 60.459 55.000 18.33 0.50 44.51 5.01
2197 2368 8.079809 AGTGAAACAAAAATATGTTCCTTACCG 58.920 33.333 0.00 0.00 42.49 4.02
2262 2441 5.810587 GCATGTTTAGTCGTCTAAGATGGAA 59.189 40.000 17.22 0.00 37.44 3.53
2264 2443 5.109210 TGCATGTTTAGTCGTCTAAGATGG 58.891 41.667 17.22 7.01 37.44 3.51
2282 2462 4.556942 TCGAAAAGCCTGATAATGCATG 57.443 40.909 0.00 0.00 0.00 4.06
2360 2540 0.326927 TTTCCTGGATCGGTGGTTCC 59.673 55.000 0.00 0.00 33.40 3.62
2368 2548 2.005451 CTCACTGCTTTTCCTGGATCG 58.995 52.381 0.00 0.00 0.00 3.69
2383 2563 0.535102 CGGCCAAACTGGAACTCACT 60.535 55.000 2.24 0.00 40.96 3.41
2397 2577 4.573201 GTGCTTATTAGATTTGTACGGCCA 59.427 41.667 2.24 0.00 0.00 5.36
2405 2585 7.533426 AGAAGTTGCTGTGCTTATTAGATTTG 58.467 34.615 0.00 0.00 0.00 2.32
2479 2663 5.207110 AGGTCACCTGATCGATCAATTAG 57.793 43.478 27.09 18.06 36.18 1.73
2484 2668 1.025041 CGAGGTCACCTGATCGATCA 58.975 55.000 25.80 25.80 37.35 2.92
2489 2673 1.142748 CCAGCGAGGTCACCTGATC 59.857 63.158 0.00 0.00 31.76 2.92
2533 2721 0.888619 CTTCCACACGGACTCTGCTA 59.111 55.000 0.00 0.00 42.67 3.49
2545 2733 1.522668 CGAACCTTGCATCTTCCACA 58.477 50.000 0.00 0.00 0.00 4.17
2554 2742 1.373748 GTAGACGCCGAACCTTGCA 60.374 57.895 0.00 0.00 0.00 4.08
2587 2775 3.680786 CCGACGAGCCACTGGTCA 61.681 66.667 9.85 0.00 38.76 4.02
2619 2807 4.351054 GGAGCACCACACCCCTGG 62.351 72.222 0.00 0.00 37.33 4.45
2666 2854 2.894387 GATGTCCCTGCTCAGCGC 60.894 66.667 0.00 0.00 39.77 5.92
2689 2877 1.007238 TCAAGAGGGGAAGGAGACGAT 59.993 52.381 0.00 0.00 0.00 3.73
2740 2928 0.978146 CGGGGTCAGAGACAGGGAAT 60.978 60.000 0.00 0.00 33.68 3.01
2803 2991 4.535781 ACTCCAATATGCCATGCAAGTAA 58.464 39.130 0.00 0.00 43.62 2.24
2827 3015 2.910479 ACCTCGATCCGCGCCATA 60.910 61.111 0.00 0.00 40.61 2.74
2873 3063 6.997239 TTCTCGAACAATAGCTACTACTGA 57.003 37.500 0.00 0.00 0.00 3.41
2874 3064 7.473366 TCTTTCTCGAACAATAGCTACTACTG 58.527 38.462 0.00 0.00 0.00 2.74
2875 3065 7.627298 TCTTTCTCGAACAATAGCTACTACT 57.373 36.000 0.00 0.00 0.00 2.57
2876 3066 9.947669 TTATCTTTCTCGAACAATAGCTACTAC 57.052 33.333 0.00 0.00 0.00 2.73
2880 3070 9.684448 CTGATTATCTTTCTCGAACAATAGCTA 57.316 33.333 0.00 0.00 0.00 3.32
2884 3074 8.696374 ACTCCTGATTATCTTTCTCGAACAATA 58.304 33.333 0.00 0.00 0.00 1.90
2885 3075 7.560368 ACTCCTGATTATCTTTCTCGAACAAT 58.440 34.615 0.00 0.00 0.00 2.71
2888 3078 6.639279 GCTACTCCTGATTATCTTTCTCGAAC 59.361 42.308 0.00 0.00 0.00 3.95
2903 3093 3.353557 AGTTCGTACATGCTACTCCTGA 58.646 45.455 0.00 0.00 0.00 3.86
2927 3117 0.668401 GCAACATTTCAGTGCCCAGC 60.668 55.000 0.00 0.00 0.00 4.85
2954 3144 0.767375 ACTGGCCTGCACCCATATAG 59.233 55.000 9.95 0.00 0.00 1.31
3099 3289 2.980475 GCCTCTGTCTGCTCTGCT 59.020 61.111 0.00 0.00 0.00 4.24
3207 3397 6.347061 AAGGGGGACTATTGAATGATTCTT 57.653 37.500 6.73 0.00 0.00 2.52
3217 3407 7.954666 TCTCATTTTAAAAGGGGGACTATTG 57.045 36.000 12.24 0.00 0.00 1.90
3219 3409 7.036132 TCCTTCTCATTTTAAAAGGGGGACTAT 60.036 37.037 12.24 0.00 39.02 2.12
3221 3411 5.075900 TCCTTCTCATTTTAAAAGGGGGACT 59.924 40.000 12.24 0.00 39.02 3.85
3222 3412 5.330233 TCCTTCTCATTTTAAAAGGGGGAC 58.670 41.667 12.24 0.00 39.02 4.46
3224 3418 6.680148 TTTCCTTCTCATTTTAAAAGGGGG 57.320 37.500 12.24 9.57 39.02 5.40
3233 3429 6.742363 GCCTGTGGATTTTTCCTTCTCATTTT 60.742 38.462 0.00 0.00 0.00 1.82
3241 3437 2.568509 CCATGCCTGTGGATTTTTCCTT 59.431 45.455 0.00 0.00 42.02 3.36
3243 3439 1.405933 GCCATGCCTGTGGATTTTTCC 60.406 52.381 4.24 0.00 42.02 3.13
3244 3440 1.551883 AGCCATGCCTGTGGATTTTTC 59.448 47.619 4.24 0.00 42.02 2.29
3252 3448 2.821366 GGTCGAGCCATGCCTGTG 60.821 66.667 2.39 0.00 37.17 3.66
3256 3452 2.660258 ATTACCGGTCGAGCCATGCC 62.660 60.000 12.40 0.00 36.97 4.40
3258 3454 0.937304 CAATTACCGGTCGAGCCATG 59.063 55.000 12.40 0.00 36.97 3.66
3261 3457 1.022451 TTGCAATTACCGGTCGAGCC 61.022 55.000 12.40 0.00 0.00 4.70
3460 3656 1.547901 GGTCTTTGGTTTAGGCTGGCT 60.548 52.381 9.28 9.28 0.00 4.75
3477 3673 3.366781 GCTTCCTGAATGCTCTTTTGGTC 60.367 47.826 0.00 0.00 0.00 4.02
3598 3794 1.108727 TGGTTTCTTGCAGCAGTGGG 61.109 55.000 0.00 0.00 0.00 4.61
3716 3912 8.940952 CATTCTAAAAGAGTCTTCTTAGTTGGG 58.059 37.037 21.40 13.02 42.80 4.12
3781 3977 1.077005 CAAATTGGTCCCCTTCCTCCA 59.923 52.381 0.00 0.00 0.00 3.86
3801 3997 2.611292 GCATCAGACTCTGGTTACATGC 59.389 50.000 11.75 11.75 31.51 4.06


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.