Multiple sequence alignment - TraesCS6D01G121500

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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 TraesCS6D01G121500 chr6D 100.000 6554 0 0 1 6554 86552687 86546134 0.000000e+00 12104.0
1 TraesCS6D01G121500 chr6D 85.903 227 24 7 3498 3720 83217864 83218086 1.100000e-57 235.0
2 TraesCS6D01G121500 chr6D 82.213 253 19 10 4307 4557 83221205 83221433 1.860000e-45 195.0
3 TraesCS6D01G121500 chr6D 94.595 74 4 0 4813 4886 83221444 83221517 1.490000e-21 115.0
4 TraesCS6D01G121500 chr6D 83.486 109 18 0 1664 1772 346830454 346830562 1.160000e-17 102.0
5 TraesCS6D01G121500 chr6D 82.883 111 15 2 1664 1772 346830574 346830682 5.410000e-16 97.1
6 TraesCS6D01G121500 chr6A 95.978 4749 129 24 1836 6554 104056449 104051733 0.000000e+00 7655.0
7 TraesCS6D01G121500 chr6A 92.375 918 34 19 843 1736 104057589 104056684 0.000000e+00 1275.0
8 TraesCS6D01G121500 chr6A 85.523 449 49 7 1 448 104058362 104057929 7.750000e-124 455.0
9 TraesCS6D01G121500 chr6A 87.931 174 8 5 669 830 104057935 104057763 6.710000e-45 193.0
10 TraesCS6D01G121500 chr6A 94.203 69 2 1 1769 1837 614534044 614533978 3.230000e-18 104.0
11 TraesCS6D01G121500 chr6A 87.805 82 4 4 1757 1837 104308568 104308492 2.520000e-14 91.6
12 TraesCS6D01G121500 chr6A 100.000 30 0 0 828 857 104057657 104057628 1.000000e-03 56.5
13 TraesCS6D01G121500 chr6B 87.323 2193 200 39 2141 4316 163972785 163970654 0.000000e+00 2438.0
14 TraesCS6D01G121500 chr6B 86.563 1094 113 16 5473 6553 163969480 163968408 0.000000e+00 1175.0
15 TraesCS6D01G121500 chr6B 87.101 783 52 21 724 1461 163974095 163973317 0.000000e+00 841.0
16 TraesCS6D01G121500 chr6B 90.693 548 38 8 4846 5389 163970023 163969485 0.000000e+00 717.0
17 TraesCS6D01G121500 chr6B 84.816 652 69 9 77 728 163975137 163974516 4.310000e-176 628.0
18 TraesCS6D01G121500 chr6B 88.845 502 40 9 4314 4812 163970513 163970025 2.610000e-168 603.0
19 TraesCS6D01G121500 chr6B 84.615 78 9 1 1770 1844 114836363 114836286 2.530000e-09 75.0
20 TraesCS6D01G121500 chr2B 91.064 235 14 3 4314 4547 256585826 256586054 1.770000e-80 311.0
21 TraesCS6D01G121500 chr2B 89.787 235 17 3 4314 4547 535679770 535679998 1.790000e-75 294.0
22 TraesCS6D01G121500 chr3B 89.787 235 17 3 4314 4547 810718887 810719115 1.790000e-75 294.0
23 TraesCS6D01G121500 chr3B 84.615 78 10 1 1771 1848 516636658 516636733 7.050000e-10 76.8
24 TraesCS6D01G121500 chr3B 85.135 74 9 1 1771 1844 641529723 641529794 2.530000e-09 75.0
25 TraesCS6D01G121500 chr7D 74.054 370 79 10 1 365 630379469 630379826 1.150000e-27 135.0
26 TraesCS6D01G121500 chr7D 81.818 110 20 0 10 119 155265856 155265965 7.000000e-15 93.5
27 TraesCS6D01G121500 chr7D 89.552 67 5 1 1771 1837 604972460 604972524 4.210000e-12 84.2
28 TraesCS6D01G121500 chr5A 95.588 68 2 1 1771 1837 376469481 376469548 2.500000e-19 108.0
29 TraesCS6D01G121500 chr1A 95.522 67 3 0 1771 1837 558328726 558328660 2.500000e-19 108.0
30 TraesCS6D01G121500 chr1A 82.727 110 16 3 1664 1772 341174886 341174993 1.950000e-15 95.3
31 TraesCS6D01G121500 chr1B 95.522 67 1 2 1771 1837 129174941 129175005 8.990000e-19 106.0
32 TraesCS6D01G121500 chr5D 94.118 68 4 0 1770 1837 41140036 41139969 3.230000e-18 104.0
33 TraesCS6D01G121500 chr5D 84.848 66 10 0 23 88 451626226 451626291 4.240000e-07 67.6
34 TraesCS6D01G121500 chr3D 83.929 112 14 3 1664 1772 588151752 588151862 3.230000e-18 104.0
35 TraesCS6D01G121500 chr3D 86.957 92 6 5 1751 1837 505937284 505937374 1.500000e-16 99.0
36 TraesCS6D01G121500 chr3D 95.082 61 3 0 1835 1895 223203819 223203759 5.410000e-16 97.1
37 TraesCS6D01G121500 chr3D 74.074 270 55 11 1 267 553726566 553726823 5.410000e-16 97.1
38 TraesCS6D01G121500 chr3D 85.714 91 11 2 1664 1753 393011957 393012046 1.950000e-15 95.3
39 TraesCS6D01G121500 chr3D 100.000 31 0 0 69 99 45022306 45022336 2.550000e-04 58.4
40 TraesCS6D01G121500 chr2D 94.030 67 3 1 1771 1837 10869122 10869057 4.180000e-17 100.0
41 TraesCS6D01G121500 chr2D 78.981 157 22 9 271 421 59822355 59822506 5.410000e-16 97.1
42 TraesCS6D01G121500 chr2D 85.870 92 11 2 1664 1753 623353215 623353306 5.410000e-16 97.1
43 TraesCS6D01G121500 chr2D 88.889 81 3 3 1763 1838 327614819 327614898 1.950000e-15 95.3
44 TraesCS6D01G121500 chrUn 88.095 84 8 2 1835 1918 388800440 388800359 1.500000e-16 99.0
45 TraesCS6D01G121500 chr7A 96.667 60 1 1 1836 1894 579481245 579481186 1.500000e-16 99.0
46 TraesCS6D01G121500 chr3A 88.095 84 8 2 1835 1918 47074 46993 1.500000e-16 99.0
47 TraesCS6D01G121500 chr3A 85.417 96 13 1 1664 1759 733533009 733533103 1.500000e-16 99.0
48 TraesCS6D01G121500 chr3A 86.111 72 7 1 1770 1838 731094873 731094944 2.530000e-09 75.0
49 TraesCS6D01G121500 chr3A 88.525 61 3 1 1782 1838 68364005 68364065 3.280000e-08 71.3
50 TraesCS6D01G121500 chr2A 93.750 64 4 0 1836 1899 718110561 718110624 5.410000e-16 97.1
51 TraesCS6D01G121500 chr2A 93.651 63 3 1 1837 1899 32514091 32514030 7.000000e-15 93.5
52 TraesCS6D01G121500 chr2A 86.667 75 5 1 1774 1843 658150139 658150065 1.960000e-10 78.7
53 TraesCS6D01G121500 chr4A 93.651 63 4 0 1826 1888 215247655 215247717 1.950000e-15 95.3
54 TraesCS6D01G121500 chr4A 91.045 67 6 0 1836 1902 47138023 47138089 2.520000e-14 91.6
55 TraesCS6D01G121500 chr4A 81.739 115 13 4 1664 1772 14736191 14736303 9.050000e-14 89.8
56 TraesCS6D01G121500 chr1D 87.500 80 4 3 1771 1844 400062901 400062980 3.260000e-13 87.9
57 TraesCS6D01G121500 chr1D 73.303 221 46 10 29 241 434598647 434598432 1.180000e-07 69.4
58 TraesCS6D01G121500 chr4B 77.500 120 23 2 267 383 497510971 497510853 1.180000e-07 69.4
59 TraesCS6D01G121500 chr4D 82.353 68 9 1 273 337 401955500 401955433 1.000000e-03 56.5


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 TraesCS6D01G121500 chr6D 86546134 86552687 6553 True 12104.0 12104 100.000000 1 6554 1 chr6D.!!$R1 6553
1 TraesCS6D01G121500 chr6A 104051733 104058362 6629 True 1926.9 7655 92.361400 1 6554 5 chr6A.!!$R3 6553
2 TraesCS6D01G121500 chr6B 163968408 163975137 6729 True 1067.0 2438 87.556833 77 6553 6 chr6B.!!$R2 6476

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
647 648 0.390340 GGCATCGAGCTTCACTCACA 60.390 55.0 6.78 0.00 46.63 3.58 F
1753 2600 0.327924 AATGCCCACACGAATCTCCA 59.672 50.0 0.00 0.00 0.00 3.86 F
1756 2603 0.392998 GCCCACACGAATCTCCATGT 60.393 55.0 0.00 0.00 0.00 3.21 F
3435 4444 0.662619 CCGCACTGTCTTCTTTTGCA 59.337 50.0 0.00 0.00 32.51 4.08 F
3614 4623 1.324740 TTGGGCCTGCTGAATCATGC 61.325 55.0 4.53 0.00 0.00 4.06 F
5414 6603 0.577269 GTGTCTGTTCAGTGCACGTC 59.423 55.0 12.01 4.05 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2438 3437 0.106268 ACACCCATTGCAACTGGTCA 60.106 50.000 16.71 0.00 31.44 4.02 R
3721 4730 2.948979 TGACTGGTGAAATGTTGGTGTC 59.051 45.455 0.00 0.00 0.00 3.67 R
3761 4770 5.163713 GCCAAGAGGAGTAATTGACAATGAC 60.164 44.000 7.51 7.51 36.89 3.06 R
5181 6366 0.393537 CTCCGAAGCTGGATTTGGCT 60.394 55.000 0.32 0.00 37.41 4.75 R
5486 6675 2.680974 AATCACACGCAGGCCACAGT 62.681 55.000 5.01 0.00 0.00 3.55 R
6290 7491 1.350684 TGGCTAGCCACATTCAGAACA 59.649 47.619 32.88 5.00 41.89 3.18 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
23 24 5.823353 GACCTTGTTAATGACAACCGAAAA 58.177 37.500 0.00 0.00 43.13 2.29
30 31 7.190871 TGTTAATGACAACCGAAAAGTCTTTC 58.809 34.615 0.00 0.00 35.43 2.62
56 57 2.747443 GCCCCTAAGGACCAGCTCC 61.747 68.421 0.00 0.00 38.24 4.70
70 71 4.394712 CTCCTTGGAGCCGCGGTT 62.395 66.667 28.70 23.32 0.00 4.44
71 72 4.697756 TCCTTGGAGCCGCGGTTG 62.698 66.667 28.70 8.62 0.00 3.77
73 74 3.423154 CTTGGAGCCGCGGTTGTC 61.423 66.667 28.70 20.17 0.00 3.18
74 75 4.243008 TTGGAGCCGCGGTTGTCA 62.243 61.111 28.70 18.09 0.00 3.58
99 100 1.134521 TGAACCCTTGAATCGATCCGG 60.135 52.381 0.00 0.00 0.00 5.14
111 112 1.227380 GATCCGGAGCGCTTGACAT 60.227 57.895 13.26 1.37 0.00 3.06
120 121 3.812053 GGAGCGCTTGACATCAGATATTT 59.188 43.478 13.26 0.00 0.00 1.40
151 152 2.037902 TGCATGACGAGAAACCCTAACA 59.962 45.455 0.00 0.00 0.00 2.41
153 154 3.689649 GCATGACGAGAAACCCTAACATT 59.310 43.478 0.00 0.00 0.00 2.71
173 174 0.391597 GTCACCCAAGGAGACGACAA 59.608 55.000 0.00 0.00 34.07 3.18
194 195 0.461961 AATCTACACCAGAGGCTCGC 59.538 55.000 9.22 0.00 36.48 5.03
209 210 0.962489 CTCGCCGACTCCATCCTAAT 59.038 55.000 0.00 0.00 0.00 1.73
246 247 3.198853 AGGATCAAAGCCTAGAAGACCAC 59.801 47.826 0.00 0.00 32.92 4.16
268 269 0.392193 CGAAGATGAAGCACTGCCCT 60.392 55.000 0.00 0.00 0.00 5.19
367 368 1.758440 GCGGCATGTAGAGGGGATGA 61.758 60.000 0.00 0.00 0.00 2.92
368 369 0.758734 CGGCATGTAGAGGGGATGAA 59.241 55.000 0.00 0.00 0.00 2.57
427 428 3.432051 CTTCACCCTAGCCGCCGAG 62.432 68.421 0.00 0.00 0.00 4.63
488 489 0.693049 ATGTGGTTGTCCAGTCCTCC 59.307 55.000 0.00 0.00 45.24 4.30
494 495 2.222027 GTTGTCCAGTCCTCCTTGTTG 58.778 52.381 0.00 0.00 0.00 3.33
496 497 0.398318 GTCCAGTCCTCCTTGTTGCT 59.602 55.000 0.00 0.00 0.00 3.91
504 505 4.711846 AGTCCTCCTTGTTGCTTTCTTTTT 59.288 37.500 0.00 0.00 0.00 1.94
510 511 4.501400 CCTTGTTGCTTTCTTTTTCGGGAT 60.501 41.667 0.00 0.00 0.00 3.85
511 512 5.278758 CCTTGTTGCTTTCTTTTTCGGGATA 60.279 40.000 0.00 0.00 0.00 2.59
512 513 5.776173 TGTTGCTTTCTTTTTCGGGATAA 57.224 34.783 0.00 0.00 0.00 1.75
513 514 5.525199 TGTTGCTTTCTTTTTCGGGATAAC 58.475 37.500 0.00 0.00 0.00 1.89
514 515 4.413495 TGCTTTCTTTTTCGGGATAACG 57.587 40.909 0.00 0.00 0.00 3.18
515 516 4.066490 TGCTTTCTTTTTCGGGATAACGA 58.934 39.130 0.00 0.00 41.76 3.85
516 517 4.698304 TGCTTTCTTTTTCGGGATAACGAT 59.302 37.500 0.00 0.00 43.11 3.73
517 518 5.182380 TGCTTTCTTTTTCGGGATAACGATT 59.818 36.000 0.00 0.00 43.11 3.34
518 519 6.090783 GCTTTCTTTTTCGGGATAACGATTT 58.909 36.000 0.00 0.00 43.11 2.17
519 520 6.033513 GCTTTCTTTTTCGGGATAACGATTTG 59.966 38.462 0.00 0.00 43.11 2.32
520 521 6.563222 TTCTTTTTCGGGATAACGATTTGT 57.437 33.333 0.00 0.00 43.11 2.83
521 522 6.563222 TCTTTTTCGGGATAACGATTTGTT 57.437 33.333 0.00 0.00 43.11 2.83
522 523 6.972722 TCTTTTTCGGGATAACGATTTGTTT 58.027 32.000 0.00 0.00 43.11 2.83
523 524 7.427214 TCTTTTTCGGGATAACGATTTGTTTT 58.573 30.769 0.00 0.00 43.11 2.43
524 525 7.921745 TCTTTTTCGGGATAACGATTTGTTTTT 59.078 29.630 0.00 0.00 43.11 1.94
525 526 7.626144 TTTTCGGGATAACGATTTGTTTTTC 57.374 32.000 0.00 0.00 43.11 2.29
526 527 5.943706 TCGGGATAACGATTTGTTTTTCA 57.056 34.783 0.00 0.00 42.09 2.69
527 528 6.503589 TCGGGATAACGATTTGTTTTTCAT 57.496 33.333 0.00 0.00 42.09 2.57
528 529 7.612668 TCGGGATAACGATTTGTTTTTCATA 57.387 32.000 0.00 0.00 42.09 2.15
529 530 8.215926 TCGGGATAACGATTTGTTTTTCATAT 57.784 30.769 0.00 0.00 42.09 1.78
530 531 8.339714 TCGGGATAACGATTTGTTTTTCATATC 58.660 33.333 0.00 0.00 42.09 1.63
536 537 6.008364 CGATTTGTTTTTCATATCGTTGCC 57.992 37.500 10.67 0.00 45.66 4.52
539 540 2.486203 TGTTTTTCATATCGTTGCCGCT 59.514 40.909 0.00 0.00 0.00 5.52
552 553 3.775654 CCGCTGGGGTCCTCTGTC 61.776 72.222 1.98 0.00 0.00 3.51
563 564 1.135333 GTCCTCTGTCTTCGACCATCC 59.865 57.143 0.00 0.00 0.00 3.51
568 569 2.632996 TCTGTCTTCGACCATCCACTTT 59.367 45.455 0.00 0.00 0.00 2.66
609 610 2.159184 TGCTTCTCTGATTCTAGTGGCG 60.159 50.000 0.00 0.00 0.00 5.69
618 619 0.973632 TTCTAGTGGCGCTTTGGAGA 59.026 50.000 5.61 0.00 0.00 3.71
621 622 2.764010 TCTAGTGGCGCTTTGGAGATTA 59.236 45.455 5.61 0.00 0.00 1.75
622 623 2.717639 AGTGGCGCTTTGGAGATTAT 57.282 45.000 7.64 0.00 0.00 1.28
630 631 1.876156 CTTTGGAGATTATGAGGCGGC 59.124 52.381 0.00 0.00 0.00 6.53
646 647 1.416813 CGGCATCGAGCTTCACTCAC 61.417 60.000 6.78 0.00 46.63 3.51
647 648 0.390340 GGCATCGAGCTTCACTCACA 60.390 55.000 6.78 0.00 46.63 3.58
648 649 0.997932 GCATCGAGCTTCACTCACAG 59.002 55.000 0.00 0.00 46.63 3.66
649 650 1.638133 CATCGAGCTTCACTCACAGG 58.362 55.000 0.00 0.00 46.63 4.00
652 653 0.668706 CGAGCTTCACTCACAGGGTG 60.669 60.000 0.00 0.00 46.63 4.61
654 655 0.394565 AGCTTCACTCACAGGGTGTC 59.605 55.000 0.00 0.00 36.25 3.67
757 1183 6.248433 AGGATTGACCAACTTTGATACATGT 58.752 36.000 2.69 2.69 42.04 3.21
759 1185 7.233348 AGGATTGACCAACTTTGATACATGTTT 59.767 33.333 2.30 0.00 42.04 2.83
796 1234 4.475028 TGTTTGCTGCATCACGATTTAAG 58.525 39.130 1.84 0.00 0.00 1.85
807 1245 4.462133 TCACGATTTAAGGAAAACACCCA 58.538 39.130 0.00 0.00 0.00 4.51
816 1254 2.430332 AGGAAAACACCCAACACATGTG 59.570 45.455 24.25 24.25 36.11 3.21
870 1469 9.985318 GTTGAGAGAAATGATTACAATCTGAAG 57.015 33.333 3.76 0.00 36.39 3.02
889 1488 6.481313 TCTGAAGATCATCTATCCGCAAAAAG 59.519 38.462 0.00 0.00 34.90 2.27
931 1534 2.755469 CGGGTTCTGGGCATTGGG 60.755 66.667 0.00 0.00 0.00 4.12
1131 1748 1.443981 ACCCTAAACCCTAACCCTCCT 59.556 52.381 0.00 0.00 0.00 3.69
1195 1816 3.228017 GGAGACCCTAGCCGCCTC 61.228 72.222 0.00 0.00 0.00 4.70
1196 1817 2.442272 GAGACCCTAGCCGCCTCA 60.442 66.667 0.00 0.00 0.00 3.86
1197 1818 2.443016 AGACCCTAGCCGCCTCAG 60.443 66.667 0.00 0.00 0.00 3.35
1230 1860 0.675522 CGCCGTACCATTTCCCTGTT 60.676 55.000 0.00 0.00 0.00 3.16
1298 1928 2.330372 CCTCGACCGAGTCCGTGAA 61.330 63.158 16.86 0.00 40.44 3.18
1299 1929 1.134901 CTCGACCGAGTCCGTGAAG 59.865 63.158 10.96 0.00 37.47 3.02
1303 1933 4.052229 CCGAGTCCGTGAAGGCGT 62.052 66.667 0.00 0.00 40.77 5.68
1328 1958 0.463116 CGGTCGATTCGGGGGATTTT 60.463 55.000 6.18 0.00 0.00 1.82
1407 2051 2.029844 GTCAGAGCACGGAGTTGGC 61.030 63.158 0.00 0.00 41.61 4.52
1425 2069 2.026262 TGGCTACCTGTTGATTTCTCCC 60.026 50.000 0.00 0.00 0.00 4.30
1426 2070 2.239907 GGCTACCTGTTGATTTCTCCCT 59.760 50.000 0.00 0.00 0.00 4.20
1609 2255 6.808212 GTGCTTGAAGTGCATAAATGTGTAAT 59.192 34.615 0.00 0.00 42.69 1.89
1674 2320 9.868277 CAATTTTAATAGTTTGATGTGCCCTAA 57.132 29.630 0.00 0.00 0.00 2.69
1705 2351 4.695455 ACATCTAAGTGACCCAATCAAACG 59.305 41.667 0.00 0.00 39.72 3.60
1706 2352 4.345859 TCTAAGTGACCCAATCAAACGT 57.654 40.909 0.00 0.00 39.72 3.99
1753 2600 0.327924 AATGCCCACACGAATCTCCA 59.672 50.000 0.00 0.00 0.00 3.86
1756 2603 0.392998 GCCCACACGAATCTCCATGT 60.393 55.000 0.00 0.00 0.00 3.21
1762 2609 5.997746 CCCACACGAATCTCCATGTAATATT 59.002 40.000 0.00 0.00 0.00 1.28
1787 2634 9.931698 TTAGTGATATACTCCCTCTGTAAAGAA 57.068 33.333 0.00 0.00 40.89 2.52
1788 2635 8.840200 AGTGATATACTCCCTCTGTAAAGAAA 57.160 34.615 0.00 0.00 33.17 2.52
1789 2636 9.440761 AGTGATATACTCCCTCTGTAAAGAAAT 57.559 33.333 0.00 0.00 33.17 2.17
1797 2644 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1798 2645 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1799 2646 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1800 2647 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1801 2648 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1996 2843 9.777297 AAATTAGCAATTTGTTGTTACCTGATT 57.223 25.926 0.00 0.00 39.50 2.57
1999 2846 9.906660 TTAGCAATTTGTTGTTACCTGATTAAG 57.093 29.630 0.00 0.00 0.00 1.85
2076 3038 3.887621 TTATGTACAGACACAGAGGGC 57.112 47.619 0.33 0.00 38.76 5.19
2096 3058 8.105829 AGAGGGCCTCATCTTAAATATTATGTG 58.894 37.037 33.86 0.00 28.47 3.21
2170 3169 5.216566 TGTATAATGTGCGCTTTGACTTC 57.783 39.130 9.73 0.00 0.00 3.01
2297 3296 9.232473 TCACATAACCTATCTATAGCTGTACTG 57.768 37.037 0.00 0.00 0.00 2.74
2307 3306 7.182817 TCTATAGCTGTACTGATTGTTGGTT 57.817 36.000 3.61 0.00 0.00 3.67
2388 3387 7.013655 CAGATGGATCATTACCCAACCTTTAAG 59.986 40.741 0.00 0.00 35.85 1.85
2396 3395 8.098912 TCATTACCCAACCTTTAAGTTAGAGAC 58.901 37.037 2.04 0.00 0.00 3.36
2397 3396 7.622502 TTACCCAACCTTTAAGTTAGAGACT 57.377 36.000 2.04 0.00 41.47 3.24
2460 3459 1.133637 ACCAGTTGCAATGGGTGTACA 60.134 47.619 20.32 0.00 42.48 2.90
2630 3629 1.332640 CGCTACATGCTTCAATCGCTG 60.333 52.381 0.00 0.00 40.11 5.18
2750 3749 7.283354 CCTATCCTTCCTTTATTCACCAAAGTC 59.717 40.741 0.00 0.00 32.23 3.01
3262 4264 6.866010 TTGGCATGAATTAGCTATGTACAG 57.134 37.500 0.33 0.00 0.00 2.74
3318 4320 6.311200 CCTGCATTTAGTTCAACCATTAAAGC 59.689 38.462 0.00 0.00 0.00 3.51
3337 4339 6.743575 AAAGCATCATCTGTAGTTTGTACC 57.256 37.500 0.00 0.00 0.00 3.34
3425 4434 4.927425 TCTCTTTATAACAACCGCACTGTC 59.073 41.667 0.00 0.00 0.00 3.51
3435 4444 0.662619 CCGCACTGTCTTCTTTTGCA 59.337 50.000 0.00 0.00 32.51 4.08
3476 4485 6.713792 AAATTTGTTTTTGTACGCACAAGT 57.286 29.167 0.78 0.00 45.17 3.16
3477 4486 5.694674 ATTTGTTTTTGTACGCACAAGTG 57.305 34.783 0.78 0.00 45.17 3.16
3543 4552 5.833131 GGGCTTTATGGATCTGGAACATTTA 59.167 40.000 0.00 0.00 38.20 1.40
3614 4623 1.324740 TTGGGCCTGCTGAATCATGC 61.325 55.000 4.53 0.00 0.00 4.06
3620 4629 2.857489 GCCTGCTGAATCATGCGAATTC 60.857 50.000 0.00 0.00 0.00 2.17
3721 4730 7.806014 TGTGCTTTTAATTTTAGCCTTCTAACG 59.194 33.333 0.00 0.00 34.71 3.18
3761 4770 4.038402 AGTCATGAAGGCCAAGTGAAAAAG 59.962 41.667 5.01 0.00 0.00 2.27
3773 4782 6.258507 GCCAAGTGAAAAAGTCATTGTCAATT 59.741 34.615 0.00 0.00 38.90 2.32
4193 5225 2.857186 TACTCAAGCTGTGCCATCAA 57.143 45.000 0.00 0.00 0.00 2.57
4239 5271 3.244033 CTCAACAGAGCCTAGGAGTTG 57.756 52.381 14.75 19.14 40.53 3.16
4271 5303 5.079643 GTGAATTATATTGGTCCTGCCCAT 58.920 41.667 0.00 0.00 33.60 4.00
4484 5666 4.036734 TGCTAGCTTCCTTTTCTTGTGTTG 59.963 41.667 17.23 0.00 0.00 3.33
4712 5896 9.021807 CCTAAATCCTGCTGATAATTGAATCAT 57.978 33.333 0.00 0.00 35.40 2.45
4763 5947 5.059404 ACTGGCAATGCATAACTAACAAC 57.941 39.130 7.79 0.00 0.00 3.32
4795 5979 9.180678 GTTTGGTGTACTTGAACTTTTATCATG 57.819 33.333 0.00 0.00 0.00 3.07
4856 6040 3.940852 TGTGTCATACTGCATGGATTCAC 59.059 43.478 0.00 0.00 35.16 3.18
5039 6224 9.740239 TCTCTATGATTACGTTACATGTAAACC 57.260 33.333 19.63 7.89 33.75 3.27
5181 6366 1.079127 GCAAGCCTAGGTTCGAGCA 60.079 57.895 11.31 0.00 0.00 4.26
5334 6522 6.877611 TTGTGATCAAACTAGGGAACTTTC 57.122 37.500 0.00 0.00 43.67 2.62
5414 6603 0.577269 GTGTCTGTTCAGTGCACGTC 59.423 55.000 12.01 4.05 0.00 4.34
5442 6631 5.791336 TCATGGCGAATGTCTATTCTAGT 57.209 39.130 0.00 0.00 40.43 2.57
5486 6675 2.637382 TGTCCTCAGTGGCTGTTCAATA 59.363 45.455 0.00 0.00 35.26 1.90
5539 6728 5.221126 GGATGCTTGGGAGTCATTTGAATAC 60.221 44.000 0.00 0.00 0.00 1.89
5560 6749 3.638160 ACATCACAAATCTGCCACAAACT 59.362 39.130 0.00 0.00 0.00 2.66
5566 6755 2.664402 ATCTGCCACAAACTGGAGTT 57.336 45.000 0.00 0.00 43.95 3.01
5567 6756 3.788227 ATCTGCCACAAACTGGAGTTA 57.212 42.857 0.00 0.00 43.95 2.24
5641 6830 9.677567 TGACAACTTAAGATTTATTTGACTTGC 57.322 29.630 10.09 0.00 0.00 4.01
5643 6837 9.683069 ACAACTTAAGATTTATTTGACTTGCAG 57.317 29.630 10.09 0.00 0.00 4.41
5647 6841 6.830873 AAGATTTATTTGACTTGCAGCTCT 57.169 33.333 0.00 0.00 0.00 4.09
5648 6842 6.192234 AGATTTATTTGACTTGCAGCTCTG 57.808 37.500 0.00 0.00 0.00 3.35
5668 6862 2.182014 GCTTGAACAACCAACGAACAC 58.818 47.619 0.00 0.00 0.00 3.32
5692 6887 6.986817 ACGATTCCACATATTCCTCTAACAAG 59.013 38.462 0.00 0.00 0.00 3.16
5727 6926 2.054799 GGCTATGGGGTGATGAGGTAA 58.945 52.381 0.00 0.00 0.00 2.85
5793 6992 4.376819 GCTACAACAGCGATAAGATGATGC 60.377 45.833 0.00 0.00 41.84 3.91
5794 6993 3.801698 ACAACAGCGATAAGATGATGCT 58.198 40.909 0.00 0.00 41.84 3.79
5864 7063 2.459934 GCAAAGAACCACAAAGAACCG 58.540 47.619 0.00 0.00 0.00 4.44
5873 7072 1.971695 CAAAGAACCGGGACAGGCC 60.972 63.158 6.32 0.00 33.69 5.19
5885 7084 0.947244 GACAGGCCACACACAAAGAG 59.053 55.000 5.01 0.00 0.00 2.85
5926 7125 2.825532 GACCAACCCATGCAGTGTAATT 59.174 45.455 0.00 0.00 0.00 1.40
6055 7254 2.716424 TGTCCTTGGGTTCCTGAAAGAT 59.284 45.455 0.00 0.00 34.07 2.40
6064 7263 3.760684 GGTTCCTGAAAGATGTCAAGCAT 59.239 43.478 0.00 0.00 41.24 3.79
6085 7284 1.580059 CCTGTTAGTGAAGGGGGCTA 58.420 55.000 0.00 0.00 0.00 3.93
6115 7314 6.883756 TCATATCAAGCATACCAACAGAACAA 59.116 34.615 0.00 0.00 0.00 2.83
6142 7341 5.817296 GCAAAAGAACAGAAGGAAATTGGTT 59.183 36.000 0.00 0.00 0.00 3.67
6163 7362 7.891561 TGGTTTGGGTTGATTCAGTTTTATAG 58.108 34.615 0.00 0.00 0.00 1.31
6239 7438 6.418101 TCTGGATCTTGAGGGAAACTTAATG 58.582 40.000 0.00 0.00 0.00 1.90
6269 7470 4.232221 CAAAATGCGCTTGAGAAACAGAT 58.768 39.130 9.73 0.00 0.00 2.90
6290 7491 1.600636 CACAGTGCGGGGTCATTGT 60.601 57.895 0.00 0.00 37.39 2.71
6292 7493 1.600636 CAGTGCGGGGTCATTGTGT 60.601 57.895 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.512741 GCAGAAAGACTTTTCGGTTGTCATTA 60.513 38.462 1.12 0.00 45.84 1.90
17 18 3.558505 CACATGCAGAAAGACTTTTCGG 58.441 45.455 1.12 0.00 45.84 4.30
18 19 2.975851 GCACATGCAGAAAGACTTTTCG 59.024 45.455 1.12 0.00 45.84 3.46
20 21 2.036346 GGGCACATGCAGAAAGACTTTT 59.964 45.455 6.15 0.00 44.36 2.27
21 22 1.615392 GGGCACATGCAGAAAGACTTT 59.385 47.619 6.15 0.00 44.36 2.66
23 24 0.610232 GGGGCACATGCAGAAAGACT 60.610 55.000 6.15 0.00 44.36 3.24
30 31 0.749454 GTCCTTAGGGGCACATGCAG 60.749 60.000 6.15 0.00 44.36 4.41
56 57 3.423154 GACAACCGCGGCTCCAAG 61.423 66.667 28.58 11.30 0.00 3.61
57 58 3.545124 ATGACAACCGCGGCTCCAA 62.545 57.895 28.58 9.25 0.00 3.53
59 60 2.746277 AATGACAACCGCGGCTCC 60.746 61.111 28.58 12.87 0.00 4.70
61 62 1.896660 AACAATGACAACCGCGGCT 60.897 52.632 28.58 11.40 0.00 5.52
62 63 1.729131 CAACAATGACAACCGCGGC 60.729 57.895 28.58 9.70 0.00 6.53
63 64 0.309302 TTCAACAATGACAACCGCGG 59.691 50.000 26.86 26.86 34.61 6.46
64 65 1.394697 GTTCAACAATGACAACCGCG 58.605 50.000 0.00 0.00 34.61 6.46
65 66 1.601914 GGGTTCAACAATGACAACCGC 60.602 52.381 0.00 0.00 37.34 5.68
66 67 1.953686 AGGGTTCAACAATGACAACCG 59.046 47.619 0.00 0.00 37.34 4.44
67 68 3.383185 TCAAGGGTTCAACAATGACAACC 59.617 43.478 0.00 0.00 36.23 3.77
68 69 4.647424 TCAAGGGTTCAACAATGACAAC 57.353 40.909 0.00 0.00 34.61 3.32
69 70 5.507149 CGATTCAAGGGTTCAACAATGACAA 60.507 40.000 0.00 0.00 34.61 3.18
70 71 4.023279 CGATTCAAGGGTTCAACAATGACA 60.023 41.667 0.00 0.00 34.61 3.58
71 72 4.215399 TCGATTCAAGGGTTCAACAATGAC 59.785 41.667 0.00 0.00 34.61 3.06
72 73 4.393834 TCGATTCAAGGGTTCAACAATGA 58.606 39.130 0.00 0.00 0.00 2.57
73 74 4.764679 TCGATTCAAGGGTTCAACAATG 57.235 40.909 0.00 0.00 0.00 2.82
74 75 4.399303 GGATCGATTCAAGGGTTCAACAAT 59.601 41.667 0.00 0.00 0.00 2.71
99 100 5.415415 AAAATATCTGATGTCAAGCGCTC 57.585 39.130 12.06 0.00 0.00 5.03
111 112 5.681337 TGCACAACGACAAAAATATCTGA 57.319 34.783 0.00 0.00 0.00 3.27
120 121 1.260297 CTCGTCATGCACAACGACAAA 59.740 47.619 18.42 2.39 42.49 2.83
151 152 1.002087 GTCGTCTCCTTGGGTGACAAT 59.998 52.381 15.79 0.00 43.78 2.71
153 154 0.757561 TGTCGTCTCCTTGGGTGACA 60.758 55.000 15.79 8.07 43.78 3.58
173 174 2.028130 CGAGCCTCTGGTGTAGATTCT 58.972 52.381 0.00 0.00 34.21 2.40
209 210 4.705110 TGATCCTTCTCAAGTTTGTCCA 57.295 40.909 0.00 0.00 0.00 4.02
246 247 1.005340 GCAGTGCTTCATCTTCGAGG 58.995 55.000 8.18 0.00 0.00 4.63
268 269 5.221783 GGTTAGGGTTTTTCAGTCCTCACTA 60.222 44.000 0.00 0.00 0.00 2.74
343 344 2.490148 CCTCTACATGCCGCTCCGA 61.490 63.158 0.00 0.00 0.00 4.55
349 350 0.758734 TTCATCCCCTCTACATGCCG 59.241 55.000 0.00 0.00 0.00 5.69
367 368 1.906574 TCTGACTAGCCCGTGGATTTT 59.093 47.619 0.00 0.00 0.00 1.82
368 369 1.482593 CTCTGACTAGCCCGTGGATTT 59.517 52.381 0.00 0.00 0.00 2.17
427 428 2.781595 TTCCTTCCTCTCAACGGCGC 62.782 60.000 6.90 0.00 0.00 6.53
488 489 4.040445 TCCCGAAAAAGAAAGCAACAAG 57.960 40.909 0.00 0.00 0.00 3.16
494 495 4.673534 TCGTTATCCCGAAAAAGAAAGC 57.326 40.909 0.00 0.00 33.15 3.51
496 497 6.972722 ACAAATCGTTATCCCGAAAAAGAAA 58.027 32.000 0.00 0.00 40.73 2.52
504 505 5.943706 TGAAAAACAAATCGTTATCCCGA 57.056 34.783 0.00 0.00 41.73 5.14
510 511 7.271653 GGCAACGATATGAAAAACAAATCGTTA 59.728 33.333 17.70 0.00 46.85 3.18
512 513 5.571357 GGCAACGATATGAAAAACAAATCGT 59.429 36.000 3.06 3.06 43.77 3.73
513 514 6.008364 GGCAACGATATGAAAAACAAATCG 57.992 37.500 0.00 0.00 36.31 3.34
535 536 3.775654 GACAGAGGACCCCAGCGG 61.776 72.222 0.00 0.00 37.81 5.52
536 537 2.232298 GAAGACAGAGGACCCCAGCG 62.232 65.000 0.00 0.00 0.00 5.18
539 540 1.463375 TCGAAGACAGAGGACCCCA 59.537 57.895 0.00 0.00 0.00 4.96
563 564 1.066257 GCACAGTGGCCACAAAGTG 59.934 57.895 33.73 33.73 35.47 3.16
568 569 0.106967 TTGTTAGCACAGTGGCCACA 60.107 50.000 36.39 13.24 33.22 4.17
575 576 3.750130 CAGAGAAGCATTGTTAGCACAGT 59.250 43.478 0.00 0.00 33.22 3.55
577 578 4.006780 TCAGAGAAGCATTGTTAGCACA 57.993 40.909 0.00 0.00 0.00 4.57
609 610 1.876156 CCGCCTCATAATCTCCAAAGC 59.124 52.381 0.00 0.00 0.00 3.51
618 619 0.671781 GCTCGATGCCGCCTCATAAT 60.672 55.000 0.00 0.00 35.15 1.28
621 622 2.985512 GAAGCTCGATGCCGCCTCAT 62.986 60.000 0.00 0.00 44.23 2.90
622 623 3.723235 GAAGCTCGATGCCGCCTCA 62.723 63.158 0.00 0.00 44.23 3.86
652 653 3.291101 TTCTACACCCGCCAGCGAC 62.291 63.158 14.67 0.00 42.83 5.19
654 655 2.501223 TTCTTCTACACCCGCCAGCG 62.501 60.000 4.75 4.75 39.44 5.18
661 662 4.806247 CGATGTCATCTTTCTTCTACACCC 59.194 45.833 11.04 0.00 0.00 4.61
728 729 9.613428 TGTATCAAAGTTGGTCAATCCTTATAG 57.387 33.333 0.00 0.00 37.07 1.31
796 1234 2.167487 ACACATGTGTTGGGTGTTTTCC 59.833 45.455 25.76 0.00 41.66 3.13
822 1260 7.823799 TCAACATGTGTGTGACATATACATTCT 59.176 33.333 11.09 0.72 43.96 2.40
823 1261 7.973601 TCAACATGTGTGTGACATATACATTC 58.026 34.615 11.09 0.00 43.96 2.67
826 1264 6.696411 TCTCAACATGTGTGTGACATATACA 58.304 36.000 0.00 4.33 43.96 2.29
870 1469 6.377327 TTTCCTTTTTGCGGATAGATGATC 57.623 37.500 0.00 0.00 0.00 2.92
906 1509 2.885644 CCAGAACCCGCGACGATG 60.886 66.667 8.23 0.00 0.00 3.84
1001 1604 1.548582 CCAGGTGGAATGGAAAGCAGT 60.549 52.381 0.00 0.00 40.51 4.40
1230 1860 0.036765 CTCAAAATCGGGACACGGGA 60.037 55.000 0.00 0.00 44.45 5.14
1298 1928 2.430382 AATCGACCGAACACACGCCT 62.430 55.000 0.00 0.00 0.00 5.52
1299 1929 1.952266 GAATCGACCGAACACACGCC 61.952 60.000 0.00 0.00 0.00 5.68
1303 1933 1.080366 CCCGAATCGACCGAACACA 60.080 57.895 3.36 0.00 0.00 3.72
1397 2041 0.034896 CAACAGGTAGCCAACTCCGT 59.965 55.000 0.00 0.00 0.00 4.69
1407 2051 7.996098 TTAAAAGGGAGAAATCAACAGGTAG 57.004 36.000 0.00 0.00 0.00 3.18
1425 2069 7.765360 TGGCCATATTCTGCAGAAATTTAAAAG 59.235 33.333 31.55 15.81 37.61 2.27
1426 2070 7.619050 TGGCCATATTCTGCAGAAATTTAAAA 58.381 30.769 31.55 13.73 37.61 1.52
1609 2255 7.450074 ACTGTCTTAGTTGGTCATTGTATCAA 58.550 34.615 0.00 0.00 35.67 2.57
1674 2320 5.754782 TGGGTCACTTAGATGTGCAATAAT 58.245 37.500 0.00 0.00 37.81 1.28
1737 2584 0.392998 ACATGGAGATTCGTGTGGGC 60.393 55.000 0.00 0.00 35.75 5.36
1762 2609 9.931698 TTTCTTTACAGAGGGAGTATATCACTA 57.068 33.333 0.00 0.00 43.76 2.74
1771 2618 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
1772 2619 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
1773 2620 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
1774 2621 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
1775 2622 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1812 2659 8.925338 CCTACTCCCTCTGTAAACAAATATACT 58.075 37.037 0.00 0.00 0.00 2.12
1813 2660 8.921205 TCCTACTCCCTCTGTAAACAAATATAC 58.079 37.037 0.00 0.00 0.00 1.47
1814 2661 8.921205 GTCCTACTCCCTCTGTAAACAAATATA 58.079 37.037 0.00 0.00 0.00 0.86
1815 2662 7.624077 AGTCCTACTCCCTCTGTAAACAAATAT 59.376 37.037 0.00 0.00 0.00 1.28
1816 2663 6.958192 AGTCCTACTCCCTCTGTAAACAAATA 59.042 38.462 0.00 0.00 0.00 1.40
1817 2664 5.785940 AGTCCTACTCCCTCTGTAAACAAAT 59.214 40.000 0.00 0.00 0.00 2.32
1818 2665 5.152934 AGTCCTACTCCCTCTGTAAACAAA 58.847 41.667 0.00 0.00 0.00 2.83
1819 2666 4.748701 AGTCCTACTCCCTCTGTAAACAA 58.251 43.478 0.00 0.00 0.00 2.83
1820 2667 4.399483 AGTCCTACTCCCTCTGTAAACA 57.601 45.455 0.00 0.00 0.00 2.83
1821 2668 6.186234 TCTAAGTCCTACTCCCTCTGTAAAC 58.814 44.000 0.00 0.00 0.00 2.01
1822 2669 6.398655 TCTAAGTCCTACTCCCTCTGTAAA 57.601 41.667 0.00 0.00 0.00 2.01
1823 2670 6.068971 ACATCTAAGTCCTACTCCCTCTGTAA 60.069 42.308 0.00 0.00 0.00 2.41
1824 2671 5.432390 ACATCTAAGTCCTACTCCCTCTGTA 59.568 44.000 0.00 0.00 0.00 2.74
1825 2672 4.230964 ACATCTAAGTCCTACTCCCTCTGT 59.769 45.833 0.00 0.00 0.00 3.41
1826 2673 4.582656 CACATCTAAGTCCTACTCCCTCTG 59.417 50.000 0.00 0.00 0.00 3.35
1827 2674 4.798882 CACATCTAAGTCCTACTCCCTCT 58.201 47.826 0.00 0.00 0.00 3.69
1828 2675 3.319689 GCACATCTAAGTCCTACTCCCTC 59.680 52.174 0.00 0.00 0.00 4.30
1829 2676 3.301274 GCACATCTAAGTCCTACTCCCT 58.699 50.000 0.00 0.00 0.00 4.20
1830 2677 3.031736 TGCACATCTAAGTCCTACTCCC 58.968 50.000 0.00 0.00 0.00 4.30
1831 2678 4.737855 TTGCACATCTAAGTCCTACTCC 57.262 45.455 0.00 0.00 0.00 3.85
1832 2679 7.045126 AGTATTGCACATCTAAGTCCTACTC 57.955 40.000 0.00 0.00 0.00 2.59
1833 2680 7.425224 AAGTATTGCACATCTAAGTCCTACT 57.575 36.000 0.00 0.00 0.00 2.57
1834 2681 7.868415 CCTAAGTATTGCACATCTAAGTCCTAC 59.132 40.741 0.00 0.00 0.00 3.18
1999 2846 9.803315 AGAAGGAAAAACTGAACAAGATTAAAC 57.197 29.630 0.00 0.00 0.00 2.01
2096 3058 8.732746 AATCACATAGGGTATACAAACAGAAC 57.267 34.615 5.01 0.00 0.00 3.01
2388 3387 8.354426 ACAAAGAACTACTTGAGAGTCTCTAAC 58.646 37.037 20.64 0.00 38.98 2.34
2438 3437 0.106268 ACACCCATTGCAACTGGTCA 60.106 50.000 16.71 0.00 31.44 4.02
2630 3629 5.122869 TGCAGATAAAGATGTTCTTGCAGTC 59.877 40.000 0.00 0.00 36.71 3.51
3157 4159 9.906660 CATTTGTTATGGCTTACTAAAAAGTGA 57.093 29.630 0.00 0.00 0.00 3.41
3236 4238 6.601217 TGTACATAGCTAATTCATGCCAAACA 59.399 34.615 0.00 0.00 0.00 2.83
3262 4264 5.422214 TCCTTCCCTCTTGACTATTGTTC 57.578 43.478 0.00 0.00 0.00 3.18
3409 4418 3.402628 AGAAGACAGTGCGGTTGTTAT 57.597 42.857 0.00 0.00 0.00 1.89
3425 4434 8.758715 CAAAGAGGAACTTAAATGCAAAAGAAG 58.241 33.333 12.26 6.64 41.55 2.85
3476 4485 6.179756 AGACAATGTATTCCTATGTTGTGCA 58.820 36.000 0.00 0.00 30.70 4.57
3477 4486 6.683974 AGACAATGTATTCCTATGTTGTGC 57.316 37.500 0.00 0.00 30.70 4.57
3620 4629 5.831525 TGATTTCATGGAAGGATCATGGAAG 59.168 40.000 0.00 0.00 41.67 3.46
3721 4730 2.948979 TGACTGGTGAAATGTTGGTGTC 59.051 45.455 0.00 0.00 0.00 3.67
3761 4770 5.163713 GCCAAGAGGAGTAATTGACAATGAC 60.164 44.000 7.51 7.51 36.89 3.06
3773 4782 2.009681 TGTCACTGCCAAGAGGAGTA 57.990 50.000 0.00 0.00 36.89 2.59
3820 4829 6.646267 AGAAAGGCAATACAATCCGTAAGTA 58.354 36.000 0.00 0.00 32.59 2.24
3826 4839 6.316390 AGAACTTAGAAAGGCAATACAATCCG 59.684 38.462 0.00 0.00 0.00 4.18
3938 4951 2.787473 TGCTTGGTCCATGTAGAAGG 57.213 50.000 6.62 0.00 0.00 3.46
4148 5180 9.897744 ATTGTGTCATCTACAAAAGTACAAATG 57.102 29.630 0.00 0.00 38.72 2.32
4193 5225 4.353777 TCTAGATTTAGGCTATGGCGGAT 58.646 43.478 0.00 0.00 39.81 4.18
4239 5271 7.339466 AGGACCAATATAATTCACAAGTTGACC 59.661 37.037 10.54 0.00 32.26 4.02
4271 5303 2.167662 TGCAGGAGATCGTACTTCACA 58.832 47.619 0.00 0.00 0.00 3.58
4360 5541 8.132362 GGTGAATAGGATGATAAGTATAGAGCG 58.868 40.741 0.00 0.00 0.00 5.03
4437 5618 7.290842 CAGAATAACACAACATACAGACACAC 58.709 38.462 0.00 0.00 0.00 3.82
4441 5622 6.727824 AGCAGAATAACACAACATACAGAC 57.272 37.500 0.00 0.00 0.00 3.51
4484 5666 5.048504 TCTCTTGCCAAAATCATTCAGTGAC 60.049 40.000 0.00 0.00 40.28 3.67
4712 5896 5.620654 CGGTTAGTTGGACTAAATCTGTCGA 60.621 44.000 2.37 0.00 41.80 4.20
4763 5947 5.365619 AGTTCAAGTACACCAAACCTACTG 58.634 41.667 0.00 0.00 0.00 2.74
4795 5979 1.604278 GGAATGCGGTGAAATAGAGCC 59.396 52.381 0.00 0.00 0.00 4.70
4856 6040 3.004106 CCAAGCAACTTTGTGGAAGAGAG 59.996 47.826 0.00 0.00 38.77 3.20
5039 6224 8.873830 AGTAGTCAAAAGACATCATAAATGACG 58.126 33.333 0.00 0.00 40.51 4.35
5181 6366 0.393537 CTCCGAAGCTGGATTTGGCT 60.394 55.000 0.32 0.00 37.41 4.75
5414 6603 7.095910 AGAATAGACATTCGCCATGAATCTAG 58.904 38.462 0.00 0.00 45.59 2.43
5486 6675 2.680974 AATCACACGCAGGCCACAGT 62.681 55.000 5.01 0.00 0.00 3.55
5539 6728 3.985279 CAGTTTGTGGCAGATTTGTGATG 59.015 43.478 0.00 0.00 0.00 3.07
5560 6749 4.634012 ATGGTTGCTGTAGTTAACTCCA 57.366 40.909 12.39 11.65 0.00 3.86
5641 6830 1.311859 TGGTTGTTCAAGCAGAGCTG 58.688 50.000 12.40 0.00 39.62 4.24
5643 6837 1.597937 CGTTGGTTGTTCAAGCAGAGC 60.598 52.381 15.17 10.12 0.00 4.09
5647 6841 1.813178 TGTTCGTTGGTTGTTCAAGCA 59.187 42.857 12.40 12.40 0.00 3.91
5648 6842 2.182014 GTGTTCGTTGGTTGTTCAAGC 58.818 47.619 7.65 7.65 0.00 4.01
5668 6862 7.169982 GTCTTGTTAGAGGAATATGTGGAATCG 59.830 40.741 0.00 0.00 0.00 3.34
5692 6887 3.511934 CCATAGCCCCTCTGTATAGTGTC 59.488 52.174 0.00 0.00 0.00 3.67
5703 6898 0.768221 TCATCACCCCATAGCCCCTC 60.768 60.000 0.00 0.00 0.00 4.30
5727 6926 3.895232 AGAGTATGTGTTCGAAGGCAT 57.105 42.857 15.71 15.71 0.00 4.40
5794 6993 9.895138 TCAGATAAATTCTTGTGAATCTGATCA 57.105 29.630 8.37 0.00 41.62 2.92
5864 7063 1.454847 TTTGTGTGTGGCCTGTCCC 60.455 57.895 3.32 0.00 0.00 4.46
5873 7072 4.955925 TGTAACCAACTCTTTGTGTGTG 57.044 40.909 0.00 0.00 0.00 3.82
5885 7084 1.737793 CTCCGCTGGATTGTAACCAAC 59.262 52.381 0.00 0.00 36.95 3.77
5926 7125 3.061322 CAAAAACGTCGTGTCTGGGATA 58.939 45.455 0.00 0.00 0.00 2.59
6055 7254 2.153645 CACTAACAGGCATGCTTGACA 58.846 47.619 33.61 19.45 30.96 3.58
6064 7263 2.074967 CCCCCTTCACTAACAGGCA 58.925 57.895 0.00 0.00 0.00 4.75
6085 7284 8.819845 TCTGTTGGTATGCTTGATATGATCTAT 58.180 33.333 0.00 0.00 0.00 1.98
6115 7314 6.484308 CCAATTTCCTTCTGTTCTTTTGCATT 59.516 34.615 0.00 0.00 0.00 3.56
6142 7341 7.450014 TCTTGCTATAAAACTGAATCAACCCAA 59.550 33.333 0.00 0.00 0.00 4.12
6163 7362 6.441093 TTGAAGAATGTGGTATCATCTTGC 57.559 37.500 0.00 0.00 0.00 4.01
6173 7372 5.625150 AGAAGTAGCTTTGAAGAATGTGGT 58.375 37.500 0.00 0.00 0.00 4.16
6239 7438 2.053627 CAAGCGCATTTTGGTCACTTC 58.946 47.619 11.47 0.00 0.00 3.01
6290 7491 1.350684 TGGCTAGCCACATTCAGAACA 59.649 47.619 32.88 5.00 41.89 3.18
6292 7493 1.630369 ACTGGCTAGCCACATTCAGAA 59.370 47.619 32.88 8.47 41.89 3.02


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

AutoCloner maintained by Alex Coulton.