Multiple sequence alignment - TraesCS5A01G327300

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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 TraesCS5A01G327300 chr5A 100.000 2669 0 0 1 2669 537018369 537021037 0.000000e+00 4929.0
1 TraesCS5A01G327300 chr5A 71.806 681 160 25 1958 2621 34325629 34324964 5.910000e-37 165.0
2 TraesCS5A01G327300 chr5B 95.246 1157 35 4 594 1730 511346419 511347575 0.000000e+00 1814.0
3 TraesCS5A01G327300 chr5B 86.111 288 21 10 46 327 511343125 511343399 2.600000e-75 292.0
4 TraesCS5A01G327300 chr5B 93.793 145 6 2 517 661 511346287 511346428 5.790000e-52 215.0
5 TraesCS5A01G327300 chr5B 86.207 174 14 9 343 514 511343385 511343550 2.110000e-41 180.0
6 TraesCS5A01G327300 chr5B 90.698 43 4 0 2 44 511342924 511342966 1.030000e-04 58.4
7 TraesCS5A01G327300 chr1B 86.278 1115 120 19 595 1678 561754086 561752974 0.000000e+00 1181.0
8 TraesCS5A01G327300 chr1B 90.769 65 4 2 1727 1789 35032172 35032236 4.730000e-13 86.1
9 TraesCS5A01G327300 chr1D 87.739 995 111 7 693 1678 415435975 415434983 0.000000e+00 1151.0
10 TraesCS5A01G327300 chr1D 77.108 332 56 13 1989 2310 319003490 319003811 9.820000e-40 174.0
11 TraesCS5A01G327300 chr1D 77.055 292 51 10 1983 2265 308129398 308129682 1.280000e-33 154.0
12 TraesCS5A01G327300 chr1A 87.311 993 119 4 693 1678 513159420 513158428 0.000000e+00 1129.0
13 TraesCS5A01G327300 chr1A 93.651 63 4 0 1727 1789 570044065 570044003 7.870000e-16 95.3
14 TraesCS5A01G327300 chr6A 86.701 985 118 6 693 1665 1031368 1030385 0.000000e+00 1081.0
15 TraesCS5A01G327300 chr6A 73.500 800 167 36 1865 2653 375383149 375382384 7.330000e-66 261.0
16 TraesCS5A01G327300 chr6D 85.787 985 127 8 693 1665 1587505 1588488 0.000000e+00 1031.0
17 TraesCS5A01G327300 chr6B 84.975 985 143 2 693 1672 4943422 4944406 0.000000e+00 994.0
18 TraesCS5A01G327300 chr6B 76.117 515 101 14 1820 2317 171340143 171339634 1.590000e-62 250.0
19 TraesCS5A01G327300 chr6B 78.912 147 28 2 697 843 130318000 130317857 2.190000e-16 97.1
20 TraesCS5A01G327300 chr6B 90.909 66 4 1 1726 1789 609649391 609649456 1.320000e-13 87.9
21 TraesCS5A01G327300 chr2D 75.561 757 162 15 1865 2613 640637589 640636848 4.230000e-93 351.0
22 TraesCS5A01G327300 chr2D 82.143 168 27 2 692 859 578939052 578938888 9.960000e-30 141.0
23 TraesCS5A01G327300 chr5D 78.738 301 56 6 2019 2315 519201130 519201426 7.540000e-46 195.0
24 TraesCS5A01G327300 chr5D 75.477 367 66 16 2041 2398 344069579 344069930 9.890000e-35 158.0
25 TraesCS5A01G327300 chr7B 75.059 425 83 14 1983 2398 317334698 317335108 2.730000e-40 176.0
26 TraesCS5A01G327300 chr7B 75.177 282 60 9 1989 2264 408410619 408410896 1.000000e-24 124.0
27 TraesCS5A01G327300 chr7B 90.769 65 4 1 1727 1789 735308362 735308298 4.730000e-13 86.1
28 TraesCS5A01G327300 chr7B 90.769 65 4 1 1727 1789 735806804 735806868 4.730000e-13 86.1
29 TraesCS5A01G327300 chr2B 75.000 420 81 15 1983 2393 221132667 221133071 3.530000e-39 172.0
30 TraesCS5A01G327300 chr2B 73.013 478 97 22 2118 2584 621080601 621080145 3.580000e-29 139.0
31 TraesCS5A01G327300 chr2B 82.099 162 26 2 698 859 695862340 695862182 4.630000e-28 135.0
32 TraesCS5A01G327300 chr3D 78.495 279 39 16 1983 2251 254650549 254650816 2.130000e-36 163.0
33 TraesCS5A01G327300 chr3D 71.704 622 136 26 2040 2646 355811876 355811280 1.290000e-28 137.0
34 TraesCS5A01G327300 chr7D 74.447 407 84 12 2040 2440 282012812 282012420 9.890000e-35 158.0
35 TraesCS5A01G327300 chr2A 82.738 168 26 2 692 859 716491205 716491041 2.140000e-31 147.0
36 TraesCS5A01G327300 chrUn 93.651 63 4 0 1727 1789 1714604 1714542 7.870000e-16 95.3
37 TraesCS5A01G327300 chrUn 93.651 63 4 0 1727 1789 189301590 189301528 7.870000e-16 95.3
38 TraesCS5A01G327300 chrUn 91.429 70 4 1 1722 1789 255004424 255004493 7.870000e-16 95.3
39 TraesCS5A01G327300 chr3A 90.769 65 4 1 1727 1789 204128010 204128074 4.730000e-13 86.1


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 TraesCS5A01G327300 chr5A 537018369 537021037 2668 False 4929.00 4929 100.000 1 2669 1 chr5A.!!$F1 2668
1 TraesCS5A01G327300 chr5B 511342924 511347575 4651 False 511.88 1814 90.411 2 1730 5 chr5B.!!$F1 1728
2 TraesCS5A01G327300 chr1B 561752974 561754086 1112 True 1181.00 1181 86.278 595 1678 1 chr1B.!!$R1 1083
3 TraesCS5A01G327300 chr1D 415434983 415435975 992 True 1151.00 1151 87.739 693 1678 1 chr1D.!!$R1 985
4 TraesCS5A01G327300 chr1A 513158428 513159420 992 True 1129.00 1129 87.311 693 1678 1 chr1A.!!$R1 985
5 TraesCS5A01G327300 chr6A 1030385 1031368 983 True 1081.00 1081 86.701 693 1665 1 chr6A.!!$R1 972
6 TraesCS5A01G327300 chr6A 375382384 375383149 765 True 261.00 261 73.500 1865 2653 1 chr6A.!!$R2 788
7 TraesCS5A01G327300 chr6D 1587505 1588488 983 False 1031.00 1031 85.787 693 1665 1 chr6D.!!$F1 972
8 TraesCS5A01G327300 chr6B 4943422 4944406 984 False 994.00 994 84.975 693 1672 1 chr6B.!!$F1 979
9 TraesCS5A01G327300 chr6B 171339634 171340143 509 True 250.00 250 76.117 1820 2317 1 chr6B.!!$R2 497
10 TraesCS5A01G327300 chr2D 640636848 640637589 741 True 351.00 351 75.561 1865 2613 1 chr2D.!!$R2 748

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
514 675 0.170116 CACTCACTCTCCACTCGCTC 59.83 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 4785 0.034767 TAAGAGAGACGCGGGAGGAA 60.035 55.0 12.47 0.0 0.0 3.36 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
30 31 3.733684 GCGTGCCAGGTTTATGTAAATGG 60.734 47.826 0.00 2.26 31.60 3.16
32 33 4.338118 CGTGCCAGGTTTATGTAAATGGAT 59.662 41.667 8.59 0.00 30.52 3.41
37 38 6.209391 GCCAGGTTTATGTAAATGGATATGCT 59.791 38.462 8.59 0.00 30.52 3.79
39 40 9.295825 CCAGGTTTATGTAAATGGATATGCTAA 57.704 33.333 0.00 0.00 30.52 3.09
59 217 3.843893 AAAAAGAAAAGGCATGCAGGT 57.156 38.095 21.36 0.00 0.00 4.00
89 247 1.370437 CAGCTCCGCTATCCATGCT 59.630 57.895 0.00 0.00 36.40 3.79
118 276 3.592856 TTCAATGTACGCCCGCGGT 62.593 57.895 26.12 8.42 44.69 5.68
122 280 2.791501 AATGTACGCCCGCGGTCTTT 62.792 55.000 26.12 7.75 44.69 2.52
123 281 1.947597 ATGTACGCCCGCGGTCTTTA 61.948 55.000 26.12 6.65 44.69 1.85
124 282 2.160853 GTACGCCCGCGGTCTTTAC 61.161 63.158 26.12 15.16 44.69 2.01
125 283 3.681961 TACGCCCGCGGTCTTTACG 62.682 63.158 26.12 18.67 44.69 3.18
161 319 0.393077 AGGAACACACGAAGACCCAG 59.607 55.000 0.00 0.00 0.00 4.45
162 320 1.228657 GGAACACACGAAGACCCAGC 61.229 60.000 0.00 0.00 0.00 4.85
165 323 1.961277 CACACGAAGACCCAGCACC 60.961 63.158 0.00 0.00 0.00 5.01
176 334 0.607489 CCCAGCACCCTTGACTTGAG 60.607 60.000 0.00 0.00 0.00 3.02
180 338 1.845809 GCACCCTTGACTTGAGCACG 61.846 60.000 0.00 0.00 0.00 5.34
213 371 3.688272 CATTGATTGCTGTCATTCGACC 58.312 45.455 0.00 0.00 41.85 4.79
228 386 6.535150 GTCATTCGACCTCATGAATTAACTGA 59.465 38.462 0.00 0.00 36.02 3.41
232 390 6.276091 TCGACCTCATGAATTAACTGATGAG 58.724 40.000 6.42 6.42 40.97 2.90
236 394 6.820656 ACCTCATGAATTAACTGATGAGTGAC 59.179 38.462 11.53 0.00 40.08 3.67
242 400 2.732412 AACTGATGAGTGACGTCCAG 57.268 50.000 14.12 13.77 33.92 3.86
257 415 4.248859 ACGTCCAGAAAGATGTCATGAAG 58.751 43.478 0.00 0.00 29.89 3.02
272 430 0.400213 TGAAGTTACTGGGCTGGTGG 59.600 55.000 0.00 0.00 0.00 4.61
273 431 0.322546 GAAGTTACTGGGCTGGTGGG 60.323 60.000 0.00 0.00 0.00 4.61
280 441 1.306654 TGGGCTGGTGGGGTACTAG 60.307 63.158 0.00 0.00 40.57 2.57
292 453 1.334243 GGGTACTAGTACTGCTGCGAG 59.666 57.143 27.71 0.00 36.36 5.03
294 455 2.288458 GGTACTAGTACTGCTGCGAGAG 59.712 54.545 27.71 0.00 36.36 3.20
306 467 2.507992 CGAGAGGGCAGACGCAAG 60.508 66.667 0.00 0.00 41.24 4.01
321 482 3.135414 CGCAAGTTGAGAGAGAGAGAG 57.865 52.381 7.16 0.00 0.00 3.20
322 483 2.746904 CGCAAGTTGAGAGAGAGAGAGA 59.253 50.000 7.16 0.00 0.00 3.10
323 484 3.181507 CGCAAGTTGAGAGAGAGAGAGAG 60.182 52.174 7.16 0.00 0.00 3.20
324 485 4.009675 GCAAGTTGAGAGAGAGAGAGAGA 58.990 47.826 7.16 0.00 0.00 3.10
325 486 4.095483 GCAAGTTGAGAGAGAGAGAGAGAG 59.905 50.000 7.16 0.00 0.00 3.20
326 487 5.491070 CAAGTTGAGAGAGAGAGAGAGAGA 58.509 45.833 0.00 0.00 0.00 3.10
327 488 5.350504 AGTTGAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
328 489 5.026121 AGTTGAGAGAGAGAGAGAGAGAGA 58.974 45.833 0.00 0.00 0.00 3.10
329 490 5.128499 AGTTGAGAGAGAGAGAGAGAGAGAG 59.872 48.000 0.00 0.00 0.00 3.20
330 491 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
331 492 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
332 493 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
333 494 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
334 495 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
335 496 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
336 497 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
337 498 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
338 499 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
339 500 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
340 501 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
341 502 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
364 525 1.134401 AGAGAGAGAGAGACGGCAGAG 60.134 57.143 0.00 0.00 0.00 3.35
368 529 1.599606 GAGAGAGACGGCAGAGGCAA 61.600 60.000 0.00 0.00 43.71 4.52
382 543 4.736759 GCAGAGGCAATGAAGATGGATTTG 60.737 45.833 0.00 0.00 40.72 2.32
389 550 5.684030 GCAATGAAGATGGATTTGAAGGCAT 60.684 40.000 0.00 0.00 0.00 4.40
413 574 1.203563 CGCGTATCCTCGTCGGTAG 59.796 63.158 0.00 0.00 0.00 3.18
416 577 0.864455 CGTATCCTCGTCGGTAGTCC 59.136 60.000 0.00 0.00 0.00 3.85
447 608 3.851955 CCGTCCGGCCTACTACAT 58.148 61.111 0.00 0.00 0.00 2.29
448 609 1.362717 CCGTCCGGCCTACTACATG 59.637 63.158 0.00 0.00 0.00 3.21
450 611 1.299926 GTCCGGCCTACTACATGCG 60.300 63.158 0.00 0.00 0.00 4.73
451 612 2.661866 CCGGCCTACTACATGCGC 60.662 66.667 0.00 0.00 0.00 6.09
453 614 2.661866 GGCCTACTACATGCGCCG 60.662 66.667 4.18 0.00 0.00 6.46
454 615 2.415843 GCCTACTACATGCGCCGA 59.584 61.111 4.18 0.00 0.00 5.54
455 616 1.661821 GCCTACTACATGCGCCGAG 60.662 63.158 4.18 0.00 0.00 4.63
456 617 2.030551 CCTACTACATGCGCCGAGA 58.969 57.895 4.18 0.00 0.00 4.04
458 619 0.945099 CTACTACATGCGCCGAGAGA 59.055 55.000 4.18 0.00 0.00 3.10
459 620 0.945099 TACTACATGCGCCGAGAGAG 59.055 55.000 4.18 0.00 0.00 3.20
460 621 1.659954 CTACATGCGCCGAGAGAGC 60.660 63.158 4.18 0.00 35.63 4.09
461 622 3.138930 TACATGCGCCGAGAGAGCC 62.139 63.158 4.18 0.00 34.50 4.70
462 623 4.519437 CATGCGCCGAGAGAGCCA 62.519 66.667 4.18 0.00 34.50 4.75
463 624 3.544607 ATGCGCCGAGAGAGCCAT 61.545 61.111 4.18 0.00 34.50 4.40
504 665 0.838122 CCCCCTCCAACACTCACTCT 60.838 60.000 0.00 0.00 0.00 3.24
505 666 0.610687 CCCCTCCAACACTCACTCTC 59.389 60.000 0.00 0.00 0.00 3.20
507 668 1.342074 CCTCCAACACTCACTCTCCA 58.658 55.000 0.00 0.00 0.00 3.86
509 670 1.967066 CTCCAACACTCACTCTCCACT 59.033 52.381 0.00 0.00 0.00 4.00
511 672 1.336332 CCAACACTCACTCTCCACTCG 60.336 57.143 0.00 0.00 0.00 4.18
512 673 0.315568 AACACTCACTCTCCACTCGC 59.684 55.000 0.00 0.00 0.00 5.03
514 675 0.170116 CACTCACTCTCCACTCGCTC 59.830 60.000 0.00 0.00 0.00 5.03
515 676 0.963355 ACTCACTCTCCACTCGCTCC 60.963 60.000 0.00 0.00 0.00 4.70
524 3417 1.251527 CCACTCGCTCCACTACACCT 61.252 60.000 0.00 0.00 0.00 4.00
557 3450 2.036958 TCTATCCACCAATGGCAACG 57.963 50.000 0.00 0.00 46.80 4.10
855 3827 0.905357 CAAGATCCCCACCGACTTCT 59.095 55.000 0.00 0.00 0.00 2.85
857 3829 0.905357 AGATCCCCACCGACTTCTTG 59.095 55.000 0.00 0.00 0.00 3.02
924 3902 2.524394 ACCTCACCAGCCACGACT 60.524 61.111 0.00 0.00 0.00 4.18
944 3922 2.357517 CTCACCGGCGTCAGCTTT 60.358 61.111 6.01 0.00 44.37 3.51
1141 4124 1.418637 TGACCAACACCTACTTCACCC 59.581 52.381 0.00 0.00 0.00 4.61
1255 4238 2.511373 GCCATGTCGCCGTCATCA 60.511 61.111 0.00 0.00 0.00 3.07
1344 4327 4.162690 GGCCCCAACGAGATCGCT 62.163 66.667 1.39 0.00 44.43 4.93
1431 4414 0.991146 TGGTGCTGGTGGACATGTAT 59.009 50.000 0.00 0.00 36.16 2.29
1721 4719 1.950216 TGCCATTTCTGTGCGTTTGTA 59.050 42.857 0.00 0.00 0.00 2.41
1730 4728 3.257375 TCTGTGCGTTTGTAGATGGTACT 59.743 43.478 0.00 0.00 0.00 2.73
1731 4729 3.581755 TGTGCGTTTGTAGATGGTACTC 58.418 45.455 0.00 0.00 0.00 2.59
1732 4730 2.928116 GTGCGTTTGTAGATGGTACTCC 59.072 50.000 0.00 0.00 0.00 3.85
1733 4731 2.093869 TGCGTTTGTAGATGGTACTCCC 60.094 50.000 0.00 0.00 0.00 4.30
1734 4732 2.167900 GCGTTTGTAGATGGTACTCCCT 59.832 50.000 0.00 0.00 0.00 4.20
1735 4733 3.737355 GCGTTTGTAGATGGTACTCCCTC 60.737 52.174 0.00 0.00 0.00 4.30
1736 4734 3.700038 CGTTTGTAGATGGTACTCCCTCT 59.300 47.826 0.00 0.00 40.75 3.69
1737 4735 4.440250 CGTTTGTAGATGGTACTCCCTCTG 60.440 50.000 0.00 0.00 38.73 3.35
1738 4736 4.332683 TTGTAGATGGTACTCCCTCTGT 57.667 45.455 0.00 0.00 38.73 3.41
1739 4737 4.332683 TGTAGATGGTACTCCCTCTGTT 57.667 45.455 0.00 0.00 38.73 3.16
1740 4738 4.684724 TGTAGATGGTACTCCCTCTGTTT 58.315 43.478 0.00 0.00 38.73 2.83
1741 4739 5.091552 TGTAGATGGTACTCCCTCTGTTTT 58.908 41.667 0.00 0.00 38.73 2.43
1742 4740 5.546499 TGTAGATGGTACTCCCTCTGTTTTT 59.454 40.000 0.00 0.00 38.73 1.94
1781 4779 7.823745 AGATTTGGTCAAAGTCAAACTATGT 57.176 32.000 2.55 0.00 35.97 2.29
1782 4780 8.237811 AGATTTGGTCAAAGTCAAACTATGTT 57.762 30.769 2.55 0.00 35.97 2.71
1783 4781 9.349713 AGATTTGGTCAAAGTCAAACTATGTTA 57.650 29.630 2.55 0.00 35.97 2.41
1784 4782 9.959749 GATTTGGTCAAAGTCAAACTATGTTAA 57.040 29.630 2.55 0.00 35.97 2.01
1785 4783 9.744468 ATTTGGTCAAAGTCAAACTATGTTAAC 57.256 29.630 0.00 0.00 35.97 2.01
1786 4784 8.514330 TTGGTCAAAGTCAAACTATGTTAACT 57.486 30.769 7.22 0.00 0.00 2.24
1787 4785 8.514330 TGGTCAAAGTCAAACTATGTTAACTT 57.486 30.769 7.22 3.03 0.00 2.66
1788 4786 8.962679 TGGTCAAAGTCAAACTATGTTAACTTT 58.037 29.630 7.22 13.36 35.26 2.66
1789 4787 9.447040 GGTCAAAGTCAAACTATGTTAACTTTC 57.553 33.333 7.22 9.18 33.63 2.62
1790 4788 9.447040 GTCAAAGTCAAACTATGTTAACTTTCC 57.553 33.333 7.22 9.22 33.63 3.13
1791 4789 9.403583 TCAAAGTCAAACTATGTTAACTTTCCT 57.596 29.630 7.22 0.00 33.63 3.36
1792 4790 9.665264 CAAAGTCAAACTATGTTAACTTTCCTC 57.335 33.333 7.22 0.00 33.63 3.71
1793 4791 7.981102 AGTCAAACTATGTTAACTTTCCTCC 57.019 36.000 7.22 0.00 0.00 4.30
1794 4792 6.940867 AGTCAAACTATGTTAACTTTCCTCCC 59.059 38.462 7.22 0.00 0.00 4.30
1795 4793 5.935789 TCAAACTATGTTAACTTTCCTCCCG 59.064 40.000 7.22 0.00 0.00 5.14
1796 4794 3.870274 ACTATGTTAACTTTCCTCCCGC 58.130 45.455 7.22 0.00 0.00 6.13
1797 4795 1.734163 ATGTTAACTTTCCTCCCGCG 58.266 50.000 7.22 0.00 0.00 6.46
1798 4796 0.393820 TGTTAACTTTCCTCCCGCGT 59.606 50.000 4.92 0.00 0.00 6.01
1799 4797 1.073964 GTTAACTTTCCTCCCGCGTC 58.926 55.000 4.92 0.00 0.00 5.19
1800 4798 0.971386 TTAACTTTCCTCCCGCGTCT 59.029 50.000 4.92 0.00 0.00 4.18
1801 4799 0.529378 TAACTTTCCTCCCGCGTCTC 59.471 55.000 4.92 0.00 0.00 3.36
1802 4800 1.186267 AACTTTCCTCCCGCGTCTCT 61.186 55.000 4.92 0.00 0.00 3.10
1803 4801 1.139947 CTTTCCTCCCGCGTCTCTC 59.860 63.158 4.92 0.00 0.00 3.20
1804 4802 1.304217 TTTCCTCCCGCGTCTCTCT 60.304 57.895 4.92 0.00 0.00 3.10
1805 4803 0.898789 TTTCCTCCCGCGTCTCTCTT 60.899 55.000 4.92 0.00 0.00 2.85
1806 4804 0.034767 TTCCTCCCGCGTCTCTCTTA 60.035 55.000 4.92 0.00 0.00 2.10
1807 4805 0.464013 TCCTCCCGCGTCTCTCTTAG 60.464 60.000 4.92 0.00 0.00 2.18
1808 4806 0.464013 CCTCCCGCGTCTCTCTTAGA 60.464 60.000 4.92 0.00 0.00 2.10
1809 4807 1.380524 CTCCCGCGTCTCTCTTAGAA 58.619 55.000 4.92 0.00 35.47 2.10
1810 4808 1.950909 CTCCCGCGTCTCTCTTAGAAT 59.049 52.381 4.92 0.00 35.47 2.40
1811 4809 3.139850 CTCCCGCGTCTCTCTTAGAATA 58.860 50.000 4.92 0.00 35.47 1.75
1812 4810 2.877168 TCCCGCGTCTCTCTTAGAATAC 59.123 50.000 4.92 0.00 35.47 1.89
1813 4811 2.617308 CCCGCGTCTCTCTTAGAATACA 59.383 50.000 4.92 0.00 35.47 2.29
1814 4812 3.304123 CCCGCGTCTCTCTTAGAATACAG 60.304 52.174 4.92 0.00 35.47 2.74
1815 4813 3.312973 CCGCGTCTCTCTTAGAATACAGT 59.687 47.826 4.92 0.00 35.47 3.55
1816 4814 4.275662 CGCGTCTCTCTTAGAATACAGTG 58.724 47.826 0.00 0.00 35.47 3.66
1817 4815 4.034163 CGCGTCTCTCTTAGAATACAGTGA 59.966 45.833 0.00 0.00 35.47 3.41
1818 4816 5.267776 GCGTCTCTCTTAGAATACAGTGAC 58.732 45.833 0.00 0.00 35.47 3.67
1827 4825 2.492484 AGAATACAGTGACCAGTCCGTC 59.508 50.000 0.00 0.00 0.00 4.79
1828 4826 0.809385 ATACAGTGACCAGTCCGTCG 59.191 55.000 0.00 0.00 35.40 5.12
1833 4831 2.126965 GACCAGTCCGTCGACACG 60.127 66.667 17.16 4.74 46.29 4.49
1859 4857 2.995258 CGAGAGCCGACTATCTAGTACC 59.005 54.545 0.00 0.00 41.76 3.34
1862 4860 4.988029 AGAGCCGACTATCTAGTACCATT 58.012 43.478 0.00 0.00 36.50 3.16
1863 4861 5.005094 AGAGCCGACTATCTAGTACCATTC 58.995 45.833 0.00 0.00 36.50 2.67
1882 4880 3.840890 TCGCATACAATTCAAACCACC 57.159 42.857 0.00 0.00 0.00 4.61
1897 4895 1.280998 ACCACCTTTCAATAGACCGGG 59.719 52.381 6.32 0.00 0.00 5.73
1915 4913 2.502295 GGGCAAAATTCATGCAAACCA 58.498 42.857 15.56 0.00 45.60 3.67
1916 4914 3.083293 GGGCAAAATTCATGCAAACCAT 58.917 40.909 15.56 0.00 45.60 3.55
1937 4936 7.461749 ACCATCTGATTTCATATAAACCGGAT 58.538 34.615 9.46 0.00 0.00 4.18
1938 4937 7.391554 ACCATCTGATTTCATATAAACCGGATG 59.608 37.037 9.46 0.00 0.00 3.51
1942 4941 9.402320 TCTGATTTCATATAAACCGGATGAAAA 57.598 29.630 23.99 12.98 46.84 2.29
1944 4943 8.961634 TGATTTCATATAAACCGGATGAAAACA 58.038 29.630 23.99 23.56 46.84 2.83
1945 4944 9.233232 GATTTCATATAAACCGGATGAAAACAC 57.767 33.333 23.99 16.88 46.84 3.32
2024 5027 2.732016 CACCCGTCGACCACTTCA 59.268 61.111 10.58 0.00 0.00 3.02
2072 5075 1.227764 CCATCTGCCGTCTCCATGG 60.228 63.158 4.97 4.97 0.00 3.66
2075 5078 3.790437 CTGCCGTCTCCATGGGCT 61.790 66.667 13.02 0.00 46.97 5.19
2105 5111 1.129058 AGACCCGTGAAGTGAAGGTT 58.871 50.000 0.00 0.00 0.00 3.50
2111 5117 2.285083 CGTGAAGTGAAGGTTTGGTCA 58.715 47.619 0.00 0.00 0.00 4.02
2114 5120 2.025793 TGAAGTGAAGGTTTGGTCACCA 60.026 45.455 0.00 0.00 44.30 4.17
2116 5122 3.312736 AGTGAAGGTTTGGTCACCAAT 57.687 42.857 10.97 0.00 43.55 3.16
2125 5134 4.082125 GTTTGGTCACCAATGAGGAAGAT 58.918 43.478 10.97 0.00 43.55 2.40
2141 5150 5.032846 AGGAAGATTAGAACATGGGAGACA 58.967 41.667 0.00 0.00 0.00 3.41
2169 5183 2.356667 CTTGGGACTCAAGCCCCC 59.643 66.667 1.18 0.45 45.24 5.40
2171 5185 4.974438 TGGGACTCAAGCCCCCGT 62.974 66.667 0.00 0.00 45.40 5.28
2172 5186 3.647771 GGGACTCAAGCCCCCGTT 61.648 66.667 0.00 0.00 39.81 4.44
2179 5193 2.852075 AAGCCCCCGTTGTCTCCA 60.852 61.111 0.00 0.00 0.00 3.86
2198 5212 1.869767 CAATGGCCTACTCATTCTCGC 59.130 52.381 3.32 0.00 33.08 5.03
2199 5213 0.394565 ATGGCCTACTCATTCTCGCC 59.605 55.000 3.32 0.00 36.91 5.54
2272 5287 1.668151 GTGGACGGTCCTTCACTGC 60.668 63.158 26.41 5.95 37.46 4.40
2280 5295 1.770110 TCCTTCACTGCCCACCTGT 60.770 57.895 0.00 0.00 0.00 4.00
2285 5300 1.357137 TCACTGCCCACCTGTCATAA 58.643 50.000 0.00 0.00 0.00 1.90
2287 5302 1.003580 CACTGCCCACCTGTCATAAGT 59.996 52.381 0.00 0.00 0.00 2.24
2292 5307 0.620556 CCACCTGTCATAAGTGCCCT 59.379 55.000 0.00 0.00 0.00 5.19
2293 5308 1.837439 CCACCTGTCATAAGTGCCCTA 59.163 52.381 0.00 0.00 0.00 3.53
2304 5319 5.191722 TCATAAGTGCCCTAGAAAGTTGGAT 59.808 40.000 0.00 0.00 0.00 3.41
2307 5322 1.340991 TGCCCTAGAAAGTTGGATGGC 60.341 52.381 0.00 0.00 38.13 4.40
2328 5343 2.510238 GCGTAGGAGGCACAGCTG 60.510 66.667 13.48 13.48 0.00 4.24
2413 5429 2.101575 CTGCGCGCCTCTACGTTA 59.898 61.111 30.77 5.02 34.88 3.18
2463 5479 1.405821 GTAGAGTGTATGCTGCTCCGT 59.594 52.381 0.00 0.00 0.00 4.69
2464 5480 0.174389 AGAGTGTATGCTGCTCCGTG 59.826 55.000 0.00 0.00 0.00 4.94
2466 5482 0.826715 AGTGTATGCTGCTCCGTGAT 59.173 50.000 0.00 0.00 0.00 3.06
2473 5489 1.160137 GCTGCTCCGTGATGAAGTTT 58.840 50.000 0.00 0.00 0.00 2.66
2476 5492 1.071542 TGCTCCGTGATGAAGTTTGGA 59.928 47.619 0.00 0.00 0.00 3.53
2511 5527 3.285371 CGCCACGGACTCCTACTT 58.715 61.111 0.00 0.00 0.00 2.24
2513 5529 0.037605 CGCCACGGACTCCTACTTTT 60.038 55.000 0.00 0.00 0.00 2.27
2532 5549 2.165301 GCGCTCGCCGTAGATTTGT 61.165 57.895 0.00 0.00 39.71 2.83
2541 5558 0.529992 CGTAGATTTGTCCCTCCGCC 60.530 60.000 0.00 0.00 0.00 6.13
2564 5581 1.819229 GATGCTGCTCGAGGAGGAA 59.181 57.895 30.13 9.23 37.38 3.36
2565 5582 0.392336 GATGCTGCTCGAGGAGGAAT 59.608 55.000 30.13 18.71 37.38 3.01
2567 5584 1.035923 TGCTGCTCGAGGAGGAATAG 58.964 55.000 31.61 9.96 33.79 1.73
2576 5593 3.028850 CGAGGAGGAATAGGTTGTACCA 58.971 50.000 0.00 0.00 41.95 3.25
2579 5596 4.031611 AGGAGGAATAGGTTGTACCACTC 58.968 47.826 0.00 0.00 41.95 3.51
2586 5603 1.149288 AGGTTGTACCACTCCTCCTCA 59.851 52.381 0.00 0.00 41.95 3.86
2589 5606 2.567615 GTTGTACCACTCCTCCTCATGT 59.432 50.000 0.00 0.00 0.00 3.21
2591 5608 1.134670 GTACCACTCCTCCTCATGTGC 60.135 57.143 0.00 0.00 0.00 4.57
2593 5610 1.222936 CACTCCTCCTCATGTGCCC 59.777 63.158 0.00 0.00 0.00 5.36
2596 5613 3.790437 CCTCCTCATGTGCCCGCT 61.790 66.667 0.00 0.00 0.00 5.52
2603 5620 1.140161 CATGTGCCCGCTGAAATGG 59.860 57.895 0.00 0.00 0.00 3.16
2623 5640 3.263170 TGGTGACATAGGTGTTAGCACAT 59.737 43.478 12.05 7.10 44.23 3.21
2624 5641 3.623060 GGTGACATAGGTGTTAGCACATG 59.377 47.826 12.05 9.77 46.95 3.21
2636 5653 1.378250 GCACATGCTGCTCCTCCTT 60.378 57.895 11.51 0.00 43.33 3.36
2637 5654 1.375098 GCACATGCTGCTCCTCCTTC 61.375 60.000 11.51 0.00 43.33 3.46
2662 5679 4.695231 CGGTGTCGACGCGAACCT 62.695 66.667 21.89 0.00 37.72 3.50
2663 5680 2.562912 GGTGTCGACGCGAACCTA 59.437 61.111 21.89 0.00 37.72 3.08
2664 5681 1.138247 GGTGTCGACGCGAACCTAT 59.862 57.895 21.89 0.00 37.72 2.57
2665 5682 1.138047 GGTGTCGACGCGAACCTATG 61.138 60.000 21.89 0.00 37.72 2.23
2666 5683 1.515519 TGTCGACGCGAACCTATGC 60.516 57.895 15.93 0.00 37.72 3.14
2667 5684 1.226603 GTCGACGCGAACCTATGCT 60.227 57.895 15.93 0.00 37.72 3.79
2668 5685 0.801067 GTCGACGCGAACCTATGCTT 60.801 55.000 15.93 0.00 37.72 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.237285 AACCTGGCACGCATCTGAAC 61.237 55.000 0.00 0.00 0.00 3.18
39 40 3.843893 ACCTGCATGCCTTTTCTTTTT 57.156 38.095 16.68 0.00 0.00 1.94
44 45 0.457443 GCCTACCTGCATGCCTTTTC 59.543 55.000 16.68 0.00 0.00 2.29
59 217 1.103803 CGGAGCTGTTGTAGAGCCTA 58.896 55.000 0.00 0.00 37.12 3.93
89 247 6.326375 GGGCGTACATTGAAATTGAATACAA 58.674 36.000 0.00 1.52 40.42 2.41
118 276 2.223745 GGGCACTGGTTTTCGTAAAGA 58.776 47.619 0.00 0.00 0.00 2.52
122 280 2.279935 ATTGGGCACTGGTTTTCGTA 57.720 45.000 0.00 0.00 0.00 3.43
123 281 2.159382 CTATTGGGCACTGGTTTTCGT 58.841 47.619 0.00 0.00 0.00 3.85
124 282 1.472480 CCTATTGGGCACTGGTTTTCG 59.528 52.381 0.00 0.00 0.00 3.46
125 283 2.802719 TCCTATTGGGCACTGGTTTTC 58.197 47.619 0.00 0.00 34.39 2.29
161 319 1.845809 CGTGCTCAAGTCAAGGGTGC 61.846 60.000 0.00 0.00 0.00 5.01
162 320 1.230635 CCGTGCTCAAGTCAAGGGTG 61.231 60.000 0.00 0.00 30.91 4.61
165 323 0.034059 ACTCCGTGCTCAAGTCAAGG 59.966 55.000 0.00 0.00 34.95 3.61
191 349 3.103738 GTCGAATGACAGCAATCAATGC 58.896 45.455 0.00 0.00 45.74 3.56
205 363 6.908870 TCAGTTAATTCATGAGGTCGAATG 57.091 37.500 0.00 0.00 32.27 2.67
213 371 6.533012 ACGTCACTCATCAGTTAATTCATGAG 59.467 38.462 9.80 9.80 45.30 2.90
228 386 3.259374 ACATCTTTCTGGACGTCACTCAT 59.741 43.478 18.91 0.00 0.00 2.90
232 390 3.026630 TGACATCTTTCTGGACGTCAC 57.973 47.619 18.91 7.49 0.00 3.67
236 394 4.248859 ACTTCATGACATCTTTCTGGACG 58.751 43.478 0.00 0.00 0.00 4.79
242 400 5.163713 GCCCAGTAACTTCATGACATCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
252 410 1.004745 CCACCAGCCCAGTAACTTCAT 59.995 52.381 0.00 0.00 0.00 2.57
257 415 1.202769 TACCCCACCAGCCCAGTAAC 61.203 60.000 0.00 0.00 0.00 2.50
272 430 1.334243 CTCGCAGCAGTACTAGTACCC 59.666 57.143 25.97 18.20 36.75 3.69
273 431 2.286872 TCTCGCAGCAGTACTAGTACC 58.713 52.381 25.97 13.92 36.75 3.34
280 441 2.202810 GCCCTCTCGCAGCAGTAC 60.203 66.667 0.00 0.00 0.00 2.73
292 453 1.294659 CTCAACTTGCGTCTGCCCTC 61.295 60.000 0.00 0.00 41.78 4.30
294 455 1.294659 CTCTCAACTTGCGTCTGCCC 61.295 60.000 0.00 0.00 41.78 5.36
303 464 5.491070 TCTCTCTCTCTCTCTCTCAACTTG 58.509 45.833 0.00 0.00 0.00 3.16
306 467 5.127845 TCTCTCTCTCTCTCTCTCTCTCAAC 59.872 48.000 0.00 0.00 0.00 3.18
307 468 5.272402 TCTCTCTCTCTCTCTCTCTCTCAA 58.728 45.833 0.00 0.00 0.00 3.02
308 469 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
310 471 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
311 472 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
312 473 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
313 474 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
314 475 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
315 476 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
316 477 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
317 478 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
318 479 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
319 480 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
320 481 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
321 482 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
322 483 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
323 484 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
324 485 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
325 486 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
326 487 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
327 488 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
328 489 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
329 490 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
330 491 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
331 492 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
332 493 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
333 494 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
334 495 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
335 496 4.261405 CGTCTCTCTCTCTCTCTCTCTCTC 60.261 54.167 0.00 0.00 0.00 3.20
336 497 3.634448 CGTCTCTCTCTCTCTCTCTCTCT 59.366 52.174 0.00 0.00 0.00 3.10
337 498 3.243569 CCGTCTCTCTCTCTCTCTCTCTC 60.244 56.522 0.00 0.00 0.00 3.20
338 499 2.695666 CCGTCTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
339 500 2.803492 GCCGTCTCTCTCTCTCTCTCTC 60.803 59.091 0.00 0.00 0.00 3.20
340 501 1.139058 GCCGTCTCTCTCTCTCTCTCT 59.861 57.143 0.00 0.00 0.00 3.10
341 502 1.134521 TGCCGTCTCTCTCTCTCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
364 525 4.690122 CCTTCAAATCCATCTTCATTGCC 58.310 43.478 0.00 0.00 0.00 4.52
368 529 4.202223 GCATGCCTTCAAATCCATCTTCAT 60.202 41.667 6.36 0.00 0.00 2.57
397 558 0.864455 GGACTACCGACGAGGATACG 59.136 60.000 8.56 0.00 45.00 3.06
406 567 3.553904 AGGATCTTGTAGGACTACCGAC 58.446 50.000 7.00 0.00 41.18 4.79
413 574 0.030908 CGGCGAGGATCTTGTAGGAC 59.969 60.000 0.00 0.00 0.00 3.85
416 577 0.030908 GGACGGCGAGGATCTTGTAG 59.969 60.000 16.62 0.00 0.00 2.74
438 599 0.039978 CTCTCGGCGCATGTAGTAGG 60.040 60.000 10.83 0.00 0.00 3.18
440 601 0.945099 CTCTCTCGGCGCATGTAGTA 59.055 55.000 10.83 0.00 0.00 1.82
441 602 1.730487 CTCTCTCGGCGCATGTAGT 59.270 57.895 10.83 0.00 0.00 2.73
442 603 1.659954 GCTCTCTCGGCGCATGTAG 60.660 63.158 10.83 0.62 0.00 2.74
443 604 2.413351 GCTCTCTCGGCGCATGTA 59.587 61.111 10.83 0.00 0.00 2.29
444 605 4.521062 GGCTCTCTCGGCGCATGT 62.521 66.667 10.83 0.00 0.00 3.21
445 606 3.804153 ATGGCTCTCTCGGCGCATG 62.804 63.158 10.83 0.00 0.00 4.06
447 608 4.519437 CATGGCTCTCTCGGCGCA 62.519 66.667 10.83 0.00 0.00 6.09
448 609 4.212913 TCATGGCTCTCTCGGCGC 62.213 66.667 0.00 0.00 0.00 6.53
450 611 2.280052 GCTCATGGCTCTCTCGGC 60.280 66.667 0.00 0.00 38.06 5.54
451 612 1.756408 ATGGCTCATGGCTCTCTCGG 61.756 60.000 6.20 0.00 41.46 4.63
453 614 0.885596 GCATGGCTCATGGCTCTCTC 60.886 60.000 14.50 0.00 41.64 3.20
454 615 1.148723 GCATGGCTCATGGCTCTCT 59.851 57.895 14.50 0.00 41.64 3.10
455 616 0.537600 ATGCATGGCTCATGGCTCTC 60.538 55.000 14.50 1.76 41.64 3.20
456 617 0.769247 TATGCATGGCTCATGGCTCT 59.231 50.000 10.16 4.93 41.64 4.09
458 619 2.076207 TTTATGCATGGCTCATGGCT 57.924 45.000 10.16 0.00 41.64 4.75
459 620 2.353406 GGATTTATGCATGGCTCATGGC 60.353 50.000 10.16 8.90 41.64 4.40
460 621 2.894765 TGGATTTATGCATGGCTCATGG 59.105 45.455 10.16 0.00 41.64 3.66
461 622 3.572682 ACTGGATTTATGCATGGCTCATG 59.427 43.478 10.16 9.94 43.91 3.07
462 623 3.840991 ACTGGATTTATGCATGGCTCAT 58.159 40.909 10.16 0.00 0.00 2.90
463 624 3.301794 ACTGGATTTATGCATGGCTCA 57.698 42.857 10.16 0.67 0.00 4.26
504 665 1.248785 GGTGTAGTGGAGCGAGTGGA 61.249 60.000 0.00 0.00 0.00 4.02
505 666 1.215647 GGTGTAGTGGAGCGAGTGG 59.784 63.158 0.00 0.00 0.00 4.00
507 668 1.878656 GCAGGTGTAGTGGAGCGAGT 61.879 60.000 0.00 0.00 0.00 4.18
509 670 1.906333 TGCAGGTGTAGTGGAGCGA 60.906 57.895 0.00 0.00 0.00 4.93
511 672 1.376037 GGTGCAGGTGTAGTGGAGC 60.376 63.158 0.00 0.00 0.00 4.70
512 673 1.079819 CGGTGCAGGTGTAGTGGAG 60.080 63.158 0.00 0.00 0.00 3.86
514 675 2.742372 GCGGTGCAGGTGTAGTGG 60.742 66.667 0.00 0.00 0.00 4.00
515 676 0.955428 AATGCGGTGCAGGTGTAGTG 60.955 55.000 0.00 0.00 43.65 2.74
524 3417 2.221169 GGATAGATTGAATGCGGTGCA 58.779 47.619 0.00 0.00 44.86 4.57
869 3841 2.204059 AGCAGGTCCTTGAGGCCT 60.204 61.111 3.86 3.86 40.66 5.19
1344 4327 2.264480 CCGGCGTTCACCATCTCA 59.736 61.111 6.01 0.00 0.00 3.27
1431 4414 4.017591 ACCATCATGTCCATAAAGAACCCA 60.018 41.667 0.00 0.00 0.00 4.51
1562 4545 1.899814 AGAACAGGTAGTCGGCAATGA 59.100 47.619 0.00 0.00 0.00 2.57
1564 4547 1.066143 CCAGAACAGGTAGTCGGCAAT 60.066 52.381 0.00 0.00 0.00 3.56
1566 4549 1.541310 CCCAGAACAGGTAGTCGGCA 61.541 60.000 0.00 0.00 0.00 5.69
1755 4753 9.349713 ACATAGTTTGACTTTGACCAAATCTTA 57.650 29.630 5.70 0.00 35.14 2.10
1756 4754 8.237811 ACATAGTTTGACTTTGACCAAATCTT 57.762 30.769 5.70 0.00 35.14 2.40
1757 4755 7.823745 ACATAGTTTGACTTTGACCAAATCT 57.176 32.000 5.70 0.00 35.14 2.40
1758 4756 9.959749 TTAACATAGTTTGACTTTGACCAAATC 57.040 29.630 5.70 0.00 35.14 2.17
1759 4757 9.744468 GTTAACATAGTTTGACTTTGACCAAAT 57.256 29.630 0.00 0.00 35.14 2.32
1760 4758 8.962679 AGTTAACATAGTTTGACTTTGACCAAA 58.037 29.630 8.61 0.00 32.57 3.28
1761 4759 8.514330 AGTTAACATAGTTTGACTTTGACCAA 57.486 30.769 8.61 0.00 32.57 3.67
1762 4760 8.514330 AAGTTAACATAGTTTGACTTTGACCA 57.486 30.769 8.61 0.00 32.87 4.02
1763 4761 9.447040 GAAAGTTAACATAGTTTGACTTTGACC 57.553 33.333 19.43 9.06 42.31 4.02
1764 4762 9.447040 GGAAAGTTAACATAGTTTGACTTTGAC 57.553 33.333 19.43 12.74 42.31 3.18
1765 4763 9.403583 AGGAAAGTTAACATAGTTTGACTTTGA 57.596 29.630 19.43 0.00 42.31 2.69
1766 4764 9.665264 GAGGAAAGTTAACATAGTTTGACTTTG 57.335 33.333 19.43 0.00 42.31 2.77
1767 4765 8.847196 GGAGGAAAGTTAACATAGTTTGACTTT 58.153 33.333 8.61 16.70 43.93 2.66
1768 4766 7.447545 GGGAGGAAAGTTAACATAGTTTGACTT 59.552 37.037 8.61 0.00 37.00 3.01
1769 4767 6.940867 GGGAGGAAAGTTAACATAGTTTGACT 59.059 38.462 8.61 0.90 0.00 3.41
1770 4768 6.128363 CGGGAGGAAAGTTAACATAGTTTGAC 60.128 42.308 8.61 0.00 0.00 3.18
1771 4769 5.935789 CGGGAGGAAAGTTAACATAGTTTGA 59.064 40.000 8.61 0.00 0.00 2.69
1772 4770 5.391629 GCGGGAGGAAAGTTAACATAGTTTG 60.392 44.000 8.61 0.00 0.00 2.93
1773 4771 4.698780 GCGGGAGGAAAGTTAACATAGTTT 59.301 41.667 8.61 0.00 0.00 2.66
1774 4772 4.259356 GCGGGAGGAAAGTTAACATAGTT 58.741 43.478 8.61 0.00 0.00 2.24
1775 4773 3.677976 CGCGGGAGGAAAGTTAACATAGT 60.678 47.826 8.61 0.00 0.00 2.12
1776 4774 2.864343 CGCGGGAGGAAAGTTAACATAG 59.136 50.000 8.61 0.00 0.00 2.23
1777 4775 2.234414 ACGCGGGAGGAAAGTTAACATA 59.766 45.455 12.47 0.00 0.00 2.29
1778 4776 1.002773 ACGCGGGAGGAAAGTTAACAT 59.997 47.619 12.47 0.00 0.00 2.71
1779 4777 0.393820 ACGCGGGAGGAAAGTTAACA 59.606 50.000 12.47 0.00 0.00 2.41
1780 4778 1.073964 GACGCGGGAGGAAAGTTAAC 58.926 55.000 12.47 0.00 0.00 2.01
1781 4779 0.971386 AGACGCGGGAGGAAAGTTAA 59.029 50.000 12.47 0.00 0.00 2.01
1782 4780 0.529378 GAGACGCGGGAGGAAAGTTA 59.471 55.000 12.47 0.00 0.00 2.24
1783 4781 1.186267 AGAGACGCGGGAGGAAAGTT 61.186 55.000 12.47 0.00 0.00 2.66
1784 4782 1.596895 GAGAGACGCGGGAGGAAAGT 61.597 60.000 12.47 0.00 0.00 2.66
1785 4783 1.139947 GAGAGACGCGGGAGGAAAG 59.860 63.158 12.47 0.00 0.00 2.62
1786 4784 0.898789 AAGAGAGACGCGGGAGGAAA 60.899 55.000 12.47 0.00 0.00 3.13
1787 4785 0.034767 TAAGAGAGACGCGGGAGGAA 60.035 55.000 12.47 0.00 0.00 3.36
1788 4786 0.464013 CTAAGAGAGACGCGGGAGGA 60.464 60.000 12.47 0.00 0.00 3.71
1789 4787 0.464013 TCTAAGAGAGACGCGGGAGG 60.464 60.000 12.47 0.00 0.00 4.30
1790 4788 1.380524 TTCTAAGAGAGACGCGGGAG 58.619 55.000 12.47 0.00 32.31 4.30
1791 4789 2.054232 ATTCTAAGAGAGACGCGGGA 57.946 50.000 12.47 0.00 32.31 5.14
1792 4790 2.617308 TGTATTCTAAGAGAGACGCGGG 59.383 50.000 12.47 0.00 32.31 6.13
1793 4791 3.312973 ACTGTATTCTAAGAGAGACGCGG 59.687 47.826 12.47 0.00 32.31 6.46
1794 4792 4.034163 TCACTGTATTCTAAGAGAGACGCG 59.966 45.833 3.53 3.53 32.31 6.01
1795 4793 5.267776 GTCACTGTATTCTAAGAGAGACGC 58.732 45.833 0.00 0.00 32.31 5.19
1796 4794 5.354513 TGGTCACTGTATTCTAAGAGAGACG 59.645 44.000 0.00 0.00 32.31 4.18
1797 4795 6.376018 ACTGGTCACTGTATTCTAAGAGAGAC 59.624 42.308 0.00 0.00 32.31 3.36
1798 4796 6.486056 ACTGGTCACTGTATTCTAAGAGAGA 58.514 40.000 0.00 0.00 0.00 3.10
1799 4797 6.183360 GGACTGGTCACTGTATTCTAAGAGAG 60.183 46.154 3.10 0.00 0.00 3.20
1800 4798 5.652891 GGACTGGTCACTGTATTCTAAGAGA 59.347 44.000 3.10 0.00 0.00 3.10
1801 4799 5.449314 CGGACTGGTCACTGTATTCTAAGAG 60.449 48.000 3.10 0.00 0.00 2.85
1802 4800 4.398358 CGGACTGGTCACTGTATTCTAAGA 59.602 45.833 3.10 0.00 0.00 2.10
1803 4801 4.158025 ACGGACTGGTCACTGTATTCTAAG 59.842 45.833 3.10 0.00 0.00 2.18
1804 4802 4.084287 ACGGACTGGTCACTGTATTCTAA 58.916 43.478 3.10 0.00 0.00 2.10
1805 4803 3.693085 GACGGACTGGTCACTGTATTCTA 59.307 47.826 3.10 0.00 36.91 2.10
1806 4804 2.492484 GACGGACTGGTCACTGTATTCT 59.508 50.000 3.10 0.00 36.91 2.40
1807 4805 2.731341 CGACGGACTGGTCACTGTATTC 60.731 54.545 3.10 0.00 36.73 1.75
1808 4806 1.201647 CGACGGACTGGTCACTGTATT 59.798 52.381 3.10 0.00 36.73 1.89
1809 4807 0.809385 CGACGGACTGGTCACTGTAT 59.191 55.000 3.10 0.00 36.73 2.29
1810 4808 0.250424 TCGACGGACTGGTCACTGTA 60.250 55.000 3.10 0.00 36.73 2.74
1811 4809 1.527611 TCGACGGACTGGTCACTGT 60.528 57.895 3.10 0.00 36.73 3.55
1812 4810 1.081376 GTCGACGGACTGGTCACTG 60.081 63.158 0.00 0.00 40.15 3.66
1813 4811 1.527611 TGTCGACGGACTGGTCACT 60.528 57.895 11.62 0.00 43.79 3.41
1814 4812 1.371389 GTGTCGACGGACTGGTCAC 60.371 63.158 11.62 0.00 43.79 3.67
1815 4813 2.900167 CGTGTCGACGGACTGGTCA 61.900 63.158 11.62 0.00 43.79 4.02
1816 4814 2.121564 TTCGTGTCGACGGACTGGTC 62.122 60.000 11.62 0.00 46.11 4.02
1817 4815 1.521450 ATTCGTGTCGACGGACTGGT 61.521 55.000 11.62 0.00 46.11 4.00
1818 4816 1.071019 CATTCGTGTCGACGGACTGG 61.071 60.000 11.62 0.00 46.11 4.00
1827 4825 2.508891 GGCTCTCGCATTCGTGTCG 61.509 63.158 0.00 0.00 38.10 4.35
1828 4826 2.508891 CGGCTCTCGCATTCGTGTC 61.509 63.158 0.00 0.00 38.10 3.67
1833 4831 1.268352 AGATAGTCGGCTCTCGCATTC 59.732 52.381 0.00 0.00 39.05 2.67
1834 4832 1.323412 AGATAGTCGGCTCTCGCATT 58.677 50.000 0.00 0.00 39.05 3.56
1847 4845 7.520451 TTGTATGCGAATGGTACTAGATAGT 57.480 36.000 0.00 0.00 40.24 2.12
1849 4847 8.581578 TGAATTGTATGCGAATGGTACTAGATA 58.418 33.333 0.00 0.00 0.00 1.98
1853 4851 7.201661 GGTTTGAATTGTATGCGAATGGTACTA 60.202 37.037 0.00 0.00 0.00 1.82
1855 4853 5.741982 GGTTTGAATTGTATGCGAATGGTAC 59.258 40.000 0.00 0.00 0.00 3.34
1856 4854 5.416013 TGGTTTGAATTGTATGCGAATGGTA 59.584 36.000 0.00 0.00 0.00 3.25
1857 4855 4.219507 TGGTTTGAATTGTATGCGAATGGT 59.780 37.500 0.00 0.00 0.00 3.55
1859 4857 4.562394 GGTGGTTTGAATTGTATGCGAATG 59.438 41.667 0.00 0.00 0.00 2.67
1862 4860 3.417101 AGGTGGTTTGAATTGTATGCGA 58.583 40.909 0.00 0.00 0.00 5.10
1863 4861 3.848272 AGGTGGTTTGAATTGTATGCG 57.152 42.857 0.00 0.00 0.00 4.73
1882 4880 4.718940 ATTTTGCCCGGTCTATTGAAAG 57.281 40.909 0.00 0.00 0.00 2.62
1897 4895 4.691685 TCAGATGGTTTGCATGAATTTTGC 59.308 37.500 0.00 7.23 40.55 3.68
1915 4913 9.573166 TTTCATCCGGTTTATATGAAATCAGAT 57.427 29.630 19.08 0.00 41.99 2.90
1916 4914 8.972458 TTTCATCCGGTTTATATGAAATCAGA 57.028 30.769 19.08 3.14 41.99 3.27
1937 4936 9.868277 AAAATGTCTGAAATGTAAGTGTTTTCA 57.132 25.926 0.00 0.00 37.11 2.69
1976 4975 3.429960 GGATAGGTTTAAGTTCGACCGCT 60.430 47.826 0.00 0.00 38.48 5.52
2016 5019 3.417101 TGCGGAATACAAATGAAGTGGT 58.583 40.909 0.00 0.00 0.00 4.16
2045 5048 0.977627 ACGGCAGATGGAGGATGTGA 60.978 55.000 0.00 0.00 0.00 3.58
2049 5052 1.118356 GGAGACGGCAGATGGAGGAT 61.118 60.000 0.00 0.00 0.00 3.24
2072 5075 1.078637 GGTCTTGAACCCCGTAGCC 60.079 63.158 0.00 0.00 42.85 3.93
2111 5117 6.125029 CCATGTTCTAATCTTCCTCATTGGT 58.875 40.000 0.00 0.00 37.07 3.67
2114 5120 6.388100 TCTCCCATGTTCTAATCTTCCTCATT 59.612 38.462 0.00 0.00 0.00 2.57
2116 5122 5.129485 GTCTCCCATGTTCTAATCTTCCTCA 59.871 44.000 0.00 0.00 0.00 3.86
2125 5134 2.496070 CGGTCTGTCTCCCATGTTCTAA 59.504 50.000 0.00 0.00 0.00 2.10
2160 5174 2.747686 GAGACAACGGGGGCTTGA 59.252 61.111 0.00 0.00 0.00 3.02
2172 5186 1.951209 TGAGTAGGCCATTGGAGACA 58.049 50.000 5.01 0.00 39.83 3.41
2179 5193 1.202698 GGCGAGAATGAGTAGGCCATT 60.203 52.381 5.01 0.00 40.24 3.16
2183 5197 1.300233 CCGGCGAGAATGAGTAGGC 60.300 63.158 9.30 0.00 0.00 3.93
2272 5287 0.394352 GGGCACTTATGACAGGTGGG 60.394 60.000 7.69 0.00 34.30 4.61
2280 5295 4.534500 TCCAACTTTCTAGGGCACTTATGA 59.466 41.667 0.00 0.00 0.00 2.15
2285 5300 2.025887 CCATCCAACTTTCTAGGGCACT 60.026 50.000 0.00 0.00 0.00 4.40
2287 5302 1.340991 GCCATCCAACTTTCTAGGGCA 60.341 52.381 0.00 0.00 39.88 5.36
2292 5307 0.742990 CGCCGCCATCCAACTTTCTA 60.743 55.000 0.00 0.00 0.00 2.10
2293 5308 2.040544 CGCCGCCATCCAACTTTCT 61.041 57.895 0.00 0.00 0.00 2.52
2333 5348 4.831307 CGGGCGAGGACGAGAACG 62.831 72.222 0.00 0.00 42.66 3.95
2396 5411 1.299165 ATAACGTAGAGGCGCGCAG 60.299 57.895 34.42 17.65 34.88 5.18
2397 5412 1.587876 CATAACGTAGAGGCGCGCA 60.588 57.895 34.42 9.57 34.88 6.09
2451 5467 1.482182 ACTTCATCACGGAGCAGCATA 59.518 47.619 0.00 0.00 0.00 3.14
2452 5468 0.251354 ACTTCATCACGGAGCAGCAT 59.749 50.000 0.00 0.00 0.00 3.79
2463 5479 1.737236 CGGCGAATCCAAACTTCATCA 59.263 47.619 0.00 0.00 34.01 3.07
2464 5480 1.531883 GCGGCGAATCCAAACTTCATC 60.532 52.381 12.98 0.00 34.01 2.92
2466 5482 0.605319 AGCGGCGAATCCAAACTTCA 60.605 50.000 12.98 0.00 34.01 3.02
2473 5489 1.227527 CATGGTAGCGGCGAATCCA 60.228 57.895 12.98 15.32 34.01 3.41
2476 5492 2.591715 GCCATGGTAGCGGCGAAT 60.592 61.111 12.98 0.00 38.82 3.34
2502 5518 1.014564 GCGAGCGCAAAAGTAGGAGT 61.015 55.000 11.47 0.00 41.49 3.85
2508 5524 2.356553 TACGGCGAGCGCAAAAGT 60.357 55.556 16.62 12.25 44.11 2.66
2509 5525 1.421410 ATCTACGGCGAGCGCAAAAG 61.421 55.000 16.62 9.74 44.11 2.27
2510 5526 1.017177 AATCTACGGCGAGCGCAAAA 61.017 50.000 16.62 0.00 44.11 2.44
2511 5527 1.017177 AAATCTACGGCGAGCGCAAA 61.017 50.000 16.62 0.30 44.11 3.68
2513 5529 2.164663 CAAATCTACGGCGAGCGCA 61.165 57.895 16.62 0.00 44.11 6.09
2547 5564 1.617850 CTATTCCTCCTCGAGCAGCAT 59.382 52.381 6.99 0.00 0.00 3.79
2550 5567 1.698506 ACCTATTCCTCCTCGAGCAG 58.301 55.000 6.99 0.15 0.00 4.24
2558 5575 3.134262 GGAGTGGTACAACCTATTCCTCC 59.866 52.174 0.00 0.00 44.16 4.30
2564 5581 3.012502 TGAGGAGGAGTGGTACAACCTAT 59.987 47.826 0.00 0.00 44.73 2.57
2565 5582 2.380932 TGAGGAGGAGTGGTACAACCTA 59.619 50.000 0.00 0.00 44.73 3.08
2567 5584 1.640917 TGAGGAGGAGTGGTACAACC 58.359 55.000 0.00 0.00 44.16 3.77
2576 5593 2.362369 CGGGCACATGAGGAGGAGT 61.362 63.158 0.00 0.00 0.00 3.85
2579 5596 3.790437 AGCGGGCACATGAGGAGG 61.790 66.667 0.00 0.00 0.00 4.30
2586 5603 1.304381 ACCATTTCAGCGGGCACAT 60.304 52.632 0.00 0.00 0.00 3.21
2589 5606 1.971167 GTCACCATTTCAGCGGGCA 60.971 57.895 0.00 0.00 0.00 5.36
2591 5608 1.942657 CTATGTCACCATTTCAGCGGG 59.057 52.381 0.00 0.00 32.29 6.13
2593 5610 2.352651 CACCTATGTCACCATTTCAGCG 59.647 50.000 0.00 0.00 32.29 5.18
2596 5613 4.941263 GCTAACACCTATGTCACCATTTCA 59.059 41.667 0.00 0.00 38.45 2.69
2603 5620 3.063997 GCATGTGCTAACACCTATGTCAC 59.936 47.826 0.00 0.00 46.86 3.67
2620 5637 1.220206 CGAAGGAGGAGCAGCATGT 59.780 57.895 0.00 0.00 39.31 3.21
2623 5640 4.087892 GGCGAAGGAGGAGCAGCA 62.088 66.667 0.00 0.00 0.00 4.41
2624 5641 3.397613 ATGGCGAAGGAGGAGCAGC 62.398 63.158 0.00 0.00 0.00 5.25
2648 5665 1.515519 GCATAGGTTCGCGTCGACA 60.516 57.895 17.16 0.00 34.89 4.35


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

AutoCloner maintained by Alex Coulton.