Multiple sequence alignment - TraesCS5B01G406900

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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 TraesCS5B01G406900 chr5B 100.000 4676 0 0 1 4676 582899066 582894391 0.000000e+00 8636.0
1 TraesCS5B01G406900 chr5B 94.521 657 27 4 2138 2794 358019667 358020314 0.000000e+00 1005.0
2 TraesCS5B01G406900 chr5B 90.019 531 46 3 1504 2031 626280629 626281155 0.000000e+00 680.0
3 TraesCS5B01G406900 chr5B 88.312 77 3 2 501 571 285934788 285934864 2.320000e-13 87.9
4 TraesCS5B01G406900 chr5D 94.630 2421 91 18 2136 4552 475516112 475513727 0.000000e+00 3714.0
5 TraesCS5B01G406900 chr5D 92.585 1389 75 14 759 2143 475517534 475516170 0.000000e+00 1969.0
6 TraesCS5B01G406900 chr5D 88.469 529 53 5 1506 2031 198385834 198386357 2.370000e-177 632.0
7 TraesCS5B01G406900 chr5D 88.258 528 54 5 1507 2031 198444045 198444567 3.970000e-175 625.0
8 TraesCS5B01G406900 chr5D 84.690 516 43 18 1 502 475519651 475519158 2.530000e-132 483.0
9 TraesCS5B01G406900 chr5D 93.204 103 6 1 4574 4676 475513521 475513420 2.910000e-32 150.0
10 TraesCS5B01G406900 chr5D 75.379 264 56 9 43 302 565508102 565508360 8.220000e-23 119.0
11 TraesCS5B01G406900 chr5D 92.857 70 5 0 2074 2143 198386358 198386427 8.280000e-18 102.0
12 TraesCS5B01G406900 chr5D 91.429 70 6 0 2074 2143 198444568 198444637 3.850000e-16 97.1
13 TraesCS5B01G406900 chr5D 88.525 61 4 2 1318 1375 475517038 475516978 2.330000e-08 71.3
14 TraesCS5B01G406900 chr5A 94.625 1842 69 12 2136 3963 594969222 594967397 0.000000e+00 2826.0
15 TraesCS5B01G406900 chr5A 92.257 904 51 14 636 1525 594970726 594969828 0.000000e+00 1264.0
16 TraesCS5B01G406900 chr5A 91.429 560 37 9 1587 2143 594969829 594969278 0.000000e+00 758.0
17 TraesCS5B01G406900 chr5A 94.444 432 19 4 4249 4676 594967328 594966898 0.000000e+00 660.0
18 TraesCS5B01G406900 chr5A 91.250 80 7 0 498 577 4610212 4610133 4.950000e-20 110.0
19 TraesCS5B01G406900 chr5A 98.387 62 1 0 3994 4055 594967401 594967340 4.950000e-20 110.0
20 TraesCS5B01G406900 chr5A 94.828 58 3 0 1318 1375 594970086 594970029 1.790000e-14 91.6
21 TraesCS5B01G406900 chr4D 94.064 657 27 3 2138 2794 451650346 451649702 0.000000e+00 987.0
22 TraesCS5B01G406900 chr4D 90.467 535 47 4 1612 2143 451650933 451650400 0.000000e+00 702.0
23 TraesCS5B01G406900 chr4D 92.593 81 4 2 499 577 20122000 20122080 1.060000e-21 115.0
24 TraesCS5B01G406900 chr1B 93.607 657 31 5 2139 2794 51418640 51419286 0.000000e+00 970.0
25 TraesCS5B01G406900 chr1B 92.846 657 37 3 2138 2794 51402361 51403007 0.000000e+00 944.0
26 TraesCS5B01G406900 chr1B 89.120 432 42 3 1603 2031 535554407 535554836 2.480000e-147 532.0
27 TraesCS5B01G406900 chr1B 76.339 224 48 5 17 238 648657983 648658203 1.060000e-21 115.0
28 TraesCS5B01G406900 chrUn 93.303 657 34 4 2138 2794 215732282 215731636 0.000000e+00 961.0
29 TraesCS5B01G406900 chr3A 92.121 660 32 7 2136 2794 11823737 11823097 0.000000e+00 913.0
30 TraesCS5B01G406900 chr4B 89.603 529 48 4 1506 2031 662787788 662787264 0.000000e+00 665.0
31 TraesCS5B01G406900 chr3B 89.036 529 49 5 1506 2031 798188933 798188411 0.000000e+00 647.0
32 TraesCS5B01G406900 chr3B 89.773 88 5 2 494 577 828548651 828548738 4.950000e-20 110.0
33 TraesCS5B01G406900 chr2B 78.201 289 50 12 14 296 15091711 15091992 6.220000e-39 172.0
34 TraesCS5B01G406900 chr2B 100.000 29 0 0 4104 4132 779248517 779248489 2.000000e-03 54.7
35 TraesCS5B01G406900 chr2D 80.258 233 40 5 68 297 481156954 481156725 2.240000e-38 171.0
36 TraesCS5B01G406900 chr2D 77.224 281 56 7 15 292 10753730 10754005 1.740000e-34 158.0
37 TraesCS5B01G406900 chr2D 75.570 307 60 12 1 301 480128771 480129068 2.270000e-28 137.0
38 TraesCS5B01G406900 chr2D 83.696 92 6 4 500 584 403345050 403345139 1.390000e-10 78.7
39 TraesCS5B01G406900 chr2D 95.833 48 1 1 540 587 617536486 617536532 5.020000e-10 76.8
40 TraesCS5B01G406900 chr2D 81.633 98 7 3 498 584 13994897 13994994 2.330000e-08 71.3
41 TraesCS5B01G406900 chr4A 94.000 100 6 0 2639 2738 610735259 610735160 8.100000e-33 152.0
42 TraesCS5B01G406900 chr4A 92.683 82 4 1 498 577 18683391 18683310 2.960000e-22 117.0
43 TraesCS5B01G406900 chr4A 91.463 82 5 1 498 577 18649578 18649497 1.380000e-20 111.0
44 TraesCS5B01G406900 chr7B 79.679 187 33 5 44 227 185043161 185043345 3.800000e-26 130.0
45 TraesCS5B01G406900 chr7B 94.231 52 2 1 540 590 168077629 168077578 1.390000e-10 78.7
46 TraesCS5B01G406900 chr1D 92.208 77 6 0 502 578 442373784 442373860 4.950000e-20 110.0
47 TraesCS5B01G406900 chr1D 75.424 236 46 8 32 262 413586483 413586255 2.300000e-18 104.0
48 TraesCS5B01G406900 chr2A 87.234 94 10 2 485 577 729674096 729674188 6.400000e-19 106.0
49 TraesCS5B01G406900 chr2A 83.750 80 6 4 500 572 540847331 540847410 8.400000e-08 69.4
50 TraesCS5B01G406900 chr7A 87.912 91 7 2 494 581 381248678 381248767 2.300000e-18 104.0
51 TraesCS5B01G406900 chr7A 85.263 95 5 4 501 587 136806190 136806097 6.440000e-14 89.8
52 TraesCS5B01G406900 chr3D 92.105 76 3 2 501 573 105151124 105151049 2.300000e-18 104.0
53 TraesCS5B01G406900 chr3D 84.043 94 7 4 501 586 180394992 180394899 3.000000e-12 84.2
54 TraesCS5B01G406900 chr3D 93.617 47 3 0 540 586 30294900 30294946 2.330000e-08 71.3


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 TraesCS5B01G406900 chr5B 582894391 582899066 4675 True 8636.00 8636 100.000000 1 4676 1 chr5B.!!$R1 4675
1 TraesCS5B01G406900 chr5B 358019667 358020314 647 False 1005.00 1005 94.521000 2138 2794 1 chr5B.!!$F2 656
2 TraesCS5B01G406900 chr5B 626280629 626281155 526 False 680.00 680 90.019000 1504 2031 1 chr5B.!!$F3 527
3 TraesCS5B01G406900 chr5D 475513420 475519651 6231 True 1277.46 3714 90.726800 1 4676 5 chr5D.!!$R1 4675
4 TraesCS5B01G406900 chr5D 198385834 198386427 593 False 367.00 632 90.663000 1506 2143 2 chr5D.!!$F2 637
5 TraesCS5B01G406900 chr5D 198444045 198444637 592 False 361.05 625 89.843500 1507 2143 2 chr5D.!!$F3 636
6 TraesCS5B01G406900 chr5A 594966898 594970726 3828 True 951.60 2826 94.328333 636 4676 6 chr5A.!!$R2 4040
7 TraesCS5B01G406900 chr4D 451649702 451650933 1231 True 844.50 987 92.265500 1612 2794 2 chr4D.!!$R1 1182
8 TraesCS5B01G406900 chr1B 51418640 51419286 646 False 970.00 970 93.607000 2139 2794 1 chr1B.!!$F2 655
9 TraesCS5B01G406900 chr1B 51402361 51403007 646 False 944.00 944 92.846000 2138 2794 1 chr1B.!!$F1 656
10 TraesCS5B01G406900 chrUn 215731636 215732282 646 True 961.00 961 93.303000 2138 2794 1 chrUn.!!$R1 656
11 TraesCS5B01G406900 chr3A 11823097 11823737 640 True 913.00 913 92.121000 2136 2794 1 chr3A.!!$R1 658
12 TraesCS5B01G406900 chr4B 662787264 662787788 524 True 665.00 665 89.603000 1506 2031 1 chr4B.!!$R1 525
13 TraesCS5B01G406900 chr3B 798188411 798188933 522 True 647.00 647 89.036000 1506 2031 1 chr3B.!!$R1 525

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
435 442 0.033109 AGTTTGCTATTGGGGAGCCC 60.033 55.0 0.00 0.0 45.71 5.19 F
1823 3297 0.037697 CGGAAACATCTCGTGGTGGA 60.038 55.0 2.40 0.0 0.00 4.02 F
2217 3766 0.171903 ATCTGCATTGCTCGTTTGGC 59.828 50.0 10.49 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 3383 0.929615 CAAGGCAAAGCACAAAACCG 59.070 50.000 0.0 0.0 0.00 4.44 R
3642 5209 2.047655 CGCCTGCTTCGGGTGTTA 60.048 61.111 0.0 0.0 35.82 2.41 R
4084 5653 1.374758 CAGGACGGAGGTTGCAGTC 60.375 63.158 0.0 0.0 33.12 3.51 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 2.558378 GTTAGCGGTGGGAAGGAATAC 58.442 52.381 0.00 0.00 0.00 1.89
54 55 0.313987 GTGGACGAAAAAGGGCAAGG 59.686 55.000 0.00 0.00 0.00 3.61
72 74 1.880340 GATTGAGTGGAGAGCGGCG 60.880 63.158 0.51 0.51 0.00 6.46
92 94 2.472029 GGGATGGAAGAAGAGAGTGGA 58.528 52.381 0.00 0.00 0.00 4.02
121 123 2.718731 CGAAAACAGTGCGGCCAA 59.281 55.556 2.24 0.00 0.00 4.52
134 136 0.804156 CGGCCAACTGCAAAAACGTT 60.804 50.000 2.24 0.00 43.89 3.99
138 140 1.639280 CAACTGCAAAAACGTTGGCT 58.361 45.000 17.24 0.00 34.43 4.75
144 146 0.378962 CAAAAACGTTGGCTCCGTCA 59.621 50.000 0.00 0.00 37.61 4.35
162 164 1.005450 TCATAGTTTTGGGTGGGCCTC 59.995 52.381 4.53 0.00 34.45 4.70
166 168 3.501040 TTTTGGGTGGGCCTCGGTC 62.501 63.158 4.53 0.00 34.45 4.79
178 180 1.153489 CTCGGTCGTCGGAGTCCTA 60.153 63.158 7.77 0.00 39.77 2.94
179 181 1.427592 CTCGGTCGTCGGAGTCCTAC 61.428 65.000 7.77 5.60 39.77 3.18
185 187 2.753043 TCGGAGTCCTACGTGGCC 60.753 66.667 7.77 0.00 38.28 5.36
201 203 4.939368 CCCGTGTCCAAACGCCCA 62.939 66.667 0.00 0.00 42.23 5.36
213 215 4.041762 CGCCCACAAGCCCCCTAA 62.042 66.667 0.00 0.00 0.00 2.69
214 216 2.689813 GCCCACAAGCCCCCTAAT 59.310 61.111 0.00 0.00 0.00 1.73
217 219 1.342574 GCCCACAAGCCCCCTAATTTA 60.343 52.381 0.00 0.00 0.00 1.40
218 220 2.666317 CCCACAAGCCCCCTAATTTAG 58.334 52.381 0.00 0.00 0.00 1.85
219 221 2.024369 CCCACAAGCCCCCTAATTTAGT 60.024 50.000 2.88 0.00 0.00 2.24
221 223 3.699538 CCACAAGCCCCCTAATTTAGTTC 59.300 47.826 2.88 0.00 0.00 3.01
223 225 2.949644 CAAGCCCCCTAATTTAGTTCCG 59.050 50.000 2.88 0.00 0.00 4.30
224 226 2.202707 AGCCCCCTAATTTAGTTCCGT 58.797 47.619 2.88 0.00 0.00 4.69
248 254 0.179073 CGAGAGAATTGCGGTCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
258 264 2.423898 CGGTCCCATACTGCTCCGT 61.424 63.158 0.00 0.00 34.38 4.69
267 273 0.817654 TACTGCTCCGTGGACTGATG 59.182 55.000 0.00 0.00 0.00 3.07
268 274 1.153489 CTGCTCCGTGGACTGATGG 60.153 63.158 0.00 0.00 0.00 3.51
274 280 2.584608 GTGGACTGATGGGGGTCG 59.415 66.667 0.00 0.00 33.70 4.79
297 303 4.115199 GGATGGCTTGCGGGGTCT 62.115 66.667 0.00 0.00 0.00 3.85
299 305 3.329542 GATGGCTTGCGGGGTCTGA 62.330 63.158 0.00 0.00 0.00 3.27
300 306 2.819984 GATGGCTTGCGGGGTCTGAA 62.820 60.000 0.00 0.00 0.00 3.02
301 307 3.056328 GGCTTGCGGGGTCTGAAC 61.056 66.667 0.00 0.00 0.00 3.18
302 308 3.423154 GCTTGCGGGGTCTGAACG 61.423 66.667 0.00 0.00 0.00 3.95
303 309 2.742372 CTTGCGGGGTCTGAACGG 60.742 66.667 0.00 0.00 0.00 4.44
304 310 4.323477 TTGCGGGGTCTGAACGGG 62.323 66.667 0.00 0.00 0.00 5.28
306 312 3.384532 GCGGGGTCTGAACGGGTA 61.385 66.667 0.00 0.00 0.00 3.69
307 313 2.575461 CGGGGTCTGAACGGGTAC 59.425 66.667 0.00 0.00 0.00 3.34
309 315 1.978617 GGGGTCTGAACGGGTACGA 60.979 63.158 0.00 0.00 44.60 3.43
310 316 1.509923 GGGTCTGAACGGGTACGAG 59.490 63.158 0.00 0.00 44.60 4.18
311 317 0.962356 GGGTCTGAACGGGTACGAGA 60.962 60.000 0.00 0.00 44.60 4.04
312 318 0.450983 GGTCTGAACGGGTACGAGAG 59.549 60.000 0.00 0.00 44.60 3.20
313 319 1.446907 GTCTGAACGGGTACGAGAGA 58.553 55.000 0.00 0.00 44.60 3.10
314 320 2.015587 GTCTGAACGGGTACGAGAGAT 58.984 52.381 0.00 0.00 44.60 2.75
315 321 2.422832 GTCTGAACGGGTACGAGAGATT 59.577 50.000 0.00 0.00 44.60 2.40
316 322 3.087031 TCTGAACGGGTACGAGAGATTT 58.913 45.455 0.00 0.00 44.60 2.17
327 333 1.403679 CGAGAGATTTGAGAGTCGGCT 59.596 52.381 0.00 0.00 0.00 5.52
329 335 3.674682 CGAGAGATTTGAGAGTCGGCTTT 60.675 47.826 0.00 0.00 0.00 3.51
331 337 3.259374 AGAGATTTGAGAGTCGGCTTTGA 59.741 43.478 0.00 0.00 0.00 2.69
393 399 7.093112 CCTCATTAAAATTGTGGTATTGGGGAA 60.093 37.037 0.00 0.00 0.00 3.97
435 442 0.033109 AGTTTGCTATTGGGGAGCCC 60.033 55.000 0.00 0.00 45.71 5.19
445 452 2.930935 GGGGAGCCCAAGTAGATGA 58.069 57.895 8.02 0.00 44.65 2.92
446 453 1.213296 GGGGAGCCCAAGTAGATGAA 58.787 55.000 8.02 0.00 44.65 2.57
448 455 2.175715 GGGGAGCCCAAGTAGATGAATT 59.824 50.000 8.02 0.00 44.65 2.17
451 458 4.711846 GGGAGCCCAAGTAGATGAATTTTT 59.288 41.667 0.00 0.00 35.81 1.94
510 524 7.786178 TGAATACAATCAATTACTCCCTTCG 57.214 36.000 0.00 0.00 0.00 3.79
511 525 7.335627 TGAATACAATCAATTACTCCCTTCGT 58.664 34.615 0.00 0.00 0.00 3.85
512 526 7.494625 TGAATACAATCAATTACTCCCTTCGTC 59.505 37.037 0.00 0.00 0.00 4.20
513 527 5.422214 ACAATCAATTACTCCCTTCGTCT 57.578 39.130 0.00 0.00 0.00 4.18
514 528 5.420409 ACAATCAATTACTCCCTTCGTCTC 58.580 41.667 0.00 0.00 0.00 3.36
515 529 5.046591 ACAATCAATTACTCCCTTCGTCTCA 60.047 40.000 0.00 0.00 0.00 3.27
516 530 5.878406 ATCAATTACTCCCTTCGTCTCAT 57.122 39.130 0.00 0.00 0.00 2.90
517 531 6.978674 ATCAATTACTCCCTTCGTCTCATA 57.021 37.500 0.00 0.00 0.00 2.15
518 532 6.785337 TCAATTACTCCCTTCGTCTCATAA 57.215 37.500 0.00 0.00 0.00 1.90
519 533 7.361457 TCAATTACTCCCTTCGTCTCATAAT 57.639 36.000 0.00 0.00 0.00 1.28
520 534 8.473358 TCAATTACTCCCTTCGTCTCATAATA 57.527 34.615 0.00 0.00 0.00 0.98
521 535 9.090103 TCAATTACTCCCTTCGTCTCATAATAT 57.910 33.333 0.00 0.00 0.00 1.28
525 539 9.803507 TTACTCCCTTCGTCTCATAATATAAGA 57.196 33.333 0.00 0.00 0.00 2.10
526 540 8.343168 ACTCCCTTCGTCTCATAATATAAGAG 57.657 38.462 0.00 0.00 0.00 2.85
527 541 7.094118 ACTCCCTTCGTCTCATAATATAAGAGC 60.094 40.741 0.00 0.00 0.00 4.09
528 542 6.030849 CCCTTCGTCTCATAATATAAGAGCG 58.969 44.000 0.00 0.00 33.46 5.03
529 543 6.349445 CCCTTCGTCTCATAATATAAGAGCGT 60.349 42.308 0.00 0.00 33.70 5.07
530 544 7.085116 CCTTCGTCTCATAATATAAGAGCGTT 58.915 38.462 0.00 0.00 33.70 4.84
531 545 7.595502 CCTTCGTCTCATAATATAAGAGCGTTT 59.404 37.037 0.00 0.00 33.70 3.60
532 546 8.867112 TTCGTCTCATAATATAAGAGCGTTTT 57.133 30.769 0.00 0.00 33.70 2.43
533 547 8.867112 TCGTCTCATAATATAAGAGCGTTTTT 57.133 30.769 0.00 0.00 33.70 1.94
554 568 7.820044 TTTTTACAATGTCAAAAACGCTCTT 57.180 28.000 3.29 0.00 30.72 2.85
555 569 8.912787 TTTTTACAATGTCAAAAACGCTCTTA 57.087 26.923 3.29 0.00 30.72 2.10
556 570 9.522804 TTTTTACAATGTCAAAAACGCTCTTAT 57.477 25.926 3.29 0.00 30.72 1.73
563 577 9.950680 AATGTCAAAAACGCTCTTATATTATGG 57.049 29.630 0.00 0.00 0.00 2.74
564 578 7.925993 TGTCAAAAACGCTCTTATATTATGGG 58.074 34.615 0.00 0.00 0.00 4.00
565 579 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
566 580 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
567 581 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
568 582 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
569 583 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
570 584 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
571 585 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
572 586 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
573 587 3.773119 TCTTATATTATGGGACGGAGGGC 59.227 47.826 0.00 0.00 0.00 5.19
574 588 0.902531 ATATTATGGGACGGAGGGCG 59.097 55.000 0.00 0.00 0.00 6.13
589 603 1.066358 AGGGCGTAGAAAAGTAGGCAC 60.066 52.381 0.00 0.00 37.45 5.01
590 604 0.997196 GGCGTAGAAAAGTAGGCACG 59.003 55.000 0.00 0.00 35.85 5.34
605 619 6.646267 AGTAGGCACGTAATTTATCCAAAGA 58.354 36.000 0.00 0.00 0.00 2.52
607 621 5.250200 AGGCACGTAATTTATCCAAAGACA 58.750 37.500 0.00 0.00 0.00 3.41
609 623 7.051623 AGGCACGTAATTTATCCAAAGACATA 58.948 34.615 0.00 0.00 0.00 2.29
612 626 8.774586 GCACGTAATTTATCCAAAGACATATCT 58.225 33.333 0.00 0.00 36.42 1.98
628 642 6.989169 AGACATATCTTCCACTTCATTGTAGC 59.011 38.462 0.00 0.00 0.00 3.58
674 688 1.884579 GATGGCCATGAATCATCGCTT 59.115 47.619 26.56 0.00 29.24 4.68
693 707 5.530171 TCGCTTATCGGTGTCTCTATAAAGT 59.470 40.000 0.00 0.00 39.05 2.66
696 712 6.238953 GCTTATCGGTGTCTCTATAAAGTCCA 60.239 42.308 0.00 0.00 0.00 4.02
710 726 9.042450 TCTATAAAGTCCAAATACTCACTTCCA 57.958 33.333 0.00 0.00 0.00 3.53
717 733 6.486993 GTCCAAATACTCACTTCCACTTTTCT 59.513 38.462 0.00 0.00 0.00 2.52
727 743 7.264947 TCACTTCCACTTTTCTTTTTCCATTC 58.735 34.615 0.00 0.00 0.00 2.67
731 747 5.660864 TCCACTTTTCTTTTTCCATTCCAGT 59.339 36.000 0.00 0.00 0.00 4.00
831 2288 2.997315 GAAGCCAAACCAGCCCCC 60.997 66.667 0.00 0.00 0.00 5.40
867 2324 0.390735 AATACCCTCGCGTCAACCAC 60.391 55.000 5.77 0.00 0.00 4.16
1719 3190 2.280628 CAAATCGAGTAGGTTCCTGGC 58.719 52.381 1.12 0.00 0.00 4.85
1735 3206 1.349026 CTGGCCATATCCCATCTCGTT 59.651 52.381 5.51 0.00 0.00 3.85
1770 3244 1.465777 CGAATTTGGTACCCGTGGTTC 59.534 52.381 10.07 6.06 37.09 3.62
1823 3297 0.037697 CGGAAACATCTCGTGGTGGA 60.038 55.000 2.40 0.00 0.00 4.02
1843 3319 2.439507 GAGGATTCTGCAGGTATTGGGA 59.560 50.000 15.13 0.00 0.00 4.37
1844 3320 2.441001 AGGATTCTGCAGGTATTGGGAG 59.559 50.000 15.13 0.00 0.00 4.30
1845 3321 2.487986 GGATTCTGCAGGTATTGGGAGG 60.488 54.545 15.13 0.00 0.00 4.30
1846 3322 0.918983 TTCTGCAGGTATTGGGAGGG 59.081 55.000 15.13 0.00 0.00 4.30
1859 3337 1.273098 TGGGAGGGTCAGAGGAGTTAC 60.273 57.143 0.00 0.00 0.00 2.50
1860 3338 1.487300 GGAGGGTCAGAGGAGTTACC 58.513 60.000 0.00 0.00 39.35 2.85
1902 3383 5.757850 ATTTAATTGCGTCTCCCTTGATC 57.242 39.130 0.00 0.00 0.00 2.92
1922 3403 1.298602 GGTTTTGTGCTTTGCCTTGG 58.701 50.000 0.00 0.00 0.00 3.61
1995 3476 4.462483 GTGATTTGGCAGGGACAAGATAAA 59.538 41.667 0.00 0.00 29.74 1.40
2007 3488 4.054671 GACAAGATAAAGGATGAGAGGCG 58.945 47.826 0.00 0.00 0.00 5.52
2044 3525 4.189188 CAATGCAGGCGCCTCAGC 62.189 66.667 30.29 28.47 37.32 4.26
2102 3583 2.738964 GCTCGTCAGATTACCCAGGTTC 60.739 54.545 0.00 0.00 0.00 3.62
2217 3766 0.171903 ATCTGCATTGCTCGTTTGGC 59.828 50.000 10.49 0.00 0.00 4.52
2232 3781 3.189287 CGTTTGGCTATTGCTTTGAGAGT 59.811 43.478 0.00 0.00 39.59 3.24
2275 3824 1.676006 GTGCCAGCCAATATTAAGCGT 59.324 47.619 4.49 0.00 0.00 5.07
2294 3843 3.932710 GCGTCCTTGTGTATCTGAATTGA 59.067 43.478 0.00 0.00 0.00 2.57
2374 3929 7.479980 TGTACTTTGCATACAAATCTATTGGC 58.520 34.615 0.00 0.00 44.54 4.52
2433 3988 1.069022 CCGTTGCAATGTTCTCCACAG 60.069 52.381 17.19 0.00 39.40 3.66
2527 4091 0.548031 ATGCATGGAGGGTACACCAG 59.452 55.000 0.00 5.50 43.89 4.00
2552 4116 7.501559 AGCAAGATGTCTATATGATGCAAAAGT 59.498 33.333 0.00 0.00 35.11 2.66
2553 4117 7.590322 GCAAGATGTCTATATGATGCAAAAGTG 59.410 37.037 0.00 0.00 33.00 3.16
3152 4717 6.271488 TGAAATCTCTGCCAAAAGTTATGG 57.729 37.500 0.00 0.00 41.08 2.74
3163 4728 3.492421 AAAGTTATGGCGAATGTGCAG 57.508 42.857 0.00 0.00 36.28 4.41
3315 4880 3.758023 TCTTCATCAACATGCCGAAACAT 59.242 39.130 0.00 0.00 0.00 2.71
3348 4913 8.893219 TCAATATCTTAATGATCTGCGAAACT 57.107 30.769 0.00 0.00 36.65 2.66
3592 5159 4.219115 TCTCATCCTATCCTTGACTGGTC 58.781 47.826 0.00 0.00 0.00 4.02
3800 5367 1.961394 ACTGTAGCGGAGTTGTCTGAA 59.039 47.619 0.00 0.00 0.00 3.02
3808 5375 3.677424 GCGGAGTTGTCTGAATCTAGCTT 60.677 47.826 0.00 0.00 0.00 3.74
3812 5379 6.503524 GGAGTTGTCTGAATCTAGCTTCTAG 58.496 44.000 7.77 4.28 0.00 2.43
3829 5396 5.762279 CTTCTAGGGGTAGACTTCTCTTCT 58.238 45.833 0.00 0.00 0.00 2.85
3832 5399 6.211272 TCTAGGGGTAGACTTCTCTTCTAGA 58.789 44.000 0.00 0.00 0.00 2.43
3833 5400 6.852908 TCTAGGGGTAGACTTCTCTTCTAGAT 59.147 42.308 0.00 0.00 33.05 1.98
3889 5456 8.246430 TCTGTAGGACTCTTGTCTTCTAAAAA 57.754 34.615 0.00 0.00 42.54 1.94
4056 5625 5.582689 AACCTTTTTGAGTCTTCCAACAG 57.417 39.130 0.00 0.00 0.00 3.16
4074 5643 5.446473 CCAACAGCTCAGAATGTAATCGAAC 60.446 44.000 0.00 0.00 37.40 3.95
4084 5653 9.611284 TCAGAATGTAATCGAACTTTTGAATTG 57.389 29.630 0.00 0.00 37.40 2.32
4089 5658 6.855914 TGTAATCGAACTTTTGAATTGACTGC 59.144 34.615 0.00 0.00 0.00 4.40
4181 5750 7.765695 ATAATCTTCTTTGACCAAAGCTGAA 57.234 32.000 15.56 6.56 45.48 3.02
4213 5782 7.563906 TGTATTGACTGTGATAATCCATGTCA 58.436 34.615 0.00 0.00 33.77 3.58
4299 5868 1.226030 ACGCGTTTAGGTTGTGAGCC 61.226 55.000 5.58 0.00 0.00 4.70
4374 5943 5.999044 ACTGTGAAATCTTCCATGCTATCT 58.001 37.500 0.00 0.00 0.00 1.98
4436 6005 8.940952 TGTTTTTGGTCAAACAAAATTTAGGAG 58.059 29.630 6.77 0.00 46.22 3.69
4500 6069 6.088824 TCGATTAGTACTCGGTGAACTTTTC 58.911 40.000 9.70 0.00 36.78 2.29
4506 6075 1.260561 CTCGGTGAACTTTTCCACACG 59.739 52.381 0.00 0.00 35.13 4.49
4508 6077 1.385528 GGTGAACTTTTCCACACGGT 58.614 50.000 0.00 0.00 35.13 4.83
4656 6411 7.404139 CGGAATAAACTATTCTACCTTTCCG 57.596 40.000 5.96 5.96 44.58 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.135527 CTTCCCACCGCTAACGTATGA 59.864 52.381 0.00 0.00 37.70 2.15
5 6 1.567504 CTTCCCACCGCTAACGTATG 58.432 55.000 0.00 0.00 37.70 2.39
6 7 0.462789 CCTTCCCACCGCTAACGTAT 59.537 55.000 0.00 0.00 37.70 3.06
7 8 0.611618 TCCTTCCCACCGCTAACGTA 60.612 55.000 0.00 0.00 37.70 3.57
8 9 1.474332 TTCCTTCCCACCGCTAACGT 61.474 55.000 0.00 0.00 37.70 3.99
30 31 1.429463 CCCTTTTTCGTCCACTCTCG 58.571 55.000 0.00 0.00 0.00 4.04
54 55 1.880340 CGCCGCTCTCCACTCAATC 60.880 63.158 0.00 0.00 0.00 2.67
66 68 3.391665 CTTCTTCCATCCCGCCGCT 62.392 63.158 0.00 0.00 0.00 5.52
68 70 1.227380 CTCTTCTTCCATCCCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
72 74 2.433970 CTCCACTCTCTTCTTCCATCCC 59.566 54.545 0.00 0.00 0.00 3.85
92 94 0.671251 TGTTTTCGCGGCAAAATCCT 59.329 45.000 6.13 0.00 0.00 3.24
121 123 0.102300 GGAGCCAACGTTTTTGCAGT 59.898 50.000 14.47 0.00 0.00 4.40
134 136 1.339631 CCCAAAACTATGACGGAGCCA 60.340 52.381 0.00 0.00 0.00 4.75
138 140 1.003812 CCCACCCAAAACTATGACGGA 59.996 52.381 0.00 0.00 0.00 4.69
144 146 0.034477 CGAGGCCCACCCAAAACTAT 60.034 55.000 0.00 0.00 36.11 2.12
162 164 3.096791 GTAGGACTCCGACGACCG 58.903 66.667 0.00 0.00 38.18 4.79
167 169 2.488820 GCCACGTAGGACTCCGAC 59.511 66.667 8.04 0.00 41.22 4.79
185 187 3.656045 GTGGGCGTTTGGACACGG 61.656 66.667 0.00 0.00 40.69 4.94
201 203 3.623954 CGGAACTAAATTAGGGGGCTTGT 60.624 47.826 4.92 0.00 0.00 3.16
210 212 6.090358 TCTCTCGCAAAACGGAACTAAATTAG 59.910 38.462 0.00 0.00 43.89 1.73
211 213 5.927689 TCTCTCGCAAAACGGAACTAAATTA 59.072 36.000 0.00 0.00 43.89 1.40
212 214 4.753107 TCTCTCGCAAAACGGAACTAAATT 59.247 37.500 0.00 0.00 43.89 1.82
213 215 4.312443 TCTCTCGCAAAACGGAACTAAAT 58.688 39.130 0.00 0.00 43.89 1.40
214 216 3.719924 TCTCTCGCAAAACGGAACTAAA 58.280 40.909 0.00 0.00 43.89 1.85
217 219 2.234300 TTCTCTCGCAAAACGGAACT 57.766 45.000 0.00 0.00 43.89 3.01
218 220 3.226347 CAATTCTCTCGCAAAACGGAAC 58.774 45.455 0.00 0.00 43.89 3.62
219 221 2.350388 GCAATTCTCTCGCAAAACGGAA 60.350 45.455 0.00 0.00 43.89 4.30
221 223 1.606606 GCAATTCTCTCGCAAAACGG 58.393 50.000 0.00 0.00 43.89 4.44
223 225 1.069227 ACCGCAATTCTCTCGCAAAAC 60.069 47.619 0.00 0.00 0.00 2.43
224 226 1.196808 GACCGCAATTCTCTCGCAAAA 59.803 47.619 0.00 0.00 0.00 2.44
248 254 0.817654 CATCAGTCCACGGAGCAGTA 59.182 55.000 0.00 0.00 0.00 2.74
256 262 2.584608 GACCCCCATCAGTCCACG 59.415 66.667 0.00 0.00 0.00 4.94
258 264 2.687200 CCGACCCCCATCAGTCCA 60.687 66.667 0.00 0.00 0.00 4.02
267 273 2.045340 CATCCAACACCGACCCCC 60.045 66.667 0.00 0.00 0.00 5.40
268 274 2.045340 CCATCCAACACCGACCCC 60.045 66.667 0.00 0.00 0.00 4.95
274 280 2.568090 CGCAAGCCATCCAACACC 59.432 61.111 0.00 0.00 0.00 4.16
297 303 2.821378 TCAAATCTCTCGTACCCGTTCA 59.179 45.455 0.00 0.00 35.01 3.18
299 305 3.087031 TCTCAAATCTCTCGTACCCGTT 58.913 45.455 0.00 0.00 35.01 4.44
300 306 2.683867 CTCTCAAATCTCTCGTACCCGT 59.316 50.000 0.00 0.00 35.01 5.28
301 307 2.683867 ACTCTCAAATCTCTCGTACCCG 59.316 50.000 0.00 0.00 0.00 5.28
302 308 3.242804 CGACTCTCAAATCTCTCGTACCC 60.243 52.174 0.00 0.00 0.00 3.69
303 309 3.242804 CCGACTCTCAAATCTCTCGTACC 60.243 52.174 0.00 0.00 0.00 3.34
304 310 3.789459 GCCGACTCTCAAATCTCTCGTAC 60.789 52.174 0.00 0.00 0.00 3.67
305 311 2.355132 GCCGACTCTCAAATCTCTCGTA 59.645 50.000 0.00 0.00 0.00 3.43
306 312 1.133407 GCCGACTCTCAAATCTCTCGT 59.867 52.381 0.00 0.00 0.00 4.18
307 313 1.403679 AGCCGACTCTCAAATCTCTCG 59.596 52.381 0.00 0.00 0.00 4.04
308 314 3.518634 AAGCCGACTCTCAAATCTCTC 57.481 47.619 0.00 0.00 0.00 3.20
309 315 3.259374 TCAAAGCCGACTCTCAAATCTCT 59.741 43.478 0.00 0.00 0.00 3.10
310 316 3.589988 TCAAAGCCGACTCTCAAATCTC 58.410 45.455 0.00 0.00 0.00 2.75
311 317 3.685139 TCAAAGCCGACTCTCAAATCT 57.315 42.857 0.00 0.00 0.00 2.40
312 318 3.997021 TCTTCAAAGCCGACTCTCAAATC 59.003 43.478 0.00 0.00 0.00 2.17
313 319 4.008074 TCTTCAAAGCCGACTCTCAAAT 57.992 40.909 0.00 0.00 0.00 2.32
314 320 3.469008 TCTTCAAAGCCGACTCTCAAA 57.531 42.857 0.00 0.00 0.00 2.69
315 321 3.329386 CATCTTCAAAGCCGACTCTCAA 58.671 45.455 0.00 0.00 0.00 3.02
316 322 2.932622 GCATCTTCAAAGCCGACTCTCA 60.933 50.000 0.00 0.00 0.00 3.27
327 333 3.719268 TGCTCTAAGGGCATCTTCAAA 57.281 42.857 0.00 0.00 36.93 2.69
359 365 5.338300 CCACAATTTTAATGAGGAAAGGGGG 60.338 44.000 0.00 0.00 31.01 5.40
372 378 6.881602 GCAATTCCCCAATACCACAATTTTAA 59.118 34.615 0.00 0.00 0.00 1.52
380 386 1.757682 TCGCAATTCCCCAATACCAC 58.242 50.000 0.00 0.00 0.00 4.16
500 514 9.451002 CTCTTATATTATGAGACGAAGGGAGTA 57.549 37.037 0.00 0.00 33.20 2.59
501 515 7.094118 GCTCTTATATTATGAGACGAAGGGAGT 60.094 40.741 0.00 0.00 33.20 3.85
502 516 7.254852 GCTCTTATATTATGAGACGAAGGGAG 58.745 42.308 0.00 0.00 33.20 4.30
503 517 6.127980 CGCTCTTATATTATGAGACGAAGGGA 60.128 42.308 11.45 0.00 34.62 4.20
504 518 6.030849 CGCTCTTATATTATGAGACGAAGGG 58.969 44.000 11.45 2.16 34.62 3.95
505 519 6.613233 ACGCTCTTATATTATGAGACGAAGG 58.387 40.000 18.20 3.81 35.57 3.46
506 520 8.508800 AAACGCTCTTATATTATGAGACGAAG 57.491 34.615 18.20 4.07 35.57 3.79
507 521 8.867112 AAAACGCTCTTATATTATGAGACGAA 57.133 30.769 18.20 0.00 35.57 3.85
508 522 8.867112 AAAAACGCTCTTATATTATGAGACGA 57.133 30.769 18.20 0.00 35.57 4.20
530 544 7.820044 AAGAGCGTTTTTGACATTGTAAAAA 57.180 28.000 7.81 7.81 34.45 1.94
537 551 9.950680 CCATAATATAAGAGCGTTTTTGACATT 57.049 29.630 0.00 0.00 0.00 2.71
538 552 8.567948 CCCATAATATAAGAGCGTTTTTGACAT 58.432 33.333 0.00 0.00 0.00 3.06
539 553 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
540 554 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
541 555 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
542 556 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
543 557 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
544 558 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
545 559 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
546 560 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
547 561 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
548 562 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
549 563 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
550 564 4.141914 GCCCTCCGTCCCATAATATAAGAG 60.142 50.000 0.00 0.00 0.00 2.85
551 565 3.773119 GCCCTCCGTCCCATAATATAAGA 59.227 47.826 0.00 0.00 0.00 2.10
552 566 3.430374 CGCCCTCCGTCCCATAATATAAG 60.430 52.174 0.00 0.00 0.00 1.73
553 567 2.498481 CGCCCTCCGTCCCATAATATAA 59.502 50.000 0.00 0.00 0.00 0.98
554 568 2.104967 CGCCCTCCGTCCCATAATATA 58.895 52.381 0.00 0.00 0.00 0.86
555 569 0.902531 CGCCCTCCGTCCCATAATAT 59.097 55.000 0.00 0.00 0.00 1.28
556 570 2.358039 CGCCCTCCGTCCCATAATA 58.642 57.895 0.00 0.00 0.00 0.98
557 571 3.148084 CGCCCTCCGTCCCATAAT 58.852 61.111 0.00 0.00 0.00 1.28
566 580 1.202382 CCTACTTTTCTACGCCCTCCG 60.202 57.143 0.00 0.00 44.21 4.63
567 581 1.472904 GCCTACTTTTCTACGCCCTCC 60.473 57.143 0.00 0.00 0.00 4.30
568 582 1.206371 TGCCTACTTTTCTACGCCCTC 59.794 52.381 0.00 0.00 0.00 4.30
569 583 1.066358 GTGCCTACTTTTCTACGCCCT 60.066 52.381 0.00 0.00 0.00 5.19
570 584 1.366679 GTGCCTACTTTTCTACGCCC 58.633 55.000 0.00 0.00 0.00 6.13
571 585 0.997196 CGTGCCTACTTTTCTACGCC 59.003 55.000 0.00 0.00 0.00 5.68
572 586 1.706443 ACGTGCCTACTTTTCTACGC 58.294 50.000 0.00 0.00 35.17 4.42
573 587 6.399204 AAATTACGTGCCTACTTTTCTACG 57.601 37.500 0.00 0.00 37.54 3.51
574 588 8.546244 GGATAAATTACGTGCCTACTTTTCTAC 58.454 37.037 0.00 0.00 0.00 2.59
605 619 5.755375 CGCTACAATGAAGTGGAAGATATGT 59.245 40.000 0.00 0.00 0.00 2.29
607 621 5.163301 ACCGCTACAATGAAGTGGAAGATAT 60.163 40.000 9.54 0.00 45.70 1.63
609 623 3.055094 ACCGCTACAATGAAGTGGAAGAT 60.055 43.478 9.54 0.00 45.70 2.40
612 626 2.037902 TCACCGCTACAATGAAGTGGAA 59.962 45.455 9.54 0.00 45.70 3.53
628 642 4.507710 TGAGATTTTGATCCTTCTCACCG 58.492 43.478 8.90 0.00 39.61 4.94
674 688 7.649533 TTTGGACTTTATAGAGACACCGATA 57.350 36.000 0.00 0.00 0.00 2.92
693 707 6.601332 AGAAAAGTGGAAGTGAGTATTTGGA 58.399 36.000 0.00 0.00 0.00 3.53
696 712 9.803315 GAAAAAGAAAAGTGGAAGTGAGTATTT 57.197 29.630 0.00 0.00 0.00 1.40
717 733 8.198109 TGAAACGAAAATACTGGAATGGAAAAA 58.802 29.630 0.00 0.00 0.00 1.94
746 762 3.695830 TTCACTTCACATACTGTCCCC 57.304 47.619 0.00 0.00 0.00 4.81
831 2288 4.383661 GGGTATTTATGGGTTTGGGCTTTG 60.384 45.833 0.00 0.00 0.00 2.77
1392 2863 2.787249 CGTTGCTGCTCCAATCGG 59.213 61.111 0.00 0.00 0.00 4.18
1395 2866 2.282391 TGGCGTTGCTGCTCCAAT 60.282 55.556 0.00 0.00 34.52 3.16
1458 2929 4.118995 TCGTACGCGGCCACGAAT 62.119 61.111 22.04 0.00 43.63 3.34
1540 3011 3.636231 TGAACGACCCTGCCCCAG 61.636 66.667 0.00 0.00 0.00 4.45
1719 3190 2.770164 GGGAACGAGATGGGATATGG 57.230 55.000 0.00 0.00 0.00 2.74
1735 3206 3.396260 AATTCGACAAGAAAGACGGGA 57.604 42.857 0.00 0.00 42.91 5.14
1782 3256 3.414700 CCCAGAACGTCACAGCGC 61.415 66.667 0.00 0.00 34.88 5.92
1823 3297 2.441001 CTCCCAATACCTGCAGAATCCT 59.559 50.000 17.39 0.00 0.00 3.24
1843 3319 3.713867 GGGTAACTCCTCTGACCCT 57.286 57.895 1.55 0.00 46.92 4.34
1859 3337 9.757227 TTAAATACACAAATTGAACAAAGAGGG 57.243 29.630 0.00 0.00 0.00 4.30
1902 3383 0.929615 CAAGGCAAAGCACAAAACCG 59.070 50.000 0.00 0.00 0.00 4.44
1922 3403 5.521372 GCAATGAGGCAAATCATTCTAAACC 59.479 40.000 7.77 0.00 44.68 3.27
1995 3476 3.071206 ACGCACGCCTCTCATCCT 61.071 61.111 0.00 0.00 0.00 3.24
2007 3488 1.436195 TTCCAACTGCTCACACGCAC 61.436 55.000 0.00 0.00 35.74 5.34
2044 3525 1.080705 GTTGGAGACTGACGGGTCG 60.081 63.158 0.00 0.00 40.76 4.79
2050 3531 2.640316 AACCCTTGTTGGAGACTGAC 57.360 50.000 0.00 0.00 38.35 3.51
2102 3583 2.510613 ACCACCCACAGAATAAAACCG 58.489 47.619 0.00 0.00 0.00 4.44
2217 3766 6.981762 AGAATGACACTCTCAAAGCAATAG 57.018 37.500 0.00 0.00 30.60 1.73
2232 3781 2.083774 GGCAATCCGTGAAGAATGACA 58.916 47.619 0.00 0.00 0.00 3.58
2257 3806 1.266989 GGACGCTTAATATTGGCTGGC 59.733 52.381 0.00 0.00 0.00 4.85
2275 3824 3.932710 GCGTCAATTCAGATACACAAGGA 59.067 43.478 0.00 0.00 0.00 3.36
2374 3929 4.245660 TGAATGAAGTAAGAACGGCTCTG 58.754 43.478 0.00 0.00 33.37 3.35
2527 4091 7.590322 CACTTTTGCATCATATAGACATCTTGC 59.410 37.037 0.00 0.00 0.00 4.01
3152 4717 5.641209 AGATAAGATAATCCTGCACATTCGC 59.359 40.000 0.00 0.00 0.00 4.70
3203 4768 4.148079 TGCCAAACAAGGATATTGTGTGA 58.852 39.130 11.57 0.00 39.41 3.58
3642 5209 2.047655 CGCCTGCTTCGGGTGTTA 60.048 61.111 0.00 0.00 35.82 2.41
3800 5367 5.374453 AGAAGTCTACCCCTAGAAGCTAGAT 59.626 44.000 0.00 0.00 30.37 1.98
3808 5375 6.211272 TCTAGAAGAGAAGTCTACCCCTAGA 58.789 44.000 0.00 0.00 31.88 2.43
3812 5379 7.235804 ACATATCTAGAAGAGAAGTCTACCCC 58.764 42.308 0.00 0.00 37.85 4.95
3859 5426 6.495181 AGAAGACAAGAGTCCTACAGATTTCA 59.505 38.462 0.00 0.00 46.15 2.69
3889 5456 9.381038 TCTACTTATAAATTGAGCCCTACAGAT 57.619 33.333 0.00 0.00 0.00 2.90
3967 5536 5.716703 ACTTTAAATGGGCTAAACTGCTGAT 59.283 36.000 0.00 0.00 0.00 2.90
4056 5625 6.831769 TCAAAAGTTCGATTACATTCTGAGC 58.168 36.000 0.00 0.00 0.00 4.26
4074 5643 4.301628 GGAGGTTGCAGTCAATTCAAAAG 58.698 43.478 0.00 0.00 34.29 2.27
4084 5653 1.374758 CAGGACGGAGGTTGCAGTC 60.375 63.158 0.00 0.00 33.12 3.51
4089 5658 2.543777 TCTTTTCAGGACGGAGGTTG 57.456 50.000 0.00 0.00 0.00 3.77
4138 5707 7.068061 AGATTATAATATACTCCCTCCGTCCC 58.932 42.308 0.00 0.00 0.00 4.46
4197 5766 7.700022 TTCAAACATGACATGGATTATCACA 57.300 32.000 19.39 0.00 33.60 3.58
4205 5774 6.402456 TGTCAAATTCAAACATGACATGGA 57.598 33.333 19.39 4.71 45.14 3.41
4299 5868 3.326747 GAATCTTGTATCCCGATTCCCG 58.673 50.000 0.00 0.00 37.91 5.14
4344 5913 4.971939 TGGAAGATTTCACAGTCACATGA 58.028 39.130 0.00 0.00 0.00 3.07
4352 5921 6.053650 TCAGATAGCATGGAAGATTTCACAG 58.946 40.000 0.00 0.00 0.00 3.66
4389 5958 2.104111 ACCTTCAACGTTCCATGTCTGA 59.896 45.455 0.00 0.00 0.00 3.27
4395 5964 4.429108 CAAAAACACCTTCAACGTTCCAT 58.571 39.130 0.00 0.00 0.00 3.41
4436 6005 2.143122 TCGACAGCAATCACCTTCAAC 58.857 47.619 0.00 0.00 0.00 3.18
4500 6069 0.321298 CCCAAGTCCTTACCGTGTGG 60.321 60.000 0.00 0.00 42.84 4.17
4506 6075 4.362470 ACAGTTTACCCAAGTCCTTACC 57.638 45.455 0.00 0.00 0.00 2.85
4508 6077 7.747690 TCAAATACAGTTTACCCAAGTCCTTA 58.252 34.615 0.00 0.00 0.00 2.69
4622 6376 3.934457 AGTTTATTCCGCAAAAGTGGG 57.066 42.857 0.00 0.00 37.44 4.61


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

AutoCloner maintained by Alex Coulton.