Multiple sequence alignment - TraesCS2A01G553400

Loading Multiple Alignment...

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 TraesCS2A01G553400 chr2A 100.000 4480 0 0 1 4480 758926327 758921848 0.000000e+00 8274.0
1 TraesCS2A01G553400 chr2A 85.237 359 44 6 207 561 289912822 289913175 1.180000e-95 361.0
2 TraesCS2A01G553400 chr2D 95.235 2875 70 21 1430 4290 629204825 629202004 0.000000e+00 4488.0
3 TraesCS2A01G553400 chr2D 87.899 595 21 15 600 1171 629205462 629204896 0.000000e+00 652.0
4 TraesCS2A01G553400 chr2D 87.288 354 40 5 209 561 318459058 318459407 2.510000e-107 399.0
5 TraesCS2A01G553400 chr2D 91.837 196 10 2 4284 4476 629201960 629201768 7.390000e-68 268.0
6 TraesCS2A01G553400 chr2D 92.222 90 7 0 1198 1287 629204898 629204809 1.310000e-25 128.0
7 TraesCS2A01G553400 chr2D 96.429 56 1 1 1288 1343 559245286 559245340 1.720000e-14 91.6
8 TraesCS2A01G553400 chr2B 90.717 3458 161 62 943 4290 772049730 772053137 0.000000e+00 4460.0
9 TraesCS2A01G553400 chr2B 92.000 125 3 4 4350 4470 772053320 772053441 7.710000e-38 169.0
10 TraesCS2A01G553400 chr2B 94.521 73 4 0 4281 4353 772053178 772053250 3.660000e-21 113.0
11 TraesCS2A01G553400 chr2B 83.186 113 11 5 727 839 772049512 772049616 3.690000e-16 97.1
12 TraesCS2A01G553400 chr6A 97.668 772 16 2 3700 4470 527380500 527379730 0.000000e+00 1325.0
13 TraesCS2A01G553400 chr6A 97.552 776 13 2 3700 4470 527457297 527456523 0.000000e+00 1323.0
14 TraesCS2A01G553400 chr6A 92.138 318 24 1 208 525 224017497 224017181 8.840000e-122 448.0
15 TraesCS2A01G553400 chrUn 92.971 313 22 0 208 520 167084460 167084772 1.470000e-124 457.0
16 TraesCS2A01G553400 chrUn 92.675 314 20 3 208 520 252262168 252261857 2.460000e-122 449.0
17 TraesCS2A01G553400 chr5A 92.652 313 23 0 208 520 696039175 696038863 6.830000e-123 451.0
18 TraesCS2A01G553400 chr5A 91.385 325 26 2 211 535 398981894 398982216 1.140000e-120 444.0
19 TraesCS2A01G553400 chr5A 93.780 209 13 0 1 209 333662455 333662247 9.350000e-82 315.0
20 TraesCS2A01G553400 chr5A 93.810 210 12 1 1 209 410197592 410197801 9.350000e-82 315.0
21 TraesCS2A01G553400 chr5A 86.296 270 34 3 292 561 79428515 79428249 1.580000e-74 291.0
22 TraesCS2A01G553400 chr7A 90.588 340 29 3 208 546 731254742 731254405 8.840000e-122 448.0
23 TraesCS2A01G553400 chr7A 93.780 209 13 0 1 209 638749649 638749857 9.350000e-82 315.0
24 TraesCS2A01G553400 chr3A 90.560 339 30 2 208 545 46032454 46032117 8.840000e-122 448.0
25 TraesCS2A01G553400 chr3A 90.173 346 29 5 208 552 456984925 456984584 3.180000e-121 446.0
26 TraesCS2A01G553400 chr3A 90.634 331 30 1 206 536 687499969 687499640 5.320000e-119 438.0
27 TraesCS2A01G553400 chr3A 94.737 209 11 0 1 209 461196613 461196821 4.320000e-85 326.0
28 TraesCS2A01G553400 chr3B 86.667 360 42 6 208 564 177683674 177683318 1.170000e-105 394.0
29 TraesCS2A01G553400 chr5D 79.966 594 68 35 12 561 481361917 481361331 1.510000e-104 390.0
30 TraesCS2A01G553400 chr5D 85.588 340 41 6 226 561 199786743 199787078 2.560000e-92 350.0
31 TraesCS2A01G553400 chr7D 87.059 340 37 6 226 561 90200346 90200010 1.180000e-100 377.0
32 TraesCS2A01G553400 chr6D 86.804 341 37 5 226 561 147609826 147609489 1.520000e-99 374.0
33 TraesCS2A01G553400 chr4A 88.710 310 30 4 3940 4245 398499618 398499310 1.520000e-99 374.0
34 TraesCS2A01G553400 chr4A 94.258 209 12 0 1 209 103861047 103861255 2.010000e-83 320.0
35 TraesCS2A01G553400 chr4A 94.258 209 12 0 1 209 188275360 188275568 2.010000e-83 320.0
36 TraesCS2A01G553400 chr4A 83.824 204 22 5 4248 4448 398491829 398491634 2.750000e-42 183.0
37 TraesCS2A01G553400 chr1A 93.810 210 13 0 1 210 247782505 247782714 2.600000e-82 316.0
38 TraesCS2A01G553400 chr1A 93.780 209 13 0 1 209 444351412 444351204 9.350000e-82 315.0
39 TraesCS2A01G553400 chr7B 93.780 209 13 0 1 209 692711776 692711984 9.350000e-82 315.0
40 TraesCS2A01G553400 chr4D 84.239 184 26 3 378 561 196535462 196535642 4.610000e-40 176.0


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 TraesCS2A01G553400 chr2A 758921848 758926327 4479 True 8274.000 8274 100.00000 1 4480 1 chr2A.!!$R1 4479
1 TraesCS2A01G553400 chr2D 629201768 629205462 3694 True 1384.000 4488 91.79825 600 4476 4 chr2D.!!$R1 3876
2 TraesCS2A01G553400 chr2B 772049512 772053441 3929 False 1209.775 4460 90.10600 727 4470 4 chr2B.!!$F1 3743
3 TraesCS2A01G553400 chr6A 527379730 527380500 770 True 1325.000 1325 97.66800 3700 4470 1 chr6A.!!$R2 770
4 TraesCS2A01G553400 chr6A 527456523 527457297 774 True 1323.000 1323 97.55200 3700 4470 1 chr6A.!!$R3 770
5 TraesCS2A01G553400 chr5D 481361331 481361917 586 True 390.000 390 79.96600 12 561 1 chr5D.!!$R1 549

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
783 829 0.176910 CCTCGCTTTCCTCCTCCTTC 59.823 60.0 0.00 0.0 0.00 3.46 F
1534 1657 0.038526 AGTCTCACGGTTTGGCTACG 60.039 55.0 0.00 0.0 0.00 3.51 F
1601 1726 0.031449 GGCTCGAGATCACACTAGGC 59.969 60.0 18.75 0.0 0.00 3.93 F
1823 1956 0.832559 AGCCTCGGTAGATTAGGGCC 60.833 60.0 0.00 0.0 40.32 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1718 0.833834 ACAGCCTCACAGCCTAGTGT 60.834 55.000 0.0 0.00 40.37 3.55 R
2629 2801 1.268234 GCTGTGACTGTGCAGTGAAAC 60.268 52.381 9.8 6.11 42.66 2.78 R
2845 3017 2.176148 TGGGCAATGATGATCCATGTCT 59.824 45.455 0.0 0.00 0.00 3.41 R
3577 3749 2.938956 AGTGGGACAACTGAAAGGAG 57.061 50.000 0.0 0.00 44.16 3.69 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 5.063204 GGTAGTATCATGCATGCCAACTAA 58.937 41.667 24.68 9.84 0.00 2.24
31 32 5.180117 GGTAGTATCATGCATGCCAACTAAG 59.820 44.000 24.68 3.62 0.00 2.18
33 34 1.836802 TCATGCATGCCAACTAAGCA 58.163 45.000 22.25 0.00 45.94 3.91
34 35 2.169330 TCATGCATGCCAACTAAGCAA 58.831 42.857 22.25 0.00 44.83 3.91
38 39 2.827322 TGCATGCCAACTAAGCAATCTT 59.173 40.909 16.68 0.00 44.83 2.40
44 45 4.766373 TGCCAACTAAGCAATCTTGATGAA 59.234 37.500 0.00 0.00 37.28 2.57
48 49 6.149973 CCAACTAAGCAATCTTGATGAAGTGA 59.850 38.462 0.00 0.00 33.85 3.41
51 52 6.883217 ACTAAGCAATCTTGATGAAGTGACAT 59.117 34.615 0.00 0.00 33.85 3.06
52 53 5.562506 AGCAATCTTGATGAAGTGACATG 57.437 39.130 0.00 0.00 0.00 3.21
53 54 4.398358 AGCAATCTTGATGAAGTGACATGG 59.602 41.667 0.00 0.00 0.00 3.66
64 65 9.022884 TGATGAAGTGACATGGAATTAAATGAA 57.977 29.630 0.00 0.00 0.00 2.57
65 66 9.859427 GATGAAGTGACATGGAATTAAATGAAA 57.141 29.630 0.00 0.00 0.00 2.69
121 125 9.719355 ACCGTATCATATTAAATGATGTGCTAA 57.281 29.630 16.73 1.63 38.98 3.09
152 156 7.263100 TCATGCATGACAATAAATGTAGTCC 57.737 36.000 25.42 0.00 44.12 3.85
153 157 7.056006 TCATGCATGACAATAAATGTAGTCCT 58.944 34.615 25.42 0.00 44.12 3.85
154 158 8.210265 TCATGCATGACAATAAATGTAGTCCTA 58.790 33.333 25.42 0.00 44.12 2.94
202 206 6.863275 TGCATTAGGGATGTAGTATCATACG 58.137 40.000 0.00 0.00 38.07 3.06
205 209 7.201794 GCATTAGGGATGTAGTATCATACGCTA 60.202 40.741 0.00 0.00 38.07 4.26
206 210 7.860918 TTAGGGATGTAGTATCATACGCTAG 57.139 40.000 0.00 0.00 30.81 3.42
207 211 5.817784 AGGGATGTAGTATCATACGCTAGT 58.182 41.667 0.00 0.00 29.96 2.57
209 213 6.822676 AGGGATGTAGTATCATACGCTAGTAC 59.177 42.308 0.00 0.00 35.39 2.73
210 214 6.822676 GGGATGTAGTATCATACGCTAGTACT 59.177 42.308 0.00 0.00 35.39 2.73
211 215 7.011295 GGGATGTAGTATCATACGCTAGTACTC 59.989 44.444 0.00 0.00 35.39 2.59
212 216 7.011295 GGATGTAGTATCATACGCTAGTACTCC 59.989 44.444 0.00 0.00 35.39 3.85
213 217 6.762333 TGTAGTATCATACGCTAGTACTCCA 58.238 40.000 0.00 0.00 35.39 3.86
214 218 7.392418 TGTAGTATCATACGCTAGTACTCCAT 58.608 38.462 0.00 0.00 35.39 3.41
215 219 6.988622 AGTATCATACGCTAGTACTCCATC 57.011 41.667 0.00 0.00 35.39 3.51
216 220 5.881443 AGTATCATACGCTAGTACTCCATCC 59.119 44.000 0.00 0.00 35.39 3.51
217 221 4.368565 TCATACGCTAGTACTCCATCCT 57.631 45.455 0.00 0.00 35.39 3.24
219 223 5.138276 TCATACGCTAGTACTCCATCCTTT 58.862 41.667 0.00 0.00 35.39 3.11
221 225 2.694109 ACGCTAGTACTCCATCCTTTCC 59.306 50.000 0.00 0.00 0.00 3.13
222 226 2.287668 CGCTAGTACTCCATCCTTTCCG 60.288 54.545 0.00 0.00 0.00 4.30
230 261 5.703730 ACTCCATCCTTTCCGGTTTATAA 57.296 39.130 0.00 0.00 0.00 0.98
254 285 7.235935 AGGCTCAATTCAAAAATCTCATCAA 57.764 32.000 0.00 0.00 0.00 2.57
255 286 7.848128 AGGCTCAATTCAAAAATCTCATCAAT 58.152 30.769 0.00 0.00 0.00 2.57
267 302 9.690913 AAAAATCTCATCAATCAAGGTAGATGA 57.309 29.630 0.00 0.00 43.14 2.92
277 312 4.352893 TCAAGGTAGATGATGAGTGGTGA 58.647 43.478 0.00 0.00 0.00 4.02
282 317 7.623999 AGGTAGATGATGAGTGGTGAAATAT 57.376 36.000 0.00 0.00 0.00 1.28
368 403 8.719560 TCAAATGTATTAATTGCAATGCATGT 57.280 26.923 13.82 2.25 39.41 3.21
436 475 5.402997 TGCAATGATTTAATGCACCTTGA 57.597 34.783 0.00 0.00 44.52 3.02
438 477 5.870433 TGCAATGATTTAATGCACCTTGAAG 59.130 36.000 0.00 0.00 44.52 3.02
443 482 6.003326 TGATTTAATGCACCTTGAAGTCTGA 58.997 36.000 0.00 0.00 0.00 3.27
453 492 5.934043 CACCTTGAAGTCTGAACATGTGATA 59.066 40.000 0.00 0.00 0.00 2.15
456 495 6.358974 TTGAAGTCTGAACATGTGATAGGA 57.641 37.500 0.00 0.00 0.00 2.94
469 510 8.415950 ACATGTGATAGGAAACAACCAAATTA 57.584 30.769 0.00 0.00 0.00 1.40
566 607 9.945904 TGTATGATACTACTCTATGATTCTCGT 57.054 33.333 4.03 0.00 0.00 4.18
568 609 7.583860 TGATACTACTCTATGATTCTCGTCG 57.416 40.000 0.00 0.00 0.00 5.12
569 610 6.590677 TGATACTACTCTATGATTCTCGTCGG 59.409 42.308 0.00 0.00 0.00 4.79
570 611 4.958509 ACTACTCTATGATTCTCGTCGGA 58.041 43.478 0.00 0.00 0.00 4.55
571 612 5.366460 ACTACTCTATGATTCTCGTCGGAA 58.634 41.667 0.00 0.00 0.00 4.30
572 613 4.822036 ACTCTATGATTCTCGTCGGAAG 57.178 45.455 0.00 0.00 0.00 3.46
573 614 4.452825 ACTCTATGATTCTCGTCGGAAGA 58.547 43.478 0.00 0.00 38.16 2.87
574 615 4.882427 ACTCTATGATTCTCGTCGGAAGAA 59.118 41.667 0.00 0.00 45.01 2.52
575 616 5.357314 ACTCTATGATTCTCGTCGGAAGAAA 59.643 40.000 1.03 0.00 45.01 2.52
576 617 6.127703 ACTCTATGATTCTCGTCGGAAGAAAA 60.128 38.462 1.03 0.00 45.01 2.29
577 618 6.266323 TCTATGATTCTCGTCGGAAGAAAAG 58.734 40.000 1.03 0.00 45.01 2.27
578 619 4.252971 TGATTCTCGTCGGAAGAAAAGT 57.747 40.909 1.03 0.00 45.01 2.66
579 620 3.987868 TGATTCTCGTCGGAAGAAAAGTG 59.012 43.478 1.03 0.00 45.01 3.16
580 621 2.433868 TCTCGTCGGAAGAAAAGTGG 57.566 50.000 0.00 0.00 45.01 4.00
581 622 1.000506 TCTCGTCGGAAGAAAAGTGGG 59.999 52.381 0.00 0.00 45.01 4.61
582 623 1.000506 CTCGTCGGAAGAAAAGTGGGA 59.999 52.381 0.00 0.00 45.01 4.37
583 624 1.621814 TCGTCGGAAGAAAAGTGGGAT 59.378 47.619 0.00 0.00 45.01 3.85
584 625 1.732259 CGTCGGAAGAAAAGTGGGATG 59.268 52.381 0.00 0.00 45.01 3.51
585 626 2.779506 GTCGGAAGAAAAGTGGGATGT 58.220 47.619 0.00 0.00 45.01 3.06
586 627 3.615592 CGTCGGAAGAAAAGTGGGATGTA 60.616 47.826 0.00 0.00 45.01 2.29
587 628 3.933332 GTCGGAAGAAAAGTGGGATGTAG 59.067 47.826 0.00 0.00 45.01 2.74
588 629 3.581332 TCGGAAGAAAAGTGGGATGTAGT 59.419 43.478 0.00 0.00 37.03 2.73
589 630 4.773674 TCGGAAGAAAAGTGGGATGTAGTA 59.226 41.667 0.00 0.00 37.03 1.82
590 631 5.105473 TCGGAAGAAAAGTGGGATGTAGTAG 60.105 44.000 0.00 0.00 37.03 2.57
591 632 5.337330 CGGAAGAAAAGTGGGATGTAGTAGT 60.337 44.000 0.00 0.00 0.00 2.73
592 633 6.127535 CGGAAGAAAAGTGGGATGTAGTAGTA 60.128 42.308 0.00 0.00 0.00 1.82
593 634 7.266400 GGAAGAAAAGTGGGATGTAGTAGTAG 58.734 42.308 0.00 0.00 0.00 2.57
594 635 6.793505 AGAAAAGTGGGATGTAGTAGTAGG 57.206 41.667 0.00 0.00 0.00 3.18
595 636 6.500336 AGAAAAGTGGGATGTAGTAGTAGGA 58.500 40.000 0.00 0.00 0.00 2.94
596 637 6.958192 AGAAAAGTGGGATGTAGTAGTAGGAA 59.042 38.462 0.00 0.00 0.00 3.36
597 638 7.624077 AGAAAAGTGGGATGTAGTAGTAGGAAT 59.376 37.037 0.00 0.00 0.00 3.01
598 639 6.980416 AAGTGGGATGTAGTAGTAGGAATC 57.020 41.667 0.00 0.00 0.00 2.52
599 640 5.071370 AGTGGGATGTAGTAGTAGGAATCG 58.929 45.833 0.00 0.00 0.00 3.34
600 641 4.826183 GTGGGATGTAGTAGTAGGAATCGT 59.174 45.833 0.00 0.00 0.00 3.73
601 642 5.301298 GTGGGATGTAGTAGTAGGAATCGTT 59.699 44.000 0.00 0.00 0.00 3.85
602 643 5.533903 TGGGATGTAGTAGTAGGAATCGTTC 59.466 44.000 0.00 0.00 0.00 3.95
603 644 5.334724 GGGATGTAGTAGTAGGAATCGTTCG 60.335 48.000 0.00 0.00 0.00 3.95
604 645 5.468072 GGATGTAGTAGTAGGAATCGTTCGA 59.532 44.000 0.00 0.00 0.00 3.71
605 646 5.980698 TGTAGTAGTAGGAATCGTTCGAG 57.019 43.478 0.80 0.00 0.00 4.04
606 647 4.813161 TGTAGTAGTAGGAATCGTTCGAGG 59.187 45.833 0.80 0.00 0.00 4.63
607 648 2.617774 AGTAGTAGGAATCGTTCGAGGC 59.382 50.000 0.80 0.00 0.00 4.70
608 649 0.381089 AGTAGGAATCGTTCGAGGCG 59.619 55.000 5.30 5.30 0.00 5.52
646 687 0.868406 CAGACTGAAACCAGCCGAAC 59.132 55.000 0.00 0.00 35.09 3.95
658 704 2.294791 CCAGCCGAACTCCTAGTCATAG 59.705 54.545 0.00 0.00 0.00 2.23
702 748 3.066190 CCGCACCACCTAGACCGA 61.066 66.667 0.00 0.00 0.00 4.69
723 769 1.361271 GACTTGTCGTCGTCCACCA 59.639 57.895 0.00 0.00 32.04 4.17
768 814 1.566018 AACTTTTTCTCGCCGCCTCG 61.566 55.000 0.00 0.00 0.00 4.63
769 815 3.368455 CTTTTTCTCGCCGCCTCGC 62.368 63.158 0.00 0.00 0.00 5.03
770 816 3.876589 TTTTTCTCGCCGCCTCGCT 62.877 57.895 0.00 0.00 0.00 4.93
771 817 3.876589 TTTTCTCGCCGCCTCGCTT 62.877 57.895 0.00 0.00 0.00 4.68
772 818 3.876589 TTTCTCGCCGCCTCGCTTT 62.877 57.895 0.00 0.00 0.00 3.51
773 819 4.796231 TCTCGCCGCCTCGCTTTC 62.796 66.667 0.00 0.00 0.00 2.62
778 824 3.775654 CCGCCTCGCTTTCCTCCT 61.776 66.667 0.00 0.00 0.00 3.69
779 825 2.202810 CGCCTCGCTTTCCTCCTC 60.203 66.667 0.00 0.00 0.00 3.71
783 829 0.176910 CCTCGCTTTCCTCCTCCTTC 59.823 60.000 0.00 0.00 0.00 3.46
814 860 3.681835 GTCGCCCAGTCGTGGTCT 61.682 66.667 0.00 0.00 43.23 3.85
815 861 3.371063 TCGCCCAGTCGTGGTCTC 61.371 66.667 0.00 0.00 43.23 3.36
816 862 4.778415 CGCCCAGTCGTGGTCTCG 62.778 72.222 0.00 0.00 43.23 4.04
817 863 3.681835 GCCCAGTCGTGGTCTCGT 61.682 66.667 0.00 0.00 43.23 4.18
823 869 1.372623 GTCGTGGTCTCGTGGAACC 60.373 63.158 0.00 0.00 0.00 3.62
874 920 2.509336 CGCTGGCGACGGAGATTT 60.509 61.111 0.00 0.00 42.83 2.17
903 949 3.855853 GCTCCCCCTCTTCCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
909 955 3.157949 CCTCTTCCTCGCCCCCTC 61.158 72.222 0.00 0.00 0.00 4.30
960 1023 1.175347 CCGCCTCCGATCTCTCATCA 61.175 60.000 0.00 0.00 36.29 3.07
961 1024 0.887247 CGCCTCCGATCTCTCATCAT 59.113 55.000 0.00 0.00 36.29 2.45
962 1025 1.135431 CGCCTCCGATCTCTCATCATC 60.135 57.143 0.00 0.00 36.29 2.92
1041 1107 2.516460 GAGCCGCTCCTCGAGGTA 60.516 66.667 30.17 16.19 41.67 3.08
1044 1110 2.416432 GCCGCTCCTCGAGGTACTT 61.416 63.158 30.17 0.00 41.55 2.24
1233 1323 4.468689 CCCCCTTCCGCTCCGTTC 62.469 72.222 0.00 0.00 0.00 3.95
1312 1407 4.664150 TTTTTGGCGATGAAAAAGGAGT 57.336 36.364 0.00 0.00 30.62 3.85
1319 1414 6.754193 TGGCGATGAAAAAGGAGTTTTATTT 58.246 32.000 0.00 0.00 39.60 1.40
1346 1441 9.307121 CAAATTGATAAGAGTTACAGTCGAGAT 57.693 33.333 0.00 0.00 0.00 2.75
1368 1480 3.548770 ACATGGTGTTCCTAGATGCATG 58.451 45.455 2.46 0.00 34.23 4.06
1376 1492 0.661552 CCTAGATGCATGCACACAGC 59.338 55.000 25.37 10.21 45.96 4.40
1400 1516 3.558033 TGGTACACTCCATGCGACTATA 58.442 45.455 0.00 0.00 31.96 1.31
1405 1521 5.276461 ACACTCCATGCGACTATAATTCA 57.724 39.130 0.00 0.00 0.00 2.57
1410 1526 6.648310 ACTCCATGCGACTATAATTCATCTTG 59.352 38.462 0.00 0.00 0.00 3.02
1414 1530 7.384932 CCATGCGACTATAATTCATCTTGTACA 59.615 37.037 0.00 0.00 0.00 2.90
1417 1533 8.141268 TGCGACTATAATTCATCTTGTACATGA 58.859 33.333 13.28 13.28 0.00 3.07
1428 1544 9.538508 TTCATCTTGTACATGATGATAGAGTTG 57.461 33.333 36.00 19.43 45.39 3.16
1433 1549 6.809869 TGTACATGATGATAGAGTTGTGAGG 58.190 40.000 0.00 0.00 0.00 3.86
1507 1630 3.084786 GCTGCTGTAATTCTTTCCCTGT 58.915 45.455 0.00 0.00 0.00 4.00
1510 1633 5.358160 GCTGCTGTAATTCTTTCCCTGTTAT 59.642 40.000 0.00 0.00 0.00 1.89
1534 1657 0.038526 AGTCTCACGGTTTGGCTACG 60.039 55.000 0.00 0.00 0.00 3.51
1538 1661 0.320073 TCACGGTTTGGCTACGAAGG 60.320 55.000 0.00 0.00 0.00 3.46
1552 1675 0.321122 CGAAGGTTGCTCTTGCTCCT 60.321 55.000 0.00 0.00 42.36 3.69
1569 1692 1.915489 TCCTGCAGAATAGGGCTTTGA 59.085 47.619 17.39 0.00 35.96 2.69
1593 1718 2.094234 TCGTCAATTTGGCTCGAGATCA 60.094 45.455 18.75 10.78 0.00 2.92
1598 1723 4.081697 TCAATTTGGCTCGAGATCACACTA 60.082 41.667 18.75 0.00 0.00 2.74
1599 1724 3.510388 TTTGGCTCGAGATCACACTAG 57.490 47.619 18.75 0.00 0.00 2.57
1600 1725 1.393603 TGGCTCGAGATCACACTAGG 58.606 55.000 18.75 0.00 0.00 3.02
1601 1726 0.031449 GGCTCGAGATCACACTAGGC 59.969 60.000 18.75 0.00 0.00 3.93
1602 1727 1.028905 GCTCGAGATCACACTAGGCT 58.971 55.000 18.75 0.00 0.00 4.58
1603 1728 1.268999 GCTCGAGATCACACTAGGCTG 60.269 57.143 18.75 0.00 0.00 4.85
1604 1729 2.020720 CTCGAGATCACACTAGGCTGT 58.979 52.381 6.58 0.00 0.00 4.40
1605 1730 1.745653 TCGAGATCACACTAGGCTGTG 59.254 52.381 13.26 13.26 42.62 3.66
1633 1758 4.839550 TGTATGTAACCAAGGTCACCACTA 59.160 41.667 0.00 0.00 0.00 2.74
1634 1759 4.986054 ATGTAACCAAGGTCACCACTAA 57.014 40.909 0.00 0.00 0.00 2.24
1637 1762 4.883006 TGTAACCAAGGTCACCACTAAAAC 59.117 41.667 0.00 0.00 0.00 2.43
1651 1776 7.172532 TCACCACTAAAACATACTTACTGCAAG 59.827 37.037 0.00 0.00 40.38 4.01
1680 1806 3.967332 AGACAGGAAATTTTGGGCATG 57.033 42.857 0.00 0.00 0.00 4.06
1684 1810 4.136051 ACAGGAAATTTTGGGCATGTTTG 58.864 39.130 0.00 0.00 0.00 2.93
1738 1871 4.406972 ACTTCTTCAGATATGCAGCAGGTA 59.593 41.667 0.00 0.00 0.00 3.08
1752 1885 3.283259 GCAGGTAGCTACAAAGGGATT 57.717 47.619 24.75 0.00 41.15 3.01
1753 1886 4.417426 GCAGGTAGCTACAAAGGGATTA 57.583 45.455 24.75 0.00 41.15 1.75
1754 1887 4.777463 GCAGGTAGCTACAAAGGGATTAA 58.223 43.478 24.75 0.00 41.15 1.40
1823 1956 0.832559 AGCCTCGGTAGATTAGGGCC 60.833 60.000 0.00 0.00 40.32 5.80
2173 2336 2.787601 AATTATCCTGCAGCAATGCG 57.212 45.000 8.66 0.00 37.69 4.73
2214 2377 4.992319 TCCGTTTAGGTAGAACAATGTGTG 59.008 41.667 0.00 0.00 41.99 3.82
2268 2431 2.435059 GGCTGTGGTCTTCGGCTC 60.435 66.667 0.00 0.00 37.35 4.70
2558 2730 7.174772 ACTGCTGTTTGATTTTGTTTCCTTTTT 59.825 29.630 0.00 0.00 0.00 1.94
2629 2801 1.746470 TCAGCATCTTCTGTGGCATG 58.254 50.000 0.00 0.00 35.63 4.06
2843 3015 4.083537 GCCGATCTTGTAAAACATGTGTGA 60.084 41.667 0.00 0.00 0.00 3.58
2845 3017 6.183360 GCCGATCTTGTAAAACATGTGTGATA 60.183 38.462 0.00 0.00 0.00 2.15
2948 3120 7.915508 TGTATCGTGAATTGTTGCTAATTAGG 58.084 34.615 14.28 0.00 30.78 2.69
3364 3536 6.156775 TCACCAACTGATATTCATGGAGAGAA 59.843 38.462 4.56 0.00 32.35 2.87
3526 3698 4.517453 GCAATGTTTACTTACCTGGTGTCA 59.483 41.667 10.23 0.00 0.00 3.58
3658 3830 4.735369 TCTTTCCACTTGGCCTTATCAAA 58.265 39.130 3.32 0.00 34.44 2.69
3940 4114 7.746703 AGATTATGTAATTAGTGGGTCCCTTC 58.253 38.462 10.00 2.42 0.00 3.46
4212 4392 3.681417 AGTTTCCGTATTCTGTAAACGCC 59.319 43.478 0.00 0.00 35.67 5.68
4342 4622 6.711277 ACTGAAGCTGGTGATGTAAAATAGA 58.289 36.000 0.00 0.00 0.00 1.98
4470 4831 3.004002 TCTCGTTGCTTTACTCGAACAGA 59.996 43.478 0.00 0.00 32.12 3.41
4472 4833 3.673338 TCGTTGCTTTACTCGAACAGATG 59.327 43.478 0.00 0.00 0.00 2.90
4476 4837 3.254060 GCTTTACTCGAACAGATGCTGA 58.746 45.455 0.82 0.00 35.18 4.26
4477 4838 3.679980 GCTTTACTCGAACAGATGCTGAA 59.320 43.478 0.82 0.00 35.18 3.02
4478 4839 4.152402 GCTTTACTCGAACAGATGCTGAAA 59.848 41.667 0.82 0.00 35.18 2.69
4479 4840 5.163814 GCTTTACTCGAACAGATGCTGAAAT 60.164 40.000 0.82 0.00 35.18 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.163550 GGCATGCATGATACTACCTACGATA 60.164 44.000 30.64 0.00 0.00 2.92
1 2 4.382040 GGCATGCATGATACTACCTACGAT 60.382 45.833 30.64 0.00 0.00 3.73
3 4 3.254060 GGCATGCATGATACTACCTACG 58.746 50.000 30.64 0.00 0.00 3.51
5 6 4.347876 AGTTGGCATGCATGATACTACCTA 59.652 41.667 30.64 13.97 0.00 3.08
8 9 5.334414 GCTTAGTTGGCATGCATGATACTAC 60.334 44.000 30.64 22.16 0.00 2.73
9 10 4.756642 GCTTAGTTGGCATGCATGATACTA 59.243 41.667 30.64 25.19 0.00 1.82
10 11 3.567164 GCTTAGTTGGCATGCATGATACT 59.433 43.478 30.64 26.11 0.00 2.12
30 31 4.398358 CCATGTCACTTCATCAAGATTGCT 59.602 41.667 0.00 0.00 33.34 3.91
31 32 4.397103 TCCATGTCACTTCATCAAGATTGC 59.603 41.667 0.00 0.00 33.34 3.56
33 34 7.713734 AATTCCATGTCACTTCATCAAGATT 57.286 32.000 0.00 0.00 33.34 2.40
34 35 8.812513 TTAATTCCATGTCACTTCATCAAGAT 57.187 30.769 0.00 0.00 33.34 2.40
38 39 8.578448 TCATTTAATTCCATGTCACTTCATCA 57.422 30.769 0.00 0.00 0.00 3.07
64 65 8.489489 TGATATGATACTCAAGCCTCTCTTTTT 58.511 33.333 0.00 0.00 31.27 1.94
65 66 8.027524 TGATATGATACTCAAGCCTCTCTTTT 57.972 34.615 0.00 0.00 31.27 2.27
113 114 4.787260 TGCATGACACAAATTAGCACAT 57.213 36.364 0.00 0.00 0.00 3.21
129 133 7.268199 AGGACTACATTTATTGTCATGCATG 57.732 36.000 21.07 21.07 39.87 4.06
161 165 9.412460 CCCTAATGCATAATATCATATGTTGGT 57.588 33.333 0.00 0.00 36.00 3.67
185 189 6.822676 AGTACTAGCGTATGATACTACATCCC 59.177 42.308 0.00 0.00 0.00 3.85
189 193 6.762333 TGGAGTACTAGCGTATGATACTACA 58.238 40.000 0.00 0.00 34.93 2.74
198 202 4.523558 GGAAAGGATGGAGTACTAGCGTAT 59.476 45.833 0.00 0.00 0.00 3.06
202 206 2.036089 CCGGAAAGGATGGAGTACTAGC 59.964 54.545 0.00 0.00 45.00 3.42
205 209 2.249309 ACCGGAAAGGATGGAGTACT 57.751 50.000 9.46 0.00 45.00 2.73
206 210 3.345508 AAACCGGAAAGGATGGAGTAC 57.654 47.619 9.46 0.00 45.00 2.73
207 211 6.183361 CCTTATAAACCGGAAAGGATGGAGTA 60.183 42.308 9.46 0.00 45.00 2.59
209 213 5.063880 CCTTATAAACCGGAAAGGATGGAG 58.936 45.833 9.46 0.00 45.00 3.86
210 214 4.687769 GCCTTATAAACCGGAAAGGATGGA 60.688 45.833 9.46 0.00 45.00 3.41
211 215 3.568430 GCCTTATAAACCGGAAAGGATGG 59.432 47.826 9.46 3.76 45.00 3.51
212 216 4.461198 AGCCTTATAAACCGGAAAGGATG 58.539 43.478 9.46 0.00 45.00 3.51
213 217 4.165372 TGAGCCTTATAAACCGGAAAGGAT 59.835 41.667 9.46 11.46 45.00 3.24
214 218 3.520317 TGAGCCTTATAAACCGGAAAGGA 59.480 43.478 9.46 0.00 45.00 3.36
216 220 6.094881 TGAATTGAGCCTTATAAACCGGAAAG 59.905 38.462 9.46 3.38 0.00 2.62
217 221 5.946972 TGAATTGAGCCTTATAAACCGGAAA 59.053 36.000 9.46 0.00 0.00 3.13
219 223 5.105567 TGAATTGAGCCTTATAAACCGGA 57.894 39.130 9.46 0.00 0.00 5.14
221 225 8.702163 ATTTTTGAATTGAGCCTTATAAACCG 57.298 30.769 0.00 0.00 0.00 4.44
222 226 9.875691 AGATTTTTGAATTGAGCCTTATAAACC 57.124 29.630 0.00 0.00 0.00 3.27
230 261 6.845758 TGATGAGATTTTTGAATTGAGCCT 57.154 33.333 0.00 0.00 0.00 4.58
251 282 5.426509 ACCACTCATCATCTACCTTGATTGA 59.573 40.000 0.00 0.00 31.50 2.57
254 285 4.964897 TCACCACTCATCATCTACCTTGAT 59.035 41.667 0.00 0.00 34.15 2.57
255 286 4.352893 TCACCACTCATCATCTACCTTGA 58.647 43.478 0.00 0.00 0.00 3.02
378 417 7.876936 AGAGAAAACTGATCAATACATGCAT 57.123 32.000 0.00 0.00 0.00 3.96
412 451 6.408035 TCAAGGTGCATTAAATCATTGCATT 58.592 32.000 4.14 0.00 46.90 3.56
436 475 6.533730 TGTTTCCTATCACATGTTCAGACTT 58.466 36.000 0.00 0.00 0.00 3.01
438 477 6.348540 GGTTGTTTCCTATCACATGTTCAGAC 60.349 42.308 0.00 0.00 0.00 3.51
443 482 6.723298 TTTGGTTGTTTCCTATCACATGTT 57.277 33.333 0.00 0.00 0.00 2.71
453 492 5.887214 AAGGCTTAATTTGGTTGTTTCCT 57.113 34.783 0.00 0.00 0.00 3.36
540 581 9.945904 ACGAGAATCATAGAGTAGTATCATACA 57.054 33.333 0.00 0.00 33.17 2.29
542 583 9.303537 CGACGAGAATCATAGAGTAGTATCATA 57.696 37.037 0.00 0.00 33.17 2.15
543 584 7.279090 CCGACGAGAATCATAGAGTAGTATCAT 59.721 40.741 0.00 0.00 33.17 2.45
544 585 6.590677 CCGACGAGAATCATAGAGTAGTATCA 59.409 42.308 0.00 0.00 33.17 2.15
545 586 6.812656 TCCGACGAGAATCATAGAGTAGTATC 59.187 42.308 0.00 0.00 33.17 2.24
546 587 6.699366 TCCGACGAGAATCATAGAGTAGTAT 58.301 40.000 0.00 0.00 33.17 2.12
547 588 6.094193 TCCGACGAGAATCATAGAGTAGTA 57.906 41.667 0.00 0.00 33.17 1.82
548 589 4.958509 TCCGACGAGAATCATAGAGTAGT 58.041 43.478 0.00 0.00 33.17 2.73
549 590 5.697178 TCTTCCGACGAGAATCATAGAGTAG 59.303 44.000 0.00 0.00 33.17 2.57
550 591 5.608449 TCTTCCGACGAGAATCATAGAGTA 58.392 41.667 0.00 0.00 33.17 2.59
551 592 4.452825 TCTTCCGACGAGAATCATAGAGT 58.547 43.478 0.00 0.00 33.17 3.24
552 593 5.425577 TTCTTCCGACGAGAATCATAGAG 57.574 43.478 0.00 0.00 33.17 2.43
553 594 5.830000 TTTCTTCCGACGAGAATCATAGA 57.170 39.130 0.00 0.00 33.48 1.98
554 595 6.020281 CACTTTTCTTCCGACGAGAATCATAG 60.020 42.308 0.00 0.00 33.48 2.23
555 596 5.805486 CACTTTTCTTCCGACGAGAATCATA 59.195 40.000 0.00 0.00 33.48 2.15
556 597 4.627467 CACTTTTCTTCCGACGAGAATCAT 59.373 41.667 0.00 0.00 33.48 2.45
557 598 3.987868 CACTTTTCTTCCGACGAGAATCA 59.012 43.478 0.00 0.00 33.48 2.57
558 599 3.368236 CCACTTTTCTTCCGACGAGAATC 59.632 47.826 0.00 0.00 33.48 2.52
559 600 3.326747 CCACTTTTCTTCCGACGAGAAT 58.673 45.455 0.00 0.00 33.48 2.40
560 601 2.547218 CCCACTTTTCTTCCGACGAGAA 60.547 50.000 0.00 0.00 0.00 2.87
561 602 1.000506 CCCACTTTTCTTCCGACGAGA 59.999 52.381 0.00 0.00 0.00 4.04
562 603 1.000506 TCCCACTTTTCTTCCGACGAG 59.999 52.381 0.00 0.00 0.00 4.18
563 604 1.042229 TCCCACTTTTCTTCCGACGA 58.958 50.000 0.00 0.00 0.00 4.20
564 605 1.732259 CATCCCACTTTTCTTCCGACG 59.268 52.381 0.00 0.00 0.00 5.12
565 606 2.779506 ACATCCCACTTTTCTTCCGAC 58.220 47.619 0.00 0.00 0.00 4.79
566 607 3.581332 ACTACATCCCACTTTTCTTCCGA 59.419 43.478 0.00 0.00 0.00 4.55
567 608 3.939066 ACTACATCCCACTTTTCTTCCG 58.061 45.455 0.00 0.00 0.00 4.30
568 609 6.051179 ACTACTACATCCCACTTTTCTTCC 57.949 41.667 0.00 0.00 0.00 3.46
569 610 7.123847 TCCTACTACTACATCCCACTTTTCTTC 59.876 40.741 0.00 0.00 0.00 2.87
570 611 6.958192 TCCTACTACTACATCCCACTTTTCTT 59.042 38.462 0.00 0.00 0.00 2.52
571 612 6.500336 TCCTACTACTACATCCCACTTTTCT 58.500 40.000 0.00 0.00 0.00 2.52
572 613 6.786967 TCCTACTACTACATCCCACTTTTC 57.213 41.667 0.00 0.00 0.00 2.29
573 614 7.417570 CGATTCCTACTACTACATCCCACTTTT 60.418 40.741 0.00 0.00 0.00 2.27
574 615 6.040616 CGATTCCTACTACTACATCCCACTTT 59.959 42.308 0.00 0.00 0.00 2.66
575 616 5.535406 CGATTCCTACTACTACATCCCACTT 59.465 44.000 0.00 0.00 0.00 3.16
576 617 5.071370 CGATTCCTACTACTACATCCCACT 58.929 45.833 0.00 0.00 0.00 4.00
577 618 4.826183 ACGATTCCTACTACTACATCCCAC 59.174 45.833 0.00 0.00 0.00 4.61
578 619 5.057843 ACGATTCCTACTACTACATCCCA 57.942 43.478 0.00 0.00 0.00 4.37
579 620 5.334724 CGAACGATTCCTACTACTACATCCC 60.335 48.000 0.00 0.00 0.00 3.85
580 621 5.468072 TCGAACGATTCCTACTACTACATCC 59.532 44.000 0.00 0.00 0.00 3.51
581 622 6.347563 CCTCGAACGATTCCTACTACTACATC 60.348 46.154 0.00 0.00 0.00 3.06
582 623 5.469421 CCTCGAACGATTCCTACTACTACAT 59.531 44.000 0.00 0.00 0.00 2.29
583 624 4.813161 CCTCGAACGATTCCTACTACTACA 59.187 45.833 0.00 0.00 0.00 2.74
584 625 4.319405 GCCTCGAACGATTCCTACTACTAC 60.319 50.000 0.00 0.00 0.00 2.73
585 626 3.812053 GCCTCGAACGATTCCTACTACTA 59.188 47.826 0.00 0.00 0.00 1.82
586 627 2.617774 GCCTCGAACGATTCCTACTACT 59.382 50.000 0.00 0.00 0.00 2.57
587 628 2.601741 CGCCTCGAACGATTCCTACTAC 60.602 54.545 1.42 0.00 0.00 2.73
588 629 1.600957 CGCCTCGAACGATTCCTACTA 59.399 52.381 1.42 0.00 0.00 1.82
589 630 0.381089 CGCCTCGAACGATTCCTACT 59.619 55.000 1.42 0.00 0.00 2.57
590 631 0.100146 ACGCCTCGAACGATTCCTAC 59.900 55.000 13.80 0.00 0.00 3.18
591 632 0.099968 CACGCCTCGAACGATTCCTA 59.900 55.000 13.80 0.00 0.00 2.94
592 633 1.153823 CACGCCTCGAACGATTCCT 60.154 57.895 13.80 0.00 0.00 3.36
593 634 2.165301 CCACGCCTCGAACGATTCC 61.165 63.158 13.80 0.00 0.00 3.01
594 635 0.527817 ATCCACGCCTCGAACGATTC 60.528 55.000 13.80 0.00 0.00 2.52
595 636 0.806102 CATCCACGCCTCGAACGATT 60.806 55.000 13.80 0.00 0.00 3.34
596 637 1.226974 CATCCACGCCTCGAACGAT 60.227 57.895 13.80 0.00 0.00 3.73
597 638 1.868987 TTCATCCACGCCTCGAACGA 61.869 55.000 13.80 0.00 0.00 3.85
598 639 1.413767 CTTCATCCACGCCTCGAACG 61.414 60.000 6.00 6.00 0.00 3.95
599 640 1.696832 GCTTCATCCACGCCTCGAAC 61.697 60.000 0.00 0.00 0.00 3.95
600 641 1.447838 GCTTCATCCACGCCTCGAA 60.448 57.895 0.00 0.00 0.00 3.71
601 642 1.035385 TAGCTTCATCCACGCCTCGA 61.035 55.000 0.00 0.00 0.00 4.04
602 643 0.179111 TTAGCTTCATCCACGCCTCG 60.179 55.000 0.00 0.00 0.00 4.63
603 644 1.134670 AGTTAGCTTCATCCACGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
604 645 0.905357 AGTTAGCTTCATCCACGCCT 59.095 50.000 0.00 0.00 0.00 5.52
605 646 1.739067 AAGTTAGCTTCATCCACGCC 58.261 50.000 0.00 0.00 0.00 5.68
606 647 3.188460 TGAAAAGTTAGCTTCATCCACGC 59.812 43.478 0.00 0.00 33.01 5.34
607 648 4.690748 TCTGAAAAGTTAGCTTCATCCACG 59.309 41.667 0.00 0.00 33.01 4.94
608 649 5.703130 AGTCTGAAAAGTTAGCTTCATCCAC 59.297 40.000 0.00 0.00 33.01 4.02
768 814 0.544223 GAGGGAAGGAGGAGGAAAGC 59.456 60.000 0.00 0.00 0.00 3.51
769 815 0.827368 CGAGGGAAGGAGGAGGAAAG 59.173 60.000 0.00 0.00 0.00 2.62
770 816 0.412244 TCGAGGGAAGGAGGAGGAAA 59.588 55.000 0.00 0.00 0.00 3.13
771 817 0.412244 TTCGAGGGAAGGAGGAGGAA 59.588 55.000 0.00 0.00 0.00 3.36
772 818 0.637195 ATTCGAGGGAAGGAGGAGGA 59.363 55.000 0.00 0.00 35.19 3.71
773 819 1.044611 GATTCGAGGGAAGGAGGAGG 58.955 60.000 0.00 0.00 35.19 4.30
774 820 1.044611 GGATTCGAGGGAAGGAGGAG 58.955 60.000 0.00 0.00 35.19 3.69
775 821 0.637195 AGGATTCGAGGGAAGGAGGA 59.363 55.000 0.00 0.00 35.19 3.71
776 822 1.414550 GAAGGATTCGAGGGAAGGAGG 59.585 57.143 0.00 0.00 34.17 4.30
777 823 2.900716 GAAGGATTCGAGGGAAGGAG 57.099 55.000 0.00 0.00 34.17 3.69
823 869 2.431683 CCTGGTGGTGGTGGAGTG 59.568 66.667 0.00 0.00 0.00 3.51
857 903 2.509336 AAATCTCCGTCGCCAGCG 60.509 61.111 5.50 5.50 41.35 5.18
858 904 3.093278 CAAATCTCCGTCGCCAGC 58.907 61.111 0.00 0.00 0.00 4.85
860 906 2.813474 CGCAAATCTCCGTCGCCA 60.813 61.111 0.00 0.00 0.00 5.69
891 937 4.806339 AGGGGGCGAGGAAGAGGG 62.806 72.222 0.00 0.00 0.00 4.30
939 985 3.984749 GAGAGATCGGAGGCGGCC 61.985 72.222 12.11 12.11 0.00 6.13
1233 1323 0.752658 TCATCCCTACCATGTCGCTG 59.247 55.000 0.00 0.00 0.00 5.18
1319 1414 8.520351 TCTCGACTGTAACTCTTATCAATTTGA 58.480 33.333 0.75 0.75 0.00 2.69
1329 1424 5.652891 ACCATGTATCTCGACTGTAACTCTT 59.347 40.000 0.00 0.00 0.00 2.85
1346 1441 4.707105 CATGCATCTAGGAACACCATGTA 58.293 43.478 0.00 0.00 0.00 2.29
1368 1480 2.280524 TGTACCACGGCTGTGTGC 60.281 61.111 23.77 15.18 44.92 4.57
1376 1492 1.809619 CGCATGGAGTGTACCACGG 60.810 63.158 0.00 0.00 43.03 4.94
1385 1501 6.352016 AGATGAATTATAGTCGCATGGAGT 57.648 37.500 0.00 0.00 0.00 3.85
1389 1505 8.298030 TGTACAAGATGAATTATAGTCGCATG 57.702 34.615 0.00 0.00 0.00 4.06
1390 1506 8.929746 CATGTACAAGATGAATTATAGTCGCAT 58.070 33.333 0.00 0.00 0.00 4.73
1405 1521 8.699130 TCACAACTCTATCATCATGTACAAGAT 58.301 33.333 7.76 7.76 0.00 2.40
1410 1526 7.013750 TCTCCTCACAACTCTATCATCATGTAC 59.986 40.741 0.00 0.00 0.00 2.90
1414 1530 5.010922 GCTCTCCTCACAACTCTATCATCAT 59.989 44.000 0.00 0.00 0.00 2.45
1417 1533 4.285020 TGCTCTCCTCACAACTCTATCAT 58.715 43.478 0.00 0.00 0.00 2.45
1422 1538 0.607620 GCTGCTCTCCTCACAACTCT 59.392 55.000 0.00 0.00 0.00 3.24
1428 1544 0.034616 ACTTGTGCTGCTCTCCTCAC 59.965 55.000 0.00 0.00 0.00 3.51
1433 1549 2.001159 CAGATGACTTGTGCTGCTCTC 58.999 52.381 0.00 0.00 0.00 3.20
1507 1630 6.646267 AGCCAAACCGTGAGACTAATAATAA 58.354 36.000 0.00 0.00 0.00 1.40
1510 1633 4.546829 AGCCAAACCGTGAGACTAATAA 57.453 40.909 0.00 0.00 0.00 1.40
1517 1640 0.675083 TTCGTAGCCAAACCGTGAGA 59.325 50.000 0.00 0.00 0.00 3.27
1534 1657 1.163554 CAGGAGCAAGAGCAACCTTC 58.836 55.000 0.00 0.00 43.62 3.46
1552 1675 3.282021 GACATCAAAGCCCTATTCTGCA 58.718 45.455 0.00 0.00 0.00 4.41
1569 1692 2.002586 CTCGAGCCAAATTGACGACAT 58.997 47.619 0.00 0.00 0.00 3.06
1593 1718 0.833834 ACAGCCTCACAGCCTAGTGT 60.834 55.000 0.00 0.00 40.37 3.55
1598 1723 1.866015 TACATACAGCCTCACAGCCT 58.134 50.000 0.00 0.00 0.00 4.58
1599 1724 2.280628 GTTACATACAGCCTCACAGCC 58.719 52.381 0.00 0.00 0.00 4.85
1600 1725 2.280628 GGTTACATACAGCCTCACAGC 58.719 52.381 0.00 0.00 0.00 4.40
1601 1726 3.610040 TGGTTACATACAGCCTCACAG 57.390 47.619 0.00 0.00 0.00 3.66
1602 1727 3.307410 CCTTGGTTACATACAGCCTCACA 60.307 47.826 0.00 0.00 0.00 3.58
1603 1728 3.270877 CCTTGGTTACATACAGCCTCAC 58.729 50.000 0.00 0.00 0.00 3.51
1604 1729 2.910319 ACCTTGGTTACATACAGCCTCA 59.090 45.455 0.00 0.00 0.00 3.86
1605 1730 3.055385 TGACCTTGGTTACATACAGCCTC 60.055 47.826 0.00 0.00 0.00 4.70
1633 1758 6.952773 TTGACCTTGCAGTAAGTATGTTTT 57.047 33.333 0.00 0.00 34.45 2.43
1634 1759 6.490040 ACATTGACCTTGCAGTAAGTATGTTT 59.510 34.615 0.00 0.00 34.45 2.83
1637 1762 7.010552 GTCTACATTGACCTTGCAGTAAGTATG 59.989 40.741 0.00 0.00 34.45 2.39
1651 1776 6.389906 CCAAAATTTCCTGTCTACATTGACC 58.610 40.000 0.00 0.00 36.21 4.02
1738 1871 9.969001 TTTACAGTTATTAATCCCTTTGTAGCT 57.031 29.630 0.00 0.00 0.00 3.32
1823 1956 7.411274 TCCAAGTAACATAAACTGAAAACACG 58.589 34.615 0.00 0.00 0.00 4.49
2079 2221 6.119536 TGAGTTGTTGTTTGTCCTACAGATT 58.880 36.000 0.00 0.00 0.00 2.40
2173 2336 2.548920 CGGAAGGAGGATGGTGATTAGC 60.549 54.545 0.00 0.00 0.00 3.09
2256 2419 3.390003 AAAAACGAGCCGAAGACCA 57.610 47.368 1.50 0.00 0.00 4.02
2558 2730 2.904866 GCCACCTGTGAAACGGCA 60.905 61.111 0.00 0.00 43.57 5.69
2629 2801 1.268234 GCTGTGACTGTGCAGTGAAAC 60.268 52.381 9.80 6.11 42.66 2.78
2843 3015 4.043686 TGGGCAATGATGATCCATGTCTAT 59.956 41.667 0.00 0.00 0.00 1.98
2845 3017 2.176148 TGGGCAATGATGATCCATGTCT 59.824 45.455 0.00 0.00 0.00 3.41
2948 3120 9.060547 CAAAAAGGCAAATAAAACAAGACAAAC 57.939 29.630 0.00 0.00 0.00 2.93
3100 3272 4.503685 AACTCTAGAGGGGGCCATATAA 57.496 45.455 23.50 0.00 0.00 0.98
3364 3536 3.751175 TCGAACAAGATTTCGCAATCCTT 59.249 39.130 4.07 0.00 46.46 3.36
3526 3698 9.125026 GGTCTACATATGAAAGGATGAAACAAT 57.875 33.333 10.38 0.00 0.00 2.71
3577 3749 2.938956 AGTGGGACAACTGAAAGGAG 57.061 50.000 0.00 0.00 44.16 3.69
3658 3830 5.670485 TGTAGAATACCGAATCTGTGCATT 58.330 37.500 0.00 0.00 42.12 3.56
3929 4103 6.655425 GCTATGATATTTTAGAAGGGACCCAC 59.345 42.308 14.60 6.45 0.00 4.61
3940 4114 8.613613 TTTGCAACAACGCTATGATATTTTAG 57.386 30.769 0.00 0.00 0.00 1.85
3999 4173 9.788960 GGTCTAATCAATTTACCAAATTCTGTC 57.211 33.333 0.00 0.00 38.97 3.51
4000 4174 9.308000 TGGTCTAATCAATTTACCAAATTCTGT 57.692 29.630 7.01 0.00 38.97 3.41
4212 4392 6.921857 GGATCAGAAAATACCATGATTGCTTG 59.078 38.462 0.00 0.00 32.68 4.01


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

AutoCloner maintained by Alex Coulton.