Multiple sequence alignment - TraesCS2A01G090200

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 TraesCS2A01G090200 chr2A 100.000 2827 0 0 1 2827 43181608 43178782 0.000000e+00 5221.0
1 TraesCS2A01G090200 chr2A 85.909 809 80 21 1934 2722 29605988 29605194 0.000000e+00 832.0
2 TraesCS2A01G090200 chr2A 86.957 391 34 6 2383 2758 758937828 758938216 9.360000e-115 424.0
3 TraesCS2A01G090200 chr2A 95.327 107 5 0 1677 1783 43163001 43162895 1.350000e-38 171.0
4 TraesCS2A01G090200 chr2A 95.000 100 0 1 1779 1873 43162864 43162765 4.880000e-33 152.0
5 TraesCS2A01G090200 chr2A 94.253 87 5 0 463 549 387038992 387038906 1.770000e-27 134.0
6 TraesCS2A01G090200 chr2D 94.746 1142 51 3 643 1782 38185067 38183933 0.000000e+00 1768.0
7 TraesCS2A01G090200 chr2D 83.890 838 90 23 1904 2722 27317718 27316907 0.000000e+00 758.0
8 TraesCS2A01G090200 chr2D 93.869 473 19 7 1 469 38185538 38185072 0.000000e+00 704.0
9 TraesCS2A01G090200 chr2D 89.831 118 10 2 525 641 76865240 76865356 1.750000e-32 150.0
10 TraesCS2A01G090200 chr2D 98.765 81 1 0 1779 1859 38183901 38183821 8.160000e-31 145.0
11 TraesCS2A01G090200 chr2D 96.875 32 1 0 2796 2827 38183794 38183763 1.000000e-03 54.7
12 TraesCS2A01G090200 chr2B 90.189 1162 66 25 643 1782 66718920 66717785 0.000000e+00 1471.0
13 TraesCS2A01G090200 chr2B 89.957 468 21 9 4 467 66719371 66718926 5.250000e-162 580.0
14 TraesCS2A01G090200 chr2B 93.750 96 2 1 1782 1873 66717750 66717655 1.060000e-29 141.0
15 TraesCS2A01G090200 chr2B 87.879 66 5 2 530 593 96110169 96110233 1.090000e-09 75.0
16 TraesCS2A01G090200 chr3B 91.611 894 47 11 1879 2753 697980907 697981791 0.000000e+00 1210.0
17 TraesCS2A01G090200 chr3B 84.606 864 95 27 1913 2753 65332103 65331255 0.000000e+00 824.0
18 TraesCS2A01G090200 chr3B 84.382 858 88 31 1918 2753 65342324 65341491 0.000000e+00 800.0
19 TraesCS2A01G090200 chr3B 97.753 89 2 0 553 641 249860973 249860885 1.360000e-33 154.0
20 TraesCS2A01G090200 chr3B 91.429 105 9 0 554 658 545181702 545181598 8.160000e-31 145.0
21 TraesCS2A01G090200 chr1A 86.480 895 88 18 1879 2753 64835461 64834580 0.000000e+00 952.0
22 TraesCS2A01G090200 chr1A 85.538 892 87 20 1879 2754 488100873 488100008 0.000000e+00 894.0
23 TraesCS2A01G090200 chr1A 84.444 180 24 3 465 641 560308053 560307875 1.040000e-39 174.0
24 TraesCS2A01G090200 chr1A 96.471 85 3 0 465 549 554524438 554524522 1.060000e-29 141.0
25 TraesCS2A01G090200 chr7B 86.374 888 87 25 1879 2757 141016550 141017412 0.000000e+00 939.0
26 TraesCS2A01G090200 chr7B 88.136 118 11 2 533 649 201496455 201496570 1.370000e-28 137.0
27 TraesCS2A01G090200 chr7A 86.161 896 85 22 1879 2753 519557458 519556581 0.000000e+00 931.0
28 TraesCS2A01G090200 chr7A 93.258 89 6 0 465 553 156937541 156937453 6.350000e-27 132.0
29 TraesCS2A01G090200 chr7A 87.611 113 12 2 530 641 131122133 131122244 2.290000e-26 130.0
30 TraesCS2A01G090200 chr5A 85.587 895 95 18 1879 2753 565725183 565726063 0.000000e+00 907.0
31 TraesCS2A01G090200 chr5A 96.774 93 2 1 549 641 626964601 626964510 1.360000e-33 154.0
32 TraesCS2A01G090200 chr5A 90.526 95 9 0 456 550 349401369 349401463 2.960000e-25 126.0
33 TraesCS2A01G090200 chrUn 86.436 752 70 14 2020 2753 94242460 94243197 0.000000e+00 795.0
34 TraesCS2A01G090200 chr3A 83.945 872 96 26 1913 2753 53297577 53296719 0.000000e+00 795.0
35 TraesCS2A01G090200 chr3A 81.844 358 46 11 1877 2223 52204992 52205341 1.660000e-72 283.0
36 TraesCS2A01G090200 chr3A 93.258 89 6 0 463 551 215966891 215966979 6.350000e-27 132.0
37 TraesCS2A01G090200 chr3D 83.871 837 89 29 1913 2724 42402322 42403137 0.000000e+00 756.0
38 TraesCS2A01G090200 chr3D 86.905 84 5 5 530 611 490039591 490039670 3.880000e-14 89.8
39 TraesCS2A01G090200 chr5B 83.750 480 40 19 2293 2754 711992429 711991970 1.210000e-113 420.0
40 TraesCS2A01G090200 chr6B 89.831 118 8 4 526 642 357123591 357123705 6.310000e-32 148.0
41 TraesCS2A01G090200 chr6B 87.931 116 8 5 527 640 478590911 478591022 6.350000e-27 132.0
42 TraesCS2A01G090200 chr6A 90.991 111 8 2 546 655 359016504 359016613 6.310000e-32 148.0
43 TraesCS2A01G090200 chr1B 90.826 109 10 0 555 663 134494635 134494743 2.270000e-31 147.0
44 TraesCS2A01G090200 chr1B 92.308 91 7 0 462 552 582741373 582741283 2.290000e-26 130.0
45 TraesCS2A01G090200 chr5D 95.506 89 4 0 461 549 458893934 458893846 2.940000e-30 143.0
46 TraesCS2A01G090200 chr5D 86.517 89 5 2 1866 1952 113744713 113744796 1.080000e-14 91.6
47 TraesCS2A01G090200 chr4A 91.489 94 7 1 464 556 24824544 24824451 8.220000e-26 128.0
48 TraesCS2A01G090200 chr7D 85.271 129 7 6 524 640 545268970 545269098 3.820000e-24 122.0
49 TraesCS2A01G090200 chr7D 74.899 247 45 13 1414 1650 111746897 111746658 2.320000e-16 97.1


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 TraesCS2A01G090200 chr2A 43178782 43181608 2826 True 5221.000000 5221 100.000000 1 2827 1 chr2A.!!$R2 2826
1 TraesCS2A01G090200 chr2A 29605194 29605988 794 True 832.000000 832 85.909000 1934 2722 1 chr2A.!!$R1 788
2 TraesCS2A01G090200 chr2D 27316907 27317718 811 True 758.000000 758 83.890000 1904 2722 1 chr2D.!!$R1 818
3 TraesCS2A01G090200 chr2D 38183763 38185538 1775 True 667.925000 1768 96.063750 1 2827 4 chr2D.!!$R2 2826
4 TraesCS2A01G090200 chr2B 66717655 66719371 1716 True 730.666667 1471 91.298667 4 1873 3 chr2B.!!$R1 1869
5 TraesCS2A01G090200 chr3B 697980907 697981791 884 False 1210.000000 1210 91.611000 1879 2753 1 chr3B.!!$F1 874
6 TraesCS2A01G090200 chr3B 65331255 65332103 848 True 824.000000 824 84.606000 1913 2753 1 chr3B.!!$R1 840
7 TraesCS2A01G090200 chr3B 65341491 65342324 833 True 800.000000 800 84.382000 1918 2753 1 chr3B.!!$R2 835
8 TraesCS2A01G090200 chr1A 64834580 64835461 881 True 952.000000 952 86.480000 1879 2753 1 chr1A.!!$R1 874
9 TraesCS2A01G090200 chr1A 488100008 488100873 865 True 894.000000 894 85.538000 1879 2754 1 chr1A.!!$R2 875
10 TraesCS2A01G090200 chr7B 141016550 141017412 862 False 939.000000 939 86.374000 1879 2757 1 chr7B.!!$F1 878
11 TraesCS2A01G090200 chr7A 519556581 519557458 877 True 931.000000 931 86.161000 1879 2753 1 chr7A.!!$R2 874
12 TraesCS2A01G090200 chr5A 565725183 565726063 880 False 907.000000 907 85.587000 1879 2753 1 chr5A.!!$F2 874
13 TraesCS2A01G090200 chrUn 94242460 94243197 737 False 795.000000 795 86.436000 2020 2753 1 chrUn.!!$F1 733
14 TraesCS2A01G090200 chr3A 53296719 53297577 858 True 795.000000 795 83.945000 1913 2753 1 chr3A.!!$R1 840
15 TraesCS2A01G090200 chr3D 42402322 42403137 815 False 756.000000 756 83.871000 1913 2724 1 chr3D.!!$F1 811

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
481 487 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.0 3.28 F
1224 1240 0.036105 TACAGACTCTACCGGCGACA 60.036 55.0 9.3 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1727 0.470456 AACGGTGGGACTGACAGGTA 60.470 55.0 7.51 0.0 0.0 3.08 R
2620 2750 0.109153 TCTCACCACATGCAAGCACT 59.891 50.0 0.00 0.0 0.0 4.40 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
22 23 2.287915 ACGCGAATGGAATAATCACAGC 59.712 45.455 15.93 0.00 0.00 4.40
62 63 8.154203 TGGAAGACAAATGTATGTAGAAAGTGA 58.846 33.333 0.00 0.00 32.57 3.41
175 176 4.155644 CAGTGAGCATTCCTCCTCTTTTTC 59.844 45.833 0.00 0.00 39.98 2.29
245 249 5.781210 TTGTTGTTGATTGATGCCTACAA 57.219 34.783 0.00 0.00 0.00 2.41
317 322 7.851228 AGGAGGAAAACAAGAAAGACATTTTT 58.149 30.769 0.00 0.00 0.00 1.94
364 369 1.507140 TGGGGACAACACAGACTTCT 58.493 50.000 0.00 0.00 37.44 2.85
365 370 1.843851 TGGGGACAACACAGACTTCTT 59.156 47.619 0.00 0.00 37.44 2.52
366 371 2.158813 TGGGGACAACACAGACTTCTTC 60.159 50.000 0.00 0.00 37.44 2.87
404 409 3.073650 ACTGCCCATCTGAACTTCTCTTT 59.926 43.478 0.00 0.00 0.00 2.52
412 418 7.826252 CCCATCTGAACTTCTCTTTATTCAAGA 59.174 37.037 0.00 0.00 39.39 3.02
469 475 8.370940 TCAGAAATTCATCATGGATACTACTCC 58.629 37.037 0.00 0.00 35.74 3.85
470 476 7.605691 CAGAAATTCATCATGGATACTACTCCC 59.394 40.741 0.00 0.00 34.12 4.30
471 477 7.515514 AGAAATTCATCATGGATACTACTCCCT 59.484 37.037 0.00 0.00 34.12 4.20
472 478 6.865834 ATTCATCATGGATACTACTCCCTC 57.134 41.667 0.00 0.00 34.12 4.30
473 479 4.678256 TCATCATGGATACTACTCCCTCC 58.322 47.826 0.00 0.00 34.12 4.30
474 480 3.156288 TCATGGATACTACTCCCTCCG 57.844 52.381 0.00 0.00 34.12 4.63
475 481 2.445905 TCATGGATACTACTCCCTCCGT 59.554 50.000 0.00 0.00 34.12 4.69
476 482 2.653234 TGGATACTACTCCCTCCGTC 57.347 55.000 0.00 0.00 34.12 4.79
477 483 1.144503 TGGATACTACTCCCTCCGTCC 59.855 57.143 0.00 0.00 34.12 4.79
478 484 1.547449 GGATACTACTCCCTCCGTCCC 60.547 61.905 0.00 0.00 0.00 4.46
479 485 1.144503 GATACTACTCCCTCCGTCCCA 59.855 57.143 0.00 0.00 0.00 4.37
480 486 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
481 487 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
482 488 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
483 489 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
484 490 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
485 491 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
486 492 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
487 493 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
488 494 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
489 495 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
490 496 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
491 497 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
492 498 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
493 499 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
494 500 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
495 501 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
496 502 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
497 503 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
553 559 7.973048 ATTTTAGGACAGAGGTAGTACATCA 57.027 36.000 16.67 0.00 30.12 3.07
554 560 7.973048 TTTTAGGACAGAGGTAGTACATCAT 57.027 36.000 16.67 4.74 30.12 2.45
555 561 9.656323 ATTTTAGGACAGAGGTAGTACATCATA 57.344 33.333 16.67 0.09 30.12 2.15
556 562 8.461249 TTTAGGACAGAGGTAGTACATCATAC 57.539 38.462 16.67 5.66 30.12 2.39
557 563 6.268855 AGGACAGAGGTAGTACATCATACT 57.731 41.667 16.67 7.76 30.12 2.12
558 564 6.300703 AGGACAGAGGTAGTACATCATACTC 58.699 44.000 16.67 5.91 30.12 2.59
559 565 5.474189 GGACAGAGGTAGTACATCATACTCC 59.526 48.000 16.67 10.07 30.12 3.85
560 566 5.386924 ACAGAGGTAGTACATCATACTCCC 58.613 45.833 16.67 0.00 30.12 4.30
561 567 5.134679 ACAGAGGTAGTACATCATACTCCCT 59.865 44.000 16.67 0.00 36.72 4.20
562 568 5.708230 CAGAGGTAGTACATCATACTCCCTC 59.292 48.000 16.67 14.66 45.52 4.30
563 569 5.000570 AGGTAGTACATCATACTCCCTCC 57.999 47.826 2.06 0.00 29.24 4.30
564 570 3.757493 GGTAGTACATCATACTCCCTCCG 59.243 52.174 2.06 0.00 0.00 4.63
565 571 3.596940 AGTACATCATACTCCCTCCGT 57.403 47.619 0.00 0.00 0.00 4.69
566 572 3.912248 AGTACATCATACTCCCTCCGTT 58.088 45.455 0.00 0.00 0.00 4.44
567 573 3.890147 AGTACATCATACTCCCTCCGTTC 59.110 47.826 0.00 0.00 0.00 3.95
568 574 2.040178 ACATCATACTCCCTCCGTTCC 58.960 52.381 0.00 0.00 0.00 3.62
569 575 2.039418 CATCATACTCCCTCCGTTCCA 58.961 52.381 0.00 0.00 0.00 3.53
570 576 2.241281 TCATACTCCCTCCGTTCCAA 57.759 50.000 0.00 0.00 0.00 3.53
571 577 2.542550 TCATACTCCCTCCGTTCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
572 578 2.907696 TCATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
573 579 3.521937 TCATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
574 580 4.717778 TCATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
575 581 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
576 582 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
577 583 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
578 584 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
579 585 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
580 586 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
581 587 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
582 588 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
583 589 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
584 590 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
585 591 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
586 592 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
587 593 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
588 594 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
589 595 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
590 596 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
591 597 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
592 598 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
593 599 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
613 619 9.638239 TTGTACTAAGTTTAGTATAACGTTGGG 57.362 33.333 11.99 0.00 45.11 4.12
614 620 8.802267 TGTACTAAGTTTAGTATAACGTTGGGT 58.198 33.333 11.99 0.00 45.11 4.51
615 621 9.290483 GTACTAAGTTTAGTATAACGTTGGGTC 57.710 37.037 11.99 0.00 45.11 4.46
616 622 7.895759 ACTAAGTTTAGTATAACGTTGGGTCA 58.104 34.615 11.99 0.00 41.92 4.02
617 623 8.534496 ACTAAGTTTAGTATAACGTTGGGTCAT 58.466 33.333 11.99 0.00 41.92 3.06
618 624 7.838771 AAGTTTAGTATAACGTTGGGTCATC 57.161 36.000 11.99 0.00 33.26 2.92
619 625 7.179076 AGTTTAGTATAACGTTGGGTCATCT 57.821 36.000 11.99 2.61 33.26 2.90
620 626 8.297470 AGTTTAGTATAACGTTGGGTCATCTA 57.703 34.615 11.99 1.71 33.26 1.98
621 627 8.921205 AGTTTAGTATAACGTTGGGTCATCTAT 58.079 33.333 11.99 0.00 33.26 1.98
622 628 9.538508 GTTTAGTATAACGTTGGGTCATCTATT 57.461 33.333 11.99 0.00 0.00 1.73
625 631 8.433421 AGTATAACGTTGGGTCATCTATTTTG 57.567 34.615 11.99 0.00 0.00 2.44
626 632 6.693315 ATAACGTTGGGTCATCTATTTTGG 57.307 37.500 11.99 0.00 0.00 3.28
627 633 4.295141 ACGTTGGGTCATCTATTTTGGA 57.705 40.909 0.00 0.00 0.00 3.53
628 634 4.658063 ACGTTGGGTCATCTATTTTGGAA 58.342 39.130 0.00 0.00 0.00 3.53
629 635 4.457949 ACGTTGGGTCATCTATTTTGGAAC 59.542 41.667 0.00 0.00 0.00 3.62
630 636 4.436852 CGTTGGGTCATCTATTTTGGAACG 60.437 45.833 0.00 0.00 0.00 3.95
631 637 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
632 638 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
633 639 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
634 640 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
635 641 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
636 642 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
637 643 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
638 644 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
639 645 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
640 646 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
641 647 1.272807 TTTGGAACGGAGGGAGTAGG 58.727 55.000 0.00 0.00 0.00 3.18
688 694 8.506437 AGCTAAAGCAAAGGCATTTTTATTTTC 58.494 29.630 4.54 0.00 45.16 2.29
963 977 7.661968 TCACCTTCTTAGATCCTTCGAATATG 58.338 38.462 0.00 0.00 0.00 1.78
1020 1036 5.460419 GCATATATATAACACGCAGAGCTCC 59.540 44.000 10.93 0.00 0.00 4.70
1062 1078 7.072961 ACCAGATTCCTAATCCACTACATCAAT 59.927 37.037 0.00 0.00 38.71 2.57
1068 1084 6.782494 TCCTAATCCACTACATCAATCAGCTA 59.218 38.462 0.00 0.00 0.00 3.32
1204 1220 2.361610 CAGCGAAGGGGCAATGGT 60.362 61.111 0.00 0.00 34.64 3.55
1206 1222 0.679640 CAGCGAAGGGGCAATGGTTA 60.680 55.000 0.00 0.00 34.64 2.85
1212 1228 1.372501 AGGGGCAATGGTTACAGACT 58.627 50.000 0.00 0.00 0.00 3.24
1213 1229 1.282157 AGGGGCAATGGTTACAGACTC 59.718 52.381 0.00 0.00 0.00 3.36
1215 1231 2.504175 GGGGCAATGGTTACAGACTCTA 59.496 50.000 0.00 0.00 0.00 2.43
1216 1232 3.532542 GGGCAATGGTTACAGACTCTAC 58.467 50.000 0.00 0.00 0.00 2.59
1218 1234 3.187700 GCAATGGTTACAGACTCTACCG 58.812 50.000 0.00 0.00 33.29 4.02
1222 1238 1.089920 GTTACAGACTCTACCGGCGA 58.910 55.000 9.30 0.00 0.00 5.54
1224 1240 0.036105 TACAGACTCTACCGGCGACA 60.036 55.000 9.30 0.00 0.00 4.35
1225 1241 0.892358 ACAGACTCTACCGGCGACAA 60.892 55.000 9.30 0.00 0.00 3.18
1227 1243 0.892358 AGACTCTACCGGCGACAACA 60.892 55.000 9.30 0.00 0.00 3.33
1228 1244 0.456312 GACTCTACCGGCGACAACAG 60.456 60.000 9.30 0.00 0.00 3.16
1392 1408 2.126618 GTGGCATCGTCGACGTCA 60.127 61.111 34.40 24.27 40.80 4.35
1437 1453 2.594592 GTGTGCCACCGGAGCTTT 60.595 61.111 9.46 0.00 0.00 3.51
1567 1589 3.220999 CTCAACCTGACGCCGGTGA 62.221 63.158 24.59 4.28 34.33 4.02
1611 1633 0.252742 GAAGGTGGGGAGAGGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
1745 1772 8.364129 TCATTCTTGTTTATTTCCACTTTTGC 57.636 30.769 0.00 0.00 0.00 3.68
1873 1939 5.375417 TCAATAGACAAAACAGTGGCATG 57.625 39.130 0.00 0.00 0.00 4.06
1874 1940 4.826733 TCAATAGACAAAACAGTGGCATGT 59.173 37.500 0.00 0.00 33.96 3.21
1875 1941 4.771590 ATAGACAAAACAGTGGCATGTG 57.228 40.909 0.00 0.00 32.52 3.21
1876 1942 2.653726 AGACAAAACAGTGGCATGTGA 58.346 42.857 6.80 0.00 32.52 3.58
1877 1943 3.225104 AGACAAAACAGTGGCATGTGAT 58.775 40.909 6.80 0.00 32.52 3.06
1909 1975 0.907704 TCTACCATGCACGGGACCTT 60.908 55.000 12.94 0.00 0.00 3.50
2311 2400 8.800972 CATTTCATAATGTTACATTGTGTGCTC 58.199 33.333 25.99 0.00 37.06 4.26
2459 2550 5.754890 GTGCTTCACCATGTTTCAGAATTTT 59.245 36.000 0.00 0.00 0.00 1.82
2503 2594 9.840427 AAATATATTCAAAAGTGGTCTCGTTTG 57.160 29.630 0.00 5.52 37.84 2.93
2620 2750 2.380064 AAAAGCATGGGTGGAACAGA 57.620 45.000 0.00 0.00 41.80 3.41
2648 2780 2.606725 GCATGTGGTGAGAGAAAGATCG 59.393 50.000 0.00 0.00 0.00 3.69
2652 2784 3.320826 TGTGGTGAGAGAAAGATCGAACA 59.679 43.478 0.00 0.00 0.00 3.18
2679 2813 3.970610 GCGAGCAGTATAAATGCATTGTG 59.029 43.478 13.82 7.10 46.31 3.33
2757 2891 3.471680 GGAGATTAGCTTTTCTCGGCAT 58.528 45.455 15.49 0.00 39.42 4.40
2758 2892 3.249559 GGAGATTAGCTTTTCTCGGCATG 59.750 47.826 15.49 0.00 39.42 4.06
2759 2893 3.873952 GAGATTAGCTTTTCTCGGCATGT 59.126 43.478 9.15 0.00 29.96 3.21
2760 2894 3.624861 AGATTAGCTTTTCTCGGCATGTG 59.375 43.478 0.00 0.00 0.00 3.21
2761 2895 2.760634 TAGCTTTTCTCGGCATGTGA 57.239 45.000 0.00 0.00 0.00 3.58
2762 2896 2.119801 AGCTTTTCTCGGCATGTGAT 57.880 45.000 0.00 0.00 0.00 3.06
2763 2897 2.012673 AGCTTTTCTCGGCATGTGATC 58.987 47.619 0.00 0.00 0.00 2.92
2764 2898 1.064654 GCTTTTCTCGGCATGTGATCC 59.935 52.381 0.00 0.00 0.00 3.36
2765 2899 2.636830 CTTTTCTCGGCATGTGATCCT 58.363 47.619 0.00 0.00 0.00 3.24
2766 2900 2.787473 TTTCTCGGCATGTGATCCTT 57.213 45.000 0.00 0.00 0.00 3.36
2767 2901 2.787473 TTCTCGGCATGTGATCCTTT 57.213 45.000 0.00 0.00 0.00 3.11
2768 2902 3.904800 TTCTCGGCATGTGATCCTTTA 57.095 42.857 0.00 0.00 0.00 1.85
2769 2903 4.422073 TTCTCGGCATGTGATCCTTTAT 57.578 40.909 0.00 0.00 0.00 1.40
2770 2904 3.995199 TCTCGGCATGTGATCCTTTATC 58.005 45.455 0.00 0.00 34.93 1.75
2771 2905 2.733552 CTCGGCATGTGATCCTTTATCG 59.266 50.000 0.00 0.00 37.42 2.92
2772 2906 1.800586 CGGCATGTGATCCTTTATCGG 59.199 52.381 0.00 0.00 37.42 4.18
2773 2907 2.547855 CGGCATGTGATCCTTTATCGGA 60.548 50.000 0.00 0.00 37.42 4.55
2774 2908 3.476552 GGCATGTGATCCTTTATCGGAA 58.523 45.455 0.00 0.00 37.42 4.30
2775 2909 3.882888 GGCATGTGATCCTTTATCGGAAA 59.117 43.478 0.00 0.00 37.42 3.13
2776 2910 4.520492 GGCATGTGATCCTTTATCGGAAAT 59.480 41.667 0.00 0.00 37.42 2.17
2777 2911 5.705441 GGCATGTGATCCTTTATCGGAAATA 59.295 40.000 0.00 0.00 37.42 1.40
2778 2912 6.128172 GGCATGTGATCCTTTATCGGAAATAG 60.128 42.308 0.00 0.00 37.42 1.73
2779 2913 6.621596 GCATGTGATCCTTTATCGGAAATAGC 60.622 42.308 0.00 0.00 37.42 2.97
2780 2914 5.924356 TGTGATCCTTTATCGGAAATAGCA 58.076 37.500 0.00 0.00 37.42 3.49
2781 2915 6.533730 TGTGATCCTTTATCGGAAATAGCAT 58.466 36.000 0.00 0.00 37.42 3.79
2782 2916 7.676004 TGTGATCCTTTATCGGAAATAGCATA 58.324 34.615 0.00 0.00 37.42 3.14
2783 2917 8.154203 TGTGATCCTTTATCGGAAATAGCATAA 58.846 33.333 0.00 0.00 37.42 1.90
2784 2918 8.999431 GTGATCCTTTATCGGAAATAGCATAAA 58.001 33.333 0.00 0.00 37.42 1.40
2785 2919 9.739276 TGATCCTTTATCGGAAATAGCATAAAT 57.261 29.630 0.00 0.00 37.42 1.40
2786 2920 9.994432 GATCCTTTATCGGAAATAGCATAAATG 57.006 33.333 0.00 0.00 36.49 2.32
2787 2921 9.739276 ATCCTTTATCGGAAATAGCATAAATGA 57.261 29.630 0.00 0.00 36.49 2.57
2788 2922 9.219603 TCCTTTATCGGAAATAGCATAAATGAG 57.780 33.333 0.00 0.00 0.00 2.90
2789 2923 9.219603 CCTTTATCGGAAATAGCATAAATGAGA 57.780 33.333 0.00 0.00 0.00 3.27
2791 2925 9.778741 TTTATCGGAAATAGCATAAATGAGAGT 57.221 29.630 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.138761 GTGATTGATTCGCTGTGATTATTCC 58.861 40.000 0.00 0.00 31.85 3.01
22 23 5.550232 TGTCTTCCATTGTGATTGATTCG 57.450 39.130 0.00 0.00 0.00 3.34
62 63 2.747446 GGACTTTCCGTGTGTGCATAAT 59.253 45.455 0.00 0.00 0.00 1.28
175 176 6.478016 TCTGTCTCGAGAATCAATATTTGCAG 59.522 38.462 18.55 14.78 33.17 4.41
317 322 3.250744 CGAACCGTCAATTTGAGAGCTA 58.749 45.455 0.00 0.00 0.00 3.32
376 381 2.107204 AGTTCAGATGGGCAGTTCTGTT 59.893 45.455 9.46 0.00 40.22 3.16
378 383 2.486472 AGTTCAGATGGGCAGTTCTG 57.514 50.000 4.70 4.70 40.58 3.02
404 409 4.312443 GTTGGACGTGTTCCTCTTGAATA 58.688 43.478 0.00 0.00 46.10 1.75
412 418 1.553704 GGATAGGTTGGACGTGTTCCT 59.446 52.381 0.00 0.00 46.10 3.36
419 425 2.279252 CCGCGGATAGGTTGGACG 60.279 66.667 24.07 0.00 0.00 4.79
469 475 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
470 476 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
471 477 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
472 478 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
527 533 9.656323 TGATGTACTACCTCTGTCCTAAAATAT 57.344 33.333 0.00 0.00 0.00 1.28
528 534 9.656323 ATGATGTACTACCTCTGTCCTAAAATA 57.344 33.333 0.00 0.00 0.00 1.40
529 535 7.973048 TGATGTACTACCTCTGTCCTAAAAT 57.027 36.000 0.00 0.00 0.00 1.82
530 536 7.973048 ATGATGTACTACCTCTGTCCTAAAA 57.027 36.000 0.00 0.00 0.00 1.52
531 537 8.280084 AGTATGATGTACTACCTCTGTCCTAAA 58.720 37.037 0.00 0.00 0.00 1.85
532 538 7.813331 AGTATGATGTACTACCTCTGTCCTAA 58.187 38.462 0.00 0.00 0.00 2.69
533 539 7.390013 AGTATGATGTACTACCTCTGTCCTA 57.610 40.000 0.00 0.00 0.00 2.94
534 540 6.268855 AGTATGATGTACTACCTCTGTCCT 57.731 41.667 0.00 0.00 0.00 3.85
535 541 5.474189 GGAGTATGATGTACTACCTCTGTCC 59.526 48.000 0.00 0.00 0.00 4.02
536 542 5.474189 GGGAGTATGATGTACTACCTCTGTC 59.526 48.000 8.85 0.00 43.64 3.51
537 543 5.386924 GGGAGTATGATGTACTACCTCTGT 58.613 45.833 8.85 0.00 43.64 3.41
538 544 5.968528 GGGAGTATGATGTACTACCTCTG 57.031 47.826 8.85 0.00 43.64 3.35
542 548 3.757493 CGGAGGGAGTATGATGTACTACC 59.243 52.174 8.17 8.17 46.61 3.18
543 549 4.396522 ACGGAGGGAGTATGATGTACTAC 58.603 47.826 0.00 0.00 0.00 2.73
544 550 4.719026 ACGGAGGGAGTATGATGTACTA 57.281 45.455 0.00 0.00 0.00 1.82
545 551 3.596940 ACGGAGGGAGTATGATGTACT 57.403 47.619 0.00 0.00 0.00 2.73
546 552 3.005578 GGAACGGAGGGAGTATGATGTAC 59.994 52.174 0.00 0.00 0.00 2.90
547 553 3.228453 GGAACGGAGGGAGTATGATGTA 58.772 50.000 0.00 0.00 0.00 2.29
548 554 2.040178 GGAACGGAGGGAGTATGATGT 58.960 52.381 0.00 0.00 0.00 3.06
549 555 2.039418 TGGAACGGAGGGAGTATGATG 58.961 52.381 0.00 0.00 0.00 3.07
550 556 2.471815 TGGAACGGAGGGAGTATGAT 57.528 50.000 0.00 0.00 0.00 2.45
551 557 2.241281 TTGGAACGGAGGGAGTATGA 57.759 50.000 0.00 0.00 0.00 2.15
552 558 3.343941 TTTTGGAACGGAGGGAGTATG 57.656 47.619 0.00 0.00 0.00 2.39
553 559 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
554 560 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
555 561 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
556 562 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
557 563 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
558 564 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
559 565 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
560 566 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
561 567 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
562 568 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
563 569 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
564 570 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
565 571 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
566 572 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
567 573 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
587 593 9.638239 CCCAACGTTATACTAAACTTAGTACAA 57.362 33.333 10.74 4.27 45.86 2.41
588 594 8.802267 ACCCAACGTTATACTAAACTTAGTACA 58.198 33.333 10.74 0.00 45.86 2.90
589 595 9.290483 GACCCAACGTTATACTAAACTTAGTAC 57.710 37.037 10.74 2.25 45.86 2.73
590 596 9.019656 TGACCCAACGTTATACTAAACTTAGTA 57.980 33.333 10.89 10.89 46.74 1.82
591 597 7.895759 TGACCCAACGTTATACTAAACTTAGT 58.104 34.615 0.00 7.27 45.39 2.24
592 598 8.937634 ATGACCCAACGTTATACTAAACTTAG 57.062 34.615 0.00 0.00 36.82 2.18
593 599 8.752187 AGATGACCCAACGTTATACTAAACTTA 58.248 33.333 0.00 0.00 0.00 2.24
594 600 7.618137 AGATGACCCAACGTTATACTAAACTT 58.382 34.615 0.00 0.00 0.00 2.66
595 601 7.179076 AGATGACCCAACGTTATACTAAACT 57.821 36.000 0.00 0.00 0.00 2.66
596 602 9.538508 AATAGATGACCCAACGTTATACTAAAC 57.461 33.333 0.00 0.00 0.00 2.01
599 605 9.537192 CAAAATAGATGACCCAACGTTATACTA 57.463 33.333 0.00 0.00 0.00 1.82
600 606 7.497909 CCAAAATAGATGACCCAACGTTATACT 59.502 37.037 0.00 0.00 0.00 2.12
601 607 7.496591 TCCAAAATAGATGACCCAACGTTATAC 59.503 37.037 0.00 0.00 0.00 1.47
602 608 7.566569 TCCAAAATAGATGACCCAACGTTATA 58.433 34.615 0.00 0.00 0.00 0.98
603 609 6.419791 TCCAAAATAGATGACCCAACGTTAT 58.580 36.000 0.00 0.00 0.00 1.89
604 610 5.806818 TCCAAAATAGATGACCCAACGTTA 58.193 37.500 0.00 0.00 0.00 3.18
605 611 4.658063 TCCAAAATAGATGACCCAACGTT 58.342 39.130 0.00 0.00 0.00 3.99
606 612 4.295141 TCCAAAATAGATGACCCAACGT 57.705 40.909 0.00 0.00 0.00 3.99
607 613 4.436852 CGTTCCAAAATAGATGACCCAACG 60.437 45.833 0.00 0.00 0.00 4.10
608 614 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
609 615 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
610 616 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
611 617 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
612 618 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
613 619 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
614 620 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
615 621 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
616 622 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
617 623 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
618 624 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
619 625 3.453353 CCTACTCCCTCCGTTCCAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
620 626 2.238898 CCTACTCCCTCCGTTCCAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
621 627 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
622 628 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
623 629 0.115745 ACCTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 0.00 3.53
624 630 0.324091 GACCTACTCCCTCCGTTCCA 60.324 60.000 0.00 0.00 0.00 3.53
625 631 0.324091 TGACCTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
626 632 1.777941 ATGACCTACTCCCTCCGTTC 58.222 55.000 0.00 0.00 0.00 3.95
627 633 2.424523 CCTATGACCTACTCCCTCCGTT 60.425 54.545 0.00 0.00 0.00 4.44
628 634 1.145325 CCTATGACCTACTCCCTCCGT 59.855 57.143 0.00 0.00 0.00 4.69
629 635 1.145325 ACCTATGACCTACTCCCTCCG 59.855 57.143 0.00 0.00 0.00 4.63
630 636 2.599677 CACCTATGACCTACTCCCTCC 58.400 57.143 0.00 0.00 0.00 4.30
631 637 1.964933 GCACCTATGACCTACTCCCTC 59.035 57.143 0.00 0.00 0.00 4.30
632 638 1.291033 TGCACCTATGACCTACTCCCT 59.709 52.381 0.00 0.00 0.00 4.20
633 639 1.789523 TGCACCTATGACCTACTCCC 58.210 55.000 0.00 0.00 0.00 4.30
634 640 2.965831 TCATGCACCTATGACCTACTCC 59.034 50.000 0.00 0.00 32.39 3.85
635 641 4.672587 TTCATGCACCTATGACCTACTC 57.327 45.455 0.00 0.00 36.84 2.59
636 642 4.655649 TGATTCATGCACCTATGACCTACT 59.344 41.667 0.00 0.00 36.84 2.57
637 643 4.960938 TGATTCATGCACCTATGACCTAC 58.039 43.478 0.00 0.00 36.84 3.18
638 644 5.104569 TGTTGATTCATGCACCTATGACCTA 60.105 40.000 0.00 0.00 36.84 3.08
639 645 4.202441 GTTGATTCATGCACCTATGACCT 58.798 43.478 0.00 0.00 36.84 3.85
640 646 3.947196 TGTTGATTCATGCACCTATGACC 59.053 43.478 0.00 0.00 36.84 4.02
641 647 4.497006 GCTGTTGATTCATGCACCTATGAC 60.497 45.833 0.00 0.00 36.84 3.06
688 694 2.758089 GCGGCTCTCCAATGTGCTG 61.758 63.158 0.00 0.00 36.32 4.41
851 865 0.250338 AGTGGTTTCCAGTTCTCCGC 60.250 55.000 0.00 0.00 32.53 5.54
852 866 1.608283 GGAGTGGTTTCCAGTTCTCCG 60.608 57.143 7.75 0.00 37.30 4.63
856 870 2.930826 TGAGGAGTGGTTTCCAGTTC 57.069 50.000 0.00 0.00 37.30 3.01
963 977 2.974165 GCAAGTGTGCGTTCTATATGC 58.026 47.619 0.00 0.00 41.93 3.14
1020 1036 4.808414 TCTGGTTTACTGAGTCCTGATG 57.192 45.455 0.00 0.00 0.00 3.07
1097 1113 0.863799 CGTCATCTTCATCATGGCCG 59.136 55.000 0.00 0.00 0.00 6.13
1182 1198 4.722700 TGCCCCTTCGCTGCTTCC 62.723 66.667 0.00 0.00 0.00 3.46
1183 1199 2.048603 ATTGCCCCTTCGCTGCTTC 61.049 57.895 0.00 0.00 0.00 3.86
1185 1201 2.753043 CATTGCCCCTTCGCTGCT 60.753 61.111 0.00 0.00 0.00 4.24
1204 1220 1.089920 GTCGCCGGTAGAGTCTGTAA 58.910 55.000 1.90 0.00 0.00 2.41
1206 1222 0.892358 TTGTCGCCGGTAGAGTCTGT 60.892 55.000 1.90 0.00 0.00 3.41
1212 1228 2.260434 GCTGTTGTCGCCGGTAGA 59.740 61.111 1.90 0.00 0.00 2.59
1213 1229 2.048597 TGCTGTTGTCGCCGGTAG 60.049 61.111 1.90 0.00 0.00 3.18
1476 1492 2.893398 GACAGCCCGTCCCAGTAG 59.107 66.667 0.00 0.00 38.85 2.57
1701 1727 0.470456 AACGGTGGGACTGACAGGTA 60.470 55.000 7.51 0.00 0.00 3.08
1745 1772 8.306761 AGTGGAAATAAACAATAGGCTCAAAAG 58.693 33.333 0.00 0.00 0.00 2.27
1873 1939 6.227298 TGGTAGAAAATCCTCTCTCATCAC 57.773 41.667 0.00 0.00 0.00 3.06
1874 1940 6.687393 GCATGGTAGAAAATCCTCTCTCATCA 60.687 42.308 0.00 0.00 0.00 3.07
1875 1941 5.700373 GCATGGTAGAAAATCCTCTCTCATC 59.300 44.000 0.00 0.00 0.00 2.92
1876 1942 5.131642 TGCATGGTAGAAAATCCTCTCTCAT 59.868 40.000 0.00 0.00 0.00 2.90
1877 1943 4.471025 TGCATGGTAGAAAATCCTCTCTCA 59.529 41.667 0.00 0.00 0.00 3.27
1909 1975 1.888638 CGATGGATGCATGCACGGA 60.889 57.895 25.37 9.82 0.00 4.69
1932 1999 8.664669 AGAAAAGGTCCCACACAATAATAAAT 57.335 30.769 0.00 0.00 0.00 1.40
2216 2297 7.493743 TTGCAAAACACAATGAAGCATTATT 57.506 28.000 0.00 0.00 32.35 1.40
2218 2299 6.915544 TTTGCAAAACACAATGAAGCATTA 57.084 29.167 10.02 0.00 32.35 1.90
2219 2300 5.814764 TTTGCAAAACACAATGAAGCATT 57.185 30.435 10.02 0.00 34.04 3.56
2221 2302 5.618056 TTTTTGCAAAACACAATGAAGCA 57.382 30.435 23.79 2.34 0.00 3.91
2311 2400 7.582435 ACTAAGAATCAGTTTGATACACACG 57.418 36.000 0.00 0.00 35.76 4.49
2503 2594 3.307782 TGTTTTTGACGACGAGACCTTTC 59.692 43.478 0.00 0.00 0.00 2.62
2620 2750 0.109153 TCTCACCACATGCAAGCACT 59.891 50.000 0.00 0.00 0.00 4.40
2679 2813 3.440173 TGATTTTTGCTTGGAGATCCGAC 59.560 43.478 0.00 0.00 39.43 4.79
2757 2891 5.924356 TGCTATTTCCGATAAAGGATCACA 58.076 37.500 0.00 0.00 40.48 3.58
2758 2892 8.547967 TTATGCTATTTCCGATAAAGGATCAC 57.452 34.615 0.00 0.00 40.48 3.06
2759 2893 9.739276 ATTTATGCTATTTCCGATAAAGGATCA 57.261 29.630 0.00 0.00 40.48 2.92
2760 2894 9.994432 CATTTATGCTATTTCCGATAAAGGATC 57.006 33.333 0.00 0.00 40.48 3.36
2761 2895 9.739276 TCATTTATGCTATTTCCGATAAAGGAT 57.261 29.630 0.00 0.00 40.48 3.24
2762 2896 9.219603 CTCATTTATGCTATTTCCGATAAAGGA 57.780 33.333 0.00 0.00 38.79 3.36
2763 2897 9.219603 TCTCATTTATGCTATTTCCGATAAAGG 57.780 33.333 0.00 0.00 0.00 3.11
2765 2899 9.778741 ACTCTCATTTATGCTATTTCCGATAAA 57.221 29.630 0.00 0.00 0.00 1.40
2798 2932 6.821616 AGTCAGAAAGAATCACTGGGATAT 57.178 37.500 0.00 0.00 34.28 1.63


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

AutoCloner maintained by Alex Coulton.