Multiple sequence alignment - TraesCS6D01G087600

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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 TraesCS6D01G087600 chr6D 100.000 9498 0 0 1 9498 52828439 52818942 0.000000e+00 17540
1 TraesCS6D01G087600 chr6D 93.694 111 7 0 576 686 323668433 323668543 5.900000e-37 167
2 TraesCS6D01G087600 chr6A 96.887 3726 91 14 697 4401 63776528 63772807 0.000000e+00 6215
3 TraesCS6D01G087600 chr6A 97.336 1952 30 2 4450 6401 63772801 63770872 0.000000e+00 3297
4 TraesCS6D01G087600 chr6A 97.587 1699 36 4 7449 9144 63769761 63768065 0.000000e+00 2905
5 TraesCS6D01G087600 chr6A 97.919 961 20 0 6484 7444 63770870 63769910 0.000000e+00 1664
6 TraesCS6D01G087600 chr6A 97.333 225 5 1 9274 9498 63768006 63767783 1.940000e-101 381
7 TraesCS6D01G087600 chr6B 94.784 3432 99 34 673 4053 119986336 119982934 0.000000e+00 5273
8 TraesCS6D01G087600 chr6B 97.192 2386 57 5 4049 6427 119982736 119980354 0.000000e+00 4026
9 TraesCS6D01G087600 chr6B 97.592 1869 41 4 6474 8340 119980276 119978410 0.000000e+00 3199
10 TraesCS6D01G087600 chr6B 95.876 1164 42 6 8339 9498 119978438 119977277 0.000000e+00 1879
11 TraesCS6D01G087600 chr6B 94.898 98 5 0 6400 6497 164810385 164810288 4.590000e-33 154
12 TraesCS6D01G087600 chr2D 98.611 576 6 1 1 576 275177329 275177902 0.000000e+00 1018
13 TraesCS6D01G087600 chr2D 92.373 118 4 5 576 693 213131299 213131411 7.630000e-36 163
14 TraesCS6D01G087600 chr2D 90.400 125 7 4 576 696 545396159 545396282 9.870000e-35 159
15 TraesCS6D01G087600 chr2D 92.233 103 7 1 6400 6502 441039185 441039084 2.760000e-30 145
16 TraesCS6D01G087600 chr2D 90.179 112 10 1 6391 6502 638464730 638464840 2.760000e-30 145
17 TraesCS6D01G087600 chr3D 98.264 576 7 2 1 576 511684361 511683789 0.000000e+00 1005
18 TraesCS6D01G087600 chr3D 96.007 576 10 1 1 576 442776804 442777366 0.000000e+00 924
19 TraesCS6D01G087600 chr3D 90.625 128 8 2 576 700 232037837 232037963 5.900000e-37 167
20 TraesCS6D01G087600 chr3D 92.373 118 5 3 576 692 259177409 259177523 2.120000e-36 165
21 TraesCS6D01G087600 chr5D 92.746 579 23 4 1 576 169968826 169969388 0.000000e+00 819
22 TraesCS6D01G087600 chr2A 90.878 592 35 5 1 576 719698166 719698754 0.000000e+00 776
23 TraesCS6D01G087600 chr4A 90.508 590 38 6 1 576 43267808 43268393 0.000000e+00 763
24 TraesCS6D01G087600 chr4A 88.793 580 31 17 1 577 618263678 618264226 0.000000e+00 680
25 TraesCS6D01G087600 chr1A 90.339 590 39 6 1 576 568651456 568652041 0.000000e+00 758
26 TraesCS6D01G087600 chr5A 88.663 591 37 12 1 577 664545557 664544983 0.000000e+00 693
27 TraesCS6D01G087600 chr3B 86.621 583 33 9 12 581 10015896 10015346 3.790000e-168 603
28 TraesCS6D01G087600 chr5B 85.059 589 44 9 1 576 393943199 393943756 2.320000e-155 560
29 TraesCS6D01G087600 chr5B 90.400 125 8 4 576 697 706217929 706218052 2.740000e-35 161
30 TraesCS6D01G087600 chr5B 96.809 94 3 0 6399 6492 482285947 482285854 3.550000e-34 158
31 TraesCS6D01G087600 chr5B 97.802 91 2 0 6399 6489 482285860 482285950 3.550000e-34 158
32 TraesCS6D01G087600 chr7B 92.562 121 5 3 576 693 542859682 542859563 4.560000e-38 171
33 TraesCS6D01G087600 chr7D 94.545 110 4 2 576 685 174964761 174964654 1.640000e-37 169
34 TraesCS6D01G087600 chr7D 93.750 112 5 2 576 686 220228859 220228749 5.900000e-37 167
35 TraesCS6D01G087600 chr2B 95.000 100 5 0 6395 6494 297439029 297438930 3.550000e-34 158
36 TraesCS6D01G087600 chr4B 96.774 93 3 0 6393 6485 599830397 599830305 1.280000e-33 156
37 TraesCS6D01G087600 chr1B 94.949 99 4 1 6400 6498 97376181 97376084 4.590000e-33 154
38 TraesCS6D01G087600 chr4D 92.308 104 8 0 6400 6503 481440702 481440599 2.140000e-31 148


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 TraesCS6D01G087600 chr6D 52818942 52828439 9497 True 17540.00 17540 100.0000 1 9498 1 chr6D.!!$R1 9497
1 TraesCS6D01G087600 chr6A 63767783 63776528 8745 True 2892.40 6215 97.4124 697 9498 5 chr6A.!!$R1 8801
2 TraesCS6D01G087600 chr6B 119977277 119986336 9059 True 3594.25 5273 96.3610 673 9498 4 chr6B.!!$R2 8825
3 TraesCS6D01G087600 chr2D 275177329 275177902 573 False 1018.00 1018 98.6110 1 576 1 chr2D.!!$F2 575
4 TraesCS6D01G087600 chr3D 511683789 511684361 572 True 1005.00 1005 98.2640 1 576 1 chr3D.!!$R1 575
5 TraesCS6D01G087600 chr3D 442776804 442777366 562 False 924.00 924 96.0070 1 576 1 chr3D.!!$F3 575
6 TraesCS6D01G087600 chr5D 169968826 169969388 562 False 819.00 819 92.7460 1 576 1 chr5D.!!$F1 575
7 TraesCS6D01G087600 chr2A 719698166 719698754 588 False 776.00 776 90.8780 1 576 1 chr2A.!!$F1 575
8 TraesCS6D01G087600 chr4A 43267808 43268393 585 False 763.00 763 90.5080 1 576 1 chr4A.!!$F1 575
9 TraesCS6D01G087600 chr4A 618263678 618264226 548 False 680.00 680 88.7930 1 577 1 chr4A.!!$F2 576
10 TraesCS6D01G087600 chr1A 568651456 568652041 585 False 758.00 758 90.3390 1 576 1 chr1A.!!$F1 575
11 TraesCS6D01G087600 chr5A 664544983 664545557 574 True 693.00 693 88.6630 1 577 1 chr5A.!!$R1 576
12 TraesCS6D01G087600 chr3B 10015346 10015896 550 True 603.00 603 86.6210 12 581 1 chr3B.!!$R1 569
13 TraesCS6D01G087600 chr5B 393943199 393943756 557 False 560.00 560 85.0590 1 576 1 chr5B.!!$F1 575


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
590 633 0.105224 CAGTGGGTACGTGGACAACA 59.895 55.000 0.00 0.00 0.00 3.33 F
591 634 0.105408 AGTGGGTACGTGGACAACAC 59.895 55.000 0.00 2.95 46.78 3.32 F
614 657 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96 F
634 677 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57 F
670 713 0.470766 AACTACTGCGTTCCCCAACA 59.529 50.000 0.00 0.00 32.14 3.33 F
671 714 0.470766 ACTACTGCGTTCCCCAACAA 59.529 50.000 0.00 0.00 32.14 2.83 F
1648 1734 0.756294 TTCAAGAACACGGAGAGCCA 59.244 50.000 0.00 0.00 0.00 4.75 F
3719 3818 0.393820 CAAACCAGCCACCATGCTTT 59.606 50.000 0.00 0.00 40.32 3.51 F
4309 4610 0.586802 GTTTGGTGCTTCTGTCGACC 59.413 55.000 14.12 0.00 0.00 4.79 F
4760 5061 1.019673 AAGTGCACTGCTCTGTTGTG 58.980 50.000 22.49 0.00 32.56 3.33 F
6416 6723 1.145325 AGATACTCCCTCCGTTCCGAT 59.855 52.381 0.00 0.00 0.00 4.18 F
8240 8725 0.179234 TCGCTTTGACACCTTGTCCA 59.821 50.000 3.91 0.00 46.40 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 1689 0.247736 GCGCTTCTTCTTCTCCCTCA 59.752 55.000 0.00 0.00 0.00 3.86 R
2063 2149 1.707632 CTTCCTCACTGCAGTCTTCG 58.292 55.000 18.64 5.91 0.00 3.79 R
2201 2287 6.012858 TGCATTGATTAAGGTACTATAGGGGG 60.013 42.308 4.43 0.00 38.49 5.40 R
2410 2496 7.176515 TGTGCATACAGTTTATCACCTTTTGAT 59.823 33.333 0.00 0.00 39.15 2.57 R
2970 3058 2.124570 CGGGGCAGTGAATCCCTG 60.125 66.667 12.72 6.85 42.25 4.45 R
2987 3075 5.383130 GGTTTTTCGCTACTCATGTTCTTC 58.617 41.667 0.00 0.00 0.00 2.87 R
3834 3933 0.398696 TGCAGTACGGGTTGGATTGT 59.601 50.000 0.00 0.00 0.00 2.71 R
4671 4972 2.276201 TGAACACAAGGAACACACTCG 58.724 47.619 0.00 0.00 0.00 4.18 R
6459 6766 2.165845 CCCTCCGTTCTGATTTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18 R
6460 6767 2.426024 TCCCTCCGTTCTGATTTACTCG 59.574 50.000 0.00 0.00 0.00 4.18 R
8330 8815 1.819288 CCACTCGGCAGACTTCTTAGA 59.181 52.381 0.00 0.00 0.00 2.10 R
9225 9713 2.109126 GCCAGCAGGTAAGAAGGCG 61.109 63.158 0.00 0.00 37.19 5.52 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
105 107 2.300956 AGTTCAGAGCAGAGGAGTGA 57.699 50.000 0.00 0.00 0.00 3.41
446 479 2.072487 GGCCCATCAGACCAGGCTA 61.072 63.158 0.00 0.00 45.07 3.93
577 620 3.775654 GAGAGGTCCGCCAGTGGG 61.776 72.222 12.15 0.59 37.19 4.61
581 624 4.446413 GGTCCGCCAGTGGGTACG 62.446 72.222 12.15 5.97 36.17 3.67
582 625 3.688159 GTCCGCCAGTGGGTACGT 61.688 66.667 12.15 0.00 36.17 3.57
583 626 3.687102 TCCGCCAGTGGGTACGTG 61.687 66.667 12.15 1.06 36.17 4.49
584 627 4.752879 CCGCCAGTGGGTACGTGG 62.753 72.222 12.15 0.00 36.17 4.94
585 628 3.687102 CGCCAGTGGGTACGTGGA 61.687 66.667 12.15 0.00 36.17 4.02
586 629 2.047560 GCCAGTGGGTACGTGGAC 60.048 66.667 12.15 0.00 36.17 4.02
587 630 2.874664 GCCAGTGGGTACGTGGACA 61.875 63.158 12.15 0.00 36.17 4.02
588 631 1.749665 CCAGTGGGTACGTGGACAA 59.250 57.895 0.00 0.00 32.60 3.18
589 632 0.601841 CCAGTGGGTACGTGGACAAC 60.602 60.000 0.00 0.00 32.60 3.32
590 633 0.105224 CAGTGGGTACGTGGACAACA 59.895 55.000 0.00 0.00 0.00 3.33
591 634 0.105408 AGTGGGTACGTGGACAACAC 59.895 55.000 0.00 2.95 46.78 3.32
599 642 2.453242 GTGGACAACACTCTCCCCT 58.547 57.895 0.00 0.00 46.72 4.79
600 643 0.321996 GTGGACAACACTCTCCCCTC 59.678 60.000 0.00 0.00 46.72 4.30
601 644 0.191064 TGGACAACACTCTCCCCTCT 59.809 55.000 0.00 0.00 0.00 3.69
602 645 0.899019 GGACAACACTCTCCCCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
603 646 0.528470 GACAACACTCTCCCCTCTCG 59.472 60.000 0.00 0.00 0.00 4.04
604 647 0.178958 ACAACACTCTCCCCTCTCGT 60.179 55.000 0.00 0.00 0.00 4.18
605 648 0.969894 CAACACTCTCCCCTCTCGTT 59.030 55.000 0.00 0.00 0.00 3.85
606 649 0.969894 AACACTCTCCCCTCTCGTTG 59.030 55.000 0.00 0.00 0.00 4.10
607 650 1.216710 CACTCTCCCCTCTCGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
608 651 1.077625 ACTCTCCCCTCTCGTTGCT 59.922 57.895 0.00 0.00 0.00 3.91
609 652 0.331954 ACTCTCCCCTCTCGTTGCTA 59.668 55.000 0.00 0.00 0.00 3.49
610 653 1.063567 ACTCTCCCCTCTCGTTGCTAT 60.064 52.381 0.00 0.00 0.00 2.97
611 654 1.339610 CTCTCCCCTCTCGTTGCTATG 59.660 57.143 0.00 0.00 0.00 2.23
612 655 0.249657 CTCCCCTCTCGTTGCTATGC 60.250 60.000 0.00 0.00 0.00 3.14
613 656 0.975556 TCCCCTCTCGTTGCTATGCA 60.976 55.000 0.00 0.00 36.47 3.96
614 657 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
615 658 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
616 659 1.202568 CCCTCTCGTTGCTATGCATCA 60.203 52.381 0.19 0.00 38.76 3.07
617 660 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
618 661 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
619 662 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
620 663 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
621 664 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
622 665 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
623 666 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
624 667 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
625 668 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
626 669 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
627 670 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
628 671 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
629 672 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
630 673 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
631 674 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
632 675 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
633 676 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
634 677 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
646 689 2.325509 GCGTGTGCGTAGGAATTTTT 57.674 45.000 0.00 0.00 40.81 1.94
666 709 4.834357 TTTTAAAACTACTGCGTTCCCC 57.166 40.909 0.00 0.00 0.00 4.81
667 710 3.488778 TTAAAACTACTGCGTTCCCCA 57.511 42.857 0.00 0.00 0.00 4.96
668 711 2.351706 AAAACTACTGCGTTCCCCAA 57.648 45.000 0.00 0.00 0.00 4.12
669 712 1.601166 AAACTACTGCGTTCCCCAAC 58.399 50.000 0.00 0.00 0.00 3.77
670 713 0.470766 AACTACTGCGTTCCCCAACA 59.529 50.000 0.00 0.00 32.14 3.33
671 714 0.470766 ACTACTGCGTTCCCCAACAA 59.529 50.000 0.00 0.00 32.14 2.83
679 722 4.310769 TGCGTTCCCCAACAATTTTTATG 58.689 39.130 0.00 0.00 32.14 1.90
682 725 5.107259 GCGTTCCCCAACAATTTTTATGTTC 60.107 40.000 0.00 0.00 38.90 3.18
691 734 9.757227 CCAACAATTTTTATGTTCTTTGAGGTA 57.243 29.630 0.00 0.00 38.90 3.08
1263 1316 1.304547 CCCACTCACTCGTCTCCCT 60.305 63.158 0.00 0.00 0.00 4.20
1277 1330 2.094234 GTCTCCCTTCTCTTGCTCAGAC 60.094 54.545 0.00 0.00 0.00 3.51
1322 1375 3.769844 GTGACTTCACCAAGGAGATCCTA 59.230 47.826 0.81 0.00 42.41 2.94
1523 1609 2.430382 AAGACGACGTGGACGCCATT 62.430 55.000 4.58 0.00 44.43 3.16
1603 1689 2.147387 ACTTGCGGAAGGAGGTGGT 61.147 57.895 21.31 0.00 40.95 4.16
1648 1734 0.756294 TTCAAGAACACGGAGAGCCA 59.244 50.000 0.00 0.00 0.00 4.75
2063 2149 1.716581 CGAGAACTTTGTCGCTCTGTC 59.283 52.381 0.00 0.00 37.16 3.51
2120 2206 3.260380 CAGGTAATGGCCCAAAATCACAA 59.740 43.478 0.00 0.00 0.00 3.33
2160 2246 7.379059 TGGGTATTCATCATAATGAGACAGT 57.621 36.000 0.00 0.00 42.72 3.55
2764 2850 5.239525 ACTGTTTGCCTAGTGTTCTTCAATC 59.760 40.000 0.00 0.00 0.00 2.67
2987 3075 1.987807 ATCAGGGATTCACTGCCCCG 61.988 60.000 11.24 0.00 45.89 5.73
3124 3212 1.817357 CAGAAGTGCAGAGCATTGGA 58.183 50.000 0.00 0.00 41.91 3.53
3588 3686 4.189639 AGAGAAGTTTAAGGTAGCACCG 57.810 45.455 0.00 0.00 44.90 4.94
3719 3818 0.393820 CAAACCAGCCACCATGCTTT 59.606 50.000 0.00 0.00 40.32 3.51
3834 3933 3.197766 AGTCGATTTGTATGGCCAGAGAA 59.802 43.478 13.05 9.18 0.00 2.87
3959 4058 1.746615 GCATCATGTGGCCGTCTGT 60.747 57.895 0.00 0.00 0.00 3.41
4097 4398 7.010183 CGGATGACTTTACATTAAGATTCACGT 59.990 37.037 0.00 0.00 0.00 4.49
4098 4399 9.309516 GGATGACTTTACATTAAGATTCACGTA 57.690 33.333 0.00 0.00 0.00 3.57
4156 4457 6.093495 CACCATCGACTTAGGCATAAGAAAAA 59.907 38.462 23.93 7.31 40.86 1.94
4174 4475 8.650143 AAGAAAAATCTTGGCCAACTTAGATA 57.350 30.769 16.05 0.00 0.00 1.98
4309 4610 0.586802 GTTTGGTGCTTCTGTCGACC 59.413 55.000 14.12 0.00 0.00 4.79
4368 4669 4.201802 TGTTGTATAACTGATGCATGCACG 60.202 41.667 25.37 16.67 37.68 5.34
4626 4927 4.972875 GCCTGTGAGCAAGGCTAT 57.027 55.556 7.20 0.00 44.72 2.97
4671 4972 2.620251 TATGTAGGTGTGGCATGCTC 57.380 50.000 18.92 11.73 0.00 4.26
4760 5061 1.019673 AAGTGCACTGCTCTGTTGTG 58.980 50.000 22.49 0.00 32.56 3.33
4871 5172 2.492088 GTTCCTCCCTTACCATTGTTGC 59.508 50.000 0.00 0.00 0.00 4.17
4978 5279 4.701651 TGTTCAACCATGGATGATCAACTC 59.298 41.667 25.38 13.48 0.00 3.01
5002 5303 3.150767 GGTAGTCTGACTGAGTGTCTGT 58.849 50.000 20.19 0.00 45.54 3.41
5149 5450 6.456181 CGAAACTTTCAGGAGCATGATAAGTC 60.456 42.308 0.00 0.00 33.43 3.01
5389 5690 3.504863 CCATGCCTTCATTTTGTTCTCG 58.495 45.455 0.00 0.00 0.00 4.04
6079 6380 4.571984 CGATAAATTCCTCATCACACAGCA 59.428 41.667 0.00 0.00 0.00 4.41
6150 6451 7.980662 TGTTACAAATCCATTGCTATTCATTGG 59.019 33.333 0.00 0.00 43.95 3.16
6217 6518 2.961526 TGAACTAAGGCGAGATGGAC 57.038 50.000 0.00 0.00 0.00 4.02
6237 6538 2.256174 CTTCAAATGACCAAGCATGCG 58.744 47.619 13.01 0.00 0.00 4.73
6368 6675 5.823045 AGTCTTTCACGTTCCAATTCTTCTT 59.177 36.000 0.00 0.00 0.00 2.52
6411 6718 6.011122 TCTTAGTTAGATACTCCCTCCGTT 57.989 41.667 0.00 0.00 38.33 4.44
6414 6721 2.267174 TAGATACTCCCTCCGTTCCG 57.733 55.000 0.00 0.00 0.00 4.30
6416 6723 1.145325 AGATACTCCCTCCGTTCCGAT 59.855 52.381 0.00 0.00 0.00 4.18
6417 6724 1.962100 GATACTCCCTCCGTTCCGATT 59.038 52.381 0.00 0.00 0.00 3.34
6422 6729 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
6427 6734 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
6428 6735 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
6430 6737 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
6431 6738 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
6432 6739 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
6434 6741 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
6435 6742 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
6436 6743 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
6438 6745 5.640218 TTTACTCGTCGTGGTTTTAGTTG 57.360 39.130 0.00 0.00 0.00 3.16
6442 6749 4.812626 ACTCGTCGTGGTTTTAGTTGAAAT 59.187 37.500 0.00 0.00 0.00 2.17
6444 6751 6.121613 TCGTCGTGGTTTTAGTTGAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
6447 6754 6.469595 CGTCGTGGTTTTAGTTGAAATTTGAA 59.530 34.615 0.00 0.00 0.00 2.69
6448 6755 7.512426 CGTCGTGGTTTTAGTTGAAATTTGAAC 60.512 37.037 12.02 12.02 0.00 3.18
6451 6758 9.291664 CGTGGTTTTAGTTGAAATTTGAACTAA 57.708 29.630 28.23 28.23 42.36 2.24
6458 6765 7.749539 AGTTGAAATTTGAACTAAAACCACG 57.250 32.000 19.68 0.00 32.83 4.94
6459 6766 7.540299 AGTTGAAATTTGAACTAAAACCACGA 58.460 30.769 19.68 0.00 32.83 4.35
6460 6767 7.486870 AGTTGAAATTTGAACTAAAACCACGAC 59.513 33.333 19.68 0.00 32.83 4.34
6461 6768 5.966503 TGAAATTTGAACTAAAACCACGACG 59.033 36.000 0.00 0.00 0.00 5.12
6462 6769 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
6463 6770 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
6466 6773 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
6467 6774 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
6470 6777 5.531634 ACTAAAACCACGACGAGTAAATCA 58.468 37.500 0.00 0.00 0.00 2.57
6471 6778 4.985044 AAAACCACGACGAGTAAATCAG 57.015 40.909 0.00 0.00 0.00 2.90
6472 6779 3.928727 AACCACGACGAGTAAATCAGA 57.071 42.857 0.00 0.00 0.00 3.27
6622 6961 4.246458 CCTAAGTGCCTCAGTGAAGTAAC 58.754 47.826 0.00 0.00 0.00 2.50
6754 7093 4.884164 AGCCCTGATTGTAAGTAAATCTGC 59.116 41.667 0.00 0.00 35.48 4.26
6760 7099 6.163476 TGATTGTAAGTAAATCTGCGACACT 58.837 36.000 0.00 0.00 35.48 3.55
6914 7253 2.689658 TCAACTTCTGGAGGAGGTGAA 58.310 47.619 0.00 0.00 34.40 3.18
7302 7642 6.650390 GGAATTGCACACACCATCTTTAATTT 59.350 34.615 0.00 0.00 0.00 1.82
7414 7754 7.573283 GCAACTTCTCTATCTTGTTTAACCCAC 60.573 40.741 0.00 0.00 0.00 4.61
7434 7774 6.961721 ACCCACTACACTTTTACTAGGGATTA 59.038 38.462 0.00 0.00 37.23 1.75
7885 8369 6.169094 ACTTGTATGAACTGATCTGAAGGTG 58.831 40.000 6.60 0.00 0.00 4.00
8240 8725 0.179234 TCGCTTTGACACCTTGTCCA 59.821 50.000 3.91 0.00 46.40 4.02
8330 8815 1.305297 TCTGCCCAGAGGTCGACAT 60.305 57.895 18.91 11.04 34.57 3.06
8368 8853 0.238553 GGTCGGCAGCAAAGAAGTTC 59.761 55.000 0.00 0.00 0.00 3.01
8506 8991 4.423625 ACAAGAGGTATAAGGGATGCAC 57.576 45.455 0.00 0.00 0.00 4.57
8606 9092 8.251750 TCATTCTTTACTGATAAAACCGTCTG 57.748 34.615 0.00 0.00 29.82 3.51
8714 9202 1.135774 GGTTGAAAGGCGAAATCCGTC 60.136 52.381 0.00 0.00 44.58 4.79
8761 9249 1.494721 ACTGGCCACCCACATAATAGG 59.505 52.381 0.00 0.00 35.79 2.57
8783 9271 2.561733 TTTCTGAGCACGTCCTATCG 57.438 50.000 0.00 0.00 0.00 2.92
8902 9390 0.387622 CACTGCCACATTTTGAGCCG 60.388 55.000 0.00 0.00 0.00 5.52
8981 9469 1.091537 AACGTGTGACCACAACAAGG 58.908 50.000 4.21 0.00 43.77 3.61
9148 9636 2.665649 ACCGATATCAAGCAACGACA 57.334 45.000 3.12 0.00 0.00 4.35
9151 9639 2.282555 CCGATATCAAGCAACGACAGTG 59.717 50.000 3.12 0.00 0.00 3.66
9157 9645 0.593128 AAGCAACGACAGTGCATTCC 59.407 50.000 0.00 0.00 0.00 3.01
9193 9681 9.423061 CATAAGGTTTAAAAGCATAAAAGCTGT 57.577 29.630 0.00 0.00 45.89 4.40
9194 9682 7.713764 AAGGTTTAAAAGCATAAAAGCTGTG 57.286 32.000 0.00 0.00 45.89 3.66
9201 9689 1.477700 GCATAAAAGCTGTGGGCATCA 59.522 47.619 0.00 0.00 44.79 3.07
9225 9713 7.706179 TCACAATTTGAACTCTGGTTTTCATTC 59.294 33.333 2.79 0.00 35.58 2.67
9244 9732 1.750780 GCCTTCTTACCTGCTGGCC 60.751 63.158 9.95 0.00 36.63 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 107 2.766828 CCTAGGGTCCGAAACTCTGAAT 59.233 50.000 0.00 0.00 39.75 2.57
446 479 3.264866 GACTCGTTCGACCGCACCT 62.265 63.158 0.00 0.00 0.00 4.00
581 624 0.321996 GAGGGGAGAGTGTTGTCCAC 59.678 60.000 0.00 0.00 40.47 4.02
582 625 0.191064 AGAGGGGAGAGTGTTGTCCA 59.809 55.000 0.00 0.00 38.50 4.02
583 626 0.899019 GAGAGGGGAGAGTGTTGTCC 59.101 60.000 0.00 0.00 36.03 4.02
584 627 0.528470 CGAGAGGGGAGAGTGTTGTC 59.472 60.000 0.00 0.00 0.00 3.18
585 628 0.178958 ACGAGAGGGGAGAGTGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
586 629 0.969894 AACGAGAGGGGAGAGTGTTG 59.030 55.000 0.00 0.00 0.00 3.33
587 630 0.969894 CAACGAGAGGGGAGAGTGTT 59.030 55.000 0.00 0.00 0.00 3.32
588 631 1.536943 GCAACGAGAGGGGAGAGTGT 61.537 60.000 0.00 0.00 0.00 3.55
589 632 1.216710 GCAACGAGAGGGGAGAGTG 59.783 63.158 0.00 0.00 0.00 3.51
590 633 0.331954 TAGCAACGAGAGGGGAGAGT 59.668 55.000 0.00 0.00 0.00 3.24
591 634 1.339610 CATAGCAACGAGAGGGGAGAG 59.660 57.143 0.00 0.00 0.00 3.20
592 635 1.403814 CATAGCAACGAGAGGGGAGA 58.596 55.000 0.00 0.00 0.00 3.71
593 636 0.249657 GCATAGCAACGAGAGGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
594 637 0.975556 TGCATAGCAACGAGAGGGGA 60.976 55.000 0.00 0.00 34.76 4.81
595 638 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
596 639 1.202568 TGATGCATAGCAACGAGAGGG 60.203 52.381 0.00 0.00 43.62 4.30
597 640 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
598 641 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
599 642 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
600 643 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
601 644 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
602 645 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
603 646 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
604 647 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
605 648 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
606 649 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
607 650 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
608 651 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
609 652 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
610 653 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
611 654 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
612 655 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
613 656 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
614 657 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
615 658 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
616 659 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
617 660 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
618 661 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
619 662 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
620 663 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
621 664 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
622 665 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
623 666 0.037697 ATTCCTACGCACACGCAAGA 60.038 50.000 0.00 0.00 45.53 3.02
624 667 0.796312 AATTCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
625 668 1.231221 AAATTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
626 669 1.231221 AAAATTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
627 670 2.325509 AAAAATTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
644 687 5.185668 GGGGAACGCAGTAGTTTTAAAAA 57.814 39.130 1.31 0.00 45.00 1.94
645 688 4.834357 GGGGAACGCAGTAGTTTTAAAA 57.166 40.909 0.00 0.00 45.00 1.52
658 701 4.311606 ACATAAAAATTGTTGGGGAACGC 58.688 39.130 0.00 0.00 43.69 4.84
659 702 6.220201 AGAACATAAAAATTGTTGGGGAACG 58.780 36.000 0.00 0.00 37.43 3.95
660 703 8.341903 CAAAGAACATAAAAATTGTTGGGGAAC 58.658 33.333 0.00 0.00 37.43 3.62
661 704 8.267894 TCAAAGAACATAAAAATTGTTGGGGAA 58.732 29.630 0.00 0.00 37.43 3.97
662 705 7.796054 TCAAAGAACATAAAAATTGTTGGGGA 58.204 30.769 0.00 0.00 37.43 4.81
663 706 7.173047 CCTCAAAGAACATAAAAATTGTTGGGG 59.827 37.037 0.00 0.00 37.43 4.96
664 707 7.714813 ACCTCAAAGAACATAAAAATTGTTGGG 59.285 33.333 0.00 0.00 37.43 4.12
665 708 8.661352 ACCTCAAAGAACATAAAAATTGTTGG 57.339 30.769 0.00 0.00 37.43 3.77
679 722 9.052759 TCAGAAGTACAAAATACCTCAAAGAAC 57.947 33.333 0.00 0.00 0.00 3.01
715 758 8.727149 TCATCAAAAAGGACCTGGATCTATTAT 58.273 33.333 0.00 0.00 0.00 1.28
716 759 8.101309 TCATCAAAAAGGACCTGGATCTATTA 57.899 34.615 0.00 0.00 0.00 0.98
718 761 6.581388 TCATCAAAAAGGACCTGGATCTAT 57.419 37.500 0.00 0.00 0.00 1.98
719 762 6.387192 TTCATCAAAAAGGACCTGGATCTA 57.613 37.500 0.00 0.00 0.00 1.98
803 846 1.748493 CCCGAGTCCTCTCAAGAGAAG 59.252 57.143 8.62 0.00 44.74 2.85
804 847 1.840737 CCCGAGTCCTCTCAAGAGAA 58.159 55.000 8.62 0.00 44.74 2.87
1223 1276 2.436646 AAATGGCGAGCGAGGGTG 60.437 61.111 0.00 0.00 0.00 4.61
1263 1316 0.541998 TCCCCGTCTGAGCAAGAGAA 60.542 55.000 0.00 0.00 34.84 2.87
1277 1330 2.038975 TTGTCCTCCTCCTCCCCG 59.961 66.667 0.00 0.00 0.00 5.73
1322 1375 7.882791 TGCATAAGAATACCGTTCAATATGGAT 59.117 33.333 11.83 0.00 36.33 3.41
1523 1609 4.411869 TCCATATCCAGTATCTTGTTGCCA 59.588 41.667 0.00 0.00 0.00 4.92
1541 1627 1.004277 GACCCTGCAAACCACTCCATA 59.996 52.381 0.00 0.00 0.00 2.74
1577 1663 0.813184 CCTTCCGCAAGTGCATCATT 59.187 50.000 3.87 0.00 42.21 2.57
1603 1689 0.247736 GCGCTTCTTCTTCTCCCTCA 59.752 55.000 0.00 0.00 0.00 3.86
1648 1734 2.650116 ATCAGCCTCGTGAAGCGGT 61.650 57.895 0.00 0.00 41.72 5.68
2063 2149 1.707632 CTTCCTCACTGCAGTCTTCG 58.292 55.000 18.64 5.91 0.00 3.79
2120 2206 8.893563 TGAATACCCAAATAGAAGGTTTTGAT 57.106 30.769 0.00 0.00 35.34 2.57
2160 2246 7.151999 ACAAACTGTGTAAGATGAAACAACA 57.848 32.000 0.00 0.00 39.29 3.33
2201 2287 6.012858 TGCATTGATTAAGGTACTATAGGGGG 60.013 42.308 4.43 0.00 38.49 5.40
2410 2496 7.176515 TGTGCATACAGTTTATCACCTTTTGAT 59.823 33.333 0.00 0.00 39.15 2.57
2970 3058 2.124570 CGGGGCAGTGAATCCCTG 60.125 66.667 12.72 6.85 42.25 4.45
2987 3075 5.383130 GGTTTTTCGCTACTCATGTTCTTC 58.617 41.667 0.00 0.00 0.00 2.87
3059 3147 3.354467 AGTACAGCCTACTCCACTACAC 58.646 50.000 0.00 0.00 0.00 2.90
3221 3313 0.829990 TGGTTCTGATAGCGATGCCA 59.170 50.000 0.00 0.00 0.00 4.92
3588 3686 2.679837 CCTGTCATATGCACCAACAGAC 59.320 50.000 18.36 8.57 39.72 3.51
3719 3818 7.015292 AGAGCGGATTATTTAGACTATGTGGAA 59.985 37.037 0.00 0.00 0.00 3.53
3834 3933 0.398696 TGCAGTACGGGTTGGATTGT 59.601 50.000 0.00 0.00 0.00 2.71
4012 4111 8.522178 AATCACAAACGACTTTTAACAAAACA 57.478 26.923 0.00 0.00 0.00 2.83
4098 4399 9.136323 GTGTGATAAAATATTTTCCCTCATCCT 57.864 33.333 16.56 0.00 0.00 3.24
4368 4669 4.243007 AGTAAAGTGCCAATGTTGCTTC 57.757 40.909 0.00 0.00 0.00 3.86
4429 4730 5.880332 TGCTCGGCATTAAGACTAAAATCTT 59.120 36.000 0.00 0.00 36.85 2.40
4448 4749 7.964559 TCAAGAATCACAAAATCTAAATGCTCG 59.035 33.333 0.00 0.00 0.00 5.03
4626 4927 2.299013 ACGACTTACCATGTGAAGCTCA 59.701 45.455 0.00 0.00 0.00 4.26
4671 4972 2.276201 TGAACACAAGGAACACACTCG 58.724 47.619 0.00 0.00 0.00 4.18
4844 5145 5.253096 ACAATGGTAAGGGAGGAACAGTATT 59.747 40.000 0.00 0.00 0.00 1.89
4948 5249 5.078949 TCATCCATGGTTGAACAATGTTCT 58.921 37.500 24.30 3.52 0.00 3.01
4978 5279 4.167554 GACACTCAGTCAGACTACCAAG 57.832 50.000 1.67 1.68 46.77 3.61
5389 5690 4.023707 GGTCAATGTCAGCAATAGGTATGC 60.024 45.833 0.00 0.00 44.15 3.14
5451 5752 6.071984 TGGCAAACAGGAATTTTTACCTCTA 58.928 36.000 0.00 0.00 33.91 2.43
6079 6380 2.564947 GGTCATAGAGCAGGATCCGAAT 59.435 50.000 5.98 0.00 0.00 3.34
6217 6518 2.256174 CGCATGCTTGGTCATTTGAAG 58.744 47.619 17.13 0.00 0.00 3.02
6237 6538 9.916397 GAATATGCGTTAATTAGTGCCATATAC 57.084 33.333 8.11 0.00 0.00 1.47
6414 6721 6.144402 TCAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
6416 6723 5.347342 TCAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
6417 6724 4.930963 TCAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
6422 6729 5.966503 TCAAATTTCAACTAAAACCACGACG 59.033 36.000 0.00 0.00 0.00 5.12
6432 6739 9.291664 CGTGGTTTTAGTTCAAATTTCAACTAA 57.708 29.630 19.70 19.70 41.31 2.24
6434 6741 7.486870 GTCGTGGTTTTAGTTCAAATTTCAACT 59.513 33.333 12.32 12.32 36.75 3.16
6435 6742 7.512426 CGTCGTGGTTTTAGTTCAAATTTCAAC 60.512 37.037 0.00 0.00 0.00 3.18
6436 6743 6.469595 CGTCGTGGTTTTAGTTCAAATTTCAA 59.530 34.615 0.00 0.00 0.00 2.69
6438 6745 6.193761 TCGTCGTGGTTTTAGTTCAAATTTC 58.806 36.000 0.00 0.00 0.00 2.17
6442 6749 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
6444 6751 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
6447 6754 5.531634 TGATTTACTCGTCGTGGTTTTAGT 58.468 37.500 0.00 0.00 0.00 2.24
6448 6755 5.860182 TCTGATTTACTCGTCGTGGTTTTAG 59.140 40.000 0.00 0.00 0.00 1.85
6451 6758 4.247267 TCTGATTTACTCGTCGTGGTTT 57.753 40.909 0.00 0.00 0.00 3.27
6452 6759 3.928727 TCTGATTTACTCGTCGTGGTT 57.071 42.857 0.00 0.00 0.00 3.67
6453 6760 3.572584 GTTCTGATTTACTCGTCGTGGT 58.427 45.455 0.00 0.00 0.00 4.16
6454 6761 2.592897 CGTTCTGATTTACTCGTCGTGG 59.407 50.000 0.00 0.00 0.00 4.94
6455 6762 2.592897 CCGTTCTGATTTACTCGTCGTG 59.407 50.000 0.00 0.00 0.00 4.35
6457 6764 3.099362 CTCCGTTCTGATTTACTCGTCG 58.901 50.000 0.00 0.00 0.00 5.12
6458 6765 3.436496 CCTCCGTTCTGATTTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
6459 6766 2.165845 CCCTCCGTTCTGATTTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
6460 6767 2.426024 TCCCTCCGTTCTGATTTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
6461 6768 3.447944 ACTCCCTCCGTTCTGATTTACTC 59.552 47.826 0.00 0.00 0.00 2.59
6462 6769 3.442076 ACTCCCTCCGTTCTGATTTACT 58.558 45.455 0.00 0.00 0.00 2.24
6463 6770 3.889520 ACTCCCTCCGTTCTGATTTAC 57.110 47.619 0.00 0.00 0.00 2.01
6466 6773 5.148502 ACATATACTCCCTCCGTTCTGATT 58.851 41.667 0.00 0.00 0.00 2.57
6467 6774 4.742012 ACATATACTCCCTCCGTTCTGAT 58.258 43.478 0.00 0.00 0.00 2.90
6470 6777 6.014499 CCATTAACATATACTCCCTCCGTTCT 60.014 42.308 0.00 0.00 0.00 3.01
6471 6778 6.164176 CCATTAACATATACTCCCTCCGTTC 58.836 44.000 0.00 0.00 0.00 3.95
6472 6779 5.605488 ACCATTAACATATACTCCCTCCGTT 59.395 40.000 0.00 0.00 0.00 4.44
6754 7093 2.943033 AGTTTTGACAGGGAAAGTGTCG 59.057 45.455 0.00 0.00 46.21 4.35
6760 7099 5.445069 TCATCTCAAGTTTTGACAGGGAAA 58.555 37.500 0.00 0.00 35.46 3.13
6914 7253 2.697147 AAACCACATGCCTGGCTCGT 62.697 55.000 21.03 13.70 34.20 4.18
6980 7319 4.281941 AGGAGCATCAATTAGCATACTCGA 59.718 41.667 0.00 0.00 36.25 4.04
7395 7735 7.612677 AGTGTAGTGGGTTAAACAAGATAGAG 58.387 38.462 0.00 0.00 0.00 2.43
7441 7781 9.968743 CTCAACCAAATAAAACGAATCTACTAC 57.031 33.333 0.00 0.00 0.00 2.73
7885 8369 4.405358 TCCATTTCCCATATTTGGCAGAAC 59.595 41.667 0.00 0.00 42.15 3.01
8240 8725 5.630415 TGGATATCCCACGAGAAGAAATT 57.370 39.130 19.34 0.00 40.82 1.82
8272 8757 4.985413 ACATCCTGCATACAAAAATGTCG 58.015 39.130 0.00 0.00 0.00 4.35
8330 8815 1.819288 CCACTCGGCAGACTTCTTAGA 59.181 52.381 0.00 0.00 0.00 2.10
8368 8853 7.148069 GGATCCTCCTTTGGTATTGTTTTGTAG 60.148 40.741 3.84 0.00 32.53 2.74
8506 8991 2.224281 TGTAACAGAAGTGGCAGAGTGG 60.224 50.000 0.00 0.00 0.00 4.00
8606 9092 5.784750 GCCAAACAATTAGAAGAAATGGC 57.215 39.130 0.00 0.00 43.31 4.40
8714 9202 4.935702 TGTCTGTTTGGCTTCAATTTGAG 58.064 39.130 0.00 0.00 0.00 3.02
8761 9249 2.080286 TAGGACGTGCTCAGAAAAGC 57.920 50.000 14.74 0.00 42.82 3.51
8902 9390 1.266989 GGTAAGTGGTCACAGCAAAGC 59.733 52.381 3.82 0.00 0.00 3.51
8981 9469 3.859411 TTGTTTCACTGTGAACAACCC 57.141 42.857 21.95 8.97 35.89 4.11
9151 9639 4.755123 ACCTTATGTTATGCGTAGGAATGC 59.245 41.667 0.00 0.00 38.18 3.56
9157 9645 8.178964 TGCTTTTAAACCTTATGTTATGCGTAG 58.821 33.333 0.00 0.00 35.67 3.51
9193 9681 3.256383 CAGAGTTCAAATTGTGATGCCCA 59.744 43.478 0.00 0.00 35.70 5.36
9194 9682 3.367703 CCAGAGTTCAAATTGTGATGCCC 60.368 47.826 0.00 0.00 35.70 5.36
9201 9689 6.697019 CGAATGAAAACCAGAGTTCAAATTGT 59.303 34.615 0.00 0.00 37.31 2.71
9203 9691 5.691754 GCGAATGAAAACCAGAGTTCAAATT 59.308 36.000 0.00 0.00 37.31 1.82
9204 9692 5.222631 GCGAATGAAAACCAGAGTTCAAAT 58.777 37.500 0.00 0.00 37.31 2.32
9225 9713 2.109126 GCCAGCAGGTAAGAAGGCG 61.109 63.158 0.00 0.00 37.19 5.52
9368 9858 2.427095 GCAAGGTTTGTGTTCTTCCACT 59.573 45.455 0.00 0.00 36.30 4.00
9369 9859 2.165437 TGCAAGGTTTGTGTTCTTCCAC 59.835 45.455 0.00 0.00 35.86 4.02
9370 9860 2.451490 TGCAAGGTTTGTGTTCTTCCA 58.549 42.857 0.00 0.00 0.00 3.53



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

AutoCloner maintained by Alex Coulton.