Multiple sequence alignment - TraesCS5A01G142700

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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 TraesCS5A01G142700 chr5A 100.000 2626 0 0 1 2626 316352515 316349890 0.000000e+00 4850.0
1 TraesCS5A01G142700 chr5D 92.786 1913 59 26 740 2626 238382623 238384482 0.000000e+00 2695.0
2 TraesCS5A01G142700 chr5D 89.855 621 61 2 1 621 238382038 238382656 0.000000e+00 797.0
3 TraesCS5A01G142700 chr5B 92.050 1912 79 26 740 2626 267114116 267112253 0.000000e+00 2621.0
4 TraesCS5A01G142700 chr5B 86.341 615 81 3 12 626 267114689 267114078 0.000000e+00 667.0
5 TraesCS5A01G142700 chr1B 100.000 143 0 0 615 757 625778272 625778130 5.570000e-67 265.0
6 TraesCS5A01G142700 chr1B 100.000 142 0 0 616 757 14629526 14629667 2.000000e-66 263.0
7 TraesCS5A01G142700 chr1B 100.000 142 0 0 616 757 24138310 24138169 2.000000e-66 263.0
8 TraesCS5A01G142700 chr1B 100.000 142 0 0 616 757 108939957 108939816 2.000000e-66 263.0
9 TraesCS5A01G142700 chr1B 100.000 142 0 0 616 757 550674955 550674814 2.000000e-66 263.0
10 TraesCS5A01G142700 chr1B 93.103 58 4 0 472 529 577211180 577211123 4.660000e-13 86.1
11 TraesCS5A01G142700 chr7A 99.315 146 0 1 613 757 18294460 18294605 2.000000e-66 263.0
12 TraesCS5A01G142700 chr6A 99.315 146 0 1 613 757 127189973 127190118 2.000000e-66 263.0
13 TraesCS5A01G142700 chr4B 100.000 142 0 0 616 757 376422916 376423057 2.000000e-66 263.0
14 TraesCS5A01G142700 chr2B 99.310 145 1 0 613 757 519190180 519190324 2.000000e-66 263.0
15 TraesCS5A01G142700 chr3D 84.810 79 11 1 112 189 413646104 413646182 7.790000e-11 78.7
16 TraesCS5A01G142700 chr7D 76.923 117 23 3 277 391 106223610 106223496 2.180000e-06 63.9
17 TraesCS5A01G142700 chr2A 100.000 28 0 0 365 392 756942831 756942804 5.000000e-03 52.8


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 TraesCS5A01G142700 chr5A 316349890 316352515 2625 True 4850 4850 100.0000 1 2626 1 chr5A.!!$R1 2625
1 TraesCS5A01G142700 chr5D 238382038 238384482 2444 False 1746 2695 91.3205 1 2626 2 chr5D.!!$F1 2625
2 TraesCS5A01G142700 chr5B 267112253 267114689 2436 True 1644 2621 89.1955 12 2626 2 chr5B.!!$R1 2614

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
843 844 0.034477 AAATTACCCAGGTGCTCCGG 60.034 55.0 0.0 0.0 39.05 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2340 0.104855 AAAGTGACAGCGCAGTGAGA 59.895 50.0 11.27 0.0 0.0 3.27 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
71 72 3.045601 ACTCCCTTGATCAACGACAAG 57.954 47.619 3.38 0.00 41.85 3.16
98 99 2.362889 GGGCATTGGTGAGGGTGG 60.363 66.667 0.00 0.00 0.00 4.61
109 110 2.772191 AGGGTGGGCGGCATGATA 60.772 61.111 12.47 0.00 0.00 2.15
172 173 1.681264 AGCACAACTTTGTAACCAGGC 59.319 47.619 0.00 0.00 39.91 4.85
189 190 4.653801 ACCAGGCCACAAAAATAGAAAACT 59.346 37.500 5.01 0.00 0.00 2.66
224 225 8.561738 AATTATTCAACGGAGTACAAGAACAT 57.438 30.769 0.00 0.00 45.00 2.71
228 229 7.789273 TTCAACGGAGTACAAGAACATAAAA 57.211 32.000 0.00 0.00 45.00 1.52
247 248 9.088987 ACATAAAAACATAGATCAACCCAAAGT 57.911 29.630 0.00 0.00 0.00 2.66
251 252 7.781324 AAACATAGATCAACCCAAAGTCATT 57.219 32.000 0.00 0.00 0.00 2.57
274 275 0.463204 CTGGCGATCTCTGTCACCAT 59.537 55.000 0.00 0.00 30.48 3.55
279 280 2.587522 CGATCTCTGTCACCATCCCTA 58.412 52.381 0.00 0.00 0.00 3.53
284 285 3.898123 TCTCTGTCACCATCCCTATAAGC 59.102 47.826 0.00 0.00 0.00 3.09
307 308 0.888619 ATGATGTGTCGTGACCTCGT 59.111 50.000 0.00 0.00 0.00 4.18
394 395 1.754555 CGGTCTAGCATACCCTCACCT 60.755 57.143 0.00 0.00 33.10 4.00
413 414 3.207778 CCTCTCTAGAATCCGTCGTCTT 58.792 50.000 0.00 0.00 0.00 3.01
423 424 1.140407 CCGTCGTCTTCATCTTCCGC 61.140 60.000 0.00 0.00 0.00 5.54
424 425 0.179161 CGTCGTCTTCATCTTCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
475 476 0.823356 TCTTGCCAAGCCCAACTGTC 60.823 55.000 0.00 0.00 0.00 3.51
507 508 0.601558 ACGACACTAGACAACGCCAT 59.398 50.000 0.00 0.00 0.00 4.40
509 510 1.402325 CGACACTAGACAACGCCATCA 60.402 52.381 0.00 0.00 0.00 3.07
514 515 3.308053 CACTAGACAACGCCATCATTCTG 59.692 47.826 0.00 0.00 0.00 3.02
543 544 7.064609 CGCGTCCATCATAGAATTTACCAATAT 59.935 37.037 0.00 0.00 0.00 1.28
617 618 2.032675 GCCAACCGGTTACGTAAACAAA 59.967 45.455 21.79 0.00 40.08 2.83
618 619 3.488216 GCCAACCGGTTACGTAAACAAAA 60.488 43.478 21.79 0.00 40.08 2.44
619 620 4.666237 CCAACCGGTTACGTAAACAAAAA 58.334 39.130 21.79 0.00 40.08 1.94
641 642 3.683365 AAAATGAAACTCCATGGGCAC 57.317 42.857 13.02 0.33 0.00 5.01
642 643 2.610438 AATGAAACTCCATGGGCACT 57.390 45.000 13.02 0.00 0.00 4.40
643 644 3.737559 AATGAAACTCCATGGGCACTA 57.262 42.857 13.02 0.00 0.00 2.74
644 645 2.787473 TGAAACTCCATGGGCACTAG 57.213 50.000 13.02 3.62 0.00 2.57
645 646 1.340017 TGAAACTCCATGGGCACTAGC 60.340 52.381 13.02 0.00 41.10 3.42
646 647 0.698238 AAACTCCATGGGCACTAGCA 59.302 50.000 13.02 0.00 44.61 3.49
648 649 1.153086 CTCCATGGGCACTAGCACC 60.153 63.158 13.02 0.00 46.13 5.01
649 650 2.124151 CCATGGGCACTAGCACCC 60.124 66.667 12.83 12.83 46.13 4.61
653 654 4.778143 GGGCACTAGCACCCACGG 62.778 72.222 14.48 0.00 46.22 4.94
654 655 4.016706 GGCACTAGCACCCACGGT 62.017 66.667 0.00 0.00 44.61 4.83
655 656 2.032071 GCACTAGCACCCACGGTT 59.968 61.111 0.00 0.00 41.58 4.44
656 657 1.599797 GCACTAGCACCCACGGTTT 60.600 57.895 0.00 0.00 41.58 3.27
657 658 1.170290 GCACTAGCACCCACGGTTTT 61.170 55.000 0.00 0.00 41.58 2.43
658 659 1.878948 GCACTAGCACCCACGGTTTTA 60.879 52.381 0.00 0.00 41.58 1.52
659 660 2.706890 CACTAGCACCCACGGTTTTAT 58.293 47.619 0.00 0.00 31.02 1.40
660 661 3.078837 CACTAGCACCCACGGTTTTATT 58.921 45.455 0.00 0.00 31.02 1.40
661 662 3.078837 ACTAGCACCCACGGTTTTATTG 58.921 45.455 0.00 0.00 31.02 1.90
662 663 2.279935 AGCACCCACGGTTTTATTGA 57.720 45.000 0.00 0.00 31.02 2.57
663 664 2.802719 AGCACCCACGGTTTTATTGAT 58.197 42.857 0.00 0.00 31.02 2.57
664 665 3.958018 AGCACCCACGGTTTTATTGATA 58.042 40.909 0.00 0.00 31.02 2.15
665 666 4.532834 AGCACCCACGGTTTTATTGATAT 58.467 39.130 0.00 0.00 31.02 1.63
666 667 5.686753 AGCACCCACGGTTTTATTGATATA 58.313 37.500 0.00 0.00 31.02 0.86
667 668 5.763204 AGCACCCACGGTTTTATTGATATAG 59.237 40.000 0.00 0.00 31.02 1.31
668 669 5.761234 GCACCCACGGTTTTATTGATATAGA 59.239 40.000 0.00 0.00 31.02 1.98
669 670 6.261381 GCACCCACGGTTTTATTGATATAGAA 59.739 38.462 0.00 0.00 31.02 2.10
670 671 7.519970 GCACCCACGGTTTTATTGATATAGAAG 60.520 40.741 0.00 0.00 31.02 2.85
671 672 7.713507 CACCCACGGTTTTATTGATATAGAAGA 59.286 37.037 0.00 0.00 31.02 2.87
672 673 8.269317 ACCCACGGTTTTATTGATATAGAAGAA 58.731 33.333 0.00 0.00 27.29 2.52
673 674 8.774586 CCCACGGTTTTATTGATATAGAAGAAG 58.225 37.037 0.00 0.00 0.00 2.85
674 675 8.283291 CCACGGTTTTATTGATATAGAAGAAGC 58.717 37.037 0.00 0.00 0.00 3.86
675 676 8.826710 CACGGTTTTATTGATATAGAAGAAGCA 58.173 33.333 0.00 0.00 0.00 3.91
676 677 9.561069 ACGGTTTTATTGATATAGAAGAAGCAT 57.439 29.630 0.00 0.00 0.00 3.79
681 682 9.950496 TTTATTGATATAGAAGAAGCATCCCTC 57.050 33.333 0.00 0.00 0.00 4.30
682 683 7.565190 ATTGATATAGAAGAAGCATCCCTCA 57.435 36.000 0.00 0.00 0.00 3.86
683 684 7.565190 TTGATATAGAAGAAGCATCCCTCAT 57.435 36.000 0.00 0.00 0.00 2.90
684 685 6.944096 TGATATAGAAGAAGCATCCCTCATG 58.056 40.000 0.00 0.00 35.29 3.07
685 686 6.727697 TGATATAGAAGAAGCATCCCTCATGA 59.272 38.462 0.00 0.00 33.80 3.07
686 687 3.842007 AGAAGAAGCATCCCTCATGAG 57.158 47.619 16.24 16.24 33.80 2.90
687 688 3.382278 AGAAGAAGCATCCCTCATGAGA 58.618 45.455 24.62 5.64 33.80 3.27
688 689 3.779183 AGAAGAAGCATCCCTCATGAGAA 59.221 43.478 24.62 11.97 33.80 2.87
689 690 4.412858 AGAAGAAGCATCCCTCATGAGAAT 59.587 41.667 24.62 13.73 33.80 2.40
690 691 4.792513 AGAAGCATCCCTCATGAGAATT 57.207 40.909 24.62 8.69 33.80 2.17
691 692 4.716794 AGAAGCATCCCTCATGAGAATTC 58.283 43.478 24.62 15.91 33.80 2.17
692 693 3.505480 AGCATCCCTCATGAGAATTCC 57.495 47.619 24.62 9.10 33.80 3.01
693 694 2.781757 AGCATCCCTCATGAGAATTCCA 59.218 45.455 24.62 0.28 33.80 3.53
694 695 3.147629 GCATCCCTCATGAGAATTCCAG 58.852 50.000 24.62 5.13 33.80 3.86
695 696 3.181447 GCATCCCTCATGAGAATTCCAGA 60.181 47.826 24.62 8.82 33.80 3.86
696 697 4.688045 GCATCCCTCATGAGAATTCCAGAA 60.688 45.833 24.62 0.00 33.80 3.02
697 698 5.443283 CATCCCTCATGAGAATTCCAGAAA 58.557 41.667 24.62 0.00 33.80 2.52
698 699 5.722172 TCCCTCATGAGAATTCCAGAAAT 57.278 39.130 24.62 0.00 0.00 2.17
699 700 6.083487 TCCCTCATGAGAATTCCAGAAATT 57.917 37.500 24.62 0.00 40.34 1.82
707 708 2.038387 ATTCCAGAAATTCGTCCCCG 57.962 50.000 0.00 0.00 0.00 5.73
708 709 0.978151 TTCCAGAAATTCGTCCCCGA 59.022 50.000 0.00 0.00 42.41 5.14
709 710 0.248289 TCCAGAAATTCGTCCCCGAC 59.752 55.000 0.00 0.00 44.13 4.79
718 719 3.136123 GTCCCCGACGTGGATCGA 61.136 66.667 1.39 0.00 45.13 3.59
719 720 2.361483 TCCCCGACGTGGATCGAA 60.361 61.111 0.00 0.00 45.13 3.71
720 721 2.202703 CCCCGACGTGGATCGAAC 60.203 66.667 0.00 0.00 45.13 3.95
721 722 2.707849 CCCCGACGTGGATCGAACT 61.708 63.158 0.00 0.00 45.13 3.01
722 723 1.226603 CCCGACGTGGATCGAACTC 60.227 63.158 0.00 0.00 45.13 3.01
723 724 1.654954 CCCGACGTGGATCGAACTCT 61.655 60.000 0.00 0.00 45.13 3.24
724 725 0.523546 CCGACGTGGATCGAACTCTG 60.524 60.000 0.00 0.00 45.13 3.35
725 726 0.523546 CGACGTGGATCGAACTCTGG 60.524 60.000 0.00 0.00 45.13 3.86
726 727 0.526662 GACGTGGATCGAACTCTGGT 59.473 55.000 0.00 0.00 42.86 4.00
727 728 0.526662 ACGTGGATCGAACTCTGGTC 59.473 55.000 0.00 0.00 42.86 4.02
728 729 0.523546 CGTGGATCGAACTCTGGTCG 60.524 60.000 0.00 0.00 42.86 4.79
729 730 0.526662 GTGGATCGAACTCTGGTCGT 59.473 55.000 4.93 0.00 0.00 4.34
730 731 1.067776 GTGGATCGAACTCTGGTCGTT 60.068 52.381 4.93 0.00 0.00 3.85
731 732 2.163010 GTGGATCGAACTCTGGTCGTTA 59.837 50.000 4.93 0.00 0.00 3.18
732 733 2.422479 TGGATCGAACTCTGGTCGTTAG 59.578 50.000 4.93 0.00 0.00 2.34
733 734 2.223525 GGATCGAACTCTGGTCGTTAGG 60.224 54.545 4.93 0.00 0.00 2.69
734 735 1.901591 TCGAACTCTGGTCGTTAGGT 58.098 50.000 4.93 0.00 0.00 3.08
735 736 2.233271 TCGAACTCTGGTCGTTAGGTT 58.767 47.619 4.93 0.00 0.00 3.50
736 737 2.624838 TCGAACTCTGGTCGTTAGGTTT 59.375 45.455 4.93 0.00 0.00 3.27
737 738 3.820467 TCGAACTCTGGTCGTTAGGTTTA 59.180 43.478 4.93 0.00 0.00 2.01
738 739 3.916776 CGAACTCTGGTCGTTAGGTTTAC 59.083 47.826 0.00 0.00 0.00 2.01
739 740 4.557296 CGAACTCTGGTCGTTAGGTTTACA 60.557 45.833 0.00 0.00 0.00 2.41
740 741 4.942761 ACTCTGGTCGTTAGGTTTACAA 57.057 40.909 0.00 0.00 0.00 2.41
741 742 5.479124 ACTCTGGTCGTTAGGTTTACAAT 57.521 39.130 0.00 0.00 0.00 2.71
742 743 5.476614 ACTCTGGTCGTTAGGTTTACAATC 58.523 41.667 0.00 0.00 0.00 2.67
743 744 5.011329 ACTCTGGTCGTTAGGTTTACAATCA 59.989 40.000 0.00 0.00 0.00 2.57
744 745 6.045072 TCTGGTCGTTAGGTTTACAATCAT 57.955 37.500 0.00 0.00 0.00 2.45
745 746 5.872617 TCTGGTCGTTAGGTTTACAATCATG 59.127 40.000 0.00 0.00 0.00 3.07
746 747 4.393680 TGGTCGTTAGGTTTACAATCATGC 59.606 41.667 0.00 0.00 0.00 4.06
747 748 4.493545 GGTCGTTAGGTTTACAATCATGCG 60.494 45.833 0.00 0.00 0.00 4.73
748 749 3.062909 TCGTTAGGTTTACAATCATGCGC 59.937 43.478 0.00 0.00 0.00 6.09
749 750 3.691498 GTTAGGTTTACAATCATGCGCC 58.309 45.455 4.18 0.00 0.00 6.53
750 751 1.102978 AGGTTTACAATCATGCGCCC 58.897 50.000 4.18 0.00 0.00 6.13
751 752 0.102300 GGTTTACAATCATGCGCCCC 59.898 55.000 4.18 0.00 0.00 5.80
752 753 0.102300 GTTTACAATCATGCGCCCCC 59.898 55.000 4.18 0.00 0.00 5.40
753 754 0.323816 TTTACAATCATGCGCCCCCA 60.324 50.000 4.18 0.00 0.00 4.96
754 755 0.323816 TTACAATCATGCGCCCCCAA 60.324 50.000 4.18 0.00 0.00 4.12
755 756 1.034838 TACAATCATGCGCCCCCAAC 61.035 55.000 4.18 0.00 0.00 3.77
756 757 2.759560 AATCATGCGCCCCCAACC 60.760 61.111 4.18 0.00 0.00 3.77
764 765 4.334118 GCCCCCAACCGGTTACGT 62.334 66.667 21.79 0.00 38.78 3.57
765 766 2.953488 GCCCCCAACCGGTTACGTA 61.953 63.158 21.79 0.00 38.78 3.57
766 767 1.676384 CCCCCAACCGGTTACGTAA 59.324 57.895 21.79 3.29 38.78 3.18
767 768 0.036022 CCCCCAACCGGTTACGTAAA 59.964 55.000 21.79 0.00 38.78 2.01
768 769 1.155889 CCCCAACCGGTTACGTAAAC 58.844 55.000 21.79 13.50 38.78 2.01
769 770 1.542108 CCCCAACCGGTTACGTAAACA 60.542 52.381 21.79 0.00 40.08 2.83
770 771 2.216898 CCCAACCGGTTACGTAAACAA 58.783 47.619 21.79 0.00 40.08 2.83
821 822 2.125512 GTGGACCGAATGCTCGCT 60.126 61.111 0.00 0.00 44.04 4.93
830 831 2.286418 CCGAATGCTCGCTCCAAATTAC 60.286 50.000 0.00 0.00 44.04 1.89
843 844 0.034477 AAATTACCCAGGTGCTCCGG 60.034 55.000 0.00 0.00 39.05 5.14
859 861 1.134521 TCCGGCGCATGATCTAAAACT 60.135 47.619 10.83 0.00 0.00 2.66
899 901 1.141254 TGCCCGTTCTTGTAACCTTGA 59.859 47.619 0.00 0.00 0.00 3.02
912 914 6.248569 TGTAACCTTGAGAGACTCCTTTTT 57.751 37.500 0.00 0.00 0.00 1.94
939 941 0.386731 ACGCAATTACACGCAAAGCC 60.387 50.000 0.00 0.00 0.00 4.35
972 974 4.485163 CGCGGAAAAGAAATGGAGAAAAT 58.515 39.130 0.00 0.00 0.00 1.82
977 979 6.470235 CGGAAAAGAAATGGAGAAAATCATCG 59.530 38.462 0.00 0.00 0.00 3.84
1058 1060 1.275421 CCTTCCCACTCCCTTCCCTC 61.275 65.000 0.00 0.00 0.00 4.30
1077 1080 2.659063 CCATCCCAGACGCCACAGA 61.659 63.158 0.00 0.00 0.00 3.41
1080 1083 4.394712 CCCAGACGCCACAGACCC 62.395 72.222 0.00 0.00 0.00 4.46
1081 1084 4.742201 CCAGACGCCACAGACCCG 62.742 72.222 0.00 0.00 0.00 5.28
1082 1085 3.680786 CAGACGCCACAGACCCGA 61.681 66.667 0.00 0.00 0.00 5.14
1367 1382 3.827898 GAGGTGGAGGCCGTCGAG 61.828 72.222 0.00 0.00 0.00 4.04
1451 1466 0.319900 GTTCTCTTGCTGGCTCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
1521 1536 8.536172 GAGATGACTCCATTCGATCTCGATCC 62.536 50.000 2.75 0.00 41.31 3.36
1575 1594 6.508030 AATTTATCTTCTTCCTCCTCCTCC 57.492 41.667 0.00 0.00 0.00 4.30
1576 1595 4.909355 TTATCTTCTTCCTCCTCCTCCT 57.091 45.455 0.00 0.00 0.00 3.69
1577 1596 2.838637 TCTTCTTCCTCCTCCTCCTC 57.161 55.000 0.00 0.00 0.00 3.71
1578 1597 2.293246 TCTTCTTCCTCCTCCTCCTCT 58.707 52.381 0.00 0.00 0.00 3.69
1579 1598 2.657459 TCTTCTTCCTCCTCCTCCTCTT 59.343 50.000 0.00 0.00 0.00 2.85
1580 1599 2.838637 TCTTCCTCCTCCTCCTCTTC 57.161 55.000 0.00 0.00 0.00 2.87
1581 1600 1.289530 TCTTCCTCCTCCTCCTCTTCC 59.710 57.143 0.00 0.00 0.00 3.46
1615 1634 4.044426 GGATTAATTTGGTGCTCGATTGC 58.956 43.478 0.00 0.00 0.00 3.56
1667 1686 3.516681 GCATATGCGTGTTGATGAGAG 57.483 47.619 12.82 0.00 0.00 3.20
1681 1700 0.249868 TGAGAGTCCAAACTGGTGCG 60.250 55.000 0.00 0.00 39.03 5.34
1682 1701 0.249911 GAGAGTCCAAACTGGTGCGT 60.250 55.000 0.00 0.00 39.03 5.24
1683 1702 0.532862 AGAGTCCAAACTGGTGCGTG 60.533 55.000 0.00 0.00 39.03 5.34
1684 1703 0.814010 GAGTCCAAACTGGTGCGTGT 60.814 55.000 0.00 0.00 39.03 4.49
1713 1732 2.561733 TCGATCGGTGAGATGAACAC 57.438 50.000 16.41 0.00 40.26 3.32
1737 1756 8.134895 CACCTTGTAATTTGTACAGATTTGTGT 58.865 33.333 15.99 5.60 38.23 3.72
1848 1867 6.998074 TCACTGAATGGAATTACACTTTGACT 59.002 34.615 0.00 0.00 36.07 3.41
1849 1868 7.173218 TCACTGAATGGAATTACACTTTGACTC 59.827 37.037 0.00 0.00 36.07 3.36
1850 1869 6.998074 ACTGAATGGAATTACACTTTGACTCA 59.002 34.615 0.00 0.00 36.07 3.41
1877 1896 0.438830 CTTTACTTCACCGAGTGCGC 59.561 55.000 0.00 0.00 35.83 6.09
1878 1897 1.279527 TTTACTTCACCGAGTGCGCG 61.280 55.000 0.00 0.00 35.83 6.86
1896 1915 2.372350 GCGCGGCTGTAAAATTATGTC 58.628 47.619 8.83 0.00 0.00 3.06
1908 1927 8.267620 TGTAAAATTATGTCATCCTGTCACTG 57.732 34.615 0.00 0.00 0.00 3.66
1929 1948 2.999507 CTAGTAGCTAGCATGGGTCG 57.000 55.000 18.83 0.00 0.00 4.79
1994 2018 4.891566 TTCGAGCCGAAGAGAAGC 57.108 55.556 6.01 0.00 41.05 3.86
1998 2022 2.680352 AGCCGAAGAGAAGCCGGA 60.680 61.111 5.05 0.00 45.58 5.14
2054 2085 0.259938 AGGCTGGGTTCCCATCATTC 59.740 55.000 11.26 0.52 35.33 2.67
2084 2115 1.956477 TGCCAGAAAAGTTTGAGAGCC 59.044 47.619 0.00 0.00 0.00 4.70
2105 2136 1.248101 ACCGCTACCCATTTGTTGGC 61.248 55.000 0.00 0.00 44.97 4.52
2173 2204 7.607607 TGATGCTGTCAGTGACTGTAATAATTT 59.392 33.333 25.42 9.88 34.68 1.82
2209 2240 1.230324 AAGTCAAGGAGCAAGCGTTC 58.770 50.000 0.00 0.00 0.00 3.95
2254 2285 1.140312 TTGGTGAGAGCTTGAAGGGT 58.860 50.000 0.00 0.00 0.00 4.34
2259 2290 3.198853 GGTGAGAGCTTGAAGGGTTATCT 59.801 47.826 0.00 0.00 0.00 1.98
2264 2295 4.719273 AGAGCTTGAAGGGTTATCTTAGCT 59.281 41.667 0.00 0.00 37.84 3.32
2301 2332 1.790696 CGTACGTAGTGTCGCTGTAC 58.209 55.000 7.22 0.48 45.73 2.90
2309 2340 5.865552 ACGTAGTGTCGCTGTACAATTAAAT 59.134 36.000 0.00 0.00 42.51 1.40
2342 2373 5.115773 GCTGTCACTTTACTAATATCGCTCG 59.884 44.000 0.00 0.00 0.00 5.03
2343 2374 4.974275 TGTCACTTTACTAATATCGCTCGC 59.026 41.667 0.00 0.00 0.00 5.03
2344 2375 5.213675 GTCACTTTACTAATATCGCTCGCT 58.786 41.667 0.00 0.00 0.00 4.93
2345 2376 5.340138 GTCACTTTACTAATATCGCTCGCTC 59.660 44.000 0.00 0.00 0.00 5.03
2378 2409 4.379243 AAGCGTGGAGACTGGCCG 62.379 66.667 0.00 0.00 0.00 6.13
2384 2415 1.076014 TGGAGACTGGCCGTCACTA 59.924 57.895 23.47 15.44 45.32 2.74
2422 2453 4.347453 CTGCCGCCAACTGCCAAC 62.347 66.667 0.00 0.00 36.24 3.77
2572 2605 2.947448 AAACGTGACTCCGTATACCC 57.053 50.000 0.00 0.00 40.85 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.734492 GCTAGCCGTCGTTGTTACTGAT 60.734 50.000 2.29 0.00 0.00 2.90
71 72 1.004679 CCAATGCCCAAACAGGTGC 60.005 57.895 0.00 0.00 34.66 5.01
98 99 0.467290 TTCCCCTTTATCATGCCGCC 60.467 55.000 0.00 0.00 0.00 6.13
105 106 4.380843 TGCTCACTTTTCCCCTTTATCA 57.619 40.909 0.00 0.00 0.00 2.15
109 110 3.374764 ACTTTGCTCACTTTTCCCCTTT 58.625 40.909 0.00 0.00 0.00 3.11
142 143 3.056607 ACAAAGTTGTGCTCAGTTTTGCT 60.057 39.130 18.77 9.53 40.49 3.91
217 218 9.308000 TGGGTTGATCTATGTTTTTATGTTCTT 57.692 29.630 0.00 0.00 0.00 2.52
224 225 8.698973 TGACTTTGGGTTGATCTATGTTTTTA 57.301 30.769 0.00 0.00 0.00 1.52
228 229 7.781324 AAATGACTTTGGGTTGATCTATGTT 57.219 32.000 0.00 0.00 0.00 2.71
247 248 3.935203 GACAGAGATCGCCAGAAAAATGA 59.065 43.478 0.00 0.00 0.00 2.57
251 252 2.612972 GGTGACAGAGATCGCCAGAAAA 60.613 50.000 0.48 0.00 46.73 2.29
274 275 5.509670 CGACACATCATCAAGCTTATAGGGA 60.510 44.000 0.00 0.00 0.00 4.20
279 280 4.568359 GTCACGACACATCATCAAGCTTAT 59.432 41.667 0.00 0.00 0.00 1.73
284 285 2.926200 GAGGTCACGACACATCATCAAG 59.074 50.000 0.00 0.00 0.00 3.02
307 308 6.329986 ACTGGATTAGATGATGTGGGTTGATA 59.670 38.462 0.00 0.00 0.00 2.15
355 356 0.389166 GGTTGGTGCTCTCGACTCAG 60.389 60.000 0.00 0.00 0.00 3.35
394 395 3.870274 TGAAGACGACGGATTCTAGAGA 58.130 45.455 13.31 0.00 0.00 3.10
423 424 5.065914 TGATCTCTTTTGAAGTTGGGACAG 58.934 41.667 0.00 0.00 42.39 3.51
424 425 5.047566 TGATCTCTTTTGAAGTTGGGACA 57.952 39.130 0.00 0.00 0.00 4.02
475 476 2.794166 GTCGTGGTGACGTCGACG 60.794 66.667 34.58 34.58 46.20 5.12
495 496 2.279741 GCAGAATGATGGCGTTGTCTA 58.720 47.619 0.00 0.00 39.69 2.59
507 508 4.733371 TGGACGCGCGCAGAATGA 62.733 61.111 32.58 6.13 39.69 2.57
509 510 3.264897 GATGGACGCGCGCAGAAT 61.265 61.111 32.58 18.55 0.00 2.40
514 515 1.284982 ATTCTATGATGGACGCGCGC 61.285 55.000 32.58 23.91 0.00 6.86
620 621 3.647590 AGTGCCCATGGAGTTTCATTTTT 59.352 39.130 15.22 0.00 0.00 1.94
621 622 3.242011 AGTGCCCATGGAGTTTCATTTT 58.758 40.909 15.22 0.00 0.00 1.82
622 623 2.893424 AGTGCCCATGGAGTTTCATTT 58.107 42.857 15.22 0.00 0.00 2.32
623 624 2.610438 AGTGCCCATGGAGTTTCATT 57.390 45.000 15.22 0.00 0.00 2.57
624 625 2.684927 GCTAGTGCCCATGGAGTTTCAT 60.685 50.000 15.22 0.00 0.00 2.57
625 626 1.340017 GCTAGTGCCCATGGAGTTTCA 60.340 52.381 15.22 0.00 0.00 2.69
626 627 1.340017 TGCTAGTGCCCATGGAGTTTC 60.340 52.381 15.22 0.00 38.71 2.78
627 628 0.698238 TGCTAGTGCCCATGGAGTTT 59.302 50.000 15.22 0.00 38.71 2.66
628 629 0.035056 GTGCTAGTGCCCATGGAGTT 60.035 55.000 15.22 0.00 38.71 3.01
629 630 1.604378 GTGCTAGTGCCCATGGAGT 59.396 57.895 15.22 0.00 38.71 3.85
630 631 1.153086 GGTGCTAGTGCCCATGGAG 60.153 63.158 15.22 2.70 38.71 3.86
631 632 2.679342 GGGTGCTAGTGCCCATGGA 61.679 63.158 15.22 0.00 44.23 3.41
632 633 2.124151 GGGTGCTAGTGCCCATGG 60.124 66.667 15.91 4.14 44.23 3.66
636 637 4.778143 CCGTGGGTGCTAGTGCCC 62.778 72.222 14.48 14.48 45.04 5.36
637 638 3.546714 AACCGTGGGTGCTAGTGCC 62.547 63.158 0.00 0.00 35.34 5.01
638 639 1.170290 AAAACCGTGGGTGCTAGTGC 61.170 55.000 0.00 0.00 35.34 4.40
639 640 2.172851 TAAAACCGTGGGTGCTAGTG 57.827 50.000 0.00 0.00 35.34 2.74
640 641 3.078837 CAATAAAACCGTGGGTGCTAGT 58.921 45.455 0.00 0.00 35.34 2.57
641 642 3.340034 TCAATAAAACCGTGGGTGCTAG 58.660 45.455 0.00 0.00 35.34 3.42
642 643 3.420300 TCAATAAAACCGTGGGTGCTA 57.580 42.857 0.00 0.00 35.34 3.49
643 644 2.279935 TCAATAAAACCGTGGGTGCT 57.720 45.000 0.00 0.00 35.34 4.40
644 645 4.911514 ATATCAATAAAACCGTGGGTGC 57.088 40.909 0.00 0.00 35.34 5.01
645 646 7.713507 TCTTCTATATCAATAAAACCGTGGGTG 59.286 37.037 0.00 0.00 35.34 4.61
646 647 7.798071 TCTTCTATATCAATAAAACCGTGGGT 58.202 34.615 0.00 0.00 37.65 4.51
647 648 8.671384 TTCTTCTATATCAATAAAACCGTGGG 57.329 34.615 0.00 0.00 0.00 4.61
648 649 8.283291 GCTTCTTCTATATCAATAAAACCGTGG 58.717 37.037 0.00 0.00 0.00 4.94
649 650 8.826710 TGCTTCTTCTATATCAATAAAACCGTG 58.173 33.333 0.00 0.00 0.00 4.94
650 651 8.958119 TGCTTCTTCTATATCAATAAAACCGT 57.042 30.769 0.00 0.00 0.00 4.83
655 656 9.950496 GAGGGATGCTTCTTCTATATCAATAAA 57.050 33.333 0.00 0.00 0.00 1.40
656 657 9.104713 TGAGGGATGCTTCTTCTATATCAATAA 57.895 33.333 0.00 0.00 0.00 1.40
657 658 8.670521 TGAGGGATGCTTCTTCTATATCAATA 57.329 34.615 0.00 0.00 0.00 1.90
658 659 7.565190 TGAGGGATGCTTCTTCTATATCAAT 57.435 36.000 0.00 0.00 0.00 2.57
659 660 7.236225 TCATGAGGGATGCTTCTTCTATATCAA 59.764 37.037 0.00 0.00 31.32 2.57
660 661 6.727697 TCATGAGGGATGCTTCTTCTATATCA 59.272 38.462 0.00 0.00 31.32 2.15
661 662 7.123997 TCTCATGAGGGATGCTTCTTCTATATC 59.876 40.741 22.42 0.00 31.32 1.63
662 663 6.958778 TCTCATGAGGGATGCTTCTTCTATAT 59.041 38.462 22.42 0.00 31.32 0.86
663 664 6.318112 TCTCATGAGGGATGCTTCTTCTATA 58.682 40.000 22.42 0.00 31.32 1.31
664 665 5.153675 TCTCATGAGGGATGCTTCTTCTAT 58.846 41.667 22.42 0.00 31.32 1.98
665 666 4.550669 TCTCATGAGGGATGCTTCTTCTA 58.449 43.478 22.42 0.00 31.32 2.10
666 667 3.382278 TCTCATGAGGGATGCTTCTTCT 58.618 45.455 22.42 0.00 31.32 2.85
667 668 3.834489 TCTCATGAGGGATGCTTCTTC 57.166 47.619 22.42 0.00 31.32 2.87
668 669 4.792513 ATTCTCATGAGGGATGCTTCTT 57.207 40.909 22.42 0.00 31.32 2.52
669 670 4.446023 GGAATTCTCATGAGGGATGCTTCT 60.446 45.833 22.42 2.49 31.32 2.85
670 671 3.819902 GGAATTCTCATGAGGGATGCTTC 59.180 47.826 22.42 14.34 31.32 3.86
671 672 3.203710 TGGAATTCTCATGAGGGATGCTT 59.796 43.478 22.42 7.33 31.32 3.91
672 673 2.781757 TGGAATTCTCATGAGGGATGCT 59.218 45.455 22.42 3.80 31.32 3.79
673 674 3.147629 CTGGAATTCTCATGAGGGATGC 58.852 50.000 22.42 14.53 31.32 3.91
674 675 4.701651 TCTGGAATTCTCATGAGGGATG 57.298 45.455 22.42 7.14 0.00 3.51
675 676 5.722172 TTTCTGGAATTCTCATGAGGGAT 57.278 39.130 22.42 13.69 0.00 3.85
676 677 5.722172 ATTTCTGGAATTCTCATGAGGGA 57.278 39.130 22.42 12.00 0.00 4.20
677 678 6.388435 GAATTTCTGGAATTCTCATGAGGG 57.612 41.667 22.42 0.00 46.59 4.30
701 702 2.703798 TTCGATCCACGTCGGGGAC 61.704 63.158 20.83 11.97 41.74 4.46
702 703 2.361483 TTCGATCCACGTCGGGGA 60.361 61.111 20.66 20.66 41.74 4.81
703 704 2.202703 GTTCGATCCACGTCGGGG 60.203 66.667 7.38 7.38 41.74 5.73
704 705 1.226603 GAGTTCGATCCACGTCGGG 60.227 63.158 0.00 0.00 41.74 5.14
705 706 0.523546 CAGAGTTCGATCCACGTCGG 60.524 60.000 0.00 0.00 41.74 4.79
706 707 0.523546 CCAGAGTTCGATCCACGTCG 60.524 60.000 0.00 0.00 43.13 5.12
707 708 0.526662 ACCAGAGTTCGATCCACGTC 59.473 55.000 0.00 0.00 43.13 4.34
708 709 0.526662 GACCAGAGTTCGATCCACGT 59.473 55.000 0.00 0.00 43.13 4.49
709 710 0.523546 CGACCAGAGTTCGATCCACG 60.524 60.000 0.00 0.00 44.09 4.94
710 711 0.526662 ACGACCAGAGTTCGATCCAC 59.473 55.000 0.00 0.00 0.00 4.02
711 712 1.254026 AACGACCAGAGTTCGATCCA 58.746 50.000 0.00 0.00 0.00 3.41
712 713 2.223525 CCTAACGACCAGAGTTCGATCC 60.224 54.545 0.00 0.00 33.42 3.36
713 714 2.422832 ACCTAACGACCAGAGTTCGATC 59.577 50.000 0.00 0.00 33.42 3.69
714 715 2.444421 ACCTAACGACCAGAGTTCGAT 58.556 47.619 0.00 0.00 33.42 3.59
715 716 1.901591 ACCTAACGACCAGAGTTCGA 58.098 50.000 0.00 0.00 33.42 3.71
716 717 2.719426 AACCTAACGACCAGAGTTCG 57.281 50.000 0.00 0.00 33.42 3.95
717 718 4.874970 TGTAAACCTAACGACCAGAGTTC 58.125 43.478 0.00 0.00 33.42 3.01
718 719 4.942761 TGTAAACCTAACGACCAGAGTT 57.057 40.909 0.00 0.00 35.75 3.01
719 720 4.942761 TTGTAAACCTAACGACCAGAGT 57.057 40.909 0.00 0.00 0.00 3.24
720 721 5.475719 TGATTGTAAACCTAACGACCAGAG 58.524 41.667 0.00 0.00 0.00 3.35
721 722 5.471556 TGATTGTAAACCTAACGACCAGA 57.528 39.130 0.00 0.00 0.00 3.86
722 723 5.447279 GCATGATTGTAAACCTAACGACCAG 60.447 44.000 0.00 0.00 0.00 4.00
723 724 4.393680 GCATGATTGTAAACCTAACGACCA 59.606 41.667 0.00 0.00 0.00 4.02
724 725 4.493545 CGCATGATTGTAAACCTAACGACC 60.494 45.833 0.00 0.00 0.00 4.79
725 726 4.574759 CGCATGATTGTAAACCTAACGAC 58.425 43.478 0.00 0.00 0.00 4.34
726 727 3.062909 GCGCATGATTGTAAACCTAACGA 59.937 43.478 0.30 0.00 0.00 3.85
727 728 3.350912 GCGCATGATTGTAAACCTAACG 58.649 45.455 0.30 0.00 0.00 3.18
728 729 3.488553 GGGCGCATGATTGTAAACCTAAC 60.489 47.826 10.83 0.00 0.00 2.34
729 730 2.685897 GGGCGCATGATTGTAAACCTAA 59.314 45.455 10.83 0.00 0.00 2.69
730 731 2.294074 GGGCGCATGATTGTAAACCTA 58.706 47.619 10.83 0.00 0.00 3.08
731 732 1.102978 GGGCGCATGATTGTAAACCT 58.897 50.000 10.83 0.00 0.00 3.50
732 733 0.102300 GGGGCGCATGATTGTAAACC 59.898 55.000 10.83 0.00 0.00 3.27
733 734 0.102300 GGGGGCGCATGATTGTAAAC 59.898 55.000 10.83 0.00 0.00 2.01
734 735 0.323816 TGGGGGCGCATGATTGTAAA 60.324 50.000 10.83 0.00 0.00 2.01
735 736 0.323816 TTGGGGGCGCATGATTGTAA 60.324 50.000 10.83 0.00 0.00 2.41
736 737 1.034838 GTTGGGGGCGCATGATTGTA 61.035 55.000 10.83 0.00 0.00 2.41
737 738 2.037049 TTGGGGGCGCATGATTGT 59.963 55.556 10.83 0.00 0.00 2.71
738 739 2.495866 GTTGGGGGCGCATGATTG 59.504 61.111 10.83 0.00 0.00 2.67
739 740 2.759560 GGTTGGGGGCGCATGATT 60.760 61.111 10.83 0.00 0.00 2.57
747 748 2.462125 TTACGTAACCGGTTGGGGGC 62.462 60.000 30.08 12.78 41.60 5.80
748 749 0.036022 TTTACGTAACCGGTTGGGGG 59.964 55.000 30.08 17.01 41.60 5.40
749 750 1.155889 GTTTACGTAACCGGTTGGGG 58.844 55.000 30.08 19.42 41.60 4.96
750 751 1.876322 TGTTTACGTAACCGGTTGGG 58.124 50.000 30.08 21.88 40.75 4.12
751 752 3.129871 TCTTGTTTACGTAACCGGTTGG 58.870 45.455 30.08 22.23 42.84 3.77
752 753 4.792528 TTCTTGTTTACGTAACCGGTTG 57.207 40.909 30.08 16.45 38.78 3.77
753 754 7.489574 TTATTTCTTGTTTACGTAACCGGTT 57.510 32.000 25.64 25.64 38.78 4.44
754 755 7.489574 TTTATTTCTTGTTTACGTAACCGGT 57.510 32.000 7.70 0.00 38.78 5.28
755 756 7.693536 GGATTTATTTCTTGTTTACGTAACCGG 59.306 37.037 7.70 0.00 38.78 5.28
756 757 8.229137 TGGATTTATTTCTTGTTTACGTAACCG 58.771 33.333 7.70 0.00 35.81 4.44
757 758 9.550811 CTGGATTTATTTCTTGTTTACGTAACC 57.449 33.333 7.70 0.86 35.81 2.85
760 761 8.938906 GGTCTGGATTTATTTCTTGTTTACGTA 58.061 33.333 0.00 0.00 0.00 3.57
761 762 7.446013 TGGTCTGGATTTATTTCTTGTTTACGT 59.554 33.333 0.00 0.00 0.00 3.57
762 763 7.749126 GTGGTCTGGATTTATTTCTTGTTTACG 59.251 37.037 0.00 0.00 0.00 3.18
763 764 8.573035 TGTGGTCTGGATTTATTTCTTGTTTAC 58.427 33.333 0.00 0.00 0.00 2.01
764 765 8.573035 GTGTGGTCTGGATTTATTTCTTGTTTA 58.427 33.333 0.00 0.00 0.00 2.01
765 766 7.069331 TGTGTGGTCTGGATTTATTTCTTGTTT 59.931 33.333 0.00 0.00 0.00 2.83
766 767 6.549364 TGTGTGGTCTGGATTTATTTCTTGTT 59.451 34.615 0.00 0.00 0.00 2.83
767 768 6.016276 GTGTGTGGTCTGGATTTATTTCTTGT 60.016 38.462 0.00 0.00 0.00 3.16
768 769 6.381801 GTGTGTGGTCTGGATTTATTTCTTG 58.618 40.000 0.00 0.00 0.00 3.02
769 770 5.181245 CGTGTGTGGTCTGGATTTATTTCTT 59.819 40.000 0.00 0.00 0.00 2.52
770 771 4.695455 CGTGTGTGGTCTGGATTTATTTCT 59.305 41.667 0.00 0.00 0.00 2.52
821 822 1.005450 GGAGCACCTGGGTAATTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
843 844 5.292101 AGTGTTCTAGTTTTAGATCATGCGC 59.708 40.000 0.00 0.00 37.72 6.09
859 861 0.599991 CCAGTGCGCACAGTGTTCTA 60.600 55.000 39.21 0.00 44.42 2.10
884 886 5.011227 AGGAGTCTCTCAAGGTTACAAGAAC 59.989 44.000 0.00 0.00 31.08 3.01
912 914 2.669434 GCGTGTAATTGCGTTAGGAGAA 59.331 45.455 0.00 0.00 0.00 2.87
948 950 0.179163 CTCCATTTCTTTTCCGCGGC 60.179 55.000 23.51 0.00 0.00 6.53
972 974 2.123251 GAGAGGGAGGGGCGATGA 60.123 66.667 0.00 0.00 0.00 2.92
1058 1060 3.687321 CTGTGGCGTCTGGGATGGG 62.687 68.421 0.00 0.00 0.00 4.00
1367 1382 3.749064 TCGGAGGAGCAGTCGCAC 61.749 66.667 0.00 0.00 42.27 5.34
1468 1483 1.440060 CACGCCTTACCTGCCGATA 59.560 57.895 0.00 0.00 0.00 2.92
1469 1484 2.186903 CACGCCTTACCTGCCGAT 59.813 61.111 0.00 0.00 0.00 4.18
1470 1485 4.077184 CCACGCCTTACCTGCCGA 62.077 66.667 0.00 0.00 0.00 5.54
1471 1486 4.388499 ACCACGCCTTACCTGCCG 62.388 66.667 0.00 0.00 0.00 5.69
1575 1594 2.764269 TCCCAATACCAGGAGGAAGAG 58.236 52.381 0.00 0.00 38.69 2.85
1576 1595 2.961536 TCCCAATACCAGGAGGAAGA 57.038 50.000 0.00 0.00 38.69 2.87
1577 1596 5.646692 TTAATCCCAATACCAGGAGGAAG 57.353 43.478 0.00 0.00 38.69 3.46
1578 1597 6.606241 AATTAATCCCAATACCAGGAGGAA 57.394 37.500 0.00 0.00 38.69 3.36
1579 1598 6.372931 CAAATTAATCCCAATACCAGGAGGA 58.627 40.000 0.00 0.00 38.69 3.71
1580 1599 5.539955 CCAAATTAATCCCAATACCAGGAGG 59.460 44.000 0.00 0.00 42.21 4.30
1581 1600 6.040842 CACCAAATTAATCCCAATACCAGGAG 59.959 42.308 0.00 0.00 35.08 3.69
1615 1634 7.402811 ACGGATATGTTAATTACATCACACG 57.597 36.000 0.00 0.00 44.15 4.49
1667 1686 1.355210 CACACGCACCAGTTTGGAC 59.645 57.895 1.40 0.00 40.96 4.02
1681 1700 2.159421 ACCGATCGATCTACACACACAC 60.159 50.000 22.43 0.00 0.00 3.82
1682 1701 2.089201 ACCGATCGATCTACACACACA 58.911 47.619 22.43 0.00 0.00 3.72
1683 1702 2.096980 TCACCGATCGATCTACACACAC 59.903 50.000 22.43 0.00 0.00 3.82
1684 1703 2.354821 CTCACCGATCGATCTACACACA 59.645 50.000 22.43 0.31 0.00 3.72
1713 1732 9.528018 AAACACAAATCTGTACAAATTACAAGG 57.472 29.630 0.00 0.00 33.22 3.61
1737 1756 3.096092 ACTGCTGGTTCCAAACAAGAAA 58.904 40.909 0.00 0.00 34.15 2.52
1800 1819 4.285863 AGCAAAGGCATCTACTCTACTCT 58.714 43.478 0.00 0.00 44.61 3.24
1801 1820 4.664150 AGCAAAGGCATCTACTCTACTC 57.336 45.455 0.00 0.00 44.61 2.59
1802 1821 4.467795 TGAAGCAAAGGCATCTACTCTACT 59.532 41.667 0.00 0.00 44.61 2.57
1803 1822 4.568760 GTGAAGCAAAGGCATCTACTCTAC 59.431 45.833 0.00 0.00 44.61 2.59
1804 1823 4.467795 AGTGAAGCAAAGGCATCTACTCTA 59.532 41.667 0.00 0.00 44.61 2.43
1805 1824 3.262915 AGTGAAGCAAAGGCATCTACTCT 59.737 43.478 0.00 0.00 44.61 3.24
1806 1825 3.373439 CAGTGAAGCAAAGGCATCTACTC 59.627 47.826 0.00 0.00 44.61 2.59
1848 1867 3.585862 GGTGAAGTAAAGCTCACGATGA 58.414 45.455 0.00 0.00 34.24 2.92
1849 1868 2.345641 CGGTGAAGTAAAGCTCACGATG 59.654 50.000 0.00 0.00 34.24 3.84
1850 1869 2.230508 TCGGTGAAGTAAAGCTCACGAT 59.769 45.455 0.00 0.00 34.24 3.73
1877 1896 3.666883 TGACATAATTTTACAGCCGCG 57.333 42.857 0.00 0.00 0.00 6.46
1878 1897 4.275936 AGGATGACATAATTTTACAGCCGC 59.724 41.667 0.00 0.00 41.12 6.53
1879 1898 5.296780 ACAGGATGACATAATTTTACAGCCG 59.703 40.000 0.00 0.00 41.12 5.52
1880 1899 6.318648 TGACAGGATGACATAATTTTACAGCC 59.681 38.462 0.00 0.00 39.69 4.85
1896 1915 2.223923 GCTACTAGCCAGTGACAGGATG 60.224 54.545 0.00 0.00 38.05 3.51
1929 1948 8.846607 CGTGCTAATTGAAAACAATACCTAAAC 58.153 33.333 0.00 0.00 0.00 2.01
1994 2018 1.874019 CACGCACGAAGAGATCCGG 60.874 63.158 0.00 0.00 0.00 5.14
1998 2022 0.389948 GGAACCACGCACGAAGAGAT 60.390 55.000 0.00 0.00 0.00 2.75
2084 2115 1.067915 CCAACAAATGGGTAGCGGTTG 60.068 52.381 0.00 0.00 46.27 3.77
2121 2152 8.641499 TTAACCTTAATTTGAGCACTGTTTTG 57.359 30.769 0.00 0.00 0.00 2.44
2173 2204 5.227569 TGACTTTGATGCAGAGGTTAAGA 57.772 39.130 0.00 0.00 0.00 2.10
2182 2213 2.156917 TGCTCCTTGACTTTGATGCAG 58.843 47.619 0.00 0.00 0.00 4.41
2252 2283 8.910351 ATCTGGTTTTGATAGCTAAGATAACC 57.090 34.615 17.55 17.55 35.51 2.85
2259 2290 5.294306 CGCTTGATCTGGTTTTGATAGCTAA 59.706 40.000 0.00 0.00 0.00 3.09
2264 2295 4.565166 CGTACGCTTGATCTGGTTTTGATA 59.435 41.667 0.52 0.00 0.00 2.15
2301 2332 4.142838 TGACAGCGCAGTGAGATTTAATTG 60.143 41.667 11.27 0.00 0.00 2.32
2309 2340 0.104855 AAAGTGACAGCGCAGTGAGA 59.895 50.000 11.27 0.00 0.00 3.27
2342 2373 2.358003 ACAAGAGCTGGTGCGAGC 60.358 61.111 0.00 0.00 45.42 5.03
2343 2374 0.601046 TTGACAAGAGCTGGTGCGAG 60.601 55.000 0.00 0.00 45.42 5.03
2344 2375 0.601046 CTTGACAAGAGCTGGTGCGA 60.601 55.000 9.76 0.00 45.42 5.10
2345 2376 1.864862 CTTGACAAGAGCTGGTGCG 59.135 57.895 9.76 0.00 45.42 5.34
2384 2415 5.001874 CAGCAATAGATATGGCACTGTGAT 58.998 41.667 12.86 0.00 35.03 3.06
2572 2605 0.379669 CCTGCCTGCGCTTTAGATTG 59.620 55.000 9.73 0.00 35.36 2.67


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

AutoCloner maintained by Alex Coulton.