Multiple sequence alignment - TraesCS7A01G228000

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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 TraesCS7A01G228000 chr7A 100.000 2921 0 0 1 2921 198650649 198653569 0.000000e+00 5395.0
1 TraesCS7A01G228000 chr7B 91.637 1686 91 26 940 2583 329365045 329363368 0.000000e+00 2287.0
2 TraesCS7A01G228000 chr7D 88.330 1731 135 26 934 2635 186418804 186417112 0.000000e+00 2015.0
3 TraesCS7A01G228000 chr7D 87.391 571 58 11 1 560 186419648 186419081 0.000000e+00 643.0
4 TraesCS7A01G228000 chr7D 90.554 307 15 3 2620 2921 186417094 186416797 7.590000e-106 394.0
5 TraesCS7A01G228000 chr4A 86.822 129 12 4 629 754 88092835 88092709 3.930000e-29 139.0
6 TraesCS7A01G228000 chr4A 82.645 121 15 2 629 749 88087631 88087517 5.150000e-18 102.0
7 TraesCS7A01G228000 chr5D 81.679 131 15 6 627 754 345965643 345965767 1.850000e-17 100.0
8 TraesCS7A01G228000 chr6D 92.593 54 4 0 168 221 13105478 13105425 8.680000e-11 78.7
9 TraesCS7A01G228000 chr2B 79.339 121 13 6 635 754 713997383 713997274 1.120000e-09 75.0
10 TraesCS7A01G228000 chr3B 92.308 52 3 1 703 754 173111138 173111188 4.040000e-09 73.1


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 TraesCS7A01G228000 chr7A 198650649 198653569 2920 False 5395.000000 5395 100.000000 1 2921 1 chr7A.!!$F1 2920
1 TraesCS7A01G228000 chr7B 329363368 329365045 1677 True 2287.000000 2287 91.637000 940 2583 1 chr7B.!!$R1 1643
2 TraesCS7A01G228000 chr7D 186416797 186419648 2851 True 1017.333333 2015 88.758333 1 2921 3 chr7D.!!$R1 2920

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
391 393 0.035598 TCCAGCGTGGAAAATCGGAA 59.964 50.0 4.51 0.0 45.00 4.30 F
1073 1161 0.032130 GAGTATCAGGCGCGATCCAA 59.968 55.0 12.10 0.0 33.17 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1822 1.521450 CTCAACCCTGCAGCAACCAG 61.521 60.0 8.66 0.0 0.0 4.00 R
2813 3003 0.251077 AGCAGAGCCAAACTTCCCAG 60.251 55.0 0.00 0.0 0.0 4.45 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
20 21 0.107017 ATGGTGGCCTGAGTGTATGC 60.107 55.000 3.32 0.00 0.00 3.14
23 24 1.079197 TGGCCTGAGTGTATGCGTG 60.079 57.895 3.32 0.00 0.00 5.34
30 31 1.079127 AGTGTATGCGTGTGCCCTC 60.079 57.895 0.00 0.00 41.78 4.30
35 36 1.884075 TATGCGTGTGCCCTCGAGTT 61.884 55.000 12.31 0.00 41.78 3.01
38 39 1.782028 GCGTGTGCCCTCGAGTTTTT 61.782 55.000 12.31 0.00 33.98 1.94
44 45 2.614983 GTGCCCTCGAGTTTTTGTTGTA 59.385 45.455 12.31 0.00 0.00 2.41
45 46 3.065648 GTGCCCTCGAGTTTTTGTTGTAA 59.934 43.478 12.31 0.00 0.00 2.41
51 52 5.133707 TCGAGTTTTTGTTGTAACGTCTG 57.866 39.130 0.00 0.00 0.00 3.51
53 54 4.023739 AGTTTTTGTTGTAACGTCTGGC 57.976 40.909 0.00 0.00 0.00 4.85
55 56 4.877251 AGTTTTTGTTGTAACGTCTGGCTA 59.123 37.500 0.00 0.00 0.00 3.93
61 62 1.337447 TGTAACGTCTGGCTAGGTTGC 60.337 52.381 0.00 0.00 32.63 4.17
66 67 0.796927 GTCTGGCTAGGTTGCGTTTC 59.203 55.000 0.00 0.00 0.00 2.78
67 68 0.321298 TCTGGCTAGGTTGCGTTTCC 60.321 55.000 0.00 0.00 0.00 3.13
126 127 6.042322 TGTCTTTGGCTAGGACTTTGTACTTA 59.958 38.462 11.89 0.00 0.00 2.24
200 201 6.092092 TGTCTTATTCGCATTGGACAAAATG 58.908 36.000 0.00 0.00 39.98 2.32
205 206 5.697473 TTCGCATTGGACAAAATGAAGTA 57.303 34.783 1.22 0.00 39.46 2.24
206 207 5.697473 TCGCATTGGACAAAATGAAGTAA 57.303 34.783 1.22 0.00 39.46 2.24
248 250 8.574251 ACAATGTACATATTTTTGCTCCACTA 57.426 30.769 9.21 0.00 0.00 2.74
268 270 9.219603 TCCACTATTTTGAAACTAACTCTCATG 57.780 33.333 0.00 0.00 0.00 3.07
270 272 8.506437 CACTATTTTGAAACTAACTCTCATGCA 58.494 33.333 0.00 0.00 0.00 3.96
283 285 1.066752 CATGCATCCCATGGCAACG 59.933 57.895 6.09 0.00 46.09 4.10
296 298 3.081133 CAACGTCGGAATCGCCTG 58.919 61.111 0.00 0.00 36.13 4.85
327 329 4.117685 ACACGAAGACACTGAAACCTAAC 58.882 43.478 0.00 0.00 0.00 2.34
330 332 5.064198 CACGAAGACACTGAAACCTAACAAA 59.936 40.000 0.00 0.00 0.00 2.83
359 361 0.773644 AAGTCCCTGTGCAACTCCAT 59.226 50.000 0.00 0.00 38.04 3.41
361 363 0.036732 GTCCCTGTGCAACTCCATGA 59.963 55.000 0.00 0.00 38.04 3.07
376 378 1.153369 ATGATCCCGTGCGTTCCAG 60.153 57.895 0.00 0.00 0.00 3.86
377 379 3.195698 GATCCCGTGCGTTCCAGC 61.196 66.667 0.00 0.00 37.71 4.85
391 393 0.035598 TCCAGCGTGGAAAATCGGAA 59.964 50.000 4.51 0.00 45.00 4.30
394 396 1.128692 CAGCGTGGAAAATCGGAAGTC 59.871 52.381 0.00 0.00 0.00 3.01
413 415 2.446341 GGAGACGAGGAAAACAGCG 58.554 57.895 0.00 0.00 0.00 5.18
415 417 0.038526 GAGACGAGGAAAACAGCGGA 60.039 55.000 0.00 0.00 0.00 5.54
417 419 0.511653 GACGAGGAAAACAGCGGAAC 59.488 55.000 0.00 0.00 0.00 3.62
447 450 0.818040 GAAGTGGGCTTTGTGTCCGT 60.818 55.000 0.00 0.00 45.26 4.69
469 472 3.708403 AGGGTTTTTCCTAGGTTACGG 57.292 47.619 9.08 0.00 34.92 4.02
557 568 8.825667 TCTTTATCCTGCAAATTAAACAAACC 57.174 30.769 0.00 0.00 0.00 3.27
560 571 5.622346 TCCTGCAAATTAAACAAACCCTT 57.378 34.783 0.00 0.00 0.00 3.95
562 573 7.125792 TCCTGCAAATTAAACAAACCCTTTA 57.874 32.000 0.00 0.00 0.00 1.85
563 574 7.565680 TCCTGCAAATTAAACAAACCCTTTAA 58.434 30.769 0.00 0.00 0.00 1.52
594 637 3.452627 CCTAAGGAATGTAGTCTGTGCCT 59.547 47.826 0.00 0.00 0.00 4.75
603 646 3.876914 TGTAGTCTGTGCCTCACAAAAAG 59.123 43.478 1.14 0.00 44.08 2.27
605 648 3.209410 AGTCTGTGCCTCACAAAAAGAG 58.791 45.455 1.14 0.00 44.08 2.85
619 662 9.618890 CTCACAAAAAGAGGAATATAATCTGGA 57.381 33.333 0.00 0.00 0.00 3.86
620 663 9.396022 TCACAAAAAGAGGAATATAATCTGGAC 57.604 33.333 0.00 0.00 0.00 4.02
621 664 8.338259 CACAAAAAGAGGAATATAATCTGGACG 58.662 37.037 0.00 0.00 0.00 4.79
622 665 8.047310 ACAAAAAGAGGAATATAATCTGGACGT 58.953 33.333 0.00 0.00 0.00 4.34
623 666 8.552034 CAAAAAGAGGAATATAATCTGGACGTC 58.448 37.037 7.13 7.13 0.00 4.34
624 667 5.630661 AGAGGAATATAATCTGGACGTCG 57.369 43.478 9.92 0.00 0.00 5.12
625 668 5.071370 AGAGGAATATAATCTGGACGTCGT 58.929 41.667 9.92 0.00 0.00 4.34
626 669 5.535406 AGAGGAATATAATCTGGACGTCGTT 59.465 40.000 9.92 4.57 0.00 3.85
627 670 6.040616 AGAGGAATATAATCTGGACGTCGTTT 59.959 38.462 9.92 3.04 0.00 3.60
628 671 6.579865 AGGAATATAATCTGGACGTCGTTTT 58.420 36.000 9.92 3.39 0.00 2.43
629 672 7.046033 AGGAATATAATCTGGACGTCGTTTTT 58.954 34.615 9.92 3.75 0.00 1.94
630 673 7.224167 AGGAATATAATCTGGACGTCGTTTTTC 59.776 37.037 9.92 3.30 0.00 2.29
631 674 7.224167 GGAATATAATCTGGACGTCGTTTTTCT 59.776 37.037 9.92 0.00 0.00 2.52
632 675 5.779806 ATAATCTGGACGTCGTTTTTCTG 57.220 39.130 9.92 0.00 0.00 3.02
633 676 2.875087 TCTGGACGTCGTTTTTCTGA 57.125 45.000 9.92 1.26 0.00 3.27
634 677 3.380479 TCTGGACGTCGTTTTTCTGAT 57.620 42.857 9.92 0.00 0.00 2.90
635 678 3.314553 TCTGGACGTCGTTTTTCTGATC 58.685 45.455 9.92 0.00 0.00 2.92
636 679 2.409975 TGGACGTCGTTTTTCTGATCC 58.590 47.619 9.92 0.00 0.00 3.36
637 680 1.730612 GGACGTCGTTTTTCTGATCCC 59.269 52.381 9.92 0.00 0.00 3.85
638 681 1.389106 GACGTCGTTTTTCTGATCCCG 59.611 52.381 0.00 0.00 0.00 5.14
639 682 1.000060 ACGTCGTTTTTCTGATCCCGA 60.000 47.619 0.00 0.00 0.00 5.14
640 683 1.654105 CGTCGTTTTTCTGATCCCGAG 59.346 52.381 0.00 0.00 0.00 4.63
641 684 1.393883 GTCGTTTTTCTGATCCCGAGC 59.606 52.381 0.00 0.00 0.00 5.03
642 685 1.275291 TCGTTTTTCTGATCCCGAGCT 59.725 47.619 0.00 0.00 0.00 4.09
643 686 1.661112 CGTTTTTCTGATCCCGAGCTC 59.339 52.381 2.73 2.73 0.00 4.09
644 687 2.699954 GTTTTTCTGATCCCGAGCTCA 58.300 47.619 15.40 0.00 0.00 4.26
645 688 2.386661 TTTTCTGATCCCGAGCTCAC 57.613 50.000 15.40 0.00 0.00 3.51
646 689 1.266178 TTTCTGATCCCGAGCTCACA 58.734 50.000 15.40 4.66 0.00 3.58
647 690 1.489481 TTCTGATCCCGAGCTCACAT 58.511 50.000 15.40 1.32 0.00 3.21
648 691 0.749049 TCTGATCCCGAGCTCACATG 59.251 55.000 15.40 0.00 0.00 3.21
649 692 0.749049 CTGATCCCGAGCTCACATGA 59.251 55.000 15.40 4.26 0.00 3.07
650 693 0.749049 TGATCCCGAGCTCACATGAG 59.251 55.000 15.40 4.43 44.75 2.90
661 704 2.898705 CTCACATGAGCTAGGGTGAAC 58.101 52.381 12.97 0.00 39.53 3.18
662 705 2.234661 CTCACATGAGCTAGGGTGAACA 59.765 50.000 12.97 0.00 39.53 3.18
663 706 2.234661 TCACATGAGCTAGGGTGAACAG 59.765 50.000 10.39 0.00 37.33 3.16
664 707 2.027745 CACATGAGCTAGGGTGAACAGT 60.028 50.000 0.00 0.00 33.16 3.55
665 708 3.195610 CACATGAGCTAGGGTGAACAGTA 59.804 47.826 0.00 0.00 33.16 2.74
666 709 3.838317 ACATGAGCTAGGGTGAACAGTAA 59.162 43.478 0.00 0.00 0.00 2.24
667 710 4.286032 ACATGAGCTAGGGTGAACAGTAAA 59.714 41.667 0.00 0.00 0.00 2.01
668 711 4.967084 TGAGCTAGGGTGAACAGTAAAA 57.033 40.909 0.00 0.00 0.00 1.52
669 712 5.499004 TGAGCTAGGGTGAACAGTAAAAT 57.501 39.130 0.00 0.00 0.00 1.82
670 713 6.614694 TGAGCTAGGGTGAACAGTAAAATA 57.385 37.500 0.00 0.00 0.00 1.40
671 714 7.011499 TGAGCTAGGGTGAACAGTAAAATAA 57.989 36.000 0.00 0.00 0.00 1.40
672 715 7.455058 TGAGCTAGGGTGAACAGTAAAATAAA 58.545 34.615 0.00 0.00 0.00 1.40
673 716 7.940137 TGAGCTAGGGTGAACAGTAAAATAAAA 59.060 33.333 0.00 0.00 0.00 1.52
674 717 8.700439 AGCTAGGGTGAACAGTAAAATAAAAA 57.300 30.769 0.00 0.00 0.00 1.94
735 778 7.953158 TGTGAAACTTTGACAAATGTTTTGA 57.047 28.000 19.95 12.48 41.29 2.69
736 779 8.545229 TGTGAAACTTTGACAAATGTTTTGAT 57.455 26.923 19.95 7.11 41.29 2.57
737 780 9.645059 TGTGAAACTTTGACAAATGTTTTGATA 57.355 25.926 19.95 11.47 41.29 2.15
739 782 9.868277 TGAAACTTTGACAAATGTTTTGATAGT 57.132 25.926 19.95 3.95 41.29 2.12
743 786 8.603181 ACTTTGACAAATGTTTTGATAGTTTGC 58.397 29.630 0.05 0.00 34.12 3.68
744 787 8.484641 TTTGACAAATGTTTTGATAGTTTGCA 57.515 26.923 6.96 0.00 34.12 4.08
745 788 8.484641 TTGACAAATGTTTTGATAGTTTGCAA 57.515 26.923 6.96 0.00 34.12 4.08
746 789 8.484641 TGACAAATGTTTTGATAGTTTGCAAA 57.515 26.923 8.05 8.05 34.12 3.68
747 790 8.939929 TGACAAATGTTTTGATAGTTTGCAAAA 58.060 25.926 14.67 0.00 40.50 2.44
748 791 9.934190 GACAAATGTTTTGATAGTTTGCAAAAT 57.066 25.926 17.11 17.11 43.37 1.82
749 792 9.934190 ACAAATGTTTTGATAGTTTGCAAAATC 57.066 25.926 16.40 15.19 43.37 2.17
752 795 9.545105 AATGTTTTGATAGTTTGCAAAATCTCA 57.455 25.926 19.69 19.69 43.37 3.27
753 796 9.715121 ATGTTTTGATAGTTTGCAAAATCTCAT 57.285 25.926 22.80 16.75 43.37 2.90
754 797 8.980610 TGTTTTGATAGTTTGCAAAATCTCATG 58.019 29.630 22.80 0.00 43.37 3.07
755 798 8.981647 GTTTTGATAGTTTGCAAAATCTCATGT 58.018 29.630 22.80 3.68 43.37 3.21
756 799 8.523523 TTTGATAGTTTGCAAAATCTCATGTG 57.476 30.769 22.80 0.00 31.64 3.21
757 800 7.451501 TGATAGTTTGCAAAATCTCATGTGA 57.548 32.000 19.69 0.00 0.00 3.58
758 801 7.307694 TGATAGTTTGCAAAATCTCATGTGAC 58.692 34.615 19.69 2.98 0.00 3.67
759 802 4.874970 AGTTTGCAAAATCTCATGTGACC 58.125 39.130 14.67 0.00 0.00 4.02
760 803 4.586001 AGTTTGCAAAATCTCATGTGACCT 59.414 37.500 14.67 0.00 0.00 3.85
761 804 4.771590 TTGCAAAATCTCATGTGACCTC 57.228 40.909 0.00 0.00 0.00 3.85
762 805 2.743664 TGCAAAATCTCATGTGACCTCG 59.256 45.455 0.00 0.00 0.00 4.63
763 806 2.096496 GCAAAATCTCATGTGACCTCGG 59.904 50.000 0.00 0.00 0.00 4.63
764 807 3.599343 CAAAATCTCATGTGACCTCGGA 58.401 45.455 0.00 0.00 0.00 4.55
765 808 3.981071 AAATCTCATGTGACCTCGGAA 57.019 42.857 0.00 0.00 0.00 4.30
766 809 4.494091 AAATCTCATGTGACCTCGGAAT 57.506 40.909 0.00 0.00 0.00 3.01
767 810 4.494091 AATCTCATGTGACCTCGGAATT 57.506 40.909 0.00 0.00 0.00 2.17
768 811 5.614324 AATCTCATGTGACCTCGGAATTA 57.386 39.130 0.00 0.00 0.00 1.40
769 812 4.655762 TCTCATGTGACCTCGGAATTAG 57.344 45.455 0.00 0.00 0.00 1.73
770 813 4.278310 TCTCATGTGACCTCGGAATTAGA 58.722 43.478 0.00 0.00 0.00 2.10
771 814 4.709886 TCTCATGTGACCTCGGAATTAGAA 59.290 41.667 0.00 0.00 0.00 2.10
772 815 4.755411 TCATGTGACCTCGGAATTAGAAC 58.245 43.478 0.00 0.00 0.00 3.01
773 816 4.221924 TCATGTGACCTCGGAATTAGAACA 59.778 41.667 0.00 0.00 0.00 3.18
774 817 4.819105 TGTGACCTCGGAATTAGAACAT 57.181 40.909 0.00 0.00 0.00 2.71
775 818 4.755411 TGTGACCTCGGAATTAGAACATC 58.245 43.478 0.00 0.00 0.00 3.06
776 819 4.221924 TGTGACCTCGGAATTAGAACATCA 59.778 41.667 0.00 0.00 0.00 3.07
777 820 4.567159 GTGACCTCGGAATTAGAACATCAC 59.433 45.833 0.00 0.00 0.00 3.06
778 821 4.466370 TGACCTCGGAATTAGAACATCACT 59.534 41.667 0.00 0.00 0.00 3.41
779 822 5.046591 TGACCTCGGAATTAGAACATCACTT 60.047 40.000 0.00 0.00 0.00 3.16
780 823 5.805728 ACCTCGGAATTAGAACATCACTTT 58.194 37.500 0.00 0.00 0.00 2.66
781 824 5.875359 ACCTCGGAATTAGAACATCACTTTC 59.125 40.000 0.00 0.00 0.00 2.62
795 838 8.723942 AACATCACTTTCAATATAGTCTGTCC 57.276 34.615 0.00 0.00 0.00 4.02
796 839 8.083828 ACATCACTTTCAATATAGTCTGTCCT 57.916 34.615 0.00 0.00 0.00 3.85
836 883 2.068834 TAGTCGTCTCCCTGGGAATC 57.931 55.000 17.81 11.36 0.00 2.52
844 891 2.317900 TCTCCCTGGGAATCTAGAACCA 59.682 50.000 17.81 14.73 0.00 3.67
870 917 9.542462 AAAAGAGGCCTTAAAATCTGTAAAAAC 57.458 29.630 6.77 0.00 31.15 2.43
887 935 0.392706 AACTGCTGATGACGTGGTGA 59.607 50.000 0.00 0.00 0.00 4.02
900 948 0.893727 GTGGTGACCCAAAGCCGAAT 60.894 55.000 0.00 0.00 44.15 3.34
922 970 1.075482 CTTGGCCCAAAGCAGAGGA 59.925 57.895 0.00 0.00 46.50 3.71
923 971 1.228552 TTGGCCCAAAGCAGAGGAC 60.229 57.895 0.00 0.00 46.50 3.85
1014 1102 2.279120 GAGATGGCGCGAGGAGTG 60.279 66.667 12.10 0.00 0.00 3.51
1073 1161 0.032130 GAGTATCAGGCGCGATCCAA 59.968 55.000 12.10 0.00 33.17 3.53
1077 1165 2.874648 ATCAGGCGCGATCCAAGCAA 62.875 55.000 12.10 0.00 34.19 3.91
1087 1175 2.735151 ATCCAAGCAAGCCTGGGCAA 62.735 55.000 14.39 0.00 44.88 4.52
1114 1202 0.820871 CTTCTTCTCCTCCACCTCCG 59.179 60.000 0.00 0.00 0.00 4.63
1140 1240 4.509737 GCCGGCTCCTCGTGGTAC 62.510 72.222 22.15 0.00 34.23 3.34
1187 1288 2.805099 GTTTCTCTCACAAGCCTGAGTG 59.195 50.000 0.00 0.00 39.08 3.51
1209 1310 7.916552 AGTGTTATGTTTCGATATTACCAAGC 58.083 34.615 0.00 0.00 0.00 4.01
1229 1330 5.426689 AGCTGAGGATGAATTAAGTGACA 57.573 39.130 0.00 0.00 0.00 3.58
1235 1336 9.166173 CTGAGGATGAATTAAGTGACAATACAA 57.834 33.333 0.00 0.00 0.00 2.41
1306 1423 5.171476 TCTTCATCTTGTTGTAGCTAGTGC 58.829 41.667 0.00 0.00 40.05 4.40
1392 1509 6.245115 TCACTTTTCATTGACTGCTGTATG 57.755 37.500 0.00 0.00 0.00 2.39
1401 1518 3.261580 TGACTGCTGTATGAATGAACCG 58.738 45.455 0.00 0.00 0.00 4.44
1466 1583 5.448654 TCATATAAACAAGCCCTGATTGCT 58.551 37.500 0.00 0.00 41.89 3.91
1467 1584 6.600388 TCATATAAACAAGCCCTGATTGCTA 58.400 36.000 0.00 0.00 38.34 3.49
1468 1585 6.712095 TCATATAAACAAGCCCTGATTGCTAG 59.288 38.462 0.00 0.00 38.34 3.42
1478 1595 4.571176 GCCCTGATTGCTAGTAGTGTTTAC 59.429 45.833 0.00 0.00 0.00 2.01
1530 1647 8.920665 TCCATAACAATCAAAGCAAAATAAACG 58.079 29.630 0.00 0.00 0.00 3.60
1537 1654 0.524414 AGCAAAATAAACGACGGGCC 59.476 50.000 0.00 0.00 0.00 5.80
1545 1662 2.736579 AAACGACGGGCCTACCAACC 62.737 60.000 0.84 0.00 40.22 3.77
1602 1719 8.218338 AGACAACATGAATATTCAGGATTGTC 57.782 34.615 34.99 34.99 45.94 3.18
1607 1724 8.812513 ACATGAATATTCAGGATTGTCAGAAA 57.187 30.769 30.88 1.41 41.15 2.52
1646 1763 6.819284 AGAGATCATTTTCATGTCTCTCCTC 58.181 40.000 4.40 0.00 40.35 3.71
1660 1777 3.834813 TCTCTCCTCATTTGCACTACAGT 59.165 43.478 0.00 0.00 0.00 3.55
1689 1808 1.880340 GCTCGCATCCTGACTTCCG 60.880 63.158 0.00 0.00 0.00 4.30
1703 1822 5.229921 TGACTTCCGCAACTATTTTATGC 57.770 39.130 0.00 0.00 36.74 3.14
1726 1845 3.368571 GCTGCAGGGTTGAGGTGC 61.369 66.667 17.12 0.00 37.73 5.01
1740 1859 1.781786 AGGTGCTCCTCGTGATATGT 58.218 50.000 0.18 0.00 40.58 2.29
1925 2044 9.076596 GCTTCTTCCATTGTCAATGTAAAATAC 57.923 33.333 21.32 5.47 37.18 1.89
1977 2098 9.371136 TGTGAAATGCTCTCAGTTTAATACTAG 57.629 33.333 0.00 0.00 34.56 2.57
2217 2348 9.257651 GCCAGTTAACTACTATGTACTTATTGG 57.742 37.037 8.04 1.57 34.56 3.16
2272 2404 9.587772 TTAGTCAGATTTCAGTAATGCTCTAAC 57.412 33.333 0.00 0.00 0.00 2.34
2318 2451 8.938906 CCAAATATAGGCAAAAATATGAATGGC 58.061 33.333 0.00 0.00 38.51 4.40
2391 2524 8.581578 TCGATGCCAAGTTAACTGACATATATA 58.418 33.333 9.34 0.00 0.00 0.86
2471 2612 8.679288 AAATTTGCGATGTTTCTAGAATGAAG 57.321 30.769 5.89 0.00 0.00 3.02
2523 2676 4.217754 GCTGAACGAAATGTAACAACCA 57.782 40.909 0.00 0.00 0.00 3.67
2677 2864 2.200373 AGAAACGTAGGCCAGCATTT 57.800 45.000 5.01 0.00 0.00 2.32
2682 2869 3.899052 ACGTAGGCCAGCATTTAGTAA 57.101 42.857 5.01 0.00 0.00 2.24
2683 2870 4.417426 ACGTAGGCCAGCATTTAGTAAT 57.583 40.909 5.01 0.00 0.00 1.89
2684 2871 5.540400 ACGTAGGCCAGCATTTAGTAATA 57.460 39.130 5.01 0.00 0.00 0.98
2685 2872 5.920903 ACGTAGGCCAGCATTTAGTAATAA 58.079 37.500 5.01 0.00 0.00 1.40
2686 2873 6.531021 ACGTAGGCCAGCATTTAGTAATAAT 58.469 36.000 5.01 0.00 0.00 1.28
2687 2874 7.673180 ACGTAGGCCAGCATTTAGTAATAATA 58.327 34.615 5.01 0.00 0.00 0.98
2688 2875 8.152246 ACGTAGGCCAGCATTTAGTAATAATAA 58.848 33.333 5.01 0.00 0.00 1.40
2689 2876 9.162764 CGTAGGCCAGCATTTAGTAATAATAAT 57.837 33.333 5.01 0.00 0.00 1.28
2721 2908 3.680490 TGGTTTCATTAAGATGCGGACA 58.320 40.909 0.00 0.00 33.14 4.02
2839 3031 2.867624 AGTTTGGCTCTGCTTTCATCA 58.132 42.857 0.00 0.00 0.00 3.07
2916 3108 4.811364 GAAGGAGCTGGGCCCTGC 62.811 72.222 38.98 38.98 40.49 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.079127 GAGGGCACACGCATACACT 60.079 57.895 0.00 0.00 41.24 3.55
20 21 0.041312 CAAAAACTCGAGGGCACACG 60.041 55.000 18.41 0.00 0.00 4.49
23 24 1.404035 ACAACAAAAACTCGAGGGCAC 59.596 47.619 18.41 0.00 0.00 5.01
30 31 4.268522 CCAGACGTTACAACAAAAACTCG 58.731 43.478 0.00 0.00 0.00 4.18
35 36 3.810941 CCTAGCCAGACGTTACAACAAAA 59.189 43.478 0.00 0.00 0.00 2.44
38 39 1.965643 ACCTAGCCAGACGTTACAACA 59.034 47.619 0.00 0.00 0.00 3.33
44 45 1.374252 CGCAACCTAGCCAGACGTT 60.374 57.895 0.00 0.00 0.00 3.99
45 46 2.095978 AACGCAACCTAGCCAGACGT 62.096 55.000 0.00 0.00 0.00 4.34
51 52 2.044555 GGGGAAACGCAACCTAGCC 61.045 63.158 0.00 0.00 43.99 3.93
53 54 4.313819 GGGGGAAACGCAACCTAG 57.686 61.111 0.00 0.00 46.93 3.02
67 68 1.530655 AACAACGAGGCAAAGGGGG 60.531 57.895 0.00 0.00 0.00 5.40
100 101 3.477530 ACAAAGTCCTAGCCAAAGACAC 58.522 45.455 0.00 0.00 32.82 3.67
168 169 7.542130 GTCCAATGCGAATAAGACAAGAATTTT 59.458 33.333 1.65 0.00 0.00 1.82
172 173 5.000591 TGTCCAATGCGAATAAGACAAGAA 58.999 37.500 6.04 0.00 31.70 2.52
244 246 8.506437 TGCATGAGAGTTAGTTTCAAAATAGTG 58.494 33.333 0.00 0.00 0.00 2.74
248 250 7.363268 GGGATGCATGAGAGTTAGTTTCAAAAT 60.363 37.037 2.46 0.00 0.00 1.82
268 270 2.800736 GACGTTGCCATGGGATGC 59.199 61.111 15.13 6.07 0.00 3.91
270 272 2.124736 CCGACGTTGCCATGGGAT 60.125 61.111 15.13 0.00 0.00 3.85
283 285 2.552585 TTCGTCCAGGCGATTCCGAC 62.553 60.000 6.79 0.00 46.21 4.79
296 298 1.257155 GTGTCTTCGTGTTGTTCGTCC 59.743 52.381 0.00 0.00 0.00 4.79
327 329 5.238583 CACAGGGACTTTAGGTCTAGTTTG 58.761 45.833 0.00 0.00 43.97 2.93
330 332 2.832733 GCACAGGGACTTTAGGTCTAGT 59.167 50.000 0.00 0.00 43.97 2.57
347 349 0.392863 CGGGATCATGGAGTTGCACA 60.393 55.000 0.00 0.00 0.00 4.57
349 351 0.392863 CACGGGATCATGGAGTTGCA 60.393 55.000 0.00 0.00 0.00 4.08
350 352 1.718757 GCACGGGATCATGGAGTTGC 61.719 60.000 0.00 0.00 0.00 4.17
359 361 2.264480 CTGGAACGCACGGGATCA 59.736 61.111 0.00 0.00 0.00 2.92
376 378 0.094730 CGACTTCCGATTTTCCACGC 59.905 55.000 0.00 0.00 41.76 5.34
377 379 0.719465 CCGACTTCCGATTTTCCACG 59.281 55.000 0.00 0.00 41.76 4.94
378 380 2.000447 CTCCGACTTCCGATTTTCCAC 59.000 52.381 0.00 0.00 41.76 4.02
379 381 1.897133 TCTCCGACTTCCGATTTTCCA 59.103 47.619 0.00 0.00 41.76 3.53
391 393 1.269998 CTGTTTTCCTCGTCTCCGACT 59.730 52.381 0.00 0.00 38.40 4.18
394 396 1.344942 CGCTGTTTTCCTCGTCTCCG 61.345 60.000 0.00 0.00 0.00 4.63
413 415 1.449070 CTTCCCTAACGGCCGTTCC 60.449 63.158 44.24 0.00 39.31 3.62
415 417 1.004200 CACTTCCCTAACGGCCGTT 60.004 57.895 41.91 41.91 41.65 4.44
417 419 2.125269 CCACTTCCCTAACGGCCG 60.125 66.667 26.86 26.86 0.00 6.13
418 420 2.271173 CCCACTTCCCTAACGGCC 59.729 66.667 0.00 0.00 0.00 6.13
419 421 2.437895 GCCCACTTCCCTAACGGC 60.438 66.667 0.00 0.00 0.00 5.68
420 422 0.037734 AAAGCCCACTTCCCTAACGG 59.962 55.000 0.00 0.00 34.05 4.44
421 423 1.165270 CAAAGCCCACTTCCCTAACG 58.835 55.000 0.00 0.00 34.05 3.18
422 424 1.886542 CACAAAGCCCACTTCCCTAAC 59.113 52.381 0.00 0.00 34.05 2.34
423 425 1.497286 ACACAAAGCCCACTTCCCTAA 59.503 47.619 0.00 0.00 34.05 2.69
424 426 1.073284 GACACAAAGCCCACTTCCCTA 59.927 52.381 0.00 0.00 34.05 3.53
447 450 4.843516 TCCGTAACCTAGGAAAAACCCTAA 59.156 41.667 17.98 0.00 38.26 2.69
522 532 7.701539 TTTGCAGGATAAAGAGCATAGAAAA 57.298 32.000 0.00 0.00 36.80 2.29
531 541 8.925700 GGTTTGTTTAATTTGCAGGATAAAGAG 58.074 33.333 0.00 0.00 0.00 2.85
533 543 7.877612 AGGGTTTGTTTAATTTGCAGGATAAAG 59.122 33.333 0.00 0.00 0.00 1.85
582 625 4.127171 TCTTTTTGTGAGGCACAGACTAC 58.873 43.478 0.24 0.00 45.39 2.73
594 637 9.396022 GTCCAGATTATATTCCTCTTTTTGTGA 57.604 33.333 0.00 0.00 0.00 3.58
603 646 5.373981 ACGACGTCCAGATTATATTCCTC 57.626 43.478 10.58 0.00 0.00 3.71
605 648 6.839820 AAAACGACGTCCAGATTATATTCC 57.160 37.500 10.58 0.00 0.00 3.01
607 650 7.762615 TCAGAAAAACGACGTCCAGATTATATT 59.237 33.333 10.58 0.00 0.00 1.28
608 651 7.262772 TCAGAAAAACGACGTCCAGATTATAT 58.737 34.615 10.58 0.00 0.00 0.86
609 652 6.623486 TCAGAAAAACGACGTCCAGATTATA 58.377 36.000 10.58 0.00 0.00 0.98
610 653 5.475719 TCAGAAAAACGACGTCCAGATTAT 58.524 37.500 10.58 0.00 0.00 1.28
611 654 4.873817 TCAGAAAAACGACGTCCAGATTA 58.126 39.130 10.58 0.00 0.00 1.75
612 655 3.724374 TCAGAAAAACGACGTCCAGATT 58.276 40.909 10.58 0.27 0.00 2.40
613 656 3.380479 TCAGAAAAACGACGTCCAGAT 57.620 42.857 10.58 0.00 0.00 2.90
614 657 2.875087 TCAGAAAAACGACGTCCAGA 57.125 45.000 10.58 0.00 0.00 3.86
615 658 2.412089 GGATCAGAAAAACGACGTCCAG 59.588 50.000 10.58 0.00 0.00 3.86
616 659 2.409975 GGATCAGAAAAACGACGTCCA 58.590 47.619 10.58 0.00 0.00 4.02
617 660 1.730612 GGGATCAGAAAAACGACGTCC 59.269 52.381 10.58 0.00 0.00 4.79
618 661 1.389106 CGGGATCAGAAAAACGACGTC 59.611 52.381 5.18 5.18 0.00 4.34
619 662 1.000060 TCGGGATCAGAAAAACGACGT 60.000 47.619 0.00 0.00 0.00 4.34
620 663 1.654105 CTCGGGATCAGAAAAACGACG 59.346 52.381 0.00 0.00 0.00 5.12
621 664 1.393883 GCTCGGGATCAGAAAAACGAC 59.606 52.381 0.00 0.00 0.00 4.34
622 665 1.275291 AGCTCGGGATCAGAAAAACGA 59.725 47.619 0.00 0.00 0.00 3.85
623 666 1.661112 GAGCTCGGGATCAGAAAAACG 59.339 52.381 0.00 0.00 0.00 3.60
624 667 2.416893 GTGAGCTCGGGATCAGAAAAAC 59.583 50.000 1.92 0.00 38.62 2.43
625 668 2.038426 TGTGAGCTCGGGATCAGAAAAA 59.962 45.455 1.92 0.00 38.62 1.94
626 669 1.623311 TGTGAGCTCGGGATCAGAAAA 59.377 47.619 1.92 0.00 38.62 2.29
627 670 1.266178 TGTGAGCTCGGGATCAGAAA 58.734 50.000 1.92 0.00 38.62 2.52
628 671 1.137675 CATGTGAGCTCGGGATCAGAA 59.862 52.381 1.92 0.00 38.62 3.02
629 672 0.749049 CATGTGAGCTCGGGATCAGA 59.251 55.000 1.92 1.80 38.62 3.27
630 673 0.749049 TCATGTGAGCTCGGGATCAG 59.251 55.000 1.92 0.00 38.62 2.90
631 674 0.749049 CTCATGTGAGCTCGGGATCA 59.251 55.000 0.00 0.00 35.34 2.92
632 675 3.584586 CTCATGTGAGCTCGGGATC 57.415 57.895 9.64 0.00 35.13 3.36
641 684 2.234661 TGTTCACCCTAGCTCATGTGAG 59.765 50.000 5.66 5.66 44.75 3.51
642 685 2.234661 CTGTTCACCCTAGCTCATGTGA 59.765 50.000 7.75 7.75 36.04 3.58
643 686 2.027745 ACTGTTCACCCTAGCTCATGTG 60.028 50.000 0.00 0.00 0.00 3.21
644 687 2.260822 ACTGTTCACCCTAGCTCATGT 58.739 47.619 0.00 0.00 0.00 3.21
645 688 4.471904 TTACTGTTCACCCTAGCTCATG 57.528 45.455 0.00 0.00 0.00 3.07
646 689 5.499004 TTTTACTGTTCACCCTAGCTCAT 57.501 39.130 0.00 0.00 0.00 2.90
647 690 4.967084 TTTTACTGTTCACCCTAGCTCA 57.033 40.909 0.00 0.00 0.00 4.26
648 691 7.916914 TTTATTTTACTGTTCACCCTAGCTC 57.083 36.000 0.00 0.00 0.00 4.09
649 692 8.700439 TTTTTATTTTACTGTTCACCCTAGCT 57.300 30.769 0.00 0.00 0.00 3.32
677 720 8.709386 TTCGGAATTTTCTGAAATTGTTTTCA 57.291 26.923 11.25 1.63 46.46 2.69
709 752 9.645059 TCAAAACATTTGTCAAAGTTTCACATA 57.355 25.926 18.13 0.00 33.45 2.29
710 753 8.545229 TCAAAACATTTGTCAAAGTTTCACAT 57.455 26.923 18.13 7.39 33.45 3.21
711 754 7.953158 TCAAAACATTTGTCAAAGTTTCACA 57.047 28.000 18.13 0.00 33.45 3.58
713 756 9.868277 ACTATCAAAACATTTGTCAAAGTTTCA 57.132 25.926 18.13 12.32 33.45 2.69
717 760 8.603181 GCAAACTATCAAAACATTTGTCAAAGT 58.397 29.630 4.03 0.09 33.70 2.66
718 761 8.602328 TGCAAACTATCAAAACATTTGTCAAAG 58.398 29.630 4.03 0.00 33.70 2.77
719 762 8.484641 TGCAAACTATCAAAACATTTGTCAAA 57.515 26.923 0.00 0.00 33.70 2.69
720 763 8.484641 TTGCAAACTATCAAAACATTTGTCAA 57.515 26.923 0.00 0.00 33.70 3.18
721 764 8.484641 TTTGCAAACTATCAAAACATTTGTCA 57.515 26.923 8.05 0.00 33.70 3.58
722 765 9.934190 ATTTTGCAAACTATCAAAACATTTGTC 57.066 25.926 12.39 0.00 42.62 3.18
723 766 9.934190 GATTTTGCAAACTATCAAAACATTTGT 57.066 25.926 12.39 0.00 42.62 2.83
726 769 9.545105 TGAGATTTTGCAAACTATCAAAACATT 57.455 25.926 20.42 2.77 42.62 2.71
727 770 9.715121 ATGAGATTTTGCAAACTATCAAAACAT 57.285 25.926 24.61 18.05 42.62 2.71
728 771 8.980610 CATGAGATTTTGCAAACTATCAAAACA 58.019 29.630 24.61 17.04 42.62 2.83
729 772 8.981647 ACATGAGATTTTGCAAACTATCAAAAC 58.018 29.630 24.61 13.43 42.62 2.43
730 773 8.980610 CACATGAGATTTTGCAAACTATCAAAA 58.019 29.630 24.61 11.32 43.55 2.44
731 774 8.358895 TCACATGAGATTTTGCAAACTATCAAA 58.641 29.630 24.61 13.26 0.00 2.69
732 775 7.809331 GTCACATGAGATTTTGCAAACTATCAA 59.191 33.333 24.61 13.53 0.00 2.57
733 776 7.307694 GTCACATGAGATTTTGCAAACTATCA 58.692 34.615 23.52 23.52 0.00 2.15
734 777 6.749118 GGTCACATGAGATTTTGCAAACTATC 59.251 38.462 12.39 14.00 0.00 2.08
735 778 6.435277 AGGTCACATGAGATTTTGCAAACTAT 59.565 34.615 12.39 3.44 0.00 2.12
736 779 5.769662 AGGTCACATGAGATTTTGCAAACTA 59.230 36.000 12.39 0.00 0.00 2.24
737 780 4.586001 AGGTCACATGAGATTTTGCAAACT 59.414 37.500 12.39 6.55 0.00 2.66
738 781 4.874970 AGGTCACATGAGATTTTGCAAAC 58.125 39.130 12.39 0.98 0.00 2.93
739 782 4.320421 CGAGGTCACATGAGATTTTGCAAA 60.320 41.667 8.05 8.05 0.00 3.68
740 783 3.189080 CGAGGTCACATGAGATTTTGCAA 59.811 43.478 0.00 0.00 0.00 4.08
741 784 2.743664 CGAGGTCACATGAGATTTTGCA 59.256 45.455 0.00 0.00 0.00 4.08
742 785 2.096496 CCGAGGTCACATGAGATTTTGC 59.904 50.000 0.00 0.00 0.00 3.68
743 786 3.599343 TCCGAGGTCACATGAGATTTTG 58.401 45.455 0.00 0.00 0.00 2.44
744 787 3.981071 TCCGAGGTCACATGAGATTTT 57.019 42.857 0.00 0.00 0.00 1.82
745 788 3.981071 TTCCGAGGTCACATGAGATTT 57.019 42.857 0.00 0.00 0.00 2.17
746 789 4.494091 AATTCCGAGGTCACATGAGATT 57.506 40.909 0.00 0.00 0.00 2.40
747 790 4.895889 TCTAATTCCGAGGTCACATGAGAT 59.104 41.667 0.00 0.00 0.00 2.75
748 791 4.278310 TCTAATTCCGAGGTCACATGAGA 58.722 43.478 0.00 0.00 0.00 3.27
749 792 4.655762 TCTAATTCCGAGGTCACATGAG 57.344 45.455 0.00 0.00 0.00 2.90
750 793 4.221924 TGTTCTAATTCCGAGGTCACATGA 59.778 41.667 0.00 0.00 0.00 3.07
751 794 4.503910 TGTTCTAATTCCGAGGTCACATG 58.496 43.478 0.00 0.00 0.00 3.21
752 795 4.819105 TGTTCTAATTCCGAGGTCACAT 57.181 40.909 0.00 0.00 0.00 3.21
753 796 4.221924 TGATGTTCTAATTCCGAGGTCACA 59.778 41.667 0.00 0.00 0.00 3.58
754 797 4.567159 GTGATGTTCTAATTCCGAGGTCAC 59.433 45.833 0.00 0.00 0.00 3.67
755 798 4.466370 AGTGATGTTCTAATTCCGAGGTCA 59.534 41.667 0.00 0.00 0.00 4.02
756 799 5.012328 AGTGATGTTCTAATTCCGAGGTC 57.988 43.478 0.00 0.00 0.00 3.85
757 800 5.422214 AAGTGATGTTCTAATTCCGAGGT 57.578 39.130 0.00 0.00 0.00 3.85
758 801 5.874810 TGAAAGTGATGTTCTAATTCCGAGG 59.125 40.000 0.00 0.00 0.00 4.63
759 802 6.968131 TGAAAGTGATGTTCTAATTCCGAG 57.032 37.500 0.00 0.00 0.00 4.63
760 803 7.921786 ATTGAAAGTGATGTTCTAATTCCGA 57.078 32.000 0.00 0.00 0.00 4.55
768 811 9.593134 GACAGACTATATTGAAAGTGATGTTCT 57.407 33.333 0.00 0.00 0.00 3.01
769 812 8.821894 GGACAGACTATATTGAAAGTGATGTTC 58.178 37.037 0.00 0.00 0.00 3.18
770 813 8.543774 AGGACAGACTATATTGAAAGTGATGTT 58.456 33.333 0.00 0.00 0.00 2.71
771 814 8.083828 AGGACAGACTATATTGAAAGTGATGT 57.916 34.615 0.00 0.00 0.00 3.06
772 815 8.954950 AAGGACAGACTATATTGAAAGTGATG 57.045 34.615 0.00 0.00 0.00 3.07
773 816 9.965902 AAAAGGACAGACTATATTGAAAGTGAT 57.034 29.630 0.00 0.00 0.00 3.06
774 817 9.793259 AAAAAGGACAGACTATATTGAAAGTGA 57.207 29.630 0.00 0.00 0.00 3.41
802 845 6.711645 GGAGACGACTATATTCCTTACAGTCT 59.288 42.308 0.00 0.00 37.85 3.24
822 869 2.701423 GGTTCTAGATTCCCAGGGAGAC 59.299 54.545 8.67 7.08 31.21 3.36
836 883 6.894339 TTTTAAGGCCTCTTTTGGTTCTAG 57.106 37.500 5.23 0.00 34.59 2.43
844 891 9.542462 GTTTTTACAGATTTTAAGGCCTCTTTT 57.458 29.630 5.23 0.00 34.59 2.27
870 917 1.016130 GGTCACCACGTCATCAGCAG 61.016 60.000 0.00 0.00 0.00 4.24
887 935 1.228552 AGCACATTCGGCTTTGGGT 60.229 52.632 0.00 0.00 38.81 4.51
900 948 2.443577 TGCTTTGGGCCAAGCACA 60.444 55.556 28.05 20.86 41.67 4.57
922 970 1.421646 GAGGAAATGGGGGATCGATGT 59.578 52.381 0.54 0.00 0.00 3.06
923 971 1.701847 AGAGGAAATGGGGGATCGATG 59.298 52.381 0.54 0.00 0.00 3.84
996 1084 3.893763 ACTCCTCGCGCCATCTCG 61.894 66.667 0.00 0.00 0.00 4.04
998 1086 3.842923 CCACTCCTCGCGCCATCT 61.843 66.667 0.00 0.00 0.00 2.90
1087 1175 0.827368 GAGGAGAAGAAGGATGCGGT 59.173 55.000 0.00 0.00 0.00 5.68
1140 1240 3.039202 CTTAGGGTTGGCGCTTGCG 62.039 63.158 7.64 10.90 40.46 4.85
1187 1288 8.138365 TCAGCTTGGTAATATCGAAACATAAC 57.862 34.615 0.00 0.00 0.00 1.89
1209 1310 8.722480 TGTATTGTCACTTAATTCATCCTCAG 57.278 34.615 0.00 0.00 0.00 3.35
1229 1330 6.976934 ATAATGGCCGATTTTCCTTGTATT 57.023 33.333 0.00 0.00 0.00 1.89
1235 1336 5.061721 ACCTAATAATGGCCGATTTTCCT 57.938 39.130 0.00 0.00 0.00 3.36
1275 1392 6.595716 GCTACAACAAGATGAAGAACTATGGT 59.404 38.462 0.00 0.00 0.00 3.55
1306 1423 2.214376 TTGGGCAGGTAACAATCCAG 57.786 50.000 0.00 0.00 41.41 3.86
1392 1509 4.985413 TGATCATTTTGCTCGGTTCATTC 58.015 39.130 0.00 0.00 0.00 2.67
1401 1518 8.915871 TTTAGCTTACAATGATCATTTTGCTC 57.084 30.769 24.71 14.04 0.00 4.26
1447 1564 4.860022 ACTAGCAATCAGGGCTTGTTTAT 58.140 39.130 0.00 0.00 43.08 1.40
1466 1583 4.873817 TGCTTTCGCAGTAAACACTACTA 58.126 39.130 0.00 0.00 42.25 1.82
1467 1584 3.724374 TGCTTTCGCAGTAAACACTACT 58.276 40.909 0.00 0.00 42.25 2.57
1515 1632 2.407026 GCCCGTCGTTTATTTTGCTTTG 59.593 45.455 0.00 0.00 0.00 2.77
1530 1647 2.120737 AACAGGTTGGTAGGCCCGTC 62.121 60.000 0.00 0.00 35.15 4.79
1537 1654 9.886132 ACTTGTAAATATAGAACAGGTTGGTAG 57.114 33.333 0.00 0.00 30.21 3.18
1571 1688 9.112725 TCCTGAATATTCATGTTGTCTTATGTG 57.887 33.333 18.26 2.14 36.46 3.21
1577 1694 7.830697 TGACAATCCTGAATATTCATGTTGTCT 59.169 33.333 34.98 21.56 39.96 3.41
1628 1745 6.034591 GCAAATGAGGAGAGACATGAAAATG 58.965 40.000 0.00 0.00 0.00 2.32
1646 1763 9.956797 GCAATAATTTAAACTGTAGTGCAAATG 57.043 29.630 16.64 0.00 37.46 2.32
1660 1777 6.318648 AGTCAGGATGCGAGCAATAATTTAAA 59.681 34.615 0.57 0.00 34.76 1.52
1703 1822 1.521450 CTCAACCCTGCAGCAACCAG 61.521 60.000 8.66 0.00 0.00 4.00
1726 1845 3.553511 GCAAGTTCACATATCACGAGGAG 59.446 47.826 0.00 0.00 0.00 3.69
1740 1859 5.551233 AGTAGAGCATACAAAGCAAGTTCA 58.449 37.500 2.43 0.00 0.00 3.18
1843 1962 4.264253 TCCTTGGTTAATCTCATGCACAG 58.736 43.478 0.00 0.00 0.00 3.66
2272 2404 2.749621 GGTCAGGCCAGTGAACAATAAG 59.250 50.000 5.01 0.00 34.00 1.73
2318 2451 9.825972 ATGAAACACAATTAACTCAGAAATACG 57.174 29.630 0.00 0.00 0.00 3.06
2391 2524 6.093633 ACTGAAACGTCTAAAAGCAAAAGAGT 59.906 34.615 0.00 0.00 0.00 3.24
2471 2612 5.355350 CCTCAACTACATCTGGTTGGAATTC 59.645 44.000 0.00 0.00 41.91 2.17
2512 2665 6.661377 TGTGCACCTATTATTGGTTGTTACAT 59.339 34.615 15.69 0.00 35.28 2.29
2513 2666 6.004574 TGTGCACCTATTATTGGTTGTTACA 58.995 36.000 15.69 0.00 35.28 2.41
2514 2667 6.503589 TGTGCACCTATTATTGGTTGTTAC 57.496 37.500 15.69 0.00 35.28 2.50
2515 2668 6.405286 GCATGTGCACCTATTATTGGTTGTTA 60.405 38.462 15.69 0.00 41.59 2.41
2516 2669 5.624281 GCATGTGCACCTATTATTGGTTGTT 60.624 40.000 15.69 0.00 41.59 2.83
2517 2670 4.142182 GCATGTGCACCTATTATTGGTTGT 60.142 41.667 15.69 0.00 41.59 3.32
2518 2671 4.362279 GCATGTGCACCTATTATTGGTTG 58.638 43.478 15.69 0.00 41.59 3.77
2519 2672 4.654091 GCATGTGCACCTATTATTGGTT 57.346 40.909 15.69 0.00 41.59 3.67
2548 2701 2.218953 TAACCTTCGCCATAAGCTCG 57.781 50.000 0.00 0.00 40.39 5.03
2652 2839 5.031066 TGCTGGCCTACGTTTCTTATATT 57.969 39.130 3.32 0.00 0.00 1.28
2653 2840 4.682778 TGCTGGCCTACGTTTCTTATAT 57.317 40.909 3.32 0.00 0.00 0.86
2699 2886 4.075682 TGTCCGCATCTTAATGAAACCAA 58.924 39.130 0.00 0.00 34.61 3.67
2721 2908 0.478942 TAGGCCCTCATCGCTAGACT 59.521 55.000 0.00 0.00 0.00 3.24
2813 3003 0.251077 AGCAGAGCCAAACTTCCCAG 60.251 55.000 0.00 0.00 0.00 4.45
2817 3007 3.254166 TGATGAAAGCAGAGCCAAACTTC 59.746 43.478 0.00 0.00 0.00 3.01
2839 3031 2.434428 CAGCAGCTCTTGGATCAGTTT 58.566 47.619 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.