Multiple sequence alignment - TraesCS4D01G047100

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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 TraesCS4D01G047100 chr4D 100.000 3934 0 0 1 3934 22578769 22582702 0.000000e+00 7265.0
1 TraesCS4D01G047100 chr4D 92.654 667 40 9 1 662 501151590 501150928 0.000000e+00 952.0
2 TraesCS4D01G047100 chr3B 85.813 2742 252 56 1267 3934 173386981 173384303 0.000000e+00 2782.0
3 TraesCS4D01G047100 chr3B 84.118 340 28 13 817 1145 173387616 173387292 4.940000e-79 305.0
4 TraesCS4D01G047100 chr3B 80.569 211 34 7 984 1188 173110900 173110691 5.260000e-34 156.0
5 TraesCS4D01G047100 chr3A 85.556 2790 250 56 1262 3934 128159974 128157221 0.000000e+00 2778.0
6 TraesCS4D01G047100 chr3A 81.399 586 55 26 1 581 405998210 405998746 2.810000e-116 429.0
7 TraesCS4D01G047100 chr3A 85.455 330 37 5 817 1145 128160591 128160272 2.270000e-87 333.0
8 TraesCS4D01G047100 chr3A 87.654 162 13 6 1 160 25489897 25490053 8.680000e-42 182.0
9 TraesCS4D01G047100 chr3A 75.431 232 36 16 2597 2812 127966125 127965899 4.190000e-15 93.5
10 TraesCS4D01G047100 chr3D 85.499 2324 191 56 1262 3492 121962673 121960403 0.000000e+00 2290.0
11 TraesCS4D01G047100 chr3D 83.299 479 47 12 817 1275 121963282 121962817 1.020000e-110 411.0
12 TraesCS4D01G047100 chr3D 81.737 449 69 8 3497 3934 121945343 121944897 2.890000e-96 363.0
13 TraesCS4D01G047100 chr3D 87.209 172 8 7 1 170 82551516 82551675 2.410000e-42 183.0
14 TraesCS4D01G047100 chr3D 81.991 211 31 7 984 1188 121538454 121538245 5.230000e-39 172.0
15 TraesCS4D01G047100 chr3D 88.679 106 8 4 2902 3003 121534731 121534626 4.130000e-25 126.0
16 TraesCS4D01G047100 chr4A 92.601 892 44 7 3051 3933 579525776 579524898 0.000000e+00 1262.0
17 TraesCS4D01G047100 chr4A 96.053 228 8 1 2831 3058 579526075 579525849 1.730000e-98 370.0
18 TraesCS4D01G047100 chr4B 87.898 785 72 11 1130 1908 34565393 34566160 0.000000e+00 902.0
19 TraesCS4D01G047100 chr4B 86.761 710 55 13 1911 2615 34567845 34568520 0.000000e+00 754.0
20 TraesCS4D01G047100 chr4B 93.671 395 16 3 2997 3388 34568923 34569311 2.040000e-162 582.0
21 TraesCS4D01G047100 chr4B 90.226 399 29 2 2565 2953 34568529 34568927 2.710000e-141 512.0
22 TraesCS4D01G047100 chr4B 90.780 141 8 3 672 808 34545682 34545821 2.410000e-42 183.0
23 TraesCS4D01G047100 chr5A 90.347 663 52 11 1 658 452521187 452520532 0.000000e+00 859.0
24 TraesCS4D01G047100 chr5A 93.728 574 30 4 90 658 296306477 296307049 0.000000e+00 856.0
25 TraesCS4D01G047100 chr5A 89.577 662 58 10 1 659 540847840 540848493 0.000000e+00 830.0
26 TraesCS4D01G047100 chr5D 93.739 575 30 4 90 660 170318366 170318938 0.000000e+00 857.0
27 TraesCS4D01G047100 chrUn 93.750 576 27 7 90 657 260712620 260712046 0.000000e+00 856.0
28 TraesCS4D01G047100 chrUn 88.805 661 63 11 1 658 229101125 229101777 0.000000e+00 800.0
29 TraesCS4D01G047100 chrUn 88.502 661 65 11 1 658 71597764 71598416 0.000000e+00 789.0
30 TraesCS4D01G047100 chr1D 93.520 571 32 5 90 658 301250935 301250368 0.000000e+00 845.0
31 TraesCS4D01G047100 chr1D 91.667 144 8 4 1 142 49610265 49610124 3.100000e-46 196.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G047100 chr4D 22578769 22582702 3933 False 7265.0 7265 100.0000 1 3934 1 chr4D.!!$F1 3933
1 TraesCS4D01G047100 chr4D 501150928 501151590 662 True 952.0 952 92.6540 1 662 1 chr4D.!!$R1 661
2 TraesCS4D01G047100 chr3B 173384303 173387616 3313 True 1543.5 2782 84.9655 817 3934 2 chr3B.!!$R2 3117
3 TraesCS4D01G047100 chr3A 128157221 128160591 3370 True 1555.5 2778 85.5055 817 3934 2 chr3A.!!$R2 3117
4 TraesCS4D01G047100 chr3A 405998210 405998746 536 False 429.0 429 81.3990 1 581 1 chr3A.!!$F2 580
5 TraesCS4D01G047100 chr3D 121960403 121963282 2879 True 1350.5 2290 84.3990 817 3492 2 chr3D.!!$R3 2675
6 TraesCS4D01G047100 chr4A 579524898 579526075 1177 True 816.0 1262 94.3270 2831 3933 2 chr4A.!!$R1 1102
7 TraesCS4D01G047100 chr4B 34565393 34569311 3918 False 687.5 902 89.6390 1130 3388 4 chr4B.!!$F2 2258
8 TraesCS4D01G047100 chr5A 452520532 452521187 655 True 859.0 859 90.3470 1 658 1 chr5A.!!$R1 657
9 TraesCS4D01G047100 chr5A 296306477 296307049 572 False 856.0 856 93.7280 90 658 1 chr5A.!!$F1 568
10 TraesCS4D01G047100 chr5A 540847840 540848493 653 False 830.0 830 89.5770 1 659 1 chr5A.!!$F2 658
11 TraesCS4D01G047100 chr5D 170318366 170318938 572 False 857.0 857 93.7390 90 660 1 chr5D.!!$F1 570
12 TraesCS4D01G047100 chrUn 260712046 260712620 574 True 856.0 856 93.7500 90 657 1 chrUn.!!$R1 567
13 TraesCS4D01G047100 chrUn 229101125 229101777 652 False 800.0 800 88.8050 1 658 1 chrUn.!!$F2 657
14 TraesCS4D01G047100 chrUn 71597764 71598416 652 False 789.0 789 88.5020 1 658 1 chrUn.!!$F1 657
15 TraesCS4D01G047100 chr1D 301250368 301250935 567 True 845.0 845 93.5200 90 658 1 chr1D.!!$R2 568

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
761 782 0.032615 AGTGTTGTCTTGGGCCCAAA 60.033 50.0 36.16 23.92 35.33 3.28 F
862 884 0.036858 AAGCGCAAAGTCTCTCCTCC 60.037 55.0 11.47 0.00 0.00 4.30 F
903 927 0.546747 ATCCCTCCCGGACAGAAACA 60.547 55.0 0.73 0.00 46.09 2.83 F
1017 1049 0.671251 AGATGGACTTCGCGGAGATC 59.329 55.0 24.16 13.95 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 3858 0.318441 CTGTTCTTCCTCGGTCTGCA 59.682 55.000 0.0 0.0 0.0 4.41 R
2074 3986 0.693049 AAGAGGGTACTTGCACTGGG 59.307 55.000 0.0 0.0 0.0 4.45 R
2716 4734 1.212935 ACTTGCAGGGTGAGACAAACT 59.787 47.619 0.0 0.0 0.0 2.66 R
2981 5008 1.701847 ACTGATTGGAGAGGCACAAGT 59.298 47.619 0.0 0.0 0.0 3.16 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
83 85 8.319585 GGAAAAACAAAACGCGTTTTCTATTTA 58.680 29.630 38.94 0.00 43.82 1.40
336 350 2.639327 GCACGGGCATGCCTCTTTT 61.639 57.895 34.70 12.87 39.86 2.27
438 456 6.938030 AGTTCGTTAAAACCTATCAACATGGA 59.062 34.615 0.00 0.00 0.00 3.41
619 640 1.299976 GCGACCTGGGAAAGTGGAT 59.700 57.895 0.00 0.00 0.00 3.41
662 683 6.758886 ACTCCTTAATTAGTGATTTCGCAGAG 59.241 38.462 0.00 0.00 38.43 3.35
663 684 6.873997 TCCTTAATTAGTGATTTCGCAGAGA 58.126 36.000 0.00 0.00 38.43 3.10
664 685 7.327975 TCCTTAATTAGTGATTTCGCAGAGAA 58.672 34.615 0.00 0.00 38.43 2.87
665 686 7.492669 TCCTTAATTAGTGATTTCGCAGAGAAG 59.507 37.037 0.00 0.00 40.40 2.85
666 687 7.492669 CCTTAATTAGTGATTTCGCAGAGAAGA 59.507 37.037 0.00 0.00 40.40 2.87
667 688 6.900568 AATTAGTGATTTCGCAGAGAAGAG 57.099 37.500 0.00 0.00 40.40 2.85
668 689 5.644977 TTAGTGATTTCGCAGAGAAGAGA 57.355 39.130 0.00 0.00 40.40 3.10
669 690 4.527509 AGTGATTTCGCAGAGAAGAGAA 57.472 40.909 0.00 0.00 40.40 2.87
670 691 4.887748 AGTGATTTCGCAGAGAAGAGAAA 58.112 39.130 0.00 0.00 40.61 2.52
671 692 4.928615 AGTGATTTCGCAGAGAAGAGAAAG 59.071 41.667 0.00 0.00 39.90 2.62
672 693 3.681897 TGATTTCGCAGAGAAGAGAAAGC 59.318 43.478 0.00 0.00 41.78 3.51
673 694 2.820059 TTCGCAGAGAAGAGAAAGCA 57.180 45.000 0.00 0.00 38.43 3.91
674 695 2.360553 TCGCAGAGAAGAGAAAGCAG 57.639 50.000 0.00 0.00 0.00 4.24
675 696 1.889170 TCGCAGAGAAGAGAAAGCAGA 59.111 47.619 0.00 0.00 0.00 4.26
676 697 2.297315 TCGCAGAGAAGAGAAAGCAGAA 59.703 45.455 0.00 0.00 0.00 3.02
677 698 3.062763 CGCAGAGAAGAGAAAGCAGAAA 58.937 45.455 0.00 0.00 0.00 2.52
678 699 3.496130 CGCAGAGAAGAGAAAGCAGAAAA 59.504 43.478 0.00 0.00 0.00 2.29
679 700 4.153835 CGCAGAGAAGAGAAAGCAGAAAAT 59.846 41.667 0.00 0.00 0.00 1.82
680 701 5.349817 CGCAGAGAAGAGAAAGCAGAAAATA 59.650 40.000 0.00 0.00 0.00 1.40
681 702 6.541969 GCAGAGAAGAGAAAGCAGAAAATAC 58.458 40.000 0.00 0.00 0.00 1.89
682 703 6.371271 GCAGAGAAGAGAAAGCAGAAAATACT 59.629 38.462 0.00 0.00 0.00 2.12
683 704 7.094848 GCAGAGAAGAGAAAGCAGAAAATACTT 60.095 37.037 0.00 0.00 0.00 2.24
684 705 8.442384 CAGAGAAGAGAAAGCAGAAAATACTTC 58.558 37.037 0.00 0.00 33.74 3.01
685 706 8.374743 AGAGAAGAGAAAGCAGAAAATACTTCT 58.625 33.333 0.00 0.00 42.29 2.85
686 707 8.916628 AGAAGAGAAAGCAGAAAATACTTCTT 57.083 30.769 0.00 0.00 38.47 2.52
690 711 9.950496 AGAGAAAGCAGAAAATACTTCTTATGA 57.050 29.630 0.00 0.00 0.00 2.15
695 716 9.994432 AAGCAGAAAATACTTCTTATGATTTCG 57.006 29.630 0.00 0.00 32.21 3.46
696 717 8.125448 AGCAGAAAATACTTCTTATGATTTCGC 58.875 33.333 0.00 0.00 32.21 4.70
697 718 7.910162 GCAGAAAATACTTCTTATGATTTCGCA 59.090 33.333 0.00 0.00 32.21 5.10
698 719 9.773328 CAGAAAATACTTCTTATGATTTCGCAA 57.227 29.630 0.00 0.00 32.21 4.85
705 726 7.182761 ACTTCTTATGATTTCGCAAAAGATCG 58.817 34.615 0.00 0.00 0.00 3.69
706 727 6.902224 TCTTATGATTTCGCAAAAGATCGA 57.098 33.333 0.00 0.00 0.00 3.59
707 728 7.482654 TCTTATGATTTCGCAAAAGATCGAT 57.517 32.000 0.00 0.00 34.48 3.59
708 729 8.587952 TCTTATGATTTCGCAAAAGATCGATA 57.412 30.769 0.00 0.00 34.48 2.92
709 730 9.040939 TCTTATGATTTCGCAAAAGATCGATAA 57.959 29.630 0.00 0.00 34.48 1.75
710 731 9.650371 CTTATGATTTCGCAAAAGATCGATAAA 57.350 29.630 0.00 0.00 34.48 1.40
712 733 8.719478 ATGATTTCGCAAAAGATCGATAAATC 57.281 30.769 14.70 14.70 33.42 2.17
713 734 7.693020 TGATTTCGCAAAAGATCGATAAATCA 58.307 30.769 18.13 18.13 36.98 2.57
714 735 8.180920 TGATTTCGCAAAAGATCGATAAATCAA 58.819 29.630 19.10 8.79 36.69 2.57
715 736 8.909708 ATTTCGCAAAAGATCGATAAATCAAA 57.090 26.923 0.00 0.00 34.48 2.69
716 737 7.719689 TTCGCAAAAGATCGATAAATCAAAC 57.280 32.000 0.00 0.00 34.48 2.93
717 738 6.836953 TCGCAAAAGATCGATAAATCAAACA 58.163 32.000 0.00 0.00 0.00 2.83
718 739 7.471721 TCGCAAAAGATCGATAAATCAAACAT 58.528 30.769 0.00 0.00 0.00 2.71
719 740 8.608317 TCGCAAAAGATCGATAAATCAAACATA 58.392 29.630 0.00 0.00 0.00 2.29
720 741 9.385902 CGCAAAAGATCGATAAATCAAACATAT 57.614 29.630 0.00 0.00 0.00 1.78
747 768 2.518349 CCAACCGGTGGCAGTGTT 60.518 61.111 8.52 0.00 41.72 3.32
748 769 2.721231 CAACCGGTGGCAGTGTTG 59.279 61.111 8.52 8.68 32.99 3.33
749 770 2.118404 CAACCGGTGGCAGTGTTGT 61.118 57.895 8.52 0.00 34.76 3.32
750 771 1.822186 AACCGGTGGCAGTGTTGTC 60.822 57.895 8.52 0.00 0.00 3.18
751 772 2.111043 CCGGTGGCAGTGTTGTCT 59.889 61.111 0.00 0.00 0.00 3.41
752 773 1.525995 CCGGTGGCAGTGTTGTCTT 60.526 57.895 0.00 0.00 0.00 3.01
753 774 1.648720 CGGTGGCAGTGTTGTCTTG 59.351 57.895 0.00 0.00 0.00 3.02
754 775 1.785041 CGGTGGCAGTGTTGTCTTGG 61.785 60.000 0.00 0.00 0.00 3.61
755 776 1.455383 GGTGGCAGTGTTGTCTTGGG 61.455 60.000 0.00 0.00 0.00 4.12
756 777 1.827789 TGGCAGTGTTGTCTTGGGC 60.828 57.895 0.00 0.00 0.00 5.36
757 778 2.564721 GGCAGTGTTGTCTTGGGCC 61.565 63.158 0.00 0.00 0.00 5.80
758 779 2.564721 GCAGTGTTGTCTTGGGCCC 61.565 63.158 17.59 17.59 0.00 5.80
759 780 1.152777 CAGTGTTGTCTTGGGCCCA 60.153 57.895 24.45 24.45 0.00 5.36
760 781 0.754957 CAGTGTTGTCTTGGGCCCAA 60.755 55.000 34.90 34.90 0.00 4.12
761 782 0.032615 AGTGTTGTCTTGGGCCCAAA 60.033 50.000 36.16 23.92 35.33 3.28
762 783 0.389025 GTGTTGTCTTGGGCCCAAAG 59.611 55.000 36.16 27.89 35.33 2.77
763 784 1.367471 GTTGTCTTGGGCCCAAAGC 59.633 57.895 36.16 29.20 42.60 3.51
772 793 3.313524 GCCCAAAGCCCCAACCAG 61.314 66.667 0.00 0.00 34.35 4.00
773 794 3.313524 CCCAAAGCCCCAACCAGC 61.314 66.667 0.00 0.00 0.00 4.85
774 795 2.523902 CCAAAGCCCCAACCAGCA 60.524 61.111 0.00 0.00 0.00 4.41
775 796 2.736531 CAAAGCCCCAACCAGCAC 59.263 61.111 0.00 0.00 0.00 4.40
776 797 1.833934 CAAAGCCCCAACCAGCACT 60.834 57.895 0.00 0.00 0.00 4.40
777 798 1.075301 AAAGCCCCAACCAGCACTT 60.075 52.632 0.00 0.00 0.00 3.16
778 799 1.115326 AAAGCCCCAACCAGCACTTC 61.115 55.000 0.00 0.00 0.00 3.01
779 800 2.203480 GCCCCAACCAGCACTTCA 60.203 61.111 0.00 0.00 0.00 3.02
780 801 2.270986 GCCCCAACCAGCACTTCAG 61.271 63.158 0.00 0.00 0.00 3.02
781 802 1.604593 CCCCAACCAGCACTTCAGG 60.605 63.158 0.00 0.00 0.00 3.86
782 803 1.604593 CCCAACCAGCACTTCAGGG 60.605 63.158 0.00 0.00 0.00 4.45
783 804 1.151450 CCAACCAGCACTTCAGGGT 59.849 57.895 0.00 0.00 34.43 4.34
784 805 0.890996 CCAACCAGCACTTCAGGGTC 60.891 60.000 0.00 0.00 32.01 4.46
785 806 0.890996 CAACCAGCACTTCAGGGTCC 60.891 60.000 0.00 0.00 32.01 4.46
786 807 1.352622 AACCAGCACTTCAGGGTCCA 61.353 55.000 0.00 0.00 32.01 4.02
787 808 1.352622 ACCAGCACTTCAGGGTCCAA 61.353 55.000 0.00 0.00 0.00 3.53
788 809 0.178992 CCAGCACTTCAGGGTCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
789 810 1.242076 CAGCACTTCAGGGTCCAAAG 58.758 55.000 0.00 0.00 0.00 2.77
790 811 0.846693 AGCACTTCAGGGTCCAAAGT 59.153 50.000 0.00 0.00 33.63 2.66
791 812 1.202818 AGCACTTCAGGGTCCAAAGTC 60.203 52.381 5.26 2.77 31.04 3.01
792 813 1.897560 CACTTCAGGGTCCAAAGTCC 58.102 55.000 5.26 0.00 31.04 3.85
793 814 1.142870 CACTTCAGGGTCCAAAGTCCA 59.857 52.381 5.26 0.00 31.04 4.02
794 815 1.850345 ACTTCAGGGTCCAAAGTCCAA 59.150 47.619 0.00 0.00 0.00 3.53
795 816 2.243736 ACTTCAGGGTCCAAAGTCCAAA 59.756 45.455 0.00 0.00 0.00 3.28
796 817 2.358322 TCAGGGTCCAAAGTCCAAAC 57.642 50.000 0.00 0.00 0.00 2.93
797 818 1.850345 TCAGGGTCCAAAGTCCAAACT 59.150 47.619 0.00 0.00 37.32 2.66
798 819 3.050089 TCAGGGTCCAAAGTCCAAACTA 58.950 45.455 0.00 0.00 33.48 2.24
799 820 3.460340 TCAGGGTCCAAAGTCCAAACTAA 59.540 43.478 0.00 0.00 33.48 2.24
800 821 3.568430 CAGGGTCCAAAGTCCAAACTAAC 59.432 47.826 0.00 0.00 33.48 2.34
801 822 2.551032 GGGTCCAAAGTCCAAACTAACG 59.449 50.000 0.00 0.00 33.48 3.18
802 823 3.469739 GGTCCAAAGTCCAAACTAACGA 58.530 45.455 0.00 0.00 33.48 3.85
803 824 3.497262 GGTCCAAAGTCCAAACTAACGAG 59.503 47.826 0.00 0.00 33.48 4.18
804 825 4.374399 GTCCAAAGTCCAAACTAACGAGA 58.626 43.478 0.00 0.00 33.48 4.04
805 826 4.812626 GTCCAAAGTCCAAACTAACGAGAA 59.187 41.667 0.00 0.00 33.48 2.87
806 827 5.050295 GTCCAAAGTCCAAACTAACGAGAAG 60.050 44.000 0.00 0.00 33.48 2.85
807 828 4.814771 CCAAAGTCCAAACTAACGAGAAGT 59.185 41.667 0.00 0.00 33.48 3.01
808 829 5.296035 CCAAAGTCCAAACTAACGAGAAGTT 59.704 40.000 0.00 0.00 46.36 2.66
809 830 5.986004 AAGTCCAAACTAACGAGAAGTTG 57.014 39.130 0.00 0.00 44.01 3.16
810 831 5.272283 AGTCCAAACTAACGAGAAGTTGA 57.728 39.130 0.00 0.00 44.01 3.18
811 832 5.855045 AGTCCAAACTAACGAGAAGTTGAT 58.145 37.500 0.00 0.00 44.01 2.57
812 833 6.289064 AGTCCAAACTAACGAGAAGTTGATT 58.711 36.000 0.00 0.00 44.01 2.57
813 834 6.424207 AGTCCAAACTAACGAGAAGTTGATTC 59.576 38.462 0.00 0.00 44.01 2.52
814 835 5.404366 TCCAAACTAACGAGAAGTTGATTCG 59.596 40.000 0.00 0.00 44.01 3.34
820 841 4.358494 ACGAGAAGTTGATTCGTCCTAG 57.642 45.455 0.00 0.00 43.35 3.02
835 856 2.749621 GTCCTAGACTTCCCGTTTCGTA 59.250 50.000 0.00 0.00 0.00 3.43
853 875 0.250727 TAGCCCAGAAAGCGCAAAGT 60.251 50.000 11.47 0.00 34.64 2.66
859 881 1.462670 CAGAAAGCGCAAAGTCTCTCC 59.537 52.381 11.47 0.00 0.00 3.71
860 882 1.346068 AGAAAGCGCAAAGTCTCTCCT 59.654 47.619 11.47 0.00 0.00 3.69
861 883 1.729517 GAAAGCGCAAAGTCTCTCCTC 59.270 52.381 11.47 0.00 0.00 3.71
862 884 0.036858 AAGCGCAAAGTCTCTCCTCC 60.037 55.000 11.47 0.00 0.00 4.30
863 885 0.902516 AGCGCAAAGTCTCTCCTCCT 60.903 55.000 11.47 0.00 0.00 3.69
865 887 1.181786 CGCAAAGTCTCTCCTCCTCT 58.818 55.000 0.00 0.00 0.00 3.69
866 888 1.135141 CGCAAAGTCTCTCCTCCTCTG 60.135 57.143 0.00 0.00 0.00 3.35
867 889 2.175202 GCAAAGTCTCTCCTCCTCTGA 58.825 52.381 0.00 0.00 0.00 3.27
869 891 2.495669 CAAAGTCTCTCCTCCTCTGACC 59.504 54.545 0.00 0.00 0.00 4.02
870 892 1.681229 AGTCTCTCCTCCTCTGACCT 58.319 55.000 0.00 0.00 0.00 3.85
874 896 0.851332 TCTCCTCCTCTGACCTCCCA 60.851 60.000 0.00 0.00 0.00 4.37
877 899 1.261238 CCTCCTCTGACCTCCCACAC 61.261 65.000 0.00 0.00 0.00 3.82
878 900 1.599606 CTCCTCTGACCTCCCACACG 61.600 65.000 0.00 0.00 0.00 4.49
903 927 0.546747 ATCCCTCCCGGACAGAAACA 60.547 55.000 0.73 0.00 46.09 2.83
909 933 1.507141 CCCGGACAGAAACACAGCAC 61.507 60.000 0.73 0.00 0.00 4.40
917 941 4.539083 AACACAGCACGGCCGACA 62.539 61.111 35.90 0.00 0.00 4.35
925 957 4.675029 ACGGCCGACAACCTTCCG 62.675 66.667 35.90 0.00 45.04 4.30
968 1000 3.000266 CCGTTAAATCGTCGGCGG 59.000 61.111 10.62 0.00 37.90 6.13
969 1001 1.516821 CCGTTAAATCGTCGGCGGA 60.517 57.895 10.62 0.00 41.45 5.54
970 1002 1.477030 CCGTTAAATCGTCGGCGGAG 61.477 60.000 10.62 0.91 41.45 4.63
1017 1049 0.671251 AGATGGACTTCGCGGAGATC 59.329 55.000 24.16 13.95 0.00 2.75
1018 1050 0.671251 GATGGACTTCGCGGAGATCT 59.329 55.000 24.16 0.00 0.00 2.75
1029 1061 1.135333 GCGGAGATCTCGAAGAAGGTT 59.865 52.381 16.46 0.00 34.09 3.50
1148 1213 2.716017 CCGTGTCTGAGGGAGGCTC 61.716 68.421 5.78 5.78 0.00 4.70
1201 1266 1.160137 GCAAAAGTCAGCCGACATCT 58.840 50.000 2.32 0.00 45.23 2.90
1216 1281 2.815945 ATCTCTGGAGGGCATGCGG 61.816 63.158 12.44 0.00 0.00 5.69
1245 1310 2.093106 GTCATAGAGGTCAGTGACGGT 58.907 52.381 16.89 6.82 32.64 4.83
1257 1322 0.966920 GTGACGGTGAGGAAGAGGAA 59.033 55.000 0.00 0.00 0.00 3.36
1277 1498 4.082081 GGAAATGGCTGTTGATGTCAATGA 60.082 41.667 0.00 0.00 38.24 2.57
1353 1577 2.357517 CGGGTGGTCAGTGACAGC 60.358 66.667 24.20 17.89 33.68 4.40
1458 1682 1.067915 GGAGTCAGTGACAGTGAGAGC 60.068 57.143 24.73 5.93 34.60 4.09
1478 1702 2.439156 GGATGGCAGTGAGGGTGC 60.439 66.667 0.00 0.00 40.42 5.01
1485 1709 1.069765 CAGTGAGGGTGCTCGTGTT 59.930 57.895 0.00 0.00 0.00 3.32
1547 1771 1.406898 TGAGAGTGAGGATGACGATGC 59.593 52.381 0.00 0.00 0.00 3.91
1559 1783 6.111382 AGGATGACGATGCTGAATTATATGG 58.889 40.000 0.00 0.00 0.00 2.74
1590 1814 3.842007 TGTTCTACTCCCGGAACAAAA 57.158 42.857 0.73 0.00 45.54 2.44
1591 1815 4.153673 TGTTCTACTCCCGGAACAAAAA 57.846 40.909 0.73 0.00 45.54 1.94
1596 1820 1.152922 TCCCGGAACAAAAAGGCGT 60.153 52.632 0.73 0.00 0.00 5.68
1617 1841 1.425412 TCGCTCGGTTAACTGAAAGC 58.575 50.000 17.63 16.38 37.60 3.51
1639 1863 3.181503 CCAATCAAAGAGAATGCGACCTG 60.182 47.826 0.00 0.00 0.00 4.00
1715 1939 8.811017 GGATGATTCAGAAGAGGATGATAGTAA 58.189 37.037 0.00 0.00 0.00 2.24
1791 2021 0.979665 CCTCAGCTGGACCAGAAGAA 59.020 55.000 26.25 5.95 32.44 2.52
1810 2040 7.911651 AGAAGAATCTGACAATGAGGAAACTA 58.088 34.615 0.00 0.00 35.78 2.24
1811 2041 8.547173 AGAAGAATCTGACAATGAGGAAACTAT 58.453 33.333 0.00 0.00 35.78 2.12
1845 2075 1.805120 GCTAGGATACGCGGCAAAAGA 60.805 52.381 12.47 0.00 46.39 2.52
1946 3858 3.535561 CTGTTTGTGCCCTCTATCGAAT 58.464 45.455 0.00 0.00 0.00 3.34
2021 3933 3.615155 GATTTAGCCAGATAGATGCCCC 58.385 50.000 0.00 0.00 0.00 5.80
2050 3962 8.965819 GGTATACCTTCTACTATTACTAAGGGC 58.034 40.741 15.09 0.00 40.86 5.19
2063 3975 9.463443 CTATTACTAAGGGCAATTAATTTGTGC 57.537 33.333 0.00 0.00 37.65 4.57
2070 3982 4.815308 GGGCAATTAATTTGTGCATATGCA 59.185 37.500 26.32 26.32 41.31 3.96
2099 4011 5.279809 CCAGTGCAAGTACCCTCTTTACTTA 60.280 44.000 0.00 0.00 37.62 2.24
2115 4027 8.752766 TCTTTACTTACACTTTAATCGACAGG 57.247 34.615 0.00 0.00 0.00 4.00
2210 4124 5.357596 TGCTCATTGTCTGCATAGCATTTTA 59.642 36.000 0.00 0.00 38.13 1.52
2213 4127 7.114529 GCTCATTGTCTGCATAGCATTTTATTC 59.885 37.037 0.00 0.00 38.13 1.75
2215 4129 4.847633 TGTCTGCATAGCATTTTATTCGC 58.152 39.130 0.00 0.00 38.13 4.70
2218 4132 5.341462 GTCTGCATAGCATTTTATTCGCATG 59.659 40.000 0.00 0.00 38.13 4.06
2219 4133 4.548494 TGCATAGCATTTTATTCGCATGG 58.452 39.130 0.00 0.00 31.71 3.66
2259 4201 6.367969 TCGCAACAAGAACTTTAATCTAGACC 59.632 38.462 0.00 0.00 0.00 3.85
2260 4202 6.147164 CGCAACAAGAACTTTAATCTAGACCA 59.853 38.462 0.00 0.00 0.00 4.02
2295 4250 6.534634 TCTTTTGTCTTTAGAGAAGAAGGGG 58.465 40.000 0.00 0.00 32.66 4.79
2299 4254 7.383156 TTGTCTTTAGAGAAGAAGGGGTTTA 57.617 36.000 0.00 0.00 32.66 2.01
2303 4258 8.034215 GTCTTTAGAGAAGAAGGGGTTTACTAC 58.966 40.741 0.00 0.00 32.66 2.73
2325 4280 5.310409 CCATTGGGGTTGATAGATACTGT 57.690 43.478 0.00 0.00 0.00 3.55
2355 4310 7.044181 ACTTGACCATGTGTTATACTGATCTG 58.956 38.462 0.00 0.00 0.00 2.90
2375 4330 7.335171 TGATCTGGATGTTCAGTTCTATTTGTG 59.665 37.037 0.00 0.00 35.57 3.33
2392 4347 8.871125 TCTATTTGTGAAGTACCTCTCTTTTCT 58.129 33.333 0.00 0.00 0.00 2.52
2417 4372 4.349048 TGTATAATGCAGGGCTTCTCAGAT 59.651 41.667 0.00 0.00 0.00 2.90
2424 4379 4.655649 TGCAGGGCTTCTCAGATTAATAGA 59.344 41.667 0.00 0.00 0.00 1.98
2457 4412 5.722021 TTTGCAAAATACTCCTCTTTCCC 57.278 39.130 10.02 0.00 0.00 3.97
2477 4432 2.431057 CCGTGTAGAAATCTAGGCCACT 59.569 50.000 5.01 0.00 0.00 4.00
2480 4435 3.623510 GTGTAGAAATCTAGGCCACTTGC 59.376 47.826 5.01 0.00 40.16 4.01
2512 4467 4.335315 TGAACTGTCAACATGTCAAACTCC 59.665 41.667 0.00 0.00 0.00 3.85
2513 4468 3.884895 ACTGTCAACATGTCAAACTCCA 58.115 40.909 0.00 0.00 0.00 3.86
2547 4502 4.214437 CGTTTGTTCTGATGCTCAAGTTC 58.786 43.478 0.00 0.00 0.00 3.01
2563 4518 6.361748 GCTCAAGTTCAGCTTTTGTTCTATTG 59.638 38.462 0.00 0.00 34.69 1.90
2567 4522 5.241728 AGTTCAGCTTTTGTTCTATTGGGTC 59.758 40.000 0.00 0.00 0.00 4.46
2570 4585 6.480763 TCAGCTTTTGTTCTATTGGGTCATA 58.519 36.000 0.00 0.00 0.00 2.15
2573 4588 5.730568 GCTTTTGTTCTATTGGGTCATAGCG 60.731 44.000 0.00 0.00 0.00 4.26
2595 4610 6.093082 AGCGTAATAAACACATAACCCAGTTC 59.907 38.462 0.00 0.00 0.00 3.01
2603 4619 4.338118 ACACATAACCCAGTTCTGTTTGTG 59.662 41.667 0.00 0.00 38.27 3.33
2683 4701 8.390354 TCATTTTTCAGCATATTACTTCAGTCG 58.610 33.333 0.00 0.00 0.00 4.18
2716 4734 8.072321 AGAGATCAAGAACTAGCATTGAACTA 57.928 34.615 12.11 0.00 36.55 2.24
2761 4788 3.396260 TTCTGTGTTTAGGGGTTCTCG 57.604 47.619 0.00 0.00 0.00 4.04
2763 4790 0.320073 TGTGTTTAGGGGTTCTCGCG 60.320 55.000 0.00 0.00 0.00 5.87
2789 4816 2.485814 GCAGTTTCTTCTGGATGGTGAC 59.514 50.000 0.00 0.00 36.12 3.67
2981 5008 5.863965 TCATATGTTGACCTTTCTGTGACA 58.136 37.500 1.90 0.00 0.00 3.58
3022 5053 8.354711 TCAGTCAGTCAGAGTCTTTTGTATAT 57.645 34.615 0.00 0.00 0.00 0.86
3023 5054 9.462606 TCAGTCAGTCAGAGTCTTTTGTATATA 57.537 33.333 0.00 0.00 0.00 0.86
3057 5168 9.538508 TTAGTTTTGTGTCTTCTTAAGTAGTCC 57.461 33.333 8.74 2.77 0.00 3.85
3199 5312 7.038729 CCTGCATAGTAAATCTATCCAAGGAGA 60.039 40.741 0.00 0.00 37.26 3.71
3246 5376 5.278660 GCTTTGTTCATGGAGTCAGAATGTT 60.279 40.000 0.00 0.00 37.40 2.71
3285 5415 5.478233 TCGTGCGCTTTAATAATGAATGT 57.522 34.783 9.73 0.00 0.00 2.71
3326 5457 1.518325 TTGTGGTGCTCAACATACGG 58.482 50.000 0.00 0.00 0.00 4.02
3409 5548 2.664402 ACCACCTGAAGCAACAAGAT 57.336 45.000 0.00 0.00 0.00 2.40
3416 5555 4.646492 ACCTGAAGCAACAAGATTTTGACT 59.354 37.500 2.48 0.00 37.73 3.41
3495 5639 7.066284 CAGGAACTATTCTGTTTATGGTTCTGG 59.934 40.741 10.49 2.48 40.92 3.86
3567 5714 5.733620 ACGAAGACAATAAGTAGGGTTGA 57.266 39.130 0.00 0.00 0.00 3.18
3614 5767 1.234821 TGTCGTGCATGTTTCCTTCC 58.765 50.000 5.68 0.00 0.00 3.46
3623 5776 2.045561 TGTTTCCTTCCTTGTTGCGA 57.954 45.000 0.00 0.00 0.00 5.10
3753 5910 7.899330 GTGAAAACTGTCATGATTTTGTTTGTG 59.101 33.333 9.64 0.00 0.00 3.33
3784 5941 9.736414 ATCATAATATGAAATCTCACCCTCTTG 57.264 33.333 7.07 0.00 43.50 3.02
3859 6016 8.596271 TGAAATGTATTGTCGTCTTTTCACTA 57.404 30.769 0.00 0.00 33.55 2.74
3870 6027 4.023193 CGTCTTTTCACTATTTGCTTGGGT 60.023 41.667 0.00 0.00 0.00 4.51
3903 6060 4.587262 ACCCTAATTCCTTTCAACGCTTTT 59.413 37.500 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 4.391140 GTGACTCTCGCGAAAGAAAAAT 57.609 40.909 17.91 0.00 0.00 1.82
438 456 5.517054 GCGTCGAGATCTTCAAAACTAGATT 59.483 40.000 0.00 0.00 0.00 2.40
619 640 3.558418 GGAGTACTCGTTGCAAAGAACAA 59.442 43.478 15.91 2.20 0.00 2.83
664 685 9.950496 TCATAAGAAGTATTTTCTGCTTTCTCT 57.050 29.630 0.00 0.00 35.25 3.10
669 690 9.994432 CGAAATCATAAGAAGTATTTTCTGCTT 57.006 29.630 0.00 0.00 37.17 3.91
670 691 8.125448 GCGAAATCATAAGAAGTATTTTCTGCT 58.875 33.333 0.00 0.00 0.00 4.24
671 692 7.910162 TGCGAAATCATAAGAAGTATTTTCTGC 59.090 33.333 0.00 0.00 30.06 4.26
672 693 9.773328 TTGCGAAATCATAAGAAGTATTTTCTG 57.227 29.630 0.00 0.00 0.00 3.02
679 700 8.328146 CGATCTTTTGCGAAATCATAAGAAGTA 58.672 33.333 0.00 0.00 37.49 2.24
680 701 7.064609 TCGATCTTTTGCGAAATCATAAGAAGT 59.935 33.333 0.00 0.00 37.49 3.01
681 702 7.401860 TCGATCTTTTGCGAAATCATAAGAAG 58.598 34.615 0.00 0.00 37.49 2.85
682 703 7.302350 TCGATCTTTTGCGAAATCATAAGAA 57.698 32.000 0.00 0.00 37.49 2.52
683 704 6.902224 TCGATCTTTTGCGAAATCATAAGA 57.098 33.333 0.00 0.00 38.02 2.10
684 705 9.650371 TTTATCGATCTTTTGCGAAATCATAAG 57.350 29.630 0.00 0.00 40.20 1.73
686 707 9.811655 GATTTATCGATCTTTTGCGAAATCATA 57.188 29.630 15.91 0.00 40.20 2.15
687 708 8.344831 TGATTTATCGATCTTTTGCGAAATCAT 58.655 29.630 18.13 0.00 36.59 2.45
688 709 7.693020 TGATTTATCGATCTTTTGCGAAATCA 58.307 30.769 18.13 18.13 37.87 2.57
689 710 8.547091 TTGATTTATCGATCTTTTGCGAAATC 57.453 30.769 0.00 9.82 40.20 2.17
690 711 8.798153 GTTTGATTTATCGATCTTTTGCGAAAT 58.202 29.630 0.00 0.00 40.20 2.17
691 712 7.805542 TGTTTGATTTATCGATCTTTTGCGAAA 59.194 29.630 0.00 0.00 40.20 3.46
692 713 7.301789 TGTTTGATTTATCGATCTTTTGCGAA 58.698 30.769 0.00 0.00 40.20 4.70
693 714 6.836953 TGTTTGATTTATCGATCTTTTGCGA 58.163 32.000 0.00 0.00 41.14 5.10
694 715 7.669438 ATGTTTGATTTATCGATCTTTTGCG 57.331 32.000 0.00 0.00 0.00 4.85
723 744 3.544772 CCACCGGTTGGGCTTTTT 58.455 55.556 2.97 0.00 42.54 1.94
731 752 2.058829 GACAACACTGCCACCGGTTG 62.059 60.000 2.97 1.36 44.57 3.77
732 753 1.822186 GACAACACTGCCACCGGTT 60.822 57.895 2.97 0.00 0.00 4.44
733 754 2.203153 GACAACACTGCCACCGGT 60.203 61.111 0.00 0.00 0.00 5.28
734 755 1.525995 AAGACAACACTGCCACCGG 60.526 57.895 0.00 0.00 0.00 5.28
735 756 1.648720 CAAGACAACACTGCCACCG 59.351 57.895 0.00 0.00 0.00 4.94
736 757 1.455383 CCCAAGACAACACTGCCACC 61.455 60.000 0.00 0.00 0.00 4.61
737 758 2.032981 CCCAAGACAACACTGCCAC 58.967 57.895 0.00 0.00 0.00 5.01
738 759 1.827789 GCCCAAGACAACACTGCCA 60.828 57.895 0.00 0.00 0.00 4.92
739 760 2.564721 GGCCCAAGACAACACTGCC 61.565 63.158 0.00 0.00 0.00 4.85
740 761 2.564721 GGGCCCAAGACAACACTGC 61.565 63.158 19.95 0.00 0.00 4.40
741 762 0.754957 TTGGGCCCAAGACAACACTG 60.755 55.000 34.07 0.00 0.00 3.66
742 763 0.032615 TTTGGGCCCAAGACAACACT 60.033 50.000 35.02 0.00 37.24 3.55
743 764 0.389025 CTTTGGGCCCAAGACAACAC 59.611 55.000 35.02 0.00 37.24 3.32
744 765 1.398958 GCTTTGGGCCCAAGACAACA 61.399 55.000 35.02 19.80 37.24 3.33
745 766 1.367471 GCTTTGGGCCCAAGACAAC 59.633 57.895 35.02 20.25 37.24 3.32
746 767 3.869481 GCTTTGGGCCCAAGACAA 58.131 55.556 35.02 20.93 37.24 3.18
755 776 3.313524 CTGGTTGGGGCTTTGGGC 61.314 66.667 0.00 0.00 40.90 5.36
756 777 3.313524 GCTGGTTGGGGCTTTGGG 61.314 66.667 0.00 0.00 0.00 4.12
757 778 2.523902 TGCTGGTTGGGGCTTTGG 60.524 61.111 0.00 0.00 0.00 3.28
758 779 1.402107 AAGTGCTGGTTGGGGCTTTG 61.402 55.000 0.00 0.00 0.00 2.77
759 780 1.075301 AAGTGCTGGTTGGGGCTTT 60.075 52.632 0.00 0.00 0.00 3.51
760 781 1.531602 GAAGTGCTGGTTGGGGCTT 60.532 57.895 0.00 0.00 0.00 4.35
761 782 2.116125 GAAGTGCTGGTTGGGGCT 59.884 61.111 0.00 0.00 0.00 5.19
762 783 2.203480 TGAAGTGCTGGTTGGGGC 60.203 61.111 0.00 0.00 0.00 5.80
763 784 1.604593 CCTGAAGTGCTGGTTGGGG 60.605 63.158 0.00 0.00 0.00 4.96
764 785 1.604593 CCCTGAAGTGCTGGTTGGG 60.605 63.158 0.00 0.00 34.00 4.12
765 786 0.890996 GACCCTGAAGTGCTGGTTGG 60.891 60.000 0.00 0.00 34.00 3.77
766 787 0.890996 GGACCCTGAAGTGCTGGTTG 60.891 60.000 0.00 0.00 34.00 3.77
767 788 1.352622 TGGACCCTGAAGTGCTGGTT 61.353 55.000 0.00 0.00 34.00 3.67
768 789 1.352622 TTGGACCCTGAAGTGCTGGT 61.353 55.000 0.00 0.00 34.00 4.00
769 790 0.178992 TTTGGACCCTGAAGTGCTGG 60.179 55.000 0.00 0.00 35.50 4.85
770 791 1.242076 CTTTGGACCCTGAAGTGCTG 58.758 55.000 0.00 0.00 0.00 4.41
771 792 0.846693 ACTTTGGACCCTGAAGTGCT 59.153 50.000 4.69 0.00 32.73 4.40
772 793 1.239347 GACTTTGGACCCTGAAGTGC 58.761 55.000 9.07 0.00 34.02 4.40
773 794 1.142870 TGGACTTTGGACCCTGAAGTG 59.857 52.381 9.07 0.00 34.02 3.16
774 795 1.518367 TGGACTTTGGACCCTGAAGT 58.482 50.000 5.07 5.07 36.40 3.01
775 796 2.623416 GTTTGGACTTTGGACCCTGAAG 59.377 50.000 0.00 0.00 0.00 3.02
776 797 2.243736 AGTTTGGACTTTGGACCCTGAA 59.756 45.455 0.00 0.00 29.87 3.02
777 798 1.850345 AGTTTGGACTTTGGACCCTGA 59.150 47.619 0.00 0.00 29.87 3.86
778 799 2.364972 AGTTTGGACTTTGGACCCTG 57.635 50.000 0.00 0.00 29.87 4.45
779 800 3.746432 CGTTAGTTTGGACTTTGGACCCT 60.746 47.826 0.00 0.00 37.33 4.34
780 801 2.551032 CGTTAGTTTGGACTTTGGACCC 59.449 50.000 0.00 0.00 37.33 4.46
781 802 3.469739 TCGTTAGTTTGGACTTTGGACC 58.530 45.455 0.00 0.00 37.33 4.46
782 803 4.374399 TCTCGTTAGTTTGGACTTTGGAC 58.626 43.478 0.00 0.00 37.33 4.02
783 804 4.675976 TCTCGTTAGTTTGGACTTTGGA 57.324 40.909 0.00 0.00 37.33 3.53
784 805 4.814771 ACTTCTCGTTAGTTTGGACTTTGG 59.185 41.667 0.00 0.00 37.33 3.28
785 806 5.986004 ACTTCTCGTTAGTTTGGACTTTG 57.014 39.130 0.00 0.00 37.33 2.77
786 807 6.110707 TCAACTTCTCGTTAGTTTGGACTTT 58.889 36.000 0.00 0.00 37.33 2.66
787 808 5.667466 TCAACTTCTCGTTAGTTTGGACTT 58.333 37.500 0.00 0.00 37.33 3.01
788 809 5.272283 TCAACTTCTCGTTAGTTTGGACT 57.728 39.130 0.00 0.00 39.97 3.85
789 810 6.541111 AATCAACTTCTCGTTAGTTTGGAC 57.459 37.500 0.00 0.00 33.73 4.02
790 811 5.404366 CGAATCAACTTCTCGTTAGTTTGGA 59.596 40.000 0.00 0.00 33.73 3.53
791 812 5.176958 ACGAATCAACTTCTCGTTAGTTTGG 59.823 40.000 0.00 0.00 42.86 3.28
792 813 6.211664 ACGAATCAACTTCTCGTTAGTTTG 57.788 37.500 0.00 0.00 42.86 2.93
793 814 5.404667 GGACGAATCAACTTCTCGTTAGTTT 59.595 40.000 0.00 0.00 45.25 2.66
794 815 4.922103 GGACGAATCAACTTCTCGTTAGTT 59.078 41.667 0.00 0.00 45.25 2.24
795 816 4.217983 AGGACGAATCAACTTCTCGTTAGT 59.782 41.667 0.00 0.00 45.25 2.24
796 817 4.734917 AGGACGAATCAACTTCTCGTTAG 58.265 43.478 0.00 0.00 45.25 2.34
797 818 4.778534 AGGACGAATCAACTTCTCGTTA 57.221 40.909 0.00 0.00 45.25 3.18
798 819 3.662247 AGGACGAATCAACTTCTCGTT 57.338 42.857 0.00 0.00 45.25 3.85
800 821 4.095185 AGTCTAGGACGAATCAACTTCTCG 59.905 45.833 0.00 0.00 37.67 4.04
801 822 5.570234 AGTCTAGGACGAATCAACTTCTC 57.430 43.478 0.00 0.00 37.67 2.87
802 823 5.105675 GGAAGTCTAGGACGAATCAACTTCT 60.106 44.000 12.29 0.00 40.43 2.85
803 824 5.103687 GGAAGTCTAGGACGAATCAACTTC 58.896 45.833 0.00 0.00 40.06 3.01
804 825 4.081586 GGGAAGTCTAGGACGAATCAACTT 60.082 45.833 0.00 0.00 37.67 2.66
805 826 3.447944 GGGAAGTCTAGGACGAATCAACT 59.552 47.826 0.00 0.00 37.67 3.16
806 827 3.734293 CGGGAAGTCTAGGACGAATCAAC 60.734 52.174 0.00 0.00 37.67 3.18
807 828 2.426024 CGGGAAGTCTAGGACGAATCAA 59.574 50.000 0.00 0.00 37.67 2.57
808 829 2.022195 CGGGAAGTCTAGGACGAATCA 58.978 52.381 0.00 0.00 37.67 2.57
809 830 2.022934 ACGGGAAGTCTAGGACGAATC 58.977 52.381 0.00 0.00 37.67 2.52
810 831 2.140839 ACGGGAAGTCTAGGACGAAT 57.859 50.000 0.00 0.00 37.67 3.34
811 832 1.915141 AACGGGAAGTCTAGGACGAA 58.085 50.000 0.00 0.00 37.67 3.85
812 833 1.815003 GAAACGGGAAGTCTAGGACGA 59.185 52.381 0.00 0.00 37.67 4.20
813 834 1.467035 CGAAACGGGAAGTCTAGGACG 60.467 57.143 0.00 0.00 37.67 4.79
814 835 1.543358 ACGAAACGGGAAGTCTAGGAC 59.457 52.381 0.00 0.00 0.00 3.85
815 836 1.915141 ACGAAACGGGAAGTCTAGGA 58.085 50.000 0.00 0.00 0.00 2.94
820 841 0.738762 GGGCTACGAAACGGGAAGTC 60.739 60.000 0.00 0.00 0.00 3.01
853 875 0.923358 GGAGGTCAGAGGAGGAGAGA 59.077 60.000 0.00 0.00 0.00 3.10
859 881 1.599606 CGTGTGGGAGGTCAGAGGAG 61.600 65.000 0.00 0.00 0.00 3.69
860 882 1.606601 CGTGTGGGAGGTCAGAGGA 60.607 63.158 0.00 0.00 0.00 3.71
861 883 2.973899 CGTGTGGGAGGTCAGAGG 59.026 66.667 0.00 0.00 0.00 3.69
862 884 2.262915 GCGTGTGGGAGGTCAGAG 59.737 66.667 0.00 0.00 0.00 3.35
863 885 2.523168 TGCGTGTGGGAGGTCAGA 60.523 61.111 0.00 0.00 0.00 3.27
865 887 3.157949 TGTGCGTGTGGGAGGTCA 61.158 61.111 0.00 0.00 0.00 4.02
866 888 2.172483 ATCTGTGCGTGTGGGAGGTC 62.172 60.000 0.00 0.00 0.00 3.85
867 889 2.172483 GATCTGTGCGTGTGGGAGGT 62.172 60.000 0.00 0.00 0.00 3.85
869 891 1.448540 GGATCTGTGCGTGTGGGAG 60.449 63.158 0.00 0.00 0.00 4.30
870 892 2.662596 GGATCTGTGCGTGTGGGA 59.337 61.111 0.00 0.00 0.00 4.37
874 896 2.660064 GGGAGGGATCTGTGCGTGT 61.660 63.158 0.00 0.00 0.00 4.49
946 978 0.921347 CCGACGATTTAACGGCAGAG 59.079 55.000 0.00 0.00 41.84 3.35
994 1026 1.883275 CTCCGCGAAGTCCATCTCTAT 59.117 52.381 8.23 0.00 0.00 1.98
995 1027 1.134189 TCTCCGCGAAGTCCATCTCTA 60.134 52.381 8.23 0.00 0.00 2.43
996 1028 0.394488 TCTCCGCGAAGTCCATCTCT 60.394 55.000 8.23 0.00 0.00 3.10
1004 1036 4.220413 TCGAGATCTCCGCGAAGT 57.780 55.556 17.13 0.00 43.81 3.01
1017 1049 1.014564 GGGCGTCAACCTTCTTCGAG 61.015 60.000 0.00 0.00 0.00 4.04
1018 1050 1.005394 GGGCGTCAACCTTCTTCGA 60.005 57.895 0.00 0.00 0.00 3.71
1120 1152 1.079543 CAGACACGGCCTTCCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
1148 1213 2.202932 CCGCCTCCAATCGACCAG 60.203 66.667 0.00 0.00 0.00 4.00
1178 1243 0.661483 GTCGGCTGACTTTTGCTTGC 60.661 55.000 18.76 0.00 42.08 4.01
1201 1266 4.100084 CACCGCATGCCCTCCAGA 62.100 66.667 13.15 0.00 0.00 3.86
1216 1281 5.752472 CACTGACCTCTATGACATGATTCAC 59.248 44.000 0.00 0.00 0.00 3.18
1245 1310 1.988107 ACAGCCATTTCCTCTTCCTCA 59.012 47.619 0.00 0.00 0.00 3.86
1257 1322 4.338012 TCTCATTGACATCAACAGCCATT 58.662 39.130 0.00 0.00 38.86 3.16
1277 1498 4.952071 ACATCATCGTCATCCAGAATCT 57.048 40.909 0.00 0.00 0.00 2.40
1342 1566 0.593618 TCACTCTCGCTGTCACTGAC 59.406 55.000 1.86 1.86 0.00 3.51
1353 1577 0.678395 CATCCCCATCCTCACTCTCG 59.322 60.000 0.00 0.00 0.00 4.04
1458 1682 2.362369 ACCCTCACTGCCATCCTCG 61.362 63.158 0.00 0.00 0.00 4.63
1478 1702 5.685511 CCAGGTTTTTGATTAACAACACGAG 59.314 40.000 2.22 0.00 38.29 4.18
1485 1709 5.659079 AGGTGAACCAGGTTTTTGATTAACA 59.341 36.000 6.21 0.00 38.89 2.41
1547 1771 4.541714 ACCCCTCCATCCCATATAATTCAG 59.458 45.833 0.00 0.00 0.00 3.02
1559 1783 1.763545 GAGTAGAACACCCCTCCATCC 59.236 57.143 0.00 0.00 0.00 3.51
1581 1805 1.117234 CGAAACGCCTTTTTGTTCCG 58.883 50.000 0.00 0.00 0.00 4.30
1596 1820 2.222445 GCTTTCAGTTAACCGAGCGAAA 59.778 45.455 0.88 3.79 0.00 3.46
1617 1841 3.012518 AGGTCGCATTCTCTTTGATTGG 58.987 45.455 0.00 0.00 0.00 3.16
1639 1863 0.878961 AACTCAAGTTCCCGACGTGC 60.879 55.000 0.00 0.00 37.61 5.34
1771 2001 0.906756 TCTTCTGGTCCAGCTGAGGG 60.907 60.000 17.39 0.00 0.00 4.30
1791 2021 8.324306 TCTTCAATAGTTTCCTCATTGTCAGAT 58.676 33.333 0.00 0.00 32.64 2.90
1810 2040 7.551585 CGTATCCTAGCCATAAGATCTTCAAT 58.448 38.462 12.24 0.00 0.00 2.57
1811 2041 6.572509 GCGTATCCTAGCCATAAGATCTTCAA 60.573 42.308 12.24 0.00 0.00 2.69
1857 2087 3.359033 TGCCTCAATCTTCCAATCCTTG 58.641 45.455 0.00 0.00 0.00 3.61
1899 2129 1.566018 GGCGAAGTTCAGGGTGTTCG 61.566 60.000 3.32 0.00 43.62 3.95
1946 3858 0.318441 CTGTTCTTCCTCGGTCTGCA 59.682 55.000 0.00 0.00 0.00 4.41
1983 3895 6.710295 GGCTAAATCCCTTTTTGTTGTGAATT 59.290 34.615 0.00 0.00 0.00 2.17
1986 3898 4.651503 TGGCTAAATCCCTTTTTGTTGTGA 59.348 37.500 0.00 0.00 0.00 3.58
2050 3962 9.311292 GGGCACTGCATATGCACAAATTAATTG 62.311 40.741 26.32 14.46 46.22 2.32
2063 3975 1.731700 GCACTGGGCACTGCATATG 59.268 57.895 2.82 0.00 43.97 1.78
2074 3986 0.693049 AAGAGGGTACTTGCACTGGG 59.307 55.000 0.00 0.00 0.00 4.45
2075 3987 2.568623 AAAGAGGGTACTTGCACTGG 57.431 50.000 0.00 0.00 0.00 4.00
2076 3988 4.273148 AGTAAAGAGGGTACTTGCACTG 57.727 45.455 0.00 0.00 30.31 3.66
2099 4011 3.244078 TGCAGACCTGTCGATTAAAGTGT 60.244 43.478 0.00 0.00 34.09 3.55
2115 4027 2.480419 GGTGATACAACTGTGTGCAGAC 59.520 50.000 7.12 7.12 45.28 3.51
2150 4062 7.422399 TGTCAGGACAAAACTAAATAGCAAAC 58.578 34.615 0.00 0.00 38.56 2.93
2154 4066 7.377766 TGATGTCAGGACAAAACTAAATAGC 57.622 36.000 6.17 0.00 45.41 2.97
2161 4073 5.010012 GTCCAAATGATGTCAGGACAAAACT 59.990 40.000 6.17 0.00 46.15 2.66
2210 4124 3.072486 GCCAAGCTGCCATGCGAAT 62.072 57.895 0.00 0.00 38.13 3.34
2219 4133 2.256461 CGAACAAGGCCAAGCTGC 59.744 61.111 5.01 0.00 0.00 5.25
2303 4258 5.065914 CACAGTATCTATCAACCCCAATGG 58.934 45.833 0.00 0.00 41.37 3.16
2308 4263 5.104900 AGTCAACACAGTATCTATCAACCCC 60.105 44.000 0.00 0.00 0.00 4.95
2316 4271 6.014584 ACATGGTCAAGTCAACACAGTATCTA 60.015 38.462 0.00 0.00 0.00 1.98
2325 4280 6.426633 CAGTATAACACATGGTCAAGTCAACA 59.573 38.462 0.00 0.00 0.00 3.33
2355 4310 7.440523 ACTTCACAAATAGAACTGAACATCC 57.559 36.000 0.00 0.00 0.00 3.51
2392 4347 5.543790 TCTGAGAAGCCCTGCATTATACATA 59.456 40.000 0.00 0.00 0.00 2.29
2447 4402 4.094476 AGATTTCTACACGGGAAAGAGGA 58.906 43.478 0.00 0.00 36.35 3.71
2448 4403 4.473477 AGATTTCTACACGGGAAAGAGG 57.527 45.455 0.00 0.00 36.35 3.69
2457 4412 3.802948 AGTGGCCTAGATTTCTACACG 57.197 47.619 3.32 0.00 31.90 4.49
2477 4432 2.206750 GACAGTTCAACCTACACGCAA 58.793 47.619 0.00 0.00 0.00 4.85
2508 4463 5.379187 ACAAACGGTACCTAAAAATGGAGT 58.621 37.500 10.90 0.00 0.00 3.85
2512 4467 6.961576 TCAGAACAAACGGTACCTAAAAATG 58.038 36.000 10.90 3.18 0.00 2.32
2513 4468 7.590279 CATCAGAACAAACGGTACCTAAAAAT 58.410 34.615 10.90 0.00 0.00 1.82
2547 4502 5.649782 ATGACCCAATAGAACAAAAGCTG 57.350 39.130 0.00 0.00 0.00 4.24
2563 4518 7.307573 GGTTATGTGTTTATTACGCTATGACCC 60.308 40.741 0.00 0.00 38.12 4.46
2567 4522 7.225931 ACTGGGTTATGTGTTTATTACGCTATG 59.774 37.037 0.00 0.00 38.12 2.23
2570 4585 5.493809 ACTGGGTTATGTGTTTATTACGCT 58.506 37.500 0.00 0.00 38.12 5.07
2573 4588 8.331730 ACAGAACTGGGTTATGTGTTTATTAC 57.668 34.615 9.40 0.00 44.56 1.89
2603 4619 8.388103 GTGGTGTGTGTTACTTATTCATATGTC 58.612 37.037 1.90 0.00 0.00 3.06
2683 4701 5.810074 GCTAGTTCTTGATCTCTTCCTCAAC 59.190 44.000 0.00 0.00 0.00 3.18
2716 4734 1.212935 ACTTGCAGGGTGAGACAAACT 59.787 47.619 0.00 0.00 0.00 2.66
2763 4790 2.080286 TCCAGAAGAAACTGCGCTAC 57.920 50.000 9.73 0.00 36.67 3.58
2981 5008 1.701847 ACTGATTGGAGAGGCACAAGT 59.298 47.619 0.00 0.00 0.00 3.16
3022 5053 9.802039 AAGAAGACACAAAACTAAACCCATATA 57.198 29.630 0.00 0.00 0.00 0.86
3023 5054 8.706322 AAGAAGACACAAAACTAAACCCATAT 57.294 30.769 0.00 0.00 0.00 1.78
3057 5168 3.793559 ACTTTAGCATGCCCTAACTACG 58.206 45.455 15.66 0.00 0.00 3.51
3199 5312 7.436118 AGCAATTGAACAATACAGAACAACAT 58.564 30.769 10.34 0.00 0.00 2.71
3246 5376 2.103373 ACGAGCAGGAGAGAAAGCATA 58.897 47.619 0.00 0.00 0.00 3.14
3285 5415 2.738587 TCCACTTTGTGCCAACCTTA 57.261 45.000 0.00 0.00 31.34 2.69
3326 5457 2.178912 TGTGGTCCGGAAATTCAGAC 57.821 50.000 5.23 6.80 0.00 3.51
3409 5548 2.028839 TGCCTCGAACCGATAGTCAAAA 60.029 45.455 0.00 0.00 34.61 2.44
3416 5555 1.945394 GTAGAGTGCCTCGAACCGATA 59.055 52.381 0.00 0.00 34.61 2.92
3567 5714 0.991920 CAGGTTCAGGTGGTGGGTAT 59.008 55.000 0.00 0.00 0.00 2.73
3614 5767 0.839477 CAACAACGCTTCGCAACAAG 59.161 50.000 0.00 0.00 0.00 3.16
3623 5776 2.254546 TGATCTCACCAACAACGCTT 57.745 45.000 0.00 0.00 0.00 4.68
3627 5780 4.275689 TGACACAATGATCTCACCAACAAC 59.724 41.667 0.00 0.00 0.00 3.32
3784 5941 6.094048 TGAACTGTAGGAAAAGCTGCAATATC 59.906 38.462 1.02 0.00 0.00 1.63
3859 6016 0.779997 AGAGACCCACCCAAGCAAAT 59.220 50.000 0.00 0.00 0.00 2.32
3903 6060 3.998341 GTGTTCAACGAGTAATTAGCCCA 59.002 43.478 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.