Multiple sequence alignment - TraesCS3D01G263700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G263700 chr3D 100.000 5469 0 0 1 5469 365537922 365532454 0.000000e+00 10100
1 TraesCS3D01G263700 chr3D 98.505 602 9 0 1 602 365546253 365545652 0.000000e+00 1062
2 TraesCS3D01G263700 chr3A 93.795 4609 140 53 942 5469 487452056 487447513 0.000000e+00 6793
3 TraesCS3D01G263700 chr3B 96.131 2869 93 10 872 3738 476045144 476042292 0.000000e+00 4667
4 TraesCS3D01G263700 chr3B 93.337 1681 67 11 3803 5469 476042213 476040564 0.000000e+00 2442
5 TraesCS3D01G263700 chr3B 94.792 96 4 1 778 872 779368985 779368890 1.230000e-31 148
6 TraesCS3D01G263700 chr1A 89.570 604 58 3 1 602 421462683 421463283 0.000000e+00 761
7 TraesCS3D01G263700 chr1A 88.907 613 63 3 1 608 421470887 421471499 0.000000e+00 750
8 TraesCS3D01G263700 chr1A 94.737 95 4 1 778 871 469201994 469202088 4.410000e-31 147
9 TraesCS3D01G263700 chr7B 91.163 430 35 3 174 602 45834502 45834929 1.020000e-161 580
10 TraesCS3D01G263700 chr7B 90.867 427 36 3 177 602 45578142 45577718 2.210000e-158 569
11 TraesCS3D01G263700 chr7B 85.915 213 16 5 2 203 48072655 48072864 1.190000e-51 215
12 TraesCS3D01G263700 chr2D 86.066 366 46 4 239 602 403776590 403776228 6.640000e-104 388
13 TraesCS3D01G263700 chr2D 85.519 366 48 4 239 602 403766913 403766551 1.440000e-100 377
14 TraesCS3D01G263700 chr2D 94.792 96 4 1 778 872 585783741 585783646 1.230000e-31 148
15 TraesCS3D01G263700 chr2D 93.684 95 4 2 778 870 492033831 492033925 2.050000e-29 141
16 TraesCS3D01G263700 chr7D 82.452 416 63 9 190 602 365301559 365301151 6.740000e-94 355
17 TraesCS3D01G263700 chr4A 84.444 360 49 7 245 602 497723722 497724076 1.130000e-91 348
18 TraesCS3D01G263700 chr6A 74.178 639 116 29 2 602 318269611 318268984 2.560000e-53 220
19 TraesCS3D01G263700 chr5D 95.699 93 4 0 780 872 352847800 352847892 3.410000e-32 150
20 TraesCS3D01G263700 chr5A 92.233 103 6 2 778 878 4117176 4117074 1.590000e-30 145
21 TraesCS3D01G263700 chr2A 93.814 97 4 1 778 872 98897509 98897413 1.590000e-30 145
22 TraesCS3D01G263700 chr4D 92.857 98 7 0 778 875 82458437 82458340 5.710000e-30 143
23 TraesCS3D01G263700 chr1B 92.157 102 5 3 778 876 42186395 42186496 2.050000e-29 141


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 TraesCS3D01G263700 chr3D 365532454 365537922 5468 True 10100.0 10100 100.000 1 5469 1 chr3D.!!$R1 5468
1 TraesCS3D01G263700 chr3D 365545652 365546253 601 True 1062.0 1062 98.505 1 602 1 chr3D.!!$R2 601
2 TraesCS3D01G263700 chr3A 487447513 487452056 4543 True 6793.0 6793 93.795 942 5469 1 chr3A.!!$R1 4527
3 TraesCS3D01G263700 chr3B 476040564 476045144 4580 True 3554.5 4667 94.734 872 5469 2 chr3B.!!$R2 4597
4 TraesCS3D01G263700 chr1A 421462683 421463283 600 False 761.0 761 89.570 1 602 1 chr1A.!!$F1 601
5 TraesCS3D01G263700 chr1A 421470887 421471499 612 False 750.0 750 88.907 1 608 1 chr1A.!!$F2 607
6 TraesCS3D01G263700 chr6A 318268984 318269611 627 True 220.0 220 74.178 2 602 1 chr6A.!!$R1 600

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
622 658 0.037447 TCCATCCGGCATTGTCAACA 59.963 50.000 0.00 0.00 0.00 3.33 F
993 1029 0.039618 TTGGCCCTCCAATCTCCAAC 59.960 55.000 0.00 0.00 46.89 3.77 F
1520 1575 0.449388 GCTATTGTGGTGCAGCTCAC 59.551 55.000 19.32 12.94 44.90 3.51 F
2206 2263 0.608640 CGAACTTCCAGCCAGTACCT 59.391 55.000 0.00 0.00 0.00 3.08 F
3210 3268 1.203187 TGGAGCTGGTCTTCCTACTGT 60.203 52.381 6.83 0.00 34.23 3.55 F
4300 4420 1.207089 TGGCTTGAGGTATGAACTCCG 59.793 52.381 0.00 0.00 34.06 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2120 0.738975 GGACATCGAGTGATCGGTGA 59.261 55.000 16.98 0.00 46.13 4.02 R
2206 2263 1.351017 CTGGTTCCCCTAAGCTTGACA 59.649 52.381 9.86 0.00 36.51 3.58 R
2527 2585 1.452651 CTGCATCCAAGGCACGGAT 60.453 57.895 2.09 2.09 44.35 4.18 R
3900 3998 1.048601 AGGGTTTCAGTCTCAGCGAA 58.951 50.000 0.00 0.00 0.00 4.70 R
4414 4534 0.539051 CATTCCAGAAGTCCCGAGCT 59.461 55.000 0.00 0.00 0.00 4.09 R
5189 5327 2.584965 TGGAGAGAGAGGATGGAGAAGT 59.415 50.000 0.00 0.00 0.00 3.01 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
519 555 3.891056 ATTTGAACTCGGTTTCGAACC 57.109 42.857 0.00 1.79 45.47 3.62
545 581 4.506217 GCGAGTTTATCAACAGTAATCGC 58.494 43.478 7.35 7.35 41.46 4.58
602 638 3.248602 GCTTAATTATCCAGGCGTCACAG 59.751 47.826 0.00 0.00 0.00 3.66
603 639 4.442706 CTTAATTATCCAGGCGTCACAGT 58.557 43.478 0.00 0.00 0.00 3.55
604 640 2.604046 ATTATCCAGGCGTCACAGTC 57.396 50.000 0.00 0.00 0.00 3.51
605 641 0.535335 TTATCCAGGCGTCACAGTCC 59.465 55.000 0.00 0.00 0.00 3.85
606 642 0.613572 TATCCAGGCGTCACAGTCCA 60.614 55.000 0.00 0.00 0.00 4.02
607 643 1.267574 ATCCAGGCGTCACAGTCCAT 61.268 55.000 0.00 0.00 0.00 3.41
608 644 1.448540 CCAGGCGTCACAGTCCATC 60.449 63.158 0.00 0.00 0.00 3.51
609 645 1.448540 CAGGCGTCACAGTCCATCC 60.449 63.158 0.00 0.00 0.00 3.51
610 646 2.509336 GGCGTCACAGTCCATCCG 60.509 66.667 0.00 0.00 0.00 4.18
611 647 2.509336 GCGTCACAGTCCATCCGG 60.509 66.667 0.00 0.00 0.00 5.14
612 648 2.509336 CGTCACAGTCCATCCGGC 60.509 66.667 0.00 0.00 0.00 6.13
613 649 2.662596 GTCACAGTCCATCCGGCA 59.337 61.111 0.00 0.00 0.00 5.69
614 650 1.221840 GTCACAGTCCATCCGGCAT 59.778 57.895 0.00 0.00 0.00 4.40
615 651 0.392998 GTCACAGTCCATCCGGCATT 60.393 55.000 0.00 0.00 0.00 3.56
616 652 0.392863 TCACAGTCCATCCGGCATTG 60.393 55.000 0.00 0.00 0.00 2.82
617 653 0.677731 CACAGTCCATCCGGCATTGT 60.678 55.000 0.00 0.00 0.00 2.71
618 654 0.392998 ACAGTCCATCCGGCATTGTC 60.393 55.000 0.00 0.00 0.00 3.18
619 655 0.392863 CAGTCCATCCGGCATTGTCA 60.393 55.000 0.00 0.00 0.00 3.58
620 656 0.327924 AGTCCATCCGGCATTGTCAA 59.672 50.000 0.00 0.00 0.00 3.18
621 657 0.451783 GTCCATCCGGCATTGTCAAC 59.548 55.000 0.00 0.00 0.00 3.18
622 658 0.037447 TCCATCCGGCATTGTCAACA 59.963 50.000 0.00 0.00 0.00 3.33
623 659 0.452987 CCATCCGGCATTGTCAACAG 59.547 55.000 0.00 0.00 0.00 3.16
624 660 1.452110 CATCCGGCATTGTCAACAGA 58.548 50.000 0.00 0.00 0.00 3.41
625 661 1.131126 CATCCGGCATTGTCAACAGAC 59.869 52.381 0.00 0.00 0.00 3.51
626 662 0.948623 TCCGGCATTGTCAACAGACG 60.949 55.000 0.00 7.87 35.00 4.18
627 663 1.227999 CCGGCATTGTCAACAGACGT 61.228 55.000 12.53 0.00 35.00 4.34
628 664 0.110688 CGGCATTGTCAACAGACGTG 60.111 55.000 0.00 0.00 35.00 4.49
629 665 0.944386 GGCATTGTCAACAGACGTGT 59.056 50.000 0.00 0.00 39.19 4.49
630 666 1.069906 GGCATTGTCAACAGACGTGTC 60.070 52.381 0.00 0.00 35.08 3.67
631 667 1.069906 GCATTGTCAACAGACGTGTCC 60.070 52.381 0.00 0.00 35.08 4.02
632 668 1.192312 CATTGTCAACAGACGTGTCCG 59.808 52.381 0.00 0.00 35.08 4.79
633 669 0.456628 TTGTCAACAGACGTGTCCGA 59.543 50.000 0.00 0.00 35.08 4.55
634 670 0.456628 TGTCAACAGACGTGTCCGAA 59.543 50.000 0.00 0.00 35.08 4.30
635 671 0.850856 GTCAACAGACGTGTCCGAAC 59.149 55.000 0.00 0.00 35.08 3.95
654 690 2.674296 GCTCCCGCGTACTTTTAGG 58.326 57.895 4.92 0.00 0.00 2.69
655 691 0.808847 GCTCCCGCGTACTTTTAGGG 60.809 60.000 4.92 0.00 43.32 3.53
656 692 0.179092 CTCCCGCGTACTTTTAGGGG 60.179 60.000 4.92 0.00 42.26 4.79
657 693 0.614415 TCCCGCGTACTTTTAGGGGA 60.614 55.000 4.92 0.00 42.26 4.81
658 694 0.466963 CCCGCGTACTTTTAGGGGAT 59.533 55.000 4.92 0.00 39.96 3.85
659 695 1.578583 CCGCGTACTTTTAGGGGATG 58.421 55.000 4.92 0.00 39.96 3.51
660 696 1.578583 CGCGTACTTTTAGGGGATGG 58.421 55.000 0.00 0.00 0.00 3.51
661 697 1.137479 CGCGTACTTTTAGGGGATGGA 59.863 52.381 0.00 0.00 0.00 3.41
662 698 2.224209 CGCGTACTTTTAGGGGATGGAT 60.224 50.000 0.00 0.00 0.00 3.41
663 699 3.743269 CGCGTACTTTTAGGGGATGGATT 60.743 47.826 0.00 0.00 0.00 3.01
664 700 4.204799 GCGTACTTTTAGGGGATGGATTT 58.795 43.478 0.00 0.00 0.00 2.17
665 701 4.036380 GCGTACTTTTAGGGGATGGATTTG 59.964 45.833 0.00 0.00 0.00 2.32
666 702 4.036380 CGTACTTTTAGGGGATGGATTTGC 59.964 45.833 0.00 0.00 0.00 3.68
667 703 3.374764 ACTTTTAGGGGATGGATTTGCC 58.625 45.455 0.00 0.00 37.10 4.52
668 704 3.012844 ACTTTTAGGGGATGGATTTGCCT 59.987 43.478 0.00 0.00 37.63 4.75
669 705 2.754012 TTAGGGGATGGATTTGCCTG 57.246 50.000 0.00 0.00 37.63 4.85
670 706 0.852842 TAGGGGATGGATTTGCCTGG 59.147 55.000 0.00 0.00 37.63 4.45
671 707 1.224003 AGGGGATGGATTTGCCTGGT 61.224 55.000 0.00 0.00 37.63 4.00
672 708 0.325577 GGGGATGGATTTGCCTGGTT 60.326 55.000 0.00 0.00 37.63 3.67
673 709 0.826062 GGGATGGATTTGCCTGGTTG 59.174 55.000 0.00 0.00 37.63 3.77
674 710 1.560505 GGATGGATTTGCCTGGTTGT 58.439 50.000 0.00 0.00 37.63 3.32
675 711 2.622977 GGGATGGATTTGCCTGGTTGTA 60.623 50.000 0.00 0.00 37.63 2.41
676 712 2.689983 GGATGGATTTGCCTGGTTGTAG 59.310 50.000 0.00 0.00 37.63 2.74
677 713 2.214376 TGGATTTGCCTGGTTGTAGG 57.786 50.000 0.00 0.00 40.95 3.18
678 714 1.427368 TGGATTTGCCTGGTTGTAGGT 59.573 47.619 0.00 0.00 40.11 3.08
679 715 1.818674 GGATTTGCCTGGTTGTAGGTG 59.181 52.381 0.00 0.00 40.11 4.00
680 716 1.818674 GATTTGCCTGGTTGTAGGTGG 59.181 52.381 0.00 0.00 40.11 4.61
681 717 0.825840 TTTGCCTGGTTGTAGGTGGC 60.826 55.000 0.00 0.00 43.49 5.01
682 718 1.715019 TTGCCTGGTTGTAGGTGGCT 61.715 55.000 0.00 0.00 43.57 4.75
683 719 0.838554 TGCCTGGTTGTAGGTGGCTA 60.839 55.000 0.00 0.00 43.57 3.93
684 720 0.326927 GCCTGGTTGTAGGTGGCTAA 59.673 55.000 0.00 0.00 40.11 3.09
685 721 1.679032 GCCTGGTTGTAGGTGGCTAAG 60.679 57.143 0.00 0.00 40.11 2.18
686 722 1.628846 CCTGGTTGTAGGTGGCTAAGT 59.371 52.381 0.00 0.00 32.99 2.24
687 723 2.835764 CCTGGTTGTAGGTGGCTAAGTA 59.164 50.000 0.00 0.00 32.99 2.24
688 724 3.118738 CCTGGTTGTAGGTGGCTAAGTAG 60.119 52.174 0.00 0.00 32.99 2.57
689 725 3.513517 TGGTTGTAGGTGGCTAAGTAGT 58.486 45.455 0.00 0.00 0.00 2.73
690 726 3.905591 TGGTTGTAGGTGGCTAAGTAGTT 59.094 43.478 0.00 0.00 0.00 2.24
691 727 4.348754 TGGTTGTAGGTGGCTAAGTAGTTT 59.651 41.667 0.00 0.00 0.00 2.66
692 728 5.163174 TGGTTGTAGGTGGCTAAGTAGTTTT 60.163 40.000 0.00 0.00 0.00 2.43
693 729 5.766670 GGTTGTAGGTGGCTAAGTAGTTTTT 59.233 40.000 0.00 0.00 0.00 1.94
717 753 6.851222 TTTTTGAAACACTGTGCAAAAGAA 57.149 29.167 17.80 7.91 40.15 2.52
718 754 6.851222 TTTTGAAACACTGTGCAAAAGAAA 57.149 29.167 15.89 6.33 35.88 2.52
719 755 7.432350 TTTTGAAACACTGTGCAAAAGAAAT 57.568 28.000 15.89 0.00 35.88 2.17
720 756 6.645700 TTGAAACACTGTGCAAAAGAAATC 57.354 33.333 7.90 0.00 0.00 2.17
721 757 5.718146 TGAAACACTGTGCAAAAGAAATCA 58.282 33.333 7.90 0.00 0.00 2.57
722 758 6.339730 TGAAACACTGTGCAAAAGAAATCAT 58.660 32.000 7.90 0.00 0.00 2.45
723 759 6.817641 TGAAACACTGTGCAAAAGAAATCATT 59.182 30.769 7.90 0.00 0.00 2.57
724 760 7.978414 TGAAACACTGTGCAAAAGAAATCATTA 59.022 29.630 7.90 0.00 0.00 1.90
725 761 8.715191 AAACACTGTGCAAAAGAAATCATTAA 57.285 26.923 7.90 0.00 0.00 1.40
726 762 8.715191 AACACTGTGCAAAAGAAATCATTAAA 57.285 26.923 7.90 0.00 0.00 1.52
727 763 8.715191 ACACTGTGCAAAAGAAATCATTAAAA 57.285 26.923 7.90 0.00 0.00 1.52
728 764 9.160496 ACACTGTGCAAAAGAAATCATTAAAAA 57.840 25.926 7.90 0.00 0.00 1.94
758 794 8.926092 ATTTAATCCTAGGAAGCAAATAGTCC 57.074 34.615 17.30 0.00 0.00 3.85
759 795 5.975988 AATCCTAGGAAGCAAATAGTCCA 57.024 39.130 17.30 0.00 33.57 4.02
760 796 5.559148 ATCCTAGGAAGCAAATAGTCCAG 57.441 43.478 17.30 0.00 33.57 3.86
761 797 4.362677 TCCTAGGAAGCAAATAGTCCAGT 58.637 43.478 9.71 0.00 33.57 4.00
762 798 5.525484 TCCTAGGAAGCAAATAGTCCAGTA 58.475 41.667 9.71 0.00 33.57 2.74
763 799 5.598830 TCCTAGGAAGCAAATAGTCCAGTAG 59.401 44.000 9.71 0.00 33.57 2.57
764 800 5.598830 CCTAGGAAGCAAATAGTCCAGTAGA 59.401 44.000 1.05 0.00 33.57 2.59
765 801 6.098409 CCTAGGAAGCAAATAGTCCAGTAGAA 59.902 42.308 1.05 0.00 33.57 2.10
766 802 6.374417 AGGAAGCAAATAGTCCAGTAGAAA 57.626 37.500 0.00 0.00 33.57 2.52
767 803 6.779860 AGGAAGCAAATAGTCCAGTAGAAAA 58.220 36.000 0.00 0.00 33.57 2.29
768 804 7.231467 AGGAAGCAAATAGTCCAGTAGAAAAA 58.769 34.615 0.00 0.00 33.57 1.94
769 805 7.890655 AGGAAGCAAATAGTCCAGTAGAAAAAT 59.109 33.333 0.00 0.00 33.57 1.82
770 806 8.184848 GGAAGCAAATAGTCCAGTAGAAAAATC 58.815 37.037 0.00 0.00 0.00 2.17
771 807 8.635765 AAGCAAATAGTCCAGTAGAAAAATCA 57.364 30.769 0.00 0.00 0.00 2.57
772 808 8.814038 AGCAAATAGTCCAGTAGAAAAATCAT 57.186 30.769 0.00 0.00 0.00 2.45
773 809 9.905713 AGCAAATAGTCCAGTAGAAAAATCATA 57.094 29.630 0.00 0.00 0.00 2.15
779 815 8.779354 AGTCCAGTAGAAAAATCATAACAGTC 57.221 34.615 0.00 0.00 0.00 3.51
780 816 8.598041 AGTCCAGTAGAAAAATCATAACAGTCT 58.402 33.333 0.00 0.00 0.00 3.24
781 817 9.871238 GTCCAGTAGAAAAATCATAACAGTCTA 57.129 33.333 0.00 0.00 0.00 2.59
782 818 9.871238 TCCAGTAGAAAAATCATAACAGTCTAC 57.129 33.333 0.00 0.00 37.38 2.59
783 819 8.808529 CCAGTAGAAAAATCATAACAGTCTACG 58.191 37.037 0.00 0.00 40.44 3.51
784 820 8.808529 CAGTAGAAAAATCATAACAGTCTACGG 58.191 37.037 0.00 0.00 40.44 4.02
785 821 8.746530 AGTAGAAAAATCATAACAGTCTACGGA 58.253 33.333 0.00 0.00 40.44 4.69
786 822 9.530633 GTAGAAAAATCATAACAGTCTACGGAT 57.469 33.333 0.00 0.00 30.12 4.18
787 823 8.649973 AGAAAAATCATAACAGTCTACGGATC 57.350 34.615 0.00 0.00 0.00 3.36
788 824 8.478877 AGAAAAATCATAACAGTCTACGGATCT 58.521 33.333 0.00 0.00 0.00 2.75
789 825 8.425577 AAAAATCATAACAGTCTACGGATCTG 57.574 34.615 0.00 0.00 35.60 2.90
790 826 5.713792 ATCATAACAGTCTACGGATCTGG 57.286 43.478 6.47 0.00 34.02 3.86
791 827 4.788679 TCATAACAGTCTACGGATCTGGA 58.211 43.478 6.47 0.00 34.02 3.86
792 828 5.386060 TCATAACAGTCTACGGATCTGGAT 58.614 41.667 6.47 0.00 34.02 3.41
793 829 5.241728 TCATAACAGTCTACGGATCTGGATG 59.758 44.000 6.47 0.00 34.02 3.51
794 830 3.019799 ACAGTCTACGGATCTGGATGT 57.980 47.619 6.47 0.00 34.02 3.06
795 831 4.166246 ACAGTCTACGGATCTGGATGTA 57.834 45.455 6.47 0.00 34.02 2.29
796 832 4.533815 ACAGTCTACGGATCTGGATGTAA 58.466 43.478 6.47 0.00 34.02 2.41
797 833 5.141182 ACAGTCTACGGATCTGGATGTAAT 58.859 41.667 6.47 0.00 34.02 1.89
798 834 5.598830 ACAGTCTACGGATCTGGATGTAATT 59.401 40.000 6.47 0.00 34.02 1.40
799 835 6.098409 ACAGTCTACGGATCTGGATGTAATTT 59.902 38.462 6.47 0.00 34.02 1.82
800 836 6.986817 CAGTCTACGGATCTGGATGTAATTTT 59.013 38.462 6.47 0.00 0.00 1.82
801 837 7.495934 CAGTCTACGGATCTGGATGTAATTTTT 59.504 37.037 6.47 0.00 0.00 1.94
802 838 8.701895 AGTCTACGGATCTGGATGTAATTTTTA 58.298 33.333 6.47 0.00 0.00 1.52
803 839 9.490379 GTCTACGGATCTGGATGTAATTTTTAT 57.510 33.333 6.47 0.00 0.00 1.40
832 868 9.863845 TTTCTATTGTTCGTTGTACTATCATGA 57.136 29.630 0.00 0.00 0.00 3.07
836 872 8.716646 ATTGTTCGTTGTACTATCATGATTGA 57.283 30.769 21.64 1.13 36.00 2.57
837 873 8.541133 TTGTTCGTTGTACTATCATGATTGAA 57.459 30.769 21.64 5.14 34.96 2.69
838 874 8.185003 TGTTCGTTGTACTATCATGATTGAAG 57.815 34.615 21.64 12.40 34.96 3.02
839 875 8.032451 TGTTCGTTGTACTATCATGATTGAAGA 58.968 33.333 21.64 6.21 34.96 2.87
840 876 9.035607 GTTCGTTGTACTATCATGATTGAAGAT 57.964 33.333 21.64 4.07 34.96 2.40
841 877 8.579682 TCGTTGTACTATCATGATTGAAGATG 57.420 34.615 21.64 10.62 34.96 2.90
842 878 8.413229 TCGTTGTACTATCATGATTGAAGATGA 58.587 33.333 21.64 12.27 34.96 2.92
843 879 9.034544 CGTTGTACTATCATGATTGAAGATGAA 57.965 33.333 21.64 4.00 34.96 2.57
895 931 6.780457 TCCTTTGAATCAAGGGAATCAATC 57.220 37.500 22.24 0.00 44.61 2.67
896 932 6.255287 TCCTTTGAATCAAGGGAATCAATCA 58.745 36.000 22.24 0.00 44.61 2.57
897 933 6.725369 TCCTTTGAATCAAGGGAATCAATCAA 59.275 34.615 22.24 0.00 44.61 2.57
993 1029 0.039618 TTGGCCCTCCAATCTCCAAC 59.960 55.000 0.00 0.00 46.89 3.77
994 1030 0.846427 TGGCCCTCCAATCTCCAACT 60.846 55.000 0.00 0.00 39.99 3.16
1010 1046 4.774124 TCCAACTAGAGCATGAGGATTTG 58.226 43.478 0.00 0.00 0.00 2.32
1226 1262 4.135153 CTCCCAGCGTCCAGTCCG 62.135 72.222 0.00 0.00 0.00 4.79
1520 1575 0.449388 GCTATTGTGGTGCAGCTCAC 59.551 55.000 19.32 12.94 44.90 3.51
1574 1629 1.420138 GTCTGACTTGAAGGGGGTGAA 59.580 52.381 0.00 0.00 0.00 3.18
1632 1687 1.967319 TGCCACAGAGGTTTCTTGAC 58.033 50.000 0.00 0.00 40.61 3.18
1676 1731 4.849926 CAGAAATCTGTCTGTCAAATTGCG 59.150 41.667 2.18 0.00 40.22 4.85
1704 1759 7.467131 GCATTGCCTTTGTTTTAGTTCAATTGT 60.467 33.333 5.13 0.00 0.00 2.71
1794 1849 3.458189 ACATTGGCTAGCGACTATTGTC 58.542 45.455 9.00 0.00 39.70 3.18
1800 1855 3.304794 GGCTAGCGACTATTGTCTACTGG 60.305 52.174 9.00 6.09 40.86 4.00
1890 1945 3.068590 CAGTGGCTCAAAACCAAATCAGT 59.931 43.478 0.00 0.00 39.39 3.41
1901 1956 6.421377 AAACCAAATCAGTTCTTTTTGTGC 57.579 33.333 0.00 0.00 0.00 4.57
1912 1967 9.023962 TCAGTTCTTTTTGTGCCTATTTCATAT 57.976 29.630 0.00 0.00 0.00 1.78
1913 1968 9.643693 CAGTTCTTTTTGTGCCTATTTCATATT 57.356 29.630 0.00 0.00 0.00 1.28
2042 2099 8.760735 CATCATCATTCATAGGACTAGGAGAAT 58.239 37.037 0.00 0.00 0.00 2.40
2063 2120 7.690256 AGAATTAATGGTTACCAGAGAGTTGT 58.310 34.615 10.74 0.00 36.75 3.32
2140 2197 3.536158 TTTCAAATCAAGCTTCGTCGG 57.464 42.857 0.00 0.00 0.00 4.79
2141 2198 2.448926 TCAAATCAAGCTTCGTCGGA 57.551 45.000 0.00 0.00 0.00 4.55
2142 2199 2.972625 TCAAATCAAGCTTCGTCGGAT 58.027 42.857 0.00 0.00 0.00 4.18
2206 2263 0.608640 CGAACTTCCAGCCAGTACCT 59.391 55.000 0.00 0.00 0.00 3.08
2337 2394 8.899427 ATCATTTGTCATGTCTCCTTGTATAG 57.101 34.615 0.00 0.00 0.00 1.31
2381 2438 4.876107 CCAAGTTTGTTGCCTCTATATCGT 59.124 41.667 0.00 0.00 0.00 3.73
2527 2585 5.190925 ACAGGTGTTTCCCTTGCATATACTA 59.809 40.000 0.00 0.00 36.75 1.82
2562 2620 1.901591 CAGGTCCAGTGATTGCTTGT 58.098 50.000 0.00 0.00 0.00 3.16
2628 2686 1.425066 TCTTGTGCCAGTTTGAGGGAT 59.575 47.619 0.00 0.00 0.00 3.85
2815 2873 7.466805 TGAAAATAGATGCTCGTTGAATGAAG 58.533 34.615 0.00 0.00 0.00 3.02
2906 2964 2.683211 AACTTTTCATGGGAGCACCT 57.317 45.000 0.00 0.00 41.11 4.00
3154 3212 6.769822 ACTCAAACTGATCATATTCCATCACC 59.230 38.462 0.00 0.00 0.00 4.02
3182 3240 7.961351 AGATATGTATATAGCTCTTCCATGGC 58.039 38.462 6.96 0.00 29.87 4.40
3210 3268 1.203187 TGGAGCTGGTCTTCCTACTGT 60.203 52.381 6.83 0.00 34.23 3.55
3690 3756 5.518847 TGCTACAGTTTAGTTCATATGCGAC 59.481 40.000 0.00 0.00 0.00 5.19
3798 3866 5.363562 TGCATTCACCTGATCATTACTCT 57.636 39.130 0.00 0.00 0.00 3.24
3801 3899 5.466058 GCATTCACCTGATCATTACTCTCTG 59.534 44.000 0.00 0.00 0.00 3.35
3841 3939 6.596621 AGTTCTCTTAGGGCATATTTCTTCC 58.403 40.000 0.00 0.00 0.00 3.46
3876 3974 7.652300 TTTATATGGCTGTAACTAGCATTCG 57.348 36.000 0.00 0.00 45.46 3.34
3896 3994 9.523730 GCATTCGTTTTAATTTGTTCCAATAAC 57.476 29.630 0.00 0.00 0.00 1.89
3900 3998 7.595502 TCGTTTTAATTTGTTCCAATAACGCAT 59.404 29.630 0.00 0.00 36.68 4.73
3902 4000 9.523730 GTTTTAATTTGTTCCAATAACGCATTC 57.476 29.630 0.00 0.00 0.00 2.67
3939 4039 4.080863 CCCTAATCTACTGGCACTTCAAGT 60.081 45.833 0.00 0.00 0.00 3.16
4123 4227 3.728373 GGATGGCCTGGAACCCGT 61.728 66.667 3.32 0.00 0.00 5.28
4159 4263 1.698506 TGAACCAAAATGGCGAACCT 58.301 45.000 0.00 0.00 42.67 3.50
4189 4293 7.260558 TCTAGACATCAAGGTTATCAGTACG 57.739 40.000 0.00 0.00 0.00 3.67
4192 4296 6.331061 AGACATCAAGGTTATCAGTACGAAC 58.669 40.000 0.00 0.00 0.00 3.95
4252 4356 6.380274 ACGAAATACTATTCTCAGGGAACTCA 59.620 38.462 0.00 0.00 40.21 3.41
4293 4413 2.749621 GGTCAACTTGGCTTGAGGTATG 59.250 50.000 0.00 0.00 30.63 2.39
4294 4414 3.559171 GGTCAACTTGGCTTGAGGTATGA 60.559 47.826 0.00 0.00 30.63 2.15
4295 4415 4.072131 GTCAACTTGGCTTGAGGTATGAA 58.928 43.478 0.00 0.00 30.63 2.57
4296 4416 4.072131 TCAACTTGGCTTGAGGTATGAAC 58.928 43.478 0.00 0.00 0.00 3.18
4297 4417 4.074970 CAACTTGGCTTGAGGTATGAACT 58.925 43.478 0.00 0.00 0.00 3.01
4298 4418 3.944087 ACTTGGCTTGAGGTATGAACTC 58.056 45.455 0.00 0.00 35.55 3.01
4299 4419 3.274288 CTTGGCTTGAGGTATGAACTCC 58.726 50.000 0.00 0.00 34.06 3.85
4300 4420 1.207089 TGGCTTGAGGTATGAACTCCG 59.793 52.381 0.00 0.00 34.06 4.63
4301 4421 1.207329 GGCTTGAGGTATGAACTCCGT 59.793 52.381 0.00 0.00 34.06 4.69
4302 4422 2.354805 GGCTTGAGGTATGAACTCCGTT 60.355 50.000 0.00 0.00 34.06 4.44
4303 4423 3.335579 GCTTGAGGTATGAACTCCGTTT 58.664 45.455 0.00 0.00 34.06 3.60
4304 4424 3.125316 GCTTGAGGTATGAACTCCGTTTG 59.875 47.826 0.00 0.00 34.06 2.93
4305 4425 2.695359 TGAGGTATGAACTCCGTTTGC 58.305 47.619 0.00 0.00 34.06 3.68
4306 4426 2.007608 GAGGTATGAACTCCGTTTGCC 58.992 52.381 0.00 0.00 0.00 4.52
4307 4427 1.349688 AGGTATGAACTCCGTTTGCCA 59.650 47.619 0.00 0.00 0.00 4.92
4308 4428 2.026262 AGGTATGAACTCCGTTTGCCAT 60.026 45.455 0.00 0.00 0.00 4.40
4358 4478 2.892852 TGGCCTTCTCAAATTTGTCTGG 59.107 45.455 17.47 15.16 0.00 3.86
4373 4493 3.534554 TGTCTGGTGTCATGTGCATATC 58.465 45.455 0.00 0.00 0.00 1.63
4414 4534 2.781174 ACCTGGAAAGAAGGTAACCACA 59.219 45.455 0.00 0.00 46.44 4.17
4606 4727 3.591527 TCCTTAGAGAAATTTGCAGGGGA 59.408 43.478 0.00 0.00 0.00 4.81
4704 4827 8.814235 CAATAATTTTCCAGATTGTCATGCTTC 58.186 33.333 0.00 0.00 0.00 3.86
4711 4834 4.569966 CCAGATTGTCATGCTTCTCTGTAC 59.430 45.833 11.62 0.00 0.00 2.90
4713 4836 5.291371 CAGATTGTCATGCTTCTCTGTACTG 59.709 44.000 0.00 0.00 0.00 2.74
4721 4844 2.739379 GCTTCTCTGTACTGTTTCCAGC 59.261 50.000 0.00 0.00 42.81 4.85
4751 4882 7.669722 AGTTACAATGTTACCTTGAATGATGGT 59.330 33.333 7.34 0.00 36.15 3.55
4812 4943 4.705991 TCATGATTTGGCTGTGATTGCTAA 59.294 37.500 0.00 0.00 0.00 3.09
4839 4970 2.939103 ACAGACTGACAGTTGAAGCAAC 59.061 45.455 10.01 2.22 43.83 4.17
4840 4971 2.289002 CAGACTGACAGTTGAAGCAACC 59.711 50.000 10.01 0.00 44.49 3.77
4865 5002 2.518949 GTGACAATGGCAAAGCATACG 58.481 47.619 0.00 0.00 0.00 3.06
4891 5028 5.298276 TCAAGAAGCCGATAACAAAACAGTT 59.702 36.000 0.00 0.00 35.55 3.16
4973 5110 8.052748 ACTGCAATAACCATTCACCTATTTAGA 58.947 33.333 0.00 0.00 0.00 2.10
4974 5111 8.815565 TGCAATAACCATTCACCTATTTAGAA 57.184 30.769 0.00 0.00 0.00 2.10
4975 5112 9.420118 TGCAATAACCATTCACCTATTTAGAAT 57.580 29.630 0.00 0.00 32.53 2.40
4976 5113 9.899226 GCAATAACCATTCACCTATTTAGAATC 57.101 33.333 0.00 0.00 30.04 2.52
4982 5119 9.838339 ACCATTCACCTATTTAGAATCACTTAG 57.162 33.333 0.00 0.00 30.04 2.18
5011 5148 1.602377 CAGGGACAACTTTCAACGGTC 59.398 52.381 0.00 0.00 0.00 4.79
5042 5179 9.624697 TGCTCAACAAATCTTACATTGAATTAC 57.375 29.630 0.00 0.00 0.00 1.89
5093 5230 5.095490 GCTGCCAAATGTTACAACTGATAC 58.905 41.667 0.00 0.00 0.00 2.24
5127 5264 4.956075 TGTATGAGGAGAACAGCAGATGTA 59.044 41.667 0.00 0.00 43.00 2.29
5128 5265 5.600069 TGTATGAGGAGAACAGCAGATGTAT 59.400 40.000 0.00 0.00 43.00 2.29
5189 5327 4.157472 TCATGTATTTGAATTCTGCCGCAA 59.843 37.500 7.05 0.00 0.00 4.85
5202 5340 1.092345 GCCGCAACTTCTCCATCCTC 61.092 60.000 0.00 0.00 0.00 3.71
5273 5411 6.509418 TTCATTAGTATCTTTTGGCACACC 57.491 37.500 0.00 0.00 39.29 4.16
5275 5413 2.969821 AGTATCTTTTGGCACACCCA 57.030 45.000 0.00 0.00 43.51 4.51
5309 5449 1.511613 CATGGAAGAGCTAGGGGGAA 58.488 55.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
402 438 8.725606 AATAATGCATAGGAAATTATGGTGGT 57.274 30.769 0.00 0.00 32.77 4.16
494 530 5.090652 TCGAAACCGAGTTCAAATTTCAG 57.909 39.130 0.00 0.00 31.11 3.02
519 555 1.983605 ACTGTTGATAAACTCGCGTCG 59.016 47.619 5.77 0.58 0.00 5.12
602 638 0.451783 GTTGACAATGCCGGATGGAC 59.548 55.000 5.05 0.47 37.49 4.02
603 639 0.037447 TGTTGACAATGCCGGATGGA 59.963 50.000 5.05 0.00 37.49 3.41
604 640 0.452987 CTGTTGACAATGCCGGATGG 59.547 55.000 5.05 0.00 38.77 3.51
605 641 1.131126 GTCTGTTGACAATGCCGGATG 59.869 52.381 5.05 2.64 42.48 3.51
606 642 1.453155 GTCTGTTGACAATGCCGGAT 58.547 50.000 5.05 0.00 42.48 4.18
607 643 0.948623 CGTCTGTTGACAATGCCGGA 60.949 55.000 5.05 0.00 43.06 5.14
608 644 1.227999 ACGTCTGTTGACAATGCCGG 61.228 55.000 0.00 0.00 43.06 6.13
609 645 0.110688 CACGTCTGTTGACAATGCCG 60.111 55.000 0.00 0.00 43.06 5.69
610 646 0.944386 ACACGTCTGTTGACAATGCC 59.056 50.000 0.00 0.00 43.06 4.40
611 647 1.069906 GGACACGTCTGTTGACAATGC 60.070 52.381 0.00 0.00 43.06 3.56
612 648 1.192312 CGGACACGTCTGTTGACAATG 59.808 52.381 0.00 0.00 43.06 2.82
613 649 1.067974 TCGGACACGTCTGTTGACAAT 59.932 47.619 5.93 0.00 43.06 2.71
614 650 0.456628 TCGGACACGTCTGTTGACAA 59.543 50.000 5.93 0.00 43.06 3.18
615 651 0.456628 TTCGGACACGTCTGTTGACA 59.543 50.000 5.93 0.00 43.06 3.58
616 652 0.850856 GTTCGGACACGTCTGTTGAC 59.149 55.000 5.93 1.28 41.85 3.18
617 653 0.593008 CGTTCGGACACGTCTGTTGA 60.593 55.000 5.93 0.00 41.85 3.18
618 654 1.844003 CGTTCGGACACGTCTGTTG 59.156 57.895 5.93 0.00 41.85 3.33
619 655 1.947642 GCGTTCGGACACGTCTGTT 60.948 57.895 5.93 0.00 42.43 3.16
620 656 2.354305 GCGTTCGGACACGTCTGT 60.354 61.111 5.93 0.00 42.43 3.41
621 657 2.050351 AGCGTTCGGACACGTCTG 60.050 61.111 0.00 0.00 42.43 3.51
622 658 2.254651 GAGCGTTCGGACACGTCT 59.745 61.111 0.00 10.00 42.43 4.18
623 659 2.804090 GGAGCGTTCGGACACGTC 60.804 66.667 0.00 9.07 42.43 4.34
624 660 4.353437 GGGAGCGTTCGGACACGT 62.353 66.667 0.00 0.00 42.43 4.49
637 673 0.179092 CCCCTAAAAGTACGCGGGAG 60.179 60.000 12.47 0.00 37.05 4.30
638 674 0.614415 TCCCCTAAAAGTACGCGGGA 60.614 55.000 12.47 0.00 37.05 5.14
639 675 0.466963 ATCCCCTAAAAGTACGCGGG 59.533 55.000 12.47 0.00 34.62 6.13
640 676 1.578583 CATCCCCTAAAAGTACGCGG 58.421 55.000 12.47 0.00 0.00 6.46
641 677 1.137479 TCCATCCCCTAAAAGTACGCG 59.863 52.381 3.53 3.53 0.00 6.01
642 678 2.994186 TCCATCCCCTAAAAGTACGC 57.006 50.000 0.00 0.00 0.00 4.42
643 679 4.036380 GCAAATCCATCCCCTAAAAGTACG 59.964 45.833 0.00 0.00 0.00 3.67
644 680 4.341235 GGCAAATCCATCCCCTAAAAGTAC 59.659 45.833 0.00 0.00 34.01 2.73
645 681 4.231890 AGGCAAATCCATCCCCTAAAAGTA 59.768 41.667 0.00 0.00 37.29 2.24
646 682 3.012844 AGGCAAATCCATCCCCTAAAAGT 59.987 43.478 0.00 0.00 37.29 2.66
647 683 3.385755 CAGGCAAATCCATCCCCTAAAAG 59.614 47.826 0.00 0.00 37.29 2.27
648 684 3.373830 CAGGCAAATCCATCCCCTAAAA 58.626 45.455 0.00 0.00 37.29 1.52
649 685 2.359143 CCAGGCAAATCCATCCCCTAAA 60.359 50.000 0.00 0.00 37.29 1.85
650 686 1.217689 CCAGGCAAATCCATCCCCTAA 59.782 52.381 0.00 0.00 37.29 2.69
651 687 0.852842 CCAGGCAAATCCATCCCCTA 59.147 55.000 0.00 0.00 37.29 3.53
652 688 1.224003 ACCAGGCAAATCCATCCCCT 61.224 55.000 0.00 0.00 37.29 4.79
653 689 0.325577 AACCAGGCAAATCCATCCCC 60.326 55.000 0.00 0.00 37.29 4.81
654 690 0.826062 CAACCAGGCAAATCCATCCC 59.174 55.000 0.00 0.00 37.29 3.85
655 691 1.560505 ACAACCAGGCAAATCCATCC 58.439 50.000 0.00 0.00 37.29 3.51
656 692 2.689983 CCTACAACCAGGCAAATCCATC 59.310 50.000 0.00 0.00 37.29 3.51
657 693 2.042979 ACCTACAACCAGGCAAATCCAT 59.957 45.455 0.00 0.00 39.53 3.41
658 694 1.427368 ACCTACAACCAGGCAAATCCA 59.573 47.619 0.00 0.00 39.53 3.41
659 695 1.818674 CACCTACAACCAGGCAAATCC 59.181 52.381 0.00 0.00 39.53 3.01
660 696 1.818674 CCACCTACAACCAGGCAAATC 59.181 52.381 0.00 0.00 39.53 2.17
661 697 1.923356 CCACCTACAACCAGGCAAAT 58.077 50.000 0.00 0.00 39.53 2.32
662 698 0.825840 GCCACCTACAACCAGGCAAA 60.826 55.000 0.00 0.00 44.59 3.68
663 699 1.228429 GCCACCTACAACCAGGCAA 60.228 57.895 0.00 0.00 44.59 4.52
664 700 2.434331 GCCACCTACAACCAGGCA 59.566 61.111 0.00 0.00 44.59 4.75
665 701 0.326927 TTAGCCACCTACAACCAGGC 59.673 55.000 0.00 0.00 45.54 4.85
666 702 1.628846 ACTTAGCCACCTACAACCAGG 59.371 52.381 0.00 0.00 41.87 4.45
667 703 3.514309 ACTACTTAGCCACCTACAACCAG 59.486 47.826 0.00 0.00 0.00 4.00
668 704 3.513517 ACTACTTAGCCACCTACAACCA 58.486 45.455 0.00 0.00 0.00 3.67
669 705 4.548451 AACTACTTAGCCACCTACAACC 57.452 45.455 0.00 0.00 0.00 3.77
670 706 6.872628 AAAAACTACTTAGCCACCTACAAC 57.127 37.500 0.00 0.00 0.00 3.32
694 730 6.851222 TTCTTTTGCACAGTGTTTCAAAAA 57.149 29.167 22.91 15.63 37.77 1.94
695 731 6.851222 TTTCTTTTGCACAGTGTTTCAAAA 57.149 29.167 22.04 22.04 37.05 2.44
696 732 6.648310 TGATTTCTTTTGCACAGTGTTTCAAA 59.352 30.769 13.54 13.54 0.00 2.69
697 733 6.162079 TGATTTCTTTTGCACAGTGTTTCAA 58.838 32.000 1.61 0.00 0.00 2.69
698 734 5.718146 TGATTTCTTTTGCACAGTGTTTCA 58.282 33.333 1.61 0.00 0.00 2.69
699 735 6.833342 ATGATTTCTTTTGCACAGTGTTTC 57.167 33.333 1.61 0.00 0.00 2.78
700 736 8.715191 TTAATGATTTCTTTTGCACAGTGTTT 57.285 26.923 1.61 0.00 0.00 2.83
701 737 8.715191 TTTAATGATTTCTTTTGCACAGTGTT 57.285 26.923 1.61 0.00 0.00 3.32
702 738 8.715191 TTTTAATGATTTCTTTTGCACAGTGT 57.285 26.923 1.61 0.00 0.00 3.55
732 768 9.355916 GGACTATTTGCTTCCTAGGATTAAATT 57.644 33.333 22.76 12.84 0.00 1.82
733 769 8.502738 TGGACTATTTGCTTCCTAGGATTAAAT 58.497 33.333 13.57 19.27 0.00 1.40
734 770 7.867921 TGGACTATTTGCTTCCTAGGATTAAA 58.132 34.615 13.57 14.06 0.00 1.52
735 771 7.127339 ACTGGACTATTTGCTTCCTAGGATTAA 59.873 37.037 13.57 5.56 0.00 1.40
736 772 6.615726 ACTGGACTATTTGCTTCCTAGGATTA 59.384 38.462 13.57 0.00 0.00 1.75
737 773 5.430089 ACTGGACTATTTGCTTCCTAGGATT 59.570 40.000 13.57 0.00 0.00 3.01
738 774 4.971924 ACTGGACTATTTGCTTCCTAGGAT 59.028 41.667 13.57 0.00 0.00 3.24
739 775 4.362677 ACTGGACTATTTGCTTCCTAGGA 58.637 43.478 7.62 7.62 0.00 2.94
740 776 4.762289 ACTGGACTATTTGCTTCCTAGG 57.238 45.455 0.82 0.82 0.00 3.02
741 777 6.716934 TCTACTGGACTATTTGCTTCCTAG 57.283 41.667 0.00 0.00 0.00 3.02
742 778 7.490657 TTTCTACTGGACTATTTGCTTCCTA 57.509 36.000 0.00 0.00 0.00 2.94
743 779 6.374417 TTTCTACTGGACTATTTGCTTCCT 57.626 37.500 0.00 0.00 0.00 3.36
744 780 7.448748 TTTTTCTACTGGACTATTTGCTTCC 57.551 36.000 0.00 0.00 0.00 3.46
745 781 8.730680 TGATTTTTCTACTGGACTATTTGCTTC 58.269 33.333 0.00 0.00 0.00 3.86
746 782 8.635765 TGATTTTTCTACTGGACTATTTGCTT 57.364 30.769 0.00 0.00 0.00 3.91
747 783 8.814038 ATGATTTTTCTACTGGACTATTTGCT 57.186 30.769 0.00 0.00 0.00 3.91
753 789 9.871238 GACTGTTATGATTTTTCTACTGGACTA 57.129 33.333 0.00 0.00 0.00 2.59
754 790 8.598041 AGACTGTTATGATTTTTCTACTGGACT 58.402 33.333 0.00 0.00 0.00 3.85
755 791 8.779354 AGACTGTTATGATTTTTCTACTGGAC 57.221 34.615 0.00 0.00 0.00 4.02
756 792 9.871238 GTAGACTGTTATGATTTTTCTACTGGA 57.129 33.333 0.00 0.00 33.95 3.86
757 793 8.808529 CGTAGACTGTTATGATTTTTCTACTGG 58.191 37.037 0.00 0.00 34.38 4.00
758 794 8.808529 CCGTAGACTGTTATGATTTTTCTACTG 58.191 37.037 0.00 0.00 34.38 2.74
759 795 8.746530 TCCGTAGACTGTTATGATTTTTCTACT 58.253 33.333 0.00 0.00 34.38 2.57
760 796 8.922058 TCCGTAGACTGTTATGATTTTTCTAC 57.078 34.615 0.00 0.00 33.58 2.59
761 797 9.745880 GATCCGTAGACTGTTATGATTTTTCTA 57.254 33.333 0.00 0.00 0.00 2.10
762 798 8.478877 AGATCCGTAGACTGTTATGATTTTTCT 58.521 33.333 0.00 0.00 0.00 2.52
763 799 8.543774 CAGATCCGTAGACTGTTATGATTTTTC 58.456 37.037 0.00 0.00 0.00 2.29
764 800 7.495934 CCAGATCCGTAGACTGTTATGATTTTT 59.504 37.037 0.00 0.00 0.00 1.94
765 801 6.986817 CCAGATCCGTAGACTGTTATGATTTT 59.013 38.462 0.00 0.00 0.00 1.82
766 802 6.323996 TCCAGATCCGTAGACTGTTATGATTT 59.676 38.462 0.00 0.00 0.00 2.17
767 803 5.833667 TCCAGATCCGTAGACTGTTATGATT 59.166 40.000 0.00 0.00 0.00 2.57
768 804 5.386060 TCCAGATCCGTAGACTGTTATGAT 58.614 41.667 0.00 0.00 0.00 2.45
769 805 4.788679 TCCAGATCCGTAGACTGTTATGA 58.211 43.478 0.00 0.00 0.00 2.15
770 806 5.010112 ACATCCAGATCCGTAGACTGTTATG 59.990 44.000 0.00 0.00 33.47 1.90
771 807 5.141182 ACATCCAGATCCGTAGACTGTTAT 58.859 41.667 0.00 0.00 0.00 1.89
772 808 4.533815 ACATCCAGATCCGTAGACTGTTA 58.466 43.478 0.00 0.00 0.00 2.41
773 809 3.366396 ACATCCAGATCCGTAGACTGTT 58.634 45.455 0.00 0.00 0.00 3.16
774 810 3.019799 ACATCCAGATCCGTAGACTGT 57.980 47.619 0.00 0.00 0.00 3.55
775 811 5.713792 ATTACATCCAGATCCGTAGACTG 57.286 43.478 0.00 0.00 0.00 3.51
776 812 6.732896 AAATTACATCCAGATCCGTAGACT 57.267 37.500 0.00 0.00 0.00 3.24
777 813 7.787725 AAAAATTACATCCAGATCCGTAGAC 57.212 36.000 0.00 0.00 0.00 2.59
806 842 9.863845 TCATGATAGTACAACGAACAATAGAAA 57.136 29.630 0.00 0.00 0.00 2.52
810 846 9.810545 TCAATCATGATAGTACAACGAACAATA 57.189 29.630 9.04 0.00 0.00 1.90
811 847 8.716646 TCAATCATGATAGTACAACGAACAAT 57.283 30.769 9.04 0.00 0.00 2.71
812 848 8.541133 TTCAATCATGATAGTACAACGAACAA 57.459 30.769 9.04 0.00 34.96 2.83
813 849 8.032451 TCTTCAATCATGATAGTACAACGAACA 58.968 33.333 9.04 0.00 34.96 3.18
814 850 8.407457 TCTTCAATCATGATAGTACAACGAAC 57.593 34.615 9.04 0.00 34.96 3.95
815 851 9.034544 CATCTTCAATCATGATAGTACAACGAA 57.965 33.333 9.04 2.03 34.96 3.85
816 852 8.413229 TCATCTTCAATCATGATAGTACAACGA 58.587 33.333 9.04 0.00 34.96 3.85
817 853 8.579682 TCATCTTCAATCATGATAGTACAACG 57.420 34.615 9.04 0.00 34.96 4.10
985 1021 3.921104 TCCTCATGCTCTAGTTGGAGAT 58.079 45.455 0.00 0.00 35.52 2.75
993 1029 2.141517 CGCCAAATCCTCATGCTCTAG 58.858 52.381 0.00 0.00 0.00 2.43
994 1030 1.486310 ACGCCAAATCCTCATGCTCTA 59.514 47.619 0.00 0.00 0.00 2.43
1265 1301 4.083862 GTGTCCAGGACCGAGGCC 62.084 72.222 17.59 0.00 0.00 5.19
1520 1575 2.129607 GCATTGCAAGACAAACCACTG 58.870 47.619 4.94 0.00 42.86 3.66
1574 1629 2.035066 GCAGTGATGCAAAGTTCTGGTT 59.965 45.455 0.00 0.00 34.41 3.67
1676 1731 5.288804 TGAACTAAAACAAAGGCAATGCTC 58.711 37.500 4.82 0.00 0.00 4.26
1704 1759 3.945981 ATTGTTCATCATGCAGCACAA 57.054 38.095 0.00 0.00 0.00 3.33
1794 1849 7.745620 AAGTACAAGAACAAAATCCCAGTAG 57.254 36.000 0.00 0.00 0.00 2.57
1843 1898 5.248870 ACAAAACTACCAAAGTCAAGCAG 57.751 39.130 0.00 0.00 37.50 4.24
1901 1956 9.161629 TGCGGTATCAATACAATATGAAATAGG 57.838 33.333 2.80 0.00 34.98 2.57
1912 1967 5.880887 TGGTTAATGTGCGGTATCAATACAA 59.119 36.000 2.80 0.00 34.98 2.41
1913 1968 5.429130 TGGTTAATGTGCGGTATCAATACA 58.571 37.500 2.80 0.00 34.98 2.29
2042 2099 6.228258 GTGACAACTCTCTGGTAACCATTAA 58.772 40.000 0.00 0.00 30.82 1.40
2063 2120 0.738975 GGACATCGAGTGATCGGTGA 59.261 55.000 16.98 0.00 46.13 4.02
2135 2192 2.410939 AGCATGAATCATCATCCGACG 58.589 47.619 0.00 0.00 44.53 5.12
2140 2197 8.725405 AATCAGATCTAGCATGAATCATCATC 57.275 34.615 0.00 0.00 44.53 2.92
2142 2199 7.819900 CAGAATCAGATCTAGCATGAATCATCA 59.180 37.037 0.00 0.00 40.57 3.07
2206 2263 1.351017 CTGGTTCCCCTAAGCTTGACA 59.649 52.381 9.86 0.00 36.51 3.58
2337 2394 5.920903 TGGGTGTATATTAACTGTACCTGC 58.079 41.667 0.00 0.00 0.00 4.85
2381 2438 3.837570 CTGCACAGGAGCTGCACCA 62.838 63.158 18.31 0.00 39.76 4.17
2527 2585 1.452651 CTGCATCCAAGGCACGGAT 60.453 57.895 2.09 2.09 44.35 4.18
2562 2620 5.562696 GCATTCATCGACAGAAAACCTTTCA 60.563 40.000 6.26 0.00 0.00 2.69
2628 2686 4.142534 GCTTTTGCATAGCAGTCAAGATGA 60.143 41.667 14.50 0.00 46.58 2.92
2838 2896 4.634004 CACAGACAGACACCACACTAAAAA 59.366 41.667 0.00 0.00 0.00 1.94
2949 3007 2.089201 CCTTGCACAGAAGCATCATCA 58.911 47.619 0.00 0.00 45.19 3.07
3170 3228 2.057137 TGTAATGGCCATGGAAGAGC 57.943 50.000 21.63 5.32 0.00 4.09
3195 3253 6.130569 AGAGGTATAACAGTAGGAAGACCAG 58.869 44.000 0.00 0.00 38.94 4.00
3406 3464 2.479566 TGGAGTCATCTTGTGGCTTC 57.520 50.000 0.00 0.00 44.48 3.86
3690 3756 9.226345 GAATTTGATAAGGATTTTAGCAAGTCG 57.774 33.333 0.00 0.00 32.78 4.18
3753 3819 1.273986 AATGGGCTTGCAATTCCCCC 61.274 55.000 25.52 20.04 39.30 5.40
3801 3899 7.524912 TAAGAGAACTTCAGTACACATCGTAC 58.475 38.462 0.00 0.00 42.36 3.67
3861 3959 9.607285 ACAAATTAAAACGAATGCTAGTTACAG 57.393 29.630 0.00 0.00 0.00 2.74
3900 3998 1.048601 AGGGTTTCAGTCTCAGCGAA 58.951 50.000 0.00 0.00 0.00 4.70
3902 4000 2.743636 TTAGGGTTTCAGTCTCAGCG 57.256 50.000 0.00 0.00 0.00 5.18
4114 4218 3.976339 CAATTTTGCACGGGTTCCA 57.024 47.368 0.00 0.00 0.00 3.53
4139 4243 2.029110 CAGGTTCGCCATTTTGGTTCAT 60.029 45.455 0.00 0.00 40.46 2.57
4293 4413 4.083003 TCATTGTTATGGCAAACGGAGTTC 60.083 41.667 0.00 0.00 40.35 3.01
4294 4414 3.823873 TCATTGTTATGGCAAACGGAGTT 59.176 39.130 0.00 0.00 41.97 3.01
4295 4415 3.190535 GTCATTGTTATGGCAAACGGAGT 59.809 43.478 0.00 0.00 38.37 3.85
4296 4416 3.190327 TGTCATTGTTATGGCAAACGGAG 59.810 43.478 0.00 0.00 43.10 4.63
4297 4417 3.149981 TGTCATTGTTATGGCAAACGGA 58.850 40.909 0.00 0.00 43.10 4.69
4298 4418 3.567576 TGTCATTGTTATGGCAAACGG 57.432 42.857 0.00 0.00 43.10 4.44
4304 4424 4.644103 AGCAGAATGTCATTGTTATGGC 57.356 40.909 1.88 0.00 39.31 4.40
4305 4425 5.957798 ACAAGCAGAATGTCATTGTTATGG 58.042 37.500 1.88 0.00 36.49 2.74
4306 4426 7.878477 AAACAAGCAGAATGTCATTGTTATG 57.122 32.000 1.88 0.85 43.37 1.90
4307 4427 7.095523 GCAAAACAAGCAGAATGTCATTGTTAT 60.096 33.333 1.88 0.00 43.37 1.89
4308 4428 6.200665 GCAAAACAAGCAGAATGTCATTGTTA 59.799 34.615 1.88 0.00 43.37 2.41
4358 4478 3.801698 AGACCTGATATGCACATGACAC 58.198 45.455 0.00 0.00 0.00 3.67
4373 4493 2.851798 GCTGAAGCTCCAAGACCTG 58.148 57.895 0.00 0.00 38.21 4.00
4414 4534 0.539051 CATTCCAGAAGTCCCGAGCT 59.461 55.000 0.00 0.00 0.00 4.09
4562 4683 6.897413 AGGATAAATGTCAACAGCCCTTTAAT 59.103 34.615 0.00 0.00 0.00 1.40
4606 4727 8.962884 ACAAAAATTAAGACCATCTTTTTGCT 57.037 26.923 15.65 5.93 44.58 3.91
4713 4836 6.803154 AACATTGTAACTAGAGCTGGAAAC 57.197 37.500 0.00 0.00 0.00 2.78
4721 4844 9.653287 TCATTCAAGGTAACATTGTAACTAGAG 57.347 33.333 0.00 0.00 41.41 2.43
4751 4882 5.760743 TGATGAAACCAACGTTATTCTGTCA 59.239 36.000 16.65 16.33 0.00 3.58
4812 4943 2.432146 TCAACTGTCAGTCTGTGAAGCT 59.568 45.455 5.82 0.00 36.74 3.74
4839 4970 0.831288 TTTGCCATTGTCACCCCTGG 60.831 55.000 0.00 0.00 0.00 4.45
4840 4971 0.604578 CTTTGCCATTGTCACCCCTG 59.395 55.000 0.00 0.00 0.00 4.45
4865 5002 5.516090 TGTTTTGTTATCGGCTTCTTGAAC 58.484 37.500 0.00 0.00 0.00 3.18
4891 5028 1.891919 GTGCCGTTTGGAGCTGTCA 60.892 57.895 0.00 0.00 37.49 3.58
4973 5110 5.940470 GTCCCTGTTGTGATTCTAAGTGATT 59.060 40.000 0.00 0.00 0.00 2.57
4974 5111 5.013079 TGTCCCTGTTGTGATTCTAAGTGAT 59.987 40.000 0.00 0.00 0.00 3.06
4975 5112 4.346709 TGTCCCTGTTGTGATTCTAAGTGA 59.653 41.667 0.00 0.00 0.00 3.41
4976 5113 4.641396 TGTCCCTGTTGTGATTCTAAGTG 58.359 43.478 0.00 0.00 0.00 3.16
4977 5114 4.974645 TGTCCCTGTTGTGATTCTAAGT 57.025 40.909 0.00 0.00 0.00 2.24
4978 5115 5.308825 AGTTGTCCCTGTTGTGATTCTAAG 58.691 41.667 0.00 0.00 0.00 2.18
4979 5116 5.304686 AGTTGTCCCTGTTGTGATTCTAA 57.695 39.130 0.00 0.00 0.00 2.10
4980 5117 4.974645 AGTTGTCCCTGTTGTGATTCTA 57.025 40.909 0.00 0.00 0.00 2.10
4981 5118 3.864789 AGTTGTCCCTGTTGTGATTCT 57.135 42.857 0.00 0.00 0.00 2.40
4982 5119 4.338118 TGAAAGTTGTCCCTGTTGTGATTC 59.662 41.667 0.00 0.00 0.00 2.52
5042 5179 2.333926 TCAGGTCGATGTTTTGCGTAG 58.666 47.619 0.00 0.00 0.00 3.51
5112 5249 9.619316 CTGTATACTTATACATCTGCTGTTCTC 57.381 37.037 9.10 0.00 45.19 2.87
5145 5282 7.448469 ACATGAAGTTAGTCCTTGCTAAAATGT 59.552 33.333 0.00 0.00 33.34 2.71
5189 5327 2.584965 TGGAGAGAGAGGATGGAGAAGT 59.415 50.000 0.00 0.00 0.00 3.01
5202 5340 4.259356 TGCAAAAGATGTCATGGAGAGAG 58.741 43.478 0.00 0.00 0.00 3.20
5273 5411 8.097078 TCTTCCATGCATTTTGTTTATTTTGG 57.903 30.769 0.00 0.00 0.00 3.28
5275 5413 7.662669 AGCTCTTCCATGCATTTTGTTTATTTT 59.337 29.630 0.00 0.00 0.00 1.82
5309 5449 5.808366 TCCCTCATTAGCGATGAAGTAAT 57.192 39.130 7.15 0.00 43.93 1.89


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

AutoCloner maintained by Alex Coulton.