Multiple sequence alignment - TraesCS1A01G129200

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 TraesCS1A01G129200 chr1A 100.000 6291 0 0 1 6291 163398226 163391936 0.000000e+00 11618.0
1 TraesCS1A01G129200 chr1B 97.105 4767 95 21 810 5565 201753662 201758396 0.000000e+00 7998.0
2 TraesCS1A01G129200 chr1B 95.531 358 15 1 5562 5918 201758553 201758910 7.080000e-159 571.0
3 TraesCS1A01G129200 chr1B 93.750 48 3 0 5979 6026 576137960 576137913 8.750000e-09 73.1
4 TraesCS1A01G129200 chr1D 96.502 4660 103 20 921 5560 134675473 134680092 0.000000e+00 7648.0
5 TraesCS1A01G129200 chr1D 91.646 395 20 10 5554 5936 134680389 134680782 9.280000e-148 534.0
6 TraesCS1A01G129200 chr1D 81.850 573 91 11 96 664 198725774 198725211 2.660000e-128 470.0
7 TraesCS1A01G129200 chrUn 100.000 384 0 0 2634 3017 480934145 480934528 0.000000e+00 710.0
8 TraesCS1A01G129200 chrUn 83.103 651 99 10 1 648 255848088 255848730 3.270000e-162 582.0
9 TraesCS1A01G129200 chrUn 83.103 651 99 10 1 648 304161220 304160578 3.270000e-162 582.0
10 TraesCS1A01G129200 chrUn 83.103 651 99 10 1 648 304165619 304164977 3.270000e-162 582.0
11 TraesCS1A01G129200 chrUn 83.103 651 99 10 1 648 325089257 325089899 3.270000e-162 582.0
12 TraesCS1A01G129200 chr5D 87.849 609 67 3 1 609 170477060 170477661 0.000000e+00 708.0
13 TraesCS1A01G129200 chr4A 83.388 608 90 5 60 666 347190810 347191407 2.560000e-153 553.0
14 TraesCS1A01G129200 chr3D 80.564 674 108 20 1 664 495931170 495931830 1.220000e-136 497.0
15 TraesCS1A01G129200 chr6A 90.710 366 16 5 5942 6291 97136770 97136407 7.380000e-129 472.0
16 TraesCS1A01G129200 chr6A 90.196 255 11 2 6051 6291 133637422 133637168 2.830000e-83 320.0
17 TraesCS1A01G129200 chr6A 95.726 117 5 0 5942 6058 133639951 133639835 8.330000e-44 189.0
18 TraesCS1A01G129200 chr6D 78.190 674 125 19 1 664 212820669 212821330 1.630000e-110 411.0
19 TraesCS1A01G129200 chr6D 83.654 208 16 5 5989 6182 62147148 62146945 5.010000e-41 180.0
20 TraesCS1A01G129200 chr6D 96.000 100 4 0 5942 6041 62147247 62147148 5.050000e-36 163.0
21 TraesCS1A01G129200 chr6D 91.429 70 5 1 5958 6026 269900254 269900323 1.870000e-15 95.3
22 TraesCS1A01G129200 chr7D 86.800 250 18 3 5942 6177 91711709 91711461 1.340000e-66 265.0
23 TraesCS1A01G129200 chr4B 95.000 80 4 0 5942 6021 547312775 547312696 6.620000e-25 126.0
24 TraesCS1A01G129200 chr2A 92.941 85 6 0 5942 6026 163532903 163532987 2.380000e-24 124.0


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 TraesCS1A01G129200 chr1A 163391936 163398226 6290 True 11618.0 11618 100.000 1 6291 1 chr1A.!!$R1 6290
1 TraesCS1A01G129200 chr1B 201753662 201758910 5248 False 4284.5 7998 96.318 810 5918 2 chr1B.!!$F1 5108
2 TraesCS1A01G129200 chr1D 134675473 134680782 5309 False 4091.0 7648 94.074 921 5936 2 chr1D.!!$F1 5015
3 TraesCS1A01G129200 chr1D 198725211 198725774 563 True 470.0 470 81.850 96 664 1 chr1D.!!$R1 568
4 TraesCS1A01G129200 chrUn 255848088 255848730 642 False 582.0 582 83.103 1 648 1 chrUn.!!$F1 647
5 TraesCS1A01G129200 chrUn 304160578 304165619 5041 True 582.0 582 83.103 1 648 2 chrUn.!!$R1 647
6 TraesCS1A01G129200 chrUn 325089257 325089899 642 False 582.0 582 83.103 1 648 1 chrUn.!!$F2 647
7 TraesCS1A01G129200 chr5D 170477060 170477661 601 False 708.0 708 87.849 1 609 1 chr5D.!!$F1 608
8 TraesCS1A01G129200 chr4A 347190810 347191407 597 False 553.0 553 83.388 60 666 1 chr4A.!!$F1 606
9 TraesCS1A01G129200 chr3D 495931170 495931830 660 False 497.0 497 80.564 1 664 1 chr3D.!!$F1 663
10 TraesCS1A01G129200 chr6A 133637168 133639951 2783 True 254.5 320 92.961 5942 6291 2 chr6A.!!$R2 349
11 TraesCS1A01G129200 chr6D 212820669 212821330 661 False 411.0 411 78.190 1 664 1 chr6D.!!$F1 663

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
758 765 0.035056 CCCCGATTCAACCAGAAGCT 60.035 55.000 0.00 0.00 40.43 3.74 F
773 780 0.244721 AAGCTTCATTTTCTGCGGGC 59.755 50.000 0.00 0.00 0.00 6.13 F
775 782 0.244721 GCTTCATTTTCTGCGGGCTT 59.755 50.000 0.00 0.00 0.00 4.35 F
983 2463 0.323629 TTCTAAGGCAACCCCACGAG 59.676 55.000 0.00 0.00 35.39 4.18 F
1152 2635 2.310233 CGGTGTCCTGCGTGTTCTG 61.310 63.158 0.00 0.00 0.00 3.02 F
1466 3231 2.472695 TTATGCGTGGTGAGCTTTCT 57.527 45.000 0.00 0.00 35.28 2.52 F
1735 3500 4.778579 AGAAGATTGGATCACATGTGAGG 58.221 43.478 30.63 4.97 43.61 3.86 F
3101 4911 3.594603 ACCTATGAACCACGACTCTTG 57.405 47.619 0.00 0.00 0.00 3.02 F
4247 6253 1.751351 TCACGACATCAGAGGACATCC 59.249 52.381 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 3773 0.762418 ACACGGAATCCAACAGACCA 59.238 50.000 0.00 0.00 0.00 4.02 R
2223 4031 2.171448 AGGTGCAGCAATAGGACTAAGG 59.829 50.000 19.63 0.00 0.00 2.69 R
2302 4110 7.202016 TCTCTTCACGCAAAATAAACAGAAT 57.798 32.000 0.00 0.00 0.00 2.40 R
3021 4831 6.684979 CGCACAAATAAAAACAAAGGGAAAAC 59.315 34.615 0.00 0.00 0.00 2.43 R
3091 4901 2.071688 ACTTAGCTGCAAGAGTCGTG 57.928 50.000 15.41 1.20 34.07 4.35 R
3101 4911 6.480320 ACAGTGCAGTAAATATACTTAGCTGC 59.520 38.462 15.46 15.46 45.42 5.25 R
4247 6253 2.309528 TCTTTGTGGGATCGATTCGG 57.690 50.000 6.18 0.00 0.00 4.30 R
4993 7004 1.532868 GAAAGACTGCGCTGTGACAAT 59.467 47.619 25.37 6.11 0.00 2.71 R
5799 8131 0.438830 CGCAGGTCGCTAACAAAGAC 59.561 55.000 0.00 0.00 39.08 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
26 28 3.366273 CCCAACATGTTGTGCATAGACAC 60.366 47.826 31.20 0.00 38.85 3.67
58 60 1.712018 CGGACGCTGTCGGACATCTA 61.712 60.000 11.86 0.00 40.69 1.98
66 68 1.103803 GTCGGACATCTAGTGGCTCA 58.896 55.000 2.62 0.00 35.58 4.26
75 77 1.289231 TCTAGTGGCTCATGAGGGTCT 59.711 52.381 23.89 3.91 0.00 3.85
94 96 2.649034 GACGTCCGGAAGCAGTCA 59.351 61.111 17.91 0.00 32.57 3.41
265 271 2.203466 TGGGGTGTGTCGGACGTA 60.203 61.111 3.34 0.00 0.00 3.57
316 322 0.317479 GTACGCAGACTGGGACTTGT 59.683 55.000 24.85 5.73 34.12 3.16
347 354 2.434185 GCTTCCATGCGTCGGACA 60.434 61.111 9.10 0.00 30.29 4.02
369 376 2.567497 GGTTCAGACCGGTCGTCCA 61.567 63.158 28.26 11.55 43.08 4.02
395 402 2.233431 CTGTAGACTTCTGGCAGCTCTT 59.767 50.000 10.34 0.00 0.00 2.85
396 403 2.232452 TGTAGACTTCTGGCAGCTCTTC 59.768 50.000 10.34 7.79 0.00 2.87
397 404 1.643310 AGACTTCTGGCAGCTCTTCT 58.357 50.000 10.34 5.81 0.00 2.85
398 405 1.977129 AGACTTCTGGCAGCTCTTCTT 59.023 47.619 10.34 0.00 0.00 2.52
399 406 2.028203 AGACTTCTGGCAGCTCTTCTTC 60.028 50.000 10.34 0.00 0.00 2.87
400 407 1.977129 ACTTCTGGCAGCTCTTCTTCT 59.023 47.619 10.34 0.00 0.00 2.85
450 457 0.946221 CCGTCTTGTCTGTCAGGTGC 60.946 60.000 0.00 0.00 0.00 5.01
488 495 3.378512 TCCTCTAAGCACCTGATCACAT 58.621 45.455 0.00 0.00 0.00 3.21
543 550 5.542635 TCTCACATGTAGGAAGTGGTAGTTT 59.457 40.000 0.00 0.00 34.17 2.66
544 551 6.722590 TCTCACATGTAGGAAGTGGTAGTTTA 59.277 38.462 0.00 0.00 34.17 2.01
550 557 5.418209 TGTAGGAAGTGGTAGTTTAGAGAGC 59.582 44.000 0.00 0.00 0.00 4.09
562 569 1.827681 TAGAGAGCAGCGAGTTCACT 58.172 50.000 0.00 0.00 33.41 3.41
609 616 2.488891 CCCTTGTCATTGGTCCAAGTGA 60.489 50.000 10.72 10.77 35.02 3.41
610 617 2.554032 CCTTGTCATTGGTCCAAGTGAC 59.446 50.000 25.19 25.19 43.67 3.67
614 621 0.790207 CATTGGTCCAAGTGACGTCG 59.210 55.000 11.62 0.00 45.46 5.12
615 622 0.391597 ATTGGTCCAAGTGACGTCGT 59.608 50.000 11.62 0.00 45.46 4.34
630 637 1.549203 GTCGTGGGAGGTGTAGGTAA 58.451 55.000 0.00 0.00 0.00 2.85
631 638 1.895131 GTCGTGGGAGGTGTAGGTAAA 59.105 52.381 0.00 0.00 0.00 2.01
640 647 3.714798 GAGGTGTAGGTAAATCCATGGGA 59.285 47.826 13.02 0.00 39.02 4.37
641 648 4.315993 AGGTGTAGGTAAATCCATGGGAT 58.684 43.478 13.02 1.07 45.46 3.85
642 649 4.104738 AGGTGTAGGTAAATCCATGGGATG 59.895 45.833 13.02 0.00 42.27 3.51
643 650 4.104102 GGTGTAGGTAAATCCATGGGATGA 59.896 45.833 13.02 0.00 42.27 2.92
646 653 5.431731 TGTAGGTAAATCCATGGGATGAACT 59.568 40.000 13.02 4.87 42.27 3.01
648 655 5.203528 AGGTAAATCCATGGGATGAACTTG 58.796 41.667 13.02 0.00 42.27 3.16
649 656 5.044179 AGGTAAATCCATGGGATGAACTTGA 60.044 40.000 13.02 0.00 42.27 3.02
651 658 4.868172 AATCCATGGGATGAACTTGAGA 57.132 40.909 13.02 0.00 42.27 3.27
652 659 5.399052 AATCCATGGGATGAACTTGAGAT 57.601 39.130 13.02 0.00 42.27 2.75
654 661 2.621998 CCATGGGATGAACTTGAGATGC 59.378 50.000 2.85 0.00 0.00 3.91
655 662 3.552875 CATGGGATGAACTTGAGATGCT 58.447 45.455 0.00 0.00 0.00 3.79
656 663 3.272574 TGGGATGAACTTGAGATGCTC 57.727 47.619 0.00 0.00 0.00 4.26
657 664 2.092753 TGGGATGAACTTGAGATGCTCC 60.093 50.000 0.00 0.00 0.00 4.70
658 665 2.208431 GGATGAACTTGAGATGCTCCG 58.792 52.381 0.00 0.00 0.00 4.63
660 667 0.321346 TGAACTTGAGATGCTCCGCA 59.679 50.000 0.00 0.00 44.86 5.69
681 688 3.272574 TCAATGCCCTTTTGTTTTGCA 57.727 38.095 0.00 0.00 36.23 4.08
684 691 1.964552 TGCCCTTTTGTTTTGCATGG 58.035 45.000 0.00 0.00 0.00 3.66
685 692 1.211457 TGCCCTTTTGTTTTGCATGGT 59.789 42.857 0.00 0.00 0.00 3.55
686 693 1.603326 GCCCTTTTGTTTTGCATGGTG 59.397 47.619 0.00 0.00 0.00 4.17
687 694 2.744494 GCCCTTTTGTTTTGCATGGTGA 60.744 45.455 0.00 0.00 0.00 4.02
688 695 3.742385 CCCTTTTGTTTTGCATGGTGAT 58.258 40.909 0.00 0.00 0.00 3.06
689 696 4.802248 GCCCTTTTGTTTTGCATGGTGATA 60.802 41.667 0.00 0.00 0.00 2.15
690 697 5.303971 CCCTTTTGTTTTGCATGGTGATAA 58.696 37.500 0.00 0.00 0.00 1.75
692 699 5.990996 CCTTTTGTTTTGCATGGTGATAAGT 59.009 36.000 0.00 0.00 0.00 2.24
693 700 7.151308 CCTTTTGTTTTGCATGGTGATAAGTA 58.849 34.615 0.00 0.00 0.00 2.24
694 701 7.818930 CCTTTTGTTTTGCATGGTGATAAGTAT 59.181 33.333 0.00 0.00 0.00 2.12
695 702 8.531622 TTTTGTTTTGCATGGTGATAAGTATG 57.468 30.769 0.00 0.00 0.00 2.39
698 705 3.862877 TGCATGGTGATAAGTATGCCT 57.137 42.857 0.00 0.00 43.89 4.75
700 707 3.392285 TGCATGGTGATAAGTATGCCTCT 59.608 43.478 0.00 0.00 43.89 3.69
701 708 3.999663 GCATGGTGATAAGTATGCCTCTC 59.000 47.826 0.00 0.00 39.88 3.20
702 709 4.262808 GCATGGTGATAAGTATGCCTCTCT 60.263 45.833 0.00 0.00 39.88 3.10
703 710 5.477510 CATGGTGATAAGTATGCCTCTCTC 58.522 45.833 0.00 0.00 0.00 3.20
704 711 4.546674 TGGTGATAAGTATGCCTCTCTCA 58.453 43.478 0.00 0.00 0.00 3.27
705 712 4.342378 TGGTGATAAGTATGCCTCTCTCAC 59.658 45.833 0.00 0.00 32.10 3.51
706 713 4.586841 GGTGATAAGTATGCCTCTCTCACT 59.413 45.833 0.00 0.00 32.78 3.41
707 714 5.508825 GGTGATAAGTATGCCTCTCTCACTG 60.509 48.000 0.00 0.00 32.78 3.66
708 715 5.300539 GTGATAAGTATGCCTCTCTCACTGA 59.699 44.000 0.00 0.00 31.17 3.41
709 716 5.893824 TGATAAGTATGCCTCTCTCACTGAA 59.106 40.000 0.00 0.00 0.00 3.02
710 717 6.552725 TGATAAGTATGCCTCTCTCACTGAAT 59.447 38.462 0.00 0.00 0.00 2.57
711 718 4.669206 AGTATGCCTCTCTCACTGAATG 57.331 45.455 0.00 0.00 0.00 2.67
712 719 4.285020 AGTATGCCTCTCTCACTGAATGA 58.715 43.478 0.00 0.00 35.45 2.57
714 721 2.250924 TGCCTCTCTCACTGAATGACA 58.749 47.619 0.00 0.00 32.37 3.58
715 722 2.836372 TGCCTCTCTCACTGAATGACAT 59.164 45.455 0.00 0.00 32.37 3.06
716 723 4.026052 TGCCTCTCTCACTGAATGACATA 58.974 43.478 0.00 0.00 32.37 2.29
717 724 4.142071 TGCCTCTCTCACTGAATGACATAC 60.142 45.833 0.00 0.00 32.37 2.39
718 725 4.142071 GCCTCTCTCACTGAATGACATACA 60.142 45.833 0.00 0.00 32.37 2.29
719 726 5.453057 GCCTCTCTCACTGAATGACATACAT 60.453 44.000 0.00 0.00 41.45 2.29
720 727 5.984323 CCTCTCTCACTGAATGACATACATG 59.016 44.000 0.00 0.00 39.39 3.21
732 739 3.185246 ACATACATGTCCTAGTGCTGC 57.815 47.619 0.00 0.00 35.87 5.25
733 740 2.158900 ACATACATGTCCTAGTGCTGCC 60.159 50.000 0.00 0.00 35.87 4.85
734 741 1.866015 TACATGTCCTAGTGCTGCCT 58.134 50.000 0.00 0.00 0.00 4.75
735 742 1.866015 ACATGTCCTAGTGCTGCCTA 58.134 50.000 0.00 0.00 0.00 3.93
736 743 1.482593 ACATGTCCTAGTGCTGCCTAC 59.517 52.381 0.00 0.00 0.00 3.18
737 744 1.482182 CATGTCCTAGTGCTGCCTACA 59.518 52.381 0.00 0.00 0.00 2.74
738 745 1.866015 TGTCCTAGTGCTGCCTACAT 58.134 50.000 0.00 0.00 0.00 2.29
739 746 1.757118 TGTCCTAGTGCTGCCTACATC 59.243 52.381 0.00 0.00 0.00 3.06
741 748 0.394565 CCTAGTGCTGCCTACATCCC 59.605 60.000 0.00 0.00 0.00 3.85
742 749 0.394565 CTAGTGCTGCCTACATCCCC 59.605 60.000 0.00 0.00 0.00 4.81
743 750 1.399744 TAGTGCTGCCTACATCCCCG 61.400 60.000 0.00 0.00 0.00 5.73
745 752 1.766059 TGCTGCCTACATCCCCGAT 60.766 57.895 0.00 0.00 0.00 4.18
747 754 0.603975 GCTGCCTACATCCCCGATTC 60.604 60.000 0.00 0.00 0.00 2.52
748 755 0.758734 CTGCCTACATCCCCGATTCA 59.241 55.000 0.00 0.00 0.00 2.57
750 757 1.134220 TGCCTACATCCCCGATTCAAC 60.134 52.381 0.00 0.00 0.00 3.18
753 760 2.485479 CCTACATCCCCGATTCAACCAG 60.485 54.545 0.00 0.00 0.00 4.00
754 761 1.285280 ACATCCCCGATTCAACCAGA 58.715 50.000 0.00 0.00 0.00 3.86
756 763 2.292267 CATCCCCGATTCAACCAGAAG 58.708 52.381 0.00 0.00 40.15 2.85
758 765 0.035056 CCCCGATTCAACCAGAAGCT 60.035 55.000 0.00 0.00 40.43 3.74
761 768 2.426522 CCGATTCAACCAGAAGCTTCA 58.573 47.619 27.57 6.04 40.43 3.02
762 769 3.012518 CCGATTCAACCAGAAGCTTCAT 58.987 45.455 27.57 10.82 40.43 2.57
763 770 3.441572 CCGATTCAACCAGAAGCTTCATT 59.558 43.478 27.57 15.61 40.43 2.57
764 771 4.082571 CCGATTCAACCAGAAGCTTCATTT 60.083 41.667 27.57 14.19 40.43 2.32
765 772 5.464168 CGATTCAACCAGAAGCTTCATTTT 58.536 37.500 27.57 13.85 40.43 1.82
766 773 5.570589 CGATTCAACCAGAAGCTTCATTTTC 59.429 40.000 27.57 11.78 40.43 2.29
767 774 6.569226 CGATTCAACCAGAAGCTTCATTTTCT 60.569 38.462 27.57 3.12 40.43 2.52
770 777 2.227388 ACCAGAAGCTTCATTTTCTGCG 59.773 45.455 27.57 12.05 45.60 5.18
771 778 2.415090 CCAGAAGCTTCATTTTCTGCGG 60.415 50.000 27.57 9.67 45.60 5.69
772 779 1.815003 AGAAGCTTCATTTTCTGCGGG 59.185 47.619 27.57 0.00 32.65 6.13
773 780 0.244721 AAGCTTCATTTTCTGCGGGC 59.755 50.000 0.00 0.00 0.00 6.13
774 781 0.610232 AGCTTCATTTTCTGCGGGCT 60.610 50.000 0.00 0.00 0.00 5.19
775 782 0.244721 GCTTCATTTTCTGCGGGCTT 59.755 50.000 0.00 0.00 0.00 4.35
776 783 1.472480 GCTTCATTTTCTGCGGGCTTA 59.528 47.619 0.00 0.00 0.00 3.09
777 784 2.478539 GCTTCATTTTCTGCGGGCTTAG 60.479 50.000 0.00 0.00 0.00 2.18
778 785 2.489938 TCATTTTCTGCGGGCTTAGT 57.510 45.000 0.00 0.00 0.00 2.24
779 786 3.620427 TCATTTTCTGCGGGCTTAGTA 57.380 42.857 0.00 0.00 0.00 1.82
780 787 3.945346 TCATTTTCTGCGGGCTTAGTAA 58.055 40.909 0.00 0.00 0.00 2.24
781 788 3.687698 TCATTTTCTGCGGGCTTAGTAAC 59.312 43.478 0.00 0.00 0.00 2.50
782 789 3.412237 TTTTCTGCGGGCTTAGTAACT 57.588 42.857 0.00 0.00 0.00 2.24
783 790 2.667473 TTCTGCGGGCTTAGTAACTC 57.333 50.000 0.00 0.00 0.00 3.01
784 791 1.848652 TCTGCGGGCTTAGTAACTCT 58.151 50.000 0.00 0.00 0.00 3.24
785 792 3.008835 TCTGCGGGCTTAGTAACTCTA 57.991 47.619 0.00 0.00 0.00 2.43
788 795 2.950309 TGCGGGCTTAGTAACTCTAGAG 59.050 50.000 18.49 18.49 0.00 2.43
789 796 3.212685 GCGGGCTTAGTAACTCTAGAGA 58.787 50.000 26.57 1.40 0.00 3.10
791 798 4.320641 GCGGGCTTAGTAACTCTAGAGATG 60.321 50.000 26.57 6.81 0.00 2.90
792 799 4.822896 CGGGCTTAGTAACTCTAGAGATGT 59.177 45.833 26.57 12.75 0.00 3.06
793 800 5.996513 CGGGCTTAGTAACTCTAGAGATGTA 59.003 44.000 26.57 11.79 0.00 2.29
794 801 6.485984 CGGGCTTAGTAACTCTAGAGATGTAA 59.514 42.308 26.57 14.45 0.00 2.41
795 802 7.520292 CGGGCTTAGTAACTCTAGAGATGTAAC 60.520 44.444 26.57 14.60 0.00 2.50
796 803 7.354257 GGCTTAGTAACTCTAGAGATGTAACG 58.646 42.308 26.57 10.14 0.00 3.18
797 804 6.852345 GCTTAGTAACTCTAGAGATGTAACGC 59.148 42.308 26.57 15.47 0.00 4.84
798 805 5.754543 AGTAACTCTAGAGATGTAACGCC 57.245 43.478 26.57 4.06 0.00 5.68
799 806 3.694535 AACTCTAGAGATGTAACGCCG 57.305 47.619 26.57 0.00 0.00 6.46
800 807 2.641305 ACTCTAGAGATGTAACGCCGT 58.359 47.619 26.57 0.00 0.00 5.68
801 808 3.801698 ACTCTAGAGATGTAACGCCGTA 58.198 45.455 26.57 0.00 0.00 4.02
802 809 4.387598 ACTCTAGAGATGTAACGCCGTAT 58.612 43.478 26.57 0.00 0.00 3.06
804 811 4.383173 TCTAGAGATGTAACGCCGTATCA 58.617 43.478 0.00 0.00 0.00 2.15
805 812 5.001874 TCTAGAGATGTAACGCCGTATCAT 58.998 41.667 6.75 6.75 0.00 2.45
806 813 4.585955 AGAGATGTAACGCCGTATCATT 57.414 40.909 8.11 0.96 0.00 2.57
807 814 4.945246 AGAGATGTAACGCCGTATCATTT 58.055 39.130 8.11 3.69 0.00 2.32
808 815 5.357257 AGAGATGTAACGCCGTATCATTTT 58.643 37.500 8.11 2.06 0.00 1.82
809 816 5.815740 AGAGATGTAACGCCGTATCATTTTT 59.184 36.000 8.11 0.00 0.00 1.94
831 838 3.829886 TTCAATAAAGTGCGCTCAAGG 57.170 42.857 9.73 0.00 0.00 3.61
832 839 2.083774 TCAATAAAGTGCGCTCAAGGG 58.916 47.619 9.73 0.00 0.00 3.95
856 863 3.222053 AAAAACGCTCCTACCGGTC 57.778 52.632 12.40 0.00 0.00 4.79
858 865 2.176314 AAAACGCTCCTACCGGTCCC 62.176 60.000 12.40 0.00 0.00 4.46
860 867 3.528370 CGCTCCTACCGGTCCCAG 61.528 72.222 12.40 2.19 0.00 4.45
865 872 1.626825 CTCCTACCGGTCCCAGAAAAA 59.373 52.381 12.40 0.00 0.00 1.94
899 2378 1.474478 GAGAATCTCACGACTCAGCCA 59.526 52.381 5.22 0.00 0.00 4.75
907 2387 3.210227 TCACGACTCAGCCAAAAATTGA 58.790 40.909 0.00 0.00 0.00 2.57
917 2397 5.010012 TCAGCCAAAAATTGAGTCTCCTTTC 59.990 40.000 0.00 0.00 0.00 2.62
919 2399 5.010415 AGCCAAAAATTGAGTCTCCTTTCTG 59.990 40.000 0.00 0.00 0.00 3.02
922 2402 6.920210 CCAAAAATTGAGTCTCCTTTCTGAAC 59.080 38.462 0.00 0.00 0.00 3.18
943 2423 2.359531 CGACCCAAAAGCTTTGGTTACA 59.640 45.455 19.19 0.00 37.88 2.41
983 2463 0.323629 TTCTAAGGCAACCCCACGAG 59.676 55.000 0.00 0.00 35.39 4.18
1152 2635 2.310233 CGGTGTCCTGCGTGTTCTG 61.310 63.158 0.00 0.00 0.00 3.02
1234 2717 2.961669 GATTTGGCGTTCGCGTGGT 61.962 57.895 5.77 0.00 43.62 4.16
1466 3231 2.472695 TTATGCGTGGTGAGCTTTCT 57.527 45.000 0.00 0.00 35.28 2.52
1551 3316 5.045942 TCAATGTGCTCCATCCTGTTTAGTA 60.046 40.000 0.00 0.00 31.75 1.82
1645 3410 6.435164 AGTGCCCTTTCAAATATATGGTCTT 58.565 36.000 0.00 0.00 0.00 3.01
1735 3500 4.778579 AGAAGATTGGATCACATGTGAGG 58.221 43.478 30.63 4.97 43.61 3.86
1973 3777 9.547753 ACTACAAGAATGATATATGTGTTGGTC 57.452 33.333 0.00 0.00 0.00 4.02
2008 3812 7.724506 TCCGTGTAGAGATGGTTTCTTAGATAT 59.275 37.037 0.00 0.00 33.74 1.63
2398 4206 6.457355 TCAGCTACTTTCATAACCAAACGTA 58.543 36.000 0.00 0.00 0.00 3.57
3091 4901 8.557029 GCACTATTACACATTTACCTATGAACC 58.443 37.037 0.00 0.00 0.00 3.62
3101 4911 3.594603 ACCTATGAACCACGACTCTTG 57.405 47.619 0.00 0.00 0.00 3.02
4247 6253 1.751351 TCACGACATCAGAGGACATCC 59.249 52.381 0.00 0.00 0.00 3.51
4406 6413 5.529800 ACGTGGCTGAAGTTTTATTACTGTT 59.470 36.000 0.00 0.00 0.00 3.16
4409 6416 7.096640 CGTGGCTGAAGTTTTATTACTGTTTTG 60.097 37.037 0.00 0.00 0.00 2.44
4411 6418 8.254508 TGGCTGAAGTTTTATTACTGTTTTGTT 58.745 29.630 0.00 0.00 0.00 2.83
4505 6512 4.673328 TTTCCCCTTTGATTCATCTGGA 57.327 40.909 0.00 0.00 0.00 3.86
4543 6550 4.323104 GCCTCCTACCCATATTTCTAGCAG 60.323 50.000 0.00 0.00 0.00 4.24
4674 6681 6.603237 TTAGAGATGTCGCACCATTTATTG 57.397 37.500 0.00 0.00 0.00 1.90
4686 6693 5.048782 GCACCATTTATTGTCAGAGTGTTCA 60.049 40.000 0.00 0.00 0.00 3.18
4900 6911 5.606348 TGCCTTTTAGTTTGTGTTGGATT 57.394 34.783 0.00 0.00 0.00 3.01
4902 6913 5.362430 TGCCTTTTAGTTTGTGTTGGATTCT 59.638 36.000 0.00 0.00 0.00 2.40
4993 7004 3.819337 CGATGGGAATTCTCTACTACCGA 59.181 47.826 6.92 0.00 0.00 4.69
5106 7117 0.962356 CTTGCTGCCGATTCAAGGGT 60.962 55.000 0.00 0.00 34.98 4.34
5314 7325 0.602638 TGTTGTCGCGCCTTCTGAAT 60.603 50.000 0.00 0.00 0.00 2.57
5372 7383 4.517285 ACATCGCTGTGTTATTTCTCCAT 58.483 39.130 0.00 0.00 33.22 3.41
5436 7447 2.440517 TATGCACAACATGGCAGGAT 57.559 45.000 5.99 0.00 44.24 3.24
5466 7477 4.947077 ATTCTTTTAGTTTGCAAACGCG 57.053 36.364 30.90 19.77 43.51 6.01
5544 7564 3.389983 TGCCCGTAGCTACTTCCATAATT 59.610 43.478 21.20 0.00 44.23 1.40
5605 7932 3.531538 GTGTTATTTCTCCTCGCCATGA 58.468 45.455 0.00 0.00 0.00 3.07
5609 7936 2.609427 TTTCTCCTCGCCATGATCTG 57.391 50.000 0.00 0.00 0.00 2.90
5633 7960 6.363088 TGATTTCACTCATCGTTTGCATTTTC 59.637 34.615 0.00 0.00 0.00 2.29
5767 8099 7.397192 ACTTTTGCACATTCATCCCTTATAGTT 59.603 33.333 0.00 0.00 0.00 2.24
5799 8131 1.165907 TGGTGCTTGGCAAGAAGTCG 61.166 55.000 30.45 4.38 41.47 4.18
5854 8563 1.077429 GCTGGATGGAAGGACCCAC 60.077 63.158 0.00 0.00 39.34 4.61
5940 8652 6.935741 AAAAATGTACTAATAGGATGCGCA 57.064 33.333 14.96 14.96 0.00 6.09
5975 8687 3.659089 TAAGCGCCCGAACAGCTCC 62.659 63.158 2.29 0.00 40.78 4.70
5996 8708 2.107953 GCGCCTGATGGAGACCTC 59.892 66.667 0.00 0.00 34.95 3.85
6003 8715 2.315176 CTGATGGAGACCTCTAGTGGG 58.685 57.143 15.12 9.03 0.00 4.61
6021 8733 2.207229 GCCGGCCCAGAAAACCTTT 61.207 57.895 18.11 0.00 0.00 3.11
6087 11219 2.550830 AAAAGAGATGTGCGTGAGGT 57.449 45.000 0.00 0.00 0.00 3.85
6092 11224 1.741770 GATGTGCGTGAGGTGGGAC 60.742 63.158 0.00 0.00 0.00 4.46
6101 11233 1.201880 GTGAGGTGGGACTCGAACTAC 59.798 57.143 0.00 0.00 40.39 2.73
6106 11238 1.135460 GTGGGACTCGAACTACGGAAG 60.135 57.143 0.00 0.00 42.82 3.46
6107 11239 0.455005 GGGACTCGAACTACGGAAGG 59.545 60.000 0.00 0.00 42.82 3.46
6108 11240 0.455005 GGACTCGAACTACGGAAGGG 59.545 60.000 0.00 0.00 42.82 3.95
6109 11241 0.455005 GACTCGAACTACGGAAGGGG 59.545 60.000 0.00 0.00 42.82 4.79
6110 11242 0.038744 ACTCGAACTACGGAAGGGGA 59.961 55.000 0.00 0.00 42.82 4.81
6111 11243 1.341778 ACTCGAACTACGGAAGGGGAT 60.342 52.381 0.00 0.00 42.82 3.85
6112 11244 1.067212 CTCGAACTACGGAAGGGGATG 59.933 57.143 0.00 0.00 42.82 3.51
6113 11245 1.108776 CGAACTACGGAAGGGGATGA 58.891 55.000 0.00 0.00 38.46 2.92
6119 11265 2.420058 ACGGAAGGGGATGAATGAAC 57.580 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 2.090831 AGACCCTCATGAGCCACTAGAT 60.091 50.000 17.76 0.00 0.00 1.98
58 60 1.270414 CCAGACCCTCATGAGCCACT 61.270 60.000 17.76 11.75 0.00 4.00
66 68 2.052690 CGGACGTCCAGACCCTCAT 61.053 63.158 32.80 0.00 35.14 2.90
75 77 2.915659 ACTGCTTCCGGACGTCCA 60.916 61.111 32.80 13.21 35.14 4.02
180 185 5.189934 ACAGAAGGGAAATTATCGGAAGTCT 59.810 40.000 0.00 0.00 0.00 3.24
299 305 1.115930 AGACAAGTCCCAGTCTGCGT 61.116 55.000 0.00 0.00 43.09 5.24
305 311 1.757306 CAGCCAGACAAGTCCCAGT 59.243 57.895 0.00 0.00 0.00 4.00
369 376 0.610687 GCCAGAAGTCTACAGCCACT 59.389 55.000 0.00 0.00 0.00 4.00
395 402 7.125792 AGTACAAGGAACAAGAAGAAGAAGA 57.874 36.000 0.00 0.00 0.00 2.87
396 403 7.254932 CCAAGTACAAGGAACAAGAAGAAGAAG 60.255 40.741 0.00 0.00 0.00 2.85
397 404 6.542370 CCAAGTACAAGGAACAAGAAGAAGAA 59.458 38.462 0.00 0.00 0.00 2.52
398 405 6.055588 CCAAGTACAAGGAACAAGAAGAAGA 58.944 40.000 0.00 0.00 0.00 2.87
399 406 5.823045 ACCAAGTACAAGGAACAAGAAGAAG 59.177 40.000 10.24 0.00 0.00 2.85
400 407 5.588648 CACCAAGTACAAGGAACAAGAAGAA 59.411 40.000 10.24 0.00 0.00 2.52
450 457 4.473520 AAGGCCACGGATCAGCGG 62.474 66.667 5.01 0.00 0.00 5.52
488 495 2.474112 ACCTCAAGCGGAAACCCTATA 58.526 47.619 0.00 0.00 0.00 1.31
543 550 1.827681 AGTGAACTCGCTGCTCTCTA 58.172 50.000 0.00 0.00 35.04 2.43
544 551 0.965439 AAGTGAACTCGCTGCTCTCT 59.035 50.000 0.00 0.00 36.72 3.10
550 557 4.166523 TCGAAGATAAAGTGAACTCGCTG 58.833 43.478 0.00 0.00 36.72 5.18
609 616 1.975407 CCTACACCTCCCACGACGT 60.975 63.158 0.00 0.00 0.00 4.34
610 617 0.677731 TACCTACACCTCCCACGACG 60.678 60.000 0.00 0.00 0.00 5.12
614 621 2.841881 TGGATTTACCTACACCTCCCAC 59.158 50.000 0.00 0.00 39.86 4.61
615 622 3.208570 TGGATTTACCTACACCTCCCA 57.791 47.619 0.00 0.00 39.86 4.37
630 637 4.868172 TCTCAAGTTCATCCCATGGATT 57.132 40.909 15.22 0.00 39.79 3.01
631 638 4.726583 CATCTCAAGTTCATCCCATGGAT 58.273 43.478 15.22 1.70 44.21 3.41
660 667 3.818180 TGCAAAACAAAAGGGCATTGAT 58.182 36.364 4.27 0.00 0.00 2.57
661 668 3.272574 TGCAAAACAAAAGGGCATTGA 57.727 38.095 4.27 0.00 0.00 2.57
662 669 3.304794 CCATGCAAAACAAAAGGGCATTG 60.305 43.478 0.00 0.00 42.81 2.82
664 671 2.158638 ACCATGCAAAACAAAAGGGCAT 60.159 40.909 0.00 0.00 45.33 4.40
666 673 1.603326 CACCATGCAAAACAAAAGGGC 59.397 47.619 0.00 0.00 0.00 5.19
667 674 3.191078 TCACCATGCAAAACAAAAGGG 57.809 42.857 0.00 0.00 0.00 3.95
668 675 5.990996 ACTTATCACCATGCAAAACAAAAGG 59.009 36.000 0.00 0.00 0.00 3.11
669 676 8.649841 CATACTTATCACCATGCAAAACAAAAG 58.350 33.333 0.00 0.00 0.00 2.27
670 677 7.117523 GCATACTTATCACCATGCAAAACAAAA 59.882 33.333 0.00 0.00 42.61 2.44
671 678 6.589523 GCATACTTATCACCATGCAAAACAAA 59.410 34.615 0.00 0.00 42.61 2.83
673 680 5.394005 GGCATACTTATCACCATGCAAAACA 60.394 40.000 7.60 0.00 44.40 2.83
674 681 5.043248 GGCATACTTATCACCATGCAAAAC 58.957 41.667 7.60 0.00 44.40 2.43
675 682 4.955450 AGGCATACTTATCACCATGCAAAA 59.045 37.500 7.60 0.00 44.40 2.44
676 683 4.535781 AGGCATACTTATCACCATGCAAA 58.464 39.130 7.60 0.00 44.40 3.68
677 684 4.136796 GAGGCATACTTATCACCATGCAA 58.863 43.478 7.60 0.00 44.40 4.08
679 686 3.999663 GAGAGGCATACTTATCACCATGC 59.000 47.826 0.00 0.00 42.39 4.06
681 688 5.011533 GTGAGAGAGGCATACTTATCACCAT 59.988 44.000 0.00 0.00 32.94 3.55
684 691 5.300539 TCAGTGAGAGAGGCATACTTATCAC 59.699 44.000 0.00 0.00 36.03 3.06
685 692 5.449553 TCAGTGAGAGAGGCATACTTATCA 58.550 41.667 0.00 0.00 0.00 2.15
686 693 6.398234 TTCAGTGAGAGAGGCATACTTATC 57.602 41.667 0.00 0.00 0.00 1.75
687 694 6.552725 TCATTCAGTGAGAGAGGCATACTTAT 59.447 38.462 0.00 0.00 31.80 1.73
688 695 5.893824 TCATTCAGTGAGAGAGGCATACTTA 59.106 40.000 0.00 0.00 31.80 2.24
689 696 4.713814 TCATTCAGTGAGAGAGGCATACTT 59.286 41.667 0.00 0.00 31.80 2.24
690 697 4.099266 GTCATTCAGTGAGAGAGGCATACT 59.901 45.833 0.00 0.00 37.56 2.12
692 699 4.026052 TGTCATTCAGTGAGAGAGGCATA 58.974 43.478 0.00 0.00 37.56 3.14
693 700 2.836372 TGTCATTCAGTGAGAGAGGCAT 59.164 45.455 0.00 0.00 37.56 4.40
694 701 2.250924 TGTCATTCAGTGAGAGAGGCA 58.749 47.619 0.00 0.00 37.56 4.75
695 702 3.540314 ATGTCATTCAGTGAGAGAGGC 57.460 47.619 0.00 0.00 37.56 4.70
698 705 6.535963 ACATGTATGTCATTCAGTGAGAGA 57.464 37.500 0.00 0.00 37.56 3.10
712 719 2.158900 GGCAGCACTAGGACATGTATGT 60.159 50.000 0.00 0.00 45.16 2.29
714 721 2.402564 AGGCAGCACTAGGACATGTAT 58.597 47.619 0.00 0.00 0.00 2.29
715 722 1.866015 AGGCAGCACTAGGACATGTA 58.134 50.000 0.00 0.00 0.00 2.29
716 723 1.482593 GTAGGCAGCACTAGGACATGT 59.517 52.381 0.00 0.00 0.00 3.21
717 724 1.482182 TGTAGGCAGCACTAGGACATG 59.518 52.381 0.00 0.00 0.00 3.21
718 725 1.866015 TGTAGGCAGCACTAGGACAT 58.134 50.000 0.00 0.00 0.00 3.06
719 726 1.757118 GATGTAGGCAGCACTAGGACA 59.243 52.381 0.00 0.00 0.00 4.02
720 727 1.069358 GGATGTAGGCAGCACTAGGAC 59.931 57.143 0.00 0.00 31.62 3.85
722 729 0.394565 GGGATGTAGGCAGCACTAGG 59.605 60.000 0.00 0.00 30.55 3.02
723 730 0.394565 GGGGATGTAGGCAGCACTAG 59.605 60.000 0.00 0.00 34.32 2.57
726 733 2.044806 ATCGGGGATGTAGGCAGCAC 62.045 60.000 0.00 0.00 32.82 4.40
727 734 1.344953 AATCGGGGATGTAGGCAGCA 61.345 55.000 0.00 0.00 31.62 4.41
730 737 1.134220 GTTGAATCGGGGATGTAGGCA 60.134 52.381 0.00 0.00 0.00 4.75
731 738 1.594331 GTTGAATCGGGGATGTAGGC 58.406 55.000 0.00 0.00 0.00 3.93
732 739 1.488812 TGGTTGAATCGGGGATGTAGG 59.511 52.381 0.00 0.00 0.00 3.18
733 740 2.434336 TCTGGTTGAATCGGGGATGTAG 59.566 50.000 0.00 0.00 0.00 2.74
734 741 2.473070 TCTGGTTGAATCGGGGATGTA 58.527 47.619 0.00 0.00 0.00 2.29
735 742 1.285280 TCTGGTTGAATCGGGGATGT 58.715 50.000 0.00 0.00 0.00 3.06
736 743 2.292267 CTTCTGGTTGAATCGGGGATG 58.708 52.381 0.00 0.00 33.71 3.51
737 744 1.408822 GCTTCTGGTTGAATCGGGGAT 60.409 52.381 0.00 0.00 33.71 3.85
738 745 0.035439 GCTTCTGGTTGAATCGGGGA 60.035 55.000 0.00 0.00 33.71 4.81
739 746 0.035056 AGCTTCTGGTTGAATCGGGG 60.035 55.000 0.00 0.00 33.71 5.73
741 748 2.426522 TGAAGCTTCTGGTTGAATCGG 58.573 47.619 26.09 0.00 33.64 4.18
742 749 4.691860 AATGAAGCTTCTGGTTGAATCG 57.308 40.909 26.09 0.00 33.64 3.34
743 750 6.585322 CAGAAAATGAAGCTTCTGGTTGAATC 59.415 38.462 26.09 15.66 43.15 2.52
745 752 5.737063 GCAGAAAATGAAGCTTCTGGTTGAA 60.737 40.000 26.09 5.44 45.71 2.69
747 754 3.985925 GCAGAAAATGAAGCTTCTGGTTG 59.014 43.478 26.09 16.71 45.71 3.77
748 755 3.304928 CGCAGAAAATGAAGCTTCTGGTT 60.305 43.478 26.09 16.40 45.71 3.67
750 757 2.415090 CCGCAGAAAATGAAGCTTCTGG 60.415 50.000 26.09 9.45 45.71 3.86
753 760 1.733718 GCCCGCAGAAAATGAAGCTTC 60.734 52.381 19.89 19.89 0.00 3.86
754 761 0.244721 GCCCGCAGAAAATGAAGCTT 59.755 50.000 0.00 0.00 0.00 3.74
756 763 0.244721 AAGCCCGCAGAAAATGAAGC 59.755 50.000 0.00 0.00 0.00 3.86
758 765 2.790433 ACTAAGCCCGCAGAAAATGAA 58.210 42.857 0.00 0.00 0.00 2.57
761 768 3.939592 GAGTTACTAAGCCCGCAGAAAAT 59.060 43.478 0.00 0.00 0.00 1.82
762 769 3.007614 AGAGTTACTAAGCCCGCAGAAAA 59.992 43.478 0.00 0.00 0.00 2.29
763 770 2.565834 AGAGTTACTAAGCCCGCAGAAA 59.434 45.455 0.00 0.00 0.00 2.52
764 771 2.176889 AGAGTTACTAAGCCCGCAGAA 58.823 47.619 0.00 0.00 0.00 3.02
765 772 1.848652 AGAGTTACTAAGCCCGCAGA 58.151 50.000 0.00 0.00 0.00 4.26
766 773 2.950309 TCTAGAGTTACTAAGCCCGCAG 59.050 50.000 0.00 0.00 0.00 5.18
767 774 2.950309 CTCTAGAGTTACTAAGCCCGCA 59.050 50.000 11.89 0.00 0.00 5.69
770 777 7.520292 CGTTACATCTCTAGAGTTACTAAGCCC 60.520 44.444 19.21 0.00 0.00 5.19
771 778 7.354257 CGTTACATCTCTAGAGTTACTAAGCC 58.646 42.308 19.21 0.90 0.00 4.35
772 779 6.852345 GCGTTACATCTCTAGAGTTACTAAGC 59.148 42.308 19.21 14.12 0.00 3.09
773 780 7.354257 GGCGTTACATCTCTAGAGTTACTAAG 58.646 42.308 19.21 8.86 0.00 2.18
774 781 6.018425 CGGCGTTACATCTCTAGAGTTACTAA 60.018 42.308 19.21 8.31 0.00 2.24
775 782 5.464722 CGGCGTTACATCTCTAGAGTTACTA 59.535 44.000 19.21 0.00 0.00 1.82
776 783 4.272991 CGGCGTTACATCTCTAGAGTTACT 59.727 45.833 19.21 3.85 0.00 2.24
777 784 4.034975 ACGGCGTTACATCTCTAGAGTTAC 59.965 45.833 19.21 10.04 0.00 2.50
778 785 4.194640 ACGGCGTTACATCTCTAGAGTTA 58.805 43.478 19.21 6.97 0.00 2.24
779 786 3.015327 ACGGCGTTACATCTCTAGAGTT 58.985 45.455 19.21 8.60 0.00 3.01
780 787 2.641305 ACGGCGTTACATCTCTAGAGT 58.359 47.619 19.21 4.03 0.00 3.24
781 788 4.451435 TGATACGGCGTTACATCTCTAGAG 59.549 45.833 21.24 13.98 0.00 2.43
782 789 4.383173 TGATACGGCGTTACATCTCTAGA 58.617 43.478 21.24 0.00 0.00 2.43
783 790 4.744136 TGATACGGCGTTACATCTCTAG 57.256 45.455 21.24 0.00 0.00 2.43
784 791 5.700722 AATGATACGGCGTTACATCTCTA 57.299 39.130 21.24 0.00 0.00 2.43
785 792 4.585955 AATGATACGGCGTTACATCTCT 57.414 40.909 21.24 6.90 0.00 3.10
808 815 4.981674 CCTTGAGCGCACTTTATTGAAAAA 59.018 37.500 11.47 0.00 0.00 1.94
809 816 4.545610 CCTTGAGCGCACTTTATTGAAAA 58.454 39.130 11.47 0.00 0.00 2.29
810 817 3.057596 CCCTTGAGCGCACTTTATTGAAA 60.058 43.478 11.47 0.00 0.00 2.69
812 819 2.083774 CCCTTGAGCGCACTTTATTGA 58.916 47.619 11.47 0.00 0.00 2.57
813 820 1.468054 GCCCTTGAGCGCACTTTATTG 60.468 52.381 11.47 0.00 0.00 1.90
814 821 0.811281 GCCCTTGAGCGCACTTTATT 59.189 50.000 11.47 0.00 0.00 1.40
843 850 3.528370 CTGGGACCGGTAGGAGCG 61.528 72.222 7.34 0.00 41.02 5.03
865 872 5.932883 GTGAGATTCTCCGGTAAGACTTTTT 59.067 40.000 11.12 0.00 0.00 1.94
866 873 5.480205 GTGAGATTCTCCGGTAAGACTTTT 58.520 41.667 11.12 0.00 0.00 2.27
868 875 3.128938 CGTGAGATTCTCCGGTAAGACTT 59.871 47.826 11.12 0.00 0.00 3.01
869 876 2.683867 CGTGAGATTCTCCGGTAAGACT 59.316 50.000 11.12 1.79 0.00 3.24
870 877 2.681848 TCGTGAGATTCTCCGGTAAGAC 59.318 50.000 18.29 6.42 33.31 3.01
873 880 2.681848 GAGTCGTGAGATTCTCCGGTAA 59.318 50.000 18.29 0.00 42.83 2.85
874 881 2.286872 GAGTCGTGAGATTCTCCGGTA 58.713 52.381 18.29 0.00 42.83 4.02
875 882 1.096416 GAGTCGTGAGATTCTCCGGT 58.904 55.000 18.29 10.31 42.83 5.28
899 2378 6.542370 TCGTTCAGAAAGGAGACTCAATTTTT 59.458 34.615 4.53 0.00 42.68 1.94
917 2397 2.543653 CCAAAGCTTTTGGGTCGTTCAG 60.544 50.000 9.53 0.00 35.96 3.02
919 2399 1.407618 ACCAAAGCTTTTGGGTCGTTC 59.592 47.619 23.11 0.00 43.71 3.95
922 2402 2.359531 TGTAACCAAAGCTTTTGGGTCG 59.640 45.455 18.64 3.69 43.71 4.79
943 2423 6.633856 AGAAATGTTAACCGGTAGTAATCGT 58.366 36.000 8.00 0.00 0.00 3.73
983 2463 1.084370 CGCAGGGATGGAACGAAGTC 61.084 60.000 0.00 0.00 45.00 3.01
997 2477 2.584418 CACGGCAGATCTCGCAGG 60.584 66.667 16.76 11.40 0.00 4.85
1152 2635 2.372690 ATGTCGACGCGCAACAGAC 61.373 57.895 5.73 11.57 0.00 3.51
1234 2717 0.337773 AGTGCCCTCTCAGATCCAGA 59.662 55.000 0.00 0.00 0.00 3.86
1466 3231 1.274358 TGGGATGAGGGGATCAAGTCA 60.274 52.381 0.00 0.00 42.53 3.41
1571 3336 4.310769 ACAACAGCTAACATGAGAGACAC 58.689 43.478 0.00 0.00 0.00 3.67
1645 3410 4.459390 AGCACATTTCAAAGCATATGCA 57.541 36.364 28.62 8.05 45.16 3.96
1735 3500 6.147821 TCTCAGCAGCTATTTGTTAAACAGTC 59.852 38.462 0.00 0.00 0.00 3.51
1817 3582 2.946329 CCTAAGAGAGCGCACTAAGAGA 59.054 50.000 11.47 0.00 0.00 3.10
1951 3755 8.442632 ACAGACCAACACATATATCATTCTTG 57.557 34.615 0.00 0.00 0.00 3.02
1966 3770 1.142060 ACGGAATCCAACAGACCAACA 59.858 47.619 0.00 0.00 0.00 3.33
1967 3771 1.535462 CACGGAATCCAACAGACCAAC 59.465 52.381 0.00 0.00 0.00 3.77
1968 3772 1.142060 ACACGGAATCCAACAGACCAA 59.858 47.619 0.00 0.00 0.00 3.67
1969 3773 0.762418 ACACGGAATCCAACAGACCA 59.238 50.000 0.00 0.00 0.00 4.02
1970 3774 2.232941 TCTACACGGAATCCAACAGACC 59.767 50.000 0.00 0.00 0.00 3.85
1971 3775 3.192844 TCTCTACACGGAATCCAACAGAC 59.807 47.826 0.00 0.00 0.00 3.51
1972 3776 3.427573 TCTCTACACGGAATCCAACAGA 58.572 45.455 0.00 0.00 0.00 3.41
1973 3777 3.868757 TCTCTACACGGAATCCAACAG 57.131 47.619 0.00 0.00 0.00 3.16
2149 3955 4.298626 AGGGCTGTGAATCTGTTATAGGA 58.701 43.478 0.00 0.00 0.00 2.94
2223 4031 2.171448 AGGTGCAGCAATAGGACTAAGG 59.829 50.000 19.63 0.00 0.00 2.69
2302 4110 7.202016 TCTCTTCACGCAAAATAAACAGAAT 57.798 32.000 0.00 0.00 0.00 2.40
3021 4831 6.684979 CGCACAAATAAAAACAAAGGGAAAAC 59.315 34.615 0.00 0.00 0.00 2.43
3091 4901 2.071688 ACTTAGCTGCAAGAGTCGTG 57.928 50.000 15.41 1.20 34.07 4.35
3101 4911 6.480320 ACAGTGCAGTAAATATACTTAGCTGC 59.520 38.462 15.46 15.46 45.42 5.25
4247 6253 2.309528 TCTTTGTGGGATCGATTCGG 57.690 50.000 6.18 0.00 0.00 4.30
4369 6376 7.101054 ACTTCAGCCACGTAATATCTGTTTTA 58.899 34.615 0.00 0.00 0.00 1.52
4375 6382 8.732746 AATAAAACTTCAGCCACGTAATATCT 57.267 30.769 0.00 0.00 0.00 1.98
4384 6391 7.704899 ACAAAACAGTAATAAAACTTCAGCCAC 59.295 33.333 0.00 0.00 0.00 5.01
4543 6550 5.529581 TTTCTGGTTGTTTCCCTCAAATC 57.470 39.130 0.00 0.00 0.00 2.17
4993 7004 1.532868 GAAAGACTGCGCTGTGACAAT 59.467 47.619 25.37 6.11 0.00 2.71
5106 7117 7.455008 TGGAAAATAATACAGGCAGGGTAAAAA 59.545 33.333 0.00 0.00 0.00 1.94
5314 7325 4.688879 CGATCAAAGTAACACCTGTAGCAA 59.311 41.667 0.00 0.00 0.00 3.91
5372 7383 6.801377 GCATCGTCATGACAAGTGAAAAATAA 59.199 34.615 24.93 0.00 30.57 1.40
5389 7400 4.641396 CCTATAATTTCCCAGCATCGTCA 58.359 43.478 0.00 0.00 0.00 4.35
5605 7932 4.696877 TGCAAACGATGAGTGAAATCAGAT 59.303 37.500 0.00 0.00 31.44 2.90
5609 7936 6.583806 AGAAAATGCAAACGATGAGTGAAATC 59.416 34.615 0.00 0.00 0.00 2.17
5767 8099 4.260985 CCAAGCACCAACAGATACATGTA 58.739 43.478 8.27 8.27 31.70 2.29
5799 8131 0.438830 CGCAGGTCGCTAACAAAGAC 59.561 55.000 0.00 0.00 39.08 3.01
5854 8563 1.831286 GCATCCCAAGCCCATCTGG 60.831 63.158 0.00 0.00 37.09 3.86
5922 8634 3.005472 GGAGTGCGCATCCTATTAGTACA 59.995 47.826 23.41 0.00 33.77 2.90
5923 8635 3.256136 AGGAGTGCGCATCCTATTAGTAC 59.744 47.826 28.70 8.52 45.58 2.73
5936 8648 3.330853 CGCCGAATAGGAGTGCGC 61.331 66.667 0.00 0.00 45.00 6.09
5938 8650 3.330853 CGCGCCGAATAGGAGTGC 61.331 66.667 0.00 0.00 43.05 4.40
5940 8652 0.457035 TTAACGCGCCGAATAGGAGT 59.543 50.000 5.73 0.00 45.00 3.85
5975 8687 3.473647 TCTCCATCAGGCGCCAGG 61.474 66.667 31.54 23.56 33.74 4.45
5987 8699 1.001760 GGCCCACTAGAGGTCTCCA 59.998 63.158 5.43 0.00 0.00 3.86
6003 8715 2.207229 AAAGGTTTTCTGGGCCGGC 61.207 57.895 21.18 21.18 0.00 6.13
6072 11204 1.448540 CCCACCTCACGCACATCTC 60.449 63.158 0.00 0.00 0.00 2.75
6087 11219 1.171308 CTTCCGTAGTTCGAGTCCCA 58.829 55.000 0.00 0.00 42.86 4.37
6092 11224 1.067212 CATCCCCTTCCGTAGTTCGAG 59.933 57.143 0.00 0.00 42.86 4.04
6101 11233 1.064758 TGGTTCATTCATCCCCTTCCG 60.065 52.381 0.00 0.00 0.00 4.30
6106 11238 2.561569 CGTAGTGGTTCATTCATCCCC 58.438 52.381 0.00 0.00 0.00 4.81
6107 11239 1.940613 GCGTAGTGGTTCATTCATCCC 59.059 52.381 0.00 0.00 0.00 3.85
6108 11240 2.906354 AGCGTAGTGGTTCATTCATCC 58.094 47.619 0.00 0.00 0.00 3.51
6109 11241 4.686554 GGATAGCGTAGTGGTTCATTCATC 59.313 45.833 0.00 0.00 0.00 2.92
6110 11242 4.100963 TGGATAGCGTAGTGGTTCATTCAT 59.899 41.667 0.00 0.00 0.00 2.57
6111 11243 3.449377 TGGATAGCGTAGTGGTTCATTCA 59.551 43.478 0.00 0.00 0.00 2.57
6112 11244 4.054780 TGGATAGCGTAGTGGTTCATTC 57.945 45.455 0.00 0.00 0.00 2.67
6113 11245 4.189231 GTTGGATAGCGTAGTGGTTCATT 58.811 43.478 0.00 0.00 0.00 2.57
6119 11265 1.535437 GGTCGTTGGATAGCGTAGTGG 60.535 57.143 0.00 0.00 0.00 4.00
6193 11339 7.486802 TCGTTACGGAAAAAGAGAGAAAAAT 57.513 32.000 4.53 0.00 0.00 1.82
6215 11361 8.628882 AGGAAATAAAAAGGCGAAATAAATCG 57.371 30.769 0.00 0.00 45.41 3.34


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

AutoCloner maintained by Alex Coulton.