Multiple sequence alignment - TraesCS4B01G299500

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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 TraesCS4B01G299500 chr4B 100.000 3219 0 0 1 3219 585965442 585962224 0.000000e+00 5945.0
1 TraesCS4B01G299500 chr4B 94.965 576 24 3 1 571 585970920 585970345 0.000000e+00 898.0
2 TraesCS4B01G299500 chr4B 84.118 913 96 20 1400 2283 585822613 585821721 0.000000e+00 837.0
3 TraesCS4B01G299500 chr4B 86.100 482 39 15 901 1366 585823166 585822697 8.020000e-136 494.0
4 TraesCS4B01G299500 chr4D 89.352 1296 67 30 1738 2988 467792426 467791157 0.000000e+00 1563.0
5 TraesCS4B01G299500 chr4D 81.635 1688 159 74 900 2481 467636907 467635265 0.000000e+00 1260.0
6 TraesCS4B01G299500 chr4D 90.846 579 35 7 828 1405 467801453 467800892 0.000000e+00 760.0
7 TraesCS4B01G299500 chr4D 96.774 62 2 0 3152 3213 467791008 467790947 1.580000e-18 104.0
8 TraesCS4B01G299500 chr4A 87.658 1264 78 27 1007 2232 3351107 3352330 0.000000e+00 1399.0
9 TraesCS4B01G299500 chr4A 82.541 1535 166 51 950 2429 3370219 3371706 0.000000e+00 1256.0
10 TraesCS4B01G299500 chr4A 86.887 816 61 15 2234 3019 3353423 3354222 0.000000e+00 872.0
11 TraesCS4B01G299500 chr4A 89.011 182 10 1 828 1009 3350663 3350834 1.940000e-52 217.0
12 TraesCS4B01G299500 chr2D 95.470 574 23 2 1 571 593401118 593401691 0.000000e+00 913.0
13 TraesCS4B01G299500 chr2D 94.746 571 19 4 1 571 126965096 126964537 0.000000e+00 878.0
14 TraesCS4B01G299500 chr2D 94.128 579 23 7 1 571 552731859 552732434 0.000000e+00 870.0
15 TraesCS4B01G299500 chr2D 93.706 572 31 2 1 571 35322275 35322842 0.000000e+00 852.0
16 TraesCS4B01G299500 chr2D 86.592 179 23 1 1472 1649 61021907 61022085 2.530000e-46 196.0
17 TraesCS4B01G299500 chr1D 95.122 574 25 2 1 571 412791014 412791587 0.000000e+00 902.0
18 TraesCS4B01G299500 chr1D 93.728 574 33 3 1 571 412876711 412877284 0.000000e+00 857.0
19 TraesCS4B01G299500 chr3D 94.291 578 25 4 1 571 27869566 27868990 0.000000e+00 878.0
20 TraesCS4B01G299500 chr5D 93.892 573 24 4 1 571 246019213 246018650 0.000000e+00 854.0
21 TraesCS4B01G299500 chr2B 85.475 179 25 1 1472 1649 95796566 95796744 5.480000e-43 185.0
22 TraesCS4B01G299500 chr2A 85.475 179 25 1 1472 1649 61488452 61488630 5.480000e-43 185.0
23 TraesCS4B01G299500 chr5A 83.815 173 28 0 1472 1644 525026124 525026296 7.140000e-37 165.0
24 TraesCS4B01G299500 chr7A 79.803 203 37 4 1439 1639 262474559 262474759 9.310000e-31 145.0
25 TraesCS4B01G299500 chr3A 96.364 55 2 0 774 828 722361896 722361842 1.230000e-14 91.6
26 TraesCS4B01G299500 chr3B 89.091 55 6 0 3033 3087 771330437 771330491 5.760000e-08 69.4


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 TraesCS4B01G299500 chr4B 585962224 585965442 3218 True 5945.000000 5945 100.000 1 3219 1 chr4B.!!$R1 3218
1 TraesCS4B01G299500 chr4B 585970345 585970920 575 True 898.000000 898 94.965 1 571 1 chr4B.!!$R2 570
2 TraesCS4B01G299500 chr4B 585821721 585823166 1445 True 665.500000 837 85.109 901 2283 2 chr4B.!!$R3 1382
3 TraesCS4B01G299500 chr4D 467635265 467636907 1642 True 1260.000000 1260 81.635 900 2481 1 chr4D.!!$R1 1581
4 TraesCS4B01G299500 chr4D 467790947 467792426 1479 True 833.500000 1563 93.063 1738 3213 2 chr4D.!!$R3 1475
5 TraesCS4B01G299500 chr4D 467800892 467801453 561 True 760.000000 760 90.846 828 1405 1 chr4D.!!$R2 577
6 TraesCS4B01G299500 chr4A 3370219 3371706 1487 False 1256.000000 1256 82.541 950 2429 1 chr4A.!!$F1 1479
7 TraesCS4B01G299500 chr4A 3350663 3354222 3559 False 829.333333 1399 87.852 828 3019 3 chr4A.!!$F2 2191
8 TraesCS4B01G299500 chr2D 593401118 593401691 573 False 913.000000 913 95.470 1 571 1 chr2D.!!$F4 570
9 TraesCS4B01G299500 chr2D 126964537 126965096 559 True 878.000000 878 94.746 1 571 1 chr2D.!!$R1 570
10 TraesCS4B01G299500 chr2D 552731859 552732434 575 False 870.000000 870 94.128 1 571 1 chr2D.!!$F3 570
11 TraesCS4B01G299500 chr2D 35322275 35322842 567 False 852.000000 852 93.706 1 571 1 chr2D.!!$F1 570
12 TraesCS4B01G299500 chr1D 412791014 412791587 573 False 902.000000 902 95.122 1 571 1 chr1D.!!$F1 570
13 TraesCS4B01G299500 chr1D 412876711 412877284 573 False 857.000000 857 93.728 1 571 1 chr1D.!!$F2 570
14 TraesCS4B01G299500 chr3D 27868990 27869566 576 True 878.000000 878 94.291 1 571 1 chr3D.!!$R1 570
15 TraesCS4B01G299500 chr5D 246018650 246019213 563 True 854.000000 854 93.892 1 571 1 chr5D.!!$R1 570

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
825 837 0.038251 CAAGCGCGCATATCCCTCTA 60.038 55.0 35.1 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 4221 2.139917 CGATGTTGGAGTGGAACGAAA 58.86 47.619 0.0 0.0 45.86 3.46 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
99 100 3.827302 GGGAGTGAGTGAACTGAGTTAGA 59.173 47.826 0.00 0.00 0.00 2.10
374 386 4.135153 GAGGAGGAGAAGCGCGCA 62.135 66.667 35.10 0.00 0.00 6.09
571 583 3.446442 AGCCCATCCATAATCCATCAC 57.554 47.619 0.00 0.00 0.00 3.06
572 584 2.991713 AGCCCATCCATAATCCATCACT 59.008 45.455 0.00 0.00 0.00 3.41
573 585 4.178339 AGCCCATCCATAATCCATCACTA 58.822 43.478 0.00 0.00 0.00 2.74
574 586 4.792426 AGCCCATCCATAATCCATCACTAT 59.208 41.667 0.00 0.00 0.00 2.12
575 587 5.104193 AGCCCATCCATAATCCATCACTATC 60.104 44.000 0.00 0.00 0.00 2.08
576 588 5.688807 CCCATCCATAATCCATCACTATCC 58.311 45.833 0.00 0.00 0.00 2.59
577 589 5.192321 CCCATCCATAATCCATCACTATCCA 59.808 44.000 0.00 0.00 0.00 3.41
578 590 6.118170 CCATCCATAATCCATCACTATCCAC 58.882 44.000 0.00 0.00 0.00 4.02
579 591 5.405935 TCCATAATCCATCACTATCCACG 57.594 43.478 0.00 0.00 0.00 4.94
580 592 5.083821 TCCATAATCCATCACTATCCACGA 58.916 41.667 0.00 0.00 0.00 4.35
581 593 5.721480 TCCATAATCCATCACTATCCACGAT 59.279 40.000 0.00 0.00 0.00 3.73
582 594 5.814188 CCATAATCCATCACTATCCACGATG 59.186 44.000 0.00 0.00 36.99 3.84
583 595 2.820059 TCCATCACTATCCACGATGC 57.180 50.000 0.00 0.00 36.12 3.91
584 596 1.344438 TCCATCACTATCCACGATGCC 59.656 52.381 0.00 0.00 36.12 4.40
585 597 1.345741 CCATCACTATCCACGATGCCT 59.654 52.381 0.00 0.00 36.12 4.75
586 598 2.224378 CCATCACTATCCACGATGCCTT 60.224 50.000 0.00 0.00 36.12 4.35
587 599 3.006859 CCATCACTATCCACGATGCCTTA 59.993 47.826 0.00 0.00 36.12 2.69
588 600 4.323028 CCATCACTATCCACGATGCCTTAT 60.323 45.833 0.00 0.00 36.12 1.73
589 601 4.257267 TCACTATCCACGATGCCTTATG 57.743 45.455 0.00 0.00 0.00 1.90
590 602 3.006859 TCACTATCCACGATGCCTTATGG 59.993 47.826 0.00 0.00 0.00 2.74
591 603 3.006859 CACTATCCACGATGCCTTATGGA 59.993 47.826 0.00 0.00 45.12 3.41
592 604 2.550830 ATCCACGATGCCTTATGGAC 57.449 50.000 0.00 0.00 43.88 4.02
593 605 1.199615 TCCACGATGCCTTATGGACA 58.800 50.000 0.00 0.00 36.30 4.02
594 606 1.557371 TCCACGATGCCTTATGGACAA 59.443 47.619 0.00 0.00 36.30 3.18
595 607 1.670811 CCACGATGCCTTATGGACAAC 59.329 52.381 0.00 0.00 33.80 3.32
596 608 2.355197 CACGATGCCTTATGGACAACA 58.645 47.619 0.00 0.00 34.57 3.33
597 609 2.945008 CACGATGCCTTATGGACAACAT 59.055 45.455 0.00 0.00 43.68 2.71
598 610 4.126437 CACGATGCCTTATGGACAACATA 58.874 43.478 0.00 0.00 41.03 2.29
599 611 4.756642 CACGATGCCTTATGGACAACATAT 59.243 41.667 0.00 0.00 41.49 1.78
600 612 5.239306 CACGATGCCTTATGGACAACATATT 59.761 40.000 0.00 0.00 41.49 1.28
601 613 5.827797 ACGATGCCTTATGGACAACATATTT 59.172 36.000 0.00 0.00 41.49 1.40
602 614 6.144854 CGATGCCTTATGGACAACATATTTG 58.855 40.000 0.00 0.00 41.49 2.32
603 615 6.238731 CGATGCCTTATGGACAACATATTTGT 60.239 38.462 0.00 3.81 41.49 2.83
604 616 6.849085 TGCCTTATGGACAACATATTTGTT 57.151 33.333 0.00 0.00 41.49 2.83
605 617 7.238486 TGCCTTATGGACAACATATTTGTTT 57.762 32.000 0.00 0.00 41.49 2.83
606 618 7.319646 TGCCTTATGGACAACATATTTGTTTC 58.680 34.615 0.00 1.85 41.49 2.78
607 619 7.039434 TGCCTTATGGACAACATATTTGTTTCA 60.039 33.333 0.00 0.02 41.49 2.69
608 620 7.275560 GCCTTATGGACAACATATTTGTTTCAC 59.724 37.037 0.00 0.00 41.49 3.18
609 621 8.522830 CCTTATGGACAACATATTTGTTTCACT 58.477 33.333 0.00 0.00 41.49 3.41
642 654 7.939784 AGTTTTCCCTTGTATCTCAATTACC 57.060 36.000 0.00 0.00 35.35 2.85
643 655 7.699878 AGTTTTCCCTTGTATCTCAATTACCT 58.300 34.615 0.00 0.00 35.35 3.08
644 656 7.611855 AGTTTTCCCTTGTATCTCAATTACCTG 59.388 37.037 0.00 0.00 35.35 4.00
645 657 5.036117 TCCCTTGTATCTCAATTACCTGC 57.964 43.478 0.00 0.00 35.35 4.85
646 658 4.721776 TCCCTTGTATCTCAATTACCTGCT 59.278 41.667 0.00 0.00 35.35 4.24
647 659 5.191722 TCCCTTGTATCTCAATTACCTGCTT 59.808 40.000 0.00 0.00 35.35 3.91
648 660 5.297776 CCCTTGTATCTCAATTACCTGCTTG 59.702 44.000 0.00 0.00 35.35 4.01
649 661 5.882557 CCTTGTATCTCAATTACCTGCTTGT 59.117 40.000 0.00 0.00 35.35 3.16
650 662 6.375455 CCTTGTATCTCAATTACCTGCTTGTT 59.625 38.462 0.00 0.00 35.35 2.83
651 663 7.094205 CCTTGTATCTCAATTACCTGCTTGTTT 60.094 37.037 0.00 0.00 35.35 2.83
652 664 8.856153 TTGTATCTCAATTACCTGCTTGTTTA 57.144 30.769 0.00 0.00 0.00 2.01
653 665 8.856153 TGTATCTCAATTACCTGCTTGTTTAA 57.144 30.769 0.00 0.00 0.00 1.52
654 666 8.726988 TGTATCTCAATTACCTGCTTGTTTAAC 58.273 33.333 0.00 0.00 0.00 2.01
655 667 8.947115 GTATCTCAATTACCTGCTTGTTTAACT 58.053 33.333 0.00 0.00 0.00 2.24
657 669 8.911918 TCTCAATTACCTGCTTGTTTAACTAA 57.088 30.769 0.00 0.00 0.00 2.24
658 670 9.515226 TCTCAATTACCTGCTTGTTTAACTAAT 57.485 29.630 0.00 0.00 0.00 1.73
686 698 9.498176 TTTTAGTTTTCCCTGTATCTCAGTTAC 57.502 33.333 0.00 0.00 42.19 2.50
687 699 6.051179 AGTTTTCCCTGTATCTCAGTTACC 57.949 41.667 0.00 0.00 42.19 2.85
688 700 5.785940 AGTTTTCCCTGTATCTCAGTTACCT 59.214 40.000 0.00 0.00 42.19 3.08
689 701 5.677319 TTTCCCTGTATCTCAGTTACCTG 57.323 43.478 0.00 0.00 42.19 4.00
690 702 4.332683 TCCCTGTATCTCAGTTACCTGT 57.667 45.455 0.00 0.00 42.19 4.00
691 703 4.023980 TCCCTGTATCTCAGTTACCTGTG 58.976 47.826 0.00 0.00 42.19 3.66
692 704 3.769844 CCCTGTATCTCAGTTACCTGTGT 59.230 47.826 0.00 0.00 42.19 3.72
693 705 4.954202 CCCTGTATCTCAGTTACCTGTGTA 59.046 45.833 0.00 0.00 42.19 2.90
694 706 5.598830 CCCTGTATCTCAGTTACCTGTGTAT 59.401 44.000 0.00 0.00 42.19 2.29
695 707 6.098409 CCCTGTATCTCAGTTACCTGTGTATT 59.902 42.308 0.00 0.00 42.19 1.89
696 708 7.364762 CCCTGTATCTCAGTTACCTGTGTATTT 60.365 40.741 0.00 0.00 42.19 1.40
697 709 8.692710 CCTGTATCTCAGTTACCTGTGTATTTA 58.307 37.037 0.00 0.00 42.19 1.40
703 715 9.595823 TCTCAGTTACCTGTGTATTTATTAAGC 57.404 33.333 0.00 0.00 39.82 3.09
704 716 8.415192 TCAGTTACCTGTGTATTTATTAAGCG 57.585 34.615 0.00 0.00 39.82 4.68
705 717 7.010738 TCAGTTACCTGTGTATTTATTAAGCGC 59.989 37.037 0.00 0.00 39.82 5.92
706 718 6.259387 AGTTACCTGTGTATTTATTAAGCGCC 59.741 38.462 2.29 0.00 0.00 6.53
707 719 3.558418 ACCTGTGTATTTATTAAGCGCCG 59.442 43.478 2.29 0.00 0.00 6.46
708 720 3.558418 CCTGTGTATTTATTAAGCGCCGT 59.442 43.478 2.29 0.00 0.00 5.68
709 721 4.514506 CTGTGTATTTATTAAGCGCCGTG 58.485 43.478 2.29 0.00 0.00 4.94
710 722 4.182339 TGTGTATTTATTAAGCGCCGTGA 58.818 39.130 2.29 0.00 0.00 4.35
711 723 4.630505 TGTGTATTTATTAAGCGCCGTGAA 59.369 37.500 2.29 0.00 0.00 3.18
712 724 4.959757 GTGTATTTATTAAGCGCCGTGAAC 59.040 41.667 2.29 0.00 0.00 3.18
713 725 4.630505 TGTATTTATTAAGCGCCGTGAACA 59.369 37.500 2.29 0.00 0.00 3.18
714 726 4.688511 ATTTATTAAGCGCCGTGAACAA 57.311 36.364 2.29 0.00 0.00 2.83
715 727 4.485024 TTTATTAAGCGCCGTGAACAAA 57.515 36.364 2.29 0.00 0.00 2.83
716 728 4.688511 TTATTAAGCGCCGTGAACAAAT 57.311 36.364 2.29 0.00 0.00 2.32
717 729 2.604969 TTAAGCGCCGTGAACAAATC 57.395 45.000 2.29 0.00 0.00 2.17
718 730 1.803334 TAAGCGCCGTGAACAAATCT 58.197 45.000 2.29 0.00 0.00 2.40
719 731 0.238289 AAGCGCCGTGAACAAATCTG 59.762 50.000 2.29 0.00 0.00 2.90
720 732 0.884704 AGCGCCGTGAACAAATCTGT 60.885 50.000 2.29 0.00 37.39 3.41
721 733 0.793861 GCGCCGTGAACAAATCTGTA 59.206 50.000 0.00 0.00 33.45 2.74
722 734 1.195900 GCGCCGTGAACAAATCTGTAA 59.804 47.619 0.00 0.00 33.45 2.41
723 735 2.724839 GCGCCGTGAACAAATCTGTAAG 60.725 50.000 0.00 0.00 33.45 2.34
750 762 5.630415 CCTAATCAAGGGATGACTAACCA 57.370 43.478 0.00 0.00 41.93 3.67
751 763 6.001449 CCTAATCAAGGGATGACTAACCAA 57.999 41.667 0.00 0.00 41.93 3.67
752 764 6.423182 CCTAATCAAGGGATGACTAACCAAA 58.577 40.000 0.00 0.00 41.93 3.28
753 765 6.889722 CCTAATCAAGGGATGACTAACCAAAA 59.110 38.462 0.00 0.00 41.93 2.44
754 766 6.590234 AATCAAGGGATGACTAACCAAAAC 57.410 37.500 0.00 0.00 41.93 2.43
755 767 5.055265 TCAAGGGATGACTAACCAAAACA 57.945 39.130 0.00 0.00 31.50 2.83
756 768 5.070001 TCAAGGGATGACTAACCAAAACAG 58.930 41.667 0.00 0.00 31.50 3.16
757 769 4.993705 AGGGATGACTAACCAAAACAGA 57.006 40.909 0.00 0.00 0.00 3.41
758 770 4.652822 AGGGATGACTAACCAAAACAGAC 58.347 43.478 0.00 0.00 0.00 3.51
759 771 4.104102 AGGGATGACTAACCAAAACAGACA 59.896 41.667 0.00 0.00 0.00 3.41
760 772 4.825085 GGGATGACTAACCAAAACAGACAA 59.175 41.667 0.00 0.00 0.00 3.18
761 773 5.278315 GGGATGACTAACCAAAACAGACAAC 60.278 44.000 0.00 0.00 0.00 3.32
762 774 5.531287 GGATGACTAACCAAAACAGACAACT 59.469 40.000 0.00 0.00 0.00 3.16
763 775 6.708949 GGATGACTAACCAAAACAGACAACTA 59.291 38.462 0.00 0.00 0.00 2.24
764 776 7.227910 GGATGACTAACCAAAACAGACAACTAA 59.772 37.037 0.00 0.00 0.00 2.24
765 777 7.925043 TGACTAACCAAAACAGACAACTAAA 57.075 32.000 0.00 0.00 0.00 1.85
766 778 7.754625 TGACTAACCAAAACAGACAACTAAAC 58.245 34.615 0.00 0.00 0.00 2.01
767 779 7.390996 TGACTAACCAAAACAGACAACTAAACA 59.609 33.333 0.00 0.00 0.00 2.83
768 780 7.758495 ACTAACCAAAACAGACAACTAAACAG 58.242 34.615 0.00 0.00 0.00 3.16
769 781 5.576447 ACCAAAACAGACAACTAAACAGG 57.424 39.130 0.00 0.00 0.00 4.00
770 782 4.142249 ACCAAAACAGACAACTAAACAGGC 60.142 41.667 0.00 0.00 0.00 4.85
771 783 4.142271 CCAAAACAGACAACTAAACAGGCA 60.142 41.667 0.00 0.00 0.00 4.75
772 784 5.406649 CAAAACAGACAACTAAACAGGCAA 58.593 37.500 0.00 0.00 0.00 4.52
773 785 5.652994 AAACAGACAACTAAACAGGCAAA 57.347 34.783 0.00 0.00 0.00 3.68
774 786 5.652994 AACAGACAACTAAACAGGCAAAA 57.347 34.783 0.00 0.00 0.00 2.44
775 787 5.652994 ACAGACAACTAAACAGGCAAAAA 57.347 34.783 0.00 0.00 0.00 1.94
794 806 3.695830 AAAATACTCACCGGCAGAAGA 57.304 42.857 0.00 0.00 0.00 2.87
795 807 3.695830 AAATACTCACCGGCAGAAGAA 57.304 42.857 0.00 0.00 0.00 2.52
796 808 2.674796 ATACTCACCGGCAGAAGAAC 57.325 50.000 0.00 0.00 0.00 3.01
797 809 0.242825 TACTCACCGGCAGAAGAACG 59.757 55.000 0.00 0.00 0.00 3.95
822 834 2.974698 GCAAGCGCGCATATCCCT 60.975 61.111 35.10 7.55 0.00 4.20
823 835 2.959357 GCAAGCGCGCATATCCCTC 61.959 63.158 35.10 9.01 0.00 4.30
824 836 1.301244 CAAGCGCGCATATCCCTCT 60.301 57.895 35.10 5.73 0.00 3.69
825 837 0.038251 CAAGCGCGCATATCCCTCTA 60.038 55.000 35.10 0.00 0.00 2.43
826 838 0.244994 AAGCGCGCATATCCCTCTAG 59.755 55.000 35.10 0.00 0.00 2.43
854 866 4.639135 ATAGAATCCGGCAAGAAAAAGC 57.361 40.909 0.00 0.00 0.00 3.51
1064 1369 6.291585 CGTGAAAGAAAAATCCAACGGAAAAG 60.292 38.462 0.00 0.00 34.34 2.27
1118 1423 4.207281 CGAAGCTGATCCCGCCGA 62.207 66.667 0.00 0.00 0.00 5.54
1119 1424 2.586357 GAAGCTGATCCCGCCGAC 60.586 66.667 0.00 0.00 0.00 4.79
1120 1425 4.514577 AAGCTGATCCCGCCGACG 62.515 66.667 0.00 0.00 39.67 5.12
1191 1499 1.678635 CCAAGAAGGGCGGCATGAA 60.679 57.895 12.47 0.00 0.00 2.57
1197 1505 1.244019 AAGGGCGGCATGAACAAGAC 61.244 55.000 12.47 0.00 0.00 3.01
1356 1673 2.614481 GGGCAACTCTCGTGGTTTCATA 60.614 50.000 0.00 0.00 0.00 2.15
1392 1735 5.190992 TCATGGCTACAATCGTTACGTAT 57.809 39.130 4.24 0.00 0.00 3.06
1394 1737 5.460748 TCATGGCTACAATCGTTACGTATTG 59.539 40.000 19.86 19.86 38.71 1.90
1640 2015 0.469144 GGCCAAAGTCAACTTCCCCA 60.469 55.000 0.00 0.00 34.61 4.96
1644 2019 1.336755 CAAAGTCAACTTCCCCAACGG 59.663 52.381 0.00 0.00 34.61 4.44
1698 2073 1.779683 GGAGAACCGCTTCGAAACG 59.220 57.895 13.80 13.80 0.00 3.60
1835 2228 0.179020 CCTGACCACTGCTTTCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2155 2582 5.677319 TCGGTTGTAAGAATCTCCATCTT 57.323 39.130 0.00 0.00 40.18 2.40
2232 2664 1.750399 CATGGCCAGGAACGAAGGG 60.750 63.158 13.35 0.00 0.00 3.95
2453 4029 3.742433 TGCGGTTGTCAATTCCAAATT 57.258 38.095 0.00 0.00 0.00 1.82
2459 4035 6.201997 GCGGTTGTCAATTCCAAATTAGTTTT 59.798 34.615 0.00 0.00 0.00 2.43
2460 4036 7.382759 GCGGTTGTCAATTCCAAATTAGTTTTA 59.617 33.333 0.00 0.00 0.00 1.52
2567 4161 2.608090 GGAATTTCGGAGGTGATTCGTC 59.392 50.000 0.00 0.00 31.03 4.20
2644 4239 3.316868 GGAAATTTCGTTCCACTCCAACA 59.683 43.478 11.95 0.00 45.57 3.33
2647 4242 1.790755 TTCGTTCCACTCCAACATCG 58.209 50.000 0.00 0.00 0.00 3.84
2651 4246 2.608506 CGTTCCACTCCAACATCGTGTA 60.609 50.000 0.00 0.00 0.00 2.90
2662 4257 7.987458 ACTCCAACATCGTGTAAAGAATCATAT 59.013 33.333 0.00 0.00 0.00 1.78
2736 4331 7.215789 AGATGACATATCACTTCATTCCTGTC 58.784 38.462 0.00 0.00 37.79 3.51
2772 4370 3.582647 TCCTGTGAATCAAAGAGGCACTA 59.417 43.478 1.15 0.00 41.55 2.74
2773 4371 4.225942 TCCTGTGAATCAAAGAGGCACTAT 59.774 41.667 1.15 0.00 41.55 2.12
2827 4425 9.436957 CTACATTGTGTAGTTGATCTTTTACCT 57.563 33.333 8.58 0.00 43.93 3.08
2828 4426 8.691661 ACATTGTGTAGTTGATCTTTTACCTT 57.308 30.769 0.00 0.00 0.00 3.50
2833 4431 9.485206 TGTGTAGTTGATCTTTTACCTTAAGAC 57.515 33.333 3.36 0.00 34.68 3.01
2848 4456 4.033358 CCTTAAGACGATGTCAATCTGTGC 59.967 45.833 3.36 0.00 34.60 4.57
2940 4552 9.866655 TTTAAGGCAAATATCTGGAATCTACAT 57.133 29.630 0.00 0.00 0.00 2.29
2955 4567 3.098377 TCTACATAACTAACCGCCACCA 58.902 45.455 0.00 0.00 0.00 4.17
2966 4578 2.954611 GCCACCACTTCGCCTTTC 59.045 61.111 0.00 0.00 0.00 2.62
2988 4632 6.477053 TCAAACCAAAAGGTTCATCATCAA 57.523 33.333 0.00 0.00 0.00 2.57
2990 4634 4.503741 ACCAAAAGGTTCATCATCAACG 57.496 40.909 0.00 0.00 0.00 4.10
3002 4646 7.872993 GGTTCATCATCAACGGAGATATTCTTA 59.127 37.037 0.00 0.00 0.00 2.10
3036 4680 9.905713 ATCTTGTGTATGTGTAAATATCTGGTT 57.094 29.630 0.00 0.00 0.00 3.67
3037 4681 9.161629 TCTTGTGTATGTGTAAATATCTGGTTG 57.838 33.333 0.00 0.00 0.00 3.77
3038 4682 8.856153 TTGTGTATGTGTAAATATCTGGTTGT 57.144 30.769 0.00 0.00 0.00 3.32
3039 4683 9.945904 TTGTGTATGTGTAAATATCTGGTTGTA 57.054 29.630 0.00 0.00 0.00 2.41
3042 4686 9.051679 TGTATGTGTAAATATCTGGTTGTATGC 57.948 33.333 0.00 0.00 0.00 3.14
3043 4687 9.051679 GTATGTGTAAATATCTGGTTGTATGCA 57.948 33.333 0.00 0.00 0.00 3.96
3044 4688 8.696043 ATGTGTAAATATCTGGTTGTATGCAT 57.304 30.769 3.79 3.79 0.00 3.96
3045 4689 8.153479 TGTGTAAATATCTGGTTGTATGCATC 57.847 34.615 0.19 0.00 0.00 3.91
3046 4690 7.042119 TGTGTAAATATCTGGTTGTATGCATCG 60.042 37.037 0.19 0.00 0.00 3.84
3047 4691 5.362556 AAATATCTGGTTGTATGCATCGC 57.637 39.130 0.19 0.00 0.00 4.58
3048 4692 1.597742 ATCTGGTTGTATGCATCGCC 58.402 50.000 0.19 1.97 0.00 5.54
3049 4693 0.463654 TCTGGTTGTATGCATCGCCC 60.464 55.000 0.19 0.00 0.00 6.13
3052 4696 0.463654 GGTTGTATGCATCGCCCAGA 60.464 55.000 0.19 0.00 0.00 3.86
3060 4704 4.872357 ATCGCCCAGATGCAGAAG 57.128 55.556 0.00 0.00 38.36 2.85
3061 4705 2.215191 ATCGCCCAGATGCAGAAGA 58.785 52.632 0.00 0.00 38.36 2.87
3063 4707 2.169789 CGCCCAGATGCAGAAGACG 61.170 63.158 0.00 0.00 0.00 4.18
3064 4708 1.817099 GCCCAGATGCAGAAGACGG 60.817 63.158 0.00 0.00 0.00 4.79
3065 4709 1.153289 CCCAGATGCAGAAGACGGG 60.153 63.158 0.00 0.00 0.00 5.28
3066 4710 1.617018 CCCAGATGCAGAAGACGGGA 61.617 60.000 0.00 0.00 33.83 5.14
3067 4711 0.250234 CCAGATGCAGAAGACGGGAA 59.750 55.000 0.00 0.00 0.00 3.97
3068 4712 1.134280 CCAGATGCAGAAGACGGGAAT 60.134 52.381 0.00 0.00 0.00 3.01
3069 4713 2.208431 CAGATGCAGAAGACGGGAATC 58.792 52.381 0.00 0.00 0.00 2.52
3070 4714 2.114616 AGATGCAGAAGACGGGAATCT 58.885 47.619 0.00 0.00 0.00 2.40
3071 4715 2.503356 AGATGCAGAAGACGGGAATCTT 59.497 45.455 0.00 0.00 41.74 2.40
3076 4720 2.605837 GAAGACGGGAATCTTCCTCC 57.394 55.000 8.78 0.00 46.04 4.30
3077 4721 2.112190 GAAGACGGGAATCTTCCTCCT 58.888 52.381 8.78 1.75 46.04 3.69
3078 4722 2.255770 AGACGGGAATCTTCCTCCTT 57.744 50.000 8.78 0.00 46.72 3.36
3079 4723 2.552367 AGACGGGAATCTTCCTCCTTT 58.448 47.619 8.78 0.00 46.72 3.11
3080 4724 2.913617 AGACGGGAATCTTCCTCCTTTT 59.086 45.455 8.78 0.00 46.72 2.27
3081 4725 3.055021 AGACGGGAATCTTCCTCCTTTTC 60.055 47.826 8.78 0.00 46.72 2.29
3082 4726 2.913617 ACGGGAATCTTCCTCCTTTTCT 59.086 45.455 8.78 0.00 46.72 2.52
3083 4727 4.101856 ACGGGAATCTTCCTCCTTTTCTA 58.898 43.478 8.78 0.00 46.72 2.10
3084 4728 4.534897 ACGGGAATCTTCCTCCTTTTCTAA 59.465 41.667 8.78 0.00 46.72 2.10
3085 4729 5.013808 ACGGGAATCTTCCTCCTTTTCTAAA 59.986 40.000 8.78 0.00 46.72 1.85
3086 4730 5.944007 CGGGAATCTTCCTCCTTTTCTAAAA 59.056 40.000 8.78 0.00 46.72 1.52
3087 4731 6.433093 CGGGAATCTTCCTCCTTTTCTAAAAA 59.567 38.462 8.78 0.00 46.72 1.94
3088 4732 7.122799 CGGGAATCTTCCTCCTTTTCTAAAAAT 59.877 37.037 8.78 0.00 46.72 1.82
3089 4733 9.475620 GGGAATCTTCCTCCTTTTCTAAAAATA 57.524 33.333 8.78 0.00 46.72 1.40
3118 4762 9.729281 ATTGAAATTAAGATGGCAATTTTCTGT 57.271 25.926 0.00 0.00 35.14 3.41
3213 4857 6.384224 ACAAAGATGTCAATATGTTGCTGTG 58.616 36.000 0.00 0.00 33.41 3.66
3214 4858 5.571784 AAGATGTCAATATGTTGCTGTGG 57.428 39.130 0.00 0.00 35.26 4.17
3215 4859 4.592942 AGATGTCAATATGTTGCTGTGGT 58.407 39.130 0.00 0.00 35.26 4.16
3216 4860 4.637534 AGATGTCAATATGTTGCTGTGGTC 59.362 41.667 0.00 0.00 35.26 4.02
3217 4861 3.081061 TGTCAATATGTTGCTGTGGTCC 58.919 45.455 0.00 0.00 35.26 4.46
3218 4862 3.244875 TGTCAATATGTTGCTGTGGTCCT 60.245 43.478 0.00 0.00 35.26 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 0.839946 ACTGGCCAGTTGAGTGAACT 59.160 50.000 33.20 5.90 46.52 3.01
352 364 3.855853 GCTTCTCCTCCTCCGCCC 61.856 72.222 0.00 0.00 0.00 6.13
366 378 1.635663 GGAGTTGTACATGCGCGCTT 61.636 55.000 33.29 24.21 0.00 4.68
374 386 4.475016 AGCTTGGGAATAGGAGTTGTACAT 59.525 41.667 0.00 0.00 0.00 2.29
478 490 2.741486 TACGGCAAGTGGTGGGAAGC 62.741 60.000 0.00 0.00 0.00 3.86
546 558 3.335748 TGGATTATGGATGGGCTTAGGT 58.664 45.455 0.00 0.00 0.00 3.08
571 583 3.006859 TGTCCATAAGGCATCGTGGATAG 59.993 47.826 7.77 0.00 42.27 2.08
572 584 2.969262 TGTCCATAAGGCATCGTGGATA 59.031 45.455 7.77 3.20 42.27 2.59
573 585 1.768275 TGTCCATAAGGCATCGTGGAT 59.232 47.619 7.77 0.00 42.27 3.41
574 586 1.199615 TGTCCATAAGGCATCGTGGA 58.800 50.000 1.02 1.02 38.37 4.02
575 587 1.670811 GTTGTCCATAAGGCATCGTGG 59.329 52.381 0.00 0.00 33.74 4.94
576 588 2.355197 TGTTGTCCATAAGGCATCGTG 58.645 47.619 0.00 0.00 33.74 4.35
577 589 2.779755 TGTTGTCCATAAGGCATCGT 57.220 45.000 0.00 0.00 33.74 3.73
578 590 5.947228 AATATGTTGTCCATAAGGCATCG 57.053 39.130 0.00 0.00 39.43 3.84
579 591 7.042797 ACAAATATGTTGTCCATAAGGCATC 57.957 36.000 0.00 0.00 39.43 3.91
616 628 9.457436 GGTAATTGAGATACAAGGGAAAACTAA 57.543 33.333 0.00 0.00 42.02 2.24
617 629 8.832735 AGGTAATTGAGATACAAGGGAAAACTA 58.167 33.333 0.00 0.00 42.02 2.24
618 630 7.611855 CAGGTAATTGAGATACAAGGGAAAACT 59.388 37.037 0.00 0.00 42.02 2.66
619 631 7.628580 GCAGGTAATTGAGATACAAGGGAAAAC 60.629 40.741 0.00 0.00 42.02 2.43
620 632 6.377146 GCAGGTAATTGAGATACAAGGGAAAA 59.623 38.462 0.00 0.00 42.02 2.29
621 633 5.885912 GCAGGTAATTGAGATACAAGGGAAA 59.114 40.000 0.00 0.00 42.02 3.13
622 634 5.191722 AGCAGGTAATTGAGATACAAGGGAA 59.808 40.000 0.00 0.00 42.02 3.97
623 635 4.721776 AGCAGGTAATTGAGATACAAGGGA 59.278 41.667 0.00 0.00 42.02 4.20
624 636 5.041191 AGCAGGTAATTGAGATACAAGGG 57.959 43.478 0.00 0.00 42.02 3.95
625 637 5.882557 ACAAGCAGGTAATTGAGATACAAGG 59.117 40.000 0.00 0.00 42.02 3.61
626 638 6.992063 ACAAGCAGGTAATTGAGATACAAG 57.008 37.500 0.00 0.00 42.02 3.16
627 639 7.759489 AAACAAGCAGGTAATTGAGATACAA 57.241 32.000 0.00 0.00 42.95 2.41
628 640 8.726988 GTTAAACAAGCAGGTAATTGAGATACA 58.273 33.333 0.00 0.00 0.00 2.29
629 641 8.947115 AGTTAAACAAGCAGGTAATTGAGATAC 58.053 33.333 0.00 0.00 0.00 2.24
631 643 9.515226 TTAGTTAAACAAGCAGGTAATTGAGAT 57.485 29.630 0.00 0.00 0.00 2.75
632 644 8.911918 TTAGTTAAACAAGCAGGTAATTGAGA 57.088 30.769 0.00 0.00 0.00 3.27
682 694 6.424683 GGCGCTTAATAAATACACAGGTAAC 58.575 40.000 7.64 0.00 32.19 2.50
683 695 5.234757 CGGCGCTTAATAAATACACAGGTAA 59.765 40.000 7.64 0.00 32.19 2.85
684 696 4.746115 CGGCGCTTAATAAATACACAGGTA 59.254 41.667 7.64 0.00 0.00 3.08
685 697 3.558418 CGGCGCTTAATAAATACACAGGT 59.442 43.478 7.64 0.00 0.00 4.00
686 698 3.558418 ACGGCGCTTAATAAATACACAGG 59.442 43.478 6.90 0.00 0.00 4.00
687 699 4.269123 TCACGGCGCTTAATAAATACACAG 59.731 41.667 6.90 0.00 0.00 3.66
688 700 4.182339 TCACGGCGCTTAATAAATACACA 58.818 39.130 6.90 0.00 0.00 3.72
689 701 4.782252 TCACGGCGCTTAATAAATACAC 57.218 40.909 6.90 0.00 0.00 2.90
690 702 4.630505 TGTTCACGGCGCTTAATAAATACA 59.369 37.500 6.90 0.00 0.00 2.29
691 703 5.146482 TGTTCACGGCGCTTAATAAATAC 57.854 39.130 6.90 0.00 0.00 1.89
692 704 5.798015 TTGTTCACGGCGCTTAATAAATA 57.202 34.783 6.90 0.00 0.00 1.40
693 705 4.688511 TTGTTCACGGCGCTTAATAAAT 57.311 36.364 6.90 0.00 0.00 1.40
694 706 4.485024 TTTGTTCACGGCGCTTAATAAA 57.515 36.364 6.90 7.03 0.00 1.40
695 707 4.393680 AGATTTGTTCACGGCGCTTAATAA 59.606 37.500 6.90 0.37 0.00 1.40
696 708 3.936453 AGATTTGTTCACGGCGCTTAATA 59.064 39.130 6.90 0.00 0.00 0.98
697 709 2.747446 AGATTTGTTCACGGCGCTTAAT 59.253 40.909 6.90 0.00 0.00 1.40
698 710 2.095969 CAGATTTGTTCACGGCGCTTAA 60.096 45.455 6.90 0.00 0.00 1.85
699 711 1.463056 CAGATTTGTTCACGGCGCTTA 59.537 47.619 6.90 0.00 0.00 3.09
700 712 0.238289 CAGATTTGTTCACGGCGCTT 59.762 50.000 6.90 0.00 0.00 4.68
701 713 0.884704 ACAGATTTGTTCACGGCGCT 60.885 50.000 6.90 0.00 32.28 5.92
702 714 0.793861 TACAGATTTGTTCACGGCGC 59.206 50.000 6.90 0.00 38.76 6.53
703 715 2.734606 TCTTACAGATTTGTTCACGGCG 59.265 45.455 4.80 4.80 38.76 6.46
704 716 3.994392 TCTCTTACAGATTTGTTCACGGC 59.006 43.478 0.00 0.00 38.76 5.68
705 717 4.389077 GGTCTCTTACAGATTTGTTCACGG 59.611 45.833 0.00 0.00 38.76 4.94
706 718 4.389077 GGGTCTCTTACAGATTTGTTCACG 59.611 45.833 0.00 0.00 38.76 4.35
707 719 5.552178 AGGGTCTCTTACAGATTTGTTCAC 58.448 41.667 0.00 0.00 38.76 3.18
708 720 5.825593 AGGGTCTCTTACAGATTTGTTCA 57.174 39.130 0.00 0.00 38.76 3.18
709 721 8.041323 TGATTAGGGTCTCTTACAGATTTGTTC 58.959 37.037 0.00 0.00 38.76 3.18
710 722 7.918076 TGATTAGGGTCTCTTACAGATTTGTT 58.082 34.615 0.00 0.00 38.76 2.83
711 723 7.496346 TGATTAGGGTCTCTTACAGATTTGT 57.504 36.000 0.00 0.00 41.39 2.83
712 724 7.497249 CCTTGATTAGGGTCTCTTACAGATTTG 59.503 40.741 0.00 0.00 40.67 2.32
713 725 7.569240 CCTTGATTAGGGTCTCTTACAGATTT 58.431 38.462 0.00 0.00 40.67 2.17
714 726 7.130681 CCTTGATTAGGGTCTCTTACAGATT 57.869 40.000 0.00 0.00 40.67 2.40
715 727 6.739331 CCTTGATTAGGGTCTCTTACAGAT 57.261 41.667 0.00 0.00 40.67 2.90
728 740 5.630415 TGGTTAGTCATCCCTTGATTAGG 57.370 43.478 0.00 0.00 44.33 2.69
729 741 7.393234 TGTTTTGGTTAGTCATCCCTTGATTAG 59.607 37.037 0.00 0.00 36.54 1.73
730 742 7.235079 TGTTTTGGTTAGTCATCCCTTGATTA 58.765 34.615 0.00 0.00 36.54 1.75
731 743 6.074648 TGTTTTGGTTAGTCATCCCTTGATT 58.925 36.000 0.00 0.00 36.54 2.57
732 744 5.640147 TGTTTTGGTTAGTCATCCCTTGAT 58.360 37.500 0.00 0.00 36.54 2.57
733 745 5.055265 TGTTTTGGTTAGTCATCCCTTGA 57.945 39.130 0.00 0.00 0.00 3.02
734 746 5.048713 GTCTGTTTTGGTTAGTCATCCCTTG 60.049 44.000 0.00 0.00 0.00 3.61
735 747 5.070685 GTCTGTTTTGGTTAGTCATCCCTT 58.929 41.667 0.00 0.00 0.00 3.95
736 748 4.104102 TGTCTGTTTTGGTTAGTCATCCCT 59.896 41.667 0.00 0.00 0.00 4.20
737 749 4.394729 TGTCTGTTTTGGTTAGTCATCCC 58.605 43.478 0.00 0.00 0.00 3.85
738 750 5.531287 AGTTGTCTGTTTTGGTTAGTCATCC 59.469 40.000 0.00 0.00 0.00 3.51
739 751 6.619801 AGTTGTCTGTTTTGGTTAGTCATC 57.380 37.500 0.00 0.00 0.00 2.92
740 752 8.403236 GTTTAGTTGTCTGTTTTGGTTAGTCAT 58.597 33.333 0.00 0.00 0.00 3.06
741 753 7.390996 TGTTTAGTTGTCTGTTTTGGTTAGTCA 59.609 33.333 0.00 0.00 0.00 3.41
742 754 7.754625 TGTTTAGTTGTCTGTTTTGGTTAGTC 58.245 34.615 0.00 0.00 0.00 2.59
743 755 7.148137 CCTGTTTAGTTGTCTGTTTTGGTTAGT 60.148 37.037 0.00 0.00 0.00 2.24
744 756 7.193595 CCTGTTTAGTTGTCTGTTTTGGTTAG 58.806 38.462 0.00 0.00 0.00 2.34
745 757 6.404954 GCCTGTTTAGTTGTCTGTTTTGGTTA 60.405 38.462 0.00 0.00 0.00 2.85
746 758 5.623596 GCCTGTTTAGTTGTCTGTTTTGGTT 60.624 40.000 0.00 0.00 0.00 3.67
747 759 4.142249 GCCTGTTTAGTTGTCTGTTTTGGT 60.142 41.667 0.00 0.00 0.00 3.67
748 760 4.142271 TGCCTGTTTAGTTGTCTGTTTTGG 60.142 41.667 0.00 0.00 0.00 3.28
749 761 4.992688 TGCCTGTTTAGTTGTCTGTTTTG 58.007 39.130 0.00 0.00 0.00 2.44
750 762 5.652994 TTGCCTGTTTAGTTGTCTGTTTT 57.347 34.783 0.00 0.00 0.00 2.43
751 763 5.652994 TTTGCCTGTTTAGTTGTCTGTTT 57.347 34.783 0.00 0.00 0.00 2.83
752 764 5.652994 TTTTGCCTGTTTAGTTGTCTGTT 57.347 34.783 0.00 0.00 0.00 3.16
753 765 5.652994 TTTTTGCCTGTTTAGTTGTCTGT 57.347 34.783 0.00 0.00 0.00 3.41
773 785 4.015872 TCTTCTGCCGGTGAGTATTTTT 57.984 40.909 1.90 0.00 0.00 1.94
774 786 3.695830 TCTTCTGCCGGTGAGTATTTT 57.304 42.857 1.90 0.00 0.00 1.82
775 787 3.335579 GTTCTTCTGCCGGTGAGTATTT 58.664 45.455 1.90 0.00 0.00 1.40
776 788 2.674177 CGTTCTTCTGCCGGTGAGTATT 60.674 50.000 1.90 0.00 0.00 1.89
777 789 1.135083 CGTTCTTCTGCCGGTGAGTAT 60.135 52.381 1.90 0.00 0.00 2.12
778 790 0.242825 CGTTCTTCTGCCGGTGAGTA 59.757 55.000 1.90 0.00 0.00 2.59
779 791 1.006102 CGTTCTTCTGCCGGTGAGT 60.006 57.895 1.90 0.00 0.00 3.41
780 792 1.738099 CCGTTCTTCTGCCGGTGAG 60.738 63.158 1.90 0.00 37.00 3.51
781 793 2.342279 CCGTTCTTCTGCCGGTGA 59.658 61.111 1.90 0.00 37.00 4.02
782 794 3.423154 GCCGTTCTTCTGCCGGTG 61.423 66.667 1.90 0.00 43.56 4.94
805 817 2.959357 GAGGGATATGCGCGCTTGC 61.959 63.158 33.29 20.82 34.07 4.01
806 818 0.038251 TAGAGGGATATGCGCGCTTG 60.038 55.000 33.29 0.00 40.03 4.01
807 819 0.244994 CTAGAGGGATATGCGCGCTT 59.755 55.000 33.29 28.14 40.03 4.68
808 820 0.896019 ACTAGAGGGATATGCGCGCT 60.896 55.000 33.29 19.73 42.06 5.92
809 821 0.038159 AACTAGAGGGATATGCGCGC 60.038 55.000 27.26 27.26 34.07 6.86
810 822 1.000163 ACAACTAGAGGGATATGCGCG 60.000 52.381 0.00 0.00 34.07 6.86
811 823 2.224066 ACACAACTAGAGGGATATGCGC 60.224 50.000 0.00 0.00 0.00 6.09
812 824 3.735237 ACACAACTAGAGGGATATGCG 57.265 47.619 0.00 0.00 0.00 4.73
813 825 7.704578 TCTATACACAACTAGAGGGATATGC 57.295 40.000 0.00 0.00 0.00 3.14
815 827 9.482175 GGATTCTATACACAACTAGAGGGATAT 57.518 37.037 0.00 0.00 0.00 1.63
816 828 7.610692 CGGATTCTATACACAACTAGAGGGATA 59.389 40.741 0.00 0.00 0.00 2.59
817 829 6.434652 CGGATTCTATACACAACTAGAGGGAT 59.565 42.308 0.00 0.00 0.00 3.85
818 830 5.768662 CGGATTCTATACACAACTAGAGGGA 59.231 44.000 0.00 0.00 0.00 4.20
819 831 5.047943 CCGGATTCTATACACAACTAGAGGG 60.048 48.000 0.00 0.00 0.00 4.30
820 832 5.565045 GCCGGATTCTATACACAACTAGAGG 60.565 48.000 5.05 0.00 0.00 3.69
821 833 5.009710 TGCCGGATTCTATACACAACTAGAG 59.990 44.000 5.05 0.00 0.00 2.43
822 834 4.891168 TGCCGGATTCTATACACAACTAGA 59.109 41.667 5.05 0.00 0.00 2.43
823 835 5.196341 TGCCGGATTCTATACACAACTAG 57.804 43.478 5.05 0.00 0.00 2.57
824 836 5.361571 TCTTGCCGGATTCTATACACAACTA 59.638 40.000 5.05 0.00 0.00 2.24
825 837 4.161565 TCTTGCCGGATTCTATACACAACT 59.838 41.667 5.05 0.00 0.00 3.16
826 838 4.439057 TCTTGCCGGATTCTATACACAAC 58.561 43.478 5.05 0.00 0.00 3.32
854 866 1.447317 AAGGAACCACAGTGCAAGCG 61.447 55.000 0.00 0.00 0.00 4.68
1052 1357 1.953686 CTCTTTGCCTTTTCCGTTGGA 59.046 47.619 0.00 0.00 0.00 3.53
1064 1369 2.666619 CGCACATTGTTCTCTCTTTGCC 60.667 50.000 0.00 0.00 0.00 4.52
1191 1499 1.889105 CTGCTGTGGTGCGTCTTGT 60.889 57.895 0.00 0.00 35.36 3.16
1265 1576 4.463879 CTCCTCCGCCTGCAGGTG 62.464 72.222 34.93 34.93 45.02 4.00
1356 1673 3.658725 AGCCATGAACCCTGTATACTCT 58.341 45.455 4.17 0.00 0.00 3.24
1392 1735 2.742053 GCTGCAAAGGAATCTACGTCAA 59.258 45.455 0.00 0.00 0.00 3.18
1394 1737 1.666189 GGCTGCAAAGGAATCTACGTC 59.334 52.381 0.50 0.00 0.00 4.34
1668 2043 3.936203 TTCTCCGGCTGGCACGTT 61.936 61.111 6.73 0.00 34.14 3.99
1669 2044 4.681978 GTTCTCCGGCTGGCACGT 62.682 66.667 6.73 0.00 34.14 4.49
1755 2148 3.338275 TTGGCCACCATAGCGTCCC 62.338 63.158 3.88 0.00 31.53 4.46
1835 2228 2.184322 CATGACAGGCGGTAGCGT 59.816 61.111 16.63 0.00 46.35 5.07
2011 2422 3.138930 ATCCTGGATGACGGCGTCG 62.139 63.158 31.90 18.52 43.02 5.12
2453 4029 9.226606 CACAAGATAACCAGGTTCATAAAACTA 57.773 33.333 8.57 0.00 28.91 2.24
2459 4035 6.367374 TGACACAAGATAACCAGGTTCATA 57.633 37.500 8.57 0.00 0.00 2.15
2460 4036 5.241403 TGACACAAGATAACCAGGTTCAT 57.759 39.130 8.57 0.97 0.00 2.57
2627 4221 2.139917 CGATGTTGGAGTGGAACGAAA 58.860 47.619 0.00 0.00 45.86 3.46
2671 4266 5.947228 ATATGGGTATTTGATTGTGCGAG 57.053 39.130 0.00 0.00 0.00 5.03
2672 4267 7.809546 TTAATATGGGTATTTGATTGTGCGA 57.190 32.000 0.00 0.00 32.84 5.10
2686 4281 9.507329 CTTTAGTACTGCATGATTAATATGGGT 57.493 33.333 5.39 0.00 0.00 4.51
2744 4339 5.415701 GCCTCTTTGATTCACAGGATTTGTA 59.584 40.000 8.94 0.00 38.16 2.41
2755 4353 6.418101 AGCTTAATAGTGCCTCTTTGATTCA 58.582 36.000 0.00 0.00 0.00 2.57
2773 4371 9.982651 GAGTACATCCAGAATTGTATAGCTTAA 57.017 33.333 0.00 0.00 31.48 1.85
2824 4422 5.171476 CACAGATTGACATCGTCTTAAGGT 58.829 41.667 1.85 0.00 34.17 3.50
2825 4423 4.033358 GCACAGATTGACATCGTCTTAAGG 59.967 45.833 1.85 0.00 34.17 2.69
2826 4424 4.867047 AGCACAGATTGACATCGTCTTAAG 59.133 41.667 0.00 0.00 34.17 1.85
2827 4425 4.627035 CAGCACAGATTGACATCGTCTTAA 59.373 41.667 0.00 0.00 34.17 1.85
2828 4426 4.176271 CAGCACAGATTGACATCGTCTTA 58.824 43.478 0.00 0.00 34.17 2.10
2831 4429 1.662629 CCAGCACAGATTGACATCGTC 59.337 52.381 0.00 0.00 34.17 4.20
2832 4430 1.002430 ACCAGCACAGATTGACATCGT 59.998 47.619 0.00 0.00 34.17 3.73
2833 4431 1.395954 CACCAGCACAGATTGACATCG 59.604 52.381 0.00 0.00 34.17 3.84
2848 4456 3.530910 AAGCCGAACGGACCACCAG 62.531 63.158 17.63 0.00 37.50 4.00
2940 4552 1.337074 CGAAGTGGTGGCGGTTAGTTA 60.337 52.381 0.00 0.00 0.00 2.24
2955 4567 3.430236 CCTTTTGGTTTGAAAGGCGAAGT 60.430 43.478 2.99 0.00 44.62 3.01
2977 4589 7.721286 AAGAATATCTCCGTTGATGATGAAC 57.279 36.000 0.00 0.00 0.00 3.18
3021 4665 7.290842 CGATGCATACAACCAGATATTTACAC 58.709 38.462 0.00 0.00 0.00 2.90
3024 4668 5.411361 GGCGATGCATACAACCAGATATTTA 59.589 40.000 0.00 0.00 0.00 1.40
3025 4669 4.216257 GGCGATGCATACAACCAGATATTT 59.784 41.667 0.00 0.00 0.00 1.40
3026 4670 3.753272 GGCGATGCATACAACCAGATATT 59.247 43.478 0.00 0.00 0.00 1.28
3027 4671 3.338249 GGCGATGCATACAACCAGATAT 58.662 45.455 0.00 0.00 0.00 1.63
3028 4672 2.549992 GGGCGATGCATACAACCAGATA 60.550 50.000 0.00 0.00 0.00 1.98
3029 4673 1.597742 GGCGATGCATACAACCAGAT 58.402 50.000 0.00 0.00 0.00 2.90
3030 4674 0.463654 GGGCGATGCATACAACCAGA 60.464 55.000 0.00 0.00 0.00 3.86
3031 4675 0.747644 TGGGCGATGCATACAACCAG 60.748 55.000 0.00 0.00 0.00 4.00
3032 4676 0.747644 CTGGGCGATGCATACAACCA 60.748 55.000 0.00 5.45 0.00 3.67
3033 4677 0.463654 TCTGGGCGATGCATACAACC 60.464 55.000 0.00 0.30 0.00 3.77
3034 4678 1.265095 CATCTGGGCGATGCATACAAC 59.735 52.381 0.00 0.00 42.75 3.32
3036 4680 3.310727 CATCTGGGCGATGCATACA 57.689 52.632 0.00 0.00 42.75 2.29
3043 4687 0.179062 GTCTTCTGCATCTGGGCGAT 60.179 55.000 0.00 0.00 36.28 4.58
3044 4688 1.219124 GTCTTCTGCATCTGGGCGA 59.781 57.895 0.00 0.00 36.28 5.54
3045 4689 2.169789 CGTCTTCTGCATCTGGGCG 61.170 63.158 0.00 0.00 36.28 6.13
3046 4690 1.817099 CCGTCTTCTGCATCTGGGC 60.817 63.158 0.00 0.00 0.00 5.36
3047 4691 1.153289 CCCGTCTTCTGCATCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
3048 4692 0.250234 TTCCCGTCTTCTGCATCTGG 59.750 55.000 0.00 0.00 0.00 3.86
3049 4693 2.158986 AGATTCCCGTCTTCTGCATCTG 60.159 50.000 0.00 0.00 0.00 2.90
3052 4696 2.911484 GAAGATTCCCGTCTTCTGCAT 58.089 47.619 8.89 0.00 46.72 3.96
3092 4736 9.729281 ACAGAAAATTGCCATCTTAATTTCAAT 57.271 25.926 0.00 0.00 35.94 2.57
3129 4773 7.044380 CGCATCTCGATTCTAGAATTATACAGC 60.044 40.741 18.88 16.61 41.67 4.40
3147 4791 4.407551 TGCAGTGATCGCATCTCG 57.592 55.556 9.33 0.00 33.55 4.04
3162 4806 4.082571 AGTTAAGGATCAACTGCACAATGC 60.083 41.667 0.00 0.00 45.29 3.56


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

AutoCloner maintained by Alex Coulton.