Multiple sequence alignment - TraesCS4D01G058500

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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 TraesCS4D01G058500 chr4D 100.000 3908 0 0 1 3908 34664725 34668632 0.000000e+00 7217.0
1 TraesCS4D01G058500 chr4D 85.156 128 18 1 376 502 119822900 119822773 3.170000e-26 130.0
2 TraesCS4D01G058500 chr4D 91.111 45 3 1 850 893 432988886 432988842 4.220000e-05 60.2
3 TraesCS4D01G058500 chr4D 100.000 31 0 0 629 659 499555654 499555684 1.520000e-04 58.4
4 TraesCS4D01G058500 chr4A 96.413 2760 66 13 1035 3781 567685847 567683108 0.000000e+00 4518.0
5 TraesCS4D01G058500 chr4A 91.791 536 37 4 13 545 567686852 567686321 0.000000e+00 739.0
6 TraesCS4D01G058500 chr4A 96.479 142 5 0 3767 3908 567682945 567682804 6.530000e-58 235.0
7 TraesCS4D01G058500 chr4A 85.827 127 15 3 376 500 450791658 450791533 8.810000e-27 132.0
8 TraesCS4D01G058500 chr4B 93.349 3007 151 25 946 3907 49740534 49743536 0.000000e+00 4399.0
9 TraesCS4D01G058500 chr4B 97.239 326 9 0 13 338 49739935 49740260 1.590000e-153 553.0
10 TraesCS4D01G058500 chr4B 89.583 144 14 1 364 507 49740261 49740403 8.630000e-42 182.0
11 TraesCS4D01G058500 chr4B 100.000 30 0 0 632 661 23845857 23845828 5.450000e-04 56.5
12 TraesCS4D01G058500 chr4B 100.000 29 0 0 631 659 134457775 134457803 2.000000e-03 54.7
13 TraesCS4D01G058500 chr4B 100.000 29 0 0 631 659 135218215 135218187 2.000000e-03 54.7
14 TraesCS4D01G058500 chr1D 82.022 178 26 6 720 893 75768271 75768096 3.150000e-31 147.0
15 TraesCS4D01G058500 chr1D 84.496 129 19 1 376 503 418194249 418194121 4.100000e-25 126.0
16 TraesCS4D01G058500 chr1A 82.759 174 21 6 720 891 59607803 59607637 3.150000e-31 147.0
17 TraesCS4D01G058500 chr7D 82.759 174 19 7 720 891 267878467 267878303 1.130000e-30 145.0
18 TraesCS4D01G058500 chr5D 88.333 120 13 1 376 494 220683190 220683309 4.070000e-30 143.0
19 TraesCS4D01G058500 chr5D 100.000 29 0 0 631 659 190923066 190923094 2.000000e-03 54.7
20 TraesCS4D01G058500 chr6A 85.106 141 15 5 370 509 38757319 38757184 5.270000e-29 139.0
21 TraesCS4D01G058500 chr6A 100.000 30 0 0 630 659 387878690 387878719 5.450000e-04 56.5
22 TraesCS4D01G058500 chr7A 85.714 126 17 1 372 496 427814847 427814972 8.810000e-27 132.0
23 TraesCS4D01G058500 chr2A 83.453 139 20 2 370 507 747272334 747272198 4.100000e-25 126.0
24 TraesCS4D01G058500 chr7B 85.217 115 13 4 509 620 645090077 645090190 8.870000e-22 115.0
25 TraesCS4D01G058500 chr2D 81.818 132 18 6 511 638 649125815 649125944 5.340000e-19 106.0
26 TraesCS4D01G058500 chr2D 100.000 30 0 0 630 659 14119481 14119510 5.450000e-04 56.5
27 TraesCS4D01G058500 chr6D 100.000 30 0 0 630 659 271599926 271599955 5.450000e-04 56.5
28 TraesCS4D01G058500 chr5B 100.000 30 0 0 630 659 578847406 578847377 5.450000e-04 56.5
29 TraesCS4D01G058500 chr3D 94.444 36 2 0 858 893 146940203 146940168 5.450000e-04 56.5


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 TraesCS4D01G058500 chr4D 34664725 34668632 3907 False 7217.000000 7217 100.000000 1 3908 1 chr4D.!!$F1 3907
1 TraesCS4D01G058500 chr4A 567682804 567686852 4048 True 1830.666667 4518 94.894333 13 3908 3 chr4A.!!$R2 3895
2 TraesCS4D01G058500 chr4B 49739935 49743536 3601 False 1711.333333 4399 93.390333 13 3907 3 chr4B.!!$F2 3894

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
258 260 0.462581 ATGCATCCCAGTGCTGTACG 60.463 55.000 0.00 0.0 45.27 3.67 F
269 271 0.899019 TGCTGTACGCCTGATGGTTA 59.101 50.000 7.13 0.0 38.05 2.85 F
802 806 1.421268 TCTGTGGCATCAAACACTCCT 59.579 47.619 0.00 0.0 38.39 3.69 F
2514 2726 1.228644 TTGCATTGCCAGCAGAGGT 60.229 52.632 6.12 0.0 43.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2470 1.184431 CCACAATGCCATGGCTTGTA 58.816 50.000 34.26 21.13 38.98 2.41 R
2451 2663 7.041107 GCTCAAGTTTCTCATCTCTGACTAAT 58.959 38.462 0.00 0.00 0.00 1.73 R
2562 2774 1.798223 TCCTTGACATGTTTCTTCGCG 59.202 47.619 0.00 0.00 0.00 5.87 R
3819 4237 1.587568 TGCAGAACATGGCATGCAC 59.412 52.632 26.70 19.55 43.34 4.57 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
187 188 9.593134 AAAAGATGTGTTTCTATAGCTAGTGAG 57.407 33.333 0.00 0.00 0.00 3.51
258 260 0.462581 ATGCATCCCAGTGCTGTACG 60.463 55.000 0.00 0.00 45.27 3.67
269 271 0.899019 TGCTGTACGCCTGATGGTTA 59.101 50.000 7.13 0.00 38.05 2.85
383 385 5.278120 GCACGTTGTAAAATTGTACTCCCTT 60.278 40.000 7.31 0.00 0.00 3.95
473 477 8.856153 ACAAACACACTAACATATGTCCATAA 57.144 30.769 9.23 0.00 0.00 1.90
481 485 9.330063 CACTAACATATGTCCATAAACATCTGT 57.670 33.333 9.23 3.15 44.25 3.41
485 489 7.919690 ACATATGTCCATAAACATCTGTTTCG 58.080 34.615 11.35 5.18 44.15 3.46
515 519 6.313519 AGTTATAAAACATCTCAGGGCTCA 57.686 37.500 0.00 0.00 38.12 4.26
520 524 3.726557 AACATCTCAGGGCTCATTTGA 57.273 42.857 0.00 0.00 0.00 2.69
523 527 4.205587 ACATCTCAGGGCTCATTTGATTC 58.794 43.478 0.00 0.00 0.00 2.52
524 528 4.204799 CATCTCAGGGCTCATTTGATTCA 58.795 43.478 0.00 0.00 0.00 2.57
525 529 4.305539 TCTCAGGGCTCATTTGATTCAA 57.694 40.909 0.00 0.00 0.00 2.69
532 536 5.486419 AGGGCTCATTTGATTCAAAGGAATT 59.514 36.000 22.41 9.40 42.17 2.17
533 537 5.814188 GGGCTCATTTGATTCAAAGGAATTC 59.186 40.000 22.41 15.46 42.17 2.17
535 539 6.534079 GGCTCATTTGATTCAAAGGAATTCTG 59.466 38.462 22.41 13.89 42.17 3.02
545 549 9.578439 GATTCAAAGGAATTCTGTAGGATTTTG 57.422 33.333 5.23 4.74 43.69 2.44
546 550 7.466746 TCAAAGGAATTCTGTAGGATTTTGG 57.533 36.000 5.23 0.00 0.00 3.28
547 551 6.437162 TCAAAGGAATTCTGTAGGATTTTGGG 59.563 38.462 5.23 0.00 0.00 4.12
553 557 5.796502 TTCTGTAGGATTTTGGGAGGATT 57.203 39.130 0.00 0.00 0.00 3.01
554 558 5.116084 TCTGTAGGATTTTGGGAGGATTG 57.884 43.478 0.00 0.00 0.00 2.67
555 559 4.788075 TCTGTAGGATTTTGGGAGGATTGA 59.212 41.667 0.00 0.00 0.00 2.57
556 560 5.252863 TCTGTAGGATTTTGGGAGGATTGAA 59.747 40.000 0.00 0.00 0.00 2.69
557 561 5.898120 TGTAGGATTTTGGGAGGATTGAAA 58.102 37.500 0.00 0.00 0.00 2.69
558 562 6.502138 TGTAGGATTTTGGGAGGATTGAAAT 58.498 36.000 0.00 0.00 0.00 2.17
559 563 7.647827 TGTAGGATTTTGGGAGGATTGAAATA 58.352 34.615 0.00 0.00 0.00 1.40
560 564 8.288812 TGTAGGATTTTGGGAGGATTGAAATAT 58.711 33.333 0.00 0.00 0.00 1.28
561 565 9.147732 GTAGGATTTTGGGAGGATTGAAATATT 57.852 33.333 0.00 0.00 0.00 1.28
568 572 9.728100 TTTGGGAGGATTGAAATATTTAGGAAT 57.272 29.630 0.00 0.48 0.00 3.01
594 598 7.969690 TTTTCTATATTGGCCCTTTGATTCA 57.030 32.000 0.00 0.00 0.00 2.57
595 599 8.551682 TTTTCTATATTGGCCCTTTGATTCAT 57.448 30.769 0.00 0.00 0.00 2.57
596 600 8.551682 TTTCTATATTGGCCCTTTGATTCATT 57.448 30.769 0.00 0.00 0.00 2.57
601 605 5.502089 TTGGCCCTTTGATTCATTGAATT 57.498 34.783 12.96 0.00 31.89 2.17
602 606 4.834534 TGGCCCTTTGATTCATTGAATTG 58.165 39.130 12.96 4.97 31.89 2.32
603 607 4.193865 GGCCCTTTGATTCATTGAATTGG 58.806 43.478 12.96 12.01 31.89 3.16
604 608 4.080975 GGCCCTTTGATTCATTGAATTGGA 60.081 41.667 12.96 0.73 31.89 3.53
606 610 6.117488 GCCCTTTGATTCATTGAATTGGATT 58.883 36.000 12.96 0.00 31.89 3.01
608 612 6.764560 CCCTTTGATTCATTGAATTGGATTCC 59.235 38.462 12.96 0.00 38.50 3.01
613 617 8.185506 TGATTCATTGAATTGGATTCCATAGG 57.814 34.615 12.96 0.00 38.50 2.57
614 618 8.005976 TGATTCATTGAATTGGATTCCATAGGA 58.994 33.333 12.96 0.00 38.50 2.94
615 619 8.967779 ATTCATTGAATTGGATTCCATAGGAT 57.032 30.769 6.15 0.00 38.50 3.24
616 620 8.786710 TTCATTGAATTGGATTCCATAGGATT 57.213 30.769 6.15 3.09 38.50 3.01
617 621 8.786710 TCATTGAATTGGATTCCATAGGATTT 57.213 30.769 6.15 0.00 38.50 2.17
618 622 9.216148 TCATTGAATTGGATTCCATAGGATTTT 57.784 29.630 6.15 0.00 38.50 1.82
619 623 9.841295 CATTGAATTGGATTCCATAGGATTTTT 57.159 29.630 6.15 0.00 38.50 1.94
621 625 8.843308 TGAATTGGATTCCATAGGATTTTTCT 57.157 30.769 6.15 0.00 38.50 2.52
622 626 8.917088 TGAATTGGATTCCATAGGATTTTTCTC 58.083 33.333 6.15 0.00 38.50 2.87
623 627 9.140874 GAATTGGATTCCATAGGATTTTTCTCT 57.859 33.333 6.15 0.00 31.53 3.10
626 630 9.578576 TTGGATTCCATAGGATTTTTCTCTATG 57.421 33.333 6.15 0.00 39.74 2.23
641 645 8.575649 TTTTCTCTATGGATTTTTGTACTCCC 57.424 34.615 0.00 0.00 0.00 4.30
642 646 7.510675 TTCTCTATGGATTTTTGTACTCCCT 57.489 36.000 0.00 0.00 0.00 4.20
643 647 7.125792 TCTCTATGGATTTTTGTACTCCCTC 57.874 40.000 0.00 0.00 0.00 4.30
644 648 6.099845 TCTCTATGGATTTTTGTACTCCCTCC 59.900 42.308 0.00 0.00 0.00 4.30
645 649 4.946160 ATGGATTTTTGTACTCCCTCCA 57.054 40.909 0.00 1.07 35.89 3.86
646 650 4.946160 TGGATTTTTGTACTCCCTCCAT 57.054 40.909 0.00 0.00 0.00 3.41
647 651 5.269554 TGGATTTTTGTACTCCCTCCATT 57.730 39.130 0.00 0.00 0.00 3.16
648 652 5.261216 TGGATTTTTGTACTCCCTCCATTC 58.739 41.667 0.00 0.00 0.00 2.67
649 653 4.645136 GGATTTTTGTACTCCCTCCATTCC 59.355 45.833 0.00 0.00 0.00 3.01
650 654 5.510430 GATTTTTGTACTCCCTCCATTCCT 58.490 41.667 0.00 0.00 0.00 3.36
651 655 6.353602 GGATTTTTGTACTCCCTCCATTCCTA 60.354 42.308 0.00 0.00 0.00 2.94
652 656 6.457159 TTTTTGTACTCCCTCCATTCCTAA 57.543 37.500 0.00 0.00 0.00 2.69
653 657 6.457159 TTTTGTACTCCCTCCATTCCTAAA 57.543 37.500 0.00 0.00 0.00 1.85
654 658 6.652205 TTTGTACTCCCTCCATTCCTAAAT 57.348 37.500 0.00 0.00 0.00 1.40
655 659 7.758820 TTTGTACTCCCTCCATTCCTAAATA 57.241 36.000 0.00 0.00 0.00 1.40
656 660 7.947782 TTGTACTCCCTCCATTCCTAAATAT 57.052 36.000 0.00 0.00 0.00 1.28
657 661 9.455144 TTTGTACTCCCTCCATTCCTAAATATA 57.545 33.333 0.00 0.00 0.00 0.86
658 662 9.455144 TTGTACTCCCTCCATTCCTAAATATAA 57.545 33.333 0.00 0.00 0.00 0.98
659 663 9.629649 TGTACTCCCTCCATTCCTAAATATAAT 57.370 33.333 0.00 0.00 0.00 1.28
663 667 9.601217 CTCCCTCCATTCCTAAATATAATAACG 57.399 37.037 0.00 0.00 0.00 3.18
664 668 9.108111 TCCCTCCATTCCTAAATATAATAACGT 57.892 33.333 0.00 0.00 0.00 3.99
665 669 9.162764 CCCTCCATTCCTAAATATAATAACGTG 57.837 37.037 0.00 0.00 0.00 4.49
666 670 9.720769 CCTCCATTCCTAAATATAATAACGTGT 57.279 33.333 0.00 0.00 0.00 4.49
711 715 9.793252 TGTAAAGAACGTCTTATATGTAGGAAC 57.207 33.333 0.00 0.00 35.27 3.62
712 716 9.793252 GTAAAGAACGTCTTATATGTAGGAACA 57.207 33.333 0.00 0.00 35.27 3.18
715 719 7.932335 AGAACGTCTTATATGTAGGAACAGAG 58.068 38.462 0.00 0.00 39.49 3.35
716 720 6.636562 ACGTCTTATATGTAGGAACAGAGG 57.363 41.667 0.00 0.00 39.49 3.69
717 721 6.363065 ACGTCTTATATGTAGGAACAGAGGA 58.637 40.000 0.00 0.00 39.49 3.71
719 723 7.013464 ACGTCTTATATGTAGGAACAGAGGAAG 59.987 40.741 0.00 0.00 39.49 3.46
721 725 9.352191 GTCTTATATGTAGGAACAGAGGAAGTA 57.648 37.037 0.00 0.00 39.49 2.24
725 729 8.694581 ATATGTAGGAACAGAGGAAGTACTAC 57.305 38.462 0.00 0.00 39.49 2.73
727 731 6.491383 TGTAGGAACAGAGGAAGTACTACAT 58.509 40.000 0.00 0.00 36.01 2.29
728 732 6.952358 TGTAGGAACAGAGGAAGTACTACATT 59.048 38.462 0.00 0.00 36.01 2.71
730 734 6.937392 AGGAACAGAGGAAGTACTACATTTC 58.063 40.000 0.00 0.00 0.00 2.17
731 735 6.497259 AGGAACAGAGGAAGTACTACATTTCA 59.503 38.462 0.00 0.00 0.00 2.69
732 736 6.590677 GGAACAGAGGAAGTACTACATTTCAC 59.409 42.308 0.00 0.00 0.00 3.18
733 737 6.665992 ACAGAGGAAGTACTACATTTCACA 57.334 37.500 0.00 0.00 0.00 3.58
736 740 7.015292 ACAGAGGAAGTACTACATTTCACAGAA 59.985 37.037 0.00 0.00 0.00 3.02
739 743 9.220767 GAGGAAGTACTACATTTCACAGAAAAT 57.779 33.333 0.00 0.00 0.00 1.82
740 744 9.220767 AGGAAGTACTACATTTCACAGAAAATC 57.779 33.333 0.00 0.00 0.00 2.17
741 745 9.220767 GGAAGTACTACATTTCACAGAAAATCT 57.779 33.333 0.00 0.00 0.00 2.40
759 763 8.547173 AGAAAATCTGACATCCACTCTAATCTT 58.453 33.333 0.00 0.00 0.00 2.40
760 764 8.729805 AAAATCTGACATCCACTCTAATCTTC 57.270 34.615 0.00 0.00 0.00 2.87
761 765 7.673641 AATCTGACATCCACTCTAATCTTCT 57.326 36.000 0.00 0.00 0.00 2.85
763 767 7.487822 TCTGACATCCACTCTAATCTTCTTT 57.512 36.000 0.00 0.00 0.00 2.52
764 768 7.911651 TCTGACATCCACTCTAATCTTCTTTT 58.088 34.615 0.00 0.00 0.00 2.27
765 769 7.821359 TCTGACATCCACTCTAATCTTCTTTTG 59.179 37.037 0.00 0.00 0.00 2.44
766 770 7.453393 TGACATCCACTCTAATCTTCTTTTGT 58.547 34.615 0.00 0.00 0.00 2.83
769 773 9.965902 ACATCCACTCTAATCTTCTTTTGTAAT 57.034 29.630 0.00 0.00 0.00 1.89
799 803 4.734398 TTTTTCTGTGGCATCAAACACT 57.266 36.364 0.00 0.00 38.39 3.55
800 804 3.988379 TTTCTGTGGCATCAAACACTC 57.012 42.857 0.00 0.00 38.39 3.51
801 805 1.896220 TCTGTGGCATCAAACACTCC 58.104 50.000 0.00 0.00 38.39 3.85
802 806 1.421268 TCTGTGGCATCAAACACTCCT 59.579 47.619 0.00 0.00 38.39 3.69
803 807 2.158623 TCTGTGGCATCAAACACTCCTT 60.159 45.455 0.00 0.00 38.39 3.36
804 808 3.072330 TCTGTGGCATCAAACACTCCTTA 59.928 43.478 0.00 0.00 38.39 2.69
805 809 3.146066 TGTGGCATCAAACACTCCTTAC 58.854 45.455 0.00 0.00 38.39 2.34
806 810 3.181445 TGTGGCATCAAACACTCCTTACT 60.181 43.478 0.00 0.00 38.39 2.24
807 811 4.041075 TGTGGCATCAAACACTCCTTACTA 59.959 41.667 0.00 0.00 38.39 1.82
808 812 5.001232 GTGGCATCAAACACTCCTTACTAA 58.999 41.667 0.00 0.00 34.84 2.24
809 813 5.648092 GTGGCATCAAACACTCCTTACTAAT 59.352 40.000 0.00 0.00 34.84 1.73
810 814 6.151144 GTGGCATCAAACACTCCTTACTAATT 59.849 38.462 0.00 0.00 34.84 1.40
811 815 6.719370 TGGCATCAAACACTCCTTACTAATTT 59.281 34.615 0.00 0.00 0.00 1.82
812 816 7.232534 TGGCATCAAACACTCCTTACTAATTTT 59.767 33.333 0.00 0.00 0.00 1.82
813 817 8.736244 GGCATCAAACACTCCTTACTAATTTTA 58.264 33.333 0.00 0.00 0.00 1.52
847 851 5.848286 TGGATATGCCACTCCAATCTTAT 57.152 39.130 0.00 0.00 43.33 1.73
848 852 6.950860 TGGATATGCCACTCCAATCTTATA 57.049 37.500 0.00 0.00 43.33 0.98
849 853 7.515004 TGGATATGCCACTCCAATCTTATAT 57.485 36.000 0.00 0.00 43.33 0.86
850 854 7.932134 TGGATATGCCACTCCAATCTTATATT 58.068 34.615 0.00 0.00 43.33 1.28
851 855 8.393259 TGGATATGCCACTCCAATCTTATATTT 58.607 33.333 0.00 0.00 43.33 1.40
852 856 9.247861 GGATATGCCACTCCAATCTTATATTTT 57.752 33.333 0.00 0.00 36.34 1.82
855 859 8.773033 ATGCCACTCCAATCTTATATTTTTCT 57.227 30.769 0.00 0.00 0.00 2.52
856 860 7.999679 TGCCACTCCAATCTTATATTTTTCTG 58.000 34.615 0.00 0.00 0.00 3.02
857 861 7.615365 TGCCACTCCAATCTTATATTTTTCTGT 59.385 33.333 0.00 0.00 0.00 3.41
858 862 8.470002 GCCACTCCAATCTTATATTTTTCTGTT 58.530 33.333 0.00 0.00 0.00 3.16
891 895 8.857694 TTTAAAATCCTACGAATCAAAGAGGT 57.142 30.769 0.00 0.00 0.00 3.85
892 896 6.986904 AAAATCCTACGAATCAAAGAGGTC 57.013 37.500 0.00 0.00 0.00 3.85
893 897 5.677319 AATCCTACGAATCAAAGAGGTCA 57.323 39.130 0.00 0.00 0.00 4.02
895 899 5.677319 TCCTACGAATCAAAGAGGTCATT 57.323 39.130 0.00 0.00 0.00 2.57
896 900 5.661458 TCCTACGAATCAAAGAGGTCATTC 58.339 41.667 0.00 0.00 0.00 2.67
897 901 5.186992 TCCTACGAATCAAAGAGGTCATTCA 59.813 40.000 0.00 0.00 0.00 2.57
899 903 6.540189 CCTACGAATCAAAGAGGTCATTCATT 59.460 38.462 0.00 0.00 0.00 2.57
900 904 7.710907 CCTACGAATCAAAGAGGTCATTCATTA 59.289 37.037 0.00 0.00 0.00 1.90
901 905 9.265901 CTACGAATCAAAGAGGTCATTCATTAT 57.734 33.333 0.00 0.00 0.00 1.28
903 907 9.265901 ACGAATCAAAGAGGTCATTCATTATAG 57.734 33.333 0.00 0.00 0.00 1.31
915 919 8.524487 GGTCATTCATTATAGTAATCTCTCCGT 58.476 37.037 0.00 0.00 0.00 4.69
916 920 9.562583 GTCATTCATTATAGTAATCTCTCCGTC 57.437 37.037 0.00 0.00 0.00 4.79
917 921 8.740906 TCATTCATTATAGTAATCTCTCCGTCC 58.259 37.037 0.00 0.00 0.00 4.79
920 924 6.659668 TCATTATAGTAATCTCTCCGTCCCAG 59.340 42.308 0.00 0.00 0.00 4.45
922 926 1.569548 AGTAATCTCTCCGTCCCAGGA 59.430 52.381 0.00 0.00 38.80 3.86
923 927 2.178106 AGTAATCTCTCCGTCCCAGGAT 59.822 50.000 0.00 0.00 39.96 3.24
926 930 4.676799 AATCTCTCCGTCCCAGGATATA 57.323 45.455 0.00 0.00 39.96 0.86
927 931 4.676799 ATCTCTCCGTCCCAGGATATAA 57.323 45.455 0.00 0.00 39.96 0.98
928 932 4.035612 TCTCTCCGTCCCAGGATATAAG 57.964 50.000 0.00 0.00 39.96 1.73
930 934 4.292571 TCTCTCCGTCCCAGGATATAAGAT 59.707 45.833 0.00 0.00 39.96 2.40
931 935 4.601084 TCTCCGTCCCAGGATATAAGATC 58.399 47.826 0.00 0.00 39.96 2.75
932 936 4.044191 TCTCCGTCCCAGGATATAAGATCA 59.956 45.833 0.00 0.00 39.96 2.92
933 937 4.747583 TCCGTCCCAGGATATAAGATCAA 58.252 43.478 0.00 0.00 34.92 2.57
934 938 5.342017 TCCGTCCCAGGATATAAGATCAAT 58.658 41.667 0.00 0.00 34.92 2.57
936 940 6.272324 TCCGTCCCAGGATATAAGATCAATTT 59.728 38.462 0.00 0.00 34.92 1.82
938 942 7.448469 CCGTCCCAGGATATAAGATCAATTTTT 59.552 37.037 0.00 0.00 0.00 1.94
969 1150 5.422012 TCAGCTGATACTATTGGTTCAGTCA 59.578 40.000 13.74 0.00 36.45 3.41
972 1153 5.023533 TGATACTATTGGTTCAGTCAGGC 57.976 43.478 0.00 0.00 0.00 4.85
1008 1201 4.696877 TCAGTTCATCACGAAATGCAATCT 59.303 37.500 0.00 0.00 46.77 2.40
1009 1202 5.181811 TCAGTTCATCACGAAATGCAATCTT 59.818 36.000 0.00 0.00 46.77 2.40
1010 1203 5.285370 CAGTTCATCACGAAATGCAATCTTG 59.715 40.000 0.00 0.00 42.23 3.02
1011 1204 4.030977 GTTCATCACGAAATGCAATCTTGC 59.969 41.667 7.96 7.96 44.33 4.01
1012 1205 7.160214 GTTCATCACGAAATGCAATCTTGCG 62.160 44.000 10.10 0.00 45.82 4.85
1057 1269 4.681744 ACATGCAGTTGTTCGTTTTCAAT 58.318 34.783 0.00 0.00 0.00 2.57
1744 1956 2.276116 AAGCTCGACGAGGCCAAGA 61.276 57.895 25.31 0.00 0.00 3.02
2514 2726 1.228644 TTGCATTGCCAGCAGAGGT 60.229 52.632 6.12 0.00 43.75 3.85
2562 2774 2.988010 TCTGGATCCATGCACTGTAC 57.012 50.000 16.63 0.00 0.00 2.90
2586 2798 3.416156 GAAGAAACATGTCAAGGAGGCT 58.584 45.455 0.00 0.00 0.00 4.58
2610 2822 2.679837 CTCGTATTGCTTGGACATGCTT 59.320 45.455 10.84 2.73 33.23 3.91
2724 2936 1.003580 GAGAAGGTGAGGTTGATGGCA 59.996 52.381 0.00 0.00 0.00 4.92
2882 3094 0.729690 GCTGACCTTTCGGATTCTGC 59.270 55.000 0.00 0.00 0.00 4.26
2918 3130 6.600882 ATTCCCGAGTTGAGTTAAACTAGA 57.399 37.500 0.00 0.00 40.48 2.43
2920 3132 5.776744 TCCCGAGTTGAGTTAAACTAGAAC 58.223 41.667 0.00 0.00 40.48 3.01
2963 3181 5.754890 ACCTTCACTTGATTGAATTGTTTGC 59.245 36.000 0.00 0.00 34.96 3.68
2984 3202 3.181500 GCGGGAGTGATTGGTTTATGAAC 60.181 47.826 0.00 0.00 34.96 3.18
3080 3300 1.112916 TGAGCCAAGTGACACTCCGA 61.113 55.000 8.93 0.00 0.00 4.55
3353 3578 7.173863 ACTACACAAGTAACAAAACTCATCG 57.826 36.000 0.00 0.00 36.36 3.84
3391 3616 8.249327 TGAAGTAGAGAGTTAGTAGTGTAACG 57.751 38.462 0.00 0.00 45.86 3.18
3447 3673 9.013229 CATGCTTATCTCTGAGATACTAAGAGT 57.987 37.037 23.42 11.57 39.49 3.24
3674 3911 7.148755 GCAGTTGCTTTTGTGGAAGTAAATATG 60.149 37.037 0.00 0.00 33.93 1.78
3676 3913 8.082242 AGTTGCTTTTGTGGAAGTAAATATGTC 58.918 33.333 0.00 0.00 33.93 3.06
3711 3948 1.605710 CTATTACATGCTGGTGCTGGC 59.394 52.381 0.00 0.00 40.48 4.85
3732 3970 7.009540 GCTGGCATTAACATTAATCAAGTTGAC 59.990 37.037 7.96 0.00 31.28 3.18
3831 4249 4.220693 TCTAGTTAAGTGCATGCCATGT 57.779 40.909 16.68 0.00 0.00 3.21
3869 4291 4.644103 ATGCTTATGTGCACTTTCATCC 57.356 40.909 19.41 1.27 46.33 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.171949 GCTGCAAGAGCCAGAGAAT 57.828 52.632 0.00 0.00 42.54 2.40
258 260 4.576463 CCAATTAGACACTAACCATCAGGC 59.424 45.833 0.00 0.00 39.06 4.85
269 271 4.104102 TCAGTTTCCACCCAATTAGACACT 59.896 41.667 0.00 0.00 0.00 3.55
499 503 4.038271 TCAAATGAGCCCTGAGATGTTT 57.962 40.909 0.00 0.00 0.00 2.83
507 511 3.765511 TCCTTTGAATCAAATGAGCCCTG 59.234 43.478 9.02 0.00 32.70 4.45
508 512 4.051661 TCCTTTGAATCAAATGAGCCCT 57.948 40.909 9.02 0.00 32.70 5.19
510 514 6.534079 CAGAATTCCTTTGAATCAAATGAGCC 59.466 38.462 9.02 5.41 40.34 4.70
511 515 7.095270 ACAGAATTCCTTTGAATCAAATGAGC 58.905 34.615 9.02 5.88 40.34 4.26
515 519 8.884124 TCCTACAGAATTCCTTTGAATCAAAT 57.116 30.769 9.02 0.00 40.34 2.32
520 524 8.534496 CCAAAATCCTACAGAATTCCTTTGAAT 58.466 33.333 0.65 0.00 43.08 2.57
523 527 6.437162 TCCCAAAATCCTACAGAATTCCTTTG 59.563 38.462 0.65 0.00 0.00 2.77
524 528 6.561294 TCCCAAAATCCTACAGAATTCCTTT 58.439 36.000 0.65 0.00 0.00 3.11
525 529 6.152638 TCCCAAAATCCTACAGAATTCCTT 57.847 37.500 0.65 0.00 0.00 3.36
532 536 4.788075 TCAATCCTCCCAAAATCCTACAGA 59.212 41.667 0.00 0.00 0.00 3.41
533 537 5.116084 TCAATCCTCCCAAAATCCTACAG 57.884 43.478 0.00 0.00 0.00 2.74
535 539 8.712228 ATATTTCAATCCTCCCAAAATCCTAC 57.288 34.615 0.00 0.00 0.00 3.18
576 580 6.811634 TTCAATGAATCAAAGGGCCAATAT 57.188 33.333 6.18 0.00 0.00 1.28
578 582 5.703730 ATTCAATGAATCAAAGGGCCAAT 57.296 34.783 6.18 0.00 0.00 3.16
579 583 5.247084 CAATTCAATGAATCAAAGGGCCAA 58.753 37.500 9.11 0.00 30.29 4.52
580 584 4.323638 CCAATTCAATGAATCAAAGGGCCA 60.324 41.667 9.11 0.00 30.29 5.36
582 586 5.088680 TCCAATTCAATGAATCAAAGGGC 57.911 39.130 9.11 0.00 30.29 5.19
585 589 8.958119 ATGGAATCCAATTCAATGAATCAAAG 57.042 30.769 5.89 0.59 41.03 2.77
588 592 8.005976 TCCTATGGAATCCAATTCAATGAATCA 58.994 33.333 5.89 1.61 41.03 2.57
590 594 8.967779 ATCCTATGGAATCCAATTCAATGAAT 57.032 30.769 5.89 2.07 41.03 2.57
593 597 9.841295 AAAAATCCTATGGAATCCAATTCAATG 57.159 29.630 5.89 0.00 41.03 2.82
595 599 9.270707 AGAAAAATCCTATGGAATCCAATTCAA 57.729 29.630 5.89 0.00 41.03 2.69
596 600 8.843308 AGAAAAATCCTATGGAATCCAATTCA 57.157 30.769 5.89 0.00 41.03 2.57
615 619 9.020731 GGGAGTACAAAAATCCATAGAGAAAAA 57.979 33.333 0.00 0.00 34.62 1.94
616 620 8.390921 AGGGAGTACAAAAATCCATAGAGAAAA 58.609 33.333 0.00 0.00 34.62 2.29
617 621 7.928873 AGGGAGTACAAAAATCCATAGAGAAA 58.071 34.615 0.00 0.00 34.62 2.52
618 622 7.365652 GGAGGGAGTACAAAAATCCATAGAGAA 60.366 40.741 0.00 0.00 34.62 2.87
619 623 6.099845 GGAGGGAGTACAAAAATCCATAGAGA 59.900 42.308 0.00 0.00 34.62 3.10
620 624 6.126768 TGGAGGGAGTACAAAAATCCATAGAG 60.127 42.308 0.00 0.00 34.62 2.43
621 625 5.729229 TGGAGGGAGTACAAAAATCCATAGA 59.271 40.000 0.00 0.00 34.62 1.98
622 626 6.001449 TGGAGGGAGTACAAAAATCCATAG 57.999 41.667 0.00 0.00 34.62 2.23
623 627 6.590656 ATGGAGGGAGTACAAAAATCCATA 57.409 37.500 14.38 0.00 42.70 2.74
624 628 4.946160 TGGAGGGAGTACAAAAATCCAT 57.054 40.909 0.00 0.00 34.62 3.41
625 629 4.946160 ATGGAGGGAGTACAAAAATCCA 57.054 40.909 8.64 8.64 39.52 3.41
626 630 4.645136 GGAATGGAGGGAGTACAAAAATCC 59.355 45.833 0.00 0.00 0.00 3.01
627 631 5.510430 AGGAATGGAGGGAGTACAAAAATC 58.490 41.667 0.00 0.00 0.00 2.17
628 632 5.536497 AGGAATGGAGGGAGTACAAAAAT 57.464 39.130 0.00 0.00 0.00 1.82
629 633 6.457159 TTAGGAATGGAGGGAGTACAAAAA 57.543 37.500 0.00 0.00 0.00 1.94
630 634 6.457159 TTTAGGAATGGAGGGAGTACAAAA 57.543 37.500 0.00 0.00 0.00 2.44
631 635 6.652205 ATTTAGGAATGGAGGGAGTACAAA 57.348 37.500 0.00 0.00 0.00 2.83
632 636 7.947782 ATATTTAGGAATGGAGGGAGTACAA 57.052 36.000 0.00 0.00 0.00 2.41
633 637 9.629649 ATTATATTTAGGAATGGAGGGAGTACA 57.370 33.333 0.00 0.00 0.00 2.90
637 641 9.601217 CGTTATTATATTTAGGAATGGAGGGAG 57.399 37.037 0.00 0.00 0.00 4.30
638 642 9.108111 ACGTTATTATATTTAGGAATGGAGGGA 57.892 33.333 0.00 0.00 0.00 4.20
639 643 9.162764 CACGTTATTATATTTAGGAATGGAGGG 57.837 37.037 0.00 0.00 0.00 4.30
640 644 9.720769 ACACGTTATTATATTTAGGAATGGAGG 57.279 33.333 0.00 0.00 0.00 4.30
685 689 9.793252 GTTCCTACATATAAGACGTTCTTTACA 57.207 33.333 5.74 0.00 37.89 2.41
686 690 9.793252 TGTTCCTACATATAAGACGTTCTTTAC 57.207 33.333 5.74 0.00 37.89 2.01
688 692 8.746530 TCTGTTCCTACATATAAGACGTTCTTT 58.253 33.333 5.74 0.00 34.33 2.52
689 693 8.289939 TCTGTTCCTACATATAAGACGTTCTT 57.710 34.615 0.00 0.00 35.69 2.52
690 694 7.013464 CCTCTGTTCCTACATATAAGACGTTCT 59.987 40.741 0.00 0.00 32.86 3.01
691 695 7.013083 TCCTCTGTTCCTACATATAAGACGTTC 59.987 40.741 0.00 0.00 32.86 3.95
692 696 6.832384 TCCTCTGTTCCTACATATAAGACGTT 59.168 38.462 0.00 0.00 32.86 3.99
693 697 6.363065 TCCTCTGTTCCTACATATAAGACGT 58.637 40.000 0.00 0.00 32.86 4.34
694 698 6.879276 TCCTCTGTTCCTACATATAAGACG 57.121 41.667 0.00 0.00 32.86 4.18
695 699 8.240267 ACTTCCTCTGTTCCTACATATAAGAC 57.760 38.462 0.00 0.00 32.86 3.01
696 700 9.352191 GTACTTCCTCTGTTCCTACATATAAGA 57.648 37.037 0.00 0.00 32.86 2.10
697 701 9.357161 AGTACTTCCTCTGTTCCTACATATAAG 57.643 37.037 0.00 0.00 32.86 1.73
699 703 9.790344 GTAGTACTTCCTCTGTTCCTACATATA 57.210 37.037 0.00 0.00 32.86 0.86
710 714 6.493802 TCTGTGAAATGTAGTACTTCCTCTGT 59.506 38.462 0.00 0.00 0.00 3.41
711 715 6.925211 TCTGTGAAATGTAGTACTTCCTCTG 58.075 40.000 0.00 0.49 0.00 3.35
712 716 7.540474 TTCTGTGAAATGTAGTACTTCCTCT 57.460 36.000 0.00 0.00 0.00 3.69
715 719 9.220767 AGATTTTCTGTGAAATGTAGTACTTCC 57.779 33.333 0.00 0.00 29.75 3.46
717 721 9.778741 TCAGATTTTCTGTGAAATGTAGTACTT 57.221 29.630 0.00 0.00 44.58 2.24
719 723 8.988934 TGTCAGATTTTCTGTGAAATGTAGTAC 58.011 33.333 4.56 0.00 44.58 2.73
721 725 8.627208 ATGTCAGATTTTCTGTGAAATGTAGT 57.373 30.769 4.56 0.00 44.58 2.73
724 728 6.491062 TGGATGTCAGATTTTCTGTGAAATGT 59.509 34.615 4.56 0.00 44.58 2.71
725 729 6.805271 GTGGATGTCAGATTTTCTGTGAAATG 59.195 38.462 4.56 0.00 44.58 2.32
727 731 6.064060 AGTGGATGTCAGATTTTCTGTGAAA 58.936 36.000 4.56 0.00 44.58 2.69
728 732 5.624159 AGTGGATGTCAGATTTTCTGTGAA 58.376 37.500 4.56 0.00 44.58 3.18
730 734 5.243981 AGAGTGGATGTCAGATTTTCTGTG 58.756 41.667 4.56 0.00 44.58 3.66
731 735 5.495926 AGAGTGGATGTCAGATTTTCTGT 57.504 39.130 4.56 0.00 44.58 3.41
732 736 7.986320 AGATTAGAGTGGATGTCAGATTTTCTG 59.014 37.037 0.00 0.00 45.59 3.02
733 737 8.088463 AGATTAGAGTGGATGTCAGATTTTCT 57.912 34.615 0.00 0.00 0.00 2.52
736 740 8.088463 AGAAGATTAGAGTGGATGTCAGATTT 57.912 34.615 0.00 0.00 0.00 2.17
739 743 7.487822 AAAGAAGATTAGAGTGGATGTCAGA 57.512 36.000 0.00 0.00 0.00 3.27
740 744 7.605691 ACAAAAGAAGATTAGAGTGGATGTCAG 59.394 37.037 0.00 0.00 0.00 3.51
741 745 7.453393 ACAAAAGAAGATTAGAGTGGATGTCA 58.547 34.615 0.00 0.00 0.00 3.58
742 746 7.913674 ACAAAAGAAGATTAGAGTGGATGTC 57.086 36.000 0.00 0.00 0.00 3.06
778 782 4.441356 GGAGTGTTTGATGCCACAGAAAAA 60.441 41.667 0.00 0.00 33.99 1.94
779 783 3.068024 GGAGTGTTTGATGCCACAGAAAA 59.932 43.478 0.00 0.00 33.99 2.29
780 784 2.622942 GGAGTGTTTGATGCCACAGAAA 59.377 45.455 0.00 0.00 33.99 2.52
781 785 2.158623 AGGAGTGTTTGATGCCACAGAA 60.159 45.455 0.00 0.00 33.99 3.02
782 786 1.421268 AGGAGTGTTTGATGCCACAGA 59.579 47.619 0.00 0.00 33.99 3.41
783 787 1.901591 AGGAGTGTTTGATGCCACAG 58.098 50.000 0.00 0.00 33.99 3.66
784 788 2.363306 AAGGAGTGTTTGATGCCACA 57.637 45.000 0.00 0.00 33.99 4.17
785 789 3.412386 AGTAAGGAGTGTTTGATGCCAC 58.588 45.455 0.00 0.00 0.00 5.01
786 790 3.788227 AGTAAGGAGTGTTTGATGCCA 57.212 42.857 0.00 0.00 0.00 4.92
787 791 6.759497 AATTAGTAAGGAGTGTTTGATGCC 57.241 37.500 0.00 0.00 0.00 4.40
809 813 9.599056 TGGCATATCCATTGAAATCCTATAAAA 57.401 29.630 0.00 0.00 40.72 1.52
825 829 5.848286 ATAAGATTGGAGTGGCATATCCA 57.152 39.130 17.56 17.56 43.87 3.41
826 830 8.814038 AAATATAAGATTGGAGTGGCATATCC 57.186 34.615 13.25 13.25 36.05 2.59
829 833 9.866655 AGAAAAATATAAGATTGGAGTGGCATA 57.133 29.630 0.00 0.00 0.00 3.14
830 834 8.636213 CAGAAAAATATAAGATTGGAGTGGCAT 58.364 33.333 0.00 0.00 0.00 4.40
831 835 7.615365 ACAGAAAAATATAAGATTGGAGTGGCA 59.385 33.333 0.00 0.00 0.00 4.92
832 836 8.000780 ACAGAAAAATATAAGATTGGAGTGGC 57.999 34.615 0.00 0.00 0.00 5.01
865 869 9.292195 ACCTCTTTGATTCGTAGGATTTTAAAA 57.708 29.630 2.51 2.51 0.00 1.52
866 870 8.857694 ACCTCTTTGATTCGTAGGATTTTAAA 57.142 30.769 0.00 0.00 0.00 1.52
867 871 8.098286 TGACCTCTTTGATTCGTAGGATTTTAA 58.902 33.333 0.00 0.00 0.00 1.52
868 872 7.617225 TGACCTCTTTGATTCGTAGGATTTTA 58.383 34.615 0.00 0.00 0.00 1.52
869 873 6.472887 TGACCTCTTTGATTCGTAGGATTTT 58.527 36.000 0.00 0.00 0.00 1.82
870 874 6.049955 TGACCTCTTTGATTCGTAGGATTT 57.950 37.500 0.00 0.00 0.00 2.17
871 875 5.677319 TGACCTCTTTGATTCGTAGGATT 57.323 39.130 0.00 0.00 0.00 3.01
878 882 9.265901 ACTATAATGAATGACCTCTTTGATTCG 57.734 33.333 0.00 0.00 0.00 3.34
888 892 8.744652 CGGAGAGATTACTATAATGAATGACCT 58.255 37.037 0.00 0.00 0.00 3.85
889 893 8.524487 ACGGAGAGATTACTATAATGAATGACC 58.476 37.037 0.00 0.00 0.00 4.02
890 894 9.562583 GACGGAGAGATTACTATAATGAATGAC 57.437 37.037 0.00 0.00 0.00 3.06
891 895 8.740906 GGACGGAGAGATTACTATAATGAATGA 58.259 37.037 0.00 0.00 0.00 2.57
892 896 7.976734 GGGACGGAGAGATTACTATAATGAATG 59.023 40.741 0.00 0.00 0.00 2.67
893 897 7.674348 TGGGACGGAGAGATTACTATAATGAAT 59.326 37.037 0.00 0.00 0.00 2.57
895 899 6.549242 TGGGACGGAGAGATTACTATAATGA 58.451 40.000 0.00 0.00 0.00 2.57
896 900 6.127591 CCTGGGACGGAGAGATTACTATAATG 60.128 46.154 0.00 0.00 36.31 1.90
897 901 5.952947 CCTGGGACGGAGAGATTACTATAAT 59.047 44.000 0.00 0.00 36.31 1.28
899 903 4.600547 TCCTGGGACGGAGAGATTACTATA 59.399 45.833 0.00 0.00 36.31 1.31
900 904 3.398292 TCCTGGGACGGAGAGATTACTAT 59.602 47.826 0.00 0.00 36.31 2.12
901 905 2.781757 TCCTGGGACGGAGAGATTACTA 59.218 50.000 0.00 0.00 36.31 1.82
902 906 1.569548 TCCTGGGACGGAGAGATTACT 59.430 52.381 0.00 0.00 36.31 2.24
903 907 2.068834 TCCTGGGACGGAGAGATTAC 57.931 55.000 0.00 0.00 36.31 1.89
906 910 4.292571 TCTTATATCCTGGGACGGAGAGAT 59.707 45.833 0.00 0.00 36.31 2.75
907 911 3.656264 TCTTATATCCTGGGACGGAGAGA 59.344 47.826 0.00 0.00 36.31 3.10
908 912 4.035612 TCTTATATCCTGGGACGGAGAG 57.964 50.000 0.00 0.00 36.31 3.20
909 913 4.044191 TGATCTTATATCCTGGGACGGAGA 59.956 45.833 0.00 0.00 36.31 3.71
910 914 4.344978 TGATCTTATATCCTGGGACGGAG 58.655 47.826 0.00 0.00 36.31 4.63
912 916 5.683876 ATTGATCTTATATCCTGGGACGG 57.316 43.478 0.00 0.00 0.00 4.79
913 917 7.986085 AAAATTGATCTTATATCCTGGGACG 57.014 36.000 0.00 0.00 0.00 4.79
926 930 9.453572 TCAGCTGATAGTGTAAAAATTGATCTT 57.546 29.630 13.74 0.00 0.00 2.40
927 931 9.624373 ATCAGCTGATAGTGTAAAAATTGATCT 57.376 29.630 27.73 0.00 32.01 2.75
930 934 9.890629 AGTATCAGCTGATAGTGTAAAAATTGA 57.109 29.630 33.52 11.70 38.77 2.57
936 940 8.924303 ACCAATAGTATCAGCTGATAGTGTAAA 58.076 33.333 37.76 25.66 40.04 2.01
938 942 8.478775 AACCAATAGTATCAGCTGATAGTGTA 57.521 34.615 37.76 27.22 40.04 2.90
940 944 7.436933 TGAACCAATAGTATCAGCTGATAGTG 58.563 38.462 37.76 27.95 40.04 2.74
941 945 7.288852 ACTGAACCAATAGTATCAGCTGATAGT 59.711 37.037 35.05 35.05 42.34 2.12
942 946 7.665690 ACTGAACCAATAGTATCAGCTGATAG 58.334 38.462 32.02 22.15 42.34 2.08
944 948 6.098838 TGACTGAACCAATAGTATCAGCTGAT 59.901 38.462 30.85 30.85 42.34 2.90
945 949 5.422012 TGACTGAACCAATAGTATCAGCTGA 59.578 40.000 20.79 20.79 42.34 4.26
946 950 5.664457 TGACTGAACCAATAGTATCAGCTG 58.336 41.667 7.63 7.63 42.34 4.24
948 952 5.053145 CCTGACTGAACCAATAGTATCAGC 58.947 45.833 1.77 0.00 42.34 4.26
949 953 5.053145 GCCTGACTGAACCAATAGTATCAG 58.947 45.833 0.00 0.00 43.79 2.90
950 954 4.441495 CGCCTGACTGAACCAATAGTATCA 60.441 45.833 0.00 0.00 0.00 2.15
951 955 4.051922 CGCCTGACTGAACCAATAGTATC 58.948 47.826 0.00 0.00 0.00 2.24
969 1150 2.321263 CTGATGATCAGTGGGCGCCT 62.321 60.000 28.56 4.40 39.58 5.52
1008 1201 2.115911 GGACACCACAACACCGCAA 61.116 57.895 0.00 0.00 0.00 4.85
1009 1202 2.515057 GGACACCACAACACCGCA 60.515 61.111 0.00 0.00 0.00 5.69
1010 1203 3.645975 CGGACACCACAACACCGC 61.646 66.667 0.00 0.00 37.32 5.68
1012 1205 1.153329 TGACGGACACCACAACACC 60.153 57.895 0.00 0.00 0.00 4.16
1013 1206 2.011453 GTGACGGACACCACAACAC 58.989 57.895 0.00 0.00 43.05 3.32
1014 1207 0.036294 TTGTGACGGACACCACAACA 60.036 50.000 8.06 0.00 45.13 3.33
1057 1269 1.879372 GCTGATCTGTTCTGTGTGCCA 60.879 52.381 1.27 0.00 0.00 4.92
2258 2470 1.184431 CCACAATGCCATGGCTTGTA 58.816 50.000 34.26 21.13 38.98 2.41
2451 2663 7.041107 GCTCAAGTTTCTCATCTCTGACTAAT 58.959 38.462 0.00 0.00 0.00 1.73
2514 2726 2.875317 TGCACTCACATTTAGTTCGCAA 59.125 40.909 0.00 0.00 0.00 4.85
2517 2729 3.684305 TCCATGCACTCACATTTAGTTCG 59.316 43.478 0.00 0.00 0.00 3.95
2562 2774 1.798223 TCCTTGACATGTTTCTTCGCG 59.202 47.619 0.00 0.00 0.00 5.87
2586 2798 2.177394 TGTCCAAGCAATACGAGCAA 57.823 45.000 0.00 0.00 0.00 3.91
2631 2843 2.034124 AGCTTTGCAAATGTGTCTGGT 58.966 42.857 13.23 1.63 0.00 4.00
2724 2936 6.859112 TTAAAGCTTACATGTCTCTCCTCT 57.141 37.500 0.00 0.00 0.00 3.69
2882 3094 3.062763 CTCGGGAATTCTTCATCATCGG 58.937 50.000 5.23 0.00 0.00 4.18
2918 3130 5.014202 GGTGTTCATTACCCACTTATGGTT 58.986 41.667 0.00 0.00 45.66 3.67
2920 3132 4.855340 AGGTGTTCATTACCCACTTATGG 58.145 43.478 0.00 0.00 46.81 2.74
2931 3143 7.815840 TTCAATCAAGTGAAGGTGTTCATTA 57.184 32.000 0.00 0.00 44.58 1.90
2963 3181 4.616181 GTTCATAAACCAATCACTCCCG 57.384 45.455 0.00 0.00 0.00 5.14
3080 3300 3.582208 GGCAGATGGACTTCAGATAGGAT 59.418 47.826 0.00 0.00 0.00 3.24
3353 3578 6.040391 ACTCTCTACTTCATAACTGATGGAGC 59.960 42.308 0.00 0.00 44.32 4.70
3391 3616 9.353999 AGTGAAACAGAAAGTTCAAAATGTAAC 57.646 29.630 0.00 0.00 40.26 2.50
3611 3847 6.567687 TGTGGATTTACATGGTTTACACAG 57.432 37.500 0.00 0.00 33.09 3.66
3711 3948 7.264947 GGGGGTCAACTTGATTAATGTTAATG 58.735 38.462 2.90 0.00 33.72 1.90
3764 4182 7.066284 GTGCACCTGATTAAAGATCAATACAGT 59.934 37.037 5.22 0.00 0.00 3.55
3785 4203 3.066760 AGCTCAAAAGGTTTAGTGTGCAC 59.933 43.478 10.75 10.75 33.94 4.57
3819 4237 1.587568 TGCAGAACATGGCATGCAC 59.412 52.632 26.70 19.55 43.34 4.57
3869 4291 2.095059 GGATAAAGCACAAGCACCAGTG 60.095 50.000 0.00 0.00 45.49 3.66


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

AutoCloner maintained by Alex Coulton.