Multiple sequence alignment - TraesCS1D01G091400

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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 TraesCS1D01G091400 chr1D 100.000 3926 0 0 1 3926 77454364 77450439 0.000000e+00 7251.0
1 TraesCS1D01G091400 chr1D 81.818 539 59 17 3 512 2215771 2215243 2.180000e-112 416.0
2 TraesCS1D01G091400 chr1D 100.000 65 0 0 589 653 269413952 269414016 1.920000e-23 121.0
3 TraesCS1D01G091400 chr1D 100.000 65 0 0 589 653 298347882 298347818 1.920000e-23 121.0
4 TraesCS1D01G091400 chr1B 91.641 2919 169 42 653 3539 121015319 121012444 0.000000e+00 3969.0
5 TraesCS1D01G091400 chr1A 94.584 2308 101 12 682 2968 108781496 108779192 0.000000e+00 3548.0
6 TraesCS1D01G091400 chr1A 89.572 374 31 5 3008 3379 108779198 108778831 5.940000e-128 468.0
7 TraesCS1D01G091400 chr1A 86.555 357 39 6 3376 3729 108778787 108778437 6.150000e-103 385.0
8 TraesCS1D01G091400 chr7A 92.423 2402 142 18 856 3249 477185542 477183173 0.000000e+00 3391.0
9 TraesCS1D01G091400 chr7A 91.200 125 9 1 3737 3859 477182645 477182521 6.750000e-38 169.0
10 TraesCS1D01G091400 chr7A 94.545 55 3 0 3855 3909 477182485 477182431 6.990000e-13 86.1
11 TraesCS1D01G091400 chr2B 85.504 1566 186 24 1586 3121 757230798 757232352 0.000000e+00 1596.0
12 TraesCS1D01G091400 chr2B 88.023 885 74 16 2340 3212 757390576 757391440 0.000000e+00 1018.0
13 TraesCS1D01G091400 chr2B 90.141 213 19 2 2051 2263 757292621 757292831 3.860000e-70 276.0
14 TraesCS1D01G091400 chr2B 83.667 300 40 4 1288 1578 757221810 757222109 1.390000e-69 274.0
15 TraesCS1D01G091400 chr2B 81.111 360 45 15 3373 3724 757015185 757015529 2.330000e-67 267.0
16 TraesCS1D01G091400 chr2B 86.992 123 12 2 975 1096 756713284 756713403 6.840000e-28 135.0
17 TraesCS1D01G091400 chr2A 86.642 1340 147 18 1739 3056 750330538 750331867 0.000000e+00 1454.0
18 TraesCS1D01G091400 chr2A 86.471 1020 105 12 2365 3379 750190767 750189776 0.000000e+00 1088.0
19 TraesCS1D01G091400 chr2A 83.232 328 40 10 3 320 660966773 660966451 1.790000e-73 287.0
20 TraesCS1D01G091400 chr2A 78.212 358 45 18 3381 3724 750189713 750189375 8.600000e-47 198.0
21 TraesCS1D01G091400 chr2A 88.816 152 9 5 2845 2990 750334905 750335054 3.120000e-41 180.0
22 TraesCS1D01G091400 chr7D 84.713 1027 115 14 2365 3379 498243302 498244298 0.000000e+00 989.0
23 TraesCS1D01G091400 chr7D 88.973 263 20 3 2089 2351 498242823 498243076 2.280000e-82 316.0
24 TraesCS1D01G091400 chr7D 86.920 237 24 5 3 234 169783486 169783252 3.890000e-65 259.0
25 TraesCS1D01G091400 chr7D 85.938 128 15 2 3383 3510 498284402 498284526 2.460000e-27 134.0
26 TraesCS1D01G091400 chr2D 87.637 728 73 8 1834 2547 619311041 619311765 0.000000e+00 830.0
27 TraesCS1D01G091400 chr2D 83.429 175 22 6 3554 3724 619311981 619312152 5.250000e-34 156.0
28 TraesCS1D01G091400 chr3D 83.491 527 52 17 3 511 302940446 302940955 3.570000e-125 459.0
29 TraesCS1D01G091400 chr3D 80.669 538 65 16 3 511 12545231 12545758 7.960000e-102 381.0
30 TraesCS1D01G091400 chr3A 87.966 349 30 8 3 351 423599542 423599206 6.110000e-108 401.0
31 TraesCS1D01G091400 chr3A 80.222 541 64 20 3 511 114788365 114788894 2.230000e-97 366.0
32 TraesCS1D01G091400 chr3A 95.349 86 4 0 426 511 423599023 423598938 1.900000e-28 137.0
33 TraesCS1D01G091400 chr5B 83.627 397 50 7 3 390 468635964 468635574 3.730000e-95 359.0
34 TraesCS1D01G091400 chr5A 83.537 328 40 9 3 320 651557206 651556883 1.070000e-75 294.0
35 TraesCS1D01G091400 chr6D 100.000 65 0 0 589 653 124524727 124524791 1.920000e-23 121.0
36 TraesCS1D01G091400 chr6D 100.000 65 0 0 589 653 458905382 458905446 1.920000e-23 121.0
37 TraesCS1D01G091400 chr4D 100.000 65 0 0 589 653 134991664 134991600 1.920000e-23 121.0
38 TraesCS1D01G091400 chr4D 100.000 65 0 0 589 653 241116839 241116775 1.920000e-23 121.0
39 TraesCS1D01G091400 chr4D 100.000 65 0 0 589 653 241277176 241277112 1.920000e-23 121.0
40 TraesCS1D01G091400 chr4D 100.000 65 0 0 589 653 398039721 398039657 1.920000e-23 121.0
41 TraesCS1D01G091400 chr4D 100.000 65 0 0 589 653 448276053 448275989 1.920000e-23 121.0


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 TraesCS1D01G091400 chr1D 77450439 77454364 3925 True 7251.000000 7251 100.000000 1 3926 1 chr1D.!!$R2 3925
1 TraesCS1D01G091400 chr1D 2215243 2215771 528 True 416.000000 416 81.818000 3 512 1 chr1D.!!$R1 509
2 TraesCS1D01G091400 chr1B 121012444 121015319 2875 True 3969.000000 3969 91.641000 653 3539 1 chr1B.!!$R1 2886
3 TraesCS1D01G091400 chr1A 108778437 108781496 3059 True 1467.000000 3548 90.237000 682 3729 3 chr1A.!!$R1 3047
4 TraesCS1D01G091400 chr7A 477182431 477185542 3111 True 1215.366667 3391 92.722667 856 3909 3 chr7A.!!$R1 3053
5 TraesCS1D01G091400 chr2B 757230798 757232352 1554 False 1596.000000 1596 85.504000 1586 3121 1 chr2B.!!$F4 1535
6 TraesCS1D01G091400 chr2B 757390576 757391440 864 False 1018.000000 1018 88.023000 2340 3212 1 chr2B.!!$F6 872
7 TraesCS1D01G091400 chr2A 750330538 750335054 4516 False 817.000000 1454 87.729000 1739 3056 2 chr2A.!!$F1 1317
8 TraesCS1D01G091400 chr2A 750189375 750190767 1392 True 643.000000 1088 82.341500 2365 3724 2 chr2A.!!$R2 1359
9 TraesCS1D01G091400 chr7D 498242823 498244298 1475 False 652.500000 989 86.843000 2089 3379 2 chr7D.!!$F2 1290
10 TraesCS1D01G091400 chr2D 619311041 619312152 1111 False 493.000000 830 85.533000 1834 3724 2 chr2D.!!$F1 1890
11 TraesCS1D01G091400 chr3D 302940446 302940955 509 False 459.000000 459 83.491000 3 511 1 chr3D.!!$F2 508
12 TraesCS1D01G091400 chr3D 12545231 12545758 527 False 381.000000 381 80.669000 3 511 1 chr3D.!!$F1 508
13 TraesCS1D01G091400 chr3A 114788365 114788894 529 False 366.000000 366 80.222000 3 511 1 chr3A.!!$F1 508
14 TraesCS1D01G091400 chr3A 423598938 423599542 604 True 269.000000 401 91.657500 3 511 2 chr3A.!!$R1 508

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
839 983 0.449388 GCTTGCAGGAAATCAGGTCG 59.551 55.0 0.0 0.0 0.00 4.79 F
1726 1925 0.325671 GGAGGAGTGGGTGAGATCCA 60.326 60.0 0.0 0.0 34.08 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2141 0.106819 AATGATCAGGCAGGCCAGAC 60.107 55.0 13.63 0.0 34.44 3.51 R
3280 3756 0.315251 GGCCTGTTGGAAGTTTCAGC 59.685 55.0 0.00 0.0 34.57 4.26 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
252 259 0.470341 TGGGTTGTGTGTTCGATCCA 59.530 50.000 0.00 0.00 30.24 3.41
266 273 1.133025 CGATCCACCAACAATGCCTTC 59.867 52.381 0.00 0.00 0.00 3.46
294 305 9.771534 TTTTACATATTTTTGTCCAGGGAAAAG 57.228 29.630 0.00 0.00 0.00 2.27
372 386 2.876581 AGGAGGTCGCCATTTCTTTTT 58.123 42.857 0.00 0.00 0.00 1.94
491 622 2.942376 ACTTTTGCAATCTGTCACACGA 59.058 40.909 0.00 0.00 0.00 4.35
511 642 4.022329 ACGATTGACATATATCGCAGTCCA 60.022 41.667 7.71 0.00 45.57 4.02
512 643 4.923281 CGATTGACATATATCGCAGTCCAA 59.077 41.667 0.00 0.00 37.45 3.53
513 644 5.405269 CGATTGACATATATCGCAGTCCAAA 59.595 40.000 0.00 0.00 37.45 3.28
514 645 6.091305 CGATTGACATATATCGCAGTCCAAAT 59.909 38.462 0.00 0.00 37.45 2.32
515 646 6.544038 TTGACATATATCGCAGTCCAAATG 57.456 37.500 0.00 0.00 0.00 2.32
516 647 5.610398 TGACATATATCGCAGTCCAAATGT 58.390 37.500 0.00 0.00 0.00 2.71
517 648 6.054941 TGACATATATCGCAGTCCAAATGTT 58.945 36.000 0.00 0.00 0.00 2.71
518 649 7.213678 TGACATATATCGCAGTCCAAATGTTA 58.786 34.615 0.00 0.00 0.00 2.41
519 650 7.713073 TGACATATATCGCAGTCCAAATGTTAA 59.287 33.333 0.00 0.00 0.00 2.01
520 651 8.445275 ACATATATCGCAGTCCAAATGTTAAA 57.555 30.769 0.00 0.00 0.00 1.52
521 652 8.342634 ACATATATCGCAGTCCAAATGTTAAAC 58.657 33.333 0.00 0.00 0.00 2.01
522 653 6.751514 ATATCGCAGTCCAAATGTTAAACA 57.248 33.333 0.00 0.00 0.00 2.83
523 654 5.643379 ATCGCAGTCCAAATGTTAAACAT 57.357 34.783 0.00 0.00 41.31 2.71
524 655 6.751514 ATCGCAGTCCAAATGTTAAACATA 57.248 33.333 0.00 0.00 37.97 2.29
525 656 6.561737 TCGCAGTCCAAATGTTAAACATAA 57.438 33.333 0.00 0.00 37.97 1.90
526 657 6.971602 TCGCAGTCCAAATGTTAAACATAAA 58.028 32.000 0.00 0.00 37.97 1.40
527 658 7.598278 TCGCAGTCCAAATGTTAAACATAAAT 58.402 30.769 0.00 0.00 37.97 1.40
528 659 7.753132 TCGCAGTCCAAATGTTAAACATAAATC 59.247 33.333 0.00 0.00 37.97 2.17
529 660 7.540400 CGCAGTCCAAATGTTAAACATAAATCA 59.460 33.333 0.00 0.00 37.97 2.57
530 661 9.369904 GCAGTCCAAATGTTAAACATAAATCAT 57.630 29.630 0.00 0.00 37.97 2.45
539 670 8.974060 TGTTAAACATAAATCATACTCCCTCC 57.026 34.615 0.00 0.00 0.00 4.30
540 671 8.553153 TGTTAAACATAAATCATACTCCCTCCA 58.447 33.333 0.00 0.00 0.00 3.86
541 672 9.574516 GTTAAACATAAATCATACTCCCTCCAT 57.425 33.333 0.00 0.00 0.00 3.41
544 675 7.259088 ACATAAATCATACTCCCTCCATACC 57.741 40.000 0.00 0.00 0.00 2.73
545 676 6.792473 ACATAAATCATACTCCCTCCATACCA 59.208 38.462 0.00 0.00 0.00 3.25
546 677 7.294720 ACATAAATCATACTCCCTCCATACCAA 59.705 37.037 0.00 0.00 0.00 3.67
547 678 6.590656 AAATCATACTCCCTCCATACCAAA 57.409 37.500 0.00 0.00 0.00 3.28
548 679 6.590656 AATCATACTCCCTCCATACCAAAA 57.409 37.500 0.00 0.00 0.00 2.44
549 680 6.786843 ATCATACTCCCTCCATACCAAAAT 57.213 37.500 0.00 0.00 0.00 1.82
550 681 7.888514 ATCATACTCCCTCCATACCAAAATA 57.111 36.000 0.00 0.00 0.00 1.40
551 682 7.074653 TCATACTCCCTCCATACCAAAATAC 57.925 40.000 0.00 0.00 0.00 1.89
552 683 6.849697 TCATACTCCCTCCATACCAAAATACT 59.150 38.462 0.00 0.00 0.00 2.12
553 684 7.349859 TCATACTCCCTCCATACCAAAATACTT 59.650 37.037 0.00 0.00 0.00 2.24
554 685 5.755849 ACTCCCTCCATACCAAAATACTTG 58.244 41.667 0.00 0.00 0.00 3.16
555 686 4.532834 TCCCTCCATACCAAAATACTTGC 58.467 43.478 0.00 0.00 0.00 4.01
556 687 4.017958 TCCCTCCATACCAAAATACTTGCA 60.018 41.667 0.00 0.00 0.00 4.08
557 688 4.709397 CCCTCCATACCAAAATACTTGCAA 59.291 41.667 0.00 0.00 0.00 4.08
558 689 5.163519 CCCTCCATACCAAAATACTTGCAAG 60.164 44.000 24.84 24.84 0.00 4.01
559 690 5.652014 CCTCCATACCAAAATACTTGCAAGA 59.348 40.000 32.50 16.27 0.00 3.02
560 691 6.404734 CCTCCATACCAAAATACTTGCAAGAC 60.405 42.308 32.50 0.00 0.00 3.01
561 692 6.007076 TCCATACCAAAATACTTGCAAGACA 58.993 36.000 32.50 19.19 0.00 3.41
562 693 6.663093 TCCATACCAAAATACTTGCAAGACAT 59.337 34.615 32.50 20.49 0.00 3.06
563 694 7.178274 TCCATACCAAAATACTTGCAAGACATT 59.822 33.333 32.50 24.43 0.00 2.71
564 695 7.818930 CCATACCAAAATACTTGCAAGACATTT 59.181 33.333 32.50 27.81 0.00 2.32
565 696 9.206870 CATACCAAAATACTTGCAAGACATTTT 57.793 29.630 32.50 30.75 36.06 1.82
566 697 9.777297 ATACCAAAATACTTGCAAGACATTTTT 57.223 25.926 31.28 25.34 34.82 1.94
567 698 7.918643 ACCAAAATACTTGCAAGACATTTTTG 58.081 30.769 31.28 29.82 34.82 2.44
580 711 8.356533 CAAGACATTTTTGCAGTTCAATTAGT 57.643 30.769 0.00 0.00 34.12 2.24
581 712 9.462174 CAAGACATTTTTGCAGTTCAATTAGTA 57.538 29.630 0.00 0.00 34.12 1.82
583 714 9.683069 AGACATTTTTGCAGTTCAATTAGTAAG 57.317 29.630 0.00 0.00 34.12 2.34
584 715 9.463443 GACATTTTTGCAGTTCAATTAGTAAGT 57.537 29.630 0.00 0.00 34.12 2.24
597 728 9.935682 TTCAATTAGTAAGTATAAGTACGGTCG 57.064 33.333 0.00 0.00 35.92 4.79
598 729 8.070171 TCAATTAGTAAGTATAAGTACGGTCGC 58.930 37.037 0.00 0.00 35.92 5.19
599 730 6.918892 TTAGTAAGTATAAGTACGGTCGCA 57.081 37.500 0.00 0.00 35.92 5.10
600 731 5.818136 AGTAAGTATAAGTACGGTCGCAA 57.182 39.130 0.00 0.00 35.92 4.85
601 732 5.814783 AGTAAGTATAAGTACGGTCGCAAG 58.185 41.667 0.00 0.00 35.92 4.01
602 733 4.970662 AAGTATAAGTACGGTCGCAAGA 57.029 40.909 0.00 0.00 39.06 3.02
613 744 3.671262 TCGCAAGACCGAAACTCAA 57.329 47.368 0.00 0.00 45.01 3.02
614 745 1.942677 TCGCAAGACCGAAACTCAAA 58.057 45.000 0.00 0.00 45.01 2.69
615 746 1.864711 TCGCAAGACCGAAACTCAAAG 59.135 47.619 0.00 0.00 45.01 2.77
616 747 1.069906 CGCAAGACCGAAACTCAAAGG 60.070 52.381 0.00 0.00 43.02 3.11
617 748 2.218603 GCAAGACCGAAACTCAAAGGA 58.781 47.619 0.00 0.00 0.00 3.36
618 749 2.616842 GCAAGACCGAAACTCAAAGGAA 59.383 45.455 0.00 0.00 0.00 3.36
619 750 3.253432 GCAAGACCGAAACTCAAAGGAAT 59.747 43.478 0.00 0.00 0.00 3.01
620 751 4.261614 GCAAGACCGAAACTCAAAGGAATT 60.262 41.667 0.00 0.00 0.00 2.17
621 752 5.215160 CAAGACCGAAACTCAAAGGAATTG 58.785 41.667 0.00 0.00 40.58 2.32
622 753 4.714632 AGACCGAAACTCAAAGGAATTGA 58.285 39.130 0.00 0.00 45.71 2.57
623 754 4.515567 AGACCGAAACTCAAAGGAATTGAC 59.484 41.667 0.00 0.00 43.08 3.18
624 755 3.250040 ACCGAAACTCAAAGGAATTGACG 59.750 43.478 0.00 0.00 43.08 4.35
625 756 3.364964 CCGAAACTCAAAGGAATTGACGG 60.365 47.826 0.00 0.00 43.08 4.79
626 757 3.364964 CGAAACTCAAAGGAATTGACGGG 60.365 47.826 0.00 0.00 43.08 5.28
627 758 2.200373 ACTCAAAGGAATTGACGGGG 57.800 50.000 0.00 0.00 43.08 5.73
628 759 1.271926 ACTCAAAGGAATTGACGGGGG 60.272 52.381 0.00 0.00 43.08 5.40
629 760 0.610785 TCAAAGGAATTGACGGGGGC 60.611 55.000 0.00 0.00 43.08 5.80
630 761 1.304962 AAAGGAATTGACGGGGGCC 60.305 57.895 0.00 0.00 0.00 5.80
631 762 1.800229 AAAGGAATTGACGGGGGCCT 61.800 55.000 0.84 0.00 0.00 5.19
632 763 2.440247 GGAATTGACGGGGGCCTG 60.440 66.667 0.84 0.00 0.00 4.85
633 764 3.140814 GAATTGACGGGGGCCTGC 61.141 66.667 0.84 0.00 0.00 4.85
634 765 3.936772 GAATTGACGGGGGCCTGCA 62.937 63.158 0.84 0.00 0.00 4.41
635 766 4.740822 ATTGACGGGGGCCTGCAC 62.741 66.667 0.84 0.00 0.00 4.57
650 781 2.872557 CACAAGCGGTGGAGCATG 59.127 61.111 0.00 0.00 44.04 4.06
651 782 2.431683 ACAAGCGGTGGAGCATGT 59.568 55.556 0.00 0.00 43.12 3.21
693 824 2.518949 CAGACACAATAAACGGCATGC 58.481 47.619 9.90 9.90 0.00 4.06
706 838 3.754965 ACGGCATGCCAGAATATATTGT 58.245 40.909 34.93 17.99 35.37 2.71
779 914 3.243267 GCATTACACGTGGAACCAGTTTT 60.243 43.478 17.16 0.00 0.00 2.43
834 978 5.651576 TGTGTATATTGCTTGCAGGAAATCA 59.348 36.000 5.09 0.00 0.00 2.57
835 979 6.183360 TGTGTATATTGCTTGCAGGAAATCAG 60.183 38.462 5.09 0.00 0.00 2.90
837 981 1.999648 TTGCTTGCAGGAAATCAGGT 58.000 45.000 0.00 0.00 0.00 4.00
839 983 0.449388 GCTTGCAGGAAATCAGGTCG 59.551 55.000 0.00 0.00 0.00 4.79
840 984 1.813513 CTTGCAGGAAATCAGGTCGT 58.186 50.000 0.00 0.00 0.00 4.34
965 1114 1.003233 GCGGCAGGAAGGAAGAAGT 60.003 57.895 0.00 0.00 0.00 3.01
966 1115 1.301677 GCGGCAGGAAGGAAGAAGTG 61.302 60.000 0.00 0.00 0.00 3.16
1106 1296 3.706373 CCTCCTCCACCACCACCG 61.706 72.222 0.00 0.00 0.00 4.94
1146 1336 1.006813 TCCTCTCCAAGCTCCTCTCT 58.993 55.000 0.00 0.00 0.00 3.10
1155 1348 3.157087 CAAGCTCCTCTCTATCTCCTCC 58.843 54.545 0.00 0.00 0.00 4.30
1425 1624 2.511145 CTCCTGCAGAAGCTCGGC 60.511 66.667 17.39 0.00 42.74 5.54
1726 1925 0.325671 GGAGGAGTGGGTGAGATCCA 60.326 60.000 0.00 0.00 34.08 3.41
1749 1948 0.832135 GGATGGAGGTGGGATCGCTA 60.832 60.000 11.46 0.00 0.00 4.26
1989 2207 0.736325 GACGCAGGTACGCACAGAAT 60.736 55.000 0.00 0.00 36.19 2.40
2031 2249 1.065491 TCCCTATTTCACAGCATGCGT 60.065 47.619 13.01 10.68 42.53 5.24
2067 2285 5.050490 CGTCCAGATAAGATAACCTTGGTG 58.950 45.833 0.00 0.00 36.34 4.17
2286 2505 1.615392 GCCTTGATTTGTGGTCTTGCT 59.385 47.619 0.00 0.00 0.00 3.91
2447 2893 4.081406 TGGTTCAATTCCTTGACATCTGG 58.919 43.478 0.00 0.00 41.05 3.86
2616 3065 5.111989 TGTCGGAAATGCAAAAATGTTGAA 58.888 33.333 0.00 0.00 0.00 2.69
2775 3237 1.337167 GGTGTCAGCAAAATTCCAGGC 60.337 52.381 0.00 0.00 0.00 4.85
2934 3400 6.119536 TCTTGATCTGGTTTAACACACAACT 58.880 36.000 0.00 0.00 0.00 3.16
2957 3423 5.212532 AGATGCAGATCAACCTCAGTATC 57.787 43.478 0.00 0.00 0.00 2.24
2969 3435 4.778579 ACCTCAGTATCGCAGTCTTACTA 58.221 43.478 0.00 0.00 0.00 1.82
3127 3601 5.336690 GGAACATTGCTTTGCATTCCTTCTA 60.337 40.000 13.17 0.00 40.20 2.10
3130 3604 6.799512 ACATTGCTTTGCATTCCTTCTATAC 58.200 36.000 0.00 0.00 38.76 1.47
3135 3609 5.983720 GCTTTGCATTCCTTCTATACGACTA 59.016 40.000 0.00 0.00 0.00 2.59
3146 3620 6.594937 CCTTCTATACGACTAGATACCAGGAC 59.405 46.154 0.00 0.00 29.19 3.85
3147 3621 6.931790 TCTATACGACTAGATACCAGGACT 57.068 41.667 0.00 0.00 0.00 3.85
3167 3642 5.181433 GGACTGAACCAGGTCTATTTTGAAC 59.819 44.000 0.00 0.00 35.51 3.18
3224 3700 3.256383 AGCATGCTTAGTCATGTGCAAAA 59.744 39.130 16.30 0.00 44.20 2.44
3226 3702 4.090930 GCATGCTTAGTCATGTGCAAAAAG 59.909 41.667 11.37 0.00 44.20 2.27
3227 3703 4.916983 TGCTTAGTCATGTGCAAAAAGT 57.083 36.364 0.00 0.00 32.12 2.66
3228 3704 5.261209 TGCTTAGTCATGTGCAAAAAGTT 57.739 34.783 0.00 0.00 32.12 2.66
3273 3749 9.739276 TCTATGAAAATACCTGATTCAGTTGTT 57.261 29.630 12.54 0.24 36.59 2.83
3280 3756 2.416547 CCTGATTCAGTTGTTGCTACCG 59.583 50.000 12.54 0.00 0.00 4.02
3281 3757 1.804151 TGATTCAGTTGTTGCTACCGC 59.196 47.619 0.00 0.00 0.00 5.68
3297 3773 0.593128 CCGCTGAAACTTCCAACAGG 59.407 55.000 0.00 0.00 0.00 4.00
3299 3775 0.315251 GCTGAAACTTCCAACAGGCC 59.685 55.000 0.00 0.00 0.00 5.19
3353 3869 2.610433 CGAGCTGTCAGAACATGCTAA 58.390 47.619 3.32 0.00 38.87 3.09
3362 3878 4.094294 GTCAGAACATGCTAAATAACCGCA 59.906 41.667 0.00 0.00 38.14 5.69
3379 3956 5.257082 ACCGCAAATATGGAAAACCATAC 57.743 39.130 10.53 0.00 35.79 2.39
3416 3994 7.382218 AGTCTAAAAGAAAAATGATTTGGCACG 59.618 33.333 0.00 0.00 0.00 5.34
3417 3995 5.671742 AAAAGAAAAATGATTTGGCACGG 57.328 34.783 0.00 0.00 0.00 4.94
3434 4012 1.910671 ACGGGCCTATTGTTGGAGTTA 59.089 47.619 0.84 0.00 0.00 2.24
3445 4023 9.369904 CCTATTGTTGGAGTTATTGGAAAAATG 57.630 33.333 0.00 0.00 0.00 2.32
3468 4046 3.801698 CATTCCAGGTGGAGTGTAGATG 58.198 50.000 12.28 3.16 46.36 2.90
3469 4047 1.866015 TCCAGGTGGAGTGTAGATGG 58.134 55.000 0.00 0.00 39.78 3.51
3473 4051 1.203313 AGGTGGAGTGTAGATGGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
3521 4102 6.750501 CCAAGTCAGCATTCATGTAGATTTTG 59.249 38.462 0.00 0.00 0.00 2.44
3530 4115 8.863049 GCATTCATGTAGATTTTGTTTTGGTAG 58.137 33.333 0.00 0.00 0.00 3.18
3552 4137 3.366052 TTCTTCAGGTAAGAATGGCCC 57.634 47.619 0.00 0.00 46.88 5.80
3592 4177 5.639506 CCTGGTTGTCTGTGTAGATTGTAAG 59.360 44.000 0.00 0.00 34.94 2.34
3660 4470 7.795047 TCTTACTGCCAGAATCATCTTGAATA 58.205 34.615 0.00 0.00 32.03 1.75
3661 4471 7.712639 TCTTACTGCCAGAATCATCTTGAATAC 59.287 37.037 0.00 0.00 32.03 1.89
3670 4482 7.437565 CAGAATCATCTTGAATACGTGACTGAT 59.562 37.037 0.00 0.00 32.03 2.90
3683 4495 6.174451 ACGTGACTGATCAATCAATTCTTG 57.826 37.500 8.70 0.00 36.31 3.02
3687 4499 7.025963 GTGACTGATCAATCAATTCTTGGAAC 58.974 38.462 8.70 0.00 36.31 3.62
3713 4529 5.545588 TGGATCAAGACAGAACTCTTTCAG 58.454 41.667 0.00 0.00 33.72 3.02
3715 4531 5.407995 GGATCAAGACAGAACTCTTTCAGTG 59.592 44.000 0.00 0.00 34.56 3.66
3724 4540 9.477484 GACAGAACTCTTTCAGTGAAATACTTA 57.523 33.333 18.35 0.00 37.60 2.24
3729 4545 8.950208 ACTCTTTCAGTGAAATACTTATAGGC 57.050 34.615 18.35 0.00 37.60 3.93
3730 4546 8.763601 ACTCTTTCAGTGAAATACTTATAGGCT 58.236 33.333 18.35 0.00 37.60 4.58
3732 4548 8.982723 TCTTTCAGTGAAATACTTATAGGCTCT 58.017 33.333 18.35 0.00 37.60 4.09
3735 4551 8.410673 TCAGTGAAATACTTATAGGCTCTAGG 57.589 38.462 0.00 0.00 37.60 3.02
3778 4624 7.442656 CGTTTCCCACTCTAACAATCCTATAT 58.557 38.462 0.00 0.00 0.00 0.86
3820 5944 3.394606 ACAGACCAAACCATCTACCACTT 59.605 43.478 0.00 0.00 0.00 3.16
3859 5985 4.023193 CACTATTTTGCTCGTTTCCAACCT 60.023 41.667 0.00 0.00 0.00 3.50
3860 5986 3.643159 ATTTTGCTCGTTTCCAACCTC 57.357 42.857 0.00 0.00 0.00 3.85
3861 5987 1.314730 TTTGCTCGTTTCCAACCTCC 58.685 50.000 0.00 0.00 0.00 4.30
3862 5988 0.536460 TTGCTCGTTTCCAACCTCCC 60.536 55.000 0.00 0.00 0.00 4.30
3909 6819 4.077300 TCAGAGAAGACTTGTGCAATGT 57.923 40.909 0.00 0.00 0.00 2.71
3911 6821 2.551459 AGAGAAGACTTGTGCAATGTGC 59.449 45.455 0.00 0.00 45.29 4.57
3921 6831 3.396491 GCAATGTGCAGTCTTCAGC 57.604 52.632 0.00 0.00 44.26 4.26
3922 6832 0.594602 GCAATGTGCAGTCTTCAGCA 59.405 50.000 0.00 0.00 44.26 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.327404 TGGGCGTCCCTTCCCTTC 61.327 66.667 2.12 0.00 45.70 3.46
1 2 3.330720 CTGGGCGTCCCTTCCCTT 61.331 66.667 2.12 0.00 45.70 3.95
17 18 3.813166 CGGTTCACATAGTTCACAAACCT 59.187 43.478 0.00 0.00 35.92 3.50
180 187 4.098501 GGGCTAGTCGGCTTTACTAACTAA 59.901 45.833 0.00 0.00 38.46 2.24
228 235 2.485903 TCGAACACACAACCCACATAC 58.514 47.619 0.00 0.00 0.00 2.39
252 259 5.606348 TGTAAAAAGAAGGCATTGTTGGT 57.394 34.783 0.00 0.00 0.00 3.67
266 273 9.771534 TTTCCCTGGACAAAAATATGTAAAAAG 57.228 29.630 0.00 0.00 32.57 2.27
294 305 0.034896 ATCCCGCGTCCACCATATTC 59.965 55.000 4.92 0.00 0.00 1.75
341 352 1.605712 GCGACCTCCTATTCAATCCCG 60.606 57.143 0.00 0.00 0.00 5.14
394 408 1.554583 GCTCCTCCCGATTATCCCCC 61.555 65.000 0.00 0.00 0.00 5.40
395 409 1.554583 GGCTCCTCCCGATTATCCCC 61.555 65.000 0.00 0.00 0.00 4.81
396 410 1.984020 GGCTCCTCCCGATTATCCC 59.016 63.158 0.00 0.00 0.00 3.85
424 438 1.536662 AACAGTCCGCCTCCTTCCT 60.537 57.895 0.00 0.00 0.00 3.36
491 622 6.712095 ACATTTGGACTGCGATATATGTCAAT 59.288 34.615 0.11 0.00 0.00 2.57
513 644 9.574516 GGAGGGAGTATGATTTATGTTTAACAT 57.425 33.333 15.22 15.22 42.35 2.71
514 645 8.553153 TGGAGGGAGTATGATTTATGTTTAACA 58.447 33.333 0.00 0.00 0.00 2.41
515 646 8.974060 TGGAGGGAGTATGATTTATGTTTAAC 57.026 34.615 0.00 0.00 0.00 2.01
518 649 8.164070 GGTATGGAGGGAGTATGATTTATGTTT 58.836 37.037 0.00 0.00 0.00 2.83
519 650 7.294720 TGGTATGGAGGGAGTATGATTTATGTT 59.705 37.037 0.00 0.00 0.00 2.71
520 651 6.792473 TGGTATGGAGGGAGTATGATTTATGT 59.208 38.462 0.00 0.00 0.00 2.29
521 652 7.257790 TGGTATGGAGGGAGTATGATTTATG 57.742 40.000 0.00 0.00 0.00 1.90
522 653 7.888514 TTGGTATGGAGGGAGTATGATTTAT 57.111 36.000 0.00 0.00 0.00 1.40
523 654 7.699709 TTTGGTATGGAGGGAGTATGATTTA 57.300 36.000 0.00 0.00 0.00 1.40
524 655 6.590656 TTTGGTATGGAGGGAGTATGATTT 57.409 37.500 0.00 0.00 0.00 2.17
525 656 6.590656 TTTTGGTATGGAGGGAGTATGATT 57.409 37.500 0.00 0.00 0.00 2.57
526 657 6.786843 ATTTTGGTATGGAGGGAGTATGAT 57.213 37.500 0.00 0.00 0.00 2.45
527 658 6.849697 AGTATTTTGGTATGGAGGGAGTATGA 59.150 38.462 0.00 0.00 0.00 2.15
528 659 7.079451 AGTATTTTGGTATGGAGGGAGTATG 57.921 40.000 0.00 0.00 0.00 2.39
529 660 7.518188 CAAGTATTTTGGTATGGAGGGAGTAT 58.482 38.462 0.00 0.00 0.00 2.12
530 661 6.634039 GCAAGTATTTTGGTATGGAGGGAGTA 60.634 42.308 0.00 0.00 0.00 2.59
531 662 5.755849 CAAGTATTTTGGTATGGAGGGAGT 58.244 41.667 0.00 0.00 0.00 3.85
532 663 4.580580 GCAAGTATTTTGGTATGGAGGGAG 59.419 45.833 0.00 0.00 0.00 4.30
533 664 4.017958 TGCAAGTATTTTGGTATGGAGGGA 60.018 41.667 0.00 0.00 0.00 4.20
534 665 4.277476 TGCAAGTATTTTGGTATGGAGGG 58.723 43.478 0.00 0.00 0.00 4.30
535 666 5.652014 TCTTGCAAGTATTTTGGTATGGAGG 59.348 40.000 25.19 0.00 0.00 4.30
536 667 6.150976 TGTCTTGCAAGTATTTTGGTATGGAG 59.849 38.462 25.19 0.00 0.00 3.86
537 668 6.007076 TGTCTTGCAAGTATTTTGGTATGGA 58.993 36.000 25.19 0.00 0.00 3.41
538 669 6.266168 TGTCTTGCAAGTATTTTGGTATGG 57.734 37.500 25.19 0.00 0.00 2.74
539 670 8.761575 AAATGTCTTGCAAGTATTTTGGTATG 57.238 30.769 25.19 0.00 0.00 2.39
540 671 9.777297 AAAAATGTCTTGCAAGTATTTTGGTAT 57.223 25.926 32.54 23.46 35.83 2.73
541 672 9.039870 CAAAAATGTCTTGCAAGTATTTTGGTA 57.960 29.630 32.54 13.41 35.83 3.25
542 673 7.467131 GCAAAAATGTCTTGCAAGTATTTTGGT 60.467 33.333 32.54 24.09 46.78 3.67
543 674 6.852345 GCAAAAATGTCTTGCAAGTATTTTGG 59.148 34.615 32.54 31.16 46.78 3.28
544 675 7.825627 GCAAAAATGTCTTGCAAGTATTTTG 57.174 32.000 32.54 31.37 46.78 2.44
555 686 8.356533 ACTAATTGAACTGCAAAAATGTCTTG 57.643 30.769 0.00 0.00 40.48 3.02
557 688 9.683069 CTTACTAATTGAACTGCAAAAATGTCT 57.317 29.630 0.00 0.00 40.48 3.41
558 689 9.463443 ACTTACTAATTGAACTGCAAAAATGTC 57.537 29.630 0.00 0.00 40.48 3.06
571 702 9.935682 CGACCGTACTTATACTTACTAATTGAA 57.064 33.333 0.00 0.00 0.00 2.69
572 703 8.070171 GCGACCGTACTTATACTTACTAATTGA 58.930 37.037 0.00 0.00 0.00 2.57
573 704 7.857389 TGCGACCGTACTTATACTTACTAATTG 59.143 37.037 0.00 0.00 0.00 2.32
574 705 7.930217 TGCGACCGTACTTATACTTACTAATT 58.070 34.615 0.00 0.00 0.00 1.40
575 706 7.496529 TGCGACCGTACTTATACTTACTAAT 57.503 36.000 0.00 0.00 0.00 1.73
576 707 6.918892 TGCGACCGTACTTATACTTACTAA 57.081 37.500 0.00 0.00 0.00 2.24
577 708 6.761242 TCTTGCGACCGTACTTATACTTACTA 59.239 38.462 0.00 0.00 0.00 1.82
578 709 5.586243 TCTTGCGACCGTACTTATACTTACT 59.414 40.000 0.00 0.00 0.00 2.24
579 710 5.678919 GTCTTGCGACCGTACTTATACTTAC 59.321 44.000 0.00 0.00 33.98 2.34
580 711 5.810525 GTCTTGCGACCGTACTTATACTTA 58.189 41.667 0.00 0.00 33.98 2.24
581 712 4.666237 GTCTTGCGACCGTACTTATACTT 58.334 43.478 0.00 0.00 33.98 2.24
582 713 4.284378 GTCTTGCGACCGTACTTATACT 57.716 45.455 0.00 0.00 33.98 2.12
594 725 1.214367 TTGAGTTTCGGTCTTGCGAC 58.786 50.000 0.00 0.00 39.49 5.19
595 726 1.864711 CTTTGAGTTTCGGTCTTGCGA 59.135 47.619 0.00 0.00 0.00 5.10
596 727 1.069906 CCTTTGAGTTTCGGTCTTGCG 60.070 52.381 0.00 0.00 0.00 4.85
597 728 2.218603 TCCTTTGAGTTTCGGTCTTGC 58.781 47.619 0.00 0.00 0.00 4.01
598 729 5.008613 TCAATTCCTTTGAGTTTCGGTCTTG 59.991 40.000 0.00 0.00 39.44 3.02
599 730 5.008712 GTCAATTCCTTTGAGTTTCGGTCTT 59.991 40.000 0.00 0.00 44.89 3.01
600 731 4.515567 GTCAATTCCTTTGAGTTTCGGTCT 59.484 41.667 0.00 0.00 44.89 3.85
601 732 4.610680 CGTCAATTCCTTTGAGTTTCGGTC 60.611 45.833 0.00 0.00 44.89 4.79
602 733 3.250040 CGTCAATTCCTTTGAGTTTCGGT 59.750 43.478 0.00 0.00 44.89 4.69
603 734 3.364964 CCGTCAATTCCTTTGAGTTTCGG 60.365 47.826 0.00 0.00 44.89 4.30
604 735 3.364964 CCCGTCAATTCCTTTGAGTTTCG 60.365 47.826 0.00 0.00 44.89 3.46
605 736 3.057526 CCCCGTCAATTCCTTTGAGTTTC 60.058 47.826 0.00 0.00 44.89 2.78
606 737 2.890945 CCCCGTCAATTCCTTTGAGTTT 59.109 45.455 0.00 0.00 44.89 2.66
607 738 2.514803 CCCCGTCAATTCCTTTGAGTT 58.485 47.619 0.00 0.00 44.89 3.01
608 739 1.271926 CCCCCGTCAATTCCTTTGAGT 60.272 52.381 0.00 0.00 44.89 3.41
609 740 1.463674 CCCCCGTCAATTCCTTTGAG 58.536 55.000 0.00 0.00 44.89 3.02
610 741 0.610785 GCCCCCGTCAATTCCTTTGA 60.611 55.000 0.00 0.00 42.09 2.69
611 742 1.604147 GGCCCCCGTCAATTCCTTTG 61.604 60.000 0.00 0.00 36.61 2.77
612 743 1.304962 GGCCCCCGTCAATTCCTTT 60.305 57.895 0.00 0.00 0.00 3.11
613 744 2.238701 AGGCCCCCGTCAATTCCTT 61.239 57.895 0.00 0.00 0.00 3.36
614 745 2.614013 AGGCCCCCGTCAATTCCT 60.614 61.111 0.00 0.00 0.00 3.36
615 746 2.440247 CAGGCCCCCGTCAATTCC 60.440 66.667 0.00 0.00 0.00 3.01
616 747 3.140814 GCAGGCCCCCGTCAATTC 61.141 66.667 0.00 0.00 0.00 2.17
617 748 3.978193 TGCAGGCCCCCGTCAATT 61.978 61.111 0.00 0.00 0.00 2.32
618 749 4.740822 GTGCAGGCCCCCGTCAAT 62.741 66.667 0.00 0.00 0.00 2.57
629 760 3.052082 CTCCACCGCTTGTGCAGG 61.052 66.667 0.00 0.00 44.01 4.85
630 761 3.730761 GCTCCACCGCTTGTGCAG 61.731 66.667 0.00 0.00 44.01 4.41
631 762 3.848301 ATGCTCCACCGCTTGTGCA 62.848 57.895 0.00 0.00 44.01 4.57
632 763 3.058160 ATGCTCCACCGCTTGTGC 61.058 61.111 0.00 0.00 44.01 4.57
633 764 1.968017 ACATGCTCCACCGCTTGTG 60.968 57.895 0.00 0.00 43.78 3.33
634 765 1.968017 CACATGCTCCACCGCTTGT 60.968 57.895 0.00 0.00 45.56 3.16
635 766 0.673333 TACACATGCTCCACCGCTTG 60.673 55.000 0.00 0.00 39.94 4.01
636 767 0.673644 GTACACATGCTCCACCGCTT 60.674 55.000 0.00 0.00 0.00 4.68
637 768 1.079127 GTACACATGCTCCACCGCT 60.079 57.895 0.00 0.00 0.00 5.52
638 769 0.953471 TTGTACACATGCTCCACCGC 60.953 55.000 0.00 0.00 0.00 5.68
639 770 1.078709 CTTGTACACATGCTCCACCG 58.921 55.000 0.00 0.00 0.00 4.94
640 771 2.185004 ACTTGTACACATGCTCCACC 57.815 50.000 0.00 0.00 0.00 4.61
641 772 5.880054 ATAAACTTGTACACATGCTCCAC 57.120 39.130 0.00 0.00 0.00 4.02
642 773 6.941857 TCTATAAACTTGTACACATGCTCCA 58.058 36.000 0.00 0.00 0.00 3.86
643 774 6.018669 GCTCTATAAACTTGTACACATGCTCC 60.019 42.308 0.00 0.00 0.00 4.70
644 775 6.018669 GGCTCTATAAACTTGTACACATGCTC 60.019 42.308 0.00 0.00 0.00 4.26
645 776 5.817816 GGCTCTATAAACTTGTACACATGCT 59.182 40.000 0.00 0.00 0.00 3.79
646 777 5.584649 TGGCTCTATAAACTTGTACACATGC 59.415 40.000 0.00 0.00 0.00 4.06
647 778 7.414098 GGTTGGCTCTATAAACTTGTACACATG 60.414 40.741 0.00 0.00 0.00 3.21
648 779 6.598064 GGTTGGCTCTATAAACTTGTACACAT 59.402 38.462 0.00 0.00 0.00 3.21
649 780 5.935789 GGTTGGCTCTATAAACTTGTACACA 59.064 40.000 0.00 0.00 0.00 3.72
650 781 5.935789 TGGTTGGCTCTATAAACTTGTACAC 59.064 40.000 0.00 0.00 0.00 2.90
651 782 6.014070 TCTGGTTGGCTCTATAAACTTGTACA 60.014 38.462 0.00 0.00 0.00 2.90
693 824 9.982651 CTATATTCCCGGTACAATATATTCTGG 57.017 37.037 13.93 0.00 30.52 3.86
706 838 8.438618 TCATTTATGTTCCTATATTCCCGGTA 57.561 34.615 0.00 0.00 0.00 4.02
779 914 3.685139 AAGTTCCGCTCAGATCAAGAA 57.315 42.857 0.00 0.00 0.00 2.52
804 939 4.779696 TGCAAGCAATATACACATCAGGA 58.220 39.130 0.00 0.00 0.00 3.86
834 978 3.315749 GCTAGCAACAGTATAGACGACCT 59.684 47.826 10.63 0.00 0.00 3.85
835 979 3.066342 TGCTAGCAACAGTATAGACGACC 59.934 47.826 16.84 0.00 0.00 4.79
837 981 4.202020 CCTTGCTAGCAACAGTATAGACGA 60.202 45.833 26.06 1.19 0.00 4.20
839 983 3.804873 GCCTTGCTAGCAACAGTATAGAC 59.195 47.826 26.06 3.39 0.00 2.59
840 984 3.450817 TGCCTTGCTAGCAACAGTATAGA 59.549 43.478 26.06 2.76 37.28 1.98
946 1095 1.746991 CTTCTTCCTTCCTGCCGCC 60.747 63.158 0.00 0.00 0.00 6.13
965 1114 4.704833 GGCAGTGCTCCTTCGGCA 62.705 66.667 16.11 0.00 37.36 5.69
966 1115 4.704833 TGGCAGTGCTCCTTCGGC 62.705 66.667 16.11 0.00 0.00 5.54
1106 1296 2.045634 GGTTGTACGGGAAGGGGC 60.046 66.667 0.00 0.00 0.00 5.80
1146 1336 1.436179 CGGAGGAGGGGGAGGAGATA 61.436 65.000 0.00 0.00 0.00 1.98
1224 1423 2.203938 AAGGAGAAGGCGGTGGGA 60.204 61.111 0.00 0.00 0.00 4.37
1329 1528 4.509737 GGGAGCGTGTAGGCGTCC 62.510 72.222 0.00 6.54 38.18 4.79
1425 1624 0.105224 TGTGGTCGTGGTTGTGTAGG 59.895 55.000 0.00 0.00 0.00 3.18
1701 1900 0.475632 TCACCCACTCCTCCAACCAT 60.476 55.000 0.00 0.00 0.00 3.55
1726 1925 3.347562 ATCCCACCTCCATCCCCGT 62.348 63.158 0.00 0.00 0.00 5.28
1782 1981 2.839632 TCCGCCATCTCTCCGCAT 60.840 61.111 0.00 0.00 0.00 4.73
1916 2117 5.359009 CAGGCCAGACAAGATTACATTCATT 59.641 40.000 5.01 0.00 0.00 2.57
1931 2141 0.106819 AATGATCAGGCAGGCCAGAC 60.107 55.000 13.63 0.00 34.44 3.51
1989 2207 0.178967 TGGCTTCCTTTGACATGCCA 60.179 50.000 0.00 0.00 46.59 4.92
2014 2232 3.677601 CTTGACGCATGCTGTGAAATAG 58.322 45.455 17.13 0.00 0.00 1.73
2031 2249 4.329545 GGACGTGCCCCTGCTTGA 62.330 66.667 0.00 0.00 38.71 3.02
2415 2861 0.820074 AATTGAACCAACGCCGACCA 60.820 50.000 0.00 0.00 0.00 4.02
2447 2893 4.202050 CGATCTTGGGAATGATTTGGAACC 60.202 45.833 0.00 0.00 0.00 3.62
2616 3065 3.134623 TGTTGATGACCTTGACACTGACT 59.865 43.478 0.00 0.00 0.00 3.41
2775 3237 1.467734 CTAACTTCAAGCCAGCTGCAG 59.532 52.381 10.11 10.11 44.83 4.41
2934 3400 5.048434 CGATACTGAGGTTGATCTGCATCTA 60.048 44.000 0.00 0.00 0.00 1.98
2957 3423 8.682016 CAGAAAACAAATTTTAGTAAGACTGCG 58.318 33.333 0.00 0.00 38.17 5.18
2969 3435 9.054922 CATGTACCAATCCAGAAAACAAATTTT 57.945 29.630 0.00 0.00 40.83 1.82
3095 3569 3.592059 CAAAGCAATGTTCCATCTTGGG 58.408 45.455 0.00 0.00 38.32 4.12
3127 3601 5.563876 TCAGTCCTGGTATCTAGTCGTAT 57.436 43.478 0.00 0.00 0.00 3.06
3130 3604 3.315749 GGTTCAGTCCTGGTATCTAGTCG 59.684 52.174 0.00 0.00 0.00 4.18
3135 3609 2.472029 CCTGGTTCAGTCCTGGTATCT 58.528 52.381 0.00 0.00 40.32 1.98
3146 3620 5.048713 GTGGTTCAAAATAGACCTGGTTCAG 60.049 44.000 0.00 0.00 0.00 3.02
3147 3621 4.825085 GTGGTTCAAAATAGACCTGGTTCA 59.175 41.667 0.00 0.00 0.00 3.18
3167 3642 5.982356 TCAAAGATCTCTGTTGATAGGTGG 58.018 41.667 4.53 0.00 0.00 4.61
3224 3700 3.974222 GCTCAAGCAGCCAAAACTT 57.026 47.368 0.00 0.00 43.17 2.66
3244 3720 9.911788 AACTGAATCAGGTATTTTCATAGACAT 57.088 29.630 15.38 0.00 35.51 3.06
3280 3756 0.315251 GGCCTGTTGGAAGTTTCAGC 59.685 55.000 0.00 0.00 34.57 4.26
3281 3757 1.691196 TGGCCTGTTGGAAGTTTCAG 58.309 50.000 3.32 0.00 34.57 3.02
3297 3773 4.186159 CTCCATTGGTGAATTGAAATGGC 58.814 43.478 1.86 0.00 45.72 4.40
3299 3775 6.028146 TGACTCCATTGGTGAATTGAAATG 57.972 37.500 11.60 0.00 0.00 2.32
3353 3869 6.287589 TGGTTTTCCATATTTGCGGTTATT 57.712 33.333 0.00 0.00 46.22 1.40
3379 3956 9.936759 ATTTTTCTTTTAGACTAGAGTCCTGAG 57.063 33.333 6.05 0.92 45.85 3.35
3416 3994 3.636764 CCAATAACTCCAACAATAGGCCC 59.363 47.826 0.00 0.00 0.00 5.80
3417 3995 4.532834 TCCAATAACTCCAACAATAGGCC 58.467 43.478 0.00 0.00 0.00 5.19
3423 4001 5.994668 GCCATTTTTCCAATAACTCCAACAA 59.005 36.000 0.00 0.00 0.00 2.83
3445 4023 0.618458 TACACTCCACCTGGAATGCC 59.382 55.000 0.00 0.00 44.70 4.40
3463 4041 3.755483 GCTCCTCTGGATACCACCATCTA 60.755 52.174 0.00 0.00 39.34 1.98
3467 4045 0.339859 AGCTCCTCTGGATACCACCA 59.660 55.000 0.00 0.00 38.33 4.17
3468 4046 1.964933 GTAGCTCCTCTGGATACCACC 59.035 57.143 0.00 0.00 0.00 4.61
3469 4047 1.609555 CGTAGCTCCTCTGGATACCAC 59.390 57.143 0.00 0.00 0.00 4.16
3473 4051 2.100916 GCAAACGTAGCTCCTCTGGATA 59.899 50.000 5.73 0.00 0.00 2.59
3559 4144 1.686587 CAGACAACCAGGGGGAAAAAC 59.313 52.381 0.00 0.00 38.05 2.43
3571 4156 5.238583 AGCTTACAATCTACACAGACAACC 58.761 41.667 0.00 0.00 32.25 3.77
3592 4177 7.327032 CCTCTGCAACAACTTTAAAAGATAAGC 59.673 37.037 0.00 0.00 0.00 3.09
3647 4457 7.267857 TGATCAGTCACGTATTCAAGATGATT 58.732 34.615 0.00 0.00 0.00 2.57
3683 4495 5.006386 AGTTCTGTCTTGATCCATTGTTCC 58.994 41.667 0.00 0.00 0.00 3.62
3687 4499 6.429078 TGAAAGAGTTCTGTCTTGATCCATTG 59.571 38.462 1.30 0.00 36.86 2.82
3713 4529 8.471609 GGATCCTAGAGCCTATAAGTATTTCAC 58.528 40.741 3.84 0.00 34.95 3.18
3729 4545 6.764085 CGGACATATAGTGTAGGATCCTAGAG 59.236 46.154 22.30 10.03 42.36 2.43
3730 4546 6.215023 ACGGACATATAGTGTAGGATCCTAGA 59.785 42.308 22.30 18.33 42.36 2.43
3732 4548 6.384342 ACGGACATATAGTGTAGGATCCTA 57.616 41.667 18.00 18.00 42.36 2.94
3734 4550 5.979288 AACGGACATATAGTGTAGGATCC 57.021 43.478 2.48 2.48 42.36 3.36
3735 4551 6.388278 GGAAACGGACATATAGTGTAGGATC 58.612 44.000 0.00 0.00 42.36 3.36
3778 4624 7.046292 TCTGTTTTGCAGTACAGAGTACTTA 57.954 36.000 22.00 5.57 44.20 2.24
3786 4632 4.351192 GTTTGGTCTGTTTTGCAGTACAG 58.649 43.478 18.96 18.96 45.23 2.74
3791 4637 2.957491 TGGTTTGGTCTGTTTTGCAG 57.043 45.000 0.00 0.00 46.34 4.41
3859 5985 0.970640 TCGAAGATTGTGAACCGGGA 59.029 50.000 6.32 0.00 0.00 5.14
3860 5986 1.803334 TTCGAAGATTGTGAACCGGG 58.197 50.000 6.32 0.00 35.04 5.73
3861 5987 3.747193 CAATTCGAAGATTGTGAACCGG 58.253 45.455 3.35 0.00 35.04 5.28
3862 5988 3.120199 AGCAATTCGAAGATTGTGAACCG 60.120 43.478 11.91 0.00 35.04 4.44


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

AutoCloner maintained by Alex Coulton.