Multiple sequence alignment - TraesCS1A01G071200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G071200 chr1A 100.000 6088 0 0 1 6088 53864110 53870197 0.000000e+00 11243.0
1 TraesCS1A01G071200 chr1A 87.648 1352 128 21 2354 3690 53851610 53852937 0.000000e+00 1535.0
2 TraesCS1A01G071200 chr1A 86.833 1162 100 28 972 2121 53850065 53851185 0.000000e+00 1249.0
3 TraesCS1A01G071200 chr1A 88.621 457 47 3 4659 5114 53853220 53853672 8.920000e-153 551.0
4 TraesCS1A01G071200 chr1A 80.963 457 51 26 26 456 377505225 377504779 4.550000e-86 329.0
5 TraesCS1A01G071200 chr1A 76.647 334 47 19 143 456 490320093 490319771 8.170000e-34 156.0
6 TraesCS1A01G071200 chr1A 88.571 70 7 1 4538 4606 53852945 53853014 3.910000e-12 84.2
7 TraesCS1A01G071200 chr1D 94.180 2749 83 22 808 3502 54903761 54906486 0.000000e+00 4119.0
8 TraesCS1A01G071200 chr1D 96.677 1625 46 7 3496 5114 54906660 54908282 0.000000e+00 2695.0
9 TraesCS1A01G071200 chr1D 87.553 707 45 14 3 674 54903064 54903762 0.000000e+00 778.0
10 TraesCS1A01G071200 chr1D 86.301 219 29 1 489 707 319433305 319433088 2.840000e-58 237.0
11 TraesCS1A01G071200 chr1D 79.042 167 23 10 213 367 426972909 426972743 3.000000e-18 104.0
12 TraesCS1A01G071200 chrUn 84.322 2462 256 72 2223 4600 3831643 3829228 0.000000e+00 2289.0
13 TraesCS1A01G071200 chrUn 86.736 1161 104 27 972 2121 3833005 3831884 0.000000e+00 1245.0
14 TraesCS1A01G071200 chrUn 89.934 457 45 1 4659 5114 3700439 3699983 6.800000e-164 588.0
15 TraesCS1A01G071200 chrUn 83.503 491 64 12 1617 2098 117283590 117284072 5.600000e-120 442.0
16 TraesCS1A01G071200 chr2B 98.665 974 11 2 5115 6088 156372723 156373694 0.000000e+00 1725.0
17 TraesCS1A01G071200 chr2B 87.671 219 27 0 489 707 562867329 562867111 7.830000e-64 255.0
18 TraesCS1A01G071200 chr2B 74.831 445 84 17 4650 5089 715313755 715313334 6.270000e-40 176.0
19 TraesCS1A01G071200 chr7A 98.566 976 10 3 5115 6088 678343279 678344252 0.000000e+00 1722.0
20 TraesCS1A01G071200 chr7A 98.566 976 10 3 5115 6088 678366349 678367322 0.000000e+00 1722.0
21 TraesCS1A01G071200 chr7A 98.463 976 11 3 5115 6088 678359499 678360472 0.000000e+00 1716.0
22 TraesCS1A01G071200 chr6B 98.274 985 10 5 5107 6088 663195458 663196438 0.000000e+00 1718.0
23 TraesCS1A01G071200 chr6B 98.465 977 10 4 5115 6088 663205612 663206586 0.000000e+00 1716.0
24 TraesCS1A01G071200 chr6B 86.301 219 27 2 490 708 22644808 22645023 1.020000e-57 235.0
25 TraesCS1A01G071200 chr6B 80.312 320 35 17 121 419 458482214 458481902 3.700000e-52 217.0
26 TraesCS1A01G071200 chr6B 84.028 144 11 5 15 146 474815252 474815109 1.780000e-25 128.0
27 TraesCS1A01G071200 chr7B 98.463 976 11 3 5115 6088 741311107 741312080 0.000000e+00 1716.0
28 TraesCS1A01G071200 chr7B 84.477 612 76 14 2156 2752 7093844 7094451 2.440000e-163 586.0
29 TraesCS1A01G071200 chr7B 83.660 612 79 15 2156 2752 676799281 676799886 1.920000e-154 556.0
30 TraesCS1A01G071200 chr6A 98.361 976 12 3 5115 6088 540553851 540552878 0.000000e+00 1711.0
31 TraesCS1A01G071200 chr6A 88.000 75 6 2 18 90 615701215 615701288 1.090000e-12 86.1
32 TraesCS1A01G071200 chr3B 98.361 976 12 3 5115 6088 274795216 274796189 0.000000e+00 1711.0
33 TraesCS1A01G071200 chr3B 84.082 490 61 12 1617 2098 51865794 51866274 2.000000e-124 457.0
34 TraesCS1A01G071200 chr3B 81.250 160 15 11 213 365 176618416 176618265 1.390000e-21 115.0
35 TraesCS1A01G071200 chr3B 87.097 93 7 4 32 122 11016121 11016032 3.880000e-17 100.0
36 TraesCS1A01G071200 chr1B 95.455 924 41 1 3149 4072 90437864 90436942 0.000000e+00 1472.0
37 TraesCS1A01G071200 chr1B 90.338 1066 33 25 4058 5114 90436922 90435918 0.000000e+00 1334.0
38 TraesCS1A01G071200 chr3D 83.762 505 66 12 1599 2098 54336367 54336860 1.200000e-126 464.0
39 TraesCS1A01G071200 chr3D 88.060 67 7 1 15 80 565010767 565010701 1.820000e-10 78.7
40 TraesCS1A01G071200 chr5B 83.629 507 68 10 1599 2098 420933501 420933999 4.300000e-126 462.0
41 TraesCS1A01G071200 chr5B 83.661 508 65 14 1599 2098 702386236 702386733 4.300000e-126 462.0
42 TraesCS1A01G071200 chr5B 83.268 508 68 12 1599 2098 581761656 581762154 9.310000e-123 451.0
43 TraesCS1A01G071200 chr5B 88.532 218 21 3 489 704 505606460 505606675 1.680000e-65 261.0
44 TraesCS1A01G071200 chr5B 86.977 215 27 1 490 704 69552749 69552536 2.190000e-59 241.0
45 TraesCS1A01G071200 chr2D 84.211 304 36 12 2165 2463 179337859 179337563 9.990000e-73 285.0
46 TraesCS1A01G071200 chr2D 76.443 433 80 11 4689 5102 590334919 590334490 1.330000e-51 215.0
47 TraesCS1A01G071200 chr5D 78.407 477 57 29 15 456 219774349 219773884 1.010000e-67 268.0
48 TraesCS1A01G071200 chr5A 88.106 227 24 3 488 713 466585486 466585262 3.620000e-67 267.0
49 TraesCS1A01G071200 chr5A 86.726 113 14 1 230 342 17525439 17525328 2.300000e-24 124.0
50 TraesCS1A01G071200 chr5A 87.179 78 10 0 755 832 293437014 293436937 8.400000e-14 89.8
51 TraesCS1A01G071200 chr6D 88.479 217 23 2 488 704 460583638 460583852 1.680000e-65 261.0
52 TraesCS1A01G071200 chr3A 86.758 219 28 1 489 707 712319134 712318917 6.100000e-60 243.0
53 TraesCS1A01G071200 chr2A 75.527 474 90 11 4650 5102 724735836 724735368 6.180000e-50 209.0
54 TraesCS1A01G071200 chr4B 78.397 287 41 15 142 410 66186951 66186668 3.770000e-37 167.0
55 TraesCS1A01G071200 chr4A 82.258 124 11 9 32 147 647183235 647183115 5.020000e-16 97.1
56 TraesCS1A01G071200 chr4D 95.000 60 1 1 22 79 318470334 318470393 6.500000e-15 93.5
57 TraesCS1A01G071200 chr4D 91.176 68 3 2 22 86 451692451 451692384 8.400000e-14 89.8
58 TraesCS1A01G071200 chr7D 82.278 79 6 8 54 130 593025513 593025585 1.830000e-05 62.1


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 TraesCS1A01G071200 chr1A 53864110 53870197 6087 False 11243.000000 11243 100.000000 1 6088 1 chr1A.!!$F1 6087
1 TraesCS1A01G071200 chr1A 53850065 53853672 3607 False 854.800000 1535 87.918250 972 5114 4 chr1A.!!$F2 4142
2 TraesCS1A01G071200 chr1D 54903064 54908282 5218 False 2530.666667 4119 92.803333 3 5114 3 chr1D.!!$F1 5111
3 TraesCS1A01G071200 chrUn 3829228 3833005 3777 True 1767.000000 2289 85.529000 972 4600 2 chrUn.!!$R2 3628
4 TraesCS1A01G071200 chr2B 156372723 156373694 971 False 1725.000000 1725 98.665000 5115 6088 1 chr2B.!!$F1 973
5 TraesCS1A01G071200 chr7A 678343279 678344252 973 False 1722.000000 1722 98.566000 5115 6088 1 chr7A.!!$F1 973
6 TraesCS1A01G071200 chr7A 678366349 678367322 973 False 1722.000000 1722 98.566000 5115 6088 1 chr7A.!!$F3 973
7 TraesCS1A01G071200 chr7A 678359499 678360472 973 False 1716.000000 1716 98.463000 5115 6088 1 chr7A.!!$F2 973
8 TraesCS1A01G071200 chr6B 663195458 663196438 980 False 1718.000000 1718 98.274000 5107 6088 1 chr6B.!!$F2 981
9 TraesCS1A01G071200 chr6B 663205612 663206586 974 False 1716.000000 1716 98.465000 5115 6088 1 chr6B.!!$F3 973
10 TraesCS1A01G071200 chr7B 741311107 741312080 973 False 1716.000000 1716 98.463000 5115 6088 1 chr7B.!!$F3 973
11 TraesCS1A01G071200 chr7B 7093844 7094451 607 False 586.000000 586 84.477000 2156 2752 1 chr7B.!!$F1 596
12 TraesCS1A01G071200 chr7B 676799281 676799886 605 False 556.000000 556 83.660000 2156 2752 1 chr7B.!!$F2 596
13 TraesCS1A01G071200 chr6A 540552878 540553851 973 True 1711.000000 1711 98.361000 5115 6088 1 chr6A.!!$R1 973
14 TraesCS1A01G071200 chr3B 274795216 274796189 973 False 1711.000000 1711 98.361000 5115 6088 1 chr3B.!!$F2 973
15 TraesCS1A01G071200 chr1B 90435918 90437864 1946 True 1403.000000 1472 92.896500 3149 5114 2 chr1B.!!$R1 1965

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
782 815 0.179129 TTTACTAGCTACGTGGGCGC 60.179 55.0 0.00 0.0 42.83 6.53 F
808 841 0.248743 GTCGGTCCAATATGACGCGA 60.249 55.0 15.93 0.0 36.38 5.87 F
1449 1482 0.258774 ATTGGTGGGTGGTCATAGGC 59.741 55.0 0.00 0.0 0.00 3.93 F
2396 2674 0.693049 CTAAGGTGTTGCCAGTCCCT 59.307 55.0 0.00 0.0 40.61 4.20 F
2888 3193 1.021968 AGACCGTTGTCAAAGTTGCC 58.978 50.0 0.00 0.0 44.33 4.52 F
3581 4073 1.125633 TATAGTTTGGCCGAGGGTCC 58.874 55.0 0.00 0.0 0.00 4.46 F
4534 5112 5.480073 AGTTGCATTACAAAAGGAGGCATAA 59.520 36.0 0.00 0.0 40.82 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 1986 2.259618 CCTTCATCAGTTACGACCACG 58.740 52.381 0.00 0.00 45.75 4.94 R
2438 2716 4.019860 ACTGATGACAGCCAGACAGTAAAT 60.020 41.667 12.84 0.00 46.95 1.40 R
3027 3332 3.933861 ATGGTGGAGAAGGAACATACC 57.066 47.619 0.00 0.00 0.00 2.73 R
3581 4073 3.420300 AGAGCTGCTTGATCCATATGG 57.580 47.619 16.25 16.25 0.00 2.74 R
4835 5572 3.118956 AGTGTAGCCATCTAAGACACTGC 60.119 47.826 5.24 0.00 32.04 4.40 R
4992 5731 2.097825 GCAAGAATCCTCTGCACCAAT 58.902 47.619 0.00 0.00 30.03 3.16 R
5762 6504 1.001503 AGTGAGAGAGAGCAGGGGG 59.998 63.158 0.00 0.00 0.00 5.40 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
161 163 7.118101 CCAAAGGAAAAATGTTGACCATGTATG 59.882 37.037 0.00 0.00 32.82 2.39
296 311 6.868339 ACTTGTATTAGAAAAATGCTGTTGGC 59.132 34.615 0.00 0.00 42.22 4.52
332 347 8.735692 AATGTTGAATGAAAACCAGAACAAAT 57.264 26.923 0.00 0.00 30.82 2.32
476 509 6.679327 AAAGCGGTAAATAGGCTCTTTTAG 57.321 37.500 3.04 0.00 35.64 1.85
490 523 7.339482 AGGCTCTTTTAGATTAATCGGAGTTT 58.661 34.615 9.78 0.00 0.00 2.66
513 546 3.319137 TCTGAACATCAGTACAGCCAC 57.681 47.619 7.21 0.00 44.58 5.01
530 563 3.325870 GCCACAAGCGCTCATATACATA 58.674 45.455 12.06 0.00 0.00 2.29
531 564 3.123621 GCCACAAGCGCTCATATACATAC 59.876 47.826 12.06 0.00 0.00 2.39
550 583 6.429151 ACATACGCATATACTCACCCCTATA 58.571 40.000 0.00 0.00 0.00 1.31
553 586 6.034161 ACGCATATACTCACCCCTATAAAC 57.966 41.667 0.00 0.00 0.00 2.01
557 590 6.640518 CATATACTCACCCCTATAAACGCAT 58.359 40.000 0.00 0.00 0.00 4.73
562 595 3.451540 TCACCCCTATAAACGCATACACA 59.548 43.478 0.00 0.00 0.00 3.72
564 597 3.198200 ACCCCTATAAACGCATACACACA 59.802 43.478 0.00 0.00 0.00 3.72
565 598 4.141574 ACCCCTATAAACGCATACACACAT 60.142 41.667 0.00 0.00 0.00 3.21
569 602 6.220930 CCTATAAACGCATACACACATACCT 58.779 40.000 0.00 0.00 0.00 3.08
574 607 3.128349 CGCATACACACATACCTTACCC 58.872 50.000 0.00 0.00 0.00 3.69
586 619 1.009675 ACCTTACCCCTATGAGCACCT 59.990 52.381 0.00 0.00 0.00 4.00
588 621 2.104963 CCTTACCCCTATGAGCACCTTC 59.895 54.545 0.00 0.00 0.00 3.46
595 628 3.181461 CCCTATGAGCACCTTCGAAAGAT 60.181 47.826 0.00 0.00 41.60 2.40
605 638 2.337583 CTTCGAAAGATTGAGCCGTCA 58.662 47.619 0.00 0.00 41.60 4.35
646 679 4.438880 CGAAGTCATCATAGACACCTCGTT 60.439 45.833 0.00 0.00 40.98 3.85
655 688 1.563111 GACACCTCGTTGTCGACAAA 58.437 50.000 31.20 16.76 41.35 2.83
674 707 1.420430 AAACGTCTCCTCCCACTGAA 58.580 50.000 0.00 0.00 0.00 3.02
675 708 1.645710 AACGTCTCCTCCCACTGAAT 58.354 50.000 0.00 0.00 0.00 2.57
676 709 2.526888 ACGTCTCCTCCCACTGAATA 57.473 50.000 0.00 0.00 0.00 1.75
677 710 2.100989 ACGTCTCCTCCCACTGAATAC 58.899 52.381 0.00 0.00 0.00 1.89
678 711 1.065701 CGTCTCCTCCCACTGAATACG 59.934 57.143 0.00 0.00 0.00 3.06
679 712 1.112113 TCTCCTCCCACTGAATACGC 58.888 55.000 0.00 0.00 0.00 4.42
680 713 0.824109 CTCCTCCCACTGAATACGCA 59.176 55.000 0.00 0.00 0.00 5.24
681 714 1.414181 CTCCTCCCACTGAATACGCAT 59.586 52.381 0.00 0.00 0.00 4.73
682 715 1.412710 TCCTCCCACTGAATACGCATC 59.587 52.381 0.00 0.00 0.00 3.91
683 716 1.491670 CTCCCACTGAATACGCATCG 58.508 55.000 0.00 0.00 0.00 3.84
684 717 0.529773 TCCCACTGAATACGCATCGC 60.530 55.000 0.00 0.00 0.00 4.58
685 718 0.530650 CCCACTGAATACGCATCGCT 60.531 55.000 0.00 0.00 0.00 4.93
686 719 0.578683 CCACTGAATACGCATCGCTG 59.421 55.000 0.00 0.00 0.00 5.18
687 720 0.578683 CACTGAATACGCATCGCTGG 59.421 55.000 0.00 0.00 0.00 4.85
688 721 0.459899 ACTGAATACGCATCGCTGGA 59.540 50.000 0.00 0.00 0.00 3.86
689 722 1.134818 ACTGAATACGCATCGCTGGAA 60.135 47.619 0.00 0.00 0.00 3.53
690 723 1.933181 CTGAATACGCATCGCTGGAAA 59.067 47.619 0.00 0.00 0.00 3.13
691 724 2.545526 CTGAATACGCATCGCTGGAAAT 59.454 45.455 0.00 0.00 0.00 2.17
692 725 2.543848 TGAATACGCATCGCTGGAAATC 59.456 45.455 0.00 0.00 0.00 2.17
693 726 1.512926 ATACGCATCGCTGGAAATCC 58.487 50.000 0.00 0.00 0.00 3.01
694 727 0.464036 TACGCATCGCTGGAAATCCT 59.536 50.000 0.44 0.00 36.82 3.24
695 728 1.091771 ACGCATCGCTGGAAATCCTG 61.092 55.000 0.44 1.39 37.93 3.86
696 729 0.811219 CGCATCGCTGGAAATCCTGA 60.811 55.000 10.20 1.98 37.15 3.86
697 730 1.382522 GCATCGCTGGAAATCCTGAA 58.617 50.000 10.20 0.00 37.15 3.02
698 731 1.745087 GCATCGCTGGAAATCCTGAAA 59.255 47.619 10.20 0.00 37.15 2.69
699 732 2.360165 GCATCGCTGGAAATCCTGAAAT 59.640 45.455 10.20 0.52 37.15 2.17
700 733 3.565482 GCATCGCTGGAAATCCTGAAATA 59.435 43.478 10.20 0.00 37.15 1.40
701 734 4.036734 GCATCGCTGGAAATCCTGAAATAA 59.963 41.667 10.20 0.00 37.15 1.40
702 735 5.450412 GCATCGCTGGAAATCCTGAAATAAA 60.450 40.000 10.20 0.00 37.15 1.40
703 736 6.736794 GCATCGCTGGAAATCCTGAAATAAAT 60.737 38.462 10.20 0.00 37.15 1.40
704 737 7.522073 GCATCGCTGGAAATCCTGAAATAAATA 60.522 37.037 10.20 0.00 37.15 1.40
705 738 7.259290 TCGCTGGAAATCCTGAAATAAATAC 57.741 36.000 10.20 0.00 37.15 1.89
706 739 6.826231 TCGCTGGAAATCCTGAAATAAATACA 59.174 34.615 10.20 0.00 37.15 2.29
707 740 7.338196 TCGCTGGAAATCCTGAAATAAATACAA 59.662 33.333 10.20 0.00 37.15 2.41
708 741 7.645340 CGCTGGAAATCCTGAAATAAATACAAG 59.355 37.037 10.20 0.00 37.15 3.16
709 742 7.436376 GCTGGAAATCCTGAAATAAATACAAGC 59.564 37.037 10.20 0.00 37.15 4.01
710 743 8.359875 TGGAAATCCTGAAATAAATACAAGCA 57.640 30.769 0.44 0.00 36.82 3.91
711 744 8.811017 TGGAAATCCTGAAATAAATACAAGCAA 58.189 29.630 0.44 0.00 36.82 3.91
712 745 9.822185 GGAAATCCTGAAATAAATACAAGCAAT 57.178 29.630 0.00 0.00 0.00 3.56
716 749 8.477984 TCCTGAAATAAATACAAGCAATTTGC 57.522 30.769 13.55 13.55 45.46 3.68
729 762 4.582441 GCAATTTGCGGGTAATTTTCTG 57.418 40.909 5.49 0.00 31.71 3.02
730 763 3.993736 GCAATTTGCGGGTAATTTTCTGT 59.006 39.130 5.49 0.00 31.71 3.41
731 764 4.143137 GCAATTTGCGGGTAATTTTCTGTG 60.143 41.667 5.49 0.00 31.71 3.66
732 765 4.864704 ATTTGCGGGTAATTTTCTGTGT 57.135 36.364 0.00 0.00 0.00 3.72
733 766 4.657436 TTTGCGGGTAATTTTCTGTGTT 57.343 36.364 0.00 0.00 0.00 3.32
734 767 4.657436 TTGCGGGTAATTTTCTGTGTTT 57.343 36.364 0.00 0.00 0.00 2.83
735 768 4.657436 TGCGGGTAATTTTCTGTGTTTT 57.343 36.364 0.00 0.00 0.00 2.43
736 769 5.012328 TGCGGGTAATTTTCTGTGTTTTT 57.988 34.783 0.00 0.00 0.00 1.94
761 794 8.628630 TTTTTGAAGGGAATTTTCTGTGTTTT 57.371 26.923 0.00 0.00 0.00 2.43
762 795 8.628630 TTTTGAAGGGAATTTTCTGTGTTTTT 57.371 26.923 0.00 0.00 0.00 1.94
781 814 2.282701 TTTTACTAGCTACGTGGGCG 57.717 50.000 0.00 0.00 44.93 6.13
782 815 0.179129 TTTACTAGCTACGTGGGCGC 60.179 55.000 0.00 0.00 42.83 6.53
783 816 2.327002 TTACTAGCTACGTGGGCGCG 62.327 60.000 0.00 0.00 42.83 6.86
784 817 3.884350 CTAGCTACGTGGGCGCGA 61.884 66.667 12.10 0.00 42.83 5.87
785 818 3.405592 CTAGCTACGTGGGCGCGAA 62.406 63.158 12.10 0.00 42.83 4.70
786 819 2.679132 CTAGCTACGTGGGCGCGAAT 62.679 60.000 12.10 0.00 42.83 3.34
787 820 2.947118 TAGCTACGTGGGCGCGAATG 62.947 60.000 12.10 1.89 42.83 2.67
788 821 3.261951 CTACGTGGGCGCGAATGG 61.262 66.667 12.10 0.00 42.83 3.16
789 822 4.823419 TACGTGGGCGCGAATGGG 62.823 66.667 12.10 0.00 42.83 4.00
799 832 4.954933 CGAATGGGTCGGTCCAAT 57.045 55.556 2.00 0.00 46.45 3.16
801 834 2.543777 CGAATGGGTCGGTCCAATAT 57.456 50.000 2.00 0.00 46.45 1.28
802 835 2.143122 CGAATGGGTCGGTCCAATATG 58.857 52.381 2.00 0.00 46.45 1.78
803 836 2.224185 CGAATGGGTCGGTCCAATATGA 60.224 50.000 2.00 0.00 46.45 2.15
804 837 2.930826 ATGGGTCGGTCCAATATGAC 57.069 50.000 2.00 0.00 40.62 3.06
805 838 0.462375 TGGGTCGGTCCAATATGACG 59.538 55.000 0.00 0.00 36.07 4.35
806 839 0.878961 GGGTCGGTCCAATATGACGC 60.879 60.000 0.00 0.00 36.07 5.19
807 840 1.213094 GGTCGGTCCAATATGACGCG 61.213 60.000 3.53 3.53 36.07 6.01
808 841 0.248743 GTCGGTCCAATATGACGCGA 60.249 55.000 15.93 0.00 36.38 5.87
814 847 1.000843 TCCAATATGACGCGATGGAGG 59.999 52.381 15.93 5.74 35.33 4.30
882 915 1.028330 TCTCGGCCCGTACTACAGTG 61.028 60.000 1.63 0.00 0.00 3.66
895 928 2.759114 CAGTGGACTGGGCCATGT 59.241 61.111 6.72 7.60 40.68 3.21
910 943 1.820519 CCATGTCCATGTCAGTTTGGG 59.179 52.381 6.53 0.00 37.11 4.12
915 948 0.540365 CCATGTCAGTTTGGGCCTGT 60.540 55.000 4.53 0.00 0.00 4.00
925 958 3.512516 GGGCCTGTCGCTTCATGC 61.513 66.667 0.84 0.00 37.74 4.06
970 1003 3.039202 GCAGAACACCCCGCGAATG 62.039 63.158 8.23 5.01 0.00 2.67
1042 1075 1.000283 CACTCGCTTCCACAGTTCTCT 60.000 52.381 0.00 0.00 0.00 3.10
1045 1078 0.320247 CGCTTCCACAGTTCTCTGCT 60.320 55.000 0.00 0.00 44.77 4.24
1046 1079 1.875576 CGCTTCCACAGTTCTCTGCTT 60.876 52.381 0.00 0.00 44.77 3.91
1047 1080 1.803555 GCTTCCACAGTTCTCTGCTTC 59.196 52.381 0.00 0.00 44.77 3.86
1048 1081 2.421619 CTTCCACAGTTCTCTGCTTCC 58.578 52.381 0.00 0.00 44.77 3.46
1049 1082 0.318441 TCCACAGTTCTCTGCTTCCG 59.682 55.000 0.00 0.00 44.77 4.30
1065 1098 4.992511 CGTTCCGCCCCACCGAAA 62.993 66.667 0.00 0.00 0.00 3.46
1251 1284 4.678743 GGCAACCTGGTGTCCCCC 62.679 72.222 0.00 0.00 0.00 5.40
1346 1379 3.518998 CCGCGTCCGAGGATGAGT 61.519 66.667 15.06 0.00 37.24 3.41
1399 1432 3.515602 AATATGAGGAGGCATGGGAAC 57.484 47.619 0.00 0.00 0.00 3.62
1424 1457 0.318614 CCAGTTTGTGCGCCGAAATT 60.319 50.000 4.18 0.00 0.00 1.82
1438 1471 1.750778 CGAAATTCCTGGATTGGTGGG 59.249 52.381 0.00 0.00 0.00 4.61
1442 1475 1.071314 TTCCTGGATTGGTGGGTGGT 61.071 55.000 0.00 0.00 0.00 4.16
1443 1476 1.000896 CCTGGATTGGTGGGTGGTC 60.001 63.158 0.00 0.00 0.00 4.02
1444 1477 1.767036 CTGGATTGGTGGGTGGTCA 59.233 57.895 0.00 0.00 0.00 4.02
1445 1478 0.332632 CTGGATTGGTGGGTGGTCAT 59.667 55.000 0.00 0.00 0.00 3.06
1446 1479 1.563879 CTGGATTGGTGGGTGGTCATA 59.436 52.381 0.00 0.00 0.00 2.15
1447 1480 1.563879 TGGATTGGTGGGTGGTCATAG 59.436 52.381 0.00 0.00 0.00 2.23
1448 1481 1.133792 GGATTGGTGGGTGGTCATAGG 60.134 57.143 0.00 0.00 0.00 2.57
1449 1482 0.258774 ATTGGTGGGTGGTCATAGGC 59.741 55.000 0.00 0.00 0.00 3.93
1461 1494 3.639561 TGGTCATAGGCTCATAGCGTTTA 59.360 43.478 0.00 0.00 43.62 2.01
1491 1524 6.097356 TGCTGTCAAGTAGTAGTAAAATCGG 58.903 40.000 0.00 0.00 0.00 4.18
1611 1648 5.638234 GGGTCGAAATGAGGTATAAGTATGC 59.362 44.000 0.00 0.00 0.00 3.14
1614 1651 5.918576 TCGAAATGAGGTATAAGTATGCGTG 59.081 40.000 0.00 0.00 0.00 5.34
1622 1659 4.152402 GGTATAAGTATGCGTGGATGCTTG 59.848 45.833 13.36 0.00 31.57 4.01
1835 1879 6.151648 ACCATCCAACATACTTGAACTGAATG 59.848 38.462 0.00 0.00 0.00 2.67
1942 1986 4.142381 GCAGGTGTTGGAAGAAATCATACC 60.142 45.833 0.00 0.00 0.00 2.73
1957 2001 3.018856 TCATACCGTGGTCGTAACTGAT 58.981 45.455 0.00 0.00 35.01 2.90
2008 2052 2.142292 GACATGGCCAGTTGGGGACT 62.142 60.000 13.05 0.00 36.67 3.85
2112 2156 1.877443 ACAACTGGTGTGCGGAAATAC 59.123 47.619 0.00 0.00 39.72 1.89
2154 2302 5.503662 TCTACAGTTGTGTTCTGTTACGA 57.496 39.130 3.98 0.00 42.50 3.43
2261 2482 1.946984 TCAGGACGATGGGGTAGTTT 58.053 50.000 0.00 0.00 0.00 2.66
2263 2484 2.640826 TCAGGACGATGGGGTAGTTTTT 59.359 45.455 0.00 0.00 0.00 1.94
2386 2664 1.493022 TGGTGCAGGAACTAAGGTGTT 59.507 47.619 0.00 0.00 36.02 3.32
2396 2674 0.693049 CTAAGGTGTTGCCAGTCCCT 59.307 55.000 0.00 0.00 40.61 4.20
2408 2686 1.534729 CAGTCCCTTGCCTTGTTACC 58.465 55.000 0.00 0.00 0.00 2.85
2438 2716 1.401761 ATGCTGTTTGTGGTGCTGAA 58.598 45.000 0.00 0.00 0.00 3.02
2615 2912 8.740906 TGTATTTAGTGGTTTTGTTCTTGTTCA 58.259 29.630 0.00 0.00 0.00 3.18
2774 3079 7.933396 TGCTATCATCAGTAATTGTGATTTGG 58.067 34.615 3.07 0.00 32.06 3.28
2888 3193 1.021968 AGACCGTTGTCAAAGTTGCC 58.978 50.000 0.00 0.00 44.33 4.52
3027 3332 5.830912 TGATTCAAGTGGCTTTGTTTACAG 58.169 37.500 3.02 0.00 0.00 2.74
3259 3570 6.381133 TCTTGTCATGTATGGTGTATCTCACT 59.619 38.462 0.00 0.00 45.50 3.41
3449 3760 2.203001 TGCCGGTGGTATGATGCG 60.203 61.111 1.90 0.00 0.00 4.73
3581 4073 1.125633 TATAGTTTGGCCGAGGGTCC 58.874 55.000 0.00 0.00 0.00 4.46
3629 4121 7.174426 GTGATTAGTTTACCTTGCACCTTAAGT 59.826 37.037 0.97 0.00 0.00 2.24
3634 4126 5.957842 TTACCTTGCACCTTAAGTTGATG 57.042 39.130 3.89 0.00 0.00 3.07
3963 4483 6.038825 AGGAAAACATCGTGTAAATGTTCACA 59.961 34.615 2.29 0.00 44.44 3.58
4091 4647 8.461222 TGAAATGTAGATTATGTGCCAGAAAAG 58.539 33.333 0.00 0.00 0.00 2.27
4534 5112 5.480073 AGTTGCATTACAAAAGGAGGCATAA 59.520 36.000 0.00 0.00 40.82 1.90
4584 5163 8.654230 TTTTCATCTGCAAGTAGATCTCATAC 57.346 34.615 0.00 0.00 35.28 2.39
4593 5172 6.625362 CAAGTAGATCTCATACCGCATATGT 58.375 40.000 0.00 0.00 41.44 2.29
4634 5234 5.637810 TCGTTATACCTTTGCACTCTTTCAG 59.362 40.000 0.00 0.00 0.00 3.02
4835 5572 8.393366 CAAACTGTGAAATACCATAGTGATGAG 58.607 37.037 0.00 0.00 38.29 2.90
5290 6029 6.475504 TGCTCTCTGAAAATATTGGACAGAA 58.524 36.000 15.34 9.19 37.20 3.02
5436 6175 5.372343 TGCCAATTATAAAGGAGCTCTGA 57.628 39.130 14.64 0.00 0.00 3.27
5782 6524 0.033208 CCCCTGCTCTCTCTCACTCT 60.033 60.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 186 7.993821 TTCAAATGCTTGATTACGTTTTTCA 57.006 28.000 0.00 0.00 41.22 2.69
185 187 8.324567 TGTTTCAAATGCTTGATTACGTTTTTC 58.675 29.630 0.00 0.00 41.22 2.29
191 193 6.932901 ACATGTTTCAAATGCTTGATTACG 57.067 33.333 0.00 0.00 41.22 3.18
308 323 9.829507 TTATTTGTTCTGGTTTTCATTCAACAT 57.170 25.926 0.00 0.00 0.00 2.71
433 461 7.306574 CCGCTTTTTCTGTTTTATTCAGTTTCC 60.307 37.037 0.00 0.00 34.86 3.13
434 462 7.222031 ACCGCTTTTTCTGTTTTATTCAGTTTC 59.778 33.333 0.00 0.00 34.86 2.78
494 527 6.145029 GCTTGTGGCTGTACTGATGTTCAG 62.145 50.000 3.61 3.03 43.01 3.02
495 528 3.402110 CTTGTGGCTGTACTGATGTTCA 58.598 45.455 3.61 0.00 0.00 3.18
496 529 2.160417 GCTTGTGGCTGTACTGATGTTC 59.840 50.000 3.61 0.00 38.06 3.18
510 543 3.364920 CGTATGTATATGAGCGCTTGTGG 59.635 47.826 13.26 0.00 0.00 4.17
513 546 2.986479 TGCGTATGTATATGAGCGCTTG 59.014 45.455 13.26 0.00 44.34 4.01
530 563 5.336213 CGTTTATAGGGGTGAGTATATGCGT 60.336 44.000 0.00 0.00 0.00 5.24
531 564 5.100259 CGTTTATAGGGGTGAGTATATGCG 58.900 45.833 0.00 0.00 0.00 4.73
550 583 4.632688 GGTAAGGTATGTGTGTATGCGTTT 59.367 41.667 0.00 0.00 0.00 3.60
553 586 3.128349 GGGTAAGGTATGTGTGTATGCG 58.872 50.000 0.00 0.00 0.00 4.73
557 590 5.779636 TCATAGGGGTAAGGTATGTGTGTA 58.220 41.667 0.00 0.00 0.00 2.90
562 595 3.646637 GTGCTCATAGGGGTAAGGTATGT 59.353 47.826 0.00 0.00 0.00 2.29
564 597 3.116317 AGGTGCTCATAGGGGTAAGGTAT 60.116 47.826 0.00 0.00 0.00 2.73
565 598 2.249214 AGGTGCTCATAGGGGTAAGGTA 59.751 50.000 0.00 0.00 0.00 3.08
569 602 1.760613 CGAAGGTGCTCATAGGGGTAA 59.239 52.381 0.00 0.00 0.00 2.85
574 607 3.526931 TCTTTCGAAGGTGCTCATAGG 57.473 47.619 7.20 0.00 0.00 2.57
586 619 2.448926 TGACGGCTCAATCTTTCGAA 57.551 45.000 0.00 0.00 0.00 3.71
588 621 4.051237 TGATATGACGGCTCAATCTTTCG 58.949 43.478 0.00 0.00 0.00 3.46
595 628 9.868277 AAATTTTAAAATGATATGACGGCTCAA 57.132 25.926 14.04 0.00 0.00 3.02
623 656 3.065510 ACGAGGTGTCTATGATGACTTCG 59.934 47.826 0.00 0.00 39.41 3.79
628 661 3.181500 CGACAACGAGGTGTCTATGATGA 60.181 47.826 17.77 0.00 44.79 2.92
629 662 3.108881 CGACAACGAGGTGTCTATGATG 58.891 50.000 17.77 0.00 44.79 3.07
631 664 2.429478 TCGACAACGAGGTGTCTATGA 58.571 47.619 17.77 6.50 44.79 2.15
632 665 2.913777 TCGACAACGAGGTGTCTATG 57.086 50.000 17.77 4.35 44.79 2.23
646 679 2.466846 GAGGAGACGTTTTTGTCGACA 58.533 47.619 15.76 15.76 43.70 4.35
650 683 1.871676 GTGGGAGGAGACGTTTTTGTC 59.128 52.381 0.00 0.00 39.21 3.18
653 686 1.766496 TCAGTGGGAGGAGACGTTTTT 59.234 47.619 0.00 0.00 0.00 1.94
655 688 1.420430 TTCAGTGGGAGGAGACGTTT 58.580 50.000 0.00 0.00 0.00 3.60
674 707 1.070758 AGGATTTCCAGCGATGCGTAT 59.929 47.619 0.00 0.00 38.89 3.06
675 708 0.464036 AGGATTTCCAGCGATGCGTA 59.536 50.000 0.00 0.00 38.89 4.42
676 709 1.091771 CAGGATTTCCAGCGATGCGT 61.092 55.000 0.00 0.00 38.89 5.24
677 710 0.811219 TCAGGATTTCCAGCGATGCG 60.811 55.000 0.00 0.00 38.89 4.73
678 711 1.382522 TTCAGGATTTCCAGCGATGC 58.617 50.000 0.00 0.00 38.89 3.91
679 712 5.756195 TTATTTCAGGATTTCCAGCGATG 57.244 39.130 0.00 0.00 38.89 3.84
680 713 6.966534 ATTTATTTCAGGATTTCCAGCGAT 57.033 33.333 0.00 0.00 38.89 4.58
681 714 6.826231 TGTATTTATTTCAGGATTTCCAGCGA 59.174 34.615 0.00 0.00 38.89 4.93
682 715 7.026631 TGTATTTATTTCAGGATTTCCAGCG 57.973 36.000 0.00 0.00 38.89 5.18
683 716 7.436376 GCTTGTATTTATTTCAGGATTTCCAGC 59.564 37.037 0.00 0.00 38.89 4.85
684 717 8.469200 TGCTTGTATTTATTTCAGGATTTCCAG 58.531 33.333 0.00 0.00 38.89 3.86
685 718 8.359875 TGCTTGTATTTATTTCAGGATTTCCA 57.640 30.769 0.00 0.00 38.89 3.53
686 719 9.822185 ATTGCTTGTATTTATTTCAGGATTTCC 57.178 29.630 0.00 0.00 0.00 3.13
690 723 9.101655 GCAAATTGCTTGTATTTATTTCAGGAT 57.898 29.630 11.19 0.00 40.96 3.24
691 724 7.275341 CGCAAATTGCTTGTATTTATTTCAGGA 59.725 33.333 16.42 0.00 42.25 3.86
692 725 7.393327 CGCAAATTGCTTGTATTTATTTCAGG 58.607 34.615 16.42 0.00 42.25 3.86
693 726 7.393327 CCGCAAATTGCTTGTATTTATTTCAG 58.607 34.615 16.42 0.00 42.25 3.02
694 727 6.312426 CCCGCAAATTGCTTGTATTTATTTCA 59.688 34.615 16.42 0.00 42.25 2.69
695 728 6.312672 ACCCGCAAATTGCTTGTATTTATTTC 59.687 34.615 16.42 0.00 42.25 2.17
696 729 6.169800 ACCCGCAAATTGCTTGTATTTATTT 58.830 32.000 16.42 0.00 42.25 1.40
697 730 5.729510 ACCCGCAAATTGCTTGTATTTATT 58.270 33.333 16.42 0.00 42.25 1.40
698 731 5.337578 ACCCGCAAATTGCTTGTATTTAT 57.662 34.783 16.42 0.00 42.25 1.40
699 732 4.792521 ACCCGCAAATTGCTTGTATTTA 57.207 36.364 16.42 0.00 42.25 1.40
700 733 3.676291 ACCCGCAAATTGCTTGTATTT 57.324 38.095 16.42 0.00 42.25 1.40
701 734 4.792521 TTACCCGCAAATTGCTTGTATT 57.207 36.364 16.42 0.00 42.25 1.89
702 735 5.337578 AATTACCCGCAAATTGCTTGTAT 57.662 34.783 16.42 1.10 42.25 2.29
703 736 4.792521 AATTACCCGCAAATTGCTTGTA 57.207 36.364 16.42 13.21 42.25 2.41
704 737 3.676291 AATTACCCGCAAATTGCTTGT 57.324 38.095 16.42 14.17 42.25 3.16
705 738 4.690280 AGAAAATTACCCGCAAATTGCTTG 59.310 37.500 16.42 9.02 42.25 4.01
706 739 4.690280 CAGAAAATTACCCGCAAATTGCTT 59.310 37.500 16.42 0.37 42.25 3.91
707 740 4.244862 CAGAAAATTACCCGCAAATTGCT 58.755 39.130 16.42 0.00 42.25 3.91
708 741 3.993736 ACAGAAAATTACCCGCAAATTGC 59.006 39.130 8.09 8.09 40.69 3.56
709 742 4.987912 ACACAGAAAATTACCCGCAAATTG 59.012 37.500 0.00 0.00 0.00 2.32
710 743 5.208463 ACACAGAAAATTACCCGCAAATT 57.792 34.783 0.00 0.00 0.00 1.82
711 744 4.864704 ACACAGAAAATTACCCGCAAAT 57.135 36.364 0.00 0.00 0.00 2.32
712 745 4.657436 AACACAGAAAATTACCCGCAAA 57.343 36.364 0.00 0.00 0.00 3.68
713 746 4.657436 AAACACAGAAAATTACCCGCAA 57.343 36.364 0.00 0.00 0.00 4.85
714 747 4.657436 AAAACACAGAAAATTACCCGCA 57.343 36.364 0.00 0.00 0.00 5.69
736 769 8.628630 AAAACACAGAAAATTCCCTTCAAAAA 57.371 26.923 0.00 0.00 0.00 1.94
737 770 8.628630 AAAAACACAGAAAATTCCCTTCAAAA 57.371 26.923 0.00 0.00 0.00 2.44
761 794 2.609350 CGCCCACGTAGCTAGTAAAAA 58.391 47.619 8.00 0.00 33.53 1.94
762 795 1.736696 GCGCCCACGTAGCTAGTAAAA 60.737 52.381 0.00 0.00 42.83 1.52
763 796 0.179129 GCGCCCACGTAGCTAGTAAA 60.179 55.000 0.00 0.00 42.83 2.01
764 797 1.434696 GCGCCCACGTAGCTAGTAA 59.565 57.895 0.00 0.00 42.83 2.24
765 798 2.827051 CGCGCCCACGTAGCTAGTA 61.827 63.158 0.00 0.00 42.83 1.82
766 799 4.189188 CGCGCCCACGTAGCTAGT 62.189 66.667 0.00 0.00 42.83 2.57
767 800 2.679132 ATTCGCGCCCACGTAGCTAG 62.679 60.000 0.00 2.52 42.83 3.42
768 801 2.777972 ATTCGCGCCCACGTAGCTA 61.778 57.895 0.00 0.00 42.83 3.32
769 802 4.143333 ATTCGCGCCCACGTAGCT 62.143 61.111 0.00 0.00 42.83 3.32
770 803 3.925238 CATTCGCGCCCACGTAGC 61.925 66.667 0.00 0.00 42.83 3.58
771 804 3.261951 CCATTCGCGCCCACGTAG 61.262 66.667 0.00 0.00 42.83 3.51
772 805 4.823419 CCCATTCGCGCCCACGTA 62.823 66.667 0.00 0.00 42.83 3.57
783 816 3.139077 GTCATATTGGACCGACCCATTC 58.861 50.000 0.00 0.00 35.87 2.67
784 817 2.484770 CGTCATATTGGACCGACCCATT 60.485 50.000 0.00 0.00 35.87 3.16
785 818 1.070134 CGTCATATTGGACCGACCCAT 59.930 52.381 0.00 0.00 35.87 4.00
786 819 0.462375 CGTCATATTGGACCGACCCA 59.538 55.000 0.00 0.00 38.00 4.51
787 820 0.878961 GCGTCATATTGGACCGACCC 60.879 60.000 0.00 0.00 38.00 4.46
788 821 1.213094 CGCGTCATATTGGACCGACC 61.213 60.000 0.00 0.00 35.13 4.79
789 822 0.248743 TCGCGTCATATTGGACCGAC 60.249 55.000 5.77 0.00 36.37 4.79
790 823 0.671796 ATCGCGTCATATTGGACCGA 59.328 50.000 5.77 0.00 41.31 4.69
791 824 0.784178 CATCGCGTCATATTGGACCG 59.216 55.000 5.77 0.00 34.24 4.79
792 825 1.148310 CCATCGCGTCATATTGGACC 58.852 55.000 5.77 0.00 34.24 4.46
793 826 2.061773 CTCCATCGCGTCATATTGGAC 58.938 52.381 5.77 0.00 33.12 4.02
794 827 1.000843 CCTCCATCGCGTCATATTGGA 59.999 52.381 5.77 9.37 35.29 3.53
795 828 1.000843 TCCTCCATCGCGTCATATTGG 59.999 52.381 5.77 5.38 0.00 3.16
796 829 2.438868 TCCTCCATCGCGTCATATTG 57.561 50.000 5.77 0.00 0.00 1.90
797 830 3.469008 TTTCCTCCATCGCGTCATATT 57.531 42.857 5.77 0.00 0.00 1.28
798 831 3.469008 TTTTCCTCCATCGCGTCATAT 57.531 42.857 5.77 0.00 0.00 1.78
799 832 2.933906 GTTTTTCCTCCATCGCGTCATA 59.066 45.455 5.77 0.00 0.00 2.15
800 833 1.737793 GTTTTTCCTCCATCGCGTCAT 59.262 47.619 5.77 0.00 0.00 3.06
801 834 1.153353 GTTTTTCCTCCATCGCGTCA 58.847 50.000 5.77 0.00 0.00 4.35
802 835 0.446616 GGTTTTTCCTCCATCGCGTC 59.553 55.000 5.77 0.00 0.00 5.19
803 836 0.036306 AGGTTTTTCCTCCATCGCGT 59.964 50.000 5.77 0.00 44.42 6.01
804 837 2.854522 AGGTTTTTCCTCCATCGCG 58.145 52.632 0.00 0.00 44.42 5.87
814 847 2.031069 GGGTTCTCGCTGAAGGTTTTTC 60.031 50.000 0.00 0.00 35.01 2.29
890 923 1.820519 CCCAAACTGACATGGACATGG 59.179 52.381 15.94 2.42 42.91 3.66
891 924 1.203052 GCCCAAACTGACATGGACATG 59.797 52.381 10.57 10.57 44.15 3.21
892 925 1.549203 GCCCAAACTGACATGGACAT 58.451 50.000 0.00 0.00 39.12 3.06
893 926 0.539438 GGCCCAAACTGACATGGACA 60.539 55.000 0.00 0.00 39.12 4.02
894 927 0.251341 AGGCCCAAACTGACATGGAC 60.251 55.000 0.00 0.00 39.12 4.02
895 928 0.251297 CAGGCCCAAACTGACATGGA 60.251 55.000 0.00 0.00 39.12 3.41
976 1009 2.338500 GGCTCTGTAGAACGGAACTTG 58.662 52.381 0.00 0.00 32.26 3.16
1049 1082 2.453379 TAGTTTCGGTGGGGCGGAAC 62.453 60.000 0.00 0.00 36.38 3.62
1065 1098 1.077265 TCCGACCGGAAACCCTAGT 59.923 57.895 9.46 0.00 42.05 2.57
1346 1379 6.697641 AATACAGTGGAGGAAAGTAAGGAA 57.302 37.500 0.00 0.00 0.00 3.36
1384 1417 2.597903 GGGTTCCCATGCCTCCTC 59.402 66.667 2.59 0.00 0.00 3.71
1418 1451 1.750778 CCCACCAATCCAGGAATTTCG 59.249 52.381 0.00 0.00 0.00 3.46
1424 1457 1.465188 ACCACCCACCAATCCAGGA 60.465 57.895 0.00 0.00 0.00 3.86
1438 1471 1.341531 ACGCTATGAGCCTATGACCAC 59.658 52.381 0.00 0.00 38.18 4.16
1442 1475 6.096673 TCAATAAACGCTATGAGCCTATGA 57.903 37.500 0.00 0.00 38.18 2.15
1443 1476 6.785488 TTCAATAAACGCTATGAGCCTATG 57.215 37.500 0.00 0.00 38.18 2.23
1444 1477 6.128172 GCATTCAATAAACGCTATGAGCCTAT 60.128 38.462 0.00 0.00 38.18 2.57
1445 1478 5.179368 GCATTCAATAAACGCTATGAGCCTA 59.821 40.000 0.00 0.00 38.18 3.93
1446 1479 4.023707 GCATTCAATAAACGCTATGAGCCT 60.024 41.667 0.00 0.00 38.18 4.58
1447 1480 4.023707 AGCATTCAATAAACGCTATGAGCC 60.024 41.667 0.00 0.00 38.18 4.70
1448 1481 4.908156 CAGCATTCAATAAACGCTATGAGC 59.092 41.667 0.00 0.00 38.02 4.26
1449 1482 6.052840 ACAGCATTCAATAAACGCTATGAG 57.947 37.500 0.00 0.00 0.00 2.90
1461 1494 9.502091 TTTTACTACTACTTGACAGCATTCAAT 57.498 29.630 0.88 0.00 34.96 2.57
1491 1524 6.560253 AGCAAAATCGATATGACCATAACC 57.440 37.500 13.63 0.00 0.00 2.85
1518 1551 2.423185 CGCTGGCAAAATGTAGGAATCA 59.577 45.455 0.00 0.00 0.00 2.57
1611 1648 5.863397 ACATAACAAAAATCAAGCATCCACG 59.137 36.000 0.00 0.00 0.00 4.94
1614 1651 8.538409 AGAAACATAACAAAAATCAAGCATCC 57.462 30.769 0.00 0.00 0.00 3.51
1835 1879 5.413523 AGAAAACATATAACACCGTTGGACC 59.586 40.000 0.00 0.00 0.00 4.46
1942 1986 2.259618 CCTTCATCAGTTACGACCACG 58.740 52.381 0.00 0.00 45.75 4.94
2154 2302 6.215636 AGGTAGATTCCAAGAACAGGTAACAT 59.784 38.462 0.00 0.00 41.41 2.71
2221 2438 8.264347 TCCTGAACAATATAAGTTCTGTATGCA 58.736 33.333 17.07 0.00 44.30 3.96
2438 2716 4.019860 ACTGATGACAGCCAGACAGTAAAT 60.020 41.667 12.84 0.00 46.95 1.40
2581 2878 6.322712 ACAAAACCACTAAATACAGCCAAAGA 59.677 34.615 0.00 0.00 0.00 2.52
2649 2946 4.402793 GGAAGACCTGCTGTACTGAATAGA 59.597 45.833 3.61 0.00 0.00 1.98
2888 3193 5.707298 AGAACCTGTATGATTTGTTCCACAG 59.293 40.000 0.00 0.00 36.78 3.66
3027 3332 3.933861 ATGGTGGAGAAGGAACATACC 57.066 47.619 0.00 0.00 0.00 2.73
3276 3587 6.998074 AGAAAGTGGACAGATGAACAATGTAA 59.002 34.615 0.00 0.00 0.00 2.41
3581 4073 3.420300 AGAGCTGCTTGATCCATATGG 57.580 47.619 16.25 16.25 0.00 2.74
3629 4121 8.812329 GCAACACAAACATAACTAAAACATCAA 58.188 29.630 0.00 0.00 0.00 2.57
3634 4126 8.125728 ACATGCAACACAAACATAACTAAAAC 57.874 30.769 0.00 0.00 0.00 2.43
3696 4189 4.458397 ACTCAATTGTCCTATGCCATCTG 58.542 43.478 5.13 0.00 0.00 2.90
3963 4483 8.023128 CAGTATGACAGGAAAACGAAAATGATT 58.977 33.333 0.00 0.00 39.69 2.57
4043 4563 9.575783 TTTCATTGGTCAAAGTTAAACACTAAC 57.424 29.630 0.00 0.00 32.94 2.34
4489 5067 9.646427 GCAACTAAACCCAAACATCATAAATAA 57.354 29.630 0.00 0.00 0.00 1.40
4584 5163 8.134895 ACAATACTATTTTCCAAACATATGCGG 58.865 33.333 1.58 1.18 0.00 5.69
4634 5234 6.800408 CACAATCAACAGAACATCAATCTGAC 59.200 38.462 10.27 0.00 45.74 3.51
4693 5429 5.565455 AAATCAAACCAATGGACCAACAT 57.435 34.783 6.16 0.00 0.00 2.71
4702 5438 5.160641 CCACGACCTAAAATCAAACCAATG 58.839 41.667 0.00 0.00 0.00 2.82
4703 5439 4.219725 CCCACGACCTAAAATCAAACCAAT 59.780 41.667 0.00 0.00 0.00 3.16
4835 5572 3.118956 AGTGTAGCCATCTAAGACACTGC 60.119 47.826 5.24 0.00 32.04 4.40
4882 5619 9.343539 GGATAATAGTATTTCAACAGGAAGCTT 57.656 33.333 0.00 0.00 36.72 3.74
4992 5731 2.097825 GCAAGAATCCTCTGCACCAAT 58.902 47.619 0.00 0.00 30.03 3.16
5436 6175 9.600432 TTTTTGCAGGGGCTAGATATATTATTT 57.400 29.630 0.00 0.00 41.91 1.40
5762 6504 1.001503 AGTGAGAGAGAGCAGGGGG 59.998 63.158 0.00 0.00 0.00 5.40
5782 6524 2.042843 GAGGGAAGAGCCGAGGGA 60.043 66.667 0.00 0.00 37.63 4.20


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

AutoCloner maintained by Alex Coulton.