Multiple sequence alignment - TraesCS5D01G432100

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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 TraesCS5D01G432100 chr5D 100.000 2984 0 0 1 2984 488427171 488424188 0.000000e+00 5511.0
1 TraesCS5D01G432100 chr5A 90.512 2793 152 47 11 2744 609260585 609257847 0.000000e+00 3585.0
2 TraesCS5D01G432100 chr5B 94.233 1890 75 16 667 2539 601407336 601405464 0.000000e+00 2856.0
3 TraesCS5D01G432100 chr5B 88.889 702 34 15 3 670 601410297 601409606 0.000000e+00 824.0
4 TraesCS5D01G432100 chr5B 87.075 147 16 1 2598 2744 601405068 601404925 2.380000e-36 163.0
5 TraesCS5D01G432100 chr5B 97.872 47 1 0 2936 2982 506993040 506992994 6.860000e-12 82.4
6 TraesCS5D01G432100 chr5B 95.918 49 2 0 2931 2979 536889463 536889415 2.470000e-11 80.5
7 TraesCS5D01G432100 chr4B 95.758 165 6 1 1524 1688 10704411 10704248 6.340000e-67 265.0
8 TraesCS5D01G432100 chr4B 97.826 46 1 0 2937 2982 560856762 560856717 2.470000e-11 80.5
9 TraesCS5D01G432100 chr4D 93.333 165 10 1 1524 1688 6078207 6078044 2.970000e-60 243.0
10 TraesCS5D01G432100 chr4D 97.826 46 1 0 2937 2982 163710536 163710491 2.470000e-11 80.5
11 TraesCS5D01G432100 chr4D 100.000 32 0 0 1624 1655 6078042 6078011 3.210000e-05 60.2
12 TraesCS5D01G432100 chr2D 100.000 48 0 0 2937 2984 549854315 549854362 4.100000e-14 89.8
13 TraesCS5D01G432100 chr6D 97.917 48 1 0 2937 2984 438954412 438954365 1.910000e-12 84.2
14 TraesCS5D01G432100 chr6D 95.349 43 2 0 2937 2979 407226219 407226177 5.340000e-08 69.4
15 TraesCS5D01G432100 chr2B 95.918 49 2 0 2936 2984 505795349 505795301 2.470000e-11 80.5
16 TraesCS5D01G432100 chr4A 97.727 44 1 0 2939 2982 669991922 669991879 3.190000e-10 76.8


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 TraesCS5D01G432100 chr5D 488424188 488427171 2983 True 5511 5511 100.000000 1 2984 1 chr5D.!!$R1 2983
1 TraesCS5D01G432100 chr5A 609257847 609260585 2738 True 3585 3585 90.512000 11 2744 1 chr5A.!!$R1 2733
2 TraesCS5D01G432100 chr5B 601404925 601410297 5372 True 1281 2856 90.065667 3 2744 3 chr5B.!!$R3 2741

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
179 205 1.06643 TCTAACCGCAAACTGGCTAGG 60.066 52.381 0.85 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 4310 0.821517 CCGGCGGCCATATATACTGA 59.178 55.0 20.71 0.0 0.0 3.41 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
35 36 5.640147 TGTCCATATTTCAAAACCTGGAGT 58.360 37.500 0.00 0.00 34.41 3.85
37 38 6.884295 TGTCCATATTTCAAAACCTGGAGTAG 59.116 38.462 0.00 0.00 34.41 2.57
49 50 4.599047 CCTGGAGTAGGTGATCTTCATC 57.401 50.000 0.00 0.00 42.00 2.92
63 64 5.361857 TGATCTTCATCAGCTGTGACATCTA 59.638 40.000 14.67 8.57 33.80 1.98
125 144 5.530171 TCACGTAGTATGTTCTATCCTCACC 59.470 44.000 0.00 0.00 41.61 4.02
126 145 5.298527 CACGTAGTATGTTCTATCCTCACCA 59.701 44.000 0.00 0.00 41.61 4.17
170 196 1.266718 CAAGCAGCTTCTAACCGCAAA 59.733 47.619 4.07 0.00 0.00 3.68
176 202 1.523758 CTTCTAACCGCAAACTGGCT 58.476 50.000 0.00 0.00 0.00 4.75
179 205 1.066430 TCTAACCGCAAACTGGCTAGG 60.066 52.381 0.85 0.00 0.00 3.02
188 214 1.187087 AACTGGCTAGGAGGACTTCG 58.813 55.000 0.85 0.00 0.00 3.79
217 243 2.610438 AGCCATGGGAAATGTTGAGT 57.390 45.000 15.13 0.00 0.00 3.41
371 397 2.622064 AATTAGGTCTGGCATCGGAC 57.378 50.000 0.00 0.00 46.01 4.79
445 473 3.179443 TGGTCTCTGGCAATTCGATAC 57.821 47.619 0.00 0.00 0.00 2.24
466 497 7.692291 CGATACATGTTGTTCCAGTGATTTTAC 59.308 37.037 2.30 0.00 0.00 2.01
467 498 6.959639 ACATGTTGTTCCAGTGATTTTACT 57.040 33.333 0.00 0.00 0.00 2.24
468 499 6.738114 ACATGTTGTTCCAGTGATTTTACTG 58.262 36.000 0.00 0.00 45.93 2.74
471 502 3.472652 TGTTCCAGTGATTTTACTGCGT 58.527 40.909 0.00 0.00 45.21 5.24
472 503 3.880490 TGTTCCAGTGATTTTACTGCGTT 59.120 39.130 0.00 0.00 45.21 4.84
473 504 4.336993 TGTTCCAGTGATTTTACTGCGTTT 59.663 37.500 0.00 0.00 45.21 3.60
474 505 5.527951 TGTTCCAGTGATTTTACTGCGTTTA 59.472 36.000 0.00 0.00 45.21 2.01
475 506 6.205853 TGTTCCAGTGATTTTACTGCGTTTAT 59.794 34.615 0.00 0.00 45.21 1.40
476 507 7.388224 TGTTCCAGTGATTTTACTGCGTTTATA 59.612 33.333 0.00 0.00 45.21 0.98
477 508 8.395633 GTTCCAGTGATTTTACTGCGTTTATAT 58.604 33.333 0.00 0.00 45.21 0.86
478 509 8.138365 TCCAGTGATTTTACTGCGTTTATATC 57.862 34.615 0.00 0.00 45.21 1.63
479 510 7.985184 TCCAGTGATTTTACTGCGTTTATATCT 59.015 33.333 0.00 0.00 45.21 1.98
480 511 8.064222 CCAGTGATTTTACTGCGTTTATATCTG 58.936 37.037 0.00 0.00 45.21 2.90
481 512 8.817100 CAGTGATTTTACTGCGTTTATATCTGA 58.183 33.333 0.00 0.00 41.31 3.27
716 3026 6.595716 AGGACATACTTTACTTTCAGTGATGC 59.404 38.462 0.00 0.00 0.00 3.91
773 3087 8.688336 TTAACGACAAAAATATGAATATCGCG 57.312 30.769 0.00 0.00 0.00 5.87
787 3102 1.139989 ATCGCGTGTTGTCTCTGTTG 58.860 50.000 5.77 0.00 0.00 3.33
789 3104 1.151777 CGCGTGTTGTCTCTGTTGGT 61.152 55.000 0.00 0.00 0.00 3.67
792 3107 1.668419 GTGTTGTCTCTGTTGGTGCT 58.332 50.000 0.00 0.00 0.00 4.40
793 3108 2.801699 CGTGTTGTCTCTGTTGGTGCTA 60.802 50.000 0.00 0.00 0.00 3.49
803 3118 1.270305 TGTTGGTGCTACTGCTGAGTC 60.270 52.381 0.00 0.00 40.48 3.36
808 3124 1.107114 TGCTACTGCTGAGTCTAGCC 58.893 55.000 10.72 0.00 43.02 3.93
811 3127 2.374184 CTACTGCTGAGTCTAGCCAGT 58.626 52.381 10.72 13.84 43.02 4.00
858 3174 1.607178 CCCAATGAGCAGCACCCAA 60.607 57.895 0.00 0.00 0.00 4.12
914 3230 1.833630 TGGATGAGATTCCACTTCGCT 59.166 47.619 0.00 0.00 40.90 4.93
1129 3447 2.358737 AGCCAAAGAAGTCGCCGG 60.359 61.111 0.00 0.00 0.00 6.13
1863 4181 1.338107 TCACCTTCAGCCTCGAGAAA 58.662 50.000 15.71 1.78 0.00 2.52
1987 4308 0.254178 GGGAAGGAGCAGATGAAGCA 59.746 55.000 0.00 0.00 0.00 3.91
1989 4310 2.652590 GGAAGGAGCAGATGAAGCATT 58.347 47.619 0.00 0.00 0.00 3.56
2143 4464 0.251121 TCAATGGTTGATGCCACGGT 60.251 50.000 0.00 0.00 41.94 4.83
2183 4511 6.800892 GTGAAGTGATGATGCTTCTTTCTTTC 59.199 38.462 0.88 7.26 41.05 2.62
2184 4512 5.893897 AGTGATGATGCTTCTTTCTTTCC 57.106 39.130 0.88 0.00 0.00 3.13
2205 4538 9.315363 CTTTCCTAGAGGATGTATAAGTACCAT 57.685 37.037 0.00 0.00 44.98 3.55
2206 4539 9.670442 TTTCCTAGAGGATGTATAAGTACCATT 57.330 33.333 0.00 0.00 44.98 3.16
2207 4540 8.651589 TCCTAGAGGATGTATAAGTACCATTG 57.348 38.462 0.00 0.00 39.78 2.82
2208 4541 8.232412 TCCTAGAGGATGTATAAGTACCATTGT 58.768 37.037 0.00 0.00 39.78 2.71
2209 4542 9.529823 CCTAGAGGATGTATAAGTACCATTGTA 57.470 37.037 0.00 0.00 37.39 2.41
2223 4556 7.303634 GTACCATTGTACCAATGAAGTAGTG 57.696 40.000 16.42 3.02 41.27 2.74
2251 4605 5.047847 GTGCCATGTGTATAGTGTTCGTAT 58.952 41.667 0.00 0.00 0.00 3.06
2252 4606 6.183360 TGTGCCATGTGTATAGTGTTCGTATA 60.183 38.462 0.00 0.00 0.00 1.47
2296 4651 4.020218 AGTCATGGAGGAAAGTTCAATCGA 60.020 41.667 0.00 0.00 0.00 3.59
2348 4703 2.309528 AGCAGAGTGAACGTGAAACA 57.690 45.000 0.00 0.00 35.74 2.83
2359 4714 1.686052 ACGTGAAACATTGTGGCCATT 59.314 42.857 9.72 0.00 35.74 3.16
2360 4715 2.060284 CGTGAAACATTGTGGCCATTG 58.940 47.619 9.72 10.36 35.74 2.82
2429 4784 1.767759 AAGTTTGCAACTGGACAGCT 58.232 45.000 0.00 0.00 41.91 4.24
2474 4830 2.669569 GCTCTGTCGCAGGCCAAA 60.670 61.111 5.01 0.00 31.51 3.28
2482 4838 2.644992 GCAGGCCAAACGGTTCTG 59.355 61.111 5.01 0.00 33.16 3.02
2494 4850 2.493713 CGGTTCTGGTAGAGGAATCG 57.506 55.000 0.00 0.00 39.18 3.34
2511 4867 1.118965 TCGAAGGGTGGAAGCAGTGA 61.119 55.000 0.00 0.00 34.77 3.41
2518 4874 1.032014 GTGGAAGCAGTGAAAGGCAA 58.968 50.000 0.00 0.00 0.00 4.52
2527 4883 1.217942 AGTGAAAGGCAAGAAGGGGTT 59.782 47.619 0.00 0.00 0.00 4.11
2528 4884 2.039418 GTGAAAGGCAAGAAGGGGTTT 58.961 47.619 0.00 0.00 0.00 3.27
2645 5338 0.250038 CCGGCTGCTACATGCTATGT 60.250 55.000 0.00 6.93 46.92 2.29
2646 5339 0.863799 CGGCTGCTACATGCTATGTG 59.136 55.000 10.77 4.25 44.60 3.21
2647 5340 0.590195 GGCTGCTACATGCTATGTGC 59.410 55.000 10.77 11.62 44.60 4.57
2749 5442 3.620785 GCTCGCCTCCCCATCGAT 61.621 66.667 0.00 0.00 0.00 3.59
2750 5443 2.341543 CTCGCCTCCCCATCGATG 59.658 66.667 18.76 18.76 0.00 3.84
2752 5445 3.550431 CGCCTCCCCATCGATGGT 61.550 66.667 36.09 0.00 46.65 3.55
2753 5446 2.427753 GCCTCCCCATCGATGGTC 59.572 66.667 36.09 18.98 46.65 4.02
2754 5447 2.737180 CCTCCCCATCGATGGTCG 59.263 66.667 36.09 26.95 46.65 4.79
2755 5448 2.134287 CCTCCCCATCGATGGTCGT 61.134 63.158 36.09 0.00 46.65 4.34
2756 5449 1.068083 CTCCCCATCGATGGTCGTG 59.932 63.158 36.09 23.86 46.65 4.35
2757 5450 2.588877 CCCCATCGATGGTCGTGC 60.589 66.667 36.09 0.00 46.65 5.34
2758 5451 2.501128 CCCATCGATGGTCGTGCT 59.499 61.111 36.09 0.00 46.65 4.40
2759 5452 1.592669 CCCATCGATGGTCGTGCTC 60.593 63.158 36.09 0.00 46.65 4.26
2760 5453 1.439228 CCATCGATGGTCGTGCTCT 59.561 57.895 32.39 0.00 43.05 4.09
2761 5454 0.596083 CCATCGATGGTCGTGCTCTC 60.596 60.000 32.39 0.00 43.05 3.20
2762 5455 0.596083 CATCGATGGTCGTGCTCTCC 60.596 60.000 17.96 0.00 41.35 3.71
2763 5456 0.753479 ATCGATGGTCGTGCTCTCCT 60.753 55.000 0.00 0.00 41.35 3.69
2764 5457 0.965866 TCGATGGTCGTGCTCTCCTT 60.966 55.000 0.00 0.00 41.35 3.36
2765 5458 0.526524 CGATGGTCGTGCTCTCCTTC 60.527 60.000 0.00 0.00 34.72 3.46
2766 5459 0.179097 GATGGTCGTGCTCTCCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
2767 5460 1.617947 ATGGTCGTGCTCTCCTTCCC 61.618 60.000 0.00 0.00 0.00 3.97
2768 5461 2.182030 GTCGTGCTCTCCTTCCCG 59.818 66.667 0.00 0.00 0.00 5.14
2769 5462 3.760035 TCGTGCTCTCCTTCCCGC 61.760 66.667 0.00 0.00 0.00 6.13
2770 5463 4.821589 CGTGCTCTCCTTCCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
2771 5464 4.475135 GTGCTCTCCTTCCCGCCC 62.475 72.222 0.00 0.00 0.00 6.13
2812 5505 2.886124 GCTAAGCGCCTCGTCACC 60.886 66.667 2.29 0.00 0.00 4.02
2813 5506 2.571757 CTAAGCGCCTCGTCACCA 59.428 61.111 2.29 0.00 0.00 4.17
2814 5507 1.805945 CTAAGCGCCTCGTCACCAC 60.806 63.158 2.29 0.00 0.00 4.16
2815 5508 2.214181 CTAAGCGCCTCGTCACCACT 62.214 60.000 2.29 0.00 0.00 4.00
2816 5509 2.209064 TAAGCGCCTCGTCACCACTC 62.209 60.000 2.29 0.00 0.00 3.51
2817 5510 4.057428 GCGCCTCGTCACCACTCT 62.057 66.667 0.00 0.00 0.00 3.24
2818 5511 2.126307 CGCCTCGTCACCACTCTG 60.126 66.667 0.00 0.00 0.00 3.35
2819 5512 2.920645 CGCCTCGTCACCACTCTGT 61.921 63.158 0.00 0.00 0.00 3.41
2820 5513 1.583495 CGCCTCGTCACCACTCTGTA 61.583 60.000 0.00 0.00 0.00 2.74
2821 5514 0.171455 GCCTCGTCACCACTCTGTAG 59.829 60.000 0.00 0.00 0.00 2.74
2822 5515 0.811915 CCTCGTCACCACTCTGTAGG 59.188 60.000 0.00 0.00 0.00 3.18
2823 5516 1.535833 CTCGTCACCACTCTGTAGGT 58.464 55.000 0.00 0.00 39.10 3.08
2824 5517 2.617276 CCTCGTCACCACTCTGTAGGTA 60.617 54.545 0.00 0.00 36.07 3.08
2825 5518 2.678836 CTCGTCACCACTCTGTAGGTAG 59.321 54.545 0.00 0.00 36.07 3.18
2826 5519 2.303890 TCGTCACCACTCTGTAGGTAGA 59.696 50.000 0.00 0.00 36.07 2.59
2827 5520 3.079578 CGTCACCACTCTGTAGGTAGAA 58.920 50.000 0.00 0.00 36.07 2.10
2828 5521 3.127203 CGTCACCACTCTGTAGGTAGAAG 59.873 52.174 0.00 0.00 36.07 2.85
2829 5522 4.333690 GTCACCACTCTGTAGGTAGAAGA 58.666 47.826 0.00 0.00 36.07 2.87
2830 5523 4.396790 GTCACCACTCTGTAGGTAGAAGAG 59.603 50.000 0.00 0.00 42.59 2.85
2832 5525 4.767928 CACCACTCTGTAGGTAGAAGAGTT 59.232 45.833 1.90 0.00 46.59 3.01
2833 5526 5.944599 CACCACTCTGTAGGTAGAAGAGTTA 59.055 44.000 1.90 0.00 46.59 2.24
2834 5527 5.945191 ACCACTCTGTAGGTAGAAGAGTTAC 59.055 44.000 1.90 0.00 46.59 2.50
2835 5528 5.944599 CCACTCTGTAGGTAGAAGAGTTACA 59.055 44.000 1.90 0.00 46.59 2.41
2836 5529 6.603997 CCACTCTGTAGGTAGAAGAGTTACAT 59.396 42.308 1.90 0.00 46.59 2.29
2837 5530 7.122948 CCACTCTGTAGGTAGAAGAGTTACATT 59.877 40.741 1.90 0.00 46.59 2.71
2838 5531 9.175312 CACTCTGTAGGTAGAAGAGTTACATTA 57.825 37.037 1.90 0.00 46.59 1.90
2839 5532 9.750783 ACTCTGTAGGTAGAAGAGTTACATTAA 57.249 33.333 0.00 0.00 46.59 1.40
2841 5534 9.186837 TCTGTAGGTAGAAGAGTTACATTAAGG 57.813 37.037 0.00 0.00 0.00 2.69
2842 5535 9.186837 CTGTAGGTAGAAGAGTTACATTAAGGA 57.813 37.037 0.00 0.00 0.00 3.36
2843 5536 8.964772 TGTAGGTAGAAGAGTTACATTAAGGAC 58.035 37.037 0.00 0.00 0.00 3.85
2844 5537 7.421087 AGGTAGAAGAGTTACATTAAGGACC 57.579 40.000 0.00 0.00 0.00 4.46
2845 5538 6.383436 AGGTAGAAGAGTTACATTAAGGACCC 59.617 42.308 0.00 0.00 0.00 4.46
2846 5539 5.695424 AGAAGAGTTACATTAAGGACCCC 57.305 43.478 0.00 0.00 0.00 4.95
2847 5540 4.473922 AGAAGAGTTACATTAAGGACCCCC 59.526 45.833 0.00 0.00 0.00 5.40
2863 5556 3.711782 CCCTCCCCTCCCCCTCTT 61.712 72.222 0.00 0.00 0.00 2.85
2864 5557 2.040359 CCTCCCCTCCCCCTCTTC 60.040 72.222 0.00 0.00 0.00 2.87
2865 5558 2.040359 CTCCCCTCCCCCTCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
2866 5559 3.707189 TCCCCTCCCCCTCTTCCC 61.707 72.222 0.00 0.00 0.00 3.97
2868 5561 4.089757 CCCTCCCCCTCTTCCCGA 62.090 72.222 0.00 0.00 0.00 5.14
2869 5562 2.287251 CCTCCCCCTCTTCCCGAT 59.713 66.667 0.00 0.00 0.00 4.18
2870 5563 1.547248 CCTCCCCCTCTTCCCGATA 59.453 63.158 0.00 0.00 0.00 2.92
2871 5564 0.543174 CCTCCCCCTCTTCCCGATAG 60.543 65.000 0.00 0.00 0.00 2.08
2888 5581 5.456192 CGATAGGTGTGAAAGCAAACTAG 57.544 43.478 0.00 0.00 32.59 2.57
2889 5582 4.201724 CGATAGGTGTGAAAGCAAACTAGC 60.202 45.833 0.00 0.00 32.59 3.42
2891 5584 3.142174 AGGTGTGAAAGCAAACTAGCTC 58.858 45.455 0.00 0.00 45.89 4.09
2892 5585 2.226674 GGTGTGAAAGCAAACTAGCTCC 59.773 50.000 0.00 0.00 45.89 4.70
2893 5586 2.096218 GTGTGAAAGCAAACTAGCTCCG 60.096 50.000 0.00 0.00 45.89 4.63
2894 5587 2.224185 TGTGAAAGCAAACTAGCTCCGA 60.224 45.455 0.00 0.00 45.89 4.55
2895 5588 2.413453 GTGAAAGCAAACTAGCTCCGAG 59.587 50.000 0.00 0.00 45.89 4.63
2896 5589 2.299013 TGAAAGCAAACTAGCTCCGAGA 59.701 45.455 0.00 0.00 45.89 4.04
2897 5590 3.244078 TGAAAGCAAACTAGCTCCGAGAA 60.244 43.478 0.00 0.00 45.89 2.87
2898 5591 2.371910 AGCAAACTAGCTCCGAGAAC 57.628 50.000 0.00 0.00 42.18 3.01
2899 5592 1.066787 AGCAAACTAGCTCCGAGAACC 60.067 52.381 0.00 0.00 42.18 3.62
2900 5593 1.337823 GCAAACTAGCTCCGAGAACCA 60.338 52.381 0.00 0.00 0.00 3.67
2901 5594 2.611518 CAAACTAGCTCCGAGAACCAG 58.388 52.381 0.00 0.00 0.00 4.00
2902 5595 0.533032 AACTAGCTCCGAGAACCAGC 59.467 55.000 0.00 0.00 0.00 4.85
2903 5596 0.612174 ACTAGCTCCGAGAACCAGCA 60.612 55.000 0.00 0.00 35.46 4.41
2904 5597 0.102120 CTAGCTCCGAGAACCAGCAG 59.898 60.000 0.00 0.00 35.46 4.24
2905 5598 1.949847 TAGCTCCGAGAACCAGCAGC 61.950 60.000 0.00 0.00 35.46 5.25
2906 5599 2.977178 CTCCGAGAACCAGCAGCT 59.023 61.111 0.00 0.00 0.00 4.24
2907 5600 1.294780 CTCCGAGAACCAGCAGCTT 59.705 57.895 0.00 0.00 0.00 3.74
2908 5601 0.532573 CTCCGAGAACCAGCAGCTTA 59.467 55.000 0.00 0.00 0.00 3.09
2909 5602 0.532573 TCCGAGAACCAGCAGCTTAG 59.467 55.000 0.00 0.00 0.00 2.18
2910 5603 0.460987 CCGAGAACCAGCAGCTTAGG 60.461 60.000 0.00 0.00 0.00 2.69
2911 5604 0.247736 CGAGAACCAGCAGCTTAGGT 59.752 55.000 0.00 0.00 37.20 3.08
2912 5605 1.476891 CGAGAACCAGCAGCTTAGGTA 59.523 52.381 4.86 0.00 34.63 3.08
2913 5606 2.101582 CGAGAACCAGCAGCTTAGGTAT 59.898 50.000 4.86 0.00 34.63 2.73
2914 5607 3.462021 GAGAACCAGCAGCTTAGGTATG 58.538 50.000 4.86 0.00 34.63 2.39
2915 5608 3.107601 AGAACCAGCAGCTTAGGTATGA 58.892 45.455 4.86 0.00 34.63 2.15
2916 5609 3.519510 AGAACCAGCAGCTTAGGTATGAA 59.480 43.478 4.86 0.00 34.63 2.57
2917 5610 3.268023 ACCAGCAGCTTAGGTATGAAC 57.732 47.619 2.46 0.00 32.92 3.18
2918 5611 2.571653 ACCAGCAGCTTAGGTATGAACA 59.428 45.455 2.46 0.00 32.92 3.18
2919 5612 3.201290 CCAGCAGCTTAGGTATGAACAG 58.799 50.000 0.00 0.00 0.00 3.16
2920 5613 3.118629 CCAGCAGCTTAGGTATGAACAGA 60.119 47.826 0.00 0.00 0.00 3.41
2921 5614 4.507710 CAGCAGCTTAGGTATGAACAGAA 58.492 43.478 0.00 0.00 0.00 3.02
2922 5615 4.937620 CAGCAGCTTAGGTATGAACAGAAA 59.062 41.667 0.00 0.00 0.00 2.52
2923 5616 4.938226 AGCAGCTTAGGTATGAACAGAAAC 59.062 41.667 0.00 0.00 0.00 2.78
2924 5617 4.095036 GCAGCTTAGGTATGAACAGAAACC 59.905 45.833 0.00 0.00 0.00 3.27
2925 5618 5.245531 CAGCTTAGGTATGAACAGAAACCA 58.754 41.667 0.00 0.00 34.29 3.67
2926 5619 5.705441 CAGCTTAGGTATGAACAGAAACCAA 59.295 40.000 0.00 0.00 34.29 3.67
2927 5620 5.705905 AGCTTAGGTATGAACAGAAACCAAC 59.294 40.000 0.00 0.00 34.29 3.77
2928 5621 5.705905 GCTTAGGTATGAACAGAAACCAACT 59.294 40.000 0.00 0.00 34.29 3.16
2929 5622 6.206829 GCTTAGGTATGAACAGAAACCAACTT 59.793 38.462 0.00 0.00 34.29 2.66
2930 5623 7.255486 GCTTAGGTATGAACAGAAACCAACTTT 60.255 37.037 0.00 0.00 34.29 2.66
2931 5624 6.391227 AGGTATGAACAGAAACCAACTTTG 57.609 37.500 0.00 0.00 34.29 2.77
2932 5625 6.126409 AGGTATGAACAGAAACCAACTTTGA 58.874 36.000 0.00 0.00 34.29 2.69
2933 5626 6.263168 AGGTATGAACAGAAACCAACTTTGAG 59.737 38.462 0.00 0.00 34.29 3.02
2934 5627 6.262273 GGTATGAACAGAAACCAACTTTGAGA 59.738 38.462 0.00 0.00 32.04 3.27
2935 5628 6.773976 ATGAACAGAAACCAACTTTGAGAA 57.226 33.333 0.00 0.00 0.00 2.87
2936 5629 6.773976 TGAACAGAAACCAACTTTGAGAAT 57.226 33.333 0.00 0.00 0.00 2.40
2937 5630 7.169158 TGAACAGAAACCAACTTTGAGAATT 57.831 32.000 0.00 0.00 0.00 2.17
2938 5631 8.287439 TGAACAGAAACCAACTTTGAGAATTA 57.713 30.769 0.00 0.00 0.00 1.40
2939 5632 8.405531 TGAACAGAAACCAACTTTGAGAATTAG 58.594 33.333 0.00 0.00 0.00 1.73
2940 5633 8.519799 AACAGAAACCAACTTTGAGAATTAGA 57.480 30.769 0.00 0.00 0.00 2.10
2941 5634 8.159344 ACAGAAACCAACTTTGAGAATTAGAG 57.841 34.615 0.00 0.00 0.00 2.43
2942 5635 7.229506 ACAGAAACCAACTTTGAGAATTAGAGG 59.770 37.037 0.00 0.00 0.00 3.69
2943 5636 7.445402 CAGAAACCAACTTTGAGAATTAGAGGA 59.555 37.037 0.00 0.00 0.00 3.71
2944 5637 8.166726 AGAAACCAACTTTGAGAATTAGAGGAT 58.833 33.333 0.00 0.00 0.00 3.24
2945 5638 7.929941 AACCAACTTTGAGAATTAGAGGATC 57.070 36.000 0.00 0.00 0.00 3.36
2957 5650 1.066587 GAGGATCTCCAGCCGTTCG 59.933 63.158 0.00 0.00 38.89 3.95
2958 5651 2.107141 GGATCTCCAGCCGTTCGG 59.893 66.667 6.90 6.90 35.64 4.30
2979 5672 3.747976 CCCAGGGCGCCGAAAAAG 61.748 66.667 22.54 5.42 0.00 2.27
2980 5673 2.671619 CCAGGGCGCCGAAAAAGA 60.672 61.111 22.54 0.00 0.00 2.52
2981 5674 2.690778 CCAGGGCGCCGAAAAAGAG 61.691 63.158 22.54 3.24 0.00 2.85
2982 5675 1.966451 CAGGGCGCCGAAAAAGAGT 60.966 57.895 22.54 0.00 0.00 3.24
2983 5676 1.966451 AGGGCGCCGAAAAAGAGTG 60.966 57.895 22.54 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.691409 TATGGACAACAGCTACCAGC 57.309 50.000 0.00 0.00 42.84 4.85
1 2 5.185454 TGAAATATGGACAACAGCTACCAG 58.815 41.667 0.00 0.00 35.84 4.00
35 36 4.026052 TCACAGCTGATGAAGATCACCTA 58.974 43.478 23.35 0.00 34.71 3.08
37 38 2.935201 GTCACAGCTGATGAAGATCACC 59.065 50.000 23.35 3.31 34.71 4.02
45 46 3.065925 CGTCTAGATGTCACAGCTGATGA 59.934 47.826 23.35 17.05 30.76 2.92
49 50 1.800655 GCCGTCTAGATGTCACAGCTG 60.801 57.143 13.48 13.48 30.76 4.24
105 106 7.783042 AGTTTGGTGAGGATAGAACATACTAC 58.217 38.462 0.00 0.00 0.00 2.73
125 144 1.151668 CCTGCGAAGACCAGAGTTTG 58.848 55.000 0.00 0.00 32.03 2.93
126 145 1.048601 TCCTGCGAAGACCAGAGTTT 58.951 50.000 0.00 0.00 32.03 2.66
170 196 0.684805 CCGAAGTCCTCCTAGCCAGT 60.685 60.000 0.00 0.00 0.00 4.00
176 202 2.297698 TGTTCACCGAAGTCCTCCTA 57.702 50.000 0.00 0.00 0.00 2.94
179 205 2.031944 GCTTTTGTTCACCGAAGTCCTC 60.032 50.000 0.00 0.00 0.00 3.71
188 214 1.337118 TCCCATGGCTTTTGTTCACC 58.663 50.000 6.09 0.00 0.00 4.02
217 243 1.279271 GCTGGGTAGGAAGAAGCTTCA 59.721 52.381 27.57 4.18 0.00 3.02
371 397 9.289303 CAAATGGATTATTAACTGGTTTCTTCG 57.711 33.333 0.00 0.00 0.00 3.79
445 473 5.630680 GCAGTAAAATCACTGGAACAACATG 59.369 40.000 5.49 0.00 45.03 3.21
466 497 5.971792 TCGACTCTTTCAGATATAAACGCAG 59.028 40.000 0.00 0.00 0.00 5.18
467 498 5.886992 TCGACTCTTTCAGATATAAACGCA 58.113 37.500 0.00 0.00 0.00 5.24
468 499 6.994868 ATCGACTCTTTCAGATATAAACGC 57.005 37.500 0.00 0.00 0.00 4.84
730 3040 7.646130 TGTCGTTAATAAAAGTGAAAAAGGCTG 59.354 33.333 0.00 0.00 0.00 4.85
765 3079 3.232213 ACAGAGACAACACGCGATATT 57.768 42.857 15.93 0.00 0.00 1.28
766 3080 2.923655 CAACAGAGACAACACGCGATAT 59.076 45.455 15.93 0.00 0.00 1.63
773 3087 1.668419 AGCACCAACAGAGACAACAC 58.332 50.000 0.00 0.00 0.00 3.32
787 3102 1.202359 GCTAGACTCAGCAGTAGCACC 60.202 57.143 0.00 0.00 45.49 5.01
789 3104 1.107114 GGCTAGACTCAGCAGTAGCA 58.893 55.000 0.00 0.00 43.67 3.49
792 3107 2.095461 CACTGGCTAGACTCAGCAGTA 58.905 52.381 3.17 0.00 43.67 2.74
793 3108 0.894141 CACTGGCTAGACTCAGCAGT 59.106 55.000 3.17 0.00 43.67 4.40
803 3118 2.093764 CCAGAAAGAGACCACTGGCTAG 60.094 54.545 0.00 0.00 42.30 3.42
808 3124 3.475566 TGAACCAGAAAGAGACCACTG 57.524 47.619 0.00 0.00 0.00 3.66
811 3127 5.532406 CAGATTTTGAACCAGAAAGAGACCA 59.468 40.000 0.00 0.00 0.00 4.02
858 3174 4.760047 GGTGATGACCTGGCGCGT 62.760 66.667 8.43 0.00 39.47 6.01
914 3230 2.923426 GAAGACGATGATGGGGCGCA 62.923 60.000 10.83 6.74 0.00 6.09
949 3267 4.515361 AGAGCTTCTTGATCTGATGGTTG 58.485 43.478 0.00 0.00 40.31 3.77
1918 4236 1.676635 TGGCCTTGAGCATGTCAGC 60.677 57.895 3.32 0.00 46.50 4.26
1920 4238 1.303561 GGTGGCCTTGAGCATGTCA 60.304 57.895 3.32 0.00 46.50 3.58
1969 4287 2.345124 ATGCTTCATCTGCTCCTTCC 57.655 50.000 0.00 0.00 0.00 3.46
1987 4308 2.158957 CCGGCGGCCATATATACTGAAT 60.159 50.000 20.71 0.00 0.00 2.57
1989 4310 0.821517 CCGGCGGCCATATATACTGA 59.178 55.000 20.71 0.00 0.00 3.41
2063 4384 3.252215 GTGGTAAGTGTACAAAGCATGCA 59.748 43.478 21.98 0.00 31.21 3.96
2064 4385 3.365969 GGTGGTAAGTGTACAAAGCATGC 60.366 47.826 10.51 10.51 31.21 4.06
2065 4386 3.120338 CGGTGGTAAGTGTACAAAGCATG 60.120 47.826 0.00 0.00 31.21 4.06
2066 4387 3.071479 CGGTGGTAAGTGTACAAAGCAT 58.929 45.455 0.00 0.00 31.21 3.79
2143 4464 2.628178 ACTTCACGATGTGAGTCAGGAA 59.372 45.455 0.00 0.00 43.69 3.36
2183 4511 8.423906 ACAATGGTACTTATACATCCTCTAGG 57.576 38.462 0.00 0.00 32.40 3.02
2206 4539 4.534500 ACATCCCACTACTTCATTGGTACA 59.466 41.667 0.00 0.00 0.00 2.90
2207 4540 4.876107 CACATCCCACTACTTCATTGGTAC 59.124 45.833 0.00 0.00 0.00 3.34
2208 4541 4.625324 GCACATCCCACTACTTCATTGGTA 60.625 45.833 0.00 0.00 0.00 3.25
2209 4542 3.873801 GCACATCCCACTACTTCATTGGT 60.874 47.826 0.00 0.00 0.00 3.67
2210 4543 2.684881 GCACATCCCACTACTTCATTGG 59.315 50.000 0.00 0.00 0.00 3.16
2211 4544 2.684881 GGCACATCCCACTACTTCATTG 59.315 50.000 0.00 0.00 0.00 2.82
2212 4545 2.308570 TGGCACATCCCACTACTTCATT 59.691 45.455 0.00 0.00 0.00 2.57
2251 4605 7.448777 TGACTTTATTTACAGCCCAACATGTTA 59.551 33.333 11.53 0.00 0.00 2.41
2252 4606 6.266558 TGACTTTATTTACAGCCCAACATGTT 59.733 34.615 4.92 4.92 0.00 2.71
2348 4703 6.564557 AAAAATAGATCCAATGGCCACAAT 57.435 33.333 8.16 0.00 0.00 2.71
2359 4714 7.004086 AGCCATCCGATTTAAAAATAGATCCA 58.996 34.615 0.00 0.00 0.00 3.41
2360 4715 7.174946 TGAGCCATCCGATTTAAAAATAGATCC 59.825 37.037 0.00 0.00 0.00 3.36
2397 4752 3.408634 TGCAAACTTACACTAGGGAAGC 58.591 45.455 0.00 0.00 0.00 3.86
2464 4820 2.978010 AGAACCGTTTGGCCTGCG 60.978 61.111 3.32 5.71 39.70 5.18
2474 4830 1.749634 CGATTCCTCTACCAGAACCGT 59.250 52.381 0.00 0.00 0.00 4.83
2482 4838 1.413077 CCACCCTTCGATTCCTCTACC 59.587 57.143 0.00 0.00 0.00 3.18
2494 4850 1.882623 CTTTCACTGCTTCCACCCTTC 59.117 52.381 0.00 0.00 0.00 3.46
2511 4867 2.319844 CTCAAACCCCTTCTTGCCTTT 58.680 47.619 0.00 0.00 0.00 3.11
2518 4874 1.128188 ACCGAGCTCAAACCCCTTCT 61.128 55.000 15.40 0.00 0.00 2.85
2527 4883 3.706373 GGAGGCCACCGAGCTCAA 61.706 66.667 15.40 0.00 0.00 3.02
2645 5338 3.399181 CCGGGTAAGGGAGCAGCA 61.399 66.667 0.00 0.00 0.00 4.41
2646 5339 3.400054 ACCGGGTAAGGGAGCAGC 61.400 66.667 6.32 0.00 35.02 5.25
2647 5340 2.584608 CACCGGGTAAGGGAGCAG 59.415 66.667 6.32 0.00 35.02 4.24
2744 5437 0.753479 AGGAGAGCACGACCATCGAT 60.753 55.000 5.04 0.00 43.74 3.59
2745 5438 0.965866 AAGGAGAGCACGACCATCGA 60.966 55.000 5.04 0.00 43.74 3.59
2746 5439 0.526524 GAAGGAGAGCACGACCATCG 60.527 60.000 0.00 0.00 46.93 3.84
2747 5440 0.179097 GGAAGGAGAGCACGACCATC 60.179 60.000 0.00 0.00 0.00 3.51
2748 5441 1.617947 GGGAAGGAGAGCACGACCAT 61.618 60.000 0.00 0.00 0.00 3.55
2749 5442 2.283529 GGGAAGGAGAGCACGACCA 61.284 63.158 0.00 0.00 0.00 4.02
2750 5443 2.579738 GGGAAGGAGAGCACGACC 59.420 66.667 0.00 0.00 0.00 4.79
2751 5444 2.182030 CGGGAAGGAGAGCACGAC 59.818 66.667 0.00 0.00 0.00 4.34
2752 5445 3.760035 GCGGGAAGGAGAGCACGA 61.760 66.667 0.00 0.00 0.00 4.35
2753 5446 4.821589 GGCGGGAAGGAGAGCACG 62.822 72.222 0.00 0.00 0.00 5.34
2754 5447 4.475135 GGGCGGGAAGGAGAGCAC 62.475 72.222 0.00 0.00 0.00 4.40
2796 5489 1.805945 GTGGTGACGAGGCGCTTAG 60.806 63.158 7.64 1.62 0.00 2.18
2797 5490 2.209064 GAGTGGTGACGAGGCGCTTA 62.209 60.000 7.64 0.00 0.00 3.09
2798 5491 3.575351 GAGTGGTGACGAGGCGCTT 62.575 63.158 7.64 0.00 0.00 4.68
2799 5492 4.057428 GAGTGGTGACGAGGCGCT 62.057 66.667 7.64 0.00 0.00 5.92
2800 5493 4.057428 AGAGTGGTGACGAGGCGC 62.057 66.667 0.00 0.00 0.00 6.53
2801 5494 1.583495 TACAGAGTGGTGACGAGGCG 61.583 60.000 0.00 0.00 0.00 5.52
2802 5495 0.171455 CTACAGAGTGGTGACGAGGC 59.829 60.000 0.00 0.00 0.00 4.70
2803 5496 0.811915 CCTACAGAGTGGTGACGAGG 59.188 60.000 0.00 0.00 0.00 4.63
2804 5497 1.535833 ACCTACAGAGTGGTGACGAG 58.464 55.000 0.00 0.00 34.90 4.18
2805 5498 2.303890 TCTACCTACAGAGTGGTGACGA 59.696 50.000 0.00 0.00 37.74 4.20
2806 5499 2.708051 TCTACCTACAGAGTGGTGACG 58.292 52.381 0.00 0.00 37.74 4.35
2807 5500 4.333690 TCTTCTACCTACAGAGTGGTGAC 58.666 47.826 0.00 0.00 37.74 3.67
2808 5501 4.043059 ACTCTTCTACCTACAGAGTGGTGA 59.957 45.833 0.25 0.00 44.57 4.02
2809 5502 4.337145 ACTCTTCTACCTACAGAGTGGTG 58.663 47.826 0.25 0.00 44.57 4.17
2810 5503 4.661247 ACTCTTCTACCTACAGAGTGGT 57.339 45.455 0.25 0.00 44.57 4.16
2811 5504 5.944599 TGTAACTCTTCTACCTACAGAGTGG 59.055 44.000 1.90 0.00 45.35 4.00
2812 5505 7.633193 ATGTAACTCTTCTACCTACAGAGTG 57.367 40.000 1.90 0.00 45.35 3.51
2815 5508 9.186837 CCTTAATGTAACTCTTCTACCTACAGA 57.813 37.037 0.00 0.00 0.00 3.41
2816 5509 9.186837 TCCTTAATGTAACTCTTCTACCTACAG 57.813 37.037 0.00 0.00 0.00 2.74
2817 5510 8.964772 GTCCTTAATGTAACTCTTCTACCTACA 58.035 37.037 0.00 0.00 0.00 2.74
2818 5511 8.412456 GGTCCTTAATGTAACTCTTCTACCTAC 58.588 40.741 0.00 0.00 0.00 3.18
2819 5512 7.562821 GGGTCCTTAATGTAACTCTTCTACCTA 59.437 40.741 0.00 0.00 0.00 3.08
2820 5513 6.383436 GGGTCCTTAATGTAACTCTTCTACCT 59.617 42.308 0.00 0.00 0.00 3.08
2821 5514 6.407865 GGGGTCCTTAATGTAACTCTTCTACC 60.408 46.154 0.00 0.00 0.00 3.18
2822 5515 6.407865 GGGGGTCCTTAATGTAACTCTTCTAC 60.408 46.154 0.00 0.00 0.00 2.59
2823 5516 5.664457 GGGGGTCCTTAATGTAACTCTTCTA 59.336 44.000 0.00 0.00 0.00 2.10
2824 5517 4.473922 GGGGGTCCTTAATGTAACTCTTCT 59.526 45.833 0.00 0.00 0.00 2.85
2825 5518 4.778579 GGGGGTCCTTAATGTAACTCTTC 58.221 47.826 0.00 0.00 0.00 2.87
2826 5519 4.857130 GGGGGTCCTTAATGTAACTCTT 57.143 45.455 0.00 0.00 0.00 2.85
2846 5539 3.711782 AAGAGGGGGAGGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
2847 5540 2.040359 GAAGAGGGGGAGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
2848 5541 2.040359 GGAAGAGGGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
2849 5542 3.707189 GGGAAGAGGGGGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
2851 5544 2.032356 TATCGGGAAGAGGGGGAGGG 62.032 65.000 0.00 0.00 0.00 4.30
2852 5545 0.543174 CTATCGGGAAGAGGGGGAGG 60.543 65.000 0.00 0.00 0.00 4.30
2853 5546 0.543174 CCTATCGGGAAGAGGGGGAG 60.543 65.000 0.00 0.00 37.23 4.30
2854 5547 1.301913 ACCTATCGGGAAGAGGGGGA 61.302 60.000 5.34 0.00 38.76 4.81
2855 5548 1.122019 CACCTATCGGGAAGAGGGGG 61.122 65.000 5.34 0.00 38.76 5.40
2856 5549 0.398664 ACACCTATCGGGAAGAGGGG 60.399 60.000 1.73 1.73 39.87 4.79
2857 5550 0.753262 CACACCTATCGGGAAGAGGG 59.247 60.000 5.34 0.00 38.76 4.30
2858 5551 1.776662 TCACACCTATCGGGAAGAGG 58.223 55.000 0.00 0.00 38.76 3.69
2859 5552 3.786635 CTTTCACACCTATCGGGAAGAG 58.213 50.000 0.00 0.00 38.76 2.85
2860 5553 2.093658 GCTTTCACACCTATCGGGAAGA 60.094 50.000 0.00 0.00 38.76 2.87
2861 5554 2.280628 GCTTTCACACCTATCGGGAAG 58.719 52.381 0.00 0.00 38.76 3.46
2862 5555 1.626321 TGCTTTCACACCTATCGGGAA 59.374 47.619 0.00 0.00 38.76 3.97
2863 5556 1.271856 TGCTTTCACACCTATCGGGA 58.728 50.000 0.00 0.00 38.76 5.14
2864 5557 2.107950 TTGCTTTCACACCTATCGGG 57.892 50.000 0.00 0.00 41.89 5.14
2865 5558 3.074412 AGTTTGCTTTCACACCTATCGG 58.926 45.455 0.00 0.00 0.00 4.18
2866 5559 4.201724 GCTAGTTTGCTTTCACACCTATCG 60.202 45.833 0.00 0.00 0.00 2.92
2867 5560 4.938226 AGCTAGTTTGCTTTCACACCTATC 59.062 41.667 0.00 0.00 40.93 2.08
2868 5561 4.911390 AGCTAGTTTGCTTTCACACCTAT 58.089 39.130 0.00 0.00 40.93 2.57
2869 5562 4.315803 GAGCTAGTTTGCTTTCACACCTA 58.684 43.478 0.00 0.00 44.17 3.08
2870 5563 3.142174 GAGCTAGTTTGCTTTCACACCT 58.858 45.455 0.00 0.00 44.17 4.00
2871 5564 2.226674 GGAGCTAGTTTGCTTTCACACC 59.773 50.000 0.00 0.00 44.17 4.16
2872 5565 2.096218 CGGAGCTAGTTTGCTTTCACAC 60.096 50.000 0.00 0.00 44.17 3.82
2873 5566 2.143122 CGGAGCTAGTTTGCTTTCACA 58.857 47.619 0.00 0.00 44.17 3.58
2874 5567 2.413453 CTCGGAGCTAGTTTGCTTTCAC 59.587 50.000 0.00 0.00 44.17 3.18
2875 5568 2.299013 TCTCGGAGCTAGTTTGCTTTCA 59.701 45.455 0.00 0.00 44.17 2.69
2876 5569 2.960819 TCTCGGAGCTAGTTTGCTTTC 58.039 47.619 0.00 0.00 44.17 2.62
2877 5570 3.067833 GTTCTCGGAGCTAGTTTGCTTT 58.932 45.455 0.00 0.00 44.17 3.51
2878 5571 2.613223 GGTTCTCGGAGCTAGTTTGCTT 60.613 50.000 0.00 0.00 44.17 3.91
2880 5573 1.337823 TGGTTCTCGGAGCTAGTTTGC 60.338 52.381 0.00 0.00 0.00 3.68
2881 5574 2.611518 CTGGTTCTCGGAGCTAGTTTG 58.388 52.381 0.00 0.00 0.00 2.93
2882 5575 1.066787 GCTGGTTCTCGGAGCTAGTTT 60.067 52.381 0.00 0.00 0.00 2.66
2883 5576 0.533032 GCTGGTTCTCGGAGCTAGTT 59.467 55.000 0.00 0.00 0.00 2.24
2884 5577 0.612174 TGCTGGTTCTCGGAGCTAGT 60.612 55.000 0.00 0.00 33.66 2.57
2885 5578 0.102120 CTGCTGGTTCTCGGAGCTAG 59.898 60.000 0.00 0.00 33.66 3.42
2886 5579 1.949847 GCTGCTGGTTCTCGGAGCTA 61.950 60.000 0.00 0.00 33.66 3.32
2887 5580 2.977178 CTGCTGGTTCTCGGAGCT 59.023 61.111 0.00 0.00 33.66 4.09
2888 5581 2.794820 AAGCTGCTGGTTCTCGGAGC 62.795 60.000 1.35 0.00 0.00 4.70
2889 5582 0.532573 TAAGCTGCTGGTTCTCGGAG 59.467 55.000 11.52 0.00 35.36 4.63
2890 5583 0.532573 CTAAGCTGCTGGTTCTCGGA 59.467 55.000 11.52 0.00 35.36 4.55
2891 5584 0.460987 CCTAAGCTGCTGGTTCTCGG 60.461 60.000 11.52 7.51 35.36 4.63
2892 5585 0.247736 ACCTAAGCTGCTGGTTCTCG 59.752 55.000 11.52 3.53 35.36 4.04
2893 5586 3.133003 TCATACCTAAGCTGCTGGTTCTC 59.867 47.826 15.80 0.00 35.48 2.87
2894 5587 3.107601 TCATACCTAAGCTGCTGGTTCT 58.892 45.455 15.80 3.23 35.48 3.01
2895 5588 3.543680 TCATACCTAAGCTGCTGGTTC 57.456 47.619 15.80 0.00 35.48 3.62
2896 5589 3.009033 TGTTCATACCTAAGCTGCTGGTT 59.991 43.478 15.80 12.76 35.48 3.67
2897 5590 2.571653 TGTTCATACCTAAGCTGCTGGT 59.428 45.455 15.07 15.07 37.83 4.00
2898 5591 3.118629 TCTGTTCATACCTAAGCTGCTGG 60.119 47.826 1.35 3.30 0.00 4.85
2899 5592 4.128925 TCTGTTCATACCTAAGCTGCTG 57.871 45.455 1.35 0.00 0.00 4.41
2900 5593 4.826274 TTCTGTTCATACCTAAGCTGCT 57.174 40.909 0.00 0.00 0.00 4.24
2901 5594 4.095036 GGTTTCTGTTCATACCTAAGCTGC 59.905 45.833 0.00 0.00 0.00 5.25
2902 5595 5.245531 TGGTTTCTGTTCATACCTAAGCTG 58.754 41.667 0.00 0.00 0.00 4.24
2903 5596 5.499004 TGGTTTCTGTTCATACCTAAGCT 57.501 39.130 0.00 0.00 0.00 3.74
2904 5597 5.705905 AGTTGGTTTCTGTTCATACCTAAGC 59.294 40.000 0.00 0.00 0.00 3.09
2905 5598 7.745620 AAGTTGGTTTCTGTTCATACCTAAG 57.254 36.000 0.00 0.00 0.00 2.18
2906 5599 7.776030 TCAAAGTTGGTTTCTGTTCATACCTAA 59.224 33.333 0.00 0.00 0.00 2.69
2907 5600 7.284074 TCAAAGTTGGTTTCTGTTCATACCTA 58.716 34.615 0.00 0.00 0.00 3.08
2908 5601 6.126409 TCAAAGTTGGTTTCTGTTCATACCT 58.874 36.000 0.00 0.00 0.00 3.08
2909 5602 6.262273 TCTCAAAGTTGGTTTCTGTTCATACC 59.738 38.462 0.00 0.00 0.00 2.73
2910 5603 7.259290 TCTCAAAGTTGGTTTCTGTTCATAC 57.741 36.000 0.00 0.00 0.00 2.39
2911 5604 7.873719 TTCTCAAAGTTGGTTTCTGTTCATA 57.126 32.000 0.00 0.00 0.00 2.15
2912 5605 6.773976 TTCTCAAAGTTGGTTTCTGTTCAT 57.226 33.333 0.00 0.00 0.00 2.57
2913 5606 6.773976 ATTCTCAAAGTTGGTTTCTGTTCA 57.226 33.333 0.00 0.00 0.00 3.18
2914 5607 8.621286 TCTAATTCTCAAAGTTGGTTTCTGTTC 58.379 33.333 0.00 0.00 0.00 3.18
2915 5608 8.519799 TCTAATTCTCAAAGTTGGTTTCTGTT 57.480 30.769 0.00 0.00 0.00 3.16
2916 5609 7.229506 CCTCTAATTCTCAAAGTTGGTTTCTGT 59.770 37.037 0.00 0.00 0.00 3.41
2917 5610 7.445402 TCCTCTAATTCTCAAAGTTGGTTTCTG 59.555 37.037 0.00 0.00 0.00 3.02
2918 5611 7.518188 TCCTCTAATTCTCAAAGTTGGTTTCT 58.482 34.615 0.00 0.00 0.00 2.52
2919 5612 7.745620 TCCTCTAATTCTCAAAGTTGGTTTC 57.254 36.000 0.00 0.00 0.00 2.78
2920 5613 8.166726 AGATCCTCTAATTCTCAAAGTTGGTTT 58.833 33.333 0.00 0.00 0.00 3.27
2921 5614 7.694093 AGATCCTCTAATTCTCAAAGTTGGTT 58.306 34.615 0.00 0.00 0.00 3.67
2922 5615 7.264294 AGATCCTCTAATTCTCAAAGTTGGT 57.736 36.000 0.00 0.00 0.00 3.67
2923 5616 6.765512 GGAGATCCTCTAATTCTCAAAGTTGG 59.234 42.308 0.00 0.00 38.08 3.77
2924 5617 7.334090 TGGAGATCCTCTAATTCTCAAAGTTG 58.666 38.462 0.00 0.00 38.08 3.16
2925 5618 7.502060 TGGAGATCCTCTAATTCTCAAAGTT 57.498 36.000 0.00 0.00 38.08 2.66
2926 5619 6.407979 GCTGGAGATCCTCTAATTCTCAAAGT 60.408 42.308 0.00 0.00 38.08 2.66
2927 5620 5.990996 GCTGGAGATCCTCTAATTCTCAAAG 59.009 44.000 0.00 0.00 38.08 2.77
2928 5621 5.163258 GGCTGGAGATCCTCTAATTCTCAAA 60.163 44.000 0.00 0.00 38.08 2.69
2929 5622 4.346418 GGCTGGAGATCCTCTAATTCTCAA 59.654 45.833 0.00 0.00 38.08 3.02
2930 5623 3.900601 GGCTGGAGATCCTCTAATTCTCA 59.099 47.826 0.00 0.00 38.08 3.27
2931 5624 3.056891 CGGCTGGAGATCCTCTAATTCTC 60.057 52.174 0.00 0.00 36.08 2.87
2932 5625 2.896685 CGGCTGGAGATCCTCTAATTCT 59.103 50.000 0.00 0.00 36.82 2.40
2933 5626 2.630580 ACGGCTGGAGATCCTCTAATTC 59.369 50.000 0.00 0.00 36.82 2.17
2934 5627 2.683768 ACGGCTGGAGATCCTCTAATT 58.316 47.619 0.00 0.00 36.82 1.40
2935 5628 2.390225 ACGGCTGGAGATCCTCTAAT 57.610 50.000 0.00 0.00 36.82 1.73
2936 5629 2.032620 GAACGGCTGGAGATCCTCTAA 58.967 52.381 0.00 0.00 36.82 2.10
2937 5630 1.693627 GAACGGCTGGAGATCCTCTA 58.306 55.000 0.00 0.00 36.82 2.43
2938 5631 1.388065 CGAACGGCTGGAGATCCTCT 61.388 60.000 0.00 0.00 36.82 3.69
2939 5632 1.066587 CGAACGGCTGGAGATCCTC 59.933 63.158 0.00 0.00 36.82 3.71
2940 5633 2.427245 CCGAACGGCTGGAGATCCT 61.427 63.158 0.00 0.00 36.82 3.24
2941 5634 2.107141 CCGAACGGCTGGAGATCC 59.893 66.667 0.00 0.00 0.00 3.36
2962 5655 3.747976 CTTTTTCGGCGCCCTGGG 61.748 66.667 23.46 8.86 0.00 4.45
2963 5656 2.671619 TCTTTTTCGGCGCCCTGG 60.672 61.111 23.46 7.26 0.00 4.45
2964 5657 1.966451 ACTCTTTTTCGGCGCCCTG 60.966 57.895 23.46 8.15 0.00 4.45
2965 5658 1.966451 CACTCTTTTTCGGCGCCCT 60.966 57.895 23.46 0.00 0.00 5.19
2966 5659 2.561373 CACTCTTTTTCGGCGCCC 59.439 61.111 23.46 2.84 0.00 6.13


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

AutoCloner maintained by Alex Coulton.