Multiple sequence alignment - TraesCS2A01G354800

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 TraesCS2A01G354800 chr2A 100.000 2929 0 0 1 2929 595985354 595988282 0.000000e+00 5409.0
1 TraesCS2A01G354800 chr2D 93.330 1814 64 24 911 2685 454733010 454731215 0.000000e+00 2627.0
2 TraesCS2A01G354800 chr2D 91.964 112 8 1 2609 2720 454731424 454731314 3.910000e-34 156.0
3 TraesCS2A01G354800 chr2D 84.746 118 6 4 2494 2599 454731290 454731173 1.110000e-19 108.0
4 TraesCS2A01G354800 chr2B 91.744 1502 73 18 808 2272 534383421 534381934 0.000000e+00 2039.0
5 TraesCS2A01G354800 chr2B 88.293 820 72 12 1 802 534386161 534385348 0.000000e+00 961.0
6 TraesCS2A01G354800 chr2B 92.617 298 18 3 2257 2550 534381907 534381610 2.700000e-115 425.0
7 TraesCS2A01G354800 chr6B 91.324 219 19 0 2711 2929 76325246 76325464 1.710000e-77 300.0
8 TraesCS2A01G354800 chr1B 85.915 284 32 4 308 585 548296187 548296468 2.210000e-76 296.0
9 TraesCS2A01G354800 chr3D 81.613 310 41 6 309 602 9068019 9068328 2.920000e-60 243.0
10 TraesCS2A01G354800 chr4A 81.696 224 38 3 63 283 620983270 620983493 1.790000e-42 183.0
11 TraesCS2A01G354800 chr4A 82.500 160 25 3 270 427 620983672 620983830 1.420000e-28 137.0
12 TraesCS2A01G354800 chr7D 83.607 61 7 2 353 411 45581041 45580982 1.000000e-03 54.7


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 TraesCS2A01G354800 chr2A 595985354 595988282 2928 False 5409.000000 5409 100.000000 1 2929 1 chr2A.!!$F1 2928
1 TraesCS2A01G354800 chr2D 454731173 454733010 1837 True 963.666667 2627 90.013333 911 2720 3 chr2D.!!$R1 1809
2 TraesCS2A01G354800 chr2B 534381610 534386161 4551 True 1141.666667 2039 90.884667 1 2550 3 chr2B.!!$R1 2549

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
229 237 0.035317 TGCGAGCCTTCACTTGACAT 59.965 50.0 0.0 0.0 0.0 3.06 F
954 2911 0.543174 AGCTCTTCCTGGTCCGACTT 60.543 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 3211 1.307866 GGGGAATGGGGAGAGTGGA 60.308 63.158 0.00 0.0 0.0 4.02 R
2898 4940 0.034896 GGAGGTCTTGGCGAAGTTCA 59.965 55.000 8.41 0.0 0.0 3.18 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
116 123 4.352600 TTTGCAACAAATGTTTTGCTGG 57.647 36.364 8.19 0.00 46.83 4.85
145 152 2.838202 AGATCCCGTTGTAGACCATTGT 59.162 45.455 0.00 0.00 0.00 2.71
156 163 7.095144 CGTTGTAGACCATTGTAACACCAAATA 60.095 37.037 0.00 0.00 0.00 1.40
202 209 2.143122 CAGAAAGCACGCCTGACTAAA 58.857 47.619 0.00 0.00 0.00 1.85
207 214 0.110373 GCACGCCTGACTAAAAACGG 60.110 55.000 0.00 0.00 0.00 4.44
229 237 0.035317 TGCGAGCCTTCACTTGACAT 59.965 50.000 0.00 0.00 0.00 3.06
240 248 2.359850 TTGACATGTGGAGGCGGC 60.360 61.111 1.15 0.00 0.00 6.53
274 282 4.336433 CGCAGGATGATGGTAAATGTTTCT 59.664 41.667 0.00 0.00 39.69 2.52
335 343 7.681939 TGACAAAAGTCTTGTTACAGAAGTT 57.318 32.000 0.00 0.00 31.96 2.66
351 359 6.739112 ACAGAAGTTAGGAAATTTGCAGAAC 58.261 36.000 12.54 14.19 0.00 3.01
366 375 3.611986 TGCAGAACTTTTTCGCAACAAAG 59.388 39.130 0.00 0.00 37.90 2.77
400 409 5.809001 AGAATTATTCTGCAACAGAGGTCA 58.191 37.500 6.67 0.00 41.75 4.02
416 425 6.435277 ACAGAGGTCATGTTGCAGAAATTTAT 59.565 34.615 0.00 0.00 0.00 1.40
438 447 4.222124 AGTCTTTTCATAACCGATGCCT 57.778 40.909 0.00 0.00 35.29 4.75
464 479 1.352622 ACCCTGCAACTGTTCCTGGA 61.353 55.000 8.78 0.00 0.00 3.86
471 486 2.704572 CAACTGTTCCTGGATGAGACC 58.295 52.381 0.00 0.00 0.00 3.85
498 513 5.949233 CGACATGATCGTGATGTTTCTAA 57.051 39.130 21.75 0.00 46.25 2.10
499 514 6.331170 CGACATGATCGTGATGTTTCTAAA 57.669 37.500 21.75 0.00 46.25 1.85
508 523 7.421530 TCGTGATGTTTCTAAAGAAGGAAAG 57.578 36.000 0.00 0.00 35.21 2.62
516 531 5.228945 TCTAAAGAAGGAAAGGTGGACAG 57.771 43.478 0.00 0.00 0.00 3.51
520 535 1.415672 AAGGAAAGGTGGACAGCGGA 61.416 55.000 0.00 0.00 0.00 5.54
522 537 1.671379 GAAAGGTGGACAGCGGACC 60.671 63.158 0.00 0.00 0.00 4.46
546 561 1.207089 CCACATGGACACGTGGTAGAT 59.793 52.381 21.57 3.14 46.31 1.98
553 568 2.223829 GGACACGTGGTAGATGATGGAG 60.224 54.545 21.57 0.00 0.00 3.86
554 569 2.688446 GACACGTGGTAGATGATGGAGA 59.312 50.000 21.57 0.00 0.00 3.71
562 577 2.969628 AGATGATGGAGACGGTTGAC 57.030 50.000 0.00 0.00 0.00 3.18
579 594 2.253414 GACGTTTGGGAGCAATCCGC 62.253 60.000 0.00 0.00 42.91 5.54
582 597 4.794648 TTGGGAGCAATCCGCCGG 62.795 66.667 0.00 0.00 44.04 6.13
589 604 4.557605 CAATCCGCCGGTGCATGC 62.558 66.667 11.82 11.82 37.32 4.06
608 626 5.125417 GCATGCTCATTTCCCTAACTTGTAA 59.875 40.000 11.37 0.00 0.00 2.41
613 631 6.403746 GCTCATTTCCCTAACTTGTAAGCTTC 60.404 42.308 0.00 0.00 0.00 3.86
617 635 4.906618 TCCCTAACTTGTAAGCTTCCAAG 58.093 43.478 25.26 25.26 42.91 3.61
622 640 7.610305 CCCTAACTTGTAAGCTTCCAAGAAATA 59.390 37.037 31.37 20.47 40.36 1.40
627 645 9.077885 ACTTGTAAGCTTCCAAGAAATAATTGA 57.922 29.630 31.37 0.00 40.36 2.57
675 693 7.669722 TGGCTAGGAGACAGTTTATTTCAAAAT 59.330 33.333 0.00 0.00 0.00 1.82
699 717 4.994217 CCAAAACAACACACCAAAAGAACT 59.006 37.500 0.00 0.00 0.00 3.01
724 742 3.077359 CCCAAATCGACTGAAAGAAGCT 58.923 45.455 0.00 0.00 37.43 3.74
732 750 3.722147 GACTGAAAGAAGCTGTGACTGA 58.278 45.455 0.00 0.00 37.43 3.41
735 753 1.795286 GAAAGAAGCTGTGACTGACCG 59.205 52.381 0.00 0.00 0.00 4.79
750 769 6.020678 GTGACTGACCGAAAAACAAAAATCAG 60.021 38.462 0.00 0.00 38.60 2.90
755 774 6.309251 TGACCGAAAAACAAAAATCAGTCAAC 59.691 34.615 0.00 0.00 29.03 3.18
769 788 1.160137 GTCAACTTGCACCTAGCCTG 58.840 55.000 0.00 0.00 44.83 4.85
777 796 4.100189 ACTTGCACCTAGCCTGTTCTATAG 59.900 45.833 0.00 0.00 44.83 1.31
802 821 8.846211 AGTTAAAACAGCGCACCATTATATTAT 58.154 29.630 11.47 0.00 0.00 1.28
803 822 9.458374 GTTAAAACAGCGCACCATTATATTATT 57.542 29.630 11.47 0.00 0.00 1.40
845 2785 2.729383 TCTGCATCCCTAGGATCCAT 57.271 50.000 15.82 1.47 40.98 3.41
875 2815 6.315393 TCGGTAGAAATTTTGCTTGGAGTATC 59.685 38.462 0.00 0.00 0.00 2.24
882 2822 9.353999 GAAATTTTGCTTGGAGTATCGTAAATT 57.646 29.630 0.00 0.00 34.37 1.82
883 2823 9.705290 AAATTTTGCTTGGAGTATCGTAAATTT 57.295 25.926 0.00 0.00 34.37 1.82
890 2846 4.936411 TGGAGTATCGTAAATTTTGCCGAA 59.064 37.500 0.00 0.00 34.37 4.30
954 2911 0.543174 AGCTCTTCCTGGTCCGACTT 60.543 55.000 0.00 0.00 0.00 3.01
989 2946 4.838152 CCACATCGGGTCCAGCCG 62.838 72.222 11.03 11.03 38.44 5.52
991 2948 3.000819 ACATCGGGTCCAGCCGAA 61.001 61.111 22.71 7.75 41.74 4.30
993 2950 3.000819 ATCGGGTCCAGCCGAACA 61.001 61.111 22.71 1.74 41.74 3.18
1254 3211 1.220206 CGAGCACCATCTCAGCCTT 59.780 57.895 0.00 0.00 33.41 4.35
1696 3653 1.791103 GATCGCGCTGCCTCTCTACT 61.791 60.000 5.56 0.00 0.00 2.57
1738 3695 2.202570 ACGATTCGAAGGACGCGG 60.203 61.111 13.95 0.00 42.26 6.46
1994 3966 1.699083 TCTGGTTCTGGATGCAGTTGA 59.301 47.619 14.43 4.12 0.00 3.18
2067 4039 1.304381 TTGGTGAGGCAGGCATTCC 60.304 57.895 0.00 0.00 0.00 3.01
2077 4049 1.030488 CAGGCATTCCTCAGGCAGTG 61.030 60.000 0.00 0.00 41.93 3.66
2102 4074 2.571653 ACCAGAGGCTAACATTGCACTA 59.428 45.455 0.00 0.00 0.00 2.74
2130 4102 5.577164 GGTGTATTGAGCTACAGTTAGTGTG 59.423 44.000 2.52 0.00 40.69 3.82
2168 4140 3.944055 TTCTCTCCTCAGTTAGTGTGC 57.056 47.619 0.00 0.00 0.00 4.57
2183 4155 7.801315 CAGTTAGTGTGCGTGTTTTATGTTTAT 59.199 33.333 0.00 0.00 0.00 1.40
2189 4161 8.907685 GTGTGCGTGTTTTATGTTTATGTTTAT 58.092 29.630 0.00 0.00 0.00 1.40
2212 4190 4.334203 TGTTGGCACCGTATATGTGAAATC 59.666 41.667 8.96 0.00 35.74 2.17
2218 4196 4.574421 CACCGTATATGTGAAATCTGGCAA 59.426 41.667 0.00 0.00 35.74 4.52
2228 4206 7.716799 TGTGAAATCTGGCAACCTATTATTT 57.283 32.000 0.00 0.00 0.00 1.40
2239 4217 7.497909 TGGCAACCTATTATTTCTAGCACTTAC 59.502 37.037 0.00 0.00 0.00 2.34
2262 4240 4.717280 CCTGTAGTCAAACTATCCTCCCTT 59.283 45.833 0.00 0.00 32.65 3.95
2307 4330 5.746990 AACCTTAGTTCTATCACTGCACT 57.253 39.130 0.00 0.00 0.00 4.40
2336 4359 4.262377 CCTGATACCACTTGAGCTCTATGG 60.262 50.000 22.40 22.40 36.46 2.74
2497 4520 7.222999 GCTACAACCTATGTTCTACTGACAATC 59.777 40.741 0.00 0.00 43.63 2.67
2506 4529 7.815840 TGTTCTACTGACAATCATTTTGGAA 57.184 32.000 0.00 0.00 0.00 3.53
2515 4538 9.357652 CTGACAATCATTTTGGAATTTTACGAT 57.642 29.630 0.00 0.00 0.00 3.73
2558 4600 1.024271 ATGCCGATTTCCGTTCATGG 58.976 50.000 0.00 0.00 36.31 3.66
2659 4701 1.738474 TCTCATGGCAGGGATATGCT 58.262 50.000 0.00 0.00 45.75 3.79
2685 4727 1.687563 CGTTCCCCAACCCCAATATC 58.312 55.000 0.00 0.00 0.00 1.63
2686 4728 1.752788 CGTTCCCCAACCCCAATATCC 60.753 57.143 0.00 0.00 0.00 2.59
2687 4729 1.289530 GTTCCCCAACCCCAATATCCA 59.710 52.381 0.00 0.00 0.00 3.41
2688 4730 1.700147 TCCCCAACCCCAATATCCAA 58.300 50.000 0.00 0.00 0.00 3.53
2689 4731 2.231348 TCCCCAACCCCAATATCCAAT 58.769 47.619 0.00 0.00 0.00 3.16
2690 4732 3.417997 TCCCCAACCCCAATATCCAATA 58.582 45.455 0.00 0.00 0.00 1.90
2691 4733 4.000649 TCCCCAACCCCAATATCCAATAT 58.999 43.478 0.00 0.00 0.00 1.28
2701 4743 8.511126 ACCCCAATATCCAATATGAAAGTTACT 58.489 33.333 0.00 0.00 0.00 2.24
2738 4780 6.971527 TTTTTGAGAAACTCGAGTACACAA 57.028 33.333 20.39 21.10 32.35 3.33
2739 4781 6.971527 TTTTGAGAAACTCGAGTACACAAA 57.028 33.333 26.76 26.76 32.35 2.83
2740 4782 7.548196 TTTTGAGAAACTCGAGTACACAAAT 57.452 32.000 28.75 11.66 31.63 2.32
2741 4783 8.651391 TTTTGAGAAACTCGAGTACACAAATA 57.349 30.769 28.75 21.84 31.63 1.40
2742 4784 7.633361 TTGAGAAACTCGAGTACACAAATAC 57.367 36.000 20.39 4.70 32.35 1.89
2743 4785 6.978338 TGAGAAACTCGAGTACACAAATACT 58.022 36.000 20.39 7.61 38.13 2.12
2744 4786 7.082602 TGAGAAACTCGAGTACACAAATACTC 58.917 38.462 20.39 15.28 45.18 2.59
2748 4790 6.746120 AACTCGAGTACACAAATACTCAAGT 58.254 36.000 20.39 7.12 46.66 3.16
2749 4791 7.444629 ACTCGAGTACACAAATACTCAAGTA 57.555 36.000 18.46 0.00 44.15 2.24
2750 4792 7.528307 ACTCGAGTACACAAATACTCAAGTAG 58.472 38.462 18.46 6.81 44.15 2.57
2751 4793 7.389884 ACTCGAGTACACAAATACTCAAGTAGA 59.610 37.037 18.46 2.05 44.15 2.59
2768 4810 3.291497 GAGGGAGTACACTCAGCCT 57.709 57.895 11.31 8.91 45.11 4.58
2769 4811 0.820871 GAGGGAGTACACTCAGCCTG 59.179 60.000 11.31 0.00 45.11 4.85
2770 4812 1.219393 GGGAGTACACTCAGCCTGC 59.781 63.158 11.31 0.00 44.60 4.85
2771 4813 1.544825 GGGAGTACACTCAGCCTGCA 61.545 60.000 11.31 0.00 44.60 4.41
2772 4814 0.539051 GGAGTACACTCAGCCTGCAT 59.461 55.000 11.31 0.00 44.60 3.96
2773 4815 1.472376 GGAGTACACTCAGCCTGCATC 60.472 57.143 11.31 0.00 44.60 3.91
2774 4816 1.205655 GAGTACACTCAGCCTGCATCA 59.794 52.381 4.48 0.00 42.42 3.07
2775 4817 1.206610 AGTACACTCAGCCTGCATCAG 59.793 52.381 0.00 0.00 0.00 2.90
2776 4818 1.205655 GTACACTCAGCCTGCATCAGA 59.794 52.381 0.00 0.00 32.44 3.27
2777 4819 0.910338 ACACTCAGCCTGCATCAGAT 59.090 50.000 0.00 0.00 32.44 2.90
2778 4820 1.281287 ACACTCAGCCTGCATCAGATT 59.719 47.619 0.00 0.00 32.44 2.40
2779 4821 1.941294 CACTCAGCCTGCATCAGATTC 59.059 52.381 0.00 0.00 32.44 2.52
2780 4822 1.558294 ACTCAGCCTGCATCAGATTCA 59.442 47.619 0.00 0.00 32.44 2.57
2781 4823 2.172930 ACTCAGCCTGCATCAGATTCAT 59.827 45.455 0.00 0.00 32.44 2.57
2782 4824 2.809119 CTCAGCCTGCATCAGATTCATC 59.191 50.000 0.00 0.00 32.44 2.92
2783 4825 2.171870 TCAGCCTGCATCAGATTCATCA 59.828 45.455 0.00 0.00 32.44 3.07
2784 4826 2.550180 CAGCCTGCATCAGATTCATCAG 59.450 50.000 0.00 0.00 32.44 2.90
2785 4827 2.172930 AGCCTGCATCAGATTCATCAGT 59.827 45.455 0.00 0.00 32.44 3.41
2786 4828 2.548904 GCCTGCATCAGATTCATCAGTC 59.451 50.000 0.00 0.00 32.44 3.51
2787 4829 3.744846 GCCTGCATCAGATTCATCAGTCT 60.745 47.826 0.00 0.00 32.44 3.24
2788 4830 3.810386 CCTGCATCAGATTCATCAGTCTG 59.190 47.826 0.00 0.00 42.46 3.51
2789 4831 4.443621 CTGCATCAGATTCATCAGTCTGT 58.556 43.478 0.00 0.00 41.92 3.41
2790 4832 4.439968 TGCATCAGATTCATCAGTCTGTC 58.560 43.478 0.00 0.00 41.92 3.51
2791 4833 3.808726 GCATCAGATTCATCAGTCTGTCC 59.191 47.826 0.00 0.00 41.92 4.02
2792 4834 3.790152 TCAGATTCATCAGTCTGTCCG 57.210 47.619 0.00 0.00 41.92 4.79
2793 4835 2.428530 TCAGATTCATCAGTCTGTCCGG 59.571 50.000 0.00 0.00 41.92 5.14
2794 4836 1.759445 AGATTCATCAGTCTGTCCGGG 59.241 52.381 0.00 0.00 0.00 5.73
2795 4837 1.757118 GATTCATCAGTCTGTCCGGGA 59.243 52.381 0.00 0.00 0.00 5.14
2796 4838 0.895530 TTCATCAGTCTGTCCGGGAC 59.104 55.000 20.36 20.36 0.00 4.46
2797 4839 0.970937 TCATCAGTCTGTCCGGGACC 60.971 60.000 23.81 9.13 34.56 4.46
2798 4840 1.686110 ATCAGTCTGTCCGGGACCC 60.686 63.158 23.81 11.90 34.56 4.46
2799 4841 2.169590 ATCAGTCTGTCCGGGACCCT 62.170 60.000 23.81 13.89 34.56 4.34
2800 4842 2.037527 AGTCTGTCCGGGACCCTC 59.962 66.667 23.81 13.31 34.56 4.30
2801 4843 3.450115 GTCTGTCCGGGACCCTCG 61.450 72.222 23.81 10.08 0.00 4.63
2805 4847 3.782443 GTCCGGGACCCTCGCAAT 61.782 66.667 16.55 0.00 0.00 3.56
2806 4848 3.781307 TCCGGGACCCTCGCAATG 61.781 66.667 9.41 0.00 0.00 2.82
2807 4849 3.781307 CCGGGACCCTCGCAATGA 61.781 66.667 9.41 0.00 0.00 2.57
2808 4850 2.202932 CGGGACCCTCGCAATGAG 60.203 66.667 9.41 0.00 44.83 2.90
2809 4851 2.514824 GGGACCCTCGCAATGAGC 60.515 66.667 2.09 0.00 43.82 4.26
2810 4852 2.586792 GGACCCTCGCAATGAGCT 59.413 61.111 0.00 0.00 43.82 4.09
2811 4853 1.817099 GGACCCTCGCAATGAGCTG 60.817 63.158 0.00 0.00 43.82 4.24
2812 4854 1.219124 GACCCTCGCAATGAGCTGA 59.781 57.895 0.00 0.00 43.82 4.26
2813 4855 0.391661 GACCCTCGCAATGAGCTGAA 60.392 55.000 0.00 0.00 43.82 3.02
2814 4856 0.392193 ACCCTCGCAATGAGCTGAAG 60.392 55.000 0.00 0.00 43.82 3.02
2815 4857 0.107993 CCCTCGCAATGAGCTGAAGA 60.108 55.000 0.00 0.00 43.82 2.87
2816 4858 1.474677 CCCTCGCAATGAGCTGAAGAT 60.475 52.381 0.00 0.00 43.82 2.40
2817 4859 1.865970 CCTCGCAATGAGCTGAAGATC 59.134 52.381 0.00 0.00 43.82 2.75
2818 4860 2.547826 CTCGCAATGAGCTGAAGATCA 58.452 47.619 0.03 0.03 45.10 2.92
2819 4861 2.274437 TCGCAATGAGCTGAAGATCAC 58.726 47.619 0.00 0.00 43.73 3.06
2820 4862 1.329906 CGCAATGAGCTGAAGATCACC 59.670 52.381 0.00 0.00 43.73 4.02
2821 4863 2.641305 GCAATGAGCTGAAGATCACCT 58.359 47.619 0.00 0.00 43.73 4.00
2822 4864 3.015327 GCAATGAGCTGAAGATCACCTT 58.985 45.455 0.00 0.00 43.73 3.50
2823 4865 3.442977 GCAATGAGCTGAAGATCACCTTT 59.557 43.478 0.00 0.00 43.73 3.11
2824 4866 4.082354 GCAATGAGCTGAAGATCACCTTTT 60.082 41.667 0.00 0.00 43.73 2.27
2825 4867 5.566230 GCAATGAGCTGAAGATCACCTTTTT 60.566 40.000 0.00 0.00 43.73 1.94
2826 4868 5.640189 ATGAGCTGAAGATCACCTTTTTG 57.360 39.130 0.00 0.00 43.73 2.44
2827 4869 4.464008 TGAGCTGAAGATCACCTTTTTGT 58.536 39.130 0.00 0.00 35.30 2.83
2828 4870 4.516698 TGAGCTGAAGATCACCTTTTTGTC 59.483 41.667 0.00 0.00 35.30 3.18
2829 4871 4.723309 AGCTGAAGATCACCTTTTTGTCT 58.277 39.130 0.00 0.00 34.68 3.41
2830 4872 5.136105 AGCTGAAGATCACCTTTTTGTCTT 58.864 37.500 0.00 0.00 34.68 3.01
2831 4873 5.009410 AGCTGAAGATCACCTTTTTGTCTTG 59.991 40.000 0.00 0.00 34.68 3.02
2832 4874 5.186996 TGAAGATCACCTTTTTGTCTTGC 57.813 39.130 0.00 0.00 34.68 4.01
2833 4875 4.037923 TGAAGATCACCTTTTTGTCTTGCC 59.962 41.667 0.00 0.00 34.68 4.52
2834 4876 3.837355 AGATCACCTTTTTGTCTTGCCT 58.163 40.909 0.00 0.00 0.00 4.75
2835 4877 3.823304 AGATCACCTTTTTGTCTTGCCTC 59.177 43.478 0.00 0.00 0.00 4.70
2836 4878 3.297134 TCACCTTTTTGTCTTGCCTCT 57.703 42.857 0.00 0.00 0.00 3.69
2837 4879 2.951642 TCACCTTTTTGTCTTGCCTCTG 59.048 45.455 0.00 0.00 0.00 3.35
2838 4880 1.683385 ACCTTTTTGTCTTGCCTCTGC 59.317 47.619 0.00 0.00 38.26 4.26
2849 4891 2.723322 TGCCTCTGCAGCTAATTCAT 57.277 45.000 9.47 0.00 44.23 2.57
2850 4892 2.294979 TGCCTCTGCAGCTAATTCATG 58.705 47.619 9.47 0.00 44.23 3.07
2851 4893 1.607628 GCCTCTGCAGCTAATTCATGG 59.392 52.381 9.47 1.07 37.47 3.66
2852 4894 2.228059 CCTCTGCAGCTAATTCATGGG 58.772 52.381 9.47 0.00 0.00 4.00
2853 4895 2.422519 CCTCTGCAGCTAATTCATGGGT 60.423 50.000 9.47 0.00 0.00 4.51
2854 4896 2.877168 CTCTGCAGCTAATTCATGGGTC 59.123 50.000 9.47 0.00 0.00 4.46
2855 4897 2.239402 TCTGCAGCTAATTCATGGGTCA 59.761 45.455 9.47 0.00 0.00 4.02
2856 4898 2.617308 CTGCAGCTAATTCATGGGTCAG 59.383 50.000 0.00 0.00 0.00 3.51
2857 4899 2.025981 TGCAGCTAATTCATGGGTCAGT 60.026 45.455 0.00 0.00 0.00 3.41
2858 4900 2.357009 GCAGCTAATTCATGGGTCAGTG 59.643 50.000 0.00 0.00 0.00 3.66
2859 4901 3.614092 CAGCTAATTCATGGGTCAGTGT 58.386 45.455 0.00 0.00 0.00 3.55
2860 4902 3.376234 CAGCTAATTCATGGGTCAGTGTG 59.624 47.826 0.00 0.00 0.00 3.82
2861 4903 3.009473 AGCTAATTCATGGGTCAGTGTGT 59.991 43.478 0.00 0.00 0.00 3.72
2862 4904 3.758554 GCTAATTCATGGGTCAGTGTGTT 59.241 43.478 0.00 0.00 0.00 3.32
2863 4905 4.379813 GCTAATTCATGGGTCAGTGTGTTG 60.380 45.833 0.00 0.00 0.00 3.33
2864 4906 1.317613 TTCATGGGTCAGTGTGTTGC 58.682 50.000 0.00 0.00 0.00 4.17
2865 4907 0.182299 TCATGGGTCAGTGTGTTGCA 59.818 50.000 0.00 0.00 0.00 4.08
2875 4917 1.317613 GTGTGTTGCACATCCTTCCA 58.682 50.000 5.22 0.00 46.32 3.53
2876 4918 1.680735 GTGTGTTGCACATCCTTCCAA 59.319 47.619 5.22 0.00 46.32 3.53
2877 4919 1.680735 TGTGTTGCACATCCTTCCAAC 59.319 47.619 0.00 0.00 39.62 3.77
2878 4920 1.680735 GTGTTGCACATCCTTCCAACA 59.319 47.619 0.00 0.00 43.51 3.33
2879 4921 2.297033 GTGTTGCACATCCTTCCAACAT 59.703 45.455 8.09 0.00 46.11 2.71
2880 4922 2.296752 TGTTGCACATCCTTCCAACATG 59.703 45.455 0.00 0.00 41.62 3.21
2881 4923 2.557924 GTTGCACATCCTTCCAACATGA 59.442 45.455 0.00 0.00 37.93 3.07
2882 4924 2.439409 TGCACATCCTTCCAACATGAG 58.561 47.619 0.00 0.00 0.00 2.90
2883 4925 1.133790 GCACATCCTTCCAACATGAGC 59.866 52.381 0.00 0.00 0.00 4.26
2884 4926 1.399440 CACATCCTTCCAACATGAGCG 59.601 52.381 0.00 0.00 0.00 5.03
2885 4927 1.278985 ACATCCTTCCAACATGAGCGA 59.721 47.619 0.00 0.00 0.00 4.93
2886 4928 1.667724 CATCCTTCCAACATGAGCGAC 59.332 52.381 0.00 0.00 0.00 5.19
2887 4929 0.684535 TCCTTCCAACATGAGCGACA 59.315 50.000 0.00 0.00 0.00 4.35
2888 4930 1.278985 TCCTTCCAACATGAGCGACAT 59.721 47.619 0.00 0.00 40.17 3.06
2889 4931 2.086869 CCTTCCAACATGAGCGACATT 58.913 47.619 0.00 0.00 37.07 2.71
2890 4932 2.159476 CCTTCCAACATGAGCGACATTG 60.159 50.000 0.00 0.00 37.07 2.82
2891 4933 2.470983 TCCAACATGAGCGACATTGA 57.529 45.000 0.00 0.00 37.07 2.57
2892 4934 2.777094 TCCAACATGAGCGACATTGAA 58.223 42.857 0.00 0.00 37.07 2.69
2893 4935 2.743664 TCCAACATGAGCGACATTGAAG 59.256 45.455 0.00 0.00 37.07 3.02
2894 4936 2.159476 CCAACATGAGCGACATTGAAGG 60.159 50.000 0.00 0.00 37.07 3.46
2895 4937 2.743664 CAACATGAGCGACATTGAAGGA 59.256 45.455 0.00 0.00 37.07 3.36
2896 4938 3.057969 ACATGAGCGACATTGAAGGAA 57.942 42.857 0.00 0.00 37.07 3.36
2897 4939 3.005554 ACATGAGCGACATTGAAGGAAG 58.994 45.455 0.00 0.00 37.07 3.46
2898 4940 2.839486 TGAGCGACATTGAAGGAAGT 57.161 45.000 0.00 0.00 0.00 3.01
2899 4941 2.416747 TGAGCGACATTGAAGGAAGTG 58.583 47.619 0.00 0.00 0.00 3.16
2900 4942 2.037121 TGAGCGACATTGAAGGAAGTGA 59.963 45.455 0.00 0.00 0.00 3.41
2901 4943 3.067106 GAGCGACATTGAAGGAAGTGAA 58.933 45.455 0.00 0.00 0.00 3.18
2902 4944 2.808543 AGCGACATTGAAGGAAGTGAAC 59.191 45.455 0.00 0.00 0.00 3.18
2903 4945 2.808543 GCGACATTGAAGGAAGTGAACT 59.191 45.455 0.00 0.00 0.00 3.01
2904 4946 3.251004 GCGACATTGAAGGAAGTGAACTT 59.749 43.478 0.00 0.00 39.23 2.66
2913 4955 2.951676 GAAGTGAACTTCGCCAAGAC 57.048 50.000 7.41 0.00 42.33 3.01
2914 4956 1.531578 GAAGTGAACTTCGCCAAGACC 59.468 52.381 7.41 0.00 42.33 3.85
2915 4957 0.759346 AGTGAACTTCGCCAAGACCT 59.241 50.000 0.00 0.00 33.34 3.85
2916 4958 1.149148 GTGAACTTCGCCAAGACCTC 58.851 55.000 0.00 0.00 33.34 3.85
2917 4959 0.034896 TGAACTTCGCCAAGACCTCC 59.965 55.000 0.00 0.00 33.34 4.30
2918 4960 0.034896 GAACTTCGCCAAGACCTCCA 59.965 55.000 0.00 0.00 33.34 3.86
2919 4961 0.693049 AACTTCGCCAAGACCTCCAT 59.307 50.000 0.00 0.00 33.34 3.41
2920 4962 0.036010 ACTTCGCCAAGACCTCCATG 60.036 55.000 0.00 0.00 33.34 3.66
2921 4963 0.250234 CTTCGCCAAGACCTCCATGA 59.750 55.000 0.00 0.00 0.00 3.07
2922 4964 0.911769 TTCGCCAAGACCTCCATGAT 59.088 50.000 0.00 0.00 0.00 2.45
2923 4965 1.788229 TCGCCAAGACCTCCATGATA 58.212 50.000 0.00 0.00 0.00 2.15
2924 4966 2.329267 TCGCCAAGACCTCCATGATAT 58.671 47.619 0.00 0.00 0.00 1.63
2925 4967 2.300152 TCGCCAAGACCTCCATGATATC 59.700 50.000 0.00 0.00 0.00 1.63
2926 4968 2.037641 CGCCAAGACCTCCATGATATCA 59.962 50.000 8.10 8.10 0.00 2.15
2927 4969 3.406764 GCCAAGACCTCCATGATATCAC 58.593 50.000 7.78 0.00 0.00 3.06
2928 4970 3.657634 CCAAGACCTCCATGATATCACG 58.342 50.000 7.78 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 69 9.669887 TCTGTTACAAGACCTTAGTTACAAAAA 57.330 29.630 0.00 0.00 0.00 1.94
116 123 5.522824 GGTCTACAACGGGATCTATGTTTTC 59.477 44.000 0.00 0.00 0.00 2.29
164 171 2.621055 TCTGCAACAACGGCTATGTTTT 59.379 40.909 2.50 0.00 38.90 2.43
181 188 0.670546 TAGTCAGGCGTGCTTTCTGC 60.671 55.000 0.35 0.00 43.25 4.26
182 189 1.795768 TTAGTCAGGCGTGCTTTCTG 58.204 50.000 0.35 0.00 0.00 3.02
190 197 2.241171 GCCGTTTTTAGTCAGGCGT 58.759 52.632 0.00 0.00 38.28 5.68
193 200 1.465689 CGCATGCCGTTTTTAGTCAGG 60.466 52.381 13.15 0.00 0.00 3.86
195 202 1.463056 CTCGCATGCCGTTTTTAGTCA 59.537 47.619 13.15 0.00 38.35 3.41
207 214 1.136147 CAAGTGAAGGCTCGCATGC 59.864 57.895 7.91 7.91 34.29 4.06
248 256 3.181440 ACATTTACCATCATCCTGCGGAT 60.181 43.478 0.00 0.00 44.21 4.18
335 343 5.689961 GCGAAAAAGTTCTGCAAATTTCCTA 59.310 36.000 0.00 0.00 35.06 2.94
351 359 4.173256 ACAAGACCTTTGTTGCGAAAAAG 58.827 39.130 9.42 9.42 33.95 2.27
366 375 7.377766 TGCAGAATAATTCTACAACAAGACC 57.622 36.000 0.00 0.00 38.11 3.85
376 385 6.946340 TGACCTCTGTTGCAGAATAATTCTA 58.054 36.000 0.37 0.00 40.18 2.10
378 387 6.094603 ACATGACCTCTGTTGCAGAATAATTC 59.905 38.462 0.00 0.00 40.18 2.17
381 390 4.910195 ACATGACCTCTGTTGCAGAATAA 58.090 39.130 0.00 0.00 40.18 1.40
392 401 4.778534 AATTTCTGCAACATGACCTCTG 57.221 40.909 0.00 0.00 0.00 3.35
416 425 5.116180 CAGGCATCGGTTATGAAAAGACTA 58.884 41.667 0.00 0.00 37.86 2.59
438 447 0.034574 ACAGTTGCAGGGTTCACACA 60.035 50.000 0.00 0.00 0.00 3.72
464 479 1.478631 TCATGTCGCTCTGGTCTCAT 58.521 50.000 0.00 0.00 0.00 2.90
497 512 2.587522 GCTGTCCACCTTTCCTTCTTT 58.412 47.619 0.00 0.00 0.00 2.52
498 513 1.543429 CGCTGTCCACCTTTCCTTCTT 60.543 52.381 0.00 0.00 0.00 2.52
499 514 0.035458 CGCTGTCCACCTTTCCTTCT 59.965 55.000 0.00 0.00 0.00 2.85
520 535 4.344865 GTGTCCATGTGGCCCGGT 62.345 66.667 0.00 0.00 34.44 5.28
522 537 4.697756 ACGTGTCCATGTGGCCCG 62.698 66.667 0.00 0.00 34.44 6.13
562 577 2.485122 GCGGATTGCTCCCAAACG 59.515 61.111 0.00 0.00 41.73 3.60
579 594 1.434696 GGAAATGAGCATGCACCGG 59.565 57.895 21.98 0.00 0.00 5.28
582 597 3.019564 AGTTAGGGAAATGAGCATGCAC 58.980 45.455 21.98 15.08 0.00 4.57
585 600 6.678900 GCTTACAAGTTAGGGAAATGAGCATG 60.679 42.308 0.00 0.00 0.00 4.06
589 604 6.094186 GGAAGCTTACAAGTTAGGGAAATGAG 59.906 42.308 2.98 0.00 0.00 2.90
608 626 6.944862 ACTCAGTCAATTATTTCTTGGAAGCT 59.055 34.615 0.00 0.00 0.00 3.74
627 645 9.153479 AGCCATCTTATATTCTAGAAACTCAGT 57.847 33.333 9.71 0.00 0.00 3.41
641 659 7.863901 AAACTGTCTCCTAGCCATCTTATAT 57.136 36.000 0.00 0.00 0.00 0.86
642 660 8.958060 ATAAACTGTCTCCTAGCCATCTTATA 57.042 34.615 0.00 0.00 0.00 0.98
675 693 4.873746 TCTTTTGGTGTGTTGTTTTGGA 57.126 36.364 0.00 0.00 0.00 3.53
682 700 2.539476 GCCAGTTCTTTTGGTGTGTTG 58.461 47.619 0.00 0.00 38.02 3.33
699 717 0.111446 TTTCAGTCGATTTGGGGCCA 59.889 50.000 4.39 0.00 0.00 5.36
724 742 4.768130 TTTTGTTTTTCGGTCAGTCACA 57.232 36.364 0.00 0.00 0.00 3.58
732 750 6.394809 AGTTGACTGATTTTTGTTTTTCGGT 58.605 32.000 0.00 0.00 0.00 4.69
735 753 7.478355 GTGCAAGTTGACTGATTTTTGTTTTTC 59.522 33.333 7.16 0.00 0.00 2.29
750 769 1.160137 CAGGCTAGGTGCAAGTTGAC 58.840 55.000 7.16 2.08 45.15 3.18
755 774 3.550437 ATAGAACAGGCTAGGTGCAAG 57.450 47.619 0.00 0.00 45.15 4.01
769 788 5.121142 TGGTGCGCTGTTTTAACTATAGAAC 59.879 40.000 9.73 0.90 0.00 3.01
777 796 9.458374 AATAATATAATGGTGCGCTGTTTTAAC 57.542 29.630 9.73 0.00 0.00 2.01
804 823 8.139989 GCAGATCAACTAATGGCATATTTCTTT 58.860 33.333 0.00 0.00 0.00 2.52
815 2755 4.096190 AGGGATGCAGATCAACTAATGG 57.904 45.455 0.00 0.00 0.00 3.16
821 2761 3.936564 GATCCTAGGGATGCAGATCAAC 58.063 50.000 9.46 0.00 43.27 3.18
845 2785 5.285651 CAAGCAAAATTTCTACCGACCAAA 58.714 37.500 0.00 0.00 0.00 3.28
875 2815 3.666797 GGTTCACTTCGGCAAAATTTACG 59.333 43.478 0.00 0.00 0.00 3.18
882 2822 3.027292 GCGGTTCACTTCGGCAAA 58.973 55.556 0.00 0.00 0.00 3.68
890 2846 1.004440 GAAGAGCTGGCGGTTCACT 60.004 57.895 12.90 0.00 0.00 3.41
954 2911 1.448893 GGTTCGCCGATGCTGGTTA 60.449 57.895 0.00 0.00 34.43 2.85
981 2938 1.652563 GGTTTGTGTTCGGCTGGAC 59.347 57.895 0.00 0.00 0.00 4.02
984 2941 2.637025 CGGGTTTGTGTTCGGCTG 59.363 61.111 0.00 0.00 0.00 4.85
986 2943 4.676586 CGCGGGTTTGTGTTCGGC 62.677 66.667 0.00 0.00 0.00 5.54
988 2945 2.549282 CTCGCGGGTTTGTGTTCG 59.451 61.111 6.13 0.00 0.00 3.95
989 2946 2.054140 TTGCTCGCGGGTTTGTGTTC 62.054 55.000 8.30 0.00 0.00 3.18
991 2948 1.452145 ATTTGCTCGCGGGTTTGTGT 61.452 50.000 8.30 0.00 0.00 3.72
993 2950 0.519961 GTATTTGCTCGCGGGTTTGT 59.480 50.000 8.30 0.00 0.00 2.83
1149 3106 2.922503 TGCTTGAGCCACCGGAGA 60.923 61.111 9.46 0.00 41.18 3.71
1254 3211 1.307866 GGGGAATGGGGAGAGTGGA 60.308 63.158 0.00 0.00 0.00 4.02
1444 3401 3.823330 GAGGTCGACGGGCACGAT 61.823 66.667 19.19 0.00 44.60 3.73
1994 3966 5.906772 ATCCCCGAACTATTTATTCCAGT 57.093 39.130 0.00 0.00 0.00 4.00
2102 4074 4.891992 ACTGTAGCTCAATACACCAACT 57.108 40.909 0.00 0.00 32.36 3.16
2148 4120 2.229062 CGCACACTAACTGAGGAGAGAA 59.771 50.000 0.00 0.00 0.00 2.87
2183 4155 5.065346 CACATATACGGTGCCAACATAAACA 59.935 40.000 0.00 0.00 0.00 2.83
2189 4161 3.336138 TTCACATATACGGTGCCAACA 57.664 42.857 0.00 0.00 36.22 3.33
2194 4172 3.058914 GCCAGATTTCACATATACGGTGC 60.059 47.826 0.00 0.00 36.22 5.01
2212 4190 6.058183 AGTGCTAGAAATAATAGGTTGCCAG 58.942 40.000 0.00 0.00 0.00 4.85
2218 4196 8.320338 ACAGGTAAGTGCTAGAAATAATAGGT 57.680 34.615 0.00 0.00 0.00 3.08
2228 4206 5.773680 AGTTTGACTACAGGTAAGTGCTAGA 59.226 40.000 0.00 0.00 0.00 2.43
2239 4217 4.290942 AGGGAGGATAGTTTGACTACAGG 58.709 47.826 0.00 0.00 32.84 4.00
2246 4224 2.912956 AGCACAAGGGAGGATAGTTTGA 59.087 45.455 0.00 0.00 0.00 2.69
2262 4240 7.387397 GGTTATCAAATTTTCCAATGAAGCACA 59.613 33.333 0.00 0.00 0.00 4.57
2292 4315 3.929610 GGACTTCAGTGCAGTGATAGAAC 59.070 47.826 24.41 19.03 36.33 3.01
2295 4318 3.194329 TCAGGACTTCAGTGCAGTGATAG 59.806 47.826 24.41 22.87 38.96 2.08
2307 4330 3.055819 GCTCAAGTGGTATCAGGACTTCA 60.056 47.826 0.00 0.00 0.00 3.02
2336 4359 5.616488 TCAACGGATAACTAAAAAGCCAC 57.384 39.130 0.00 0.00 0.00 5.01
2449 4472 4.836825 CCAGAACATTCTAGGAGAAGCAA 58.163 43.478 0.00 0.00 37.69 3.91
2497 4520 8.519492 AGACAACATCGTAAAATTCCAAAATG 57.481 30.769 0.00 0.00 0.00 2.32
2506 4529 7.530010 CCATGAGAAAGACAACATCGTAAAAT 58.470 34.615 0.00 0.00 0.00 1.82
2515 4538 2.507484 CCTGCCATGAGAAAGACAACA 58.493 47.619 0.00 0.00 0.00 3.33
2544 4567 5.642063 TCAGTAACTTCCATGAACGGAAATC 59.358 40.000 0.00 0.00 44.42 2.17
2618 4660 7.102847 AGAAAAACAACCTCGTAAAAATCCA 57.897 32.000 0.00 0.00 0.00 3.41
2659 4701 0.251430 GGGTTGGGGAACGGAAATCA 60.251 55.000 0.00 0.00 0.00 2.57
2716 4758 6.971527 TTTGTGTACTCGAGTTTCTCAAAA 57.028 33.333 27.71 19.71 30.20 2.44
2720 4762 7.495339 GAGTATTTGTGTACTCGAGTTTCTC 57.505 40.000 25.44 17.14 40.66 2.87
2730 4772 6.952358 TCCCTCTACTTGAGTATTTGTGTACT 59.048 38.462 0.00 0.00 41.11 2.73
2731 4773 7.093858 ACTCCCTCTACTTGAGTATTTGTGTAC 60.094 40.741 0.00 0.00 41.11 2.90
2732 4774 6.952358 ACTCCCTCTACTTGAGTATTTGTGTA 59.048 38.462 0.00 0.00 41.11 2.90
2733 4775 5.780793 ACTCCCTCTACTTGAGTATTTGTGT 59.219 40.000 0.00 0.00 41.11 3.72
2734 4776 6.287589 ACTCCCTCTACTTGAGTATTTGTG 57.712 41.667 0.00 0.00 41.11 3.33
2735 4777 6.952358 TGTACTCCCTCTACTTGAGTATTTGT 59.048 38.462 0.00 0.00 41.96 2.83
2736 4778 7.122948 AGTGTACTCCCTCTACTTGAGTATTTG 59.877 40.741 0.00 0.00 41.96 2.32
2737 4779 7.183460 AGTGTACTCCCTCTACTTGAGTATTT 58.817 38.462 0.00 0.00 41.96 1.40
2738 4780 6.733509 AGTGTACTCCCTCTACTTGAGTATT 58.266 40.000 0.00 0.00 41.96 1.89
2739 4781 6.069556 TGAGTGTACTCCCTCTACTTGAGTAT 60.070 42.308 9.37 0.00 41.96 2.12
2740 4782 5.250082 TGAGTGTACTCCCTCTACTTGAGTA 59.750 44.000 9.37 0.00 42.20 2.59
2741 4783 4.043059 TGAGTGTACTCCCTCTACTTGAGT 59.957 45.833 9.37 0.00 42.20 3.41
2742 4784 4.590918 TGAGTGTACTCCCTCTACTTGAG 58.409 47.826 9.37 0.00 42.20 3.02
2743 4785 4.590918 CTGAGTGTACTCCCTCTACTTGA 58.409 47.826 9.37 0.00 42.20 3.02
2744 4786 3.129638 GCTGAGTGTACTCCCTCTACTTG 59.870 52.174 9.37 0.00 42.20 3.16
2745 4787 3.358118 GCTGAGTGTACTCCCTCTACTT 58.642 50.000 9.37 0.00 42.20 2.24
2746 4788 2.357361 GGCTGAGTGTACTCCCTCTACT 60.357 54.545 9.37 0.00 42.20 2.57
2747 4789 2.025898 GGCTGAGTGTACTCCCTCTAC 58.974 57.143 9.37 0.00 42.20 2.59
2748 4790 1.923850 AGGCTGAGTGTACTCCCTCTA 59.076 52.381 9.37 0.00 42.20 2.43
2749 4791 0.707616 AGGCTGAGTGTACTCCCTCT 59.292 55.000 9.37 1.91 42.20 3.69
2750 4792 0.820871 CAGGCTGAGTGTACTCCCTC 59.179 60.000 9.42 0.00 42.20 4.30
2751 4793 1.261238 GCAGGCTGAGTGTACTCCCT 61.261 60.000 20.86 6.77 42.20 4.20
2752 4794 1.219393 GCAGGCTGAGTGTACTCCC 59.781 63.158 20.86 4.69 42.20 4.30
2753 4795 0.539051 ATGCAGGCTGAGTGTACTCC 59.461 55.000 20.86 0.00 42.20 3.85
2754 4796 1.205655 TGATGCAGGCTGAGTGTACTC 59.794 52.381 20.86 5.09 43.15 2.59
2755 4797 1.206610 CTGATGCAGGCTGAGTGTACT 59.793 52.381 20.86 0.00 0.00 2.73
2756 4798 1.205655 TCTGATGCAGGCTGAGTGTAC 59.794 52.381 20.86 0.00 31.51 2.90
2757 4799 1.560505 TCTGATGCAGGCTGAGTGTA 58.439 50.000 20.86 0.00 31.51 2.90
2758 4800 0.910338 ATCTGATGCAGGCTGAGTGT 59.090 50.000 20.86 0.00 31.51 3.55
2759 4801 1.941294 GAATCTGATGCAGGCTGAGTG 59.059 52.381 20.86 2.93 31.51 3.51
2760 4802 1.558294 TGAATCTGATGCAGGCTGAGT 59.442 47.619 20.86 5.06 31.51 3.41
2761 4803 2.327200 TGAATCTGATGCAGGCTGAG 57.673 50.000 20.86 6.64 31.51 3.35
2762 4804 2.171870 TGATGAATCTGATGCAGGCTGA 59.828 45.455 20.86 3.68 31.51 4.26
2763 4805 2.550180 CTGATGAATCTGATGCAGGCTG 59.450 50.000 10.94 10.94 31.51 4.85
2764 4806 2.172930 ACTGATGAATCTGATGCAGGCT 59.827 45.455 4.36 0.00 31.51 4.58
2765 4807 2.548904 GACTGATGAATCTGATGCAGGC 59.451 50.000 4.36 2.86 31.51 4.85
2766 4808 3.810386 CAGACTGATGAATCTGATGCAGG 59.190 47.826 4.36 0.31 44.32 4.85
2767 4809 4.443621 ACAGACTGATGAATCTGATGCAG 58.556 43.478 10.08 6.52 44.32 4.41
2768 4810 4.439968 GACAGACTGATGAATCTGATGCA 58.560 43.478 10.08 0.00 44.32 3.96
2769 4811 3.808726 GGACAGACTGATGAATCTGATGC 59.191 47.826 10.08 0.00 44.32 3.91
2770 4812 4.049869 CGGACAGACTGATGAATCTGATG 58.950 47.826 10.08 5.35 44.32 3.07
2771 4813 3.069300 CCGGACAGACTGATGAATCTGAT 59.931 47.826 10.08 0.00 44.32 2.90
2772 4814 2.428530 CCGGACAGACTGATGAATCTGA 59.571 50.000 10.08 0.00 44.32 3.27
2773 4815 2.482664 CCCGGACAGACTGATGAATCTG 60.483 54.545 10.08 0.60 46.49 2.90
2774 4816 1.759445 CCCGGACAGACTGATGAATCT 59.241 52.381 10.08 0.00 0.00 2.40
2775 4817 1.757118 TCCCGGACAGACTGATGAATC 59.243 52.381 10.08 0.00 0.00 2.52
2776 4818 1.482593 GTCCCGGACAGACTGATGAAT 59.517 52.381 13.05 0.00 32.09 2.57
2777 4819 0.895530 GTCCCGGACAGACTGATGAA 59.104 55.000 13.05 0.00 32.09 2.57
2778 4820 0.970937 GGTCCCGGACAGACTGATGA 60.971 60.000 19.43 0.00 33.68 2.92
2779 4821 1.517832 GGTCCCGGACAGACTGATG 59.482 63.158 19.43 0.00 33.68 3.07
2780 4822 1.686110 GGGTCCCGGACAGACTGAT 60.686 63.158 19.43 0.00 33.68 2.90
2781 4823 2.283676 GGGTCCCGGACAGACTGA 60.284 66.667 19.43 0.00 33.68 3.41
2782 4824 2.283966 AGGGTCCCGGACAGACTG 60.284 66.667 19.43 0.00 33.68 3.51
2783 4825 2.037527 GAGGGTCCCGGACAGACT 59.962 66.667 19.43 13.21 33.68 3.24
2784 4826 3.450115 CGAGGGTCCCGGACAGAC 61.450 72.222 19.43 8.73 33.68 3.51
2788 4830 3.782443 ATTGCGAGGGTCCCGGAC 61.782 66.667 9.30 9.30 0.00 4.79
2789 4831 3.781307 CATTGCGAGGGTCCCGGA 61.781 66.667 0.73 0.00 0.00 5.14
2790 4832 3.740128 CTCATTGCGAGGGTCCCGG 62.740 68.421 0.99 0.00 38.18 5.73
2791 4833 2.202932 CTCATTGCGAGGGTCCCG 60.203 66.667 0.99 0.00 38.18 5.14
2792 4834 2.514824 GCTCATTGCGAGGGTCCC 60.515 66.667 0.00 0.00 42.55 4.46
2808 4850 5.218139 CAAGACAAAAAGGTGATCTTCAGC 58.782 41.667 0.00 0.00 44.62 4.26
2809 4851 5.218139 GCAAGACAAAAAGGTGATCTTCAG 58.782 41.667 0.00 0.00 33.94 3.02
2810 4852 4.037923 GGCAAGACAAAAAGGTGATCTTCA 59.962 41.667 0.00 0.00 33.94 3.02
2811 4853 4.279420 AGGCAAGACAAAAAGGTGATCTTC 59.721 41.667 0.00 0.00 33.94 2.87
2812 4854 4.218312 AGGCAAGACAAAAAGGTGATCTT 58.782 39.130 0.00 0.00 37.28 2.40
2813 4855 3.823304 GAGGCAAGACAAAAAGGTGATCT 59.177 43.478 0.00 0.00 0.00 2.75
2814 4856 3.823304 AGAGGCAAGACAAAAAGGTGATC 59.177 43.478 0.00 0.00 0.00 2.92
2815 4857 3.571401 CAGAGGCAAGACAAAAAGGTGAT 59.429 43.478 0.00 0.00 0.00 3.06
2816 4858 2.951642 CAGAGGCAAGACAAAAAGGTGA 59.048 45.455 0.00 0.00 0.00 4.02
2817 4859 2.544486 GCAGAGGCAAGACAAAAAGGTG 60.544 50.000 0.00 0.00 40.72 4.00
2818 4860 1.683385 GCAGAGGCAAGACAAAAAGGT 59.317 47.619 0.00 0.00 40.72 3.50
2819 4861 2.428888 GCAGAGGCAAGACAAAAAGG 57.571 50.000 0.00 0.00 40.72 3.11
2831 4873 1.607628 CCATGAATTAGCTGCAGAGGC 59.392 52.381 20.43 2.30 41.68 4.70
2832 4874 2.228059 CCCATGAATTAGCTGCAGAGG 58.772 52.381 20.43 3.96 0.00 3.69
2833 4875 2.877168 GACCCATGAATTAGCTGCAGAG 59.123 50.000 20.43 0.00 0.00 3.35
2834 4876 2.239402 TGACCCATGAATTAGCTGCAGA 59.761 45.455 20.43 0.00 0.00 4.26
2835 4877 2.617308 CTGACCCATGAATTAGCTGCAG 59.383 50.000 10.11 10.11 0.00 4.41
2836 4878 2.025981 ACTGACCCATGAATTAGCTGCA 60.026 45.455 1.02 0.00 0.00 4.41
2837 4879 2.357009 CACTGACCCATGAATTAGCTGC 59.643 50.000 0.00 0.00 0.00 5.25
2838 4880 3.376234 CACACTGACCCATGAATTAGCTG 59.624 47.826 0.00 0.00 0.00 4.24
2839 4881 3.009473 ACACACTGACCCATGAATTAGCT 59.991 43.478 0.00 0.00 0.00 3.32
2840 4882 3.347216 ACACACTGACCCATGAATTAGC 58.653 45.455 0.00 0.00 0.00 3.09
2841 4883 4.379813 GCAACACACTGACCCATGAATTAG 60.380 45.833 0.00 0.00 0.00 1.73
2842 4884 3.505680 GCAACACACTGACCCATGAATTA 59.494 43.478 0.00 0.00 0.00 1.40
2843 4885 2.297033 GCAACACACTGACCCATGAATT 59.703 45.455 0.00 0.00 0.00 2.17
2844 4886 1.888512 GCAACACACTGACCCATGAAT 59.111 47.619 0.00 0.00 0.00 2.57
2845 4887 1.317613 GCAACACACTGACCCATGAA 58.682 50.000 0.00 0.00 0.00 2.57
2846 4888 0.182299 TGCAACACACTGACCCATGA 59.818 50.000 0.00 0.00 0.00 3.07
2847 4889 0.311790 GTGCAACACACTGACCCATG 59.688 55.000 0.00 0.00 46.41 3.66
2848 4890 0.106769 TGTGCAACACACTGACCCAT 60.107 50.000 0.00 0.00 45.67 4.00
2849 4891 1.301293 TGTGCAACACACTGACCCA 59.699 52.632 0.00 0.00 45.67 4.51
2850 4892 4.234019 TGTGCAACACACTGACCC 57.766 55.556 0.00 0.00 45.67 4.46
2860 4902 2.557924 TCATGTTGGAAGGATGTGCAAC 59.442 45.455 2.99 2.99 46.60 4.17
2861 4903 2.821378 CTCATGTTGGAAGGATGTGCAA 59.179 45.455 0.00 0.00 0.00 4.08
2862 4904 2.439409 CTCATGTTGGAAGGATGTGCA 58.561 47.619 0.00 0.00 0.00 4.57
2863 4905 1.133790 GCTCATGTTGGAAGGATGTGC 59.866 52.381 0.00 0.00 31.64 4.57
2864 4906 1.399440 CGCTCATGTTGGAAGGATGTG 59.601 52.381 0.00 0.00 0.00 3.21
2865 4907 1.278985 TCGCTCATGTTGGAAGGATGT 59.721 47.619 0.00 0.00 0.00 3.06
2866 4908 1.667724 GTCGCTCATGTTGGAAGGATG 59.332 52.381 0.00 0.00 0.00 3.51
2867 4909 1.278985 TGTCGCTCATGTTGGAAGGAT 59.721 47.619 0.00 0.00 0.00 3.24
2868 4910 0.684535 TGTCGCTCATGTTGGAAGGA 59.315 50.000 0.00 0.00 0.00 3.36
2869 4911 1.742761 ATGTCGCTCATGTTGGAAGG 58.257 50.000 0.00 0.00 35.19 3.46
2870 4912 2.743664 TCAATGTCGCTCATGTTGGAAG 59.256 45.455 0.00 0.00 36.81 3.46
2871 4913 2.777094 TCAATGTCGCTCATGTTGGAA 58.223 42.857 0.00 0.00 36.81 3.53
2872 4914 2.470983 TCAATGTCGCTCATGTTGGA 57.529 45.000 0.00 0.00 36.81 3.53
2873 4915 2.159476 CCTTCAATGTCGCTCATGTTGG 60.159 50.000 0.00 0.00 36.81 3.77
2874 4916 2.743664 TCCTTCAATGTCGCTCATGTTG 59.256 45.455 0.00 0.00 36.81 3.33
2875 4917 3.057969 TCCTTCAATGTCGCTCATGTT 57.942 42.857 0.00 0.00 36.81 2.71
2876 4918 2.768253 TCCTTCAATGTCGCTCATGT 57.232 45.000 0.00 0.00 36.81 3.21
2877 4919 3.005554 ACTTCCTTCAATGTCGCTCATG 58.994 45.455 0.00 0.00 36.81 3.07
2878 4920 3.005554 CACTTCCTTCAATGTCGCTCAT 58.994 45.455 0.00 0.00 38.57 2.90
2879 4921 2.037121 TCACTTCCTTCAATGTCGCTCA 59.963 45.455 0.00 0.00 0.00 4.26
2880 4922 2.688507 TCACTTCCTTCAATGTCGCTC 58.311 47.619 0.00 0.00 0.00 5.03
2881 4923 2.808543 GTTCACTTCCTTCAATGTCGCT 59.191 45.455 0.00 0.00 0.00 4.93
2882 4924 2.808543 AGTTCACTTCCTTCAATGTCGC 59.191 45.455 0.00 0.00 0.00 5.19
2883 4925 5.023551 GAAGTTCACTTCCTTCAATGTCG 57.976 43.478 8.31 0.00 44.93 4.35
2894 4936 1.531578 GGTCTTGGCGAAGTTCACTTC 59.468 52.381 8.41 9.33 46.63 3.01
2895 4937 1.141053 AGGTCTTGGCGAAGTTCACTT 59.859 47.619 8.41 0.00 39.23 3.16
2896 4938 0.759346 AGGTCTTGGCGAAGTTCACT 59.241 50.000 8.41 0.59 0.00 3.41
2897 4939 1.149148 GAGGTCTTGGCGAAGTTCAC 58.851 55.000 8.41 0.00 0.00 3.18
2898 4940 0.034896 GGAGGTCTTGGCGAAGTTCA 59.965 55.000 8.41 0.00 0.00 3.18
2899 4941 0.034896 TGGAGGTCTTGGCGAAGTTC 59.965 55.000 8.41 5.35 0.00 3.01
2900 4942 0.693049 ATGGAGGTCTTGGCGAAGTT 59.307 50.000 8.41 0.00 0.00 2.66
2901 4943 0.036010 CATGGAGGTCTTGGCGAAGT 60.036 55.000 8.41 0.00 0.00 3.01
2902 4944 0.250234 TCATGGAGGTCTTGGCGAAG 59.750 55.000 1.39 1.39 0.00 3.79
2903 4945 0.911769 ATCATGGAGGTCTTGGCGAA 59.088 50.000 0.00 0.00 0.00 4.70
2904 4946 1.788229 TATCATGGAGGTCTTGGCGA 58.212 50.000 0.00 0.00 0.00 5.54
2905 4947 2.037641 TGATATCATGGAGGTCTTGGCG 59.962 50.000 0.00 0.00 0.00 5.69
2906 4948 3.406764 GTGATATCATGGAGGTCTTGGC 58.593 50.000 9.02 0.00 0.00 4.52
2907 4949 3.657634 CGTGATATCATGGAGGTCTTGG 58.342 50.000 15.99 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.