Multiple sequence alignment - TraesCS6B01G179000

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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 TraesCS6B01G179000 chr6B 100.000 3666 0 0 1 3666 198987331 198983666 0.000000e+00 6770.0
1 TraesCS6B01G179000 chr6B 77.083 240 46 6 2932 3166 42765941 42766176 2.970000e-26 130.0
2 TraesCS6B01G179000 chr6B 94.872 78 4 0 542 619 198978788 198978711 4.970000e-24 122.0
3 TraesCS6B01G179000 chr6D 91.051 2827 104 47 40 2787 110445722 110442966 0.000000e+00 3681.0
4 TraesCS6B01G179000 chr6D 95.000 260 13 0 2932 3191 467769409 467769150 3.410000e-110 409.0
5 TraesCS6B01G179000 chr6D 95.946 148 4 1 3384 3531 467766952 467766807 4.730000e-59 239.0
6 TraesCS6B01G179000 chr6D 92.086 139 10 1 3195 3332 467769079 467768941 1.040000e-45 195.0
7 TraesCS6B01G179000 chr6A 90.323 2821 122 61 40 2787 134950472 134947730 0.000000e+00 3557.0
8 TraesCS6B01G179000 chr6A 85.057 87 12 1 2930 3015 570521232 570521318 1.810000e-13 87.9
9 TraesCS6B01G179000 chr5A 93.561 264 17 0 2932 3195 653936193 653936456 9.540000e-106 394.0
10 TraesCS6B01G179000 chr5A 93.562 233 8 2 3331 3558 653936737 653936967 1.260000e-89 340.0
11 TraesCS6B01G179000 chr5A 92.806 139 9 1 3195 3332 653936523 653936661 2.230000e-47 200.0
12 TraesCS6B01G179000 chr5D 87.977 341 24 6 3331 3666 139937618 139937290 1.600000e-103 387.0
13 TraesCS6B01G179000 chr5D 89.773 264 27 0 2932 3195 139938164 139937901 4.530000e-89 339.0
14 TraesCS6B01G179000 chr5D 91.429 140 10 2 3195 3332 139937833 139937694 1.340000e-44 191.0
15 TraesCS6B01G179000 chr4B 88.302 265 31 0 2931 3195 25557968 25557704 5.910000e-83 318.0
16 TraesCS6B01G179000 chr4B 95.804 143 5 1 3334 3476 25555384 25555243 2.850000e-56 230.0
17 TraesCS6B01G179000 chr4B 95.105 143 6 1 3334 3476 25556238 25556097 1.320000e-54 224.0
18 TraesCS6B01G179000 chr7A 86.935 199 23 2 2137 2335 686937954 686938149 1.710000e-53 220.0
19 TraesCS6B01G179000 chr7D 85.930 199 25 2 2137 2335 594729870 594729675 3.710000e-50 209.0
20 TraesCS6B01G179000 chr7B 86.387 191 23 2 2137 2327 667070583 667070396 4.800000e-49 206.0
21 TraesCS6B01G179000 chr7B 91.150 113 10 0 3210 3322 1333755 1333643 1.760000e-33 154.0
22 TraesCS6B01G179000 chr2B 88.554 166 16 3 2143 2306 530307315 530307479 8.030000e-47 198.0
23 TraesCS6B01G179000 chr2D 88.485 165 16 3 2144 2306 450235651 450235814 2.890000e-46 196.0
24 TraesCS6B01G179000 chr2A 88.415 164 16 3 2143 2304 594581072 594581234 1.040000e-45 195.0
25 TraesCS6B01G179000 chr1B 81.250 240 43 2 2929 3167 102142357 102142595 3.740000e-45 193.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G179000 chr6B 198983666 198987331 3665 True 6770.000000 6770 100.000000 1 3666 1 chr6B.!!$R2 3665
1 TraesCS6B01G179000 chr6D 110442966 110445722 2756 True 3681.000000 3681 91.051000 40 2787 1 chr6D.!!$R1 2747
2 TraesCS6B01G179000 chr6D 467766807 467769409 2602 True 281.000000 409 94.344000 2932 3531 3 chr6D.!!$R2 599
3 TraesCS6B01G179000 chr6A 134947730 134950472 2742 True 3557.000000 3557 90.323000 40 2787 1 chr6A.!!$R1 2747
4 TraesCS6B01G179000 chr5A 653936193 653936967 774 False 311.333333 394 93.309667 2932 3558 3 chr5A.!!$F1 626
5 TraesCS6B01G179000 chr5D 139937290 139938164 874 True 305.666667 387 89.726333 2932 3666 3 chr5D.!!$R1 734
6 TraesCS6B01G179000 chr4B 25555243 25557968 2725 True 257.333333 318 93.070333 2931 3476 3 chr4B.!!$R1 545

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
354 373 0.092351 CATGTGACGCGTTTACGGAC 59.908 55.0 15.53 0.0 40.23 4.79 F
679 723 0.107165 GTCCAGGCCTCCGCTTAATT 60.107 55.0 0.00 0.0 34.44 1.40 F
1536 1622 0.241213 CTGAACGACGCTCTGGAAGA 59.759 55.0 0.00 0.0 43.69 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1900 0.326264 GATCAGGAAGGTGCACCAGT 59.674 55.000 36.39 24.24 38.89 4.00 R
1839 1933 1.407437 CGAGCCCTGCTAAATGGAAGT 60.407 52.381 0.00 0.00 39.88 3.01 R
2961 3070 0.036732 TCAAATCGCTGTGGAGGCTT 59.963 50.000 0.00 0.00 0.00 4.35 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
25 26 8.522542 AGTATCGACTACTATTTCCAGAAAGT 57.477 34.615 5.94 0.00 38.96 2.66
26 27 8.968969 AGTATCGACTACTATTTCCAGAAAGTT 58.031 33.333 5.94 0.00 38.96 2.66
27 28 9.235537 GTATCGACTACTATTTCCAGAAAGTTC 57.764 37.037 0.00 0.00 33.32 3.01
28 29 6.320171 TCGACTACTATTTCCAGAAAGTTCG 58.680 40.000 0.00 0.86 33.32 3.95
29 30 5.004535 CGACTACTATTTCCAGAAAGTTCGC 59.995 44.000 0.00 0.00 33.32 4.70
30 31 5.790593 ACTACTATTTCCAGAAAGTTCGCA 58.209 37.500 0.00 0.00 33.32 5.10
31 32 6.228258 ACTACTATTTCCAGAAAGTTCGCAA 58.772 36.000 0.00 0.00 33.32 4.85
32 33 5.613358 ACTATTTCCAGAAAGTTCGCAAG 57.387 39.130 0.00 0.00 33.32 4.01
33 34 2.774439 TTTCCAGAAAGTTCGCAAGC 57.226 45.000 0.00 0.00 37.18 4.01
34 35 1.967319 TTCCAGAAAGTTCGCAAGCT 58.033 45.000 0.00 0.00 37.18 3.74
35 36 2.831685 TCCAGAAAGTTCGCAAGCTA 57.168 45.000 0.00 0.00 37.18 3.32
36 37 3.120321 TCCAGAAAGTTCGCAAGCTAA 57.880 42.857 0.00 0.00 37.18 3.09
37 38 3.674997 TCCAGAAAGTTCGCAAGCTAAT 58.325 40.909 0.00 0.00 37.18 1.73
38 39 3.684788 TCCAGAAAGTTCGCAAGCTAATC 59.315 43.478 0.00 0.00 37.18 1.75
39 40 3.686726 CCAGAAAGTTCGCAAGCTAATCT 59.313 43.478 0.00 0.00 37.18 2.40
40 41 4.870426 CCAGAAAGTTCGCAAGCTAATCTA 59.130 41.667 0.00 0.00 37.18 1.98
41 42 5.525378 CCAGAAAGTTCGCAAGCTAATCTAT 59.475 40.000 0.00 0.00 37.18 1.98
42 43 6.037610 CCAGAAAGTTCGCAAGCTAATCTATT 59.962 38.462 0.00 0.00 37.18 1.73
43 44 7.224753 CCAGAAAGTTCGCAAGCTAATCTATTA 59.775 37.037 0.00 0.00 37.18 0.98
68 69 0.250901 TCCACCTTTTGAGCTCAGCC 60.251 55.000 17.43 0.00 0.00 4.85
71 72 2.694760 CCTTTTGAGCTCAGCCGGC 61.695 63.158 21.89 21.89 0.00 6.13
72 73 1.673665 CTTTTGAGCTCAGCCGGCT 60.674 57.895 27.08 27.08 43.26 5.52
73 74 1.919956 CTTTTGAGCTCAGCCGGCTG 61.920 60.000 44.24 44.24 44.86 4.85
74 75 3.907260 TTTGAGCTCAGCCGGCTGG 62.907 63.158 46.58 37.51 43.75 4.85
81 82 4.767255 CAGCCGGCTGGGAGTGTC 62.767 72.222 42.81 4.22 40.17 3.67
103 104 3.170991 AGGAAGAGCCAGCGGTATATA 57.829 47.619 0.00 0.00 40.02 0.86
212 231 3.006940 GCGGTCACAGGTTAATGATGAA 58.993 45.455 0.00 0.00 0.00 2.57
333 352 1.273327 CTTCCACCTTTGGGACATTGC 59.727 52.381 0.00 0.00 44.11 3.56
334 353 0.187117 TCCACCTTTGGGACATTGCA 59.813 50.000 0.00 0.00 44.11 4.08
354 373 0.092351 CATGTGACGCGTTTACGGAC 59.908 55.000 15.53 0.00 40.23 4.79
361 380 1.962306 GCGTTTACGGACTGCCCAA 60.962 57.895 4.29 0.00 40.23 4.12
362 381 1.864176 CGTTTACGGACTGCCCAAC 59.136 57.895 0.00 0.00 35.37 3.77
365 384 1.951602 GTTTACGGACTGCCCAACTTT 59.048 47.619 0.00 0.00 34.14 2.66
366 385 1.886886 TTACGGACTGCCCAACTTTC 58.113 50.000 0.00 0.00 34.14 2.62
367 386 0.320073 TACGGACTGCCCAACTTTCG 60.320 55.000 0.00 0.00 34.14 3.46
368 387 1.597027 CGGACTGCCCAACTTTCGT 60.597 57.895 0.00 0.00 34.14 3.85
369 388 1.566018 CGGACTGCCCAACTTTCGTC 61.566 60.000 0.00 0.00 34.14 4.20
370 389 0.534203 GGACTGCCCAACTTTCGTCA 60.534 55.000 0.00 0.00 34.14 4.35
371 390 0.586802 GACTGCCCAACTTTCGTCAC 59.413 55.000 0.00 0.00 0.00 3.67
372 391 0.107410 ACTGCCCAACTTTCGTCACA 60.107 50.000 0.00 0.00 0.00 3.58
373 392 0.588252 CTGCCCAACTTTCGTCACAG 59.412 55.000 0.00 0.00 0.00 3.66
424 464 7.467403 GCTTACTTAATAATTCCACAGCTGTCC 60.467 40.741 18.64 0.00 0.00 4.02
458 498 2.438975 AGGCGCATGATGGTGGTG 60.439 61.111 10.83 0.00 0.00 4.17
533 573 2.999355 GCAAGAGCAACTTCTAGACCAG 59.001 50.000 0.00 0.00 41.58 4.00
554 594 2.474816 CTTAGCTGTCCCATAAGCGAC 58.525 52.381 0.00 0.00 44.34 5.19
579 623 6.919662 CGGTGCTTATAAACCTAAGACGATAA 59.080 38.462 5.09 0.00 34.06 1.75
666 710 1.303309 GCTTTGATCATCCGTCCAGG 58.697 55.000 0.00 0.00 42.97 4.45
669 713 0.982852 TTGATCATCCGTCCAGGCCT 60.983 55.000 0.00 0.00 40.77 5.19
670 714 1.369321 GATCATCCGTCCAGGCCTC 59.631 63.158 0.00 0.00 40.77 4.70
671 715 2.105806 GATCATCCGTCCAGGCCTCC 62.106 65.000 0.00 0.00 40.77 4.30
672 716 4.227134 CATCCGTCCAGGCCTCCG 62.227 72.222 0.00 5.53 40.77 4.63
679 723 0.107165 GTCCAGGCCTCCGCTTAATT 60.107 55.000 0.00 0.00 34.44 1.40
937 1003 2.499685 GGATTCCCTCCCACGACG 59.500 66.667 0.00 0.00 38.19 5.12
939 1005 4.143333 ATTCCCTCCCACGACGCG 62.143 66.667 3.53 3.53 0.00 6.01
1046 1117 1.768870 GGAAATCCTGGTAGCTGGCTA 59.231 52.381 12.65 0.00 0.00 3.93
1453 1533 2.716017 CGAGGGACAGGAGCAGGAC 61.716 68.421 0.00 0.00 0.00 3.85
1495 1581 3.834799 GCGGTCGACGGGGAGAAT 61.835 66.667 22.64 0.00 44.51 2.40
1496 1582 2.484062 GCGGTCGACGGGGAGAATA 61.484 63.158 22.64 0.00 44.51 1.75
1534 1620 1.289066 CCTGAACGACGCTCTGGAA 59.711 57.895 16.61 0.00 34.66 3.53
1536 1622 0.241213 CTGAACGACGCTCTGGAAGA 59.759 55.000 0.00 0.00 43.69 2.87
1567 1653 1.149148 GGAAGGACAACGTGAAGCTC 58.851 55.000 0.00 0.00 0.00 4.09
1811 1900 1.674441 CTTACCCTCGCGTCATCTGTA 59.326 52.381 5.77 0.00 0.00 2.74
1814 1903 0.248661 CCCTCGCGTCATCTGTACTG 60.249 60.000 5.77 0.00 0.00 2.74
1816 1905 0.452184 CTCGCGTCATCTGTACTGGT 59.548 55.000 5.77 0.00 0.00 4.00
1839 1933 4.018506 TGCACCTTCCTGATCTTTATTGGA 60.019 41.667 0.00 0.00 0.00 3.53
1874 1968 4.687215 TCGTCGTCGGAGGTCGGT 62.687 66.667 15.05 0.00 39.77 4.69
2013 2107 5.785243 CCTAACCAGATTAGCTAGCTAACC 58.215 45.833 33.80 27.17 40.76 2.85
2014 2108 5.540719 CCTAACCAGATTAGCTAGCTAACCT 59.459 44.000 33.80 28.88 40.76 3.50
2015 2109 5.538849 AACCAGATTAGCTAGCTAACCTC 57.461 43.478 33.80 27.55 40.76 3.85
2018 2112 6.374588 ACCAGATTAGCTAGCTAACCTCTTA 58.625 40.000 33.80 14.94 40.76 2.10
2019 2113 6.839657 ACCAGATTAGCTAGCTAACCTCTTAA 59.160 38.462 33.80 15.90 40.76 1.85
2020 2114 7.149307 CCAGATTAGCTAGCTAACCTCTTAAC 58.851 42.308 33.80 18.45 40.76 2.01
2021 2115 7.014808 CCAGATTAGCTAGCTAACCTCTTAACT 59.985 40.741 33.80 18.03 40.76 2.24
2022 2116 7.865385 CAGATTAGCTAGCTAACCTCTTAACTG 59.135 40.741 33.80 24.69 40.76 3.16
2023 2117 7.562088 AGATTAGCTAGCTAACCTCTTAACTGT 59.438 37.037 33.80 16.88 40.76 3.55
2024 2118 7.477945 TTAGCTAGCTAACCTCTTAACTGTT 57.522 36.000 29.22 0.00 34.02 3.16
2025 2119 6.361768 AGCTAGCTAACCTCTTAACTGTTT 57.638 37.500 17.69 0.00 0.00 2.83
2055 2149 6.631016 ACGAGTACATGTAATTGATCACTGT 58.369 36.000 23.81 8.37 0.00 3.55
2084 2180 2.297698 TAAACAGGTCTCCTCGGTGA 57.702 50.000 0.00 0.00 0.00 4.02
2479 2575 1.265905 GGTGCCTAATTAAATCCGGCG 59.734 52.381 0.00 0.00 43.54 6.46
2582 2690 0.592754 GATCGCTGGCTCGAGTGTAC 60.593 60.000 15.13 3.07 42.14 2.90
2602 2710 8.134895 AGTGTACTATACTACTCTACTCGACAC 58.865 40.741 0.00 0.00 32.99 3.67
2603 2711 7.112844 GTGTACTATACTACTCTACTCGACACG 59.887 44.444 0.00 0.00 0.00 4.49
2604 2712 4.981674 ACTATACTACTCTACTCGACACGC 59.018 45.833 0.00 0.00 0.00 5.34
2605 2713 2.090400 ACTACTCTACTCGACACGCA 57.910 50.000 0.00 0.00 0.00 5.24
2606 2714 1.731160 ACTACTCTACTCGACACGCAC 59.269 52.381 0.00 0.00 0.00 5.34
2685 2793 9.796180 CTAGTTGATAAGTCTACTACCCTGTAT 57.204 37.037 0.00 0.00 40.23 2.29
2695 2804 6.380560 GTCTACTACCCTGTATCCTTTTCTGT 59.619 42.308 0.00 0.00 0.00 3.41
2699 2808 3.274288 CCCTGTATCCTTTTCTGTGCTC 58.726 50.000 0.00 0.00 0.00 4.26
2766 2875 5.181433 GGAACAGCTTAGTTCTAGTTTTGGG 59.819 44.000 14.54 0.00 45.52 4.12
2774 2883 5.319043 AGTTCTAGTTTTGGGATCCACAA 57.681 39.130 15.23 12.48 30.78 3.33
2777 2886 5.576563 TCTAGTTTTGGGATCCACAAGAA 57.423 39.130 15.23 9.42 30.78 2.52
2787 2896 4.811557 GGGATCCACAAGAAACTTATCTCG 59.188 45.833 15.23 0.00 0.00 4.04
2788 2897 4.271291 GGATCCACAAGAAACTTATCTCGC 59.729 45.833 6.95 0.00 0.00 5.03
2789 2898 3.250744 TCCACAAGAAACTTATCTCGCG 58.749 45.455 0.00 0.00 0.00 5.87
2790 2899 2.993899 CCACAAGAAACTTATCTCGCGT 59.006 45.455 5.77 0.00 0.00 6.01
2791 2900 3.432252 CCACAAGAAACTTATCTCGCGTT 59.568 43.478 5.77 0.00 0.00 4.84
2792 2901 4.084013 CCACAAGAAACTTATCTCGCGTTT 60.084 41.667 5.77 0.00 33.91 3.60
2793 2902 5.440685 CACAAGAAACTTATCTCGCGTTTT 58.559 37.500 5.77 0.00 31.60 2.43
2794 2903 6.347079 CCACAAGAAACTTATCTCGCGTTTTA 60.347 38.462 5.77 0.00 31.60 1.52
2795 2904 6.515340 CACAAGAAACTTATCTCGCGTTTTAC 59.485 38.462 5.77 0.00 31.60 2.01
2796 2905 6.201425 ACAAGAAACTTATCTCGCGTTTTACA 59.799 34.615 5.77 0.00 31.60 2.41
2797 2906 6.963049 AGAAACTTATCTCGCGTTTTACAT 57.037 33.333 5.77 0.00 31.60 2.29
2798 2907 8.377681 CAAGAAACTTATCTCGCGTTTTACATA 58.622 33.333 5.77 0.00 31.60 2.29
2799 2908 7.892803 AGAAACTTATCTCGCGTTTTACATAC 58.107 34.615 5.77 0.00 31.60 2.39
2800 2909 6.579491 AACTTATCTCGCGTTTTACATACC 57.421 37.500 5.77 0.00 0.00 2.73
2801 2910 5.653507 ACTTATCTCGCGTTTTACATACCA 58.346 37.500 5.77 0.00 0.00 3.25
2802 2911 6.101332 ACTTATCTCGCGTTTTACATACCAA 58.899 36.000 5.77 0.00 0.00 3.67
2803 2912 6.255020 ACTTATCTCGCGTTTTACATACCAAG 59.745 38.462 5.77 0.00 0.00 3.61
2804 2913 3.255725 TCTCGCGTTTTACATACCAAGG 58.744 45.455 5.77 0.00 0.00 3.61
2805 2914 2.997986 CTCGCGTTTTACATACCAAGGT 59.002 45.455 5.77 0.00 0.00 3.50
2806 2915 3.401182 TCGCGTTTTACATACCAAGGTT 58.599 40.909 5.77 0.00 0.00 3.50
2807 2916 4.564041 TCGCGTTTTACATACCAAGGTTA 58.436 39.130 5.77 0.00 0.00 2.85
2808 2917 4.993584 TCGCGTTTTACATACCAAGGTTAA 59.006 37.500 5.77 0.00 0.00 2.01
2809 2918 5.120519 TCGCGTTTTACATACCAAGGTTAAG 59.879 40.000 5.77 0.00 0.00 1.85
2810 2919 5.106987 CGCGTTTTACATACCAAGGTTAAGT 60.107 40.000 0.00 0.00 0.00 2.24
2811 2920 6.081693 GCGTTTTACATACCAAGGTTAAGTG 58.918 40.000 0.00 0.00 0.00 3.16
2812 2921 6.073112 GCGTTTTACATACCAAGGTTAAGTGA 60.073 38.462 0.00 0.00 0.00 3.41
2813 2922 7.361457 GCGTTTTACATACCAAGGTTAAGTGAT 60.361 37.037 0.00 0.00 0.00 3.06
2814 2923 7.960738 CGTTTTACATACCAAGGTTAAGTGATG 59.039 37.037 0.00 0.00 0.00 3.07
2815 2924 6.995511 TTACATACCAAGGTTAAGTGATGC 57.004 37.500 0.00 0.00 0.00 3.91
2816 2925 4.917385 ACATACCAAGGTTAAGTGATGCA 58.083 39.130 0.00 0.00 0.00 3.96
2817 2926 5.509498 ACATACCAAGGTTAAGTGATGCAT 58.491 37.500 0.00 0.00 0.00 3.96
2818 2927 5.590259 ACATACCAAGGTTAAGTGATGCATC 59.410 40.000 20.14 20.14 0.00 3.91
2819 2928 4.032960 ACCAAGGTTAAGTGATGCATCA 57.967 40.909 25.42 25.42 0.00 3.07
2820 2929 4.406456 ACCAAGGTTAAGTGATGCATCAA 58.594 39.130 30.24 13.22 38.75 2.57
2821 2930 5.018809 ACCAAGGTTAAGTGATGCATCAAT 58.981 37.500 30.24 26.70 38.75 2.57
2822 2931 5.481473 ACCAAGGTTAAGTGATGCATCAATT 59.519 36.000 35.88 35.88 45.63 2.32
2823 2932 6.014327 ACCAAGGTTAAGTGATGCATCAATTT 60.014 34.615 37.90 30.00 41.70 1.82
2824 2933 6.311935 CCAAGGTTAAGTGATGCATCAATTTG 59.688 38.462 37.90 29.47 41.70 2.32
2825 2934 6.594788 AGGTTAAGTGATGCATCAATTTGT 57.405 33.333 37.90 22.46 41.70 2.83
2826 2935 7.701539 AGGTTAAGTGATGCATCAATTTGTA 57.298 32.000 37.90 22.98 41.70 2.41
2827 2936 7.538575 AGGTTAAGTGATGCATCAATTTGTAC 58.461 34.615 37.90 30.46 41.70 2.90
2828 2937 6.751888 GGTTAAGTGATGCATCAATTTGTACC 59.248 38.462 37.90 33.50 41.70 3.34
2829 2938 5.981088 AAGTGATGCATCAATTTGTACCA 57.019 34.783 30.93 5.00 41.70 3.25
2830 2939 5.571784 AGTGATGCATCAATTTGTACCAG 57.428 39.130 30.24 0.00 38.75 4.00
2831 2940 5.012239 AGTGATGCATCAATTTGTACCAGT 58.988 37.500 30.24 5.13 38.75 4.00
2832 2941 5.097529 GTGATGCATCAATTTGTACCAGTG 58.902 41.667 30.24 0.00 38.75 3.66
2833 2942 4.158209 TGATGCATCAATTTGTACCAGTGG 59.842 41.667 26.87 7.91 33.08 4.00
2834 2943 2.230992 TGCATCAATTTGTACCAGTGGC 59.769 45.455 9.78 0.00 0.00 5.01
2835 2944 2.230992 GCATCAATTTGTACCAGTGGCA 59.769 45.455 9.78 0.00 0.00 4.92
2836 2945 3.305950 GCATCAATTTGTACCAGTGGCAA 60.306 43.478 9.78 3.32 0.00 4.52
2837 2946 4.236935 CATCAATTTGTACCAGTGGCAAC 58.763 43.478 9.78 8.76 0.00 4.17
2838 2947 2.292016 TCAATTTGTACCAGTGGCAACG 59.708 45.455 9.78 0.00 42.51 4.10
2848 2957 2.202946 TGGCAACGCACGTCTCAA 60.203 55.556 0.00 0.00 42.51 3.02
2849 2958 2.243957 TGGCAACGCACGTCTCAAG 61.244 57.895 0.00 0.00 42.51 3.02
2850 2959 2.127609 GCAACGCACGTCTCAAGC 60.128 61.111 0.00 0.00 0.00 4.01
2851 2960 2.881266 GCAACGCACGTCTCAAGCA 61.881 57.895 0.00 0.00 0.00 3.91
2852 2961 1.862123 CAACGCACGTCTCAAGCAT 59.138 52.632 0.00 0.00 0.00 3.79
2853 2962 0.235665 CAACGCACGTCTCAAGCATT 59.764 50.000 0.00 0.00 0.00 3.56
2868 2977 5.171147 CAAGCATTGGTCAGATGAGATTC 57.829 43.478 0.00 0.00 43.94 2.52
2869 2978 4.498894 AGCATTGGTCAGATGAGATTCA 57.501 40.909 0.00 0.00 0.00 2.57
2870 2979 4.197750 AGCATTGGTCAGATGAGATTCAC 58.802 43.478 0.00 0.00 0.00 3.18
2871 2980 3.943381 GCATTGGTCAGATGAGATTCACA 59.057 43.478 0.00 0.00 0.00 3.58
2872 2981 4.035324 GCATTGGTCAGATGAGATTCACAG 59.965 45.833 0.00 0.00 0.00 3.66
2873 2982 3.257469 TGGTCAGATGAGATTCACAGC 57.743 47.619 0.00 0.00 0.00 4.40
2874 2983 2.200067 GGTCAGATGAGATTCACAGCG 58.800 52.381 0.00 0.00 0.00 5.18
2875 2984 2.200067 GTCAGATGAGATTCACAGCGG 58.800 52.381 0.00 0.00 0.00 5.52
2876 2985 0.935898 CAGATGAGATTCACAGCGGC 59.064 55.000 0.00 0.00 0.00 6.53
2877 2986 0.538584 AGATGAGATTCACAGCGGCA 59.461 50.000 1.45 0.00 0.00 5.69
2878 2987 1.140452 AGATGAGATTCACAGCGGCAT 59.860 47.619 1.45 0.00 0.00 4.40
2879 2988 2.366590 AGATGAGATTCACAGCGGCATA 59.633 45.455 1.45 0.00 0.00 3.14
2880 2989 2.689553 TGAGATTCACAGCGGCATAA 57.310 45.000 1.45 0.00 0.00 1.90
2881 2990 2.984562 TGAGATTCACAGCGGCATAAA 58.015 42.857 1.45 0.00 0.00 1.40
2882 2991 3.342719 TGAGATTCACAGCGGCATAAAA 58.657 40.909 1.45 0.00 0.00 1.52
2883 2992 3.755905 TGAGATTCACAGCGGCATAAAAA 59.244 39.130 1.45 0.00 0.00 1.94
2884 2993 4.398988 TGAGATTCACAGCGGCATAAAAAT 59.601 37.500 1.45 0.00 0.00 1.82
2885 2994 5.588246 TGAGATTCACAGCGGCATAAAAATA 59.412 36.000 1.45 0.00 0.00 1.40
2886 2995 6.064846 AGATTCACAGCGGCATAAAAATAG 57.935 37.500 1.45 0.00 0.00 1.73
2887 2996 5.822519 AGATTCACAGCGGCATAAAAATAGA 59.177 36.000 1.45 0.00 0.00 1.98
2888 2997 5.888691 TTCACAGCGGCATAAAAATAGAA 57.111 34.783 1.45 0.00 0.00 2.10
2889 2998 6.449635 TTCACAGCGGCATAAAAATAGAAT 57.550 33.333 1.45 0.00 0.00 2.40
2890 2999 5.820131 TCACAGCGGCATAAAAATAGAATG 58.180 37.500 1.45 0.00 0.00 2.67
2891 3000 5.588246 TCACAGCGGCATAAAAATAGAATGA 59.412 36.000 1.45 0.00 0.00 2.57
2892 3001 5.682862 CACAGCGGCATAAAAATAGAATGAC 59.317 40.000 1.45 0.00 0.00 3.06
2893 3002 5.356751 ACAGCGGCATAAAAATAGAATGACA 59.643 36.000 1.45 0.00 0.00 3.58
2894 3003 6.127758 ACAGCGGCATAAAAATAGAATGACAA 60.128 34.615 1.45 0.00 0.00 3.18
2895 3004 6.919662 CAGCGGCATAAAAATAGAATGACAAT 59.080 34.615 1.45 0.00 0.00 2.71
2896 3005 8.075574 CAGCGGCATAAAAATAGAATGACAATA 58.924 33.333 1.45 0.00 0.00 1.90
2897 3006 8.629158 AGCGGCATAAAAATAGAATGACAATAA 58.371 29.630 1.45 0.00 0.00 1.40
2898 3007 9.243637 GCGGCATAAAAATAGAATGACAATAAA 57.756 29.630 0.00 0.00 0.00 1.40
2928 3037 9.834628 TCTAAAATGTATGAATGAAACGGAAAC 57.165 29.630 0.00 0.00 0.00 2.78
2929 3038 9.619316 CTAAAATGTATGAATGAAACGGAAACA 57.381 29.630 0.00 0.00 0.00 2.83
2961 3070 7.555554 AGAAACAGTATAACGAGGCTAGTTAGA 59.444 37.037 21.79 16.37 37.47 2.10
2990 3099 3.434641 CACAGCGATTTGATTGTCTCAGT 59.565 43.478 0.00 0.00 34.68 3.41
2991 3100 4.067896 ACAGCGATTTGATTGTCTCAGTT 58.932 39.130 0.00 0.00 34.68 3.16
3024 3133 9.067986 TCTTTCAATCTACGATCTAGATTAGCA 57.932 33.333 18.81 9.53 40.99 3.49
3097 3206 1.078426 CCACGGAATGACCTGGTCC 60.078 63.158 23.42 8.26 34.50 4.46
3175 3284 1.334419 CCACGTCGTACAGTTTCGAGT 60.334 52.381 0.00 1.10 36.76 4.18
3191 3300 1.825242 CGAGTGCTATCCCTCCCATCT 60.825 57.143 0.00 0.00 0.00 2.90
3195 3304 1.274712 GCTATCCCTCCCATCTCAGG 58.725 60.000 0.00 0.00 0.00 3.86
3202 3311 3.313874 CCCATCTCAGGGCGAGTT 58.686 61.111 0.00 0.00 43.10 3.01
3203 3312 1.144936 CCCATCTCAGGGCGAGTTC 59.855 63.158 0.00 0.00 43.10 3.01
3204 3313 1.227089 CCATCTCAGGGCGAGTTCG 60.227 63.158 0.00 0.00 42.88 3.95
3253 4857 1.064685 GTCCCATCCGTCCCAATCTTT 60.065 52.381 0.00 0.00 0.00 2.52
3433 7579 5.379706 AAGAATCTTGGATCCCCAACTAG 57.620 43.478 9.90 0.00 46.94 2.57
3552 7703 9.308000 ACTCTCTAAGAAGGGTGATAATGATAG 57.692 37.037 0.00 0.00 0.00 2.08
3564 7715 6.127897 GGTGATAATGATAGCCCACAAATAGC 60.128 42.308 0.00 0.00 0.00 2.97
3565 7716 6.656693 GTGATAATGATAGCCCACAAATAGCT 59.343 38.462 0.00 0.00 40.66 3.32
3599 7750 7.441760 TGTTGTTGGTACTTATATGTCGTTTGT 59.558 33.333 0.00 0.00 0.00 2.83
3600 7751 7.585286 TGTTGGTACTTATATGTCGTTTGTC 57.415 36.000 0.00 0.00 0.00 3.18
3620 7771 8.925700 GTTTGTCTCCAATTTTATTTGACATCC 58.074 33.333 0.00 0.00 33.80 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.522542 ACTTTCTGGAAATAGTAGTCGATACT 57.477 34.615 10.84 10.84 46.70 2.12
1 2 9.235537 GAACTTTCTGGAAATAGTAGTCGATAC 57.764 37.037 0.00 0.00 34.30 2.24
3 4 6.973474 CGAACTTTCTGGAAATAGTAGTCGAT 59.027 38.462 0.00 0.00 0.00 3.59
5 6 5.004535 GCGAACTTTCTGGAAATAGTAGTCG 59.995 44.000 0.00 0.00 0.00 4.18
6 7 5.867716 TGCGAACTTTCTGGAAATAGTAGTC 59.132 40.000 0.00 0.00 0.00 2.59
7 8 5.790593 TGCGAACTTTCTGGAAATAGTAGT 58.209 37.500 0.00 0.00 0.00 2.73
8 9 6.673316 GCTTGCGAACTTTCTGGAAATAGTAG 60.673 42.308 0.00 0.00 0.00 2.57
9 10 5.121768 GCTTGCGAACTTTCTGGAAATAGTA 59.878 40.000 0.00 0.00 0.00 1.82
10 11 4.083271 GCTTGCGAACTTTCTGGAAATAGT 60.083 41.667 0.00 0.00 0.00 2.12
11 12 4.154918 AGCTTGCGAACTTTCTGGAAATAG 59.845 41.667 0.00 0.00 0.00 1.73
12 13 4.072131 AGCTTGCGAACTTTCTGGAAATA 58.928 39.130 0.00 0.00 0.00 1.40
13 14 2.887152 AGCTTGCGAACTTTCTGGAAAT 59.113 40.909 0.00 0.00 0.00 2.17
14 15 2.297701 AGCTTGCGAACTTTCTGGAAA 58.702 42.857 0.00 0.00 0.00 3.13
15 16 1.967319 AGCTTGCGAACTTTCTGGAA 58.033 45.000 0.00 0.00 0.00 3.53
16 17 2.831685 TAGCTTGCGAACTTTCTGGA 57.168 45.000 0.00 0.00 0.00 3.86
17 18 3.686726 AGATTAGCTTGCGAACTTTCTGG 59.313 43.478 0.00 0.00 0.00 3.86
18 19 4.935885 AGATTAGCTTGCGAACTTTCTG 57.064 40.909 0.00 0.00 0.00 3.02
19 20 8.894768 ATAATAGATTAGCTTGCGAACTTTCT 57.105 30.769 0.00 0.00 0.00 2.52
20 21 9.937175 AAATAATAGATTAGCTTGCGAACTTTC 57.063 29.630 0.00 0.00 0.00 2.62
21 22 9.722056 CAAATAATAGATTAGCTTGCGAACTTT 57.278 29.630 0.00 0.00 0.00 2.66
22 23 8.345565 CCAAATAATAGATTAGCTTGCGAACTT 58.654 33.333 0.00 0.00 0.00 2.66
23 24 7.499232 ACCAAATAATAGATTAGCTTGCGAACT 59.501 33.333 0.00 0.00 0.00 3.01
24 25 7.639945 ACCAAATAATAGATTAGCTTGCGAAC 58.360 34.615 0.00 0.00 0.00 3.95
25 26 7.041372 GGACCAAATAATAGATTAGCTTGCGAA 60.041 37.037 0.00 0.00 0.00 4.70
26 27 6.426937 GGACCAAATAATAGATTAGCTTGCGA 59.573 38.462 0.00 0.00 0.00 5.10
27 28 6.204688 TGGACCAAATAATAGATTAGCTTGCG 59.795 38.462 0.00 0.00 0.00 4.85
28 29 7.363431 GTGGACCAAATAATAGATTAGCTTGC 58.637 38.462 0.00 0.00 0.00 4.01
29 30 7.721399 AGGTGGACCAAATAATAGATTAGCTTG 59.279 37.037 0.00 0.00 38.89 4.01
30 31 7.816411 AGGTGGACCAAATAATAGATTAGCTT 58.184 34.615 0.00 0.00 38.89 3.74
31 32 7.394144 AGGTGGACCAAATAATAGATTAGCT 57.606 36.000 0.00 0.00 38.89 3.32
32 33 8.465273 AAAGGTGGACCAAATAATAGATTAGC 57.535 34.615 0.00 0.00 38.89 3.09
34 35 9.983024 TCAAAAGGTGGACCAAATAATAGATTA 57.017 29.630 0.00 0.00 38.89 1.75
35 36 8.893563 TCAAAAGGTGGACCAAATAATAGATT 57.106 30.769 0.00 0.00 38.89 2.40
36 37 7.068716 GCTCAAAAGGTGGACCAAATAATAGAT 59.931 37.037 0.00 0.00 38.89 1.98
37 38 6.377146 GCTCAAAAGGTGGACCAAATAATAGA 59.623 38.462 0.00 0.00 38.89 1.98
38 39 6.378280 AGCTCAAAAGGTGGACCAAATAATAG 59.622 38.462 0.00 0.00 38.89 1.73
39 40 6.252995 AGCTCAAAAGGTGGACCAAATAATA 58.747 36.000 0.00 0.00 38.89 0.98
40 41 5.086621 AGCTCAAAAGGTGGACCAAATAAT 58.913 37.500 0.00 0.00 38.89 1.28
41 42 4.479158 AGCTCAAAAGGTGGACCAAATAA 58.521 39.130 0.00 0.00 38.89 1.40
42 43 4.079253 GAGCTCAAAAGGTGGACCAAATA 58.921 43.478 9.40 0.00 38.89 1.40
43 44 2.893489 GAGCTCAAAAGGTGGACCAAAT 59.107 45.455 9.40 0.00 38.89 2.32
68 69 2.046892 CCTTGACACTCCCAGCCG 60.047 66.667 0.00 0.00 0.00 5.52
71 72 1.338579 GCTCTTCCTTGACACTCCCAG 60.339 57.143 0.00 0.00 0.00 4.45
72 73 0.687354 GCTCTTCCTTGACACTCCCA 59.313 55.000 0.00 0.00 0.00 4.37
73 74 0.035915 GGCTCTTCCTTGACACTCCC 60.036 60.000 0.00 0.00 0.00 4.30
74 75 0.687354 TGGCTCTTCCTTGACACTCC 59.313 55.000 0.00 0.00 35.26 3.85
81 82 0.179000 ATACCGCTGGCTCTTCCTTG 59.821 55.000 0.00 0.00 35.26 3.61
116 117 4.278419 CCGAAATGTCAGAAAAGTCCCTTT 59.722 41.667 0.00 0.00 34.94 3.11
122 140 1.886542 GGCCCGAAATGTCAGAAAAGT 59.113 47.619 0.00 0.00 0.00 2.66
212 231 2.754946 TAATTCACCGCCTTTCGTCT 57.245 45.000 0.00 0.00 36.19 4.18
333 352 0.179260 CCGTAAACGCGTCACATGTG 60.179 55.000 20.18 20.18 38.18 3.21
334 353 0.318869 TCCGTAAACGCGTCACATGT 60.319 50.000 14.44 0.00 38.18 3.21
382 419 3.573967 AGTAAGCAACCCAAACTTGATGG 59.426 43.478 0.00 0.00 37.71 3.51
424 464 1.019278 CCTGGTTGACGATGTTCCCG 61.019 60.000 0.00 0.00 0.00 5.14
445 485 0.394216 TAGCACCACCACCATCATGC 60.394 55.000 0.00 0.00 0.00 4.06
554 594 4.675510 TCGTCTTAGGTTTATAAGCACCG 58.324 43.478 1.55 0.00 38.21 4.94
579 623 6.221659 GGTTAGTGCTAATTAATACTCCGCT 58.778 40.000 4.95 0.00 0.00 5.52
666 710 3.275999 TGGACTTAAATTAAGCGGAGGC 58.724 45.455 12.28 0.00 39.39 4.70
669 713 3.275999 GGCTGGACTTAAATTAAGCGGA 58.724 45.455 12.28 0.00 39.39 5.54
670 714 2.357952 GGGCTGGACTTAAATTAAGCGG 59.642 50.000 12.28 4.20 39.39 5.52
671 715 2.031683 CGGGCTGGACTTAAATTAAGCG 59.968 50.000 12.28 3.07 39.39 4.68
672 716 3.014623 ACGGGCTGGACTTAAATTAAGC 58.985 45.455 12.28 5.81 39.39 3.09
673 717 4.258543 TCACGGGCTGGACTTAAATTAAG 58.741 43.478 10.92 10.92 41.51 1.85
679 723 1.066430 GTCATCACGGGCTGGACTTAA 60.066 52.381 0.00 0.00 0.00 1.85
725 769 2.607892 AAGGCAAAGACGCGACAGC 61.608 57.895 15.93 12.64 40.74 4.40
726 770 1.205064 CAAGGCAAAGACGCGACAG 59.795 57.895 15.93 1.76 0.00 3.51
906 972 1.208293 GGAATCCCAGCCCGAGATATC 59.792 57.143 0.00 0.00 0.00 1.63
939 1005 4.179579 GGCAAATCTGGCGGCGTC 62.180 66.667 3.62 3.62 38.51 5.19
1441 1521 3.575351 GAACGCGTCCTGCTCCTGT 62.575 63.158 14.44 0.00 43.27 4.00
1453 1533 1.055235 GAACGACATCACGAACGCG 59.945 57.895 3.53 3.53 44.79 6.01
1495 1581 3.006728 CCCACGGGGTCCTGCTTA 61.007 66.667 1.28 0.00 38.25 3.09
1512 1598 1.009389 CAGAGCGTCGTTCAGGTTCC 61.009 60.000 11.82 0.00 0.00 3.62
1567 1653 2.087009 GTCCGCGAACAGGAAGTCG 61.087 63.158 8.23 0.00 39.84 4.18
1661 1747 1.079543 CACCGAAGTCCAGCTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
1811 1900 0.326264 GATCAGGAAGGTGCACCAGT 59.674 55.000 36.39 24.24 38.89 4.00
1814 1903 2.206576 AAAGATCAGGAAGGTGCACC 57.793 50.000 29.22 29.22 0.00 5.01
1816 1905 4.018506 TCCAATAAAGATCAGGAAGGTGCA 60.019 41.667 0.00 0.00 0.00 4.57
1839 1933 1.407437 CGAGCCCTGCTAAATGGAAGT 60.407 52.381 0.00 0.00 39.88 3.01
1874 1968 4.690719 ATCGCGTCCGGCACCAAA 62.691 61.111 5.77 0.00 43.84 3.28
1955 2049 1.602605 GCTTGGTGTGGGGGTGTAC 60.603 63.158 0.00 0.00 0.00 2.90
1975 2069 3.259902 GGTTAGGCACTTACAGTACTGC 58.740 50.000 22.90 8.38 40.09 4.40
1996 2090 7.865385 CAGTTAAGAGGTTAGCTAGCTAATCTG 59.135 40.741 41.50 27.06 46.47 2.90
2013 2107 9.188588 TGTACTCGTTGATAAAACAGTTAAGAG 57.811 33.333 0.00 0.00 0.00 2.85
2014 2108 9.701098 ATGTACTCGTTGATAAAACAGTTAAGA 57.299 29.630 0.00 0.00 0.00 2.10
2015 2109 9.741168 CATGTACTCGTTGATAAAACAGTTAAG 57.259 33.333 0.00 0.00 0.00 1.85
2018 2112 7.724305 ACATGTACTCGTTGATAAAACAGTT 57.276 32.000 0.00 0.00 0.00 3.16
2019 2113 8.821147 TTACATGTACTCGTTGATAAAACAGT 57.179 30.769 4.68 0.00 0.00 3.55
2025 2119 9.810545 TGATCAATTACATGTACTCGTTGATAA 57.189 29.630 22.14 17.08 35.62 1.75
2055 2149 6.187727 AGGAGACCTGTTTAATCACAAGAA 57.812 37.500 0.00 0.00 29.57 2.52
2084 2180 2.671619 CGGCACCGACCCAACATT 60.672 61.111 2.01 0.00 42.83 2.71
2365 2461 3.175240 CCGAAGTCGAGCACGCAG 61.175 66.667 1.43 0.00 43.02 5.18
2582 2690 4.981054 TGCGTGTCGAGTAGAGTAGTATAG 59.019 45.833 0.00 0.00 0.00 1.31
2667 2775 8.342270 AGAAAAGGATACAGGGTAGTAGACTTA 58.658 37.037 0.00 0.00 41.41 2.24
2668 2776 7.124448 CAGAAAAGGATACAGGGTAGTAGACTT 59.876 40.741 0.00 0.00 41.41 3.01
2685 2793 1.202639 TCAAGCGAGCACAGAAAAGGA 60.203 47.619 0.00 0.00 0.00 3.36
2695 2804 0.889994 AATTTGCCATCAAGCGAGCA 59.110 45.000 0.00 0.00 33.12 4.26
2699 2808 1.406539 AGCCTAATTTGCCATCAAGCG 59.593 47.619 0.00 0.00 33.12 4.68
2766 2875 4.026475 CGCGAGATAAGTTTCTTGTGGATC 60.026 45.833 0.00 0.00 35.06 3.36
2774 2883 6.963049 ATGTAAAACGCGAGATAAGTTTCT 57.037 33.333 15.93 0.00 37.13 2.52
2777 2886 6.101332 TGGTATGTAAAACGCGAGATAAGTT 58.899 36.000 15.93 0.00 0.00 2.66
2787 2896 6.073112 TCACTTAACCTTGGTATGTAAAACGC 60.073 38.462 0.00 0.00 0.00 4.84
2788 2897 7.424227 TCACTTAACCTTGGTATGTAAAACG 57.576 36.000 0.00 0.00 0.00 3.60
2789 2898 7.753580 GCATCACTTAACCTTGGTATGTAAAAC 59.246 37.037 0.00 0.00 0.00 2.43
2790 2899 7.448777 TGCATCACTTAACCTTGGTATGTAAAA 59.551 33.333 0.00 0.00 0.00 1.52
2791 2900 6.943146 TGCATCACTTAACCTTGGTATGTAAA 59.057 34.615 0.00 0.00 0.00 2.01
2792 2901 6.477253 TGCATCACTTAACCTTGGTATGTAA 58.523 36.000 0.00 0.00 0.00 2.41
2793 2902 6.056090 TGCATCACTTAACCTTGGTATGTA 57.944 37.500 0.00 0.00 0.00 2.29
2794 2903 4.917385 TGCATCACTTAACCTTGGTATGT 58.083 39.130 0.00 0.00 0.00 2.29
2795 2904 5.589855 TGATGCATCACTTAACCTTGGTATG 59.410 40.000 25.42 0.00 0.00 2.39
2796 2905 5.754782 TGATGCATCACTTAACCTTGGTAT 58.245 37.500 25.42 0.00 0.00 2.73
2797 2906 5.172687 TGATGCATCACTTAACCTTGGTA 57.827 39.130 25.42 0.00 0.00 3.25
2798 2907 4.032960 TGATGCATCACTTAACCTTGGT 57.967 40.909 25.42 0.00 0.00 3.67
2799 2908 5.587388 ATTGATGCATCACTTAACCTTGG 57.413 39.130 28.72 0.00 36.36 3.61
2800 2909 6.869913 ACAAATTGATGCATCACTTAACCTTG 59.130 34.615 28.72 22.77 36.36 3.61
2801 2910 6.996509 ACAAATTGATGCATCACTTAACCTT 58.003 32.000 28.72 11.44 36.36 3.50
2802 2911 6.594788 ACAAATTGATGCATCACTTAACCT 57.405 33.333 28.72 11.79 36.36 3.50
2803 2912 6.751888 GGTACAAATTGATGCATCACTTAACC 59.248 38.462 28.72 26.84 36.36 2.85
2804 2913 7.312154 TGGTACAAATTGATGCATCACTTAAC 58.688 34.615 28.72 23.23 32.86 2.01
2805 2914 7.176515 ACTGGTACAAATTGATGCATCACTTAA 59.823 33.333 28.72 14.90 38.70 1.85
2806 2915 6.658816 ACTGGTACAAATTGATGCATCACTTA 59.341 34.615 28.72 15.29 38.70 2.24
2807 2916 5.477984 ACTGGTACAAATTGATGCATCACTT 59.522 36.000 28.72 25.32 38.70 3.16
2808 2917 5.012239 ACTGGTACAAATTGATGCATCACT 58.988 37.500 28.72 20.90 38.70 3.41
2809 2918 5.097529 CACTGGTACAAATTGATGCATCAC 58.902 41.667 28.72 14.94 38.70 3.06
2810 2919 4.158209 CCACTGGTACAAATTGATGCATCA 59.842 41.667 25.42 25.42 38.70 3.07
2811 2920 4.675510 CCACTGGTACAAATTGATGCATC 58.324 43.478 20.14 20.14 38.70 3.91
2812 2921 3.119029 GCCACTGGTACAAATTGATGCAT 60.119 43.478 0.00 0.00 38.70 3.96
2813 2922 2.230992 GCCACTGGTACAAATTGATGCA 59.769 45.455 0.00 0.00 38.70 3.96
2814 2923 2.230992 TGCCACTGGTACAAATTGATGC 59.769 45.455 0.00 0.00 38.70 3.91
2815 2924 4.236935 GTTGCCACTGGTACAAATTGATG 58.763 43.478 0.00 0.00 38.70 3.07
2816 2925 3.057596 CGTTGCCACTGGTACAAATTGAT 60.058 43.478 0.00 0.00 38.70 2.57
2817 2926 2.292016 CGTTGCCACTGGTACAAATTGA 59.708 45.455 0.00 0.00 38.70 2.57
2818 2927 2.660490 CGTTGCCACTGGTACAAATTG 58.340 47.619 0.00 0.00 38.70 2.32
2819 2928 1.000717 GCGTTGCCACTGGTACAAATT 60.001 47.619 0.00 0.00 38.70 1.82
2820 2929 0.596082 GCGTTGCCACTGGTACAAAT 59.404 50.000 0.00 0.00 38.70 2.32
2821 2930 0.748367 TGCGTTGCCACTGGTACAAA 60.748 50.000 0.00 0.00 38.70 2.83
2822 2931 1.153147 TGCGTTGCCACTGGTACAA 60.153 52.632 0.00 0.00 38.70 2.41
2823 2932 1.890041 GTGCGTTGCCACTGGTACA 60.890 57.895 0.00 0.00 33.02 2.90
2824 2933 2.943653 GTGCGTTGCCACTGGTAC 59.056 61.111 0.00 0.00 33.02 3.34
2825 2934 2.663520 CGTGCGTTGCCACTGGTA 60.664 61.111 0.00 0.00 33.60 3.25
2826 2935 4.849310 ACGTGCGTTGCCACTGGT 62.849 61.111 0.00 0.00 33.60 4.00
2827 2936 4.012895 GACGTGCGTTGCCACTGG 62.013 66.667 0.00 0.00 33.60 4.00
2828 2937 2.943345 GAGACGTGCGTTGCCACTG 61.943 63.158 0.00 0.00 33.60 3.66
2829 2938 2.661866 GAGACGTGCGTTGCCACT 60.662 61.111 0.00 0.00 33.60 4.00
2830 2939 2.430080 CTTGAGACGTGCGTTGCCAC 62.430 60.000 0.00 0.00 0.00 5.01
2831 2940 2.202946 TTGAGACGTGCGTTGCCA 60.203 55.556 0.00 0.00 0.00 4.92
2832 2941 2.551270 CTTGAGACGTGCGTTGCC 59.449 61.111 0.00 0.00 0.00 4.52
2833 2942 2.127609 GCTTGAGACGTGCGTTGC 60.128 61.111 0.00 0.00 0.00 4.17
2834 2943 0.235665 AATGCTTGAGACGTGCGTTG 59.764 50.000 0.00 0.00 35.03 4.10
2835 2944 0.235665 CAATGCTTGAGACGTGCGTT 59.764 50.000 0.00 0.00 36.51 4.84
2836 2945 1.568612 CCAATGCTTGAGACGTGCGT 61.569 55.000 0.00 0.00 0.00 5.24
2837 2946 1.133253 CCAATGCTTGAGACGTGCG 59.867 57.895 0.00 0.00 0.00 5.34
2838 2947 0.166814 GACCAATGCTTGAGACGTGC 59.833 55.000 0.00 0.00 0.00 5.34
2839 2948 1.462283 CTGACCAATGCTTGAGACGTG 59.538 52.381 0.00 0.00 0.00 4.49
2840 2949 1.344438 TCTGACCAATGCTTGAGACGT 59.656 47.619 0.00 0.00 0.00 4.34
2841 2950 2.084610 TCTGACCAATGCTTGAGACG 57.915 50.000 0.00 0.00 0.00 4.18
2842 2951 3.603532 TCATCTGACCAATGCTTGAGAC 58.396 45.455 0.00 0.00 0.00 3.36
2843 2952 3.516700 TCTCATCTGACCAATGCTTGAGA 59.483 43.478 0.00 0.00 36.65 3.27
2844 2953 3.870274 TCTCATCTGACCAATGCTTGAG 58.130 45.455 0.00 0.00 0.00 3.02
2845 2954 3.986996 TCTCATCTGACCAATGCTTGA 57.013 42.857 0.00 0.00 0.00 3.02
2846 2955 4.638865 TGAATCTCATCTGACCAATGCTTG 59.361 41.667 0.00 0.00 0.00 4.01
2847 2956 4.639310 GTGAATCTCATCTGACCAATGCTT 59.361 41.667 0.00 0.00 0.00 3.91
2848 2957 4.197750 GTGAATCTCATCTGACCAATGCT 58.802 43.478 0.00 0.00 0.00 3.79
2849 2958 3.943381 TGTGAATCTCATCTGACCAATGC 59.057 43.478 0.00 0.00 0.00 3.56
2850 2959 4.035324 GCTGTGAATCTCATCTGACCAATG 59.965 45.833 0.00 0.00 0.00 2.82
2851 2960 4.197750 GCTGTGAATCTCATCTGACCAAT 58.802 43.478 0.00 0.00 0.00 3.16
2852 2961 3.603532 GCTGTGAATCTCATCTGACCAA 58.396 45.455 0.00 0.00 0.00 3.67
2853 2962 2.417787 CGCTGTGAATCTCATCTGACCA 60.418 50.000 0.00 0.00 0.00 4.02
2854 2963 2.200067 CGCTGTGAATCTCATCTGACC 58.800 52.381 0.00 0.00 0.00 4.02
2855 2964 2.200067 CCGCTGTGAATCTCATCTGAC 58.800 52.381 0.00 0.00 0.00 3.51
2856 2965 1.472201 GCCGCTGTGAATCTCATCTGA 60.472 52.381 0.00 0.00 0.00 3.27
2857 2966 0.935898 GCCGCTGTGAATCTCATCTG 59.064 55.000 0.00 0.00 0.00 2.90
2858 2967 0.538584 TGCCGCTGTGAATCTCATCT 59.461 50.000 0.00 0.00 0.00 2.90
2859 2968 1.590932 ATGCCGCTGTGAATCTCATC 58.409 50.000 0.00 0.00 0.00 2.92
2860 2969 2.916702 TATGCCGCTGTGAATCTCAT 57.083 45.000 0.00 0.00 0.00 2.90
2861 2970 2.689553 TTATGCCGCTGTGAATCTCA 57.310 45.000 0.00 0.00 0.00 3.27
2862 2971 4.355543 TTTTTATGCCGCTGTGAATCTC 57.644 40.909 0.00 0.00 0.00 2.75
2863 2972 4.989279 ATTTTTATGCCGCTGTGAATCT 57.011 36.364 0.00 0.00 0.00 2.40
2864 2973 6.060028 TCTATTTTTATGCCGCTGTGAATC 57.940 37.500 0.00 0.00 0.00 2.52
2865 2974 6.449635 TTCTATTTTTATGCCGCTGTGAAT 57.550 33.333 0.00 0.00 0.00 2.57
2866 2975 5.888691 TTCTATTTTTATGCCGCTGTGAA 57.111 34.783 0.00 0.00 0.00 3.18
2867 2976 5.588246 TCATTCTATTTTTATGCCGCTGTGA 59.412 36.000 0.00 0.00 0.00 3.58
2868 2977 5.682862 GTCATTCTATTTTTATGCCGCTGTG 59.317 40.000 0.00 0.00 0.00 3.66
2869 2978 5.356751 TGTCATTCTATTTTTATGCCGCTGT 59.643 36.000 0.00 0.00 0.00 4.40
2870 2979 5.820131 TGTCATTCTATTTTTATGCCGCTG 58.180 37.500 0.00 0.00 0.00 5.18
2871 2980 6.449635 TTGTCATTCTATTTTTATGCCGCT 57.550 33.333 0.00 0.00 0.00 5.52
2872 2981 8.795786 TTATTGTCATTCTATTTTTATGCCGC 57.204 30.769 0.00 0.00 0.00 6.53
2902 3011 9.834628 GTTTCCGTTTCATTCATACATTTTAGA 57.165 29.630 0.00 0.00 0.00 2.10
2903 3012 9.619316 TGTTTCCGTTTCATTCATACATTTTAG 57.381 29.630 0.00 0.00 0.00 1.85
2904 3013 9.400638 GTGTTTCCGTTTCATTCATACATTTTA 57.599 29.630 0.00 0.00 0.00 1.52
2905 3014 7.923344 TGTGTTTCCGTTTCATTCATACATTTT 59.077 29.630 0.00 0.00 0.00 1.82
2906 3015 7.429633 TGTGTTTCCGTTTCATTCATACATTT 58.570 30.769 0.00 0.00 0.00 2.32
2907 3016 6.976088 TGTGTTTCCGTTTCATTCATACATT 58.024 32.000 0.00 0.00 0.00 2.71
2908 3017 6.567687 TGTGTTTCCGTTTCATTCATACAT 57.432 33.333 0.00 0.00 0.00 2.29
2909 3018 6.567687 ATGTGTTTCCGTTTCATTCATACA 57.432 33.333 0.00 0.00 0.00 2.29
2910 3019 7.081349 TCAATGTGTTTCCGTTTCATTCATAC 58.919 34.615 0.00 0.00 0.00 2.39
2911 3020 7.174080 TCTCAATGTGTTTCCGTTTCATTCATA 59.826 33.333 0.00 0.00 0.00 2.15
2912 3021 6.016360 TCTCAATGTGTTTCCGTTTCATTCAT 60.016 34.615 0.00 0.00 0.00 2.57
2913 3022 5.298026 TCTCAATGTGTTTCCGTTTCATTCA 59.702 36.000 0.00 0.00 0.00 2.57
2914 3023 5.757886 TCTCAATGTGTTTCCGTTTCATTC 58.242 37.500 0.00 0.00 0.00 2.67
2915 3024 5.766150 TCTCAATGTGTTTCCGTTTCATT 57.234 34.783 0.00 0.00 0.00 2.57
2916 3025 5.766150 TTCTCAATGTGTTTCCGTTTCAT 57.234 34.783 0.00 0.00 0.00 2.57
2917 3026 5.106118 TGTTTCTCAATGTGTTTCCGTTTCA 60.106 36.000 0.00 0.00 0.00 2.69
2918 3027 5.336744 TGTTTCTCAATGTGTTTCCGTTTC 58.663 37.500 0.00 0.00 0.00 2.78
2919 3028 5.105917 ACTGTTTCTCAATGTGTTTCCGTTT 60.106 36.000 0.00 0.00 0.00 3.60
2920 3029 4.398044 ACTGTTTCTCAATGTGTTTCCGTT 59.602 37.500 0.00 0.00 0.00 4.44
2921 3030 3.945285 ACTGTTTCTCAATGTGTTTCCGT 59.055 39.130 0.00 0.00 0.00 4.69
2922 3031 4.552166 ACTGTTTCTCAATGTGTTTCCG 57.448 40.909 0.00 0.00 0.00 4.30
2923 3032 7.744715 CGTTATACTGTTTCTCAATGTGTTTCC 59.255 37.037 0.00 0.00 0.00 3.13
2924 3033 8.492748 TCGTTATACTGTTTCTCAATGTGTTTC 58.507 33.333 0.00 0.00 0.00 2.78
2925 3034 8.373048 TCGTTATACTGTTTCTCAATGTGTTT 57.627 30.769 0.00 0.00 0.00 2.83
2926 3035 7.117812 CCTCGTTATACTGTTTCTCAATGTGTT 59.882 37.037 0.00 0.00 0.00 3.32
2927 3036 6.590292 CCTCGTTATACTGTTTCTCAATGTGT 59.410 38.462 0.00 0.00 0.00 3.72
2928 3037 6.455646 GCCTCGTTATACTGTTTCTCAATGTG 60.456 42.308 0.00 0.00 0.00 3.21
2929 3038 5.581085 GCCTCGTTATACTGTTTCTCAATGT 59.419 40.000 0.00 0.00 0.00 2.71
2961 3070 0.036732 TCAAATCGCTGTGGAGGCTT 59.963 50.000 0.00 0.00 0.00 4.35
2990 3099 7.776107 AGATCGTAGATTGAAAGATCTGACAA 58.224 34.615 14.33 14.33 44.22 3.18
2991 3100 7.340122 AGATCGTAGATTGAAAGATCTGACA 57.660 36.000 0.00 0.00 44.22 3.58
3097 3206 1.269831 CGGCCCGATTAAGGAGAGAAG 60.270 57.143 0.00 0.00 0.00 2.85
3175 3284 1.483876 CCTGAGATGGGAGGGATAGCA 60.484 57.143 0.00 0.00 0.00 3.49
3197 3306 2.202440 ACGATCGTGGCGAACTCG 60.202 61.111 22.06 11.34 41.86 4.18
3198 3307 2.789203 GCACGATCGTGGCGAACTC 61.789 63.158 40.19 23.08 45.49 3.01
3199 3308 2.809601 GCACGATCGTGGCGAACT 60.810 61.111 40.19 7.58 45.49 3.01
3200 3309 4.191485 CGCACGATCGTGGCGAAC 62.191 66.667 37.92 26.41 45.49 3.95
3451 7597 7.062956 GCATATATAGCATACTTACACGTGCAA 59.937 37.037 17.22 8.50 39.94 4.08
3552 7703 0.529119 GCATGCAGCTATTTGTGGGC 60.529 55.000 14.21 0.00 41.15 5.36
3564 7715 2.294233 AGTACCAACAACAAGCATGCAG 59.706 45.455 21.98 14.52 0.00 4.41
3565 7716 2.305928 AGTACCAACAACAAGCATGCA 58.694 42.857 21.98 0.00 0.00 3.96
3636 7787 9.710818 TGTCCCTTAGTCTAAGTAGTAAATCAT 57.289 33.333 16.69 0.00 33.96 2.45


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

AutoCloner maintained by Alex Coulton.