Multiple sequence alignment - TraesCS2D01G548600

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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 TraesCS2D01G548600 chr2D 100.000 6020 0 0 1 6020 624302138 624308157 0.000000e+00 11117.0
1 TraesCS2D01G548600 chr2D 96.000 950 35 2 1115 2064 63545727 63544781 0.000000e+00 1541.0
2 TraesCS2D01G548600 chr2D 97.196 107 3 0 614 720 624302698 624302804 1.330000e-41 182.0
3 TraesCS2D01G548600 chr2D 97.196 107 3 0 561 667 624302751 624302857 1.330000e-41 182.0
4 TraesCS2D01G548600 chr2A 92.005 3940 227 43 666 4578 755702628 755706506 0.000000e+00 5450.0
5 TraesCS2D01G548600 chr2A 89.001 1091 72 24 4945 6017 755710267 755711327 0.000000e+00 1306.0
6 TraesCS2D01G548600 chr2A 86.341 615 59 15 3 608 755702078 755702676 0.000000e+00 647.0
7 TraesCS2D01G548600 chr2A 93.351 376 20 3 4576 4950 755706552 755706923 8.820000e-153 551.0
8 TraesCS2D01G548600 chr2B 91.557 3885 215 44 726 4578 766231591 766235394 0.000000e+00 5252.0
9 TraesCS2D01G548600 chr2B 90.226 1463 90 19 4576 6020 766235439 766236866 0.000000e+00 1860.0
10 TraesCS2D01G548600 chr2B 89.788 519 45 4 1 514 766229771 766230286 0.000000e+00 658.0
11 TraesCS2D01G548600 chr2B 89.189 222 23 1 381 601 766231371 766231592 5.940000e-70 276.0
12 TraesCS2D01G548600 chr2B 93.750 112 5 2 551 661 766231248 766231358 3.730000e-37 167.0
13 TraesCS2D01G548600 chr2B 96.040 101 4 0 614 714 766231258 766231358 1.340000e-36 165.0
14 TraesCS2D01G548600 chr2B 75.904 166 28 11 4314 4474 166612698 166612856 2.330000e-09 75.0
15 TraesCS2D01G548600 chr2B 97.222 36 0 1 3095 3130 359311959 359311993 6.520000e-05 60.2
16 TraesCS2D01G548600 chr3A 79.348 1380 218 39 984 2350 568018304 568019629 0.000000e+00 907.0
17 TraesCS2D01G548600 chr3A 82.545 888 130 13 1466 2348 567976283 567977150 0.000000e+00 758.0
18 TraesCS2D01G548600 chr3A 81.116 466 64 16 2626 3072 568096708 568097168 9.600000e-93 351.0
19 TraesCS2D01G548600 chr3D 79.275 1380 222 37 984 2350 429786759 429788087 0.000000e+00 905.0
20 TraesCS2D01G548600 chr3D 78.997 1276 220 29 1067 2336 430050462 430051695 0.000000e+00 828.0
21 TraesCS2D01G548600 chr3D 78.727 1288 229 26 1066 2350 429909589 429910834 0.000000e+00 819.0
22 TraesCS2D01G548600 chr3D 83.072 892 118 18 1455 2336 429724712 429725580 0.000000e+00 780.0
23 TraesCS2D01G548600 chr3D 77.267 849 157 22 3226 4071 429727212 429728027 3.290000e-127 466.0
24 TraesCS2D01G548600 chr3D 82.035 462 64 15 2622 3070 430051916 430052371 5.700000e-100 375.0
25 TraesCS2D01G548600 chr3D 79.431 457 77 14 2622 3071 429911125 429911571 2.110000e-79 307.0
26 TraesCS2D01G548600 chr3D 74.717 265 47 12 4314 4567 597141964 597141709 3.840000e-17 100.0
27 TraesCS2D01G548600 chr3B 79.305 1295 215 32 1066 2350 562273027 562274278 0.000000e+00 857.0
28 TraesCS2D01G548600 chr3B 78.654 1293 222 30 1067 2350 562401819 562403066 0.000000e+00 809.0
29 TraesCS2D01G548600 chr3B 83.562 876 122 14 1466 2336 561971184 561972042 0.000000e+00 800.0
30 TraesCS2D01G548600 chr3B 77.636 863 149 27 3215 4071 561973748 561974572 9.070000e-133 484.0
31 TraesCS2D01G548600 chr3B 91.489 235 18 2 2840 3072 562403575 562403809 7.530000e-84 322.0
32 TraesCS2D01G548600 chrUn 95.946 148 6 0 518 665 23192666 23192813 2.170000e-59 241.0
33 TraesCS2D01G548600 chrUn 97.059 102 3 0 614 715 23192709 23192810 8.020000e-39 172.0
34 TraesCS2D01G548600 chrUn 79.545 220 16 18 526 720 23192547 23192762 4.900000e-26 130.0
35 TraesCS2D01G548600 chrUn 89.041 73 2 3 667 739 23192582 23192648 1.080000e-12 86.1
36 TraesCS2D01G548600 chrUn 100.000 41 0 0 614 654 23192582 23192622 6.470000e-10 76.8
37 TraesCS2D01G548600 chrUn 82.558 86 12 3 405 488 111009569 111009653 8.370000e-09 73.1
38 TraesCS2D01G548600 chrUn 79.439 107 12 6 440 544 111062325 111062423 3.890000e-07 67.6
39 TraesCS2D01G548600 chr5A 82.609 138 15 6 391 521 701785506 701785641 4.930000e-21 113.0
40 TraesCS2D01G548600 chr4B 78.142 183 26 10 383 554 660766779 660766600 2.970000e-18 104.0
41 TraesCS2D01G548600 chr6B 97.059 34 1 0 3103 3136 372319382 372319415 2.340000e-04 58.4
42 TraesCS2D01G548600 chr6D 94.286 35 1 1 3095 3129 254240385 254240418 1.100000e-02 52.8
43 TraesCS2D01G548600 chr6A 94.286 35 1 1 3095 3129 364621889 364621856 1.100000e-02 52.8


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 TraesCS2D01G548600 chr2D 624302138 624308157 6019 False 11117.000000 11117 100.000000 1 6020 1 chr2D.!!$F1 6019
1 TraesCS2D01G548600 chr2D 63544781 63545727 946 True 1541.000000 1541 96.000000 1115 2064 1 chr2D.!!$R1 949
2 TraesCS2D01G548600 chr2A 755702078 755711327 9249 False 1988.500000 5450 90.174500 3 6017 4 chr2A.!!$F1 6014
3 TraesCS2D01G548600 chr2B 766229771 766236866 7095 False 1396.333333 5252 91.758333 1 6020 6 chr2B.!!$F3 6019
4 TraesCS2D01G548600 chr3A 568018304 568019629 1325 False 907.000000 907 79.348000 984 2350 1 chr3A.!!$F2 1366
5 TraesCS2D01G548600 chr3A 567976283 567977150 867 False 758.000000 758 82.545000 1466 2348 1 chr3A.!!$F1 882
6 TraesCS2D01G548600 chr3D 429786759 429788087 1328 False 905.000000 905 79.275000 984 2350 1 chr3D.!!$F1 1366
7 TraesCS2D01G548600 chr3D 429724712 429728027 3315 False 623.000000 780 80.169500 1455 4071 2 chr3D.!!$F2 2616
8 TraesCS2D01G548600 chr3D 430050462 430052371 1909 False 601.500000 828 80.516000 1067 3070 2 chr3D.!!$F4 2003
9 TraesCS2D01G548600 chr3D 429909589 429911571 1982 False 563.000000 819 79.079000 1066 3071 2 chr3D.!!$F3 2005
10 TraesCS2D01G548600 chr3B 562273027 562274278 1251 False 857.000000 857 79.305000 1066 2350 1 chr3B.!!$F1 1284
11 TraesCS2D01G548600 chr3B 561971184 561974572 3388 False 642.000000 800 80.599000 1466 4071 2 chr3B.!!$F2 2605
12 TraesCS2D01G548600 chr3B 562401819 562403809 1990 False 565.500000 809 85.071500 1067 3072 2 chr3B.!!$F3 2005

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
539 573 0.461339 ACATGGATACGCGTGGAACC 60.461 55.0 24.59 18.72 42.51 3.62 F
778 1909 0.657840 GCGCACAGTGAAGTTCAGTT 59.342 50.0 10.62 0.00 0.00 3.16 F
1291 2438 1.309499 CGGCGTCCTCACTCTCTCTT 61.309 60.0 0.00 0.00 0.00 2.85 F
2167 3329 0.325933 CATGGACCAGTGCAGGAAGA 59.674 55.0 0.00 0.00 34.64 2.87 F
2813 4924 0.601046 TCAGCTCTCCGTTGTGCTTG 60.601 55.0 0.00 0.00 35.01 4.01 F
3662 5845 1.103803 TGGTGCTAGAGATCGTCACC 58.896 55.0 13.94 13.94 45.43 4.02 F
4036 6219 1.361204 TGAGCCTGGAGGAAACATCA 58.639 50.0 0.00 0.00 37.39 3.07 F
4835 7072 0.461548 TTGTCCTGCTATCTCCAGCG 59.538 55.0 0.00 0.00 44.88 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2629 0.888736 TGTCCGTCGGGTAGTCGAAA 60.889 55.000 12.29 0.00 41.05 3.46 R
2143 3305 0.957395 CTGCACTGGTCCATGGTCAC 60.957 60.000 12.58 2.96 0.00 3.67 R
2785 4867 0.028770 CGGAGAGCTGAGTGATCGAC 59.971 60.000 0.00 0.00 35.99 4.20 R
3662 5845 0.460987 AGCCTCGATTCTTCTTGCCG 60.461 55.000 0.00 0.00 0.00 5.69 R
4322 6506 0.108585 AAGCCCACCATATAGCACCG 59.891 55.000 0.00 0.00 0.00 4.94 R
4644 6881 0.393077 ATTGTTCTCTATCGCCCCGG 59.607 55.000 0.00 0.00 0.00 5.73 R
5016 10603 0.798776 CAGCCTTCCACGACATTCAC 59.201 55.000 0.00 0.00 0.00 3.18 R
5897 11502 2.745821 ACGCATGCACATGGATGATATC 59.254 45.455 19.57 0.00 45.22 1.63 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
83 84 0.626382 TGTCAGGTTTGGTGGTTCCA 59.374 50.000 0.00 0.00 45.60 3.53
152 153 5.765176 GCATAGACAATAATGCAATGCTGA 58.235 37.500 6.82 0.00 46.19 4.26
153 154 5.628193 GCATAGACAATAATGCAATGCTGAC 59.372 40.000 6.82 0.00 46.19 3.51
162 168 5.664294 AATGCAATGCTGACAGGAATTTA 57.336 34.783 6.82 0.00 0.00 1.40
163 169 5.664294 ATGCAATGCTGACAGGAATTTAA 57.336 34.783 6.82 0.00 0.00 1.52
182 188 7.656707 ATTTAATGAACAAGGTTTCACATGC 57.343 32.000 0.00 0.00 38.31 4.06
195 201 2.722094 TCACATGCACCCCTTATGAAC 58.278 47.619 0.00 0.00 0.00 3.18
206 212 7.617723 TGCACCCCTTATGAACAGTATAAATTT 59.382 33.333 0.00 0.00 0.00 1.82
381 388 8.181904 ACATTGTTTCATGAACATTAAGGTCT 57.818 30.769 7.89 0.00 46.99 3.85
412 419 5.988310 TTTCTTCACTAAGGATACCACGA 57.012 39.130 0.00 0.00 33.22 4.35
424 431 3.865745 GGATACCACGAGTGTCATTTCTG 59.134 47.826 2.36 0.00 38.31 3.02
427 434 3.650139 ACCACGAGTGTCATTTCTGTAC 58.350 45.455 2.36 0.00 0.00 2.90
429 436 3.561503 CACGAGTGTCATTTCTGTACGA 58.438 45.455 0.00 0.00 0.00 3.43
434 441 5.854866 CGAGTGTCATTTCTGTACGAAACTA 59.145 40.000 12.77 4.54 43.90 2.24
475 482 6.868339 GTCAACCAAGTTTGATATCCCAAAAG 59.132 38.462 0.00 0.00 37.80 2.27
478 485 6.993079 ACCAAGTTTGATATCCCAAAAGTTC 58.007 36.000 0.00 0.00 37.72 3.01
488 495 9.927668 TGATATCCCAAAAGTTCAGAATTTTTC 57.072 29.630 12.25 2.70 29.27 2.29
539 573 0.461339 ACATGGATACGCGTGGAACC 60.461 55.000 24.59 18.72 42.51 3.62
582 1514 7.362802 ACTACTAATCTACTCCAATCCAACC 57.637 40.000 0.00 0.00 0.00 3.77
583 1515 6.901300 ACTACTAATCTACTCCAATCCAACCA 59.099 38.462 0.00 0.00 0.00 3.67
585 1517 7.213178 ACTAATCTACTCCAATCCAACCAAT 57.787 36.000 0.00 0.00 0.00 3.16
589 1521 7.797121 ATCTACTCCAATCCAACCAATTTTT 57.203 32.000 0.00 0.00 0.00 1.94
644 1576 7.695055 TCTACTCCAATCCAACCAAATTTCTA 58.305 34.615 0.00 0.00 0.00 2.10
661 1593 7.439108 AATTTCTACTACTAGTCAAGCCCAT 57.561 36.000 0.00 0.00 0.00 4.00
662 1594 6.466885 TTTCTACTACTAGTCAAGCCCATC 57.533 41.667 0.00 0.00 0.00 3.51
664 1596 5.378332 TCTACTACTAGTCAAGCCCATCTC 58.622 45.833 0.00 0.00 0.00 2.75
714 1845 7.439108 AATTTCTACTACTAGTCAAGCCCAT 57.561 36.000 0.00 0.00 0.00 4.00
715 1846 6.869206 TTTCTACTACTAGTCAAGCCCATT 57.131 37.500 0.00 0.00 0.00 3.16
744 1875 3.243816 TCTGCTGCTCCTGCACCA 61.244 61.111 0.00 0.00 45.31 4.17
754 1885 2.821366 CTGCACCAGCGATGGACC 60.821 66.667 29.47 16.65 46.23 4.46
775 1906 2.243957 CGGCGCACAGTGAAGTTCA 61.244 57.895 10.83 0.08 0.00 3.18
776 1907 1.571460 GGCGCACAGTGAAGTTCAG 59.429 57.895 10.83 0.00 0.00 3.02
777 1908 1.160329 GGCGCACAGTGAAGTTCAGT 61.160 55.000 10.83 6.60 0.00 3.41
778 1909 0.657840 GCGCACAGTGAAGTTCAGTT 59.342 50.000 10.62 0.00 0.00 3.16
779 1910 1.333258 GCGCACAGTGAAGTTCAGTTC 60.333 52.381 10.62 2.97 0.00 3.01
902 2033 3.560278 GGATAACCACCACGCGCG 61.560 66.667 30.96 30.96 35.97 6.86
903 2034 2.812178 GATAACCACCACGCGCGT 60.812 61.111 32.73 32.73 0.00 6.01
1036 2183 1.970352 CTCCCTGCTTCCTCTCCTGC 61.970 65.000 0.00 0.00 0.00 4.85
1164 2311 2.970639 CTCGGCTTCTTCGTCCCA 59.029 61.111 0.00 0.00 0.00 4.37
1291 2438 1.309499 CGGCGTCCTCACTCTCTCTT 61.309 60.000 0.00 0.00 0.00 2.85
1348 2495 3.299977 CCGTGTGGTCCTCCGACA 61.300 66.667 0.00 0.00 41.13 4.35
2164 3326 1.841302 GACCATGGACCAGTGCAGGA 61.841 60.000 21.47 0.00 34.64 3.86
2167 3329 0.325933 CATGGACCAGTGCAGGAAGA 59.674 55.000 0.00 0.00 34.64 2.87
2343 3505 3.512516 GATGCCTTGACCGCTGCC 61.513 66.667 0.00 0.00 0.00 4.85
2409 3636 8.239314 TCCAAATTTCTCATTTCAATTCGAGAG 58.761 33.333 0.00 0.00 35.99 3.20
2464 4465 4.147322 CGTGGTTGTGATCGCCGC 62.147 66.667 3.31 1.72 0.00 6.53
2667 4704 3.462021 GAAGATGATCTTGACCTTCGGG 58.538 50.000 13.18 0.00 36.73 5.14
2700 4737 1.971167 GTGATTCTGGCCGCCACAA 60.971 57.895 8.43 5.05 0.00 3.33
2711 4748 1.355210 CGCCACAAACAACTTCGCT 59.645 52.632 0.00 0.00 0.00 4.93
2761 4798 2.116238 TGGCCCTGTCTATCTGGTAAC 58.884 52.381 0.00 0.00 33.97 2.50
2764 4801 3.574826 GGCCCTGTCTATCTGGTAACTAG 59.425 52.174 0.00 0.00 33.97 2.57
2792 4874 9.599866 AAGATCAAGTAATAACAATGTCGATCA 57.400 29.630 0.00 0.00 0.00 2.92
2793 4875 9.035607 AGATCAAGTAATAACAATGTCGATCAC 57.964 33.333 0.00 0.00 0.00 3.06
2794 4876 8.948631 ATCAAGTAATAACAATGTCGATCACT 57.051 30.769 0.00 0.00 0.00 3.41
2795 4877 8.407457 TCAAGTAATAACAATGTCGATCACTC 57.593 34.615 0.00 0.00 0.00 3.51
2796 4878 8.032451 TCAAGTAATAACAATGTCGATCACTCA 58.968 33.333 0.00 0.00 0.00 3.41
2798 4880 5.725110 AATAACAATGTCGATCACTCAGC 57.275 39.130 0.00 0.00 0.00 4.26
2800 4882 2.886081 ACAATGTCGATCACTCAGCTC 58.114 47.619 0.00 0.00 0.00 4.09
2801 4883 2.495270 ACAATGTCGATCACTCAGCTCT 59.505 45.455 0.00 0.00 0.00 4.09
2802 4884 3.114809 CAATGTCGATCACTCAGCTCTC 58.885 50.000 0.00 0.00 0.00 3.20
2813 4924 0.601046 TCAGCTCTCCGTTGTGCTTG 60.601 55.000 0.00 0.00 35.01 4.01
2818 4929 1.267806 CTCTCCGTTGTGCTTGCAAAT 59.732 47.619 0.00 0.00 0.00 2.32
2820 4989 2.881513 TCTCCGTTGTGCTTGCAAATAA 59.118 40.909 0.00 0.00 0.00 1.40
2824 4993 5.053145 TCCGTTGTGCTTGCAAATAAAAAT 58.947 33.333 0.00 0.00 0.00 1.82
2825 4994 5.050499 TCCGTTGTGCTTGCAAATAAAAATG 60.050 36.000 0.00 0.00 0.00 2.32
2826 4995 5.050499 CCGTTGTGCTTGCAAATAAAAATGA 60.050 36.000 0.00 0.00 0.00 2.57
2827 4996 6.066410 CGTTGTGCTTGCAAATAAAAATGAG 58.934 36.000 0.00 0.00 0.00 2.90
2828 4997 5.594724 TGTGCTTGCAAATAAAAATGAGC 57.405 34.783 0.00 0.00 0.00 4.26
2829 4998 5.055144 TGTGCTTGCAAATAAAAATGAGCA 58.945 33.333 0.00 0.00 0.00 4.26
2830 4999 5.050227 TGTGCTTGCAAATAAAAATGAGCAC 60.050 36.000 20.44 20.44 46.00 4.40
2831 5000 4.150274 TGCTTGCAAATAAAAATGAGCACG 59.850 37.500 0.00 0.00 0.00 5.34
2832 5001 4.150451 GCTTGCAAATAAAAATGAGCACGT 59.850 37.500 0.00 0.00 0.00 4.49
2833 5002 5.344665 GCTTGCAAATAAAAATGAGCACGTA 59.655 36.000 0.00 0.00 0.00 3.57
2834 5003 6.667386 GCTTGCAAATAAAAATGAGCACGTAC 60.667 38.462 0.00 0.00 0.00 3.67
2835 5004 4.848841 TGCAAATAAAAATGAGCACGTACG 59.151 37.500 15.01 15.01 0.00 3.67
2836 5005 4.849383 GCAAATAAAAATGAGCACGTACGT 59.151 37.500 16.72 16.72 0.00 3.57
2837 5006 6.016718 GCAAATAAAAATGAGCACGTACGTA 58.983 36.000 22.34 5.72 0.00 3.57
2838 5007 6.022794 GCAAATAAAAATGAGCACGTACGTAC 60.023 38.462 22.34 16.33 0.00 3.67
2842 5011 1.556564 ATGAGCACGTACGTACATGC 58.443 50.000 32.92 32.92 44.86 4.06
3077 5248 4.002906 TGGTGGTCAGTTCATCTTACAC 57.997 45.455 0.00 0.00 0.00 2.90
3207 5378 6.381801 CACCCTTAGTTGAATCAATGACAAC 58.618 40.000 8.21 8.21 42.51 3.32
3401 5583 3.010138 TGATCCCCAAAATCTCGGACTTT 59.990 43.478 0.00 0.00 0.00 2.66
3483 5665 5.301298 GGGACATAGTACGTGAGAACCTATT 59.699 44.000 0.00 0.00 0.00 1.73
3487 5669 8.743085 ACATAGTACGTGAGAACCTATTTCTA 57.257 34.615 0.00 0.00 45.24 2.10
3491 5673 7.318893 AGTACGTGAGAACCTATTTCTAAACC 58.681 38.462 0.00 0.00 45.24 3.27
3493 5675 6.164176 ACGTGAGAACCTATTTCTAAACCAG 58.836 40.000 0.00 0.00 45.24 4.00
3494 5676 5.063564 CGTGAGAACCTATTTCTAAACCAGC 59.936 44.000 0.00 0.00 45.24 4.85
3495 5677 6.174049 GTGAGAACCTATTTCTAAACCAGCT 58.826 40.000 0.00 0.00 45.24 4.24
3498 5680 5.940470 AGAACCTATTTCTAAACCAGCTGTG 59.060 40.000 13.81 6.81 43.27 3.66
3513 5696 8.943909 AACCAGCTGTGTATAGTACTATTTTC 57.056 34.615 20.21 11.70 0.00 2.29
3517 5700 8.543774 CAGCTGTGTATAGTACTATTTTCAAGC 58.456 37.037 20.21 19.68 0.00 4.01
3532 5715 3.057969 TCAAGCTGGGTGTGTTATCAG 57.942 47.619 0.00 0.00 0.00 2.90
3533 5716 2.637382 TCAAGCTGGGTGTGTTATCAGA 59.363 45.455 0.00 0.00 0.00 3.27
3539 5722 4.993584 GCTGGGTGTGTTATCAGAGATATG 59.006 45.833 0.00 0.00 0.00 1.78
3662 5845 1.103803 TGGTGCTAGAGATCGTCACC 58.896 55.000 13.94 13.94 45.43 4.02
3751 5934 2.880890 GCACGAGCATGATTAATTCCCT 59.119 45.455 0.00 0.00 41.58 4.20
3753 5936 3.185188 CACGAGCATGATTAATTCCCTCG 59.815 47.826 18.63 18.63 39.90 4.63
3762 5945 5.989477 TGATTAATTCCCTCGTGTGATTCT 58.011 37.500 0.00 0.00 0.00 2.40
3799 5982 9.394767 ACTGTGTTACTAATATGCAATCAATCA 57.605 29.630 0.00 0.00 0.00 2.57
3813 5996 7.311408 TGCAATCAATCATGTTGATCGTTTTA 58.689 30.769 17.93 5.71 35.76 1.52
3986 6169 4.516698 GTCTTCAGTTGTCATGATGTTGGT 59.483 41.667 0.00 0.00 0.00 3.67
3987 6170 5.009010 GTCTTCAGTTGTCATGATGTTGGTT 59.991 40.000 0.00 0.00 0.00 3.67
4036 6219 1.361204 TGAGCCTGGAGGAAACATCA 58.639 50.000 0.00 0.00 37.39 3.07
4093 6276 5.518848 TCAAAGTGAGTTGACCGTAACTA 57.481 39.130 0.00 0.00 40.78 2.24
4154 6337 1.997928 GCGGAAGAGGGCATGCTTTC 61.998 60.000 18.92 14.97 0.00 2.62
4223 6406 9.654663 AGTTGTTGATAGGTTGTTTCTATAGAC 57.345 33.333 0.67 0.00 0.00 2.59
4298 6481 7.475840 TGAGAAAAAGAAAGAGACTCAAAAGC 58.524 34.615 5.02 0.00 31.51 3.51
4327 6511 7.081976 AGTTGTCATAATTTTCTTTACGGTGC 58.918 34.615 0.00 0.00 0.00 5.01
4328 6512 6.811253 TGTCATAATTTTCTTTACGGTGCT 57.189 33.333 0.00 0.00 0.00 4.40
4357 6541 3.599285 CTTACGCCGGCCTGAACCA 62.599 63.158 23.46 0.00 0.00 3.67
4377 6561 5.906073 ACCATTGCATTAATAAACCAGAGC 58.094 37.500 0.00 0.00 0.00 4.09
4424 6613 6.354938 GGGGTAGGGTAAGAAAGTGAAATAG 58.645 44.000 0.00 0.00 0.00 1.73
4426 6615 7.147355 GGGGTAGGGTAAGAAAGTGAAATAGAT 60.147 40.741 0.00 0.00 0.00 1.98
4474 6663 7.680730 AGATAAGTGAAACAACATGGTACTCT 58.319 34.615 0.00 0.00 41.43 3.24
4477 6666 5.238583 AGTGAAACAACATGGTACTCTAGC 58.761 41.667 0.00 0.00 41.43 3.42
4478 6667 4.994852 GTGAAACAACATGGTACTCTAGCA 59.005 41.667 0.00 0.00 37.41 3.49
4479 6668 5.643777 GTGAAACAACATGGTACTCTAGCAT 59.356 40.000 0.00 0.00 41.62 3.79
4556 6745 2.009774 CAGAACAAGCGATTAGGTGGG 58.990 52.381 0.00 0.00 0.00 4.61
4558 6747 2.039879 AGAACAAGCGATTAGGTGGGTT 59.960 45.455 0.00 0.00 33.35 4.11
4607 6844 4.574828 TGGAGCGAACTTTATTATGAAGGC 59.425 41.667 1.93 0.00 0.00 4.35
4614 6851 3.627577 ACTTTATTATGAAGGCCAGTGCG 59.372 43.478 5.01 0.00 38.85 5.34
4644 6881 3.209410 GACTCATGTCATGGGGAATCAC 58.791 50.000 17.11 0.00 42.48 3.06
4658 6895 0.469331 AATCACCGGGGCGATAGAGA 60.469 55.000 6.32 0.00 39.76 3.10
4673 6910 5.664262 CGATAGAGAACAATTCTTCGCATG 58.336 41.667 0.58 0.00 40.87 4.06
4702 6939 3.631145 TGATTTTGACAGTGAAGCAGC 57.369 42.857 0.00 0.00 0.00 5.25
4830 7067 5.283457 ACCTTGTATTGTCCTGCTATCTC 57.717 43.478 0.00 0.00 0.00 2.75
4835 7072 0.461548 TTGTCCTGCTATCTCCAGCG 59.538 55.000 0.00 0.00 44.88 5.18
4865 7102 4.652881 TCATGGTGCTAGAGATCTTCACAT 59.347 41.667 15.38 5.12 33.12 3.21
4906 7143 7.065563 GGCAATTAGGATGTCTAGCTTGATATG 59.934 40.741 11.79 0.00 30.42 1.78
4916 7153 3.185246 AGCTTGATATGAACCTCACCG 57.815 47.619 0.00 0.00 0.00 4.94
5016 10603 3.187637 TCATTTTGGTCGTTTTCTAGGCG 59.812 43.478 0.00 0.00 0.00 5.52
5077 10664 1.706305 AGGTGGGGTTGGACGAAATTA 59.294 47.619 0.00 0.00 0.00 1.40
5080 10667 3.086282 GTGGGGTTGGACGAAATTATGT 58.914 45.455 0.00 0.00 0.00 2.29
5178 10765 5.501156 GGGACAAAGACCAAGAAGATACAT 58.499 41.667 0.00 0.00 0.00 2.29
5330 10918 5.991328 TGCACAAACTCAAAAGAGTAGAG 57.009 39.130 0.00 0.00 34.56 2.43
5331 10919 4.816385 TGCACAAACTCAAAAGAGTAGAGG 59.184 41.667 0.00 0.00 34.56 3.69
5504 11092 4.399303 CCTCATGTTTGGTTTACTCCATCC 59.601 45.833 0.00 0.00 37.33 3.51
5506 11094 2.785562 TGTTTGGTTTACTCCATCCGG 58.214 47.619 0.00 0.00 37.33 5.14
5650 11239 8.528917 AACACAAAAGAGTACCTTTCAAAAAC 57.471 30.769 9.02 0.00 43.90 2.43
5651 11240 7.892609 ACACAAAAGAGTACCTTTCAAAAACT 58.107 30.769 9.02 0.00 43.90 2.66
5711 11303 7.547285 GCGCTCGCAAAAATATATTTTATCA 57.453 32.000 20.90 7.45 38.92 2.15
5712 11304 7.429284 GCGCTCGCAAAAATATATTTTATCAC 58.571 34.615 20.90 11.29 38.92 3.06
5713 11305 7.112844 GCGCTCGCAAAAATATATTTTATCACA 59.887 33.333 20.90 6.60 38.92 3.58
5714 11306 8.952979 CGCTCGCAAAAATATATTTTATCACAA 58.047 29.630 20.90 7.02 38.92 3.33
5727 11319 9.997482 ATATTTTATCACAAACGTCACCATAAC 57.003 29.630 0.00 0.00 0.00 1.89
5728 11320 7.499321 TTTTATCACAAACGTCACCATAACT 57.501 32.000 0.00 0.00 0.00 2.24
5729 11321 7.499321 TTTATCACAAACGTCACCATAACTT 57.501 32.000 0.00 0.00 0.00 2.66
5730 11322 7.499321 TTATCACAAACGTCACCATAACTTT 57.501 32.000 0.00 0.00 0.00 2.66
5731 11323 5.821516 TCACAAACGTCACCATAACTTTT 57.178 34.783 0.00 0.00 0.00 2.27
5732 11324 6.197364 TCACAAACGTCACCATAACTTTTT 57.803 33.333 0.00 0.00 0.00 1.94
5776 11375 3.148340 GGGGGATGTACGTTGTGTC 57.852 57.895 0.00 0.00 0.00 3.67
5819 11419 9.850198 TCATGGAAATGACAATATGTATCTTGA 57.150 29.630 0.00 0.00 0.00 3.02
5973 11589 9.071276 AGTATGATTATGGCAGGAAAACATTAG 57.929 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 7.092079 TGTTCATTAAATTCCTGTCAGCATTG 58.908 34.615 0.00 0.00 0.00 2.82
151 152 8.141268 TGAAACCTTGTTCATTAAATTCCTGTC 58.859 33.333 0.00 0.00 32.56 3.51
152 153 7.926018 GTGAAACCTTGTTCATTAAATTCCTGT 59.074 33.333 0.00 0.00 39.61 4.00
153 154 7.925483 TGTGAAACCTTGTTCATTAAATTCCTG 59.075 33.333 0.00 0.00 39.61 3.86
162 168 4.370917 GTGCATGTGAAACCTTGTTCATT 58.629 39.130 0.00 0.00 39.61 2.57
163 169 3.243839 GGTGCATGTGAAACCTTGTTCAT 60.244 43.478 0.00 0.00 39.61 2.57
263 269 9.547753 GTTCATACACCAATATATGAGTTGACT 57.452 33.333 0.00 0.00 38.65 3.41
264 270 9.547753 AGTTCATACACCAATATATGAGTTGAC 57.452 33.333 0.00 0.00 38.65 3.18
277 283 7.789273 TTCTTCGTAAAAGTTCATACACCAA 57.211 32.000 0.00 0.00 0.00 3.67
309 315 7.901029 TGTCATTTTAGCCAAAAATACCATGA 58.099 30.769 6.96 0.00 44.27 3.07
365 372 6.668541 ACAATCGAGACCTTAATGTTCATG 57.331 37.500 0.00 0.00 0.00 3.07
371 378 9.098355 TGAAGAAATACAATCGAGACCTTAATG 57.902 33.333 0.00 0.00 0.00 1.90
381 388 9.745880 GTATCCTTAGTGAAGAAATACAATCGA 57.254 33.333 0.00 0.00 34.50 3.59
427 434 9.476202 TGACCATTCTATTCATATGTAGTTTCG 57.524 33.333 1.90 0.00 0.00 3.46
434 441 8.055181 ACTTGGTTGACCATTCTATTCATATGT 58.945 33.333 3.28 0.00 46.97 2.29
522 556 0.468226 ATGGTTCCACGCGTATCCAT 59.532 50.000 13.44 19.32 0.00 3.41
525 559 0.928229 GACATGGTTCCACGCGTATC 59.072 55.000 13.44 0.00 0.00 2.24
589 1521 4.579340 CGAGATGGGCTTGACTAGTAGTAA 59.421 45.833 1.88 0.00 0.00 2.24
590 1522 4.135306 CGAGATGGGCTTGACTAGTAGTA 58.865 47.826 1.88 0.00 0.00 1.82
644 1576 2.952978 CGAGATGGGCTTGACTAGTAGT 59.047 50.000 1.37 1.37 0.00 2.73
661 1593 6.598503 TGGATTGGAGTAGATTAGTACGAGA 58.401 40.000 0.00 0.00 0.00 4.04
662 1594 6.879276 TGGATTGGAGTAGATTAGTACGAG 57.121 41.667 0.00 0.00 0.00 4.18
664 1596 6.183360 TGGTTGGATTGGAGTAGATTAGTACG 60.183 42.308 0.00 0.00 0.00 3.67
714 1845 4.870305 GCAGAGAGCGAGACGAAA 57.130 55.556 0.00 0.00 0.00 3.46
754 1885 3.114616 CTTCACTGTGCGCCGAGG 61.115 66.667 4.18 0.00 0.00 4.63
903 2034 4.830765 GACCTGTATGGGCGCGCA 62.831 66.667 34.42 30.06 41.11 6.09
911 2042 0.465705 ACTGGATGCCGACCTGTATG 59.534 55.000 0.00 0.00 37.71 2.39
1016 2163 1.002792 AGGAGAGGAAGCAGGGAGG 59.997 63.158 0.00 0.00 0.00 4.30
1023 2170 2.202864 GCGAGCAGGAGAGGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
1222 2369 2.732658 GACCCACACGACCGTCTT 59.267 61.111 0.00 0.00 0.00 3.01
1482 2629 0.888736 TGTCCGTCGGGTAGTCGAAA 60.889 55.000 12.29 0.00 41.05 3.46
2143 3305 0.957395 CTGCACTGGTCCATGGTCAC 60.957 60.000 12.58 2.96 0.00 3.67
2343 3505 4.413087 CAGAGTTGTAGTGCTACTAACCG 58.587 47.826 10.28 3.19 37.00 4.44
2382 3544 8.575589 TCTCGAATTGAAATGAGAAATTTGGAA 58.424 29.630 0.00 0.00 34.72 3.53
2409 3636 2.012673 AGCTGAAGAAATCGACATGGC 58.987 47.619 0.00 0.00 0.00 4.40
2667 4704 2.015736 ATCACTGCCAGATCGAACAC 57.984 50.000 0.00 0.00 0.00 3.32
2700 4737 1.498865 CTGTCGGCAGCGAAGTTGTT 61.499 55.000 3.01 0.00 42.08 2.83
2711 4748 1.621317 TGTCCAATCTTACTGTCGGCA 59.379 47.619 0.00 0.00 0.00 5.69
2778 4860 4.158579 AGAGCTGAGTGATCGACATTGTTA 59.841 41.667 0.00 0.00 35.99 2.41
2780 4862 2.495270 AGAGCTGAGTGATCGACATTGT 59.505 45.455 0.00 0.00 35.99 2.71
2781 4863 3.114809 GAGAGCTGAGTGATCGACATTG 58.885 50.000 0.00 0.00 35.99 2.82
2783 4865 1.680735 GGAGAGCTGAGTGATCGACAT 59.319 52.381 0.00 0.00 35.99 3.06
2785 4867 0.028770 CGGAGAGCTGAGTGATCGAC 59.971 60.000 0.00 0.00 35.99 4.20
2786 4868 0.393132 ACGGAGAGCTGAGTGATCGA 60.393 55.000 0.00 0.00 35.99 3.59
2787 4869 0.453793 AACGGAGAGCTGAGTGATCG 59.546 55.000 0.00 0.00 35.99 3.69
2788 4870 1.203523 ACAACGGAGAGCTGAGTGATC 59.796 52.381 0.00 0.00 0.00 2.92
2789 4871 1.067283 CACAACGGAGAGCTGAGTGAT 60.067 52.381 0.00 0.00 34.33 3.06
2790 4872 0.315251 CACAACGGAGAGCTGAGTGA 59.685 55.000 0.00 0.00 34.33 3.41
2791 4873 1.287730 GCACAACGGAGAGCTGAGTG 61.288 60.000 0.00 0.00 35.00 3.51
2792 4874 1.005630 GCACAACGGAGAGCTGAGT 60.006 57.895 0.00 0.00 0.00 3.41
2793 4875 0.320247 AAGCACAACGGAGAGCTGAG 60.320 55.000 0.00 0.00 37.41 3.35
2794 4876 0.601046 CAAGCACAACGGAGAGCTGA 60.601 55.000 0.00 0.00 37.41 4.26
2795 4877 1.864862 CAAGCACAACGGAGAGCTG 59.135 57.895 0.00 0.00 37.41 4.24
2796 4878 1.963338 GCAAGCACAACGGAGAGCT 60.963 57.895 0.00 0.00 39.37 4.09
2798 4880 0.662619 TTTGCAAGCACAACGGAGAG 59.337 50.000 0.00 0.00 0.00 3.20
2800 4882 2.987413 TATTTGCAAGCACAACGGAG 57.013 45.000 0.00 0.00 0.00 4.63
2801 4883 3.717400 TTTATTTGCAAGCACAACGGA 57.283 38.095 0.00 0.00 0.00 4.69
2802 4884 4.785669 TTTTTATTTGCAAGCACAACGG 57.214 36.364 0.00 0.00 0.00 4.44
2813 4924 4.849383 ACGTACGTGCTCATTTTTATTTGC 59.151 37.500 22.14 0.00 0.00 3.68
2818 4929 6.085121 CATGTACGTACGTGCTCATTTTTA 57.915 37.500 31.45 13.50 36.53 1.52
2820 4989 4.577687 CATGTACGTACGTGCTCATTTT 57.422 40.909 31.45 11.74 36.53 1.82
2828 4997 1.623809 CTGCGCATGTACGTACGTG 59.376 57.895 33.70 33.70 44.10 4.49
2829 4998 1.515519 CCTGCGCATGTACGTACGT 60.516 57.895 25.98 25.98 34.88 3.57
2830 4999 2.228241 CCCTGCGCATGTACGTACG 61.228 63.158 20.18 15.01 34.88 3.67
2831 5000 0.458889 TTCCCTGCGCATGTACGTAC 60.459 55.000 18.90 18.90 34.88 3.67
2832 5001 0.179121 CTTCCCTGCGCATGTACGTA 60.179 55.000 12.24 0.00 34.88 3.57
2833 5002 1.447838 CTTCCCTGCGCATGTACGT 60.448 57.895 12.24 0.00 34.88 3.57
2834 5003 2.173669 CCTTCCCTGCGCATGTACG 61.174 63.158 12.24 0.00 0.00 3.67
2835 5004 2.472909 GCCTTCCCTGCGCATGTAC 61.473 63.158 12.24 0.00 0.00 2.90
2836 5005 2.124736 GCCTTCCCTGCGCATGTA 60.125 61.111 12.24 0.00 0.00 2.29
2837 5006 3.574074 AAGCCTTCCCTGCGCATGT 62.574 57.895 12.24 0.00 0.00 3.21
2838 5007 2.753043 AAGCCTTCCCTGCGCATG 60.753 61.111 12.24 8.49 0.00 4.06
2842 5011 2.262774 ATCCTCAAGCCTTCCCTGCG 62.263 60.000 0.00 0.00 0.00 5.18
3077 5248 1.021390 GGAATGAGCAGACCACCGTG 61.021 60.000 0.00 0.00 0.00 4.94
3207 5378 5.794687 TCTGCATGACCAAAATTAGTACG 57.205 39.130 0.00 0.00 0.00 3.67
3401 5583 1.368345 CGAACATCCTCGCAATGCCA 61.368 55.000 0.00 0.00 31.04 4.92
3483 5665 7.713734 AGTACTATACACAGCTGGTTTAGAA 57.286 36.000 25.04 7.91 0.00 2.10
3487 5669 9.379791 GAAAATAGTACTATACACAGCTGGTTT 57.620 33.333 19.93 10.56 0.00 3.27
3491 5673 8.543774 GCTTGAAAATAGTACTATACACAGCTG 58.456 37.037 15.74 13.48 0.00 4.24
3493 5675 8.543774 CAGCTTGAAAATAGTACTATACACAGC 58.456 37.037 15.74 20.36 0.00 4.40
3494 5676 9.035607 CCAGCTTGAAAATAGTACTATACACAG 57.964 37.037 15.74 14.47 0.00 3.66
3495 5677 7.985184 CCCAGCTTGAAAATAGTACTATACACA 59.015 37.037 15.74 12.26 0.00 3.72
3498 5680 7.985752 ACACCCAGCTTGAAAATAGTACTATAC 59.014 37.037 15.74 10.72 0.00 1.47
3513 5696 3.005554 CTCTGATAACACACCCAGCTTG 58.994 50.000 0.00 0.00 0.00 4.01
3517 5700 5.987953 CACATATCTCTGATAACACACCCAG 59.012 44.000 0.00 0.00 0.00 4.45
3532 5715 5.003692 TCTCACAAGTCAGCACATATCTC 57.996 43.478 0.00 0.00 0.00 2.75
3533 5716 5.358090 CATCTCACAAGTCAGCACATATCT 58.642 41.667 0.00 0.00 0.00 1.98
3539 5722 0.801251 GCCATCTCACAAGTCAGCAC 59.199 55.000 0.00 0.00 0.00 4.40
3662 5845 0.460987 AGCCTCGATTCTTCTTGCCG 60.461 55.000 0.00 0.00 0.00 5.69
3749 5932 8.883731 AGTTAATCAAATAAGAATCACACGAGG 58.116 33.333 0.00 0.00 0.00 4.63
3751 5934 9.214957 ACAGTTAATCAAATAAGAATCACACGA 57.785 29.630 0.00 0.00 0.00 4.35
3796 5979 4.201812 CGCCTGTAAAACGATCAACATGAT 60.202 41.667 0.00 0.00 40.34 2.45
3797 5980 3.124466 CGCCTGTAAAACGATCAACATGA 59.876 43.478 0.00 0.00 0.00 3.07
3798 5981 3.120338 ACGCCTGTAAAACGATCAACATG 60.120 43.478 0.00 0.00 0.00 3.21
3799 5982 3.071479 ACGCCTGTAAAACGATCAACAT 58.929 40.909 0.00 0.00 0.00 2.71
3813 5996 2.587753 CACAACGTCCACGCCTGT 60.588 61.111 0.00 0.38 44.43 4.00
3986 6169 3.430862 GCGTGGCATTCTCGGCAA 61.431 61.111 0.00 0.00 43.86 4.52
3987 6170 4.393155 AGCGTGGCATTCTCGGCA 62.393 61.111 0.00 0.00 39.46 5.69
4036 6219 2.963371 GTCCGACGTGCTCCTTCT 59.037 61.111 0.00 0.00 0.00 2.85
4093 6276 4.038402 CCCAAACTACCGAGTATCCGTTAT 59.962 45.833 0.00 0.00 33.58 1.89
4154 6337 8.239314 ACAATTAGATTTGTATGCTTCACACAG 58.761 33.333 0.00 0.00 38.04 3.66
4187 6370 6.465439 ACCTATCAACAACTATGTGATCGA 57.535 37.500 0.00 0.00 40.46 3.59
4223 6406 8.932945 ATATGTAGCACGATGTAAAGGATATG 57.067 34.615 0.00 0.00 0.00 1.78
4265 6448 9.838339 AGTCTCTTTCTTTTTCTCATCAAGTTA 57.162 29.630 0.00 0.00 0.00 2.24
4298 6481 9.755064 CCGTAAAGAAAATTATGACAACTACTG 57.245 33.333 0.00 0.00 0.00 2.74
4322 6506 0.108585 AAGCCCACCATATAGCACCG 59.891 55.000 0.00 0.00 0.00 4.94
4357 6541 6.528537 TGTGCTCTGGTTTATTAATGCAAT 57.471 33.333 0.00 0.00 0.00 3.56
4377 6561 4.615121 CCAATCCGTTTCGTTGTAAATGTG 59.385 41.667 0.00 0.00 33.60 3.21
4474 6663 2.299867 TGAGCAGGCATCGAATATGCTA 59.700 45.455 15.06 4.84 46.67 3.49
4477 6666 3.119955 CCAATGAGCAGGCATCGAATATG 60.120 47.826 0.00 0.00 0.00 1.78
4478 6667 3.079578 CCAATGAGCAGGCATCGAATAT 58.920 45.455 0.00 0.00 0.00 1.28
4479 6668 2.158769 ACCAATGAGCAGGCATCGAATA 60.159 45.455 0.00 0.00 0.00 1.75
4556 6745 2.295349 TCAGGGACGACACTCAACTAAC 59.705 50.000 0.00 0.00 0.00 2.34
4558 6747 2.281539 TCAGGGACGACACTCAACTA 57.718 50.000 0.00 0.00 0.00 2.24
4600 6837 0.537143 TTTGACGCACTGGCCTTCAT 60.537 50.000 3.32 0.00 36.38 2.57
4629 6866 1.607071 CCGGTGATTCCCCATGACA 59.393 57.895 0.00 0.00 0.00 3.58
4639 6876 0.469331 TCTCTATCGCCCCGGTGATT 60.469 55.000 14.69 0.67 41.96 2.57
4644 6881 0.393077 ATTGTTCTCTATCGCCCCGG 59.607 55.000 0.00 0.00 0.00 5.73
4658 6895 2.421424 GCTCTCCATGCGAAGAATTGTT 59.579 45.455 0.00 0.00 0.00 2.83
4673 6910 4.456911 TCACTGTCAAAATCAATGCTCTCC 59.543 41.667 0.00 0.00 0.00 3.71
4702 6939 1.739562 GCTGCTTCGAGACCACCAG 60.740 63.158 0.00 0.00 0.00 4.00
4793 7030 1.074566 CAAGGTTTGAGCCCTCCTTCT 59.925 52.381 0.00 0.00 38.09 2.85
4794 7031 1.202940 ACAAGGTTTGAGCCCTCCTTC 60.203 52.381 0.00 0.00 38.09 3.46
4795 7032 0.853530 ACAAGGTTTGAGCCCTCCTT 59.146 50.000 0.00 0.00 40.38 3.36
4830 7067 2.815211 CCATGACACCGACGCTGG 60.815 66.667 0.00 0.00 0.00 4.85
4835 7072 0.530744 TCTAGCACCATGACACCGAC 59.469 55.000 0.00 0.00 0.00 4.79
4865 7102 6.663093 TCCTAATTGCCTTAATTCTTCTTGCA 59.337 34.615 0.00 0.00 39.61 4.08
4878 7115 5.104360 TCAAGCTAGACATCCTAATTGCCTT 60.104 40.000 0.00 0.00 30.23 4.35
4906 7143 2.973694 TTACATAGCCGGTGAGGTTC 57.026 50.000 1.90 0.00 43.70 3.62
4916 7153 4.916249 GCTCGTGTAGTGTATTACATAGCC 59.084 45.833 0.00 0.00 38.33 3.93
5016 10603 0.798776 CAGCCTTCCACGACATTCAC 59.201 55.000 0.00 0.00 0.00 3.18
5077 10664 7.592938 TGCAATCACGAAAAATCTTTAGACAT 58.407 30.769 0.00 0.00 0.00 3.06
5080 10667 7.870826 TCTTGCAATCACGAAAAATCTTTAGA 58.129 30.769 0.00 0.00 0.00 2.10
5096 10683 6.162777 AGACTAGTCAGAACTTCTTGCAATC 58.837 40.000 24.44 0.00 36.92 2.67
5154 10741 2.543777 TCTTCTTGGTCTTTGTCCCG 57.456 50.000 0.00 0.00 0.00 5.14
5275 10863 8.676401 ACATGGCCTAATTTTATTTTTCAATGC 58.324 29.630 3.32 0.00 0.00 3.56
5291 10879 3.323115 TGTGCATTTCAAACATGGCCTAA 59.677 39.130 3.32 0.00 0.00 2.69
5376 10964 8.423906 TGGGTTTGCTTCCTACAAATATTTAA 57.576 30.769 0.00 0.00 39.09 1.52
5504 11092 6.770785 TCCCTACTTCCAATAATTTTCATCCG 59.229 38.462 0.00 0.00 0.00 4.18
5587 11176 9.733556 ACAAAGGAAACAAACTTAGGAATTTTT 57.266 25.926 0.00 0.00 0.00 1.94
5589 11178 9.378551 GAACAAAGGAAACAAACTTAGGAATTT 57.621 29.630 0.00 0.00 0.00 1.82
5708 11300 6.385649 AAAAGTTATGGTGACGTTTGTGAT 57.614 33.333 0.00 0.00 29.70 3.06
5709 11301 5.821516 AAAAGTTATGGTGACGTTTGTGA 57.178 34.783 0.00 0.00 29.70 3.58
5733 11325 9.297037 CCCAAAATTAGAACTTCTCCTTCTAAA 57.703 33.333 0.00 0.00 41.39 1.85
5734 11326 7.888546 CCCCAAAATTAGAACTTCTCCTTCTAA 59.111 37.037 0.00 3.70 41.97 2.10
5735 11327 7.402862 CCCCAAAATTAGAACTTCTCCTTCTA 58.597 38.462 0.00 0.00 0.00 2.10
5736 11328 6.249192 CCCCAAAATTAGAACTTCTCCTTCT 58.751 40.000 0.00 0.00 0.00 2.85
5737 11329 5.419155 CCCCCAAAATTAGAACTTCTCCTTC 59.581 44.000 0.00 0.00 0.00 3.46
5738 11330 5.333581 CCCCCAAAATTAGAACTTCTCCTT 58.666 41.667 0.00 0.00 0.00 3.36
5739 11331 4.935578 CCCCCAAAATTAGAACTTCTCCT 58.064 43.478 0.00 0.00 0.00 3.69
5776 11375 3.242413 CCATGAATTTAGAACACGCGAGG 60.242 47.826 15.93 7.12 0.00 4.63
5897 11502 2.745821 ACGCATGCACATGGATGATATC 59.254 45.455 19.57 0.00 45.22 1.63


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

AutoCloner maintained by Alex Coulton.