Multiple sequence alignment - TraesCS3A01G181800

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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 TraesCS3A01G181800 chr3A 100.000 5608 0 0 1 5608 210251632 210246025 0.000000e+00 10357
1 TraesCS3A01G181800 chr3A 92.593 135 10 0 2982 3116 659015374 659015508 1.590000e-45 195
2 TraesCS3A01G181800 chr3D 92.497 2719 128 20 1928 4615 172357763 172355090 0.000000e+00 3821
3 TraesCS3A01G181800 chr3D 90.453 1016 60 20 816 1809 172360443 172359443 0.000000e+00 1304
4 TraesCS3A01G181800 chr3D 92.722 687 46 2 4923 5608 26040264 26040947 0.000000e+00 989
5 TraesCS3A01G181800 chr3D 89.177 656 59 10 1 654 172361205 172360560 0.000000e+00 808
6 TraesCS3A01G181800 chr3D 83.487 757 102 9 3113 3855 329442932 329443679 0.000000e+00 684
7 TraesCS3A01G181800 chr3D 79.301 744 104 23 3184 3892 352617752 352618480 5.080000e-130 475
8 TraesCS3A01G181800 chr3D 95.668 277 10 2 4629 4905 172354966 172354692 1.430000e-120 444
9 TraesCS3A01G181800 chr3D 95.161 124 5 1 1806 1929 172359207 172359085 1.590000e-45 195
10 TraesCS3A01G181800 chr3B 94.415 1898 82 7 1395 3291 250806719 250804845 0.000000e+00 2896
11 TraesCS3A01G181800 chr3B 93.091 1650 55 12 3284 4905 250804450 250802832 0.000000e+00 2361
12 TraesCS3A01G181800 chr3B 87.789 778 71 9 10 775 250813537 250812772 0.000000e+00 889
13 TraesCS3A01G181800 chr3B 86.161 607 29 14 816 1398 250812771 250812196 6.210000e-169 604
14 TraesCS3A01G181800 chr1D 87.954 689 61 10 4923 5608 377982892 377983561 0.000000e+00 793
15 TraesCS3A01G181800 chr1D 82.587 804 104 13 3113 3890 175817199 175817992 0.000000e+00 676
16 TraesCS3A01G181800 chr6B 86.057 667 70 12 4922 5580 551804684 551805335 0.000000e+00 695
17 TraesCS3A01G181800 chr6B 92.188 128 10 0 2989 3116 46424795 46424668 1.240000e-41 182
18 TraesCS3A01G181800 chr2B 85.907 667 70 11 4923 5580 423904370 423903719 0.000000e+00 689
19 TraesCS3A01G181800 chr2B 83.409 663 84 12 4922 5580 655899603 655900243 4.840000e-165 592
20 TraesCS3A01G181800 chr2B 94.030 134 8 0 2982 3115 185812825 185812958 2.650000e-48 204
21 TraesCS3A01G181800 chr2B 92.366 131 10 0 2986 3116 572791052 572791182 2.670000e-43 187
22 TraesCS3A01G181800 chr2B 81.395 129 22 2 4922 5049 178046219 178046092 2.760000e-18 104
23 TraesCS3A01G181800 chr1B 85.973 663 72 11 4923 5580 391577494 391578140 0.000000e+00 689
24 TraesCS3A01G181800 chr1B 83.289 760 101 8 3113 3855 322467461 322468211 0.000000e+00 676
25 TraesCS3A01G181800 chr7D 84.241 698 87 8 3113 3798 369457678 369456992 0.000000e+00 658
26 TraesCS3A01G181800 chr7D 80.074 813 116 24 3113 3892 188574352 188575151 3.790000e-156 562
27 TraesCS3A01G181800 chr7D 89.971 349 31 4 2644 2989 332695917 332696264 1.110000e-121 448
28 TraesCS3A01G181800 chr2D 82.517 755 107 8 3113 3855 218750439 218751180 1.700000e-179 640
29 TraesCS3A01G181800 chr2D 91.040 346 27 4 2642 2985 380416526 380416869 1.100000e-126 464
30 TraesCS3A01G181800 chr2D 90.116 344 29 5 2645 2985 388833663 388834004 5.160000e-120 442
31 TraesCS3A01G181800 chr4A 82.947 733 100 12 3113 3830 504674781 504675503 6.130000e-179 638
32 TraesCS3A01G181800 chr4A 89.489 352 28 5 2641 2985 119071495 119071844 2.400000e-118 436
33 TraesCS3A01G181800 chr4A 88.396 293 29 3 5289 5580 42255334 42255622 1.160000e-91 348
34 TraesCS3A01G181800 chr4A 92.308 130 10 0 2989 3118 60654285 60654156 9.590000e-43 185
35 TraesCS3A01G181800 chr4A 85.135 148 21 1 4923 5069 120561466 120561613 3.500000e-32 150
36 TraesCS3A01G181800 chr4A 83.750 160 23 3 4923 5080 681889713 681889871 1.260000e-31 148
37 TraesCS3A01G181800 chr5B 81.328 798 117 9 3116 3890 383526095 383525307 2.220000e-173 619
38 TraesCS3A01G181800 chr1A 82.024 751 114 8 3115 3855 357772785 357772046 2.220000e-173 619
39 TraesCS3A01G181800 chr1A 83.333 162 22 5 4922 5080 398892351 398892192 1.630000e-30 145
40 TraesCS3A01G181800 chr5A 88.341 446 49 3 4923 5366 665950143 665950587 2.970000e-147 532
41 TraesCS3A01G181800 chr5A 88.942 208 19 1 5398 5605 665950589 665950792 2.590000e-63 254
42 TraesCS3A01G181800 chr5A 85.062 241 33 3 4923 5161 665966869 665966630 5.610000e-60 243
43 TraesCS3A01G181800 chr5D 90.652 353 27 6 2645 2993 360541857 360542207 1.100000e-126 464
44 TraesCS3A01G181800 chr5D 93.750 128 8 0 2988 3115 412263324 412263451 5.730000e-45 193
45 TraesCS3A01G181800 chr7B 91.071 336 25 5 2659 2991 254836798 254836465 3.080000e-122 449
46 TraesCS3A01G181800 chr2A 89.831 354 31 5 2641 2991 515951638 515951989 3.080000e-122 449
47 TraesCS3A01G181800 chr2A 91.603 131 11 0 2986 3116 632952299 632952429 1.240000e-41 182
48 TraesCS3A01G181800 chr4D 86.577 149 18 2 4923 5069 25435884 25435736 4.500000e-36 163
49 TraesCS3A01G181800 chr7A 84.375 160 22 3 4923 5080 539047 538889 2.710000e-33 154


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 TraesCS3A01G181800 chr3A 210246025 210251632 5607 True 10357.0 10357 100.0000 1 5608 1 chr3A.!!$R1 5607
1 TraesCS3A01G181800 chr3D 172354692 172361205 6513 True 1314.4 3821 92.5912 1 4905 5 chr3D.!!$R1 4904
2 TraesCS3A01G181800 chr3D 26040264 26040947 683 False 989.0 989 92.7220 4923 5608 1 chr3D.!!$F1 685
3 TraesCS3A01G181800 chr3D 329442932 329443679 747 False 684.0 684 83.4870 3113 3855 1 chr3D.!!$F2 742
4 TraesCS3A01G181800 chr3D 352617752 352618480 728 False 475.0 475 79.3010 3184 3892 1 chr3D.!!$F3 708
5 TraesCS3A01G181800 chr3B 250802832 250806719 3887 True 2628.5 2896 93.7530 1395 4905 2 chr3B.!!$R1 3510
6 TraesCS3A01G181800 chr3B 250812196 250813537 1341 True 746.5 889 86.9750 10 1398 2 chr3B.!!$R2 1388
7 TraesCS3A01G181800 chr1D 377982892 377983561 669 False 793.0 793 87.9540 4923 5608 1 chr1D.!!$F2 685
8 TraesCS3A01G181800 chr1D 175817199 175817992 793 False 676.0 676 82.5870 3113 3890 1 chr1D.!!$F1 777
9 TraesCS3A01G181800 chr6B 551804684 551805335 651 False 695.0 695 86.0570 4922 5580 1 chr6B.!!$F1 658
10 TraesCS3A01G181800 chr2B 423903719 423904370 651 True 689.0 689 85.9070 4923 5580 1 chr2B.!!$R2 657
11 TraesCS3A01G181800 chr2B 655899603 655900243 640 False 592.0 592 83.4090 4922 5580 1 chr2B.!!$F3 658
12 TraesCS3A01G181800 chr1B 391577494 391578140 646 False 689.0 689 85.9730 4923 5580 1 chr1B.!!$F2 657
13 TraesCS3A01G181800 chr1B 322467461 322468211 750 False 676.0 676 83.2890 3113 3855 1 chr1B.!!$F1 742
14 TraesCS3A01G181800 chr7D 369456992 369457678 686 True 658.0 658 84.2410 3113 3798 1 chr7D.!!$R1 685
15 TraesCS3A01G181800 chr7D 188574352 188575151 799 False 562.0 562 80.0740 3113 3892 1 chr7D.!!$F1 779
16 TraesCS3A01G181800 chr2D 218750439 218751180 741 False 640.0 640 82.5170 3113 3855 1 chr2D.!!$F1 742
17 TraesCS3A01G181800 chr4A 504674781 504675503 722 False 638.0 638 82.9470 3113 3830 1 chr4A.!!$F4 717
18 TraesCS3A01G181800 chr5B 383525307 383526095 788 True 619.0 619 81.3280 3116 3890 1 chr5B.!!$R1 774
19 TraesCS3A01G181800 chr1A 357772046 357772785 739 True 619.0 619 82.0240 3115 3855 1 chr1A.!!$R1 740
20 TraesCS3A01G181800 chr5A 665950143 665950792 649 False 393.0 532 88.6415 4923 5605 2 chr5A.!!$F1 682

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
717 732 0.108585 GTCACCTTTGAGTCCTGGCA 59.891 55.000 0.00 0.00 30.10 4.92 F
721 736 0.111253 CCTTTGAGTCCTGGCAGGTT 59.889 55.000 31.60 21.36 36.53 3.50 F
1369 1408 0.395586 GTATGCATGGGTGGGCAAGA 60.396 55.000 10.16 0.00 44.20 3.02 F
1878 2171 0.890542 TCTGTCTGCCAATGCACACC 60.891 55.000 0.00 0.00 44.23 4.16 F
2940 4558 1.066430 TGCCCGAACCATCTTAGACAC 60.066 52.381 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1610 2.430248 TGTAGGATGAGCCGTAGACA 57.570 50.000 0.00 0.0 43.43 3.41 R
2318 3934 3.814504 AAATTGGCTTTGAGAGGAGGA 57.185 42.857 0.00 0.0 0.00 3.71 R
3242 4861 1.206371 AGGACGGGGATTCAACTTACG 59.794 52.381 0.00 0.0 0.00 3.18 R
3646 5683 2.104281 TGGTGATGATGGATGAGCTCAG 59.896 50.000 22.96 0.0 0.00 3.35 R
5326 7531 0.037232 GCCGTCCAACTAGCTTCAGT 60.037 55.000 0.00 0.0 0.00 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.735662 GAACACAAAACGTATAGCCACA 57.264 40.909 0.00 0.00 0.00 4.17
29 30 2.228059 ACGTATAGCCACAGATAGCGT 58.772 47.619 0.00 0.00 0.00 5.07
33 34 1.763968 TAGCCACAGATAGCGTGACT 58.236 50.000 4.85 1.82 36.43 3.41
60 61 9.606631 GAGACAAACCTACATGAGAGAAATAAT 57.393 33.333 0.00 0.00 0.00 1.28
62 63 8.425577 ACAAACCTACATGAGAGAAATAATCG 57.574 34.615 0.00 0.00 0.00 3.34
68 69 7.758980 CCTACATGAGAGAAATAATCGGATCTG 59.241 40.741 0.00 0.00 0.00 2.90
86 87 2.434336 TCTGGGGACACATAATCTTCCG 59.566 50.000 0.00 0.00 35.60 4.30
102 103 0.965866 TCCGCACTCCTCTCAACGAT 60.966 55.000 0.00 0.00 0.00 3.73
113 114 2.778928 CTCTCAACGATACGAAGAAGCG 59.221 50.000 0.00 0.00 37.29 4.68
122 123 1.154654 CGAAGAAGCGCCGTCAAAC 60.155 57.895 2.29 0.00 0.00 2.93
123 124 1.206831 GAAGAAGCGCCGTCAAACC 59.793 57.895 2.29 0.00 0.00 3.27
129 130 2.125673 CGCCGTCAAACCGAGGAT 60.126 61.111 0.00 0.00 0.00 3.24
135 136 1.084370 GTCAAACCGAGGATGAGGCG 61.084 60.000 0.00 0.00 0.00 5.52
157 158 3.181443 GGGGGACTTTATTCCATGTCGAT 60.181 47.826 0.00 0.00 37.40 3.59
159 160 3.251004 GGGACTTTATTCCATGTCGATGC 59.749 47.826 0.00 0.00 37.40 3.91
161 162 4.130118 GACTTTATTCCATGTCGATGCCT 58.870 43.478 0.00 0.00 0.00 4.75
162 163 4.130118 ACTTTATTCCATGTCGATGCCTC 58.870 43.478 0.00 0.00 0.00 4.70
184 185 1.300971 CCATCGTCTTGCCACCACTG 61.301 60.000 0.00 0.00 0.00 3.66
202 203 2.445905 ACTGATCGGAGACATACCCCTA 59.554 50.000 9.00 0.00 42.51 3.53
238 239 1.299976 GCCTCCATTGGACCGAAGT 59.700 57.895 0.00 0.00 0.00 3.01
248 249 2.522436 ACCGAAGTCGTGGGGTCA 60.522 61.111 0.00 0.00 37.74 4.02
264 265 0.909610 GTCACCACCCTCTCCCATCA 60.910 60.000 0.00 0.00 0.00 3.07
265 266 0.909610 TCACCACCCTCTCCCATCAC 60.910 60.000 0.00 0.00 0.00 3.06
266 267 1.160870 ACCACCCTCTCCCATCACA 59.839 57.895 0.00 0.00 0.00 3.58
290 291 1.081481 TGACAGACAGAGGGGTAGGA 58.919 55.000 0.00 0.00 0.00 2.94
334 335 1.006454 GGTTAGATAGGCCGCCGTC 60.006 63.158 3.05 6.75 0.00 4.79
375 376 5.336293 GGATGAGGAAAAGAAAGCTTTGGAG 60.336 44.000 18.30 0.00 43.32 3.86
397 398 5.715429 GCACATAGCACATATATCTGCTC 57.285 43.478 17.51 1.52 42.86 4.26
455 456 7.133133 TCATGCTATATGAGATGTATGCCAT 57.867 36.000 0.00 0.00 36.13 4.40
471 472 7.424803 TGTATGCCATAAATGTATGTTGAAGC 58.575 34.615 2.19 0.00 36.16 3.86
668 672 2.226437 AGTTGGCTTTGTGTATTCGCAG 59.774 45.455 0.00 0.00 35.43 5.18
669 673 0.521291 TGGCTTTGTGTATTCGCAGC 59.479 50.000 0.00 0.00 35.43 5.25
678 682 2.032178 GTGTATTCGCAGCTGGAAATCC 59.968 50.000 17.12 9.52 0.00 3.01
679 683 2.092968 TGTATTCGCAGCTGGAAATCCT 60.093 45.455 17.12 5.15 36.82 3.24
692 696 6.331307 AGCTGGAAATCCTAGGAGATAAACAT 59.669 38.462 18.34 0.00 36.82 2.71
695 699 8.980481 TGGAAATCCTAGGAGATAAACATTTC 57.020 34.615 18.34 17.34 36.82 2.17
700 704 9.620259 AATCCTAGGAGATAAACATTTCTTGTC 57.380 33.333 18.34 0.00 37.68 3.18
703 718 7.281100 CCTAGGAGATAAACATTTCTTGTCACC 59.719 40.741 1.05 0.00 37.68 4.02
717 732 0.108585 GTCACCTTTGAGTCCTGGCA 59.891 55.000 0.00 0.00 30.10 4.92
721 736 0.111253 CCTTTGAGTCCTGGCAGGTT 59.889 55.000 31.60 21.36 36.53 3.50
772 787 6.730507 TCCCTCCATATCACAATATAAGAGCA 59.269 38.462 0.00 0.00 31.77 4.26
775 790 9.458727 CCTCCATATCACAATATAAGAGCATTT 57.541 33.333 0.00 0.00 31.77 2.32
791 806 7.907214 AGAGCATTTTTAACCTACACTAGTG 57.093 36.000 21.44 21.44 0.00 2.74
792 807 7.450903 AGAGCATTTTTAACCTACACTAGTGT 58.549 34.615 30.13 30.13 46.87 3.55
793 808 8.591072 AGAGCATTTTTAACCTACACTAGTGTA 58.409 33.333 29.21 29.21 44.42 2.90
794 809 9.379791 GAGCATTTTTAACCTACACTAGTGTAT 57.620 33.333 30.78 20.73 44.15 2.29
795 810 9.734984 AGCATTTTTAACCTACACTAGTGTATT 57.265 29.630 30.78 24.99 44.15 1.89
796 811 9.983804 GCATTTTTAACCTACACTAGTGTATTC 57.016 33.333 30.78 9.31 44.15 1.75
824 839 4.873746 TGTGAAACAGAGGGAGTAGAAG 57.126 45.455 0.00 0.00 45.67 2.85
837 852 7.020827 AGGGAGTAGAAGACATTCATTTTCA 57.979 36.000 0.00 0.00 37.94 2.69
840 855 9.396022 GGGAGTAGAAGACATTCATTTTCATAA 57.604 33.333 0.00 0.00 37.94 1.90
891 907 5.126545 ACCAGCGTGATGTGATAAGTAGTAA 59.873 40.000 0.00 0.00 0.00 2.24
892 908 6.040247 CCAGCGTGATGTGATAAGTAGTAAA 58.960 40.000 0.00 0.00 0.00 2.01
895 911 6.096423 AGCGTGATGTGATAAGTAGTAAAGGA 59.904 38.462 0.00 0.00 0.00 3.36
930 946 4.058817 GAGCGGAGAGAAGAAAACTTCAA 58.941 43.478 11.59 0.00 35.91 2.69
931 947 4.451900 AGCGGAGAGAAGAAAACTTCAAA 58.548 39.130 11.59 0.00 35.91 2.69
932 948 4.881850 AGCGGAGAGAAGAAAACTTCAAAA 59.118 37.500 11.59 0.00 35.91 2.44
949 976 8.707938 ACTTCAAAAGAAGTTCCATGAAAAAG 57.292 30.769 13.41 7.45 42.16 2.27
950 977 8.531146 ACTTCAAAAGAAGTTCCATGAAAAAGA 58.469 29.630 13.41 0.00 42.16 2.52
951 978 9.369904 CTTCAAAAGAAGTTCCATGAAAAAGAA 57.630 29.630 13.41 0.00 0.00 2.52
952 979 9.889128 TTCAAAAGAAGTTCCATGAAAAAGAAT 57.111 25.926 11.18 0.00 0.00 2.40
977 1004 1.336755 GGAAAGAAGCGCAAAAGACCA 59.663 47.619 11.47 0.00 0.00 4.02
1325 1356 0.701731 TGGTTGGGGACGGATCAAAT 59.298 50.000 0.00 0.00 0.00 2.32
1351 1384 1.227438 CGAGGGGAAACACACACGT 60.227 57.895 0.00 0.00 34.58 4.49
1357 1390 1.810151 GGGAAACACACACGTATGCAT 59.190 47.619 3.79 3.79 0.00 3.96
1369 1408 0.395586 GTATGCATGGGTGGGCAAGA 60.396 55.000 10.16 0.00 44.20 3.02
1373 1412 1.063038 TGCATGGGTGGGCAAGATATT 60.063 47.619 0.00 0.00 37.03 1.28
1385 1424 8.691797 GGTGGGCAAGATATTTGTTAGATTTAA 58.308 33.333 0.00 0.00 0.00 1.52
1419 1458 6.345096 TCCCCATCAATCAAGAAAGAAAAC 57.655 37.500 0.00 0.00 0.00 2.43
1440 1479 2.866762 CAAGCGAATAGAGGTTAGGTGC 59.133 50.000 0.00 0.00 0.00 5.01
1446 1485 4.202264 CGAATAGAGGTTAGGTGCTGGAAT 60.202 45.833 0.00 0.00 0.00 3.01
1461 1500 8.052748 AGGTGCTGGAATAGTTTGATACAATTA 58.947 33.333 0.00 0.00 0.00 1.40
1507 1551 3.070018 CGGATGCTCTCTTGAACAGTTT 58.930 45.455 0.00 0.00 0.00 2.66
1508 1552 4.021456 TCGGATGCTCTCTTGAACAGTTTA 60.021 41.667 0.00 0.00 0.00 2.01
1509 1553 4.690748 CGGATGCTCTCTTGAACAGTTTAA 59.309 41.667 0.00 0.00 0.00 1.52
1510 1554 5.179368 CGGATGCTCTCTTGAACAGTTTAAA 59.821 40.000 0.00 0.00 0.00 1.52
1511 1555 6.128172 CGGATGCTCTCTTGAACAGTTTAAAT 60.128 38.462 0.00 0.00 0.00 1.40
1523 1567 3.498397 ACAGTTTAAATGACTCTGCCACG 59.502 43.478 0.00 0.00 0.00 4.94
1566 1610 1.754226 ACGTTTTGCACTGTTCCCATT 59.246 42.857 0.00 0.00 0.00 3.16
1638 1693 5.003160 TGTTGTGTGATGAAAATCCGAGAT 58.997 37.500 0.00 0.00 0.00 2.75
1656 1711 8.475331 TCCGAGATACTTTTTGTAGCTAAAAG 57.525 34.615 15.53 15.53 46.54 2.27
1657 1712 8.308931 TCCGAGATACTTTTTGTAGCTAAAAGA 58.691 33.333 21.49 5.13 46.54 2.52
1672 1727 5.290885 AGCTAAAAGAAAAACTGGTTTTGCG 59.709 36.000 8.36 0.00 41.77 4.85
1878 2171 0.890542 TCTGTCTGCCAATGCACACC 60.891 55.000 0.00 0.00 44.23 4.16
1956 3572 3.540314 TTGTTTTGCAAGATGCTGGTT 57.460 38.095 0.00 0.00 45.31 3.67
1962 3578 7.385267 TGTTTTGCAAGATGCTGGTTTATAAT 58.615 30.769 0.00 0.00 45.31 1.28
1964 3580 6.772360 TTGCAAGATGCTGGTTTATAATCA 57.228 33.333 0.00 0.00 45.31 2.57
2050 3666 5.119694 GCTTAGCTTAGCTTTGGATAGTGT 58.880 41.667 17.24 0.00 40.44 3.55
2213 3829 3.531538 ACTATGTGGGAATGTTACAGCG 58.468 45.455 0.00 0.00 0.00 5.18
2318 3934 8.918202 TTACTACAGATTCTTGAAATGGTGTT 57.082 30.769 0.00 0.00 0.00 3.32
2336 3952 2.376518 TGTTCCTCCTCTCAAAGCCAAT 59.623 45.455 0.00 0.00 0.00 3.16
2462 4078 7.962964 TGGACTCCAATATAATTCGATGTTC 57.037 36.000 0.00 0.00 0.00 3.18
2550 4166 5.623956 TTTGTTCTGACCTGAGGAAGTTA 57.376 39.130 4.99 0.00 0.00 2.24
2580 4196 2.756840 TGCAACTGGACAGATGAGAG 57.243 50.000 12.94 0.00 33.63 3.20
2655 4271 8.091449 TCAAGTTTACCTTTTCAACAACAACAT 58.909 29.630 0.00 0.00 0.00 2.71
2695 4311 1.555533 ACAAGTTGGGTAGGCTAGAGC 59.444 52.381 7.96 0.00 41.14 4.09
2844 4461 3.392947 TCCCATGTCAAGTTTGGTCTACA 59.607 43.478 0.00 0.00 0.00 2.74
2912 4530 2.985282 CGCTTTTGGAGGCCTGCA 60.985 61.111 24.87 24.87 0.00 4.41
2940 4558 1.066430 TGCCCGAACCATCTTAGACAC 60.066 52.381 0.00 0.00 0.00 3.67
3011 4629 4.914177 TTACCTCCGTCCCAAATTAGTT 57.086 40.909 0.00 0.00 0.00 2.24
3067 4685 7.061905 CCAACACTAAAACGTGTCTAGATACAG 59.938 40.741 18.39 13.21 46.71 2.74
3086 4704 2.543012 CAGCCGCATCTAGACAAATCTG 59.457 50.000 0.00 0.00 36.29 2.90
3133 4751 5.424252 GGAGTATATCATTATTCCGGACCCA 59.576 44.000 1.83 0.00 0.00 4.51
3169 4788 4.572389 GTGACCACATATCCATCTCAACAC 59.428 45.833 0.00 0.00 0.00 3.32
3242 4861 3.753272 ACCATTCAGCGCCATACAATATC 59.247 43.478 2.29 0.00 0.00 1.63
3289 5309 3.493334 ACCCACCTTTTACCTTTAGTGC 58.507 45.455 0.00 0.00 0.00 4.40
3612 5649 1.361668 CCACATCGTCCGCAAAGAGG 61.362 60.000 0.00 0.00 0.00 3.69
3621 5658 1.066430 TCCGCAAAGAGGATACACCAC 60.066 52.381 0.00 0.00 42.04 4.16
3646 5683 6.508777 GCGATATCTCCTTGTATATCCCTTC 58.491 44.000 0.34 0.00 33.38 3.46
3734 5777 0.670546 CAGAAAGGCATCGGTGTCGT 60.671 55.000 0.00 0.00 34.36 4.34
3755 5798 3.119792 GTCATCACTCGTTCGAACACTTC 59.880 47.826 26.71 0.69 0.00 3.01
3763 5806 2.858344 CGTTCGAACACTTCTCACAACT 59.142 45.455 26.71 0.00 0.00 3.16
3896 5965 5.313280 TGCAGGTCCTTCTTTTACCTTTA 57.687 39.130 0.00 0.00 41.75 1.85
3932 6001 3.950397 TGAATTAGCACCTCAAACCGAT 58.050 40.909 0.00 0.00 0.00 4.18
4073 6142 1.405821 GATCACCACTCCGATCTCGTT 59.594 52.381 0.00 0.00 36.04 3.85
4076 6145 1.202582 CACCACTCCGATCTCGTTCTT 59.797 52.381 0.00 0.00 37.74 2.52
4079 6148 1.397343 CACTCCGATCTCGTTCTTCGA 59.603 52.381 0.00 0.00 46.83 3.71
4116 6185 7.066284 CCTGCTTTACTGATGTTAGTGCTTTAT 59.934 37.037 0.00 0.00 32.19 1.40
4117 6186 8.335532 TGCTTTACTGATGTTAGTGCTTTATT 57.664 30.769 0.00 0.00 32.19 1.40
4118 6187 9.443323 TGCTTTACTGATGTTAGTGCTTTATTA 57.557 29.630 0.00 0.00 32.19 0.98
4206 6275 5.587844 ACCTCTGTTGTTATCATCATCTTGC 59.412 40.000 0.00 0.00 0.00 4.01
4252 6321 3.318313 AGTCGAATATTCCCCCAGTCAT 58.682 45.455 9.87 0.00 0.00 3.06
4272 6341 7.272731 CAGTCATTTGTCAGCTTGTTCATTATG 59.727 37.037 0.00 0.00 0.00 1.90
4400 6469 3.665544 GCATGTGTGTGCAAACCTT 57.334 47.368 4.11 0.00 44.43 3.50
4402 6471 2.393764 GCATGTGTGTGCAAACCTTAC 58.606 47.619 4.11 0.00 44.43 2.34
4412 6496 2.007608 GCAAACCTTACGGAGATCACC 58.992 52.381 0.00 0.00 0.00 4.02
4650 6844 3.365472 CAGGGAAGGGTTTCTATTTGGG 58.635 50.000 0.00 0.00 33.68 4.12
4668 6862 2.979678 TGGGGAGTTAGAGCTGTTTTCT 59.020 45.455 0.00 0.00 0.00 2.52
4905 7102 0.684805 CCGAACTGCCCTCTCCTAGT 60.685 60.000 0.00 0.00 0.00 2.57
4906 7103 1.187087 CGAACTGCCCTCTCCTAGTT 58.813 55.000 0.00 0.00 36.18 2.24
4907 7104 1.135333 CGAACTGCCCTCTCCTAGTTC 59.865 57.143 0.00 0.00 43.32 3.01
4908 7105 2.462723 GAACTGCCCTCTCCTAGTTCT 58.537 52.381 0.00 0.00 43.38 3.01
4909 7106 3.633418 GAACTGCCCTCTCCTAGTTCTA 58.367 50.000 0.00 0.00 43.38 2.10
4910 7107 3.306472 ACTGCCCTCTCCTAGTTCTAG 57.694 52.381 0.31 0.31 0.00 2.43
4911 7108 2.853707 ACTGCCCTCTCCTAGTTCTAGA 59.146 50.000 8.26 0.00 0.00 2.43
4912 7109 3.219281 CTGCCCTCTCCTAGTTCTAGAC 58.781 54.545 8.26 0.00 0.00 2.59
4913 7110 2.853707 TGCCCTCTCCTAGTTCTAGACT 59.146 50.000 8.26 0.00 42.55 3.24
4914 7111 3.117813 TGCCCTCTCCTAGTTCTAGACTC 60.118 52.174 8.26 0.00 39.86 3.36
4915 7112 3.749632 GCCCTCTCCTAGTTCTAGACTCC 60.750 56.522 8.26 0.00 39.86 3.85
4916 7113 3.720002 CCCTCTCCTAGTTCTAGACTCCT 59.280 52.174 8.26 0.00 39.86 3.69
4917 7114 4.909088 CCCTCTCCTAGTTCTAGACTCCTA 59.091 50.000 8.26 0.00 39.86 2.94
4918 7115 5.221783 CCCTCTCCTAGTTCTAGACTCCTAC 60.222 52.000 8.26 0.00 39.86 3.18
4919 7116 5.221783 CCTCTCCTAGTTCTAGACTCCTACC 60.222 52.000 8.26 0.00 39.86 3.18
4920 7117 4.659835 TCTCCTAGTTCTAGACTCCTACCC 59.340 50.000 8.26 0.00 39.86 3.69
4961 7158 2.168521 GTCCTCATACTTGCTGGCTACA 59.831 50.000 0.00 0.00 0.00 2.74
4977 7174 2.497675 GCTACATCCACTTCAGTCCTGA 59.502 50.000 0.00 0.00 37.91 3.86
4987 7184 1.581934 TCAGTCCTGAAACTTGCGTG 58.418 50.000 0.00 0.00 36.53 5.34
5005 7202 0.821517 TGTTGCATCGATACGGTCCT 59.178 50.000 0.00 0.00 0.00 3.85
5007 7204 1.107945 TTGCATCGATACGGTCCTGA 58.892 50.000 0.00 0.00 0.00 3.86
5024 7221 6.292168 CGGTCCTGATACATGAAAATACGTTC 60.292 42.308 0.00 0.00 0.00 3.95
5042 7239 3.444034 CGTTCTCAATACAGTCCCTGAGA 59.556 47.826 0.00 5.45 41.89 3.27
5049 7246 6.962182 TCAATACAGTCCCTGAGATTGAAAT 58.038 36.000 16.56 0.00 40.50 2.17
5055 7252 2.577563 TCCCTGAGATTGAAATGCCAGA 59.422 45.455 0.00 0.00 0.00 3.86
5089 7287 2.861935 GTGCACTACGTACAACACACTT 59.138 45.455 10.32 0.00 0.00 3.16
5094 7292 2.780065 ACGTACAACACACTTCGCTA 57.220 45.000 0.00 0.00 0.00 4.26
5095 7293 3.082698 ACGTACAACACACTTCGCTAA 57.917 42.857 0.00 0.00 0.00 3.09
5110 7308 1.026718 GCTAAATGCCACGTCAGCCT 61.027 55.000 4.72 0.00 35.15 4.58
5121 7319 2.611800 TCAGCCTGGGCCTCACAT 60.612 61.111 4.53 0.00 43.17 3.21
5142 7340 0.192566 TCAGGTAGGACCCACCAGTT 59.807 55.000 12.00 0.00 39.75 3.16
5224 7428 2.531685 CCCTGTTCTCCCCCACCA 60.532 66.667 0.00 0.00 0.00 4.17
5382 7587 1.885157 CTGTTTGGTGGCGATGCAT 59.115 52.632 0.00 0.00 0.00 3.96
5386 7591 3.942377 TTGGTGGCGATGCATGGCT 62.942 57.895 29.20 0.00 0.00 4.75
5469 7674 6.978659 TCACTAGGTCGATTTGATGTACATTC 59.021 38.462 10.30 2.46 0.00 2.67
5506 7711 9.545105 AAAAATGTTTCTTTGCTGTGATTATGA 57.455 25.926 0.00 0.00 0.00 2.15
5588 7793 6.681729 TTCTAGGGTTTCAGTATGTTGAGT 57.318 37.500 0.00 0.00 37.40 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.276868 GCTATCTGTGGCTATACGTTTTGTG 60.277 44.000 0.00 0.00 0.00 3.33
8 9 2.621998 ACGCTATCTGTGGCTATACGTT 59.378 45.455 0.00 0.00 0.00 3.99
21 22 3.367498 GGTTTGTCTCAGTCACGCTATCT 60.367 47.826 0.00 0.00 0.00 1.98
29 30 4.832823 TCTCATGTAGGTTTGTCTCAGTCA 59.167 41.667 0.00 0.00 0.00 3.41
33 34 6.419484 TTTCTCTCATGTAGGTTTGTCTCA 57.581 37.500 0.00 0.00 0.00 3.27
60 61 2.168458 TTATGTGTCCCCAGATCCGA 57.832 50.000 0.00 0.00 0.00 4.55
62 63 4.505742 GGAAGATTATGTGTCCCCAGATCC 60.506 50.000 0.00 0.00 0.00 3.36
68 69 1.134220 TGCGGAAGATTATGTGTCCCC 60.134 52.381 0.00 0.00 0.00 4.81
86 87 1.400846 TCGTATCGTTGAGAGGAGTGC 59.599 52.381 0.00 0.00 0.00 4.40
102 103 0.318869 TTTGACGGCGCTTCTTCGTA 60.319 50.000 6.90 0.00 37.25 3.43
113 114 1.079405 TCATCCTCGGTTTGACGGC 60.079 57.895 0.00 0.00 0.00 5.68
129 130 0.544697 GAATAAAGTCCCCCGCCTCA 59.455 55.000 0.00 0.00 0.00 3.86
135 136 2.171870 TCGACATGGAATAAAGTCCCCC 59.828 50.000 0.00 0.00 36.80 5.40
159 160 2.892425 GCAAGACGATGGCGGAGG 60.892 66.667 0.00 0.00 43.17 4.30
184 185 2.169330 GGTAGGGGTATGTCTCCGATC 58.831 57.143 0.00 0.00 42.70 3.69
202 203 1.829849 GGCGGAGTTAGGAGTAAAGGT 59.170 52.381 0.00 0.00 0.00 3.50
248 249 0.911525 CTGTGATGGGAGAGGGTGGT 60.912 60.000 0.00 0.00 0.00 4.16
264 265 1.626686 CCTCTGTCTGTCACTCCTGT 58.373 55.000 0.00 0.00 0.00 4.00
265 266 0.894141 CCCTCTGTCTGTCACTCCTG 59.106 60.000 0.00 0.00 0.00 3.86
266 267 0.252012 CCCCTCTGTCTGTCACTCCT 60.252 60.000 0.00 0.00 0.00 3.69
271 272 1.006043 CTCCTACCCCTCTGTCTGTCA 59.994 57.143 0.00 0.00 0.00 3.58
290 291 2.032071 CGTCGAAACCAAGGGCCT 59.968 61.111 0.00 0.00 0.00 5.19
334 335 0.260230 TCCTCCTCCAGCCACTAGAG 59.740 60.000 0.00 0.00 0.00 2.43
471 472 8.792830 TCACTAGAAACTCCTTTGAAATATGG 57.207 34.615 0.00 0.00 0.00 2.74
619 623 9.656040 ATTATGAAATAAGATGCAAAACAGCAA 57.344 25.926 0.00 0.00 44.63 3.91
668 672 5.930135 TGTTTATCTCCTAGGATTTCCAGC 58.070 41.667 13.12 1.40 38.89 4.85
669 673 8.986929 AAATGTTTATCTCCTAGGATTTCCAG 57.013 34.615 13.12 0.00 38.89 3.86
678 682 8.043710 AGGTGACAAGAAATGTTTATCTCCTAG 58.956 37.037 0.00 0.00 44.12 3.02
679 683 7.918076 AGGTGACAAGAAATGTTTATCTCCTA 58.082 34.615 0.00 0.00 44.12 2.94
692 696 4.199310 CAGGACTCAAAGGTGACAAGAAA 58.801 43.478 0.00 0.00 0.00 2.52
695 699 2.498167 CCAGGACTCAAAGGTGACAAG 58.502 52.381 0.00 0.00 0.00 3.16
698 702 0.108585 TGCCAGGACTCAAAGGTGAC 59.891 55.000 0.00 0.00 0.00 3.67
700 704 0.607489 CCTGCCAGGACTCAAAGGTG 60.607 60.000 4.15 0.00 37.67 4.00
703 718 1.882623 GAAACCTGCCAGGACTCAAAG 59.117 52.381 19.90 0.00 37.67 2.77
743 758 9.837681 TCTTATATTGTGATATGGAGGGAGTAA 57.162 33.333 0.00 0.00 31.09 2.24
790 805 9.613428 CCCTCTGTTTCACAATATAAGAATACA 57.387 33.333 0.00 0.00 0.00 2.29
791 806 9.832445 TCCCTCTGTTTCACAATATAAGAATAC 57.168 33.333 0.00 0.00 0.00 1.89
793 808 8.552296 ACTCCCTCTGTTTCACAATATAAGAAT 58.448 33.333 0.00 0.00 0.00 2.40
794 809 7.918076 ACTCCCTCTGTTTCACAATATAAGAA 58.082 34.615 0.00 0.00 0.00 2.52
795 810 7.496346 ACTCCCTCTGTTTCACAATATAAGA 57.504 36.000 0.00 0.00 0.00 2.10
796 811 8.696374 TCTACTCCCTCTGTTTCACAATATAAG 58.304 37.037 0.00 0.00 0.00 1.73
797 812 8.603898 TCTACTCCCTCTGTTTCACAATATAA 57.396 34.615 0.00 0.00 0.00 0.98
798 813 8.603898 TTCTACTCCCTCTGTTTCACAATATA 57.396 34.615 0.00 0.00 0.00 0.86
799 814 7.400339 TCTTCTACTCCCTCTGTTTCACAATAT 59.600 37.037 0.00 0.00 0.00 1.28
800 815 6.724441 TCTTCTACTCCCTCTGTTTCACAATA 59.276 38.462 0.00 0.00 0.00 1.90
801 816 5.544176 TCTTCTACTCCCTCTGTTTCACAAT 59.456 40.000 0.00 0.00 0.00 2.71
802 817 4.899457 TCTTCTACTCCCTCTGTTTCACAA 59.101 41.667 0.00 0.00 0.00 3.33
803 818 4.281182 GTCTTCTACTCCCTCTGTTTCACA 59.719 45.833 0.00 0.00 0.00 3.58
804 819 4.281182 TGTCTTCTACTCCCTCTGTTTCAC 59.719 45.833 0.00 0.00 0.00 3.18
805 820 4.480115 TGTCTTCTACTCCCTCTGTTTCA 58.520 43.478 0.00 0.00 0.00 2.69
806 821 5.669164 ATGTCTTCTACTCCCTCTGTTTC 57.331 43.478 0.00 0.00 0.00 2.78
807 822 5.544176 TGAATGTCTTCTACTCCCTCTGTTT 59.456 40.000 0.00 0.00 32.29 2.83
808 823 5.087323 TGAATGTCTTCTACTCCCTCTGTT 58.913 41.667 0.00 0.00 32.29 3.16
809 824 4.678256 TGAATGTCTTCTACTCCCTCTGT 58.322 43.478 0.00 0.00 32.29 3.41
810 825 5.867903 ATGAATGTCTTCTACTCCCTCTG 57.132 43.478 0.00 0.00 32.29 3.35
811 826 6.882768 AAATGAATGTCTTCTACTCCCTCT 57.117 37.500 0.00 0.00 32.29 3.69
812 827 7.106239 TGAAAATGAATGTCTTCTACTCCCTC 58.894 38.462 0.00 0.00 32.29 4.30
813 828 7.020827 TGAAAATGAATGTCTTCTACTCCCT 57.979 36.000 0.00 0.00 32.29 4.20
814 829 7.872113 ATGAAAATGAATGTCTTCTACTCCC 57.128 36.000 0.00 0.00 32.29 4.30
847 862 8.440059 CGCTGGTTTTTAAAAACTTTCTTTCTT 58.560 29.630 32.06 0.00 45.70 2.52
849 864 7.686529 CACGCTGGTTTTTAAAAACTTTCTTTC 59.313 33.333 32.06 19.46 45.70 2.62
853 868 6.635166 TCACGCTGGTTTTTAAAAACTTTC 57.365 33.333 32.06 21.10 45.70 2.62
855 870 6.035542 CACATCACGCTGGTTTTTAAAAACTT 59.964 34.615 32.06 15.74 45.70 2.66
857 872 5.517054 TCACATCACGCTGGTTTTTAAAAAC 59.483 36.000 28.10 28.10 45.70 2.43
858 873 5.651530 TCACATCACGCTGGTTTTTAAAAA 58.348 33.333 9.31 9.31 0.00 1.94
859 874 5.250235 TCACATCACGCTGGTTTTTAAAA 57.750 34.783 0.00 0.00 0.00 1.52
860 875 4.902443 TCACATCACGCTGGTTTTTAAA 57.098 36.364 0.00 0.00 0.00 1.52
861 876 6.205853 ACTTATCACATCACGCTGGTTTTTAA 59.794 34.615 0.00 0.00 0.00 1.52
891 907 8.575649 TCTCCGCTCTTTATTTTATTTTCCTT 57.424 30.769 0.00 0.00 0.00 3.36
892 908 8.047310 TCTCTCCGCTCTTTATTTTATTTTCCT 58.953 33.333 0.00 0.00 0.00 3.36
895 911 9.449719 TCTTCTCTCCGCTCTTTATTTTATTTT 57.550 29.630 0.00 0.00 0.00 1.82
932 948 8.964772 CCTGATATTCTTTTTCATGGAACTTCT 58.035 33.333 0.00 0.00 0.00 2.85
943 970 6.470556 GCGCTTCTTTCCTGATATTCTTTTTC 59.529 38.462 0.00 0.00 0.00 2.29
949 976 4.882671 TTGCGCTTCTTTCCTGATATTC 57.117 40.909 9.73 0.00 0.00 1.75
950 977 5.415701 TCTTTTGCGCTTCTTTCCTGATATT 59.584 36.000 9.73 0.00 0.00 1.28
951 978 4.943705 TCTTTTGCGCTTCTTTCCTGATAT 59.056 37.500 9.73 0.00 0.00 1.63
952 979 4.154195 GTCTTTTGCGCTTCTTTCCTGATA 59.846 41.667 9.73 0.00 0.00 2.15
977 1004 1.070786 TCGCCGTTTCTTTGCCTCT 59.929 52.632 0.00 0.00 0.00 3.69
1080 1108 1.596934 GAACCCACGGAGCAGATCA 59.403 57.895 0.00 0.00 0.00 2.92
1182 1213 1.205893 GAGTGCAGGTCTAGGGTTGAG 59.794 57.143 0.00 0.00 0.00 3.02
1184 1215 0.108615 CGAGTGCAGGTCTAGGGTTG 60.109 60.000 0.00 0.00 0.00 3.77
1193 1224 4.008933 GGGTGCTCGAGTGCAGGT 62.009 66.667 15.13 0.00 44.20 4.00
1325 1356 2.602267 TTTCCCCTCGACGCCAGA 60.602 61.111 0.00 0.00 0.00 3.86
1351 1384 0.557238 ATCTTGCCCACCCATGCATA 59.443 50.000 0.00 0.00 37.33 3.14
1357 1390 2.917713 ACAAATATCTTGCCCACCCA 57.082 45.000 0.00 0.00 0.00 4.51
1373 1412 8.241367 GGGAAAATTCTCGCTTAAATCTAACAA 58.759 33.333 0.00 0.00 0.00 2.83
1385 1424 2.806945 TGATGGGGAAAATTCTCGCT 57.193 45.000 0.00 0.00 0.00 4.93
1419 1458 2.866762 GCACCTAACCTCTATTCGCTTG 59.133 50.000 0.00 0.00 0.00 4.01
1546 1590 2.875188 TGGGAACAGTGCAAAACGT 58.125 47.368 0.00 0.00 35.01 3.99
1566 1610 2.430248 TGTAGGATGAGCCGTAGACA 57.570 50.000 0.00 0.00 43.43 3.41
1656 1711 5.570262 GGTTATCGCAAAACCAGTTTTTC 57.430 39.130 5.78 1.01 44.83 2.29
1672 1727 5.028549 ACAGAGTGATGGACATGGTTATC 57.971 43.478 0.00 0.00 0.00 1.75
1780 1835 6.367969 TCGTTATCTTGCTTAAGTCCAAAGAC 59.632 38.462 4.02 0.00 43.89 3.01
1782 1837 6.721571 TCGTTATCTTGCTTAAGTCCAAAG 57.278 37.500 4.02 4.08 0.00 2.77
1817 2110 9.533831 TTAAGATACTGCTATCAGGACATATGA 57.466 33.333 10.38 0.00 44.54 2.15
1878 2171 5.516996 TGGTTTATAGAATAGTCGTCAGCG 58.483 41.667 0.00 0.00 39.92 5.18
1962 3578 6.121776 ACCACAGTTCTTAACCATACATGA 57.878 37.500 0.00 0.00 0.00 3.07
1964 3580 6.303839 ACAACCACAGTTCTTAACCATACAT 58.696 36.000 0.00 0.00 32.45 2.29
2213 3829 6.532657 CCTGTGTTGAGCAATCATTAAATTCC 59.467 38.462 0.00 0.00 0.00 3.01
2318 3934 3.814504 AAATTGGCTTTGAGAGGAGGA 57.185 42.857 0.00 0.00 0.00 3.71
2462 4078 9.691362 ACTGGTGTTTTTATACAGCTTTTTATG 57.309 29.630 7.37 0.00 44.62 1.90
2550 4166 4.858850 TGTCCAGTTGCATCTCCATAATT 58.141 39.130 0.00 0.00 0.00 1.40
2580 4196 4.457257 AGCACAGAAGAGCCAACTTTAATC 59.543 41.667 0.00 0.00 31.08 1.75
2655 4271 4.787551 TGTTTTGGACTCTAAGGCTTTGA 58.212 39.130 4.45 8.31 0.00 2.69
2695 4311 5.294552 GGTTTCGAGATCTTATGGGTTTCAG 59.705 44.000 0.00 0.00 0.00 3.02
2844 4461 4.023980 TGATAATGTCAAGAGAGGTCGGT 58.976 43.478 0.00 0.00 32.78 4.69
2912 4530 4.640771 AGATGGTTCGGGCATATACAAT 57.359 40.909 0.00 0.00 0.00 2.71
2940 4558 3.470709 TGAAGAGAAGCTTGTCCAACAG 58.529 45.455 19.26 0.00 36.83 3.16
3011 4629 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3067 4685 2.799412 CTCAGATTTGTCTAGATGCGGC 59.201 50.000 0.00 0.00 0.00 6.53
3086 4704 2.165030 TCCGTCCCGAATTAGTTGACTC 59.835 50.000 0.00 0.00 0.00 3.36
3169 4788 3.323136 GTGTAGCGGAGATGCGCG 61.323 66.667 13.02 0.00 40.67 6.86
3242 4861 1.206371 AGGACGGGGATTCAACTTACG 59.794 52.381 0.00 0.00 0.00 3.18
3289 5309 2.625314 TGTGAGACTGACAAGAGAGTGG 59.375 50.000 0.00 0.00 0.00 4.00
3345 5367 3.705043 AAGCCATCGAATCAAAGATGC 57.295 42.857 0.00 0.00 41.98 3.91
3501 5534 9.722184 AAGGTTTTAGGCTTAGTAGAACTAAAG 57.278 33.333 0.00 0.00 39.89 1.85
3612 5649 2.488545 AGGAGATATCGCGTGGTGTATC 59.511 50.000 5.77 7.87 0.00 2.24
3621 5658 4.580995 AGGGATATACAAGGAGATATCGCG 59.419 45.833 0.00 0.00 45.59 5.87
3646 5683 2.104281 TGGTGATGATGGATGAGCTCAG 59.896 50.000 22.96 0.00 0.00 3.35
3734 5777 3.004419 AGAAGTGTTCGAACGAGTGATGA 59.996 43.478 22.48 0.06 34.02 2.92
3755 5798 7.672983 AGGACATGTACAATAAAGTTGTGAG 57.327 36.000 11.55 0.00 34.11 3.51
3896 5965 8.424133 GGTGCTAATTCAATTTTCCCTAATGAT 58.576 33.333 0.00 0.00 0.00 2.45
3932 6001 8.939201 TTGCAAATGAAAATTGACAAGTCTTA 57.061 26.923 0.00 0.00 0.00 2.10
4056 6125 0.811915 AGAACGAGATCGGAGTGGTG 59.188 55.000 7.22 0.00 44.95 4.17
4073 6142 2.033049 GCAGGCGAAGTACTATCGAAGA 59.967 50.000 22.93 0.00 42.76 2.87
4076 6145 1.676746 AGCAGGCGAAGTACTATCGA 58.323 50.000 22.93 0.00 42.76 3.59
4079 6148 4.401519 TCAGTAAAGCAGGCGAAGTACTAT 59.598 41.667 0.00 0.00 0.00 2.12
4117 6186 9.856488 GTAATGCCGATAGAGAAGAATGTATTA 57.144 33.333 0.00 0.00 39.76 0.98
4118 6187 7.819900 GGTAATGCCGATAGAGAAGAATGTATT 59.180 37.037 0.00 0.00 39.76 1.89
4119 6188 7.179338 AGGTAATGCCGATAGAGAAGAATGTAT 59.821 37.037 0.00 0.00 43.70 2.29
4120 6189 6.493802 AGGTAATGCCGATAGAGAAGAATGTA 59.506 38.462 0.00 0.00 43.70 2.29
4206 6275 5.971895 AAAAGTGCAGCAAAAACAGTATG 57.028 34.783 0.00 0.00 46.00 2.39
4238 6307 3.624707 GCTGACAAATGACTGGGGGAATA 60.625 47.826 0.00 0.00 0.00 1.75
4239 6308 2.885554 GCTGACAAATGACTGGGGGAAT 60.886 50.000 0.00 0.00 0.00 3.01
4252 6321 7.648908 CAGAAACATAATGAACAAGCTGACAAA 59.351 33.333 0.00 0.00 0.00 2.83
4272 6341 3.253432 GTCTGATCCAACCAACCAGAAAC 59.747 47.826 0.00 0.00 35.89 2.78
4442 6526 4.087892 GCCTCCTTCAGAGCGGCA 62.088 66.667 1.45 0.00 41.74 5.69
4650 6844 7.674471 ACAATAAGAAAACAGCTCTAACTCC 57.326 36.000 0.00 0.00 0.00 3.85
4668 6862 7.353497 TCACTTGTCGCGAAAATAAACAATAA 58.647 30.769 13.05 0.00 0.00 1.40
4791 6986 6.128929 GCTCCGGACAAAATTTGAAATAACAC 60.129 38.462 13.19 0.00 0.00 3.32
4861 7058 1.726853 CAAGAGACATCGTTGGACCC 58.273 55.000 0.00 0.00 0.00 4.46
4905 7102 6.843473 TTATCTCTGGGTAGGAGTCTAGAA 57.157 41.667 0.00 0.00 33.06 2.10
4906 7103 7.235079 CAATTATCTCTGGGTAGGAGTCTAGA 58.765 42.308 0.00 0.00 33.06 2.43
4907 7104 6.071616 GCAATTATCTCTGGGTAGGAGTCTAG 60.072 46.154 0.00 0.00 33.06 2.43
4908 7105 5.775701 GCAATTATCTCTGGGTAGGAGTCTA 59.224 44.000 0.00 0.00 33.06 2.59
4909 7106 4.591072 GCAATTATCTCTGGGTAGGAGTCT 59.409 45.833 0.00 0.00 33.06 3.24
4910 7107 4.345257 TGCAATTATCTCTGGGTAGGAGTC 59.655 45.833 0.00 0.00 33.06 3.36
4911 7108 4.298626 TGCAATTATCTCTGGGTAGGAGT 58.701 43.478 0.00 0.00 33.06 3.85
4912 7109 4.963318 TGCAATTATCTCTGGGTAGGAG 57.037 45.455 0.00 0.00 0.00 3.69
4913 7110 5.158141 AGATGCAATTATCTCTGGGTAGGA 58.842 41.667 0.00 0.00 31.97 2.94
4914 7111 5.495926 AGATGCAATTATCTCTGGGTAGG 57.504 43.478 0.00 0.00 31.97 3.18
4915 7112 8.976353 ACTATAGATGCAATTATCTCTGGGTAG 58.024 37.037 6.78 0.00 38.35 3.18
4916 7113 8.901472 ACTATAGATGCAATTATCTCTGGGTA 57.099 34.615 6.78 0.00 38.35 3.69
4917 7114 7.093112 GGACTATAGATGCAATTATCTCTGGGT 60.093 40.741 6.78 0.00 38.35 4.51
4918 7115 7.125507 AGGACTATAGATGCAATTATCTCTGGG 59.874 40.741 6.78 0.00 38.35 4.45
4919 7116 8.076910 AGGACTATAGATGCAATTATCTCTGG 57.923 38.462 6.78 0.00 38.35 3.86
4920 7117 8.747471 TGAGGACTATAGATGCAATTATCTCTG 58.253 37.037 6.78 0.00 38.35 3.35
4987 7184 1.202371 TCAGGACCGTATCGATGCAAC 60.202 52.381 14.06 0.42 0.00 4.17
5055 7252 3.238497 TGCACGTGTAGGCCAGGT 61.238 61.111 18.38 0.00 42.69 4.00
5084 7282 3.748916 GACGTGGCATTTAGCGAAGTGT 61.749 50.000 0.00 0.00 42.91 3.55
5085 7283 1.201921 GACGTGGCATTTAGCGAAGTG 60.202 52.381 0.00 0.00 42.91 3.16
5094 7292 1.973281 CCAGGCTGACGTGGCATTT 60.973 57.895 17.94 0.00 44.34 2.32
5095 7293 2.360350 CCAGGCTGACGTGGCATT 60.360 61.111 17.94 0.00 44.34 3.56
5110 7308 0.546507 TACCTGACATGTGAGGCCCA 60.547 55.000 28.86 13.23 37.49 5.36
5114 7312 1.482593 GGTCCTACCTGACATGTGAGG 59.517 57.143 27.56 27.56 40.01 3.86
5116 7314 1.203250 TGGGTCCTACCTGACATGTGA 60.203 52.381 1.15 0.00 38.64 3.58
5121 7319 0.544357 CTGGTGGGTCCTACCTGACA 60.544 60.000 23.78 4.10 38.88 3.58
5142 7340 3.399181 CGGGTGGGCCTCAAGCTA 61.399 66.667 4.53 0.00 43.05 3.32
5224 7428 3.181469 TGTTTCGCACTCCTCTGTTTAGT 60.181 43.478 0.00 0.00 0.00 2.24
5326 7531 0.037232 GCCGTCCAACTAGCTTCAGT 60.037 55.000 0.00 0.00 0.00 3.41
5482 7687 7.326789 CGTCATAATCACAGCAAAGAAACATTT 59.673 33.333 0.00 0.00 0.00 2.32
5483 7688 6.803320 CGTCATAATCACAGCAAAGAAACATT 59.197 34.615 0.00 0.00 0.00 2.71
5484 7689 6.072508 ACGTCATAATCACAGCAAAGAAACAT 60.073 34.615 0.00 0.00 0.00 2.71
5506 7711 2.825532 AGAAATAGCATGGGCAAAACGT 59.174 40.909 0.00 0.00 44.61 3.99


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

AutoCloner maintained by Alex Coulton.