Multiple sequence alignment - TraesCS5A01G384400

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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 TraesCS5A01G384400 chr5A 100.000 3867 0 0 1 3867 582380772 582384638 0.000000e+00 7142.0
1 TraesCS5A01G384400 chr5A 97.345 113 3 0 3520 3632 346203862 346203974 3.940000e-45 193.0
2 TraesCS5A01G384400 chr5A 89.655 58 6 0 3355 3412 667304821 667304878 1.490000e-09 75.0
3 TraesCS5A01G384400 chr5D 95.094 2446 101 7 579 3021 462074043 462076472 0.000000e+00 3834.0
4 TraesCS5A01G384400 chr5D 93.923 543 17 5 2990 3524 462076482 462077016 0.000000e+00 806.0
5 TraesCS5A01G384400 chr5D 86.071 560 71 7 1 557 351337871 351337316 2.570000e-166 595.0
6 TraesCS5A01G384400 chr5D 92.083 240 4 2 3629 3867 462077015 462077240 1.340000e-84 324.0
7 TraesCS5A01G384400 chr5D 88.136 59 7 0 3351 3409 126572372 126572430 1.930000e-08 71.3
8 TraesCS5A01G384400 chr5B 94.082 2281 99 11 581 2859 568401394 568403640 0.000000e+00 3432.0
9 TraesCS5A01G384400 chr5B 93.148 540 25 3 2990 3524 568403867 568404399 0.000000e+00 782.0
10 TraesCS5A01G384400 chr5B 93.333 240 15 1 3629 3867 568404398 568404637 1.710000e-93 353.0
11 TraesCS5A01G384400 chr5B 87.324 213 25 1 2809 3021 568403647 568403857 3.860000e-60 243.0
12 TraesCS5A01G384400 chr4A 88.592 561 52 9 1 557 463875772 463876324 0.000000e+00 671.0
13 TraesCS5A01G384400 chr4A 97.297 111 3 0 3523 3633 274959061 274958951 5.100000e-44 189.0
14 TraesCS5A01G384400 chr4A 89.655 58 6 0 3355 3412 501972649 501972592 1.490000e-09 75.0
15 TraesCS5A01G384400 chr1D 87.567 563 58 9 1 560 495132931 495132378 3.260000e-180 641.0
16 TraesCS5A01G384400 chr1D 87.034 563 59 10 1 560 25698039 25698590 1.180000e-174 623.0
17 TraesCS5A01G384400 chr1D 86.380 558 59 12 1 555 465933604 465934147 9.250000e-166 593.0
18 TraesCS5A01G384400 chr1D 84.252 127 15 5 3198 3319 317439607 317439481 6.790000e-23 119.0
19 TraesCS5A01G384400 chr7A 86.170 564 65 10 1 560 188657095 188657649 7.150000e-167 597.0
20 TraesCS5A01G384400 chr7A 97.345 113 3 0 3520 3632 685837619 685837731 3.940000e-45 193.0
21 TraesCS5A01G384400 chr7A 79.866 149 26 3 3207 3355 177333672 177333528 5.280000e-19 106.0
22 TraesCS5A01G384400 chr3D 86.121 562 66 7 1 560 550991057 550991608 2.570000e-166 595.0
23 TraesCS5A01G384400 chr3D 86.047 559 67 9 1 557 18336813 18337362 1.200000e-164 590.0
24 TraesCS5A01G384400 chr3D 95.690 116 4 1 3516 3631 487231572 487231686 6.600000e-43 185.0
25 TraesCS5A01G384400 chr4D 85.487 565 72 9 1 563 98454861 98454305 7.200000e-162 580.0
26 TraesCS5A01G384400 chr4D 84.404 109 13 3 3199 3306 486932222 486932117 1.900000e-18 104.0
27 TraesCS5A01G384400 chr4D 93.443 61 4 0 3351 3411 486932153 486932213 1.480000e-14 91.6
28 TraesCS5A01G384400 chr4D 80.159 126 16 8 3198 3318 67791793 67791914 6.880000e-13 86.1
29 TraesCS5A01G384400 chr7D 88.000 200 17 4 658 852 21085034 21084837 3.010000e-56 230.0
30 TraesCS5A01G384400 chr7D 80.537 149 25 3 3207 3355 175652620 175652476 1.140000e-20 111.0
31 TraesCS5A01G384400 chr2A 97.458 118 2 1 3514 3630 647958048 647957931 2.360000e-47 200.0
32 TraesCS5A01G384400 chr2A 95.652 115 5 0 3516 3630 256792653 256792767 6.600000e-43 185.0
33 TraesCS5A01G384400 chr7B 96.581 117 4 0 3514 3630 34608161 34608277 1.100000e-45 195.0
34 TraesCS5A01G384400 chr7B 92.969 128 6 2 3516 3640 733859804 733859677 2.370000e-42 183.0
35 TraesCS5A01G384400 chr6D 94.118 119 7 0 3522 3640 307291338 307291456 8.530000e-42 182.0
36 TraesCS5A01G384400 chr1A 84.375 128 14 4 3198 3319 398461003 398460876 1.890000e-23 121.0
37 TraesCS5A01G384400 chr4B 79.137 139 19 9 3198 3331 100314579 100314712 1.910000e-13 87.9
38 TraesCS5A01G384400 chr1B 93.103 58 4 0 3355 3412 565664619 565664562 6.880000e-13 86.1
39 TraesCS5A01G384400 chr2D 92.727 55 4 0 3355 3409 394525142 394525196 3.200000e-11 80.5
40 TraesCS5A01G384400 chr2B 92.727 55 4 0 3355 3409 466165250 466165304 3.200000e-11 80.5


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 TraesCS5A01G384400 chr5A 582380772 582384638 3866 False 7142.000000 7142 100.00000 1 3867 1 chr5A.!!$F2 3866
1 TraesCS5A01G384400 chr5D 462074043 462077240 3197 False 1654.666667 3834 93.70000 579 3867 3 chr5D.!!$F2 3288
2 TraesCS5A01G384400 chr5D 351337316 351337871 555 True 595.000000 595 86.07100 1 557 1 chr5D.!!$R1 556
3 TraesCS5A01G384400 chr5B 568401394 568404637 3243 False 1202.500000 3432 91.97175 581 3867 4 chr5B.!!$F1 3286
4 TraesCS5A01G384400 chr4A 463875772 463876324 552 False 671.000000 671 88.59200 1 557 1 chr4A.!!$F1 556
5 TraesCS5A01G384400 chr1D 495132378 495132931 553 True 641.000000 641 87.56700 1 560 1 chr1D.!!$R2 559
6 TraesCS5A01G384400 chr1D 25698039 25698590 551 False 623.000000 623 87.03400 1 560 1 chr1D.!!$F1 559
7 TraesCS5A01G384400 chr1D 465933604 465934147 543 False 593.000000 593 86.38000 1 555 1 chr1D.!!$F2 554
8 TraesCS5A01G384400 chr7A 188657095 188657649 554 False 597.000000 597 86.17000 1 560 1 chr7A.!!$F1 559
9 TraesCS5A01G384400 chr3D 550991057 550991608 551 False 595.000000 595 86.12100 1 560 1 chr3D.!!$F3 559
10 TraesCS5A01G384400 chr3D 18336813 18337362 549 False 590.000000 590 86.04700 1 557 1 chr3D.!!$F1 556
11 TraesCS5A01G384400 chr4D 98454305 98454861 556 True 580.000000 580 85.48700 1 563 1 chr4D.!!$R1 562

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
452 465 0.179121 CGTTGCATAGTAGGGTGCGA 60.179 55.0 0.0 0.0 44.11 5.10 F
822 840 0.322187 ACCATTCACAACCCCTACGC 60.322 55.0 0.0 0.0 0.00 4.42 F
2517 2538 0.766131 TCCTGAAGGGTTTTACGCCA 59.234 50.0 0.0 0.0 36.25 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2391 0.180171 TGTGGCATATGAGGAACCGG 59.820 55.0 6.97 0.0 0.00 5.28 R
2690 2711 0.244450 CATGGCCACAAGCGTTTGAT 59.756 50.0 19.42 0.0 45.17 2.57 R
3699 3826 0.881118 TTGGACTCGCCTTTCAATGC 59.119 50.0 0.00 0.0 37.63 3.56 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
109 110 2.173996 ACGGAGGAAAAGAAAGGGAACA 59.826 45.455 0.00 0.00 0.00 3.18
120 121 5.906772 AGAAAGGGAACAGAGGAGTTTAA 57.093 39.130 0.00 0.00 0.00 1.52
165 166 4.080582 TCGAATCCAGGGCTAAAATCTTCA 60.081 41.667 0.00 0.00 0.00 3.02
172 173 6.386927 TCCAGGGCTAAAATCTTCAAGATCTA 59.613 38.462 0.00 0.00 32.89 1.98
176 177 8.722422 AGGGCTAAAATCTTCAAGATCTAAGAT 58.278 33.333 12.99 12.99 42.78 2.40
181 182 8.517062 AAAATCTTCAAGATCTAAGATGGGTG 57.483 34.615 17.63 1.67 40.66 4.61
182 183 6.821616 ATCTTCAAGATCTAAGATGGGTGT 57.178 37.500 16.61 0.00 40.17 4.16
183 184 5.982356 TCTTCAAGATCTAAGATGGGTGTG 58.018 41.667 4.15 0.00 0.00 3.82
184 185 5.485353 TCTTCAAGATCTAAGATGGGTGTGT 59.515 40.000 4.15 0.00 0.00 3.72
185 186 5.089970 TCAAGATCTAAGATGGGTGTGTG 57.910 43.478 0.00 0.00 0.00 3.82
186 187 4.080919 TCAAGATCTAAGATGGGTGTGTGG 60.081 45.833 0.00 0.00 0.00 4.17
242 254 4.814147 TCTGTACAGAGAGCAACTTCATG 58.186 43.478 21.74 0.00 32.82 3.07
268 280 1.575447 GGGGAAGAACTGCCTGGGAT 61.575 60.000 0.00 0.00 35.37 3.85
307 320 3.466791 AAGTCACAGTGCAGCGCCT 62.467 57.895 2.29 0.00 0.00 5.52
334 347 2.169832 AGTCGCTGCACATTACACTT 57.830 45.000 0.00 0.00 0.00 3.16
366 379 2.744768 GCTTAGGCGCTGCACTGTC 61.745 63.158 7.64 0.00 0.00 3.51
440 453 1.072331 CCTAAGGGATAGGCGTTGCAT 59.928 52.381 0.00 0.00 44.72 3.96
452 465 0.179121 CGTTGCATAGTAGGGTGCGA 60.179 55.000 0.00 0.00 44.11 5.10
462 475 4.752879 GGGTGCGACGCCTTGCTA 62.753 66.667 18.69 0.00 33.98 3.49
475 488 3.323758 TTGCTATCGGGCGCCACTT 62.324 57.895 30.85 14.24 34.52 3.16
486 499 1.244019 GCGCCACTTGAAAGGGTCAT 61.244 55.000 0.00 0.00 35.70 3.06
560 578 4.082787 AGGTCAAATATGTGTTTTCTGCCG 60.083 41.667 0.00 0.00 0.00 5.69
563 581 5.342259 GTCAAATATGTGTTTTCTGCCGTTC 59.658 40.000 0.00 0.00 0.00 3.95
564 582 4.434713 AATATGTGTTTTCTGCCGTTCC 57.565 40.909 0.00 0.00 0.00 3.62
565 583 1.981256 ATGTGTTTTCTGCCGTTCCT 58.019 45.000 0.00 0.00 0.00 3.36
566 584 1.757682 TGTGTTTTCTGCCGTTCCTT 58.242 45.000 0.00 0.00 0.00 3.36
567 585 1.403679 TGTGTTTTCTGCCGTTCCTTG 59.596 47.619 0.00 0.00 0.00 3.61
568 586 0.383949 TGTTTTCTGCCGTTCCTTGC 59.616 50.000 0.00 0.00 0.00 4.01
569 587 0.383949 GTTTTCTGCCGTTCCTTGCA 59.616 50.000 0.00 0.00 35.86 4.08
570 588 1.107114 TTTTCTGCCGTTCCTTGCAA 58.893 45.000 0.00 0.00 36.98 4.08
571 589 1.327303 TTTCTGCCGTTCCTTGCAAT 58.673 45.000 0.00 0.00 36.98 3.56
572 590 1.327303 TTCTGCCGTTCCTTGCAATT 58.673 45.000 0.00 0.00 36.98 2.32
573 591 2.192664 TCTGCCGTTCCTTGCAATTA 57.807 45.000 0.00 0.00 36.98 1.40
574 592 2.509569 TCTGCCGTTCCTTGCAATTAA 58.490 42.857 0.00 0.00 36.98 1.40
575 593 2.227865 TCTGCCGTTCCTTGCAATTAAC 59.772 45.455 0.00 6.78 36.98 2.01
576 594 2.228822 CTGCCGTTCCTTGCAATTAACT 59.771 45.455 17.17 0.00 36.98 2.24
577 595 2.227865 TGCCGTTCCTTGCAATTAACTC 59.772 45.455 17.17 11.45 33.87 3.01
610 628 2.001361 GCTCTAGTACTTCGCCGCCA 62.001 60.000 0.00 0.00 0.00 5.69
735 753 0.671781 CACAACTCCTTCCTCCGCTG 60.672 60.000 0.00 0.00 0.00 5.18
798 816 1.047002 CATCTAGCTAGCAGCCCACT 58.953 55.000 18.83 0.00 43.77 4.00
821 839 1.278127 AGACCATTCACAACCCCTACG 59.722 52.381 0.00 0.00 0.00 3.51
822 840 0.322187 ACCATTCACAACCCCTACGC 60.322 55.000 0.00 0.00 0.00 4.42
885 903 2.283604 TGCTAGTGGTCGCCCTGA 60.284 61.111 0.00 0.00 0.00 3.86
903 921 2.185867 GGCCGGTCACGATTAGCA 59.814 61.111 0.00 0.00 44.60 3.49
1036 1057 2.741985 TCATTGTGTCGCAGCCGG 60.742 61.111 0.00 0.00 34.56 6.13
1148 1169 1.079127 ACGGCGACTCCTTTGATGG 60.079 57.895 16.62 0.00 0.00 3.51
1518 1539 7.284074 TGGTTGACATACTAGGAAAGTTCAAA 58.716 34.615 0.00 0.00 35.34 2.69
1701 1722 3.866651 AGACACCACAGCTATGAATGTC 58.133 45.455 17.05 17.05 36.85 3.06
2370 2391 6.564328 CAAAAGGCAATGGATAAAGGTACTC 58.436 40.000 0.00 0.00 38.49 2.59
2394 2415 3.316308 GGTTCCTCATATGCCACATGTTC 59.684 47.826 0.00 0.00 0.00 3.18
2397 2418 2.882761 CCTCATATGCCACATGTTCAGG 59.117 50.000 0.00 0.00 0.00 3.86
2403 2424 1.355381 TGCCACATGTTCAGGAAGGAT 59.645 47.619 4.91 0.00 0.00 3.24
2484 2505 1.155042 CTGCTCAGTCTTGCCTGTTC 58.845 55.000 0.00 0.00 34.02 3.18
2499 2520 2.093235 CCTGTTCTTGGAGGAGATGGTC 60.093 54.545 0.00 0.00 0.00 4.02
2517 2538 0.766131 TCCTGAAGGGTTTTACGCCA 59.234 50.000 0.00 0.00 36.25 5.69
2542 2563 5.821204 AGAAAGAAACGTTTGATCTTGTGG 58.179 37.500 20.10 0.00 33.86 4.17
2543 2564 5.357032 AGAAAGAAACGTTTGATCTTGTGGT 59.643 36.000 20.10 0.62 33.86 4.16
2544 2565 4.552166 AGAAACGTTTGATCTTGTGGTG 57.448 40.909 20.10 0.00 0.00 4.17
2562 2583 2.356125 GGTGGAGAAGCTTGATAAGGCA 60.356 50.000 2.10 0.00 0.00 4.75
2577 2598 1.386533 AGGCAAATCTCCATTCAGCG 58.613 50.000 0.00 0.00 0.00 5.18
2587 2608 3.753272 TCTCCATTCAGCGAAGAAAAAGG 59.247 43.478 0.00 0.00 0.00 3.11
2622 2643 2.979676 CGGGCAGCTGCTGTGAAA 60.980 61.111 35.82 0.00 41.70 2.69
2623 2644 2.960170 GGGCAGCTGCTGTGAAAG 59.040 61.111 35.82 4.79 41.70 2.62
2624 2645 1.900498 GGGCAGCTGCTGTGAAAGT 60.900 57.895 35.82 0.00 41.70 2.66
2625 2646 1.285023 GGCAGCTGCTGTGAAAGTG 59.715 57.895 35.82 4.24 41.70 3.16
2648 2669 2.271944 AGCACACTGGTTTCCCTTAC 57.728 50.000 0.00 0.00 0.00 2.34
2649 2670 1.493022 AGCACACTGGTTTCCCTTACA 59.507 47.619 0.00 0.00 0.00 2.41
2675 2696 1.303561 GGATGGTGCTGCTGGACAA 60.304 57.895 16.64 6.16 36.16 3.18
2690 2711 5.420739 TGCTGGACAACATAGTGACATACTA 59.579 40.000 0.00 0.00 45.50 1.82
2706 2727 1.165270 ACTATCAAACGCTTGTGGCC 58.835 50.000 0.00 0.00 37.74 5.36
2718 2739 2.879756 GCTTGTGGCCATGAACCTTAGA 60.880 50.000 9.72 0.00 34.27 2.10
2726 2747 4.176271 GCCATGAACCTTAGAACAAATGC 58.824 43.478 0.00 0.00 0.00 3.56
2739 2760 5.278604 AGAACAAATGCGAAGGTACAAAAC 58.721 37.500 0.00 0.00 0.00 2.43
2771 2792 5.421056 ACAAGTTTATCACTCGACCTATCCA 59.579 40.000 0.00 0.00 32.94 3.41
2782 2803 4.617959 TCGACCTATCCATTCATCGAAAC 58.382 43.478 0.00 0.00 35.80 2.78
2822 2900 7.441836 ACACTGTCACTGATCTGTTACAATTA 58.558 34.615 17.21 0.00 0.00 1.40
2836 2914 7.770433 TCTGTTACAATTATGTTGCTCTGCTAT 59.230 33.333 0.00 0.00 41.05 2.97
2837 2915 7.696755 TGTTACAATTATGTTGCTCTGCTATG 58.303 34.615 0.00 0.00 41.05 2.23
2840 2918 6.558009 ACAATTATGTTGCTCTGCTATGTTG 58.442 36.000 0.00 0.00 35.91 3.33
2859 2937 5.242434 TGTTGAACTATATTCGCAACACCT 58.758 37.500 0.00 0.00 42.49 4.00
2860 2938 5.703592 TGTTGAACTATATTCGCAACACCTT 59.296 36.000 0.00 0.00 42.49 3.50
2861 2939 6.874664 TGTTGAACTATATTCGCAACACCTTA 59.125 34.615 0.00 0.00 42.49 2.69
2862 2940 7.388224 TGTTGAACTATATTCGCAACACCTTAA 59.612 33.333 0.00 0.00 42.49 1.85
2917 2995 1.822425 TTGGTCAAGTCCCCTACCAA 58.178 50.000 1.77 1.77 46.88 3.67
2921 2999 1.697982 GTCAAGTCCCCTACCAACTGT 59.302 52.381 0.00 0.00 0.00 3.55
2923 3001 1.697432 CAAGTCCCCTACCAACTGTCA 59.303 52.381 0.00 0.00 0.00 3.58
2930 3008 5.771165 GTCCCCTACCAACTGTCAATTTTAA 59.229 40.000 0.00 0.00 0.00 1.52
2935 3013 7.362920 CCCTACCAACTGTCAATTTTAATCCTG 60.363 40.741 0.00 0.00 0.00 3.86
2942 3020 7.530010 ACTGTCAATTTTAATCCTGTTCATCG 58.470 34.615 0.00 0.00 0.00 3.84
2952 3030 0.987715 CTGTTCATCGACGTCTGCAG 59.012 55.000 14.70 7.63 0.00 4.41
2962 3040 5.050644 TCGACGTCTGCAGTATAAAAAGA 57.949 39.130 14.67 2.04 0.00 2.52
2983 3061 0.179004 TGTGGAAGCGGTTCACCATT 60.179 50.000 26.94 0.00 33.93 3.16
2984 3062 0.958822 GTGGAAGCGGTTCACCATTT 59.041 50.000 26.94 0.00 33.93 2.32
2988 3066 0.802494 AAGCGGTTCACCATTTAGCG 59.198 50.000 0.00 0.00 35.14 4.26
2992 3111 2.846693 CGGTTCACCATTTAGCGTTTC 58.153 47.619 0.00 0.00 35.14 2.78
3069 3188 6.314400 GCAACTGGACATGCAAAATCAAATAT 59.686 34.615 0.00 0.00 42.12 1.28
3109 3228 6.620678 TCACAAAATCAGCAGCCTTATTTAC 58.379 36.000 0.00 0.00 27.74 2.01
3172 3292 6.926272 GCCTTTCTGATACCATAGAGTTACAG 59.074 42.308 0.00 0.00 0.00 2.74
3178 3298 5.838521 TGATACCATAGAGTTACAGGCATGA 59.161 40.000 4.84 0.00 0.00 3.07
3249 3369 7.280356 AGTTCTAGCTTTGTCCTAAGTCAAAA 58.720 34.615 0.00 0.00 31.97 2.44
3464 3591 3.756434 GCCTGCACCTCATGTTTTACTTA 59.244 43.478 0.00 0.00 0.00 2.24
3486 3613 9.801873 ACTTATAATGTACAATTCCATTTGCAC 57.198 29.630 0.00 0.00 33.54 4.57
3490 3617 7.466746 AATGTACAATTCCATTTGCACTAGT 57.533 32.000 0.00 0.00 0.00 2.57
3493 3620 8.039603 TGTACAATTCCATTTGCACTAGTTAG 57.960 34.615 0.00 0.00 0.00 2.34
3520 3647 7.272978 AGTTACAGAAAGTGCTACTGAAAGAA 58.727 34.615 0.00 0.00 37.43 2.52
3524 3651 6.702282 ACAGAAAGTGCTACTGAAAGAACTAC 59.298 38.462 0.00 0.00 37.43 2.73
3525 3652 6.926272 CAGAAAGTGCTACTGAAAGAACTACT 59.074 38.462 0.00 0.00 37.43 2.57
3526 3653 7.115663 CAGAAAGTGCTACTGAAAGAACTACTC 59.884 40.741 0.00 0.00 37.43 2.59
3527 3654 5.394224 AGTGCTACTGAAAGAACTACTCC 57.606 43.478 0.00 0.00 37.43 3.85
3528 3655 4.221041 AGTGCTACTGAAAGAACTACTCCC 59.779 45.833 0.00 0.00 37.43 4.30
3529 3656 4.221041 GTGCTACTGAAAGAACTACTCCCT 59.779 45.833 0.00 0.00 37.43 4.20
3530 3657 4.463186 TGCTACTGAAAGAACTACTCCCTC 59.537 45.833 0.00 0.00 37.43 4.30
3531 3658 4.142116 GCTACTGAAAGAACTACTCCCTCC 60.142 50.000 0.00 0.00 37.43 4.30
3532 3659 4.134933 ACTGAAAGAACTACTCCCTCCT 57.865 45.455 0.00 0.00 37.43 3.69
3533 3660 4.494591 ACTGAAAGAACTACTCCCTCCTT 58.505 43.478 0.00 0.00 37.43 3.36
3534 3661 4.908481 ACTGAAAGAACTACTCCCTCCTTT 59.092 41.667 0.00 0.00 37.43 3.11
3535 3662 5.012251 ACTGAAAGAACTACTCCCTCCTTTC 59.988 44.000 0.00 0.00 39.64 2.62
3536 3663 4.905456 TGAAAGAACTACTCCCTCCTTTCA 59.095 41.667 0.00 0.00 43.80 2.69
3537 3664 4.893829 AAGAACTACTCCCTCCTTTCAC 57.106 45.455 0.00 0.00 0.00 3.18
3538 3665 4.134933 AGAACTACTCCCTCCTTTCACT 57.865 45.455 0.00 0.00 0.00 3.41
3539 3666 4.494591 AGAACTACTCCCTCCTTTCACTT 58.505 43.478 0.00 0.00 0.00 3.16
3540 3667 4.908481 AGAACTACTCCCTCCTTTCACTTT 59.092 41.667 0.00 0.00 0.00 2.66
3541 3668 5.369993 AGAACTACTCCCTCCTTTCACTTTT 59.630 40.000 0.00 0.00 0.00 2.27
3542 3669 4.974399 ACTACTCCCTCCTTTCACTTTTG 58.026 43.478 0.00 0.00 0.00 2.44
3543 3670 3.953542 ACTCCCTCCTTTCACTTTTGT 57.046 42.857 0.00 0.00 0.00 2.83
3544 3671 5.605488 ACTACTCCCTCCTTTCACTTTTGTA 59.395 40.000 0.00 0.00 0.00 2.41
3545 3672 5.382664 ACTCCCTCCTTTCACTTTTGTAA 57.617 39.130 0.00 0.00 0.00 2.41
3546 3673 5.377478 ACTCCCTCCTTTCACTTTTGTAAG 58.623 41.667 0.00 0.00 37.40 2.34
3547 3674 5.104067 ACTCCCTCCTTTCACTTTTGTAAGT 60.104 40.000 0.00 0.00 45.40 2.24
3548 3675 5.374071 TCCCTCCTTTCACTTTTGTAAGTC 58.626 41.667 0.00 0.00 42.67 3.01
3549 3676 5.104277 TCCCTCCTTTCACTTTTGTAAGTCA 60.104 40.000 0.00 0.00 42.67 3.41
3550 3677 5.770162 CCCTCCTTTCACTTTTGTAAGTCAT 59.230 40.000 0.00 0.00 42.67 3.06
3551 3678 6.265422 CCCTCCTTTCACTTTTGTAAGTCATT 59.735 38.462 0.00 0.00 42.67 2.57
3552 3679 7.201911 CCCTCCTTTCACTTTTGTAAGTCATTT 60.202 37.037 0.00 0.00 42.67 2.32
3553 3680 7.862873 CCTCCTTTCACTTTTGTAAGTCATTTC 59.137 37.037 0.00 0.00 42.67 2.17
3554 3681 8.287439 TCCTTTCACTTTTGTAAGTCATTTCA 57.713 30.769 0.00 0.00 42.67 2.69
3555 3682 8.405531 TCCTTTCACTTTTGTAAGTCATTTCAG 58.594 33.333 0.00 0.00 42.67 3.02
3556 3683 8.405531 CCTTTCACTTTTGTAAGTCATTTCAGA 58.594 33.333 0.00 0.00 42.67 3.27
3557 3684 9.226345 CTTTCACTTTTGTAAGTCATTTCAGAC 57.774 33.333 0.00 0.00 42.67 3.51
3558 3685 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
3559 3686 8.275015 TCACTTTTGTAAGTCATTTCAGACAA 57.725 30.769 0.00 0.00 42.67 3.18
3560 3687 8.181573 TCACTTTTGTAAGTCATTTCAGACAAC 58.818 33.333 0.00 0.00 42.67 3.32
3561 3688 8.184192 CACTTTTGTAAGTCATTTCAGACAACT 58.816 33.333 0.00 0.00 42.67 3.16
3562 3689 8.398665 ACTTTTGTAAGTCATTTCAGACAACTC 58.601 33.333 0.00 0.00 40.60 3.01
3563 3690 7.857734 TTTGTAAGTCATTTCAGACAACTCA 57.142 32.000 0.00 0.00 40.98 3.41
3564 3691 7.857734 TTGTAAGTCATTTCAGACAACTCAA 57.142 32.000 0.00 0.00 40.98 3.02
3565 3692 7.857734 TGTAAGTCATTTCAGACAACTCAAA 57.142 32.000 0.00 0.00 40.98 2.69
3566 3693 8.275015 TGTAAGTCATTTCAGACAACTCAAAA 57.725 30.769 0.00 0.00 40.98 2.44
3567 3694 8.902806 TGTAAGTCATTTCAGACAACTCAAAAT 58.097 29.630 0.00 0.00 40.98 1.82
3568 3695 9.173939 GTAAGTCATTTCAGACAACTCAAAATG 57.826 33.333 0.00 0.00 40.98 2.32
3569 3696 6.742109 AGTCATTTCAGACAACTCAAAATGG 58.258 36.000 0.00 0.00 40.98 3.16
3570 3697 5.922544 GTCATTTCAGACAACTCAAAATGGG 59.077 40.000 0.00 0.00 37.16 4.00
3571 3698 5.832595 TCATTTCAGACAACTCAAAATGGGA 59.167 36.000 0.00 0.00 37.16 4.37
3572 3699 6.494491 TCATTTCAGACAACTCAAAATGGGAT 59.506 34.615 0.00 0.00 37.16 3.85
3573 3700 5.710513 TTCAGACAACTCAAAATGGGATG 57.289 39.130 0.00 0.00 0.00 3.51
3574 3701 4.728772 TCAGACAACTCAAAATGGGATGT 58.271 39.130 0.00 0.00 0.00 3.06
3575 3702 5.139727 TCAGACAACTCAAAATGGGATGTT 58.860 37.500 0.00 0.00 0.00 2.71
3576 3703 5.598005 TCAGACAACTCAAAATGGGATGTTT 59.402 36.000 0.00 0.00 0.00 2.83
3577 3704 6.098124 TCAGACAACTCAAAATGGGATGTTTT 59.902 34.615 0.00 0.00 0.00 2.43
3578 3705 6.201425 CAGACAACTCAAAATGGGATGTTTTG 59.799 38.462 5.27 5.27 44.10 2.44
3579 3706 5.988287 ACAACTCAAAATGGGATGTTTTGT 58.012 33.333 10.12 0.00 43.52 2.83
3580 3707 7.069331 AGACAACTCAAAATGGGATGTTTTGTA 59.931 33.333 10.12 0.00 43.52 2.41
3581 3708 6.983890 ACAACTCAAAATGGGATGTTTTGTAC 59.016 34.615 10.12 0.00 43.52 2.90
3582 3709 6.723298 ACTCAAAATGGGATGTTTTGTACA 57.277 33.333 10.12 0.00 43.52 2.90
3596 3723 8.801715 ATGTTTTGTACATTGTCTGAAATGTC 57.198 30.769 16.13 11.24 45.47 3.06
3597 3724 7.995289 TGTTTTGTACATTGTCTGAAATGTCT 58.005 30.769 16.13 3.09 45.47 3.41
3598 3725 8.465999 TGTTTTGTACATTGTCTGAAATGTCTT 58.534 29.630 16.13 2.61 45.47 3.01
3599 3726 8.958043 GTTTTGTACATTGTCTGAAATGTCTTC 58.042 33.333 16.13 11.26 45.47 2.87
3600 3727 7.800155 TTGTACATTGTCTGAAATGTCTTCA 57.200 32.000 16.13 12.76 45.47 3.02
3601 3728 7.800155 TGTACATTGTCTGAAATGTCTTCAA 57.200 32.000 16.13 0.18 45.47 2.69
3602 3729 7.864686 TGTACATTGTCTGAAATGTCTTCAAG 58.135 34.615 16.13 0.00 45.47 3.02
3603 3730 6.323203 ACATTGTCTGAAATGTCTTCAAGG 57.677 37.500 10.41 0.00 45.47 3.61
3604 3731 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
3605 3732 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
3606 3733 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
3607 3734 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
3608 3735 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
3609 3736 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
3610 3737 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
3611 3738 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
3617 3744 9.793259 AATGTCTTCAAGGTCTTATAAAAGTGA 57.207 29.630 0.00 0.00 34.13 3.41
3618 3745 9.793259 ATGTCTTCAAGGTCTTATAAAAGTGAA 57.207 29.630 0.00 0.00 34.13 3.18
3619 3746 9.052759 TGTCTTCAAGGTCTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 34.13 3.18
3620 3747 9.052759 GTCTTCAAGGTCTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 34.13 3.18
3621 3748 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
3622 3749 9.273016 CTTCAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
3623 3750 8.833231 TCAAGGTCTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 34.13 3.35
3624 3751 7.878127 TCAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
3625 3752 7.554959 AGGTCTTATAAAAGTGAACAGAGGA 57.445 36.000 0.00 0.00 34.13 3.71
3626 3753 7.974504 AGGTCTTATAAAAGTGAACAGAGGAA 58.025 34.615 0.00 0.00 34.13 3.36
3627 3754 8.097662 AGGTCTTATAAAAGTGAACAGAGGAAG 58.902 37.037 0.00 0.00 34.13 3.46
3628 3755 7.878644 GGTCTTATAAAAGTGAACAGAGGAAGT 59.121 37.037 0.00 0.00 34.13 3.01
3629 3756 9.924650 GTCTTATAAAAGTGAACAGAGGAAGTA 57.075 33.333 0.00 0.00 34.13 2.24
3640 3767 7.542824 GTGAACAGAGGAAGTAGTACAAATCTC 59.457 40.741 2.52 4.34 0.00 2.75
3699 3826 5.235516 ACTACGTAAGGTCAACTTCAATGG 58.764 41.667 0.00 0.00 46.39 3.16
3701 3828 2.811431 CGTAAGGTCAACTTCAATGGCA 59.189 45.455 0.00 0.00 40.64 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 5.341031 CCCTCCTACTAGGTTAAACTCCTCT 60.341 48.000 0.00 0.00 36.53 3.69
120 121 3.140143 TCTCCAATCCCTCCTACTAGGT 58.860 50.000 1.83 0.00 36.53 3.08
165 166 3.200825 CCCACACACCCATCTTAGATCTT 59.799 47.826 0.00 0.00 0.00 2.40
172 173 1.460255 CCACCCACACACCCATCTT 59.540 57.895 0.00 0.00 0.00 2.40
181 182 4.109675 CGGATCCCCCACCCACAC 62.110 72.222 6.06 0.00 34.14 3.82
182 183 3.874370 TTCGGATCCCCCACCCACA 62.874 63.158 6.06 0.00 34.14 4.17
183 184 3.012722 TTCGGATCCCCCACCCAC 61.013 66.667 6.06 0.00 34.14 4.61
184 185 2.690881 CTTCGGATCCCCCACCCA 60.691 66.667 6.06 0.00 34.14 4.51
185 186 3.489513 CCTTCGGATCCCCCACCC 61.490 72.222 6.06 0.00 34.14 4.61
186 187 2.366435 TCCTTCGGATCCCCCACC 60.366 66.667 6.06 0.00 34.14 4.61
240 252 0.423544 AGTTCTTCCCCCTCTCCCAT 59.576 55.000 0.00 0.00 0.00 4.00
242 254 1.916206 GCAGTTCTTCCCCCTCTCCC 61.916 65.000 0.00 0.00 0.00 4.30
279 292 0.108585 ACTGTGACTTGACCCGCATT 59.891 50.000 0.00 0.00 0.00 3.56
286 299 1.566563 CGCTGCACTGTGACTTGAC 59.433 57.895 12.86 0.00 0.00 3.18
288 301 2.250485 GCGCTGCACTGTGACTTG 59.750 61.111 12.86 0.00 0.00 3.16
317 330 2.032117 CACAAAGTGTAATGTGCAGCGA 60.032 45.455 0.00 0.00 40.32 4.93
440 453 1.679977 AAGGCGTCGCACCCTACTA 60.680 57.895 20.50 0.00 0.00 1.82
462 475 2.033448 TTTCAAGTGGCGCCCGAT 59.967 55.556 26.77 6.65 0.00 4.18
475 488 0.684535 TCACGCTGATGACCCTTTCA 59.315 50.000 0.00 0.00 39.11 2.69
610 628 2.981909 TGGTCTCGTCTCGCGGTT 60.982 61.111 6.13 0.00 41.72 4.44
735 753 4.491409 GCGGGGAAGGGGAGCTTC 62.491 72.222 0.00 0.00 0.00 3.86
780 798 2.109128 TCTAGTGGGCTGCTAGCTAGAT 59.891 50.000 25.15 0.00 41.99 1.98
798 816 2.915869 AGGGGTTGTGAATGGTCTCTA 58.084 47.619 0.00 0.00 0.00 2.43
848 866 1.770324 CCTGAAAGAGCTTGGGGGT 59.230 57.895 0.00 0.00 34.07 4.95
851 869 1.246737 GCACCCTGAAAGAGCTTGGG 61.247 60.000 0.00 0.00 43.26 4.12
852 870 0.251077 AGCACCCTGAAAGAGCTTGG 60.251 55.000 0.00 0.00 33.72 3.61
853 871 2.289945 ACTAGCACCCTGAAAGAGCTTG 60.290 50.000 0.00 0.00 37.50 4.01
854 872 1.981495 ACTAGCACCCTGAAAGAGCTT 59.019 47.619 0.00 0.00 37.50 3.74
885 903 2.355986 TGCTAATCGTGACCGGCCT 61.356 57.895 0.00 0.00 33.95 5.19
903 921 2.129146 TCAAGGACACACCGTCGGT 61.129 57.895 12.23 12.23 46.42 4.69
1036 1057 3.680620 TATGTGGCCGGAGCACAGC 62.681 63.158 5.05 0.00 42.56 4.40
1148 1169 4.386652 GCACAAATTTGTCATGGTCATCAC 59.613 41.667 20.85 0.00 39.91 3.06
1162 1183 3.157087 ACTTGATCGGGAGCACAAATTT 58.843 40.909 0.00 0.00 0.00 1.82
1518 1539 2.299867 GCCCCACATCAAATCAAACTGT 59.700 45.455 0.00 0.00 0.00 3.55
1631 1652 1.560860 GAAGGCGTCTATGGCATCGC 61.561 60.000 19.98 19.98 46.42 4.58
1701 1722 1.153745 GCACAGCGTGTCTAGGAGG 60.154 63.158 9.76 0.00 35.75 4.30
2370 2391 0.180171 TGTGGCATATGAGGAACCGG 59.820 55.000 6.97 0.00 0.00 5.28
2394 2415 2.694397 TCAGGGGTGATATCCTTCCTG 58.306 52.381 20.43 20.43 42.10 3.86
2397 2418 5.310409 TGAAATCAGGGGTGATATCCTTC 57.690 43.478 0.00 0.00 0.00 3.46
2403 2424 2.092429 GGTGCTGAAATCAGGGGTGATA 60.092 50.000 12.09 0.00 43.94 2.15
2454 2475 1.743252 CTGAGCAGGCTTCCCGTTC 60.743 63.158 0.00 0.00 35.76 3.95
2466 2487 0.761187 AGAACAGGCAAGACTGAGCA 59.239 50.000 10.44 0.00 40.97 4.26
2469 2490 1.768275 TCCAAGAACAGGCAAGACTGA 59.232 47.619 10.44 0.00 40.97 3.41
2499 2520 1.611519 TTGGCGTAAAACCCTTCAGG 58.388 50.000 0.00 0.00 43.78 3.86
2517 2538 6.751888 CCACAAGATCAAACGTTTCTTTCTTT 59.248 34.615 19.37 12.27 0.00 2.52
2542 2563 2.991250 TGCCTTATCAAGCTTCTCCAC 58.009 47.619 0.00 0.00 0.00 4.02
2543 2564 3.719268 TTGCCTTATCAAGCTTCTCCA 57.281 42.857 0.00 0.00 0.00 3.86
2544 2565 4.886489 AGATTTGCCTTATCAAGCTTCTCC 59.114 41.667 0.00 0.00 0.00 3.71
2562 2583 5.964958 TTTTCTTCGCTGAATGGAGATTT 57.035 34.783 0.00 0.00 0.00 2.17
2577 2598 6.266323 GGTGAGAAGTTGAACCTTTTTCTTC 58.734 40.000 0.00 0.00 33.73 2.87
2587 2608 0.868406 CGCAGGGTGAGAAGTTGAAC 59.132 55.000 0.00 0.00 0.00 3.18
2641 2662 3.591527 ACCATCCTTGTTCATGTAAGGGA 59.408 43.478 18.99 10.63 42.92 4.20
2648 2669 1.135199 GCAGCACCATCCTTGTTCATG 60.135 52.381 0.00 0.00 0.00 3.07
2649 2670 1.180029 GCAGCACCATCCTTGTTCAT 58.820 50.000 0.00 0.00 0.00 2.57
2690 2711 0.244450 CATGGCCACAAGCGTTTGAT 59.756 50.000 19.42 0.00 45.17 2.57
2706 2727 5.295431 TCGCATTTGTTCTAAGGTTCATG 57.705 39.130 0.00 0.00 0.00 3.07
2718 2739 4.364860 GGTTTTGTACCTTCGCATTTGTT 58.635 39.130 0.00 0.00 44.10 2.83
2739 2760 7.222224 GGTCGAGTGATAAACTTGTATTACTGG 59.778 40.741 0.00 0.00 40.07 4.00
2755 2776 4.082517 CGATGAATGGATAGGTCGAGTGAT 60.083 45.833 0.00 0.00 0.00 3.06
2759 2780 4.505313 TTCGATGAATGGATAGGTCGAG 57.495 45.455 0.00 0.00 38.99 4.04
2806 2827 8.121086 CAGAGCAACATAATTGTAACAGATCAG 58.879 37.037 0.00 0.00 34.06 2.90
2822 2900 4.330250 AGTTCAACATAGCAGAGCAACAT 58.670 39.130 0.00 0.00 0.00 2.71
2836 2914 5.242434 AGGTGTTGCGAATATAGTTCAACA 58.758 37.500 13.99 13.99 42.95 3.33
2837 2915 5.796350 AGGTGTTGCGAATATAGTTCAAC 57.204 39.130 10.41 10.41 37.94 3.18
2872 2950 4.777896 TCCTTACTGCTATGGAACTTCTGT 59.222 41.667 0.00 0.00 0.00 3.41
2917 2995 7.390440 TCGATGAACAGGATTAAAATTGACAGT 59.610 33.333 0.00 0.00 0.00 3.55
2921 2999 6.370442 ACGTCGATGAACAGGATTAAAATTGA 59.630 34.615 12.58 0.00 0.00 2.57
2923 3001 6.594159 AGACGTCGATGAACAGGATTAAAATT 59.406 34.615 12.58 0.00 0.00 1.82
2930 3008 1.469940 GCAGACGTCGATGAACAGGAT 60.470 52.381 12.58 0.00 0.00 3.24
2935 3013 2.257974 TACTGCAGACGTCGATGAAC 57.742 50.000 23.35 5.11 0.00 3.18
2942 3020 6.955963 CACATTCTTTTTATACTGCAGACGTC 59.044 38.462 23.35 7.70 0.00 4.34
2952 3030 6.190954 ACCGCTTCCACATTCTTTTTATAC 57.809 37.500 0.00 0.00 0.00 1.47
2962 3040 0.179004 TGGTGAACCGCTTCCACATT 60.179 50.000 0.00 0.00 39.43 2.71
2983 3061 8.657074 ACTGTTTATATATGCTGAAACGCTAA 57.343 30.769 0.00 0.00 35.09 3.09
2984 3062 8.657074 AACTGTTTATATATGCTGAAACGCTA 57.343 30.769 0.00 0.00 35.09 4.26
3069 3188 3.473923 TGTGAAGTCTGAATGCTGTCA 57.526 42.857 0.00 0.00 0.00 3.58
3109 3228 2.711542 ACTGTTGGAAATAAGGGAGCG 58.288 47.619 0.00 0.00 0.00 5.03
3360 3480 8.403236 GCTTTGTCCTAAGTTGAACTTCTTTAA 58.597 33.333 14.64 2.69 39.51 1.52
3361 3481 7.773690 AGCTTTGTCCTAAGTTGAACTTCTTTA 59.226 33.333 14.64 0.00 39.51 1.85
3464 3591 9.189156 ACTAGTGCAAATGGAATTGTACATTAT 57.811 29.630 10.14 0.00 45.00 1.28
3484 3611 8.298140 AGCACTTTCTGTAACTACTAACTAGTG 58.702 37.037 0.00 0.00 35.70 2.74
3485 3612 8.406730 AGCACTTTCTGTAACTACTAACTAGT 57.593 34.615 0.00 0.00 37.28 2.57
3486 3613 9.771915 GTAGCACTTTCTGTAACTACTAACTAG 57.228 37.037 0.00 0.00 35.92 2.57
3487 3614 9.512588 AGTAGCACTTTCTGTAACTACTAACTA 57.487 33.333 0.00 0.00 41.78 2.24
3488 3615 8.298140 CAGTAGCACTTTCTGTAACTACTAACT 58.702 37.037 0.00 0.00 41.73 2.24
3489 3616 8.295288 TCAGTAGCACTTTCTGTAACTACTAAC 58.705 37.037 0.00 0.00 41.73 2.34
3490 3617 8.400184 TCAGTAGCACTTTCTGTAACTACTAA 57.600 34.615 0.00 0.00 41.73 2.24
3493 3620 7.866393 TCTTTCAGTAGCACTTTCTGTAACTAC 59.134 37.037 0.00 0.00 37.58 2.73
3520 3647 4.412528 ACAAAAGTGAAAGGAGGGAGTAGT 59.587 41.667 0.00 0.00 0.00 2.73
3524 3651 5.377478 ACTTACAAAAGTGAAAGGAGGGAG 58.623 41.667 0.00 0.00 44.40 4.30
3525 3652 5.104277 TGACTTACAAAAGTGAAAGGAGGGA 60.104 40.000 0.00 0.00 46.09 4.20
3526 3653 5.130350 TGACTTACAAAAGTGAAAGGAGGG 58.870 41.667 0.00 0.00 46.09 4.30
3527 3654 6.884280 ATGACTTACAAAAGTGAAAGGAGG 57.116 37.500 0.00 0.00 46.09 4.30
3528 3655 8.405531 TGAAATGACTTACAAAAGTGAAAGGAG 58.594 33.333 0.00 0.00 46.09 3.69
3529 3656 8.287439 TGAAATGACTTACAAAAGTGAAAGGA 57.713 30.769 0.00 0.00 46.09 3.36
3530 3657 8.405531 TCTGAAATGACTTACAAAAGTGAAAGG 58.594 33.333 0.00 0.00 46.09 3.11
3531 3658 9.226345 GTCTGAAATGACTTACAAAAGTGAAAG 57.774 33.333 0.00 0.00 46.09 2.62
3532 3659 8.735315 TGTCTGAAATGACTTACAAAAGTGAAA 58.265 29.630 0.00 0.00 46.09 2.69
3533 3660 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
3534 3661 7.857734 TGTCTGAAATGACTTACAAAAGTGA 57.142 32.000 0.00 0.00 46.09 3.41
3535 3662 8.184192 AGTTGTCTGAAATGACTTACAAAAGTG 58.816 33.333 0.00 0.00 46.09 3.16
3537 3664 8.397906 TGAGTTGTCTGAAATGACTTACAAAAG 58.602 33.333 0.00 0.00 37.79 2.27
3538 3665 8.275015 TGAGTTGTCTGAAATGACTTACAAAA 57.725 30.769 0.00 0.00 37.79 2.44
3539 3666 7.857734 TGAGTTGTCTGAAATGACTTACAAA 57.142 32.000 0.00 0.00 37.79 2.83
3540 3667 7.857734 TTGAGTTGTCTGAAATGACTTACAA 57.142 32.000 0.00 0.00 37.79 2.41
3541 3668 7.857734 TTTGAGTTGTCTGAAATGACTTACA 57.142 32.000 0.00 0.00 37.79 2.41
3542 3669 9.173939 CATTTTGAGTTGTCTGAAATGACTTAC 57.826 33.333 0.00 0.00 38.18 2.34
3543 3670 8.352201 CCATTTTGAGTTGTCTGAAATGACTTA 58.648 33.333 8.27 0.00 38.18 2.24
3544 3671 7.205297 CCATTTTGAGTTGTCTGAAATGACTT 58.795 34.615 8.27 0.00 38.18 3.01
3545 3672 6.239120 CCCATTTTGAGTTGTCTGAAATGACT 60.239 38.462 8.27 0.00 38.18 3.41
3546 3673 5.922544 CCCATTTTGAGTTGTCTGAAATGAC 59.077 40.000 8.27 0.00 38.18 3.06
3547 3674 5.832595 TCCCATTTTGAGTTGTCTGAAATGA 59.167 36.000 8.27 0.00 38.18 2.57
3548 3675 6.088016 TCCCATTTTGAGTTGTCTGAAATG 57.912 37.500 0.00 0.00 37.04 2.32
3549 3676 6.268387 ACATCCCATTTTGAGTTGTCTGAAAT 59.732 34.615 0.00 0.00 0.00 2.17
3550 3677 5.598005 ACATCCCATTTTGAGTTGTCTGAAA 59.402 36.000 0.00 0.00 0.00 2.69
3551 3678 5.139727 ACATCCCATTTTGAGTTGTCTGAA 58.860 37.500 0.00 0.00 0.00 3.02
3552 3679 4.728772 ACATCCCATTTTGAGTTGTCTGA 58.271 39.130 0.00 0.00 0.00 3.27
3553 3680 5.458041 AACATCCCATTTTGAGTTGTCTG 57.542 39.130 0.00 0.00 0.00 3.51
3554 3681 6.127083 ACAAAACATCCCATTTTGAGTTGTCT 60.127 34.615 15.13 0.00 45.75 3.41
3555 3682 6.048509 ACAAAACATCCCATTTTGAGTTGTC 58.951 36.000 15.13 0.00 45.75 3.18
3556 3683 5.988287 ACAAAACATCCCATTTTGAGTTGT 58.012 33.333 15.13 0.00 45.75 3.32
3557 3684 6.983307 TGTACAAAACATCCCATTTTGAGTTG 59.017 34.615 15.13 0.00 45.75 3.16
3558 3685 7.118496 TGTACAAAACATCCCATTTTGAGTT 57.882 32.000 15.13 0.00 45.75 3.01
3559 3686 6.723298 TGTACAAAACATCCCATTTTGAGT 57.277 33.333 15.13 0.00 45.75 3.41
3572 3699 7.995289 AGACATTTCAGACAATGTACAAAACA 58.005 30.769 0.00 0.00 45.55 2.83
3573 3700 8.856490 AAGACATTTCAGACAATGTACAAAAC 57.144 30.769 0.00 0.00 45.55 2.43
3574 3701 8.681806 TGAAGACATTTCAGACAATGTACAAAA 58.318 29.630 0.00 0.00 45.55 2.44
3575 3702 8.219546 TGAAGACATTTCAGACAATGTACAAA 57.780 30.769 0.00 0.00 45.55 2.83
3576 3703 7.800155 TGAAGACATTTCAGACAATGTACAA 57.200 32.000 0.00 0.00 45.55 2.41
3577 3704 7.041167 CCTTGAAGACATTTCAGACAATGTACA 60.041 37.037 0.00 0.00 45.55 2.90
3578 3705 7.041098 ACCTTGAAGACATTTCAGACAATGTAC 60.041 37.037 9.58 0.00 45.55 2.90
3579 3706 6.998074 ACCTTGAAGACATTTCAGACAATGTA 59.002 34.615 9.58 0.00 45.55 2.29
3581 3708 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
3582 3709 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
3583 3710 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
3584 3711 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
3585 3712 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
3591 3718 9.793259 TCACTTTTATAAGACCTTGAAGACATT 57.207 29.630 0.00 0.00 35.30 2.71
3592 3719 9.793259 TTCACTTTTATAAGACCTTGAAGACAT 57.207 29.630 0.00 0.00 35.30 3.06
3593 3720 9.052759 GTTCACTTTTATAAGACCTTGAAGACA 57.947 33.333 0.00 0.00 35.30 3.41
3594 3721 9.052759 TGTTCACTTTTATAAGACCTTGAAGAC 57.947 33.333 0.00 0.00 35.30 3.01
3595 3722 9.273016 CTGTTCACTTTTATAAGACCTTGAAGA 57.727 33.333 0.00 0.00 35.30 2.87
3596 3723 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
3597 3724 9.273016 CTCTGTTCACTTTTATAAGACCTTGAA 57.727 33.333 0.00 0.00 35.30 2.69
3598 3725 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
3599 3726 7.878127 TCCTCTGTTCACTTTTATAAGACCTTG 59.122 37.037 0.00 0.00 35.30 3.61
3600 3727 7.974504 TCCTCTGTTCACTTTTATAAGACCTT 58.025 34.615 0.00 0.00 35.30 3.50
3601 3728 7.554959 TCCTCTGTTCACTTTTATAAGACCT 57.445 36.000 0.00 0.00 35.30 3.85
3602 3729 7.878644 ACTTCCTCTGTTCACTTTTATAAGACC 59.121 37.037 0.00 0.00 35.30 3.85
3603 3730 8.834749 ACTTCCTCTGTTCACTTTTATAAGAC 57.165 34.615 0.00 0.00 35.30 3.01
3605 3732 9.930693 ACTACTTCCTCTGTTCACTTTTATAAG 57.069 33.333 0.00 0.00 37.40 1.73
3608 3735 8.867097 TGTACTACTTCCTCTGTTCACTTTTAT 58.133 33.333 0.00 0.00 0.00 1.40
3609 3736 8.241497 TGTACTACTTCCTCTGTTCACTTTTA 57.759 34.615 0.00 0.00 0.00 1.52
3610 3737 7.120923 TGTACTACTTCCTCTGTTCACTTTT 57.879 36.000 0.00 0.00 0.00 2.27
3611 3738 6.726490 TGTACTACTTCCTCTGTTCACTTT 57.274 37.500 0.00 0.00 0.00 2.66
3612 3739 6.726490 TTGTACTACTTCCTCTGTTCACTT 57.274 37.500 0.00 0.00 0.00 3.16
3613 3740 6.726490 TTTGTACTACTTCCTCTGTTCACT 57.274 37.500 0.00 0.00 0.00 3.41
3614 3741 7.379750 AGATTTGTACTACTTCCTCTGTTCAC 58.620 38.462 0.00 0.00 0.00 3.18
3615 3742 7.232737 TGAGATTTGTACTACTTCCTCTGTTCA 59.767 37.037 0.00 0.00 0.00 3.18
3616 3743 7.603651 TGAGATTTGTACTACTTCCTCTGTTC 58.396 38.462 0.00 0.00 0.00 3.18
3617 3744 7.540474 TGAGATTTGTACTACTTCCTCTGTT 57.460 36.000 0.00 0.00 0.00 3.16
3618 3745 7.364232 CCATGAGATTTGTACTACTTCCTCTGT 60.364 40.741 0.00 0.00 0.00 3.41
3619 3746 6.983307 CCATGAGATTTGTACTACTTCCTCTG 59.017 42.308 0.00 0.00 0.00 3.35
3620 3747 6.897966 TCCATGAGATTTGTACTACTTCCTCT 59.102 38.462 0.00 0.00 0.00 3.69
3621 3748 7.113658 TCCATGAGATTTGTACTACTTCCTC 57.886 40.000 0.00 0.00 0.00 3.71
3622 3749 7.419518 CCATCCATGAGATTTGTACTACTTCCT 60.420 40.741 0.00 0.00 30.59 3.36
3623 3750 6.708054 CCATCCATGAGATTTGTACTACTTCC 59.292 42.308 0.00 0.00 30.59 3.46
3624 3751 7.500992 TCCATCCATGAGATTTGTACTACTTC 58.499 38.462 0.00 0.00 30.59 3.01
3625 3752 7.345653 TCTCCATCCATGAGATTTGTACTACTT 59.654 37.037 0.00 0.00 30.59 2.24
3626 3753 6.841229 TCTCCATCCATGAGATTTGTACTACT 59.159 38.462 0.00 0.00 30.59 2.57
3627 3754 7.055667 TCTCCATCCATGAGATTTGTACTAC 57.944 40.000 0.00 0.00 30.59 2.73
3628 3755 7.675161 TTCTCCATCCATGAGATTTGTACTA 57.325 36.000 0.00 0.00 30.59 1.82
3629 3756 6.566079 TTCTCCATCCATGAGATTTGTACT 57.434 37.500 0.00 0.00 30.59 2.73
3640 3767 9.404848 AGCACATAATATTATTCTCCATCCATG 57.595 33.333 5.18 0.00 0.00 3.66
3699 3826 0.881118 TTGGACTCGCCTTTCAATGC 59.119 50.000 0.00 0.00 37.63 3.56
3701 3828 2.568623 ACTTGGACTCGCCTTTCAAT 57.431 45.000 0.00 0.00 37.63 2.57
3840 3968 4.036734 GCTGATTCAAGAAACAACACCTCA 59.963 41.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.