Multiple sequence alignment - TraesCS1B01G408400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G408400 chr1B 100.000 3488 0 0 1 3488 635977554 635981041 0.000000e+00 6442.0
1 TraesCS1B01G408400 chr1B 97.770 269 5 1 2626 2893 120470613 120470345 2.450000e-126 462.0
2 TraesCS1B01G408400 chr1B 86.780 295 37 2 84 377 2356969 2356676 9.330000e-86 327.0
3 TraesCS1B01G408400 chr1B 75.085 293 59 10 87 375 22824274 22823992 1.310000e-24 124.0
4 TraesCS1B01G408400 chr1B 92.683 41 3 0 620 660 326018423 326018383 3.760000e-05 60.2
5 TraesCS1B01G408400 chr5A 99.147 1994 16 1 607 2599 549934965 549936958 0.000000e+00 3587.0
6 TraesCS1B01G408400 chr5A 99.333 600 3 1 2890 3488 549936949 549937548 0.000000e+00 1085.0
7 TraesCS1B01G408400 chr4A 98.597 1996 21 3 607 2599 697442323 697444314 0.000000e+00 3524.0
8 TraesCS1B01G408400 chr4A 98.333 600 9 1 2890 3488 697444305 697444904 0.000000e+00 1051.0
9 TraesCS1B01G408400 chr4A 92.251 271 20 1 2621 2891 4244652 4244383 1.960000e-102 383.0
10 TraesCS1B01G408400 chr4A 78.451 297 56 3 80 375 714897295 714897584 1.650000e-43 187.0
11 TraesCS1B01G408400 chr6A 91.736 605 45 4 6 610 1338858 1338259 0.000000e+00 835.0
12 TraesCS1B01G408400 chr6D 86.964 606 41 6 3 607 543874 544442 0.000000e+00 647.0
13 TraesCS1B01G408400 chr6D 73.890 563 109 21 68 607 1445336 1445883 1.280000e-44 191.0
14 TraesCS1B01G408400 chr6D 79.200 125 21 4 481 601 501747 501624 8.020000e-12 82.4
15 TraesCS1B01G408400 chr7A 92.647 272 19 1 2621 2892 734568619 734568349 1.170000e-104 390.0
16 TraesCS1B01G408400 chr2A 91.912 272 22 0 2621 2892 613211682 613211411 7.060000e-102 381.0
17 TraesCS1B01G408400 chr4B 92.857 266 6 1 2624 2889 424283579 424283831 1.180000e-99 374.0
18 TraesCS1B01G408400 chr3A 87.132 272 22 2 2621 2892 691701781 691701523 2.630000e-76 296.0
19 TraesCS1B01G408400 chr3A 85.663 279 32 4 2621 2892 738909835 738910112 1.580000e-73 287.0
20 TraesCS1B01G408400 chrUn 82.803 314 45 4 74 378 51444018 51444331 4.440000e-69 272.0
21 TraesCS1B01G408400 chrUn 82.653 294 51 0 84 377 228623816 228624109 9.600000e-66 261.0
22 TraesCS1B01G408400 chrUn 78.231 294 56 3 83 375 314280328 314280042 7.690000e-42 182.0
23 TraesCS1B01G408400 chrUn 84.112 107 14 2 481 584 228624172 228624278 2.220000e-17 100.0
24 TraesCS1B01G408400 chr3D 79.360 344 44 19 951 1278 474454130 474454462 2.110000e-52 217.0
25 TraesCS1B01G408400 chr6B 78.635 337 41 19 954 1275 500249150 500248830 9.880000e-46 195.0
26 TraesCS1B01G408400 chr2B 83.200 125 16 4 481 601 755627915 755628038 3.680000e-20 110.0
27 TraesCS1B01G408400 chr2B 90.196 51 1 3 2848 2898 105393422 105393376 2.910000e-06 63.9
28 TraesCS1B01G408400 chr2B 100.000 30 0 0 620 649 676686473 676686444 4.860000e-04 56.5
29 TraesCS1B01G408400 chr1D 97.826 46 1 0 614 659 7835843 7835888 2.890000e-11 80.5
30 TraesCS1B01G408400 chr5B 93.478 46 2 1 2848 2892 32641014 32641059 2.250000e-07 67.6
31 TraesCS1B01G408400 chr5B 92.683 41 3 0 620 660 548529819 548529779 3.760000e-05 60.2
32 TraesCS1B01G408400 chr1A 96.970 33 1 0 2542 2574 532281132 532281100 4.860000e-04 56.5


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 TraesCS1B01G408400 chr1B 635977554 635981041 3487 False 6442.0 6442 100.000 1 3488 1 chr1B.!!$F1 3487
1 TraesCS1B01G408400 chr5A 549934965 549937548 2583 False 2336.0 3587 99.240 607 3488 2 chr5A.!!$F1 2881
2 TraesCS1B01G408400 chr4A 697442323 697444904 2581 False 2287.5 3524 98.465 607 3488 2 chr4A.!!$F2 2881
3 TraesCS1B01G408400 chr6A 1338259 1338858 599 True 835.0 835 91.736 6 610 1 chr6A.!!$R1 604
4 TraesCS1B01G408400 chr6D 543874 544442 568 False 647.0 647 86.964 3 607 1 chr6D.!!$F1 604

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
205 207 0.109132 CCCTCGTGCTTGATTTTGCC 60.109 55.0 0.0 0.0 0.00 4.52 F
292 294 0.461870 ACAGCTCTTGTGTCAACGCA 60.462 50.0 0.0 0.0 38.99 5.24 F
344 346 0.676782 GGACCATTACGCTGGCAACT 60.677 55.0 0.0 0.0 40.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 1678 1.432807 ACCCCATTTTGGTCATGTCCT 59.567 47.619 10.43 0.0 35.17 3.85 R
2232 2237 0.988832 TATCCCTGAAACGGTGGCTT 59.011 50.000 0.00 0.0 0.00 4.35 R
2589 2594 1.969103 GCACTTTGCGATCAAACCTC 58.031 50.000 0.00 0.0 37.28 3.85 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
70 71 2.509336 ATGCCGCACAGCTACGAC 60.509 61.111 0.00 0.00 0.00 4.34
153 155 2.835605 CCGACTTGTACGGCAACAT 58.164 52.632 0.00 0.00 43.74 2.71
163 165 1.999051 CGGCAACATGACGCTACTC 59.001 57.895 0.00 0.00 44.33 2.59
166 168 1.804151 GGCAACATGACGCTACTCAAA 59.196 47.619 0.00 0.00 0.00 2.69
205 207 0.109132 CCCTCGTGCTTGATTTTGCC 60.109 55.000 0.00 0.00 0.00 4.52
238 240 2.725203 CTTGTCCGGCGGAAGGTCAA 62.725 60.000 32.91 26.89 35.94 3.18
292 294 0.461870 ACAGCTCTTGTGTCAACGCA 60.462 50.000 0.00 0.00 38.99 5.24
324 326 3.136763 CTGGCTATATCTGCAGGTGTTG 58.863 50.000 15.13 7.39 0.00 3.33
344 346 0.676782 GGACCATTACGCTGGCAACT 60.677 55.000 0.00 0.00 40.15 3.16
383 385 2.691526 TGCCAAGGTACATACTCCTACG 59.308 50.000 0.00 0.00 33.27 3.51
588 590 2.417243 GCAGGATGGGAATGAAAAACGG 60.417 50.000 0.00 0.00 35.86 4.44
607 609 2.031465 GGCGAACGGGGAAACTGA 59.969 61.111 0.00 0.00 0.00 3.41
1675 1678 7.031372 GGATTTGTCAGTGTATGTACGTTCTA 58.969 38.462 0.00 0.00 0.00 2.10
1747 1750 5.185828 GGATTCTTAGAACATGGCCAAAGTT 59.814 40.000 22.53 22.53 0.00 2.66
2232 2237 8.637986 ACTTTTTGTTTATAATCTGTTCTGCCA 58.362 29.630 0.00 0.00 0.00 4.92
2592 2597 9.003658 AGATTAAATTAGTTGTGACTTGTGAGG 57.996 33.333 0.00 0.00 37.33 3.86
2593 2598 8.691661 ATTAAATTAGTTGTGACTTGTGAGGT 57.308 30.769 0.00 0.00 37.33 3.85
2594 2599 8.514330 TTAAATTAGTTGTGACTTGTGAGGTT 57.486 30.769 0.00 0.00 37.33 3.50
2595 2600 7.404671 AAATTAGTTGTGACTTGTGAGGTTT 57.595 32.000 0.00 0.00 37.33 3.27
2596 2601 5.811399 TTAGTTGTGACTTGTGAGGTTTG 57.189 39.130 0.00 0.00 37.33 2.93
2597 2602 3.950397 AGTTGTGACTTGTGAGGTTTGA 58.050 40.909 0.00 0.00 29.87 2.69
2598 2603 4.526970 AGTTGTGACTTGTGAGGTTTGAT 58.473 39.130 0.00 0.00 29.87 2.57
2599 2604 4.576463 AGTTGTGACTTGTGAGGTTTGATC 59.424 41.667 0.00 0.00 29.87 2.92
2600 2605 3.130633 TGTGACTTGTGAGGTTTGATCG 58.869 45.455 0.00 0.00 0.00 3.69
2601 2606 2.096218 GTGACTTGTGAGGTTTGATCGC 60.096 50.000 0.00 0.00 0.00 4.58
2602 2607 2.143122 GACTTGTGAGGTTTGATCGCA 58.857 47.619 0.00 0.00 35.48 5.10
2603 2608 2.548057 GACTTGTGAGGTTTGATCGCAA 59.452 45.455 2.39 2.39 43.03 4.85
2604 2609 2.948979 ACTTGTGAGGTTTGATCGCAAA 59.051 40.909 3.83 0.00 44.16 3.68
2605 2610 3.003689 ACTTGTGAGGTTTGATCGCAAAG 59.996 43.478 3.83 1.90 44.16 2.77
2606 2611 2.571212 TGTGAGGTTTGATCGCAAAGT 58.429 42.857 0.00 0.00 44.12 2.66
2607 2612 2.290367 TGTGAGGTTTGATCGCAAAGTG 59.710 45.455 0.00 0.00 44.12 3.16
2608 2613 1.266718 TGAGGTTTGATCGCAAAGTGC 59.733 47.619 0.00 0.00 44.12 4.40
2609 2614 1.266718 GAGGTTTGATCGCAAAGTGCA 59.733 47.619 0.61 0.00 45.36 4.57
2610 2615 1.888512 AGGTTTGATCGCAAAGTGCAT 59.111 42.857 0.61 0.00 45.36 3.96
2611 2616 2.297033 AGGTTTGATCGCAAAGTGCATT 59.703 40.909 0.61 0.00 45.36 3.56
2612 2617 3.505680 AGGTTTGATCGCAAAGTGCATTA 59.494 39.130 0.61 0.00 45.36 1.90
2613 2618 4.158394 AGGTTTGATCGCAAAGTGCATTAT 59.842 37.500 0.61 0.00 45.36 1.28
2614 2619 4.266029 GGTTTGATCGCAAAGTGCATTATG 59.734 41.667 0.61 0.00 45.36 1.90
2615 2620 4.700268 TTGATCGCAAAGTGCATTATGT 57.300 36.364 0.61 0.00 45.36 2.29
2616 2621 4.700268 TGATCGCAAAGTGCATTATGTT 57.300 36.364 0.61 0.00 45.36 2.71
2617 2622 4.413969 TGATCGCAAAGTGCATTATGTTG 58.586 39.130 0.61 0.00 45.36 3.33
2618 2623 2.594321 TCGCAAAGTGCATTATGTTGC 58.406 42.857 6.95 6.95 45.36 4.17
2619 2624 1.655099 CGCAAAGTGCATTATGTTGCC 59.345 47.619 10.41 0.00 45.36 4.52
2620 2625 2.686235 GCAAAGTGCATTATGTTGCCA 58.314 42.857 5.96 0.00 44.26 4.92
2621 2626 2.669434 GCAAAGTGCATTATGTTGCCAG 59.331 45.455 5.96 0.00 44.26 4.85
2622 2627 3.255725 CAAAGTGCATTATGTTGCCAGG 58.744 45.455 0.00 0.00 42.06 4.45
2623 2628 2.512692 AGTGCATTATGTTGCCAGGA 57.487 45.000 0.00 0.00 42.06 3.86
2624 2629 2.806434 AGTGCATTATGTTGCCAGGAA 58.194 42.857 0.00 0.00 42.06 3.36
2625 2630 3.164268 AGTGCATTATGTTGCCAGGAAA 58.836 40.909 0.00 0.00 42.06 3.13
2626 2631 3.194116 AGTGCATTATGTTGCCAGGAAAG 59.806 43.478 0.00 0.00 42.06 2.62
2627 2632 2.496871 TGCATTATGTTGCCAGGAAAGG 59.503 45.455 0.00 0.00 42.06 3.11
2628 2633 2.760092 GCATTATGTTGCCAGGAAAGGA 59.240 45.455 0.00 0.00 36.60 3.36
2629 2634 3.195396 GCATTATGTTGCCAGGAAAGGAA 59.805 43.478 0.00 0.00 36.60 3.36
2630 2635 4.141869 GCATTATGTTGCCAGGAAAGGAAT 60.142 41.667 0.00 0.00 36.60 3.01
2631 2636 5.353938 CATTATGTTGCCAGGAAAGGAATG 58.646 41.667 0.00 0.00 0.00 2.67
2632 2637 0.968405 TGTTGCCAGGAAAGGAATGC 59.032 50.000 0.00 0.00 0.00 3.56
2633 2638 1.260544 GTTGCCAGGAAAGGAATGCT 58.739 50.000 0.00 0.00 0.00 3.79
2634 2639 2.224992 TGTTGCCAGGAAAGGAATGCTA 60.225 45.455 0.00 0.00 0.00 3.49
2635 2640 2.424956 GTTGCCAGGAAAGGAATGCTAG 59.575 50.000 0.00 0.00 0.00 3.42
2636 2641 1.064463 TGCCAGGAAAGGAATGCTAGG 60.064 52.381 0.00 0.00 0.00 3.02
2637 2642 1.212935 GCCAGGAAAGGAATGCTAGGA 59.787 52.381 0.00 0.00 0.00 2.94
2638 2643 2.158549 GCCAGGAAAGGAATGCTAGGAT 60.159 50.000 0.00 0.00 0.00 3.24
2639 2644 3.749226 CCAGGAAAGGAATGCTAGGATC 58.251 50.000 0.00 0.00 0.00 3.36
2640 2645 3.393941 CCAGGAAAGGAATGCTAGGATCT 59.606 47.826 0.00 0.00 0.00 2.75
2641 2646 4.141298 CCAGGAAAGGAATGCTAGGATCTT 60.141 45.833 0.00 0.00 0.00 2.40
2642 2647 5.444176 CAGGAAAGGAATGCTAGGATCTTT 58.556 41.667 9.71 9.71 0.00 2.52
2643 2648 5.298777 CAGGAAAGGAATGCTAGGATCTTTG 59.701 44.000 13.44 0.51 0.00 2.77
2644 2649 5.192522 AGGAAAGGAATGCTAGGATCTTTGA 59.807 40.000 13.44 0.00 0.00 2.69
2645 2650 5.888161 GGAAAGGAATGCTAGGATCTTTGAA 59.112 40.000 13.44 0.00 0.00 2.69
2646 2651 6.183360 GGAAAGGAATGCTAGGATCTTTGAAC 60.183 42.308 13.44 2.84 0.00 3.18
2647 2652 5.441718 AGGAATGCTAGGATCTTTGAACA 57.558 39.130 0.00 0.00 0.00 3.18
2648 2653 5.189180 AGGAATGCTAGGATCTTTGAACAC 58.811 41.667 0.00 0.00 0.00 3.32
2649 2654 4.943705 GGAATGCTAGGATCTTTGAACACA 59.056 41.667 0.00 0.00 0.00 3.72
2650 2655 5.163713 GGAATGCTAGGATCTTTGAACACAC 60.164 44.000 0.00 0.00 0.00 3.82
2651 2656 3.674997 TGCTAGGATCTTTGAACACACC 58.325 45.455 0.00 0.00 0.00 4.16
2652 2657 2.673368 GCTAGGATCTTTGAACACACCG 59.327 50.000 0.00 0.00 0.00 4.94
2653 2658 1.523758 AGGATCTTTGAACACACCGC 58.476 50.000 0.00 0.00 0.00 5.68
2654 2659 0.521735 GGATCTTTGAACACACCGCC 59.478 55.000 0.00 0.00 0.00 6.13
2655 2660 1.234821 GATCTTTGAACACACCGCCA 58.765 50.000 0.00 0.00 0.00 5.69
2656 2661 1.197721 GATCTTTGAACACACCGCCAG 59.802 52.381 0.00 0.00 0.00 4.85
2657 2662 0.107410 TCTTTGAACACACCGCCAGT 60.107 50.000 0.00 0.00 0.00 4.00
2658 2663 1.139256 TCTTTGAACACACCGCCAGTA 59.861 47.619 0.00 0.00 0.00 2.74
2659 2664 2.151202 CTTTGAACACACCGCCAGTAT 58.849 47.619 0.00 0.00 0.00 2.12
2660 2665 1.803334 TTGAACACACCGCCAGTATC 58.197 50.000 0.00 0.00 0.00 2.24
2661 2666 0.389296 TGAACACACCGCCAGTATCG 60.389 55.000 0.00 0.00 0.00 2.92
2662 2667 0.389426 GAACACACCGCCAGTATCGT 60.389 55.000 0.00 0.00 0.00 3.73
2663 2668 0.389426 AACACACCGCCAGTATCGTC 60.389 55.000 0.00 0.00 0.00 4.20
2664 2669 1.872234 CACACCGCCAGTATCGTCG 60.872 63.158 0.00 0.00 0.00 5.12
2665 2670 2.042259 ACACCGCCAGTATCGTCGA 61.042 57.895 0.00 0.00 0.00 4.20
2666 2671 1.585521 CACCGCCAGTATCGTCGAC 60.586 63.158 5.18 5.18 0.00 4.20
2667 2672 2.042259 ACCGCCAGTATCGTCGACA 61.042 57.895 17.16 3.13 0.00 4.35
2668 2673 1.298413 CCGCCAGTATCGTCGACAG 60.298 63.158 17.16 8.67 0.00 3.51
2669 2674 1.712018 CCGCCAGTATCGTCGACAGA 61.712 60.000 17.16 13.90 0.00 3.41
2670 2675 0.316278 CGCCAGTATCGTCGACAGAG 60.316 60.000 17.16 0.00 0.00 3.35
2671 2676 0.733729 GCCAGTATCGTCGACAGAGT 59.266 55.000 17.16 0.00 0.00 3.24
2672 2677 1.132643 GCCAGTATCGTCGACAGAGTT 59.867 52.381 17.16 2.97 0.00 3.01
2673 2678 2.415625 GCCAGTATCGTCGACAGAGTTT 60.416 50.000 17.16 2.30 0.00 2.66
2674 2679 3.834610 CCAGTATCGTCGACAGAGTTTT 58.165 45.455 17.16 1.97 0.00 2.43
2675 2680 3.608506 CCAGTATCGTCGACAGAGTTTTG 59.391 47.826 17.16 10.35 0.00 2.44
2676 2681 3.608506 CAGTATCGTCGACAGAGTTTTGG 59.391 47.826 17.16 0.00 0.00 3.28
2677 2682 3.504906 AGTATCGTCGACAGAGTTTTGGA 59.495 43.478 17.16 1.22 0.00 3.53
2678 2683 2.129823 TCGTCGACAGAGTTTTGGAC 57.870 50.000 17.16 0.00 0.00 4.02
2679 2684 1.137513 CGTCGACAGAGTTTTGGACC 58.862 55.000 17.16 0.00 0.00 4.46
2680 2685 1.537348 CGTCGACAGAGTTTTGGACCA 60.537 52.381 17.16 0.00 0.00 4.02
2681 2686 2.135933 GTCGACAGAGTTTTGGACCAG 58.864 52.381 11.55 0.00 0.00 4.00
2682 2687 2.036387 TCGACAGAGTTTTGGACCAGA 58.964 47.619 0.00 0.00 0.00 3.86
2683 2688 2.632996 TCGACAGAGTTTTGGACCAGAT 59.367 45.455 0.00 0.00 0.00 2.90
2684 2689 3.071023 TCGACAGAGTTTTGGACCAGATT 59.929 43.478 0.00 0.00 0.00 2.40
2685 2690 4.282449 TCGACAGAGTTTTGGACCAGATTA 59.718 41.667 0.00 0.00 0.00 1.75
2686 2691 4.627467 CGACAGAGTTTTGGACCAGATTAG 59.373 45.833 0.00 0.00 0.00 1.73
2687 2692 5.566826 CGACAGAGTTTTGGACCAGATTAGA 60.567 44.000 0.00 0.00 0.00 2.10
2688 2693 5.799213 ACAGAGTTTTGGACCAGATTAGAG 58.201 41.667 0.00 0.00 0.00 2.43
2689 2694 5.544176 ACAGAGTTTTGGACCAGATTAGAGA 59.456 40.000 0.00 0.00 0.00 3.10
2690 2695 6.043243 ACAGAGTTTTGGACCAGATTAGAGAA 59.957 38.462 0.00 0.00 0.00 2.87
2691 2696 6.593382 CAGAGTTTTGGACCAGATTAGAGAAG 59.407 42.308 0.00 0.00 0.00 2.85
2692 2697 6.498651 AGAGTTTTGGACCAGATTAGAGAAGA 59.501 38.462 0.00 0.00 0.00 2.87
2693 2698 7.181845 AGAGTTTTGGACCAGATTAGAGAAGAT 59.818 37.037 0.00 0.00 0.00 2.40
2694 2699 7.334858 AGTTTTGGACCAGATTAGAGAAGATC 58.665 38.462 0.00 0.00 0.00 2.75
2695 2700 7.181845 AGTTTTGGACCAGATTAGAGAAGATCT 59.818 37.037 0.00 0.00 42.47 2.75
2696 2701 7.502060 TTTGGACCAGATTAGAGAAGATCTT 57.498 36.000 7.95 7.95 39.64 2.40
2697 2702 6.723298 TGGACCAGATTAGAGAAGATCTTC 57.277 41.667 25.20 25.20 39.64 2.87
2698 2703 6.197903 TGGACCAGATTAGAGAAGATCTTCA 58.802 40.000 31.79 15.50 41.84 3.02
2699 2704 6.669591 TGGACCAGATTAGAGAAGATCTTCAA 59.330 38.462 31.79 20.18 41.84 2.69
2700 2705 7.147759 TGGACCAGATTAGAGAAGATCTTCAAG 60.148 40.741 31.79 14.39 41.84 3.02
2701 2706 7.147742 GGACCAGATTAGAGAAGATCTTCAAGT 60.148 40.741 31.79 19.72 41.84 3.16
2702 2707 7.781056 ACCAGATTAGAGAAGATCTTCAAGTC 58.219 38.462 31.79 22.05 41.84 3.01
2703 2708 7.619302 ACCAGATTAGAGAAGATCTTCAAGTCT 59.381 37.037 31.79 26.54 41.84 3.24
2704 2709 7.922278 CCAGATTAGAGAAGATCTTCAAGTCTG 59.078 40.741 31.79 29.63 41.84 3.51
2705 2710 7.922278 CAGATTAGAGAAGATCTTCAAGTCTGG 59.078 40.741 31.79 18.13 41.84 3.86
2706 2711 7.838696 AGATTAGAGAAGATCTTCAAGTCTGGA 59.161 37.037 31.79 19.57 41.84 3.86
2707 2712 5.920193 AGAGAAGATCTTCAAGTCTGGAG 57.080 43.478 31.79 0.00 41.84 3.86
2708 2713 4.711355 AGAGAAGATCTTCAAGTCTGGAGG 59.289 45.833 31.79 0.00 41.84 4.30
2709 2714 3.774216 AGAAGATCTTCAAGTCTGGAGGG 59.226 47.826 31.79 0.00 41.84 4.30
2710 2715 1.836802 AGATCTTCAAGTCTGGAGGGC 59.163 52.381 0.00 0.00 0.00 5.19
2711 2716 1.556911 GATCTTCAAGTCTGGAGGGCA 59.443 52.381 0.00 0.00 0.00 5.36
2712 2717 0.979665 TCTTCAAGTCTGGAGGGCAG 59.020 55.000 0.00 0.00 0.00 4.85
2713 2718 0.676151 CTTCAAGTCTGGAGGGCAGC 60.676 60.000 0.00 0.00 0.00 5.25
2714 2719 2.435586 CAAGTCTGGAGGGCAGCG 60.436 66.667 0.00 0.00 0.00 5.18
2715 2720 3.710722 AAGTCTGGAGGGCAGCGG 61.711 66.667 0.00 0.00 0.00 5.52
2725 2730 4.643387 GGCAGCGGGGTGTGTTCT 62.643 66.667 0.00 0.00 0.00 3.01
2726 2731 3.357079 GCAGCGGGGTGTGTTCTG 61.357 66.667 0.00 0.00 0.00 3.02
2727 2732 2.669569 CAGCGGGGTGTGTTCTGG 60.670 66.667 0.00 0.00 0.00 3.86
2728 2733 2.847234 AGCGGGGTGTGTTCTGGA 60.847 61.111 0.00 0.00 0.00 3.86
2729 2734 2.224159 AGCGGGGTGTGTTCTGGAT 61.224 57.895 0.00 0.00 0.00 3.41
2730 2735 1.745489 GCGGGGTGTGTTCTGGATC 60.745 63.158 0.00 0.00 0.00 3.36
2731 2736 1.983224 CGGGGTGTGTTCTGGATCT 59.017 57.895 0.00 0.00 0.00 2.75
2732 2737 0.324943 CGGGGTGTGTTCTGGATCTT 59.675 55.000 0.00 0.00 0.00 2.40
2733 2738 1.553248 CGGGGTGTGTTCTGGATCTTA 59.447 52.381 0.00 0.00 0.00 2.10
2734 2739 2.677037 CGGGGTGTGTTCTGGATCTTAC 60.677 54.545 0.00 0.00 0.00 2.34
2735 2740 2.572104 GGGGTGTGTTCTGGATCTTACT 59.428 50.000 0.00 0.00 0.00 2.24
2736 2741 3.009143 GGGGTGTGTTCTGGATCTTACTT 59.991 47.826 0.00 0.00 0.00 2.24
2737 2742 4.506802 GGGGTGTGTTCTGGATCTTACTTT 60.507 45.833 0.00 0.00 0.00 2.66
2738 2743 4.455877 GGGTGTGTTCTGGATCTTACTTTG 59.544 45.833 0.00 0.00 0.00 2.77
2739 2744 5.063880 GGTGTGTTCTGGATCTTACTTTGT 58.936 41.667 0.00 0.00 0.00 2.83
2740 2745 6.228258 GGTGTGTTCTGGATCTTACTTTGTA 58.772 40.000 0.00 0.00 0.00 2.41
2741 2746 6.708949 GGTGTGTTCTGGATCTTACTTTGTAA 59.291 38.462 0.00 0.00 0.00 2.41
2742 2747 7.227910 GGTGTGTTCTGGATCTTACTTTGTAAA 59.772 37.037 0.00 0.00 0.00 2.01
2743 2748 8.617809 GTGTGTTCTGGATCTTACTTTGTAAAA 58.382 33.333 0.00 0.00 0.00 1.52
2744 2749 8.836413 TGTGTTCTGGATCTTACTTTGTAAAAG 58.164 33.333 0.00 0.00 0.00 2.27
2745 2750 7.803659 GTGTTCTGGATCTTACTTTGTAAAAGC 59.196 37.037 0.00 0.00 0.00 3.51
2746 2751 7.040686 TGTTCTGGATCTTACTTTGTAAAAGCC 60.041 37.037 0.00 0.00 0.00 4.35
2747 2752 6.779860 TCTGGATCTTACTTTGTAAAAGCCT 58.220 36.000 0.00 0.00 0.00 4.58
2748 2753 6.879458 TCTGGATCTTACTTTGTAAAAGCCTC 59.121 38.462 0.00 0.00 0.00 4.70
2749 2754 6.779860 TGGATCTTACTTTGTAAAAGCCTCT 58.220 36.000 0.00 0.00 0.00 3.69
2750 2755 7.231467 TGGATCTTACTTTGTAAAAGCCTCTT 58.769 34.615 0.00 0.00 0.00 2.85
2751 2756 8.380099 TGGATCTTACTTTGTAAAAGCCTCTTA 58.620 33.333 0.00 0.00 0.00 2.10
2752 2757 9.397280 GGATCTTACTTTGTAAAAGCCTCTTAT 57.603 33.333 0.00 0.00 0.00 1.73
2759 2764 8.304596 ACTTTGTAAAAGCCTCTTATAAAAGCC 58.695 33.333 0.00 0.00 32.36 4.35
2760 2765 8.417273 TTTGTAAAAGCCTCTTATAAAAGCCT 57.583 30.769 0.00 0.00 32.36 4.58
2761 2766 7.625828 TGTAAAAGCCTCTTATAAAAGCCTC 57.374 36.000 0.00 0.00 32.36 4.70
2762 2767 7.402862 TGTAAAAGCCTCTTATAAAAGCCTCT 58.597 34.615 0.00 0.00 32.36 3.69
2763 2768 7.888546 TGTAAAAGCCTCTTATAAAAGCCTCTT 59.111 33.333 0.00 0.00 32.36 2.85
2764 2769 6.765915 AAAGCCTCTTATAAAAGCCTCTTG 57.234 37.500 0.00 0.00 32.36 3.02
2765 2770 5.443230 AGCCTCTTATAAAAGCCTCTTGT 57.557 39.130 0.00 0.00 32.36 3.16
2766 2771 6.561519 AGCCTCTTATAAAAGCCTCTTGTA 57.438 37.500 0.00 0.00 32.36 2.41
2767 2772 6.958767 AGCCTCTTATAAAAGCCTCTTGTAA 58.041 36.000 0.00 0.00 32.36 2.41
2768 2773 7.578203 AGCCTCTTATAAAAGCCTCTTGTAAT 58.422 34.615 0.00 0.00 32.36 1.89
2769 2774 8.055790 AGCCTCTTATAAAAGCCTCTTGTAATT 58.944 33.333 0.00 0.00 32.36 1.40
2770 2775 8.131731 GCCTCTTATAAAAGCCTCTTGTAATTG 58.868 37.037 0.00 0.00 32.36 2.32
2771 2776 8.624776 CCTCTTATAAAAGCCTCTTGTAATTGG 58.375 37.037 0.00 0.00 32.36 3.16
2772 2777 8.519799 TCTTATAAAAGCCTCTTGTAATTGGG 57.480 34.615 0.00 0.00 32.36 4.12
2773 2778 7.559897 TCTTATAAAAGCCTCTTGTAATTGGGG 59.440 37.037 0.00 0.00 32.36 4.96
2774 2779 3.542969 AAAGCCTCTTGTAATTGGGGT 57.457 42.857 0.00 0.00 0.00 4.95
2775 2780 2.514458 AGCCTCTTGTAATTGGGGTG 57.486 50.000 0.00 0.00 0.00 4.61
2776 2781 1.710809 AGCCTCTTGTAATTGGGGTGT 59.289 47.619 0.00 0.00 0.00 4.16
2777 2782 2.110011 AGCCTCTTGTAATTGGGGTGTT 59.890 45.455 0.00 0.00 0.00 3.32
2778 2783 2.492088 GCCTCTTGTAATTGGGGTGTTC 59.508 50.000 0.00 0.00 0.00 3.18
2779 2784 3.814316 GCCTCTTGTAATTGGGGTGTTCT 60.814 47.826 0.00 0.00 0.00 3.01
2780 2785 4.566907 GCCTCTTGTAATTGGGGTGTTCTA 60.567 45.833 0.00 0.00 0.00 2.10
2781 2786 5.755849 CCTCTTGTAATTGGGGTGTTCTAT 58.244 41.667 0.00 0.00 0.00 1.98
2782 2787 5.823045 CCTCTTGTAATTGGGGTGTTCTATC 59.177 44.000 0.00 0.00 0.00 2.08
2783 2788 5.751586 TCTTGTAATTGGGGTGTTCTATCC 58.248 41.667 0.00 0.00 0.00 2.59
2784 2789 5.491078 TCTTGTAATTGGGGTGTTCTATCCT 59.509 40.000 0.00 0.00 0.00 3.24
2785 2790 5.110814 TGTAATTGGGGTGTTCTATCCTG 57.889 43.478 0.00 0.00 0.00 3.86
2786 2791 3.669939 AATTGGGGTGTTCTATCCTGG 57.330 47.619 0.00 0.00 0.00 4.45
2787 2792 1.295020 TTGGGGTGTTCTATCCTGGG 58.705 55.000 0.00 0.00 0.00 4.45
2788 2793 0.623324 TGGGGTGTTCTATCCTGGGG 60.623 60.000 0.00 0.00 0.00 4.96
2789 2794 1.353394 GGGGTGTTCTATCCTGGGGG 61.353 65.000 0.00 0.00 0.00 5.40
2790 2795 0.623617 GGGTGTTCTATCCTGGGGGT 60.624 60.000 0.00 0.00 0.00 4.95
2791 2796 0.546598 GGTGTTCTATCCTGGGGGTG 59.453 60.000 0.00 0.00 0.00 4.61
2792 2797 0.546598 GTGTTCTATCCTGGGGGTGG 59.453 60.000 0.00 0.00 0.00 4.61
2793 2798 1.279025 TGTTCTATCCTGGGGGTGGC 61.279 60.000 0.00 0.00 0.00 5.01
2794 2799 2.070039 TTCTATCCTGGGGGTGGCG 61.070 63.158 0.00 0.00 0.00 5.69
2795 2800 4.256180 CTATCCTGGGGGTGGCGC 62.256 72.222 0.00 0.00 0.00 6.53
2814 2819 2.672414 CCTCGGGAGGTCTTTCAGT 58.328 57.895 6.56 0.00 43.61 3.41
2815 2820 0.247736 CCTCGGGAGGTCTTTCAGTG 59.752 60.000 6.56 0.00 43.61 3.66
2816 2821 0.390472 CTCGGGAGGTCTTTCAGTGC 60.390 60.000 0.00 0.00 0.00 4.40
2817 2822 1.738099 CGGGAGGTCTTTCAGTGCG 60.738 63.158 0.00 0.00 0.00 5.34
2818 2823 1.671742 GGGAGGTCTTTCAGTGCGA 59.328 57.895 0.00 0.00 0.00 5.10
2819 2824 0.390472 GGGAGGTCTTTCAGTGCGAG 60.390 60.000 0.00 0.00 0.00 5.03
2820 2825 0.603569 GGAGGTCTTTCAGTGCGAGA 59.396 55.000 0.00 0.00 0.00 4.04
2821 2826 1.670380 GGAGGTCTTTCAGTGCGAGAC 60.670 57.143 14.02 14.02 39.19 3.36
2823 2828 1.009389 GGTCTTTCAGTGCGAGACCG 61.009 60.000 21.47 0.00 46.96 4.79
2833 2838 3.141488 CGAGACCGCCTAGCCTGT 61.141 66.667 0.00 0.00 0.00 4.00
2834 2839 2.809010 GAGACCGCCTAGCCTGTC 59.191 66.667 0.00 0.00 0.00 3.51
2835 2840 1.755008 GAGACCGCCTAGCCTGTCT 60.755 63.158 0.00 0.00 38.99 3.41
2836 2841 2.010582 GAGACCGCCTAGCCTGTCTG 62.011 65.000 2.36 0.00 37.31 3.51
2837 2842 2.037367 ACCGCCTAGCCTGTCTGA 59.963 61.111 0.00 0.00 0.00 3.27
2838 2843 2.286127 GACCGCCTAGCCTGTCTGAC 62.286 65.000 0.00 0.00 0.00 3.51
2839 2844 2.496817 CGCCTAGCCTGTCTGACC 59.503 66.667 5.17 0.00 0.00 4.02
2840 2845 2.055042 CGCCTAGCCTGTCTGACCT 61.055 63.158 5.17 0.00 0.00 3.85
2841 2846 1.608717 CGCCTAGCCTGTCTGACCTT 61.609 60.000 5.17 0.00 0.00 3.50
2842 2847 0.107945 GCCTAGCCTGTCTGACCTTG 60.108 60.000 5.17 0.00 0.00 3.61
2843 2848 1.270907 CCTAGCCTGTCTGACCTTGT 58.729 55.000 5.17 0.00 0.00 3.16
2844 2849 1.625818 CCTAGCCTGTCTGACCTTGTT 59.374 52.381 5.17 0.00 0.00 2.83
2845 2850 2.613977 CCTAGCCTGTCTGACCTTGTTG 60.614 54.545 5.17 0.00 0.00 3.33
2846 2851 0.839946 AGCCTGTCTGACCTTGTTGT 59.160 50.000 5.17 0.00 0.00 3.32
2847 2852 2.047061 AGCCTGTCTGACCTTGTTGTA 58.953 47.619 5.17 0.00 0.00 2.41
2848 2853 2.143925 GCCTGTCTGACCTTGTTGTAC 58.856 52.381 5.17 0.00 0.00 2.90
2849 2854 2.224305 GCCTGTCTGACCTTGTTGTACT 60.224 50.000 5.17 0.00 0.00 2.73
2850 2855 3.654414 CCTGTCTGACCTTGTTGTACTC 58.346 50.000 5.17 0.00 0.00 2.59
2851 2856 3.322254 CCTGTCTGACCTTGTTGTACTCT 59.678 47.826 5.17 0.00 0.00 3.24
2852 2857 4.202264 CCTGTCTGACCTTGTTGTACTCTT 60.202 45.833 5.17 0.00 0.00 2.85
2853 2858 4.945246 TGTCTGACCTTGTTGTACTCTTC 58.055 43.478 5.17 0.00 0.00 2.87
2854 2859 4.649674 TGTCTGACCTTGTTGTACTCTTCT 59.350 41.667 5.17 0.00 0.00 2.85
2855 2860 5.221263 TGTCTGACCTTGTTGTACTCTTCTC 60.221 44.000 5.17 0.00 0.00 2.87
2856 2861 4.281182 TCTGACCTTGTTGTACTCTTCTCC 59.719 45.833 0.00 0.00 0.00 3.71
2857 2862 4.223953 TGACCTTGTTGTACTCTTCTCCT 58.776 43.478 0.00 0.00 0.00 3.69
2858 2863 4.281182 TGACCTTGTTGTACTCTTCTCCTC 59.719 45.833 0.00 0.00 0.00 3.71
2859 2864 4.484912 ACCTTGTTGTACTCTTCTCCTCT 58.515 43.478 0.00 0.00 0.00 3.69
2860 2865 4.902448 ACCTTGTTGTACTCTTCTCCTCTT 59.098 41.667 0.00 0.00 0.00 2.85
2861 2866 5.367060 ACCTTGTTGTACTCTTCTCCTCTTT 59.633 40.000 0.00 0.00 0.00 2.52
2862 2867 5.929415 CCTTGTTGTACTCTTCTCCTCTTTC 59.071 44.000 0.00 0.00 0.00 2.62
2863 2868 6.239458 CCTTGTTGTACTCTTCTCCTCTTTCT 60.239 42.308 0.00 0.00 0.00 2.52
2864 2869 7.039644 CCTTGTTGTACTCTTCTCCTCTTTCTA 60.040 40.741 0.00 0.00 0.00 2.10
2865 2870 7.834881 TGTTGTACTCTTCTCCTCTTTCTAA 57.165 36.000 0.00 0.00 0.00 2.10
2866 2871 8.423906 TGTTGTACTCTTCTCCTCTTTCTAAT 57.576 34.615 0.00 0.00 0.00 1.73
2867 2872 9.529823 TGTTGTACTCTTCTCCTCTTTCTAATA 57.470 33.333 0.00 0.00 0.00 0.98
2875 2880 9.601217 TCTTCTCCTCTTTCTAATAAAATTCGG 57.399 33.333 0.00 0.00 0.00 4.30
2876 2881 7.787725 TCTCCTCTTTCTAATAAAATTCGGC 57.212 36.000 0.00 0.00 0.00 5.54
2877 2882 6.766467 TCTCCTCTTTCTAATAAAATTCGGCC 59.234 38.462 0.00 0.00 0.00 6.13
2878 2883 6.419791 TCCTCTTTCTAATAAAATTCGGCCA 58.580 36.000 2.24 0.00 0.00 5.36
2879 2884 6.887545 TCCTCTTTCTAATAAAATTCGGCCAA 59.112 34.615 2.24 0.00 0.00 4.52
2880 2885 6.972901 CCTCTTTCTAATAAAATTCGGCCAAC 59.027 38.462 2.24 0.00 0.00 3.77
2881 2886 6.548171 TCTTTCTAATAAAATTCGGCCAACG 58.452 36.000 2.24 0.00 46.11 4.10
2882 2887 4.886247 TCTAATAAAATTCGGCCAACGG 57.114 40.909 2.24 0.00 44.45 4.44
3448 3455 0.185175 GGGTGTGGGTTGTTCCTTCT 59.815 55.000 0.00 0.00 36.25 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.215742 TTGCCGGGGCGATACTCG 62.216 66.667 2.18 0.00 45.51 4.18
153 155 3.135994 GGGTTCTTTTTGAGTAGCGTCA 58.864 45.455 0.00 0.00 0.00 4.35
163 165 2.579657 GCCCCGGGGGTTCTTTTTG 61.580 63.158 40.58 11.89 46.51 2.44
185 187 0.598065 GCAAAATCAAGCACGAGGGT 59.402 50.000 0.00 0.00 0.00 4.34
205 207 1.566018 GACAAGAAGTGTTCCCGGCG 61.566 60.000 0.00 0.00 41.96 6.46
299 301 1.066286 CCTGCAGATATAGCCAGGAGC 60.066 57.143 17.39 0.00 44.25 4.70
324 326 1.377987 TTGCCAGCGTAATGGTCCC 60.378 57.895 5.54 0.00 42.75 4.46
344 346 2.159099 GGCATCCGTGAGTGATGTAAGA 60.159 50.000 0.00 0.00 39.45 2.10
460 462 6.419791 TGAAGGAAGAACCAACACTTTTCTA 58.580 36.000 0.00 0.00 42.04 2.10
474 476 5.936372 CACTCATCAATGTCTGAAGGAAGAA 59.064 40.000 0.00 0.00 37.67 2.52
574 576 0.388006 CGCCACCGTTTTTCATTCCC 60.388 55.000 0.00 0.00 0.00 3.97
588 590 2.281276 AGTTTCCCCGTTCGCCAC 60.281 61.111 0.00 0.00 0.00 5.01
1330 1332 8.236084 AGTCAAGTAAACAATACACATACGAC 57.764 34.615 0.00 0.00 0.00 4.34
1675 1678 1.432807 ACCCCATTTTGGTCATGTCCT 59.567 47.619 10.43 0.00 35.17 3.85
2232 2237 0.988832 TATCCCTGAAACGGTGGCTT 59.011 50.000 0.00 0.00 0.00 4.35
2589 2594 1.969103 GCACTTTGCGATCAAACCTC 58.031 50.000 0.00 0.00 37.28 3.85
2597 2602 6.408083 TGGCAACATAATGCACTTTGCGAT 62.408 41.667 11.29 0.00 45.68 4.58
2598 2603 5.164129 TGGCAACATAATGCACTTTGCGA 62.164 43.478 11.29 6.77 45.68 5.10
2599 2604 2.925732 TGGCAACATAATGCACTTTGCG 60.926 45.455 11.29 0.00 45.68 4.85
2614 2619 1.260544 AGCATTCCTTTCCTGGCAAC 58.739 50.000 0.00 0.00 0.00 4.17
2615 2620 2.621407 CCTAGCATTCCTTTCCTGGCAA 60.621 50.000 0.00 0.00 0.00 4.52
2616 2621 1.064463 CCTAGCATTCCTTTCCTGGCA 60.064 52.381 0.00 0.00 0.00 4.92
2617 2622 1.212935 TCCTAGCATTCCTTTCCTGGC 59.787 52.381 0.00 0.00 0.00 4.85
2618 2623 3.393941 AGATCCTAGCATTCCTTTCCTGG 59.606 47.826 0.00 0.00 0.00 4.45
2619 2624 4.703379 AGATCCTAGCATTCCTTTCCTG 57.297 45.455 0.00 0.00 0.00 3.86
2620 2625 5.192522 TCAAAGATCCTAGCATTCCTTTCCT 59.807 40.000 0.00 0.00 0.00 3.36
2621 2626 5.440610 TCAAAGATCCTAGCATTCCTTTCC 58.559 41.667 0.00 0.00 0.00 3.13
2622 2627 6.375455 TGTTCAAAGATCCTAGCATTCCTTTC 59.625 38.462 0.00 0.00 0.00 2.62
2623 2628 6.151817 GTGTTCAAAGATCCTAGCATTCCTTT 59.848 38.462 0.00 0.00 0.00 3.11
2624 2629 5.649831 GTGTTCAAAGATCCTAGCATTCCTT 59.350 40.000 0.00 0.00 0.00 3.36
2625 2630 5.189180 GTGTTCAAAGATCCTAGCATTCCT 58.811 41.667 0.00 0.00 0.00 3.36
2626 2631 4.943705 TGTGTTCAAAGATCCTAGCATTCC 59.056 41.667 0.00 0.00 0.00 3.01
2627 2632 5.163713 GGTGTGTTCAAAGATCCTAGCATTC 60.164 44.000 0.00 0.00 0.00 2.67
2628 2633 4.702131 GGTGTGTTCAAAGATCCTAGCATT 59.298 41.667 0.00 0.00 0.00 3.56
2629 2634 4.265073 GGTGTGTTCAAAGATCCTAGCAT 58.735 43.478 0.00 0.00 0.00 3.79
2630 2635 3.674997 GGTGTGTTCAAAGATCCTAGCA 58.325 45.455 0.00 0.00 0.00 3.49
2631 2636 2.673368 CGGTGTGTTCAAAGATCCTAGC 59.327 50.000 0.00 0.00 0.00 3.42
2632 2637 2.673368 GCGGTGTGTTCAAAGATCCTAG 59.327 50.000 0.00 0.00 0.00 3.02
2633 2638 2.614481 GGCGGTGTGTTCAAAGATCCTA 60.614 50.000 0.00 0.00 0.00 2.94
2634 2639 1.523758 GCGGTGTGTTCAAAGATCCT 58.476 50.000 0.00 0.00 0.00 3.24
2635 2640 0.521735 GGCGGTGTGTTCAAAGATCC 59.478 55.000 0.00 0.00 0.00 3.36
2636 2641 1.197721 CTGGCGGTGTGTTCAAAGATC 59.802 52.381 0.00 0.00 0.00 2.75
2637 2642 1.238439 CTGGCGGTGTGTTCAAAGAT 58.762 50.000 0.00 0.00 0.00 2.40
2638 2643 0.107410 ACTGGCGGTGTGTTCAAAGA 60.107 50.000 0.00 0.00 0.00 2.52
2639 2644 1.588674 TACTGGCGGTGTGTTCAAAG 58.411 50.000 9.79 0.00 0.00 2.77
2640 2645 2.147958 GATACTGGCGGTGTGTTCAAA 58.852 47.619 9.79 0.00 0.00 2.69
2641 2646 1.803334 GATACTGGCGGTGTGTTCAA 58.197 50.000 9.79 0.00 0.00 2.69
2642 2647 0.389296 CGATACTGGCGGTGTGTTCA 60.389 55.000 9.79 0.00 0.00 3.18
2643 2648 0.389426 ACGATACTGGCGGTGTGTTC 60.389 55.000 9.79 0.12 0.00 3.18
2644 2649 0.389426 GACGATACTGGCGGTGTGTT 60.389 55.000 9.79 0.00 0.00 3.32
2645 2650 1.214589 GACGATACTGGCGGTGTGT 59.785 57.895 9.79 4.44 0.00 3.72
2646 2651 1.872234 CGACGATACTGGCGGTGTG 60.872 63.158 9.79 0.87 0.00 3.82
2647 2652 2.042259 TCGACGATACTGGCGGTGT 61.042 57.895 9.79 1.08 0.00 4.16
2648 2653 1.585521 GTCGACGATACTGGCGGTG 60.586 63.158 9.79 0.00 0.00 4.94
2649 2654 1.989966 CTGTCGACGATACTGGCGGT 61.990 60.000 11.62 3.57 0.00 5.68
2650 2655 1.298413 CTGTCGACGATACTGGCGG 60.298 63.158 11.62 0.00 0.00 6.13
2651 2656 0.316278 CTCTGTCGACGATACTGGCG 60.316 60.000 11.62 0.00 0.00 5.69
2652 2657 0.733729 ACTCTGTCGACGATACTGGC 59.266 55.000 11.62 0.00 0.00 4.85
2653 2658 3.489180 AAACTCTGTCGACGATACTGG 57.511 47.619 11.62 2.21 0.00 4.00
2654 2659 3.608506 CCAAAACTCTGTCGACGATACTG 59.391 47.826 11.62 2.31 0.00 2.74
2655 2660 3.504906 TCCAAAACTCTGTCGACGATACT 59.495 43.478 11.62 0.00 0.00 2.12
2656 2661 3.607209 GTCCAAAACTCTGTCGACGATAC 59.393 47.826 11.62 0.00 0.00 2.24
2657 2662 3.366679 GGTCCAAAACTCTGTCGACGATA 60.367 47.826 11.62 0.00 0.00 2.92
2658 2663 2.609737 GGTCCAAAACTCTGTCGACGAT 60.610 50.000 11.62 0.00 0.00 3.73
2659 2664 1.269413 GGTCCAAAACTCTGTCGACGA 60.269 52.381 11.62 10.20 0.00 4.20
2660 2665 1.137513 GGTCCAAAACTCTGTCGACG 58.862 55.000 11.62 6.07 0.00 5.12
2661 2666 2.135933 CTGGTCCAAAACTCTGTCGAC 58.864 52.381 9.11 9.11 0.00 4.20
2662 2667 2.036387 TCTGGTCCAAAACTCTGTCGA 58.964 47.619 0.00 0.00 0.00 4.20
2663 2668 2.526304 TCTGGTCCAAAACTCTGTCG 57.474 50.000 0.00 0.00 0.00 4.35
2664 2669 5.794894 TCTAATCTGGTCCAAAACTCTGTC 58.205 41.667 0.00 0.00 0.00 3.51
2665 2670 5.544176 TCTCTAATCTGGTCCAAAACTCTGT 59.456 40.000 0.00 0.00 0.00 3.41
2666 2671 6.042638 TCTCTAATCTGGTCCAAAACTCTG 57.957 41.667 0.00 0.00 0.00 3.35
2667 2672 6.498651 TCTTCTCTAATCTGGTCCAAAACTCT 59.501 38.462 0.00 0.00 0.00 3.24
2668 2673 6.702329 TCTTCTCTAATCTGGTCCAAAACTC 58.298 40.000 0.00 0.00 0.00 3.01
2669 2674 6.688073 TCTTCTCTAATCTGGTCCAAAACT 57.312 37.500 0.00 0.00 0.00 2.66
2670 2675 7.334858 AGATCTTCTCTAATCTGGTCCAAAAC 58.665 38.462 0.00 0.00 31.09 2.43
2671 2676 7.502060 AGATCTTCTCTAATCTGGTCCAAAA 57.498 36.000 0.00 0.00 31.09 2.44
2672 2677 7.180946 TGAAGATCTTCTCTAATCTGGTCCAAA 59.819 37.037 30.45 6.56 40.14 3.28
2673 2678 6.669591 TGAAGATCTTCTCTAATCTGGTCCAA 59.330 38.462 30.45 6.91 40.14 3.53
2674 2679 6.197903 TGAAGATCTTCTCTAATCTGGTCCA 58.802 40.000 30.45 8.08 40.14 4.02
2675 2680 6.723298 TGAAGATCTTCTCTAATCTGGTCC 57.277 41.667 30.45 5.69 40.14 4.46
2676 2681 7.781056 ACTTGAAGATCTTCTCTAATCTGGTC 58.219 38.462 30.45 6.19 40.14 4.02
2677 2682 7.619302 AGACTTGAAGATCTTCTCTAATCTGGT 59.381 37.037 30.45 14.02 40.14 4.00
2678 2683 7.922278 CAGACTTGAAGATCTTCTCTAATCTGG 59.078 40.741 30.45 17.04 40.14 3.86
2679 2684 7.922278 CCAGACTTGAAGATCTTCTCTAATCTG 59.078 40.741 30.45 28.49 40.14 2.90
2680 2685 7.838696 TCCAGACTTGAAGATCTTCTCTAATCT 59.161 37.037 30.45 22.27 40.14 2.40
2681 2686 8.006298 TCCAGACTTGAAGATCTTCTCTAATC 57.994 38.462 30.45 20.84 40.14 1.75
2682 2687 7.069826 CCTCCAGACTTGAAGATCTTCTCTAAT 59.930 40.741 30.45 15.02 40.14 1.73
2683 2688 6.379703 CCTCCAGACTTGAAGATCTTCTCTAA 59.620 42.308 30.45 18.35 40.14 2.10
2684 2689 5.890985 CCTCCAGACTTGAAGATCTTCTCTA 59.109 44.000 30.45 17.41 40.14 2.43
2685 2690 4.711355 CCTCCAGACTTGAAGATCTTCTCT 59.289 45.833 30.45 23.05 40.14 3.10
2686 2691 4.141959 CCCTCCAGACTTGAAGATCTTCTC 60.142 50.000 30.45 21.47 40.14 2.87
2687 2692 3.774216 CCCTCCAGACTTGAAGATCTTCT 59.226 47.826 30.45 14.98 40.14 2.85
2688 2693 3.681313 GCCCTCCAGACTTGAAGATCTTC 60.681 52.174 25.68 25.68 39.91 2.87
2689 2694 2.238395 GCCCTCCAGACTTGAAGATCTT 59.762 50.000 7.95 7.95 0.00 2.40
2690 2695 1.836802 GCCCTCCAGACTTGAAGATCT 59.163 52.381 0.00 0.00 0.00 2.75
2691 2696 1.556911 TGCCCTCCAGACTTGAAGATC 59.443 52.381 0.00 0.00 0.00 2.75
2692 2697 1.558756 CTGCCCTCCAGACTTGAAGAT 59.441 52.381 0.00 0.00 44.64 2.40
2693 2698 0.979665 CTGCCCTCCAGACTTGAAGA 59.020 55.000 0.00 0.00 44.64 2.87
2694 2699 0.676151 GCTGCCCTCCAGACTTGAAG 60.676 60.000 0.00 0.00 44.64 3.02
2695 2700 1.376466 GCTGCCCTCCAGACTTGAA 59.624 57.895 0.00 0.00 44.64 2.69
2696 2701 2.947532 CGCTGCCCTCCAGACTTGA 61.948 63.158 0.00 0.00 44.64 3.02
2697 2702 2.435586 CGCTGCCCTCCAGACTTG 60.436 66.667 0.00 0.00 44.64 3.16
2698 2703 3.710722 CCGCTGCCCTCCAGACTT 61.711 66.667 0.00 0.00 44.64 3.01
2708 2713 4.643387 AGAACACACCCCGCTGCC 62.643 66.667 0.00 0.00 0.00 4.85
2709 2714 3.357079 CAGAACACACCCCGCTGC 61.357 66.667 0.00 0.00 0.00 5.25
2710 2715 2.469465 ATCCAGAACACACCCCGCTG 62.469 60.000 0.00 0.00 0.00 5.18
2711 2716 2.185310 GATCCAGAACACACCCCGCT 62.185 60.000 0.00 0.00 0.00 5.52
2712 2717 1.745489 GATCCAGAACACACCCCGC 60.745 63.158 0.00 0.00 0.00 6.13
2713 2718 0.324943 AAGATCCAGAACACACCCCG 59.675 55.000 0.00 0.00 0.00 5.73
2714 2719 2.572104 AGTAAGATCCAGAACACACCCC 59.428 50.000 0.00 0.00 0.00 4.95
2715 2720 3.983044 AGTAAGATCCAGAACACACCC 57.017 47.619 0.00 0.00 0.00 4.61
2716 2721 5.063880 ACAAAGTAAGATCCAGAACACACC 58.936 41.667 0.00 0.00 0.00 4.16
2717 2722 7.724305 TTACAAAGTAAGATCCAGAACACAC 57.276 36.000 0.00 0.00 0.00 3.82
2718 2723 8.740123 TTTTACAAAGTAAGATCCAGAACACA 57.260 30.769 0.00 0.00 0.00 3.72
2719 2724 7.803659 GCTTTTACAAAGTAAGATCCAGAACAC 59.196 37.037 0.00 0.00 0.00 3.32
2720 2725 7.040686 GGCTTTTACAAAGTAAGATCCAGAACA 60.041 37.037 0.00 0.00 0.00 3.18
2721 2726 7.175119 AGGCTTTTACAAAGTAAGATCCAGAAC 59.825 37.037 0.00 0.00 0.00 3.01
2722 2727 7.231467 AGGCTTTTACAAAGTAAGATCCAGAA 58.769 34.615 0.00 0.00 0.00 3.02
2723 2728 6.779860 AGGCTTTTACAAAGTAAGATCCAGA 58.220 36.000 0.00 0.00 0.00 3.86
2724 2729 6.881602 AGAGGCTTTTACAAAGTAAGATCCAG 59.118 38.462 0.00 0.00 0.00 3.86
2725 2730 6.779860 AGAGGCTTTTACAAAGTAAGATCCA 58.220 36.000 0.00 0.00 0.00 3.41
2726 2731 7.689446 AAGAGGCTTTTACAAAGTAAGATCC 57.311 36.000 0.00 0.00 0.00 3.36
2733 2738 8.304596 GGCTTTTATAAGAGGCTTTTACAAAGT 58.695 33.333 18.95 4.19 35.73 2.66
2734 2739 8.523658 AGGCTTTTATAAGAGGCTTTTACAAAG 58.476 33.333 22.07 18.20 45.31 2.77
2735 2740 8.417273 AGGCTTTTATAAGAGGCTTTTACAAA 57.583 30.769 22.07 0.00 45.31 2.83
2744 2749 7.809546 ATTACAAGAGGCTTTTATAAGAGGC 57.190 36.000 18.68 18.68 38.61 4.70
2745 2750 8.624776 CCAATTACAAGAGGCTTTTATAAGAGG 58.375 37.037 5.26 0.00 32.92 3.69
2746 2751 8.624776 CCCAATTACAAGAGGCTTTTATAAGAG 58.375 37.037 0.00 0.00 32.92 2.85
2747 2752 7.559897 CCCCAATTACAAGAGGCTTTTATAAGA 59.440 37.037 0.00 0.00 32.92 2.10
2748 2753 7.342026 ACCCCAATTACAAGAGGCTTTTATAAG 59.658 37.037 0.00 0.00 34.36 1.73
2749 2754 7.123547 CACCCCAATTACAAGAGGCTTTTATAA 59.876 37.037 0.00 0.00 0.00 0.98
2750 2755 6.605594 CACCCCAATTACAAGAGGCTTTTATA 59.394 38.462 0.00 0.00 0.00 0.98
2751 2756 5.422012 CACCCCAATTACAAGAGGCTTTTAT 59.578 40.000 0.00 0.00 0.00 1.40
2752 2757 4.770010 CACCCCAATTACAAGAGGCTTTTA 59.230 41.667 0.00 0.00 0.00 1.52
2753 2758 3.578282 CACCCCAATTACAAGAGGCTTTT 59.422 43.478 0.00 0.00 0.00 2.27
2754 2759 3.165071 CACCCCAATTACAAGAGGCTTT 58.835 45.455 0.00 0.00 0.00 3.51
2755 2760 2.110011 ACACCCCAATTACAAGAGGCTT 59.890 45.455 0.00 0.00 0.00 4.35
2756 2761 1.710809 ACACCCCAATTACAAGAGGCT 59.289 47.619 0.00 0.00 0.00 4.58
2757 2762 2.215942 ACACCCCAATTACAAGAGGC 57.784 50.000 0.00 0.00 0.00 4.70
2758 2763 4.034285 AGAACACCCCAATTACAAGAGG 57.966 45.455 0.00 0.00 0.00 3.69
2759 2764 5.823045 GGATAGAACACCCCAATTACAAGAG 59.177 44.000 0.00 0.00 0.00 2.85
2760 2765 5.491078 AGGATAGAACACCCCAATTACAAGA 59.509 40.000 0.00 0.00 0.00 3.02
2761 2766 5.590259 CAGGATAGAACACCCCAATTACAAG 59.410 44.000 0.00 0.00 0.00 3.16
2762 2767 5.505780 CAGGATAGAACACCCCAATTACAA 58.494 41.667 0.00 0.00 0.00 2.41
2763 2768 4.080015 CCAGGATAGAACACCCCAATTACA 60.080 45.833 0.00 0.00 0.00 2.41
2764 2769 4.461198 CCAGGATAGAACACCCCAATTAC 58.539 47.826 0.00 0.00 0.00 1.89
2765 2770 3.461831 CCCAGGATAGAACACCCCAATTA 59.538 47.826 0.00 0.00 0.00 1.40
2766 2771 2.244769 CCCAGGATAGAACACCCCAATT 59.755 50.000 0.00 0.00 0.00 2.32
2767 2772 1.852965 CCCAGGATAGAACACCCCAAT 59.147 52.381 0.00 0.00 0.00 3.16
2768 2773 1.295020 CCCAGGATAGAACACCCCAA 58.705 55.000 0.00 0.00 0.00 4.12
2769 2774 0.623324 CCCCAGGATAGAACACCCCA 60.623 60.000 0.00 0.00 0.00 4.96
2770 2775 1.353394 CCCCCAGGATAGAACACCCC 61.353 65.000 0.00 0.00 33.47 4.95
2771 2776 0.623617 ACCCCCAGGATAGAACACCC 60.624 60.000 0.00 0.00 36.73 4.61
2772 2777 0.546598 CACCCCCAGGATAGAACACC 59.453 60.000 0.00 0.00 36.73 4.16
2773 2778 0.546598 CCACCCCCAGGATAGAACAC 59.453 60.000 0.00 0.00 36.73 3.32
2774 2779 1.279025 GCCACCCCCAGGATAGAACA 61.279 60.000 0.00 0.00 36.73 3.18
2775 2780 1.532238 GCCACCCCCAGGATAGAAC 59.468 63.158 0.00 0.00 36.73 3.01
2776 2781 2.070039 CGCCACCCCCAGGATAGAA 61.070 63.158 0.00 0.00 36.73 2.10
2777 2782 2.445845 CGCCACCCCCAGGATAGA 60.446 66.667 0.00 0.00 36.73 1.98
2778 2783 4.256180 GCGCCACCCCCAGGATAG 62.256 72.222 0.00 0.00 36.73 2.08
2795 2800 0.905337 ACTGAAAGACCTCCCGAGGG 60.905 60.000 15.16 0.65 45.70 4.30
2796 2801 0.247736 CACTGAAAGACCTCCCGAGG 59.752 60.000 9.29 9.29 46.43 4.63
2797 2802 0.390472 GCACTGAAAGACCTCCCGAG 60.390 60.000 0.00 0.00 37.43 4.63
2798 2803 1.671742 GCACTGAAAGACCTCCCGA 59.328 57.895 0.00 0.00 37.43 5.14
2799 2804 1.738099 CGCACTGAAAGACCTCCCG 60.738 63.158 0.00 0.00 37.43 5.14
2800 2805 0.390472 CTCGCACTGAAAGACCTCCC 60.390 60.000 0.00 0.00 37.43 4.30
2801 2806 0.603569 TCTCGCACTGAAAGACCTCC 59.396 55.000 0.00 0.00 37.43 4.30
2802 2807 1.704070 GTCTCGCACTGAAAGACCTC 58.296 55.000 0.00 0.00 37.43 3.85
2803 2808 3.896317 GTCTCGCACTGAAAGACCT 57.104 52.632 0.00 0.00 37.43 3.85
2805 2810 2.435741 CGGTCTCGCACTGAAAGAC 58.564 57.895 0.00 0.00 38.94 3.01
2806 2811 4.966005 CGGTCTCGCACTGAAAGA 57.034 55.556 0.00 0.00 37.43 2.52
2816 2821 3.127352 GACAGGCTAGGCGGTCTCG 62.127 68.421 32.48 12.92 39.81 4.04
2817 2822 1.755008 AGACAGGCTAGGCGGTCTC 60.755 63.158 35.38 19.64 38.73 3.36
2818 2823 2.055042 CAGACAGGCTAGGCGGTCT 61.055 63.158 35.38 35.38 41.87 3.85
2819 2824 2.052690 TCAGACAGGCTAGGCGGTC 61.053 63.158 32.66 32.66 35.03 4.79
2820 2825 2.037367 TCAGACAGGCTAGGCGGT 59.963 61.111 21.57 21.57 0.00 5.68
2821 2826 2.496817 GTCAGACAGGCTAGGCGG 59.503 66.667 14.82 14.82 0.00 6.13
2822 2827 1.608717 AAGGTCAGACAGGCTAGGCG 61.609 60.000 11.10 8.51 0.00 5.52
2823 2828 0.107945 CAAGGTCAGACAGGCTAGGC 60.108 60.000 8.55 8.55 0.00 3.93
2824 2829 1.270907 ACAAGGTCAGACAGGCTAGG 58.729 55.000 2.17 0.00 0.00 3.02
2825 2830 2.037772 ACAACAAGGTCAGACAGGCTAG 59.962 50.000 2.17 0.00 0.00 3.42
2826 2831 2.047061 ACAACAAGGTCAGACAGGCTA 58.953 47.619 2.17 0.00 0.00 3.93
2827 2832 0.839946 ACAACAAGGTCAGACAGGCT 59.160 50.000 2.17 0.00 0.00 4.58
2828 2833 2.143925 GTACAACAAGGTCAGACAGGC 58.856 52.381 2.17 0.00 0.00 4.85
2829 2834 3.322254 AGAGTACAACAAGGTCAGACAGG 59.678 47.826 2.17 0.00 0.00 4.00
2830 2835 4.592485 AGAGTACAACAAGGTCAGACAG 57.408 45.455 2.17 0.00 0.00 3.51
2831 2836 4.649674 AGAAGAGTACAACAAGGTCAGACA 59.350 41.667 2.17 0.00 0.00 3.41
2832 2837 5.203060 AGAAGAGTACAACAAGGTCAGAC 57.797 43.478 0.00 0.00 0.00 3.51
2833 2838 4.281182 GGAGAAGAGTACAACAAGGTCAGA 59.719 45.833 0.00 0.00 0.00 3.27
2834 2839 4.282195 AGGAGAAGAGTACAACAAGGTCAG 59.718 45.833 0.00 0.00 0.00 3.51
2835 2840 4.223953 AGGAGAAGAGTACAACAAGGTCA 58.776 43.478 0.00 0.00 0.00 4.02
2836 2841 4.525100 AGAGGAGAAGAGTACAACAAGGTC 59.475 45.833 0.00 0.00 0.00 3.85
2837 2842 4.484912 AGAGGAGAAGAGTACAACAAGGT 58.515 43.478 0.00 0.00 0.00 3.50
2838 2843 5.476091 AAGAGGAGAAGAGTACAACAAGG 57.524 43.478 0.00 0.00 0.00 3.61
2839 2844 6.754193 AGAAAGAGGAGAAGAGTACAACAAG 58.246 40.000 0.00 0.00 0.00 3.16
2840 2845 6.732896 AGAAAGAGGAGAAGAGTACAACAA 57.267 37.500 0.00 0.00 0.00 2.83
2841 2846 7.834881 TTAGAAAGAGGAGAAGAGTACAACA 57.165 36.000 0.00 0.00 0.00 3.33
2849 2854 9.601217 CCGAATTTTATTAGAAAGAGGAGAAGA 57.399 33.333 0.00 0.00 0.00 2.87
2850 2855 8.338986 GCCGAATTTTATTAGAAAGAGGAGAAG 58.661 37.037 0.00 0.00 0.00 2.85
2851 2856 7.282450 GGCCGAATTTTATTAGAAAGAGGAGAA 59.718 37.037 0.00 0.00 0.00 2.87
2852 2857 6.766467 GGCCGAATTTTATTAGAAAGAGGAGA 59.234 38.462 0.00 0.00 0.00 3.71
2853 2858 6.542370 TGGCCGAATTTTATTAGAAAGAGGAG 59.458 38.462 0.00 0.00 0.00 3.69
2854 2859 6.419791 TGGCCGAATTTTATTAGAAAGAGGA 58.580 36.000 0.00 0.00 0.00 3.71
2855 2860 6.693315 TGGCCGAATTTTATTAGAAAGAGG 57.307 37.500 0.00 0.00 0.00 3.69
2856 2861 6.687105 CGTTGGCCGAATTTTATTAGAAAGAG 59.313 38.462 0.00 0.00 39.56 2.85
2857 2862 6.403855 CCGTTGGCCGAATTTTATTAGAAAGA 60.404 38.462 0.00 0.00 39.56 2.52
2858 2863 5.741982 CCGTTGGCCGAATTTTATTAGAAAG 59.258 40.000 0.00 0.00 39.56 2.62
2859 2864 5.642686 CCGTTGGCCGAATTTTATTAGAAA 58.357 37.500 0.00 0.00 39.56 2.52
2860 2865 4.439016 GCCGTTGGCCGAATTTTATTAGAA 60.439 41.667 0.00 0.00 44.06 2.10
2861 2866 3.065648 GCCGTTGGCCGAATTTTATTAGA 59.934 43.478 0.00 0.00 44.06 2.10
2862 2867 3.368495 GCCGTTGGCCGAATTTTATTAG 58.632 45.455 0.00 0.00 44.06 1.73
2863 2868 3.423996 GCCGTTGGCCGAATTTTATTA 57.576 42.857 0.00 0.00 44.06 0.98
2864 2869 2.287393 GCCGTTGGCCGAATTTTATT 57.713 45.000 0.00 0.00 44.06 1.40
2876 2881 3.546714 AACCTCGAAGGGCCGTTGG 62.547 63.158 16.93 14.98 40.58 3.77
2877 2882 1.599797 AAACCTCGAAGGGCCGTTG 60.600 57.895 16.93 8.25 40.58 4.10
2878 2883 1.599797 CAAACCTCGAAGGGCCGTT 60.600 57.895 11.21 11.21 40.58 4.44
2879 2884 1.838073 ATCAAACCTCGAAGGGCCGT 61.838 55.000 0.00 0.00 40.58 5.68
2880 2885 1.078426 ATCAAACCTCGAAGGGCCG 60.078 57.895 0.00 0.00 40.58 6.13
2881 2886 1.657751 GCATCAAACCTCGAAGGGCC 61.658 60.000 0.00 0.00 40.58 5.80
2882 2887 1.657751 GGCATCAAACCTCGAAGGGC 61.658 60.000 5.98 0.00 40.58 5.19
2883 2888 0.322456 TGGCATCAAACCTCGAAGGG 60.322 55.000 5.98 0.00 40.58 3.95
2884 2889 1.672881 GATGGCATCAAACCTCGAAGG 59.327 52.381 22.23 0.00 42.49 3.46
2885 2890 2.358957 TGATGGCATCAAACCTCGAAG 58.641 47.619 27.03 0.00 36.11 3.79
2886 2891 2.488204 TGATGGCATCAAACCTCGAA 57.512 45.000 27.03 0.75 36.11 3.71
2887 2892 2.291365 CATGATGGCATCAAACCTCGA 58.709 47.619 31.81 8.27 43.50 4.04
2888 2893 2.019249 ACATGATGGCATCAAACCTCG 58.981 47.619 31.81 18.04 43.50 4.63
3448 3455 1.416401 AGGTTTCTCTGTTCTTCCGCA 59.584 47.619 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.