Multiple sequence alignment - TraesCS6A01G393200

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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 TraesCS6A01G393200 chr6A 100.000 3197 0 0 1 3197 607056652 607059848 0.000000e+00 5904.0
1 TraesCS6A01G393200 chr6B 95.578 1764 59 7 1 1760 702245272 702247020 0.000000e+00 2808.0
2 TraesCS6A01G393200 chr6B 89.676 649 62 5 1739 2383 702247032 702247679 0.000000e+00 822.0
3 TraesCS6A01G393200 chr6B 87.912 182 20 2 150 329 702247924 702248105 2.500000e-51 213.0
4 TraesCS6A01G393200 chr6B 85.366 205 17 9 2764 2958 702245421 702245622 1.940000e-47 200.0
5 TraesCS6A01G393200 chr6B 78.548 303 43 13 2748 3047 702247908 702248191 2.530000e-41 180.0
6 TraesCS6A01G393200 chr6B 84.507 71 6 5 2740 2805 702267932 702268002 7.400000e-07 65.8
7 TraesCS6A01G393200 chr6B 96.875 32 1 0 179 210 702270807 702270838 2.000000e-03 54.7
8 TraesCS6A01G393200 chr6D 89.487 1617 131 26 779 2371 460791160 460792761 0.000000e+00 2008.0
9 TraesCS6A01G393200 chr6D 90.753 757 56 8 1 751 460790423 460791171 0.000000e+00 998.0
10 TraesCS6A01G393200 chr6D 84.593 344 45 7 446 782 460792915 460793257 5.110000e-88 335.0
11 TraesCS6A01G393200 chr6D 87.629 97 11 1 2426 2521 460792764 460792860 9.370000e-21 111.0
12 TraesCS6A01G393200 chr3B 93.955 397 22 2 1 397 739118128 739117734 1.640000e-167 599.0
13 TraesCS6A01G393200 chr3B 93.939 396 22 2 2 397 13127335 13127728 5.900000e-167 597.0
14 TraesCS6A01G393200 chr3B 83.774 265 37 5 1037 1300 13127819 13128078 2.460000e-61 246.0
15 TraesCS6A01G393200 chr3B 83.704 270 34 8 1040 1306 739117639 739117377 2.460000e-61 246.0
16 TraesCS6A01G393200 chr3B 95.604 91 3 1 530 620 739117733 739117644 9.240000e-31 145.0
17 TraesCS6A01G393200 chr7B 98.404 188 3 0 2561 2748 83032716 83032903 6.610000e-87 331.0
18 TraesCS6A01G393200 chr7B 96.447 197 5 1 2547 2743 41525075 41524881 1.110000e-84 324.0
19 TraesCS6A01G393200 chr2A 98.396 187 3 0 2561 2747 649490204 649490018 2.380000e-86 329.0
20 TraesCS6A01G393200 chr2A 97.895 190 3 1 2561 2749 117158988 117158799 8.550000e-86 327.0
21 TraesCS6A01G393200 chr5A 97.884 189 4 0 2560 2748 596662161 596662349 8.550000e-86 327.0
22 TraesCS6A01G393200 chr5A 97.382 191 5 0 2561 2751 13889430 13889620 3.080000e-85 326.0
23 TraesCS6A01G393200 chr7A 95.545 202 7 2 2560 2759 253535778 253535979 3.980000e-84 322.0
24 TraesCS6A01G393200 chr4B 92.760 221 14 2 2533 2753 596317437 596317219 5.150000e-83 318.0
25 TraesCS6A01G393200 chr2B 95.939 197 7 1 2554 2749 409336371 409336567 5.150000e-83 318.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G393200 chr6A 607056652 607059848 3196 False 5904.0 5904 100.000000 1 3197 1 chr6A.!!$F1 3196
1 TraesCS6A01G393200 chr6B 702245272 702248191 2919 False 844.6 2808 87.416000 1 3047 5 chr6B.!!$F1 3046
2 TraesCS6A01G393200 chr6D 460790423 460793257 2834 False 863.0 2008 88.115500 1 2521 4 chr6D.!!$F1 2520
3 TraesCS6A01G393200 chr3B 13127335 13128078 743 False 421.5 597 88.856500 2 1300 2 chr3B.!!$F1 1298
4 TraesCS6A01G393200 chr3B 739117377 739118128 751 True 330.0 599 91.087667 1 1306 3 chr3B.!!$R1 1305

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
330 331 0.182299 TGCATGGACAACTGGTGACA 59.818 50.0 0.0 0.0 39.59 3.58 F
1897 1965 0.458543 ATCTCAACTGCTACACGCCG 60.459 55.0 0.0 0.0 38.05 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2129 1.072159 CCTCCATGCCTCGGGAATC 59.928 63.158 0.00 0.0 31.58 2.52 R
2981 3131 1.024046 ACACACGCACTGCACAGAAA 61.024 50.000 4.31 0.0 0.00 2.52 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
73 74 2.921754 GCGTACAAAGTAGCAGTGTAGG 59.078 50.000 0.00 0.00 36.93 3.18
109 110 1.059584 TGAGTGGGGGAAAGACTGCA 61.060 55.000 0.00 0.00 0.00 4.41
330 331 0.182299 TGCATGGACAACTGGTGACA 59.818 50.000 0.00 0.00 39.59 3.58
519 520 8.647143 ATCAAAACCAACAACTCACAATTTAG 57.353 30.769 0.00 0.00 0.00 1.85
587 588 3.960102 ACTCCATGGTCAATGTGTTGTTT 59.040 39.130 12.58 0.00 36.69 2.83
670 672 9.216117 GGCAAACTACTGACTTTTCTTAATCTA 57.784 33.333 0.00 0.00 0.00 1.98
891 905 2.223711 GGTGATGACCAACCACAACAAC 60.224 50.000 0.00 0.00 42.59 3.32
921 935 1.021202 TCGTTTGTGCTCCACCTTTG 58.979 50.000 0.00 0.00 32.73 2.77
1106 1120 9.770097 TGAGATTGAGGTGTTCTTATGAATATC 57.230 33.333 0.00 0.00 34.40 1.63
1260 1275 2.476185 GCACGTCGCTTAAATGAGCATT 60.476 45.455 0.00 0.00 42.83 3.56
1495 1510 5.645067 CAGAAGCATGTGAAGATAGAAACCA 59.355 40.000 0.00 0.00 0.00 3.67
1501 1516 7.025963 GCATGTGAAGATAGAAACCAAAAGAG 58.974 38.462 0.00 0.00 0.00 2.85
1591 1606 6.381481 TTTCAGGCTAATAAGTCGATCGTA 57.619 37.500 15.94 0.11 30.45 3.43
1608 1623 6.312672 TCGATCGTACATCAAAATCACAATGT 59.687 34.615 15.94 0.00 36.40 2.71
1656 1673 7.122055 GTCAAATGATGGTGGTAGGAAATACAA 59.878 37.037 0.00 0.00 35.96 2.41
1687 1704 3.181510 GCTGTTAAATCGGTCGAGCATTT 60.182 43.478 15.89 18.89 0.00 2.32
1696 1713 2.542824 CGGTCGAGCATTTGTTTTGGTT 60.543 45.455 15.89 0.00 0.00 3.67
1725 1742 4.944962 TGCAGTTATTCCTTCATGTTCG 57.055 40.909 0.00 0.00 0.00 3.95
1738 1755 0.673644 ATGTTCGTCTTTCGCTGGGG 60.674 55.000 0.00 0.00 39.67 4.96
1842 1893 5.448438 TCTTGTAATCGATGTTGTTTGTGC 58.552 37.500 0.00 0.00 0.00 4.57
1877 1945 3.006940 TCATGTTCGTATTTGCCTCCAC 58.993 45.455 0.00 0.00 0.00 4.02
1878 1946 2.552599 TGTTCGTATTTGCCTCCACA 57.447 45.000 0.00 0.00 0.00 4.17
1897 1965 0.458543 ATCTCAACTGCTACACGCCG 60.459 55.000 0.00 0.00 38.05 6.46
1898 1966 2.048597 TCAACTGCTACACGCCGG 60.049 61.111 0.00 0.00 38.05 6.13
1938 2006 4.164796 TCACCAGCTATGAACCATCTGATT 59.835 41.667 0.00 0.00 0.00 2.57
1941 2009 6.713903 CACCAGCTATGAACCATCTGATTTAT 59.286 38.462 0.00 0.00 0.00 1.40
2006 2074 1.606224 GGTTACTTCCGGCTTGTTCGA 60.606 52.381 0.00 0.00 0.00 3.71
2045 2113 4.332828 GAAAGCCCAGTAACACCTGTTAT 58.667 43.478 1.32 0.00 41.85 1.89
2052 2120 2.565834 AGTAACACCTGTTATGCCGAGT 59.434 45.455 1.32 0.00 41.85 4.18
2217 2285 3.146104 AGGCTTATTCAACAGCACAGT 57.854 42.857 0.00 0.00 37.81 3.55
2228 2296 0.883370 CAGCACAGTCAGCAGAAGCA 60.883 55.000 0.00 0.00 45.49 3.91
2229 2297 0.603172 AGCACAGTCAGCAGAAGCAG 60.603 55.000 0.00 0.00 45.49 4.24
2253 2321 0.311165 CACTCTGTCGTCACCTTCGT 59.689 55.000 0.00 0.00 0.00 3.85
2271 2340 4.145876 TCGTTTTGTGCTAGCTGATTTG 57.854 40.909 17.23 0.77 0.00 2.32
2277 2346 3.475575 TGTGCTAGCTGATTTGTTGTCA 58.524 40.909 17.23 0.00 0.00 3.58
2308 2377 3.508845 TTCTGCCAAGAGCTTTAACCT 57.491 42.857 0.00 0.00 44.23 3.50
2309 2378 2.783135 TCTGCCAAGAGCTTTAACCTG 58.217 47.619 0.00 0.00 44.23 4.00
2327 2396 3.311596 ACCTGCGTGTTCTTTGTTTCTAC 59.688 43.478 0.00 0.00 0.00 2.59
2372 2441 3.874543 TGCTCTCTTTTGCTTCGTTGTTA 59.125 39.130 0.00 0.00 0.00 2.41
2375 2444 5.565638 GCTCTCTTTTGCTTCGTTGTTAATC 59.434 40.000 0.00 0.00 0.00 1.75
2378 2447 2.604969 TTGCTTCGTTGTTAATCCGC 57.395 45.000 0.00 0.00 0.00 5.54
2383 2452 0.648441 TCGTTGTTAATCCGCGATGC 59.352 50.000 8.23 0.00 0.00 3.91
2385 2454 1.062002 CGTTGTTAATCCGCGATGCTT 59.938 47.619 8.23 0.00 0.00 3.91
2388 2457 2.080693 TGTTAATCCGCGATGCTTTGT 58.919 42.857 8.23 0.00 0.00 2.83
2390 2459 3.062909 TGTTAATCCGCGATGCTTTGTAC 59.937 43.478 8.23 0.00 0.00 2.90
2391 2460 1.732941 AATCCGCGATGCTTTGTACA 58.267 45.000 8.23 0.00 0.00 2.90
2441 2563 4.022416 GGGTTAGATTGTCATGTTGTGCAA 60.022 41.667 0.00 0.00 0.00 4.08
2447 2569 7.686438 AGATTGTCATGTTGTGCAATAGTAA 57.314 32.000 0.00 0.00 35.87 2.24
2459 2581 8.682710 GTTGTGCAATAGTAAATAGGAATCCAA 58.317 33.333 0.61 0.00 0.00 3.53
2465 2587 8.660435 CAATAGTAAATAGGAATCCAAGGGAGA 58.340 37.037 0.61 0.00 34.05 3.71
2477 2599 2.027100 CCAAGGGAGAAGTGTAGGAACC 60.027 54.545 0.00 0.00 0.00 3.62
2521 2643 2.048603 GTCAATGGGCTGGCTGGAC 61.049 63.158 0.00 0.75 0.00 4.02
2522 2644 3.136123 CAATGGGCTGGCTGGACG 61.136 66.667 0.00 0.00 0.00 4.79
2553 2693 4.023279 TGTTTTATTGCTGCGATGAGTTGT 60.023 37.500 12.66 0.00 0.00 3.32
2560 2700 0.587768 TGCGATGAGTTGTGCAAGTG 59.412 50.000 0.00 0.00 33.80 3.16
2561 2701 0.867746 GCGATGAGTTGTGCAAGTGA 59.132 50.000 0.00 0.00 0.00 3.41
2562 2702 1.264020 GCGATGAGTTGTGCAAGTGAA 59.736 47.619 0.00 0.00 0.00 3.18
2563 2703 2.663879 GCGATGAGTTGTGCAAGTGAAG 60.664 50.000 0.00 0.00 0.00 3.02
2564 2704 2.096069 CGATGAGTTGTGCAAGTGAAGG 60.096 50.000 0.00 0.00 0.00 3.46
2565 2705 1.679139 TGAGTTGTGCAAGTGAAGGG 58.321 50.000 0.00 0.00 0.00 3.95
2566 2706 0.954452 GAGTTGTGCAAGTGAAGGGG 59.046 55.000 0.00 0.00 0.00 4.79
2567 2707 0.550914 AGTTGTGCAAGTGAAGGGGA 59.449 50.000 0.00 0.00 0.00 4.81
2568 2708 0.954452 GTTGTGCAAGTGAAGGGGAG 59.046 55.000 0.00 0.00 0.00 4.30
2569 2709 0.823356 TTGTGCAAGTGAAGGGGAGC 60.823 55.000 0.00 0.00 0.00 4.70
2570 2710 1.973812 GTGCAAGTGAAGGGGAGCC 60.974 63.158 0.00 0.00 0.00 4.70
2571 2711 2.156098 TGCAAGTGAAGGGGAGCCT 61.156 57.895 0.00 0.00 0.00 4.58
2572 2712 1.075659 GCAAGTGAAGGGGAGCCTT 59.924 57.895 0.00 0.00 0.00 4.35
2573 2713 0.328258 GCAAGTGAAGGGGAGCCTTA 59.672 55.000 0.00 0.00 0.00 2.69
2574 2714 1.680249 GCAAGTGAAGGGGAGCCTTAG 60.680 57.143 0.00 0.00 0.00 2.18
2575 2715 0.621082 AAGTGAAGGGGAGCCTTAGC 59.379 55.000 0.00 0.00 40.32 3.09
2576 2716 1.153349 GTGAAGGGGAGCCTTAGCG 60.153 63.158 0.00 0.00 46.67 4.26
2577 2717 2.203084 GAAGGGGAGCCTTAGCGC 60.203 66.667 0.00 0.00 46.67 5.92
2578 2718 3.009115 AAGGGGAGCCTTAGCGCA 61.009 61.111 11.47 0.00 46.67 6.09
2579 2719 2.932130 GAAGGGGAGCCTTAGCGCAG 62.932 65.000 11.47 0.00 46.67 5.18
2580 2720 3.787001 GGGGAGCCTTAGCGCAGT 61.787 66.667 11.47 0.00 46.67 4.40
2581 2721 2.432300 GGGGAGCCTTAGCGCAGTA 61.432 63.158 11.47 0.00 46.67 2.74
2582 2722 1.068250 GGGAGCCTTAGCGCAGTAG 59.932 63.158 11.47 2.99 46.67 2.57
2583 2723 1.677637 GGGAGCCTTAGCGCAGTAGT 61.678 60.000 11.47 0.00 46.67 2.73
2584 2724 1.030457 GGAGCCTTAGCGCAGTAGTA 58.970 55.000 11.47 0.00 46.67 1.82
2585 2725 1.407979 GGAGCCTTAGCGCAGTAGTAA 59.592 52.381 11.47 0.00 46.67 2.24
2586 2726 2.159142 GGAGCCTTAGCGCAGTAGTAAA 60.159 50.000 11.47 0.00 46.67 2.01
2587 2727 3.492829 GGAGCCTTAGCGCAGTAGTAAAT 60.493 47.826 11.47 0.00 46.67 1.40
2588 2728 3.718815 AGCCTTAGCGCAGTAGTAAATC 58.281 45.455 11.47 0.00 46.67 2.17
2589 2729 3.385111 AGCCTTAGCGCAGTAGTAAATCT 59.615 43.478 11.47 0.00 46.67 2.40
2590 2730 3.491267 GCCTTAGCGCAGTAGTAAATCTG 59.509 47.826 11.47 0.00 35.12 2.90
2598 2738 4.871993 CAGTAGTAAATCTGCTGCCTTG 57.128 45.455 0.00 0.00 46.35 3.61
2599 2739 4.256920 CAGTAGTAAATCTGCTGCCTTGT 58.743 43.478 0.00 0.00 46.35 3.16
2600 2740 4.093998 CAGTAGTAAATCTGCTGCCTTGTG 59.906 45.833 0.00 0.00 46.35 3.33
2601 2741 3.423539 AGTAAATCTGCTGCCTTGTGA 57.576 42.857 0.00 0.00 0.00 3.58
2602 2742 3.077359 AGTAAATCTGCTGCCTTGTGAC 58.923 45.455 0.00 0.00 0.00 3.67
2603 2743 1.251251 AAATCTGCTGCCTTGTGACC 58.749 50.000 0.00 0.00 0.00 4.02
2604 2744 0.111061 AATCTGCTGCCTTGTGACCA 59.889 50.000 0.00 0.00 0.00 4.02
2605 2745 0.330604 ATCTGCTGCCTTGTGACCAT 59.669 50.000 0.00 0.00 0.00 3.55
2606 2746 0.607217 TCTGCTGCCTTGTGACCATG 60.607 55.000 0.00 0.00 0.00 3.66
2607 2747 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2608 2748 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2609 2749 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2619 2759 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2620 2760 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2621 2761 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2622 2762 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2623 2763 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2624 2764 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2625 2765 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2626 2766 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2627 2767 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2628 2768 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2629 2769 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2630 2770 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2631 2771 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2632 2772 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2633 2773 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2647 2787 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2648 2788 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2649 2789 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2650 2790 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2651 2791 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2652 2792 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2653 2793 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2654 2794 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2655 2795 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2656 2796 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2657 2797 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2658 2798 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2659 2799 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2660 2800 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2661 2801 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2662 2802 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2663 2803 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2664 2804 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2665 2805 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2666 2806 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2667 2807 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2668 2808 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2669 2809 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2670 2810 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2671 2811 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2672 2812 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2673 2813 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2674 2814 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2675 2815 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2676 2816 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2677 2817 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
2678 2818 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2679 2819 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2680 2820 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
2681 2821 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
2682 2822 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
2683 2823 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
2684 2824 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
2689 2829 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2690 2830 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2691 2831 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2692 2832 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2693 2833 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2694 2834 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2695 2835 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2696 2836 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2697 2837 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2698 2838 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
2699 2839 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
2700 2840 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
2701 2841 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
2702 2842 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
2703 2843 2.125225 GGACCCTTCCCCAGACCT 59.875 66.667 0.00 0.00 35.57 3.85
2704 2844 1.541620 GGACCCTTCCCCAGACCTT 60.542 63.158 0.00 0.00 35.57 3.50
2705 2845 1.685820 GACCCTTCCCCAGACCTTG 59.314 63.158 0.00 0.00 0.00 3.61
2706 2846 2.356667 CCCTTCCCCAGACCTTGC 59.643 66.667 0.00 0.00 0.00 4.01
2707 2847 2.045926 CCTTCCCCAGACCTTGCG 60.046 66.667 0.00 0.00 0.00 4.85
2708 2848 2.747855 CTTCCCCAGACCTTGCGC 60.748 66.667 0.00 0.00 0.00 6.09
2709 2849 3.551496 CTTCCCCAGACCTTGCGCA 62.551 63.158 5.66 5.66 0.00 6.09
2710 2850 3.126703 TTCCCCAGACCTTGCGCAA 62.127 57.895 23.48 23.48 0.00 4.85
2711 2851 3.058160 CCCCAGACCTTGCGCAAG 61.058 66.667 37.33 37.33 38.14 4.01
2729 2869 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
2730 2870 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2731 2871 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
2732 2872 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
2733 2873 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
2734 2874 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
2735 2875 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2736 2876 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2737 2877 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
2742 2882 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
2743 2883 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
2770 2910 9.809096 TTTTGATGAGTTGTGCAAGTAAATTTA 57.191 25.926 0.00 0.00 0.00 1.40
2774 2914 7.801716 TGAGTTGTGCAAGTAAATTTAGTCT 57.198 32.000 6.01 0.00 0.00 3.24
2784 2924 8.899771 GCAAGTAAATTTAGTCTAATGCCCTAA 58.100 33.333 13.17 0.00 0.00 2.69
2792 2932 8.974060 TTTAGTCTAATGCCCTAAAATACCAG 57.026 34.615 0.00 0.00 30.07 4.00
2805 2945 9.855021 CCCTAAAATACCAGTAAAAATTGTCAG 57.145 33.333 0.00 0.00 0.00 3.51
2814 2954 9.349713 ACCAGTAAAAATTGTCAGTAATCTTCA 57.650 29.630 0.00 0.00 0.00 3.02
2838 2978 3.916761 TGCATGCTGGTTTTCATTCTTC 58.083 40.909 20.33 0.00 0.00 2.87
2841 2981 4.387862 GCATGCTGGTTTTCATTCTTCTTG 59.612 41.667 11.37 0.00 0.00 3.02
2852 2992 9.968743 GTTTTCATTCTTCTTGTAAGTATACGG 57.031 33.333 0.00 0.00 34.60 4.02
2877 3017 9.547753 GGTGAAGATTTACAGCAGAGATATTTA 57.452 33.333 0.00 0.00 35.10 1.40
2887 3027 7.655490 ACAGCAGAGATATTTATTTGAATGGC 58.345 34.615 0.00 0.00 0.00 4.40
2888 3028 7.504911 ACAGCAGAGATATTTATTTGAATGGCT 59.495 33.333 0.00 0.00 0.00 4.75
2890 3030 6.585322 GCAGAGATATTTATTTGAATGGCTGC 59.415 38.462 0.00 0.00 0.00 5.25
2892 3032 8.304596 CAGAGATATTTATTTGAATGGCTGCAT 58.695 33.333 0.50 0.00 0.00 3.96
2893 3033 8.304596 AGAGATATTTATTTGAATGGCTGCATG 58.695 33.333 0.50 0.00 0.00 4.06
2895 3035 8.644216 AGATATTTATTTGAATGGCTGCATGAA 58.356 29.630 0.50 0.00 0.00 2.57
2896 3036 9.263538 GATATTTATTTGAATGGCTGCATGAAA 57.736 29.630 0.50 0.00 0.00 2.69
2897 3037 9.787435 ATATTTATTTGAATGGCTGCATGAAAT 57.213 25.926 0.50 2.35 0.00 2.17
2918 3068 2.555325 TGAAACAAGGCTCATGCTCTTG 59.445 45.455 15.83 15.83 44.92 3.02
2938 3088 1.542915 GCATTGACAACTGGTGATGCT 59.457 47.619 9.78 0.00 40.16 3.79
2939 3089 2.749076 GCATTGACAACTGGTGATGCTA 59.251 45.455 9.78 0.00 40.16 3.49
2940 3090 3.191162 GCATTGACAACTGGTGATGCTAA 59.809 43.478 9.78 0.00 40.16 3.09
2941 3091 4.142315 GCATTGACAACTGGTGATGCTAAT 60.142 41.667 9.78 0.00 40.16 1.73
2942 3092 5.337554 CATTGACAACTGGTGATGCTAATG 58.662 41.667 0.00 0.00 0.00 1.90
2943 3093 2.749076 TGACAACTGGTGATGCTAATGC 59.251 45.455 0.00 0.00 40.20 3.56
2961 3111 6.638468 GCTAATGCAAATATTTGTGGACTAGC 59.362 38.462 25.15 22.52 40.24 3.42
2962 3112 4.981806 TGCAAATATTTGTGGACTAGCC 57.018 40.909 25.15 9.19 40.24 3.93
2981 3131 6.942576 ACTAGCCATGACATTACTTGTTTCTT 59.057 34.615 0.00 0.00 39.18 2.52
3017 3167 5.137403 CGTGTGTTAACTAAGCATGTGTTC 58.863 41.667 7.22 0.00 0.00 3.18
3022 3172 8.194104 TGTGTTAACTAAGCATGTGTTCAAAAT 58.806 29.630 7.22 0.00 0.00 1.82
3030 3180 4.931002 AGCATGTGTTCAAAATATGTTGGC 59.069 37.500 5.78 0.00 0.00 4.52
3035 3185 5.182950 TGTGTTCAAAATATGTTGGCGATCT 59.817 36.000 5.78 0.00 0.00 2.75
3036 3186 5.512788 GTGTTCAAAATATGTTGGCGATCTG 59.487 40.000 5.78 0.00 0.00 2.90
3101 3251 6.524101 AACCAACAACTCACAGTTTAATGT 57.476 33.333 0.00 0.00 36.03 2.71
3116 3266 9.502091 ACAGTTTAATGTAGATTAACAGCTGAA 57.498 29.630 23.35 5.34 34.41 3.02
3123 3273 9.726438 AATGTAGATTAACAGCTGAACTTAACT 57.274 29.630 23.35 15.14 31.70 2.24
3124 3274 8.758633 TGTAGATTAACAGCTGAACTTAACTC 57.241 34.615 23.35 13.00 0.00 3.01
3125 3275 8.585881 TGTAGATTAACAGCTGAACTTAACTCT 58.414 33.333 23.35 18.03 0.00 3.24
3126 3276 7.897575 AGATTAACAGCTGAACTTAACTCTG 57.102 36.000 23.35 0.00 0.00 3.35
3127 3277 5.924475 TTAACAGCTGAACTTAACTCTGC 57.076 39.130 23.35 4.39 37.86 4.26
3128 3278 2.772287 ACAGCTGAACTTAACTCTGCC 58.228 47.619 23.35 0.00 38.21 4.85
3129 3279 2.104792 ACAGCTGAACTTAACTCTGCCA 59.895 45.455 23.35 0.00 38.21 4.92
3130 3280 2.740981 CAGCTGAACTTAACTCTGCCAG 59.259 50.000 8.42 0.00 38.21 4.85
3131 3281 2.370189 AGCTGAACTTAACTCTGCCAGT 59.630 45.455 0.00 0.00 38.21 4.00
3132 3282 2.739379 GCTGAACTTAACTCTGCCAGTC 59.261 50.000 0.00 0.00 32.30 3.51
3133 3283 3.330267 CTGAACTTAACTCTGCCAGTCC 58.670 50.000 0.00 0.00 32.30 3.85
3134 3284 2.038557 TGAACTTAACTCTGCCAGTCCC 59.961 50.000 0.00 0.00 32.30 4.46
3135 3285 2.031495 ACTTAACTCTGCCAGTCCCT 57.969 50.000 0.00 0.00 32.30 4.20
3136 3286 3.185880 ACTTAACTCTGCCAGTCCCTA 57.814 47.619 0.00 0.00 32.30 3.53
3137 3287 3.517612 ACTTAACTCTGCCAGTCCCTAA 58.482 45.455 0.00 0.00 32.30 2.69
3138 3288 3.908103 ACTTAACTCTGCCAGTCCCTAAA 59.092 43.478 0.00 0.00 32.30 1.85
3139 3289 4.349930 ACTTAACTCTGCCAGTCCCTAAAA 59.650 41.667 0.00 0.00 32.30 1.52
3140 3290 3.876309 AACTCTGCCAGTCCCTAAAAA 57.124 42.857 0.00 0.00 32.30 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.957402 ACCTTTCTCACCATTGCAGA 57.043 45.000 0.00 0.00 0.00 4.26
73 74 6.381801 CCCACTCATATTGTGTCTGAAAAAC 58.618 40.000 5.28 0.00 33.92 2.43
109 110 4.289672 AGAAACCATCTCACTATGTTGGGT 59.710 41.667 0.00 0.00 30.46 4.51
330 331 8.353423 AGTTTGTCCAGAATATTTGCATTAGT 57.647 30.769 0.00 0.00 0.00 2.24
519 520 0.801251 GGTCAGCTGTCAATCTGCAC 59.199 55.000 14.67 0.36 42.26 4.57
564 565 3.149196 ACAACACATTGACCATGGAGTC 58.851 45.455 21.47 7.13 39.30 3.36
891 905 2.290641 AGCACAAACGAAAAGGTAGCTG 59.709 45.455 0.00 0.00 0.00 4.24
921 935 9.781834 GATTGTAGTATGATATACAGAGAGCAC 57.218 37.037 2.24 0.00 33.66 4.40
1106 1120 4.556233 TGTTCTCGTATTGTTCCTGTCAG 58.444 43.478 0.00 0.00 0.00 3.51
1397 1412 1.101635 TATCACCTCTGCCGTCTCCG 61.102 60.000 0.00 0.00 0.00 4.63
1495 1510 3.769844 TCTCCTTCAGATACGGCTCTTTT 59.230 43.478 0.00 0.00 0.00 2.27
1501 1516 3.190874 CAGTTTCTCCTTCAGATACGGC 58.809 50.000 0.00 0.00 37.95 5.68
1624 1639 8.966155 TCCTACCACCATCATTTGACTATATA 57.034 34.615 0.00 0.00 0.00 0.86
1625 1640 7.872061 TCCTACCACCATCATTTGACTATAT 57.128 36.000 0.00 0.00 0.00 0.86
1687 1704 6.403866 AACTGCATCAATAGAACCAAAACA 57.596 33.333 0.00 0.00 0.00 2.83
1696 1713 7.994911 ACATGAAGGAATAACTGCATCAATAGA 59.005 33.333 0.00 0.00 34.43 1.98
1725 1742 1.314730 TTGTTTCCCCAGCGAAAGAC 58.685 50.000 0.00 0.00 32.52 3.01
1738 1755 8.358895 GTCCTACTCCTATGTACCTATTGTTTC 58.641 40.741 0.00 0.00 0.00 2.78
1842 1893 1.631405 ACATGATGTGGGTGTTTGGG 58.369 50.000 0.00 0.00 0.00 4.12
1897 1965 4.151121 GGTGACCTACTATCTTCCTACCC 58.849 52.174 0.00 0.00 0.00 3.69
1898 1966 4.801164 TGGTGACCTACTATCTTCCTACC 58.199 47.826 2.11 0.00 0.00 3.18
2006 2074 3.369576 GCTTTCCTCTGGTAAGTCCGAAT 60.370 47.826 5.20 0.00 39.52 3.34
2061 2129 1.072159 CCTCCATGCCTCGGGAATC 59.928 63.158 0.00 0.00 31.58 2.52
2085 2153 1.201429 ATCTCTGGGAAGGCACGGTT 61.201 55.000 0.00 0.00 0.00 4.44
2154 2222 2.418910 CCCCTCGATGTCAGACGCT 61.419 63.158 0.00 0.00 0.00 5.07
2228 2296 2.203082 TGACGACAGAGTGCAGCCT 61.203 57.895 0.00 0.00 0.00 4.58
2229 2297 2.024319 GTGACGACAGAGTGCAGCC 61.024 63.158 0.00 0.00 0.00 4.85
2253 2321 5.163571 TGACAACAAATCAGCTAGCACAAAA 60.164 36.000 18.83 0.00 0.00 2.44
2271 2340 3.664025 GCAGAAAATACTTGCGTGACAAC 59.336 43.478 0.00 0.00 33.68 3.32
2277 2346 3.146066 TCTTGGCAGAAAATACTTGCGT 58.854 40.909 0.00 0.00 0.00 5.24
2284 2353 6.010219 AGGTTAAAGCTCTTGGCAGAAAATA 58.990 36.000 0.00 0.00 44.79 1.40
2308 2377 2.614983 GGGTAGAAACAAAGAACACGCA 59.385 45.455 0.00 0.00 0.00 5.24
2309 2378 2.349155 CGGGTAGAAACAAAGAACACGC 60.349 50.000 0.00 0.00 29.39 5.34
2327 2396 2.086510 CGTGTCATTAAGCCACGGG 58.913 57.895 13.50 0.00 45.97 5.28
2372 2441 1.732941 TGTACAAAGCATCGCGGATT 58.267 45.000 6.13 0.00 0.00 3.01
2375 2444 1.396648 TGATTGTACAAAGCATCGCGG 59.603 47.619 13.23 0.00 0.00 6.46
2378 2447 4.201841 TGCTGATGATTGTACAAAGCATCG 60.202 41.667 29.69 26.23 38.05 3.84
2383 2452 5.647589 AGCAATGCTGATGATTGTACAAAG 58.352 37.500 13.23 6.13 37.57 2.77
2385 2454 5.404096 CAAGCAATGCTGATGATTGTACAA 58.596 37.500 9.14 11.41 39.62 2.41
2409 2531 3.627123 TGACAATCTAACCCGCATTGATG 59.373 43.478 0.00 0.00 32.73 3.07
2412 2534 3.378112 ACATGACAATCTAACCCGCATTG 59.622 43.478 0.00 0.00 34.29 2.82
2415 2537 2.746904 CAACATGACAATCTAACCCGCA 59.253 45.455 0.00 0.00 0.00 5.69
2441 2563 8.814448 TTCTCCCTTGGATTCCTATTTACTAT 57.186 34.615 3.95 0.00 0.00 2.12
2447 2569 4.790790 ACACTTCTCCCTTGGATTCCTATT 59.209 41.667 3.95 0.00 0.00 1.73
2459 2581 1.558233 CGGTTCCTACACTTCTCCCT 58.442 55.000 0.00 0.00 0.00 4.20
2465 2587 0.035439 CATGCCCGGTTCCTACACTT 60.035 55.000 0.00 0.00 0.00 3.16
2493 2615 1.346395 AGCCCATTGACACGTAAGACA 59.654 47.619 0.00 0.00 43.62 3.41
2497 2619 0.958382 GCCAGCCCATTGACACGTAA 60.958 55.000 0.00 0.00 0.00 3.18
2521 2643 1.470098 AGCAATAAAACAGAGCAGCCG 59.530 47.619 0.00 0.00 0.00 5.52
2522 2644 2.872370 CAGCAATAAAACAGAGCAGCC 58.128 47.619 0.00 0.00 0.00 4.85
2553 2693 2.156098 AGGCTCCCCTTCACTTGCA 61.156 57.895 0.00 0.00 38.74 4.08
2562 2702 2.873557 TACTGCGCTAAGGCTCCCCT 62.874 60.000 9.73 0.00 45.77 4.79
2563 2703 2.370647 CTACTGCGCTAAGGCTCCCC 62.371 65.000 9.73 0.00 36.09 4.81
2564 2704 1.068250 CTACTGCGCTAAGGCTCCC 59.932 63.158 9.73 0.00 36.09 4.30
2565 2705 1.030457 TACTACTGCGCTAAGGCTCC 58.970 55.000 9.73 0.00 36.09 4.70
2566 2706 2.865343 TTACTACTGCGCTAAGGCTC 57.135 50.000 9.73 0.00 36.09 4.70
2567 2707 3.385111 AGATTTACTACTGCGCTAAGGCT 59.615 43.478 9.73 0.00 36.09 4.58
2568 2708 3.491267 CAGATTTACTACTGCGCTAAGGC 59.509 47.826 9.73 0.00 0.00 4.35
2577 2717 4.093998 CACAAGGCAGCAGATTTACTACTG 59.906 45.833 0.00 0.00 41.52 2.74
2578 2718 4.020218 TCACAAGGCAGCAGATTTACTACT 60.020 41.667 0.00 0.00 0.00 2.57
2579 2719 4.093556 GTCACAAGGCAGCAGATTTACTAC 59.906 45.833 0.00 0.00 0.00 2.73
2580 2720 4.253685 GTCACAAGGCAGCAGATTTACTA 58.746 43.478 0.00 0.00 0.00 1.82
2581 2721 3.077359 GTCACAAGGCAGCAGATTTACT 58.923 45.455 0.00 0.00 0.00 2.24
2582 2722 2.162408 GGTCACAAGGCAGCAGATTTAC 59.838 50.000 0.00 0.00 0.00 2.01
2583 2723 2.224744 TGGTCACAAGGCAGCAGATTTA 60.225 45.455 0.00 0.00 0.00 1.40
2584 2724 1.251251 GGTCACAAGGCAGCAGATTT 58.749 50.000 0.00 0.00 0.00 2.17
2585 2725 0.111061 TGGTCACAAGGCAGCAGATT 59.889 50.000 0.00 0.00 0.00 2.40
2586 2726 0.330604 ATGGTCACAAGGCAGCAGAT 59.669 50.000 0.00 0.00 0.00 2.90
2587 2727 0.607217 CATGGTCACAAGGCAGCAGA 60.607 55.000 0.00 0.00 0.00 4.26
2588 2728 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2589 2729 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2590 2730 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2591 2731 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2592 2732 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2603 2743 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2604 2744 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2605 2745 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2606 2746 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2607 2747 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2608 2748 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2609 2749 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2610 2750 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2611 2751 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2612 2752 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2613 2753 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2614 2754 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2615 2755 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2616 2756 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2617 2757 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2618 2758 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2619 2759 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2620 2760 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2621 2761 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2622 2762 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2623 2763 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2624 2764 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2625 2765 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2637 2777 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2638 2778 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2639 2779 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2640 2780 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2641 2781 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2642 2782 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2643 2783 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2644 2784 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2645 2785 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2646 2786 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2647 2787 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2648 2788 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2649 2789 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2650 2790 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2651 2791 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2652 2792 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2653 2793 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2654 2794 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2655 2795 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2656 2796 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2657 2797 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2658 2798 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2659 2799 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2660 2800 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2661 2801 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2662 2802 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2663 2803 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
2673 2813 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2674 2814 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2675 2815 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2676 2816 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2677 2817 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2678 2818 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2679 2819 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2680 2820 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2681 2821 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
2682 2822 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2683 2823 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2684 2824 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2685 2825 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2686 2826 1.541620 AAGGTCTGGGGAAGGGTCC 60.542 63.158 0.00 0.00 44.10 4.46
2687 2827 1.685820 CAAGGTCTGGGGAAGGGTC 59.314 63.158 0.00 0.00 0.00 4.46
2688 2828 2.539081 GCAAGGTCTGGGGAAGGGT 61.539 63.158 0.00 0.00 0.00 4.34
2689 2829 2.356667 GCAAGGTCTGGGGAAGGG 59.643 66.667 0.00 0.00 0.00 3.95
2690 2830 2.045926 CGCAAGGTCTGGGGAAGG 60.046 66.667 0.00 0.00 34.37 3.46
2691 2831 2.747855 GCGCAAGGTCTGGGGAAG 60.748 66.667 0.30 0.00 38.41 3.46
2692 2832 3.126703 TTGCGCAAGGTCTGGGGAA 62.127 57.895 21.02 0.00 44.40 3.97
2693 2833 3.551496 CTTGCGCAAGGTCTGGGGA 62.551 63.158 36.86 6.58 38.41 4.81
2694 2834 3.058160 CTTGCGCAAGGTCTGGGG 61.058 66.667 36.86 14.30 38.41 4.96
2695 2835 3.741476 GCTTGCGCAAGGTCTGGG 61.741 66.667 41.83 22.68 38.80 4.45
2696 2836 4.093952 CGCTTGCGCAAGGTCTGG 62.094 66.667 41.83 23.36 38.80 3.86
2697 2837 4.093952 CCGCTTGCGCAAGGTCTG 62.094 66.667 41.83 23.74 38.80 3.51
2703 2843 4.386951 TAGCTCCCGCTTGCGCAA 62.387 61.111 23.48 23.48 46.47 4.85
2706 2846 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2707 2847 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2708 2848 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2709 2849 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2711 2851 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
2712 2852 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2713 2853 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
2714 2854 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
2715 2855 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
2716 2856 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
2717 2857 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2718 2858 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2719 2859 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
2743 2883 8.715191 AATTTACTTGCACAACTCATCAAAAA 57.285 26.923 0.00 0.00 0.00 1.94
2744 2884 8.715191 AAATTTACTTGCACAACTCATCAAAA 57.285 26.923 0.00 0.00 0.00 2.44
2745 2885 9.462174 CTAAATTTACTTGCACAACTCATCAAA 57.538 29.630 0.00 0.00 0.00 2.69
2746 2886 8.629158 ACTAAATTTACTTGCACAACTCATCAA 58.371 29.630 0.00 0.00 0.00 2.57
2747 2887 8.165239 ACTAAATTTACTTGCACAACTCATCA 57.835 30.769 0.00 0.00 0.00 3.07
2748 2888 8.507249 AGACTAAATTTACTTGCACAACTCATC 58.493 33.333 0.00 0.00 0.00 2.92
2749 2889 8.396272 AGACTAAATTTACTTGCACAACTCAT 57.604 30.769 0.00 0.00 0.00 2.90
2750 2890 7.801716 AGACTAAATTTACTTGCACAACTCA 57.198 32.000 0.00 0.00 0.00 3.41
2753 2893 8.850452 GCATTAGACTAAATTTACTTGCACAAC 58.150 33.333 8.97 0.00 0.00 3.32
2754 2894 8.026607 GGCATTAGACTAAATTTACTTGCACAA 58.973 33.333 13.76 0.00 0.00 3.33
2755 2895 7.362574 GGGCATTAGACTAAATTTACTTGCACA 60.363 37.037 13.76 0.00 30.44 4.57
2756 2896 6.972901 GGGCATTAGACTAAATTTACTTGCAC 59.027 38.462 13.76 8.49 0.00 4.57
2757 2897 6.889722 AGGGCATTAGACTAAATTTACTTGCA 59.110 34.615 13.76 0.00 0.00 4.08
2758 2898 7.334844 AGGGCATTAGACTAAATTTACTTGC 57.665 36.000 0.00 2.89 0.00 4.01
2770 2910 6.576778 ACTGGTATTTTAGGGCATTAGACT 57.423 37.500 0.00 0.00 0.00 3.24
2777 2917 8.196378 ACAATTTTTACTGGTATTTTAGGGCA 57.804 30.769 0.00 0.00 0.00 5.36
2789 2929 9.831737 CTGAAGATTACTGACAATTTTTACTGG 57.168 33.333 0.00 0.00 0.00 4.00
2799 2939 5.065602 GCATGCATCTGAAGATTACTGACAA 59.934 40.000 14.21 0.00 31.21 3.18
2805 2945 3.881688 ACCAGCATGCATCTGAAGATTAC 59.118 43.478 21.98 0.00 33.54 1.89
2807 2947 3.014304 ACCAGCATGCATCTGAAGATT 57.986 42.857 21.98 0.00 33.54 2.40
2813 2953 3.520290 ATGAAAACCAGCATGCATCTG 57.480 42.857 21.98 9.58 31.97 2.90
2814 2954 3.767673 AGAATGAAAACCAGCATGCATCT 59.232 39.130 21.98 0.00 31.97 2.90
2838 2978 9.577110 TGTAAATCTTCACCGTATACTTACAAG 57.423 33.333 0.56 0.00 0.00 3.16
2841 2981 7.703621 TGCTGTAAATCTTCACCGTATACTTAC 59.296 37.037 0.56 0.90 0.00 2.34
2849 2989 3.258372 TCTCTGCTGTAAATCTTCACCGT 59.742 43.478 0.00 0.00 0.00 4.83
2850 2990 3.849911 TCTCTGCTGTAAATCTTCACCG 58.150 45.455 0.00 0.00 0.00 4.94
2877 3017 5.092554 TCATTTCATGCAGCCATTCAAAT 57.907 34.783 0.00 0.00 0.00 2.32
2886 3026 2.414138 GCCTTGTTTCATTTCATGCAGC 59.586 45.455 0.00 0.00 0.00 5.25
2887 3027 3.921677 AGCCTTGTTTCATTTCATGCAG 58.078 40.909 0.00 0.00 0.00 4.41
2888 3028 3.321396 TGAGCCTTGTTTCATTTCATGCA 59.679 39.130 0.00 0.00 0.00 3.96
2890 3030 4.328983 GCATGAGCCTTGTTTCATTTCATG 59.671 41.667 0.00 7.09 41.87 3.07
2892 3032 3.575256 AGCATGAGCCTTGTTTCATTTCA 59.425 39.130 0.00 0.00 43.56 2.69
2893 3033 4.082354 AGAGCATGAGCCTTGTTTCATTTC 60.082 41.667 0.00 0.00 43.56 2.17
2895 3035 3.428532 AGAGCATGAGCCTTGTTTCATT 58.571 40.909 0.00 0.00 43.56 2.57
2896 3036 3.083122 AGAGCATGAGCCTTGTTTCAT 57.917 42.857 0.00 0.00 43.56 2.57
2897 3037 2.555325 CAAGAGCATGAGCCTTGTTTCA 59.445 45.455 0.00 0.00 43.56 2.69
2918 3068 1.542915 AGCATCACCAGTTGTCAATGC 59.457 47.619 0.00 0.00 40.82 3.56
2923 3073 3.411415 GCATTAGCATCACCAGTTGTC 57.589 47.619 0.00 0.00 41.58 3.18
2938 3088 6.605194 TGGCTAGTCCACAAATATTTGCATTA 59.395 34.615 24.82 11.15 40.72 1.90
2939 3089 5.421693 TGGCTAGTCCACAAATATTTGCATT 59.578 36.000 24.82 10.67 40.72 3.56
2940 3090 4.955450 TGGCTAGTCCACAAATATTTGCAT 59.045 37.500 24.82 6.78 40.72 3.96
2941 3091 4.339748 TGGCTAGTCCACAAATATTTGCA 58.660 39.130 24.82 10.71 40.72 4.08
2942 3092 4.981806 TGGCTAGTCCACAAATATTTGC 57.018 40.909 24.82 10.92 40.72 3.68
2950 3100 9.586541 ACAAGTAATGTCATGGCTAGTCCACAA 62.587 40.741 7.89 0.00 43.29 3.33
2951 3101 8.209703 ACAAGTAATGTCATGGCTAGTCCACA 62.210 42.308 7.89 1.22 43.29 4.17
2952 3102 5.858243 ACAAGTAATGTCATGGCTAGTCCAC 60.858 44.000 7.89 0.00 43.29 4.02
2953 3103 4.225042 ACAAGTAATGTCATGGCTAGTCCA 59.775 41.667 8.12 8.12 44.26 4.02
2954 3104 4.770795 ACAAGTAATGTCATGGCTAGTCC 58.229 43.478 0.00 0.00 37.96 3.85
2955 3105 6.595716 AGAAACAAGTAATGTCATGGCTAGTC 59.404 38.462 0.00 0.00 42.99 2.59
2956 3106 6.476378 AGAAACAAGTAATGTCATGGCTAGT 58.524 36.000 0.00 0.00 42.99 2.57
2957 3107 6.992063 AGAAACAAGTAATGTCATGGCTAG 57.008 37.500 0.00 0.00 42.99 3.42
2958 3108 7.759489 AAAGAAACAAGTAATGTCATGGCTA 57.241 32.000 0.00 0.00 42.99 3.93
2959 3109 6.655078 AAAGAAACAAGTAATGTCATGGCT 57.345 33.333 0.00 0.00 42.99 4.75
2960 3110 7.115378 CAGAAAAGAAACAAGTAATGTCATGGC 59.885 37.037 0.00 0.00 42.99 4.40
2961 3111 8.137437 ACAGAAAAGAAACAAGTAATGTCATGG 58.863 33.333 0.00 0.00 42.99 3.66
2962 3112 8.961092 CACAGAAAAGAAACAAGTAATGTCATG 58.039 33.333 0.00 0.00 42.99 3.07
2972 3122 3.549070 GCACTGCACAGAAAAGAAACAAG 59.451 43.478 4.31 0.00 0.00 3.16
2981 3131 1.024046 ACACACGCACTGCACAGAAA 61.024 50.000 4.31 0.00 0.00 2.52
3017 3167 7.579589 TTTTTCAGATCGCCAACATATTTTG 57.420 32.000 0.00 0.00 0.00 2.44
3062 3212 4.448537 TTGGTTTTGACCAACTCACTTG 57.551 40.909 6.91 0.00 44.11 3.16
3088 3238 8.935844 CAGCTGTTAATCTACATTAAACTGTGA 58.064 33.333 5.25 0.00 36.43 3.58
3101 3251 7.545965 GCAGAGTTAAGTTCAGCTGTTAATCTA 59.454 37.037 14.67 0.00 0.00 1.98
3107 3257 3.142174 GGCAGAGTTAAGTTCAGCTGTT 58.858 45.455 14.67 3.23 0.00 3.16
3116 3266 2.031495 AGGGACTGGCAGAGTTAAGT 57.969 50.000 23.66 0.00 37.18 2.24
3119 3269 4.986054 TTTTTAGGGACTGGCAGAGTTA 57.014 40.909 23.66 5.17 41.52 2.24
3120 3270 3.876309 TTTTTAGGGACTGGCAGAGTT 57.124 42.857 23.66 0.00 41.52 3.01
3163 3313 3.638160 AGCACATTGACCATGAAGTGTTT 59.362 39.130 0.00 0.00 36.24 2.83


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

AutoCloner maintained by Alex Coulton.