Multiple sequence alignment - TraesCS4B01G180600

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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 TraesCS4B01G180600 chr4B 100.000 5864 0 0 954 6817 395605069 395610932 0.000000e+00 10829
1 TraesCS4B01G180600 chr4B 100.000 479 0 0 1 479 395604116 395604594 0.000000e+00 885
2 TraesCS4B01G180600 chr4B 90.265 113 11 0 2793 2905 178081153 178081265 1.530000e-31 148
3 TraesCS4B01G180600 chr4B 96.875 64 2 0 2694 2757 590011371 590011434 2.600000e-19 108
4 TraesCS4B01G180600 chr4D 91.678 4266 186 47 956 5101 318285231 318289447 0.000000e+00 5755
5 TraesCS4B01G180600 chr4D 93.229 1536 74 17 5308 6817 318291180 318292711 0.000000e+00 2233
6 TraesCS4B01G180600 chr4D 94.421 466 14 6 1 455 318284766 318285230 0.000000e+00 706
7 TraesCS4B01G180600 chr4D 96.825 63 2 0 2695 2757 455326602 455326540 9.350000e-19 106
8 TraesCS4B01G180600 chr4D 95.312 64 3 0 2694 2757 314930300 314930363 1.210000e-17 102
9 TraesCS4B01G180600 chr4A 90.355 1804 64 36 969 2697 156140708 156138940 0.000000e+00 2266
10 TraesCS4B01G180600 chr4A 92.612 934 45 12 5301 6220 156136018 156135095 0.000000e+00 1321
11 TraesCS4B01G180600 chr4A 91.973 897 57 9 3630 4516 156138069 156137178 0.000000e+00 1243
12 TraesCS4B01G180600 chr4A 97.561 656 16 0 4502 5157 156137162 156136507 0.000000e+00 1123
13 TraesCS4B01G180600 chr4A 93.460 474 11 3 1 454 156141182 156140709 0.000000e+00 686
14 TraesCS4B01G180600 chr4A 87.500 576 32 15 3072 3629 156138820 156138267 4.490000e-176 628
15 TraesCS4B01G180600 chr4A 86.807 379 37 9 6437 6811 156134322 156133953 1.770000e-110 411
16 TraesCS4B01G180600 chr4A 92.994 157 11 0 5143 5299 156136236 156136080 5.320000e-56 230
17 TraesCS4B01G180600 chr4A 92.466 146 10 1 6248 6392 156134906 156134761 2.490000e-49 207
18 TraesCS4B01G180600 chr4A 92.593 135 10 0 6388 6522 156134457 156134323 1.940000e-45 195
19 TraesCS4B01G180600 chr2D 90.517 116 9 2 2791 2905 624365886 624365772 1.180000e-32 152
20 TraesCS4B01G180600 chr2D 89.655 116 12 0 2791 2906 556926980 556927095 1.530000e-31 148
21 TraesCS4B01G180600 chr2D 87.200 125 14 1 2793 2917 43687561 43687439 2.560000e-29 141
22 TraesCS4B01G180600 chr2D 95.455 66 3 0 2692 2757 498106261 498106196 9.350000e-19 106
23 TraesCS4B01G180600 chr1A 88.189 127 13 2 2779 2904 564757213 564757338 4.260000e-32 150
24 TraesCS4B01G180600 chr1A 88.430 121 14 0 2791 2911 534913871 534913751 5.510000e-31 147
25 TraesCS4B01G180600 chr2B 89.655 116 10 2 2791 2905 766565416 766565302 5.510000e-31 147
26 TraesCS4B01G180600 chr2B 96.774 62 2 0 2696 2757 109974475 109974414 3.360000e-18 104
27 TraesCS4B01G180600 chr2A 87.302 126 16 0 2779 2904 696850752 696850877 1.980000e-30 145
28 TraesCS4B01G180600 chr7A 96.774 62 2 0 2694 2755 494786827 494786888 3.360000e-18 104
29 TraesCS4B01G180600 chr6B 96.774 62 2 0 2696 2757 16269668 16269729 3.360000e-18 104
30 TraesCS4B01G180600 chr5A 96.774 62 2 0 2696 2757 136396778 136396839 3.360000e-18 104


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 TraesCS4B01G180600 chr4B 395604116 395610932 6816 False 5857 10829 100.000000 1 6817 2 chr4B.!!$F3 6816
1 TraesCS4B01G180600 chr4D 318284766 318292711 7945 False 2898 5755 93.109333 1 6817 3 chr4D.!!$F2 6816
2 TraesCS4B01G180600 chr4A 156133953 156141182 7229 True 831 2266 91.832100 1 6811 10 chr4A.!!$R1 6810

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
458 480 0.105913 CCCTAGGACCCAGGTCTCTC 60.106 65.0 11.48 0.38 44.04 3.20 F
1682 1740 0.032217 AAGAGAGGCAGAGAGAGGGG 60.032 60.0 0.00 0.00 0.00 4.79 F
3506 3685 0.613853 TCTACCAGACCAGGAACCCG 60.614 60.0 0.00 0.00 0.00 5.28 F
5203 6016 0.105593 CGCTGTGTCCCTCATGCTAT 59.894 55.0 0.00 0.00 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2403 0.259938 ATCATCAACAAGGAGGGGGC 59.740 55.0 0.00 0.0 0.00 5.80 R
3587 3766 0.889994 GCCAACACAGGATGCAATGA 59.110 50.0 0.00 0.0 42.53 2.57 R
5299 6112 0.652592 GCATGGTACGCATCACAGAC 59.347 55.0 0.00 0.0 0.00 3.51 R
6109 8363 0.373716 GTGCGCCATAAACCTCTTCG 59.626 55.0 4.18 0.0 0.00 3.79 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
33 34 1.408683 CGCTCCCATTCTTGAATCCCA 60.409 52.381 0.00 0.00 0.00 4.37
51 63 8.026607 TGAATCCCATTACGTTTCTGAAATTTC 58.973 33.333 11.41 11.41 0.00 2.17
92 110 1.016130 CGACGCTGCCAACTCTGATT 61.016 55.000 0.00 0.00 0.00 2.57
139 158 1.447489 CGGAGAGCAGTGCTGGAAG 60.447 63.158 25.35 7.62 39.88 3.46
173 192 1.537202 GCAGTAGGGACAAAACAGCAG 59.463 52.381 0.00 0.00 0.00 4.24
328 350 2.165845 CCGCCTCCCCTATAAATACGAG 59.834 54.545 0.00 0.00 0.00 4.18
414 436 3.997952 GGGCCCCCTTTTGCTCCT 61.998 66.667 12.23 0.00 0.00 3.69
455 477 1.827492 AAGCCCTAGGACCCAGGTCT 61.827 60.000 11.48 0.00 44.04 3.85
456 478 1.762858 GCCCTAGGACCCAGGTCTC 60.763 68.421 11.48 6.95 44.04 3.36
457 479 2.020137 CCCTAGGACCCAGGTCTCT 58.980 63.158 11.48 13.30 44.04 3.10
458 480 0.105913 CCCTAGGACCCAGGTCTCTC 60.106 65.000 11.48 0.38 44.04 3.20
459 481 0.930726 CCTAGGACCCAGGTCTCTCT 59.069 60.000 16.18 7.87 44.04 3.10
460 482 1.133606 CCTAGGACCCAGGTCTCTCTC 60.134 61.905 16.18 0.00 44.04 3.20
461 483 1.850345 CTAGGACCCAGGTCTCTCTCT 59.150 57.143 16.18 7.20 44.04 3.10
462 484 0.629058 AGGACCCAGGTCTCTCTCTC 59.371 60.000 16.18 0.00 44.04 3.20
463 485 0.629058 GGACCCAGGTCTCTCTCTCT 59.371 60.000 16.18 0.00 44.04 3.10
464 486 1.409661 GGACCCAGGTCTCTCTCTCTC 60.410 61.905 16.18 0.00 44.04 3.20
465 487 1.564348 GACCCAGGTCTCTCTCTCTCT 59.436 57.143 9.67 0.00 41.57 3.10
466 488 1.564348 ACCCAGGTCTCTCTCTCTCTC 59.436 57.143 0.00 0.00 0.00 3.20
467 489 1.846439 CCCAGGTCTCTCTCTCTCTCT 59.154 57.143 0.00 0.00 0.00 3.10
468 490 2.158755 CCCAGGTCTCTCTCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
469 491 2.774234 CCAGGTCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
470 492 3.181461 CCAGGTCTCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
471 493 3.708631 CAGGTCTCTCTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
472 494 3.964031 AGGTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
473 495 3.964031 GGTCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
474 496 4.038642 GGTCTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 0.00 3.20
475 497 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
476 498 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
477 499 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
478 500 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1382 1440 3.134804 CCCTCCCCAAAGTAGTAGTCATG 59.865 52.174 0.00 0.00 0.00 3.07
1422 1480 3.953775 AGGCACCGGTGGACCAAG 61.954 66.667 34.58 9.21 35.14 3.61
1517 1575 1.694150 TCTCATGATCCCCGGCTTAAG 59.306 52.381 0.00 0.00 0.00 1.85
1518 1576 1.694150 CTCATGATCCCCGGCTTAAGA 59.306 52.381 6.67 0.00 0.00 2.10
1519 1577 2.104792 CTCATGATCCCCGGCTTAAGAA 59.895 50.000 6.67 0.00 0.00 2.52
1520 1578 2.158813 TCATGATCCCCGGCTTAAGAAC 60.159 50.000 6.67 0.00 0.00 3.01
1521 1579 1.281419 TGATCCCCGGCTTAAGAACA 58.719 50.000 6.67 0.00 0.00 3.18
1522 1580 1.631388 TGATCCCCGGCTTAAGAACAA 59.369 47.619 6.67 0.00 0.00 2.83
1558 1616 3.187700 GCTAATCTGAACATCGACGGTT 58.812 45.455 4.13 4.13 0.00 4.44
1582 1640 7.026631 TGCGATTATTTAGATCTTGGTTTGG 57.973 36.000 0.00 0.00 0.00 3.28
1680 1738 1.750778 GTGAAGAGAGGCAGAGAGAGG 59.249 57.143 0.00 0.00 0.00 3.69
1682 1740 0.032217 AAGAGAGGCAGAGAGAGGGG 60.032 60.000 0.00 0.00 0.00 4.79
1748 1808 4.230657 GTGTATGATGATGACGAGGTAGC 58.769 47.826 0.00 0.00 0.00 3.58
1790 1853 4.636435 CGGACCCACCACCACCAC 62.636 72.222 0.00 0.00 38.90 4.16
1791 1854 4.280019 GGACCCACCACCACCACC 62.280 72.222 0.00 0.00 38.79 4.61
1821 1884 2.418060 CGCCTTCTTTCTCTCTCCTTCC 60.418 54.545 0.00 0.00 0.00 3.46
1858 1921 2.230660 GGGGCAATACCAATGTCTAGC 58.769 52.381 0.00 0.00 42.05 3.42
1869 1932 6.696441 ACCAATGTCTAGCAGTAGTAGTAC 57.304 41.667 0.00 0.00 0.00 2.73
1870 1933 6.424883 ACCAATGTCTAGCAGTAGTAGTACT 58.575 40.000 8.14 8.14 40.38 2.73
1871 1934 7.571919 ACCAATGTCTAGCAGTAGTAGTACTA 58.428 38.462 9.94 5.90 37.40 1.82
1902 1965 2.472695 TCGATTGTGTTTGGGAGAGG 57.527 50.000 0.00 0.00 0.00 3.69
1945 2009 6.667558 TGAAACAATTAACCGGGGTAAAAT 57.332 33.333 8.90 0.00 0.00 1.82
1946 2010 7.063934 TGAAACAATTAACCGGGGTAAAATT 57.936 32.000 8.90 0.00 0.00 1.82
1947 2011 6.929606 TGAAACAATTAACCGGGGTAAAATTG 59.070 34.615 23.55 23.55 41.81 2.32
1957 2024 3.512496 GGGGTAAAATTGGTTTCCCTGA 58.488 45.455 4.98 0.00 37.04 3.86
1969 2036 4.038162 TGGTTTCCCTGAACAAAAATACGG 59.962 41.667 0.00 0.00 0.00 4.02
1993 2060 2.850130 TTGGCGTGGGTAGGTGGT 60.850 61.111 0.00 0.00 0.00 4.16
1994 2061 3.185299 TTGGCGTGGGTAGGTGGTG 62.185 63.158 0.00 0.00 0.00 4.17
1997 2064 2.285024 GCGTGGGTAGGTGGTGGTA 61.285 63.158 0.00 0.00 0.00 3.25
1998 2065 1.895238 CGTGGGTAGGTGGTGGTAG 59.105 63.158 0.00 0.00 0.00 3.18
1999 2066 0.901580 CGTGGGTAGGTGGTGGTAGT 60.902 60.000 0.00 0.00 0.00 2.73
2012 2093 2.225727 GGTGGTAGTTTGCAAGTACAGC 59.774 50.000 17.92 11.88 38.72 4.40
2057 2138 0.955919 CGGGTCTTCTGTTTCCAGCC 60.956 60.000 0.00 0.00 38.66 4.85
2059 2140 1.272147 GGGTCTTCTGTTTCCAGCCAT 60.272 52.381 0.00 0.00 38.66 4.40
2069 2150 4.823157 TGTTTCCAGCCATTTCATTCATG 58.177 39.130 0.00 0.00 0.00 3.07
2141 2222 3.935450 TCTTCTTTTCTGTTTGCGTTCG 58.065 40.909 0.00 0.00 0.00 3.95
2193 2274 3.239861 CAGCCTCTTGAGGTTGGAC 57.760 57.895 21.02 4.76 36.66 4.02
2445 2552 5.774690 AGATGTACTCCAATCCAAGCAAAAA 59.225 36.000 0.00 0.00 0.00 1.94
2449 2556 6.491745 TGTACTCCAATCCAAGCAAAAACATA 59.508 34.615 0.00 0.00 0.00 2.29
2462 2569 2.057137 AAACATATCTGGCGCATGGT 57.943 45.000 10.83 0.00 0.00 3.55
2518 2639 1.888512 CTGCACAGGCCACTTATGTTT 59.111 47.619 5.01 0.00 40.13 2.83
2671 2798 3.045601 AGGTCCAATCAACGAGTTCTG 57.954 47.619 0.00 0.00 0.00 3.02
2689 2816 7.742089 CGAGTTCTGATAGTTTCATTTTGTGTC 59.258 37.037 0.00 0.00 32.72 3.67
2691 2818 6.480524 TCTGATAGTTTCATTTTGTGTCCG 57.519 37.500 0.00 0.00 32.72 4.79
2705 2832 2.439701 TCCGCACTACTCCCTCCG 60.440 66.667 0.00 0.00 0.00 4.63
2761 2888 1.075525 ACTACATAGGGAGCGGCCA 60.076 57.895 2.24 0.00 38.95 5.36
2775 2902 1.000019 GGCCAGGGGTTTAACCTCC 60.000 63.158 10.86 11.50 40.56 4.30
2783 2910 5.458508 CCAGGGGTTTAACCTCCTTTTCTAA 60.459 44.000 17.59 0.00 40.56 2.10
2816 2944 4.759693 ACATACGGAGCAAAATGACTGAAA 59.240 37.500 0.00 0.00 0.00 2.69
2865 2993 4.563337 TCCGGATGTAGTTCGTATTGAG 57.437 45.455 0.00 0.00 0.00 3.02
2996 3154 8.341173 CAGGGTAGTACTCTTACTAAATGTACG 58.659 40.741 0.00 0.00 41.55 3.67
3187 3362 6.438425 AGGAAATATTGCCAGTCAAAGTGAAT 59.562 34.615 15.30 0.00 38.34 2.57
3191 3366 2.844946 TGCCAGTCAAAGTGAATTCGA 58.155 42.857 0.04 0.00 0.00 3.71
3271 3448 8.976715 TTATTTCGTTCTACTGTTTTCGAAAC 57.023 30.769 10.79 6.80 45.18 2.78
3300 3477 4.700213 GGCAGATTGCTAAACTTAACTCCA 59.300 41.667 0.67 0.00 44.28 3.86
3304 3482 3.048337 TGCTAAACTTAACTCCACCCG 57.952 47.619 0.00 0.00 0.00 5.28
3327 3505 6.255453 CCGCTTTTCATTATTGTTATTGTGGG 59.745 38.462 0.00 0.00 0.00 4.61
3330 3508 7.280652 GCTTTTCATTATTGTTATTGTGGGCAT 59.719 33.333 0.00 0.00 0.00 4.40
3348 3526 4.423732 GGCATTTCAATACGTTGAGCAAT 58.576 39.130 0.00 0.00 44.62 3.56
3386 3564 2.693069 ACTCGCTGTCAAAATCCTCTG 58.307 47.619 0.00 0.00 0.00 3.35
3393 3572 2.438434 AAAATCCTCTGCCCGCCG 60.438 61.111 0.00 0.00 0.00 6.46
3394 3573 3.268103 AAAATCCTCTGCCCGCCGT 62.268 57.895 0.00 0.00 0.00 5.68
3409 3588 1.435577 GCCGTCCGTAAATGTTCTGT 58.564 50.000 0.00 0.00 0.00 3.41
3411 3590 2.412325 GCCGTCCGTAAATGTTCTGTTG 60.412 50.000 0.00 0.00 0.00 3.33
3422 3601 9.530129 CGTAAATGTTCTGTTGACTTTATTCTC 57.470 33.333 0.00 0.00 0.00 2.87
3448 3627 6.820335 TGTACAGATCATATCTTGGTCTTGG 58.180 40.000 0.00 0.00 43.58 3.61
3482 3661 1.065102 GCATGGTGCATGACTCATGTC 59.935 52.381 18.36 11.98 43.81 3.06
3506 3685 0.613853 TCTACCAGACCAGGAACCCG 60.614 60.000 0.00 0.00 0.00 5.28
3535 3714 3.868077 CAGTTCAAGTAGGAGCACTATGC 59.132 47.826 0.00 0.00 45.46 3.14
3599 3779 4.443913 TCAAATGTGTCATTGCATCCTG 57.556 40.909 0.00 0.00 0.00 3.86
3605 3785 1.887854 TGTCATTGCATCCTGTGTTGG 59.112 47.619 0.00 0.00 0.00 3.77
3721 4104 7.173735 TGAATTTAGCATAGATCGCATGTCAAT 59.826 33.333 10.76 5.61 0.00 2.57
3722 4105 5.851047 TTAGCATAGATCGCATGTCAATG 57.149 39.130 10.76 0.00 36.82 2.82
3723 4106 3.736720 AGCATAGATCGCATGTCAATGT 58.263 40.909 10.76 0.00 36.08 2.71
3733 4116 5.582550 TCGCATGTCAATGTTGTTGTTAAA 58.417 33.333 0.00 0.00 36.08 1.52
3760 4143 6.513180 ACATCTACGTTATACAGGAACATGG 58.487 40.000 0.00 0.00 0.00 3.66
3782 4165 8.956426 CATGGTGTCTATTTGTAAGTAACCAAT 58.044 33.333 0.00 0.00 35.59 3.16
3801 4184 6.435164 ACCAATTTTAGCTCAGAATGGGTAT 58.565 36.000 11.90 0.00 40.30 2.73
3842 4228 1.206132 CAATGTGTGCATGGAGGCAAT 59.794 47.619 0.00 0.00 46.93 3.56
3882 4268 5.945784 TGAATATTTTGCTCAGTTAGGTGCT 59.054 36.000 0.00 0.00 0.00 4.40
3908 4294 0.317020 GCGCGGTGCATCTATTTTCC 60.317 55.000 8.83 0.00 45.45 3.13
3959 4345 8.545420 GCATGTTTTCTCTATGCATTTATTTGG 58.455 33.333 3.54 0.00 44.88 3.28
4000 4387 5.036737 CAGTTCAAACTAACTTGGCTTGTG 58.963 41.667 0.00 0.00 37.61 3.33
4023 4410 7.013750 TGTGTTGTCTACCATTTTTATGCTTGA 59.986 33.333 0.00 0.00 0.00 3.02
4045 4432 4.609018 CTGGCGACTATGCGGGGG 62.609 72.222 0.00 0.00 35.06 5.40
4048 4435 4.547367 GCGACTATGCGGGGGCTT 62.547 66.667 0.00 0.00 0.00 4.35
4051 4438 1.436983 CGACTATGCGGGGGCTTTTC 61.437 60.000 0.00 0.00 0.00 2.29
4089 4476 5.163437 GGTATGAACAGTTACCTCCTACCTG 60.163 48.000 0.00 0.00 35.89 4.00
4110 4497 6.439375 ACCTGTTATATTAGTGTGTCCTGTCA 59.561 38.462 0.00 0.00 0.00 3.58
4135 4522 6.839124 TTCAGCATCACATTTGGTAGAAAT 57.161 33.333 0.00 0.00 0.00 2.17
4160 4547 8.723942 TTTAAAAGCAATGTTTGGTATTGTGT 57.276 26.923 0.00 0.00 41.14 3.72
4310 4697 7.907045 GCATTGATGTGTGTGTTTCTTCTATAG 59.093 37.037 0.00 0.00 0.00 1.31
4532 4950 7.175293 AGTTTTATTCGGTTGTGCTAAATGGTA 59.825 33.333 0.00 0.00 0.00 3.25
4741 5159 2.734606 CAGGCATCATGTTTTGTGCTTG 59.265 45.455 0.00 0.72 35.17 4.01
4882 5300 8.373981 ACTATAGGAATCCATCAGTTTGATCAG 58.626 37.037 0.61 0.00 34.28 2.90
4908 5326 3.306917 TCCGCGTCAGTTAAAATCTGA 57.693 42.857 4.92 0.00 39.25 3.27
5044 5462 1.477295 AGCGCCTCTAGTTGACTAACC 59.523 52.381 2.29 0.00 37.52 2.85
5186 5999 4.634184 TGAACAGAGAGTAAGATACCGC 57.366 45.455 0.00 0.00 0.00 5.68
5193 6006 2.688958 AGAGTAAGATACCGCTGTGTCC 59.311 50.000 1.43 0.00 33.41 4.02
5203 6016 0.105593 CGCTGTGTCCCTCATGCTAT 59.894 55.000 0.00 0.00 0.00 2.97
5237 6050 8.838365 ACTTCAGATCTAATACTACCGTTAGTG 58.162 37.037 2.45 0.00 39.06 2.74
5253 6066 4.792189 CGTTAGTGTTGATACGAGTTCCTC 59.208 45.833 0.00 0.00 36.16 3.71
5301 6114 2.825086 AACAGTTCGTTGCAGTTGTC 57.175 45.000 0.00 0.00 36.12 3.18
5303 6116 1.665679 ACAGTTCGTTGCAGTTGTCTG 59.334 47.619 8.13 8.13 43.87 3.51
5304 6117 1.665679 CAGTTCGTTGCAGTTGTCTGT 59.334 47.619 0.00 0.00 43.05 3.41
5305 6118 1.665679 AGTTCGTTGCAGTTGTCTGTG 59.334 47.619 0.00 0.00 43.05 3.66
5306 6119 1.663643 GTTCGTTGCAGTTGTCTGTGA 59.336 47.619 0.00 0.00 43.05 3.58
5310 7544 0.587768 TTGCAGTTGTCTGTGATGCG 59.412 50.000 0.00 0.00 43.05 4.73
5343 7577 1.660167 TGATTGATTGGCTCAGCTCG 58.340 50.000 0.00 0.00 34.68 5.03
5480 7714 0.252197 GGTACAACCTGGAGGCGATT 59.748 55.000 0.00 0.00 39.32 3.34
5558 7792 3.429141 CCAGCACCAGAAGCGCAG 61.429 66.667 11.47 0.00 37.01 5.18
5582 7816 1.135333 GAGATCACCTTCGTGTCCTCC 59.865 57.143 0.00 0.00 41.09 4.30
5587 7821 2.344203 CCTTCGTGTCCTCCGCTCT 61.344 63.158 0.00 0.00 0.00 4.09
5597 7831 1.299468 CTCCGCTCTTCCGATTCCG 60.299 63.158 0.00 0.00 0.00 4.30
5645 7879 0.902531 CACCTTATGTCCTCCACGGT 59.097 55.000 0.00 0.00 0.00 4.83
5905 8140 2.807108 GCTGGGACGGAGGTGATATTTC 60.807 54.545 0.00 0.00 36.31 2.17
5908 8143 1.068741 GGACGGAGGTGATATTTCGCT 59.931 52.381 0.00 0.00 32.76 4.93
5939 8174 1.562008 TGGAACTCACCACCTGAACAA 59.438 47.619 0.00 0.00 34.77 2.83
5941 8176 2.618709 GGAACTCACCACCTGAACAAAG 59.381 50.000 0.00 0.00 0.00 2.77
5942 8177 2.348411 ACTCACCACCTGAACAAAGG 57.652 50.000 0.00 0.00 43.57 3.11
5943 8178 1.133792 ACTCACCACCTGAACAAAGGG 60.134 52.381 0.00 0.00 42.11 3.95
5945 8180 1.286553 TCACCACCTGAACAAAGGGTT 59.713 47.619 0.00 0.00 42.11 4.11
5946 8181 2.107366 CACCACCTGAACAAAGGGTTT 58.893 47.619 0.00 0.00 42.11 3.27
5947 8182 2.100749 CACCACCTGAACAAAGGGTTTC 59.899 50.000 0.00 0.00 42.11 2.78
5948 8183 1.686587 CCACCTGAACAAAGGGTTTCC 59.313 52.381 0.00 0.00 42.11 3.13
5949 8184 2.383855 CACCTGAACAAAGGGTTTCCA 58.616 47.619 0.00 0.00 42.11 3.53
5950 8185 2.965147 CACCTGAACAAAGGGTTTCCAT 59.035 45.455 0.00 0.00 42.11 3.41
5951 8186 4.148838 CACCTGAACAAAGGGTTTCCATA 58.851 43.478 0.00 0.00 42.11 2.74
5982 8230 5.330233 TCCAGTTGTCCTCTTCTATGTGTA 58.670 41.667 0.00 0.00 0.00 2.90
6068 8322 0.606673 GCGAAAGAAGCTCCAAGGGT 60.607 55.000 0.00 0.00 0.00 4.34
6075 8329 0.693049 AAGCTCCAAGGGTGGTAGTG 59.307 55.000 0.00 0.00 46.11 2.74
6078 8332 1.151899 TCCAAGGGTGGTAGTGGCT 60.152 57.895 0.00 0.00 46.11 4.75
6109 8363 1.273606 TGCTGTGTAGAGCAGTTCCTC 59.726 52.381 0.00 0.00 44.16 3.71
6198 8452 1.213296 ACAAGGAGTGGACAAGTGGT 58.787 50.000 0.00 0.00 0.00 4.16
6201 8455 2.368875 CAAGGAGTGGACAAGTGGTACT 59.631 50.000 0.00 0.00 0.00 2.73
6271 8686 3.071023 CCTTCTGTTCCCTTCACAGTGTA 59.929 47.826 0.00 0.00 42.12 2.90
6272 8687 4.444306 CCTTCTGTTCCCTTCACAGTGTAA 60.444 45.833 0.00 0.00 42.12 2.41
6273 8688 4.764050 TCTGTTCCCTTCACAGTGTAAA 57.236 40.909 0.00 0.00 42.12 2.01
6300 8715 7.394641 GTCATTCTTCTTACCAAAAGGAGGATT 59.605 37.037 0.00 0.00 0.00 3.01
6325 8740 7.790823 ACCTCTATCTTAAACGAGTAGTCTC 57.209 40.000 0.00 0.00 37.35 3.36
6443 9167 5.989168 TCAAATCGGTTATATGTAGCCTGTG 59.011 40.000 1.06 0.00 0.00 3.66
6457 9181 1.141657 GCCTGTGCTATCATCTCCCAA 59.858 52.381 0.00 0.00 33.53 4.12
6481 9205 3.806949 TTGCCTTCAAAGACCATAGGT 57.193 42.857 0.00 0.00 39.44 3.08
6494 9218 6.080969 AGACCATAGGTTCTCTCACTTCTA 57.919 41.667 0.00 0.00 35.25 2.10
6547 9359 0.251354 ATCCAGATGCGCAACAGACT 59.749 50.000 17.11 6.39 0.00 3.24
6548 9360 0.894835 TCCAGATGCGCAACAGACTA 59.105 50.000 17.11 0.00 0.00 2.59
6549 9361 1.275010 TCCAGATGCGCAACAGACTAA 59.725 47.619 17.11 0.00 0.00 2.24
6550 9362 1.394917 CCAGATGCGCAACAGACTAAC 59.605 52.381 17.11 0.00 0.00 2.34
6551 9363 1.394917 CAGATGCGCAACAGACTAACC 59.605 52.381 17.11 0.00 0.00 2.85
6552 9364 1.276421 AGATGCGCAACAGACTAACCT 59.724 47.619 17.11 0.00 0.00 3.50
6553 9365 1.394917 GATGCGCAACAGACTAACCTG 59.605 52.381 17.11 0.00 39.93 4.00
6616 9431 5.705609 TTTCAACAGTTCCAAATAGCTCC 57.294 39.130 0.00 0.00 0.00 4.70
6624 9439 6.948309 ACAGTTCCAAATAGCTCCAAGTAATT 59.052 34.615 0.00 0.00 0.00 1.40
6628 9443 6.480763 TCCAAATAGCTCCAAGTAATTCACA 58.519 36.000 0.00 0.00 0.00 3.58
6651 9466 3.764237 ACTCCCACGTGAATTAGTGTT 57.236 42.857 19.30 0.00 36.69 3.32
6652 9467 3.399330 ACTCCCACGTGAATTAGTGTTG 58.601 45.455 19.30 0.00 36.69 3.33
6718 9535 7.411808 TGGAGATACTATTAGATGGAGGTACC 58.588 42.308 2.73 2.73 39.54 3.34
6726 9543 3.621682 AGATGGAGGTACCTTAGAGGG 57.378 52.381 17.53 0.00 40.58 4.30
6762 9579 5.938125 CGGCATAATAACTTAGCTATTGGGT 59.062 40.000 0.00 0.00 0.00 4.51
6803 9620 1.847818 TCGTTTTCTCGTGGTCACAG 58.152 50.000 1.90 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.607689 TGCATCGAAATTTCAGAAACGTAAT 58.392 32.000 17.99 0.00 0.00 1.89
51 63 2.781923 TGGTGGAATGGATATGCATCG 58.218 47.619 10.42 0.00 31.33 3.84
127 146 3.782244 CGCGACTTCCAGCACTGC 61.782 66.667 0.00 0.00 0.00 4.40
139 158 0.863144 TACTGCCTTTTGTTCGCGAC 59.137 50.000 9.15 4.85 0.00 5.19
397 419 3.965026 GAGGAGCAAAAGGGGGCCC 62.965 68.421 15.76 15.76 0.00 5.80
414 436 0.768622 AATGGGGTTTGACGTGAGGA 59.231 50.000 0.00 0.00 0.00 3.71
455 477 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
456 478 5.452078 GAGAGAGAGAGAGAGAGAGAGAG 57.548 52.174 0.00 0.00 0.00 3.20
953 975 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
954 976 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
955 977 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
956 978 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
957 979 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
958 980 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
959 981 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
960 982 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
961 983 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
962 984 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
963 985 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
964 986 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1157 1202 4.052229 CGTCGTTGCGGGAGGACT 62.052 66.667 6.04 0.00 33.48 3.85
1382 1440 2.020016 CGCATCGCACGTGTTAGC 59.980 61.111 18.38 14.71 0.00 3.09
1467 1525 1.959226 GCGTCCCTTGCGTTTCTGA 60.959 57.895 0.00 0.00 0.00 3.27
1517 1575 2.536928 GCGGCGAGATTATGTGTTGTTC 60.537 50.000 12.98 0.00 0.00 3.18
1518 1576 1.396996 GCGGCGAGATTATGTGTTGTT 59.603 47.619 12.98 0.00 0.00 2.83
1519 1577 1.006832 GCGGCGAGATTATGTGTTGT 58.993 50.000 12.98 0.00 0.00 3.32
1520 1578 1.290203 AGCGGCGAGATTATGTGTTG 58.710 50.000 12.98 0.00 0.00 3.33
1521 1579 2.882927 TAGCGGCGAGATTATGTGTT 57.117 45.000 12.98 0.00 0.00 3.32
1522 1580 2.882927 TTAGCGGCGAGATTATGTGT 57.117 45.000 12.98 0.00 0.00 3.72
1558 1616 6.601613 ACCAAACCAAGATCTAAATAATCGCA 59.398 34.615 0.00 0.00 0.00 5.10
1582 1640 1.706287 GAAAGATCCGAGCCCGCAAC 61.706 60.000 0.00 0.00 0.00 4.17
1624 1682 1.841556 GGCATCCCATCGGGTCCTA 60.842 63.158 0.00 0.00 44.74 2.94
1680 1738 4.477975 CACGCGACGTCTCTCCCC 62.478 72.222 15.93 0.00 38.32 4.81
1682 1740 4.104417 AGCACGCGACGTCTCTCC 62.104 66.667 15.93 0.00 38.32 3.71
1789 1852 0.765510 AAGAAGGCGGTCAAAGAGGT 59.234 50.000 0.00 0.00 0.00 3.85
1790 1853 1.807142 GAAAGAAGGCGGTCAAAGAGG 59.193 52.381 0.00 0.00 0.00 3.69
1791 1854 2.739379 GAGAAAGAAGGCGGTCAAAGAG 59.261 50.000 0.00 0.00 0.00 2.85
1821 1884 1.609555 CCCCGAGAAATACGAGAGGAG 59.390 57.143 0.00 0.00 0.00 3.69
1869 1932 7.966157 AACACAATCGAAATCGTACTACTAG 57.034 36.000 2.41 0.00 40.80 2.57
1870 1933 7.274033 CCAAACACAATCGAAATCGTACTACTA 59.726 37.037 2.41 0.00 40.80 1.82
1871 1934 6.090358 CCAAACACAATCGAAATCGTACTACT 59.910 38.462 2.41 0.00 40.80 2.57
1902 1965 1.008995 CTAGCGCGCTCTCTTCTCC 60.009 63.158 40.23 0.00 0.00 3.71
1957 2024 5.859648 CGCCAAGATTAACCGTATTTTTGTT 59.140 36.000 0.00 0.00 0.00 2.83
1969 2036 2.285977 CCTACCCACGCCAAGATTAAC 58.714 52.381 0.00 0.00 0.00 2.01
1993 2060 2.139917 CGCTGTACTTGCAAACTACCA 58.860 47.619 0.00 0.00 0.00 3.25
1994 2061 2.409975 TCGCTGTACTTGCAAACTACC 58.590 47.619 0.00 0.00 0.00 3.18
1997 2064 0.868406 GCTCGCTGTACTTGCAAACT 59.132 50.000 0.00 0.00 0.00 2.66
1998 2065 0.586319 TGCTCGCTGTACTTGCAAAC 59.414 50.000 0.00 0.00 0.00 2.93
1999 2066 0.586319 GTGCTCGCTGTACTTGCAAA 59.414 50.000 0.00 0.00 35.34 3.68
2012 2093 2.127118 CAAAAGGCTGCGTGCTCG 60.127 61.111 3.31 3.31 42.39 5.03
2057 2138 3.834435 CACGCATGCATGAATGAAATG 57.166 42.857 30.64 11.87 0.00 2.32
2084 2165 3.864789 AGAAGAAAGAAGCTGACCCAA 57.135 42.857 0.00 0.00 0.00 4.12
2141 2222 3.375782 AAAAACAGATTGCTGGCAGAC 57.624 42.857 20.86 10.37 46.60 3.51
2191 2272 3.629438 TCAAAATTCGAAAACCCCGTC 57.371 42.857 0.00 0.00 0.00 4.79
2192 2273 4.388378 TTTCAAAATTCGAAAACCCCGT 57.612 36.364 0.00 0.00 29.63 5.28
2193 2274 4.151512 CCATTTCAAAATTCGAAAACCCCG 59.848 41.667 0.00 0.00 36.06 5.73
2263 2344 1.900016 TGTCCTTGCTTGCTGGCTG 60.900 57.895 3.49 0.00 0.00 4.85
2264 2345 1.900498 GTGTCCTTGCTTGCTGGCT 60.900 57.895 3.49 0.00 0.00 4.75
2265 2346 2.138656 CTGTGTCCTTGCTTGCTGGC 62.139 60.000 0.00 0.00 0.00 4.85
2266 2347 1.954528 CTGTGTCCTTGCTTGCTGG 59.045 57.895 0.00 0.00 0.00 4.85
2267 2348 1.170919 AGCTGTGTCCTTGCTTGCTG 61.171 55.000 0.00 0.00 32.61 4.41
2268 2349 0.397941 TAGCTGTGTCCTTGCTTGCT 59.602 50.000 0.00 0.00 38.15 3.91
2269 2350 1.198637 CTTAGCTGTGTCCTTGCTTGC 59.801 52.381 0.00 0.00 38.15 4.01
2270 2351 1.198637 GCTTAGCTGTGTCCTTGCTTG 59.801 52.381 0.00 0.00 38.15 4.01
2319 2403 0.259938 ATCATCAACAAGGAGGGGGC 59.740 55.000 0.00 0.00 0.00 5.80
2323 2407 2.681848 GTGCTGATCATCAACAAGGAGG 59.318 50.000 0.00 0.00 0.00 4.30
2445 2552 0.601046 CGACCATGCGCCAGATATGT 60.601 55.000 4.18 0.00 0.00 2.29
2449 2556 2.512286 CACGACCATGCGCCAGAT 60.512 61.111 4.18 0.00 33.86 2.90
2660 2787 8.070171 ACAAAATGAAACTATCAGAACTCGTTG 58.930 33.333 0.00 0.00 42.53 4.10
2671 2798 4.851558 GTGCGGACACAAAATGAAACTATC 59.148 41.667 0.63 0.00 46.61 2.08
2689 2816 2.280823 GAACGGAGGGAGTAGTGCGG 62.281 65.000 0.00 0.00 0.00 5.69
2691 2818 0.971447 AGGAACGGAGGGAGTAGTGC 60.971 60.000 0.00 0.00 0.00 4.40
2761 2888 5.935668 TTAGAAAAGGAGGTTAAACCCCT 57.064 39.130 0.00 0.00 39.75 4.79
2794 2922 4.944962 TTCAGTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2842 2970 4.866921 TCAATACGAACTACATCCGGATG 58.133 43.478 37.23 37.23 44.15 3.51
2890 3018 9.675464 TTGAACTAAATAATACTCCATCCGTTT 57.325 29.630 0.00 0.00 0.00 3.60
2893 3021 8.888579 AGTTGAACTAAATAATACTCCATCCG 57.111 34.615 0.00 0.00 0.00 4.18
2940 3071 8.429641 TGAAACTAAGAACTTCAGGAGTAACAT 58.570 33.333 0.00 0.00 37.72 2.71
3032 3190 7.834881 AACATAATGATCGGAAGGACTACTA 57.165 36.000 0.00 0.00 0.00 1.82
3036 3194 5.523916 CGAAAACATAATGATCGGAAGGACT 59.476 40.000 0.00 0.00 0.00 3.85
3092 3251 1.856597 ACGAACGAAAAACGAGTCTGG 59.143 47.619 0.14 0.00 45.77 3.86
3241 3418 9.640974 CGAAAACAGTAGAACGAAATAAGAAAA 57.359 29.630 0.00 0.00 0.00 2.29
3245 3422 9.089123 GTTTCGAAAACAGTAGAACGAAATAAG 57.911 33.333 13.10 0.00 45.93 1.73
3259 3436 4.803088 TCTGCCAAATTGTTTCGAAAACAG 59.197 37.500 13.10 9.82 0.00 3.16
3271 3448 7.599998 AGTTAAGTTTAGCAATCTGCCAAATTG 59.400 33.333 0.00 0.00 46.52 2.32
3300 3477 6.811170 CACAATAACAATAATGAAAAGCGGGT 59.189 34.615 0.00 0.00 0.00 5.28
3304 3482 6.593382 TGCCCACAATAACAATAATGAAAAGC 59.407 34.615 0.00 0.00 0.00 3.51
3327 3505 5.335127 AGATTGCTCAACGTATTGAAATGC 58.665 37.500 0.00 0.00 44.28 3.56
3330 3508 6.801539 AGAAGATTGCTCAACGTATTGAAA 57.198 33.333 0.00 0.00 44.28 2.69
3348 3526 5.874810 AGCGAGTATGCAACATAAAAGAAGA 59.125 36.000 0.00 0.00 37.31 2.87
3386 3564 3.569690 CATTTACGGACGGCGGGC 61.570 66.667 13.24 2.03 0.00 6.13
3393 3572 5.668558 AAGTCAACAGAACATTTACGGAC 57.331 39.130 0.00 0.00 0.00 4.79
3394 3573 7.972832 ATAAAGTCAACAGAACATTTACGGA 57.027 32.000 0.00 0.00 0.00 4.69
3422 3601 7.387122 CCAAGACCAAGATATGATCTGTACATG 59.613 40.741 0.00 0.00 40.13 3.21
3436 3615 2.107204 ACAGAAGTGCCAAGACCAAGAT 59.893 45.455 0.00 0.00 0.00 2.40
3506 3685 2.417933 CTCCTACTTGAACTGCATGCAC 59.582 50.000 18.46 8.19 0.00 4.57
3579 3758 3.924073 CACAGGATGCAATGACACATTTG 59.076 43.478 0.00 0.00 42.53 2.32
3587 3766 0.889994 GCCAACACAGGATGCAATGA 59.110 50.000 0.00 0.00 42.53 2.57
3692 4075 7.358066 ACATGCGATCTATGCTAAATTCAAAG 58.642 34.615 0.00 0.00 0.00 2.77
3696 4079 6.471976 TGACATGCGATCTATGCTAAATTC 57.528 37.500 0.00 0.00 0.00 2.17
3705 4088 5.355071 ACAACAACATTGACATGCGATCTAT 59.645 36.000 0.00 0.00 33.05 1.98
3733 4116 6.927416 TGTTCCTGTATAACGTAGATGTTGT 58.073 36.000 0.00 0.00 33.32 3.32
3746 4129 7.857456 ACAAATAGACACCATGTTCCTGTATA 58.143 34.615 0.00 0.00 0.00 1.47
3815 4200 4.449131 CTCCATGCACACATTGAGATACT 58.551 43.478 0.00 0.00 44.89 2.12
3818 4203 2.651455 CCTCCATGCACACATTGAGAT 58.349 47.619 8.30 0.00 44.89 2.75
3822 4207 0.604073 TTGCCTCCATGCACACATTG 59.396 50.000 0.00 0.00 41.88 2.82
3823 4208 1.563924 ATTGCCTCCATGCACACATT 58.436 45.000 0.00 0.00 41.88 2.71
3825 4210 1.271817 TGTATTGCCTCCATGCACACA 60.272 47.619 0.00 0.00 41.88 3.72
3830 4215 5.242393 AGTTATGATTGTATTGCCTCCATGC 59.758 40.000 0.00 0.00 0.00 4.06
3882 4268 1.948104 AGATGCACCGCGCTTAATTA 58.052 45.000 5.56 0.00 43.06 1.40
3965 4352 5.392767 AGTTTGAACTGATAGCGAAGAGA 57.607 39.130 0.00 0.00 37.98 3.10
3966 4353 6.809196 AGTTAGTTTGAACTGATAGCGAAGAG 59.191 38.462 6.64 0.00 38.25 2.85
3967 4354 6.688578 AGTTAGTTTGAACTGATAGCGAAGA 58.311 36.000 6.64 0.00 38.25 2.87
3968 4355 6.952935 AGTTAGTTTGAACTGATAGCGAAG 57.047 37.500 6.64 0.00 38.25 3.79
3970 4357 5.637810 CCAAGTTAGTTTGAACTGATAGCGA 59.362 40.000 6.64 0.00 39.62 4.93
3971 4358 5.671329 GCCAAGTTAGTTTGAACTGATAGCG 60.671 44.000 6.64 0.00 39.62 4.26
3972 4359 5.412904 AGCCAAGTTAGTTTGAACTGATAGC 59.587 40.000 6.64 2.92 39.62 2.97
3973 4360 7.041098 ACAAGCCAAGTTAGTTTGAACTGATAG 60.041 37.037 5.00 0.00 39.62 2.08
3979 4366 4.993905 ACACAAGCCAAGTTAGTTTGAAC 58.006 39.130 5.00 0.00 0.00 3.18
3983 4370 4.705023 AGACAACACAAGCCAAGTTAGTTT 59.295 37.500 0.00 0.00 0.00 2.66
4023 4410 1.066858 CCCGCATAGTCGCCAGATTAT 60.067 52.381 0.00 0.00 30.60 1.28
4045 4432 5.515797 ACCCAAGTAAACTGAAGAAAAGC 57.484 39.130 0.00 0.00 0.00 3.51
4048 4435 7.776030 TGTTCATACCCAAGTAAACTGAAGAAA 59.224 33.333 0.00 0.00 29.77 2.52
4051 4438 6.710744 ACTGTTCATACCCAAGTAAACTGAAG 59.289 38.462 0.00 0.00 29.77 3.02
4089 4476 9.378551 TGAAATGACAGGACACACTAATATAAC 57.621 33.333 0.00 0.00 0.00 1.89
4110 4497 6.839124 TTCTACCAAATGTGATGCTGAAAT 57.161 33.333 0.00 0.00 0.00 2.17
4135 4522 8.723942 ACACAATACCAAACATTGCTTTTAAA 57.276 26.923 0.00 0.00 36.96 1.52
4155 4542 5.626142 TCTTTTTCATAGCCACCTACACAA 58.374 37.500 0.00 0.00 0.00 3.33
4157 4544 5.938125 TCTTCTTTTTCATAGCCACCTACAC 59.062 40.000 0.00 0.00 0.00 2.90
4160 4547 7.420214 CCCTATCTTCTTTTTCATAGCCACCTA 60.420 40.741 0.00 0.00 0.00 3.08
4741 5159 1.198637 GATCACCAAGCAGACAGTTGC 59.801 52.381 0.00 0.82 44.41 4.17
4882 5300 4.650545 TTTTAACTGACGCGGAACATAC 57.349 40.909 12.47 0.00 0.00 2.39
4908 5326 3.394940 TCACTATCAGGGACTAGGTCGAT 59.605 47.826 0.00 0.00 36.02 3.59
5044 5462 7.205992 TCTTTGGAATGAAGAGAGATATCACG 58.794 38.462 5.32 0.00 0.00 4.35
5186 5999 2.169144 TGTCATAGCATGAGGGACACAG 59.831 50.000 0.00 0.00 40.53 3.66
5215 6028 8.618677 TCAACACTAACGGTAGTATTAGATCTG 58.381 37.037 13.91 0.00 38.58 2.90
5269 6082 2.096909 CGAACTGTTGACGGTGAACATC 60.097 50.000 13.40 8.50 35.26 3.06
5299 6112 0.652592 GCATGGTACGCATCACAGAC 59.347 55.000 0.00 0.00 0.00 3.51
5301 6114 0.654160 CTGCATGGTACGCATCACAG 59.346 55.000 0.00 3.07 39.02 3.66
5303 6116 1.934589 TACTGCATGGTACGCATCAC 58.065 50.000 0.00 0.00 39.02 3.06
5304 6117 2.682155 TTACTGCATGGTACGCATCA 57.318 45.000 0.00 0.00 39.02 3.07
5305 6118 3.130633 TCATTACTGCATGGTACGCATC 58.869 45.455 0.00 0.00 39.02 3.91
5306 6119 3.192541 TCATTACTGCATGGTACGCAT 57.807 42.857 0.00 0.00 39.02 4.73
5310 7544 6.441274 CCAATCAATCATTACTGCATGGTAC 58.559 40.000 0.00 0.00 0.00 3.34
5587 7821 1.447838 GACTGCTGCGGAATCGGAA 60.448 57.895 16.72 0.00 36.03 4.30
5607 7841 4.374702 CACTTGCACGTCGCTGCC 62.375 66.667 14.37 1.78 43.06 4.85
5612 7846 4.012895 GGTGGCACTTGCACGTCG 62.013 66.667 18.45 0.00 44.36 5.12
5645 7879 2.667418 GCCTGGAGCTGCAGAAGA 59.333 61.111 34.12 0.00 38.99 2.87
5684 7918 2.109126 GCTGTAGCTGGAAAGCGGG 61.109 63.158 0.00 0.00 40.27 6.13
5810 8044 0.736053 GAGAGCCCAGAGACTACACG 59.264 60.000 0.00 0.00 0.00 4.49
5905 8140 0.594796 GTTCCAAACCAGCAACAGCG 60.595 55.000 0.00 0.00 0.00 5.18
5908 8143 1.748493 GTGAGTTCCAAACCAGCAACA 59.252 47.619 0.00 0.00 0.00 3.33
5948 8183 2.749621 GGACAACTGGAACCAAGCTATG 59.250 50.000 0.00 0.00 0.00 2.23
5949 8184 2.644798 AGGACAACTGGAACCAAGCTAT 59.355 45.455 0.00 0.00 0.00 2.97
5950 8185 2.038557 GAGGACAACTGGAACCAAGCTA 59.961 50.000 0.00 0.00 0.00 3.32
5951 8186 0.846693 AGGACAACTGGAACCAAGCT 59.153 50.000 0.00 0.00 0.00 3.74
5982 8230 7.876582 AGTTCGCTAACTGTCTTAATAACCTTT 59.123 33.333 2.31 0.00 44.40 3.11
6068 8322 0.908910 CCCACATACAGCCACTACCA 59.091 55.000 0.00 0.00 0.00 3.25
6075 8329 2.117156 CAGCAGCCCACATACAGCC 61.117 63.158 0.00 0.00 0.00 4.85
6078 8332 0.980423 TACACAGCAGCCCACATACA 59.020 50.000 0.00 0.00 0.00 2.29
6109 8363 0.373716 GTGCGCCATAAACCTCTTCG 59.626 55.000 4.18 0.00 0.00 3.79
6198 8452 6.237901 AGAACATAACATCTGCCAACAAGTA 58.762 36.000 0.00 0.00 0.00 2.24
6201 8455 6.403866 AAAGAACATAACATCTGCCAACAA 57.596 33.333 0.00 0.00 0.00 2.83
6271 8686 7.231519 CCTCCTTTTGGTAAGAAGAATGACTTT 59.768 37.037 0.00 0.00 38.78 2.66
6272 8687 6.717084 CCTCCTTTTGGTAAGAAGAATGACTT 59.283 38.462 0.00 0.00 40.23 3.01
6273 8688 6.044404 TCCTCCTTTTGGTAAGAAGAATGACT 59.956 38.462 0.00 0.00 41.38 3.41
6300 8715 8.481314 TGAGACTACTCGTTTAAGATAGAGGTA 58.519 37.037 0.00 0.00 45.25 3.08
6309 8724 7.759465 TCATACCTTGAGACTACTCGTTTAAG 58.241 38.462 0.00 0.00 45.25 1.85
6369 8784 2.365582 AGGTTGCCGGCTATTTGTTAG 58.634 47.619 29.70 0.00 0.00 2.34
6443 9167 2.481952 GCAATCGTTGGGAGATGATAGC 59.518 50.000 1.01 0.00 0.00 2.97
6457 9181 2.270352 TGGTCTTTGAAGGCAATCGT 57.730 45.000 0.00 0.00 33.25 3.73
6616 9431 5.212194 CGTGGGAGTTTTGTGAATTACTTG 58.788 41.667 0.00 0.00 0.00 3.16
6624 9439 2.404923 TTCACGTGGGAGTTTTGTGA 57.595 45.000 17.00 0.00 37.76 3.58
6628 9443 4.457466 ACACTAATTCACGTGGGAGTTTT 58.543 39.130 17.00 3.59 35.51 2.43
6651 9466 2.038033 GGTGGTTGAGCCTAGTACAACA 59.962 50.000 18.50 8.12 43.51 3.33
6652 9467 2.302157 AGGTGGTTGAGCCTAGTACAAC 59.698 50.000 12.41 12.41 41.79 3.32
6708 9525 1.294068 TGCCCTCTAAGGTACCTCCAT 59.706 52.381 16.64 1.70 39.02 3.41
6736 9553 6.313905 CCCAATAGCTAAGTTATTATGCCGAG 59.686 42.308 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.