Multiple sequence alignment - TraesCS1D01G244200

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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 TraesCS1D01G244200 chr1D 100.000 3146 0 0 1 3146 335034955 335031810 0.000000e+00 5810.0
1 TraesCS1D01G244200 chr1A 89.072 2489 151 57 534 2952 432560740 432558303 0.000000e+00 2977.0
2 TraesCS1D01G244200 chr1A 83.939 523 39 20 4 503 432561233 432560733 2.860000e-125 459.0
3 TraesCS1D01G244200 chr1A 88.406 69 5 3 3063 3129 432558191 432558124 2.600000e-11 80.5
4 TraesCS1D01G244200 chr1B 93.141 2012 84 15 559 2528 450454227 450452228 0.000000e+00 2902.0
5 TraesCS1D01G244200 chr1B 80.792 682 82 35 2472 3133 450452246 450451594 3.650000e-134 488.0
6 TraesCS1D01G244200 chr1B 86.062 452 30 16 1 424 450454727 450454281 3.700000e-124 455.0


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 TraesCS1D01G244200 chr1D 335031810 335034955 3145 True 5810.000000 5810 100.000 1 3146 1 chr1D.!!$R1 3145
1 TraesCS1D01G244200 chr1A 432558124 432561233 3109 True 1172.166667 2977 87.139 4 3129 3 chr1A.!!$R1 3125
2 TraesCS1D01G244200 chr1B 450451594 450454727 3133 True 1281.666667 2902 86.665 1 3133 3 chr1B.!!$R1 3132

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
287 301 0.110486 AACCATTTGACCGGCACTCT 59.890 50.0 0.0 0.0 0.0 3.24 F
289 303 0.321564 CCATTTGACCGGCACTCTGA 60.322 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1580 1.313812 GGAAGACGGAGGAGAAGCGA 61.314 60.0 0.0 0.0 0.00 4.93 R
2185 2298 2.173126 ATCAGCCTTACTCAGCTCCT 57.827 50.0 0.0 0.0 37.18 3.69 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
20 21 4.179579 GCAACGGCGAGCCAATCC 62.180 66.667 16.62 0.00 35.37 3.01
140 149 1.889105 ACGTGTTGCTCTGCACCAG 60.889 57.895 0.00 0.00 38.71 4.00
160 169 0.392998 CGGTGAGGGAAATGAGGGTG 60.393 60.000 0.00 0.00 0.00 4.61
177 186 4.132336 AGGGTGAAACGAGAAAGTAAACC 58.868 43.478 0.00 0.00 38.12 3.27
178 187 3.878699 GGGTGAAACGAGAAAGTAAACCA 59.121 43.478 0.00 0.00 38.12 3.67
179 188 4.260907 GGGTGAAACGAGAAAGTAAACCAC 60.261 45.833 0.00 0.00 38.12 4.16
180 189 4.511734 GTGAAACGAGAAAGTAAACCACG 58.488 43.478 0.00 0.00 0.00 4.94
196 210 2.691011 ACCACGTGTTGCTGGTAAAAAT 59.309 40.909 15.65 0.00 39.11 1.82
202 216 4.915085 CGTGTTGCTGGTAAAAATACAAGG 59.085 41.667 0.00 0.00 0.00 3.61
251 265 8.837389 ACTGAAATTCACCTGTTTTAAGACTAC 58.163 33.333 0.00 0.00 0.00 2.73
263 277 8.997621 TGTTTTAAGACTACATATGAGTGACC 57.002 34.615 10.38 0.00 0.00 4.02
264 278 8.590204 TGTTTTAAGACTACATATGAGTGACCA 58.410 33.333 10.38 0.00 0.00 4.02
272 286 4.101114 ACATATGAGTGACCACCTAACCA 58.899 43.478 10.38 0.00 0.00 3.67
282 296 0.808755 CACCTAACCATTTGACCGGC 59.191 55.000 0.00 0.00 0.00 6.13
285 299 1.613255 CCTAACCATTTGACCGGCACT 60.613 52.381 0.00 0.00 0.00 4.40
286 300 1.737793 CTAACCATTTGACCGGCACTC 59.262 52.381 0.00 0.00 0.00 3.51
287 301 0.110486 AACCATTTGACCGGCACTCT 59.890 50.000 0.00 0.00 0.00 3.24
289 303 0.321564 CCATTTGACCGGCACTCTGA 60.322 55.000 0.00 0.00 0.00 3.27
336 372 8.563949 CAGCGTAAATGTACAACTTTAAATTCG 58.436 33.333 0.00 2.99 0.00 3.34
452 488 9.824216 ACTATATATGTACTGTACCACCTCAAT 57.176 33.333 14.91 3.22 0.00 2.57
462 498 1.960689 ACCACCTCAATTTTCAACCCG 59.039 47.619 0.00 0.00 0.00 5.28
463 499 1.960689 CCACCTCAATTTTCAACCCGT 59.039 47.619 0.00 0.00 0.00 5.28
472 511 5.236911 TCAATTTTCAACCCGTGTACAGTAC 59.763 40.000 3.49 3.49 0.00 2.73
501 540 5.833406 CCAATCATGCATGGTAGTACAAA 57.167 39.130 25.97 4.08 31.84 2.83
502 541 5.824429 CCAATCATGCATGGTAGTACAAAG 58.176 41.667 25.97 3.29 31.84 2.77
503 542 5.357878 CCAATCATGCATGGTAGTACAAAGT 59.642 40.000 25.97 0.00 31.84 2.66
504 543 6.458751 CCAATCATGCATGGTAGTACAAAGTC 60.459 42.308 25.97 0.00 31.84 3.01
505 544 4.513442 TCATGCATGGTAGTACAAAGTCC 58.487 43.478 25.97 0.00 0.00 3.85
506 545 4.019771 TCATGCATGGTAGTACAAAGTCCA 60.020 41.667 25.97 0.00 0.00 4.02
507 546 4.568072 TGCATGGTAGTACAAAGTCCAT 57.432 40.909 2.06 0.00 39.14 3.41
508 547 4.513442 TGCATGGTAGTACAAAGTCCATC 58.487 43.478 2.06 0.00 36.86 3.51
509 548 4.225042 TGCATGGTAGTACAAAGTCCATCT 59.775 41.667 2.06 0.00 36.86 2.90
510 549 4.811557 GCATGGTAGTACAAAGTCCATCTC 59.188 45.833 2.06 0.00 36.86 2.75
511 550 5.626809 GCATGGTAGTACAAAGTCCATCTCA 60.627 44.000 2.06 0.00 36.86 3.27
512 551 6.406370 CATGGTAGTACAAAGTCCATCTCAA 58.594 40.000 2.06 0.00 36.86 3.02
513 552 6.428083 TGGTAGTACAAAGTCCATCTCAAA 57.572 37.500 2.06 0.00 0.00 2.69
514 553 6.228258 TGGTAGTACAAAGTCCATCTCAAAC 58.772 40.000 2.06 0.00 0.00 2.93
515 554 6.183361 TGGTAGTACAAAGTCCATCTCAAACA 60.183 38.462 2.06 0.00 0.00 2.83
516 555 6.147328 GGTAGTACAAAGTCCATCTCAAACAC 59.853 42.308 2.06 0.00 0.00 3.32
517 556 5.930135 AGTACAAAGTCCATCTCAAACACT 58.070 37.500 0.00 0.00 0.00 3.55
518 557 5.760253 AGTACAAAGTCCATCTCAAACACTG 59.240 40.000 0.00 0.00 0.00 3.66
519 558 3.316308 ACAAAGTCCATCTCAAACACTGC 59.684 43.478 0.00 0.00 0.00 4.40
520 559 2.936919 AGTCCATCTCAAACACTGCA 57.063 45.000 0.00 0.00 0.00 4.41
521 560 3.430042 AGTCCATCTCAAACACTGCAT 57.570 42.857 0.00 0.00 0.00 3.96
522 561 3.759581 AGTCCATCTCAAACACTGCATT 58.240 40.909 0.00 0.00 0.00 3.56
523 562 4.147321 AGTCCATCTCAAACACTGCATTT 58.853 39.130 0.00 0.00 0.00 2.32
524 563 4.022589 AGTCCATCTCAAACACTGCATTTG 60.023 41.667 5.12 5.12 38.21 2.32
525 564 4.022935 GTCCATCTCAAACACTGCATTTGA 60.023 41.667 12.19 12.19 42.37 2.69
532 571 6.245115 TCAAACACTGCATTTGAGAGTATG 57.755 37.500 9.38 0.00 40.32 2.39
562 601 6.772716 ACAGAAGCTTTACCAGAATTTCAGAA 59.227 34.615 0.00 0.00 0.00 3.02
571 610 3.503748 CCAGAATTTCAGAAGAAACGGCT 59.496 43.478 0.00 0.00 45.79 5.52
588 627 2.480416 CGGCTCAGTTACAGTGAGGATC 60.480 54.545 10.02 0.00 44.00 3.36
597 636 6.589523 CAGTTACAGTGAGGATCTGAGAAAAG 59.410 42.308 0.00 0.00 36.81 2.27
630 669 2.220133 CCAAACACTGGTCGAAACGTAG 59.780 50.000 0.00 0.00 40.78 3.51
631 670 4.287081 CCAAACACTGGTCGAAACGTAGT 61.287 47.826 0.00 0.00 41.88 2.73
632 671 3.988379 AACACTGGTCGAAACGTAGTA 57.012 42.857 0.00 0.00 45.00 1.82
740 794 2.181021 GTCGATCGAACGGCTGGT 59.819 61.111 21.31 0.00 34.94 4.00
774 838 1.660607 CATGTGACTGACGGTGCATAC 59.339 52.381 0.00 0.00 0.00 2.39
791 855 2.453650 TACGCATCTTTCTCGTCTCG 57.546 50.000 0.00 0.00 37.61 4.04
868 936 7.482169 AAAAGTTTTCACCTTTCTTCCTTCT 57.518 32.000 0.00 0.00 31.11 2.85
869 937 7.482169 AAAGTTTTCACCTTTCTTCCTTCTT 57.518 32.000 0.00 0.00 0.00 2.52
870 938 6.701145 AGTTTTCACCTTTCTTCCTTCTTC 57.299 37.500 0.00 0.00 0.00 2.87
871 939 6.427441 AGTTTTCACCTTTCTTCCTTCTTCT 58.573 36.000 0.00 0.00 0.00 2.85
872 940 6.544197 AGTTTTCACCTTTCTTCCTTCTTCTC 59.456 38.462 0.00 0.00 0.00 2.87
873 941 5.630415 TTCACCTTTCTTCCTTCTTCTCA 57.370 39.130 0.00 0.00 0.00 3.27
891 964 1.080354 ACTTCCCATCCCACCTCGA 59.920 57.895 0.00 0.00 0.00 4.04
943 1016 3.707640 CTCTCCTCCTCCCGCGACT 62.708 68.421 8.23 0.00 0.00 4.18
980 1053 2.499685 GAACCCGCAGCGTAGGAT 59.500 61.111 15.05 3.01 0.00 3.24
981 1054 1.737816 GAACCCGCAGCGTAGGATA 59.262 57.895 15.05 0.00 0.00 2.59
983 1056 2.049063 CCCGCAGCGTAGGATAGC 60.049 66.667 15.05 0.00 0.00 2.97
984 1057 2.728180 CCGCAGCGTAGGATAGCA 59.272 61.111 15.05 0.00 35.48 3.49
1338 1424 4.717629 TTCTCCACCGACTGCGCG 62.718 66.667 0.00 0.00 35.83 6.86
1421 1507 3.579302 CCACCCCAACCTGCTCCA 61.579 66.667 0.00 0.00 0.00 3.86
1494 1580 2.344203 CCTCTCGTCCTTCGCCACT 61.344 63.158 0.00 0.00 39.67 4.00
1815 1916 0.319641 ACTCAAACTCGTTCTCCGGC 60.320 55.000 0.00 0.00 37.11 6.13
2185 2298 4.806571 GCACTAGGATTCGTGCGA 57.193 55.556 0.00 0.00 45.74 5.10
2329 2442 6.383147 TCGAAGGGGTAAAATGAGACTCTAAT 59.617 38.462 3.68 0.00 0.00 1.73
2330 2443 6.702282 CGAAGGGGTAAAATGAGACTCTAATC 59.298 42.308 3.68 0.00 0.00 1.75
2331 2444 6.502074 AGGGGTAAAATGAGACTCTAATCC 57.498 41.667 3.68 0.00 0.00 3.01
2359 2472 0.601841 TTGGACGTCTTTTCTCCCGC 60.602 55.000 16.46 0.00 0.00 6.13
2379 2492 1.002900 CAGTGTGAAATTTGCGTCGGT 60.003 47.619 0.00 0.00 0.00 4.69
2396 2509 1.676006 CGGTGTCCTCCAAATATTGCC 59.324 52.381 0.00 0.00 0.00 4.52
2404 2517 6.377146 TGTCCTCCAAATATTGCCTCTAAAAC 59.623 38.462 0.00 0.00 0.00 2.43
2406 2519 5.893824 CCTCCAAATATTGCCTCTAAAACCT 59.106 40.000 0.00 0.00 0.00 3.50
2407 2520 7.060421 CCTCCAAATATTGCCTCTAAAACCTA 58.940 38.462 0.00 0.00 0.00 3.08
2419 2532 9.474313 TGCCTCTAAAACCTAAATACATCAAAT 57.526 29.630 0.00 0.00 0.00 2.32
2453 2566 9.914131 AGAAGATTTAAAAGTTACTGGAAATGC 57.086 29.630 0.00 0.00 0.00 3.56
2455 2568 9.914131 AAGATTTAAAAGTTACTGGAAATGCTC 57.086 29.630 0.00 0.00 0.00 4.26
2457 2570 9.561270 GATTTAAAAGTTACTGGAAATGCTCTC 57.439 33.333 0.00 0.00 0.00 3.20
2459 2572 8.635765 TTAAAAGTTACTGGAAATGCTCTCAT 57.364 30.769 0.00 0.00 33.53 2.90
2468 2581 6.100279 ACTGGAAATGCTCTCATATAGGTTGA 59.900 38.462 0.00 0.00 31.46 3.18
2476 2589 8.706322 TGCTCTCATATAGGTTGAGTGTATTA 57.294 34.615 10.16 0.00 41.13 0.98
2480 2631 8.577296 TCTCATATAGGTTGAGTGTATTACAGC 58.423 37.037 0.00 0.00 41.13 4.40
2482 2633 3.247006 AGGTTGAGTGTATTACAGCGG 57.753 47.619 0.00 0.00 0.00 5.52
2486 2637 4.634443 GGTTGAGTGTATTACAGCGGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
2495 2646 8.086522 GTGTATTACAGCGGAAATATCCTAGAA 58.913 37.037 0.00 0.00 44.17 2.10
2507 2658 9.508642 GGAAATATCCTAGAATCTTAAGTTGGG 57.491 37.037 1.63 0.00 42.93 4.12
2509 2660 9.853177 AAATATCCTAGAATCTTAAGTTGGGTG 57.147 33.333 1.63 0.00 0.00 4.61
2515 2666 9.110502 CCTAGAATCTTAAGTTGGGTGTATTTC 57.889 37.037 1.63 0.00 0.00 2.17
2516 2667 9.667107 CTAGAATCTTAAGTTGGGTGTATTTCA 57.333 33.333 1.63 0.00 0.00 2.69
2576 2757 9.075678 TGTAAAATTTGCCAAATGAAATCCATT 57.924 25.926 2.91 0.00 46.86 3.16
2578 2759 6.518208 AATTTGCCAAATGAAATCCATTGG 57.482 33.333 2.91 0.00 44.28 3.16
2588 2769 7.543359 AATGAAATCCATTGGTTTGAGAAGA 57.457 32.000 1.86 0.00 43.46 2.87
2589 2770 6.975196 TGAAATCCATTGGTTTGAGAAGAA 57.025 33.333 1.86 0.00 0.00 2.52
2590 2771 6.985117 TGAAATCCATTGGTTTGAGAAGAAG 58.015 36.000 1.86 0.00 0.00 2.85
2591 2772 5.397142 AATCCATTGGTTTGAGAAGAAGC 57.603 39.130 1.86 0.00 0.00 3.86
2612 2793 2.959465 GGGGGTTGCTAGCATTCTAT 57.041 50.000 20.13 0.00 0.00 1.98
2613 2794 2.784347 GGGGGTTGCTAGCATTCTATC 58.216 52.381 20.13 3.17 0.00 2.08
2624 2806 5.411053 GCTAGCATTCTATCCCATCAAGTTC 59.589 44.000 10.63 0.00 0.00 3.01
2632 2814 9.736414 ATTCTATCCCATCAAGTTCAGAATATG 57.264 33.333 0.00 0.00 31.52 1.78
2657 2840 7.814107 TGAATCTGCCAACTTAAATTTGTGATC 59.186 33.333 0.00 0.00 0.00 2.92
2665 2848 5.003804 ACTTAAATTTGTGATCGAGGTGCT 58.996 37.500 0.00 0.00 0.00 4.40
2711 2894 3.840666 AGAAGAGGTGTGCAGAATCCTTA 59.159 43.478 0.00 0.00 0.00 2.69
2718 2901 4.395231 GGTGTGCAGAATCCTTAGTTAACC 59.605 45.833 0.88 0.00 0.00 2.85
2727 2910 1.208776 CCTTAGTTAACCAGACCGGGG 59.791 57.143 6.32 0.00 40.22 5.73
2730 2913 0.689055 AGTTAACCAGACCGGGGTTC 59.311 55.000 15.88 4.63 45.26 3.62
2731 2914 0.321919 GTTAACCAGACCGGGGTTCC 60.322 60.000 15.88 6.04 45.26 3.62
2734 2917 2.933834 CCAGACCGGGGTTCCCTT 60.934 66.667 6.32 0.00 42.67 3.95
2762 2953 2.311841 AGGTTAGGAGTGGGATTTTGGG 59.688 50.000 0.00 0.00 0.00 4.12
2763 2954 2.042569 GGTTAGGAGTGGGATTTTGGGT 59.957 50.000 0.00 0.00 0.00 4.51
2767 2960 3.197983 AGGAGTGGGATTTTGGGTATGA 58.802 45.455 0.00 0.00 0.00 2.15
2773 2966 3.270696 TGGGATTTTGGGTATGATGTGGA 59.729 43.478 0.00 0.00 0.00 4.02
2774 2967 4.264577 TGGGATTTTGGGTATGATGTGGAA 60.265 41.667 0.00 0.00 0.00 3.53
2779 2972 3.912496 TGGGTATGATGTGGAAGTCTG 57.088 47.619 0.00 0.00 0.00 3.51
2786 2979 3.701664 TGATGTGGAAGTCTGAGCTAGA 58.298 45.455 0.00 0.00 0.00 2.43
2811 3004 9.092876 GAGGTGTCAAATTTTGTTTTGTAATGA 57.907 29.630 8.89 0.00 37.73 2.57
2844 3037 7.398024 AGACAAGTGTTTATTCAGCTAATCCT 58.602 34.615 0.00 0.00 0.00 3.24
2845 3038 7.550906 AGACAAGTGTTTATTCAGCTAATCCTC 59.449 37.037 0.00 0.00 0.00 3.71
2846 3039 6.599638 ACAAGTGTTTATTCAGCTAATCCTCC 59.400 38.462 0.00 0.00 0.00 4.30
2859 3052 8.314751 TCAGCTAATCCTCCTAATATAGTTTGC 58.685 37.037 0.00 0.00 0.00 3.68
2900 3096 5.458015 TGGTGTATGATTAGTATCGCTTCG 58.542 41.667 0.00 0.00 33.23 3.79
2906 3102 5.389642 TGATTAGTATCGCTTCGCAAAAG 57.610 39.130 0.00 0.00 33.23 2.27
2909 3105 5.691508 TTAGTATCGCTTCGCAAAAGTAC 57.308 39.130 0.00 0.00 0.00 2.73
2910 3106 3.581755 AGTATCGCTTCGCAAAAGTACA 58.418 40.909 0.00 0.00 0.00 2.90
2914 3113 2.546368 TCGCTTCGCAAAAGTACAATGT 59.454 40.909 0.00 0.00 0.00 2.71
2915 3114 2.902484 CGCTTCGCAAAAGTACAATGTC 59.098 45.455 0.00 0.00 0.00 3.06
2925 3124 3.525800 AGTACAATGTCTTTTGCCCCT 57.474 42.857 0.00 0.00 0.00 4.79
2928 3127 0.897621 CAATGTCTTTTGCCCCTCCC 59.102 55.000 0.00 0.00 0.00 4.30
2930 3129 2.361230 GTCTTTTGCCCCTCCCCG 60.361 66.667 0.00 0.00 0.00 5.73
2933 3132 1.533033 CTTTTGCCCCTCCCCGTTT 60.533 57.895 0.00 0.00 0.00 3.60
2972 3171 7.716799 TTAATTGTATGCTCCCTTGATTGTT 57.283 32.000 0.00 0.00 0.00 2.83
2974 3173 7.902920 AATTGTATGCTCCCTTGATTGTTAT 57.097 32.000 0.00 0.00 0.00 1.89
2975 3174 6.698008 TTGTATGCTCCCTTGATTGTTATG 57.302 37.500 0.00 0.00 0.00 1.90
2976 3175 4.580167 TGTATGCTCCCTTGATTGTTATGC 59.420 41.667 0.00 0.00 0.00 3.14
2977 3176 3.084536 TGCTCCCTTGATTGTTATGCA 57.915 42.857 0.00 0.00 0.00 3.96
2979 3178 4.790937 TGCTCCCTTGATTGTTATGCATA 58.209 39.130 1.16 1.16 0.00 3.14
2980 3179 5.387788 TGCTCCCTTGATTGTTATGCATAT 58.612 37.500 7.36 0.00 0.00 1.78
2982 3181 6.324512 TGCTCCCTTGATTGTTATGCATATTT 59.675 34.615 7.36 0.00 0.00 1.40
2983 3182 7.505248 TGCTCCCTTGATTGTTATGCATATTTA 59.495 33.333 7.36 0.00 0.00 1.40
2984 3183 8.025445 GCTCCCTTGATTGTTATGCATATTTAG 58.975 37.037 7.36 0.00 0.00 1.85
2985 3184 8.995027 TCCCTTGATTGTTATGCATATTTAGT 57.005 30.769 7.36 0.00 0.00 2.24
2986 3185 9.420118 TCCCTTGATTGTTATGCATATTTAGTT 57.580 29.630 7.36 0.00 0.00 2.24
2996 3195 9.604626 GTTATGCATATTTAGTTCTCAATGAGC 57.395 33.333 7.36 0.00 0.00 4.26
2999 3198 6.038603 TGCATATTTAGTTCTCAATGAGCACC 59.961 38.462 9.32 0.00 0.00 5.01
3001 3200 5.886960 ATTTAGTTCTCAATGAGCACCAC 57.113 39.130 9.32 2.22 0.00 4.16
3002 3201 4.623932 TTAGTTCTCAATGAGCACCACT 57.376 40.909 9.32 8.84 0.00 4.00
3003 3202 3.051081 AGTTCTCAATGAGCACCACTC 57.949 47.619 9.32 0.00 46.45 3.51
3013 3212 2.210116 GAGCACCACTCAGAAAAACGA 58.790 47.619 0.00 0.00 45.49 3.85
3014 3213 2.612212 GAGCACCACTCAGAAAAACGAA 59.388 45.455 0.00 0.00 45.49 3.85
3015 3214 2.614057 AGCACCACTCAGAAAAACGAAG 59.386 45.455 0.00 0.00 0.00 3.79
3032 3238 3.751698 ACGAAGTTCCCAATTAGCACTTC 59.248 43.478 8.97 8.97 37.78 3.01
3042 3248 3.659183 ATTAGCACTTCCCATCAGCTT 57.341 42.857 0.00 0.00 36.80 3.74
3043 3249 2.408271 TAGCACTTCCCATCAGCTTG 57.592 50.000 0.00 0.00 36.80 4.01
3044 3250 0.403271 AGCACTTCCCATCAGCTTGT 59.597 50.000 0.00 0.00 29.98 3.16
3045 3251 0.807496 GCACTTCCCATCAGCTTGTC 59.193 55.000 0.00 0.00 0.00 3.18
3046 3252 1.883638 GCACTTCCCATCAGCTTGTCA 60.884 52.381 0.00 0.00 0.00 3.58
3047 3253 2.719739 CACTTCCCATCAGCTTGTCAT 58.280 47.619 0.00 0.00 0.00 3.06
3057 3263 5.121611 CCATCAGCTTGTCATTAACGTACAA 59.878 40.000 1.25 1.25 0.00 2.41
3061 3268 6.584942 TCAGCTTGTCATTAACGTACAACTAG 59.415 38.462 0.00 0.00 0.00 2.57
3066 3273 8.821147 TTGTCATTAACGTACAACTAGTGAAT 57.179 30.769 0.00 0.00 0.00 2.57
3070 3277 9.647797 TCATTAACGTACAACTAGTGAATCAAT 57.352 29.630 0.00 0.00 0.00 2.57
3130 3338 2.684104 TCTCGTGGGAGAGGGGAG 59.316 66.667 0.00 0.00 44.28 4.30
3131 3339 3.151022 CTCGTGGGAGAGGGGAGC 61.151 72.222 0.00 0.00 43.27 4.70
3132 3340 3.670629 CTCGTGGGAGAGGGGAGCT 62.671 68.421 0.00 0.00 43.27 4.09
3133 3341 3.465403 CGTGGGAGAGGGGAGCTG 61.465 72.222 0.00 0.00 0.00 4.24
3134 3342 3.791586 GTGGGAGAGGGGAGCTGC 61.792 72.222 0.00 0.00 0.00 5.25
3135 3343 4.337304 TGGGAGAGGGGAGCTGCA 62.337 66.667 7.79 0.00 0.00 4.41
3136 3344 3.478274 GGGAGAGGGGAGCTGCAG 61.478 72.222 10.11 10.11 0.00 4.41
3137 3345 2.686835 GGAGAGGGGAGCTGCAGT 60.687 66.667 16.64 1.59 0.00 4.40
3138 3346 2.583520 GAGAGGGGAGCTGCAGTG 59.416 66.667 16.64 0.00 0.00 3.66
3139 3347 3.007920 AGAGGGGAGCTGCAGTGG 61.008 66.667 16.64 0.00 0.00 4.00
3140 3348 3.005539 GAGGGGAGCTGCAGTGGA 61.006 66.667 16.64 0.00 0.00 4.02
3141 3349 2.285969 AGGGGAGCTGCAGTGGAT 60.286 61.111 16.64 0.00 0.00 3.41
3142 3350 2.191641 GGGGAGCTGCAGTGGATC 59.808 66.667 16.64 8.54 0.00 3.36
3143 3351 2.191641 GGGAGCTGCAGTGGATCC 59.808 66.667 16.64 16.51 38.41 3.36
3144 3352 2.202987 GGAGCTGCAGTGGATCCG 60.203 66.667 16.64 0.00 29.47 4.18
3145 3353 2.725312 GGAGCTGCAGTGGATCCGA 61.725 63.158 16.64 0.00 29.47 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.401674 CGTATGATGATATCCATGCAGATCG 59.598 44.000 0.00 0.00 35.17 3.69
59 68 4.814294 CGCTGTAGCCACGTCCCC 62.814 72.222 0.00 0.00 37.91 4.81
140 149 1.452108 CCCTCATTTCCCTCACCGC 60.452 63.158 0.00 0.00 0.00 5.68
144 153 2.552155 CGTTTCACCCTCATTTCCCTCA 60.552 50.000 0.00 0.00 0.00 3.86
147 156 2.084546 CTCGTTTCACCCTCATTTCCC 58.915 52.381 0.00 0.00 0.00 3.97
160 169 4.033243 ACACGTGGTTTACTTTCTCGTTTC 59.967 41.667 21.57 0.00 0.00 2.78
177 186 4.849883 TGTATTTTTACCAGCAACACGTG 58.150 39.130 15.48 15.48 0.00 4.49
178 187 5.502153 TTGTATTTTTACCAGCAACACGT 57.498 34.783 0.00 0.00 0.00 4.49
179 188 4.915085 CCTTGTATTTTTACCAGCAACACG 59.085 41.667 0.00 0.00 0.00 4.49
180 189 5.838529 ACCTTGTATTTTTACCAGCAACAC 58.161 37.500 0.00 0.00 0.00 3.32
196 210 4.600111 AGACCATAGAAACCCAACCTTGTA 59.400 41.667 0.00 0.00 0.00 2.41
202 216 4.394729 TCAACAGACCATAGAAACCCAAC 58.605 43.478 0.00 0.00 0.00 3.77
251 265 4.753516 TGGTTAGGTGGTCACTCATATG 57.246 45.455 0.00 0.00 0.00 1.78
255 269 3.392947 TCAAATGGTTAGGTGGTCACTCA 59.607 43.478 0.93 0.00 0.00 3.41
256 270 3.751698 GTCAAATGGTTAGGTGGTCACTC 59.248 47.826 0.93 0.00 0.00 3.51
263 277 0.808755 GCCGGTCAAATGGTTAGGTG 59.191 55.000 1.90 0.00 0.00 4.00
264 278 0.402504 TGCCGGTCAAATGGTTAGGT 59.597 50.000 1.90 0.00 0.00 3.08
272 286 2.270352 TTTCAGAGTGCCGGTCAAAT 57.730 45.000 1.90 0.00 0.00 2.32
282 296 7.173907 ACCAGAGTATTGTTTCATTTCAGAGTG 59.826 37.037 0.00 0.00 0.00 3.51
285 299 8.154203 TGTACCAGAGTATTGTTTCATTTCAGA 58.846 33.333 0.00 0.00 0.00 3.27
286 300 8.322906 TGTACCAGAGTATTGTTTCATTTCAG 57.677 34.615 0.00 0.00 0.00 3.02
287 301 7.094805 GCTGTACCAGAGTATTGTTTCATTTCA 60.095 37.037 0.00 0.00 32.44 2.69
289 303 6.128282 CGCTGTACCAGAGTATTGTTTCATTT 60.128 38.462 0.00 0.00 32.44 2.32
319 355 6.073112 GCCCTACACGAATTTAAAGTTGTACA 60.073 38.462 8.16 0.00 0.00 2.90
320 356 6.073112 TGCCCTACACGAATTTAAAGTTGTAC 60.073 38.462 8.16 0.00 0.00 2.90
336 372 2.628657 CCTACTATGTCCTGCCCTACAC 59.371 54.545 0.00 0.00 0.00 2.90
434 470 5.931294 TGAAAATTGAGGTGGTACAGTACA 58.069 37.500 12.89 0.00 41.80 2.90
436 472 5.766174 GGTTGAAAATTGAGGTGGTACAGTA 59.234 40.000 0.00 0.00 41.80 2.74
437 473 4.583073 GGTTGAAAATTGAGGTGGTACAGT 59.417 41.667 0.00 0.00 41.80 3.55
438 474 4.022329 GGGTTGAAAATTGAGGTGGTACAG 60.022 45.833 0.00 0.00 41.80 2.74
439 475 3.892588 GGGTTGAAAATTGAGGTGGTACA 59.107 43.478 0.00 0.00 0.00 2.90
440 476 3.057806 CGGGTTGAAAATTGAGGTGGTAC 60.058 47.826 0.00 0.00 0.00 3.34
441 477 3.150767 CGGGTTGAAAATTGAGGTGGTA 58.849 45.455 0.00 0.00 0.00 3.25
442 478 1.960689 CGGGTTGAAAATTGAGGTGGT 59.039 47.619 0.00 0.00 0.00 4.16
452 488 4.134379 TGTACTGTACACGGGTTGAAAA 57.866 40.909 16.26 0.00 32.89 2.29
463 499 5.037383 TGATTGGTTTGGTGTACTGTACA 57.963 39.130 16.26 16.26 36.08 2.90
472 511 2.027929 ACCATGCATGATTGGTTTGGTG 60.028 45.455 28.31 8.80 43.73 4.17
480 519 6.441093 ACTTTGTACTACCATGCATGATTG 57.559 37.500 28.31 14.96 0.00 2.67
495 534 5.560953 GCAGTGTTTGAGATGGACTTTGTAC 60.561 44.000 0.00 0.00 0.00 2.90
496 535 4.515191 GCAGTGTTTGAGATGGACTTTGTA 59.485 41.667 0.00 0.00 0.00 2.41
497 536 3.316308 GCAGTGTTTGAGATGGACTTTGT 59.684 43.478 0.00 0.00 0.00 2.83
498 537 3.316029 TGCAGTGTTTGAGATGGACTTTG 59.684 43.478 0.00 0.00 0.00 2.77
499 538 3.554934 TGCAGTGTTTGAGATGGACTTT 58.445 40.909 0.00 0.00 0.00 2.66
500 539 3.213206 TGCAGTGTTTGAGATGGACTT 57.787 42.857 0.00 0.00 0.00 3.01
501 540 2.936919 TGCAGTGTTTGAGATGGACT 57.063 45.000 0.00 0.00 0.00 3.85
502 541 4.022935 TCAAATGCAGTGTTTGAGATGGAC 60.023 41.667 9.38 0.00 39.81 4.02
503 542 4.143543 TCAAATGCAGTGTTTGAGATGGA 58.856 39.130 9.38 0.00 39.81 3.41
504 543 4.508461 TCAAATGCAGTGTTTGAGATGG 57.492 40.909 9.38 0.00 39.81 3.51
509 548 5.335113 GCATACTCTCAAATGCAGTGTTTGA 60.335 40.000 12.19 12.19 46.19 2.69
510 549 4.855388 GCATACTCTCAAATGCAGTGTTTG 59.145 41.667 5.12 5.12 46.19 2.93
511 550 5.051891 GCATACTCTCAAATGCAGTGTTT 57.948 39.130 0.00 0.00 46.19 2.83
512 551 4.691860 GCATACTCTCAAATGCAGTGTT 57.308 40.909 0.00 0.00 46.19 3.32
519 558 6.238049 GCTTCTGTGTAGCATACTCTCAAATG 60.238 42.308 0.00 0.00 43.54 2.32
520 559 5.814705 GCTTCTGTGTAGCATACTCTCAAAT 59.185 40.000 0.00 0.00 43.54 2.32
521 560 5.047021 AGCTTCTGTGTAGCATACTCTCAAA 60.047 40.000 0.00 0.00 43.54 2.69
522 561 4.464244 AGCTTCTGTGTAGCATACTCTCAA 59.536 41.667 0.00 0.00 43.54 3.02
523 562 4.019858 AGCTTCTGTGTAGCATACTCTCA 58.980 43.478 0.00 0.00 43.54 3.27
524 563 4.647424 AGCTTCTGTGTAGCATACTCTC 57.353 45.455 0.00 0.00 43.54 3.20
525 564 5.413309 AAAGCTTCTGTGTAGCATACTCT 57.587 39.130 0.00 0.00 43.54 3.24
526 565 5.520649 GGTAAAGCTTCTGTGTAGCATACTC 59.479 44.000 0.00 0.00 43.54 2.59
527 566 5.046591 TGGTAAAGCTTCTGTGTAGCATACT 60.047 40.000 0.00 0.00 43.54 2.12
528 567 5.175859 TGGTAAAGCTTCTGTGTAGCATAC 58.824 41.667 0.00 0.00 43.42 2.39
529 568 5.186992 TCTGGTAAAGCTTCTGTGTAGCATA 59.813 40.000 0.00 0.00 41.11 3.14
530 569 4.020218 TCTGGTAAAGCTTCTGTGTAGCAT 60.020 41.667 0.00 0.00 41.11 3.79
531 570 3.323691 TCTGGTAAAGCTTCTGTGTAGCA 59.676 43.478 0.00 3.05 41.11 3.49
532 571 3.926616 TCTGGTAAAGCTTCTGTGTAGC 58.073 45.455 0.00 0.00 38.93 3.58
562 601 2.364324 TCACTGTAACTGAGCCGTTTCT 59.636 45.455 0.00 0.00 0.00 2.52
571 610 4.923415 TCTCAGATCCTCACTGTAACTGA 58.077 43.478 0.00 0.00 36.81 3.41
588 627 2.821991 ACACGGGACTCTTTTCTCAG 57.178 50.000 0.00 0.00 0.00 3.35
597 636 3.390003 TGTTTGGAACACGGGACTC 57.610 52.632 0.00 0.00 39.29 3.36
630 669 8.319143 TGAAACTCTGGCAGTAAAGTTTATAC 57.681 34.615 24.36 16.27 40.89 1.47
631 670 7.119262 GCTGAAACTCTGGCAGTAAAGTTTATA 59.881 37.037 24.36 17.73 40.89 0.98
632 671 6.072452 GCTGAAACTCTGGCAGTAAAGTTTAT 60.072 38.462 24.36 10.70 40.89 1.40
774 838 0.098905 TCCGAGACGAGAAAGATGCG 59.901 55.000 0.00 0.00 0.00 4.73
868 936 0.991920 GGTGGGATGGGAAGTGAGAA 59.008 55.000 0.00 0.00 0.00 2.87
869 937 0.119155 AGGTGGGATGGGAAGTGAGA 59.881 55.000 0.00 0.00 0.00 3.27
870 938 0.543749 GAGGTGGGATGGGAAGTGAG 59.456 60.000 0.00 0.00 0.00 3.51
871 939 1.264749 CGAGGTGGGATGGGAAGTGA 61.265 60.000 0.00 0.00 0.00 3.41
872 940 1.221840 CGAGGTGGGATGGGAAGTG 59.778 63.158 0.00 0.00 0.00 3.16
873 941 0.326618 ATCGAGGTGGGATGGGAAGT 60.327 55.000 0.00 0.00 0.00 3.01
891 964 4.521062 GCGGTCGGCAGAGCAGAT 62.521 66.667 16.14 0.00 44.60 2.90
913 986 0.755327 GAGGAGAGGAGTGGAGAGGC 60.755 65.000 0.00 0.00 0.00 4.70
949 1022 2.686816 GGTTCGTTCATGGCGTGGG 61.687 63.158 6.90 0.00 0.00 4.61
980 1053 1.957186 GTTGGTTCACGGCGTGCTA 60.957 57.895 33.59 21.16 32.98 3.49
981 1054 3.276846 GTTGGTTCACGGCGTGCT 61.277 61.111 33.59 0.00 32.98 4.40
983 1056 2.258013 ATGGTTGGTTCACGGCGTG 61.258 57.895 32.75 32.75 34.45 5.34
984 1057 2.112297 ATGGTTGGTTCACGGCGT 59.888 55.556 6.77 6.77 0.00 5.68
1035 1121 2.741211 GGGAACGACTTGACGCCC 60.741 66.667 0.00 0.00 36.70 6.13
1421 1507 2.758737 CGTAGGAGGCGGTTCCCT 60.759 66.667 0.00 0.00 38.02 4.20
1494 1580 1.313812 GGAAGACGGAGGAGAAGCGA 61.314 60.000 0.00 0.00 0.00 4.93
1775 1876 3.179265 CGTACTTGCCGGTGCTCG 61.179 66.667 1.90 0.00 38.71 5.03
2185 2298 2.173126 ATCAGCCTTACTCAGCTCCT 57.827 50.000 0.00 0.00 37.18 3.69
2329 2442 0.974383 GACGTCCAAAGGAAGGAGGA 59.026 55.000 3.51 0.00 42.19 3.71
2330 2443 0.977395 AGACGTCCAAAGGAAGGAGG 59.023 55.000 13.01 0.00 44.45 4.30
2331 2444 2.841442 AAGACGTCCAAAGGAAGGAG 57.159 50.000 13.01 0.00 35.56 3.69
2359 2472 1.002900 ACCGACGCAAATTTCACACTG 60.003 47.619 0.00 0.00 0.00 3.66
2374 2487 2.354821 GCAATATTTGGAGGACACCGAC 59.645 50.000 0.00 0.00 0.00 4.79
2379 2492 5.708736 TTAGAGGCAATATTTGGAGGACA 57.291 39.130 0.00 0.00 0.00 4.02
2432 2545 9.077885 TGAGAGCATTTCCAGTAACTTTTAAAT 57.922 29.630 0.00 0.00 0.00 1.40
2433 2546 8.458573 TGAGAGCATTTCCAGTAACTTTTAAA 57.541 30.769 0.00 0.00 0.00 1.52
2434 2547 8.635765 ATGAGAGCATTTCCAGTAACTTTTAA 57.364 30.769 0.00 0.00 0.00 1.52
2443 2556 6.100279 TCAACCTATATGAGAGCATTTCCAGT 59.900 38.462 0.00 0.00 35.94 4.00
2445 2558 6.100279 ACTCAACCTATATGAGAGCATTTCCA 59.900 38.462 10.27 0.00 45.74 3.53
2457 2570 6.586463 CCGCTGTAATACACTCAACCTATATG 59.414 42.308 0.00 0.00 0.00 1.78
2459 2572 5.829391 TCCGCTGTAATACACTCAACCTATA 59.171 40.000 0.00 0.00 0.00 1.31
2486 2637 7.989947 ACACCCAACTTAAGATTCTAGGATA 57.010 36.000 10.09 0.00 0.00 2.59
2495 2646 7.458397 TCACTGAAATACACCCAACTTAAGAT 58.542 34.615 10.09 0.00 0.00 2.40
2533 2684 0.040058 ACAATGCAGAGGCCATCCAA 59.960 50.000 5.01 0.00 40.13 3.53
2541 2692 4.567971 TGGCAAATTTTACAATGCAGAGG 58.432 39.130 0.00 0.00 40.51 3.69
2576 2757 0.250727 CCCCGCTTCTTCTCAAACCA 60.251 55.000 0.00 0.00 0.00 3.67
2578 2759 2.556286 CCCCCGCTTCTTCTCAAAC 58.444 57.895 0.00 0.00 0.00 2.93
2597 2778 4.645535 TGATGGGATAGAATGCTAGCAAC 58.354 43.478 23.54 18.25 34.73 4.17
2604 2785 5.371526 TCTGAACTTGATGGGATAGAATGC 58.628 41.667 0.00 0.00 0.00 3.56
2612 2793 7.718314 CAGATTCATATTCTGAACTTGATGGGA 59.282 37.037 0.00 0.00 46.37 4.37
2613 2794 7.521748 GCAGATTCATATTCTGAACTTGATGGG 60.522 40.741 7.02 0.00 46.37 4.00
2632 2814 7.008628 CGATCACAAATTTAAGTTGGCAGATTC 59.991 37.037 9.88 4.50 0.00 2.52
2665 2848 3.216800 GGAGCATGAGGTATTTGCATCA 58.783 45.455 0.00 0.00 38.84 3.07
2711 2894 0.689055 GAACCCCGGTCTGGTTAACT 59.311 55.000 12.93 0.00 45.93 2.24
2727 2910 4.476297 TCCTAACCTTTTTGGAAGGGAAC 58.524 43.478 9.42 0.00 41.71 3.62
2729 2912 3.725267 ACTCCTAACCTTTTTGGAAGGGA 59.275 43.478 9.42 0.00 41.71 4.20
2730 2913 3.826729 CACTCCTAACCTTTTTGGAAGGG 59.173 47.826 9.42 0.00 41.71 3.95
2731 2914 3.826729 CCACTCCTAACCTTTTTGGAAGG 59.173 47.826 3.35 3.35 41.04 3.46
2734 2917 3.057586 TCCCACTCCTAACCTTTTTGGA 58.942 45.455 0.00 0.00 39.71 3.53
2762 2953 4.399004 AGCTCAGACTTCCACATCATAC 57.601 45.455 0.00 0.00 0.00 2.39
2763 2954 5.449553 TCTAGCTCAGACTTCCACATCATA 58.550 41.667 0.00 0.00 0.00 2.15
2767 2960 3.030291 CCTCTAGCTCAGACTTCCACAT 58.970 50.000 0.00 0.00 0.00 3.21
2773 2966 3.162147 TGACACCTCTAGCTCAGACTT 57.838 47.619 0.00 0.00 0.00 3.01
2774 2967 2.889170 TGACACCTCTAGCTCAGACT 57.111 50.000 0.00 0.00 0.00 3.24
2779 2972 5.948992 ACAAAATTTGACACCTCTAGCTC 57.051 39.130 13.19 0.00 0.00 4.09
2786 2979 9.612066 ATCATTACAAAACAAAATTTGACACCT 57.388 25.926 13.19 0.00 41.73 4.00
2844 3037 7.073854 AGTACAGGAGGCAAACTATATTAGGA 58.926 38.462 0.00 0.00 0.00 2.94
2845 3038 7.304497 AGTACAGGAGGCAAACTATATTAGG 57.696 40.000 0.00 0.00 0.00 2.69
2846 3039 8.421784 TCAAGTACAGGAGGCAAACTATATTAG 58.578 37.037 0.00 0.00 0.00 1.73
2859 3052 4.256920 CACCAAATCTCAAGTACAGGAGG 58.743 47.826 12.24 2.07 0.00 4.30
2894 3090 7.696791 AAAAGACATTGTACTTTTGCGAAGCG 61.697 38.462 18.08 0.00 45.56 4.68
2906 3102 2.492088 GGAGGGGCAAAAGACATTGTAC 59.508 50.000 0.00 0.00 32.80 2.90
2909 3105 0.897621 GGGAGGGGCAAAAGACATTG 59.102 55.000 0.00 0.00 0.00 2.82
2910 3106 0.252239 GGGGAGGGGCAAAAGACATT 60.252 55.000 0.00 0.00 0.00 2.71
2914 3113 2.014033 AAACGGGGAGGGGCAAAAGA 62.014 55.000 0.00 0.00 0.00 2.52
2915 3114 1.532604 GAAACGGGGAGGGGCAAAAG 61.533 60.000 0.00 0.00 0.00 2.27
2921 3120 1.378514 CACATGAAACGGGGAGGGG 60.379 63.158 0.00 0.00 0.00 4.79
2922 3121 0.251165 AACACATGAAACGGGGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
2925 3124 2.577606 ATGAACACATGAAACGGGGA 57.422 45.000 0.00 0.00 0.00 4.81
2950 3149 7.685155 GCATAACAATCAAGGGAGCATACAATT 60.685 37.037 0.00 0.00 0.00 2.32
2951 3150 6.239120 GCATAACAATCAAGGGAGCATACAAT 60.239 38.462 0.00 0.00 0.00 2.71
2952 3151 5.067674 GCATAACAATCAAGGGAGCATACAA 59.932 40.000 0.00 0.00 0.00 2.41
2954 3153 4.580167 TGCATAACAATCAAGGGAGCATAC 59.420 41.667 0.00 0.00 0.00 2.39
2958 3157 5.972107 ATATGCATAACAATCAAGGGAGC 57.028 39.130 11.13 0.00 0.00 4.70
2960 3159 8.995027 ACTAAATATGCATAACAATCAAGGGA 57.005 30.769 11.13 0.00 0.00 4.20
2970 3169 9.604626 GCTCATTGAGAACTAAATATGCATAAC 57.395 33.333 17.87 0.00 0.00 1.89
2972 3171 8.777413 GTGCTCATTGAGAACTAAATATGCATA 58.223 33.333 17.87 9.27 35.44 3.14
2974 3173 6.038603 GGTGCTCATTGAGAACTAAATATGCA 59.961 38.462 21.56 4.97 38.25 3.96
2975 3174 6.038603 TGGTGCTCATTGAGAACTAAATATGC 59.961 38.462 21.56 5.79 38.25 3.14
2976 3175 7.281774 AGTGGTGCTCATTGAGAACTAAATATG 59.718 37.037 21.56 0.00 38.25 1.78
2977 3176 7.341805 AGTGGTGCTCATTGAGAACTAAATAT 58.658 34.615 21.56 3.42 38.25 1.28
2979 3178 5.564550 AGTGGTGCTCATTGAGAACTAAAT 58.435 37.500 21.56 9.28 38.25 1.40
2980 3179 4.973168 AGTGGTGCTCATTGAGAACTAAA 58.027 39.130 21.56 7.74 38.25 1.85
2982 3181 4.193826 GAGTGGTGCTCATTGAGAACTA 57.806 45.455 21.56 14.78 43.58 2.24
2983 3182 3.051081 GAGTGGTGCTCATTGAGAACT 57.949 47.619 21.56 15.19 43.58 3.01
2994 3193 2.325583 TCGTTTTTCTGAGTGGTGCT 57.674 45.000 0.00 0.00 0.00 4.40
2995 3194 2.354821 ACTTCGTTTTTCTGAGTGGTGC 59.645 45.455 0.00 0.00 0.00 5.01
2996 3195 4.495844 GGAACTTCGTTTTTCTGAGTGGTG 60.496 45.833 0.00 0.00 0.00 4.17
2999 3198 3.625764 TGGGAACTTCGTTTTTCTGAGTG 59.374 43.478 0.00 0.00 0.00 3.51
3001 3200 4.893424 TTGGGAACTTCGTTTTTCTGAG 57.107 40.909 0.00 0.00 0.00 3.35
3002 3201 5.845391 AATTGGGAACTTCGTTTTTCTGA 57.155 34.783 0.00 0.00 0.00 3.27
3003 3202 5.629435 GCTAATTGGGAACTTCGTTTTTCTG 59.371 40.000 0.00 0.00 0.00 3.02
3004 3203 5.300792 TGCTAATTGGGAACTTCGTTTTTCT 59.699 36.000 0.00 0.00 0.00 2.52
3005 3204 5.401376 GTGCTAATTGGGAACTTCGTTTTTC 59.599 40.000 0.00 0.00 0.00 2.29
3006 3205 5.068591 AGTGCTAATTGGGAACTTCGTTTTT 59.931 36.000 0.00 0.00 0.00 1.94
3009 3208 3.751518 AGTGCTAATTGGGAACTTCGTT 58.248 40.909 0.00 0.00 0.00 3.85
3010 3209 3.418684 AGTGCTAATTGGGAACTTCGT 57.581 42.857 0.00 0.00 0.00 3.85
3011 3210 3.127030 GGAAGTGCTAATTGGGAACTTCG 59.873 47.826 19.16 0.00 45.51 3.79
3013 3212 3.181423 TGGGAAGTGCTAATTGGGAACTT 60.181 43.478 6.39 6.39 35.46 2.66
3014 3213 2.378547 TGGGAAGTGCTAATTGGGAACT 59.621 45.455 0.00 0.00 0.00 3.01
3015 3214 2.802719 TGGGAAGTGCTAATTGGGAAC 58.197 47.619 0.00 0.00 0.00 3.62
3018 3217 2.954318 CTGATGGGAAGTGCTAATTGGG 59.046 50.000 0.00 0.00 0.00 4.12
3019 3218 2.360165 GCTGATGGGAAGTGCTAATTGG 59.640 50.000 0.00 0.00 0.00 3.16
3020 3219 3.285484 AGCTGATGGGAAGTGCTAATTG 58.715 45.455 0.00 0.00 31.71 2.32
3024 3230 1.630369 ACAAGCTGATGGGAAGTGCTA 59.370 47.619 0.00 0.00 33.28 3.49
3032 3238 3.009723 ACGTTAATGACAAGCTGATGGG 58.990 45.455 0.58 0.00 0.00 4.00
3042 3248 8.083462 TGATTCACTAGTTGTACGTTAATGACA 58.917 33.333 0.58 0.00 0.00 3.58
3043 3249 8.456904 TGATTCACTAGTTGTACGTTAATGAC 57.543 34.615 0.58 0.00 0.00 3.06
3044 3250 9.647797 ATTGATTCACTAGTTGTACGTTAATGA 57.352 29.630 0.58 0.00 0.00 2.57
3077 3284 7.272244 GCCTAATGTAGGGTTGCAAATAATTT 58.728 34.615 0.00 0.00 46.32 1.82
3080 3287 4.647399 GGCCTAATGTAGGGTTGCAAATAA 59.353 41.667 0.00 0.00 46.32 1.40
3082 3289 3.031013 GGCCTAATGTAGGGTTGCAAAT 58.969 45.455 0.00 0.00 46.32 2.32
3083 3290 2.452505 GGCCTAATGTAGGGTTGCAAA 58.547 47.619 0.00 0.00 46.32 3.68
3125 3333 2.191641 GATCCACTGCAGCTCCCC 59.808 66.667 15.27 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.