Multiple sequence alignment - TraesCS2A01G297700

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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 TraesCS2A01G297700 chr2A 100.000 3010 0 0 1 3010 511924525 511921516 0.000000e+00 5559
1 TraesCS2A01G297700 chr2A 91.200 125 11 0 2886 3010 505159816 505159940 1.430000e-38 171
2 TraesCS2A01G297700 chr2B 91.956 2362 91 35 520 2853 449121474 449119184 0.000000e+00 3217
3 TraesCS2A01G297700 chr2B 91.182 499 27 4 11 499 449121953 449121462 0.000000e+00 662
4 TraesCS2A01G297700 chr2D 91.454 2387 89 44 517 2853 377504421 377502100 0.000000e+00 3171
5 TraesCS2A01G297700 chr2D 94.024 502 21 4 1 498 377504903 377504407 0.000000e+00 752
6 TraesCS2A01G297700 chr5D 80.403 347 68 0 1565 1911 528230435 528230089 6.400000e-67 265
7 TraesCS2A01G297700 chr5A 80.352 341 67 0 1565 1905 656210529 656210189 2.980000e-65 259
8 TraesCS2A01G297700 chr5A 92.800 125 9 0 2886 3010 159668716 159668592 6.630000e-42 182
9 TraesCS2A01G297700 chr5A 90.400 125 12 0 2886 3010 510796571 510796695 6.680000e-37 165
10 TraesCS2A01G297700 chr5B 79.769 346 68 2 1567 1911 664998549 664998205 1.790000e-62 250
11 TraesCS2A01G297700 chr7A 92.000 125 10 0 2886 3010 419412577 419412453 3.080000e-40 176
12 TraesCS2A01G297700 chr7A 91.200 125 11 0 2886 3010 259321175 259321051 1.430000e-38 171
13 TraesCS2A01G297700 chr7A 91.057 123 11 0 2888 3010 175321966 175322088 1.860000e-37 167
14 TraesCS2A01G297700 chr3A 91.200 125 11 0 2886 3010 506628713 506628589 1.430000e-38 171
15 TraesCS2A01G297700 chr6A 89.600 125 13 0 2886 3010 571105599 571105475 3.110000e-35 159
16 TraesCS2A01G297700 chr1A 89.600 125 13 0 2886 3010 81944789 81944665 3.110000e-35 159


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 TraesCS2A01G297700 chr2A 511921516 511924525 3009 True 5559.0 5559 100.000 1 3010 1 chr2A.!!$R1 3009
1 TraesCS2A01G297700 chr2B 449119184 449121953 2769 True 1939.5 3217 91.569 11 2853 2 chr2B.!!$R1 2842
2 TraesCS2A01G297700 chr2D 377502100 377504903 2803 True 1961.5 3171 92.739 1 2853 2 chr2D.!!$R1 2852

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
493 508 0.388659 TGCAATGCAAGACACCAACC 59.611 50.0 5.01 0.0 34.76 3.77 F
1213 1246 0.396811 CTCCCTTGACGTCCAGGTTT 59.603 55.0 28.43 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1592 0.176680 GATGGTCACCTGCGTCAGAT 59.823 55.0 8.2 0.0 32.44 2.9 R
2568 2622 0.107508 CCGACCTCCAATGATGCTGT 60.108 55.0 0.0 0.0 0.00 4.4 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
332 347 3.944087 AGTTAGGCTTTGAGCGAAGAAT 58.056 40.909 0.00 0.00 43.62 2.40
357 372 1.873591 CAGTGTTTAACGGCTCTGCTT 59.126 47.619 0.00 0.00 0.00 3.91
433 448 1.786937 TGACAGGCCAACCACAAAAT 58.213 45.000 5.01 0.00 39.06 1.82
434 449 2.950781 TGACAGGCCAACCACAAAATA 58.049 42.857 5.01 0.00 39.06 1.40
436 451 3.320541 TGACAGGCCAACCACAAAATAAG 59.679 43.478 5.01 0.00 39.06 1.73
437 452 2.632512 ACAGGCCAACCACAAAATAAGG 59.367 45.455 5.01 0.00 39.06 2.69
491 506 2.442212 CATGCAATGCAAGACACCAA 57.558 45.000 13.45 0.00 43.62 3.67
492 507 2.063266 CATGCAATGCAAGACACCAAC 58.937 47.619 13.45 0.00 43.62 3.77
493 508 0.388659 TGCAATGCAAGACACCAACC 59.611 50.000 5.01 0.00 34.76 3.77
494 509 0.675633 GCAATGCAAGACACCAACCT 59.324 50.000 0.00 0.00 0.00 3.50
495 510 1.069049 GCAATGCAAGACACCAACCTT 59.931 47.619 0.00 0.00 0.00 3.50
496 511 2.863704 GCAATGCAAGACACCAACCTTC 60.864 50.000 0.00 0.00 0.00 3.46
497 512 2.361757 CAATGCAAGACACCAACCTTCA 59.638 45.455 0.00 0.00 0.00 3.02
498 513 2.363306 TGCAAGACACCAACCTTCAT 57.637 45.000 0.00 0.00 0.00 2.57
499 514 2.665165 TGCAAGACACCAACCTTCATT 58.335 42.857 0.00 0.00 0.00 2.57
500 515 3.030291 TGCAAGACACCAACCTTCATTT 58.970 40.909 0.00 0.00 0.00 2.32
501 516 3.450457 TGCAAGACACCAACCTTCATTTT 59.550 39.130 0.00 0.00 0.00 1.82
502 517 4.081198 TGCAAGACACCAACCTTCATTTTT 60.081 37.500 0.00 0.00 0.00 1.94
503 518 4.507756 GCAAGACACCAACCTTCATTTTTC 59.492 41.667 0.00 0.00 0.00 2.29
504 519 5.682212 GCAAGACACCAACCTTCATTTTTCT 60.682 40.000 0.00 0.00 0.00 2.52
505 520 6.340522 CAAGACACCAACCTTCATTTTTCTT 58.659 36.000 0.00 0.00 0.00 2.52
506 521 6.544928 AGACACCAACCTTCATTTTTCTTT 57.455 33.333 0.00 0.00 0.00 2.52
507 522 6.946340 AGACACCAACCTTCATTTTTCTTTT 58.054 32.000 0.00 0.00 0.00 2.27
508 523 7.394016 AGACACCAACCTTCATTTTTCTTTTT 58.606 30.769 0.00 0.00 0.00 1.94
509 524 8.536175 AGACACCAACCTTCATTTTTCTTTTTA 58.464 29.630 0.00 0.00 0.00 1.52
510 525 9.157104 GACACCAACCTTCATTTTTCTTTTTAA 57.843 29.630 0.00 0.00 0.00 1.52
511 526 9.508642 ACACCAACCTTCATTTTTCTTTTTAAA 57.491 25.926 0.00 0.00 0.00 1.52
512 527 9.767684 CACCAACCTTCATTTTTCTTTTTAAAC 57.232 29.630 0.00 0.00 0.00 2.01
513 528 9.508642 ACCAACCTTCATTTTTCTTTTTAAACA 57.491 25.926 0.00 0.00 0.00 2.83
514 529 9.986833 CCAACCTTCATTTTTCTTTTTAAACAG 57.013 29.630 0.00 0.00 0.00 3.16
515 530 9.986833 CAACCTTCATTTTTCTTTTTAAACAGG 57.013 29.630 1.66 0.00 0.00 4.00
516 531 9.952030 AACCTTCATTTTTCTTTTTAAACAGGA 57.048 25.926 1.66 0.00 0.00 3.86
517 532 9.599866 ACCTTCATTTTTCTTTTTAAACAGGAG 57.400 29.630 1.66 0.00 0.00 3.69
518 533 9.816354 CCTTCATTTTTCTTTTTAAACAGGAGA 57.184 29.630 1.66 0.00 0.00 3.71
580 599 0.946221 GACGCACTTGACCACCTGAG 60.946 60.000 0.00 0.00 0.00 3.35
581 600 1.367471 CGCACTTGACCACCTGAGA 59.633 57.895 0.00 0.00 0.00 3.27
674 700 4.616143 GCAGCGATCTCGGATTAACAGATA 60.616 45.833 1.34 0.00 40.23 1.98
695 721 8.849168 CAGATAGATAGATAGGTAAGCTCCATG 58.151 40.741 0.00 0.00 0.00 3.66
702 728 3.466314 TAAGCTCCATGCCGCCGA 61.466 61.111 0.00 0.00 44.23 5.54
744 770 3.124297 GCAGAAGAATCTTCGTCAGTTGG 59.876 47.826 16.35 2.99 38.01 3.77
825 851 4.577677 ATGCGCCACACCACACCA 62.578 61.111 4.18 0.00 0.00 4.17
828 854 3.582120 CGCCACACCACACCACAC 61.582 66.667 0.00 0.00 0.00 3.82
829 855 3.216292 GCCACACCACACCACACC 61.216 66.667 0.00 0.00 0.00 4.16
887 913 2.672098 CTATAGCCACTCCCACTCACT 58.328 52.381 0.00 0.00 0.00 3.41
894 920 2.680352 TCCCACTCACTCCGAGCC 60.680 66.667 0.00 0.00 46.63 4.70
927 953 1.128507 ACATGCTACACATCGCAAACG 59.871 47.619 0.00 0.00 39.89 3.60
938 964 3.670377 GCAAACGGCCACAGTCCC 61.670 66.667 2.24 0.00 36.11 4.46
941 967 4.643387 AACGGCCACAGTCCCAGC 62.643 66.667 2.24 0.00 0.00 4.85
951 977 3.086600 GTCCCAGCTAGCAGCCCT 61.087 66.667 18.83 0.00 43.77 5.19
959 985 1.893786 CTAGCAGCCCTTCACTCGT 59.106 57.895 0.00 0.00 0.00 4.18
961 987 0.815734 TAGCAGCCCTTCACTCGTAC 59.184 55.000 0.00 0.00 0.00 3.67
967 993 1.935300 GCCCTTCACTCGTACACACAG 60.935 57.143 0.00 0.00 0.00 3.66
969 995 2.351835 CCCTTCACTCGTACACACAGAG 60.352 54.545 0.00 0.00 37.96 3.35
972 998 2.847441 TCACTCGTACACACAGAGACT 58.153 47.619 2.23 0.00 36.03 3.24
973 999 2.548480 TCACTCGTACACACAGAGACTG 59.452 50.000 2.23 0.00 37.52 3.51
995 1028 1.211457 GCCCAGTTGATCAGATCAGGT 59.789 52.381 12.97 2.31 40.94 4.00
1213 1246 0.396811 CTCCCTTGACGTCCAGGTTT 59.603 55.000 28.43 0.00 0.00 3.27
1232 1265 5.878261 GTTTGCACATCTCAAACTTCTTG 57.122 39.130 10.32 0.00 45.77 3.02
1267 1300 2.741878 CGGACAGTTCACAGTTTGGTCT 60.742 50.000 0.00 0.00 0.00 3.85
1272 1305 3.809832 CAGTTCACAGTTTGGTCTTCGAT 59.190 43.478 0.00 0.00 0.00 3.59
1277 1310 2.105821 ACAGTTTGGTCTTCGATCCCAA 59.894 45.455 6.81 6.81 36.49 4.12
1278 1311 3.244911 ACAGTTTGGTCTTCGATCCCAAT 60.245 43.478 10.60 0.00 38.02 3.16
1280 1313 4.941263 CAGTTTGGTCTTCGATCCCAATTA 59.059 41.667 10.60 0.00 38.02 1.40
1281 1314 5.065218 CAGTTTGGTCTTCGATCCCAATTAG 59.935 44.000 10.60 2.60 38.02 1.73
1282 1315 3.838244 TGGTCTTCGATCCCAATTAGG 57.162 47.619 0.00 0.00 37.03 2.69
1283 1316 2.158813 TGGTCTTCGATCCCAATTAGGC 60.159 50.000 0.00 0.00 35.39 3.93
1284 1317 2.158813 GGTCTTCGATCCCAATTAGGCA 60.159 50.000 0.00 0.00 35.39 4.75
1285 1318 3.541632 GTCTTCGATCCCAATTAGGCAA 58.458 45.455 0.00 0.00 35.39 4.52
1286 1319 3.312697 GTCTTCGATCCCAATTAGGCAAC 59.687 47.826 0.00 0.00 35.39 4.17
1287 1320 3.054728 TCTTCGATCCCAATTAGGCAACA 60.055 43.478 0.00 0.00 41.41 3.33
1288 1321 3.358111 TCGATCCCAATTAGGCAACAA 57.642 42.857 0.00 0.00 41.41 2.83
1289 1322 3.278574 TCGATCCCAATTAGGCAACAAG 58.721 45.455 0.00 0.00 41.41 3.16
1314 1348 5.342259 GCACAAAATTAGTAAAAGCGACTGG 59.658 40.000 0.00 0.00 0.00 4.00
1383 1417 9.800572 AGAGCTACTATAGTTAGTGAATCATGA 57.199 33.333 11.40 0.00 39.08 3.07
1412 1446 8.079809 GCTAGTAGGAGTATGAGAGAATGTTTC 58.920 40.741 0.00 0.00 0.00 2.78
1485 1519 5.243954 TCGTAGTCAGCTAAGCATATCCAAT 59.756 40.000 0.00 0.00 0.00 3.16
1490 1524 6.604795 AGTCAGCTAAGCATATCCAATTTTGT 59.395 34.615 0.00 0.00 0.00 2.83
1491 1525 6.914757 GTCAGCTAAGCATATCCAATTTTGTC 59.085 38.462 0.00 0.00 0.00 3.18
1492 1526 6.602803 TCAGCTAAGCATATCCAATTTTGTCA 59.397 34.615 0.00 0.00 0.00 3.58
1514 1548 8.994170 TGTCATCACGAAATAAAGTACATTTCA 58.006 29.630 14.18 0.47 40.76 2.69
1554 1588 6.109156 TCTGAAACAGTATTTGCTCTGGTA 57.891 37.500 0.00 0.00 36.17 3.25
1555 1589 6.711277 TCTGAAACAGTATTTGCTCTGGTAT 58.289 36.000 0.00 0.00 36.17 2.73
1556 1590 7.847096 TCTGAAACAGTATTTGCTCTGGTATA 58.153 34.615 0.00 0.00 36.17 1.47
1557 1591 8.486210 TCTGAAACAGTATTTGCTCTGGTATAT 58.514 33.333 0.00 0.00 36.17 0.86
1558 1592 9.764363 CTGAAACAGTATTTGCTCTGGTATATA 57.236 33.333 0.00 0.00 36.17 0.86
1565 1599 8.462811 AGTATTTGCTCTGGTATATATCTGACG 58.537 37.037 0.00 0.00 0.00 4.35
2000 2034 2.654877 CCGTCCTACTGCACCGTT 59.345 61.111 0.00 0.00 0.00 4.44
2096 2130 8.506168 TTATTTGCAGGAGTAAATCTTGTAGG 57.494 34.615 0.00 0.00 40.04 3.18
2107 2141 7.402862 AGTAAATCTTGTAGGGTAGCAACAAT 58.597 34.615 11.14 2.10 33.01 2.71
2258 2297 5.534207 TTGTTTCTCATTTGGCAATCTGT 57.466 34.783 0.00 0.00 0.00 3.41
2262 2301 3.937814 TCTCATTTGGCAATCTGTACGT 58.062 40.909 0.00 0.00 0.00 3.57
2330 2372 0.036105 TGCATCTCAGTGTCCGCATT 60.036 50.000 0.00 0.00 0.00 3.56
2336 2378 1.208358 CAGTGTCCGCATTGCTGTG 59.792 57.895 7.12 0.00 0.00 3.66
2337 2379 1.227943 AGTGTCCGCATTGCTGTGT 60.228 52.632 7.12 0.00 0.00 3.72
2401 2447 7.814107 TGCAAAAGAGGAATGTACAATGATTTC 59.186 33.333 0.00 0.00 0.00 2.17
2414 2461 8.481314 TGTACAATGATTTCTTGAGCTAGAGAT 58.519 33.333 0.00 0.00 0.00 2.75
2431 2478 0.615331 GATGGAGAGTGACAGGCCAA 59.385 55.000 5.01 0.00 31.53 4.52
2432 2479 0.326264 ATGGAGAGTGACAGGCCAAC 59.674 55.000 5.01 0.00 31.53 3.77
2433 2480 1.374758 GGAGAGTGACAGGCCAACG 60.375 63.158 5.01 0.00 0.00 4.10
2434 2481 2.029844 GAGAGTGACAGGCCAACGC 61.030 63.158 5.01 2.03 0.00 4.84
2474 2521 4.834892 CGGAATTTGGCAGCGCGG 62.835 66.667 8.83 2.11 0.00 6.46
2529 2583 1.339438 CCAGTGTCACAGCCTAGCATT 60.339 52.381 5.62 0.00 0.00 3.56
2533 2587 1.554617 TGTCACAGCCTAGCATTAGCA 59.445 47.619 0.00 0.00 45.49 3.49
2537 2591 1.139853 ACAGCCTAGCATTAGCAGGTC 59.860 52.381 0.00 0.00 45.49 3.85
2559 2613 3.486043 CGACTGAGACTAAGGATCGTGTG 60.486 52.174 0.00 0.00 0.00 3.82
2560 2614 2.755655 ACTGAGACTAAGGATCGTGTGG 59.244 50.000 0.00 0.00 0.00 4.17
2568 2622 0.396435 AGGATCGTGTGGCAAACAGA 59.604 50.000 8.81 6.71 40.26 3.41
2593 2647 1.746615 CATTGGAGGTCGGCAGGTG 60.747 63.158 0.00 0.00 0.00 4.00
2637 2691 8.763049 AGCAAGTTTATTAGCCTGAAAAATTC 57.237 30.769 0.00 0.00 0.00 2.17
2656 2710 4.901123 CCCGCACCGACACACACA 62.901 66.667 0.00 0.00 0.00 3.72
2657 2711 3.636043 CCGCACCGACACACACAC 61.636 66.667 0.00 0.00 0.00 3.82
2671 2725 0.532640 ACACACGCATGACAGCTTCA 60.533 50.000 0.00 1.85 39.11 3.02
2673 2727 1.081892 ACACGCATGACAGCTTCATC 58.918 50.000 0.00 0.00 43.68 2.92
2823 2891 4.799473 CGTTGCTGCGCCGTGATG 62.799 66.667 4.18 0.00 0.00 3.07
2853 2921 1.595929 GGAAACACCGCTTCGACCA 60.596 57.895 0.00 0.00 0.00 4.02
2854 2922 1.566018 GGAAACACCGCTTCGACCAG 61.566 60.000 0.00 0.00 0.00 4.00
2855 2923 0.599204 GAAACACCGCTTCGACCAGA 60.599 55.000 0.00 0.00 0.00 3.86
2856 2924 0.179067 AAACACCGCTTCGACCAGAA 60.179 50.000 0.00 0.00 37.31 3.02
2857 2925 0.878961 AACACCGCTTCGACCAGAAC 60.879 55.000 0.00 0.00 34.66 3.01
2858 2926 1.300620 CACCGCTTCGACCAGAACA 60.301 57.895 0.00 0.00 34.66 3.18
2859 2927 0.878523 CACCGCTTCGACCAGAACAA 60.879 55.000 0.00 0.00 34.66 2.83
2860 2928 0.179067 ACCGCTTCGACCAGAACAAA 60.179 50.000 0.00 0.00 34.66 2.83
2861 2929 1.156736 CCGCTTCGACCAGAACAAAT 58.843 50.000 0.00 0.00 34.66 2.32
2862 2930 1.128692 CCGCTTCGACCAGAACAAATC 59.871 52.381 0.00 0.00 34.66 2.17
2863 2931 1.798223 CGCTTCGACCAGAACAAATCA 59.202 47.619 0.00 0.00 34.66 2.57
2864 2932 2.416547 CGCTTCGACCAGAACAAATCAT 59.583 45.455 0.00 0.00 34.66 2.45
2865 2933 3.120199 CGCTTCGACCAGAACAAATCATT 60.120 43.478 0.00 0.00 34.66 2.57
2866 2934 4.092821 CGCTTCGACCAGAACAAATCATTA 59.907 41.667 0.00 0.00 34.66 1.90
2867 2935 5.390461 CGCTTCGACCAGAACAAATCATTAA 60.390 40.000 0.00 0.00 34.66 1.40
2868 2936 5.795441 GCTTCGACCAGAACAAATCATTAAC 59.205 40.000 0.00 0.00 34.66 2.01
2869 2937 6.567701 GCTTCGACCAGAACAAATCATTAACA 60.568 38.462 0.00 0.00 34.66 2.41
2870 2938 6.236017 TCGACCAGAACAAATCATTAACAC 57.764 37.500 0.00 0.00 0.00 3.32
2871 2939 5.079406 CGACCAGAACAAATCATTAACACG 58.921 41.667 0.00 0.00 0.00 4.49
2872 2940 5.107259 CGACCAGAACAAATCATTAACACGA 60.107 40.000 0.00 0.00 0.00 4.35
2873 2941 6.402118 CGACCAGAACAAATCATTAACACGAT 60.402 38.462 0.00 0.00 0.00 3.73
2874 2942 6.611381 ACCAGAACAAATCATTAACACGATG 58.389 36.000 0.00 0.00 0.00 3.84
2875 2943 6.429692 ACCAGAACAAATCATTAACACGATGA 59.570 34.615 0.00 0.00 37.86 2.92
2876 2944 7.040755 ACCAGAACAAATCATTAACACGATGAA 60.041 33.333 0.00 0.00 37.11 2.57
2877 2945 7.970061 CCAGAACAAATCATTAACACGATGAAT 59.030 33.333 0.00 0.00 37.11 2.57
2878 2946 9.986833 CAGAACAAATCATTAACACGATGAATA 57.013 29.630 0.00 0.00 37.11 1.75
2879 2947 9.988350 AGAACAAATCATTAACACGATGAATAC 57.012 29.630 0.00 0.00 37.11 1.89
2880 2948 9.767684 GAACAAATCATTAACACGATGAATACA 57.232 29.630 0.00 0.00 37.11 2.29
2882 2950 9.720667 ACAAATCATTAACACGATGAATACATG 57.279 29.630 0.00 0.00 37.11 3.21
2883 2951 9.934190 CAAATCATTAACACGATGAATACATGA 57.066 29.630 0.00 0.00 37.11 3.07
2891 2959 7.848223 ACACGATGAATACATGAATTTCTCA 57.152 32.000 0.00 0.00 36.82 3.27
2892 2960 8.267620 ACACGATGAATACATGAATTTCTCAA 57.732 30.769 0.00 0.00 37.67 3.02
2893 2961 8.729756 ACACGATGAATACATGAATTTCTCAAA 58.270 29.630 0.00 0.00 37.67 2.69
2894 2962 9.003112 CACGATGAATACATGAATTTCTCAAAC 57.997 33.333 0.00 0.00 37.67 2.93
2895 2963 8.184192 ACGATGAATACATGAATTTCTCAAACC 58.816 33.333 0.00 0.00 37.67 3.27
2896 2964 7.374228 CGATGAATACATGAATTTCTCAAACCG 59.626 37.037 0.00 0.00 37.67 4.44
2897 2965 7.447374 TGAATACATGAATTTCTCAAACCGT 57.553 32.000 0.00 0.00 37.67 4.83
2898 2966 8.554835 TGAATACATGAATTTCTCAAACCGTA 57.445 30.769 0.00 0.00 37.67 4.02
2899 2967 9.004717 TGAATACATGAATTTCTCAAACCGTAA 57.995 29.630 0.00 0.00 37.67 3.18
2901 2969 9.787532 AATACATGAATTTCTCAAACCGTAATG 57.212 29.630 0.00 0.00 37.67 1.90
2902 2970 7.447374 ACATGAATTTCTCAAACCGTAATGA 57.553 32.000 0.00 0.00 37.67 2.57
2903 2971 7.305474 ACATGAATTTCTCAAACCGTAATGAC 58.695 34.615 0.00 0.00 37.67 3.06
2904 2972 6.465781 CATGAATTTCTCAAACCGTAATGACG 59.534 38.462 0.00 0.00 42.53 4.35
2905 2973 6.148811 ATGAATTTCTCAAACCGTAATGACGT 59.851 34.615 1.04 0.00 41.84 4.34
2906 2974 7.623506 ATGAATTTCTCAAACCGTAATGACGTC 60.624 37.037 9.11 9.11 41.84 4.34
2919 2987 7.745022 CGTAATGACGTCCATACTTCTTTAA 57.255 36.000 14.12 0.00 44.31 1.52
2920 2988 8.348983 CGTAATGACGTCCATACTTCTTTAAT 57.651 34.615 14.12 0.00 44.31 1.40
2921 2989 9.454585 CGTAATGACGTCCATACTTCTTTAATA 57.545 33.333 14.12 0.00 44.31 0.98
2926 2994 9.932207 TGACGTCCATACTTCTTTAATAGAAAA 57.068 29.630 14.12 0.00 42.19 2.29
2941 3009 4.397348 AAAAATGCTCGCCGGAGT 57.603 50.000 5.05 0.00 42.53 3.85
2942 3010 3.543884 AAAAATGCTCGCCGGAGTA 57.456 47.368 5.05 0.00 42.53 2.59
2943 3011 2.038387 AAAAATGCTCGCCGGAGTAT 57.962 45.000 5.05 0.00 46.01 2.12
2944 3012 2.902705 AAAATGCTCGCCGGAGTATA 57.097 45.000 5.05 0.00 43.70 1.47
2945 3013 3.402628 AAAATGCTCGCCGGAGTATAT 57.597 42.857 5.05 0.00 43.70 0.86
2946 3014 2.656560 AATGCTCGCCGGAGTATATC 57.343 50.000 5.05 0.00 43.70 1.63
2947 3015 0.818296 ATGCTCGCCGGAGTATATCC 59.182 55.000 5.05 0.00 42.83 2.59
2957 3025 3.859411 GGAGTATATCCGAAGAGGCTG 57.141 52.381 0.00 0.00 38.67 4.85
2958 3026 2.094442 GGAGTATATCCGAAGAGGCTGC 60.094 54.545 0.00 0.00 38.67 5.25
2959 3027 1.896465 AGTATATCCGAAGAGGCTGCC 59.104 52.381 11.65 11.65 40.77 4.85
2960 3028 0.888619 TATATCCGAAGAGGCTGCCG 59.111 55.000 13.96 0.13 40.77 5.69
2961 3029 1.115930 ATATCCGAAGAGGCTGCCGT 61.116 55.000 13.96 1.28 40.77 5.68
2962 3030 1.327690 TATCCGAAGAGGCTGCCGTT 61.328 55.000 13.96 11.09 40.77 4.44
2963 3031 2.579684 ATCCGAAGAGGCTGCCGTTC 62.580 60.000 20.60 20.60 40.77 3.95
2964 3032 2.048222 CGAAGAGGCTGCCGTTCA 60.048 61.111 26.26 0.00 0.00 3.18
2965 3033 2.383527 CGAAGAGGCTGCCGTTCAC 61.384 63.158 26.26 13.72 0.00 3.18
2966 3034 2.357517 AAGAGGCTGCCGTTCACG 60.358 61.111 13.96 0.00 39.44 4.35
2972 3040 4.680237 CTGCCGTTCACGCCTCCA 62.680 66.667 0.00 0.00 38.18 3.86
2973 3041 3.958147 CTGCCGTTCACGCCTCCAT 62.958 63.158 0.00 0.00 38.18 3.41
2974 3042 3.195698 GCCGTTCACGCCTCCATC 61.196 66.667 0.00 0.00 38.18 3.51
2975 3043 2.264480 CCGTTCACGCCTCCATCA 59.736 61.111 0.00 0.00 38.18 3.07
2976 3044 1.811266 CCGTTCACGCCTCCATCAG 60.811 63.158 0.00 0.00 38.18 2.90
2977 3045 1.079819 CGTTCACGCCTCCATCAGT 60.080 57.895 0.00 0.00 0.00 3.41
2978 3046 1.078759 CGTTCACGCCTCCATCAGTC 61.079 60.000 0.00 0.00 0.00 3.51
2979 3047 1.078759 GTTCACGCCTCCATCAGTCG 61.079 60.000 0.00 0.00 0.00 4.18
2980 3048 2.202797 CACGCCTCCATCAGTCGG 60.203 66.667 0.00 0.00 0.00 4.79
2981 3049 3.461773 ACGCCTCCATCAGTCGGG 61.462 66.667 0.00 0.00 0.00 5.14
2982 3050 4.899239 CGCCTCCATCAGTCGGGC 62.899 72.222 0.00 0.00 39.43 6.13
2983 3051 3.474570 GCCTCCATCAGTCGGGCT 61.475 66.667 0.00 0.00 39.68 5.19
2984 3052 3.036429 GCCTCCATCAGTCGGGCTT 62.036 63.158 0.00 0.00 39.68 4.35
2985 3053 1.144936 CCTCCATCAGTCGGGCTTC 59.855 63.158 0.00 0.00 0.00 3.86
2986 3054 1.617018 CCTCCATCAGTCGGGCTTCA 61.617 60.000 0.00 0.00 0.00 3.02
2987 3055 0.179089 CTCCATCAGTCGGGCTTCAG 60.179 60.000 0.00 0.00 0.00 3.02
2988 3056 1.153289 CCATCAGTCGGGCTTCAGG 60.153 63.158 0.00 0.00 0.00 3.86
2989 3057 1.153289 CATCAGTCGGGCTTCAGGG 60.153 63.158 0.00 0.00 0.00 4.45
2990 3058 3.036429 ATCAGTCGGGCTTCAGGGC 62.036 63.158 0.00 0.00 40.05 5.19
2997 3065 4.115199 GGCTTCAGGGCCGGACAT 62.115 66.667 11.00 0.00 42.82 3.06
2998 3066 2.742116 GGCTTCAGGGCCGGACATA 61.742 63.158 11.00 0.00 42.82 2.29
2999 3067 1.227674 GCTTCAGGGCCGGACATAG 60.228 63.158 11.00 0.00 0.00 2.23
3000 3068 1.686325 GCTTCAGGGCCGGACATAGA 61.686 60.000 11.00 0.00 0.00 1.98
3001 3069 0.390860 CTTCAGGGCCGGACATAGAG 59.609 60.000 11.00 0.00 0.00 2.43
3002 3070 1.048724 TTCAGGGCCGGACATAGAGG 61.049 60.000 11.00 0.00 0.00 3.69
3006 3074 3.224324 GCCGGACATAGAGGCGGA 61.224 66.667 5.05 0.00 41.53 5.54
3007 3075 2.792947 GCCGGACATAGAGGCGGAA 61.793 63.158 5.05 0.00 41.53 4.30
3008 3076 1.364171 CCGGACATAGAGGCGGAAG 59.636 63.158 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.142966 CGCGTACTAGTAGCATAGCACATA 60.143 45.833 18.33 0.00 0.00 2.29
8 9 3.365064 CGCGTACTAGTAGCATAGCACAT 60.365 47.826 18.33 0.00 0.00 3.21
116 127 2.285950 GCGCGCAATAATTTAGACCGAA 60.286 45.455 29.10 0.00 0.00 4.30
119 130 1.659211 CGGCGCGCAATAATTTAGACC 60.659 52.381 34.42 9.35 0.00 3.85
120 131 1.658968 CGGCGCGCAATAATTTAGAC 58.341 50.000 34.42 9.57 0.00 2.59
316 331 3.190535 TGGTTAATTCTTCGCTCAAAGCC 59.809 43.478 0.00 0.00 38.18 4.35
332 347 3.810941 CAGAGCCGTTAAACACTGGTTAA 59.189 43.478 0.00 0.00 35.82 2.01
371 386 5.008019 CGGTGCTGAAATTTCATACTGCTAT 59.992 40.000 20.76 0.00 36.46 2.97
375 390 3.127548 AGCGGTGCTGAAATTTCATACTG 59.872 43.478 25.51 25.51 37.57 2.74
420 435 3.860754 GCTGACCTTATTTTGTGGTTGGC 60.861 47.826 0.00 0.00 33.74 4.52
433 448 4.089361 TCTGAGAACATGAGCTGACCTTA 58.911 43.478 0.00 0.00 0.00 2.69
434 449 2.902486 TCTGAGAACATGAGCTGACCTT 59.098 45.455 0.00 0.00 0.00 3.50
436 451 3.260740 CTTCTGAGAACATGAGCTGACC 58.739 50.000 0.00 0.00 0.00 4.02
437 452 3.924144 ACTTCTGAGAACATGAGCTGAC 58.076 45.455 0.00 0.00 0.00 3.51
488 503 9.986833 CTGTTTAAAAAGAAAAATGAAGGTTGG 57.013 29.630 0.00 0.00 0.00 3.77
489 504 9.986833 CCTGTTTAAAAAGAAAAATGAAGGTTG 57.013 29.630 6.98 0.00 0.00 3.77
490 505 9.952030 TCCTGTTTAAAAAGAAAAATGAAGGTT 57.048 25.926 6.98 0.00 0.00 3.50
491 506 9.599866 CTCCTGTTTAAAAAGAAAAATGAAGGT 57.400 29.630 6.98 0.00 0.00 3.50
492 507 9.816354 TCTCCTGTTTAAAAAGAAAAATGAAGG 57.184 29.630 6.98 0.00 0.00 3.46
495 510 9.581099 GTGTCTCCTGTTTAAAAAGAAAAATGA 57.419 29.630 6.98 0.00 0.00 2.57
496 511 8.817100 GGTGTCTCCTGTTTAAAAAGAAAAATG 58.183 33.333 6.98 0.00 0.00 2.32
497 512 8.536175 TGGTGTCTCCTGTTTAAAAAGAAAAAT 58.464 29.630 6.98 0.00 37.07 1.82
498 513 7.897864 TGGTGTCTCCTGTTTAAAAAGAAAAA 58.102 30.769 6.98 0.00 37.07 1.94
499 514 7.469537 TGGTGTCTCCTGTTTAAAAAGAAAA 57.530 32.000 6.98 0.00 37.07 2.29
500 515 7.317390 GTTGGTGTCTCCTGTTTAAAAAGAAA 58.683 34.615 6.98 0.00 37.07 2.52
501 516 6.127563 GGTTGGTGTCTCCTGTTTAAAAAGAA 60.128 38.462 6.98 0.00 37.07 2.52
502 517 5.358725 GGTTGGTGTCTCCTGTTTAAAAAGA 59.641 40.000 6.98 0.00 37.07 2.52
503 518 5.359860 AGGTTGGTGTCTCCTGTTTAAAAAG 59.640 40.000 0.00 0.00 37.07 2.27
504 519 5.265989 AGGTTGGTGTCTCCTGTTTAAAAA 58.734 37.500 0.00 0.00 37.07 1.94
505 520 4.862371 AGGTTGGTGTCTCCTGTTTAAAA 58.138 39.130 0.00 0.00 37.07 1.52
506 521 4.513406 AGGTTGGTGTCTCCTGTTTAAA 57.487 40.909 0.00 0.00 37.07 1.52
507 522 4.080243 TGAAGGTTGGTGTCTCCTGTTTAA 60.080 41.667 0.00 0.00 37.07 1.52
508 523 3.456644 TGAAGGTTGGTGTCTCCTGTTTA 59.543 43.478 0.00 0.00 37.07 2.01
509 524 2.241176 TGAAGGTTGGTGTCTCCTGTTT 59.759 45.455 0.00 0.00 37.07 2.83
510 525 1.843851 TGAAGGTTGGTGTCTCCTGTT 59.156 47.619 0.00 0.00 37.07 3.16
511 526 1.507140 TGAAGGTTGGTGTCTCCTGT 58.493 50.000 0.00 0.00 37.07 4.00
512 527 2.867109 ATGAAGGTTGGTGTCTCCTG 57.133 50.000 0.00 0.00 37.07 3.86
513 528 3.521727 ACTATGAAGGTTGGTGTCTCCT 58.478 45.455 0.00 0.00 37.07 3.69
514 529 3.983044 ACTATGAAGGTTGGTGTCTCC 57.017 47.619 0.00 0.00 0.00 3.71
515 530 6.371825 CCTTTTACTATGAAGGTTGGTGTCTC 59.628 42.308 0.00 0.00 38.07 3.36
516 531 6.238648 CCTTTTACTATGAAGGTTGGTGTCT 58.761 40.000 0.00 0.00 38.07 3.41
517 532 6.496338 CCTTTTACTATGAAGGTTGGTGTC 57.504 41.667 0.00 0.00 38.07 3.67
580 599 2.287849 TGCGATTCACTCCGATCTCATC 60.288 50.000 0.00 0.00 0.00 2.92
581 600 1.683385 TGCGATTCACTCCGATCTCAT 59.317 47.619 0.00 0.00 0.00 2.90
612 631 0.952984 GAGTCTGGTGTGCTTCTGGC 60.953 60.000 0.00 0.00 42.22 4.85
651 677 1.789464 CTGTTAATCCGAGATCGCTGC 59.211 52.381 0.00 0.00 38.18 5.25
653 679 5.004448 TCTATCTGTTAATCCGAGATCGCT 58.996 41.667 0.00 0.00 38.18 4.93
674 700 4.714308 GGCATGGAGCTTACCTATCTATCT 59.286 45.833 0.00 0.00 44.79 1.98
702 728 3.330720 CTTCTTCCTGGGCCCCGT 61.331 66.667 22.27 0.00 0.00 5.28
825 851 1.404479 TTACACGCAGGAGGTGGTGT 61.404 55.000 1.12 1.12 41.06 4.16
826 852 0.036388 ATTACACGCAGGAGGTGGTG 60.036 55.000 0.00 0.00 39.69 4.17
827 853 0.249398 GATTACACGCAGGAGGTGGT 59.751 55.000 0.00 0.00 39.69 4.16
828 854 0.537188 AGATTACACGCAGGAGGTGG 59.463 55.000 0.00 0.00 39.69 4.61
829 855 3.735237 ATAGATTACACGCAGGAGGTG 57.265 47.619 0.00 0.00 41.15 4.00
887 913 2.348888 GGTCGAAGGAAGGCTCGGA 61.349 63.158 0.00 0.00 35.76 4.55
894 920 0.036010 AGCATGTGGGTCGAAGGAAG 60.036 55.000 0.00 0.00 0.00 3.46
927 953 2.586792 CTAGCTGGGACTGTGGCC 59.413 66.667 0.00 0.00 0.00 5.36
938 964 0.461693 GAGTGAAGGGCTGCTAGCTG 60.462 60.000 17.23 16.92 41.99 4.24
941 967 1.103803 TACGAGTGAAGGGCTGCTAG 58.896 55.000 0.00 0.00 0.00 3.42
951 977 3.003378 CAGTCTCTGTGTGTACGAGTGAA 59.997 47.826 0.00 0.00 32.80 3.18
959 985 1.257743 GGGCTCAGTCTCTGTGTGTA 58.742 55.000 0.00 0.00 32.61 2.90
961 987 0.037512 CTGGGCTCAGTCTCTGTGTG 60.038 60.000 5.06 0.00 36.30 3.82
972 998 2.169978 CTGATCTGATCAACTGGGCTCA 59.830 50.000 19.95 0.00 39.11 4.26
973 999 2.485124 CCTGATCTGATCAACTGGGCTC 60.485 54.545 19.95 0.00 39.11 4.70
983 1016 3.803021 GCTCATGGTGACCTGATCTGATC 60.803 52.174 10.72 10.72 0.00 2.92
984 1017 2.104451 GCTCATGGTGACCTGATCTGAT 59.896 50.000 2.11 0.00 0.00 2.90
985 1018 1.483827 GCTCATGGTGACCTGATCTGA 59.516 52.381 2.11 0.00 0.00 3.27
986 1019 1.208776 TGCTCATGGTGACCTGATCTG 59.791 52.381 2.11 0.00 0.00 2.90
987 1020 1.576577 TGCTCATGGTGACCTGATCT 58.423 50.000 2.11 0.00 0.00 2.75
995 1028 0.609957 CTTGCCCTTGCTCATGGTGA 60.610 55.000 0.00 0.00 38.71 4.02
1232 1265 5.179368 TGAACTGTCCGAGATGAATGAAAAC 59.821 40.000 0.00 0.00 0.00 2.43
1267 1300 3.358111 TGTTGCCTAATTGGGATCGAA 57.642 42.857 12.81 0.00 35.58 3.71
1272 1305 1.203112 TGCCTTGTTGCCTAATTGGGA 60.203 47.619 12.81 0.00 36.00 4.37
1277 1310 4.622260 ATTTTGTGCCTTGTTGCCTAAT 57.378 36.364 0.00 0.00 0.00 1.73
1278 1311 4.414337 AATTTTGTGCCTTGTTGCCTAA 57.586 36.364 0.00 0.00 0.00 2.69
1280 1313 3.387699 ACTAATTTTGTGCCTTGTTGCCT 59.612 39.130 0.00 0.00 0.00 4.75
1281 1314 3.727726 ACTAATTTTGTGCCTTGTTGCC 58.272 40.909 0.00 0.00 0.00 4.52
1282 1315 6.836577 TTTACTAATTTTGTGCCTTGTTGC 57.163 33.333 0.00 0.00 0.00 4.17
1283 1316 7.344441 GCTTTTACTAATTTTGTGCCTTGTTG 58.656 34.615 0.00 0.00 0.00 3.33
1284 1317 6.200097 CGCTTTTACTAATTTTGTGCCTTGTT 59.800 34.615 0.00 0.00 0.00 2.83
1285 1318 5.689961 CGCTTTTACTAATTTTGTGCCTTGT 59.310 36.000 0.00 0.00 0.00 3.16
1286 1319 5.918011 TCGCTTTTACTAATTTTGTGCCTTG 59.082 36.000 0.00 0.00 0.00 3.61
1287 1320 5.918576 GTCGCTTTTACTAATTTTGTGCCTT 59.081 36.000 0.00 0.00 0.00 4.35
1288 1321 5.240844 AGTCGCTTTTACTAATTTTGTGCCT 59.759 36.000 0.00 0.00 0.00 4.75
1289 1322 5.342259 CAGTCGCTTTTACTAATTTTGTGCC 59.658 40.000 0.00 0.00 0.00 5.01
1314 1348 4.547406 AAACAGAAACAGGACGCTAAAC 57.453 40.909 0.00 0.00 0.00 2.01
1383 1417 8.611257 ACATTCTCTCATACTCCTACTAGCTAT 58.389 37.037 0.00 0.00 0.00 2.97
1426 1460 5.458595 TCCCTCATACTGATGTAGTGATGT 58.541 41.667 0.00 0.00 40.65 3.06
1427 1461 6.410942 TTCCCTCATACTGATGTAGTGATG 57.589 41.667 0.00 0.00 40.65 3.07
1428 1462 7.015680 AGATTCCCTCATACTGATGTAGTGAT 58.984 38.462 0.00 0.00 40.65 3.06
1429 1463 6.377080 AGATTCCCTCATACTGATGTAGTGA 58.623 40.000 0.00 0.00 40.65 3.41
1430 1464 6.662865 AGATTCCCTCATACTGATGTAGTG 57.337 41.667 0.00 0.00 40.65 2.74
1431 1465 6.435904 GCTAGATTCCCTCATACTGATGTAGT 59.564 42.308 0.00 0.00 43.56 2.73
1432 1466 6.663093 AGCTAGATTCCCTCATACTGATGTAG 59.337 42.308 0.00 0.00 34.41 2.74
1433 1467 6.435591 CAGCTAGATTCCCTCATACTGATGTA 59.564 42.308 0.00 0.00 34.41 2.29
1537 1571 9.314133 TCAGATATATACCAGAGCAAATACTGT 57.686 33.333 0.00 0.00 32.93 3.55
1544 1578 4.522789 TGCGTCAGATATATACCAGAGCAA 59.477 41.667 0.00 0.00 0.00 3.91
1554 1588 3.230976 TGGTCACCTGCGTCAGATATAT 58.769 45.455 8.20 0.00 32.44 0.86
1555 1589 2.661718 TGGTCACCTGCGTCAGATATA 58.338 47.619 8.20 0.00 32.44 0.86
1556 1590 1.485124 TGGTCACCTGCGTCAGATAT 58.515 50.000 8.20 0.00 32.44 1.63
1557 1591 1.409064 GATGGTCACCTGCGTCAGATA 59.591 52.381 8.20 0.00 32.44 1.98
1558 1592 0.176680 GATGGTCACCTGCGTCAGAT 59.823 55.000 8.20 0.00 32.44 2.90
1565 1599 3.188786 GACGCGATGGTCACCTGC 61.189 66.667 15.93 0.00 36.91 4.85
1860 1894 2.563179 AGTTGACGAAGATGTGGTAGCT 59.437 45.455 0.00 0.00 0.00 3.32
1959 1993 0.233332 GTGAACTTGAGCGTGACTGC 59.767 55.000 0.00 0.00 0.00 4.40
1961 1995 1.215655 GCGTGAACTTGAGCGTGACT 61.216 55.000 0.00 0.00 0.00 3.41
1965 1999 2.598632 GCTGCGTGAACTTGAGCGT 61.599 57.895 0.00 0.00 0.00 5.07
2000 2034 2.353030 CGCGTCACTCACACGTCA 60.353 61.111 0.00 0.00 39.54 4.35
2156 2190 5.434408 AGCATTATTCTGCACAGATTCAGA 58.566 37.500 0.31 0.00 44.77 3.27
2215 2249 8.664669 AACAAATTTGATACTCAGGGGTAAAT 57.335 30.769 24.64 0.00 0.00 1.40
2216 2250 8.485578 AAACAAATTTGATACTCAGGGGTAAA 57.514 30.769 24.64 0.00 0.00 2.01
2258 2297 3.506096 CTCTGCTCGCCCGACGTA 61.506 66.667 0.00 0.00 44.19 3.57
2262 2301 2.113433 GTAGACTCTGCTCGCCCGA 61.113 63.158 0.00 0.00 0.00 5.14
2330 2372 3.167093 CACGTACGTGTACACAGCA 57.833 52.632 34.48 6.93 40.91 4.41
2401 2447 4.036734 GTCACTCTCCATCTCTAGCTCAAG 59.963 50.000 0.00 0.00 0.00 3.02
2414 2461 1.754745 GTTGGCCTGTCACTCTCCA 59.245 57.895 3.32 0.00 0.00 3.86
2479 2526 2.037136 CCCTTTGCACGGAGCTGAG 61.037 63.158 0.00 0.00 45.94 3.35
2480 2527 2.032528 CCCTTTGCACGGAGCTGA 59.967 61.111 0.00 0.00 45.94 4.26
2481 2528 3.741476 GCCCTTTGCACGGAGCTG 61.741 66.667 0.00 0.00 45.94 4.24
2529 2583 3.271729 CTTAGTCTCAGTCGACCTGCTA 58.728 50.000 13.01 5.48 41.25 3.49
2533 2587 3.547746 GATCCTTAGTCTCAGTCGACCT 58.452 50.000 13.01 4.11 34.46 3.85
2537 2591 2.678836 ACACGATCCTTAGTCTCAGTCG 59.321 50.000 0.00 0.00 0.00 4.18
2544 2598 2.380084 TTGCCACACGATCCTTAGTC 57.620 50.000 0.00 0.00 0.00 2.59
2559 2613 2.602878 CAATGATGCTGTCTGTTTGCC 58.397 47.619 0.00 0.00 0.00 4.52
2560 2614 2.229543 TCCAATGATGCTGTCTGTTTGC 59.770 45.455 0.00 0.00 0.00 3.68
2568 2622 0.107508 CCGACCTCCAATGATGCTGT 60.108 55.000 0.00 0.00 0.00 4.40
2770 2824 3.414700 CGCCTCCGTCACAAGTGC 61.415 66.667 0.00 0.00 0.00 4.40
2823 2891 2.808321 GTTTCCGTCCTCGTCGCC 60.808 66.667 0.00 0.00 35.01 5.54
2850 2918 6.429692 TCATCGTGTTAATGATTTGTTCTGGT 59.570 34.615 0.00 0.00 29.05 4.00
2853 2921 9.988350 GTATTCATCGTGTTAATGATTTGTTCT 57.012 29.630 0.00 0.00 33.36 3.01
2854 2922 9.767684 TGTATTCATCGTGTTAATGATTTGTTC 57.232 29.630 0.00 0.00 33.36 3.18
2856 2924 9.720667 CATGTATTCATCGTGTTAATGATTTGT 57.279 29.630 0.00 0.00 33.36 2.83
2857 2925 9.934190 TCATGTATTCATCGTGTTAATGATTTG 57.066 29.630 0.00 0.00 33.36 2.32
2865 2933 9.377312 TGAGAAATTCATGTATTCATCGTGTTA 57.623 29.630 0.00 0.00 31.15 2.41
2866 2934 8.267620 TGAGAAATTCATGTATTCATCGTGTT 57.732 30.769 0.00 0.00 31.15 3.32
2867 2935 7.848223 TGAGAAATTCATGTATTCATCGTGT 57.152 32.000 0.00 0.00 31.15 4.49
2868 2936 9.003112 GTTTGAGAAATTCATGTATTCATCGTG 57.997 33.333 0.00 0.00 35.27 4.35
2869 2937 8.184192 GGTTTGAGAAATTCATGTATTCATCGT 58.816 33.333 0.00 0.00 35.27 3.73
2870 2938 7.374228 CGGTTTGAGAAATTCATGTATTCATCG 59.626 37.037 0.00 0.00 35.27 3.84
2871 2939 8.184192 ACGGTTTGAGAAATTCATGTATTCATC 58.816 33.333 0.00 1.28 35.27 2.92
2872 2940 8.055279 ACGGTTTGAGAAATTCATGTATTCAT 57.945 30.769 0.00 0.00 35.27 2.57
2873 2941 7.447374 ACGGTTTGAGAAATTCATGTATTCA 57.553 32.000 0.00 0.00 35.27 2.57
2875 2943 9.787532 CATTACGGTTTGAGAAATTCATGTATT 57.212 29.630 0.00 0.00 35.27 1.89
2876 2944 9.173021 TCATTACGGTTTGAGAAATTCATGTAT 57.827 29.630 0.00 0.00 35.27 2.29
2877 2945 8.447833 GTCATTACGGTTTGAGAAATTCATGTA 58.552 33.333 0.00 0.00 35.27 2.29
2878 2946 7.305474 GTCATTACGGTTTGAGAAATTCATGT 58.695 34.615 0.00 0.00 35.27 3.21
2879 2947 6.465781 CGTCATTACGGTTTGAGAAATTCATG 59.534 38.462 0.00 0.00 45.50 3.07
2880 2948 6.542852 CGTCATTACGGTTTGAGAAATTCAT 58.457 36.000 0.00 0.00 45.50 2.57
2881 2949 5.922546 CGTCATTACGGTTTGAGAAATTCA 58.077 37.500 0.00 0.00 45.50 2.57
2900 2968 9.932207 TTTTCTATTAAAGAAGTATGGACGTCA 57.068 29.630 18.91 3.91 44.95 4.35
2924 2992 2.038387 ATACTCCGGCGAGCATTTTT 57.962 45.000 9.30 0.00 40.03 1.94
2925 2993 2.902705 TATACTCCGGCGAGCATTTT 57.097 45.000 9.30 0.00 40.03 1.82
2926 2994 2.353803 GGATATACTCCGGCGAGCATTT 60.354 50.000 9.30 0.00 40.03 2.32
2927 2995 1.204941 GGATATACTCCGGCGAGCATT 59.795 52.381 9.30 0.00 40.03 3.56
2928 2996 0.818296 GGATATACTCCGGCGAGCAT 59.182 55.000 9.30 2.86 40.03 3.79
2929 2997 2.264124 GGATATACTCCGGCGAGCA 58.736 57.895 9.30 0.00 40.03 4.26
2937 3005 2.094442 GCAGCCTCTTCGGATATACTCC 60.094 54.545 0.00 0.00 41.07 3.85
2938 3006 2.094442 GGCAGCCTCTTCGGATATACTC 60.094 54.545 3.29 0.00 33.16 2.59
2939 3007 1.896465 GGCAGCCTCTTCGGATATACT 59.104 52.381 3.29 0.00 33.16 2.12
2940 3008 1.402984 CGGCAGCCTCTTCGGATATAC 60.403 57.143 10.54 0.00 33.16 1.47
2941 3009 0.888619 CGGCAGCCTCTTCGGATATA 59.111 55.000 10.54 0.00 33.16 0.86
2942 3010 1.115930 ACGGCAGCCTCTTCGGATAT 61.116 55.000 10.54 0.00 33.16 1.63
2943 3011 1.327690 AACGGCAGCCTCTTCGGATA 61.328 55.000 10.54 0.00 33.16 2.59
2944 3012 2.579684 GAACGGCAGCCTCTTCGGAT 62.580 60.000 10.54 0.00 33.16 4.18
2945 3013 3.296709 GAACGGCAGCCTCTTCGGA 62.297 63.158 10.54 0.00 33.16 4.55
2946 3014 2.815647 GAACGGCAGCCTCTTCGG 60.816 66.667 10.54 0.00 0.00 4.30
2947 3015 2.048222 TGAACGGCAGCCTCTTCG 60.048 61.111 10.54 0.00 0.00 3.79
2948 3016 2.383527 CGTGAACGGCAGCCTCTTC 61.384 63.158 10.54 10.56 35.37 2.87
2949 3017 2.357517 CGTGAACGGCAGCCTCTT 60.358 61.111 10.54 0.00 35.37 2.85
2958 3026 1.811266 CTGATGGAGGCGTGAACGG 60.811 63.158 4.84 0.00 40.23 4.44
2959 3027 1.078759 GACTGATGGAGGCGTGAACG 61.079 60.000 0.00 0.00 43.27 3.95
2960 3028 2.755929 GACTGATGGAGGCGTGAAC 58.244 57.895 0.00 0.00 0.00 3.18
2966 3034 2.932130 GAAGCCCGACTGATGGAGGC 62.932 65.000 0.00 0.00 44.20 4.70
2967 3035 1.144936 GAAGCCCGACTGATGGAGG 59.855 63.158 0.00 0.00 0.00 4.30
2968 3036 0.179089 CTGAAGCCCGACTGATGGAG 60.179 60.000 0.00 0.00 0.00 3.86
2969 3037 1.617018 CCTGAAGCCCGACTGATGGA 61.617 60.000 0.00 0.00 0.00 3.41
2970 3038 1.153289 CCTGAAGCCCGACTGATGG 60.153 63.158 0.00 0.00 0.00 3.51
2971 3039 1.153289 CCCTGAAGCCCGACTGATG 60.153 63.158 0.00 0.00 0.00 3.07
2972 3040 3.036429 GCCCTGAAGCCCGACTGAT 62.036 63.158 0.00 0.00 0.00 2.90
2973 3041 3.706373 GCCCTGAAGCCCGACTGA 61.706 66.667 0.00 0.00 0.00 3.41
2981 3049 1.227674 CTATGTCCGGCCCTGAAGC 60.228 63.158 0.00 0.00 0.00 3.86
2982 3050 0.390860 CTCTATGTCCGGCCCTGAAG 59.609 60.000 0.00 0.00 0.00 3.02
2983 3051 1.048724 CCTCTATGTCCGGCCCTGAA 61.049 60.000 0.00 0.00 0.00 3.02
2984 3052 1.457643 CCTCTATGTCCGGCCCTGA 60.458 63.158 0.00 0.00 0.00 3.86
2985 3053 3.142393 CCTCTATGTCCGGCCCTG 58.858 66.667 0.00 0.00 0.00 4.45
2986 3054 2.844839 GCCTCTATGTCCGGCCCT 60.845 66.667 0.00 0.00 37.86 5.19
2987 3055 4.301027 CGCCTCTATGTCCGGCCC 62.301 72.222 0.00 0.00 40.70 5.80
2988 3056 4.301027 CCGCCTCTATGTCCGGCC 62.301 72.222 0.00 0.00 40.70 6.13
2989 3057 2.701163 CTTCCGCCTCTATGTCCGGC 62.701 65.000 0.00 0.00 40.49 6.13
2990 3058 1.364171 CTTCCGCCTCTATGTCCGG 59.636 63.158 0.00 0.00 41.97 5.14
2991 3059 1.300233 GCTTCCGCCTCTATGTCCG 60.300 63.158 0.00 0.00 0.00 4.79
2992 3060 4.760757 GCTTCCGCCTCTATGTCC 57.239 61.111 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.