Multiple sequence alignment - TraesCS3D01G025300

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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 TraesCS3D01G025300 chr3D 100.000 2840 0 0 1 2840 8563460 8566299 0.000000e+00 5245.0
1 TraesCS3D01G025300 chr3D 81.794 379 57 10 2200 2568 546665215 546664839 9.880000e-80 307.0
2 TraesCS3D01G025300 chr3D 84.571 175 18 6 661 833 431447810 431447643 6.290000e-37 165.0
3 TraesCS3D01G025300 chr3B 93.113 1728 80 17 926 2639 10406538 10408240 0.000000e+00 2495.0
4 TraesCS3D01G025300 chr3B 85.240 874 99 16 985 1851 10573438 10572588 0.000000e+00 872.0
5 TraesCS3D01G025300 chr3B 81.509 530 75 18 276 793 10405833 10406351 5.660000e-112 414.0
6 TraesCS3D01G025300 chr3B 76.077 418 72 20 106 512 797634511 797634911 2.890000e-45 193.0
7 TraesCS3D01G025300 chr6D 87.444 446 46 5 2202 2639 454998756 454999199 3.270000e-139 505.0
8 TraesCS3D01G025300 chr6D 81.301 369 57 9 2200 2559 456332295 456332660 3.580000e-74 289.0
9 TraesCS3D01G025300 chr7D 83.596 445 65 6 2202 2639 11916661 11916218 7.320000e-111 411.0
10 TraesCS3D01G025300 chr7D 83.467 375 50 10 2202 2567 592974630 592974259 3.500000e-89 339.0
11 TraesCS3D01G025300 chr6B 86.577 298 32 8 2197 2487 682642757 682643053 3.530000e-84 322.0
12 TraesCS3D01G025300 chr6B 84.762 315 37 6 2202 2507 228662550 228662862 3.550000e-79 305.0
13 TraesCS3D01G025300 chr6B 76.471 476 82 18 110 564 185112028 185111562 6.120000e-57 231.0
14 TraesCS3D01G025300 chr2B 81.283 374 59 10 2202 2567 17069646 17069276 2.770000e-75 292.0
15 TraesCS3D01G025300 chr2B 76.673 493 88 18 141 610 251106566 251107054 6.080000e-62 248.0
16 TraesCS3D01G025300 chr2B 74.919 614 93 28 92 672 786239325 786239910 1.020000e-54 224.0
17 TraesCS3D01G025300 chr2B 78.779 344 52 15 2232 2567 493231763 493232093 7.970000e-51 211.0
18 TraesCS3D01G025300 chr2B 84.106 151 21 3 672 822 41555701 41555554 2.950000e-30 143.0
19 TraesCS3D01G025300 chr2B 80.556 180 30 5 134 310 150346680 150346503 1.780000e-27 134.0
20 TraesCS3D01G025300 chr2B 90.769 65 6 0 544 608 113288236 113288172 1.400000e-13 87.9
21 TraesCS3D01G025300 chr1B 80.679 383 59 12 2196 2568 642674478 642674101 1.670000e-72 283.0
22 TraesCS3D01G025300 chr1A 76.128 532 96 22 105 614 56099527 56099005 1.690000e-62 250.0
23 TraesCS3D01G025300 chr1A 84.091 220 28 7 147 362 238209652 238209436 3.710000e-49 206.0
24 TraesCS3D01G025300 chr1A 88.148 135 13 2 661 793 331927591 331927458 1.050000e-34 158.0
25 TraesCS3D01G025300 chr5A 76.559 465 84 15 134 574 568358409 568358872 6.120000e-57 231.0
26 TraesCS3D01G025300 chr3A 75.103 486 78 24 136 610 458808643 458808190 1.340000e-43 187.0
27 TraesCS3D01G025300 chr3A 83.007 153 23 3 661 812 728617602 728617452 4.940000e-28 135.0
28 TraesCS3D01G025300 chr3A 96.875 32 1 0 547 578 42034018 42034049 1.000000e-03 54.7
29 TraesCS3D01G025300 chr2A 74.312 545 87 24 110 609 210038652 210039188 6.250000e-42 182.0
30 TraesCS3D01G025300 chr2D 86.585 164 20 1 672 833 50159126 50158963 2.250000e-41 180.0
31 TraesCS3D01G025300 chr2D 83.889 180 27 2 134 311 98719338 98719159 1.350000e-38 171.0
32 TraesCS3D01G025300 chr2D 82.781 151 25 1 460 610 636198400 636198549 1.780000e-27 134.0
33 TraesCS3D01G025300 chr2D 73.889 180 34 12 410 584 379698087 379698258 3.060000e-05 60.2
34 TraesCS3D01G025300 chr4B 78.929 280 42 12 92 360 626056366 626056639 1.050000e-39 174.0
35 TraesCS3D01G025300 chr7A 78.571 266 39 12 110 362 903835 903575 2.930000e-35 159.0
36 TraesCS3D01G025300 chr7A 83.851 161 23 2 454 614 92477601 92477444 1.760000e-32 150.0
37 TraesCS3D01G025300 chr7A 100.000 30 0 0 543 572 150447505 150447476 3.950000e-04 56.5
38 TraesCS3D01G025300 chr5B 81.443 194 32 4 661 852 127708635 127708444 3.790000e-34 156.0
39 TraesCS3D01G025300 chr4A 83.030 165 24 4 661 822 497093407 497093570 2.280000e-31 147.0
40 TraesCS3D01G025300 chr7B 85.926 135 17 1 661 793 107086232 107086366 2.950000e-30 143.0
41 TraesCS3D01G025300 chr7B 95.122 41 1 1 544 584 30378771 30378810 2.360000e-06 63.9
42 TraesCS3D01G025300 chr5D 85.106 141 16 5 180 318 42933663 42933526 3.820000e-29 139.0


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 TraesCS3D01G025300 chr3D 8563460 8566299 2839 False 5245.0 5245 100.000 1 2840 1 chr3D.!!$F1 2839
1 TraesCS3D01G025300 chr3B 10405833 10408240 2407 False 1454.5 2495 87.311 276 2639 2 chr3B.!!$F2 2363
2 TraesCS3D01G025300 chr3B 10572588 10573438 850 True 872.0 872 85.240 985 1851 1 chr3B.!!$R1 866
3 TraesCS3D01G025300 chr2B 786239325 786239910 585 False 224.0 224 74.919 92 672 1 chr2B.!!$F3 580
4 TraesCS3D01G025300 chr1A 56099005 56099527 522 True 250.0 250 76.128 105 614 1 chr1A.!!$R1 509

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
969 1147 0.860533 CAAAACCATTGCGCCAAGTG 59.139 50.0 4.18 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 2810 0.035458 CATCTACAATCGGGCCCCTC 59.965 60.0 18.66 0.0 0.0 4.3 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
236 239 7.489757 TCCTAAAATTTCAAAAACTGTTCGTGG 59.510 33.333 0.00 0.00 0.00 4.94
304 326 9.325150 CAGAAAATGATCATGCATTTCAAAAAC 57.675 29.630 23.63 6.01 45.09 2.43
310 332 5.886715 TCATGCATTTCAAAAACTGTTCG 57.113 34.783 0.00 0.00 0.00 3.95
311 333 4.744137 TCATGCATTTCAAAAACTGTTCGG 59.256 37.500 0.00 0.00 0.00 4.30
312 334 4.116747 TGCATTTCAAAAACTGTTCGGT 57.883 36.364 0.00 0.00 0.00 4.69
313 335 4.499183 TGCATTTCAAAAACTGTTCGGTT 58.501 34.783 0.00 0.00 0.00 4.44
314 336 4.328440 TGCATTTCAAAAACTGTTCGGTTG 59.672 37.500 0.00 0.00 0.00 3.77
315 337 4.564769 GCATTTCAAAAACTGTTCGGTTGA 59.435 37.500 9.06 9.06 0.00 3.18
316 338 5.062809 GCATTTCAAAAACTGTTCGGTTGAA 59.937 36.000 16.54 16.54 36.64 2.69
317 339 6.401581 GCATTTCAAAAACTGTTCGGTTGAAA 60.402 34.615 25.35 25.35 46.43 2.69
318 340 7.513968 CATTTCAAAAACTGTTCGGTTGAAAA 58.486 30.769 26.11 17.39 45.86 2.29
319 341 7.478520 TTTCAAAAACTGTTCGGTTGAAAAA 57.521 28.000 23.23 12.01 42.27 1.94
387 427 8.538409 AATGTTCACCTATTCAAGAAAAATGC 57.462 30.769 0.00 0.00 0.00 3.56
448 489 9.169592 TGCACATAGGATATATGTTGATGAATG 57.830 33.333 0.00 0.00 36.13 2.67
461 502 8.610248 ATGTTGATGAATGCAGAAAATTTTCA 57.390 26.923 28.00 12.45 39.61 2.69
463 504 9.708092 TGTTGATGAATGCAGAAAATTTTCATA 57.292 25.926 28.00 16.06 37.20 2.15
545 587 8.774586 ACCATTGCAGATATATTTACGAGTTTC 58.225 33.333 0.00 0.00 0.00 2.78
546 588 8.773645 CCATTGCAGATATATTTACGAGTTTCA 58.226 33.333 0.00 0.00 0.00 2.69
590 653 7.168972 TGAAAAATTGGTCATGATTTCACGAAC 59.831 33.333 13.36 0.00 31.36 3.95
622 709 3.889859 AGTGTATCATGGCCATTGGAT 57.110 42.857 17.92 18.85 0.00 3.41
630 717 7.557358 TGTATCATGGCCATTGGATATTATGAC 59.443 37.037 22.19 14.45 0.00 3.06
657 748 1.163420 TCTTCCGTTGCAATGCACGT 61.163 50.000 21.52 0.00 38.71 4.49
893 1048 1.073199 AAGGTTGTGGCCTTCCTCG 59.927 57.895 3.32 0.00 45.03 4.63
895 1050 3.423154 GTTGTGGCCTTCCTCGCG 61.423 66.667 3.32 0.00 0.00 5.87
901 1056 4.235762 GCCTTCCTCGCGCCCATA 62.236 66.667 0.00 0.00 0.00 2.74
902 1057 2.743718 CCTTCCTCGCGCCCATAT 59.256 61.111 0.00 0.00 0.00 1.78
903 1058 1.669115 CCTTCCTCGCGCCCATATG 60.669 63.158 0.00 0.00 0.00 1.78
904 1059 2.280797 TTCCTCGCGCCCATATGC 60.281 61.111 0.00 0.00 0.00 3.14
905 1060 3.825160 TTCCTCGCGCCCATATGCC 62.825 63.158 0.00 0.00 0.00 4.40
914 1069 4.217210 CCATATGCCCGCCCCCAA 62.217 66.667 0.00 0.00 0.00 4.12
916 1071 1.760086 CATATGCCCGCCCCCAAAA 60.760 57.895 0.00 0.00 0.00 2.44
918 1073 3.966930 TATGCCCGCCCCCAAAACC 62.967 63.158 0.00 0.00 0.00 3.27
921 1076 4.924187 CCCGCCCCCAAAACCACA 62.924 66.667 0.00 0.00 0.00 4.17
922 1077 3.611674 CCGCCCCCAAAACCACAC 61.612 66.667 0.00 0.00 0.00 3.82
923 1078 3.611674 CGCCCCCAAAACCACACC 61.612 66.667 0.00 0.00 0.00 4.16
924 1079 2.444895 GCCCCCAAAACCACACCA 60.445 61.111 0.00 0.00 0.00 4.17
965 1143 2.739784 CCCAAAACCATTGCGCCA 59.260 55.556 4.18 0.00 0.00 5.69
966 1144 1.070445 CCCAAAACCATTGCGCCAA 59.930 52.632 4.18 0.00 0.00 4.52
969 1147 0.860533 CAAAACCATTGCGCCAAGTG 59.139 50.000 4.18 0.00 0.00 3.16
978 1156 3.345808 CGCCAAGTGTGACGGTGG 61.346 66.667 0.00 0.00 33.15 4.61
1172 1356 2.149803 TACCAGTCCAACGTCCGCAG 62.150 60.000 0.00 0.00 0.00 5.18
1176 1360 3.936203 TCCAACGTCCGCAGCCTT 61.936 61.111 0.00 0.00 0.00 4.35
1179 1363 1.961277 CAACGTCCGCAGCCTTCTT 60.961 57.895 0.00 0.00 0.00 2.52
1371 1555 2.115052 AGGTGCATGGGCGTCAAA 59.885 55.556 0.00 0.00 45.35 2.69
1863 2050 1.885163 CGCCACCTACTTCTCCCGTT 61.885 60.000 0.00 0.00 0.00 4.44
1865 2052 0.535797 CCACCTACTTCTCCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
1902 2089 8.243426 CAGACTGCAGGTATTCTATCTTCTATC 58.757 40.741 19.93 0.00 0.00 2.08
1904 2091 9.456147 GACTGCAGGTATTCTATCTTCTATCTA 57.544 37.037 19.93 0.00 0.00 1.98
1905 2092 9.989296 ACTGCAGGTATTCTATCTTCTATCTAT 57.011 33.333 19.93 0.00 0.00 1.98
1940 2127 0.892755 ACTTGTTACCTGCCGATCGA 59.107 50.000 18.66 0.00 0.00 3.59
1951 2138 3.317150 CTGCCGATCGATTGCATACTTA 58.683 45.455 18.66 0.00 33.97 2.24
2019 2206 7.928908 TGACATTTTTATCTGCAACTTTGAC 57.071 32.000 0.00 0.00 0.00 3.18
2222 2410 0.179073 AGCATCATCAGCCACGTACC 60.179 55.000 0.00 0.00 0.00 3.34
2230 2418 3.795623 TCAGCCACGTACCTCTAATTC 57.204 47.619 0.00 0.00 0.00 2.17
2246 2434 1.838073 ATTCGACCCCTCAAACGCCT 61.838 55.000 0.00 0.00 0.00 5.52
2267 2455 4.034258 GACGCGTCCGGTCAGTGA 62.034 66.667 28.61 0.00 39.22 3.41
2268 2456 4.338539 ACGCGTCCGGTCAGTGAC 62.339 66.667 15.24 15.24 39.22 3.67
2299 2487 2.228103 CCGTTTTCAGCCCCTACTTTTC 59.772 50.000 0.00 0.00 0.00 2.29
2332 2526 7.095313 CGCAGCTCTCATATTTTTCTCATATGT 60.095 37.037 1.90 0.00 36.41 2.29
2355 2549 1.888512 GGTCACTTGCACATGATTGGT 59.111 47.619 0.00 0.00 0.00 3.67
2373 2567 4.119556 TGGTGGAGAAGAAGAGAGAGAA 57.880 45.455 0.00 0.00 0.00 2.87
2374 2568 4.483950 TGGTGGAGAAGAAGAGAGAGAAA 58.516 43.478 0.00 0.00 0.00 2.52
2416 2610 2.650226 AAAAAGGTGGTCCGGGGTGG 62.650 60.000 0.00 0.00 39.05 4.61
2429 2623 1.342672 GGGGTGGGGTCGTGTCATAT 61.343 60.000 0.00 0.00 0.00 1.78
2440 2634 1.929169 CGTGTCATATGTGGCAGACTG 59.071 52.381 0.00 0.00 41.38 3.51
2479 2673 1.530655 TCCGCGAGCCCTCATATCA 60.531 57.895 8.23 0.00 0.00 2.15
2493 2687 6.541641 GCCCTCATATCATCCTCATATTTGAC 59.458 42.308 0.00 0.00 0.00 3.18
2503 2697 9.828039 TCATCCTCATATTTGACATAGATATGC 57.172 33.333 0.00 0.00 37.19 3.14
2511 2705 1.276421 GACATAGATATGCGGGGTGCT 59.724 52.381 0.00 0.00 46.63 4.40
2512 2706 2.496070 GACATAGATATGCGGGGTGCTA 59.504 50.000 0.00 0.00 46.63 3.49
2516 2710 0.679505 GATATGCGGGGTGCTAGTCA 59.320 55.000 0.00 0.00 46.63 3.41
2531 2725 1.595929 GTCAGTCCGGGCGTTTGAA 60.596 57.895 0.00 0.00 0.00 2.69
2534 2728 0.673644 CAGTCCGGGCGTTTGAAGAT 60.674 55.000 0.00 0.00 0.00 2.40
2543 2737 4.152402 CGGGCGTTTGAAGATGGATATAAG 59.848 45.833 0.00 0.00 0.00 1.73
2545 2739 4.455877 GGCGTTTGAAGATGGATATAAGGG 59.544 45.833 0.00 0.00 0.00 3.95
2551 2745 2.834113 AGATGGATATAAGGGGTCCGG 58.166 52.381 0.00 0.00 34.72 5.14
2555 2749 2.332117 GGATATAAGGGGTCCGGTTGA 58.668 52.381 0.00 0.00 0.00 3.18
2589 2783 0.959372 ACCGGTCACTGACTAGACGG 60.959 60.000 17.92 17.92 35.63 4.79
2594 2788 2.152830 GTCACTGACTAGACGGTCTGT 58.847 52.381 20.58 15.34 44.92 3.41
2609 2803 2.027625 CTGTCCGGGCGTTTGAGAC 61.028 63.158 0.00 0.00 0.00 3.36
2616 2810 1.369625 GGGCGTTTGAGACAGGTATG 58.630 55.000 0.00 0.00 0.00 2.39
2622 2816 1.204146 TTGAGACAGGTATGAGGGGC 58.796 55.000 0.00 0.00 0.00 5.80
2624 2818 1.384643 AGACAGGTATGAGGGGCCC 60.385 63.158 17.12 17.12 0.00 5.80
2626 2820 2.445845 CAGGTATGAGGGGCCCGA 60.446 66.667 18.95 8.60 0.00 5.14
2639 2833 0.946221 GGCCCGATTGTAGATGCTCG 60.946 60.000 0.00 0.00 0.00 5.03
2640 2834 1.560860 GCCCGATTGTAGATGCTCGC 61.561 60.000 0.00 0.00 0.00 5.03
2641 2835 0.249447 CCCGATTGTAGATGCTCGCA 60.249 55.000 0.00 0.00 0.00 5.10
2642 2836 0.855349 CCGATTGTAGATGCTCGCAC 59.145 55.000 0.00 0.00 0.00 5.34
2643 2837 0.500178 CGATTGTAGATGCTCGCACG 59.500 55.000 0.00 0.00 0.00 5.34
2644 2838 1.840181 GATTGTAGATGCTCGCACGA 58.160 50.000 0.00 0.00 0.00 4.35
2645 2839 1.518929 GATTGTAGATGCTCGCACGAC 59.481 52.381 0.00 0.00 0.00 4.34
2646 2840 0.526211 TTGTAGATGCTCGCACGACT 59.474 50.000 0.00 0.00 0.00 4.18
2647 2841 0.098905 TGTAGATGCTCGCACGACTC 59.901 55.000 0.00 0.00 0.00 3.36
2648 2842 0.926174 GTAGATGCTCGCACGACTCG 60.926 60.000 0.00 0.00 0.00 4.18
2649 2843 2.648320 TAGATGCTCGCACGACTCGC 62.648 60.000 0.00 0.00 0.00 5.03
2656 2850 3.255379 GCACGACTCGCGAATCCC 61.255 66.667 12.49 0.00 44.57 3.85
2657 2851 2.949678 CACGACTCGCGAATCCCG 60.950 66.667 12.49 13.70 44.57 5.14
2658 2852 3.129502 ACGACTCGCGAATCCCGA 61.130 61.111 12.49 0.00 44.57 5.14
2659 2853 2.651232 CGACTCGCGAATCCCGAC 60.651 66.667 12.49 0.00 44.57 4.79
2660 2854 2.278661 GACTCGCGAATCCCGACC 60.279 66.667 11.33 0.00 41.76 4.79
2661 2855 3.769875 GACTCGCGAATCCCGACCC 62.770 68.421 11.33 0.00 41.76 4.46
2662 2856 3.528370 CTCGCGAATCCCGACCCT 61.528 66.667 11.33 0.00 41.76 4.34
2663 2857 3.774959 CTCGCGAATCCCGACCCTG 62.775 68.421 11.33 0.00 41.76 4.45
2664 2858 4.143333 CGCGAATCCCGACCCTGT 62.143 66.667 0.00 0.00 41.76 4.00
2665 2859 2.202892 GCGAATCCCGACCCTGTC 60.203 66.667 0.00 0.00 41.76 3.51
2674 2868 2.603776 GACCCTGTCGTCCCCTGT 60.604 66.667 0.00 0.00 0.00 4.00
2675 2869 2.923035 ACCCTGTCGTCCCCTGTG 60.923 66.667 0.00 0.00 0.00 3.66
2676 2870 3.706373 CCCTGTCGTCCCCTGTGG 61.706 72.222 0.00 0.00 0.00 4.17
2677 2871 2.923035 CCTGTCGTCCCCTGTGGT 60.923 66.667 0.00 0.00 34.77 4.16
2678 2872 2.516888 CCTGTCGTCCCCTGTGGTT 61.517 63.158 0.00 0.00 34.77 3.67
2679 2873 1.301716 CTGTCGTCCCCTGTGGTTG 60.302 63.158 0.00 0.00 34.77 3.77
2680 2874 2.032071 GTCGTCCCCTGTGGTTGG 59.968 66.667 0.00 0.00 34.77 3.77
2681 2875 2.446994 TCGTCCCCTGTGGTTGGT 60.447 61.111 0.00 0.00 34.77 3.67
2682 2876 2.281484 CGTCCCCTGTGGTTGGTG 60.281 66.667 0.00 0.00 34.77 4.17
2683 2877 2.923837 GTCCCCTGTGGTTGGTGT 59.076 61.111 0.00 0.00 34.77 4.16
2684 2878 1.229076 GTCCCCTGTGGTTGGTGTT 59.771 57.895 0.00 0.00 34.77 3.32
2685 2879 1.106944 GTCCCCTGTGGTTGGTGTTG 61.107 60.000 0.00 0.00 34.77 3.33
2686 2880 1.076339 CCCCTGTGGTTGGTGTTGT 60.076 57.895 0.00 0.00 0.00 3.32
2687 2881 1.391157 CCCCTGTGGTTGGTGTTGTG 61.391 60.000 0.00 0.00 0.00 3.33
2688 2882 1.391157 CCCTGTGGTTGGTGTTGTGG 61.391 60.000 0.00 0.00 0.00 4.17
2689 2883 1.391157 CCTGTGGTTGGTGTTGTGGG 61.391 60.000 0.00 0.00 0.00 4.61
2690 2884 0.682855 CTGTGGTTGGTGTTGTGGGT 60.683 55.000 0.00 0.00 0.00 4.51
2691 2885 0.251832 TGTGGTTGGTGTTGTGGGTT 60.252 50.000 0.00 0.00 0.00 4.11
2692 2886 0.458260 GTGGTTGGTGTTGTGGGTTC 59.542 55.000 0.00 0.00 0.00 3.62
2693 2887 1.032657 TGGTTGGTGTTGTGGGTTCG 61.033 55.000 0.00 0.00 0.00 3.95
2694 2888 0.748729 GGTTGGTGTTGTGGGTTCGA 60.749 55.000 0.00 0.00 0.00 3.71
2695 2889 0.661020 GTTGGTGTTGTGGGTTCGAG 59.339 55.000 0.00 0.00 0.00 4.04
2696 2890 1.098712 TTGGTGTTGTGGGTTCGAGC 61.099 55.000 0.00 0.00 0.00 5.03
2697 2891 2.258726 GGTGTTGTGGGTTCGAGCC 61.259 63.158 10.28 10.28 36.00 4.70
2698 2892 2.280524 TGTTGTGGGTTCGAGCCG 60.281 61.111 12.54 0.00 38.98 5.52
2699 2893 3.047877 GTTGTGGGTTCGAGCCGG 61.048 66.667 12.54 0.00 38.98 6.13
2700 2894 4.323477 TTGTGGGTTCGAGCCGGG 62.323 66.667 12.54 0.00 38.98 5.73
2724 2918 3.081409 GGCGCCAGGGGTCTCTAA 61.081 66.667 24.80 0.00 0.00 2.10
2725 2919 2.666098 GGCGCCAGGGGTCTCTAAA 61.666 63.158 24.80 0.00 0.00 1.85
2726 2920 1.153349 GCGCCAGGGGTCTCTAAAG 60.153 63.158 5.22 0.00 0.00 1.85
2727 2921 1.522569 CGCCAGGGGTCTCTAAAGG 59.477 63.158 0.00 0.00 0.00 3.11
2728 2922 1.915983 GCCAGGGGTCTCTAAAGGG 59.084 63.158 0.00 0.00 0.00 3.95
2729 2923 1.915983 CCAGGGGTCTCTAAAGGGC 59.084 63.158 0.00 0.00 0.00 5.19
2730 2924 0.621862 CCAGGGGTCTCTAAAGGGCT 60.622 60.000 0.00 0.00 0.00 5.19
2731 2925 1.344087 CCAGGGGTCTCTAAAGGGCTA 60.344 57.143 0.00 0.00 0.00 3.93
2732 2926 2.043227 CAGGGGTCTCTAAAGGGCTAG 58.957 57.143 0.00 0.00 0.00 3.42
2733 2927 1.938069 AGGGGTCTCTAAAGGGCTAGA 59.062 52.381 0.00 0.00 0.00 2.43
2734 2928 2.040939 GGGGTCTCTAAAGGGCTAGAC 58.959 57.143 0.00 0.00 38.08 2.59
2735 2929 2.626149 GGGGTCTCTAAAGGGCTAGACA 60.626 54.545 0.00 0.00 40.09 3.41
2736 2930 2.696187 GGGTCTCTAAAGGGCTAGACAG 59.304 54.545 0.00 0.00 40.09 3.51
2737 2931 2.696187 GGTCTCTAAAGGGCTAGACAGG 59.304 54.545 0.00 0.00 40.09 4.00
2738 2932 3.627747 GGTCTCTAAAGGGCTAGACAGGA 60.628 52.174 0.00 0.00 40.09 3.86
2739 2933 4.219919 GTCTCTAAAGGGCTAGACAGGAT 58.780 47.826 0.00 0.00 38.56 3.24
2740 2934 4.279922 GTCTCTAAAGGGCTAGACAGGATC 59.720 50.000 0.00 0.00 38.56 3.36
2741 2935 3.576550 CTCTAAAGGGCTAGACAGGATCC 59.423 52.174 2.48 2.48 0.00 3.36
2742 2936 2.577772 AAAGGGCTAGACAGGATCCT 57.422 50.000 9.02 9.02 0.00 3.24
2743 2937 2.095604 AAGGGCTAGACAGGATCCTC 57.904 55.000 12.69 1.33 0.00 3.71
2744 2938 0.178975 AGGGCTAGACAGGATCCTCG 60.179 60.000 12.69 10.40 0.00 4.63
2745 2939 0.468400 GGGCTAGACAGGATCCTCGT 60.468 60.000 12.69 13.76 0.00 4.18
2746 2940 0.671251 GGCTAGACAGGATCCTCGTG 59.329 60.000 12.69 4.37 38.16 4.35
2747 2941 0.671251 GCTAGACAGGATCCTCGTGG 59.329 60.000 12.69 2.85 36.65 4.94
2748 2942 0.671251 CTAGACAGGATCCTCGTGGC 59.329 60.000 12.69 3.85 40.40 5.01
2749 2943 1.101635 TAGACAGGATCCTCGTGGCG 61.102 60.000 12.69 1.57 44.48 5.69
2750 2944 3.432051 GACAGGATCCTCGTGGCGG 62.432 68.421 12.69 0.73 36.65 6.13
2751 2945 3.147595 CAGGATCCTCGTGGCGGA 61.148 66.667 12.69 0.00 34.52 5.54
2752 2946 2.123251 AGGATCCTCGTGGCGGAT 60.123 61.111 9.02 0.00 43.77 4.18
2753 2947 1.762460 AGGATCCTCGTGGCGGATT 60.762 57.895 9.02 0.00 41.24 3.01
2754 2948 1.146263 GGATCCTCGTGGCGGATTT 59.854 57.895 3.84 0.00 41.24 2.17
2755 2949 0.391597 GGATCCTCGTGGCGGATTTA 59.608 55.000 3.84 0.00 41.24 1.40
2756 2950 1.605712 GGATCCTCGTGGCGGATTTAG 60.606 57.143 3.84 0.00 41.24 1.85
2757 2951 1.068741 GATCCTCGTGGCGGATTTAGT 59.931 52.381 0.00 0.00 41.24 2.24
2758 2952 1.766494 TCCTCGTGGCGGATTTAGTA 58.234 50.000 0.00 0.00 0.00 1.82
2759 2953 1.406539 TCCTCGTGGCGGATTTAGTAC 59.593 52.381 0.00 0.00 0.00 2.73
2760 2954 1.135527 CCTCGTGGCGGATTTAGTACA 59.864 52.381 0.00 0.00 0.00 2.90
2761 2955 2.223971 CCTCGTGGCGGATTTAGTACAT 60.224 50.000 0.00 0.00 0.00 2.29
2762 2956 2.794910 CTCGTGGCGGATTTAGTACATG 59.205 50.000 0.00 0.00 0.00 3.21
2763 2957 1.864711 CGTGGCGGATTTAGTACATGG 59.135 52.381 0.00 0.00 0.00 3.66
2764 2958 1.602377 GTGGCGGATTTAGTACATGGC 59.398 52.381 0.00 0.00 0.00 4.40
2765 2959 1.210722 TGGCGGATTTAGTACATGGCA 59.789 47.619 0.00 0.00 0.00 4.92
2766 2960 1.602377 GGCGGATTTAGTACATGGCAC 59.398 52.381 0.00 0.00 0.00 5.01
2767 2961 1.260561 GCGGATTTAGTACATGGCACG 59.739 52.381 0.00 0.00 0.00 5.34
2768 2962 1.260561 CGGATTTAGTACATGGCACGC 59.739 52.381 0.00 0.00 0.00 5.34
2769 2963 2.561569 GGATTTAGTACATGGCACGCT 58.438 47.619 0.00 0.00 0.00 5.07
2770 2964 2.287915 GGATTTAGTACATGGCACGCTG 59.712 50.000 0.00 0.00 0.00 5.18
2771 2965 2.753055 TTTAGTACATGGCACGCTGA 57.247 45.000 0.00 0.00 0.00 4.26
2772 2966 2.293677 TTAGTACATGGCACGCTGAG 57.706 50.000 0.00 0.00 0.00 3.35
2773 2967 0.179111 TAGTACATGGCACGCTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
2788 2982 2.410466 GAGCGAGATCGTTCTCCCT 58.590 57.895 16.05 12.99 44.76 4.20
2789 2983 0.309612 GAGCGAGATCGTTCTCCCTC 59.690 60.000 17.87 17.87 44.76 4.30
2790 2984 0.106918 AGCGAGATCGTTCTCCCTCT 60.107 55.000 16.05 9.06 44.76 3.69
2791 2985 1.141254 AGCGAGATCGTTCTCCCTCTA 59.859 52.381 16.05 0.00 44.76 2.43
2792 2986 1.948145 GCGAGATCGTTCTCCCTCTAA 59.052 52.381 16.05 0.00 44.76 2.10
2793 2987 2.031508 GCGAGATCGTTCTCCCTCTAAG 60.032 54.545 16.05 3.61 44.76 2.18
2794 2988 3.468770 CGAGATCGTTCTCCCTCTAAGA 58.531 50.000 16.05 0.00 44.76 2.10
2795 2989 3.878103 CGAGATCGTTCTCCCTCTAAGAA 59.122 47.826 16.05 0.00 44.76 2.52
2796 2990 4.024387 CGAGATCGTTCTCCCTCTAAGAAG 60.024 50.000 16.05 0.00 44.76 2.85
2797 2991 5.118729 AGATCGTTCTCCCTCTAAGAAGA 57.881 43.478 0.00 0.00 33.57 2.87
2798 2992 5.238650 GAGATCGTTCTCCCTCTAAGAAGAG 59.761 48.000 11.73 0.00 42.46 2.85
2809 3003 5.337578 CTCTAAGAAGAGGGAACAAGAGG 57.662 47.826 0.00 0.00 44.82 3.69
2810 3004 4.097418 TCTAAGAAGAGGGAACAAGAGGG 58.903 47.826 0.00 0.00 0.00 4.30
2811 3005 2.723530 AGAAGAGGGAACAAGAGGGA 57.276 50.000 0.00 0.00 0.00 4.20
2812 3006 3.213160 AGAAGAGGGAACAAGAGGGAT 57.787 47.619 0.00 0.00 0.00 3.85
2813 3007 3.111484 AGAAGAGGGAACAAGAGGGATC 58.889 50.000 0.00 0.00 0.00 3.36
2814 3008 1.886422 AGAGGGAACAAGAGGGATCC 58.114 55.000 1.92 1.92 0.00 3.36
2815 3009 1.081174 AGAGGGAACAAGAGGGATCCA 59.919 52.381 15.23 0.00 33.48 3.41
2816 3010 1.488393 GAGGGAACAAGAGGGATCCAG 59.512 57.143 15.23 0.00 33.48 3.86
2817 3011 1.081174 AGGGAACAAGAGGGATCCAGA 59.919 52.381 15.23 0.00 33.48 3.86
2818 3012 1.488393 GGGAACAAGAGGGATCCAGAG 59.512 57.143 15.23 0.64 33.48 3.35
2819 3013 2.192263 GGAACAAGAGGGATCCAGAGT 58.808 52.381 15.23 1.31 32.08 3.24
2820 3014 2.093235 GGAACAAGAGGGATCCAGAGTG 60.093 54.545 15.23 8.54 32.08 3.51
2821 3015 0.908198 ACAAGAGGGATCCAGAGTGC 59.092 55.000 15.23 0.00 0.00 4.40
2822 3016 0.179936 CAAGAGGGATCCAGAGTGCC 59.820 60.000 15.23 0.00 0.00 5.01
2823 3017 0.985490 AAGAGGGATCCAGAGTGCCC 60.985 60.000 15.23 0.00 41.00 5.36
2824 3018 1.690633 GAGGGATCCAGAGTGCCCA 60.691 63.158 15.23 0.00 43.20 5.36
2825 3019 1.977293 GAGGGATCCAGAGTGCCCAC 61.977 65.000 15.23 0.00 43.20 4.61
2826 3020 2.592308 GGATCCAGAGTGCCCACC 59.408 66.667 6.95 0.00 0.00 4.61
2827 3021 2.592308 GATCCAGAGTGCCCACCC 59.408 66.667 0.00 0.00 0.00 4.61
2828 3022 2.204136 ATCCAGAGTGCCCACCCA 60.204 61.111 0.00 0.00 0.00 4.51
2829 3023 1.620589 ATCCAGAGTGCCCACCCAT 60.621 57.895 0.00 0.00 0.00 4.00
2830 3024 1.929860 ATCCAGAGTGCCCACCCATG 61.930 60.000 0.00 0.00 0.00 3.66
2831 3025 2.753043 CAGAGTGCCCACCCATGC 60.753 66.667 0.00 0.00 0.00 4.06
2832 3026 4.052518 AGAGTGCCCACCCATGCC 62.053 66.667 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 220 3.859411 AGCCACGAACAGTTTTTGAAA 57.141 38.095 0.00 0.00 0.00 2.69
250 253 8.512966 TCACCGGACATTTTATGAATTGATAA 57.487 30.769 9.46 0.00 0.00 1.75
254 257 7.257003 TGAATCACCGGACATTTTATGAATTG 58.743 34.615 9.46 0.00 0.00 2.32
255 258 7.339212 TCTGAATCACCGGACATTTTATGAATT 59.661 33.333 9.46 0.00 0.00 2.17
269 272 5.516996 CATGATCATTTTCTGAATCACCGG 58.483 41.667 5.16 0.00 37.44 5.28
272 275 8.420374 AAATGCATGATCATTTTCTGAATCAC 57.580 30.769 5.16 0.00 42.21 3.06
319 341 8.882736 GGAACAATTTCTGAAATTCACAAACTT 58.117 29.630 22.00 7.84 38.97 2.66
320 342 8.040132 TGGAACAATTTCTGAAATTCACAAACT 58.960 29.630 22.00 0.35 38.97 2.66
321 343 8.116136 GTGGAACAATTTCTGAAATTCACAAAC 58.884 33.333 25.10 17.78 44.16 2.93
322 344 7.279758 GGTGGAACAATTTCTGAAATTCACAAA 59.720 33.333 27.95 14.85 44.16 2.83
323 345 6.760770 GGTGGAACAATTTCTGAAATTCACAA 59.239 34.615 27.95 15.65 44.16 3.33
324 346 6.127225 TGGTGGAACAATTTCTGAAATTCACA 60.127 34.615 27.95 20.20 44.16 3.58
426 466 9.609346 TCTGCATTCATCAACATATATCCTATG 57.391 33.333 0.00 0.00 0.00 2.23
513 554 9.729023 CGTAAATATATCTGCAATGGTGAAAAA 57.271 29.630 0.00 0.00 0.00 1.94
571 613 4.819088 TCAAGTTCGTGAAATCATGACCAA 59.181 37.500 0.00 0.00 41.18 3.67
574 618 5.406780 ACTCTCAAGTTCGTGAAATCATGAC 59.593 40.000 0.00 2.01 41.18 3.06
590 653 5.925397 GCCATGATACACTATCACTCTCAAG 59.075 44.000 0.00 0.00 46.94 3.02
641 732 2.636462 CACGTGCATTGCAACGGA 59.364 55.556 25.86 0.00 41.47 4.69
651 742 0.240678 CTAGCAAAATGGCACGTGCA 59.759 50.000 38.60 25.68 44.36 4.57
657 748 7.175816 TGTTGAATAAGTACTAGCAAAATGGCA 59.824 33.333 0.00 0.00 35.83 4.92
888 1043 4.314440 GGCATATGGGCGCGAGGA 62.314 66.667 12.10 0.00 33.57 3.71
899 1054 1.760480 GTTTTGGGGGCGGGCATAT 60.760 57.895 3.27 0.00 0.00 1.78
900 1055 2.363147 GTTTTGGGGGCGGGCATA 60.363 61.111 3.27 0.00 0.00 3.14
904 1059 4.924187 TGTGGTTTTGGGGGCGGG 62.924 66.667 0.00 0.00 0.00 6.13
905 1060 3.611674 GTGTGGTTTTGGGGGCGG 61.612 66.667 0.00 0.00 0.00 6.13
906 1061 3.611674 GGTGTGGTTTTGGGGGCG 61.612 66.667 0.00 0.00 0.00 6.13
907 1062 2.444895 TGGTGTGGTTTTGGGGGC 60.445 61.111 0.00 0.00 0.00 5.80
908 1063 0.689412 AAGTGGTGTGGTTTTGGGGG 60.689 55.000 0.00 0.00 0.00 5.40
909 1064 2.074729 TAAGTGGTGTGGTTTTGGGG 57.925 50.000 0.00 0.00 0.00 4.96
910 1065 3.739830 GCTTTAAGTGGTGTGGTTTTGGG 60.740 47.826 0.00 0.00 0.00 4.12
911 1066 3.453424 GCTTTAAGTGGTGTGGTTTTGG 58.547 45.455 0.00 0.00 0.00 3.28
914 1069 2.616842 CTCGCTTTAAGTGGTGTGGTTT 59.383 45.455 5.65 0.00 0.00 3.27
916 1071 1.414919 TCTCGCTTTAAGTGGTGTGGT 59.585 47.619 5.65 0.00 0.00 4.16
918 1073 2.479837 TGTCTCGCTTTAAGTGGTGTG 58.520 47.619 5.65 0.00 0.00 3.82
919 1074 2.902705 TGTCTCGCTTTAAGTGGTGT 57.097 45.000 5.65 0.00 0.00 4.16
920 1075 3.865745 CCTATGTCTCGCTTTAAGTGGTG 59.134 47.826 5.65 0.10 0.00 4.17
921 1076 3.118738 CCCTATGTCTCGCTTTAAGTGGT 60.119 47.826 5.65 0.00 0.00 4.16
922 1077 3.458189 CCCTATGTCTCGCTTTAAGTGG 58.542 50.000 5.65 0.00 0.00 4.00
923 1078 2.866762 GCCCTATGTCTCGCTTTAAGTG 59.133 50.000 0.00 0.00 0.00 3.16
924 1079 2.481449 CGCCCTATGTCTCGCTTTAAGT 60.481 50.000 0.00 0.00 0.00 2.24
950 1128 0.860533 CACTTGGCGCAATGGTTTTG 59.139 50.000 10.83 0.00 0.00 2.44
965 1143 1.364901 CCGTACCACCGTCACACTT 59.635 57.895 0.00 0.00 0.00 3.16
966 1144 2.567497 CCCGTACCACCGTCACACT 61.567 63.158 0.00 0.00 0.00 3.55
992 1170 2.158559 GGTGTATGTCCATGTTGTGCA 58.841 47.619 0.00 0.00 0.00 4.57
1172 1356 2.815647 CGAGGGACGCAAGAAGGC 60.816 66.667 0.00 0.00 43.62 4.35
1371 1555 2.419324 GTCGTAGAAGATGGACACGTCT 59.581 50.000 0.00 0.00 44.75 4.18
1863 2050 1.456892 AGTCTGGTGTGTGGACGGA 60.457 57.895 0.00 0.00 35.42 4.69
1865 2052 1.956170 GCAGTCTGGTGTGTGGACG 60.956 63.158 1.14 0.00 35.42 4.79
1904 2091 9.396022 GGTAACAAGTAAGCCATATATGCATAT 57.604 33.333 22.31 22.31 0.00 1.78
1905 2092 8.602424 AGGTAACAAGTAAGCCATATATGCATA 58.398 33.333 9.27 9.27 41.41 3.14
1906 2093 7.391554 CAGGTAACAAGTAAGCCATATATGCAT 59.608 37.037 3.79 3.79 41.41 3.96
1907 2094 6.710295 CAGGTAACAAGTAAGCCATATATGCA 59.290 38.462 7.24 0.00 41.41 3.96
1908 2095 6.348540 GCAGGTAACAAGTAAGCCATATATGC 60.349 42.308 7.24 3.40 41.41 3.14
1909 2096 6.149474 GGCAGGTAACAAGTAAGCCATATATG 59.851 42.308 5.68 5.68 40.29 1.78
1910 2097 6.238648 GGCAGGTAACAAGTAAGCCATATAT 58.761 40.000 0.00 0.00 40.29 0.86
1911 2098 5.617252 GGCAGGTAACAAGTAAGCCATATA 58.383 41.667 0.00 0.00 40.29 0.86
1940 2127 7.097192 ACAATCGATACGGATAAGTATGCAAT 58.903 34.615 0.00 0.00 37.43 3.56
1951 2138 9.362539 GTATGGTATAAAACAATCGATACGGAT 57.637 33.333 0.00 0.00 0.00 4.18
2188 2376 9.681692 GCTGATGATGCTCTTATATATACTCTG 57.318 37.037 0.00 0.00 0.00 3.35
2213 2401 2.457970 GTCGAATTAGAGGTACGTGGC 58.542 52.381 0.00 0.00 0.00 5.01
2222 2410 3.187700 CGTTTGAGGGGTCGAATTAGAG 58.812 50.000 0.00 0.00 0.00 2.43
2230 2418 2.742372 CAGGCGTTTGAGGGGTCG 60.742 66.667 0.00 0.00 0.00 4.79
2260 2448 1.664965 GACACGCCTGGTCACTGAC 60.665 63.158 0.00 0.00 35.36 3.51
2261 2449 2.734591 GACACGCCTGGTCACTGA 59.265 61.111 0.00 0.00 35.36 3.41
2262 2450 2.357517 GGACACGCCTGGTCACTG 60.358 66.667 0.00 0.00 37.00 3.66
2263 2451 3.991051 CGGACACGCCTGGTCACT 61.991 66.667 0.00 0.00 37.00 3.41
2264 2452 3.802418 AACGGACACGCCTGGTCAC 62.802 63.158 0.00 0.00 46.04 3.67
2265 2453 2.596553 AAAACGGACACGCCTGGTCA 62.597 55.000 0.00 0.00 46.04 4.02
2266 2454 1.838568 GAAAACGGACACGCCTGGTC 61.839 60.000 0.00 0.00 46.04 4.02
2267 2455 1.890510 GAAAACGGACACGCCTGGT 60.891 57.895 0.00 0.00 46.04 4.00
2268 2456 1.841663 CTGAAAACGGACACGCCTGG 61.842 60.000 0.00 0.00 46.04 4.45
2269 2457 1.569493 CTGAAAACGGACACGCCTG 59.431 57.895 0.00 0.00 46.04 4.85
2270 2458 2.251642 GCTGAAAACGGACACGCCT 61.252 57.895 0.00 0.00 46.04 5.52
2271 2459 2.251371 GCTGAAAACGGACACGCC 59.749 61.111 0.00 0.00 46.04 5.68
2272 2460 2.251371 GGCTGAAAACGGACACGC 59.749 61.111 0.00 0.00 46.04 5.34
2274 2462 0.035739 TAGGGGCTGAAAACGGACAC 59.964 55.000 0.00 0.00 0.00 3.67
2275 2463 0.035739 GTAGGGGCTGAAAACGGACA 59.964 55.000 0.00 0.00 0.00 4.02
2312 2500 7.735917 ACCGGACATATGAGAAAAATATGAGA 58.264 34.615 9.46 0.00 39.40 3.27
2313 2501 7.657354 TGACCGGACATATGAGAAAAATATGAG 59.343 37.037 9.46 2.53 39.40 2.90
2323 2517 2.159099 GCAAGTGACCGGACATATGAGA 60.159 50.000 20.15 0.00 0.00 3.27
2332 2526 0.324614 ATCATGTGCAAGTGACCGGA 59.675 50.000 9.46 0.00 0.00 5.14
2355 2549 6.985653 TTTCTTTCTCTCTCTTCTTCTCCA 57.014 37.500 0.00 0.00 0.00 3.86
2416 2610 0.107897 TGCCACATATGACACGACCC 60.108 55.000 10.38 0.00 0.00 4.46
2421 2615 3.251479 TCAGTCTGCCACATATGACAC 57.749 47.619 10.38 0.00 32.41 3.67
2422 2616 3.491447 CGATCAGTCTGCCACATATGACA 60.491 47.826 10.38 3.82 32.41 3.58
2426 2620 1.345741 CCCGATCAGTCTGCCACATAT 59.654 52.381 0.00 0.00 0.00 1.78
2429 2623 2.981302 CCCGATCAGTCTGCCACA 59.019 61.111 0.00 0.00 0.00 4.17
2458 2652 2.088674 ATATGAGGGCTCGCGGACAC 62.089 60.000 6.13 0.00 0.00 3.67
2459 2653 1.806461 GATATGAGGGCTCGCGGACA 61.806 60.000 6.13 0.00 0.00 4.02
2463 2657 0.459237 GGATGATATGAGGGCTCGCG 60.459 60.000 0.00 0.00 0.00 5.87
2479 2673 8.883954 CGCATATCTATGTCAAATATGAGGAT 57.116 34.615 13.41 0.00 36.08 3.24
2493 2687 2.497675 ACTAGCACCCCGCATATCTATG 59.502 50.000 0.00 0.00 46.13 2.23
2503 2697 2.893398 GGACTGACTAGCACCCCG 59.107 66.667 0.00 0.00 0.00 5.73
2511 2705 1.180456 TCAAACGCCCGGACTGACTA 61.180 55.000 0.73 0.00 0.00 2.59
2512 2706 2.030562 CAAACGCCCGGACTGACT 59.969 61.111 0.73 0.00 0.00 3.41
2516 2710 0.673644 CATCTTCAAACGCCCGGACT 60.674 55.000 0.73 0.00 0.00 3.85
2531 2725 2.113777 ACCGGACCCCTTATATCCATCT 59.886 50.000 9.46 0.00 32.35 2.90
2534 2728 2.051692 CAACCGGACCCCTTATATCCA 58.948 52.381 9.46 0.00 32.35 3.41
2543 2737 4.754667 GCGACTCAACCGGACCCC 62.755 72.222 9.46 0.00 0.00 4.95
2545 2739 3.853597 AACGCGACTCAACCGGACC 62.854 63.158 15.93 0.00 0.00 4.46
2551 2745 2.098870 GTCACAAAAACGCGACTCAAC 58.901 47.619 15.93 0.00 0.00 3.18
2555 2749 1.639534 CGGTCACAAAAACGCGACT 59.360 52.632 15.93 0.00 0.00 4.18
2572 2766 0.447011 GACCGTCTAGTCAGTGACCG 59.553 60.000 19.71 14.99 36.73 4.79
2589 2783 2.027625 CTCAAACGCCCGGACAGAC 61.028 63.158 0.73 0.00 0.00 3.51
2594 2788 2.342279 CTGTCTCAAACGCCCGGA 59.658 61.111 0.73 0.00 0.00 5.14
2596 2790 0.108329 ATACCTGTCTCAAACGCCCG 60.108 55.000 0.00 0.00 0.00 6.13
2609 2803 1.418908 AATCGGGCCCCTCATACCTG 61.419 60.000 18.66 0.00 0.00 4.00
2616 2810 0.035458 CATCTACAATCGGGCCCCTC 59.965 60.000 18.66 0.00 0.00 4.30
2622 2816 0.249447 TGCGAGCATCTACAATCGGG 60.249 55.000 0.00 0.00 35.76 5.14
2624 2818 0.500178 CGTGCGAGCATCTACAATCG 59.500 55.000 0.00 0.00 38.19 3.34
2626 2820 1.135139 AGTCGTGCGAGCATCTACAAT 59.865 47.619 0.00 0.00 0.00 2.71
2639 2833 3.255379 GGGATTCGCGAGTCGTGC 61.255 66.667 22.98 10.99 37.28 5.34
2640 2834 2.949678 CGGGATTCGCGAGTCGTG 60.950 66.667 22.98 19.86 42.31 4.35
2641 2835 3.129502 TCGGGATTCGCGAGTCGT 61.130 61.111 22.98 5.38 43.39 4.34
2646 2840 3.833645 CAGGGTCGGGATTCGCGA 61.834 66.667 20.28 20.28 45.83 5.87
2647 2841 4.143333 ACAGGGTCGGGATTCGCG 62.143 66.667 16.18 16.18 41.10 5.87
2648 2842 2.202892 GACAGGGTCGGGATTCGC 60.203 66.667 0.00 0.00 39.05 4.70
2657 2851 2.603776 ACAGGGGACGACAGGGTC 60.604 66.667 0.00 0.00 36.18 4.46
2658 2852 2.923035 CACAGGGGACGACAGGGT 60.923 66.667 0.00 0.00 0.00 4.34
2659 2853 3.706373 CCACAGGGGACGACAGGG 61.706 72.222 0.00 0.00 40.01 4.45
2660 2854 2.516888 AACCACAGGGGACGACAGG 61.517 63.158 0.00 0.00 41.15 4.00
2661 2855 1.301716 CAACCACAGGGGACGACAG 60.302 63.158 0.00 0.00 41.15 3.51
2662 2856 2.813726 CCAACCACAGGGGACGACA 61.814 63.158 0.00 0.00 41.15 4.35
2663 2857 2.032071 CCAACCACAGGGGACGAC 59.968 66.667 0.00 0.00 41.15 4.34
2664 2858 2.446994 ACCAACCACAGGGGACGA 60.447 61.111 0.00 0.00 41.15 4.20
2665 2859 2.281484 CACCAACCACAGGGGACG 60.281 66.667 0.00 0.00 41.15 4.79
2666 2860 1.106944 CAACACCAACCACAGGGGAC 61.107 60.000 0.00 0.00 41.15 4.46
2667 2861 1.228793 CAACACCAACCACAGGGGA 59.771 57.895 0.00 0.00 41.15 4.81
2668 2862 1.076339 ACAACACCAACCACAGGGG 60.076 57.895 0.00 0.00 44.81 4.79
2669 2863 1.391157 CCACAACACCAACCACAGGG 61.391 60.000 0.00 0.00 41.29 4.45
2670 2864 1.391157 CCCACAACACCAACCACAGG 61.391 60.000 0.00 0.00 0.00 4.00
2671 2865 0.682855 ACCCACAACACCAACCACAG 60.683 55.000 0.00 0.00 0.00 3.66
2672 2866 0.251832 AACCCACAACACCAACCACA 60.252 50.000 0.00 0.00 0.00 4.17
2673 2867 0.458260 GAACCCACAACACCAACCAC 59.542 55.000 0.00 0.00 0.00 4.16
2674 2868 1.032657 CGAACCCACAACACCAACCA 61.033 55.000 0.00 0.00 0.00 3.67
2675 2869 0.748729 TCGAACCCACAACACCAACC 60.749 55.000 0.00 0.00 0.00 3.77
2676 2870 0.661020 CTCGAACCCACAACACCAAC 59.339 55.000 0.00 0.00 0.00 3.77
2677 2871 1.098712 GCTCGAACCCACAACACCAA 61.099 55.000 0.00 0.00 0.00 3.67
2678 2872 1.525077 GCTCGAACCCACAACACCA 60.525 57.895 0.00 0.00 0.00 4.17
2679 2873 2.258726 GGCTCGAACCCACAACACC 61.259 63.158 0.00 0.00 0.00 4.16
2680 2874 2.604174 CGGCTCGAACCCACAACAC 61.604 63.158 0.00 0.00 0.00 3.32
2681 2875 2.280524 CGGCTCGAACCCACAACA 60.281 61.111 0.00 0.00 0.00 3.33
2682 2876 3.047877 CCGGCTCGAACCCACAAC 61.048 66.667 0.00 0.00 0.00 3.32
2683 2877 4.323477 CCCGGCTCGAACCCACAA 62.323 66.667 0.00 0.00 0.00 3.33
2707 2901 2.595009 CTTTAGAGACCCCTGGCGCC 62.595 65.000 22.73 22.73 0.00 6.53
2708 2902 1.153349 CTTTAGAGACCCCTGGCGC 60.153 63.158 0.00 0.00 0.00 6.53
2709 2903 1.522569 CCTTTAGAGACCCCTGGCG 59.477 63.158 0.00 0.00 0.00 5.69
2710 2904 1.915983 CCCTTTAGAGACCCCTGGC 59.084 63.158 0.00 0.00 0.00 4.85
2711 2905 0.621862 AGCCCTTTAGAGACCCCTGG 60.622 60.000 0.00 0.00 0.00 4.45
2712 2906 2.043227 CTAGCCCTTTAGAGACCCCTG 58.957 57.143 0.00 0.00 0.00 4.45
2713 2907 1.938069 TCTAGCCCTTTAGAGACCCCT 59.062 52.381 0.00 0.00 0.00 4.79
2714 2908 2.040939 GTCTAGCCCTTTAGAGACCCC 58.959 57.143 0.00 0.00 33.64 4.95
2715 2909 2.696187 CTGTCTAGCCCTTTAGAGACCC 59.304 54.545 0.00 0.00 38.01 4.46
2716 2910 2.696187 CCTGTCTAGCCCTTTAGAGACC 59.304 54.545 0.00 0.00 38.01 3.85
2717 2911 3.633418 TCCTGTCTAGCCCTTTAGAGAC 58.367 50.000 0.00 0.00 39.03 3.36
2718 2912 4.475345 GATCCTGTCTAGCCCTTTAGAGA 58.525 47.826 0.00 0.00 30.62 3.10
2719 2913 3.576550 GGATCCTGTCTAGCCCTTTAGAG 59.423 52.174 3.84 0.00 30.62 2.43
2720 2914 3.207777 AGGATCCTGTCTAGCCCTTTAGA 59.792 47.826 15.29 0.00 0.00 2.10
2721 2915 3.576550 GAGGATCCTGTCTAGCCCTTTAG 59.423 52.174 22.02 0.00 0.00 1.85
2722 2916 3.577919 GAGGATCCTGTCTAGCCCTTTA 58.422 50.000 22.02 0.00 0.00 1.85
2723 2917 2.403561 GAGGATCCTGTCTAGCCCTTT 58.596 52.381 22.02 0.00 0.00 3.11
2724 2918 1.755977 CGAGGATCCTGTCTAGCCCTT 60.756 57.143 22.02 0.00 0.00 3.95
2725 2919 0.178975 CGAGGATCCTGTCTAGCCCT 60.179 60.000 22.02 0.00 0.00 5.19
2726 2920 0.468400 ACGAGGATCCTGTCTAGCCC 60.468 60.000 22.02 0.15 0.00 5.19
2727 2921 0.671251 CACGAGGATCCTGTCTAGCC 59.329 60.000 22.02 1.00 0.00 3.93
2728 2922 0.671251 CCACGAGGATCCTGTCTAGC 59.329 60.000 22.02 1.85 36.89 3.42
2729 2923 0.671251 GCCACGAGGATCCTGTCTAG 59.329 60.000 22.02 7.57 36.89 2.43
2730 2924 1.101635 CGCCACGAGGATCCTGTCTA 61.102 60.000 22.02 0.00 36.89 2.59
2731 2925 2.418910 CGCCACGAGGATCCTGTCT 61.419 63.158 22.02 0.00 36.89 3.41
2732 2926 2.105128 CGCCACGAGGATCCTGTC 59.895 66.667 22.02 4.74 36.89 3.51
2733 2927 3.461773 CCGCCACGAGGATCCTGT 61.462 66.667 22.02 14.74 36.89 4.00
2734 2928 2.032860 AATCCGCCACGAGGATCCTG 62.033 60.000 22.02 14.05 46.99 3.86
2735 2929 1.338136 AAATCCGCCACGAGGATCCT 61.338 55.000 16.13 16.13 46.99 3.24
2736 2930 0.391597 TAAATCCGCCACGAGGATCC 59.608 55.000 2.48 2.48 46.99 3.36
2737 2931 1.068741 ACTAAATCCGCCACGAGGATC 59.931 52.381 1.86 0.00 46.99 3.36
2739 2933 1.406539 GTACTAAATCCGCCACGAGGA 59.593 52.381 1.86 0.00 42.69 3.71
2740 2934 1.135527 TGTACTAAATCCGCCACGAGG 59.864 52.381 0.00 0.00 38.23 4.63
2741 2935 2.572191 TGTACTAAATCCGCCACGAG 57.428 50.000 0.00 0.00 0.00 4.18
2742 2936 2.482316 CCATGTACTAAATCCGCCACGA 60.482 50.000 0.00 0.00 0.00 4.35
2743 2937 1.864711 CCATGTACTAAATCCGCCACG 59.135 52.381 0.00 0.00 0.00 4.94
2744 2938 1.602377 GCCATGTACTAAATCCGCCAC 59.398 52.381 0.00 0.00 0.00 5.01
2745 2939 1.210722 TGCCATGTACTAAATCCGCCA 59.789 47.619 0.00 0.00 0.00 5.69
2746 2940 1.602377 GTGCCATGTACTAAATCCGCC 59.398 52.381 0.00 0.00 0.00 6.13
2747 2941 1.260561 CGTGCCATGTACTAAATCCGC 59.739 52.381 0.00 0.00 0.00 5.54
2748 2942 1.260561 GCGTGCCATGTACTAAATCCG 59.739 52.381 0.00 0.00 0.00 4.18
2749 2943 2.287915 CAGCGTGCCATGTACTAAATCC 59.712 50.000 0.00 0.00 0.00 3.01
2750 2944 3.194861 TCAGCGTGCCATGTACTAAATC 58.805 45.455 0.00 0.00 0.00 2.17
2751 2945 3.198068 CTCAGCGTGCCATGTACTAAAT 58.802 45.455 0.00 0.00 0.00 1.40
2752 2946 2.616960 CTCAGCGTGCCATGTACTAAA 58.383 47.619 0.00 0.00 0.00 1.85
2753 2947 1.739035 GCTCAGCGTGCCATGTACTAA 60.739 52.381 0.00 0.00 0.00 2.24
2754 2948 0.179111 GCTCAGCGTGCCATGTACTA 60.179 55.000 0.00 0.00 0.00 1.82
2755 2949 1.448540 GCTCAGCGTGCCATGTACT 60.449 57.895 0.00 0.00 0.00 2.73
2756 2950 3.093278 GCTCAGCGTGCCATGTAC 58.907 61.111 0.00 0.00 0.00 2.90
2767 2961 2.866688 GAGAACGATCTCGCTCAGC 58.133 57.895 6.96 0.00 42.54 4.26
2773 2967 7.938034 CTCTTCTTAGAGGGAGAACGATCTCG 61.938 50.000 15.53 0.00 44.30 4.04
2774 2968 5.238650 CTCTTCTTAGAGGGAGAACGATCTC 59.761 48.000 13.91 13.91 43.58 2.75
2775 2969 5.118729 TCTTCTTAGAGGGAGAACGATCT 57.881 43.478 0.00 0.00 39.10 2.75
2776 2970 5.432885 CTCTTCTTAGAGGGAGAACGATC 57.567 47.826 8.01 0.00 43.52 3.69
2787 2981 4.161377 CCCTCTTGTTCCCTCTTCTTAGAG 59.839 50.000 0.00 0.00 46.24 2.43
2788 2982 4.097418 CCCTCTTGTTCCCTCTTCTTAGA 58.903 47.826 0.00 0.00 0.00 2.10
2789 2983 4.097418 TCCCTCTTGTTCCCTCTTCTTAG 58.903 47.826 0.00 0.00 0.00 2.18
2790 2984 4.141990 TCCCTCTTGTTCCCTCTTCTTA 57.858 45.455 0.00 0.00 0.00 2.10
2791 2985 2.991580 TCCCTCTTGTTCCCTCTTCTT 58.008 47.619 0.00 0.00 0.00 2.52
2792 2986 2.723530 TCCCTCTTGTTCCCTCTTCT 57.276 50.000 0.00 0.00 0.00 2.85
2793 2987 2.171659 GGATCCCTCTTGTTCCCTCTTC 59.828 54.545 0.00 0.00 0.00 2.87
2794 2988 2.200955 GGATCCCTCTTGTTCCCTCTT 58.799 52.381 0.00 0.00 0.00 2.85
2795 2989 1.081174 TGGATCCCTCTTGTTCCCTCT 59.919 52.381 9.90 0.00 0.00 3.69
2796 2990 1.488393 CTGGATCCCTCTTGTTCCCTC 59.512 57.143 9.90 0.00 0.00 4.30
2797 2991 1.081174 TCTGGATCCCTCTTGTTCCCT 59.919 52.381 9.90 0.00 0.00 4.20
2798 2992 1.488393 CTCTGGATCCCTCTTGTTCCC 59.512 57.143 9.90 0.00 0.00 3.97
2799 2993 2.093235 CACTCTGGATCCCTCTTGTTCC 60.093 54.545 9.90 0.00 0.00 3.62
2800 2994 2.679349 GCACTCTGGATCCCTCTTGTTC 60.679 54.545 9.90 0.00 0.00 3.18
2801 2995 1.280421 GCACTCTGGATCCCTCTTGTT 59.720 52.381 9.90 0.00 0.00 2.83
2802 2996 0.908198 GCACTCTGGATCCCTCTTGT 59.092 55.000 9.90 0.00 0.00 3.16
2803 2997 0.179936 GGCACTCTGGATCCCTCTTG 59.820 60.000 9.90 2.69 0.00 3.02
2804 2998 0.985490 GGGCACTCTGGATCCCTCTT 60.985 60.000 9.90 0.00 35.87 2.85
2805 2999 1.383803 GGGCACTCTGGATCCCTCT 60.384 63.158 9.90 0.00 35.87 3.69
2806 3000 1.690633 TGGGCACTCTGGATCCCTC 60.691 63.158 9.90 0.00 39.49 4.30
2807 3001 1.997874 GTGGGCACTCTGGATCCCT 60.998 63.158 9.90 0.00 39.49 4.20
2808 3002 2.592308 GTGGGCACTCTGGATCCC 59.408 66.667 9.90 0.00 39.22 3.85
2809 3003 2.592308 GGTGGGCACTCTGGATCC 59.408 66.667 4.20 4.20 0.00 3.36
2810 3004 1.639635 ATGGGTGGGCACTCTGGATC 61.640 60.000 0.00 0.00 31.68 3.36
2811 3005 1.620589 ATGGGTGGGCACTCTGGAT 60.621 57.895 0.00 0.00 31.68 3.41
2812 3006 2.204136 ATGGGTGGGCACTCTGGA 60.204 61.111 0.00 0.00 31.68 3.86
2813 3007 2.044650 CATGGGTGGGCACTCTGG 60.045 66.667 0.00 0.00 31.68 3.86
2814 3008 2.753043 GCATGGGTGGGCACTCTG 60.753 66.667 0.00 0.00 31.68 3.35
2815 3009 4.052518 GGCATGGGTGGGCACTCT 62.053 66.667 0.00 0.00 31.68 3.24


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

AutoCloner maintained by Alex Coulton.