Multiple sequence alignment - TraesCS4A01G056900

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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 TraesCS4A01G056900 chr4A 100.000 2776 0 0 1 2776 47655583 47658358 0.000000e+00 5127.0
1 TraesCS4A01G056900 chr4A 77.563 1658 326 30 9 1653 739718645 739717021 0.000000e+00 959.0
2 TraesCS4A01G056900 chr4A 77.680 1586 306 37 9 1574 740087310 740088867 0.000000e+00 924.0
3 TraesCS4A01G056900 chr4A 77.083 1680 311 45 7 1664 733781374 733783001 0.000000e+00 902.0
4 TraesCS4A01G056900 chr4A 76.435 1672 327 43 9 1667 742113852 742112235 0.000000e+00 843.0
5 TraesCS4A01G056900 chr4A 78.713 606 113 12 1063 1662 722930870 722931465 9.320000e-105 390.0
6 TraesCS4A01G056900 chr4A 75.719 556 108 23 593 1139 740162766 740163303 1.280000e-63 254.0
7 TraesCS4A01G056900 chr4A 74.159 565 117 24 7 555 621130856 621131407 1.010000e-49 207.0
8 TraesCS4A01G056900 chr4A 82.051 117 18 3 2340 2455 661589787 661589673 2.280000e-16 97.1
9 TraesCS4A01G056900 chr4D 96.194 1997 70 6 395 2388 416403242 416401249 0.000000e+00 3262.0
10 TraesCS4A01G056900 chr4D 96.500 400 12 2 1 400 416413622 416413225 0.000000e+00 660.0
11 TraesCS4A01G056900 chr4D 95.107 327 16 0 1 327 416425572 416425246 1.470000e-142 516.0
12 TraesCS4A01G056900 chr4D 93.069 101 4 2 2380 2478 416205949 416205850 8.010000e-31 145.0
13 TraesCS4A01G056900 chr4B 89.668 2381 173 29 1 2341 513058578 513056231 0.000000e+00 2966.0
14 TraesCS4A01G056900 chr6B 79.370 1682 297 38 10 1670 75519870 75518218 0.000000e+00 1138.0
15 TraesCS4A01G056900 chr6B 80.374 107 14 6 2078 2184 75517831 75517732 1.070000e-09 75.0
16 TraesCS4A01G056900 chr7D 77.099 1965 384 45 3 1929 2494508 2492572 0.000000e+00 1075.0
17 TraesCS4A01G056900 chr7D 83.036 112 18 1 2344 2455 632854188 632854078 1.760000e-17 100.0
18 TraesCS4A01G056900 chr5A 78.580 1676 309 36 7 1664 18675026 18673383 0.000000e+00 1061.0
19 TraesCS4A01G056900 chr5A 89.474 95 8 2 2361 2455 148050859 148050767 4.860000e-23 119.0
20 TraesCS4A01G056900 chr6D 79.167 1560 279 37 9 1548 36077176 36075643 0.000000e+00 1038.0
21 TraesCS4A01G056900 chr6D 76.115 314 40 16 2497 2776 207083254 207082942 6.240000e-27 132.0
22 TraesCS4A01G056900 chr6D 83.036 112 16 3 2344 2455 29378335 29378227 6.330000e-17 99.0
23 TraesCS4A01G056900 chr6D 79.439 107 15 6 2078 2184 36075374 36075275 4.960000e-08 69.4
24 TraesCS4A01G056900 chr2A 71.767 1392 324 52 308 1664 15879838 15881195 2.060000e-86 329.0
25 TraesCS4A01G056900 chr2A 78.261 253 51 3 1 251 15879420 15879670 2.860000e-35 159.0
26 TraesCS4A01G056900 chr2B 73.638 918 197 34 770 1664 24915973 24915078 2.080000e-81 313.0
27 TraesCS4A01G056900 chr2B 78.367 245 49 3 7 249 24916835 24916593 3.700000e-34 156.0
28 TraesCS4A01G056900 chr2B 87.500 112 12 2 2344 2455 556216763 556216872 8.070000e-26 128.0
29 TraesCS4A01G056900 chr7A 70.457 1706 387 90 7 1668 701251640 701253272 1.650000e-62 250.0
30 TraesCS4A01G056900 chr7A 86.000 100 10 3 2356 2455 37119496 37119401 1.360000e-18 104.0
31 TraesCS4A01G056900 chr1B 84.898 245 27 6 2533 2773 624703996 624703758 3.570000e-59 239.0
32 TraesCS4A01G056900 chr1B 83.929 112 16 2 2344 2455 467616754 467616863 3.780000e-19 106.0
33 TraesCS4A01G056900 chr6A 86.486 111 10 5 2494 2601 13081886 13081994 1.750000e-22 117.0
34 TraesCS4A01G056900 chr1A 83.186 113 16 3 2344 2455 547694138 547694248 1.760000e-17 100.0
35 TraesCS4A01G056900 chr2D 80.620 129 23 2 1526 1653 478636 478763 6.330000e-17 99.0


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 TraesCS4A01G056900 chr4A 47655583 47658358 2775 False 5127.0 5127 100.0000 1 2776 1 chr4A.!!$F1 2775
1 TraesCS4A01G056900 chr4A 739717021 739718645 1624 True 959.0 959 77.5630 9 1653 1 chr4A.!!$R2 1644
2 TraesCS4A01G056900 chr4A 740087310 740088867 1557 False 924.0 924 77.6800 9 1574 1 chr4A.!!$F5 1565
3 TraesCS4A01G056900 chr4A 733781374 733783001 1627 False 902.0 902 77.0830 7 1664 1 chr4A.!!$F4 1657
4 TraesCS4A01G056900 chr4A 742112235 742113852 1617 True 843.0 843 76.4350 9 1667 1 chr4A.!!$R3 1658
5 TraesCS4A01G056900 chr4A 722930870 722931465 595 False 390.0 390 78.7130 1063 1662 1 chr4A.!!$F3 599
6 TraesCS4A01G056900 chr4A 740162766 740163303 537 False 254.0 254 75.7190 593 1139 1 chr4A.!!$F6 546
7 TraesCS4A01G056900 chr4A 621130856 621131407 551 False 207.0 207 74.1590 7 555 1 chr4A.!!$F2 548
8 TraesCS4A01G056900 chr4D 416401249 416403242 1993 True 3262.0 3262 96.1940 395 2388 1 chr4D.!!$R2 1993
9 TraesCS4A01G056900 chr4B 513056231 513058578 2347 True 2966.0 2966 89.6680 1 2341 1 chr4B.!!$R1 2340
10 TraesCS4A01G056900 chr6B 75517732 75519870 2138 True 606.5 1138 79.8720 10 2184 2 chr6B.!!$R1 2174
11 TraesCS4A01G056900 chr7D 2492572 2494508 1936 True 1075.0 1075 77.0990 3 1929 1 chr7D.!!$R1 1926
12 TraesCS4A01G056900 chr5A 18673383 18675026 1643 True 1061.0 1061 78.5800 7 1664 1 chr5A.!!$R1 1657
13 TraesCS4A01G056900 chr6D 36075275 36077176 1901 True 553.7 1038 79.3030 9 2184 2 chr6D.!!$R3 2175
14 TraesCS4A01G056900 chr2A 15879420 15881195 1775 False 244.0 329 75.0140 1 1664 2 chr2A.!!$F1 1663
15 TraesCS4A01G056900 chr2B 24915078 24916835 1757 True 234.5 313 76.0025 7 1664 2 chr2B.!!$R1 1657
16 TraesCS4A01G056900 chr7A 701251640 701253272 1632 False 250.0 250 70.4570 7 1668 1 chr7A.!!$F1 1661

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
414 540 0.461693 GACCTCTCTGGCACATCTGC 60.462 60.0 0.00 0.0 43.41 4.26 F
1163 1327 0.855598 ATGGCCTATTGCATCTGGGT 59.144 50.0 3.32 0.0 43.89 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 1658 0.551377 TCAGGCCCCAACAATCCCTA 60.551 55.0 0.00 0.0 0.0 3.53 R
2513 2805 0.036294 GAAGGAGGCGGCTTACAAGT 60.036 55.0 14.76 0.0 0.0 3.16 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
106 107 9.130661 TCGGGTAACATTCATATGAAATCATTT 57.869 29.630 21.50 12.18 37.61 2.32
188 195 0.745845 GCATGTTGCACTCGAGGGAT 60.746 55.000 21.51 0.00 44.26 3.85
414 540 0.461693 GACCTCTCTGGCACATCTGC 60.462 60.000 0.00 0.00 43.41 4.26
446 578 2.567615 GACCTCTGTACAATGGGTGTCT 59.432 50.000 15.74 0.00 41.98 3.41
464 596 3.058155 TGTCTCACGACTCAAGAAGCTAC 60.058 47.826 0.00 0.00 40.86 3.58
545 680 9.862371 CATTAGAAGTTCTACATGTAGACACTT 57.138 33.333 34.14 34.14 41.48 3.16
620 755 6.578163 TTGGGTTACTTATGGCTTTTACAC 57.422 37.500 0.00 0.00 0.00 2.90
653 788 1.002069 TTGGTCTGCAATGAGGGGAT 58.998 50.000 0.00 0.00 0.00 3.85
690 825 2.010145 ATGTACAGCTACAAGGTGCG 57.990 50.000 0.33 0.00 46.94 5.34
836 974 2.906354 AGAAGGATATTGTCACGTGCC 58.094 47.619 11.67 0.00 0.00 5.01
957 1112 9.508567 GAAGATTGCAAATTTTCCATAGACTAC 57.491 33.333 1.71 0.00 0.00 2.73
1020 1175 2.504519 GTCCTTCCGGGGGAATCG 59.495 66.667 16.56 0.00 41.23 3.34
1163 1327 0.855598 ATGGCCTATTGCATCTGGGT 59.144 50.000 3.32 0.00 43.89 4.51
1232 1402 5.125417 ACATATACTTGCACAATTGTCCACC 59.875 40.000 8.48 0.00 0.00 4.61
1447 1635 3.189495 CGATACTAGACTGATCACCGCAT 59.811 47.826 0.00 0.00 0.00 4.73
1470 1658 1.410882 GCCTTAGAGACGATCAGCCTT 59.589 52.381 0.00 0.00 0.00 4.35
1511 1699 2.657237 GCTACCAGCCGTGTCACT 59.343 61.111 0.65 0.00 34.48 3.41
1622 1810 0.396435 TTCAAGACATGCCACTCGGT 59.604 50.000 0.00 0.00 33.28 4.69
1631 1819 2.736144 TGCCACTCGGTTTACTACAG 57.264 50.000 0.00 0.00 33.28 2.74
1810 2008 1.749634 AGGGAGGTTGATCGACTTACG 59.250 52.381 12.89 0.00 44.09 3.18
1819 2017 4.968812 TGATCGACTTACGTTGACCATA 57.031 40.909 0.00 0.00 43.13 2.74
1883 2129 5.067805 ACAACTCTCAAGTGTTTCCCATTTC 59.932 40.000 0.00 0.00 35.36 2.17
1929 2176 2.703416 TGTCACAAGATCCATCTGCAC 58.297 47.619 0.00 0.00 37.19 4.57
1991 2239 6.343716 TGCACAATGAAGAATAAATGGTGT 57.656 33.333 0.00 0.00 0.00 4.16
2351 2643 9.535170 CCATCTTAATATAGTACTCTCCCTTCA 57.465 37.037 0.00 0.00 0.00 3.02
2413 2705 8.709386 AGACTACATATAAAGCAAACTGAGTG 57.291 34.615 0.00 0.00 0.00 3.51
2414 2706 8.531982 AGACTACATATAAAGCAAACTGAGTGA 58.468 33.333 0.00 0.00 0.00 3.41
2415 2707 9.151471 GACTACATATAAAGCAAACTGAGTGAA 57.849 33.333 0.00 0.00 0.00 3.18
2416 2708 9.672673 ACTACATATAAAGCAAACTGAGTGAAT 57.327 29.630 0.00 0.00 0.00 2.57
2418 2710 8.798859 ACATATAAAGCAAACTGAGTGAATCT 57.201 30.769 0.00 0.00 0.00 2.40
2419 2711 9.890629 ACATATAAAGCAAACTGAGTGAATCTA 57.109 29.630 0.00 0.00 0.00 1.98
2421 2713 9.890629 ATATAAAGCAAACTGAGTGAATCTACA 57.109 29.630 0.00 0.00 0.00 2.74
2422 2714 5.931441 AAGCAAACTGAGTGAATCTACAC 57.069 39.130 0.00 0.00 40.60 2.90
2484 2776 7.784790 TTTTTACGAATACGCAAAGGAATTC 57.215 32.000 0.00 0.00 43.96 2.17
2485 2777 6.483385 TTTACGAATACGCAAAGGAATTCA 57.517 33.333 7.93 0.00 43.96 2.57
2486 2778 4.336532 ACGAATACGCAAAGGAATTCAC 57.663 40.909 7.93 0.00 43.96 3.18
2487 2779 4.000988 ACGAATACGCAAAGGAATTCACT 58.999 39.130 7.93 0.00 43.96 3.41
2488 2780 4.454504 ACGAATACGCAAAGGAATTCACTT 59.545 37.500 7.93 5.64 43.96 3.16
2489 2781 5.048991 ACGAATACGCAAAGGAATTCACTTT 60.049 36.000 7.93 11.17 43.96 2.66
2498 2790 5.966742 AAGGAATTCACTTTGCTTCTACC 57.033 39.130 7.93 0.00 32.56 3.18
2499 2791 4.003648 AGGAATTCACTTTGCTTCTACCG 58.996 43.478 7.93 0.00 0.00 4.02
2500 2792 3.127030 GGAATTCACTTTGCTTCTACCGG 59.873 47.826 7.93 0.00 0.00 5.28
2501 2793 1.519408 TTCACTTTGCTTCTACCGGC 58.481 50.000 0.00 0.00 0.00 6.13
2502 2794 0.685097 TCACTTTGCTTCTACCGGCT 59.315 50.000 0.00 0.00 0.00 5.52
2503 2795 0.798776 CACTTTGCTTCTACCGGCTG 59.201 55.000 0.00 0.00 0.00 4.85
2504 2796 0.685097 ACTTTGCTTCTACCGGCTGA 59.315 50.000 0.00 0.00 0.00 4.26
2505 2797 1.279271 ACTTTGCTTCTACCGGCTGAT 59.721 47.619 0.00 0.00 0.00 2.90
2506 2798 2.500098 ACTTTGCTTCTACCGGCTGATA 59.500 45.455 0.00 0.00 0.00 2.15
2507 2799 3.055385 ACTTTGCTTCTACCGGCTGATAA 60.055 43.478 0.00 0.00 0.00 1.75
2508 2800 3.838244 TTGCTTCTACCGGCTGATAAT 57.162 42.857 0.00 0.00 0.00 1.28
2509 2801 4.948341 TTGCTTCTACCGGCTGATAATA 57.052 40.909 0.00 0.00 0.00 0.98
2510 2802 4.252971 TGCTTCTACCGGCTGATAATAC 57.747 45.455 0.00 0.00 0.00 1.89
2511 2803 3.243336 GCTTCTACCGGCTGATAATACG 58.757 50.000 0.00 0.00 0.00 3.06
2512 2804 3.243336 CTTCTACCGGCTGATAATACGC 58.757 50.000 0.00 0.00 0.00 4.42
2513 2805 2.232399 TCTACCGGCTGATAATACGCA 58.768 47.619 0.00 0.00 0.00 5.24
2514 2806 2.030540 TCTACCGGCTGATAATACGCAC 60.031 50.000 0.00 0.00 0.00 5.34
2515 2807 0.750850 ACCGGCTGATAATACGCACT 59.249 50.000 0.00 0.00 0.00 4.40
2516 2808 1.138266 ACCGGCTGATAATACGCACTT 59.862 47.619 0.00 0.00 0.00 3.16
2517 2809 1.526887 CCGGCTGATAATACGCACTTG 59.473 52.381 0.00 0.00 0.00 3.16
2518 2810 2.201732 CGGCTGATAATACGCACTTGT 58.798 47.619 0.00 0.00 0.00 3.16
2519 2811 3.377439 CGGCTGATAATACGCACTTGTA 58.623 45.455 0.00 0.00 0.00 2.41
2520 2812 3.799963 CGGCTGATAATACGCACTTGTAA 59.200 43.478 0.00 0.00 0.00 2.41
2521 2813 4.085055 CGGCTGATAATACGCACTTGTAAG 60.085 45.833 0.00 0.00 0.00 2.34
2522 2814 4.318831 GGCTGATAATACGCACTTGTAAGC 60.319 45.833 0.00 0.00 0.00 3.09
2523 2815 4.318831 GCTGATAATACGCACTTGTAAGCC 60.319 45.833 0.00 0.00 0.00 4.35
2524 2816 3.799963 TGATAATACGCACTTGTAAGCCG 59.200 43.478 4.44 4.44 0.00 5.52
2525 2817 0.725117 AATACGCACTTGTAAGCCGC 59.275 50.000 5.54 2.11 0.00 6.53
2526 2818 1.087771 ATACGCACTTGTAAGCCGCC 61.088 55.000 5.54 0.00 0.00 6.13
2527 2819 2.162338 TACGCACTTGTAAGCCGCCT 62.162 55.000 5.54 0.00 0.00 5.52
2528 2820 2.740714 CGCACTTGTAAGCCGCCTC 61.741 63.158 0.00 0.00 0.00 4.70
2529 2821 2.399356 GCACTTGTAAGCCGCCTCC 61.399 63.158 0.00 0.00 0.00 4.30
2530 2822 1.296715 CACTTGTAAGCCGCCTCCT 59.703 57.895 0.00 0.00 0.00 3.69
2531 2823 0.321653 CACTTGTAAGCCGCCTCCTT 60.322 55.000 0.00 0.00 0.00 3.36
2532 2824 0.036294 ACTTGTAAGCCGCCTCCTTC 60.036 55.000 0.00 0.00 0.00 3.46
2533 2825 0.250513 CTTGTAAGCCGCCTCCTTCT 59.749 55.000 0.00 0.00 0.00 2.85
2534 2826 0.690762 TTGTAAGCCGCCTCCTTCTT 59.309 50.000 0.00 0.00 0.00 2.52
2535 2827 0.036388 TGTAAGCCGCCTCCTTCTTG 60.036 55.000 0.00 0.00 0.00 3.02
2536 2828 0.036294 GTAAGCCGCCTCCTTCTTGT 60.036 55.000 0.00 0.00 0.00 3.16
2537 2829 0.036388 TAAGCCGCCTCCTTCTTGTG 60.036 55.000 0.00 0.00 0.00 3.33
2538 2830 1.768684 AAGCCGCCTCCTTCTTGTGA 61.769 55.000 0.00 0.00 0.00 3.58
2539 2831 1.078143 GCCGCCTCCTTCTTGTGAT 60.078 57.895 0.00 0.00 0.00 3.06
2540 2832 1.372087 GCCGCCTCCTTCTTGTGATG 61.372 60.000 0.00 0.00 0.00 3.07
2541 2833 1.372087 CCGCCTCCTTCTTGTGATGC 61.372 60.000 0.00 0.00 0.00 3.91
2542 2834 1.699656 CGCCTCCTTCTTGTGATGCG 61.700 60.000 0.00 0.00 38.78 4.73
2543 2835 0.674895 GCCTCCTTCTTGTGATGCGT 60.675 55.000 0.00 0.00 0.00 5.24
2544 2836 1.081892 CCTCCTTCTTGTGATGCGTG 58.918 55.000 0.00 0.00 0.00 5.34
2545 2837 1.609061 CCTCCTTCTTGTGATGCGTGT 60.609 52.381 0.00 0.00 0.00 4.49
2546 2838 1.728971 CTCCTTCTTGTGATGCGTGTC 59.271 52.381 0.00 0.00 0.00 3.67
2547 2839 0.798776 CCTTCTTGTGATGCGTGTCC 59.201 55.000 0.00 0.00 0.00 4.02
2548 2840 0.798776 CTTCTTGTGATGCGTGTCCC 59.201 55.000 0.00 0.00 0.00 4.46
2549 2841 0.948623 TTCTTGTGATGCGTGTCCCG 60.949 55.000 0.00 0.00 40.40 5.14
2575 2867 2.523168 TCACCACTCGCCCTGTCA 60.523 61.111 0.00 0.00 0.00 3.58
2581 2873 2.821366 CTCGCCCTGTCATGTGCC 60.821 66.667 0.00 0.00 0.00 5.01
2583 2875 2.360350 CGCCCTGTCATGTGCCTT 60.360 61.111 0.00 0.00 0.00 4.35
2584 2876 1.973281 CGCCCTGTCATGTGCCTTT 60.973 57.895 0.00 0.00 0.00 3.11
2585 2877 1.526575 CGCCCTGTCATGTGCCTTTT 61.527 55.000 0.00 0.00 0.00 2.27
2586 2878 0.037975 GCCCTGTCATGTGCCTTTTG 60.038 55.000 0.00 0.00 0.00 2.44
2588 2880 0.963962 CCTGTCATGTGCCTTTTGCT 59.036 50.000 0.00 0.00 42.00 3.91
2589 2881 1.342174 CCTGTCATGTGCCTTTTGCTT 59.658 47.619 0.00 0.00 42.00 3.91
2590 2882 2.608752 CCTGTCATGTGCCTTTTGCTTC 60.609 50.000 0.00 0.00 42.00 3.86
2591 2883 1.340889 TGTCATGTGCCTTTTGCTTCC 59.659 47.619 0.00 0.00 42.00 3.46
2592 2884 0.968405 TCATGTGCCTTTTGCTTCCC 59.032 50.000 0.00 0.00 42.00 3.97
2593 2885 0.680618 CATGTGCCTTTTGCTTCCCA 59.319 50.000 0.00 0.00 42.00 4.37
2594 2886 0.681175 ATGTGCCTTTTGCTTCCCAC 59.319 50.000 0.00 0.00 42.00 4.61
2595 2887 1.367471 GTGCCTTTTGCTTCCCACC 59.633 57.895 0.00 0.00 42.00 4.61
2596 2888 2.199652 TGCCTTTTGCTTCCCACCG 61.200 57.895 0.00 0.00 42.00 4.94
2597 2889 2.650778 CCTTTTGCTTCCCACCGC 59.349 61.111 0.00 0.00 0.00 5.68
2598 2890 2.199652 CCTTTTGCTTCCCACCGCA 61.200 57.895 0.00 0.00 0.00 5.69
2599 2891 1.286880 CTTTTGCTTCCCACCGCAG 59.713 57.895 0.00 0.00 37.46 5.18
2600 2892 1.152860 TTTTGCTTCCCACCGCAGA 60.153 52.632 0.00 0.00 37.46 4.26
2601 2893 0.753479 TTTTGCTTCCCACCGCAGAA 60.753 50.000 0.00 0.00 37.46 3.02
2602 2894 0.753479 TTTGCTTCCCACCGCAGAAA 60.753 50.000 0.00 0.00 37.46 2.52
2603 2895 1.172180 TTGCTTCCCACCGCAGAAAG 61.172 55.000 0.00 0.00 37.46 2.62
2604 2896 2.982744 GCTTCCCACCGCAGAAAGC 61.983 63.158 0.00 0.00 40.87 3.51
2605 2897 2.282180 TTCCCACCGCAGAAAGCC 60.282 61.111 0.00 0.00 41.38 4.35
2606 2898 3.860930 TTCCCACCGCAGAAAGCCC 62.861 63.158 0.00 0.00 41.38 5.19
2608 2900 4.351054 CCACCGCAGAAAGCCCCT 62.351 66.667 0.00 0.00 41.38 4.79
2609 2901 2.747855 CACCGCAGAAAGCCCCTC 60.748 66.667 0.00 0.00 41.38 4.30
2610 2902 2.930562 ACCGCAGAAAGCCCCTCT 60.931 61.111 0.00 0.00 41.38 3.69
2611 2903 2.352805 CCGCAGAAAGCCCCTCTT 59.647 61.111 0.00 0.00 41.38 2.85
2612 2904 1.746991 CCGCAGAAAGCCCCTCTTC 60.747 63.158 0.00 0.00 41.38 2.87
2613 2905 1.746991 CGCAGAAAGCCCCTCTTCC 60.747 63.158 0.00 0.00 41.38 3.46
2614 2906 1.688211 GCAGAAAGCCCCTCTTCCT 59.312 57.895 0.00 0.00 37.23 3.36
2615 2907 0.393673 GCAGAAAGCCCCTCTTCCTC 60.394 60.000 0.00 0.00 37.23 3.71
2616 2908 1.284313 CAGAAAGCCCCTCTTCCTCT 58.716 55.000 0.00 0.00 32.88 3.69
2617 2909 1.209261 CAGAAAGCCCCTCTTCCTCTC 59.791 57.143 0.00 0.00 32.88 3.20
2618 2910 1.080329 AGAAAGCCCCTCTTCCTCTCT 59.920 52.381 0.00 0.00 32.88 3.10
2619 2911 1.912731 GAAAGCCCCTCTTCCTCTCTT 59.087 52.381 0.00 0.00 32.88 2.85
2620 2912 1.578897 AAGCCCCTCTTCCTCTCTTC 58.421 55.000 0.00 0.00 0.00 2.87
2621 2913 0.326143 AGCCCCTCTTCCTCTCTTCC 60.326 60.000 0.00 0.00 0.00 3.46
2622 2914 0.326143 GCCCCTCTTCCTCTCTTCCT 60.326 60.000 0.00 0.00 0.00 3.36
2623 2915 1.494960 CCCCTCTTCCTCTCTTCCTG 58.505 60.000 0.00 0.00 0.00 3.86
2624 2916 1.273552 CCCCTCTTCCTCTCTTCCTGT 60.274 57.143 0.00 0.00 0.00 4.00
2625 2917 2.023888 CCCCTCTTCCTCTCTTCCTGTA 60.024 54.545 0.00 0.00 0.00 2.74
2626 2918 3.295973 CCCTCTTCCTCTCTTCCTGTAG 58.704 54.545 0.00 0.00 0.00 2.74
2627 2919 3.309556 CCCTCTTCCTCTCTTCCTGTAGT 60.310 52.174 0.00 0.00 0.00 2.73
2628 2920 3.951680 CCTCTTCCTCTCTTCCTGTAGTC 59.048 52.174 0.00 0.00 0.00 2.59
2629 2921 4.325030 CCTCTTCCTCTCTTCCTGTAGTCT 60.325 50.000 0.00 0.00 0.00 3.24
2630 2922 4.850680 TCTTCCTCTCTTCCTGTAGTCTC 58.149 47.826 0.00 0.00 0.00 3.36
2631 2923 4.289934 TCTTCCTCTCTTCCTGTAGTCTCA 59.710 45.833 0.00 0.00 0.00 3.27
2632 2924 4.659529 TCCTCTCTTCCTGTAGTCTCAA 57.340 45.455 0.00 0.00 0.00 3.02
2633 2925 5.199982 TCCTCTCTTCCTGTAGTCTCAAT 57.800 43.478 0.00 0.00 0.00 2.57
2634 2926 5.197451 TCCTCTCTTCCTGTAGTCTCAATC 58.803 45.833 0.00 0.00 0.00 2.67
2635 2927 4.340950 CCTCTCTTCCTGTAGTCTCAATCC 59.659 50.000 0.00 0.00 0.00 3.01
2636 2928 4.282496 TCTCTTCCTGTAGTCTCAATCCC 58.718 47.826 0.00 0.00 0.00 3.85
2637 2929 4.026744 CTCTTCCTGTAGTCTCAATCCCA 58.973 47.826 0.00 0.00 0.00 4.37
2638 2930 4.624913 TCTTCCTGTAGTCTCAATCCCAT 58.375 43.478 0.00 0.00 0.00 4.00
2639 2931 4.651503 TCTTCCTGTAGTCTCAATCCCATC 59.348 45.833 0.00 0.00 0.00 3.51
2640 2932 4.271807 TCCTGTAGTCTCAATCCCATCT 57.728 45.455 0.00 0.00 0.00 2.90
2641 2933 4.219115 TCCTGTAGTCTCAATCCCATCTC 58.781 47.826 0.00 0.00 0.00 2.75
2642 2934 3.963374 CCTGTAGTCTCAATCCCATCTCA 59.037 47.826 0.00 0.00 0.00 3.27
2643 2935 4.202202 CCTGTAGTCTCAATCCCATCTCAC 60.202 50.000 0.00 0.00 0.00 3.51
2644 2936 3.706594 TGTAGTCTCAATCCCATCTCACC 59.293 47.826 0.00 0.00 0.00 4.02
2645 2937 2.837947 AGTCTCAATCCCATCTCACCA 58.162 47.619 0.00 0.00 0.00 4.17
2646 2938 3.184628 AGTCTCAATCCCATCTCACCAA 58.815 45.455 0.00 0.00 0.00 3.67
2647 2939 3.199508 AGTCTCAATCCCATCTCACCAAG 59.800 47.826 0.00 0.00 0.00 3.61
2648 2940 2.507058 TCTCAATCCCATCTCACCAAGG 59.493 50.000 0.00 0.00 0.00 3.61
2649 2941 1.064463 TCAATCCCATCTCACCAAGGC 60.064 52.381 0.00 0.00 0.00 4.35
2650 2942 1.002069 AATCCCATCTCACCAAGGCA 58.998 50.000 0.00 0.00 0.00 4.75
2651 2943 0.549950 ATCCCATCTCACCAAGGCAG 59.450 55.000 0.00 0.00 0.00 4.85
2652 2944 0.842030 TCCCATCTCACCAAGGCAGT 60.842 55.000 0.00 0.00 0.00 4.40
2653 2945 0.911769 CCCATCTCACCAAGGCAGTA 59.088 55.000 0.00 0.00 0.00 2.74
2654 2946 1.281867 CCCATCTCACCAAGGCAGTAA 59.718 52.381 0.00 0.00 0.00 2.24
2655 2947 2.636830 CCATCTCACCAAGGCAGTAAG 58.363 52.381 0.00 0.00 0.00 2.34
2656 2948 2.012673 CATCTCACCAAGGCAGTAAGC 58.987 52.381 0.00 0.00 44.65 3.09
2665 2957 2.953821 GCAGTAAGCAAGCCGCAA 59.046 55.556 0.00 0.00 46.13 4.85
2666 2958 1.508088 GCAGTAAGCAAGCCGCAAT 59.492 52.632 0.00 0.00 46.13 3.56
2667 2959 0.109132 GCAGTAAGCAAGCCGCAATT 60.109 50.000 0.00 0.00 46.13 2.32
2668 2960 1.621107 CAGTAAGCAAGCCGCAATTG 58.379 50.000 0.00 0.00 46.13 2.32
2669 2961 1.068333 CAGTAAGCAAGCCGCAATTGT 60.068 47.619 7.40 0.00 46.13 2.71
2670 2962 1.068333 AGTAAGCAAGCCGCAATTGTG 60.068 47.619 12.16 12.16 46.13 3.33
2671 2963 0.958091 TAAGCAAGCCGCAATTGTGT 59.042 45.000 17.34 0.00 46.13 3.72
2672 2964 0.958091 AAGCAAGCCGCAATTGTGTA 59.042 45.000 17.34 0.00 46.13 2.90
2673 2965 0.240945 AGCAAGCCGCAATTGTGTAC 59.759 50.000 17.34 9.34 46.13 2.90
2674 2966 0.039617 GCAAGCCGCAATTGTGTACA 60.040 50.000 17.34 0.00 41.79 2.90
2675 2967 1.685302 CAAGCCGCAATTGTGTACAC 58.315 50.000 19.36 19.36 0.00 2.90
2676 2968 0.237235 AAGCCGCAATTGTGTACACG 59.763 50.000 20.61 7.85 0.00 4.49
2677 2969 1.154301 GCCGCAATTGTGTACACGG 60.154 57.895 20.61 17.16 43.37 4.94
2678 2970 1.570347 GCCGCAATTGTGTACACGGA 61.570 55.000 20.73 13.14 43.19 4.69
2679 2971 0.442310 CCGCAATTGTGTACACGGAG 59.558 55.000 20.61 11.50 43.19 4.63
2680 2972 1.424403 CGCAATTGTGTACACGGAGA 58.576 50.000 20.61 7.48 0.00 3.71
2681 2973 1.126113 CGCAATTGTGTACACGGAGAC 59.874 52.381 20.61 9.38 0.00 3.36
2716 3008 2.124819 CCGCTCCTGCTGCAAGAT 60.125 61.111 3.02 0.00 34.07 2.40
2717 3009 2.178890 CCGCTCCTGCTGCAAGATC 61.179 63.158 3.02 0.00 34.07 2.75
2718 3010 2.178890 CGCTCCTGCTGCAAGATCC 61.179 63.158 3.02 0.00 34.07 3.36
2719 3011 1.823041 GCTCCTGCTGCAAGATCCC 60.823 63.158 3.02 0.00 34.07 3.85
2720 3012 1.523258 CTCCTGCTGCAAGATCCCG 60.523 63.158 3.02 0.00 34.07 5.14
2721 3013 2.249413 CTCCTGCTGCAAGATCCCGT 62.249 60.000 3.02 0.00 34.07 5.28
2722 3014 1.817099 CCTGCTGCAAGATCCCGTC 60.817 63.158 3.02 0.00 34.07 4.79
2723 3015 1.078918 CTGCTGCAAGATCCCGTCA 60.079 57.895 3.02 0.00 34.07 4.35
2724 3016 1.364626 CTGCTGCAAGATCCCGTCAC 61.365 60.000 3.02 0.00 34.07 3.67
2725 3017 1.375908 GCTGCAAGATCCCGTCACA 60.376 57.895 0.00 0.00 34.07 3.58
2726 3018 1.639298 GCTGCAAGATCCCGTCACAC 61.639 60.000 0.00 0.00 34.07 3.82
2727 3019 1.354337 CTGCAAGATCCCGTCACACG 61.354 60.000 0.00 0.00 37.51 4.49
2728 3020 1.080093 GCAAGATCCCGTCACACGA 60.080 57.895 0.00 0.00 46.05 4.35
2729 3021 0.460284 GCAAGATCCCGTCACACGAT 60.460 55.000 0.00 0.00 46.05 3.73
2730 3022 2.007049 GCAAGATCCCGTCACACGATT 61.007 52.381 0.00 0.00 46.05 3.34
2731 3023 1.660607 CAAGATCCCGTCACACGATTG 59.339 52.381 0.00 0.00 46.05 2.67
2732 3024 0.460284 AGATCCCGTCACACGATTGC 60.460 55.000 0.00 0.00 46.05 3.56
2733 3025 0.460284 GATCCCGTCACACGATTGCT 60.460 55.000 0.00 0.00 46.05 3.91
2734 3026 0.460284 ATCCCGTCACACGATTGCTC 60.460 55.000 0.00 0.00 46.05 4.26
2735 3027 2.100631 CCCGTCACACGATTGCTCC 61.101 63.158 0.00 0.00 46.05 4.70
2736 3028 2.444624 CCGTCACACGATTGCTCCG 61.445 63.158 0.00 0.00 46.05 4.63
2737 3029 1.443702 CGTCACACGATTGCTCCGA 60.444 57.895 0.00 0.00 46.05 4.55
2738 3030 0.802222 CGTCACACGATTGCTCCGAT 60.802 55.000 0.00 0.00 46.05 4.18
2739 3031 0.647410 GTCACACGATTGCTCCGATG 59.353 55.000 0.00 0.00 0.00 3.84
2740 3032 1.083806 TCACACGATTGCTCCGATGC 61.084 55.000 0.00 0.00 0.00 3.91
2741 3033 1.086067 CACACGATTGCTCCGATGCT 61.086 55.000 0.00 0.00 0.00 3.79
2742 3034 1.086067 ACACGATTGCTCCGATGCTG 61.086 55.000 0.00 0.00 0.00 4.41
2743 3035 2.176273 ACGATTGCTCCGATGCTGC 61.176 57.895 0.00 0.00 0.00 5.25
2744 3036 2.175621 CGATTGCTCCGATGCTGCA 61.176 57.895 4.13 4.13 34.69 4.41
2745 3037 1.647629 GATTGCTCCGATGCTGCAG 59.352 57.895 10.11 10.11 38.01 4.41
2746 3038 1.783031 GATTGCTCCGATGCTGCAGG 61.783 60.000 17.12 4.92 38.01 4.85
2747 3039 2.261430 ATTGCTCCGATGCTGCAGGA 62.261 55.000 17.12 14.45 38.01 3.86
2749 3041 2.108566 CTCCGATGCTGCAGGAGG 59.891 66.667 23.38 18.24 45.77 4.30
2750 3042 2.364186 TCCGATGCTGCAGGAGGA 60.364 61.111 17.12 14.02 0.00 3.71
2751 3043 2.108566 CCGATGCTGCAGGAGGAG 59.891 66.667 17.12 8.07 36.10 3.69
2752 3044 2.108566 CGATGCTGCAGGAGGAGG 59.891 66.667 17.12 0.00 33.18 4.30
2753 3045 2.203181 GATGCTGCAGGAGGAGGC 60.203 66.667 17.12 0.00 33.18 4.70
2754 3046 2.691623 ATGCTGCAGGAGGAGGCT 60.692 61.111 17.12 0.00 33.18 4.58
2755 3047 2.663423 GATGCTGCAGGAGGAGGCTC 62.663 65.000 17.12 5.78 33.18 4.70
2756 3048 4.173924 GCTGCAGGAGGAGGCTCC 62.174 72.222 26.42 26.42 43.65 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.386049 CGTGATAACATCTAAGGATTCGGC 59.614 45.833 0.00 0.00 0.00 5.54
106 107 1.208776 CCTGATGATGACACTGCAGGA 59.791 52.381 19.93 0.00 41.47 3.86
188 195 1.248486 CTCTCGAGTTGTGGAGTGGA 58.752 55.000 13.13 0.00 30.75 4.02
414 540 7.307989 CCATTGTACAGAGGTCAAGTGTTTTAG 60.308 40.741 7.34 0.00 0.00 1.85
446 578 3.413327 AGAGTAGCTTCTTGAGTCGTGA 58.587 45.455 0.00 0.00 0.00 4.35
464 596 0.535780 TGCTCACAACCCAGCAAGAG 60.536 55.000 0.00 0.00 42.74 2.85
545 680 2.158475 ACAATGGTTTGCTCTTCCCTCA 60.158 45.455 0.00 0.00 36.22 3.86
620 755 3.305608 GCAGACCAAAAGAACCTTCCATG 60.306 47.826 0.00 0.00 0.00 3.66
653 788 4.574674 ACATAGAACTCTGCCAATGGAA 57.425 40.909 2.05 0.00 0.00 3.53
690 825 5.247110 TGGATTGTAGAAGAGATATGGAGGC 59.753 44.000 0.00 0.00 0.00 4.70
836 974 2.032071 GTCCCACACCAAGGACCG 59.968 66.667 0.00 0.00 45.76 4.79
1020 1175 4.576216 TTCTAGACGCATCCAAGATCTC 57.424 45.455 0.00 0.00 0.00 2.75
1163 1327 6.372659 GGAAGAGTGATGACAAATGCTTCTAA 59.627 38.462 0.00 0.00 33.09 2.10
1232 1402 2.781681 AGGGAGGATAAACACCAACG 57.218 50.000 0.00 0.00 0.00 4.10
1243 1413 4.413851 GGTGAAGGAAGAAATAGGGAGGAT 59.586 45.833 0.00 0.00 0.00 3.24
1447 1635 1.309950 CTGATCGTCTCTAAGGCCGA 58.690 55.000 0.00 0.00 0.00 5.54
1470 1658 0.551377 TCAGGCCCCAACAATCCCTA 60.551 55.000 0.00 0.00 0.00 3.53
1511 1699 2.434331 CCGGCTTGGGACCTTCAA 59.566 61.111 0.00 0.00 0.00 2.69
1701 1899 5.015515 TGAATCAATGACACTTGCCCAATA 58.984 37.500 0.00 0.00 0.00 1.90
1765 1963 4.161565 TGCGTGATTCAGATTACCTAAGGT 59.838 41.667 0.00 0.00 40.16 3.50
1768 1966 5.584649 CCTTTGCGTGATTCAGATTACCTAA 59.415 40.000 0.00 0.00 0.00 2.69
1810 2008 6.258727 CACCAATAGACTGATGTATGGTCAAC 59.741 42.308 0.00 0.00 32.98 3.18
1819 2017 4.890158 TGTGACACCAATAGACTGATGT 57.110 40.909 2.45 0.00 0.00 3.06
1883 2129 2.095768 CACCTAGTTGCAAATCACACGG 60.096 50.000 1.02 0.25 0.00 4.94
2200 2492 8.834465 GCTCAGTTTATAGTTCATCAATCACAT 58.166 33.333 0.00 0.00 0.00 3.21
2388 2680 8.531982 TCACTCAGTTTGCTTTATATGTAGTCT 58.468 33.333 0.00 0.00 0.00 3.24
2389 2681 8.703604 TCACTCAGTTTGCTTTATATGTAGTC 57.296 34.615 0.00 0.00 0.00 2.59
2390 2682 9.672673 ATTCACTCAGTTTGCTTTATATGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
2392 2684 9.890629 AGATTCACTCAGTTTGCTTTATATGTA 57.109 29.630 0.00 0.00 0.00 2.29
2393 2685 8.798859 AGATTCACTCAGTTTGCTTTATATGT 57.201 30.769 0.00 0.00 0.00 2.29
2395 2687 9.890629 TGTAGATTCACTCAGTTTGCTTTATAT 57.109 29.630 0.00 0.00 0.00 0.86
2396 2688 9.151471 GTGTAGATTCACTCAGTTTGCTTTATA 57.849 33.333 0.00 0.00 35.68 0.98
2397 2689 7.880195 AGTGTAGATTCACTCAGTTTGCTTTAT 59.120 33.333 0.00 0.00 44.07 1.40
2398 2690 7.217200 AGTGTAGATTCACTCAGTTTGCTTTA 58.783 34.615 0.00 0.00 44.07 1.85
2399 2691 6.058183 AGTGTAGATTCACTCAGTTTGCTTT 58.942 36.000 0.00 0.00 44.07 3.51
2400 2692 5.615289 AGTGTAGATTCACTCAGTTTGCTT 58.385 37.500 0.00 0.00 44.07 3.91
2401 2693 5.220710 AGTGTAGATTCACTCAGTTTGCT 57.779 39.130 0.00 0.00 44.07 3.91
2402 2694 5.931441 AAGTGTAGATTCACTCAGTTTGC 57.069 39.130 0.00 0.00 46.25 3.68
2460 2752 7.324135 GTGAATTCCTTTGCGTATTCGTAAAAA 59.676 33.333 9.05 2.96 46.77 1.94
2461 2753 6.797995 GTGAATTCCTTTGCGTATTCGTAAAA 59.202 34.615 9.05 2.90 46.77 1.52
2462 2754 6.148150 AGTGAATTCCTTTGCGTATTCGTAAA 59.852 34.615 7.66 7.66 45.82 2.01
2463 2755 5.640357 AGTGAATTCCTTTGCGTATTCGTAA 59.360 36.000 2.27 0.00 39.59 3.18
2464 2756 5.172934 AGTGAATTCCTTTGCGTATTCGTA 58.827 37.500 2.27 0.00 39.49 3.43
2465 2757 4.000988 AGTGAATTCCTTTGCGTATTCGT 58.999 39.130 2.27 0.00 39.49 3.85
2466 2758 4.600012 AGTGAATTCCTTTGCGTATTCG 57.400 40.909 2.27 0.00 40.37 3.34
2467 2759 6.617289 CAAAGTGAATTCCTTTGCGTATTC 57.383 37.500 24.10 0.00 41.46 1.75
2475 2767 5.048713 CGGTAGAAGCAAAGTGAATTCCTTT 60.049 40.000 13.15 13.15 32.48 3.11
2476 2768 4.455877 CGGTAGAAGCAAAGTGAATTCCTT 59.544 41.667 2.27 3.32 0.00 3.36
2477 2769 4.003648 CGGTAGAAGCAAAGTGAATTCCT 58.996 43.478 2.27 0.00 0.00 3.36
2478 2770 3.127030 CCGGTAGAAGCAAAGTGAATTCC 59.873 47.826 2.27 0.00 0.00 3.01
2479 2771 3.426292 GCCGGTAGAAGCAAAGTGAATTC 60.426 47.826 1.90 0.00 0.00 2.17
2480 2772 2.488153 GCCGGTAGAAGCAAAGTGAATT 59.512 45.455 1.90 0.00 0.00 2.17
2481 2773 2.084546 GCCGGTAGAAGCAAAGTGAAT 58.915 47.619 1.90 0.00 0.00 2.57
2482 2774 1.071699 AGCCGGTAGAAGCAAAGTGAA 59.928 47.619 1.90 0.00 0.00 3.18
2483 2775 0.685097 AGCCGGTAGAAGCAAAGTGA 59.315 50.000 1.90 0.00 0.00 3.41
2484 2776 0.798776 CAGCCGGTAGAAGCAAAGTG 59.201 55.000 1.90 0.00 0.00 3.16
2485 2777 0.685097 TCAGCCGGTAGAAGCAAAGT 59.315 50.000 1.90 0.00 0.00 2.66
2486 2778 2.029838 ATCAGCCGGTAGAAGCAAAG 57.970 50.000 1.90 0.00 0.00 2.77
2487 2779 3.620427 TTATCAGCCGGTAGAAGCAAA 57.380 42.857 1.90 0.00 0.00 3.68
2488 2780 3.838244 ATTATCAGCCGGTAGAAGCAA 57.162 42.857 1.90 0.00 0.00 3.91
2489 2781 3.305131 CGTATTATCAGCCGGTAGAAGCA 60.305 47.826 1.90 0.00 0.00 3.91
2490 2782 3.243336 CGTATTATCAGCCGGTAGAAGC 58.757 50.000 1.90 0.00 0.00 3.86
2491 2783 3.243336 GCGTATTATCAGCCGGTAGAAG 58.757 50.000 1.90 0.00 0.00 2.85
2492 2784 2.624364 TGCGTATTATCAGCCGGTAGAA 59.376 45.455 1.90 0.00 0.00 2.10
2493 2785 2.030540 GTGCGTATTATCAGCCGGTAGA 60.031 50.000 1.90 1.04 0.00 2.59
2494 2786 2.030185 AGTGCGTATTATCAGCCGGTAG 60.030 50.000 1.90 0.00 0.00 3.18
2495 2787 1.958579 AGTGCGTATTATCAGCCGGTA 59.041 47.619 1.90 0.00 0.00 4.02
2496 2788 0.750850 AGTGCGTATTATCAGCCGGT 59.249 50.000 1.90 0.00 0.00 5.28
2497 2789 1.526887 CAAGTGCGTATTATCAGCCGG 59.473 52.381 0.00 0.00 0.00 6.13
2498 2790 2.201732 ACAAGTGCGTATTATCAGCCG 58.798 47.619 0.00 0.00 0.00 5.52
2499 2791 4.318831 GCTTACAAGTGCGTATTATCAGCC 60.319 45.833 0.00 0.00 0.00 4.85
2500 2792 4.318831 GGCTTACAAGTGCGTATTATCAGC 60.319 45.833 0.00 0.00 0.00 4.26
2501 2793 4.085055 CGGCTTACAAGTGCGTATTATCAG 60.085 45.833 0.00 0.00 0.00 2.90
2502 2794 3.799963 CGGCTTACAAGTGCGTATTATCA 59.200 43.478 0.00 0.00 0.00 2.15
2503 2795 3.362693 GCGGCTTACAAGTGCGTATTATC 60.363 47.826 0.00 0.00 0.00 1.75
2504 2796 2.542595 GCGGCTTACAAGTGCGTATTAT 59.457 45.455 0.00 0.00 0.00 1.28
2505 2797 1.928503 GCGGCTTACAAGTGCGTATTA 59.071 47.619 0.00 0.00 0.00 0.98
2506 2798 0.725117 GCGGCTTACAAGTGCGTATT 59.275 50.000 0.00 0.00 0.00 1.89
2507 2799 1.087771 GGCGGCTTACAAGTGCGTAT 61.088 55.000 0.00 0.00 32.64 3.06
2508 2800 1.738830 GGCGGCTTACAAGTGCGTA 60.739 57.895 0.00 0.00 32.64 4.42
2509 2801 3.047877 GGCGGCTTACAAGTGCGT 61.048 61.111 0.00 0.00 32.64 5.24
2510 2802 2.740714 GAGGCGGCTTACAAGTGCG 61.741 63.158 14.76 0.00 32.64 5.34
2511 2803 2.399356 GGAGGCGGCTTACAAGTGC 61.399 63.158 14.76 0.00 0.00 4.40
2512 2804 0.321653 AAGGAGGCGGCTTACAAGTG 60.322 55.000 14.76 0.00 0.00 3.16
2513 2805 0.036294 GAAGGAGGCGGCTTACAAGT 60.036 55.000 14.76 0.00 0.00 3.16
2514 2806 0.250513 AGAAGGAGGCGGCTTACAAG 59.749 55.000 14.76 0.00 0.00 3.16
2515 2807 0.690762 AAGAAGGAGGCGGCTTACAA 59.309 50.000 14.76 0.00 0.00 2.41
2516 2808 0.036388 CAAGAAGGAGGCGGCTTACA 60.036 55.000 14.76 0.00 0.00 2.41
2517 2809 0.036294 ACAAGAAGGAGGCGGCTTAC 60.036 55.000 14.76 9.90 0.00 2.34
2518 2810 0.036388 CACAAGAAGGAGGCGGCTTA 60.036 55.000 14.76 0.00 0.00 3.09
2519 2811 1.302832 CACAAGAAGGAGGCGGCTT 60.303 57.895 14.76 0.00 0.00 4.35
2520 2812 1.557269 ATCACAAGAAGGAGGCGGCT 61.557 55.000 13.09 13.09 0.00 5.52
2521 2813 1.078143 ATCACAAGAAGGAGGCGGC 60.078 57.895 0.00 0.00 0.00 6.53
2522 2814 1.372087 GCATCACAAGAAGGAGGCGG 61.372 60.000 0.00 0.00 30.80 6.13
2523 2815 2.093216 GCATCACAAGAAGGAGGCG 58.907 57.895 0.00 0.00 30.80 5.52
2524 2816 0.674895 ACGCATCACAAGAAGGAGGC 60.675 55.000 0.00 0.00 37.46 4.70
2525 2817 1.081892 CACGCATCACAAGAAGGAGG 58.918 55.000 0.00 0.00 0.00 4.30
2526 2818 1.728971 GACACGCATCACAAGAAGGAG 59.271 52.381 0.00 0.00 0.00 3.69
2527 2819 1.608025 GGACACGCATCACAAGAAGGA 60.608 52.381 0.00 0.00 0.00 3.36
2528 2820 0.798776 GGACACGCATCACAAGAAGG 59.201 55.000 0.00 0.00 0.00 3.46
2529 2821 0.798776 GGGACACGCATCACAAGAAG 59.201 55.000 0.00 0.00 0.00 2.85
2530 2822 0.948623 CGGGACACGCATCACAAGAA 60.949 55.000 0.00 0.00 34.82 2.52
2531 2823 1.374125 CGGGACACGCATCACAAGA 60.374 57.895 0.00 0.00 34.82 3.02
2532 2824 3.168271 CGGGACACGCATCACAAG 58.832 61.111 0.00 0.00 34.82 3.16
2552 2844 3.311110 GGCGAGTGGTGAGACCCA 61.311 66.667 0.00 0.00 37.50 4.51
2553 2845 4.083862 GGGCGAGTGGTGAGACCC 62.084 72.222 0.00 0.00 37.50 4.46
2554 2846 2.997897 AGGGCGAGTGGTGAGACC 60.998 66.667 0.00 0.00 39.22 3.85
2555 2847 2.262915 CAGGGCGAGTGGTGAGAC 59.737 66.667 0.00 0.00 0.00 3.36
2556 2848 2.203640 ACAGGGCGAGTGGTGAGA 60.204 61.111 0.00 0.00 0.00 3.27
2557 2849 1.892819 ATGACAGGGCGAGTGGTGAG 61.893 60.000 0.00 0.00 0.00 3.51
2558 2850 1.913262 ATGACAGGGCGAGTGGTGA 60.913 57.895 0.00 0.00 0.00 4.02
2559 2851 1.742880 CATGACAGGGCGAGTGGTG 60.743 63.158 0.00 0.00 0.00 4.17
2560 2852 2.217038 ACATGACAGGGCGAGTGGT 61.217 57.895 0.00 0.00 0.00 4.16
2561 2853 1.742880 CACATGACAGGGCGAGTGG 60.743 63.158 0.00 0.00 0.00 4.00
2562 2854 2.393768 GCACATGACAGGGCGAGTG 61.394 63.158 0.00 0.00 0.00 3.51
2563 2855 2.046892 GCACATGACAGGGCGAGT 60.047 61.111 0.00 0.00 0.00 4.18
2564 2856 2.809861 AAGGCACATGACAGGGCGAG 62.810 60.000 0.00 0.00 0.00 5.03
2565 2857 2.410322 AAAGGCACATGACAGGGCGA 62.410 55.000 0.00 0.00 0.00 5.54
2566 2858 1.526575 AAAAGGCACATGACAGGGCG 61.527 55.000 0.00 0.00 0.00 6.13
2567 2859 0.037975 CAAAAGGCACATGACAGGGC 60.038 55.000 0.00 0.00 0.00 5.19
2568 2860 0.037975 GCAAAAGGCACATGACAGGG 60.038 55.000 0.00 0.00 43.97 4.45
2581 2873 1.172180 TCTGCGGTGGGAAGCAAAAG 61.172 55.000 0.00 0.00 43.31 2.27
2583 2875 0.753479 TTTCTGCGGTGGGAAGCAAA 60.753 50.000 0.00 0.00 43.31 3.68
2584 2876 1.152860 TTTCTGCGGTGGGAAGCAA 60.153 52.632 0.00 0.00 43.31 3.91
2585 2877 1.600636 CTTTCTGCGGTGGGAAGCA 60.601 57.895 0.00 0.00 41.55 3.91
2586 2878 2.982744 GCTTTCTGCGGTGGGAAGC 61.983 63.158 8.91 8.91 0.00 3.86
2588 2880 2.282180 GGCTTTCTGCGGTGGGAA 60.282 61.111 0.00 0.00 44.05 3.97
2589 2881 4.344865 GGGCTTTCTGCGGTGGGA 62.345 66.667 0.00 0.00 44.05 4.37
2591 2883 4.351054 AGGGGCTTTCTGCGGTGG 62.351 66.667 0.00 0.00 44.05 4.61
2592 2884 2.747855 GAGGGGCTTTCTGCGGTG 60.748 66.667 0.00 0.00 44.05 4.94
2593 2885 2.470938 GAAGAGGGGCTTTCTGCGGT 62.471 60.000 0.00 0.00 44.05 5.68
2594 2886 1.746991 GAAGAGGGGCTTTCTGCGG 60.747 63.158 0.00 0.00 44.05 5.69
2595 2887 1.746991 GGAAGAGGGGCTTTCTGCG 60.747 63.158 0.00 0.00 44.05 5.18
2596 2888 0.393673 GAGGAAGAGGGGCTTTCTGC 60.394 60.000 0.00 0.00 42.70 4.26
2597 2889 1.209261 GAGAGGAAGAGGGGCTTTCTG 59.791 57.143 0.00 0.00 42.70 3.02
2598 2890 1.080329 AGAGAGGAAGAGGGGCTTTCT 59.920 52.381 0.00 0.00 45.41 2.52
2599 2891 1.578897 AGAGAGGAAGAGGGGCTTTC 58.421 55.000 0.00 0.00 36.83 2.62
2600 2892 1.912731 GAAGAGAGGAAGAGGGGCTTT 59.087 52.381 0.00 0.00 36.83 3.51
2601 2893 1.578897 GAAGAGAGGAAGAGGGGCTT 58.421 55.000 0.00 0.00 40.25 4.35
2602 2894 0.326143 GGAAGAGAGGAAGAGGGGCT 60.326 60.000 0.00 0.00 0.00 5.19
2603 2895 0.326143 AGGAAGAGAGGAAGAGGGGC 60.326 60.000 0.00 0.00 0.00 5.80
2604 2896 1.273552 ACAGGAAGAGAGGAAGAGGGG 60.274 57.143 0.00 0.00 0.00 4.79
2605 2897 2.246091 ACAGGAAGAGAGGAAGAGGG 57.754 55.000 0.00 0.00 0.00 4.30
2606 2898 3.951680 GACTACAGGAAGAGAGGAAGAGG 59.048 52.174 0.00 0.00 0.00 3.69
2607 2899 4.855340 AGACTACAGGAAGAGAGGAAGAG 58.145 47.826 0.00 0.00 0.00 2.85
2608 2900 4.289934 TGAGACTACAGGAAGAGAGGAAGA 59.710 45.833 0.00 0.00 0.00 2.87
2609 2901 4.594970 TGAGACTACAGGAAGAGAGGAAG 58.405 47.826 0.00 0.00 0.00 3.46
2610 2902 4.659529 TGAGACTACAGGAAGAGAGGAA 57.340 45.455 0.00 0.00 0.00 3.36
2611 2903 4.659529 TTGAGACTACAGGAAGAGAGGA 57.340 45.455 0.00 0.00 0.00 3.71
2612 2904 4.340950 GGATTGAGACTACAGGAAGAGAGG 59.659 50.000 0.00 0.00 0.00 3.69
2613 2905 4.340950 GGGATTGAGACTACAGGAAGAGAG 59.659 50.000 0.00 0.00 0.00 3.20
2614 2906 4.264397 TGGGATTGAGACTACAGGAAGAGA 60.264 45.833 0.00 0.00 0.00 3.10
2615 2907 4.026744 TGGGATTGAGACTACAGGAAGAG 58.973 47.826 0.00 0.00 0.00 2.85
2616 2908 4.061131 TGGGATTGAGACTACAGGAAGA 57.939 45.455 0.00 0.00 0.00 2.87
2617 2909 4.653341 AGATGGGATTGAGACTACAGGAAG 59.347 45.833 0.00 0.00 0.00 3.46
2618 2910 4.624913 AGATGGGATTGAGACTACAGGAA 58.375 43.478 0.00 0.00 0.00 3.36
2619 2911 4.219115 GAGATGGGATTGAGACTACAGGA 58.781 47.826 0.00 0.00 0.00 3.86
2620 2912 3.963374 TGAGATGGGATTGAGACTACAGG 59.037 47.826 0.00 0.00 0.00 4.00
2621 2913 4.202202 GGTGAGATGGGATTGAGACTACAG 60.202 50.000 0.00 0.00 0.00 2.74
2622 2914 3.706594 GGTGAGATGGGATTGAGACTACA 59.293 47.826 0.00 0.00 0.00 2.74
2623 2915 3.706594 TGGTGAGATGGGATTGAGACTAC 59.293 47.826 0.00 0.00 0.00 2.73
2624 2916 3.994317 TGGTGAGATGGGATTGAGACTA 58.006 45.455 0.00 0.00 0.00 2.59
2625 2917 2.837947 TGGTGAGATGGGATTGAGACT 58.162 47.619 0.00 0.00 0.00 3.24
2626 2918 3.539604 CTTGGTGAGATGGGATTGAGAC 58.460 50.000 0.00 0.00 0.00 3.36
2627 2919 2.507058 CCTTGGTGAGATGGGATTGAGA 59.493 50.000 0.00 0.00 0.00 3.27
2628 2920 2.928334 CCTTGGTGAGATGGGATTGAG 58.072 52.381 0.00 0.00 0.00 3.02
2629 2921 1.064463 GCCTTGGTGAGATGGGATTGA 60.064 52.381 0.00 0.00 0.00 2.57
2630 2922 1.341285 TGCCTTGGTGAGATGGGATTG 60.341 52.381 0.00 0.00 0.00 2.67
2631 2923 1.002069 TGCCTTGGTGAGATGGGATT 58.998 50.000 0.00 0.00 0.00 3.01
2632 2924 0.549950 CTGCCTTGGTGAGATGGGAT 59.450 55.000 0.00 0.00 0.00 3.85
2633 2925 0.842030 ACTGCCTTGGTGAGATGGGA 60.842 55.000 0.00 0.00 0.00 4.37
2634 2926 0.911769 TACTGCCTTGGTGAGATGGG 59.088 55.000 0.00 0.00 0.00 4.00
2635 2927 2.636830 CTTACTGCCTTGGTGAGATGG 58.363 52.381 0.00 0.00 0.00 3.51
2636 2928 2.012673 GCTTACTGCCTTGGTGAGATG 58.987 52.381 0.00 0.00 35.15 2.90
2637 2929 1.630369 TGCTTACTGCCTTGGTGAGAT 59.370 47.619 0.00 0.00 42.00 2.75
2638 2930 1.055849 TGCTTACTGCCTTGGTGAGA 58.944 50.000 0.00 0.00 42.00 3.27
2639 2931 1.808945 CTTGCTTACTGCCTTGGTGAG 59.191 52.381 0.00 0.00 42.00 3.51
2640 2932 1.896220 CTTGCTTACTGCCTTGGTGA 58.104 50.000 0.00 0.00 42.00 4.02
2641 2933 0.242017 GCTTGCTTACTGCCTTGGTG 59.758 55.000 0.00 0.00 42.00 4.17
2642 2934 0.895559 GGCTTGCTTACTGCCTTGGT 60.896 55.000 0.00 0.00 43.05 3.67
2643 2935 1.885871 GGCTTGCTTACTGCCTTGG 59.114 57.895 0.00 0.00 43.05 3.61
2644 2936 1.503542 CGGCTTGCTTACTGCCTTG 59.496 57.895 0.00 0.00 44.09 3.61
2645 2937 2.335712 GCGGCTTGCTTACTGCCTT 61.336 57.895 0.00 0.00 44.09 4.35
2646 2938 2.747855 GCGGCTTGCTTACTGCCT 60.748 61.111 0.00 0.00 44.09 4.75
2647 2939 1.937546 ATTGCGGCTTGCTTACTGCC 61.938 55.000 0.00 0.00 46.63 4.85
2648 2940 0.109132 AATTGCGGCTTGCTTACTGC 60.109 50.000 0.00 0.00 46.63 4.40
2649 2941 1.068333 ACAATTGCGGCTTGCTTACTG 60.068 47.619 5.05 0.00 46.63 2.74
2650 2942 1.068333 CACAATTGCGGCTTGCTTACT 60.068 47.619 5.05 0.00 46.63 2.24
2651 2943 1.335872 ACACAATTGCGGCTTGCTTAC 60.336 47.619 5.05 0.00 46.63 2.34
2652 2944 0.958091 ACACAATTGCGGCTTGCTTA 59.042 45.000 5.05 0.00 46.63 3.09
2653 2945 0.958091 TACACAATTGCGGCTTGCTT 59.042 45.000 5.05 0.00 46.63 3.91
2654 2946 0.240945 GTACACAATTGCGGCTTGCT 59.759 50.000 5.05 0.00 46.63 3.91
2655 2947 0.039617 TGTACACAATTGCGGCTTGC 60.040 50.000 5.05 0.00 46.70 4.01
2656 2948 1.685302 GTGTACACAATTGCGGCTTG 58.315 50.000 21.14 0.53 0.00 4.01
2657 2949 0.237235 CGTGTACACAATTGCGGCTT 59.763 50.000 24.98 0.00 0.00 4.35
2658 2950 1.573829 CCGTGTACACAATTGCGGCT 61.574 55.000 24.98 0.00 32.73 5.52
2659 2951 1.154301 CCGTGTACACAATTGCGGC 60.154 57.895 24.98 0.00 32.73 6.53
2660 2952 0.442310 CTCCGTGTACACAATTGCGG 59.558 55.000 24.98 18.56 40.43 5.69
2661 2953 1.126113 GTCTCCGTGTACACAATTGCG 59.874 52.381 24.98 10.29 0.00 4.85
2662 2954 1.126113 CGTCTCCGTGTACACAATTGC 59.874 52.381 24.98 10.96 0.00 3.56
2701 2993 1.823041 GGGATCTTGCAGCAGGAGC 60.823 63.158 14.14 14.14 42.56 4.70
2702 2994 1.523258 CGGGATCTTGCAGCAGGAG 60.523 63.158 13.35 0.15 0.00 3.69
2703 2995 2.244117 GACGGGATCTTGCAGCAGGA 62.244 60.000 10.05 10.05 0.00 3.86
2704 2996 1.817099 GACGGGATCTTGCAGCAGG 60.817 63.158 0.00 0.00 0.00 4.85
2705 2997 1.078918 TGACGGGATCTTGCAGCAG 60.079 57.895 0.00 0.00 0.00 4.24
2706 2998 1.375908 GTGACGGGATCTTGCAGCA 60.376 57.895 0.00 0.00 0.00 4.41
2707 2999 1.375908 TGTGACGGGATCTTGCAGC 60.376 57.895 0.00 0.00 0.00 5.25
2708 3000 1.354337 CGTGTGACGGGATCTTGCAG 61.354 60.000 0.00 0.00 38.08 4.41
2709 3001 1.374125 CGTGTGACGGGATCTTGCA 60.374 57.895 0.00 0.00 38.08 4.08
2710 3002 0.460284 ATCGTGTGACGGGATCTTGC 60.460 55.000 0.00 0.00 42.81 4.01
2711 3003 1.660607 CAATCGTGTGACGGGATCTTG 59.339 52.381 0.00 0.00 42.81 3.02
2712 3004 2.007049 GCAATCGTGTGACGGGATCTT 61.007 52.381 0.00 0.00 42.81 2.40
2713 3005 0.460284 GCAATCGTGTGACGGGATCT 60.460 55.000 0.00 0.00 42.81 2.75
2714 3006 0.460284 AGCAATCGTGTGACGGGATC 60.460 55.000 0.00 0.00 42.81 3.36
2715 3007 0.460284 GAGCAATCGTGTGACGGGAT 60.460 55.000 0.00 0.00 42.81 3.85
2716 3008 1.080093 GAGCAATCGTGTGACGGGA 60.080 57.895 0.00 0.00 42.81 5.14
2717 3009 2.100631 GGAGCAATCGTGTGACGGG 61.101 63.158 0.00 0.00 42.81 5.28
2718 3010 2.444624 CGGAGCAATCGTGTGACGG 61.445 63.158 0.00 0.00 42.81 4.79
2719 3011 0.802222 ATCGGAGCAATCGTGTGACG 60.802 55.000 0.00 0.00 44.19 4.35
2720 3012 0.647410 CATCGGAGCAATCGTGTGAC 59.353 55.000 0.00 0.00 0.00 3.67
2721 3013 1.083806 GCATCGGAGCAATCGTGTGA 61.084 55.000 0.00 0.00 0.00 3.58
2722 3014 1.086067 AGCATCGGAGCAATCGTGTG 61.086 55.000 3.00 0.00 36.85 3.82
2723 3015 1.086067 CAGCATCGGAGCAATCGTGT 61.086 55.000 3.00 0.00 36.85 4.49
2724 3016 1.640069 CAGCATCGGAGCAATCGTG 59.360 57.895 3.00 0.00 36.85 4.35
2725 3017 2.176273 GCAGCATCGGAGCAATCGT 61.176 57.895 3.00 0.00 36.85 3.73
2726 3018 2.102394 CTGCAGCATCGGAGCAATCG 62.102 60.000 0.00 0.00 37.89 3.34
2727 3019 1.647629 CTGCAGCATCGGAGCAATC 59.352 57.895 0.00 0.00 37.89 2.67
2728 3020 1.822613 CCTGCAGCATCGGAGCAAT 60.823 57.895 8.66 0.00 37.89 3.56
2729 3021 2.437180 CCTGCAGCATCGGAGCAA 60.437 61.111 8.66 0.00 37.89 3.91
2730 3022 3.381333 CTCCTGCAGCATCGGAGCA 62.381 63.158 15.86 0.00 38.05 4.26
2731 3023 2.588314 CTCCTGCAGCATCGGAGC 60.588 66.667 15.86 0.00 38.05 4.70
2732 3024 2.108566 CCTCCTGCAGCATCGGAG 59.891 66.667 19.66 19.66 43.11 4.63
2733 3025 2.364186 TCCTCCTGCAGCATCGGA 60.364 61.111 8.66 7.77 0.00 4.55
2734 3026 2.108566 CTCCTCCTGCAGCATCGG 59.891 66.667 8.66 5.35 0.00 4.18
2735 3027 2.108566 CCTCCTCCTGCAGCATCG 59.891 66.667 8.66 0.00 0.00 3.84
2736 3028 2.203181 GCCTCCTCCTGCAGCATC 60.203 66.667 8.66 0.00 0.00 3.91
2737 3029 2.691623 AGCCTCCTCCTGCAGCAT 60.692 61.111 8.66 0.00 0.00 3.79
2738 3030 3.397439 GAGCCTCCTCCTGCAGCA 61.397 66.667 8.66 0.00 31.68 4.41


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

AutoCloner maintained by Alex Coulton.