Multiple sequence alignment - TraesCS4D01G194700

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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 TraesCS4D01G194700 chr4D 100.000 3446 0 0 1 3446 337472684 337469239 0.000000e+00 6364.0
1 TraesCS4D01G194700 chr4D 98.875 622 5 2 2826 3446 28466639 28466019 0.000000e+00 1109.0
2 TraesCS4D01G194700 chr4B 91.147 2293 98 45 385 2610 416626173 416623919 0.000000e+00 3013.0
3 TraesCS4D01G194700 chr4B 96.645 626 19 2 2823 3446 171097438 171098063 0.000000e+00 1038.0
4 TraesCS4D01G194700 chr4B 89.385 358 25 5 34 390 416626547 416626202 4.080000e-119 438.0
5 TraesCS4D01G194700 chr4A 90.755 1882 92 22 685 2521 134550001 134551845 0.000000e+00 2436.0
6 TraesCS4D01G194700 chr4A 91.200 375 20 8 15 385 134549339 134549704 6.640000e-137 497.0
7 TraesCS4D01G194700 chr4A 86.466 266 13 3 385 638 134549743 134549997 1.580000e-68 270.0
8 TraesCS4D01G194700 chr4A 83.838 99 14 2 2514 2610 134552880 134552978 3.660000e-15 93.5
9 TraesCS4D01G194700 chr6D 98.400 625 9 1 2823 3446 132391025 132391649 0.000000e+00 1098.0
10 TraesCS4D01G194700 chr6D 98.240 625 8 3 2823 3446 60312608 60313230 0.000000e+00 1090.0
11 TraesCS4D01G194700 chr2D 98.400 625 8 2 2823 3446 126956248 126956871 0.000000e+00 1098.0
12 TraesCS4D01G194700 chr3D 98.240 625 10 1 2823 3446 569379599 569380223 0.000000e+00 1092.0
13 TraesCS4D01G194700 chr3D 96.800 625 16 3 2823 3446 264598605 264599226 0.000000e+00 1040.0
14 TraesCS4D01G194700 chr1D 97.910 622 11 2 2826 3446 163482446 163481826 0.000000e+00 1075.0
15 TraesCS4D01G194700 chr1D 83.234 167 19 8 2640 2801 356220826 356220664 9.970000e-31 145.0
16 TraesCS4D01G194700 chr5B 96.940 621 17 2 2828 3446 521394115 521394735 0.000000e+00 1040.0
17 TraesCS4D01G194700 chr6B 89.362 188 19 1 2640 2827 578687208 578687022 5.750000e-58 235.0
18 TraesCS4D01G194700 chr6B 85.650 223 23 2 2613 2827 549712937 549712716 3.460000e-55 226.0
19 TraesCS4D01G194700 chr2B 81.448 221 34 6 2613 2827 669948320 669948539 1.270000e-39 174.0
20 TraesCS4D01G194700 chr5D 80.319 188 33 2 2640 2827 495223564 495223381 4.640000e-29 139.0
21 TraesCS4D01G194700 chr1A 81.633 147 22 5 2640 2784 533183425 533183282 2.170000e-22 117.0


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 TraesCS4D01G194700 chr4D 337469239 337472684 3445 True 6364.000 6364 100.00000 1 3446 1 chr4D.!!$R2 3445
1 TraesCS4D01G194700 chr4D 28466019 28466639 620 True 1109.000 1109 98.87500 2826 3446 1 chr4D.!!$R1 620
2 TraesCS4D01G194700 chr4B 416623919 416626547 2628 True 1725.500 3013 90.26600 34 2610 2 chr4B.!!$R1 2576
3 TraesCS4D01G194700 chr4B 171097438 171098063 625 False 1038.000 1038 96.64500 2823 3446 1 chr4B.!!$F1 623
4 TraesCS4D01G194700 chr4A 134549339 134552978 3639 False 824.125 2436 88.06475 15 2610 4 chr4A.!!$F1 2595
5 TraesCS4D01G194700 chr6D 132391025 132391649 624 False 1098.000 1098 98.40000 2823 3446 1 chr6D.!!$F2 623
6 TraesCS4D01G194700 chr6D 60312608 60313230 622 False 1090.000 1090 98.24000 2823 3446 1 chr6D.!!$F1 623
7 TraesCS4D01G194700 chr2D 126956248 126956871 623 False 1098.000 1098 98.40000 2823 3446 1 chr2D.!!$F1 623
8 TraesCS4D01G194700 chr3D 569379599 569380223 624 False 1092.000 1092 98.24000 2823 3446 1 chr3D.!!$F2 623
9 TraesCS4D01G194700 chr3D 264598605 264599226 621 False 1040.000 1040 96.80000 2823 3446 1 chr3D.!!$F1 623
10 TraesCS4D01G194700 chr1D 163481826 163482446 620 True 1075.000 1075 97.91000 2826 3446 1 chr1D.!!$R1 620
11 TraesCS4D01G194700 chr5B 521394115 521394735 620 False 1040.000 1040 96.94000 2828 3446 1 chr5B.!!$F1 618

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
265 270 0.100682 GTCTCTTGGATGCGAGCGTA 59.899 55.0 0.0 0.0 0.0 4.42 F
818 884 0.243636 CAAAAGTAAGCCCGCCCAAG 59.756 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2362 1.341976 ACCCAGACCCACATTTATGGC 60.342 52.381 0.0 0.0 38.55 4.4 R
2743 3932 0.034863 TTGTACCCTTCATTCGGGCC 60.035 55.000 0.0 0.0 46.04 5.8 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
24 25 1.237458 GTAGCCATCCCTCCCCTCT 59.763 63.158 0.00 0.00 0.00 3.69
25 26 0.834261 GTAGCCATCCCTCCCCTCTC 60.834 65.000 0.00 0.00 0.00 3.20
26 27 2.037304 TAGCCATCCCTCCCCTCTCC 62.037 65.000 0.00 0.00 0.00 3.71
27 28 3.041365 CCATCCCTCCCCTCTCCT 58.959 66.667 0.00 0.00 0.00 3.69
28 29 1.319799 CCATCCCTCCCCTCTCCTT 59.680 63.158 0.00 0.00 0.00 3.36
29 30 1.059006 CCATCCCTCCCCTCTCCTTG 61.059 65.000 0.00 0.00 0.00 3.61
30 31 1.059006 CATCCCTCCCCTCTCCTTGG 61.059 65.000 0.00 0.00 0.00 3.61
32 33 3.474570 CCTCCCCTCTCCTTGGCG 61.475 72.222 0.00 0.00 0.00 5.69
98 99 4.019312 TGGCCATGTCAGCAGCGA 62.019 61.111 0.00 0.00 0.00 4.93
125 126 1.204146 GCTCCAGATGAGTGGGGTAA 58.796 55.000 0.00 0.00 40.68 2.85
231 236 6.942576 AGATATCACGAGAAATATTTTGGGGG 59.057 38.462 5.32 0.00 0.00 5.40
265 270 0.100682 GTCTCTTGGATGCGAGCGTA 59.899 55.000 0.00 0.00 0.00 4.42
359 364 4.562143 GCTCAAGGACATGCCAAGATTTTT 60.562 41.667 8.58 0.00 40.02 1.94
471 523 2.034685 CCTCGACTATTCCTGATTCGCA 59.965 50.000 0.00 0.00 0.00 5.10
481 533 4.159377 TCCTGATTCGCAATGTTCAAAC 57.841 40.909 0.00 0.00 0.00 2.93
524 588 4.998051 ACACCCATCCATATATCCAAACC 58.002 43.478 0.00 0.00 0.00 3.27
544 608 2.346803 CGAACCGTGATCCATCAAAGT 58.653 47.619 0.00 0.00 38.75 2.66
546 610 2.113860 ACCGTGATCCATCAAAGTGG 57.886 50.000 0.00 0.00 38.75 4.00
610 674 0.870307 CCCCGAAGACGATAACAGCG 60.870 60.000 0.00 0.00 42.66 5.18
680 744 1.953686 GAGAGAGGCCTACTGCTACTG 59.046 57.143 4.42 0.00 40.92 2.74
681 745 0.387565 GAGAGGCCTACTGCTACTGC 59.612 60.000 4.42 0.00 40.92 4.40
683 747 1.215673 AGAGGCCTACTGCTACTGCTA 59.784 52.381 4.42 0.00 40.92 3.49
693 759 2.285977 TGCTACTGCTAGTCGATCGAA 58.714 47.619 21.31 4.08 40.48 3.71
705 771 5.122512 AGTCGATCGAATTATTCCGTGAT 57.877 39.130 21.31 0.00 0.00 3.06
706 772 6.250344 AGTCGATCGAATTATTCCGTGATA 57.750 37.500 21.31 0.00 0.00 2.15
707 773 6.315551 AGTCGATCGAATTATTCCGTGATAG 58.684 40.000 21.31 0.00 0.00 2.08
808 874 2.663119 GCAAATCGCTGCCAAAAGTAAG 59.337 45.455 0.00 0.00 36.25 2.34
814 880 2.212900 CTGCCAAAAGTAAGCCCGCC 62.213 60.000 0.00 0.00 0.00 6.13
816 882 1.605165 CCAAAAGTAAGCCCGCCCA 60.605 57.895 0.00 0.00 0.00 5.36
817 883 1.182385 CCAAAAGTAAGCCCGCCCAA 61.182 55.000 0.00 0.00 0.00 4.12
818 884 0.243636 CAAAAGTAAGCCCGCCCAAG 59.756 55.000 0.00 0.00 0.00 3.61
870 943 3.066342 CACCTATATATACGCCACCCTCG 59.934 52.174 0.00 0.00 0.00 4.63
902 975 1.131638 TCTTGCAACTCCTCACACCT 58.868 50.000 0.00 0.00 0.00 4.00
903 976 1.490490 TCTTGCAACTCCTCACACCTT 59.510 47.619 0.00 0.00 0.00 3.50
904 977 1.876156 CTTGCAACTCCTCACACCTTC 59.124 52.381 0.00 0.00 0.00 3.46
905 978 1.131638 TGCAACTCCTCACACCTTCT 58.868 50.000 0.00 0.00 0.00 2.85
906 979 1.202687 TGCAACTCCTCACACCTTCTG 60.203 52.381 0.00 0.00 0.00 3.02
907 980 1.517242 CAACTCCTCACACCTTCTGC 58.483 55.000 0.00 0.00 0.00 4.26
908 981 1.071385 CAACTCCTCACACCTTCTGCT 59.929 52.381 0.00 0.00 0.00 4.24
909 982 0.972883 ACTCCTCACACCTTCTGCTC 59.027 55.000 0.00 0.00 0.00 4.26
910 983 0.248843 CTCCTCACACCTTCTGCTCC 59.751 60.000 0.00 0.00 0.00 4.70
996 1098 1.226323 CCACTCGTCGTCGTCCATC 60.226 63.158 1.33 0.00 38.33 3.51
1179 1292 3.602513 CTTGAGGCGGCTGTGCTCT 62.603 63.158 19.63 0.00 34.52 4.09
1678 1791 4.151582 ACATCGGTTACGGCGGGG 62.152 66.667 13.24 0.00 41.39 5.73
1908 2039 1.352404 GTCGTCCGACATCGAGGAG 59.648 63.158 14.48 0.00 44.02 3.69
1995 2126 3.112709 GTGCGCGAGTTGGAGGAC 61.113 66.667 12.10 0.00 0.00 3.85
2045 2176 3.063084 ACCGCCCAGTCTCGAGAC 61.063 66.667 33.52 33.52 45.08 3.36
2231 2362 2.880879 CGACGATCGCTGTGGGTG 60.881 66.667 16.60 0.00 31.14 4.61
2266 2397 1.452108 GGGTTTGATCGGCCTCCTG 60.452 63.158 0.00 0.00 0.00 3.86
2373 2507 4.151157 GCAGCCAGTGAATTGATGTTTTTC 59.849 41.667 0.00 0.00 0.00 2.29
2446 2583 6.293004 TCTTTGGTGGTTTTGACTTTTGAT 57.707 33.333 0.00 0.00 0.00 2.57
2447 2584 7.411486 TCTTTGGTGGTTTTGACTTTTGATA 57.589 32.000 0.00 0.00 0.00 2.15
2451 2592 5.988561 TGGTGGTTTTGACTTTTGATATTGC 59.011 36.000 0.00 0.00 0.00 3.56
2456 2597 7.090173 GGTTTTGACTTTTGATATTGCTGCTA 58.910 34.615 0.00 0.00 0.00 3.49
2470 2611 1.825474 GCTGCTACTAGTTGGGTGAGA 59.175 52.381 0.00 0.00 0.00 3.27
2474 2615 2.100087 GCTACTAGTTGGGTGAGAGAGC 59.900 54.545 0.00 0.00 0.00 4.09
2481 2622 3.706373 GGTGAGAGAGCCGGCCAA 61.706 66.667 26.15 0.00 0.00 4.52
2482 2623 2.125350 GTGAGAGAGCCGGCCAAG 60.125 66.667 26.15 0.00 0.00 3.61
2483 2624 2.283894 TGAGAGAGCCGGCCAAGA 60.284 61.111 26.15 0.00 0.00 3.02
2484 2625 1.687146 TGAGAGAGCCGGCCAAGAT 60.687 57.895 26.15 2.91 0.00 2.40
2485 2626 0.397114 TGAGAGAGCCGGCCAAGATA 60.397 55.000 26.15 2.88 0.00 1.98
2522 3705 1.152756 GTGGTGTGTTTGCTCCCCT 60.153 57.895 0.00 0.00 0.00 4.79
2524 3707 0.467290 TGGTGTGTTTGCTCCCCTTC 60.467 55.000 0.00 0.00 0.00 3.46
2525 3708 0.178990 GGTGTGTTTGCTCCCCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
2527 3710 1.609072 GTGTGTTTGCTCCCCTTCTTC 59.391 52.381 0.00 0.00 0.00 2.87
2555 3740 2.602568 CCAGCCTTGCCTTGCCTT 60.603 61.111 0.00 0.00 0.00 4.35
2557 3742 3.308705 AGCCTTGCCTTGCCTTGC 61.309 61.111 0.00 0.00 0.00 4.01
2558 3743 4.383861 GCCTTGCCTTGCCTTGCC 62.384 66.667 0.00 0.00 0.00 4.52
2610 3799 0.455633 CGCTTGCCTTCAGATGTTGC 60.456 55.000 0.00 0.00 0.00 4.17
2611 3800 0.108945 GCTTGCCTTCAGATGTTGCC 60.109 55.000 0.00 0.00 0.00 4.52
2612 3801 1.542492 CTTGCCTTCAGATGTTGCCT 58.458 50.000 0.00 0.00 0.00 4.75
2613 3802 1.891150 CTTGCCTTCAGATGTTGCCTT 59.109 47.619 0.00 0.00 0.00 4.35
2614 3803 1.999648 TGCCTTCAGATGTTGCCTTT 58.000 45.000 0.00 0.00 0.00 3.11
2615 3804 2.318908 TGCCTTCAGATGTTGCCTTTT 58.681 42.857 0.00 0.00 0.00 2.27
2616 3805 2.699846 TGCCTTCAGATGTTGCCTTTTT 59.300 40.909 0.00 0.00 0.00 1.94
2617 3806 3.243839 TGCCTTCAGATGTTGCCTTTTTC 60.244 43.478 0.00 0.00 0.00 2.29
2618 3807 3.568538 CCTTCAGATGTTGCCTTTTTCG 58.431 45.455 0.00 0.00 0.00 3.46
2619 3808 2.704725 TCAGATGTTGCCTTTTTCGC 57.295 45.000 0.00 0.00 0.00 4.70
2620 3809 1.069296 TCAGATGTTGCCTTTTTCGCG 60.069 47.619 0.00 0.00 0.00 5.87
2621 3810 1.069296 CAGATGTTGCCTTTTTCGCGA 60.069 47.619 3.71 3.71 0.00 5.87
2622 3811 1.606668 AGATGTTGCCTTTTTCGCGAA 59.393 42.857 19.38 19.38 0.00 4.70
2623 3812 2.228822 AGATGTTGCCTTTTTCGCGAAT 59.771 40.909 24.05 2.73 0.00 3.34
2624 3813 3.438781 AGATGTTGCCTTTTTCGCGAATA 59.561 39.130 24.05 15.77 0.00 1.75
2625 3814 2.923643 TGTTGCCTTTTTCGCGAATAC 58.076 42.857 24.05 10.84 0.00 1.89
2626 3815 1.902504 GTTGCCTTTTTCGCGAATACG 59.097 47.619 24.05 15.23 42.93 3.06
2627 3816 0.444651 TGCCTTTTTCGCGAATACGG 59.555 50.000 24.05 24.07 40.15 4.02
2628 3817 0.722848 GCCTTTTTCGCGAATACGGA 59.277 50.000 29.77 11.94 40.15 4.69
2629 3818 1.267383 GCCTTTTTCGCGAATACGGAG 60.267 52.381 29.77 17.17 40.15 4.63
2630 3819 2.264813 CCTTTTTCGCGAATACGGAGA 58.735 47.619 24.09 6.05 40.15 3.71
2631 3820 2.281762 CCTTTTTCGCGAATACGGAGAG 59.718 50.000 24.09 13.33 40.15 3.20
2632 3821 1.274596 TTTTCGCGAATACGGAGAGC 58.725 50.000 24.05 0.00 40.15 4.09
2633 3822 0.454600 TTTCGCGAATACGGAGAGCT 59.545 50.000 24.05 0.00 40.15 4.09
2634 3823 0.454600 TTCGCGAATACGGAGAGCTT 59.545 50.000 19.38 0.00 40.15 3.74
2635 3824 0.248498 TCGCGAATACGGAGAGCTTG 60.248 55.000 6.20 0.00 40.15 4.01
2636 3825 1.812214 CGCGAATACGGAGAGCTTGC 61.812 60.000 0.00 0.00 40.15 4.01
2643 3832 3.345737 CGGAGAGCTTGCGTATTGA 57.654 52.632 0.00 0.00 35.71 2.57
2644 3833 1.858091 CGGAGAGCTTGCGTATTGAT 58.142 50.000 0.00 0.00 35.71 2.57
2645 3834 3.013276 CGGAGAGCTTGCGTATTGATA 57.987 47.619 0.00 0.00 35.71 2.15
2646 3835 2.983136 CGGAGAGCTTGCGTATTGATAG 59.017 50.000 0.00 0.00 35.71 2.08
2647 3836 3.304726 CGGAGAGCTTGCGTATTGATAGA 60.305 47.826 0.00 0.00 35.71 1.98
2648 3837 4.621991 GGAGAGCTTGCGTATTGATAGAA 58.378 43.478 0.00 0.00 0.00 2.10
2649 3838 4.683781 GGAGAGCTTGCGTATTGATAGAAG 59.316 45.833 0.00 0.00 0.00 2.85
2650 3839 5.508153 GGAGAGCTTGCGTATTGATAGAAGA 60.508 44.000 0.00 0.00 0.00 2.87
2651 3840 5.907207 AGAGCTTGCGTATTGATAGAAGAA 58.093 37.500 0.00 0.00 0.00 2.52
2652 3841 6.341316 AGAGCTTGCGTATTGATAGAAGAAA 58.659 36.000 0.00 0.00 0.00 2.52
2653 3842 6.256757 AGAGCTTGCGTATTGATAGAAGAAAC 59.743 38.462 0.00 0.00 0.00 2.78
2654 3843 5.874810 AGCTTGCGTATTGATAGAAGAAACA 59.125 36.000 0.00 0.00 0.00 2.83
2655 3844 6.371548 AGCTTGCGTATTGATAGAAGAAACAA 59.628 34.615 0.00 0.00 0.00 2.83
2656 3845 7.021196 GCTTGCGTATTGATAGAAGAAACAAA 58.979 34.615 0.00 0.00 0.00 2.83
2657 3846 7.537306 GCTTGCGTATTGATAGAAGAAACAAAA 59.463 33.333 0.00 0.00 0.00 2.44
2658 3847 9.559958 CTTGCGTATTGATAGAAGAAACAAAAT 57.440 29.630 0.00 0.00 0.00 1.82
2659 3848 8.894409 TGCGTATTGATAGAAGAAACAAAATG 57.106 30.769 0.00 0.00 0.00 2.32
2660 3849 8.726068 TGCGTATTGATAGAAGAAACAAAATGA 58.274 29.630 0.00 0.00 0.00 2.57
2661 3850 9.214953 GCGTATTGATAGAAGAAACAAAATGAG 57.785 33.333 0.00 0.00 0.00 2.90
2683 3872 9.733556 ATGAGTACAAATAAAGGATACAACACA 57.266 29.630 0.00 0.00 41.41 3.72
2684 3873 9.733556 TGAGTACAAATAAAGGATACAACACAT 57.266 29.630 0.00 0.00 41.41 3.21
2685 3874 9.988350 GAGTACAAATAAAGGATACAACACATG 57.012 33.333 0.00 0.00 41.41 3.21
2686 3875 9.733556 AGTACAAATAAAGGATACAACACATGA 57.266 29.630 0.00 0.00 41.41 3.07
2687 3876 9.769093 GTACAAATAAAGGATACAACACATGAC 57.231 33.333 0.00 0.00 41.41 3.06
2688 3877 8.402798 ACAAATAAAGGATACAACACATGACA 57.597 30.769 0.00 0.00 41.41 3.58
2689 3878 9.023962 ACAAATAAAGGATACAACACATGACAT 57.976 29.630 0.00 0.00 41.41 3.06
2690 3879 9.292846 CAAATAAAGGATACAACACATGACATG 57.707 33.333 14.02 14.02 41.41 3.21
2691 3880 8.806429 AATAAAGGATACAACACATGACATGA 57.194 30.769 22.19 0.00 41.41 3.07
2692 3881 8.806429 ATAAAGGATACAACACATGACATGAA 57.194 30.769 22.19 0.91 41.41 2.57
2693 3882 6.500684 AAGGATACAACACATGACATGAAC 57.499 37.500 22.19 0.00 41.41 3.18
2694 3883 5.559770 AGGATACAACACATGACATGAACA 58.440 37.500 22.19 0.00 41.41 3.18
2695 3884 5.412594 AGGATACAACACATGACATGAACAC 59.587 40.000 22.19 4.97 41.41 3.32
2696 3885 5.181056 GGATACAACACATGACATGAACACA 59.819 40.000 22.19 3.09 0.00 3.72
2697 3886 4.556942 ACAACACATGACATGAACACAG 57.443 40.909 22.19 8.68 0.00 3.66
2698 3887 4.198530 ACAACACATGACATGAACACAGA 58.801 39.130 22.19 0.00 0.00 3.41
2699 3888 4.035558 ACAACACATGACATGAACACAGAC 59.964 41.667 22.19 0.00 0.00 3.51
2700 3889 3.807553 ACACATGACATGAACACAGACA 58.192 40.909 22.19 0.00 0.00 3.41
2701 3890 4.392047 ACACATGACATGAACACAGACAT 58.608 39.130 22.19 0.00 0.00 3.06
2702 3891 4.214758 ACACATGACATGAACACAGACATG 59.785 41.667 22.19 7.95 46.11 3.21
2703 3892 3.189910 ACATGACATGAACACAGACATGC 59.810 43.478 22.19 0.00 45.03 4.06
2704 3893 1.799994 TGACATGAACACAGACATGCG 59.200 47.619 0.00 0.00 45.03 4.73
2705 3894 1.800586 GACATGAACACAGACATGCGT 59.199 47.619 0.00 0.00 45.03 5.24
2706 3895 1.532437 ACATGAACACAGACATGCGTG 59.468 47.619 3.82 3.82 45.03 5.34
2707 3896 1.799994 CATGAACACAGACATGCGTGA 59.200 47.619 14.17 0.00 37.62 4.35
2708 3897 1.946745 TGAACACAGACATGCGTGAA 58.053 45.000 14.17 1.15 36.91 3.18
2709 3898 1.597195 TGAACACAGACATGCGTGAAC 59.403 47.619 14.17 6.35 36.91 3.18
2710 3899 1.597195 GAACACAGACATGCGTGAACA 59.403 47.619 14.17 0.00 36.91 3.18
2711 3900 1.882912 ACACAGACATGCGTGAACAT 58.117 45.000 14.17 0.00 36.91 2.71
2719 3908 2.112380 ATGCGTGAACATGATGTCCA 57.888 45.000 0.00 0.00 0.00 4.02
2720 3909 1.889545 TGCGTGAACATGATGTCCAA 58.110 45.000 0.00 0.00 0.00 3.53
2721 3910 2.225467 TGCGTGAACATGATGTCCAAA 58.775 42.857 0.00 0.00 0.00 3.28
2722 3911 2.226200 TGCGTGAACATGATGTCCAAAG 59.774 45.455 0.00 0.00 0.00 2.77
2723 3912 2.855180 CGTGAACATGATGTCCAAAGC 58.145 47.619 0.00 0.00 0.00 3.51
2724 3913 2.226200 CGTGAACATGATGTCCAAAGCA 59.774 45.455 0.00 0.00 0.00 3.91
2725 3914 3.668757 CGTGAACATGATGTCCAAAGCAG 60.669 47.826 0.00 0.00 0.00 4.24
2726 3915 3.503363 GTGAACATGATGTCCAAAGCAGA 59.497 43.478 0.00 0.00 0.00 4.26
2727 3916 3.754850 TGAACATGATGTCCAAAGCAGAG 59.245 43.478 0.00 0.00 0.00 3.35
2728 3917 3.708403 ACATGATGTCCAAAGCAGAGA 57.292 42.857 0.00 0.00 0.00 3.10
2729 3918 4.025040 ACATGATGTCCAAAGCAGAGAA 57.975 40.909 0.00 0.00 0.00 2.87
2730 3919 4.401022 ACATGATGTCCAAAGCAGAGAAA 58.599 39.130 0.00 0.00 0.00 2.52
2731 3920 4.217118 ACATGATGTCCAAAGCAGAGAAAC 59.783 41.667 0.00 0.00 0.00 2.78
2732 3921 3.819368 TGATGTCCAAAGCAGAGAAACA 58.181 40.909 0.00 0.00 0.00 2.83
2733 3922 4.206375 TGATGTCCAAAGCAGAGAAACAA 58.794 39.130 0.00 0.00 0.00 2.83
2734 3923 4.276678 TGATGTCCAAAGCAGAGAAACAAG 59.723 41.667 0.00 0.00 0.00 3.16
2735 3924 2.951642 TGTCCAAAGCAGAGAAACAAGG 59.048 45.455 0.00 0.00 0.00 3.61
2736 3925 2.294512 GTCCAAAGCAGAGAAACAAGGG 59.705 50.000 0.00 0.00 0.00 3.95
2737 3926 2.174639 TCCAAAGCAGAGAAACAAGGGA 59.825 45.455 0.00 0.00 0.00 4.20
2738 3927 3.160269 CCAAAGCAGAGAAACAAGGGAT 58.840 45.455 0.00 0.00 0.00 3.85
2739 3928 3.057033 CCAAAGCAGAGAAACAAGGGATG 60.057 47.826 0.00 0.00 0.00 3.51
2740 3929 1.831580 AGCAGAGAAACAAGGGATGC 58.168 50.000 0.00 0.00 0.00 3.91
2741 3930 1.353694 AGCAGAGAAACAAGGGATGCT 59.646 47.619 0.00 0.00 37.69 3.79
2742 3931 1.742268 GCAGAGAAACAAGGGATGCTC 59.258 52.381 0.00 0.00 0.00 4.26
2743 3932 2.005451 CAGAGAAACAAGGGATGCTCG 58.995 52.381 0.00 0.00 0.00 5.03
2744 3933 1.065854 AGAGAAACAAGGGATGCTCGG 60.066 52.381 0.00 0.00 0.00 4.63
2745 3934 0.678048 AGAAACAAGGGATGCTCGGC 60.678 55.000 0.00 0.00 0.00 5.54
2746 3935 1.657751 GAAACAAGGGATGCTCGGCC 61.658 60.000 0.00 0.00 0.00 6.13
2747 3936 3.645268 AACAAGGGATGCTCGGCCC 62.645 63.158 0.00 0.00 45.04 5.80
2751 3940 4.256180 GGGATGCTCGGCCCGAAT 62.256 66.667 7.50 0.00 34.74 3.34
2752 3941 2.974698 GGATGCTCGGCCCGAATG 60.975 66.667 7.50 0.00 34.74 2.67
2753 3942 2.108976 GATGCTCGGCCCGAATGA 59.891 61.111 7.50 0.00 34.74 2.57
2754 3943 1.523711 GATGCTCGGCCCGAATGAA 60.524 57.895 7.50 0.00 34.74 2.57
2755 3944 1.502163 GATGCTCGGCCCGAATGAAG 61.502 60.000 7.50 0.00 34.74 3.02
2756 3945 2.897350 GCTCGGCCCGAATGAAGG 60.897 66.667 7.50 0.00 34.74 3.46
2764 3953 2.483014 CCCGAATGAAGGGTACAACA 57.517 50.000 0.00 0.00 43.89 3.33
2765 3954 2.081462 CCCGAATGAAGGGTACAACAC 58.919 52.381 0.00 0.00 43.89 3.32
2766 3955 2.551287 CCCGAATGAAGGGTACAACACA 60.551 50.000 0.00 0.00 43.89 3.72
2767 3956 2.742053 CCGAATGAAGGGTACAACACAG 59.258 50.000 0.00 0.00 0.00 3.66
2768 3957 2.159627 CGAATGAAGGGTACAACACAGC 59.840 50.000 0.00 0.00 0.00 4.40
2769 3958 3.412386 GAATGAAGGGTACAACACAGCT 58.588 45.455 0.00 0.00 0.00 4.24
2770 3959 4.575885 GAATGAAGGGTACAACACAGCTA 58.424 43.478 0.00 0.00 0.00 3.32
2771 3960 4.634012 ATGAAGGGTACAACACAGCTAA 57.366 40.909 0.00 0.00 0.00 3.09
2772 3961 4.425180 TGAAGGGTACAACACAGCTAAA 57.575 40.909 0.00 0.00 0.00 1.85
2773 3962 4.131596 TGAAGGGTACAACACAGCTAAAC 58.868 43.478 0.00 0.00 0.00 2.01
2774 3963 3.136009 AGGGTACAACACAGCTAAACC 57.864 47.619 0.00 0.00 0.00 3.27
2775 3964 2.709397 AGGGTACAACACAGCTAAACCT 59.291 45.455 0.00 0.00 0.00 3.50
2776 3965 3.905591 AGGGTACAACACAGCTAAACCTA 59.094 43.478 0.00 0.00 0.00 3.08
2777 3966 3.999001 GGGTACAACACAGCTAAACCTAC 59.001 47.826 0.00 0.00 0.00 3.18
2778 3967 4.503643 GGGTACAACACAGCTAAACCTACA 60.504 45.833 0.00 0.00 0.00 2.74
2779 3968 5.058490 GGTACAACACAGCTAAACCTACAA 58.942 41.667 0.00 0.00 0.00 2.41
2780 3969 5.528320 GGTACAACACAGCTAAACCTACAAA 59.472 40.000 0.00 0.00 0.00 2.83
2781 3970 6.038492 GGTACAACACAGCTAAACCTACAAAA 59.962 38.462 0.00 0.00 0.00 2.44
2782 3971 5.886992 ACAACACAGCTAAACCTACAAAAC 58.113 37.500 0.00 0.00 0.00 2.43
2783 3972 5.163591 ACAACACAGCTAAACCTACAAAACC 60.164 40.000 0.00 0.00 0.00 3.27
2784 3973 3.887110 ACACAGCTAAACCTACAAAACCC 59.113 43.478 0.00 0.00 0.00 4.11
2785 3974 3.058501 CACAGCTAAACCTACAAAACCCG 60.059 47.826 0.00 0.00 0.00 5.28
2786 3975 3.181452 ACAGCTAAACCTACAAAACCCGA 60.181 43.478 0.00 0.00 0.00 5.14
2787 3976 3.187842 CAGCTAAACCTACAAAACCCGAC 59.812 47.826 0.00 0.00 0.00 4.79
2788 3977 2.485426 GCTAAACCTACAAAACCCGACC 59.515 50.000 0.00 0.00 0.00 4.79
2789 3978 1.985473 AAACCTACAAAACCCGACCC 58.015 50.000 0.00 0.00 0.00 4.46
2790 3979 0.845337 AACCTACAAAACCCGACCCA 59.155 50.000 0.00 0.00 0.00 4.51
2791 3980 0.845337 ACCTACAAAACCCGACCCAA 59.155 50.000 0.00 0.00 0.00 4.12
2792 3981 1.202842 ACCTACAAAACCCGACCCAAG 60.203 52.381 0.00 0.00 0.00 3.61
2793 3982 1.530323 CTACAAAACCCGACCCAAGG 58.470 55.000 0.00 0.00 0.00 3.61
2802 3991 3.451894 GACCCAAGGGCGGCAATG 61.452 66.667 12.47 8.87 39.32 2.82
2815 4004 2.368655 GGCAATGCCTAACCAACAAG 57.631 50.000 18.47 0.00 46.69 3.16
2816 4005 1.892474 GGCAATGCCTAACCAACAAGA 59.108 47.619 18.47 0.00 46.69 3.02
2817 4006 2.094545 GGCAATGCCTAACCAACAAGAG 60.095 50.000 18.47 0.00 46.69 2.85
2818 4007 2.672195 GCAATGCCTAACCAACAAGAGC 60.672 50.000 0.00 0.00 0.00 4.09
2819 4008 2.557924 CAATGCCTAACCAACAAGAGCA 59.442 45.455 0.00 0.00 0.00 4.26
2820 4009 1.604604 TGCCTAACCAACAAGAGCAC 58.395 50.000 0.00 0.00 0.00 4.40
2821 4010 0.881796 GCCTAACCAACAAGAGCACC 59.118 55.000 0.00 0.00 0.00 5.01
2824 4013 1.537202 CTAACCAACAAGAGCACCAGC 59.463 52.381 0.00 0.00 42.56 4.85
2839 4028 2.050350 CAGCATTGAGGCAGGGTGG 61.050 63.158 0.00 0.00 35.83 4.61
3286 4476 5.385198 TGGAAGGAAAAATTACTGTCTGCT 58.615 37.500 0.00 0.00 0.00 4.24
3352 4542 4.038763 CCTACCTATGCAATGTCGGTCTTA 59.961 45.833 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.301027 GAGGGATGGCTACGCGGG 62.301 72.222 12.47 3.66 0.00 6.13
2 3 4.301027 GGAGGGATGGCTACGCGG 62.301 72.222 12.47 0.00 0.00 6.46
3 4 4.301027 GGGAGGGATGGCTACGCG 62.301 72.222 3.53 3.53 0.00 6.01
4 5 3.942439 GGGGAGGGATGGCTACGC 61.942 72.222 0.00 0.00 0.00 4.42
5 6 2.122813 AGGGGAGGGATGGCTACG 60.123 66.667 0.00 0.00 0.00 3.51
6 7 0.834261 GAGAGGGGAGGGATGGCTAC 60.834 65.000 0.00 0.00 0.00 3.58
7 8 1.549297 GAGAGGGGAGGGATGGCTA 59.451 63.158 0.00 0.00 0.00 3.93
8 9 2.288643 GAGAGGGGAGGGATGGCT 59.711 66.667 0.00 0.00 0.00 4.75
9 10 2.851588 GGAGAGGGGAGGGATGGC 60.852 72.222 0.00 0.00 0.00 4.40
10 11 1.059006 CAAGGAGAGGGGAGGGATGG 61.059 65.000 0.00 0.00 0.00 3.51
11 12 1.059006 CCAAGGAGAGGGGAGGGATG 61.059 65.000 0.00 0.00 0.00 3.51
12 13 1.319799 CCAAGGAGAGGGGAGGGAT 59.680 63.158 0.00 0.00 0.00 3.85
13 14 2.787866 CCAAGGAGAGGGGAGGGA 59.212 66.667 0.00 0.00 0.00 4.20
74 75 2.606213 TGACATGGCCACCGGAGA 60.606 61.111 8.16 0.00 0.00 3.71
243 248 1.086634 GCTCGCATCCAAGAGACCAC 61.087 60.000 0.00 0.00 36.65 4.16
265 270 2.429610 ACTCAGTTGTCCACACGTAACT 59.570 45.455 0.00 0.00 33.94 2.24
280 285 2.519771 TATGGTGTACCGGACTCAGT 57.480 50.000 9.46 0.00 39.43 3.41
289 294 3.987868 CACATCACGCTATATGGTGTACC 59.012 47.826 4.84 0.00 39.42 3.34
290 295 4.617959 ACACATCACGCTATATGGTGTAC 58.382 43.478 4.84 0.00 39.42 2.90
427 479 2.159212 TGCACTGCATTGCCATATGTTC 60.159 45.455 24.31 0.00 42.25 3.18
471 523 2.167487 ACGCACCTTTGGTTTGAACATT 59.833 40.909 0.00 0.00 31.02 2.71
481 533 2.128853 ATCAACGCACGCACCTTTGG 62.129 55.000 0.00 0.00 0.00 3.28
524 588 2.094258 CACTTTGATGGATCACGGTTCG 59.906 50.000 0.00 0.00 36.36 3.95
610 674 1.009675 CGAGTGGTGTGCAACTTGC 60.010 57.895 6.82 6.82 45.29 4.01
680 744 4.321217 CACGGAATAATTCGATCGACTAGC 59.679 45.833 19.26 8.52 0.00 3.42
681 745 5.686834 TCACGGAATAATTCGATCGACTAG 58.313 41.667 19.26 6.18 0.00 2.57
683 747 4.563337 TCACGGAATAATTCGATCGACT 57.437 40.909 19.26 10.21 0.00 4.18
705 771 8.495160 TTCTTTCCGGGTTCCATATAATACTA 57.505 34.615 0.00 0.00 0.00 1.82
706 772 7.383156 TTCTTTCCGGGTTCCATATAATACT 57.617 36.000 0.00 0.00 0.00 2.12
707 773 7.935210 TCTTTCTTTCCGGGTTCCATATAATAC 59.065 37.037 0.00 0.00 0.00 1.89
808 874 2.342279 GGTTTTTCTTGGGCGGGC 59.658 61.111 0.00 0.00 0.00 6.13
814 880 1.669795 GCTGCATCGGGTTTTTCTTGG 60.670 52.381 0.00 0.00 0.00 3.61
816 882 0.240945 CGCTGCATCGGGTTTTTCTT 59.759 50.000 1.09 0.00 0.00 2.52
817 883 1.875963 CGCTGCATCGGGTTTTTCT 59.124 52.632 1.09 0.00 0.00 2.52
818 884 1.801512 GCGCTGCATCGGGTTTTTC 60.802 57.895 12.41 0.00 0.00 2.29
870 943 2.873288 CAAGAAGAGGGCAAGCGC 59.127 61.111 0.00 0.00 37.44 5.92
902 975 4.080863 GTGAATAAAGGGAGAGGAGCAGAA 60.081 45.833 0.00 0.00 0.00 3.02
903 976 3.452627 GTGAATAAAGGGAGAGGAGCAGA 59.547 47.826 0.00 0.00 0.00 4.26
904 977 3.454082 AGTGAATAAAGGGAGAGGAGCAG 59.546 47.826 0.00 0.00 0.00 4.24
905 978 3.452627 GAGTGAATAAAGGGAGAGGAGCA 59.547 47.826 0.00 0.00 0.00 4.26
906 979 3.181459 GGAGTGAATAAAGGGAGAGGAGC 60.181 52.174 0.00 0.00 0.00 4.70
907 980 4.294347 AGGAGTGAATAAAGGGAGAGGAG 58.706 47.826 0.00 0.00 0.00 3.69
908 981 4.264850 TGAGGAGTGAATAAAGGGAGAGGA 60.265 45.833 0.00 0.00 0.00 3.71
909 982 4.033709 TGAGGAGTGAATAAAGGGAGAGG 58.966 47.826 0.00 0.00 0.00 3.69
910 983 4.141824 GGTGAGGAGTGAATAAAGGGAGAG 60.142 50.000 0.00 0.00 0.00 3.20
996 1098 2.456119 GCGCGTCCACTCCATCTTG 61.456 63.158 8.43 0.00 0.00 3.02
1179 1292 2.740440 TACGCCACGACGTACGGA 60.740 61.111 21.06 13.88 46.19 4.69
1695 1808 3.749064 GAGTCGGAGAGGCACGCA 61.749 66.667 0.00 0.00 36.95 5.24
1908 2039 1.596477 GCTCGCCATGATCACCTCC 60.596 63.158 0.00 0.00 0.00 4.30
2045 2176 4.585364 CAGTACTACTACATCGGTTGACG 58.415 47.826 0.00 0.00 46.11 4.35
2231 2362 1.341976 ACCCAGACCCACATTTATGGC 60.342 52.381 0.00 0.00 38.55 4.40
2373 2507 2.151202 ACCGAACCAGCAACTGTAATG 58.849 47.619 0.00 0.00 0.00 1.90
2446 2583 3.772572 TCACCCAACTAGTAGCAGCAATA 59.227 43.478 0.00 0.00 0.00 1.90
2447 2584 2.571653 TCACCCAACTAGTAGCAGCAAT 59.428 45.455 0.00 0.00 0.00 3.56
2451 2592 3.357203 TCTCTCACCCAACTAGTAGCAG 58.643 50.000 0.00 0.00 0.00 4.24
2456 2597 1.562783 GGCTCTCTCACCCAACTAGT 58.437 55.000 0.00 0.00 0.00 2.57
2470 2611 0.912486 AACTTATCTTGGCCGGCTCT 59.088 50.000 28.56 9.12 0.00 4.09
2474 2615 1.339631 TGACCAACTTATCTTGGCCGG 60.340 52.381 0.00 0.00 44.19 6.13
2481 2622 2.009042 GCGCTGCTGACCAACTTATCT 61.009 52.381 0.00 0.00 0.00 1.98
2482 2623 0.375106 GCGCTGCTGACCAACTTATC 59.625 55.000 0.00 0.00 0.00 1.75
2483 2624 1.361668 CGCGCTGCTGACCAACTTAT 61.362 55.000 5.56 0.00 0.00 1.73
2484 2625 2.027073 CGCGCTGCTGACCAACTTA 61.027 57.895 5.56 0.00 0.00 2.24
2485 2626 3.349006 CGCGCTGCTGACCAACTT 61.349 61.111 5.56 0.00 0.00 2.66
2522 3705 1.001181 GCTGGCATTGGCAAAGAAGAA 59.999 47.619 14.35 0.00 43.71 2.52
2524 3707 0.390735 GGCTGGCATTGGCAAAGAAG 60.391 55.000 14.35 2.62 43.71 2.85
2525 3708 0.832983 AGGCTGGCATTGGCAAAGAA 60.833 50.000 14.35 0.00 43.71 2.52
2527 3710 0.672401 CAAGGCTGGCATTGGCAAAG 60.672 55.000 14.35 0.00 43.71 2.77
2597 3786 3.568538 CGAAAAAGGCAACATCTGAAGG 58.431 45.455 0.00 0.00 41.41 3.46
2610 3799 2.264813 TCTCCGTATTCGCGAAAAAGG 58.735 47.619 27.23 25.59 35.54 3.11
2611 3800 2.285084 GCTCTCCGTATTCGCGAAAAAG 60.285 50.000 27.23 18.22 35.54 2.27
2612 3801 1.657094 GCTCTCCGTATTCGCGAAAAA 59.343 47.619 27.23 14.43 35.54 1.94
2613 3802 1.135199 AGCTCTCCGTATTCGCGAAAA 60.135 47.619 27.23 3.73 35.54 2.29
2614 3803 0.454600 AGCTCTCCGTATTCGCGAAA 59.545 50.000 27.23 12.42 35.54 3.46
2615 3804 0.454600 AAGCTCTCCGTATTCGCGAA 59.545 50.000 25.66 25.66 35.54 4.70
2616 3805 0.248498 CAAGCTCTCCGTATTCGCGA 60.248 55.000 3.71 3.71 35.54 5.87
2617 3806 1.812214 GCAAGCTCTCCGTATTCGCG 61.812 60.000 0.00 0.00 35.54 5.87
2618 3807 1.812214 CGCAAGCTCTCCGTATTCGC 61.812 60.000 0.00 0.00 35.54 4.70
2619 3808 0.525668 ACGCAAGCTCTCCGTATTCG 60.526 55.000 4.70 0.00 45.62 3.34
2620 3809 2.486951 TACGCAAGCTCTCCGTATTC 57.513 50.000 8.74 0.00 45.62 1.75
2621 3810 3.454371 AATACGCAAGCTCTCCGTATT 57.546 42.857 22.52 22.52 46.88 1.89
2622 3811 2.361119 TCAATACGCAAGCTCTCCGTAT 59.639 45.455 15.98 15.98 46.46 3.06
2623 3812 1.746787 TCAATACGCAAGCTCTCCGTA 59.253 47.619 13.45 13.45 45.62 4.02
2624 3813 0.530744 TCAATACGCAAGCTCTCCGT 59.469 50.000 10.42 10.42 45.62 4.69
2625 3814 1.858091 ATCAATACGCAAGCTCTCCG 58.142 50.000 0.00 0.00 45.62 4.63
2626 3815 4.244425 TCTATCAATACGCAAGCTCTCC 57.756 45.455 0.00 0.00 45.62 3.71
2627 3816 5.524284 TCTTCTATCAATACGCAAGCTCTC 58.476 41.667 0.00 0.00 45.62 3.20
2628 3817 5.521906 TCTTCTATCAATACGCAAGCTCT 57.478 39.130 0.00 0.00 45.62 4.09
2629 3818 6.036083 TGTTTCTTCTATCAATACGCAAGCTC 59.964 38.462 0.00 0.00 45.62 4.09
2630 3819 5.874810 TGTTTCTTCTATCAATACGCAAGCT 59.125 36.000 0.00 0.00 45.62 3.74
2631 3820 6.106877 TGTTTCTTCTATCAATACGCAAGC 57.893 37.500 0.00 0.00 45.62 4.01
2633 3822 9.340695 CATTTTGTTTCTTCTATCAATACGCAA 57.659 29.630 0.00 0.00 0.00 4.85
2634 3823 8.726068 TCATTTTGTTTCTTCTATCAATACGCA 58.274 29.630 0.00 0.00 0.00 5.24
2635 3824 9.214953 CTCATTTTGTTTCTTCTATCAATACGC 57.785 33.333 0.00 0.00 0.00 4.42
2657 3846 9.733556 TGTGTTGTATCCTTTATTTGTACTCAT 57.266 29.630 0.00 0.00 0.00 2.90
2658 3847 9.733556 ATGTGTTGTATCCTTTATTTGTACTCA 57.266 29.630 0.00 0.00 0.00 3.41
2659 3848 9.988350 CATGTGTTGTATCCTTTATTTGTACTC 57.012 33.333 0.00 0.00 0.00 2.59
2660 3849 9.733556 TCATGTGTTGTATCCTTTATTTGTACT 57.266 29.630 0.00 0.00 0.00 2.73
2661 3850 9.769093 GTCATGTGTTGTATCCTTTATTTGTAC 57.231 33.333 0.00 0.00 0.00 2.90
2662 3851 9.508642 TGTCATGTGTTGTATCCTTTATTTGTA 57.491 29.630 0.00 0.00 0.00 2.41
2663 3852 8.402798 TGTCATGTGTTGTATCCTTTATTTGT 57.597 30.769 0.00 0.00 0.00 2.83
2664 3853 9.292846 CATGTCATGTGTTGTATCCTTTATTTG 57.707 33.333 4.53 0.00 0.00 2.32
2665 3854 9.241919 TCATGTCATGTGTTGTATCCTTTATTT 57.758 29.630 12.54 0.00 0.00 1.40
2666 3855 8.806429 TCATGTCATGTGTTGTATCCTTTATT 57.194 30.769 12.54 0.00 0.00 1.40
2667 3856 8.677300 GTTCATGTCATGTGTTGTATCCTTTAT 58.323 33.333 12.54 0.00 0.00 1.40
2668 3857 7.663493 TGTTCATGTCATGTGTTGTATCCTTTA 59.337 33.333 12.54 0.00 0.00 1.85
2669 3858 6.489700 TGTTCATGTCATGTGTTGTATCCTTT 59.510 34.615 12.54 0.00 0.00 3.11
2670 3859 6.003326 TGTTCATGTCATGTGTTGTATCCTT 58.997 36.000 12.54 0.00 0.00 3.36
2671 3860 5.412594 GTGTTCATGTCATGTGTTGTATCCT 59.587 40.000 12.54 0.00 0.00 3.24
2672 3861 5.181056 TGTGTTCATGTCATGTGTTGTATCC 59.819 40.000 12.54 0.00 0.00 2.59
2673 3862 6.147656 TCTGTGTTCATGTCATGTGTTGTATC 59.852 38.462 12.54 0.00 0.00 2.24
2674 3863 5.997129 TCTGTGTTCATGTCATGTGTTGTAT 59.003 36.000 12.54 0.00 0.00 2.29
2675 3864 5.236263 GTCTGTGTTCATGTCATGTGTTGTA 59.764 40.000 12.54 0.00 0.00 2.41
2676 3865 4.035558 GTCTGTGTTCATGTCATGTGTTGT 59.964 41.667 12.54 0.00 0.00 3.32
2677 3866 4.035441 TGTCTGTGTTCATGTCATGTGTTG 59.965 41.667 12.54 1.03 0.00 3.33
2678 3867 4.198530 TGTCTGTGTTCATGTCATGTGTT 58.801 39.130 12.54 0.00 0.00 3.32
2679 3868 3.807553 TGTCTGTGTTCATGTCATGTGT 58.192 40.909 12.54 0.00 0.00 3.72
2680 3869 4.719040 CATGTCTGTGTTCATGTCATGTG 58.281 43.478 12.54 0.00 37.31 3.21
2681 3870 3.189910 GCATGTCTGTGTTCATGTCATGT 59.810 43.478 12.54 0.00 42.09 3.21
2682 3871 3.726782 CGCATGTCTGTGTTCATGTCATG 60.727 47.826 6.47 6.47 42.09 3.07
2683 3872 2.417586 CGCATGTCTGTGTTCATGTCAT 59.582 45.455 0.00 0.00 42.09 3.06
2684 3873 1.799994 CGCATGTCTGTGTTCATGTCA 59.200 47.619 0.00 0.00 42.09 3.58
2685 3874 1.800586 ACGCATGTCTGTGTTCATGTC 59.199 47.619 0.00 0.00 43.48 3.06
2686 3875 1.532437 CACGCATGTCTGTGTTCATGT 59.468 47.619 0.00 0.00 43.48 3.21
2687 3876 1.799994 TCACGCATGTCTGTGTTCATG 59.200 47.619 12.46 0.00 43.48 3.07
2688 3877 2.168326 TCACGCATGTCTGTGTTCAT 57.832 45.000 12.46 0.00 43.48 2.57
2689 3878 1.597195 GTTCACGCATGTCTGTGTTCA 59.403 47.619 12.46 0.13 43.48 3.18
2690 3879 1.597195 TGTTCACGCATGTCTGTGTTC 59.403 47.619 12.46 8.71 43.48 3.18
2691 3880 1.662517 TGTTCACGCATGTCTGTGTT 58.337 45.000 12.46 0.00 43.48 3.32
2692 3881 1.532437 CATGTTCACGCATGTCTGTGT 59.468 47.619 12.46 0.00 46.85 3.72
2693 3882 1.799994 TCATGTTCACGCATGTCTGTG 59.200 47.619 8.11 8.11 44.68 3.66
2694 3883 2.168326 TCATGTTCACGCATGTCTGT 57.832 45.000 6.04 0.00 44.68 3.41
2695 3884 2.417586 ACATCATGTTCACGCATGTCTG 59.582 45.455 6.04 7.52 44.68 3.51
2696 3885 2.674852 GACATCATGTTCACGCATGTCT 59.325 45.455 12.00 0.00 44.68 3.41
2697 3886 2.223112 GGACATCATGTTCACGCATGTC 60.223 50.000 11.19 11.19 44.68 3.06
2698 3887 1.739466 GGACATCATGTTCACGCATGT 59.261 47.619 0.00 0.00 44.68 3.21
2699 3888 1.738908 TGGACATCATGTTCACGCATG 59.261 47.619 0.00 0.00 45.48 4.06
2700 3889 2.112380 TGGACATCATGTTCACGCAT 57.888 45.000 0.00 0.00 29.19 4.73
2701 3890 1.889545 TTGGACATCATGTTCACGCA 58.110 45.000 0.00 0.00 35.17 5.24
2702 3891 2.855180 CTTTGGACATCATGTTCACGC 58.145 47.619 0.00 0.00 35.17 5.34
2703 3892 2.226200 TGCTTTGGACATCATGTTCACG 59.774 45.455 0.00 0.00 35.17 4.35
2704 3893 3.503363 TCTGCTTTGGACATCATGTTCAC 59.497 43.478 0.00 0.00 35.17 3.18
2705 3894 3.753815 TCTGCTTTGGACATCATGTTCA 58.246 40.909 0.00 0.00 33.18 3.18
2706 3895 4.005650 TCTCTGCTTTGGACATCATGTTC 58.994 43.478 0.00 0.00 0.00 3.18
2707 3896 4.025040 TCTCTGCTTTGGACATCATGTT 57.975 40.909 0.00 0.00 0.00 2.71
2708 3897 3.708403 TCTCTGCTTTGGACATCATGT 57.292 42.857 0.00 0.00 0.00 3.21
2709 3898 4.216902 TGTTTCTCTGCTTTGGACATCATG 59.783 41.667 0.00 0.00 0.00 3.07
2710 3899 4.401022 TGTTTCTCTGCTTTGGACATCAT 58.599 39.130 0.00 0.00 0.00 2.45
2711 3900 3.819368 TGTTTCTCTGCTTTGGACATCA 58.181 40.909 0.00 0.00 0.00 3.07
2712 3901 4.320788 CCTTGTTTCTCTGCTTTGGACATC 60.321 45.833 0.00 0.00 0.00 3.06
2713 3902 3.571401 CCTTGTTTCTCTGCTTTGGACAT 59.429 43.478 0.00 0.00 0.00 3.06
2714 3903 2.951642 CCTTGTTTCTCTGCTTTGGACA 59.048 45.455 0.00 0.00 0.00 4.02
2715 3904 2.294512 CCCTTGTTTCTCTGCTTTGGAC 59.705 50.000 0.00 0.00 0.00 4.02
2716 3905 2.174639 TCCCTTGTTTCTCTGCTTTGGA 59.825 45.455 0.00 0.00 0.00 3.53
2717 3906 2.586425 TCCCTTGTTTCTCTGCTTTGG 58.414 47.619 0.00 0.00 0.00 3.28
2718 3907 3.613432 GCATCCCTTGTTTCTCTGCTTTG 60.613 47.826 0.00 0.00 0.00 2.77
2719 3908 2.560105 GCATCCCTTGTTTCTCTGCTTT 59.440 45.455 0.00 0.00 0.00 3.51
2720 3909 2.165998 GCATCCCTTGTTTCTCTGCTT 58.834 47.619 0.00 0.00 0.00 3.91
2721 3910 1.353694 AGCATCCCTTGTTTCTCTGCT 59.646 47.619 0.00 0.00 33.89 4.24
2722 3911 1.742268 GAGCATCCCTTGTTTCTCTGC 59.258 52.381 0.00 0.00 0.00 4.26
2723 3912 2.005451 CGAGCATCCCTTGTTTCTCTG 58.995 52.381 0.00 0.00 0.00 3.35
2724 3913 1.065854 CCGAGCATCCCTTGTTTCTCT 60.066 52.381 0.00 0.00 0.00 3.10
2725 3914 1.373570 CCGAGCATCCCTTGTTTCTC 58.626 55.000 0.00 0.00 0.00 2.87
2726 3915 0.678048 GCCGAGCATCCCTTGTTTCT 60.678 55.000 0.00 0.00 0.00 2.52
2727 3916 1.657751 GGCCGAGCATCCCTTGTTTC 61.658 60.000 0.00 0.00 0.00 2.78
2728 3917 1.678970 GGCCGAGCATCCCTTGTTT 60.679 57.895 0.00 0.00 0.00 2.83
2729 3918 2.044946 GGCCGAGCATCCCTTGTT 60.045 61.111 0.00 0.00 0.00 2.83
2730 3919 4.115199 GGGCCGAGCATCCCTTGT 62.115 66.667 0.00 0.00 39.46 3.16
2734 3923 4.256180 ATTCGGGCCGAGCATCCC 62.256 66.667 29.30 0.00 37.14 3.85
2735 3924 2.940890 TTCATTCGGGCCGAGCATCC 62.941 60.000 29.30 0.00 37.14 3.51
2736 3925 1.502163 CTTCATTCGGGCCGAGCATC 61.502 60.000 29.30 0.00 37.14 3.91
2737 3926 1.524621 CTTCATTCGGGCCGAGCAT 60.525 57.895 29.30 18.12 37.14 3.79
2738 3927 2.125147 CTTCATTCGGGCCGAGCA 60.125 61.111 29.30 16.41 37.14 4.26
2739 3928 2.897350 CCTTCATTCGGGCCGAGC 60.897 66.667 29.30 0.00 37.14 5.03
2740 3929 1.682451 TACCCTTCATTCGGGCCGAG 61.682 60.000 29.30 18.72 46.04 4.63
2741 3930 1.686455 TACCCTTCATTCGGGCCGA 60.686 57.895 27.46 27.46 46.04 5.54
2742 3931 1.523032 GTACCCTTCATTCGGGCCG 60.523 63.158 22.51 22.51 46.04 6.13
2743 3932 0.034863 TTGTACCCTTCATTCGGGCC 60.035 55.000 0.00 0.00 46.04 5.80
2744 3933 1.092348 GTTGTACCCTTCATTCGGGC 58.908 55.000 0.00 0.00 46.04 6.13
2746 3935 2.742053 CTGTGTTGTACCCTTCATTCGG 59.258 50.000 0.00 0.00 0.00 4.30
2747 3936 2.159627 GCTGTGTTGTACCCTTCATTCG 59.840 50.000 0.00 0.00 0.00 3.34
2748 3937 3.412386 AGCTGTGTTGTACCCTTCATTC 58.588 45.455 0.00 0.00 0.00 2.67
2749 3938 3.508845 AGCTGTGTTGTACCCTTCATT 57.491 42.857 0.00 0.00 0.00 2.57
2750 3939 4.634012 TTAGCTGTGTTGTACCCTTCAT 57.366 40.909 0.00 0.00 0.00 2.57
2751 3940 4.131596 GTTTAGCTGTGTTGTACCCTTCA 58.868 43.478 0.00 0.00 0.00 3.02
2752 3941 3.501062 GGTTTAGCTGTGTTGTACCCTTC 59.499 47.826 0.00 0.00 0.00 3.46
2753 3942 3.137728 AGGTTTAGCTGTGTTGTACCCTT 59.862 43.478 0.00 0.00 0.00 3.95
2754 3943 2.709397 AGGTTTAGCTGTGTTGTACCCT 59.291 45.455 0.00 0.00 0.00 4.34
2755 3944 3.136009 AGGTTTAGCTGTGTTGTACCC 57.864 47.619 0.00 0.00 0.00 3.69
2756 3945 4.634199 TGTAGGTTTAGCTGTGTTGTACC 58.366 43.478 0.00 0.00 0.00 3.34
2757 3946 6.607735 TTTGTAGGTTTAGCTGTGTTGTAC 57.392 37.500 0.00 0.00 0.00 2.90
2758 3947 6.038492 GGTTTTGTAGGTTTAGCTGTGTTGTA 59.962 38.462 0.00 0.00 0.00 2.41
2759 3948 5.163591 GGTTTTGTAGGTTTAGCTGTGTTGT 60.164 40.000 0.00 0.00 0.00 3.32
2760 3949 5.278604 GGTTTTGTAGGTTTAGCTGTGTTG 58.721 41.667 0.00 0.00 0.00 3.33
2761 3950 4.340097 GGGTTTTGTAGGTTTAGCTGTGTT 59.660 41.667 0.00 0.00 0.00 3.32
2762 3951 3.887110 GGGTTTTGTAGGTTTAGCTGTGT 59.113 43.478 0.00 0.00 0.00 3.72
2763 3952 3.058501 CGGGTTTTGTAGGTTTAGCTGTG 60.059 47.826 0.00 0.00 0.00 3.66
2764 3953 3.143728 CGGGTTTTGTAGGTTTAGCTGT 58.856 45.455 0.00 0.00 0.00 4.40
2765 3954 3.187842 GTCGGGTTTTGTAGGTTTAGCTG 59.812 47.826 0.00 0.00 0.00 4.24
2766 3955 3.405831 GTCGGGTTTTGTAGGTTTAGCT 58.594 45.455 0.00 0.00 0.00 3.32
2767 3956 2.485426 GGTCGGGTTTTGTAGGTTTAGC 59.515 50.000 0.00 0.00 0.00 3.09
2768 3957 3.076621 GGGTCGGGTTTTGTAGGTTTAG 58.923 50.000 0.00 0.00 0.00 1.85
2769 3958 2.441001 TGGGTCGGGTTTTGTAGGTTTA 59.559 45.455 0.00 0.00 0.00 2.01
2770 3959 1.214923 TGGGTCGGGTTTTGTAGGTTT 59.785 47.619 0.00 0.00 0.00 3.27
2771 3960 0.845337 TGGGTCGGGTTTTGTAGGTT 59.155 50.000 0.00 0.00 0.00 3.50
2772 3961 0.845337 TTGGGTCGGGTTTTGTAGGT 59.155 50.000 0.00 0.00 0.00 3.08
2773 3962 1.530323 CTTGGGTCGGGTTTTGTAGG 58.470 55.000 0.00 0.00 0.00 3.18
2774 3963 1.530323 CCTTGGGTCGGGTTTTGTAG 58.470 55.000 0.00 0.00 0.00 2.74
2775 3964 0.110869 CCCTTGGGTCGGGTTTTGTA 59.889 55.000 0.00 0.00 36.91 2.41
2776 3965 1.152631 CCCTTGGGTCGGGTTTTGT 60.153 57.895 0.00 0.00 36.91 2.83
2777 3966 2.570284 GCCCTTGGGTCGGGTTTTG 61.570 63.158 7.61 0.00 43.92 2.44
2778 3967 2.203582 GCCCTTGGGTCGGGTTTT 60.204 61.111 7.61 0.00 43.92 2.43
2779 3968 4.653888 CGCCCTTGGGTCGGGTTT 62.654 66.667 7.61 0.00 43.92 3.27
2785 3974 3.451894 CATTGCCGCCCTTGGGTC 61.452 66.667 7.61 0.00 0.00 4.46
2797 3986 2.672195 GCTCTTGTTGGTTAGGCATTGC 60.672 50.000 0.00 0.00 0.00 3.56
2798 3987 2.557924 TGCTCTTGTTGGTTAGGCATTG 59.442 45.455 0.00 0.00 0.00 2.82
2799 3988 2.558359 GTGCTCTTGTTGGTTAGGCATT 59.442 45.455 0.00 0.00 0.00 3.56
2800 3989 2.162681 GTGCTCTTGTTGGTTAGGCAT 58.837 47.619 0.00 0.00 0.00 4.40
2801 3990 1.604604 GTGCTCTTGTTGGTTAGGCA 58.395 50.000 0.00 0.00 0.00 4.75
2802 3991 0.881796 GGTGCTCTTGTTGGTTAGGC 59.118 55.000 0.00 0.00 0.00 3.93
2803 3992 2.154462 CTGGTGCTCTTGTTGGTTAGG 58.846 52.381 0.00 0.00 0.00 2.69
2804 3993 1.537202 GCTGGTGCTCTTGTTGGTTAG 59.463 52.381 0.00 0.00 36.03 2.34
2805 3994 1.133945 TGCTGGTGCTCTTGTTGGTTA 60.134 47.619 0.00 0.00 40.48 2.85
2806 3995 0.395586 TGCTGGTGCTCTTGTTGGTT 60.396 50.000 0.00 0.00 40.48 3.67
2807 3996 0.178981 ATGCTGGTGCTCTTGTTGGT 60.179 50.000 0.00 0.00 40.48 3.67
2808 3997 0.963962 AATGCTGGTGCTCTTGTTGG 59.036 50.000 0.00 0.00 40.48 3.77
2809 3998 1.610038 TCAATGCTGGTGCTCTTGTTG 59.390 47.619 0.00 0.00 40.48 3.33
2810 3999 1.884579 CTCAATGCTGGTGCTCTTGTT 59.115 47.619 0.00 0.00 40.48 2.83
2811 4000 1.531423 CTCAATGCTGGTGCTCTTGT 58.469 50.000 0.00 0.00 40.48 3.16
2812 4001 0.809385 CCTCAATGCTGGTGCTCTTG 59.191 55.000 0.00 0.00 40.48 3.02
2813 4002 0.964358 GCCTCAATGCTGGTGCTCTT 60.964 55.000 0.00 0.00 40.48 2.85
2814 4003 1.378250 GCCTCAATGCTGGTGCTCT 60.378 57.895 0.00 0.00 40.48 4.09
2815 4004 1.654954 CTGCCTCAATGCTGGTGCTC 61.655 60.000 0.00 0.00 40.48 4.26
2816 4005 1.677966 CTGCCTCAATGCTGGTGCT 60.678 57.895 0.00 0.00 40.48 4.40
2817 4006 2.707849 CCTGCCTCAATGCTGGTGC 61.708 63.158 0.00 0.00 43.24 5.01
2818 4007 2.050350 CCCTGCCTCAATGCTGGTG 61.050 63.158 7.93 0.00 45.84 4.17
2819 4008 2.357836 CCCTGCCTCAATGCTGGT 59.642 61.111 7.93 0.00 45.84 4.00
2820 4009 2.050350 CACCCTGCCTCAATGCTGG 61.050 63.158 2.33 2.33 46.57 4.85
2821 4010 2.050350 CCACCCTGCCTCAATGCTG 61.050 63.158 0.00 0.00 0.00 4.41
2824 4013 1.379044 GGACCACCCTGCCTCAATG 60.379 63.158 0.00 0.00 0.00 2.82
2839 4028 2.240279 AGAGGTATGGTGATAGCGGAC 58.760 52.381 0.00 0.00 37.58 4.79


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

AutoCloner maintained by Alex Coulton.