Multiple sequence alignment - TraesCS2A01G495700

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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 TraesCS2A01G495700 chr2A 100.000 3574 0 0 1 3574 727185138 727181565 0.000000e+00 6601.0
1 TraesCS2A01G495700 chr2A 82.950 827 85 27 1041 1847 288599644 288598854 0.000000e+00 695.0
2 TraesCS2A01G495700 chr2A 96.711 152 5 0 541 692 155780172 155780323 1.650000e-63 254.0
3 TraesCS2A01G495700 chr2A 86.179 123 13 2 2927 3046 162803547 162803668 2.900000e-26 130.0
4 TraesCS2A01G495700 chr2D 91.502 2424 92 36 705 3051 592627390 592625004 0.000000e+00 3230.0
5 TraesCS2A01G495700 chr2D 98.329 359 6 0 1 359 592628126 592627768 6.510000e-177 630.0
6 TraesCS2A01G495700 chr2D 90.642 374 13 7 3151 3503 592625030 592624658 8.980000e-131 477.0
7 TraesCS2A01G495700 chr2D 88.837 215 17 7 1660 1870 80828704 80828915 1.270000e-64 257.0
8 TraesCS2A01G495700 chr2D 93.382 136 7 2 3046 3181 592468113 592467980 2.180000e-47 200.0
9 TraesCS2A01G495700 chr2D 85.246 61 5 4 482 542 523024843 523024787 3.850000e-05 60.2
10 TraesCS2A01G495700 chr2B 88.159 929 74 25 1038 1939 718595962 718595043 0.000000e+00 1074.0
11 TraesCS2A01G495700 chr2B 87.500 792 74 15 2154 2931 718594603 718593823 0.000000e+00 891.0
12 TraesCS2A01G495700 chr2B 95.833 360 9 3 1 359 718597095 718596741 8.600000e-161 577.0
13 TraesCS2A01G495700 chr2B 92.926 311 5 3 3176 3469 718593821 718593511 1.520000e-118 436.0
14 TraesCS2A01G495700 chr2B 82.544 338 20 18 702 1006 718596380 718596049 9.840000e-66 261.0
15 TraesCS2A01G495700 chr2B 96.000 50 1 1 995 1043 718596030 718595981 2.960000e-11 80.5
16 TraesCS2A01G495700 chr2B 81.553 103 8 7 361 462 718596675 718596583 1.380000e-09 75.0
17 TraesCS2A01G495700 chr2B 85.455 55 7 1 482 536 476564426 476564373 4.980000e-04 56.5
18 TraesCS2A01G495700 chr3B 91.748 618 39 10 1534 2145 184209497 184208886 0.000000e+00 848.0
19 TraesCS2A01G495700 chr3B 97.333 150 4 0 543 692 2103302 2103153 4.580000e-64 255.0
20 TraesCS2A01G495700 chr3B 94.444 162 8 1 532 692 18858970 18858809 7.660000e-62 248.0
21 TraesCS2A01G495700 chr3B 89.062 192 20 1 1470 1661 808608520 808608710 1.660000e-58 237.0
22 TraesCS2A01G495700 chr3B 88.506 174 17 2 3012 3184 802923715 802923544 1.300000e-49 207.0
23 TraesCS2A01G495700 chr3B 94.118 136 6 2 3049 3183 760589111 760588977 4.680000e-49 206.0
24 TraesCS2A01G495700 chr3B 95.349 129 4 2 3050 3178 793003112 793003238 1.680000e-48 204.0
25 TraesCS2A01G495700 chr3B 83.969 131 13 7 2928 3053 550661387 550661260 6.270000e-23 119.0
26 TraesCS2A01G495700 chr4A 91.262 618 42 10 1534 2145 669508043 669507432 0.000000e+00 832.0
27 TraesCS2A01G495700 chr4A 91.262 618 42 10 1534 2145 731142783 731142172 0.000000e+00 832.0
28 TraesCS2A01G495700 chr4A 84.525 769 74 21 1041 1798 614805409 614804675 0.000000e+00 719.0
29 TraesCS2A01G495700 chr4A 95.652 253 7 1 1927 2175 519261645 519261393 1.550000e-108 403.0
30 TraesCS2A01G495700 chr4A 89.744 234 17 7 1660 1889 519261873 519261643 3.490000e-75 292.0
31 TraesCS2A01G495700 chr4A 93.382 136 8 1 3047 3182 652849883 652849749 2.180000e-47 200.0
32 TraesCS2A01G495700 chr7A 83.615 769 97 14 1042 1799 478038506 478037756 0.000000e+00 695.0
33 TraesCS2A01G495700 chr7A 95.302 149 7 0 544 692 12118755 12118607 1.660000e-58 237.0
34 TraesCS2A01G495700 chr3A 83.615 769 81 21 1035 1792 301210511 301211245 0.000000e+00 680.0
35 TraesCS2A01G495700 chr3A 83.158 760 83 24 1041 1790 256404148 256403424 0.000000e+00 652.0
36 TraesCS2A01G495700 chr3A 82.620 771 91 20 1032 1792 727324592 727325329 3.010000e-180 641.0
37 TraesCS2A01G495700 chr3A 96.732 153 5 0 540 692 7202019 7201867 4.580000e-64 255.0
38 TraesCS2A01G495700 chr3A 96.711 152 5 0 541 692 710866862 710866711 1.650000e-63 254.0
39 TraesCS2A01G495700 chr3A 95.541 157 6 1 537 692 157045211 157045367 2.130000e-62 250.0
40 TraesCS2A01G495700 chr5A 83.180 761 83 21 1041 1790 699174509 699173783 0.000000e+00 654.0
41 TraesCS2A01G495700 chr5A 87.786 131 12 2 2925 3051 622770092 622769962 2.220000e-32 150.0
42 TraesCS2A01G495700 chr5A 85.484 124 14 2 2927 3046 521206523 521206646 3.750000e-25 126.0
43 TraesCS2A01G495700 chr5B 97.510 241 6 0 1935 2175 43550302 43550542 2.570000e-111 412.0
44 TraesCS2A01G495700 chr5D 97.095 241 7 0 1927 2167 25521888 25522128 1.190000e-109 407.0
45 TraesCS2A01G495700 chr5D 90.171 234 16 7 1660 1889 25521660 25521890 7.500000e-77 298.0
46 TraesCS2A01G495700 chr1A 95.257 253 8 1 1927 2175 212155626 212155374 7.190000e-107 398.0
47 TraesCS2A01G495700 chr1A 88.462 234 20 7 1660 1889 212155854 212155624 3.510000e-70 276.0
48 TraesCS2A01G495700 chr1A 84.553 123 15 2 2927 3046 459639434 459639313 6.270000e-23 119.0
49 TraesCS2A01G495700 chr6A 95.181 249 12 0 1927 2175 87407856 87407608 9.300000e-106 394.0
50 TraesCS2A01G495700 chr6A 95.000 120 5 1 1769 1887 587390182 587390301 1.690000e-43 187.0
51 TraesCS2A01G495700 chr6B 96.104 154 6 0 539 692 114057205 114057052 5.920000e-63 252.0
52 TraesCS2A01G495700 chr4B 95.570 158 5 2 536 692 658178333 658178177 5.920000e-63 252.0
53 TraesCS2A01G495700 chr4B 84.211 57 9 0 481 537 60326716 60326772 4.980000e-04 56.5
54 TraesCS2A01G495700 chr7B 96.094 128 4 1 3050 3177 578434541 578434415 1.300000e-49 207.0
55 TraesCS2A01G495700 chr7B 96.063 127 4 1 3049 3175 377050545 377050670 4.680000e-49 206.0
56 TraesCS2A01G495700 chr7B 95.349 129 5 1 3050 3178 72021755 72021882 1.680000e-48 204.0
57 TraesCS2A01G495700 chr4D 91.667 144 9 3 3050 3192 127555116 127554975 2.810000e-46 196.0
58 TraesCS2A01G495700 chr4D 89.362 47 4 1 491 537 41723889 41723934 1.390000e-04 58.4
59 TraesCS2A01G495700 chr4D 85.185 54 6 1 482 533 462801221 462801274 2.000000e-03 54.7
60 TraesCS2A01G495700 chr6D 85.366 123 15 1 2927 3046 97403732 97403610 1.350000e-24 124.0
61 TraesCS2A01G495700 chr6D 87.273 55 7 0 483 537 408903077 408903023 2.980000e-06 63.9
62 TraesCS2A01G495700 chr3D 84.553 123 16 1 2927 3046 178107899 178108021 6.270000e-23 119.0
63 TraesCS2A01G495700 chr3D 76.265 257 41 15 2928 3177 351086868 351086625 6.270000e-23 119.0
64 TraesCS2A01G495700 chr3D 85.965 57 5 2 482 537 29167352 29167298 1.390000e-04 58.4
65 TraesCS2A01G495700 chr1D 85.965 57 5 2 482 537 246650036 246649982 1.390000e-04 58.4
66 TraesCS2A01G495700 chr1B 85.965 57 5 2 482 537 331419515 331419569 1.390000e-04 58.4


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 TraesCS2A01G495700 chr2A 727181565 727185138 3573 True 6601.000000 6601 100.000000 1 3574 1 chr2A.!!$R2 3573
1 TraesCS2A01G495700 chr2A 288598854 288599644 790 True 695.000000 695 82.950000 1041 1847 1 chr2A.!!$R1 806
2 TraesCS2A01G495700 chr2D 592624658 592628126 3468 True 1445.666667 3230 93.491000 1 3503 3 chr2D.!!$R3 3502
3 TraesCS2A01G495700 chr2B 718593511 718597095 3584 True 484.928571 1074 89.216429 1 3469 7 chr2B.!!$R2 3468
4 TraesCS2A01G495700 chr3B 184208886 184209497 611 True 848.000000 848 91.748000 1534 2145 1 chr3B.!!$R3 611
5 TraesCS2A01G495700 chr4A 669507432 669508043 611 True 832.000000 832 91.262000 1534 2145 1 chr4A.!!$R3 611
6 TraesCS2A01G495700 chr4A 731142172 731142783 611 True 832.000000 832 91.262000 1534 2145 1 chr4A.!!$R4 611
7 TraesCS2A01G495700 chr4A 614804675 614805409 734 True 719.000000 719 84.525000 1041 1798 1 chr4A.!!$R1 757
8 TraesCS2A01G495700 chr7A 478037756 478038506 750 True 695.000000 695 83.615000 1042 1799 1 chr7A.!!$R2 757
9 TraesCS2A01G495700 chr3A 301210511 301211245 734 False 680.000000 680 83.615000 1035 1792 1 chr3A.!!$F2 757
10 TraesCS2A01G495700 chr3A 256403424 256404148 724 True 652.000000 652 83.158000 1041 1790 1 chr3A.!!$R2 749
11 TraesCS2A01G495700 chr3A 727324592 727325329 737 False 641.000000 641 82.620000 1032 1792 1 chr3A.!!$F3 760
12 TraesCS2A01G495700 chr5A 699173783 699174509 726 True 654.000000 654 83.180000 1041 1790 1 chr5A.!!$R2 749

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
462 528 1.410153 AGCACAGAAAAGGCAACCAAG 59.590 47.619 0.00 0.0 37.17 3.61 F
1026 1431 0.846427 TCCCCTCTTTCACATGGCCT 60.846 55.000 3.32 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2375 0.038166 ACCGGTGTGATGCCAGAAAT 59.962 50.0 6.12 0.0 0.0 2.17 R
2890 3618 0.517316 GATCACGGCCAAGTTCACAC 59.483 55.0 2.24 0.0 0.0 3.82 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
336 337 5.280945 CCAGTTTACAATGTTGTCTTGGTG 58.719 41.667 0.99 0.00 42.35 4.17
349 350 3.644265 TGTCTTGGTGCTTTGGTAGAGTA 59.356 43.478 0.00 0.00 0.00 2.59
355 356 3.510360 GGTGCTTTGGTAGAGTAGTCAGA 59.490 47.826 0.00 0.00 0.00 3.27
367 368 5.054390 GAGTAGTCAGACTCTTTGGACAG 57.946 47.826 6.27 0.00 42.26 3.51
369 370 5.329399 AGTAGTCAGACTCTTTGGACAGAT 58.671 41.667 6.27 0.00 32.79 2.90
375 440 5.046304 TCAGACTCTTTGGACAGATAAAGGG 60.046 44.000 0.00 0.00 39.65 3.95
399 464 4.099380 TCAAACACCAAACGAAAGAACC 57.901 40.909 0.00 0.00 0.00 3.62
420 485 9.352191 AGAACCTACTTGTACAGTTATATCGAT 57.648 33.333 2.16 2.16 36.88 3.59
421 486 9.395707 GAACCTACTTGTACAGTTATATCGATG 57.604 37.037 8.54 0.00 36.88 3.84
422 487 7.368833 ACCTACTTGTACAGTTATATCGATGC 58.631 38.462 8.54 0.00 36.88 3.91
423 488 7.230913 ACCTACTTGTACAGTTATATCGATGCT 59.769 37.037 8.54 0.00 36.88 3.79
462 528 1.410153 AGCACAGAAAAGGCAACCAAG 59.590 47.619 0.00 0.00 37.17 3.61
464 530 2.799562 GCACAGAAAAGGCAACCAAGAC 60.800 50.000 0.00 0.00 37.17 3.01
468 534 4.580580 ACAGAAAAGGCAACCAAGACTAAG 59.419 41.667 0.00 0.00 37.17 2.18
470 536 5.049129 CAGAAAAGGCAACCAAGACTAAGAG 60.049 44.000 0.00 0.00 37.17 2.85
471 537 4.706842 AAAGGCAACCAAGACTAAGAGA 57.293 40.909 0.00 0.00 37.17 3.10
473 539 4.278975 AGGCAACCAAGACTAAGAGAAG 57.721 45.455 0.00 0.00 37.17 2.85
474 540 3.008485 AGGCAACCAAGACTAAGAGAAGG 59.992 47.826 0.00 0.00 37.17 3.46
475 541 3.339141 GCAACCAAGACTAAGAGAAGGG 58.661 50.000 0.00 0.00 0.00 3.95
476 542 3.008049 GCAACCAAGACTAAGAGAAGGGA 59.992 47.826 0.00 0.00 0.00 4.20
479 545 6.241645 CAACCAAGACTAAGAGAAGGGAAAT 58.758 40.000 0.00 0.00 0.00 2.17
480 546 6.056090 ACCAAGACTAAGAGAAGGGAAATC 57.944 41.667 0.00 0.00 0.00 2.17
496 670 7.384524 AGGGAAATCATACATCTGATTCAGA 57.615 36.000 18.29 18.29 43.37 3.27
504 678 8.498054 TCATACATCTGATTCAGAAAAGTTCC 57.502 34.615 19.73 0.00 44.04 3.62
512 692 8.378565 TCTGATTCAGAAAAGTTCCTAGAACAT 58.621 33.333 13.96 0.00 37.57 2.71
531 711 8.786826 AGAACATCTTATATTTGTGAACGGAA 57.213 30.769 0.00 0.00 0.00 4.30
557 737 6.936968 AGTTCATACTACTCCCTCTGTTTT 57.063 37.500 0.00 0.00 31.21 2.43
558 738 7.317722 AGTTCATACTACTCCCTCTGTTTTT 57.682 36.000 0.00 0.00 31.21 1.94
559 739 8.431910 AGTTCATACTACTCCCTCTGTTTTTA 57.568 34.615 0.00 0.00 31.21 1.52
560 740 8.877195 AGTTCATACTACTCCCTCTGTTTTTAA 58.123 33.333 0.00 0.00 31.21 1.52
561 741 9.498176 GTTCATACTACTCCCTCTGTTTTTAAA 57.502 33.333 0.00 0.00 0.00 1.52
570 750 9.588096 ACTCCCTCTGTTTTTAAATATTTGTCT 57.412 29.630 11.05 0.00 0.00 3.41
594 774 9.778741 TCTTTGTAGACATTTCAAATGACTACT 57.221 29.630 33.32 21.35 42.98 2.57
597 777 9.990360 TTGTAGACATTTCAAATGACTACTACA 57.010 29.630 33.32 27.89 42.98 2.74
601 781 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
602 782 8.420374 ACATTTCAAATGACTACTACATACGG 57.580 34.615 17.30 0.00 0.00 4.02
603 783 8.255206 ACATTTCAAATGACTACTACATACGGA 58.745 33.333 17.30 0.00 0.00 4.69
604 784 9.261180 CATTTCAAATGACTACTACATACGGAT 57.739 33.333 3.82 0.00 0.00 4.18
605 785 8.642908 TTTCAAATGACTACTACATACGGATG 57.357 34.615 5.94 5.94 39.16 3.51
607 787 8.454570 TCAAATGACTACTACATACGGATGTA 57.545 34.615 19.32 19.32 44.77 2.29
608 788 9.074576 TCAAATGACTACTACATACGGATGTAT 57.925 33.333 20.64 13.02 45.42 2.29
648 828 7.516198 AGTGTAGATTCACTCATTTTGCTTT 57.484 32.000 0.00 0.00 44.07 3.51
649 829 7.365741 AGTGTAGATTCACTCATTTTGCTTTG 58.634 34.615 0.00 0.00 44.07 2.77
650 830 7.013655 AGTGTAGATTCACTCATTTTGCTTTGT 59.986 33.333 0.00 0.00 44.07 2.83
651 831 8.289618 GTGTAGATTCACTCATTTTGCTTTGTA 58.710 33.333 0.00 0.00 35.68 2.41
652 832 9.013229 TGTAGATTCACTCATTTTGCTTTGTAT 57.987 29.630 0.00 0.00 0.00 2.29
653 833 9.282247 GTAGATTCACTCATTTTGCTTTGTATG 57.718 33.333 0.00 0.00 0.00 2.39
654 834 7.889469 AGATTCACTCATTTTGCTTTGTATGT 58.111 30.769 0.00 0.00 0.00 2.29
655 835 9.013229 AGATTCACTCATTTTGCTTTGTATGTA 57.987 29.630 0.00 0.00 0.00 2.29
656 836 9.282247 GATTCACTCATTTTGCTTTGTATGTAG 57.718 33.333 0.00 0.00 0.00 2.74
657 837 7.744087 TCACTCATTTTGCTTTGTATGTAGT 57.256 32.000 0.00 0.00 0.00 2.73
658 838 7.806690 TCACTCATTTTGCTTTGTATGTAGTC 58.193 34.615 0.00 0.00 0.00 2.59
659 839 7.443879 TCACTCATTTTGCTTTGTATGTAGTCA 59.556 33.333 0.00 0.00 0.00 3.41
660 840 7.535258 CACTCATTTTGCTTTGTATGTAGTCAC 59.465 37.037 0.00 0.00 0.00 3.67
661 841 7.445402 ACTCATTTTGCTTTGTATGTAGTCACT 59.555 33.333 0.00 0.00 0.00 3.41
662 842 8.165239 TCATTTTGCTTTGTATGTAGTCACTT 57.835 30.769 0.00 0.00 0.00 3.16
663 843 8.075574 TCATTTTGCTTTGTATGTAGTCACTTG 58.924 33.333 0.00 0.00 0.00 3.16
664 844 6.935741 TTTGCTTTGTATGTAGTCACTTGT 57.064 33.333 0.00 0.00 0.00 3.16
665 845 6.935741 TTGCTTTGTATGTAGTCACTTGTT 57.064 33.333 0.00 0.00 0.00 2.83
666 846 6.299023 TGCTTTGTATGTAGTCACTTGTTG 57.701 37.500 0.00 0.00 0.00 3.33
667 847 6.052360 TGCTTTGTATGTAGTCACTTGTTGA 58.948 36.000 0.00 0.00 0.00 3.18
668 848 6.540551 TGCTTTGTATGTAGTCACTTGTTGAA 59.459 34.615 0.00 0.00 35.39 2.69
669 849 7.066404 TGCTTTGTATGTAGTCACTTGTTGAAA 59.934 33.333 0.00 0.00 35.39 2.69
670 850 8.076178 GCTTTGTATGTAGTCACTTGTTGAAAT 58.924 33.333 0.00 0.00 35.39 2.17
671 851 9.385902 CTTTGTATGTAGTCACTTGTTGAAATG 57.614 33.333 0.00 0.00 35.39 2.32
672 852 6.898041 TGTATGTAGTCACTTGTTGAAATGC 58.102 36.000 0.00 0.00 35.39 3.56
673 853 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
674 854 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
675 855 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
676 856 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
677 857 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
678 858 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
679 859 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
680 860 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
681 861 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
682 862 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
683 863 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
684 864 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
685 865 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
710 1037 9.507329 AGTATTTAACTTTCTGATTCTGAAGCA 57.493 29.630 8.20 8.20 33.35 3.91
736 1064 4.591072 GCTATCTCCAGATTAGTTCCAGGT 59.409 45.833 0.00 0.00 36.05 4.00
757 1090 6.925165 CAGGTTTGAATTTGTTATCTGCTGTT 59.075 34.615 0.00 0.00 0.00 3.16
787 1120 7.334171 ACCGAATTGGAATTGGAATTTGAATTC 59.666 33.333 7.73 7.73 41.35 2.17
814 1150 8.596380 GCTGCTGAAATAAGAATATACGGATAC 58.404 37.037 0.00 0.00 0.00 2.24
827 1163 8.732746 AATATACGGATACAAAAGCTTCAACT 57.267 30.769 0.00 0.00 0.00 3.16
869 1205 3.543670 GAACGCGCATAGTAGTACTCTC 58.456 50.000 5.73 0.00 0.00 3.20
870 1206 2.558378 ACGCGCATAGTAGTACTCTCA 58.442 47.619 5.73 0.00 0.00 3.27
882 1229 4.120946 AGTACTCTCAACTCAACCTCCT 57.879 45.455 0.00 0.00 0.00 3.69
959 1333 2.420890 GCGATCAGCCCAGAGAGG 59.579 66.667 0.00 0.00 40.81 3.69
1026 1431 0.846427 TCCCCTCTTTCACATGGCCT 60.846 55.000 3.32 0.00 0.00 5.19
1376 1809 2.650322 GATCTCGTCCTCCACTTCTCT 58.350 52.381 0.00 0.00 0.00 3.10
1377 1810 1.827681 TCTCGTCCTCCACTTCTCTG 58.172 55.000 0.00 0.00 0.00 3.35
1408 1845 5.057149 GGCTCTGAAGTCTCAAACTGTAAA 58.943 41.667 0.00 0.00 38.58 2.01
1532 1973 3.887621 ACATCTTGCCGTAAGCTCTTA 57.112 42.857 0.00 0.00 44.23 2.10
1559 2001 1.734117 GCTTTCGCCCATGTGCAAC 60.734 57.895 0.00 0.00 37.35 4.17
1618 2060 3.366985 GGTGGTGTCGAATTTTTGGATCC 60.367 47.826 4.20 4.20 0.00 3.36
1658 2101 2.235891 CAACCTGTTCCTTAACACCCC 58.764 52.381 0.00 0.00 40.69 4.95
1733 2187 6.003950 ACTGTGCTGTCCTTGTACATAAAAT 58.996 36.000 0.00 0.00 30.36 1.82
1734 2188 6.149474 ACTGTGCTGTCCTTGTACATAAAATC 59.851 38.462 0.00 0.00 30.36 2.17
1736 2190 5.414454 GTGCTGTCCTTGTACATAAAATCCA 59.586 40.000 0.00 0.00 0.00 3.41
1737 2191 5.647658 TGCTGTCCTTGTACATAAAATCCAG 59.352 40.000 0.00 0.00 0.00 3.86
1738 2192 5.449177 GCTGTCCTTGTACATAAAATCCAGC 60.449 44.000 0.00 5.15 34.42 4.85
1767 2221 9.790344 AAAGGGATTGTCATCTGAAGATAATAG 57.210 33.333 5.11 0.00 32.63 1.73
1811 2265 5.588648 CCTGTATATGTGTTGAAATTCCCGT 59.411 40.000 0.00 0.00 0.00 5.28
1850 2311 3.495001 GTGGTCTCTGTTTGCTGAAGTAC 59.505 47.826 0.00 0.00 0.00 2.73
1904 2365 3.697045 AGCTACAGTACTGGTGCTCTTAG 59.303 47.826 27.83 18.93 38.27 2.18
1914 2375 8.154856 AGTACTGGTGCTCTTAGTTTCATAAAA 58.845 33.333 0.00 0.00 0.00 1.52
2000 2645 3.441572 GGTGATTGCTCATTGCTGTACTT 59.558 43.478 0.00 0.00 43.37 2.24
2192 2909 8.227791 GGCTAACATTATTGGTTATCATGTACG 58.772 37.037 0.00 0.00 31.43 3.67
2193 2910 8.227791 GCTAACATTATTGGTTATCATGTACGG 58.772 37.037 0.00 0.00 31.43 4.02
2322 3045 5.077134 TGTGTTGTGGTCATCATAGAGAG 57.923 43.478 0.00 0.00 0.00 3.20
2368 3091 4.148128 ACTCTAATTCTGTCCTGCCATG 57.852 45.455 0.00 0.00 0.00 3.66
2376 3099 1.212688 CTGTCCTGCCATGGGTTATCA 59.787 52.381 15.13 0.88 0.00 2.15
2382 3105 2.824936 CTGCCATGGGTTATCAACAACA 59.175 45.455 15.13 0.00 0.00 3.33
2516 3244 1.487976 GAGGTGGAGATGCAGGAATCA 59.512 52.381 0.00 0.00 0.00 2.57
2606 3334 5.412904 GCTGATGGCATATTAGGTAAGGTTC 59.587 44.000 0.00 0.00 41.35 3.62
2657 3385 8.668510 TCCAACTTATTTCAGAGCTCATATTC 57.331 34.615 17.77 0.00 0.00 1.75
2890 3618 1.466167 GTGCACTGACATGTAAGCTGG 59.534 52.381 10.40 1.66 0.00 4.85
2956 3684 1.611491 CGCCCCAAAAAGCTTGTCTTA 59.389 47.619 0.00 0.00 33.88 2.10
2977 3705 3.931578 AGATTTGCCTAGATACGGATGC 58.068 45.455 0.00 0.00 0.00 3.91
3009 3741 6.292389 ACGTAGTGTTAGATACATCCGTAC 57.708 41.667 0.00 0.00 42.51 3.67
3031 3763 7.808856 CGTACCTAGATAAATCTAAGACAAGCC 59.191 40.741 3.20 0.00 38.80 4.35
3051 3783 3.538591 CCTTTTGGGACGGAGGTAATAC 58.461 50.000 0.00 0.00 37.23 1.89
3052 3784 3.199289 CCTTTTGGGACGGAGGTAATACT 59.801 47.826 0.00 0.00 37.23 2.12
3053 3785 4.439968 CTTTTGGGACGGAGGTAATACTC 58.560 47.826 0.00 0.00 36.76 2.59
3054 3786 7.653482 CCTTTTGGGACGGAGGTAATACTCC 62.653 52.000 2.18 2.18 44.72 3.85
3062 3794 3.226682 GAGGTAATACTCCCTCCGTCT 57.773 52.381 0.00 0.00 41.22 4.18
3063 3795 2.885894 GAGGTAATACTCCCTCCGTCTG 59.114 54.545 0.00 0.00 41.22 3.51
3064 3796 2.512896 AGGTAATACTCCCTCCGTCTGA 59.487 50.000 0.00 0.00 0.00 3.27
3065 3797 3.053095 AGGTAATACTCCCTCCGTCTGAA 60.053 47.826 0.00 0.00 0.00 3.02
3066 3798 3.703052 GGTAATACTCCCTCCGTCTGAAA 59.297 47.826 0.00 0.00 0.00 2.69
3067 3799 4.161001 GGTAATACTCCCTCCGTCTGAAAA 59.839 45.833 0.00 0.00 0.00 2.29
3068 3800 5.163332 GGTAATACTCCCTCCGTCTGAAAAT 60.163 44.000 0.00 0.00 0.00 1.82
3069 3801 6.041296 GGTAATACTCCCTCCGTCTGAAAATA 59.959 42.308 0.00 0.00 0.00 1.40
3070 3802 3.889520 ACTCCCTCCGTCTGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3071 3803 3.442076 ACTCCCTCCGTCTGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3072 3804 3.838903 ACTCCCTCCGTCTGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3073 3805 4.184629 CTCCCTCCGTCTGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3074 3806 3.581332 TCCCTCCGTCTGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3075 3807 3.933332 CCCTCCGTCTGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3076 3808 4.562757 CCCTCCGTCTGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
3077 3809 5.178797 CCTCCGTCTGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
3078 3810 5.292101 CCTCCGTCTGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
3079 3811 5.789521 TCCGTCTGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
3080 3812 6.227522 TCCGTCTGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
3081 3813 6.708502 TCCGTCTGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
3082 3814 7.227711 TCCGTCTGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
3083 3815 8.023128 CCGTCTGAAAATACTTGTCATCAAAAT 58.977 33.333 0.00 0.00 32.87 1.82
3084 3816 8.843733 CGTCTGAAAATACTTGTCATCAAAATG 58.156 33.333 0.00 0.00 32.87 2.32
3085 3817 9.897744 GTCTGAAAATACTTGTCATCAAAATGA 57.102 29.630 0.00 0.00 39.63 2.57
3097 3829 6.581388 TCATCAAAATGACTAGAAGGGGAT 57.419 37.500 0.00 0.00 36.98 3.85
3098 3830 6.359804 TCATCAAAATGACTAGAAGGGGATG 58.640 40.000 0.00 0.00 36.98 3.51
3099 3831 5.779241 TCAAAATGACTAGAAGGGGATGT 57.221 39.130 0.00 0.00 0.00 3.06
3100 3832 6.884472 TCAAAATGACTAGAAGGGGATGTA 57.116 37.500 0.00 0.00 0.00 2.29
3101 3833 7.451731 TCAAAATGACTAGAAGGGGATGTAT 57.548 36.000 0.00 0.00 0.00 2.29
3102 3834 7.509546 TCAAAATGACTAGAAGGGGATGTATC 58.490 38.462 0.00 0.00 0.00 2.24
3103 3835 7.348274 TCAAAATGACTAGAAGGGGATGTATCT 59.652 37.037 0.00 0.00 0.00 1.98
3104 3836 8.651389 CAAAATGACTAGAAGGGGATGTATCTA 58.349 37.037 0.00 0.00 0.00 1.98
3105 3837 8.429237 AAATGACTAGAAGGGGATGTATCTAG 57.571 38.462 0.00 7.03 44.39 2.43
3106 3838 6.781857 TGACTAGAAGGGGATGTATCTAGA 57.218 41.667 13.85 0.00 42.48 2.43
3107 3839 7.350044 TGACTAGAAGGGGATGTATCTAGAT 57.650 40.000 10.73 10.73 42.48 1.98
3108 3840 7.178573 TGACTAGAAGGGGATGTATCTAGATG 58.821 42.308 15.79 0.00 42.48 2.90
3109 3841 7.109901 ACTAGAAGGGGATGTATCTAGATGT 57.890 40.000 15.79 1.25 42.48 3.06
3110 3842 8.233349 ACTAGAAGGGGATGTATCTAGATGTA 57.767 38.462 15.79 4.44 42.48 2.29
3111 3843 8.851876 ACTAGAAGGGGATGTATCTAGATGTAT 58.148 37.037 15.79 9.11 42.48 2.29
3164 3896 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
3165 3897 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
3166 3898 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
3167 3899 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3168 3900 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3169 3901 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3170 3902 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3171 3903 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3172 3904 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3173 3905 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3174 3906 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3235 3967 3.485394 TGTTTGAGGCATTCACAGCTTA 58.515 40.909 0.00 0.00 34.94 3.09
3481 4234 7.962917 ACAAATTGATGCGAAATATTTGTTCC 58.037 30.769 5.17 0.00 43.20 3.62
3514 4267 9.658799 AAGTCAATACCATAGTATGATGCATAC 57.341 33.333 11.91 9.03 44.81 2.39
3515 4268 8.815912 AGTCAATACCATAGTATGATGCATACA 58.184 33.333 11.91 0.00 46.30 2.29
3516 4269 9.435688 GTCAATACCATAGTATGATGCATACAA 57.564 33.333 11.91 0.00 46.30 2.41
3522 4275 9.658799 ACCATAGTATGATGCATACAATACTTC 57.341 33.333 23.65 3.51 46.30 3.01
3523 4276 9.102757 CCATAGTATGATGCATACAATACTTCC 57.897 37.037 23.65 2.18 46.30 3.46
3524 4277 9.881649 CATAGTATGATGCATACAATACTTCCT 57.118 33.333 23.65 12.87 46.30 3.36
3526 4279 7.390027 AGTATGATGCATACAATACTTCCTCC 58.610 38.462 17.38 0.00 46.30 4.30
3527 4280 5.628797 TGATGCATACAATACTTCCTCCA 57.371 39.130 0.00 0.00 0.00 3.86
3528 4281 6.191657 TGATGCATACAATACTTCCTCCAT 57.808 37.500 0.00 0.00 0.00 3.41
3529 4282 7.315066 TGATGCATACAATACTTCCTCCATA 57.685 36.000 0.00 0.00 0.00 2.74
3530 4283 7.161404 TGATGCATACAATACTTCCTCCATAC 58.839 38.462 0.00 0.00 0.00 2.39
3531 4284 5.538118 TGCATACAATACTTCCTCCATACG 58.462 41.667 0.00 0.00 0.00 3.06
3532 4285 4.929808 GCATACAATACTTCCTCCATACGG 59.070 45.833 0.00 0.00 0.00 4.02
3533 4286 5.279306 GCATACAATACTTCCTCCATACGGA 60.279 44.000 0.00 0.00 39.79 4.69
3534 4287 6.740401 GCATACAATACTTCCTCCATACGGAA 60.740 42.308 0.00 0.00 42.21 4.30
3535 4288 5.888982 ACAATACTTCCTCCATACGGAAT 57.111 39.130 0.00 0.00 42.21 3.01
3536 4289 6.989155 ACAATACTTCCTCCATACGGAATA 57.011 37.500 0.00 0.00 42.21 1.75
3537 4290 6.756221 ACAATACTTCCTCCATACGGAATAC 58.244 40.000 0.00 0.00 42.21 1.89
3552 4305 4.096311 CGGAATACGCTTAGATACATCCG 58.904 47.826 0.00 0.00 40.92 4.18
3553 4306 3.858238 GGAATACGCTTAGATACATCCGC 59.142 47.826 0.00 0.00 0.00 5.54
3554 4307 4.380655 GGAATACGCTTAGATACATCCGCT 60.381 45.833 0.00 0.00 0.00 5.52
3555 4308 4.785511 ATACGCTTAGATACATCCGCTT 57.214 40.909 0.00 0.00 0.00 4.68
3556 4309 2.743938 ACGCTTAGATACATCCGCTTG 58.256 47.619 0.00 0.00 0.00 4.01
3557 4310 2.361119 ACGCTTAGATACATCCGCTTGA 59.639 45.455 0.00 0.00 0.00 3.02
3558 4311 2.983136 CGCTTAGATACATCCGCTTGAG 59.017 50.000 0.00 0.00 0.00 3.02
3559 4312 2.734079 GCTTAGATACATCCGCTTGAGC 59.266 50.000 0.00 0.00 37.78 4.26
3573 4326 4.404507 GCTTGAGCGTGAACTAATTCAA 57.595 40.909 0.00 0.00 46.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
297 298 7.867752 TGTAAACTGGCAGTAATGTTTCTAAC 58.132 34.615 22.37 6.98 34.88 2.34
336 337 4.989044 GAGTCTGACTACTCTACCAAAGC 58.011 47.826 10.86 0.00 42.21 3.51
349 350 6.295575 CCTTTATCTGTCCAAAGAGTCTGACT 60.296 42.308 10.66 10.66 34.35 3.41
355 356 5.843019 TTCCCTTTATCTGTCCAAAGAGT 57.157 39.130 0.00 0.00 34.35 3.24
359 360 6.780031 TGTTTGATTCCCTTTATCTGTCCAAA 59.220 34.615 0.00 0.00 0.00 3.28
360 361 6.208599 GTGTTTGATTCCCTTTATCTGTCCAA 59.791 38.462 0.00 0.00 0.00 3.53
361 362 5.710099 GTGTTTGATTCCCTTTATCTGTCCA 59.290 40.000 0.00 0.00 0.00 4.02
364 365 5.640147 TGGTGTTTGATTCCCTTTATCTGT 58.360 37.500 0.00 0.00 0.00 3.41
365 366 6.588719 TTGGTGTTTGATTCCCTTTATCTG 57.411 37.500 0.00 0.00 0.00 2.90
367 368 5.861787 CGTTTGGTGTTTGATTCCCTTTATC 59.138 40.000 0.00 0.00 0.00 1.75
369 370 4.888239 TCGTTTGGTGTTTGATTCCCTTTA 59.112 37.500 0.00 0.00 0.00 1.85
375 440 5.231357 GGTTCTTTCGTTTGGTGTTTGATTC 59.769 40.000 0.00 0.00 0.00 2.52
399 464 7.751348 GGAGCATCGATATAACTGTACAAGTAG 59.249 40.741 0.00 0.00 34.52 2.57
420 485 5.409214 GCTAAAGCAATCAAATTTTGGAGCA 59.591 36.000 17.28 0.00 41.59 4.26
421 486 5.861725 GCTAAAGCAATCAAATTTTGGAGC 58.138 37.500 9.18 10.27 41.59 4.70
462 528 8.646900 AGATGTATGATTTCCCTTCTCTTAGTC 58.353 37.037 0.00 0.00 0.00 2.59
464 530 8.646004 TCAGATGTATGATTTCCCTTCTCTTAG 58.354 37.037 0.00 0.00 0.00 2.18
479 545 8.324306 AGGAACTTTTCTGAATCAGATGTATGA 58.676 33.333 14.31 0.00 36.04 2.15
480 546 8.503458 AGGAACTTTTCTGAATCAGATGTATG 57.497 34.615 14.31 7.59 36.04 2.39
502 676 9.529325 CGTTCACAAATATAAGATGTTCTAGGA 57.471 33.333 0.00 0.00 0.00 2.94
503 677 8.765219 CCGTTCACAAATATAAGATGTTCTAGG 58.235 37.037 0.00 0.00 0.00 3.02
504 678 9.529325 TCCGTTCACAAATATAAGATGTTCTAG 57.471 33.333 0.00 0.00 0.00 2.43
512 692 9.362539 GAACTACTTCCGTTCACAAATATAAGA 57.637 33.333 0.00 0.00 40.27 2.10
533 713 8.431910 AAAAACAGAGGGAGTAGTATGAACTA 57.568 34.615 0.00 0.00 37.15 2.24
544 724 9.588096 AGACAAATATTTAAAAACAGAGGGAGT 57.412 29.630 0.00 0.00 0.00 3.85
568 748 9.778741 AGTAGTCATTTGAAATGTCTACAAAGA 57.221 29.630 34.42 14.49 40.54 2.52
571 751 9.990360 TGTAGTAGTCATTTGAAATGTCTACAA 57.010 29.630 34.42 24.59 40.54 2.41
575 755 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
576 756 8.540492 CCGTATGTAGTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
577 757 8.255206 TCCGTATGTAGTAGTCATTTGAAATGT 58.745 33.333 16.62 2.38 0.00 2.71
578 758 8.642908 TCCGTATGTAGTAGTCATTTGAAATG 57.357 34.615 11.54 11.54 0.00 2.32
579 759 9.261180 CATCCGTATGTAGTAGTCATTTGAAAT 57.739 33.333 0.00 0.00 0.00 2.17
580 760 8.255206 ACATCCGTATGTAGTAGTCATTTGAAA 58.745 33.333 0.00 0.00 44.66 2.69
581 761 7.778083 ACATCCGTATGTAGTAGTCATTTGAA 58.222 34.615 0.00 0.00 44.66 2.69
582 762 7.342769 ACATCCGTATGTAGTAGTCATTTGA 57.657 36.000 0.00 0.00 44.66 2.69
625 805 7.141363 ACAAAGCAAAATGAGTGAATCTACAC 58.859 34.615 0.00 0.00 40.60 2.90
626 806 7.275888 ACAAAGCAAAATGAGTGAATCTACA 57.724 32.000 0.00 0.00 0.00 2.74
627 807 9.282247 CATACAAAGCAAAATGAGTGAATCTAC 57.718 33.333 0.00 0.00 0.00 2.59
628 808 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
629 809 7.889469 ACATACAAAGCAAAATGAGTGAATCT 58.111 30.769 0.00 0.00 0.00 2.40
630 810 9.282247 CTACATACAAAGCAAAATGAGTGAATC 57.718 33.333 0.00 0.00 0.00 2.52
631 811 8.796475 ACTACATACAAAGCAAAATGAGTGAAT 58.204 29.630 0.00 0.00 0.00 2.57
632 812 8.165239 ACTACATACAAAGCAAAATGAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
633 813 7.443879 TGACTACATACAAAGCAAAATGAGTGA 59.556 33.333 0.00 0.00 0.00 3.41
634 814 7.535258 GTGACTACATACAAAGCAAAATGAGTG 59.465 37.037 0.00 0.00 0.00 3.51
635 815 7.445402 AGTGACTACATACAAAGCAAAATGAGT 59.555 33.333 0.00 0.00 0.00 3.41
636 816 7.810658 AGTGACTACATACAAAGCAAAATGAG 58.189 34.615 0.00 0.00 0.00 2.90
637 817 7.744087 AGTGACTACATACAAAGCAAAATGA 57.256 32.000 0.00 0.00 0.00 2.57
638 818 7.862372 ACAAGTGACTACATACAAAGCAAAATG 59.138 33.333 0.00 0.00 0.00 2.32
639 819 7.940850 ACAAGTGACTACATACAAAGCAAAAT 58.059 30.769 0.00 0.00 0.00 1.82
640 820 7.328277 ACAAGTGACTACATACAAAGCAAAA 57.672 32.000 0.00 0.00 0.00 2.44
641 821 6.935741 ACAAGTGACTACATACAAAGCAAA 57.064 33.333 0.00 0.00 0.00 3.68
642 822 6.540551 TCAACAAGTGACTACATACAAAGCAA 59.459 34.615 0.00 0.00 0.00 3.91
643 823 6.052360 TCAACAAGTGACTACATACAAAGCA 58.948 36.000 0.00 0.00 0.00 3.91
644 824 6.539649 TCAACAAGTGACTACATACAAAGC 57.460 37.500 0.00 0.00 0.00 3.51
645 825 9.385902 CATTTCAACAAGTGACTACATACAAAG 57.614 33.333 0.00 0.00 35.39 2.77
646 826 7.860373 GCATTTCAACAAGTGACTACATACAAA 59.140 33.333 0.00 0.00 35.39 2.83
647 827 7.359595 GCATTTCAACAAGTGACTACATACAA 58.640 34.615 0.00 0.00 35.39 2.41
648 828 6.072728 GGCATTTCAACAAGTGACTACATACA 60.073 38.462 0.00 0.00 35.39 2.29
649 829 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
650 830 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
651 831 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
652 832 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
653 833 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
654 834 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
655 835 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
656 836 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
657 837 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
658 838 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
659 839 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
660 840 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
661 841 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
662 842 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
663 843 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
664 844 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
665 845 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
668 848 9.740710 AGTTAAATACTTGTCTTTCTAGGCATT 57.259 29.630 0.00 0.00 35.56 3.56
669 849 9.740710 AAGTTAAATACTTGTCTTTCTAGGCAT 57.259 29.630 0.00 0.00 45.33 4.40
670 850 9.569122 AAAGTTAAATACTTGTCTTTCTAGGCA 57.431 29.630 0.00 0.00 46.34 4.75
684 864 9.507329 TGCTTCAGAATCAGAAAGTTAAATACT 57.493 29.630 0.00 0.00 39.32 2.12
697 877 5.179742 GGAGATAGCAATGCTTCAGAATCAG 59.820 44.000 14.85 0.00 40.44 2.90
698 878 5.061853 GGAGATAGCAATGCTTCAGAATCA 58.938 41.667 14.85 0.00 40.44 2.57
699 879 5.061853 TGGAGATAGCAATGCTTCAGAATC 58.938 41.667 14.85 9.98 40.44 2.52
700 880 5.045012 TGGAGATAGCAATGCTTCAGAAT 57.955 39.130 14.85 0.00 40.44 2.40
710 1037 6.239829 CCTGGAACTAATCTGGAGATAGCAAT 60.240 42.308 0.00 0.00 33.73 3.56
736 1064 8.816144 GTTTCAACAGCAGATAACAAATTCAAA 58.184 29.630 0.00 0.00 0.00 2.69
757 1090 5.736951 ATTCCAATTCCAATTCGGTTTCA 57.263 34.783 0.00 0.00 35.57 2.69
787 1120 5.633601 TCCGTATATTCTTATTTCAGCAGCG 59.366 40.000 0.00 0.00 0.00 5.18
827 1163 3.328343 TCCCCGTCTTTAAACTTCATCCA 59.672 43.478 0.00 0.00 0.00 3.41
869 1205 1.376037 GGCGGAGGAGGTTGAGTTG 60.376 63.158 0.00 0.00 0.00 3.16
870 1206 2.943978 CGGCGGAGGAGGTTGAGTT 61.944 63.158 0.00 0.00 0.00 3.01
1377 1810 9.617387 AGTTTGAGACTTCAGAGCCATCTCTTC 62.617 44.444 0.00 0.00 40.23 2.87
1391 1828 5.985781 TCGCAATTTACAGTTTGAGACTTC 58.014 37.500 0.00 0.00 36.10 3.01
1393 1830 5.122396 GGATCGCAATTTACAGTTTGAGACT 59.878 40.000 0.00 0.00 39.89 3.24
1408 1845 0.749454 GTTCCTGCAGGGATCGCAAT 60.749 55.000 32.23 0.00 44.66 3.56
1618 2060 6.155393 AGGTTGGACTAGAATTCCTAACTGAG 59.845 42.308 0.65 0.00 34.97 3.35
1640 2082 1.525175 TGGGGTGTTAAGGAACAGGT 58.475 50.000 0.00 0.00 46.20 4.00
1710 2157 5.940192 TTTTATGTACAAGGACAGCACAG 57.060 39.130 0.00 0.00 31.51 3.66
1733 2187 1.146774 TGACAATCCCTTTTGGCTGGA 59.853 47.619 0.00 0.00 35.54 3.86
1734 2188 1.631405 TGACAATCCCTTTTGGCTGG 58.369 50.000 0.00 0.00 35.54 4.85
1736 2190 3.094572 CAGATGACAATCCCTTTTGGCT 58.905 45.455 0.00 0.00 35.54 4.75
1737 2191 3.091545 TCAGATGACAATCCCTTTTGGC 58.908 45.455 0.00 0.00 38.58 4.52
1738 2192 5.012239 TCTTCAGATGACAATCCCTTTTGG 58.988 41.667 0.00 0.00 39.97 3.28
1767 2221 6.398918 ACAGGTACTCACATTTGACATAGTC 58.601 40.000 0.00 0.00 34.60 2.59
1811 2265 5.630121 AGACCACACTTTACATTTGATCCA 58.370 37.500 0.00 0.00 0.00 3.41
1850 2311 2.755103 GGAAGCATTACACCTCAAAGGG 59.245 50.000 0.00 0.00 40.58 3.95
1904 2365 7.148590 GGTGTGATGCCAGAAATTTTATGAAAC 60.149 37.037 5.35 0.00 0.00 2.78
1914 2375 0.038166 ACCGGTGTGATGCCAGAAAT 59.962 50.000 6.12 0.00 0.00 2.17
2000 2645 5.472478 TCTTTCAGTAAGTCGAAGCTAGTGA 59.528 40.000 0.00 0.00 35.28 3.41
2192 2909 8.463930 TCCATATAAAATTTGGTCTCATCACC 57.536 34.615 0.00 0.00 36.90 4.02
2193 2910 9.903682 CATCCATATAAAATTTGGTCTCATCAC 57.096 33.333 0.00 0.00 33.68 3.06
2271 2990 3.644884 TCTCGGTTCTCAAGTCTCAAC 57.355 47.619 0.00 0.00 0.00 3.18
2343 3066 4.962362 TGGCAGGACAGAATTAGAGTATCA 59.038 41.667 0.00 0.00 37.82 2.15
2344 3067 5.537300 TGGCAGGACAGAATTAGAGTATC 57.463 43.478 0.00 0.00 0.00 2.24
2368 3091 9.482627 TTTAAATGTTGATGTTGTTGATAACCC 57.517 29.630 0.00 0.00 0.00 4.11
2516 3244 6.428159 ACGTTTGAGATTCTCTACTGCATTTT 59.572 34.615 14.54 0.00 0.00 1.82
2606 3334 4.100529 CAATTTTGATACTGCTGCTTCCG 58.899 43.478 0.00 0.00 0.00 4.30
2634 3362 9.322773 TGAGAATATGAGCTCTGAAATAAGTTG 57.677 33.333 16.19 0.00 32.44 3.16
2641 3369 6.070596 TCCAACTGAGAATATGAGCTCTGAAA 60.071 38.462 16.19 0.00 35.08 2.69
2657 3385 0.987294 ACCTGGGTCATCCAACTGAG 59.013 55.000 0.00 0.00 46.51 3.35
2806 3534 2.487762 CGTGCTGCCTCAAAATTCCTAA 59.512 45.455 0.00 0.00 0.00 2.69
2890 3618 0.517316 GATCACGGCCAAGTTCACAC 59.483 55.000 2.24 0.00 0.00 3.82
2956 3684 3.324846 TGCATCCGTATCTAGGCAAATCT 59.675 43.478 0.00 0.00 0.00 2.40
2977 3705 8.139521 TGTATCTAACACTACGTGTCTAGATG 57.860 38.462 23.47 0.00 46.79 2.90
3003 3735 8.985315 TTGTCTTAGATTTATCTAGGTACGGA 57.015 34.615 8.26 0.00 40.23 4.69
3009 3741 9.620259 AAAAGGCTTGTCTTAGATTTATCTAGG 57.380 33.333 0.00 3.24 40.23 3.02
3031 3763 4.439968 GAGTATTACCTCCGTCCCAAAAG 58.560 47.826 0.00 0.00 0.00 2.27
3051 3783 4.184629 CAAGTATTTTCAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3052 3784 3.581332 ACAAGTATTTTCAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3053 3785 3.933332 GACAAGTATTTTCAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3054 3786 4.566004 TGACAAGTATTTTCAGACGGAGG 58.434 43.478 0.00 0.00 0.00 4.30
3055 3787 5.869344 TGATGACAAGTATTTTCAGACGGAG 59.131 40.000 0.00 0.00 0.00 4.63
3056 3788 5.789521 TGATGACAAGTATTTTCAGACGGA 58.210 37.500 0.00 0.00 0.00 4.69
3057 3789 6.480524 TTGATGACAAGTATTTTCAGACGG 57.519 37.500 0.00 0.00 0.00 4.79
3058 3790 8.843733 CATTTTGATGACAAGTATTTTCAGACG 58.156 33.333 0.00 0.00 37.32 4.18
3059 3791 9.897744 TCATTTTGATGACAAGTATTTTCAGAC 57.102 29.630 0.00 0.00 37.32 3.51
3074 3806 6.069440 ACATCCCCTTCTAGTCATTTTGATGA 60.069 38.462 0.00 0.00 32.39 2.92
3075 3807 6.125029 ACATCCCCTTCTAGTCATTTTGATG 58.875 40.000 0.00 0.00 33.80 3.07
3076 3808 6.332976 ACATCCCCTTCTAGTCATTTTGAT 57.667 37.500 0.00 0.00 0.00 2.57
3077 3809 5.779241 ACATCCCCTTCTAGTCATTTTGA 57.221 39.130 0.00 0.00 0.00 2.69
3078 3810 7.512992 AGATACATCCCCTTCTAGTCATTTTG 58.487 38.462 0.00 0.00 0.00 2.44
3079 3811 7.698163 AGATACATCCCCTTCTAGTCATTTT 57.302 36.000 0.00 0.00 0.00 1.82
3080 3812 8.235230 TCTAGATACATCCCCTTCTAGTCATTT 58.765 37.037 0.00 0.00 39.03 2.32
3081 3813 7.770662 TCTAGATACATCCCCTTCTAGTCATT 58.229 38.462 0.00 0.00 39.03 2.57
3082 3814 7.350044 TCTAGATACATCCCCTTCTAGTCAT 57.650 40.000 0.00 0.00 39.03 3.06
3083 3815 6.781857 TCTAGATACATCCCCTTCTAGTCA 57.218 41.667 0.00 0.00 39.03 3.41
3084 3816 7.179269 ACATCTAGATACATCCCCTTCTAGTC 58.821 42.308 4.54 0.00 39.03 2.59
3085 3817 7.109901 ACATCTAGATACATCCCCTTCTAGT 57.890 40.000 4.54 0.00 39.03 2.57
3138 3870 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
3139 3871 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
3140 3872 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
3141 3873 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3142 3874 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3143 3875 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3144 3876 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3145 3877 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3146 3878 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3147 3879 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3148 3880 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3149 3881 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3150 3882 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3151 3883 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3152 3884 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3153 3885 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3154 3886 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3155 3887 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3156 3888 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3157 3889 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3158 3890 1.753073 GATACTCCCTCCGTCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
3159 3891 1.064166 AGATACTCCCTCCGTCCGAAA 60.064 52.381 0.00 0.00 0.00 3.46
3160 3892 0.549950 AGATACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
3161 3893 0.549950 AAGATACTCCCTCCGTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
3162 3894 1.400737 AAAGATACTCCCTCCGTCCG 58.599 55.000 0.00 0.00 0.00 4.79
3163 3895 4.344390 ACATAAAAGATACTCCCTCCGTCC 59.656 45.833 0.00 0.00 0.00 4.79
3164 3896 5.532664 ACATAAAAGATACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
3165 3897 7.509659 AGAATACATAAAAGATACTCCCTCCGT 59.490 37.037 0.00 0.00 0.00 4.69
3166 3898 7.897864 AGAATACATAAAAGATACTCCCTCCG 58.102 38.462 0.00 0.00 0.00 4.63
3167 3899 9.495572 CAAGAATACATAAAAGATACTCCCTCC 57.504 37.037 0.00 0.00 0.00 4.30
3169 3901 9.838339 CACAAGAATACATAAAAGATACTCCCT 57.162 33.333 0.00 0.00 0.00 4.20
3170 3902 8.560374 GCACAAGAATACATAAAAGATACTCCC 58.440 37.037 0.00 0.00 0.00 4.30
3171 3903 8.276325 CGCACAAGAATACATAAAAGATACTCC 58.724 37.037 0.00 0.00 0.00 3.85
3172 3904 8.276325 CCGCACAAGAATACATAAAAGATACTC 58.724 37.037 0.00 0.00 0.00 2.59
3173 3905 7.226720 CCCGCACAAGAATACATAAAAGATACT 59.773 37.037 0.00 0.00 0.00 2.12
3174 3906 7.352739 CCCGCACAAGAATACATAAAAGATAC 58.647 38.462 0.00 0.00 0.00 2.24
3235 3967 2.980233 GCTGGGCAGCGAAACAGT 60.980 61.111 0.00 0.00 45.29 3.55
3269 4006 2.574006 TCAGTGCAGCAGAATTTCCT 57.426 45.000 0.00 0.00 0.00 3.36
3503 4256 7.315066 TGGAGGAAGTATTGTATGCATCATA 57.685 36.000 0.19 0.00 0.00 2.15
3504 4257 6.191657 TGGAGGAAGTATTGTATGCATCAT 57.808 37.500 0.19 0.00 0.00 2.45
3505 4258 5.628797 TGGAGGAAGTATTGTATGCATCA 57.371 39.130 0.19 0.00 0.00 3.07
3506 4259 6.311445 CGTATGGAGGAAGTATTGTATGCATC 59.689 42.308 0.19 0.00 0.00 3.91
3507 4260 6.166279 CGTATGGAGGAAGTATTGTATGCAT 58.834 40.000 3.79 3.79 0.00 3.96
3508 4261 5.510690 CCGTATGGAGGAAGTATTGTATGCA 60.511 44.000 0.00 0.00 37.49 3.96
3509 4262 4.929808 CCGTATGGAGGAAGTATTGTATGC 59.070 45.833 0.00 0.00 37.49 3.14
3510 4263 6.340962 TCCGTATGGAGGAAGTATTGTATG 57.659 41.667 0.00 0.00 40.17 2.39
3524 4277 5.706833 TGTATCTAAGCGTATTCCGTATGGA 59.293 40.000 0.00 0.00 44.61 3.41
3525 4278 5.946298 TGTATCTAAGCGTATTCCGTATGG 58.054 41.667 0.00 0.00 39.32 2.74
3526 4279 6.691818 GGATGTATCTAAGCGTATTCCGTATG 59.308 42.308 0.00 0.00 39.32 2.39
3527 4280 6.457934 CGGATGTATCTAAGCGTATTCCGTAT 60.458 42.308 0.00 0.00 39.32 3.06
3528 4281 5.163824 CGGATGTATCTAAGCGTATTCCGTA 60.164 44.000 0.00 0.00 39.32 4.02
3529 4282 4.379186 CGGATGTATCTAAGCGTATTCCGT 60.379 45.833 0.00 0.00 39.32 4.69
3530 4283 4.096311 CGGATGTATCTAAGCGTATTCCG 58.904 47.826 0.00 0.00 40.40 4.30
3531 4284 3.858238 GCGGATGTATCTAAGCGTATTCC 59.142 47.826 0.00 0.00 0.00 3.01
3532 4285 4.734917 AGCGGATGTATCTAAGCGTATTC 58.265 43.478 0.00 0.00 0.00 1.75
3533 4286 4.785511 AGCGGATGTATCTAAGCGTATT 57.214 40.909 0.00 0.00 0.00 1.89
3534 4287 4.217767 TCAAGCGGATGTATCTAAGCGTAT 59.782 41.667 0.00 0.00 0.00 3.06
3535 4288 3.566742 TCAAGCGGATGTATCTAAGCGTA 59.433 43.478 0.00 0.00 0.00 4.42
3536 4289 2.361119 TCAAGCGGATGTATCTAAGCGT 59.639 45.455 0.00 0.00 0.00 5.07
3537 4290 2.983136 CTCAAGCGGATGTATCTAAGCG 59.017 50.000 0.00 0.00 0.00 4.68
3538 4291 2.734079 GCTCAAGCGGATGTATCTAAGC 59.266 50.000 0.00 0.00 0.00 3.09
3552 4305 4.404507 TTGAATTAGTTCACGCTCAAGC 57.595 40.909 0.00 0.00 43.72 4.01


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

AutoCloner maintained by Alex Coulton.