Multiple sequence alignment - TraesCS2B01G287700

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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 TraesCS2B01G287700 chr2B 100.000 3104 0 0 1 3104 397012467 397009364 0.000000e+00 5733.0
1 TraesCS2B01G287700 chr2B 100.000 2742 0 0 3352 6093 397009116 397006375 0.000000e+00 5064.0
2 TraesCS2B01G287700 chr2B 92.029 138 10 1 1761 1897 77137515 77137378 6.230000e-45 193.0
3 TraesCS2B01G287700 chr2B 79.592 147 18 6 714 848 140234048 140233902 1.810000e-15 95.3
4 TraesCS2B01G287700 chr2D 95.560 2703 77 22 3352 6041 327756556 327753884 0.000000e+00 4287.0
5 TraesCS2B01G287700 chr2D 89.854 1232 90 15 1887 3104 327757859 327756649 0.000000e+00 1550.0
6 TraesCS2B01G287700 chr2D 97.209 824 22 1 943 1766 327758678 327757856 0.000000e+00 1393.0
7 TraesCS2B01G287700 chr2D 84.233 704 93 10 26 714 89390362 89391062 0.000000e+00 669.0
8 TraesCS2B01G287700 chr2D 84.211 589 90 3 1890 2476 43276641 43276054 2.460000e-158 569.0
9 TraesCS2B01G287700 chr2D 84.941 591 55 17 329 898 327759255 327758678 8.860000e-158 568.0
10 TraesCS2B01G287700 chr2D 83.400 500 69 6 2477 2976 43276001 43275516 9.310000e-123 451.0
11 TraesCS2B01G287700 chr2A 95.587 1722 49 15 4259 5966 433361655 433359947 0.000000e+00 2734.0
12 TraesCS2B01G287700 chr2A 90.279 1790 126 23 1 1766 433370917 433369152 0.000000e+00 2298.0
13 TraesCS2B01G287700 chr2A 94.951 911 40 5 3352 4257 433362812 433361903 0.000000e+00 1423.0
14 TraesCS2B01G287700 chr2A 88.387 1128 114 10 1887 2997 433369155 433368028 0.000000e+00 1341.0
15 TraesCS2B01G287700 chr2A 99.219 128 1 0 5962 6089 433359916 433359789 1.320000e-56 231.0
16 TraesCS2B01G287700 chr2A 78.912 147 19 6 714 848 62393232 62393086 8.410000e-14 89.8
17 TraesCS2B01G287700 chr1D 86.676 728 82 7 1 714 60313580 60314306 0.000000e+00 793.0
18 TraesCS2B01G287700 chr1D 84.636 729 88 16 1 709 397172013 397172737 0.000000e+00 704.0
19 TraesCS2B01G287700 chr1D 81.361 735 96 18 1 721 365301061 365300354 1.480000e-155 560.0
20 TraesCS2B01G287700 chr1D 83.810 525 79 5 2474 2997 334245811 334246330 1.530000e-135 494.0
21 TraesCS2B01G287700 chr1D 79.874 636 100 18 2477 3098 139549347 139549968 2.020000e-119 440.0
22 TraesCS2B01G287700 chr7B 85.675 733 91 6 1 719 221322708 221321976 0.000000e+00 760.0
23 TraesCS2B01G287700 chr7B 82.916 679 96 10 1 661 387821313 387820637 1.460000e-165 593.0
24 TraesCS2B01G287700 chr7B 92.537 134 9 1 1762 1894 126893118 126893251 2.240000e-44 191.0
25 TraesCS2B01G287700 chr7B 77.239 268 42 11 401 654 610723839 610724101 8.240000e-29 139.0
26 TraesCS2B01G287700 chr7B 86.517 89 5 5 1683 1765 65375441 65375354 2.340000e-14 91.6
27 TraesCS2B01G287700 chr7B 85.882 85 11 1 1683 1766 745741934 745742018 8.410000e-14 89.8
28 TraesCS2B01G287700 chr7B 79.021 143 19 5 717 848 632936613 632936471 3.030000e-13 87.9
29 TraesCS2B01G287700 chr7B 100.000 31 0 0 818 848 303720335 303720365 2.370000e-04 58.4
30 TraesCS2B01G287700 chr6D 85.417 720 85 10 8 712 456514678 456515392 0.000000e+00 730.0
31 TraesCS2B01G287700 chr6D 84.060 734 97 12 1 717 321771154 321771884 0.000000e+00 689.0
32 TraesCS2B01G287700 chr6D 84.317 593 84 9 1887 2476 143356360 143356946 6.850000e-159 571.0
33 TraesCS2B01G287700 chr6D 86.170 94 5 5 1680 1765 119968022 119967929 1.810000e-15 95.3
34 TraesCS2B01G287700 chr5D 84.795 730 95 8 1 717 404478637 404477911 0.000000e+00 719.0
35 TraesCS2B01G287700 chr5D 86.115 677 77 10 1 662 373778183 373777509 0.000000e+00 713.0
36 TraesCS2B01G287700 chr5D 85.606 660 88 6 1 655 475386252 475386909 0.000000e+00 686.0
37 TraesCS2B01G287700 chr5D 82.897 725 99 15 1 716 495896308 495897016 4.010000e-176 628.0
38 TraesCS2B01G287700 chr5D 82.524 721 91 15 9 714 77862352 77863052 8.740000e-168 601.0
39 TraesCS2B01G287700 chr5D 83.871 589 88 7 1889 2476 318815058 318814476 6.900000e-154 555.0
40 TraesCS2B01G287700 chr5D 81.166 669 81 23 2477 3104 421996571 421995907 4.240000e-136 496.0
41 TraesCS2B01G287700 chr5D 100.000 30 0 0 819 848 10356583 10356554 8.530000e-04 56.5
42 TraesCS2B01G287700 chr3B 84.521 730 92 11 2 714 12762156 12761431 0.000000e+00 702.0
43 TraesCS2B01G287700 chr3B 83.989 737 91 13 2 714 13051610 13050877 0.000000e+00 682.0
44 TraesCS2B01G287700 chr5B 84.401 718 89 15 17 715 67534852 67535565 0.000000e+00 684.0
45 TraesCS2B01G287700 chr5B 81.559 667 81 22 2479 3104 508684903 508684238 4.210000e-141 512.0
46 TraesCS2B01G287700 chr5B 78.322 143 20 5 717 848 592863300 592863442 1.410000e-11 82.4
47 TraesCS2B01G287700 chr3D 86.142 635 79 6 8 633 505054132 505053498 0.000000e+00 676.0
48 TraesCS2B01G287700 chr3D 83.221 745 96 13 1 722 458326234 458325496 0.000000e+00 656.0
49 TraesCS2B01G287700 chr3D 84.486 593 81 6 1887 2476 516852373 516852957 5.300000e-160 575.0
50 TraesCS2B01G287700 chr3D 83.117 308 39 5 419 714 330259756 330259450 1.010000e-67 268.0
51 TraesCS2B01G287700 chr3D 83.389 301 37 7 426 714 33290876 33291175 3.620000e-67 267.0
52 TraesCS2B01G287700 chr6A 85.068 663 82 11 69 717 475417091 475416432 0.000000e+00 660.0
53 TraesCS2B01G287700 chr6A 82.400 625 88 14 1 608 481254755 481255374 5.410000e-145 525.0
54 TraesCS2B01G287700 chr6A 80.423 378 57 9 356 717 580218449 580218073 7.780000e-69 272.0
55 TraesCS2B01G287700 chr3A 82.877 730 109 8 1 716 45772643 45773370 5.150000e-180 641.0
56 TraesCS2B01G287700 chr3A 85.065 154 20 3 1756 1907 17665723 17665875 2.940000e-33 154.0
57 TraesCS2B01G287700 chr3A 84.564 149 20 3 1762 1908 17803340 17803193 1.770000e-30 145.0
58 TraesCS2B01G287700 chr6B 85.086 637 81 7 1 624 501776378 501775743 6.660000e-179 638.0
59 TraesCS2B01G287700 chr6B 82.466 730 106 11 1 715 475039028 475038306 2.410000e-173 619.0
60 TraesCS2B01G287700 chr6B 81.633 735 111 16 1 714 646142985 646143716 6.800000e-164 588.0
61 TraesCS2B01G287700 chr6B 93.233 133 7 2 1763 1893 207511029 207510897 1.730000e-45 195.0
62 TraesCS2B01G287700 chr6B 77.124 153 23 6 708 848 680821341 680821189 1.820000e-10 78.7
63 TraesCS2B01G287700 chr1B 80.926 734 119 12 1 716 178726507 178725777 1.480000e-155 560.0
64 TraesCS2B01G287700 chr1B 84.321 574 81 7 1887 2458 95300093 95299527 2.480000e-153 553.0
65 TraesCS2B01G287700 chr1B 79.012 729 126 18 1 714 595471354 595472070 1.990000e-129 473.0
66 TraesCS2B01G287700 chr1B 75.705 745 138 29 1 716 564857552 564856822 3.520000e-87 333.0
67 TraesCS2B01G287700 chr1B 81.185 287 44 2 413 689 193469613 193469327 7.950000e-54 222.0
68 TraesCS2B01G287700 chr1B 95.385 130 5 1 1765 1893 56324101 56323972 8.010000e-49 206.0
69 TraesCS2B01G287700 chr1B 78.169 142 21 4 717 848 608959425 608959284 1.410000e-11 82.4
70 TraesCS2B01G287700 chr4D 83.953 592 86 7 1887 2476 105893894 105894478 5.330000e-155 558.0
71 TraesCS2B01G287700 chr4D 80.507 631 96 17 1 610 499735584 499736208 5.570000e-125 459.0
72 TraesCS2B01G287700 chr4D 80.218 551 91 9 178 714 28888272 28887726 1.230000e-106 398.0
73 TraesCS2B01G287700 chr4D 84.615 104 8 5 1681 1776 81984640 81984537 5.030000e-16 97.1
74 TraesCS2B01G287700 chr7A 83.474 593 90 7 1887 2476 384512940 384512353 4.150000e-151 545.0
75 TraesCS2B01G287700 chr7A 87.633 469 52 5 1 465 182324027 182323561 1.930000e-149 540.0
76 TraesCS2B01G287700 chr7A 93.284 134 8 1 1762 1894 319588730 319588863 4.820000e-46 196.0
77 TraesCS2B01G287700 chr7A 87.500 80 9 1 1680 1759 731240248 731240170 2.340000e-14 91.6
78 TraesCS2B01G287700 chr7A 88.406 69 8 0 852 920 219130221 219130153 3.910000e-12 84.2
79 TraesCS2B01G287700 chr1A 81.873 662 104 7 1 649 38736705 38737363 1.490000e-150 544.0
80 TraesCS2B01G287700 chr1A 81.349 504 79 8 103 592 502642830 502642328 4.430000e-106 396.0
81 TraesCS2B01G287700 chr1A 82.759 203 25 4 390 583 28640344 28640143 8.120000e-39 172.0
82 TraesCS2B01G287700 chr1A 80.769 104 19 1 601 703 30775412 30775309 5.060000e-11 80.5
83 TraesCS2B01G287700 chr5A 85.855 509 65 5 2477 2980 535532307 535531801 8.990000e-148 534.0
84 TraesCS2B01G287700 chr5A 89.610 77 6 2 1829 1904 7108142 7108067 5.030000e-16 97.1
85 TraesCS2B01G287700 chr5A 77.922 154 22 6 705 846 180140589 180140742 1.090000e-12 86.1
86 TraesCS2B01G287700 chr5A 76.761 142 23 4 717 848 640409764 640409623 3.050000e-08 71.3
87 TraesCS2B01G287700 chr4A 84.615 546 62 12 186 717 689650982 689651519 1.950000e-144 523.0
88 TraesCS2B01G287700 chr4A 83.083 532 83 6 2474 3003 613769870 613770396 1.540000e-130 477.0
89 TraesCS2B01G287700 chr4A 92.701 137 8 2 1756 1890 623322239 623322103 4.820000e-46 196.0
90 TraesCS2B01G287700 chr4A 92.593 135 7 3 1762 1893 223857832 223857966 2.240000e-44 191.0
91 TraesCS2B01G287700 chr4A 76.596 141 22 8 717 846 426335410 426335270 3.940000e-07 67.6
92 TraesCS2B01G287700 chr4B 78.319 595 94 19 2539 3104 149699783 149700371 9.720000e-93 351.0
93 TraesCS2B01G287700 chr4B 90.411 146 10 4 1751 1893 63765836 63765692 8.060000e-44 189.0
94 TraesCS2B01G287700 chr4B 89.286 140 13 2 1765 1903 300811448 300811310 2.260000e-39 174.0
95 TraesCS2B01G287700 chrUn 78.998 519 90 15 2485 2997 63406520 63407025 2.720000e-88 337.0
96 TraesCS2B01G287700 chrUn 79.389 262 50 3 2605 2863 352559942 352559682 1.350000e-41 182.0
97 TraesCS2B01G287700 chr7D 83.077 260 32 4 380 627 401775319 401775578 6.140000e-55 226.0
98 TraesCS2B01G287700 chr7D 91.971 137 9 2 1755 1890 135442289 135442154 2.240000e-44 191.0
99 TraesCS2B01G287700 chr7D 87.778 90 8 3 1680 1766 10543468 10543379 1.080000e-17 102.0
100 TraesCS2B01G287700 chr7D 85.185 108 7 5 1678 1776 63006868 63006975 1.080000e-17 102.0
101 TraesCS2B01G287700 chr7D 100.000 31 0 0 818 848 312467736 312467766 2.370000e-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 TraesCS2B01G287700 chr2B 397006375 397012467 6092 True 5398.500000 5733 100.000000 1 6093 2 chr2B.!!$R3 6092
1 TraesCS2B01G287700 chr2D 327753884 327759255 5371 True 1949.500000 4287 91.891000 329 6041 4 chr2D.!!$R2 5712
2 TraesCS2B01G287700 chr2D 89390362 89391062 700 False 669.000000 669 84.233000 26 714 1 chr2D.!!$F1 688
3 TraesCS2B01G287700 chr2D 43275516 43276641 1125 True 510.000000 569 83.805500 1890 2976 2 chr2D.!!$R1 1086
4 TraesCS2B01G287700 chr2A 433368028 433370917 2889 True 1819.500000 2298 89.333000 1 2997 2 chr2A.!!$R3 2996
5 TraesCS2B01G287700 chr2A 433359789 433362812 3023 True 1462.666667 2734 96.585667 3352 6089 3 chr2A.!!$R2 2737
6 TraesCS2B01G287700 chr1D 60313580 60314306 726 False 793.000000 793 86.676000 1 714 1 chr1D.!!$F1 713
7 TraesCS2B01G287700 chr1D 397172013 397172737 724 False 704.000000 704 84.636000 1 709 1 chr1D.!!$F4 708
8 TraesCS2B01G287700 chr1D 365300354 365301061 707 True 560.000000 560 81.361000 1 721 1 chr1D.!!$R1 720
9 TraesCS2B01G287700 chr1D 334245811 334246330 519 False 494.000000 494 83.810000 2474 2997 1 chr1D.!!$F3 523
10 TraesCS2B01G287700 chr1D 139549347 139549968 621 False 440.000000 440 79.874000 2477 3098 1 chr1D.!!$F2 621
11 TraesCS2B01G287700 chr7B 221321976 221322708 732 True 760.000000 760 85.675000 1 719 1 chr7B.!!$R2 718
12 TraesCS2B01G287700 chr7B 387820637 387821313 676 True 593.000000 593 82.916000 1 661 1 chr7B.!!$R3 660
13 TraesCS2B01G287700 chr6D 456514678 456515392 714 False 730.000000 730 85.417000 8 712 1 chr6D.!!$F3 704
14 TraesCS2B01G287700 chr6D 321771154 321771884 730 False 689.000000 689 84.060000 1 717 1 chr6D.!!$F2 716
15 TraesCS2B01G287700 chr6D 143356360 143356946 586 False 571.000000 571 84.317000 1887 2476 1 chr6D.!!$F1 589
16 TraesCS2B01G287700 chr5D 404477911 404478637 726 True 719.000000 719 84.795000 1 717 1 chr5D.!!$R4 716
17 TraesCS2B01G287700 chr5D 373777509 373778183 674 True 713.000000 713 86.115000 1 662 1 chr5D.!!$R3 661
18 TraesCS2B01G287700 chr5D 475386252 475386909 657 False 686.000000 686 85.606000 1 655 1 chr5D.!!$F2 654
19 TraesCS2B01G287700 chr5D 495896308 495897016 708 False 628.000000 628 82.897000 1 716 1 chr5D.!!$F3 715
20 TraesCS2B01G287700 chr5D 77862352 77863052 700 False 601.000000 601 82.524000 9 714 1 chr5D.!!$F1 705
21 TraesCS2B01G287700 chr5D 318814476 318815058 582 True 555.000000 555 83.871000 1889 2476 1 chr5D.!!$R2 587
22 TraesCS2B01G287700 chr5D 421995907 421996571 664 True 496.000000 496 81.166000 2477 3104 1 chr5D.!!$R5 627
23 TraesCS2B01G287700 chr3B 12761431 12762156 725 True 702.000000 702 84.521000 2 714 1 chr3B.!!$R1 712
24 TraesCS2B01G287700 chr3B 13050877 13051610 733 True 682.000000 682 83.989000 2 714 1 chr3B.!!$R2 712
25 TraesCS2B01G287700 chr5B 67534852 67535565 713 False 684.000000 684 84.401000 17 715 1 chr5B.!!$F1 698
26 TraesCS2B01G287700 chr5B 508684238 508684903 665 True 512.000000 512 81.559000 2479 3104 1 chr5B.!!$R1 625
27 TraesCS2B01G287700 chr3D 505053498 505054132 634 True 676.000000 676 86.142000 8 633 1 chr3D.!!$R3 625
28 TraesCS2B01G287700 chr3D 458325496 458326234 738 True 656.000000 656 83.221000 1 722 1 chr3D.!!$R2 721
29 TraesCS2B01G287700 chr3D 516852373 516852957 584 False 575.000000 575 84.486000 1887 2476 1 chr3D.!!$F2 589
30 TraesCS2B01G287700 chr6A 475416432 475417091 659 True 660.000000 660 85.068000 69 717 1 chr6A.!!$R1 648
31 TraesCS2B01G287700 chr6A 481254755 481255374 619 False 525.000000 525 82.400000 1 608 1 chr6A.!!$F1 607
32 TraesCS2B01G287700 chr3A 45772643 45773370 727 False 641.000000 641 82.877000 1 716 1 chr3A.!!$F2 715
33 TraesCS2B01G287700 chr6B 501775743 501776378 635 True 638.000000 638 85.086000 1 624 1 chr6B.!!$R3 623
34 TraesCS2B01G287700 chr6B 475038306 475039028 722 True 619.000000 619 82.466000 1 715 1 chr6B.!!$R2 714
35 TraesCS2B01G287700 chr6B 646142985 646143716 731 False 588.000000 588 81.633000 1 714 1 chr6B.!!$F1 713
36 TraesCS2B01G287700 chr1B 178725777 178726507 730 True 560.000000 560 80.926000 1 716 1 chr1B.!!$R3 715
37 TraesCS2B01G287700 chr1B 95299527 95300093 566 True 553.000000 553 84.321000 1887 2458 1 chr1B.!!$R2 571
38 TraesCS2B01G287700 chr1B 595471354 595472070 716 False 473.000000 473 79.012000 1 714 1 chr1B.!!$F1 713
39 TraesCS2B01G287700 chr1B 564856822 564857552 730 True 333.000000 333 75.705000 1 716 1 chr1B.!!$R5 715
40 TraesCS2B01G287700 chr4D 105893894 105894478 584 False 558.000000 558 83.953000 1887 2476 1 chr4D.!!$F1 589
41 TraesCS2B01G287700 chr4D 499735584 499736208 624 False 459.000000 459 80.507000 1 610 1 chr4D.!!$F2 609
42 TraesCS2B01G287700 chr4D 28887726 28888272 546 True 398.000000 398 80.218000 178 714 1 chr4D.!!$R1 536
43 TraesCS2B01G287700 chr7A 384512353 384512940 587 True 545.000000 545 83.474000 1887 2476 1 chr7A.!!$R3 589
44 TraesCS2B01G287700 chr1A 38736705 38737363 658 False 544.000000 544 81.873000 1 649 1 chr1A.!!$F1 648
45 TraesCS2B01G287700 chr1A 502642328 502642830 502 True 396.000000 396 81.349000 103 592 1 chr1A.!!$R3 489
46 TraesCS2B01G287700 chr5A 535531801 535532307 506 True 534.000000 534 85.855000 2477 2980 1 chr5A.!!$R2 503
47 TraesCS2B01G287700 chr4A 689650982 689651519 537 False 523.000000 523 84.615000 186 717 1 chr4A.!!$F3 531
48 TraesCS2B01G287700 chr4A 613769870 613770396 526 False 477.000000 477 83.083000 2474 3003 1 chr4A.!!$F2 529
49 TraesCS2B01G287700 chr4B 149699783 149700371 588 False 351.000000 351 78.319000 2539 3104 1 chr4B.!!$F1 565
50 TraesCS2B01G287700 chrUn 63406520 63407025 505 False 337.000000 337 78.998000 2485 2997 1 chrUn.!!$F1 512

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
783 883 0.037326 TCGACAGAATCACCTGCCAC 60.037 55.000 0.00 0.0 37.68 5.01 F
1537 1644 0.844503 CGCGCTCGGTAAATAGTGTC 59.155 55.000 5.56 0.0 0.00 3.67 F
1783 1891 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 F
2372 2493 0.250467 GAGGGAGCAACACAAGAGCA 60.250 55.000 0.00 0.0 0.00 4.26 F
4072 4318 1.381056 TTGGCCAAACACCAGCTGT 60.381 52.632 17.98 0.0 38.73 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1872 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 R
2408 2531 0.325765 AACTCCTCCTGCTACCTCCC 60.326 60.000 0.00 0.00 0.00 4.30 R
3084 3323 1.306226 AGGTCCTCTTCCTTCCCGG 60.306 63.158 0.00 0.00 30.18 5.73 R
4243 4489 0.880441 TCAAACCGTGCCATGTCATG 59.120 50.000 5.79 5.79 0.00 3.07 R
5279 5772 0.172803 CAGACAGGGTACAGGCGTAC 59.827 60.000 9.98 9.98 46.18 3.67 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
96 103 3.973657 AGCAAGTGCATGAAAGTTTCAG 58.026 40.909 22.03 15.02 45.16 3.02
453 513 5.768317 ACATGATCCGTTCGTGAAAAATTT 58.232 33.333 0.00 0.00 42.99 1.82
454 514 5.629020 ACATGATCCGTTCGTGAAAAATTTG 59.371 36.000 0.00 0.00 42.99 2.32
455 515 5.176407 TGATCCGTTCGTGAAAAATTTGT 57.824 34.783 0.00 0.00 0.00 2.83
456 516 5.583495 TGATCCGTTCGTGAAAAATTTGTT 58.417 33.333 0.00 0.00 0.00 2.83
501 572 8.617290 ACCTTGTTGTACTAGACTTAATTTGG 57.383 34.615 0.00 0.00 0.00 3.28
565 649 3.996363 TCGATGAATATCAGCCGATTTGG 59.004 43.478 0.00 0.00 32.99 3.28
740 839 4.114794 CCAATTCTTTTCGCCATGATTCC 58.885 43.478 0.00 0.00 0.00 3.01
782 882 0.684535 TTCGACAGAATCACCTGCCA 59.315 50.000 0.00 0.00 37.68 4.92
783 883 0.037326 TCGACAGAATCACCTGCCAC 60.037 55.000 0.00 0.00 37.68 5.01
795 895 1.308069 CCTGCCACCAGAATCAACCG 61.308 60.000 0.00 0.00 41.77 4.44
804 906 2.996621 CCAGAATCAACCGTCAGTTCTC 59.003 50.000 0.00 0.00 36.18 2.87
848 950 3.696281 TGAGTTGTGTGCTGAAATGTG 57.304 42.857 0.00 0.00 0.00 3.21
849 951 2.358582 TGAGTTGTGTGCTGAAATGTGG 59.641 45.455 0.00 0.00 0.00 4.17
850 952 2.358898 GAGTTGTGTGCTGAAATGTGGT 59.641 45.455 0.00 0.00 0.00 4.16
856 963 4.455533 TGTGTGCTGAAATGTGGTTAGATC 59.544 41.667 0.00 0.00 0.00 2.75
913 1020 3.571571 TCGGACAGTTTCACGTCTAATG 58.428 45.455 0.00 0.00 32.57 1.90
922 1029 7.279313 ACAGTTTCACGTCTAATGTAAACAACT 59.721 33.333 0.00 0.00 31.02 3.16
971 1078 5.363868 TCTTCTCTTCTTCACACTTTCCTCA 59.636 40.000 0.00 0.00 0.00 3.86
1384 1491 4.194720 GCGAGATCGAGGCCGTGT 62.195 66.667 6.39 0.00 43.02 4.49
1537 1644 0.844503 CGCGCTCGGTAAATAGTGTC 59.155 55.000 5.56 0.00 0.00 3.67
1615 1722 3.228453 GGTCATCAATCTGGGCATTCAT 58.772 45.455 0.00 0.00 0.00 2.57
1769 1877 8.603242 TTCACAAAGATCTTACAAAGTACTCC 57.397 34.615 8.75 0.00 0.00 3.85
1770 1878 7.159372 TCACAAAGATCTTACAAAGTACTCCC 58.841 38.462 8.75 0.00 0.00 4.30
1771 1879 7.016268 TCACAAAGATCTTACAAAGTACTCCCT 59.984 37.037 8.75 0.00 0.00 4.20
1772 1880 7.332182 CACAAAGATCTTACAAAGTACTCCCTC 59.668 40.741 8.75 0.00 0.00 4.30
1773 1881 6.547930 AAGATCTTACAAAGTACTCCCTCC 57.452 41.667 6.06 0.00 0.00 4.30
1774 1882 4.645588 AGATCTTACAAAGTACTCCCTCCG 59.354 45.833 0.00 0.00 0.00 4.63
1775 1883 3.771216 TCTTACAAAGTACTCCCTCCGT 58.229 45.455 0.00 0.00 0.00 4.69
1776 1884 3.760684 TCTTACAAAGTACTCCCTCCGTC 59.239 47.826 0.00 0.00 0.00 4.79
1777 1885 1.264295 ACAAAGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
1778 1886 0.172803 CAAAGTACTCCCTCCGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
1779 1887 0.969409 AAAGTACTCCCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
1780 1888 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1781 1889 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1782 1890 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1783 1891 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1784 1892 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1785 1893 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
1786 1894 1.692519 CTCCCTCCGTCCGGAAATATT 59.307 52.381 5.23 0.00 44.66 1.28
1787 1895 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
1788 1896 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
1789 1897 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
1790 1898 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
1791 1899 3.527533 CTCCGTCCGGAAATATTTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
1792 1900 3.264104 TCCGTCCGGAAATATTTGTCAC 58.736 45.455 5.23 0.00 42.05 3.67
1793 1901 2.353579 CCGTCCGGAAATATTTGTCACC 59.646 50.000 5.23 0.00 37.50 4.02
1794 1902 3.004171 CGTCCGGAAATATTTGTCACCA 58.996 45.455 5.23 0.00 0.00 4.17
1795 1903 3.437395 CGTCCGGAAATATTTGTCACCAA 59.563 43.478 5.23 0.00 0.00 3.67
1796 1904 4.083217 CGTCCGGAAATATTTGTCACCAAA 60.083 41.667 5.23 0.00 44.27 3.28
1797 1905 5.563085 CGTCCGGAAATATTTGTCACCAAAA 60.563 40.000 5.23 0.00 43.43 2.44
1798 1906 6.394809 GTCCGGAAATATTTGTCACCAAAAT 58.605 36.000 5.23 0.00 43.43 1.82
1799 1907 6.310224 GTCCGGAAATATTTGTCACCAAAATG 59.690 38.462 5.23 0.00 43.43 2.32
1800 1908 5.580297 CCGGAAATATTTGTCACCAAAATGG 59.420 40.000 5.17 0.00 43.43 3.16
1801 1909 6.393990 CGGAAATATTTGTCACCAAAATGGA 58.606 36.000 5.17 0.00 43.43 3.41
1802 1910 7.041107 CGGAAATATTTGTCACCAAAATGGAT 58.959 34.615 5.17 0.00 43.43 3.41
1803 1911 8.194104 CGGAAATATTTGTCACCAAAATGGATA 58.806 33.333 5.17 0.00 43.43 2.59
1804 1912 9.883142 GGAAATATTTGTCACCAAAATGGATAA 57.117 29.630 5.17 0.00 43.43 1.75
1808 1916 9.889128 ATATTTGTCACCAAAATGGATAAAAGG 57.111 29.630 2.85 0.00 43.43 3.11
1809 1917 5.736951 TGTCACCAAAATGGATAAAAGGG 57.263 39.130 2.85 0.00 40.96 3.95
1810 1918 4.530161 TGTCACCAAAATGGATAAAAGGGG 59.470 41.667 2.85 0.00 40.96 4.79
1811 1919 4.775253 GTCACCAAAATGGATAAAAGGGGA 59.225 41.667 2.85 0.00 40.96 4.81
1812 1920 5.425217 GTCACCAAAATGGATAAAAGGGGAT 59.575 40.000 2.85 0.00 40.96 3.85
1813 1921 5.424895 TCACCAAAATGGATAAAAGGGGATG 59.575 40.000 2.85 0.00 40.96 3.51
1814 1922 5.189539 CACCAAAATGGATAAAAGGGGATGT 59.810 40.000 2.85 0.00 40.96 3.06
1815 1923 6.382570 CACCAAAATGGATAAAAGGGGATGTA 59.617 38.462 2.85 0.00 40.96 2.29
1816 1924 7.071071 CACCAAAATGGATAAAAGGGGATGTAT 59.929 37.037 2.85 0.00 40.96 2.29
1817 1925 7.290014 ACCAAAATGGATAAAAGGGGATGTATC 59.710 37.037 2.85 0.00 40.96 2.24
1818 1926 7.510343 CCAAAATGGATAAAAGGGGATGTATCT 59.490 37.037 0.00 0.00 40.96 1.98
1819 1927 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
1820 1928 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
1821 1929 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
1822 1930 7.554959 TGGATAAAAGGGGATGTATCTAGAC 57.445 40.000 0.00 0.00 0.00 2.59
1823 1931 7.313731 TGGATAAAAGGGGATGTATCTAGACT 58.686 38.462 0.00 0.00 0.00 3.24
1824 1932 8.461854 TGGATAAAAGGGGATGTATCTAGACTA 58.538 37.037 0.00 0.00 0.00 2.59
1825 1933 9.495382 GGATAAAAGGGGATGTATCTAGACTAT 57.505 37.037 0.00 0.00 0.00 2.12
1831 1939 9.900112 AAGGGGATGTATCTAGACTATTTTAGT 57.100 33.333 0.00 0.00 42.86 2.24
1832 1940 9.900112 AGGGGATGTATCTAGACTATTTTAGTT 57.100 33.333 0.00 0.00 39.59 2.24
1845 1953 9.482175 AGACTATTTTAGTTCTAGACACATCCT 57.518 33.333 0.00 0.00 39.59 3.24
1877 1985 9.748708 ATCCATTTTGATGACAAATATTTACGG 57.251 29.630 0.00 0.00 43.99 4.02
1878 1986 8.961634 TCCATTTTGATGACAAATATTTACGGA 58.038 29.630 0.00 0.00 43.99 4.69
1879 1987 9.019764 CCATTTTGATGACAAATATTTACGGAC 57.980 33.333 0.00 0.00 43.99 4.79
1880 1988 8.733128 CATTTTGATGACAAATATTTACGGACG 58.267 33.333 0.00 0.00 43.99 4.79
1881 1989 5.977171 TGATGACAAATATTTACGGACGG 57.023 39.130 0.00 0.00 0.00 4.79
1882 1990 5.662456 TGATGACAAATATTTACGGACGGA 58.338 37.500 0.00 0.00 0.00 4.69
1883 1991 5.751509 TGATGACAAATATTTACGGACGGAG 59.248 40.000 0.00 0.00 0.00 4.63
1884 1992 4.435425 TGACAAATATTTACGGACGGAGG 58.565 43.478 0.00 0.00 0.00 4.30
1885 1993 3.800531 ACAAATATTTACGGACGGAGGG 58.199 45.455 0.00 0.00 0.00 4.30
1899 2007 3.231818 ACGGAGGGAGTAATACATCAGG 58.768 50.000 0.00 0.00 0.00 3.86
1971 2079 0.546747 TGAAGGGGTCCCGATTGTCT 60.547 55.000 0.48 0.00 41.95 3.41
2084 2192 0.965439 GTCCAGTGCACTCTCAGTCT 59.035 55.000 18.64 0.00 0.00 3.24
2086 2194 0.964700 CCAGTGCACTCTCAGTCTCA 59.035 55.000 18.64 0.00 0.00 3.27
2088 2196 1.885233 CAGTGCACTCTCAGTCTCAGA 59.115 52.381 18.64 0.00 0.00 3.27
2131 2248 3.954904 GTCCATCTTCAGAGCAGGTACTA 59.045 47.826 0.00 0.00 36.02 1.82
2190 2307 4.182433 TGCCAGACAACGCCACCA 62.182 61.111 0.00 0.00 0.00 4.17
2202 2319 4.814294 CCACCACCCTACTCGCGC 62.814 72.222 0.00 0.00 0.00 6.86
2207 2324 3.081409 ACCCTACTCGCGCCCATT 61.081 61.111 0.00 0.00 0.00 3.16
2233 2350 3.411114 ATCCGTCGCCGAGACCCTA 62.411 63.158 0.00 0.00 46.92 3.53
2236 2353 2.753043 GTCGCCGAGACCCTACCA 60.753 66.667 0.00 0.00 43.95 3.25
2267 2384 1.209640 GAGACTCCACACCGTCGAC 59.790 63.158 5.18 5.18 35.38 4.20
2278 2395 2.799502 CGTCGACGCGTGACATGT 60.800 61.111 26.59 0.00 36.11 3.21
2372 2493 0.250467 GAGGGAGCAACACAAGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
2408 2531 4.002982 TCAACTGATCAAGGATTTCACCG 58.997 43.478 0.00 0.00 34.73 4.94
2497 2672 4.145052 GTCTGTCCCAAGAAAATCCAACT 58.855 43.478 0.00 0.00 0.00 3.16
2535 2710 2.034221 GACCGCCTTCAAAGCCCT 59.966 61.111 0.00 0.00 0.00 5.19
2554 2729 4.658063 CCCTAGATCTAGTCGTCCAGATT 58.342 47.826 24.80 0.00 31.63 2.40
2633 2809 2.374525 TGTGTGCCACCACTGGAGT 61.375 57.895 0.71 0.00 40.55 3.85
2776 2952 2.285368 TCCGCCTTGGACAGGGAT 60.285 61.111 4.47 0.00 43.74 3.85
2827 3003 2.758089 GCTTCACCTGCTGCCATCG 61.758 63.158 0.00 0.00 0.00 3.84
2967 3175 2.574955 AAGCTCTTCCACGTCGCCT 61.575 57.895 0.00 0.00 0.00 5.52
2999 3210 3.941188 CTCTGCCCACCACCACGT 61.941 66.667 0.00 0.00 0.00 4.49
3004 3215 4.619227 CCCACCACCACGTCGCTT 62.619 66.667 0.00 0.00 0.00 4.68
3084 3323 2.725008 CCTCACTCGATCTCGGCC 59.275 66.667 0.00 0.00 40.29 6.13
3464 3705 9.384682 CCATAATTTTTGCTCAATGTTTTGTTC 57.615 29.630 0.00 0.00 34.32 3.18
3744 3989 5.940192 TGCTACGGGAAATTATAGCAATG 57.060 39.130 2.43 0.00 45.27 2.82
3866 4112 8.652290 GTGGAGATAAATAGGTTAGTGAGGATT 58.348 37.037 0.00 0.00 0.00 3.01
4072 4318 1.381056 TTGGCCAAACACCAGCTGT 60.381 52.632 17.98 0.00 38.73 4.40
4128 4374 6.615726 AGCCTAATCTCTTATGGAGGTTGTTA 59.384 38.462 6.36 0.00 44.33 2.41
4231 4477 7.400439 AGTTTTAGTTCCTTATCCTGGGTTAC 58.600 38.462 0.00 0.00 0.00 2.50
4243 4489 2.618053 CTGGGTTACGTGGATTCAGTC 58.382 52.381 0.00 0.00 0.00 3.51
4483 4975 8.534333 TGTGTAGTAATTGCTTACTTTCTCAG 57.466 34.615 0.00 0.00 44.07 3.35
4489 4981 2.715046 TGCTTACTTTCTCAGGCCATG 58.285 47.619 5.01 0.00 0.00 3.66
4500 4992 5.245584 TCTCAGGCCATGAATATGCATAA 57.754 39.130 11.13 0.00 37.52 1.90
4826 5319 7.977293 TGCCAAGTGATCATATTTTCATTTCTG 59.023 33.333 0.00 0.00 0.00 3.02
4863 5356 8.435187 TGCTATGAAGATTACCATTTCTCTCAT 58.565 33.333 0.00 0.00 0.00 2.90
5006 5499 4.271291 GTCTGCCCTTGAACGAAGATAATC 59.729 45.833 0.00 0.00 32.82 1.75
5057 5550 3.181487 GCTTGGAGAAAGTCTTGCACAAA 60.181 43.478 0.00 0.00 38.25 2.83
5277 5770 8.275632 GGTGAAATTCTTCATTGTTTTGTTAGC 58.724 33.333 0.00 0.00 43.39 3.09
5278 5771 9.034544 GTGAAATTCTTCATTGTTTTGTTAGCT 57.965 29.630 0.00 0.00 43.39 3.32
5279 5772 9.033481 TGAAATTCTTCATTGTTTTGTTAGCTG 57.967 29.630 0.00 0.00 36.62 4.24
5280 5773 8.947055 AAATTCTTCATTGTTTTGTTAGCTGT 57.053 26.923 0.00 0.00 0.00 4.40
5282 5775 9.463443 AATTCTTCATTGTTTTGTTAGCTGTAC 57.537 29.630 0.00 0.00 0.00 2.90
5283 5776 6.655062 TCTTCATTGTTTTGTTAGCTGTACG 58.345 36.000 0.00 0.00 0.00 3.67
5284 5777 4.778904 TCATTGTTTTGTTAGCTGTACGC 58.221 39.130 0.00 2.08 39.57 4.42
5285 5778 3.612472 TTGTTTTGTTAGCTGTACGCC 57.388 42.857 0.00 0.00 40.39 5.68
5451 5945 9.612066 ATTTGGTTTCTTTTTCAAGATAAGCAA 57.388 25.926 13.96 13.96 40.66 3.91
5559 6062 3.364964 CGCAGTGTGGACCTATTGTTTTC 60.365 47.826 0.00 0.00 0.00 2.29
5631 6134 0.261991 TCCTATCTCTTGCTCCGGGT 59.738 55.000 0.00 0.00 0.00 5.28
5706 6209 5.453567 AAATTTCAGTTTCCTTCCTTCCG 57.546 39.130 0.00 0.00 0.00 4.30
5724 6228 0.865769 CGGTTAGCGTCACTTTGCTT 59.134 50.000 0.00 0.00 42.48 3.91
5788 6292 0.674581 GCTTCCCAATTTTGCAGGGC 60.675 55.000 3.03 0.00 42.52 5.19
5840 6344 2.047061 TGACAGTACCCTTGCAAGACT 58.953 47.619 28.05 19.40 0.00 3.24
5849 6353 2.497138 CCTTGCAAGACTGTCATGACA 58.503 47.619 28.05 26.33 39.32 3.58
5890 6394 4.244066 GCATTGTAACATTTGCACATCCA 58.756 39.130 0.00 0.00 35.22 3.41
6089 6632 1.069358 CCTCTAGGATCCGCAAGAACC 59.931 57.143 5.98 0.00 37.71 3.62
6091 6634 3.223435 CTCTAGGATCCGCAAGAACCTA 58.777 50.000 5.98 8.82 45.56 3.08
6092 6635 2.957006 TCTAGGATCCGCAAGAACCTAC 59.043 50.000 5.98 0.00 45.56 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 77 1.985473 ACTTTCATGCACTTGCTCCA 58.015 45.000 2.33 0.00 42.66 3.86
96 103 1.620413 GCGCAATGTGCTTTCTTGCC 61.620 55.000 12.00 0.00 42.25 4.52
456 516 3.334691 GTCTCAAATTCGTGGATGTCCA 58.665 45.455 0.00 0.00 45.30 4.02
501 572 6.150641 AGCATAAATCATCCACACATAGCATC 59.849 38.462 0.00 0.00 0.00 3.91
565 649 9.931210 ATTTTAACTAATCGGACGAAATTCATC 57.069 29.630 0.00 0.00 0.00 2.92
697 795 1.668419 CTTAGGGCATCTTCAACGGG 58.332 55.000 0.00 0.00 0.00 5.28
740 839 4.764172 AGTTTCCAGAATCTGATTCTCCG 58.236 43.478 25.89 19.27 46.17 4.63
749 848 5.215252 TCTGTCGAAAGTTTCCAGAATCT 57.785 39.130 17.27 0.00 0.00 2.40
763 863 0.684535 TGGCAGGTGATTCTGTCGAA 59.315 50.000 0.00 0.00 41.89 3.71
764 864 0.037326 GTGGCAGGTGATTCTGTCGA 60.037 55.000 0.00 0.00 41.89 4.20
782 882 2.368875 AGAACTGACGGTTGATTCTGGT 59.631 45.455 3.87 0.00 38.41 4.00
783 883 2.996621 GAGAACTGACGGTTGATTCTGG 59.003 50.000 3.87 0.00 38.41 3.86
848 950 2.166664 AGCACTCAGTTCCGATCTAACC 59.833 50.000 4.66 0.00 0.00 2.85
849 951 3.119459 TCAGCACTCAGTTCCGATCTAAC 60.119 47.826 0.00 0.00 0.00 2.34
850 952 3.089284 TCAGCACTCAGTTCCGATCTAA 58.911 45.455 0.00 0.00 0.00 2.10
856 963 2.146342 ACATTTCAGCACTCAGTTCCG 58.854 47.619 0.00 0.00 0.00 4.30
913 1020 4.594136 AGCGTTAGTTGCAAGTTGTTTAC 58.406 39.130 12.95 3.14 33.85 2.01
922 1029 1.001815 GGCTTCAAGCGTTAGTTGCAA 60.002 47.619 2.54 0.00 43.62 4.08
1384 1491 0.546747 CTCTCCCCCTGGTACCACAA 60.547 60.000 11.60 0.00 0.00 3.33
1537 1644 5.618195 GCCATGCCAAAAATGAAGACAAATG 60.618 40.000 0.00 0.00 0.00 2.32
1615 1722 4.027674 TGTCCAAAATTGCTAGCCTGTA 57.972 40.909 13.29 0.00 0.00 2.74
1689 1796 1.000359 CGGGGCCATCCTCCTTTTT 60.000 57.895 4.39 0.00 35.33 1.94
1747 1855 7.317722 AGGGAGTACTTTGTAAGATCTTTGT 57.682 36.000 14.36 7.89 0.00 2.83
1754 1862 3.760684 GACGGAGGGAGTACTTTGTAAGA 59.239 47.826 0.00 0.00 0.00 2.10
1762 1870 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
1763 1871 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
1764 1872 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1765 1873 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1766 1874 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
1767 1875 1.797320 AATATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
1768 1876 2.218603 CAAATATTTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
1769 1877 2.870411 GACAAATATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
1770 1878 3.308866 GTGACAAATATTTCCGGACGGAG 59.691 47.826 13.64 3.15 46.06 4.63
1771 1879 3.264104 GTGACAAATATTTCCGGACGGA 58.736 45.455 1.83 9.76 43.52 4.69
1772 1880 2.353579 GGTGACAAATATTTCCGGACGG 59.646 50.000 1.83 3.96 0.00 4.79
1773 1881 3.004171 TGGTGACAAATATTTCCGGACG 58.996 45.455 1.83 0.00 37.44 4.79
1787 1895 4.530161 CCCCTTTTATCCATTTTGGTGACA 59.470 41.667 0.00 0.00 39.03 3.58
1788 1896 4.775253 TCCCCTTTTATCCATTTTGGTGAC 59.225 41.667 0.00 0.00 39.03 3.67
1789 1897 5.017093 TCCCCTTTTATCCATTTTGGTGA 57.983 39.130 0.00 0.00 39.03 4.02
1790 1898 5.189539 ACATCCCCTTTTATCCATTTTGGTG 59.810 40.000 0.00 0.00 39.03 4.17
1791 1899 5.349690 ACATCCCCTTTTATCCATTTTGGT 58.650 37.500 0.00 0.00 39.03 3.67
1792 1900 5.955961 ACATCCCCTTTTATCCATTTTGG 57.044 39.130 0.00 0.00 39.43 3.28
1793 1901 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
1794 1902 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
1795 1903 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
1796 1904 8.606830 GTCTAGATACATCCCCTTTTATCCATT 58.393 37.037 0.00 0.00 0.00 3.16
1797 1905 7.964293 AGTCTAGATACATCCCCTTTTATCCAT 59.036 37.037 0.00 0.00 0.00 3.41
1798 1906 7.313731 AGTCTAGATACATCCCCTTTTATCCA 58.686 38.462 0.00 0.00 0.00 3.41
1799 1907 7.800300 AGTCTAGATACATCCCCTTTTATCC 57.200 40.000 0.00 0.00 0.00 2.59
1805 1913 9.900112 ACTAAAATAGTCTAGATACATCCCCTT 57.100 33.333 0.00 0.00 32.47 3.95
1806 1914 9.900112 AACTAAAATAGTCTAGATACATCCCCT 57.100 33.333 0.00 0.00 38.26 4.79
1819 1927 9.482175 AGGATGTGTCTAGAACTAAAATAGTCT 57.518 33.333 0.00 0.00 38.26 3.24
1851 1959 9.748708 CCGTAAATATTTGTCATCAAAATGGAT 57.251 29.630 11.05 0.00 44.97 3.41
1852 1960 8.961634 TCCGTAAATATTTGTCATCAAAATGGA 58.038 29.630 11.05 5.04 44.97 3.41
1853 1961 9.019764 GTCCGTAAATATTTGTCATCAAAATGG 57.980 33.333 11.05 2.82 44.97 3.16
1854 1962 8.733128 CGTCCGTAAATATTTGTCATCAAAATG 58.267 33.333 11.05 0.00 44.97 2.32
1855 1963 7.913297 CCGTCCGTAAATATTTGTCATCAAAAT 59.087 33.333 11.05 0.00 44.97 1.82
1856 1964 7.119407 TCCGTCCGTAAATATTTGTCATCAAAA 59.881 33.333 11.05 0.00 44.97 2.44
1857 1965 6.594547 TCCGTCCGTAAATATTTGTCATCAAA 59.405 34.615 11.05 0.00 45.71 2.69
1858 1966 6.107343 TCCGTCCGTAAATATTTGTCATCAA 58.893 36.000 11.05 0.00 0.00 2.57
1859 1967 5.662456 TCCGTCCGTAAATATTTGTCATCA 58.338 37.500 11.05 0.00 0.00 3.07
1860 1968 5.176958 CCTCCGTCCGTAAATATTTGTCATC 59.823 44.000 11.05 0.00 0.00 2.92
1861 1969 5.054477 CCTCCGTCCGTAAATATTTGTCAT 58.946 41.667 11.05 0.00 0.00 3.06
1862 1970 4.435425 CCTCCGTCCGTAAATATTTGTCA 58.565 43.478 11.05 0.00 0.00 3.58
1863 1971 3.805971 CCCTCCGTCCGTAAATATTTGTC 59.194 47.826 11.05 3.49 0.00 3.18
1864 1972 3.451902 TCCCTCCGTCCGTAAATATTTGT 59.548 43.478 11.05 0.00 0.00 2.83
1865 1973 4.056050 CTCCCTCCGTCCGTAAATATTTG 58.944 47.826 11.05 0.00 0.00 2.32
1866 1974 3.708121 ACTCCCTCCGTCCGTAAATATTT 59.292 43.478 5.89 5.89 0.00 1.40
1867 1975 3.303049 ACTCCCTCCGTCCGTAAATATT 58.697 45.455 0.00 0.00 0.00 1.28
1868 1976 2.954792 ACTCCCTCCGTCCGTAAATAT 58.045 47.619 0.00 0.00 0.00 1.28
1869 1977 2.442236 ACTCCCTCCGTCCGTAAATA 57.558 50.000 0.00 0.00 0.00 1.40
1870 1978 2.442236 TACTCCCTCCGTCCGTAAAT 57.558 50.000 0.00 0.00 0.00 1.40
1871 1979 2.214376 TTACTCCCTCCGTCCGTAAA 57.786 50.000 0.00 0.00 0.00 2.01
1872 1980 2.442236 ATTACTCCCTCCGTCCGTAA 57.558 50.000 0.00 0.00 0.00 3.18
1873 1981 2.172505 TGTATTACTCCCTCCGTCCGTA 59.827 50.000 0.00 0.00 0.00 4.02
1874 1982 1.064463 TGTATTACTCCCTCCGTCCGT 60.064 52.381 0.00 0.00 0.00 4.69
1875 1983 1.683943 TGTATTACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
1876 1984 3.228453 TGATGTATTACTCCCTCCGTCC 58.772 50.000 0.00 0.00 0.00 4.79
1877 1985 3.256136 CCTGATGTATTACTCCCTCCGTC 59.744 52.174 0.00 0.00 0.00 4.79
1878 1986 3.117246 TCCTGATGTATTACTCCCTCCGT 60.117 47.826 0.00 0.00 0.00 4.69
1879 1987 3.497332 TCCTGATGTATTACTCCCTCCG 58.503 50.000 0.00 0.00 0.00 4.63
1880 1988 4.902448 ACTTCCTGATGTATTACTCCCTCC 59.098 45.833 0.00 0.00 0.00 4.30
1881 1989 5.836358 AGACTTCCTGATGTATTACTCCCTC 59.164 44.000 0.00 0.00 0.00 4.30
1882 1990 5.600484 CAGACTTCCTGATGTATTACTCCCT 59.400 44.000 0.00 0.00 45.78 4.20
1883 1991 5.598830 TCAGACTTCCTGATGTATTACTCCC 59.401 44.000 0.00 0.00 46.38 4.30
1884 1992 6.716934 TCAGACTTCCTGATGTATTACTCC 57.283 41.667 0.00 0.00 46.38 3.85
1899 2007 3.190118 CCAAGATGGTTGCTTCAGACTTC 59.810 47.826 0.00 0.00 31.35 3.01
1961 2069 3.871594 GGTATTTGACTCAGACAATCGGG 59.128 47.826 0.00 0.00 0.00 5.14
1971 2079 6.653320 GTGAGGTATGTTTGGTATTTGACTCA 59.347 38.462 0.00 0.00 0.00 3.41
2131 2248 1.878102 GCCTGACAAGGTCGATGTGTT 60.878 52.381 0.00 0.00 46.43 3.32
2190 2307 1.119574 ATAATGGGCGCGAGTAGGGT 61.120 55.000 12.10 0.00 34.93 4.34
2202 2319 2.135139 CGACGGATGTGTGATAATGGG 58.865 52.381 0.00 0.00 0.00 4.00
2278 2395 0.458260 TTAGCGATGGAGCAGCGTTA 59.542 50.000 0.00 0.00 45.34 3.18
2284 2401 0.036765 ACGGTTTTAGCGATGGAGCA 60.037 50.000 5.21 0.00 42.41 4.26
2372 2493 1.141657 CAGTTGATCGGATGATGGGGT 59.858 52.381 0.00 0.00 34.09 4.95
2400 2522 0.541863 CTGCTACCTCCCGGTGAAAT 59.458 55.000 0.00 0.00 45.18 2.17
2408 2531 0.325765 AACTCCTCCTGCTACCTCCC 60.326 60.000 0.00 0.00 0.00 4.30
2497 2672 1.225855 GGACGATGCACAAGTTGTCA 58.774 50.000 5.27 7.97 0.00 3.58
2535 2710 5.211174 TCGAATCTGGACGACTAGATCTA 57.789 43.478 13.45 1.69 42.14 1.98
2554 2729 1.135489 GCTGTTGTGGATAGTCGTCGA 60.135 52.381 0.00 0.00 0.00 4.20
2562 2737 0.399833 TGGCAGTGCTGTTGTGGATA 59.600 50.000 16.11 0.00 0.00 2.59
2949 3157 2.048127 GGCGACGTGGAAGAGCTT 60.048 61.111 0.11 0.00 0.00 3.74
2950 3158 2.574955 AAGGCGACGTGGAAGAGCT 61.575 57.895 0.11 0.00 0.00 4.09
3084 3323 1.306226 AGGTCCTCTTCCTTCCCGG 60.306 63.158 0.00 0.00 30.18 5.73
3464 3705 8.718102 ATGGTTGCTATTTTGTAGTACTAGTG 57.282 34.615 5.39 0.00 0.00 2.74
3541 3782 5.050091 ACATTTTGACTCTTCAACTACAGCG 60.050 40.000 0.00 0.00 41.64 5.18
3738 3983 7.879160 ACAACAAATCCATCAAAATACATTGCT 59.121 29.630 0.00 0.00 0.00 3.91
3744 3989 9.868277 TTCCATACAACAAATCCATCAAAATAC 57.132 29.630 0.00 0.00 0.00 1.89
3940 4186 9.507329 AGAACGGGTATCTTAATCGTATAAGTA 57.493 33.333 8.92 1.64 35.01 2.24
3944 4190 7.448161 TCCAAGAACGGGTATCTTAATCGTATA 59.552 37.037 0.00 0.00 35.43 1.47
4017 4263 2.032204 GCATTATGCTTGCTTCTCCTCG 60.032 50.000 10.27 0.00 40.96 4.63
4072 4318 3.333029 TGTTCATCTCGATTGGCTTCA 57.667 42.857 0.00 0.00 0.00 3.02
4128 4374 7.015195 ACCAAAATTATACTTTTCACTGGCTGT 59.985 33.333 0.00 0.00 0.00 4.40
4231 4477 2.610833 CCATGTCATGACTGAATCCACG 59.389 50.000 25.55 0.00 31.85 4.94
4243 4489 0.880441 TCAAACCGTGCCATGTCATG 59.120 50.000 5.79 5.79 0.00 3.07
4483 4975 9.439500 AAATTACAATTATGCATATTCATGGCC 57.561 29.630 7.36 0.00 32.36 5.36
4863 5356 8.458052 CAACCTGTTTTAGTGCATACATAATCA 58.542 33.333 0.00 0.00 0.00 2.57
5006 5499 2.417933 GTGCTTCAGTGGTAAGATGCAG 59.582 50.000 0.00 0.00 42.93 4.41
5057 5550 7.717875 TGCTTGTAAAAAGTTACTGATGTAGGT 59.282 33.333 0.00 0.00 40.35 3.08
5279 5772 0.172803 CAGACAGGGTACAGGCGTAC 59.827 60.000 9.98 9.98 46.18 3.67
5280 5773 0.251474 ACAGACAGGGTACAGGCGTA 60.251 55.000 0.00 0.00 0.00 4.42
5281 5774 1.533273 ACAGACAGGGTACAGGCGT 60.533 57.895 0.00 0.00 0.00 5.68
5282 5775 1.079819 CACAGACAGGGTACAGGCG 60.080 63.158 0.00 0.00 0.00 5.52
5283 5776 0.396811 AACACAGACAGGGTACAGGC 59.603 55.000 0.00 0.00 29.80 4.85
5284 5777 2.368875 AGAAACACAGACAGGGTACAGG 59.631 50.000 0.00 0.00 29.80 4.00
5285 5778 3.753294 AGAAACACAGACAGGGTACAG 57.247 47.619 0.00 0.00 29.80 2.74
5296 5789 9.737427 ACGATATCTATACAAGAAGAAACACAG 57.263 33.333 0.34 0.00 37.89 3.66
5451 5945 9.911788 ACCAGTGAGAAAAGTATTCATATGATT 57.088 29.630 6.17 5.79 0.00 2.57
5559 6062 4.580580 ACCACAGAGCAACTAAAAGGAAAG 59.419 41.667 0.00 0.00 0.00 2.62
5572 6075 4.301072 AAGCCTAAATTACCACAGAGCA 57.699 40.909 0.00 0.00 0.00 4.26
5601 6104 6.240894 AGCAAGAGATAGGACACAAATTGAA 58.759 36.000 0.00 0.00 0.00 2.69
5602 6105 5.809001 AGCAAGAGATAGGACACAAATTGA 58.191 37.500 0.00 0.00 0.00 2.57
5611 6114 0.676736 CCCGGAGCAAGAGATAGGAC 59.323 60.000 0.73 0.00 0.00 3.85
5631 6134 2.381961 AGATAGGAAACAAAGGGGGCAA 59.618 45.455 0.00 0.00 0.00 4.52
5682 6185 5.691754 CGGAAGGAAGGAAACTGAAATTTTG 59.308 40.000 0.00 0.00 42.68 2.44
5706 6209 1.871039 TCAAGCAAAGTGACGCTAACC 59.129 47.619 0.00 0.00 37.54 2.85
5724 6228 6.262273 GGAGGTCACAACAGTTTAAAAGATCA 59.738 38.462 0.00 0.00 0.00 2.92
5840 6344 8.642935 TCCAAATATAAAAGGTTGTCATGACA 57.357 30.769 24.56 24.56 39.98 3.58
5849 6353 7.917003 ACAATGCCTTCCAAATATAAAAGGTT 58.083 30.769 0.00 0.00 40.36 3.50
5890 6394 8.296713 ACATGATTTTTATTCGCTTTGTACTGT 58.703 29.630 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.