Multiple sequence alignment - TraesCS2D01G176600

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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 TraesCS2D01G176600 chr2D 100.000 7001 0 0 1 7001 120098720 120091720 0.000000e+00 12892.0
1 TraesCS2D01G176600 chr2D 96.361 797 15 3 1 783 634844134 634844930 0.000000e+00 1299.0
2 TraesCS2D01G176600 chr2D 95.358 797 23 5 1 783 324353762 324354558 0.000000e+00 1254.0
3 TraesCS2D01G176600 chr2D 95.346 795 23 5 1 781 51186849 51186055 0.000000e+00 1251.0
4 TraesCS2D01G176600 chr2D 77.887 710 58 40 6376 6997 33361406 33362104 4.020000e-92 350.0
5 TraesCS2D01G176600 chr2D 76.765 680 77 35 6392 6997 494648101 494647429 8.820000e-79 305.0
6 TraesCS2D01G176600 chr2D 83.133 249 32 8 6503 6744 74924670 74924425 1.180000e-52 219.0
7 TraesCS2D01G176600 chr2D 92.045 88 7 0 6914 7001 579200616 579200529 2.650000e-24 124.0
8 TraesCS2D01G176600 chr2D 100.000 42 0 0 3299 3340 120095382 120095341 2.090000e-10 78.7
9 TraesCS2D01G176600 chr2D 100.000 42 0 0 3339 3380 120095422 120095381 2.090000e-10 78.7
10 TraesCS2D01G176600 chr2B 95.591 5421 134 30 794 6150 172895472 172890093 0.000000e+00 8589.0
11 TraesCS2D01G176600 chr2B 93.750 64 4 0 6329 6392 172880101 172880038 5.780000e-16 97.1
12 TraesCS2D01G176600 chr2B 96.226 53 2 0 2186 2238 172894108 172894056 3.480000e-13 87.9
13 TraesCS2D01G176600 chr2A 95.125 3549 122 30 3466 7001 123516951 123513441 0.000000e+00 5548.0
14 TraesCS2D01G176600 chr2A 97.968 2559 42 2 930 3478 123519527 123516969 0.000000e+00 4429.0
15 TraesCS2D01G176600 chr2A 98.000 50 1 0 2189 2238 123518306 123518257 3.480000e-13 87.9
16 TraesCS2D01G176600 chr2A 94.231 52 2 1 3299 3349 123517108 123517057 2.090000e-10 78.7
17 TraesCS2D01G176600 chr2A 81.818 88 14 2 6461 6546 416006100 416006013 9.740000e-09 73.1
18 TraesCS2D01G176600 chr4D 96.919 779 13 5 1 768 294010731 294011509 0.000000e+00 1295.0
19 TraesCS2D01G176600 chr4D 95.483 797 21 4 1 783 35528476 35527681 0.000000e+00 1258.0
20 TraesCS2D01G176600 chr4D 94.949 792 23 4 1 778 136491872 136492660 0.000000e+00 1225.0
21 TraesCS2D01G176600 chr4D 82.236 501 51 21 6457 6923 101392499 101392995 1.410000e-106 398.0
22 TraesCS2D01G176600 chr4D 77.138 538 57 28 6518 6997 66772231 66771702 1.170000e-62 252.0
23 TraesCS2D01G176600 chr4D 75.248 606 72 29 6457 6997 385519234 385519826 4.250000e-52 217.0
24 TraesCS2D01G176600 chr4D 74.949 487 62 30 6475 6927 502752901 502753361 1.210000e-37 169.0
25 TraesCS2D01G176600 chr4D 77.551 245 37 10 6459 6690 3842425 3842664 1.580000e-26 132.0
26 TraesCS2D01G176600 chr4D 73.150 473 82 35 6463 6908 23218713 23219167 2.050000e-25 128.0
27 TraesCS2D01G176600 chr4D 89.286 84 6 3 6918 6999 10996109 10996027 1.240000e-17 102.0
28 TraesCS2D01G176600 chr5D 96.110 797 17 3 1 783 440942585 440943381 0.000000e+00 1288.0
29 TraesCS2D01G176600 chr5D 95.226 796 23 4 3 783 298037049 298036254 0.000000e+00 1245.0
30 TraesCS2D01G176600 chr5D 80.830 506 48 28 6461 6923 95867061 95866562 1.120000e-92 351.0
31 TraesCS2D01G176600 chr5D 78.536 601 58 39 6459 6997 498647425 498648016 5.240000e-86 329.0
32 TraesCS2D01G176600 chr5D 79.654 462 55 28 6481 6909 510358068 510358523 5.310000e-76 296.0
33 TraesCS2D01G176600 chr5D 76.736 576 66 31 6475 6997 302325164 302324604 6.970000e-65 259.0
34 TraesCS2D01G176600 chr5D 83.945 218 27 7 6475 6690 435670983 435671194 1.190000e-47 202.0
35 TraesCS2D01G176600 chr5D 79.085 306 42 16 6401 6690 114967216 114967515 2.580000e-44 191.0
36 TraesCS2D01G176600 chr5D 92.771 83 6 0 6915 6997 466525243 466525325 3.430000e-23 121.0
37 TraesCS2D01G176600 chr6D 95.739 798 19 5 1 783 413394456 413393659 0.000000e+00 1271.0
38 TraesCS2D01G176600 chr6D 94.571 792 29 5 1 778 157656328 157655537 0.000000e+00 1212.0
39 TraesCS2D01G176600 chr6D 94.852 777 25 6 1 763 363010385 363011160 0.000000e+00 1199.0
40 TraesCS2D01G176600 chr6D 95.687 626 12 4 171 781 108536191 108535566 0.000000e+00 992.0
41 TraesCS2D01G176600 chr6D 79.764 593 62 24 6457 6997 349102447 349103033 1.840000e-100 377.0
42 TraesCS2D01G176600 chr6D 82.650 317 36 12 6535 6840 266442471 266442779 5.390000e-66 263.0
43 TraesCS2D01G176600 chr6D 98.649 148 0 2 6153 6298 459701993 459701846 1.940000e-65 261.0
44 TraesCS2D01G176600 chr6D 97.203 143 4 0 6150 6292 440963294 440963436 7.020000e-60 243.0
45 TraesCS2D01G176600 chr6D 75.712 597 70 29 6470 6997 316627915 316628505 5.460000e-56 230.0
46 TraesCS2D01G176600 chr6D 77.500 360 55 15 6461 6806 164802928 164802581 7.170000e-45 193.0
47 TraesCS2D01G176600 chr6D 78.413 315 42 17 6549 6844 156455739 156456046 1.550000e-41 182.0
48 TraesCS2D01G176600 chr6D 90.805 87 8 0 6911 6997 242997697 242997783 4.440000e-22 117.0
49 TraesCS2D01G176600 chr6D 83.333 84 13 1 6830 6913 174343324 174343406 7.530000e-10 76.8
50 TraesCS2D01G176600 chr6D 86.567 67 9 0 6857 6923 324556386 324556320 2.710000e-09 75.0
51 TraesCS2D01G176600 chr1D 95.597 795 21 6 1 781 24093512 24092718 0.000000e+00 1262.0
52 TraesCS2D01G176600 chr1D 95.472 795 22 5 1 781 366012851 366013645 0.000000e+00 1256.0
53 TraesCS2D01G176600 chr1D 79.102 579 55 29 6392 6923 490949814 490950373 8.700000e-89 339.0
54 TraesCS2D01G176600 chr1D 83.033 389 44 16 6541 6923 202354491 202354863 4.050000e-87 333.0
55 TraesCS2D01G176600 chr1D 99.301 143 1 0 6150 6292 99547539 99547681 6.970000e-65 259.0
56 TraesCS2D01G176600 chr1D 76.923 546 62 25 6503 6997 443793171 443793703 1.170000e-62 252.0
57 TraesCS2D01G176600 chr1D 77.629 447 50 24 6393 6797 483355657 483355219 7.070000e-55 226.0
58 TraesCS2D01G176600 chr1D 74.783 345 43 21 6459 6793 459628116 459628426 1.600000e-21 115.0
59 TraesCS2D01G176600 chr1D 88.506 87 10 0 6911 6997 296975768 296975854 9.600000e-19 106.0
60 TraesCS2D01G176600 chr1D 83.673 98 12 2 6832 6925 433144636 433144539 9.670000e-14 89.8
61 TraesCS2D01G176600 chr3D 95.483 797 22 5 1 783 12303672 12304468 0.000000e+00 1260.0
62 TraesCS2D01G176600 chr3D 95.220 795 24 5 1 781 209460164 209460958 0.000000e+00 1245.0
63 TraesCS2D01G176600 chr3D 78.231 588 68 22 6461 6997 578901262 578900684 8.760000e-84 322.0
64 TraesCS2D01G176600 chr3D 78.815 439 49 20 6392 6791 551515788 551516221 9.010000e-64 255.0
65 TraesCS2D01G176600 chr3D 76.144 612 70 40 6383 6923 273475491 273474885 1.170000e-62 252.0
66 TraesCS2D01G176600 chr3D 94.245 139 8 0 6151 6289 18361996 18361858 5.500000e-51 213.0
67 TraesCS2D01G176600 chr3D 75.826 484 81 28 6460 6923 315470258 315469791 5.500000e-51 213.0
68 TraesCS2D01G176600 chr3D 76.123 423 68 22 6523 6923 474538901 474538490 2.580000e-44 191.0
69 TraesCS2D01G176600 chr3D 94.253 87 5 0 6911 6997 551554692 551554778 4.410000e-27 134.0
70 TraesCS2D01G176600 chr3D 88.732 71 8 0 6856 6926 315745576 315745506 3.480000e-13 87.9
71 TraesCS2D01G176600 chr7D 95.358 797 23 7 1 783 628532630 628531834 0.000000e+00 1254.0
72 TraesCS2D01G176600 chr7D 100.000 142 0 0 6151 6292 618707278 618707137 5.390000e-66 263.0
73 TraesCS2D01G176600 chr7D 76.285 603 74 25 6457 6997 368568097 368568692 2.510000e-64 257.0
74 TraesCS2D01G176600 chr7D 77.362 508 49 22 6555 7001 233065840 233066342 2.520000e-59 241.0
75 TraesCS2D01G176600 chr7D 74.386 570 91 38 6392 6923 116341112 116341664 7.170000e-45 193.0
76 TraesCS2D01G176600 chr6A 86.906 779 93 6 1 771 326233310 326234087 0.000000e+00 865.0
77 TraesCS2D01G176600 chr6A 94.891 137 7 0 6153 6289 605337143 605337279 1.530000e-51 215.0
78 TraesCS2D01G176600 chr6A 91.667 84 7 0 6914 6997 219702287 219702204 4.440000e-22 117.0
79 TraesCS2D01G176600 chr5A 80.929 409 49 19 6531 6923 565485867 565486262 5.310000e-76 296.0
80 TraesCS2D01G176600 chr5A 75.868 576 78 31 6392 6923 112039943 112040501 3.260000e-58 237.0
81 TraesCS2D01G176600 chr5A 95.918 49 2 0 6878 6926 407932408 407932360 5.820000e-11 80.5
82 TraesCS2D01G176600 chr5B 76.706 674 69 44 6392 6992 125841351 125842009 1.910000e-75 294.0
83 TraesCS2D01G176600 chr5B 93.525 139 9 0 6154 6292 680974853 680974991 2.560000e-49 207.0
84 TraesCS2D01G176600 chr5B 90.260 154 14 1 6143 6296 647934328 647934480 4.280000e-47 200.0
85 TraesCS2D01G176600 chr5B 89.510 143 15 0 6150 6292 705847037 705847179 1.550000e-41 182.0
86 TraesCS2D01G176600 chr5B 88.095 84 10 0 6840 6923 372201841 372201924 4.470000e-17 100.0
87 TraesCS2D01G176600 chr6B 77.052 536 74 33 6418 6923 508937152 508936636 5.390000e-66 263.0
88 TraesCS2D01G176600 chr6B 93.182 88 6 0 6914 7001 492195320 492195233 5.700000e-26 130.0
89 TraesCS2D01G176600 chr6B 73.090 301 44 15 6388 6655 632232492 632232788 9.740000e-09 73.1
90 TraesCS2D01G176600 chr7B 78.079 479 56 28 6406 6842 442374177 442374648 2.510000e-64 257.0
91 TraesCS2D01G176600 chr7B 96.429 140 5 0 6153 6292 247261442 247261581 1.520000e-56 231.0
92 TraesCS2D01G176600 chr3A 79.500 400 46 22 6555 6923 724263629 724264023 1.170000e-62 252.0
93 TraesCS2D01G176600 chr3A 83.333 156 23 2 6535 6690 364450141 364450293 2.630000e-29 141.0
94 TraesCS2D01G176600 chr3A 74.453 411 60 38 6535 6921 60285597 60285986 1.220000e-27 135.0
95 TraesCS2D01G176600 chr3A 93.407 91 6 0 6911 7001 357299117 357299207 1.220000e-27 135.0
96 TraesCS2D01G176600 chr7A 78.220 427 51 28 6535 6923 12814532 12814110 1.170000e-57 235.0
97 TraesCS2D01G176600 chr7A 76.963 191 27 14 6475 6655 14299361 14299544 7.480000e-15 93.5
98 TraesCS2D01G176600 chr4A 94.667 150 8 0 6151 6300 462223872 462224021 4.220000e-57 233.0
99 TraesCS2D01G176600 chr4A 93.662 142 9 0 6151 6292 175752704 175752845 5.500000e-51 213.0
100 TraesCS2D01G176600 chr3B 95.833 144 5 1 6153 6295 765923816 765923673 1.520000e-56 231.0
101 TraesCS2D01G176600 chr3B 95.139 144 6 1 6153 6295 335132327 335132184 7.070000e-55 226.0
102 TraesCS2D01G176600 chr3B 93.333 90 6 0 6908 6997 72723822 72723911 4.410000e-27 134.0
103 TraesCS2D01G176600 chr3B 89.583 48 5 0 6878 6925 169926911 169926864 2.110000e-05 62.1
104 TraesCS2D01G176600 chrUn 81.818 209 26 5 6459 6655 124658248 124658040 1.560000e-36 165.0
105 TraesCS2D01G176600 chrUn 90.361 83 8 0 6914 6996 78905221 78905139 7.420000e-20 110.0


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 TraesCS2D01G176600 chr2D 120091720 120098720 7000 True 4349.80 12892 100.0000 1 7001 3 chr2D.!!$R5 7000
1 TraesCS2D01G176600 chr2D 634844134 634844930 796 False 1299.00 1299 96.3610 1 783 1 chr2D.!!$F3 782
2 TraesCS2D01G176600 chr2D 324353762 324354558 796 False 1254.00 1254 95.3580 1 783 1 chr2D.!!$F2 782
3 TraesCS2D01G176600 chr2D 51186055 51186849 794 True 1251.00 1251 95.3460 1 781 1 chr2D.!!$R1 780
4 TraesCS2D01G176600 chr2D 33361406 33362104 698 False 350.00 350 77.8870 6376 6997 1 chr2D.!!$F1 621
5 TraesCS2D01G176600 chr2D 494647429 494648101 672 True 305.00 305 76.7650 6392 6997 1 chr2D.!!$R3 605
6 TraesCS2D01G176600 chr2B 172890093 172895472 5379 True 4338.45 8589 95.9085 794 6150 2 chr2B.!!$R2 5356
7 TraesCS2D01G176600 chr2A 123513441 123519527 6086 True 2535.90 5548 96.3310 930 7001 4 chr2A.!!$R2 6071
8 TraesCS2D01G176600 chr4D 294010731 294011509 778 False 1295.00 1295 96.9190 1 768 1 chr4D.!!$F5 767
9 TraesCS2D01G176600 chr4D 35527681 35528476 795 True 1258.00 1258 95.4830 1 783 1 chr4D.!!$R2 782
10 TraesCS2D01G176600 chr4D 136491872 136492660 788 False 1225.00 1225 94.9490 1 778 1 chr4D.!!$F4 777
11 TraesCS2D01G176600 chr4D 66771702 66772231 529 True 252.00 252 77.1380 6518 6997 1 chr4D.!!$R3 479
12 TraesCS2D01G176600 chr4D 385519234 385519826 592 False 217.00 217 75.2480 6457 6997 1 chr4D.!!$F6 540
13 TraesCS2D01G176600 chr5D 440942585 440943381 796 False 1288.00 1288 96.1100 1 783 1 chr5D.!!$F3 782
14 TraesCS2D01G176600 chr5D 298036254 298037049 795 True 1245.00 1245 95.2260 3 783 1 chr5D.!!$R2 780
15 TraesCS2D01G176600 chr5D 498647425 498648016 591 False 329.00 329 78.5360 6459 6997 1 chr5D.!!$F5 538
16 TraesCS2D01G176600 chr5D 302324604 302325164 560 True 259.00 259 76.7360 6475 6997 1 chr5D.!!$R3 522
17 TraesCS2D01G176600 chr6D 413393659 413394456 797 True 1271.00 1271 95.7390 1 783 1 chr6D.!!$R5 782
18 TraesCS2D01G176600 chr6D 157655537 157656328 791 True 1212.00 1212 94.5710 1 778 1 chr6D.!!$R2 777
19 TraesCS2D01G176600 chr6D 363010385 363011160 775 False 1199.00 1199 94.8520 1 763 1 chr6D.!!$F7 762
20 TraesCS2D01G176600 chr6D 108535566 108536191 625 True 992.00 992 95.6870 171 781 1 chr6D.!!$R1 610
21 TraesCS2D01G176600 chr6D 349102447 349103033 586 False 377.00 377 79.7640 6457 6997 1 chr6D.!!$F6 540
22 TraesCS2D01G176600 chr6D 316627915 316628505 590 False 230.00 230 75.7120 6470 6997 1 chr6D.!!$F5 527
23 TraesCS2D01G176600 chr1D 24092718 24093512 794 True 1262.00 1262 95.5970 1 781 1 chr1D.!!$R1 780
24 TraesCS2D01G176600 chr1D 366012851 366013645 794 False 1256.00 1256 95.4720 1 781 1 chr1D.!!$F4 780
25 TraesCS2D01G176600 chr1D 490949814 490950373 559 False 339.00 339 79.1020 6392 6923 1 chr1D.!!$F7 531
26 TraesCS2D01G176600 chr1D 443793171 443793703 532 False 252.00 252 76.9230 6503 6997 1 chr1D.!!$F5 494
27 TraesCS2D01G176600 chr3D 12303672 12304468 796 False 1260.00 1260 95.4830 1 783 1 chr3D.!!$F1 782
28 TraesCS2D01G176600 chr3D 209460164 209460958 794 False 1245.00 1245 95.2200 1 781 1 chr3D.!!$F2 780
29 TraesCS2D01G176600 chr3D 578900684 578901262 578 True 322.00 322 78.2310 6461 6997 1 chr3D.!!$R6 536
30 TraesCS2D01G176600 chr3D 273474885 273475491 606 True 252.00 252 76.1440 6383 6923 1 chr3D.!!$R2 540
31 TraesCS2D01G176600 chr7D 628531834 628532630 796 True 1254.00 1254 95.3580 1 783 1 chr7D.!!$R2 782
32 TraesCS2D01G176600 chr7D 368568097 368568692 595 False 257.00 257 76.2850 6457 6997 1 chr7D.!!$F3 540
33 TraesCS2D01G176600 chr7D 233065840 233066342 502 False 241.00 241 77.3620 6555 7001 1 chr7D.!!$F2 446
34 TraesCS2D01G176600 chr6A 326233310 326234087 777 False 865.00 865 86.9060 1 771 1 chr6A.!!$F1 770
35 TraesCS2D01G176600 chr5A 112039943 112040501 558 False 237.00 237 75.8680 6392 6923 1 chr5A.!!$F1 531
36 TraesCS2D01G176600 chr5B 125841351 125842009 658 False 294.00 294 76.7060 6392 6992 1 chr5B.!!$F1 600
37 TraesCS2D01G176600 chr6B 508936636 508937152 516 True 263.00 263 77.0520 6418 6923 1 chr6B.!!$R2 505

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
617 632 3.394836 GAGCGGAGGTGGGAAGCT 61.395 66.667 0.00 0.00 39.88 3.74 F
2558 2596 2.203084 TGTTCCTTCGGCGCAACA 60.203 55.556 10.83 7.24 0.00 3.33 F
2560 2598 1.357334 GTTCCTTCGGCGCAACAAA 59.643 52.632 10.83 0.00 0.00 2.83 F
4047 4131 1.001181 GCACAATCCAGCAACCACAAT 59.999 47.619 0.00 0.00 0.00 2.71 F
4830 4914 0.174617 ACCAACTGCAAAAACACCGG 59.825 50.000 0.00 0.00 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2560 2598 1.133792 ACTTACAGCCTGCCTTGTTGT 60.134 47.619 0.00 0.0 0.00 3.32 R
3919 4003 3.567478 AGAGTCAGTTGGAAAAGCTGT 57.433 42.857 0.00 0.0 0.00 4.40 R
4294 4378 5.358442 AGCACGAGTAGAATGAGTACTGAAT 59.642 40.000 0.00 0.0 30.60 2.57 R
5654 5739 1.202245 TGCCACAGCGACAAAAACTTC 60.202 47.619 0.00 0.0 44.31 3.01 R
6111 6219 0.179148 GGCGCCGGTCAATTAAAAGG 60.179 55.000 12.58 0.0 0.00 3.11 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
617 632 3.394836 GAGCGGAGGTGGGAAGCT 61.395 66.667 0.00 0.00 39.88 3.74
816 832 4.458989 GTGGACAATAAATGGACTGCTTGA 59.541 41.667 0.00 0.00 0.00 3.02
849 865 3.894759 AGACATTGTGCCATAGCTGATT 58.105 40.909 0.00 0.00 40.80 2.57
1301 1317 3.203040 ACCCCGGATGAGATCAGAAATTT 59.797 43.478 0.73 0.00 0.00 1.82
1722 1738 7.442364 TCAGTTCATTTCTGACCTTTCTTACAG 59.558 37.037 0.00 0.00 37.07 2.74
2022 2057 4.994852 ACACATATAATGGGCACGTACATC 59.005 41.667 0.00 0.00 37.11 3.06
2024 2059 5.348724 CACATATAATGGGCACGTACATCTC 59.651 44.000 0.00 0.00 33.60 2.75
2383 2421 7.217201 CACACAAAAAGTTTTCAAACGTACAG 58.783 34.615 0.32 0.00 43.51 2.74
2558 2596 2.203084 TGTTCCTTCGGCGCAACA 60.203 55.556 10.83 7.24 0.00 3.33
2560 2598 1.357334 GTTCCTTCGGCGCAACAAA 59.643 52.632 10.83 0.00 0.00 2.83
2692 2730 4.188462 CAGTGTCAGTGTCACCTTTTGTA 58.812 43.478 15.57 0.00 36.58 2.41
2733 2771 3.679980 CGAGCAGTTACTATGTGTTTGCT 59.320 43.478 0.00 0.00 40.08 3.91
2889 2927 2.178912 TACTTTAGGCTGTGGTGTGC 57.821 50.000 0.00 0.00 0.00 4.57
3061 3099 2.031420 GTGCCCTTTTCGAACTTACCAC 60.031 50.000 0.00 0.00 0.00 4.16
3184 3228 9.927668 GGGTCTCAAATTTCTCAATTATTTTGA 57.072 29.630 0.00 0.00 31.89 2.69
3243 3287 4.635765 TGCTTTTGATAGAGATTTGACCGG 59.364 41.667 0.00 0.00 0.00 5.28
3325 3369 9.760660 CAGTTTGCTACTATCATGTTTACTTTC 57.239 33.333 0.00 0.00 34.56 2.62
3387 3431 5.726397 TCGTGTGCTAATACACCTTTATGT 58.274 37.500 0.00 0.00 46.28 2.29
3450 3494 7.334421 GGTGAGTGATCTTTTCTTTGCTGTATA 59.666 37.037 0.00 0.00 0.00 1.47
3919 4003 5.643348 GGCATTGATGTGGATTATGACGATA 59.357 40.000 0.00 0.00 0.00 2.92
4047 4131 1.001181 GCACAATCCAGCAACCACAAT 59.999 47.619 0.00 0.00 0.00 2.71
4294 4378 2.108168 CAAGGATCTTCGTCCACCCTA 58.892 52.381 0.00 0.00 40.90 3.53
4361 4445 5.426689 TTTCACATGTTATCTGCTCCTCT 57.573 39.130 0.00 0.00 0.00 3.69
4781 4865 4.625135 CGTCGCTACTGTTTGTTATGTTC 58.375 43.478 0.00 0.00 0.00 3.18
4830 4914 0.174617 ACCAACTGCAAAAACACCGG 59.825 50.000 0.00 0.00 0.00 5.28
5001 5085 4.455533 CCACTTTGCACTGCTCAGTATAAA 59.544 41.667 1.79 6.48 40.20 1.40
5002 5086 5.391310 CCACTTTGCACTGCTCAGTATAAAG 60.391 44.000 22.58 22.58 42.65 1.85
5247 5332 0.736325 AATCCCGTCGCAGTTTCTCG 60.736 55.000 0.00 0.00 0.00 4.04
5653 5738 1.021202 TTCACCCGAAGCAACACTTG 58.979 50.000 0.00 0.00 39.29 3.16
5654 5739 0.817634 TCACCCGAAGCAACACTTGG 60.818 55.000 0.00 0.00 39.29 3.61
5842 5933 4.159135 AGTGGGAAATTTCTCATGACATGC 59.841 41.667 23.16 8.99 40.32 4.06
5851 5942 2.573009 TCTCATGACATGCCTTCAGGAA 59.427 45.455 10.76 0.00 33.65 3.36
6018 6112 1.285950 GAAAGTTCACGGCTTGGCC 59.714 57.895 0.00 0.00 46.75 5.36
6111 6219 2.010145 TTCATCTCTGTTAGTGGCGC 57.990 50.000 0.00 0.00 0.00 6.53
6182 6290 2.961526 GGAATCACTCCGCTCTGTAA 57.038 50.000 0.00 0.00 33.37 2.41
6183 6291 2.541556 GGAATCACTCCGCTCTGTAAC 58.458 52.381 0.00 0.00 33.37 2.50
6184 6292 2.166664 GGAATCACTCCGCTCTGTAACT 59.833 50.000 0.00 0.00 33.37 2.24
6185 6293 3.440228 GAATCACTCCGCTCTGTAACTC 58.560 50.000 0.00 0.00 0.00 3.01
6186 6294 1.174783 TCACTCCGCTCTGTAACTCC 58.825 55.000 0.00 0.00 0.00 3.85
6187 6295 0.179161 CACTCCGCTCTGTAACTCCG 60.179 60.000 0.00 0.00 0.00 4.63
6188 6296 1.226717 CTCCGCTCTGTAACTCCGC 60.227 63.158 0.00 0.00 0.00 5.54
6189 6297 2.202756 CCGCTCTGTAACTCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
6190 6298 2.579787 CGCTCTGTAACTCCGCCG 60.580 66.667 0.00 0.00 0.00 6.46
6223 6331 2.986479 GGCAACCAGTTCAATTTTAGCG 59.014 45.455 0.00 0.00 0.00 4.26
6229 6337 1.130561 AGTTCAATTTTAGCGAGCGGC 59.869 47.619 0.00 0.00 44.05 6.53
6282 6390 1.745264 GAGGAGCAGAGGATTCCCG 59.255 63.158 0.00 0.00 37.58 5.14
6293 6401 0.608035 GGATTCCCGAACACAGCCAA 60.608 55.000 0.00 0.00 0.00 4.52
6294 6402 1.243902 GATTCCCGAACACAGCCAAA 58.756 50.000 0.00 0.00 0.00 3.28
6315 6423 1.537814 TATGACGCACCCTCGGTTGT 61.538 55.000 0.00 0.00 31.02 3.32
6336 6444 2.224185 TGTTGGACGTGTGCTAATCTGT 60.224 45.455 0.00 0.00 0.00 3.41
6356 6464 4.998788 TGTAGCTGTGACTATGCTGTAAG 58.001 43.478 0.00 0.00 37.62 2.34
6362 6470 2.678336 GTGACTATGCTGTAAGGGCAAC 59.322 50.000 0.00 0.00 43.14 4.17
6390 6498 1.927174 CGGACGGACTCATCAAATGTC 59.073 52.381 0.00 0.00 0.00 3.06
6428 6543 1.464198 AACAGGACCCTCCAAGGCT 60.464 57.895 0.00 0.00 39.61 4.58
6430 6545 1.614824 CAGGACCCTCCAAGGCTCT 60.615 63.158 0.00 0.00 39.61 4.09
6676 6837 1.316651 GCCAGCCTTCCATTGAGATC 58.683 55.000 0.00 0.00 0.00 2.75
6726 6900 3.787001 CTTCCCCTCCCTCCACGC 61.787 72.222 0.00 0.00 0.00 5.34
6805 7013 4.154347 CTCACCCGCAGCCTCTCC 62.154 72.222 0.00 0.00 0.00 3.71
6873 7113 0.104855 CCGATGGGAGAGCGATTTCA 59.895 55.000 0.00 0.00 34.57 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
512 527 1.004918 GTACGTGGCAGCTTGTCCT 60.005 57.895 0.00 0.00 0.00 3.85
617 632 4.720902 TACCTCGACGCCGTCCCA 62.721 66.667 12.26 0.00 37.05 4.37
657 672 2.277949 GCACGCGCTACTCATCGA 60.278 61.111 5.73 0.00 34.30 3.59
816 832 6.653020 TGGCACAATGTCTATAATCAACTCT 58.347 36.000 0.00 0.00 31.92 3.24
1455 1471 9.841295 ACGCCTTTTATACAGGAAGATTATAAA 57.159 29.630 1.76 0.00 32.41 1.40
1932 1955 5.795972 TGCATGAACAAAATTGACATCCAT 58.204 33.333 0.00 0.00 31.19 3.41
2011 2046 3.243334 GGGTAGTTAGAGATGTACGTGCC 60.243 52.174 0.00 0.00 0.00 5.01
2022 2057 4.038642 GCATCAGAAGGAGGGTAGTTAGAG 59.961 50.000 0.00 0.00 0.00 2.43
2024 2059 3.706594 TGCATCAGAAGGAGGGTAGTTAG 59.293 47.826 0.00 0.00 0.00 2.34
2165 2200 6.436847 TGCAACAGGAATTTCATCCATCTTAA 59.563 34.615 0.00 0.00 42.27 1.85
2383 2421 6.205853 TCAGAGAGAACTTTCTGTGTACTCTC 59.794 42.308 17.59 0.00 43.29 3.20
2558 2596 2.065899 TACAGCCTGCCTTGTTGTTT 57.934 45.000 0.00 0.00 0.00 2.83
2560 2598 1.133792 ACTTACAGCCTGCCTTGTTGT 60.134 47.619 0.00 0.00 0.00 3.32
2692 2730 6.184789 TGCTCGGGGTAAAGAATAAAAGAAT 58.815 36.000 0.00 0.00 0.00 2.40
2733 2771 3.595173 CATCCAGTTTACATGTCCACGA 58.405 45.455 0.00 0.00 0.00 4.35
3050 3088 8.488651 AAATAATACTTCAGGTGGTAAGTTCG 57.511 34.615 0.00 0.00 37.19 3.95
3061 3099 9.113838 AGCTGAACATGTAAATAATACTTCAGG 57.886 33.333 15.11 2.40 35.80 3.86
3105 3143 8.621532 TTATATGTGCCCAAGATTCAATCTAC 57.378 34.615 0.00 0.00 39.08 2.59
3184 3228 8.133024 TGCCAAATAAAGAACAGTCCATAAAT 57.867 30.769 0.00 0.00 0.00 1.40
3218 3262 5.563842 GGTCAAATCTCTATCAAAAGCACG 58.436 41.667 0.00 0.00 0.00 5.34
3243 3287 6.098017 AGTCAAACCTACTCGTAAATAGCAC 58.902 40.000 0.00 0.00 0.00 4.40
3387 3431 7.232534 ACCATTTGCTTCTGTCCTGTTAAATAA 59.767 33.333 0.00 0.00 0.00 1.40
3450 3494 7.333423 ACAACAACAACATATATACAAGCGACT 59.667 33.333 0.00 0.00 0.00 4.18
3919 4003 3.567478 AGAGTCAGTTGGAAAAGCTGT 57.433 42.857 0.00 0.00 0.00 4.40
4294 4378 5.358442 AGCACGAGTAGAATGAGTACTGAAT 59.642 40.000 0.00 0.00 30.60 2.57
4575 4659 9.722056 GAATACAACATATGCTTTTCCTACAAG 57.278 33.333 1.58 0.00 0.00 3.16
4781 4865 1.203052 GGTGCCATCATGTGAAACTGG 59.797 52.381 0.00 0.00 38.04 4.00
4830 4914 9.525409 TTAATATAAAGCTCTGTTAGTTCCGAC 57.475 33.333 0.00 0.00 0.00 4.79
5247 5332 9.013490 GTTGCATTGATATCATGTACAGAAAAC 57.987 33.333 6.17 0.00 0.00 2.43
5505 5590 1.270358 GCAAACGACTTCCTCTCACCT 60.270 52.381 0.00 0.00 0.00 4.00
5653 5738 1.864029 GCCACAGCGACAAAAACTTCC 60.864 52.381 0.00 0.00 0.00 3.46
5654 5739 1.202245 TGCCACAGCGACAAAAACTTC 60.202 47.619 0.00 0.00 44.31 3.01
5842 5933 3.431486 GGCACTACTCTGATTCCTGAAGG 60.431 52.174 0.00 0.00 0.00 3.46
5851 5942 2.359531 GCTTCTACGGCACTACTCTGAT 59.640 50.000 0.00 0.00 0.00 2.90
5999 6093 1.285950 GCCAAGCCGTGAACTTTCC 59.714 57.895 0.00 0.00 0.00 3.13
6018 6112 5.163764 TGCGGTACATTTAGCAGAAAAGATG 60.164 40.000 0.00 0.00 34.39 2.90
6099 6207 4.083003 TCAATTAAAAGGCGCCACTAACAG 60.083 41.667 31.54 16.61 0.00 3.16
6111 6219 0.179148 GGCGCCGGTCAATTAAAAGG 60.179 55.000 12.58 0.00 0.00 3.11
6198 6306 0.598065 AATTGAACTGGTTGCCGCTC 59.402 50.000 0.00 0.00 0.00 5.03
6206 6314 2.159627 CGCTCGCTAAAATTGAACTGGT 59.840 45.455 0.00 0.00 0.00 4.00
6207 6315 2.476185 CCGCTCGCTAAAATTGAACTGG 60.476 50.000 0.00 0.00 0.00 4.00
6264 6372 0.757188 TCGGGAATCCTCTGCTCCTC 60.757 60.000 0.00 0.00 0.00 3.71
6282 6390 2.412847 GCGTCATACTTTGGCTGTGTTC 60.413 50.000 0.00 0.00 0.00 3.18
6293 6401 1.255667 ACCGAGGGTGCGTCATACTT 61.256 55.000 0.00 0.00 32.98 2.24
6294 6402 1.255667 AACCGAGGGTGCGTCATACT 61.256 55.000 0.00 0.00 35.34 2.12
6315 6423 2.224185 ACAGATTAGCACACGTCCAACA 60.224 45.455 0.00 0.00 0.00 3.33
6336 6444 3.384789 CCCTTACAGCATAGTCACAGCTA 59.615 47.826 0.00 0.00 36.73 3.32
6390 6498 1.694133 GGGGGAGTGGAGATGCTCTG 61.694 65.000 0.00 0.00 32.67 3.35
6493 6622 1.352156 CTGAGTCCGCCAACGCTAAC 61.352 60.000 0.00 0.00 38.22 2.34
6707 6881 3.412408 GTGGAGGGAGGGGAAGGC 61.412 72.222 0.00 0.00 0.00 4.35
6715 6889 2.181021 GTGTACGCGTGGAGGGAG 59.819 66.667 24.59 0.00 36.53 4.30
6718 6892 2.503375 GACGTGTACGCGTGGAGG 60.503 66.667 36.45 15.58 45.79 4.30
6719 6893 1.796355 CAGACGTGTACGCGTGGAG 60.796 63.158 36.45 21.59 45.79 3.86
6720 6894 2.253154 CAGACGTGTACGCGTGGA 59.747 61.111 36.45 4.71 45.79 4.02
6721 6895 3.467119 GCAGACGTGTACGCGTGG 61.467 66.667 36.45 27.16 45.79 4.94
6727 6901 4.367023 TGGGCGGCAGACGTGTAC 62.367 66.667 12.47 0.00 46.52 2.90


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

AutoCloner maintained by Alex Coulton.