Multiple sequence alignment - TraesCS2D01G590500

Loading Multiple Alignment...

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 TraesCS2D01G590500 chr2D 100.000 2372 0 0 1 2372 646478031 646475660 0.000000e+00 4381.0
1 TraesCS2D01G590500 chr2D 92.920 565 30 9 1453 2011 439660072 439659512 0.000000e+00 813.0
2 TraesCS2D01G590500 chr2D 92.434 304 21 2 6 307 348187958 348187655 1.300000e-117 433.0
3 TraesCS2D01G590500 chr2D 93.684 95 6 0 1360 1454 294551115 294551021 2.460000e-30 143.0
4 TraesCS2D01G590500 chr7B 95.227 1676 53 6 722 2372 257652461 257654134 0.000000e+00 2627.0
5 TraesCS2D01G590500 chr7A 94.928 1676 58 6 722 2372 299313389 299311716 0.000000e+00 2599.0
6 TraesCS2D01G590500 chr2A 94.806 1675 60 6 723 2372 166818343 166816671 0.000000e+00 2586.0
7 TraesCS2D01G590500 chr2A 93.746 1679 59 15 725 2372 395710741 395709078 0.000000e+00 2477.0
8 TraesCS2D01G590500 chr2A 91.935 310 22 3 1 307 737466454 737466763 4.680000e-117 431.0
9 TraesCS2D01G590500 chr5A 95.003 1661 55 7 737 2372 484830714 484832371 0.000000e+00 2582.0
10 TraesCS2D01G590500 chr5A 94.816 926 43 4 1448 2372 613191751 613190830 0.000000e+00 1439.0
11 TraesCS2D01G590500 chr1A 94.687 1675 62 10 723 2372 546232106 546233778 0.000000e+00 2575.0
12 TraesCS2D01G590500 chr1A 92.991 428 24 4 292 714 19500533 19500107 9.310000e-174 619.0
13 TraesCS2D01G590500 chr1A 91.593 452 28 7 1566 2011 244556137 244555690 1.200000e-172 616.0
14 TraesCS2D01G590500 chr1A 85.000 240 26 7 2096 2333 186715934 186715703 3.940000e-58 235.0
15 TraesCS2D01G590500 chr1A 96.330 109 4 0 1453 1561 244556292 244556184 1.870000e-41 180.0
16 TraesCS2D01G590500 chr1A 97.143 70 2 0 1383 1452 244556394 244556325 4.140000e-23 119.0
17 TraesCS2D01G590500 chr1A 91.429 70 4 2 783 851 12001398 12001466 6.980000e-16 95.3
18 TraesCS2D01G590500 chr1A 93.651 63 4 0 1392 1454 554812620 554812558 6.980000e-16 95.3
19 TraesCS2D01G590500 chr5B 94.740 1673 55 7 731 2372 47328170 47326500 0.000000e+00 2571.0
20 TraesCS2D01G590500 chr5B 94.385 1674 60 10 731 2372 47323125 47321454 0.000000e+00 2540.0
21 TraesCS2D01G590500 chr6B 94.342 1679 63 8 725 2372 246983362 246985039 0.000000e+00 2545.0
22 TraesCS2D01G590500 chr6B 93.145 1663 76 9 742 2372 420862196 420863852 0.000000e+00 2405.0
23 TraesCS2D01G590500 chr6B 91.958 1430 68 20 722 2122 63359432 63360843 0.000000e+00 1960.0
24 TraesCS2D01G590500 chr6B 97.628 253 5 1 2120 2372 63360942 63361193 1.300000e-117 433.0
25 TraesCS2D01G590500 chr1B 93.970 1675 60 10 723 2372 526807649 526809307 0.000000e+00 2495.0
26 TraesCS2D01G590500 chr1B 92.289 1219 61 10 723 1915 408552530 408553741 0.000000e+00 1700.0
27 TraesCS2D01G590500 chr1B 93.888 409 21 2 292 697 687569407 687569000 4.330000e-172 614.0
28 TraesCS2D01G590500 chr7D 90.040 753 40 14 734 1454 618884906 618884157 0.000000e+00 942.0
29 TraesCS2D01G590500 chr7D 96.053 532 18 1 1448 1979 618884131 618883603 0.000000e+00 863.0
30 TraesCS2D01G590500 chr7D 97.872 329 7 0 2044 2372 618883356 618883028 9.510000e-159 569.0
31 TraesCS2D01G590500 chr7D 96.405 306 9 2 2031 2335 84434123 84434427 9.790000e-139 503.0
32 TraesCS2D01G590500 chr7D 87.619 105 8 2 1862 1961 84434014 84434118 1.490000e-22 117.0
33 TraesCS2D01G590500 chr4A 92.727 440 23 7 292 723 78259630 78260068 5.570000e-176 627.0
34 TraesCS2D01G590500 chr3B 93.192 426 18 7 295 715 9536188 9535769 1.200000e-172 616.0
35 TraesCS2D01G590500 chr2B 92.637 421 21 8 308 721 13786204 13785787 4.360000e-167 597.0
36 TraesCS2D01G590500 chr2B 93.548 403 22 3 296 695 117978571 117978170 4.360000e-167 597.0
37 TraesCS2D01G590500 chr4B 92.754 414 25 3 292 702 584448931 584449342 5.640000e-166 593.0
38 TraesCS2D01G590500 chr4B 92.754 414 25 3 298 708 584771666 584771255 5.640000e-166 593.0
39 TraesCS2D01G590500 chr4B 92.718 412 24 3 292 698 672304297 672304707 7.300000e-165 590.0
40 TraesCS2D01G590500 chr4B 94.718 284 15 0 1 284 560235719 560235436 2.160000e-120 442.0
41 TraesCS2D01G590500 chr4B 87.013 154 19 1 719 871 1878432 1878585 3.130000e-39 172.0
42 TraesCS2D01G590500 chrUn 95.775 284 12 0 1 284 67785919 67785636 2.150000e-125 459.0
43 TraesCS2D01G590500 chrUn 94.718 284 14 1 1 284 89359604 89359886 7.780000e-120 440.0
44 TraesCS2D01G590500 chrUn 88.333 300 6 8 1184 1454 478715850 478716149 1.360000e-87 333.0
45 TraesCS2D01G590500 chrUn 81.557 244 30 9 2096 2333 22416427 22416661 1.120000e-43 187.0
46 TraesCS2D01G590500 chr4D 93.750 304 17 1 6 307 233092765 233093068 2.780000e-124 455.0
47 TraesCS2D01G590500 chr5D 95.053 283 13 1 1 283 298859493 298859774 6.020000e-121 444.0
48 TraesCS2D01G590500 chr3D 94.700 283 15 0 1 283 254401805 254402087 7.780000e-120 440.0
49 TraesCS2D01G590500 chr3D 94.366 284 16 0 1 284 576631410 576631127 1.010000e-118 436.0
50 TraesCS2D01G590500 chr3D 84.000 325 39 3 1465 1788 80635168 80634856 1.380000e-77 300.0
51 TraesCS2D01G590500 chr3D 85.496 131 17 2 729 858 61039872 61039743 4.110000e-28 135.0
52 TraesCS2D01G590500 chr6A 82.917 240 30 7 2096 2333 338191319 338191089 3.090000e-49 206.0
53 TraesCS2D01G590500 chr1D 82.979 235 30 7 2096 2328 456924484 456924710 1.110000e-48 204.0
54 TraesCS2D01G590500 chr6D 84.545 110 17 0 749 858 160875422 160875531 2.490000e-20 110.0
55 TraesCS2D01G590500 chr6D 78.571 140 22 7 721 857 308581041 308581175 4.200000e-13 86.1


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 TraesCS2D01G590500 chr2D 646475660 646478031 2371 True 4381.000000 4381 100.0000 1 2372 1 chr2D.!!$R4 2371
1 TraesCS2D01G590500 chr2D 439659512 439660072 560 True 813.000000 813 92.9200 1453 2011 1 chr2D.!!$R3 558
2 TraesCS2D01G590500 chr7B 257652461 257654134 1673 False 2627.000000 2627 95.2270 722 2372 1 chr7B.!!$F1 1650
3 TraesCS2D01G590500 chr7A 299311716 299313389 1673 True 2599.000000 2599 94.9280 722 2372 1 chr7A.!!$R1 1650
4 TraesCS2D01G590500 chr2A 166816671 166818343 1672 True 2586.000000 2586 94.8060 723 2372 1 chr2A.!!$R1 1649
5 TraesCS2D01G590500 chr2A 395709078 395710741 1663 True 2477.000000 2477 93.7460 725 2372 1 chr2A.!!$R2 1647
6 TraesCS2D01G590500 chr5A 484830714 484832371 1657 False 2582.000000 2582 95.0030 737 2372 1 chr5A.!!$F1 1635
7 TraesCS2D01G590500 chr5A 613190830 613191751 921 True 1439.000000 1439 94.8160 1448 2372 1 chr5A.!!$R1 924
8 TraesCS2D01G590500 chr1A 546232106 546233778 1672 False 2575.000000 2575 94.6870 723 2372 1 chr1A.!!$F2 1649
9 TraesCS2D01G590500 chr1A 244555690 244556394 704 True 305.000000 616 95.0220 1383 2011 3 chr1A.!!$R4 628
10 TraesCS2D01G590500 chr5B 47321454 47328170 6716 True 2555.500000 2571 94.5625 731 2372 2 chr5B.!!$R1 1641
11 TraesCS2D01G590500 chr6B 246983362 246985039 1677 False 2545.000000 2545 94.3420 725 2372 1 chr6B.!!$F1 1647
12 TraesCS2D01G590500 chr6B 420862196 420863852 1656 False 2405.000000 2405 93.1450 742 2372 1 chr6B.!!$F2 1630
13 TraesCS2D01G590500 chr6B 63359432 63361193 1761 False 1196.500000 1960 94.7930 722 2372 2 chr6B.!!$F3 1650
14 TraesCS2D01G590500 chr1B 526807649 526809307 1658 False 2495.000000 2495 93.9700 723 2372 1 chr1B.!!$F2 1649
15 TraesCS2D01G590500 chr1B 408552530 408553741 1211 False 1700.000000 1700 92.2890 723 1915 1 chr1B.!!$F1 1192
16 TraesCS2D01G590500 chr7D 618883028 618884906 1878 True 791.333333 942 94.6550 734 2372 3 chr7D.!!$R1 1638

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
948 956 0.179045 AACCACACAGAGAGCACACC 60.179 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 2006 3.008049 AGGTACACGCTCAGAGGAATTTT 59.992 43.478 0.0 0.0 0.0 1.82 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
25 26 8.922058 AACCAAGAGTATGTACGTTTAGTATG 57.078 34.615 0.00 0.00 37.69 2.39
26 27 8.059798 ACCAAGAGTATGTACGTTTAGTATGT 57.940 34.615 0.00 0.00 37.69 2.29
27 28 9.177608 ACCAAGAGTATGTACGTTTAGTATGTA 57.822 33.333 0.00 0.00 37.69 2.29
28 29 9.661187 CCAAGAGTATGTACGTTTAGTATGTAG 57.339 37.037 0.00 0.00 37.69 2.74
89 90 9.727859 TTTTGGCTAGTATGTACTATGTTTTGA 57.272 29.630 0.69 0.00 38.06 2.69
90 91 8.942338 TTGGCTAGTATGTACTATGTTTTGAG 57.058 34.615 0.69 0.00 38.06 3.02
91 92 8.074613 TGGCTAGTATGTACTATGTTTTGAGT 57.925 34.615 0.69 0.00 38.06 3.41
92 93 9.192642 TGGCTAGTATGTACTATGTTTTGAGTA 57.807 33.333 0.69 0.00 38.06 2.59
97 98 9.751542 AGTATGTACTATGTTTTGAGTATGCTC 57.248 33.333 3.51 3.51 37.22 4.26
98 99 9.751542 GTATGTACTATGTTTTGAGTATGCTCT 57.248 33.333 12.30 0.00 42.13 4.09
100 101 9.672673 ATGTACTATGTTTTGAGTATGCTCTTT 57.327 29.630 12.30 0.00 42.13 2.52
101 102 9.502091 TGTACTATGTTTTGAGTATGCTCTTTT 57.498 29.630 12.30 0.00 42.13 2.27
102 103 9.974750 GTACTATGTTTTGAGTATGCTCTTTTC 57.025 33.333 12.30 1.87 42.13 2.29
103 104 8.854614 ACTATGTTTTGAGTATGCTCTTTTCT 57.145 30.769 12.30 0.00 42.13 2.52
104 105 9.944376 ACTATGTTTTGAGTATGCTCTTTTCTA 57.056 29.630 12.30 0.00 42.13 2.10
107 108 8.621532 TGTTTTGAGTATGCTCTTTTCTATGT 57.378 30.769 12.30 0.00 42.13 2.29
108 109 9.719355 TGTTTTGAGTATGCTCTTTTCTATGTA 57.281 29.630 12.30 0.00 42.13 2.29
159 160 7.701539 AACAAAAACTATGGACTCATATGCA 57.298 32.000 0.00 0.00 35.53 3.96
160 161 7.701539 ACAAAAACTATGGACTCATATGCAA 57.298 32.000 0.00 0.00 35.53 4.08
161 162 8.297470 ACAAAAACTATGGACTCATATGCAAT 57.703 30.769 0.00 0.00 35.53 3.56
162 163 8.752187 ACAAAAACTATGGACTCATATGCAATT 58.248 29.630 0.00 0.00 35.53 2.32
163 164 9.590451 CAAAAACTATGGACTCATATGCAATTT 57.410 29.630 0.00 0.00 35.53 1.82
268 269 8.200120 CACATGGTAGTATATGAGATATGTGGG 58.800 40.741 0.00 0.00 39.22 4.61
269 270 7.345653 ACATGGTAGTATATGAGATATGTGGGG 59.654 40.741 0.00 0.00 0.00 4.96
270 271 6.811574 TGGTAGTATATGAGATATGTGGGGT 58.188 40.000 0.00 0.00 0.00 4.95
271 272 7.946381 TGGTAGTATATGAGATATGTGGGGTA 58.054 38.462 0.00 0.00 0.00 3.69
272 273 8.403474 TGGTAGTATATGAGATATGTGGGGTAA 58.597 37.037 0.00 0.00 0.00 2.85
273 274 8.693625 GGTAGTATATGAGATATGTGGGGTAAC 58.306 40.741 0.00 0.00 0.00 2.50
274 275 9.476928 GTAGTATATGAGATATGTGGGGTAACT 57.523 37.037 0.00 0.00 0.00 2.24
276 277 9.476928 AGTATATGAGATATGTGGGGTAACTAC 57.523 37.037 0.00 0.00 0.00 2.73
277 278 7.735326 ATATGAGATATGTGGGGTAACTACC 57.265 40.000 0.00 0.00 45.71 3.18
288 289 3.354948 GGTAACTACCACCGGGATTTT 57.645 47.619 6.32 0.00 45.73 1.82
289 290 3.689347 GGTAACTACCACCGGGATTTTT 58.311 45.455 6.32 0.00 45.73 1.94
290 291 3.691118 GGTAACTACCACCGGGATTTTTC 59.309 47.826 6.32 0.00 45.73 2.29
291 292 3.512219 AACTACCACCGGGATTTTTCA 57.488 42.857 6.32 0.00 38.05 2.69
292 293 3.732048 ACTACCACCGGGATTTTTCAT 57.268 42.857 6.32 0.00 38.05 2.57
293 294 4.847990 ACTACCACCGGGATTTTTCATA 57.152 40.909 6.32 0.00 38.05 2.15
294 295 5.382664 ACTACCACCGGGATTTTTCATAT 57.617 39.130 6.32 0.00 38.05 1.78
295 296 6.503560 ACTACCACCGGGATTTTTCATATA 57.496 37.500 6.32 0.00 38.05 0.86
296 297 7.086685 ACTACCACCGGGATTTTTCATATAT 57.913 36.000 6.32 0.00 38.05 0.86
297 298 8.209802 ACTACCACCGGGATTTTTCATATATA 57.790 34.615 6.32 0.00 38.05 0.86
298 299 8.832735 ACTACCACCGGGATTTTTCATATATAT 58.167 33.333 6.32 0.00 38.05 0.86
327 328 3.804036 TGGAAAATGCATCCTACTACCG 58.196 45.455 0.00 0.00 37.85 4.02
328 329 3.139077 GGAAAATGCATCCTACTACCGG 58.861 50.000 0.00 0.00 33.98 5.28
329 330 2.930826 AAATGCATCCTACTACCGGG 57.069 50.000 6.32 0.00 0.00 5.73
330 331 1.802553 AATGCATCCTACTACCGGGT 58.197 50.000 6.32 4.46 0.00 5.28
331 332 1.048601 ATGCATCCTACTACCGGGTG 58.951 55.000 10.66 0.00 35.71 4.61
332 333 0.324923 TGCATCCTACTACCGGGTGT 60.325 55.000 10.66 6.62 35.06 4.16
333 334 1.063792 TGCATCCTACTACCGGGTGTA 60.064 52.381 10.66 7.54 35.06 2.90
463 464 4.530710 AAAATTGCATGTGAGCTCATGT 57.469 36.364 21.47 8.91 44.68 3.21
464 465 4.530710 AAATTGCATGTGAGCTCATGTT 57.469 36.364 21.47 4.89 44.68 2.71
465 466 4.530710 AATTGCATGTGAGCTCATGTTT 57.469 36.364 21.47 7.86 44.68 2.83
466 467 4.530710 ATTGCATGTGAGCTCATGTTTT 57.469 36.364 21.47 0.26 44.68 2.43
467 468 4.325028 TTGCATGTGAGCTCATGTTTTT 57.675 36.364 21.47 0.00 44.68 1.94
468 469 5.450592 TTGCATGTGAGCTCATGTTTTTA 57.549 34.783 21.47 0.86 44.68 1.52
469 470 5.648178 TGCATGTGAGCTCATGTTTTTAT 57.352 34.783 21.47 3.62 44.68 1.40
470 471 6.756299 TGCATGTGAGCTCATGTTTTTATA 57.244 33.333 21.47 0.00 44.68 0.98
471 472 7.155655 TGCATGTGAGCTCATGTTTTTATAA 57.844 32.000 21.47 0.00 44.68 0.98
472 473 7.774134 TGCATGTGAGCTCATGTTTTTATAAT 58.226 30.769 21.47 0.00 44.68 1.28
473 474 8.901793 TGCATGTGAGCTCATGTTTTTATAATA 58.098 29.630 21.47 0.00 44.68 0.98
474 475 9.903682 GCATGTGAGCTCATGTTTTTATAATAT 57.096 29.630 21.47 0.00 44.68 1.28
518 519 7.949903 TTGTACGTAAAAAGAAGTATGCTCA 57.050 32.000 0.00 0.00 0.00 4.26
519 520 7.949903 TGTACGTAAAAAGAAGTATGCTCAA 57.050 32.000 0.00 0.00 0.00 3.02
520 521 8.367943 TGTACGTAAAAAGAAGTATGCTCAAA 57.632 30.769 0.00 0.00 0.00 2.69
521 522 8.828644 TGTACGTAAAAAGAAGTATGCTCAAAA 58.171 29.630 0.00 0.00 0.00 2.44
522 523 9.821662 GTACGTAAAAAGAAGTATGCTCAAAAT 57.178 29.630 0.00 0.00 0.00 1.82
595 596 9.492973 TCTTACATACTACATACTATGCGTACA 57.507 33.333 0.00 0.00 0.00 2.90
599 600 9.445878 ACATACTACATACTATGCGTACATACT 57.554 33.333 0.00 0.00 37.74 2.12
600 601 9.917872 CATACTACATACTATGCGTACATACTC 57.082 37.037 0.00 0.00 37.74 2.59
601 602 9.887629 ATACTACATACTATGCGTACATACTCT 57.112 33.333 0.00 0.00 37.74 3.24
602 603 8.254178 ACTACATACTATGCGTACATACTCTC 57.746 38.462 0.00 0.00 37.74 3.20
603 604 6.497785 ACATACTATGCGTACATACTCTCC 57.502 41.667 0.00 0.00 37.74 3.71
604 605 5.121925 ACATACTATGCGTACATACTCTCCG 59.878 44.000 0.00 0.00 37.74 4.63
605 606 3.736720 ACTATGCGTACATACTCTCCGA 58.263 45.455 0.00 0.00 37.74 4.55
606 607 4.325119 ACTATGCGTACATACTCTCCGAT 58.675 43.478 0.00 0.00 37.74 4.18
607 608 5.485620 ACTATGCGTACATACTCTCCGATA 58.514 41.667 0.00 0.00 37.74 2.92
608 609 6.114089 ACTATGCGTACATACTCTCCGATAT 58.886 40.000 0.00 0.00 37.74 1.63
609 610 7.270779 ACTATGCGTACATACTCTCCGATATA 58.729 38.462 0.00 0.00 37.74 0.86
610 611 6.997239 ATGCGTACATACTCTCCGATATAA 57.003 37.500 0.00 0.00 33.67 0.98
611 612 6.997239 TGCGTACATACTCTCCGATATAAT 57.003 37.500 0.00 0.00 0.00 1.28
612 613 8.672823 ATGCGTACATACTCTCCGATATAATA 57.327 34.615 0.00 0.00 33.67 0.98
613 614 8.139521 TGCGTACATACTCTCCGATATAATAG 57.860 38.462 0.00 0.00 0.00 1.73
614 615 7.983484 TGCGTACATACTCTCCGATATAATAGA 59.017 37.037 0.00 0.00 0.00 1.98
615 616 8.991026 GCGTACATACTCTCCGATATAATAGAT 58.009 37.037 0.00 0.00 0.00 1.98
638 639 9.852091 AGATACTACCTAGAACGTAAACAAAAG 57.148 33.333 0.00 0.00 0.00 2.27
639 640 9.631452 GATACTACCTAGAACGTAAACAAAAGT 57.369 33.333 0.00 0.00 0.00 2.66
640 641 7.704789 ACTACCTAGAACGTAAACAAAAGTG 57.295 36.000 0.00 0.00 0.00 3.16
641 642 5.996669 ACCTAGAACGTAAACAAAAGTGG 57.003 39.130 0.00 0.00 0.00 4.00
642 643 4.818005 ACCTAGAACGTAAACAAAAGTGGG 59.182 41.667 0.00 0.00 0.00 4.61
643 644 5.058490 CCTAGAACGTAAACAAAAGTGGGA 58.942 41.667 0.00 0.00 0.00 4.37
644 645 5.178809 CCTAGAACGTAAACAAAAGTGGGAG 59.821 44.000 0.00 0.00 0.00 4.30
645 646 4.520179 AGAACGTAAACAAAAGTGGGAGT 58.480 39.130 0.00 0.00 0.00 3.85
646 647 5.673514 AGAACGTAAACAAAAGTGGGAGTA 58.326 37.500 0.00 0.00 0.00 2.59
647 648 6.114767 AGAACGTAAACAAAAGTGGGAGTAA 58.885 36.000 0.00 0.00 0.00 2.24
648 649 5.739752 ACGTAAACAAAAGTGGGAGTAAC 57.260 39.130 0.00 0.00 0.00 2.50
649 650 5.430886 ACGTAAACAAAAGTGGGAGTAACT 58.569 37.500 0.00 0.00 0.00 2.24
650 651 6.581712 ACGTAAACAAAAGTGGGAGTAACTA 58.418 36.000 0.00 0.00 0.00 2.24
651 652 6.479990 ACGTAAACAAAAGTGGGAGTAACTAC 59.520 38.462 0.00 0.00 0.00 2.73
652 653 6.479660 CGTAAACAAAAGTGGGAGTAACTACA 59.520 38.462 0.00 0.00 0.00 2.74
653 654 6.688637 AAACAAAAGTGGGAGTAACTACAC 57.311 37.500 0.00 0.00 0.00 2.90
654 655 4.711399 ACAAAAGTGGGAGTAACTACACC 58.289 43.478 0.00 0.00 36.39 4.16
658 659 2.982026 GGGAGTAACTACACCCGGT 58.018 57.895 0.00 0.00 45.03 5.28
659 660 2.143876 GGGAGTAACTACACCCGGTA 57.856 55.000 0.00 0.00 45.03 4.02
670 671 3.801307 ACACCCGGTAGAAGGAAAAAT 57.199 42.857 0.00 0.00 0.00 1.82
671 672 4.108501 ACACCCGGTAGAAGGAAAAATT 57.891 40.909 0.00 0.00 0.00 1.82
672 673 4.476297 ACACCCGGTAGAAGGAAAAATTT 58.524 39.130 0.00 0.00 0.00 1.82
673 674 4.279922 ACACCCGGTAGAAGGAAAAATTTG 59.720 41.667 0.00 0.00 0.00 2.32
674 675 4.279922 CACCCGGTAGAAGGAAAAATTTGT 59.720 41.667 0.00 0.00 0.00 2.83
675 676 4.521639 ACCCGGTAGAAGGAAAAATTTGTC 59.478 41.667 0.00 0.00 0.00 3.18
676 677 4.521256 CCCGGTAGAAGGAAAAATTTGTCA 59.479 41.667 10.53 0.00 0.00 3.58
677 678 5.185056 CCCGGTAGAAGGAAAAATTTGTCAT 59.815 40.000 10.53 0.00 0.00 3.06
678 679 6.376018 CCCGGTAGAAGGAAAAATTTGTCATA 59.624 38.462 10.53 0.00 0.00 2.15
679 680 7.068226 CCCGGTAGAAGGAAAAATTTGTCATAT 59.932 37.037 10.53 0.00 0.00 1.78
680 681 9.116067 CCGGTAGAAGGAAAAATTTGTCATATA 57.884 33.333 10.53 0.00 0.00 0.86
757 758 4.124351 CCACGCATTGCTGCTGGG 62.124 66.667 7.12 2.67 46.65 4.45
847 850 0.310854 GTGGCACTCTGGAAAAACGG 59.689 55.000 11.13 0.00 0.00 4.44
858 861 5.725362 TCTGGAAAAACGGTTCATTTTTGT 58.275 33.333 0.00 0.00 38.92 2.83
866 869 7.653767 AAACGGTTCATTTTTGTGTAAAACA 57.346 28.000 0.00 0.00 38.48 2.83
895 898 1.623359 TTGGACAATTAAATGCGCGC 58.377 45.000 27.26 27.26 0.00 6.86
948 956 0.179045 AACCACACAGAGAGCACACC 60.179 55.000 0.00 0.00 0.00 4.16
951 959 2.134287 ACACAGAGAGCACACCGGT 61.134 57.895 0.00 0.00 0.00 5.28
1356 1397 3.528078 AGGTTTTATCCCTCCTTTCCTCC 59.472 47.826 0.00 0.00 0.00 4.30
1357 1398 3.268595 GGTTTTATCCCTCCTTTCCTCCA 59.731 47.826 0.00 0.00 0.00 3.86
1561 1651 7.888424 TGTAGTCTGTAGCTTTATGTGTTACA 58.112 34.615 0.00 0.00 0.00 2.41
1829 1966 5.048504 GCTCAGTTCAGGATGTGATTTTCAA 60.049 40.000 0.00 0.00 37.40 2.69
2089 2411 6.430925 AGTGTCAAAAAGCAGCAGTGATAATA 59.569 34.615 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.526147 ACATACTAAACGTACATACTCTTGGTT 58.474 33.333 0.00 0.00 0.00 3.67
2 3 9.661187 CTACATACTAAACGTACATACTCTTGG 57.339 37.037 0.00 0.00 0.00 3.61
63 64 9.727859 TCAAAACATAGTACATACTAGCCAAAA 57.272 29.630 5.11 0.00 41.62 2.44
64 65 9.378551 CTCAAAACATAGTACATACTAGCCAAA 57.621 33.333 5.11 0.00 41.62 3.28
65 66 8.537016 ACTCAAAACATAGTACATACTAGCCAA 58.463 33.333 5.11 0.00 41.62 4.52
66 67 8.074613 ACTCAAAACATAGTACATACTAGCCA 57.925 34.615 5.11 0.00 41.62 4.75
71 72 9.751542 GAGCATACTCAAAACATAGTACATACT 57.248 33.333 0.00 0.00 42.93 2.12
72 73 9.751542 AGAGCATACTCAAAACATAGTACATAC 57.248 33.333 0.00 0.00 46.09 2.39
74 75 9.672673 AAAGAGCATACTCAAAACATAGTACAT 57.327 29.630 0.00 0.00 46.09 2.29
75 76 9.502091 AAAAGAGCATACTCAAAACATAGTACA 57.498 29.630 0.00 0.00 46.09 2.90
76 77 9.974750 GAAAAGAGCATACTCAAAACATAGTAC 57.025 33.333 0.00 0.00 46.09 2.73
77 78 9.944376 AGAAAAGAGCATACTCAAAACATAGTA 57.056 29.630 0.00 0.00 46.09 1.82
78 79 8.854614 AGAAAAGAGCATACTCAAAACATAGT 57.145 30.769 0.00 0.00 46.09 2.12
81 82 9.236006 ACATAGAAAAGAGCATACTCAAAACAT 57.764 29.630 0.00 0.00 46.09 2.71
82 83 8.621532 ACATAGAAAAGAGCATACTCAAAACA 57.378 30.769 0.00 0.00 46.09 2.83
133 134 9.407380 TGCATATGAGTCCATAGTTTTTGTTAT 57.593 29.630 6.97 0.00 38.53 1.89
134 135 8.800370 TGCATATGAGTCCATAGTTTTTGTTA 57.200 30.769 6.97 0.00 38.53 2.41
135 136 7.701539 TGCATATGAGTCCATAGTTTTTGTT 57.298 32.000 6.97 0.00 38.53 2.83
136 137 7.701539 TTGCATATGAGTCCATAGTTTTTGT 57.298 32.000 6.97 0.00 38.53 2.83
137 138 9.590451 AAATTGCATATGAGTCCATAGTTTTTG 57.410 29.630 6.97 0.00 38.53 2.44
242 243 8.200120 CCCACATATCTCATATACTACCATGTG 58.800 40.741 0.00 0.00 40.08 3.21
243 244 7.345653 CCCCACATATCTCATATACTACCATGT 59.654 40.741 0.00 0.00 0.00 3.21
244 245 7.345653 ACCCCACATATCTCATATACTACCATG 59.654 40.741 0.00 0.00 0.00 3.66
245 246 7.430844 ACCCCACATATCTCATATACTACCAT 58.569 38.462 0.00 0.00 0.00 3.55
246 247 6.811574 ACCCCACATATCTCATATACTACCA 58.188 40.000 0.00 0.00 0.00 3.25
247 248 8.693625 GTTACCCCACATATCTCATATACTACC 58.306 40.741 0.00 0.00 0.00 3.18
248 249 9.476928 AGTTACCCCACATATCTCATATACTAC 57.523 37.037 0.00 0.00 0.00 2.73
250 251 9.476928 GTAGTTACCCCACATATCTCATATACT 57.523 37.037 0.00 0.00 0.00 2.12
251 252 8.693625 GGTAGTTACCCCACATATCTCATATAC 58.306 40.741 0.00 0.00 40.53 1.47
252 253 8.403474 TGGTAGTTACCCCACATATCTCATATA 58.597 37.037 5.90 0.00 45.87 0.86
253 254 7.253421 TGGTAGTTACCCCACATATCTCATAT 58.747 38.462 5.90 0.00 45.87 1.78
254 255 6.626238 TGGTAGTTACCCCACATATCTCATA 58.374 40.000 5.90 0.00 45.87 2.15
255 256 5.473273 TGGTAGTTACCCCACATATCTCAT 58.527 41.667 5.90 0.00 45.87 2.90
256 257 4.886163 TGGTAGTTACCCCACATATCTCA 58.114 43.478 5.90 0.00 45.87 3.27
265 266 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
266 267 0.692083 ATCCCGGTGGTAGTTACCCC 60.692 60.000 0.00 5.97 45.87 4.95
267 268 1.206878 AATCCCGGTGGTAGTTACCC 58.793 55.000 0.00 0.00 45.87 3.69
268 269 3.354948 AAAATCCCGGTGGTAGTTACC 57.645 47.619 0.00 1.25 46.62 2.85
269 270 4.325972 TGAAAAATCCCGGTGGTAGTTAC 58.674 43.478 0.00 0.00 0.00 2.50
270 271 4.637387 TGAAAAATCCCGGTGGTAGTTA 57.363 40.909 0.00 0.00 0.00 2.24
271 272 3.512219 TGAAAAATCCCGGTGGTAGTT 57.488 42.857 0.00 0.00 0.00 2.24
272 273 3.732048 ATGAAAAATCCCGGTGGTAGT 57.268 42.857 0.00 0.00 0.00 2.73
301 302 7.987458 CGGTAGTAGGATGCATTTTCCATATAT 59.013 37.037 0.00 0.00 35.59 0.86
302 303 7.327975 CGGTAGTAGGATGCATTTTCCATATA 58.672 38.462 0.00 0.00 35.59 0.86
303 304 6.173339 CGGTAGTAGGATGCATTTTCCATAT 58.827 40.000 0.00 0.00 35.59 1.78
304 305 5.512404 CCGGTAGTAGGATGCATTTTCCATA 60.512 44.000 0.00 0.00 35.59 2.74
305 306 4.389374 CGGTAGTAGGATGCATTTTCCAT 58.611 43.478 0.00 0.00 35.59 3.41
306 307 3.433031 CCGGTAGTAGGATGCATTTTCCA 60.433 47.826 0.00 0.00 35.59 3.53
307 308 3.139077 CCGGTAGTAGGATGCATTTTCC 58.861 50.000 0.00 0.00 0.00 3.13
308 309 3.139077 CCCGGTAGTAGGATGCATTTTC 58.861 50.000 0.00 0.00 0.00 2.29
309 310 2.508300 ACCCGGTAGTAGGATGCATTTT 59.492 45.455 0.00 0.00 0.00 1.82
310 311 2.124411 ACCCGGTAGTAGGATGCATTT 58.876 47.619 0.00 0.00 0.00 2.32
311 312 1.416401 CACCCGGTAGTAGGATGCATT 59.584 52.381 0.00 0.00 0.00 3.56
312 313 1.048601 CACCCGGTAGTAGGATGCAT 58.951 55.000 0.00 0.00 0.00 3.96
313 314 0.324923 ACACCCGGTAGTAGGATGCA 60.325 55.000 0.00 0.00 0.00 3.96
314 315 1.612463 CTACACCCGGTAGTAGGATGC 59.388 57.143 18.15 0.00 43.73 3.91
492 493 8.995220 TGAGCATACTTCTTTTTACGTACAAAT 58.005 29.630 7.32 0.00 0.00 2.32
493 494 8.367943 TGAGCATACTTCTTTTTACGTACAAA 57.632 30.769 6.71 6.71 0.00 2.83
494 495 7.949903 TGAGCATACTTCTTTTTACGTACAA 57.050 32.000 0.00 0.00 0.00 2.41
495 496 7.949903 TTGAGCATACTTCTTTTTACGTACA 57.050 32.000 0.00 0.00 0.00 2.90
496 497 9.821662 ATTTTGAGCATACTTCTTTTTACGTAC 57.178 29.630 0.00 0.00 0.00 3.67
569 570 9.492973 TGTACGCATAGTATGTAGTATGTAAGA 57.507 33.333 17.44 1.21 40.22 2.10
573 574 9.445878 AGTATGTACGCATAGTATGTAGTATGT 57.554 33.333 17.44 13.36 40.22 2.29
574 575 9.917872 GAGTATGTACGCATAGTATGTAGTATG 57.082 37.037 17.44 9.51 40.32 2.39
575 576 9.887629 AGAGTATGTACGCATAGTATGTAGTAT 57.112 33.333 17.44 10.33 40.32 2.12
576 577 9.363763 GAGAGTATGTACGCATAGTATGTAGTA 57.636 37.037 11.73 12.57 40.32 1.82
577 578 7.333921 GGAGAGTATGTACGCATAGTATGTAGT 59.666 40.741 11.73 13.44 40.32 2.73
578 579 7.464311 CGGAGAGTATGTACGCATAGTATGTAG 60.464 44.444 11.73 8.70 40.32 2.74
579 580 6.312180 CGGAGAGTATGTACGCATAGTATGTA 59.688 42.308 11.73 0.00 40.32 2.29
580 581 5.121925 CGGAGAGTATGTACGCATAGTATGT 59.878 44.000 11.73 0.00 40.32 2.29
581 582 5.350640 TCGGAGAGTATGTACGCATAGTATG 59.649 44.000 5.73 5.73 40.32 2.39
582 583 5.485620 TCGGAGAGTATGTACGCATAGTAT 58.514 41.667 0.00 0.00 40.32 2.12
583 584 4.886579 TCGGAGAGTATGTACGCATAGTA 58.113 43.478 0.00 0.00 40.32 1.82
584 585 3.736720 TCGGAGAGTATGTACGCATAGT 58.263 45.455 0.00 0.00 42.27 2.12
585 586 4.948608 ATCGGAGAGTATGTACGCATAG 57.051 45.455 0.00 0.00 43.63 2.23
586 587 8.672823 ATTATATCGGAGAGTATGTACGCATA 57.327 34.615 0.00 0.00 43.63 3.14
587 588 6.997239 TTATATCGGAGAGTATGTACGCAT 57.003 37.500 0.00 0.00 43.63 4.73
588 589 6.997239 ATTATATCGGAGAGTATGTACGCA 57.003 37.500 0.00 0.00 43.63 5.24
589 590 8.362860 TCTATTATATCGGAGAGTATGTACGC 57.637 38.462 0.00 0.00 43.63 4.42
612 613 9.852091 CTTTTGTTTACGTTCTAGGTAGTATCT 57.148 33.333 0.00 0.00 0.00 1.98
613 614 9.631452 ACTTTTGTTTACGTTCTAGGTAGTATC 57.369 33.333 0.00 0.00 0.00 2.24
614 615 9.415544 CACTTTTGTTTACGTTCTAGGTAGTAT 57.584 33.333 0.00 0.00 0.00 2.12
615 616 7.867403 CCACTTTTGTTTACGTTCTAGGTAGTA 59.133 37.037 0.00 0.00 0.00 1.82
616 617 6.703165 CCACTTTTGTTTACGTTCTAGGTAGT 59.297 38.462 0.00 0.00 0.00 2.73
617 618 6.146673 CCCACTTTTGTTTACGTTCTAGGTAG 59.853 42.308 0.00 0.00 0.00 3.18
618 619 5.990996 CCCACTTTTGTTTACGTTCTAGGTA 59.009 40.000 0.00 0.00 0.00 3.08
619 620 4.818005 CCCACTTTTGTTTACGTTCTAGGT 59.182 41.667 0.00 0.00 0.00 3.08
620 621 5.058490 TCCCACTTTTGTTTACGTTCTAGG 58.942 41.667 0.00 0.00 0.00 3.02
621 622 5.756833 ACTCCCACTTTTGTTTACGTTCTAG 59.243 40.000 0.00 0.00 0.00 2.43
622 623 5.673514 ACTCCCACTTTTGTTTACGTTCTA 58.326 37.500 0.00 0.00 0.00 2.10
623 624 4.520179 ACTCCCACTTTTGTTTACGTTCT 58.480 39.130 0.00 0.00 0.00 3.01
624 625 4.888038 ACTCCCACTTTTGTTTACGTTC 57.112 40.909 0.00 0.00 0.00 3.95
625 626 5.882000 AGTTACTCCCACTTTTGTTTACGTT 59.118 36.000 0.00 0.00 0.00 3.99
626 627 5.430886 AGTTACTCCCACTTTTGTTTACGT 58.569 37.500 0.00 0.00 0.00 3.57
627 628 5.996669 AGTTACTCCCACTTTTGTTTACG 57.003 39.130 0.00 0.00 0.00 3.18
628 629 7.254898 GGTGTAGTTACTCCCACTTTTGTTTAC 60.255 40.741 12.62 0.00 34.61 2.01
629 630 6.767423 GGTGTAGTTACTCCCACTTTTGTTTA 59.233 38.462 12.62 0.00 34.61 2.01
630 631 5.591472 GGTGTAGTTACTCCCACTTTTGTTT 59.409 40.000 12.62 0.00 34.61 2.83
631 632 5.128205 GGTGTAGTTACTCCCACTTTTGTT 58.872 41.667 12.62 0.00 34.61 2.83
632 633 4.711399 GGTGTAGTTACTCCCACTTTTGT 58.289 43.478 12.62 0.00 34.61 2.83
641 642 3.004752 TCTACCGGGTGTAGTTACTCC 57.995 52.381 10.66 2.51 45.99 3.85
642 643 3.379688 CCTTCTACCGGGTGTAGTTACTC 59.620 52.174 10.66 0.00 45.99 2.59
643 644 3.010584 TCCTTCTACCGGGTGTAGTTACT 59.989 47.826 10.66 0.00 45.99 2.24
644 645 3.356290 TCCTTCTACCGGGTGTAGTTAC 58.644 50.000 10.66 0.00 45.99 2.50
645 646 3.737559 TCCTTCTACCGGGTGTAGTTA 57.262 47.619 10.66 0.00 45.99 2.24
646 647 2.610438 TCCTTCTACCGGGTGTAGTT 57.390 50.000 10.66 0.00 45.99 2.24
647 648 2.610438 TTCCTTCTACCGGGTGTAGT 57.390 50.000 10.66 0.00 45.99 2.73
649 650 4.914177 ATTTTTCCTTCTACCGGGTGTA 57.086 40.909 10.66 0.00 0.00 2.90
650 651 3.801307 ATTTTTCCTTCTACCGGGTGT 57.199 42.857 10.66 0.00 0.00 4.16
651 652 4.279922 ACAAATTTTTCCTTCTACCGGGTG 59.720 41.667 10.66 0.00 0.00 4.61
652 653 4.476297 ACAAATTTTTCCTTCTACCGGGT 58.524 39.130 6.32 4.46 0.00 5.28
653 654 4.521256 TGACAAATTTTTCCTTCTACCGGG 59.479 41.667 6.32 0.00 0.00 5.73
654 655 5.699097 TGACAAATTTTTCCTTCTACCGG 57.301 39.130 0.00 0.00 0.00 5.28
719 720 8.571336 GCGTGGTTTATTAGTAGGTAGAGATTA 58.429 37.037 0.00 0.00 0.00 1.75
720 721 7.069085 TGCGTGGTTTATTAGTAGGTAGAGATT 59.931 37.037 0.00 0.00 0.00 2.40
788 789 6.374333 CGGGTTGATTTCAAAGAAATAGAGGA 59.626 38.462 5.07 0.00 37.63 3.71
858 861 2.683867 CCAAACGACAGGGTGTTTTACA 59.316 45.455 0.00 0.00 36.22 2.41
882 885 1.798813 GCTTGGAGCGCGCATTTAATT 60.799 47.619 35.10 10.81 0.00 1.40
886 889 3.332493 CTGCTTGGAGCGCGCATTT 62.332 57.895 35.10 13.58 46.26 2.32
895 898 7.826260 TTTTTCTTTACAAAACTGCTTGGAG 57.174 32.000 0.00 0.00 0.00 3.86
948 956 3.839432 GGGAGAGGAGGCGAACCG 61.839 72.222 0.00 0.00 42.76 4.44
951 959 1.380515 CAGAGGGAGAGGAGGCGAA 60.381 63.158 0.00 0.00 0.00 4.70
1314 1355 0.622136 TGAGGAGCTGCATGTCCATT 59.378 50.000 8.35 0.00 35.02 3.16
1561 1651 9.240734 AGCAATCTTCAAGTTCAATCTTAAGAT 57.759 29.630 12.37 12.37 34.02 2.40
1829 1966 7.334171 GTGCCAAAAGTATCAAATGCCTAAAAT 59.666 33.333 0.00 0.00 0.00 1.82
1866 2005 3.751698 GGTACACGCTCAGAGGAATTTTT 59.248 43.478 0.00 0.00 0.00 1.94
1867 2006 3.008049 AGGTACACGCTCAGAGGAATTTT 59.992 43.478 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.