Multiple sequence alignment - TraesCS4A01G157800

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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 TraesCS4A01G157800 chr4A 100.000 2738 0 0 1 2738 323784110 323786847 0.000000e+00 5057.0
1 TraesCS4A01G157800 chr4A 95.739 2441 103 1 1 2441 322074986 322072547 0.000000e+00 3930.0
2 TraesCS4A01G157800 chr4A 92.708 480 34 1 672 1150 302615391 302615870 0.000000e+00 691.0
3 TraesCS4A01G157800 chr4A 92.083 480 37 1 672 1150 302607484 302607963 0.000000e+00 675.0
4 TraesCS4A01G157800 chr4A 92.067 479 37 1 673 1150 412705883 412706361 0.000000e+00 673.0
5 TraesCS4A01G157800 chr4A 91.807 476 38 1 672 1146 366968331 366968806 0.000000e+00 662.0
6 TraesCS4A01G157800 chr4A 88.957 489 52 2 2103 2590 428706938 428707425 1.080000e-168 603.0
7 TraesCS4A01G157800 chr4A 88.776 490 51 4 2103 2590 428712937 428713424 5.050000e-167 597.0
8 TraesCS4A01G157800 chr4A 88.172 465 49 6 1894 2354 443312811 443313273 1.430000e-152 549.0
9 TraesCS4A01G157800 chr4A 91.293 379 32 1 1022 1399 245001871 245001493 1.450000e-142 516.0
10 TraesCS4A01G157800 chr4A 90.000 380 37 1 1021 1399 245009888 245009509 8.810000e-135 490.0
11 TraesCS4A01G157800 chr4A 90.966 321 23 6 1 316 236052235 236052554 7.010000e-116 427.0
12 TraesCS4A01G157800 chr4A 93.704 270 17 0 316 585 422962139 422962408 3.280000e-109 405.0
13 TraesCS4A01G157800 chr4A 92.509 267 19 1 316 582 422987625 422987890 5.530000e-102 381.0
14 TraesCS4A01G157800 chr4A 78.489 609 96 31 1 587 127985634 127985039 1.550000e-97 366.0
15 TraesCS4A01G157800 chr4A 93.600 125 4 3 2616 2738 401302938 401302816 1.670000e-42 183.0
16 TraesCS4A01G157800 chr4A 84.211 133 18 3 1361 1491 316704933 316705064 2.860000e-25 126.0
17 TraesCS4A01G157800 chr4A 78.616 159 19 11 1738 1887 78905549 78905397 1.040000e-14 91.6
18 TraesCS4A01G157800 chr4A 77.987 159 20 11 1738 1887 78898693 78898541 4.860000e-13 86.1
19 TraesCS4A01G157800 chr4A 92.308 52 2 2 2686 2736 429009289 429009239 3.780000e-09 73.1
20 TraesCS4A01G157800 chr2A 92.005 788 55 3 995 1775 86565855 86565069 0.000000e+00 1099.0
21 TraesCS4A01G157800 chr2A 92.179 780 52 3 997 1775 86522419 86521648 0.000000e+00 1094.0
22 TraesCS4A01G157800 chr2A 92.308 468 35 1 684 1150 156218661 156218194 0.000000e+00 664.0
23 TraesCS4A01G157800 chr2A 91.983 474 36 2 678 1150 156226646 156226174 0.000000e+00 664.0
24 TraesCS4A01G157800 chr2A 89.388 490 47 5 2103 2590 166451994 166451508 1.800000e-171 612.0
25 TraesCS4A01G157800 chr2A 88.595 491 50 6 2103 2590 224331819 224332306 2.350000e-165 592.0
26 TraesCS4A01G157800 chr2A 87.234 470 53 7 1894 2360 335750959 335750494 1.870000e-146 529.0
27 TraesCS4A01G157800 chr2A 85.319 470 63 6 1894 2360 335780077 335779611 5.300000e-132 481.0
28 TraesCS4A01G157800 chr2A 91.875 320 18 7 1 316 667771150 667771465 9.000000e-120 440.0
29 TraesCS4A01G157800 chr2A 91.250 320 22 5 1 316 30468929 30469246 5.420000e-117 431.0
30 TraesCS4A01G157800 chr2A 79.749 479 60 20 315 771 698949355 698948892 2.050000e-81 313.0
31 TraesCS4A01G157800 chr2A 79.406 471 70 18 316 771 462861058 462860600 9.520000e-80 307.0
32 TraesCS4A01G157800 chr2A 78.914 479 64 21 315 771 698913224 698912761 9.590000e-75 291.0
33 TraesCS4A01G157800 chr2A 91.608 143 6 6 1764 1902 211540598 211540738 2.780000e-45 193.0
34 TraesCS4A01G157800 chr2A 90.909 143 7 6 1764 1902 211532402 211532542 1.290000e-43 187.0
35 TraesCS4A01G157800 chr2A 88.119 101 8 4 600 699 166445665 166445568 1.720000e-22 117.0
36 TraesCS4A01G157800 chr6A 91.571 783 63 3 997 1777 296141860 296141079 0.000000e+00 1077.0
37 TraesCS4A01G157800 chr6A 89.057 594 54 9 1 585 216351956 216351365 0.000000e+00 726.0
38 TraesCS4A01G157800 chr6A 91.717 495 37 4 709 1201 346131668 346131176 0.000000e+00 684.0
39 TraesCS4A01G157800 chr6A 91.717 495 37 4 709 1201 346160704 346160212 0.000000e+00 684.0
40 TraesCS4A01G157800 chr6A 89.608 510 45 8 2084 2590 422631901 422631397 2.300000e-180 641.0
41 TraesCS4A01G157800 chr6A 90.441 272 23 3 1504 1774 472187907 472187638 3.350000e-94 355.0
42 TraesCS4A01G157800 chr6A 90.551 127 6 6 1749 1873 397479172 397479294 2.180000e-36 163.0
43 TraesCS4A01G157800 chr6A 89.764 127 7 6 1749 1873 397471769 397471891 1.020000e-34 158.0
44 TraesCS4A01G157800 chr5A 91.635 526 41 3 678 1201 96333042 96332518 0.000000e+00 725.0
45 TraesCS4A01G157800 chr5A 92.708 480 34 1 672 1150 267785718 267786197 0.000000e+00 691.0
46 TraesCS4A01G157800 chr5A 88.595 491 49 7 2103 2590 378682390 378681904 8.440000e-165 590.0
47 TraesCS4A01G157800 chr5A 92.674 273 15 5 1504 1774 574157412 574157143 3.310000e-104 388.0
48 TraesCS4A01G157800 chr3A 90.188 479 40 6 2041 2515 266616417 266615942 3.870000e-173 617.0
49 TraesCS4A01G157800 chr3A 88.958 480 45 6 2041 2515 290810572 290810096 1.090000e-163 586.0
50 TraesCS4A01G157800 chr3A 93.122 378 26 0 995 1372 137335477 137335100 3.080000e-154 555.0
51 TraesCS4A01G157800 chr3A 92.308 338 23 3 1513 1849 694920680 694921015 6.860000e-131 477.0
52 TraesCS4A01G157800 chr3A 89.058 329 31 5 1 328 389525117 389525441 1.180000e-108 403.0
53 TraesCS4A01G157800 chr3A 78.431 612 93 31 1 587 273507776 273508373 2.000000e-96 363.0
54 TraesCS4A01G157800 chr3A 83.085 402 54 10 367 757 256664189 256663791 1.210000e-93 353.0
55 TraesCS4A01G157800 chr3A 78.069 611 95 32 1 587 273485590 273486185 1.560000e-92 350.0
56 TraesCS4A01G157800 chr3A 92.308 52 2 2 2686 2736 362416695 362416645 3.780000e-09 73.1
57 TraesCS4A01G157800 chr3A 92.308 52 2 2 2686 2736 364875596 364875646 3.780000e-09 73.1
58 TraesCS4A01G157800 chr7A 88.641 493 50 6 2103 2592 586191721 586192210 1.820000e-166 595.0
59 TraesCS4A01G157800 chr7A 91.774 389 31 1 995 1382 301858856 301859244 8.630000e-150 540.0
60 TraesCS4A01G157800 chr7A 90.956 387 34 1 995 1381 301845512 301845897 1.120000e-143 520.0
61 TraesCS4A01G157800 chr7A 88.810 420 36 10 1949 2360 669043244 669042828 3.150000e-139 505.0
62 TraesCS4A01G157800 chr7A 88.333 420 37 11 1949 2360 403212052 403211637 6.810000e-136 494.0
63 TraesCS4A01G157800 chr7A 88.193 415 42 6 1946 2354 492314759 492315172 3.170000e-134 488.0
64 TraesCS4A01G157800 chr7A 90.938 320 21 8 1 316 266818683 266818998 9.060000e-115 424.0
65 TraesCS4A01G157800 chr7A 94.403 268 15 0 316 583 399557372 399557105 1.960000e-111 412.0
66 TraesCS4A01G157800 chr7A 93.333 270 18 0 316 585 504422200 504422469 1.530000e-107 399.0
67 TraesCS4A01G157800 chr7A 92.593 270 19 1 316 585 399520232 399519964 1.190000e-103 387.0
68 TraesCS4A01G157800 chr7A 81.974 466 57 16 316 771 165252570 165252122 1.200000e-98 370.0
69 TraesCS4A01G157800 chr7A 81.935 465 59 16 316 771 165299868 165299420 1.200000e-98 370.0
70 TraesCS4A01G157800 chr7A 90.110 273 22 4 1504 1774 693671896 693671627 1.560000e-92 350.0
71 TraesCS4A01G157800 chr7A 79.778 450 55 21 336 771 271998375 271998802 7.410000e-76 294.0
72 TraesCS4A01G157800 chr7A 85.526 228 28 5 1367 1591 301853450 301853675 1.640000e-57 233.0
73 TraesCS4A01G157800 chr1A 92.607 257 15 3 1595 1849 93889359 93889613 1.550000e-97 366.0
74 TraesCS4A01G157800 chr1A 97.436 39 1 0 2595 2633 408155230 408155268 1.760000e-07 67.6
75 TraesCS4A01G157800 chr6D 92.208 77 5 1 2636 2711 125385163 125385239 1.040000e-19 108.0
76 TraesCS4A01G157800 chr6D 92.647 68 5 0 2636 2703 125394505 125394572 6.240000e-17 99.0
77 TraesCS4A01G157800 chr7D 92.537 67 5 0 2636 2702 343666016 343666082 2.240000e-16 97.1
78 TraesCS4A01G157800 chr7D 89.855 69 3 4 2644 2711 343674261 343674326 4.860000e-13 86.1
79 TraesCS4A01G157800 chr2D 85.227 88 10 3 2627 2713 226337756 226337841 1.350000e-13 87.9
80 TraesCS4A01G157800 chr2D 83.158 95 13 3 2627 2721 226296785 226296876 1.750000e-12 84.2
81 TraesCS4A01G157800 chr4D 97.619 42 1 0 2591 2632 273989677 273989636 3.780000e-09 73.1


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 TraesCS4A01G157800 chr4A 323784110 323786847 2737 False 5057 5057 100.000 1 2738 1 chr4A.!!$F5 2737
1 TraesCS4A01G157800 chr4A 322072547 322074986 2439 True 3930 3930 95.739 1 2441 1 chr4A.!!$R6 2440
2 TraesCS4A01G157800 chr4A 127985039 127985634 595 True 366 366 78.489 1 587 1 chr4A.!!$R3 586
3 TraesCS4A01G157800 chr2A 86565069 86565855 786 True 1099 1099 92.005 995 1775 1 chr2A.!!$R2 780
4 TraesCS4A01G157800 chr2A 86521648 86522419 771 True 1094 1094 92.179 997 1775 1 chr2A.!!$R1 778
5 TraesCS4A01G157800 chr6A 296141079 296141860 781 True 1077 1077 91.571 997 1777 1 chr6A.!!$R2 780
6 TraesCS4A01G157800 chr6A 216351365 216351956 591 True 726 726 89.057 1 585 1 chr6A.!!$R1 584
7 TraesCS4A01G157800 chr6A 422631397 422631901 504 True 641 641 89.608 2084 2590 1 chr6A.!!$R5 506
8 TraesCS4A01G157800 chr5A 96332518 96333042 524 True 725 725 91.635 678 1201 1 chr5A.!!$R1 523
9 TraesCS4A01G157800 chr3A 273507776 273508373 597 False 363 363 78.431 1 587 1 chr3A.!!$F2 586
10 TraesCS4A01G157800 chr3A 273485590 273486185 595 False 350 350 78.069 1 587 1 chr3A.!!$F1 586

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
748 776 0.031585 CGAGGAACTTGACGTCCACA 59.968 55.0 14.12 0.0 44.22 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2597 0.036952 ATGCGTCAGGTGTCTTCCAG 60.037 55.0 0.0 0.0 0.0 3.86 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
107 111 2.733956 AGGCATTTTAAATGAGGCCGA 58.266 42.857 20.37 0.00 45.79 5.54
127 131 5.234116 GCCGAAAACATCAAACAACAATTCT 59.766 36.000 0.00 0.00 0.00 2.40
207 216 4.512571 TGTTGTTATCATGATGCGGATGAG 59.487 41.667 18.72 0.00 33.38 2.90
208 217 4.341366 TGTTATCATGATGCGGATGAGT 57.659 40.909 18.72 0.00 33.38 3.41
212 221 6.095300 TGTTATCATGATGCGGATGAGTTTTT 59.905 34.615 18.72 0.00 33.38 1.94
295 306 1.132881 TGGAAAGAAAAGGGGTGCCAT 60.133 47.619 0.00 0.00 0.00 4.40
416 435 1.754226 GTGGCAAGGAAACAAGGAACA 59.246 47.619 0.00 0.00 0.00 3.18
480 502 2.013400 ACAACACATCACAAGCGTTCA 58.987 42.857 0.00 0.00 0.00 3.18
515 539 4.960469 TCGTCTCAGGGTTATACCTTTGAT 59.040 41.667 0.00 0.00 39.34 2.57
587 614 2.095567 GCGACGGTAGTGAAAGTAGTCA 60.096 50.000 0.00 0.00 0.00 3.41
594 621 8.517062 ACGGTAGTGAAAGTAGTCATACTATT 57.483 34.615 0.00 0.00 41.54 1.73
621 648 1.269102 CGGCGATGGTAGTGGAAGTAG 60.269 57.143 0.00 0.00 0.00 2.57
635 662 1.345415 GAAGTAGTGGTTCCCGGTTCA 59.655 52.381 0.00 0.00 0.00 3.18
643 670 2.534493 TCCCGGTTCAGAGGGGAA 59.466 61.111 0.00 0.00 46.81 3.97
655 682 1.555533 AGAGGGGAACTTGACGAATCC 59.444 52.381 0.00 0.00 0.00 3.01
664 691 2.094649 ACTTGACGAATCCGAGTCCTTC 60.095 50.000 0.00 0.00 39.50 3.46
748 776 0.031585 CGAGGAACTTGACGTCCACA 59.968 55.000 14.12 0.00 44.22 4.17
778 806 2.491621 GTCGGCGGTAGTGGTACC 59.508 66.667 7.21 4.43 44.99 3.34
931 959 0.108992 GTTCACGACGATGGTAGCCA 60.109 55.000 0.00 0.00 38.19 4.75
968 996 4.381292 CGAAGGGGTACTTGACGAATAACT 60.381 45.833 0.00 0.00 40.21 2.24
1077 1105 5.413833 TGTAGACGTACTTTCGAAGAGGAAT 59.586 40.000 0.00 0.00 38.43 3.01
1103 1131 1.533625 CGTCCCAAAATGAGCAAGGA 58.466 50.000 0.00 0.00 0.00 3.36
1115 1143 1.080501 GCAAGGAAAAAGCCCTCGC 60.081 57.895 0.00 0.00 32.57 5.03
1128 1156 2.811317 CTCGCTCAACGGTGCTCC 60.811 66.667 0.00 0.00 43.89 4.70
1142 1171 2.293399 GGTGCTCCAACTTGACGAAATT 59.707 45.455 0.00 0.00 0.00 1.82
1154 1183 3.379240 TGACGAAATTCACGAACGGTTA 58.621 40.909 11.01 0.00 34.70 2.85
1268 1298 4.452733 CCAACGAGGGGCGAGGTC 62.453 72.222 0.00 0.00 44.57 3.85
1778 1822 0.825840 GGATCGAGAGGTGAGGAGGG 60.826 65.000 0.00 0.00 0.00 4.30
1869 1913 1.227292 GCTCGCTAGGGTTAGTGGC 60.227 63.158 6.70 0.43 37.86 5.01
1932 1976 1.553690 GGTGAGAGGCCTGGTTGCTA 61.554 60.000 12.00 0.00 0.00 3.49
1939 1983 2.821366 CCTGGTTGCTAGGCTGCG 60.821 66.667 0.00 0.00 35.36 5.18
2006 2050 2.817396 GCGGCTGGTCTGAAGCTC 60.817 66.667 0.00 0.00 40.64 4.09
2007 2051 2.125350 CGGCTGGTCTGAAGCTCC 60.125 66.667 1.74 0.00 40.64 4.70
2056 2100 7.649306 TCAAGCAGAAAATAAAGAGAAAAGCAC 59.351 33.333 0.00 0.00 0.00 4.40
2138 2182 9.829507 CATGCCCTATTTGATAAAATTGGTTTA 57.170 29.630 13.19 2.37 34.60 2.01
2200 2244 8.937634 ATATCATTCAAACTTGAGGCATTTTC 57.062 30.769 0.00 0.00 38.61 2.29
2336 2381 9.612066 ACTTGCAAAAATGAAAGGAATAAGAAA 57.388 25.926 0.00 0.00 0.00 2.52
2451 2496 4.739587 ATGCAATGCACATGGTGATAAA 57.260 36.364 11.23 0.00 43.04 1.40
2483 2528 2.747460 TGGCAAGAGGCACGATGC 60.747 61.111 7.09 7.09 46.46 3.91
2499 2544 3.676172 ACGATGCAAAGCAAACAATGATG 59.324 39.130 0.00 0.00 43.62 3.07
2524 2569 6.717413 ACATGATGAAATGCAACAAACAAAC 58.283 32.000 0.00 0.00 32.72 2.93
2528 2573 7.759465 TGATGAAATGCAACAAACAAACAAAT 58.241 26.923 0.00 0.00 0.00 2.32
2529 2574 7.696872 TGATGAAATGCAACAAACAAACAAATG 59.303 29.630 0.00 0.00 0.00 2.32
2532 2577 6.492007 AATGCAACAAACAAACAAATGACA 57.508 29.167 0.00 0.00 0.00 3.58
2533 2578 6.680874 ATGCAACAAACAAACAAATGACAT 57.319 29.167 0.00 0.00 0.00 3.06
2536 2581 5.163774 GCAACAAACAAACAAATGACATGGT 60.164 36.000 0.00 0.00 0.00 3.55
2537 2582 6.036517 GCAACAAACAAACAAATGACATGGTA 59.963 34.615 0.00 0.00 0.00 3.25
2567 2612 4.691216 GTGAATAACTGGAAGACACCTGAC 59.309 45.833 0.00 0.00 37.43 3.51
2570 2615 1.367471 CTGGAAGACACCTGACGCA 59.633 57.895 0.00 0.00 34.07 5.24
2582 2627 4.570663 GACGCATCGGTCTCGGGG 62.571 72.222 0.00 0.00 36.95 5.73
2586 2631 4.570663 CATCGGTCTCGGGGCGTC 62.571 72.222 0.00 0.00 36.95 5.19
2590 2635 4.436998 GGTCTCGGGGCGTCACAG 62.437 72.222 0.00 0.00 0.00 3.66
2591 2636 3.681835 GTCTCGGGGCGTCACAGT 61.682 66.667 0.00 0.00 0.00 3.55
2592 2637 2.915659 TCTCGGGGCGTCACAGTT 60.916 61.111 0.00 0.00 0.00 3.16
2593 2638 1.604308 TCTCGGGGCGTCACAGTTA 60.604 57.895 0.00 0.00 0.00 2.24
2594 2639 1.153823 CTCGGGGCGTCACAGTTAG 60.154 63.158 0.00 0.00 0.00 2.34
2595 2640 2.813908 CGGGGCGTCACAGTTAGC 60.814 66.667 0.00 0.00 0.00 3.09
2596 2641 2.663196 GGGGCGTCACAGTTAGCT 59.337 61.111 0.00 0.00 0.00 3.32
2597 2642 1.895238 GGGGCGTCACAGTTAGCTA 59.105 57.895 0.00 0.00 0.00 3.32
2598 2643 0.179108 GGGGCGTCACAGTTAGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
2599 2644 0.179108 GGGCGTCACAGTTAGCTAGG 60.179 60.000 0.00 0.00 0.00 3.02
2600 2645 0.179108 GGCGTCACAGTTAGCTAGGG 60.179 60.000 0.00 0.00 0.00 3.53
2601 2646 0.531200 GCGTCACAGTTAGCTAGGGT 59.469 55.000 0.00 0.00 0.00 4.34
2602 2647 1.067071 GCGTCACAGTTAGCTAGGGTT 60.067 52.381 0.00 0.00 0.00 4.11
2603 2648 2.877335 CGTCACAGTTAGCTAGGGTTC 58.123 52.381 0.00 0.00 0.00 3.62
2604 2649 2.731341 CGTCACAGTTAGCTAGGGTTCG 60.731 54.545 0.00 0.00 0.00 3.95
2605 2650 1.822990 TCACAGTTAGCTAGGGTTCGG 59.177 52.381 0.00 0.00 0.00 4.30
2606 2651 1.822990 CACAGTTAGCTAGGGTTCGGA 59.177 52.381 0.00 0.00 0.00 4.55
2607 2652 2.100989 ACAGTTAGCTAGGGTTCGGAG 58.899 52.381 0.00 0.00 0.00 4.63
2608 2653 1.409427 CAGTTAGCTAGGGTTCGGAGG 59.591 57.143 0.00 0.00 0.00 4.30
2609 2654 0.751452 GTTAGCTAGGGTTCGGAGGG 59.249 60.000 0.00 0.00 0.00 4.30
2610 2655 0.398098 TTAGCTAGGGTTCGGAGGGG 60.398 60.000 0.00 0.00 0.00 4.79
2611 2656 1.587522 TAGCTAGGGTTCGGAGGGGT 61.588 60.000 0.00 0.00 0.00 4.95
2612 2657 2.732619 GCTAGGGTTCGGAGGGGTG 61.733 68.421 0.00 0.00 0.00 4.61
2613 2658 2.686106 TAGGGTTCGGAGGGGTGC 60.686 66.667 0.00 0.00 0.00 5.01
2635 2680 3.628989 TGGGCTACAGATGGGTCG 58.371 61.111 0.00 0.00 0.00 4.79
2636 2681 2.063979 TGGGCTACAGATGGGTCGG 61.064 63.158 0.00 0.00 0.00 4.79
2637 2682 2.109181 GGCTACAGATGGGTCGGC 59.891 66.667 0.00 0.00 0.00 5.54
2638 2683 2.279517 GCTACAGATGGGTCGGCG 60.280 66.667 0.00 0.00 0.00 6.46
2639 2684 2.417516 CTACAGATGGGTCGGCGG 59.582 66.667 7.21 0.00 0.00 6.13
2640 2685 2.043752 TACAGATGGGTCGGCGGA 60.044 61.111 7.21 0.00 0.00 5.54
2641 2686 2.076622 CTACAGATGGGTCGGCGGAG 62.077 65.000 7.21 0.00 0.00 4.63
2642 2687 2.561467 TACAGATGGGTCGGCGGAGA 62.561 60.000 7.21 0.00 0.00 3.71
2643 2688 2.835431 AGATGGGTCGGCGGAGAG 60.835 66.667 7.21 0.00 0.00 3.20
2644 2689 3.917760 GATGGGTCGGCGGAGAGG 61.918 72.222 7.21 0.00 0.00 3.69
2648 2693 3.387947 GGTCGGCGGAGAGGGAAA 61.388 66.667 7.21 0.00 0.00 3.13
2649 2694 2.125633 GTCGGCGGAGAGGGAAAC 60.126 66.667 7.21 0.00 0.00 2.78
2650 2695 3.755628 TCGGCGGAGAGGGAAACG 61.756 66.667 7.21 0.00 0.00 3.60
2651 2696 4.814294 CGGCGGAGAGGGAAACGG 62.814 72.222 0.00 0.00 0.00 4.44
2654 2699 3.702048 CGGAGAGGGAAACGGCCA 61.702 66.667 2.24 0.00 0.00 5.36
2655 2700 2.998949 GGAGAGGGAAACGGCCAT 59.001 61.111 2.24 0.00 0.00 4.40
2656 2701 1.682451 CGGAGAGGGAAACGGCCATA 61.682 60.000 2.24 0.00 0.00 2.74
2657 2702 0.106894 GGAGAGGGAAACGGCCATAG 59.893 60.000 2.24 0.00 0.00 2.23
2658 2703 0.106894 GAGAGGGAAACGGCCATAGG 59.893 60.000 2.24 0.00 0.00 2.57
2683 2728 4.982701 GGCTGGGCTGCTGGTTGT 62.983 66.667 0.00 0.00 0.00 3.32
2684 2729 3.677648 GCTGGGCTGCTGGTTGTG 61.678 66.667 0.00 0.00 0.00 3.33
2685 2730 3.677648 CTGGGCTGCTGGTTGTGC 61.678 66.667 0.00 0.00 0.00 4.57
2686 2731 4.208403 TGGGCTGCTGGTTGTGCT 62.208 61.111 0.00 0.00 0.00 4.40
2687 2732 3.368571 GGGCTGCTGGTTGTGCTC 61.369 66.667 0.00 0.00 0.00 4.26
2688 2733 2.282040 GGCTGCTGGTTGTGCTCT 60.282 61.111 0.00 0.00 0.00 4.09
2689 2734 2.331132 GGCTGCTGGTTGTGCTCTC 61.331 63.158 0.00 0.00 0.00 3.20
2690 2735 1.302351 GCTGCTGGTTGTGCTCTCT 60.302 57.895 0.00 0.00 0.00 3.10
2691 2736 1.297456 GCTGCTGGTTGTGCTCTCTC 61.297 60.000 0.00 0.00 0.00 3.20
2692 2737 0.321021 CTGCTGGTTGTGCTCTCTCT 59.679 55.000 0.00 0.00 0.00 3.10
2693 2738 0.319728 TGCTGGTTGTGCTCTCTCTC 59.680 55.000 0.00 0.00 0.00 3.20
2694 2739 0.607620 GCTGGTTGTGCTCTCTCTCT 59.392 55.000 0.00 0.00 0.00 3.10
2695 2740 1.404047 GCTGGTTGTGCTCTCTCTCTC 60.404 57.143 0.00 0.00 0.00 3.20
2696 2741 2.170166 CTGGTTGTGCTCTCTCTCTCT 58.830 52.381 0.00 0.00 0.00 3.10
2697 2742 2.164219 CTGGTTGTGCTCTCTCTCTCTC 59.836 54.545 0.00 0.00 0.00 3.20
2698 2743 1.476488 GGTTGTGCTCTCTCTCTCTCC 59.524 57.143 0.00 0.00 0.00 3.71
2699 2744 1.476488 GTTGTGCTCTCTCTCTCTCCC 59.524 57.143 0.00 0.00 0.00 4.30
2700 2745 0.998928 TGTGCTCTCTCTCTCTCCCT 59.001 55.000 0.00 0.00 0.00 4.20
2701 2746 1.064758 TGTGCTCTCTCTCTCTCCCTC 60.065 57.143 0.00 0.00 0.00 4.30
2702 2747 1.064758 GTGCTCTCTCTCTCTCCCTCA 60.065 57.143 0.00 0.00 0.00 3.86
2703 2748 1.852309 TGCTCTCTCTCTCTCCCTCAT 59.148 52.381 0.00 0.00 0.00 2.90
2704 2749 3.052329 TGCTCTCTCTCTCTCCCTCATA 58.948 50.000 0.00 0.00 0.00 2.15
2705 2750 3.657239 TGCTCTCTCTCTCTCCCTCATAT 59.343 47.826 0.00 0.00 0.00 1.78
2706 2751 4.106179 TGCTCTCTCTCTCTCCCTCATATT 59.894 45.833 0.00 0.00 0.00 1.28
2707 2752 5.079643 GCTCTCTCTCTCTCCCTCATATTT 58.920 45.833 0.00 0.00 0.00 1.40
2708 2753 5.539955 GCTCTCTCTCTCTCCCTCATATTTT 59.460 44.000 0.00 0.00 0.00 1.82
2709 2754 6.294731 GCTCTCTCTCTCTCCCTCATATTTTC 60.295 46.154 0.00 0.00 0.00 2.29
2710 2755 6.921412 TCTCTCTCTCTCCCTCATATTTTCT 58.079 40.000 0.00 0.00 0.00 2.52
2711 2756 7.361438 TCTCTCTCTCTCCCTCATATTTTCTT 58.639 38.462 0.00 0.00 0.00 2.52
2712 2757 7.843760 TCTCTCTCTCTCCCTCATATTTTCTTT 59.156 37.037 0.00 0.00 0.00 2.52
2713 2758 9.142014 CTCTCTCTCTCCCTCATATTTTCTTTA 57.858 37.037 0.00 0.00 0.00 1.85
2714 2759 9.494055 TCTCTCTCTCCCTCATATTTTCTTTAA 57.506 33.333 0.00 0.00 0.00 1.52
2715 2760 9.541143 CTCTCTCTCCCTCATATTTTCTTTAAC 57.459 37.037 0.00 0.00 0.00 2.01
2716 2761 9.046846 TCTCTCTCCCTCATATTTTCTTTAACA 57.953 33.333 0.00 0.00 0.00 2.41
2717 2762 9.323985 CTCTCTCCCTCATATTTTCTTTAACAG 57.676 37.037 0.00 0.00 0.00 3.16
2718 2763 9.046846 TCTCTCCCTCATATTTTCTTTAACAGA 57.953 33.333 0.00 0.00 0.00 3.41
2719 2764 9.672673 CTCTCCCTCATATTTTCTTTAACAGAA 57.327 33.333 0.00 0.00 39.99 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.421424 GCTTCACCTCTTGCCATGTTAG 59.579 50.000 0.00 0.00 0.00 2.34
107 111 9.442047 TTTACCAGAATTGTTGTTTGATGTTTT 57.558 25.926 0.00 0.00 0.00 2.43
127 131 2.844654 ATGCATGTGGGGATTTACCA 57.155 45.000 0.00 0.00 41.20 3.25
295 306 1.194997 CCGTTTTCGTTATCGTTGCCA 59.805 47.619 0.00 0.00 42.35 4.92
416 435 0.250640 GCCCGATCTGATCCTTGCAT 60.251 55.000 11.84 0.00 0.00 3.96
480 502 0.675837 TGAGACGACCGTCCGAGAAT 60.676 55.000 17.62 0.00 45.59 2.40
515 539 2.325166 GTTCCGAAAACGCACGCA 59.675 55.556 0.00 0.00 0.00 5.24
587 614 1.991121 TCGCCGAGGACCAATAGTAT 58.009 50.000 0.00 0.00 0.00 2.12
594 621 2.043752 TACCATCGCCGAGGACCA 60.044 61.111 0.00 0.00 0.00 4.02
635 662 1.555533 GGATTCGTCAAGTTCCCCTCT 59.444 52.381 0.00 0.00 0.00 3.69
643 670 1.546961 AGGACTCGGATTCGTCAAGT 58.453 50.000 0.00 0.00 37.69 3.16
664 691 1.065273 CCACTATCGTCGAACCCCG 59.935 63.158 0.00 0.00 40.25 5.73
748 776 2.637383 GCCGACCCTCGAAGACACT 61.637 63.158 0.00 0.00 43.74 3.55
778 806 0.453282 CTCGACGTGCATTTTGGCAG 60.453 55.000 0.00 0.00 45.96 4.85
931 959 2.514803 CCCTTCGGATCACCAAGTTTT 58.485 47.619 0.00 0.00 35.59 2.43
968 996 0.031043 CACCAAGTACCACGACGACA 59.969 55.000 0.00 0.00 0.00 4.35
1077 1105 1.265635 CTCATTTTGGGACGCGACAAA 59.734 47.619 15.93 17.84 35.01 2.83
1115 1143 0.588252 CAAGTTGGAGCACCGTTGAG 59.412 55.000 0.00 0.00 39.42 3.02
1128 1156 3.653113 CGTTCGTGAATTTCGTCAAGTTG 59.347 43.478 0.00 0.00 0.00 3.16
1142 1171 0.319727 ACGCCAATAACCGTTCGTGA 60.320 50.000 0.00 0.00 33.26 4.35
1154 1183 1.134098 CCAAGACCAGGATACGCCAAT 60.134 52.381 0.00 0.00 46.39 3.16
1268 1298 2.249309 CAGGCAACAACAGCGTCG 59.751 61.111 0.00 0.00 41.41 5.12
1494 1538 3.391382 CCGCCGTCCTTCTCCCTT 61.391 66.667 0.00 0.00 0.00 3.95
1778 1822 1.671261 CCATCTCCATTCGCTCGATCC 60.671 57.143 0.00 0.00 0.00 3.36
1932 1976 4.351054 CACCCTTTCCCGCAGCCT 62.351 66.667 0.00 0.00 0.00 4.58
1938 1982 2.590092 CTAGGCCACCCTTTCCCG 59.410 66.667 5.01 0.00 42.87 5.14
1939 1983 1.929088 ACCTAGGCCACCCTTTCCC 60.929 63.158 9.30 0.00 42.87 3.97
1987 2031 3.123620 GCTTCAGACCAGCCGCAG 61.124 66.667 0.00 0.00 0.00 5.18
2006 2050 7.880195 TGAAGAAAATTAGAGAGAGGAAACAGG 59.120 37.037 0.00 0.00 0.00 4.00
2007 2051 8.839310 TGAAGAAAATTAGAGAGAGGAAACAG 57.161 34.615 0.00 0.00 0.00 3.16
2056 2100 1.068121 ACACCTCTCCTTTTCCCCTG 58.932 55.000 0.00 0.00 0.00 4.45
2200 2244 3.628487 TGGAGTTGTTTTGGTTAGGTTCG 59.372 43.478 0.00 0.00 0.00 3.95
2336 2381 2.369860 TGTGTCATCACTGCCTTCTTCT 59.630 45.455 0.00 0.00 44.14 2.85
2451 2496 5.155278 TCTTGCCATTTTGCATTTCATCT 57.845 34.783 0.00 0.00 41.70 2.90
2474 2519 0.597118 TGTTTGCTTTGCATCGTGCC 60.597 50.000 7.38 0.00 44.23 5.01
2478 2523 3.921630 TCATCATTGTTTGCTTTGCATCG 59.078 39.130 0.00 0.00 38.76 3.84
2483 2528 6.588373 TCATCATGTCATCATTGTTTGCTTTG 59.412 34.615 0.00 0.00 31.15 2.77
2499 2544 6.528014 TTGTTTGTTGCATTTCATCATGTC 57.472 33.333 0.00 0.00 0.00 3.06
2524 2569 6.070897 TCACTGTTGTTACCATGTCATTTG 57.929 37.500 0.00 0.00 0.00 2.32
2528 2573 6.995686 AGTTATTCACTGTTGTTACCATGTCA 59.004 34.615 0.00 0.00 32.83 3.58
2529 2574 7.435068 AGTTATTCACTGTTGTTACCATGTC 57.565 36.000 0.00 0.00 32.83 3.06
2543 2588 4.593206 TCAGGTGTCTTCCAGTTATTCACT 59.407 41.667 0.00 0.00 35.35 3.41
2544 2589 4.691216 GTCAGGTGTCTTCCAGTTATTCAC 59.309 45.833 0.00 0.00 0.00 3.18
2545 2590 4.560716 CGTCAGGTGTCTTCCAGTTATTCA 60.561 45.833 0.00 0.00 0.00 2.57
2549 2594 1.000506 GCGTCAGGTGTCTTCCAGTTA 59.999 52.381 0.00 0.00 0.00 2.24
2551 2596 1.367840 GCGTCAGGTGTCTTCCAGT 59.632 57.895 0.00 0.00 0.00 4.00
2552 2597 0.036952 ATGCGTCAGGTGTCTTCCAG 60.037 55.000 0.00 0.00 0.00 3.86
2561 2606 2.885861 GAGACCGATGCGTCAGGT 59.114 61.111 18.36 18.36 41.63 4.00
2562 2607 2.278206 CGAGACCGATGCGTCAGG 60.278 66.667 6.75 10.58 38.22 3.86
2582 2627 0.531200 ACCCTAGCTAACTGTGACGC 59.469 55.000 0.00 0.00 0.00 5.19
2583 2628 2.731341 CGAACCCTAGCTAACTGTGACG 60.731 54.545 0.00 0.00 0.00 4.35
2584 2629 2.416972 CCGAACCCTAGCTAACTGTGAC 60.417 54.545 0.00 0.00 0.00 3.67
2586 2631 1.822990 TCCGAACCCTAGCTAACTGTG 59.177 52.381 0.00 0.00 0.00 3.66
2587 2632 2.100989 CTCCGAACCCTAGCTAACTGT 58.899 52.381 0.00 0.00 0.00 3.55
2588 2633 1.409427 CCTCCGAACCCTAGCTAACTG 59.591 57.143 0.00 0.00 0.00 3.16
2589 2634 1.688627 CCCTCCGAACCCTAGCTAACT 60.689 57.143 0.00 0.00 0.00 2.24
2590 2635 0.751452 CCCTCCGAACCCTAGCTAAC 59.249 60.000 0.00 0.00 0.00 2.34
2591 2636 0.398098 CCCCTCCGAACCCTAGCTAA 60.398 60.000 0.00 0.00 0.00 3.09
2592 2637 1.232216 CCCCTCCGAACCCTAGCTA 59.768 63.158 0.00 0.00 0.00 3.32
2593 2638 2.041819 CCCCTCCGAACCCTAGCT 60.042 66.667 0.00 0.00 0.00 3.32
2594 2639 2.365237 ACCCCTCCGAACCCTAGC 60.365 66.667 0.00 0.00 0.00 3.42
2595 2640 2.732619 GCACCCCTCCGAACCCTAG 61.733 68.421 0.00 0.00 0.00 3.02
2596 2641 2.686106 GCACCCCTCCGAACCCTA 60.686 66.667 0.00 0.00 0.00 3.53
2612 2657 3.866582 ATCTGTAGCCCAGCCCGC 61.867 66.667 0.00 0.00 41.25 6.13
2613 2658 2.109799 CATCTGTAGCCCAGCCCG 59.890 66.667 0.00 0.00 41.25 6.13
2614 2659 2.512896 CCATCTGTAGCCCAGCCC 59.487 66.667 0.00 0.00 41.25 5.19
2615 2660 2.330924 GACCCATCTGTAGCCCAGCC 62.331 65.000 0.00 0.00 41.25 4.85
2616 2661 1.147153 GACCCATCTGTAGCCCAGC 59.853 63.158 0.00 0.00 41.25 4.85
2617 2662 1.443407 CGACCCATCTGTAGCCCAG 59.557 63.158 0.00 0.00 42.97 4.45
2618 2663 2.063979 CCGACCCATCTGTAGCCCA 61.064 63.158 0.00 0.00 0.00 5.36
2619 2664 2.822399 CCGACCCATCTGTAGCCC 59.178 66.667 0.00 0.00 0.00 5.19
2620 2665 2.109181 GCCGACCCATCTGTAGCC 59.891 66.667 0.00 0.00 0.00 3.93
2621 2666 2.279517 CGCCGACCCATCTGTAGC 60.280 66.667 0.00 0.00 0.00 3.58
2622 2667 2.076622 CTCCGCCGACCCATCTGTAG 62.077 65.000 0.00 0.00 0.00 2.74
2623 2668 2.043752 TCCGCCGACCCATCTGTA 60.044 61.111 0.00 0.00 0.00 2.74
2624 2669 3.461773 CTCCGCCGACCCATCTGT 61.462 66.667 0.00 0.00 0.00 3.41
2625 2670 3.144120 CTCTCCGCCGACCCATCTG 62.144 68.421 0.00 0.00 0.00 2.90
2626 2671 2.835431 CTCTCCGCCGACCCATCT 60.835 66.667 0.00 0.00 0.00 2.90
2627 2672 3.917760 CCTCTCCGCCGACCCATC 61.918 72.222 0.00 0.00 0.00 3.51
2631 2676 3.387947 TTTCCCTCTCCGCCGACC 61.388 66.667 0.00 0.00 0.00 4.79
2632 2677 2.125633 GTTTCCCTCTCCGCCGAC 60.126 66.667 0.00 0.00 0.00 4.79
2633 2678 3.755628 CGTTTCCCTCTCCGCCGA 61.756 66.667 0.00 0.00 0.00 5.54
2634 2679 4.814294 CCGTTTCCCTCTCCGCCG 62.814 72.222 0.00 0.00 0.00 6.46
2637 2682 1.682451 TATGGCCGTTTCCCTCTCCG 61.682 60.000 0.77 0.00 0.00 4.63
2638 2683 0.106894 CTATGGCCGTTTCCCTCTCC 59.893 60.000 0.77 0.00 0.00 3.71
2639 2684 0.106894 CCTATGGCCGTTTCCCTCTC 59.893 60.000 0.77 0.00 0.00 3.20
2640 2685 1.984288 GCCTATGGCCGTTTCCCTCT 61.984 60.000 0.77 0.00 44.06 3.69
2641 2686 1.526225 GCCTATGGCCGTTTCCCTC 60.526 63.158 0.77 0.00 44.06 4.30
2642 2687 2.595655 GCCTATGGCCGTTTCCCT 59.404 61.111 0.77 0.00 44.06 4.20
2666 2711 4.982701 ACAACCAGCAGCCCAGCC 62.983 66.667 0.00 0.00 34.23 4.85
2667 2712 3.677648 CACAACCAGCAGCCCAGC 61.678 66.667 0.00 0.00 0.00 4.85
2668 2713 3.677648 GCACAACCAGCAGCCCAG 61.678 66.667 0.00 0.00 0.00 4.45
2669 2714 4.208403 AGCACAACCAGCAGCCCA 62.208 61.111 0.00 0.00 0.00 5.36
2670 2715 3.368571 GAGCACAACCAGCAGCCC 61.369 66.667 0.00 0.00 0.00 5.19
2671 2716 2.282040 AGAGCACAACCAGCAGCC 60.282 61.111 0.00 0.00 0.00 4.85
2672 2717 1.297456 GAGAGAGCACAACCAGCAGC 61.297 60.000 0.00 0.00 0.00 5.25
2673 2718 0.321021 AGAGAGAGCACAACCAGCAG 59.679 55.000 0.00 0.00 0.00 4.24
2674 2719 0.319728 GAGAGAGAGCACAACCAGCA 59.680 55.000 0.00 0.00 0.00 4.41
2675 2720 0.607620 AGAGAGAGAGCACAACCAGC 59.392 55.000 0.00 0.00 0.00 4.85
2676 2721 2.164219 GAGAGAGAGAGAGCACAACCAG 59.836 54.545 0.00 0.00 0.00 4.00
2677 2722 2.166829 GAGAGAGAGAGAGCACAACCA 58.833 52.381 0.00 0.00 0.00 3.67
2678 2723 1.476488 GGAGAGAGAGAGAGCACAACC 59.524 57.143 0.00 0.00 0.00 3.77
2679 2724 1.476488 GGGAGAGAGAGAGAGCACAAC 59.524 57.143 0.00 0.00 0.00 3.32
2680 2725 1.357420 AGGGAGAGAGAGAGAGCACAA 59.643 52.381 0.00 0.00 0.00 3.33
2681 2726 0.998928 AGGGAGAGAGAGAGAGCACA 59.001 55.000 0.00 0.00 0.00 4.57
2682 2727 1.064758 TGAGGGAGAGAGAGAGAGCAC 60.065 57.143 0.00 0.00 0.00 4.40
2683 2728 1.294041 TGAGGGAGAGAGAGAGAGCA 58.706 55.000 0.00 0.00 0.00 4.26
2684 2729 2.664402 ATGAGGGAGAGAGAGAGAGC 57.336 55.000 0.00 0.00 0.00 4.09
2685 2730 7.006509 AGAAAATATGAGGGAGAGAGAGAGAG 58.993 42.308 0.00 0.00 0.00 3.20
2686 2731 6.921412 AGAAAATATGAGGGAGAGAGAGAGA 58.079 40.000 0.00 0.00 0.00 3.10
2687 2732 7.601705 AAGAAAATATGAGGGAGAGAGAGAG 57.398 40.000 0.00 0.00 0.00 3.20
2688 2733 7.986553 AAAGAAAATATGAGGGAGAGAGAGA 57.013 36.000 0.00 0.00 0.00 3.10
2689 2734 9.541143 GTTAAAGAAAATATGAGGGAGAGAGAG 57.459 37.037 0.00 0.00 0.00 3.20
2690 2735 9.046846 TGTTAAAGAAAATATGAGGGAGAGAGA 57.953 33.333 0.00 0.00 0.00 3.10
2691 2736 9.323985 CTGTTAAAGAAAATATGAGGGAGAGAG 57.676 37.037 0.00 0.00 0.00 3.20
2692 2737 9.046846 TCTGTTAAAGAAAATATGAGGGAGAGA 57.953 33.333 0.00 0.00 29.54 3.10
2693 2738 9.672673 TTCTGTTAAAGAAAATATGAGGGAGAG 57.327 33.333 0.00 0.00 42.09 3.20


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

AutoCloner maintained by Alex Coulton.