Multiple sequence alignment - TraesCS1B01G397900

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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 TraesCS1B01G397900 chr1B 100.000 2513 0 0 1 2513 629091201 629093713 0.000000e+00 4641.0
1 TraesCS1B01G397900 chr1B 92.461 1963 129 8 1 1946 628810454 628812414 0.000000e+00 2787.0
2 TraesCS1B01G397900 chr1B 94.770 1415 64 8 1 1408 629052938 629054349 0.000000e+00 2194.0
3 TraesCS1B01G397900 chr1B 91.987 1535 88 15 1 1507 628993595 628995122 0.000000e+00 2121.0
4 TraesCS1B01G397900 chr1B 93.503 1416 81 9 1 1408 628917249 628918661 0.000000e+00 2095.0
5 TraesCS1B01G397900 chr1B 92.873 1319 81 3 640 1946 628975167 628976484 0.000000e+00 1903.0
6 TraesCS1B01G397900 chr1B 90.820 1329 92 9 640 1946 628856096 628857416 0.000000e+00 1751.0
7 TraesCS1B01G397900 chr1B 93.506 770 49 1 640 1408 628898949 628899718 0.000000e+00 1144.0
8 TraesCS1B01G397900 chr1B 87.444 900 93 13 25 920 628996743 628997626 0.000000e+00 1018.0
9 TraesCS1B01G397900 chr1B 87.111 900 96 13 25 920 628920421 628921304 0.000000e+00 1002.0
10 TraesCS1B01G397900 chr1B 86.222 900 104 13 25 920 629056106 629056989 0.000000e+00 957.0
11 TraesCS1B01G397900 chr1B 93.497 569 36 1 1378 1946 628899744 628900311 0.000000e+00 845.0
12 TraesCS1B01G397900 chr1B 85.907 518 51 4 1945 2440 8617135 8616618 1.320000e-147 532.0
13 TraesCS1B01G397900 chr1D 86.741 1976 149 51 1 1946 458272052 458273944 0.000000e+00 2093.0
14 TraesCS1B01G397900 chr1D 80.899 1513 196 55 4 1458 458206625 458208102 0.000000e+00 1107.0
15 TraesCS1B01G397900 chr1D 91.114 799 54 10 716 1506 458229790 458230579 0.000000e+00 1066.0
16 TraesCS1B01G397900 chr1D 86.827 539 45 7 1945 2458 341233343 341232806 1.680000e-161 579.0
17 TraesCS1B01G397900 chr1D 85.385 520 51 8 1945 2439 102828172 102828691 1.330000e-142 516.0
18 TraesCS1B01G397900 chr1D 80.775 645 84 18 1 618 458204486 458205117 3.780000e-128 468.0
19 TraesCS1B01G397900 chr1D 83.174 523 64 3 1945 2444 462094852 462095373 8.190000e-125 457.0
20 TraesCS1B01G397900 chr1D 95.775 71 3 0 2443 2513 458113965 458114035 5.680000e-22 115.0
21 TraesCS1B01G397900 chr1A 88.567 1417 108 14 1 1408 550792330 550793701 0.000000e+00 1670.0
22 TraesCS1B01G397900 chr1A 82.102 1989 214 75 4 1946 550823546 550825438 0.000000e+00 1570.0
23 TraesCS1B01G397900 chr1A 83.877 1501 180 37 468 1946 550654885 550656345 0.000000e+00 1375.0
24 TraesCS1B01G397900 chr1A 83.916 1287 155 34 669 1946 550695218 550696461 0.000000e+00 1182.0
25 TraesCS1B01G397900 chr1A 91.009 456 38 3 1492 1946 550669683 550670136 1.650000e-171 612.0
26 TraesCS1B01G397900 chr7D 86.293 518 48 5 1945 2439 104667794 104668311 2.200000e-150 542.0
27 TraesCS1B01G397900 chr7D 86.631 187 25 0 2258 2444 189174572 189174758 9.110000e-50 207.0
28 TraesCS1B01G397900 chr7D 90.141 71 7 0 2443 2513 12913100 12913170 2.660000e-15 93.5
29 TraesCS1B01G397900 chr3A 85.687 517 51 5 1945 2438 696473658 696474174 7.960000e-145 523.0
30 TraesCS1B01G397900 chr3A 80.344 524 77 11 1948 2447 565358783 565358262 8.490000e-100 374.0
31 TraesCS1B01G397900 chr3A 95.775 71 3 0 2443 2513 86383233 86383163 5.680000e-22 115.0
32 TraesCS1B01G397900 chr5D 85.164 519 50 11 1945 2439 433196161 433196676 8.020000e-140 507.0
33 TraesCS1B01G397900 chr3B 84.942 518 55 5 1945 2439 37980816 37980299 1.040000e-138 503.0
34 TraesCS1B01G397900 chr3B 84.749 518 56 3 1945 2439 405834467 405833950 4.830000e-137 497.0
35 TraesCS1B01G397900 chr3B 82.236 501 65 7 1945 2422 794366727 794367226 6.470000e-111 411.0
36 TraesCS1B01G397900 chr6D 84.720 517 57 5 1945 2439 207063740 207063224 4.830000e-137 497.0
37 TraesCS1B01G397900 chr6D 79.151 518 80 15 1945 2438 265310263 265309750 1.440000e-87 333.0
38 TraesCS1B01G397900 chr6D 87.324 71 9 0 2443 2513 15360910 15360980 5.760000e-12 82.4
39 TraesCS1B01G397900 chrUn 89.342 319 28 3 1945 2257 283974147 283973829 1.810000e-106 396.0
40 TraesCS1B01G397900 chr5A 84.195 329 34 4 2133 2444 516799918 516800245 1.130000e-78 303.0
41 TraesCS1B01G397900 chr7A 78.027 446 75 6 2022 2444 706342717 706342272 2.480000e-65 259.0
42 TraesCS1B01G397900 chr3D 97.183 71 2 0 2443 2513 26308410 26308340 1.220000e-23 121.0
43 TraesCS1B01G397900 chr3D 95.714 70 3 0 2444 2513 545791790 545791721 2.040000e-21 113.0
44 TraesCS1B01G397900 chr2D 92.958 71 5 0 2443 2513 150912820 150912750 1.230000e-18 104.0
45 TraesCS1B01G397900 chr6B 92.958 71 4 1 2443 2513 73180178 73180247 4.420000e-18 102.0
46 TraesCS1B01G397900 chr4B 90.000 70 7 0 2443 2512 567437765 567437834 9.570000e-15 91.6


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 TraesCS1B01G397900 chr1B 629091201 629093713 2512 False 4641.0 4641 100.0000 1 2513 1 chr1B.!!$F4 2512
1 TraesCS1B01G397900 chr1B 628810454 628812414 1960 False 2787.0 2787 92.4610 1 1946 1 chr1B.!!$F1 1945
2 TraesCS1B01G397900 chr1B 628975167 628976484 1317 False 1903.0 1903 92.8730 640 1946 1 chr1B.!!$F3 1306
3 TraesCS1B01G397900 chr1B 628856096 628857416 1320 False 1751.0 1751 90.8200 640 1946 1 chr1B.!!$F2 1306
4 TraesCS1B01G397900 chr1B 629052938 629056989 4051 False 1575.5 2194 90.4960 1 1408 2 chr1B.!!$F8 1407
5 TraesCS1B01G397900 chr1B 628993595 628997626 4031 False 1569.5 2121 89.7155 1 1507 2 chr1B.!!$F7 1506
6 TraesCS1B01G397900 chr1B 628917249 628921304 4055 False 1548.5 2095 90.3070 1 1408 2 chr1B.!!$F6 1407
7 TraesCS1B01G397900 chr1B 628898949 628900311 1362 False 994.5 1144 93.5015 640 1946 2 chr1B.!!$F5 1306
8 TraesCS1B01G397900 chr1B 8616618 8617135 517 True 532.0 532 85.9070 1945 2440 1 chr1B.!!$R1 495
9 TraesCS1B01G397900 chr1D 458272052 458273944 1892 False 2093.0 2093 86.7410 1 1946 1 chr1D.!!$F4 1945
10 TraesCS1B01G397900 chr1D 458229790 458230579 789 False 1066.0 1066 91.1140 716 1506 1 chr1D.!!$F3 790
11 TraesCS1B01G397900 chr1D 458204486 458208102 3616 False 787.5 1107 80.8370 1 1458 2 chr1D.!!$F6 1457
12 TraesCS1B01G397900 chr1D 341232806 341233343 537 True 579.0 579 86.8270 1945 2458 1 chr1D.!!$R1 513
13 TraesCS1B01G397900 chr1D 102828172 102828691 519 False 516.0 516 85.3850 1945 2439 1 chr1D.!!$F1 494
14 TraesCS1B01G397900 chr1D 462094852 462095373 521 False 457.0 457 83.1740 1945 2444 1 chr1D.!!$F5 499
15 TraesCS1B01G397900 chr1A 550792330 550793701 1371 False 1670.0 1670 88.5670 1 1408 1 chr1A.!!$F4 1407
16 TraesCS1B01G397900 chr1A 550823546 550825438 1892 False 1570.0 1570 82.1020 4 1946 1 chr1A.!!$F5 1942
17 TraesCS1B01G397900 chr1A 550654885 550656345 1460 False 1375.0 1375 83.8770 468 1946 1 chr1A.!!$F1 1478
18 TraesCS1B01G397900 chr1A 550695218 550696461 1243 False 1182.0 1182 83.9160 669 1946 1 chr1A.!!$F3 1277
19 TraesCS1B01G397900 chr7D 104667794 104668311 517 False 542.0 542 86.2930 1945 2439 1 chr7D.!!$F2 494
20 TraesCS1B01G397900 chr3A 696473658 696474174 516 False 523.0 523 85.6870 1945 2438 1 chr3A.!!$F1 493
21 TraesCS1B01G397900 chr3A 565358262 565358783 521 True 374.0 374 80.3440 1948 2447 1 chr3A.!!$R2 499
22 TraesCS1B01G397900 chr5D 433196161 433196676 515 False 507.0 507 85.1640 1945 2439 1 chr5D.!!$F1 494
23 TraesCS1B01G397900 chr3B 37980299 37980816 517 True 503.0 503 84.9420 1945 2439 1 chr3B.!!$R1 494
24 TraesCS1B01G397900 chr3B 405833950 405834467 517 True 497.0 497 84.7490 1945 2439 1 chr3B.!!$R2 494
25 TraesCS1B01G397900 chr6D 207063224 207063740 516 True 497.0 497 84.7200 1945 2439 1 chr6D.!!$R1 494
26 TraesCS1B01G397900 chr6D 265309750 265310263 513 True 333.0 333 79.1510 1945 2438 1 chr6D.!!$R2 493

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
27 30 0.243636 GTTTTCAATGGGTGGCGAGG 59.756 55.0 0.00 0.0 0.0 4.63 F
478 2618 0.450583 TACGAGCGGTCACTAAGCAG 59.549 55.0 15.89 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 3495 0.105964 CCCTCCAGTAGAGCTGCCTA 60.106 60.0 0.00 0.00 43.71 3.93 R
1802 5555 0.107897 TTCAGTCCCAATATGCGCGT 60.108 50.0 8.43 7.55 0.00 6.01 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
27 30 0.243636 GTTTTCAATGGGTGGCGAGG 59.756 55.000 0.00 0.00 0.00 4.63
61 64 0.749454 ATGCAGCCATCCGTTCTTCC 60.749 55.000 0.00 0.00 0.00 3.46
62 65 1.377202 GCAGCCATCCGTTCTTCCA 60.377 57.895 0.00 0.00 0.00 3.53
202 213 2.166459 CAGAGACGAAGGGCAACAGATA 59.834 50.000 0.00 0.00 39.74 1.98
300 327 4.222810 TGCTAGATCTGTACAAAAGCCTGA 59.777 41.667 5.18 0.00 0.00 3.86
402 2539 6.413052 CATCATCTTTCTTCTTCTTCTCCCA 58.587 40.000 0.00 0.00 0.00 4.37
478 2618 0.450583 TACGAGCGGTCACTAAGCAG 59.549 55.000 15.89 0.00 0.00 4.24
603 2751 1.845809 CGAACCTGAGCACCAGCAAC 61.846 60.000 1.06 0.00 45.49 4.17
685 2871 2.714259 GTGGCAAGCACCAACACTA 58.286 52.632 0.00 0.00 42.70 2.74
844 3052 4.744237 ACTGTAGGGTGTGTAGTTTAGGA 58.256 43.478 0.00 0.00 0.00 2.94
861 3069 1.551883 AGGATGGCAATGGCAAAAGAC 59.448 47.619 14.81 2.69 42.43 3.01
1010 3263 2.565210 TCCGCGAGCTTATAAAACGA 57.435 45.000 8.23 0.00 0.00 3.85
1189 3445 1.144057 CGGAAGATGACGGAAGGGG 59.856 63.158 0.00 0.00 0.00 4.79
1190 3446 1.527370 GGAAGATGACGGAAGGGGG 59.473 63.158 0.00 0.00 0.00 5.40
1326 3585 3.173151 TGACATCAAGAGCTACTCCCAA 58.827 45.455 0.00 0.00 0.00 4.12
1369 3632 1.596477 GCCCATCGCCTCTAGCAAG 60.596 63.158 0.00 0.00 44.04 4.01
1374 3637 0.687757 ATCGCCTCTAGCAAGACCCA 60.688 55.000 0.00 0.00 44.04 4.51
1465 3812 1.795286 CTGGAGAGTTTGAAGTGTCGC 59.205 52.381 0.00 0.00 0.00 5.19
1663 4015 2.186826 AAGCCGTCACTTGCCACAC 61.187 57.895 0.00 0.00 0.00 3.82
1736 5296 3.184683 CGGTGCTTCTCTCGCTGC 61.185 66.667 0.00 0.00 0.00 5.25
1737 5297 2.264166 GGTGCTTCTCTCGCTGCT 59.736 61.111 0.00 0.00 0.00 4.24
1767 5448 9.565213 GTCATTTTATTCTTGAGATGAAACCAG 57.435 33.333 0.00 0.00 0.00 4.00
1778 5459 6.822442 TGAGATGAAACCAGTGTAGTGTTAA 58.178 36.000 0.00 0.00 0.00 2.01
1852 6230 3.788797 GCGATGTTAATTTTCAGGAGGCG 60.789 47.826 0.00 0.00 0.00 5.52
1879 6306 6.471942 TTTGGAACCCTCCCTTATAAAAGA 57.528 37.500 0.00 0.00 41.64 2.52
1885 6312 9.078990 GGAACCCTCCCTTATAAAAGATTATTG 57.921 37.037 0.00 0.00 35.42 1.90
1927 6355 8.525290 ACCATGAGATTAAAACTTATCCCTTG 57.475 34.615 0.00 0.00 0.00 3.61
2042 6470 8.480501 AGTAGGAAGTGTAGTTTTTGTACTCAA 58.519 33.333 0.00 0.00 0.00 3.02
2137 6565 3.886505 TCCAATTTGTATCCGCCCATAAC 59.113 43.478 0.00 0.00 0.00 1.89
2179 6613 6.313658 GGTCATTGGTTGAATTTCAAATAGGC 59.686 38.462 13.21 1.33 38.22 3.93
2261 6713 7.373493 AGAAATGATTTGATTTTCGAGTTGCT 58.627 30.769 0.00 0.00 35.14 3.91
2299 6751 1.438651 GCACTTGCTTCGTACATGGA 58.561 50.000 0.00 0.00 38.21 3.41
2300 6752 2.009774 GCACTTGCTTCGTACATGGAT 58.990 47.619 0.00 0.00 38.21 3.41
2440 6894 2.359900 CACCTCCTTCAACATAGGCAC 58.640 52.381 0.00 0.00 32.59 5.01
2447 6901 4.469586 TCCTTCAACATAGGCACAGTATCA 59.530 41.667 0.00 0.00 32.59 2.15
2448 6902 5.130975 TCCTTCAACATAGGCACAGTATCAT 59.869 40.000 0.00 0.00 32.59 2.45
2452 6906 5.104569 TCAACATAGGCACAGTATCATTCCA 60.105 40.000 0.00 0.00 0.00 3.53
2453 6907 5.573380 ACATAGGCACAGTATCATTCCAT 57.427 39.130 0.00 0.00 0.00 3.41
2455 6909 5.766670 ACATAGGCACAGTATCATTCCATTG 59.233 40.000 0.00 0.00 0.00 2.82
2456 6910 4.508551 AGGCACAGTATCATTCCATTGA 57.491 40.909 0.00 0.00 0.00 2.57
2457 6911 5.057843 AGGCACAGTATCATTCCATTGAT 57.942 39.130 0.00 0.00 39.60 2.57
2459 6913 6.236409 AGGCACAGTATCATTCCATTGATAG 58.764 40.000 0.00 0.00 38.83 2.08
2460 6914 6.043590 AGGCACAGTATCATTCCATTGATAGA 59.956 38.462 0.00 0.00 38.83 1.98
2461 6915 6.712095 GGCACAGTATCATTCCATTGATAGAA 59.288 38.462 0.00 0.00 38.83 2.10
2462 6916 7.094890 GGCACAGTATCATTCCATTGATAGAAG 60.095 40.741 0.00 0.00 38.83 2.85
2463 6917 7.094890 GCACAGTATCATTCCATTGATAGAAGG 60.095 40.741 0.00 0.00 38.83 3.46
2464 6918 8.152898 CACAGTATCATTCCATTGATAGAAGGA 58.847 37.037 0.00 0.00 38.83 3.36
2465 6919 8.373981 ACAGTATCATTCCATTGATAGAAGGAG 58.626 37.037 0.00 0.00 38.83 3.69
2466 6920 8.373981 CAGTATCATTCCATTGATAGAAGGAGT 58.626 37.037 0.00 0.00 38.83 3.85
2467 6921 8.943085 AGTATCATTCCATTGATAGAAGGAGTT 58.057 33.333 0.00 0.00 38.83 3.01
2470 6924 7.739825 TCATTCCATTGATAGAAGGAGTTAGG 58.260 38.462 0.00 0.00 30.08 2.69
2471 6925 7.568738 TCATTCCATTGATAGAAGGAGTTAGGA 59.431 37.037 0.00 0.00 30.08 2.94
2472 6926 6.732896 TCCATTGATAGAAGGAGTTAGGAC 57.267 41.667 0.00 0.00 0.00 3.85
2473 6927 6.202331 TCCATTGATAGAAGGAGTTAGGACA 58.798 40.000 0.00 0.00 0.00 4.02
2474 6928 6.672218 TCCATTGATAGAAGGAGTTAGGACAA 59.328 38.462 0.00 0.00 0.00 3.18
2475 6929 6.989169 CCATTGATAGAAGGAGTTAGGACAAG 59.011 42.308 0.00 0.00 0.00 3.16
2476 6930 7.365117 CCATTGATAGAAGGAGTTAGGACAAGT 60.365 40.741 0.00 0.00 0.00 3.16
2477 6931 8.696374 CATTGATAGAAGGAGTTAGGACAAGTA 58.304 37.037 0.00 0.00 0.00 2.24
2478 6932 7.642082 TGATAGAAGGAGTTAGGACAAGTAC 57.358 40.000 0.00 0.00 0.00 2.73
2479 6933 7.179966 TGATAGAAGGAGTTAGGACAAGTACA 58.820 38.462 0.00 0.00 0.00 2.90
2480 6934 7.672660 TGATAGAAGGAGTTAGGACAAGTACAA 59.327 37.037 0.00 0.00 0.00 2.41
2481 6935 6.347859 AGAAGGAGTTAGGACAAGTACAAG 57.652 41.667 0.00 0.00 0.00 3.16
2482 6936 6.075984 AGAAGGAGTTAGGACAAGTACAAGA 58.924 40.000 0.00 0.00 0.00 3.02
2483 6937 6.553852 AGAAGGAGTTAGGACAAGTACAAGAA 59.446 38.462 0.00 0.00 0.00 2.52
2484 6938 6.347859 AGGAGTTAGGACAAGTACAAGAAG 57.652 41.667 0.00 0.00 0.00 2.85
2485 6939 5.839606 AGGAGTTAGGACAAGTACAAGAAGT 59.160 40.000 0.00 0.00 0.00 3.01
2486 6940 5.927115 GGAGTTAGGACAAGTACAAGAAGTG 59.073 44.000 0.00 0.00 0.00 3.16
2487 6941 5.855045 AGTTAGGACAAGTACAAGAAGTGG 58.145 41.667 0.00 0.00 0.00 4.00
2488 6942 5.365895 AGTTAGGACAAGTACAAGAAGTGGT 59.634 40.000 0.00 0.00 0.00 4.16
2489 6943 6.552350 AGTTAGGACAAGTACAAGAAGTGGTA 59.448 38.462 0.00 0.00 0.00 3.25
2490 6944 5.211174 AGGACAAGTACAAGAAGTGGTAC 57.789 43.478 0.00 0.00 40.06 3.34
2491 6945 4.652421 AGGACAAGTACAAGAAGTGGTACA 59.348 41.667 0.00 0.00 41.74 2.90
2492 6946 5.129815 AGGACAAGTACAAGAAGTGGTACAA 59.870 40.000 0.00 0.00 44.16 2.41
2493 6947 5.235831 GGACAAGTACAAGAAGTGGTACAAC 59.764 44.000 0.00 0.00 44.16 3.32
2494 6948 5.736813 ACAAGTACAAGAAGTGGTACAACA 58.263 37.500 2.54 0.00 44.16 3.33
2495 6949 5.583457 ACAAGTACAAGAAGTGGTACAACAC 59.417 40.000 2.54 0.00 44.16 3.32
2496 6950 5.347620 AGTACAAGAAGTGGTACAACACA 57.652 39.130 2.54 0.00 44.16 3.72
2497 6951 5.925509 AGTACAAGAAGTGGTACAACACAT 58.074 37.500 2.54 0.00 44.16 3.21
2498 6952 5.758296 AGTACAAGAAGTGGTACAACACATG 59.242 40.000 2.54 2.66 44.16 3.21
2499 6953 4.776349 ACAAGAAGTGGTACAACACATGA 58.224 39.130 2.54 0.00 44.16 3.07
2500 6954 4.574828 ACAAGAAGTGGTACAACACATGAC 59.425 41.667 2.54 0.00 44.16 3.06
2501 6955 4.415881 AGAAGTGGTACAACACATGACA 57.584 40.909 2.54 0.00 44.16 3.58
2502 6956 4.127171 AGAAGTGGTACAACACATGACAC 58.873 43.478 2.54 0.00 44.16 3.67
2503 6957 2.479837 AGTGGTACAACACATGACACG 58.520 47.619 2.54 0.00 44.16 4.49
2504 6958 1.529438 GTGGTACAACACATGACACGG 59.471 52.381 0.00 0.00 44.16 4.94
2505 6959 1.413077 TGGTACAACACATGACACGGA 59.587 47.619 0.00 0.00 31.92 4.69
2506 6960 1.796459 GGTACAACACATGACACGGAC 59.204 52.381 0.00 0.00 0.00 4.79
2507 6961 1.454276 GTACAACACATGACACGGACG 59.546 52.381 0.00 0.00 0.00 4.79
2508 6962 1.204062 CAACACATGACACGGACGC 59.796 57.895 0.00 0.00 0.00 5.19
2509 6963 1.227409 AACACATGACACGGACGCA 60.227 52.632 0.00 0.00 0.00 5.24
2510 6964 0.812014 AACACATGACACGGACGCAA 60.812 50.000 0.00 0.00 0.00 4.85
2512 6966 1.667830 ACATGACACGGACGCAAGG 60.668 57.895 0.00 0.00 46.39 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 30 1.400846 CTGCATGCACACAGATTCTCC 59.599 52.381 18.46 0.00 35.90 3.71
202 213 3.227250 GCCAGTACCTACCGGCAT 58.773 61.111 0.00 0.00 46.50 4.40
264 276 9.587772 GTACAGATCTAGCATTTTCAACTTCTA 57.412 33.333 0.00 0.00 0.00 2.10
283 295 5.189736 TGAGGTATCAGGCTTTTGTACAGAT 59.810 40.000 0.00 0.00 0.00 2.90
349 379 0.665068 TGACGCTTTACACGCACGAT 60.665 50.000 0.00 0.00 0.00 3.73
466 2606 0.737715 CGTGCTCCTGCTTAGTGACC 60.738 60.000 0.00 0.00 40.48 4.02
478 2618 0.889186 ATGTTGGAACCACGTGCTCC 60.889 55.000 21.88 21.88 0.00 4.70
603 2751 1.480137 AGAGAAGAAGCACTGGATCGG 59.520 52.381 0.00 0.00 0.00 4.18
685 2871 0.106819 GCTTGAGGCATCCATCCACT 60.107 55.000 0.00 0.00 41.35 4.00
844 3052 0.390209 GCGTCTTTTGCCATTGCCAT 60.390 50.000 0.00 0.00 36.33 4.40
861 3069 1.632422 GCAAAATCACATTCCAGGCG 58.368 50.000 0.00 0.00 0.00 5.52
1236 3495 0.105964 CCCTCCAGTAGAGCTGCCTA 60.106 60.000 0.00 0.00 43.71 3.93
1369 3632 3.056465 AGAAGAAGAAGACGATGTGGGTC 60.056 47.826 0.00 0.00 34.62 4.46
1374 3637 6.339587 AGAAGAAGAAGAAGAAGACGATGT 57.660 37.500 0.00 0.00 0.00 3.06
1663 4015 8.195436 ACATAAATTGCTGAAATCTCATTCCAG 58.805 33.333 0.00 0.00 0.00 3.86
1736 5296 5.801350 TCTCAAGAATAAAATGACCGCAG 57.199 39.130 0.00 0.00 0.00 5.18
1737 5297 5.879777 TCATCTCAAGAATAAAATGACCGCA 59.120 36.000 0.00 0.00 0.00 5.69
1740 5300 8.522830 TGGTTTCATCTCAAGAATAAAATGACC 58.477 33.333 0.00 0.00 0.00 4.02
1767 5448 6.812160 AGCTTAGCTACACATTAACACTACAC 59.188 38.462 4.30 0.00 36.99 2.90
1778 5459 7.382488 CGTATATCAAACAGCTTAGCTACACAT 59.618 37.037 6.35 0.00 36.40 3.21
1802 5555 0.107897 TTCAGTCCCAATATGCGCGT 60.108 50.000 8.43 7.55 0.00 6.01
1852 6230 4.797912 ATAAGGGAGGGTTCCAAATCTC 57.202 45.455 0.00 0.00 45.98 2.75
1885 6312 8.492673 TCTCATGGTTGATCTACATACAAAAC 57.507 34.615 9.51 0.00 0.00 2.43
1902 6329 7.561356 CCAAGGGATAAGTTTTAATCTCATGGT 59.439 37.037 0.00 0.00 36.92 3.55
1904 6331 8.752005 TCCAAGGGATAAGTTTTAATCTCATG 57.248 34.615 0.00 0.00 0.00 3.07
1963 6391 4.360951 TTGGTTAGTACAACTCCCCTTG 57.639 45.455 0.00 0.00 0.00 3.61
2020 6448 6.512903 GCCTTGAGTACAAAAACTACACTTCC 60.513 42.308 0.00 0.00 35.49 3.46
2137 6565 7.818930 ACCAATGACCAAAAATATTAGCAACAG 59.181 33.333 0.00 0.00 0.00 3.16
2179 6613 3.574614 CCACCCAAATTAGCGTTTTGAG 58.425 45.455 9.66 1.25 36.40 3.02
2261 6713 4.272991 AGTGCGTACAACGAAAAATAACCA 59.727 37.500 6.38 0.00 46.05 3.67
2299 6751 6.322969 TGATACTCCATTCGGTGTAGTGTAAT 59.677 38.462 0.00 0.00 42.86 1.89
2300 6752 5.653330 TGATACTCCATTCGGTGTAGTGTAA 59.347 40.000 0.00 0.00 42.86 2.41
2397 6851 2.172505 TGCACCAATCCGGAGATTATGT 59.827 45.455 11.34 0.00 40.89 2.29
2440 6894 8.373981 ACTCCTTCTATCAATGGAATGATACTG 58.626 37.037 0.00 0.00 40.44 2.74
2447 6901 7.348274 TGTCCTAACTCCTTCTATCAATGGAAT 59.652 37.037 0.00 0.00 0.00 3.01
2448 6902 6.672218 TGTCCTAACTCCTTCTATCAATGGAA 59.328 38.462 0.00 0.00 0.00 3.53
2452 6906 7.741554 ACTTGTCCTAACTCCTTCTATCAAT 57.258 36.000 0.00 0.00 0.00 2.57
2453 6907 7.672660 TGTACTTGTCCTAACTCCTTCTATCAA 59.327 37.037 0.00 0.00 0.00 2.57
2455 6909 7.642082 TGTACTTGTCCTAACTCCTTCTATC 57.358 40.000 0.00 0.00 0.00 2.08
2456 6910 7.894364 TCTTGTACTTGTCCTAACTCCTTCTAT 59.106 37.037 0.00 0.00 0.00 1.98
2457 6911 7.236529 TCTTGTACTTGTCCTAACTCCTTCTA 58.763 38.462 0.00 0.00 0.00 2.10
2459 6913 6.342338 TCTTGTACTTGTCCTAACTCCTTC 57.658 41.667 0.00 0.00 0.00 3.46
2460 6914 6.326843 ACTTCTTGTACTTGTCCTAACTCCTT 59.673 38.462 0.00 0.00 0.00 3.36
2461 6915 5.839606 ACTTCTTGTACTTGTCCTAACTCCT 59.160 40.000 0.00 0.00 0.00 3.69
2462 6916 5.927115 CACTTCTTGTACTTGTCCTAACTCC 59.073 44.000 0.00 0.00 0.00 3.85
2463 6917 5.927115 CCACTTCTTGTACTTGTCCTAACTC 59.073 44.000 0.00 0.00 0.00 3.01
2464 6918 5.365895 ACCACTTCTTGTACTTGTCCTAACT 59.634 40.000 0.00 0.00 0.00 2.24
2465 6919 5.608449 ACCACTTCTTGTACTTGTCCTAAC 58.392 41.667 0.00 0.00 0.00 2.34
2466 6920 5.881923 ACCACTTCTTGTACTTGTCCTAA 57.118 39.130 0.00 0.00 0.00 2.69
2467 6921 5.834742 TGTACCACTTCTTGTACTTGTCCTA 59.165 40.000 0.00 0.00 38.48 2.94
2468 6922 4.652421 TGTACCACTTCTTGTACTTGTCCT 59.348 41.667 0.00 0.00 38.48 3.85
2469 6923 4.952460 TGTACCACTTCTTGTACTTGTCC 58.048 43.478 0.00 0.00 38.48 4.02
2470 6924 5.813672 TGTTGTACCACTTCTTGTACTTGTC 59.186 40.000 0.00 0.00 38.48 3.18
2471 6925 5.583457 GTGTTGTACCACTTCTTGTACTTGT 59.417 40.000 0.00 0.00 38.48 3.16
2472 6926 5.583061 TGTGTTGTACCACTTCTTGTACTTG 59.417 40.000 0.00 0.00 38.48 3.16
2473 6927 5.736813 TGTGTTGTACCACTTCTTGTACTT 58.263 37.500 0.00 0.00 38.48 2.24
2474 6928 5.347620 TGTGTTGTACCACTTCTTGTACT 57.652 39.130 0.00 0.00 38.48 2.73
2475 6929 5.756347 TCATGTGTTGTACCACTTCTTGTAC 59.244 40.000 0.00 0.00 38.22 2.90
2476 6930 5.756347 GTCATGTGTTGTACCACTTCTTGTA 59.244 40.000 0.00 0.00 36.30 2.41
2477 6931 4.574828 GTCATGTGTTGTACCACTTCTTGT 59.425 41.667 0.00 0.00 36.30 3.16
2478 6932 4.574421 TGTCATGTGTTGTACCACTTCTTG 59.426 41.667 0.00 1.90 36.30 3.02
2479 6933 4.574828 GTGTCATGTGTTGTACCACTTCTT 59.425 41.667 0.00 0.00 36.30 2.52
2480 6934 4.127171 GTGTCATGTGTTGTACCACTTCT 58.873 43.478 0.00 0.00 36.30 2.85
2481 6935 3.059868 CGTGTCATGTGTTGTACCACTTC 60.060 47.826 0.00 0.00 36.30 3.01
2482 6936 2.869801 CGTGTCATGTGTTGTACCACTT 59.130 45.455 0.00 0.00 36.30 3.16
2483 6937 2.479837 CGTGTCATGTGTTGTACCACT 58.520 47.619 0.00 0.00 36.30 4.00
2484 6938 1.529438 CCGTGTCATGTGTTGTACCAC 59.471 52.381 0.00 0.00 35.86 4.16
2485 6939 1.413077 TCCGTGTCATGTGTTGTACCA 59.587 47.619 0.00 0.00 0.00 3.25
2486 6940 1.796459 GTCCGTGTCATGTGTTGTACC 59.204 52.381 0.00 0.00 0.00 3.34
2487 6941 1.454276 CGTCCGTGTCATGTGTTGTAC 59.546 52.381 0.00 0.00 0.00 2.90
2488 6942 1.773410 CGTCCGTGTCATGTGTTGTA 58.227 50.000 0.00 0.00 0.00 2.41
2489 6943 1.495584 GCGTCCGTGTCATGTGTTGT 61.496 55.000 0.00 0.00 0.00 3.32
2490 6944 1.204062 GCGTCCGTGTCATGTGTTG 59.796 57.895 0.00 0.00 0.00 3.33
2491 6945 0.812014 TTGCGTCCGTGTCATGTGTT 60.812 50.000 0.00 0.00 0.00 3.32
2492 6946 1.221466 CTTGCGTCCGTGTCATGTGT 61.221 55.000 0.00 0.00 0.00 3.72
2493 6947 1.492873 CTTGCGTCCGTGTCATGTG 59.507 57.895 0.00 0.00 0.00 3.21
2494 6948 1.667830 CCTTGCGTCCGTGTCATGT 60.668 57.895 0.00 0.00 0.00 3.21
2495 6949 3.168271 CCTTGCGTCCGTGTCATG 58.832 61.111 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.