Multiple sequence alignment - TraesCS6B01G443600

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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 TraesCS6B01G443600 chr6B 100.000 8583 0 0 1 8583 706581836 706590418 0.000000e+00 15850.0
1 TraesCS6B01G443600 chr6B 97.744 7137 110 14 1322 8441 706468790 706475892 0.000000e+00 12240.0
2 TraesCS6B01G443600 chr6B 91.010 901 53 13 446 1330 706463193 706464081 0.000000e+00 1190.0
3 TraesCS6B01G443600 chr6B 90.993 544 24 8 888 1417 624609938 624609406 0.000000e+00 710.0
4 TraesCS6B01G443600 chr6B 87.414 437 45 3 7135 7565 706632141 706632573 2.150000e-135 494.0
5 TraesCS6B01G443600 chr6B 95.862 145 5 1 8440 8583 662147516 662147372 5.180000e-57 233.0
6 TraesCS6B01G443600 chr6B 96.454 141 5 0 8440 8580 706475928 706476068 5.180000e-57 233.0
7 TraesCS6B01G443600 chr6B 96.454 141 5 0 8440 8580 719751774 719751914 5.180000e-57 233.0
8 TraesCS6B01G443600 chr6B 87.368 95 8 3 7188 7282 706632572 706632662 1.180000e-18 106.0
9 TraesCS6B01G443600 chr6B 91.781 73 6 0 2 74 81664531 81664603 1.520000e-17 102.0
10 TraesCS6B01G443600 chr6B 98.148 54 1 0 1363 1416 706464144 706464197 2.550000e-15 95.3
11 TraesCS6B01G443600 chr6B 90.000 70 4 2 1204 1273 706466985 706467051 4.270000e-13 87.9
12 TraesCS6B01G443600 chr6B 97.959 49 1 0 766 814 624609944 624609992 1.540000e-12 86.1
13 TraesCS6B01G443600 chr6A 88.613 2178 191 29 6212 8361 609845208 609847356 0.000000e+00 2595.0
14 TraesCS6B01G443600 chr6A 92.097 1860 117 8 1295 3135 609840106 609841954 0.000000e+00 2593.0
15 TraesCS6B01G443600 chr6A 86.634 1429 112 46 3855 5264 609842393 609843761 0.000000e+00 1507.0
16 TraesCS6B01G443600 chr6A 88.681 857 73 13 5261 6100 609843980 609844829 0.000000e+00 1024.0
17 TraesCS6B01G443600 chr6A 87.865 857 78 14 2 848 609830111 609830951 0.000000e+00 983.0
18 TraesCS6B01G443600 chr6A 83.529 850 92 19 3024 3862 609978206 609979018 0.000000e+00 750.0
19 TraesCS6B01G443600 chr6A 87.500 512 40 9 837 1330 609836645 609837150 3.480000e-158 569.0
20 TraesCS6B01G443600 chr6A 88.249 434 33 7 3438 3863 609841951 609842374 3.580000e-138 503.0
21 TraesCS6B01G443600 chr6A 98.630 73 1 0 2 74 46766434 46766362 6.990000e-26 130.0
22 TraesCS6B01G443600 chr6A 98.113 53 1 0 1363 1415 609837215 609837267 9.170000e-15 93.5
23 TraesCS6B01G443600 chr6A 91.429 70 3 2 1204 1273 609840041 609840107 9.170000e-15 93.5
24 TraesCS6B01G443600 chr6D 81.779 933 118 21 2684 3593 463221404 463222307 0.000000e+00 734.0
25 TraesCS6B01G443600 chr6D 86.405 662 60 16 2 653 463218698 463219339 0.000000e+00 697.0
26 TraesCS6B01G443600 chr6D 84.501 471 51 11 4919 5381 463222632 463223088 6.110000e-121 446.0
27 TraesCS6B01G443600 chr6D 87.234 235 30 0 7315 7549 463459863 463460097 1.420000e-67 268.0
28 TraesCS6B01G443600 chr6D 79.845 258 28 8 4300 4543 463222304 463222551 5.330000e-37 167.0
29 TraesCS6B01G443600 chr6D 90.411 73 7 0 2630 2702 405759160 405759088 7.090000e-16 97.1
30 TraesCS6B01G443600 chr7D 89.277 401 35 6 4984 5382 369462216 369461822 5.980000e-136 496.0
31 TraesCS6B01G443600 chr7D 87.179 273 25 5 5421 5692 369461837 369461574 1.400000e-77 302.0
32 TraesCS6B01G443600 chr7D 82.692 156 24 3 309 463 510005661 510005508 1.500000e-27 135.0
33 TraesCS6B01G443600 chr7D 90.196 102 7 1 2333 2431 369461561 369461460 6.990000e-26 130.0
34 TraesCS6B01G443600 chr7D 100.000 36 0 0 8406 8441 412474780 412474745 5.560000e-07 67.6
35 TraesCS6B01G443600 chr7B 89.796 392 31 6 4995 5382 315732678 315732292 2.150000e-135 494.0
36 TraesCS6B01G443600 chr7B 83.937 442 32 16 5709 6129 315731985 315731562 3.760000e-103 387.0
37 TraesCS6B01G443600 chr7B 95.745 141 6 0 8440 8580 548371769 548371909 2.410000e-55 228.0
38 TraesCS6B01G443600 chr7B 100.000 36 0 0 8406 8441 612083660 612083695 5.560000e-07 67.6
39 TraesCS6B01G443600 chr7A 87.817 394 29 11 4992 5382 411528600 411528977 2.200000e-120 444.0
40 TraesCS6B01G443600 chr7A 83.784 444 33 18 5707 6129 411529280 411529705 1.350000e-102 385.0
41 TraesCS6B01G443600 chr7A 87.546 273 24 5 5421 5692 411528962 411529225 3.010000e-79 307.0
42 TraesCS6B01G443600 chr7A 83.772 228 35 2 7508 7734 194057731 194057957 1.880000e-51 215.0
43 TraesCS6B01G443600 chr7A 90.196 102 7 1 2333 2431 411529238 411529339 6.990000e-26 130.0
44 TraesCS6B01G443600 chr7A 86.275 102 12 2 7513 7613 680338748 680338648 9.110000e-20 110.0
45 TraesCS6B01G443600 chr1D 79.535 430 67 19 181 601 109081926 109082343 3.920000e-73 287.0
46 TraesCS6B01G443600 chr1D 84.674 261 40 0 7518 7778 394456100 394456360 2.380000e-65 261.0
47 TraesCS6B01G443600 chr1D 82.745 255 42 2 2847 3100 462743222 462742969 8.670000e-55 226.0
48 TraesCS6B01G443600 chr1D 77.880 217 28 12 2090 2286 462744791 462744575 5.440000e-22 117.0
49 TraesCS6B01G443600 chr1D 85.088 114 15 2 2453 2565 462744347 462744235 1.960000e-21 115.0
50 TraesCS6B01G443600 chr1D 90.411 73 7 0 2630 2702 89984874 89984802 7.090000e-16 97.1
51 TraesCS6B01G443600 chr1D 90.411 73 7 0 2627 2699 261887233 261887305 7.090000e-16 97.1
52 TraesCS6B01G443600 chr5A 86.038 265 37 0 7514 7778 52281152 52281416 1.410000e-72 285.0
53 TraesCS6B01G443600 chr5A 78.906 384 61 18 187 557 12149664 12149288 8.610000e-60 243.0
54 TraesCS6B01G443600 chr1B 85.019 267 39 1 7518 7784 279904491 279904756 3.950000e-68 270.0
55 TraesCS6B01G443600 chr1B 81.148 122 20 3 2436 2556 637831132 637831013 2.550000e-15 95.3
56 TraesCS6B01G443600 chr1B 88.235 68 6 2 1503 1569 637832602 637832536 7.140000e-11 80.5
57 TraesCS6B01G443600 chr2D 84.848 264 39 1 7516 7778 76002727 76002990 1.840000e-66 265.0
58 TraesCS6B01G443600 chr2D 100.000 36 0 0 8406 8441 566983576 566983541 5.560000e-07 67.6
59 TraesCS6B01G443600 chr5D 80.163 368 56 14 197 553 519804745 519804384 8.550000e-65 259.0
60 TraesCS6B01G443600 chr5D 78.846 312 51 12 175 476 357609908 357610214 6.800000e-46 196.0
61 TraesCS6B01G443600 chr5D 74.793 484 81 33 174 640 538155741 538156200 6.850000e-41 180.0
62 TraesCS6B01G443600 chr5D 76.703 279 54 7 7509 7777 447395611 447395334 2.500000e-30 145.0
63 TraesCS6B01G443600 chr5D 90.411 73 7 0 2630 2702 40677264 40677192 7.090000e-16 97.1
64 TraesCS6B01G443600 chr3A 84.074 270 41 2 7510 7778 179503211 179502943 8.550000e-65 259.0
65 TraesCS6B01G443600 chr3A 84.411 263 40 1 7516 7778 429624787 429625048 3.070000e-64 257.0
66 TraesCS6B01G443600 chr5B 81.231 325 49 11 183 499 654760100 654759780 1.430000e-62 252.0
67 TraesCS6B01G443600 chr5B 96.454 141 5 0 8440 8580 614364205 614364345 5.180000e-57 233.0
68 TraesCS6B01G443600 chr5B 100.000 36 0 0 8406 8441 358896332 358896367 5.560000e-07 67.6
69 TraesCS6B01G443600 chr1A 83.835 266 40 3 7516 7778 82734224 82734489 5.140000e-62 250.0
70 TraesCS6B01G443600 chr1A 77.880 217 28 12 2090 2286 554533369 554533153 5.440000e-22 117.0
71 TraesCS6B01G443600 chr1A 84.211 114 16 2 2453 2565 554532925 554532813 9.110000e-20 110.0
72 TraesCS6B01G443600 chr3B 97.872 141 3 0 8440 8580 429580970 429581110 2.390000e-60 244.0
73 TraesCS6B01G443600 chr3B 80.952 126 14 10 430 548 518408107 518407985 3.300000e-14 91.6
74 TraesCS6B01G443600 chr3B 100.000 36 0 0 8406 8441 64251220 64251255 5.560000e-07 67.6
75 TraesCS6B01G443600 chr3B 100.000 33 0 0 8406 8438 462072522 462072554 2.590000e-05 62.1
76 TraesCS6B01G443600 chr3B 100.000 29 0 0 786 814 558194520 558194492 4.000000e-03 54.7
77 TraesCS6B01G443600 chr2B 97.163 141 4 0 8440 8580 733998186 733998326 1.110000e-58 239.0
78 TraesCS6B01G443600 chrUn 95.172 145 6 1 8440 8583 2576985 2576841 2.410000e-55 228.0
79 TraesCS6B01G443600 chr4B 95.139 144 7 0 8440 8583 7828065 7827922 2.410000e-55 228.0
80 TraesCS6B01G443600 chr4B 90.411 73 7 0 2627 2699 187553577 187553649 7.090000e-16 97.1
81 TraesCS6B01G443600 chr4D 78.125 352 44 27 170 511 342914945 342915273 8.790000e-45 193.0
82 TraesCS6B01G443600 chr4D 90.411 73 7 0 2630 2702 261524252 261524180 7.090000e-16 97.1
83 TraesCS6B01G443600 chr4D 90.411 73 7 0 2630 2702 266112602 266112530 7.090000e-16 97.1
84 TraesCS6B01G443600 chr4D 100.000 38 0 0 8404 8441 5549707 5549670 4.300000e-08 71.3
85 TraesCS6B01G443600 chr4A 75.849 265 60 4 7516 7778 589491199 589490937 1.940000e-26 132.0
86 TraesCS6B01G443600 chr3D 100.000 36 0 0 8406 8441 528948873 528948838 5.560000e-07 67.6


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 TraesCS6B01G443600 chr6B 706581836 706590418 8582 False 15850.000000 15850 100.00000 1 8583 1 chr6B.!!$F3 8582
1 TraesCS6B01G443600 chr6B 706463193 706476068 12875 False 2769.240000 12240 94.67120 446 8580 5 chr6B.!!$F5 8134
2 TraesCS6B01G443600 chr6B 624609406 624609938 532 True 710.000000 710 90.99300 888 1417 1 chr6B.!!$R1 529
3 TraesCS6B01G443600 chr6B 706632141 706632662 521 False 300.000000 494 87.39100 7135 7565 2 chr6B.!!$F6 430
4 TraesCS6B01G443600 chr6A 609836645 609847356 10711 False 1122.250000 2595 90.16450 837 8361 8 chr6A.!!$F3 7524
5 TraesCS6B01G443600 chr6A 609830111 609830951 840 False 983.000000 983 87.86500 2 848 1 chr6A.!!$F1 846
6 TraesCS6B01G443600 chr6A 609978206 609979018 812 False 750.000000 750 83.52900 3024 3862 1 chr6A.!!$F2 838
7 TraesCS6B01G443600 chr6D 463218698 463223088 4390 False 511.000000 734 83.13250 2 5381 4 chr6D.!!$F2 5379
8 TraesCS6B01G443600 chr7D 369461460 369462216 756 True 309.333333 496 88.88400 2333 5692 3 chr7D.!!$R3 3359
9 TraesCS6B01G443600 chr7B 315731562 315732678 1116 True 440.500000 494 86.86650 4995 6129 2 chr7B.!!$R1 1134
10 TraesCS6B01G443600 chr7A 411528600 411529705 1105 False 316.500000 444 87.33575 2333 6129 4 chr7A.!!$F2 3796

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
716 725 0.251341 ACAGTCAAACCCATGGGCTC 60.251 55.000 31.73 15.77 39.32 4.70 F
1519 6333 1.305930 GGGTTCCGGCAAGTCATCAC 61.306 60.000 0.00 0.00 0.00 3.06 F
3014 8553 0.888619 CCAGGTGTAGAGAGCGTGAA 59.111 55.000 0.00 0.00 0.00 3.18 F
3518 9358 0.517316 GCTTGTTTAGTGCCACCTCG 59.483 55.000 0.00 0.00 0.00 4.63 F
5189 11106 2.191354 CTGCATGTCCAGTTGGTGCG 62.191 60.000 7.47 0.94 37.48 5.34 F
6100 12324 5.798125 TCTGACTCTTTGAGACATTGTCT 57.202 39.130 19.05 19.05 46.42 3.41 F
6438 12929 2.159448 CCACAAGTTCGTTTCAGCAACA 60.159 45.455 0.00 0.00 34.68 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 6788 3.525537 ACATGATCTGAACAGCTTACCG 58.474 45.455 0.00 0.00 0.00 4.02 R
3452 9292 2.038426 TCTAAAACTGCTAGTGCCTGCA 59.962 45.455 0.00 0.00 38.71 4.41 R
4338 10222 5.917541 ATGCTTGCTTTTGAACATCAAAG 57.082 34.783 5.75 2.94 45.77 2.77 R
5385 11527 1.177401 AGCGGGATGAAAGCCTTTTC 58.823 50.000 0.00 0.00 46.10 2.29 R
6129 12353 2.097160 GCTGCAGCACAACGATCG 59.903 61.111 33.36 14.88 41.59 3.69 R
7231 13732 1.000060 GCAACCTTCTTCTTGCATGCA 60.000 47.619 18.46 18.46 42.05 3.96 R
8269 14787 3.926616 AGTGTATTCTCGTGTTTGAGGG 58.073 45.455 0.00 0.00 36.61 4.30 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
45 46 3.518705 TGGGAGTTGCAATATTTTGGCAT 59.481 39.130 0.59 0.00 33.22 4.40
95 96 2.869801 GGCGATTCATATTTGACGTCCA 59.130 45.455 14.12 0.00 0.00 4.02
100 101 6.357980 CGATTCATATTTGACGTCCATGAAG 58.642 40.000 23.90 14.78 38.58 3.02
111 112 1.002134 CCATGAAGGTCAAGCGGGT 60.002 57.895 0.00 0.00 0.00 5.28
127 128 1.598130 GGTGTGGCTTCGCTGAAGT 60.598 57.895 16.09 0.00 41.27 3.01
130 131 2.110835 TGGCTTCGCTGAAGTGCA 59.889 55.556 16.09 0.00 41.27 4.57
131 132 1.525765 TGGCTTCGCTGAAGTGCAA 60.526 52.632 16.09 0.00 41.27 4.08
179 180 1.666888 CCATGGTTGCTTCGCTGTTTC 60.667 52.381 2.57 0.00 0.00 2.78
180 181 1.267806 CATGGTTGCTTCGCTGTTTCT 59.732 47.619 0.00 0.00 0.00 2.52
181 182 2.248280 TGGTTGCTTCGCTGTTTCTA 57.752 45.000 0.00 0.00 0.00 2.10
266 271 7.716768 TTGTGTATCATACAAAGTTCGTTGA 57.283 32.000 0.00 0.00 40.93 3.18
283 288 8.241367 AGTTCGTTGAGTCTTACAAAAATGTTT 58.759 29.630 0.00 0.00 0.00 2.83
287 292 9.658475 CGTTGAGTCTTACAAAAATGTTTATCA 57.342 29.630 0.00 0.00 0.00 2.15
702 711 1.270147 ACAGTTTGGACCGCTACAGTC 60.270 52.381 0.00 0.00 0.00 3.51
716 725 0.251341 ACAGTCAAACCCATGGGCTC 60.251 55.000 31.73 15.77 39.32 4.70
752 762 3.323403 TCAATTTTCGGCTTCCAACCAAT 59.677 39.130 0.00 0.00 0.00 3.16
935 952 1.502640 CCGATCGATAGTCTCCCGC 59.497 63.158 18.66 0.00 37.40 6.13
938 955 1.596895 GATCGATAGTCTCCCGCCCC 61.597 65.000 0.00 0.00 37.40 5.80
939 956 3.303928 CGATAGTCTCCCGCCCCC 61.304 72.222 0.00 0.00 0.00 5.40
1014 1048 2.105128 GCGATGGAGGACCTGACG 59.895 66.667 0.00 0.09 37.04 4.35
1064 1098 2.254350 CACTCTCGCCGACAACGA 59.746 61.111 0.00 0.00 42.66 3.85
1117 1151 3.664025 CTGCCCTTCATCGCCGTCA 62.664 63.158 0.00 0.00 0.00 4.35
1147 1181 2.047655 TGCGTGCCCTTAGAACCG 60.048 61.111 0.00 0.00 0.00 4.44
1172 1206 2.387125 TTTTCTTGTGCAGACGCGGC 62.387 55.000 12.47 7.86 42.97 6.53
1300 1349 2.562296 AGTGAGAGAGAGGGAGAGAGT 58.438 52.381 0.00 0.00 0.00 3.24
1334 6136 3.904339 AGAAATAGCACCGGTGATCCTAT 59.096 43.478 38.30 28.15 0.00 2.57
1519 6333 1.305930 GGGTTCCGGCAAGTCATCAC 61.306 60.000 0.00 0.00 0.00 3.06
1593 6407 5.518848 TCTTGAACTCGTACAGTTTGGTA 57.481 39.130 10.65 0.00 46.10 3.25
1649 6471 9.243637 TGTCTTTTTATTTGATTTGTGTACAGC 57.756 29.630 0.00 0.00 0.00 4.40
1705 6527 9.807921 ATCTATTTAAAACTGAAGAAGGAACCA 57.192 29.630 0.00 0.00 0.00 3.67
1769 6591 7.336931 TGAAGATTTTGGTAATGGCTCTACTTC 59.663 37.037 0.00 0.00 0.00 3.01
1780 6602 7.646548 AATGGCTCTACTTCCCTTTTTATTC 57.353 36.000 0.00 0.00 0.00 1.75
1878 6700 3.407424 TGTTGCAGCTGAAGTCAGTAT 57.593 42.857 20.43 0.00 45.45 2.12
1887 6709 5.301551 CAGCTGAAGTCAGTATGGAGATAGT 59.698 44.000 8.42 0.00 45.45 2.12
1966 6788 5.579119 CCGTTTAAGCATATTTTCCCCAAAC 59.421 40.000 0.00 0.00 0.00 2.93
1984 6806 3.678056 AACGGTAAGCTGTTCAGATCA 57.322 42.857 3.84 0.00 39.88 2.92
2006 6828 4.829064 TGTACTGTTGGATTGTTGCTTC 57.171 40.909 0.00 0.00 0.00 3.86
2188 7713 9.299963 CTTTTGATGTTCAGTTTGTTCATTGTA 57.700 29.630 0.00 0.00 0.00 2.41
2222 7747 4.960938 TGGCTTTATGCTTATCAGACGAT 58.039 39.130 0.00 0.00 42.39 3.73
2444 7982 4.744631 GGTAACTTGTTCAGCATTTTGGTG 59.255 41.667 0.38 0.38 46.40 4.17
2762 8301 6.893554 TCACCAAAATTGATCTGATGGAGAAT 59.106 34.615 0.00 0.00 33.12 2.40
3014 8553 0.888619 CCAGGTGTAGAGAGCGTGAA 59.111 55.000 0.00 0.00 0.00 3.18
3174 8715 2.039216 TGATCTACTTGGTCCGGCAAAA 59.961 45.455 0.00 0.00 0.00 2.44
3286 8827 5.411669 GTCCCACGTCAAGAGTTCAATAAAT 59.588 40.000 0.00 0.00 0.00 1.40
3357 8913 2.815478 GCTTAAGCTAGTCATCGTGCT 58.185 47.619 20.38 0.00 38.21 4.40
3452 9292 6.077993 AGCCTTTTTATCTTTGGAGTTCCTT 58.922 36.000 0.00 0.00 36.82 3.36
3518 9358 0.517316 GCTTGTTTAGTGCCACCTCG 59.483 55.000 0.00 0.00 0.00 4.63
3719 9568 5.470047 ACAAAGGTGTTATTCTCGACTCT 57.530 39.130 0.00 0.00 32.58 3.24
3720 9569 5.471257 ACAAAGGTGTTATTCTCGACTCTC 58.529 41.667 0.00 0.00 32.58 3.20
3721 9570 4.358494 AAGGTGTTATTCTCGACTCTCG 57.642 45.455 0.00 0.00 42.10 4.04
3722 9571 7.956410 ACAAAGGTGTTATTCTCGACTCTCGA 61.956 42.308 0.00 0.00 40.08 4.04
3984 9866 2.231478 CTGTCACAGACATACCTTCGGT 59.769 50.000 0.00 0.00 41.94 4.69
4191 10073 4.503741 TTGCCTCTTTGCTAACATGTTC 57.496 40.909 15.85 1.96 0.00 3.18
4338 10222 2.285488 GCGTAGGATTTGCTGAGCTAAC 59.715 50.000 5.83 0.00 0.00 2.34
4507 10408 5.622346 AATCTACAGGTGATTTCCTCCTC 57.378 43.478 0.00 0.00 36.67 3.71
4508 10409 4.338795 TCTACAGGTGATTTCCTCCTCT 57.661 45.455 0.00 0.00 36.67 3.69
4509 10410 4.282496 TCTACAGGTGATTTCCTCCTCTC 58.718 47.826 0.00 0.00 36.67 3.20
4510 10411 3.197927 ACAGGTGATTTCCTCCTCTCT 57.802 47.619 0.00 0.00 36.67 3.10
5189 11106 2.191354 CTGCATGTCCAGTTGGTGCG 62.191 60.000 7.47 0.94 37.48 5.34
5385 11527 6.148811 ACTTTCAATGACTGTAACATTACCGG 59.851 38.462 0.00 0.00 36.40 5.28
5714 11899 6.680810 CATTTGTAAAATCAAGTGGCAGAGA 58.319 36.000 0.00 0.00 33.47 3.10
6100 12324 5.798125 TCTGACTCTTTGAGACATTGTCT 57.202 39.130 19.05 19.05 46.42 3.41
6438 12929 2.159448 CCACAAGTTCGTTTCAGCAACA 60.159 45.455 0.00 0.00 34.68 3.33
7231 13732 5.700402 AGGTTGGACTTCTGCTACAATAT 57.300 39.130 0.00 0.00 0.00 1.28
7550 14066 7.069331 TCCGGTCCTTTTTACTCCGTATATTAA 59.931 37.037 0.00 0.00 39.62 1.40
8365 14888 2.480419 GTGTCCCGCATGTAAGCATATC 59.520 50.000 0.00 0.00 33.30 1.63
8487 15047 8.635765 AGTTTAGATTTTTAGGCTGTTCATCA 57.364 30.769 0.00 0.00 0.00 3.07
8503 15063 0.451783 ATCATCTTTGTTTCGGCGGC 59.548 50.000 7.21 0.00 0.00 6.53
8543 15103 6.992715 TGAATAAAGATTCTTCGGATCCTTCC 59.007 38.462 10.75 0.00 41.87 3.46
8567 15127 1.063717 ACAAGGCCATTGGTCCTATGG 60.064 52.381 23.74 23.74 43.68 2.74
8580 15140 2.040412 GTCCTATGGTTGGGGATGGATC 59.960 54.545 0.00 0.00 0.00 3.36
8581 15141 2.089408 TCCTATGGTTGGGGATGGATCT 60.089 50.000 0.00 0.00 0.00 2.75
8582 15142 2.040813 CCTATGGTTGGGGATGGATCTG 59.959 54.545 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.905480 TCATGGACGTCAAATATGAATCG 57.095 39.130 18.91 0.00 37.30 3.34
82 83 5.097742 TGACCTTCATGGACGTCAAATAT 57.902 39.130 18.91 3.01 39.71 1.28
95 96 0.606401 CACACCCGCTTGACCTTCAT 60.606 55.000 0.00 0.00 0.00 2.57
100 101 4.643387 AGCCACACCCGCTTGACC 62.643 66.667 0.00 0.00 30.57 4.02
250 255 7.402811 TGTAAGACTCAACGAACTTTGTATG 57.597 36.000 0.00 0.00 0.00 2.39
389 395 5.163903 GGCTGAACAAATTTCAAAAACACGT 60.164 36.000 0.00 0.00 0.00 4.49
391 397 6.421377 AGGCTGAACAAATTTCAAAAACAC 57.579 33.333 0.00 0.00 0.00 3.32
558 564 4.536364 ACACACGATGAACTCTTTTGTG 57.464 40.909 0.00 0.00 0.00 3.33
565 571 7.298122 ACATTTCAATAACACACGATGAACTC 58.702 34.615 0.00 0.00 30.34 3.01
702 711 1.278537 ATTTGGAGCCCATGGGTTTG 58.721 50.000 31.58 7.03 37.65 2.93
716 725 4.097892 CGAAAATTGAGACCCCCTATTTGG 59.902 45.833 0.00 0.00 0.00 3.28
865 881 1.274447 CGACTCCCGAGGGTTTAAGTT 59.726 52.381 8.20 0.00 41.76 2.66
938 955 4.924187 AGATCGAGGGGGCGAGGG 62.924 72.222 0.00 0.00 44.26 4.30
939 956 3.299190 GAGATCGAGGGGGCGAGG 61.299 72.222 0.00 0.00 44.26 4.63
941 958 2.833582 GTGAGATCGAGGGGGCGA 60.834 66.667 0.00 0.00 45.22 5.54
942 959 3.917760 GGTGAGATCGAGGGGGCG 61.918 72.222 0.00 0.00 0.00 6.13
943 960 3.551407 GGGTGAGATCGAGGGGGC 61.551 72.222 0.00 0.00 0.00 5.80
1014 1048 1.569479 GCAGCTTGTTGACGAGGGAC 61.569 60.000 0.00 0.00 0.00 4.46
1086 1120 3.695606 GGCAGCTCGTCCCAGTCA 61.696 66.667 0.00 0.00 0.00 3.41
1139 1173 1.717194 AGAAAATCGCGCGGTTCTAA 58.283 45.000 30.53 9.30 0.00 2.10
1147 1181 0.110238 TCTGCACAAGAAAATCGCGC 60.110 50.000 0.00 0.00 29.54 6.86
1172 1206 0.035317 TCACTGGTGCTACTGCCAAG 59.965 55.000 0.00 0.00 38.71 3.61
1300 1349 6.537301 CCGGTGCTATTTCTGAACAAGTATTA 59.463 38.462 0.00 0.00 0.00 0.98
1334 6136 0.105658 ACCAGGCGCCTCCTTAGATA 60.106 55.000 30.29 0.00 44.75 1.98
1355 6157 1.586422 ATCCATGCATGCAGTACGTC 58.414 50.000 26.69 0.00 0.00 4.34
1878 6700 5.624509 CGGTCAGTTTCATCAACTATCTCCA 60.625 44.000 0.00 0.00 44.60 3.86
1887 6709 3.813166 GGTTTCTCGGTCAGTTTCATCAA 59.187 43.478 0.00 0.00 0.00 2.57
1966 6788 3.525537 ACATGATCTGAACAGCTTACCG 58.474 45.455 0.00 0.00 0.00 4.02
1984 6806 4.826733 TGAAGCAACAATCCAACAGTACAT 59.173 37.500 0.00 0.00 0.00 2.29
2006 6828 5.401550 ACGTGGCTGTTTTGATATTTGATG 58.598 37.500 0.00 0.00 0.00 3.07
2222 7747 4.023980 CCTGAACTATACTGACTGACCCA 58.976 47.826 0.00 0.00 0.00 4.51
2230 7755 9.567776 TGTTTTCAATTTCCTGAACTATACTGA 57.432 29.630 0.00 0.00 35.07 3.41
2762 8301 5.756347 ACTTACATTAACAACACTTGCTCGA 59.244 36.000 0.00 0.00 0.00 4.04
3286 8827 4.890158 ACACAATGACTGACACCTGATA 57.110 40.909 0.00 0.00 0.00 2.15
3452 9292 2.038426 TCTAAAACTGCTAGTGCCTGCA 59.962 45.455 0.00 0.00 38.71 4.41
3518 9358 9.813080 GTTACTTCAGATGTTTATTGAACTCAC 57.187 33.333 0.00 0.00 39.08 3.51
3789 9639 8.311109 TCTGTAGAGTACAAATGCTTGAACATA 58.689 33.333 0.00 0.00 38.38 2.29
4338 10222 5.917541 ATGCTTGCTTTTGAACATCAAAG 57.082 34.783 5.75 2.94 45.77 2.77
5189 11106 1.339151 CCCACAGAAGTAGAGCAACCC 60.339 57.143 0.00 0.00 0.00 4.11
5385 11527 1.177401 AGCGGGATGAAAGCCTTTTC 58.823 50.000 0.00 0.00 46.10 2.29
6129 12353 2.097160 GCTGCAGCACAACGATCG 59.903 61.111 33.36 14.88 41.59 3.69
7231 13732 1.000060 GCAACCTTCTTCTTGCATGCA 60.000 47.619 18.46 18.46 42.05 3.96
7550 14066 7.151999 TGTACAGTTTGACTTGACACAAATT 57.848 32.000 0.00 0.00 38.09 1.82
7635 14151 7.182361 AGATTCATTATGCAATGTAGTGTCG 57.818 36.000 0.00 0.00 41.96 4.35
8269 14787 3.926616 AGTGTATTCTCGTGTTTGAGGG 58.073 45.455 0.00 0.00 36.61 4.30
8365 14888 4.324402 GCCGCACAATGTTAATTTTCTCTG 59.676 41.667 0.00 0.00 0.00 3.35
8441 14964 7.793907 AACTACGAGAGAGTAAAAACGATTC 57.206 36.000 0.00 0.00 0.00 2.52
8442 14965 9.339492 CTAAACTACGAGAGAGTAAAAACGATT 57.661 33.333 0.00 0.00 0.00 3.34
8487 15047 1.669760 TCGCCGCCGAAACAAAGAT 60.670 52.632 0.00 0.00 41.17 2.40
8503 15063 1.142185 ATTCAGCGCTGTCATCGTCG 61.142 55.000 34.70 8.33 0.00 5.12
8543 15103 0.890683 GGACCAATGGCCTTGTCAAG 59.109 55.000 3.32 5.53 32.61 3.02


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

AutoCloner maintained by Alex Coulton.