Multiple sequence alignment - TraesCS6B01G115000

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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 TraesCS6B01G115000 chr6B 100.000 2604 0 0 2806 5409 98985701 98988304 0.000000e+00 4809
1 TraesCS6B01G115000 chr6B 100.000 2504 0 0 1 2504 98982896 98985399 0.000000e+00 4625
2 TraesCS6B01G115000 chr6B 82.873 543 62 9 4883 5409 654496182 654495655 4.940000e-125 459
3 TraesCS6B01G115000 chr6B 84.438 347 38 4 5077 5409 404182740 404183084 1.450000e-85 327
4 TraesCS6B01G115000 chrUn 94.372 2523 79 23 2 2504 20932793 20930314 0.000000e+00 3814
5 TraesCS6B01G115000 chrUn 96.320 1902 46 9 2806 4689 20930238 20928343 0.000000e+00 3103
6 TraesCS6B01G115000 chrUn 85.526 304 16 11 4767 5069 20928331 20928055 5.300000e-75 292
7 TraesCS6B01G115000 chr6A 94.604 2020 79 13 257 2260 55700218 55702223 0.000000e+00 3099
8 TraesCS6B01G115000 chr6A 96.477 1192 35 6 3712 4902 55704335 55705520 0.000000e+00 1962
9 TraesCS6B01G115000 chr6A 94.498 927 33 6 2811 3720 55702546 55703471 0.000000e+00 1413
10 TraesCS6B01G115000 chr6A 96.218 238 9 0 2258 2495 55702254 55702491 1.830000e-104 390
11 TraesCS6B01G115000 chr6A 81.702 235 17 10 4835 5069 55705535 55705743 7.200000e-39 172
12 TraesCS6B01G115000 chr7B 97.005 434 13 0 4451 4884 731876501 731876934 0.000000e+00 730
13 TraesCS6B01G115000 chr7B 84.133 542 59 6 4883 5409 41710859 41710330 2.910000e-137 499
14 TraesCS6B01G115000 chr5B 85.028 541 55 9 4883 5409 466842531 466842003 1.330000e-145 527
15 TraesCS6B01G115000 chr5B 84.074 540 62 3 4883 5409 466862713 466863241 2.910000e-137 499
16 TraesCS6B01G115000 chr5B 83.179 541 65 9 4883 5409 575145411 575144883 6.340000e-129 472
17 TraesCS6B01G115000 chr4A 84.658 541 54 9 4883 5409 55920695 55921220 3.740000e-141 512
18 TraesCS6B01G115000 chr3A 84.444 540 60 3 4883 5409 671262723 671262195 1.340000e-140 510
19 TraesCS6B01G115000 chr1D 84.444 540 59 4 4883 5409 336584746 336585273 4.830000e-140 508
20 TraesCS6B01G115000 chr2D 84.288 541 60 4 4883 5409 610042750 610042221 6.250000e-139 505
21 TraesCS6B01G115000 chr4D 83.919 541 61 5 4883 5409 150559841 150560369 1.350000e-135 494
22 TraesCS6B01G115000 chr3B 84.015 538 59 13 4883 5409 592881060 592880539 4.870000e-135 492
23 TraesCS6B01G115000 chr3B 83.704 540 63 6 4883 5409 587961774 587961247 2.260000e-133 486
24 TraesCS6B01G115000 chr6D 83.889 540 60 5 4883 5409 456921120 456920595 1.750000e-134 490
25 TraesCS6B01G115000 chr3D 83.919 541 54 10 4883 5409 159724609 159725130 2.260000e-133 486
26 TraesCS6B01G115000 chr4B 83.519 540 64 5 4883 5409 434314228 434314755 1.050000e-131 481
27 TraesCS6B01G115000 chr4B 83.333 546 60 9 4883 5409 53866945 53866412 4.900000e-130 475
28 TraesCS6B01G115000 chr5A 81.031 543 71 8 4883 5409 194111258 194111784 2.350000e-108 403


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 TraesCS6B01G115000 chr6B 98982896 98988304 5408 False 4717.0 4809 100.000000 1 5409 2 chr6B.!!$F2 5408
1 TraesCS6B01G115000 chr6B 654495655 654496182 527 True 459.0 459 82.873000 4883 5409 1 chr6B.!!$R1 526
2 TraesCS6B01G115000 chrUn 20928055 20932793 4738 True 2403.0 3814 92.072667 2 5069 3 chrUn.!!$R1 5067
3 TraesCS6B01G115000 chr6A 55700218 55705743 5525 False 1407.2 3099 92.699800 257 5069 5 chr6A.!!$F1 4812
4 TraesCS6B01G115000 chr7B 41710330 41710859 529 True 499.0 499 84.133000 4883 5409 1 chr7B.!!$R1 526
5 TraesCS6B01G115000 chr5B 466842003 466842531 528 True 527.0 527 85.028000 4883 5409 1 chr5B.!!$R1 526
6 TraesCS6B01G115000 chr5B 466862713 466863241 528 False 499.0 499 84.074000 4883 5409 1 chr5B.!!$F1 526
7 TraesCS6B01G115000 chr5B 575144883 575145411 528 True 472.0 472 83.179000 4883 5409 1 chr5B.!!$R2 526
8 TraesCS6B01G115000 chr4A 55920695 55921220 525 False 512.0 512 84.658000 4883 5409 1 chr4A.!!$F1 526
9 TraesCS6B01G115000 chr3A 671262195 671262723 528 True 510.0 510 84.444000 4883 5409 1 chr3A.!!$R1 526
10 TraesCS6B01G115000 chr1D 336584746 336585273 527 False 508.0 508 84.444000 4883 5409 1 chr1D.!!$F1 526
11 TraesCS6B01G115000 chr2D 610042221 610042750 529 True 505.0 505 84.288000 4883 5409 1 chr2D.!!$R1 526
12 TraesCS6B01G115000 chr4D 150559841 150560369 528 False 494.0 494 83.919000 4883 5409 1 chr4D.!!$F1 526
13 TraesCS6B01G115000 chr3B 592880539 592881060 521 True 492.0 492 84.015000 4883 5409 1 chr3B.!!$R2 526
14 TraesCS6B01G115000 chr3B 587961247 587961774 527 True 486.0 486 83.704000 4883 5409 1 chr3B.!!$R1 526
15 TraesCS6B01G115000 chr6D 456920595 456921120 525 True 490.0 490 83.889000 4883 5409 1 chr6D.!!$R1 526
16 TraesCS6B01G115000 chr3D 159724609 159725130 521 False 486.0 486 83.919000 4883 5409 1 chr3D.!!$F1 526
17 TraesCS6B01G115000 chr4B 434314228 434314755 527 False 481.0 481 83.519000 4883 5409 1 chr4B.!!$F1 526
18 TraesCS6B01G115000 chr4B 53866412 53866945 533 True 475.0 475 83.333000 4883 5409 1 chr4B.!!$R1 526
19 TraesCS6B01G115000 chr5A 194111258 194111784 526 False 403.0 403 81.031000 4883 5409 1 chr5A.!!$F1 526

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
34 35 0.107214 GGCTTGTACATGCAGGGCTA 60.107 55.000 28.60 0.00 37.87 3.93 F
180 181 0.187361 TCAAGGTTGGGAAGGGGTTG 59.813 55.000 0.00 0.00 0.00 3.77 F
269 270 0.554865 TCCCCCTTCCAATCACCCAT 60.555 55.000 0.00 0.00 0.00 4.00 F
843 846 1.464997 GAGAATCCGGTGTTGAACAGC 59.535 52.381 16.85 16.85 42.72 4.40 F
2031 2039 0.981183 AGTAGGCCGAAACATCCACA 59.019 50.000 0.00 0.00 0.00 4.17 F
3063 3117 1.082104 CGAAGGCGCTTTCAACCAC 60.082 57.895 28.63 4.79 0.00 4.16 F
3313 3367 3.252215 CGTTGGGCTTCTGTTTAATGTGA 59.748 43.478 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1086 0.890996 GGTTCTTGTCAGGGTGCCAG 60.891 60.000 0.00 0.00 0.00 4.85 R
2013 2021 1.084289 GTGTGGATGTTTCGGCCTAC 58.916 55.000 0.00 0.00 0.00 3.18 R
2031 2039 3.004524 GGTCGTAGTCTTGTCTTGAGTGT 59.995 47.826 0.00 0.00 0.00 3.55 R
2434 2488 0.673333 CATCACGTACTGCAAGCCCA 60.673 55.000 0.00 0.00 37.60 5.36 R
3697 3768 1.143813 AGTAGCCATGCCCTTGCTAT 58.856 50.000 4.28 0.00 39.56 2.97 R
4096 5052 0.107703 GGGGCTTCATGTCGATGACA 60.108 55.000 1.65 1.65 46.90 3.58 R
4425 5381 0.179111 TGAATCGATCCACTGTCGCC 60.179 55.000 0.00 0.00 38.88 5.54 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
34 35 0.107214 GGCTTGTACATGCAGGGCTA 60.107 55.000 28.60 0.00 37.87 3.93
45 46 2.675423 AGGGCTACGAGTCGCACA 60.675 61.111 13.59 0.00 30.23 4.57
68 69 4.612264 TGTAGTTGTTTCACCCTCTACC 57.388 45.455 0.00 0.00 0.00 3.18
70 71 4.657039 TGTAGTTGTTTCACCCTCTACCTT 59.343 41.667 0.00 0.00 0.00 3.50
76 77 6.442541 TGTTTCACCCTCTACCTTTCAATA 57.557 37.500 0.00 0.00 0.00 1.90
81 82 7.938140 TCACCCTCTACCTTTCAATAAAATG 57.062 36.000 0.00 0.00 0.00 2.32
102 103 7.552458 AATGATACACAATCTTGCGTATTCA 57.448 32.000 5.38 5.79 36.76 2.57
103 104 7.734924 ATGATACACAATCTTGCGTATTCAT 57.265 32.000 5.38 7.26 36.76 2.57
109 110 6.803320 ACACAATCTTGCGTATTCATGAAAAG 59.197 34.615 13.09 10.99 0.00 2.27
115 116 5.203358 TGCGTATTCATGAAAAGAGAACG 57.797 39.130 13.09 14.99 0.00 3.95
118 119 5.062308 GCGTATTCATGAAAAGAGAACGAGT 59.938 40.000 13.09 0.00 31.02 4.18
119 120 6.461816 CGTATTCATGAAAAGAGAACGAGTG 58.538 40.000 13.09 0.00 31.02 3.51
124 125 6.459066 TCATGAAAAGAGAACGAGTGAAGAT 58.541 36.000 0.00 0.00 0.00 2.40
125 126 7.602753 TCATGAAAAGAGAACGAGTGAAGATA 58.397 34.615 0.00 0.00 0.00 1.98
126 127 8.253810 TCATGAAAAGAGAACGAGTGAAGATAT 58.746 33.333 0.00 0.00 0.00 1.63
127 128 8.538856 CATGAAAAGAGAACGAGTGAAGATATC 58.461 37.037 0.00 0.00 0.00 1.63
128 129 6.747739 TGAAAAGAGAACGAGTGAAGATATCG 59.252 38.462 0.00 0.00 42.04 2.92
129 130 4.822036 AGAGAACGAGTGAAGATATCGG 57.178 45.455 0.00 0.00 40.67 4.18
130 131 4.200874 AGAGAACGAGTGAAGATATCGGT 58.799 43.478 0.00 0.00 39.49 4.69
132 133 4.555348 GAACGAGTGAAGATATCGGTCT 57.445 45.455 4.72 2.83 46.81 3.85
133 134 5.670149 GAACGAGTGAAGATATCGGTCTA 57.330 43.478 4.72 0.00 46.81 2.59
134 135 6.057627 GAACGAGTGAAGATATCGGTCTAA 57.942 41.667 4.72 0.00 46.81 2.10
135 136 6.636562 AACGAGTGAAGATATCGGTCTAAT 57.363 37.500 9.87 0.00 40.67 1.73
136 137 6.636562 ACGAGTGAAGATATCGGTCTAATT 57.363 37.500 9.87 0.00 40.67 1.40
137 138 7.040473 ACGAGTGAAGATATCGGTCTAATTT 57.960 36.000 9.87 0.00 40.67 1.82
140 141 8.903723 CGAGTGAAGATATCGGTCTAATTTAAC 58.096 37.037 9.87 0.00 32.93 2.01
151 152 2.923020 TCTAATTTAACCGAACCGTCGC 59.077 45.455 0.00 0.00 46.28 5.19
157 158 4.409218 CCGAACCGTCGCCGAGAA 62.409 66.667 0.00 0.00 46.28 2.87
177 178 0.409484 ATGTCAAGGTTGGGAAGGGG 59.591 55.000 0.00 0.00 0.00 4.79
178 179 0.996762 TGTCAAGGTTGGGAAGGGGT 60.997 55.000 0.00 0.00 0.00 4.95
179 180 0.187606 GTCAAGGTTGGGAAGGGGTT 59.812 55.000 0.00 0.00 0.00 4.11
180 181 0.187361 TCAAGGTTGGGAAGGGGTTG 59.813 55.000 0.00 0.00 0.00 3.77
181 182 1.152333 AAGGTTGGGAAGGGGTTGC 60.152 57.895 0.00 0.00 0.00 4.17
183 184 2.114411 GTTGGGAAGGGGTTGCGA 59.886 61.111 0.00 0.00 0.00 5.10
185 186 2.758207 TTGGGAAGGGGTTGCGACA 61.758 57.895 6.39 0.00 0.00 4.35
186 187 2.114411 GGGAAGGGGTTGCGACAA 59.886 61.111 6.39 0.00 0.00 3.18
187 188 1.529713 GGGAAGGGGTTGCGACAAA 60.530 57.895 6.39 0.00 0.00 2.83
188 189 1.110518 GGGAAGGGGTTGCGACAAAA 61.111 55.000 6.39 0.00 0.00 2.44
189 190 0.747852 GGAAGGGGTTGCGACAAAAA 59.252 50.000 6.39 0.00 0.00 1.94
190 191 1.269569 GGAAGGGGTTGCGACAAAAAG 60.270 52.381 6.39 0.00 0.00 2.27
191 192 1.407618 GAAGGGGTTGCGACAAAAAGT 59.592 47.619 6.39 0.00 0.00 2.66
192 193 1.480789 AGGGGTTGCGACAAAAAGTT 58.519 45.000 6.39 0.00 0.00 2.66
193 194 1.136110 AGGGGTTGCGACAAAAAGTTG 59.864 47.619 6.39 0.00 40.84 3.16
194 195 1.566404 GGGTTGCGACAAAAAGTTGG 58.434 50.000 6.39 0.00 39.22 3.77
201 202 2.030335 GCGACAAAAAGTTGGGCAAAAG 59.970 45.455 0.00 0.00 39.22 2.27
254 255 2.660189 CACAGATGTGCAATTTCCCC 57.340 50.000 0.00 0.00 39.39 4.81
255 256 1.205417 CACAGATGTGCAATTTCCCCC 59.795 52.381 0.00 0.00 39.39 5.40
269 270 0.554865 TCCCCCTTCCAATCACCCAT 60.555 55.000 0.00 0.00 0.00 4.00
287 288 4.849310 TGAATAGCCGCCGCACCC 62.849 66.667 0.00 0.00 37.52 4.61
301 302 2.609350 CGCACCCATTTCAAAATCAGG 58.391 47.619 0.00 1.30 0.00 3.86
306 307 4.161942 CACCCATTTCAAAATCAGGCCATA 59.838 41.667 5.01 0.00 0.00 2.74
346 347 1.690985 CCCACTCCTCCCCTTCCTC 60.691 68.421 0.00 0.00 0.00 3.71
684 687 1.579429 GGCGCTGTTTGGTTGTAGG 59.421 57.895 7.64 0.00 0.00 3.18
691 694 2.735134 CTGTTTGGTTGTAGGTAGACGC 59.265 50.000 0.00 0.00 0.00 5.19
712 715 4.527157 GCACGATCTTGCGGCTGC 62.527 66.667 11.65 11.65 43.20 5.25
735 738 2.791927 GTCGAATTCTTGCCGGGC 59.208 61.111 13.32 13.32 0.00 6.13
843 846 1.464997 GAGAATCCGGTGTTGAACAGC 59.535 52.381 16.85 16.85 42.72 4.40
870 873 2.758979 GTGGACGAAAGGTAGGATCTGA 59.241 50.000 0.00 0.00 0.00 3.27
985 988 1.999024 GTGGTTTGCTTGTGTTTGTGG 59.001 47.619 0.00 0.00 0.00 4.17
1092 1095 2.689034 GCTAGGACCTGGCACCCT 60.689 66.667 23.91 7.82 37.89 4.34
1236 1239 2.125673 ATTCGGTGCCGGTTCGAG 60.126 61.111 10.94 0.00 40.25 4.04
1277 1280 3.244582 TGTGGGGAGCTTCTAGTGTTAA 58.755 45.455 0.00 0.00 0.00 2.01
1278 1281 3.844211 TGTGGGGAGCTTCTAGTGTTAAT 59.156 43.478 0.00 0.00 0.00 1.40
1279 1282 5.027460 TGTGGGGAGCTTCTAGTGTTAATA 58.973 41.667 0.00 0.00 0.00 0.98
1280 1283 5.486063 TGTGGGGAGCTTCTAGTGTTAATAA 59.514 40.000 0.00 0.00 0.00 1.40
1734 1739 6.417258 TGAGATCTGCAATTTTGTATCCTGA 58.583 36.000 0.00 0.00 0.00 3.86
1984 1992 4.509970 CCGTATCGGTGCATTGATAGAAAA 59.490 41.667 10.18 0.00 42.73 2.29
2007 2015 9.844790 AAAAAGTAAGTTACAACTGTACAAACC 57.155 29.630 15.28 0.00 39.66 3.27
2013 2021 8.658499 AAGTTACAACTGTACAAACCTAAGAG 57.342 34.615 0.00 0.00 39.66 2.85
2031 2039 0.981183 AGTAGGCCGAAACATCCACA 59.019 50.000 0.00 0.00 0.00 4.17
2447 2501 1.581447 GTTGCTGGGCTTGCAGTAC 59.419 57.895 5.30 0.00 41.71 2.73
2495 2549 6.548622 AGGAAAGCATCAGTTATACAATGCAT 59.451 34.615 15.08 0.00 45.39 3.96
3063 3117 1.082104 CGAAGGCGCTTTCAACCAC 60.082 57.895 28.63 4.79 0.00 4.16
3188 3242 5.350091 GGAGAAGACATTACTTTGCACTCTC 59.650 44.000 0.00 0.00 0.00 3.20
3313 3367 3.252215 CGTTGGGCTTCTGTTTAATGTGA 59.748 43.478 0.00 0.00 0.00 3.58
3329 3383 9.334693 GTTTAATGTGAGAACATTAAGCTTGAG 57.665 33.333 21.18 0.89 46.61 3.02
3434 3490 4.141846 TGCCAAGTCCATTTTTGCAAGTAA 60.142 37.500 0.00 0.00 0.00 2.24
3467 3534 5.769662 AGTGTGGATCATCAAAAGCTTAACA 59.230 36.000 0.00 0.00 0.00 2.41
3583 3650 8.734386 AGAGCACCTTTTCATATTTTACTCTTG 58.266 33.333 0.00 0.00 0.00 3.02
3584 3651 8.409358 AGCACCTTTTCATATTTTACTCTTGT 57.591 30.769 0.00 0.00 0.00 3.16
3586 3653 8.915654 GCACCTTTTCATATTTTACTCTTGTTG 58.084 33.333 0.00 0.00 0.00 3.33
3587 3654 8.915654 CACCTTTTCATATTTTACTCTTGTTGC 58.084 33.333 0.00 0.00 0.00 4.17
3588 3655 8.637986 ACCTTTTCATATTTTACTCTTGTTGCA 58.362 29.630 0.00 0.00 0.00 4.08
3652 3723 9.009675 TCCTTTTATATCCAGTTAAATCCTCCA 57.990 33.333 0.00 0.00 0.00 3.86
4132 5088 1.482593 CCCCATGACACCTACACTCTC 59.517 57.143 0.00 0.00 0.00 3.20
4276 5232 2.431954 CTGGCCAGGAGATTGTGATT 57.568 50.000 26.14 0.00 0.00 2.57
4300 5256 3.467226 GAAGGGTGGCCGATCCGA 61.467 66.667 0.00 0.00 37.80 4.55
4425 5381 2.884304 GCTAACCAGGGAAAAGAAGGGG 60.884 54.545 0.00 0.00 0.00 4.79
4543 5499 7.389232 TGTTCATCTGTTGTTCATAGATCAGT 58.611 34.615 0.00 0.00 0.00 3.41
4603 5559 2.445453 TCGCAAGTGACGTTGTTTTC 57.555 45.000 0.00 0.00 39.48 2.29
4606 5562 3.120130 TCGCAAGTGACGTTGTTTTCTTT 60.120 39.130 0.00 0.00 39.48 2.52
4607 5563 3.606346 CGCAAGTGACGTTGTTTTCTTTT 59.394 39.130 0.00 0.00 0.00 2.27
4608 5564 4.258860 CGCAAGTGACGTTGTTTTCTTTTC 60.259 41.667 0.00 0.00 0.00 2.29
4611 5567 3.437741 AGTGACGTTGTTTTCTTTTCGGT 59.562 39.130 0.00 0.00 0.00 4.69
4617 5573 4.494410 CGTTGTTTTCTTTTCGGTGACTTC 59.506 41.667 0.00 0.00 0.00 3.01
4727 5683 6.862090 GCTTTTCTTAAGATGGATCATCATGC 59.138 38.462 5.89 0.00 42.72 4.06
4728 5684 6.889301 TTTCTTAAGATGGATCATCATGCC 57.111 37.500 5.89 0.00 42.72 4.40
4745 5701 1.682854 TGCCATGGCTTAGCATTTAGC 59.317 47.619 35.53 6.54 42.47 3.09
4764 5720 6.539649 TTAGCACACAGATTTGACAGTTAC 57.460 37.500 0.00 0.00 0.00 2.50
4765 5721 3.494626 AGCACACAGATTTGACAGTTACG 59.505 43.478 0.00 0.00 0.00 3.18
4820 5776 1.944024 TGTTCGTCTTCGTTTTGCCAT 59.056 42.857 0.00 0.00 38.33 4.40
4825 5781 2.993899 CGTCTTCGTTTTGCCATAGAGT 59.006 45.455 0.00 0.00 0.00 3.24
4852 5808 9.836864 AATAGATGCATACAGTTTATTCACTCA 57.163 29.630 0.00 0.00 0.00 3.41
4934 5957 1.611977 CTACACAACCTCACCGACTGA 59.388 52.381 0.00 0.00 0.00 3.41
4936 5959 0.600255 CACAACCTCACCGACTGACC 60.600 60.000 0.00 0.00 0.00 4.02
4958 5981 5.240623 ACCGCAAACATAAACTCAGAAATCA 59.759 36.000 0.00 0.00 0.00 2.57
4994 6021 2.105821 TGGAACAGTTGGGGAGTACTTG 59.894 50.000 0.00 0.00 0.00 3.16
5008 6035 4.438472 GGAGTACTTGTACTAGAAGCACCG 60.438 50.000 11.43 0.00 0.00 4.94
5010 6037 4.948621 AGTACTTGTACTAGAAGCACCGAT 59.051 41.667 11.43 0.00 0.00 4.18
5011 6038 4.111375 ACTTGTACTAGAAGCACCGATG 57.889 45.455 11.43 0.00 0.00 3.84
5012 6039 3.762288 ACTTGTACTAGAAGCACCGATGA 59.238 43.478 11.43 0.00 0.00 2.92
5013 6040 4.219944 ACTTGTACTAGAAGCACCGATGAA 59.780 41.667 11.43 0.00 0.00 2.57
5014 6041 4.371855 TGTACTAGAAGCACCGATGAAG 57.628 45.455 0.00 0.00 0.00 3.02
5015 6042 2.301577 ACTAGAAGCACCGATGAAGC 57.698 50.000 0.00 0.00 0.00 3.86
5016 6043 1.550524 ACTAGAAGCACCGATGAAGCA 59.449 47.619 0.00 0.00 0.00 3.91
5017 6044 2.169352 ACTAGAAGCACCGATGAAGCAT 59.831 45.455 0.00 0.00 0.00 3.79
5018 6045 1.661341 AGAAGCACCGATGAAGCATC 58.339 50.000 0.00 0.00 37.50 3.91
5019 6046 1.209019 AGAAGCACCGATGAAGCATCT 59.791 47.619 5.94 0.00 38.59 2.90
5020 6047 1.329906 GAAGCACCGATGAAGCATCTG 59.670 52.381 5.94 2.18 38.59 2.90
5070 6097 5.755409 TGAAGGGTAAATTAGTGAGCTCA 57.245 39.130 13.74 13.74 0.00 4.26
5120 6147 3.242608 GCCTCGCGCTGTAATTAATTTCA 60.243 43.478 5.56 6.67 0.00 2.69
5133 6160 7.865385 TGTAATTAATTTCAGGACAACTTGCAC 59.135 33.333 5.91 0.00 0.00 4.57
5178 6205 4.851843 TCAAGACCTCAAATGATGCATCT 58.148 39.130 26.32 10.21 0.00 2.90
5224 6255 3.010027 TCAAACACCATCTTATCTGGCCA 59.990 43.478 4.71 4.71 37.27 5.36
5229 6260 4.130118 CACCATCTTATCTGGCCACTAAC 58.870 47.826 0.00 0.00 37.27 2.34
5293 6324 7.010923 GTGAAGTTGTAGCTAGAAATCTGATGG 59.989 40.741 4.66 0.00 0.00 3.51
5339 6383 5.914898 ACTAAGATAATGGTTTTGCCCAC 57.085 39.130 0.00 0.00 37.31 4.61
5343 6387 0.875728 TAATGGTTTTGCCCACGTCG 59.124 50.000 0.00 0.00 37.31 5.12
5345 6389 1.104577 ATGGTTTTGCCCACGTCGTT 61.105 50.000 0.00 0.00 37.31 3.85
5357 6401 1.862201 CACGTCGTTCTTTGGTTGCTA 59.138 47.619 0.00 0.00 0.00 3.49
5363 6407 5.163893 CGTCGTTCTTTGGTTGCTATAATGT 60.164 40.000 0.00 0.00 0.00 2.71
5403 6447 4.156556 GCATAAACCTCACTCTTTGATGCA 59.843 41.667 0.00 0.00 34.29 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.877071 AAGCCTGTCGTGATTGCAAG 59.123 50.000 4.94 0.00 0.00 4.01
12 13 0.322816 CCCTGCATGTACAAGCCTGT 60.323 55.000 19.55 0.00 39.75 4.00
15 16 0.107214 TAGCCCTGCATGTACAAGCC 60.107 55.000 19.55 4.92 0.00 4.35
34 35 2.058798 CAACTACAATGTGCGACTCGT 58.941 47.619 0.00 0.00 0.00 4.18
45 46 5.309806 AGGTAGAGGGTGAAACAACTACAAT 59.690 40.000 0.00 0.00 38.76 2.71
70 71 9.288124 CGCAAGATTGTGTATCATTTTATTGAA 57.712 29.630 0.00 0.00 43.02 2.69
102 103 7.433719 CGATATCTTCACTCGTTCTCTTTTCAT 59.566 37.037 0.34 0.00 0.00 2.57
103 104 6.747739 CGATATCTTCACTCGTTCTCTTTTCA 59.252 38.462 0.34 0.00 0.00 2.69
109 110 4.273969 AGACCGATATCTTCACTCGTTCTC 59.726 45.833 0.34 0.00 29.70 2.87
115 116 9.194271 GGTTAAATTAGACCGATATCTTCACTC 57.806 37.037 0.34 0.00 0.00 3.51
128 129 3.304293 CGACGGTTCGGTTAAATTAGACC 59.696 47.826 1.04 1.04 41.89 3.85
129 130 3.241773 GCGACGGTTCGGTTAAATTAGAC 60.242 47.826 0.00 0.00 45.98 2.59
130 131 2.923020 GCGACGGTTCGGTTAAATTAGA 59.077 45.455 0.00 0.00 45.98 2.10
131 132 2.029606 GGCGACGGTTCGGTTAAATTAG 59.970 50.000 0.00 0.00 45.98 1.73
132 133 1.999024 GGCGACGGTTCGGTTAAATTA 59.001 47.619 0.00 0.00 45.98 1.40
133 134 0.798159 GGCGACGGTTCGGTTAAATT 59.202 50.000 0.00 0.00 45.98 1.82
134 135 2.459245 GGCGACGGTTCGGTTAAAT 58.541 52.632 0.00 0.00 45.98 1.40
135 136 3.949855 GGCGACGGTTCGGTTAAA 58.050 55.556 0.00 0.00 45.98 1.52
147 148 0.721718 CCTTGACATTTCTCGGCGAC 59.278 55.000 4.99 0.00 0.00 5.19
151 152 1.812571 CCCAACCTTGACATTTCTCGG 59.187 52.381 0.00 0.00 0.00 4.63
157 158 1.203174 CCCCTTCCCAACCTTGACATT 60.203 52.381 0.00 0.00 0.00 2.71
177 178 0.927537 GCCCAACTTTTTGTCGCAAC 59.072 50.000 0.00 0.00 0.00 4.17
178 179 0.532573 TGCCCAACTTTTTGTCGCAA 59.467 45.000 0.00 0.00 34.70 4.85
179 180 0.532573 TTGCCCAACTTTTTGTCGCA 59.467 45.000 0.00 0.00 35.41 5.10
180 181 1.646189 TTTGCCCAACTTTTTGTCGC 58.354 45.000 0.00 0.00 0.00 5.19
181 182 3.516615 TCTTTTGCCCAACTTTTTGTCG 58.483 40.909 0.00 0.00 0.00 4.35
183 184 6.641169 TTTTTCTTTTGCCCAACTTTTTGT 57.359 29.167 0.00 0.00 0.00 2.83
219 220 7.815641 CACATCTGTGTAAAACATACCATCAA 58.184 34.615 2.09 0.00 40.96 2.57
245 246 2.501316 GGTGATTGGAAGGGGGAAATTG 59.499 50.000 0.00 0.00 0.00 2.32
251 252 0.339510 AATGGGTGATTGGAAGGGGG 59.660 55.000 0.00 0.00 0.00 5.40
252 253 1.006998 TCAATGGGTGATTGGAAGGGG 59.993 52.381 0.00 0.00 41.76 4.79
253 254 2.530460 TCAATGGGTGATTGGAAGGG 57.470 50.000 0.00 0.00 41.76 3.95
254 255 4.038402 GCTATTCAATGGGTGATTGGAAGG 59.962 45.833 0.00 0.00 41.76 3.46
255 256 4.038402 GGCTATTCAATGGGTGATTGGAAG 59.962 45.833 0.00 0.00 41.76 3.46
269 270 2.822255 GGTGCGGCGGCTATTCAA 60.822 61.111 17.76 0.00 40.82 2.69
287 288 5.341872 TGGTATGGCCTGATTTTGAAATG 57.658 39.130 3.32 0.00 38.35 2.32
301 302 2.223711 CCGTATGGCTTTTTGGTATGGC 60.224 50.000 0.00 0.00 0.00 4.40
306 307 2.579410 ACTCCGTATGGCTTTTTGGT 57.421 45.000 0.00 0.00 34.14 3.67
684 687 0.179134 AGATCGTGCCTTGCGTCTAC 60.179 55.000 0.00 0.00 0.00 2.59
691 694 2.787249 CCGCAAGATCGTGCCTTG 59.213 61.111 24.91 12.86 41.73 3.61
715 718 2.461110 CCGGCAAGAATTCGACGGG 61.461 63.158 17.27 11.96 37.80 5.28
719 722 0.468226 ATAGCCCGGCAAGAATTCGA 59.532 50.000 13.15 0.00 0.00 3.71
721 724 3.686726 CAGATATAGCCCGGCAAGAATTC 59.313 47.826 13.15 0.00 0.00 2.17
729 732 1.490574 ATCCTCAGATATAGCCCGGC 58.509 55.000 0.00 0.00 0.00 6.13
735 738 5.406649 GCGACCTTCAATCCTCAGATATAG 58.593 45.833 0.00 0.00 30.42 1.31
843 846 0.320073 TACCTTTCGTCCACCGCAAG 60.320 55.000 0.00 0.00 39.17 4.01
870 873 3.094484 TCAGACAAACTTTGGGTGGTT 57.906 42.857 6.47 0.00 34.12 3.67
985 988 0.392998 TCCATCGCCTCTTTGCCTTC 60.393 55.000 0.00 0.00 0.00 3.46
1083 1086 0.890996 GGTTCTTGTCAGGGTGCCAG 60.891 60.000 0.00 0.00 0.00 4.85
1236 1239 7.271511 CCCACAGGAATAGCTATCATTCTATC 58.728 42.308 6.72 0.00 33.70 2.08
1360 1363 8.627403 CACAGCTAAATGGTCAATCTTCATAAT 58.373 33.333 0.00 0.00 0.00 1.28
1552 1555 9.010366 CAAGTACTAAACTGCAAAGAAGAAAAC 57.990 33.333 0.00 0.00 38.88 2.43
1734 1739 9.381038 TGGAGAAAAGTATAGCTACTTATGGAT 57.619 33.333 2.32 0.00 45.40 3.41
1753 1758 6.595682 ACTTTTGACTTCTGAGATGGAGAAA 58.404 36.000 0.29 0.00 0.00 2.52
1940 1948 4.614535 CGGAAGCTTTGTGATTTCTCAAGG 60.615 45.833 0.00 1.48 31.85 3.61
1984 1992 9.889128 TTAGGTTTGTACAGTTGTAACTTACTT 57.111 29.630 7.18 0.00 37.08 2.24
2007 2015 3.132289 TGGATGTTTCGGCCTACTCTTAG 59.868 47.826 0.00 0.00 0.00 2.18
2013 2021 1.084289 GTGTGGATGTTTCGGCCTAC 58.916 55.000 0.00 0.00 0.00 3.18
2031 2039 3.004524 GGTCGTAGTCTTGTCTTGAGTGT 59.995 47.826 0.00 0.00 0.00 3.55
2434 2488 0.673333 CATCACGTACTGCAAGCCCA 60.673 55.000 0.00 0.00 37.60 5.36
2447 2501 6.967767 CCTAGAAGAAAGTACAGTACATCACG 59.032 42.308 13.37 0.00 0.00 4.35
3063 3117 3.596066 CTGCTGAGGTCCGGTGTGG 62.596 68.421 0.00 0.00 40.09 4.17
3188 3242 6.662414 TTTGTTCCATTATACAGCTCTTCG 57.338 37.500 0.00 0.00 0.00 3.79
3313 3367 5.819901 GGCTCATACTCAAGCTTAATGTTCT 59.180 40.000 0.00 0.00 38.58 3.01
3329 3383 5.010516 ACATCATGTCAGTAGAGGCTCATAC 59.989 44.000 18.26 15.09 0.00 2.39
3379 3433 8.817100 CAATGATAACGCAGTAGAGAATACAAA 58.183 33.333 0.00 0.00 45.00 2.83
3444 3500 6.012658 TGTTAAGCTTTTGATGATCCACAC 57.987 37.500 3.20 0.00 0.00 3.82
3467 3534 8.963725 ACAATCAGATAACACACATGAATTCAT 58.036 29.630 15.36 15.36 36.96 2.57
3697 3768 1.143813 AGTAGCCATGCCCTTGCTAT 58.856 50.000 4.28 0.00 39.56 2.97
3750 4693 2.755103 CCTTTATCAACCACCTGGCTTC 59.245 50.000 0.00 0.00 39.32 3.86
4096 5052 0.107703 GGGGCTTCATGTCGATGACA 60.108 55.000 1.65 1.65 46.90 3.58
4132 5088 0.321653 CCAGGAGGTTGTTCCCTTCG 60.322 60.000 0.00 0.00 38.02 3.79
4261 5217 5.434408 TCATTCTCAATCACAATCTCCTGG 58.566 41.667 0.00 0.00 0.00 4.45
4276 5232 1.198094 TCGGCCACCCTTCATTCTCA 61.198 55.000 2.24 0.00 0.00 3.27
4300 5256 0.701147 CCTTCTTCCCTGGCTCCTTT 59.299 55.000 0.00 0.00 0.00 3.11
4425 5381 0.179111 TGAATCGATCCACTGTCGCC 60.179 55.000 0.00 0.00 38.88 5.54
4543 5499 2.006888 GAATTAGTGCTGCACCGCTAA 58.993 47.619 27.74 19.65 40.75 3.09
4603 5559 2.287009 GCCAACAGAAGTCACCGAAAAG 60.287 50.000 0.00 0.00 0.00 2.27
4606 5562 0.534203 GGCCAACAGAAGTCACCGAA 60.534 55.000 0.00 0.00 0.00 4.30
4607 5563 1.070786 GGCCAACAGAAGTCACCGA 59.929 57.895 0.00 0.00 0.00 4.69
4608 5564 0.606401 ATGGCCAACAGAAGTCACCG 60.606 55.000 10.96 0.00 0.00 4.94
4611 5567 2.224744 TGCTAATGGCCAACAGAAGTCA 60.225 45.455 10.96 0.09 40.92 3.41
4617 5573 1.203052 CCAACTGCTAATGGCCAACAG 59.797 52.381 10.96 17.56 40.92 3.16
4681 5637 5.560148 AGCGCTAATTATCAACAAAAGTCG 58.440 37.500 8.99 0.00 0.00 4.18
4727 5683 2.689471 TGTGCTAAATGCTAAGCCATGG 59.311 45.455 7.63 7.63 43.37 3.66
4728 5684 3.129113 TGTGTGCTAAATGCTAAGCCATG 59.871 43.478 0.00 0.00 43.37 3.66
4745 5701 4.084537 GGTCGTAACTGTCAAATCTGTGTG 60.085 45.833 0.00 0.00 0.00 3.82
4756 5712 1.014564 GGCAGCAGGTCGTAACTGTC 61.015 60.000 0.00 0.00 38.22 3.51
4764 5720 0.811616 GACCATTAGGCAGCAGGTCG 60.812 60.000 0.00 0.00 39.33 4.79
4765 5721 0.253044 TGACCATTAGGCAGCAGGTC 59.747 55.000 10.91 10.91 46.86 3.85
4852 5808 5.055144 CACTGCATATACAGCATCTGAACT 58.945 41.667 2.65 0.00 41.82 3.01
4915 5872 1.338973 GTCAGTCGGTGAGGTTGTGTA 59.661 52.381 0.00 0.00 35.13 2.90
4934 5957 5.240623 TGATTTCTGAGTTTATGTTTGCGGT 59.759 36.000 0.00 0.00 0.00 5.68
4936 5959 6.142139 TGTGATTTCTGAGTTTATGTTTGCG 58.858 36.000 0.00 0.00 0.00 4.85
4958 5981 2.644299 TGTTCCATGTGAAGGAGGATGT 59.356 45.455 0.00 0.00 36.33 3.06
4994 6021 3.117046 GCTTCATCGGTGCTTCTAGTAC 58.883 50.000 0.00 0.00 0.00 2.73
5014 6041 3.526931 TCACACCTAACTAGCAGATGC 57.473 47.619 0.00 0.00 42.49 3.91
5015 6042 5.700832 TGTTTTCACACCTAACTAGCAGATG 59.299 40.000 0.00 0.00 0.00 2.90
5016 6043 5.865085 TGTTTTCACACCTAACTAGCAGAT 58.135 37.500 0.00 0.00 0.00 2.90
5017 6044 5.284861 TGTTTTCACACCTAACTAGCAGA 57.715 39.130 0.00 0.00 0.00 4.26
5018 6045 5.527582 AGTTGTTTTCACACCTAACTAGCAG 59.472 40.000 0.00 0.00 30.32 4.24
5019 6046 5.433526 AGTTGTTTTCACACCTAACTAGCA 58.566 37.500 0.00 0.00 30.32 3.49
5020 6047 5.526111 TGAGTTGTTTTCACACCTAACTAGC 59.474 40.000 0.00 0.00 30.32 3.42
5070 6097 3.555966 AGTTTGCTCCTGCTACAACTTT 58.444 40.909 0.00 0.00 40.48 2.66
5120 6147 0.818040 GTTCCCGTGCAAGTTGTCCT 60.818 55.000 4.48 0.00 0.00 3.85
5133 6160 3.245048 GTCAAAAATTGTGCAAGTTCCCG 59.755 43.478 0.00 0.00 0.00 5.14
5185 6216 8.690884 TGGTGTTTGAAGTCATCTTTCATTAAA 58.309 29.630 0.00 0.00 33.64 1.52
5186 6217 8.231692 TGGTGTTTGAAGTCATCTTTCATTAA 57.768 30.769 0.00 0.00 33.64 1.40
5207 6238 4.130118 GTTAGTGGCCAGATAAGATGGTG 58.870 47.826 5.11 0.00 40.17 4.17
5216 6247 0.673644 GCACGTGTTAGTGGCCAGAT 60.674 55.000 18.38 0.00 42.09 2.90
5224 6255 1.920610 AGGGTCTAGCACGTGTTAGT 58.079 50.000 30.59 14.83 31.81 2.24
5229 6260 2.853731 CTAGAAGGGTCTAGCACGTG 57.146 55.000 12.28 12.28 45.29 4.49
5258 6289 5.291905 AGCTACAACTTCACACCTAAACT 57.708 39.130 0.00 0.00 0.00 2.66
5293 6324 2.493675 GGAAGCTTTGGGAGAAATGACC 59.506 50.000 0.00 0.00 0.00 4.02
5339 6383 4.914312 TTATAGCAACCAAAGAACGACG 57.086 40.909 0.00 0.00 0.00 5.12
5384 6428 4.021719 CCAATGCATCAAAGAGTGAGGTTT 60.022 41.667 0.00 0.00 40.27 3.27


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

AutoCloner maintained by Alex Coulton.