Multiple sequence alignment - TraesCS7D01G497400

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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 TraesCS7D01G497400 chr7D 100.000 2629 0 0 1 2629 603981571 603984199 0.000000e+00 4855
1 TraesCS7D01G497400 chr7D 89.170 1579 118 34 520 2069 604530609 604532163 0.000000e+00 1919
2 TraesCS7D01G497400 chr7D 84.141 1507 139 54 619 2069 603847518 603848980 0.000000e+00 1367
3 TraesCS7D01G497400 chr7D 100.000 658 0 0 2959 3616 603984529 603985186 0.000000e+00 1216
4 TraesCS7D01G497400 chr7D 86.126 1146 116 24 960 2069 604475308 604476446 0.000000e+00 1195
5 TraesCS7D01G497400 chr7D 83.793 290 44 2 148 434 4582520 4582231 4.600000e-69 272
6 TraesCS7D01G497400 chr7D 81.818 297 50 4 142 435 184674848 184675143 2.790000e-61 246
7 TraesCS7D01G497400 chr7A 93.771 2087 107 12 291 2362 696624177 696622099 0.000000e+00 3112
8 TraesCS7D01G497400 chr7A 83.649 1688 151 64 440 2069 696723997 696722377 0.000000e+00 1472
9 TraesCS7D01G497400 chr7A 86.268 1136 113 17 960 2069 696552633 696553751 0.000000e+00 1194
10 TraesCS7D01G497400 chr7A 82.570 677 65 27 2959 3614 696621389 696620745 6.830000e-152 547
11 TraesCS7D01G497400 chr7A 83.578 341 26 13 442 759 696552150 696552483 3.530000e-75 292
12 TraesCS7D01G497400 chr7A 82.877 146 20 4 1 143 696625056 696624913 3.790000e-25 126
13 TraesCS7D01G497400 chr7B 88.918 2265 184 33 148 2364 686889305 686887060 0.000000e+00 2730
14 TraesCS7D01G497400 chr7B 82.889 1724 149 51 440 2069 686849487 686851158 0.000000e+00 1415
15 TraesCS7D01G497400 chr7B 85.380 1197 117 27 901 2069 688162997 688164163 0.000000e+00 1188
16 TraesCS7D01G497400 chr7B 84.553 1243 129 28 861 2069 686966576 686965363 0.000000e+00 1173
17 TraesCS7D01G497400 chr7B 84.583 480 28 18 3136 3585 686886255 686885792 5.540000e-118 435
18 TraesCS7D01G497400 chr7B 84.881 377 32 11 435 797 686966935 686966570 1.230000e-94 357
19 TraesCS7D01G497400 chr7B 92.969 128 9 0 440 567 688162670 688162797 1.710000e-43 187
20 TraesCS7D01G497400 chr6D 84.828 290 41 2 148 434 5735721 5735432 4.570000e-74 289
21 TraesCS7D01G497400 chr6D 92.157 102 8 0 1985 2086 104454152 104454051 1.050000e-30 145
22 TraesCS7D01G497400 chr2D 84.175 297 43 3 148 440 453626010 453625714 5.910000e-73 285
23 TraesCS7D01G497400 chr2D 83.784 296 44 4 142 434 13594133 13594427 9.890000e-71 278
24 TraesCS7D01G497400 chr2D 83.498 303 44 5 142 439 357443094 357443395 9.890000e-71 278
25 TraesCS7D01G497400 chr4D 83.498 303 44 5 148 445 11871813 11871512 9.890000e-71 278
26 TraesCS7D01G497400 chr4A 83.737 289 45 2 148 434 94978583 94978295 4.600000e-69 272


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 TraesCS7D01G497400 chr7D 603981571 603985186 3615 False 3035.500000 4855 100.0000 1 3616 2 chr7D.!!$F5 3615
1 TraesCS7D01G497400 chr7D 604530609 604532163 1554 False 1919.000000 1919 89.1700 520 2069 1 chr7D.!!$F4 1549
2 TraesCS7D01G497400 chr7D 603847518 603848980 1462 False 1367.000000 1367 84.1410 619 2069 1 chr7D.!!$F2 1450
3 TraesCS7D01G497400 chr7D 604475308 604476446 1138 False 1195.000000 1195 86.1260 960 2069 1 chr7D.!!$F3 1109
4 TraesCS7D01G497400 chr7A 696722377 696723997 1620 True 1472.000000 1472 83.6490 440 2069 1 chr7A.!!$R1 1629
5 TraesCS7D01G497400 chr7A 696620745 696625056 4311 True 1261.666667 3112 86.4060 1 3614 3 chr7A.!!$R2 3613
6 TraesCS7D01G497400 chr7A 696552150 696553751 1601 False 743.000000 1194 84.9230 442 2069 2 chr7A.!!$F1 1627
7 TraesCS7D01G497400 chr7B 686885792 686889305 3513 True 1582.500000 2730 86.7505 148 3585 2 chr7B.!!$R1 3437
8 TraesCS7D01G497400 chr7B 686849487 686851158 1671 False 1415.000000 1415 82.8890 440 2069 1 chr7B.!!$F1 1629
9 TraesCS7D01G497400 chr7B 686965363 686966935 1572 True 765.000000 1173 84.7170 435 2069 2 chr7B.!!$R2 1634
10 TraesCS7D01G497400 chr7B 688162670 688164163 1493 False 687.500000 1188 89.1745 440 2069 2 chr7B.!!$F2 1629

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
208 343 0.107410 TGGTTTCTGTTCTGGTGCGT 60.107 50.0 0.00 0.0 0.00 5.24 F
465 1065 0.112995 AAGAACATCAAGGCAGGCCA 59.887 50.0 13.63 0.0 38.92 5.36 F
1571 2296 0.466543 AGTAACGAACACCCAGCACA 59.533 50.0 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1788 0.404426 TGAAGTCCTCCTCCACGAGA 59.596 55.0 0.00 0.0 30.97 4.04 R
2161 2928 0.524816 GACATGACCGCGTACGTGAT 60.525 55.0 29.24 14.1 37.70 3.06 R
3347 4682 0.169672 CATGCTGCTTCTGTTTCCGG 59.830 55.0 0.00 0.0 0.00 5.14 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
30 32 2.028190 CGATGCCGGAGCTGGTAG 59.972 66.667 5.05 0.00 40.80 3.18
38 40 2.294078 GGAGCTGGTAGGTGCTGGT 61.294 63.158 0.00 0.00 39.91 4.00
43 45 2.359975 GGTAGGTGCTGGTGGTGC 60.360 66.667 0.00 0.00 0.00 5.01
47 49 0.620410 TAGGTGCTGGTGGTGCCTAT 60.620 55.000 0.00 0.00 38.35 2.57
62 64 1.650912 CTATTGCATGCGTGGAGGC 59.349 57.895 14.09 0.00 0.00 4.70
67 69 4.758251 CATGCGTGGAGGCGGTGA 62.758 66.667 0.00 0.00 35.06 4.02
68 70 3.785859 ATGCGTGGAGGCGGTGAT 61.786 61.111 0.00 0.00 35.06 3.06
70 72 2.746277 GCGTGGAGGCGGTGATTT 60.746 61.111 0.00 0.00 0.00 2.17
72 74 1.501741 CGTGGAGGCGGTGATTTTG 59.498 57.895 0.00 0.00 0.00 2.44
103 105 1.378514 CGCTTAGGTGGGCCATGTT 60.379 57.895 10.70 0.38 37.19 2.71
126 128 3.728373 CCAAGGCGGGTTAGGGCT 61.728 66.667 0.00 0.00 42.77 5.19
133 135 1.289380 CGGGTTAGGGCTATCGCTC 59.711 63.158 0.00 0.00 36.78 5.03
139 141 1.782201 TAGGGCTATCGCTCCGGGTA 61.782 60.000 0.00 0.00 37.33 3.69
143 145 1.957562 CTATCGCTCCGGGTAGGTG 59.042 63.158 0.00 0.00 41.99 4.00
145 147 0.111832 TATCGCTCCGGGTAGGTGAT 59.888 55.000 0.00 9.86 41.99 3.06
146 148 1.179814 ATCGCTCCGGGTAGGTGATC 61.180 60.000 0.00 0.00 41.99 2.92
154 289 3.139584 TCCGGGTAGGTGATCTCAGATTA 59.860 47.826 0.00 0.00 41.99 1.75
194 329 3.366052 ACTCTTCAACAGTGGTGGTTT 57.634 42.857 8.65 0.00 0.00 3.27
195 330 3.279434 ACTCTTCAACAGTGGTGGTTTC 58.721 45.455 8.65 0.00 0.00 2.78
208 343 0.107410 TGGTTTCTGTTCTGGTGCGT 60.107 50.000 0.00 0.00 0.00 5.24
251 386 2.606725 CGACGACTTACCGACTGTCTAT 59.393 50.000 6.21 0.00 0.00 1.98
253 388 4.341099 GACGACTTACCGACTGTCTATTG 58.659 47.826 6.21 0.00 0.00 1.90
314 449 2.031012 CGGCACACCTTCAGCTCA 59.969 61.111 0.00 0.00 0.00 4.26
343 478 1.812235 TTGTAGTCGTCGCTAGGTGA 58.188 50.000 0.00 0.00 0.00 4.02
390 988 0.306533 ATTCGTGGTGTTCGTTGCAC 59.693 50.000 0.00 0.00 36.22 4.57
395 993 2.052237 GTGTTCGTTGCACCGCTG 60.052 61.111 0.00 0.00 0.00 5.18
465 1065 0.112995 AAGAACATCAAGGCAGGCCA 59.887 50.000 13.63 0.00 38.92 5.36
469 1069 0.682209 ACATCAAGGCAGGCCACATC 60.682 55.000 13.63 0.00 38.92 3.06
497 1097 3.309296 TCTTTGTTGGGGTGCCAAAATA 58.691 40.909 0.00 0.00 0.00 1.40
670 1296 3.742385 TCATGCTGATTGTCAGTGTCAA 58.258 40.909 5.27 5.27 45.94 3.18
967 1646 8.360390 GTCTTCTTCTTCTTCTTCTTCTTCTCT 58.640 37.037 0.00 0.00 0.00 3.10
1098 1788 2.526046 CCCTCCGGTGACCAAGGTT 61.526 63.158 16.33 0.00 0.00 3.50
1194 1884 1.893919 GCGAGGAGAACAGGAGGCTT 61.894 60.000 0.00 0.00 0.00 4.35
1229 1919 2.034879 CGCTGGTGGCCAAGTACTG 61.035 63.158 7.24 3.70 37.74 2.74
1506 2223 3.256178 TGCAAGGCCAGCAGGGTA 61.256 61.111 17.76 0.00 37.02 3.69
1518 2235 2.412591 AGCAGGGTATCCAAGCTGTAT 58.587 47.619 10.84 0.00 42.46 2.29
1536 2253 4.570663 GTCCACGCCGATCCCTCG 62.571 72.222 0.00 0.00 44.62 4.63
1571 2296 0.466543 AGTAACGAACACCCAGCACA 59.533 50.000 0.00 0.00 0.00 4.57
1622 2360 0.856641 TCGAAAGTTTCTTGCCGTCG 59.143 50.000 13.56 0.00 0.00 5.12
1872 2622 3.984193 GATGCAAGGCTCTGGCGGT 62.984 63.158 0.00 0.00 39.81 5.68
1952 2706 1.153289 AGCCGAAGCAGCAATCGAT 60.153 52.632 19.02 0.00 43.56 3.59
2025 2779 4.988716 ACGCTGACGAGGGACCCA 62.989 66.667 14.60 0.00 43.93 4.51
2028 2782 2.037367 CTGACGAGGGACCCAGGA 59.963 66.667 14.60 0.00 0.00 3.86
2132 2886 3.547413 CGTTTTCGTTTTGGTCTCCCTTC 60.547 47.826 0.00 0.00 38.65 3.46
2167 2934 7.667043 TGTAGCTGAAAATTTTAGATCACGT 57.333 32.000 2.75 0.00 0.00 4.49
2168 2935 8.766000 TGTAGCTGAAAATTTTAGATCACGTA 57.234 30.769 2.75 0.00 0.00 3.57
2169 2936 8.653338 TGTAGCTGAAAATTTTAGATCACGTAC 58.347 33.333 2.75 1.70 0.00 3.67
2170 2937 6.762108 AGCTGAAAATTTTAGATCACGTACG 58.238 36.000 15.01 15.01 0.00 3.67
2171 2938 5.448162 GCTGAAAATTTTAGATCACGTACGC 59.552 40.000 16.72 0.00 0.00 4.42
2172 2939 5.543716 TGAAAATTTTAGATCACGTACGCG 58.456 37.500 16.72 3.53 44.93 6.01
2173 2940 4.509915 AAATTTTAGATCACGTACGCGG 57.490 40.909 16.72 8.28 43.45 6.46
2174 2941 2.634982 TTTTAGATCACGTACGCGGT 57.365 45.000 16.72 0.42 43.45 5.68
2175 2942 2.178474 TTTAGATCACGTACGCGGTC 57.822 50.000 16.72 12.32 43.45 4.79
2176 2943 1.085893 TTAGATCACGTACGCGGTCA 58.914 50.000 18.01 2.48 43.45 4.02
2177 2944 1.302366 TAGATCACGTACGCGGTCAT 58.698 50.000 18.01 6.54 43.45 3.06
2201 2968 5.576384 TGTCATTAATTTTGAATTGCTCGCC 59.424 36.000 0.00 0.00 0.00 5.54
2292 3061 0.524862 CTGGAGTGGATGCAGCAAAC 59.475 55.000 3.51 0.97 40.79 2.93
2301 3071 6.066690 AGTGGATGCAGCAAACATATATTCT 58.933 36.000 3.51 0.00 0.00 2.40
2354 3124 9.554395 TTAGTACAACTTTCATGAATTCACAGA 57.446 29.630 11.07 9.26 0.00 3.41
2355 3125 8.627208 AGTACAACTTTCATGAATTCACAGAT 57.373 30.769 11.07 0.00 0.00 2.90
2356 3126 9.725019 AGTACAACTTTCATGAATTCACAGATA 57.275 29.630 11.07 6.51 0.00 1.98
2357 3127 9.979270 GTACAACTTTCATGAATTCACAGATAG 57.021 33.333 11.07 16.76 0.00 2.08
2358 3128 8.853077 ACAACTTTCATGAATTCACAGATAGA 57.147 30.769 24.17 10.72 0.00 1.98
2359 3129 9.288576 ACAACTTTCATGAATTCACAGATAGAA 57.711 29.630 24.17 14.43 0.00 2.10
2365 3135 8.812513 TCATGAATTCACAGATAGAAAATGGT 57.187 30.769 11.07 0.00 0.00 3.55
2400 3571 8.500753 AAATACAGCAATGTATTTACGGAAGA 57.499 30.769 19.55 0.00 46.78 2.87
2403 3574 5.296780 ACAGCAATGTATTTACGGAAGATGG 59.703 40.000 0.00 0.00 0.00 3.51
2404 3575 4.275936 AGCAATGTATTTACGGAAGATGGC 59.724 41.667 0.00 0.00 0.00 4.40
2428 3599 7.814587 GGCTACAGAAATATGCTTGTTTTTCTT 59.185 33.333 0.00 0.00 36.54 2.52
2429 3600 9.196552 GCTACAGAAATATGCTTGTTTTTCTTT 57.803 29.630 0.00 0.00 36.54 2.52
2434 3605 8.915654 AGAAATATGCTTGTTTTTCTTTAAGCG 58.084 29.630 0.00 0.00 46.31 4.68
2449 3620 3.162448 AGCGCCGGTGCTTATTTTA 57.838 47.368 36.21 0.00 44.46 1.52
2453 3624 2.538939 GCGCCGGTGCTTATTTTAAGAG 60.539 50.000 32.27 0.00 34.43 2.85
2456 3629 3.064958 GCCGGTGCTTATTTTAAGAGGAC 59.935 47.826 1.90 0.00 33.53 3.85
2458 3631 4.881850 CCGGTGCTTATTTTAAGAGGACAT 59.118 41.667 0.00 0.00 33.96 3.06
2461 3634 6.537301 CGGTGCTTATTTTAAGAGGACATACA 59.463 38.462 0.00 0.00 33.96 2.29
2479 3652 8.142551 GGACATACACTTAATTAGAGATCCGTT 58.857 37.037 0.00 0.00 0.00 4.44
2483 3656 6.043411 ACACTTAATTAGAGATCCGTTCTGC 58.957 40.000 0.00 0.00 33.74 4.26
2487 3660 5.344743 AATTAGAGATCCGTTCTGCAGAA 57.655 39.130 25.16 25.16 33.74 3.02
2491 3664 5.543507 AGAGATCCGTTCTGCAGAAATAT 57.456 39.130 29.99 21.68 35.58 1.28
2504 3677 9.534565 TTCTGCAGAAATATGACTAGTGATTAC 57.465 33.333 26.61 0.00 0.00 1.89
2536 3813 8.994429 TTGATTTCTTTTACAAAGCACTTTCA 57.006 26.923 0.00 0.00 29.14 2.69
2554 3831 5.183904 ACTTTCATAAGAACCCTGCATTGTC 59.816 40.000 0.00 0.00 35.30 3.18
2563 3840 1.377725 CTGCATTGTCCGAGGCCTT 60.378 57.895 6.77 0.00 0.00 4.35
2594 3871 3.017442 GTGGGGTTTTAGCTTGAGGATC 58.983 50.000 0.00 0.00 0.00 3.36
2613 3890 1.783031 CGATGTAGGCTACGCGAGGT 61.783 60.000 25.83 7.72 32.99 3.85
2614 3891 1.233019 GATGTAGGCTACGCGAGGTA 58.767 55.000 15.93 0.68 0.00 3.08
2615 3892 1.605710 GATGTAGGCTACGCGAGGTAA 59.394 52.381 15.93 0.00 0.00 2.85
2617 3894 2.849942 TGTAGGCTACGCGAGGTAATA 58.150 47.619 15.93 0.00 0.00 0.98
2618 3895 3.213506 TGTAGGCTACGCGAGGTAATAA 58.786 45.455 15.93 0.00 0.00 1.40
2620 3897 3.366440 AGGCTACGCGAGGTAATAAAG 57.634 47.619 15.93 0.00 0.00 1.85
2621 3898 2.954318 AGGCTACGCGAGGTAATAAAGA 59.046 45.455 15.93 0.00 0.00 2.52
2626 3903 3.778618 ACGCGAGGTAATAAAGAAGACC 58.221 45.455 15.93 0.00 0.00 3.85
3000 4303 2.354510 TGTGGCTGTTTTCGAAGTTCTG 59.645 45.455 0.00 0.00 0.00 3.02
3052 4355 7.716998 ACAGATATGAGTGTGCTATTTAAAGGG 59.283 37.037 0.00 0.00 0.00 3.95
3053 4356 7.933577 CAGATATGAGTGTGCTATTTAAAGGGA 59.066 37.037 0.00 0.00 0.00 4.20
3054 4357 8.153550 AGATATGAGTGTGCTATTTAAAGGGAG 58.846 37.037 0.00 0.00 0.00 4.30
3062 4365 8.523658 GTGTGCTATTTAAAGGGAGAAAAATCT 58.476 33.333 0.00 0.00 0.00 2.40
3065 4368 8.458843 TGCTATTTAAAGGGAGAAAAATCTTCG 58.541 33.333 0.00 0.00 0.00 3.79
3083 4386 5.767269 TCTTCGTTGCTTTTCATTGCATTA 58.233 33.333 0.00 0.00 39.07 1.90
3090 4413 9.201424 CGTTGCTTTTCATTGCATTATATTTTG 57.799 29.630 0.00 0.00 39.07 2.44
3119 4442 4.009675 TGCCCTCTACATTAAACAAGCAG 58.990 43.478 0.00 0.00 0.00 4.24
3125 4457 6.481644 CCTCTACATTAAACAAGCAGGATCTC 59.518 42.308 0.00 0.00 0.00 2.75
3127 4459 7.268586 TCTACATTAAACAAGCAGGATCTCTC 58.731 38.462 0.00 0.00 0.00 3.20
3129 4461 6.112058 ACATTAAACAAGCAGGATCTCTCTC 58.888 40.000 0.00 0.00 0.00 3.20
3132 4464 4.906747 AACAAGCAGGATCTCTCTCTTT 57.093 40.909 0.00 0.00 0.00 2.52
3133 4465 4.906747 ACAAGCAGGATCTCTCTCTTTT 57.093 40.909 0.00 0.00 0.00 2.27
3134 4466 5.240013 ACAAGCAGGATCTCTCTCTTTTT 57.760 39.130 0.00 0.00 0.00 1.94
3181 4513 0.900547 GAAAACGCGCATCATGTTCG 59.099 50.000 5.73 0.13 0.00 3.95
3182 4514 0.515127 AAAACGCGCATCATGTTCGA 59.485 45.000 5.73 0.00 0.00 3.71
3183 4515 0.515127 AAACGCGCATCATGTTCGAA 59.485 45.000 5.73 0.00 0.00 3.71
3184 4516 0.515127 AACGCGCATCATGTTCGAAA 59.485 45.000 5.73 0.00 0.00 3.46
3185 4517 0.726827 ACGCGCATCATGTTCGAAAT 59.273 45.000 5.73 0.00 0.00 2.17
3186 4518 1.930503 ACGCGCATCATGTTCGAAATA 59.069 42.857 5.73 0.00 0.00 1.40
3187 4519 2.350192 ACGCGCATCATGTTCGAAATAA 59.650 40.909 5.73 0.00 0.00 1.40
3188 4520 2.960266 CGCGCATCATGTTCGAAATAAG 59.040 45.455 8.75 0.00 0.00 1.73
3189 4521 3.302415 CGCGCATCATGTTCGAAATAAGA 60.302 43.478 8.75 0.00 0.00 2.10
3190 4522 4.609113 CGCGCATCATGTTCGAAATAAGAT 60.609 41.667 8.75 0.00 0.00 2.40
3191 4523 4.610122 GCGCATCATGTTCGAAATAAGATG 59.390 41.667 18.91 18.91 35.67 2.90
3192 4524 5.558844 GCGCATCATGTTCGAAATAAGATGA 60.559 40.000 23.78 13.55 41.63 2.92
3193 4525 6.069563 CGCATCATGTTCGAAATAAGATGAG 58.930 40.000 23.78 19.44 40.99 2.90
3275 4610 1.227205 CAGTCGGAGATCTGCTGCC 60.227 63.158 12.78 0.18 40.67 4.85
3331 4666 1.582968 CGAAGGACGACGGAGGAAA 59.417 57.895 0.00 0.00 45.77 3.13
3347 4682 0.461163 GAAAGAGAGAGGAAGCCGGC 60.461 60.000 21.89 21.89 0.00 6.13
3394 4744 1.841556 GGGGCCACGATGGGATCTA 60.842 63.158 4.39 0.00 38.19 1.98
3436 4786 1.553195 CGGTCAAACACGTGCGATGA 61.553 55.000 17.22 14.52 0.00 2.92
3440 4790 2.325082 AAACACGTGCGATGAGGCC 61.325 57.895 17.22 0.00 0.00 5.19
3480 4830 1.517257 GTCATCTCGTCCACGCTGG 60.517 63.158 0.00 0.00 39.43 4.85
3481 4831 2.202797 CATCTCGTCCACGCTGGG 60.203 66.667 4.52 0.00 38.32 4.45
3483 4833 1.758514 ATCTCGTCCACGCTGGGAT 60.759 57.895 0.00 0.00 39.62 3.85
3484 4834 2.021068 ATCTCGTCCACGCTGGGATG 62.021 60.000 0.00 6.43 43.93 3.51
3537 4897 4.491676 CAAATGCCTTTCTCACTGGAATG 58.508 43.478 0.00 0.00 0.00 2.67
3538 4900 1.538047 TGCCTTTCTCACTGGAATGC 58.462 50.000 0.00 0.00 0.00 3.56
3591 4955 2.702592 TTCATTAAGTACCCGCCCTG 57.297 50.000 0.00 0.00 0.00 4.45
3592 4956 1.575419 TCATTAAGTACCCGCCCTGT 58.425 50.000 0.00 0.00 0.00 4.00
3611 4976 5.428253 CCTGTTGCTAGATTAGTTTAGGCA 58.572 41.667 0.00 0.00 0.00 4.75
3614 4979 6.889198 TGTTGCTAGATTAGTTTAGGCATCT 58.111 36.000 0.00 0.00 0.00 2.90
3615 4980 7.338710 TGTTGCTAGATTAGTTTAGGCATCTT 58.661 34.615 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.365635 ACCTACCAGCTCCGGCAT 60.366 61.111 0.00 0.00 41.70 4.40
16 17 3.390521 CACCTACCAGCTCCGGCA 61.391 66.667 0.00 0.00 41.70 5.69
18 19 3.077556 AGCACCTACCAGCTCCGG 61.078 66.667 0.00 0.00 36.00 5.14
19 20 2.185350 CAGCACCTACCAGCTCCG 59.815 66.667 0.00 0.00 39.50 4.63
20 21 2.294078 ACCAGCACCTACCAGCTCC 61.294 63.158 0.00 0.00 39.50 4.70
22 23 2.596851 CCACCAGCACCTACCAGCT 61.597 63.158 0.00 0.00 42.94 4.24
23 24 2.045926 CCACCAGCACCTACCAGC 60.046 66.667 0.00 0.00 0.00 4.85
24 25 1.003355 CACCACCAGCACCTACCAG 60.003 63.158 0.00 0.00 0.00 4.00
26 27 2.359975 GCACCACCAGCACCTACC 60.360 66.667 0.00 0.00 0.00 3.18
30 32 1.000896 AATAGGCACCACCAGCACC 60.001 57.895 0.00 0.00 43.14 5.01
43 45 1.789078 GCCTCCACGCATGCAATAGG 61.789 60.000 19.57 17.97 0.00 2.57
55 57 0.521735 GTCAAAATCACCGCCTCCAC 59.478 55.000 0.00 0.00 0.00 4.02
56 58 0.608035 GGTCAAAATCACCGCCTCCA 60.608 55.000 0.00 0.00 0.00 3.86
62 64 1.065418 AGCCCTAGGTCAAAATCACCG 60.065 52.381 8.29 0.00 39.13 4.94
126 128 0.111832 ATCACCTACCCGGAGCGATA 59.888 55.000 0.73 0.00 36.31 2.92
133 135 2.002505 ATCTGAGATCACCTACCCGG 57.997 55.000 0.00 0.00 39.35 5.73
170 305 2.224281 CCACCACTGTTGAAGAGTAGCA 60.224 50.000 0.00 0.00 0.00 3.49
172 307 3.753294 ACCACCACTGTTGAAGAGTAG 57.247 47.619 0.00 0.00 0.00 2.57
194 329 0.531974 GACCAACGCACCAGAACAGA 60.532 55.000 0.00 0.00 0.00 3.41
195 330 1.507141 GGACCAACGCACCAGAACAG 61.507 60.000 0.00 0.00 0.00 3.16
208 343 3.451178 GTGCTAAGACTCCATAGGACCAA 59.549 47.826 0.00 0.00 35.26 3.67
296 431 3.426568 GAGCTGAAGGTGTGCCGC 61.427 66.667 0.00 0.00 40.50 6.53
314 449 3.822996 CGACGACTACAATCACTGAAGT 58.177 45.455 0.00 0.00 0.00 3.01
465 1065 4.411869 ACCCCAACAAAGAAAATTGGATGT 59.588 37.500 3.80 0.00 44.84 3.06
469 1069 2.877786 GCACCCCAACAAAGAAAATTGG 59.122 45.455 0.00 0.00 42.21 3.16
497 1097 3.228453 CTGGGGATGCTTTCATGCTTAT 58.772 45.455 0.00 0.00 40.41 1.73
967 1646 5.045651 TGAATTCCCAGTAGCTCAAGAATGA 60.046 40.000 2.27 0.00 0.00 2.57
984 1663 4.695455 TCGTCCATGTCTTTCTTGAATTCC 59.305 41.667 2.27 0.00 0.00 3.01
1098 1788 0.404426 TGAAGTCCTCCTCCACGAGA 59.596 55.000 0.00 0.00 30.97 4.04
1506 2223 1.743772 GCGTGGACATACAGCTTGGAT 60.744 52.381 0.00 0.00 0.00 3.41
1515 2232 1.300697 GGGATCGGCGTGGACATAC 60.301 63.158 6.85 0.00 0.00 2.39
1518 2235 3.458163 GAGGGATCGGCGTGGACA 61.458 66.667 6.85 0.00 0.00 4.02
1536 2253 1.760192 TACTTACGAGGCTGAGGTCC 58.240 55.000 0.00 0.00 0.00 4.46
1571 2296 2.104170 GAGGAAGAAGATGGACGGACT 58.896 52.381 0.00 0.00 0.00 3.85
1622 2360 6.687105 ACGAAGCGCAAATTGATTAGTTAATC 59.313 34.615 11.47 5.18 41.81 1.75
1872 2622 3.818787 GCGTCGGCGGACTTCCTA 61.819 66.667 20.54 0.00 41.16 2.94
2025 2779 4.101448 AGCGCCGCCTTGAATCCT 62.101 61.111 4.98 0.00 0.00 3.24
2028 2782 4.760047 ACGAGCGCCGCCTTGAAT 62.760 61.111 16.48 0.00 43.32 2.57
2161 2928 0.524816 GACATGACCGCGTACGTGAT 60.525 55.000 29.24 14.10 37.70 3.06
2165 2932 1.830086 TAATGACATGACCGCGTACG 58.170 50.000 11.84 11.84 39.67 3.67
2167 2934 5.351740 TCAAAATTAATGACATGACCGCGTA 59.648 36.000 4.92 0.00 0.00 4.42
2168 2935 4.155099 TCAAAATTAATGACATGACCGCGT 59.845 37.500 4.92 0.00 0.00 6.01
2169 2936 4.657055 TCAAAATTAATGACATGACCGCG 58.343 39.130 0.00 0.00 0.00 6.46
2170 2937 7.393327 CAATTCAAAATTAATGACATGACCGC 58.607 34.615 0.00 0.00 0.00 5.68
2171 2938 7.276218 AGCAATTCAAAATTAATGACATGACCG 59.724 33.333 0.00 0.00 0.00 4.79
2172 2939 8.483307 AGCAATTCAAAATTAATGACATGACC 57.517 30.769 0.00 0.00 0.00 4.02
2173 2940 8.316046 CGAGCAATTCAAAATTAATGACATGAC 58.684 33.333 0.00 0.00 0.00 3.06
2174 2941 7.009448 GCGAGCAATTCAAAATTAATGACATGA 59.991 33.333 0.00 0.00 0.00 3.07
2175 2942 7.114920 GCGAGCAATTCAAAATTAATGACATG 58.885 34.615 0.00 0.00 0.00 3.21
2176 2943 6.256321 GGCGAGCAATTCAAAATTAATGACAT 59.744 34.615 0.00 0.00 0.00 3.06
2177 2944 5.576384 GGCGAGCAATTCAAAATTAATGACA 59.424 36.000 0.00 0.00 0.00 3.58
2362 3132 9.461312 ACATTGCTGTATTTTTCTATCTAACCA 57.539 29.630 0.00 0.00 32.49 3.67
2386 3557 5.361571 TCTGTAGCCATCTTCCGTAAATACA 59.638 40.000 0.00 0.00 0.00 2.29
2389 3560 5.353394 TTCTGTAGCCATCTTCCGTAAAT 57.647 39.130 0.00 0.00 0.00 1.40
2394 3565 4.153117 GCATATTTCTGTAGCCATCTTCCG 59.847 45.833 0.00 0.00 0.00 4.30
2400 3571 6.780457 AAACAAGCATATTTCTGTAGCCAT 57.220 33.333 0.00 0.00 0.00 4.40
2403 3574 8.748380 AAGAAAAACAAGCATATTTCTGTAGC 57.252 30.769 0.00 0.00 40.28 3.58
2434 3605 3.064958 GTCCTCTTAAAATAAGCACCGGC 59.935 47.826 0.00 0.00 41.61 6.13
2453 3624 7.659186 ACGGATCTCTAATTAAGTGTATGTCC 58.341 38.462 0.00 0.00 0.00 4.02
2456 3629 9.186323 CAGAACGGATCTCTAATTAAGTGTATG 57.814 37.037 0.00 0.00 35.73 2.39
2458 3631 7.147966 TGCAGAACGGATCTCTAATTAAGTGTA 60.148 37.037 0.00 0.00 35.73 2.90
2461 3634 6.096987 TCTGCAGAACGGATCTCTAATTAAGT 59.903 38.462 15.67 0.00 35.73 2.24
2471 3644 5.053145 GTCATATTTCTGCAGAACGGATCT 58.947 41.667 28.46 9.83 39.68 2.75
2472 3645 5.053145 AGTCATATTTCTGCAGAACGGATC 58.947 41.667 28.46 16.26 33.13 3.36
2479 3652 8.695456 TGTAATCACTAGTCATATTTCTGCAGA 58.305 33.333 13.74 13.74 0.00 4.26
2510 3688 9.429359 TGAAAGTGCTTTGTAAAAGAAATCAAA 57.571 25.926 1.51 0.00 32.11 2.69
2518 3696 8.968242 GGTTCTTATGAAAGTGCTTTGTAAAAG 58.032 33.333 1.51 0.00 33.52 2.27
2536 3813 2.238646 TCGGACAATGCAGGGTTCTTAT 59.761 45.455 0.00 0.00 0.00 1.73
2563 3840 4.911522 AGCTAAAACCCCACATAGCCTATA 59.088 41.667 0.00 0.00 41.25 1.31
2971 4274 3.119316 TCGAAAACAGCCACACAAACAAT 60.119 39.130 0.00 0.00 0.00 2.71
2980 4283 2.854805 GCAGAACTTCGAAAACAGCCAC 60.855 50.000 0.00 0.00 0.00 5.01
3027 4330 7.933577 TCCCTTTAAATAGCACACTCATATCTG 59.066 37.037 0.00 0.00 0.00 2.90
3052 4355 7.629027 ATGAAAAGCAACGAAGATTTTTCTC 57.371 32.000 8.64 0.00 38.14 2.87
3053 4356 7.517259 GCAATGAAAAGCAACGAAGATTTTTCT 60.517 33.333 8.64 0.00 38.14 2.52
3054 4357 6.571154 GCAATGAAAAGCAACGAAGATTTTTC 59.429 34.615 8.64 8.67 37.92 2.29
3062 4365 8.700722 AATATAATGCAATGAAAAGCAACGAA 57.299 26.923 0.00 0.00 44.88 3.85
3083 4386 7.716799 TGTAGAGGGCAATCAAACAAAATAT 57.283 32.000 0.00 0.00 0.00 1.28
3090 4413 6.919721 TGTTTAATGTAGAGGGCAATCAAAC 58.080 36.000 0.00 0.00 0.00 2.93
3094 4417 5.125417 TGCTTGTTTAATGTAGAGGGCAATC 59.875 40.000 0.00 0.00 0.00 2.67
3134 4466 1.406860 GCTGGTTGCCCCCTCAAAAA 61.407 55.000 0.00 0.00 35.15 1.94
3135 4467 1.836604 GCTGGTTGCCCCCTCAAAA 60.837 57.895 0.00 0.00 35.15 2.44
3136 4468 2.203625 GCTGGTTGCCCCCTCAAA 60.204 61.111 0.00 0.00 35.15 2.69
3137 4469 3.506743 TGCTGGTTGCCCCCTCAA 61.507 61.111 0.00 0.00 42.00 3.02
3138 4470 3.970410 CTGCTGGTTGCCCCCTCA 61.970 66.667 0.00 0.00 42.00 3.86
3139 4471 4.748144 CCTGCTGGTTGCCCCCTC 62.748 72.222 0.51 0.00 42.00 4.30
3145 4477 1.538047 TTCAAGATCCTGCTGGTTGC 58.462 50.000 9.73 0.71 43.25 4.17
3186 4518 9.076781 TCGATCTTGATCTTATTCTCTCATCTT 57.923 33.333 8.70 0.00 0.00 2.40
3187 4519 8.634335 TCGATCTTGATCTTATTCTCTCATCT 57.366 34.615 8.70 0.00 0.00 2.90
3188 4520 9.507280 GATCGATCTTGATCTTATTCTCTCATC 57.493 37.037 18.29 0.00 41.26 2.92
3189 4521 8.469200 GGATCGATCTTGATCTTATTCTCTCAT 58.531 37.037 23.96 0.00 43.46 2.90
3190 4522 7.449704 TGGATCGATCTTGATCTTATTCTCTCA 59.550 37.037 23.96 5.30 43.46 3.27
3191 4523 7.825681 TGGATCGATCTTGATCTTATTCTCTC 58.174 38.462 23.96 2.77 43.46 3.20
3192 4524 7.577426 GCTGGATCGATCTTGATCTTATTCTCT 60.577 40.741 23.96 0.00 43.46 3.10
3193 4525 6.531240 GCTGGATCGATCTTGATCTTATTCTC 59.469 42.308 23.96 3.75 43.46 2.87
3275 4610 2.474359 CACTCGTTTTCTCTGCTGTCTG 59.526 50.000 0.00 0.00 0.00 3.51
3324 4659 1.484653 GGCTTCCTCTCTCTTTCCTCC 59.515 57.143 0.00 0.00 0.00 4.30
3331 4666 2.762043 GGCCGGCTTCCTCTCTCT 60.762 66.667 28.56 0.00 0.00 3.10
3347 4682 0.169672 CATGCTGCTTCTGTTTCCGG 59.830 55.000 0.00 0.00 0.00 5.14
3378 4728 0.759346 AACTAGATCCCATCGTGGCC 59.241 55.000 0.00 0.00 35.79 5.36
3379 4729 2.213499 CAAACTAGATCCCATCGTGGC 58.787 52.381 0.00 0.00 35.79 5.01
3394 4744 4.048504 GCACGAATTAAACAAGCCAAACT 58.951 39.130 0.00 0.00 0.00 2.66
3465 4815 1.758514 ATCCCAGCGTGGACGAGAT 60.759 57.895 2.73 0.00 40.96 2.75
3480 4830 1.648467 GAAGGAGTTGTGCCGCATCC 61.648 60.000 0.00 0.00 0.00 3.51
3481 4831 1.796796 GAAGGAGTTGTGCCGCATC 59.203 57.895 0.00 0.00 0.00 3.91
3483 4833 2.449031 ATCGAAGGAGTTGTGCCGCA 62.449 55.000 0.00 0.00 0.00 5.69
3484 4834 1.696832 GATCGAAGGAGTTGTGCCGC 61.697 60.000 0.00 0.00 0.00 6.53
3492 4852 2.451490 TGCAGAAGAGATCGAAGGAGT 58.549 47.619 0.00 0.00 0.00 3.85
3526 4886 5.471456 AGTTAGACAAAAGCATTCCAGTGAG 59.529 40.000 0.00 0.00 0.00 3.51
3537 4897 5.178809 ACACGTGGAATAGTTAGACAAAAGC 59.821 40.000 21.57 0.00 0.00 3.51
3538 4900 6.780706 ACACGTGGAATAGTTAGACAAAAG 57.219 37.500 21.57 0.00 0.00 2.27
3591 4955 7.793927 AAGATGCCTAAACTAATCTAGCAAC 57.206 36.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.