Multiple sequence alignment - TraesCS7D01G262700

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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 TraesCS7D01G262700 chr7D 100.000 4397 0 0 1 4397 241880075 241884471 0.000000e+00 8120.0
1 TraesCS7D01G262700 chr7D 81.053 95 13 4 225 314 394049711 394049805 2.190000e-08 71.3
2 TraesCS7D01G262700 chr7D 81.053 95 13 5 225 314 546540254 546540348 2.190000e-08 71.3
3 TraesCS7D01G262700 chr7B 93.126 3404 115 52 538 3883 217623480 217626822 0.000000e+00 4879.0
4 TraesCS7D01G262700 chr7B 90.726 496 16 16 3926 4393 217626830 217627323 6.200000e-178 634.0
5 TraesCS7D01G262700 chr7B 83.607 305 42 6 224 524 217620205 217620505 3.350000e-71 279.0
6 TraesCS7D01G262700 chr7A 92.564 3066 109 52 792 3779 256215796 256212772 0.000000e+00 4289.0
7 TraesCS7D01G262700 chr7A 89.106 817 79 5 1 807 256216658 256215842 0.000000e+00 1007.0
8 TraesCS7D01G262700 chr7A 82.661 496 40 26 3926 4394 256212689 256212213 8.860000e-107 398.0
9 TraesCS7D01G262700 chr7A 78.505 107 19 4 387 491 517888679 517888575 2.840000e-07 67.6
10 TraesCS7D01G262700 chr5B 81.639 305 49 5 224 526 689868965 689868666 3.400000e-61 246.0
11 TraesCS7D01G262700 chr5B 87.895 190 18 3 9 193 87108676 87108865 7.400000e-53 219.0
12 TraesCS7D01G262700 chr3D 85.169 236 27 5 224 457 322768901 322768672 7.350000e-58 235.0
13 TraesCS7D01G262700 chr3D 88.083 193 18 4 7 194 17955884 17955692 1.590000e-54 224.0
14 TraesCS7D01G262700 chr3D 88.021 192 18 3 7 193 170309026 170308835 5.720000e-54 222.0
15 TraesCS7D01G262700 chr6B 87.817 197 20 3 1 193 606918080 606918276 1.230000e-55 228.0
16 TraesCS7D01G262700 chr6B 86.869 198 20 5 1 193 372569910 372570106 2.660000e-52 217.0
17 TraesCS7D01G262700 chr6B 82.667 150 22 4 3055 3202 471630547 471630694 3.570000e-26 130.0
18 TraesCS7D01G262700 chr4D 88.021 192 18 3 7 193 336023318 336023127 5.720000e-54 222.0
19 TraesCS7D01G262700 chr4D 78.523 149 32 0 2253 2401 381888642 381888494 1.010000e-16 99.0
20 TraesCS7D01G262700 chr2D 87.435 191 20 2 7 193 308244994 308244804 2.660000e-52 217.0
21 TraesCS7D01G262700 chr4B 86.911 191 21 3 7 193 87794591 87794401 1.240000e-50 211.0
22 TraesCS7D01G262700 chr4B 77.852 149 33 0 2253 2401 469034938 469034790 4.680000e-15 93.5
23 TraesCS7D01G262700 chr3A 80.889 225 35 6 235 457 400752298 400752516 2.100000e-38 171.0
24 TraesCS7D01G262700 chr6A 82.550 149 24 2 3055 3202 409413831 409413978 3.570000e-26 130.0
25 TraesCS7D01G262700 chr6D 81.013 158 28 2 3055 3211 305179756 305179600 1.660000e-24 124.0
26 TraesCS7D01G262700 chr1B 78.857 175 35 1 237 409 11414411 11414585 2.780000e-22 117.0
27 TraesCS7D01G262700 chr4A 71.899 516 104 36 1884 2386 81800034 81800521 1.290000e-20 111.0
28 TraesCS7D01G262700 chr3B 73.606 269 67 3 244 508 53205177 53205445 2.800000e-17 100.0
29 TraesCS7D01G262700 chr3B 79.412 136 25 2 283 415 53201487 53201622 4.680000e-15 93.5
30 TraesCS7D01G262700 chr3B 83.951 81 13 0 443 523 2036890 2036970 1.310000e-10 78.7
31 TraesCS7D01G262700 chr5D 81.481 81 13 2 391 470 89578771 89578850 1.020000e-06 65.8
32 TraesCS7D01G262700 chr5D 80.247 81 9 5 397 474 193197483 193197407 2.000000e-03 54.7


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 TraesCS7D01G262700 chr7D 241880075 241884471 4396 False 8120.000000 8120 100.000000 1 4397 1 chr7D.!!$F1 4396
1 TraesCS7D01G262700 chr7B 217620205 217627323 7118 False 1930.666667 4879 89.153000 224 4393 3 chr7B.!!$F1 4169
2 TraesCS7D01G262700 chr7A 256212213 256216658 4445 True 1898.000000 4289 88.110333 1 4394 3 chr7A.!!$R2 4393

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
382 386 0.034380 GTTTAGGTCTGGCCCCCTTC 60.034 60.0 10.66 0.62 38.26 3.46 F
1104 4153 0.967380 CCTTCCTCACAACCCCATGC 60.967 60.0 0.00 0.00 0.00 4.06 F
1490 4540 0.035152 TTACCTGCAGCATCCCTGTG 60.035 55.0 8.66 0.00 43.71 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 4373 0.459237 CAACCTGCGCAAACAAACCA 60.459 50.0 13.05 0.00 0.0 3.67 R
2584 5663 0.031043 CATCTCTGCTCTGCTCTCCG 59.969 60.0 0.00 0.00 0.0 4.63 R
3489 6619 0.319211 ACGTACTACAGCGCTGCAAA 60.319 50.0 36.28 20.92 0.0 3.68 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
18 19 1.227089 CGATCAGCTGTTCGAGGGG 60.227 63.158 33.40 10.89 38.99 4.79
40 42 0.109226 CGGACGAGGAGGAGACAAAC 60.109 60.000 0.00 0.00 0.00 2.93
49 51 2.741211 GAGACAAACCCCGCGGAC 60.741 66.667 30.73 8.51 0.00 4.79
68 70 1.635663 CGCGCTACCCCAACTCTTTG 61.636 60.000 5.56 0.00 0.00 2.77
71 73 1.002087 CGCTACCCCAACTCTTTGTCT 59.998 52.381 0.00 0.00 0.00 3.41
73 75 2.427506 CTACCCCAACTCTTTGTCTGC 58.572 52.381 0.00 0.00 0.00 4.26
78 80 1.884579 CCAACTCTTTGTCTGCTGCAT 59.115 47.619 1.31 0.00 0.00 3.96
83 85 0.530744 CTTTGTCTGCTGCATGGCAT 59.469 50.000 1.31 0.00 41.63 4.40
88 90 4.805231 TGCTGCATGGCATTGCGC 62.805 61.111 19.97 19.97 45.77 6.09
90 92 4.485834 CTGCATGGCATTGCGCGT 62.486 61.111 8.43 0.00 45.77 6.01
91 93 4.479542 TGCATGGCATTGCGCGTC 62.480 61.111 8.43 0.00 45.77 5.19
99 101 0.804544 GCATTGCGCGTCTAGTGGTA 60.805 55.000 8.43 0.00 0.00 3.25
120 122 0.961753 CGATCCGTGATCCATCTCCA 59.038 55.000 7.91 0.00 35.83 3.86
131 133 3.827008 TCCATCTCCAGTAGCATGTTC 57.173 47.619 0.00 0.00 0.00 3.18
141 143 3.624861 CAGTAGCATGTTCCTGGATGTTC 59.375 47.826 0.00 0.00 0.00 3.18
154 156 1.065709 GGATGTTCTGCGGGTAGGAAA 60.066 52.381 0.00 0.00 0.00 3.13
178 182 2.506438 GCAGTCGACGCACCCTAC 60.506 66.667 21.73 0.77 0.00 3.18
179 183 2.991076 GCAGTCGACGCACCCTACT 61.991 63.158 21.73 0.00 0.00 2.57
201 205 9.832445 CTACTGTAGAACCCAACATTACATATT 57.168 33.333 9.22 0.00 0.00 1.28
212 216 8.840321 CCCAACATTACATATTTTCTACCTCTG 58.160 37.037 0.00 0.00 0.00 3.35
232 236 7.178628 ACCTCTGCTACTTCTGTATGTTCTAAA 59.821 37.037 0.00 0.00 0.00 1.85
233 237 8.200792 CCTCTGCTACTTCTGTATGTTCTAAAT 58.799 37.037 0.00 0.00 0.00 1.40
264 268 0.249868 TGACCGCACCTTCACTTCAG 60.250 55.000 0.00 0.00 0.00 3.02
287 291 3.650907 TTTATCGCCGCCGCTCACA 62.651 57.895 0.00 0.00 0.00 3.58
300 304 1.513158 CTCACAGAGACGGCGGATT 59.487 57.895 13.24 0.00 0.00 3.01
372 376 3.286353 GCCGTAGTCTAGGTTTAGGTCT 58.714 50.000 0.00 0.00 0.00 3.85
375 379 3.066481 CGTAGTCTAGGTTTAGGTCTGGC 59.934 52.174 0.00 0.00 0.00 4.85
382 386 0.034380 GTTTAGGTCTGGCCCCCTTC 60.034 60.000 10.66 0.62 38.26 3.46
395 399 3.195610 GGCCCCCTTCTGTTAATGAAAAG 59.804 47.826 0.00 0.00 0.00 2.27
432 436 3.758023 TGAATGTGCTCCAGTTTGTATGG 59.242 43.478 0.00 0.00 39.33 2.74
440 444 6.488006 GTGCTCCAGTTTGTATGGATATCAAT 59.512 38.462 4.83 0.77 45.64 2.57
475 479 6.752815 TGAATTTTGTTCGGTTAGTTGAAACC 59.247 34.615 0.00 0.00 44.63 3.27
519 532 2.886730 ATTGGATGACCGGTTCCCGC 62.887 60.000 20.37 3.07 46.86 6.13
524 3497 2.511600 GACCGGTTCCCGCATCTG 60.512 66.667 9.42 0.00 46.86 2.90
531 3504 1.069090 TTCCCGCATCTGTATCCGC 59.931 57.895 0.00 0.00 0.00 5.54
535 3508 1.080501 CGCATCTGTATCCGCGGAT 60.081 57.895 39.97 39.97 43.84 4.18
541 3514 4.555708 GCATCTGTATCCGCGGATAGATAG 60.556 50.000 40.85 34.43 37.72 2.08
557 3530 2.104281 AGATAGGGTGTCCGGTTTATGC 59.896 50.000 0.00 0.00 38.33 3.14
560 3533 1.641123 GGGTGTCCGGTTTATGCGTG 61.641 60.000 0.00 0.00 0.00 5.34
747 3725 6.564328 AGAAAAGAGAACACAAATCCACAAC 58.436 36.000 0.00 0.00 0.00 3.32
846 3886 2.739379 GCTTCAGCCTTCAGAGTACAAC 59.261 50.000 0.00 0.00 34.31 3.32
874 3914 1.074850 GGGAGGAGGAAGAGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
875 3915 1.595058 GGGAGGAGGAAGAGGAGGGA 61.595 65.000 0.00 0.00 0.00 4.20
879 3919 1.074850 GAGGAAGAGGAGGGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
880 3920 2.770475 GGAAGAGGAGGGAGGGGC 60.770 72.222 0.00 0.00 0.00 5.80
881 3921 3.157949 GAAGAGGAGGGAGGGGCG 61.158 72.222 0.00 0.00 0.00 6.13
1104 4153 0.967380 CCTTCCTCACAACCCCATGC 60.967 60.000 0.00 0.00 0.00 4.06
1115 4164 1.277580 ACCCCATGCTCTTCCTCCTG 61.278 60.000 0.00 0.00 0.00 3.86
1130 4180 1.059584 TCCTGTCTGCCCCTTTGACA 61.060 55.000 0.00 0.00 38.24 3.58
1170 4220 1.593296 CTGCTGCTCCTTGGCCTTTC 61.593 60.000 3.32 0.00 0.00 2.62
1300 4350 3.476552 TCTGTGCCGACATTTCTTTTCT 58.523 40.909 0.00 0.00 0.00 2.52
1305 4355 2.405025 GCCGACATTTCTTTTCTTTGCG 59.595 45.455 0.00 0.00 0.00 4.85
1329 4379 1.540267 TATTTCCCACGCCTGGTTTG 58.460 50.000 0.86 0.00 35.46 2.93
1490 4540 0.035152 TTACCTGCAGCATCCCTGTG 60.035 55.000 8.66 0.00 43.71 3.66
1533 4583 0.536006 AGCGTGCCTTTCTGCTTTCT 60.536 50.000 0.00 0.00 32.89 2.52
1574 4625 4.695455 TCCGTCTTTTCCAATCTTGATGAC 59.305 41.667 0.00 0.00 0.00 3.06
1674 4728 8.154649 ACAGAATTGAACAGGTAAAGTACAAG 57.845 34.615 0.00 0.00 0.00 3.16
1712 4766 1.534595 GCTGCCTGCGAATTAATGGTG 60.535 52.381 0.00 0.00 0.00 4.17
1806 4864 5.704515 AGGATTGTGTTGATTTCAGTCTCTG 59.295 40.000 0.00 0.00 0.00 3.35
2418 5488 1.229359 CTCCGAGGCCTACCAGGTA 59.771 63.158 4.42 0.00 37.80 3.08
2424 5494 4.886121 GCCTACCAGGTACGCGCC 62.886 72.222 5.73 0.00 37.80 6.53
2499 5577 1.294780 CAGTGCCACTCTCCAGTCC 59.705 63.158 0.00 0.00 0.00 3.85
2500 5578 1.152247 AGTGCCACTCTCCAGTCCA 60.152 57.895 0.00 0.00 0.00 4.02
2501 5579 1.190833 AGTGCCACTCTCCAGTCCAG 61.191 60.000 0.00 0.00 0.00 3.86
2502 5580 1.152247 TGCCACTCTCCAGTCCAGT 60.152 57.895 0.00 0.00 0.00 4.00
2503 5581 0.114364 TGCCACTCTCCAGTCCAGTA 59.886 55.000 0.00 0.00 0.00 2.74
2504 5582 0.533032 GCCACTCTCCAGTCCAGTAC 59.467 60.000 0.00 0.00 0.00 2.73
2505 5583 1.893210 GCCACTCTCCAGTCCAGTACT 60.893 57.143 0.00 0.00 39.81 2.73
2527 5606 0.878416 TACACAGCATTTTCACCGGC 59.122 50.000 0.00 0.00 0.00 6.13
2530 5609 0.250901 ACAGCATTTTCACCGGCTCT 60.251 50.000 0.00 0.00 33.60 4.09
2562 5641 1.468520 CATCGCATTTCTTTGACCGGT 59.531 47.619 6.92 6.92 0.00 5.28
2563 5642 2.459060 TCGCATTTCTTTGACCGGTA 57.541 45.000 7.34 0.00 0.00 4.02
2564 5643 2.343101 TCGCATTTCTTTGACCGGTAG 58.657 47.619 7.34 0.45 0.00 3.18
2565 5644 2.073816 CGCATTTCTTTGACCGGTAGT 58.926 47.619 7.34 0.00 0.00 2.73
2942 6052 8.712228 TCATCATCATATAACTAGTCCAGTGT 57.288 34.615 0.00 0.00 37.63 3.55
2943 6053 9.807921 TCATCATCATATAACTAGTCCAGTGTA 57.192 33.333 0.00 0.00 37.63 2.90
3267 6384 0.526524 GCGACGAGATCCTCTTGGTG 60.527 60.000 0.00 0.00 32.07 4.17
3270 6387 2.094700 CGACGAGATCCTCTTGGTGAAA 60.095 50.000 0.00 0.00 32.07 2.69
3496 6626 2.475666 CCTAGCTCAGGTTTGCAGC 58.524 57.895 0.00 0.00 39.91 5.25
3617 6754 0.110373 GGAACGTGCATGTTTCGTCC 60.110 55.000 24.49 17.32 36.80 4.79
3624 6761 2.744202 GTGCATGTTTCGTCCTCAATCT 59.256 45.455 0.00 0.00 0.00 2.40
3687 6827 5.509716 TCATTTGCCATATCTTGCTTCTG 57.490 39.130 0.00 0.00 0.00 3.02
3725 6879 1.301322 TCAGCATCGACGTGGCAAA 60.301 52.632 14.03 1.47 0.00 3.68
3728 6882 0.168788 AGCATCGACGTGGCAAATTG 59.831 50.000 14.03 0.00 0.00 2.32
3731 6885 0.447801 ATCGACGTGGCAAATTGAGC 59.552 50.000 0.00 0.00 0.00 4.26
3753 6907 2.195389 CCACGAATCACGAGGGGTA 58.805 57.895 0.00 0.00 46.11 3.69
3772 6926 1.878953 AGAAATTGACCTGCGAACGT 58.121 45.000 0.00 0.00 0.00 3.99
3773 6927 3.034721 AGAAATTGACCTGCGAACGTA 57.965 42.857 0.00 0.00 0.00 3.57
3774 6928 2.735134 AGAAATTGACCTGCGAACGTAC 59.265 45.455 0.00 0.00 0.00 3.67
3814 6968 2.045561 TGAACGAAAGGCAGGAACAA 57.954 45.000 0.00 0.00 0.00 2.83
3818 6974 2.767505 ACGAAAGGCAGGAACAAGTAG 58.232 47.619 0.00 0.00 0.00 2.57
3820 6976 2.437413 GAAAGGCAGGAACAAGTAGGG 58.563 52.381 0.00 0.00 0.00 3.53
3834 6990 1.651770 AGTAGGGAGACTCAATGGGGA 59.348 52.381 4.53 0.00 0.00 4.81
3847 7004 1.244697 ATGGGGATCGATCGAGGTCG 61.245 60.000 23.84 1.99 42.74 4.79
3851 7008 0.935366 GGATCGATCGAGGTCGTTGC 60.935 60.000 23.84 6.93 42.07 4.17
3883 7040 0.743345 AGCAAGCGGGGTTCGTTATC 60.743 55.000 0.00 0.00 41.72 1.75
3884 7041 2.003672 CAAGCGGGGTTCGTTATCG 58.996 57.895 0.00 0.00 41.72 2.92
3885 7042 0.458889 CAAGCGGGGTTCGTTATCGA 60.459 55.000 0.00 0.00 44.66 3.59
3886 7043 0.462789 AAGCGGGGTTCGTTATCGAT 59.537 50.000 2.16 2.16 45.65 3.59
3887 7044 1.321474 AGCGGGGTTCGTTATCGATA 58.679 50.000 0.00 0.00 45.65 2.92
3888 7045 1.891150 AGCGGGGTTCGTTATCGATAT 59.109 47.619 5.84 0.00 45.65 1.63
3889 7046 3.084039 AGCGGGGTTCGTTATCGATATA 58.916 45.455 5.84 0.00 45.65 0.86
3890 7047 3.507233 AGCGGGGTTCGTTATCGATATAA 59.493 43.478 5.84 0.00 45.65 0.98
3891 7048 4.159135 AGCGGGGTTCGTTATCGATATAAT 59.841 41.667 5.84 0.00 45.65 1.28
3892 7049 5.357878 AGCGGGGTTCGTTATCGATATAATA 59.642 40.000 5.84 0.00 45.65 0.98
3893 7050 6.040166 AGCGGGGTTCGTTATCGATATAATAT 59.960 38.462 5.84 0.00 45.65 1.28
3894 7051 6.143438 GCGGGGTTCGTTATCGATATAATATG 59.857 42.308 5.84 0.00 45.65 1.78
3895 7052 6.143438 CGGGGTTCGTTATCGATATAATATGC 59.857 42.308 5.84 0.00 45.65 3.14
3896 7053 6.982141 GGGGTTCGTTATCGATATAATATGCA 59.018 38.462 5.84 0.00 45.65 3.96
3897 7054 7.656137 GGGGTTCGTTATCGATATAATATGCAT 59.344 37.037 5.84 3.79 45.65 3.96
3898 7055 8.487970 GGGTTCGTTATCGATATAATATGCATG 58.512 37.037 10.16 0.00 45.65 4.06
3899 7056 8.004344 GGTTCGTTATCGATATAATATGCATGC 58.996 37.037 11.82 11.82 45.65 4.06
3900 7057 8.755941 GTTCGTTATCGATATAATATGCATGCT 58.244 33.333 20.33 7.07 45.65 3.79
3901 7058 8.871686 TCGTTATCGATATAATATGCATGCTT 57.128 30.769 20.33 15.55 41.35 3.91
3902 7059 8.755018 TCGTTATCGATATAATATGCATGCTTG 58.245 33.333 20.33 0.00 41.35 4.01
3903 7060 7.528516 CGTTATCGATATAATATGCATGCTTGC 59.471 37.037 20.33 17.19 43.65 4.01
3904 7061 8.337532 GTTATCGATATAATATGCATGCTTGCA 58.662 33.333 27.09 27.09 44.57 4.08
3918 7075 4.621068 TGCTTGCATCAAGTACTAATGC 57.379 40.909 25.47 25.47 42.77 3.56
3919 7076 3.063861 TGCTTGCATCAAGTACTAATGCG 59.936 43.478 25.95 18.42 46.86 4.73
3920 7077 3.546815 GCTTGCATCAAGTACTAATGCGG 60.547 47.826 25.95 22.61 46.86 5.69
3921 7078 3.535280 TGCATCAAGTACTAATGCGGA 57.465 42.857 25.95 14.58 46.86 5.54
3922 7079 4.071961 TGCATCAAGTACTAATGCGGAT 57.928 40.909 25.95 9.92 46.86 4.18
3923 7080 4.058124 TGCATCAAGTACTAATGCGGATC 58.942 43.478 25.95 10.22 46.86 3.36
3924 7081 3.121944 GCATCAAGTACTAATGCGGATCG 59.878 47.826 20.92 0.00 36.75 3.69
3932 7089 1.723542 CTAATGCGGATCGATGCACTC 59.276 52.381 17.54 5.87 45.07 3.51
3944 7101 3.766691 GCACTCGGGCCGGTCTAA 61.767 66.667 27.98 4.85 0.00 2.10
3979 7139 2.029623 CAAAGGATGCTTAGCCATGCT 58.970 47.619 0.00 3.42 44.39 3.79
4013 7175 4.749099 GCTAGATGAGTACTGCCATTCAAG 59.251 45.833 0.00 0.00 0.00 3.02
4330 7530 4.109050 GCATCGTTCAAAGTTTCAAACCA 58.891 39.130 0.00 0.00 0.00 3.67
4360 7564 2.457366 ATGTGTTCTCCTGACGAACC 57.543 50.000 0.00 0.00 39.92 3.62
4384 7588 6.376177 CACAGTAATACAGTAACACGTCAGA 58.624 40.000 0.00 0.00 0.00 3.27
4386 7590 6.429078 ACAGTAATACAGTAACACGTCAGAGA 59.571 38.462 0.00 0.00 0.00 3.10
4388 7592 6.877855 AGTAATACAGTAACACGTCAGAGAGA 59.122 38.462 0.00 0.00 0.00 3.10
4395 7599 3.627395 ACACGTCAGAGAGAGAGAGAT 57.373 47.619 0.00 0.00 0.00 2.75
4396 7600 3.531538 ACACGTCAGAGAGAGAGAGATC 58.468 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.816984 TCTCCTCCTCGTCCGCCC 62.817 72.222 0.00 0.00 0.00 6.13
20 21 1.874345 TTTGTCTCCTCCTCGTCCGC 61.874 60.000 0.00 0.00 0.00 5.54
26 28 1.597461 CGGGGTTTGTCTCCTCCTC 59.403 63.158 0.00 0.00 33.68 3.71
49 51 1.375523 AAAGAGTTGGGGTAGCGCG 60.376 57.895 0.00 0.00 0.00 6.86
52 54 2.427506 CAGACAAAGAGTTGGGGTAGC 58.572 52.381 0.00 0.00 39.22 3.58
55 57 0.846693 AGCAGACAAAGAGTTGGGGT 59.153 50.000 0.00 0.00 39.22 4.95
71 73 4.805231 GCGCAATGCCATGCAGCA 62.805 61.111 0.30 2.80 46.76 4.41
73 75 4.485834 ACGCGCAATGCCATGCAG 62.486 61.111 5.73 6.67 46.76 4.41
78 80 2.100031 CACTAGACGCGCAATGCCA 61.100 57.895 5.73 0.00 42.08 4.92
83 85 0.730155 CGTTACCACTAGACGCGCAA 60.730 55.000 5.73 0.00 0.00 4.85
88 90 1.667724 ACGGATCGTTACCACTAGACG 59.332 52.381 0.00 0.00 36.35 4.18
89 91 2.679837 TCACGGATCGTTACCACTAGAC 59.320 50.000 0.00 0.00 38.32 2.59
90 92 2.989909 TCACGGATCGTTACCACTAGA 58.010 47.619 0.00 0.00 38.32 2.43
91 93 3.304525 GGATCACGGATCGTTACCACTAG 60.305 52.174 0.00 0.00 39.72 2.57
99 101 1.341531 GGAGATGGATCACGGATCGTT 59.658 52.381 0.00 0.00 39.72 3.85
120 122 3.521126 AGAACATCCAGGAACATGCTACT 59.479 43.478 0.00 0.00 0.00 2.57
131 133 0.179073 CTACCCGCAGAACATCCAGG 60.179 60.000 0.00 0.00 0.00 4.45
141 143 3.380004 TGCATTAAATTTCCTACCCGCAG 59.620 43.478 0.00 0.00 0.00 5.18
154 156 1.396996 GGTGCGTCGACTGCATTAAAT 59.603 47.619 28.33 0.00 45.34 1.40
179 183 9.747898 AGAAAATATGTAATGTTGGGTTCTACA 57.252 29.630 0.00 0.00 33.58 2.74
201 205 6.663953 ACATACAGAAGTAGCAGAGGTAGAAA 59.336 38.462 0.00 0.00 32.86 2.52
212 216 9.384764 AGGAAATTTAGAACATACAGAAGTAGC 57.615 33.333 0.00 0.00 32.86 3.58
219 223 5.276868 CGGCGAGGAAATTTAGAACATACAG 60.277 44.000 0.00 0.00 0.00 2.74
232 236 2.267961 GGTCACCGGCGAGGAAAT 59.732 61.111 9.30 0.00 45.00 2.17
233 237 4.367023 CGGTCACCGGCGAGGAAA 62.367 66.667 8.94 0.00 44.15 3.13
264 268 3.579232 CGGCGGCGATAAAACCCC 61.579 66.667 29.19 0.00 0.00 4.95
287 291 1.379977 TCCTCAATCCGCCGTCTCT 60.380 57.895 0.00 0.00 0.00 3.10
317 321 3.031013 CCAAGTCCTTGTTGTTCCCTTT 58.969 45.455 6.31 0.00 38.85 3.11
350 354 3.019564 GACCTAAACCTAGACTACGGCA 58.980 50.000 0.00 0.00 0.00 5.69
372 376 1.377690 TCATTAACAGAAGGGGGCCA 58.622 50.000 4.39 0.00 0.00 5.36
375 379 4.832823 ACACTTTTCATTAACAGAAGGGGG 59.167 41.667 0.00 0.00 0.00 5.40
382 386 7.138736 ACATTTCGGACACTTTTCATTAACAG 58.861 34.615 0.00 0.00 0.00 3.16
395 399 4.669197 GCACATTCACTACATTTCGGACAC 60.669 45.833 0.00 0.00 0.00 3.67
440 444 5.352569 ACCGAACAAAATTCATGCAAACAAA 59.647 32.000 0.00 0.00 0.00 2.83
492 500 3.583228 ACCGGTCATCCAATACTATCCA 58.417 45.455 0.00 0.00 0.00 3.41
519 532 4.023622 CCTATCTATCCGCGGATACAGATG 60.024 50.000 39.57 31.73 36.17 2.90
524 3497 2.358267 CACCCTATCTATCCGCGGATAC 59.642 54.545 37.73 0.00 36.17 2.24
535 3508 3.322828 GCATAAACCGGACACCCTATCTA 59.677 47.826 9.46 0.00 0.00 1.98
541 3514 1.376295 ACGCATAAACCGGACACCC 60.376 57.895 9.46 0.00 0.00 4.61
557 3530 1.501741 CGCATTTCCAACCCTCACG 59.498 57.895 0.00 0.00 0.00 4.35
560 3533 2.885113 GGCGCATTTCCAACCCTC 59.115 61.111 10.83 0.00 0.00 4.30
609 3582 2.534990 CCAATGGGGGCTTTGTTTCTA 58.465 47.619 0.00 0.00 0.00 2.10
747 3725 4.922206 AGATAGAGAGAGGACATGGCTAG 58.078 47.826 0.00 0.00 0.00 3.42
846 3886 2.673523 CTCCTCCCCTGTTGCTGG 59.326 66.667 0.00 0.00 0.00 4.85
880 3920 3.055719 GTGGTGATGGTGGTGGCG 61.056 66.667 0.00 0.00 0.00 5.69
881 3921 2.676471 GGTGGTGATGGTGGTGGC 60.676 66.667 0.00 0.00 0.00 5.01
882 3922 1.603455 GTGGTGGTGATGGTGGTGG 60.603 63.158 0.00 0.00 0.00 4.61
883 3923 1.603455 GGTGGTGGTGATGGTGGTG 60.603 63.158 0.00 0.00 0.00 4.17
884 3924 2.081787 TGGTGGTGGTGATGGTGGT 61.082 57.895 0.00 0.00 0.00 4.16
885 3925 1.603455 GTGGTGGTGGTGATGGTGG 60.603 63.158 0.00 0.00 0.00 4.61
886 3926 0.467106 TTGTGGTGGTGGTGATGGTG 60.467 55.000 0.00 0.00 0.00 4.17
887 3927 0.178992 CTTGTGGTGGTGGTGATGGT 60.179 55.000 0.00 0.00 0.00 3.55
888 3928 0.178992 ACTTGTGGTGGTGGTGATGG 60.179 55.000 0.00 0.00 0.00 3.51
889 3929 2.151202 GTACTTGTGGTGGTGGTGATG 58.849 52.381 0.00 0.00 0.00 3.07
890 3930 1.771854 TGTACTTGTGGTGGTGGTGAT 59.228 47.619 0.00 0.00 0.00 3.06
891 3931 1.134340 GTGTACTTGTGGTGGTGGTGA 60.134 52.381 0.00 0.00 0.00 4.02
1104 4153 1.621672 GGGGCAGACAGGAGGAAGAG 61.622 65.000 0.00 0.00 0.00 2.85
1115 4164 1.271597 ACAGATGTCAAAGGGGCAGAC 60.272 52.381 0.00 0.00 0.00 3.51
1130 4180 3.073062 AGCACAGTTAACAAGGGACAGAT 59.927 43.478 8.61 0.00 0.00 2.90
1170 4220 1.966451 GGTGACCCTGCAAGTTCCG 60.966 63.158 0.00 0.00 0.00 4.30
1256 4306 0.823356 TGCAGCAGGAACCAAGAACC 60.823 55.000 0.00 0.00 0.00 3.62
1305 4355 3.982576 CCAGGCGTGGGAAATAATTAC 57.017 47.619 17.92 0.00 40.67 1.89
1323 4373 0.459237 CAACCTGCGCAAACAAACCA 60.459 50.000 13.05 0.00 0.00 3.67
1329 4379 1.658409 GCTGTCAACCTGCGCAAAC 60.658 57.895 13.05 5.59 0.00 2.93
1380 4430 0.611896 TCAGATCGGTCAGCACCTGA 60.612 55.000 0.00 0.00 41.17 3.86
1472 4522 1.200760 ACACAGGGATGCTGCAGGTA 61.201 55.000 17.12 0.00 0.00 3.08
1490 4540 5.257262 AGCTTCCTCCTTAATCTTTCCAAC 58.743 41.667 0.00 0.00 0.00 3.77
1533 4583 4.886247 CGGAAAGATTTACGCCCAAATA 57.114 40.909 0.00 0.00 37.72 1.40
1674 4728 2.187073 CTGCACAAGCTGGGATTCC 58.813 57.895 0.00 0.00 42.74 3.01
1712 4766 1.676967 CTCTGCCTTTGCCAGGGAC 60.677 63.158 1.35 0.00 44.16 4.46
2424 5494 1.152567 ATCAGGGAGAGGAGAGCGG 60.153 63.158 0.00 0.00 0.00 5.52
2499 5577 5.120830 GTGAAAATGCTGTGTAGGAGTACTG 59.879 44.000 0.00 0.00 0.00 2.74
2500 5578 5.238583 GTGAAAATGCTGTGTAGGAGTACT 58.761 41.667 0.00 0.00 0.00 2.73
2501 5579 4.392138 GGTGAAAATGCTGTGTAGGAGTAC 59.608 45.833 0.00 0.00 0.00 2.73
2502 5580 4.575885 GGTGAAAATGCTGTGTAGGAGTA 58.424 43.478 0.00 0.00 0.00 2.59
2503 5581 3.412386 GGTGAAAATGCTGTGTAGGAGT 58.588 45.455 0.00 0.00 0.00 3.85
2504 5582 2.416547 CGGTGAAAATGCTGTGTAGGAG 59.583 50.000 0.00 0.00 0.00 3.69
2505 5583 2.422597 CGGTGAAAATGCTGTGTAGGA 58.577 47.619 0.00 0.00 0.00 2.94
2562 5641 4.442706 GGTACCACTAGCGTGTACTACTA 58.557 47.826 7.15 0.00 39.55 1.82
2563 5642 3.274288 GGTACCACTAGCGTGTACTACT 58.726 50.000 7.15 0.00 39.55 2.57
2564 5643 2.030946 CGGTACCACTAGCGTGTACTAC 59.969 54.545 13.54 0.00 39.55 2.73
2565 5644 2.279741 CGGTACCACTAGCGTGTACTA 58.720 52.381 13.54 0.00 39.55 1.82
2584 5663 0.031043 CATCTCTGCTCTGCTCTCCG 59.969 60.000 0.00 0.00 0.00 4.63
2742 5846 3.503363 TCTTTTCCGTTCTGCTCGTAGTA 59.497 43.478 0.00 0.00 0.00 1.82
2743 5847 2.295349 TCTTTTCCGTTCTGCTCGTAGT 59.705 45.455 0.00 0.00 0.00 2.73
2744 5848 2.662156 GTCTTTTCCGTTCTGCTCGTAG 59.338 50.000 0.00 0.00 0.00 3.51
2942 6052 3.181474 TGTGTCCGAACCGAATGCATATA 60.181 43.478 0.00 0.00 0.00 0.86
2943 6053 2.210116 GTGTCCGAACCGAATGCATAT 58.790 47.619 0.00 0.00 0.00 1.78
2944 6054 1.066787 TGTGTCCGAACCGAATGCATA 60.067 47.619 0.00 0.00 0.00 3.14
2952 6062 2.289547 AGAATGTTTTGTGTCCGAACCG 59.710 45.455 0.00 0.00 0.00 4.44
3489 6619 0.319211 ACGTACTACAGCGCTGCAAA 60.319 50.000 36.28 20.92 0.00 3.68
3496 6626 4.047822 AGTAGCTACTACGTACTACAGCG 58.952 47.826 24.97 0.21 41.37 5.18
3559 6693 1.880027 ACAAGGATCGTTGACAAAGGC 59.120 47.619 29.52 0.00 0.00 4.35
3617 6754 9.539825 AGAATATTTACACTGCTACAGATTGAG 57.460 33.333 0.78 0.00 35.18 3.02
3624 6761 9.890629 AAGATTGAGAATATTTACACTGCTACA 57.109 29.630 0.00 0.00 0.00 2.74
3687 6827 1.210155 GCGGACACAAGCAATCCAC 59.790 57.895 0.00 0.00 32.35 4.02
3722 6876 5.088739 GTGATTCGTGGTTAGCTCAATTTG 58.911 41.667 0.00 0.00 0.00 2.32
3725 6879 2.930040 CGTGATTCGTGGTTAGCTCAAT 59.070 45.455 0.00 0.00 34.52 2.57
3728 6882 2.186076 CTCGTGATTCGTGGTTAGCTC 58.814 52.381 0.00 0.00 40.80 4.09
3749 6903 2.396590 TCGCAGGTCAATTTCTACCC 57.603 50.000 0.00 0.00 36.34 3.69
3750 6904 2.093783 CGTTCGCAGGTCAATTTCTACC 59.906 50.000 0.00 0.00 35.91 3.18
3753 6907 1.878953 ACGTTCGCAGGTCAATTTCT 58.121 45.000 0.00 0.00 0.00 2.52
3772 6926 4.343231 TCCAGTCCAATACCAACGTAGTA 58.657 43.478 0.00 0.00 45.00 1.82
3774 6928 3.880047 TCCAGTCCAATACCAACGTAG 57.120 47.619 0.00 0.00 0.00 3.51
3790 6944 1.089920 CCTGCCTTTCGTTCATCCAG 58.910 55.000 0.00 0.00 0.00 3.86
3814 6968 1.651770 TCCCCATTGAGTCTCCCTACT 59.348 52.381 0.00 0.00 0.00 2.57
3818 6974 0.394565 CGATCCCCATTGAGTCTCCC 59.605 60.000 0.00 0.00 0.00 4.30
3820 6976 2.352225 CGATCGATCCCCATTGAGTCTC 60.352 54.545 19.51 0.00 0.00 3.36
3834 6990 1.298413 CGCAACGACCTCGATCGAT 60.298 57.895 19.78 4.24 45.13 3.59
3847 7004 2.580589 TGCTTTAATCTTTCGCGCAAC 58.419 42.857 8.75 0.00 0.00 4.17
3851 7008 1.834178 CGCTTGCTTTAATCTTTCGCG 59.166 47.619 0.00 0.00 0.00 5.87
3895 7052 4.974275 GCATTAGTACTTGATGCAAGCATG 59.026 41.667 26.41 0.73 44.43 4.06
3896 7053 4.260907 CGCATTAGTACTTGATGCAAGCAT 60.261 41.667 28.53 7.35 44.43 3.79
3897 7054 3.063861 CGCATTAGTACTTGATGCAAGCA 59.936 43.478 28.53 0.00 44.43 3.91
3898 7055 3.546815 CCGCATTAGTACTTGATGCAAGC 60.547 47.826 28.53 13.04 44.43 4.01
3899 7056 3.871006 TCCGCATTAGTACTTGATGCAAG 59.129 43.478 28.53 22.50 44.81 4.01
3900 7057 3.867857 TCCGCATTAGTACTTGATGCAA 58.132 40.909 28.53 19.41 44.81 4.08
3901 7058 3.535280 TCCGCATTAGTACTTGATGCA 57.465 42.857 28.53 16.39 44.81 3.96
3902 7059 3.121944 CGATCCGCATTAGTACTTGATGC 59.878 47.826 23.64 23.64 41.99 3.91
3903 7060 4.546570 TCGATCCGCATTAGTACTTGATG 58.453 43.478 0.00 7.59 0.00 3.07
3904 7061 4.848562 TCGATCCGCATTAGTACTTGAT 57.151 40.909 0.00 0.00 0.00 2.57
3905 7062 4.546570 CATCGATCCGCATTAGTACTTGA 58.453 43.478 0.00 0.00 0.00 3.02
3906 7063 3.121944 GCATCGATCCGCATTAGTACTTG 59.878 47.826 0.00 0.00 0.00 3.16
3907 7064 3.243737 TGCATCGATCCGCATTAGTACTT 60.244 43.478 0.00 0.00 31.95 2.24
3908 7065 2.296190 TGCATCGATCCGCATTAGTACT 59.704 45.455 6.33 0.00 31.95 2.73
3909 7066 2.408704 GTGCATCGATCCGCATTAGTAC 59.591 50.000 12.90 0.00 40.89 2.73
3910 7067 2.296190 AGTGCATCGATCCGCATTAGTA 59.704 45.455 12.90 0.00 40.89 1.82
3911 7068 1.069204 AGTGCATCGATCCGCATTAGT 59.931 47.619 12.90 0.00 40.89 2.24
3912 7069 1.723542 GAGTGCATCGATCCGCATTAG 59.276 52.381 12.90 0.00 40.89 1.73
3913 7070 1.783284 GAGTGCATCGATCCGCATTA 58.217 50.000 12.90 0.00 40.89 1.90
3914 7071 2.609825 GAGTGCATCGATCCGCATT 58.390 52.632 12.90 9.23 40.89 3.56
3915 7072 4.350620 GAGTGCATCGATCCGCAT 57.649 55.556 12.90 3.71 40.89 4.73
3932 7089 2.125269 CACCTTTAGACCGGCCCG 60.125 66.667 0.00 0.00 0.00 6.13
3936 7093 0.682852 TGACACCACCTTTAGACCGG 59.317 55.000 0.00 0.00 0.00 5.28
3943 7100 3.835395 TCCTTTGTTTTGACACCACCTTT 59.165 39.130 0.00 0.00 0.00 3.11
3944 7101 3.436243 TCCTTTGTTTTGACACCACCTT 58.564 40.909 0.00 0.00 0.00 3.50
3991 7151 5.752472 CACTTGAATGGCAGTACTCATCTAG 59.248 44.000 0.00 0.00 0.00 2.43
4013 7175 0.861450 GCGCCGTACATGATTTGCAC 60.861 55.000 0.00 0.00 0.00 4.57
4137 7325 3.496884 ACGCACGTGATGACAAAGTAAAT 59.503 39.130 22.23 0.00 0.00 1.40
4330 7530 3.388024 AGGAGAACACATACACACACTGT 59.612 43.478 0.00 0.00 36.82 3.55
4360 7564 6.376177 TCTGACGTGTTACTGTATTACTGTG 58.624 40.000 14.53 2.70 32.45 3.66


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

AutoCloner maintained by Alex Coulton.