Multiple sequence alignment - TraesCS1A01G153900

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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 TraesCS1A01G153900 chr1A 100.000 9047 0 0 862 9908 267794536 267803582 0.000000e+00 16707.0
1 TraesCS1A01G153900 chr1A 100.000 438 0 0 1 438 267793675 267794112 0.000000e+00 809.0
2 TraesCS1A01G153900 chr1B 96.481 4234 89 18 5694 9908 304515031 304510839 0.000000e+00 6938.0
3 TraesCS1A01G153900 chr1B 91.715 1545 73 18 1875 3391 304518251 304516734 0.000000e+00 2093.0
4 TraesCS1A01G153900 chr1B 97.036 1147 20 3 4132 5267 304516716 304515573 0.000000e+00 1917.0
5 TraesCS1A01G153900 chr1B 95.726 1053 21 2 862 1892 304519664 304518614 0.000000e+00 1674.0
6 TraesCS1A01G153900 chr1B 96.536 433 14 1 5265 5697 304515542 304515111 0.000000e+00 715.0
7 TraesCS1A01G153900 chr1B 95.631 206 4 1 238 438 304520350 304520145 9.600000e-85 326.0
8 TraesCS1A01G153900 chr1B 87.243 243 29 2 1 242 304520691 304520450 9.800000e-70 276.0
9 TraesCS1A01G153900 chr1B 86.885 122 14 2 3372 3491 406341868 406341747 1.740000e-27 135.0
10 TraesCS1A01G153900 chr1B 100.000 39 0 0 4095 4133 304516740 304516702 1.380000e-08 73.1
11 TraesCS1A01G153900 chr1D 96.713 2708 54 12 5265 7956 211954890 211957578 0.000000e+00 4475.0
12 TraesCS1A01G153900 chr1D 96.478 2243 47 7 3032 5264 211952636 211954856 0.000000e+00 3675.0
13 TraesCS1A01G153900 chr1D 96.880 1891 38 4 8026 9908 211957572 211959449 0.000000e+00 3145.0
14 TraesCS1A01G153900 chr1D 95.310 1386 22 7 862 2205 211950634 211952018 0.000000e+00 2159.0
15 TraesCS1A01G153900 chr1D 96.166 626 20 2 2287 2908 211952012 211952637 0.000000e+00 1020.0
16 TraesCS1A01G153900 chr1D 97.484 159 4 0 280 438 211950292 211950450 1.270000e-68 272.0
17 TraesCS1A01G153900 chr1D 83.962 212 31 2 21 229 211942568 211942779 6.070000e-47 200.0
18 TraesCS1A01G153900 chr1D 84.694 98 9 2 6803 6898 211956298 211956391 1.060000e-14 93.5
19 TraesCS1A01G153900 chr2A 97.015 134 4 0 2903 3036 486500220 486500087 1.000000e-54 226.0
20 TraesCS1A01G153900 chr2A 95.745 94 1 3 3390 3480 729165685 729165592 2.230000e-31 148.0
21 TraesCS1A01G153900 chr7A 98.438 128 1 1 2907 3034 81861245 81861119 3.600000e-54 224.0
22 TraesCS1A01G153900 chr7A 94.928 138 6 1 2906 3043 454048957 454049093 2.170000e-51 215.0
23 TraesCS1A01G153900 chr7B 96.970 132 4 0 2903 3034 41253299 41253430 1.300000e-53 222.0
24 TraesCS1A01G153900 chr3D 97.674 129 3 0 2907 3035 260333004 260332876 1.300000e-53 222.0
25 TraesCS1A01G153900 chr3B 94.964 139 7 0 2902 3040 76508246 76508384 1.680000e-52 219.0
26 TraesCS1A01G153900 chr3B 92.000 150 10 2 2903 3052 741865980 741865833 1.010000e-49 209.0
27 TraesCS1A01G153900 chr3B 93.000 100 2 4 3387 3484 551513883 551513979 3.730000e-29 141.0
28 TraesCS1A01G153900 chr5D 93.706 143 8 1 2903 3044 115924518 115924660 7.800000e-51 213.0
29 TraesCS1A01G153900 chr5D 96.629 89 1 2 3393 3479 526559650 526559562 8.020000e-31 147.0
30 TraesCS1A01G153900 chr5D 92.929 99 6 1 3383 3480 452219492 452219394 1.040000e-29 143.0
31 TraesCS1A01G153900 chr6B 90.909 154 10 3 2901 3054 582866936 582867085 4.690000e-48 204.0
32 TraesCS1A01G153900 chr5B 95.726 117 4 1 9792 9908 20974083 20974198 4.720000e-43 187.0
33 TraesCS1A01G153900 chr5B 96.667 90 2 1 3393 3481 269975155 269975244 2.230000e-31 148.0
34 TraesCS1A01G153900 chr6A 95.789 95 3 1 3383 3476 407093164 407093070 1.720000e-32 152.0
35 TraesCS1A01G153900 chr4D 93.750 96 5 1 3393 3487 252173789 252173694 1.040000e-29 143.0


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 TraesCS1A01G153900 chr1A 267793675 267803582 9907 False 8758.000000 16707 100.000000 1 9908 2 chr1A.!!$F1 9907
1 TraesCS1A01G153900 chr1B 304510839 304520691 9852 True 1751.512500 6938 95.046000 1 9908 8 chr1B.!!$R2 9907
2 TraesCS1A01G153900 chr1D 211950292 211959449 9157 False 2119.928571 4475 94.817857 280 9908 7 chr1D.!!$F2 9628

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
82 83 0.038159 CGACACTTTTCCCGCTCTCT 60.038 55.000 0.0 0.0 0.00 3.10 F
1362 1552 0.249398 AAGCCGAGGATACAAAGCGT 59.751 50.000 0.0 0.0 41.41 5.07 F
2926 3521 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.0 0.0 0.00 1.82 F
3121 3716 2.429610 TCCCTAAGCTGTCGTGATAACC 59.570 50.000 0.0 0.0 0.00 2.85 F
4509 5115 2.400399 TCAAGTAGTTCTTTGCCGTCG 58.600 47.619 0.0 0.0 33.63 5.12 F
5181 5791 2.205022 TTGGAGGGCACTGAGAAATG 57.795 50.000 0.0 0.0 0.00 2.32 F
6449 7188 2.026636 ACAGATACCCTTTTTAGCCGCA 60.027 45.455 0.0 0.0 0.00 5.69 F
7982 8727 2.910199 TGAGAGCAATTCCATCCTTCG 58.090 47.619 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1960 1.072331 ACCACTGCGAAAATGTCCTCT 59.928 47.619 0.00 0.00 0.00 3.69 R
3016 3611 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12 R
4509 5115 2.014068 GCACTACCAGCAGGGAACATC 61.014 57.143 0.00 0.00 41.15 3.06 R
4692 5302 8.510243 ACATGAATAATAACAAGCACAGATGA 57.490 30.769 0.00 0.00 0.00 2.92 R
6200 6930 3.369756 ACAACACATAACAGCGATTACCG 59.630 43.478 0.00 0.00 42.21 4.02 R
6581 7320 2.359981 TCTACGATCGGTTCCAGGAT 57.640 50.000 20.98 0.00 0.00 3.24 R
8016 8761 2.246719 ATGCCTCGAGACCAAATAGC 57.753 50.000 15.71 6.54 0.00 2.97 R
9385 10140 0.911769 AATTCTCTGCATGACGGGGA 59.088 50.000 0.00 0.00 29.70 4.81 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
32 33 0.397941 ACGGTCCGACGGGAGATATA 59.602 55.000 20.51 0.00 44.97 0.86
42 43 3.759618 GACGGGAGATATAGAAGGAGGTG 59.240 52.174 0.00 0.00 0.00 4.00
72 73 2.143925 GTAGAGCAAGGCGACACTTTT 58.856 47.619 0.00 0.00 0.00 2.27
82 83 0.038159 CGACACTTTTCCCGCTCTCT 60.038 55.000 0.00 0.00 0.00 3.10
86 87 3.863041 ACACTTTTCCCGCTCTCTTATC 58.137 45.455 0.00 0.00 0.00 1.75
91 92 0.556258 TCCCGCTCTCTTATCCCTGA 59.444 55.000 0.00 0.00 0.00 3.86
94 95 2.242926 CCGCTCTCTTATCCCTGATGA 58.757 52.381 0.00 0.00 0.00 2.92
105 106 3.577805 TCCCTGATGATGTCTCTACGA 57.422 47.619 0.00 0.00 0.00 3.43
126 127 5.738370 CGAGATGGTCGGTCAAATTAAATC 58.262 41.667 0.00 0.00 45.58 2.17
130 131 5.873179 TGGTCGGTCAAATTAAATCAGAC 57.127 39.130 0.00 0.00 0.00 3.51
132 133 6.703319 TGGTCGGTCAAATTAAATCAGACTA 58.297 36.000 0.00 0.00 0.00 2.59
133 134 6.592607 TGGTCGGTCAAATTAAATCAGACTAC 59.407 38.462 0.00 0.00 0.00 2.73
134 135 6.592607 GGTCGGTCAAATTAAATCAGACTACA 59.407 38.462 0.00 0.00 0.00 2.74
150 151 5.010933 AGACTACATCTCACTTCTTTCGGA 58.989 41.667 0.00 0.00 28.16 4.55
161 162 4.309254 CTTCTTTCGGAAGCGTCTTAAC 57.691 45.455 0.00 0.00 43.88 2.01
167 168 1.067071 CGGAAGCGTCTTAACCTCCTT 60.067 52.381 0.00 0.00 0.00 3.36
211 212 9.434420 TTTTCAACCAAATATCATCCAAATGAC 57.566 29.630 0.00 0.00 44.51 3.06
212 213 7.111247 TCAACCAAATATCATCCAAATGACC 57.889 36.000 0.00 0.00 44.51 4.02
213 214 6.666980 TCAACCAAATATCATCCAAATGACCA 59.333 34.615 0.00 0.00 44.51 4.02
218 219 8.640651 CCAAATATCATCCAAATGACCATACAA 58.359 33.333 0.00 0.00 44.51 2.41
285 396 5.440234 AGCATCGACTCTTATCATTACGT 57.560 39.130 0.00 0.00 0.00 3.57
433 544 0.385098 TCCGCTGTTATATCGACGCG 60.385 55.000 3.53 3.53 38.64 6.01
1065 1233 2.671963 CTGCTGCAGCTGCCAGAA 60.672 61.111 36.61 23.77 42.66 3.02
1303 1493 0.739112 GTGCTGCAGTGCCTCTCTAC 60.739 60.000 16.64 0.00 0.00 2.59
1316 1506 4.098044 TGCCTCTCTACGAGTTTAGATTGG 59.902 45.833 0.00 0.00 38.11 3.16
1362 1552 0.249398 AAGCCGAGGATACAAAGCGT 59.751 50.000 0.00 0.00 41.41 5.07
1538 1728 4.214119 TCTTGAACTGATGTGCTTACTTGC 59.786 41.667 0.00 0.00 0.00 4.01
1563 1753 2.107953 GAGATGAGCCCTCACCGC 59.892 66.667 0.00 0.00 43.11 5.68
1703 1893 6.690530 AGATCTAGTGCTATCAAAGATCTGC 58.309 40.000 16.30 0.00 44.39 4.26
1826 2016 2.430465 TCTGGCTTGAATTGTCTGCTC 58.570 47.619 0.00 0.00 0.00 4.26
1998 2568 5.756347 AGTGTTCTTGATAGTAAAACGTGCA 59.244 36.000 0.00 0.00 0.00 4.57
1999 2569 5.844396 GTGTTCTTGATAGTAAAACGTGCAC 59.156 40.000 6.82 6.82 0.00 4.57
2000 2570 5.049954 TGTTCTTGATAGTAAAACGTGCACC 60.050 40.000 12.15 0.00 0.00 5.01
2054 2643 5.567552 GCAATCTGTTTGAGTATTGCTCTC 58.432 41.667 10.71 0.00 46.71 3.20
2089 2678 4.597004 AGTCAATGGCTTCATGTGAGAAT 58.403 39.130 0.00 0.00 0.00 2.40
2092 2681 4.768448 TCAATGGCTTCATGTGAGAATGTT 59.232 37.500 0.00 0.00 0.00 2.71
2205 2795 9.464714 ACATAGACTATATAGCTTTTGTTGACG 57.535 33.333 9.78 0.00 0.00 4.35
2234 2824 1.136891 ACTTTGCAGGCCAAACTTGTC 59.863 47.619 5.01 0.00 38.46 3.18
2238 2828 2.161855 TGCAGGCCAAACTTGTCTATG 58.838 47.619 5.01 0.00 0.00 2.23
2262 2852 5.681105 GCAATATTGCGTAGTAAACACATGG 59.319 40.000 23.77 0.00 45.11 3.66
2353 2943 4.347000 TCTCAAGGCTTTACCACTAGTGTT 59.653 41.667 21.18 10.30 43.14 3.32
2412 3002 7.062839 TGTTTTGTCTGCTTTGTTATGTTGAAC 59.937 33.333 0.00 0.00 0.00 3.18
2429 3019 7.022055 TGTTGAACGTTGTCTTGAATGTTAT 57.978 32.000 5.00 0.00 35.61 1.89
2435 3025 7.724305 ACGTTGTCTTGAATGTTATGTAGTT 57.276 32.000 0.00 0.00 0.00 2.24
2509 3101 7.154656 CGGGAGACATGATGTTATCAAATAGA 58.845 38.462 0.00 0.00 43.50 1.98
2542 3134 1.290324 GACTGCTTGCCTCGACTGA 59.710 57.895 0.00 0.00 0.00 3.41
2603 3195 1.131826 CGGCCTTTTGTAGTTCGCG 59.868 57.895 0.00 0.00 0.00 5.87
2848 3443 4.422073 TGATGTTCTGTTGTCTTCAGGT 57.578 40.909 0.00 0.00 34.15 4.00
2924 3519 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2926 3521 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2933 3528 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2934 3529 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2935 3530 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2938 3533 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2939 3534 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2941 3536 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2942 3537 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2943 3538 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2944 3539 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2973 3568 7.120923 ACGGATGTATCTAACACTAAACCAT 57.879 36.000 0.00 0.00 42.09 3.55
2974 3569 6.984474 ACGGATGTATCTAACACTAAACCATG 59.016 38.462 0.00 0.00 42.09 3.66
2975 3570 7.147794 ACGGATGTATCTAACACTAAACCATGA 60.148 37.037 0.00 0.00 42.09 3.07
2988 3583 6.863645 CACTAAACCATGACTAGATACATCCG 59.136 42.308 0.00 0.00 0.00 4.18
2991 3586 7.540474 AAACCATGACTAGATACATCCGTAT 57.460 36.000 0.00 0.00 41.16 3.06
3121 3716 2.429610 TCCCTAAGCTGTCGTGATAACC 59.570 50.000 0.00 0.00 0.00 2.85
3270 3867 7.593273 TGATTTTTCACGTGTGATTATTTGACC 59.407 33.333 16.51 0.00 39.64 4.02
3327 3924 6.317391 GCTGGCTTCTTACATCTTGTATTTCT 59.683 38.462 0.00 0.00 32.20 2.52
3394 3993 7.676947 GGTTTAACCTCTCTGCATATATGGTA 58.323 38.462 14.51 0.00 34.73 3.25
3490 4089 6.115446 CAGAGGGAGTGTATGCTTGAAATAA 58.885 40.000 0.00 0.00 0.00 1.40
3550 4149 7.282450 GGTTTGTTCTATACTTCATTAGTGGGG 59.718 40.741 0.00 0.00 37.73 4.96
3559 4158 6.335781 ACTTCATTAGTGGGGCCTTAAATA 57.664 37.500 0.84 0.00 35.19 1.40
3566 4165 3.513912 AGTGGGGCCTTAAATAAAGTTGC 59.486 43.478 0.84 0.00 32.89 4.17
3621 4220 5.991328 CAGCTACACTGTTTTTCTCTTGA 57.009 39.130 0.00 0.00 41.86 3.02
3644 4243 5.265989 AGTTTGTTGTTTCTTGGGTCCTTA 58.734 37.500 0.00 0.00 0.00 2.69
3796 4395 9.892130 ACAGATTAGTCCGAGATTTTTCTAAAT 57.108 29.630 0.00 0.00 36.68 1.40
3919 4518 6.148811 TCCGAGGCACTAGAACTTTTAATTTG 59.851 38.462 0.00 0.00 41.55 2.32
3958 4557 7.011499 TCTTGGCTTTGGTTACTCTGTTATA 57.989 36.000 0.00 0.00 0.00 0.98
3964 4563 8.610035 GGCTTTGGTTACTCTGTTATATTACAC 58.390 37.037 0.00 0.00 0.00 2.90
3965 4564 9.379791 GCTTTGGTTACTCTGTTATATTACACT 57.620 33.333 0.00 0.00 0.00 3.55
3984 4583 5.842907 ACACTTCAAATTTCTTAAGGTGGC 58.157 37.500 1.85 0.00 0.00 5.01
4004 4603 6.553953 TGGCACACCTATAATTCTAACTCA 57.446 37.500 0.00 0.00 36.63 3.41
4133 4732 7.366847 ACTGCTCAGGTTCTGTATATATGTT 57.633 36.000 1.66 0.00 32.61 2.71
4134 4733 7.437748 ACTGCTCAGGTTCTGTATATATGTTC 58.562 38.462 1.66 0.00 32.61 3.18
4135 4734 7.288852 ACTGCTCAGGTTCTGTATATATGTTCT 59.711 37.037 1.66 0.00 32.61 3.01
4136 4735 7.436933 TGCTCAGGTTCTGTATATATGTTCTG 58.563 38.462 0.00 0.00 32.61 3.02
4137 4736 7.069950 TGCTCAGGTTCTGTATATATGTTCTGT 59.930 37.037 0.00 0.00 32.61 3.41
4138 4737 8.577296 GCTCAGGTTCTGTATATATGTTCTGTA 58.423 37.037 0.00 0.00 32.61 2.74
4204 4810 8.897752 ACTGCTCTTCTGTTTTTGATAATATCC 58.102 33.333 0.00 0.00 0.00 2.59
4509 5115 2.400399 TCAAGTAGTTCTTTGCCGTCG 58.600 47.619 0.00 0.00 33.63 5.12
4943 5553 6.318144 TGTTTTGTCCACATTGAAATGCATTT 59.682 30.769 24.33 24.33 40.04 2.32
4952 5562 9.384682 CCACATTGAAATGCATTTTTAACTTTC 57.615 29.630 24.81 11.55 40.04 2.62
5119 5729 4.314961 TCAACATGGCTACACTAGTGTTG 58.685 43.478 32.15 29.18 44.57 3.33
5181 5791 2.205022 TTGGAGGGCACTGAGAAATG 57.795 50.000 0.00 0.00 0.00 2.32
5272 5915 5.724370 TGGAACATTAACCTGTCTCCATAGA 59.276 40.000 8.08 0.00 34.40 1.98
5295 5938 8.025243 AGAAAAATTAGCATTTGATTGCACAG 57.975 30.769 0.00 0.00 45.23 3.66
5470 6113 7.227156 CCATTATAATTAGGCAGACCAGAAGT 58.773 38.462 0.00 0.00 39.06 3.01
5598 6241 2.635714 CAGTGTGCATGCTTCTGGATA 58.364 47.619 20.33 0.00 0.00 2.59
5676 6319 7.775561 GGACTAGGATGTCAGGTTTCATTTATT 59.224 37.037 0.00 0.00 38.61 1.40
5929 6659 5.351189 TGACAATAAGATCACAATGGACACG 59.649 40.000 0.00 0.00 0.00 4.49
6200 6930 2.758979 TCCCGAGTTTCAGGACAGATAC 59.241 50.000 0.00 0.00 0.00 2.24
6241 6971 5.295787 TGTTGTTCAAGTTGCCTAGTAGTTG 59.704 40.000 0.00 0.00 0.00 3.16
6298 7028 6.456853 GCATTAGACGTGCATTTTGAGTCATA 60.457 38.462 0.00 0.00 42.08 2.15
6328 7058 9.412460 TCTTTCAAAAGCCAATGATGATAGTAT 57.588 29.630 0.00 0.00 35.99 2.12
6449 7188 2.026636 ACAGATACCCTTTTTAGCCGCA 60.027 45.455 0.00 0.00 0.00 5.69
6516 7255 9.139174 CACTGAAATAAAATAAGGCATCGTTTT 57.861 29.630 0.00 0.00 0.00 2.43
6581 7320 4.362677 AGCCTGAGATGGTAGTAAGGAAA 58.637 43.478 0.00 0.00 0.00 3.13
6708 7449 5.250200 TCTACAATAAACCTGTCGGCATTT 58.750 37.500 0.00 0.00 0.00 2.32
7098 7839 5.348986 GTGATTTGCTGCATCTCATTCATT 58.651 37.500 15.00 0.00 0.00 2.57
7364 8105 7.709182 TCAGTAGAATATGGTTTCCATTACACG 59.291 37.037 6.59 0.00 42.23 4.49
7409 8150 3.744660 TGTTCTTTCAAGAGCTCCTTCC 58.255 45.455 10.93 0.00 37.20 3.46
7907 8652 5.542635 TGAGTACTGGTAATTGTGTTCTCCT 59.457 40.000 0.00 0.00 0.00 3.69
7930 8675 8.160765 TCCTGGTTTGATATGTCTTCTGTTTTA 58.839 33.333 0.00 0.00 0.00 1.52
7982 8727 2.910199 TGAGAGCAATTCCATCCTTCG 58.090 47.619 0.00 0.00 0.00 3.79
8016 8761 0.904649 TGTCTAGTCCCCATGCTGTG 59.095 55.000 0.00 0.00 0.00 3.66
8147 8892 9.912634 CTACAAATTTCCAACATGAAGTTATGT 57.087 29.630 0.00 0.00 42.82 2.29
8238 8983 4.442706 TCCTTCATCTATTGAAACGCCTC 58.557 43.478 0.00 0.00 43.64 4.70
8239 8984 4.081142 TCCTTCATCTATTGAAACGCCTCA 60.081 41.667 0.00 0.00 43.64 3.86
8246 8993 1.865865 TTGAAACGCCTCACACTCTC 58.134 50.000 0.00 0.00 0.00 3.20
8936 9683 3.826729 TGAGTGCTACTAGTGCTTTCTGA 59.173 43.478 5.39 0.63 0.00 3.27
8952 9699 8.078596 GTGCTTTCTGAATGAACTTACAGATTT 58.921 33.333 7.40 0.00 38.79 2.17
9119 9874 4.706842 TGCATTATTCCCTCTTAGACCC 57.293 45.455 0.00 0.00 0.00 4.46
9191 9946 6.935167 ACATGTTTTCAATTCCCAACCTATC 58.065 36.000 0.00 0.00 0.00 2.08
9339 10094 6.449635 TCAGCAGTAAAAACTGAATTGTGT 57.550 33.333 9.63 0.00 39.99 3.72
9385 10140 6.980593 TGCTGTCAAGTATACTGCAATTTTT 58.019 32.000 6.06 0.00 45.18 1.94
9514 10269 0.107993 CTGGTCATCGGTGCAGATGT 60.108 55.000 13.81 0.00 45.96 3.06
9555 10310 0.819259 TTGCTTCCTGCGTCTTTGCT 60.819 50.000 0.00 0.00 46.63 3.91
9629 10384 1.790755 TGGTGAGTTTCGTCCAATCG 58.209 50.000 0.00 0.00 0.00 3.34
9659 10414 8.627208 ATTACTCTGGCCATTCATATTAGTTG 57.373 34.615 5.51 0.00 0.00 3.16
9692 10447 6.654582 AGAATTTGTGCCAGTCAAAACTTTTT 59.345 30.769 0.00 0.00 38.11 1.94
9771 10526 7.428826 AGATTTTTCATGAAGTCAAAGTGTCC 58.571 34.615 8.41 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.170919 ATATCTCCCGTCGGACCGTG 61.171 60.000 14.39 7.84 33.32 4.94
32 33 7.014808 GCTCTACTTATTATGACACCTCCTTCT 59.985 40.741 0.00 0.00 0.00 2.85
42 43 5.402867 GTCGCCTTGCTCTACTTATTATGAC 59.597 44.000 0.00 0.00 0.00 3.06
72 73 0.556258 TCAGGGATAAGAGAGCGGGA 59.444 55.000 0.00 0.00 0.00 5.14
82 83 5.631119 TCGTAGAGACATCATCAGGGATAA 58.369 41.667 0.00 0.00 0.00 1.75
105 106 6.316390 GTCTGATTTAATTTGACCGACCATCT 59.684 38.462 0.00 0.00 0.00 2.90
126 127 5.098893 CCGAAAGAAGTGAGATGTAGTCTG 58.901 45.833 0.00 0.00 37.29 3.51
145 146 1.067354 GGAGGTTAAGACGCTTCCGAA 60.067 52.381 0.00 0.00 38.29 4.30
150 151 8.803397 AATTATAAAAGGAGGTTAAGACGCTT 57.197 30.769 0.00 0.00 0.00 4.68
185 186 9.434420 GTCATTTGGATGATATTTGGTTGAAAA 57.566 29.630 0.00 0.00 43.76 2.29
267 373 7.080353 TCTTTCACGTAATGATAAGAGTCGA 57.920 36.000 0.00 0.00 37.11 4.20
268 374 7.736031 TTCTTTCACGTAATGATAAGAGTCG 57.264 36.000 0.00 0.00 36.59 4.18
285 396 8.244802 TGTGTTTTTCGGTTCTATTTTCTTTCA 58.755 29.630 0.00 0.00 0.00 2.69
1303 1493 7.646526 TGATACGAACATACCAATCTAAACTCG 59.353 37.037 0.00 0.00 0.00 4.18
1316 1506 5.346281 GCTAGCAATCCTGATACGAACATAC 59.654 44.000 10.63 0.00 0.00 2.39
1362 1552 1.553248 CTTTGATGTACCAGACCCCGA 59.447 52.381 0.00 0.00 0.00 5.14
1508 1698 4.044426 GCACATCAGTTCAAGAAACCAAC 58.956 43.478 0.00 0.00 38.76 3.77
1538 1728 1.740025 GAGGGCTCATCTCAAAAACCG 59.260 52.381 0.00 0.00 0.00 4.44
1770 1960 1.072331 ACCACTGCGAAAATGTCCTCT 59.928 47.619 0.00 0.00 0.00 3.69
1826 2016 8.507249 CAATCTAAAGTAACCCAAAGAGACAAG 58.493 37.037 0.00 0.00 0.00 3.16
1998 2568 3.242011 AGCAACTTCAAATTCCATGGGT 58.758 40.909 13.02 0.00 0.00 4.51
1999 2569 3.967332 AGCAACTTCAAATTCCATGGG 57.033 42.857 13.02 0.00 0.00 4.00
2000 2570 6.536224 GGAAATAGCAACTTCAAATTCCATGG 59.464 38.462 4.97 4.97 36.09 3.66
2054 2643 3.990469 GCCATTGACTATCACCTATCACG 59.010 47.826 0.00 0.00 0.00 4.35
2089 2678 2.020720 ACACGGAGCAACAATTCAACA 58.979 42.857 0.00 0.00 0.00 3.33
2092 2681 0.310543 GCACACGGAGCAACAATTCA 59.689 50.000 0.00 0.00 0.00 2.57
2205 2795 1.477014 GGCCTGCAAAGTAGGTATCCC 60.477 57.143 0.00 0.00 37.64 3.85
2299 2889 9.688592 GATAACACTACAGGTAACACCATATAC 57.311 37.037 0.00 0.00 41.95 1.47
2353 2943 2.756760 GCATCATTTGGGAGAGCAAGAA 59.243 45.455 0.00 0.00 0.00 2.52
2429 3019 4.938575 ATGTCCACCCCATAAAACTACA 57.061 40.909 0.00 0.00 0.00 2.74
2435 3025 1.841277 ACGCTATGTCCACCCCATAAA 59.159 47.619 0.00 0.00 0.00 1.40
2542 3134 0.178950 TCTGTCTCCTGGACTGCTGT 60.179 55.000 0.00 0.00 44.74 4.40
2579 3171 0.949105 ACTACAAAAGGCCGACAGCG 60.949 55.000 0.00 0.00 45.17 5.18
2848 3443 1.686052 GCCACTTGGTCCAAAACATCA 59.314 47.619 5.64 0.00 37.57 3.07
2926 3521 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2947 3542 8.241497 TGGTTTAGTGTTAGATACATCCGTAT 57.759 34.615 0.00 0.00 41.16 3.06
2948 3543 7.643569 TGGTTTAGTGTTAGATACATCCGTA 57.356 36.000 0.00 0.00 39.39 4.02
2949 3544 6.534475 TGGTTTAGTGTTAGATACATCCGT 57.466 37.500 0.00 0.00 39.39 4.69
2950 3545 7.169308 GTCATGGTTTAGTGTTAGATACATCCG 59.831 40.741 0.00 0.00 39.39 4.18
2962 3557 7.470147 CGGATGTATCTAGTCATGGTTTAGTGT 60.470 40.741 0.00 0.00 0.00 3.55
2963 3558 6.863645 CGGATGTATCTAGTCATGGTTTAGTG 59.136 42.308 0.00 0.00 0.00 2.74
2970 3565 6.516739 ACATACGGATGTATCTAGTCATGG 57.483 41.667 12.79 0.00 44.77 3.66
2971 3566 8.494016 TCTACATACGGATGTATCTAGTCATG 57.506 38.462 20.64 6.28 45.42 3.07
2997 3592 8.726988 CGTCCCAAAATTCTTGTCTTAGATTTA 58.273 33.333 0.00 0.00 0.00 1.40
2998 3593 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3001 3596 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3002 3597 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3003 3598 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3005 3600 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3006 3601 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3007 3602 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3008 3603 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3009 3604 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3011 3606 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3012 3607 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3013 3608 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3014 3609 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
3015 3610 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
3016 3611 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3017 3612 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
3018 3613 0.751452 GAACATACTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
3019 3614 1.777941 AGAACATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3020 3615 5.393243 GCATATAGAACATACTCCCTCCGTC 60.393 48.000 0.00 0.00 0.00 4.79
3121 3716 6.443792 TCCAATACATGTATAGCACTACACG 58.556 40.000 18.56 0.00 34.59 4.49
3154 3749 9.426837 CAGTCAAATAATCACACATGGAAAATT 57.573 29.630 0.00 0.00 0.00 1.82
3270 3867 6.882140 AGTAGATCTATATTGTCCTGACTCCG 59.118 42.308 5.57 0.00 0.00 4.63
3300 3897 2.307098 ACAAGATGTAAGAAGCCAGCCT 59.693 45.455 0.00 0.00 0.00 4.58
3394 3993 8.379331 GCTCTTATATTTCTTTATGGAGGGAGT 58.621 37.037 0.00 0.00 0.00 3.85
3550 4149 4.412207 CGGACTGCAACTTTATTTAAGGC 58.588 43.478 0.00 0.00 38.23 4.35
3566 4165 2.924290 GCTACAAGAAACTAGCGGACTG 59.076 50.000 0.00 0.00 0.00 3.51
3621 4220 3.708451 AGGACCCAAGAAACAACAAACT 58.292 40.909 0.00 0.00 0.00 2.66
3644 4243 2.008242 TGGCAAGTACAAAATGGCCT 57.992 45.000 3.32 0.00 41.86 5.19
3720 4319 2.726066 GCTGATACAAGCACGCAACTTC 60.726 50.000 0.00 0.00 43.01 3.01
3764 4363 9.667107 AAAAATCTCGGACTAATCTGTTCAATA 57.333 29.630 0.00 0.00 32.47 1.90
3797 4396 7.001674 TGATTGGACTAGCCTCTGTTTAAAAA 58.998 34.615 5.06 0.00 37.63 1.94
3798 4397 6.539173 TGATTGGACTAGCCTCTGTTTAAAA 58.461 36.000 5.06 0.00 37.63 1.52
3801 4400 5.755409 TTGATTGGACTAGCCTCTGTTTA 57.245 39.130 5.06 0.00 37.63 2.01
3805 4404 6.438741 TCCTATATTGATTGGACTAGCCTCTG 59.561 42.308 5.06 0.00 32.72 3.35
3867 4466 6.403636 GCCTATTGTCACAATTCCAAGTACAG 60.404 42.308 8.69 0.00 0.00 2.74
3919 4518 3.005155 AGCCAAGAAAAGAGCACACAATC 59.995 43.478 0.00 0.00 0.00 2.67
3958 4557 8.088365 GCCACCTTAAGAAATTTGAAGTGTAAT 58.912 33.333 3.36 0.00 0.00 1.89
3964 4563 5.691754 GTGTGCCACCTTAAGAAATTTGAAG 59.308 40.000 3.36 0.00 0.00 3.02
3965 4564 5.596845 GTGTGCCACCTTAAGAAATTTGAA 58.403 37.500 3.36 0.00 0.00 2.69
4068 4667 9.823647 AATGTTCACCAAATTACAATGTGTTAA 57.176 25.926 0.00 0.00 0.00 2.01
4403 5009 9.442047 CTTCAATCAAAGATTTCACCTAGTAGT 57.558 33.333 0.00 0.00 0.00 2.73
4509 5115 2.014068 GCACTACCAGCAGGGAACATC 61.014 57.143 0.00 0.00 41.15 3.06
4692 5302 8.510243 ACATGAATAATAACAAGCACAGATGA 57.490 30.769 0.00 0.00 0.00 2.92
4943 5553 9.809096 TGTGCAAATAAGACATTGAAAGTTAAA 57.191 25.926 0.00 0.00 0.00 1.52
4952 5562 9.961265 ATTCTGATATGTGCAAATAAGACATTG 57.039 29.630 0.00 0.00 32.59 2.82
5164 5774 0.034670 AGCATTTCTCAGTGCCCTCC 60.035 55.000 0.00 0.00 42.20 4.30
5181 5791 1.065102 CATGTGGTAGCTGCATGAAGC 59.935 52.381 18.84 18.84 41.62 3.86
5272 5915 6.348704 GGCTGTGCAATCAAATGCTAATTTTT 60.349 34.615 0.00 0.00 46.54 1.94
5295 5938 1.956477 ACACAGATTTCCAACACTGGC 59.044 47.619 0.00 0.00 43.17 4.85
5598 6241 8.546597 AATTTACAAACACAAGCAAGAAAACT 57.453 26.923 0.00 0.00 0.00 2.66
5929 6659 9.220767 CTTAGTATTTCAAATATCTGGGTAGCC 57.779 37.037 3.29 3.29 0.00 3.93
6200 6930 3.369756 ACAACACATAACAGCGATTACCG 59.630 43.478 0.00 0.00 42.21 4.02
6241 6971 5.675538 ACAAAGAATACTGGTGATAGAGCC 58.324 41.667 0.00 0.00 0.00 4.70
6281 7011 5.872635 AGAACATATGACTCAAAATGCACG 58.127 37.500 10.38 0.00 0.00 5.34
6298 7028 6.761312 TCATCATTGGCTTTTGAAAGAACAT 58.239 32.000 7.63 0.00 38.28 2.71
6397 7127 5.538813 AGATGCGGAGGACATAACTACATTA 59.461 40.000 0.00 0.00 0.00 1.90
6516 7255 6.020971 TCTACGCAAACAGAACTATGAAGA 57.979 37.500 0.00 0.00 0.00 2.87
6581 7320 2.359981 TCTACGATCGGTTCCAGGAT 57.640 50.000 20.98 0.00 0.00 3.24
6708 7449 4.023980 AGATGTTGATACGGAGAGTTCCA 58.976 43.478 0.00 0.00 44.26 3.53
7237 7978 6.813293 TTGTTGATATCCTCTTCCTCATCA 57.187 37.500 0.00 0.00 0.00 3.07
7364 8105 5.755861 AGAATTCGTAAGGAGCTAAAGCATC 59.244 40.000 4.54 0.00 40.49 3.91
7409 8150 2.445427 TGGCCATCACAACCACATAAG 58.555 47.619 0.00 0.00 0.00 1.73
7544 8285 7.630026 TGCAGTAGATTACATAAAAATGCTCG 58.370 34.615 0.00 0.00 0.00 5.03
7907 8652 7.942341 AGGTAAAACAGAAGACATATCAAACCA 59.058 33.333 0.00 0.00 0.00 3.67
7930 8675 8.047310 CCCTCAGATAATAAAACAGTTACAGGT 58.953 37.037 0.00 0.00 0.00 4.00
7982 8727 7.173390 GGGGACTAGACATTTAAGCATACATTC 59.827 40.741 0.00 0.00 0.00 2.67
8016 8761 2.246719 ATGCCTCGAGACCAAATAGC 57.753 50.000 15.71 6.54 0.00 2.97
8147 8892 9.777008 TGATATAACATATAGGTGTCCCATACA 57.223 33.333 0.00 0.00 35.06 2.29
8238 8983 4.686554 GCACTTAAACCTGTAGAGAGTGTG 59.313 45.833 7.29 0.00 36.36 3.82
8239 8984 4.344102 TGCACTTAAACCTGTAGAGAGTGT 59.656 41.667 7.29 0.00 36.36 3.55
8246 8993 6.992063 AGATCAATGCACTTAAACCTGTAG 57.008 37.500 0.00 0.00 0.00 2.74
8655 9402 4.455877 AGGAATGGATCACGAGTTTCAAAC 59.544 41.667 0.00 0.00 0.00 2.93
8820 9567 1.137675 TCTTCCATCGACAGCCTGATG 59.862 52.381 0.00 0.00 41.27 3.07
8952 9699 7.235399 TCCATAATTCACTAGCCATCTGTATCA 59.765 37.037 0.00 0.00 0.00 2.15
9119 9874 2.412870 TGTGTGTCACTATGAAAGGCG 58.587 47.619 4.27 0.00 35.11 5.52
9261 10016 5.121221 ACGGAACTTAAGAAATTGCCAAG 57.879 39.130 10.09 0.00 0.00 3.61
9339 10094 4.859798 CAGTTTTTGCGTAAACCACTCAAA 59.140 37.500 0.00 0.00 39.46 2.69
9385 10140 0.911769 AATTCTCTGCATGACGGGGA 59.088 50.000 0.00 0.00 29.70 4.81
9476 10231 7.952671 TGACCAGCTTATACGAGAGATAAAAT 58.047 34.615 0.00 0.00 0.00 1.82
9534 10289 1.927710 GCAAAGACGCAGGAAGCAAAG 60.928 52.381 0.00 0.00 46.13 2.77
9555 10310 7.441890 TTTAACTTGATAAACATCGAAGGCA 57.558 32.000 0.00 0.00 0.00 4.75
9590 10345 5.472478 CACCAATCGTACTGGCTACTATAGA 59.528 44.000 6.78 0.00 37.48 1.98
9629 10384 5.841957 ATGAATGGCCAGAGTAATTGTTC 57.158 39.130 13.05 7.31 0.00 3.18
9659 10414 5.932303 TGACTGGCACAAATTCTAGAACTAC 59.068 40.000 7.48 0.00 38.70 2.73
9677 10432 6.533723 GGTCAAACCTAAAAAGTTTTGACTGG 59.466 38.462 20.59 4.90 35.28 4.00


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

AutoCloner maintained by Alex Coulton.