Multiple sequence alignment - TraesCS2D01G277400

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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 TraesCS2D01G277400 chr2D 100.000 4097 0 0 1 4097 347790888 347794984 0.000000e+00 7566.0
1 TraesCS2D01G277400 chr2D 78.424 1701 278 47 913 2553 347807276 347808947 0.000000e+00 1026.0
2 TraesCS2D01G277400 chr2B 94.905 3415 109 14 1 3351 412989134 412992547 0.000000e+00 5282.0
3 TraesCS2D01G277400 chr2B 94.937 553 23 4 3350 3898 412992594 412993145 0.000000e+00 861.0
4 TraesCS2D01G277400 chr2A 94.377 2294 84 19 1 2259 461388282 461390565 0.000000e+00 3480.0
5 TraesCS2D01G277400 chr2A 93.016 1532 74 22 2256 3755 461390645 461392175 0.000000e+00 2206.0
6 TraesCS2D01G277400 chr2A 94.681 94 5 0 3817 3910 461399366 461399459 3.300000e-31 147.0
7 TraesCS2D01G277400 chr2A 96.512 86 2 1 3740 3825 461392196 461392280 1.540000e-29 141.0
8 TraesCS2D01G277400 chr5A 78.838 1687 273 56 913 2553 569224765 569223117 0.000000e+00 1061.0
9 TraesCS2D01G277400 chr5A 79.002 1624 261 55 962 2553 569183932 569182357 0.000000e+00 1037.0
10 TraesCS2D01G277400 chr5A 79.363 1318 215 36 932 2211 569151632 569152930 0.000000e+00 874.0
11 TraesCS2D01G277400 chr7B 78.002 1782 292 61 1064 2772 733750414 733752168 0.000000e+00 1027.0
12 TraesCS2D01G277400 chr7B 83.253 1033 134 30 1064 2063 733359501 733358475 0.000000e+00 913.0
13 TraesCS2D01G277400 chr7B 80.872 1192 169 41 1060 2207 733787983 733789159 0.000000e+00 883.0
14 TraesCS2D01G277400 chr5D 77.772 1777 298 57 832 2553 449936312 449934578 0.000000e+00 1003.0
15 TraesCS2D01G277400 chr5D 80.562 1317 197 31 935 2211 449940975 449939678 0.000000e+00 959.0
16 TraesCS2D01G277400 chr5D 80.418 1195 184 35 935 2089 449983278 449982094 0.000000e+00 865.0
17 TraesCS2D01G277400 chr5D 81.349 949 128 28 973 1890 449883760 449884690 0.000000e+00 726.0
18 TraesCS2D01G277400 chr5D 77.219 338 49 18 2646 2963 449981461 449981132 5.440000e-39 172.0
19 TraesCS2D01G277400 chr5D 76.667 330 56 11 2648 2962 449939148 449938825 3.280000e-36 163.0
20 TraesCS2D01G277400 chr7A 81.255 1195 160 44 1064 2200 726859482 726858294 0.000000e+00 907.0
21 TraesCS2D01G277400 chr7A 80.167 479 68 20 2307 2772 726858223 726857759 2.360000e-87 333.0
22 TraesCS2D01G277400 chr5B 82.240 991 137 24 935 1890 549954194 549953208 0.000000e+00 819.0
23 TraesCS2D01G277400 chr4A 94.872 39 1 1 4050 4087 699620486 699620524 4.420000e-05 60.2


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 TraesCS2D01G277400 chr2D 347790888 347794984 4096 False 7566.000000 7566 100.000000 1 4097 1 chr2D.!!$F1 4096
1 TraesCS2D01G277400 chr2D 347807276 347808947 1671 False 1026.000000 1026 78.424000 913 2553 1 chr2D.!!$F2 1640
2 TraesCS2D01G277400 chr2B 412989134 412993145 4011 False 3071.500000 5282 94.921000 1 3898 2 chr2B.!!$F1 3897
3 TraesCS2D01G277400 chr2A 461388282 461392280 3998 False 1942.333333 3480 94.635000 1 3825 3 chr2A.!!$F2 3824
4 TraesCS2D01G277400 chr5A 569223117 569224765 1648 True 1061.000000 1061 78.838000 913 2553 1 chr5A.!!$R2 1640
5 TraesCS2D01G277400 chr5A 569182357 569183932 1575 True 1037.000000 1037 79.002000 962 2553 1 chr5A.!!$R1 1591
6 TraesCS2D01G277400 chr5A 569151632 569152930 1298 False 874.000000 874 79.363000 932 2211 1 chr5A.!!$F1 1279
7 TraesCS2D01G277400 chr7B 733750414 733752168 1754 False 1027.000000 1027 78.002000 1064 2772 1 chr7B.!!$F1 1708
8 TraesCS2D01G277400 chr7B 733358475 733359501 1026 True 913.000000 913 83.253000 1064 2063 1 chr7B.!!$R1 999
9 TraesCS2D01G277400 chr7B 733787983 733789159 1176 False 883.000000 883 80.872000 1060 2207 1 chr7B.!!$F2 1147
10 TraesCS2D01G277400 chr5D 449883760 449884690 930 False 726.000000 726 81.349000 973 1890 1 chr5D.!!$F1 917
11 TraesCS2D01G277400 chr5D 449934578 449940975 6397 True 708.333333 1003 78.333667 832 2962 3 chr5D.!!$R1 2130
12 TraesCS2D01G277400 chr5D 449981132 449983278 2146 True 518.500000 865 78.818500 935 2963 2 chr5D.!!$R2 2028
13 TraesCS2D01G277400 chr7A 726857759 726859482 1723 True 620.000000 907 80.711000 1064 2772 2 chr7A.!!$R1 1708
14 TraesCS2D01G277400 chr5B 549953208 549954194 986 True 819.000000 819 82.240000 935 1890 1 chr5B.!!$R1 955

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
341 343 0.247736 AATCACAGGGCTCGTCAGTC 59.752 55.0 0.0 0.0 0.00 3.51 F
557 581 0.252513 TCGGGAAAGGGAGTCCATGA 60.253 55.0 12.3 0.0 36.83 3.07 F
1623 1734 0.865111 CAAACGCAGAACATCGTCCA 59.135 50.0 0.0 0.0 38.03 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1693 1.302511 GAACCGGACATGGCACTGT 60.303 57.895 9.46 0.0 0.0 3.55 R
2381 7485 0.389166 GCTCGACACAAGACCCAGAG 60.389 60.000 0.00 0.0 0.0 3.35 R
3126 8358 1.222567 TCTCCCTGGCTAATTTCCCC 58.777 55.000 0.00 0.0 0.0 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
203 205 2.450619 GAGCGACAGAGTTTGCTCC 58.549 57.895 11.79 0.00 46.21 4.70
244 246 3.751518 TCTTAGGAGGTTCTGTTTTGCC 58.248 45.455 0.00 0.00 0.00 4.52
272 274 7.032598 AGAGGAGGGATGTCTTGAATTTTTA 57.967 36.000 0.00 0.00 0.00 1.52
274 276 5.952347 AGGAGGGATGTCTTGAATTTTTACC 59.048 40.000 0.00 0.00 0.00 2.85
331 333 0.251916 TGCGGTTCCTAATCACAGGG 59.748 55.000 0.00 0.00 36.26 4.45
341 343 0.247736 AATCACAGGGCTCGTCAGTC 59.752 55.000 0.00 0.00 0.00 3.51
550 574 0.389948 CAACGAGTCGGGAAAGGGAG 60.390 60.000 18.30 0.00 0.00 4.30
557 581 0.252513 TCGGGAAAGGGAGTCCATGA 60.253 55.000 12.30 0.00 36.83 3.07
695 742 1.742761 ATTCACTGCAGATTGTCGGG 58.257 50.000 23.35 0.00 0.00 5.14
706 753 4.508124 GCAGATTGTCGGGTAGTTATTCTG 59.492 45.833 0.00 0.00 33.07 3.02
876 923 4.040461 TCTGTTTCCTCTCGATTTCCTGTT 59.960 41.667 0.00 0.00 0.00 3.16
1116 1177 2.062177 GTACCTTGCCGGGCCTCTA 61.062 63.158 17.97 0.00 36.97 2.43
1260 1323 8.454106 GGCTTCAGCTTGTTGGTATATATATTG 58.546 37.037 0.00 0.00 41.70 1.90
1293 1377 7.437713 TCATCTCTTACATATGTTGGACCTT 57.562 36.000 14.77 0.00 0.00 3.50
1329 1440 2.490509 TCAGCTGGCTTTGTTCATGATG 59.509 45.455 15.13 0.00 0.00 3.07
1582 1693 2.438254 TTCGTCTACGGCCCGCTA 60.438 61.111 1.23 0.00 40.29 4.26
1623 1734 0.865111 CAAACGCAGAACATCGTCCA 59.135 50.000 0.00 0.00 38.03 4.02
1884 1995 3.370846 CCATCTGCTCTCATGGTTTGGTA 60.371 47.826 0.00 0.00 35.67 3.25
1892 2003 5.009610 GCTCTCATGGTTTGGTAAGTTTGAA 59.990 40.000 0.00 0.00 0.00 2.69
1927 2054 9.241919 TCTAATTGCAGGTAGAATTTTTCATCA 57.758 29.630 6.08 0.00 0.00 3.07
2509 7613 3.101437 AGAATGATGCCAATTCTTGCCA 58.899 40.909 1.01 0.00 31.21 4.92
2570 7674 3.306502 GGTAAGTGCAGTGTAGGTGCTTA 60.307 47.826 0.00 0.00 41.78 3.09
2612 7718 5.599999 ATTATAAGGAGCCTGCGTATAGG 57.400 43.478 0.00 0.00 40.95 2.57
2744 7961 1.336755 CCCGCGGCTTTATATTTTGCT 59.663 47.619 22.85 0.00 0.00 3.91
2784 8001 8.343168 TGGTGGAATGGTACTTATTTTACTTG 57.657 34.615 0.00 0.00 0.00 3.16
2788 8005 9.005777 TGGAATGGTACTTATTTTACTTGTGTC 57.994 33.333 0.00 0.00 0.00 3.67
3006 8238 5.408299 GTGAGTTTTGTTTTGTTGGCTTCTT 59.592 36.000 0.00 0.00 0.00 2.52
3126 8358 5.981315 ACAAGACAAGATGCACAATTTTCTG 59.019 36.000 0.00 0.00 0.00 3.02
3263 8495 5.060446 CGATCCGCTTTGGTAAAAACAATTC 59.940 40.000 0.00 0.00 39.52 2.17
3268 8500 5.164100 CGCTTTGGTAAAAACAATTCGGATG 60.164 40.000 0.00 0.00 0.00 3.51
3308 8542 1.835494 TGAGTAGAGGCGCAGTACTT 58.165 50.000 10.83 0.00 0.00 2.24
3316 8550 1.019805 GGCGCAGTACTTCCCTTGAC 61.020 60.000 10.83 0.00 0.00 3.18
3446 8733 3.055819 TGCTTGGTTTTTGTGCTTGGTAA 60.056 39.130 0.00 0.00 0.00 2.85
3480 8767 3.511934 GGGATGAGGACGCTAGTGATTAT 59.488 47.826 10.99 0.00 0.00 1.28
3647 8937 3.519908 TTTTGAGCTTTCGTGATCGTG 57.480 42.857 0.00 0.00 38.33 4.35
3693 8987 0.968393 AAACTTGGTGTTGGTGCGGT 60.968 50.000 0.00 0.00 39.13 5.68
3756 9086 5.479306 GTTGTGTTCCTGATCTAGTGCTAA 58.521 41.667 0.00 0.00 0.00 3.09
3805 9136 7.996758 ATGGGGAGAAGACTAGAATAGAAAA 57.003 36.000 0.00 0.00 42.77 2.29
3831 9162 2.340337 GGTGTGCAAAAATGAGATGCC 58.660 47.619 0.00 0.00 39.31 4.40
3894 9225 4.186926 TGATGCTATCAAGACAGCTCAAC 58.813 43.478 1.74 0.00 38.63 3.18
3898 9229 2.820059 ATCAAGACAGCTCAACGTGA 57.180 45.000 0.00 0.00 0.00 4.35
3899 9230 2.595124 TCAAGACAGCTCAACGTGAA 57.405 45.000 0.00 0.00 0.00 3.18
3900 9231 2.201732 TCAAGACAGCTCAACGTGAAC 58.798 47.619 0.00 0.00 0.00 3.18
3901 9232 1.933181 CAAGACAGCTCAACGTGAACA 59.067 47.619 0.00 0.00 0.00 3.18
3902 9233 2.309528 AGACAGCTCAACGTGAACAA 57.690 45.000 0.00 0.00 0.00 2.83
3903 9234 2.627945 AGACAGCTCAACGTGAACAAA 58.372 42.857 0.00 0.00 0.00 2.83
3904 9235 3.006940 AGACAGCTCAACGTGAACAAAA 58.993 40.909 0.00 0.00 0.00 2.44
3905 9236 3.627577 AGACAGCTCAACGTGAACAAAAT 59.372 39.130 0.00 0.00 0.00 1.82
3906 9237 4.096382 AGACAGCTCAACGTGAACAAAATT 59.904 37.500 0.00 0.00 0.00 1.82
3907 9238 4.104776 ACAGCTCAACGTGAACAAAATTG 58.895 39.130 0.00 0.00 0.00 2.32
3908 9239 4.104776 CAGCTCAACGTGAACAAAATTGT 58.895 39.130 0.00 0.00 44.72 2.71
3909 9240 5.163703 ACAGCTCAACGTGAACAAAATTGTA 60.164 36.000 0.00 0.00 41.31 2.41
3910 9241 5.171337 CAGCTCAACGTGAACAAAATTGTAC 59.829 40.000 0.00 0.00 41.31 2.90
3911 9242 5.065988 AGCTCAACGTGAACAAAATTGTACT 59.934 36.000 0.00 0.00 41.31 2.73
3912 9243 5.395486 GCTCAACGTGAACAAAATTGTACTC 59.605 40.000 0.00 0.00 41.31 2.59
3913 9244 5.812652 TCAACGTGAACAAAATTGTACTCC 58.187 37.500 0.00 0.00 41.31 3.85
3914 9245 4.461992 ACGTGAACAAAATTGTACTCCG 57.538 40.909 0.00 3.28 41.31 4.63
3915 9246 3.872771 ACGTGAACAAAATTGTACTCCGT 59.127 39.130 0.00 3.84 41.31 4.69
3916 9247 4.025480 ACGTGAACAAAATTGTACTCCGTC 60.025 41.667 0.00 0.00 41.31 4.79
3917 9248 4.609783 CGTGAACAAAATTGTACTCCGTCC 60.610 45.833 0.00 0.00 41.31 4.79
3918 9249 3.816523 TGAACAAAATTGTACTCCGTCCC 59.183 43.478 0.00 0.00 41.31 4.46
3919 9250 3.495434 ACAAAATTGTACTCCGTCCCA 57.505 42.857 0.00 0.00 40.16 4.37
3920 9251 3.822940 ACAAAATTGTACTCCGTCCCAA 58.177 40.909 0.00 0.00 40.16 4.12
3921 9252 4.208746 ACAAAATTGTACTCCGTCCCAAA 58.791 39.130 0.00 0.00 40.16 3.28
3922 9253 4.645588 ACAAAATTGTACTCCGTCCCAAAA 59.354 37.500 0.00 0.00 40.16 2.44
3923 9254 5.303333 ACAAAATTGTACTCCGTCCCAAAAT 59.697 36.000 0.00 0.00 40.16 1.82
3924 9255 6.490721 ACAAAATTGTACTCCGTCCCAAAATA 59.509 34.615 0.00 0.00 40.16 1.40
3925 9256 7.014422 ACAAAATTGTACTCCGTCCCAAAATAA 59.986 33.333 0.00 0.00 40.16 1.40
3926 9257 7.712204 AAATTGTACTCCGTCCCAAAATAAT 57.288 32.000 0.00 0.00 0.00 1.28
3927 9258 7.712204 AATTGTACTCCGTCCCAAAATAATT 57.288 32.000 0.00 0.00 0.00 1.40
3928 9259 6.503589 TTGTACTCCGTCCCAAAATAATTG 57.496 37.500 0.00 0.00 0.00 2.32
3929 9260 5.562635 TGTACTCCGTCCCAAAATAATTGT 58.437 37.500 0.00 0.00 0.00 2.71
3930 9261 5.413213 TGTACTCCGTCCCAAAATAATTGTG 59.587 40.000 0.00 0.00 0.00 3.33
3931 9262 4.658063 ACTCCGTCCCAAAATAATTGTGA 58.342 39.130 0.00 0.00 0.00 3.58
3932 9263 4.457949 ACTCCGTCCCAAAATAATTGTGAC 59.542 41.667 0.00 0.00 0.00 3.67
3933 9264 3.759618 TCCGTCCCAAAATAATTGTGACC 59.240 43.478 0.00 0.00 0.00 4.02
3934 9265 3.119280 CCGTCCCAAAATAATTGTGACCC 60.119 47.826 0.00 0.00 0.00 4.46
3935 9266 3.761752 CGTCCCAAAATAATTGTGACCCT 59.238 43.478 0.00 0.00 0.00 4.34
3936 9267 4.219725 CGTCCCAAAATAATTGTGACCCTT 59.780 41.667 0.00 0.00 0.00 3.95
3937 9268 5.279256 CGTCCCAAAATAATTGTGACCCTTT 60.279 40.000 0.00 0.00 0.00 3.11
3938 9269 6.530120 GTCCCAAAATAATTGTGACCCTTTT 58.470 36.000 0.00 0.00 0.00 2.27
3939 9270 6.426633 GTCCCAAAATAATTGTGACCCTTTTG 59.573 38.462 0.00 0.00 34.81 2.44
3940 9271 6.327626 TCCCAAAATAATTGTGACCCTTTTGA 59.672 34.615 7.03 0.00 36.28 2.69
3941 9272 7.017056 TCCCAAAATAATTGTGACCCTTTTGAT 59.983 33.333 7.03 0.00 36.28 2.57
3942 9273 8.317679 CCCAAAATAATTGTGACCCTTTTGATA 58.682 33.333 7.03 0.00 36.28 2.15
3943 9274 9.889128 CCAAAATAATTGTGACCCTTTTGATAT 57.111 29.630 7.03 0.00 36.28 1.63
3945 9276 9.801873 AAAATAATTGTGACCCTTTTGATATCG 57.198 29.630 0.00 0.00 0.00 2.92
3946 9277 5.835113 AATTGTGACCCTTTTGATATCGG 57.165 39.130 0.00 0.00 0.00 4.18
3947 9278 3.275617 TGTGACCCTTTTGATATCGGG 57.724 47.619 10.89 10.89 42.53 5.14
3955 9286 6.985188 CCCTTTTGATATCGGGTACATATG 57.015 41.667 0.00 0.00 31.89 1.78
3956 9287 6.472887 CCCTTTTGATATCGGGTACATATGT 58.527 40.000 13.93 13.93 31.89 2.29
3957 9288 6.940298 CCCTTTTGATATCGGGTACATATGTT 59.060 38.462 14.77 0.00 31.89 2.71
3958 9289 7.119262 CCCTTTTGATATCGGGTACATATGTTC 59.881 40.741 14.77 8.93 31.89 3.18
3959 9290 7.878127 CCTTTTGATATCGGGTACATATGTTCT 59.122 37.037 14.77 0.00 0.00 3.01
3960 9291 9.923143 CTTTTGATATCGGGTACATATGTTCTA 57.077 33.333 14.77 0.00 0.00 2.10
3969 9300 9.578576 TCGGGTACATATGTTCTATTTAGTACT 57.421 33.333 14.77 0.00 33.16 2.73
3983 9314 9.364653 TCTATTTAGTACTACTTTCTCCATCCC 57.635 37.037 0.91 0.00 0.00 3.85
3984 9315 7.989947 ATTTAGTACTACTTTCTCCATCCCA 57.010 36.000 0.91 0.00 0.00 4.37
3985 9316 7.989947 TTTAGTACTACTTTCTCCATCCCAT 57.010 36.000 0.91 0.00 0.00 4.00
3986 9317 9.670442 ATTTAGTACTACTTTCTCCATCCCATA 57.330 33.333 0.91 0.00 0.00 2.74
3987 9318 9.670442 TTTAGTACTACTTTCTCCATCCCATAT 57.330 33.333 0.91 0.00 0.00 1.78
3988 9319 9.670442 TTAGTACTACTTTCTCCATCCCATATT 57.330 33.333 0.91 0.00 0.00 1.28
3990 9321 9.845214 AGTACTACTTTCTCCATCCCATATTAT 57.155 33.333 0.00 0.00 0.00 1.28
3996 9327 9.398921 ACTTTCTCCATCCCATATTATTAGAGT 57.601 33.333 0.00 0.00 0.00 3.24
3997 9328 9.664332 CTTTCTCCATCCCATATTATTAGAGTG 57.336 37.037 0.00 0.00 0.00 3.51
3998 9329 8.742125 TTCTCCATCCCATATTATTAGAGTGT 57.258 34.615 0.00 0.00 0.00 3.55
3999 9330 8.742125 TCTCCATCCCATATTATTAGAGTGTT 57.258 34.615 0.00 0.00 0.00 3.32
4000 9331 9.170890 TCTCCATCCCATATTATTAGAGTGTTT 57.829 33.333 0.00 0.00 0.00 2.83
4001 9332 9.799106 CTCCATCCCATATTATTAGAGTGTTTT 57.201 33.333 0.00 0.00 0.00 2.43
4046 9377 6.499234 ACACTTTACGGTGTTTTAGTTGTT 57.501 33.333 0.00 0.00 46.71 2.83
4047 9378 6.912082 ACACTTTACGGTGTTTTAGTTGTTT 58.088 32.000 0.00 0.00 46.71 2.83
4048 9379 7.369607 ACACTTTACGGTGTTTTAGTTGTTTT 58.630 30.769 0.00 0.00 46.71 2.43
4049 9380 7.866898 ACACTTTACGGTGTTTTAGTTGTTTTT 59.133 29.630 0.00 0.00 46.71 1.94
4050 9381 8.157183 CACTTTACGGTGTTTTAGTTGTTTTTG 58.843 33.333 0.00 0.00 33.04 2.44
4051 9382 7.866898 ACTTTACGGTGTTTTAGTTGTTTTTGT 59.133 29.630 0.00 0.00 0.00 2.83
4052 9383 8.585189 TTTACGGTGTTTTAGTTGTTTTTGTT 57.415 26.923 0.00 0.00 0.00 2.83
4053 9384 9.683069 TTTACGGTGTTTTAGTTGTTTTTGTTA 57.317 25.926 0.00 0.00 0.00 2.41
4054 9385 7.800015 ACGGTGTTTTAGTTGTTTTTGTTAG 57.200 32.000 0.00 0.00 0.00 2.34
4055 9386 7.592051 ACGGTGTTTTAGTTGTTTTTGTTAGA 58.408 30.769 0.00 0.00 0.00 2.10
4056 9387 7.751793 ACGGTGTTTTAGTTGTTTTTGTTAGAG 59.248 33.333 0.00 0.00 0.00 2.43
4057 9388 7.964011 CGGTGTTTTAGTTGTTTTTGTTAGAGA 59.036 33.333 0.00 0.00 0.00 3.10
4058 9389 9.797556 GGTGTTTTAGTTGTTTTTGTTAGAGAT 57.202 29.630 0.00 0.00 0.00 2.75
4082 9413 9.953697 GATATATTTAGTAGTAGAGATTGCCCG 57.046 37.037 0.00 0.00 0.00 6.13
4083 9414 4.931661 TTTAGTAGTAGAGATTGCCCGG 57.068 45.455 0.00 0.00 0.00 5.73
4084 9415 2.750141 AGTAGTAGAGATTGCCCGGA 57.250 50.000 0.73 0.00 0.00 5.14
4085 9416 3.246416 AGTAGTAGAGATTGCCCGGAT 57.754 47.619 0.73 0.00 0.00 4.18
4086 9417 3.577919 AGTAGTAGAGATTGCCCGGATT 58.422 45.455 0.73 0.00 0.00 3.01
4087 9418 3.967987 AGTAGTAGAGATTGCCCGGATTT 59.032 43.478 0.73 0.00 0.00 2.17
4088 9419 5.145564 AGTAGTAGAGATTGCCCGGATTTA 58.854 41.667 0.73 0.00 0.00 1.40
4089 9420 5.780793 AGTAGTAGAGATTGCCCGGATTTAT 59.219 40.000 0.73 0.00 0.00 1.40
4090 9421 6.952358 AGTAGTAGAGATTGCCCGGATTTATA 59.048 38.462 0.73 0.00 0.00 0.98
4091 9422 6.875972 AGTAGAGATTGCCCGGATTTATAT 57.124 37.500 0.73 0.00 0.00 0.86
4092 9423 7.973048 AGTAGAGATTGCCCGGATTTATATA 57.027 36.000 0.73 0.00 0.00 0.86
4093 9424 8.012957 AGTAGAGATTGCCCGGATTTATATAG 57.987 38.462 0.73 0.00 0.00 1.31
4094 9425 7.839705 AGTAGAGATTGCCCGGATTTATATAGA 59.160 37.037 0.73 0.00 0.00 1.98
4095 9426 7.118496 AGAGATTGCCCGGATTTATATAGAG 57.882 40.000 0.73 0.00 0.00 2.43
4096 9427 6.670027 AGAGATTGCCCGGATTTATATAGAGT 59.330 38.462 0.73 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.742649 AGAGGGAGAGCACCGCGA 62.743 66.667 8.23 0.00 32.63 5.87
203 205 6.506500 AAGATGTACTTCAAAATGAGGCAG 57.493 37.500 11.02 0.00 32.91 4.85
244 246 1.683917 CAAGACATCCCTCCTCTACGG 59.316 57.143 0.00 0.00 0.00 4.02
272 274 1.408822 GCTTCTTGAATCCATCCGGGT 60.409 52.381 0.00 0.00 38.11 5.28
274 276 1.312815 GGCTTCTTGAATCCATCCGG 58.687 55.000 0.00 0.00 0.00 5.14
341 343 1.230635 CCAGGGCCATTAGCGAATCG 61.231 60.000 6.18 0.00 45.17 3.34
461 482 1.365699 GGCCAATCGTTTCTAAGCGA 58.634 50.000 0.00 4.15 45.30 4.93
539 563 0.839946 ATCATGGACTCCCTTTCCCG 59.160 55.000 0.00 0.00 31.33 5.14
542 566 5.653769 TGAAATCAATCATGGACTCCCTTTC 59.346 40.000 0.00 0.00 0.00 2.62
550 574 8.682936 AGGTACTAATGAAATCAATCATGGAC 57.317 34.615 0.00 0.00 39.90 4.02
588 616 7.986889 TGCACTTAGATCTGCAATACTAATCAA 59.013 33.333 5.18 0.00 40.45 2.57
695 742 7.709269 TCAACACAACTGACAGAATAACTAC 57.291 36.000 10.08 0.00 0.00 2.73
706 753 2.365582 ACCAGGTTCAACACAACTGAC 58.634 47.619 0.00 0.00 0.00 3.51
1293 1377 4.318332 CCAGCTGATGTTAGTTGTTCAGA 58.682 43.478 17.39 0.00 38.25 3.27
1329 1440 1.729881 GACATGCCGGCCTCAAATC 59.270 57.895 26.77 9.22 0.00 2.17
1582 1693 1.302511 GAACCGGACATGGCACTGT 60.303 57.895 9.46 0.00 0.00 3.55
1623 1734 3.005539 AGCTCAGCATCACCGGGT 61.006 61.111 6.32 0.00 0.00 5.28
1884 1995 7.178983 TGCAATTAGAGGGATCAATTCAAACTT 59.821 33.333 0.00 0.00 0.00 2.66
1892 2003 4.803329 ACCTGCAATTAGAGGGATCAAT 57.197 40.909 6.83 0.00 33.16 2.57
1927 2054 4.916041 TGAAGTTCAGTTGGAGATGGAT 57.084 40.909 0.08 0.00 0.00 3.41
2287 2604 4.379394 GCTACAGAGGCGAGAGATAATGAG 60.379 50.000 0.00 0.00 0.00 2.90
2381 7485 0.389166 GCTCGACACAAGACCCAGAG 60.389 60.000 0.00 0.00 0.00 3.35
2509 7613 5.336213 GCAGGTCATCAAACAAGAATGTCAT 60.336 40.000 0.00 0.00 39.40 3.06
2612 7718 9.295214 CGATCACAGATATTGTTCATCCTATAC 57.705 37.037 0.00 0.00 38.16 1.47
2788 8005 9.774742 GGTCAACTTAGAGCTTTTTGTATAATG 57.225 33.333 0.00 0.00 33.41 1.90
3126 8358 1.222567 TCTCCCTGGCTAATTTCCCC 58.777 55.000 0.00 0.00 0.00 4.81
3263 8495 5.685511 CCTAACATTTTATTTTCCGCATCCG 59.314 40.000 0.00 0.00 0.00 4.18
3268 8500 7.480810 ACTCATCCTAACATTTTATTTTCCGC 58.519 34.615 0.00 0.00 0.00 5.54
3446 8733 2.781757 TCCTCATCCCTCAGAAATGCAT 59.218 45.455 0.00 0.00 0.00 3.96
3480 8767 1.855295 TACGTAGTGGCCCTCAATCA 58.145 50.000 0.00 0.00 45.73 2.57
3663 8957 2.616842 ACACCAAGTTTTGCCGACTTAG 59.383 45.455 0.00 0.00 35.68 2.18
3665 8959 1.470051 ACACCAAGTTTTGCCGACTT 58.530 45.000 0.00 0.00 37.82 3.01
3693 8987 1.752310 CAATACATGGCCGGCACCA 60.752 57.895 30.85 19.02 45.82 4.17
3831 9162 2.224523 TGTGGCAGACTTTAAGGGACAG 60.225 50.000 0.00 0.00 0.00 3.51
3894 9225 4.461992 ACGGAGTACAATTTTGTTCACG 57.538 40.909 0.63 8.06 41.94 4.35
3910 9241 4.981794 GTCACAATTATTTTGGGACGGAG 58.018 43.478 5.09 0.00 42.14 4.63
3915 9246 6.327626 TCAAAAGGGTCACAATTATTTTGGGA 59.672 34.615 7.98 0.00 37.90 4.37
3916 9247 6.529220 TCAAAAGGGTCACAATTATTTTGGG 58.471 36.000 7.98 0.00 37.90 4.12
3917 9248 9.889128 ATATCAAAAGGGTCACAATTATTTTGG 57.111 29.630 7.98 0.00 37.90 3.28
3919 9250 9.801873 CGATATCAAAAGGGTCACAATTATTTT 57.198 29.630 3.12 0.00 0.00 1.82
3920 9251 8.413229 CCGATATCAAAAGGGTCACAATTATTT 58.587 33.333 3.12 0.00 0.00 1.40
3921 9252 7.014230 CCCGATATCAAAAGGGTCACAATTATT 59.986 37.037 3.12 0.00 39.05 1.40
3922 9253 6.490040 CCCGATATCAAAAGGGTCACAATTAT 59.510 38.462 3.12 0.00 39.05 1.28
3923 9254 5.825679 CCCGATATCAAAAGGGTCACAATTA 59.174 40.000 3.12 0.00 39.05 1.40
3924 9255 4.644685 CCCGATATCAAAAGGGTCACAATT 59.355 41.667 3.12 0.00 39.05 2.32
3925 9256 4.207165 CCCGATATCAAAAGGGTCACAAT 58.793 43.478 3.12 0.00 39.05 2.71
3926 9257 3.616219 CCCGATATCAAAAGGGTCACAA 58.384 45.455 3.12 0.00 39.05 3.33
3927 9258 3.275617 CCCGATATCAAAAGGGTCACA 57.724 47.619 3.12 0.00 39.05 3.58
3933 9264 7.878127 AGAACATATGTACCCGATATCAAAAGG 59.122 37.037 9.21 0.30 0.00 3.11
3934 9265 8.833231 AGAACATATGTACCCGATATCAAAAG 57.167 34.615 9.21 0.00 0.00 2.27
3943 9274 9.578576 AGTACTAAATAGAACATATGTACCCGA 57.421 33.333 9.21 0.00 32.15 5.14
3957 9288 9.364653 GGGATGGAGAAAGTAGTACTAAATAGA 57.635 37.037 3.61 0.00 0.00 1.98
3958 9289 9.144298 TGGGATGGAGAAAGTAGTACTAAATAG 57.856 37.037 3.61 0.00 0.00 1.73
3959 9290 9.670442 ATGGGATGGAGAAAGTAGTACTAAATA 57.330 33.333 3.61 0.00 0.00 1.40
3960 9291 7.989947 TGGGATGGAGAAAGTAGTACTAAAT 57.010 36.000 3.61 0.00 0.00 1.40
3961 9292 7.989947 ATGGGATGGAGAAAGTAGTACTAAA 57.010 36.000 3.61 0.00 0.00 1.85
3962 9293 9.670442 AATATGGGATGGAGAAAGTAGTACTAA 57.330 33.333 3.61 0.00 0.00 2.24
3964 9295 9.845214 ATAATATGGGATGGAGAAAGTAGTACT 57.155 33.333 0.00 0.00 0.00 2.73
3970 9301 9.398921 ACTCTAATAATATGGGATGGAGAAAGT 57.601 33.333 0.00 0.00 0.00 2.66
3971 9302 9.664332 CACTCTAATAATATGGGATGGAGAAAG 57.336 37.037 0.00 0.00 0.00 2.62
3972 9303 9.170890 ACACTCTAATAATATGGGATGGAGAAA 57.829 33.333 0.00 0.00 0.00 2.52
3973 9304 8.742125 ACACTCTAATAATATGGGATGGAGAA 57.258 34.615 0.00 0.00 0.00 2.87
3974 9305 8.742125 AACACTCTAATAATATGGGATGGAGA 57.258 34.615 0.00 0.00 0.00 3.71
3975 9306 9.799106 AAAACACTCTAATAATATGGGATGGAG 57.201 33.333 0.00 0.00 0.00 3.86
4024 9355 7.800015 AAAACAACTAAAACACCGTAAAGTG 57.200 32.000 0.00 0.00 43.65 3.16
4025 9356 7.866898 ACAAAAACAACTAAAACACCGTAAAGT 59.133 29.630 0.00 0.00 0.00 2.66
4026 9357 8.230112 ACAAAAACAACTAAAACACCGTAAAG 57.770 30.769 0.00 0.00 0.00 1.85
4027 9358 8.585189 AACAAAAACAACTAAAACACCGTAAA 57.415 26.923 0.00 0.00 0.00 2.01
4028 9359 9.339492 CTAACAAAAACAACTAAAACACCGTAA 57.661 29.630 0.00 0.00 0.00 3.18
4029 9360 8.725148 TCTAACAAAAACAACTAAAACACCGTA 58.275 29.630 0.00 0.00 0.00 4.02
4030 9361 7.592051 TCTAACAAAAACAACTAAAACACCGT 58.408 30.769 0.00 0.00 0.00 4.83
4031 9362 7.964011 TCTCTAACAAAAACAACTAAAACACCG 59.036 33.333 0.00 0.00 0.00 4.94
4032 9363 9.797556 ATCTCTAACAAAAACAACTAAAACACC 57.202 29.630 0.00 0.00 0.00 4.16
4056 9387 9.953697 CGGGCAATCTCTACTACTAAATATATC 57.046 37.037 0.00 0.00 0.00 1.63
4057 9388 8.915036 CCGGGCAATCTCTACTACTAAATATAT 58.085 37.037 0.00 0.00 0.00 0.86
4058 9389 8.111545 TCCGGGCAATCTCTACTACTAAATATA 58.888 37.037 0.00 0.00 0.00 0.86
4059 9390 6.952358 TCCGGGCAATCTCTACTACTAAATAT 59.048 38.462 0.00 0.00 0.00 1.28
4060 9391 6.309357 TCCGGGCAATCTCTACTACTAAATA 58.691 40.000 0.00 0.00 0.00 1.40
4061 9392 5.145564 TCCGGGCAATCTCTACTACTAAAT 58.854 41.667 0.00 0.00 0.00 1.40
4062 9393 4.539726 TCCGGGCAATCTCTACTACTAAA 58.460 43.478 0.00 0.00 0.00 1.85
4063 9394 4.174704 TCCGGGCAATCTCTACTACTAA 57.825 45.455 0.00 0.00 0.00 2.24
4064 9395 3.870538 TCCGGGCAATCTCTACTACTA 57.129 47.619 0.00 0.00 0.00 1.82
4065 9396 2.750141 TCCGGGCAATCTCTACTACT 57.250 50.000 0.00 0.00 0.00 2.57
4066 9397 4.338379 AAATCCGGGCAATCTCTACTAC 57.662 45.455 0.00 0.00 0.00 2.73
4067 9398 7.973048 ATATAAATCCGGGCAATCTCTACTA 57.027 36.000 0.00 0.00 0.00 1.82
4068 9399 6.875972 ATATAAATCCGGGCAATCTCTACT 57.124 37.500 0.00 0.00 0.00 2.57
4069 9400 8.008513 TCTATATAAATCCGGGCAATCTCTAC 57.991 38.462 0.00 0.00 0.00 2.59
4070 9401 7.839705 ACTCTATATAAATCCGGGCAATCTCTA 59.160 37.037 0.00 0.00 0.00 2.43
4071 9402 6.670027 ACTCTATATAAATCCGGGCAATCTCT 59.330 38.462 0.00 0.00 0.00 3.10
4072 9403 6.879400 ACTCTATATAAATCCGGGCAATCTC 58.121 40.000 0.00 0.00 0.00 2.75
4073 9404 6.875972 ACTCTATATAAATCCGGGCAATCT 57.124 37.500 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.