Multiple sequence alignment - TraesCS6A01G245900

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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 TraesCS6A01G245900 chr6A 100.000 2860 0 0 1 2860 457096862 457094003 0.000000e+00 5282.0
1 TraesCS6A01G245900 chr6A 76.862 376 60 22 205 567 77604154 77604515 1.350000e-43 187.0
2 TraesCS6A01G245900 chr6B 90.981 1131 68 20 847 1973 503933601 503934701 0.000000e+00 1493.0
3 TraesCS6A01G245900 chr6B 91.624 394 28 4 2461 2852 666090484 666090094 9.010000e-150 540.0
4 TraesCS6A01G245900 chr6B 83.794 543 54 19 1 534 503931033 503931550 4.280000e-133 484.0
5 TraesCS6A01G245900 chr6B 90.099 303 22 6 2195 2496 666090782 666090487 1.240000e-103 387.0
6 TraesCS6A01G245900 chr6B 90.476 147 11 3 525 668 503931833 503931979 1.050000e-44 191.0
7 TraesCS6A01G245900 chr6B 77.104 297 45 22 120 408 720043644 720043363 1.780000e-32 150.0
8 TraesCS6A01G245900 chr6B 91.358 81 5 1 682 762 503932280 503932358 3.010000e-20 110.0
9 TraesCS6A01G245900 chr6D 95.688 603 20 5 1489 2087 319290547 319289947 0.000000e+00 965.0
10 TraesCS6A01G245900 chr6D 90.587 733 46 7 2088 2819 319289531 319288821 0.000000e+00 950.0
11 TraesCS6A01G245900 chr6D 91.806 659 33 7 855 1497 319291341 319290688 0.000000e+00 898.0
12 TraesCS6A01G245900 chr6D 86.137 541 39 19 5 534 319293884 319293369 4.160000e-153 551.0
13 TraesCS6A01G245900 chr6D 90.295 237 19 3 525 760 319293087 319292854 9.950000e-80 307.0
14 TraesCS6A01G245900 chr6D 79.528 254 41 9 77 324 53543275 53543523 1.360000e-38 171.0
15 TraesCS6A01G245900 chr2B 88.102 706 59 14 2164 2852 197992321 197993018 0.000000e+00 815.0
16 TraesCS6A01G245900 chr2D 93.228 443 27 3 2419 2860 9184565 9185005 0.000000e+00 649.0
17 TraesCS6A01G245900 chr2D 93.228 443 27 3 2419 2860 74518351 74518791 0.000000e+00 649.0
18 TraesCS6A01G245900 chr2D 92.777 443 28 4 2419 2860 31398318 31397879 3.110000e-179 638.0
19 TraesCS6A01G245900 chr2D 75.057 441 70 27 69 491 476798983 476799401 4.900000e-38 169.0
20 TraesCS6A01G245900 chr4A 92.551 443 29 4 2419 2860 154317690 154318129 1.450000e-177 632.0
21 TraesCS6A01G245900 chr4A 87.786 262 28 2 2164 2425 666808432 666808689 1.290000e-78 303.0
22 TraesCS6A01G245900 chr3A 92.239 451 25 4 2419 2860 680732779 680733228 5.200000e-177 630.0
23 TraesCS6A01G245900 chr3B 91.648 443 30 3 2419 2860 719422656 719423092 8.760000e-170 606.0
24 TraesCS6A01G245900 chr3B 87.500 264 26 5 2163 2425 164468925 164469182 5.990000e-77 298.0
25 TraesCS6A01G245900 chr3B 87.405 262 29 2 2164 2425 610313805 610313548 5.990000e-77 298.0
26 TraesCS6A01G245900 chr3D 91.076 437 32 6 2419 2853 543767903 543768334 4.110000e-163 584.0
27 TraesCS6A01G245900 chr3D 87.833 263 27 3 2163 2425 118514165 118513908 1.290000e-78 303.0
28 TraesCS6A01G245900 chr3D 86.087 230 24 6 2197 2425 118273128 118272906 1.020000e-59 241.0
29 TraesCS6A01G245900 chr1D 87.452 263 27 4 2164 2425 202275947 202276204 5.990000e-77 298.0
30 TraesCS6A01G245900 chr7B 87.442 215 23 2 2164 2378 700382766 700382976 7.920000e-61 244.0
31 TraesCS6A01G245900 chr5D 75.467 428 78 24 68 483 393910406 393910818 1.750000e-42 183.0
32 TraesCS6A01G245900 chr5A 80.269 223 40 4 255 477 461716601 461716819 6.340000e-37 165.0
33 TraesCS6A01G245900 chr5A 76.639 244 41 14 95 328 597242586 597242349 1.390000e-23 121.0
34 TraesCS6A01G245900 chr2A 75.831 331 64 14 82 408 60988809 60989127 1.370000e-33 154.0
35 TraesCS6A01G245900 chr7D 83.465 127 15 5 331 456 568766521 568766642 2.330000e-21 113.0
36 TraesCS6A01G245900 chr5B 86.957 69 8 1 503 570 513961717 513961649 3.060000e-10 76.8


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 TraesCS6A01G245900 chr6A 457094003 457096862 2859 True 5282.0 5282 100.00000 1 2860 1 chr6A.!!$R1 2859
1 TraesCS6A01G245900 chr6B 503931033 503934701 3668 False 569.5 1493 89.15225 1 1973 4 chr6B.!!$F1 1972
2 TraesCS6A01G245900 chr6B 666090094 666090782 688 True 463.5 540 90.86150 2195 2852 2 chr6B.!!$R2 657
3 TraesCS6A01G245900 chr6D 319288821 319293884 5063 True 734.2 965 90.90260 5 2819 5 chr6D.!!$R1 2814
4 TraesCS6A01G245900 chr2B 197992321 197993018 697 False 815.0 815 88.10200 2164 2852 1 chr2B.!!$F1 688

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
713 1310 0.250793 ACGAGTTGGGTTGTGTGTGA 59.749 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 4840 0.391793 CGGGTGAGAAAAGAGGAGCC 60.392 60.0 0.0 0.0 0.0 4.7 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
38 39 3.525609 TCTGTAATACCAATGCCCCTGAA 59.474 43.478 0.00 0.00 0.00 3.02
53 54 6.129179 TGCCCCTGAATAATTCTTTCTTAGG 58.871 40.000 0.00 0.00 0.00 2.69
226 233 9.199982 GATTCCAATGCCACTAATTCATTATTG 57.800 33.333 0.00 0.00 0.00 1.90
267 274 9.109393 TCTTGTCAAACTTCCACTATTATATGC 57.891 33.333 0.00 0.00 0.00 3.14
268 275 8.800370 TTGTCAAACTTCCACTATTATATGCA 57.200 30.769 0.00 0.00 0.00 3.96
270 277 8.839343 TGTCAAACTTCCACTATTATATGCATG 58.161 33.333 10.16 0.00 0.00 4.06
302 310 5.844301 ATTGTAAAAAGGCGCAATTTCTG 57.156 34.783 10.83 0.00 0.00 3.02
311 319 5.637006 AGGCGCAATTTCTGTGTAAATTA 57.363 34.783 10.83 0.00 37.03 1.40
338 346 7.917505 TGTGCAAATTTTGTCAACTTTTGTTTT 59.082 25.926 10.65 0.00 41.35 2.43
339 347 9.387123 GTGCAAATTTTGTCAACTTTTGTTTTA 57.613 25.926 10.65 4.14 41.35 1.52
385 397 6.678547 TCTTAAAGGGTAATACCAATGCCAT 58.321 36.000 12.03 0.00 41.02 4.40
396 408 9.423061 GTAATACCAATGCCATTAATTCATTCC 57.577 33.333 8.85 0.00 0.00 3.01
398 410 6.564557 ACCAATGCCATTAATTCATTCCTT 57.435 33.333 8.85 0.00 0.00 3.36
478 491 6.772716 TCTCTAAGGATAATTTCAATGCCACC 59.227 38.462 0.00 0.00 0.00 4.61
484 497 7.729116 AGGATAATTTCAATGCCACCAATTAG 58.271 34.615 0.00 0.00 0.00 1.73
487 500 8.947055 ATAATTTCAATGCCACCAATTAGTTC 57.053 30.769 0.00 0.00 0.00 3.01
491 504 4.220382 TCAATGCCACCAATTAGTTCCTTG 59.780 41.667 0.00 0.00 0.00 3.61
498 513 5.955355 CCACCAATTAGTTCCTTGGGAATTA 59.045 40.000 2.20 0.30 44.04 1.40
612 921 2.223852 GGAGAGAGACAAAGGCCGATAC 60.224 54.545 0.00 0.00 0.00 2.24
616 925 2.832129 AGAGACAAAGGCCGATACTGAA 59.168 45.455 0.00 0.00 0.00 3.02
626 935 3.181465 GGCCGATACTGAAAGAGAATGGA 60.181 47.826 0.00 0.00 37.43 3.41
627 936 3.804873 GCCGATACTGAAAGAGAATGGAC 59.195 47.826 0.00 0.00 37.43 4.02
632 941 6.294010 CGATACTGAAAGAGAATGGACCGATA 60.294 42.308 0.00 0.00 37.43 2.92
647 956 4.223923 GGACCGATAGAGGGATCATGATTT 59.776 45.833 10.14 0.00 39.76 2.17
669 979 1.475213 GGGCTGTTACTATGGACTGGC 60.475 57.143 0.00 0.00 38.81 4.85
680 990 2.261671 GACTGGCACCACGTCGAT 59.738 61.111 0.00 0.00 0.00 3.59
711 1308 0.463116 GGACGAGTTGGGTTGTGTGT 60.463 55.000 0.00 0.00 0.00 3.72
712 1309 0.655733 GACGAGTTGGGTTGTGTGTG 59.344 55.000 0.00 0.00 0.00 3.82
713 1310 0.250793 ACGAGTTGGGTTGTGTGTGA 59.749 50.000 0.00 0.00 0.00 3.58
714 1311 1.134220 ACGAGTTGGGTTGTGTGTGAT 60.134 47.619 0.00 0.00 0.00 3.06
715 1312 1.264020 CGAGTTGGGTTGTGTGTGATG 59.736 52.381 0.00 0.00 0.00 3.07
716 1313 1.608590 GAGTTGGGTTGTGTGTGATGG 59.391 52.381 0.00 0.00 0.00 3.51
718 1315 2.028130 GTTGGGTTGTGTGTGATGGAA 58.972 47.619 0.00 0.00 0.00 3.53
719 1316 2.428890 GTTGGGTTGTGTGTGATGGAAA 59.571 45.455 0.00 0.00 0.00 3.13
720 1317 2.028130 TGGGTTGTGTGTGATGGAAAC 58.972 47.619 0.00 0.00 0.00 2.78
752 1349 4.928661 AAAATTTCGGTCAGTCGATCAG 57.071 40.909 0.00 0.00 39.03 2.90
762 1359 4.272018 GGTCAGTCGATCAGAATTGAATGG 59.728 45.833 0.00 0.00 40.33 3.16
763 1360 4.272018 GTCAGTCGATCAGAATTGAATGGG 59.728 45.833 0.00 0.00 40.33 4.00
768 1365 5.178996 GTCGATCAGAATTGAATGGGAGATG 59.821 44.000 0.00 0.00 36.78 2.90
769 1366 4.083431 CGATCAGAATTGAATGGGAGATGC 60.083 45.833 0.00 0.00 36.78 3.91
771 1368 4.995881 ATCAGAATTGAATGGGAGATGCCC 60.996 45.833 0.00 0.00 46.78 5.36
812 1409 9.623000 ATGAATGACAGATGAAAATATGACTGA 57.377 29.630 0.00 0.00 0.00 3.41
813 1410 8.886719 TGAATGACAGATGAAAATATGACTGAC 58.113 33.333 0.00 0.00 0.00 3.51
814 1411 7.798596 ATGACAGATGAAAATATGACTGACC 57.201 36.000 0.00 0.00 0.00 4.02
815 1412 6.115446 TGACAGATGAAAATATGACTGACCC 58.885 40.000 0.00 0.00 0.00 4.46
816 1413 6.065976 ACAGATGAAAATATGACTGACCCA 57.934 37.500 0.00 0.00 0.00 4.51
817 1414 6.484288 ACAGATGAAAATATGACTGACCCAA 58.516 36.000 0.00 0.00 0.00 4.12
818 1415 6.947733 ACAGATGAAAATATGACTGACCCAAA 59.052 34.615 0.00 0.00 0.00 3.28
819 1416 7.451255 ACAGATGAAAATATGACTGACCCAAAA 59.549 33.333 0.00 0.00 0.00 2.44
820 1417 8.472413 CAGATGAAAATATGACTGACCCAAAAT 58.528 33.333 0.00 0.00 0.00 1.82
821 1418 9.699410 AGATGAAAATATGACTGACCCAAAATA 57.301 29.630 0.00 0.00 0.00 1.40
838 1435 7.714813 ACCCAAAATAAATTTTCAGTCACCTTG 59.285 33.333 0.00 0.00 37.86 3.61
839 1436 7.714813 CCCAAAATAAATTTTCAGTCACCTTGT 59.285 33.333 0.00 0.00 37.86 3.16
840 1437 9.108284 CCAAAATAAATTTTCAGTCACCTTGTT 57.892 29.630 0.00 0.00 37.86 2.83
844 1441 9.965824 AATAAATTTTCAGTCACCTTGTTACTG 57.034 29.630 0.00 2.85 38.62 2.74
845 1442 7.404671 AAATTTTCAGTCACCTTGTTACTGT 57.595 32.000 8.05 0.00 38.46 3.55
850 2960 5.839621 TCAGTCACCTTGTTACTGTTAGTC 58.160 41.667 8.05 0.00 38.46 2.59
853 2963 5.243283 AGTCACCTTGTTACTGTTAGTCGAT 59.757 40.000 0.00 0.00 0.00 3.59
864 2974 8.601476 GTTACTGTTAGTCGATCCCTTAAATTG 58.399 37.037 0.00 0.00 0.00 2.32
866 2976 6.070424 ACTGTTAGTCGATCCCTTAAATTGGA 60.070 38.462 0.00 0.00 34.54 3.53
884 2994 8.965986 AAATTGGAGCGTTTCTTCTAATTAAC 57.034 30.769 0.00 0.00 0.00 2.01
895 3005 5.412640 TCTTCTAATTAACGCGTCCAATGA 58.587 37.500 14.44 7.81 0.00 2.57
989 3107 2.250939 CGCGTTTGTGCCCTCTTGA 61.251 57.895 0.00 0.00 0.00 3.02
998 3116 1.065410 TGCCCTCTTGACCCCTTTCA 61.065 55.000 0.00 0.00 0.00 2.69
1110 3228 2.117156 ATCCCGCATCACAAGCTGC 61.117 57.895 0.00 0.00 33.67 5.25
1111 3229 3.818787 CCCGCATCACAAGCTGCC 61.819 66.667 0.00 0.00 33.44 4.85
1112 3230 2.749044 CCGCATCACAAGCTGCCT 60.749 61.111 0.00 0.00 33.44 4.75
1113 3231 2.483745 CGCATCACAAGCTGCCTG 59.516 61.111 0.00 0.00 33.44 4.85
1114 3232 2.181021 GCATCACAAGCTGCCTGC 59.819 61.111 0.00 0.00 43.29 4.85
1115 3233 2.632544 GCATCACAAGCTGCCTGCA 61.633 57.895 0.00 0.00 45.94 4.41
1116 3234 1.961378 CATCACAAGCTGCCTGCAA 59.039 52.632 0.00 0.00 45.94 4.08
1117 3235 0.388134 CATCACAAGCTGCCTGCAAC 60.388 55.000 0.00 0.00 45.94 4.17
1118 3236 1.530013 ATCACAAGCTGCCTGCAACC 61.530 55.000 0.00 0.00 45.94 3.77
1129 3247 0.464373 CCTGCAACCTCGTGGCATAT 60.464 55.000 2.76 0.00 41.99 1.78
1131 3249 0.541392 TGCAACCTCGTGGCATATCT 59.459 50.000 2.76 0.00 37.59 1.98
1137 3258 2.750166 ACCTCGTGGCATATCTAGATCG 59.250 50.000 8.95 5.71 36.63 3.69
1211 3332 3.616721 AGTGCGGCGACCAGTTCT 61.617 61.111 12.98 0.00 0.00 3.01
1261 3382 6.335777 ACATTCTTCTCCAATGCAAATTAGC 58.664 36.000 0.00 0.00 35.02 3.09
1298 3427 2.755650 AGAAACGCTCGTGTCTGAATT 58.244 42.857 13.70 0.00 40.86 2.17
1300 3429 3.184581 AGAAACGCTCGTGTCTGAATTTC 59.815 43.478 13.70 3.26 40.86 2.17
1302 3431 3.570926 ACGCTCGTGTCTGAATTTCTA 57.429 42.857 0.00 0.00 0.00 2.10
1311 3440 5.692204 CGTGTCTGAATTTCTAACAGTGTCT 59.308 40.000 0.00 0.00 33.93 3.41
1338 3468 4.307834 CTGTAAGGACGTTCGTGATTTG 57.692 45.455 1.74 0.00 0.00 2.32
1340 3470 3.737266 TGTAAGGACGTTCGTGATTTGAC 59.263 43.478 1.74 0.00 0.00 3.18
1483 3613 0.389948 ACACTCTGGTCGGCGAAATC 60.390 55.000 12.92 5.09 0.00 2.17
1524 3803 4.489771 CTCCATCCACCGTGCCCC 62.490 72.222 0.00 0.00 0.00 5.80
1790 4069 1.734465 CCCTTTCTGAACATCACGCTC 59.266 52.381 0.00 0.00 0.00 5.03
1862 4141 2.365582 TGGACGACGAGAGAATGATCA 58.634 47.619 0.00 0.00 0.00 2.92
1863 4142 2.097629 TGGACGACGAGAGAATGATCAC 59.902 50.000 0.00 0.00 0.00 3.06
1879 4158 1.952133 CACTGAAAACGCCCGTCGA 60.952 57.895 0.00 0.00 41.67 4.20
1961 4240 3.807622 TCTGTCAAAATGTGTCGAACTCC 59.192 43.478 0.00 0.00 0.00 3.85
2012 4291 1.003851 CCGGTGCATACGTAGTTTGG 58.996 55.000 11.89 0.00 37.78 3.28
2023 4302 7.014905 TGCATACGTAGTTTGGAGGATATAAGT 59.985 37.037 0.08 0.00 37.78 2.24
2138 4836 5.093849 TCTCCCCACTTTTATAAACGAGG 57.906 43.478 8.56 9.42 0.00 4.63
2142 4840 4.093850 CCCCACTTTTATAAACGAGGTTCG 59.906 45.833 14.27 0.00 46.93 3.95
2147 4845 2.877043 TATAAACGAGGTTCGGCTCC 57.123 50.000 3.37 0.00 45.59 4.70
2157 4855 1.002087 GGTTCGGCTCCTCTTTTCTCA 59.998 52.381 0.00 0.00 0.00 3.27
2160 4858 0.391793 CGGCTCCTCTTTTCTCACCC 60.392 60.000 0.00 0.00 0.00 4.61
2187 4885 3.379688 GCCTCATTTGACAGAAAGGGATC 59.620 47.826 0.00 0.00 0.00 3.36
2188 4886 4.592942 CCTCATTTGACAGAAAGGGATCA 58.407 43.478 0.00 0.00 0.00 2.92
2193 4891 4.656100 TTGACAGAAAGGGATCATGGAA 57.344 40.909 0.00 0.00 0.00 3.53
2216 4914 4.106341 AGTTTTGAGAGGAGGGGATTTCAA 59.894 41.667 0.00 0.00 0.00 2.69
2217 4915 3.721087 TTGAGAGGAGGGGATTTCAAC 57.279 47.619 0.00 0.00 0.00 3.18
2240 4938 3.713003 GATTTGGTGAATCCCCCTCTTT 58.287 45.455 0.00 0.00 38.57 2.52
2255 4953 2.580783 CCTCTTTCACCCAATCCCCTTA 59.419 50.000 0.00 0.00 0.00 2.69
2263 4961 2.043939 ACCCAATCCCCTTAAAACCTCC 59.956 50.000 0.00 0.00 0.00 4.30
2264 4962 2.043801 CCCAATCCCCTTAAAACCTCCA 59.956 50.000 0.00 0.00 0.00 3.86
2265 4963 3.365472 CCAATCCCCTTAAAACCTCCAG 58.635 50.000 0.00 0.00 0.00 3.86
2266 4964 2.760650 CAATCCCCTTAAAACCTCCAGC 59.239 50.000 0.00 0.00 0.00 4.85
2267 4965 0.702316 TCCCCTTAAAACCTCCAGCC 59.298 55.000 0.00 0.00 0.00 4.85
2274 4972 0.786435 AAAACCTCCAGCCAATCCCT 59.214 50.000 0.00 0.00 0.00 4.20
2294 4992 2.262774 CTCCAGCCACACATCCCCTC 62.263 65.000 0.00 0.00 0.00 4.30
2296 4994 2.204136 AGCCACACATCCCCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
2298 4996 1.454479 GCCACACATCCCCTCCATG 60.454 63.158 0.00 0.00 0.00 3.66
2322 5020 4.520111 CAGAACATTGTTTGACAGGGATGA 59.480 41.667 3.08 0.00 0.00 2.92
2389 5087 8.579006 TCTAATCTTGCAACAATTCTTCACATT 58.421 29.630 0.00 0.00 0.00 2.71
2413 5111 9.979578 ATTAACAACATAATTTGCTTGACTTGA 57.020 25.926 0.00 0.00 0.00 3.02
2480 5179 6.357367 AGGAACCAACAATATCAGTATCCAC 58.643 40.000 0.00 0.00 0.00 4.02
2524 5260 0.108992 TTTGACCTACTACGCAGGCG 60.109 55.000 12.71 12.71 46.03 5.52
2539 5275 1.826487 GGCGGGACAAACCACACTT 60.826 57.895 0.00 0.00 41.20 3.16
2676 5413 0.329596 AGTTCATCCAGGGACCTTGC 59.670 55.000 0.00 0.00 0.00 4.01
2712 5449 2.957402 AAGCTCATCCAGAAACACCA 57.043 45.000 0.00 0.00 0.00 4.17
2728 5465 7.425606 AGAAACACCATAATTTCTGTCAACAC 58.574 34.615 0.00 0.00 42.27 3.32
2736 5473 5.576447 AATTTCTGTCAACACGAAAACCT 57.424 34.783 0.00 0.68 31.76 3.50
2782 5519 3.577919 AGGTACTGGTTCTCACAAGAGT 58.422 45.455 0.00 0.00 39.50 3.24
2852 5589 0.383590 AGTCTCATCGATGGACGCAG 59.616 55.000 26.93 17.98 42.26 5.18
2853 5590 1.066422 TCTCATCGATGGACGCAGC 59.934 57.895 24.61 0.00 42.26 5.25
2854 5591 1.227060 CTCATCGATGGACGCAGCA 60.227 57.895 24.61 2.33 42.26 4.41
2855 5592 0.807275 CTCATCGATGGACGCAGCAA 60.807 55.000 24.61 1.59 42.26 3.91
2856 5593 0.390998 TCATCGATGGACGCAGCAAA 60.391 50.000 24.61 0.00 42.26 3.68
2857 5594 0.247814 CATCGATGGACGCAGCAAAC 60.248 55.000 17.96 0.00 42.26 2.93
2858 5595 0.391661 ATCGATGGACGCAGCAAACT 60.392 50.000 0.00 0.00 42.26 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.286775 GGGGCATTGGTATTACAGAAGAAATAA 59.713 37.037 0.00 0.00 0.00 1.40
9 10 6.775629 GGGGCATTGGTATTACAGAAGAAATA 59.224 38.462 0.00 0.00 0.00 1.40
17 18 3.576078 TCAGGGGCATTGGTATTACAG 57.424 47.619 0.00 0.00 0.00 2.74
193 200 9.768662 GAATTAGTGGCATTGGAATCATTAAAT 57.231 29.630 0.00 0.00 0.00 1.40
201 208 8.707449 ACAATAATGAATTAGTGGCATTGGAAT 58.293 29.630 13.31 0.00 41.22 3.01
203 210 7.658525 ACAATAATGAATTAGTGGCATTGGA 57.341 32.000 13.31 0.00 41.22 3.53
249 256 9.632638 AAGAACATGCATATAATAGTGGAAGTT 57.367 29.630 0.00 0.00 31.85 2.66
267 274 7.463119 CGCCTTTTTACAATATGCAAGAACATG 60.463 37.037 0.00 0.00 0.00 3.21
268 275 6.531240 CGCCTTTTTACAATATGCAAGAACAT 59.469 34.615 0.00 0.00 0.00 2.71
270 277 5.220209 GCGCCTTTTTACAATATGCAAGAAC 60.220 40.000 0.00 0.00 0.00 3.01
311 319 7.143514 ACAAAAGTTGACAAAATTTGCACAT 57.856 28.000 19.31 0.00 34.05 3.21
352 360 9.643735 TGGTATTACCCTTTAAGAAGAAAACAA 57.356 29.630 10.37 0.00 37.50 2.83
353 361 9.643735 TTGGTATTACCCTTTAAGAAGAAAACA 57.356 29.630 10.37 0.00 37.50 2.83
356 364 8.745590 GCATTGGTATTACCCTTTAAGAAGAAA 58.254 33.333 10.37 0.00 37.50 2.52
357 365 7.340999 GGCATTGGTATTACCCTTTAAGAAGAA 59.659 37.037 10.37 0.00 37.50 2.52
358 366 6.831868 GGCATTGGTATTACCCTTTAAGAAGA 59.168 38.462 10.37 0.00 37.50 2.87
359 367 6.605594 TGGCATTGGTATTACCCTTTAAGAAG 59.394 38.462 10.37 0.00 37.50 2.85
362 370 6.976934 ATGGCATTGGTATTACCCTTTAAG 57.023 37.500 10.37 0.00 37.50 1.85
368 380 7.296628 TGAATTAATGGCATTGGTATTACCC 57.703 36.000 22.57 8.28 37.50 3.69
376 388 6.823497 AGAAGGAATGAATTAATGGCATTGG 58.177 36.000 22.57 0.00 32.80 3.16
377 389 9.472361 CTAAGAAGGAATGAATTAATGGCATTG 57.528 33.333 22.57 0.00 32.80 2.82
478 491 8.882736 GCAAAATAATTCCCAAGGAACTAATTG 58.117 33.333 0.00 4.31 45.07 2.32
484 497 7.503521 TTTTGCAAAATAATTCCCAAGGAAC 57.496 32.000 20.46 0.00 45.07 3.62
558 867 4.439305 AGCACGCATGACAATTTACATT 57.561 36.364 0.00 0.00 0.00 2.71
612 921 5.508825 CCTCTATCGGTCCATTCTCTTTCAG 60.509 48.000 0.00 0.00 0.00 3.02
616 925 3.117093 TCCCTCTATCGGTCCATTCTCTT 60.117 47.826 0.00 0.00 0.00 2.85
626 935 5.513788 CCAAAATCATGATCCCTCTATCGGT 60.514 44.000 9.06 0.00 0.00 4.69
627 936 4.940046 CCAAAATCATGATCCCTCTATCGG 59.060 45.833 9.06 0.00 0.00 4.18
632 941 2.517127 AGCCCAAAATCATGATCCCTCT 59.483 45.455 9.06 0.00 0.00 3.69
647 956 2.238646 CCAGTCCATAGTAACAGCCCAA 59.761 50.000 0.00 0.00 0.00 4.12
669 979 3.804518 TTTGATTCAATCGACGTGGTG 57.195 42.857 0.00 0.00 0.00 4.17
680 990 4.022416 CCCAACTCGTCCATTTTGATTCAA 60.022 41.667 0.00 0.00 0.00 2.69
711 1308 8.463930 AATTTTAAGTCAGTCTGTTTCCATCA 57.536 30.769 0.00 0.00 0.00 3.07
712 1309 9.399403 GAAATTTTAAGTCAGTCTGTTTCCATC 57.601 33.333 0.00 0.00 0.00 3.51
713 1310 8.076178 CGAAATTTTAAGTCAGTCTGTTTCCAT 58.924 33.333 0.00 0.00 0.00 3.41
714 1311 7.414436 CGAAATTTTAAGTCAGTCTGTTTCCA 58.586 34.615 0.00 0.00 0.00 3.53
715 1312 6.856426 CCGAAATTTTAAGTCAGTCTGTTTCC 59.144 38.462 0.00 0.00 0.00 3.13
716 1313 7.415229 ACCGAAATTTTAAGTCAGTCTGTTTC 58.585 34.615 0.00 0.00 0.00 2.78
718 1315 6.540914 TGACCGAAATTTTAAGTCAGTCTGTT 59.459 34.615 12.29 0.00 32.75 3.16
719 1316 6.053005 TGACCGAAATTTTAAGTCAGTCTGT 58.947 36.000 12.29 0.00 32.75 3.41
720 1317 6.539649 TGACCGAAATTTTAAGTCAGTCTG 57.460 37.500 12.29 0.00 32.75 3.51
721 1318 6.787085 CTGACCGAAATTTTAAGTCAGTCT 57.213 37.500 24.14 0.00 45.95 3.24
730 1327 5.716094 TCTGATCGACTGACCGAAATTTTA 58.284 37.500 0.00 0.00 42.22 1.52
786 1383 9.623000 TCAGTCATATTTTCATCTGTCATTCAT 57.377 29.630 0.00 0.00 0.00 2.57
787 1384 8.886719 GTCAGTCATATTTTCATCTGTCATTCA 58.113 33.333 0.00 0.00 0.00 2.57
788 1385 8.341173 GGTCAGTCATATTTTCATCTGTCATTC 58.659 37.037 0.00 0.00 0.00 2.67
789 1386 7.284034 GGGTCAGTCATATTTTCATCTGTCATT 59.716 37.037 0.00 0.00 0.00 2.57
790 1387 6.769822 GGGTCAGTCATATTTTCATCTGTCAT 59.230 38.462 0.00 0.00 0.00 3.06
791 1388 6.115446 GGGTCAGTCATATTTTCATCTGTCA 58.885 40.000 0.00 0.00 0.00 3.58
792 1389 6.115446 TGGGTCAGTCATATTTTCATCTGTC 58.885 40.000 0.00 0.00 0.00 3.51
793 1390 6.065976 TGGGTCAGTCATATTTTCATCTGT 57.934 37.500 0.00 0.00 0.00 3.41
794 1391 7.395190 TTTGGGTCAGTCATATTTTCATCTG 57.605 36.000 0.00 0.00 0.00 2.90
795 1392 8.599624 ATTTTGGGTCAGTCATATTTTCATCT 57.400 30.769 0.00 0.00 0.00 2.90
805 1402 8.650490 ACTGAAAATTTATTTTGGGTCAGTCAT 58.350 29.630 10.62 0.00 38.64 3.06
806 1403 8.017418 ACTGAAAATTTATTTTGGGTCAGTCA 57.983 30.769 10.62 0.00 38.64 3.41
807 1404 8.520835 GACTGAAAATTTATTTTGGGTCAGTC 57.479 34.615 20.88 20.88 44.62 3.51
808 1405 7.926018 GTGACTGAAAATTTATTTTGGGTCAGT 59.074 33.333 20.43 14.60 42.33 3.41
809 1406 7.384932 GGTGACTGAAAATTTATTTTGGGTCAG 59.615 37.037 20.43 16.04 42.02 3.51
810 1407 7.070571 AGGTGACTGAAAATTTATTTTGGGTCA 59.929 33.333 18.25 18.25 40.82 4.02
811 1408 7.441836 AGGTGACTGAAAATTTATTTTGGGTC 58.558 34.615 5.24 11.73 39.86 4.46
812 1409 7.373617 AGGTGACTGAAAATTTATTTTGGGT 57.626 32.000 5.24 4.27 39.86 4.51
813 1410 7.714813 ACAAGGTGACTGAAAATTTATTTTGGG 59.285 33.333 5.24 1.56 42.68 4.12
814 1411 8.661352 ACAAGGTGACTGAAAATTTATTTTGG 57.339 30.769 5.24 1.85 42.68 3.28
818 1415 9.965824 CAGTAACAAGGTGACTGAAAATTTATT 57.034 29.630 7.94 0.00 45.33 1.40
819 1416 9.131791 ACAGTAACAAGGTGACTGAAAATTTAT 57.868 29.630 18.41 0.00 45.33 1.40
820 1417 8.514330 ACAGTAACAAGGTGACTGAAAATTTA 57.486 30.769 18.41 0.00 45.33 1.40
821 1418 7.404671 ACAGTAACAAGGTGACTGAAAATTT 57.595 32.000 18.41 0.00 45.33 1.82
822 1419 7.404671 AACAGTAACAAGGTGACTGAAAATT 57.595 32.000 18.41 2.16 45.33 1.82
838 1435 8.601476 CAATTTAAGGGATCGACTAACAGTAAC 58.399 37.037 0.00 0.00 0.00 2.50
839 1436 7.767198 CCAATTTAAGGGATCGACTAACAGTAA 59.233 37.037 0.00 0.00 0.00 2.24
840 1437 7.124599 TCCAATTTAAGGGATCGACTAACAGTA 59.875 37.037 0.00 0.00 0.00 2.74
841 1438 6.070424 TCCAATTTAAGGGATCGACTAACAGT 60.070 38.462 0.00 0.00 0.00 3.55
843 1440 6.302535 TCCAATTTAAGGGATCGACTAACA 57.697 37.500 0.00 0.00 0.00 2.41
844 1441 5.236695 GCTCCAATTTAAGGGATCGACTAAC 59.763 44.000 0.00 0.00 31.57 2.34
845 1442 5.365619 GCTCCAATTTAAGGGATCGACTAA 58.634 41.667 0.00 0.00 31.57 2.24
850 2960 2.561569 ACGCTCCAATTTAAGGGATCG 58.438 47.619 11.93 11.93 45.52 3.69
853 2963 4.028993 AGAAACGCTCCAATTTAAGGGA 57.971 40.909 7.63 0.00 0.00 4.20
884 2994 1.794222 GGGAGTTTCATTGGACGCG 59.206 57.895 3.53 3.53 0.00 6.01
895 3005 7.008021 TGGAAATTAAGTAGTACGGGAGTTT 57.992 36.000 0.00 0.00 43.33 2.66
981 3099 0.771127 TGTGAAAGGGGTCAAGAGGG 59.229 55.000 0.00 0.00 0.00 4.30
982 3100 2.440409 CATGTGAAAGGGGTCAAGAGG 58.560 52.381 0.00 0.00 0.00 3.69
989 3107 0.324943 CGTCTCCATGTGAAAGGGGT 59.675 55.000 0.00 0.00 0.00 4.95
998 3116 2.178521 GCGTCGTCGTCTCCATGT 59.821 61.111 3.66 0.00 39.49 3.21
1110 3228 0.464373 ATATGCCACGAGGTTGCAGG 60.464 55.000 0.00 0.00 37.60 4.85
1111 3229 0.940126 GATATGCCACGAGGTTGCAG 59.060 55.000 0.00 0.00 37.60 4.41
1112 3230 0.541392 AGATATGCCACGAGGTTGCA 59.459 50.000 0.00 0.00 38.50 4.08
1113 3231 2.035961 TCTAGATATGCCACGAGGTTGC 59.964 50.000 0.00 0.00 37.19 4.17
1114 3232 4.489810 GATCTAGATATGCCACGAGGTTG 58.510 47.826 4.89 0.00 37.19 3.77
1115 3233 3.191581 CGATCTAGATATGCCACGAGGTT 59.808 47.826 4.89 0.00 37.19 3.50
1116 3234 2.750166 CGATCTAGATATGCCACGAGGT 59.250 50.000 4.89 0.00 37.19 3.85
1117 3235 2.478709 GCGATCTAGATATGCCACGAGG 60.479 54.545 15.37 0.00 38.23 4.63
1118 3236 2.421775 AGCGATCTAGATATGCCACGAG 59.578 50.000 20.29 0.00 0.00 4.18
1129 3247 0.741326 GGTGAGCACAGCGATCTAGA 59.259 55.000 0.00 0.00 34.87 2.43
1137 3258 3.248029 CTCAACGGTGAGCACAGC 58.752 61.111 19.17 3.00 44.74 4.40
1211 3332 2.289274 CGTGTGTGATTTTACTGGTGCA 59.711 45.455 0.00 0.00 0.00 4.57
1237 3358 6.071221 TGCTAATTTGCATTGGAGAAGAATGT 60.071 34.615 10.62 0.00 38.12 2.71
1261 3382 5.061808 GCGTTTCTACAATGTGGTAGTACTG 59.938 44.000 5.39 0.00 41.20 2.74
1270 3391 2.475111 ACACGAGCGTTTCTACAATGTG 59.525 45.455 0.00 0.00 0.00 3.21
1298 3427 3.388024 ACAGGCTTCAGACACTGTTAGAA 59.612 43.478 0.00 0.00 41.03 2.10
1300 3429 3.393089 ACAGGCTTCAGACACTGTTAG 57.607 47.619 0.00 0.00 41.03 2.34
1302 3431 3.495100 CCTTACAGGCTTCAGACACTGTT 60.495 47.826 0.00 0.00 41.03 3.16
1311 3440 1.336517 CGAACGTCCTTACAGGCTTCA 60.337 52.381 0.00 0.00 34.61 3.02
1338 3468 1.741770 CTGTGCTTACCTGGGCGTC 60.742 63.158 0.00 0.00 0.00 5.19
1340 3470 2.436646 CCTGTGCTTACCTGGGCG 60.437 66.667 0.00 0.00 0.00 6.13
1505 3784 2.125106 GGCACGGTGGATGGAGTC 60.125 66.667 10.60 0.00 0.00 3.36
1528 3807 1.594293 ACTTGCACAAGGTCGTCGG 60.594 57.895 14.51 0.00 42.53 4.79
1565 3844 0.831288 CCTCCCTGATGATCTCGCCT 60.831 60.000 0.00 0.00 0.00 5.52
1847 4126 5.220117 CGTTTTCAGTGATCATTCTCTCGTC 60.220 44.000 0.00 0.00 0.00 4.20
1848 4127 4.623167 CGTTTTCAGTGATCATTCTCTCGT 59.377 41.667 0.00 0.00 0.00 4.18
1862 4141 1.005394 ATCGACGGGCGTTTTCAGT 60.005 52.632 1.89 0.00 41.80 3.41
1863 4142 1.419922 CATCGACGGGCGTTTTCAG 59.580 57.895 1.89 0.00 41.80 3.02
1961 4240 1.165907 TTTCACGGCCACAGCTCAAG 61.166 55.000 2.24 0.00 39.73 3.02
2012 4291 9.788960 CCAAACAAAAGCTTAACTTATATCCTC 57.211 33.333 0.00 0.00 37.75 3.71
2086 4784 8.945057 GCTCTGGATATTTCCTTTCTATTCATC 58.055 37.037 3.72 0.00 43.07 2.92
2099 4797 4.384940 GGGAGAACTGCTCTGGATATTTC 58.615 47.826 0.00 0.00 43.43 2.17
2117 4815 4.840271 ACCTCGTTTATAAAAGTGGGGAG 58.160 43.478 25.70 14.27 36.03 4.30
2138 4836 2.070028 GTGAGAAAAGAGGAGCCGAAC 58.930 52.381 0.00 0.00 0.00 3.95
2142 4840 0.391793 CGGGTGAGAAAAGAGGAGCC 60.392 60.000 0.00 0.00 0.00 4.70
2147 4845 1.301677 GCCTGCGGGTGAGAAAAGAG 61.302 60.000 14.55 0.00 34.45 2.85
2157 4855 2.361610 CAAATGAGGCCTGCGGGT 60.362 61.111 12.00 0.00 34.45 5.28
2160 4858 0.674581 TCTGTCAAATGAGGCCTGCG 60.675 55.000 12.00 0.00 0.00 5.18
2170 4868 5.197224 TCCATGATCCCTTTCTGTCAAAT 57.803 39.130 0.00 0.00 0.00 2.32
2187 4885 3.350833 CCCTCCTCTCAAAACTTCCATG 58.649 50.000 0.00 0.00 0.00 3.66
2188 4886 2.310052 CCCCTCCTCTCAAAACTTCCAT 59.690 50.000 0.00 0.00 0.00 3.41
2193 4891 3.657727 TGAAATCCCCTCCTCTCAAAACT 59.342 43.478 0.00 0.00 0.00 2.66
2240 4938 2.725227 AGGTTTTAAGGGGATTGGGTGA 59.275 45.455 0.00 0.00 0.00 4.02
2255 4953 0.786435 AGGGATTGGCTGGAGGTTTT 59.214 50.000 0.00 0.00 0.00 2.43
2263 4961 1.153005 GCTGGAGAGGGATTGGCTG 60.153 63.158 0.00 0.00 0.00 4.85
2264 4962 2.381941 GGCTGGAGAGGGATTGGCT 61.382 63.158 0.00 0.00 0.00 4.75
2265 4963 2.194326 GGCTGGAGAGGGATTGGC 59.806 66.667 0.00 0.00 0.00 4.52
2266 4964 1.225704 GTGGCTGGAGAGGGATTGG 59.774 63.158 0.00 0.00 0.00 3.16
2267 4965 0.393537 GTGTGGCTGGAGAGGGATTG 60.394 60.000 0.00 0.00 0.00 2.67
2274 4972 2.300967 GGGGATGTGTGGCTGGAGA 61.301 63.158 0.00 0.00 0.00 3.71
2294 4992 3.979948 TGTCAAACAATGTTCTGCATGG 58.020 40.909 0.00 0.00 37.96 3.66
2296 4994 3.006110 CCCTGTCAAACAATGTTCTGCAT 59.994 43.478 0.00 0.00 40.03 3.96
2298 4996 2.622942 TCCCTGTCAAACAATGTTCTGC 59.377 45.455 0.00 0.00 0.00 4.26
2389 5087 9.809096 TTTCAAGTCAAGCAAATTATGTTGTTA 57.191 25.926 0.00 0.00 0.00 2.41
2413 5111 5.536951 TGGTCCCCATCCATAAATTGATTT 58.463 37.500 0.00 0.00 0.00 2.17
2480 5179 2.930950 TCCACTGTCCCTTTGTTTCAG 58.069 47.619 0.00 0.00 0.00 3.02
2524 5260 9.984190 TTAAATAATTAAAGTGTGGTTTGTCCC 57.016 29.630 0.00 0.00 34.77 4.46
2576 5312 5.130705 TCTGGACTAGAAGCAAGATCCTA 57.869 43.478 0.00 0.00 30.84 2.94
2581 5318 5.300752 CAAAGTTCTGGACTAGAAGCAAGA 58.699 41.667 0.82 0.00 45.71 3.02
2676 5413 7.965107 GGATGAGCTTTTACATTGACAGTAAAG 59.035 37.037 0.00 0.00 41.06 1.85
2712 5449 7.272037 AGGTTTTCGTGTTGACAGAAATTAT 57.728 32.000 8.50 0.00 34.40 1.28
2728 5465 9.543018 GAATTTTGATAGAAGTGTAGGTTTTCG 57.457 33.333 0.00 0.00 0.00 3.46
2782 5519 3.088532 CCTGAAAATCATTGGAACCCGA 58.911 45.455 0.00 0.00 0.00 5.14
2831 5568 0.596083 GCGTCCATCGATGAGACTGG 60.596 60.000 28.60 20.80 42.86 4.00


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

AutoCloner maintained by Alex Coulton.