Multiple sequence alignment - TraesCS5D01G407500

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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 TraesCS5D01G407500 chr5D 100.000 3716 0 0 1 3716 472625769 472629484 0.000000e+00 6863.0
1 TraesCS5D01G407500 chr5D 92.880 955 65 2 1059 2010 472568521 472569475 0.000000e+00 1384.0
2 TraesCS5D01G407500 chr5D 87.802 951 107 6 1068 2015 472520403 472521347 0.000000e+00 1105.0
3 TraesCS5D01G407500 chr5D 92.458 769 50 5 2027 2793 472570486 472571248 0.000000e+00 1092.0
4 TraesCS5D01G407500 chr5D 84.676 633 97 0 2096 2728 472522071 472522703 1.880000e-177 632.0
5 TraesCS5D01G407500 chr5D 88.235 272 23 6 7 272 468303361 468303093 2.150000e-82 316.0
6 TraesCS5D01G407500 chr5D 82.258 248 42 2 271 516 375469655 375469408 2.910000e-51 213.0
7 TraesCS5D01G407500 chr5D 83.444 151 19 5 454 602 514869307 514869453 6.470000e-28 135.0
8 TraesCS5D01G407500 chr5A 92.849 2615 117 29 273 2853 592197448 592200026 0.000000e+00 3729.0
9 TraesCS5D01G407500 chr5A 90.806 1055 78 9 2027 3069 592124391 592125438 0.000000e+00 1393.0
10 TraesCS5D01G407500 chr5A 91.946 956 66 6 1059 2010 592122406 592123354 0.000000e+00 1328.0
11 TraesCS5D01G407500 chr5A 86.779 953 98 10 1068 2015 592034051 592034980 0.000000e+00 1037.0
12 TraesCS5D01G407500 chr5A 84.194 639 99 1 2092 2728 592035647 592036285 1.470000e-173 619.0
13 TraesCS5D01G407500 chr5A 88.254 315 27 9 2859 3171 592201667 592201973 5.860000e-98 368.0
14 TraesCS5D01G407500 chr5A 91.498 247 12 5 3470 3716 592204633 592204870 7.690000e-87 331.0
15 TraesCS5D01G407500 chr5A 80.588 170 10 10 3545 3714 592126212 592126358 3.920000e-20 110.0
16 TraesCS5D01G407500 chr5A 96.774 31 1 0 917 947 592122199 592122229 7.000000e-03 52.8
17 TraesCS5D01G407500 chr5B 93.525 1359 64 10 658 2010 580072844 580074184 0.000000e+00 2001.0
18 TraesCS5D01G407500 chr5B 91.738 1174 62 16 2027 3170 580074442 580075610 0.000000e+00 1598.0
19 TraesCS5D01G407500 chr5B 91.975 947 67 3 1067 2010 579590938 579591878 0.000000e+00 1319.0
20 TraesCS5D01G407500 chr5B 91.552 947 71 3 1067 2010 579807424 579808364 0.000000e+00 1297.0
21 TraesCS5D01G407500 chr5B 88.701 947 69 17 2027 2953 579809488 579810416 0.000000e+00 1122.0
22 TraesCS5D01G407500 chr5B 93.544 728 35 3 2027 2753 579593654 579594370 0.000000e+00 1074.0
23 TraesCS5D01G407500 chr5B 86.853 966 105 11 1061 2015 579520130 579521084 0.000000e+00 1061.0
24 TraesCS5D01G407500 chr5B 84.518 633 97 1 2099 2731 579521509 579522140 3.150000e-175 625.0
25 TraesCS5D01G407500 chr5B 87.059 340 34 6 1 333 580072413 580072749 3.500000e-100 375.0
26 TraesCS5D01G407500 chr5B 88.584 219 23 2 3213 3430 580075614 580075831 7.910000e-67 265.0
27 TraesCS5D01G407500 chr5B 85.802 162 5 5 3515 3676 580076038 580076181 4.970000e-34 156.0
28 TraesCS5D01G407500 chr5B 96.774 31 1 0 917 947 579590777 579590807 7.000000e-03 52.8
29 TraesCS5D01G407500 chr1D 89.377 273 26 3 1 272 114303030 114303300 1.280000e-89 340.0
30 TraesCS5D01G407500 chr1D 88.722 266 24 4 9 268 209408468 209408203 1.670000e-83 320.0
31 TraesCS5D01G407500 chr4B 88.043 276 27 4 1 270 440618121 440617846 4.630000e-84 322.0
32 TraesCS5D01G407500 chr4D 87.500 280 28 5 1 273 357430354 357430075 2.150000e-82 316.0
33 TraesCS5D01G407500 chr4D 87.823 271 27 2 9 273 443182180 443182450 2.790000e-81 313.0
34 TraesCS5D01G407500 chr4D 79.630 108 20 2 274 380 48723142 48723248 3.980000e-10 76.8
35 TraesCS5D01G407500 chr6A 88.148 270 25 4 9 272 426598785 426599053 7.750000e-82 315.0
36 TraesCS5D01G407500 chr1B 87.868 272 25 7 7 272 312045327 312045058 2.790000e-81 313.0
37 TraesCS5D01G407500 chr2B 82.622 328 52 5 274 598 516727819 516728144 6.070000e-73 285.0
38 TraesCS5D01G407500 chr2D 80.110 181 35 1 273 452 436000978 436000798 2.330000e-27 134.0
39 TraesCS5D01G407500 chr3A 72.930 314 62 14 273 579 595460472 595460769 1.840000e-13 87.9
40 TraesCS5D01G407500 chr7D 94.872 39 1 1 543 581 73121800 73121837 4.010000e-05 60.2
41 TraesCS5D01G407500 chr4A 100.000 28 0 0 272 299 698836007 698836034 7.000000e-03 52.8


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 TraesCS5D01G407500 chr5D 472625769 472629484 3715 False 6863.000000 6863 100.000000 1 3716 1 chr5D.!!$F1 3715
1 TraesCS5D01G407500 chr5D 472568521 472571248 2727 False 1238.000000 1384 92.669000 1059 2793 2 chr5D.!!$F4 1734
2 TraesCS5D01G407500 chr5D 472520403 472522703 2300 False 868.500000 1105 86.239000 1068 2728 2 chr5D.!!$F3 1660
3 TraesCS5D01G407500 chr5A 592197448 592204870 7422 False 1476.000000 3729 90.867000 273 3716 3 chr5A.!!$F3 3443
4 TraesCS5D01G407500 chr5A 592034051 592036285 2234 False 828.000000 1037 85.486500 1068 2728 2 chr5A.!!$F1 1660
5 TraesCS5D01G407500 chr5A 592122199 592126358 4159 False 720.950000 1393 90.028500 917 3714 4 chr5A.!!$F2 2797
6 TraesCS5D01G407500 chr5B 579807424 579810416 2992 False 1209.500000 1297 90.126500 1067 2953 2 chr5B.!!$F3 1886
7 TraesCS5D01G407500 chr5B 580072413 580076181 3768 False 879.000000 2001 89.341600 1 3676 5 chr5B.!!$F4 3675
8 TraesCS5D01G407500 chr5B 579520130 579522140 2010 False 843.000000 1061 85.685500 1061 2731 2 chr5B.!!$F1 1670
9 TraesCS5D01G407500 chr5B 579590777 579594370 3593 False 815.266667 1319 94.097667 917 2753 3 chr5B.!!$F2 1836

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
542 553 0.164217 GCGGCGTACAATCGAACAAA 59.836 50.000 9.37 0.00 0.00 2.83 F
787 825 0.710567 GCGTATGGATGCGAATCTCG 59.289 55.000 2.72 5.12 43.89 4.04 F
956 1019 0.746563 GGCGTATGCAGGTTAAGCCA 60.747 55.000 15.26 0.00 45.35 4.75 F
1653 1776 1.078918 CCTCAGCGTGCTCATGGAA 60.079 57.895 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1776 1.002134 CTTGGTCTGGGCGATGGTT 60.002 57.895 0.00 0.00 0.0 3.67 R
2094 5264 1.344114 GCCCCAAACAAATTCTGCAGA 59.656 47.619 13.74 13.74 0.0 4.26 R
2604 5785 2.662596 GTCATGTCCACCTCCGCA 59.337 61.111 0.00 0.00 0.0 5.69 R
3379 10806 0.178068 AACCATTGGAGATCGACCCG 59.822 55.000 10.37 0.00 0.0 5.28 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
34 35 8.593679 TCATATTCTCAAAGTTGTTCTAGGACA 58.406 33.333 0.00 0.00 0.00 4.02
50 51 7.218228 TCTAGGACAATCGTTACACTTAACA 57.782 36.000 0.00 0.00 37.99 2.41
52 53 8.308931 TCTAGGACAATCGTTACACTTAACAAT 58.691 33.333 0.00 0.00 37.99 2.71
83 90 2.817258 TCCGGAAAACATGATCAACACC 59.183 45.455 0.00 0.00 0.00 4.16
88 95 4.479619 GAAAACATGATCAACACCTGAGC 58.520 43.478 0.00 0.00 41.07 4.26
90 97 4.558226 AACATGATCAACACCTGAGCTA 57.442 40.909 0.00 0.00 41.27 3.32
93 100 4.019860 ACATGATCAACACCTGAGCTAGTT 60.020 41.667 0.00 0.00 41.27 2.24
100 107 4.810191 ACACCTGAGCTAGTTTTAGAGG 57.190 45.455 0.00 0.00 0.00 3.69
106 113 4.822026 TGAGCTAGTTTTAGAGGCAAGAC 58.178 43.478 0.00 0.00 0.00 3.01
110 117 5.128008 AGCTAGTTTTAGAGGCAAGACTAGG 59.872 44.000 12.62 0.66 40.77 3.02
113 120 6.628644 AGTTTTAGAGGCAAGACTAGGAAT 57.371 37.500 0.00 0.00 0.00 3.01
141 148 5.533533 TTTACCGTTTATCATTCCACACG 57.466 39.130 0.00 0.00 0.00 4.49
151 158 3.197265 TCATTCCACACGTGCATATGAG 58.803 45.455 17.22 0.53 0.00 2.90
156 163 3.435327 TCCACACGTGCATATGAGTTTTC 59.565 43.478 17.22 0.00 0.00 2.29
186 193 4.176271 TCGCATATTTCAGGATCATAGCG 58.824 43.478 0.00 0.00 42.42 4.26
196 203 4.082190 TCAGGATCATAGCGGTTATAGCAC 60.082 45.833 0.00 0.00 37.01 4.40
290 301 2.029828 ACAGCGACTTCGACATCTTCTT 60.030 45.455 2.02 0.00 43.02 2.52
291 302 2.596419 CAGCGACTTCGACATCTTCTTC 59.404 50.000 2.02 0.00 43.02 2.87
292 303 2.490115 AGCGACTTCGACATCTTCTTCT 59.510 45.455 2.02 0.00 43.02 2.85
299 310 6.102663 ACTTCGACATCTTCTTCTATGTTGG 58.897 40.000 0.00 0.00 37.85 3.77
336 347 2.505405 GTTTCTCCAACCCTCTGAACC 58.495 52.381 0.00 0.00 0.00 3.62
337 348 0.685097 TTCTCCAACCCTCTGAACCG 59.315 55.000 0.00 0.00 0.00 4.44
338 349 1.192146 TCTCCAACCCTCTGAACCGG 61.192 60.000 0.00 0.00 0.00 5.28
352 363 0.965363 AACCGGTGGTGATGGATTGC 60.965 55.000 8.52 0.00 35.34 3.56
354 365 0.964860 CCGGTGGTGATGGATTGCAA 60.965 55.000 0.00 0.00 0.00 4.08
357 368 0.174162 GTGGTGATGGATTGCAAGCC 59.826 55.000 26.78 26.78 34.32 4.35
361 372 2.417787 GGTGATGGATTGCAAGCCTTTC 60.418 50.000 32.05 26.60 34.95 2.62
363 374 2.105766 GATGGATTGCAAGCCTTTCCT 58.894 47.619 32.05 13.12 34.95 3.36
374 385 1.188863 GCCTTTCCTACGTAGGGTGA 58.811 55.000 35.39 21.49 43.79 4.02
375 386 1.761198 GCCTTTCCTACGTAGGGTGAT 59.239 52.381 35.39 0.00 43.79 3.06
376 387 2.483188 GCCTTTCCTACGTAGGGTGATG 60.483 54.545 35.39 22.99 43.79 3.07
377 388 2.483188 CCTTTCCTACGTAGGGTGATGC 60.483 54.545 35.39 0.00 43.79 3.91
378 389 2.154567 TTCCTACGTAGGGTGATGCT 57.845 50.000 35.39 0.00 43.79 3.79
379 390 1.688772 TCCTACGTAGGGTGATGCTC 58.311 55.000 35.39 0.00 43.79 4.26
380 391 0.674534 CCTACGTAGGGTGATGCTCC 59.325 60.000 30.62 0.00 39.86 4.70
381 392 1.399714 CTACGTAGGGTGATGCTCCA 58.600 55.000 15.07 0.00 0.00 3.86
382 393 1.338337 CTACGTAGGGTGATGCTCCAG 59.662 57.143 15.07 0.00 0.00 3.86
383 394 0.614979 ACGTAGGGTGATGCTCCAGT 60.615 55.000 0.00 0.00 0.00 4.00
384 395 0.537188 CGTAGGGTGATGCTCCAGTT 59.463 55.000 0.00 0.00 0.00 3.16
385 396 1.740380 CGTAGGGTGATGCTCCAGTTG 60.740 57.143 0.00 0.00 0.00 3.16
386 397 1.555075 GTAGGGTGATGCTCCAGTTGA 59.445 52.381 0.00 0.00 0.00 3.18
387 398 1.293062 AGGGTGATGCTCCAGTTGAT 58.707 50.000 0.00 0.00 0.00 2.57
388 399 1.064906 AGGGTGATGCTCCAGTTGATG 60.065 52.381 0.00 0.00 0.00 3.07
389 400 1.340405 GGGTGATGCTCCAGTTGATGT 60.340 52.381 0.00 0.00 0.00 3.06
397 408 2.294233 GCTCCAGTTGATGTTGCTTCAA 59.706 45.455 0.00 0.00 0.00 2.69
413 424 7.763985 TGTTGCTTCAACGATTTATAGATCTCA 59.236 33.333 0.00 0.00 46.13 3.27
422 433 7.835822 ACGATTTATAGATCTCATCTCAAGGG 58.164 38.462 0.00 0.00 40.76 3.95
426 437 2.392662 AGATCTCATCTCAAGGGCGAA 58.607 47.619 0.00 0.00 33.42 4.70
448 459 4.134563 ACAACTATTGCGGTCTTCAAAGT 58.865 39.130 0.00 0.00 0.00 2.66
449 460 4.213482 ACAACTATTGCGGTCTTCAAAGTC 59.787 41.667 0.00 0.00 0.00 3.01
451 462 3.997021 ACTATTGCGGTCTTCAAAGTCTG 59.003 43.478 0.00 0.00 0.00 3.51
452 463 2.613026 TTGCGGTCTTCAAAGTCTGA 57.387 45.000 0.81 0.00 0.00 3.27
459 470 4.500837 CGGTCTTCAAAGTCTGATATGACG 59.499 45.833 0.00 0.00 41.47 4.35
461 472 6.100004 GGTCTTCAAAGTCTGATATGACGAA 58.900 40.000 0.00 0.00 41.47 3.85
484 495 1.477105 GTTTGCAGGTGTCGCTTTTC 58.523 50.000 0.00 0.00 0.00 2.29
499 510 1.682854 CTTTTCCTTGCTGTTGGCTCA 59.317 47.619 0.00 0.00 42.39 4.26
504 515 2.453773 CTTGCTGTTGGCTCAGTGCG 62.454 60.000 10.70 0.00 44.05 5.34
516 527 3.486542 GGCTCAGTGCGATTTTCAATCTC 60.487 47.826 0.00 0.00 44.05 2.75
520 531 4.701651 TCAGTGCGATTTTCAATCTCCAAT 59.298 37.500 0.00 0.00 0.00 3.16
522 533 4.107622 GTGCGATTTTCAATCTCCAATGG 58.892 43.478 0.00 0.00 0.00 3.16
524 535 3.709987 CGATTTTCAATCTCCAATGGGC 58.290 45.455 0.00 0.00 0.00 5.36
527 538 1.037030 TTCAATCTCCAATGGGCGGC 61.037 55.000 0.00 0.00 0.00 6.53
538 549 2.509786 GGGCGGCGTACAATCGAA 60.510 61.111 9.37 0.00 0.00 3.71
539 550 2.699212 GGCGGCGTACAATCGAAC 59.301 61.111 9.37 0.00 0.00 3.95
542 553 0.164217 GCGGCGTACAATCGAACAAA 59.836 50.000 9.37 0.00 0.00 2.83
543 554 1.398705 GCGGCGTACAATCGAACAAAA 60.399 47.619 9.37 0.00 0.00 2.44
544 555 2.906153 CGGCGTACAATCGAACAAAAA 58.094 42.857 0.00 0.00 0.00 1.94
545 556 2.900046 CGGCGTACAATCGAACAAAAAG 59.100 45.455 0.00 0.00 0.00 2.27
597 608 2.401583 TACCGGCTGTTCTACGTCTA 57.598 50.000 0.00 0.00 0.00 2.59
604 615 3.913163 GGCTGTTCTACGTCTATATTCGC 59.087 47.826 0.00 0.00 0.00 4.70
618 629 8.761497 CGTCTATATTCGCCTTTATTTTTCTCA 58.239 33.333 0.00 0.00 0.00 3.27
760 798 4.504689 CCAAAGCAAAAGGCCTCCAAATAA 60.505 41.667 5.23 0.00 46.50 1.40
773 811 6.095440 GGCCTCCAAATAATAATCATGCGTAT 59.905 38.462 0.00 0.00 0.00 3.06
787 825 0.710567 GCGTATGGATGCGAATCTCG 59.289 55.000 2.72 5.12 43.89 4.04
794 832 4.118093 TGGATGCGAATCTCGAGTTTTA 57.882 40.909 13.13 2.24 43.74 1.52
856 895 2.590575 CCGCACGGACAACAAGGT 60.591 61.111 2.01 0.00 37.50 3.50
913 952 4.215399 TCTTTCAACATTTCCACGATCCAC 59.785 41.667 0.00 0.00 0.00 4.02
914 953 3.133141 TCAACATTTCCACGATCCACA 57.867 42.857 0.00 0.00 0.00 4.17
918 957 3.955471 ACATTTCCACGATCCACAGATT 58.045 40.909 0.00 0.00 30.90 2.40
956 1019 0.746563 GGCGTATGCAGGTTAAGCCA 60.747 55.000 15.26 0.00 45.35 4.75
957 1020 1.308998 GCGTATGCAGGTTAAGCCAT 58.691 50.000 0.89 1.56 42.15 4.40
958 1021 1.264288 GCGTATGCAGGTTAAGCCATC 59.736 52.381 0.89 0.00 42.15 3.51
959 1022 2.838736 CGTATGCAGGTTAAGCCATCT 58.161 47.619 0.00 0.00 40.61 2.90
960 1023 3.802329 GCGTATGCAGGTTAAGCCATCTA 60.802 47.826 0.89 0.00 42.15 1.98
961 1024 3.990469 CGTATGCAGGTTAAGCCATCTAG 59.010 47.826 0.00 0.00 40.61 2.43
1048 1167 2.884012 TCCAATCAACGCACATCACTTT 59.116 40.909 0.00 0.00 0.00 2.66
1056 1175 3.009723 ACGCACATCACTTTCCCTTATG 58.990 45.455 0.00 0.00 0.00 1.90
1083 1203 6.716628 CACAGTTAACCATGGATAAGGCATAT 59.283 38.462 21.47 0.00 0.00 1.78
1086 1206 9.113838 CAGTTAACCATGGATAAGGCATATATC 57.886 37.037 21.47 2.06 0.00 1.63
1653 1776 1.078918 CCTCAGCGTGCTCATGGAA 60.079 57.895 0.00 0.00 0.00 3.53
2041 5211 6.153851 TCCAATAACACTCGGTGAATTCTCTA 59.846 38.462 7.05 0.00 36.96 2.43
2086 5256 7.582435 TCTCATCAATAACACTCGTTTTCTC 57.418 36.000 0.00 0.00 36.52 2.87
2087 5257 7.151976 TCTCATCAATAACACTCGTTTTCTCA 58.848 34.615 0.00 0.00 36.52 3.27
2088 5258 7.116376 TCTCATCAATAACACTCGTTTTCTCAC 59.884 37.037 0.00 0.00 36.52 3.51
2089 5259 6.929049 TCATCAATAACACTCGTTTTCTCACT 59.071 34.615 0.00 0.00 36.52 3.41
2090 5260 6.525121 TCAATAACACTCGTTTTCTCACTG 57.475 37.500 0.00 0.00 36.52 3.66
2091 5261 6.277605 TCAATAACACTCGTTTTCTCACTGA 58.722 36.000 0.00 0.00 36.52 3.41
2092 5262 6.759356 TCAATAACACTCGTTTTCTCACTGAA 59.241 34.615 0.00 0.00 36.52 3.02
2093 5263 4.859629 AACACTCGTTTTCTCACTGAAC 57.140 40.909 0.00 0.00 33.88 3.18
2094 5264 4.124851 ACACTCGTTTTCTCACTGAACT 57.875 40.909 0.00 0.00 33.88 3.01
2626 5807 0.970937 GGAGGTGGACATGACGGAGA 60.971 60.000 0.00 0.00 0.00 3.71
2769 5956 2.280797 GACTGGTGGCGTGCTGAA 60.281 61.111 0.00 0.00 0.00 3.02
2770 5957 1.891919 GACTGGTGGCGTGCTGAAA 60.892 57.895 0.00 0.00 0.00 2.69
2884 7742 4.757594 GCTATCTAGGTAGCTAGCTCGTA 58.242 47.826 27.84 17.10 42.02 3.43
2888 7746 5.132897 TCTAGGTAGCTAGCTCGTAGTAC 57.867 47.826 27.84 12.65 35.39 2.73
3128 8025 2.880268 TGCAAATAAGCGGATGATGGAG 59.120 45.455 0.00 0.00 37.31 3.86
3171 8068 7.169158 GGAAATATCCACCTGTGAATTTTCA 57.831 36.000 0.00 0.00 45.79 2.69
3192 10504 7.956508 TTCATGCGGTTTTGTTATTTATACG 57.043 32.000 0.00 0.00 0.00 3.06
3193 10505 6.487960 TCATGCGGTTTTGTTATTTATACGG 58.512 36.000 0.00 0.00 0.00 4.02
3194 10506 5.876612 TGCGGTTTTGTTATTTATACGGT 57.123 34.783 0.00 0.00 0.00 4.83
3195 10507 6.251655 TGCGGTTTTGTTATTTATACGGTT 57.748 33.333 0.00 0.00 0.00 4.44
3196 10508 7.369803 TGCGGTTTTGTTATTTATACGGTTA 57.630 32.000 0.00 0.00 0.00 2.85
3197 10509 7.239972 TGCGGTTTTGTTATTTATACGGTTAC 58.760 34.615 0.00 0.00 0.00 2.50
3198 10510 6.686679 GCGGTTTTGTTATTTATACGGTTACC 59.313 38.462 0.00 0.00 0.00 2.85
3199 10511 7.413988 GCGGTTTTGTTATTTATACGGTTACCT 60.414 37.037 0.00 0.00 0.00 3.08
3200 10512 8.450180 CGGTTTTGTTATTTATACGGTTACCTT 58.550 33.333 0.00 0.00 0.00 3.50
3284 10596 3.053849 GAGCGACACTCCGAGGTCC 62.054 68.421 0.00 0.46 39.75 4.46
3293 10605 4.715130 CCGAGGTCCAGGTGGGGA 62.715 72.222 0.00 0.00 37.22 4.81
3333 10645 1.337260 CCAGAACCTCGTTGGAGACTG 60.337 57.143 4.38 0.00 43.27 3.51
3340 10700 1.070134 CTCGTTGGAGACTGGGACAAA 59.930 52.381 0.00 0.00 43.27 2.83
3348 10775 2.391724 GACTGGGACAAAGGCGGTGA 62.392 60.000 0.00 0.00 38.70 4.02
3374 10801 0.469917 GAGGAAGATGAATGGGCCGA 59.530 55.000 0.00 0.00 0.00 5.54
3379 10806 1.887707 GATGAATGGGCCGACCGTC 60.888 63.158 0.00 0.00 44.64 4.79
3413 10840 1.209383 GGTTCGGCCGAAAAGAAGC 59.791 57.895 40.13 26.07 35.75 3.86
3417 10844 2.126850 GGCCGAAAAGAAGCGTGC 60.127 61.111 0.00 0.00 0.00 5.34
3452 10887 2.028748 GCACAATGCTGTCCCATTTTCT 60.029 45.455 0.00 0.00 40.96 2.52
3455 10890 2.997986 CAATGCTGTCCCATTTTCTTGC 59.002 45.455 0.00 0.00 33.35 4.01
3481 10916 7.610865 TGTTTGGTCCCATTTTCTTATGATTC 58.389 34.615 0.00 0.00 0.00 2.52
3488 10923 5.359576 CCCATTTTCTTATGATTCCCGTCAA 59.640 40.000 0.00 0.00 0.00 3.18
3492 10927 8.673711 CATTTTCTTATGATTCCCGTCAAACTA 58.326 33.333 0.00 0.00 0.00 2.24
3598 11363 7.575414 TGTTGATTCTTTGTTGCTTACCTAA 57.425 32.000 0.00 0.00 0.00 2.69
3599 11364 7.648142 TGTTGATTCTTTGTTGCTTACCTAAG 58.352 34.615 0.00 0.00 36.40 2.18
3630 11395 1.633432 CATTGGGTTGGGTCAGGACTA 59.367 52.381 0.00 0.00 0.00 2.59
3704 11469 0.168128 CCCAATCGCGTTTCAACCTC 59.832 55.000 5.77 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.605275 CCTAGAACAACTTTGAGAATATGATGA 57.395 33.333 0.00 0.00 0.00 2.92
7 8 9.606631 GTCCTAGAACAACTTTGAGAATATGAT 57.393 33.333 0.00 0.00 0.00 2.45
27 28 7.878477 TTGTTAAGTGTAACGATTGTCCTAG 57.122 36.000 0.00 0.00 45.86 3.02
52 53 9.402320 TGATCATGTTTTCCGGATCTTAAAATA 57.598 29.630 4.15 0.58 37.60 1.40
56 57 6.657117 TGTTGATCATGTTTTCCGGATCTTAA 59.343 34.615 4.15 0.00 37.60 1.85
57 58 6.093495 GTGTTGATCATGTTTTCCGGATCTTA 59.907 38.462 4.15 0.00 37.60 2.10
70 71 3.517100 ACTAGCTCAGGTGTTGATCATGT 59.483 43.478 0.00 0.00 34.68 3.21
83 90 4.867608 GTCTTGCCTCTAAAACTAGCTCAG 59.132 45.833 0.00 0.00 0.00 3.35
88 95 6.777213 TCCTAGTCTTGCCTCTAAAACTAG 57.223 41.667 0.00 0.00 37.18 2.57
90 97 6.213600 TGATTCCTAGTCTTGCCTCTAAAACT 59.786 38.462 0.00 0.00 0.00 2.66
93 100 5.129485 CCTGATTCCTAGTCTTGCCTCTAAA 59.871 44.000 0.00 0.00 0.00 1.85
100 107 5.354513 GGTAAAACCTGATTCCTAGTCTTGC 59.645 44.000 0.00 0.00 34.73 4.01
106 113 7.767198 TGATAAACGGTAAAACCTGATTCCTAG 59.233 37.037 0.00 0.00 35.66 3.02
110 117 7.913821 GGAATGATAAACGGTAAAACCTGATTC 59.086 37.037 0.00 0.00 35.66 2.52
113 120 6.149807 GTGGAATGATAAACGGTAAAACCTGA 59.850 38.462 0.00 0.00 35.66 3.86
141 148 5.627499 TTCAGTGGAAAACTCATATGCAC 57.373 39.130 0.00 0.00 36.83 4.57
151 158 6.321717 TGAAATATGCGATTCAGTGGAAAAC 58.678 36.000 0.00 0.00 36.43 2.43
256 264 1.742831 GTCGCTGTTGGAAATATGCCA 59.257 47.619 0.00 0.00 0.00 4.92
258 266 3.685058 GAAGTCGCTGTTGGAAATATGC 58.315 45.455 0.00 0.00 0.00 3.14
271 279 2.490115 AGAAGAAGATGTCGAAGTCGCT 59.510 45.455 0.00 0.00 39.60 4.93
290 301 2.290260 CCAAGCCACAGACCAACATAGA 60.290 50.000 0.00 0.00 0.00 1.98
291 302 2.086869 CCAAGCCACAGACCAACATAG 58.913 52.381 0.00 0.00 0.00 2.23
292 303 1.423541 ACCAAGCCACAGACCAACATA 59.576 47.619 0.00 0.00 0.00 2.29
299 310 2.358737 CCGGACCAAGCCACAGAC 60.359 66.667 0.00 0.00 0.00 3.51
336 347 0.452987 CTTGCAATCCATCACCACCG 59.547 55.000 0.00 0.00 0.00 4.94
337 348 0.174162 GCTTGCAATCCATCACCACC 59.826 55.000 0.00 0.00 0.00 4.61
338 349 0.174162 GGCTTGCAATCCATCACCAC 59.826 55.000 14.43 0.00 0.00 4.16
352 363 1.553704 ACCCTACGTAGGAAAGGCTTG 59.446 52.381 37.76 22.29 46.63 4.01
354 365 1.192428 CACCCTACGTAGGAAAGGCT 58.808 55.000 37.76 13.17 46.63 4.58
357 368 2.431057 AGCATCACCCTACGTAGGAAAG 59.569 50.000 37.76 26.20 46.63 2.62
361 372 0.674534 GGAGCATCACCCTACGTAGG 59.325 60.000 31.17 31.17 39.25 3.18
363 374 1.341679 ACTGGAGCATCACCCTACGTA 60.342 52.381 0.00 0.00 36.25 3.57
374 385 2.211250 AGCAACATCAACTGGAGCAT 57.789 45.000 0.00 0.00 32.91 3.79
375 386 1.881973 GAAGCAACATCAACTGGAGCA 59.118 47.619 0.00 0.00 32.91 4.26
376 387 1.881973 TGAAGCAACATCAACTGGAGC 59.118 47.619 0.00 0.00 0.00 4.70
383 394 8.262715 TCTATAAATCGTTGAAGCAACATCAA 57.737 30.769 10.48 0.00 43.70 2.57
384 395 7.841915 TCTATAAATCGTTGAAGCAACATCA 57.158 32.000 10.48 0.00 43.70 3.07
385 396 8.768955 AGATCTATAAATCGTTGAAGCAACATC 58.231 33.333 10.48 3.24 43.70 3.06
386 397 8.668510 AGATCTATAAATCGTTGAAGCAACAT 57.331 30.769 10.48 1.55 43.70 2.71
387 398 7.763985 TGAGATCTATAAATCGTTGAAGCAACA 59.236 33.333 10.48 0.00 43.70 3.33
388 399 8.131455 TGAGATCTATAAATCGTTGAAGCAAC 57.869 34.615 0.00 0.00 40.54 4.17
389 400 8.893219 ATGAGATCTATAAATCGTTGAAGCAA 57.107 30.769 0.00 0.00 0.00 3.91
397 408 7.578571 GCCCTTGAGATGAGATCTATAAATCGT 60.579 40.741 0.00 0.00 40.38 3.73
413 424 3.914426 ATAGTTGTTCGCCCTTGAGAT 57.086 42.857 0.00 0.00 0.00 2.75
422 433 1.076332 AGACCGCAATAGTTGTTCGC 58.924 50.000 0.00 0.00 0.00 4.70
426 437 4.134563 ACTTTGAAGACCGCAATAGTTGT 58.865 39.130 0.00 0.00 0.00 3.32
459 470 1.282875 GACACCTGCAAACGCCTTC 59.717 57.895 0.00 0.00 0.00 3.46
461 472 2.972505 CGACACCTGCAAACGCCT 60.973 61.111 0.00 0.00 0.00 5.52
499 510 4.142315 CCATTGGAGATTGAAAATCGCACT 60.142 41.667 0.00 0.00 0.00 4.40
504 515 3.491447 CCGCCCATTGGAGATTGAAAATC 60.491 47.826 3.62 0.00 32.25 2.17
516 527 2.058829 GATTGTACGCCGCCCATTGG 62.059 60.000 0.00 0.00 0.00 3.16
520 531 3.298115 TTCGATTGTACGCCGCCCA 62.298 57.895 0.00 0.00 0.00 5.36
522 533 1.628447 TTGTTCGATTGTACGCCGCC 61.628 55.000 0.00 0.00 0.00 6.13
524 535 2.580729 TTTTGTTCGATTGTACGCCG 57.419 45.000 0.00 0.00 0.00 6.46
527 538 7.101993 ACTAGTCTTTTTGTTCGATTGTACG 57.898 36.000 0.00 0.00 0.00 3.67
581 592 4.149617 CGAATATAGACGTAGAACAGCCG 58.850 47.826 0.00 0.00 0.00 5.52
583 594 3.913163 GGCGAATATAGACGTAGAACAGC 59.087 47.826 0.00 0.00 0.00 4.40
702 740 1.134580 CGAGGAGAGCCATGTCAATGT 60.135 52.381 0.00 0.00 36.29 2.71
748 786 4.218417 ACGCATGATTATTATTTGGAGGCC 59.782 41.667 0.00 0.00 0.00 5.19
760 798 3.860641 TCGCATCCATACGCATGATTAT 58.139 40.909 0.00 0.00 33.67 1.28
773 811 2.672961 AAACTCGAGATTCGCATCCA 57.327 45.000 21.68 0.00 40.21 3.41
856 895 1.070105 AGCAAACGGTCGTGGCTTA 59.930 52.632 14.30 0.00 36.58 3.09
913 952 1.012086 CTGACGTCCATGGCAATCTG 58.988 55.000 14.12 4.31 0.00 2.90
914 953 0.107508 CCTGACGTCCATGGCAATCT 60.108 55.000 14.12 0.00 0.00 2.40
956 1019 8.691797 GTGGTTCATCTTCTTCTAGAACTAGAT 58.308 37.037 14.59 14.59 41.37 1.98
957 1020 7.148222 CGTGGTTCATCTTCTTCTAGAACTAGA 60.148 40.741 0.00 7.57 40.17 2.43
958 1021 6.970043 CGTGGTTCATCTTCTTCTAGAACTAG 59.030 42.308 0.00 2.11 38.78 2.57
959 1022 6.625300 GCGTGGTTCATCTTCTTCTAGAACTA 60.625 42.308 0.00 0.00 38.78 2.24
960 1023 5.715070 CGTGGTTCATCTTCTTCTAGAACT 58.285 41.667 0.00 0.00 38.78 3.01
961 1024 4.327627 GCGTGGTTCATCTTCTTCTAGAAC 59.672 45.833 0.00 0.00 38.22 3.01
1048 1167 5.496556 CATGGTTAACTGTGTCATAAGGGA 58.503 41.667 5.42 0.00 0.00 4.20
1056 1175 4.335594 GCCTTATCCATGGTTAACTGTGTC 59.664 45.833 12.58 0.00 0.00 3.67
1083 1203 1.248486 CGAAGGAGAGGATGGCGATA 58.752 55.000 0.00 0.00 0.00 2.92
1086 1206 2.279784 GCGAAGGAGAGGATGGCG 60.280 66.667 0.00 0.00 0.00 5.69
1190 1310 3.470888 CGAGGAACGGGATGGCCT 61.471 66.667 3.32 0.00 38.46 5.19
1653 1776 1.002134 CTTGGTCTGGGCGATGGTT 60.002 57.895 0.00 0.00 0.00 3.67
2086 5256 4.825546 ACAAATTCTGCAGAGTTCAGTG 57.174 40.909 22.94 19.23 33.48 3.66
2087 5257 5.450965 CCAAACAAATTCTGCAGAGTTCAGT 60.451 40.000 22.94 20.25 33.48 3.41
2088 5258 4.980434 CCAAACAAATTCTGCAGAGTTCAG 59.020 41.667 22.94 19.70 0.00 3.02
2089 5259 4.202141 CCCAAACAAATTCTGCAGAGTTCA 60.202 41.667 22.94 6.61 0.00 3.18
2090 5260 4.301628 CCCAAACAAATTCTGCAGAGTTC 58.698 43.478 22.94 0.00 0.00 3.01
2091 5261 3.070015 CCCCAAACAAATTCTGCAGAGTT 59.930 43.478 17.94 17.94 0.00 3.01
2092 5262 2.629617 CCCCAAACAAATTCTGCAGAGT 59.370 45.455 17.43 11.77 0.00 3.24
2093 5263 2.611224 GCCCCAAACAAATTCTGCAGAG 60.611 50.000 17.43 7.86 0.00 3.35
2094 5264 1.344114 GCCCCAAACAAATTCTGCAGA 59.656 47.619 13.74 13.74 0.00 4.26
2604 5785 2.662596 GTCATGTCCACCTCCGCA 59.337 61.111 0.00 0.00 0.00 5.69
2884 7742 5.137551 ACAAATTGCTGGTTTGGTAGTACT 58.862 37.500 0.00 0.00 40.08 2.73
2888 7746 7.961325 AAATTACAAATTGCTGGTTTGGTAG 57.039 32.000 11.68 0.00 40.08 3.18
2988 7847 0.947180 ACCATGAACGTTCGTTCCCG 60.947 55.000 27.22 19.86 42.56 5.14
3006 7865 1.737793 CAGATCGGTGTAAGCCCAAAC 59.262 52.381 0.00 0.00 0.00 2.93
3099 7996 6.264832 TCATCCGCTTATTTGCAAATACAAG 58.735 36.000 27.44 24.56 31.03 3.16
3100 7997 6.201226 TCATCCGCTTATTTGCAAATACAA 57.799 33.333 27.44 16.96 31.03 2.41
3128 8025 0.237498 CCGCTTCCGTTTTCTGTTCC 59.763 55.000 0.00 0.00 0.00 3.62
3171 8068 6.439675 ACCGTATAAATAACAAAACCGCAT 57.560 33.333 0.00 0.00 0.00 4.73
3202 10514 7.337436 CAGGTAACCGTATAAATCCCTCAAAAA 59.663 37.037 0.00 0.00 37.17 1.94
3203 10515 6.824704 CAGGTAACCGTATAAATCCCTCAAAA 59.175 38.462 0.00 0.00 37.17 2.44
3204 10516 6.156602 TCAGGTAACCGTATAAATCCCTCAAA 59.843 38.462 0.00 0.00 37.17 2.69
3205 10517 5.662208 TCAGGTAACCGTATAAATCCCTCAA 59.338 40.000 0.00 0.00 37.17 3.02
3206 10518 5.210430 TCAGGTAACCGTATAAATCCCTCA 58.790 41.667 0.00 0.00 37.17 3.86
3207 10519 5.796424 TCAGGTAACCGTATAAATCCCTC 57.204 43.478 0.00 0.00 37.17 4.30
3208 10520 6.564557 TTTCAGGTAACCGTATAAATCCCT 57.435 37.500 0.00 0.00 37.17 4.20
3209 10521 6.238184 CGTTTTCAGGTAACCGTATAAATCCC 60.238 42.308 0.00 0.00 37.17 3.85
3210 10522 6.534793 TCGTTTTCAGGTAACCGTATAAATCC 59.465 38.462 0.00 0.00 37.17 3.01
3211 10523 7.524294 TCGTTTTCAGGTAACCGTATAAATC 57.476 36.000 0.00 0.00 37.17 2.17
3301 10613 4.697756 TTCTGGACCGGCCTTGCG 62.698 66.667 14.76 0.00 37.63 4.85
3302 10614 3.056328 GTTCTGGACCGGCCTTGC 61.056 66.667 14.76 0.00 37.63 4.01
3314 10626 1.337260 CCAGTCTCCAACGAGGTTCTG 60.337 57.143 0.00 2.14 39.02 3.02
3333 10645 2.046285 CCATCACCGCCTTTGTCCC 61.046 63.158 0.00 0.00 0.00 4.46
3340 10700 2.765807 CTCCTCCCATCACCGCCT 60.766 66.667 0.00 0.00 0.00 5.52
3348 10775 2.715336 CCATTCATCTTCCTCCTCCCAT 59.285 50.000 0.00 0.00 0.00 4.00
3379 10806 0.178068 AACCATTGGAGATCGACCCG 59.822 55.000 10.37 0.00 0.00 5.28
3417 10844 3.728864 GCATTGTGCATCTAAACGTCCTG 60.729 47.826 0.00 0.00 44.26 3.86
3452 10887 3.037549 AGAAAATGGGACCAAACAGCAA 58.962 40.909 0.00 0.00 0.00 3.91
3455 10890 6.588719 TCATAAGAAAATGGGACCAAACAG 57.411 37.500 0.00 0.00 0.00 3.16
3481 10916 3.731089 TGTAAACTGGTAGTTTGACGGG 58.269 45.455 15.17 0.00 46.83 5.28


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

AutoCloner maintained by Alex Coulton.