Multiple sequence alignment - TraesCS4D01G004600

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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 TraesCS4D01G004600 chr4D 100.000 2432 0 0 1 2432 2075094 2072663 0.000000e+00 4492.0
1 TraesCS4D01G004600 chr4D 81.028 253 47 1 2098 2350 363683715 363683966 1.470000e-47 200.0
2 TraesCS4D01G004600 chrUn 88.468 1899 164 33 526 2410 47872536 47874393 0.000000e+00 2242.0
3 TraesCS4D01G004600 chrUn 88.452 1576 127 31 526 2088 47728045 47726512 0.000000e+00 1851.0
4 TraesCS4D01G004600 chrUn 85.637 369 27 12 201 545 47728422 47728056 4.940000e-97 364.0
5 TraesCS4D01G004600 chrUn 85.792 366 26 12 201 542 47872159 47872522 4.940000e-97 364.0
6 TraesCS4D01G004600 chrUn 88.889 144 12 1 56 195 47871978 47872121 8.940000e-40 174.0
7 TraesCS4D01G004600 chr4B 91.421 373 17 11 1214 1586 2410536 2410179 4.670000e-137 497.0
8 TraesCS4D01G004600 chr4B 87.915 422 18 4 1 422 2410926 2410538 1.320000e-127 466.0
9 TraesCS4D01G004600 chr4B 90.476 231 12 2 2202 2432 411852398 411852178 1.830000e-76 296.0
10 TraesCS4D01G004600 chr6D 78.450 529 93 15 912 1435 1572410 1571898 2.330000e-85 326.0
11 TraesCS4D01G004600 chr6D 82.143 252 42 3 2098 2348 68074973 68075222 1.890000e-51 213.0
12 TraesCS4D01G004600 chr6D 87.273 55 7 0 748 802 1572940 1572886 2.020000e-06 63.9
13 TraesCS4D01G004600 chr6B 89.583 240 15 2 2193 2432 187211577 187211806 1.830000e-76 296.0
14 TraesCS4D01G004600 chr3A 89.583 240 15 2 2193 2432 139327982 139328211 1.830000e-76 296.0
15 TraesCS4D01G004600 chr2A 89.583 240 15 3 2193 2432 273356971 273357200 1.830000e-76 296.0
16 TraesCS4D01G004600 chr2A 81.467 259 43 5 2098 2354 119341796 119342051 8.810000e-50 207.0
17 TraesCS4D01G004600 chr3B 89.167 240 16 2 2193 2432 810690861 810691090 8.510000e-75 291.0
18 TraesCS4D01G004600 chr1B 89.167 240 15 3 2193 2432 331815170 331815398 3.060000e-74 289.0
19 TraesCS4D01G004600 chr7B 88.750 240 17 2 2193 2432 385434202 385434431 3.960000e-73 285.0
20 TraesCS4D01G004600 chr7B 84.127 63 6 3 392 454 745137860 745137802 9.390000e-05 58.4
21 TraesCS4D01G004600 chr5A 88.750 240 17 2 2193 2432 418902562 418902791 3.960000e-73 285.0
22 TraesCS4D01G004600 chr5D 84.706 255 34 5 2099 2350 475008036 475008288 1.440000e-62 250.0
23 TraesCS4D01G004600 chr5D 80.309 259 49 2 2092 2350 269336243 269336499 6.860000e-46 195.0
24 TraesCS4D01G004600 chr2D 82.129 263 42 5 2099 2358 8321038 8321298 1.130000e-53 220.0
25 TraesCS4D01G004600 chr6A 80.657 274 47 6 2084 2354 555925321 555925591 8.810000e-50 207.0
26 TraesCS4D01G004600 chr6A 89.091 55 6 0 748 802 1056413 1056467 4.340000e-08 69.4
27 TraesCS4D01G004600 chr4A 81.081 259 48 1 2098 2356 101743650 101743393 3.170000e-49 206.0
28 TraesCS4D01G004600 chr7D 87.500 56 3 2 399 454 632157976 632157925 7.260000e-06 62.1


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 TraesCS4D01G004600 chr4D 2072663 2075094 2431 True 4492.000000 4492 100.000000 1 2432 1 chr4D.!!$R1 2431
1 TraesCS4D01G004600 chrUn 47726512 47728422 1910 True 1107.500000 1851 87.044500 201 2088 2 chrUn.!!$R1 1887
2 TraesCS4D01G004600 chrUn 47871978 47874393 2415 False 926.666667 2242 87.716333 56 2410 3 chrUn.!!$F1 2354
3 TraesCS4D01G004600 chr4B 2410179 2410926 747 True 481.500000 497 89.668000 1 1586 2 chr4B.!!$R2 1585

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
248 285 0.036164 CGGGATCCAACAGGTTGACA 59.964 55.0 15.23 0.5 42.93 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1785 0.171007 TAACCCGGCTACTCGAAACG 59.829 55.0 0.0 0.0 0.0 3.6 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 1.586154 GGGTGTCGGTGGAGCAAATG 61.586 60.000 0.00 0.00 0.00 2.32
195 200 6.986817 GTCATGTGTATATAGAACTTGCTGGT 59.013 38.462 0.00 0.00 0.00 4.00
196 201 6.986231 TCATGTGTATATAGAACTTGCTGGTG 59.014 38.462 0.00 0.00 0.00 4.17
197 202 6.294361 TGTGTATATAGAACTTGCTGGTGT 57.706 37.500 0.00 0.00 0.00 4.16
228 265 2.132762 ACTCGTGTGTTGATTCGTTCC 58.867 47.619 0.00 0.00 0.00 3.62
248 285 0.036164 CGGGATCCAACAGGTTGACA 59.964 55.000 15.23 0.50 42.93 3.58
256 293 2.353011 CCAACAGGTTGACATTGCATCC 60.353 50.000 13.47 0.00 42.93 3.51
261 298 2.756760 AGGTTGACATTGCATCCATCAC 59.243 45.455 0.00 0.00 31.46 3.06
272 309 2.476619 GCATCCATCACTAAACCGATCG 59.523 50.000 8.51 8.51 0.00 3.69
369 410 3.873952 GTCGATCCAAGAAAGAATCAGGG 59.126 47.826 0.00 0.00 0.00 4.45
370 411 3.774766 TCGATCCAAGAAAGAATCAGGGA 59.225 43.478 0.00 0.00 37.07 4.20
371 412 4.225042 TCGATCCAAGAAAGAATCAGGGAA 59.775 41.667 0.00 0.00 36.49 3.97
372 413 4.943705 CGATCCAAGAAAGAATCAGGGAAA 59.056 41.667 0.00 0.00 36.49 3.13
373 414 5.163713 CGATCCAAGAAAGAATCAGGGAAAC 60.164 44.000 0.00 0.00 36.49 2.78
374 415 5.060427 TCCAAGAAAGAATCAGGGAAACA 57.940 39.130 0.00 0.00 31.78 2.83
375 416 5.454062 TCCAAGAAAGAATCAGGGAAACAA 58.546 37.500 0.00 0.00 31.78 2.83
376 417 6.077322 TCCAAGAAAGAATCAGGGAAACAAT 58.923 36.000 0.00 0.00 31.78 2.71
389 438 3.058501 GGGAAACAATCGTGTGATTCGTT 60.059 43.478 5.51 0.00 42.94 3.85
395 444 5.657474 ACAATCGTGTGATTCGTTATAGGT 58.343 37.500 0.00 0.00 42.94 3.08
455 504 0.647410 GCTGTGTTGTCGATCCGATG 59.353 55.000 0.00 0.00 38.42 3.84
456 505 1.735700 GCTGTGTTGTCGATCCGATGA 60.736 52.381 0.00 0.00 38.42 2.92
458 507 3.190079 CTGTGTTGTCGATCCGATGAAT 58.810 45.455 0.00 0.00 38.42 2.57
459 508 3.186909 TGTGTTGTCGATCCGATGAATC 58.813 45.455 0.00 0.00 38.42 2.52
460 509 3.186909 GTGTTGTCGATCCGATGAATCA 58.813 45.455 0.00 0.00 38.42 2.57
461 510 3.616821 GTGTTGTCGATCCGATGAATCAA 59.383 43.478 0.00 0.00 38.42 2.57
462 511 3.616821 TGTTGTCGATCCGATGAATCAAC 59.383 43.478 10.68 10.68 37.90 3.18
463 512 2.459934 TGTCGATCCGATGAATCAACG 58.540 47.619 5.92 5.92 38.42 4.10
464 513 2.098443 TGTCGATCCGATGAATCAACGA 59.902 45.455 14.42 1.47 38.42 3.85
465 514 3.243401 TGTCGATCCGATGAATCAACGAT 60.243 43.478 14.42 6.10 38.42 3.73
467 516 2.663602 CGATCCGATGAATCAACGATCC 59.336 50.000 14.42 2.15 31.46 3.36
468 517 2.134201 TCCGATGAATCAACGATCCG 57.866 50.000 14.42 0.00 31.46 4.18
469 518 1.407618 TCCGATGAATCAACGATCCGT 59.592 47.619 14.42 0.00 43.97 4.69
470 519 1.787155 CCGATGAATCAACGATCCGTC 59.213 52.381 14.42 0.00 39.99 4.79
482 551 1.860950 CGATCCGTCATGTGGTCAATC 59.139 52.381 6.63 3.00 0.00 2.67
494 563 1.103398 GGTCAATCCATCCGGGCTTG 61.103 60.000 0.00 0.00 42.84 4.01
505 574 1.021968 CCGGGCTTGGTTATGCTTAC 58.978 55.000 0.00 0.00 0.00 2.34
542 611 5.705441 TCCTATTAAGTGCCACAACTTGAAG 59.295 40.000 0.00 0.00 40.58 3.02
549 648 2.157738 GCCACAACTTGAAGATGCTCT 58.842 47.619 0.00 0.00 0.00 4.09
566 665 6.765036 AGATGCTCTTCATGTTAAATCGTCAT 59.235 34.615 0.00 0.00 35.05 3.06
574 673 6.287525 TCATGTTAAATCGTCATATCTGGCA 58.712 36.000 0.00 0.00 0.00 4.92
596 696 8.150945 TGGCATTAATGGAACTTAGATAGACTC 58.849 37.037 17.02 0.00 0.00 3.36
608 708 1.067821 GATAGACTCGCTGACCCCAAG 59.932 57.143 0.00 0.00 0.00 3.61
609 709 0.970937 TAGACTCGCTGACCCCAAGG 60.971 60.000 0.00 0.00 40.04 3.61
626 726 4.021981 CCCAAGGGAACTCATCAAAACTTC 60.022 45.833 0.00 0.00 42.68 3.01
675 775 8.609176 GCTTCAATTAATTCATCCTTACGTACA 58.391 33.333 0.00 0.00 0.00 2.90
714 814 4.188462 TGTTACCACACAGACAGAAACTG 58.812 43.478 0.00 0.00 40.68 3.16
726 826 3.079578 ACAGAAACTGACATGGCATCTG 58.920 45.455 23.35 23.35 38.91 2.90
733 833 0.460811 GACATGGCATCTGACAGCGA 60.461 55.000 0.00 0.00 35.91 4.93
745 848 4.014406 TCTGACAGCGAAAGTCCTGTATA 58.986 43.478 0.00 0.00 42.01 1.47
765 868 8.702163 TGTATATGTATGTATTGAATGGAGCG 57.298 34.615 0.00 0.00 0.00 5.03
772 875 2.246719 ATTGAATGGAGCGGCTACTC 57.753 50.000 14.37 4.07 35.86 2.59
802 905 6.714810 TCAGGTCAACTTTAGTAACATGCATT 59.285 34.615 0.00 0.00 0.00 3.56
803 906 7.230510 TCAGGTCAACTTTAGTAACATGCATTT 59.769 33.333 0.00 0.00 0.00 2.32
804 907 8.511321 CAGGTCAACTTTAGTAACATGCATTTA 58.489 33.333 0.00 0.00 0.00 1.40
805 908 8.730680 AGGTCAACTTTAGTAACATGCATTTAG 58.269 33.333 0.00 0.00 0.00 1.85
806 909 7.484959 GGTCAACTTTAGTAACATGCATTTAGC 59.515 37.037 0.00 0.00 45.96 3.09
807 910 7.484959 GTCAACTTTAGTAACATGCATTTAGCC 59.515 37.037 0.00 0.00 44.83 3.93
808 911 7.175816 TCAACTTTAGTAACATGCATTTAGCCA 59.824 33.333 0.00 0.00 44.83 4.75
809 912 7.088589 ACTTTAGTAACATGCATTTAGCCAG 57.911 36.000 0.00 0.00 44.83 4.85
810 913 6.095440 ACTTTAGTAACATGCATTTAGCCAGG 59.905 38.462 0.00 0.00 44.83 4.45
811 914 3.968265 AGTAACATGCATTTAGCCAGGT 58.032 40.909 0.00 0.00 44.83 4.00
812 915 3.947834 AGTAACATGCATTTAGCCAGGTC 59.052 43.478 0.00 0.00 44.83 3.85
813 916 2.512692 ACATGCATTTAGCCAGGTCA 57.487 45.000 0.00 0.00 44.83 4.02
814 917 2.806434 ACATGCATTTAGCCAGGTCAA 58.194 42.857 0.00 0.00 44.83 3.18
815 918 2.493278 ACATGCATTTAGCCAGGTCAAC 59.507 45.455 0.00 0.00 44.83 3.18
816 919 2.584835 TGCATTTAGCCAGGTCAACT 57.415 45.000 0.00 0.00 44.83 3.16
817 920 2.875296 TGCATTTAGCCAGGTCAACTT 58.125 42.857 0.00 0.00 44.83 2.66
818 921 3.230134 TGCATTTAGCCAGGTCAACTTT 58.770 40.909 0.00 0.00 44.83 2.66
819 922 4.402829 TGCATTTAGCCAGGTCAACTTTA 58.597 39.130 0.00 0.00 44.83 1.85
820 923 4.458989 TGCATTTAGCCAGGTCAACTTTAG 59.541 41.667 0.00 0.00 44.83 1.85
821 924 4.459337 GCATTTAGCCAGGTCAACTTTAGT 59.541 41.667 0.00 0.00 37.23 2.24
822 925 5.646360 GCATTTAGCCAGGTCAACTTTAGTA 59.354 40.000 0.00 0.00 37.23 1.82
823 926 6.150474 GCATTTAGCCAGGTCAACTTTAGTAA 59.850 38.462 0.00 0.00 37.23 2.24
824 927 7.527457 CATTTAGCCAGGTCAACTTTAGTAAC 58.473 38.462 0.00 0.00 0.00 2.50
825 928 4.699925 AGCCAGGTCAACTTTAGTAACA 57.300 40.909 0.00 0.00 0.00 2.41
826 929 5.242795 AGCCAGGTCAACTTTAGTAACAT 57.757 39.130 0.00 0.00 0.00 2.71
859 962 3.780850 AGTTGCATTTAGCTAGTACCCCT 59.219 43.478 0.00 0.00 45.94 4.79
864 967 4.369182 CATTTAGCTAGTACCCCTGTTCG 58.631 47.826 0.00 0.00 0.00 3.95
867 970 3.309600 AGCTAGTACCCCTGTTCGTAT 57.690 47.619 0.00 0.00 0.00 3.06
885 988 8.582437 TGTTCGTATCCCTGTCTTATAAATAGG 58.418 37.037 0.00 0.00 0.00 2.57
913 1016 1.202698 GGTGCTCTATCCCATGGACAC 60.203 57.143 15.22 9.13 32.98 3.67
920 1023 1.673767 ATCCCATGGACACTGAGGTT 58.326 50.000 15.22 0.00 32.98 3.50
942 1045 2.493278 GTCTCTTCTCTTGCTCTCTGCT 59.507 50.000 0.00 0.00 43.37 4.24
949 1052 7.001073 TCTTCTCTTGCTCTCTGCTATATACA 58.999 38.462 0.00 0.00 43.37 2.29
950 1053 6.816134 TCTCTTGCTCTCTGCTATATACAG 57.184 41.667 6.17 6.17 43.37 2.74
951 1054 6.303054 TCTCTTGCTCTCTGCTATATACAGT 58.697 40.000 10.29 0.00 43.37 3.55
952 1055 7.454225 TCTCTTGCTCTCTGCTATATACAGTA 58.546 38.462 10.29 0.00 43.37 2.74
953 1056 7.389330 TCTCTTGCTCTCTGCTATATACAGTAC 59.611 40.741 10.29 0.00 43.37 2.73
954 1057 7.227873 TCTTGCTCTCTGCTATATACAGTACT 58.772 38.462 0.00 0.00 43.37 2.73
955 1058 8.376270 TCTTGCTCTCTGCTATATACAGTACTA 58.624 37.037 0.00 0.00 43.37 1.82
956 1059 8.919777 TTGCTCTCTGCTATATACAGTACTAA 57.080 34.615 0.00 0.00 43.37 2.24
957 1060 9.521841 TTGCTCTCTGCTATATACAGTACTAAT 57.478 33.333 0.00 0.00 43.37 1.73
1046 1149 0.685097 ACTGTGTTAGCGGTGATGGT 59.315 50.000 0.00 0.00 0.00 3.55
1104 1207 1.430632 CATGACGGCATGCAAGGAC 59.569 57.895 20.25 8.91 44.76 3.85
1185 1288 4.057428 GCCGACTGCAGTCCGACT 62.057 66.667 35.07 6.62 41.86 4.18
1255 1358 1.902918 TGCTTGAGGGCGTGCAAAT 60.903 52.632 0.00 0.00 32.12 2.32
1317 1420 1.585297 GCAATTGCAGCAACCAAAGT 58.415 45.000 25.36 0.00 41.59 2.66
1329 1436 0.107831 ACCAAAGTAGCTTGTGCGGA 59.892 50.000 0.00 0.00 45.42 5.54
1331 1438 1.512926 CAAAGTAGCTTGTGCGGAGT 58.487 50.000 0.00 0.00 45.42 3.85
1349 1456 4.753877 CGTCTGCGGCGAGTCGAA 62.754 66.667 18.61 0.00 0.00 3.71
1511 1618 4.147449 CTCATCGGCGCCTCACCA 62.147 66.667 26.68 2.85 0.00 4.17
1539 1646 4.335416 CCACATGTCAGTGAAATAAGGGT 58.665 43.478 0.00 0.00 42.05 4.34
1572 1679 8.556194 TGCAAATCCTTAATTACGTGCTATAAG 58.444 33.333 0.00 1.99 32.28 1.73
1576 1683 8.603242 ATCCTTAATTACGTGCTATAAGGTTG 57.397 34.615 20.83 6.17 42.03 3.77
1601 1708 7.285401 TGTGAAACTTAGGAGCTTCATTTTCTT 59.715 33.333 0.00 0.00 39.44 2.52
1604 1711 6.809630 ACTTAGGAGCTTCATTTTCTTCAC 57.190 37.500 0.00 0.00 0.00 3.18
1652 1759 6.603201 TGTTTTCCCTTTAGCATCTTGATAGG 59.397 38.462 0.00 0.00 0.00 2.57
1657 1764 7.867921 TCCCTTTAGCATCTTGATAGGTTTTA 58.132 34.615 0.00 0.00 0.00 1.52
1661 1768 9.125026 CTTTAGCATCTTGATAGGTTTTACCAT 57.875 33.333 0.00 0.00 41.95 3.55
1662 1769 9.474313 TTTAGCATCTTGATAGGTTTTACCATT 57.526 29.630 0.00 0.00 41.95 3.16
1668 1775 8.106247 TCTTGATAGGTTTTACCATTGTGTTC 57.894 34.615 0.00 0.00 41.95 3.18
1671 1778 9.575868 TTGATAGGTTTTACCATTGTGTTCTTA 57.424 29.630 0.00 0.00 41.95 2.10
1676 1783 9.758651 AGGTTTTACCATTGTGTTCTTAATTTC 57.241 29.630 0.00 0.00 41.95 2.17
1679 1786 9.672086 TTTTACCATTGTGTTCTTAATTTCTCG 57.328 29.630 0.00 0.00 0.00 4.04
1683 1790 7.860872 ACCATTGTGTTCTTAATTTCTCGTTTC 59.139 33.333 0.00 0.00 0.00 2.78
1695 1802 1.973281 TCGTTTCGAGTAGCCGGGT 60.973 57.895 12.58 12.58 0.00 5.28
1696 1803 1.080298 CGTTTCGAGTAGCCGGGTT 60.080 57.895 13.43 0.00 0.00 4.11
1697 1804 0.171007 CGTTTCGAGTAGCCGGGTTA 59.829 55.000 13.43 0.00 0.00 2.85
1698 1805 1.633561 GTTTCGAGTAGCCGGGTTAC 58.366 55.000 13.43 12.62 0.00 2.50
1699 1806 1.203287 GTTTCGAGTAGCCGGGTTACT 59.797 52.381 21.66 21.66 32.52 2.24
1700 1807 2.418368 TTCGAGTAGCCGGGTTACTA 57.582 50.000 21.56 6.49 30.12 1.82
1701 1808 2.418368 TCGAGTAGCCGGGTTACTAA 57.582 50.000 21.56 11.49 30.12 2.24
1702 1809 2.936202 TCGAGTAGCCGGGTTACTAAT 58.064 47.619 21.56 0.00 30.12 1.73
1774 1882 7.897575 ATTTTGTTGCTTCAGTTTACAAACA 57.102 28.000 7.53 0.00 41.30 2.83
1820 1930 6.887002 ACTCCTCCAAGTAAAATTTGAGATCC 59.113 38.462 0.00 0.00 0.00 3.36
1907 2018 5.441718 TGGAGATCAGCTTTATCCAACTT 57.558 39.130 7.21 0.00 37.12 2.66
1912 2023 7.201956 GGAGATCAGCTTTATCCAACTTCTCTA 60.202 40.741 0.00 0.00 0.00 2.43
1977 2088 7.595819 AAGTTCTCGGAGATCATCTTTATCT 57.404 36.000 16.22 0.00 36.40 1.98
2008 2120 6.564709 TGGTATGCTAAGATTGAATCATGC 57.435 37.500 8.03 8.68 0.00 4.06
2012 2124 8.396390 GGTATGCTAAGATTGAATCATGCATAG 58.604 37.037 25.10 13.94 40.68 2.23
2080 2192 2.750166 CACACAACACACACACCCTTAA 59.250 45.455 0.00 0.00 0.00 1.85
2091 2203 9.796180 ACACACACACCCTTAAAGTATATTTAA 57.204 29.630 0.00 0.00 0.00 1.52
2135 2247 1.790623 CCGCATATTAACTTCGACCGG 59.209 52.381 0.00 0.00 0.00 5.28
2145 2257 1.411612 ACTTCGACCGGAGTCAAACTT 59.588 47.619 9.46 0.00 43.73 2.66
2153 2265 4.995487 GACCGGAGTCAAACTTCATAAAGT 59.005 41.667 9.46 0.00 44.01 2.66
2247 2361 8.388853 CGATGATGAATCTGATGGTATTGATTC 58.611 37.037 0.00 0.00 42.77 2.52
2253 2367 8.777413 TGAATCTGATGGTATTGATTCGATTTC 58.223 33.333 0.00 0.00 44.35 2.17
2350 2464 5.814188 GTCGAGTAAATAAAAACGGAGGGAT 59.186 40.000 0.00 0.00 0.00 3.85
2353 2467 7.492344 TCGAGTAAATAAAAACGGAGGGATTAC 59.508 37.037 0.00 0.00 0.00 1.89
2360 2474 4.482952 AAACGGAGGGATTACTAGGTTG 57.517 45.455 0.00 0.00 0.00 3.77
2363 2477 3.956848 ACGGAGGGATTACTAGGTTGTAC 59.043 47.826 0.00 0.00 0.00 2.90
2410 2524 3.928727 ATCATCAGCCAACAAACTGTG 57.071 42.857 0.00 0.00 35.37 3.66
2411 2525 1.955778 TCATCAGCCAACAAACTGTGG 59.044 47.619 0.00 0.00 35.37 4.17
2412 2526 1.000060 CATCAGCCAACAAACTGTGGG 60.000 52.381 0.00 0.00 44.50 4.61
2413 2527 0.257328 TCAGCCAACAAACTGTGGGA 59.743 50.000 4.29 0.00 44.46 4.37
2414 2528 1.110442 CAGCCAACAAACTGTGGGAA 58.890 50.000 4.29 0.00 44.46 3.97
2415 2529 1.067516 CAGCCAACAAACTGTGGGAAG 59.932 52.381 4.29 0.00 44.46 3.46
2416 2530 0.389025 GCCAACAAACTGTGGGAAGG 59.611 55.000 4.29 0.00 44.46 3.46
2417 2531 2.026905 GCCAACAAACTGTGGGAAGGA 61.027 52.381 4.29 0.00 44.46 3.36
2418 2532 2.597455 CCAACAAACTGTGGGAAGGAT 58.403 47.619 0.00 0.00 44.46 3.24
2419 2533 3.761897 CCAACAAACTGTGGGAAGGATA 58.238 45.455 0.00 0.00 44.46 2.59
2420 2534 4.344104 CCAACAAACTGTGGGAAGGATAT 58.656 43.478 0.00 0.00 44.46 1.63
2421 2535 4.772100 CCAACAAACTGTGGGAAGGATATT 59.228 41.667 0.00 0.00 44.46 1.28
2422 2536 5.245977 CCAACAAACTGTGGGAAGGATATTT 59.754 40.000 0.00 0.00 44.46 1.40
2423 2537 6.239572 CCAACAAACTGTGGGAAGGATATTTT 60.240 38.462 0.00 0.00 44.46 1.82
2424 2538 6.345096 ACAAACTGTGGGAAGGATATTTTG 57.655 37.500 0.00 0.00 0.00 2.44
2425 2539 5.838521 ACAAACTGTGGGAAGGATATTTTGT 59.161 36.000 0.00 0.00 31.51 2.83
2426 2540 5.982890 AACTGTGGGAAGGATATTTTGTG 57.017 39.130 0.00 0.00 0.00 3.33
2427 2541 4.344104 ACTGTGGGAAGGATATTTTGTGG 58.656 43.478 0.00 0.00 0.00 4.17
2428 2542 3.096092 TGTGGGAAGGATATTTTGTGGC 58.904 45.455 0.00 0.00 0.00 5.01
2429 2543 2.430694 GTGGGAAGGATATTTTGTGGCC 59.569 50.000 0.00 0.00 0.00 5.36
2430 2544 2.043664 TGGGAAGGATATTTTGTGGCCA 59.956 45.455 0.00 0.00 0.00 5.36
2431 2545 2.695147 GGGAAGGATATTTTGTGGCCAG 59.305 50.000 5.11 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.438021 TGGCAAGACTTGTGGAGTAAGT 59.562 45.455 16.39 0.00 39.19 2.24
52 53 2.808543 GTGGCAAGACTTGTGGAGTAAG 59.191 50.000 16.39 0.00 39.19 2.34
53 54 2.438021 AGTGGCAAGACTTGTGGAGTAA 59.562 45.455 16.39 0.00 39.19 2.24
54 55 2.047061 AGTGGCAAGACTTGTGGAGTA 58.953 47.619 16.39 0.00 39.19 2.59
207 244 2.155155 GGAACGAATCAACACACGAGTC 59.845 50.000 0.00 0.00 0.00 3.36
228 265 0.676782 GTCAACCTGTTGGATCCCGG 60.677 60.000 9.90 7.10 40.78 5.73
248 285 3.884895 TCGGTTTAGTGATGGATGCAAT 58.115 40.909 0.00 0.00 0.00 3.56
256 293 6.089551 GGATATGAACGATCGGTTTAGTGATG 59.910 42.308 20.98 0.00 39.50 3.07
261 298 5.983720 ACTTGGATATGAACGATCGGTTTAG 59.016 40.000 20.98 5.34 39.50 1.85
272 309 6.170506 TCACTTGGTGTACTTGGATATGAAC 58.829 40.000 0.00 0.00 34.79 3.18
369 410 7.117454 CCTATAACGAATCACACGATTGTTTC 58.883 38.462 0.00 0.00 42.06 2.78
370 411 6.592607 ACCTATAACGAATCACACGATTGTTT 59.407 34.615 0.00 0.00 42.06 2.83
371 412 6.103997 ACCTATAACGAATCACACGATTGTT 58.896 36.000 0.00 0.00 42.06 2.83
372 413 5.657474 ACCTATAACGAATCACACGATTGT 58.343 37.500 0.00 0.00 42.06 2.71
373 414 6.410845 CAACCTATAACGAATCACACGATTG 58.589 40.000 0.00 0.00 42.06 2.67
374 415 5.522460 CCAACCTATAACGAATCACACGATT 59.478 40.000 0.00 0.00 44.75 3.34
375 416 5.047847 CCAACCTATAACGAATCACACGAT 58.952 41.667 0.00 0.00 34.70 3.73
376 417 4.158209 TCCAACCTATAACGAATCACACGA 59.842 41.667 0.00 0.00 34.70 4.35
389 438 2.969950 CGGGAACTCCATCCAACCTATA 59.030 50.000 0.00 0.00 41.55 1.31
395 444 1.195115 CTCTCGGGAACTCCATCCAA 58.805 55.000 0.00 0.00 41.55 3.53
455 504 2.285220 CCACATGACGGATCGTTGATTC 59.715 50.000 0.00 0.00 41.37 2.52
456 505 2.279741 CCACATGACGGATCGTTGATT 58.720 47.619 0.00 0.00 41.37 2.57
458 507 0.606096 ACCACATGACGGATCGTTGA 59.394 50.000 12.07 0.00 41.37 3.18
459 508 0.999406 GACCACATGACGGATCGTTG 59.001 55.000 12.07 0.00 41.37 4.10
460 509 0.606096 TGACCACATGACGGATCGTT 59.394 50.000 12.07 0.00 41.37 3.85
461 510 0.606096 TTGACCACATGACGGATCGT 59.394 50.000 12.07 0.00 45.10 3.73
462 511 1.860950 GATTGACCACATGACGGATCG 59.139 52.381 12.07 0.00 0.00 3.69
463 512 2.213499 GGATTGACCACATGACGGATC 58.787 52.381 12.07 5.57 38.79 3.36
464 513 1.559219 TGGATTGACCACATGACGGAT 59.441 47.619 12.07 0.00 44.64 4.18
465 514 0.980423 TGGATTGACCACATGACGGA 59.020 50.000 12.07 0.00 44.64 4.69
482 551 1.455383 GCATAACCAAGCCCGGATGG 61.455 60.000 16.48 16.48 42.60 3.51
487 556 0.655733 CGTAAGCATAACCAAGCCCG 59.344 55.000 0.00 0.00 0.00 6.13
505 574 7.281484 GCACTTAATAGGACGATTTAACATCG 58.719 38.462 14.42 14.42 46.02 3.84
522 591 5.565439 GCATCTTCAAGTTGTGGCACTTAAT 60.565 40.000 19.83 3.26 35.10 1.40
527 596 1.610522 AGCATCTTCAAGTTGTGGCAC 59.389 47.619 11.55 11.55 0.00 5.01
542 611 6.349973 TGACGATTTAACATGAAGAGCATC 57.650 37.500 0.00 0.00 34.15 3.91
549 648 6.765512 TGCCAGATATGACGATTTAACATGAA 59.234 34.615 0.00 0.00 0.00 2.57
551 650 6.544038 TGCCAGATATGACGATTTAACATG 57.456 37.500 0.00 0.00 0.00 3.21
574 673 8.085296 CAGCGAGTCTATCTAAGTTCCATTAAT 58.915 37.037 0.00 0.00 0.00 1.40
596 696 2.359975 GTTCCCTTGGGGTCAGCG 60.360 66.667 5.78 0.00 44.74 5.18
616 716 5.562890 GCCTTGAGCTTAACGAAGTTTTGAT 60.563 40.000 0.00 0.00 44.48 2.57
618 718 3.975035 GCCTTGAGCTTAACGAAGTTTTG 59.025 43.478 0.00 0.00 44.48 2.44
626 726 1.136336 GTCAACGCCTTGAGCTTAACG 60.136 52.381 0.00 0.00 37.06 3.18
641 741 6.251376 GGATGAATTAATTGAAGCGTGTCAAC 59.749 38.462 5.17 0.00 40.22 3.18
661 761 2.025898 TGCCGATGTACGTAAGGATGA 58.974 47.619 11.97 0.00 46.39 2.92
675 775 2.042686 ACATGTATGCAAGTGCCGAT 57.957 45.000 0.00 0.00 41.18 4.18
676 776 1.819928 AACATGTATGCAAGTGCCGA 58.180 45.000 0.00 0.00 41.18 5.54
714 814 0.460811 TCGCTGTCAGATGCCATGTC 60.461 55.000 3.32 0.00 0.00 3.06
726 826 4.683832 ACATATACAGGACTTTCGCTGTC 58.316 43.478 0.00 0.00 32.70 3.51
745 848 3.753272 GCCGCTCCATTCAATACATACAT 59.247 43.478 0.00 0.00 0.00 2.29
765 868 1.174783 TGACCTGAAGACGAGTAGCC 58.825 55.000 0.00 0.00 0.00 3.93
772 875 5.981315 TGTTACTAAAGTTGACCTGAAGACG 59.019 40.000 0.00 0.00 0.00 4.18
802 905 6.177310 TGTTACTAAAGTTGACCTGGCTAA 57.823 37.500 0.00 0.00 0.00 3.09
803 906 5.811796 TGTTACTAAAGTTGACCTGGCTA 57.188 39.130 0.00 0.00 0.00 3.93
804 907 4.699925 TGTTACTAAAGTTGACCTGGCT 57.300 40.909 0.00 0.00 0.00 4.75
805 908 4.156008 CCATGTTACTAAAGTTGACCTGGC 59.844 45.833 0.00 0.00 29.57 4.85
806 909 5.313712 ACCATGTTACTAAAGTTGACCTGG 58.686 41.667 13.82 13.82 36.14 4.45
807 910 6.092259 GCTACCATGTTACTAAAGTTGACCTG 59.908 42.308 0.00 0.00 0.00 4.00
808 911 6.013639 AGCTACCATGTTACTAAAGTTGACCT 60.014 38.462 0.00 0.00 0.00 3.85
809 912 6.171213 AGCTACCATGTTACTAAAGTTGACC 58.829 40.000 0.00 0.00 0.00 4.02
810 913 7.816031 TGTAGCTACCATGTTACTAAAGTTGAC 59.184 37.037 21.01 0.00 0.00 3.18
811 914 7.898918 TGTAGCTACCATGTTACTAAAGTTGA 58.101 34.615 21.01 0.00 0.00 3.18
812 915 8.542497 TTGTAGCTACCATGTTACTAAAGTTG 57.458 34.615 21.01 0.00 0.00 3.16
813 916 8.373220 ACTTGTAGCTACCATGTTACTAAAGTT 58.627 33.333 21.01 3.00 0.00 2.66
814 917 7.904205 ACTTGTAGCTACCATGTTACTAAAGT 58.096 34.615 21.01 15.28 0.00 2.66
815 918 8.656849 CAACTTGTAGCTACCATGTTACTAAAG 58.343 37.037 21.01 14.70 0.00 1.85
816 919 7.118680 GCAACTTGTAGCTACCATGTTACTAAA 59.881 37.037 21.01 3.86 0.00 1.85
817 920 6.592607 GCAACTTGTAGCTACCATGTTACTAA 59.407 38.462 21.01 4.56 0.00 2.24
818 921 6.103997 GCAACTTGTAGCTACCATGTTACTA 58.896 40.000 21.01 0.00 0.00 1.82
819 922 4.935808 GCAACTTGTAGCTACCATGTTACT 59.064 41.667 21.01 0.61 0.00 2.24
820 923 4.693566 TGCAACTTGTAGCTACCATGTTAC 59.306 41.667 21.01 16.00 0.00 2.50
821 924 4.900684 TGCAACTTGTAGCTACCATGTTA 58.099 39.130 21.01 6.74 0.00 2.41
822 925 3.750371 TGCAACTTGTAGCTACCATGTT 58.250 40.909 21.01 17.87 0.00 2.71
823 926 3.417069 TGCAACTTGTAGCTACCATGT 57.583 42.857 21.01 13.38 0.00 3.21
824 927 4.970662 AATGCAACTTGTAGCTACCATG 57.029 40.909 21.01 14.36 0.00 3.66
825 928 5.066505 GCTAAATGCAACTTGTAGCTACCAT 59.933 40.000 21.01 12.46 42.31 3.55
826 929 4.394920 GCTAAATGCAACTTGTAGCTACCA 59.605 41.667 21.01 9.50 42.31 3.25
859 962 8.582437 CCTATTTATAAGACAGGGATACGAACA 58.418 37.037 0.00 0.00 37.60 3.18
913 1016 3.006752 AGCAAGAGAAGAGACAACCTCAG 59.993 47.826 0.00 0.00 44.40 3.35
920 1023 2.230992 GCAGAGAGCAAGAGAAGAGACA 59.769 50.000 0.00 0.00 44.79 3.41
997 1100 1.006337 TTTGTGAAGGCGCCATTGC 60.006 52.632 31.54 16.34 0.00 3.56
998 1101 0.314935 ACTTTGTGAAGGCGCCATTG 59.685 50.000 31.54 11.55 37.19 2.82
1038 1141 0.598065 GCACAAGGACAACCATCACC 59.402 55.000 0.00 0.00 38.94 4.02
1046 1149 1.529010 CCCAGCAGCACAAGGACAA 60.529 57.895 0.00 0.00 0.00 3.18
1109 1212 4.600576 TCGAGTTGCACTGCGGCA 62.601 61.111 1.29 1.29 43.19 5.69
1112 1215 3.030308 ACGTCGAGTTGCACTGCG 61.030 61.111 0.00 0.00 0.00 5.18
1191 1294 3.859414 GAGAGGCAGCCCGAGCAT 61.859 66.667 8.22 0.00 43.56 3.79
1317 1420 1.211969 GACGACTCCGCACAAGCTA 59.788 57.895 0.00 0.00 39.95 3.32
1329 1436 4.104417 GACTCGCCGCAGACGACT 62.104 66.667 0.00 0.00 43.93 4.18
1511 1618 0.756294 TCACTGACATGTGGGTCGTT 59.244 50.000 1.15 0.00 40.72 3.85
1572 1679 4.134563 TGAAGCTCCTAAGTTTCACAACC 58.865 43.478 1.24 0.00 44.69 3.77
1601 1708 5.136068 TGCCCCTAATGATTATTTGGTGA 57.864 39.130 9.28 0.00 37.45 4.02
1604 1711 5.867903 TGTTGCCCCTAATGATTATTTGG 57.132 39.130 4.06 4.06 38.44 3.28
1657 1764 6.877611 ACGAGAAATTAAGAACACAATGGT 57.122 33.333 0.00 0.00 0.00 3.55
1661 1768 7.236674 TCGAAACGAGAAATTAAGAACACAA 57.763 32.000 0.00 0.00 0.00 3.33
1662 1769 6.831727 TCGAAACGAGAAATTAAGAACACA 57.168 33.333 0.00 0.00 0.00 3.72
1678 1785 0.171007 TAACCCGGCTACTCGAAACG 59.829 55.000 0.00 0.00 0.00 3.60
1679 1786 1.203287 AGTAACCCGGCTACTCGAAAC 59.797 52.381 8.29 0.00 0.00 2.78
1683 1790 3.722728 AATTAGTAACCCGGCTACTCG 57.277 47.619 15.54 0.00 31.98 4.18
1686 1793 8.442632 AATTTCTTAATTAGTAACCCGGCTAC 57.557 34.615 0.00 0.00 32.25 3.58
1688 1795 9.281371 GATAATTTCTTAATTAGTAACCCGGCT 57.719 33.333 0.00 0.00 39.05 5.52
1689 1796 9.281371 AGATAATTTCTTAATTAGTAACCCGGC 57.719 33.333 0.00 0.00 39.05 6.13
1832 1942 3.694072 GCTTGGCCATGACATACAAGTAA 59.306 43.478 22.21 0.00 40.35 2.24
1848 1958 4.164988 AGGGGATGACATATATAGCTTGGC 59.835 45.833 0.00 0.00 0.00 4.52
1894 2005 9.717942 ATGACATATAGAGAAGTTGGATAAAGC 57.282 33.333 0.00 0.00 0.00 3.51
1907 2018 7.423844 ACAGTTTGGTCATGACATATAGAGA 57.576 36.000 26.47 1.56 0.00 3.10
1936 2047 3.111741 ACTTACTTGGAGGGGTACGAT 57.888 47.619 0.00 0.00 0.00 3.73
1989 2101 8.678199 CATCTATGCATGATTCAATCTTAGCAT 58.322 33.333 20.67 20.67 43.16 3.79
2008 2120 7.871463 TCTTCTGTCTAATCACATGCATCTATG 59.129 37.037 0.00 0.00 0.00 2.23
2012 2124 5.051173 CGTCTTCTGTCTAATCACATGCATC 60.051 44.000 0.00 0.00 0.00 3.91
2048 2160 4.177026 GTGTGTTGTGTGTTTAATGCCAA 58.823 39.130 0.00 0.00 0.00 4.52
2059 2171 1.173043 AAGGGTGTGTGTGTTGTGTG 58.827 50.000 0.00 0.00 0.00 3.82
2091 2203 9.264719 CGGACTAAATAAAAACGGAGGTAATAT 57.735 33.333 0.00 0.00 0.00 1.28
2094 2206 5.351189 GCGGACTAAATAAAAACGGAGGTAA 59.649 40.000 0.00 0.00 0.00 2.85
2096 2208 3.686241 GCGGACTAAATAAAAACGGAGGT 59.314 43.478 0.00 0.00 0.00 3.85
2097 2209 3.685756 TGCGGACTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
2108 2220 6.423001 GGTCGAAGTTAATATGCGGACTAAAT 59.577 38.462 0.00 0.00 0.00 1.40
2112 2224 3.714391 GGTCGAAGTTAATATGCGGACT 58.286 45.455 0.00 0.00 0.00 3.85
2129 2241 2.080286 ATGAAGTTTGACTCCGGTCG 57.920 50.000 0.00 0.00 44.83 4.79
2145 2257 9.621629 TTCTAGAAACTTGGTCAAACTTTATGA 57.378 29.630 1.68 0.00 0.00 2.15
2205 2317 9.814899 ATTCATCATCGAATATATTCTCACCTC 57.185 33.333 20.47 0.00 33.82 3.85
2206 2318 9.814899 GATTCATCATCGAATATATTCTCACCT 57.185 33.333 20.47 3.22 35.74 4.00
2222 2336 8.388853 CGAATCAATACCATCAGATTCATCATC 58.611 37.037 12.68 0.00 43.96 2.92
2279 2393 8.807581 CAAACTTTACAAACTTTGACCAAGATC 58.192 33.333 8.55 0.00 36.21 2.75
2283 2397 7.662897 AGTCAAACTTTACAAACTTTGACCAA 58.337 30.769 22.51 0.00 44.13 3.67
2327 2441 5.404466 TCCCTCCGTTTTTATTTACTCGA 57.596 39.130 0.00 0.00 0.00 4.04
2328 2442 6.673154 AATCCCTCCGTTTTTATTTACTCG 57.327 37.500 0.00 0.00 0.00 4.18
2350 2464 9.316730 CAAACACACTTAAGTACAACCTAGTAA 57.683 33.333 8.04 0.00 0.00 2.24
2353 2467 7.781548 ACAAACACACTTAAGTACAACCTAG 57.218 36.000 8.04 0.00 0.00 3.02
2390 2504 2.559668 CCACAGTTTGTTGGCTGATGAT 59.440 45.455 0.00 0.00 36.62 2.45
2395 2509 1.067516 CTTCCCACAGTTTGTTGGCTG 59.932 52.381 0.00 0.00 33.53 4.85
2410 2524 2.695147 CTGGCCACAAAATATCCTTCCC 59.305 50.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.