Multiple sequence alignment - TraesCS3D01G117300

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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 TraesCS3D01G117300 chr3D 100.000 4762 0 0 1 4762 70724322 70729083 0.000000e+00 8794
1 TraesCS3D01G117300 chr3D 98.516 1348 12 4 2372 3715 510300220 510301563 0.000000e+00 2372
2 TraesCS3D01G117300 chr3D 90.546 1428 80 27 1836 3218 71496610 71495193 0.000000e+00 1838
3 TraesCS3D01G117300 chr3D 92.593 108 4 4 4064 4170 19535175 19535071 8.250000e-33 152
4 TraesCS3D01G117300 chr3D 91.667 108 5 4 4064 4170 19360322 19360218 3.840000e-31 147
5 TraesCS3D01G117300 chr3A 91.126 3099 138 53 1145 4170 82440137 82443171 0.000000e+00 4072
6 TraesCS3D01G117300 chr3A 92.242 1289 71 17 1836 3102 83725419 83724138 0.000000e+00 1799
7 TraesCS3D01G117300 chr3A 86.719 1152 79 27 1 1126 82438983 82440086 0.000000e+00 1212
8 TraesCS3D01G117300 chr3B 92.314 2368 96 30 1833 4170 116191294 116193605 0.000000e+00 3286
9 TraesCS3D01G117300 chr3B 86.784 1536 94 44 2265 3763 117553667 117552204 0.000000e+00 1611
10 TraesCS3D01G117300 chr3B 89.039 1113 68 27 726 1820 116190097 116191173 0.000000e+00 1330
11 TraesCS3D01G117300 chr3B 99.129 574 5 0 4189 4762 613815716 613815143 0.000000e+00 1033
12 TraesCS3D01G117300 chr3B 91.009 634 42 10 1 625 116189374 116190001 0.000000e+00 841
13 TraesCS3D01G117300 chr3B 90.244 369 16 6 1875 2241 117553999 117553649 9.330000e-127 464
14 TraesCS3D01G117300 chr3B 97.802 91 2 0 4092 4182 117554477 117554387 1.770000e-34 158
15 TraesCS3D01G117300 chr4D 98.583 1341 14 3 2375 3715 497616139 497614804 0.000000e+00 2366
16 TraesCS3D01G117300 chr7D 99.826 575 0 1 4189 4762 37274712 37275286 0.000000e+00 1055
17 TraesCS3D01G117300 chr7D 99.477 574 3 0 4189 4762 219843678 219843105 0.000000e+00 1044
18 TraesCS3D01G117300 chr7D 98.791 579 7 0 4184 4762 291502563 291501985 0.000000e+00 1031
19 TraesCS3D01G117300 chr2D 99.475 571 3 0 4192 4762 503850988 503851558 0.000000e+00 1038
20 TraesCS3D01G117300 chr2D 99.129 574 5 0 4189 4762 422778800 422778227 0.000000e+00 1033
21 TraesCS3D01G117300 chr2D 80.802 349 49 12 1278 1618 6722809 6723147 1.700000e-64 257
22 TraesCS3D01G117300 chr4A 98.962 578 6 0 4185 4762 85145657 85145080 0.000000e+00 1035
23 TraesCS3D01G117300 chr4A 99.129 574 5 0 4189 4762 84922888 84923461 0.000000e+00 1033
24 TraesCS3D01G117300 chr4A 98.780 82 1 0 4089 4170 137968564 137968483 3.840000e-31 147
25 TraesCS3D01G117300 chr5D 99.299 571 4 0 4192 4762 384072604 384073174 0.000000e+00 1033
26 TraesCS3D01G117300 chr4B 77.654 358 63 11 1288 1638 579786563 579786910 8.080000e-48 202
27 TraesCS3D01G117300 chr4B 89.908 109 8 3 4076 4184 631578956 631578851 2.310000e-28 137
28 TraesCS3D01G117300 chr1A 96.875 96 1 2 4089 4184 132795544 132795451 4.930000e-35 159
29 TraesCS3D01G117300 chr1A 96.703 91 0 3 4082 4170 490796168 490796257 1.070000e-31 148
30 TraesCS3D01G117300 chr1D 95.876 97 2 2 4089 4184 478271240 478271335 6.380000e-34 156
31 TraesCS3D01G117300 chr6A 94.681 94 4 1 4094 4187 7983737 7983645 1.380000e-30 145


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 TraesCS3D01G117300 chr3D 70724322 70729083 4761 False 8794.000000 8794 100.000000 1 4762 1 chr3D.!!$F1 4761
1 TraesCS3D01G117300 chr3D 510300220 510301563 1343 False 2372.000000 2372 98.516000 2372 3715 1 chr3D.!!$F2 1343
2 TraesCS3D01G117300 chr3D 71495193 71496610 1417 True 1838.000000 1838 90.546000 1836 3218 1 chr3D.!!$R3 1382
3 TraesCS3D01G117300 chr3A 82438983 82443171 4188 False 2642.000000 4072 88.922500 1 4170 2 chr3A.!!$F1 4169
4 TraesCS3D01G117300 chr3A 83724138 83725419 1281 True 1799.000000 1799 92.242000 1836 3102 1 chr3A.!!$R1 1266
5 TraesCS3D01G117300 chr3B 116189374 116193605 4231 False 1819.000000 3286 90.787333 1 4170 3 chr3B.!!$F1 4169
6 TraesCS3D01G117300 chr3B 613815143 613815716 573 True 1033.000000 1033 99.129000 4189 4762 1 chr3B.!!$R1 573
7 TraesCS3D01G117300 chr3B 117552204 117554477 2273 True 744.333333 1611 91.610000 1875 4182 3 chr3B.!!$R2 2307
8 TraesCS3D01G117300 chr4D 497614804 497616139 1335 True 2366.000000 2366 98.583000 2375 3715 1 chr4D.!!$R1 1340
9 TraesCS3D01G117300 chr7D 37274712 37275286 574 False 1055.000000 1055 99.826000 4189 4762 1 chr7D.!!$F1 573
10 TraesCS3D01G117300 chr7D 219843105 219843678 573 True 1044.000000 1044 99.477000 4189 4762 1 chr7D.!!$R1 573
11 TraesCS3D01G117300 chr7D 291501985 291502563 578 True 1031.000000 1031 98.791000 4184 4762 1 chr7D.!!$R2 578
12 TraesCS3D01G117300 chr2D 503850988 503851558 570 False 1038.000000 1038 99.475000 4192 4762 1 chr2D.!!$F2 570
13 TraesCS3D01G117300 chr2D 422778227 422778800 573 True 1033.000000 1033 99.129000 4189 4762 1 chr2D.!!$R1 573
14 TraesCS3D01G117300 chr4A 85145080 85145657 577 True 1035.000000 1035 98.962000 4185 4762 1 chr4A.!!$R1 577
15 TraesCS3D01G117300 chr4A 84922888 84923461 573 False 1033.000000 1033 99.129000 4189 4762 1 chr4A.!!$F1 573
16 TraesCS3D01G117300 chr5D 384072604 384073174 570 False 1033.000000 1033 99.299000 4192 4762 1 chr5D.!!$F1 570

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
627 641 0.033504 ATTGAAGTCGTCTGCACCGT 59.966 50.0 0.0 0.0 0.0 4.83 F
731 763 0.690762 CCGGGGTTTCTCTCTTTCCA 59.309 55.0 0.0 0.0 0.0 3.53 F
1750 1837 0.102481 CTACCAGATTCCCACCGTCG 59.898 60.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1819 0.323633 TCGACGGTGGGAATCTGGTA 60.324 55.000 0.00 0.00 0.00 3.25 R
1900 2097 0.393537 CAGGGTGGCTCATGAGGAAC 60.394 60.000 23.89 7.53 0.00 3.62 R
3768 4078 1.064463 GGTGAGATGCCCCTCAATTCA 60.064 52.381 6.70 0.00 43.94 2.57 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
81 83 5.649831 AGCTAATCAAGAAGCAACTAAAGGG 59.350 40.000 0.00 0.00 41.32 3.95
132 134 1.846648 GTAATCAGGATCGTGCGCG 59.153 57.895 14.79 14.79 39.92 6.86
178 181 2.125912 GCTCACAGATCGTGCCGT 60.126 61.111 11.34 0.00 45.92 5.68
208 212 0.486879 TTTCAAGGGGGTCCATGCTT 59.513 50.000 0.00 0.00 32.17 3.91
317 324 4.081142 CCCCATGGTTTTTACAGGGAATTC 60.081 45.833 11.73 0.00 42.09 2.17
354 361 3.248602 CCACTAGCGCAGGAAAATGATAC 59.751 47.826 11.47 0.00 0.00 2.24
382 393 2.425143 ATGCTCCATGATTCGGTTGT 57.575 45.000 0.00 0.00 0.00 3.32
417 430 3.444034 CAGGAGACGACCTACTTGATTCA 59.556 47.826 0.00 0.00 38.32 2.57
507 521 3.830744 TCGGAAGAGGAACACAAAAGA 57.169 42.857 0.00 0.00 34.84 2.52
509 523 3.875134 TCGGAAGAGGAACACAAAAGAAC 59.125 43.478 0.00 0.00 34.84 3.01
511 525 4.260784 CGGAAGAGGAACACAAAAGAACAG 60.261 45.833 0.00 0.00 0.00 3.16
515 529 6.834168 AGAGGAACACAAAAGAACAGAAAA 57.166 33.333 0.00 0.00 0.00 2.29
516 530 7.227049 AGAGGAACACAAAAGAACAGAAAAA 57.773 32.000 0.00 0.00 0.00 1.94
557 571 4.026804 GTCAGTGAGTCAACAAACACGTAG 60.027 45.833 0.00 0.00 38.15 3.51
608 622 9.074576 CATCATTCTTAATCCCATTCTGATCAA 57.925 33.333 0.00 0.00 0.00 2.57
609 623 9.824216 ATCATTCTTAATCCCATTCTGATCAAT 57.176 29.630 0.00 0.00 0.00 2.57
623 637 3.663025 TGATCAATTGAAGTCGTCTGCA 58.337 40.909 13.09 0.00 0.00 4.41
625 639 2.143122 TCAATTGAAGTCGTCTGCACC 58.857 47.619 5.45 0.00 0.00 5.01
626 640 1.136252 CAATTGAAGTCGTCTGCACCG 60.136 52.381 0.00 0.00 0.00 4.94
627 641 0.033504 ATTGAAGTCGTCTGCACCGT 59.966 50.000 0.00 0.00 0.00 4.83
669 683 2.034687 CCCAACTCCCAGCCACAG 59.965 66.667 0.00 0.00 0.00 3.66
670 684 2.674380 CCAACTCCCAGCCACAGC 60.674 66.667 0.00 0.00 40.32 4.40
675 689 1.226542 CTCCCAGCCACAGCATGAT 59.773 57.895 0.00 0.00 43.56 2.45
681 695 0.844660 AGCCACAGCATGATCAGGAT 59.155 50.000 12.39 0.50 43.56 3.24
683 697 2.440627 AGCCACAGCATGATCAGGATAA 59.559 45.455 12.39 0.00 43.56 1.75
684 698 2.551459 GCCACAGCATGATCAGGATAAC 59.449 50.000 12.39 0.00 39.69 1.89
685 699 3.144506 CCACAGCATGATCAGGATAACC 58.855 50.000 12.39 0.00 39.69 2.85
686 700 3.434024 CCACAGCATGATCAGGATAACCA 60.434 47.826 12.39 0.00 39.69 3.67
687 701 4.395625 CACAGCATGATCAGGATAACCAT 58.604 43.478 12.39 0.00 39.69 3.55
688 702 5.513614 CCACAGCATGATCAGGATAACCATA 60.514 44.000 12.39 0.00 39.69 2.74
689 703 5.410746 CACAGCATGATCAGGATAACCATAC 59.589 44.000 12.39 0.00 39.69 2.39
690 704 5.309020 ACAGCATGATCAGGATAACCATACT 59.691 40.000 12.39 0.00 39.69 2.12
691 705 6.498303 ACAGCATGATCAGGATAACCATACTA 59.502 38.462 12.39 0.00 39.69 1.82
692 706 7.181665 ACAGCATGATCAGGATAACCATACTAT 59.818 37.037 12.39 0.00 39.69 2.12
694 708 9.444668 AGCATGATCAGGATAACCATACTATAT 57.555 33.333 12.39 0.00 38.94 0.86
695 709 9.486497 GCATGATCAGGATAACCATACTATATG 57.514 37.037 12.39 0.00 38.94 1.78
696 710 9.993454 CATGATCAGGATAACCATACTATATGG 57.007 37.037 12.42 12.42 44.54 2.74
697 711 8.023021 TGATCAGGATAACCATACTATATGGC 57.977 38.462 13.68 0.00 42.82 4.40
698 712 7.623278 TGATCAGGATAACCATACTATATGGCA 59.377 37.037 13.68 0.00 42.82 4.92
699 713 7.182817 TCAGGATAACCATACTATATGGCAC 57.817 40.000 13.68 4.42 42.82 5.01
700 714 6.042777 CAGGATAACCATACTATATGGCACG 58.957 44.000 13.68 0.00 42.82 5.34
701 715 5.128827 AGGATAACCATACTATATGGCACGG 59.871 44.000 13.68 0.00 42.82 4.94
702 716 3.695830 AACCATACTATATGGCACGGG 57.304 47.619 13.68 0.00 42.82 5.28
703 717 2.616524 ACCATACTATATGGCACGGGT 58.383 47.619 13.68 0.00 42.82 5.28
704 718 2.976882 ACCATACTATATGGCACGGGTT 59.023 45.455 13.68 0.00 42.82 4.11
705 719 4.161876 ACCATACTATATGGCACGGGTTA 58.838 43.478 13.68 0.00 42.82 2.85
707 721 5.249852 ACCATACTATATGGCACGGGTTAAT 59.750 40.000 13.68 0.00 42.82 1.40
709 723 7.038160 ACCATACTATATGGCACGGGTTAATTA 60.038 37.037 13.68 0.00 42.82 1.40
710 724 7.825270 CCATACTATATGGCACGGGTTAATTAA 59.175 37.037 1.98 0.00 31.75 1.40
711 725 8.662141 CATACTATATGGCACGGGTTAATTAAC 58.338 37.037 18.30 18.30 35.50 2.01
722 736 3.700538 GGTTAATTAACCCGGGGTTTCT 58.299 45.455 34.78 21.19 44.33 2.52
723 737 3.696051 GGTTAATTAACCCGGGGTTTCTC 59.304 47.826 34.78 18.49 44.33 2.87
731 763 0.690762 CCGGGGTTTCTCTCTTTCCA 59.309 55.000 0.00 0.00 0.00 3.53
734 766 2.224548 CGGGGTTTCTCTCTTTCCAGTT 60.225 50.000 0.00 0.00 0.00 3.16
741 773 8.268605 GGGTTTCTCTCTTTCCAGTTAAGATAT 58.731 37.037 0.00 0.00 31.66 1.63
804 837 3.304911 TCAAATGTCAACAGGTTGGGA 57.695 42.857 11.87 0.21 40.78 4.37
814 847 3.208747 ACAGGTTGGGATAATTAGGCG 57.791 47.619 0.00 0.00 0.00 5.52
896 929 4.969196 CCCGCCCGTCGATGGATG 62.969 72.222 25.65 15.68 41.67 3.51
902 935 4.806571 CGTCGATGGATGGAACGT 57.193 55.556 0.00 0.00 0.00 3.99
903 936 2.578369 CGTCGATGGATGGAACGTC 58.422 57.895 0.00 0.00 0.00 4.34
904 937 1.200474 CGTCGATGGATGGAACGTCG 61.200 60.000 0.00 0.00 45.89 5.12
923 956 4.689812 CGTCGTCTCCCCTATATATATCCG 59.310 50.000 0.00 0.00 0.00 4.18
1000 1033 1.298340 CATGTGCCCTTGTCCCGTA 59.702 57.895 0.00 0.00 0.00 4.02
1006 1039 1.146263 CCCTTGTCCCGTATGAGCC 59.854 63.158 0.00 0.00 0.00 4.70
1082 1118 1.717937 CAGGCGGCTTTCAGATTCG 59.282 57.895 9.66 0.00 0.00 3.34
1084 1120 2.405191 GCGGCTTTCAGATTCGGC 59.595 61.111 0.00 0.00 0.00 5.54
1129 1165 5.249393 AGCACAGGGAAGAAGAAGAAGAATA 59.751 40.000 0.00 0.00 0.00 1.75
1132 1168 7.390027 CACAGGGAAGAAGAAGAAGAATAAGA 58.610 38.462 0.00 0.00 0.00 2.10
1134 1170 8.100164 ACAGGGAAGAAGAAGAAGAATAAGAAG 58.900 37.037 0.00 0.00 0.00 2.85
1135 1171 8.317679 CAGGGAAGAAGAAGAAGAATAAGAAGA 58.682 37.037 0.00 0.00 0.00 2.87
1142 1178 9.087424 GAAGAAGAAGAATAAGAAGAAGAGCTC 57.913 37.037 5.27 5.27 0.00 4.09
1143 1179 8.366359 AGAAGAAGAATAAGAAGAAGAGCTCT 57.634 34.615 11.45 11.45 35.13 4.09
1229 1297 2.725312 GCTCAGAGCCCGTCCATCA 61.725 63.158 11.84 0.00 34.48 3.07
1232 1304 1.817099 CAGAGCCCGTCCATCAAGC 60.817 63.158 0.00 0.00 0.00 4.01
1237 1309 1.515954 CCCGTCCATCAAGCGTAGT 59.484 57.895 0.00 0.00 0.00 2.73
1240 1312 1.133598 CCGTCCATCAAGCGTAGTGTA 59.866 52.381 0.00 0.00 0.00 2.90
1241 1313 2.451132 CGTCCATCAAGCGTAGTGTAG 58.549 52.381 0.00 0.00 0.00 2.74
1248 1320 2.363038 TCAAGCGTAGTGTAGGTGTGTT 59.637 45.455 0.00 0.00 0.00 3.32
1249 1321 2.719426 AGCGTAGTGTAGGTGTGTTC 57.281 50.000 0.00 0.00 0.00 3.18
1250 1322 2.236766 AGCGTAGTGTAGGTGTGTTCT 58.763 47.619 0.00 0.00 0.00 3.01
1252 1324 2.985139 GCGTAGTGTAGGTGTGTTCTTC 59.015 50.000 0.00 0.00 0.00 2.87
1278 1352 5.128499 TGTTCTTGGTGATTGATTTGGTGTT 59.872 36.000 0.00 0.00 0.00 3.32
1279 1353 5.199024 TCTTGGTGATTGATTTGGTGTTG 57.801 39.130 0.00 0.00 0.00 3.33
1284 1358 3.490526 GTGATTGATTTGGTGTTGTGTGC 59.509 43.478 0.00 0.00 0.00 4.57
1285 1359 3.131755 TGATTGATTTGGTGTTGTGTGCA 59.868 39.130 0.00 0.00 0.00 4.57
1407 1490 3.166434 CAAGGTGGGTGGGTGCTA 58.834 61.111 0.00 0.00 0.00 3.49
1409 1492 2.907179 AAGGTGGGTGGGTGCTAGC 61.907 63.158 8.10 8.10 0.00 3.42
1410 1493 4.426313 GGTGGGTGGGTGCTAGCC 62.426 72.222 13.29 3.27 36.00 3.93
1411 1494 3.330720 GTGGGTGGGTGCTAGCCT 61.331 66.667 13.29 0.00 36.53 4.58
1424 1507 2.346099 CTAGCCTAGCAAGATCGAGC 57.654 55.000 0.00 0.00 0.00 5.03
1654 1740 3.460672 TTCCGCGGATCCATGAGGC 62.461 63.158 31.56 5.48 33.74 4.70
1732 1819 1.922447 TGGGGAAACATGGCTGATACT 59.078 47.619 0.00 0.00 0.00 2.12
1750 1837 0.102481 CTACCAGATTCCCACCGTCG 59.898 60.000 0.00 0.00 0.00 5.12
1766 1853 2.159366 CCGTCGAAAGTAGATCAGTGCT 60.159 50.000 0.00 0.00 0.00 4.40
1767 1854 2.848887 CGTCGAAAGTAGATCAGTGCTG 59.151 50.000 0.00 0.00 0.00 4.41
1782 1869 2.558359 AGTGCTGGTACTTGATTTTGGC 59.442 45.455 0.00 0.00 0.00 4.52
1900 2097 6.428385 AATCGGAAGCAAAATTCAGAGTAG 57.572 37.500 0.00 0.00 36.93 2.57
2071 2288 3.630148 CGATCGCGGCGCATTTCT 61.630 61.111 32.61 10.56 0.00 2.52
2533 2758 3.713902 GCCATGGTGGACATAGAGG 57.286 57.895 14.67 0.00 40.96 3.69
2534 2759 1.131638 GCCATGGTGGACATAGAGGA 58.868 55.000 14.67 0.00 40.96 3.71
3768 4078 1.141053 ACCTCGAGTTTTGAGCTGGTT 59.859 47.619 12.31 0.00 31.98 3.67
3769 4079 1.532868 CCTCGAGTTTTGAGCTGGTTG 59.467 52.381 12.31 0.00 31.98 3.77
3770 4080 2.483876 CTCGAGTTTTGAGCTGGTTGA 58.516 47.619 3.62 0.00 0.00 3.18
3771 4081 2.872245 CTCGAGTTTTGAGCTGGTTGAA 59.128 45.455 3.62 0.00 0.00 2.69
3772 4082 3.476552 TCGAGTTTTGAGCTGGTTGAAT 58.523 40.909 0.00 0.00 0.00 2.57
3773 4083 3.882888 TCGAGTTTTGAGCTGGTTGAATT 59.117 39.130 0.00 0.00 0.00 2.17
3786 4096 2.621407 GGTTGAATTGAGGGGCATCTCA 60.621 50.000 5.81 5.81 41.51 3.27
3818 4149 0.874390 AACACGACATGGACATGCAC 59.126 50.000 11.96 6.19 42.39 4.57
3819 4150 1.291184 ACACGACATGGACATGCACG 61.291 55.000 21.50 21.50 42.39 5.34
3907 4239 1.581934 AACATGTGTGACGGTGTCAG 58.418 50.000 0.00 0.00 43.57 3.51
3908 4240 0.880278 ACATGTGTGACGGTGTCAGC 60.880 55.000 0.00 0.00 43.57 4.26
3909 4241 1.301716 ATGTGTGACGGTGTCAGCC 60.302 57.895 0.00 0.00 43.57 4.85
3917 4249 3.626924 GGTGTCAGCCGGTCTGGT 61.627 66.667 20.90 0.00 43.06 4.00
3918 4250 2.357517 GTGTCAGCCGGTCTGGTG 60.358 66.667 20.90 4.43 43.06 4.17
3919 4251 3.625897 TGTCAGCCGGTCTGGTGG 61.626 66.667 20.90 1.51 43.06 4.61
3920 4252 3.626924 GTCAGCCGGTCTGGTGGT 61.627 66.667 20.90 0.00 43.06 4.16
3921 4253 3.625897 TCAGCCGGTCTGGTGGTG 61.626 66.667 20.90 2.77 43.06 4.17
3922 4254 3.941188 CAGCCGGTCTGGTGGTGT 61.941 66.667 15.59 0.00 41.21 4.16
3923 4255 2.203728 AGCCGGTCTGGTGGTGTA 60.204 61.111 1.90 0.00 41.21 2.90
3924 4256 1.839747 AGCCGGTCTGGTGGTGTAA 60.840 57.895 1.90 0.00 41.21 2.41
3925 4257 1.198759 AGCCGGTCTGGTGGTGTAAT 61.199 55.000 1.90 0.00 41.21 1.89
3926 4258 0.743345 GCCGGTCTGGTGGTGTAATC 60.743 60.000 1.90 0.00 41.21 1.75
3927 4259 0.611200 CCGGTCTGGTGGTGTAATCA 59.389 55.000 0.00 0.00 0.00 2.57
3928 4260 1.209504 CCGGTCTGGTGGTGTAATCAT 59.790 52.381 0.00 0.00 0.00 2.45
3929 4261 2.550978 CGGTCTGGTGGTGTAATCATC 58.449 52.381 0.00 0.00 0.00 2.92
3930 4262 2.550978 GGTCTGGTGGTGTAATCATCG 58.449 52.381 0.00 0.00 0.00 3.84
3931 4263 2.550978 GTCTGGTGGTGTAATCATCGG 58.449 52.381 0.00 0.00 0.00 4.18
3932 4264 1.134521 TCTGGTGGTGTAATCATCGGC 60.135 52.381 0.00 0.00 0.00 5.54
3933 4265 0.615850 TGGTGGTGTAATCATCGGCA 59.384 50.000 0.00 0.00 0.00 5.69
3934 4266 1.299541 GGTGGTGTAATCATCGGCAG 58.700 55.000 0.00 0.00 0.00 4.85
3935 4267 1.134521 GGTGGTGTAATCATCGGCAGA 60.135 52.381 0.00 0.00 0.00 4.26
3936 4268 2.485479 GGTGGTGTAATCATCGGCAGAT 60.485 50.000 0.00 0.00 37.65 2.90
3998 4369 2.638363 GTTACCTTTCTCCCCTGTCAGT 59.362 50.000 0.00 0.00 0.00 3.41
3999 4370 2.715763 ACCTTTCTCCCCTGTCAGTA 57.284 50.000 0.00 0.00 0.00 2.74
4001 4372 4.348020 ACCTTTCTCCCCTGTCAGTATA 57.652 45.455 0.00 0.00 0.00 1.47
4002 4373 4.031611 ACCTTTCTCCCCTGTCAGTATAC 58.968 47.826 0.00 0.00 0.00 1.47
4003 4374 3.068307 CCTTTCTCCCCTGTCAGTATACG 59.932 52.174 0.00 0.00 0.00 3.06
4004 4375 2.359981 TCTCCCCTGTCAGTATACGG 57.640 55.000 0.00 0.00 0.00 4.02
4172 4559 2.960819 CACTAGACCACTGGTGCTAAC 58.039 52.381 5.10 0.00 45.52 2.34
4173 4560 2.299013 CACTAGACCACTGGTGCTAACA 59.701 50.000 5.10 0.00 45.52 2.41
4174 4561 2.969950 ACTAGACCACTGGTGCTAACAA 59.030 45.455 5.10 0.00 36.51 2.83
4175 4562 3.583086 ACTAGACCACTGGTGCTAACAAT 59.417 43.478 5.10 0.00 36.51 2.71
4176 4563 2.783135 AGACCACTGGTGCTAACAATG 58.217 47.619 5.10 0.00 35.25 2.82
4177 4564 2.106511 AGACCACTGGTGCTAACAATGT 59.893 45.455 5.10 0.00 35.25 2.71
4178 4565 2.884639 GACCACTGGTGCTAACAATGTT 59.115 45.455 5.10 3.43 35.25 2.71
4179 4566 4.069304 GACCACTGGTGCTAACAATGTTA 58.931 43.478 5.10 5.66 35.25 2.41
4180 4567 4.465886 ACCACTGGTGCTAACAATGTTAA 58.534 39.130 7.30 0.00 32.98 2.01
4181 4568 5.076873 ACCACTGGTGCTAACAATGTTAAT 58.923 37.500 7.30 0.00 32.98 1.40
4182 4569 5.538433 ACCACTGGTGCTAACAATGTTAATT 59.462 36.000 7.30 0.00 32.98 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.282674 TTGCTTGGGCTCTGCTGG 60.283 61.111 4.00 0.00 39.59 4.85
81 83 7.018235 CAGAGGCGATTAAGACTTTTCTTTTC 58.982 38.462 0.00 0.00 39.17 2.29
144 146 3.122850 CAATGATTGGAGGGGCGC 58.877 61.111 0.00 0.00 0.00 6.53
178 181 2.769095 CCCCCTTGAAAGTTTGAAACCA 59.231 45.455 4.14 0.00 0.00 3.67
208 212 2.161078 TATCACCGTGTGGCAAGCGA 62.161 55.000 12.54 0.00 39.70 4.93
238 245 0.598158 TAAACGTGTCTCACCGTGGC 60.598 55.000 0.00 0.00 0.00 5.01
252 259 5.373262 GCACATTTTCCTGCATTTTAAACG 58.627 37.500 0.00 0.00 33.31 3.60
335 342 4.143242 CGATGTATCATTTTCCTGCGCTAG 60.143 45.833 9.73 4.25 0.00 3.42
336 343 3.740832 CGATGTATCATTTTCCTGCGCTA 59.259 43.478 9.73 0.00 0.00 4.26
337 344 2.545526 CGATGTATCATTTTCCTGCGCT 59.454 45.455 9.73 0.00 0.00 5.92
339 346 2.224079 CCCGATGTATCATTTTCCTGCG 59.776 50.000 0.00 0.00 0.00 5.18
342 349 5.473504 GCATAACCCGATGTATCATTTTCCT 59.526 40.000 0.00 0.00 0.00 3.36
354 361 2.549064 TCATGGAGCATAACCCGATG 57.451 50.000 0.00 0.00 0.00 3.84
382 393 3.320826 TCGTCTCCTGATCACTTTGAACA 59.679 43.478 0.00 0.00 0.00 3.18
417 430 5.298527 CACAATCTATGCCACATGATGAAGT 59.701 40.000 0.00 0.00 0.00 3.01
525 539 2.147204 GACTCACTGACACGCGTTGC 62.147 60.000 10.22 4.83 0.00 4.17
557 571 2.655685 GTCGAATCTCTCGGCCGC 60.656 66.667 23.51 2.90 46.75 6.53
608 622 0.033504 ACGGTGCAGACGACTTCAAT 59.966 50.000 16.62 0.00 34.93 2.57
609 623 0.874175 CACGGTGCAGACGACTTCAA 60.874 55.000 16.62 0.00 34.93 2.69
623 637 0.676782 GTGCAGAATAAGGCCACGGT 60.677 55.000 5.01 0.00 0.00 4.83
625 639 2.309528 TAGTGCAGAATAAGGCCACG 57.690 50.000 5.01 0.00 0.00 4.94
626 640 3.808728 TGATAGTGCAGAATAAGGCCAC 58.191 45.455 5.01 0.00 0.00 5.01
627 641 3.711190 TCTGATAGTGCAGAATAAGGCCA 59.289 43.478 5.01 0.00 41.65 5.36
669 683 9.486497 CATATAGTATGGTTATCCTGATCATGC 57.514 37.037 0.00 0.00 34.23 4.06
670 684 9.993454 CCATATAGTATGGTTATCCTGATCATG 57.007 37.037 0.00 0.00 34.56 3.07
675 689 6.127451 CGTGCCATATAGTATGGTTATCCTGA 60.127 42.308 15.36 0.00 41.17 3.86
681 695 4.161876 ACCCGTGCCATATAGTATGGTTA 58.838 43.478 15.36 4.94 41.17 2.85
683 697 2.616524 ACCCGTGCCATATAGTATGGT 58.383 47.619 15.36 0.00 41.17 3.55
684 698 3.695830 AACCCGTGCCATATAGTATGG 57.304 47.619 10.88 10.88 41.99 2.74
685 699 8.662141 GTTAATTAACCCGTGCCATATAGTATG 58.338 37.037 16.14 0.00 0.00 2.39
686 700 8.782339 GTTAATTAACCCGTGCCATATAGTAT 57.218 34.615 16.14 0.00 0.00 2.12
702 716 4.592942 AGAGAAACCCCGGGTTAATTAAC 58.407 43.478 22.69 18.30 46.20 2.01
703 717 4.537288 AGAGAGAAACCCCGGGTTAATTAA 59.463 41.667 22.69 0.00 46.20 1.40
704 718 4.106324 AGAGAGAAACCCCGGGTTAATTA 58.894 43.478 22.69 0.00 46.20 1.40
705 719 2.917600 AGAGAGAAACCCCGGGTTAATT 59.082 45.455 22.69 7.02 46.20 1.40
707 721 2.034436 AGAGAGAAACCCCGGGTTAA 57.966 50.000 22.69 0.00 46.20 2.01
710 724 0.691332 GAAAGAGAGAAACCCCGGGT 59.309 55.000 21.85 2.03 37.65 5.28
711 725 0.035343 GGAAAGAGAGAAACCCCGGG 60.035 60.000 15.80 15.80 0.00 5.73
712 726 0.690762 TGGAAAGAGAGAAACCCCGG 59.309 55.000 0.00 0.00 0.00 5.73
713 727 1.348036 ACTGGAAAGAGAGAAACCCCG 59.652 52.381 0.00 0.00 0.00 5.73
714 728 3.510531 AACTGGAAAGAGAGAAACCCC 57.489 47.619 0.00 0.00 0.00 4.95
715 729 5.866207 TCTTAACTGGAAAGAGAGAAACCC 58.134 41.667 0.00 0.00 0.00 4.11
716 730 9.674068 AATATCTTAACTGGAAAGAGAGAAACC 57.326 33.333 0.00 0.00 36.46 3.27
741 773 5.421277 CATGGCCTGCTGAAATAAAATGAA 58.579 37.500 3.32 0.00 0.00 2.57
804 837 0.602905 GCTGACGCCCGCCTAATTAT 60.603 55.000 0.00 0.00 0.00 1.28
882 915 1.887707 GTTCCATCCATCGACGGGC 60.888 63.158 0.00 0.00 0.00 6.13
886 919 0.179145 ACGACGTTCCATCCATCGAC 60.179 55.000 0.00 0.00 36.64 4.20
896 929 1.972872 TATAGGGGAGACGACGTTCC 58.027 55.000 16.25 16.25 0.00 3.62
902 935 4.506271 GGCGGATATATATAGGGGAGACGA 60.506 50.000 0.00 0.00 0.00 4.20
903 936 3.757493 GGCGGATATATATAGGGGAGACG 59.243 52.174 0.00 0.00 0.00 4.18
904 937 3.757493 CGGCGGATATATATAGGGGAGAC 59.243 52.174 0.00 0.00 0.00 3.36
1000 1033 1.645034 CGACAACGATTCTGGCTCAT 58.355 50.000 0.00 0.00 42.66 2.90
1006 1039 0.792640 AGCTTGCGACAACGATTCTG 59.207 50.000 0.00 0.00 42.66 3.02
1129 1165 3.099141 CTCTCCCAGAGCTCTTCTTCTT 58.901 50.000 15.27 0.00 35.30 2.52
1157 1225 1.769098 CTGATTCTGCGCCACCATCG 61.769 60.000 4.18 0.00 0.00 3.84
1167 1235 1.880340 CGGCGTCCTCTGATTCTGC 60.880 63.158 0.00 0.00 0.00 4.26
1217 1285 2.298158 CTACGCTTGATGGACGGGCT 62.298 60.000 0.00 0.00 0.00 5.19
1225 1293 2.923655 CACACCTACACTACGCTTGATG 59.076 50.000 0.00 0.00 0.00 3.07
1229 1297 2.626743 AGAACACACCTACACTACGCTT 59.373 45.455 0.00 0.00 0.00 4.68
1232 1304 3.231965 CGAAGAACACACCTACACTACG 58.768 50.000 0.00 0.00 0.00 3.51
1237 1309 3.131577 AGAACACGAAGAACACACCTACA 59.868 43.478 0.00 0.00 0.00 2.74
1240 1312 2.936498 CAAGAACACGAAGAACACACCT 59.064 45.455 0.00 0.00 0.00 4.00
1241 1313 2.031683 CCAAGAACACGAAGAACACACC 59.968 50.000 0.00 0.00 0.00 4.16
1248 1320 4.066646 TCAATCACCAAGAACACGAAGA 57.933 40.909 0.00 0.00 0.00 2.87
1249 1321 5.362556 AATCAATCACCAAGAACACGAAG 57.637 39.130 0.00 0.00 0.00 3.79
1250 1322 5.507149 CCAAATCAATCACCAAGAACACGAA 60.507 40.000 0.00 0.00 0.00 3.85
1252 1324 4.229096 CCAAATCAATCACCAAGAACACG 58.771 43.478 0.00 0.00 0.00 4.49
1278 1352 2.437537 AACACCTGCGTGCACACA 60.438 55.556 18.64 12.99 44.40 3.72
1279 1353 2.180204 AGAACACCTGCGTGCACAC 61.180 57.895 18.64 7.98 44.40 3.82
1284 1358 3.357079 GGCCAGAACACCTGCGTG 61.357 66.667 0.00 0.00 46.11 5.34
1285 1359 4.643387 GGGCCAGAACACCTGCGT 62.643 66.667 4.39 0.00 41.57 5.24
1407 1490 0.673437 GAGCTCGATCTTGCTAGGCT 59.327 55.000 0.00 0.00 39.91 4.58
1409 1492 0.316841 GGGAGCTCGATCTTGCTAGG 59.683 60.000 7.83 0.00 39.91 3.02
1410 1493 0.039617 CGGGAGCTCGATCTTGCTAG 60.040 60.000 7.83 0.00 39.91 3.42
1411 1494 1.456196 CCGGGAGCTCGATCTTGCTA 61.456 60.000 7.83 0.00 39.91 3.49
1424 1507 1.445582 CCGAAACTCGAACCGGGAG 60.446 63.158 6.32 5.41 43.74 4.30
1503 1589 1.304052 AGCTCTCCTCTGCACGAGT 60.304 57.895 10.86 0.00 38.11 4.18
1654 1740 4.291783 GTCTTCAGGATCGGATAAGAACG 58.708 47.826 3.21 0.00 0.00 3.95
1723 1810 2.972713 TGGGAATCTGGTAGTATCAGCC 59.027 50.000 5.47 2.01 32.63 4.85
1732 1819 0.323633 TCGACGGTGGGAATCTGGTA 60.324 55.000 0.00 0.00 0.00 3.25
1750 1837 5.331876 AGTACCAGCACTGATCTACTTTC 57.668 43.478 0.00 0.00 0.00 2.62
1766 1853 3.073798 TCCTCAGCCAAAATCAAGTACCA 59.926 43.478 0.00 0.00 0.00 3.25
1767 1854 3.440522 GTCCTCAGCCAAAATCAAGTACC 59.559 47.826 0.00 0.00 0.00 3.34
1782 1869 4.377841 GCAAAATCGACAAGAAGTCCTCAG 60.378 45.833 0.00 0.00 44.66 3.35
1864 2060 6.615264 TGCTTCCGATTAGTACTACTAGTG 57.385 41.667 5.39 0.00 31.47 2.74
1900 2097 0.393537 CAGGGTGGCTCATGAGGAAC 60.394 60.000 23.89 7.53 0.00 3.62
2071 2288 0.941542 CCAAGAACCGCGAGAAAACA 59.058 50.000 8.23 0.00 0.00 2.83
2526 2751 0.461548 TTGGCTGCTCGTCCTCTATG 59.538 55.000 0.00 0.00 0.00 2.23
2527 2752 0.749649 CTTGGCTGCTCGTCCTCTAT 59.250 55.000 0.00 0.00 0.00 1.98
2528 2753 1.323271 CCTTGGCTGCTCGTCCTCTA 61.323 60.000 0.00 0.00 0.00 2.43
2529 2754 2.654079 CCTTGGCTGCTCGTCCTCT 61.654 63.158 0.00 0.00 0.00 3.69
2530 2755 2.125350 CCTTGGCTGCTCGTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
2531 2756 3.710722 CCCTTGGCTGCTCGTCCT 61.711 66.667 0.00 0.00 0.00 3.85
3768 4078 1.064463 GGTGAGATGCCCCTCAATTCA 60.064 52.381 6.70 0.00 43.94 2.57
3769 4079 1.685148 GGTGAGATGCCCCTCAATTC 58.315 55.000 6.70 0.00 43.94 2.17
3770 4080 0.107017 CGGTGAGATGCCCCTCAATT 60.107 55.000 6.70 0.00 43.94 2.32
3771 4081 1.528824 CGGTGAGATGCCCCTCAAT 59.471 57.895 6.70 0.00 43.94 2.57
3772 4082 2.669133 CCGGTGAGATGCCCCTCAA 61.669 63.158 6.70 0.00 43.94 3.02
3773 4083 3.083349 CCGGTGAGATGCCCCTCA 61.083 66.667 0.00 1.50 40.57 3.86
3794 4104 2.431771 TCCATGTCGTGTTCGGCG 60.432 61.111 0.00 0.00 45.30 6.46
3818 4149 0.091344 CGACGCAGCTGAAAACTACG 59.909 55.000 20.43 12.08 0.00 3.51
3819 4150 1.124477 GTCGACGCAGCTGAAAACTAC 59.876 52.381 20.43 3.81 0.00 2.73
3907 4239 0.743345 GATTACACCACCAGACCGGC 60.743 60.000 0.00 0.00 39.03 6.13
3908 4240 0.611200 TGATTACACCACCAGACCGG 59.389 55.000 0.00 0.00 42.50 5.28
3909 4241 2.550978 GATGATTACACCACCAGACCG 58.449 52.381 0.00 0.00 0.00 4.79
3911 4243 2.550978 CCGATGATTACACCACCAGAC 58.449 52.381 0.00 0.00 0.00 3.51
3912 4244 1.134521 GCCGATGATTACACCACCAGA 60.135 52.381 0.00 0.00 0.00 3.86
3913 4245 1.299541 GCCGATGATTACACCACCAG 58.700 55.000 0.00 0.00 0.00 4.00
3914 4246 0.615850 TGCCGATGATTACACCACCA 59.384 50.000 0.00 0.00 0.00 4.17
3915 4247 1.134521 TCTGCCGATGATTACACCACC 60.135 52.381 0.00 0.00 0.00 4.61
3916 4248 2.309528 TCTGCCGATGATTACACCAC 57.690 50.000 0.00 0.00 0.00 4.16
3917 4249 2.433970 TGATCTGCCGATGATTACACCA 59.566 45.455 0.00 0.00 0.00 4.17
3918 4250 3.111853 TGATCTGCCGATGATTACACC 57.888 47.619 0.00 0.00 0.00 4.16
3919 4251 4.751600 TCATTGATCTGCCGATGATTACAC 59.248 41.667 0.00 0.00 33.29 2.90
3920 4252 4.959723 TCATTGATCTGCCGATGATTACA 58.040 39.130 0.00 0.00 33.29 2.41
3921 4253 5.929697 TTCATTGATCTGCCGATGATTAC 57.070 39.130 0.00 0.00 36.96 1.89
3922 4254 7.514784 AAATTCATTGATCTGCCGATGATTA 57.485 32.000 0.00 0.00 36.96 1.75
3923 4255 6.401047 AAATTCATTGATCTGCCGATGATT 57.599 33.333 0.00 0.00 36.96 2.57
3924 4256 7.698506 ATAAATTCATTGATCTGCCGATGAT 57.301 32.000 0.00 0.00 36.96 2.45
3925 4257 7.335171 CCTATAAATTCATTGATCTGCCGATGA 59.665 37.037 0.00 0.00 35.68 2.92
3926 4258 7.335171 TCCTATAAATTCATTGATCTGCCGATG 59.665 37.037 0.00 0.00 0.00 3.84
3927 4259 7.397221 TCCTATAAATTCATTGATCTGCCGAT 58.603 34.615 0.00 0.00 0.00 4.18
3928 4260 6.768483 TCCTATAAATTCATTGATCTGCCGA 58.232 36.000 0.00 0.00 0.00 5.54
3929 4261 7.621428 ATCCTATAAATTCATTGATCTGCCG 57.379 36.000 0.00 0.00 0.00 5.69
3998 4369 2.490509 CACACTGTCTCACCACCGTATA 59.509 50.000 0.00 0.00 0.00 1.47
3999 4370 1.272490 CACACTGTCTCACCACCGTAT 59.728 52.381 0.00 0.00 0.00 3.06
4001 4372 1.441729 CACACTGTCTCACCACCGT 59.558 57.895 0.00 0.00 0.00 4.83
4002 4373 1.956170 GCACACTGTCTCACCACCG 60.956 63.158 0.00 0.00 0.00 4.94
4003 4374 0.882042 CAGCACACTGTCTCACCACC 60.882 60.000 0.00 0.00 39.22 4.61
4004 4375 2.609825 CAGCACACTGTCTCACCAC 58.390 57.895 0.00 0.00 39.22 4.16
4180 4567 8.804204 CGGAACAGAGGGAGTAGTATATAAAAT 58.196 37.037 0.00 0.00 0.00 1.82
4181 4568 8.000709 TCGGAACAGAGGGAGTAGTATATAAAA 58.999 37.037 0.00 0.00 0.00 1.52
4182 4569 7.520798 TCGGAACAGAGGGAGTAGTATATAAA 58.479 38.462 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.