Multiple sequence alignment - TraesCS6D01G372000

Loading Multiple Alignment...

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 TraesCS6D01G372000 chr6D 100.000 3349 0 0 1 3349 457474290 457470942 0.000000e+00 6185.0
1 TraesCS6D01G372000 chr6D 89.576 1650 112 41 718 2349 457347444 457345837 0.000000e+00 2039.0
2 TraesCS6D01G372000 chr6D 78.392 199 41 2 2125 2322 292376608 292376805 9.750000e-26 128.0
3 TraesCS6D01G372000 chr6A 91.597 2047 106 35 718 2740 604294545 604296549 0.000000e+00 2767.0
4 TraesCS6D01G372000 chr6A 88.923 1652 118 42 718 2349 604384365 604385971 0.000000e+00 1977.0
5 TraesCS6D01G372000 chr6A 89.897 485 23 3 103 572 18528997 18529470 4.780000e-168 601.0
6 TraesCS6D01G372000 chr6A 92.982 342 15 6 2736 3070 604297220 604297559 1.080000e-134 490.0
7 TraesCS6D01G372000 chr6A 93.600 250 15 1 3101 3349 604297558 604297807 4.080000e-99 372.0
8 TraesCS6D01G372000 chr6A 94.444 90 5 0 11 100 604384281 604384370 4.510000e-29 139.0
9 TraesCS6D01G372000 chr6A 86.364 88 12 0 1677 1764 430342818 430342731 2.750000e-16 97.1
10 TraesCS6D01G372000 chr6B 88.037 1931 113 55 718 2550 695936689 695938599 0.000000e+00 2178.0
11 TraesCS6D01G372000 chr6B 84.043 94 15 0 1671 1764 455414413 455414506 1.280000e-14 91.6
12 TraesCS6D01G372000 chr5A 89.241 790 50 25 718 1488 531241425 531240652 0.000000e+00 955.0
13 TraesCS6D01G372000 chr5A 75.745 738 144 24 1595 2322 454720580 454721292 4.140000e-89 339.0
14 TraesCS6D01G372000 chrUn 94.652 617 27 4 103 715 278087772 278087158 0.000000e+00 952.0
15 TraesCS6D01G372000 chr7D 94.652 617 27 4 103 715 15948205 15947591 0.000000e+00 952.0
16 TraesCS6D01G372000 chr7D 94.652 617 27 4 103 715 16034806 16034192 0.000000e+00 952.0
17 TraesCS6D01G372000 chr7B 84.340 530 49 11 207 712 605998116 605997597 3.880000e-134 488.0
18 TraesCS6D01G372000 chr7B 83.929 112 18 0 1378 1489 102782876 102782765 1.270000e-19 108.0
19 TraesCS6D01G372000 chr2B 83.567 499 56 11 243 717 51465886 51466382 8.530000e-121 444.0
20 TraesCS6D01G372000 chr2B 81.182 457 43 19 299 717 778478313 778477862 8.960000e-86 327.0
21 TraesCS6D01G372000 chr2B 84.956 113 15 2 1378 1489 544982032 544982143 2.730000e-21 113.0
22 TraesCS6D01G372000 chr5D 74.924 981 189 42 1359 2322 353763000 353763940 2.420000e-106 396.0
23 TraesCS6D01G372000 chr5D 96.875 64 2 0 103 166 483824347 483824410 1.270000e-19 108.0
24 TraesCS6D01G372000 chr5D 79.762 84 16 1 103 185 390356963 390357046 3.610000e-05 60.2
25 TraesCS6D01G372000 chr3A 82.018 456 42 15 299 718 14077871 14077420 5.320000e-93 351.0
26 TraesCS6D01G372000 chr5B 75.848 737 145 22 1595 2322 417874961 417875673 8.900000e-91 344.0
27 TraesCS6D01G372000 chr1D 97.326 187 5 0 527 713 463162412 463162598 5.390000e-83 318.0
28 TraesCS6D01G372000 chr1D 86.667 150 15 4 1075 1222 199623993 199624139 9.620000e-36 161.0
29 TraesCS6D01G372000 chr1D 95.122 82 3 1 103 183 463162321 463162402 9.750000e-26 128.0
30 TraesCS6D01G372000 chr1D 100.000 28 0 0 103 130 395100332 395100305 6.000000e-03 52.8
31 TraesCS6D01G372000 chr3D 82.713 376 35 9 373 721 607570066 607570438 1.170000e-79 307.0
32 TraesCS6D01G372000 chr3D 90.698 86 7 1 103 187 517155677 517155762 2.730000e-21 113.0
33 TraesCS6D01G372000 chr3D 100.000 28 0 0 103 130 57022982 57023009 6.000000e-03 52.8
34 TraesCS6D01G372000 chr1A 86.667 150 15 4 1075 1222 251376415 251376561 9.620000e-36 161.0
35 TraesCS6D01G372000 chr1A 82.308 130 22 1 1701 1830 251376999 251377127 9.820000e-21 111.0
36 TraesCS6D01G372000 chr1B 85.333 150 17 4 1075 1222 280181997 280182143 2.080000e-32 150.0
37 TraesCS6D01G372000 chr2D 84.000 150 19 4 1075 1222 16057125 16057271 4.510000e-29 139.0
38 TraesCS6D01G372000 chr2D 86.726 113 13 2 1378 1489 462197753 462197864 1.260000e-24 124.0
39 TraesCS6D01G372000 chr2D 82.540 126 22 0 1705 1830 16057713 16057838 9.820000e-21 111.0
40 TraesCS6D01G372000 chr2A 73.759 423 74 26 1378 1788 607476495 607476892 7.540000e-27 132.0


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 TraesCS6D01G372000 chr6D 457470942 457474290 3348 True 6185.000000 6185 100.000000 1 3349 1 chr6D.!!$R2 3348
1 TraesCS6D01G372000 chr6D 457345837 457347444 1607 True 2039.000000 2039 89.576000 718 2349 1 chr6D.!!$R1 1631
2 TraesCS6D01G372000 chr6A 604294545 604297807 3262 False 1209.666667 2767 92.726333 718 3349 3 chr6A.!!$F2 2631
3 TraesCS6D01G372000 chr6A 604384281 604385971 1690 False 1058.000000 1977 91.683500 11 2349 2 chr6A.!!$F3 2338
4 TraesCS6D01G372000 chr6B 695936689 695938599 1910 False 2178.000000 2178 88.037000 718 2550 1 chr6B.!!$F2 1832
5 TraesCS6D01G372000 chr5A 531240652 531241425 773 True 955.000000 955 89.241000 718 1488 1 chr5A.!!$R1 770
6 TraesCS6D01G372000 chr5A 454720580 454721292 712 False 339.000000 339 75.745000 1595 2322 1 chr5A.!!$F1 727
7 TraesCS6D01G372000 chrUn 278087158 278087772 614 True 952.000000 952 94.652000 103 715 1 chrUn.!!$R1 612
8 TraesCS6D01G372000 chr7D 15947591 15948205 614 True 952.000000 952 94.652000 103 715 1 chr7D.!!$R1 612
9 TraesCS6D01G372000 chr7D 16034192 16034806 614 True 952.000000 952 94.652000 103 715 1 chr7D.!!$R2 612
10 TraesCS6D01G372000 chr7B 605997597 605998116 519 True 488.000000 488 84.340000 207 712 1 chr7B.!!$R2 505
11 TraesCS6D01G372000 chr5D 353763000 353763940 940 False 396.000000 396 74.924000 1359 2322 1 chr5D.!!$F1 963
12 TraesCS6D01G372000 chr5B 417874961 417875673 712 False 344.000000 344 75.848000 1595 2322 1 chr5B.!!$F1 727

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
555 584 0.454957 CTCAAGCGCCCAAATCGTTG 60.455 55.0 2.29 0.0 34.25 4.1 F
1835 2027 1.045407 TGTCCGAGTACAAGCAGGTT 58.955 50.0 0.00 0.0 0.00 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2228 0.390603 CCACGAACACCGCTCCATTA 60.391 55.000 0.00 0.0 43.32 1.90 R
3077 3998 1.220750 AGGACTCCGGGAATCTATGGT 59.779 52.381 5.37 0.0 0.00 3.55 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
32 33 3.129813 GCAAAGATCCAATGCACATCTGA 59.870 43.478 9.40 0.00 39.81 3.27
67 68 1.068921 CAAACCCCAAAACCGGCAG 59.931 57.895 0.00 0.00 0.00 4.85
86 87 3.126343 GCAGGGAATTACTGTAAACCACG 59.874 47.826 20.44 14.47 38.22 4.94
94 95 5.480642 TTACTGTAAACCACGGGACATAA 57.519 39.130 0.00 0.00 37.90 1.90
95 96 4.563140 ACTGTAAACCACGGGACATAAT 57.437 40.909 0.00 0.00 37.90 1.28
96 97 4.913784 ACTGTAAACCACGGGACATAATT 58.086 39.130 0.00 0.00 37.90 1.40
97 98 6.052405 ACTGTAAACCACGGGACATAATTA 57.948 37.500 0.00 0.00 37.90 1.40
98 99 5.876460 ACTGTAAACCACGGGACATAATTAC 59.124 40.000 0.00 0.00 37.90 1.89
99 100 5.184711 TGTAAACCACGGGACATAATTACC 58.815 41.667 0.00 0.00 0.00 2.85
141 142 4.081031 CCCTGGTACTCCTTTTTCCTAGAC 60.081 50.000 0.00 0.00 34.23 2.59
143 144 4.410099 TGGTACTCCTTTTTCCTAGACGA 58.590 43.478 0.00 0.00 34.23 4.20
178 179 3.773560 TCTAACCATTGGTTCAAAGGGG 58.226 45.455 24.04 7.62 43.05 4.79
188 189 4.557705 TGGTTCAAAGGGGTAATTTTGGA 58.442 39.130 0.00 0.00 35.52 3.53
345 350 0.607489 GCACTTGCAGTGGAGGATGT 60.607 55.000 15.16 0.00 46.01 3.06
363 368 2.039418 TGTAACGCAGGCATAGATCCT 58.961 47.619 0.00 0.00 0.00 3.24
481 486 3.173240 GCTTGTCGTCGGCTCGTC 61.173 66.667 0.00 0.00 0.00 4.20
555 584 0.454957 CTCAAGCGCCCAAATCGTTG 60.455 55.000 2.29 0.00 34.25 4.10
568 597 6.338146 CCCAAATCGTTGATTAGTCTACAGA 58.662 40.000 1.28 0.42 36.83 3.41
634 663 1.218316 GGTACTCCCTGCCACTTCG 59.782 63.158 0.00 0.00 0.00 3.79
715 744 4.102681 ACTTCAGGGTACTGTAAAAGTGCT 59.897 41.667 0.00 0.00 45.14 4.40
716 745 4.267349 TCAGGGTACTGTAAAAGTGCTC 57.733 45.455 0.00 0.00 45.14 4.26
833 874 1.560923 GACGACGACATGATCCAAGG 58.439 55.000 0.00 0.00 0.00 3.61
892 955 6.665680 AGGATAGACGATGCTCTATAAATGGT 59.334 38.462 0.00 0.00 34.21 3.55
948 1023 3.690628 TGTACACGCATACACTAGCTACA 59.309 43.478 0.00 0.00 29.97 2.74
955 1030 5.043903 CGCATACACTAGCTACAACATCTT 58.956 41.667 0.00 0.00 0.00 2.40
959 1034 7.380065 GCATACACTAGCTACAACATCTTACTC 59.620 40.741 0.00 0.00 0.00 2.59
1260 1345 1.534729 TCAGTTGAGTAGCGAGCTCA 58.465 50.000 15.40 4.26 40.76 4.26
1266 1351 1.138337 GAGTAGCGAGCTCATGCATG 58.862 55.000 21.07 21.07 42.74 4.06
1291 1383 4.827692 TGGATACACATACACTTCACACC 58.172 43.478 0.00 0.00 46.17 4.16
1292 1384 3.863424 GGATACACATACACTTCACACCG 59.137 47.826 0.00 0.00 0.00 4.94
1305 1397 2.590575 CACCGTTCACCAGCCGTT 60.591 61.111 0.00 0.00 0.00 4.44
1306 1398 2.184167 CACCGTTCACCAGCCGTTT 61.184 57.895 0.00 0.00 0.00 3.60
1310 1402 1.299089 GTTCACCAGCCGTTTGTGC 60.299 57.895 0.00 0.00 0.00 4.57
1311 1403 1.750780 TTCACCAGCCGTTTGTGCA 60.751 52.632 0.00 0.00 0.00 4.57
1312 1404 1.723608 TTCACCAGCCGTTTGTGCAG 61.724 55.000 0.00 0.00 0.00 4.41
1313 1405 2.186160 CACCAGCCGTTTGTGCAGA 61.186 57.895 0.00 0.00 0.00 4.26
1314 1406 1.228245 ACCAGCCGTTTGTGCAGAT 60.228 52.632 0.00 0.00 0.00 2.90
1318 1422 2.030363 CCAGCCGTTTGTGCAGATTTTA 60.030 45.455 0.00 0.00 0.00 1.52
1321 1426 3.568007 AGCCGTTTGTGCAGATTTTAAGA 59.432 39.130 0.00 0.00 0.00 2.10
1323 1428 4.226761 CCGTTTGTGCAGATTTTAAGACC 58.773 43.478 0.00 0.00 0.00 3.85
1344 1455 9.840427 AAGACCAACTGATTGATTTAATTAACG 57.160 29.630 0.00 0.00 38.15 3.18
1371 1482 2.664518 GCAGGCGAGCAGATAGGC 60.665 66.667 0.00 0.00 0.00 3.93
1500 1617 1.719780 CAGTTCGTACGTGCTTCCTTC 59.280 52.381 16.05 0.00 0.00 3.46
1589 1722 3.009140 GCTCCGTGCATCATCGTG 58.991 61.111 0.00 0.00 42.31 4.35
1590 1723 3.009140 CTCCGTGCATCATCGTGC 58.991 61.111 0.00 0.00 45.25 5.34
1835 2027 1.045407 TGTCCGAGTACAAGCAGGTT 58.955 50.000 0.00 0.00 0.00 3.50
2405 2627 7.698130 AGTTCGATTGCTTATGCTTTTTCATAC 59.302 33.333 1.96 0.00 40.48 2.39
2555 2788 4.520492 CCAGCAGATAAATCCATGGTTACC 59.480 45.833 12.58 0.00 0.00 2.85
2630 2863 2.884639 CGGGTGGGTGATAATTGAATCC 59.115 50.000 0.00 0.00 0.00 3.01
2638 2871 7.121759 GTGGGTGATAATTGAATCCTGGATATG 59.878 40.741 10.13 0.00 0.00 1.78
2639 2872 7.018449 TGGGTGATAATTGAATCCTGGATATGA 59.982 37.037 10.13 0.00 0.00 2.15
2640 2873 8.057623 GGGTGATAATTGAATCCTGGATATGAT 58.942 37.037 10.13 0.00 0.00 2.45
2641 2874 9.118300 GGTGATAATTGAATCCTGGATATGATC 57.882 37.037 10.13 8.67 0.00 2.92
2642 2875 9.676861 GTGATAATTGAATCCTGGATATGATCA 57.323 33.333 10.13 11.04 0.00 2.92
2647 2880 9.824216 AATTGAATCCTGGATATGATCAAGATT 57.176 29.630 20.30 11.93 31.67 2.40
2648 2881 8.859236 TTGAATCCTGGATATGATCAAGATTC 57.141 34.615 10.13 9.58 39.03 2.52
2649 2882 8.215954 TGAATCCTGGATATGATCAAGATTCT 57.784 34.615 10.13 0.00 39.16 2.40
2650 2883 8.319881 TGAATCCTGGATATGATCAAGATTCTC 58.680 37.037 10.13 0.00 39.16 2.87
2662 2895 7.547227 TGATCAAGATTCTCGATTGTTCAGTA 58.453 34.615 0.00 0.00 32.04 2.74
2664 2897 9.684448 GATCAAGATTCTCGATTGTTCAGTATA 57.316 33.333 0.00 0.00 0.00 1.47
2692 2925 9.831737 CTAGTTTCATTGTCTGAATCGATTTTT 57.168 29.630 12.81 0.00 43.30 1.94
2697 2932 2.491693 TGTCTGAATCGATTTTTGGCCC 59.508 45.455 12.81 0.00 0.00 5.80
2724 2959 4.281688 GCATATCTGGCCCATGTTTTACAT 59.718 41.667 0.00 0.00 39.91 2.29
2762 3683 7.569226 GCCCGCGTTTTATAATTTTCGACTATA 60.569 37.037 4.92 0.00 0.00 1.31
2778 3699 4.793216 CGACTATATGCTTTGTTTGGTTGC 59.207 41.667 0.00 0.00 0.00 4.17
2779 3700 5.618863 CGACTATATGCTTTGTTTGGTTGCA 60.619 40.000 0.00 0.00 38.05 4.08
2780 3701 5.469479 ACTATATGCTTTGTTTGGTTGCAC 58.531 37.500 0.00 0.00 36.44 4.57
2781 3702 2.687700 ATGCTTTGTTTGGTTGCACA 57.312 40.000 0.00 0.00 36.44 4.57
2880 3801 5.230182 TGCATGTTACAACACAACAAAACA 58.770 33.333 0.00 0.00 42.51 2.83
2928 3849 3.391296 AGTTCTTCAGCTCACTTAACCCA 59.609 43.478 0.00 0.00 0.00 4.51
3000 3921 6.318396 ACGAACTTGTACTACTAATCCTCTCC 59.682 42.308 0.00 0.00 0.00 3.71
3029 3950 8.160765 CCTCTCTAGTCACAAATCCTCTATAGA 58.839 40.741 1.69 1.69 0.00 1.98
3051 3972 7.417496 AGAAACTATTCTTGTAACCGTTCAC 57.583 36.000 0.00 0.00 43.43 3.18
3054 3975 5.235516 ACTATTCTTGTAACCGTTCACCTG 58.764 41.667 0.00 0.00 0.00 4.00
3064 3985 0.950836 CGTTCACCTGTTCATGGCAA 59.049 50.000 0.00 0.00 0.00 4.52
3065 3986 1.541147 CGTTCACCTGTTCATGGCAAT 59.459 47.619 0.00 0.00 0.00 3.56
3066 3987 2.669113 CGTTCACCTGTTCATGGCAATG 60.669 50.000 0.00 0.00 34.88 2.82
3067 3988 2.291209 TCACCTGTTCATGGCAATGT 57.709 45.000 0.00 0.00 35.15 2.71
3068 3989 2.161855 TCACCTGTTCATGGCAATGTC 58.838 47.619 0.00 0.00 35.15 3.06
3069 3990 2.165167 CACCTGTTCATGGCAATGTCT 58.835 47.619 0.00 0.00 35.15 3.41
3070 3991 2.094906 CACCTGTTCATGGCAATGTCTG 60.095 50.000 0.00 0.79 35.15 3.51
3079 4000 3.727419 GCAATGTCTGCCATGAACC 57.273 52.632 0.00 0.00 46.13 3.62
3080 4001 0.889994 GCAATGTCTGCCATGAACCA 59.110 50.000 0.00 0.00 46.13 3.67
3081 4002 1.479323 GCAATGTCTGCCATGAACCAT 59.521 47.619 0.00 0.00 46.13 3.55
3082 4003 2.689471 GCAATGTCTGCCATGAACCATA 59.311 45.455 0.00 0.00 46.13 2.74
3083 4004 3.243301 GCAATGTCTGCCATGAACCATAG 60.243 47.826 0.00 0.00 46.13 2.23
3084 4005 4.201657 CAATGTCTGCCATGAACCATAGA 58.798 43.478 0.00 0.00 32.82 1.98
3085 4006 4.719026 ATGTCTGCCATGAACCATAGAT 57.281 40.909 0.00 0.00 30.69 1.98
3086 4007 4.508551 TGTCTGCCATGAACCATAGATT 57.491 40.909 0.00 0.00 0.00 2.40
3087 4008 4.454678 TGTCTGCCATGAACCATAGATTC 58.545 43.478 0.00 0.00 0.00 2.52
3088 4009 3.817647 GTCTGCCATGAACCATAGATTCC 59.182 47.826 0.00 0.00 0.00 3.01
3089 4010 3.152341 CTGCCATGAACCATAGATTCCC 58.848 50.000 0.00 0.00 0.00 3.97
3090 4011 2.154462 GCCATGAACCATAGATTCCCG 58.846 52.381 0.00 0.00 0.00 5.14
3091 4012 2.783135 CCATGAACCATAGATTCCCGG 58.217 52.381 0.00 0.00 0.00 5.73
3092 4013 2.371841 CCATGAACCATAGATTCCCGGA 59.628 50.000 0.73 0.00 0.00 5.14
3093 4014 3.557898 CCATGAACCATAGATTCCCGGAG 60.558 52.174 0.73 0.00 0.00 4.63
3094 4015 2.759355 TGAACCATAGATTCCCGGAGT 58.241 47.619 0.73 0.00 0.00 3.85
3095 4016 2.698797 TGAACCATAGATTCCCGGAGTC 59.301 50.000 0.73 1.61 0.00 3.36
3096 4017 1.718280 ACCATAGATTCCCGGAGTCC 58.282 55.000 0.73 0.00 0.00 3.85
3097 4018 1.220750 ACCATAGATTCCCGGAGTCCT 59.779 52.381 0.73 0.00 0.00 3.85
3098 4019 1.896465 CCATAGATTCCCGGAGTCCTC 59.104 57.143 0.73 0.00 0.00 3.71
3099 4020 1.896465 CATAGATTCCCGGAGTCCTCC 59.104 57.143 0.73 3.09 46.18 4.30
3152 4073 6.372185 CAAGACAGAAGAGCAAGATTTCAAG 58.628 40.000 0.00 0.00 0.00 3.02
3159 4080 5.118642 AGAGCAAGATTTCAAGAAGCAAC 57.881 39.130 0.00 0.00 0.00 4.17
3209 4130 5.334414 GGAATAGAAGCAACATAAGGATGCG 60.334 44.000 0.00 0.00 44.60 4.73
3221 4142 1.144057 GGATGCGTCACTACCAGGG 59.856 63.158 8.47 0.00 0.00 4.45
3222 4143 1.327690 GGATGCGTCACTACCAGGGA 61.328 60.000 8.47 0.00 0.00 4.20
3240 4161 5.844516 CCAGGGAAAACCCTATAGATAGACA 59.155 44.000 7.53 0.00 41.63 3.41
3259 4180 3.295973 ACACTTAACAACAATGCTGGGT 58.704 40.909 0.00 0.00 0.00 4.51
3263 4184 2.969821 AACAACAATGCTGGGTAGGA 57.030 45.000 0.00 0.00 0.00 2.94
3264 4185 2.496899 ACAACAATGCTGGGTAGGAG 57.503 50.000 0.00 0.00 0.00 3.69
3265 4186 1.098050 CAACAATGCTGGGTAGGAGC 58.902 55.000 0.00 0.00 36.95 4.70
3293 4215 6.237755 CCACTATTGTTACTTAGTAGCAACGC 60.238 42.308 20.65 0.00 40.73 4.84
3307 4229 1.956297 CAACGCGGGGATTAATACCA 58.044 50.000 18.78 0.00 29.87 3.25
3308 4230 2.290464 CAACGCGGGGATTAATACCAA 58.710 47.619 18.78 0.00 29.87 3.67
3321 4243 9.127277 GGGATTAATACCAAGCTACAAATAACA 57.873 33.333 12.23 0.00 0.00 2.41
3335 4257 5.235516 ACAAATAACAAGTAGTAGCAGCGT 58.764 37.500 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.266718 TGGATCTTTGCACGCTGTTTC 59.733 47.619 0.00 0.00 0.00 2.78
1 2 1.317613 TGGATCTTTGCACGCTGTTT 58.682 45.000 0.00 0.00 0.00 2.83
2 3 1.317613 TTGGATCTTTGCACGCTGTT 58.682 45.000 0.00 0.00 0.00 3.16
3 4 1.200716 CATTGGATCTTTGCACGCTGT 59.799 47.619 0.00 0.00 0.00 4.40
4 5 1.904144 CATTGGATCTTTGCACGCTG 58.096 50.000 0.00 0.00 0.00 5.18
5 6 0.171903 GCATTGGATCTTTGCACGCT 59.828 50.000 9.27 0.00 36.40 5.07
6 7 0.109179 TGCATTGGATCTTTGCACGC 60.109 50.000 11.85 0.35 41.18 5.34
9 10 3.093814 AGATGTGCATTGGATCTTTGCA 58.906 40.909 11.85 11.85 43.63 4.08
18 19 2.933906 GGCATTTTCAGATGTGCATTGG 59.066 45.455 0.00 0.00 39.27 3.16
27 28 2.299867 GTTGGTGTGGGCATTTTCAGAT 59.700 45.455 0.00 0.00 0.00 2.90
32 33 1.207791 TTGGTTGGTGTGGGCATTTT 58.792 45.000 0.00 0.00 0.00 1.82
67 68 3.011818 CCCGTGGTTTACAGTAATTCCC 58.988 50.000 10.65 5.40 0.00 3.97
86 87 2.052468 ACCTCCCGGTAATTATGTCCC 58.948 52.381 0.00 0.00 43.29 4.46
141 142 3.861689 GGTTAGATTTGACGGGTACTTCG 59.138 47.826 7.42 7.42 0.00 3.79
143 144 4.895668 TGGTTAGATTTGACGGGTACTT 57.104 40.909 0.00 0.00 0.00 2.24
151 152 6.868339 CCTTTGAACCAATGGTTAGATTTGAC 59.132 38.462 18.76 3.47 46.95 3.18
188 189 5.732247 GCGGCGGAATTACTAATGACAAAAT 60.732 40.000 9.78 0.00 0.00 1.82
278 282 5.106197 CCATCTCCATTGATCGTTTTGACAA 60.106 40.000 0.00 0.00 0.00 3.18
345 350 3.466836 CAAAGGATCTATGCCTGCGTTA 58.533 45.455 0.00 0.00 35.50 3.18
423 428 0.545171 TCACTCTATCTCCCGGTCGT 59.455 55.000 0.00 0.00 0.00 4.34
715 744 5.190132 TGGACCTTTAATTCTCCGGTAATGA 59.810 40.000 0.00 0.00 0.00 2.57
716 745 5.296035 GTGGACCTTTAATTCTCCGGTAATG 59.704 44.000 0.00 0.00 0.00 1.90
833 874 2.482839 GCATCTAGTGAGTGGCCTCTTC 60.483 54.545 9.08 5.88 38.61 2.87
863 924 9.688091 ATTTATAGAGCATCGTCTATCCTTCTA 57.312 33.333 0.00 0.00 42.67 2.10
864 925 8.465999 CATTTATAGAGCATCGTCTATCCTTCT 58.534 37.037 0.00 0.00 42.67 2.85
865 926 7.704472 CCATTTATAGAGCATCGTCTATCCTTC 59.296 40.741 0.00 0.00 42.67 3.46
866 927 7.179338 ACCATTTATAGAGCATCGTCTATCCTT 59.821 37.037 0.00 0.00 42.67 3.36
867 928 6.665680 ACCATTTATAGAGCATCGTCTATCCT 59.334 38.462 0.00 0.00 42.67 3.24
868 929 6.754209 CACCATTTATAGAGCATCGTCTATCC 59.246 42.308 0.00 0.00 42.67 2.59
869 930 7.486551 GTCACCATTTATAGAGCATCGTCTATC 59.513 40.741 0.00 0.00 42.67 2.08
870 931 7.177568 AGTCACCATTTATAGAGCATCGTCTAT 59.822 37.037 0.00 0.00 42.67 1.98
871 932 6.490381 AGTCACCATTTATAGAGCATCGTCTA 59.510 38.462 0.00 0.00 42.67 2.59
872 933 5.303078 AGTCACCATTTATAGAGCATCGTCT 59.697 40.000 0.00 0.00 42.67 4.18
874 935 5.292765 CAGTCACCATTTATAGAGCATCGT 58.707 41.667 0.00 0.00 42.67 3.73
875 936 4.151335 GCAGTCACCATTTATAGAGCATCG 59.849 45.833 0.00 0.00 42.67 3.84
892 955 1.350319 GAAACGTTGCGTGCAGTCA 59.650 52.632 0.00 0.00 39.99 3.41
948 1023 4.040952 AGTTGCCACTGAGAGTAAGATGTT 59.959 41.667 0.00 0.00 0.00 2.71
1207 1292 1.227999 TTCTTGCCGTTGGAGAAGCG 61.228 55.000 0.00 0.00 0.00 4.68
1209 1294 0.512952 CGTTCTTGCCGTTGGAGAAG 59.487 55.000 0.00 0.00 30.66 2.85
1260 1345 4.216902 GTGTATGTGTATCCATGCATGCAT 59.783 41.667 27.46 27.46 39.19 3.96
1266 1351 4.875536 TGTGAAGTGTATGTGTATCCATGC 59.124 41.667 0.00 0.00 0.00 4.06
1274 1359 2.902705 ACGGTGTGAAGTGTATGTGT 57.097 45.000 0.00 0.00 0.00 3.72
1278 1370 2.103432 TGGTGAACGGTGTGAAGTGTAT 59.897 45.455 0.00 0.00 0.00 2.29
1279 1371 1.481363 TGGTGAACGGTGTGAAGTGTA 59.519 47.619 0.00 0.00 0.00 2.90
1280 1372 0.250793 TGGTGAACGGTGTGAAGTGT 59.749 50.000 0.00 0.00 0.00 3.55
1281 1373 0.937304 CTGGTGAACGGTGTGAAGTG 59.063 55.000 0.00 0.00 0.00 3.16
1282 1374 0.814010 GCTGGTGAACGGTGTGAAGT 60.814 55.000 0.00 0.00 0.00 3.01
1283 1375 1.507141 GGCTGGTGAACGGTGTGAAG 61.507 60.000 0.00 0.00 0.00 3.02
1284 1376 1.525077 GGCTGGTGAACGGTGTGAA 60.525 57.895 0.00 0.00 0.00 3.18
1285 1377 2.110213 GGCTGGTGAACGGTGTGA 59.890 61.111 0.00 0.00 0.00 3.58
1286 1378 3.345808 CGGCTGGTGAACGGTGTG 61.346 66.667 0.00 0.00 0.00 3.82
1287 1379 2.879813 AAACGGCTGGTGAACGGTGT 62.880 55.000 0.00 0.00 0.00 4.16
1288 1380 2.184167 AAACGGCTGGTGAACGGTG 61.184 57.895 0.00 0.00 0.00 4.94
1289 1381 2.184167 CAAACGGCTGGTGAACGGT 61.184 57.895 0.00 0.00 0.00 4.83
1290 1382 2.184167 ACAAACGGCTGGTGAACGG 61.184 57.895 5.56 0.00 0.00 4.44
1291 1383 1.010125 CACAAACGGCTGGTGAACG 60.010 57.895 5.56 0.00 34.52 3.95
1292 1384 1.299089 GCACAAACGGCTGGTGAAC 60.299 57.895 4.76 0.00 34.52 3.18
1305 1397 5.592282 TCAGTTGGTCTTAAAATCTGCACAA 59.408 36.000 0.00 0.00 0.00 3.33
1306 1398 5.129634 TCAGTTGGTCTTAAAATCTGCACA 58.870 37.500 0.00 0.00 0.00 4.57
1310 1402 9.918630 AAATCAATCAGTTGGTCTTAAAATCTG 57.081 29.630 0.00 0.00 35.99 2.90
1318 1422 9.840427 CGTTAATTAAATCAATCAGTTGGTCTT 57.160 29.630 0.00 0.00 35.99 3.01
1321 1426 9.787532 CATCGTTAATTAAATCAATCAGTTGGT 57.212 29.630 0.00 0.00 35.99 3.67
1344 1455 3.372676 CTCGCCTGCGTGCAACATC 62.373 63.158 11.68 0.00 40.74 3.06
1513 1630 5.921976 TGAATGAAGTGTGCATTGATGAAAC 59.078 36.000 0.00 0.00 36.19 2.78
1514 1631 6.086785 TGAATGAAGTGTGCATTGATGAAA 57.913 33.333 0.00 0.00 36.19 2.69
1516 1633 5.708877 TTGAATGAAGTGTGCATTGATGA 57.291 34.783 0.00 0.00 36.19 2.92
1517 1634 8.642908 ATTATTGAATGAAGTGTGCATTGATG 57.357 30.769 0.00 0.00 36.19 3.07
1589 1722 3.044059 GATGTTGGCCTGCACGAGC 62.044 63.158 3.32 0.00 42.57 5.03
1590 1723 1.028330 ATGATGTTGGCCTGCACGAG 61.028 55.000 3.32 0.00 0.00 4.18
1772 1964 4.516195 GAGAACTCCCGGGAGCGC 62.516 72.222 44.15 35.17 45.54 5.92
1793 1985 2.953466 TGTACTTGATGTAGTCCGGC 57.047 50.000 0.00 0.00 0.00 6.13
2031 2223 2.895372 CACCGCTCCATTACCGCC 60.895 66.667 0.00 0.00 0.00 6.13
2032 2224 1.702491 GAACACCGCTCCATTACCGC 61.702 60.000 0.00 0.00 0.00 5.68
2036 2228 0.390603 CCACGAACACCGCTCCATTA 60.391 55.000 0.00 0.00 43.32 1.90
2039 2231 4.980805 GCCACGAACACCGCTCCA 62.981 66.667 0.00 0.00 43.32 3.86
2148 2340 2.746277 GCCGATGCCGTTGAACCT 60.746 61.111 0.00 0.00 0.00 3.50
2405 2627 2.892852 TGACAAAATCAAGAAGGCCAGG 59.107 45.455 5.01 0.00 33.02 4.45
2528 2761 4.141181 ACCATGGATTTATCTGCTGGCTAA 60.141 41.667 21.47 0.00 0.00 3.09
2555 2788 2.029380 TGACACCACAAGTACCTCGATG 60.029 50.000 0.00 0.00 0.00 3.84
2630 2863 7.818446 ACAATCGAGAATCTTGATCATATCCAG 59.182 37.037 13.04 0.00 33.85 3.86
2638 2871 6.900568 ACTGAACAATCGAGAATCTTGATC 57.099 37.500 13.04 3.09 33.85 2.92
2639 2872 9.689976 CTATACTGAACAATCGAGAATCTTGAT 57.310 33.333 7.17 7.17 36.26 2.57
2640 2873 7.649705 GCTATACTGAACAATCGAGAATCTTGA 59.350 37.037 2.18 2.18 0.00 3.02
2641 2874 7.651304 AGCTATACTGAACAATCGAGAATCTTG 59.349 37.037 0.00 0.00 0.00 3.02
2642 2875 7.721402 AGCTATACTGAACAATCGAGAATCTT 58.279 34.615 0.00 0.00 0.00 2.40
2643 2876 7.283625 AGCTATACTGAACAATCGAGAATCT 57.716 36.000 0.00 0.00 0.00 2.40
2644 2877 8.293867 ACTAGCTATACTGAACAATCGAGAATC 58.706 37.037 0.00 0.00 0.00 2.52
2647 2880 7.569639 AACTAGCTATACTGAACAATCGAGA 57.430 36.000 0.00 0.00 0.00 4.04
2648 2881 7.915923 TGAAACTAGCTATACTGAACAATCGAG 59.084 37.037 0.00 0.00 0.00 4.04
2649 2882 7.768240 TGAAACTAGCTATACTGAACAATCGA 58.232 34.615 0.00 0.00 0.00 3.59
2650 2883 7.987268 TGAAACTAGCTATACTGAACAATCG 57.013 36.000 0.00 0.00 0.00 3.34
2692 2925 1.538167 CCAGATATGCAAGGGGCCA 59.462 57.895 4.39 0.00 43.89 5.36
2697 2932 1.254026 CATGGGCCAGATATGCAAGG 58.746 55.000 13.78 0.00 0.00 3.61
2762 3683 2.278854 GTGTGCAACCAAACAAAGCAT 58.721 42.857 0.00 0.00 37.56 3.79
2780 3701 4.393062 GGTAATCACATCAGACACAAGGTG 59.607 45.833 0.00 0.00 39.75 4.00
2781 3702 4.287067 AGGTAATCACATCAGACACAAGGT 59.713 41.667 0.00 0.00 0.00 3.50
2835 3756 5.346822 GCAGTAAAAGCATTGATTTGAGTGG 59.653 40.000 17.35 4.18 27.10 4.00
2889 3810 8.335532 TGAAGAACTTCATAATTTTCGTCCAT 57.664 30.769 12.40 0.00 43.90 3.41
2977 3898 6.834969 AGGGAGAGGATTAGTAGTACAAGTTC 59.165 42.308 2.52 0.00 0.00 3.01
3000 3921 4.285863 AGGATTTGTGACTAGAGAGGAGG 58.714 47.826 0.00 0.00 0.00 4.30
3029 3950 6.204108 CAGGTGAACGGTTACAAGAATAGTTT 59.796 38.462 0.00 0.00 0.00 2.66
3051 3972 2.933495 CAGACATTGCCATGAACAGG 57.067 50.000 4.52 0.00 34.11 4.00
3064 3985 4.719026 ATCTATGGTTCATGGCAGACAT 57.281 40.909 0.00 0.00 41.57 3.06
3065 3986 4.454678 GAATCTATGGTTCATGGCAGACA 58.545 43.478 0.00 0.00 0.00 3.41
3066 3987 3.817647 GGAATCTATGGTTCATGGCAGAC 59.182 47.826 0.00 0.00 0.00 3.51
3067 3988 3.181440 GGGAATCTATGGTTCATGGCAGA 60.181 47.826 0.00 0.00 0.00 4.26
3068 3989 3.152341 GGGAATCTATGGTTCATGGCAG 58.848 50.000 0.00 0.00 0.00 4.85
3069 3990 2.487086 CGGGAATCTATGGTTCATGGCA 60.487 50.000 0.00 0.00 0.00 4.92
3070 3991 2.154462 CGGGAATCTATGGTTCATGGC 58.846 52.381 0.00 0.00 0.00 4.40
3071 3992 2.371841 TCCGGGAATCTATGGTTCATGG 59.628 50.000 0.00 0.00 0.00 3.66
3072 3993 3.071602 ACTCCGGGAATCTATGGTTCATG 59.928 47.826 0.00 0.00 0.00 3.07
3073 3994 3.318313 ACTCCGGGAATCTATGGTTCAT 58.682 45.455 0.00 0.00 0.00 2.57
3074 3995 2.698797 GACTCCGGGAATCTATGGTTCA 59.301 50.000 0.00 0.00 0.00 3.18
3075 3996 2.037381 GGACTCCGGGAATCTATGGTTC 59.963 54.545 5.37 0.00 0.00 3.62
3076 3997 2.047830 GGACTCCGGGAATCTATGGTT 58.952 52.381 5.37 0.00 0.00 3.67
3077 3998 1.220750 AGGACTCCGGGAATCTATGGT 59.779 52.381 5.37 0.00 0.00 3.55
3078 3999 1.896465 GAGGACTCCGGGAATCTATGG 59.104 57.143 5.37 0.00 0.00 2.74
3079 4000 1.896465 GGAGGACTCCGGGAATCTATG 59.104 57.143 5.37 0.00 40.36 2.23
3080 4001 2.312424 GGAGGACTCCGGGAATCTAT 57.688 55.000 5.37 0.00 40.36 1.98
3081 4002 3.844161 GGAGGACTCCGGGAATCTA 57.156 57.895 5.37 0.00 40.36 1.98
3082 4003 4.709690 GGAGGACTCCGGGAATCT 57.290 61.111 5.37 0.00 40.36 2.40
3091 4012 4.279145 TGTCATGTACTTAGGGAGGACTC 58.721 47.826 0.00 0.00 40.15 3.36
3092 4013 4.332683 TGTCATGTACTTAGGGAGGACT 57.667 45.455 0.00 0.00 40.15 3.85
3093 4014 4.039366 GGATGTCATGTACTTAGGGAGGAC 59.961 50.000 0.00 0.00 39.89 3.85
3094 4015 4.223953 GGATGTCATGTACTTAGGGAGGA 58.776 47.826 0.00 0.00 0.00 3.71
3095 4016 3.967326 TGGATGTCATGTACTTAGGGAGG 59.033 47.826 0.00 0.00 0.00 4.30
3096 4017 4.651503 AGTGGATGTCATGTACTTAGGGAG 59.348 45.833 0.00 0.00 0.00 4.30
3097 4018 4.620723 AGTGGATGTCATGTACTTAGGGA 58.379 43.478 0.00 0.00 0.00 4.20
3098 4019 5.104941 TGAAGTGGATGTCATGTACTTAGGG 60.105 44.000 9.95 0.00 32.23 3.53
3099 4020 5.977635 TGAAGTGGATGTCATGTACTTAGG 58.022 41.667 9.95 0.00 32.23 2.69
3152 4073 6.088085 GTGTTATGTGTTGCTAATGTTGCTTC 59.912 38.462 0.00 0.00 0.00 3.86
3159 4080 9.012448 CATATGTTGTGTTATGTGTTGCTAATG 57.988 33.333 0.00 0.00 0.00 1.90
3240 4161 4.079253 CCTACCCAGCATTGTTGTTAAGT 58.921 43.478 0.00 0.00 0.00 2.24
3259 4180 2.280308 AACAATAGTGGGGGCTCCTA 57.720 50.000 4.32 0.00 36.20 2.94
3263 4184 4.109320 ACTAAGTAACAATAGTGGGGGCT 58.891 43.478 0.00 0.00 31.35 5.19
3264 4185 4.498894 ACTAAGTAACAATAGTGGGGGC 57.501 45.455 0.00 0.00 31.35 5.80
3265 4186 5.129815 TGCTACTAAGTAACAATAGTGGGGG 59.870 44.000 0.00 0.00 34.37 5.40
3293 4215 4.345859 TGTAGCTTGGTATTAATCCCCG 57.654 45.455 0.00 0.00 0.00 5.73
3321 4243 1.765230 AGCCTACGCTGCTACTACTT 58.235 50.000 0.00 0.00 46.19 2.24


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

AutoCloner maintained by Alex Coulton.