Multiple sequence alignment - TraesCS3D01G424000

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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 TraesCS3D01G424000 chr3D 100.000 5715 0 0 1 5715 536240260 536245974 0.000000e+00 10554.0
1 TraesCS3D01G424000 chr3D 87.514 897 80 16 1740 2619 536241102 536241983 0.000000e+00 1007.0
2 TraesCS3D01G424000 chr3D 87.514 897 80 16 843 1724 536241999 536242878 0.000000e+00 1007.0
3 TraesCS3D01G424000 chr3D 91.033 736 52 9 1421 2153 536216419 536217143 0.000000e+00 981.0
4 TraesCS3D01G424000 chr3D 89.681 407 37 3 843 1245 536216735 536217140 1.100000e-141 514.0
5 TraesCS3D01G424000 chr3D 90.885 373 24 5 316 683 536213034 536213401 5.140000e-135 492.0
6 TraesCS3D01G424000 chr3D 86.908 359 29 9 691 1044 536213464 536213809 2.500000e-103 387.0
7 TraesCS3D01G424000 chr3D 89.420 293 22 5 2334 2620 536216433 536216722 1.510000e-95 361.0
8 TraesCS3D01G424000 chr3D 84.211 342 23 17 1 319 536212004 536212337 2.590000e-78 303.0
9 TraesCS3D01G424000 chr3D 81.152 382 58 11 3721 4095 535650912 535650538 1.560000e-75 294.0
10 TraesCS3D01G424000 chr3D 80.371 377 66 8 3723 4095 535644740 535644368 4.360000e-71 279.0
11 TraesCS3D01G424000 chr3D 92.105 190 12 1 2113 2302 536214401 536214587 1.220000e-66 265.0
12 TraesCS3D01G424000 chr3D 88.208 212 22 1 1000 1208 536201483 536201694 3.420000e-62 250.0
13 TraesCS3D01G424000 chr3D 87.097 217 18 5 1208 1416 536214401 536214615 2.660000e-58 237.0
14 TraesCS3D01G424000 chr3D 87.129 202 20 2 1915 2113 536201496 536201694 2.070000e-54 224.0
15 TraesCS3D01G424000 chr3D 88.083 193 17 5 1740 1932 536213609 536213795 2.070000e-54 224.0
16 TraesCS3D01G424000 chr3D 82.609 69 9 3 2571 2637 570507381 570507314 2.220000e-04 58.4
17 TraesCS3D01G424000 chr3D 96.774 31 1 0 2583 2613 195097994 195097964 1.000000e-02 52.8
18 TraesCS3D01G424000 chr3B 88.563 1329 115 25 1421 2728 708488303 708489615 0.000000e+00 1578.0
19 TraesCS3D01G424000 chr3B 92.473 1116 59 12 3875 4972 708490735 708491843 0.000000e+00 1572.0
20 TraesCS3D01G424000 chr3B 87.639 898 79 15 843 1718 708488613 708489500 0.000000e+00 1014.0
21 TraesCS3D01G424000 chr3B 91.612 608 34 4 5049 5646 708491977 708492577 0.000000e+00 824.0
22 TraesCS3D01G424000 chr3B 84.218 735 63 26 687 1416 708487102 708487788 0.000000e+00 665.0
23 TraesCS3D01G424000 chr3B 86.054 588 46 16 1715 2296 708487204 708487761 2.950000e-167 599.0
24 TraesCS3D01G424000 chr3B 88.608 395 26 10 691 1075 708423847 708424232 4.030000e-126 462.0
25 TraesCS3D01G424000 chr3B 91.468 293 19 2 1977 2267 708455678 708455966 1.150000e-106 398.0
26 TraesCS3D01G424000 chr3B 91.096 292 21 3 1070 1357 708455676 708455966 1.930000e-104 390.0
27 TraesCS3D01G424000 chr3B 85.246 366 49 5 3736 4099 708311137 708310775 6.990000e-99 372.0
28 TraesCS3D01G424000 chr3B 83.295 431 34 17 36 442 708479014 708479430 4.210000e-96 363.0
29 TraesCS3D01G424000 chr3B 82.112 464 38 23 1 432 708416746 708417196 7.040000e-94 355.0
30 TraesCS3D01G424000 chr3B 80.940 383 57 13 3721 4095 707128692 707128318 7.250000e-74 289.0
31 TraesCS3D01G424000 chr3B 85.664 286 26 10 2339 2619 708488322 708488597 2.610000e-73 287.0
32 TraesCS3D01G424000 chr3B 86.220 254 15 7 441 685 708486807 708487049 2.040000e-64 257.0
33 TraesCS3D01G424000 chr3B 89.286 196 19 2 1000 1194 708410090 708410284 1.590000e-60 244.0
34 TraesCS3D01G424000 chr3B 86.341 205 23 2 1895 2099 708410085 708410284 9.640000e-53 219.0
35 TraesCS3D01G424000 chr3B 89.937 159 11 3 2047 2202 708423296 708423452 3.490000e-47 200.0
36 TraesCS3D01G424000 chr3B 97.222 36 1 0 5674 5709 708492575 708492610 1.720000e-05 62.1
37 TraesCS3D01G424000 chr3A 91.902 1099 61 13 3717 4814 671722945 671724016 0.000000e+00 1511.0
38 TraesCS3D01G424000 chr3A 91.029 680 41 12 5049 5709 671725075 671725753 0.000000e+00 900.0
39 TraesCS3D01G424000 chr3A 83.333 708 66 24 16 685 671717884 671718577 1.760000e-169 606.0
40 TraesCS3D01G424000 chr3A 85.792 366 47 5 3736 4099 671661137 671660775 3.230000e-102 383.0
41 TraesCS3D01G424000 chr3A 85.676 370 39 11 928 1285 671718864 671719231 1.500000e-100 377.0
42 TraesCS3D01G424000 chr3A 81.154 520 46 26 1 491 671704405 671704901 2.520000e-98 370.0
43 TraesCS3D01G424000 chr3A 85.960 349 37 8 1826 2168 671718864 671719206 4.210000e-96 363.0
44 TraesCS3D01G424000 chr3A 80.628 382 60 11 3721 4095 670834597 670834223 3.370000e-72 283.0
45 TraesCS3D01G424000 chr3A 86.932 176 12 5 691 861 671718661 671718830 2.720000e-43 187.0
46 TraesCS3D01G424000 chr3A 89.024 82 7 2 4969 5049 671724966 671725046 3.640000e-17 100.0
47 TraesCS3D01G424000 chr5D 88.769 837 81 12 2715 3542 545912441 545911609 0.000000e+00 1013.0
48 TraesCS3D01G424000 chr5D 88.381 809 80 9 2736 3535 230014645 230013842 0.000000e+00 961.0
49 TraesCS3D01G424000 chr4D 88.956 824 75 8 2717 3535 324234348 324233536 0.000000e+00 1003.0
50 TraesCS3D01G424000 chr4D 88.286 811 82 10 2733 3535 449735614 449736419 0.000000e+00 959.0
51 TraesCS3D01G424000 chr7D 89.122 809 75 11 2735 3535 1105630 1104827 0.000000e+00 994.0
52 TraesCS3D01G424000 chr7D 88.271 827 77 10 2725 3543 594070777 594071591 0.000000e+00 972.0
53 TraesCS3D01G424000 chr6B 88.186 838 84 11 2716 3545 706133611 706134441 0.000000e+00 985.0
54 TraesCS3D01G424000 chr6B 87.787 827 88 10 2721 3542 153351435 153350617 0.000000e+00 955.0
55 TraesCS3D01G424000 chr6B 88.119 808 84 10 2733 3535 478881951 478882751 0.000000e+00 950.0
56 TraesCS3D01G424000 chr1D 81.679 393 54 16 3719 4099 419999951 419999565 1.550000e-80 311.0
57 TraesCS3D01G424000 chr1D 94.737 38 2 0 2588 2625 9000191 9000154 6.180000e-05 60.2
58 TraesCS3D01G424000 chr1B 81.633 392 54 16 3721 4099 566983455 566983069 5.560000e-80 309.0


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 TraesCS3D01G424000 chr3D 536240260 536245974 5714 False 10554.000000 10554 100.000000 1 5715 1 chr3D.!!$F1 5714
1 TraesCS3D01G424000 chr3D 536241102 536242878 1776 False 1007.000000 1007 87.514000 843 2619 2 chr3D.!!$F4 1776
2 TraesCS3D01G424000 chr3D 536212004 536217143 5139 False 418.222222 981 88.824778 1 2620 9 chr3D.!!$F3 2619
3 TraesCS3D01G424000 chr3B 708486807 708492610 5803 False 762.011111 1578 88.851667 441 5709 9 chr3B.!!$F6 5268
4 TraesCS3D01G424000 chr3B 708423296 708424232 936 False 331.000000 462 89.272500 691 2202 2 chr3B.!!$F4 1511
5 TraesCS3D01G424000 chr3A 671717884 671725753 7869 False 577.714286 1511 87.693714 16 5709 7 chr3A.!!$F2 5693
6 TraesCS3D01G424000 chr5D 545911609 545912441 832 True 1013.000000 1013 88.769000 2715 3542 1 chr5D.!!$R2 827
7 TraesCS3D01G424000 chr5D 230013842 230014645 803 True 961.000000 961 88.381000 2736 3535 1 chr5D.!!$R1 799
8 TraesCS3D01G424000 chr4D 324233536 324234348 812 True 1003.000000 1003 88.956000 2717 3535 1 chr4D.!!$R1 818
9 TraesCS3D01G424000 chr4D 449735614 449736419 805 False 959.000000 959 88.286000 2733 3535 1 chr4D.!!$F1 802
10 TraesCS3D01G424000 chr7D 1104827 1105630 803 True 994.000000 994 89.122000 2735 3535 1 chr7D.!!$R1 800
11 TraesCS3D01G424000 chr7D 594070777 594071591 814 False 972.000000 972 88.271000 2725 3543 1 chr7D.!!$F1 818
12 TraesCS3D01G424000 chr6B 706133611 706134441 830 False 985.000000 985 88.186000 2716 3545 1 chr6B.!!$F2 829
13 TraesCS3D01G424000 chr6B 153350617 153351435 818 True 955.000000 955 87.787000 2721 3542 1 chr6B.!!$R1 821
14 TraesCS3D01G424000 chr6B 478881951 478882751 800 False 950.000000 950 88.119000 2733 3535 1 chr6B.!!$F1 802

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
569 1318 0.107654 ATTCAGCAAGGTCGCCCTAC 60.108 55.0 0.00 0.00 41.56 3.18 F
736 1573 0.394192 GCCCCCTGGGTAACGTATAC 59.606 60.0 12.71 0.00 46.51 1.47 F
2654 6759 0.105408 AATGCGGATGGGGTACGTAC 59.895 55.0 17.56 17.56 36.21 3.67 F
3640 7761 0.250727 TGGGCTAGCTTCACACAACC 60.251 55.0 15.72 4.25 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 6732 0.944386 CCCATCCGCATTTTAGTCGG 59.056 55.000 0.00 0.00 44.16 4.79 R
2775 6881 0.826256 AGCGGTGATGGAGGCGTATA 60.826 55.000 0.00 0.00 0.00 1.47 R
4012 10514 0.108756 GACCAGTTCGAGGTACTGCC 60.109 60.000 9.75 1.64 41.55 4.85 R
4857 12146 1.345741 TCTCCCTCTGAAACTGCACTG 59.654 52.381 0.00 0.00 0.00 3.66 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
21 22 0.893270 TGGGGTGCATGTACACTTGC 60.893 55.000 16.13 13.42 44.38 4.01
46 48 7.121315 GCACTGATAGGTGAATAATATTTCCCC 59.879 40.741 0.00 0.00 39.34 4.81
79 81 6.179906 TGGAGAAAGGCTATTCTTGGATAG 57.820 41.667 11.47 0.00 39.70 2.08
88 90 9.920946 AAGGCTATTCTTGGATAGAAAATACAA 57.079 29.630 0.34 0.00 45.62 2.41
90 92 9.343539 GGCTATTCTTGGATAGAAAATACAAGT 57.656 33.333 9.24 0.00 45.62 3.16
94 96 9.753674 ATTCTTGGATAGAAAATACAAGTTGGA 57.246 29.630 7.96 0.00 45.62 3.53
95 97 8.561738 TCTTGGATAGAAAATACAAGTTGGAC 57.438 34.615 7.96 0.00 39.49 4.02
97 99 6.184789 TGGATAGAAAATACAAGTTGGACCC 58.815 40.000 7.96 0.00 0.00 4.46
98 100 5.296035 GGATAGAAAATACAAGTTGGACCCG 59.704 44.000 7.96 0.00 0.00 5.28
100 102 3.818773 AGAAAATACAAGTTGGACCCGTG 59.181 43.478 7.96 0.00 0.00 4.94
101 103 2.943036 AATACAAGTTGGACCCGTGT 57.057 45.000 7.96 0.00 0.00 4.49
102 104 2.467566 ATACAAGTTGGACCCGTGTC 57.532 50.000 7.96 0.00 40.98 3.67
121 137 0.999406 CGTTGGCGATTACAGGTCAG 59.001 55.000 0.00 0.00 41.33 3.51
124 140 0.613260 TGGCGATTACAGGTCAGCTT 59.387 50.000 0.00 0.00 0.00 3.74
137 157 4.946157 CAGGTCAGCTTTATTGGTCAATCT 59.054 41.667 0.00 0.00 32.50 2.40
149 169 9.973661 TTTATTGGTCAATCTAGGAGAAATGAA 57.026 29.630 0.00 0.00 29.71 2.57
230 255 6.795098 AATAATGTCTCGTTGTGTAGCAAA 57.205 33.333 0.00 0.00 39.03 3.68
276 301 6.147164 TGTTAGACTTTTGCCTAGTTTCATCG 59.853 38.462 0.00 0.00 0.00 3.84
546 1289 6.180771 AGTCTACTACTGTTTCTACGCTTC 57.819 41.667 0.00 0.00 36.93 3.86
569 1318 0.107654 ATTCAGCAAGGTCGCCCTAC 60.108 55.000 0.00 0.00 41.56 3.18
613 1370 1.898574 GCACAGGTGGTCCAAGGTG 60.899 63.158 12.30 12.30 36.40 4.00
655 1412 9.999883 GTACAACTAAACTAAACGTGTCAATAG 57.000 33.333 0.00 0.00 0.00 1.73
685 1442 4.753107 GTGTCTAGAAAACCCGAAACATCA 59.247 41.667 0.00 0.00 0.00 3.07
692 1527 1.382629 CCCGAAACATCAACCCCCT 59.617 57.895 0.00 0.00 0.00 4.79
701 1536 1.605058 ATCAACCCCCTCGTCGACAG 61.605 60.000 17.16 11.67 0.00 3.51
716 1551 1.128692 CGACAGTCGAAGAAATTGCCC 59.871 52.381 18.63 0.00 43.74 5.36
733 1570 3.076278 CGCCCCCTGGGTAACGTA 61.076 66.667 12.71 0.00 46.51 3.57
734 1571 2.437396 CGCCCCCTGGGTAACGTAT 61.437 63.158 12.71 0.00 46.51 3.06
735 1572 1.114722 CGCCCCCTGGGTAACGTATA 61.115 60.000 12.71 0.00 46.51 1.47
736 1573 0.394192 GCCCCCTGGGTAACGTATAC 59.606 60.000 12.71 0.00 46.51 1.47
737 1574 0.675633 CCCCCTGGGTAACGTATACG 59.324 60.000 23.24 23.24 40.94 3.06
809 1646 3.382865 TGATCGATCCTCTGGAAGAACAG 59.617 47.826 22.31 0.00 46.34 3.16
2627 6732 6.462073 TGACTTAAGACAAATCTTGTACGC 57.538 37.500 10.09 0.00 45.17 4.42
2650 6755 2.876550 GACTAAAATGCGGATGGGGTAC 59.123 50.000 0.00 0.00 0.00 3.34
2654 6759 0.105408 AATGCGGATGGGGTACGTAC 59.895 55.000 17.56 17.56 36.21 3.67
2658 6763 1.547372 GCGGATGGGGTACGTACATAT 59.453 52.381 26.02 16.23 36.21 1.78
2670 6775 6.404623 GGGTACGTACATATACAGTCACACAA 60.405 42.308 26.02 0.00 0.00 3.33
2717 6822 5.941788 AGTATCAAGGTTGACAAGGTCTTT 58.058 37.500 0.00 0.00 40.49 2.52
2720 6825 3.202151 TCAAGGTTGACAAGGTCTTTCCT 59.798 43.478 0.00 0.99 39.30 3.36
2792 6898 1.068472 GTCTATACGCCTCCATCACCG 60.068 57.143 0.00 0.00 0.00 4.94
2949 7058 9.627123 CTTCAAAACTAGACCCCATATTGATAA 57.373 33.333 0.00 0.00 0.00 1.75
2962 7071 7.041372 CCCCATATTGATAAGTTTCGACGAAAT 60.041 37.037 24.48 13.13 33.97 2.17
2989 7099 0.534652 TTGCCCAAAAGTTGCCATGC 60.535 50.000 0.00 0.00 0.00 4.06
3037 7147 5.300539 TGCTTAAACTAAAGTTGCCATGTGA 59.699 36.000 0.00 0.00 38.44 3.58
3136 7249 4.579454 AAGTGCATGTATCATGGCAATC 57.421 40.909 10.96 1.42 38.10 2.67
3150 7263 7.716799 TCATGGCAATCTTAGTTTATGGTTT 57.283 32.000 0.00 0.00 0.00 3.27
3160 7273 8.644374 TCTTAGTTTATGGTTTATGGCAAGTT 57.356 30.769 0.00 0.00 0.00 2.66
3243 7356 7.534723 AATAGCTGAAACATATCATGGCAAT 57.465 32.000 0.00 0.00 33.60 3.56
3266 7379 4.764679 TCAGTGTAAACATCATGGCAAC 57.235 40.909 0.00 0.00 0.00 4.17
3294 7407 4.622740 GTGCAATAGACATGGCAACTTTTC 59.377 41.667 0.00 0.00 42.87 2.29
3472 7592 1.301401 GCGGTGAAGTGGCACAGTA 60.301 57.895 21.41 1.74 43.84 2.74
3552 7672 5.514914 GCGTTGTTCAAAAAGATTGACAAGA 59.485 36.000 0.00 0.00 0.00 3.02
3612 7732 2.484594 GCTCCTCCCAGATTTACAGAGC 60.485 54.545 0.00 0.00 38.76 4.09
3624 7745 0.965866 TACAGAGCGGTCAGAGTGGG 60.966 60.000 18.15 0.00 0.00 4.61
3637 7758 0.321671 GAGTGGGCTAGCTTCACACA 59.678 55.000 29.19 13.47 34.65 3.72
3638 7759 0.764890 AGTGGGCTAGCTTCACACAA 59.235 50.000 29.19 2.65 34.65 3.33
3639 7760 0.875059 GTGGGCTAGCTTCACACAAC 59.125 55.000 25.60 7.34 32.58 3.32
3640 7761 0.250727 TGGGCTAGCTTCACACAACC 60.251 55.000 15.72 4.25 0.00 3.77
3642 7763 1.278127 GGGCTAGCTTCACACAACCTA 59.722 52.381 15.72 0.00 0.00 3.08
3643 7764 2.622436 GGCTAGCTTCACACAACCTAG 58.378 52.381 15.72 0.00 0.00 3.02
3645 7766 2.354203 GCTAGCTTCACACAACCTAGCT 60.354 50.000 7.70 0.00 44.56 3.32
3646 7767 3.119101 GCTAGCTTCACACAACCTAGCTA 60.119 47.826 7.70 0.00 44.56 3.32
3647 7768 3.320673 AGCTTCACACAACCTAGCTAC 57.679 47.619 0.00 0.00 40.19 3.58
3648 7769 2.632996 AGCTTCACACAACCTAGCTACA 59.367 45.455 0.00 0.00 40.19 2.74
3649 7770 3.071023 AGCTTCACACAACCTAGCTACAA 59.929 43.478 0.00 0.00 40.19 2.41
3651 7772 3.040147 TCACACAACCTAGCTACAAGC 57.960 47.619 0.00 0.00 42.84 4.01
3653 7774 1.978580 ACACAACCTAGCTACAAGCCT 59.021 47.619 0.00 0.00 43.77 4.58
3654 7775 2.372172 ACACAACCTAGCTACAAGCCTT 59.628 45.455 0.00 0.00 43.77 4.35
3655 7776 3.181443 ACACAACCTAGCTACAAGCCTTT 60.181 43.478 0.00 0.00 43.77 3.11
3658 7779 3.790089 ACCTAGCTACAAGCCTTTTGT 57.210 42.857 0.00 0.00 43.77 2.83
3661 7782 5.429130 ACCTAGCTACAAGCCTTTTGTATC 58.571 41.667 0.00 0.00 43.77 2.24
3663 7784 4.576330 AGCTACAAGCCTTTTGTATCCT 57.424 40.909 0.73 0.00 43.77 3.24
3664 7785 5.693769 AGCTACAAGCCTTTTGTATCCTA 57.306 39.130 0.73 0.00 43.77 2.94
3667 7788 3.007635 ACAAGCCTTTTGTATCCTACGC 58.992 45.455 0.00 0.00 0.00 4.42
3668 7789 1.935933 AGCCTTTTGTATCCTACGCG 58.064 50.000 3.53 3.53 0.00 6.01
3670 7791 2.428171 AGCCTTTTGTATCCTACGCGTA 59.572 45.455 19.40 19.40 0.00 4.42
3683 7804 4.868067 CCTACGCGTAGGTTTTCATATCT 58.132 43.478 43.50 8.48 45.93 1.98
3684 7805 4.680110 CCTACGCGTAGGTTTTCATATCTG 59.320 45.833 43.50 22.04 45.93 2.90
3685 7806 4.380841 ACGCGTAGGTTTTCATATCTGA 57.619 40.909 11.67 0.00 0.00 3.27
3687 7808 5.172934 ACGCGTAGGTTTTCATATCTGAAA 58.827 37.500 11.67 2.34 46.92 2.69
3700 7821 9.693739 TTTCATATCTGAAACTAAAATAGCCCA 57.306 29.630 2.34 0.00 44.46 5.36
3701 7822 8.677148 TCATATCTGAAACTAAAATAGCCCAC 57.323 34.615 0.00 0.00 0.00 4.61
3702 7823 8.494433 TCATATCTGAAACTAAAATAGCCCACT 58.506 33.333 0.00 0.00 0.00 4.00
3743 10245 2.444256 GGTGGAGAGATTCCCGGGG 61.444 68.421 23.50 6.77 46.19 5.73
3746 10248 2.512355 GGAGAGATTCCCGGGGCTC 61.512 68.421 23.50 23.34 40.37 4.70
3860 10362 2.098443 CCTCTACCTCGAGAGCTTCAAC 59.902 54.545 15.71 0.00 41.51 3.18
4012 10514 2.819595 CGCCCGGTTCATGTCCAG 60.820 66.667 0.00 0.00 0.00 3.86
4120 10628 3.716006 CGAACGCCACAGCACCAG 61.716 66.667 0.00 0.00 39.83 4.00
4137 10650 4.560919 GCACCAGTACTACTTGCTAACACT 60.561 45.833 12.92 0.00 31.19 3.55
4143 10656 6.807230 CAGTACTACTTGCTAACACTACAAGG 59.193 42.308 0.00 0.00 44.01 3.61
4148 10661 6.115448 ACTTGCTAACACTACAAGGAGAAT 57.885 37.500 6.89 0.00 44.01 2.40
4163 10676 6.548622 ACAAGGAGAATTAATCCATGGTGATG 59.451 38.462 12.58 0.00 39.34 3.07
4174 10687 5.792188 AATCCATGGTGATGGGTATCTATCA 59.208 40.000 12.58 0.00 42.90 2.15
4182 10695 6.191657 TGATGGGTATCTATCACTTGCATT 57.808 37.500 0.00 0.00 36.21 3.56
4608 11122 0.108756 GCCGACTGGAAGAGGTACAC 60.109 60.000 0.00 0.00 37.54 2.90
4610 11124 0.456312 CGACTGGAAGAGGTACACGC 60.456 60.000 0.00 0.00 37.43 5.34
4649 11163 3.995506 AAGAAGGCGGGCGGGAATG 62.996 63.158 0.00 0.00 0.00 2.67
4723 11237 3.047807 GCACCCCTGATGGCAGCTA 62.048 63.158 3.69 0.00 40.91 3.32
4737 11251 2.735663 GGCAGCTACAGATCGATTGATG 59.264 50.000 0.00 1.91 34.09 3.07
4738 11252 2.735663 GCAGCTACAGATCGATTGATGG 59.264 50.000 0.00 0.00 34.09 3.51
4750 11265 7.861872 CAGATCGATTGATGGCTGATATACTAG 59.138 40.741 0.00 0.00 34.09 2.57
4752 11267 6.856895 TCGATTGATGGCTGATATACTAGTG 58.143 40.000 5.39 0.00 0.00 2.74
4792 11312 5.514169 TGACATTGCCCAGGATTTATGTAA 58.486 37.500 0.00 0.00 0.00 2.41
4820 12109 9.478019 CGTACTGAATAAATTGTTGATGAGAAC 57.522 33.333 0.00 0.00 0.00 3.01
4823 12112 9.850628 ACTGAATAAATTGTTGATGAGAACATG 57.149 29.630 0.00 0.00 35.77 3.21
4824 12113 9.850628 CTGAATAAATTGTTGATGAGAACATGT 57.149 29.630 0.00 0.00 35.77 3.21
4839 12128 5.288543 GAACATGTGCTTAGTTCTGAAGG 57.711 43.478 0.00 0.00 38.79 3.46
4857 12146 1.349357 AGGGTTTGAGAGAGGAACAGC 59.651 52.381 0.00 0.00 0.00 4.40
4909 12198 4.536364 TTCTTTCAGAAAACTGTCGCAG 57.464 40.909 0.00 5.47 32.47 5.18
4915 12204 2.225019 CAGAAAACTGTCGCAGATTGCT 59.775 45.455 12.77 8.66 42.25 3.91
4916 12205 3.433274 CAGAAAACTGTCGCAGATTGCTA 59.567 43.478 12.77 0.00 42.25 3.49
4917 12206 3.433615 AGAAAACTGTCGCAGATTGCTAC 59.566 43.478 12.77 0.00 42.25 3.58
4918 12207 1.350193 AACTGTCGCAGATTGCTACG 58.650 50.000 12.77 0.00 41.33 3.51
4957 12246 4.688419 CACCTGCCAAGCAACGCG 62.688 66.667 3.53 3.53 38.41 6.01
4981 12302 5.448768 GGTCTCTTGATCGAGTTCGTATGAA 60.449 44.000 9.87 0.00 40.80 2.57
5026 12348 2.172717 CTCAACCGGATCCCCTACATTT 59.827 50.000 9.46 0.00 0.00 2.32
5084 12435 3.648545 AGCAAAGGAGGAGTAACAAGTCT 59.351 43.478 0.00 0.00 0.00 3.24
5123 12475 6.574350 AGAGAACAGACAAAATATAGTCCGG 58.426 40.000 0.00 0.00 35.38 5.14
5134 12486 7.092935 ACAAAATATAGTCCGGGTAAACCTACA 60.093 37.037 0.00 0.00 36.97 2.74
5208 12564 2.433664 GGTACACTTGTCGGGCCG 60.434 66.667 22.51 22.51 0.00 6.13
5230 12586 1.201429 ATCGGGGTGAGCTTCAGGTT 61.201 55.000 0.00 0.00 0.00 3.50
5276 12632 4.025360 TGGTTCCAATCATGATTCCCAAG 58.975 43.478 18.16 6.83 0.00 3.61
5297 12653 4.260170 AGAAATCATCACTGCTGAAGGAC 58.740 43.478 0.00 0.00 0.00 3.85
5312 12668 5.334724 GCTGAAGGACAATTTGTGAAGAGAG 60.335 44.000 6.80 0.00 0.00 3.20
5313 12669 5.928976 TGAAGGACAATTTGTGAAGAGAGA 58.071 37.500 6.80 0.00 0.00 3.10
5384 12751 6.027749 CCTCAACGCATAAGTTATTTTGGTC 58.972 40.000 0.00 0.00 32.35 4.02
5577 12956 4.301628 GTCATTCTTGGTGCTTTCAAAGG 58.698 43.478 0.00 0.00 0.00 3.11
5663 13042 1.073199 AGCTGGGTTTCCACCGAAG 59.927 57.895 0.00 0.00 45.39 3.79
5668 13047 1.228154 GGTTTCCACCGAAGCCACT 60.228 57.895 1.35 0.00 45.97 4.00
5670 13049 1.228124 TTTCCACCGAAGCCACTGG 60.228 57.895 0.00 0.00 0.00 4.00
5709 13088 2.051345 CAAAGTTGTCGCCGCCAC 60.051 61.111 0.00 0.00 0.00 5.01
5710 13089 3.284449 AAAGTTGTCGCCGCCACC 61.284 61.111 0.00 0.00 0.00 4.61
5711 13090 4.555709 AAGTTGTCGCCGCCACCA 62.556 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 9.343539 ACTTGTATTTTCTATCCAAGAATAGCC 57.656 33.333 0.00 0.00 43.75 3.93
79 81 3.566742 ACACGGGTCCAACTTGTATTTTC 59.433 43.478 0.00 0.00 0.00 2.29
88 90 1.227438 CAACGACACGGGTCCAACT 60.227 57.895 13.25 0.00 41.13 3.16
90 92 2.109387 CCAACGACACGGGTCCAA 59.891 61.111 13.25 0.00 41.13 3.53
91 93 4.612412 GCCAACGACACGGGTCCA 62.612 66.667 13.25 0.00 41.13 4.02
93 95 4.651008 TCGCCAACGACACGGGTC 62.651 66.667 8.05 8.05 45.12 4.46
102 104 0.999406 CTGACCTGTAATCGCCAACG 59.001 55.000 0.00 0.00 42.01 4.10
114 130 4.946157 AGATTGACCAATAAAGCTGACCTG 59.054 41.667 0.00 0.00 0.00 4.00
121 137 7.865706 TTTCTCCTAGATTGACCAATAAAGC 57.134 36.000 0.00 0.00 0.00 3.51
149 169 8.917088 CCCAACAAATAACATCAGGATAGAAAT 58.083 33.333 0.00 0.00 0.00 2.17
160 180 4.156008 AGCGAGAACCCAACAAATAACATC 59.844 41.667 0.00 0.00 0.00 3.06
164 184 4.138290 TCAAGCGAGAACCCAACAAATAA 58.862 39.130 0.00 0.00 0.00 1.40
207 227 6.795098 TTTGCTACACAACGAGACATTATT 57.205 33.333 0.00 0.00 38.23 1.40
238 263 9.087424 GCAAAAGTCTAACAAGTGAATTCTTTT 57.913 29.630 7.05 0.00 34.43 2.27
240 265 7.068716 AGGCAAAAGTCTAACAAGTGAATTCTT 59.931 33.333 7.05 0.00 0.00 2.52
241 266 6.547510 AGGCAAAAGTCTAACAAGTGAATTCT 59.452 34.615 7.05 0.00 0.00 2.40
546 1289 0.861837 GGCGACCTTGCTGAATATCG 59.138 55.000 0.00 0.00 34.52 2.92
613 1370 0.179153 GTACGCGGTCAGAGGTTACC 60.179 60.000 12.47 0.00 0.00 2.85
659 1416 5.187687 TGTTTCGGGTTTTCTAGACACTTT 58.812 37.500 0.00 0.00 0.00 2.66
674 1431 0.679960 GAGGGGGTTGATGTTTCGGG 60.680 60.000 0.00 0.00 0.00 5.14
685 1442 2.203596 ACTGTCGACGAGGGGGTT 60.204 61.111 11.62 0.00 0.00 4.11
701 1536 1.136774 GGCGGGCAATTTCTTCGAC 59.863 57.895 0.00 0.00 0.00 4.20
730 1567 2.935201 CCCTAGCTAGCCTACGTATACG 59.065 54.545 23.24 23.24 46.33 3.06
731 1568 4.213564 TCCCTAGCTAGCCTACGTATAC 57.786 50.000 15.74 0.00 0.00 1.47
732 1569 4.141528 GGATCCCTAGCTAGCCTACGTATA 60.142 50.000 15.74 0.00 0.00 1.47
733 1570 3.371810 GGATCCCTAGCTAGCCTACGTAT 60.372 52.174 15.74 0.00 0.00 3.06
734 1571 2.026449 GGATCCCTAGCTAGCCTACGTA 60.026 54.545 15.74 0.00 0.00 3.57
735 1572 1.272037 GGATCCCTAGCTAGCCTACGT 60.272 57.143 15.74 0.00 0.00 3.57
736 1573 1.271982 TGGATCCCTAGCTAGCCTACG 60.272 57.143 15.74 1.06 0.00 3.51
737 1574 2.606751 TGGATCCCTAGCTAGCCTAC 57.393 55.000 15.74 6.48 0.00 3.18
809 1646 9.319143 GTCATAGCTGTATATATGAATTGGTCC 57.681 37.037 0.00 0.00 39.46 4.46
2627 6732 0.944386 CCCATCCGCATTTTAGTCGG 59.056 55.000 0.00 0.00 44.16 4.79
2650 6755 5.090757 ACGTTGTGTGACTGTATATGTACG 58.909 41.667 0.00 0.00 33.36 3.67
2670 6775 1.202639 TGATTGGTTCTCAGCACACGT 60.203 47.619 0.00 0.00 0.00 4.49
2674 6779 3.316308 ACTTTGTGATTGGTTCTCAGCAC 59.684 43.478 0.00 0.00 34.89 4.40
2775 6881 0.826256 AGCGGTGATGGAGGCGTATA 60.826 55.000 0.00 0.00 0.00 1.47
2777 6883 1.038681 TAAGCGGTGATGGAGGCGTA 61.039 55.000 0.00 0.00 0.00 4.42
2792 6898 4.728534 TGTTCATACGTGGCAAAATAAGC 58.271 39.130 0.00 0.00 0.00 3.09
2886 6992 9.720569 CGAATTTAATGGTGAAAACGTATTTTG 57.279 29.630 0.00 0.00 38.17 2.44
2910 7017 5.122512 AGTTTTGAAGATCTTCGAGACGA 57.877 39.130 28.04 13.38 40.82 4.20
2989 7099 7.957484 GCACTATGACAACTACAATGTAAACAG 59.043 37.037 0.00 0.00 0.00 3.16
3053 7164 9.378551 GGTCAAAGTACTGTAATTGTCATCATA 57.621 33.333 0.00 0.00 0.00 2.15
3060 7171 8.458573 TTTCATGGTCAAAGTACTGTAATTGT 57.541 30.769 0.00 0.00 0.00 2.71
3096 7208 5.412286 GCACTTAAAATTGCCATGGTTCATT 59.588 36.000 14.67 6.49 32.21 2.57
3150 7263 9.528489 AGGAATTAAGAAACTAAACTTGCCATA 57.472 29.630 0.00 0.00 0.00 2.74
3243 7356 5.301551 AGTTGCCATGATGTTTACACTGAAA 59.698 36.000 0.00 0.00 0.00 2.69
3350 7468 5.151454 TGTTTTCACCATTAAATCCCCAGT 58.849 37.500 0.00 0.00 0.00 4.00
3472 7592 3.411446 CCACATGTCCTGTAACACACAT 58.589 45.455 0.00 0.00 35.91 3.21
3482 7602 3.567579 AACCCGCCCACATGTCCTG 62.568 63.158 0.00 0.00 0.00 3.86
3535 7655 9.709495 CCCATTAAATCTTGTCAATCTTTTTGA 57.291 29.630 0.00 0.00 0.00 2.69
3557 7677 7.223584 CCATTTGGAAAAGTAGAAAAACCCAT 58.776 34.615 0.00 0.00 37.39 4.00
3566 7686 5.365314 ACAAAAGCCCATTTGGAAAAGTAGA 59.635 36.000 10.75 0.00 43.10 2.59
3576 7696 1.345415 AGGAGCACAAAAGCCCATTTG 59.655 47.619 5.87 5.87 44.11 2.32
3612 7732 1.608717 AAGCTAGCCCACTCTGACCG 61.609 60.000 12.13 0.00 0.00 4.79
3637 7758 4.100279 ACAAAAGGCTTGTAGCTAGGTT 57.900 40.909 0.00 0.00 41.99 3.50
3638 7759 3.790089 ACAAAAGGCTTGTAGCTAGGT 57.210 42.857 0.00 0.00 41.99 3.08
3639 7760 4.816925 GGATACAAAAGGCTTGTAGCTAGG 59.183 45.833 12.74 0.00 41.99 3.02
3640 7761 5.675538 AGGATACAAAAGGCTTGTAGCTAG 58.324 41.667 12.74 0.00 40.14 3.42
3642 7763 4.576330 AGGATACAAAAGGCTTGTAGCT 57.424 40.909 12.74 0.00 40.14 3.32
3643 7764 4.270325 CGTAGGATACAAAAGGCTTGTAGC 59.730 45.833 0.00 3.02 43.24 3.58
3645 7766 4.186159 GCGTAGGATACAAAAGGCTTGTA 58.814 43.478 0.00 0.15 43.24 2.41
3646 7767 3.007635 GCGTAGGATACAAAAGGCTTGT 58.992 45.455 0.00 0.00 43.24 3.16
3647 7768 2.030457 CGCGTAGGATACAAAAGGCTTG 59.970 50.000 0.00 0.00 43.24 4.01
3648 7769 2.277084 CGCGTAGGATACAAAAGGCTT 58.723 47.619 0.00 0.00 43.24 4.35
3649 7770 1.206371 ACGCGTAGGATACAAAAGGCT 59.794 47.619 11.67 0.00 43.24 4.58
3663 7784 5.503662 TCAGATATGAAAACCTACGCGTA 57.496 39.130 19.40 19.40 0.00 4.42
3664 7785 4.380841 TCAGATATGAAAACCTACGCGT 57.619 40.909 19.17 19.17 0.00 6.01
3674 7795 9.693739 TGGGCTATTTTAGTTTCAGATATGAAA 57.306 29.630 11.38 11.38 35.67 2.69
3675 7796 9.120538 GTGGGCTATTTTAGTTTCAGATATGAA 57.879 33.333 0.00 0.00 0.00 2.57
3676 7797 8.494433 AGTGGGCTATTTTAGTTTCAGATATGA 58.506 33.333 0.00 0.00 0.00 2.15
3677 7798 8.682936 AGTGGGCTATTTTAGTTTCAGATATG 57.317 34.615 0.00 0.00 0.00 1.78
3699 7820 3.790789 GCGCGAAACCCCAAATTATAGTG 60.791 47.826 12.10 0.00 0.00 2.74
3700 7821 2.356695 GCGCGAAACCCCAAATTATAGT 59.643 45.455 12.10 0.00 0.00 2.12
3701 7822 2.601266 CGCGCGAAACCCCAAATTATAG 60.601 50.000 28.94 0.00 0.00 1.31
3702 7823 1.331138 CGCGCGAAACCCCAAATTATA 59.669 47.619 28.94 0.00 0.00 0.98
3705 7826 2.257067 CGCGCGAAACCCCAAATT 59.743 55.556 28.94 0.00 0.00 1.82
3706 7827 4.413800 GCGCGCGAAACCCCAAAT 62.414 61.111 37.18 0.00 0.00 2.32
3749 10251 4.357279 ACCTTGGGCAGCAGCTCC 62.357 66.667 0.00 0.00 41.98 4.70
3750 10252 3.060615 CACCTTGGGCAGCAGCTC 61.061 66.667 0.00 0.00 43.38 4.09
3761 10263 1.961277 GTCCTCCGTGCACACCTTG 60.961 63.158 18.64 0.00 0.00 3.61
3836 10338 2.313267 GCTCTCGAGGTAGAGGTCG 58.687 63.158 13.56 0.00 42.79 4.79
4012 10514 0.108756 GACCAGTTCGAGGTACTGCC 60.109 60.000 9.75 1.64 41.55 4.85
4103 10605 3.716006 CTGGTGCTGTGGCGTTCG 61.716 66.667 0.00 0.00 42.25 3.95
4120 10628 6.917533 TCCTTGTAGTGTTAGCAAGTAGTAC 58.082 40.000 0.00 0.00 38.24 2.73
4137 10650 7.206789 TCACCATGGATTAATTCTCCTTGTA 57.793 36.000 21.47 0.00 36.62 2.41
4163 10676 7.986085 ACATAAATGCAAGTGATAGATACCC 57.014 36.000 0.00 0.00 0.00 3.69
4165 10678 9.929180 TCCTACATAAATGCAAGTGATAGATAC 57.071 33.333 0.00 0.00 0.00 2.24
4174 10687 3.938963 CGGTGTCCTACATAAATGCAAGT 59.061 43.478 0.00 0.00 0.00 3.16
4182 10695 2.764010 AGCATGTCGGTGTCCTACATAA 59.236 45.455 5.79 0.00 37.75 1.90
4352 10866 1.741770 CCCGCCAGTACTTGAGCAC 60.742 63.158 9.34 0.00 0.00 4.40
4599 11113 2.184322 CCATGCGCGTGTACCTCT 59.816 61.111 26.86 0.00 0.00 3.69
4649 11163 2.746277 GGGCACCGTCCATGTCAC 60.746 66.667 0.00 0.00 40.86 3.67
4723 11237 3.766068 ATCAGCCATCAATCGATCTGT 57.234 42.857 0.00 0.00 29.63 3.41
4737 11251 6.927294 AAAAACTGCACTAGTATATCAGCC 57.073 37.500 0.00 0.00 39.18 4.85
4792 11312 9.214957 TCTCATCAACAATTTATTCAGTACGTT 57.785 29.630 0.00 0.00 0.00 3.99
4814 11334 5.213891 TCAGAACTAAGCACATGTTCTCA 57.786 39.130 0.00 0.00 45.67 3.27
4815 11335 5.121454 CCTTCAGAACTAAGCACATGTTCTC 59.879 44.000 0.00 0.00 45.67 2.87
4820 12109 3.679389 ACCCTTCAGAACTAAGCACATG 58.321 45.455 0.00 0.00 0.00 3.21
4823 12112 4.134563 TCAAACCCTTCAGAACTAAGCAC 58.865 43.478 0.00 0.00 0.00 4.40
4824 12113 4.102524 TCTCAAACCCTTCAGAACTAAGCA 59.897 41.667 0.00 0.00 0.00 3.91
4839 12128 2.224402 ACTGCTGTTCCTCTCTCAAACC 60.224 50.000 0.00 0.00 0.00 3.27
4857 12146 1.345741 TCTCCCTCTGAAACTGCACTG 59.654 52.381 0.00 0.00 0.00 3.66
4909 12198 4.634443 ACCCATTCAAAGTACGTAGCAATC 59.366 41.667 0.00 0.00 0.00 2.67
4915 12204 5.471556 TCTGAACCCATTCAAAGTACGTA 57.528 39.130 0.00 0.00 44.28 3.57
4916 12205 4.345859 TCTGAACCCATTCAAAGTACGT 57.654 40.909 0.00 0.00 44.28 3.57
4917 12206 4.378459 GCTTCTGAACCCATTCAAAGTACG 60.378 45.833 10.68 0.00 44.28 3.67
4918 12207 4.518970 TGCTTCTGAACCCATTCAAAGTAC 59.481 41.667 10.68 0.00 44.28 2.73
4957 12246 2.923605 ACGAACTCGATCAAGAGACC 57.076 50.000 6.05 0.00 43.02 3.85
4972 12261 5.750524 TCCTTTTCCATCCATTCATACGAA 58.249 37.500 0.00 0.00 35.05 3.85
4974 12263 4.023707 GCTCCTTTTCCATCCATTCATACG 60.024 45.833 0.00 0.00 0.00 3.06
4981 12302 3.744940 TTCTGCTCCTTTTCCATCCAT 57.255 42.857 0.00 0.00 0.00 3.41
5038 12360 8.616076 GCTGTTTTCTATTATGTAGAATGCAGT 58.384 33.333 19.92 0.00 37.63 4.40
5052 12374 5.635120 ACTCCTCCTTTGCTGTTTTCTATT 58.365 37.500 0.00 0.00 0.00 1.73
5053 12375 5.248380 ACTCCTCCTTTGCTGTTTTCTAT 57.752 39.130 0.00 0.00 0.00 1.98
5054 12376 4.706842 ACTCCTCCTTTGCTGTTTTCTA 57.293 40.909 0.00 0.00 0.00 2.10
5068 12419 2.904434 TCCCAAGACTTGTTACTCCTCC 59.096 50.000 14.03 0.00 0.00 4.30
5084 12435 3.073798 TGTTCTCTTTGCCTACATCCCAA 59.926 43.478 0.00 0.00 0.00 4.12
5157 12512 3.524095 TTGGTGACCACAAGGATCATT 57.476 42.857 2.46 0.00 38.69 2.57
5208 12564 1.473434 CCTGAAGCTCACCCCGATAAC 60.473 57.143 0.00 0.00 0.00 1.89
5217 12573 1.967319 TCAACCAACCTGAAGCTCAC 58.033 50.000 0.00 0.00 0.00 3.51
5263 12619 6.320418 CAGTGATGATTTCTTGGGAATCATGA 59.680 38.462 16.04 7.47 33.85 3.07
5276 12632 4.005650 TGTCCTTCAGCAGTGATGATTTC 58.994 43.478 12.63 4.44 30.85 2.17
5333 12690 5.238432 ACAATGAGAATGCACGTTCAGTTTA 59.762 36.000 5.46 0.00 0.00 2.01
5342 12699 2.079158 AGGTGACAATGAGAATGCACG 58.921 47.619 0.00 0.00 0.00 5.34
5384 12751 8.050778 ACTACTTTCTTGATGACTGTCTAGAG 57.949 38.462 9.51 2.62 32.92 2.43
5566 12945 2.031120 CTGGTTCCACCTTTGAAAGCA 58.969 47.619 0.00 0.00 39.58 3.91
5670 13049 2.027460 CGGCAACTTTGGTGGTGC 59.973 61.111 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.