Multiple sequence alignment - TraesCS7D01G410800

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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 TraesCS7D01G410800 chr7D 100.000 3152 0 0 1 3152 529775278 529772127 0.000000e+00 5821.0
1 TraesCS7D01G410800 chr7D 89.868 2043 115 33 855 2860 529680230 529682217 0.000000e+00 2542.0
2 TraesCS7D01G410800 chr7D 87.302 252 25 2 445 693 564641278 564641031 6.660000e-72 281.0
3 TraesCS7D01G410800 chr7D 80.417 240 24 7 2906 3144 529682230 529682447 9.050000e-36 161.0
4 TraesCS7D01G410800 chr7D 91.489 94 3 3 691 780 234347304 234347212 1.190000e-24 124.0
5 TraesCS7D01G410800 chr7B 94.142 1229 49 11 1020 2230 567635381 567636604 0.000000e+00 1849.0
6 TraesCS7D01G410800 chr7B 93.640 1195 63 7 1020 2210 567884897 567883712 0.000000e+00 1773.0
7 TraesCS7D01G410800 chr7B 91.485 916 56 9 2231 3144 567883268 567882373 0.000000e+00 1240.0
8 TraesCS7D01G410800 chr7B 97.260 365 10 0 2325 2689 567636723 567637087 1.240000e-173 619.0
9 TraesCS7D01G410800 chr7B 87.526 489 34 15 2683 3152 567638817 567639297 9.950000e-150 540.0
10 TraesCS7D01G410800 chr7B 88.048 251 5 6 780 1021 567635119 567635353 1.110000e-69 274.0
11 TraesCS7D01G410800 chr7A 93.223 1092 63 2 1020 2100 609339999 609338908 0.000000e+00 1596.0
12 TraesCS7D01G410800 chr7A 90.420 929 43 21 2227 3146 609336307 609335416 0.000000e+00 1181.0
13 TraesCS7D01G410800 chr7A 93.458 749 49 0 1020 1768 609133557 609134305 0.000000e+00 1112.0
14 TraesCS7D01G410800 chr7A 93.843 536 26 3 2325 2860 609172252 609172780 0.000000e+00 800.0
15 TraesCS7D01G410800 chr7A 95.673 208 9 0 1797 2004 609134304 609134511 5.040000e-88 335.0
16 TraesCS7D01G410800 chr7A 85.098 255 19 13 2903 3144 609172789 609173037 3.140000e-60 243.0
17 TraesCS7D01G410800 chr7A 90.184 163 7 3 861 1019 609133359 609133516 1.480000e-48 204.0
18 TraesCS7D01G410800 chr7A 93.750 96 2 1 780 871 609131174 609131269 1.180000e-29 141.0
19 TraesCS7D01G410800 chr3D 97.767 627 10 1 69 695 108245078 108244456 0.000000e+00 1077.0
20 TraesCS7D01G410800 chr3D 91.398 93 4 2 691 780 298464941 298464850 1.190000e-24 124.0
21 TraesCS7D01G410800 chr3D 94.286 35 2 0 498 532 359636915 359636949 2.000000e-03 54.7
22 TraesCS7D01G410800 chr2D 95.032 624 3 8 70 692 121728420 121727824 0.000000e+00 955.0
23 TraesCS7D01G410800 chr2D 93.478 92 4 1 691 780 537187866 537187775 5.480000e-28 135.0
24 TraesCS7D01G410800 chr2D 91.489 94 3 2 691 780 476697586 476697678 1.190000e-24 124.0
25 TraesCS7D01G410800 chr2D 93.750 64 4 0 379 442 647501278 647501341 2.590000e-16 97.1
26 TraesCS7D01G410800 chr4A 94.195 379 21 1 67 444 11839714 11840092 7.580000e-161 577.0
27 TraesCS7D01G410800 chr4A 90.769 260 24 0 70 329 291973018 291973277 6.470000e-92 348.0
28 TraesCS7D01G410800 chr4A 89.767 215 17 4 445 659 11840129 11840338 1.440000e-68 270.0
29 TraesCS7D01G410800 chr4A 86.735 196 20 4 497 692 291975229 291975418 2.460000e-51 213.0
30 TraesCS7D01G410800 chr4A 91.398 93 5 3 691 780 711210387 711210479 1.190000e-24 124.0
31 TraesCS7D01G410800 chr4A 91.525 59 3 2 17 75 711243604 711243660 2.610000e-11 80.5
32 TraesCS7D01G410800 chr2B 82.157 510 81 10 1150 1654 52689525 52690029 2.250000e-116 429.0
33 TraesCS7D01G410800 chr2B 91.064 235 21 0 72 306 795606691 795606925 5.070000e-83 318.0
34 TraesCS7D01G410800 chr2B 90.213 235 22 1 72 306 144972616 144972849 3.950000e-79 305.0
35 TraesCS7D01G410800 chr2B 85.632 174 20 4 519 692 529269302 529269134 8.980000e-41 178.0
36 TraesCS7D01G410800 chr2B 95.349 86 3 1 296 380 795606985 795607070 5.480000e-28 135.0
37 TraesCS7D01G410800 chr2B 91.489 94 3 2 691 780 685044584 685044492 1.190000e-24 124.0
38 TraesCS7D01G410800 chr2B 90.909 66 6 0 379 444 144973080 144973145 4.330000e-14 89.8
39 TraesCS7D01G410800 chr2B 92.063 63 5 0 379 441 795607156 795607218 4.330000e-14 89.8
40 TraesCS7D01G410800 chr2B 91.667 60 4 1 13 71 47534217 47534158 7.250000e-12 82.4
41 TraesCS7D01G410800 chr6A 79.256 511 94 10 1150 1654 53500385 53500889 2.330000e-91 346.0
42 TraesCS7D01G410800 chr1A 91.903 247 15 3 445 690 58478718 58478960 1.080000e-89 340.0
43 TraesCS7D01G410800 chr1A 92.982 57 2 2 14 70 549554823 549554769 7.250000e-12 82.4
44 TraesCS7D01G410800 chr1D 90.496 242 23 0 71 312 90163671 90163430 1.410000e-83 320.0
45 TraesCS7D01G410800 chr1D 90.213 235 23 0 70 304 167393091 167392857 1.100000e-79 307.0
46 TraesCS7D01G410800 chr1D 88.095 168 16 3 528 695 167392786 167392623 2.480000e-46 196.0
47 TraesCS7D01G410800 chr6B 78.304 507 100 9 1153 1654 103703036 103702535 5.070000e-83 318.0
48 TraesCS7D01G410800 chr6B 77.996 509 104 6 1150 1654 17959105 17959609 2.360000e-81 313.0
49 TraesCS7D01G410800 chr6B 94.186 86 4 1 296 380 356571987 356571902 2.550000e-26 130.0
50 TraesCS7D01G410800 chr6B 92.424 66 5 0 379 444 356571815 356571750 9.310000e-16 95.3
51 TraesCS7D01G410800 chr3B 90.213 235 23 0 72 306 778635246 778635480 1.100000e-79 307.0
52 TraesCS7D01G410800 chr3B 87.083 240 25 4 445 683 778635812 778636046 1.860000e-67 267.0
53 TraesCS7D01G410800 chr3B 94.186 86 3 2 296 380 778635540 778635624 2.550000e-26 130.0
54 TraesCS7D01G410800 chr3B 98.077 52 1 0 379 430 778635711 778635762 1.200000e-14 91.6
55 TraesCS7D01G410800 chrUn 91.228 114 6 3 582 695 215714289 215714180 5.450000e-33 152.0
56 TraesCS7D01G410800 chrUn 97.917 48 1 0 24 71 20618775 20618822 2.010000e-12 84.2
57 TraesCS7D01G410800 chr4D 93.333 90 5 1 691 780 165765655 165765567 7.090000e-27 132.0
58 TraesCS7D01G410800 chr4D 91.489 94 3 2 691 780 35722438 35722346 1.190000e-24 124.0
59 TraesCS7D01G410800 chr4B 94.186 86 3 2 296 380 601870331 601870415 2.550000e-26 130.0
60 TraesCS7D01G410800 chr4B 78.049 164 26 6 2306 2463 654751577 654751736 9.310000e-16 95.3
61 TraesCS7D01G410800 chr4B 77.439 164 27 6 2306 2463 654761816 654761975 4.330000e-14 89.8
62 TraesCS7D01G410800 chr4B 77.439 164 27 6 2306 2463 654774022 654774181 4.330000e-14 89.8
63 TraesCS7D01G410800 chr4B 76.829 164 28 6 2306 2463 654699082 654699241 2.010000e-12 84.2
64 TraesCS7D01G410800 chr4B 86.957 69 6 3 4 71 159604368 159604434 1.210000e-09 75.0
65 TraesCS7D01G410800 chr2A 92.308 91 3 4 694 780 526068040 526068130 3.300000e-25 126.0
66 TraesCS7D01G410800 chr2A 93.023 86 5 1 296 380 21291243 21291328 1.190000e-24 124.0
67 TraesCS7D01G410800 chr2A 93.023 86 5 1 296 380 21315729 21315814 1.190000e-24 124.0
68 TraesCS7D01G410800 chr2A 90.769 65 3 3 9 71 77350876 77350939 2.010000e-12 84.2
69 TraesCS7D01G410800 chr2A 96.078 51 1 1 25 75 18055782 18055733 7.250000e-12 82.4
70 TraesCS7D01G410800 chr5A 96.774 62 2 0 381 442 580102858 580102919 1.550000e-18 104.0
71 TraesCS7D01G410800 chr3A 100.000 46 0 0 25 70 13377023 13376978 5.600000e-13 86.1
72 TraesCS7D01G410800 chr5D 88.235 68 5 3 7 71 447632053 447632120 9.370000e-11 78.7


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 TraesCS7D01G410800 chr7D 529772127 529775278 3151 True 5821.0 5821 100.00000 1 3152 1 chr7D.!!$R2 3151
1 TraesCS7D01G410800 chr7D 529680230 529682447 2217 False 1351.5 2542 85.14250 855 3144 2 chr7D.!!$F1 2289
2 TraesCS7D01G410800 chr7B 567882373 567884897 2524 True 1506.5 1773 92.56250 1020 3144 2 chr7B.!!$R1 2124
3 TraesCS7D01G410800 chr7B 567635119 567639297 4178 False 820.5 1849 91.74400 780 3152 4 chr7B.!!$F1 2372
4 TraesCS7D01G410800 chr7A 609335416 609339999 4583 True 1388.5 1596 91.82150 1020 3146 2 chr7A.!!$R1 2126
5 TraesCS7D01G410800 chr7A 609172252 609173037 785 False 521.5 800 89.47050 2325 3144 2 chr7A.!!$F2 819
6 TraesCS7D01G410800 chr7A 609131174 609134511 3337 False 448.0 1112 93.26625 780 2004 4 chr7A.!!$F1 1224
7 TraesCS7D01G410800 chr3D 108244456 108245078 622 True 1077.0 1077 97.76700 69 695 1 chr3D.!!$R1 626
8 TraesCS7D01G410800 chr2D 121727824 121728420 596 True 955.0 955 95.03200 70 692 1 chr2D.!!$R1 622
9 TraesCS7D01G410800 chr4A 11839714 11840338 624 False 423.5 577 91.98100 67 659 2 chr4A.!!$F3 592
10 TraesCS7D01G410800 chr4A 291973018 291975418 2400 False 280.5 348 88.75200 70 692 2 chr4A.!!$F4 622
11 TraesCS7D01G410800 chr2B 52689525 52690029 504 False 429.0 429 82.15700 1150 1654 1 chr2B.!!$F1 504
12 TraesCS7D01G410800 chr6A 53500385 53500889 504 False 346.0 346 79.25600 1150 1654 1 chr6A.!!$F1 504
13 TraesCS7D01G410800 chr6B 103702535 103703036 501 True 318.0 318 78.30400 1153 1654 1 chr6B.!!$R1 501
14 TraesCS7D01G410800 chr6B 17959105 17959609 504 False 313.0 313 77.99600 1150 1654 1 chr6B.!!$F1 504

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
704 2491 0.251165 GCACCCTAAGCTCCCACAAA 60.251 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 9199 0.327259 CGCCTGATCCATCCATCCAT 59.673 55.0 0.0 0.0 0.0 3.41 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
620 2407 8.298140 TCCAAACAACCCAAAGTATTTAATACG 58.702 33.333 9.16 0.00 35.03 3.06
676 2463 8.994429 TTCAGAAAACTGCAAAAATACTTTGA 57.006 26.923 1.49 0.00 0.00 2.69
695 2482 1.132453 GAATCCAAACGCACCCTAAGC 59.868 52.381 0.00 0.00 0.00 3.09
696 2483 0.328258 ATCCAAACGCACCCTAAGCT 59.672 50.000 0.00 0.00 0.00 3.74
697 2484 0.321298 TCCAAACGCACCCTAAGCTC 60.321 55.000 0.00 0.00 0.00 4.09
698 2485 1.305930 CCAAACGCACCCTAAGCTCC 61.306 60.000 0.00 0.00 0.00 4.70
699 2486 1.002502 AAACGCACCCTAAGCTCCC 60.003 57.895 0.00 0.00 0.00 4.30
700 2487 1.774894 AAACGCACCCTAAGCTCCCA 61.775 55.000 0.00 0.00 0.00 4.37
701 2488 2.125106 CGCACCCTAAGCTCCCAC 60.125 66.667 0.00 0.00 0.00 4.61
702 2489 2.954684 CGCACCCTAAGCTCCCACA 61.955 63.158 0.00 0.00 0.00 4.17
703 2490 1.378762 GCACCCTAAGCTCCCACAA 59.621 57.895 0.00 0.00 0.00 3.33
704 2491 0.251165 GCACCCTAAGCTCCCACAAA 60.251 55.000 0.00 0.00 0.00 2.83
705 2492 1.616994 GCACCCTAAGCTCCCACAAAT 60.617 52.381 0.00 0.00 0.00 2.32
706 2493 2.356741 GCACCCTAAGCTCCCACAAATA 60.357 50.000 0.00 0.00 0.00 1.40
707 2494 3.279434 CACCCTAAGCTCCCACAAATAC 58.721 50.000 0.00 0.00 0.00 1.89
708 2495 2.916934 ACCCTAAGCTCCCACAAATACA 59.083 45.455 0.00 0.00 0.00 2.29
709 2496 3.527665 ACCCTAAGCTCCCACAAATACAT 59.472 43.478 0.00 0.00 0.00 2.29
710 2497 4.724798 ACCCTAAGCTCCCACAAATACATA 59.275 41.667 0.00 0.00 0.00 2.29
711 2498 5.192923 ACCCTAAGCTCCCACAAATACATAA 59.807 40.000 0.00 0.00 0.00 1.90
712 2499 6.126185 ACCCTAAGCTCCCACAAATACATAAT 60.126 38.462 0.00 0.00 0.00 1.28
713 2500 6.207417 CCCTAAGCTCCCACAAATACATAATG 59.793 42.308 0.00 0.00 0.00 1.90
714 2501 5.520376 AAGCTCCCACAAATACATAATGC 57.480 39.130 0.00 0.00 0.00 3.56
715 2502 4.535781 AGCTCCCACAAATACATAATGCA 58.464 39.130 0.00 0.00 0.00 3.96
716 2503 4.581824 AGCTCCCACAAATACATAATGCAG 59.418 41.667 0.00 0.00 0.00 4.41
717 2504 4.794003 GCTCCCACAAATACATAATGCAGC 60.794 45.833 0.00 0.00 0.00 5.25
718 2505 4.276642 TCCCACAAATACATAATGCAGCA 58.723 39.130 0.00 0.00 0.00 4.41
719 2506 4.708909 TCCCACAAATACATAATGCAGCAA 59.291 37.500 0.00 0.00 0.00 3.91
720 2507 4.805192 CCCACAAATACATAATGCAGCAAC 59.195 41.667 0.00 0.00 0.00 4.17
721 2508 5.409211 CCACAAATACATAATGCAGCAACA 58.591 37.500 0.00 0.00 0.00 3.33
722 2509 5.868258 CCACAAATACATAATGCAGCAACAA 59.132 36.000 0.00 0.00 0.00 2.83
723 2510 6.035220 CCACAAATACATAATGCAGCAACAAG 59.965 38.462 0.00 0.00 0.00 3.16
724 2511 6.807720 CACAAATACATAATGCAGCAACAAGA 59.192 34.615 0.00 0.00 0.00 3.02
725 2512 7.328982 CACAAATACATAATGCAGCAACAAGAA 59.671 33.333 0.00 0.00 0.00 2.52
726 2513 7.871973 ACAAATACATAATGCAGCAACAAGAAA 59.128 29.630 0.00 0.00 0.00 2.52
727 2514 7.816945 AATACATAATGCAGCAACAAGAAAC 57.183 32.000 0.00 0.00 0.00 2.78
728 2515 5.199024 ACATAATGCAGCAACAAGAAACA 57.801 34.783 0.00 0.00 0.00 2.83
729 2516 5.599732 ACATAATGCAGCAACAAGAAACAA 58.400 33.333 0.00 0.00 0.00 2.83
730 2517 6.047870 ACATAATGCAGCAACAAGAAACAAA 58.952 32.000 0.00 0.00 0.00 2.83
731 2518 6.538021 ACATAATGCAGCAACAAGAAACAAAA 59.462 30.769 0.00 0.00 0.00 2.44
732 2519 5.876612 AATGCAGCAACAAGAAACAAAAA 57.123 30.435 0.00 0.00 0.00 1.94
761 2548 9.349713 ACTAGGACAAAATAAATCACAAACAGA 57.650 29.630 0.00 0.00 0.00 3.41
762 2549 9.831737 CTAGGACAAAATAAATCACAAACAGAG 57.168 33.333 0.00 0.00 0.00 3.35
763 2550 8.237811 AGGACAAAATAAATCACAAACAGAGT 57.762 30.769 0.00 0.00 0.00 3.24
764 2551 8.137437 AGGACAAAATAAATCACAAACAGAGTG 58.863 33.333 0.00 0.00 38.32 3.51
765 2552 7.382218 GGACAAAATAAATCACAAACAGAGTGG 59.618 37.037 0.00 0.00 37.58 4.00
766 2553 8.006298 ACAAAATAAATCACAAACAGAGTGGA 57.994 30.769 0.00 0.00 37.58 4.02
767 2554 7.920682 ACAAAATAAATCACAAACAGAGTGGAC 59.079 33.333 0.00 0.00 37.58 4.02
768 2555 7.581213 AAATAAATCACAAACAGAGTGGACA 57.419 32.000 0.00 0.00 37.58 4.02
769 2556 7.765695 AATAAATCACAAACAGAGTGGACAT 57.234 32.000 0.00 0.00 37.58 3.06
770 2557 5.695851 AAATCACAAACAGAGTGGACATC 57.304 39.130 0.00 0.00 37.58 3.06
771 2558 3.836365 TCACAAACAGAGTGGACATCA 57.164 42.857 0.00 0.00 37.58 3.07
772 2559 3.732212 TCACAAACAGAGTGGACATCAG 58.268 45.455 0.00 0.00 37.58 2.90
773 2560 2.225019 CACAAACAGAGTGGACATCAGC 59.775 50.000 0.00 0.00 33.43 4.26
774 2561 2.105477 ACAAACAGAGTGGACATCAGCT 59.895 45.455 0.00 0.00 0.00 4.24
775 2562 3.144506 CAAACAGAGTGGACATCAGCTT 58.855 45.455 0.00 0.00 0.00 3.74
776 2563 4.202357 ACAAACAGAGTGGACATCAGCTTA 60.202 41.667 0.00 0.00 0.00 3.09
777 2564 3.883830 ACAGAGTGGACATCAGCTTAG 57.116 47.619 0.00 0.00 0.00 2.18
778 2565 3.435275 ACAGAGTGGACATCAGCTTAGA 58.565 45.455 0.00 0.00 0.00 2.10
821 2612 3.001414 GACTTCGGTTTCTTTCCTAGGC 58.999 50.000 2.96 0.00 0.00 3.93
1001 4899 2.549926 CAAAGTTCCAAACCCAACTGC 58.450 47.619 0.00 0.00 33.01 4.40
1166 5107 2.948720 GCGGCTCACCAAGGTCTCT 61.949 63.158 0.00 0.00 34.57 3.10
2039 5994 2.125912 CTCACCGGCCACGAAGAG 60.126 66.667 0.00 0.00 44.60 2.85
2041 5996 2.125912 CACCGGCCACGAAGAGAG 60.126 66.667 0.00 0.00 44.60 3.20
2042 5997 4.070552 ACCGGCCACGAAGAGAGC 62.071 66.667 0.00 0.00 44.60 4.09
2052 6007 2.604686 AAGAGAGCACCCTCCGCA 60.605 61.111 0.00 0.00 38.96 5.69
2115 6070 5.460646 GCCTATAATTAAACGTGCATGCAT 58.539 37.500 25.64 10.48 0.00 3.96
2116 6071 5.343058 GCCTATAATTAAACGTGCATGCATG 59.657 40.000 33.18 33.18 38.78 4.06
2139 7666 4.499183 CTTCCAGAGACTGCGAATAAACT 58.501 43.478 0.00 0.00 0.00 2.66
2153 7680 4.865925 CGAATAAACTGACCGTGACCATAA 59.134 41.667 0.00 0.00 0.00 1.90
2197 8614 9.410556 CAGTGATTTTTATTCGAGGAAAATGTT 57.589 29.630 15.58 3.65 34.22 2.71
2229 8676 1.885887 GTGCACAAGCTGGGAATTACA 59.114 47.619 13.17 0.00 42.74 2.41
2253 9112 4.966965 TGTTGATAACCAAAACACACGT 57.033 36.364 0.00 0.00 36.36 4.49
2277 9164 1.130411 CACGTACACGCACATGCAG 59.870 57.895 4.49 0.00 44.43 4.41
2314 9201 2.541288 GCTGATGCCTCGATGGATG 58.459 57.895 0.00 0.00 38.35 3.51
2315 9202 0.954449 GCTGATGCCTCGATGGATGG 60.954 60.000 0.00 0.00 38.35 3.51
2316 9203 0.683412 CTGATGCCTCGATGGATGGA 59.317 55.000 0.00 0.00 38.35 3.41
2317 9204 1.278413 CTGATGCCTCGATGGATGGAT 59.722 52.381 0.00 0.00 38.35 3.41
2318 9205 1.002773 TGATGCCTCGATGGATGGATG 59.997 52.381 0.00 0.00 38.35 3.51
2322 9209 1.678123 GCCTCGATGGATGGATGGATG 60.678 57.143 5.24 0.00 38.35 3.51
2713 11336 2.362760 TGGATGCCGCCATTGCTT 60.363 55.556 0.00 0.00 31.66 3.91
2779 11421 4.981806 AGTTTGCTTTAGCTTTGTGACA 57.018 36.364 0.00 0.00 42.66 3.58
2798 11440 4.142160 TGACAGTGAGTGAGTATATGGCAC 60.142 45.833 0.00 0.00 0.00 5.01
2821 11463 6.498651 CACTGATCTGGAGGGTATTTATAGGT 59.501 42.308 4.49 0.00 0.00 3.08
2889 11532 1.203001 ACCGATTGGCCTTTTTCTGGA 60.203 47.619 3.32 0.00 39.70 3.86
2915 11558 0.878086 GCTAGCTCAGGGCAATCGAC 60.878 60.000 7.70 0.00 44.79 4.20
3013 11669 4.317291 GTCGATTTGTGAAATTGCGTGTAC 59.683 41.667 0.00 0.00 33.19 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.175104 AGCCTTAGATGTGACATCCTTAAAAA 58.825 34.615 21.05 6.46 0.00 1.94
49 50 6.721318 AGCCTTAGATGTGACATCCTTAAAA 58.279 36.000 21.05 8.00 0.00 1.52
50 51 6.313519 AGCCTTAGATGTGACATCCTTAAA 57.686 37.500 21.05 10.18 0.00 1.52
51 52 5.957771 AGCCTTAGATGTGACATCCTTAA 57.042 39.130 21.05 13.11 0.00 1.85
52 53 5.957771 AAGCCTTAGATGTGACATCCTTA 57.042 39.130 21.05 6.22 0.00 2.69
53 54 4.851639 AAGCCTTAGATGTGACATCCTT 57.148 40.909 21.05 13.69 0.00 3.36
54 55 4.965532 ACTAAGCCTTAGATGTGACATCCT 59.034 41.667 21.05 8.52 36.73 3.24
55 56 5.283457 ACTAAGCCTTAGATGTGACATCC 57.717 43.478 21.05 6.33 36.73 3.51
56 57 6.037610 CCAAACTAAGCCTTAGATGTGACATC 59.962 42.308 18.14 17.46 36.73 3.06
57 58 5.882557 CCAAACTAAGCCTTAGATGTGACAT 59.117 40.000 18.14 0.00 36.73 3.06
58 59 5.245531 CCAAACTAAGCCTTAGATGTGACA 58.754 41.667 18.14 0.00 36.73 3.58
59 60 4.095036 GCCAAACTAAGCCTTAGATGTGAC 59.905 45.833 18.14 2.19 36.73 3.67
60 61 4.261801 GCCAAACTAAGCCTTAGATGTGA 58.738 43.478 18.14 0.00 36.73 3.58
61 62 4.009675 TGCCAAACTAAGCCTTAGATGTG 58.990 43.478 18.14 11.38 36.73 3.21
62 63 4.265073 CTGCCAAACTAAGCCTTAGATGT 58.735 43.478 18.14 0.41 36.73 3.06
63 64 3.065925 GCTGCCAAACTAAGCCTTAGATG 59.934 47.826 18.14 14.60 36.73 2.90
64 65 3.054065 AGCTGCCAAACTAAGCCTTAGAT 60.054 43.478 18.14 3.29 37.68 1.98
65 66 2.305927 AGCTGCCAAACTAAGCCTTAGA 59.694 45.455 18.14 0.00 37.68 2.10
66 67 2.680339 GAGCTGCCAAACTAAGCCTTAG 59.320 50.000 9.95 9.95 37.68 2.18
67 68 2.305927 AGAGCTGCCAAACTAAGCCTTA 59.694 45.455 0.00 0.00 37.68 2.69
602 2389 8.860780 TTTGGTACGTATTAAATACTTTGGGT 57.139 30.769 0.00 0.00 33.59 4.51
617 2404 7.714377 TGGTTTCTGAAATAACTTTGGTACGTA 59.286 33.333 6.06 0.00 0.00 3.57
618 2405 6.543100 TGGTTTCTGAAATAACTTTGGTACGT 59.457 34.615 6.06 0.00 0.00 3.57
619 2406 6.854381 GTGGTTTCTGAAATAACTTTGGTACG 59.146 38.462 6.06 0.00 0.00 3.67
620 2407 7.708998 TGTGGTTTCTGAAATAACTTTGGTAC 58.291 34.615 6.06 0.00 0.00 3.34
676 2463 1.173913 GCTTAGGGTGCGTTTGGATT 58.826 50.000 0.00 0.00 0.00 3.01
695 2482 4.338964 TGCTGCATTATGTATTTGTGGGAG 59.661 41.667 0.00 0.00 0.00 4.30
696 2483 4.276642 TGCTGCATTATGTATTTGTGGGA 58.723 39.130 0.00 0.00 0.00 4.37
697 2484 4.652421 TGCTGCATTATGTATTTGTGGG 57.348 40.909 0.00 0.00 0.00 4.61
698 2485 5.409211 TGTTGCTGCATTATGTATTTGTGG 58.591 37.500 1.84 0.00 0.00 4.17
699 2486 6.807720 TCTTGTTGCTGCATTATGTATTTGTG 59.192 34.615 1.84 0.00 0.00 3.33
700 2487 6.923012 TCTTGTTGCTGCATTATGTATTTGT 58.077 32.000 1.84 0.00 0.00 2.83
701 2488 7.815398 TTCTTGTTGCTGCATTATGTATTTG 57.185 32.000 1.84 0.00 0.00 2.32
702 2489 7.871973 TGTTTCTTGTTGCTGCATTATGTATTT 59.128 29.630 1.84 0.00 0.00 1.40
703 2490 7.377398 TGTTTCTTGTTGCTGCATTATGTATT 58.623 30.769 1.84 0.00 0.00 1.89
704 2491 6.923012 TGTTTCTTGTTGCTGCATTATGTAT 58.077 32.000 1.84 0.00 0.00 2.29
705 2492 6.324561 TGTTTCTTGTTGCTGCATTATGTA 57.675 33.333 1.84 0.00 0.00 2.29
706 2493 5.199024 TGTTTCTTGTTGCTGCATTATGT 57.801 34.783 1.84 0.00 0.00 2.29
707 2494 6.528014 TTTGTTTCTTGTTGCTGCATTATG 57.472 33.333 1.84 0.00 0.00 1.90
708 2495 7.551035 TTTTTGTTTCTTGTTGCTGCATTAT 57.449 28.000 1.84 0.00 0.00 1.28
709 2496 6.974932 TTTTTGTTTCTTGTTGCTGCATTA 57.025 29.167 1.84 0.00 0.00 1.90
710 2497 5.876612 TTTTTGTTTCTTGTTGCTGCATT 57.123 30.435 1.84 0.00 0.00 3.56
735 2522 9.349713 TCTGTTTGTGATTTATTTTGTCCTAGT 57.650 29.630 0.00 0.00 0.00 2.57
736 2523 9.831737 CTCTGTTTGTGATTTATTTTGTCCTAG 57.168 33.333 0.00 0.00 0.00 3.02
737 2524 9.349713 ACTCTGTTTGTGATTTATTTTGTCCTA 57.650 29.630 0.00 0.00 0.00 2.94
738 2525 8.137437 CACTCTGTTTGTGATTTATTTTGTCCT 58.863 33.333 0.00 0.00 37.60 3.85
739 2526 7.382218 CCACTCTGTTTGTGATTTATTTTGTCC 59.618 37.037 0.00 0.00 37.60 4.02
740 2527 8.134895 TCCACTCTGTTTGTGATTTATTTTGTC 58.865 33.333 0.00 0.00 37.60 3.18
741 2528 7.920682 GTCCACTCTGTTTGTGATTTATTTTGT 59.079 33.333 0.00 0.00 37.60 2.83
742 2529 7.920151 TGTCCACTCTGTTTGTGATTTATTTTG 59.080 33.333 0.00 0.00 37.60 2.44
743 2530 8.006298 TGTCCACTCTGTTTGTGATTTATTTT 57.994 30.769 0.00 0.00 37.60 1.82
744 2531 7.581213 TGTCCACTCTGTTTGTGATTTATTT 57.419 32.000 0.00 0.00 37.60 1.40
745 2532 7.448161 TGATGTCCACTCTGTTTGTGATTTATT 59.552 33.333 0.00 0.00 37.60 1.40
746 2533 6.942005 TGATGTCCACTCTGTTTGTGATTTAT 59.058 34.615 0.00 0.00 37.60 1.40
747 2534 6.295249 TGATGTCCACTCTGTTTGTGATTTA 58.705 36.000 0.00 0.00 37.60 1.40
748 2535 5.132502 TGATGTCCACTCTGTTTGTGATTT 58.867 37.500 0.00 0.00 37.60 2.17
749 2536 4.717877 TGATGTCCACTCTGTTTGTGATT 58.282 39.130 0.00 0.00 37.60 2.57
750 2537 4.321718 CTGATGTCCACTCTGTTTGTGAT 58.678 43.478 0.00 0.00 37.60 3.06
751 2538 3.732212 CTGATGTCCACTCTGTTTGTGA 58.268 45.455 0.00 0.00 37.60 3.58
752 2539 2.225019 GCTGATGTCCACTCTGTTTGTG 59.775 50.000 0.00 0.00 35.39 3.33
753 2540 2.105477 AGCTGATGTCCACTCTGTTTGT 59.895 45.455 0.00 0.00 0.00 2.83
754 2541 2.775890 AGCTGATGTCCACTCTGTTTG 58.224 47.619 0.00 0.00 0.00 2.93
755 2542 3.498774 AAGCTGATGTCCACTCTGTTT 57.501 42.857 0.00 0.00 0.00 2.83
756 2543 3.834813 TCTAAGCTGATGTCCACTCTGTT 59.165 43.478 0.00 0.00 0.00 3.16
757 2544 3.435275 TCTAAGCTGATGTCCACTCTGT 58.565 45.455 0.00 0.00 0.00 3.41
758 2545 4.669206 ATCTAAGCTGATGTCCACTCTG 57.331 45.455 0.00 0.00 0.00 3.35
759 2546 6.992664 ATAATCTAAGCTGATGTCCACTCT 57.007 37.500 0.00 0.00 0.00 3.24
760 2547 9.717942 ATAAATAATCTAAGCTGATGTCCACTC 57.282 33.333 0.00 0.00 0.00 3.51
766 2553 9.561069 ACGGAAATAAATAATCTAAGCTGATGT 57.439 29.630 0.00 0.00 0.00 3.06
768 2555 9.778741 TGACGGAAATAAATAATCTAAGCTGAT 57.221 29.630 0.00 0.00 0.00 2.90
769 2556 9.607988 TTGACGGAAATAAATAATCTAAGCTGA 57.392 29.630 0.00 0.00 0.00 4.26
770 2557 9.651718 GTTGACGGAAATAAATAATCTAAGCTG 57.348 33.333 0.00 0.00 0.00 4.24
771 2558 9.391006 TGTTGACGGAAATAAATAATCTAAGCT 57.609 29.630 0.00 0.00 0.00 3.74
821 2612 0.319555 TTGTCTGTCGGGAAAGCGAG 60.320 55.000 0.00 0.00 0.00 5.03
931 4824 6.293955 GCTGAGAGCTCTCCTACTTATACTTG 60.294 46.154 35.07 9.21 42.20 3.16
932 4825 5.768164 GCTGAGAGCTCTCCTACTTATACTT 59.232 44.000 35.07 1.42 42.20 2.24
933 4826 5.313712 GCTGAGAGCTCTCCTACTTATACT 58.686 45.833 35.07 1.90 42.20 2.12
1001 4899 3.805971 TCATGATATTGTGCTTGCTCGAG 59.194 43.478 8.45 8.45 0.00 4.04
2031 5986 1.216710 GGAGGGTGCTCTCTTCGTG 59.783 63.158 0.00 0.00 34.39 4.35
2039 5994 4.459089 GACCTGCGGAGGGTGCTC 62.459 72.222 27.88 11.76 44.84 4.26
2115 6070 0.610174 ATTCGCAGTCTCTGGAAGCA 59.390 50.000 0.00 0.00 29.46 3.91
2116 6071 2.586258 TATTCGCAGTCTCTGGAAGC 57.414 50.000 0.00 0.00 29.46 3.86
2139 7666 5.904941 ACGTATATTTTATGGTCACGGTCA 58.095 37.500 0.00 0.00 32.52 4.02
2176 8586 8.831715 AAGCAACATTTTCCTCGAATAAAAAT 57.168 26.923 8.22 7.24 33.94 1.82
2185 8596 5.108405 CGTTGTAAAAGCAACATTTTCCTCG 60.108 40.000 9.20 0.00 46.47 4.63
2197 8614 2.791567 CTTGTGCACGTTGTAAAAGCA 58.208 42.857 13.13 0.00 0.00 3.91
2210 8630 2.161855 CTGTAATTCCCAGCTTGTGCA 58.838 47.619 0.00 0.00 42.74 4.57
2229 8676 5.298276 ACGTGTGTTTTGGTTATCAACATCT 59.702 36.000 0.00 0.00 34.67 2.90
2253 9112 1.008194 GTGCGTGTACGTGTCAGGA 60.008 57.895 15.61 0.00 42.22 3.86
2306 9193 2.237893 TGATCCATCCATCCATCCATCG 59.762 50.000 0.00 0.00 0.00 3.84
2310 9197 1.340795 GCCTGATCCATCCATCCATCC 60.341 57.143 0.00 0.00 0.00 3.51
2311 9198 1.678123 CGCCTGATCCATCCATCCATC 60.678 57.143 0.00 0.00 0.00 3.51
2312 9199 0.327259 CGCCTGATCCATCCATCCAT 59.673 55.000 0.00 0.00 0.00 3.41
2313 9200 1.756665 CGCCTGATCCATCCATCCA 59.243 57.895 0.00 0.00 0.00 3.41
2314 9201 1.673665 GCGCCTGATCCATCCATCC 60.674 63.158 0.00 0.00 0.00 3.51
2315 9202 0.954449 CTGCGCCTGATCCATCCATC 60.954 60.000 4.18 0.00 0.00 3.51
2316 9203 1.072678 CTGCGCCTGATCCATCCAT 59.927 57.895 4.18 0.00 0.00 3.41
2317 9204 2.507452 CTGCGCCTGATCCATCCA 59.493 61.111 4.18 0.00 0.00 3.41
2318 9205 2.976903 GCTGCGCCTGATCCATCC 60.977 66.667 4.18 0.00 0.00 3.51
2322 9209 4.838152 TTCCGCTGCGCCTGATCC 62.838 66.667 18.00 0.00 0.00 3.36
2342 9229 2.575461 GATGCAAGGTGCCCAAGC 59.425 61.111 0.00 0.00 44.23 4.01
2713 11336 0.888619 CCCACTCACGAACTAGAGCA 59.111 55.000 0.00 0.00 35.28 4.26
2779 11421 4.281657 TCAGTGCCATATACTCACTCACT 58.718 43.478 0.00 0.00 38.85 3.41
2798 11440 6.726299 TCACCTATAAATACCCTCCAGATCAG 59.274 42.308 0.00 0.00 0.00 2.90
2821 11463 0.950836 CGGCCACACAGTTTTGATCA 59.049 50.000 2.24 0.00 0.00 2.92
2915 11558 3.985279 CACTTCAGTGTGCAAATCATTGG 59.015 43.478 0.00 0.00 40.96 3.16
3013 11669 2.794631 GCCGGCCGATTACAAGAATTTG 60.795 50.000 30.73 5.15 40.24 2.32


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

AutoCloner maintained by Alex Coulton.