Multiple sequence alignment - TraesCS1D01G038100

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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 TraesCS1D01G038100 chr1D 100.000 3364 0 0 1 3364 18244464 18241101 0.000000e+00 6213.0
1 TraesCS1D01G038100 chr1D 83.495 927 92 17 987 1901 18223596 18222719 0.000000e+00 808.0
2 TraesCS1D01G038100 chr1D 83.144 878 93 33 2510 3362 18222013 18221166 0.000000e+00 750.0
3 TraesCS1D01G038100 chr1D 87.153 576 66 4 1933 2507 18222723 18222155 0.000000e+00 647.0
4 TraesCS1D01G038100 chr1D 75.956 732 133 28 1 703 476432741 476433458 1.500000e-88 337.0
5 TraesCS1D01G038100 chr1D 72.429 1099 249 43 1291 2368 474877356 474876291 5.450000e-78 302.0
6 TraesCS1D01G038100 chr1D 83.482 224 33 4 1291 1512 474883613 474883392 4.400000e-49 206.0
7 TraesCS1D01G038100 chr1D 95.238 42 2 0 2652 2693 18241765 18241724 2.170000e-07 67.6
8 TraesCS1D01G038100 chr1D 95.238 42 2 0 2700 2741 18241813 18241772 2.170000e-07 67.6
9 TraesCS1D01G038100 chr1A 93.238 1952 108 10 752 2693 20246394 20244457 0.000000e+00 2852.0
10 TraesCS1D01G038100 chr1A 86.002 2429 241 51 984 3364 20237985 20235608 0.000000e+00 2510.0
11 TraesCS1D01G038100 chr1A 84.602 565 66 10 109 657 20247570 20247011 2.950000e-150 542.0
12 TraesCS1D01G038100 chr1A 81.856 485 40 19 2700 3144 20244498 20244022 6.860000e-97 364.0
13 TraesCS1D01G038100 chr1A 85.714 238 19 5 3130 3364 20243815 20243590 1.560000e-58 237.0
14 TraesCS1D01G038100 chr1A 81.349 252 43 4 1262 1511 570388622 570388373 5.690000e-48 202.0
15 TraesCS1D01G038100 chr1A 83.111 225 32 6 1291 1512 570374456 570374235 2.050000e-47 200.0
16 TraesCS1D01G038100 chr1A 95.238 42 2 0 2700 2741 20236318 20236277 2.170000e-07 67.6
17 TraesCS1D01G038100 chr4B 85.227 704 89 6 16 705 599397921 599397219 0.000000e+00 710.0
18 TraesCS1D01G038100 chr4B 88.235 85 7 2 621 703 53119633 53119716 7.680000e-17 99.0
19 TraesCS1D01G038100 chr3A 84.349 722 98 6 1 708 388805604 388804884 0.000000e+00 693.0
20 TraesCS1D01G038100 chr3A 84.082 534 64 12 191 705 635332223 635332754 2.330000e-136 496.0
21 TraesCS1D01G038100 chr1B 83.961 717 98 12 1 704 508551400 508552112 0.000000e+00 671.0
22 TraesCS1D01G038100 chr2D 83.894 714 99 11 1 699 16850650 16851362 0.000000e+00 667.0
23 TraesCS1D01G038100 chr2D 77.982 654 110 21 74 707 596661781 596662420 2.450000e-101 379.0
24 TraesCS1D01G038100 chr4A 84.091 704 97 10 17 706 550458875 550459577 0.000000e+00 665.0
25 TraesCS1D01G038100 chr3B 83.705 718 81 19 1 704 151215898 151216593 0.000000e+00 645.0
26 TraesCS1D01G038100 chr2B 83.053 714 95 11 1 697 28761595 28762299 2.850000e-175 625.0
27 TraesCS1D01G038100 chr2B 82.361 720 101 14 1 702 68822553 68821842 1.340000e-168 603.0
28 TraesCS1D01G038100 chr6D 73.654 1207 259 40 1293 2474 319244389 319245561 2.420000e-111 412.0
29 TraesCS1D01G038100 chr6D 76.200 479 94 15 1298 1766 7567551 7567083 5.610000e-58 235.0
30 TraesCS1D01G038100 chr6A 73.074 1311 288 40 1298 2572 457072524 457073805 4.040000e-109 405.0
31 TraesCS1D01G038100 chr6B 77.292 480 89 14 1298 1767 14251806 14251337 7.160000e-67 265.0
32 TraesCS1D01G038100 chr6B 77.066 484 89 17 1295 1767 13960165 13960637 3.330000e-65 259.0
33 TraesCS1D01G038100 chr7A 77.002 487 78 19 229 708 581363338 581362879 7.210000e-62 248.0
34 TraesCS1D01G038100 chr7A 77.002 487 78 19 229 708 700428177 700427718 7.210000e-62 248.0
35 TraesCS1D01G038100 chr7A 75.876 485 83 19 229 706 498488188 498488645 2.030000e-52 217.0
36 TraesCS1D01G038100 chr7A 72.770 426 101 11 1874 2293 118241033 118241449 2.720000e-26 130.0
37 TraesCS1D01G038100 chr7B 73.253 501 110 18 1874 2367 72509143 72509626 9.660000e-36 161.0
38 TraesCS1D01G038100 chr5B 90.476 84 7 1 621 703 599272697 599272780 3.550000e-20 110.0
39 TraesCS1D01G038100 chr7D 70.957 575 131 27 1737 2293 113118376 113118932 1.650000e-18 104.0
40 TraesCS1D01G038100 chr7D 100.000 33 0 0 1737 1769 113158948 113158980 1.010000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G038100 chr1D 18241101 18244464 3363 True 2116.066667 6213 96.825333 1 3364 3 chr1D.!!$R4 3363
1 TraesCS1D01G038100 chr1D 18221166 18223596 2430 True 735.000000 808 84.597333 987 3362 3 chr1D.!!$R3 2375
2 TraesCS1D01G038100 chr1D 476432741 476433458 717 False 337.000000 337 75.956000 1 703 1 chr1D.!!$F1 702
3 TraesCS1D01G038100 chr1D 474876291 474877356 1065 True 302.000000 302 72.429000 1291 2368 1 chr1D.!!$R1 1077
4 TraesCS1D01G038100 chr1A 20235608 20237985 2377 True 1288.800000 2510 90.620000 984 3364 2 chr1A.!!$R3 2380
5 TraesCS1D01G038100 chr1A 20243590 20247570 3980 True 998.750000 2852 86.352500 109 3364 4 chr1A.!!$R4 3255
6 TraesCS1D01G038100 chr4B 599397219 599397921 702 True 710.000000 710 85.227000 16 705 1 chr4B.!!$R1 689
7 TraesCS1D01G038100 chr3A 388804884 388805604 720 True 693.000000 693 84.349000 1 708 1 chr3A.!!$R1 707
8 TraesCS1D01G038100 chr3A 635332223 635332754 531 False 496.000000 496 84.082000 191 705 1 chr3A.!!$F1 514
9 TraesCS1D01G038100 chr1B 508551400 508552112 712 False 671.000000 671 83.961000 1 704 1 chr1B.!!$F1 703
10 TraesCS1D01G038100 chr2D 16850650 16851362 712 False 667.000000 667 83.894000 1 699 1 chr2D.!!$F1 698
11 TraesCS1D01G038100 chr2D 596661781 596662420 639 False 379.000000 379 77.982000 74 707 1 chr2D.!!$F2 633
12 TraesCS1D01G038100 chr4A 550458875 550459577 702 False 665.000000 665 84.091000 17 706 1 chr4A.!!$F1 689
13 TraesCS1D01G038100 chr3B 151215898 151216593 695 False 645.000000 645 83.705000 1 704 1 chr3B.!!$F1 703
14 TraesCS1D01G038100 chr2B 28761595 28762299 704 False 625.000000 625 83.053000 1 697 1 chr2B.!!$F1 696
15 TraesCS1D01G038100 chr2B 68821842 68822553 711 True 603.000000 603 82.361000 1 702 1 chr2B.!!$R1 701
16 TraesCS1D01G038100 chr6D 319244389 319245561 1172 False 412.000000 412 73.654000 1293 2474 1 chr6D.!!$F1 1181
17 TraesCS1D01G038100 chr6A 457072524 457073805 1281 False 405.000000 405 73.074000 1298 2572 1 chr6A.!!$F1 1274

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
878 1476 0.034477 CCCTACCCTGGCAAATCGTT 60.034 55.0 0.0 0.0 0.00 3.85 F
887 1485 0.109919 GGCAAATCGTTCGTTCCCAC 60.110 55.0 0.0 0.0 0.00 4.61 F
1640 2265 0.179000 CTATGACAGGGCAGTGGACC 59.821 60.0 0.0 0.0 45.66 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2788 0.178992 TGCCTCCCAAACAGTTCTGG 60.179 55.0 4.82 7.27 0.0 3.86 R
2228 2877 0.754957 CTGCCATCTCCTCCTCGTCT 60.755 60.0 0.00 0.00 0.0 4.18 R
3048 3913 0.661020 AACGGCTAACTTGTGTGCAC 59.339 50.0 10.75 10.75 0.0 4.57 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
38 39 3.657038 TACGCTCCCTTCCGGCTCT 62.657 63.158 0.00 0.00 0.00 4.09
72 73 1.525442 CCGGTCACCATTCTACCCC 59.475 63.158 0.00 0.00 0.00 4.95
123 124 1.301479 GACCCCGTCAACACTCACC 60.301 63.158 0.00 0.00 32.09 4.02
169 172 1.483595 TTCCAGCAGCAGGTGTAGCT 61.484 55.000 7.56 0.00 44.62 3.32
298 304 2.106938 CTCGGCTTGCCGATGCTA 59.893 61.111 32.45 13.75 41.47 3.49
337 349 1.767692 GTTTCCCTTCCTGGAGGCA 59.232 57.895 0.00 0.00 38.35 4.75
356 369 0.929244 ACTGCCATGGCCTTTATCCT 59.071 50.000 33.44 4.11 41.09 3.24
359 372 1.287442 TGCCATGGCCTTTATCCTTGA 59.713 47.619 33.44 7.63 41.09 3.02
421 435 4.854924 TCGGATGGTGGCGGCATG 62.855 66.667 17.19 1.38 0.00 4.06
435 450 2.603247 GCATGACAACGTCGCACCA 61.603 57.895 0.00 0.00 34.95 4.17
442 457 1.202440 ACAACGTCGCACCACTTCTTA 60.202 47.619 0.00 0.00 0.00 2.10
495 513 2.996631 AGTGCTGGATTTGGAGATGTC 58.003 47.619 0.00 0.00 0.00 3.06
532 552 1.610624 CGGCCTGCCTTTCTGTTTAGA 60.611 52.381 6.60 0.00 0.00 2.10
539 559 6.598064 GCCTGCCTTTCTGTTTAGAATTAGTA 59.402 38.462 0.00 0.00 42.25 1.82
619 656 0.035152 ATGCCTCCTTGCGTTCATGA 60.035 50.000 0.00 0.00 0.00 3.07
625 662 3.261580 CTCCTTGCGTTCATGACATGTA 58.738 45.455 14.98 2.82 0.00 2.29
723 763 0.323629 AAAATTCCGAGTCTCCCGCA 59.676 50.000 0.00 0.00 0.00 5.69
726 766 4.710167 TCCGAGTCTCCCGCACGA 62.710 66.667 0.00 0.00 0.00 4.35
750 790 4.724279 ACCAACCACTCTAGACCAAATT 57.276 40.909 0.00 0.00 0.00 1.82
769 1367 1.196012 TTGTTTTTGGGTTCCCGCTT 58.804 45.000 3.27 0.00 0.00 4.68
770 1368 1.196012 TGTTTTTGGGTTCCCGCTTT 58.804 45.000 3.27 0.00 0.00 3.51
808 1406 5.132502 TCACTTTGTTTGGATCATGTGACT 58.867 37.500 0.00 0.00 0.00 3.41
832 1430 0.597377 CCAGCACGAAAAGCCCAAAC 60.597 55.000 0.00 0.00 0.00 2.93
837 1435 2.832563 CACGAAAAGCCCAAACCAAAT 58.167 42.857 0.00 0.00 0.00 2.32
848 1446 3.055891 CCCAAACCAAATCACATTCCTCC 60.056 47.826 0.00 0.00 0.00 4.30
855 1453 1.418334 ATCACATTCCTCCCTCCTCG 58.582 55.000 0.00 0.00 0.00 4.63
868 1466 1.400737 CTCCTCGTAACCCTACCCTG 58.599 60.000 0.00 0.00 0.00 4.45
878 1476 0.034477 CCCTACCCTGGCAAATCGTT 60.034 55.000 0.00 0.00 0.00 3.85
880 1478 1.006832 CTACCCTGGCAAATCGTTCG 58.993 55.000 0.00 0.00 0.00 3.95
887 1485 0.109919 GGCAAATCGTTCGTTCCCAC 60.110 55.000 0.00 0.00 0.00 4.61
888 1486 0.872388 GCAAATCGTTCGTTCCCACT 59.128 50.000 0.00 0.00 0.00 4.00
924 1524 4.457496 CTCTCACGCCGCCACCAT 62.457 66.667 0.00 0.00 0.00 3.55
951 1551 2.283676 TCCGGCGAACTCTCCCTT 60.284 61.111 9.30 0.00 0.00 3.95
958 1558 0.820871 CGAACTCTCCCTTCTCCCAG 59.179 60.000 0.00 0.00 0.00 4.45
975 1575 3.888930 TCCCAGTCTTGAATCCAACAAAC 59.111 43.478 0.00 0.00 0.00 2.93
1171 1778 1.023719 TATGTTCCCCTCCTCTCCCA 58.976 55.000 0.00 0.00 0.00 4.37
1202 1809 7.431249 CAATCTTGAATCCAATCCAATACAGG 58.569 38.462 0.00 0.00 0.00 4.00
1438 2054 1.073923 GGGCTTCTTCTTCAAGGACCA 59.926 52.381 0.00 0.00 0.00 4.02
1587 2206 5.466058 TGCAAATGTTTGAAATCACATCACC 59.534 36.000 9.53 0.00 40.55 4.02
1604 2229 1.667724 CACCAGGAAGATGAATGCGAC 59.332 52.381 0.00 0.00 0.00 5.19
1640 2265 0.179000 CTATGACAGGGCAGTGGACC 59.821 60.000 0.00 0.00 45.66 4.46
1736 2379 2.315386 GGGTTTCGACGTGGCAGTC 61.315 63.158 0.00 0.00 37.76 3.51
1895 2541 2.688507 TCAGAATGCGTCTTCCTCAAC 58.311 47.619 0.00 0.00 32.70 3.18
1944 2593 2.095567 GCTTTAGTAGTCACCGTCGACA 60.096 50.000 17.16 0.00 38.43 4.35
2054 2703 3.573598 CTTGTATGCGTGGCAAATTGAA 58.426 40.909 0.00 0.00 43.62 2.69
2098 2747 5.939883 TCTATGTGTGGGTTCTTGAAGATTG 59.060 40.000 0.00 0.00 0.00 2.67
2139 2788 6.393171 ACCCTCAAGTATACTGTTAACGTTC 58.607 40.000 2.82 0.00 0.00 3.95
2150 2799 4.939439 ACTGTTAACGTTCCAGAACTGTTT 59.061 37.500 25.92 6.89 38.23 2.83
2222 2871 9.953565 ATTCATCCAGATTGTGATTTGATTTTT 57.046 25.926 0.00 0.00 0.00 1.94
2228 2877 9.695526 CCAGATTGTGATTTGATTTTTCTTACA 57.304 29.630 0.00 0.00 0.00 2.41
2249 2898 0.259065 ACGAGGAGGAGATGGCAGTA 59.741 55.000 0.00 0.00 0.00 2.74
2405 3060 0.037326 TCCTTAGCGTGGCACTTCAG 60.037 55.000 16.72 6.08 0.00 3.02
2429 3084 0.610785 AGCGGTTGTTGGGTATTGGG 60.611 55.000 0.00 0.00 0.00 4.12
2430 3085 0.896479 GCGGTTGTTGGGTATTGGGT 60.896 55.000 0.00 0.00 0.00 4.51
2433 3088 3.358118 CGGTTGTTGGGTATTGGGTATT 58.642 45.455 0.00 0.00 0.00 1.89
2438 3093 2.693074 GTTGGGTATTGGGTATTGCCTG 59.307 50.000 0.00 0.00 37.43 4.85
2485 3149 4.094830 TGGATGTGTCCTAGCGTCTATA 57.905 45.455 0.00 0.00 45.32 1.31
2499 3163 5.665459 AGCGTCTATATCTGCTTCAGTTTT 58.335 37.500 0.00 0.00 32.89 2.43
2546 3353 3.964031 TCTAATGGGTTTTGTGGCTTTGT 59.036 39.130 0.00 0.00 0.00 2.83
2549 3356 1.757699 TGGGTTTTGTGGCTTTGTACC 59.242 47.619 0.00 0.00 0.00 3.34
2592 3400 2.647299 TCTGCAAGGGACCCTTAATTGA 59.353 45.455 25.83 17.10 42.67 2.57
2633 3441 3.838317 TGTCACCTTGTTAGCTCCTATGT 59.162 43.478 0.00 0.00 0.00 2.29
2639 3447 3.408157 TGTTAGCTCCTATGTGGGGTA 57.592 47.619 0.00 0.00 38.99 3.69
2698 3506 9.871238 ATTTACATCGTACAAGTGTCTTATCTT 57.129 29.630 0.00 0.00 0.00 2.40
2701 3509 7.152645 ACATCGTACAAGTGTCTTATCTTTGT 58.847 34.615 0.00 0.00 0.00 2.83
2708 3516 7.920738 ACAAGTGTCTTATCTTTGTCAAACTC 58.079 34.615 0.00 0.00 0.00 3.01
2709 3517 7.012421 ACAAGTGTCTTATCTTTGTCAAACTCC 59.988 37.037 0.00 0.00 0.00 3.85
2720 3528 8.299990 TCTTTGTCAAACTCCTTTTATTTCCA 57.700 30.769 0.00 0.00 0.00 3.53
2723 3531 9.898152 TTTGTCAAACTCCTTTTATTTCCATTT 57.102 25.926 0.00 0.00 0.00 2.32
2725 3533 9.974980 TGTCAAACTCCTTTTATTTCCATTTAC 57.025 29.630 0.00 0.00 0.00 2.01
2726 3534 9.974980 GTCAAACTCCTTTTATTTCCATTTACA 57.025 29.630 0.00 0.00 0.00 2.41
2772 3593 6.817765 ATTGGTTATCTTTTGATGTCGTGT 57.182 33.333 0.00 0.00 39.88 4.49
2789 3610 4.616802 GTCGTGTTGTTATTCTGCATTTGG 59.383 41.667 0.00 0.00 0.00 3.28
2796 3617 8.243426 TGTTGTTATTCTGCATTTGGAACTATC 58.757 33.333 0.00 0.00 0.00 2.08
2806 3629 6.660521 TGCATTTGGAACTATCACTCTCATTT 59.339 34.615 0.00 0.00 0.00 2.32
2810 3633 4.019411 TGGAACTATCACTCTCATTTGCCA 60.019 41.667 0.00 0.00 0.00 4.92
2857 3680 2.540383 TGGAACATGTCAGAGTAGCCT 58.460 47.619 0.00 0.00 0.00 4.58
2886 3710 4.640771 TGCAGAGAGGGTAAAAATCTGT 57.359 40.909 0.00 0.00 39.63 3.41
2913 3737 5.036737 GTGTTCCATTGTTGTTTCAGTCTG 58.963 41.667 0.00 0.00 0.00 3.51
2930 3760 8.818141 TTCAGTCTGTATATATGCAGCTTAAC 57.182 34.615 22.06 15.85 39.87 2.01
2932 3762 8.421002 TCAGTCTGTATATATGCAGCTTAACAA 58.579 33.333 22.06 4.40 39.87 2.83
3048 3913 4.035112 TGTAGGTAAGACAGGGGTAATGG 58.965 47.826 0.00 0.00 0.00 3.16
3078 3943 6.034683 CACAAGTTAGCCGTTCATTACTACTC 59.965 42.308 0.00 0.00 0.00 2.59
3079 3944 6.071503 ACAAGTTAGCCGTTCATTACTACTCT 60.072 38.462 0.00 0.00 0.00 3.24
3084 3949 6.616774 AGCCGTTCATTACTACTCTACTAC 57.383 41.667 0.00 0.00 0.00 2.73
3125 3990 4.741676 CAGCTCCACTGTTCATTTTTGTTC 59.258 41.667 0.00 0.00 41.86 3.18
3181 4267 2.961062 AGCTGCCCATGACCAATATTTC 59.039 45.455 0.00 0.00 0.00 2.17
3200 4286 9.868277 AATATTTCTCTACTTGACTTCTCACTG 57.132 33.333 0.00 0.00 0.00 3.66
3225 4317 7.041372 TGGTCTGTTAAGATTCTAAGTTGTTGC 60.041 37.037 0.00 0.00 34.13 4.17
3239 4331 8.475639 TCTAAGTTGTTGCCCTACTAAATCTAG 58.524 37.037 0.00 0.00 0.00 2.43
3240 4332 6.622427 AGTTGTTGCCCTACTAAATCTAGT 57.378 37.500 0.00 0.00 41.43 2.57
3241 4333 7.729124 AGTTGTTGCCCTACTAAATCTAGTA 57.271 36.000 0.00 0.00 39.23 1.82
3251 4343 9.589461 CCCTACTAAATCTAGTATTTCTGAGGA 57.411 37.037 14.75 3.97 39.40 3.71
3309 4403 6.267070 CAGATTCTTCTCGTCCTTTACCTAC 58.733 44.000 0.00 0.00 0.00 3.18
3310 4404 4.691860 TTCTTCTCGTCCTTTACCTACG 57.308 45.455 0.00 0.00 37.96 3.51
3311 4405 3.679389 TCTTCTCGTCCTTTACCTACGT 58.321 45.455 0.00 0.00 37.83 3.57
3312 4406 3.438087 TCTTCTCGTCCTTTACCTACGTG 59.562 47.826 0.00 0.00 37.83 4.49
3313 4407 2.783135 TCTCGTCCTTTACCTACGTGT 58.217 47.619 0.00 0.00 37.83 4.49
3314 4408 2.744202 TCTCGTCCTTTACCTACGTGTC 59.256 50.000 0.00 0.00 37.83 3.67
3315 4409 2.485426 CTCGTCCTTTACCTACGTGTCA 59.515 50.000 0.00 0.00 37.83 3.58
3316 4410 3.084039 TCGTCCTTTACCTACGTGTCAT 58.916 45.455 0.00 0.00 37.83 3.06
3318 4412 4.699735 TCGTCCTTTACCTACGTGTCATTA 59.300 41.667 0.00 0.00 37.83 1.90
3319 4413 5.032863 CGTCCTTTACCTACGTGTCATTAG 58.967 45.833 0.00 0.00 32.16 1.73
3320 4414 4.802563 GTCCTTTACCTACGTGTCATTAGC 59.197 45.833 0.00 0.00 0.00 3.09
3321 4415 4.463539 TCCTTTACCTACGTGTCATTAGCA 59.536 41.667 0.00 0.00 0.00 3.49
3322 4416 5.128171 TCCTTTACCTACGTGTCATTAGCAT 59.872 40.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.026522 GAGCGTAGATCCGAGCTGT 58.973 57.895 10.55 0.00 40.39 4.40
79 80 1.723870 CAGCATGGTAGAAAGCCGC 59.276 57.895 0.00 0.00 0.00 6.53
114 115 1.896220 AATGACATGCGGTGAGTGTT 58.104 45.000 0.00 0.00 0.00 3.32
123 124 2.591148 CGAGCTTTGAAAATGACATGCG 59.409 45.455 0.00 0.00 0.00 4.73
169 172 1.191535 CCCGATAGTGAAGTGGTGGA 58.808 55.000 0.00 0.00 0.00 4.02
180 184 2.561956 CGACCGCCATCCCGATAGT 61.562 63.158 0.00 0.00 0.00 2.12
337 349 0.929244 AGGATAAAGGCCATGGCAGT 59.071 50.000 36.56 21.47 44.11 4.40
421 435 0.874607 AGAAGTGGTGCGACGTTGTC 60.875 55.000 4.37 0.00 0.00 3.18
435 450 7.224949 GTGAATAAGATAGCGCCTTTAAGAAGT 59.775 37.037 2.29 0.00 0.00 3.01
442 457 4.051922 CGAGTGAATAAGATAGCGCCTTT 58.948 43.478 2.29 0.00 0.00 3.11
495 513 1.265568 CCGAACTAACACGATGTCGG 58.734 55.000 7.38 0.00 44.95 4.79
506 524 0.690762 AGAAAGGCAGGCCGAACTAA 59.309 50.000 4.37 0.00 41.95 2.24
539 559 4.141018 AGGGGAAATGACACAACTAAACCT 60.141 41.667 0.00 0.00 0.00 3.50
619 656 8.998277 AGTACAGTAGAGGATACAATACATGT 57.002 34.615 2.69 2.69 46.36 3.21
625 662 9.073475 GAGAATGAGTACAGTAGAGGATACAAT 57.927 37.037 0.00 0.00 41.41 2.71
711 751 1.372499 TTTTCGTGCGGGAGACTCG 60.372 57.895 0.00 0.00 0.00 4.18
715 755 1.146485 TTGGTTTTCGTGCGGGAGA 59.854 52.632 0.00 0.00 0.00 3.71
723 763 3.493873 GGTCTAGAGTGGTTGGTTTTCGT 60.494 47.826 0.00 0.00 0.00 3.85
726 766 4.513406 TTGGTCTAGAGTGGTTGGTTTT 57.487 40.909 0.00 0.00 0.00 2.43
808 1406 2.668212 CTTTTCGTGCTGGGCCGA 60.668 61.111 0.00 0.00 31.78 5.54
820 1418 3.802866 TGTGATTTGGTTTGGGCTTTTC 58.197 40.909 0.00 0.00 0.00 2.29
832 1430 2.243221 AGGAGGGAGGAATGTGATTTGG 59.757 50.000 0.00 0.00 0.00 3.28
837 1435 0.041238 ACGAGGAGGGAGGAATGTGA 59.959 55.000 0.00 0.00 0.00 3.58
848 1446 0.261109 AGGGTAGGGTTACGAGGAGG 59.739 60.000 0.00 0.00 0.00 4.30
855 1453 2.651455 GATTTGCCAGGGTAGGGTTAC 58.349 52.381 0.00 0.00 0.00 2.50
868 1466 0.109919 GTGGGAACGAACGATTTGCC 60.110 55.000 0.14 1.47 33.94 4.52
928 1528 3.069318 GAGTTCGCCGGAGAGGGT 61.069 66.667 5.05 0.00 41.48 4.34
951 1551 2.978978 TGTTGGATTCAAGACTGGGAGA 59.021 45.455 0.00 0.00 32.92 3.71
958 1558 4.287720 GTTCCGTTTGTTGGATTCAAGAC 58.712 43.478 0.00 0.00 34.91 3.01
975 1575 0.673644 GATGGTGGACACAGGTTCCG 60.674 60.000 4.69 0.00 0.00 4.30
1136 1736 6.270231 GGGGAACATATTACATACCTCAGACT 59.730 42.308 0.00 0.00 0.00 3.24
1171 1778 6.437755 TGGATTGGATTCAAGATTGGAAGAT 58.562 36.000 0.00 0.00 36.19 2.40
1202 1809 4.084380 CGTTTAGGTTCAGTTTAACGTCCC 60.084 45.833 0.00 0.00 35.11 4.46
1379 1995 3.569049 CTTGCGGACGTTCGGGTCT 62.569 63.158 19.64 0.00 37.12 3.85
1418 2034 1.073923 TGGTCCTTGAAGAAGAAGCCC 59.926 52.381 0.00 0.00 0.00 5.19
1438 2054 0.965363 ACGGAAATTGAAGCGGCCAT 60.965 50.000 2.24 0.00 0.00 4.40
1587 2206 2.791560 CGTAGTCGCATTCATCTTCCTG 59.208 50.000 0.00 0.00 0.00 3.86
1604 2229 2.554806 TAGGATTGCACACGACGTAG 57.445 50.000 0.00 0.00 0.00 3.51
1640 2265 2.733590 TCCTATAGGAGGCAGCACG 58.266 57.895 18.00 0.00 46.25 5.34
1657 2282 0.755686 ATCCTCTTCGTCCAGCCATC 59.244 55.000 0.00 0.00 0.00 3.51
1895 2541 4.424566 GCCAAGTGCATGGTGCCG 62.425 66.667 8.13 0.00 44.23 5.69
1907 2553 5.133221 ACTAAAGCATAATGGGTAGCCAAG 58.867 41.667 19.29 9.74 0.00 3.61
1944 2593 1.462627 TCCAAACCTTCCCCTCCGT 60.463 57.895 0.00 0.00 0.00 4.69
2054 2703 3.118482 AGAGTTGGCAATCATGATCGTCT 60.118 43.478 9.06 2.52 0.00 4.18
2098 2747 0.822121 GGTCCACTTTCCACCACCAC 60.822 60.000 0.00 0.00 0.00 4.16
2139 2788 0.178992 TGCCTCCCAAACAGTTCTGG 60.179 55.000 4.82 7.27 0.00 3.86
2166 2815 9.784531 AAACACCTTATAGGACATATCATCTTG 57.215 33.333 0.00 0.00 37.67 3.02
2222 2871 3.546724 CATCTCCTCCTCGTCTGTAAGA 58.453 50.000 0.00 0.00 43.69 2.10
2228 2877 0.754957 CTGCCATCTCCTCCTCGTCT 60.755 60.000 0.00 0.00 0.00 4.18
2249 2898 8.811017 ACTTTCTGATTCTCCATATCATACGAT 58.189 33.333 0.00 0.00 32.00 3.73
2405 3060 3.653539 ATACCCAACAACCGCTTTTTC 57.346 42.857 0.00 0.00 0.00 2.29
2429 3084 6.583806 CACAAAACAAGAAGATCAGGCAATAC 59.416 38.462 0.00 0.00 0.00 1.89
2430 3085 6.294675 CCACAAAACAAGAAGATCAGGCAATA 60.295 38.462 0.00 0.00 0.00 1.90
2433 3088 3.318839 CCACAAAACAAGAAGATCAGGCA 59.681 43.478 0.00 0.00 0.00 4.75
2438 3093 4.293415 CAGTGCCACAAAACAAGAAGATC 58.707 43.478 0.00 0.00 0.00 2.75
2485 3149 6.956497 AGAGGAAGATAAAACTGAAGCAGAT 58.044 36.000 0.82 0.00 35.18 2.90
2499 3163 3.181329 TCAGGGCACAAAGAGGAAGATA 58.819 45.455 0.00 0.00 0.00 1.98
2566 3373 1.376649 AGGGTCCCTTGCAGATTCTT 58.623 50.000 3.85 0.00 0.00 2.52
2592 3400 9.857656 AGGTGACATCAATAAGACAATAATGAT 57.142 29.630 0.00 0.00 0.00 2.45
2633 3441 6.884472 TTGACATCTCTTAGATTTACCCCA 57.116 37.500 0.00 0.00 31.32 4.96
2639 3447 9.579932 AAAAGGAGTTTGACATCTCTTAGATTT 57.420 29.630 7.69 0.00 31.32 2.17
2772 3593 8.243426 GTGATAGTTCCAAATGCAGAATAACAA 58.757 33.333 0.00 0.00 0.00 2.83
2789 3610 5.423015 TCTGGCAAATGAGAGTGATAGTTC 58.577 41.667 0.00 0.00 0.00 3.01
2796 3617 3.760151 TCCAAATCTGGCAAATGAGAGTG 59.240 43.478 0.00 0.00 43.17 3.51
2806 3629 3.303938 TGAAAACCTTCCAAATCTGGCA 58.696 40.909 0.00 0.00 43.17 4.92
2834 3657 4.018960 AGGCTACTCTGACATGTTCCATTT 60.019 41.667 0.00 0.00 0.00 2.32
2838 3661 3.172229 GAGGCTACTCTGACATGTTCC 57.828 52.381 0.00 0.00 40.68 3.62
2866 3689 5.529060 CCATACAGATTTTTACCCTCTCTGC 59.471 44.000 0.00 0.00 37.45 4.26
2872 3695 5.949952 GGAACACCATACAGATTTTTACCCT 59.050 40.000 0.00 0.00 0.00 4.34
2874 3697 6.827586 TGGAACACCATACAGATTTTTACC 57.172 37.500 0.00 0.00 0.00 2.85
2930 3760 8.767478 AAGAAATGATAATTTGTCCAGCTTTG 57.233 30.769 0.00 0.00 0.00 2.77
2932 3762 9.783081 AAAAAGAAATGATAATTTGTCCAGCTT 57.217 25.926 0.00 0.00 0.00 3.74
3048 3913 0.661020 AACGGCTAACTTGTGTGCAC 59.339 50.000 10.75 10.75 0.00 4.57
3078 3943 8.434733 TGCATGACTAGTAAGTACTGTAGTAG 57.565 38.462 16.94 16.94 35.56 2.57
3079 3944 7.012138 GCTGCATGACTAGTAAGTACTGTAGTA 59.988 40.741 11.09 6.28 35.56 1.82
3084 3949 5.255710 AGCTGCATGACTAGTAAGTACTG 57.744 43.478 1.02 0.00 35.56 2.74
3125 3990 3.393089 AGCCACGGATAGCTTAATCAG 57.607 47.619 0.00 0.00 35.22 2.90
3181 4267 4.764823 AGACCAGTGAGAAGTCAAGTAGAG 59.235 45.833 0.00 0.00 33.27 2.43
3200 4286 7.298854 GCAACAACTTAGAATCTTAACAGACC 58.701 38.462 0.00 0.00 0.00 3.85
3225 4317 9.589461 TCCTCAGAAATACTAGATTTAGTAGGG 57.411 37.037 8.88 0.00 43.64 3.53
3282 4374 2.957491 AGGACGAGAAGAATCTGCAG 57.043 50.000 7.63 7.63 35.54 4.41
3309 4403 2.223340 GCCTTGGAATGCTAATGACACG 60.223 50.000 0.00 0.00 0.00 4.49
3310 4404 3.019564 AGCCTTGGAATGCTAATGACAC 58.980 45.455 0.00 0.00 35.69 3.67
3311 4405 3.370840 AGCCTTGGAATGCTAATGACA 57.629 42.857 0.00 0.00 35.69 3.58
3312 4406 3.736126 GCAAGCCTTGGAATGCTAATGAC 60.736 47.826 6.57 0.00 36.66 3.06
3313 4407 2.428171 GCAAGCCTTGGAATGCTAATGA 59.572 45.455 6.57 0.00 36.66 2.57
3314 4408 2.166870 TGCAAGCCTTGGAATGCTAATG 59.833 45.455 6.57 0.00 39.49 1.90
3315 4409 2.459644 TGCAAGCCTTGGAATGCTAAT 58.540 42.857 6.57 0.00 39.49 1.73
3316 4410 1.921982 TGCAAGCCTTGGAATGCTAA 58.078 45.000 6.57 0.00 39.49 3.09
3318 4412 1.066430 CAATGCAAGCCTTGGAATGCT 60.066 47.619 1.80 0.00 39.49 3.79
3319 4413 1.066716 TCAATGCAAGCCTTGGAATGC 60.067 47.619 8.95 9.26 39.22 3.56
3320 4414 2.232941 ACTCAATGCAAGCCTTGGAATG 59.767 45.455 7.62 7.62 33.74 2.67
3321 4415 2.532843 ACTCAATGCAAGCCTTGGAAT 58.467 42.857 1.80 0.00 33.68 3.01
3322 4416 1.999648 ACTCAATGCAAGCCTTGGAA 58.000 45.000 1.80 0.00 33.68 3.53


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

AutoCloner maintained by Alex Coulton.