Multiple sequence alignment - TraesCS2A01G139200

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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 TraesCS2A01G139200 chr2A 100.000 4599 0 0 1 4599 84556098 84551500 0.000000e+00 8493.0
1 TraesCS2A01G139200 chr2A 91.365 359 23 5 933 1284 84586877 84586520 6.920000e-133 484.0
2 TraesCS2A01G139200 chr2A 78.387 620 115 12 23 626 771523030 771522414 7.220000e-103 385.0
3 TraesCS2A01G139200 chr2A 79.130 575 70 19 3872 4405 85596050 85596615 7.320000e-93 351.0
4 TraesCS2A01G139200 chr2A 81.720 186 20 7 684 859 752911152 752910971 4.800000e-30 143.0
5 TraesCS2A01G139200 chr2D 92.176 3387 177 40 1 3326 83825791 83822432 0.000000e+00 4706.0
6 TraesCS2A01G139200 chr2D 93.836 438 22 2 3387 3823 83822395 83821962 0.000000e+00 654.0
7 TraesCS2A01G139200 chr2D 94.041 386 17 4 4055 4440 83821766 83821387 8.580000e-162 580.0
8 TraesCS2A01G139200 chr2D 89.239 381 20 6 933 1307 83833640 83833275 1.510000e-124 457.0
9 TraesCS2A01G139200 chr2D 78.955 670 106 23 17 660 49348677 49348017 1.530000e-114 424.0
10 TraesCS2A01G139200 chr2D 78.487 595 100 21 53 625 144999893 144999305 9.400000e-97 364.0
11 TraesCS2A01G139200 chr2D 78.910 422 72 15 3872 4284 84760871 84761284 2.110000e-68 270.0
12 TraesCS2A01G139200 chr2D 93.293 164 11 0 3834 3997 83821926 83821763 4.600000e-60 243.0
13 TraesCS2A01G139200 chr2D 73.923 418 90 16 102 506 38759548 38759137 2.870000e-32 150.0
14 TraesCS2A01G139200 chr2D 95.556 45 0 1 4406 4450 84761492 84761534 2.300000e-08 71.3
15 TraesCS2A01G139200 chr2B 93.473 2436 122 17 907 3326 135694360 135691946 0.000000e+00 3583.0
16 TraesCS2A01G139200 chr2B 91.736 605 32 5 3379 3966 135691915 135691312 0.000000e+00 824.0
17 TraesCS2A01G139200 chr2B 83.443 912 103 22 3 871 135695329 135694423 0.000000e+00 804.0
18 TraesCS2A01G139200 chr2B 88.701 531 26 18 4075 4599 135691314 135690812 6.540000e-173 617.0
19 TraesCS2A01G139200 chr2B 89.751 361 30 4 933 1287 135697945 135697586 5.420000e-124 455.0
20 TraesCS2A01G139200 chr2B 77.586 290 58 5 23 311 797436241 797435958 7.910000e-38 169.0
21 TraesCS2A01G139200 chr2B 81.183 186 21 7 684 859 762025284 762025103 2.230000e-28 137.0
22 TraesCS2A01G139200 chr2B 90.566 53 1 3 4406 4457 136620692 136620741 2.970000e-07 67.6
23 TraesCS2A01G139200 chr6D 84.276 2105 201 70 1621 3672 435306166 435308193 0.000000e+00 1934.0
24 TraesCS2A01G139200 chr6D 80.573 628 91 25 23 626 15861275 15861895 5.420000e-124 455.0
25 TraesCS2A01G139200 chr6D 87.725 334 26 10 985 1303 435300377 435300710 4.340000e-100 375.0
26 TraesCS2A01G139200 chr6B 85.291 1890 190 49 1817 3672 658295890 658297725 0.000000e+00 1869.0
27 TraesCS2A01G139200 chr6B 88.184 347 29 9 971 1306 658275962 658276307 1.990000e-108 403.0
28 TraesCS2A01G139200 chr6B 88.685 327 19 11 993 1309 658291323 658291641 2.600000e-102 383.0
29 TraesCS2A01G139200 chr6B 85.799 169 16 7 3702 3867 658297779 658297942 6.120000e-39 172.0
30 TraesCS2A01G139200 chr6A 86.814 857 94 9 1767 2614 582252702 582253548 0.000000e+00 939.0
31 TraesCS2A01G139200 chr6A 84.792 697 55 21 2657 3326 582253559 582254231 0.000000e+00 652.0
32 TraesCS2A01G139200 chr6A 88.685 327 16 12 993 1309 582248688 582249003 3.360000e-101 379.0
33 TraesCS2A01G139200 chr6A 85.235 298 32 7 3384 3672 582254266 582254560 3.480000e-76 296.0
34 TraesCS2A01G139200 chr1A 82.723 573 93 6 1806 2375 15345950 15345381 5.310000e-139 505.0
35 TraesCS2A01G139200 chr1A 84.472 161 21 3 3167 3326 15344394 15344237 6.160000e-34 156.0
36 TraesCS2A01G139200 chr1A 80.392 102 16 4 570 668 560239615 560239715 1.770000e-09 75.0
37 TraesCS2A01G139200 chr1A 82.432 74 12 1 551 623 157311145 157311218 3.840000e-06 63.9
38 TraesCS2A01G139200 chr7D 81.071 523 79 7 3 508 162199428 162199947 2.580000e-107 399.0
39 TraesCS2A01G139200 chr7D 76.434 488 91 13 1 467 563902374 563901890 4.600000e-60 243.0
40 TraesCS2A01G139200 chr1D 79.356 528 93 12 2799 3319 14708558 14709076 1.570000e-94 357.0
41 TraesCS2A01G139200 chr1D 76.423 615 121 21 23 621 347782562 347781956 1.240000e-80 311.0
42 TraesCS2A01G139200 chr5D 76.230 610 114 23 40 626 77862463 77861862 1.250000e-75 294.0
43 TraesCS2A01G139200 chr5D 78.755 466 78 16 57 506 445066559 445066099 4.500000e-75 292.0
44 TraesCS2A01G139200 chr4D 76.938 516 91 19 17 509 94872776 94872266 7.580000e-68 268.0
45 TraesCS2A01G139200 chr3D 78.571 392 64 12 17 396 501047880 501048263 1.650000e-59 241.0
46 TraesCS2A01G139200 chr4B 76.688 459 72 21 15 443 134377570 134377117 5.990000e-54 222.0
47 TraesCS2A01G139200 chr5A 76.687 163 20 10 702 851 76728032 76727875 1.770000e-09 75.0


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 TraesCS2A01G139200 chr2A 84551500 84556098 4598 True 8493.00 8493 100.0000 1 4599 1 chr2A.!!$R1 4598
1 TraesCS2A01G139200 chr2A 771522414 771523030 616 True 385.00 385 78.3870 23 626 1 chr2A.!!$R4 603
2 TraesCS2A01G139200 chr2A 85596050 85596615 565 False 351.00 351 79.1300 3872 4405 1 chr2A.!!$F1 533
3 TraesCS2A01G139200 chr2D 83821387 83825791 4404 True 1545.75 4706 93.3365 1 4440 4 chr2D.!!$R5 4439
4 TraesCS2A01G139200 chr2D 49348017 49348677 660 True 424.00 424 78.9550 17 660 1 chr2D.!!$R2 643
5 TraesCS2A01G139200 chr2D 144999305 144999893 588 True 364.00 364 78.4870 53 625 1 chr2D.!!$R4 572
6 TraesCS2A01G139200 chr2B 135690812 135697945 7133 True 1256.60 3583 89.4208 3 4599 5 chr2B.!!$R3 4596
7 TraesCS2A01G139200 chr6D 435306166 435308193 2027 False 1934.00 1934 84.2760 1621 3672 1 chr6D.!!$F3 2051
8 TraesCS2A01G139200 chr6D 15861275 15861895 620 False 455.00 455 80.5730 23 626 1 chr6D.!!$F1 603
9 TraesCS2A01G139200 chr6B 658295890 658297942 2052 False 1020.50 1869 85.5450 1817 3867 2 chr6B.!!$F3 2050
10 TraesCS2A01G139200 chr6A 582248688 582254560 5872 False 566.50 939 86.3815 993 3672 4 chr6A.!!$F1 2679
11 TraesCS2A01G139200 chr1A 15344237 15345950 1713 True 330.50 505 83.5975 1806 3326 2 chr1A.!!$R1 1520
12 TraesCS2A01G139200 chr7D 162199428 162199947 519 False 399.00 399 81.0710 3 508 1 chr7D.!!$F1 505
13 TraesCS2A01G139200 chr1D 14708558 14709076 518 False 357.00 357 79.3560 2799 3319 1 chr1D.!!$F1 520
14 TraesCS2A01G139200 chr1D 347781956 347782562 606 True 311.00 311 76.4230 23 621 1 chr1D.!!$R1 598
15 TraesCS2A01G139200 chr5D 77861862 77862463 601 True 294.00 294 76.2300 40 626 1 chr5D.!!$R1 586
16 TraesCS2A01G139200 chr4D 94872266 94872776 510 True 268.00 268 76.9380 17 509 1 chr4D.!!$R1 492

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
873 3550 0.104855 TTGGATTGCTATCTCGCGCT 59.895 50.0 5.56 0.0 0.00 5.92 F
874 3551 0.598419 TGGATTGCTATCTCGCGCTG 60.598 55.0 5.56 0.0 0.00 5.18 F
1419 4182 0.864377 TCGAAGTTCGATTAGGCGCG 60.864 55.0 23.54 0.0 44.82 6.86 F
2855 9175 0.322366 TGGACATGGCGAAGAATGCA 60.322 50.0 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 8665 1.536496 GCTGCATGCACTCAACAAACA 60.536 47.619 18.46 0.00 42.31 2.83 R
2762 9063 4.154195 ACAATGAAATAACAGGTCGTGCTC 59.846 41.667 0.00 0.00 0.00 4.26 R
3356 9847 0.323178 ACCCGTCTAGACACATCCGT 60.323 55.000 22.37 5.81 0.00 4.69 R
3790 10324 0.323269 TCCACGTCCCGGTATGTACA 60.323 55.000 0.00 0.00 0.00 2.90 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
94 2711 1.952367 GCACTTGCTGCCATAAGGTCT 60.952 52.381 0.00 0.00 40.42 3.85
98 2715 2.877097 TGCTGCCATAAGGTCTTTCA 57.123 45.000 0.00 0.00 37.19 2.69
196 2824 1.597663 CCGCCATCCTTAAATCGACAC 59.402 52.381 0.00 0.00 0.00 3.67
298 2931 2.631545 GCGGAGTGTACCTGGGTATAAT 59.368 50.000 2.63 0.00 32.82 1.28
373 3006 2.288152 GGTTGCGAATGTCCAACAATGT 60.288 45.455 5.95 0.00 42.26 2.71
559 3207 1.946768 CTTTGTCTCCACTTTGCGGAA 59.053 47.619 0.00 0.00 30.33 4.30
586 3234 3.842923 CCAGACCGCCGAGCAGAT 61.843 66.667 0.00 0.00 0.00 2.90
656 3305 2.177580 CGTATGCGGGCGGTTTGAT 61.178 57.895 0.00 0.00 0.00 2.57
661 3310 2.359354 CGGGCGGTTTGATGGTCA 60.359 61.111 0.00 0.00 0.00 4.02
663 3312 2.700773 GGGCGGTTTGATGGTCAGC 61.701 63.158 0.00 0.00 0.00 4.26
688 3364 8.395633 GCGTTGCTAGGAAGAATTTATTTTCTA 58.604 33.333 0.00 0.00 34.89 2.10
718 3395 3.734463 TGTTGGAAGCAATCACGACTTA 58.266 40.909 0.00 0.00 0.00 2.24
860 3537 6.355747 TGGAAAGCAGTTTTCAATTTGGATT 58.644 32.000 11.44 0.00 45.70 3.01
868 3545 7.009907 GCAGTTTTCAATTTGGATTGCTATCTC 59.990 37.037 8.06 0.00 41.94 2.75
869 3546 7.219535 CAGTTTTCAATTTGGATTGCTATCTCG 59.780 37.037 8.06 0.00 41.94 4.04
870 3547 4.818534 TCAATTTGGATTGCTATCTCGC 57.181 40.909 8.06 0.00 41.94 5.03
871 3548 3.248363 TCAATTTGGATTGCTATCTCGCG 59.752 43.478 0.00 0.00 41.94 5.87
872 3549 0.937304 TTTGGATTGCTATCTCGCGC 59.063 50.000 0.00 0.00 0.00 6.86
873 3550 0.104855 TTGGATTGCTATCTCGCGCT 59.895 50.000 5.56 0.00 0.00 5.92
874 3551 0.598419 TGGATTGCTATCTCGCGCTG 60.598 55.000 5.56 0.00 0.00 5.18
877 3562 4.592192 TGCTATCTCGCGCTGGCC 62.592 66.667 5.56 0.00 35.02 5.36
904 3648 4.880537 CCGCTCACCCGCTGCTAG 62.881 72.222 0.00 0.00 0.00 3.42
907 3651 3.465403 CTCACCCGCTGCTAGCCT 61.465 66.667 13.29 0.00 38.18 4.58
908 3652 3.729965 CTCACCCGCTGCTAGCCTG 62.730 68.421 13.29 6.36 38.18 4.85
911 3655 3.540751 CCCGCTGCTAGCCTGCTA 61.541 66.667 21.86 0.00 38.18 3.49
981 3725 4.214327 GCCGAGCTCTTCTCCCCG 62.214 72.222 12.85 0.00 38.62 5.73
1012 3756 2.264480 CCGACATGTCCTCGGCAA 59.736 61.111 20.03 0.00 44.04 4.52
1371 4130 4.827692 TCGATAATTTGCTACCACACACT 58.172 39.130 0.00 0.00 0.00 3.55
1373 4132 4.870426 CGATAATTTGCTACCACACACTCT 59.130 41.667 0.00 0.00 0.00 3.24
1418 4181 2.953669 TCGAAGTTCGATTAGGCGC 58.046 52.632 23.54 0.00 44.82 6.53
1419 4182 0.864377 TCGAAGTTCGATTAGGCGCG 60.864 55.000 23.54 0.00 44.82 6.86
1433 4200 6.681178 CGATTAGGCGCGTATTAATTAATTGG 59.319 38.462 15.64 9.32 0.00 3.16
1437 4204 4.214758 GGCGCGTATTAATTAATTGGACCT 59.785 41.667 15.64 0.00 0.00 3.85
1469 4236 4.385146 GCTGTGTGATCGATGATACATCTG 59.615 45.833 14.21 5.24 0.00 2.90
1700 7591 5.508200 AAAAACAATTCAGGCGACTTACA 57.492 34.783 0.00 0.00 40.21 2.41
1762 7686 1.466856 ACATTGTCGCATTGCATCCT 58.533 45.000 9.69 0.00 0.00 3.24
1763 7687 1.402968 ACATTGTCGCATTGCATCCTC 59.597 47.619 9.69 0.00 0.00 3.71
1764 7688 1.402613 CATTGTCGCATTGCATCCTCA 59.597 47.619 9.69 0.00 0.00 3.86
1765 7689 1.753930 TTGTCGCATTGCATCCTCAT 58.246 45.000 9.69 0.00 0.00 2.90
1782 7706 7.285401 GCATCCTCATTAACTCCTAAAATCCAA 59.715 37.037 0.00 0.00 0.00 3.53
1786 7712 8.802267 CCTCATTAACTCCTAAAATCCAACAAA 58.198 33.333 0.00 0.00 0.00 2.83
1787 7713 9.846248 CTCATTAACTCCTAAAATCCAACAAAG 57.154 33.333 0.00 0.00 0.00 2.77
1788 7714 9.362151 TCATTAACTCCTAAAATCCAACAAAGT 57.638 29.630 0.00 0.00 0.00 2.66
1835 8027 4.405680 TGATCATTTCAGACCGGTATGAGT 59.594 41.667 29.04 19.99 31.96 3.41
2187 8379 4.980805 TGGTGAACGTGCTCGGCC 62.981 66.667 13.32 9.27 41.85 6.13
2386 8580 6.533730 TGGTTTGGTCAGTCCATATATGATC 58.466 40.000 14.54 6.64 46.60 2.92
2762 9063 6.536582 TCTCAAGTTCTTTCTTTGTCTCTGTG 59.463 38.462 0.00 0.00 0.00 3.66
2797 9117 7.914465 TGTTATTTCATTGTTTGCACCTTTTC 58.086 30.769 0.00 0.00 0.00 2.29
2855 9175 0.322366 TGGACATGGCGAAGAATGCA 60.322 50.000 0.00 0.00 0.00 3.96
3326 9817 3.995048 GCTCAACTTCTACACCAAGGTAC 59.005 47.826 0.00 0.00 0.00 3.34
3343 9834 5.584551 AGGTACTTCCTTTGTCCAGAATT 57.415 39.130 0.00 0.00 45.67 2.17
3346 9837 6.272558 AGGTACTTCCTTTGTCCAGAATTAGT 59.727 38.462 0.00 0.00 45.67 2.24
3348 9839 6.884280 ACTTCCTTTGTCCAGAATTAGTTG 57.116 37.500 0.00 0.00 0.00 3.16
3351 9842 5.313712 TCCTTTGTCCAGAATTAGTTGTCC 58.686 41.667 0.00 0.00 0.00 4.02
3352 9843 5.073144 TCCTTTGTCCAGAATTAGTTGTCCT 59.927 40.000 0.00 0.00 0.00 3.85
3354 9845 5.560722 TTGTCCAGAATTAGTTGTCCTCA 57.439 39.130 0.00 0.00 0.00 3.86
3355 9846 5.560722 TGTCCAGAATTAGTTGTCCTCAA 57.439 39.130 0.00 0.00 0.00 3.02
3356 9847 5.935945 TGTCCAGAATTAGTTGTCCTCAAA 58.064 37.500 0.00 0.00 35.20 2.69
3357 9848 5.763204 TGTCCAGAATTAGTTGTCCTCAAAC 59.237 40.000 0.00 0.00 35.20 2.93
3358 9849 4.994852 TCCAGAATTAGTTGTCCTCAAACG 59.005 41.667 0.00 0.00 35.20 3.60
3359 9850 4.154195 CCAGAATTAGTTGTCCTCAAACGG 59.846 45.833 0.00 0.00 35.20 4.44
3362 9853 5.643777 AGAATTAGTTGTCCTCAAACGGATG 59.356 40.000 0.00 0.00 35.11 3.51
3363 9854 2.930826 AGTTGTCCTCAAACGGATGT 57.069 45.000 0.00 0.00 35.11 3.06
3364 9855 2.494059 AGTTGTCCTCAAACGGATGTG 58.506 47.619 0.00 0.00 35.11 3.21
3365 9856 2.158813 AGTTGTCCTCAAACGGATGTGT 60.159 45.455 0.00 0.00 35.11 3.72
3366 9857 2.163818 TGTCCTCAAACGGATGTGTC 57.836 50.000 0.00 0.00 35.11 3.67
3367 9858 1.691976 TGTCCTCAAACGGATGTGTCT 59.308 47.619 0.00 0.00 35.11 3.41
3368 9859 2.894765 TGTCCTCAAACGGATGTGTCTA 59.105 45.455 0.00 0.00 35.11 2.59
3369 9860 3.056821 TGTCCTCAAACGGATGTGTCTAG 60.057 47.826 0.00 0.00 35.11 2.43
3370 9861 3.192844 GTCCTCAAACGGATGTGTCTAGA 59.807 47.826 0.00 0.00 35.11 2.43
3371 9862 3.192844 TCCTCAAACGGATGTGTCTAGAC 59.807 47.826 16.32 16.32 0.00 2.59
3372 9863 3.172050 CTCAAACGGATGTGTCTAGACG 58.828 50.000 17.85 7.46 0.00 4.18
3373 9864 2.094906 TCAAACGGATGTGTCTAGACGG 60.095 50.000 17.85 5.55 0.00 4.79
3374 9865 0.815734 AACGGATGTGTCTAGACGGG 59.184 55.000 17.85 5.88 0.00 5.28
3375 9866 0.323178 ACGGATGTGTCTAGACGGGT 60.323 55.000 17.85 5.95 0.00 5.28
3376 9867 1.065199 ACGGATGTGTCTAGACGGGTA 60.065 52.381 17.85 4.71 0.00 3.69
3377 9868 2.019249 CGGATGTGTCTAGACGGGTAA 58.981 52.381 17.85 2.21 0.00 2.85
3378 9869 2.424601 CGGATGTGTCTAGACGGGTAAA 59.575 50.000 17.85 0.00 0.00 2.01
3379 9870 3.067742 CGGATGTGTCTAGACGGGTAAAT 59.932 47.826 17.85 0.92 0.00 1.40
3380 9871 4.441079 CGGATGTGTCTAGACGGGTAAATT 60.441 45.833 17.85 0.00 0.00 1.82
3381 9872 4.809426 GGATGTGTCTAGACGGGTAAATTG 59.191 45.833 17.85 0.00 0.00 2.32
3382 9873 5.394883 GGATGTGTCTAGACGGGTAAATTGA 60.395 44.000 17.85 0.00 0.00 2.57
3393 9885 3.086282 GGGTAAATTGACGGAATGTGGT 58.914 45.455 0.00 0.00 0.00 4.16
3517 10021 2.233271 CTGACTTGCCAAACCATCACT 58.767 47.619 0.00 0.00 0.00 3.41
3611 10116 8.244113 ACTATGTCGCTTGATCGATAATATTGA 58.756 33.333 0.00 0.00 40.84 2.57
3625 10130 3.912496 ATATTGAGTGTGGCTAGCACA 57.088 42.857 18.24 15.55 39.17 4.57
3790 10324 5.459982 ACCAGAGAGTATACAGGAGAAGT 57.540 43.478 5.50 0.00 0.00 3.01
3791 10325 5.197451 ACCAGAGAGTATACAGGAGAAGTG 58.803 45.833 5.50 0.00 0.00 3.16
3850 10409 4.557296 CGCACCCATGGATGTTCATATTTC 60.557 45.833 15.22 0.00 0.00 2.17
3856 10415 5.599656 CCATGGATGTTCATATTTCCAAGGT 59.400 40.000 5.56 0.00 40.55 3.50
3859 10418 4.881850 GGATGTTCATATTTCCAAGGTCGT 59.118 41.667 0.00 0.00 0.00 4.34
3870 10429 3.517602 TCCAAGGTCGTGAAATATGTCG 58.482 45.455 0.00 0.00 0.00 4.35
3906 10471 2.092212 CCTTGCCAATACCAGGACATCT 60.092 50.000 0.00 0.00 0.00 2.90
3913 10478 3.498774 ATACCAGGACATCTTCATGCC 57.501 47.619 0.00 0.00 34.49 4.40
3999 10564 1.203287 TCGAGAGTGAGGTGCATTCAG 59.797 52.381 4.32 0.00 35.83 3.02
4007 10572 2.543578 GGTGCATTCAGCTCAACGA 58.456 52.632 0.00 0.00 45.94 3.85
4036 10601 6.567687 TTCTCCGTTTTTCAATGCATCTAA 57.432 33.333 0.00 0.00 0.00 2.10
4038 10603 7.857734 TCTCCGTTTTTCAATGCATCTAATA 57.142 32.000 0.00 0.00 0.00 0.98
4040 10605 9.554395 TCTCCGTTTTTCAATGCATCTAATATA 57.446 29.630 0.00 0.00 0.00 0.86
4041 10606 9.817365 CTCCGTTTTTCAATGCATCTAATATAG 57.183 33.333 0.00 0.00 0.00 1.31
4042 10607 9.337396 TCCGTTTTTCAATGCATCTAATATAGT 57.663 29.630 0.00 0.00 0.00 2.12
4043 10608 9.385902 CCGTTTTTCAATGCATCTAATATAGTG 57.614 33.333 0.00 0.00 0.00 2.74
4046 10611 9.734620 TTTTTCAATGCATCTAATATAGTGCAC 57.265 29.630 9.40 9.40 41.75 4.57
4049 10614 7.219322 TCAATGCATCTAATATAGTGCACACT 58.781 34.615 21.04 8.57 41.75 3.55
4051 10616 8.992073 CAATGCATCTAATATAGTGCACACTAA 58.008 33.333 21.04 1.29 45.87 2.24
4052 10617 9.730705 AATGCATCTAATATAGTGCACACTAAT 57.269 29.630 21.04 9.23 45.87 1.73
4065 10646 7.711846 AGTGCACACTAATTCATGTTTTTACA 58.288 30.769 21.04 0.00 40.43 2.41
4123 10705 3.199071 TCCCATGGTCGCTAACAAATAGT 59.801 43.478 11.73 0.00 33.87 2.12
4124 10706 4.406326 TCCCATGGTCGCTAACAAATAGTA 59.594 41.667 11.73 0.00 33.87 1.82
4125 10707 4.750098 CCCATGGTCGCTAACAAATAGTAG 59.250 45.833 11.73 0.00 33.87 2.57
4126 10708 4.211374 CCATGGTCGCTAACAAATAGTAGC 59.789 45.833 2.57 0.00 33.87 3.58
4127 10709 4.730949 TGGTCGCTAACAAATAGTAGCT 57.269 40.909 0.00 0.00 33.87 3.32
4141 10724 8.554011 ACAAATAGTAGCTTATGGGTTCCTTAA 58.446 33.333 0.00 0.00 0.00 1.85
4150 10733 1.967779 TGGGTTCCTTAAAAAGCAGGC 59.032 47.619 0.00 0.00 0.00 4.85
4174 10757 7.174253 GGCACGAATTAAACCCATAGATAATCA 59.826 37.037 0.00 0.00 0.00 2.57
4211 10794 7.417116 CCAATTGCCTCATTATTTAGTCAAGCT 60.417 37.037 0.00 0.00 0.00 3.74
4300 10906 1.035139 ATTGCTTTCGATGATGGCCC 58.965 50.000 0.00 0.00 0.00 5.80
4323 10929 5.295292 CCATAATACTTCAGAGCCACAACAG 59.705 44.000 0.00 0.00 0.00 3.16
4325 10931 0.536006 ACTTCAGAGCCACAACAGCC 60.536 55.000 0.00 0.00 0.00 4.85
4338 10944 1.455383 AACAGCCGAACAAGCAAGGG 61.455 55.000 0.00 0.00 0.00 3.95
4346 10952 0.899720 AACAAGCAAGGGCATGATGG 59.100 50.000 0.00 0.00 41.08 3.51
4482 11089 3.173953 AGAAGTCATTGGCCATGGAAA 57.826 42.857 18.40 9.53 33.07 3.13
4496 11103 7.499292 TGGCCATGGAAAATGTTTCTAATATG 58.501 34.615 18.40 0.00 0.00 1.78
4516 11123 7.767745 ATATGATGTCTATATTGCGCTTGAG 57.232 36.000 9.73 0.00 0.00 3.02
4542 11149 7.340699 GCAACTCAACGATGTCTATGAATTAG 58.659 38.462 0.00 0.00 0.00 1.73
4550 11157 9.823647 AACGATGTCTATGAATTAGATTTCTGT 57.176 29.630 0.00 0.00 39.14 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 2628 4.163839 TGACATACACATCATCCATGACCA 59.836 41.667 0.00 0.00 40.03 4.02
43 2658 5.341993 CGTTTCATGCACGAAAATACATTGT 59.658 36.000 9.87 0.00 40.20 2.71
94 2711 2.773661 TCATAGGCAGGAGCAGATGAAA 59.226 45.455 0.00 0.00 44.61 2.69
98 2715 3.244840 GGATTTCATAGGCAGGAGCAGAT 60.245 47.826 0.00 0.00 44.61 2.90
196 2824 3.196007 TGAGCTTATTTTCAAACGCCG 57.804 42.857 0.00 0.00 0.00 6.46
373 3006 3.283684 CTTCGGCCGCCACACAAA 61.284 61.111 23.51 6.64 0.00 2.83
432 3071 1.381327 CTCCGCCACTTCTCCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
476 3117 1.561542 CACCTCAGGCCCACTAAATCT 59.438 52.381 0.00 0.00 0.00 2.40
559 3207 4.421479 CGGTCTGGACGCGCTCTT 62.421 66.667 5.73 0.00 0.00 2.85
583 3231 4.160439 TCCAAAGCAGTCTTGTATCGATCT 59.840 41.667 0.00 0.00 31.78 2.75
586 3234 3.953712 TCCAAAGCAGTCTTGTATCGA 57.046 42.857 0.00 0.00 31.78 3.59
627 3275 1.359117 CGCATACGTCTGGATCCGT 59.641 57.895 7.39 3.52 40.87 4.69
656 3305 0.037326 CTTCCTAGCAACGCTGACCA 60.037 55.000 0.00 0.00 40.10 4.02
661 3310 6.759497 AAATAAATTCTTCCTAGCAACGCT 57.241 33.333 0.00 0.00 43.41 5.07
688 3364 6.365789 CGTGATTGCTTCCAACAAACAAATAT 59.634 34.615 0.00 0.00 32.54 1.28
860 3537 4.592192 GGCCAGCGCGAGATAGCA 62.592 66.667 12.10 0.00 36.85 3.49
909 3653 1.614413 GGACTGGAGATTAGCGGGTAG 59.386 57.143 0.00 0.00 0.00 3.18
910 3654 1.063492 TGGACTGGAGATTAGCGGGTA 60.063 52.381 0.00 0.00 0.00 3.69
911 3655 0.325296 TGGACTGGAGATTAGCGGGT 60.325 55.000 0.00 0.00 0.00 5.28
1350 4109 4.870426 AGAGTGTGTGGTAGCAAATTATCG 59.130 41.667 0.00 0.00 0.00 2.92
1364 4123 3.381272 ACCCAACAAATCAAGAGTGTGTG 59.619 43.478 0.00 0.00 0.00 3.82
1365 4124 3.631250 ACCCAACAAATCAAGAGTGTGT 58.369 40.909 0.00 0.00 0.00 3.72
1371 4130 6.553100 ACCAAGATTAACCCAACAAATCAAGA 59.447 34.615 0.00 0.00 33.06 3.02
1373 4132 6.739331 ACCAAGATTAACCCAACAAATCAA 57.261 33.333 0.00 0.00 33.06 2.57
1415 4178 5.178809 AGAGGTCCAATTAATTAATACGCGC 59.821 40.000 5.73 0.00 0.00 6.86
1416 4179 6.780706 AGAGGTCCAATTAATTAATACGCG 57.219 37.500 11.07 3.53 0.00 6.01
1417 4180 8.149973 TGAAGAGGTCCAATTAATTAATACGC 57.850 34.615 11.07 3.08 0.00 4.42
1418 4181 9.542462 TCTGAAGAGGTCCAATTAATTAATACG 57.458 33.333 11.07 5.96 0.00 3.06
1433 4200 0.315568 ACACAGCGTCTGAAGAGGTC 59.684 55.000 12.77 0.00 35.18 3.85
1437 4204 1.401539 CGATCACACAGCGTCTGAAGA 60.402 52.381 12.77 7.96 35.18 2.87
1557 4814 0.244721 GCTTTTGAAATCGGCTGGCT 59.755 50.000 0.00 0.00 0.00 4.75
1659 7542 6.978080 TGTTTTTAATGCAAGTCACCTTCTTC 59.022 34.615 0.00 0.00 0.00 2.87
1683 7573 6.313905 AGTCTATTTGTAAGTCGCCTGAATTG 59.686 38.462 0.00 0.00 33.81 2.32
1700 7591 6.636454 TGGACTTATTGGGACAGTCTATTT 57.364 37.500 0.00 0.00 42.39 1.40
1762 7686 9.362151 ACTTTGTTGGATTTTAGGAGTTAATGA 57.638 29.630 0.00 0.00 0.00 2.57
1765 7689 9.856162 ACTACTTTGTTGGATTTTAGGAGTTAA 57.144 29.630 0.00 0.00 0.00 2.01
1782 7706 6.935741 TTTGCATGTGAGTTACTACTTTGT 57.064 33.333 0.00 0.00 33.84 2.83
1815 8007 3.118775 CCACTCATACCGGTCTGAAATGA 60.119 47.826 24.49 20.17 0.00 2.57
1867 8059 2.970868 GGTATAGTTGGGCGCCGC 60.971 66.667 22.54 14.37 0.00 6.53
2386 8580 7.375808 GCGTGGTTGACAATAATATTGTGTATG 59.624 37.037 21.80 10.09 31.96 2.39
2449 8665 1.536496 GCTGCATGCACTCAACAAACA 60.536 47.619 18.46 0.00 42.31 2.83
2721 8986 5.292765 ACTTGAGATCATGCATACCTTACG 58.707 41.667 0.00 0.00 0.00 3.18
2732 8997 8.097078 AGACAAAGAAAGAACTTGAGATCATG 57.903 34.615 0.00 0.00 0.00 3.07
2762 9063 4.154195 ACAATGAAATAACAGGTCGTGCTC 59.846 41.667 0.00 0.00 0.00 4.26
2949 9269 2.835431 CCCGATCACCTCGCTCCT 60.835 66.667 0.00 0.00 46.25 3.69
2963 9283 3.564027 GCCGCGAATTCTGACCCG 61.564 66.667 8.23 0.00 0.00 5.28
2965 9285 1.776034 GATGGCCGCGAATTCTGACC 61.776 60.000 8.23 0.00 0.00 4.02
2967 9287 1.089481 GTGATGGCCGCGAATTCTGA 61.089 55.000 8.23 0.00 0.00 3.27
3326 9817 6.072452 GGACAACTAATTCTGGACAAAGGAAG 60.072 42.308 0.00 0.00 0.00 3.46
3329 9820 5.316987 AGGACAACTAATTCTGGACAAAGG 58.683 41.667 0.00 0.00 0.00 3.11
3330 9821 5.997746 TGAGGACAACTAATTCTGGACAAAG 59.002 40.000 0.00 0.00 0.00 2.77
3333 9824 5.560722 TTGAGGACAACTAATTCTGGACA 57.439 39.130 0.00 0.00 0.00 4.02
3334 9825 5.107065 CGTTTGAGGACAACTAATTCTGGAC 60.107 44.000 0.00 0.00 35.63 4.02
3335 9826 4.994852 CGTTTGAGGACAACTAATTCTGGA 59.005 41.667 0.00 0.00 35.63 3.86
3337 9828 4.994852 TCCGTTTGAGGACAACTAATTCTG 59.005 41.667 0.00 0.00 34.92 3.02
3339 9830 5.411669 ACATCCGTTTGAGGACAACTAATTC 59.588 40.000 0.00 0.00 44.07 2.17
3340 9831 5.181245 CACATCCGTTTGAGGACAACTAATT 59.819 40.000 0.00 0.00 44.07 1.40
3342 9833 4.062293 CACATCCGTTTGAGGACAACTAA 58.938 43.478 0.00 0.00 44.07 2.24
3343 9834 3.070446 ACACATCCGTTTGAGGACAACTA 59.930 43.478 0.00 0.00 44.07 2.24
3346 9837 2.104111 AGACACATCCGTTTGAGGACAA 59.896 45.455 0.00 0.00 44.07 3.18
3348 9839 2.457366 AGACACATCCGTTTGAGGAC 57.543 50.000 0.00 0.00 44.07 3.85
3351 9842 3.172050 CGTCTAGACACATCCGTTTGAG 58.828 50.000 22.37 0.00 0.00 3.02
3352 9843 2.094906 CCGTCTAGACACATCCGTTTGA 60.095 50.000 22.37 0.00 0.00 2.69
3354 9845 1.203994 CCCGTCTAGACACATCCGTTT 59.796 52.381 22.37 0.00 0.00 3.60
3355 9846 0.815734 CCCGTCTAGACACATCCGTT 59.184 55.000 22.37 0.00 0.00 4.44
3356 9847 0.323178 ACCCGTCTAGACACATCCGT 60.323 55.000 22.37 5.81 0.00 4.69
3357 9848 1.671979 TACCCGTCTAGACACATCCG 58.328 55.000 22.37 7.40 0.00 4.18
3358 9849 4.667519 ATTTACCCGTCTAGACACATCC 57.332 45.455 22.37 0.00 0.00 3.51
3359 9850 5.519206 GTCAATTTACCCGTCTAGACACATC 59.481 44.000 22.37 0.00 0.00 3.06
3362 9853 3.855950 CGTCAATTTACCCGTCTAGACAC 59.144 47.826 22.37 7.95 0.00 3.67
3363 9854 3.119388 CCGTCAATTTACCCGTCTAGACA 60.119 47.826 22.37 2.19 0.00 3.41
3364 9855 3.129287 TCCGTCAATTTACCCGTCTAGAC 59.871 47.826 13.18 13.18 0.00 2.59
3365 9856 3.355378 TCCGTCAATTTACCCGTCTAGA 58.645 45.455 0.00 0.00 0.00 2.43
3366 9857 3.788333 TCCGTCAATTTACCCGTCTAG 57.212 47.619 0.00 0.00 0.00 2.43
3367 9858 4.081531 ACATTCCGTCAATTTACCCGTCTA 60.082 41.667 0.00 0.00 0.00 2.59
3368 9859 3.267483 CATTCCGTCAATTTACCCGTCT 58.733 45.455 0.00 0.00 0.00 4.18
3369 9860 3.004862 ACATTCCGTCAATTTACCCGTC 58.995 45.455 0.00 0.00 0.00 4.79
3370 9861 2.745281 CACATTCCGTCAATTTACCCGT 59.255 45.455 0.00 0.00 0.00 5.28
3371 9862 2.096819 CCACATTCCGTCAATTTACCCG 59.903 50.000 0.00 0.00 0.00 5.28
3372 9863 3.086282 ACCACATTCCGTCAATTTACCC 58.914 45.455 0.00 0.00 0.00 3.69
3373 9864 6.293244 GCTATACCACATTCCGTCAATTTACC 60.293 42.308 0.00 0.00 0.00 2.85
3374 9865 6.259167 TGCTATACCACATTCCGTCAATTTAC 59.741 38.462 0.00 0.00 0.00 2.01
3375 9866 6.350103 TGCTATACCACATTCCGTCAATTTA 58.650 36.000 0.00 0.00 0.00 1.40
3376 9867 5.189928 TGCTATACCACATTCCGTCAATTT 58.810 37.500 0.00 0.00 0.00 1.82
3377 9868 4.776349 TGCTATACCACATTCCGTCAATT 58.224 39.130 0.00 0.00 0.00 2.32
3378 9869 4.415881 TGCTATACCACATTCCGTCAAT 57.584 40.909 0.00 0.00 0.00 2.57
3379 9870 3.897141 TGCTATACCACATTCCGTCAA 57.103 42.857 0.00 0.00 0.00 3.18
3380 9871 3.792401 CTTGCTATACCACATTCCGTCA 58.208 45.455 0.00 0.00 0.00 4.35
3381 9872 2.544267 GCTTGCTATACCACATTCCGTC 59.456 50.000 0.00 0.00 0.00 4.79
3382 9873 2.093181 TGCTTGCTATACCACATTCCGT 60.093 45.455 0.00 0.00 0.00 4.69
3625 10130 4.020039 TCTCACAAAACCCCGTACATACAT 60.020 41.667 0.00 0.00 0.00 2.29
3790 10324 0.323269 TCCACGTCCCGGTATGTACA 60.323 55.000 0.00 0.00 0.00 2.90
3791 10325 1.035139 ATCCACGTCCCGGTATGTAC 58.965 55.000 0.00 0.00 0.00 2.90
3850 10409 3.062099 CACGACATATTTCACGACCTTGG 59.938 47.826 0.00 0.00 0.00 3.61
3856 10415 2.267426 CCAGCACGACATATTTCACGA 58.733 47.619 0.00 0.00 0.00 4.35
3859 10418 2.009051 CAGCCAGCACGACATATTTCA 58.991 47.619 0.00 0.00 0.00 2.69
3906 10471 6.710278 TGATATTCTCATTATCCGGCATGAA 58.290 36.000 0.00 0.00 0.00 2.57
3913 10478 9.138062 CTTCAGAGTTGATATTCTCATTATCCG 57.862 37.037 0.00 0.00 32.72 4.18
4013 10578 6.567687 TTAGATGCATTGAAAAACGGAGAA 57.432 33.333 0.00 0.00 0.00 2.87
4018 10583 8.895845 GCACTATATTAGATGCATTGAAAAACG 58.104 33.333 0.00 0.00 34.87 3.60
4038 10603 9.840427 GTAAAAACATGAATTAGTGTGCACTAT 57.160 29.630 19.41 9.00 42.83 2.12
4040 10605 7.711846 TGTAAAAACATGAATTAGTGTGCACT 58.288 30.769 19.41 9.90 45.02 4.40
4041 10606 7.358352 GCTGTAAAAACATGAATTAGTGTGCAC 60.358 37.037 10.75 10.75 0.00 4.57
4042 10607 6.640499 GCTGTAAAAACATGAATTAGTGTGCA 59.360 34.615 0.00 0.00 0.00 4.57
4043 10608 6.089417 GGCTGTAAAAACATGAATTAGTGTGC 59.911 38.462 0.00 0.00 0.00 4.57
4046 10611 7.592938 TCAGGCTGTAAAAACATGAATTAGTG 58.407 34.615 15.27 0.00 0.00 2.74
4051 10616 9.023962 TCTTATTCAGGCTGTAAAAACATGAAT 57.976 29.630 15.27 5.54 38.86 2.57
4052 10617 8.402798 TCTTATTCAGGCTGTAAAAACATGAA 57.597 30.769 15.27 0.00 0.00 2.57
4065 10646 2.046292 GCCTCCTCTCTTATTCAGGCT 58.954 52.381 0.34 0.00 42.74 4.58
4123 10705 6.249951 TGCTTTTTAAGGAACCCATAAGCTA 58.750 36.000 0.00 0.00 38.02 3.32
4124 10706 5.083821 TGCTTTTTAAGGAACCCATAAGCT 58.916 37.500 0.00 0.00 38.02 3.74
4125 10707 5.400066 TGCTTTTTAAGGAACCCATAAGC 57.600 39.130 0.00 0.00 37.76 3.09
4126 10708 5.624509 GCCTGCTTTTTAAGGAACCCATAAG 60.625 44.000 0.00 0.00 0.00 1.73
4127 10709 4.221924 GCCTGCTTTTTAAGGAACCCATAA 59.778 41.667 0.00 0.00 0.00 1.90
4141 10724 3.554129 GGGTTTAATTCGTGCCTGCTTTT 60.554 43.478 0.00 0.00 0.00 2.27
4174 10757 5.176741 TGAGGCAATTGGGCATTAAAAAT 57.823 34.783 7.72 0.00 46.44 1.82
4300 10906 5.220739 GCTGTTGTGGCTCTGAAGTATTATG 60.221 44.000 0.00 0.00 0.00 1.90
4323 10929 2.639327 ATGCCCTTGCTTGTTCGGC 61.639 57.895 0.00 0.00 40.16 5.54
4325 10931 0.813184 ATCATGCCCTTGCTTGTTCG 59.187 50.000 0.00 0.00 41.89 3.95
4338 10944 7.438757 TCATTGTAAATGTTTATGCCATCATGC 59.561 33.333 0.26 0.00 34.22 4.06
4346 10952 6.473455 GCAGACCTCATTGTAAATGTTTATGC 59.527 38.462 0.26 2.39 0.00 3.14
4496 11103 3.124297 GCCTCAAGCGCAATATAGACATC 59.876 47.826 11.47 0.00 0.00 3.06
4516 11123 3.521560 TCATAGACATCGTTGAGTTGCC 58.478 45.455 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.