Multiple sequence alignment - TraesCS4D01G236900

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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 TraesCS4D01G236900 chr4D 100.000 6172 0 0 1 6172 398913698 398907527 0.000000e+00 11398.0
1 TraesCS4D01G236900 chr4A 90.058 4496 253 94 442 4794 56271692 56267248 0.000000e+00 5648.0
2 TraesCS4D01G236900 chr4A 89.265 1183 73 22 4848 5991 56267262 56266095 0.000000e+00 1432.0
3 TraesCS4D01G236900 chr4A 92.800 375 27 0 1989 2363 557106830 557107204 1.510000e-150 544.0
4 TraesCS4D01G236900 chr4A 92.179 358 19 4 1 351 56272072 56271717 1.190000e-136 497.0
5 TraesCS4D01G236900 chr4A 92.058 277 22 0 2544 2820 557107332 557107608 2.090000e-104 390.0
6 TraesCS4D01G236900 chr4A 91.327 196 16 1 5977 6172 56265055 56264861 3.670000e-67 267.0
7 TraesCS4D01G236900 chr4A 91.667 60 4 1 4790 4848 695685609 695685668 1.430000e-11 82.4
8 TraesCS4D01G236900 chr4B 92.894 3462 138 47 1991 5382 491837118 491833695 0.000000e+00 4931.0
9 TraesCS4D01G236900 chr4B 90.670 1404 71 24 582 1947 491838501 491837120 0.000000e+00 1812.0
10 TraesCS4D01G236900 chr4B 92.200 500 25 8 93 584 491839067 491838574 0.000000e+00 695.0
11 TraesCS4D01G236900 chr4B 87.636 275 22 7 5380 5643 491833592 491833319 6.010000e-80 309.0
12 TraesCS4D01G236900 chr4B 84.483 174 15 5 5738 5908 491833324 491833160 1.780000e-35 161.0
13 TraesCS4D01G236900 chr4B 89.796 49 3 1 4802 4848 4581975 4581927 1.860000e-05 62.1
14 TraesCS4D01G236900 chr4B 87.273 55 5 2 4794 4848 344463471 344463523 1.860000e-05 62.1
15 TraesCS4D01G236900 chr3A 89.648 483 32 6 1991 2469 411272675 411272207 3.180000e-167 599.0
16 TraesCS4D01G236900 chr3A 93.067 375 26 0 1989 2363 193871996 193871622 3.250000e-152 549.0
17 TraesCS4D01G236900 chr3A 90.055 362 25 5 2544 2894 193871494 193871133 5.640000e-125 459.0
18 TraesCS4D01G236900 chr3A 87.143 350 14 9 2556 2894 411272186 411271857 9.770000e-98 368.0
19 TraesCS4D01G236900 chr3A 92.857 98 5 2 5648 5744 660903636 660903540 2.320000e-29 141.0
20 TraesCS4D01G236900 chr5A 93.333 375 25 0 1989 2363 510197888 510198262 6.990000e-154 555.0
21 TraesCS4D01G236900 chr5A 90.331 362 24 5 2544 2894 510198390 510198751 1.210000e-126 464.0
22 TraesCS4D01G236900 chr5A 90.000 100 8 2 5638 5736 75022597 75022695 1.810000e-25 128.0
23 TraesCS4D01G236900 chr5A 88.073 109 10 3 5638 5745 660186737 660186843 6.490000e-25 126.0
24 TraesCS4D01G236900 chr5B 87.759 482 37 10 1991 2469 397293479 397293017 1.510000e-150 544.0
25 TraesCS4D01G236900 chr5B 89.503 362 27 5 2544 2894 397292988 397292627 1.220000e-121 448.0
26 TraesCS4D01G236900 chr6D 90.404 396 23 4 1991 2386 79969687 79970067 1.990000e-139 507.0
27 TraesCS4D01G236900 chr6D 94.297 263 15 0 2553 2815 79970197 79970459 2.680000e-108 403.0
28 TraesCS4D01G236900 chr7B 86.364 440 44 10 1010 1447 640919619 640920044 3.370000e-127 466.0
29 TraesCS4D01G236900 chr7B 96.226 53 1 1 4797 4848 610089117 610089065 1.100000e-12 86.1
30 TraesCS4D01G236900 chr7B 97.872 47 1 0 4802 4848 609921837 609921791 1.430000e-11 82.4
31 TraesCS4D01G236900 chr7B 97.872 47 1 0 4802 4848 610171919 610171873 1.430000e-11 82.4
32 TraesCS4D01G236900 chr2A 85.465 344 38 7 873 1215 16531613 16531945 1.270000e-91 348.0
33 TraesCS4D01G236900 chr2D 91.919 99 7 1 5637 5734 22200874 22200972 3.000000e-28 137.0
34 TraesCS4D01G236900 chr7A 91.000 100 7 2 5638 5736 288053431 288053529 3.880000e-27 134.0
35 TraesCS4D01G236900 chr7A 90.722 97 7 2 5641 5736 395735115 395735020 1.810000e-25 128.0
36 TraesCS4D01G236900 chr1A 90.722 97 6 3 5638 5733 586291363 586291457 6.490000e-25 126.0
37 TraesCS4D01G236900 chr6A 85.000 120 14 4 5638 5754 101983085 101983203 1.090000e-22 119.0
38 TraesCS4D01G236900 chrUn 91.667 60 4 1 4790 4848 304131050 304131109 1.430000e-11 82.4
39 TraesCS4D01G236900 chr6B 97.872 47 1 0 4802 4848 715815519 715815473 1.430000e-11 82.4
40 TraesCS4D01G236900 chr7D 100.000 29 0 0 1946 1974 157101302 157101274 3.000000e-03 54.7


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 TraesCS4D01G236900 chr4D 398907527 398913698 6171 True 11398.0 11398 100.00000 1 6172 1 chr4D.!!$R1 6171
1 TraesCS4D01G236900 chr4A 56264861 56272072 7211 True 1961.0 5648 90.70725 1 6172 4 chr4A.!!$R1 6171
2 TraesCS4D01G236900 chr4A 557106830 557107608 778 False 467.0 544 92.42900 1989 2820 2 chr4A.!!$F2 831
3 TraesCS4D01G236900 chr4B 491833160 491839067 5907 True 1581.6 4931 89.57660 93 5908 5 chr4B.!!$R2 5815
4 TraesCS4D01G236900 chr3A 193871133 193871996 863 True 504.0 549 91.56100 1989 2894 2 chr3A.!!$R2 905
5 TraesCS4D01G236900 chr3A 411271857 411272675 818 True 483.5 599 88.39550 1991 2894 2 chr3A.!!$R3 903
6 TraesCS4D01G236900 chr5A 510197888 510198751 863 False 509.5 555 91.83200 1989 2894 2 chr5A.!!$F3 905
7 TraesCS4D01G236900 chr5B 397292627 397293479 852 True 496.0 544 88.63100 1991 2894 2 chr5B.!!$R1 903
8 TraesCS4D01G236900 chr6D 79969687 79970459 772 False 455.0 507 92.35050 1991 2815 2 chr6D.!!$F1 824

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
971 1100 0.908180 AGAAACCCCCGAGGAACGAT 60.908 55.0 0.0 0.0 45.77 3.73 F
2193 2380 0.911769 TCCATGCCCTCTCGTTCAAT 59.088 50.0 0.0 0.0 0.00 2.57 F
3805 4057 0.250124 CGTGGTTGCACCTCAGGTAA 60.250 55.0 0.0 0.0 39.58 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2561 0.173481 TATCGCTCACTGTGTGGAGC 59.827 55.000 7.79 8.64 35.24 4.70 R
4045 4312 1.545428 GCAACAGTCATTCCTCCACCA 60.545 52.381 0.00 0.00 0.00 4.17 R
5389 5828 0.250295 AGTTAGAACAGCAGGCGCAA 60.250 50.000 10.83 0.00 42.27 4.85 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
23 24 3.453070 GACCCGGAGCTGAGATGGC 62.453 68.421 0.73 0.00 0.00 4.40
24 25 4.598894 CCCGGAGCTGAGATGGCG 62.599 72.222 0.73 0.00 34.52 5.69
27 28 3.859414 GGAGCTGAGATGGCGCCT 61.859 66.667 29.70 13.55 44.29 5.52
28 29 2.588314 GAGCTGAGATGGCGCCTG 60.588 66.667 29.70 11.43 34.52 4.85
29 30 4.853050 AGCTGAGATGGCGCCTGC 62.853 66.667 29.70 19.28 41.71 4.85
322 331 1.260561 GTGCACGTTTCACTCGTCAAT 59.739 47.619 0.00 0.00 39.55 2.57
385 394 2.225293 ACTGGGTGCTACTCCTACTCAA 60.225 50.000 0.00 0.00 0.00 3.02
391 400 2.565834 TGCTACTCCTACTCAACAACCC 59.434 50.000 0.00 0.00 0.00 4.11
401 410 0.948623 TCAACAACCCACATCGAGCG 60.949 55.000 0.00 0.00 0.00 5.03
412 421 1.133407 ACATCGAGCGTCTTCTTCCTC 59.867 52.381 0.00 0.00 0.00 3.71
429 439 5.711976 TCTTCCTCCTTAAAATGCTTGGAAG 59.288 40.000 11.00 11.00 46.15 3.46
430 440 4.998051 TCCTCCTTAAAATGCTTGGAAGT 58.002 39.130 0.00 0.00 0.00 3.01
431 441 6.134535 TCCTCCTTAAAATGCTTGGAAGTA 57.865 37.500 0.00 0.00 0.00 2.24
432 442 6.180472 TCCTCCTTAAAATGCTTGGAAGTAG 58.820 40.000 0.00 0.00 0.00 2.57
433 443 5.946377 CCTCCTTAAAATGCTTGGAAGTAGT 59.054 40.000 0.00 0.00 0.00 2.73
434 444 6.127897 CCTCCTTAAAATGCTTGGAAGTAGTG 60.128 42.308 0.00 0.00 0.00 2.74
435 445 6.303839 TCCTTAAAATGCTTGGAAGTAGTGT 58.696 36.000 0.00 0.00 0.00 3.55
436 446 7.455058 TCCTTAAAATGCTTGGAAGTAGTGTA 58.545 34.615 0.00 0.00 0.00 2.90
437 447 7.389607 TCCTTAAAATGCTTGGAAGTAGTGTAC 59.610 37.037 0.00 0.00 0.00 2.90
448 458 5.767665 TGGAAGTAGTGTACGTACCTACAAA 59.232 40.000 32.58 21.55 34.88 2.83
484 494 7.894708 TCAAAATTTGAGAGATGCATGGTTTA 58.105 30.769 2.46 0.00 34.08 2.01
486 496 9.806203 CAAAATTTGAGAGATGCATGGTTTATA 57.194 29.630 2.46 0.00 0.00 0.98
552 567 1.952102 ATGATACGGACCGTGGCGTT 61.952 55.000 29.55 8.73 41.39 4.84
573 588 5.502706 CGTTGTTTTCGTCCTCATGTGTTAA 60.503 40.000 0.00 0.00 0.00 2.01
693 787 6.015504 CGAACATATTCCAAGAGAAAACACG 58.984 40.000 0.00 0.00 38.21 4.49
936 1060 1.306642 ACACGCAAACCCAACGAACA 61.307 50.000 0.00 0.00 0.00 3.18
940 1064 1.652930 CAAACCCAACGAACACGCG 60.653 57.895 3.53 3.53 37.29 6.01
971 1100 0.908180 AGAAACCCCCGAGGAACGAT 60.908 55.000 0.00 0.00 45.77 3.73
1312 1444 1.916273 TTCCGCTGGTTAGGCAGGA 60.916 57.895 0.00 0.00 33.34 3.86
1382 1517 5.390567 GCAAGAACGAAGACCGAATTTGTAT 60.391 40.000 0.00 0.00 41.76 2.29
1395 1533 6.072119 ACCGAATTTGTATTCAAAGGAGAACC 60.072 38.462 8.09 0.00 45.01 3.62
1475 1615 7.687005 CGAAGGATCAAGTAGACAATCTAAC 57.313 40.000 0.00 0.00 29.58 2.34
1500 1643 4.881850 ACAAAACACCTCTCGATTCAGTTT 59.118 37.500 0.00 0.00 0.00 2.66
1655 1801 4.986659 GCATGCAGGGAATAATTGTGATTC 59.013 41.667 14.21 0.00 33.34 2.52
1715 1862 5.846473 GTGAAAGCGAAGTCTGTTATTTGTC 59.154 40.000 0.00 0.00 0.00 3.18
1718 1865 3.433615 AGCGAAGTCTGTTATTTGTCTGC 59.566 43.478 0.00 0.00 0.00 4.26
1852 2006 1.577328 CCCTGTGTCCACGCATCAAC 61.577 60.000 0.00 0.00 35.63 3.18
1891 2052 2.046023 CATGGCACGCTTGGAGGA 60.046 61.111 0.00 0.00 0.00 3.71
1938 2103 6.828785 GGTGGGAGAATAATACACACAAGAAT 59.171 38.462 0.00 0.00 33.91 2.40
1955 2121 6.923508 CACAAGAATTTTGTTTTACTCCCTCC 59.076 38.462 4.05 0.00 0.00 4.30
1972 2138 6.729100 ACTCCCTCCGATCCATATTAATTGTA 59.271 38.462 0.00 0.00 0.00 2.41
1973 2139 6.942976 TCCCTCCGATCCATATTAATTGTAC 58.057 40.000 0.00 0.00 0.00 2.90
1974 2140 6.499000 TCCCTCCGATCCATATTAATTGTACA 59.501 38.462 0.00 0.00 0.00 2.90
1975 2141 7.016760 TCCCTCCGATCCATATTAATTGTACAA 59.983 37.037 11.41 11.41 0.00 2.41
1976 2142 7.119262 CCCTCCGATCCATATTAATTGTACAAC 59.881 40.741 11.22 0.00 0.00 3.32
1978 2144 8.966069 TCCGATCCATATTAATTGTACAACAA 57.034 30.769 11.22 8.61 42.95 2.83
1979 2145 8.832521 TCCGATCCATATTAATTGTACAACAAC 58.167 33.333 11.22 0.00 41.40 3.32
1980 2146 7.796660 CCGATCCATATTAATTGTACAACAACG 59.203 37.037 11.22 6.18 41.40 4.10
2024 2211 3.229276 TGCCTTACAAAAATCATGCCG 57.771 42.857 0.00 0.00 0.00 5.69
2042 2229 2.653115 GGGCTGCCTTGCAAGTTC 59.347 61.111 24.35 15.82 38.41 3.01
2193 2380 0.911769 TCCATGCCCTCTCGTTCAAT 59.088 50.000 0.00 0.00 0.00 2.57
2358 2547 7.061094 CGAGTTATTGAACTTGATTCTTTTGGC 59.939 37.037 0.00 0.00 46.42 4.52
2372 2561 8.020819 TGATTCTTTTGGCTTTGTTCGTAATAG 58.979 33.333 0.00 0.00 0.00 1.73
2387 2576 2.393271 AATAGCTCCACACAGTGAGC 57.607 50.000 7.81 6.06 37.15 4.26
2459 2685 1.215647 GTGTACCAGCCGAGAGTGG 59.784 63.158 0.00 0.00 39.98 4.00
2498 2724 9.658799 CCTCATGAAAATACAGTATATACCTGG 57.341 37.037 9.32 2.66 0.00 4.45
2533 2759 4.115516 CGTGATGACCCTAGTTTCATCTG 58.884 47.826 22.26 15.04 45.71 2.90
2612 2846 8.034804 GGTGCATTACTGTTATCTTGGATTTTT 58.965 33.333 0.00 0.00 0.00 1.94
2654 2888 1.327303 TTTTGGTGACACAGGATGGC 58.673 50.000 8.08 0.00 43.62 4.40
2684 2918 5.069781 GGTGCATGTTATAGAGAGAGACCTT 59.930 44.000 0.00 0.00 0.00 3.50
2693 2927 2.028876 GAGAGAGACCTTACAGAGCCC 58.971 57.143 0.00 0.00 0.00 5.19
2723 2957 2.959707 TGTGGGTGAATTGTTACAACCC 59.040 45.455 14.31 14.31 42.55 4.11
2835 3080 9.632638 AGGCAATGTATACTGACTATTTGATTT 57.367 29.630 4.17 0.00 0.00 2.17
3106 3351 4.579340 TCATCTGGTATCCTTCTACGTGAC 59.421 45.833 0.00 0.00 0.00 3.67
3128 3373 6.071616 TGACAAGTTCATTTTACCCATAAGCC 60.072 38.462 0.00 0.00 0.00 4.35
3133 3378 4.285020 TCATTTTACCCATAAGCCATGCA 58.715 39.130 0.00 0.00 32.84 3.96
3171 3422 1.079888 CGGCCCTTTGCAATGGTTC 60.080 57.895 25.10 17.40 43.89 3.62
3187 3438 3.023119 TGGTTCAATTCTGCTTGTGTGT 58.977 40.909 0.00 0.00 0.00 3.72
3197 3448 4.513442 TCTGCTTGTGTGTAAGTTCTTGT 58.487 39.130 0.00 0.00 0.00 3.16
3230 3482 8.077991 TGTATTTGCTCTCATGTTCTTTTCAAG 58.922 33.333 0.00 0.00 0.00 3.02
3285 3537 9.741168 CTTCACATAAATCTAACTGTTTACACG 57.259 33.333 0.00 0.00 0.00 4.49
3290 3542 2.409975 TCTAACTGTTTACACGCCTGC 58.590 47.619 0.00 0.00 0.00 4.85
3295 3547 0.660488 TGTTTACACGCCTGCACTTG 59.340 50.000 0.00 0.00 0.00 3.16
3497 3749 0.321298 TAAGACGTGCCCTTTGCTCC 60.321 55.000 0.00 0.00 42.00 4.70
3537 3789 8.138074 TCTCACATTATACTCACTGCTGATTAC 58.862 37.037 0.00 0.00 0.00 1.89
3805 4057 0.250124 CGTGGTTGCACCTCAGGTAA 60.250 55.000 0.00 0.00 39.58 2.85
3807 4059 2.084546 GTGGTTGCACCTCAGGTAATC 58.915 52.381 0.00 0.00 39.58 1.75
4018 4285 1.541588 GGTGCACTTTTGATGGGAGAC 59.458 52.381 17.98 0.00 0.00 3.36
4045 4312 4.839121 TCAATATGCGACACCCTTTAACT 58.161 39.130 0.00 0.00 0.00 2.24
4297 4572 0.892358 ACACATTGGCTGGTGCTCTG 60.892 55.000 0.00 0.00 38.57 3.35
4318 4593 5.362717 TCTGTACAAAGTCTTCAGTTCCTCA 59.637 40.000 0.00 0.00 0.00 3.86
4468 4743 5.049129 ACACTTCTTTGCTGTTGCTATCTTC 60.049 40.000 0.00 0.00 40.48 2.87
4569 4858 7.037658 TCCCCCGATCTTCAATGATTTCATATA 60.038 37.037 0.00 0.00 35.10 0.86
4623 4912 4.579869 TGAAGGCAGTGATTAGAAGGAAC 58.420 43.478 0.00 0.00 0.00 3.62
4795 5084 7.924412 GCATAACTGCTGTATGTTAGTACCTTA 59.076 37.037 0.00 0.00 45.32 2.69
4870 5159 8.208224 CCATGTATGTTAGTACCTGGTTTCATA 58.792 37.037 3.84 5.07 36.31 2.15
4886 5175 6.172630 GGTTTCATAAAGTTTTGGCATCCAT 58.827 36.000 0.00 0.00 31.53 3.41
4985 5295 4.079558 AGACTGGCCATCTTTGGATGTTAT 60.080 41.667 5.51 0.00 46.92 1.89
5176 5486 3.320541 CCTGAAGCGGAGTTCTGATCTAT 59.679 47.826 0.00 0.00 0.00 1.98
5303 5637 2.401766 CGTTGGGTGCTGATCCTGC 61.402 63.158 1.38 1.38 0.00 4.85
5309 5643 0.529378 GGTGCTGATCCTGCTTTTGG 59.471 55.000 8.84 0.00 0.00 3.28
5316 5650 4.741342 CTGATCCTGCTTTTGGAATGTTC 58.259 43.478 0.00 0.00 37.13 3.18
5328 5662 2.892215 TGGAATGTTCTGAATTGCTGCA 59.108 40.909 0.00 0.00 0.00 4.41
5377 5711 9.546909 CTAGCTAAATTGTACATCTTTGTTGTG 57.453 33.333 12.01 0.00 37.28 3.33
5389 5828 8.340618 ACATCTTTGTTGTGCTACTAATGAAT 57.659 30.769 0.00 0.00 29.55 2.57
5416 5855 3.368531 CCTGCTGTTCTAACTAGTGGACC 60.369 52.174 0.00 0.00 0.00 4.46
5421 5860 4.228824 TGTTCTAACTAGTGGACCAAGGT 58.771 43.478 0.00 0.00 0.00 3.50
5453 5892 2.162608 GTCTACTGATCGTGAGCTGTGT 59.837 50.000 7.74 0.00 31.53 3.72
5530 5975 3.567164 GGACCATGATATGCCTTCAGTTG 59.433 47.826 0.00 0.00 0.00 3.16
5542 5987 0.323360 TTCAGTTGTATGGGCCAGCC 60.323 55.000 13.78 5.20 0.00 4.85
5560 6005 2.025037 AGCCCATCAAATGTGGAGCTTA 60.025 45.455 0.00 0.00 38.97 3.09
5561 6006 2.961062 GCCCATCAAATGTGGAGCTTAT 59.039 45.455 0.00 0.00 39.12 1.73
5562 6007 3.005155 GCCCATCAAATGTGGAGCTTATC 59.995 47.826 0.00 0.00 39.12 1.75
5576 6022 4.768448 GGAGCTTATCCCTTACCTAGAGTC 59.232 50.000 0.00 0.00 43.01 3.36
5649 6099 9.495572 CCTATGAGAGTTTGAATAAAGATACCC 57.504 37.037 0.00 0.00 0.00 3.69
5697 6147 7.500720 TGACATAGGATTTAGATGTGCAATG 57.499 36.000 0.00 0.00 33.99 2.82
5704 6154 6.774170 AGGATTTAGATGTGCAATGCTTATGA 59.226 34.615 6.82 0.00 0.00 2.15
5811 6261 7.147230 ACCCCTCAATAAATAAAGCAGAGAGAT 60.147 37.037 0.00 0.00 0.00 2.75
5889 6339 7.258441 AGCAGATCATTTCATCTTGTCAATTG 58.742 34.615 0.00 0.00 30.07 2.32
5922 6376 4.293494 TGTGAAGCTAGAAGATGGAGGAT 58.707 43.478 0.00 0.00 0.00 3.24
5946 6400 4.653801 AGTGTATATACTGCACCATCCACA 59.346 41.667 13.89 0.00 41.00 4.17
5949 6403 0.107017 ATACTGCACCATCCACAGGC 60.107 55.000 0.00 0.00 35.70 4.85
5985 6439 1.887956 CGCCCAAATCTCCCCCATATG 60.888 57.143 0.00 0.00 0.00 1.78
6008 7515 6.068010 TGTTTTATGTTTGGACCAGATGTCT 58.932 36.000 0.00 0.00 43.89 3.41
6009 7516 6.016360 TGTTTTATGTTTGGACCAGATGTCTG 60.016 38.462 3.01 3.01 43.89 3.51
6018 7525 7.595819 TTGGACCAGATGTCTGTAAATTTTT 57.404 32.000 9.03 0.00 43.89 1.94
6019 7526 6.980593 TGGACCAGATGTCTGTAAATTTTTG 58.019 36.000 9.03 0.00 43.89 2.44
6032 7539 1.265236 ATTTTTGGGCCTTCATCGCA 58.735 45.000 4.53 0.00 0.00 5.10
6055 7562 3.448340 CCATTTTGGGCCCGACCG 61.448 66.667 19.37 5.88 40.62 4.79
6058 7565 3.931190 ATTTTGGGCCCGACCGGTC 62.931 63.158 25.28 25.28 40.62 4.79
6074 7581 1.334599 CGGTCCAAAACGTCCACAATG 60.335 52.381 0.00 0.00 0.00 2.82
6084 7591 3.660865 ACGTCCACAATGTCCTAAGTTC 58.339 45.455 0.00 0.00 0.00 3.01
6096 7603 1.609841 CCTAAGTTCGACCCCAACCAC 60.610 57.143 0.00 0.00 0.00 4.16
6138 7645 1.528309 CACCCAAAACCCTGACGCT 60.528 57.895 0.00 0.00 0.00 5.07
6155 7662 4.277174 TGACGCTGGTGTATTTTCACAATT 59.723 37.500 0.00 0.00 39.76 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 1.291588 GCTGGATCGATCGCATCCT 59.708 57.895 29.81 9.71 40.66 3.24
322 331 2.094906 ACTACGCTACGCTGAAACATCA 60.095 45.455 0.00 0.00 0.00 3.07
356 365 3.215975 GAGTAGCACCCAGTACTCCTAG 58.784 54.545 0.00 0.00 39.45 3.02
364 373 1.358103 TGAGTAGGAGTAGCACCCAGT 59.642 52.381 0.00 0.00 0.00 4.00
385 394 1.374252 GACGCTCGATGTGGGTTGT 60.374 57.895 0.00 0.00 0.00 3.32
391 400 1.135257 AGGAAGAAGACGCTCGATGTG 60.135 52.381 0.00 0.00 0.00 3.21
401 410 6.349694 CCAAGCATTTTAAGGAGGAAGAAGAC 60.350 42.308 0.00 0.00 0.00 3.01
412 421 6.575162 ACACTACTTCCAAGCATTTTAAGG 57.425 37.500 0.00 0.00 0.00 2.69
429 439 7.756558 AGAAGATTTGTAGGTACGTACACTAC 58.243 38.462 28.81 28.81 38.02 2.73
430 440 7.928307 AGAAGATTTGTAGGTACGTACACTA 57.072 36.000 26.02 20.09 32.53 2.74
431 441 6.830873 AGAAGATTTGTAGGTACGTACACT 57.169 37.500 26.02 21.00 32.53 3.55
432 442 7.086376 TGAAGAAGATTTGTAGGTACGTACAC 58.914 38.462 26.02 17.00 32.53 2.90
433 443 7.218228 TGAAGAAGATTTGTAGGTACGTACA 57.782 36.000 26.02 21.34 0.00 2.90
434 444 8.699283 AATGAAGAAGATTTGTAGGTACGTAC 57.301 34.615 17.56 17.56 0.00 3.67
435 445 8.525316 TGAATGAAGAAGATTTGTAGGTACGTA 58.475 33.333 0.00 0.00 0.00 3.57
436 446 7.383687 TGAATGAAGAAGATTTGTAGGTACGT 58.616 34.615 0.00 0.00 0.00 3.57
437 447 7.827819 TGAATGAAGAAGATTTGTAGGTACG 57.172 36.000 0.00 0.00 0.00 3.67
484 494 5.046735 CAGCTGGCCTGACTTGAGTATATAT 60.047 44.000 14.77 0.00 44.64 0.86
486 496 3.070734 CAGCTGGCCTGACTTGAGTATAT 59.929 47.826 14.77 0.00 44.64 0.86
488 498 1.209019 CAGCTGGCCTGACTTGAGTAT 59.791 52.381 14.77 0.00 44.64 2.12
489 499 0.610174 CAGCTGGCCTGACTTGAGTA 59.390 55.000 14.77 0.00 44.64 2.59
490 500 1.374190 CAGCTGGCCTGACTTGAGT 59.626 57.895 14.77 0.00 44.64 3.41
491 501 2.039405 GCAGCTGGCCTGACTTGAG 61.039 63.158 17.12 0.00 44.64 3.02
552 567 7.915293 ATATTAACACATGAGGACGAAAACA 57.085 32.000 0.00 0.00 0.00 2.83
607 697 4.793071 CATTTGTGGCGATCAGTTTGTAA 58.207 39.130 0.00 0.00 0.00 2.41
615 705 0.957362 TGTTGCATTTGTGGCGATCA 59.043 45.000 0.00 0.00 0.00 2.92
657 749 6.936279 TGGAATATGTTCGTTCTCTTCTCTT 58.064 36.000 0.00 0.00 35.10 2.85
661 753 7.036220 TCTCTTGGAATATGTTCGTTCTCTTC 58.964 38.462 0.00 0.00 35.10 2.87
693 787 3.997021 TGTCTCTTCGCTGGATTTTTCTC 59.003 43.478 0.00 0.00 0.00 2.87
913 1037 2.043852 TTGGGTTTGCGTGTGGGT 60.044 55.556 0.00 0.00 0.00 4.51
940 1064 4.736631 GTTTCTCAACGCGGCGCC 62.737 66.667 27.87 19.07 0.00 6.53
1016 1145 3.782244 CAACGAGCTGCCAGACGC 61.782 66.667 10.63 0.00 38.31 5.19
1113 1245 3.930012 GGGATCCCTTCGAGCGGG 61.930 72.222 24.69 14.08 43.38 6.13
1117 1249 4.286320 CGCGGGGATCCCTTCGAG 62.286 72.222 30.08 22.51 42.67 4.04
1312 1444 5.066593 CCAGTCTAAAAGAAACAGGAGCTT 58.933 41.667 0.00 0.00 0.00 3.74
1382 1517 3.326588 TCAATCTCGGGTTCTCCTTTGAA 59.673 43.478 0.00 0.00 0.00 2.69
1395 1533 3.797256 GTCGAATACCAGTTCAATCTCGG 59.203 47.826 0.00 0.00 0.00 4.63
1475 1615 4.273480 ACTGAATCGAGAGGTGTTTTGTTG 59.727 41.667 0.00 0.00 0.00 3.33
1500 1643 0.035881 CAGAGCAGTTGCCTTCCTGA 59.964 55.000 0.00 0.00 43.38 3.86
1561 1707 3.689649 AGATCAAAAGCCGTTACATGACC 59.310 43.478 0.00 0.00 0.00 4.02
1684 1831 1.275573 GACTTCGCTTTCACCTAGGGT 59.724 52.381 14.81 0.00 35.62 4.34
1687 1834 3.305398 ACAGACTTCGCTTTCACCTAG 57.695 47.619 0.00 0.00 0.00 3.02
1852 2006 1.547372 CCACCAGAAAGCAGGAATTGG 59.453 52.381 0.00 0.00 0.00 3.16
1891 2052 3.883489 CGTTCTTTCCCCTCTTTTCTGTT 59.117 43.478 0.00 0.00 0.00 3.16
1938 2103 4.202482 TGGATCGGAGGGAGTAAAACAAAA 60.202 41.667 0.00 0.00 0.00 2.44
1955 2121 7.796660 CCGTTGTTGTACAATTAATATGGATCG 59.203 37.037 12.26 8.10 40.59 3.69
1972 2138 4.895668 TTATTACTCCCTCCGTTGTTGT 57.104 40.909 0.00 0.00 0.00 3.32
1973 2139 6.753107 AATTTATTACTCCCTCCGTTGTTG 57.247 37.500 0.00 0.00 0.00 3.33
1974 2140 6.717997 ACAAATTTATTACTCCCTCCGTTGTT 59.282 34.615 0.00 0.00 0.00 2.83
1975 2141 6.243148 ACAAATTTATTACTCCCTCCGTTGT 58.757 36.000 0.00 0.00 0.00 3.32
1976 2142 6.753107 ACAAATTTATTACTCCCTCCGTTG 57.247 37.500 0.00 0.00 0.00 4.10
1978 2144 9.470399 AAATAACAAATTTATTACTCCCTCCGT 57.530 29.630 0.00 0.00 0.00 4.69
1979 2145 9.730420 CAAATAACAAATTTATTACTCCCTCCG 57.270 33.333 0.00 0.00 0.00 4.63
1980 2146 9.529325 GCAAATAACAAATTTATTACTCCCTCC 57.471 33.333 0.00 0.00 0.00 4.30
2010 2196 0.904394 AGCCCCGGCATGATTTTTGT 60.904 50.000 8.74 0.00 44.88 2.83
2024 2211 2.919328 AACTTGCAAGGCAGCCCC 60.919 61.111 29.18 0.00 40.61 5.80
2069 2256 6.151648 CACCCACATGTTCTCATTCATTTAGT 59.848 38.462 0.00 0.00 31.15 2.24
2193 2380 2.319844 TCAAGTCTCTGTTGGAGCAGA 58.680 47.619 0.00 0.00 42.56 4.26
2358 2547 4.688879 TGTGTGGAGCTATTACGAACAAAG 59.311 41.667 0.00 0.00 0.00 2.77
2372 2561 0.173481 TATCGCTCACTGTGTGGAGC 59.827 55.000 7.79 8.64 35.24 4.70
2452 2678 6.065374 TGAGGATCTGTATCTTACCACTCTC 58.935 44.000 0.00 0.00 34.92 3.20
2493 2719 2.764572 CACGGTAATACTCCTTCCAGGT 59.235 50.000 0.00 0.00 36.53 4.00
2497 2723 4.501058 GGTCATCACGGTAATACTCCTTCC 60.501 50.000 0.00 0.00 0.00 3.46
2498 2724 4.501058 GGGTCATCACGGTAATACTCCTTC 60.501 50.000 0.00 0.00 0.00 3.46
2636 2870 0.539438 GGCCATCCTGTGTCACCAAA 60.539 55.000 0.00 0.00 0.00 3.28
2654 2888 1.067974 TCTATAACATGCACCCGTCGG 59.932 52.381 3.60 3.60 0.00 4.79
2684 2918 3.069586 CCACAATTCTATCGGGCTCTGTA 59.930 47.826 0.00 0.00 0.00 2.74
2693 2927 5.818136 ACAATTCACCCACAATTCTATCG 57.182 39.130 0.00 0.00 0.00 2.92
2723 2957 2.691409 TCAATTTCAGGTAGCCTCCG 57.309 50.000 0.00 0.00 0.00 4.63
2801 3035 5.405571 GTCAGTATACATTGCCTATGGTTCG 59.594 44.000 5.50 0.00 38.64 3.95
2835 3080 1.621317 TCATCAACGCAGTCTGGGTAA 59.379 47.619 21.59 13.77 45.00 2.85
3106 3351 6.279513 TGGCTTATGGGTAAAATGAACTTG 57.720 37.500 0.00 0.00 0.00 3.16
3128 3373 7.691050 CGCACAGTATTATCATTCTAATGCATG 59.309 37.037 0.00 0.00 36.36 4.06
3133 3378 5.643777 GGCCGCACAGTATTATCATTCTAAT 59.356 40.000 0.00 0.00 0.00 1.73
3171 3422 6.064846 AGAACTTACACACAAGCAGAATTG 57.935 37.500 0.00 0.00 36.22 2.32
3187 3438 9.073475 AGCAAATACACCAAATACAAGAACTTA 57.927 29.630 0.00 0.00 0.00 2.24
3197 3448 7.611467 AGAACATGAGAGCAAATACACCAAATA 59.389 33.333 0.00 0.00 0.00 1.40
3237 3489 8.885722 TGAAGCTAACCCGTTTAAAATGTATAG 58.114 33.333 0.00 0.00 0.00 1.31
3290 3542 7.113965 GTCAAACATTATTCTCAGTTGCAAGTG 59.886 37.037 25.44 25.44 0.00 3.16
3295 3547 8.454106 AGTATGTCAAACATTATTCTCAGTTGC 58.546 33.333 0.00 0.00 39.88 4.17
3497 3749 3.485463 TGTGAGAACTGTACCTTTGGG 57.515 47.619 0.00 0.00 38.88 4.12
3805 4057 4.298103 AGGACAAGATCAACTGCAAGAT 57.702 40.909 0.00 0.00 37.43 2.40
3807 4059 4.999950 ACTTAGGACAAGATCAACTGCAAG 59.000 41.667 0.00 0.00 42.29 4.01
3877 4144 6.479006 AGGAATCTGAGAAATGACAACATCA 58.521 36.000 0.00 0.00 43.13 3.07
3878 4145 6.038050 GGAGGAATCTGAGAAATGACAACATC 59.962 42.308 0.00 0.00 35.50 3.06
4045 4312 1.545428 GCAACAGTCATTCCTCCACCA 60.545 52.381 0.00 0.00 0.00 4.17
4081 4348 4.119862 GCTTGATAAGATTACGCAGGACA 58.880 43.478 0.00 0.00 0.00 4.02
4202 4477 8.603242 ACTGTATTACACTACACTGGAAAAAG 57.397 34.615 0.00 0.00 0.00 2.27
4203 4478 8.967664 AACTGTATTACACTACACTGGAAAAA 57.032 30.769 0.00 0.00 0.00 1.94
4237 4512 5.289675 CGGCTGAATAAGTTACAGAACTGAG 59.710 44.000 8.87 0.00 45.50 3.35
4241 4516 4.251268 ACCGGCTGAATAAGTTACAGAAC 58.749 43.478 0.00 0.00 34.07 3.01
4246 4521 3.400505 GCAACCGGCTGAATAAGTTAC 57.599 47.619 9.57 0.00 40.25 2.50
4297 4572 4.750598 GGTGAGGAACTGAAGACTTTGTAC 59.249 45.833 0.00 0.00 41.55 2.90
4318 4593 1.207791 CATCCCTAGCCTTGTCAGGT 58.792 55.000 0.00 0.00 43.18 4.00
4354 4629 4.766891 CCTCCAAGGCTCAAGTAATCAAAA 59.233 41.667 0.00 0.00 0.00 2.44
4468 4743 1.626654 GCATCAGTCGTCCAACACCG 61.627 60.000 0.00 0.00 0.00 4.94
4589 4878 5.865085 TCACTGCCTTCATGTTAGTACTTT 58.135 37.500 0.00 0.00 0.00 2.66
4590 4879 5.483685 TCACTGCCTTCATGTTAGTACTT 57.516 39.130 0.00 0.00 0.00 2.24
4623 4912 6.969828 AAAGATAGAAAACAGCTAGTTCCG 57.030 37.500 0.00 0.00 40.26 4.30
4837 5126 4.570772 GGTACTAACATACATGGCTGTGTG 59.429 45.833 0.00 10.57 46.56 3.82
4870 5159 9.768662 GATGAATATAATGGATGCCAAAACTTT 57.231 29.630 0.00 0.00 36.95 2.66
4985 5295 7.121020 TGTGCAGCTTTATCAAACAATAGATCA 59.879 33.333 0.00 0.00 0.00 2.92
5176 5486 2.159184 CGAGAGATTAGCTGCACCTTCA 60.159 50.000 1.02 0.00 0.00 3.02
5303 5637 5.107220 GCAGCAATTCAGAACATTCCAAAAG 60.107 40.000 0.00 0.00 0.00 2.27
5309 5643 3.789756 CGATGCAGCAATTCAGAACATTC 59.210 43.478 1.53 0.00 0.00 2.67
5316 5650 3.616935 CACCGATGCAGCAATTCAG 57.383 52.632 1.53 0.00 0.00 3.02
5377 5711 2.603173 GCAGGCGCAATTCATTAGTAGC 60.603 50.000 10.83 0.00 38.36 3.58
5389 5828 0.250295 AGTTAGAACAGCAGGCGCAA 60.250 50.000 10.83 0.00 42.27 4.85
5421 5860 3.056821 CGATCAGTAGACAAGGAACACCA 60.057 47.826 0.00 0.00 0.00 4.17
5453 5892 3.488384 GGTCTGATTTGAAACGCACACAA 60.488 43.478 0.00 0.00 0.00 3.33
5542 5987 3.571401 GGGATAAGCTCCACATTTGATGG 59.429 47.826 0.00 0.00 46.98 3.51
5560 6005 2.866454 ACTGGGACTCTAGGTAAGGGAT 59.134 50.000 0.00 0.00 0.00 3.85
5561 6006 2.295143 ACTGGGACTCTAGGTAAGGGA 58.705 52.381 0.00 0.00 0.00 4.20
5562 6007 2.766828 CAACTGGGACTCTAGGTAAGGG 59.233 54.545 0.00 0.00 0.00 3.95
5563 6008 3.709587 TCAACTGGGACTCTAGGTAAGG 58.290 50.000 0.00 0.00 0.00 2.69
5565 6010 6.127140 GCTTAATCAACTGGGACTCTAGGTAA 60.127 42.308 0.00 0.00 0.00 2.85
5567 6012 4.162509 GCTTAATCAACTGGGACTCTAGGT 59.837 45.833 0.00 0.00 0.00 3.08
5568 6013 4.162320 TGCTTAATCAACTGGGACTCTAGG 59.838 45.833 0.00 0.00 0.00 3.02
5576 6022 4.521146 AGAGACATGCTTAATCAACTGGG 58.479 43.478 0.00 0.00 0.00 4.45
5844 6294 9.678260 ATCTGCTACTCACATAAAGAAAAGATT 57.322 29.630 0.00 0.00 0.00 2.40
5845 6295 9.323985 GATCTGCTACTCACATAAAGAAAAGAT 57.676 33.333 0.00 0.00 0.00 2.40
5846 6296 8.314021 TGATCTGCTACTCACATAAAGAAAAGA 58.686 33.333 0.00 0.00 0.00 2.52
5847 6297 8.484641 TGATCTGCTACTCACATAAAGAAAAG 57.515 34.615 0.00 0.00 0.00 2.27
5848 6298 9.453572 AATGATCTGCTACTCACATAAAGAAAA 57.546 29.630 0.00 0.00 0.00 2.29
5849 6299 9.453572 AAATGATCTGCTACTCACATAAAGAAA 57.546 29.630 0.00 0.00 0.00 2.52
5889 6339 5.003692 TCTAGCTTCACATGTCATCAGTC 57.996 43.478 0.00 0.00 0.00 3.51
5922 6376 5.836358 TGTGGATGGTGCAGTATATACACTA 59.164 40.000 15.18 3.40 34.70 2.74
5962 6416 2.124278 GGGGAGATTTGGGCGTCC 60.124 66.667 0.00 0.00 0.00 4.79
6008 7515 4.815269 CGATGAAGGCCCAAAAATTTACA 58.185 39.130 0.00 0.00 0.00 2.41
6009 7516 3.616821 GCGATGAAGGCCCAAAAATTTAC 59.383 43.478 0.00 0.00 0.00 2.01
6018 7525 3.720601 AGCTGCGATGAAGGCCCA 61.721 61.111 0.00 0.00 0.00 5.36
6019 7526 3.207669 CAGCTGCGATGAAGGCCC 61.208 66.667 0.00 0.00 0.00 5.80
6050 7557 2.312436 GGACGTTTTGGACCGGTCG 61.312 63.158 27.68 18.29 0.00 4.79
6054 7561 0.948678 ATTGTGGACGTTTTGGACCG 59.051 50.000 0.00 0.00 0.00 4.79
6055 7562 1.679153 ACATTGTGGACGTTTTGGACC 59.321 47.619 0.00 0.00 0.00 4.46
6058 7565 1.953686 AGGACATTGTGGACGTTTTGG 59.046 47.619 0.00 0.00 0.00 3.28
6074 7581 1.338484 GGTTGGGGTCGAACTTAGGAC 60.338 57.143 0.00 0.00 0.00 3.85
6096 7603 1.006102 GGACCATCATAGGCCGACG 60.006 63.158 0.00 0.00 0.00 5.12
6138 7645 4.302455 CGGCAAATTGTGAAAATACACCA 58.698 39.130 0.00 0.00 39.69 4.17


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

AutoCloner maintained by Alex Coulton.