Multiple sequence alignment - TraesCS1D01G125300

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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 TraesCS1D01G125300 chr1D 100.000 6736 0 0 908 7643 133564040 133570775 0.000000e+00 12440.0
1 TraesCS1D01G125300 chr1D 100.000 410 0 0 1 410 133563133 133563542 0.000000e+00 758.0
2 TraesCS1D01G125300 chr1D 86.667 90 8 1 7426 7511 25453927 25454016 6.310000e-16 97.1
3 TraesCS1D01G125300 chr1D 82.759 87 13 2 2846 2931 17188419 17188334 8.220000e-10 76.8
4 TraesCS1D01G125300 chr1B 95.853 3593 88 18 3301 6856 202009939 202006371 0.000000e+00 5753.0
5 TraesCS1D01G125300 chr1B 96.657 2393 48 8 908 3298 202012444 202010082 0.000000e+00 3947.0
6 TraesCS1D01G125300 chr1B 96.629 267 9 0 6847 7113 202006271 202006005 1.960000e-120 444.0
7 TraesCS1D01G125300 chr1B 95.652 253 11 0 98 350 202013485 202013233 2.570000e-109 407.0
8 TraesCS1D01G125300 chr1B 87.291 299 14 7 7302 7592 202005954 202005672 3.440000e-83 320.0
9 TraesCS1D01G125300 chr1B 91.892 185 15 0 7330 7514 180834851 180835035 7.610000e-65 259.0
10 TraesCS1D01G125300 chr1B 98.969 97 1 0 16 112 202014740 202014644 2.840000e-39 174.0
11 TraesCS1D01G125300 chr1B 90.164 122 8 2 7333 7454 40819372 40819489 1.030000e-33 156.0
12 TraesCS1D01G125300 chr1A 95.474 3005 82 21 3443 6408 165176025 165173036 0.000000e+00 4747.0
13 TraesCS1D01G125300 chr1A 97.701 2392 44 7 908 3296 165178777 165176394 0.000000e+00 4102.0
14 TraesCS1D01G125300 chr1A 93.470 781 39 3 6446 7216 165173034 165172256 0.000000e+00 1149.0
15 TraesCS1D01G125300 chr1A 95.467 353 13 3 18 369 165179468 165179118 1.860000e-155 560.0
16 TraesCS1D01G125300 chr1A 82.456 399 35 11 7219 7592 165172214 165171826 4.450000e-82 316.0
17 TraesCS1D01G125300 chr1A 96.528 144 5 0 3301 3444 165176250 165176107 9.910000e-59 239.0
18 TraesCS1D01G125300 chr1A 89.441 161 13 1 7330 7486 26491315 26491475 4.680000e-47 200.0
19 TraesCS1D01G125300 chr2A 91.351 185 15 1 7330 7513 676466290 676466474 1.270000e-62 252.0
20 TraesCS1D01G125300 chr2A 84.286 70 9 2 2863 2931 423179308 423179240 4.950000e-07 67.6
21 TraesCS1D01G125300 chr2B 88.816 152 17 0 7339 7490 349521603 349521452 3.640000e-43 187.0
22 TraesCS1D01G125300 chr2B 87.500 56 6 1 2879 2933 133007662 133007607 6.400000e-06 63.9
23 TraesCS1D01G125300 chr5D 91.071 112 9 1 7404 7514 514559883 514559772 4.780000e-32 150.0
24 TraesCS1D01G125300 chr5D 94.595 37 1 1 2842 2878 454108959 454108924 1.000000e-03 56.5
25 TraesCS1D01G125300 chr5B 92.079 101 8 0 7404 7504 646675889 646675789 7.990000e-30 143.0
26 TraesCS1D01G125300 chr4D 87.234 94 10 2 2846 2938 122695543 122695635 1.050000e-18 106.0
27 TraesCS1D01G125300 chr4D 93.617 47 0 2 2889 2933 107440535 107440580 4.950000e-07 67.6
28 TraesCS1D01G125300 chr7D 90.411 73 7 0 3665 3737 2788906 2788978 6.310000e-16 97.1
29 TraesCS1D01G125300 chr6D 90.411 73 7 0 3665 3737 15675429 15675357 6.310000e-16 97.1
30 TraesCS1D01G125300 chr3B 90.278 72 7 0 3665 3736 216396411 216396340 2.270000e-15 95.3
31 TraesCS1D01G125300 chr3B 78.495 93 15 5 2841 2931 569597973 569597884 1.000000e-03 56.5
32 TraesCS1D01G125300 chr4B 81.818 88 14 2 2846 2932 18087472 18087558 1.060000e-08 73.1
33 TraesCS1D01G125300 chr4B 93.617 47 0 2 2889 2933 169582417 169582372 4.950000e-07 67.6


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 TraesCS1D01G125300 chr1D 133563133 133570775 7642 False 6599.000000 12440 100.000000 1 7643 2 chr1D.!!$F2 7642
1 TraesCS1D01G125300 chr1B 202005672 202014740 9068 True 1840.833333 5753 95.175167 16 7592 6 chr1B.!!$R1 7576
2 TraesCS1D01G125300 chr1A 165171826 165179468 7642 True 1852.166667 4747 93.516000 18 7592 6 chr1A.!!$R1 7574

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
399 1573 0.881118 CCCCAATCACCAAACACTCG 59.119 55.000 0.0 0.0 0.00 4.18 F
1826 3231 1.174783 GAGGTCGCTACTCTCAACCA 58.825 55.000 0.0 0.0 32.25 3.67 F
2046 3455 1.442526 CCCTGGATGTCATTCTGCGC 61.443 60.000 0.0 0.0 0.00 6.09 F
2386 3796 2.415893 GCGCACCATTTTCAGCAATAGT 60.416 45.455 0.3 0.0 0.00 2.12 F
2727 4137 2.415893 GGTTTGATCAATGCCCGTCTTG 60.416 50.000 9.4 0.0 0.00 3.02 F
4115 5757 1.083489 TATGTCTTTCCTTTGCCGCG 58.917 50.000 0.0 0.0 0.00 6.46 F
5496 7143 0.463620 TGGGGTTTTGCTCAGTTTGC 59.536 50.000 0.0 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 3796 3.389983 TCGGGAGAAAAACTGAGGAAAGA 59.610 43.478 0.00 0.0 34.75 2.52 R
2872 4282 4.279659 AGCTAGCTTGAAAAACGAAAACG 58.720 39.130 12.68 0.0 0.00 3.60 R
3677 5313 4.418392 CAGCAGTGTATCTGAAAATTGGC 58.582 43.478 0.00 0.0 46.27 4.52 R
4115 5757 2.549329 CCTGCAAGAAACAAAATTGGCC 59.451 45.455 0.00 0.0 34.07 5.36 R
4291 5934 4.689071 TGTATAGCAACCTACAATGGACG 58.311 43.478 0.00 0.0 0.00 4.79 R
5853 7511 1.279271 ACTTGTCCAGGAAAGGGATCG 59.721 52.381 13.08 0.0 36.67 3.69 R
7282 9116 0.244450 TCCACGGACGAGCGTAAAAT 59.756 50.000 0.00 0.0 0.00 1.82 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
52 53 2.751436 CCACGGCCCATTCACCAG 60.751 66.667 0.00 0.00 0.00 4.00
144 1318 4.933483 GAGTATCCGCTCGCTCAG 57.067 61.111 0.00 0.00 0.00 3.35
350 1524 4.103103 TCTCTCACCGCGCACTCG 62.103 66.667 8.75 0.00 39.07 4.18
364 1538 4.052229 CTCGGACGCCAGAACCGT 62.052 66.667 0.00 0.00 45.71 4.83
368 1542 4.754667 GACGCCAGAACCGTCCCC 62.755 72.222 2.79 0.00 46.78 4.81
371 1545 4.097361 GCCAGAACCGTCCCCCTC 62.097 72.222 0.00 0.00 0.00 4.30
372 1546 3.400054 CCAGAACCGTCCCCCTCC 61.400 72.222 0.00 0.00 0.00 4.30
373 1547 3.400054 CAGAACCGTCCCCCTCCC 61.400 72.222 0.00 0.00 0.00 4.30
374 1548 3.612607 AGAACCGTCCCCCTCCCT 61.613 66.667 0.00 0.00 0.00 4.20
375 1549 3.082055 GAACCGTCCCCCTCCCTC 61.082 72.222 0.00 0.00 0.00 4.30
376 1550 4.735599 AACCGTCCCCCTCCCTCC 62.736 72.222 0.00 0.00 0.00 4.30
397 1571 3.455737 CCCCCAATCACCAAACACT 57.544 52.632 0.00 0.00 0.00 3.55
398 1572 1.256812 CCCCCAATCACCAAACACTC 58.743 55.000 0.00 0.00 0.00 3.51
399 1573 0.881118 CCCCAATCACCAAACACTCG 59.119 55.000 0.00 0.00 0.00 4.18
400 1574 1.604604 CCCAATCACCAAACACTCGT 58.395 50.000 0.00 0.00 0.00 4.18
401 1575 1.535462 CCCAATCACCAAACACTCGTC 59.465 52.381 0.00 0.00 0.00 4.20
402 1576 2.494059 CCAATCACCAAACACTCGTCT 58.506 47.619 0.00 0.00 0.00 4.18
403 1577 3.556213 CCCAATCACCAAACACTCGTCTA 60.556 47.826 0.00 0.00 0.00 2.59
404 1578 3.679980 CCAATCACCAAACACTCGTCTAG 59.320 47.826 0.00 0.00 0.00 2.43
405 1579 4.556233 CAATCACCAAACACTCGTCTAGA 58.444 43.478 0.00 0.00 0.00 2.43
406 1580 5.171476 CAATCACCAAACACTCGTCTAGAT 58.829 41.667 0.00 0.00 0.00 1.98
407 1581 4.436242 TCACCAAACACTCGTCTAGATC 57.564 45.455 0.00 0.00 0.00 2.75
408 1582 3.192844 TCACCAAACACTCGTCTAGATCC 59.807 47.826 0.00 0.00 0.00 3.36
409 1583 3.056821 CACCAAACACTCGTCTAGATCCA 60.057 47.826 0.00 0.00 0.00 3.41
1446 2851 8.620116 ATGTGGCAAAAGCTTTATAATTGTTT 57.380 26.923 13.10 0.00 0.00 2.83
1545 2950 9.525826 AGAATTTGATTTTAGATCCAGTTGACT 57.474 29.630 0.00 0.00 0.00 3.41
1584 2989 7.418408 TCTATACACTTTGCTCTGTTAGATCG 58.582 38.462 0.00 0.00 0.00 3.69
1595 3000 6.096423 TGCTCTGTTAGATCGTAGGTGTAATT 59.904 38.462 0.00 0.00 0.00 1.40
1826 3231 1.174783 GAGGTCGCTACTCTCAACCA 58.825 55.000 0.00 0.00 32.25 3.67
1835 3240 6.205076 GTCGCTACTCTCAACCATATCTTCTA 59.795 42.308 0.00 0.00 0.00 2.10
1877 3282 7.071069 AGCAATGTATCTAATGATGGACTCA 57.929 36.000 0.00 0.00 38.53 3.41
1878 3283 7.687388 AGCAATGTATCTAATGATGGACTCAT 58.313 34.615 0.00 0.00 46.87 2.90
1879 3284 7.606839 AGCAATGTATCTAATGATGGACTCATG 59.393 37.037 0.00 0.00 44.03 3.07
1880 3285 7.389884 GCAATGTATCTAATGATGGACTCATGT 59.610 37.037 0.00 0.00 44.03 3.21
2046 3455 1.442526 CCCTGGATGTCATTCTGCGC 61.443 60.000 0.00 0.00 0.00 6.09
2386 3796 2.415893 GCGCACCATTTTCAGCAATAGT 60.416 45.455 0.30 0.00 0.00 2.12
2670 4080 6.423862 CATTCCAAGAAAAACATTGCAAGTG 58.576 36.000 4.94 6.32 0.00 3.16
2721 4131 3.055963 TCATGTTGGTTTGATCAATGCCC 60.056 43.478 20.29 15.72 0.00 5.36
2727 4137 2.415893 GGTTTGATCAATGCCCGTCTTG 60.416 50.000 9.40 0.00 0.00 3.02
2872 4282 5.071788 TCCCTCTGTCCCACAATATAACATC 59.928 44.000 0.00 0.00 0.00 3.06
2873 4283 4.991056 CCTCTGTCCCACAATATAACATCG 59.009 45.833 0.00 0.00 0.00 3.84
2874 4284 5.453339 CCTCTGTCCCACAATATAACATCGT 60.453 44.000 0.00 0.00 0.00 3.73
2875 4285 5.984725 TCTGTCCCACAATATAACATCGTT 58.015 37.500 0.00 0.00 0.00 3.85
2876 4286 6.411376 TCTGTCCCACAATATAACATCGTTT 58.589 36.000 0.00 0.00 0.00 3.60
2877 4287 6.882140 TCTGTCCCACAATATAACATCGTTTT 59.118 34.615 0.00 0.00 0.00 2.43
2878 4288 7.065324 TCTGTCCCACAATATAACATCGTTTTC 59.935 37.037 0.00 0.00 0.00 2.29
2957 4368 5.756195 TTACATATTGATTGAGCAGCCAC 57.244 39.130 0.00 0.00 0.00 5.01
2971 4382 2.555123 GCCACGAGCATTCCTTTCA 58.445 52.632 0.00 0.00 42.97 2.69
3298 4710 9.788960 GTATTCTTATGTCCATGGTTCTTTTTC 57.211 33.333 12.58 0.00 0.00 2.29
3299 4711 6.834168 TCTTATGTCCATGGTTCTTTTTCC 57.166 37.500 12.58 0.00 0.00 3.13
3360 4912 8.055279 TCAATAGAAGAACCATTGGTGAATTC 57.945 34.615 9.62 13.25 35.34 2.17
3469 5104 8.189119 TCTTTTAAAAGACCACAAATATGGCT 57.811 30.769 23.65 0.00 39.95 4.75
3752 5388 4.074526 TCCTCGTCTGCTGCTGGC 62.075 66.667 6.69 3.75 42.22 4.85
3782 5418 2.639065 ACTGTTGCGAAAGAACCTGAA 58.361 42.857 0.00 0.00 0.00 3.02
3915 5557 8.948631 TGATAGAAGTCTGCTTAGGTAAAATG 57.051 34.615 0.00 0.00 34.61 2.32
4063 5705 3.146847 GTTGTAAACTGCTGGCTAGGTT 58.853 45.455 0.00 0.00 45.32 3.50
4115 5757 1.083489 TATGTCTTTCCTTTGCCGCG 58.917 50.000 0.00 0.00 0.00 6.46
4251 5893 3.562176 GGCTATTACTGCCCATGCCTTAT 60.562 47.826 0.00 0.00 44.32 1.73
4256 5898 3.893326 ACTGCCCATGCCTTATTTTTC 57.107 42.857 0.00 0.00 36.33 2.29
4265 5908 6.460676 CCCATGCCTTATTTTTCTCACTGATC 60.461 42.308 0.00 0.00 0.00 2.92
4291 5934 9.185192 CTGAAACCTTGAGTGACAATTTTATTC 57.815 33.333 0.00 0.00 37.88 1.75
4520 6167 9.170734 CCTTTCTGTTTGAATCATGAGATCTTA 57.829 33.333 0.09 0.00 34.24 2.10
4809 6456 6.017026 GGGAGCTTGGCTATTAATCAACTTAC 60.017 42.308 0.00 0.00 39.88 2.34
5043 6690 6.889177 TCAATATTAGGATTGGTTGTCTGCAA 59.111 34.615 0.00 0.00 37.41 4.08
5067 6714 3.500448 TGTTCTTGAAGCACCACCATA 57.500 42.857 0.00 0.00 0.00 2.74
5131 6778 4.095483 GGATCAACTTACAATCTGCCTGTG 59.905 45.833 0.00 0.00 0.00 3.66
5481 7128 9.586732 TCACTATTTCTAAAATGGATATTGGGG 57.413 33.333 3.22 0.00 0.00 4.96
5496 7143 0.463620 TGGGGTTTTGCTCAGTTTGC 59.536 50.000 0.00 0.00 0.00 3.68
5511 7158 8.023128 TGCTCAGTTTGCTTTGTTCTAATAATC 58.977 33.333 0.00 0.00 0.00 1.75
5519 7166 5.672819 GCTTTGTTCTAATAATCGTTGCCGT 60.673 40.000 0.00 0.00 35.01 5.68
5913 7571 2.106511 AGGCTCTAGGTTCAAGCACAAA 59.893 45.455 3.12 0.00 37.78 2.83
5981 7639 8.083462 CACAAACGTTACCCTTATTTGGTAATT 58.917 33.333 0.00 0.00 46.84 1.40
5982 7640 8.640651 ACAAACGTTACCCTTATTTGGTAATTT 58.359 29.630 0.00 1.29 46.84 1.82
6150 7825 5.197451 CACTTGCCCCCACTTGTAATATAA 58.803 41.667 0.00 0.00 0.00 0.98
6193 7868 5.637006 TGTAACAACTGCAAACTTTCACT 57.363 34.783 0.00 0.00 0.00 3.41
6436 8114 6.640499 TGAAAATTTCCGAACTACTTGCATTG 59.360 34.615 3.00 0.00 0.00 2.82
6472 8150 1.545841 AGGCATGTAGTCACGAGTCA 58.454 50.000 0.00 0.00 0.00 3.41
6498 8176 8.484641 TTTGCATGTTTACTGAAATTTTGTCA 57.515 26.923 0.00 0.00 0.00 3.58
6624 8302 1.992557 AGAATCCTGGCTGTTAACCCA 59.007 47.619 2.48 3.29 0.00 4.51
6754 8434 7.041576 TGTCATGCTCTAGAAATGATATGTTGC 60.042 37.037 16.76 3.81 33.19 4.17
7086 8883 1.891811 TCGTTGTACATTCGGGTGGTA 59.108 47.619 16.81 0.00 0.00 3.25
7105 8902 1.153958 GCACCAAATCCGCTTCAGC 60.154 57.895 0.00 0.00 37.78 4.26
7174 8971 6.854496 TTATGCGATAATGTGACTAAACCC 57.146 37.500 0.00 0.00 0.00 4.11
7226 9060 1.077501 CATGAAGCGGACCCCACAT 60.078 57.895 0.00 0.00 0.00 3.21
7228 9062 0.180406 ATGAAGCGGACCCCACATAC 59.820 55.000 0.00 0.00 0.00 2.39
7246 9080 2.918712 ACGATTTAGGGCATCTCCAG 57.081 50.000 0.00 0.00 36.21 3.86
7252 9086 2.030262 GGGCATCTCCAGCGCTAG 59.970 66.667 10.99 1.56 41.20 3.42
7261 9095 0.107848 TCCAGCGCTAGCCCTTAAAC 60.108 55.000 10.99 0.00 46.67 2.01
7280 9114 1.820519 ACGGACATCACGTAGGCTTAA 59.179 47.619 0.00 0.00 43.60 1.85
7281 9115 2.231964 ACGGACATCACGTAGGCTTAAA 59.768 45.455 0.00 0.00 43.60 1.52
7282 9116 3.255725 CGGACATCACGTAGGCTTAAAA 58.744 45.455 0.00 0.00 0.00 1.52
7283 9117 3.869246 CGGACATCACGTAGGCTTAAAAT 59.131 43.478 0.00 0.00 0.00 1.82
7284 9118 4.331717 CGGACATCACGTAGGCTTAAAATT 59.668 41.667 0.00 0.00 0.00 1.82
7285 9119 5.163794 CGGACATCACGTAGGCTTAAAATTT 60.164 40.000 0.00 0.00 0.00 1.82
7287 9121 7.413219 CGGACATCACGTAGGCTTAAAATTTTA 60.413 37.037 6.54 6.54 0.00 1.52
7288 9122 7.695201 GGACATCACGTAGGCTTAAAATTTTAC 59.305 37.037 10.18 0.51 0.00 2.01
7289 9123 7.238571 ACATCACGTAGGCTTAAAATTTTACG 58.761 34.615 16.19 16.19 39.59 3.18
7290 9124 5.620467 TCACGTAGGCTTAAAATTTTACGC 58.380 37.500 24.01 24.01 37.87 4.42
7298 9146 4.667415 GCTTAAAATTTTACGCTCGTCCGT 60.667 41.667 24.49 8.05 44.62 4.69
7393 9243 8.031277 CAGATTTCTTAGCTAAATTTGCAAGGT 58.969 33.333 7.74 0.00 0.00 3.50
7464 9319 3.555139 CAGTTCTATTAGCTGCAGACTGC 59.445 47.826 20.43 20.86 45.29 4.40
7503 9358 9.535878 AATTAATAAAGCTTTCGGTTTTCAACA 57.464 25.926 16.57 0.00 40.88 3.33
7612 9471 2.044650 GCTTGAGCTGCCCATCCA 60.045 61.111 0.00 0.00 38.21 3.41
7613 9472 1.455217 GCTTGAGCTGCCCATCCAT 60.455 57.895 0.00 0.00 38.21 3.41
7614 9473 1.735376 GCTTGAGCTGCCCATCCATG 61.735 60.000 0.00 0.00 38.21 3.66
7616 9475 1.866483 TTGAGCTGCCCATCCATGGT 61.866 55.000 12.58 0.00 46.65 3.55
7617 9476 1.826921 GAGCTGCCCATCCATGGTG 60.827 63.158 12.58 9.37 46.65 4.17
7618 9477 2.836360 GCTGCCCATCCATGGTGG 60.836 66.667 20.51 20.51 46.65 4.61
7619 9478 2.836360 CTGCCCATCCATGGTGGC 60.836 66.667 25.91 25.91 46.65 5.01
7620 9479 3.665515 CTGCCCATCCATGGTGGCA 62.666 63.158 30.11 30.11 46.65 4.92
7621 9480 3.149648 GCCCATCCATGGTGGCAC 61.150 66.667 26.97 9.70 46.65 5.01
7622 9481 2.829914 CCCATCCATGGTGGCACG 60.830 66.667 21.52 9.55 46.65 5.34
7623 9482 2.045045 CCATCCATGGTGGCACGT 60.045 61.111 12.58 0.00 43.05 4.49
7624 9483 2.409055 CCATCCATGGTGGCACGTG 61.409 63.158 12.28 12.28 43.05 4.49
7625 9484 2.045045 ATCCATGGTGGCACGTGG 60.045 61.111 25.96 25.96 46.66 4.94
7626 9485 3.643595 ATCCATGGTGGCACGTGGG 62.644 63.158 29.01 21.44 45.59 4.61
7627 9486 4.343323 CCATGGTGGCACGTGGGA 62.343 66.667 24.84 4.10 42.58 4.37
7628 9487 2.282110 CATGGTGGCACGTGGGAA 60.282 61.111 18.88 0.00 0.00 3.97
7629 9488 2.034066 ATGGTGGCACGTGGGAAG 59.966 61.111 18.88 0.00 0.00 3.46
7630 9489 2.525124 ATGGTGGCACGTGGGAAGA 61.525 57.895 18.88 0.00 0.00 2.87
7631 9490 1.852157 ATGGTGGCACGTGGGAAGAT 61.852 55.000 18.88 0.00 0.00 2.40
7632 9491 2.040544 GGTGGCACGTGGGAAGATG 61.041 63.158 18.88 0.00 0.00 2.90
7633 9492 1.003839 GTGGCACGTGGGAAGATGA 60.004 57.895 18.88 0.00 0.00 2.92
7634 9493 1.021390 GTGGCACGTGGGAAGATGAG 61.021 60.000 18.88 0.00 0.00 2.90
7635 9494 1.191489 TGGCACGTGGGAAGATGAGA 61.191 55.000 18.88 0.00 0.00 3.27
7636 9495 0.460987 GGCACGTGGGAAGATGAGAG 60.461 60.000 18.88 0.00 0.00 3.20
7637 9496 0.460987 GCACGTGGGAAGATGAGAGG 60.461 60.000 18.88 0.00 0.00 3.69
7638 9497 0.460987 CACGTGGGAAGATGAGAGGC 60.461 60.000 7.95 0.00 0.00 4.70
7639 9498 1.227089 CGTGGGAAGATGAGAGGCG 60.227 63.158 0.00 0.00 0.00 5.52
7640 9499 1.144936 GTGGGAAGATGAGAGGCGG 59.855 63.158 0.00 0.00 0.00 6.13
7641 9500 1.001631 TGGGAAGATGAGAGGCGGA 59.998 57.895 0.00 0.00 0.00 5.54
7642 9501 0.617535 TGGGAAGATGAGAGGCGGAA 60.618 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.007608 GCAACGACCCAACTCCTATTC 58.992 52.381 0.00 0.00 0.00 1.75
1 2 1.674817 CGCAACGACCCAACTCCTATT 60.675 52.381 0.00 0.00 0.00 1.73
2 3 0.108329 CGCAACGACCCAACTCCTAT 60.108 55.000 0.00 0.00 0.00 2.57
3 4 1.180456 TCGCAACGACCCAACTCCTA 61.180 55.000 0.00 0.00 0.00 2.94
4 5 2.030562 CGCAACGACCCAACTCCT 59.969 61.111 0.00 0.00 0.00 3.69
5 6 2.027625 CTCGCAACGACCCAACTCC 61.028 63.158 0.00 0.00 0.00 3.85
6 7 2.027625 CCTCGCAACGACCCAACTC 61.028 63.158 0.00 0.00 0.00 3.01
7 8 2.030562 CCTCGCAACGACCCAACT 59.969 61.111 0.00 0.00 0.00 3.16
8 9 2.027625 CTCCTCGCAACGACCCAAC 61.028 63.158 0.00 0.00 0.00 3.77
9 10 2.154798 CTCTCCTCGCAACGACCCAA 62.155 60.000 0.00 0.00 0.00 4.12
10 11 2.599281 TCTCCTCGCAACGACCCA 60.599 61.111 0.00 0.00 0.00 4.51
11 12 2.182030 CTCTCCTCGCAACGACCC 59.818 66.667 0.00 0.00 0.00 4.46
12 13 1.153997 GACTCTCCTCGCAACGACC 60.154 63.158 0.00 0.00 0.00 4.79
13 14 1.153997 GGACTCTCCTCGCAACGAC 60.154 63.158 0.00 0.00 32.53 4.34
14 15 1.176619 TTGGACTCTCCTCGCAACGA 61.177 55.000 0.00 0.00 37.46 3.85
144 1318 1.543429 CCACACCACTTGAGGAGAACC 60.543 57.143 0.00 0.00 38.19 3.62
379 1553 1.256812 GAGTGTTTGGTGATTGGGGG 58.743 55.000 0.00 0.00 0.00 5.40
380 1554 0.881118 CGAGTGTTTGGTGATTGGGG 59.119 55.000 0.00 0.00 0.00 4.96
381 1555 1.535462 GACGAGTGTTTGGTGATTGGG 59.465 52.381 0.00 0.00 0.00 4.12
382 1556 2.494059 AGACGAGTGTTTGGTGATTGG 58.506 47.619 0.00 0.00 0.00 3.16
383 1557 4.556233 TCTAGACGAGTGTTTGGTGATTG 58.444 43.478 0.00 0.00 0.00 2.67
384 1558 4.866508 TCTAGACGAGTGTTTGGTGATT 57.133 40.909 0.00 0.00 0.00 2.57
385 1559 4.142138 GGATCTAGACGAGTGTTTGGTGAT 60.142 45.833 0.00 0.00 0.00 3.06
386 1560 3.192844 GGATCTAGACGAGTGTTTGGTGA 59.807 47.826 0.00 0.00 0.00 4.02
387 1561 3.056821 TGGATCTAGACGAGTGTTTGGTG 60.057 47.826 0.00 0.00 0.00 4.17
388 1562 3.162666 TGGATCTAGACGAGTGTTTGGT 58.837 45.455 0.00 0.00 0.00 3.67
389 1563 3.868757 TGGATCTAGACGAGTGTTTGG 57.131 47.619 0.00 0.00 0.00 3.28
1446 2851 5.820423 TGCAGCAGTTAAAGACAGAAGTTTA 59.180 36.000 0.00 0.00 0.00 2.01
1489 2894 8.579850 ACACTGCTCCTTGAATTCATTTAATA 57.420 30.769 9.40 0.00 0.00 0.98
1545 2950 9.371136 CAAAGTGTATAGAAATTAGACTGCAGA 57.629 33.333 23.35 0.00 0.00 4.26
1557 2962 9.587772 GATCTAACAGAGCAAAGTGTATAGAAA 57.412 33.333 0.00 0.00 29.54 2.52
1584 2989 8.565416 GCCACCAAGATATTAAATTACACCTAC 58.435 37.037 0.00 0.00 0.00 3.18
1595 3000 3.660970 TGGCAGCCACCAAGATATTAA 57.339 42.857 11.22 0.00 36.55 1.40
1877 3282 5.997746 ACGCATATTATTGGCTGAAGTACAT 59.002 36.000 0.00 0.00 0.00 2.29
1878 3283 5.364778 ACGCATATTATTGGCTGAAGTACA 58.635 37.500 0.00 0.00 0.00 2.90
1879 3284 5.924475 ACGCATATTATTGGCTGAAGTAC 57.076 39.130 0.00 0.00 0.00 2.73
1880 3285 8.503196 CATTAACGCATATTATTGGCTGAAGTA 58.497 33.333 0.00 0.00 0.00 2.24
2046 3455 3.618351 AGCCTTCTCAACAATCTCATGG 58.382 45.455 0.00 0.00 0.00 3.66
2098 3507 5.968528 ACCACAACAAAGTAACAGTGAAA 57.031 34.783 0.00 0.00 0.00 2.69
2101 3511 4.862018 CCAAACCACAACAAAGTAACAGTG 59.138 41.667 0.00 0.00 0.00 3.66
2386 3796 3.389983 TCGGGAGAAAAACTGAGGAAAGA 59.610 43.478 0.00 0.00 34.75 2.52
2597 4007 9.268282 TGAAACAGTACCTCTCCTCTAATTTAT 57.732 33.333 0.00 0.00 0.00 1.40
2721 4131 7.621832 TGCTCAAATGAAAAATAACAAGACG 57.378 32.000 0.00 0.00 0.00 4.18
2727 4137 8.330302 GGTATGCATGCTCAAATGAAAAATAAC 58.670 33.333 20.33 2.46 0.00 1.89
2872 4282 4.279659 AGCTAGCTTGAAAAACGAAAACG 58.720 39.130 12.68 0.00 0.00 3.60
2919 4330 9.837681 TCAATATGTAATCTAATACTCCCTCCA 57.162 33.333 0.00 0.00 0.00 3.86
3298 4710 6.425210 TTCTCTGAATGATACTATGGGTGG 57.575 41.667 0.00 0.00 0.00 4.61
3299 4711 6.370994 GCATTCTCTGAATGATACTATGGGTG 59.629 42.308 20.36 0.00 0.00 4.61
3390 4942 5.049474 GGCCAAATTCAACAAAAGTCATTCC 60.049 40.000 0.00 0.00 0.00 3.01
3530 5165 4.510571 ACACCTTGTATGGTATTTCGACC 58.489 43.478 0.00 0.00 38.45 4.79
3534 5169 7.807977 ATCATGACACCTTGTATGGTATTTC 57.192 36.000 0.00 0.00 38.45 2.17
3626 5261 4.828939 TGAAGCATCAAGTCAAGGACAAAT 59.171 37.500 0.00 0.00 34.60 2.32
3677 5313 4.418392 CAGCAGTGTATCTGAAAATTGGC 58.582 43.478 0.00 0.00 46.27 4.52
3782 5418 4.830600 ACCTCAATACAAAATTCACCGGTT 59.169 37.500 2.97 0.00 0.00 4.44
4063 5705 7.230510 AGCAAGATTGTACATAAACCAAGTGAA 59.769 33.333 0.00 0.00 0.00 3.18
4115 5757 2.549329 CCTGCAAGAAACAAAATTGGCC 59.451 45.455 0.00 0.00 34.07 5.36
4251 5893 6.828273 TCAAGGTTTCAGATCAGTGAGAAAAA 59.172 34.615 7.41 0.00 32.44 1.94
4256 5898 4.689812 CACTCAAGGTTTCAGATCAGTGAG 59.310 45.833 0.00 0.00 37.77 3.51
4265 5908 9.185192 GAATAAAATTGTCACTCAAGGTTTCAG 57.815 33.333 0.00 0.00 39.55 3.02
4291 5934 4.689071 TGTATAGCAACCTACAATGGACG 58.311 43.478 0.00 0.00 0.00 4.79
4488 6135 7.605449 TCATGATTCAAACAGAAAGGGATTTC 58.395 34.615 0.00 0.00 40.22 2.17
4520 6167 7.255730 GGGATTGCAGCAGTATTAGATTCAATT 60.256 37.037 0.00 0.00 0.00 2.32
4521 6168 6.208204 GGGATTGCAGCAGTATTAGATTCAAT 59.792 38.462 0.00 0.00 0.00 2.57
5043 6690 3.450457 TGGTGGTGCTTCAAGAACAAAAT 59.550 39.130 0.00 0.00 0.00 1.82
5131 6778 6.402442 GGCAAATCAATCAATGCAAGGTAAAC 60.402 38.462 0.00 0.00 40.51 2.01
5333 6980 4.046462 CACTTGATTCCACACTGCAAAAG 58.954 43.478 0.00 0.00 0.00 2.27
5480 7127 3.261580 ACAAAGCAAACTGAGCAAAACC 58.738 40.909 0.00 0.00 0.00 3.27
5481 7128 4.627035 AGAACAAAGCAAACTGAGCAAAAC 59.373 37.500 0.00 0.00 0.00 2.43
5548 7195 2.672961 TAATCACCTCTGCTGGTTCG 57.327 50.000 0.00 0.00 38.45 3.95
5599 7246 4.141711 ACCAAAGCTTGTGTAACTCTCTGA 60.142 41.667 0.00 0.00 38.04 3.27
5791 7440 5.277538 GCGTTTGGAATGGCTTCTAATCTAG 60.278 44.000 0.00 0.00 32.65 2.43
5853 7511 1.279271 ACTTGTCCAGGAAAGGGATCG 59.721 52.381 13.08 0.00 36.67 3.69
5855 7513 2.348472 TCACTTGTCCAGGAAAGGGAT 58.652 47.619 10.64 0.00 36.67 3.85
5984 7642 9.559732 AAGCATAATTAGCACATACATAAGACA 57.440 29.630 8.84 0.00 0.00 3.41
6103 7778 8.458843 GTGTATAAAATCACAGGCACATAACTT 58.541 33.333 0.00 0.00 35.04 2.66
6150 7825 9.410556 GTTACAAAATTCTTAAGCATCACACAT 57.589 29.630 0.00 0.00 0.00 3.21
6193 7868 0.118346 TTCCTGGGTTAGCTGGGAGA 59.882 55.000 0.00 0.00 0.00 3.71
6424 8102 6.300703 TGTACCCTTTTACAATGCAAGTAGT 58.699 36.000 0.00 0.00 0.00 2.73
6436 8114 5.650543 CATGCCTTTCATGTACCCTTTTAC 58.349 41.667 0.00 0.00 45.79 2.01
6459 8137 3.679980 ACATGCAAATGACTCGTGACTAC 59.320 43.478 0.00 0.00 0.00 2.73
6466 8144 5.281693 TCAGTAAACATGCAAATGACTCG 57.718 39.130 0.00 0.00 0.00 4.18
6467 8145 8.524870 AATTTCAGTAAACATGCAAATGACTC 57.475 30.769 0.00 0.00 0.00 3.36
6472 8150 9.107177 TGACAAAATTTCAGTAAACATGCAAAT 57.893 25.926 0.00 0.00 0.00 2.32
6583 8261 4.473520 CTCCGATGCCCTTGCCGT 62.474 66.667 0.00 0.00 36.33 5.68
6698 8376 3.994392 GTCTTCCGTTTGAATGTCTGCTA 59.006 43.478 0.00 0.00 31.06 3.49
6754 8434 2.276740 GGAAGGGGATGGCAGGTG 59.723 66.667 0.00 0.00 0.00 4.00
6853 8642 4.145807 ACCATGAAACGGTGGAAAATACA 58.854 39.130 0.00 0.00 38.86 2.29
6938 8727 3.916776 GCAAACAATAGCTGAGAGCAAAC 59.083 43.478 0.00 0.00 45.56 2.93
7086 8883 1.589716 GCTGAAGCGGATTTGGTGCT 61.590 55.000 0.00 0.00 41.60 4.40
7155 8952 5.353123 TCTTTGGGTTTAGTCACATTATCGC 59.647 40.000 0.00 0.00 0.00 4.58
7156 8953 6.594159 ACTCTTTGGGTTTAGTCACATTATCG 59.406 38.462 0.00 0.00 0.00 2.92
7203 9000 2.700773 GGGTCCGCTTCATGCCAAC 61.701 63.158 0.00 0.00 38.78 3.77
7216 9013 2.224450 CCCTAAATCGTATGTGGGGTCC 60.224 54.545 0.00 0.00 0.00 4.46
7218 9015 1.142262 GCCCTAAATCGTATGTGGGGT 59.858 52.381 7.83 0.00 35.41 4.95
7219 9016 1.142060 TGCCCTAAATCGTATGTGGGG 59.858 52.381 0.00 3.12 35.41 4.96
7220 9017 2.631160 TGCCCTAAATCGTATGTGGG 57.369 50.000 0.00 0.00 37.76 4.61
7223 9057 3.646162 TGGAGATGCCCTAAATCGTATGT 59.354 43.478 0.00 0.00 34.97 2.29
7226 9060 2.037251 GCTGGAGATGCCCTAAATCGTA 59.963 50.000 0.00 0.00 34.97 3.43
7228 9062 1.517242 GCTGGAGATGCCCTAAATCG 58.483 55.000 0.00 0.00 34.97 3.34
7246 9080 1.153509 TCCGTTTAAGGGCTAGCGC 60.154 57.895 23.33 23.33 0.00 5.92
7251 9085 1.674817 CGTGATGTCCGTTTAAGGGCT 60.675 52.381 0.00 0.00 36.69 5.19
7252 9086 0.725117 CGTGATGTCCGTTTAAGGGC 59.275 55.000 0.00 0.00 36.18 5.19
7261 9095 2.572191 TTAAGCCTACGTGATGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
7280 9114 1.461897 CCACGGACGAGCGTAAAATTT 59.538 47.619 0.00 0.00 0.00 1.82
7281 9115 1.073177 CCACGGACGAGCGTAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
7282 9116 0.244450 TCCACGGACGAGCGTAAAAT 59.756 50.000 0.00 0.00 0.00 1.82
7283 9117 0.664166 GTCCACGGACGAGCGTAAAA 60.664 55.000 0.00 0.00 35.30 1.52
7284 9118 1.081242 GTCCACGGACGAGCGTAAA 60.081 57.895 0.00 0.00 35.30 2.01
7285 9119 2.562912 GTCCACGGACGAGCGTAA 59.437 61.111 0.00 0.00 35.30 3.18
7393 9243 4.526262 CCAAACATTGGTTAGATGTTCCCA 59.474 41.667 3.28 0.00 44.55 4.37
7513 9372 1.099879 CCATGGCTGCCTGACTTAGC 61.100 60.000 21.03 0.00 36.74 3.09
7514 9373 0.465097 CCCATGGCTGCCTGACTTAG 60.465 60.000 21.03 1.63 0.00 2.18
7515 9374 1.609239 CCCATGGCTGCCTGACTTA 59.391 57.895 21.03 0.00 0.00 2.24
7595 9454 1.455217 ATGGATGGGCAGCTCAAGC 60.455 57.895 0.00 0.00 42.49 4.01
7596 9455 1.107538 CCATGGATGGGCAGCTCAAG 61.108 60.000 5.56 0.00 44.31 3.02
7597 9456 1.076559 CCATGGATGGGCAGCTCAA 60.077 57.895 5.56 0.00 44.31 3.02
7598 9457 2.599032 CCATGGATGGGCAGCTCA 59.401 61.111 5.56 0.00 44.31 4.26
7607 9466 2.409055 CCACGTGCCACCATGGATG 61.409 63.158 21.47 12.84 40.96 3.51
7608 9467 2.045045 CCACGTGCCACCATGGAT 60.045 61.111 21.47 0.00 40.96 3.41
7609 9468 4.343323 CCCACGTGCCACCATGGA 62.343 66.667 21.47 0.00 40.96 3.41
7610 9469 3.859118 TTCCCACGTGCCACCATGG 62.859 63.158 11.19 11.19 41.55 3.66
7611 9470 2.282110 TTCCCACGTGCCACCATG 60.282 61.111 10.91 0.00 0.00 3.66
7612 9471 1.852157 ATCTTCCCACGTGCCACCAT 61.852 55.000 10.91 0.00 0.00 3.55
7613 9472 2.525124 ATCTTCCCACGTGCCACCA 61.525 57.895 10.91 0.00 0.00 4.17
7614 9473 2.040544 CATCTTCCCACGTGCCACC 61.041 63.158 10.91 0.00 0.00 4.61
7615 9474 1.003839 TCATCTTCCCACGTGCCAC 60.004 57.895 10.91 0.00 0.00 5.01
7616 9475 1.191489 TCTCATCTTCCCACGTGCCA 61.191 55.000 10.91 0.00 0.00 4.92
7617 9476 0.460987 CTCTCATCTTCCCACGTGCC 60.461 60.000 10.91 0.00 0.00 5.01
7618 9477 0.460987 CCTCTCATCTTCCCACGTGC 60.461 60.000 10.91 0.00 0.00 5.34
7619 9478 0.460987 GCCTCTCATCTTCCCACGTG 60.461 60.000 9.08 9.08 0.00 4.49
7620 9479 1.901085 GCCTCTCATCTTCCCACGT 59.099 57.895 0.00 0.00 0.00 4.49
7621 9480 1.227089 CGCCTCTCATCTTCCCACG 60.227 63.158 0.00 0.00 0.00 4.94
7622 9481 1.144936 CCGCCTCTCATCTTCCCAC 59.855 63.158 0.00 0.00 0.00 4.61
7623 9482 0.617535 TTCCGCCTCTCATCTTCCCA 60.618 55.000 0.00 0.00 0.00 4.37
7624 9483 2.212327 TTCCGCCTCTCATCTTCCC 58.788 57.895 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.