Multiple sequence alignment - TraesCS4D01G118200

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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 TraesCS4D01G118200 chr4D 100.000 4843 0 0 1 4843 98882888 98887730 0.000000e+00 8944.0
1 TraesCS4D01G118200 chr4D 100.000 3824 0 0 5058 8881 98887945 98891768 0.000000e+00 7062.0
2 TraesCS4D01G118200 chr4D 85.180 2888 352 45 561 3418 98576064 98578905 0.000000e+00 2892.0
3 TraesCS4D01G118200 chr4D 85.833 120 13 2 6636 6752 447157320 447157438 3.370000e-24 124.0
4 TraesCS4D01G118200 chr4A 96.185 4849 139 16 1 4843 477067810 477063002 0.000000e+00 7888.0
5 TraesCS4D01G118200 chr4A 85.312 2628 322 34 817 3418 477313281 477310692 0.000000e+00 2656.0
6 TraesCS4D01G118200 chr4A 93.063 1629 68 19 7019 8632 477058560 477056962 0.000000e+00 2340.0
7 TraesCS4D01G118200 chr4A 90.766 1083 38 14 5995 7020 477059731 477058654 0.000000e+00 1389.0
8 TraesCS4D01G118200 chr4A 96.366 798 24 5 5216 6011 477060845 477060051 0.000000e+00 1308.0
9 TraesCS4D01G118200 chr4A 91.667 156 9 2 8628 8780 477056571 477056417 6.980000e-51 213.0
10 TraesCS4D01G118200 chr4A 98.837 86 0 1 5113 5198 477061815 477061731 1.540000e-32 152.0
11 TraesCS4D01G118200 chr4A 88.750 80 7 2 8781 8859 477056379 477056301 7.340000e-16 97.1
12 TraesCS4D01G118200 chr4A 97.561 41 1 0 5072 5112 477062109 477062069 4.450000e-08 71.3
13 TraesCS4D01G118200 chr4B 95.390 4816 166 27 37 4843 140700946 140705714 0.000000e+00 7613.0
14 TraesCS4D01G118200 chr4B 93.084 2270 61 22 5058 7275 140706473 140708698 0.000000e+00 3234.0
15 TraesCS4D01G118200 chr4B 84.522 2888 371 45 561 3418 140594960 140592119 0.000000e+00 2787.0
16 TraesCS4D01G118200 chr4B 93.794 1289 52 13 7496 8779 140709991 140711256 0.000000e+00 1912.0
17 TraesCS4D01G118200 chr4B 97.500 200 4 1 7308 7507 140708699 140708897 3.070000e-89 340.0
18 TraesCS4D01G118200 chr4B 80.672 119 20 3 6623 6738 5733999 5734117 1.230000e-13 89.8
19 TraesCS4D01G118200 chr7D 90.794 315 26 3 5215 5529 274697745 274697434 1.380000e-112 418.0
20 TraesCS4D01G118200 chr7D 88.288 111 8 5 4075 4184 426558989 426558883 2.600000e-25 128.0
21 TraesCS4D01G118200 chr1B 92.308 286 18 1 5240 5525 250417305 250417586 3.860000e-108 403.0
22 TraesCS4D01G118200 chr1B 93.407 91 4 2 4074 4163 279914450 279914361 5.590000e-27 134.0
23 TraesCS4D01G118200 chr1B 89.899 99 8 2 4075 4172 188791858 188791955 9.360000e-25 126.0
24 TraesCS4D01G118200 chr1A 92.308 286 17 2 5240 5525 171462710 171462430 1.390000e-107 401.0
25 TraesCS4D01G118200 chr1A 91.489 94 7 1 4075 4167 91047547 91047454 2.600000e-25 128.0
26 TraesCS4D01G118200 chr7A 89.557 316 29 4 5215 5529 307960207 307959895 1.800000e-106 398.0
27 TraesCS4D01G118200 chr3D 90.508 295 28 0 5229 5523 469481231 469481525 3.010000e-104 390.0
28 TraesCS4D01G118200 chr3D 88.660 97 8 3 6658 6753 312750108 312750014 2.030000e-21 115.0
29 TraesCS4D01G118200 chr2D 90.301 299 27 2 5224 5522 373676438 373676734 3.010000e-104 390.0
30 TraesCS4D01G118200 chr2D 89.216 102 8 3 4076 4177 341665947 341665849 3.370000e-24 124.0
31 TraesCS4D01G118200 chr5D 90.066 302 25 5 5225 5522 287426638 287426938 3.890000e-103 387.0
32 TraesCS4D01G118200 chr5D 90.110 91 7 2 6662 6752 448923428 448923516 5.630000e-22 117.0
33 TraesCS4D01G118200 chr5D 89.535 86 7 2 6658 6742 434565445 434565361 3.390000e-19 108.0
34 TraesCS4D01G118200 chr5A 94.505 91 4 1 4077 4166 698639638 698639728 1.200000e-28 139.0
35 TraesCS4D01G118200 chr5A 95.294 85 4 0 6673 6757 46575497 46575413 1.560000e-27 135.0
36 TraesCS4D01G118200 chr7B 84.559 136 17 2 6623 6755 147722372 147722506 2.010000e-26 132.0
37 TraesCS4D01G118200 chr6B 91.667 96 7 1 4073 4167 55999760 55999855 2.010000e-26 132.0
38 TraesCS4D01G118200 chr3B 90.526 95 9 0 6659 6753 786077179 786077273 9.360000e-25 126.0
39 TraesCS4D01G118200 chr2B 82.927 123 18 2 6623 6742 587480026 587480148 3.390000e-19 108.0
40 TraesCS4D01G118200 chr6D 88.372 86 8 2 6658 6742 224607 224523 1.580000e-17 102.0
41 TraesCS4D01G118200 chr6D 88.372 86 8 2 6658 6742 2899089 2899005 1.580000e-17 102.0


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 TraesCS4D01G118200 chr4D 98882888 98891768 8880 False 8003.00 8944 100.000000 1 8881 2 chr4D.!!$F3 8880
1 TraesCS4D01G118200 chr4D 98576064 98578905 2841 False 2892.00 2892 85.180000 561 3418 1 chr4D.!!$F1 2857
2 TraesCS4D01G118200 chr4A 477310692 477313281 2589 True 2656.00 2656 85.312000 817 3418 1 chr4A.!!$R1 2601
3 TraesCS4D01G118200 chr4A 477056301 477067810 11509 True 1682.30 7888 94.149375 1 8859 8 chr4A.!!$R2 8858
4 TraesCS4D01G118200 chr4B 140700946 140711256 10310 False 3274.75 7613 94.942000 37 8779 4 chr4B.!!$F2 8742
5 TraesCS4D01G118200 chr4B 140592119 140594960 2841 True 2787.00 2787 84.522000 561 3418 1 chr4B.!!$R1 2857

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
611 624 0.537371 CCGACCAAACCAAAGAGGCT 60.537 55.000 0.00 0.00 43.14 4.58 F
1500 1534 2.031163 GACCTGCAGTGTTCCGCT 59.969 61.111 13.81 0.00 0.00 5.52 F
2283 2323 0.253044 GAGATACCCAACCTGCAGCA 59.747 55.000 8.66 0.00 0.00 4.41 F
3462 3509 0.877071 ACATTTTCTGCAGCGGTCAG 59.123 50.000 9.47 7.48 0.00 3.51 F
4560 4608 1.073897 GTGGTGGGCAGAAGAGCTT 59.926 57.895 0.00 0.00 34.17 3.74 F
4798 4846 1.608025 CGTTGGTGTGCATGTAGGACT 60.608 52.381 0.00 0.00 39.64 3.85 F
6317 8495 0.183014 CAGCTTGCATCCCTCCAGAT 59.817 55.000 0.00 0.00 0.00 2.90 F
6325 8503 0.975135 ATCCCTCCAGATCTCGCATG 59.025 55.000 0.00 0.00 0.00 4.06 F
7103 9439 3.013921 GTGAGAAAGGTTGGTGTGTTCA 58.986 45.455 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2062 1.572085 CTGTCCCAACTCTTGCTGCG 61.572 60.000 0.00 0.0 0.0 5.18 R
3245 3292 1.467920 CTGGAAGGGTGATTTCTGCC 58.532 55.000 0.00 0.0 0.0 4.85 R
4180 4228 1.142667 TGTTCCAGATGCCAGTTGACA 59.857 47.619 0.00 0.0 0.0 3.58 R
4628 4676 1.144298 CGTTATAAAGGGGGAAGGGGG 59.856 57.143 0.00 0.0 0.0 5.40 R
6167 8338 0.706433 ATGGTTGATTGGGTGGCTCT 59.294 50.000 0.00 0.0 0.0 4.09 R
6709 8932 1.245732 AGCGTGTAGAGAACCGTCTT 58.754 50.000 0.00 0.0 32.8 3.01 R
7142 9478 0.387565 AAGATTGCCGTGCCGTTTTT 59.612 45.000 0.00 0.0 0.0 1.94 R
7582 11025 0.802494 GGTAACATGCCAACACTCGG 59.198 55.000 0.00 0.0 0.0 4.63 R
8413 11870 0.606401 CACACGCCCAGATTTGGTCT 60.606 55.000 0.96 0.0 43.4 3.85 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
54 55 3.059166 GGGCTGTGCACATAAAAACTTG 58.941 45.455 22.00 6.27 0.00 3.16
55 56 2.476241 GGCTGTGCACATAAAAACTTGC 59.524 45.455 22.00 16.17 35.45 4.01
286 288 8.576442 CCAACTTCAATTAATGAGTTGTTACCT 58.424 33.333 23.74 1.69 41.04 3.08
340 342 2.292267 TCGTCCATCGTAAGGTAGACC 58.708 52.381 0.00 0.00 40.80 3.85
354 356 3.166679 GGTAGACCAGTGACTTCTCCTT 58.833 50.000 0.00 0.00 35.64 3.36
425 427 1.741327 TTATGGACCGGCGGCTACTC 61.741 60.000 28.71 16.19 0.00 2.59
431 433 3.227276 CGGCGGCTACTCCCTCAT 61.227 66.667 7.61 0.00 0.00 2.90
439 441 4.246458 CGGCTACTCCCTCATATAAAAGC 58.754 47.826 0.00 0.00 0.00 3.51
445 447 8.722394 GCTACTCCCTCATATAAAAGCAATTAC 58.278 37.037 0.00 0.00 0.00 1.89
472 475 3.991773 CGTTCGGAGGTAGAAAAATGTCA 59.008 43.478 0.00 0.00 0.00 3.58
484 487 7.494952 GGTAGAAAAATGTCACTATCTGGTACC 59.505 40.741 4.43 4.43 0.00 3.34
485 488 7.016153 AGAAAAATGTCACTATCTGGTACCA 57.984 36.000 15.39 15.39 0.00 3.25
486 489 7.633789 AGAAAAATGTCACTATCTGGTACCAT 58.366 34.615 16.75 3.80 0.00 3.55
487 490 8.109634 AGAAAAATGTCACTATCTGGTACCATT 58.890 33.333 16.75 8.90 0.00 3.16
488 491 8.650143 AAAAATGTCACTATCTGGTACCATTT 57.350 30.769 16.75 8.51 33.84 2.32
548 556 8.641541 AGCAATCCAAAAATGACTAGAGAAAAA 58.358 29.630 0.00 0.00 0.00 1.94
569 578 4.160736 AGAGGCAAAAATGACGCTTTAC 57.839 40.909 0.00 0.00 0.00 2.01
611 624 0.537371 CCGACCAAACCAAAGAGGCT 60.537 55.000 0.00 0.00 43.14 4.58
621 634 3.103742 ACCAAAGAGGCTAGAGGAAGAG 58.896 50.000 0.00 0.00 43.14 2.85
1500 1534 2.031163 GACCTGCAGTGTTCCGCT 59.969 61.111 13.81 0.00 0.00 5.52
1878 1912 2.632512 GGAGAAGGATGCTAGGAAGGAG 59.367 54.545 0.00 0.00 0.00 3.69
2028 2062 1.608717 ATGAGACAGACAGGCGGGAC 61.609 60.000 0.00 0.00 0.00 4.46
2283 2323 0.253044 GAGATACCCAACCTGCAGCA 59.747 55.000 8.66 0.00 0.00 4.41
2434 2481 3.605634 TCACCCAATTGACCATCTTACG 58.394 45.455 7.12 0.00 0.00 3.18
2461 2508 9.593134 TTTAATTATTTGTGTTCTGCTTTGTGT 57.407 25.926 0.00 0.00 0.00 3.72
2550 2597 1.905354 AGCTGCAGTTTCCCCTTGC 60.905 57.895 16.64 0.00 38.30 4.01
2634 2681 3.375782 AGCAGCGCTCAAAATTTTCTT 57.624 38.095 7.13 0.00 30.62 2.52
3245 3292 4.033932 TCTGAATGACAACGATTTATGGCG 59.966 41.667 0.00 0.00 0.00 5.69
3267 3314 2.089980 CAGAAATCACCCTTCCAGCAG 58.910 52.381 0.00 0.00 0.00 4.24
3330 3377 7.530010 ACATGTCAGAAAATGCTATACACAAC 58.470 34.615 0.00 0.00 0.00 3.32
3462 3509 0.877071 ACATTTTCTGCAGCGGTCAG 59.123 50.000 9.47 7.48 0.00 3.51
3473 3520 2.699954 CAGCGGTCAGGTTTTGTATCT 58.300 47.619 0.00 0.00 0.00 1.98
3522 3569 1.173913 GCTTAAAACTCGGGCCATGT 58.826 50.000 4.39 0.00 0.00 3.21
3752 3800 7.596749 TTGAAGCTTACACTTTATAGACAGC 57.403 36.000 0.00 0.00 0.00 4.40
3859 3907 3.538591 TCTGCAATATTCTGTGCTGGAG 58.461 45.455 4.71 0.00 41.48 3.86
3864 3912 4.763073 CAATATTCTGTGCTGGAGTGAGA 58.237 43.478 0.00 0.00 0.00 3.27
3865 3913 4.669206 ATATTCTGTGCTGGAGTGAGAG 57.331 45.455 0.00 0.00 0.00 3.20
4071 4119 7.681903 ACGAATCGTCATACCATTTTAACTTC 58.318 34.615 0.96 0.00 33.69 3.01
4092 4140 6.325286 ACTTCAGAAATATACTCCCTCTGTCC 59.675 42.308 0.00 0.00 35.93 4.02
4110 4158 4.901868 TGTCCCATAATATAAGGGCGTTC 58.098 43.478 0.00 0.00 42.52 3.95
4166 4214 4.996788 TTATGGAACGGAGGAGTAGTTC 57.003 45.455 0.00 0.00 42.36 3.01
4190 4238 8.677148 TCCTTATTTCTATATTGTCAACTGGC 57.323 34.615 0.00 0.00 0.00 4.85
4307 4355 4.447616 CCACAAATGGCAGATAGGGGAATA 60.448 45.833 0.00 0.00 39.82 1.75
4407 4455 9.155975 AGTTTAGTCTACAGCATGAAATACAAG 57.844 33.333 0.00 0.00 39.69 3.16
4479 4527 4.367450 ACATGGTGTTGTGTTAATGCAAC 58.633 39.130 14.37 14.37 43.60 4.17
4501 4549 5.748592 ACGAATTTAGTGCACTTTGACTTC 58.251 37.500 27.06 17.92 0.00 3.01
4513 4561 4.518211 CACTTTGACTTCTCAATTCCAGCT 59.482 41.667 0.00 0.00 36.26 4.24
4560 4608 1.073897 GTGGTGGGCAGAAGAGCTT 59.926 57.895 0.00 0.00 34.17 3.74
4596 4644 3.377172 ACTGTCCTGTTTTGTTGCTACAC 59.623 43.478 0.00 0.00 32.98 2.90
4623 4671 4.799419 TTAATGCGTTTTATAGCGACCC 57.201 40.909 0.00 0.00 35.87 4.46
4691 4739 4.081642 TGACAACATAGACCAACCTAGCTC 60.082 45.833 0.00 0.00 0.00 4.09
4798 4846 1.608025 CGTTGGTGTGCATGTAGGACT 60.608 52.381 0.00 0.00 39.64 3.85
5488 7322 8.337118 TCCTACAAAATTCCTATCCTTCAGAT 57.663 34.615 0.00 0.00 39.15 2.90
5769 7603 6.151144 GGCGATTGGCTACCTTCATATATTTT 59.849 38.462 0.00 0.00 42.94 1.82
5771 7605 7.094805 GCGATTGGCTACCTTCATATATTTTGA 60.095 37.037 0.00 0.00 39.11 2.69
5909 7743 4.685628 CACCAAAATGTGCACATTCTTACC 59.314 41.667 37.80 1.64 45.06 2.85
5973 7807 3.476552 CTGTCCAACTGGCAGAAACTTA 58.523 45.455 23.66 2.38 39.83 2.24
6048 8219 3.377172 GCTAGCCAAAATTTTAGCCGAGA 59.623 43.478 16.26 1.34 34.00 4.04
6126 8297 3.126879 CGCATGGAGCCGCTGAAA 61.127 61.111 0.00 0.00 41.38 2.69
6167 8338 2.556559 GGAAACCCTTAGTTCCATGCCA 60.557 50.000 0.00 0.00 37.88 4.92
6221 8399 5.643176 TGATAACATATGCATCCCATTGGT 58.357 37.500 0.19 0.00 35.34 3.67
6229 8407 3.439154 TGCATCCCATTGGTTGTTATGT 58.561 40.909 1.20 0.00 34.38 2.29
6237 8415 4.644234 CCATTGGTTGTTATGTATGCCTGA 59.356 41.667 0.00 0.00 0.00 3.86
6280 8458 1.138266 TGCGATCCCTACCTAGCAAAC 59.862 52.381 0.00 0.00 0.00 2.93
6317 8495 0.183014 CAGCTTGCATCCCTCCAGAT 59.817 55.000 0.00 0.00 0.00 2.90
6325 8503 0.975135 ATCCCTCCAGATCTCGCATG 59.025 55.000 0.00 0.00 0.00 4.06
6480 8687 6.206634 CCTTCTGTTGAAAATTGCTGGTAGTA 59.793 38.462 0.00 0.00 0.00 1.82
6709 8932 9.448438 AGACATTGTACACTGATTTATTTAGCA 57.552 29.630 19.02 0.00 0.00 3.49
6853 9077 3.500448 TTCACTTTGTGTAGGGCATGA 57.500 42.857 0.00 0.00 34.79 3.07
7091 9427 4.826274 TGGTAGGAATCTGTGAGAAAGG 57.174 45.455 0.00 0.00 0.00 3.11
7103 9439 3.013921 GTGAGAAAGGTTGGTGTGTTCA 58.986 45.455 0.00 0.00 0.00 3.18
7104 9440 3.632145 GTGAGAAAGGTTGGTGTGTTCAT 59.368 43.478 0.00 0.00 0.00 2.57
7105 9441 4.097892 GTGAGAAAGGTTGGTGTGTTCATT 59.902 41.667 0.00 0.00 0.00 2.57
7131 9467 7.251321 TGGCAACCAAGTTCCAAATAATTAT 57.749 32.000 0.00 0.00 0.00 1.28
7256 9594 6.488006 ACAGTAACTTCTGCATTCTTGAATGT 59.512 34.615 20.23 5.71 38.84 2.71
7292 9630 7.801752 GGTGCAAGCTAGATAATTTGATCTAC 58.198 38.462 0.00 0.00 37.38 2.59
7479 9817 4.678622 CTGCAATTTCATAAGATGCTGCA 58.321 39.130 4.13 4.13 37.86 4.41
7530 10973 6.352516 TGTTTAAAATGTTGGTCTTGGCAAT 58.647 32.000 0.00 0.00 0.00 3.56
7545 10988 6.091441 GTCTTGGCAATGAGTAACAGACTTAG 59.909 42.308 0.00 0.00 39.06 2.18
7588 11031 1.504359 TCCGTTAAAGTTGCCGAGTG 58.496 50.000 0.00 0.00 0.00 3.51
7781 11225 2.923020 GCATGCTGGTTTATTTCCAACG 59.077 45.455 11.37 0.00 34.35 4.10
7793 11237 3.311486 TTTCCAACGAATCCAAATGCC 57.689 42.857 0.00 0.00 0.00 4.40
7889 11333 3.634910 GTCTAGGGAGTTGAGGAGACATC 59.365 52.174 0.00 0.00 34.71 3.06
7977 11421 0.596082 ACCTGTTAACATTGTGCGCC 59.404 50.000 9.13 0.00 0.00 6.53
8049 11493 2.676632 TGGTGGATTCAATGCAATGC 57.323 45.000 0.00 0.00 30.45 3.56
8050 11494 1.900486 TGGTGGATTCAATGCAATGCA 59.100 42.857 11.44 11.44 44.86 3.96
8051 11495 2.302157 TGGTGGATTCAATGCAATGCAA 59.698 40.909 13.45 0.00 43.62 4.08
8052 11496 3.055021 TGGTGGATTCAATGCAATGCAAT 60.055 39.130 13.45 0.00 43.62 3.56
8053 11497 4.161754 TGGTGGATTCAATGCAATGCAATA 59.838 37.500 13.45 0.00 43.62 1.90
8054 11498 5.163290 TGGTGGATTCAATGCAATGCAATAT 60.163 36.000 13.45 3.19 43.62 1.28
8055 11499 5.178623 GGTGGATTCAATGCAATGCAATATG 59.821 40.000 13.45 12.06 43.62 1.78
8131 11580 3.434309 TGAGTGACCAGTGAGATCATCA 58.566 45.455 0.00 0.00 34.79 3.07
8211 11663 5.239306 TGCTTGGTTGAACACTGAATCTTAG 59.761 40.000 0.00 0.00 0.00 2.18
8212 11664 5.470098 GCTTGGTTGAACACTGAATCTTAGA 59.530 40.000 0.00 0.00 0.00 2.10
8214 11666 7.334421 GCTTGGTTGAACACTGAATCTTAGATA 59.666 37.037 0.00 0.00 0.00 1.98
8215 11667 8.777865 TTGGTTGAACACTGAATCTTAGATAG 57.222 34.615 0.00 0.00 0.00 2.08
8413 11870 1.136695 CAGCTTGGTTGACAAAGGCAA 59.863 47.619 0.75 0.00 38.91 4.52
8453 11910 1.086696 GCGAAAAGTGAGCAGCCATA 58.913 50.000 0.00 0.00 0.00 2.74
8514 11971 4.495422 CGGCTGCCTAACTCGATTAATAT 58.505 43.478 17.92 0.00 0.00 1.28
8517 11974 6.109359 GGCTGCCTAACTCGATTAATATCAT 58.891 40.000 12.43 0.00 0.00 2.45
8600 12062 0.869880 GTCCGTTTGGTTGTTGCTGC 60.870 55.000 0.00 0.00 36.30 5.25
8641 12498 0.597118 TTTGACTTGGTTGCGCATGC 60.597 50.000 12.75 7.91 43.20 4.06
8666 12523 2.103094 TGAAGAATGGGCAGATACTCCG 59.897 50.000 0.00 0.00 0.00 4.63
8694 12551 5.369409 GGCCATCCCTTTTTACTACTACT 57.631 43.478 0.00 0.00 0.00 2.57
8740 12600 1.130054 ATCGGGCATGCATCTACCCT 61.130 55.000 21.36 6.25 40.45 4.34
8750 12610 4.336889 TGCATCTACCCTACTTACATGC 57.663 45.455 0.00 0.00 36.51 4.06
8817 12714 7.859009 CCCTTAGGATATGGACATTGTCCTTTT 60.859 40.741 30.71 21.40 44.16 2.27
8828 12725 7.724305 GACATTGTCCTTTTGTAGTGACTTA 57.276 36.000 5.44 0.00 0.00 2.24
8829 12726 8.324163 GACATTGTCCTTTTGTAGTGACTTAT 57.676 34.615 5.44 0.00 0.00 1.73
8831 12728 8.567948 ACATTGTCCTTTTGTAGTGACTTATTG 58.432 33.333 0.00 0.00 0.00 1.90
8832 12729 8.783093 CATTGTCCTTTTGTAGTGACTTATTGA 58.217 33.333 0.00 0.00 0.00 2.57
8833 12730 7.962964 TGTCCTTTTGTAGTGACTTATTGAG 57.037 36.000 0.00 0.00 0.00 3.02
8834 12731 7.732025 TGTCCTTTTGTAGTGACTTATTGAGA 58.268 34.615 0.00 0.00 0.00 3.27
8835 12732 7.656137 TGTCCTTTTGTAGTGACTTATTGAGAC 59.344 37.037 0.00 0.00 0.00 3.36
8837 12734 7.016268 TCCTTTTGTAGTGACTTATTGAGACCT 59.984 37.037 0.00 0.00 0.00 3.85
8838 12735 8.311836 CCTTTTGTAGTGACTTATTGAGACCTA 58.688 37.037 0.00 0.00 0.00 3.08
8839 12736 9.141400 CTTTTGTAGTGACTTATTGAGACCTAC 57.859 37.037 0.00 0.00 31.42 3.18
8840 12737 8.418597 TTTGTAGTGACTTATTGAGACCTACT 57.581 34.615 0.00 0.00 31.71 2.57
8844 12741 5.422650 AGTGACTTATTGAGACCTACTTCCC 59.577 44.000 0.00 0.00 0.00 3.97
8848 12745 7.676893 TGACTTATTGAGACCTACTTCCCTTTA 59.323 37.037 0.00 0.00 0.00 1.85
8855 12752 8.674925 TGAGACCTACTTCCCTTTATAAAGAA 57.325 34.615 23.95 11.99 38.28 2.52
8864 12761 9.682465 ACTTCCCTTTATAAAGAAATACTCCAC 57.318 33.333 23.95 0.00 38.28 4.02
8865 12762 9.121658 CTTCCCTTTATAAAGAAATACTCCACC 57.878 37.037 23.95 0.00 38.28 4.61
8866 12763 7.580007 TCCCTTTATAAAGAAATACTCCACCC 58.420 38.462 23.95 0.00 38.28 4.61
8867 12764 6.485648 CCCTTTATAAAGAAATACTCCACCCG 59.514 42.308 23.95 4.52 38.28 5.28
8868 12765 7.052248 CCTTTATAAAGAAATACTCCACCCGT 58.948 38.462 23.95 0.00 38.28 5.28
8869 12766 7.555195 CCTTTATAAAGAAATACTCCACCCGTT 59.445 37.037 23.95 0.00 38.28 4.44
8870 12767 8.866970 TTTATAAAGAAATACTCCACCCGTTT 57.133 30.769 0.00 0.00 0.00 3.60
8871 12768 6.997239 ATAAAGAAATACTCCACCCGTTTC 57.003 37.500 0.00 0.00 0.00 2.78
8872 12769 4.360951 AAGAAATACTCCACCCGTTTCA 57.639 40.909 0.00 0.00 32.66 2.69
8873 12770 4.360951 AGAAATACTCCACCCGTTTCAA 57.639 40.909 0.00 0.00 32.66 2.69
8874 12771 4.721132 AGAAATACTCCACCCGTTTCAAA 58.279 39.130 0.00 0.00 32.66 2.69
8875 12772 5.134661 AGAAATACTCCACCCGTTTCAAAA 58.865 37.500 0.00 0.00 32.66 2.44
8876 12773 5.773176 AGAAATACTCCACCCGTTTCAAAAT 59.227 36.000 0.00 0.00 32.66 1.82
8877 12774 6.943718 AGAAATACTCCACCCGTTTCAAAATA 59.056 34.615 0.00 0.00 32.66 1.40
8878 12775 6.753107 AATACTCCACCCGTTTCAAAATAG 57.247 37.500 0.00 0.00 0.00 1.73
8879 12776 4.360951 ACTCCACCCGTTTCAAAATAGA 57.639 40.909 0.00 0.00 0.00 1.98
8880 12777 4.918588 ACTCCACCCGTTTCAAAATAGAT 58.081 39.130 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.661437 TCTCGGGGATTCATTTATATTCACAAG 59.339 37.037 0.00 0.00 0.00 3.16
90 91 7.513856 TCTCGGGGATTCATTTATATTCACAA 58.486 34.615 0.00 0.00 0.00 3.33
92 93 7.979444 TTCTCGGGGATTCATTTATATTCAC 57.021 36.000 0.00 0.00 0.00 3.18
231 233 3.996150 ACTCTTCCACATGCAAGTTTG 57.004 42.857 0.00 0.00 0.00 2.93
340 342 3.405831 TGCATGAAAGGAGAAGTCACTG 58.594 45.455 0.00 0.00 0.00 3.66
354 356 5.065859 CGGTCCATAATTACTGTTGCATGAA 59.934 40.000 0.00 0.00 0.00 2.57
383 385 9.739276 ATAATTACTTTTGTGTGAGAGATGGAA 57.261 29.630 0.00 0.00 0.00 3.53
385 387 8.400947 CCATAATTACTTTTGTGTGAGAGATGG 58.599 37.037 0.00 0.00 0.00 3.51
425 427 8.017373 CGATGTGTAATTGCTTTTATATGAGGG 58.983 37.037 0.00 0.00 0.00 4.30
431 433 7.278203 TCCGAACGATGTGTAATTGCTTTTATA 59.722 33.333 0.00 0.00 0.00 0.98
439 441 3.259064 ACCTCCGAACGATGTGTAATTG 58.741 45.455 0.00 0.00 0.00 2.32
445 447 2.933495 TTCTACCTCCGAACGATGTG 57.067 50.000 0.00 0.00 0.00 3.21
548 556 3.364964 CGTAAAGCGTCATTTTTGCCTCT 60.365 43.478 0.00 0.00 35.54 3.69
569 578 0.608308 GGGGAGAAGGGAAAACCACG 60.608 60.000 0.00 0.00 43.89 4.94
1500 1534 4.270834 AGAAGCCTGAGTACGAGTTATCA 58.729 43.478 0.00 0.00 0.00 2.15
1581 1615 2.304761 GTCCACTGATGACCCAAACCTA 59.695 50.000 0.00 0.00 0.00 3.08
2028 2062 1.572085 CTGTCCCAACTCTTGCTGCG 61.572 60.000 0.00 0.00 0.00 5.18
2199 2233 4.074970 CCTTGTTAGCTTGATGAACAGGT 58.925 43.478 0.00 0.00 34.72 4.00
2434 2481 9.848172 CACAAAGCAGAACACAAATAATTAAAC 57.152 29.630 0.00 0.00 0.00 2.01
2461 2508 4.165180 TGCCTGCATATTTGGACTAACCTA 59.835 41.667 0.00 0.00 39.86 3.08
2550 2597 1.656652 CTGAAGCAGTAACATCGGGG 58.343 55.000 0.00 0.00 0.00 5.73
3245 3292 1.467920 CTGGAAGGGTGATTTCTGCC 58.532 55.000 0.00 0.00 0.00 4.85
3267 3314 5.982516 CAGACTATCTGTATCAAGAGGCAAC 59.017 44.000 0.00 0.00 39.58 4.17
3330 3377 2.084546 GGAGATCCAAAACCCAAGTCG 58.915 52.381 0.00 0.00 35.64 4.18
3462 3509 9.535878 TCAAACAATTGGTAAAGATACAAAACC 57.464 29.630 10.83 0.00 37.15 3.27
3522 3569 6.647334 TCAGGTGATTATTCTTTTGCAACA 57.353 33.333 0.00 0.00 0.00 3.33
3859 3907 5.294306 TCACAAACAACAAGATGACTCTCAC 59.706 40.000 0.00 0.00 0.00 3.51
4071 4119 4.901849 TGGGACAGAGGGAGTATATTTCTG 59.098 45.833 0.00 0.00 40.73 3.02
4088 4136 4.263156 GGAACGCCCTTATATTATGGGACA 60.263 45.833 9.14 0.00 43.93 4.02
4092 4140 4.935808 GTCAGGAACGCCCTTATATTATGG 59.064 45.833 0.00 0.00 44.85 2.74
4166 4214 8.450578 TGCCAGTTGACAATATAGAAATAAGG 57.549 34.615 0.00 0.00 0.00 2.69
4180 4228 1.142667 TGTTCCAGATGCCAGTTGACA 59.857 47.619 0.00 0.00 0.00 3.58
4479 4527 5.990408 AGAAGTCAAAGTGCACTAAATTCG 58.010 37.500 22.01 5.32 0.00 3.34
4501 4549 3.192844 AGAATGCACAAGCTGGAATTGAG 59.807 43.478 0.00 0.00 42.74 3.02
4513 4561 3.441222 CAGATAAGCCACAGAATGCACAA 59.559 43.478 0.00 0.00 42.53 3.33
4560 4608 5.925509 ACAGGACAGTTTTAGCTTCAAGTA 58.074 37.500 0.00 0.00 0.00 2.24
4573 4621 4.013728 TGTAGCAACAAAACAGGACAGTT 58.986 39.130 0.00 0.00 30.91 3.16
4586 4634 5.980116 ACGCATTAAAAATTGTGTAGCAACA 59.020 32.000 0.00 0.00 40.28 3.33
4596 4644 8.047859 GGTCGCTATAAAACGCATTAAAAATTG 58.952 33.333 0.00 0.00 0.00 2.32
4628 4676 1.144298 CGTTATAAAGGGGGAAGGGGG 59.856 57.143 0.00 0.00 0.00 5.40
4629 4677 1.478105 GCGTTATAAAGGGGGAAGGGG 60.478 57.143 0.52 0.00 0.00 4.79
4630 4678 1.493446 AGCGTTATAAAGGGGGAAGGG 59.507 52.381 0.52 0.00 0.00 3.95
4631 4679 3.292492 AAGCGTTATAAAGGGGGAAGG 57.708 47.619 0.52 0.00 0.00 3.46
4632 4680 4.760204 CCATAAGCGTTATAAAGGGGGAAG 59.240 45.833 0.52 0.00 0.00 3.46
4633 4681 4.721132 CCATAAGCGTTATAAAGGGGGAA 58.279 43.478 0.52 0.00 0.00 3.97
4634 4682 3.497227 GCCATAAGCGTTATAAAGGGGGA 60.497 47.826 0.52 0.00 0.00 4.81
4635 4683 2.817844 GCCATAAGCGTTATAAAGGGGG 59.182 50.000 0.52 0.00 0.00 5.40
4814 4862 7.870509 ATTCTATCTTGCTTGTTGCTCAATA 57.129 32.000 0.00 0.00 43.37 1.90
5064 5771 6.077838 CAGAGTTTTAAAACCATCAGTACGC 58.922 40.000 24.06 2.51 39.71 4.42
5193 6158 6.653020 TCCAACATCTAAACTGAGCATATGT 58.347 36.000 4.29 0.00 0.00 2.29
5769 7603 2.372264 GCTCATCCAAATGAAGGCTCA 58.628 47.619 0.00 0.00 41.33 4.26
5771 7605 1.006281 TGGCTCATCCAAATGAAGGCT 59.994 47.619 0.00 0.00 43.21 4.58
5909 7743 5.976534 TCTTGAACCAAATCAAATGTCAACG 59.023 36.000 0.00 0.00 38.75 4.10
6126 8297 2.726821 CAGCATGGGGTTTATGAGTGT 58.273 47.619 0.00 0.00 0.00 3.55
6167 8338 0.706433 ATGGTTGATTGGGTGGCTCT 59.294 50.000 0.00 0.00 0.00 4.09
6245 8423 2.809706 GCATGCATGACGGCCAAT 59.190 55.556 30.64 0.00 0.00 3.16
6280 8458 2.455032 CTGACAGCGAGATAGAAACCG 58.545 52.381 0.00 0.00 0.00 4.44
6317 8495 3.133691 GTTTCTGGATATGCATGCGAGA 58.866 45.455 14.09 10.41 0.00 4.04
6325 8503 6.866248 GTCTAGAAGCTAGTTTCTGGATATGC 59.134 42.308 29.03 17.31 43.56 3.14
6480 8687 1.880027 GATCAGAAAACCAGCAACGGT 59.120 47.619 0.00 0.00 42.71 4.83
6671 8887 5.041287 TGTACAATGTCTCGCTAATAGCAC 58.959 41.667 13.15 3.79 42.58 4.40
6709 8932 1.245732 AGCGTGTAGAGAACCGTCTT 58.754 50.000 0.00 0.00 32.80 3.01
6853 9077 1.209019 CCTGCTGCACCTAGAGAATGT 59.791 52.381 0.00 0.00 0.00 2.71
7091 9427 2.898705 TGCCAAAATGAACACACCAAC 58.101 42.857 0.00 0.00 0.00 3.77
7103 9439 3.922171 TTGGAACTTGGTTGCCAAAAT 57.078 38.095 2.07 0.00 43.44 1.82
7104 9440 3.703001 TTTGGAACTTGGTTGCCAAAA 57.297 38.095 16.59 4.87 43.44 2.44
7105 9441 3.922171 ATTTGGAACTTGGTTGCCAAA 57.078 38.095 18.95 18.95 43.44 3.28
7142 9478 0.387565 AAGATTGCCGTGCCGTTTTT 59.612 45.000 0.00 0.00 0.00 1.94
7147 9483 1.444212 CCAAAAGATTGCCGTGCCG 60.444 57.895 0.00 0.00 35.10 5.69
7292 9630 6.576185 AGGGCACTCATAAATAATGCTTTTG 58.424 36.000 0.00 0.00 36.52 2.44
7400 9738 8.156994 ACTGCCGTAAAACTAAAAAGTGAATA 57.843 30.769 0.00 0.00 0.00 1.75
7530 10973 6.301486 TCAGTGGTACTAAGTCTGTTACTCA 58.699 40.000 0.00 0.00 37.50 3.41
7582 11025 0.802494 GGTAACATGCCAACACTCGG 59.198 55.000 0.00 0.00 0.00 4.63
7588 11031 2.489938 TCTCTGGGTAACATGCCAAC 57.510 50.000 0.00 0.00 39.74 3.77
7628 11071 8.582433 AATAAAATACACAACAAAAACTCCGG 57.418 30.769 0.00 0.00 0.00 5.14
7742 11186 4.697756 CCTCCAGTTGGCGGCGAA 62.698 66.667 12.98 0.00 32.66 4.70
7781 11225 3.703052 AGACTGATTGGGCATTTGGATTC 59.297 43.478 0.00 0.00 0.00 2.52
7793 11237 2.766313 TCAAACGACCAGACTGATTGG 58.234 47.619 3.32 0.00 41.60 3.16
7977 11421 4.876107 AGAAACCTAACACGGATGCATAAG 59.124 41.667 0.00 0.00 0.00 1.73
8049 11493 4.761739 AGATAACCCGACCATTGCATATTG 59.238 41.667 0.00 0.00 0.00 1.90
8050 11494 4.985538 AGATAACCCGACCATTGCATATT 58.014 39.130 0.00 0.00 0.00 1.28
8051 11495 4.579869 GAGATAACCCGACCATTGCATAT 58.420 43.478 0.00 0.00 0.00 1.78
8052 11496 3.554129 CGAGATAACCCGACCATTGCATA 60.554 47.826 0.00 0.00 0.00 3.14
8053 11497 2.806745 CGAGATAACCCGACCATTGCAT 60.807 50.000 0.00 0.00 0.00 3.96
8054 11498 1.472552 CGAGATAACCCGACCATTGCA 60.473 52.381 0.00 0.00 0.00 4.08
8055 11499 1.217882 CGAGATAACCCGACCATTGC 58.782 55.000 0.00 0.00 0.00 3.56
8063 11512 1.807981 TGCGCAACGAGATAACCCG 60.808 57.895 8.16 0.00 0.00 5.28
8131 11580 1.628846 ACAATTGACTCCGGGTAAGCT 59.371 47.619 13.59 0.00 0.00 3.74
8172 11622 1.987770 CAAGCATGCGCGAAAAGAAAT 59.012 42.857 12.10 0.00 45.49 2.17
8211 11663 3.777465 TGCTTCACACGGACTACTATC 57.223 47.619 0.00 0.00 0.00 2.08
8212 11664 3.181475 CCATGCTTCACACGGACTACTAT 60.181 47.826 0.00 0.00 0.00 2.12
8214 11666 1.066858 CCATGCTTCACACGGACTACT 60.067 52.381 0.00 0.00 0.00 2.57
8215 11667 1.359848 CCATGCTTCACACGGACTAC 58.640 55.000 0.00 0.00 0.00 2.73
8413 11870 0.606401 CACACGCCCAGATTTGGTCT 60.606 55.000 0.96 0.00 43.40 3.85
8453 11910 2.158755 ACTAGTGAACCACTTGCAAGCT 60.159 45.455 26.27 14.94 42.59 3.74
8514 11971 2.555006 CCACCACCAAAGGACATGATGA 60.555 50.000 0.00 0.00 0.00 2.92
8517 11974 0.850100 ACCACCACCAAAGGACATGA 59.150 50.000 0.00 0.00 0.00 3.07
8547 12004 2.622942 TGTCACCCAAGAATGCAACTTC 59.377 45.455 6.55 0.00 0.00 3.01
8553 12010 1.474077 GTCCATGTCACCCAAGAATGC 59.526 52.381 0.00 0.00 0.00 3.56
8600 12062 1.413767 CCGTCCGAGCTTTCGTCATG 61.414 60.000 0.00 0.00 0.00 3.07
8694 12551 5.353938 ACACGCAAAGACAAAAGAGTAGTA 58.646 37.500 0.00 0.00 0.00 1.82
8740 12600 1.837439 CCTCCCACAGGCATGTAAGTA 59.163 52.381 2.51 0.00 37.65 2.24
8750 12610 0.773644 CCATATTCCCCTCCCACAGG 59.226 60.000 0.00 0.00 43.01 4.00
8817 12714 7.122353 GGAAGTAGGTCTCAATAAGTCACTACA 59.878 40.741 0.00 0.00 33.27 2.74
8818 12715 7.416551 GGGAAGTAGGTCTCAATAAGTCACTAC 60.417 44.444 0.00 0.00 32.16 2.73
8828 12725 9.280456 TCTTTATAAAGGGAAGTAGGTCTCAAT 57.720 33.333 22.11 0.00 36.67 2.57
8829 12726 8.674925 TCTTTATAAAGGGAAGTAGGTCTCAA 57.325 34.615 22.11 0.00 36.67 3.02
8838 12735 9.682465 GTGGAGTATTTCTTTATAAAGGGAAGT 57.318 33.333 22.11 11.37 36.67 3.01
8839 12736 9.121658 GGTGGAGTATTTCTTTATAAAGGGAAG 57.878 37.037 22.11 0.42 36.67 3.46
8840 12737 8.057011 GGGTGGAGTATTTCTTTATAAAGGGAA 58.943 37.037 22.11 17.35 36.67 3.97
8844 12741 8.502105 AACGGGTGGAGTATTTCTTTATAAAG 57.498 34.615 17.60 17.60 37.36 1.85
8848 12745 6.478129 TGAAACGGGTGGAGTATTTCTTTAT 58.522 36.000 0.00 0.00 31.86 1.40
8853 12750 5.441709 TTTTGAAACGGGTGGAGTATTTC 57.558 39.130 0.00 0.00 0.00 2.17
8855 12752 6.478129 TCTATTTTGAAACGGGTGGAGTATT 58.522 36.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.