Multiple sequence alignment - TraesCS4D01G239900

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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 TraesCS4D01G239900 chr4D 100.000 7436 0 0 1 7436 402241208 402233773 0.000000e+00 13732
1 TraesCS4D01G239900 chr4A 95.017 2649 70 14 4093 6701 59674912 59672286 0.000000e+00 4104
2 TraesCS4D01G239900 chr4A 95.351 2151 72 13 1949 4094 59677110 59674983 0.000000e+00 3393
3 TraesCS4D01G239900 chr4A 94.144 1981 68 23 1 1951 59679100 59677138 0.000000e+00 2972
4 TraesCS4D01G239900 chr4A 87.344 719 42 22 6734 7431 59672190 59671500 0.000000e+00 778
5 TraesCS4D01G239900 chr4B 95.938 2511 84 11 1952 4458 497866942 497864446 0.000000e+00 4056
6 TraesCS4D01G239900 chr4B 95.147 2081 59 7 4676 6735 497864447 497862388 0.000000e+00 3245
7 TraesCS4D01G239900 chr4B 93.573 1976 59 23 1 1951 497868906 497866974 0.000000e+00 2883
8 TraesCS4D01G239900 chr4B 91.068 459 18 9 6735 7171 497862354 497861897 3.840000e-167 599
9 TraesCS4D01G239900 chr4B 86.207 116 8 5 7178 7285 497861930 497861815 1.310000e-22 119


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 TraesCS4D01G239900 chr4D 402233773 402241208 7435 True 13732.00 13732 100.0000 1 7436 1 chr4D.!!$R1 7435
1 TraesCS4D01G239900 chr4A 59671500 59679100 7600 True 2811.75 4104 92.9640 1 7431 4 chr4A.!!$R1 7430
2 TraesCS4D01G239900 chr4B 497861815 497868906 7091 True 2180.40 4056 92.3866 1 7285 5 chr4B.!!$R1 7284

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
308 310 0.764369 TTATGGCCAGCGAGGAGGAT 60.764 55.000 13.05 0.00 41.22 3.24 F
1177 1209 0.747644 CTTGCTGTGGTGTGGTGTCA 60.748 55.000 0.00 0.00 0.00 3.58 F
1812 1847 0.835276 CCATCTGATCAGGGCTGACA 59.165 55.000 22.42 1.49 43.11 3.58 F
3174 3243 0.682855 AGGACGCTCTTCCCTGAGAG 60.683 60.000 0.00 0.00 44.79 3.20 F
3296 3365 2.168521 ACGCATTATACTGTCACTGCCT 59.831 45.455 0.00 0.00 0.00 4.75 F
3612 3682 2.557924 GTTCACTTGTGAATGGGATGCA 59.442 45.455 17.56 0.00 0.00 3.96 F
5208 5412 0.552363 ATCCATATGGTGTGCCTGCA 59.448 50.000 21.28 0.00 36.34 4.41 F
5471 5675 0.318762 GCGGCATTACCCCAAAACAA 59.681 50.000 0.00 0.00 33.26 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1500 1.280133 CCTGCTCAGATTCTTCCCACA 59.720 52.381 0.00 0.00 0.00 4.17 R
2543 2610 1.301322 TCCGATTGCAACACGAGCA 60.301 52.632 23.21 8.84 40.85 4.26 R
3331 3401 0.662619 TGGAGCAGAAAACAACGCAG 59.337 50.000 0.00 0.00 0.00 5.18 R
4694 4850 3.005261 AGGAGATAACTAGCATGTCAGCG 59.995 47.826 0.00 0.00 40.15 5.18 R
5208 5412 1.484240 GAGGCCACTTGAGCACTAGAT 59.516 52.381 5.01 0.00 0.00 1.98 R
5471 5675 0.323178 CATTCTTCCAGCTGCAGGGT 60.323 55.000 17.12 0.00 0.00 4.34 R
6327 6531 0.314935 CATCCACTGCAAAGCGGTTT 59.685 50.000 6.80 6.80 46.97 3.27 R
7398 7692 0.743701 CGCAGAAGGCAGCTCTGATT 60.744 55.000 14.42 0.00 42.51 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.243704 GCAATGGCAACCTTTACAAGACA 60.244 43.478 0.00 0.00 40.72 3.41
187 188 1.464734 CTAGCTCGACCAGTGGAAGA 58.535 55.000 18.40 13.28 0.00 2.87
308 310 0.764369 TTATGGCCAGCGAGGAGGAT 60.764 55.000 13.05 0.00 41.22 3.24
310 312 3.157252 GGCCAGCGAGGAGGATCA 61.157 66.667 0.00 0.00 41.22 2.92
317 319 0.816018 GCGAGGAGGATCACTCTCGA 60.816 60.000 24.73 0.00 45.83 4.04
342 344 0.928908 GTATGCAGCTCGTACCGTCG 60.929 60.000 0.00 0.00 32.29 5.12
430 433 3.303132 CCAGCGAATATTAACAGCCGTTC 60.303 47.826 0.00 0.00 36.52 3.95
431 434 2.538449 AGCGAATATTAACAGCCGTTCG 59.462 45.455 0.00 0.00 40.76 3.95
432 435 2.348218 GCGAATATTAACAGCCGTTCGG 60.348 50.000 6.90 6.90 38.92 4.30
494 514 6.039382 GCGTAAACAAGGGAAGGAAATCATAT 59.961 38.462 0.00 0.00 0.00 1.78
690 717 5.639931 GGAATCATTAACTCCTAATCGCTCC 59.360 44.000 0.00 0.00 0.00 4.70
691 718 6.426646 AATCATTAACTCCTAATCGCTCCT 57.573 37.500 0.00 0.00 0.00 3.69
1177 1209 0.747644 CTTGCTGTGGTGTGGTGTCA 60.748 55.000 0.00 0.00 0.00 3.58
1253 1285 2.955068 GCTCCGTAACTTCGTAGCC 58.045 57.895 0.00 0.00 36.93 3.93
1264 1296 1.193874 CTTCGTAGCCGTGTTTTGGTC 59.806 52.381 0.00 0.00 35.01 4.02
1266 1298 1.202557 TCGTAGCCGTGTTTTGGTCTT 60.203 47.619 0.00 0.00 35.01 3.01
1466 1499 2.208431 GAGATCTGGCTGGATTCGTTG 58.792 52.381 0.00 0.00 0.00 4.10
1467 1500 1.556911 AGATCTGGCTGGATTCGTTGT 59.443 47.619 0.00 0.00 0.00 3.32
1468 1501 1.667724 GATCTGGCTGGATTCGTTGTG 59.332 52.381 0.00 0.00 0.00 3.33
1491 1524 1.569708 GAAGAATCTGAGCAGGCTCG 58.430 55.000 15.83 10.85 45.48 5.03
1689 1722 6.426025 CACCGTAGTAATCTTATTTTAGGCCC 59.574 42.308 0.00 0.00 0.00 5.80
1755 1788 7.363431 GGAACAGTAAGTTAGTACACGTACTT 58.637 38.462 14.67 4.68 45.02 2.24
1795 1830 1.420514 TCCAACGGGAAACATGTACCA 59.579 47.619 19.16 0.58 41.32 3.25
1812 1847 0.835276 CCATCTGATCAGGGCTGACA 59.165 55.000 22.42 1.49 43.11 3.58
1834 1869 2.970974 GAGTGTTTCCCTGCGCTGC 61.971 63.158 9.73 0.00 0.00 5.25
1841 1876 4.897357 CCCTGCGCTGCGATGCTA 62.897 66.667 28.07 4.78 0.00 3.49
1865 1900 4.495844 GCTCAACCCAATTAGTAACGATGC 60.496 45.833 0.00 0.00 0.00 3.91
2003 2069 7.182930 AGGGAAATAGTGTAAGAAGAGAACCAT 59.817 37.037 0.00 0.00 0.00 3.55
2030 2096 8.673711 GCTCCTGATTGTGTTGTATTGTTATTA 58.326 33.333 0.00 0.00 0.00 0.98
2056 2122 8.633561 ACTGCTATTGCTTAATTTTCCTATTCC 58.366 33.333 0.00 0.00 40.48 3.01
2068 2134 3.452755 TCCTATTCCGTGCATAGTGTG 57.547 47.619 0.00 0.00 0.00 3.82
2089 2155 2.291741 GCTTACTAGGCATTCATGTGGC 59.708 50.000 1.98 1.98 44.31 5.01
2176 2242 4.633126 ACAGTAAGTGTGCTATGAATGCTG 59.367 41.667 0.00 0.00 38.28 4.41
2310 2377 6.647334 TGTTGCTCCAGTTGAATGATTTTA 57.353 33.333 0.00 0.00 0.00 1.52
2311 2378 7.048629 TGTTGCTCCAGTTGAATGATTTTAA 57.951 32.000 0.00 0.00 0.00 1.52
2387 2454 1.063972 GCTTGCTTGTGTCGCAACA 59.936 52.632 0.00 0.00 41.97 3.33
2491 2558 2.335316 AAGTAGTTGGCACCGTTTCA 57.665 45.000 0.00 0.00 0.00 2.69
2496 2563 1.822371 AGTTGGCACCGTTTCAAAAGT 59.178 42.857 0.00 0.00 0.00 2.66
2543 2610 2.845784 TGGCACCACCATCTGCTT 59.154 55.556 0.00 0.00 46.36 3.91
2692 2759 3.115554 GTTGTTGCTTTTCAATCGCACT 58.884 40.909 0.00 0.00 36.99 4.40
2713 2780 6.759827 GCACTTCAAATAATGATCCATTTGCT 59.240 34.615 14.88 3.44 40.41 3.91
2777 2846 8.576442 CCCACTTGTACTTATTTCAGTGAAATT 58.424 33.333 30.62 18.28 41.64 1.82
2829 2898 4.202419 TGGTGATTTAGTGCAGTTGGTAGT 60.202 41.667 0.00 0.00 0.00 2.73
3169 3238 1.684049 CTGGAGGACGCTCTTCCCT 60.684 63.158 11.65 0.00 41.51 4.20
3174 3243 0.682855 AGGACGCTCTTCCCTGAGAG 60.683 60.000 0.00 0.00 44.79 3.20
3255 3324 6.525578 TGAAACGTTCTGTCTGGATATACT 57.474 37.500 0.00 0.00 0.00 2.12
3296 3365 2.168521 ACGCATTATACTGTCACTGCCT 59.831 45.455 0.00 0.00 0.00 4.75
3315 3385 3.005554 CCTCCAGTGTAATGTTGCTCTG 58.994 50.000 6.10 6.10 35.24 3.35
3329 3399 7.886629 ATGTTGCTCTGTCCAATATATGTTT 57.113 32.000 0.00 0.00 0.00 2.83
3330 3400 8.978874 ATGTTGCTCTGTCCAATATATGTTTA 57.021 30.769 0.00 0.00 0.00 2.01
3331 3401 8.208718 TGTTGCTCTGTCCAATATATGTTTAC 57.791 34.615 0.00 0.00 0.00 2.01
3332 3402 8.046708 TGTTGCTCTGTCCAATATATGTTTACT 58.953 33.333 0.00 0.00 0.00 2.24
3333 3403 8.338259 GTTGCTCTGTCCAATATATGTTTACTG 58.662 37.037 0.00 0.00 0.00 2.74
3334 3404 6.483307 TGCTCTGTCCAATATATGTTTACTGC 59.517 38.462 0.00 0.00 0.00 4.40
3335 3405 6.346919 GCTCTGTCCAATATATGTTTACTGCG 60.347 42.308 0.00 0.00 0.00 5.18
3572 3642 4.434857 CCTGCGTTCGAGAAAAAGATTCTC 60.435 45.833 7.90 7.90 41.03 2.87
3612 3682 2.557924 GTTCACTTGTGAATGGGATGCA 59.442 45.455 17.56 0.00 0.00 3.96
3696 3766 5.659440 TGAAAGGAATAAAACATGGAGCC 57.341 39.130 0.00 0.00 0.00 4.70
4064 4134 4.505313 AGCTTTTGTTACCTGCTTTAGC 57.495 40.909 0.00 0.00 42.50 3.09
4259 4405 4.702831 TGTTCCCAAGAAAATTTTGGAGC 58.297 39.130 8.47 10.89 46.42 4.70
4330 4476 7.315142 TGCAGGTTTGATTATTGTCTTCAATC 58.685 34.615 0.00 0.00 42.45 2.67
4333 4479 9.350357 CAGGTTTGATTATTGTCTTCAATCTTG 57.650 33.333 0.00 0.00 42.45 3.02
4473 4619 4.764823 CAGTATCCCTAGCTCGAAGAATCT 59.235 45.833 0.00 0.00 34.09 2.40
4507 4653 9.289782 CTTAGTTAGCAATATGAATTAAGGGCT 57.710 33.333 0.00 0.00 0.00 5.19
4694 4850 6.811665 GCATTCCCTATTTTTAGTGGTTTGAC 59.188 38.462 0.00 0.00 0.00 3.18
4811 4987 7.290948 ACCTCCAGATTCATCATATAAGTGACA 59.709 37.037 0.00 0.00 0.00 3.58
4968 5172 9.313118 TGTTAGTCTTGTACATATGCTGTATTG 57.687 33.333 1.58 0.00 42.21 1.90
5088 5292 4.250464 TCTTGCGGTAACTTTATGTCAGG 58.750 43.478 0.00 0.00 0.00 3.86
5208 5412 0.552363 ATCCATATGGTGTGCCTGCA 59.448 50.000 21.28 0.00 36.34 4.41
5362 5566 1.573108 TGGAAGGGACCAGTCATCTC 58.427 55.000 0.00 0.00 34.77 2.75
5471 5675 0.318762 GCGGCATTACCCCAAAACAA 59.681 50.000 0.00 0.00 33.26 2.83
5473 5677 1.337354 CGGCATTACCCCAAAACAACC 60.337 52.381 0.00 0.00 33.26 3.77
5480 5684 1.069596 CCCAAAACAACCCTGCAGC 59.930 57.895 8.66 0.00 0.00 5.25
5544 5748 6.715280 ACTTGGTATGTCAGATTCAATGAGT 58.285 36.000 0.00 0.00 0.00 3.41
5709 5913 2.932130 CTTTCCCAGCTAGCGAGGGC 62.932 65.000 31.95 2.48 42.52 5.19
5716 5920 2.855514 GCTAGCGAGGGCCTCTCTG 61.856 68.421 31.31 22.12 40.30 3.35
6261 6465 1.471684 CAGAGTTCAAATGCAGCCCTC 59.528 52.381 0.00 0.00 0.00 4.30
6316 6520 2.008242 TGGATTTGTTGGGAAGGGTG 57.992 50.000 0.00 0.00 0.00 4.61
6327 6531 1.304381 GAAGGGTGCTTGCATCCCA 60.304 57.895 20.04 0.00 43.31 4.37
6417 6621 0.253044 ACATCCAGGACATGTTCGGG 59.747 55.000 16.71 16.71 29.75 5.14
6488 6692 6.086765 GCATCATTTCGTAGTCAACTTTGTTG 59.913 38.462 4.25 4.25 0.00 3.33
6489 6693 6.671614 TCATTTCGTAGTCAACTTTGTTGT 57.328 33.333 9.78 0.00 0.00 3.32
6490 6694 7.773864 TCATTTCGTAGTCAACTTTGTTGTA 57.226 32.000 9.78 0.00 0.00 2.41
6539 6743 9.023962 TGGACAATAATAGATTTTGTCAGCTTT 57.976 29.630 19.91 0.00 46.98 3.51
6540 6744 9.508567 GGACAATAATAGATTTTGTCAGCTTTC 57.491 33.333 19.91 8.10 46.98 2.62
6543 6747 9.017669 CAATAATAGATTTTGTCAGCTTTCAGC 57.982 33.333 0.00 0.00 42.84 4.26
6603 6807 9.880064 TTTTGATGCATTGATTTATTTGTTGTG 57.120 25.926 0.00 0.00 0.00 3.33
6604 6808 8.604640 TTGATGCATTGATTTATTTGTTGTGT 57.395 26.923 0.00 0.00 0.00 3.72
6605 6809 9.702494 TTGATGCATTGATTTATTTGTTGTGTA 57.298 25.926 0.00 0.00 0.00 2.90
6606 6810 9.872721 TGATGCATTGATTTATTTGTTGTGTAT 57.127 25.926 0.00 0.00 0.00 2.29
6682 6886 7.441836 TCAACTTCACATACTCTTCAAGCTAA 58.558 34.615 0.00 0.00 0.00 3.09
6701 6905 6.394025 GCTAATCTAGCCGTAGCCTATTAT 57.606 41.667 7.54 0.00 45.95 1.28
6727 6946 7.118723 AGACCCTTGTGAATTATGCTCATTAA 58.881 34.615 0.00 0.00 0.00 1.40
6728 6947 7.781693 AGACCCTTGTGAATTATGCTCATTAAT 59.218 33.333 0.00 0.00 0.00 1.40
6731 6950 9.037737 CCCTTGTGAATTATGCTCATTAATTTG 57.962 33.333 0.00 0.00 0.00 2.32
6732 6951 9.590451 CCTTGTGAATTATGCTCATTAATTTGT 57.410 29.630 0.00 0.00 0.00 2.83
6846 7114 7.816945 ATGGTTGCTCTTATTTTTCATTTCG 57.183 32.000 0.00 0.00 0.00 3.46
6900 7169 4.114794 GGGAATAATTTGTGACAGCATGC 58.885 43.478 10.51 10.51 42.53 4.06
6931 7200 6.790285 TGGTTTATAGAAAGTTGTTCGGTC 57.210 37.500 0.00 0.00 0.00 4.79
6976 7245 0.898326 TGTCTGCCGTAGCTCCTTGA 60.898 55.000 0.00 0.00 40.80 3.02
6994 7263 4.213482 CCTTGACCTAGTTAACTTGTGTGC 59.787 45.833 14.49 7.11 0.00 4.57
7020 7292 8.036273 TCGTTTAGTCCCATCTAACATTTTTC 57.964 34.615 0.00 0.00 30.87 2.29
7066 7339 3.630769 TCATCTAACTCGTATGCCGTCTT 59.369 43.478 0.00 0.00 37.94 3.01
7085 7358 7.957550 CGTCTTCGATACTGGAAATCAGGGG 62.958 52.000 0.00 0.00 42.64 4.79
7126 7417 9.859427 TTTGTTTAGAGGATTAAGAATTGCATG 57.141 29.630 0.00 0.00 0.00 4.06
7127 7418 7.999679 TGTTTAGAGGATTAAGAATTGCATGG 58.000 34.615 0.00 0.00 0.00 3.66
7137 7428 2.957006 AGAATTGCATGGGAGATCTTGC 59.043 45.455 9.71 9.71 38.02 4.01
7156 7447 4.169059 TGCCTTGAACATATGGCTGTAT 57.831 40.909 7.80 0.00 45.11 2.29
7176 7467 5.867174 TGTATAGCGCGTAAATTGCATCTAT 59.133 36.000 8.43 4.44 34.38 1.98
7177 7468 5.862924 ATAGCGCGTAAATTGCATCTATT 57.137 34.783 8.43 0.00 29.20 1.73
7178 7469 4.133856 AGCGCGTAAATTGCATCTATTC 57.866 40.909 8.43 0.00 0.00 1.75
7217 7509 0.457443 GCCTGTAAATTGCCTCCTGC 59.543 55.000 0.00 0.00 41.77 4.85
7260 7554 5.806654 ACATTTTTGTCCATTTGGCTAGT 57.193 34.783 0.00 0.00 34.44 2.57
7262 7556 5.539955 ACATTTTTGTCCATTTGGCTAGTCT 59.460 36.000 0.00 0.00 34.44 3.24
7264 7558 7.232534 ACATTTTTGTCCATTTGGCTAGTCTTA 59.767 33.333 0.00 0.00 34.44 2.10
7265 7559 6.817765 TTTTGTCCATTTGGCTAGTCTTAG 57.182 37.500 0.00 0.00 34.44 2.18
7266 7560 5.755409 TTGTCCATTTGGCTAGTCTTAGA 57.245 39.130 0.00 0.00 34.44 2.10
7267 7561 5.957771 TGTCCATTTGGCTAGTCTTAGAT 57.042 39.130 0.00 0.00 34.44 1.98
7268 7562 7.432148 TTGTCCATTTGGCTAGTCTTAGATA 57.568 36.000 0.00 0.00 34.44 1.98
7269 7563 7.618019 TGTCCATTTGGCTAGTCTTAGATAT 57.382 36.000 0.00 0.00 34.44 1.63
7270 7564 7.445121 TGTCCATTTGGCTAGTCTTAGATATG 58.555 38.462 0.00 0.00 34.44 1.78
7271 7565 7.071196 TGTCCATTTGGCTAGTCTTAGATATGT 59.929 37.037 0.00 0.00 34.44 2.29
7272 7566 7.934120 GTCCATTTGGCTAGTCTTAGATATGTT 59.066 37.037 0.00 0.00 34.44 2.71
7273 7567 7.933577 TCCATTTGGCTAGTCTTAGATATGTTG 59.066 37.037 0.00 0.00 34.44 3.33
7274 7568 7.308229 CCATTTGGCTAGTCTTAGATATGTTGC 60.308 40.741 0.00 0.00 0.00 4.17
7275 7569 6.485830 TTGGCTAGTCTTAGATATGTTGCT 57.514 37.500 0.00 0.00 0.00 3.91
7276 7570 7.597288 TTGGCTAGTCTTAGATATGTTGCTA 57.403 36.000 0.00 0.00 0.00 3.49
7277 7571 7.220741 TGGCTAGTCTTAGATATGTTGCTAG 57.779 40.000 0.00 0.00 0.00 3.42
7278 7572 6.778069 TGGCTAGTCTTAGATATGTTGCTAGT 59.222 38.462 0.00 0.00 0.00 2.57
7279 7573 7.040340 TGGCTAGTCTTAGATATGTTGCTAGTC 60.040 40.741 0.00 0.00 32.48 2.59
7280 7574 7.040340 GGCTAGTCTTAGATATGTTGCTAGTCA 60.040 40.741 0.00 0.00 32.23 3.41
7281 7575 8.519526 GCTAGTCTTAGATATGTTGCTAGTCAT 58.480 37.037 0.00 0.00 0.00 3.06
7284 7578 9.757227 AGTCTTAGATATGTTGCTAGTCATTTC 57.243 33.333 0.00 0.38 0.00 2.17
7285 7579 9.534565 GTCTTAGATATGTTGCTAGTCATTTCA 57.465 33.333 12.91 4.92 0.00 2.69
7320 7614 1.694150 TGTTGCTAGTCACTTCTGGCT 59.306 47.619 4.02 0.00 41.41 4.75
7355 7649 1.926426 AAGCCATCCACCCCAGTAGC 61.926 60.000 0.00 0.00 0.00 3.58
7367 7661 3.011482 ACCCCAGTAGCAGTACTAGAAGT 59.989 47.826 0.00 0.00 37.40 3.01
7373 7667 6.293735 CCAGTAGCAGTACTAGAAGTAGCATC 60.294 46.154 0.00 0.00 37.40 3.91
7385 7679 3.883830 AGTAGCATCTTCACAGTCCTG 57.116 47.619 0.00 0.00 0.00 3.86
7389 7683 2.636893 AGCATCTTCACAGTCCTGTTCT 59.363 45.455 0.00 0.00 42.83 3.01
7392 7686 3.753294 TCTTCACAGTCCTGTTCTTCC 57.247 47.619 0.00 0.00 42.83 3.46
7398 7692 3.621805 TCCTGTTCTTCCGGCGCA 61.622 61.111 10.83 0.00 0.00 6.09
7400 7694 2.040544 CCTGTTCTTCCGGCGCAAT 61.041 57.895 10.83 0.00 0.00 3.56
7407 7701 3.315142 TTCCGGCGCAATCAGAGCT 62.315 57.895 10.83 0.00 43.21 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 1.065854 GTGCACTAGCCACTCCATCTT 60.066 52.381 10.32 0.00 41.13 2.40
308 310 2.940410 TGCATACACGTATCGAGAGTGA 59.060 45.455 19.87 7.93 39.04 3.41
310 312 2.287069 GCTGCATACACGTATCGAGAGT 60.287 50.000 0.00 0.00 0.00 3.24
317 319 2.287427 GGTACGAGCTGCATACACGTAT 60.287 50.000 17.73 0.00 40.49 3.06
342 344 1.809684 AAGGACTAGAAAACTGGCGC 58.190 50.000 0.00 0.00 0.00 6.53
374 376 4.224818 TGGCCATAAATTTCCAAAGAAGGG 59.775 41.667 0.00 0.00 32.35 3.95
430 433 2.352388 TGATTAACTTTCCTTCGGCCG 58.648 47.619 22.12 22.12 0.00 6.13
431 434 4.983671 ATTGATTAACTTTCCTTCGGCC 57.016 40.909 0.00 0.00 0.00 6.13
432 435 5.105917 TGGAATTGATTAACTTTCCTTCGGC 60.106 40.000 4.72 0.00 38.73 5.54
434 437 7.912250 CAGATGGAATTGATTAACTTTCCTTCG 59.088 37.037 10.38 5.34 42.66 3.79
690 717 4.464947 GGGATTAAATTCTGTCAGGGGAG 58.535 47.826 0.00 0.00 0.00 4.30
691 718 3.118038 CGGGATTAAATTCTGTCAGGGGA 60.118 47.826 0.00 0.00 0.00 4.81
776 803 2.837291 CTGCGGAGGAGGAGGGAG 60.837 72.222 0.00 0.00 44.33 4.30
1177 1209 3.058160 GCGGCACCAGAGCAACAT 61.058 61.111 0.00 0.00 35.83 2.71
1242 1274 1.600485 CCAAAACACGGCTACGAAGTT 59.400 47.619 0.00 0.00 37.78 2.66
1295 1327 3.058914 ACGGAAAGAGCAAATCAAACTCG 60.059 43.478 0.00 0.00 35.56 4.18
1466 1499 2.354259 CTGCTCAGATTCTTCCCACAC 58.646 52.381 0.00 0.00 0.00 3.82
1467 1500 1.280133 CCTGCTCAGATTCTTCCCACA 59.720 52.381 0.00 0.00 0.00 4.17
1468 1501 2.016096 GCCTGCTCAGATTCTTCCCAC 61.016 57.143 0.00 0.00 0.00 4.61
1526 1559 6.064060 TCCTAATACTCCTGCAAATGGATTG 58.936 40.000 0.00 0.00 42.21 2.67
1664 1697 6.426025 GGGCCTAAAATAAGATTACTACGGTG 59.574 42.308 0.84 0.00 0.00 4.94
1689 1722 4.808558 ACATCAACCATTTTCGGTCATTG 58.191 39.130 0.00 0.00 38.76 2.82
1755 1788 5.423886 TGGATTATATTGACAGCGTGTTGA 58.576 37.500 0.00 0.00 0.00 3.18
1795 1830 1.420514 CCATGTCAGCCCTGATCAGAT 59.579 52.381 24.62 6.76 42.18 2.90
1834 1869 1.959042 ATTGGGTTGAGCTAGCATCG 58.041 50.000 18.83 0.00 0.00 3.84
1841 1876 4.546829 TCGTTACTAATTGGGTTGAGCT 57.453 40.909 0.00 0.00 0.00 4.09
1865 1900 6.039047 AGGCATTACAGTTGAGCAAATAGATG 59.961 38.462 0.00 0.00 0.00 2.90
2003 2069 4.397420 ACAATACAACACAATCAGGAGCA 58.603 39.130 0.00 0.00 0.00 4.26
2030 2096 8.633561 GGAATAGGAAAATTAAGCAATAGCAGT 58.366 33.333 0.00 0.00 45.49 4.40
2068 2134 2.291741 GCCACATGAATGCCTAGTAAGC 59.708 50.000 0.00 0.00 0.00 3.09
2089 2155 2.838202 TCCTAGGACAAAAGCTACCCAG 59.162 50.000 7.62 0.00 0.00 4.45
2103 2169 4.164981 TGTAACCTTCAAGCTTCCTAGGA 58.835 43.478 19.71 7.62 0.00 2.94
2176 2242 9.841295 TCCTACATATTAGATTTGTACCAAACC 57.159 33.333 0.00 0.00 0.00 3.27
2235 2302 5.111989 TCTGATGCTAATTTTCTCGACCAG 58.888 41.667 0.00 0.00 0.00 4.00
2238 2305 4.025313 GCCTCTGATGCTAATTTTCTCGAC 60.025 45.833 0.00 0.00 0.00 4.20
2387 2454 6.413892 ACAATCAAATCCAACACCTTGTTTT 58.586 32.000 0.00 0.00 38.77 2.43
2469 2536 3.069872 TGAAACGGTGCCAACTACTTAGA 59.930 43.478 0.00 0.00 0.00 2.10
2491 2558 2.554032 CAAGGATGCTGAACCGACTTTT 59.446 45.455 0.00 0.00 0.00 2.27
2496 2563 1.377202 GCCAAGGATGCTGAACCGA 60.377 57.895 0.00 0.00 0.00 4.69
2543 2610 1.301322 TCCGATTGCAACACGAGCA 60.301 52.632 23.21 8.84 40.85 4.26
2620 2687 2.622452 CCCATGCACCCAGAAGAGAAAT 60.622 50.000 0.00 0.00 0.00 2.17
2692 2759 9.893634 AATGAAGCAAATGGATCATTATTTGAA 57.106 25.926 22.74 11.56 43.51 2.69
2713 2780 8.155510 AGATCTTGCTGCAGAAGATATAATGAA 58.844 33.333 27.08 9.43 39.72 2.57
2723 2790 4.761235 TTTGAAGATCTTGCTGCAGAAG 57.239 40.909 20.43 17.37 0.00 2.85
2777 2846 1.888436 CGCAGAAGGCAGGACCACTA 61.888 60.000 0.00 0.00 45.17 2.74
2829 2898 4.098501 AGACGACATGAGATGTAATGCTCA 59.901 41.667 0.00 0.00 45.03 4.26
3169 3238 4.226384 TCTATATTTGGGAGCAGCTCTCA 58.774 43.478 21.95 21.95 43.70 3.27
3174 3243 3.817647 CCTGTTCTATATTTGGGAGCAGC 59.182 47.826 0.00 0.00 37.12 5.25
3175 3244 5.059833 GTCCTGTTCTATATTTGGGAGCAG 58.940 45.833 0.00 0.00 37.81 4.24
3176 3245 4.473196 TGTCCTGTTCTATATTTGGGAGCA 59.527 41.667 0.00 0.00 0.00 4.26
3255 3324 4.802039 GCGTCTACCGAATGAATAAGTCAA 59.198 41.667 0.00 0.00 38.24 3.18
3296 3365 3.557054 GGACAGAGCAACATTACACTGGA 60.557 47.826 0.00 0.00 0.00 3.86
3315 3385 7.011828 ACAACGCAGTAAACATATATTGGAC 57.988 36.000 0.00 0.00 45.00 4.02
3329 3399 1.871039 GGAGCAGAAAACAACGCAGTA 59.129 47.619 0.00 0.00 45.00 2.74
3331 3401 0.662619 TGGAGCAGAAAACAACGCAG 59.337 50.000 0.00 0.00 0.00 5.18
3332 3402 1.266718 GATGGAGCAGAAAACAACGCA 59.733 47.619 0.00 0.00 0.00 5.24
3333 3403 1.266718 TGATGGAGCAGAAAACAACGC 59.733 47.619 0.00 0.00 0.00 4.84
3334 3404 3.837213 ATGATGGAGCAGAAAACAACG 57.163 42.857 0.00 0.00 0.00 4.10
3335 3405 8.078596 GGATTATATGATGGAGCAGAAAACAAC 58.921 37.037 0.00 0.00 0.00 3.32
3572 3642 8.415950 AGTGAACATACTGAATAGGAGATAGG 57.584 38.462 0.00 0.00 0.00 2.57
3612 3682 9.846248 GAAATGTCATCAACAAGCTTTAGTATT 57.154 29.630 0.00 0.00 42.37 1.89
3696 3766 9.778993 CTGACAGGTTTAATCAAATAATCACAG 57.221 33.333 0.00 0.00 0.00 3.66
3858 3928 3.014623 CTCAGCTCCATCATTTGCAGAA 58.985 45.455 0.00 0.00 0.00 3.02
4152 4294 9.436957 CTAAATCATAGGTGTTCAACAGTAACT 57.563 33.333 0.00 0.00 0.00 2.24
4259 4405 5.256474 AGTTAAACCAGGGACATTCATCAG 58.744 41.667 0.00 0.00 0.00 2.90
4382 4528 5.978814 ACAGTAAAATAGAGAAGTCGCCAT 58.021 37.500 0.00 0.00 0.00 4.40
4650 4806 6.763135 GGAATGCTTCTTGTCATACATCTACA 59.237 38.462 0.00 0.00 0.00 2.74
4694 4850 3.005261 AGGAGATAACTAGCATGTCAGCG 59.995 47.826 0.00 0.00 40.15 5.18
4811 4987 3.896888 TGACTGAAGGCATGTCCAAAAAT 59.103 39.130 8.58 0.00 37.29 1.82
4968 5172 8.324163 AGATGTAACTTTGACCACTGATTTAC 57.676 34.615 0.00 0.00 0.00 2.01
5208 5412 1.484240 GAGGCCACTTGAGCACTAGAT 59.516 52.381 5.01 0.00 0.00 1.98
5471 5675 0.323178 CATTCTTCCAGCTGCAGGGT 60.323 55.000 17.12 0.00 0.00 4.34
5473 5677 1.664321 GGCATTCTTCCAGCTGCAGG 61.664 60.000 17.12 4.46 36.34 4.85
5544 5748 6.186957 AGAATTATTCACATTACCCAGTGCA 58.813 36.000 7.74 0.00 35.76 4.57
5709 5913 6.600822 TCAAGGAATTTTGATTAGCAGAGAGG 59.399 38.462 0.00 0.00 32.39 3.69
5904 6108 4.028852 TGAGTTACGATTCATGAGACCG 57.971 45.455 10.54 10.54 0.00 4.79
6261 6465 1.406539 CCTTGATCTGGCAATTTCCCG 59.593 52.381 0.00 0.00 0.00 5.14
6316 6520 2.125952 GCGGTTTGGGATGCAAGC 60.126 61.111 0.00 0.00 0.00 4.01
6327 6531 0.314935 CATCCACTGCAAAGCGGTTT 59.685 50.000 6.80 6.80 46.97 3.27
6404 6608 2.290071 CCACTAAACCCGAACATGTCCT 60.290 50.000 0.00 0.00 0.00 3.85
6405 6609 2.081462 CCACTAAACCCGAACATGTCC 58.919 52.381 0.00 0.00 0.00 4.02
6417 6621 3.437049 GCCTTCACATCTGTCCACTAAAC 59.563 47.826 0.00 0.00 0.00 2.01
6489 6693 9.226606 CCAAAAGAAACAGTACCATGAATACTA 57.773 33.333 8.72 0.00 31.53 1.82
6490 6694 7.942341 TCCAAAAGAAACAGTACCATGAATACT 59.058 33.333 0.00 0.00 32.98 2.12
6539 6743 0.820226 AGCGAGATGTTGCTAGCTGA 59.180 50.000 17.23 1.37 43.71 4.26
6540 6744 1.649664 AAGCGAGATGTTGCTAGCTG 58.350 50.000 17.23 0.00 44.43 4.24
6541 6745 2.275318 GAAAGCGAGATGTTGCTAGCT 58.725 47.619 17.23 0.00 46.64 3.32
6542 6746 1.328986 GGAAAGCGAGATGTTGCTAGC 59.671 52.381 8.10 8.10 43.28 3.42
6543 6747 1.936547 GGGAAAGCGAGATGTTGCTAG 59.063 52.381 4.77 0.00 43.28 3.42
6544 6748 1.555075 AGGGAAAGCGAGATGTTGCTA 59.445 47.619 4.77 0.00 43.28 3.49
6629 6833 1.528129 GCTGCAAGAGCTACCAAGTT 58.472 50.000 0.00 0.00 45.21 2.66
6682 6886 6.063404 GGTCTATAATAGGCTACGGCTAGAT 58.937 44.000 0.00 2.66 43.64 1.98
6701 6905 5.692115 TGAGCATAATTCACAAGGGTCTA 57.308 39.130 0.00 0.00 0.00 2.59
6976 7245 3.069158 ACGAGCACACAAGTTAACTAGGT 59.931 43.478 8.92 7.76 0.00 3.08
6994 7263 7.611213 AAAATGTTAGATGGGACTAAACGAG 57.389 36.000 0.00 0.00 34.74 4.18
7066 7339 2.434336 CACCCCTGATTTCCAGTATCGA 59.566 50.000 0.00 0.00 41.33 3.59
7102 7393 7.068593 CCCATGCAATTCTTAATCCTCTAAACA 59.931 37.037 0.00 0.00 0.00 2.83
7126 7417 2.496899 TGTTCAAGGCAAGATCTCCC 57.503 50.000 0.00 0.00 0.00 4.30
7127 7418 4.518211 CCATATGTTCAAGGCAAGATCTCC 59.482 45.833 0.00 0.00 0.00 3.71
7137 7428 4.389992 CGCTATACAGCCATATGTTCAAGG 59.610 45.833 1.24 0.00 45.64 3.61
7156 7447 4.988540 AGAATAGATGCAATTTACGCGCTA 59.011 37.500 5.73 0.00 0.00 4.26
7160 7451 9.831737 ATATTCAAGAATAGATGCAATTTACGC 57.168 29.630 8.34 0.00 36.79 4.42
7252 7546 6.485830 AGCAACATATCTAAGACTAGCCAA 57.514 37.500 0.00 0.00 0.00 4.52
7254 7548 7.040340 TGACTAGCAACATATCTAAGACTAGCC 60.040 40.741 0.00 0.00 31.22 3.93
7259 7553 9.534565 TGAAATGACTAGCAACATATCTAAGAC 57.465 33.333 0.00 0.00 0.00 3.01
7266 7560 8.944029 GCATAGATGAAATGACTAGCAACATAT 58.056 33.333 0.00 0.00 0.00 1.78
7267 7561 8.152898 AGCATAGATGAAATGACTAGCAACATA 58.847 33.333 0.00 0.00 0.00 2.29
7268 7562 6.996879 AGCATAGATGAAATGACTAGCAACAT 59.003 34.615 0.00 0.00 0.00 2.71
7269 7563 6.351711 AGCATAGATGAAATGACTAGCAACA 58.648 36.000 0.00 0.00 0.00 3.33
7270 7564 6.857777 AGCATAGATGAAATGACTAGCAAC 57.142 37.500 0.00 0.00 0.00 4.17
7271 7565 8.424133 TCTAAGCATAGATGAAATGACTAGCAA 58.576 33.333 0.00 0.00 33.17 3.91
7272 7566 7.955918 TCTAAGCATAGATGAAATGACTAGCA 58.044 34.615 0.00 0.00 33.17 3.49
7279 7573 9.770503 GCAACATATCTAAGCATAGATGAAATG 57.229 33.333 19.27 16.52 46.15 2.32
7280 7574 9.736414 AGCAACATATCTAAGCATAGATGAAAT 57.264 29.630 19.27 4.64 46.15 2.17
7282 7576 9.866798 CTAGCAACATATCTAAGCATAGATGAA 57.133 33.333 19.27 3.19 46.15 2.57
7283 7577 9.029368 ACTAGCAACATATCTAAGCATAGATGA 57.971 33.333 19.27 6.25 46.15 2.92
7284 7578 9.299963 GACTAGCAACATATCTAAGCATAGATG 57.700 37.037 19.27 9.36 46.15 2.90
7286 7580 8.300286 GTGACTAGCAACATATCTAAGCATAGA 58.700 37.037 0.38 0.38 42.23 1.98
7287 7581 8.303156 AGTGACTAGCAACATATCTAAGCATAG 58.697 37.037 0.00 0.00 0.00 2.23
7288 7582 8.183104 AGTGACTAGCAACATATCTAAGCATA 57.817 34.615 0.00 0.00 0.00 3.14
7289 7583 7.060383 AGTGACTAGCAACATATCTAAGCAT 57.940 36.000 0.00 0.00 0.00 3.79
7290 7584 6.471233 AGTGACTAGCAACATATCTAAGCA 57.529 37.500 0.00 0.00 0.00 3.91
7291 7585 7.168972 CAGAAGTGACTAGCAACATATCTAAGC 59.831 40.741 0.00 0.00 0.00 3.09
7320 7614 2.099405 GGCTTAAACCAGGCATTGCTA 58.901 47.619 8.82 0.00 39.20 3.49
7355 7649 7.089770 TGTGAAGATGCTACTTCTAGTACTG 57.910 40.000 18.59 0.00 44.34 2.74
7367 7661 3.834813 AGAACAGGACTGTGAAGATGCTA 59.165 43.478 5.63 0.00 44.13 3.49
7373 7667 2.408050 CGGAAGAACAGGACTGTGAAG 58.592 52.381 5.63 0.00 44.13 3.02
7385 7679 1.019278 TCTGATTGCGCCGGAAGAAC 61.019 55.000 5.05 0.00 0.00 3.01
7389 7683 2.819595 GCTCTGATTGCGCCGGAA 60.820 61.111 5.05 0.00 0.00 4.30
7392 7686 4.233635 GCAGCTCTGATTGCGCCG 62.234 66.667 4.18 0.00 35.28 6.46
7398 7692 0.743701 CGCAGAAGGCAGCTCTGATT 60.744 55.000 14.42 0.00 42.51 2.57
7400 7694 2.263852 CGCAGAAGGCAGCTCTGA 59.736 61.111 14.42 0.00 42.51 3.27


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

AutoCloner maintained by Alex Coulton.