Multiple sequence alignment - TraesCS3B01G603600

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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 TraesCS3B01G603600 chr3B 100.000 6655 0 0 1 6655 822967033 822973687 0.000000e+00 12290.0
1 TraesCS3B01G603600 chr3B 82.204 1107 160 24 4594 5680 822971572 822972661 0.000000e+00 918.0
2 TraesCS3B01G603600 chr3B 82.204 1107 160 24 4540 5629 822971626 822972712 0.000000e+00 918.0
3 TraesCS3B01G603600 chr3B 83.131 658 82 21 2284 2914 822969139 822969794 2.080000e-159 573.0
4 TraesCS3B01G603600 chr3B 76.039 722 133 24 4564 5269 822971968 822972665 8.270000e-89 339.0
5 TraesCS3B01G603600 chr3A 94.770 2677 107 9 2905 5578 749403936 749406582 0.000000e+00 4137.0
6 TraesCS3B01G603600 chr3A 88.424 2030 134 29 1 1976 749400878 749402860 0.000000e+00 2353.0
7 TraesCS3B01G603600 chr3A 93.127 1033 66 3 1877 2908 749402860 749403888 0.000000e+00 1509.0
8 TraesCS3B01G603600 chr3A 83.084 1673 230 34 4648 6301 749405553 749407191 0.000000e+00 1472.0
9 TraesCS3B01G603600 chr3A 82.498 1057 159 19 4594 5641 749405553 749406592 0.000000e+00 904.0
10 TraesCS3B01G603600 chr3A 83.131 658 82 19 2284 2914 749403087 749403742 2.080000e-159 573.0
11 TraesCS3B01G603600 chr3A 80.749 774 115 26 2107 2875 749403264 749404008 2.080000e-159 573.0
12 TraesCS3B01G603600 chr3A 77.434 904 161 29 4536 5425 749405708 749406582 3.580000e-137 499.0
13 TraesCS3B01G603600 chr3A 93.077 130 6 1 6350 6476 749407197 749407326 3.170000e-43 187.0
14 TraesCS3B01G603600 chr3A 78.073 301 55 8 5390 5680 749405560 749405859 5.300000e-41 180.0
15 TraesCS3B01G603600 chr3A 80.952 126 15 5 2904 3023 749403782 749403904 2.560000e-14 91.6
16 TraesCS3B01G603600 chr3D 91.896 2937 160 28 1 2908 613731701 613734588 0.000000e+00 4034.0
17 TraesCS3B01G603600 chr3D 93.455 2674 109 12 2905 5578 613734636 613737243 0.000000e+00 3908.0
18 TraesCS3B01G603600 chr3D 82.195 1932 215 72 4696 6575 613736235 613738089 0.000000e+00 1543.0
19 TraesCS3B01G603600 chr3D 82.648 657 87 19 2284 2914 613733784 613734439 2.100000e-154 556.0
20 TraesCS3B01G603600 chr3D 85.256 468 60 5 4594 5058 613736238 613736699 2.170000e-129 473.0
21 TraesCS3B01G603600 chr3D 82.008 528 82 9 5107 5629 613736724 613737243 2.850000e-118 436.0
22 TraesCS3B01G603600 chr3D 81.148 366 50 13 4540 4900 613736346 613736697 6.570000e-70 276.0
23 TraesCS3B01G603600 chr3D 78.205 156 22 7 2904 3050 613734479 613734631 9.190000e-14 89.8


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 TraesCS3B01G603600 chr3B 822967033 822973687 6654 False 12290.000000 12290 100.000000 1 6655 1 chr3B.!!$F1 6654
1 TraesCS3B01G603600 chr3B 822969139 822972712 3573 False 687.000000 918 80.894500 2284 5680 4 chr3B.!!$F2 3396
2 TraesCS3B01G603600 chr3A 749400878 749407326 6448 False 1134.418182 4137 85.029000 1 6476 11 chr3A.!!$F1 6475
3 TraesCS3B01G603600 chr3D 613731701 613738089 6388 False 1414.475000 4034 84.601375 1 6575 8 chr3D.!!$F1 6574

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
771 796 0.188342 CCCCGATTCCCCATTCCATT 59.812 55.000 0.00 0.00 0.00 3.16 F
1353 1395 0.324460 CCTACTTCTGGGACCGGACT 60.324 60.000 9.46 0.00 0.00 3.85 F
1837 1891 1.226491 GATGTGGCAGCAACATCGC 60.226 57.895 24.38 6.51 43.16 4.58 F
2178 2334 1.222567 AAGACACCCCCAAAGACACT 58.777 50.000 0.00 0.00 0.00 3.55 F
4173 4419 0.106708 GCGATATGTCTTCCCAGCCA 59.893 55.000 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1666 0.102481 AGCGCCGAAATGTAGTCGAT 59.898 50.000 2.29 0.0 41.02 3.59 R
2178 2334 0.747255 GAGACTCGCCCTTATCTGCA 59.253 55.000 0.00 0.0 0.00 4.41 R
2942 3152 2.418060 GGCTCTTGCAGAGACTCCTTAC 60.418 54.545 14.86 0.0 46.93 2.34 R
4175 4421 1.777272 ACCTTTTGGAAGAGACAGGCT 59.223 47.619 0.00 0.0 44.07 4.58 R
5884 6130 0.038801 GCCTTGTCTTGCTGGCTTTC 60.039 55.000 0.00 0.0 41.92 2.62 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 6.610741 GTCAAAGAGTCTGATGAACAAACT 57.389 37.500 9.76 0.00 31.90 2.66
56 57 1.485480 GTAACAAGCTACCCCTCTCCC 59.515 57.143 0.00 0.00 0.00 4.30
234 235 3.058432 CGATATACACCGTCCGTTCATCT 60.058 47.826 0.00 0.00 0.00 2.90
235 236 4.152938 CGATATACACCGTCCGTTCATCTA 59.847 45.833 0.00 0.00 0.00 1.98
243 244 5.010933 ACCGTCCGTTCATCTATATCAGAT 58.989 41.667 0.00 0.00 45.35 2.90
298 299 0.895530 ACACATCGTCCGTTCATCCT 59.104 50.000 0.00 0.00 0.00 3.24
304 309 3.710326 TCGTCCGTTCATCCTTATCAG 57.290 47.619 0.00 0.00 0.00 2.90
386 391 8.334632 TGTATCTGACAAATTACGTTGCATATG 58.665 33.333 0.00 0.00 34.15 1.78
417 422 6.094603 CCAGCTGGAATCCATAAATGCTATAC 59.905 42.308 29.88 0.00 37.39 1.47
418 423 6.656270 CAGCTGGAATCCATAAATGCTATACA 59.344 38.462 11.84 0.00 30.60 2.29
419 424 7.338703 CAGCTGGAATCCATAAATGCTATACAT 59.661 37.037 11.84 0.00 34.52 2.29
420 425 7.338703 AGCTGGAATCCATAAATGCTATACATG 59.661 37.037 10.72 0.00 33.69 3.21
421 426 7.121759 GCTGGAATCCATAAATGCTATACATGT 59.878 37.037 0.87 2.69 33.69 3.21
422 427 9.671279 CTGGAATCCATAAATGCTATACATGTA 57.329 33.333 8.27 8.27 33.69 2.29
436 441 9.740710 TGCTATACATGTACATAGTGTCTATCT 57.259 33.333 7.96 0.00 0.00 1.98
479 484 3.761752 ACACGGGTATTTCATTTTGGGAG 59.238 43.478 0.00 0.00 0.00 4.30
494 499 8.673711 TCATTTTGGGAGAATTCATTTACTACG 58.326 33.333 8.44 0.00 0.00 3.51
551 556 3.855689 AAGAAATTTCACCATCAGGCG 57.144 42.857 19.99 0.00 39.06 5.52
554 559 1.322538 AATTTCACCATCAGGCGGGC 61.323 55.000 0.00 0.00 39.06 6.13
622 627 8.174085 TGTGAAAATAAAGGAGAAATAAGGGGA 58.826 33.333 0.00 0.00 0.00 4.81
680 690 0.614697 ATTTACCAGTGGCCCCTTGC 60.615 55.000 9.78 0.00 40.16 4.01
701 711 3.885738 GCCCTAACCAGAATTCCCCAAAT 60.886 47.826 0.65 0.00 0.00 2.32
708 718 3.294214 CAGAATTCCCCAAATCCTCCAG 58.706 50.000 0.65 0.00 0.00 3.86
710 720 0.262876 ATTCCCCAAATCCTCCAGCC 59.737 55.000 0.00 0.00 0.00 4.85
717 727 2.305009 CAAATCCTCCAGCCATTCCTC 58.695 52.381 0.00 0.00 0.00 3.71
720 730 1.207791 TCCTCCAGCCATTCCTCTTC 58.792 55.000 0.00 0.00 0.00 2.87
734 755 4.650972 TCCTCTTCCTCTATAGGCTCTC 57.349 50.000 0.00 0.00 43.31 3.20
770 795 1.729267 CCCCCGATTCCCCATTCCAT 61.729 60.000 0.00 0.00 0.00 3.41
771 796 0.188342 CCCCGATTCCCCATTCCATT 59.812 55.000 0.00 0.00 0.00 3.16
1353 1395 0.324460 CCTACTTCTGGGACCGGACT 60.324 60.000 9.46 0.00 0.00 3.85
1624 1666 3.126703 TTCCGTGCCAAGCCCTTCA 62.127 57.895 0.00 0.00 0.00 3.02
1785 1827 2.358003 GAGGACGTTGCTGCTGCT 60.358 61.111 17.00 0.00 40.48 4.24
1837 1891 1.226491 GATGTGGCAGCAACATCGC 60.226 57.895 24.38 6.51 43.16 4.58
1838 1892 2.603135 GATGTGGCAGCAACATCGCC 62.603 60.000 24.38 5.80 43.16 5.54
1905 2061 3.526534 GACCAAGGAGGAGAAGAAATCG 58.473 50.000 0.00 0.00 41.22 3.34
1942 2098 1.309950 CTCGTCGCCCAAGAGAGATA 58.690 55.000 0.00 0.00 34.13 1.98
1981 2137 2.885135 AGTGGCCATTGATGTTGAGA 57.115 45.000 9.72 0.00 0.00 3.27
2069 2225 2.555325 CTCCTGCAAACAAAGATGCTGA 59.445 45.455 6.26 0.00 42.12 4.26
2074 2230 2.991190 GCAAACAAAGATGCTGACATGG 59.009 45.455 0.00 0.00 39.46 3.66
2075 2231 3.553508 GCAAACAAAGATGCTGACATGGT 60.554 43.478 0.00 0.00 39.46 3.55
2076 2232 4.624015 CAAACAAAGATGCTGACATGGTT 58.376 39.130 0.00 0.00 36.35 3.67
2137 2293 3.971245 AGTCAAAGAGAGGTAGCAAGG 57.029 47.619 0.00 0.00 0.00 3.61
2167 2323 5.506483 GCTGAGAAAAAGAAGAAAGACACCC 60.506 44.000 0.00 0.00 0.00 4.61
2178 2334 1.222567 AAGACACCCCCAAAGACACT 58.777 50.000 0.00 0.00 0.00 3.55
2237 2393 5.011586 TGCCAAAGAAGATGATGTGAATGA 58.988 37.500 0.00 0.00 0.00 2.57
2942 3152 3.658709 AGAAGAAGAAGAAAGACGCAGG 58.341 45.455 0.00 0.00 0.00 4.85
4168 4414 4.744795 ATATCAGGCGATATGTCTTCCC 57.255 45.455 9.85 0.00 42.19 3.97
4169 4415 1.788229 TCAGGCGATATGTCTTCCCA 58.212 50.000 0.00 0.00 0.00 4.37
4170 4416 1.688735 TCAGGCGATATGTCTTCCCAG 59.311 52.381 0.00 0.00 0.00 4.45
4171 4417 0.394565 AGGCGATATGTCTTCCCAGC 59.605 55.000 0.00 0.00 0.00 4.85
4172 4418 0.603975 GGCGATATGTCTTCCCAGCC 60.604 60.000 0.00 0.00 36.32 4.85
4173 4419 0.106708 GCGATATGTCTTCCCAGCCA 59.893 55.000 0.00 0.00 0.00 4.75
4174 4420 1.875576 GCGATATGTCTTCCCAGCCAG 60.876 57.143 0.00 0.00 0.00 4.85
4175 4421 1.688735 CGATATGTCTTCCCAGCCAGA 59.311 52.381 0.00 0.00 0.00 3.86
4176 4422 2.288702 CGATATGTCTTCCCAGCCAGAG 60.289 54.545 0.00 0.00 0.00 3.35
4177 4423 0.833287 TATGTCTTCCCAGCCAGAGC 59.167 55.000 0.00 0.00 40.32 4.09
4178 4424 1.919600 ATGTCTTCCCAGCCAGAGCC 61.920 60.000 0.00 0.00 41.25 4.70
4179 4425 2.123632 TCTTCCCAGCCAGAGCCT 59.876 61.111 0.00 0.00 41.25 4.58
4180 4426 2.271497 CTTCCCAGCCAGAGCCTG 59.729 66.667 0.00 0.00 41.25 4.85
4181 4427 2.530151 TTCCCAGCCAGAGCCTGT 60.530 61.111 2.18 0.00 41.25 4.00
4182 4428 2.533974 CTTCCCAGCCAGAGCCTGTC 62.534 65.000 2.18 0.00 41.25 3.51
4183 4429 3.007920 CCCAGCCAGAGCCTGTCT 61.008 66.667 2.18 0.00 41.25 3.41
4184 4430 2.583520 CCAGCCAGAGCCTGTCTC 59.416 66.667 2.18 0.00 41.25 3.36
5680 5926 1.627329 AGATGTCTGAGAAGGCAGCAA 59.373 47.619 0.00 0.00 35.86 3.91
5681 5927 2.008329 GATGTCTGAGAAGGCAGCAAG 58.992 52.381 0.00 0.00 35.86 4.01
5743 5989 5.468540 TCATATGAAGGACGATTACTGGG 57.531 43.478 1.98 0.00 0.00 4.45
5766 6012 4.391830 GCTGACATTCTCATAAACGTGGAA 59.608 41.667 0.00 0.00 0.00 3.53
5783 6029 1.544691 GGAAGAACCGCTGTCTAGTCA 59.455 52.381 0.00 0.00 0.00 3.41
5864 6110 3.478509 AGATGAAGCAAGATGAGATGCC 58.521 45.455 0.00 0.00 43.57 4.40
5865 6111 2.048444 TGAAGCAAGATGAGATGCCC 57.952 50.000 0.00 0.00 43.57 5.36
5866 6112 0.942962 GAAGCAAGATGAGATGCCCG 59.057 55.000 0.00 0.00 43.57 6.13
5867 6113 1.099879 AAGCAAGATGAGATGCCCGC 61.100 55.000 0.00 0.00 43.57 6.13
5868 6114 2.890109 GCAAGATGAGATGCCCGCG 61.890 63.158 0.00 0.00 36.56 6.46
5869 6115 2.109799 AAGATGAGATGCCCGCGG 59.890 61.111 21.04 21.04 0.00 6.46
5870 6116 2.434843 AAGATGAGATGCCCGCGGA 61.435 57.895 30.73 8.21 0.00 5.54
5871 6117 2.356793 GATGAGATGCCCGCGGAG 60.357 66.667 30.73 18.40 0.00 4.63
5872 6118 3.873026 GATGAGATGCCCGCGGAGG 62.873 68.421 30.73 12.70 40.63 4.30
5874 6120 3.849951 GAGATGCCCGCGGAGGAA 61.850 66.667 30.73 5.36 45.00 3.36
5875 6121 3.798954 GAGATGCCCGCGGAGGAAG 62.799 68.421 30.73 10.90 45.00 3.46
5880 6126 3.127533 CCCGCGGAGGAAGCAAAG 61.128 66.667 30.73 0.44 45.00 2.77
5881 6127 3.127533 CCGCGGAGGAAGCAAAGG 61.128 66.667 24.07 0.00 45.00 3.11
5882 6128 3.804193 CGCGGAGGAAGCAAAGGC 61.804 66.667 0.00 0.00 41.61 4.35
5883 6129 3.443925 GCGGAGGAAGCAAAGGCC 61.444 66.667 0.00 0.00 42.56 5.19
5884 6130 3.127533 CGGAGGAAGCAAAGGCCG 61.128 66.667 0.00 0.00 42.56 6.13
5885 6131 2.351276 GGAGGAAGCAAAGGCCGA 59.649 61.111 0.00 0.00 42.56 5.54
5886 6132 1.303317 GGAGGAAGCAAAGGCCGAA 60.303 57.895 0.00 0.00 42.56 4.30
5887 6133 0.893727 GGAGGAAGCAAAGGCCGAAA 60.894 55.000 0.00 0.00 42.56 3.46
6341 6614 0.554792 ATGATGCTTCCCTTCCCTGG 59.445 55.000 0.00 0.00 0.00 4.45
6342 6615 0.846427 TGATGCTTCCCTTCCCTGGT 60.846 55.000 0.00 0.00 0.00 4.00
6343 6616 0.394899 GATGCTTCCCTTCCCTGGTG 60.395 60.000 0.00 0.00 0.00 4.17
6344 6617 0.846427 ATGCTTCCCTTCCCTGGTGA 60.846 55.000 0.00 0.00 0.00 4.02
6345 6618 0.846427 TGCTTCCCTTCCCTGGTGAT 60.846 55.000 0.00 0.00 0.00 3.06
6346 6619 0.332972 GCTTCCCTTCCCTGGTGATT 59.667 55.000 0.00 0.00 0.00 2.57
6347 6620 1.272704 GCTTCCCTTCCCTGGTGATTT 60.273 52.381 0.00 0.00 0.00 2.17
6348 6621 2.025321 GCTTCCCTTCCCTGGTGATTTA 60.025 50.000 0.00 0.00 0.00 1.40
6409 6683 3.766591 TGTGTTGTTGGTTTCAGGTGAAT 59.233 39.130 0.00 0.00 33.54 2.57
6416 6690 2.711009 TGGTTTCAGGTGAATGAGGAGT 59.289 45.455 0.00 0.00 33.54 3.85
6432 6709 4.003648 GAGGAGTGGAGGTGTTTGTTATG 58.996 47.826 0.00 0.00 0.00 1.90
6453 6730 1.435256 AGGTGGTGGTAGCTTTCTGT 58.565 50.000 0.00 0.00 0.00 3.41
6455 6732 1.880027 GGTGGTGGTAGCTTTCTGTTG 59.120 52.381 0.00 0.00 0.00 3.33
6477 6754 6.110411 TGGTGTTAAAAGGAGGAGTAAGAG 57.890 41.667 0.00 0.00 0.00 2.85
6489 6768 5.163488 GGAGGAGTAAGAGGAGTAAGAAAGC 60.163 48.000 0.00 0.00 0.00 3.51
6495 6774 4.566426 AGAGGAGTAAGAAAGCAAGCAT 57.434 40.909 0.00 0.00 0.00 3.79
6496 6775 4.916183 AGAGGAGTAAGAAAGCAAGCATT 58.084 39.130 0.00 0.00 0.00 3.56
6510 6789 1.373748 GCATTGTGGCTTGCTGGTG 60.374 57.895 0.00 0.00 35.95 4.17
6522 6801 1.691196 TGCTGGTGTCTTTTTGGAGG 58.309 50.000 0.00 0.00 0.00 4.30
6523 6802 0.315251 GCTGGTGTCTTTTTGGAGGC 59.685 55.000 0.00 0.00 0.00 4.70
6526 6805 0.822121 GGTGTCTTTTTGGAGGCGGT 60.822 55.000 0.00 0.00 0.00 5.68
6527 6806 0.310854 GTGTCTTTTTGGAGGCGGTG 59.689 55.000 0.00 0.00 0.00 4.94
6528 6807 0.821711 TGTCTTTTTGGAGGCGGTGG 60.822 55.000 0.00 0.00 0.00 4.61
6529 6808 1.901464 TCTTTTTGGAGGCGGTGGC 60.901 57.895 0.00 0.00 38.90 5.01
6530 6809 2.123683 TTTTTGGAGGCGGTGGCA 60.124 55.556 0.00 0.00 42.47 4.92
6531 6810 1.532794 TTTTTGGAGGCGGTGGCAT 60.533 52.632 0.00 0.00 42.47 4.40
6532 6811 1.814772 TTTTTGGAGGCGGTGGCATG 61.815 55.000 0.00 0.00 42.47 4.06
6533 6812 4.738998 TTGGAGGCGGTGGCATGG 62.739 66.667 0.00 0.00 42.47 3.66
6575 6854 2.155279 GATGCTGATGCTGATGCTGAT 58.845 47.619 0.00 0.00 40.48 2.90
6576 6855 1.308998 TGCTGATGCTGATGCTGATG 58.691 50.000 0.00 0.00 40.48 3.07
6577 6856 0.039978 GCTGATGCTGATGCTGATGC 60.040 55.000 0.00 0.00 40.48 3.91
6578 6857 1.598882 CTGATGCTGATGCTGATGCT 58.401 50.000 0.00 0.00 40.48 3.79
6579 6858 1.265365 CTGATGCTGATGCTGATGCTG 59.735 52.381 0.00 0.00 40.48 4.41
6580 6859 1.134220 TGATGCTGATGCTGATGCTGA 60.134 47.619 0.00 0.00 40.48 4.26
6581 6860 2.155279 GATGCTGATGCTGATGCTGAT 58.845 47.619 0.00 0.00 40.48 2.90
6582 6861 1.308998 TGCTGATGCTGATGCTGATG 58.691 50.000 0.00 0.00 40.48 3.07
6583 6862 0.039978 GCTGATGCTGATGCTGATGC 60.040 55.000 0.00 0.00 40.48 3.91
6584 6863 1.598882 CTGATGCTGATGCTGATGCT 58.401 50.000 0.00 0.00 40.48 3.79
6585 6864 1.265365 CTGATGCTGATGCTGATGCTG 59.735 52.381 0.00 0.00 40.48 4.41
6586 6865 1.134220 TGATGCTGATGCTGATGCTGA 60.134 47.619 0.00 0.00 40.48 4.26
6587 6866 1.533299 GATGCTGATGCTGATGCTGAG 59.467 52.381 0.00 0.00 40.48 3.35
6588 6867 0.539986 TGCTGATGCTGATGCTGAGA 59.460 50.000 0.00 0.00 40.48 3.27
6589 6868 1.222300 GCTGATGCTGATGCTGAGAG 58.778 55.000 0.00 0.00 40.48 3.20
6590 6869 1.872388 CTGATGCTGATGCTGAGAGG 58.128 55.000 0.00 0.00 40.48 3.69
6591 6870 1.139256 CTGATGCTGATGCTGAGAGGT 59.861 52.381 0.00 0.00 40.48 3.85
6592 6871 1.134491 TGATGCTGATGCTGAGAGGTG 60.134 52.381 0.00 0.00 40.48 4.00
6593 6872 0.910338 ATGCTGATGCTGAGAGGTGT 59.090 50.000 0.00 0.00 40.48 4.16
6594 6873 0.689055 TGCTGATGCTGAGAGGTGTT 59.311 50.000 0.00 0.00 40.48 3.32
6595 6874 1.072806 TGCTGATGCTGAGAGGTGTTT 59.927 47.619 0.00 0.00 40.48 2.83
6596 6875 1.467734 GCTGATGCTGAGAGGTGTTTG 59.532 52.381 0.00 0.00 36.03 2.93
6597 6876 2.775890 CTGATGCTGAGAGGTGTTTGT 58.224 47.619 0.00 0.00 0.00 2.83
6598 6877 3.144506 CTGATGCTGAGAGGTGTTTGTT 58.855 45.455 0.00 0.00 0.00 2.83
6599 6878 4.318332 CTGATGCTGAGAGGTGTTTGTTA 58.682 43.478 0.00 0.00 0.00 2.41
6600 6879 4.910195 TGATGCTGAGAGGTGTTTGTTAT 58.090 39.130 0.00 0.00 0.00 1.89
6601 6880 5.316167 TGATGCTGAGAGGTGTTTGTTATT 58.684 37.500 0.00 0.00 0.00 1.40
6602 6881 5.769662 TGATGCTGAGAGGTGTTTGTTATTT 59.230 36.000 0.00 0.00 0.00 1.40
6603 6882 6.939730 TGATGCTGAGAGGTGTTTGTTATTTA 59.060 34.615 0.00 0.00 0.00 1.40
6604 6883 6.801539 TGCTGAGAGGTGTTTGTTATTTAG 57.198 37.500 0.00 0.00 0.00 1.85
6605 6884 6.296026 TGCTGAGAGGTGTTTGTTATTTAGT 58.704 36.000 0.00 0.00 0.00 2.24
6606 6885 7.446769 TGCTGAGAGGTGTTTGTTATTTAGTA 58.553 34.615 0.00 0.00 0.00 1.82
6607 6886 7.934665 TGCTGAGAGGTGTTTGTTATTTAGTAA 59.065 33.333 0.00 0.00 0.00 2.24
6608 6887 8.443937 GCTGAGAGGTGTTTGTTATTTAGTAAG 58.556 37.037 0.00 0.00 0.00 2.34
6609 6888 9.706691 CTGAGAGGTGTTTGTTATTTAGTAAGA 57.293 33.333 0.00 0.00 0.00 2.10
6629 6908 9.686683 AGTAAGATGTAAAAAGAGTTATGGCAT 57.313 29.630 4.88 4.88 0.00 4.40
6630 6909 9.722056 GTAAGATGTAAAAAGAGTTATGGCATG 57.278 33.333 10.98 0.00 0.00 4.06
6631 6910 6.799512 AGATGTAAAAAGAGTTATGGCATGC 58.200 36.000 9.90 9.90 0.00 4.06
6632 6911 5.973899 TGTAAAAAGAGTTATGGCATGCA 57.026 34.783 21.36 6.13 0.00 3.96
6633 6912 6.528537 TGTAAAAAGAGTTATGGCATGCAT 57.471 33.333 21.36 13.33 0.00 3.96
6634 6913 6.331845 TGTAAAAAGAGTTATGGCATGCATG 58.668 36.000 22.70 22.70 0.00 4.06
6635 6914 4.395959 AAAAGAGTTATGGCATGCATGG 57.604 40.909 27.34 10.03 0.00 3.66
6636 6915 2.742428 AGAGTTATGGCATGCATGGT 57.258 45.000 27.34 4.31 0.00 3.55
6637 6916 3.022557 AGAGTTATGGCATGCATGGTT 57.977 42.857 27.34 0.00 0.00 3.67
6638 6917 2.691526 AGAGTTATGGCATGCATGGTTG 59.308 45.455 27.34 4.59 0.00 3.77
6650 6929 2.414994 CATGGTTGCATCTGAGGACT 57.585 50.000 0.00 0.00 0.00 3.85
6651 6930 2.014857 CATGGTTGCATCTGAGGACTG 58.985 52.381 0.00 0.00 0.00 3.51
6652 6931 0.325933 TGGTTGCATCTGAGGACTGG 59.674 55.000 0.00 0.00 0.00 4.00
6653 6932 0.615331 GGTTGCATCTGAGGACTGGA 59.385 55.000 0.00 0.00 0.00 3.86
6654 6933 1.211457 GGTTGCATCTGAGGACTGGAT 59.789 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.144297 AGCTTGTTACTGATTTTGCTGGA 58.856 39.130 0.00 0.00 0.00 3.86
177 178 2.640346 GGTTTTTGTCAACCACACGT 57.360 45.000 0.00 0.00 45.12 4.49
284 285 3.066342 GTCTGATAAGGATGAACGGACGA 59.934 47.826 0.00 0.00 0.00 4.20
317 322 9.875691 GTATTGATTCCAGTAGTATCATATGCA 57.124 33.333 0.00 0.00 0.00 3.96
428 433 7.381408 GCGGCGCAATATAATTATAGATAGACA 59.619 37.037 29.21 0.00 0.00 3.41
431 436 6.742472 CGCGGCGCAATATAATTATAGATAG 58.258 40.000 32.61 4.41 0.00 2.08
542 547 2.033141 CCTATGCCCGCCTGATGG 59.967 66.667 0.00 0.00 0.00 3.51
551 556 0.323178 CATGATGCCTCCCTATGCCC 60.323 60.000 0.00 0.00 0.00 5.36
554 559 4.202182 CCAAAAACATGATGCCTCCCTATG 60.202 45.833 0.00 0.00 0.00 2.23
597 602 8.467598 GTCCCCTTATTTCTCCTTTATTTTCAC 58.532 37.037 0.00 0.00 0.00 3.18
606 611 4.357097 AGTTTGGTCCCCTTATTTCTCCTT 59.643 41.667 0.00 0.00 0.00 3.36
615 620 2.757894 TTTGCAGTTTGGTCCCCTTA 57.242 45.000 0.00 0.00 0.00 2.69
622 627 3.450457 TCTGGTTCATTTTGCAGTTTGGT 59.550 39.130 0.00 0.00 0.00 3.67
628 633 1.614903 TGCCTCTGGTTCATTTTGCAG 59.385 47.619 0.00 0.00 0.00 4.41
680 690 3.466395 TTTGGGGAATTCTGGTTAGGG 57.534 47.619 5.23 0.00 0.00 3.53
687 697 3.294214 CTGGAGGATTTGGGGAATTCTG 58.706 50.000 5.23 0.00 33.52 3.02
701 711 1.207791 GAAGAGGAATGGCTGGAGGA 58.792 55.000 0.00 0.00 0.00 3.71
717 727 8.844592 TGGGAACAGAGAGCCTATAGAGGAAG 62.845 50.000 7.84 0.00 39.83 3.46
720 730 3.161866 GGGAACAGAGAGCCTATAGAGG 58.838 54.545 0.00 0.00 46.93 3.69
770 795 2.044650 GATGGCAGCTGGCTGGAA 60.045 61.111 36.39 20.07 43.77 3.53
771 796 4.119363 GGATGGCAGCTGGCTGGA 62.119 66.667 36.39 20.44 43.77 3.86
850 875 2.041819 AGAGGAGGGGCTTACCGG 60.042 66.667 0.00 0.00 41.60 5.28
1322 1364 4.753662 AGTAGGCGACGAGGGGCA 62.754 66.667 0.00 0.00 0.00 5.36
1353 1395 2.674754 GGGTCCATCCAGGCGAAA 59.325 61.111 0.00 0.00 38.11 3.46
1620 1662 2.216488 CGCCGAAATGTAGTCGATGAAG 59.784 50.000 0.00 0.00 41.02 3.02
1624 1666 0.102481 AGCGCCGAAATGTAGTCGAT 59.898 50.000 2.29 0.00 41.02 3.59
1698 1740 1.609061 CGGTTGAATGACCTGAGCTGT 60.609 52.381 0.00 0.00 37.56 4.40
1785 1827 1.675801 CTCAGCCTCAGGAGCAACA 59.324 57.895 0.00 0.00 0.00 3.33
1834 1888 2.048222 CCTCTTTGTCTGCGGCGA 60.048 61.111 12.98 0.00 0.00 5.54
1835 1889 1.630244 CTTCCTCTTTGTCTGCGGCG 61.630 60.000 0.51 0.51 0.00 6.46
1836 1890 0.320771 TCTTCCTCTTTGTCTGCGGC 60.321 55.000 0.00 0.00 0.00 6.53
1837 1891 1.674221 CCTCTTCCTCTTTGTCTGCGG 60.674 57.143 0.00 0.00 0.00 5.69
1838 1892 1.273606 TCCTCTTCCTCTTTGTCTGCG 59.726 52.381 0.00 0.00 0.00 5.18
1839 1893 2.694213 GTCCTCTTCCTCTTTGTCTGC 58.306 52.381 0.00 0.00 0.00 4.26
1905 2061 4.200283 CTCTCGCCACGCCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
1926 2082 1.537135 GCAGTATCTCTCTTGGGCGAC 60.537 57.143 0.00 0.00 0.00 5.19
1931 2087 2.975732 TGCAGCAGTATCTCTCTTGG 57.024 50.000 0.00 0.00 0.00 3.61
1942 2098 0.183492 TCTGGTTCCTTTGCAGCAGT 59.817 50.000 0.00 0.00 39.18 4.40
1981 2137 0.921896 ATGGGCATAGGAGTGCTGTT 59.078 50.000 0.00 0.00 44.45 3.16
1987 2143 1.135094 CTGTCCATGGGCATAGGAGT 58.865 55.000 21.71 0.00 30.78 3.85
2000 2156 0.911769 GGTGTCCATGATCCTGTCCA 59.088 55.000 0.00 0.00 0.00 4.02
2069 2225 1.981256 GGTGTCCTCAACAACCATGT 58.019 50.000 0.00 0.00 39.89 3.21
2137 2293 5.429957 TTCTTCTTTTTCTCAGCTGAAGC 57.570 39.130 18.85 0.00 42.49 3.86
2167 2323 3.012518 CCTTATCTGCAGTGTCTTTGGG 58.987 50.000 14.67 3.16 0.00 4.12
2178 2334 0.747255 GAGACTCGCCCTTATCTGCA 59.253 55.000 0.00 0.00 0.00 4.41
2942 3152 2.418060 GGCTCTTGCAGAGACTCCTTAC 60.418 54.545 14.86 0.00 46.93 2.34
4174 4420 2.224646 ACCTTTTGGAAGAGACAGGCTC 60.225 50.000 0.00 0.00 44.07 4.70
4175 4421 1.777272 ACCTTTTGGAAGAGACAGGCT 59.223 47.619 0.00 0.00 44.07 4.58
4176 4422 2.155279 GACCTTTTGGAAGAGACAGGC 58.845 52.381 0.00 0.00 44.07 4.85
4177 4423 2.784347 GGACCTTTTGGAAGAGACAGG 58.216 52.381 0.00 0.00 44.07 4.00
4178 4424 2.417719 CGGACCTTTTGGAAGAGACAG 58.582 52.381 0.00 0.00 44.07 3.51
4179 4425 1.542547 GCGGACCTTTTGGAAGAGACA 60.543 52.381 0.00 0.00 44.07 3.41
4180 4426 1.157585 GCGGACCTTTTGGAAGAGAC 58.842 55.000 0.00 0.00 44.07 3.36
4181 4427 0.762418 TGCGGACCTTTTGGAAGAGA 59.238 50.000 0.00 0.00 44.07 3.10
4182 4428 1.537202 CTTGCGGACCTTTTGGAAGAG 59.463 52.381 0.00 0.00 44.07 2.85
4183 4429 1.604604 CTTGCGGACCTTTTGGAAGA 58.395 50.000 0.00 0.00 44.07 2.87
4184 4430 0.598065 CCTTGCGGACCTTTTGGAAG 59.402 55.000 0.00 0.00 44.07 3.46
4185 4431 1.460273 GCCTTGCGGACCTTTTGGAA 61.460 55.000 0.00 0.00 44.07 3.53
4186 4432 1.901464 GCCTTGCGGACCTTTTGGA 60.901 57.895 0.00 0.00 44.07 3.53
5714 5960 2.296190 TCGTCCTTCATATGATCACCCG 59.704 50.000 6.17 6.17 0.00 5.28
5722 5968 3.997021 GCCCAGTAATCGTCCTTCATATG 59.003 47.826 0.00 0.00 0.00 1.78
5743 5989 3.932710 TCCACGTTTATGAGAATGTCAGC 59.067 43.478 0.00 0.00 39.07 4.26
5766 6012 1.178276 CCTGACTAGACAGCGGTTCT 58.822 55.000 15.66 0.00 36.67 3.01
5783 6029 2.489802 CCCTTGTCCTTCTTCTTTGCCT 60.490 50.000 0.00 0.00 0.00 4.75
5864 6110 3.127533 CCTTTGCTTCCTCCGCGG 61.128 66.667 22.12 22.12 0.00 6.46
5865 6111 3.804193 GCCTTTGCTTCCTCCGCG 61.804 66.667 0.00 0.00 33.53 6.46
5866 6112 3.443925 GGCCTTTGCTTCCTCCGC 61.444 66.667 0.00 0.00 37.74 5.54
5867 6113 3.127533 CGGCCTTTGCTTCCTCCG 61.128 66.667 0.00 0.00 37.74 4.63
5868 6114 0.893727 TTTCGGCCTTTGCTTCCTCC 60.894 55.000 0.00 0.00 37.74 4.30
5869 6115 0.523519 CTTTCGGCCTTTGCTTCCTC 59.476 55.000 0.00 0.00 37.74 3.71
5870 6116 1.527433 GCTTTCGGCCTTTGCTTCCT 61.527 55.000 0.00 0.00 37.74 3.36
5871 6117 1.080501 GCTTTCGGCCTTTGCTTCC 60.081 57.895 0.00 0.00 37.74 3.46
5872 6118 4.559835 GCTTTCGGCCTTTGCTTC 57.440 55.556 0.00 0.00 37.74 3.86
5882 6128 0.239347 CTTGTCTTGCTGGCTTTCGG 59.761 55.000 0.00 0.00 0.00 4.30
5883 6129 0.239347 CCTTGTCTTGCTGGCTTTCG 59.761 55.000 0.00 0.00 0.00 3.46
5884 6130 0.038801 GCCTTGTCTTGCTGGCTTTC 60.039 55.000 0.00 0.00 41.92 2.62
5885 6131 0.756442 TGCCTTGTCTTGCTGGCTTT 60.756 50.000 0.00 0.00 45.11 3.51
5886 6132 1.152694 TGCCTTGTCTTGCTGGCTT 60.153 52.632 0.00 0.00 45.11 4.35
5887 6133 1.602888 CTGCCTTGTCTTGCTGGCT 60.603 57.895 0.00 0.00 45.11 4.75
6015 6282 3.369381 CCCGTACTGGCTGAAGATG 57.631 57.895 0.00 0.00 35.87 2.90
6072 6339 3.325753 ACCACCTGGGCTGAGCTC 61.326 66.667 6.82 6.82 42.05 4.09
6078 6345 2.833913 CCTGAACACCACCTGGGCT 61.834 63.158 0.00 0.00 42.05 5.19
6156 6423 4.069232 CGGAAGCTGTCGAGGCCA 62.069 66.667 5.01 0.00 0.00 5.36
6239 6506 2.121992 CTCCAGCAGCCCTGTTCACT 62.122 60.000 0.00 0.00 40.06 3.41
6341 6614 6.671402 GCAGCTCAATGCAACAAATAAATCAC 60.671 38.462 0.00 0.00 45.77 3.06
6342 6615 5.349270 GCAGCTCAATGCAACAAATAAATCA 59.651 36.000 0.00 0.00 45.77 2.57
6343 6616 5.792631 GCAGCTCAATGCAACAAATAAATC 58.207 37.500 0.00 0.00 45.77 2.17
6344 6617 5.789710 GCAGCTCAATGCAACAAATAAAT 57.210 34.783 0.00 0.00 45.77 1.40
6409 6683 1.507140 ACAAACACCTCCACTCCTCA 58.493 50.000 0.00 0.00 0.00 3.86
6416 6690 4.505918 CCACCTACATAACAAACACCTCCA 60.506 45.833 0.00 0.00 0.00 3.86
6432 6709 2.302157 ACAGAAAGCTACCACCACCTAC 59.698 50.000 0.00 0.00 0.00 3.18
6453 6730 6.465321 CCTCTTACTCCTCCTTTTAACACCAA 60.465 42.308 0.00 0.00 0.00 3.67
6455 6732 5.247792 TCCTCTTACTCCTCCTTTTAACACC 59.752 44.000 0.00 0.00 0.00 4.16
6477 6754 4.479619 CACAATGCTTGCTTTCTTACTCC 58.520 43.478 0.00 0.00 0.00 3.85
6495 6774 0.395586 AAGACACCAGCAAGCCACAA 60.396 50.000 0.00 0.00 0.00 3.33
6496 6775 0.395586 AAAGACACCAGCAAGCCACA 60.396 50.000 0.00 0.00 0.00 4.17
6498 6777 1.136695 CAAAAAGACACCAGCAAGCCA 59.863 47.619 0.00 0.00 0.00 4.75
6499 6778 1.538849 CCAAAAAGACACCAGCAAGCC 60.539 52.381 0.00 0.00 0.00 4.35
6500 6779 1.408702 TCCAAAAAGACACCAGCAAGC 59.591 47.619 0.00 0.00 0.00 4.01
6501 6780 2.035066 CCTCCAAAAAGACACCAGCAAG 59.965 50.000 0.00 0.00 0.00 4.01
6502 6781 2.031120 CCTCCAAAAAGACACCAGCAA 58.969 47.619 0.00 0.00 0.00 3.91
6505 6784 0.593128 CGCCTCCAAAAAGACACCAG 59.407 55.000 0.00 0.00 0.00 4.00
6510 6789 1.956802 CCACCGCCTCCAAAAAGAC 59.043 57.895 0.00 0.00 0.00 3.01
6526 6805 3.157949 CCATGCCATGCCATGCCA 61.158 61.111 11.13 0.00 40.92 4.92
6527 6806 4.619227 GCCATGCCATGCCATGCC 62.619 66.667 11.13 0.00 40.92 4.40
6528 6807 3.177194 ATGCCATGCCATGCCATGC 62.177 57.895 11.13 7.49 40.92 4.06
6529 6808 1.301637 CATGCCATGCCATGCCATG 60.302 57.895 13.50 13.50 41.71 3.66
6530 6809 3.147132 CATGCCATGCCATGCCAT 58.853 55.556 3.39 0.00 36.52 4.40
6575 6854 0.689055 AACACCTCTCAGCATCAGCA 59.311 50.000 0.00 0.00 45.49 4.41
6576 6855 1.467734 CAAACACCTCTCAGCATCAGC 59.532 52.381 0.00 0.00 42.56 4.26
6577 6856 2.775890 ACAAACACCTCTCAGCATCAG 58.224 47.619 0.00 0.00 0.00 2.90
6578 6857 2.936919 ACAAACACCTCTCAGCATCA 57.063 45.000 0.00 0.00 0.00 3.07
6579 6858 5.886960 AATAACAAACACCTCTCAGCATC 57.113 39.130 0.00 0.00 0.00 3.91
6580 6859 6.942576 ACTAAATAACAAACACCTCTCAGCAT 59.057 34.615 0.00 0.00 0.00 3.79
6581 6860 6.296026 ACTAAATAACAAACACCTCTCAGCA 58.704 36.000 0.00 0.00 0.00 4.41
6582 6861 6.803154 ACTAAATAACAAACACCTCTCAGC 57.197 37.500 0.00 0.00 0.00 4.26
6583 6862 9.706691 TCTTACTAAATAACAAACACCTCTCAG 57.293 33.333 0.00 0.00 0.00 3.35
6603 6882 9.686683 ATGCCATAACTCTTTTTACATCTTACT 57.313 29.630 0.00 0.00 0.00 2.24
6604 6883 9.722056 CATGCCATAACTCTTTTTACATCTTAC 57.278 33.333 0.00 0.00 0.00 2.34
6605 6884 8.405531 GCATGCCATAACTCTTTTTACATCTTA 58.594 33.333 6.36 0.00 0.00 2.10
6606 6885 7.093814 TGCATGCCATAACTCTTTTTACATCTT 60.094 33.333 16.68 0.00 0.00 2.40
6607 6886 6.377996 TGCATGCCATAACTCTTTTTACATCT 59.622 34.615 16.68 0.00 0.00 2.90
6608 6887 6.563422 TGCATGCCATAACTCTTTTTACATC 58.437 36.000 16.68 0.00 0.00 3.06
6609 6888 6.528537 TGCATGCCATAACTCTTTTTACAT 57.471 33.333 16.68 0.00 0.00 2.29
6610 6889 5.973899 TGCATGCCATAACTCTTTTTACA 57.026 34.783 16.68 0.00 0.00 2.41
6611 6890 5.750067 CCATGCATGCCATAACTCTTTTTAC 59.250 40.000 21.69 0.00 31.47 2.01
6612 6891 5.421693 ACCATGCATGCCATAACTCTTTTTA 59.578 36.000 21.69 0.00 31.47 1.52
6613 6892 4.223477 ACCATGCATGCCATAACTCTTTTT 59.777 37.500 21.69 0.00 31.47 1.94
6614 6893 3.770933 ACCATGCATGCCATAACTCTTTT 59.229 39.130 21.69 0.00 31.47 2.27
6615 6894 3.368248 ACCATGCATGCCATAACTCTTT 58.632 40.909 21.69 0.00 31.47 2.52
6616 6895 3.022557 ACCATGCATGCCATAACTCTT 57.977 42.857 21.69 0.00 31.47 2.85
6617 6896 2.691526 CAACCATGCATGCCATAACTCT 59.308 45.455 21.69 0.00 31.47 3.24
6618 6897 3.088194 CAACCATGCATGCCATAACTC 57.912 47.619 21.69 0.00 31.47 3.01
6631 6910 2.014857 CAGTCCTCAGATGCAACCATG 58.985 52.381 0.00 0.00 0.00 3.66
6632 6911 1.064906 CCAGTCCTCAGATGCAACCAT 60.065 52.381 0.00 0.00 0.00 3.55
6633 6912 0.325933 CCAGTCCTCAGATGCAACCA 59.674 55.000 0.00 0.00 0.00 3.67
6634 6913 0.615331 TCCAGTCCTCAGATGCAACC 59.385 55.000 0.00 0.00 0.00 3.77
6635 6914 2.706339 ATCCAGTCCTCAGATGCAAC 57.294 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.