Multiple sequence alignment - TraesCS2B01G410000

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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 TraesCS2B01G410000 chr2B 100.000 4055 0 0 1 4055 583557802 583553748 0.000000e+00 7489
1 TraesCS2B01G410000 chr2B 85.496 393 51 4 3666 4053 13146357 13146748 4.880000e-109 405
2 TraesCS2B01G410000 chr2A 91.573 2670 161 21 2 2655 641797717 641795096 0.000000e+00 3626
3 TraesCS2B01G410000 chr2A 93.381 846 47 5 2723 3565 641794954 641794115 0.000000e+00 1243
4 TraesCS2B01G410000 chr2A 85.751 393 50 4 3666 4053 724505765 724506156 1.050000e-110 411
5 TraesCS2B01G410000 chr2A 83.541 401 57 8 3657 4049 750101554 750101953 2.300000e-97 366
6 TraesCS2B01G410000 chr2D 91.415 2679 146 23 2 2654 496640556 496637936 0.000000e+00 3596
7 TraesCS2B01G410000 chr2D 86.927 872 62 20 2723 3575 496637786 496636948 0.000000e+00 931
8 TraesCS2B01G410000 chr2D 88.228 773 73 6 3282 4053 496634015 496633260 0.000000e+00 907
9 TraesCS2B01G410000 chr2D 89.807 569 35 8 2723 3284 496634728 496634176 0.000000e+00 708
10 TraesCS2B01G410000 chr5A 84.772 394 52 6 3666 4053 680877439 680877830 4.910000e-104 388
11 TraesCS2B01G410000 chr3B 85.027 374 50 4 3666 4034 817045887 817045515 3.830000e-100 375
12 TraesCS2B01G410000 chr7B 82.995 394 59 6 3666 4053 742381061 742380670 2.320000e-92 350
13 TraesCS2B01G410000 chr6D 84.348 345 38 11 1037 1374 315818577 315818242 1.410000e-84 324
14 TraesCS2B01G410000 chr6D 80.506 395 62 13 3667 4053 44259096 44259483 5.130000e-74 289
15 TraesCS2B01G410000 chr6B 84.058 345 39 11 1037 1374 509257704 509258039 6.540000e-83 318
16 TraesCS2B01G410000 chr6A 83.862 347 36 18 1037 1374 453572383 453572048 3.040000e-81 313
17 TraesCS2B01G410000 chr6A 80.714 140 23 3 3697 3832 462007617 462007478 5.540000e-19 106


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 TraesCS2B01G410000 chr2B 583553748 583557802 4054 True 7489.0 7489 100.00000 1 4055 1 chr2B.!!$R1 4054
1 TraesCS2B01G410000 chr2A 641794115 641797717 3602 True 2434.5 3626 92.47700 2 3565 2 chr2A.!!$R1 3563
2 TraesCS2B01G410000 chr2D 496633260 496640556 7296 True 1535.5 3596 89.09425 2 4053 4 chr2D.!!$R1 4051

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
938 946 0.025770 GCGTACACACACACACACAC 59.974 55.0 0.0 0.0 0.00 3.82 F
2187 2209 0.102844 CACACCAAACACCAAGCAGG 59.897 55.0 0.0 0.0 45.67 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 5910 0.179137 TAACATCTGCGAGACCAGCG 60.179 55.0 0.00 0.0 37.44 5.18 R
3088 6270 0.461339 CCCCTGTACATGTACGCACC 60.461 60.0 26.59 7.4 38.85 5.01 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
127 128 2.357154 GGGTGATCCTGGCTATGTTGTT 60.357 50.000 0.00 0.00 0.00 2.83
135 136 0.108662 GGCTATGTTGTTGCCCTTGC 60.109 55.000 0.00 0.00 42.11 4.01
150 151 0.175760 CTTGCTAGCGGCTAAGACCA 59.824 55.000 11.39 3.58 42.39 4.02
161 162 3.181461 CGGCTAAGACCAGATCCAGATTT 60.181 47.826 0.00 0.00 0.00 2.17
187 188 0.168348 CTCAGTCGTCGTAGTGGGTG 59.832 60.000 0.00 0.00 0.00 4.61
191 192 2.012673 AGTCGTCGTAGTGGGTGTATC 58.987 52.381 0.00 0.00 0.00 2.24
195 196 1.064654 GTCGTAGTGGGTGTATCGTCC 59.935 57.143 0.00 0.00 0.00 4.79
203 204 1.153429 GTGTATCGTCCTGGTGGGC 60.153 63.158 0.00 0.00 34.39 5.36
236 237 4.641645 CCCTTGGCGAGGTGTGCA 62.642 66.667 19.53 0.00 44.71 4.57
279 280 1.153429 GCCTTGGGCTAACGACGAT 60.153 57.895 0.00 0.00 46.69 3.73
351 352 1.244019 GCCAACGCTCAGGGTGAAAT 61.244 55.000 0.00 0.00 0.00 2.17
365 366 3.146847 GGTGAAATCCCTTGTTCGTTCT 58.853 45.455 0.00 0.00 0.00 3.01
375 376 1.737008 GTTCGTTCTGGGAGACGGC 60.737 63.158 0.00 0.00 0.00 5.68
382 383 3.551496 CTGGGAGACGGCCTTTGCA 62.551 63.158 0.00 0.00 40.13 4.08
422 423 2.901839 AGTCGTTGGTTAGTGTGGGTAT 59.098 45.455 0.00 0.00 0.00 2.73
434 435 0.108520 GTGGGTATCTTTCGGTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
451 452 1.574702 GCAGTAGCGTGTTTGGGGTC 61.575 60.000 0.00 0.00 0.00 4.46
502 504 2.701780 CGTGGCTAGTGGTCTCGCT 61.702 63.158 0.00 0.00 37.51 4.93
531 533 6.151144 GCCTTTCCTTTACATGTGACATAGTT 59.849 38.462 9.11 0.00 0.00 2.24
575 577 5.397142 TGATAGATTGATGGTCCTCGATG 57.603 43.478 0.00 0.00 0.00 3.84
650 652 4.736464 GCGACAAAGTCCAATGGTTTCTTT 60.736 41.667 0.00 6.61 0.00 2.52
654 656 6.106003 ACAAAGTCCAATGGTTTCTTTCAAC 58.894 36.000 13.28 0.00 0.00 3.18
661 663 0.383949 GGTTTCTTTCAACTGGCGCA 59.616 50.000 10.83 0.00 0.00 6.09
666 668 1.680735 TCTTTCAACTGGCGCATGTTT 59.319 42.857 10.83 0.00 0.00 2.83
692 694 3.866379 ATGAGCGGCCTTGGTTGCA 62.866 57.895 0.00 0.00 0.00 4.08
837 845 5.160607 AGGATTTTCTCAACGTCATGGTA 57.839 39.130 0.00 0.00 0.00 3.25
931 939 0.179132 AACTCACGCGTACACACACA 60.179 50.000 13.44 0.00 0.00 3.72
932 940 0.868602 ACTCACGCGTACACACACAC 60.869 55.000 13.44 0.00 0.00 3.82
933 941 0.868177 CTCACGCGTACACACACACA 60.868 55.000 13.44 0.00 0.00 3.72
934 942 1.140999 TCACGCGTACACACACACAC 61.141 55.000 13.44 0.00 0.00 3.82
935 943 1.153804 ACGCGTACACACACACACA 60.154 52.632 11.67 0.00 0.00 3.72
936 944 1.271549 CGCGTACACACACACACAC 59.728 57.895 0.00 0.00 0.00 3.82
937 945 1.414527 CGCGTACACACACACACACA 61.415 55.000 0.00 0.00 0.00 3.72
938 946 0.025770 GCGTACACACACACACACAC 59.974 55.000 0.00 0.00 0.00 3.82
939 947 1.351153 CGTACACACACACACACACA 58.649 50.000 0.00 0.00 0.00 3.72
940 948 1.059979 CGTACACACACACACACACAC 59.940 52.381 0.00 0.00 0.00 3.82
1066 1074 1.906824 GTGGTGGACGTCCTCTCCA 60.907 63.158 33.39 30.73 35.29 3.86
1166 1174 4.508128 GGCGATGACGAAGCCCGA 62.508 66.667 2.99 0.00 44.80 5.14
1373 1381 4.184629 GACATGTGAGTTCTCGCCTTAAT 58.815 43.478 1.15 0.00 0.00 1.40
1405 1413 0.459899 TCACGAGTATGATTGGCGCT 59.540 50.000 7.64 0.00 0.00 5.92
1412 1420 4.058124 GAGTATGATTGGCGCTTGTATGA 58.942 43.478 7.64 0.00 0.00 2.15
1436 1444 5.776744 TCGAGTTCCTACCTAGTTTGTTTC 58.223 41.667 0.00 0.00 0.00 2.78
1443 1451 5.987347 TCCTACCTAGTTTGTTTCGAAAGTG 59.013 40.000 11.66 0.00 0.00 3.16
1451 1459 5.799936 AGTTTGTTTCGAAAGTGATGTGTTG 59.200 36.000 11.66 0.00 0.00 3.33
1471 1479 2.266055 GAGGCCAGTTGGTCCTCG 59.734 66.667 19.06 0.00 43.41 4.63
1543 1551 5.242171 GGAATTCTCTAGACCAGGCTACTAC 59.758 48.000 5.23 0.00 0.00 2.73
1544 1552 5.656549 ATTCTCTAGACCAGGCTACTACT 57.343 43.478 0.00 0.00 0.00 2.57
1545 1553 6.766997 ATTCTCTAGACCAGGCTACTACTA 57.233 41.667 0.00 0.00 0.00 1.82
1582 1590 8.770828 TGACAAAAATAGTTTTAGGAAGACTCG 58.229 33.333 0.00 0.00 35.12 4.18
1703 1711 3.549070 GCAGCTTTATCCGCTTGATTTTG 59.451 43.478 0.00 0.00 35.07 2.44
1754 1762 4.314961 TCTTATCTGTTGCTTCTTTGCGA 58.685 39.130 0.00 0.00 35.36 5.10
1758 1766 0.588252 TGTTGCTTCTTTGCGAGCTC 59.412 50.000 2.73 2.73 35.36 4.09
1761 1769 0.390340 TGCTTCTTTGCGAGCTCGAT 60.390 50.000 38.74 0.00 43.02 3.59
1811 1820 4.691216 GCTGGGACCTTAATTAATCTAGCG 59.309 45.833 0.00 0.00 0.00 4.26
1812 1821 4.638304 TGGGACCTTAATTAATCTAGCGC 58.362 43.478 0.00 0.00 0.00 5.92
1820 1829 6.073765 CCTTAATTAATCTAGCGCGTCAACAT 60.074 38.462 8.43 0.00 0.00 2.71
1873 1882 1.195674 GCTTCTCTGCCGTTCAAGTTC 59.804 52.381 0.00 0.00 0.00 3.01
1890 1899 5.922544 TCAAGTTCGTGCTAAACTAACTACC 59.077 40.000 0.00 0.00 42.33 3.18
1891 1900 4.479619 AGTTCGTGCTAAACTAACTACCG 58.520 43.478 0.00 0.00 41.60 4.02
1930 1939 2.159043 TGTTCTATAGAGCCACTGCAGC 60.159 50.000 15.27 0.00 41.13 5.25
1957 1969 6.633500 TTTGTTGAGTTGTTCATAGAAGGG 57.367 37.500 0.00 0.00 35.27 3.95
1959 1971 5.063204 TGTTGAGTTGTTCATAGAAGGGTG 58.937 41.667 0.00 0.00 35.27 4.61
1976 1988 2.289694 GGGTGTGATGGGATAAGATCGG 60.290 54.545 0.00 0.00 0.00 4.18
2017 2029 1.134487 CACGTAGGTTGCATTGGCG 59.866 57.895 0.00 0.00 45.35 5.69
2062 2074 1.272480 CCCAACAACCCCTTCCCTAAG 60.272 57.143 0.00 0.00 0.00 2.18
2083 2095 5.242795 AGTCCTAACAAGTACAGGCAATT 57.757 39.130 0.00 0.00 0.00 2.32
2112 2124 5.195001 TGCACCCACTATCAAAAGAAAAC 57.805 39.130 0.00 0.00 0.00 2.43
2113 2125 4.226761 GCACCCACTATCAAAAGAAAACG 58.773 43.478 0.00 0.00 0.00 3.60
2117 2129 5.766174 ACCCACTATCAAAAGAAAACGCTAA 59.234 36.000 0.00 0.00 0.00 3.09
2119 2131 7.608761 ACCCACTATCAAAAGAAAACGCTAATA 59.391 33.333 0.00 0.00 0.00 0.98
2137 2149 7.123190 CGCTAATACTAACGATTTGCATTTGA 58.877 34.615 0.00 0.00 35.57 2.69
2145 2159 6.710692 AACGATTTGCATTTGAAGAATTCC 57.289 33.333 0.65 0.00 46.93 3.01
2187 2209 0.102844 CACACCAAACACCAAGCAGG 59.897 55.000 0.00 0.00 45.67 4.85
2275 2297 3.831727 AATGGTGGCCCTGCTGCAA 62.832 57.895 3.02 0.00 0.00 4.08
2469 2492 2.183478 TGGATGCACACTACCTGTTG 57.817 50.000 0.00 0.00 0.00 3.33
2487 2510 2.045536 CAACTCCCTCCTGCCAGC 60.046 66.667 0.00 0.00 0.00 4.85
2592 2615 8.598916 TCACTATGGTTATTCTTAGTTTGGACA 58.401 33.333 0.00 0.00 0.00 4.02
2649 5737 5.048782 TCTGAATAACTGATTTGGTGTGTGC 60.049 40.000 0.00 0.00 0.00 4.57
2650 5738 4.022416 TGAATAACTGATTTGGTGTGTGCC 60.022 41.667 0.00 0.00 0.00 5.01
2651 5739 2.071778 AACTGATTTGGTGTGTGCCT 57.928 45.000 0.00 0.00 0.00 4.75
2654 5742 2.233271 CTGATTTGGTGTGTGCCTCTT 58.767 47.619 0.00 0.00 0.00 2.85
2655 5743 3.181445 ACTGATTTGGTGTGTGCCTCTTA 60.181 43.478 0.00 0.00 0.00 2.10
2656 5744 3.820467 CTGATTTGGTGTGTGCCTCTTAA 59.180 43.478 0.00 0.00 0.00 1.85
2657 5745 3.820467 TGATTTGGTGTGTGCCTCTTAAG 59.180 43.478 0.00 0.00 0.00 1.85
2658 5746 1.604604 TTGGTGTGTGCCTCTTAAGC 58.395 50.000 0.00 0.00 0.00 3.09
2660 5748 0.320421 GGTGTGTGCCTCTTAAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
2661 5749 1.071605 GTGTGTGCCTCTTAAGCGAG 58.928 55.000 0.00 0.00 0.00 5.03
2671 5824 4.909894 CCTCTTAAGCGAGGCAAAATAAC 58.090 43.478 0.00 0.00 43.69 1.89
2679 5832 3.914364 GCGAGGCAAAATAACAAGACTTG 59.086 43.478 13.77 13.77 0.00 3.16
2682 5835 5.453567 AGGCAAAATAACAAGACTTGACC 57.546 39.130 21.95 9.01 0.00 4.02
2686 5839 6.145535 GCAAAATAACAAGACTTGACCTGAG 58.854 40.000 21.95 6.94 0.00 3.35
2689 5842 2.246719 ACAAGACTTGACCTGAGTGC 57.753 50.000 21.95 0.00 0.00 4.40
2693 5848 3.883830 AGACTTGACCTGAGTGCTATG 57.116 47.619 0.00 0.00 0.00 2.23
2694 5849 3.435275 AGACTTGACCTGAGTGCTATGA 58.565 45.455 0.00 0.00 0.00 2.15
2698 5853 6.155221 AGACTTGACCTGAGTGCTATGAATAA 59.845 38.462 0.00 0.00 0.00 1.40
2701 5856 5.419542 TGACCTGAGTGCTATGAATAACAC 58.580 41.667 0.00 0.00 31.31 3.32
2706 5861 6.539826 CCTGAGTGCTATGAATAACACATGAA 59.460 38.462 0.00 0.00 33.08 2.57
2714 5869 7.795734 GCTATGAATAACACATGAACTGAATCG 59.204 37.037 0.00 0.00 0.00 3.34
2719 5874 4.934075 ACACATGAACTGAATCGTGATG 57.066 40.909 0.00 9.54 38.37 3.07
2731 5904 6.707608 ACTGAATCGTGATGCATAACATATGT 59.292 34.615 14.73 1.41 39.84 2.29
2737 5910 5.455392 GTGATGCATAACATATGTTGCCTC 58.545 41.667 27.62 24.07 39.84 4.70
2742 5915 1.382522 AACATATGTTGCCTCGCTGG 58.617 50.000 20.19 0.00 36.80 4.85
2754 5927 2.182791 CGCTGGTCTCGCAGATGT 59.817 61.111 0.00 0.00 33.89 3.06
2835 6008 0.905337 AGGTGGACTTCCTCTTCGGG 60.905 60.000 0.00 0.00 36.82 5.14
2853 6026 3.464628 GTCGGCTTCGAGCTCAAC 58.535 61.111 15.40 0.00 44.17 3.18
2883 6056 2.048503 ACGTTCGGCCACTACTGC 60.049 61.111 2.24 0.00 0.00 4.40
2885 6058 2.260434 GTTCGGCCACTACTGCGA 59.740 61.111 2.24 0.00 0.00 5.10
2910 6083 0.323816 TCCAGTCCGAGATGCTCTGT 60.324 55.000 0.00 0.00 0.00 3.41
2946 6126 0.919780 AGCCCCTTCTTCCCCCTAAC 60.920 60.000 0.00 0.00 0.00 2.34
3001 6181 1.203287 TCTCTGAAGACGATGGCACTG 59.797 52.381 0.00 0.00 0.00 3.66
3107 6289 0.461339 GGTGCGTACATGTACAGGGG 60.461 60.000 30.17 17.60 35.87 4.79
3174 6356 0.877743 GCTGCTGTTTGGTTCCTCTC 59.122 55.000 0.00 0.00 0.00 3.20
3252 6434 3.010420 GAGGGAGTTGAATACAAGGTGC 58.990 50.000 0.00 0.00 36.64 5.01
3255 6437 2.415512 GGAGTTGAATACAAGGTGCGTC 59.584 50.000 0.00 0.00 36.64 5.19
3307 6652 9.869844 GTATATTGTTGGATCATTTTCTTCTCG 57.130 33.333 0.00 0.00 0.00 4.04
3317 6662 7.043059 GGATCATTTTCTTCTCGTTGCTACTAG 60.043 40.741 0.00 0.00 0.00 2.57
3318 6663 6.688578 TCATTTTCTTCTCGTTGCTACTAGT 58.311 36.000 0.00 0.00 0.00 2.57
3319 6664 7.823665 TCATTTTCTTCTCGTTGCTACTAGTA 58.176 34.615 1.89 1.89 0.00 1.82
3326 6671 3.623703 TCGTTGCTACTAGTACATGGGA 58.376 45.455 0.00 0.00 0.00 4.37
3332 6677 3.555168 GCTACTAGTACATGGGATGGCAC 60.555 52.174 0.00 0.00 33.60 5.01
3345 6690 4.968719 TGGGATGGCACTTAGAATCTCTAA 59.031 41.667 0.00 0.00 36.68 2.10
3351 6696 7.246171 TGGCACTTAGAATCTCTAACTCTTT 57.754 36.000 0.00 0.00 34.30 2.52
3374 6719 6.635030 TCCTCAAAAAGCTTTAACTCCTTC 57.365 37.500 13.10 0.00 0.00 3.46
3405 6750 5.612725 AGAATTTCTAGCTCTTCCCTCAG 57.387 43.478 0.00 0.00 0.00 3.35
3424 6769 5.304686 TCAGAAAGCTTTACCTCCTTCAA 57.695 39.130 12.68 0.00 0.00 2.69
3426 6772 6.126409 TCAGAAAGCTTTACCTCCTTCAAAA 58.874 36.000 12.68 0.00 0.00 2.44
3457 6803 7.016268 TGTTTTAAGGAGTTAGACTCAGACCAT 59.984 37.037 9.99 0.00 46.79 3.55
3461 6807 4.020543 GGAGTTAGACTCAGACCATGACT 58.979 47.826 9.99 0.00 46.79 3.41
3550 6896 2.827322 TCCCACCAATTCTGCTCAAATG 59.173 45.455 0.00 0.00 0.00 2.32
3565 6911 6.162777 TGCTCAAATGTTTATGGTTTTAGCC 58.837 36.000 0.00 0.00 33.41 3.93
3568 6914 5.782845 TCAAATGTTTATGGTTTTAGCCCCT 59.217 36.000 0.00 0.00 0.00 4.79
3570 6916 3.349022 TGTTTATGGTTTTAGCCCCTCG 58.651 45.455 0.00 0.00 0.00 4.63
3571 6917 2.047002 TTATGGTTTTAGCCCCTCGC 57.953 50.000 0.00 0.00 37.98 5.03
3574 6920 2.439701 GTTTTAGCCCCTCGCCCC 60.440 66.667 0.00 0.00 38.78 5.80
3575 6921 3.735097 TTTTAGCCCCTCGCCCCC 61.735 66.667 0.00 0.00 38.78 5.40
3576 6922 4.752594 TTTAGCCCCTCGCCCCCT 62.753 66.667 0.00 0.00 38.78 4.79
3653 6999 9.699410 ATTATCTTGATTTAATCAGGTTGGTCA 57.301 29.630 15.05 0.00 40.94 4.02
3702 7048 1.421382 ACAATGCGCTGCACAAATTC 58.579 45.000 9.73 0.00 43.04 2.17
3704 7050 1.996898 CAATGCGCTGCACAAATTCAT 59.003 42.857 9.73 0.00 43.04 2.57
3711 7057 2.350676 GCTGCACAAATTCATCGACACA 60.351 45.455 0.00 0.00 0.00 3.72
3712 7058 3.852939 GCTGCACAAATTCATCGACACAA 60.853 43.478 0.00 0.00 0.00 3.33
3732 7078 7.261325 ACACAACAAATATGCACACTAAACAA 58.739 30.769 0.00 0.00 0.00 2.83
3736 7082 6.446318 ACAAATATGCACACTAAACAACCTG 58.554 36.000 0.00 0.00 0.00 4.00
3769 7115 4.517285 AGTGAACTTTGAGAACAGCTTCA 58.483 39.130 0.00 0.00 0.00 3.02
3779 7125 2.689983 AGAACAGCTTCAACCAACAAGG 59.310 45.455 0.00 0.00 45.67 3.61
3782 7128 1.000938 CAGCTTCAACCAACAAGGAGC 60.001 52.381 0.00 0.00 41.22 4.70
3808 7154 5.641783 ATAGCACAAACAACATGCACATA 57.358 34.783 0.00 0.00 41.97 2.29
3816 7162 5.450592 AACAACATGCACATATGACACAA 57.549 34.783 10.38 0.00 0.00 3.33
3817 7163 5.050644 ACAACATGCACATATGACACAAG 57.949 39.130 10.38 4.16 0.00 3.16
3825 7171 7.446001 TGCACATATGACACAAGATTTAACA 57.554 32.000 10.38 0.00 0.00 2.41
3826 7172 7.529158 TGCACATATGACACAAGATTTAACAG 58.471 34.615 10.38 0.00 0.00 3.16
3833 7179 7.411486 TGACACAAGATTTAACAGGGAAAAA 57.589 32.000 0.00 0.00 0.00 1.94
3865 7211 1.154197 GAGGAGTAAACAACCACGGC 58.846 55.000 0.00 0.00 0.00 5.68
3893 7239 1.597663 CGACCAGTCCACAAACTTCAC 59.402 52.381 0.00 0.00 0.00 3.18
3894 7240 2.741878 CGACCAGTCCACAAACTTCACT 60.742 50.000 0.00 0.00 0.00 3.41
3904 7250 8.375506 AGTCCACAAACTTCACTTATGAGAATA 58.624 33.333 0.00 0.00 35.83 1.75
3917 7263 9.862371 CACTTATGAGAATAGTGAGTACAAAGT 57.138 33.333 0.00 0.00 41.33 2.66
3923 7269 8.861086 TGAGAATAGTGAGTACAAAGTCTTCTT 58.139 33.333 0.00 0.00 35.14 2.52
3950 7296 6.214412 AGAACCTCCAGAGAGATTTACAACAT 59.786 38.462 0.00 0.00 43.39 2.71
3952 7298 5.121811 CCTCCAGAGAGATTTACAACATGG 58.878 45.833 0.00 0.00 43.39 3.66
3954 7300 5.734720 TCCAGAGAGATTTACAACATGGTC 58.265 41.667 0.00 0.00 0.00 4.02
3960 7306 6.957631 AGAGATTTACAACATGGTCACCATA 58.042 36.000 9.68 0.00 43.15 2.74
3997 7343 3.821033 GAGCAACAACAACCATAAGAGGT 59.179 43.478 0.00 0.00 45.91 3.85
4012 7358 7.669722 ACCATAAGAGGTAAGATTTCAGCAAAA 59.330 33.333 0.00 0.00 40.98 2.44
4026 7372 6.698359 TTCAGCAAAACAAAGTTTACACAC 57.302 33.333 0.00 0.00 0.00 3.82
4032 7378 6.183360 GCAAAACAAAGTTTACACACCTTCTG 60.183 38.462 0.00 0.00 0.00 3.02
4040 7386 4.602340 TTACACACCTTCTGTCTCCTTC 57.398 45.455 0.00 0.00 0.00 3.46
4042 7388 2.103263 ACACACCTTCTGTCTCCTTCAC 59.897 50.000 0.00 0.00 0.00 3.18
4044 7390 2.366916 ACACCTTCTGTCTCCTTCACTG 59.633 50.000 0.00 0.00 0.00 3.66
4050 7396 5.467063 CCTTCTGTCTCCTTCACTGTTTTAC 59.533 44.000 0.00 0.00 0.00 2.01
4053 7399 6.591935 TCTGTCTCCTTCACTGTTTTACAAT 58.408 36.000 0.00 0.00 0.00 2.71
4054 7400 6.706270 TCTGTCTCCTTCACTGTTTTACAATC 59.294 38.462 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 1.271102 GGATCTGGTCTTAGCCGCTAG 59.729 57.143 0.00 0.00 0.00 3.42
161 162 0.322648 TACGACGACTGAGGACTCCA 59.677 55.000 0.00 0.00 0.00 3.86
187 188 2.504519 GGCCCACCAGGACGATAC 59.495 66.667 0.00 0.00 38.24 2.24
195 196 2.606587 AAGCTACCAGGCCCACCAG 61.607 63.158 0.00 0.00 39.06 4.00
203 204 3.545703 CAAGGGTATTCAAGCTACCAGG 58.454 50.000 5.02 0.00 40.41 4.45
209 210 0.618458 TCGCCAAGGGTATTCAAGCT 59.382 50.000 0.00 0.00 0.00 3.74
279 280 1.575922 GCGACACTTGCAAGCATCA 59.424 52.632 26.27 0.00 0.00 3.07
320 321 2.275380 CGTTGGCAAAAGGGGGAGG 61.275 63.158 0.00 0.00 0.00 4.30
351 352 0.685097 CTCCCAGAACGAACAAGGGA 59.315 55.000 0.00 0.00 45.94 4.20
365 366 2.819984 GATGCAAAGGCCGTCTCCCA 62.820 60.000 0.00 0.00 40.13 4.37
375 376 3.555586 CCAAAAGGGTCAAGATGCAAAGG 60.556 47.826 0.00 0.00 0.00 3.11
422 423 4.883026 GCTACTGCGACCGAAAGA 57.117 55.556 0.00 0.00 0.00 2.52
434 435 1.005394 CGACCCCAAACACGCTACT 60.005 57.895 0.00 0.00 0.00 2.57
440 441 1.152922 TCCCAACGACCCCAAACAC 60.153 57.895 0.00 0.00 0.00 3.32
451 452 1.079503 GTTGCTTAGAGCTCCCAACG 58.920 55.000 10.93 0.00 42.97 4.10
502 504 2.030363 CACATGTAAAGGAAAGGCGCAA 60.030 45.455 10.83 0.00 0.00 4.85
564 566 3.838271 GCTCCGCATCGAGGACCA 61.838 66.667 0.00 0.00 33.58 4.02
566 568 3.815569 CTCGCTCCGCATCGAGGAC 62.816 68.421 0.00 0.00 45.89 3.85
650 652 1.007502 GCAAACATGCGCCAGTTGA 60.008 52.632 14.19 0.00 0.00 3.18
654 656 2.202388 CGAGCAAACATGCGCCAG 60.202 61.111 4.18 0.00 40.27 4.85
674 676 3.064324 GCAACCAAGGCCGCTCAT 61.064 61.111 0.00 0.00 0.00 2.90
692 694 2.515901 GCCGGGCCACCATAAGAT 59.484 61.111 8.12 0.00 36.13 2.40
829 837 3.213249 AGAGAAACGTCGTACCATGAC 57.787 47.619 0.00 0.00 0.00 3.06
837 845 2.487372 GAGGAAGGTAGAGAAACGTCGT 59.513 50.000 0.00 0.00 0.00 4.34
931 939 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
932 940 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
933 941 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
934 942 0.447406 CCTGTGTGTGTGTGTGTGTG 59.553 55.000 0.00 0.00 0.00 3.82
935 943 1.305219 GCCTGTGTGTGTGTGTGTGT 61.305 55.000 0.00 0.00 0.00 3.72
936 944 1.429021 GCCTGTGTGTGTGTGTGTG 59.571 57.895 0.00 0.00 0.00 3.82
937 945 2.106074 CGCCTGTGTGTGTGTGTGT 61.106 57.895 0.00 0.00 0.00 3.72
938 946 2.708865 CGCCTGTGTGTGTGTGTG 59.291 61.111 0.00 0.00 0.00 3.82
939 947 3.202001 GCGCCTGTGTGTGTGTGT 61.202 61.111 0.00 0.00 0.00 3.72
940 948 3.201297 TGCGCCTGTGTGTGTGTG 61.201 61.111 4.18 0.00 0.00 3.82
1055 1063 3.063084 GGAGCGTGGAGAGGACGT 61.063 66.667 0.00 0.00 39.08 4.34
1227 1235 4.105057 AGGTAGATGTAACCCACCACAAAA 59.895 41.667 0.00 0.00 37.77 2.44
1230 1238 2.835764 GAGGTAGATGTAACCCACCACA 59.164 50.000 0.00 0.00 37.77 4.17
1373 1381 0.684479 CTCGTGATCAGGGGGTGAGA 60.684 60.000 15.05 0.00 39.07 3.27
1405 1413 6.363065 ACTAGGTAGGAACTCGATCATACAA 58.637 40.000 11.63 0.97 41.75 2.41
1412 1420 5.997384 AACAAACTAGGTAGGAACTCGAT 57.003 39.130 0.00 0.00 41.75 3.59
1436 1444 3.849645 GCCTCAACAACACATCACTTTCG 60.850 47.826 0.00 0.00 0.00 3.46
1443 1451 1.609208 ACTGGCCTCAACAACACATC 58.391 50.000 3.32 0.00 0.00 3.06
1451 1459 1.456287 AGGACCAACTGGCCTCAAC 59.544 57.895 3.32 0.00 37.20 3.18
1471 1479 0.034089 AAGGTGGGCATTAGCAGACC 60.034 55.000 0.00 0.00 44.61 3.85
1567 1575 4.995487 ACACCAATCGAGTCTTCCTAAAAC 59.005 41.667 0.00 0.00 0.00 2.43
1703 1711 1.264288 GTGCGATAATGCTTGGCCTAC 59.736 52.381 3.32 0.00 35.36 3.18
1754 1762 5.330455 TGACAGTGATCTTTTATCGAGCT 57.670 39.130 0.00 0.00 0.00 4.09
1758 1766 6.099579 CTGGTTGACAGTGATCTTTTATCG 57.900 41.667 0.00 0.00 42.42 2.92
1802 1811 4.928601 AGTTATGTTGACGCGCTAGATTA 58.071 39.130 5.73 0.00 0.00 1.75
1811 1820 4.165779 CAATCCCAAAGTTATGTTGACGC 58.834 43.478 0.00 0.00 0.00 5.19
1812 1821 4.165779 GCAATCCCAAAGTTATGTTGACG 58.834 43.478 0.00 0.00 0.00 4.35
1839 1848 3.102972 AGAGAAGCAGACTAATCAGCCA 58.897 45.455 0.00 0.00 38.08 4.75
1873 1882 3.722780 CGATCGGTAGTTAGTTTAGCACG 59.277 47.826 7.38 0.00 0.00 5.34
1890 1899 1.070821 ATGCAACACTGACACGATCG 58.929 50.000 14.88 14.88 0.00 3.69
1891 1900 1.800586 ACATGCAACACTGACACGATC 59.199 47.619 0.00 0.00 0.00 3.69
1930 1939 7.596248 CCTTCTATGAACAACTCAACAAATTGG 59.404 37.037 0.00 0.00 37.67 3.16
1957 1969 2.224281 TGCCGATCTTATCCCATCACAC 60.224 50.000 0.00 0.00 0.00 3.82
1959 1971 2.839486 TGCCGATCTTATCCCATCAC 57.161 50.000 0.00 0.00 0.00 3.06
2017 2029 7.301789 GTTCTGCTTCTTAAAGAATGTTCTCC 58.698 38.462 0.00 0.00 36.28 3.71
2062 2074 5.001232 TCAATTGCCTGTACTTGTTAGGAC 58.999 41.667 0.00 0.00 35.63 3.85
2083 2095 0.253044 GATAGTGGGTGCAGCCTTCA 59.747 55.000 33.29 18.96 37.43 3.02
2112 2124 7.123190 TCAAATGCAAATCGTTAGTATTAGCG 58.877 34.615 0.00 0.00 35.17 4.26
2113 2125 8.835467 TTCAAATGCAAATCGTTAGTATTAGC 57.165 30.769 0.00 0.00 0.00 3.09
2119 2131 7.542130 GGAATTCTTCAAATGCAAATCGTTAGT 59.458 33.333 5.23 0.00 0.00 2.24
2123 2135 6.029346 AGGAATTCTTCAAATGCAAATCGT 57.971 33.333 5.23 0.00 0.00 3.73
2137 2149 5.136105 GGGCAGATGACATAAGGAATTCTT 58.864 41.667 5.23 0.00 39.40 2.52
2145 2159 1.884579 GGCATGGGCAGATGACATAAG 59.115 52.381 0.00 0.00 43.71 1.73
2187 2209 6.435904 ACCTCATGAGCAGATAATACTCTACC 59.564 42.308 17.76 0.00 0.00 3.18
2275 2297 0.851469 ATGGATGGAAGGAGCAGCAT 59.149 50.000 0.00 0.00 0.00 3.79
2469 2492 2.045536 CTGGCAGGAGGGAGTTGC 60.046 66.667 6.61 0.00 37.11 4.17
2487 2510 0.763652 ACAGATAGGGCTGGATGCTG 59.236 55.000 0.00 0.00 40.20 4.41
2650 5738 5.545658 TGTTATTTTGCCTCGCTTAAGAG 57.454 39.130 6.67 2.60 37.97 2.85
2651 5739 5.703592 TCTTGTTATTTTGCCTCGCTTAAGA 59.296 36.000 6.67 0.00 0.00 2.10
2654 5742 5.001232 AGTCTTGTTATTTTGCCTCGCTTA 58.999 37.500 0.00 0.00 0.00 3.09
2655 5743 3.821033 AGTCTTGTTATTTTGCCTCGCTT 59.179 39.130 0.00 0.00 0.00 4.68
2656 5744 3.412386 AGTCTTGTTATTTTGCCTCGCT 58.588 40.909 0.00 0.00 0.00 4.93
2657 5745 3.831715 AGTCTTGTTATTTTGCCTCGC 57.168 42.857 0.00 0.00 0.00 5.03
2658 5746 5.147162 GTCAAGTCTTGTTATTTTGCCTCG 58.853 41.667 12.30 0.00 0.00 4.63
2660 5748 5.010012 CAGGTCAAGTCTTGTTATTTTGCCT 59.990 40.000 12.30 5.92 0.00 4.75
2661 5749 5.009610 TCAGGTCAAGTCTTGTTATTTTGCC 59.990 40.000 12.30 4.08 0.00 4.52
2662 5750 6.072112 TCAGGTCAAGTCTTGTTATTTTGC 57.928 37.500 12.30 0.00 0.00 3.68
2663 5751 7.134815 CACTCAGGTCAAGTCTTGTTATTTTG 58.865 38.462 12.30 4.73 0.00 2.44
2668 5821 3.388024 AGCACTCAGGTCAAGTCTTGTTA 59.612 43.478 12.30 0.00 0.00 2.41
2671 5824 2.540265 AGCACTCAGGTCAAGTCTTG 57.460 50.000 6.21 6.21 0.00 3.02
2679 5832 5.419542 TGTGTTATTCATAGCACTCAGGTC 58.580 41.667 13.12 0.00 42.62 3.85
2682 5835 7.279536 AGTTCATGTGTTATTCATAGCACTCAG 59.720 37.037 13.12 5.40 42.62 3.35
2686 5839 7.307493 TCAGTTCATGTGTTATTCATAGCAC 57.693 36.000 6.81 6.81 42.52 4.40
2689 5842 8.820933 ACGATTCAGTTCATGTGTTATTCATAG 58.179 33.333 0.00 0.00 0.00 2.23
2693 5848 7.060600 TCACGATTCAGTTCATGTGTTATTC 57.939 36.000 0.00 0.00 0.00 1.75
2694 5849 7.466805 CATCACGATTCAGTTCATGTGTTATT 58.533 34.615 0.00 0.00 0.00 1.40
2698 5853 3.125829 GCATCACGATTCAGTTCATGTGT 59.874 43.478 0.00 0.00 0.00 3.72
2701 5856 4.547406 ATGCATCACGATTCAGTTCATG 57.453 40.909 0.00 0.00 0.00 3.07
2706 5861 6.707608 ACATATGTTATGCATCACGATTCAGT 59.292 34.615 0.19 0.00 38.94 3.41
2714 5869 5.443185 AGGCAACATATGTTATGCATCAC 57.557 39.130 26.05 13.63 37.88 3.06
2719 5874 2.549754 AGCGAGGCAACATATGTTATGC 59.450 45.455 20.39 20.08 36.32 3.14
2731 5904 4.742201 GCGAGACCAGCGAGGCAA 62.742 66.667 0.00 0.00 43.14 4.52
2737 5910 0.179137 TAACATCTGCGAGACCAGCG 60.179 55.000 0.00 0.00 37.44 5.18
2742 5915 3.421826 CGTTGTTGTAACATCTGCGAGAC 60.422 47.826 0.00 0.00 38.95 3.36
2754 5927 1.794116 GCGAAGTAGGCGTTGTTGTAA 59.206 47.619 0.00 0.00 0.00 2.41
2835 6008 2.095252 GTTGAGCTCGAAGCCGACC 61.095 63.158 4.86 0.00 43.77 4.79
2853 6026 4.695231 AACGTCTCCGGCGACACG 62.695 66.667 23.51 14.03 36.58 4.49
2883 6056 0.748367 TCTCGGACTGGAGGATGTCG 60.748 60.000 0.00 0.00 34.74 4.35
2885 6058 1.407936 CATCTCGGACTGGAGGATGT 58.592 55.000 0.00 0.00 34.74 3.06
2910 6083 4.382541 TCCGGCTCCAGCTCCAGA 62.383 66.667 0.00 0.00 41.70 3.86
3017 6197 2.886862 CTGCTGAGTACTGCTGCTAT 57.113 50.000 0.00 0.00 40.71 2.97
3088 6270 0.461339 CCCCTGTACATGTACGCACC 60.461 60.000 26.59 7.40 38.85 5.01
3120 6302 2.649349 CTCGCGTACTCTGCTCGC 60.649 66.667 5.77 0.00 45.28 5.03
3174 6356 7.997107 TTGTCACCTAAACAAGCTATATACG 57.003 36.000 0.00 0.00 32.98 3.06
3252 6434 1.202348 TGTGGACTAGAGCACATGACG 59.798 52.381 0.00 0.00 0.00 4.35
3255 6437 2.998670 CACTTGTGGACTAGAGCACATG 59.001 50.000 0.00 0.00 0.00 3.21
3301 6646 5.274718 CCATGTACTAGTAGCAACGAGAAG 58.725 45.833 1.87 0.00 33.04 2.85
3307 6652 4.632153 CCATCCCATGTACTAGTAGCAAC 58.368 47.826 1.87 0.00 0.00 4.17
3317 6662 3.838244 TCTAAGTGCCATCCCATGTAC 57.162 47.619 0.00 0.00 0.00 2.90
3318 6663 4.660303 AGATTCTAAGTGCCATCCCATGTA 59.340 41.667 0.00 0.00 0.00 2.29
3319 6664 3.461085 AGATTCTAAGTGCCATCCCATGT 59.539 43.478 0.00 0.00 0.00 3.21
3326 6671 7.430760 AAGAGTTAGAGATTCTAAGTGCCAT 57.569 36.000 10.13 0.00 41.35 4.40
3345 6690 7.201830 GGAGTTAAAGCTTTTTGAGGAAAGAGT 60.202 37.037 18.47 0.00 38.60 3.24
3351 6696 5.238650 CGAAGGAGTTAAAGCTTTTTGAGGA 59.761 40.000 18.47 0.00 0.00 3.71
3374 6719 8.760569 GGAAGAGCTAGAAATTCTTCTAATTCG 58.239 37.037 18.11 0.00 42.35 3.34
3405 6750 8.144478 AGAAATTTTGAAGGAGGTAAAGCTTTC 58.856 33.333 16.57 7.49 0.00 2.62
3426 6772 9.495572 CTGAGTCTAACTCCTTAAAACAGAAAT 57.504 33.333 4.74 0.00 44.44 2.17
3457 6803 9.323985 CAAAATTTTGAGGAAAATGGTTAGTCA 57.676 29.630 23.72 0.00 40.27 3.41
3550 6896 2.098607 GCGAGGGGCTAAAACCATAAAC 59.901 50.000 0.00 0.00 39.11 2.01
3643 6989 2.358737 GTCCGGCTGACCAACCTG 60.359 66.667 0.00 0.00 38.09 4.00
3651 6997 1.216977 CAACATACGGTCCGGCTGA 59.783 57.895 17.28 0.00 0.00 4.26
3653 6999 1.956629 CTCCAACATACGGTCCGGCT 61.957 60.000 17.28 0.00 0.00 5.52
3686 7032 1.796253 CGATGAATTTGTGCAGCGCAT 60.796 47.619 11.47 0.00 41.91 4.73
3689 7035 1.136000 TGTCGATGAATTTGTGCAGCG 60.136 47.619 0.00 0.00 44.36 5.18
3691 7037 3.541071 TGTGTCGATGAATTTGTGCAG 57.459 42.857 0.00 0.00 0.00 4.41
3702 7048 4.554586 GTGTGCATATTTGTTGTGTCGATG 59.445 41.667 0.00 0.00 0.00 3.84
3704 7050 3.812609 AGTGTGCATATTTGTTGTGTCGA 59.187 39.130 0.00 0.00 0.00 4.20
3711 7057 6.922957 CAGGTTGTTTAGTGTGCATATTTGTT 59.077 34.615 0.00 0.00 0.00 2.83
3712 7058 6.446318 CAGGTTGTTTAGTGTGCATATTTGT 58.554 36.000 0.00 0.00 0.00 2.83
3732 7078 3.588277 CACTACACGTGAAGCAGGT 57.412 52.632 25.01 8.12 46.81 4.00
3760 7106 2.689983 CTCCTTGTTGGTTGAAGCTGTT 59.310 45.455 0.00 0.00 37.07 3.16
3769 7115 2.488153 GCTATTTCGCTCCTTGTTGGTT 59.512 45.455 0.00 0.00 37.07 3.67
3779 7125 3.884169 TGTTGTTTGTGCTATTTCGCTC 58.116 40.909 0.00 0.00 0.00 5.03
3782 7128 3.980134 TGCATGTTGTTTGTGCTATTTCG 59.020 39.130 0.00 0.00 39.52 3.46
3808 7154 7.595819 TTTTCCCTGTTAAATCTTGTGTCAT 57.404 32.000 0.00 0.00 0.00 3.06
3833 7179 6.650120 TGTTTACTCCTCAAGTTGAAGAGTT 58.350 36.000 31.96 20.18 43.53 3.01
3834 7180 6.235231 TGTTTACTCCTCAAGTTGAAGAGT 57.765 37.500 30.42 30.42 46.55 3.24
3838 7184 5.355910 GTGGTTGTTTACTCCTCAAGTTGAA 59.644 40.000 7.06 0.00 39.55 2.69
3848 7194 0.872388 CAGCCGTGGTTGTTTACTCC 59.128 55.000 0.00 0.00 0.00 3.85
3877 7223 5.991606 TCTCATAAGTGAAGTTTGTGGACTG 59.008 40.000 0.00 0.00 33.05 3.51
3904 7250 7.927092 GGTTCTAAAGAAGACTTTGTACTCACT 59.073 37.037 0.00 0.00 44.67 3.41
3917 7263 5.893500 TCTCTCTGGAGGTTCTAAAGAAGA 58.106 41.667 0.00 0.00 39.86 2.87
3923 7269 7.234782 TGTTGTAAATCTCTCTGGAGGTTCTAA 59.765 37.037 0.00 0.00 41.57 2.10
3928 7274 5.338708 CCATGTTGTAAATCTCTCTGGAGGT 60.339 44.000 0.00 0.00 39.86 3.85
3950 7296 1.846007 GGTTGGCAATATGGTGACCA 58.154 50.000 6.84 6.84 38.19 4.02
3952 7298 0.738389 CCGGTTGGCAATATGGTGAC 59.262 55.000 1.92 0.00 0.00 3.67
3972 7318 3.745975 TCTTATGGTTGTTGTTGCTCTCG 59.254 43.478 0.00 0.00 0.00 4.04
3973 7319 4.154918 CCTCTTATGGTTGTTGTTGCTCTC 59.845 45.833 0.00 0.00 0.00 3.20
3997 7343 9.862371 TGTAAACTTTGTTTTGCTGAAATCTTA 57.138 25.926 0.94 0.00 0.00 2.10
4012 7358 5.497474 AGACAGAAGGTGTGTAAACTTTGT 58.503 37.500 0.00 0.00 40.56 2.83
4026 7372 3.760580 AACAGTGAAGGAGACAGAAGG 57.239 47.619 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.