Multiple sequence alignment - TraesCS2A01G586300

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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 TraesCS2A01G586300 chr2A 100.000 5691 0 0 1 5691 776599184 776604874 0.000000e+00 10510.0
1 TraesCS2A01G586300 chr2A 76.786 112 24 2 2129 2239 691530578 691530688 1.710000e-05 62.1
2 TraesCS2A01G586300 chr2D 92.486 2635 126 18 1 2602 651073025 651070430 0.000000e+00 3703.0
3 TraesCS2A01G586300 chr2D 91.554 2072 140 17 2770 4826 651070021 651067970 0.000000e+00 2824.0
4 TraesCS2A01G586300 chr2D 90.621 821 74 3 4824 5643 651067919 651067101 0.000000e+00 1086.0
5 TraesCS2A01G586300 chr2D 78.505 107 21 2 2134 2239 548632169 548632274 1.020000e-07 69.4
6 TraesCS2A01G586300 chr2D 77.679 112 23 2 2147 2257 548447572 548447682 3.680000e-07 67.6
7 TraesCS2A01G586300 chr2B 91.303 2610 143 27 1 2604 780017998 780015467 0.000000e+00 3485.0
8 TraesCS2A01G586300 chr2B 96.856 986 30 1 3803 4788 780013731 780012747 0.000000e+00 1648.0
9 TraesCS2A01G586300 chr2B 93.676 1091 46 6 2605 3682 780015437 780014357 0.000000e+00 1611.0
10 TraesCS2A01G586300 chr2B 90.283 813 74 5 4833 5643 780012660 780011851 0.000000e+00 1059.0
11 TraesCS2A01G586300 chr2B 84.689 209 28 4 2704 2911 784603844 784603639 7.470000e-49 206.0
12 TraesCS2A01G586300 chr2B 95.775 71 3 0 3735 3805 780014050 780013980 1.300000e-21 115.0
13 TraesCS2A01G586300 chr3B 85.000 740 100 10 4826 5560 79271999 79271266 0.000000e+00 741.0
14 TraesCS2A01G586300 chr3B 72.165 291 67 10 1208 1492 13246271 13246553 6.110000e-10 76.8
15 TraesCS2A01G586300 chr5B 83.167 802 122 12 4827 5622 619031 619825 0.000000e+00 721.0
16 TraesCS2A01G586300 chr5B 83.191 821 99 22 4850 5640 158909054 158909865 0.000000e+00 715.0
17 TraesCS2A01G586300 chr1B 82.718 839 113 19 4827 5642 675463766 675464595 0.000000e+00 717.0
18 TraesCS2A01G586300 chr5D 85.131 686 92 7 4830 5510 396813385 396812705 0.000000e+00 693.0
19 TraesCS2A01G586300 chr4B 82.241 839 116 15 4830 5640 3910880 3910047 0.000000e+00 693.0
20 TraesCS2A01G586300 chr4B 80.399 602 116 2 4034 4634 576166920 576167520 1.870000e-124 457.0
21 TraesCS2A01G586300 chr3A 81.764 839 120 14 4827 5637 742042474 742043307 0.000000e+00 671.0
22 TraesCS2A01G586300 chr3A 71.821 291 70 8 1207 1492 16009458 16009741 7.910000e-09 73.1
23 TraesCS2A01G586300 chr4A 79.620 579 114 4 4034 4610 7441747 7441171 4.100000e-111 412.0
24 TraesCS2A01G586300 chr6D 87.081 209 24 2 2704 2911 440639514 440639720 3.430000e-57 233.0
25 TraesCS2A01G586300 chr6D 83.871 217 32 3 2695 2911 433481168 433481381 2.690000e-48 204.0
26 TraesCS2A01G586300 chr6D 98.182 55 1 0 5637 5691 39105370 39105424 4.690000e-16 97.1
27 TraesCS2A01G586300 chr1D 86.603 209 24 3 2704 2911 467628087 467628292 1.600000e-55 228.0
28 TraesCS2A01G586300 chr1D 98.182 55 1 0 5637 5691 143476253 143476199 4.690000e-16 97.1
29 TraesCS2A01G586300 chr1D 98.182 55 1 0 5637 5691 208607711 208607657 4.690000e-16 97.1
30 TraesCS2A01G586300 chr1D 98.182 55 1 0 5637 5691 278873400 278873454 4.690000e-16 97.1
31 TraesCS2A01G586300 chr1D 98.182 55 1 0 5637 5691 305569923 305569977 4.690000e-16 97.1
32 TraesCS2A01G586300 chr1D 98.182 55 1 0 5637 5691 348279368 348279422 4.690000e-16 97.1
33 TraesCS2A01G586300 chr6A 85.646 209 27 3 2704 2911 601961147 601961353 3.450000e-52 217.0
34 TraesCS2A01G586300 chr4D 85.238 210 24 6 2704 2911 109270154 109270358 5.780000e-50 209.0
35 TraesCS2A01G586300 chr4D 74.074 297 57 13 1172 1458 460955845 460956131 2.800000e-18 104.0
36 TraesCS2A01G586300 chr4D 98.182 55 1 0 5637 5691 158875491 158875437 4.690000e-16 97.1
37 TraesCS2A01G586300 chr4D 98.182 55 1 0 5637 5691 213010891 213010837 4.690000e-16 97.1
38 TraesCS2A01G586300 chr4D 98.182 55 1 0 5637 5691 370088692 370088638 4.690000e-16 97.1
39 TraesCS2A01G586300 chr1A 84.135 208 30 3 2704 2911 569353848 569353644 1.250000e-46 198.0
40 TraesCS2A01G586300 chr3D 71.898 274 63 10 1225 1492 5409970 5409705 3.680000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G586300 chr2A 776599184 776604874 5690 False 10510.000000 10510 100.000000 1 5691 1 chr2A.!!$F2 5690
1 TraesCS2A01G586300 chr2D 651067101 651073025 5924 True 2537.666667 3703 91.553667 1 5643 3 chr2D.!!$R1 5642
2 TraesCS2A01G586300 chr2B 780011851 780017998 6147 True 1583.600000 3485 93.578600 1 5643 5 chr2B.!!$R2 5642
3 TraesCS2A01G586300 chr3B 79271266 79271999 733 True 741.000000 741 85.000000 4826 5560 1 chr3B.!!$R1 734
4 TraesCS2A01G586300 chr5B 619031 619825 794 False 721.000000 721 83.167000 4827 5622 1 chr5B.!!$F1 795
5 TraesCS2A01G586300 chr5B 158909054 158909865 811 False 715.000000 715 83.191000 4850 5640 1 chr5B.!!$F2 790
6 TraesCS2A01G586300 chr1B 675463766 675464595 829 False 717.000000 717 82.718000 4827 5642 1 chr1B.!!$F1 815
7 TraesCS2A01G586300 chr5D 396812705 396813385 680 True 693.000000 693 85.131000 4830 5510 1 chr5D.!!$R1 680
8 TraesCS2A01G586300 chr4B 3910047 3910880 833 True 693.000000 693 82.241000 4830 5640 1 chr4B.!!$R1 810
9 TraesCS2A01G586300 chr4B 576166920 576167520 600 False 457.000000 457 80.399000 4034 4634 1 chr4B.!!$F1 600
10 TraesCS2A01G586300 chr3A 742042474 742043307 833 False 671.000000 671 81.764000 4827 5637 1 chr3A.!!$F2 810
11 TraesCS2A01G586300 chr4A 7441171 7441747 576 True 412.000000 412 79.620000 4034 4610 1 chr4A.!!$R1 576

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
623 624 0.823356 AGATGGAGAGAGAGAGCGCC 60.823 60.0 2.29 0.0 0.00 6.53 F
1560 1592 0.108945 CGAACGTCACCTTCTACCCC 60.109 60.0 0.00 0.0 0.00 4.95 F
1860 1892 0.460987 CTGCTGCTTCCCCTAGTTCG 60.461 60.0 0.00 0.0 0.00 3.95 F
2607 2674 0.517316 CGTCAGTGGTAAGGCAAAGC 59.483 55.0 0.00 0.0 0.00 3.51 F
3516 3805 0.882474 GATACTAGCATCGAGGGCGT 59.118 55.0 0.00 0.0 38.98 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1667 0.032813 CCATCCCCACTTCATGCCTT 60.033 55.000 0.00 0.0 0.00 4.35 R
2421 2459 0.763223 AAACGGAGTGGTCAGGGTCT 60.763 55.000 0.00 0.0 45.00 3.85 R
3500 3789 1.141881 CAACGCCCTCGATGCTAGT 59.858 57.895 5.65 0.0 39.41 2.57 R
4296 5100 0.534412 CTGGAGGATGCTTGACGTCT 59.466 55.000 17.92 0.0 34.46 4.18 R
5283 6149 1.272769 GACTTCAAGACCGTGGTAGCT 59.727 52.381 0.00 0.0 0.00 3.32 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
85 86 1.273606 TGACCCTGAGAAGAAGAAGCG 59.726 52.381 0.00 0.00 0.00 4.68
123 124 6.830114 TTCAAGAACGTCTCTTCTCTTTTC 57.170 37.500 9.20 0.00 42.84 2.29
129 130 2.914214 CGTCTCTTCTCTTTTCGAGCTG 59.086 50.000 0.00 0.00 39.70 4.24
303 304 1.874299 ATGAGGCCCCGGATGGTTTT 61.874 55.000 0.73 0.00 0.00 2.43
312 313 2.267045 GGATGGTTTTCCGCTGCTT 58.733 52.632 0.00 0.00 44.36 3.91
343 344 3.355378 CTTCCACTTGAACATGCCCATA 58.645 45.455 0.00 0.00 0.00 2.74
352 353 3.519107 TGAACATGCCCATACTCTTGAGA 59.481 43.478 4.49 0.00 0.00 3.27
357 358 3.653164 TGCCCATACTCTTGAGATGGTA 58.347 45.455 18.55 10.57 38.82 3.25
363 364 6.207810 CCCATACTCTTGAGATGGTAGTAGAC 59.792 46.154 18.55 0.00 38.82 2.59
365 366 5.100344 ACTCTTGAGATGGTAGTAGACGA 57.900 43.478 4.49 0.00 0.00 4.20
366 367 4.877251 ACTCTTGAGATGGTAGTAGACGAC 59.123 45.833 4.49 0.00 0.00 4.34
587 588 5.697473 TTTTTAACACATGAAGATGGCGA 57.303 34.783 0.00 0.00 33.39 5.54
588 589 5.895636 TTTTAACACATGAAGATGGCGAT 57.104 34.783 0.00 0.00 33.39 4.58
607 608 2.623878 TCGAGTAGAAGCCGAGAGAT 57.376 50.000 0.00 0.00 0.00 2.75
609 610 1.265635 CGAGTAGAAGCCGAGAGATGG 59.734 57.143 0.00 0.00 0.00 3.51
610 611 2.577700 GAGTAGAAGCCGAGAGATGGA 58.422 52.381 0.00 0.00 0.00 3.41
623 624 0.823356 AGATGGAGAGAGAGAGCGCC 60.823 60.000 2.29 0.00 0.00 6.53
830 846 3.307480 CGGTTAATGACTCCCCAAACTCT 60.307 47.826 0.00 0.00 0.00 3.24
843 859 4.218417 CCCCAAACTCTGTTTGTCTAATGG 59.782 45.833 18.05 12.11 0.00 3.16
853 869 8.974060 TCTGTTTGTCTAATGGTTTATATCCC 57.026 34.615 0.00 0.00 0.00 3.85
867 886 9.797732 TGGTTTATATCCCATATTCCTATCTGA 57.202 33.333 0.00 0.00 0.00 3.27
902 921 3.040477 CACCCATCCTGGCCAATAAATT 58.960 45.455 7.01 0.00 35.79 1.82
903 922 3.455543 CACCCATCCTGGCCAATAAATTT 59.544 43.478 7.01 0.00 35.79 1.82
905 924 4.653801 ACCCATCCTGGCCAATAAATTTAC 59.346 41.667 7.01 0.00 35.79 2.01
906 925 4.261994 CCCATCCTGGCCAATAAATTTACG 60.262 45.833 7.01 0.00 35.79 3.18
907 926 4.582656 CCATCCTGGCCAATAAATTTACGA 59.417 41.667 7.01 0.00 0.00 3.43
910 929 6.591750 TCCTGGCCAATAAATTTACGAAAA 57.408 33.333 7.01 0.00 0.00 2.29
911 930 7.176589 TCCTGGCCAATAAATTTACGAAAAT 57.823 32.000 7.01 0.00 36.87 1.82
912 931 7.262048 TCCTGGCCAATAAATTTACGAAAATC 58.738 34.615 7.01 0.00 34.12 2.17
913 932 6.478673 CCTGGCCAATAAATTTACGAAAATCC 59.521 38.462 7.01 0.00 34.12 3.01
914 933 7.176589 TGGCCAATAAATTTACGAAAATCCT 57.823 32.000 0.61 0.00 34.12 3.24
915 934 8.294954 TGGCCAATAAATTTACGAAAATCCTA 57.705 30.769 0.61 0.00 34.12 2.94
916 935 8.919145 TGGCCAATAAATTTACGAAAATCCTAT 58.081 29.630 0.61 0.00 34.12 2.57
938 957 2.067091 TTACGATCGGCCACCTAGCG 62.067 60.000 20.98 1.55 0.00 4.26
940 959 2.027751 GATCGGCCACCTAGCGAC 59.972 66.667 2.24 0.00 0.00 5.19
941 960 3.825833 GATCGGCCACCTAGCGACG 62.826 68.421 2.24 0.00 0.00 5.12
964 984 7.222872 ACGGCGCCTAGTATATATATCTACTT 58.777 38.462 26.68 2.36 30.98 2.24
970 990 7.307870 GCCTAGTATATATATCTACTTGCGCGT 60.308 40.741 14.07 0.00 30.98 6.01
1008 1028 4.252971 TCGAGAAGAAAAGATGGACGTT 57.747 40.909 0.00 0.00 0.00 3.99
1033 1065 1.066716 TCGCCGCACCTACAACTAATT 60.067 47.619 0.00 0.00 0.00 1.40
1087 1119 2.125147 TTGGCATTCTCGCTCCGG 60.125 61.111 0.00 0.00 0.00 5.14
1151 1183 1.021390 ATCGACGGCTTGCCTTTCAG 61.021 55.000 10.12 0.00 0.00 3.02
1498 1530 0.603707 CGAGTCACCAACCATGCAGT 60.604 55.000 0.00 0.00 0.00 4.40
1501 1533 3.146066 GAGTCACCAACCATGCAGTTAA 58.854 45.455 0.00 0.00 0.00 2.01
1560 1592 0.108945 CGAACGTCACCTTCTACCCC 60.109 60.000 0.00 0.00 0.00 4.95
1600 1632 3.060615 ACCCCTCGGTCGTCTTCG 61.061 66.667 0.00 0.00 38.28 3.79
1634 1666 1.271379 GCTAAGTGGCCACTGGAAGAA 60.271 52.381 38.35 17.96 41.58 2.52
1635 1667 2.814097 GCTAAGTGGCCACTGGAAGAAA 60.814 50.000 38.35 16.30 41.58 2.52
1652 1684 2.043526 AGAAAAGGCATGAAGTGGGGAT 59.956 45.455 0.00 0.00 0.00 3.85
1697 1729 0.608640 GTCCTTGTCCACTGGATCGT 59.391 55.000 0.00 0.00 32.73 3.73
1730 1762 2.201022 ACACGGACGAGCAGTTCCT 61.201 57.895 0.00 0.00 0.00 3.36
1736 1768 2.125912 CGAGCAGTTCCTCCACGG 60.126 66.667 0.00 0.00 0.00 4.94
1761 1793 1.884928 GCTCCTCCGGCTTACCAAAAA 60.885 52.381 0.00 0.00 34.57 1.94
1779 1811 7.238710 ACCAAAAACCTGAGAACCTAATGTAT 58.761 34.615 0.00 0.00 0.00 2.29
1787 1819 6.481644 CCTGAGAACCTAATGTATTTCTGCTC 59.518 42.308 0.00 0.00 0.00 4.26
1837 1869 0.737715 CCGTTGCTTCCTCCGAGAAG 60.738 60.000 0.00 5.70 45.05 2.85
1860 1892 0.460987 CTGCTGCTTCCCCTAGTTCG 60.461 60.000 0.00 0.00 0.00 3.95
1866 1898 2.093128 TGCTTCCCCTAGTTCGGAAATC 60.093 50.000 0.00 2.11 37.69 2.17
1887 1919 5.343307 TCGATTCTCTTCATGATCCACAA 57.657 39.130 0.00 0.00 0.00 3.33
1928 1960 3.153130 CTGATGATAGCTCCTCTTCCGA 58.847 50.000 0.00 0.00 0.00 4.55
1929 1961 3.566351 TGATGATAGCTCCTCTTCCGAA 58.434 45.455 0.00 0.00 0.00 4.30
1930 1962 3.571828 TGATGATAGCTCCTCTTCCGAAG 59.428 47.826 1.30 1.30 0.00 3.79
1931 1963 3.298686 TGATAGCTCCTCTTCCGAAGA 57.701 47.619 10.44 10.44 35.87 2.87
1932 1964 3.632333 TGATAGCTCCTCTTCCGAAGAA 58.368 45.455 11.94 0.00 37.02 2.52
1965 1997 2.975489 AGAAGAAGAAGAGGTTGAGCCA 59.025 45.455 0.00 0.00 40.61 4.75
1983 2015 1.143183 ATCGCCGCCATCGTTAACT 59.857 52.632 3.71 0.00 0.00 2.24
2024 2056 2.430332 CAGTGGACAAGGAGGAGAGATC 59.570 54.545 0.00 0.00 0.00 2.75
2025 2057 1.407258 GTGGACAAGGAGGAGAGATCG 59.593 57.143 0.00 0.00 0.00 3.69
2056 2088 3.963733 CTGAGGAAGCCCATGTTCA 57.036 52.632 0.00 0.00 33.88 3.18
2062 2094 1.408266 GGAAGCCCATGTTCATACGGT 60.408 52.381 0.00 0.00 0.00 4.83
2092 2124 2.991076 GCACGACGAGGCTACCAGT 61.991 63.158 0.00 0.00 0.00 4.00
2093 2125 1.154016 CACGACGAGGCTACCAGTG 60.154 63.158 0.00 0.00 0.00 3.66
2095 2127 2.341101 CGACGAGGCTACCAGTGGT 61.341 63.158 20.91 20.91 40.16 4.16
2099 2134 3.372554 GAGGCTACCAGTGGTCGGC 62.373 68.421 27.35 27.35 42.71 5.54
2143 2178 4.961511 GCACTCGCACCACCGTCA 62.962 66.667 0.00 0.00 38.36 4.35
2274 2312 1.795889 GCTCGAGATGACGACTTCACC 60.796 57.143 18.75 0.00 36.92 4.02
2279 2317 2.573609 GATGACGACTTCACCGGGGG 62.574 65.000 2.42 0.00 36.92 5.40
2337 2375 2.063015 ATTCCAAGGACCACACGGCA 62.063 55.000 0.00 0.00 34.57 5.69
2421 2459 5.008712 CGTTAGTGTGTATGATCTAGGCAGA 59.991 44.000 0.00 0.00 34.56 4.26
2511 2549 3.964875 GCACGGCAACCACAGGTG 61.965 66.667 0.00 0.00 35.34 4.00
2607 2674 0.517316 CGTCAGTGGTAAGGCAAAGC 59.483 55.000 0.00 0.00 0.00 3.51
3129 3418 8.310382 GCTGATGTGGTATCTATCTAGAAACAT 58.690 37.037 0.00 0.00 35.69 2.71
3167 3456 9.926751 CTATCAACTTAACTATGCATCACAAAG 57.073 33.333 0.19 6.36 0.00 2.77
3256 3545 7.016661 CCAACAGATACTAGGAATATCCAAGGT 59.983 40.741 0.00 0.00 39.61 3.50
3441 3730 3.830192 GGATTTGCCAGCTGCGGG 61.830 66.667 14.82 14.82 45.60 6.13
3489 3778 2.420827 CGCATGTATCCTTGGGTGGTAA 60.421 50.000 0.00 0.00 0.00 2.85
3500 3789 4.342951 CCTTGGGTGGTAATCACGTAGATA 59.657 45.833 0.00 0.00 46.96 1.98
3516 3805 0.882474 GATACTAGCATCGAGGGCGT 59.118 55.000 0.00 0.00 38.98 5.68
3546 3835 1.550976 GGTCGTCTTTCCTCCAGTGAT 59.449 52.381 0.00 0.00 0.00 3.06
3561 3850 4.047822 CCAGTGATAAGAAGCGATGAGAC 58.952 47.826 0.00 0.00 0.00 3.36
3578 3867 2.261361 CTGGCGACGGTGATGTCA 59.739 61.111 0.00 0.00 38.84 3.58
3581 3870 1.374252 GGCGACGGTGATGTCAAGT 60.374 57.895 0.00 0.00 38.84 3.16
3630 3919 4.631377 CACTGGTGATGATGACACGTTAAT 59.369 41.667 0.00 0.00 38.90 1.40
3684 3973 2.433436 GGACCACCATTACCTTGACAC 58.567 52.381 0.00 0.00 35.97 3.67
3703 3992 1.809619 CATGGACCAGGTACGTGCG 60.810 63.158 11.42 6.31 0.00 5.34
3714 4003 2.314647 TACGTGCGCCAAGACAAGC 61.315 57.895 4.18 0.00 0.00 4.01
3717 4006 2.203195 TGCGCCAAGACAAGCTGT 60.203 55.556 4.18 0.00 0.00 4.40
3720 4009 1.576421 CGCCAAGACAAGCTGTTCC 59.424 57.895 0.00 0.00 0.00 3.62
3724 4013 2.287849 GCCAAGACAAGCTGTTCCTTTC 60.288 50.000 0.00 0.00 0.00 2.62
3727 4016 1.202940 AGACAAGCTGTTCCTTTCCCC 60.203 52.381 0.00 0.00 0.00 4.81
3888 4682 3.326747 CTGGGTTAAGACGGTTCAGAAG 58.673 50.000 0.00 0.00 0.00 2.85
4000 4800 4.503123 GCCCCAATTAATAATGAACTGGCC 60.503 45.833 0.00 0.00 0.00 5.36
4001 4801 4.901250 CCCCAATTAATAATGAACTGGCCT 59.099 41.667 3.32 0.00 0.00 5.19
4014 4814 2.203070 GGCCTTGGCATCGACGAT 60.203 61.111 14.04 4.05 0.00 3.73
4634 5438 1.227263 GGCTTCAGGATCGCGCTTA 60.227 57.895 5.56 0.00 0.00 3.09
4677 5481 1.523154 GCCGCCTTCACAAACATGGA 61.523 55.000 0.00 0.00 0.00 3.41
4684 5488 3.822735 CCTTCACAAACATGGACACTCAT 59.177 43.478 0.00 0.00 0.00 2.90
4711 5515 8.919661 GGGTAGCATTTACAAACTACGTATATC 58.080 37.037 0.00 0.00 36.65 1.63
4784 5589 2.557317 ACGTGTTGTCGTGAGGATTTT 58.443 42.857 0.00 0.00 42.56 1.82
4818 5623 1.207329 GAGTAAGGGCATCTCCAACGT 59.793 52.381 0.00 0.00 36.21 3.99
4819 5624 1.628846 AGTAAGGGCATCTCCAACGTT 59.371 47.619 0.00 0.00 36.21 3.99
4925 5784 5.352293 GCATATCAAGCCCAAAAGAAAAAGG 59.648 40.000 0.00 0.00 0.00 3.11
4928 5787 5.428184 TCAAGCCCAAAAGAAAAAGGAAA 57.572 34.783 0.00 0.00 0.00 3.13
4977 5836 2.095768 CGACAAAGCACAAATGATCCGT 60.096 45.455 0.00 0.00 0.00 4.69
5075 5939 4.707840 GACGCGACGTCGACGACA 62.708 66.667 39.92 0.00 46.56 4.35
5156 6022 2.657237 CGACGCCCTTCAGGAAGT 59.343 61.111 8.14 0.00 38.24 3.01
5159 6025 1.736032 CGACGCCCTTCAGGAAGTAAG 60.736 57.143 8.14 1.87 38.24 2.34
5213 6079 0.740737 GATGAACCGGCAGGGATTTG 59.259 55.000 8.08 0.00 43.47 2.32
5283 6149 0.463654 CTTGCCACCCGCTAGCATAA 60.464 55.000 16.45 0.00 38.78 1.90
5373 6239 3.467226 GGGACGCCAGGAATCGGA 61.467 66.667 0.00 0.00 0.00 4.55
5418 6285 2.033602 GGAACCACCTTCCCACCG 59.966 66.667 0.00 0.00 42.75 4.94
5424 6291 2.841044 ACCTTCCCACCGTCGTGT 60.841 61.111 0.00 0.00 38.41 4.49
5433 6300 4.415332 CCGTCGTGTGGGACTCCG 62.415 72.222 0.00 0.00 34.75 4.63
5496 6363 2.440599 GGCACACCAACCCATCCT 59.559 61.111 0.00 0.00 35.26 3.24
5515 6404 3.605664 GCCCGCAAAGCCACTGTT 61.606 61.111 0.00 0.00 0.00 3.16
5609 6499 2.237143 AGCTCCACCATCGATGAAGAAA 59.763 45.455 26.86 7.07 0.00 2.52
5610 6500 3.118112 AGCTCCACCATCGATGAAGAAAT 60.118 43.478 26.86 8.15 0.00 2.17
5645 6535 3.402681 CCAGATGGGGCCTGACGT 61.403 66.667 0.84 0.00 33.65 4.34
5646 6536 2.124983 CAGATGGGGCCTGACGTG 60.125 66.667 0.84 0.00 33.65 4.49
5647 6537 2.607750 AGATGGGGCCTGACGTGT 60.608 61.111 0.84 0.00 0.00 4.49
5648 6538 2.125106 GATGGGGCCTGACGTGTC 60.125 66.667 0.84 0.00 0.00 3.67
5649 6539 2.927856 ATGGGGCCTGACGTGTCA 60.928 61.111 0.84 2.28 38.06 3.58
5659 6549 2.163818 TGACGTGTCAGGTGAAATCC 57.836 50.000 2.23 0.00 34.14 3.01
5660 6550 1.414550 TGACGTGTCAGGTGAAATCCA 59.585 47.619 2.23 0.00 34.14 3.41
5661 6551 2.038426 TGACGTGTCAGGTGAAATCCAT 59.962 45.455 2.23 0.00 34.14 3.41
5662 6552 2.673368 GACGTGTCAGGTGAAATCCATC 59.327 50.000 2.23 0.00 0.00 3.51
5663 6553 2.009774 CGTGTCAGGTGAAATCCATCC 58.990 52.381 0.00 0.00 0.00 3.51
5664 6554 2.615240 CGTGTCAGGTGAAATCCATCCA 60.615 50.000 0.00 0.00 0.00 3.41
5665 6555 3.420893 GTGTCAGGTGAAATCCATCCAA 58.579 45.455 0.00 0.00 0.00 3.53
5666 6556 4.019174 GTGTCAGGTGAAATCCATCCAAT 58.981 43.478 0.00 0.00 0.00 3.16
5667 6557 5.192927 GTGTCAGGTGAAATCCATCCAATA 58.807 41.667 0.00 0.00 0.00 1.90
5668 6558 5.829924 GTGTCAGGTGAAATCCATCCAATAT 59.170 40.000 0.00 0.00 0.00 1.28
5669 6559 5.829391 TGTCAGGTGAAATCCATCCAATATG 59.171 40.000 0.00 0.00 0.00 1.78
5670 6560 5.829924 GTCAGGTGAAATCCATCCAATATGT 59.170 40.000 0.00 0.00 0.00 2.29
5671 6561 6.322201 GTCAGGTGAAATCCATCCAATATGTT 59.678 38.462 0.00 0.00 0.00 2.71
5672 6562 6.896860 TCAGGTGAAATCCATCCAATATGTTT 59.103 34.615 0.00 0.00 0.00 2.83
5673 6563 7.399765 TCAGGTGAAATCCATCCAATATGTTTT 59.600 33.333 0.00 0.00 0.00 2.43
5674 6564 8.042515 CAGGTGAAATCCATCCAATATGTTTTT 58.957 33.333 0.00 0.00 0.00 1.94
5675 6565 9.265862 AGGTGAAATCCATCCAATATGTTTTTA 57.734 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.362077 TCTTGAAAACAAGAGCAAGGCC 59.638 45.455 8.32 0.00 38.53 5.19
203 204 1.859841 TACCTGGTGCCGAGAGAGGA 61.860 60.000 10.23 0.00 0.00 3.71
303 304 1.241315 GGCCTACAAAAAGCAGCGGA 61.241 55.000 0.00 0.00 0.00 5.54
312 313 3.586470 TCAAGTGGAAGGCCTACAAAA 57.414 42.857 5.16 0.00 34.31 2.44
343 344 4.877251 GTCGTCTACTACCATCTCAAGAGT 59.123 45.833 0.00 0.00 0.00 3.24
352 353 1.293924 CGACGGTCGTCTACTACCAT 58.706 55.000 21.68 0.00 42.54 3.55
579 580 1.268352 GCTTCTACTCGATCGCCATCT 59.732 52.381 11.09 0.00 0.00 2.90
582 583 1.734137 GGCTTCTACTCGATCGCCA 59.266 57.895 11.09 0.00 38.06 5.69
586 587 2.485903 TCTCTCGGCTTCTACTCGATC 58.514 52.381 0.00 0.00 32.32 3.69
587 588 2.623878 TCTCTCGGCTTCTACTCGAT 57.376 50.000 0.00 0.00 32.32 3.59
588 589 2.214347 CATCTCTCGGCTTCTACTCGA 58.786 52.381 0.00 0.00 0.00 4.04
607 608 1.076412 ATGGCGCTCTCTCTCTCCA 60.076 57.895 7.64 0.00 0.00 3.86
609 610 1.163420 TCGATGGCGCTCTCTCTCTC 61.163 60.000 7.64 0.00 37.46 3.20
610 611 0.537143 ATCGATGGCGCTCTCTCTCT 60.537 55.000 7.64 0.00 37.46 3.10
623 624 2.185262 ACGTTCACATGTCGATCGATG 58.815 47.619 22.50 18.46 31.64 3.84
725 728 6.284891 TCGATTGATGATGATATGGTAGCA 57.715 37.500 0.00 0.00 0.00 3.49
853 869 6.642950 GGTGTTCGAGTTCAGATAGGAATATG 59.357 42.308 0.00 0.00 0.00 1.78
863 879 0.761323 TGGGGGTGTTCGAGTTCAGA 60.761 55.000 0.00 0.00 0.00 3.27
867 886 2.826003 GGGTGGGGGTGTTCGAGTT 61.826 63.158 0.00 0.00 0.00 3.01
902 921 8.017373 CCGATCGTAAGTATAGGATTTTCGTAA 58.983 37.037 15.09 0.00 36.91 3.18
903 922 7.521529 CCGATCGTAAGTATAGGATTTTCGTA 58.478 38.462 15.09 0.00 36.91 3.43
905 924 5.285607 GCCGATCGTAAGTATAGGATTTTCG 59.714 44.000 15.09 0.00 36.91 3.46
906 925 5.575995 GGCCGATCGTAAGTATAGGATTTTC 59.424 44.000 15.09 0.00 36.91 2.29
907 926 5.011329 TGGCCGATCGTAAGTATAGGATTTT 59.989 40.000 15.09 0.00 36.91 1.82
910 929 3.442977 GTGGCCGATCGTAAGTATAGGAT 59.557 47.826 15.09 0.00 38.88 3.24
911 930 2.816087 GTGGCCGATCGTAAGTATAGGA 59.184 50.000 15.09 0.00 39.48 2.94
912 931 2.094854 GGTGGCCGATCGTAAGTATAGG 60.095 54.545 15.09 0.00 39.48 2.57
913 932 2.818432 AGGTGGCCGATCGTAAGTATAG 59.182 50.000 15.09 0.00 39.48 1.31
914 933 2.867624 AGGTGGCCGATCGTAAGTATA 58.132 47.619 15.09 0.00 39.48 1.47
915 934 1.700955 AGGTGGCCGATCGTAAGTAT 58.299 50.000 15.09 0.00 39.48 2.12
916 935 2.224606 CTAGGTGGCCGATCGTAAGTA 58.775 52.381 15.09 0.00 39.48 2.24
917 936 1.030457 CTAGGTGGCCGATCGTAAGT 58.970 55.000 15.09 0.00 39.48 2.24
918 937 0.318784 GCTAGGTGGCCGATCGTAAG 60.319 60.000 15.09 0.00 0.00 2.34
919 938 1.737816 GCTAGGTGGCCGATCGTAA 59.262 57.895 15.09 0.00 0.00 3.18
920 939 2.549198 CGCTAGGTGGCCGATCGTA 61.549 63.158 15.09 0.00 0.00 3.43
921 940 3.900892 CGCTAGGTGGCCGATCGT 61.901 66.667 15.09 0.00 0.00 3.73
938 957 6.873076 AGTAGATATATATACTAGGCGCCGTC 59.127 42.308 23.20 0.00 33.43 4.79
940 959 7.519843 CAAGTAGATATATATACTAGGCGCCG 58.480 42.308 23.20 10.77 34.02 6.46
941 960 7.306953 GCAAGTAGATATATATACTAGGCGCC 58.693 42.308 21.89 21.89 34.02 6.53
944 963 7.016466 CGCGCAAGTAGATATATATACTAGGC 58.984 42.308 22.14 22.14 34.02 3.93
945 964 8.085720 ACGCGCAAGTAGATATATATACTAGG 57.914 38.462 18.05 14.52 34.02 3.02
964 984 4.617486 CGCCGGAGTATACGCGCA 62.617 66.667 5.05 0.00 0.00 6.09
1033 1065 0.393820 ACGAGGTCTTGCCCGTAAAA 59.606 50.000 0.00 0.00 40.56 1.52
1151 1183 4.704833 TGTCGCCAGCCTCCTTGC 62.705 66.667 0.00 0.00 0.00 4.01
1278 1310 3.299977 CCACGGTCCACGAGGTCA 61.300 66.667 0.00 0.00 46.49 4.02
1299 1331 2.915659 ACTTCCCCTGTCGCGTCA 60.916 61.111 5.77 5.79 0.00 4.35
1302 1334 1.519455 GATGACTTCCCCTGTCGCG 60.519 63.158 0.00 0.00 37.26 5.87
1485 1517 1.256812 GCCTTAACTGCATGGTTGGT 58.743 50.000 1.78 0.00 0.00 3.67
1498 1530 2.290287 TGCTCTCTGCCGGCCTTAA 61.290 57.895 26.77 3.41 42.00 1.85
1590 1622 4.144703 GCCCCTCCGAAGACGACC 62.145 72.222 0.00 0.00 42.66 4.79
1634 1666 1.620524 CCATCCCCACTTCATGCCTTT 60.621 52.381 0.00 0.00 0.00 3.11
1635 1667 0.032813 CCATCCCCACTTCATGCCTT 60.033 55.000 0.00 0.00 0.00 4.35
1652 1684 0.692476 CATCTCCACCTTGGTCACCA 59.308 55.000 0.00 0.00 39.03 4.17
1704 1736 3.678717 CTCGTCCGTGTGGCCGTAG 62.679 68.421 0.00 0.00 34.14 3.51
1710 1742 2.022129 GAACTGCTCGTCCGTGTGG 61.022 63.158 0.00 0.00 0.00 4.17
1711 1743 2.022129 GGAACTGCTCGTCCGTGTG 61.022 63.158 0.00 0.00 0.00 3.82
1725 1757 4.754667 GCGGACCCGTGGAGGAAC 62.755 72.222 10.37 0.00 45.00 3.62
1749 1781 3.005472 GGTTCTCAGGTTTTTGGTAAGCC 59.995 47.826 0.00 0.00 0.00 4.35
1761 1793 6.069963 AGCAGAAATACATTAGGTTCTCAGGT 60.070 38.462 0.00 0.00 0.00 4.00
1787 1819 4.778415 AGCTGCACTCGTACGCGG 62.778 66.667 12.47 8.42 38.89 6.46
1860 1892 5.994054 TGGATCATGAAGAGAATCGATTTCC 59.006 40.000 12.81 11.13 42.67 3.13
1866 1898 4.872124 TGTTGTGGATCATGAAGAGAATCG 59.128 41.667 0.00 0.00 42.67 3.34
1887 1919 2.105477 AGATTGCAGTGAACTCTGGTGT 59.895 45.455 0.00 0.00 36.12 4.16
1928 1960 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1929 1961 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1930 1962 9.196552 CTCTTCTTCTTCTTCTTCTTCTTCTTC 57.803 37.037 0.00 0.00 0.00 2.87
1931 1963 8.150296 CCTCTTCTTCTTCTTCTTCTTCTTCTT 58.850 37.037 0.00 0.00 0.00 2.52
1932 1964 7.290014 ACCTCTTCTTCTTCTTCTTCTTCTTCT 59.710 37.037 0.00 0.00 0.00 2.85
1933 1965 7.441836 ACCTCTTCTTCTTCTTCTTCTTCTTC 58.558 38.462 0.00 0.00 0.00 2.87
1934 1966 7.373617 ACCTCTTCTTCTTCTTCTTCTTCTT 57.626 36.000 0.00 0.00 0.00 2.52
1935 1967 6.994421 ACCTCTTCTTCTTCTTCTTCTTCT 57.006 37.500 0.00 0.00 0.00 2.85
1936 1968 7.213678 TCAACCTCTTCTTCTTCTTCTTCTTC 58.786 38.462 0.00 0.00 0.00 2.87
1937 1969 7.130681 TCAACCTCTTCTTCTTCTTCTTCTT 57.869 36.000 0.00 0.00 0.00 2.52
1938 1970 6.739331 TCAACCTCTTCTTCTTCTTCTTCT 57.261 37.500 0.00 0.00 0.00 2.85
1939 1971 5.408299 GCTCAACCTCTTCTTCTTCTTCTTC 59.592 44.000 0.00 0.00 0.00 2.87
1940 1972 5.304778 GCTCAACCTCTTCTTCTTCTTCTT 58.695 41.667 0.00 0.00 0.00 2.52
1941 1973 4.262851 GGCTCAACCTCTTCTTCTTCTTCT 60.263 45.833 0.00 0.00 34.51 2.85
1942 1974 4.000325 GGCTCAACCTCTTCTTCTTCTTC 59.000 47.826 0.00 0.00 34.51 2.87
1965 1997 1.143183 AGTTAACGATGGCGGCGAT 59.857 52.632 12.98 0.00 43.17 4.58
2056 2088 1.305549 CCCGCCCCCTATACCGTAT 60.306 63.158 0.00 0.00 0.00 3.06
2062 2094 4.543361 TCGTGCCCGCCCCCTATA 62.543 66.667 0.00 0.00 0.00 1.31
2076 2108 2.341101 CCACTGGTAGCCTCGTCGT 61.341 63.158 0.00 0.00 0.00 4.34
2143 2178 2.177580 CGTCCTGCCACAACACGTT 61.178 57.895 0.00 0.00 0.00 3.99
2253 2288 1.135660 GTGAAGTCGTCATCTCGAGCA 60.136 52.381 7.81 0.00 40.52 4.26
2337 2375 1.593196 CCTTGAACCACGACACATGT 58.407 50.000 0.00 0.00 0.00 3.21
2371 2409 2.511600 GTCGCATTCCACCTCCCG 60.512 66.667 0.00 0.00 0.00 5.14
2421 2459 0.763223 AAACGGAGTGGTCAGGGTCT 60.763 55.000 0.00 0.00 45.00 3.85
2511 2549 1.672881 CCAACCCATGAAAGATCGAGC 59.327 52.381 0.00 0.00 0.00 5.03
2593 2631 3.366985 GGTACATTGCTTTGCCTTACCAC 60.367 47.826 0.00 0.00 0.00 4.16
3041 3330 2.044946 AGTCGCCCATTTCAGCCC 60.045 61.111 0.00 0.00 0.00 5.19
3167 3456 5.929992 TGCCACATTATTAGTAAGATACGGC 59.070 40.000 0.00 0.00 0.00 5.68
3256 3545 2.429930 CCGTCTTCAACCCTGGCA 59.570 61.111 0.00 0.00 0.00 4.92
3386 3675 3.002862 GTGCGGTTGACAAGATACAACAA 59.997 43.478 0.00 0.00 45.27 2.83
3387 3676 2.546368 GTGCGGTTGACAAGATACAACA 59.454 45.455 0.00 0.00 45.27 3.33
3388 3677 2.546368 TGTGCGGTTGACAAGATACAAC 59.454 45.455 0.00 0.00 43.53 3.32
3441 3730 3.060138 CACTTCAACAACATTGTGCATGC 60.060 43.478 11.82 11.82 41.31 4.06
3489 3778 4.632251 CCTCGATGCTAGTATCTACGTGAT 59.368 45.833 17.34 1.82 39.11 3.06
3500 3789 1.141881 CAACGCCCTCGATGCTAGT 59.858 57.895 5.65 0.00 39.41 2.57
3546 3835 1.202302 CGCCAGTCTCATCGCTTCTTA 60.202 52.381 0.00 0.00 0.00 2.10
3561 3850 1.354337 CTTGACATCACCGTCGCCAG 61.354 60.000 0.00 0.00 38.84 4.85
3578 3867 1.515954 CCGACCTCACCGCATACTT 59.484 57.895 0.00 0.00 0.00 2.24
3581 3870 2.043752 TCCCGACCTCACCGCATA 60.044 61.111 0.00 0.00 0.00 3.14
3630 3919 4.453136 GCACTACGTCAAAGTTTGGGAATA 59.547 41.667 15.47 3.37 0.00 1.75
3684 3973 1.449601 GCACGTACCTGGTCCATGG 60.450 63.158 4.97 4.97 0.00 3.66
3703 3992 1.322442 AAGGAACAGCTTGTCTTGGC 58.678 50.000 0.00 0.00 0.00 4.52
3727 4016 9.889128 AATGATAAAAACCTGTGAAAATATGGG 57.111 29.630 0.00 0.00 0.00 4.00
3794 4337 3.363673 GCTAGCACTGGTTAACGTTTGTC 60.364 47.826 10.63 0.00 0.00 3.18
3888 4682 4.674281 ATCCTCGAGTATTTTCCACTCC 57.326 45.455 12.31 0.00 39.43 3.85
4000 4800 2.492019 TGTAGATCGTCGATGCCAAG 57.508 50.000 13.54 0.00 0.00 3.61
4001 4801 4.783764 ATATGTAGATCGTCGATGCCAA 57.216 40.909 13.54 0.00 0.00 4.52
4296 5100 0.534412 CTGGAGGATGCTTGACGTCT 59.466 55.000 17.92 0.00 34.46 4.18
4307 5111 1.187087 GAGACGACAACCTGGAGGAT 58.813 55.000 0.00 0.00 38.94 3.24
4385 5189 4.351938 CTCCGGCGTGTCGACCAA 62.352 66.667 14.12 0.00 0.00 3.67
4677 5481 4.568072 TGTAAATGCTACCCATGAGTGT 57.432 40.909 0.00 0.00 33.49 3.55
4684 5488 4.897140 ACGTAGTTTGTAAATGCTACCCA 58.103 39.130 0.00 0.00 37.78 4.51
4765 5569 3.602390 AAAAATCCTCACGACAACACG 57.398 42.857 0.00 0.00 39.31 4.49
4784 5589 5.186021 TGCCCTTACTCAAAAAGTTCACAAA 59.814 36.000 0.00 0.00 39.55 2.83
4792 5597 4.335416 TGGAGATGCCCTTACTCAAAAAG 58.665 43.478 0.00 0.00 34.97 2.27
4872 5731 4.141287 CCCCAACAGTTATCTTGTGTTCA 58.859 43.478 0.00 0.00 32.01 3.18
4925 5784 5.107875 CGTTGTTGGCATTTAGCTCTTTTTC 60.108 40.000 0.00 0.00 44.79 2.29
4928 5787 3.305335 CCGTTGTTGGCATTTAGCTCTTT 60.305 43.478 0.00 0.00 44.79 2.52
5032 5894 2.738587 TGGAGGTGCTTTTTGGTACA 57.261 45.000 0.00 0.00 0.00 2.90
5075 5939 2.584608 GTATGTCCGGGCAGCAGT 59.415 61.111 16.89 0.00 0.00 4.40
5108 5972 3.691342 CCACTCCCTTCCGCGTGA 61.691 66.667 4.92 0.00 0.00 4.35
5213 6079 2.340328 GGTGTTTGGGATGCGGGAC 61.340 63.158 0.00 0.00 0.00 4.46
5283 6149 1.272769 GACTTCAAGACCGTGGTAGCT 59.727 52.381 0.00 0.00 0.00 3.32
5286 6152 2.232941 GGATGACTTCAAGACCGTGGTA 59.767 50.000 0.00 0.00 0.00 3.25
5373 6239 4.357279 GCTCTGGTGCTGCCCCTT 62.357 66.667 2.15 0.00 36.04 3.95
5386 6252 4.704103 TCCCTCTGGCACGGCTCT 62.704 66.667 0.00 0.00 32.53 4.09
5418 6285 3.300765 ACCGGAGTCCCACACGAC 61.301 66.667 9.46 0.00 0.00 4.34
5643 6533 2.009774 GGATGGATTTCACCTGACACG 58.990 52.381 0.00 0.00 0.00 4.49
5644 6534 3.071874 TGGATGGATTTCACCTGACAC 57.928 47.619 0.00 0.00 0.00 3.67
5645 6535 3.805066 TTGGATGGATTTCACCTGACA 57.195 42.857 0.00 0.00 0.00 3.58
5646 6536 5.829924 ACATATTGGATGGATTTCACCTGAC 59.170 40.000 0.00 0.00 0.00 3.51
5647 6537 6.017211 ACATATTGGATGGATTTCACCTGA 57.983 37.500 0.00 0.00 0.00 3.86
5648 6538 6.720112 AACATATTGGATGGATTTCACCTG 57.280 37.500 0.00 0.00 0.00 4.00
5649 6539 7.738437 AAAACATATTGGATGGATTTCACCT 57.262 32.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.