Multiple sequence alignment - TraesCS2A01G591200

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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 TraesCS2A01G591200 chr2A 100.000 2750 0 0 1 2750 778913739 778916488 0.000000e+00 5079.0
1 TraesCS2A01G591200 chr2A 86.874 1059 89 28 779 1817 778876133 778877161 0.000000e+00 1140.0
2 TraesCS2A01G591200 chr2A 89.151 636 42 12 1236 1862 778827510 778828127 0.000000e+00 767.0
3 TraesCS2A01G591200 chr2A 80.801 1073 105 49 768 1819 778759821 778760813 0.000000e+00 747.0
4 TraesCS2A01G591200 chr2A 77.244 1437 180 93 412 1773 778788300 778789664 0.000000e+00 706.0
5 TraesCS2A01G591200 chr2A 78.860 1140 126 68 40 1119 778826339 778827423 0.000000e+00 664.0
6 TraesCS2A01G591200 chr2A 83.740 246 23 8 577 815 778814083 778814318 1.660000e-52 217.0
7 TraesCS2A01G591200 chr2A 82.114 246 24 14 1584 1819 778814331 778814566 2.790000e-45 193.0
8 TraesCS2A01G591200 chr2A 80.000 295 26 15 679 958 778875855 778876131 1.300000e-43 187.0
9 TraesCS2A01G591200 chr2A 92.424 66 4 1 240 305 778869853 778869917 2.920000e-15 93.5
10 TraesCS2A01G591200 chr2D 83.965 2164 151 91 1 2077 634483424 634481370 0.000000e+00 1893.0
11 TraesCS2A01G591200 chr2D 88.679 636 44 13 1236 1862 634556369 634555753 0.000000e+00 750.0
12 TraesCS2A01G591200 chr2D 79.058 1189 128 75 683 1813 634575828 634574703 0.000000e+00 704.0
13 TraesCS2A01G591200 chr2D 81.195 904 87 42 939 1819 634658874 634658031 0.000000e+00 651.0
14 TraesCS2A01G591200 chr2D 82.448 433 32 23 458 882 634557175 634556779 3.390000e-89 339.0
15 TraesCS2A01G591200 chr2D 82.562 281 21 18 43 305 634557618 634557348 3.560000e-54 222.0
16 TraesCS2A01G591200 chr2D 89.855 138 7 2 903 1037 634556641 634556508 1.310000e-38 171.0
17 TraesCS2A01G591200 chr2D 89.062 64 7 0 43 106 634659661 634659598 2.270000e-11 80.5
18 TraesCS2A01G591200 chr2B 82.289 1660 120 81 3 1585 777522949 777521387 0.000000e+00 1277.0
19 TraesCS2A01G591200 chr2B 83.926 1350 106 52 505 1817 777549974 777548699 0.000000e+00 1188.0
20 TraesCS2A01G591200 chr2B 80.847 1180 120 61 683 1819 777619230 777618114 0.000000e+00 830.0
21 TraesCS2A01G591200 chr2B 90.576 573 40 7 2181 2749 777520811 777520249 0.000000e+00 747.0
22 TraesCS2A01G591200 chr2B 81.718 1001 76 50 856 1819 777659098 777658168 0.000000e+00 736.0
23 TraesCS2A01G591200 chr2B 83.404 705 41 33 768 1466 777635396 777634762 3.950000e-163 584.0
24 TraesCS2A01G591200 chr2B 83.922 510 42 15 1657 2157 777521384 777520906 4.180000e-123 451.0
25 TraesCS2A01G591200 chr2B 80.969 289 30 13 1527 1803 777633950 777633675 3.590000e-49 206.0
26 TraesCS2A01G591200 chr2B 86.260 131 11 4 906 1036 777605828 777605705 4.780000e-28 135.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G591200 chr2A 778913739 778916488 2749 False 5079.00 5079 100.000000 1 2750 1 chr2A.!!$F4 2749
1 TraesCS2A01G591200 chr2A 778759821 778760813 992 False 747.00 747 80.801000 768 1819 1 chr2A.!!$F1 1051
2 TraesCS2A01G591200 chr2A 778826339 778828127 1788 False 715.50 767 84.005500 40 1862 2 chr2A.!!$F6 1822
3 TraesCS2A01G591200 chr2A 778788300 778789664 1364 False 706.00 706 77.244000 412 1773 1 chr2A.!!$F2 1361
4 TraesCS2A01G591200 chr2A 778875855 778877161 1306 False 663.50 1140 83.437000 679 1817 2 chr2A.!!$F7 1138
5 TraesCS2A01G591200 chr2D 634481370 634483424 2054 True 1893.00 1893 83.965000 1 2077 1 chr2D.!!$R1 2076
6 TraesCS2A01G591200 chr2D 634574703 634575828 1125 True 704.00 704 79.058000 683 1813 1 chr2D.!!$R2 1130
7 TraesCS2A01G591200 chr2D 634555753 634557618 1865 True 370.50 750 85.886000 43 1862 4 chr2D.!!$R3 1819
8 TraesCS2A01G591200 chr2D 634658031 634659661 1630 True 365.75 651 85.128500 43 1819 2 chr2D.!!$R4 1776
9 TraesCS2A01G591200 chr2B 777548699 777549974 1275 True 1188.00 1188 83.926000 505 1817 1 chr2B.!!$R1 1312
10 TraesCS2A01G591200 chr2B 777618114 777619230 1116 True 830.00 830 80.847000 683 1819 1 chr2B.!!$R3 1136
11 TraesCS2A01G591200 chr2B 777520249 777522949 2700 True 825.00 1277 85.595667 3 2749 3 chr2B.!!$R5 2746
12 TraesCS2A01G591200 chr2B 777658168 777659098 930 True 736.00 736 81.718000 856 1819 1 chr2B.!!$R4 963
13 TraesCS2A01G591200 chr2B 777633675 777635396 1721 True 395.00 584 82.186500 768 1803 2 chr2B.!!$R6 1035

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
432 570 0.040499 ACACTCCAGTCTCCTCTCCC 59.96 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 3347 0.105593 AGACACACTGCAGACTGGTG 59.894 55.0 23.35 22.29 37.05 4.17 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
166 183 2.777972 CCCACTAACGCCGATCCGA 61.778 63.158 0.00 0.00 0.00 4.55
204 233 3.121676 ACGCACGCACAACACACA 61.122 55.556 0.00 0.00 0.00 3.72
219 249 0.671781 ACACAGGATGCTTGAGTCGC 60.672 55.000 4.03 0.00 42.53 5.19
291 391 0.455464 CACTCGCCGATCACGTACAA 60.455 55.000 5.18 0.00 37.88 2.41
310 410 5.556355 ACAACGTCGATCACAGTATCTTA 57.444 39.130 0.00 0.00 0.00 2.10
339 455 2.097160 CGCGTGCATGCTTGTCTC 59.903 61.111 27.33 0.00 0.00 3.36
353 487 3.062466 TCTCGACTGGACTGGGCG 61.062 66.667 0.00 0.00 0.00 6.13
375 509 1.672881 CTTGCAAGATTCCGTCCATCC 59.327 52.381 22.31 0.00 0.00 3.51
377 511 1.776034 GCAAGATTCCGTCCATCCGC 61.776 60.000 0.00 0.00 0.00 5.54
401 539 2.202272 CGACGACGGACCGAGAAC 60.202 66.667 23.38 12.01 35.72 3.01
402 540 2.949106 GACGACGGACCGAGAACA 59.051 61.111 23.38 0.00 0.00 3.18
403 541 1.441682 GACGACGGACCGAGAACAC 60.442 63.158 23.38 2.96 0.00 3.32
404 542 1.849976 GACGACGGACCGAGAACACT 61.850 60.000 23.38 0.00 0.00 3.55
405 543 1.154263 CGACGGACCGAGAACACTC 60.154 63.158 23.38 4.47 0.00 3.51
406 544 1.212229 GACGGACCGAGAACACTCC 59.788 63.158 23.38 0.00 0.00 3.85
407 545 2.178521 CGGACCGAGAACACTCCG 59.821 66.667 8.64 0.00 39.78 4.63
408 546 2.572284 GGACCGAGAACACTCCGG 59.428 66.667 0.00 0.00 33.77 5.14
409 547 1.975407 GGACCGAGAACACTCCGGA 60.975 63.158 2.93 2.93 32.77 5.14
410 548 1.212229 GACCGAGAACACTCCGGAC 59.788 63.158 0.00 0.00 32.77 4.79
415 553 0.313043 GAGAACACTCCGGACGAACA 59.687 55.000 0.00 0.00 0.00 3.18
432 570 0.040499 ACACTCCAGTCTCCTCTCCC 59.960 60.000 0.00 0.00 0.00 4.30
437 593 1.079256 CAGTCTCCTCTCCCCACCA 59.921 63.158 0.00 0.00 0.00 4.17
438 594 1.079438 AGTCTCCTCTCCCCACCAC 59.921 63.158 0.00 0.00 0.00 4.16
443 599 3.402681 CTCTCCCCACCACGCCAT 61.403 66.667 0.00 0.00 0.00 4.40
444 600 3.687321 CTCTCCCCACCACGCCATG 62.687 68.421 0.00 0.00 0.00 3.66
445 601 3.716195 CTCCCCACCACGCCATGA 61.716 66.667 0.00 0.00 0.00 3.07
446 602 3.253061 TCCCCACCACGCCATGAA 61.253 61.111 0.00 0.00 0.00 2.57
447 603 3.061848 CCCCACCACGCCATGAAC 61.062 66.667 0.00 0.00 0.00 3.18
448 604 2.282110 CCCACCACGCCATGAACA 60.282 61.111 0.00 0.00 0.00 3.18
449 605 2.625823 CCCACCACGCCATGAACAC 61.626 63.158 0.00 0.00 0.00 3.32
451 607 1.577328 CCACCACGCCATGAACACTC 61.577 60.000 0.00 0.00 0.00 3.51
453 609 1.302431 CCACGCCATGAACACTCCA 60.302 57.895 0.00 0.00 0.00 3.86
456 612 0.320771 ACGCCATGAACACTCCAGTC 60.321 55.000 0.00 0.00 0.00 3.51
482 650 1.205655 GGTAAACTGACCGGACCTACC 59.794 57.143 9.46 7.13 0.00 3.18
483 651 1.895131 GTAAACTGACCGGACCTACCA 59.105 52.381 9.46 0.00 38.90 3.25
485 653 0.178941 AACTGACCGGACCTACCAGT 60.179 55.000 9.46 8.40 39.49 4.00
486 654 0.700564 ACTGACCGGACCTACCAGTA 59.299 55.000 9.46 0.00 36.44 2.74
487 655 1.101331 CTGACCGGACCTACCAGTAC 58.899 60.000 9.46 0.00 38.90 2.73
488 656 0.323725 TGACCGGACCTACCAGTACC 60.324 60.000 9.46 0.00 38.90 3.34
489 657 0.323725 GACCGGACCTACCAGTACCA 60.324 60.000 9.46 0.00 38.90 3.25
490 658 0.114954 ACCGGACCTACCAGTACCAA 59.885 55.000 9.46 0.00 38.90 3.67
551 745 1.084370 GTCGTGCCAGCCAGACATAC 61.084 60.000 8.95 0.00 34.09 2.39
552 746 2.167219 CGTGCCAGCCAGACATACG 61.167 63.158 0.00 0.00 0.00 3.06
553 747 1.079127 GTGCCAGCCAGACATACGT 60.079 57.895 0.00 0.00 0.00 3.57
554 748 0.174845 GTGCCAGCCAGACATACGTA 59.825 55.000 0.00 0.00 0.00 3.57
555 749 1.119684 TGCCAGCCAGACATACGTAT 58.880 50.000 1.14 1.14 0.00 3.06
556 750 2.035449 GTGCCAGCCAGACATACGTATA 59.965 50.000 7.96 0.00 0.00 1.47
557 751 2.296190 TGCCAGCCAGACATACGTATAG 59.704 50.000 7.96 5.68 0.00 1.31
558 752 2.557056 GCCAGCCAGACATACGTATAGA 59.443 50.000 7.96 0.00 0.00 1.98
559 753 3.366476 GCCAGCCAGACATACGTATAGAG 60.366 52.174 7.96 0.00 0.00 2.43
560 754 3.366476 CCAGCCAGACATACGTATAGAGC 60.366 52.174 7.96 7.35 0.00 4.09
561 755 2.484651 AGCCAGACATACGTATAGAGCG 59.515 50.000 7.96 0.00 0.00 5.03
562 756 2.852748 CCAGACATACGTATAGAGCGC 58.147 52.381 7.96 0.00 0.00 5.92
646 861 0.460311 CATCTACTTCTCCGGCCGTT 59.540 55.000 26.12 3.07 0.00 4.44
1124 1763 0.173255 GTCAGTCTCTGCTCTGCTCC 59.827 60.000 0.00 0.00 0.00 4.70
1128 1767 1.303643 TCTCTGCTCTGCTCCGTGA 60.304 57.895 0.00 0.00 0.00 4.35
1159 1804 2.510238 CTCTTCTCCGGCAAGCGG 60.510 66.667 0.00 0.00 0.00 5.52
1160 1805 4.760047 TCTTCTCCGGCAAGCGGC 62.760 66.667 0.00 0.00 43.74 6.53
1214 1882 0.399949 AACTGTGGTGACCAGGAGGA 60.400 55.000 3.58 0.00 38.69 3.71
1545 2988 1.080025 CTTCCCGTTCCTCACCGAC 60.080 63.158 0.00 0.00 0.00 4.79
1698 3168 4.115199 GCATGGGAGGGCTTCGGT 62.115 66.667 0.00 0.00 0.00 4.69
1725 3216 3.625897 CTCACCTGGCCACCGTCA 61.626 66.667 0.00 0.00 0.00 4.35
1764 3255 1.946156 CTGATGGTCGGCGTCATCG 60.946 63.158 26.65 20.89 41.78 3.84
1767 3260 2.607668 GATGGTCGGCGTCATCGTGA 62.608 60.000 21.99 0.00 39.49 4.35
1841 3347 4.315803 TCAGCTAGTTGTTGCTTACCTTC 58.684 43.478 6.47 0.00 37.44 3.46
1869 3380 2.360138 CAGTGTGTCTGCCTCCTCT 58.640 57.895 0.00 0.00 37.36 3.69
1891 3402 8.531622 CTCTGCTAGGAATTAATGTACTCATG 57.468 38.462 0.00 0.00 34.19 3.07
1892 3403 6.931281 TCTGCTAGGAATTAATGTACTCATGC 59.069 38.462 0.00 0.00 34.19 4.06
1901 3412 2.320745 TGTACTCATGCAGCTCCATG 57.679 50.000 11.67 11.67 43.04 3.66
1906 3417 1.072489 CTCATGCAGCTCCATGGATCT 59.928 52.381 17.57 14.38 42.19 2.75
1909 3420 0.913924 TGCAGCTCCATGGATCTTCA 59.086 50.000 16.63 14.57 0.00 3.02
1911 3422 1.134159 GCAGCTCCATGGATCTTCACT 60.134 52.381 16.63 3.42 0.00 3.41
1912 3423 2.562635 CAGCTCCATGGATCTTCACTG 58.437 52.381 16.63 11.90 0.00 3.66
1913 3424 2.093075 CAGCTCCATGGATCTTCACTGT 60.093 50.000 16.63 0.00 0.00 3.55
1914 3425 2.093075 AGCTCCATGGATCTTCACTGTG 60.093 50.000 16.63 0.17 0.00 3.66
1915 3426 2.355513 GCTCCATGGATCTTCACTGTGT 60.356 50.000 16.63 0.00 0.00 3.72
1916 3427 3.871463 GCTCCATGGATCTTCACTGTGTT 60.871 47.826 16.63 0.00 0.00 3.32
1917 3428 4.330250 CTCCATGGATCTTCACTGTGTTT 58.670 43.478 16.63 0.00 0.00 2.83
1918 3429 4.326826 TCCATGGATCTTCACTGTGTTTC 58.673 43.478 11.44 1.33 0.00 2.78
1945 3456 8.908786 TTCTTCTCATGCTTAGGTATAAATGG 57.091 34.615 0.00 0.00 0.00 3.16
1946 3457 8.262601 TCTTCTCATGCTTAGGTATAAATGGA 57.737 34.615 0.00 0.00 0.00 3.41
1947 3458 8.884323 TCTTCTCATGCTTAGGTATAAATGGAT 58.116 33.333 0.00 0.00 0.00 3.41
1948 3459 8.853077 TTCTCATGCTTAGGTATAAATGGATG 57.147 34.615 0.00 0.00 0.00 3.51
1958 3469 4.154195 GGTATAAATGGATGATGTGGCGAC 59.846 45.833 0.00 0.00 0.00 5.19
1982 3493 4.202202 TGTTGTTTGAACCAATGGACCATC 60.202 41.667 6.16 0.00 0.00 3.51
2042 3561 7.234661 TGGTCCGTGCAGTGATATAATATTA 57.765 36.000 0.00 0.00 0.00 0.98
2088 3607 1.803334 TACGGTGTGGTTGCTCAATC 58.197 50.000 0.00 0.00 0.00 2.67
2126 3645 2.845363 AAAATAGTGGGGAACGACGT 57.155 45.000 0.00 0.00 44.74 4.34
2135 3654 3.934579 GTGGGGAACGACGTAATGTTATT 59.065 43.478 0.00 0.00 0.00 1.40
2138 3657 5.106634 TGGGGAACGACGTAATGTTATTTTG 60.107 40.000 0.00 0.00 0.00 2.44
2154 3673 7.432059 TGTTATTTTGATCATGAACTTGCACA 58.568 30.769 0.00 0.00 0.00 4.57
2157 3676 3.564235 TGATCATGAACTTGCACAAGC 57.436 42.857 10.26 0.00 41.99 4.01
2158 3677 3.151554 TGATCATGAACTTGCACAAGCT 58.848 40.909 10.26 0.00 41.99 3.74
2160 3679 4.945543 TGATCATGAACTTGCACAAGCTAT 59.054 37.500 10.26 0.38 41.99 2.97
2161 3680 4.952262 TCATGAACTTGCACAAGCTATC 57.048 40.909 10.26 7.25 41.99 2.08
2162 3681 4.582869 TCATGAACTTGCACAAGCTATCT 58.417 39.130 10.26 0.00 41.99 1.98
2164 3683 5.814188 TCATGAACTTGCACAAGCTATCTAG 59.186 40.000 10.26 4.58 41.99 2.43
2165 3684 5.152623 TGAACTTGCACAAGCTATCTAGT 57.847 39.130 10.26 0.00 41.99 2.57
2167 3686 6.878317 TGAACTTGCACAAGCTATCTAGTAT 58.122 36.000 10.26 0.00 41.99 2.12
2169 3688 7.492669 TGAACTTGCACAAGCTATCTAGTATTC 59.507 37.037 10.26 3.82 41.99 1.75
2170 3689 7.118496 ACTTGCACAAGCTATCTAGTATTCT 57.882 36.000 10.26 0.00 41.99 2.40
2171 3690 6.983307 ACTTGCACAAGCTATCTAGTATTCTG 59.017 38.462 10.26 0.00 41.99 3.02
2173 3692 7.582667 TGCACAAGCTATCTAGTATTCTGTA 57.417 36.000 0.00 0.00 42.74 2.74
2174 3693 8.007405 TGCACAAGCTATCTAGTATTCTGTAA 57.993 34.615 0.00 0.00 42.74 2.41
2175 3694 8.642432 TGCACAAGCTATCTAGTATTCTGTAAT 58.358 33.333 0.00 0.00 42.74 1.89
2203 3793 2.551459 CTCAAGGCACCAAAACAGAGAG 59.449 50.000 0.00 0.00 0.00 3.20
2229 3819 7.814264 ACTTTCAACAGAGTGATCTCAAAAT 57.186 32.000 0.00 0.00 42.66 1.82
2237 3829 7.771183 ACAGAGTGATCTCAAAATAGAGACTC 58.229 38.462 0.00 0.00 46.58 3.36
2271 3863 4.459390 TTTCTACCACGCAAGCTACATA 57.541 40.909 0.00 0.00 45.62 2.29
2272 3864 3.431922 TCTACCACGCAAGCTACATAC 57.568 47.619 0.00 0.00 45.62 2.39
2288 3880 1.345741 CATACCATGCCTCGATCCACT 59.654 52.381 0.00 0.00 0.00 4.00
2301 3893 4.133820 TCGATCCACTGTTGAATGTGTTT 58.866 39.130 0.00 0.00 32.76 2.83
2345 3937 6.656314 TTTGCTGATATACGACGAAACATT 57.344 33.333 0.00 0.00 0.00 2.71
2361 3953 8.786826 ACGAAACATTAAGATACATCCTCAAA 57.213 30.769 0.00 0.00 0.00 2.69
2363 3955 7.846107 CGAAACATTAAGATACATCCTCAAACG 59.154 37.037 0.00 0.00 0.00 3.60
2364 3956 8.561738 AAACATTAAGATACATCCTCAAACGT 57.438 30.769 0.00 0.00 0.00 3.99
2367 3959 7.822334 ACATTAAGATACATCCTCAAACGTGAA 59.178 33.333 0.00 0.00 31.88 3.18
2372 3964 6.591834 AGATACATCCTCAAACGTGAAGAAAG 59.408 38.462 0.00 0.00 31.88 2.62
2375 3967 1.069906 CCTCAAACGTGAAGAAAGCCG 60.070 52.381 0.00 0.00 31.88 5.52
2388 3980 7.527457 GTGAAGAAAGCCGATAAAAACTGTAT 58.473 34.615 0.00 0.00 0.00 2.29
2389 3981 8.662141 GTGAAGAAAGCCGATAAAAACTGTATA 58.338 33.333 0.00 0.00 0.00 1.47
2390 3982 8.879759 TGAAGAAAGCCGATAAAAACTGTATAG 58.120 33.333 0.00 0.00 0.00 1.31
2391 3983 8.788325 AAGAAAGCCGATAAAAACTGTATAGT 57.212 30.769 0.00 0.00 39.32 2.12
2582 4175 2.736400 GCTAAGCATGGCAAATCACACC 60.736 50.000 0.00 0.00 32.44 4.16
2620 4213 6.744112 TCTTTTAACAATCACGGCAAATTCT 58.256 32.000 0.00 0.00 0.00 2.40
2651 4244 1.545582 CGGAACATGGAAACTGCCATT 59.454 47.619 0.00 0.00 46.29 3.16
2653 4246 3.192422 CGGAACATGGAAACTGCCATTAA 59.808 43.478 0.00 0.00 46.29 1.40
2654 4247 4.675146 CGGAACATGGAAACTGCCATTAAG 60.675 45.833 0.00 0.00 46.29 1.85
2663 4256 4.766404 AACTGCCATTAAGAAAGGTTCG 57.234 40.909 0.00 0.00 34.02 3.95
2668 4261 3.673338 GCCATTAAGAAAGGTTCGTTTGC 59.327 43.478 0.00 0.00 34.02 3.68
2681 4274 3.170791 TCGTTTGCCATGCTTGAAAAA 57.829 38.095 0.22 0.00 0.00 1.94
2682 4275 3.726607 TCGTTTGCCATGCTTGAAAAAT 58.273 36.364 0.22 0.00 0.00 1.82
2685 4278 4.025061 CGTTTGCCATGCTTGAAAAATTGA 60.025 37.500 0.22 0.00 0.00 2.57
2695 4289 5.473846 TGCTTGAAAAATTGACGTACCCATA 59.526 36.000 0.00 0.00 0.00 2.74
2749 4343 8.567948 TCAAAGTCCTAAAAGAAACATCATGAC 58.432 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 13 0.397816 CTCGGGGGAGAGAGGACAAT 60.398 60.000 0.00 0.00 40.57 2.71
152 169 2.027169 GGGTCGGATCGGCGTTAG 59.973 66.667 6.85 0.00 29.52 2.34
204 233 2.185350 CGGCGACTCAAGCATCCT 59.815 61.111 0.00 0.00 36.08 3.24
291 391 3.626217 TGCTAAGATACTGTGATCGACGT 59.374 43.478 0.00 0.00 0.00 4.34
296 396 4.505922 GCACTGTGCTAAGATACTGTGATC 59.494 45.833 24.68 0.00 44.49 2.92
339 455 2.932234 AAGTCGCCCAGTCCAGTCG 61.932 63.158 0.00 0.00 0.00 4.18
353 487 1.808411 TGGACGGAATCTTGCAAGTC 58.192 50.000 25.19 16.30 0.00 3.01
398 536 0.031721 AGTGTTCGTCCGGAGTGTTC 59.968 55.000 3.06 0.00 0.00 3.18
399 537 0.031721 GAGTGTTCGTCCGGAGTGTT 59.968 55.000 3.06 0.00 0.00 3.32
400 538 1.658673 GAGTGTTCGTCCGGAGTGT 59.341 57.895 3.06 0.00 0.00 3.55
401 539 1.080705 GGAGTGTTCGTCCGGAGTG 60.081 63.158 3.06 0.00 0.00 3.51
402 540 1.524863 CTGGAGTGTTCGTCCGGAGT 61.525 60.000 3.06 0.00 42.44 3.85
403 541 1.213013 CTGGAGTGTTCGTCCGGAG 59.787 63.158 3.06 0.00 42.44 4.63
404 542 1.521450 GACTGGAGTGTTCGTCCGGA 61.521 60.000 0.00 0.00 42.44 5.14
405 543 1.080705 GACTGGAGTGTTCGTCCGG 60.081 63.158 0.00 0.00 44.98 5.14
406 544 0.109689 GAGACTGGAGTGTTCGTCCG 60.110 60.000 0.00 0.00 36.82 4.79
407 545 0.244178 GGAGACTGGAGTGTTCGTCC 59.756 60.000 0.00 0.00 34.31 4.79
408 546 1.200484 GAGGAGACTGGAGTGTTCGTC 59.800 57.143 0.00 0.00 44.43 4.20
409 547 1.202952 AGAGGAGACTGGAGTGTTCGT 60.203 52.381 0.00 0.00 44.43 3.85
410 548 1.470890 GAGAGGAGACTGGAGTGTTCG 59.529 57.143 0.00 0.00 44.43 3.95
415 553 1.149782 TGGGGAGAGGAGACTGGAGT 61.150 60.000 0.00 0.00 44.43 3.85
432 570 1.577328 GAGTGTTCATGGCGTGGTGG 61.577 60.000 6.90 0.00 0.00 4.61
437 593 0.320771 GACTGGAGTGTTCATGGCGT 60.321 55.000 0.00 0.00 0.00 5.68
438 594 0.036952 AGACTGGAGTGTTCATGGCG 60.037 55.000 0.00 0.00 0.00 5.69
443 599 1.248486 CGAGGAGACTGGAGTGTTCA 58.752 55.000 0.00 0.00 44.43 3.18
444 600 0.528470 CCGAGGAGACTGGAGTGTTC 59.472 60.000 0.00 0.00 44.43 3.18
445 601 0.178958 ACCGAGGAGACTGGAGTGTT 60.179 55.000 0.00 0.00 44.43 3.32
446 602 0.697079 TACCGAGGAGACTGGAGTGT 59.303 55.000 0.00 0.00 44.43 3.55
447 603 1.835494 TTACCGAGGAGACTGGAGTG 58.165 55.000 0.00 0.00 44.43 3.51
448 604 2.169330 GTTTACCGAGGAGACTGGAGT 58.831 52.381 0.00 0.00 44.43 3.85
449 605 2.164624 CAGTTTACCGAGGAGACTGGAG 59.835 54.545 12.72 0.00 44.43 3.86
451 607 2.094649 GTCAGTTTACCGAGGAGACTGG 60.095 54.545 17.13 0.00 44.43 4.00
482 650 3.627395 TGCCTCTTGGTATTGGTACTG 57.373 47.619 0.00 0.00 35.27 2.74
483 651 3.117888 CCATGCCTCTTGGTATTGGTACT 60.118 47.826 0.00 0.00 36.50 2.73
485 653 2.422803 GCCATGCCTCTTGGTATTGGTA 60.423 50.000 0.00 0.00 36.50 3.25
486 654 1.686115 GCCATGCCTCTTGGTATTGGT 60.686 52.381 0.00 0.00 36.50 3.67
487 655 1.035139 GCCATGCCTCTTGGTATTGG 58.965 55.000 0.00 0.00 36.50 3.16
488 656 1.035139 GGCCATGCCTCTTGGTATTG 58.965 55.000 0.00 0.00 46.69 1.90
489 657 3.520623 GGCCATGCCTCTTGGTATT 57.479 52.632 0.00 0.00 46.69 1.89
542 732 2.725145 CGCGCTCTATACGTATGTCTGG 60.725 54.545 18.37 5.95 0.00 3.86
545 739 2.869358 TCGCGCTCTATACGTATGTC 57.131 50.000 18.37 3.66 0.00 3.06
588 782 2.045926 GCTTCCTCCACGGTGCAT 60.046 61.111 1.68 0.00 34.91 3.96
594 809 1.743252 GAAGGCAGCTTCCTCCACG 60.743 63.158 5.03 0.00 34.82 4.94
623 838 0.318275 GCCGGAGAAGTAGATGCTCG 60.318 60.000 5.05 0.00 0.00 5.03
633 848 2.506438 GACGAACGGCCGGAGAAG 60.506 66.667 31.76 17.61 0.00 2.85
771 1030 0.600557 GAGCTGACGGATCGATGGAT 59.399 55.000 0.54 0.00 34.96 3.41
827 1279 1.530655 TCAGTGTGAGCTGGACCGA 60.531 57.895 0.00 0.00 37.12 4.69
828 1280 1.373497 GTCAGTGTGAGCTGGACCG 60.373 63.158 0.00 0.00 37.12 4.79
829 1281 1.004440 GGTCAGTGTGAGCTGGACC 60.004 63.158 0.00 0.00 41.34 4.46
830 1282 1.373497 CGGTCAGTGTGAGCTGGAC 60.373 63.158 0.00 0.00 42.30 4.02
1124 1763 3.270027 AGAGAGAGACAGAGTGATCACG 58.730 50.000 19.85 8.81 36.20 4.35
1128 1767 4.526970 GGAGAAGAGAGAGACAGAGTGAT 58.473 47.826 0.00 0.00 0.00 3.06
1214 1882 1.594331 GTTCTTCTTGGTCACCGCTT 58.406 50.000 0.00 0.00 0.00 4.68
1272 1964 0.830444 ACTTGGTGTCGGTGGAGCTA 60.830 55.000 0.00 0.00 0.00 3.32
1698 3168 3.385384 CAGGTGAGCTCGAGGCCA 61.385 66.667 15.58 4.56 43.05 5.36
1841 3347 0.105593 AGACACACTGCAGACTGGTG 59.894 55.000 23.35 22.29 37.05 4.17
1868 3379 6.707608 TGCATGAGTACATTAATTCCTAGCAG 59.292 38.462 0.00 0.00 34.15 4.24
1869 3380 6.591001 TGCATGAGTACATTAATTCCTAGCA 58.409 36.000 0.00 0.00 34.15 3.49
1879 3390 4.383173 CATGGAGCTGCATGAGTACATTA 58.617 43.478 36.82 0.00 34.15 1.90
1880 3391 3.211865 CATGGAGCTGCATGAGTACATT 58.788 45.455 36.82 4.25 34.15 2.71
1881 3392 2.486727 CCATGGAGCTGCATGAGTACAT 60.487 50.000 40.06 8.83 37.19 2.29
1882 3393 1.134310 CCATGGAGCTGCATGAGTACA 60.134 52.381 40.06 4.87 0.00 2.90
1891 3402 1.134159 AGTGAAGATCCATGGAGCTGC 60.134 52.381 32.24 30.28 40.26 5.25
1892 3403 2.093075 ACAGTGAAGATCCATGGAGCTG 60.093 50.000 32.24 21.78 40.26 4.24
1901 3412 6.484977 AGAAGAAAGAAACACAGTGAAGATCC 59.515 38.462 7.81 0.00 0.00 3.36
1906 3417 6.458751 GCATGAGAAGAAAGAAACACAGTGAA 60.459 38.462 7.81 0.00 0.00 3.18
1909 3420 5.128919 AGCATGAGAAGAAAGAAACACAGT 58.871 37.500 0.00 0.00 0.00 3.55
1911 3422 6.205464 CCTAAGCATGAGAAGAAAGAAACACA 59.795 38.462 0.00 0.00 0.00 3.72
1912 3423 6.205658 ACCTAAGCATGAGAAGAAAGAAACAC 59.794 38.462 0.00 0.00 0.00 3.32
1913 3424 6.299141 ACCTAAGCATGAGAAGAAAGAAACA 58.701 36.000 0.00 0.00 0.00 2.83
1914 3425 6.809630 ACCTAAGCATGAGAAGAAAGAAAC 57.190 37.500 0.00 0.00 0.00 2.78
1945 3456 1.442769 ACAACAGTCGCCACATCATC 58.557 50.000 0.00 0.00 0.00 2.92
1946 3457 1.896220 AACAACAGTCGCCACATCAT 58.104 45.000 0.00 0.00 0.00 2.45
1947 3458 1.333308 CAAACAACAGTCGCCACATCA 59.667 47.619 0.00 0.00 0.00 3.07
1948 3459 1.601903 TCAAACAACAGTCGCCACATC 59.398 47.619 0.00 0.00 0.00 3.06
1958 3469 3.131933 TGGTCCATTGGTTCAAACAACAG 59.868 43.478 1.86 0.00 0.00 3.16
1982 3493 1.275505 CTGCTGCTACACGACTGATG 58.724 55.000 0.00 0.00 0.00 3.07
2052 3571 8.842280 CCACACCGTATAACCATTTATTATTGT 58.158 33.333 0.00 0.00 0.00 2.71
2088 3607 3.731652 TTTTCTTGCCAGTGACCAATG 57.268 42.857 0.00 0.00 0.00 2.82
2111 3630 2.170166 ACATTACGTCGTTCCCCACTA 58.830 47.619 1.78 0.00 0.00 2.74
2122 3641 9.988350 AGTTCATGATCAAAATAACATTACGTC 57.012 29.630 0.00 0.00 0.00 4.34
2135 3654 4.038282 AGCTTGTGCAAGTTCATGATCAAA 59.962 37.500 12.75 0.00 42.74 2.69
2138 3657 3.844577 AGCTTGTGCAAGTTCATGATC 57.155 42.857 12.75 0.00 42.74 2.92
2150 3669 8.920665 CATTACAGAATACTAGATAGCTTGTGC 58.079 37.037 5.31 0.00 40.05 4.57
2164 3683 7.764443 TGCCTTGAGAGTAACATTACAGAATAC 59.236 37.037 4.67 0.00 36.12 1.89
2165 3684 7.764443 GTGCCTTGAGAGTAACATTACAGAATA 59.236 37.037 4.67 0.00 36.12 1.75
2167 3686 5.932303 GTGCCTTGAGAGTAACATTACAGAA 59.068 40.000 4.67 0.00 36.12 3.02
2169 3688 4.631813 GGTGCCTTGAGAGTAACATTACAG 59.368 45.833 4.67 0.00 36.12 2.74
2170 3689 4.041075 TGGTGCCTTGAGAGTAACATTACA 59.959 41.667 4.67 0.00 36.12 2.41
2171 3690 4.575885 TGGTGCCTTGAGAGTAACATTAC 58.424 43.478 0.00 0.00 0.00 1.89
2173 3692 3.788227 TGGTGCCTTGAGAGTAACATT 57.212 42.857 0.00 0.00 0.00 2.71
2174 3693 3.788227 TTGGTGCCTTGAGAGTAACAT 57.212 42.857 0.00 0.00 0.00 2.71
2175 3694 3.569194 TTTGGTGCCTTGAGAGTAACA 57.431 42.857 0.00 0.00 0.00 2.41
2178 3697 3.135712 TCTGTTTTGGTGCCTTGAGAGTA 59.864 43.478 0.00 0.00 0.00 2.59
2179 3698 2.092429 TCTGTTTTGGTGCCTTGAGAGT 60.092 45.455 0.00 0.00 0.00 3.24
2203 3793 6.851222 TTGAGATCACTCTGTTGAAAGTTC 57.149 37.500 0.00 0.00 42.99 3.01
2229 3819 5.723672 AAAATGACCGTTGAGAGTCTCTA 57.276 39.130 20.64 10.95 34.02 2.43
2237 3829 4.377022 CGTGGTAGAAAAATGACCGTTGAG 60.377 45.833 0.00 0.00 35.91 3.02
2264 3856 2.611518 GATCGAGGCATGGTATGTAGC 58.388 52.381 0.00 0.00 0.00 3.58
2271 3863 1.267574 ACAGTGGATCGAGGCATGGT 61.268 55.000 0.00 0.00 0.00 3.55
2272 3864 0.107508 AACAGTGGATCGAGGCATGG 60.108 55.000 0.00 0.00 0.00 3.66
2288 3880 6.862608 GCATGAATCACTAAACACATTCAACA 59.137 34.615 0.00 0.00 38.44 3.33
2301 3893 3.558931 ATTGGGACGCATGAATCACTA 57.441 42.857 0.00 0.00 0.00 2.74
2345 3937 7.165460 TCTTCACGTTTGAGGATGTATCTTA 57.835 36.000 0.00 0.00 33.09 2.10
2361 3953 4.514066 AGTTTTTATCGGCTTTCTTCACGT 59.486 37.500 0.00 0.00 0.00 4.49
2363 3955 5.758924 ACAGTTTTTATCGGCTTTCTTCAC 58.241 37.500 0.00 0.00 0.00 3.18
2364 3956 7.681939 ATACAGTTTTTATCGGCTTTCTTCA 57.318 32.000 0.00 0.00 0.00 3.02
2367 3959 9.310716 GTACTATACAGTTTTTATCGGCTTTCT 57.689 33.333 0.00 0.00 36.14 2.52
2456 4048 7.730332 ACTTCTATTTTCTGGGGTTTCTTCATT 59.270 33.333 0.00 0.00 0.00 2.57
2457 4049 7.241628 ACTTCTATTTTCTGGGGTTTCTTCAT 58.758 34.615 0.00 0.00 0.00 2.57
2552 4145 0.729116 CCATGCTTAGCCAGTGAACG 59.271 55.000 0.29 0.00 0.00 3.95
2590 4183 4.679654 GCCGTGATTGTTAAAAGAAAGTGG 59.320 41.667 0.00 0.00 0.00 4.00
2593 4186 6.820470 TTTGCCGTGATTGTTAAAAGAAAG 57.180 33.333 0.00 0.00 0.00 2.62
2631 4224 1.176527 ATGGCAGTTTCCATGTTCCG 58.823 50.000 0.00 0.00 44.72 4.30
2632 4225 4.462483 TCTTAATGGCAGTTTCCATGTTCC 59.538 41.667 0.00 0.00 45.64 3.62
2644 4237 4.766404 AACGAACCTTTCTTAATGGCAG 57.234 40.909 0.00 0.00 0.00 4.85
2651 4244 3.305064 GCATGGCAAACGAACCTTTCTTA 60.305 43.478 0.00 0.00 0.00 2.10
2653 4246 1.000274 GCATGGCAAACGAACCTTTCT 60.000 47.619 0.00 0.00 0.00 2.52
2654 4247 1.000274 AGCATGGCAAACGAACCTTTC 60.000 47.619 0.00 0.00 0.00 2.62
2663 4256 5.207033 GTCAATTTTTCAAGCATGGCAAAC 58.793 37.500 0.00 0.00 0.00 2.93
2668 4261 4.621034 GGTACGTCAATTTTTCAAGCATGG 59.379 41.667 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.