Multiple sequence alignment - TraesCS1D01G151600

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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 TraesCS1D01G151600 chr1D 100.000 3751 0 0 1 3751 211616756 211620506 0.000000e+00 6927.0
1 TraesCS1D01G151600 chr1B 96.965 1977 43 6 765 2725 305271920 305269945 0.000000e+00 3302.0
2 TraesCS1D01G151600 chr1B 88.136 944 78 17 2834 3751 305267283 305266348 0.000000e+00 1092.0
3 TraesCS1D01G151600 chr1B 90.971 731 57 7 1 729 305272793 305272070 0.000000e+00 976.0
4 TraesCS1D01G151600 chr1A 87.970 931 65 24 2835 3751 266878397 266879294 0.000000e+00 1055.0
5 TraesCS1D01G151600 chr6A 86.416 692 85 3 3061 3751 8866978 8866295 0.000000e+00 749.0
6 TraesCS1D01G151600 chr6A 84.670 698 88 10 3061 3751 8790636 8789951 0.000000e+00 678.0
7 TraesCS1D01G151600 chr7D 85.673 691 86 5 3061 3749 257512110 257511431 0.000000e+00 715.0
8 TraesCS1D01G151600 chr7D 81.752 685 82 15 3068 3748 45538716 45538071 1.980000e-147 532.0
9 TraesCS1D01G151600 chr6D 85.362 690 93 4 3061 3749 18192615 18193297 0.000000e+00 708.0
10 TraesCS1D01G151600 chr6D 82.979 658 100 9 3096 3749 99551709 99552358 5.400000e-163 584.0
11 TraesCS1D01G151600 chr5D 85.823 656 82 6 3096 3749 216159286 216159932 0.000000e+00 686.0
12 TraesCS1D01G151600 chr5D 86.618 553 67 3 3197 3749 335659343 335658798 4.140000e-169 604.0
13 TraesCS1D01G151600 chr7B 84.615 702 86 13 3061 3749 638734445 638735137 0.000000e+00 678.0
14 TraesCS1D01G151600 chr2D 86.111 288 32 6 3061 3347 349588042 349588322 1.690000e-78 303.0
15 TraesCS1D01G151600 chr2B 90.217 92 8 1 2743 2833 679560619 679560710 6.580000e-23 119.0
16 TraesCS1D01G151600 chr7A 80.769 78 14 1 314 391 209691714 209691790 4.050000e-05 60.2
17 TraesCS1D01G151600 chr5A 94.286 35 2 0 413 447 569541337 569541371 2.000000e-03 54.7


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 TraesCS1D01G151600 chr1D 211616756 211620506 3750 False 6927 6927 100.000 1 3751 1 chr1D.!!$F1 3750
1 TraesCS1D01G151600 chr1B 305266348 305272793 6445 True 1790 3302 92.024 1 3751 3 chr1B.!!$R1 3750
2 TraesCS1D01G151600 chr1A 266878397 266879294 897 False 1055 1055 87.970 2835 3751 1 chr1A.!!$F1 916
3 TraesCS1D01G151600 chr6A 8866295 8866978 683 True 749 749 86.416 3061 3751 1 chr6A.!!$R2 690
4 TraesCS1D01G151600 chr6A 8789951 8790636 685 True 678 678 84.670 3061 3751 1 chr6A.!!$R1 690
5 TraesCS1D01G151600 chr7D 257511431 257512110 679 True 715 715 85.673 3061 3749 1 chr7D.!!$R2 688
6 TraesCS1D01G151600 chr7D 45538071 45538716 645 True 532 532 81.752 3068 3748 1 chr7D.!!$R1 680
7 TraesCS1D01G151600 chr6D 18192615 18193297 682 False 708 708 85.362 3061 3749 1 chr6D.!!$F1 688
8 TraesCS1D01G151600 chr6D 99551709 99552358 649 False 584 584 82.979 3096 3749 1 chr6D.!!$F2 653
9 TraesCS1D01G151600 chr5D 216159286 216159932 646 False 686 686 85.823 3096 3749 1 chr5D.!!$F1 653
10 TraesCS1D01G151600 chr5D 335658798 335659343 545 True 604 604 86.618 3197 3749 1 chr5D.!!$R1 552
11 TraesCS1D01G151600 chr7B 638734445 638735137 692 False 678 678 84.615 3061 3749 1 chr7B.!!$F1 688

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
739 741 0.093026 CGAAATTCACTGTCGCCGTC 59.907 55.0 0.0 0.0 0.00 4.79 F
740 742 0.093026 GAAATTCACTGTCGCCGTCG 59.907 55.0 0.0 0.0 0.00 5.12 F
763 765 0.179086 CCACCAGCAAAAACCGCTTT 60.179 50.0 0.0 0.0 37.72 3.51 F
1089 1219 0.250295 TCCCCGCAACACTCTCTTTG 60.250 55.0 0.0 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2735 2867 1.063912 TGCGATCATGGATTTTGACGC 59.936 47.619 0.0 0.0 40.59 5.19 R
2736 2868 2.352651 AGTGCGATCATGGATTTTGACG 59.647 45.455 0.0 0.0 0.00 4.35 R
2749 2881 0.654683 GCCAACTGATGAGTGCGATC 59.345 55.000 0.0 0.0 30.61 3.69 R
2987 5691 0.465705 TCACTGGCGATCCAATCTCC 59.534 55.000 0.0 0.0 42.91 3.71 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
22 23 3.807538 GCTGACGTCGACGCCCTA 61.808 66.667 35.92 18.85 44.43 3.53
33 34 4.741676 CGTCGACGCCCTATTTAAATAGTT 59.258 41.667 26.59 12.61 37.30 2.24
42 43 6.074648 CCCTATTTAAATAGTTGGGGCATGA 58.925 40.000 26.18 0.00 37.30 3.07
43 44 6.209391 CCCTATTTAAATAGTTGGGGCATGAG 59.791 42.308 26.18 11.49 37.30 2.90
44 45 7.004086 CCTATTTAAATAGTTGGGGCATGAGA 58.996 38.462 26.18 0.00 37.30 3.27
60 61 1.282930 GAGAACCGACACCGCTTCAC 61.283 60.000 0.00 0.00 33.93 3.18
67 68 1.004277 GACACCGCTTCACTGAGTCG 61.004 60.000 0.00 0.00 0.00 4.18
69 70 2.259818 CCGCTTCACTGAGTCGCT 59.740 61.111 0.00 0.00 0.00 4.93
124 125 2.430921 CGACACCACTGCCTCGTC 60.431 66.667 0.00 0.00 0.00 4.20
131 132 2.680352 ACTGCCTCGTCCGGTCAT 60.680 61.111 0.00 0.00 0.00 3.06
132 133 2.202797 CTGCCTCGTCCGGTCATG 60.203 66.667 0.00 0.00 0.00 3.07
133 134 2.994995 TGCCTCGTCCGGTCATGT 60.995 61.111 0.00 0.00 0.00 3.21
135 136 2.102357 CCTCGTCCGGTCATGTCG 59.898 66.667 0.00 0.00 0.00 4.35
136 137 2.579787 CTCGTCCGGTCATGTCGC 60.580 66.667 0.00 0.00 0.00 5.19
137 138 4.124351 TCGTCCGGTCATGTCGCC 62.124 66.667 0.00 0.00 0.00 5.54
139 140 3.771160 GTCCGGTCATGTCGCCCT 61.771 66.667 0.00 0.00 0.00 5.19
155 156 0.617413 CCCTGACTGGCATCAAGACT 59.383 55.000 0.00 0.00 0.00 3.24
171 172 4.717629 CTGTTGAGTCGCGCCCGA 62.718 66.667 0.00 0.00 42.01 5.14
198 199 1.533625 CGGTGGACCAACATGAATGT 58.466 50.000 10.87 0.00 44.20 2.71
248 249 0.609131 CGATGACTTTGGTTGGGGCT 60.609 55.000 0.00 0.00 0.00 5.19
286 287 5.107607 CGTACGTGGCATGAGTTAAATATCC 60.108 44.000 14.82 0.00 0.00 2.59
300 301 2.292785 ATATCCCCCGGGTTTGGTGC 62.293 60.000 21.85 0.00 36.47 5.01
308 309 0.390860 CGGGTTTGGTGCCATTTTGA 59.609 50.000 0.00 0.00 0.00 2.69
351 352 0.677288 TCCGTGGACGTTTCTGACAT 59.323 50.000 0.00 0.00 37.74 3.06
431 432 1.134946 GGCACAACATTGTAGATGCCC 59.865 52.381 20.42 8.86 39.35 5.36
432 433 2.094675 GCACAACATTGTAGATGCCCT 58.905 47.619 0.00 0.00 39.91 5.19
455 456 0.976641 AGCATCTTCAACAGTCCCGA 59.023 50.000 0.00 0.00 0.00 5.14
492 493 5.070001 CCACCATTTAGGAGAAGTTCAACA 58.930 41.667 5.50 0.00 41.22 3.33
494 495 6.209391 CCACCATTTAGGAGAAGTTCAACAAT 59.791 38.462 5.50 0.00 41.22 2.71
524 525 4.440940 CCAACAGTTCCTTTAAACCCACAC 60.441 45.833 0.00 0.00 0.00 3.82
525 526 3.970842 ACAGTTCCTTTAAACCCACACA 58.029 40.909 0.00 0.00 0.00 3.72
535 537 8.171400 TCCTTTAAACCCACACATTTTATAGGA 58.829 33.333 7.85 7.85 39.04 2.94
539 541 5.061721 ACCCACACATTTTATAGGATCCC 57.938 43.478 8.55 0.00 0.00 3.85
542 544 5.221762 CCCACACATTTTATAGGATCCCGTA 60.222 44.000 8.55 0.00 0.00 4.02
551 553 8.597662 TTTTATAGGATCCCGTAAATTCTTCG 57.402 34.615 8.55 0.00 0.00 3.79
558 560 6.128090 GGATCCCGTAAATTCTTCGAAACTTT 60.128 38.462 0.00 2.20 0.00 2.66
570 572 5.696724 TCTTCGAAACTTTCACTCCATCTTC 59.303 40.000 0.00 0.00 0.00 2.87
571 573 4.956085 TCGAAACTTTCACTCCATCTTCA 58.044 39.130 2.49 0.00 0.00 3.02
595 597 4.153475 CGAAGATGGCTCTTTCCGTAAAAA 59.847 41.667 1.66 0.00 41.87 1.94
598 600 3.569250 TGGCTCTTTCCGTAAAAATGC 57.431 42.857 0.00 0.00 0.00 3.56
604 606 5.523438 TCTTTCCGTAAAAATGCCAAGTT 57.477 34.783 0.00 0.00 0.00 2.66
618 620 4.119862 TGCCAAGTTAGCTAATCGTCATC 58.880 43.478 9.88 0.00 0.00 2.92
619 621 4.119862 GCCAAGTTAGCTAATCGTCATCA 58.880 43.478 9.88 0.00 0.00 3.07
620 622 4.570772 GCCAAGTTAGCTAATCGTCATCAA 59.429 41.667 9.88 0.00 0.00 2.57
625 627 7.988904 AGTTAGCTAATCGTCATCAAAGTAC 57.011 36.000 9.88 0.00 0.00 2.73
628 630 3.060473 GCTAATCGTCATCAAAGTACGCC 60.060 47.826 0.00 0.00 36.60 5.68
668 670 2.390599 CGACCACCACCTGCAATCG 61.391 63.158 0.00 0.00 0.00 3.34
669 671 2.672996 ACCACCACCTGCAATCGC 60.673 61.111 0.00 0.00 39.24 4.58
719 721 3.702048 CCGACCACCACCGTCCAT 61.702 66.667 0.00 0.00 0.00 3.41
720 722 2.125673 CGACCACCACCGTCCATC 60.126 66.667 0.00 0.00 0.00 3.51
729 731 1.396996 CCACCGTCCATCGAAATTCAC 59.603 52.381 0.00 0.00 42.86 3.18
730 732 2.346803 CACCGTCCATCGAAATTCACT 58.653 47.619 0.00 0.00 42.86 3.41
731 733 2.094258 CACCGTCCATCGAAATTCACTG 59.906 50.000 0.00 0.00 42.86 3.66
732 734 2.289444 ACCGTCCATCGAAATTCACTGT 60.289 45.455 0.00 0.00 42.86 3.55
734 736 2.028045 CGTCCATCGAAATTCACTGTCG 59.972 50.000 0.00 0.00 42.86 4.35
735 737 1.999735 TCCATCGAAATTCACTGTCGC 59.000 47.619 0.00 0.00 34.80 5.19
736 738 1.062587 CCATCGAAATTCACTGTCGCC 59.937 52.381 0.00 0.00 34.80 5.54
737 739 0.999406 ATCGAAATTCACTGTCGCCG 59.001 50.000 0.00 0.00 34.80 6.46
738 740 0.319211 TCGAAATTCACTGTCGCCGT 60.319 50.000 0.00 0.00 34.80 5.68
739 741 0.093026 CGAAATTCACTGTCGCCGTC 59.907 55.000 0.00 0.00 0.00 4.79
740 742 0.093026 GAAATTCACTGTCGCCGTCG 59.907 55.000 0.00 0.00 0.00 5.12
741 743 1.897398 AAATTCACTGTCGCCGTCGC 61.897 55.000 0.00 0.00 35.26 5.19
756 758 4.277593 CGCCGCCACCAGCAAAAA 62.278 61.111 0.00 0.00 44.04 1.94
757 759 2.661537 GCCGCCACCAGCAAAAAC 60.662 61.111 0.00 0.00 44.04 2.43
759 761 2.354539 CGCCACCAGCAAAAACCG 60.355 61.111 0.00 0.00 44.04 4.44
761 763 3.128375 CCACCAGCAAAAACCGCT 58.872 55.556 0.00 0.00 41.47 5.52
763 765 0.179086 CCACCAGCAAAAACCGCTTT 60.179 50.000 0.00 0.00 37.72 3.51
840 956 5.188434 CAGGAGCTGTTGGAAATGATCTTA 58.812 41.667 0.00 0.00 0.00 2.10
842 958 4.034510 GGAGCTGTTGGAAATGATCTTACG 59.965 45.833 0.00 0.00 0.00 3.18
843 959 3.375299 AGCTGTTGGAAATGATCTTACGC 59.625 43.478 0.00 0.00 0.00 4.42
844 960 3.785505 GCTGTTGGAAATGATCTTACGCG 60.786 47.826 3.53 3.53 0.00 6.01
853 983 7.483375 TGGAAATGATCTTACGCGTTTATTTTG 59.517 33.333 20.78 0.07 0.00 2.44
930 1060 1.136147 GCGAGAAGACGGCGAAGTA 59.864 57.895 16.62 0.00 0.00 2.24
1011 1141 2.103143 CGAGAGATGAAGCGGCGT 59.897 61.111 9.37 0.00 0.00 5.68
1089 1219 0.250295 TCCCCGCAACACTCTCTTTG 60.250 55.000 0.00 0.00 0.00 2.77
1098 1228 1.980765 ACACTCTCTTTGGAGGCATGA 59.019 47.619 0.00 0.00 39.86 3.07
1208 1338 3.774959 GACACGAGGGCGCGATCAT 62.775 63.158 12.10 0.00 42.48 2.45
1270 1400 5.656416 TCCAAGAGGATGTTTTTCTGTGTTT 59.344 36.000 0.00 0.00 39.61 2.83
1319 1449 4.737578 TCCTGTGAAGTAGTAGTTGGTCT 58.262 43.478 0.00 0.00 0.00 3.85
1534 1664 7.728981 TCAAGTACTAGGAAAGAGAAGAGGAAA 59.271 37.037 0.00 0.00 0.00 3.13
1573 1703 7.962995 TGCCCCTATGTGTATTTATTTTGAA 57.037 32.000 0.00 0.00 0.00 2.69
1612 1742 2.830370 GGCTCCATTTCTGCGGGG 60.830 66.667 0.00 0.00 0.00 5.73
1637 1767 6.094603 GTCAGGAGAAATTGTGCTTCATATGT 59.905 38.462 1.90 0.00 0.00 2.29
1671 1801 9.778993 CTTATGATGCTACAAATGGCAATATAC 57.221 33.333 0.00 0.00 46.47 1.47
1712 1842 7.413657 GCAGTGTTTGTAGTGAGTAGTGAAAAA 60.414 37.037 0.00 0.00 0.00 1.94
1761 1891 6.717997 ACCTAATGTTGGTTTCTTTCGGTAAT 59.282 34.615 0.00 0.00 33.34 1.89
1812 1942 2.298163 CAGAATTTGATGGCCCCATAGC 59.702 50.000 0.00 0.00 36.70 2.97
1848 1978 5.253330 TCACTCAGTTTGTGGAACTCTTTT 58.747 37.500 0.00 0.00 45.40 2.27
1856 1986 8.455682 CAGTTTGTGGAACTCTTTTAAGTGTTA 58.544 33.333 9.23 0.00 45.40 2.41
1871 2001 9.906660 TTTTAAGTGTTATCGCTCATTTTCAAT 57.093 25.926 0.00 0.00 32.83 2.57
1875 2005 5.453587 GTGTTATCGCTCATTTTCAATCAGC 59.546 40.000 0.00 0.00 0.00 4.26
1917 2047 5.512232 CCTTAGGCATCCTGGATTAAGAGTC 60.512 48.000 20.65 7.57 34.61 3.36
2094 2226 8.477984 TTGCTATGATTATTTCCTTTTGTTGC 57.522 30.769 0.00 0.00 0.00 4.17
2194 2326 5.367644 TGTATGTCCAGATCCATGTGAAGAT 59.632 40.000 0.00 0.00 0.00 2.40
2250 2382 8.556194 GCACCGATACAGTTGATCATATTAAAA 58.444 33.333 0.00 0.00 0.00 1.52
2287 2419 3.173953 TGAGGGGATTGACAAATGCTT 57.826 42.857 0.00 0.00 34.70 3.91
2309 2441 4.655963 TGCAAGAGCTATTCTTTTCTGGT 58.344 39.130 0.00 0.00 43.68 4.00
2355 2487 4.945543 AGCTTGCTGATTACAACATCATGA 59.054 37.500 0.00 0.00 32.59 3.07
2369 2501 6.319658 ACAACATCATGACAAACTCTTCTGTT 59.680 34.615 0.00 0.00 0.00 3.16
2384 2516 3.536956 TCTGTTGACCTTTTCGTCACT 57.463 42.857 0.00 0.00 42.37 3.41
2387 2519 3.804036 TGTTGACCTTTTCGTCACTGAT 58.196 40.909 0.00 0.00 42.37 2.90
2400 2532 3.119388 CGTCACTGATGGGATGCAAATTT 60.119 43.478 0.00 0.00 0.00 1.82
2456 2588 6.151648 TCAATCTCAATGTCAGGAAATCCAAC 59.848 38.462 1.67 0.49 38.89 3.77
2627 2759 2.972505 CCGGTTGACAAGCTGCGT 60.973 61.111 14.96 0.00 0.00 5.24
2725 2857 3.299503 TGATGATTGAGACATCGGAGGA 58.700 45.455 0.00 0.00 44.64 3.71
2726 2858 3.068732 TGATGATTGAGACATCGGAGGAC 59.931 47.826 0.00 0.00 44.64 3.85
2727 2859 2.456577 TGATTGAGACATCGGAGGACA 58.543 47.619 0.00 0.00 0.00 4.02
2729 2861 3.068732 TGATTGAGACATCGGAGGACATC 59.931 47.826 0.00 0.00 0.00 3.06
2730 2862 2.143876 TGAGACATCGGAGGACATCA 57.856 50.000 0.00 0.00 0.00 3.07
2731 2863 2.456577 TGAGACATCGGAGGACATCAA 58.543 47.619 0.00 0.00 0.00 2.57
2733 2865 3.260632 TGAGACATCGGAGGACATCAAAA 59.739 43.478 0.00 0.00 0.00 2.44
2734 2866 3.866651 AGACATCGGAGGACATCAAAAG 58.133 45.455 0.00 0.00 0.00 2.27
2735 2867 2.939103 GACATCGGAGGACATCAAAAGG 59.061 50.000 0.00 0.00 0.00 3.11
2736 2868 1.672881 CATCGGAGGACATCAAAAGGC 59.327 52.381 0.00 0.00 0.00 4.35
2737 2869 0.391130 TCGGAGGACATCAAAAGGCG 60.391 55.000 0.00 0.00 0.00 5.52
2738 2870 0.673644 CGGAGGACATCAAAAGGCGT 60.674 55.000 0.00 0.00 0.00 5.68
2739 2871 1.087501 GGAGGACATCAAAAGGCGTC 58.912 55.000 0.00 0.00 0.00 5.19
2740 2872 1.610624 GGAGGACATCAAAAGGCGTCA 60.611 52.381 0.00 0.00 0.00 4.35
2742 2874 2.552315 GAGGACATCAAAAGGCGTCAAA 59.448 45.455 0.00 0.00 0.00 2.69
2745 2877 3.920412 GGACATCAAAAGGCGTCAAAATC 59.080 43.478 0.00 0.00 0.00 2.17
2746 2878 3.913089 ACATCAAAAGGCGTCAAAATCC 58.087 40.909 0.00 0.00 0.00 3.01
2748 2880 4.021192 ACATCAAAAGGCGTCAAAATCCAT 60.021 37.500 0.00 0.00 0.00 3.41
2749 2881 3.911868 TCAAAAGGCGTCAAAATCCATG 58.088 40.909 0.00 0.00 0.00 3.66
2750 2882 3.571828 TCAAAAGGCGTCAAAATCCATGA 59.428 39.130 0.00 0.00 0.00 3.07
2751 2883 4.220382 TCAAAAGGCGTCAAAATCCATGAT 59.780 37.500 0.00 0.00 0.00 2.45
2776 4032 2.290260 ACTCATCAGTTGGCGGATTTGA 60.290 45.455 0.00 0.00 0.00 2.69
2784 4040 3.826157 AGTTGGCGGATTTGAATGAAGAA 59.174 39.130 0.00 0.00 0.00 2.52
2788 4044 4.156556 TGGCGGATTTGAATGAAGAAGAAG 59.843 41.667 0.00 0.00 0.00 2.85
2791 4047 4.439289 CGGATTTGAATGAAGAAGAAGGCC 60.439 45.833 0.00 0.00 0.00 5.19
2800 4056 4.985538 TGAAGAAGAAGGCCTATGTGTTT 58.014 39.130 5.16 0.00 0.00 2.83
2809 4065 5.104259 AGGCCTATGTGTTTAGAGGAAAG 57.896 43.478 1.29 0.00 0.00 2.62
2854 5540 1.092348 TCGGACATGTACGTGAGGAG 58.908 55.000 28.76 9.57 38.28 3.69
2886 5572 3.687212 GTCTAGCCTTGCTTTCCTCTTTC 59.313 47.826 0.00 0.00 40.44 2.62
3022 5728 3.904339 CCAGTGAGTATAGCCAACCCTAT 59.096 47.826 0.00 0.00 32.95 2.57
3024 5730 5.542635 CCAGTGAGTATAGCCAACCCTATAA 59.457 44.000 0.00 0.00 33.39 0.98
3025 5731 6.456501 CAGTGAGTATAGCCAACCCTATAAC 58.543 44.000 0.00 0.00 33.39 1.89
3026 5732 6.041637 CAGTGAGTATAGCCAACCCTATAACA 59.958 42.308 0.00 0.00 33.39 2.41
3165 5878 2.469516 CCGCGCACACCTTATTCCC 61.470 63.158 8.75 0.00 0.00 3.97
3218 5934 3.269538 AGTCTCTCTAGAAGCACGCTA 57.730 47.619 0.00 0.00 32.16 4.26
3356 6077 2.935740 CGGAGCTCACCTCTGTGCA 61.936 63.158 17.19 0.00 42.46 4.57
3364 6093 1.139989 CACCTCTGTGCAGTTACACG 58.860 55.000 0.00 0.00 43.74 4.49
3370 6099 1.330521 CTGTGCAGTTACACGCAACTT 59.669 47.619 1.16 0.00 43.74 2.66
3400 6130 4.517453 CCAAATTGAGACCAAACCGTAAGA 59.483 41.667 0.00 0.00 35.86 2.10
3426 6160 0.179048 CCTCGGCCATAAGTGCATCA 60.179 55.000 2.24 0.00 0.00 3.07
3593 6336 2.159184 AGTCATGTCGCTTGATCGTCAT 60.159 45.455 0.00 0.00 38.38 3.06
3595 6338 2.159254 TCATGTCGCTTGATCGTCATCA 60.159 45.455 0.00 0.00 36.42 3.07
3606 6349 4.193865 TGATCGTCATCATTGCATCACTT 58.806 39.130 0.00 0.00 33.80 3.16
3626 6369 9.745018 ATCACTTGCCATAGTATAATTAGCAAT 57.255 29.630 6.52 0.00 38.02 3.56
3702 6445 7.741554 ATACACTAACTTTCTCCTCTTCCAT 57.258 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.098266 GGTTCTCATGCCCCAACTATTTAAAT 59.902 38.462 5.89 5.89 0.00 1.40
33 34 2.220586 TGTCGGTTCTCATGCCCCA 61.221 57.895 0.00 0.00 0.00 4.96
67 68 4.874977 GCCTACTCCGGTCGCAGC 62.875 72.222 0.00 0.00 0.00 5.25
69 70 2.678934 AAGCCTACTCCGGTCGCA 60.679 61.111 0.00 0.00 0.00 5.10
75 76 3.121019 CCCGAGAAGCCTACTCCG 58.879 66.667 0.00 0.00 0.00 4.63
103 104 1.227556 GAGGCAGTGGTGTCGTTGT 60.228 57.895 0.00 0.00 31.53 3.32
136 137 0.617413 AGTCTTGATGCCAGTCAGGG 59.383 55.000 0.00 0.00 38.09 4.45
137 138 1.002888 ACAGTCTTGATGCCAGTCAGG 59.997 52.381 0.00 0.00 41.84 3.86
138 139 2.469274 ACAGTCTTGATGCCAGTCAG 57.531 50.000 0.00 0.00 0.00 3.51
139 140 2.104622 TCAACAGTCTTGATGCCAGTCA 59.895 45.455 0.00 0.00 0.00 3.41
155 156 2.011741 ATATCGGGCGCGACTCAACA 62.012 55.000 28.99 9.64 0.00 3.33
171 172 0.393808 GTTGGTCCACCGCACCATAT 60.394 55.000 0.00 0.00 43.66 1.78
198 199 2.036098 TCTAGAACCGTCCCCGCA 59.964 61.111 0.00 0.00 0.00 5.69
219 220 2.932614 CCAAAGTCATCGTCATGAGTCC 59.067 50.000 0.00 0.00 41.21 3.85
248 249 3.051479 TACGCGTCCGCTCACTCA 61.051 61.111 18.63 0.00 39.32 3.41
267 268 3.826729 GGGGGATATTTAACTCATGCCAC 59.173 47.826 0.00 0.00 32.19 5.01
286 287 4.694987 ATGGCACCAAACCCGGGG 62.695 66.667 27.92 12.73 0.00 5.73
300 301 2.684881 CGTCTGAATCCCCTCAAAATGG 59.315 50.000 0.00 0.00 0.00 3.16
308 309 3.376935 CTGCGCGTCTGAATCCCCT 62.377 63.158 8.43 0.00 0.00 4.79
348 349 4.829872 ATTTTGCCATCCAACATGATGT 57.170 36.364 0.00 0.00 40.43 3.06
351 352 3.327172 ACCAATTTTGCCATCCAACATGA 59.673 39.130 0.00 0.00 31.97 3.07
377 378 3.857093 GCGAATGTTTGAACTGTGTTGTT 59.143 39.130 0.00 0.00 0.00 2.83
431 432 4.187694 GGGACTGTTGAAGATGCTCTAAG 58.812 47.826 0.00 0.00 0.00 2.18
432 433 3.368427 CGGGACTGTTGAAGATGCTCTAA 60.368 47.826 0.00 0.00 0.00 2.10
443 444 2.927580 GCGGAGTCGGGACTGTTGA 61.928 63.158 5.98 0.00 42.66 3.18
455 456 2.279935 TGGTGGTTATTTTGCGGAGT 57.720 45.000 0.00 0.00 0.00 3.85
519 520 4.714632 ACGGGATCCTATAAAATGTGTGG 58.285 43.478 12.58 0.00 0.00 4.17
525 526 9.216117 CGAAGAATTTACGGGATCCTATAAAAT 57.784 33.333 18.77 13.52 0.00 1.82
535 537 6.428771 TGAAAGTTTCGAAGAATTTACGGGAT 59.571 34.615 10.92 0.00 45.90 3.85
539 541 6.790825 GGAGTGAAAGTTTCGAAGAATTTACG 59.209 38.462 10.92 0.00 45.90 3.18
542 544 6.693315 TGGAGTGAAAGTTTCGAAGAATTT 57.307 33.333 10.92 1.97 45.90 1.82
551 553 4.750098 TCGTGAAGATGGAGTGAAAGTTTC 59.250 41.667 8.75 8.75 0.00 2.78
570 572 1.002366 CGGAAAGAGCCATCTTCGTG 58.998 55.000 0.00 0.00 45.25 4.35
571 573 0.608640 ACGGAAAGAGCCATCTTCGT 59.391 50.000 0.00 0.53 45.25 3.85
595 597 4.137116 TGACGATTAGCTAACTTGGCAT 57.863 40.909 8.70 0.00 0.00 4.40
598 600 6.313905 ACTTTGATGACGATTAGCTAACTTGG 59.686 38.462 8.70 0.00 0.00 3.61
604 606 4.974275 GCGTACTTTGATGACGATTAGCTA 59.026 41.667 0.00 0.00 38.88 3.32
652 654 2.672996 GCGATTGCAGGTGGTGGT 60.673 61.111 0.00 0.00 42.15 4.16
711 713 2.289444 ACAGTGAATTTCGATGGACGGT 60.289 45.455 0.00 0.00 42.82 4.83
719 721 0.319211 ACGGCGACAGTGAATTTCGA 60.319 50.000 16.62 0.00 34.62 3.71
720 722 0.093026 GACGGCGACAGTGAATTTCG 59.907 55.000 16.62 0.00 35.82 3.46
739 741 4.277593 TTTTTGCTGGTGGCGGCG 62.278 61.111 0.51 0.51 45.43 6.46
740 742 2.661537 GTTTTTGCTGGTGGCGGC 60.662 61.111 0.00 0.00 45.43 6.53
741 743 2.028925 GGTTTTTGCTGGTGGCGG 59.971 61.111 0.00 0.00 45.43 6.13
742 744 2.354539 CGGTTTTTGCTGGTGGCG 60.355 61.111 0.00 0.00 45.43 5.69
743 745 2.642996 AAGCGGTTTTTGCTGGTGGC 62.643 55.000 0.00 0.00 43.14 5.01
744 746 0.179086 AAAGCGGTTTTTGCTGGTGG 60.179 50.000 6.80 0.00 43.14 4.61
745 747 2.393764 CTAAAGCGGTTTTTGCTGGTG 58.606 47.619 18.81 0.00 43.14 4.17
746 748 1.339929 CCTAAAGCGGTTTTTGCTGGT 59.660 47.619 18.81 0.00 43.14 4.00
748 750 1.336795 CCCCTAAAGCGGTTTTTGCTG 60.337 52.381 18.81 3.24 43.14 4.41
749 751 0.966179 CCCCTAAAGCGGTTTTTGCT 59.034 50.000 18.81 0.00 46.68 3.91
750 752 0.963225 TCCCCTAAAGCGGTTTTTGC 59.037 50.000 18.81 0.00 0.00 3.68
751 753 2.626266 AGTTCCCCTAAAGCGGTTTTTG 59.374 45.455 18.81 11.26 0.00 2.44
755 757 2.670019 AAAGTTCCCCTAAAGCGGTT 57.330 45.000 0.00 0.00 0.00 4.44
756 758 2.670019 AAAAGTTCCCCTAAAGCGGT 57.330 45.000 0.00 0.00 0.00 5.68
757 759 4.142249 CCATAAAAAGTTCCCCTAAAGCGG 60.142 45.833 0.00 0.00 0.00 5.52
759 761 6.599356 TTCCATAAAAAGTTCCCCTAAAGC 57.401 37.500 0.00 0.00 0.00 3.51
761 763 7.785506 TCAGTTTCCATAAAAAGTTCCCCTAAA 59.214 33.333 0.00 0.00 0.00 1.85
763 765 6.854578 TCAGTTTCCATAAAAAGTTCCCCTA 58.145 36.000 0.00 0.00 0.00 3.53
812 928 4.761739 TCATTTCCAACAGCTCCTGTAAAG 59.238 41.667 0.00 0.00 44.62 1.85
840 956 3.570559 CATTCACCCAAAATAAACGCGT 58.429 40.909 5.58 5.58 0.00 6.01
842 958 3.258228 CCCATTCACCCAAAATAAACGC 58.742 45.455 0.00 0.00 0.00 4.84
843 959 3.258228 GCCCATTCACCCAAAATAAACG 58.742 45.455 0.00 0.00 0.00 3.60
844 960 3.605634 GGCCCATTCACCCAAAATAAAC 58.394 45.455 0.00 0.00 0.00 2.01
853 983 2.364186 CAAGGGGCCCATTCACCC 60.364 66.667 27.72 3.49 46.24 4.61
948 1078 2.579684 AAGGAGTGGAATCGGCTCGC 62.580 60.000 0.00 0.00 0.00 5.03
994 1124 2.103143 ACGCCGCTTCATCTCTCG 59.897 61.111 0.00 0.00 0.00 4.04
1049 1179 1.132640 CGAGCGCAAACCTTGTAGC 59.867 57.895 11.47 2.31 36.94 3.58
1089 1219 1.204146 TCAACCTAGGTCATGCCTCC 58.796 55.000 16.64 3.10 46.96 4.30
1098 1228 2.906389 TCACAAGCAGATCAACCTAGGT 59.094 45.455 9.21 9.21 0.00 3.08
1197 1327 2.203070 AGACCAATGATCGCGCCC 60.203 61.111 0.00 0.00 0.00 6.13
1208 1338 0.178955 TCACTACCCCGTGAGACCAA 60.179 55.000 0.00 0.00 38.89 3.67
1270 1400 1.705873 GCTTAGAGGCTAGGGCTACA 58.294 55.000 0.00 0.00 38.98 2.74
1435 1565 0.480252 AGAAGGAACCCAGCTTTGCT 59.520 50.000 0.00 0.00 40.77 3.91
1534 1664 7.558807 CACATAGGGGCATTTCACATGATATAT 59.441 37.037 0.00 0.00 0.00 0.86
1573 1703 6.845975 AGCCCAGATGGTTGGAATTTATAATT 59.154 34.615 0.00 0.00 40.87 1.40
1612 1742 6.094603 ACATATGAAGCACAATTTCTCCTGAC 59.905 38.462 10.38 0.00 0.00 3.51
1637 1767 7.384932 CCATTTGTAGCATCATAAGACGATGTA 59.615 37.037 0.00 0.00 41.91 2.29
1671 1801 6.072508 ACAAACACTGCAATATAACAGTCTGG 60.073 38.462 4.53 1.51 45.15 3.86
1812 1942 4.527509 ACTGAGTGAAGTAGACATGTGG 57.472 45.455 1.15 0.00 0.00 4.17
1848 1978 8.262715 TGATTGAAAATGAGCGATAACACTTA 57.737 30.769 0.00 0.00 0.00 2.24
1856 1986 4.097437 ACATGCTGATTGAAAATGAGCGAT 59.903 37.500 6.88 0.00 32.05 4.58
1917 2047 5.978934 ACCACTCGGTTATTATTTAAGCG 57.021 39.130 9.87 9.87 46.31 4.68
1939 2069 4.801330 TTCTGCTTTCCTTCTCATCGTA 57.199 40.909 0.00 0.00 0.00 3.43
2094 2226 5.617529 TTCTTGTTAGAAATGCATCTGTGCG 60.618 40.000 0.00 0.00 44.50 5.34
2157 2289 9.632807 GATCTGGACATACAATAGTGAAGATAC 57.367 37.037 0.00 0.00 0.00 2.24
2250 2382 4.567747 CCCCTCAATGGCACTAACTTTAGT 60.568 45.833 0.00 0.00 44.42 2.24
2287 2419 4.655963 ACCAGAAAAGAATAGCTCTTGCA 58.344 39.130 0.00 0.00 44.00 4.08
2309 2441 7.609146 AGCTTGTCATCATTCTTCAAGTGAATA 59.391 33.333 0.00 0.00 38.09 1.75
2355 2487 5.163754 CGAAAAGGTCAACAGAAGAGTTTGT 60.164 40.000 0.00 0.00 0.00 2.83
2369 2501 2.549992 CCCATCAGTGACGAAAAGGTCA 60.550 50.000 0.00 0.00 44.25 4.02
2384 2516 4.087907 TGACAGAAATTTGCATCCCATCA 58.912 39.130 0.00 0.00 0.00 3.07
2387 2519 4.151121 TCTTGACAGAAATTTGCATCCCA 58.849 39.130 0.00 0.00 0.00 4.37
2400 2532 1.938585 ACCGAGGGAATCTTGACAGA 58.061 50.000 0.00 0.00 0.00 3.41
2456 2588 1.068055 GCTTTGACATCAGCCACCTTG 60.068 52.381 0.00 0.00 0.00 3.61
2725 2857 3.320541 TGGATTTTGACGCCTTTTGATGT 59.679 39.130 0.00 0.00 0.00 3.06
2726 2858 3.911868 TGGATTTTGACGCCTTTTGATG 58.088 40.909 0.00 0.00 0.00 3.07
2727 2859 4.220382 TCATGGATTTTGACGCCTTTTGAT 59.780 37.500 0.00 0.00 0.00 2.57
2729 2861 3.911868 TCATGGATTTTGACGCCTTTTG 58.088 40.909 0.00 0.00 0.00 2.44
2730 2862 4.675146 CGATCATGGATTTTGACGCCTTTT 60.675 41.667 0.00 0.00 0.00 2.27
2731 2863 3.181497 CGATCATGGATTTTGACGCCTTT 60.181 43.478 0.00 0.00 0.00 3.11
2733 2865 1.942657 CGATCATGGATTTTGACGCCT 59.057 47.619 0.00 0.00 0.00 5.52
2734 2866 1.597937 GCGATCATGGATTTTGACGCC 60.598 52.381 0.00 0.00 37.51 5.68
2735 2867 1.063912 TGCGATCATGGATTTTGACGC 59.936 47.619 0.00 0.00 40.59 5.19
2736 2868 2.352651 AGTGCGATCATGGATTTTGACG 59.647 45.455 0.00 0.00 0.00 4.35
2737 2869 3.374988 TGAGTGCGATCATGGATTTTGAC 59.625 43.478 0.00 0.00 0.00 3.18
2738 2870 3.608796 TGAGTGCGATCATGGATTTTGA 58.391 40.909 0.00 0.00 0.00 2.69
2739 2871 4.035909 TGATGAGTGCGATCATGGATTTTG 59.964 41.667 8.09 0.00 40.02 2.44
2740 2872 4.201657 TGATGAGTGCGATCATGGATTTT 58.798 39.130 8.09 0.00 40.02 1.82
2742 2874 3.181457 ACTGATGAGTGCGATCATGGATT 60.181 43.478 8.09 0.00 40.02 3.01
2745 2877 2.235845 ACTGATGAGTGCGATCATGG 57.764 50.000 8.09 4.27 40.02 3.66
2746 2878 2.287103 CCAACTGATGAGTGCGATCATG 59.713 50.000 8.09 0.00 40.02 3.07
2748 2880 2.008543 GCCAACTGATGAGTGCGATCA 61.009 52.381 0.00 0.00 30.61 2.92
2749 2881 0.654683 GCCAACTGATGAGTGCGATC 59.345 55.000 0.00 0.00 30.61 3.69
2750 2882 1.086067 CGCCAACTGATGAGTGCGAT 61.086 55.000 10.78 0.00 43.73 4.58
2751 2883 1.737735 CGCCAACTGATGAGTGCGA 60.738 57.895 10.78 0.00 43.73 5.10
2776 4032 5.184892 ACACATAGGCCTTCTTCTTCATT 57.815 39.130 12.58 0.00 0.00 2.57
2784 4040 4.362677 TCCTCTAAACACATAGGCCTTCT 58.637 43.478 12.58 0.00 0.00 2.85
2788 4044 3.628032 GCTTTCCTCTAAACACATAGGCC 59.372 47.826 0.00 0.00 0.00 5.19
2791 4047 5.749109 CGGTAGCTTTCCTCTAAACACATAG 59.251 44.000 0.00 0.00 0.00 2.23
2826 4082 3.130516 ACGTACATGTCCGAAGATGATGT 59.869 43.478 18.30 0.00 34.23 3.06
2854 5540 3.102097 GGCTAGACGCATGCCAAC 58.898 61.111 13.15 3.65 45.46 3.77
2905 5591 5.187186 AGGAGAGAGCGATAAAGGTGTTTAA 59.813 40.000 0.00 0.00 31.81 1.52
2906 5592 4.710375 AGGAGAGAGCGATAAAGGTGTTTA 59.290 41.667 0.00 0.00 32.60 2.01
2975 5679 2.838202 TCCAATCTCCGTTAAGAGCCTT 59.162 45.455 0.00 0.00 33.66 4.35
2976 5680 2.467880 TCCAATCTCCGTTAAGAGCCT 58.532 47.619 0.00 0.00 33.66 4.58
2977 5681 2.981859 TCCAATCTCCGTTAAGAGCC 57.018 50.000 0.00 0.00 33.66 4.70
2978 5682 3.053455 CGATCCAATCTCCGTTAAGAGC 58.947 50.000 0.00 0.00 33.66 4.09
2979 5683 3.053455 GCGATCCAATCTCCGTTAAGAG 58.947 50.000 0.00 0.00 35.04 2.85
2980 5684 2.223971 GGCGATCCAATCTCCGTTAAGA 60.224 50.000 0.00 0.00 0.00 2.10
2982 5686 1.483004 TGGCGATCCAATCTCCGTTAA 59.517 47.619 0.00 0.00 39.99 2.01
2983 5687 1.068588 CTGGCGATCCAATCTCCGTTA 59.931 52.381 0.00 0.00 42.91 3.18
2986 5690 0.877649 CACTGGCGATCCAATCTCCG 60.878 60.000 0.00 0.00 42.91 4.63
2987 5691 0.465705 TCACTGGCGATCCAATCTCC 59.534 55.000 0.00 0.00 42.91 3.71
2988 5692 1.137872 ACTCACTGGCGATCCAATCTC 59.862 52.381 0.00 0.00 42.91 2.75
2989 5693 1.198713 ACTCACTGGCGATCCAATCT 58.801 50.000 0.00 0.00 42.91 2.40
2990 5694 2.890808 TACTCACTGGCGATCCAATC 57.109 50.000 0.00 0.00 42.91 2.67
2991 5695 3.306364 GCTATACTCACTGGCGATCCAAT 60.306 47.826 0.00 0.00 42.91 3.16
3002 5706 6.141083 TGTTATAGGGTTGGCTATACTCACT 58.859 40.000 0.00 0.00 0.00 3.41
3022 5728 5.106317 CCCTAAGTAACGTACCGTCTTGTTA 60.106 44.000 0.00 0.00 39.99 2.41
3024 5730 3.191371 CCCTAAGTAACGTACCGTCTTGT 59.809 47.826 0.00 0.00 39.99 3.16
3025 5731 3.191371 ACCCTAAGTAACGTACCGTCTTG 59.809 47.826 0.00 0.00 39.99 3.02
3026 5732 3.421844 ACCCTAAGTAACGTACCGTCTT 58.578 45.455 0.00 0.00 39.99 3.01
3066 5775 7.994911 TGATGATCACCTTGCAATAAAGAGTAT 59.005 33.333 0.00 0.00 0.00 2.12
3131 5844 1.528824 CGGGGTGCATGGAAGATCT 59.471 57.895 0.00 0.00 0.00 2.75
3165 5878 8.345565 GCTACCCATGATTTAGTCAAACTATTG 58.654 37.037 0.00 0.00 40.97 1.90
3225 5942 6.795114 CGTGTGATTTCCCGCATATTATTTAC 59.205 38.462 0.00 0.00 0.00 2.01
3226 5943 6.566942 GCGTGTGATTTCCCGCATATTATTTA 60.567 38.462 0.00 0.00 45.12 1.40
3370 6099 5.452636 GGTTTGGTCTCAATTTGGCAACTAA 60.453 40.000 0.00 0.00 35.29 2.24
3426 6160 1.029947 GGGAAATCGATTGGTGCGGT 61.030 55.000 12.25 0.00 0.00 5.68
3606 6349 8.514594 GCTTTGATTGCTAATTATACTATGGCA 58.485 33.333 0.00 0.00 0.00 4.92
3626 6369 9.230122 TCATAGTAATGACAATCAAAGCTTTGA 57.770 29.630 36.74 36.74 42.69 2.69
3680 6423 5.544176 TGATGGAAGAGGAGAAAGTTAGTGT 59.456 40.000 0.00 0.00 0.00 3.55
3702 6445 5.427157 TGCTACTGGTTCCTGGTATTTATGA 59.573 40.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.