Multiple sequence alignment - TraesCS2D01G338200

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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 TraesCS2D01G338200 chr2D 100.000 5728 0 0 1 5728 431681920 431676193 0.000000e+00 10578.0
1 TraesCS2D01G338200 chr2D 73.920 602 124 27 112 696 121009507 121010092 1.620000e-50 211.0
2 TraesCS2D01G338200 chr2D 97.059 34 0 1 801 834 431681034 431681002 8.020000e-04 56.5
3 TraesCS2D01G338200 chr2D 97.059 34 0 1 887 919 431681120 431681087 8.020000e-04 56.5
4 TraesCS2D01G338200 chr2A 93.694 2664 106 25 824 3457 554737036 554739667 0.000000e+00 3932.0
5 TraesCS2D01G338200 chr2A 94.473 2316 93 13 3443 5728 554739683 554741993 0.000000e+00 3535.0
6 TraesCS2D01G338200 chr2A 92.169 498 39 0 1 498 554533486 554533983 0.000000e+00 704.0
7 TraesCS2D01G338200 chr2A 89.299 271 26 2 491 761 554534119 554534386 2.560000e-88 337.0
8 TraesCS2D01G338200 chr2B 95.438 1600 48 10 2711 4306 510590404 510588826 0.000000e+00 2527.0
9 TraesCS2D01G338200 chr2B 93.766 1604 69 15 1124 2712 510592105 510590518 0.000000e+00 2379.0
10 TraesCS2D01G338200 chr2B 92.369 1376 80 9 4377 5728 510588837 510587463 0.000000e+00 1936.0
11 TraesCS2D01G338200 chr2B 89.535 430 20 5 698 1127 510592614 510592210 6.580000e-144 521.0
12 TraesCS2D01G338200 chr2B 97.059 34 0 1 801 834 510592446 510592414 8.020000e-04 56.5
13 TraesCS2D01G338200 chr7B 82.719 787 73 28 1809 2592 599801348 599802074 4.840000e-180 641.0
14 TraesCS2D01G338200 chr7A 84.562 434 37 14 2159 2592 639271651 639272054 2.490000e-108 403.0
15 TraesCS2D01G338200 chr7A 72.954 562 99 37 97 625 580543158 580543699 4.620000e-31 147.0
16 TraesCS2D01G338200 chr6B 80.000 315 44 12 111 415 702567422 702567727 1.250000e-51 215.0
17 TraesCS2D01G338200 chr6A 73.729 354 81 8 124 475 126538838 126538495 1.680000e-25 128.0
18 TraesCS2D01G338200 chr3A 88.889 63 6 1 500 562 705395297 705395358 6.150000e-10 76.8
19 TraesCS2D01G338200 chrUn 87.273 55 4 3 4318 4372 1923567 1923618 6.200000e-05 60.2
20 TraesCS2D01G338200 chr1D 87.273 55 4 3 4318 4372 482355370 482355421 6.200000e-05 60.2


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 TraesCS2D01G338200 chr2D 431676193 431681920 5727 True 3563.666667 10578 98.039333 1 5728 3 chr2D.!!$R1 5727
1 TraesCS2D01G338200 chr2D 121009507 121010092 585 False 211.000000 211 73.920000 112 696 1 chr2D.!!$F1 584
2 TraesCS2D01G338200 chr2A 554737036 554741993 4957 False 3733.500000 3932 94.083500 824 5728 2 chr2A.!!$F2 4904
3 TraesCS2D01G338200 chr2A 554533486 554534386 900 False 520.500000 704 90.734000 1 761 2 chr2A.!!$F1 760
4 TraesCS2D01G338200 chr2B 510587463 510592614 5151 True 1483.900000 2527 93.633400 698 5728 5 chr2B.!!$R1 5030
5 TraesCS2D01G338200 chr7B 599801348 599802074 726 False 641.000000 641 82.719000 1809 2592 1 chr7B.!!$F1 783

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
627 771 0.106708 GCGTCCCATATCAGCCTGAA 59.893 55.0 0.00 0.00 0.00 3.02 F
763 907 0.754217 TTGGGAGGATACGAGGTCCG 60.754 60.0 0.00 0.00 46.39 4.79 F
807 951 0.976073 TGAGGTTCCCAGATCGTCCC 60.976 60.0 0.00 0.00 0.00 4.46 F
1780 2055 1.000145 GCGGAATGGTCGACTCTTTC 59.000 55.0 16.46 16.84 0.00 2.62 F
2302 2585 0.885196 TAATTTGCCGCACCCTTCAC 59.115 50.0 0.00 0.00 0.00 3.18 F
3489 3926 1.612676 AGAGCAAGCATGAAACAGCA 58.387 45.0 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2031 0.460311 AGTCGACCATTCCGCTAAGG 59.540 55.000 13.01 0.00 42.97 2.69 R
1945 2224 0.607620 GCAAGTAAGCCATTTGCCCA 59.392 50.000 5.19 0.00 42.43 5.36 R
1947 2226 2.167075 AGATGCAAGTAAGCCATTTGCC 59.833 45.455 11.90 0.89 46.38 4.52 R
3629 4067 1.765904 TGCACTCCTGGTTTGTCACTA 59.234 47.619 0.00 0.00 0.00 2.74 R
3918 4356 0.689623 AGTTTCCAGCTCCCTGACAG 59.310 55.000 0.00 0.00 41.77 3.51 R
5016 5470 0.107017 ATCGGGCAGTTCATTCCAGG 60.107 55.000 0.00 0.00 0.00 4.45 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
54 55 1.214062 GTCCACTGACTCTGCCTCG 59.786 63.158 0.00 0.00 38.53 4.63
80 81 0.742635 GCCGAAGCTCCCTCTTCTTG 60.743 60.000 0.00 0.00 40.11 3.02
88 89 1.003355 CCCTCTTCTTGAAGGCGCA 60.003 57.895 10.83 0.00 0.00 6.09
89 90 0.393537 CCCTCTTCTTGAAGGCGCAT 60.394 55.000 10.83 0.00 0.00 4.73
95 96 1.748950 TCTTGAAGGCGCATATGCAA 58.251 45.000 26.52 11.51 42.21 4.08
104 105 2.039085 GCGCATATGCAATTCTCGTTG 58.961 47.619 26.52 7.89 42.21 4.10
189 190 2.385091 CCACCTAAACGGTTCCGCG 61.385 63.158 11.32 0.00 46.37 6.46
270 271 4.935495 CATGATCCACCGGCCCCG 62.935 72.222 0.00 0.00 39.44 5.73
288 289 2.433318 GCGGATCCTAGCGCCATC 60.433 66.667 10.75 0.19 0.00 3.51
293 294 1.404851 GGATCCTAGCGCCATCTTAGC 60.405 57.143 2.29 0.00 0.00 3.09
309 310 3.118261 TCTTAGCGAAGGCAATGGATTCT 60.118 43.478 6.73 0.00 43.41 2.40
310 311 1.673168 AGCGAAGGCAATGGATTCTC 58.327 50.000 0.00 0.00 43.41 2.87
328 329 2.166459 TCTCGCTGGATCGATGAAAACT 59.834 45.455 0.54 0.00 37.87 2.66
338 339 3.561120 ATGAAAACTGCGGGCGGGA 62.561 57.895 4.29 0.00 0.00 5.14
342 343 4.778143 AACTGCGGGCGGGATCAC 62.778 66.667 4.29 0.00 0.00 3.06
351 352 2.801631 GCGGGATCACTCCTCTGGG 61.802 68.421 0.00 0.00 41.74 4.45
352 353 1.075970 CGGGATCACTCCTCTGGGA 60.076 63.158 0.00 0.00 41.74 4.37
390 391 1.067000 GGATGATCATCTGCTCCTCCG 60.067 57.143 29.85 0.00 37.92 4.63
418 419 1.008938 AGGTATGAGCTCCCAGTCCTT 59.991 52.381 12.15 0.00 0.00 3.36
439 440 4.826274 TGGATCCGAAAATCTCAGAGTT 57.174 40.909 7.39 0.00 0.00 3.01
446 447 3.553511 CGAAAATCTCAGAGTTGGATCCG 59.446 47.826 7.39 0.00 0.00 4.18
451 452 0.904865 TCAGAGTTGGATCCGGTGCT 60.905 55.000 7.39 2.00 0.00 4.40
459 460 0.886490 GGATCCGGTGCTTGCCATAG 60.886 60.000 0.00 0.00 0.00 2.23
481 482 1.811645 GAGTATGCCGGAGAGGAGCC 61.812 65.000 5.05 0.00 45.00 4.70
504 648 0.389948 GTAGTGTGGAAGGCGAGTGG 60.390 60.000 0.00 0.00 0.00 4.00
524 668 0.838122 AGTGGAGTGCAGCTAGGGTT 60.838 55.000 0.00 0.00 0.00 4.11
531 675 1.197036 GTGCAGCTAGGGTTTCGTTTC 59.803 52.381 0.00 0.00 0.00 2.78
532 676 1.202710 TGCAGCTAGGGTTTCGTTTCA 60.203 47.619 0.00 0.00 0.00 2.69
535 679 2.996621 CAGCTAGGGTTTCGTTTCAGAG 59.003 50.000 0.00 0.00 0.00 3.35
541 685 1.214367 GTTTCGTTTCAGAGTGCGGA 58.786 50.000 0.00 0.00 0.00 5.54
546 690 2.425668 TCGTTTCAGAGTGCGGATATGA 59.574 45.455 0.00 0.00 0.00 2.15
547 691 3.068165 TCGTTTCAGAGTGCGGATATGAT 59.932 43.478 0.00 0.00 0.00 2.45
576 720 2.046292 TGTGAGGTCAGATGGTCACAA 58.954 47.619 9.08 0.00 44.79 3.33
583 727 1.077501 AGATGGTCACAATGGGCCG 60.078 57.895 0.00 0.00 0.00 6.13
589 733 2.901840 CACAATGGGCCGGATCCG 60.902 66.667 27.65 27.65 39.44 4.18
620 764 1.671166 CATCCGGCGTCCCATATCA 59.329 57.895 6.01 0.00 0.00 2.15
625 769 1.302033 GGCGTCCCATATCAGCCTG 60.302 63.158 0.00 0.00 44.06 4.85
627 771 0.106708 GCGTCCCATATCAGCCTGAA 59.893 55.000 0.00 0.00 0.00 3.02
629 773 2.213499 CGTCCCATATCAGCCTGAAAC 58.787 52.381 0.00 0.00 0.00 2.78
632 776 4.503123 CGTCCCATATCAGCCTGAAACATA 60.503 45.833 0.00 0.00 0.00 2.29
635 779 5.132648 TCCCATATCAGCCTGAAACATAAGT 59.867 40.000 0.00 0.00 0.00 2.24
644 788 5.307196 AGCCTGAAACATAAGTCGGGTATAT 59.693 40.000 0.77 0.00 41.65 0.86
645 789 6.495872 AGCCTGAAACATAAGTCGGGTATATA 59.504 38.462 0.77 0.00 41.65 0.86
646 790 6.812160 GCCTGAAACATAAGTCGGGTATATAG 59.188 42.308 0.77 0.00 41.65 1.31
647 791 7.309621 GCCTGAAACATAAGTCGGGTATATAGA 60.310 40.741 0.77 0.00 41.65 1.98
657 801 8.488308 AAGTCGGGTATATAGAAAGTACCATT 57.512 34.615 3.52 0.00 39.67 3.16
671 815 8.316214 AGAAAGTACCATTAGTTCGGACATTTA 58.684 33.333 0.00 0.00 0.00 1.40
672 816 8.851541 AAAGTACCATTAGTTCGGACATTTAA 57.148 30.769 0.00 0.00 0.00 1.52
683 827 3.372822 TCGGACATTTAAGTCGGATTTGC 59.627 43.478 0.00 0.00 41.19 3.68
763 907 0.754217 TTGGGAGGATACGAGGTCCG 60.754 60.000 0.00 0.00 46.39 4.79
764 908 1.150081 GGGAGGATACGAGGTCCGA 59.850 63.158 0.00 0.00 46.39 4.55
802 946 4.227864 ACTTTGATGAGGTTCCCAGATC 57.772 45.455 0.00 0.00 0.00 2.75
803 947 2.988010 TTGATGAGGTTCCCAGATCG 57.012 50.000 0.00 0.00 0.00 3.69
804 948 1.866015 TGATGAGGTTCCCAGATCGT 58.134 50.000 0.00 0.00 0.00 3.73
805 949 1.757118 TGATGAGGTTCCCAGATCGTC 59.243 52.381 0.00 0.00 0.00 4.20
806 950 1.069358 GATGAGGTTCCCAGATCGTCC 59.931 57.143 0.00 0.00 0.00 4.79
807 951 0.976073 TGAGGTTCCCAGATCGTCCC 60.976 60.000 0.00 0.00 0.00 4.46
808 952 2.017559 GAGGTTCCCAGATCGTCCCG 62.018 65.000 0.00 0.00 0.00 5.14
809 953 2.202892 GTTCCCAGATCGTCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
810 954 3.833645 TTCCCAGATCGTCCCGCG 61.834 66.667 0.00 0.00 43.01 6.46
812 956 4.570663 CCCAGATCGTCCCGCGTC 62.571 72.222 4.92 0.00 42.13 5.19
813 957 3.822192 CCAGATCGTCCCGCGTCA 61.822 66.667 4.92 0.00 42.13 4.35
814 958 2.413351 CAGATCGTCCCGCGTCAT 59.587 61.111 4.92 0.00 42.13 3.06
815 959 1.658717 CAGATCGTCCCGCGTCATC 60.659 63.158 4.92 0.00 42.13 2.92
816 960 2.726180 GATCGTCCCGCGTCATCG 60.726 66.667 4.92 4.59 42.13 3.84
846 990 2.787567 GGAGGCTCTACCGCTCACC 61.788 68.421 15.23 0.00 46.52 4.02
991 1143 5.171339 AGCTTATCCATGCGATTCCTATT 57.829 39.130 2.58 0.00 31.92 1.73
992 1144 4.940046 AGCTTATCCATGCGATTCCTATTG 59.060 41.667 2.58 0.00 31.92 1.90
993 1145 4.095483 GCTTATCCATGCGATTCCTATTGG 59.905 45.833 2.58 0.00 31.92 3.16
994 1146 1.896220 TCCATGCGATTCCTATTGGC 58.104 50.000 0.00 0.00 0.00 4.52
1371 1637 1.194781 ATGTGTTCTCCCTCGGCACT 61.195 55.000 0.00 0.00 0.00 4.40
1437 1703 2.711311 CGCGTCGGTCCGAGATAA 59.289 61.111 15.95 0.00 36.23 1.75
1517 1791 2.609299 TGGATGGCCCCGAAGACA 60.609 61.111 0.00 0.00 0.00 3.41
1527 1801 4.717629 CGAAGACAGGCGCGGACA 62.718 66.667 8.83 0.00 0.00 4.02
1585 1859 1.229853 AGAAGACGGGGAATGGGGT 60.230 57.895 0.00 0.00 0.00 4.95
1616 1890 1.142748 GTACGCTCTGATGCTGCCT 59.857 57.895 0.00 0.00 0.00 4.75
1618 1892 1.607801 TACGCTCTGATGCTGCCTGT 61.608 55.000 0.00 0.00 0.00 4.00
1713 1987 1.876156 GGCAGACTTCACCTTGACTTG 59.124 52.381 0.00 0.00 0.00 3.16
1721 1995 4.217118 ACTTCACCTTGACTTGATGAATGC 59.783 41.667 0.00 0.00 0.00 3.56
1734 2008 2.804986 TGAATGCTATGGTGCTTGGA 57.195 45.000 0.00 0.00 0.00 3.53
1740 2014 2.754552 TGCTATGGTGCTTGGATCAAAC 59.245 45.455 0.00 0.00 0.00 2.93
1752 2026 2.229543 TGGATCAAACTGTGCAATGCTC 59.770 45.455 6.82 3.08 0.00 4.26
1756 2031 2.046313 CAAACTGTGCAATGCTCGAAC 58.954 47.619 6.82 0.00 0.00 3.95
1762 2037 1.086696 TGCAATGCTCGAACCTTAGC 58.913 50.000 6.82 0.00 39.25 3.09
1780 2055 1.000145 GCGGAATGGTCGACTCTTTC 59.000 55.000 16.46 16.84 0.00 2.62
1813 2088 2.432456 GTGCAGACGATGGACGCA 60.432 61.111 0.00 0.00 46.94 5.24
1898 2176 9.109393 TCAAGTAATTCCATACTCAAATGCTAC 57.891 33.333 0.00 0.00 35.09 3.58
1914 2192 4.683501 TGCTACATTACGACTACAACGA 57.316 40.909 0.00 0.00 34.70 3.85
1921 2199 2.342910 ACGACTACAACGACATGGAC 57.657 50.000 0.00 0.00 34.70 4.02
1949 2228 4.799564 TTTGTTCTATGTGGAAATGGGC 57.200 40.909 0.00 0.00 0.00 5.36
1950 2229 3.448093 TGTTCTATGTGGAAATGGGCA 57.552 42.857 0.00 0.00 0.00 5.36
1951 2230 3.772387 TGTTCTATGTGGAAATGGGCAA 58.228 40.909 0.00 0.00 0.00 4.52
1952 2231 4.155709 TGTTCTATGTGGAAATGGGCAAA 58.844 39.130 0.00 0.00 0.00 3.68
1972 2251 5.717119 CAAATGGCTTACTTGCATCTTCTT 58.283 37.500 0.00 0.00 34.04 2.52
2095 2378 5.235186 GGTTGTTGATCTTGGACATATCTCG 59.765 44.000 0.00 0.00 0.00 4.04
2118 2401 8.777865 TCGATTTATTTGATTCTGACAAGTCT 57.222 30.769 1.53 0.00 0.00 3.24
2302 2585 0.885196 TAATTTGCCGCACCCTTCAC 59.115 50.000 0.00 0.00 0.00 3.18
2312 2595 4.321378 GCCGCACCCTTCACTTTTATTTTA 60.321 41.667 0.00 0.00 0.00 1.52
2313 2596 5.623596 GCCGCACCCTTCACTTTTATTTTAT 60.624 40.000 0.00 0.00 0.00 1.40
2495 2779 6.450545 TCTTCTTGAAGAGACTGTGTATGTG 58.549 40.000 8.80 0.00 33.02 3.21
3225 3632 9.650539 GCTATGTACATAGAATCTGACATGATT 57.349 33.333 36.28 2.92 42.55 2.57
3402 3809 2.632377 AGTGAGATTATTGTGCACCCG 58.368 47.619 15.69 0.00 0.00 5.28
3416 3823 3.749609 GTGCACCCGTTAGTTTGATTAGT 59.250 43.478 5.22 0.00 0.00 2.24
3489 3926 1.612676 AGAGCAAGCATGAAACAGCA 58.387 45.000 0.00 0.00 0.00 4.41
3501 3938 4.524316 TGAAACAGCAGAATTTCATGGG 57.476 40.909 0.00 0.00 39.34 4.00
3548 3986 6.462347 GGTGGTGTTTATGTCAGGTGATTTTT 60.462 38.462 0.00 0.00 0.00 1.94
3620 4058 7.014518 TGCTTGATGTATAAATTTCTCCCCATG 59.985 37.037 0.00 0.00 0.00 3.66
3668 4106 4.614284 GTGCACGATTTCAATGTTCTGAAG 59.386 41.667 0.00 0.00 36.69 3.02
3671 4109 5.914635 GCACGATTTCAATGTTCTGAAGAAA 59.085 36.000 5.40 5.40 36.69 2.52
3806 4244 6.403866 ACACACATCAATTTAGCTTTTCCA 57.596 33.333 0.00 0.00 0.00 3.53
3814 4252 7.346751 TCAATTTAGCTTTTCCAGTTTGTCT 57.653 32.000 0.00 0.00 0.00 3.41
3843 4281 9.249457 TGCTAATCTATTTGACGAAGAATACTG 57.751 33.333 0.00 0.00 0.00 2.74
3918 4356 1.278238 CTGCCGTCGGAGTATTCAAC 58.722 55.000 17.49 0.00 0.00 3.18
4312 4750 6.371548 GCTTACATTTGTTGAGACTGTATGGA 59.628 38.462 0.00 0.00 0.00 3.41
4316 4754 2.892374 TGTTGAGACTGTATGGATGCG 58.108 47.619 0.00 0.00 0.00 4.73
4343 4781 4.314522 TTCATTCTGGTTAATGGAGCCA 57.685 40.909 0.00 0.00 37.44 4.75
4487 4925 3.812053 GACTGCTCAACATGTTCAACTCT 59.188 43.478 8.48 0.00 0.00 3.24
4583 5021 0.095762 GACGTTTTGGGGCGTATTCG 59.904 55.000 0.00 0.00 41.70 3.34
4619 5057 1.923204 CTCTGTAGAGTTGATGCGCAC 59.077 52.381 14.90 7.75 37.40 5.34
4673 5111 4.691175 TGCTAGCATTTGATCTCTCAGAC 58.309 43.478 14.93 0.00 31.68 3.51
4676 5114 2.158986 AGCATTTGATCTCTCAGACGGG 60.159 50.000 0.00 0.00 31.68 5.28
4677 5115 2.208431 CATTTGATCTCTCAGACGGGC 58.792 52.381 0.00 0.00 31.68 6.13
4692 5130 2.592861 GGCCTTCCCATAGCAGCG 60.593 66.667 0.00 0.00 0.00 5.18
4695 5133 1.522092 CCTTCCCATAGCAGCGTCA 59.478 57.895 0.00 0.00 0.00 4.35
4805 5243 2.762535 TCATTTCTCGGAGACCAACC 57.237 50.000 7.33 0.00 0.00 3.77
4862 5300 0.250901 TGCCTCCCAGCTTCTGAAAC 60.251 55.000 0.00 0.00 32.44 2.78
4891 5329 2.932614 CTGCTCACCGGATTTAGAAGTG 59.067 50.000 9.46 0.00 0.00 3.16
4913 5360 0.505231 TTCATGTCGCGTCGTGTTTC 59.495 50.000 21.76 0.00 0.00 2.78
4957 5406 5.585820 TCTGTGTCGTTATGGCTGTTATA 57.414 39.130 0.00 0.00 0.00 0.98
4958 5407 5.588240 TCTGTGTCGTTATGGCTGTTATAG 58.412 41.667 0.00 0.00 0.00 1.31
4971 5420 3.612860 GCTGTTATAGTCTGTTGGACACG 59.387 47.826 0.00 0.00 46.72 4.49
4973 5422 5.456548 TGTTATAGTCTGTTGGACACGAA 57.543 39.130 0.00 0.00 46.72 3.85
4974 5423 5.224888 TGTTATAGTCTGTTGGACACGAAC 58.775 41.667 0.00 0.00 46.72 3.95
4976 5425 0.828022 AGTCTGTTGGACACGAACCA 59.172 50.000 0.00 0.00 46.72 3.67
4983 5432 5.533154 TCTGTTGGACACGAACCAAAATTAT 59.467 36.000 12.32 0.00 46.77 1.28
4988 5441 7.931578 TGGACACGAACCAAAATTATAGATT 57.068 32.000 0.00 0.00 34.25 2.40
5028 5482 7.405292 TGTGAGATTATTTCCTGGAATGAACT 58.595 34.615 10.45 6.66 0.00 3.01
5030 5484 6.319658 TGAGATTATTTCCTGGAATGAACTGC 59.680 38.462 10.45 0.00 0.00 4.40
5032 5486 1.923356 TTTCCTGGAATGAACTGCCC 58.077 50.000 10.45 0.00 0.00 5.36
5038 5492 1.818060 TGGAATGAACTGCCCGATTTG 59.182 47.619 0.00 0.00 0.00 2.32
5166 5623 1.812571 CCTTTGCAGCTACAACGGATT 59.187 47.619 15.54 0.00 40.47 3.01
5191 5652 4.451096 GTGCACCTATACAATTATGTCGGG 59.549 45.833 5.22 0.00 41.05 5.14
5344 5805 4.393155 TTGTCCGCGCTCAGGCAT 62.393 61.111 5.56 0.00 38.60 4.40
5346 5807 4.521062 GTCCGCGCTCAGGCATCT 62.521 66.667 5.56 0.00 38.60 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.194781 AAGAAGAGGGAGCTTCGGCA 61.195 55.000 0.00 0.00 46.81 5.69
63 64 2.615869 CTTCAAGAAGAGGGAGCTTCG 58.384 52.381 3.76 0.00 46.81 3.79
80 81 2.663879 CGAGAATTGCATATGCGCCTTC 60.664 50.000 22.21 21.18 45.83 3.46
88 89 4.675146 GCAACCACAACGAGAATTGCATAT 60.675 41.667 0.00 0.00 41.56 1.78
89 90 3.365868 GCAACCACAACGAGAATTGCATA 60.366 43.478 0.00 0.00 41.56 3.14
95 96 1.263217 GTTCGCAACCACAACGAGAAT 59.737 47.619 0.00 0.00 37.11 2.40
122 123 0.738389 AAACGGAGGCCATATTTGCG 59.262 50.000 5.01 2.77 0.00 4.85
126 127 1.675552 CCGAAAACGGAGGCCATATT 58.324 50.000 5.01 0.00 0.00 1.28
189 190 2.027460 CGCAACCTTGTTGTGCCC 59.973 61.111 7.49 0.00 0.00 5.36
288 289 3.209410 AGAATCCATTGCCTTCGCTAAG 58.791 45.455 0.00 0.00 35.36 2.18
293 294 0.305922 GCGAGAATCCATTGCCTTCG 59.694 55.000 0.00 0.00 0.00 3.79
309 310 2.270923 CAGTTTTCATCGATCCAGCGA 58.729 47.619 0.00 0.00 45.22 4.93
310 311 1.267732 GCAGTTTTCATCGATCCAGCG 60.268 52.381 0.00 0.00 0.00 5.18
338 339 1.187087 GACGTTCCCAGAGGAGTGAT 58.813 55.000 0.00 0.00 45.19 3.06
342 343 1.658686 CTCCGACGTTCCCAGAGGAG 61.659 65.000 0.00 0.00 45.19 3.69
351 352 2.089349 GCACTGCTCTCCGACGTTC 61.089 63.158 0.00 0.00 0.00 3.95
352 353 2.049063 GCACTGCTCTCCGACGTT 60.049 61.111 0.00 0.00 0.00 3.99
390 391 3.451178 TGGGAGCTCATACCTTGTAGTTC 59.549 47.826 17.19 0.00 0.00 3.01
418 419 4.507710 CAACTCTGAGATTTTCGGATCCA 58.492 43.478 13.41 0.00 40.39 3.41
425 426 3.873952 CCGGATCCAACTCTGAGATTTTC 59.126 47.826 13.41 1.83 0.00 2.29
439 440 1.631071 TATGGCAAGCACCGGATCCA 61.631 55.000 9.46 6.00 0.00 3.41
446 447 0.543749 ACTCCTCTATGGCAAGCACC 59.456 55.000 0.00 0.00 35.26 5.01
451 452 1.344438 CGGCATACTCCTCTATGGCAA 59.656 52.381 11.83 0.00 45.62 4.52
459 460 0.178987 TCCTCTCCGGCATACTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
481 482 1.079127 CGCCTTCCACACTACCCAG 60.079 63.158 0.00 0.00 0.00 4.45
504 648 1.261238 ACCCTAGCTGCACTCCACTC 61.261 60.000 1.02 0.00 0.00 3.51
524 668 3.119280 TCATATCCGCACTCTGAAACGAA 60.119 43.478 0.00 0.00 0.00 3.85
546 690 9.950496 GACCATCTGACCTCACATATATTTAAT 57.050 33.333 0.00 0.00 0.00 1.40
547 691 8.933653 TGACCATCTGACCTCACATATATTTAA 58.066 33.333 0.00 0.00 0.00 1.52
564 708 1.378882 CGGCCCATTGTGACCATCTG 61.379 60.000 0.00 0.00 0.00 2.90
567 711 1.936767 ATCCGGCCCATTGTGACCAT 61.937 55.000 0.00 0.00 0.00 3.55
608 752 0.106708 TTCAGGCTGATATGGGACGC 59.893 55.000 19.50 0.00 0.00 5.19
620 764 1.628846 ACCCGACTTATGTTTCAGGCT 59.371 47.619 0.00 0.00 0.00 4.58
625 769 9.978044 ACTTTCTATATACCCGACTTATGTTTC 57.022 33.333 0.00 0.00 0.00 2.78
629 773 9.017509 TGGTACTTTCTATATACCCGACTTATG 57.982 37.037 0.00 0.00 38.07 1.90
632 776 8.488308 AATGGTACTTTCTATATACCCGACTT 57.512 34.615 0.00 0.00 38.07 3.01
635 779 9.592196 AACTAATGGTACTTTCTATATACCCGA 57.408 33.333 0.00 0.00 38.07 5.14
644 788 6.839124 TGTCCGAACTAATGGTACTTTCTA 57.161 37.500 0.00 0.00 0.00 2.10
645 789 5.733620 TGTCCGAACTAATGGTACTTTCT 57.266 39.130 0.00 0.00 0.00 2.52
646 790 6.980051 AATGTCCGAACTAATGGTACTTTC 57.020 37.500 0.00 0.00 0.00 2.62
647 791 8.851541 TTAAATGTCCGAACTAATGGTACTTT 57.148 30.769 0.00 0.00 0.00 2.66
657 801 5.587388 ATCCGACTTAAATGTCCGAACTA 57.413 39.130 0.00 0.00 33.70 2.24
671 815 1.589716 GCAGCTGGCAAATCCGACTT 61.590 55.000 17.12 0.00 43.97 3.01
672 816 2.042831 GCAGCTGGCAAATCCGACT 61.043 57.895 17.12 0.00 43.97 4.18
683 827 1.164411 TAACATTCAACCGCAGCTGG 58.836 50.000 17.12 1.39 0.00 4.85
820 964 4.753662 TAGAGCCTCCCCGTGCGT 62.754 66.667 0.00 0.00 0.00 5.24
821 965 4.208686 GTAGAGCCTCCCCGTGCG 62.209 72.222 0.00 0.00 0.00 5.34
822 966 3.851128 GGTAGAGCCTCCCCGTGC 61.851 72.222 0.00 0.00 0.00 5.34
826 970 3.228017 GAGCGGTAGAGCCTCCCC 61.228 72.222 0.00 0.00 38.01 4.81
846 990 4.379243 AGACTTGCCCGCCGACAG 62.379 66.667 0.00 0.00 0.00 3.51
966 1118 2.740981 GGAATCGCATGGATAAGCTCAG 59.259 50.000 0.00 0.00 34.08 3.35
991 1143 4.147449 CCTCGTCATCGCCAGCCA 62.147 66.667 0.00 0.00 36.96 4.75
993 1145 4.521062 AGCCTCGTCATCGCCAGC 62.521 66.667 0.00 0.00 36.96 4.85
994 1146 2.584418 CAGCCTCGTCATCGCCAG 60.584 66.667 0.00 0.00 36.96 4.85
1146 1412 1.135915 CTGGGATGAGTTGAGGAGACG 59.864 57.143 0.00 0.00 0.00 4.18
1148 1414 1.198713 GCTGGGATGAGTTGAGGAGA 58.801 55.000 0.00 0.00 0.00 3.71
1150 1416 1.900351 CGCTGGGATGAGTTGAGGA 59.100 57.895 0.00 0.00 0.00 3.71
1155 1421 2.045926 GTGGCGCTGGGATGAGTT 60.046 61.111 7.64 0.00 0.00 3.01
1353 1619 0.541063 TAGTGCCGAGGGAGAACACA 60.541 55.000 0.00 0.00 33.69 3.72
1356 1622 0.389757 GGATAGTGCCGAGGGAGAAC 59.610 60.000 0.00 0.00 0.00 3.01
1371 1637 2.225675 TGTGACCACCTACTTGGGGATA 60.226 50.000 0.00 0.00 43.63 2.59
1437 1703 1.229428 CACAGCAACCATCACGAACT 58.771 50.000 0.00 0.00 0.00 3.01
1585 1859 2.969806 GCGTACACCGTGTCCTCGA 61.970 63.158 20.23 0.00 39.32 4.04
1713 1987 3.216800 TCCAAGCACCATAGCATTCATC 58.783 45.455 0.00 0.00 36.85 2.92
1721 1995 4.012374 ACAGTTTGATCCAAGCACCATAG 58.988 43.478 0.00 0.00 0.00 2.23
1734 2008 2.153645 TCGAGCATTGCACAGTTTGAT 58.846 42.857 11.91 0.00 0.00 2.57
1740 2014 0.877071 AAGGTTCGAGCATTGCACAG 59.123 50.000 11.91 1.62 0.00 3.66
1752 2026 1.287425 GACCATTCCGCTAAGGTTCG 58.713 55.000 0.00 0.00 41.99 3.95
1756 2031 0.460311 AGTCGACCATTCCGCTAAGG 59.540 55.000 13.01 0.00 42.97 2.69
1762 2037 1.204941 AGGAAAGAGTCGACCATTCCG 59.795 52.381 26.11 0.00 43.38 4.30
1780 2055 1.764723 TGCACATCAGGATCACCTAGG 59.235 52.381 7.41 7.41 45.94 3.02
1813 2088 2.665649 TGACGAATACCGCATCAACT 57.334 45.000 0.00 0.00 43.32 3.16
1881 2156 6.700081 GTCGTAATGTAGCATTTGAGTATGGA 59.300 38.462 0.00 0.00 0.00 3.41
1894 2172 4.406069 TGTCGTTGTAGTCGTAATGTAGC 58.594 43.478 0.00 0.00 0.00 3.58
1898 2176 4.264614 GTCCATGTCGTTGTAGTCGTAATG 59.735 45.833 0.00 0.00 0.00 1.90
1944 2223 1.207811 GCAAGTAAGCCATTTGCCCAT 59.792 47.619 5.19 0.00 42.43 4.00
1945 2224 0.607620 GCAAGTAAGCCATTTGCCCA 59.392 50.000 5.19 0.00 42.43 5.36
1946 2225 0.607620 TGCAAGTAAGCCATTTGCCC 59.392 50.000 11.90 0.00 46.38 5.36
1947 2226 2.167075 AGATGCAAGTAAGCCATTTGCC 59.833 45.455 11.90 0.89 46.38 4.52
1948 2227 3.515330 AGATGCAAGTAAGCCATTTGC 57.485 42.857 8.63 8.63 46.92 3.68
1949 2228 5.320549 AGAAGATGCAAGTAAGCCATTTG 57.679 39.130 0.00 0.00 0.00 2.32
1950 2229 5.990120 AAGAAGATGCAAGTAAGCCATTT 57.010 34.783 0.00 0.00 0.00 2.32
1951 2230 5.990120 AAAGAAGATGCAAGTAAGCCATT 57.010 34.783 0.00 0.00 0.00 3.16
1952 2231 5.591877 CCTAAAGAAGATGCAAGTAAGCCAT 59.408 40.000 0.00 0.00 0.00 4.40
2108 2391 8.411318 AGCAAATTTACAAAAAGACTTGTCAG 57.589 30.769 3.49 0.00 40.08 3.51
2252 2535 7.383687 AGAACACATGCAAATCAAAGATCAAT 58.616 30.769 0.00 0.00 0.00 2.57
2312 2595 6.552008 TGAAGGAGGTGTATTCAGGAAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
2313 2596 5.947663 TGAAGGAGGTGTATTCAGGAAAAA 58.052 37.500 0.00 0.00 0.00 1.94
3416 3823 6.423905 GCTGACACTAAAGTACAGAAATGTGA 59.576 38.462 15.76 0.00 35.32 3.58
3466 3903 4.219070 TGCTGTTTCATGCTTGCTCTTTAT 59.781 37.500 0.00 0.00 0.00 1.40
3489 3926 2.423947 CCTAGCTGCCCCATGAAATTCT 60.424 50.000 0.00 0.00 0.00 2.40
3548 3986 5.647658 CCACACCTGAAGAAAATGCACTATA 59.352 40.000 0.00 0.00 0.00 1.31
3553 3991 2.361757 CACCACACCTGAAGAAAATGCA 59.638 45.455 0.00 0.00 0.00 3.96
3620 4058 6.170506 TCCTGGTTTGTCACTACATATCAAC 58.829 40.000 0.00 0.00 34.97 3.18
3629 4067 1.765904 TGCACTCCTGGTTTGTCACTA 59.234 47.619 0.00 0.00 0.00 2.74
3668 4106 4.327680 AGCCATCTGGTAGAACAAGTTTC 58.672 43.478 0.00 0.00 37.57 2.78
3671 4109 2.093973 CGAGCCATCTGGTAGAACAAGT 60.094 50.000 0.00 0.00 37.57 3.16
3790 4228 7.202526 CAGACAAACTGGAAAAGCTAAATTGA 58.797 34.615 0.00 0.00 42.39 2.57
3802 4240 2.928801 TAGCAGCAGACAAACTGGAA 57.071 45.000 0.00 0.00 45.82 3.53
3806 4244 6.881065 TCAAATAGATTAGCAGCAGACAAACT 59.119 34.615 0.00 0.00 0.00 2.66
3814 4252 5.660460 TCTTCGTCAAATAGATTAGCAGCA 58.340 37.500 0.00 0.00 0.00 4.41
3843 4281 5.189180 AGACTGCCCAAGAGTTAATGAATC 58.811 41.667 0.00 0.00 0.00 2.52
3918 4356 0.689623 AGTTTCCAGCTCCCTGACAG 59.310 55.000 0.00 0.00 41.77 3.51
4312 4750 2.238521 ACCAGAATGAAACCAACGCAT 58.761 42.857 0.00 0.00 39.69 4.73
4316 4754 6.339587 TCCATTAACCAGAATGAAACCAAC 57.660 37.500 0.00 0.00 39.69 3.77
4372 4810 7.665559 TGAAGTAATCTAGGCTCAACAAATGTT 59.334 33.333 0.00 0.00 39.12 2.71
4487 4925 4.662961 CTGTCGAGTGCGCCACCA 62.663 66.667 4.18 0.00 34.49 4.17
4562 5000 1.300266 AATACGCCCCAAAACGTCCG 61.300 55.000 0.00 0.00 42.46 4.79
4583 5021 3.724914 GAGTGCCGGCCTAGCAGAC 62.725 68.421 26.77 13.80 41.87 3.51
4649 5087 5.583854 GTCTGAGAGATCAAATGCTAGCAAA 59.416 40.000 23.54 8.20 0.00 3.68
4676 5114 1.889573 GACGCTGCTATGGGAAGGC 60.890 63.158 0.00 0.00 0.00 4.35
4677 5115 0.531532 CTGACGCTGCTATGGGAAGG 60.532 60.000 0.00 0.00 0.00 3.46
4685 5123 2.359214 CTCTATGTTCCTGACGCTGCTA 59.641 50.000 0.00 0.00 0.00 3.49
4805 5243 3.621268 CCACCACGGTATAAACATCAGTG 59.379 47.826 0.00 0.00 0.00 3.66
4857 5295 3.745975 CGGTGAGCAGAGTAATTGTTTCA 59.254 43.478 0.00 0.00 0.00 2.69
4862 5300 2.672961 TCCGGTGAGCAGAGTAATTG 57.327 50.000 0.00 0.00 0.00 2.32
4891 5329 1.127817 CACGACGCGACATGAACAC 59.872 57.895 15.93 0.00 0.00 3.32
4913 5360 3.109547 ACACGCATACGCACACGG 61.110 61.111 0.00 0.00 46.04 4.94
4957 5406 0.828022 TGGTTCGTGTCCAACAGACT 59.172 50.000 0.00 0.00 46.46 3.24
4958 5407 1.658994 TTGGTTCGTGTCCAACAGAC 58.341 50.000 5.06 0.00 46.51 3.51
5000 5453 8.827832 TCATTCCAGGAAATAATCTCACAAAT 57.172 30.769 5.81 0.00 0.00 2.32
5004 5458 7.680588 GCAGTTCATTCCAGGAAATAATCTCAC 60.681 40.741 5.81 0.00 0.00 3.51
5016 5470 0.107017 ATCGGGCAGTTCATTCCAGG 60.107 55.000 0.00 0.00 0.00 4.45
5030 5484 1.216178 CCAAGCTTGCCAAATCGGG 59.784 57.895 21.43 0.00 34.06 5.14
5032 5486 1.216178 CCCCAAGCTTGCCAAATCG 59.784 57.895 21.43 5.31 0.00 3.34
5038 5492 3.464494 GATGGCCCCAAGCTTGCC 61.464 66.667 21.43 19.12 45.56 4.52
5166 5623 4.979815 CGACATAATTGTATAGGTGCACGA 59.020 41.667 11.45 0.98 35.79 4.35
5203 5664 2.299993 AGATTCGCTCGCTTTGATCA 57.700 45.000 0.00 0.00 0.00 2.92
5344 5805 2.110213 GTCACCAACCCGTGCAGA 59.890 61.111 0.00 0.00 33.57 4.26


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

AutoCloner maintained by Alex Coulton.