Multiple sequence alignment - TraesCS1B01G156100

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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 TraesCS1B01G156100 chr1B 100.000 4077 0 0 1 4077 263750834 263746758 0.000000e+00 7529.0
1 TraesCS1B01G156100 chr1D 94.635 2330 83 14 847 3148 189886944 189884629 0.000000e+00 3572.0
2 TraesCS1B01G156100 chr1D 94.845 582 26 3 3496 4077 189884385 189883808 0.000000e+00 905.0
3 TraesCS1B01G156100 chr1D 95.406 283 11 2 3150 3431 189884665 189884384 2.240000e-122 449.0
4 TraesCS1B01G156100 chr1D 81.687 486 77 6 364 847 361707030 361706555 1.060000e-105 394.0
5 TraesCS1B01G156100 chr1D 81.264 459 72 8 392 847 312937298 312937745 3.870000e-95 359.0
6 TraesCS1B01G156100 chr1A 94.437 2265 98 9 891 3145 167800169 167802415 0.000000e+00 3459.0
7 TraesCS1B01G156100 chr1A 94.198 586 28 3 3496 4077 167802668 167803251 0.000000e+00 889.0
8 TraesCS1B01G156100 chr1A 90.034 291 18 5 3150 3431 167802381 167802669 2.320000e-97 366.0
9 TraesCS1B01G156100 chr1A 80.526 190 25 7 3886 4075 94836252 94836075 7.110000e-28 135.0
10 TraesCS1B01G156100 chr2D 87.588 854 85 11 1 851 463935533 463934698 0.000000e+00 970.0
11 TraesCS1B01G156100 chr4A 86.926 849 99 6 1 847 97769714 97770552 0.000000e+00 942.0
12 TraesCS1B01G156100 chr3B 87.201 836 94 7 13 846 505300663 505299839 0.000000e+00 939.0
13 TraesCS1B01G156100 chr3B 85.849 848 106 10 1 847 216317416 216318250 0.000000e+00 889.0
14 TraesCS1B01G156100 chr3B 84.800 375 44 7 476 848 646731056 646731419 8.330000e-97 364.0
15 TraesCS1B01G156100 chr3B 81.441 458 68 11 394 847 679454188 679453744 3.870000e-95 359.0
16 TraesCS1B01G156100 chr3B 78.585 523 92 15 327 844 235331651 235332158 1.090000e-85 327.0
17 TraesCS1B01G156100 chr3B 87.805 82 6 4 3418 3498 54754989 54754911 4.340000e-15 93.5
18 TraesCS1B01G156100 chr4B 86.889 839 98 9 1 838 304858483 304859310 0.000000e+00 929.0
19 TraesCS1B01G156100 chr4B 85.664 851 106 10 1 846 253189672 253188833 0.000000e+00 881.0
20 TraesCS1B01G156100 chr4B 86.207 87 8 4 3412 3497 618591676 618591759 1.560000e-14 91.6
21 TraesCS1B01G156100 chr6D 85.833 840 105 8 1 837 206871720 206872548 0.000000e+00 880.0
22 TraesCS1B01G156100 chr6D 86.517 89 8 4 3412 3499 81746847 81746932 1.210000e-15 95.3
23 TraesCS1B01G156100 chr7B 85.647 843 108 9 1 841 369882041 369881210 0.000000e+00 874.0
24 TraesCS1B01G156100 chr7B 82.143 616 88 13 238 846 149404630 149404030 3.640000e-140 508.0
25 TraesCS1B01G156100 chr7B 80.233 430 71 11 413 839 345923544 345923962 1.100000e-80 311.0
26 TraesCS1B01G156100 chr4D 88.235 595 68 2 1 594 357045329 357044736 0.000000e+00 710.0
27 TraesCS1B01G156100 chr4D 81.602 462 69 9 392 849 93877729 93877280 6.440000e-98 368.0
28 TraesCS1B01G156100 chr4D 84.946 93 9 5 3411 3501 501060477 501060388 5.610000e-14 89.8
29 TraesCS1B01G156100 chr3A 81.890 508 78 8 343 847 512843554 512844050 2.270000e-112 416.0
30 TraesCS1B01G156100 chr3D 88.506 87 6 4 3418 3503 355882441 355882358 7.210000e-18 102.0
31 TraesCS1B01G156100 chr6B 87.356 87 7 4 3412 3497 690750873 690750956 3.350000e-16 97.1
32 TraesCS1B01G156100 chr6B 86.364 88 8 4 3412 3498 229680863 229680947 4.340000e-15 93.5
33 TraesCS1B01G156100 chr5D 86.022 93 9 4 3408 3499 557506303 557506392 3.350000e-16 97.1
34 TraesCS1B01G156100 chr5B 88.095 84 6 4 3418 3500 706458200 706458120 3.350000e-16 97.1


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 TraesCS1B01G156100 chr1B 263746758 263750834 4076 True 7529.000000 7529 100.000000 1 4077 1 chr1B.!!$R1 4076
1 TraesCS1B01G156100 chr1D 189883808 189886944 3136 True 1642.000000 3572 94.962000 847 4077 3 chr1D.!!$R2 3230
2 TraesCS1B01G156100 chr1A 167800169 167803251 3082 False 1571.333333 3459 92.889667 891 4077 3 chr1A.!!$F1 3186
3 TraesCS1B01G156100 chr2D 463934698 463935533 835 True 970.000000 970 87.588000 1 851 1 chr2D.!!$R1 850
4 TraesCS1B01G156100 chr4A 97769714 97770552 838 False 942.000000 942 86.926000 1 847 1 chr4A.!!$F1 846
5 TraesCS1B01G156100 chr3B 505299839 505300663 824 True 939.000000 939 87.201000 13 846 1 chr3B.!!$R2 833
6 TraesCS1B01G156100 chr3B 216317416 216318250 834 False 889.000000 889 85.849000 1 847 1 chr3B.!!$F1 846
7 TraesCS1B01G156100 chr3B 235331651 235332158 507 False 327.000000 327 78.585000 327 844 1 chr3B.!!$F2 517
8 TraesCS1B01G156100 chr4B 304858483 304859310 827 False 929.000000 929 86.889000 1 838 1 chr4B.!!$F1 837
9 TraesCS1B01G156100 chr4B 253188833 253189672 839 True 881.000000 881 85.664000 1 846 1 chr4B.!!$R1 845
10 TraesCS1B01G156100 chr6D 206871720 206872548 828 False 880.000000 880 85.833000 1 837 1 chr6D.!!$F2 836
11 TraesCS1B01G156100 chr7B 369881210 369882041 831 True 874.000000 874 85.647000 1 841 1 chr7B.!!$R2 840
12 TraesCS1B01G156100 chr7B 149404030 149404630 600 True 508.000000 508 82.143000 238 846 1 chr7B.!!$R1 608
13 TraesCS1B01G156100 chr4D 357044736 357045329 593 True 710.000000 710 88.235000 1 594 1 chr4D.!!$R2 593

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
505 508 0.038890 TGGTTCCATCGGCCAATGAA 59.961 50.0 4.85 0.0 0.00 2.57 F
599 616 0.318614 TTAACGACAACCCGACGACC 60.319 55.0 0.00 0.0 36.58 4.79 F
632 649 0.531657 CCACGTGTCGGTTACCCATA 59.468 55.0 15.65 0.0 0.00 2.74 F
902 920 1.008875 TTGCTCGTGCTAGTGCTTCG 61.009 55.0 11.19 0.0 40.48 3.79 F
2316 2355 0.319900 GCACAGGACGGCGATCATAT 60.320 55.0 16.62 0.0 0.00 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1596 0.251354 GCCAATGCCAGTGAGAGAGA 59.749 55.0 0.00 0.0 0.00 3.10 R
1570 1597 0.252479 AGCCAATGCCAGTGAGAGAG 59.748 55.0 0.00 0.0 38.69 3.20 R
1878 1905 0.311790 CTGCTGCAATGGTGTCGTTT 59.688 50.0 3.02 0.0 0.00 3.60 R
2803 2848 0.255604 CCATGACATACACCAGGCCA 59.744 55.0 5.01 0.0 0.00 5.36 R
3183 3229 0.039618 TGCCTGGGAAGGACATTTCC 59.960 55.0 0.00 0.0 44.82 3.13 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
39 41 5.072736 AGTTGATGGGCTGAATCTGATATGA 59.927 40.000 0.00 0.00 0.00 2.15
67 69 8.477256 CCATAATTTAGCCCAAAGAATGAAAGA 58.523 33.333 0.00 0.00 29.66 2.52
98 100 0.462047 CCGGATCTAATATGGGCCGC 60.462 60.000 0.00 0.00 37.57 6.53
117 119 0.381801 CAATATGGCCCAGAACGTGC 59.618 55.000 0.00 0.00 0.00 5.34
153 155 1.361197 TCGGATCTCATATGGGCCCTA 59.639 52.381 25.70 13.40 0.00 3.53
185 187 4.397420 ACAACATGGCAGACTGTTAATGA 58.603 39.130 16.26 0.00 33.96 2.57
186 188 5.012239 ACAACATGGCAGACTGTTAATGAT 58.988 37.500 16.26 6.27 33.96 2.45
225 228 2.181954 GCATTTGGCCCAAAACATGA 57.818 45.000 13.87 0.00 36.90 3.07
259 262 1.677552 CCGGCCCACTAGTGTCTTT 59.322 57.895 21.18 0.00 0.00 2.52
291 294 4.115199 CTTTAGCTGGGCCGGCCT 62.115 66.667 42.70 27.02 36.20 5.19
335 338 4.115199 CTTTAGCTGGGCCGGCCT 62.115 66.667 42.70 27.02 36.20 5.19
427 430 1.346365 CGGTCCACGTGTCAACATAG 58.654 55.000 15.65 0.00 37.93 2.23
435 438 4.440940 CCACGTGTCAACATAGCATAGGTA 60.441 45.833 15.65 0.00 32.50 3.08
455 458 1.212688 ACATCTCGCCCATTGGATGAA 59.787 47.619 3.62 0.00 38.91 2.57
460 463 0.308684 CGCCCATTGGATGAATGACG 59.691 55.000 3.62 0.00 43.87 4.35
467 470 3.436001 GGATGAATGACGTCCGTGT 57.564 52.632 14.12 0.00 43.60 4.49
505 508 0.038890 TGGTTCCATCGGCCAATGAA 59.961 50.000 4.85 0.00 0.00 2.57
532 536 5.908916 TTACACGTGAAAATCGTCATTGA 57.091 34.783 25.01 0.00 39.55 2.57
536 540 3.678072 ACGTGAAAATCGTCATTGATCGT 59.322 39.130 0.00 0.00 36.85 3.73
550 554 0.459585 GATCGTTGGCTGTTAGCGGA 60.460 55.000 0.00 0.00 43.62 5.54
559 563 2.059541 GCTGTTAGCGGATTATCGGAC 58.940 52.381 3.91 0.00 0.00 4.79
561 565 2.033372 TGTTAGCGGATTATCGGACCA 58.967 47.619 3.91 0.00 0.00 4.02
588 605 0.527565 GACCCGGTAGCTTAACGACA 59.472 55.000 0.00 0.00 42.61 4.35
594 611 1.067635 GGTAGCTTAACGACAACCCGA 60.068 52.381 0.00 0.00 0.00 5.14
595 612 1.988467 GTAGCTTAACGACAACCCGAC 59.012 52.381 0.00 0.00 0.00 4.79
597 614 0.664166 GCTTAACGACAACCCGACGA 60.664 55.000 0.00 0.00 36.58 4.20
598 615 1.055338 CTTAACGACAACCCGACGAC 58.945 55.000 0.00 0.00 36.58 4.34
599 616 0.318614 TTAACGACAACCCGACGACC 60.319 55.000 0.00 0.00 36.58 4.79
600 617 2.141122 TAACGACAACCCGACGACCC 62.141 60.000 0.00 0.00 36.58 4.46
602 619 3.982241 GACAACCCGACGACCCGT 61.982 66.667 0.00 0.00 45.10 5.28
603 620 3.504524 GACAACCCGACGACCCGTT 62.505 63.158 0.00 0.00 41.37 4.44
604 621 2.141122 GACAACCCGACGACCCGTTA 62.141 60.000 0.00 0.00 41.37 3.18
605 622 1.734117 CAACCCGACGACCCGTTAC 60.734 63.158 0.00 0.00 41.37 2.50
606 623 3.267597 AACCCGACGACCCGTTACG 62.268 63.158 0.00 0.00 41.37 3.18
630 647 2.735883 CCACGTGTCGGTTACCCA 59.264 61.111 15.65 0.00 0.00 4.51
632 649 0.531657 CCACGTGTCGGTTACCCATA 59.468 55.000 15.65 0.00 0.00 2.74
642 659 2.940410 CGGTTACCCATAACGAAAGCAT 59.060 45.455 0.00 0.00 41.52 3.79
649 666 6.767524 ACCCATAACGAAAGCATTTTCATA 57.232 33.333 0.00 0.00 42.27 2.15
676 693 4.803613 CGTCATTTATCGTCATGGAAGTGA 59.196 41.667 0.00 0.00 0.00 3.41
677 694 5.051441 CGTCATTTATCGTCATGGAAGTGAG 60.051 44.000 0.00 0.00 0.00 3.51
678 695 5.812642 GTCATTTATCGTCATGGAAGTGAGT 59.187 40.000 0.00 0.00 0.00 3.41
703 720 7.316544 ACTTCCGTGATGATAATTTTGGTAC 57.683 36.000 0.00 0.00 0.00 3.34
711 728 8.892723 GTGATGATAATTTTGGTACTGTCATGA 58.107 33.333 0.00 0.00 0.00 3.07
715 732 8.233868 TGATAATTTTGGTACTGTCATGAAACG 58.766 33.333 0.00 0.00 0.00 3.60
794 812 6.969828 TGTACATGCATGACAAATAACGTA 57.030 33.333 32.75 7.91 0.00 3.57
902 920 1.008875 TTGCTCGTGCTAGTGCTTCG 61.009 55.000 11.19 0.00 40.48 3.79
1087 1114 3.067601 TGAAGAAAAGAAAAAGGCGGGAC 59.932 43.478 0.00 0.00 0.00 4.46
1437 1464 2.885861 GACGTGCGTCTCCTCCAT 59.114 61.111 16.33 0.00 41.57 3.41
1463 1490 1.665916 GACGTCTCAGCAGCAGCAA 60.666 57.895 8.70 0.00 45.49 3.91
1468 1495 2.203238 TCAGCAGCAGCAACAGCA 60.203 55.556 3.17 0.00 45.49 4.41
1526 1553 7.306205 TGTACAACTTTTATAATGCCGTACC 57.694 36.000 0.00 0.00 0.00 3.34
1568 1595 4.676459 CGAGCATCTTGTAGTCTCACACAT 60.676 45.833 0.00 0.00 0.00 3.21
1569 1596 5.157940 AGCATCTTGTAGTCTCACACATT 57.842 39.130 0.00 0.00 0.00 2.71
1570 1597 5.174395 AGCATCTTGTAGTCTCACACATTC 58.826 41.667 0.00 0.00 0.00 2.67
1580 1607 4.218200 AGTCTCACACATTCTCTCTCACTG 59.782 45.833 0.00 0.00 0.00 3.66
1581 1608 3.509184 TCTCACACATTCTCTCTCACTGG 59.491 47.826 0.00 0.00 0.00 4.00
1591 1618 1.093159 CTCTCACTGGCATTGGCTTC 58.907 55.000 11.84 0.00 40.87 3.86
1731 1758 3.787001 CACTTCCCGGAGCTCCCC 61.787 72.222 27.20 3.97 0.00 4.81
1819 1846 2.444706 CCAGGGAGATCCTCGGCA 60.445 66.667 0.00 0.00 46.12 5.69
1878 1905 1.609501 CGAGTCCAAGACCAGGGGA 60.610 63.158 0.00 0.00 32.18 4.81
1880 1907 1.064825 GAGTCCAAGACCAGGGGAAA 58.935 55.000 0.00 0.00 32.18 3.13
1904 1931 1.199327 CACCATTGCAGCAGAGTTCTG 59.801 52.381 4.77 4.77 46.40 3.02
1928 1955 3.992317 GCTCGGGATAGGGGCGAC 61.992 72.222 0.00 0.00 0.00 5.19
2019 2046 1.764723 CACTGGCTGTCCATGATCCTA 59.235 52.381 0.00 0.00 42.51 2.94
2197 2236 4.200283 CAGGCCTCTCTCGACGGC 62.200 72.222 0.00 0.00 43.03 5.68
2268 2307 0.464916 GGGTCCAACTTCACCGTGTT 60.465 55.000 0.00 0.00 32.89 3.32
2315 2354 1.067416 GCACAGGACGGCGATCATA 59.933 57.895 16.62 0.00 0.00 2.15
2316 2355 0.319900 GCACAGGACGGCGATCATAT 60.320 55.000 16.62 0.00 0.00 1.78
2440 2479 3.390003 GTTCAACAACCTCGGGACA 57.610 52.632 0.00 0.00 0.00 4.02
2488 2527 1.464198 ACAAAGGGGCACTCCTCCT 60.464 57.895 0.00 0.00 35.80 3.69
2489 2528 1.301293 CAAAGGGGCACTCCTCCTC 59.699 63.158 0.00 0.00 35.80 3.71
2490 2529 1.925972 AAAGGGGCACTCCTCCTCC 60.926 63.158 0.00 0.00 35.80 4.30
2722 2767 3.083997 GGAGTGAGGATGGGCGGT 61.084 66.667 0.00 0.00 0.00 5.68
2723 2768 2.187946 GAGTGAGGATGGGCGGTG 59.812 66.667 0.00 0.00 0.00 4.94
2917 2962 6.343716 TCACAATGCATGGTTTATGTTCTT 57.656 33.333 3.20 0.00 39.08 2.52
3127 3172 9.982651 TTAGTACCTGATTTATCTTCTATGCAC 57.017 33.333 0.00 0.00 0.00 4.57
3147 3193 2.092429 ACCTCTTGCAAGTTGAACAGGA 60.092 45.455 27.49 7.63 0.00 3.86
3148 3194 2.291741 CCTCTTGCAAGTTGAACAGGAC 59.708 50.000 25.19 0.00 0.00 3.85
3149 3195 2.945008 CTCTTGCAAGTTGAACAGGACA 59.055 45.455 25.19 1.23 0.00 4.02
3150 3196 3.554934 TCTTGCAAGTTGAACAGGACAT 58.445 40.909 25.19 0.00 0.00 3.06
3151 3197 3.953612 TCTTGCAAGTTGAACAGGACATT 59.046 39.130 25.19 0.00 0.00 2.71
3152 3198 4.402155 TCTTGCAAGTTGAACAGGACATTT 59.598 37.500 25.19 0.00 0.00 2.32
3153 3199 5.592282 TCTTGCAAGTTGAACAGGACATTTA 59.408 36.000 25.19 0.00 0.00 1.40
3154 3200 6.265196 TCTTGCAAGTTGAACAGGACATTTAT 59.735 34.615 25.19 0.00 0.00 1.40
3155 3201 6.012658 TGCAAGTTGAACAGGACATTTATC 57.987 37.500 7.16 0.00 0.00 1.75
3156 3202 5.769662 TGCAAGTTGAACAGGACATTTATCT 59.230 36.000 7.16 0.00 0.00 1.98
3157 3203 6.265196 TGCAAGTTGAACAGGACATTTATCTT 59.735 34.615 7.16 0.00 0.00 2.40
3158 3204 6.803807 GCAAGTTGAACAGGACATTTATCTTC 59.196 38.462 7.16 0.00 0.00 2.87
3159 3205 6.727824 AGTTGAACAGGACATTTATCTTCG 57.272 37.500 0.00 0.00 0.00 3.79
3160 3206 6.464222 AGTTGAACAGGACATTTATCTTCGA 58.536 36.000 0.00 0.00 0.00 3.71
3161 3207 7.106239 AGTTGAACAGGACATTTATCTTCGAT 58.894 34.615 0.00 0.00 0.00 3.59
3162 3208 6.908870 TGAACAGGACATTTATCTTCGATG 57.091 37.500 0.00 0.00 0.00 3.84
3163 3209 5.294306 TGAACAGGACATTTATCTTCGATGC 59.706 40.000 0.00 0.00 0.00 3.91
3164 3210 4.769688 ACAGGACATTTATCTTCGATGCA 58.230 39.130 0.00 0.00 0.00 3.96
3165 3211 5.371526 ACAGGACATTTATCTTCGATGCAT 58.628 37.500 0.00 0.00 0.00 3.96
3166 3212 5.468072 ACAGGACATTTATCTTCGATGCATC 59.532 40.000 17.10 17.10 0.00 3.91
3167 3213 5.699915 CAGGACATTTATCTTCGATGCATCT 59.300 40.000 23.73 7.83 0.00 2.90
3168 3214 5.931146 AGGACATTTATCTTCGATGCATCTC 59.069 40.000 23.73 9.90 0.00 2.75
3169 3215 5.931146 GGACATTTATCTTCGATGCATCTCT 59.069 40.000 23.73 6.82 0.00 3.10
3170 3216 6.426328 GGACATTTATCTTCGATGCATCTCTT 59.574 38.462 23.73 7.31 0.00 2.85
3171 3217 7.187244 ACATTTATCTTCGATGCATCTCTTG 57.813 36.000 23.73 8.91 0.00 3.02
3184 3230 4.156664 CATCTCTTGCAAGTTGAACAGG 57.843 45.455 25.19 12.02 0.00 4.00
3185 3231 3.558931 TCTCTTGCAAGTTGAACAGGA 57.441 42.857 25.19 9.37 0.00 3.86
3290 3342 4.599047 TTACCAAGTTTCAAATGGCCAG 57.401 40.909 13.05 0.00 37.77 4.85
3295 3347 4.443315 CCAAGTTTCAAATGGCCAGAACTT 60.443 41.667 13.05 17.53 0.00 2.66
3331 3384 6.546428 ACACTATACAAGCACCAAGTCTAT 57.454 37.500 0.00 0.00 0.00 1.98
3355 3408 4.590918 TCGTAAATACTGCATTTTCCCCA 58.409 39.130 0.00 0.00 37.93 4.96
3431 3486 7.440556 ACATTTACACAAAAACATGCAGCATAA 59.559 29.630 7.82 0.00 0.00 1.90
3432 3487 7.776933 TTTACACAAAAACATGCAGCATAAA 57.223 28.000 7.82 0.00 0.00 1.40
3433 3488 7.959689 TTACACAAAAACATGCAGCATAAAT 57.040 28.000 7.82 0.00 0.00 1.40
3434 3489 6.470557 ACACAAAAACATGCAGCATAAATC 57.529 33.333 7.82 0.00 0.00 2.17
3435 3490 5.409214 ACACAAAAACATGCAGCATAAATCC 59.591 36.000 7.82 0.00 0.00 3.01
3436 3491 5.640357 CACAAAAACATGCAGCATAAATCCT 59.360 36.000 7.82 0.00 0.00 3.24
3437 3492 5.870978 ACAAAAACATGCAGCATAAATCCTC 59.129 36.000 7.82 0.00 0.00 3.71
3438 3493 4.660789 AAACATGCAGCATAAATCCTCC 57.339 40.909 7.82 0.00 0.00 4.30
3439 3494 2.224606 ACATGCAGCATAAATCCTCCG 58.775 47.619 7.82 0.00 0.00 4.63
3440 3495 2.224606 CATGCAGCATAAATCCTCCGT 58.775 47.619 7.82 0.00 0.00 4.69
3441 3496 3.181455 ACATGCAGCATAAATCCTCCGTA 60.181 43.478 7.82 0.00 0.00 4.02
3442 3497 3.769739 TGCAGCATAAATCCTCCGTAT 57.230 42.857 0.00 0.00 0.00 3.06
3443 3498 3.402110 TGCAGCATAAATCCTCCGTATG 58.598 45.455 0.00 0.00 0.00 2.39
3444 3499 3.181455 TGCAGCATAAATCCTCCGTATGT 60.181 43.478 0.00 0.00 0.00 2.29
3445 3500 4.039852 TGCAGCATAAATCCTCCGTATGTA 59.960 41.667 0.00 0.00 0.00 2.29
3446 3501 4.627467 GCAGCATAAATCCTCCGTATGTAG 59.373 45.833 0.00 0.00 0.00 2.74
3447 3502 5.784177 CAGCATAAATCCTCCGTATGTAGT 58.216 41.667 0.00 0.00 0.00 2.73
3448 3503 6.223852 CAGCATAAATCCTCCGTATGTAGTT 58.776 40.000 0.00 0.00 0.00 2.24
3449 3504 6.366332 CAGCATAAATCCTCCGTATGTAGTTC 59.634 42.308 0.00 0.00 0.00 3.01
3450 3505 6.041637 AGCATAAATCCTCCGTATGTAGTTCA 59.958 38.462 0.00 0.00 0.00 3.18
3451 3506 6.874134 GCATAAATCCTCCGTATGTAGTTCAT 59.126 38.462 0.00 0.00 40.25 2.57
3452 3507 8.033038 GCATAAATCCTCCGTATGTAGTTCATA 58.967 37.037 0.00 0.00 37.91 2.15
3453 3508 9.574458 CATAAATCCTCCGTATGTAGTTCATAG 57.426 37.037 0.00 0.00 39.36 2.23
3454 3509 7.598759 AAATCCTCCGTATGTAGTTCATAGT 57.401 36.000 0.00 0.00 39.36 2.12
3455 3510 6.576662 ATCCTCCGTATGTAGTTCATAGTG 57.423 41.667 0.00 0.00 39.36 2.74
3456 3511 4.825634 TCCTCCGTATGTAGTTCATAGTGG 59.174 45.833 2.99 2.99 39.36 4.00
3457 3512 4.825634 CCTCCGTATGTAGTTCATAGTGGA 59.174 45.833 9.16 9.16 39.94 4.02
3458 3513 5.301045 CCTCCGTATGTAGTTCATAGTGGAA 59.699 44.000 10.20 0.00 40.80 3.53
3459 3514 6.015350 CCTCCGTATGTAGTTCATAGTGGAAT 60.015 42.308 10.20 0.00 40.80 3.01
3460 3515 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
3461 3516 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
3462 3517 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
3463 3518 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
3464 3519 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
3494 3549 9.819267 AAAACTTATATTTAGGAACGGAGAGAG 57.181 33.333 0.00 0.00 0.00 3.20
3495 3550 8.536340 AACTTATATTTAGGAACGGAGAGAGT 57.464 34.615 0.00 0.00 0.00 3.24
3496 3551 9.638176 AACTTATATTTAGGAACGGAGAGAGTA 57.362 33.333 0.00 0.00 0.00 2.59
3497 3552 9.810870 ACTTATATTTAGGAACGGAGAGAGTAT 57.189 33.333 0.00 0.00 0.00 2.12
3593 3648 1.330521 CAGACCAAACAACTGTGTCCG 59.669 52.381 0.00 0.00 36.80 4.79
3633 3688 4.000988 GTGTACAACATACAGGTTCCCAG 58.999 47.826 0.00 0.00 0.00 4.45
3637 3692 3.081804 CAACATACAGGTTCCCAGTTCC 58.918 50.000 0.00 0.00 0.00 3.62
3653 3708 2.103263 AGTTCCTAGATAAGGCCAAGCG 59.897 50.000 5.01 0.00 46.10 4.68
3772 3827 5.852282 AACTTAATTGAACACAGGTTGCT 57.148 34.783 0.00 0.00 37.36 3.91
3784 3839 6.368779 ACACAGGTTGCTATTAAGGTTCTA 57.631 37.500 0.00 0.00 0.00 2.10
3860 3915 9.698309 CAAAACTCTCCTGTATACGATGATTAT 57.302 33.333 0.00 0.00 0.00 1.28
3884 3939 4.017808 ACTAACTCATACGGTGCTTCTCT 58.982 43.478 0.00 0.00 0.00 3.10
3894 3949 2.221981 CGGTGCTTCTCTGTTTTCTGTC 59.778 50.000 0.00 0.00 0.00 3.51
3916 3975 4.895889 TCTTCACCGACTCATCCATCTATT 59.104 41.667 0.00 0.00 0.00 1.73
3923 3982 7.971168 CACCGACTCATCCATCTATTTATCTAC 59.029 40.741 0.00 0.00 0.00 2.59
3948 4007 4.039366 AGACTACTTGGAACAGAACTGGAC 59.961 45.833 6.76 0.38 42.39 4.02
4006 4065 3.476552 AGACAAAAGCAAGATCAACCGA 58.523 40.909 0.00 0.00 0.00 4.69
4052 4111 1.673329 GCGTTCTCCTTCCTGACTTCC 60.673 57.143 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 5.898972 TCATTCTTTGGGCTAAATTATGGCT 59.101 36.000 13.77 0.00 0.00 4.75
67 69 1.880941 AGATCCGGCCCTTTAAGAGT 58.119 50.000 0.00 0.00 0.00 3.24
98 100 0.381801 GCACGTTCTGGGCCATATTG 59.618 55.000 6.72 0.00 0.00 1.90
117 119 2.233271 TCCGACCCGTTAATAGCCTAG 58.767 52.381 0.00 0.00 0.00 3.02
164 166 5.449588 GGATCATTAACAGTCTGCCATGTTG 60.450 44.000 0.00 0.00 39.83 3.33
185 187 5.563592 TGCCGATTCATATTTGATCTGGAT 58.436 37.500 0.00 0.00 0.00 3.41
186 188 4.971939 TGCCGATTCATATTTGATCTGGA 58.028 39.130 0.00 0.00 0.00 3.86
225 228 0.965363 CCGGCCCATTAACAAGCTGT 60.965 55.000 0.00 0.00 0.00 4.40
259 262 4.462483 CAGCTAAAGGCCCACAAGATTTTA 59.538 41.667 0.00 0.00 43.05 1.52
291 294 6.096705 CCCACAAGATTTTGCAGACCATAATA 59.903 38.462 0.00 0.00 37.85 0.98
335 338 6.096705 CCCACAAGATTTTGCAGACCATAATA 59.903 38.462 0.00 0.00 37.85 0.98
427 430 0.679505 TGGGCGAGATGTACCTATGC 59.320 55.000 0.00 0.00 0.00 3.14
435 438 0.839277 TCATCCAATGGGCGAGATGT 59.161 50.000 0.00 0.00 37.84 3.06
455 458 2.126463 CGCTGACACGGACGTCAT 60.126 61.111 18.91 1.15 44.61 3.06
505 508 8.476142 CAATGACGATTTTCACGTGTAAAATTT 58.524 29.630 25.49 19.62 43.97 1.82
532 536 0.178068 ATCCGCTAACAGCCAACGAT 59.822 50.000 0.00 0.00 38.18 3.73
536 540 2.479837 CGATAATCCGCTAACAGCCAA 58.520 47.619 0.00 0.00 38.18 4.52
588 605 2.650778 GTAACGGGTCGTCGGGTT 59.349 61.111 0.00 0.00 39.99 4.11
600 617 1.153901 ACGTGGCATCTCCGTAACG 60.154 57.895 0.00 0.00 37.66 3.18
602 619 0.108992 GACACGTGGCATCTCCGTAA 60.109 55.000 18.77 0.00 37.80 3.18
603 620 1.509463 GACACGTGGCATCTCCGTA 59.491 57.895 18.77 0.00 37.80 4.02
604 621 2.261671 GACACGTGGCATCTCCGT 59.738 61.111 18.77 0.00 37.80 4.69
605 622 2.880879 CGACACGTGGCATCTCCG 60.881 66.667 23.63 8.18 37.80 4.63
606 623 2.509336 CCGACACGTGGCATCTCC 60.509 66.667 23.63 0.00 0.00 3.71
607 624 0.108992 TAACCGACACGTGGCATCTC 60.109 55.000 23.63 7.66 0.00 2.75
608 625 0.389426 GTAACCGACACGTGGCATCT 60.389 55.000 23.63 6.78 0.00 2.90
630 647 5.451023 CGCGTTATGAAAATGCTTTCGTTAT 59.549 36.000 0.00 0.00 43.40 1.89
632 649 3.602062 CGCGTTATGAAAATGCTTTCGTT 59.398 39.130 0.00 0.00 43.40 3.85
642 659 6.097156 ACGATAAATGACGCGTTATGAAAA 57.903 33.333 17.85 4.00 32.42 2.29
649 666 2.284150 CCATGACGATAAATGACGCGTT 59.716 45.455 15.53 0.00 37.07 4.84
703 720 4.211164 TGTTGTAGAAGCGTTTCATGACAG 59.789 41.667 14.70 0.00 35.70 3.51
711 728 4.095782 ACATGTGTTGTTGTAGAAGCGTTT 59.904 37.500 0.00 0.00 33.74 3.60
715 732 6.147821 AGTCATACATGTGTTGTTGTAGAAGC 59.852 38.462 9.11 0.00 39.87 3.86
746 763 9.159364 CATCCATGACGATTATATGACAGAATT 57.841 33.333 0.00 0.00 0.00 2.17
758 775 4.954875 TGCATGTACATCCATGACGATTA 58.045 39.130 5.07 0.00 43.99 1.75
810 828 7.873719 AAAACCATTTCCATGATGATACGTA 57.126 32.000 0.00 0.00 31.07 3.57
864 882 4.530094 CAAGAAACTGTTGCAACGTCTA 57.470 40.909 23.79 6.14 0.00 2.59
902 920 5.046910 TGCAAAAGATCCGTTCATTTCTC 57.953 39.130 0.00 0.00 0.00 2.87
1056 1083 1.878953 TCTTTTCTTCACGGTGCCTC 58.121 50.000 2.51 0.00 0.00 4.70
1526 1553 2.993220 TCGGTCGTCTTTGTGAATCATG 59.007 45.455 0.00 0.00 0.00 3.07
1568 1595 1.339438 GCCAATGCCAGTGAGAGAGAA 60.339 52.381 0.00 0.00 0.00 2.87
1569 1596 0.251354 GCCAATGCCAGTGAGAGAGA 59.749 55.000 0.00 0.00 0.00 3.10
1570 1597 0.252479 AGCCAATGCCAGTGAGAGAG 59.748 55.000 0.00 0.00 38.69 3.20
1580 1607 4.503314 GCAGCCGAAGCCAATGCC 62.503 66.667 0.00 0.00 41.25 4.40
1581 1608 3.695022 CTGCAGCCGAAGCCAATGC 62.695 63.158 0.00 0.00 41.25 3.56
1591 1618 1.033746 ATGATTTCACCCTGCAGCCG 61.034 55.000 8.66 2.46 0.00 5.52
1788 1815 2.432628 CTGGCGTGGTCGAACTCC 60.433 66.667 0.33 0.69 39.71 3.85
1819 1846 4.016706 CGTCCTGTTCCCCGCCTT 62.017 66.667 0.00 0.00 0.00 4.35
1878 1905 0.311790 CTGCTGCAATGGTGTCGTTT 59.688 50.000 3.02 0.00 0.00 3.60
1880 1907 0.952497 CTCTGCTGCAATGGTGTCGT 60.952 55.000 3.02 0.00 0.00 4.34
1904 1931 1.227674 CCTATCCCGAGCTTGGTGC 60.228 63.158 19.14 0.00 43.29 5.01
1910 1937 4.220163 TCGCCCCTATCCCGAGCT 62.220 66.667 0.00 0.00 0.00 4.09
1928 1955 1.597461 GTGTCTTCTTCCCCGAGGG 59.403 63.158 0.00 0.00 46.11 4.30
1930 1957 1.215647 CGGTGTCTTCTTCCCCGAG 59.784 63.158 0.00 0.00 41.08 4.63
2197 2236 3.291101 TTCCGAGAACGAAGGCGGG 62.291 63.158 0.00 0.00 43.71 6.13
2414 2453 2.327228 GGTTGTTGAACCGGGACAG 58.673 57.895 6.32 0.00 42.47 3.51
2488 2527 1.066143 GGAGCAAGAAGAATGTCCGGA 60.066 52.381 0.00 0.00 0.00 5.14
2489 2528 1.373570 GGAGCAAGAAGAATGTCCGG 58.626 55.000 0.00 0.00 0.00 5.14
2490 2529 1.339055 TGGGAGCAAGAAGAATGTCCG 60.339 52.381 0.00 0.00 0.00 4.79
2623 2668 0.978146 CGGACCACCCTTCCATCTCT 60.978 60.000 0.00 0.00 31.94 3.10
2803 2848 0.255604 CCATGACATACACCAGGCCA 59.744 55.000 5.01 0.00 0.00 5.36
2917 2962 1.609208 GCAGTTGCAGGGAAGAAGAA 58.391 50.000 0.00 0.00 41.59 2.52
2969 3014 2.678336 CCACGAACTAGCAAGATTTCCC 59.322 50.000 0.00 0.00 0.00 3.97
3084 3129 7.824289 CAGGTACTAACATCTTTCCATTCTGAA 59.176 37.037 0.00 0.00 36.02 3.02
3127 3172 2.291741 GTCCTGTTCAACTTGCAAGAGG 59.708 50.000 32.50 24.83 34.92 3.69
3147 3193 7.187244 CAAGAGATGCATCGAAGATAAATGT 57.813 36.000 20.67 0.00 45.12 2.71
3163 3209 3.817084 TCCTGTTCAACTTGCAAGAGATG 59.183 43.478 32.50 24.38 0.00 2.90
3164 3210 4.090761 TCCTGTTCAACTTGCAAGAGAT 57.909 40.909 32.50 15.00 0.00 2.75
3165 3211 3.558931 TCCTGTTCAACTTGCAAGAGA 57.441 42.857 32.50 24.22 0.00 3.10
3166 3212 4.637483 TTTCCTGTTCAACTTGCAAGAG 57.363 40.909 32.50 22.46 0.00 2.85
3167 3213 4.402155 ACATTTCCTGTTCAACTTGCAAGA 59.598 37.500 32.50 8.21 32.90 3.02
3168 3214 4.685924 ACATTTCCTGTTCAACTTGCAAG 58.314 39.130 24.84 24.84 32.90 4.01
3169 3215 4.441356 GGACATTTCCTGTTCAACTTGCAA 60.441 41.667 0.00 0.00 38.54 4.08
3170 3216 3.068024 GGACATTTCCTGTTCAACTTGCA 59.932 43.478 0.00 0.00 38.54 4.08
3171 3217 3.642705 GGACATTTCCTGTTCAACTTGC 58.357 45.455 0.00 0.00 38.54 4.01
3183 3229 0.039618 TGCCTGGGAAGGACATTTCC 59.960 55.000 0.00 0.00 44.82 3.13
3184 3230 1.546029 GTTGCCTGGGAAGGACATTTC 59.454 52.381 0.00 0.00 0.00 2.17
3185 3231 1.133199 TGTTGCCTGGGAAGGACATTT 60.133 47.619 0.00 0.00 0.00 2.32
3196 3242 9.241919 TCATATTAATATATGGTTGTTGCCTGG 57.758 33.333 7.65 0.00 42.53 4.45
3331 3384 5.477291 TGGGGAAAATGCAGTATTTACGAAA 59.523 36.000 0.00 0.00 38.01 3.46
3431 3486 6.015350 CCACTATGAACTACATACGGAGGATT 60.015 42.308 0.00 0.00 40.07 3.01
3432 3487 5.477291 CCACTATGAACTACATACGGAGGAT 59.523 44.000 0.00 0.00 40.07 3.24
3433 3488 4.825634 CCACTATGAACTACATACGGAGGA 59.174 45.833 0.00 0.00 40.07 3.71
3434 3489 4.825634 TCCACTATGAACTACATACGGAGG 59.174 45.833 0.00 0.00 40.07 4.30
3435 3490 6.387041 TTCCACTATGAACTACATACGGAG 57.613 41.667 0.00 0.00 38.29 4.63
3436 3491 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
3437 3492 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
3438 3493 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
3468 3523 9.819267 CTCTCTCCGTTCCTAAATATAAGTTTT 57.181 33.333 0.00 0.00 0.00 2.43
3469 3524 8.979534 ACTCTCTCCGTTCCTAAATATAAGTTT 58.020 33.333 0.00 0.00 0.00 2.66
3470 3525 8.536340 ACTCTCTCCGTTCCTAAATATAAGTT 57.464 34.615 0.00 0.00 0.00 2.66
3471 3526 9.810870 ATACTCTCTCCGTTCCTAAATATAAGT 57.189 33.333 0.00 0.00 0.00 2.24
3477 3532 9.584008 TGTAATATACTCTCTCCGTTCCTAAAT 57.416 33.333 0.00 0.00 0.00 1.40
3478 3533 8.985315 TGTAATATACTCTCTCCGTTCCTAAA 57.015 34.615 0.00 0.00 0.00 1.85
3479 3534 8.985315 TTGTAATATACTCTCTCCGTTCCTAA 57.015 34.615 0.00 0.00 0.00 2.69
3480 3535 7.174599 GCTTGTAATATACTCTCTCCGTTCCTA 59.825 40.741 0.00 0.00 0.00 2.94
3481 3536 6.016108 GCTTGTAATATACTCTCTCCGTTCCT 60.016 42.308 0.00 0.00 0.00 3.36
3482 3537 6.016108 AGCTTGTAATATACTCTCTCCGTTCC 60.016 42.308 0.00 0.00 0.00 3.62
3483 3538 6.972722 AGCTTGTAATATACTCTCTCCGTTC 58.027 40.000 0.00 0.00 0.00 3.95
3484 3539 6.963083 AGCTTGTAATATACTCTCTCCGTT 57.037 37.500 0.00 0.00 0.00 4.44
3485 3540 6.963083 AAGCTTGTAATATACTCTCTCCGT 57.037 37.500 0.00 0.00 0.00 4.69
3486 3541 9.915629 AATTAAGCTTGTAATATACTCTCTCCG 57.084 33.333 9.86 0.00 0.00 4.63
3498 3553 9.392259 GACTAGGGTACAAATTAAGCTTGTAAT 57.608 33.333 9.86 0.00 40.11 1.89
3637 3692 1.871080 CCACGCTTGGCCTTATCTAG 58.129 55.000 3.32 0.00 35.56 2.43
3772 3827 7.185318 TGGTTGAATCGGTAGAACCTTAATA 57.815 36.000 9.53 0.00 38.96 0.98
3784 3839 3.057806 GGTTTCGAAATGGTTGAATCGGT 60.058 43.478 14.69 0.00 36.05 4.69
3860 3915 5.651139 AGAGAAGCACCGTATGAGTTAGTTA 59.349 40.000 0.00 0.00 0.00 2.24
3861 3916 4.463186 AGAGAAGCACCGTATGAGTTAGTT 59.537 41.667 0.00 0.00 0.00 2.24
3868 3923 3.678056 AAACAGAGAAGCACCGTATGA 57.322 42.857 0.00 0.00 0.00 2.15
3884 3939 3.118920 TGAGTCGGTGAAGACAGAAAACA 60.119 43.478 0.00 0.00 43.24 2.83
3894 3949 4.862902 ATAGATGGATGAGTCGGTGAAG 57.137 45.455 0.00 0.00 0.00 3.02
3916 3975 7.179966 TCTGTTCCAAGTAGTCTGGTAGATAA 58.820 38.462 0.00 0.00 0.00 1.75
3923 3982 4.310769 CAGTTCTGTTCCAAGTAGTCTGG 58.689 47.826 0.00 0.00 0.00 3.86
3948 4007 5.051816 TGGTTTCAAGTACAAGTCCTTACG 58.948 41.667 0.00 0.00 0.00 3.18
4006 4065 4.336280 GGCCTTTGAGGACTAAAAGATGT 58.664 43.478 10.18 0.00 41.45 3.06


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

AutoCloner maintained by Alex Coulton.