Multiple sequence alignment - TraesCS2D01G426300

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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 TraesCS2D01G426300 chr2D 100.000 3762 0 0 1 3762 538596498 538600259 0.000000e+00 6948.0
1 TraesCS2D01G426300 chr2D 84.677 124 16 3 3579 3700 539017406 539017528 1.840000e-23 121.0
2 TraesCS2D01G426300 chr2B 92.901 2113 94 23 697 2762 641193068 641195171 0.000000e+00 3020.0
3 TraesCS2D01G426300 chr2B 84.561 285 9 12 2752 3032 641195306 641195559 2.240000e-62 250.0
4 TraesCS2D01G426300 chr2A 92.525 2087 95 19 889 2921 680548007 680550086 0.000000e+00 2933.0
5 TraesCS2D01G426300 chr2A 88.300 453 45 7 1 452 680546988 680547433 1.540000e-148 536.0
6 TraesCS2D01G426300 chr2A 85.743 505 30 12 3262 3759 680551078 680551547 2.610000e-136 496.0
7 TraesCS2D01G426300 chr2A 91.077 325 27 1 2930 3254 680550618 680550940 4.460000e-119 438.0
8 TraesCS2D01G426300 chr2A 84.615 208 16 11 635 841 680547679 680547871 3.830000e-45 193.0
9 TraesCS2D01G426300 chr5B 83.057 1027 136 26 941 1946 375225014 375224005 0.000000e+00 898.0
10 TraesCS2D01G426300 chr5B 83.706 939 137 11 995 1921 378903370 378904304 0.000000e+00 872.0
11 TraesCS2D01G426300 chr5B 83.227 942 140 14 995 1921 378853288 378852350 0.000000e+00 848.0
12 TraesCS2D01G426300 chr5B 83.560 663 107 2 2097 2759 375223910 375223250 1.480000e-173 619.0
13 TraesCS2D01G426300 chr5A 84.590 915 128 12 1018 1921 429998156 429997244 0.000000e+00 896.0
14 TraesCS2D01G426300 chr5A 83.642 972 130 20 996 1946 419830895 419829932 0.000000e+00 887.0
15 TraesCS2D01G426300 chr5A 84.009 938 135 14 996 1921 430041588 430042522 0.000000e+00 887.0
16 TraesCS2D01G426300 chr5A 82.282 666 106 5 2097 2762 419829837 419829184 1.960000e-157 566.0
17 TraesCS2D01G426300 chr5A 79.621 633 118 3 2118 2749 429996714 429996092 9.590000e-121 444.0
18 TraesCS2D01G426300 chr5A 82.237 304 46 8 3461 3762 338886642 338886345 4.820000e-64 255.0
19 TraesCS2D01G426300 chr5D 84.337 913 132 6 1019 1921 326384550 326383639 0.000000e+00 883.0
20 TraesCS2D01G426300 chr5D 83.494 933 143 6 995 1917 326402830 326403761 0.000000e+00 859.0
21 TraesCS2D01G426300 chr5D 78.351 291 50 8 3474 3754 557945631 557945344 3.860000e-40 176.0
22 TraesCS2D01G426300 chr5D 76.730 159 28 6 472 623 380094591 380094747 3.110000e-11 80.5
23 TraesCS2D01G426300 chr3D 80.731 301 48 9 3461 3755 441158063 441157767 3.780000e-55 226.0
24 TraesCS2D01G426300 chr3D 81.034 116 17 4 514 625 592009216 592009102 1.860000e-13 87.9
25 TraesCS2D01G426300 chr3D 94.231 52 3 0 3704 3755 441157894 441157843 3.110000e-11 80.5
26 TraesCS2D01G426300 chr3B 79.038 291 52 7 3471 3755 99539184 99538897 1.380000e-44 191.0
27 TraesCS2D01G426300 chr1D 76.829 164 26 5 3599 3755 89596366 89596524 8.660000e-12 82.4
28 TraesCS2D01G426300 chr1D 100.000 29 0 0 3726 3754 478804595 478804623 2.000000e-03 54.7
29 TraesCS2D01G426300 chr7D 87.143 70 9 0 3630 3699 611367271 611367340 3.110000e-11 80.5
30 TraesCS2D01G426300 chr7A 94.231 52 3 0 3704 3755 198473853 198473802 3.110000e-11 80.5
31 TraesCS2D01G426300 chr7A 88.235 51 6 0 3704 3754 725584042 725584092 1.130000e-05 62.1


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 TraesCS2D01G426300 chr2D 538596498 538600259 3761 False 6948.0 6948 100.0000 1 3762 1 chr2D.!!$F1 3761
1 TraesCS2D01G426300 chr2B 641193068 641195559 2491 False 1635.0 3020 88.7310 697 3032 2 chr2B.!!$F1 2335
2 TraesCS2D01G426300 chr2A 680546988 680551547 4559 False 919.2 2933 88.4520 1 3759 5 chr2A.!!$F1 3758
3 TraesCS2D01G426300 chr5B 378903370 378904304 934 False 872.0 872 83.7060 995 1921 1 chr5B.!!$F1 926
4 TraesCS2D01G426300 chr5B 378852350 378853288 938 True 848.0 848 83.2270 995 1921 1 chr5B.!!$R1 926
5 TraesCS2D01G426300 chr5B 375223250 375225014 1764 True 758.5 898 83.3085 941 2759 2 chr5B.!!$R2 1818
6 TraesCS2D01G426300 chr5A 430041588 430042522 934 False 887.0 887 84.0090 996 1921 1 chr5A.!!$F1 925
7 TraesCS2D01G426300 chr5A 419829184 419830895 1711 True 726.5 887 82.9620 996 2762 2 chr5A.!!$R2 1766
8 TraesCS2D01G426300 chr5A 429996092 429998156 2064 True 670.0 896 82.1055 1018 2749 2 chr5A.!!$R3 1731
9 TraesCS2D01G426300 chr5D 326383639 326384550 911 True 883.0 883 84.3370 1019 1921 1 chr5D.!!$R1 902
10 TraesCS2D01G426300 chr5D 326402830 326403761 931 False 859.0 859 83.4940 995 1917 1 chr5D.!!$F1 922

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
930 1121 0.670546 AGCGGTTGATCGGTCACTTG 60.671 55.000 0.0 0.0 35.95 3.16 F
2137 2702 1.145598 CATGCAGGACCTCATCGCT 59.854 57.895 0.0 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2759 0.841289 TGGAGAACACCTCGGGTTTT 59.159 50.0 0.00 0.0 42.89 2.43 R
3495 4870 0.104304 GAGGCGGCGGATCTTTTAGA 59.896 55.0 9.78 0.0 0.00 2.10 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
19 20 1.871418 CTCCCTCCATCTCCTCAACA 58.129 55.000 0.00 0.00 0.00 3.33
22 23 2.022625 TCCCTCCATCTCCTCAACATCT 60.023 50.000 0.00 0.00 0.00 2.90
30 31 4.609866 TCTCCTCAACATCTTCCTCCTA 57.390 45.455 0.00 0.00 0.00 2.94
35 36 3.024547 TCAACATCTTCCTCCTACTCCG 58.975 50.000 0.00 0.00 0.00 4.63
36 37 3.024547 CAACATCTTCCTCCTACTCCGA 58.975 50.000 0.00 0.00 0.00 4.55
92 93 1.351017 ACCACCTCCATCGTGATTTGT 59.649 47.619 0.00 0.00 32.77 2.83
93 94 1.739466 CCACCTCCATCGTGATTTGTG 59.261 52.381 0.00 0.00 32.77 3.33
94 95 1.131126 CACCTCCATCGTGATTTGTGC 59.869 52.381 0.00 0.00 32.77 4.57
99 100 2.019249 CCATCGTGATTTGTGCCTGAT 58.981 47.619 0.00 0.00 0.00 2.90
128 129 4.495422 CGAAGAGCTTGGTGTAGTATGTT 58.505 43.478 0.00 0.00 0.00 2.71
129 130 4.327357 CGAAGAGCTTGGTGTAGTATGTTG 59.673 45.833 0.00 0.00 0.00 3.33
132 133 1.743394 GCTTGGTGTAGTATGTTGGGC 59.257 52.381 0.00 0.00 0.00 5.36
139 140 2.916502 TAGTATGTTGGGCGGCTGCG 62.917 60.000 12.29 0.00 44.10 5.18
164 165 2.752807 GGTATGGATGGCGGGGTGT 61.753 63.158 0.00 0.00 0.00 4.16
166 167 0.818040 GTATGGATGGCGGGGTGTTC 60.818 60.000 0.00 0.00 0.00 3.18
172 173 4.941309 GGCGGGGTGTTCGTTGGT 62.941 66.667 0.00 0.00 0.00 3.67
173 174 3.656045 GCGGGGTGTTCGTTGGTG 61.656 66.667 0.00 0.00 0.00 4.17
174 175 3.656045 CGGGGTGTTCGTTGGTGC 61.656 66.667 0.00 0.00 0.00 5.01
175 176 2.203294 GGGGTGTTCGTTGGTGCT 60.203 61.111 0.00 0.00 0.00 4.40
178 179 2.248431 GTGTTCGTTGGTGCTCGC 59.752 61.111 0.00 0.00 0.00 5.03
179 180 3.334751 TGTTCGTTGGTGCTCGCG 61.335 61.111 0.00 0.00 0.00 5.87
230 231 2.660258 AAATAGGGTGGCGCGCCTAG 62.660 60.000 45.79 0.33 36.94 3.02
245 246 1.450312 CTAGGGTTTGGCTCTGGCG 60.450 63.158 0.00 0.00 39.81 5.69
325 326 3.181455 TGCACCATAAATACGGCTGAGAT 60.181 43.478 0.00 0.00 0.00 2.75
335 336 3.244033 ACGGCTGAGATGAAGAGAAAG 57.756 47.619 0.00 0.00 0.00 2.62
348 349 6.891306 TGAAGAGAAAGGGATTTGAGGATA 57.109 37.500 0.00 0.00 0.00 2.59
352 353 8.759481 AAGAGAAAGGGATTTGAGGATAATTC 57.241 34.615 0.00 0.00 0.00 2.17
353 354 7.876371 AGAGAAAGGGATTTGAGGATAATTCA 58.124 34.615 0.00 0.00 0.00 2.57
382 383 4.448537 TTGCTCCAATTTATTTGACCCG 57.551 40.909 0.00 0.00 37.53 5.28
410 412 6.159751 TGGGTAAGCTATGAGGGATAACTTTT 59.840 38.462 0.00 0.00 28.08 2.27
414 416 9.174166 GTAAGCTATGAGGGATAACTTTTCAAA 57.826 33.333 0.00 0.00 28.08 2.69
455 495 1.151413 TGGGAGAAGGACTAGTTGGGT 59.849 52.381 0.00 0.00 0.00 4.51
458 498 3.451540 GGGAGAAGGACTAGTTGGGTTAG 59.548 52.174 0.00 0.00 0.00 2.34
469 509 6.226052 ACTAGTTGGGTTAGTTTCCTAAACG 58.774 40.000 0.00 0.00 45.88 3.60
470 510 5.294734 AGTTGGGTTAGTTTCCTAAACGA 57.705 39.130 0.00 0.00 45.88 3.85
471 511 5.872963 AGTTGGGTTAGTTTCCTAAACGAT 58.127 37.500 0.00 0.00 45.88 3.73
521 562 8.066612 TCAGTTCATCATCTGTCATAGTACAA 57.933 34.615 0.00 0.00 33.89 2.41
525 566 7.660030 TCATCATCTGTCATAGTACAAGGAA 57.340 36.000 0.00 0.00 0.00 3.36
529 570 6.437477 TCATCTGTCATAGTACAAGGAACACT 59.563 38.462 0.00 0.00 0.00 3.55
531 572 7.770366 TCTGTCATAGTACAAGGAACACTAA 57.230 36.000 0.00 0.00 0.00 2.24
533 574 8.812972 TCTGTCATAGTACAAGGAACACTAAAT 58.187 33.333 0.00 0.00 0.00 1.40
581 622 2.622942 ACCACCTAACGACGACTACAAA 59.377 45.455 0.00 0.00 0.00 2.83
584 625 3.423206 CACCTAACGACGACTACAAACAC 59.577 47.826 0.00 0.00 0.00 3.32
585 626 3.316308 ACCTAACGACGACTACAAACACT 59.684 43.478 0.00 0.00 0.00 3.55
586 627 4.515191 ACCTAACGACGACTACAAACACTA 59.485 41.667 0.00 0.00 0.00 2.74
591 632 3.558505 GACGACTACAAACACTAAGCGA 58.441 45.455 0.00 0.00 0.00 4.93
599 640 1.641577 AACACTAAGCGATCCGAAGC 58.358 50.000 0.00 0.00 0.00 3.86
619 660 1.818555 GCATTGCCTTCATCACCCC 59.181 57.895 0.00 0.00 0.00 4.95
625 666 1.575447 GCCTTCATCACCCCTCCCTT 61.575 60.000 0.00 0.00 0.00 3.95
626 667 1.893315 CCTTCATCACCCCTCCCTTA 58.107 55.000 0.00 0.00 0.00 2.69
628 669 3.598264 CCTTCATCACCCCTCCCTTATA 58.402 50.000 0.00 0.00 0.00 0.98
629 670 3.980698 CCTTCATCACCCCTCCCTTATAA 59.019 47.826 0.00 0.00 0.00 0.98
630 671 4.042187 CCTTCATCACCCCTCCCTTATAAG 59.958 50.000 5.43 5.43 0.00 1.73
631 672 4.295905 TCATCACCCCTCCCTTATAAGT 57.704 45.455 11.50 0.00 0.00 2.24
633 674 2.771688 TCACCCCTCCCTTATAAGTGG 58.228 52.381 11.50 11.62 0.00 4.00
639 717 3.136626 CCCTCCCTTATAAGTGGTGGAAG 59.863 52.174 26.50 14.96 34.60 3.46
645 723 6.889722 TCCCTTATAAGTGGTGGAAGAAATTG 59.110 38.462 11.50 0.00 0.00 2.32
646 724 6.405842 CCCTTATAAGTGGTGGAAGAAATTGC 60.406 42.308 11.50 0.00 0.00 3.56
648 726 5.904362 ATAAGTGGTGGAAGAAATTGCTC 57.096 39.130 0.00 0.00 0.00 4.26
650 728 3.837355 AGTGGTGGAAGAAATTGCTCTT 58.163 40.909 0.00 0.00 38.39 2.85
651 729 4.985538 AGTGGTGGAAGAAATTGCTCTTA 58.014 39.130 0.00 0.00 35.76 2.10
658 736 4.568760 GGAAGAAATTGCTCTTAGACCTCG 59.431 45.833 0.00 0.00 35.76 4.63
662 740 6.334202 AGAAATTGCTCTTAGACCTCGTTAG 58.666 40.000 0.00 0.00 0.00 2.34
669 747 4.974591 TCTTAGACCTCGTTAGCGTTAAC 58.025 43.478 11.72 11.72 39.49 2.01
731 809 3.817084 CGGACATATGGTGATTGATGCTT 59.183 43.478 7.80 0.00 0.00 3.91
733 811 5.221106 CGGACATATGGTGATTGATGCTTTT 60.221 40.000 7.80 0.00 0.00 2.27
786 866 1.066858 GGAAGCGTCCTTGTCTGATGA 60.067 52.381 11.87 0.00 41.24 2.92
787 867 2.266554 GAAGCGTCCTTGTCTGATGAG 58.733 52.381 0.00 0.00 0.00 2.90
822 903 9.807921 TTGGGACTTCATCTAATTTTTAGAAGT 57.192 29.630 12.76 12.76 45.76 3.01
842 923 7.553334 AGAAGTAAACTGACACAAGACTAACA 58.447 34.615 0.00 0.00 0.00 2.41
844 925 7.772332 AGTAAACTGACACAAGACTAACAAG 57.228 36.000 0.00 0.00 0.00 3.16
847 928 4.694339 ACTGACACAAGACTAACAAGTCC 58.306 43.478 2.00 0.00 39.50 3.85
849 930 4.693283 TGACACAAGACTAACAAGTCCAG 58.307 43.478 2.00 0.00 39.50 3.86
930 1121 0.670546 AGCGGTTGATCGGTCACTTG 60.671 55.000 0.00 0.00 35.95 3.16
1434 1646 2.716244 CGGCTCGAGTCGTATGCT 59.284 61.111 30.28 0.00 38.51 3.79
1586 1807 3.710722 CCTGGAGAAGCAGGCGGT 61.711 66.667 0.00 0.00 0.00 5.68
1905 2129 2.098298 CGGAATGGCGTCAAAGCG 59.902 61.111 0.00 0.00 38.18 4.68
1923 2147 1.608025 GCGTTCATTCAGGTCAGTCCA 60.608 52.381 0.00 0.00 39.02 4.02
1959 2195 6.512903 CGTTATTCAGTATACGAGCCAGAAGA 60.513 42.308 0.00 0.00 0.00 2.87
1989 2242 2.055042 GCCAGGAAGCTCTCGGAGA 61.055 63.158 7.60 7.60 0.00 3.71
2137 2702 1.145598 CATGCAGGACCTCATCGCT 59.854 57.895 0.00 0.00 0.00 4.93
2194 2759 1.089112 CCATGTCGCAGATGCTCAAA 58.911 50.000 2.95 0.00 40.67 2.69
2321 2886 0.871722 CGTCAAAGAAACCATGCGGA 59.128 50.000 0.00 0.00 35.59 5.54
2716 3281 1.183676 AGTTCCCGCTACAGGTCGTT 61.184 55.000 0.00 0.00 0.00 3.85
2762 3327 2.431057 CTCTACGCAAGGGGTCATTAGT 59.569 50.000 0.00 0.00 46.39 2.24
2769 3483 3.066760 GCAAGGGGTCATTAGTGTATTGC 59.933 47.826 0.00 0.00 34.46 3.56
2821 3535 3.392769 TTGTGTTCTTGTGTTGCGTAC 57.607 42.857 0.00 0.00 0.00 3.67
2839 3553 4.393680 GCGTACAGTCATGTGGGAAAATAA 59.606 41.667 0.00 0.00 40.79 1.40
2840 3554 5.106475 GCGTACAGTCATGTGGGAAAATAAA 60.106 40.000 0.00 0.00 40.79 1.40
2841 3555 6.568844 GCGTACAGTCATGTGGGAAAATAAAA 60.569 38.462 0.00 0.00 40.79 1.52
2888 3605 8.518430 TTGTCCATAAGATGCTTGCTAATTAA 57.482 30.769 0.00 0.00 0.00 1.40
2897 3614 6.550854 AGATGCTTGCTAATTAAGGGCATTTA 59.449 34.615 12.71 0.00 38.73 1.40
2900 3617 6.154363 TGCTTGCTAATTAAGGGCATTTAACT 59.846 34.615 0.00 0.00 35.84 2.24
2902 3619 7.549134 GCTTGCTAATTAAGGGCATTTAACTTT 59.451 33.333 0.00 0.00 35.84 2.66
3036 4276 9.809096 GTCTCATCTAACTTCTACATCATTTGA 57.191 33.333 0.00 0.00 0.00 2.69
3064 4304 4.946784 ATGGAGACTTGTATGCGTTTTC 57.053 40.909 0.00 0.00 0.00 2.29
3150 4390 2.882742 GAGTCATGAACTCGTTTGGC 57.117 50.000 0.00 0.00 44.79 4.52
3152 4392 2.808543 GAGTCATGAACTCGTTTGGCTT 59.191 45.455 0.00 0.00 44.79 4.35
3159 4399 3.250762 TGAACTCGTTTGGCTTCATTCTG 59.749 43.478 0.00 0.00 0.00 3.02
3161 4401 2.154462 CTCGTTTGGCTTCATTCTGGT 58.846 47.619 0.00 0.00 0.00 4.00
3235 4475 7.411804 GCAAATGTACATAACAGAAAATGTGCC 60.412 37.037 9.21 0.00 43.00 5.01
3254 4494 3.270877 GCCACCTTATTCACACCACTAG 58.729 50.000 0.00 0.00 0.00 2.57
3255 4495 3.873910 CCACCTTATTCACACCACTAGG 58.126 50.000 0.00 0.00 42.21 3.02
3256 4496 3.270877 CACCTTATTCACACCACTAGGC 58.729 50.000 0.00 0.00 39.06 3.93
3258 4498 4.161565 CACCTTATTCACACCACTAGGCTA 59.838 45.833 0.00 0.00 39.06 3.93
3259 4499 4.781087 ACCTTATTCACACCACTAGGCTAA 59.219 41.667 0.00 0.00 39.06 3.09
3260 4500 5.116882 CCTTATTCACACCACTAGGCTAAC 58.883 45.833 0.00 0.00 39.06 2.34
3268 4638 0.807667 CACTAGGCTAACCGCTGCAG 60.808 60.000 10.11 10.11 42.76 4.41
3280 4650 1.006922 GCTGCAGCCAACAAAGACC 60.007 57.895 28.76 0.00 34.31 3.85
3281 4651 1.737355 GCTGCAGCCAACAAAGACCA 61.737 55.000 28.76 0.00 34.31 4.02
3314 4684 2.810400 CGGACCATCACAAACCTTCACT 60.810 50.000 0.00 0.00 0.00 3.41
3354 4725 3.202595 TCCTCCTCTCTACCTAGACAACC 59.797 52.174 0.00 0.00 0.00 3.77
3355 4726 3.203487 CCTCCTCTCTACCTAGACAACCT 59.797 52.174 0.00 0.00 0.00 3.50
3356 4727 4.325501 CCTCCTCTCTACCTAGACAACCTT 60.326 50.000 0.00 0.00 0.00 3.50
3357 4728 4.601084 TCCTCTCTACCTAGACAACCTTG 58.399 47.826 0.00 0.00 0.00 3.61
3358 4729 4.291513 TCCTCTCTACCTAGACAACCTTGA 59.708 45.833 0.00 0.00 0.00 3.02
3359 4730 5.044030 TCCTCTCTACCTAGACAACCTTGAT 60.044 44.000 0.00 0.00 0.00 2.57
3379 4750 6.312399 TGATCAAGGTGTATTTGTGTGTTC 57.688 37.500 0.00 0.00 0.00 3.18
3434 4809 1.852895 CTATGTTAGTCCGCGTTGCTC 59.147 52.381 4.92 0.00 0.00 4.26
3442 4817 0.239879 TCCGCGTTGCTCAAAATTCC 59.760 50.000 4.92 0.00 0.00 3.01
3448 4823 4.295051 GCGTTGCTCAAAATTCCAACTAA 58.705 39.130 0.00 0.00 36.36 2.24
3478 4853 4.179926 ACTATATGGAGCATGCTACGTG 57.820 45.455 31.22 18.64 0.00 4.49
3479 4854 3.574396 ACTATATGGAGCATGCTACGTGT 59.426 43.478 31.22 27.08 0.00 4.49
3480 4855 2.509052 TATGGAGCATGCTACGTGTC 57.491 50.000 31.22 13.80 0.00 3.67
3481 4856 0.179073 ATGGAGCATGCTACGTGTCC 60.179 55.000 24.19 18.09 0.00 4.02
3482 4857 1.878522 GGAGCATGCTACGTGTCCG 60.879 63.158 22.74 0.00 40.83 4.79
3483 4858 2.509336 AGCATGCTACGTGTCCGC 60.509 61.111 21.21 0.00 37.70 5.54
3484 4859 2.509336 GCATGCTACGTGTCCGCT 60.509 61.111 11.37 0.00 37.70 5.52
3485 4860 1.226859 GCATGCTACGTGTCCGCTA 60.227 57.895 11.37 0.00 37.70 4.26
3486 4861 1.209275 GCATGCTACGTGTCCGCTAG 61.209 60.000 11.37 0.00 37.70 3.42
3487 4862 1.065928 ATGCTACGTGTCCGCTAGC 59.934 57.895 4.06 4.06 40.69 3.42
3488 4863 2.651232 GCTACGTGTCCGCTAGCG 60.651 66.667 29.93 29.93 35.56 4.26
3515 4890 1.215655 CTAAAAGATCCGCCGCCTCG 61.216 60.000 0.00 0.00 0.00 4.63
3541 4916 2.567169 CTGTTAGATCTGGTGTCACCCA 59.433 50.000 19.57 6.38 37.50 4.51
3547 4922 3.850098 CTGGTGTCACCCAGTGGCC 62.850 68.421 19.57 0.00 45.81 5.36
3571 4946 1.081892 CTCGTCCTCACCATTGCAAG 58.918 55.000 4.94 0.00 0.00 4.01
3605 4982 2.627699 ACACACCCTTTTGCAACATAGG 59.372 45.455 0.00 6.55 0.00 2.57
3620 4997 5.789643 AACATAGGTGTTGTTGCAGAATT 57.210 34.783 0.00 0.00 46.43 2.17
3621 4998 5.789643 ACATAGGTGTTGTTGCAGAATTT 57.210 34.783 0.00 0.00 34.01 1.82
3623 5000 6.581712 ACATAGGTGTTGTTGCAGAATTTTT 58.418 32.000 0.00 0.00 34.01 1.94
3650 5027 6.384015 TCCTTCCTCACTTTTCTGCTATATGA 59.616 38.462 0.00 0.00 0.00 2.15
3660 5037 7.445402 ACTTTTCTGCTATATGAGTGTTGTTGT 59.555 33.333 0.00 0.00 0.00 3.32
3681 5058 5.486526 TGTGGAAGAAACTTTTGCAACATT 58.513 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.708631 GAGGAAGATGTTGAGGAGATGGA 59.291 47.826 0.00 0.00 0.00 3.41
65 66 3.995506 GATGGAGGTGGTTGCGGGG 62.996 68.421 0.00 0.00 0.00 5.73
69 70 0.392998 ATCACGATGGAGGTGGTTGC 60.393 55.000 0.00 0.00 36.09 4.17
81 82 2.019249 CCATCAGGCACAAATCACGAT 58.981 47.619 0.00 0.00 0.00 3.73
94 95 4.161295 TCTTCGCCGCCCATCAGG 62.161 66.667 0.00 0.00 39.47 3.86
105 106 2.649331 TACTACACCAAGCTCTTCGC 57.351 50.000 0.00 0.00 39.57 4.70
108 109 4.565652 CCCAACATACTACACCAAGCTCTT 60.566 45.833 0.00 0.00 0.00 2.85
121 122 2.438434 GCAGCCGCCCAACATACT 60.438 61.111 0.00 0.00 0.00 2.12
183 184 2.618368 ATTATCCCCCAACCCACGCG 62.618 60.000 3.53 3.53 0.00 6.01
184 185 0.822121 GATTATCCCCCAACCCACGC 60.822 60.000 0.00 0.00 0.00 5.34
185 186 0.179001 GGATTATCCCCCAACCCACG 60.179 60.000 0.00 0.00 0.00 4.94
186 187 0.179001 CGGATTATCCCCCAACCCAC 60.179 60.000 5.56 0.00 31.13 4.61
187 188 0.327673 TCGGATTATCCCCCAACCCA 60.328 55.000 5.56 0.00 31.13 4.51
188 189 0.848053 TTCGGATTATCCCCCAACCC 59.152 55.000 5.56 0.00 31.13 4.11
189 190 1.202891 CCTTCGGATTATCCCCCAACC 60.203 57.143 5.56 0.00 31.13 3.77
197 198 5.705905 CCACCCTATTTTCCTTCGGATTATC 59.294 44.000 0.00 0.00 0.00 1.75
230 231 3.365265 CACGCCAGAGCCAAACCC 61.365 66.667 0.00 0.00 34.57 4.11
306 307 4.955811 TCATCTCAGCCGTATTTATGGT 57.044 40.909 0.00 0.00 34.78 3.55
311 312 5.344743 TTCTCTTCATCTCAGCCGTATTT 57.655 39.130 0.00 0.00 0.00 1.40
325 326 5.786121 ATCCTCAAATCCCTTTCTCTTCA 57.214 39.130 0.00 0.00 0.00 3.02
382 383 4.917906 ATCCCTCATAGCTTACCCATTC 57.082 45.455 0.00 0.00 0.00 2.67
414 416 8.300752 TCCCAAACCTATAATCCCTCAAATAT 57.699 34.615 0.00 0.00 0.00 1.28
432 434 3.559384 CCCAACTAGTCCTTCTCCCAAAC 60.559 52.174 0.00 0.00 0.00 2.93
486 526 6.062749 CAGATGATGAACTGATTGGAAGGAT 58.937 40.000 0.00 0.00 36.38 3.24
492 532 6.990939 ACTATGACAGATGATGAACTGATTGG 59.009 38.462 0.00 0.00 37.54 3.16
494 534 8.699130 TGTACTATGACAGATGATGAACTGATT 58.301 33.333 0.00 0.00 37.54 2.57
499 539 7.492524 TCCTTGTACTATGACAGATGATGAAC 58.507 38.462 0.00 0.00 0.00 3.18
505 545 6.634805 AGTGTTCCTTGTACTATGACAGATG 58.365 40.000 0.00 0.00 0.00 2.90
538 579 8.495148 GTGGTTTGTGAATTTGGATGTAATTTC 58.505 33.333 0.00 0.00 0.00 2.17
545 586 4.605640 AGGTGGTTTGTGAATTTGGATG 57.394 40.909 0.00 0.00 0.00 3.51
546 587 5.278758 CGTTAGGTGGTTTGTGAATTTGGAT 60.279 40.000 0.00 0.00 0.00 3.41
547 588 4.036971 CGTTAGGTGGTTTGTGAATTTGGA 59.963 41.667 0.00 0.00 0.00 3.53
548 589 4.036971 TCGTTAGGTGGTTTGTGAATTTGG 59.963 41.667 0.00 0.00 0.00 3.28
549 590 4.973663 GTCGTTAGGTGGTTTGTGAATTTG 59.026 41.667 0.00 0.00 0.00 2.32
551 592 3.249080 CGTCGTTAGGTGGTTTGTGAATT 59.751 43.478 0.00 0.00 0.00 2.17
554 595 1.408340 TCGTCGTTAGGTGGTTTGTGA 59.592 47.619 0.00 0.00 0.00 3.58
555 596 1.523934 GTCGTCGTTAGGTGGTTTGTG 59.476 52.381 0.00 0.00 0.00 3.33
556 597 1.410153 AGTCGTCGTTAGGTGGTTTGT 59.590 47.619 0.00 0.00 0.00 2.83
557 598 2.144482 AGTCGTCGTTAGGTGGTTTG 57.856 50.000 0.00 0.00 0.00 2.93
558 599 2.622942 TGTAGTCGTCGTTAGGTGGTTT 59.377 45.455 0.00 0.00 0.00 3.27
559 600 2.229792 TGTAGTCGTCGTTAGGTGGTT 58.770 47.619 0.00 0.00 0.00 3.67
560 601 1.896220 TGTAGTCGTCGTTAGGTGGT 58.104 50.000 0.00 0.00 0.00 4.16
561 602 2.982470 GTTTGTAGTCGTCGTTAGGTGG 59.018 50.000 0.00 0.00 0.00 4.61
581 622 0.179108 GGCTTCGGATCGCTTAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
584 625 2.303676 GCGGCTTCGGATCGCTTAG 61.304 63.158 11.67 0.00 45.16 2.18
585 626 2.279252 GCGGCTTCGGATCGCTTA 60.279 61.111 11.67 0.00 45.16 3.09
591 632 3.211963 GGCAATGCGGCTTCGGAT 61.212 61.111 0.00 0.00 46.65 4.18
599 640 1.434696 GGTGATGAAGGCAATGCGG 59.565 57.895 0.00 0.00 0.00 5.69
619 660 5.693769 TTCTTCCACCACTTATAAGGGAG 57.306 43.478 16.63 12.05 0.00 4.30
625 666 6.721318 AGAGCAATTTCTTCCACCACTTATA 58.279 36.000 0.00 0.00 0.00 0.98
626 667 5.574188 AGAGCAATTTCTTCCACCACTTAT 58.426 37.500 0.00 0.00 0.00 1.73
628 669 3.837355 AGAGCAATTTCTTCCACCACTT 58.163 40.909 0.00 0.00 0.00 3.16
629 670 3.515602 AGAGCAATTTCTTCCACCACT 57.484 42.857 0.00 0.00 0.00 4.00
630 671 5.003804 TCTAAGAGCAATTTCTTCCACCAC 58.996 41.667 0.00 0.00 38.35 4.16
631 672 5.003804 GTCTAAGAGCAATTTCTTCCACCA 58.996 41.667 0.00 0.00 38.35 4.17
633 674 5.249420 AGGTCTAAGAGCAATTTCTTCCAC 58.751 41.667 0.00 0.00 38.35 4.02
639 717 5.005875 GCTAACGAGGTCTAAGAGCAATTTC 59.994 44.000 0.00 0.00 31.89 2.17
645 723 1.401199 ACGCTAACGAGGTCTAAGAGC 59.599 52.381 0.00 0.00 43.93 4.09
646 724 3.761311 AACGCTAACGAGGTCTAAGAG 57.239 47.619 0.00 0.00 43.93 2.85
648 726 4.101235 GGTTAACGCTAACGAGGTCTAAG 58.899 47.826 2.82 0.00 43.93 2.18
650 728 3.347216 AGGTTAACGCTAACGAGGTCTA 58.653 45.455 2.82 0.00 43.93 2.59
651 729 2.165998 AGGTTAACGCTAACGAGGTCT 58.834 47.619 2.82 0.00 43.93 3.85
658 736 6.366877 TGTTCTTGTGATAGGTTAACGCTAAC 59.633 38.462 0.00 0.00 37.30 2.34
662 740 4.449743 TGTGTTCTTGTGATAGGTTAACGC 59.550 41.667 0.00 0.00 0.00 4.84
669 747 8.380644 CGTAATTAGTTGTGTTCTTGTGATAGG 58.619 37.037 0.00 0.00 0.00 2.57
731 809 0.108567 TACGTCTGCCTATGCGCAAA 60.109 50.000 17.11 0.00 41.78 3.68
733 811 0.104120 AATACGTCTGCCTATGCGCA 59.896 50.000 14.96 14.96 41.78 6.09
786 866 1.421268 TGAAGTCCCAAGCACATGACT 59.579 47.619 0.00 0.00 39.66 3.41
787 867 1.896220 TGAAGTCCCAAGCACATGAC 58.104 50.000 0.00 0.00 0.00 3.06
822 903 7.766219 GACTTGTTAGTCTTGTGTCAGTTTA 57.234 36.000 0.00 0.00 45.99 2.01
842 923 8.047310 TCTCTTAGTCAAAAAGAAACTGGACTT 58.953 33.333 0.00 0.00 36.95 3.01
844 925 7.519168 GCTCTCTTAGTCAAAAAGAAACTGGAC 60.519 40.741 0.00 0.00 32.77 4.02
847 928 6.018669 ACGCTCTCTTAGTCAAAAAGAAACTG 60.019 38.462 0.00 0.00 32.77 3.16
849 930 6.288426 ACGCTCTCTTAGTCAAAAAGAAAC 57.712 37.500 0.00 0.00 32.77 2.78
890 1076 1.873863 CGAGCCATCGCGGAGTATA 59.126 57.895 6.13 0.00 42.97 1.47
891 1077 2.645567 CGAGCCATCGCGGAGTAT 59.354 61.111 6.13 0.00 42.97 2.12
930 1121 4.367039 TCCTATTATTAAGTGGCTGGCC 57.633 45.455 4.43 4.43 0.00 5.36
1434 1646 3.133767 CTCCTCGCGGCGGATGTAA 62.134 63.158 23.46 0.13 0.00 2.41
1797 2021 2.681778 CTCTCACCCTGGAGGCGT 60.682 66.667 0.00 0.00 40.58 5.68
1809 2033 1.285950 CCGTGACACGAAGCTCTCA 59.714 57.895 28.83 0.00 46.05 3.27
1905 2129 3.274288 GGATGGACTGACCTGAATGAAC 58.726 50.000 0.00 0.00 39.86 3.18
1923 2147 7.813148 CGTATACTGAATAACGGAAAGATGGAT 59.187 37.037 0.56 0.00 0.00 3.41
1959 2195 1.210204 TTCCTGGCCTCCAATCTGCT 61.210 55.000 3.32 0.00 30.80 4.24
2001 2254 5.412526 TGTTTTAACTGTAAAGGTCAGCG 57.587 39.130 0.00 0.00 36.50 5.18
2002 2255 8.468720 TTTTTGTTTTAACTGTAAAGGTCAGC 57.531 30.769 0.00 0.00 36.50 4.26
2194 2759 0.841289 TGGAGAACACCTCGGGTTTT 59.159 50.000 0.00 0.00 42.89 2.43
2716 3281 1.284785 CCCTGGAGCTTGGGTTTCATA 59.715 52.381 11.02 0.00 38.65 2.15
2762 3327 3.314913 CACAACAAGTGGACAGCAATACA 59.685 43.478 0.00 0.00 44.69 2.29
2821 3535 6.594937 CCCATTTTTATTTTCCCACATGACTG 59.405 38.462 0.00 0.00 0.00 3.51
2839 3553 4.038402 GCATCCATCGAATCTTCCCATTTT 59.962 41.667 0.00 0.00 0.00 1.82
2840 3554 3.571401 GCATCCATCGAATCTTCCCATTT 59.429 43.478 0.00 0.00 0.00 2.32
2841 3555 3.152341 GCATCCATCGAATCTTCCCATT 58.848 45.455 0.00 0.00 0.00 3.16
2897 3614 9.432982 TGCAAATGGGAGGATTATATAAAAGTT 57.567 29.630 0.00 0.00 0.00 2.66
2902 3619 9.378504 ACAAATGCAAATGGGAGGATTATATAA 57.621 29.630 0.00 0.00 0.00 0.98
2912 3629 6.254157 CGAGATAAAACAAATGCAAATGGGAG 59.746 38.462 6.99 0.00 0.00 4.30
2915 3632 6.949578 ACGAGATAAAACAAATGCAAATGG 57.050 33.333 6.99 0.00 0.00 3.16
3036 4276 9.944376 AAACGCATACAAGTCTCCATATATAAT 57.056 29.630 0.00 0.00 0.00 1.28
3039 4279 7.387948 GGAAAACGCATACAAGTCTCCATATAT 59.612 37.037 0.00 0.00 0.00 0.86
3042 4282 4.873827 GGAAAACGCATACAAGTCTCCATA 59.126 41.667 0.00 0.00 0.00 2.74
3045 4285 3.071479 TGGAAAACGCATACAAGTCTCC 58.929 45.455 0.00 0.00 0.00 3.71
3086 4326 9.614792 AAGTCGCATCTAAAACCTATAAGATTT 57.385 29.630 0.00 0.00 0.00 2.17
3152 4392 2.421388 CCCGGCTTCATTACCAGAATGA 60.421 50.000 0.00 0.00 39.69 2.57
3159 4399 0.106894 CTCTCCCCGGCTTCATTACC 59.893 60.000 0.00 0.00 0.00 2.85
3161 4401 1.696097 GGCTCTCCCCGGCTTCATTA 61.696 60.000 0.00 0.00 0.00 1.90
3235 4475 3.055094 AGCCTAGTGGTGTGAATAAGGTG 60.055 47.826 0.00 0.00 35.27 4.00
3256 4496 1.514678 TTGTTGGCTGCAGCGGTTAG 61.515 55.000 31.19 0.00 43.26 2.34
3258 4498 2.354074 CTTTGTTGGCTGCAGCGGTT 62.354 55.000 31.19 0.00 43.26 4.44
3259 4499 2.832661 TTTGTTGGCTGCAGCGGT 60.833 55.556 31.19 0.00 43.26 5.68
3260 4500 2.049802 CTTTGTTGGCTGCAGCGG 60.050 61.111 31.19 11.53 43.26 5.52
3268 4638 3.552890 GGAAGTCATTGGTCTTTGTTGGC 60.553 47.826 0.00 0.00 0.00 4.52
3280 4650 2.401583 TGGTCCGATGGAAGTCATTG 57.598 50.000 0.00 0.00 35.97 2.82
3281 4651 2.505407 TGATGGTCCGATGGAAGTCATT 59.495 45.455 0.00 0.00 35.97 2.57
3314 4684 0.534203 GAGCAACACGGAAGGAACCA 60.534 55.000 0.00 0.00 0.00 3.67
3318 4688 1.671742 GAGGAGCAACACGGAAGGA 59.328 57.895 0.00 0.00 0.00 3.36
3320 4690 0.390472 GAGGAGGAGCAACACGGAAG 60.390 60.000 0.00 0.00 0.00 3.46
3354 4725 6.317789 ACACACAAATACACCTTGATCAAG 57.682 37.500 25.75 25.75 38.14 3.02
3355 4726 6.238897 GGAACACACAAATACACCTTGATCAA 60.239 38.462 8.12 8.12 0.00 2.57
3356 4727 5.240623 GGAACACACAAATACACCTTGATCA 59.759 40.000 0.00 0.00 0.00 2.92
3357 4728 5.335661 GGGAACACACAAATACACCTTGATC 60.336 44.000 0.00 0.00 0.00 2.92
3358 4729 4.522789 GGGAACACACAAATACACCTTGAT 59.477 41.667 0.00 0.00 0.00 2.57
3359 4730 3.886505 GGGAACACACAAATACACCTTGA 59.113 43.478 0.00 0.00 0.00 3.02
3379 4750 2.492773 GCGGGCCTCATTTGATGGG 61.493 63.158 0.84 0.00 0.00 4.00
3415 4786 1.202817 TGAGCAACGCGGACTAACATA 59.797 47.619 12.47 0.00 0.00 2.29
3469 4844 1.065928 GCTAGCGGACACGTAGCAT 59.934 57.895 0.00 0.00 43.10 3.79
3480 4855 4.261489 TCTTTTAGAAGTATCCGCTAGCGG 60.261 45.833 43.57 43.57 45.43 5.52
3481 4856 4.856664 TCTTTTAGAAGTATCCGCTAGCG 58.143 43.478 29.93 29.93 35.36 4.26
3482 4857 5.865013 GGATCTTTTAGAAGTATCCGCTAGC 59.135 44.000 4.06 4.06 33.73 3.42
3483 4858 6.087522 CGGATCTTTTAGAAGTATCCGCTAG 58.912 44.000 21.99 7.62 45.17 3.42
3484 4859 6.010294 CGGATCTTTTAGAAGTATCCGCTA 57.990 41.667 21.99 0.00 45.17 4.26
3485 4860 4.872664 CGGATCTTTTAGAAGTATCCGCT 58.127 43.478 21.99 0.00 45.17 5.52
3488 4863 3.988517 CGGCGGATCTTTTAGAAGTATCC 59.011 47.826 0.00 11.36 36.85 2.59
3489 4864 3.429207 GCGGCGGATCTTTTAGAAGTATC 59.571 47.826 9.78 0.00 34.41 2.24
3490 4865 3.391049 GCGGCGGATCTTTTAGAAGTAT 58.609 45.455 9.78 0.00 34.41 2.12
3491 4866 2.482490 GGCGGCGGATCTTTTAGAAGTA 60.482 50.000 9.78 0.00 34.41 2.24
3492 4867 1.653151 GCGGCGGATCTTTTAGAAGT 58.347 50.000 9.78 0.00 34.41 3.01
3493 4868 0.938008 GGCGGCGGATCTTTTAGAAG 59.062 55.000 9.78 0.00 0.00 2.85
3494 4869 0.539986 AGGCGGCGGATCTTTTAGAA 59.460 50.000 9.78 0.00 0.00 2.10
3495 4870 0.104304 GAGGCGGCGGATCTTTTAGA 59.896 55.000 9.78 0.00 0.00 2.10
3496 4871 1.215655 CGAGGCGGCGGATCTTTTAG 61.216 60.000 9.78 0.00 0.00 1.85
3497 4872 1.227147 CGAGGCGGCGGATCTTTTA 60.227 57.895 9.78 0.00 0.00 1.52
3498 4873 2.511600 CGAGGCGGCGGATCTTTT 60.512 61.111 9.78 0.00 0.00 2.27
3515 4890 3.118629 TGACACCAGATCTAACAGATGGC 60.119 47.826 0.00 0.00 34.53 4.40
3547 4922 1.115467 AATGGTGAGGACGAGGCTAG 58.885 55.000 0.00 0.00 0.00 3.42
3621 4998 4.956075 AGCAGAAAAGTGAGGAAGGAAAAA 59.044 37.500 0.00 0.00 0.00 1.94
3623 5000 4.170468 AGCAGAAAAGTGAGGAAGGAAA 57.830 40.909 0.00 0.00 0.00 3.13
3624 5001 3.864789 AGCAGAAAAGTGAGGAAGGAA 57.135 42.857 0.00 0.00 0.00 3.36
3625 5002 6.384015 TCATATAGCAGAAAAGTGAGGAAGGA 59.616 38.462 0.00 0.00 0.00 3.36
3626 5003 6.586344 TCATATAGCAGAAAAGTGAGGAAGG 58.414 40.000 0.00 0.00 0.00 3.46
3627 5004 7.224362 CACTCATATAGCAGAAAAGTGAGGAAG 59.776 40.741 0.00 0.00 36.74 3.46
3628 5005 7.044181 CACTCATATAGCAGAAAAGTGAGGAA 58.956 38.462 0.00 0.00 36.74 3.36
3650 5027 5.722021 AAAGTTTCTTCCACAACAACACT 57.278 34.783 0.00 0.00 0.00 3.55
3660 5037 5.728471 TCAATGTTGCAAAAGTTTCTTCCA 58.272 33.333 0.00 0.00 0.00 3.53
3701 5078 2.867624 TGCTGCAGGAAAGTGAAGATT 58.132 42.857 17.12 0.00 0.00 2.40
3702 5079 2.574006 TGCTGCAGGAAAGTGAAGAT 57.426 45.000 17.12 0.00 0.00 2.40
3716 5093 1.000233 CGCAACAACACTCATGCTGC 61.000 55.000 0.00 0.00 36.67 5.25


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

AutoCloner maintained by Alex Coulton.