Multiple sequence alignment - TraesCS2D01G573700

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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 TraesCS2D01G573700 chr2D 100.000 5618 0 0 1 5618 638723120 638728737 0.000000e+00 10375
1 TraesCS2D01G573700 chr2D 92.495 4570 308 20 1048 5599 638804309 638808861 0.000000e+00 6506
2 TraesCS2D01G573700 chr2D 79.651 688 99 21 4158 4829 638785419 638786081 1.840000e-124 457
3 TraesCS2D01G573700 chr2B 94.222 4915 181 28 778 5618 798128001 798132886 0.000000e+00 7408
4 TraesCS2D01G573700 chr2B 87.543 3195 339 31 919 4095 784188512 784191665 0.000000e+00 3640
5 TraesCS2D01G573700 chr2B 88.005 792 56 16 1 780 798127295 798128059 0.000000e+00 900
6 TraesCS2D01G573700 chr2B 82.810 669 78 23 4092 4747 784191695 784192339 1.060000e-156 564
7 TraesCS2D01G573700 chr2B 84.254 489 71 5 2026 2511 780594543 780595028 6.590000e-129 472
8 TraesCS2D01G573700 chr2B 85.301 415 59 2 1598 2011 780594011 780594424 1.450000e-115 427
9 TraesCS2D01G573700 chr2A 88.456 3621 382 24 1062 4665 764309000 764312601 0.000000e+00 4338
10 TraesCS2D01G573700 chr2A 88.009 3386 379 18 1370 4748 764256506 764259871 0.000000e+00 3978
11 TraesCS2D01G573700 chr7D 80.767 3546 581 59 1129 4625 460279814 460283307 0.000000e+00 2676
12 TraesCS2D01G573700 chr7D 78.061 2981 595 33 1130 4089 459790135 459787193 0.000000e+00 1827
13 TraesCS2D01G573700 chr7B 81.072 2985 509 32 1129 4097 482684460 482687404 0.000000e+00 2331
14 TraesCS2D01G573700 chr7B 78.202 2826 576 27 1269 4089 482078227 482075437 0.000000e+00 1770
15 TraesCS2D01G573700 chr7B 76.761 2655 507 75 2013 4619 482487450 482490042 0.000000e+00 1384
16 TraesCS2D01G573700 chr7A 77.371 2594 487 66 2082 4631 539448612 539446075 0.000000e+00 1447
17 TraesCS2D01G573700 chr7A 80.939 703 85 29 3942 4619 539403682 539403004 1.400000e-140 510


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 TraesCS2D01G573700 chr2D 638723120 638728737 5617 False 10375.0 10375 100.0000 1 5618 1 chr2D.!!$F1 5617
1 TraesCS2D01G573700 chr2D 638804309 638808861 4552 False 6506.0 6506 92.4950 1048 5599 1 chr2D.!!$F3 4551
2 TraesCS2D01G573700 chr2D 638785419 638786081 662 False 457.0 457 79.6510 4158 4829 1 chr2D.!!$F2 671
3 TraesCS2D01G573700 chr2B 798127295 798132886 5591 False 4154.0 7408 91.1135 1 5618 2 chr2B.!!$F3 5617
4 TraesCS2D01G573700 chr2B 784188512 784192339 3827 False 2102.0 3640 85.1765 919 4747 2 chr2B.!!$F2 3828
5 TraesCS2D01G573700 chr2B 780594011 780595028 1017 False 449.5 472 84.7775 1598 2511 2 chr2B.!!$F1 913
6 TraesCS2D01G573700 chr2A 764309000 764312601 3601 False 4338.0 4338 88.4560 1062 4665 1 chr2A.!!$F2 3603
7 TraesCS2D01G573700 chr2A 764256506 764259871 3365 False 3978.0 3978 88.0090 1370 4748 1 chr2A.!!$F1 3378
8 TraesCS2D01G573700 chr7D 460279814 460283307 3493 False 2676.0 2676 80.7670 1129 4625 1 chr7D.!!$F1 3496
9 TraesCS2D01G573700 chr7D 459787193 459790135 2942 True 1827.0 1827 78.0610 1130 4089 1 chr7D.!!$R1 2959
10 TraesCS2D01G573700 chr7B 482684460 482687404 2944 False 2331.0 2331 81.0720 1129 4097 1 chr7B.!!$F2 2968
11 TraesCS2D01G573700 chr7B 482075437 482078227 2790 True 1770.0 1770 78.2020 1269 4089 1 chr7B.!!$R1 2820
12 TraesCS2D01G573700 chr7B 482487450 482490042 2592 False 1384.0 1384 76.7610 2013 4619 1 chr7B.!!$F1 2606
13 TraesCS2D01G573700 chr7A 539446075 539448612 2537 True 1447.0 1447 77.3710 2082 4631 1 chr7A.!!$R2 2549
14 TraesCS2D01G573700 chr7A 539403004 539403682 678 True 510.0 510 80.9390 3942 4619 1 chr7A.!!$R1 677

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
688 699 1.061546 TGGAAGCGGGTATATTCCCC 58.938 55.000 11.58 6.01 44.32 4.81 F
1262 1279 0.108774 TGGTCCGGTGTTACATGCAA 59.891 50.000 0.00 0.00 0.00 4.08 F
1926 1959 0.583438 CGAATATTGCTGGCTCACCG 59.417 55.000 0.00 0.00 39.70 4.94 F
2194 2333 0.897621 GGCAGGGGAAATTCCAACTG 59.102 55.000 23.19 23.19 42.41 3.16 F
2415 2554 3.075134 AGGCAGGAGATTGGTCTTTCTTT 59.925 43.478 0.00 0.00 33.97 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2574 2713 2.033299 ACGTTTGATGTTTGTGAGCTGG 59.967 45.455 0.00 0.0 0.00 4.85 R
3069 3208 5.973565 GCCTCTCAAATTCGTGAAATATTGG 59.026 40.000 0.00 0.0 0.00 3.16 R
3321 3460 2.233431 TGAGGTGTGCAGCTTTTGTTTT 59.767 40.909 5.34 0.0 39.57 2.43 R
3377 3516 4.419522 ACGCATGATAACAGAACCAAAC 57.580 40.909 0.00 0.0 0.00 2.93 R
5547 5798 2.344203 CCTTCTCTCACCGTCGGCT 61.344 63.158 12.28 0.0 0.00 5.52 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
18 19 1.152963 CGGTATGGAGCCTTTGGGG 60.153 63.158 0.00 0.00 38.36 4.96
107 110 5.801350 TTATGTGCATCTGCTTTACTGTC 57.199 39.130 3.53 0.00 42.66 3.51
112 115 4.690748 GTGCATCTGCTTTACTGTCACTAA 59.309 41.667 3.53 0.00 42.66 2.24
125 128 4.400529 TGTCACTAAACAGAGAACTGCA 57.599 40.909 0.00 0.00 46.95 4.41
127 130 3.182572 GTCACTAAACAGAGAACTGCACG 59.817 47.826 0.00 0.00 46.95 5.34
134 137 2.099921 ACAGAGAACTGCACGCCTATAG 59.900 50.000 0.00 0.00 46.95 1.31
156 159 3.914364 GTGCGATTTGGTTTAGAAAGCTG 59.086 43.478 5.84 0.00 37.31 4.24
157 160 3.568007 TGCGATTTGGTTTAGAAAGCTGT 59.432 39.130 5.84 0.00 37.31 4.40
158 161 4.757657 TGCGATTTGGTTTAGAAAGCTGTA 59.242 37.500 5.84 0.00 37.31 2.74
159 162 5.086727 GCGATTTGGTTTAGAAAGCTGTAC 58.913 41.667 5.84 0.00 37.31 2.90
160 163 5.106673 GCGATTTGGTTTAGAAAGCTGTACT 60.107 40.000 5.84 0.00 37.31 2.73
161 164 6.091713 GCGATTTGGTTTAGAAAGCTGTACTA 59.908 38.462 5.84 0.00 37.31 1.82
162 165 7.453838 CGATTTGGTTTAGAAAGCTGTACTAC 58.546 38.462 5.84 0.00 37.31 2.73
163 166 7.117236 CGATTTGGTTTAGAAAGCTGTACTACA 59.883 37.037 5.84 0.00 37.31 2.74
164 167 8.685838 ATTTGGTTTAGAAAGCTGTACTACAA 57.314 30.769 5.84 0.00 37.31 2.41
165 168 8.685838 TTTGGTTTAGAAAGCTGTACTACAAT 57.314 30.769 5.84 0.00 37.31 2.71
166 169 7.667043 TGGTTTAGAAAGCTGTACTACAATG 57.333 36.000 5.84 0.00 37.31 2.82
167 170 7.221450 TGGTTTAGAAAGCTGTACTACAATGT 58.779 34.615 5.84 0.00 37.31 2.71
168 171 7.386848 TGGTTTAGAAAGCTGTACTACAATGTC 59.613 37.037 5.84 0.00 37.31 3.06
169 172 7.386848 GGTTTAGAAAGCTGTACTACAATGTCA 59.613 37.037 0.00 0.00 33.81 3.58
170 173 8.770828 GTTTAGAAAGCTGTACTACAATGTCAA 58.229 33.333 0.00 0.00 0.00 3.18
171 174 8.896320 TTAGAAAGCTGTACTACAATGTCAAA 57.104 30.769 0.00 0.00 0.00 2.69
172 175 7.801716 AGAAAGCTGTACTACAATGTCAAAA 57.198 32.000 0.00 0.00 0.00 2.44
173 176 7.639945 AGAAAGCTGTACTACAATGTCAAAAC 58.360 34.615 0.00 0.00 0.00 2.43
174 177 5.941948 AGCTGTACTACAATGTCAAAACC 57.058 39.130 0.00 0.00 0.00 3.27
175 178 5.621193 AGCTGTACTACAATGTCAAAACCT 58.379 37.500 0.00 0.00 0.00 3.50
176 179 6.062095 AGCTGTACTACAATGTCAAAACCTT 58.938 36.000 0.00 0.00 0.00 3.50
177 180 7.221450 AGCTGTACTACAATGTCAAAACCTTA 58.779 34.615 0.00 0.00 0.00 2.69
178 181 7.883311 AGCTGTACTACAATGTCAAAACCTTAT 59.117 33.333 0.00 0.00 0.00 1.73
179 182 9.158233 GCTGTACTACAATGTCAAAACCTTATA 57.842 33.333 0.00 0.00 0.00 0.98
199 202 9.970395 CCTTATACAACATGAATACTTACCGTA 57.030 33.333 0.00 0.00 0.00 4.02
203 206 9.745880 ATACAACATGAATACTTACCGTAAGAG 57.254 33.333 22.48 0.79 39.09 2.85
211 214 4.263018 ACTTACCGTAAGAGGGTGAAAC 57.737 45.455 22.48 0.00 36.93 2.78
212 215 3.642848 ACTTACCGTAAGAGGGTGAAACA 59.357 43.478 22.48 0.00 36.93 2.83
219 222 3.920093 GAGGGTGAAACAGGGCCGG 62.920 68.421 0.79 0.79 39.98 6.13
241 244 2.830370 GCACTGGGGCATACAGGC 60.830 66.667 7.77 5.00 40.23 4.85
250 253 2.686816 GCATACAGGCGCGTTGGTT 61.687 57.895 8.43 0.00 0.00 3.67
258 261 1.066716 AGGCGCGTTGGTTGAGTATAA 60.067 47.619 8.43 0.00 0.00 0.98
292 295 1.460305 AGTGGTCCTGCTCACCTGT 60.460 57.895 0.00 0.00 34.66 4.00
313 317 4.646945 TGTTAAAAACATCAGGGCTGTGAA 59.353 37.500 0.00 0.00 36.25 3.18
319 323 4.032960 ACATCAGGGCTGTGAACAAATA 57.967 40.909 0.00 0.00 0.00 1.40
323 327 5.860941 TCAGGGCTGTGAACAAATAAAAA 57.139 34.783 0.00 0.00 0.00 1.94
464 468 2.156917 CAGGCAGAAGCAGATCACAAA 58.843 47.619 0.00 0.00 44.61 2.83
501 505 6.623486 CATGGTAAGCAACTGAATCAAATGA 58.377 36.000 0.00 0.00 0.00 2.57
520 524 7.880713 TCAAATGACAAGTGCTAGGTAACATTA 59.119 33.333 0.00 0.00 41.41 1.90
521 525 8.677300 CAAATGACAAGTGCTAGGTAACATTAT 58.323 33.333 0.00 0.00 41.41 1.28
522 526 8.807948 AATGACAAGTGCTAGGTAACATTATT 57.192 30.769 0.00 0.00 41.41 1.40
533 537 9.343539 GCTAGGTAACATTATTCTTCCTGAATT 57.656 33.333 0.00 0.00 42.08 2.17
544 548 4.214310 TCTTCCTGAATTGCCTTTGTGAA 58.786 39.130 0.00 0.00 0.00 3.18
579 583 3.073274 AGTTAGCACCAAGATGGAACC 57.927 47.619 2.85 0.00 40.96 3.62
583 587 2.676748 AGCACCAAGATGGAACCAAAA 58.323 42.857 2.85 0.00 40.96 2.44
610 614 1.860950 CGGCGTACTGGAAATCATCAG 59.139 52.381 0.00 0.00 37.07 2.90
622 626 6.705302 TGGAAATCATCAGCACCTATCTATC 58.295 40.000 0.00 0.00 0.00 2.08
666 677 6.773976 TGAAGTGAACTTTGACTGGAAATT 57.226 33.333 0.00 0.00 36.11 1.82
667 678 7.169158 TGAAGTGAACTTTGACTGGAAATTT 57.831 32.000 0.00 0.00 36.11 1.82
688 699 1.061546 TGGAAGCGGGTATATTCCCC 58.938 55.000 11.58 6.01 44.32 4.81
705 716 1.133976 CCCCGGCTTCTTCATTGATCT 60.134 52.381 0.00 0.00 0.00 2.75
706 717 1.945394 CCCGGCTTCTTCATTGATCTG 59.055 52.381 0.00 0.00 0.00 2.90
711 722 4.205587 GGCTTCTTCATTGATCTGGATGT 58.794 43.478 0.00 0.00 0.00 3.06
714 725 5.220815 GCTTCTTCATTGATCTGGATGTCAC 60.221 44.000 0.00 0.00 0.00 3.67
717 728 6.053650 TCTTCATTGATCTGGATGTCACATC 58.946 40.000 9.53 9.53 0.00 3.06
718 729 5.362105 TCATTGATCTGGATGTCACATCA 57.638 39.130 19.61 5.09 30.59 3.07
719 730 5.937111 TCATTGATCTGGATGTCACATCAT 58.063 37.500 19.61 4.47 32.25 2.45
726 737 2.240414 TGGATGTCACATCATCTTGGCT 59.760 45.455 19.61 0.00 42.45 4.75
743 754 5.184864 TCTTGGCTGTGTCTTTCAAAGAAAA 59.815 36.000 0.00 0.00 39.67 2.29
745 756 5.976458 TGGCTGTGTCTTTCAAAGAAAAAT 58.024 33.333 0.00 0.00 39.67 1.82
761 772 9.217223 CAAAGAAAAATTCAAAGTCTTTGCATG 57.783 29.630 18.80 0.00 44.65 4.06
772 783 5.779529 AGTCTTTGCATGACTTCACAATT 57.220 34.783 14.68 0.00 41.45 2.32
773 784 6.152932 AGTCTTTGCATGACTTCACAATTT 57.847 33.333 14.68 0.00 41.45 1.82
774 785 5.981315 AGTCTTTGCATGACTTCACAATTTG 59.019 36.000 14.68 0.00 41.45 2.32
775 786 5.978919 GTCTTTGCATGACTTCACAATTTGA 59.021 36.000 2.79 0.00 0.00 2.69
776 787 6.476380 GTCTTTGCATGACTTCACAATTTGAA 59.524 34.615 2.79 3.95 42.26 2.69
777 788 7.170320 GTCTTTGCATGACTTCACAATTTGAAT 59.830 33.333 2.79 0.00 43.54 2.57
778 789 6.772770 TTGCATGACTTCACAATTTGAATG 57.227 33.333 2.79 0.00 43.54 2.67
779 790 5.231702 TGCATGACTTCACAATTTGAATGG 58.768 37.500 2.79 0.00 43.54 3.16
780 791 4.092383 GCATGACTTCACAATTTGAATGGC 59.908 41.667 2.79 0.00 43.54 4.40
781 792 4.255833 TGACTTCACAATTTGAATGGCC 57.744 40.909 2.79 0.00 43.54 5.36
782 793 3.244976 GACTTCACAATTTGAATGGCCG 58.755 45.455 2.79 0.00 43.54 6.13
783 794 2.627699 ACTTCACAATTTGAATGGCCGT 59.372 40.909 2.79 0.00 43.54 5.68
784 795 2.721274 TCACAATTTGAATGGCCGTG 57.279 45.000 0.00 0.00 0.00 4.94
785 796 1.959985 TCACAATTTGAATGGCCGTGT 59.040 42.857 0.00 0.00 0.00 4.49
786 797 2.030363 TCACAATTTGAATGGCCGTGTC 60.030 45.455 0.00 0.00 0.00 3.67
787 798 2.030007 CACAATTTGAATGGCCGTGTCT 60.030 45.455 0.00 0.00 0.00 3.41
788 799 2.627699 ACAATTTGAATGGCCGTGTCTT 59.372 40.909 0.00 0.00 0.00 3.01
789 800 3.069443 ACAATTTGAATGGCCGTGTCTTT 59.931 39.130 0.00 0.00 0.00 2.52
790 801 3.575965 ATTTGAATGGCCGTGTCTTTC 57.424 42.857 0.00 0.00 0.00 2.62
791 802 1.974265 TTGAATGGCCGTGTCTTTCA 58.026 45.000 0.00 0.00 31.28 2.69
792 803 1.974265 TGAATGGCCGTGTCTTTCAA 58.026 45.000 0.00 0.00 30.47 2.69
793 804 2.302260 TGAATGGCCGTGTCTTTCAAA 58.698 42.857 0.00 0.00 30.47 2.69
794 805 2.293122 TGAATGGCCGTGTCTTTCAAAG 59.707 45.455 0.00 0.00 30.47 2.77
795 806 2.270352 ATGGCCGTGTCTTTCAAAGA 57.730 45.000 0.00 0.00 34.51 2.52
796 807 2.270352 TGGCCGTGTCTTTCAAAGAT 57.730 45.000 2.39 0.00 40.18 2.40
797 808 1.879380 TGGCCGTGTCTTTCAAAGATG 59.121 47.619 2.39 0.00 40.18 2.90
798 809 2.151202 GGCCGTGTCTTTCAAAGATGA 58.849 47.619 2.39 0.00 40.18 2.92
799 810 2.552315 GGCCGTGTCTTTCAAAGATGAA 59.448 45.455 2.39 0.00 43.70 2.57
800 811 3.365364 GGCCGTGTCTTTCAAAGATGAAG 60.365 47.826 2.39 0.00 45.82 3.02
801 812 3.251004 GCCGTGTCTTTCAAAGATGAAGT 59.749 43.478 2.39 0.00 45.82 3.01
802 813 4.611581 GCCGTGTCTTTCAAAGATGAAGTC 60.612 45.833 2.39 0.00 45.82 3.01
803 814 4.511454 CCGTGTCTTTCAAAGATGAAGTCA 59.489 41.667 2.39 0.00 45.82 3.41
804 815 5.007626 CCGTGTCTTTCAAAGATGAAGTCAA 59.992 40.000 2.39 0.00 45.82 3.18
805 816 6.458206 CCGTGTCTTTCAAAGATGAAGTCAAA 60.458 38.462 2.39 0.00 45.82 2.69
806 817 6.630443 CGTGTCTTTCAAAGATGAAGTCAAAG 59.370 38.462 2.39 0.00 45.82 2.77
807 818 7.475840 GTGTCTTTCAAAGATGAAGTCAAAGT 58.524 34.615 2.39 0.00 45.82 2.66
808 819 7.641802 GTGTCTTTCAAAGATGAAGTCAAAGTC 59.358 37.037 2.39 0.00 45.82 3.01
809 820 7.554118 TGTCTTTCAAAGATGAAGTCAAAGTCT 59.446 33.333 2.39 0.00 45.82 3.24
810 821 8.401709 GTCTTTCAAAGATGAAGTCAAAGTCTT 58.598 33.333 2.39 0.00 45.82 3.01
811 822 8.960591 TCTTTCAAAGATGAAGTCAAAGTCTTT 58.039 29.630 0.00 3.58 45.82 2.52
814 825 7.031226 CAAAGATGAAGTCAAAGTCTTTGGA 57.969 36.000 22.23 8.88 45.87 3.53
815 826 7.655490 CAAAGATGAAGTCAAAGTCTTTGGAT 58.345 34.615 22.23 10.53 45.87 3.41
816 827 6.814506 AGATGAAGTCAAAGTCTTTGGATG 57.185 37.500 22.23 0.86 40.98 3.51
817 828 6.537355 AGATGAAGTCAAAGTCTTTGGATGA 58.463 36.000 22.23 3.28 40.98 2.92
818 829 6.429385 AGATGAAGTCAAAGTCTTTGGATGAC 59.571 38.462 22.23 14.37 40.98 3.06
868 882 8.940768 AGTTGCAGTACTACTACTACTACTAC 57.059 38.462 8.25 0.00 33.22 2.73
893 907 9.635520 ACTACTACTTGTGTTTCATATGTACAC 57.364 33.333 24.34 24.34 41.85 2.90
947 961 8.775527 TCAGCGTTCTATAAATACACTAGAGAG 58.224 37.037 0.00 0.00 0.00 3.20
1095 1112 1.747924 TCCTCTCTTCTGACATGCTCG 59.252 52.381 0.00 0.00 0.00 5.03
1198 1215 1.877258 GCACTTCTTCTGCTGCACTCT 60.877 52.381 0.00 0.00 0.00 3.24
1262 1279 0.108774 TGGTCCGGTGTTACATGCAA 59.891 50.000 0.00 0.00 0.00 4.08
1431 1457 9.499479 CATCTGAATAGGTTGCAGTATCTTAAT 57.501 33.333 0.00 0.00 0.00 1.40
1476 1502 3.441163 CATGATCCCAAGCAATTTGTCG 58.559 45.455 0.00 0.00 34.87 4.35
1524 1550 9.753674 ATTGATCTTGGGAGTAACTTCATAAAA 57.246 29.630 0.00 0.00 0.00 1.52
1890 1923 5.717654 TGGAAAGAACAACTTTACTGGGTTT 59.282 36.000 0.00 0.00 46.46 3.27
1926 1959 0.583438 CGAATATTGCTGGCTCACCG 59.417 55.000 0.00 0.00 39.70 4.94
1985 2018 3.568853 GGCGCAATACCTTCTACTCTAGA 59.431 47.826 10.83 0.00 0.00 2.43
2111 2249 5.364446 TGAGTTACAACTACTTGTCAGGGAA 59.636 40.000 0.00 0.00 41.15 3.97
2194 2333 0.897621 GGCAGGGGAAATTCCAACTG 59.102 55.000 23.19 23.19 42.41 3.16
2293 2432 4.977963 CACTAGCCAACACAACAAATCTTG 59.022 41.667 0.00 0.00 0.00 3.02
2415 2554 3.075134 AGGCAGGAGATTGGTCTTTCTTT 59.925 43.478 0.00 0.00 33.97 2.52
2574 2713 4.221041 GGCCCTATACCACAAGAGATAGAC 59.779 50.000 0.00 0.00 0.00 2.59
3057 3196 5.509501 GCACATGGAGAGGAACAATTTTCAA 60.510 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.554822 TTATCAAAATCGTAACAGGCCAC 57.445 39.130 5.01 0.00 0.00 5.01
87 90 3.438087 GTGACAGTAAAGCAGATGCACAT 59.562 43.478 7.68 0.00 45.16 3.21
96 99 6.156748 TCTCTGTTTAGTGACAGTAAAGCA 57.843 37.500 14.46 13.60 45.64 3.91
107 110 2.096713 GCGTGCAGTTCTCTGTTTAGTG 60.097 50.000 0.00 0.00 43.05 2.74
112 115 0.679505 TAGGCGTGCAGTTCTCTGTT 59.320 50.000 0.00 0.00 43.05 3.16
127 130 5.054477 TCTAAACCAAATCGCACTATAGGC 58.946 41.667 4.43 4.06 0.00 3.93
134 137 3.914364 CAGCTTTCTAAACCAAATCGCAC 59.086 43.478 0.00 0.00 0.00 5.34
140 143 8.564574 CATTGTAGTACAGCTTTCTAAACCAAA 58.435 33.333 2.68 0.00 0.00 3.28
158 161 9.344772 TGTTGTATAAGGTTTTGACATTGTAGT 57.655 29.630 0.00 0.00 0.00 2.73
161 164 8.855110 TCATGTTGTATAAGGTTTTGACATTGT 58.145 29.630 0.00 0.00 0.00 2.71
162 165 9.689976 TTCATGTTGTATAAGGTTTTGACATTG 57.310 29.630 0.00 0.00 0.00 2.82
171 174 9.321562 CGGTAAGTATTCATGTTGTATAAGGTT 57.678 33.333 0.00 0.00 0.00 3.50
172 175 8.480501 ACGGTAAGTATTCATGTTGTATAAGGT 58.519 33.333 0.00 0.00 0.00 3.50
173 176 8.882415 ACGGTAAGTATTCATGTTGTATAAGG 57.118 34.615 0.00 0.00 0.00 2.69
177 180 9.745880 CTCTTACGGTAAGTATTCATGTTGTAT 57.254 33.333 23.27 0.00 37.10 2.29
178 181 8.192774 CCTCTTACGGTAAGTATTCATGTTGTA 58.807 37.037 23.27 3.16 37.10 2.41
179 182 7.039882 CCTCTTACGGTAAGTATTCATGTTGT 58.960 38.462 23.27 0.00 37.10 3.32
180 183 6.479001 CCCTCTTACGGTAAGTATTCATGTTG 59.521 42.308 23.27 0.00 37.10 3.33
199 202 1.460699 GGCCCTGTTTCACCCTCTT 59.539 57.895 0.00 0.00 0.00 2.85
232 235 2.686816 AACCAACGCGCCTGTATGC 61.687 57.895 5.73 0.00 0.00 3.14
233 236 1.134487 CAACCAACGCGCCTGTATG 59.866 57.895 5.73 1.38 0.00 2.39
241 244 2.613691 ACCTTATACTCAACCAACGCG 58.386 47.619 3.53 3.53 0.00 6.01
243 246 5.350640 GGAGAAACCTTATACTCAACCAACG 59.649 44.000 0.00 0.00 35.41 4.10
250 253 3.449737 CCCACGGAGAAACCTTATACTCA 59.550 47.826 0.00 0.00 36.31 3.41
280 283 4.278170 TGATGTTTTTAACAGGTGAGCAGG 59.722 41.667 0.00 0.00 45.95 4.85
281 284 5.437289 TGATGTTTTTAACAGGTGAGCAG 57.563 39.130 0.00 0.00 45.95 4.24
292 295 4.646945 TGTTCACAGCCCTGATGTTTTTAA 59.353 37.500 1.69 0.00 26.01 1.52
313 317 7.504574 ACCTTGTAGTACAGGCTTTTTATTTGT 59.495 33.333 14.93 0.22 0.00 2.83
319 323 7.885009 TTTAACCTTGTAGTACAGGCTTTTT 57.115 32.000 14.93 7.60 0.00 1.94
323 327 5.932455 TGTTTTAACCTTGTAGTACAGGCT 58.068 37.500 14.93 8.49 0.00 4.58
464 468 3.441572 GCTTACCATGCTCATGTTGTTCT 59.558 43.478 8.81 0.00 37.11 3.01
501 505 7.553044 GGAAGAATAATGTTACCTAGCACTTGT 59.447 37.037 0.00 0.00 0.00 3.16
520 524 9.357742 CCTTCACAAAGGCAATTCAGGAAGAAT 62.358 40.741 0.00 0.00 45.79 2.40
521 525 4.214310 TCACAAAGGCAATTCAGGAAGAA 58.786 39.130 0.00 0.00 41.28 2.52
522 526 3.831323 TCACAAAGGCAATTCAGGAAGA 58.169 40.909 0.00 0.00 0.00 2.87
551 555 5.104900 CCATCTTGGTGCTAACTAACTAGGT 60.105 44.000 0.00 0.00 31.35 3.08
558 562 3.585289 TGGTTCCATCTTGGTGCTAACTA 59.415 43.478 0.00 0.00 39.03 2.24
579 583 0.242555 AGTACGCCGGCCAATTTTTG 59.757 50.000 23.46 6.49 0.00 2.44
583 587 2.437716 CCAGTACGCCGGCCAATT 60.438 61.111 23.46 5.18 0.00 2.32
594 598 3.878778 AGGTGCTGATGATTTCCAGTAC 58.121 45.455 0.00 0.00 42.62 2.73
641 645 5.818136 TTCCAGTCAAAGTTCACTTCAAG 57.182 39.130 0.00 0.00 34.61 3.02
666 677 2.158726 GGGAATATACCCGCTTCCACAA 60.159 50.000 4.80 0.00 40.20 3.33
667 678 1.418637 GGGAATATACCCGCTTCCACA 59.581 52.381 4.80 0.00 40.20 4.17
688 699 2.910199 TCCAGATCAATGAAGAAGCCG 58.090 47.619 0.00 0.00 0.00 5.52
691 702 5.878669 TGTGACATCCAGATCAATGAAGAAG 59.121 40.000 9.06 0.00 0.00 2.85
705 716 2.240414 AGCCAAGATGATGTGACATCCA 59.760 45.455 21.68 10.94 45.20 3.41
706 717 2.617308 CAGCCAAGATGATGTGACATCC 59.383 50.000 21.68 8.27 45.20 3.51
711 722 2.303890 AGACACAGCCAAGATGATGTGA 59.696 45.455 15.36 0.00 44.56 3.58
714 725 3.754850 TGAAAGACACAGCCAAGATGATG 59.245 43.478 0.00 0.00 0.00 3.07
717 728 4.276678 TCTTTGAAAGACACAGCCAAGATG 59.723 41.667 3.02 0.00 31.20 2.90
718 729 4.464008 TCTTTGAAAGACACAGCCAAGAT 58.536 39.130 3.02 0.00 31.20 2.40
719 730 3.884895 TCTTTGAAAGACACAGCCAAGA 58.115 40.909 3.02 0.00 31.20 3.02
726 737 9.487790 ACTTTGAATTTTTCTTTGAAAGACACA 57.512 25.926 7.21 0.00 37.23 3.72
765 776 1.959985 ACACGGCCATTCAAATTGTGA 59.040 42.857 2.24 0.00 0.00 3.58
766 777 2.030007 AGACACGGCCATTCAAATTGTG 60.030 45.455 2.24 1.32 0.00 3.33
771 782 2.302260 TGAAAGACACGGCCATTCAAA 58.698 42.857 2.24 0.00 0.00 2.69
772 783 1.974265 TGAAAGACACGGCCATTCAA 58.026 45.000 2.24 0.00 0.00 2.69
773 784 1.974265 TTGAAAGACACGGCCATTCA 58.026 45.000 2.24 0.18 0.00 2.57
774 785 2.552315 TCTTTGAAAGACACGGCCATTC 59.448 45.455 3.02 0.00 31.20 2.67
775 786 2.582052 TCTTTGAAAGACACGGCCATT 58.418 42.857 3.02 0.00 31.20 3.16
776 787 2.270352 TCTTTGAAAGACACGGCCAT 57.730 45.000 3.02 0.00 31.20 4.40
777 788 1.879380 CATCTTTGAAAGACACGGCCA 59.121 47.619 10.18 0.00 41.01 5.36
778 789 2.151202 TCATCTTTGAAAGACACGGCC 58.849 47.619 10.18 0.00 41.01 6.13
779 790 3.251004 ACTTCATCTTTGAAAGACACGGC 59.749 43.478 10.18 0.00 41.22 5.68
780 791 4.511454 TGACTTCATCTTTGAAAGACACGG 59.489 41.667 10.18 4.33 41.22 4.94
781 792 5.657470 TGACTTCATCTTTGAAAGACACG 57.343 39.130 10.18 2.35 41.22 4.49
782 793 7.475840 ACTTTGACTTCATCTTTGAAAGACAC 58.524 34.615 10.18 0.00 41.22 3.67
783 794 7.554118 AGACTTTGACTTCATCTTTGAAAGACA 59.446 33.333 10.18 0.00 41.22 3.41
784 795 7.924940 AGACTTTGACTTCATCTTTGAAAGAC 58.075 34.615 10.18 0.00 41.22 3.01
785 796 8.511604 AAGACTTTGACTTCATCTTTGAAAGA 57.488 30.769 10.39 10.39 41.22 2.52
791 802 7.503566 TCATCCAAAGACTTTGACTTCATCTTT 59.496 33.333 26.14 0.16 43.26 2.52
792 803 7.000472 TCATCCAAAGACTTTGACTTCATCTT 59.000 34.615 26.14 0.00 43.26 2.40
793 804 6.429385 GTCATCCAAAGACTTTGACTTCATCT 59.571 38.462 26.14 2.21 43.26 2.90
794 805 6.429385 AGTCATCCAAAGACTTTGACTTCATC 59.571 38.462 26.14 11.58 43.24 2.92
795 806 6.302269 AGTCATCCAAAGACTTTGACTTCAT 58.698 36.000 26.14 9.20 43.24 2.57
796 807 5.684704 AGTCATCCAAAGACTTTGACTTCA 58.315 37.500 26.14 7.51 43.24 3.02
806 817 6.738114 TCAAATTGTCAAGTCATCCAAAGAC 58.262 36.000 0.00 0.00 36.26 3.01
807 818 6.957920 TCAAATTGTCAAGTCATCCAAAGA 57.042 33.333 0.00 0.00 0.00 2.52
808 819 7.117236 CCATTCAAATTGTCAAGTCATCCAAAG 59.883 37.037 0.00 0.00 0.00 2.77
809 820 6.930164 CCATTCAAATTGTCAAGTCATCCAAA 59.070 34.615 0.00 0.00 0.00 3.28
810 821 6.457355 CCATTCAAATTGTCAAGTCATCCAA 58.543 36.000 0.00 0.00 0.00 3.53
811 822 5.047164 CCCATTCAAATTGTCAAGTCATCCA 60.047 40.000 0.00 0.00 0.00 3.41
812 823 5.185635 TCCCATTCAAATTGTCAAGTCATCC 59.814 40.000 0.00 0.00 0.00 3.51
813 824 6.271488 TCCCATTCAAATTGTCAAGTCATC 57.729 37.500 0.00 0.00 0.00 2.92
814 825 6.669125 TTCCCATTCAAATTGTCAAGTCAT 57.331 33.333 0.00 0.00 0.00 3.06
815 826 6.570186 CGATTCCCATTCAAATTGTCAAGTCA 60.570 38.462 0.00 0.00 0.00 3.41
816 827 5.801947 CGATTCCCATTCAAATTGTCAAGTC 59.198 40.000 0.00 0.00 0.00 3.01
817 828 5.336690 CCGATTCCCATTCAAATTGTCAAGT 60.337 40.000 0.00 0.00 0.00 3.16
818 829 5.104374 CCGATTCCCATTCAAATTGTCAAG 58.896 41.667 0.00 0.00 0.00 3.02
819 830 4.526262 ACCGATTCCCATTCAAATTGTCAA 59.474 37.500 0.00 0.00 0.00 3.18
820 831 4.085733 ACCGATTCCCATTCAAATTGTCA 58.914 39.130 0.00 0.00 0.00 3.58
821 832 4.718940 ACCGATTCCCATTCAAATTGTC 57.281 40.909 0.00 0.00 0.00 3.18
822 833 5.261216 ACTACCGATTCCCATTCAAATTGT 58.739 37.500 0.00 0.00 0.00 2.71
823 834 5.835113 ACTACCGATTCCCATTCAAATTG 57.165 39.130 0.00 0.00 0.00 2.32
824 835 5.394115 GCAACTACCGATTCCCATTCAAATT 60.394 40.000 0.00 0.00 0.00 1.82
825 836 4.097892 GCAACTACCGATTCCCATTCAAAT 59.902 41.667 0.00 0.00 0.00 2.32
883 897 7.134163 CCAATGCTTGTGTATGTGTACATATG 58.866 38.462 14.76 0.00 42.43 1.78
893 907 2.159338 GGACTGCCAATGCTTGTGTATG 60.159 50.000 0.00 0.00 38.71 2.39
894 908 2.094675 GGACTGCCAATGCTTGTGTAT 58.905 47.619 0.00 0.00 38.71 2.29
895 909 1.073763 AGGACTGCCAATGCTTGTGTA 59.926 47.619 0.00 0.00 38.71 2.90
896 910 0.178981 AGGACTGCCAATGCTTGTGT 60.179 50.000 0.00 0.00 38.71 3.72
897 911 0.242825 CAGGACTGCCAATGCTTGTG 59.757 55.000 0.00 0.00 38.71 3.33
898 912 2.649831 CAGGACTGCCAATGCTTGT 58.350 52.632 0.00 0.00 38.71 3.16
947 961 4.813161 CGGATGATACATTGAGATATGGGC 59.187 45.833 0.00 0.00 0.00 5.36
1095 1112 3.119065 GGAGAGCTGTGGAACCTACTAAC 60.119 52.174 0.00 0.00 34.36 2.34
1262 1279 1.396996 GTGCAACAACACGAGACTTGT 59.603 47.619 0.00 0.00 36.32 3.16
1339 1365 2.626840 GTGGATTCTTGTGAGGAGAGC 58.373 52.381 0.00 0.00 0.00 4.09
1407 1433 8.928448 AGATTAAGATACTGCAACCTATTCAGA 58.072 33.333 0.00 0.00 0.00 3.27
1431 1457 5.305585 CCACTAAGGTTGTTTGAGCTAAGA 58.694 41.667 0.00 0.00 0.00 2.10
1476 1502 1.005340 CTCGAAGCTGAGAACATGCC 58.995 55.000 0.00 0.00 38.28 4.40
1890 1923 3.985019 TTCGGGAAAACAGCAGGTATA 57.015 42.857 0.00 0.00 0.00 1.47
1926 1959 5.528690 TGATGCCAAGATAAGATACTGCAAC 59.471 40.000 0.00 0.00 0.00 4.17
1985 2018 5.052481 GCCAGCAAAGTGAAGAAAAATTCT 58.948 37.500 0.00 0.00 43.15 2.40
2111 2249 4.525487 TGTTGTAAATAGAGACTGGGACGT 59.475 41.667 0.00 0.00 0.00 4.34
2166 2305 4.039609 GGAATTTCCCCTGCCAGAATATTG 59.960 45.833 3.89 0.00 0.00 1.90
2194 2333 3.545703 CTGGAAGGGTGTATCCAATGTC 58.454 50.000 0.00 0.00 44.77 3.06
2232 2371 4.382254 CCATGGAATTTGTTCACTCCCATG 60.382 45.833 5.56 0.00 45.39 3.66
2293 2432 5.554822 TTATTGCCGAGGTAAATGTGTTC 57.445 39.130 0.00 0.00 0.00 3.18
2415 2554 2.552155 GGTGCAGTTGGTCAATGAGGTA 60.552 50.000 0.00 0.00 0.00 3.08
2554 2693 5.047660 GCTGGTCTATCTCTTGTGGTATAGG 60.048 48.000 0.00 0.00 0.00 2.57
2574 2713 2.033299 ACGTTTGATGTTTGTGAGCTGG 59.967 45.455 0.00 0.00 0.00 4.85
3069 3208 5.973565 GCCTCTCAAATTCGTGAAATATTGG 59.026 40.000 0.00 0.00 0.00 3.16
3321 3460 2.233431 TGAGGTGTGCAGCTTTTGTTTT 59.767 40.909 5.34 0.00 39.57 2.43
3377 3516 4.419522 ACGCATGATAACAGAACCAAAC 57.580 40.909 0.00 0.00 0.00 2.93
5547 5798 2.344203 CCTTCTCTCACCGTCGGCT 61.344 63.158 12.28 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.