Multiple sequence alignment - TraesCS1A01G249300

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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 TraesCS1A01G249300 chr1A 100.000 2822 0 0 1 2822 441185702 441182881 0.000000e+00 5212.0
1 TraesCS1A01G249300 chr1A 89.127 699 61 8 1007 1690 589867237 589866539 0.000000e+00 856.0
2 TraesCS1A01G249300 chr1A 83.096 491 57 15 1224 1709 441112904 441112435 9.350000e-115 424.0
3 TraesCS1A01G249300 chr1B 88.641 1435 98 33 536 1937 457380088 457378686 0.000000e+00 1687.0
4 TraesCS1A01G249300 chr1B 84.838 587 36 24 1 551 457380672 457380103 2.470000e-150 542.0
5 TraesCS1A01G249300 chr1B 88.915 424 29 11 2370 2785 457378187 457377774 9.020000e-140 507.0
6 TraesCS1A01G249300 chr1B 85.595 479 50 12 1232 1709 457322698 457322238 4.230000e-133 484.0
7 TraesCS1A01G249300 chr1B 86.014 286 26 4 2097 2369 457378507 457378223 7.640000e-76 294.0
8 TraesCS1A01G249300 chr1B 91.667 132 10 1 1946 2076 457378621 457378490 6.210000e-42 182.0
9 TraesCS1A01G249300 chr1D 90.941 1126 65 13 960 2073 341494975 341493875 0.000000e+00 1480.0
10 TraesCS1A01G249300 chr1D 82.985 670 46 38 1 624 341496093 341495446 6.880000e-151 544.0
11 TraesCS1A01G249300 chr1D 84.043 564 48 25 1224 1779 341478285 341477756 3.240000e-139 505.0
12 TraesCS1A01G249300 chr1D 88.995 418 16 10 2370 2785 341493569 341493180 9.080000e-135 490.0
13 TraesCS1A01G249300 chr1D 86.713 286 24 5 2097 2369 341493889 341493605 3.530000e-79 305.0
14 TraesCS1A01G249300 chr3A 89.100 422 27 5 1326 1738 31808744 31808333 9.020000e-140 507.0
15 TraesCS1A01G249300 chr3A 91.418 268 23 0 1007 1274 31809343 31809076 4.440000e-98 368.0
16 TraesCS1A01G249300 chr7A 100.000 32 0 0 2615 2646 204187791 204187760 3.040000e-05 60.2
17 TraesCS1A01G249300 chr3D 100.000 29 0 0 2618 2646 81825987 81825959 1.000000e-03 54.7
18 TraesCS1A01G249300 chr3B 100.000 29 0 0 2618 2646 423810229 423810201 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G249300 chr1A 441182881 441185702 2821 True 5212.00 5212 100.0000 1 2822 1 chr1A.!!$R2 2821
1 TraesCS1A01G249300 chr1A 589866539 589867237 698 True 856.00 856 89.1270 1007 1690 1 chr1A.!!$R3 683
2 TraesCS1A01G249300 chr1B 457377774 457380672 2898 True 642.40 1687 88.0150 1 2785 5 chr1B.!!$R2 2784
3 TraesCS1A01G249300 chr1D 341493180 341496093 2913 True 704.75 1480 87.4085 1 2785 4 chr1D.!!$R2 2784
4 TraesCS1A01G249300 chr1D 341477756 341478285 529 True 505.00 505 84.0430 1224 1779 1 chr1D.!!$R1 555
5 TraesCS1A01G249300 chr3A 31808333 31809343 1010 True 437.50 507 90.2590 1007 1738 2 chr3A.!!$R1 731

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
261 301 0.037590 TTGCGGCATTTGGGTCTACT 59.962 50.0 2.28 0.0 0.0 2.57 F
826 990 0.110823 CGGCTCCGCATTTTATACGC 60.111 55.0 0.00 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 2150 0.530870 GCAGTAGCTCCCGAATGTCC 60.531 60.0 0.00 0.00 37.91 4.02 R
2366 2978 0.234884 GTGTTGACGCTGCAGGTTAC 59.765 55.0 17.12 13.25 0.00 2.50 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
20 21 1.870055 CTTTGCTGCTGCCGTTCCAT 61.870 55.000 13.47 0.00 38.71 3.41
38 39 0.461961 ATCCGAAAAGGCGAGGAGAG 59.538 55.000 0.00 0.00 40.77 3.20
39 40 0.611062 TCCGAAAAGGCGAGGAGAGA 60.611 55.000 0.00 0.00 40.77 3.10
40 41 0.458716 CCGAAAAGGCGAGGAGAGAC 60.459 60.000 0.00 0.00 0.00 3.36
41 42 0.798771 CGAAAAGGCGAGGAGAGACG 60.799 60.000 0.00 0.00 0.00 4.18
76 98 2.752238 CGTGGGGAGAGCTCGAGT 60.752 66.667 15.13 0.23 0.00 4.18
98 120 4.357918 TCAACCCTGAAGAAGAAGAAGG 57.642 45.455 0.00 0.00 0.00 3.46
100 122 1.352687 ACCCTGAAGAAGAAGAAGGCC 59.647 52.381 0.00 0.00 0.00 5.19
101 123 1.632920 CCCTGAAGAAGAAGAAGGCCT 59.367 52.381 0.00 0.00 0.00 5.19
102 124 2.355615 CCCTGAAGAAGAAGAAGGCCTC 60.356 54.545 5.23 0.00 0.00 4.70
103 125 2.355615 CCTGAAGAAGAAGAAGGCCTCC 60.356 54.545 5.23 0.00 0.00 4.30
104 126 2.571202 CTGAAGAAGAAGAAGGCCTCCT 59.429 50.000 5.23 0.00 33.87 3.69
105 127 2.304180 TGAAGAAGAAGAAGGCCTCCTG 59.696 50.000 5.23 0.00 32.13 3.86
115 143 4.120755 GCCTCCTGCCCTTCCCTG 62.121 72.222 0.00 0.00 0.00 4.45
144 172 2.979240 GCCTAGAGCAAAGCTGTAAGT 58.021 47.619 0.00 0.00 39.88 2.24
145 173 2.933260 GCCTAGAGCAAAGCTGTAAGTC 59.067 50.000 0.00 0.00 39.88 3.01
150 178 3.056179 AGAGCAAAGCTGTAAGTCTCTCC 60.056 47.826 0.00 0.00 39.88 3.71
151 179 2.027653 AGCAAAGCTGTAAGTCTCTCCC 60.028 50.000 0.00 0.00 37.57 4.30
154 182 2.153034 AGCTGTAAGTCTCTCCCTCC 57.847 55.000 0.00 0.00 35.30 4.30
229 268 5.665459 GCATAATGCTATCCTACCTACCTG 58.335 45.833 0.00 0.00 40.96 4.00
234 273 2.487372 GCTATCCTACCTACCTGCGTAC 59.513 54.545 0.00 0.00 0.00 3.67
235 274 3.810033 GCTATCCTACCTACCTGCGTACT 60.810 52.174 0.00 0.00 0.00 2.73
236 275 4.564406 GCTATCCTACCTACCTGCGTACTA 60.564 50.000 0.00 0.00 0.00 1.82
237 276 4.654389 ATCCTACCTACCTGCGTACTAT 57.346 45.455 0.00 0.00 0.00 2.12
238 277 4.013267 TCCTACCTACCTGCGTACTATC 57.987 50.000 0.00 0.00 0.00 2.08
239 278 3.649981 TCCTACCTACCTGCGTACTATCT 59.350 47.826 0.00 0.00 0.00 1.98
240 279 4.002316 CCTACCTACCTGCGTACTATCTC 58.998 52.174 0.00 0.00 0.00 2.75
241 280 2.861274 ACCTACCTGCGTACTATCTCC 58.139 52.381 0.00 0.00 0.00 3.71
242 281 2.442502 ACCTACCTGCGTACTATCTCCT 59.557 50.000 0.00 0.00 0.00 3.69
260 300 0.451783 CTTGCGGCATTTGGGTCTAC 59.548 55.000 2.28 0.00 0.00 2.59
261 301 0.037590 TTGCGGCATTTGGGTCTACT 59.962 50.000 2.28 0.00 0.00 2.57
286 326 0.259938 GGATTCCCACCCAATCTGCT 59.740 55.000 0.00 0.00 31.82 4.24
292 332 1.303888 CACCCAATCTGCTGTGCCT 60.304 57.895 0.00 0.00 0.00 4.75
299 339 2.283145 ATCTGCTGTGCCTTTCTTGT 57.717 45.000 0.00 0.00 0.00 3.16
300 340 1.311859 TCTGCTGTGCCTTTCTTGTG 58.688 50.000 0.00 0.00 0.00 3.33
414 463 3.440415 GTGCCGGCTACTTTGGGC 61.440 66.667 29.70 0.00 45.76 5.36
419 468 4.815108 GGCTACTTTGGGCGGGGG 62.815 72.222 0.00 0.00 0.00 5.40
421 470 4.041762 CTACTTTGGGCGGGGGCA 62.042 66.667 0.00 0.00 0.00 5.36
433 482 2.445155 GGGGCAGTGGATTTGGGT 59.555 61.111 0.00 0.00 0.00 4.51
436 485 2.568090 GCAGTGGATTTGGGTGCG 59.432 61.111 0.00 0.00 0.00 5.34
470 519 1.202818 GGAGTGTTTCTTGCCACCTCT 60.203 52.381 0.00 0.00 31.88 3.69
528 577 9.656323 AGGGTTTAGGATTTCCCTTTATAAATC 57.344 33.333 0.00 0.00 46.99 2.17
539 588 7.739498 TCCCTTTATAAATCAGGCGAAATAC 57.261 36.000 0.00 0.00 0.00 1.89
545 623 8.827177 TTATAAATCAGGCGAAATACTACCAG 57.173 34.615 0.00 0.00 0.00 4.00
602 680 0.902531 GGAGCAACACCCAGCTACTA 59.097 55.000 0.00 0.00 42.04 1.82
603 681 1.405661 GGAGCAACACCCAGCTACTAC 60.406 57.143 0.00 0.00 42.04 2.73
604 682 1.550976 GAGCAACACCCAGCTACTACT 59.449 52.381 0.00 0.00 42.04 2.57
607 685 2.484264 GCAACACCCAGCTACTACTTTG 59.516 50.000 0.00 0.00 0.00 2.77
608 686 3.740115 CAACACCCAGCTACTACTTTGT 58.260 45.455 0.00 0.00 0.00 2.83
610 688 4.432980 ACACCCAGCTACTACTTTGTTT 57.567 40.909 0.00 0.00 0.00 2.83
611 689 4.134563 ACACCCAGCTACTACTTTGTTTG 58.865 43.478 0.00 0.00 0.00 2.93
613 691 4.578928 CACCCAGCTACTACTTTGTTTGTT 59.421 41.667 0.00 0.00 0.00 2.83
614 692 4.578928 ACCCAGCTACTACTTTGTTTGTTG 59.421 41.667 0.00 0.00 0.00 3.33
615 693 4.537015 CCAGCTACTACTTTGTTTGTTGC 58.463 43.478 0.00 0.00 0.00 4.17
616 694 4.537015 CAGCTACTACTTTGTTTGTTGCC 58.463 43.478 0.00 0.00 33.13 4.52
617 695 4.275936 CAGCTACTACTTTGTTTGTTGCCT 59.724 41.667 0.00 0.00 33.13 4.75
618 696 5.468746 CAGCTACTACTTTGTTTGTTGCCTA 59.531 40.000 0.00 0.00 33.13 3.93
620 698 6.371825 AGCTACTACTTTGTTTGTTGCCTATC 59.628 38.462 0.00 0.00 33.13 2.08
621 699 6.371825 GCTACTACTTTGTTTGTTGCCTATCT 59.628 38.462 0.00 0.00 0.00 1.98
622 700 7.094762 GCTACTACTTTGTTTGTTGCCTATCTT 60.095 37.037 0.00 0.00 0.00 2.40
623 701 7.203255 ACTACTTTGTTTGTTGCCTATCTTC 57.797 36.000 0.00 0.00 0.00 2.87
641 738 7.281999 CCTATCTTCATCTTCTGAAAGGGAAAC 59.718 40.741 0.00 0.00 43.20 2.78
647 744 3.073946 TCTTCTGAAAGGGAAACGGGAAT 59.926 43.478 0.00 0.00 33.03 3.01
651 748 2.888414 TGAAAGGGAAACGGGAATGAAC 59.112 45.455 0.00 0.00 0.00 3.18
690 845 5.804473 TGCTTGTTAAATTCTTGTGTGTGTG 59.196 36.000 0.00 0.00 0.00 3.82
693 848 6.260870 TGTTAAATTCTTGTGTGTGTGTGT 57.739 33.333 0.00 0.00 0.00 3.72
694 849 6.089476 TGTTAAATTCTTGTGTGTGTGTGTG 58.911 36.000 0.00 0.00 0.00 3.82
695 850 4.782019 AAATTCTTGTGTGTGTGTGTGT 57.218 36.364 0.00 0.00 0.00 3.72
743 901 7.118422 GGAAACTGTATTCCGATTAGTATGC 57.882 40.000 6.17 0.00 39.54 3.14
746 904 5.230942 ACTGTATTCCGATTAGTATGCTGC 58.769 41.667 0.00 0.00 0.00 5.25
749 907 0.663269 TCCGATTAGTATGCTGCGCG 60.663 55.000 0.00 0.00 0.00 6.86
755 913 0.664466 TAGTATGCTGCGCGATGAGC 60.664 55.000 12.10 14.51 43.95 4.26
768 926 4.452890 GCGATGAGCGAGCTAAATTTAA 57.547 40.909 0.00 0.00 44.57 1.52
771 929 5.502544 GCGATGAGCGAGCTAAATTTAAAGT 60.503 40.000 0.00 0.00 44.57 2.66
773 931 6.625310 CGATGAGCGAGCTAAATTTAAAGTTC 59.375 38.462 3.84 0.00 44.57 3.01
774 932 6.795098 TGAGCGAGCTAAATTTAAAGTTCA 57.205 33.333 3.84 2.77 0.00 3.18
801 965 2.414138 GAGGTACCAAACAACGGAATCG 59.586 50.000 15.94 0.00 43.02 3.34
821 985 1.817941 GGCTCGGCTCCGCATTTTA 60.818 57.895 2.96 0.00 39.59 1.52
826 990 0.110823 CGGCTCCGCATTTTATACGC 60.111 55.000 0.00 0.00 0.00 4.42
827 991 0.941542 GGCTCCGCATTTTATACGCA 59.058 50.000 0.00 0.00 0.00 5.24
828 992 1.069906 GGCTCCGCATTTTATACGCAG 60.070 52.381 0.00 0.00 0.00 5.18
831 995 3.423645 GCTCCGCATTTTATACGCAGATC 60.424 47.826 0.00 0.00 0.00 2.75
859 1025 3.119602 AGCTATGAGTTTGTGCAATGCTG 60.120 43.478 6.82 0.00 0.00 4.41
861 1027 3.738830 ATGAGTTTGTGCAATGCTGTT 57.261 38.095 6.82 0.00 0.00 3.16
863 1029 3.963665 TGAGTTTGTGCAATGCTGTTAC 58.036 40.909 6.82 0.00 0.00 2.50
864 1030 3.379688 TGAGTTTGTGCAATGCTGTTACA 59.620 39.130 6.82 0.00 0.00 2.41
865 1031 3.968649 AGTTTGTGCAATGCTGTTACAG 58.031 40.909 8.18 8.18 34.12 2.74
913 1134 4.767409 ACTAGGATCAACTTTCTTTTGCCC 59.233 41.667 0.00 0.00 0.00 5.36
933 1154 5.486063 TGCCCAACCTTCAAAGTATCTACTA 59.514 40.000 0.00 0.00 34.99 1.82
940 1161 7.721402 ACCTTCAAAGTATCTACTATCTGCTG 58.279 38.462 0.00 0.00 34.99 4.41
942 1163 7.651304 CCTTCAAAGTATCTACTATCTGCTGTG 59.349 40.741 0.00 0.00 34.99 3.66
949 1170 2.814805 ACTATCTGCTGTGCCCATTT 57.185 45.000 0.00 0.00 0.00 2.32
950 1171 3.931907 ACTATCTGCTGTGCCCATTTA 57.068 42.857 0.00 0.00 0.00 1.40
956 1177 4.819769 TCTGCTGTGCCCATTTATTTTTC 58.180 39.130 0.00 0.00 0.00 2.29
968 1189 7.360017 GCCCATTTATTTTTCACTAACAACTGC 60.360 37.037 0.00 0.00 0.00 4.40
970 1191 9.260002 CCATTTATTTTTCACTAACAACTGCTT 57.740 29.630 0.00 0.00 0.00 3.91
1013 1236 2.435805 GTCTGCCCATGGAGTCATCTAA 59.564 50.000 15.22 0.00 0.00 2.10
1024 1247 5.508567 TGGAGTCATCTAAAATTGATGCCA 58.491 37.500 0.00 0.00 40.59 4.92
1086 1309 6.174720 ACAGTATCACAGTCAAAGAAAGGA 57.825 37.500 0.00 0.00 0.00 3.36
1088 1311 6.708054 ACAGTATCACAGTCAAAGAAAGGAAG 59.292 38.462 0.00 0.00 0.00 3.46
1164 1387 9.212641 TCAGTTCAGAAGAATGAAGAATTACTG 57.787 33.333 0.00 0.00 39.78 2.74
1197 1420 5.424252 TGGAATAAAGGAGTCGACCACTATT 59.576 40.000 13.01 8.18 34.41 1.73
1445 1956 4.325472 GCAACTGCAATTCAGCTGTATTTC 59.675 41.667 15.16 11.61 46.76 2.17
1446 1957 5.706916 CAACTGCAATTCAGCTGTATTTCT 58.293 37.500 15.16 0.00 46.76 2.52
1447 1958 5.972107 ACTGCAATTCAGCTGTATTTCTT 57.028 34.783 15.16 1.18 46.76 2.52
1448 1959 6.336842 ACTGCAATTCAGCTGTATTTCTTT 57.663 33.333 15.16 0.87 46.76 2.52
1533 2061 6.402442 GGTTTTTCAACAATGCATTCTATGCC 60.402 38.462 9.53 1.98 44.23 4.40
1622 2150 2.303022 TCAGGCTGAAAGTGAACCTAGG 59.697 50.000 16.28 7.41 35.30 3.02
1686 2216 0.178950 TGTCACCAGAGAGACTGCCT 60.179 55.000 0.00 0.00 44.52 4.75
1729 2259 7.391554 TCAGTGTCAAAGGATCTAAAGATTTGG 59.608 37.037 0.00 0.00 34.37 3.28
1758 2288 3.367743 AGTGGTAGCGCCGACGAA 61.368 61.111 2.29 0.00 43.93 3.85
1938 2479 5.339695 GGGGTGTTTGATTAGTAGGGATTCA 60.340 44.000 0.00 0.00 0.00 2.57
1942 2483 9.403583 GGTGTTTGATTAGTAGGGATTCAATTA 57.596 33.333 0.00 0.00 0.00 1.40
1976 2573 6.954944 TCTGTAACACTGTAATTCTTGCAAC 58.045 36.000 0.00 0.00 0.00 4.17
2032 2629 1.530323 ACAACCGGCCTGAACATTAC 58.470 50.000 10.96 0.00 0.00 1.89
2057 2655 1.768275 TCCTGTGATATCCAATGCCGT 59.232 47.619 0.00 0.00 0.00 5.68
2058 2656 1.875514 CCTGTGATATCCAATGCCGTG 59.124 52.381 0.00 0.00 0.00 4.94
2059 2657 1.875514 CTGTGATATCCAATGCCGTGG 59.124 52.381 0.00 0.00 40.33 4.94
2060 2658 1.211703 TGTGATATCCAATGCCGTGGT 59.788 47.619 0.00 0.00 39.88 4.16
2061 2659 2.297701 GTGATATCCAATGCCGTGGTT 58.702 47.619 0.00 0.00 39.88 3.67
2062 2660 2.687935 GTGATATCCAATGCCGTGGTTT 59.312 45.455 0.00 0.00 39.88 3.27
2063 2661 3.880490 GTGATATCCAATGCCGTGGTTTA 59.120 43.478 0.00 0.00 39.88 2.01
2064 2662 4.336993 GTGATATCCAATGCCGTGGTTTAA 59.663 41.667 0.00 0.00 39.88 1.52
2065 2663 4.336993 TGATATCCAATGCCGTGGTTTAAC 59.663 41.667 0.00 0.00 39.88 2.01
2066 2664 2.279935 TCCAATGCCGTGGTTTAACT 57.720 45.000 2.91 0.00 39.88 2.24
2067 2665 1.883275 TCCAATGCCGTGGTTTAACTG 59.117 47.619 2.91 0.00 39.88 3.16
2068 2666 1.067915 CCAATGCCGTGGTTTAACTGG 60.068 52.381 0.00 0.00 33.63 4.00
2069 2667 1.883275 CAATGCCGTGGTTTAACTGGA 59.117 47.619 5.93 0.00 0.00 3.86
2070 2668 2.491693 CAATGCCGTGGTTTAACTGGAT 59.508 45.455 5.93 0.00 0.00 3.41
2071 2669 1.816074 TGCCGTGGTTTAACTGGATC 58.184 50.000 5.93 0.00 0.00 3.36
2072 2670 1.349688 TGCCGTGGTTTAACTGGATCT 59.650 47.619 5.93 0.00 0.00 2.75
2073 2671 2.568062 TGCCGTGGTTTAACTGGATCTA 59.432 45.455 5.93 0.00 0.00 1.98
2074 2672 3.199071 TGCCGTGGTTTAACTGGATCTAT 59.801 43.478 5.93 0.00 0.00 1.98
2075 2673 4.196971 GCCGTGGTTTAACTGGATCTATT 58.803 43.478 5.93 0.00 0.00 1.73
2076 2674 5.104859 TGCCGTGGTTTAACTGGATCTATTA 60.105 40.000 5.93 0.00 0.00 0.98
2077 2675 5.995897 GCCGTGGTTTAACTGGATCTATTAT 59.004 40.000 5.93 0.00 0.00 1.28
2078 2676 6.485648 GCCGTGGTTTAACTGGATCTATTATT 59.514 38.462 5.93 0.00 0.00 1.40
2079 2677 7.012989 GCCGTGGTTTAACTGGATCTATTATTT 59.987 37.037 5.93 0.00 0.00 1.40
2080 2678 9.550406 CCGTGGTTTAACTGGATCTATTATTTA 57.450 33.333 0.00 0.00 0.00 1.40
2128 2726 3.290948 TCTGTTGCCAAGTAACCTGTT 57.709 42.857 0.00 0.00 0.00 3.16
2160 2759 2.440409 TCTGGCTTTTCCAAGATCTGC 58.560 47.619 0.00 0.00 46.01 4.26
2171 2772 1.099879 AAGATCTGCGAATGGCCTGC 61.100 55.000 3.32 3.35 42.61 4.85
2173 2774 1.077212 ATCTGCGAATGGCCTGCTT 60.077 52.632 3.32 0.00 42.61 3.91
2174 2775 1.099879 ATCTGCGAATGGCCTGCTTC 61.100 55.000 3.32 3.70 42.61 3.86
2183 2786 2.350514 GCCTGCTTCCTCTGTGCT 59.649 61.111 0.00 0.00 0.00 4.40
2188 2791 2.027745 CCTGCTTCCTCTGTGCTTCTTA 60.028 50.000 0.00 0.00 0.00 2.10
2200 2803 7.369803 TCTGTGCTTCTTATGATTCTGTTTC 57.630 36.000 0.00 0.00 0.00 2.78
2233 2836 6.305272 ACAGGATCTGTGATGATTTACACT 57.695 37.500 0.00 0.00 43.63 3.55
2296 2899 5.437946 TCCTGAACACGAGACTATGACTAT 58.562 41.667 0.00 0.00 0.00 2.12
2300 2903 5.880887 TGAACACGAGACTATGACTATGAGT 59.119 40.000 0.00 0.00 0.00 3.41
2366 2978 6.699204 AGTCAGAATATTTGAGTGATGTAGCG 59.301 38.462 6.99 0.00 0.00 4.26
2378 3025 0.806102 ATGTAGCGTAACCTGCAGCG 60.806 55.000 8.66 7.71 31.03 5.18
2389 3036 3.832237 CTGCAGCGTCAACACCCCT 62.832 63.158 0.00 0.00 0.00 4.79
2390 3037 2.345991 GCAGCGTCAACACCCCTA 59.654 61.111 0.00 0.00 0.00 3.53
2391 3038 2.033194 GCAGCGTCAACACCCCTAC 61.033 63.158 0.00 0.00 0.00 3.18
2392 3039 1.736645 CAGCGTCAACACCCCTACG 60.737 63.158 0.00 0.00 38.34 3.51
2393 3040 2.433664 GCGTCAACACCCCTACGG 60.434 66.667 0.00 0.00 35.93 4.02
2420 3067 8.684520 ACGCTACTCTAGTTTTGTTATCTGTAT 58.315 33.333 0.00 0.00 0.00 2.29
2479 3127 5.010282 AGAAACCATCCATACTGGTGTTTC 58.990 41.667 19.27 19.27 46.29 2.78
2491 3139 7.418368 CCATACTGGTGTTTCTCTGTCTGATAT 60.418 40.741 0.00 0.00 31.35 1.63
2509 3157 9.230932 GTCTGATATTCAGCTTTAAATTTCTGC 57.769 33.333 0.00 0.00 43.95 4.26
2605 3253 4.973168 AGAAAGCCACAATTCTAGTCACA 58.027 39.130 0.00 0.00 34.24 3.58
2633 3283 7.422089 GGGGATTGTAAAATTATACTCCCTCCA 60.422 40.741 18.41 0.00 38.99 3.86
2656 3306 5.941555 ATCCATATTAATCGAGAGGGGAC 57.058 43.478 0.00 0.00 0.00 4.46
2670 3322 5.662456 GAGAGGGGACTGTACTACAATTTC 58.338 45.833 0.00 0.00 44.43 2.17
2671 3323 5.091552 AGAGGGGACTGTACTACAATTTCA 58.908 41.667 0.00 0.00 44.43 2.69
2718 3370 4.828829 TCCTACGATTTTTCCTCCACTTC 58.171 43.478 0.00 0.00 0.00 3.01
2736 3388 7.334090 TCCACTTCTCCTATGAATCAAAGAAG 58.666 38.462 18.17 18.17 43.29 2.85
2754 3406 5.461032 AGAAGAACTTGTCACCAGAGTAG 57.539 43.478 0.00 0.00 0.00 2.57
2763 3415 7.607250 ACTTGTCACCAGAGTAGAAAGATAAG 58.393 38.462 0.00 0.00 0.00 1.73
2801 3456 9.545105 AATGTGATAGAATTTGCTCAAAACAAA 57.455 25.926 0.00 0.00 40.98 2.83
2802 3457 9.715121 ATGTGATAGAATTTGCTCAAAACAAAT 57.285 25.926 0.00 0.00 46.85 2.32
2807 3462 9.691362 ATAGAATTTGCTCAAAACAAATAACGT 57.309 25.926 2.45 0.00 44.76 3.99
2808 3463 7.840489 AGAATTTGCTCAAAACAAATAACGTG 58.160 30.769 2.45 0.00 44.76 4.49
2809 3464 7.704472 AGAATTTGCTCAAAACAAATAACGTGA 59.296 29.630 2.45 0.00 44.76 4.35
2810 3465 7.945033 ATTTGCTCAAAACAAATAACGTGAT 57.055 28.000 0.00 0.00 43.94 3.06
2811 3466 9.469807 AATTTGCTCAAAACAAATAACGTGATA 57.530 25.926 2.45 0.00 44.76 2.15
2812 3467 8.500837 TTTGCTCAAAACAAATAACGTGATAG 57.499 30.769 0.00 0.00 32.27 2.08
2813 3468 7.197071 TGCTCAAAACAAATAACGTGATAGT 57.803 32.000 0.00 0.00 0.00 2.12
2814 3469 8.312896 TGCTCAAAACAAATAACGTGATAGTA 57.687 30.769 0.00 0.00 0.00 1.82
2815 3470 8.440059 TGCTCAAAACAAATAACGTGATAGTAG 58.560 33.333 0.00 0.00 0.00 2.57
2816 3471 8.440833 GCTCAAAACAAATAACGTGATAGTAGT 58.559 33.333 0.00 0.00 0.00 2.73
2821 3476 9.695526 AAACAAATAACGTGATAGTAGTACACA 57.304 29.630 2.52 0.00 34.69 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.017177 TCGCCTTTTCGGATGGAACG 61.017 55.000 0.00 0.00 33.42 3.95
20 21 0.611062 TCTCTCCTCGCCTTTTCGGA 60.611 55.000 0.00 0.00 33.16 4.55
76 98 4.718961 CCTTCTTCTTCTTCAGGGTTGAA 58.281 43.478 0.00 0.00 40.92 2.69
98 120 4.120755 CAGGGAAGGGCAGGAGGC 62.121 72.222 0.00 0.00 43.74 4.70
100 122 2.285668 TCCAGGGAAGGGCAGGAG 60.286 66.667 0.00 0.00 0.00 3.69
101 123 2.285668 CTCCAGGGAAGGGCAGGA 60.286 66.667 0.00 0.00 0.00 3.86
102 124 4.120755 GCTCCAGGGAAGGGCAGG 62.121 72.222 0.00 0.00 0.00 4.85
103 125 3.013932 AGCTCCAGGGAAGGGCAG 61.014 66.667 1.56 0.00 0.00 4.85
104 126 3.011517 GAGCTCCAGGGAAGGGCA 61.012 66.667 0.87 0.00 0.00 5.36
105 127 2.549169 CTTGAGCTCCAGGGAAGGGC 62.549 65.000 12.15 0.00 0.00 5.19
144 172 2.015726 GGAGGGAGGGAGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
145 173 2.612251 GGAGGGAGGGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
241 280 0.451783 GTAGACCCAAATGCCGCAAG 59.548 55.000 0.00 0.00 0.00 4.01
242 281 0.037590 AGTAGACCCAAATGCCGCAA 59.962 50.000 0.00 0.00 0.00 4.85
286 326 1.881973 GATGAGCACAAGAAAGGCACA 59.118 47.619 0.00 0.00 32.93 4.57
292 332 4.631131 TCGAAAGAGATGAGCACAAGAAA 58.369 39.130 0.00 0.00 34.84 2.52
358 407 2.414594 GGCATGCAGATTTCCGCC 59.585 61.111 21.36 0.00 0.00 6.13
361 410 2.414594 GCGGGCATGCAGATTTCC 59.585 61.111 21.36 9.23 34.15 3.13
414 463 2.755469 CCAAATCCACTGCCCCCG 60.755 66.667 0.00 0.00 0.00 5.73
415 464 2.364186 CCCAAATCCACTGCCCCC 60.364 66.667 0.00 0.00 0.00 5.40
416 465 1.984026 CACCCAAATCCACTGCCCC 60.984 63.158 0.00 0.00 0.00 5.80
417 466 2.649129 GCACCCAAATCCACTGCCC 61.649 63.158 0.00 0.00 0.00 5.36
418 467 2.973082 GCACCCAAATCCACTGCC 59.027 61.111 0.00 0.00 0.00 4.85
419 468 2.568090 CGCACCCAAATCCACTGC 59.432 61.111 0.00 0.00 0.00 4.40
420 469 2.993471 GCCGCACCCAAATCCACTG 61.993 63.158 0.00 0.00 0.00 3.66
421 470 2.676471 GCCGCACCCAAATCCACT 60.676 61.111 0.00 0.00 0.00 4.00
436 485 0.747283 CACTCCTTCCTGATGCAGCC 60.747 60.000 0.00 0.00 0.00 4.85
470 519 6.160483 AGGAGGGGATAAACAACCATAAAA 57.840 37.500 0.00 0.00 0.00 1.52
528 577 6.513180 TCTATTTCTGGTAGTATTTCGCCTG 58.487 40.000 0.00 0.00 0.00 4.85
539 588 8.151596 GGGTTATTCCTCTTCTATTTCTGGTAG 58.848 40.741 0.00 0.00 36.25 3.18
602 680 6.491403 AGATGAAGATAGGCAACAAACAAAGT 59.509 34.615 0.00 0.00 41.41 2.66
603 681 6.917533 AGATGAAGATAGGCAACAAACAAAG 58.082 36.000 0.00 0.00 41.41 2.77
604 682 6.899393 AGATGAAGATAGGCAACAAACAAA 57.101 33.333 0.00 0.00 41.41 2.83
607 685 6.372659 TCAGAAGATGAAGATAGGCAACAAAC 59.627 38.462 0.00 0.00 34.48 2.93
608 686 6.475504 TCAGAAGATGAAGATAGGCAACAAA 58.524 36.000 0.00 0.00 34.48 2.83
610 688 5.682234 TCAGAAGATGAAGATAGGCAACA 57.318 39.130 0.00 0.00 34.48 3.33
621 699 4.072131 CCGTTTCCCTTTCAGAAGATGAA 58.928 43.478 0.00 0.00 46.31 2.57
622 700 3.559171 CCCGTTTCCCTTTCAGAAGATGA 60.559 47.826 0.00 0.00 34.71 2.92
623 701 2.749621 CCCGTTTCCCTTTCAGAAGATG 59.250 50.000 0.00 0.00 34.71 2.90
690 845 2.865551 CAAGGAATGCACCAAAACACAC 59.134 45.455 0.00 0.00 0.00 3.82
749 907 7.464358 TGAACTTTAAATTTAGCTCGCTCATC 58.536 34.615 0.00 0.00 0.00 2.92
755 913 6.797033 CCACACTGAACTTTAAATTTAGCTCG 59.203 38.462 0.00 0.00 0.00 5.03
768 926 2.404559 TGGTACCTCCACACTGAACTT 58.595 47.619 14.36 0.00 41.93 2.66
818 982 2.381589 CTGCGTCGATCTGCGTATAAA 58.618 47.619 0.00 0.00 41.80 1.40
821 985 1.658717 GCTGCGTCGATCTGCGTAT 60.659 57.895 0.00 0.00 41.80 3.06
826 990 1.001924 ACTCATAGCTGCGTCGATCTG 60.002 52.381 0.00 0.00 0.00 2.90
827 991 1.313772 ACTCATAGCTGCGTCGATCT 58.686 50.000 0.00 0.00 0.00 2.75
828 992 2.126914 AACTCATAGCTGCGTCGATC 57.873 50.000 0.00 0.00 0.00 3.69
831 995 1.059692 CACAAACTCATAGCTGCGTCG 59.940 52.381 0.00 0.00 0.00 5.12
859 1025 3.945921 GAGGTATTTTCCCAGGCTGTAAC 59.054 47.826 14.43 0.38 0.00 2.50
861 1027 2.508300 GGAGGTATTTTCCCAGGCTGTA 59.492 50.000 14.43 0.00 0.00 2.74
863 1029 1.284785 TGGAGGTATTTTCCCAGGCTG 59.715 52.381 7.75 7.75 33.62 4.85
864 1030 1.566231 CTGGAGGTATTTTCCCAGGCT 59.434 52.381 0.00 0.00 41.76 4.58
865 1031 1.564348 TCTGGAGGTATTTTCCCAGGC 59.436 52.381 0.00 0.00 44.66 4.85
866 1032 4.079787 TCAATCTGGAGGTATTTTCCCAGG 60.080 45.833 0.00 0.00 44.66 4.45
867 1033 5.116084 TCAATCTGGAGGTATTTTCCCAG 57.884 43.478 0.00 0.00 45.63 4.45
868 1034 5.015178 AGTTCAATCTGGAGGTATTTTCCCA 59.985 40.000 0.00 0.00 33.62 4.37
913 1134 8.200792 AGCAGATAGTAGATACTTTGAAGGTTG 58.799 37.037 0.00 0.00 37.73 3.77
933 1154 5.046448 TGAAAAATAAATGGGCACAGCAGAT 60.046 36.000 0.00 0.00 0.00 2.90
940 1161 7.655732 AGTTGTTAGTGAAAAATAAATGGGCAC 59.344 33.333 0.00 0.00 0.00 5.01
942 1163 7.360017 GCAGTTGTTAGTGAAAAATAAATGGGC 60.360 37.037 0.00 0.00 0.00 5.36
972 1193 9.765795 GGCAGACATAAGTACTGTATAAAAGAT 57.234 33.333 0.00 0.00 34.60 2.40
975 1198 7.853299 TGGGCAGACATAAGTACTGTATAAAA 58.147 34.615 0.00 0.00 34.60 1.52
976 1199 7.426606 TGGGCAGACATAAGTACTGTATAAA 57.573 36.000 0.00 0.00 34.60 1.40
979 1202 5.221722 CCATGGGCAGACATAAGTACTGTAT 60.222 44.000 2.85 0.00 34.60 2.29
1013 1236 2.629137 TGCTTGTCACTGGCATCAATTT 59.371 40.909 0.00 0.00 0.00 1.82
1024 1247 1.066286 GCTCTCCAGATGCTTGTCACT 60.066 52.381 0.00 0.00 0.00 3.41
1086 1309 5.238624 GGACCTTAGGAAACTTGGTACTT 57.761 43.478 4.77 0.00 43.24 2.24
1088 1311 4.041321 ACAGGACCTTAGGAAACTTGGTAC 59.959 45.833 4.77 0.00 43.24 3.34
1101 1324 1.337823 GCAAGAAGCGACAGGACCTTA 60.338 52.381 0.00 0.00 0.00 2.69
1135 1358 6.957984 TTCTTCATTCTTCTGAACTGATCG 57.042 37.500 0.00 0.00 34.71 3.69
1164 1387 5.758784 CGACTCCTTTATTCCATTAGAACCC 59.241 44.000 0.00 0.00 37.29 4.11
1197 1420 0.968405 GCACCTTCTGGCCATGAAAA 59.032 50.000 5.51 0.00 36.63 2.29
1533 2061 0.907486 TGCTGATTCCTCCCACTCTG 59.093 55.000 0.00 0.00 0.00 3.35
1622 2150 0.530870 GCAGTAGCTCCCGAATGTCC 60.531 60.000 0.00 0.00 37.91 4.02
1686 2216 3.627123 CACTGACACAATGAACCTGAACA 59.373 43.478 0.00 0.00 0.00 3.18
1897 2427 2.110011 ACCCCCAGAACAACTTAATGCT 59.890 45.455 0.00 0.00 0.00 3.79
1976 2573 7.602517 TTGTGAACATTTTAAACAAAGTGGG 57.397 32.000 0.00 0.00 0.00 4.61
2018 2615 2.271800 GACTGAGTAATGTTCAGGCCG 58.728 52.381 0.00 0.00 43.51 6.13
2021 2618 4.021104 TCACAGGACTGAGTAATGTTCAGG 60.021 45.833 6.29 0.00 44.96 3.86
2032 2629 4.063689 GCATTGGATATCACAGGACTGAG 58.936 47.826 6.29 0.00 0.00 3.35
2091 2689 9.295308 TGGCAACAGATCAGGTTAAACCTTTTC 62.295 40.741 0.00 0.00 45.76 2.29
2092 2690 7.592923 TGGCAACAGATCAGGTTAAACCTTTT 61.593 38.462 0.00 0.00 45.76 2.27
2093 2691 6.160285 TGGCAACAGATCAGGTTAAACCTTT 61.160 40.000 0.00 0.00 45.76 3.11
2094 2692 4.691376 TGGCAACAGATCAGGTTAAACCTT 60.691 41.667 0.00 0.00 45.76 3.50
2128 2726 2.519771 AAGCCAGATTCATCTTGCCA 57.480 45.000 8.83 0.00 44.17 4.92
2160 2759 1.094073 CAGAGGAAGCAGGCCATTCG 61.094 60.000 5.01 0.00 0.00 3.34
2171 2772 6.258287 CAGAATCATAAGAAGCACAGAGGAAG 59.742 42.308 0.00 0.00 0.00 3.46
2173 2774 5.188555 ACAGAATCATAAGAAGCACAGAGGA 59.811 40.000 0.00 0.00 0.00 3.71
2174 2775 5.426504 ACAGAATCATAAGAAGCACAGAGG 58.573 41.667 0.00 0.00 0.00 3.69
2183 2786 5.931724 TGCGACTGAAACAGAATCATAAGAA 59.068 36.000 5.76 0.00 35.18 2.52
2188 2791 5.643348 TGTTATGCGACTGAAACAGAATCAT 59.357 36.000 5.76 7.41 35.18 2.45
2200 2803 2.862536 CACAGATCCTGTTATGCGACTG 59.137 50.000 0.00 0.00 42.59 3.51
2296 2899 0.250252 TGCTTTGGCGATGTCACTCA 60.250 50.000 0.00 0.00 42.25 3.41
2300 2903 1.532523 TTCATGCTTTGGCGATGTCA 58.467 45.000 0.00 0.00 42.25 3.58
2366 2978 0.234884 GTGTTGACGCTGCAGGTTAC 59.765 55.000 17.12 13.25 0.00 2.50
2389 3036 3.753272 ACAAAACTAGAGTAGCGTCCGTA 59.247 43.478 0.00 0.00 0.00 4.02
2390 3037 2.555757 ACAAAACTAGAGTAGCGTCCGT 59.444 45.455 0.00 0.00 0.00 4.69
2391 3038 3.213249 ACAAAACTAGAGTAGCGTCCG 57.787 47.619 0.00 0.00 0.00 4.79
2392 3039 6.472808 CAGATAACAAAACTAGAGTAGCGTCC 59.527 42.308 0.00 0.00 0.00 4.79
2393 3040 7.028361 ACAGATAACAAAACTAGAGTAGCGTC 58.972 38.462 0.00 0.00 0.00 5.19
2491 3139 6.514947 ACACATGCAGAAATTTAAAGCTGAA 58.485 32.000 15.60 8.49 0.00 3.02
2509 3157 2.092753 AGGACTGCCCAGATAACACATG 60.093 50.000 1.69 0.00 37.41 3.21
2605 3253 8.126241 AGGGAGTATAATTTTACAATCCCCTT 57.874 34.615 20.49 8.47 45.25 3.95
2633 3283 6.026186 AGTCCCCTCTCGATTAATATGGATT 58.974 40.000 0.00 0.00 0.00 3.01
2656 3306 5.700832 TCCTTGCACTGAAATTGTAGTACAG 59.299 40.000 2.68 0.00 35.14 2.74
2670 3322 4.947645 TGAATTTTCCTTTCCTTGCACTG 58.052 39.130 0.00 0.00 0.00 3.66
2671 3323 5.813513 ATGAATTTTCCTTTCCTTGCACT 57.186 34.783 0.00 0.00 0.00 4.40
2701 3353 3.944087 AGGAGAAGTGGAGGAAAAATCG 58.056 45.455 0.00 0.00 0.00 3.34
2703 3355 6.642733 TCATAGGAGAAGTGGAGGAAAAAT 57.357 37.500 0.00 0.00 0.00 1.82
2718 3370 8.558973 ACAAGTTCTTCTTTGATTCATAGGAG 57.441 34.615 6.17 6.17 33.63 3.69
2736 3388 5.844004 TCTTTCTACTCTGGTGACAAGTTC 58.156 41.667 0.00 0.00 42.06 3.01
2785 3440 7.763172 TCACGTTATTTGTTTTGAGCAAATT 57.237 28.000 7.81 0.00 41.96 1.82
2786 3441 7.945033 ATCACGTTATTTGTTTTGAGCAAAT 57.055 28.000 7.66 7.66 45.22 2.32
2787 3442 8.132362 ACTATCACGTTATTTGTTTTGAGCAAA 58.868 29.630 0.00 0.00 39.69 3.68
2788 3443 7.644490 ACTATCACGTTATTTGTTTTGAGCAA 58.356 30.769 0.00 0.00 0.00 3.91
2789 3444 7.197071 ACTATCACGTTATTTGTTTTGAGCA 57.803 32.000 0.00 0.00 0.00 4.26
2790 3445 8.440833 ACTACTATCACGTTATTTGTTTTGAGC 58.559 33.333 0.00 0.00 0.00 4.26
2795 3450 9.695526 TGTGTACTACTATCACGTTATTTGTTT 57.304 29.630 0.00 0.00 35.20 2.83


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

AutoCloner maintained by Alex Coulton.