Multiple sequence alignment - TraesCS1B01G229700

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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 TraesCS1B01G229700 chr1B 100.000 5405 0 0 1 5405 412259399 412253995 0.000000e+00 9982.0
1 TraesCS1B01G229700 chr1D 94.229 4176 138 36 833 4995 305111119 305115204 0.000000e+00 6281.0
2 TraesCS1B01G229700 chr1D 91.859 823 49 2 3 825 470590765 470591569 0.000000e+00 1133.0
3 TraesCS1B01G229700 chr1D 88.462 702 60 10 138 832 78978474 78977787 0.000000e+00 828.0
4 TraesCS1B01G229700 chr1D 84.956 339 38 8 5041 5368 305115463 305115799 1.120000e-86 331.0
5 TraesCS1B01G229700 chr1D 91.057 123 11 0 13 135 78978708 78978586 3.350000e-37 167.0
6 TraesCS1B01G229700 chr1A 94.534 1555 52 10 2091 3636 382229388 382230918 0.000000e+00 2370.0
7 TraesCS1B01G229700 chr1A 93.135 1617 57 23 3627 5218 382232856 382234443 0.000000e+00 2322.0
8 TraesCS1B01G229700 chr1A 93.299 970 35 11 833 1801 382228297 382229237 0.000000e+00 1404.0
9 TraesCS1B01G229700 chr1A 96.855 159 1 2 1916 2074 382229246 382229400 4.150000e-66 263.0
10 TraesCS1B01G229700 chr5B 99.640 833 3 0 1 833 641042052 641041220 0.000000e+00 1522.0
11 TraesCS1B01G229700 chr5B 83.746 1292 141 27 3453 4741 420934080 420935305 0.000000e+00 1158.0
12 TraesCS1B01G229700 chr5B 83.230 1294 145 37 3453 4741 581762235 581763461 0.000000e+00 1122.0
13 TraesCS1B01G229700 chr3D 84.734 1297 135 35 3450 4741 15296385 15297623 0.000000e+00 1240.0
14 TraesCS1B01G229700 chr3D 84.462 1300 140 31 3446 4741 54336934 54338175 0.000000e+00 1225.0
15 TraesCS1B01G229700 chr3D 88.068 176 20 1 658 833 24173241 24173415 1.970000e-49 207.0
16 TraesCS1B01G229700 chr6A 84.231 1300 143 25 3446 4741 585065575 585066816 0.000000e+00 1208.0
17 TraesCS1B01G229700 chrUn 83.913 1293 137 35 3453 4741 117284153 117285378 0.000000e+00 1170.0
18 TraesCS1B01G229700 chr4A 94.980 737 37 0 97 833 546013826 546014562 0.000000e+00 1157.0
19 TraesCS1B01G229700 chr4A 93.548 62 4 0 1 62 546013762 546013823 5.760000e-15 93.5
20 TraesCS1B01G229700 chr6B 93.540 743 43 1 97 839 209373756 209373019 0.000000e+00 1101.0
21 TraesCS1B01G229700 chr3B 82.521 1293 137 42 3453 4741 51866355 51867562 0.000000e+00 1053.0
22 TraesCS1B01G229700 chr7B 92.672 696 33 2 145 840 10565456 10564779 0.000000e+00 987.0
23 TraesCS1B01G229700 chr7B 94.937 79 4 0 1 79 10565541 10565463 2.040000e-24 124.0
24 TraesCS1B01G229700 chr2D 88.202 178 20 1 658 835 133054060 133054236 1.530000e-50 211.0
25 TraesCS1B01G229700 chr2D 83.019 212 34 2 1263 1473 114532607 114532817 1.990000e-44 191.0
26 TraesCS1B01G229700 chr2A 83.491 212 33 2 1263 1473 115753429 115753639 4.270000e-46 196.0
27 TraesCS1B01G229700 chr5D 85.556 180 25 1 656 835 488190925 488191103 2.570000e-43 187.0


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 TraesCS1B01G229700 chr1B 412253995 412259399 5404 True 9982.00 9982 100.00000 1 5405 1 chr1B.!!$R1 5404
1 TraesCS1B01G229700 chr1D 305111119 305115799 4680 False 3306.00 6281 89.59250 833 5368 2 chr1D.!!$F2 4535
2 TraesCS1B01G229700 chr1D 470590765 470591569 804 False 1133.00 1133 91.85900 3 825 1 chr1D.!!$F1 822
3 TraesCS1B01G229700 chr1D 78977787 78978708 921 True 497.50 828 89.75950 13 832 2 chr1D.!!$R1 819
4 TraesCS1B01G229700 chr1A 382228297 382234443 6146 False 1589.75 2370 94.45575 833 5218 4 chr1A.!!$F1 4385
5 TraesCS1B01G229700 chr5B 641041220 641042052 832 True 1522.00 1522 99.64000 1 833 1 chr5B.!!$R1 832
6 TraesCS1B01G229700 chr5B 420934080 420935305 1225 False 1158.00 1158 83.74600 3453 4741 1 chr5B.!!$F1 1288
7 TraesCS1B01G229700 chr5B 581762235 581763461 1226 False 1122.00 1122 83.23000 3453 4741 1 chr5B.!!$F2 1288
8 TraesCS1B01G229700 chr3D 15296385 15297623 1238 False 1240.00 1240 84.73400 3450 4741 1 chr3D.!!$F1 1291
9 TraesCS1B01G229700 chr3D 54336934 54338175 1241 False 1225.00 1225 84.46200 3446 4741 1 chr3D.!!$F3 1295
10 TraesCS1B01G229700 chr6A 585065575 585066816 1241 False 1208.00 1208 84.23100 3446 4741 1 chr6A.!!$F1 1295
11 TraesCS1B01G229700 chrUn 117284153 117285378 1225 False 1170.00 1170 83.91300 3453 4741 1 chrUn.!!$F1 1288
12 TraesCS1B01G229700 chr4A 546013762 546014562 800 False 625.25 1157 94.26400 1 833 2 chr4A.!!$F1 832
13 TraesCS1B01G229700 chr6B 209373019 209373756 737 True 1101.00 1101 93.54000 97 839 1 chr6B.!!$R1 742
14 TraesCS1B01G229700 chr3B 51866355 51867562 1207 False 1053.00 1053 82.52100 3453 4741 1 chr3B.!!$F1 1288
15 TraesCS1B01G229700 chr7B 10564779 10565541 762 True 555.50 987 93.80450 1 840 2 chr7B.!!$R1 839

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
171 281 1.400737 GTAGACTATGCGGTGGAGGT 58.599 55.000 0.00 0.0 0.00 3.85 F
1404 1522 2.749865 CGCCAACAACATCCGCGAT 61.750 57.895 8.23 0.0 45.41 4.58 F
2382 2503 0.179073 CACTGCCGTCCTATCAAGGG 60.179 60.000 0.00 0.0 43.84 3.95 F
2541 2662 0.244178 GAGTCACCGAGTGGAACCTC 59.756 60.000 4.52 0.0 37.80 3.85 F
2578 2699 0.537188 CACGCAGGGAGACAGGTAAT 59.463 55.000 0.00 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1583 1.186267 AGTGGGAGTCGGACCTTGAC 61.186 60.000 4.14 0.00 36.60 3.18 R
3289 3414 0.107456 AGACCATATGGAGGCAAGCG 59.893 55.000 28.77 0.00 38.94 4.68 R
3298 3423 2.979814 TGTCACCGAAGACCATATGG 57.020 50.000 20.68 20.68 37.73 2.74 R
3351 3476 4.116747 ACAACGAAATGCAAACCTTCAA 57.883 36.364 0.00 0.00 0.00 2.69 R
4558 6639 0.034756 AGCACAATCCGTACTGCACA 59.965 50.000 5.46 0.00 31.71 4.57 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
171 281 1.400737 GTAGACTATGCGGTGGAGGT 58.599 55.000 0.00 0.00 0.00 3.85
931 1049 2.930040 GCCACTGCATATATATTCGCGT 59.070 45.455 5.77 0.00 37.47 6.01
1281 1399 4.572571 TTCCCGCCGCTGGTGTTT 62.573 61.111 0.26 0.00 0.00 2.83
1291 1409 3.172106 TGGTGTTTGCGGGGGAGA 61.172 61.111 0.00 0.00 0.00 3.71
1404 1522 2.749865 CGCCAACAACATCCGCGAT 61.750 57.895 8.23 0.00 45.41 4.58
1499 1617 3.554934 TCCCACTTTCATCCATGCATAC 58.445 45.455 0.00 0.00 0.00 2.39
1500 1618 2.291465 CCCACTTTCATCCATGCATACG 59.709 50.000 0.00 0.00 0.00 3.06
1558 1676 2.522638 CCTACCGTTGGATTCGCGC 61.523 63.158 0.00 0.00 0.00 6.86
1601 1719 3.565482 TGTCCTTCTGACTTGTGAATTGC 59.435 43.478 0.00 0.00 44.75 3.56
1645 1763 1.743394 CGGGATTTGGTTCCTGTAAGC 59.257 52.381 0.00 0.00 37.38 3.09
1817 1935 5.292765 ACTGTCATAGGCTGTTATGAATCG 58.707 41.667 0.00 0.00 40.64 3.34
1858 1976 5.416271 TTTTACTCTCTTTCCTATGGCGT 57.584 39.130 0.00 0.00 0.00 5.68
1859 1977 5.416271 TTTACTCTCTTTCCTATGGCGTT 57.584 39.130 0.00 0.00 0.00 4.84
1860 1978 6.534475 TTTACTCTCTTTCCTATGGCGTTA 57.466 37.500 0.00 0.00 0.00 3.18
1861 1979 4.388378 ACTCTCTTTCCTATGGCGTTAC 57.612 45.455 0.00 0.00 0.00 2.50
1862 1980 3.767673 ACTCTCTTTCCTATGGCGTTACA 59.232 43.478 0.00 0.00 0.00 2.41
1863 1981 4.142138 ACTCTCTTTCCTATGGCGTTACAG 60.142 45.833 0.00 0.00 0.00 2.74
1864 1982 3.767673 TCTCTTTCCTATGGCGTTACAGT 59.232 43.478 0.00 0.00 0.00 3.55
1865 1983 4.222145 TCTCTTTCCTATGGCGTTACAGTT 59.778 41.667 0.00 0.00 0.00 3.16
1866 1984 4.901868 TCTTTCCTATGGCGTTACAGTTT 58.098 39.130 0.00 0.00 0.00 2.66
1867 1985 5.310451 TCTTTCCTATGGCGTTACAGTTTT 58.690 37.500 0.00 0.00 0.00 2.43
1868 1986 6.465948 TCTTTCCTATGGCGTTACAGTTTTA 58.534 36.000 0.00 0.00 0.00 1.52
1886 2004 3.478857 TTAAAGGTCTTGCCGAGAACA 57.521 42.857 0.00 0.00 45.00 3.18
1894 2012 4.184629 GTCTTGCCGAGAACATAGATTGT 58.815 43.478 0.00 0.00 41.53 2.71
1913 2031 5.666969 TTGTTGTGTTGTGTATACTGCTC 57.333 39.130 4.17 0.00 0.00 4.26
1914 2032 4.698575 TGTTGTGTTGTGTATACTGCTCA 58.301 39.130 4.17 0.00 0.00 4.26
2022 2142 3.685836 TGCATTCGATTCATCTGCAAG 57.314 42.857 0.89 0.00 39.68 4.01
2024 2144 2.223409 GCATTCGATTCATCTGCAAGCA 60.223 45.455 0.00 0.00 33.13 3.91
2026 2146 4.417506 CATTCGATTCATCTGCAAGCAAA 58.582 39.130 0.00 0.00 0.00 3.68
2027 2147 3.476295 TCGATTCATCTGCAAGCAAAC 57.524 42.857 0.00 0.00 0.00 2.93
2028 2148 3.076621 TCGATTCATCTGCAAGCAAACT 58.923 40.909 0.00 0.00 0.00 2.66
2029 2149 4.252878 TCGATTCATCTGCAAGCAAACTA 58.747 39.130 0.00 0.00 0.00 2.24
2030 2150 4.330894 TCGATTCATCTGCAAGCAAACTAG 59.669 41.667 0.00 0.00 0.00 2.57
2031 2151 4.093998 CGATTCATCTGCAAGCAAACTAGT 59.906 41.667 0.00 0.00 0.00 2.57
2080 2200 7.539712 ACATGAAACTATGAAATGTAGTCCG 57.460 36.000 0.00 0.00 31.44 4.79
2081 2201 7.103641 ACATGAAACTATGAAATGTAGTCCGT 58.896 34.615 0.00 0.00 31.44 4.69
2082 2202 7.606456 ACATGAAACTATGAAATGTAGTCCGTT 59.394 33.333 0.00 0.00 31.44 4.44
2083 2203 7.591006 TGAAACTATGAAATGTAGTCCGTTC 57.409 36.000 0.00 0.00 31.44 3.95
2084 2204 7.383687 TGAAACTATGAAATGTAGTCCGTTCT 58.616 34.615 0.00 0.00 31.44 3.01
2085 2205 8.525316 TGAAACTATGAAATGTAGTCCGTTCTA 58.475 33.333 0.00 0.00 31.44 2.10
2086 2206 9.362539 GAAACTATGAAATGTAGTCCGTTCTAA 57.637 33.333 0.00 0.00 31.44 2.10
2087 2207 9.715121 AAACTATGAAATGTAGTCCGTTCTAAA 57.285 29.630 0.00 0.00 31.44 1.85
2088 2208 9.715121 AACTATGAAATGTAGTCCGTTCTAAAA 57.285 29.630 0.00 0.00 31.44 1.52
2089 2209 9.715121 ACTATGAAATGTAGTCCGTTCTAAAAA 57.285 29.630 0.00 0.00 0.00 1.94
2188 2309 4.970662 TGTTATGCTGAAGAGAAATGCC 57.029 40.909 0.00 0.00 0.00 4.40
2364 2485 3.197983 TCGAGACTAGAGATGGAGTGACA 59.802 47.826 0.00 0.00 0.00 3.58
2382 2503 0.179073 CACTGCCGTCCTATCAAGGG 60.179 60.000 0.00 0.00 43.84 3.95
2400 2521 1.737793 GGGGACATCATCAACAACGAC 59.262 52.381 0.00 0.00 0.00 4.34
2541 2662 0.244178 GAGTCACCGAGTGGAACCTC 59.756 60.000 4.52 0.00 37.80 3.85
2576 2697 2.646175 GCACGCAGGGAGACAGGTA 61.646 63.158 0.00 0.00 0.00 3.08
2578 2699 0.537188 CACGCAGGGAGACAGGTAAT 59.463 55.000 0.00 0.00 0.00 1.89
2585 2706 5.357032 CGCAGGGAGACAGGTAATTAAATTT 59.643 40.000 0.00 0.00 0.00 1.82
2632 2753 5.541845 AGCCTTTATGCAAAACTCTTTTCC 58.458 37.500 0.00 0.00 0.00 3.13
2635 2756 5.221621 CCTTTATGCAAAACTCTTTTCCCCA 60.222 40.000 0.00 0.00 0.00 4.96
2716 2839 1.202440 CCCCATTCAATGTCATTGCCG 60.202 52.381 19.02 10.21 40.05 5.69
2759 2882 9.089601 CAACGGTTCTGGTTTAATTTTTACTTT 57.910 29.630 0.00 0.00 0.00 2.66
2782 2905 6.642707 TTGACCTCGTTTGTGGATAATTTT 57.357 33.333 0.00 0.00 32.93 1.82
2865 2988 4.421058 GACAGCATCAGTCACGTGTAATA 58.579 43.478 16.51 0.53 36.06 0.98
2993 3118 3.196469 TGTTCTTCTCTGAGCAGGTATGG 59.804 47.826 4.52 0.00 0.00 2.74
3018 3143 1.002069 TTGCCCAGAGGGTTCATGAT 58.998 50.000 0.00 0.00 46.51 2.45
3289 3414 1.815003 CCAAAGCACCCATCAGAGTTC 59.185 52.381 0.00 0.00 0.00 3.01
3298 3423 1.005340 CATCAGAGTTCGCTTGCCTC 58.995 55.000 0.00 0.00 0.00 4.70
3321 3446 4.443457 CCATATGGTCTTCGGTGACATCTT 60.443 45.833 14.09 0.00 38.61 2.40
3334 3459 6.258507 TCGGTGACATCTTTTCATATGACATG 59.741 38.462 4.48 8.02 32.12 3.21
3338 3463 7.695201 GTGACATCTTTTCATATGACATGTGTG 59.305 37.037 17.42 13.10 32.12 3.82
3351 3476 5.670485 TGACATGTGTGTTTACTGAAGTCT 58.330 37.500 1.15 0.00 39.09 3.24
3463 3588 3.890756 ACCATCAATGCTTCACAAGTCAA 59.109 39.130 0.00 0.00 0.00 3.18
3495 3620 1.843851 TCAGTTTTGTGGTCTCCAGGT 59.156 47.619 0.00 0.00 32.34 4.00
3995 6073 6.742559 ACCTACTTATGGTCGGTATTTCAT 57.257 37.500 0.00 0.00 41.42 2.57
3998 6076 5.036117 ACTTATGGTCGGTATTTCATGCT 57.964 39.130 0.00 0.00 0.00 3.79
4045 6123 1.336440 TGTTTTCTGGAACCACATGCG 59.664 47.619 0.00 0.00 0.00 4.73
4308 6386 4.329545 GACCCCAGGCTGAACGCA 62.330 66.667 17.94 0.00 41.67 5.24
4320 6398 2.730672 GAACGCATCGCAGTCGCTT 61.731 57.895 0.00 0.00 35.30 4.68
4433 6511 6.118170 TCAATCTTAGATTTCTTCCCTGCAG 58.882 40.000 6.78 6.78 0.00 4.41
4568 6649 2.755836 AGCTGTTTTTGTGCAGTACG 57.244 45.000 0.00 0.00 35.33 3.67
4569 6650 1.333619 AGCTGTTTTTGTGCAGTACGG 59.666 47.619 0.00 0.00 35.33 4.02
4663 6744 6.815089 AGAGATTACATGAGACCTGACAATC 58.185 40.000 0.00 0.00 0.00 2.67
4781 6863 4.069232 TTCTCAGCCACTCGCCCG 62.069 66.667 0.00 0.00 38.78 6.13
4785 6867 2.436646 CAGCCACTCGCCCGATTT 60.437 61.111 0.00 0.00 38.78 2.17
4799 6881 3.366374 GCCCGATTTTTCTTCCTCTGTTG 60.366 47.826 0.00 0.00 0.00 3.33
4800 6882 3.366374 CCCGATTTTTCTTCCTCTGTTGC 60.366 47.826 0.00 0.00 0.00 4.17
4827 6909 1.503347 GGGATCTCCTCCTCCTCTCTT 59.497 57.143 0.00 0.00 44.28 2.85
4900 6983 2.563179 TCCCCTCGTTTTTCTCTCTCAG 59.437 50.000 0.00 0.00 0.00 3.35
4912 6995 0.455005 TCTCTCAGCTGCATCTGTCG 59.545 55.000 16.66 9.71 35.63 4.35
4980 7063 3.524606 GGCTAGTGTCGGCGCCTA 61.525 66.667 26.68 11.79 39.42 3.93
5014 7253 2.835420 TGCTACAACCAGCAGCCA 59.165 55.556 0.00 0.00 46.41 4.75
5015 7254 1.600636 TGCTACAACCAGCAGCCAC 60.601 57.895 0.00 0.00 46.41 5.01
5016 7255 2.335712 GCTACAACCAGCAGCCACC 61.336 63.158 0.00 0.00 41.40 4.61
5060 7302 2.693074 TCCGATGCTGCAACTGTAGATA 59.307 45.455 6.36 0.00 0.00 1.98
5063 7308 4.151335 CCGATGCTGCAACTGTAGATATTC 59.849 45.833 6.36 0.00 0.00 1.75
5074 7319 7.678218 GCAACTGTAGATATTCTTTTGCTGGAG 60.678 40.741 0.00 0.00 36.13 3.86
5191 7489 0.449388 GCCTCGAACCAGCAAGAATG 59.551 55.000 0.00 0.00 0.00 2.67
5193 7491 2.154462 CCTCGAACCAGCAAGAATGTT 58.846 47.619 0.00 0.00 0.00 2.71
5194 7492 2.554032 CCTCGAACCAGCAAGAATGTTT 59.446 45.455 0.00 0.00 0.00 2.83
5195 7493 3.558505 CTCGAACCAGCAAGAATGTTTG 58.441 45.455 0.00 0.00 0.00 2.93
5204 7502 2.750948 CAAGAATGTTTGCTTGCTGCT 58.249 42.857 0.00 0.00 43.37 4.24
5206 7504 1.000506 AGAATGTTTGCTTGCTGCTGG 59.999 47.619 0.00 0.00 43.37 4.85
5277 7597 1.472552 CGGCGAGGTTACATCCATTGA 60.473 52.381 0.00 0.00 0.00 2.57
5283 7603 1.593006 GGTTACATCCATTGAGCGACG 59.407 52.381 0.00 0.00 0.00 5.12
5288 7608 2.811431 ACATCCATTGAGCGACGAAAAA 59.189 40.909 0.00 0.00 0.00 1.94
5293 7613 3.300009 CATTGAGCGACGAAAAAGCTTT 58.700 40.909 5.69 5.69 41.84 3.51
5352 7672 1.352622 TGGGAGTTGCAACCCTCACT 61.353 55.000 25.62 6.02 45.74 3.41
5368 7688 1.073025 ACTGGCGAAGTTGCATCCA 59.927 52.632 0.00 0.00 34.57 3.41
5369 7689 0.537143 ACTGGCGAAGTTGCATCCAA 60.537 50.000 0.00 0.00 34.57 3.53
5387 7707 2.281070 CAGTGGAGCTGCAACCGT 60.281 61.111 10.44 0.00 38.52 4.83
5388 7708 1.893808 CAGTGGAGCTGCAACCGTT 60.894 57.895 10.44 0.00 38.52 4.44
5389 7709 1.152963 AGTGGAGCTGCAACCGTTT 60.153 52.632 10.44 0.00 0.00 3.60
5390 7710 1.166531 AGTGGAGCTGCAACCGTTTC 61.167 55.000 10.44 0.00 0.00 2.78
5391 7711 1.153066 TGGAGCTGCAACCGTTTCA 60.153 52.632 5.01 0.00 0.00 2.69
5392 7712 0.537143 TGGAGCTGCAACCGTTTCAT 60.537 50.000 5.01 0.00 0.00 2.57
5393 7713 1.271108 TGGAGCTGCAACCGTTTCATA 60.271 47.619 5.01 0.00 0.00 2.15
5394 7714 1.398390 GGAGCTGCAACCGTTTCATAG 59.602 52.381 0.00 0.00 0.00 2.23
5395 7715 2.076863 GAGCTGCAACCGTTTCATAGT 58.923 47.619 1.02 0.00 0.00 2.12
5396 7716 1.806542 AGCTGCAACCGTTTCATAGTG 59.193 47.619 1.02 0.00 0.00 2.74
5397 7717 1.135689 GCTGCAACCGTTTCATAGTGG 60.136 52.381 0.00 0.00 0.00 4.00
5398 7718 0.878416 TGCAACCGTTTCATAGTGGC 59.122 50.000 0.00 0.00 0.00 5.01
5399 7719 0.179200 GCAACCGTTTCATAGTGGCG 60.179 55.000 0.00 0.00 0.00 5.69
5400 7720 0.179200 CAACCGTTTCATAGTGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
5401 7721 0.321298 AACCGTTTCATAGTGGCGCT 60.321 50.000 7.64 5.62 0.00 5.92
5402 7722 1.019278 ACCGTTTCATAGTGGCGCTG 61.019 55.000 11.58 0.00 0.00 5.18
5403 7723 1.060937 CGTTTCATAGTGGCGCTGC 59.939 57.895 11.58 0.00 0.00 5.25
5404 7724 1.634757 CGTTTCATAGTGGCGCTGCA 61.635 55.000 11.58 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 1.792026 AGAGGCAGGAGGATGAGGATA 59.208 52.381 0.00 0.00 0.00 2.59
171 281 2.662596 GGTCACTCCGTGGCATGA 59.337 61.111 8.63 0.00 40.26 3.07
908 1026 2.285834 GCGAATATATATGCAGTGGCGC 60.286 50.000 0.00 0.00 45.35 6.53
931 1049 0.391130 ATGCCGCGAGAAGCTGTAAA 60.391 50.000 8.23 0.00 45.59 2.01
1039 1157 4.373116 GAAGGGCGACAGGTGCGA 62.373 66.667 0.00 0.00 0.00 5.10
1213 1331 4.430765 CGCTGCGTCCGGGTACTT 62.431 66.667 14.93 0.00 0.00 2.24
1452 1570 1.442526 CCTTGACGATGGGCATCTGC 61.443 60.000 0.00 0.00 41.14 4.26
1465 1583 1.186267 AGTGGGAGTCGGACCTTGAC 61.186 60.000 4.14 0.00 36.60 3.18
1499 1617 2.951229 ATTAAGGAAGGGGTATGCCG 57.049 50.000 0.00 0.00 34.97 5.69
1500 1618 4.341235 GTCAAATTAAGGAAGGGGTATGCC 59.659 45.833 0.00 0.00 0.00 4.40
1558 1676 2.225382 AAACCCTCGTTAATTGGGGG 57.775 50.000 12.83 12.83 44.97 5.40
1601 1719 3.129109 CCATGACAGGACTTGATCATCG 58.871 50.000 0.00 0.00 30.33 3.84
1645 1763 3.611057 GCAAAGTCTGAACTGCATTGAGG 60.611 47.826 0.00 0.00 35.36 3.86
1853 1971 4.453751 AGACCTTTAAAACTGTAACGCCA 58.546 39.130 0.00 0.00 0.00 5.69
1854 1972 5.209977 CAAGACCTTTAAAACTGTAACGCC 58.790 41.667 0.00 0.00 0.00 5.68
1855 1973 4.673761 GCAAGACCTTTAAAACTGTAACGC 59.326 41.667 0.00 0.00 0.00 4.84
1856 1974 5.209977 GGCAAGACCTTTAAAACTGTAACG 58.790 41.667 0.00 0.00 34.51 3.18
1857 1975 5.007921 TCGGCAAGACCTTTAAAACTGTAAC 59.992 40.000 0.00 0.00 35.61 2.50
1858 1976 5.124645 TCGGCAAGACCTTTAAAACTGTAA 58.875 37.500 0.00 0.00 35.61 2.41
1859 1977 4.706035 TCGGCAAGACCTTTAAAACTGTA 58.294 39.130 0.00 0.00 35.61 2.74
1860 1978 3.547746 TCGGCAAGACCTTTAAAACTGT 58.452 40.909 0.00 0.00 35.61 3.55
1861 1979 3.813166 TCTCGGCAAGACCTTTAAAACTG 59.187 43.478 0.00 0.00 35.61 3.16
1862 1980 4.081322 TCTCGGCAAGACCTTTAAAACT 57.919 40.909 0.00 0.00 35.61 2.66
1863 1981 4.035909 TGTTCTCGGCAAGACCTTTAAAAC 59.964 41.667 0.00 0.00 35.61 2.43
1864 1982 4.200874 TGTTCTCGGCAAGACCTTTAAAA 58.799 39.130 0.00 0.00 35.61 1.52
1865 1983 3.811083 TGTTCTCGGCAAGACCTTTAAA 58.189 40.909 0.00 0.00 35.61 1.52
1866 1984 3.478857 TGTTCTCGGCAAGACCTTTAA 57.521 42.857 0.00 0.00 35.61 1.52
1867 1985 3.695830 ATGTTCTCGGCAAGACCTTTA 57.304 42.857 0.00 0.00 35.61 1.85
1868 1986 2.568623 ATGTTCTCGGCAAGACCTTT 57.431 45.000 0.00 0.00 35.61 3.11
1886 2004 7.824289 AGCAGTATACACAACACAACAATCTAT 59.176 33.333 5.50 0.00 0.00 1.98
1894 2012 5.546526 TCATGAGCAGTATACACAACACAA 58.453 37.500 5.50 0.00 0.00 3.33
1913 2031 2.355756 CCCAACAGTTATTCCGCTCATG 59.644 50.000 0.00 0.00 0.00 3.07
1914 2032 2.643551 CCCAACAGTTATTCCGCTCAT 58.356 47.619 0.00 0.00 0.00 2.90
2092 2212 9.905713 ACATGGTTAATCACTACATTTCATAGT 57.094 29.630 0.00 0.00 32.98 2.12
2095 2215 9.241919 TGAACATGGTTAATCACTACATTTCAT 57.758 29.630 0.00 0.00 0.00 2.57
2096 2216 8.628630 TGAACATGGTTAATCACTACATTTCA 57.371 30.769 0.00 0.00 0.00 2.69
2188 2309 7.928103 CAATCATGGAAGGAGAACATTTAGAG 58.072 38.462 0.00 0.00 0.00 2.43
2264 2385 6.913170 ACATAGTGCCACAAATCTTTTGTAG 58.087 36.000 5.38 0.38 0.00 2.74
2364 2485 1.338136 CCCCTTGATAGGACGGCAGT 61.338 60.000 0.00 0.00 45.05 4.40
2382 2503 2.333926 TCGTCGTTGTTGATGATGTCC 58.666 47.619 0.00 0.00 32.98 4.02
2541 2662 0.601046 TGCTGTGCCTCAGAAAGTCG 60.601 55.000 9.68 0.00 46.27 4.18
2606 2727 7.116376 GGAAAAGAGTTTTGCATAAAGGCTAAC 59.884 37.037 0.00 0.00 40.24 2.34
2607 2728 7.151976 GGAAAAGAGTTTTGCATAAAGGCTAA 58.848 34.615 0.00 0.00 40.24 3.09
2632 2753 2.849942 TCAGATGATATTTGCGGTGGG 58.150 47.619 0.00 0.00 0.00 4.61
2635 2756 6.698008 TTGAATTCAGATGATATTTGCGGT 57.302 33.333 8.41 0.00 0.00 5.68
2741 2864 8.964150 CGAGGTCAAAAGTAAAAATTAAACCAG 58.036 33.333 0.00 0.00 0.00 4.00
2759 2882 6.263392 TGAAAATTATCCACAAACGAGGTCAA 59.737 34.615 0.00 0.00 0.00 3.18
2766 2889 6.442952 TGGACTTGAAAATTATCCACAAACG 58.557 36.000 0.00 0.00 34.50 3.60
2782 2905 6.376864 TGACAAAATCACTTTTCTGGACTTGA 59.623 34.615 0.00 0.00 32.21 3.02
2865 2988 7.945278 TCCTAGAGGATGAATACCTAGCTATT 58.055 38.462 0.00 0.00 39.78 1.73
2882 3005 8.657387 TGATATTTCCTACAGAATCCTAGAGG 57.343 38.462 0.00 0.00 33.44 3.69
2993 3118 4.120755 CCCTCTGGGCAAGCTCCC 62.121 72.222 3.41 3.41 46.73 4.30
3018 3143 1.001020 AAGCATGAACCCGATGGCA 60.001 52.632 0.00 0.00 33.59 4.92
3289 3414 0.107456 AGACCATATGGAGGCAAGCG 59.893 55.000 28.77 0.00 38.94 4.68
3298 3423 2.979814 TGTCACCGAAGACCATATGG 57.020 50.000 20.68 20.68 37.73 2.74
3321 3446 8.614469 TCAGTAAACACACATGTCATATGAAA 57.386 30.769 7.07 1.58 38.45 2.69
3334 3459 5.585047 ACCTTCAAGACTTCAGTAAACACAC 59.415 40.000 0.00 0.00 0.00 3.82
3338 3463 5.971792 GCAAACCTTCAAGACTTCAGTAAAC 59.028 40.000 0.00 0.00 0.00 2.01
3351 3476 4.116747 ACAACGAAATGCAAACCTTCAA 57.883 36.364 0.00 0.00 0.00 2.69
3411 3536 7.575414 TTTGCAATGGAAGTTGAAGTACTTA 57.425 32.000 8.42 0.00 38.43 2.24
3463 3588 8.598041 AGACCACAAAACTGAAAGATCTATACT 58.402 33.333 0.00 0.00 37.43 2.12
3558 3683 8.666573 TCTTCATAGTTGTTAAAAACACGACAA 58.333 29.630 11.11 0.00 41.97 3.18
3995 6073 5.278414 CCATGTCTCATTGTAACAAACAGCA 60.278 40.000 0.00 0.00 39.87 4.41
3998 6076 6.017192 CAGTCCATGTCTCATTGTAACAAACA 60.017 38.462 0.00 0.00 35.88 2.83
4045 6123 6.630444 ACAATGCTATTGGATGTCTCAATC 57.370 37.500 11.76 0.00 36.40 2.67
4088 6166 5.716228 AGTGAAAATTCTGAACCATGCCATA 59.284 36.000 0.00 0.00 0.00 2.74
4433 6511 4.582656 TCCTCTAGCAGCTGAAGATAGTTC 59.417 45.833 20.43 0.00 0.00 3.01
4482 6561 5.505173 TCAAACGGCACCTATACTACTAC 57.495 43.478 0.00 0.00 0.00 2.73
4558 6639 0.034756 AGCACAATCCGTACTGCACA 59.965 50.000 5.46 0.00 31.71 4.57
4568 6649 4.630111 TGAAATTGAACCAAGCACAATCC 58.370 39.130 0.00 0.00 33.90 3.01
4569 6650 5.291971 ACTGAAATTGAACCAAGCACAATC 58.708 37.500 0.00 0.00 33.90 2.67
4663 6744 5.462068 TCAGCAAATACCGAATGAGTAATCG 59.538 40.000 0.00 0.00 38.74 3.34
4781 6863 3.237628 GCGCAACAGAGGAAGAAAAATC 58.762 45.455 0.30 0.00 0.00 2.17
4785 6867 0.889186 GGGCGCAACAGAGGAAGAAA 60.889 55.000 10.83 0.00 0.00 2.52
4827 6909 1.176619 TCACCGGAGAAGACAGCGAA 61.177 55.000 9.46 0.00 0.00 4.70
4854 6937 2.668550 GGCTCGACGGTTGGCTTT 60.669 61.111 0.00 0.00 0.00 3.51
4912 6995 2.181777 TGGTCATCGTCGAGCAGC 59.818 61.111 0.00 0.00 38.43 5.25
4924 7007 2.653115 CTGTCGCAGCTCTGGTCA 59.347 61.111 0.00 0.00 0.00 4.02
4980 7063 4.722700 AAAGCATCAGCCGCCGGT 62.723 61.111 4.45 0.00 43.56 5.28
5043 7282 7.478322 CAAAAGAATATCTACAGTTGCAGCAT 58.522 34.615 2.55 0.00 0.00 3.79
5060 7302 1.203100 AGGTGGCTCCAGCAAAAGAAT 60.203 47.619 18.90 0.00 45.79 2.40
5063 7308 1.530013 CCAGGTGGCTCCAGCAAAAG 61.530 60.000 18.90 6.83 45.79 2.27
5172 7470 0.449388 CATTCTTGCTGGTTCGAGGC 59.551 55.000 0.00 0.00 0.00 4.70
5173 7471 1.813513 ACATTCTTGCTGGTTCGAGG 58.186 50.000 0.00 0.00 0.00 4.63
5174 7472 3.558505 CAAACATTCTTGCTGGTTCGAG 58.441 45.455 0.00 0.00 0.00 4.04
5175 7473 2.287547 GCAAACATTCTTGCTGGTTCGA 60.288 45.455 1.15 0.00 46.66 3.71
5176 7474 2.053627 GCAAACATTCTTGCTGGTTCG 58.946 47.619 1.15 0.00 46.66 3.95
5195 7493 2.821688 GATCTCGCCAGCAGCAAGC 61.822 63.158 0.00 0.00 44.04 4.01
5196 7494 0.743701 AAGATCTCGCCAGCAGCAAG 60.744 55.000 0.00 0.00 44.04 4.01
5277 7597 2.614983 TGGTTAAAGCTTTTTCGTCGCT 59.385 40.909 18.47 0.00 35.09 4.93
5283 7603 2.609491 CCCCGCTGGTTAAAGCTTTTTC 60.609 50.000 18.47 10.53 41.24 2.29
5288 7608 2.361230 GCCCCGCTGGTTAAAGCT 60.361 61.111 0.00 0.00 41.24 3.74
5322 7642 3.785122 AACTCCCACCCACGTTGGC 62.785 63.158 5.40 0.00 35.79 4.52
5352 7672 0.821301 TGTTGGATGCAACTTCGCCA 60.821 50.000 27.36 6.62 36.15 5.69
5371 7691 1.152963 AAACGGTTGCAGCTCCACT 60.153 52.632 0.00 0.00 0.00 4.00
5372 7692 1.282875 GAAACGGTTGCAGCTCCAC 59.717 57.895 0.00 0.00 0.00 4.02
5373 7693 0.537143 ATGAAACGGTTGCAGCTCCA 60.537 50.000 7.73 0.00 0.00 3.86
5374 7694 1.398390 CTATGAAACGGTTGCAGCTCC 59.602 52.381 7.73 0.00 0.00 4.70
5375 7695 2.076863 ACTATGAAACGGTTGCAGCTC 58.923 47.619 7.73 0.00 0.00 4.09
5376 7696 1.806542 CACTATGAAACGGTTGCAGCT 59.193 47.619 7.73 0.00 0.00 4.24
5377 7697 1.135689 CCACTATGAAACGGTTGCAGC 60.136 52.381 7.73 0.00 0.00 5.25
5378 7698 1.135689 GCCACTATGAAACGGTTGCAG 60.136 52.381 7.73 0.00 0.00 4.41
5379 7699 0.878416 GCCACTATGAAACGGTTGCA 59.122 50.000 3.56 3.56 0.00 4.08
5380 7700 0.179200 CGCCACTATGAAACGGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
5381 7701 0.179200 GCGCCACTATGAAACGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
5382 7702 0.321298 AGCGCCACTATGAAACGGTT 60.321 50.000 2.29 0.00 0.00 4.44
5383 7703 1.019278 CAGCGCCACTATGAAACGGT 61.019 55.000 2.29 0.00 34.40 4.83
5384 7704 1.715585 CAGCGCCACTATGAAACGG 59.284 57.895 2.29 0.00 0.00 4.44
5385 7705 1.060937 GCAGCGCCACTATGAAACG 59.939 57.895 2.29 0.00 0.00 3.60
5386 7706 2.170738 TGCAGCGCCACTATGAAAC 58.829 52.632 2.29 0.00 0.00 2.78
5387 7707 4.711892 TGCAGCGCCACTATGAAA 57.288 50.000 2.29 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.