Multiple sequence alignment - TraesCS2B01G584400

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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 TraesCS2B01G584400 chr2B 100.000 2408 0 0 1 2408 771412997 771415404 0.000000e+00 4447.0
1 TraesCS2B01G584400 chr2B 88.345 429 30 14 925 1335 771968258 771967832 4.620000e-137 497.0
2 TraesCS2B01G584400 chr2B 96.078 51 2 0 820 870 771968327 771968277 1.530000e-12 84.2
3 TraesCS2B01G584400 chr2B 100.000 30 0 0 276 305 771413212 771413241 3.340000e-04 56.5
4 TraesCS2B01G584400 chr2B 100.000 30 0 0 216 245 771413272 771413301 3.340000e-04 56.5
5 TraesCS2B01G584400 chr2A 84.514 1524 122 59 784 2252 758588338 758589802 0.000000e+00 1402.0
6 TraesCS2B01G584400 chr2A 91.892 259 11 4 7 261 758710656 758710404 1.060000e-93 353.0
7 TraesCS2B01G584400 chr2A 81.517 211 18 11 653 848 758567886 758568090 1.150000e-33 154.0
8 TraesCS2B01G584400 chr2A 87.200 125 8 1 865 981 758581948 758582072 4.180000e-28 135.0
9 TraesCS2B01G584400 chr2A 89.691 97 4 5 865 956 758580536 758580631 4.210000e-23 119.0
10 TraesCS2B01G584400 chr2D 84.797 1184 63 59 497 1651 628269742 628270837 0.000000e+00 1081.0
11 TraesCS2B01G584400 chr2D 89.401 651 43 11 1633 2274 628573807 628573174 0.000000e+00 797.0
12 TraesCS2B01G584400 chr2D 84.356 831 53 19 671 1470 628574870 628574086 0.000000e+00 743.0
13 TraesCS2B01G584400 chr2D 84.715 772 46 21 864 1610 628984908 628984184 0.000000e+00 706.0
14 TraesCS2B01G584400 chr2D 97.318 261 7 0 1 261 628268994 628269254 6.110000e-121 444.0
15 TraesCS2B01G584400 chr2D 97.628 253 5 1 10 261 628655192 628655444 1.320000e-117 433.0
16 TraesCS2B01G584400 chr2D 95.057 263 8 3 1 261 628576417 628576158 2.230000e-110 409.0
17 TraesCS2B01G584400 chr2D 96.970 165 4 1 319 483 628269403 628269566 2.360000e-70 276.0
18 TraesCS2B01G584400 chr2D 96.825 126 4 0 302 427 628576150 628576025 6.740000e-51 211.0
19 TraesCS2B01G584400 chr2D 86.290 124 10 4 858 981 628583047 628582931 6.990000e-26 128.0
20 TraesCS2B01G584400 chr2D 83.942 137 14 4 639 768 628269583 628269718 9.040000e-25 124.0
21 TraesCS2B01G584400 chr2D 73.638 459 53 37 568 981 628262195 628262630 5.440000e-22 115.0
22 TraesCS2B01G584400 chr2D 100.000 49 0 0 819 867 628984974 628984926 9.170000e-15 91.6
23 TraesCS2B01G584400 chr2D 95.918 49 2 0 301 349 628655450 628655498 1.980000e-11 80.5
24 TraesCS2B01G584400 chr2D 100.000 28 0 0 278 305 628655401 628655428 4.000000e-03 52.8
25 TraesCS2B01G584400 chr5D 81.941 443 38 18 586 992 15558749 15558313 1.070000e-88 337.0
26 TraesCS2B01G584400 chr6A 95.495 111 4 1 2274 2384 616057243 616057134 2.460000e-40 176.0
27 TraesCS2B01G584400 chr3A 91.200 125 7 4 2268 2390 574318544 574318666 1.480000e-37 167.0
28 TraesCS2B01G584400 chr6D 95.833 96 4 0 2274 2369 471104244 471104339 3.210000e-34 156.0
29 TraesCS2B01G584400 chr6D 90.476 105 9 1 2280 2384 471277114 471277011 1.160000e-28 137.0


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 TraesCS2B01G584400 chr2B 771412997 771415404 2407 False 1520.00 4447 100.00000 1 2408 3 chr2B.!!$F1 2407
1 TraesCS2B01G584400 chr2A 758588338 758589802 1464 False 1402.00 1402 84.51400 784 2252 1 chr2A.!!$F2 1468
2 TraesCS2B01G584400 chr2D 628573174 628576417 3243 True 540.00 797 91.40975 1 2274 4 chr2D.!!$R2 2273
3 TraesCS2B01G584400 chr2D 628268994 628270837 1843 False 481.25 1081 90.75675 1 1651 4 chr2D.!!$F2 1650
4 TraesCS2B01G584400 chr2D 628984184 628984974 790 True 398.80 706 92.35750 819 1610 2 chr2D.!!$R3 791

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
763 2068 0.042708 CAATACATCTGCGTCGCTGC 60.043 55.0 19.5 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 3301 1.268352 GGTGCACACAATTCGGCTTAA 59.732 47.619 20.43 0.0 0.0 1.85 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
63 64 2.825532 ACATGAACCCCATTTTCTTCGG 59.174 45.455 0.00 0.00 31.94 4.30
261 264 8.856153 TTAATTGTTCCTGTAACTTATGCTCA 57.144 30.769 0.00 0.00 38.99 4.26
264 267 6.299805 TGTTCCTGTAACTTATGCTCATCT 57.700 37.500 0.00 0.00 38.99 2.90
265 268 6.341316 TGTTCCTGTAACTTATGCTCATCTC 58.659 40.000 0.00 0.00 38.99 2.75
267 270 7.342026 TGTTCCTGTAACTTATGCTCATCTCTA 59.658 37.037 0.00 0.00 38.99 2.43
268 271 7.278461 TCCTGTAACTTATGCTCATCTCTAC 57.722 40.000 0.00 0.00 0.00 2.59
269 272 6.265649 TCCTGTAACTTATGCTCATCTCTACC 59.734 42.308 0.00 0.00 0.00 3.18
270 273 6.266558 CCTGTAACTTATGCTCATCTCTACCT 59.733 42.308 0.00 0.00 0.00 3.08
271 274 7.448777 CCTGTAACTTATGCTCATCTCTACCTA 59.551 40.741 0.00 0.00 0.00 3.08
272 275 8.167605 TGTAACTTATGCTCATCTCTACCTAC 57.832 38.462 0.00 0.00 0.00 3.18
273 276 7.999545 TGTAACTTATGCTCATCTCTACCTACT 59.000 37.037 0.00 0.00 0.00 2.57
274 277 7.906199 AACTTATGCTCATCTCTACCTACTT 57.094 36.000 0.00 0.00 0.00 2.24
275 278 8.998277 AACTTATGCTCATCTCTACCTACTTA 57.002 34.615 0.00 0.00 0.00 2.24
276 279 9.594936 AACTTATGCTCATCTCTACCTACTTAT 57.405 33.333 0.00 0.00 0.00 1.73
277 280 9.019656 ACTTATGCTCATCTCTACCTACTTATG 57.980 37.037 0.00 0.00 0.00 1.90
278 281 5.713792 TGCTCATCTCTACCTACTTATGC 57.286 43.478 0.00 0.00 0.00 3.14
279 282 5.140454 TGCTCATCTCTACCTACTTATGCA 58.860 41.667 0.00 0.00 0.00 3.96
280 283 5.777223 TGCTCATCTCTACCTACTTATGCAT 59.223 40.000 3.79 3.79 0.00 3.96
281 284 6.948309 TGCTCATCTCTACCTACTTATGCATA 59.052 38.462 1.16 1.16 0.00 3.14
282 285 7.617329 TGCTCATCTCTACCTACTTATGCATAT 59.383 37.037 7.36 0.00 0.00 1.78
283 286 8.474025 GCTCATCTCTACCTACTTATGCATATT 58.526 37.037 7.36 0.32 0.00 1.28
285 288 9.533831 TCATCTCTACCTACTTATGCATATTCA 57.466 33.333 7.36 0.00 0.00 2.57
292 295 8.854614 ACCTACTTATGCATATTCAAATCTCC 57.145 34.615 7.36 0.00 0.00 3.71
293 296 8.439971 ACCTACTTATGCATATTCAAATCTCCA 58.560 33.333 7.36 0.00 0.00 3.86
294 297 9.288576 CCTACTTATGCATATTCAAATCTCCAA 57.711 33.333 7.36 0.00 0.00 3.53
296 299 8.757982 ACTTATGCATATTCAAATCTCCAACT 57.242 30.769 7.36 0.00 0.00 3.16
297 300 9.193806 ACTTATGCATATTCAAATCTCCAACTT 57.806 29.630 7.36 0.00 0.00 2.66
529 1834 6.157994 ACCCTGTCTTTATATGCTAGTTGGAA 59.842 38.462 0.00 0.00 0.00 3.53
546 1851 5.535030 AGTTGGAAGGTTTAATCTGGTTGTC 59.465 40.000 0.00 0.00 0.00 3.18
554 1859 8.250143 AGGTTTAATCTGGTTGTCTTTTCATT 57.750 30.769 0.00 0.00 0.00 2.57
561 1866 7.587037 TCTGGTTGTCTTTTCATTCATTTCT 57.413 32.000 0.00 0.00 0.00 2.52
562 1867 7.428020 TCTGGTTGTCTTTTCATTCATTTCTG 58.572 34.615 0.00 0.00 0.00 3.02
563 1868 7.068593 TCTGGTTGTCTTTTCATTCATTTCTGT 59.931 33.333 0.00 0.00 0.00 3.41
564 1869 7.555087 TGGTTGTCTTTTCATTCATTTCTGTT 58.445 30.769 0.00 0.00 0.00 3.16
568 1873 8.633075 TGTCTTTTCATTCATTTCTGTTTGTC 57.367 30.769 0.00 0.00 0.00 3.18
758 2063 1.004927 GGCGTTCAATACATCTGCGTC 60.005 52.381 0.00 0.00 0.00 5.19
762 2067 1.559831 TCAATACATCTGCGTCGCTG 58.440 50.000 19.50 18.22 0.00 5.18
763 2068 0.042708 CAATACATCTGCGTCGCTGC 60.043 55.000 19.50 0.00 0.00 5.25
764 2069 0.179100 AATACATCTGCGTCGCTGCT 60.179 50.000 19.50 6.71 35.36 4.24
765 2070 0.873312 ATACATCTGCGTCGCTGCTG 60.873 55.000 21.51 21.51 35.36 4.41
766 2071 1.933115 TACATCTGCGTCGCTGCTGA 61.933 55.000 27.42 16.65 45.10 4.26
767 2072 2.498248 ATCTGCGTCGCTGCTGAT 59.502 55.556 19.50 13.04 44.90 2.90
768 2073 2.507769 TCTGCGTCGCTGCTGATG 60.508 61.111 19.50 3.86 37.82 3.07
1156 2550 4.261614 GCAGGAATTCCGTTGTTTCTTTCT 60.262 41.667 18.82 0.00 42.08 2.52
1165 2559 6.725246 TCCGTTGTTTCTTTCTTTCATCTTC 58.275 36.000 0.00 0.00 0.00 2.87
1221 2627 3.399181 CCCAGGAAGCGGCACCTA 61.399 66.667 16.03 0.00 34.87 3.08
1250 2656 0.595588 CTCGGTGAGGATGAGATCGG 59.404 60.000 0.00 0.00 31.31 4.18
1283 2692 2.610694 AAGGCGAGACGACGACGAA 61.611 57.895 15.32 0.00 46.71 3.85
1306 2715 3.191539 CGCCTTCTCAAGCCTCGC 61.192 66.667 0.00 0.00 0.00 5.03
1312 2721 4.821589 CTCAAGCCTCGCCGTCCC 62.822 72.222 0.00 0.00 0.00 4.46
1340 2749 4.030452 GTTGCCGCTGCCACTGTC 62.030 66.667 0.00 0.00 36.33 3.51
1346 2755 4.767255 GCTGCCACTGTCCCCTCG 62.767 72.222 0.00 0.00 0.00 4.63
1347 2756 4.767255 CTGCCACTGTCCCCTCGC 62.767 72.222 0.00 0.00 0.00 5.03
1349 2758 4.767255 GCCACTGTCCCCTCGCTG 62.767 72.222 0.00 0.00 0.00 5.18
1350 2759 4.767255 CCACTGTCCCCTCGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
1368 2777 4.329545 GGTTGTCCCCTCGCTGCA 62.330 66.667 0.00 0.00 0.00 4.41
1369 2778 3.050275 GTTGTCCCCTCGCTGCAC 61.050 66.667 0.00 0.00 0.00 4.57
1370 2779 4.329545 TTGTCCCCTCGCTGCACC 62.330 66.667 0.00 0.00 0.00 5.01
1374 2783 4.077184 CCCCTCGCTGCACCGTTA 62.077 66.667 0.64 0.00 0.00 3.18
1433 2854 1.141881 GGAGCAGGAGAATCGCGAA 59.858 57.895 15.24 0.00 34.37 4.70
1443 2864 0.505231 GAATCGCGAACACAACGACA 59.495 50.000 15.24 0.00 38.85 4.35
1471 2925 4.761227 TGCAGCAGAACATGAGTAATTGAA 59.239 37.500 0.00 0.00 0.00 2.69
1508 2993 3.226777 TCCCACGACCAAAAATGAATGT 58.773 40.909 0.00 0.00 0.00 2.71
1509 2994 3.005261 TCCCACGACCAAAAATGAATGTG 59.995 43.478 0.00 0.00 0.00 3.21
1583 3076 8.668510 ACTTTGATTAGCCTTGTCATACATAG 57.331 34.615 0.00 0.00 0.00 2.23
1623 3185 9.628746 GGTTAGCTTTCTATAGTAGCTCATTAC 57.371 37.037 25.11 19.57 43.75 1.89
1651 3218 8.526218 TTATCATCGCATCTTGTAGATCTTTC 57.474 34.615 0.00 0.00 31.32 2.62
1658 3225 5.163814 GCATCTTGTAGATCTTTCTGCGTTT 60.164 40.000 0.00 0.00 37.40 3.60
1694 3261 2.948979 AGGAGATGCAAACAAACGACAA 59.051 40.909 0.00 0.00 0.00 3.18
1701 3268 5.236655 TGCAAACAAACGACAAATCTGTA 57.763 34.783 0.00 0.00 35.30 2.74
1702 3269 5.641709 TGCAAACAAACGACAAATCTGTAA 58.358 33.333 0.00 0.00 35.30 2.41
1748 3317 6.422776 AGATTAGTTAAGCCGAATTGTGTG 57.577 37.500 0.00 0.00 0.00 3.82
1769 3338 3.302555 GCACCATCATGCATATTTGTCG 58.697 45.455 0.00 0.00 45.39 4.35
1825 3402 6.038271 AGTTCAACGCACAAGAAAAATACTCT 59.962 34.615 0.00 0.00 0.00 3.24
1826 3403 7.225931 AGTTCAACGCACAAGAAAAATACTCTA 59.774 33.333 0.00 0.00 0.00 2.43
1827 3404 7.485418 TCAACGCACAAGAAAAATACTCTAA 57.515 32.000 0.00 0.00 0.00 2.10
1828 3405 8.094798 TCAACGCACAAGAAAAATACTCTAAT 57.905 30.769 0.00 0.00 0.00 1.73
1829 3406 9.210329 TCAACGCACAAGAAAAATACTCTAATA 57.790 29.630 0.00 0.00 0.00 0.98
1830 3407 9.988350 CAACGCACAAGAAAAATACTCTAATAT 57.012 29.630 0.00 0.00 0.00 1.28
1942 3519 1.319541 AGAGTATGGACGATGACGGG 58.680 55.000 0.00 0.00 44.46 5.28
1961 3538 2.289444 GGGGGCCAGCTTAAAGAAAAAC 60.289 50.000 4.39 0.00 0.00 2.43
1981 3558 3.898482 ACCCACATGACCTTTATAAGCC 58.102 45.455 0.00 0.00 0.00 4.35
1989 3566 8.103305 CACATGACCTTTATAAGCCCATATAGT 58.897 37.037 0.00 0.00 0.00 2.12
2025 3602 8.421673 AATGAAGTTAAGAGTATAGCGGAAAC 57.578 34.615 0.00 0.00 0.00 2.78
2100 3677 4.269363 AGCTTATATTGTTACACGGCGAAC 59.731 41.667 16.62 8.64 0.00 3.95
2119 3696 4.155644 CGAACGAGGTTAAGAGTAAGGACT 59.844 45.833 0.00 0.00 39.20 3.85
2130 3707 2.885894 GAGTAAGGACTATGACGGGGAG 59.114 54.545 0.00 0.00 35.45 4.30
2137 3714 3.181478 GGACTATGACGGGGAGTAGTTTG 60.181 52.174 0.00 0.00 0.00 2.93
2158 3735 3.763360 TGCAATGACACCATTTCCTTAGG 59.237 43.478 0.00 0.00 40.81 2.69
2184 3761 5.171337 GCATATAAACGCCAATCAAAAGACG 59.829 40.000 0.00 0.00 0.00 4.18
2190 3767 2.095768 CGCCAATCAAAAGACGTGTGAT 60.096 45.455 0.00 0.00 33.41 3.06
2271 3849 6.213600 TCTCTATGGGTTTAGAAGAGCTTTGT 59.786 38.462 0.00 0.00 34.89 2.83
2274 3852 4.985538 TGGGTTTAGAAGAGCTTTGTCAT 58.014 39.130 0.00 0.00 0.00 3.06
2275 3853 6.121776 TGGGTTTAGAAGAGCTTTGTCATA 57.878 37.500 0.00 0.00 0.00 2.15
2276 3854 6.721318 TGGGTTTAGAAGAGCTTTGTCATAT 58.279 36.000 0.00 0.00 0.00 1.78
2277 3855 6.599244 TGGGTTTAGAAGAGCTTTGTCATATG 59.401 38.462 0.00 0.00 0.00 1.78
2278 3856 6.038714 GGGTTTAGAAGAGCTTTGTCATATGG 59.961 42.308 2.13 0.00 0.00 2.74
2279 3857 6.823689 GGTTTAGAAGAGCTTTGTCATATGGA 59.176 38.462 2.13 0.00 0.00 3.41
2280 3858 7.336931 GGTTTAGAAGAGCTTTGTCATATGGAA 59.663 37.037 2.13 0.00 0.00 3.53
2281 3859 8.730680 GTTTAGAAGAGCTTTGTCATATGGAAA 58.269 33.333 2.13 2.16 0.00 3.13
2282 3860 9.466497 TTTAGAAGAGCTTTGTCATATGGAAAT 57.534 29.630 2.13 0.00 0.00 2.17
2284 3862 8.443953 AGAAGAGCTTTGTCATATGGAAATAC 57.556 34.615 2.13 0.00 0.00 1.89
2285 3863 8.270744 AGAAGAGCTTTGTCATATGGAAATACT 58.729 33.333 2.13 3.86 0.00 2.12
2286 3864 8.443953 AAGAGCTTTGTCATATGGAAATACTC 57.556 34.615 2.13 11.19 0.00 2.59
2287 3865 7.800092 AGAGCTTTGTCATATGGAAATACTCT 58.200 34.615 17.25 17.25 0.00 3.24
2288 3866 7.714377 AGAGCTTTGTCATATGGAAATACTCTG 59.286 37.037 19.55 6.11 0.00 3.35
2289 3867 7.341805 AGCTTTGTCATATGGAAATACTCTGT 58.658 34.615 2.13 0.00 0.00 3.41
2290 3868 7.831193 AGCTTTGTCATATGGAAATACTCTGTT 59.169 33.333 2.13 0.00 0.00 3.16
2291 3869 8.462016 GCTTTGTCATATGGAAATACTCTGTTT 58.538 33.333 2.13 0.00 0.00 2.83
2292 3870 9.994432 CTTTGTCATATGGAAATACTCTGTTTC 57.006 33.333 2.13 0.00 35.38 2.78
2293 3871 9.739276 TTTGTCATATGGAAATACTCTGTTTCT 57.261 29.630 2.13 0.00 36.18 2.52
2303 3881 9.989869 GGAAATACTCTGTTTCTAGTTAATTGC 57.010 33.333 0.00 0.00 36.18 3.56
2307 3885 7.801716 ACTCTGTTTCTAGTTAATTGCAACA 57.198 32.000 0.00 0.00 0.00 3.33
2308 3886 8.220755 ACTCTGTTTCTAGTTAATTGCAACAA 57.779 30.769 0.00 0.00 0.00 2.83
2309 3887 8.682710 ACTCTGTTTCTAGTTAATTGCAACAAA 58.317 29.630 0.00 0.00 0.00 2.83
2310 3888 9.173939 CTCTGTTTCTAGTTAATTGCAACAAAG 57.826 33.333 0.00 0.00 0.00 2.77
2311 3889 8.682710 TCTGTTTCTAGTTAATTGCAACAAAGT 58.317 29.630 0.00 4.71 0.00 2.66
2312 3890 9.301153 CTGTTTCTAGTTAATTGCAACAAAGTT 57.699 29.630 0.00 0.00 0.00 2.66
2313 3891 9.081997 TGTTTCTAGTTAATTGCAACAAAGTTG 57.918 29.630 0.00 5.56 0.00 3.16
2314 3892 9.296400 GTTTCTAGTTAATTGCAACAAAGTTGA 57.704 29.630 13.58 5.94 0.00 3.18
2315 3893 8.850454 TTCTAGTTAATTGCAACAAAGTTGAC 57.150 30.769 13.58 0.00 0.00 3.18
2316 3894 8.220755 TCTAGTTAATTGCAACAAAGTTGACT 57.779 30.769 13.58 6.83 0.00 3.41
2317 3895 8.342634 TCTAGTTAATTGCAACAAAGTTGACTC 58.657 33.333 13.58 0.00 0.00 3.36
2318 3896 7.100458 AGTTAATTGCAACAAAGTTGACTCT 57.900 32.000 13.58 0.00 0.00 3.24
2319 3897 7.547227 AGTTAATTGCAACAAAGTTGACTCTT 58.453 30.769 13.58 4.09 0.00 2.85
2320 3898 8.034804 AGTTAATTGCAACAAAGTTGACTCTTT 58.965 29.630 13.58 0.00 38.04 2.52
2321 3899 9.296400 GTTAATTGCAACAAAGTTGACTCTTTA 57.704 29.630 13.58 0.00 36.12 1.85
2323 3901 7.935338 ATTGCAACAAAGTTGACTCTTTATG 57.065 32.000 13.58 0.00 36.12 1.90
2324 3902 6.691754 TGCAACAAAGTTGACTCTTTATGA 57.308 33.333 13.58 0.00 36.12 2.15
2325 3903 7.094508 TGCAACAAAGTTGACTCTTTATGAA 57.905 32.000 13.58 0.00 36.12 2.57
2326 3904 7.542890 TGCAACAAAGTTGACTCTTTATGAAA 58.457 30.769 13.58 0.00 36.12 2.69
2327 3905 7.701924 TGCAACAAAGTTGACTCTTTATGAAAG 59.298 33.333 13.58 0.00 36.12 2.62
2328 3906 7.915397 GCAACAAAGTTGACTCTTTATGAAAGA 59.085 33.333 13.58 1.93 44.82 2.52
2329 3907 9.787532 CAACAAAGTTGACTCTTTATGAAAGAA 57.212 29.630 3.91 0.00 46.13 2.52
2330 3908 9.788960 AACAAAGTTGACTCTTTATGAAAGAAC 57.211 29.630 3.44 0.00 46.13 3.01
2331 3909 8.406297 ACAAAGTTGACTCTTTATGAAAGAACC 58.594 33.333 3.44 0.00 46.13 3.62
2332 3910 6.787085 AGTTGACTCTTTATGAAAGAACCG 57.213 37.500 3.44 0.00 46.13 4.44
2333 3911 5.179555 AGTTGACTCTTTATGAAAGAACCGC 59.820 40.000 3.44 0.00 46.13 5.68
2334 3912 4.637276 TGACTCTTTATGAAAGAACCGCA 58.363 39.130 3.44 0.00 46.13 5.69
2335 3913 5.060506 TGACTCTTTATGAAAGAACCGCAA 58.939 37.500 3.44 0.00 46.13 4.85
2336 3914 5.049680 TGACTCTTTATGAAAGAACCGCAAC 60.050 40.000 3.44 0.00 46.13 4.17
2337 3915 4.819630 ACTCTTTATGAAAGAACCGCAACA 59.180 37.500 3.44 0.00 46.13 3.33
2338 3916 5.473504 ACTCTTTATGAAAGAACCGCAACAT 59.526 36.000 3.44 0.00 46.13 2.71
2339 3917 6.653320 ACTCTTTATGAAAGAACCGCAACATA 59.347 34.615 3.44 0.00 46.13 2.29
2340 3918 7.072177 TCTTTATGAAAGAACCGCAACATAG 57.928 36.000 0.00 0.00 44.10 2.23
2341 3919 6.653320 TCTTTATGAAAGAACCGCAACATAGT 59.347 34.615 0.00 0.00 44.10 2.12
2342 3920 6.811253 TTATGAAAGAACCGCAACATAGTT 57.189 33.333 0.00 0.00 0.00 2.24
2343 3921 5.705609 ATGAAAGAACCGCAACATAGTTT 57.294 34.783 0.00 0.00 0.00 2.66
2344 3922 5.508200 TGAAAGAACCGCAACATAGTTTT 57.492 34.783 0.00 0.00 0.00 2.43
2345 3923 5.897050 TGAAAGAACCGCAACATAGTTTTT 58.103 33.333 0.00 0.00 0.00 1.94
2365 3943 6.916360 TTTTTCTCCTGATAAAACCAGCAT 57.084 33.333 0.00 0.00 0.00 3.79
2366 3944 6.916360 TTTTCTCCTGATAAAACCAGCATT 57.084 33.333 0.00 0.00 0.00 3.56
2367 3945 8.415950 TTTTTCTCCTGATAAAACCAGCATTA 57.584 30.769 0.00 0.00 0.00 1.90
2368 3946 8.415950 TTTTCTCCTGATAAAACCAGCATTAA 57.584 30.769 0.00 0.00 0.00 1.40
2369 3947 8.593945 TTTCTCCTGATAAAACCAGCATTAAT 57.406 30.769 0.00 0.00 0.00 1.40
2370 3948 8.593945 TTCTCCTGATAAAACCAGCATTAATT 57.406 30.769 0.00 0.00 0.00 1.40
2371 3949 8.593945 TCTCCTGATAAAACCAGCATTAATTT 57.406 30.769 0.00 0.00 0.00 1.82
2372 3950 9.034800 TCTCCTGATAAAACCAGCATTAATTTT 57.965 29.630 0.00 0.00 0.00 1.82
2373 3951 9.090692 CTCCTGATAAAACCAGCATTAATTTTG 57.909 33.333 0.00 0.00 0.00 2.44
2374 3952 8.592809 TCCTGATAAAACCAGCATTAATTTTGT 58.407 29.630 0.00 0.00 0.00 2.83
2375 3953 9.218440 CCTGATAAAACCAGCATTAATTTTGTT 57.782 29.630 0.00 0.00 0.00 2.83
2377 3955 9.770097 TGATAAAACCAGCATTAATTTTGTTCA 57.230 25.926 0.00 0.00 0.00 3.18
2380 3958 7.437793 AAACCAGCATTAATTTTGTTCATGG 57.562 32.000 0.00 0.00 0.00 3.66
2381 3959 4.937015 ACCAGCATTAATTTTGTTCATGGC 59.063 37.500 0.00 0.00 0.00 4.40
2382 3960 4.333372 CCAGCATTAATTTTGTTCATGGCC 59.667 41.667 0.00 0.00 0.00 5.36
2383 3961 5.180271 CAGCATTAATTTTGTTCATGGCCT 58.820 37.500 3.32 0.00 0.00 5.19
2384 3962 6.339730 CAGCATTAATTTTGTTCATGGCCTA 58.660 36.000 3.32 0.00 0.00 3.93
2385 3963 6.987992 CAGCATTAATTTTGTTCATGGCCTAT 59.012 34.615 3.32 0.00 0.00 2.57
2386 3964 7.496591 CAGCATTAATTTTGTTCATGGCCTATT 59.503 33.333 3.32 0.00 0.00 1.73
2387 3965 8.048514 AGCATTAATTTTGTTCATGGCCTATTT 58.951 29.630 3.32 0.00 0.00 1.40
2388 3966 8.676401 GCATTAATTTTGTTCATGGCCTATTTT 58.324 29.630 3.32 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.714798 TGGTACCTTCAGAAACACTTCCT 59.285 43.478 14.36 0.00 31.28 3.36
63 64 1.266718 TCTGGCACAAATTGTCGAAGC 59.733 47.619 0.00 0.00 38.70 3.86
246 249 7.283625 AGGTAGAGATGAGCATAAGTTACAG 57.716 40.000 0.00 0.00 0.00 2.74
267 270 8.439971 TGGAGATTTGAATATGCATAAGTAGGT 58.560 33.333 11.13 0.00 0.00 3.08
268 271 8.853077 TGGAGATTTGAATATGCATAAGTAGG 57.147 34.615 11.13 0.00 0.00 3.18
270 273 9.851686 AGTTGGAGATTTGAATATGCATAAGTA 57.148 29.630 11.13 0.00 28.25 2.24
271 274 8.757982 AGTTGGAGATTTGAATATGCATAAGT 57.242 30.769 11.13 1.39 28.25 2.24
276 279 9.806203 CAATTAAGTTGGAGATTTGAATATGCA 57.194 29.630 0.00 0.00 34.06 3.96
277 280 9.807649 ACAATTAAGTTGGAGATTTGAATATGC 57.192 29.630 0.00 0.00 42.28 3.14
292 295 3.059166 GGTGCAGCCAACAATTAAGTTG 58.941 45.455 4.03 2.43 46.44 3.16
293 296 2.965147 AGGTGCAGCCAACAATTAAGTT 59.035 40.909 13.29 0.00 40.61 2.66
294 297 2.597455 AGGTGCAGCCAACAATTAAGT 58.403 42.857 13.29 0.00 40.61 2.24
295 298 3.005684 TGAAGGTGCAGCCAACAATTAAG 59.994 43.478 13.29 0.00 40.61 1.85
296 299 2.961741 TGAAGGTGCAGCCAACAATTAA 59.038 40.909 13.29 0.00 40.61 1.40
297 300 2.591923 TGAAGGTGCAGCCAACAATTA 58.408 42.857 13.29 0.00 40.61 1.40
298 301 1.412079 TGAAGGTGCAGCCAACAATT 58.588 45.000 13.29 0.00 40.61 2.32
299 302 1.636148 ATGAAGGTGCAGCCAACAAT 58.364 45.000 13.29 0.00 40.61 2.71
307 310 6.892658 AGACTAGATAGTATGAAGGTGCAG 57.107 41.667 0.00 0.00 36.50 4.41
480 1614 5.580691 TCAAATTTGACCTACTGCGTATCTG 59.419 40.000 16.91 0.00 31.01 2.90
495 1629 7.615365 AGCATATAAAGACAGGGTCAAATTTGA 59.385 33.333 16.91 16.91 34.60 2.69
506 1808 6.708054 CCTTCCAACTAGCATATAAAGACAGG 59.292 42.308 0.00 0.00 0.00 4.00
529 1834 7.839680 ATGAAAAGACAACCAGATTAAACCT 57.160 32.000 0.00 0.00 0.00 3.50
554 1859 6.597672 ACCGCATATTAGACAAACAGAAATGA 59.402 34.615 0.00 0.00 0.00 2.57
561 1866 4.124238 GCCTACCGCATATTAGACAAACA 58.876 43.478 0.00 0.00 37.47 2.83
562 1867 3.497262 GGCCTACCGCATATTAGACAAAC 59.503 47.826 0.00 0.00 40.31 2.93
563 1868 3.134985 TGGCCTACCGCATATTAGACAAA 59.865 43.478 3.32 0.00 40.31 2.83
564 1869 2.701423 TGGCCTACCGCATATTAGACAA 59.299 45.455 3.32 0.00 40.31 3.18
568 1873 3.935203 CAGATTGGCCTACCGCATATTAG 59.065 47.826 3.32 0.00 40.31 1.73
641 1946 7.977818 TCTAACAAGCCATCAGACCATATAAT 58.022 34.615 0.00 0.00 0.00 1.28
749 2054 1.881709 ATCAGCAGCGACGCAGATG 60.882 57.895 22.37 22.37 36.84 2.90
781 2086 0.455633 GCTTCTTCATTGGCGTGCAG 60.456 55.000 0.00 0.00 0.00 4.41
782 2087 1.580942 GCTTCTTCATTGGCGTGCA 59.419 52.632 0.00 0.00 0.00 4.57
783 2088 1.153958 GGCTTCTTCATTGGCGTGC 60.154 57.895 0.00 0.00 0.00 5.34
784 2089 1.737838 TAGGCTTCTTCATTGGCGTG 58.262 50.000 0.00 0.00 0.00 5.34
785 2090 2.717639 ATAGGCTTCTTCATTGGCGT 57.282 45.000 0.00 0.00 0.00 5.68
786 2091 2.945008 TGAATAGGCTTCTTCATTGGCG 59.055 45.455 7.80 0.00 0.00 5.69
1180 2574 2.350522 CATCTGGTTCCTAGCACACAC 58.649 52.381 0.00 0.00 0.00 3.82
1182 2576 1.555075 TCCATCTGGTTCCTAGCACAC 59.445 52.381 0.00 0.00 36.34 3.82
1221 2627 2.824489 TCACCGAGCGCGATCTCT 60.824 61.111 23.21 2.70 40.82 3.10
1266 2672 3.024782 CTTCGTCGTCGTCTCGCCT 62.025 63.158 1.33 0.00 38.33 5.52
1283 2692 1.217779 GCTTGAGAAGGCGAGCTCT 59.782 57.895 12.85 0.00 41.20 4.09
1351 2760 4.329545 TGCAGCGAGGGGACAACC 62.330 66.667 0.00 0.00 39.11 3.77
1352 2761 3.050275 GTGCAGCGAGGGGACAAC 61.050 66.667 0.00 0.00 0.00 3.32
1353 2762 4.329545 GGTGCAGCGAGGGGACAA 62.330 66.667 0.00 0.00 0.00 3.18
1357 2766 4.077184 TAACGGTGCAGCGAGGGG 62.077 66.667 41.29 15.49 0.00 4.79
1358 2767 2.813908 GTAACGGTGCAGCGAGGG 60.814 66.667 41.29 15.88 0.00 4.30
1359 2768 2.813908 GGTAACGGTGCAGCGAGG 60.814 66.667 41.29 16.27 0.00 4.63
1371 2780 1.516603 GCAGCGAGGAGACGGTAAC 60.517 63.158 0.00 0.00 41.95 2.50
1372 2781 2.882876 GCAGCGAGGAGACGGTAA 59.117 61.111 0.00 0.00 41.95 2.85
1373 2782 3.506096 CGCAGCGAGGAGACGGTA 61.506 66.667 9.98 0.00 41.95 4.02
1433 2854 1.078072 TGCAGGGTTGTCGTTGTGT 60.078 52.632 0.00 0.00 0.00 3.72
1443 2864 0.111061 TCATGTTCTGCTGCAGGGTT 59.889 50.000 27.79 9.28 31.51 4.11
1471 2925 3.108376 GTGGGAGAAGAGGATACAACCT 58.892 50.000 0.00 0.00 43.64 3.50
1508 2993 4.380843 TTTGTATCCAAAAGGAGCCTCA 57.619 40.909 0.00 0.00 37.62 3.86
1527 3014 7.724305 ACGTATGTATGAGAACAACACTTTT 57.276 32.000 0.00 0.00 32.02 2.27
1610 3172 8.357402 TGCGATGATAAAAGTAATGAGCTACTA 58.643 33.333 0.00 0.00 31.72 1.82
1611 3173 7.210174 TGCGATGATAAAAGTAATGAGCTACT 58.790 34.615 0.00 0.00 33.41 2.57
1623 3185 8.531622 AGATCTACAAGATGCGATGATAAAAG 57.468 34.615 0.00 0.00 34.53 2.27
1630 3192 5.333187 GCAGAAAGATCTACAAGATGCGATG 60.333 44.000 0.00 0.00 34.53 3.84
1631 3193 4.749099 GCAGAAAGATCTACAAGATGCGAT 59.251 41.667 0.00 0.00 34.53 4.58
1633 3195 3.060674 CGCAGAAAGATCTACAAGATGCG 60.061 47.826 17.30 17.30 34.53 4.73
1651 3218 4.287720 TCGCTAGATATACACAAACGCAG 58.712 43.478 0.00 0.00 0.00 5.18
1658 3225 4.396478 GCATCTCCTCGCTAGATATACACA 59.604 45.833 0.00 0.00 32.40 3.72
1713 3282 9.275231 CGGCTTAACTAATCTATATCTTGTACG 57.725 37.037 0.00 0.00 0.00 3.67
1732 3301 1.268352 GGTGCACACAATTCGGCTTAA 59.732 47.619 20.43 0.00 0.00 1.85
1748 3317 3.302555 CGACAAATATGCATGATGGTGC 58.697 45.455 10.16 0.00 45.25 5.01
1830 3407 9.848710 ACAAGTACTAGACTATTCTGCAGTATA 57.151 33.333 14.67 13.11 37.44 1.47
1831 3408 8.754991 ACAAGTACTAGACTATTCTGCAGTAT 57.245 34.615 14.67 12.60 37.44 2.12
1832 3409 9.848710 ATACAAGTACTAGACTATTCTGCAGTA 57.151 33.333 14.67 4.08 37.44 2.74
1916 3493 3.318275 TCATCGTCCATACTCTTAGCCAC 59.682 47.826 0.00 0.00 0.00 5.01
1942 3519 2.289444 GGGTTTTTCTTTAAGCTGGCCC 60.289 50.000 0.00 0.00 0.00 5.80
1961 3538 3.222603 GGGCTTATAAAGGTCATGTGGG 58.777 50.000 0.00 0.00 0.00 4.61
1981 3558 4.986034 TCATTCGCCGTGTAAACTATATGG 59.014 41.667 0.00 0.00 0.00 2.74
1989 3566 4.989797 TCTTAACTTCATTCGCCGTGTAAA 59.010 37.500 0.00 0.00 0.00 2.01
2033 3610 2.500504 AGTCCCCGTCATTCTCTTTACC 59.499 50.000 0.00 0.00 0.00 2.85
2038 3615 2.830651 ACTAGTCCCCGTCATTCTCT 57.169 50.000 0.00 0.00 0.00 3.10
2048 3625 7.292713 TGGATTTTTGTTTAAACTAGTCCCC 57.707 36.000 18.72 13.05 0.00 4.81
2100 3677 6.511444 CGTCATAGTCCTTACTCTTAACCTCG 60.511 46.154 0.00 0.00 37.15 4.63
2103 3680 5.221204 CCCGTCATAGTCCTTACTCTTAACC 60.221 48.000 0.00 0.00 37.15 2.85
2119 3696 2.181125 TGCAAACTACTCCCCGTCATA 58.819 47.619 0.00 0.00 0.00 2.15
2130 3707 4.923281 GGAAATGGTGTCATTGCAAACTAC 59.077 41.667 1.71 2.57 42.29 2.73
2137 3714 3.429410 GCCTAAGGAAATGGTGTCATTGC 60.429 47.826 0.00 0.00 42.29 3.56
2184 3761 8.677300 AGAATGTCCATATAAACAACATCACAC 58.323 33.333 0.00 0.00 30.56 3.82
2214 3791 1.514678 TTGTGTGCCATTGCGACCTC 61.515 55.000 0.00 0.00 41.78 3.85
2277 3855 9.989869 GCAATTAACTAGAAACAGAGTATTTCC 57.010 33.333 0.00 0.00 36.84 3.13
2281 3859 9.502091 TGTTGCAATTAACTAGAAACAGAGTAT 57.498 29.630 0.59 0.00 0.00 2.12
2282 3860 8.896320 TGTTGCAATTAACTAGAAACAGAGTA 57.104 30.769 0.59 0.00 0.00 2.59
2283 3861 7.801716 TGTTGCAATTAACTAGAAACAGAGT 57.198 32.000 0.59 0.00 0.00 3.24
2284 3862 9.173939 CTTTGTTGCAATTAACTAGAAACAGAG 57.826 33.333 0.59 0.00 0.00 3.35
2285 3863 8.682710 ACTTTGTTGCAATTAACTAGAAACAGA 58.317 29.630 0.59 0.00 0.00 3.41
2286 3864 8.856490 ACTTTGTTGCAATTAACTAGAAACAG 57.144 30.769 0.59 0.00 0.00 3.16
2287 3865 9.081997 CAACTTTGTTGCAATTAACTAGAAACA 57.918 29.630 0.59 0.00 0.00 2.83
2288 3866 9.296400 TCAACTTTGTTGCAATTAACTAGAAAC 57.704 29.630 0.59 0.00 0.00 2.78
2289 3867 9.296400 GTCAACTTTGTTGCAATTAACTAGAAA 57.704 29.630 0.59 0.00 0.00 2.52
2290 3868 8.682710 AGTCAACTTTGTTGCAATTAACTAGAA 58.317 29.630 0.59 0.00 0.00 2.10
2291 3869 8.220755 AGTCAACTTTGTTGCAATTAACTAGA 57.779 30.769 0.59 0.00 0.00 2.43
2292 3870 8.345565 AGAGTCAACTTTGTTGCAATTAACTAG 58.654 33.333 0.59 0.00 0.00 2.57
2293 3871 8.220755 AGAGTCAACTTTGTTGCAATTAACTA 57.779 30.769 0.59 0.00 0.00 2.24
2294 3872 7.100458 AGAGTCAACTTTGTTGCAATTAACT 57.900 32.000 0.59 0.00 0.00 2.24
2295 3873 7.755582 AAGAGTCAACTTTGTTGCAATTAAC 57.244 32.000 0.59 0.00 0.00 2.01
2297 3875 9.462174 CATAAAGAGTCAACTTTGTTGCAATTA 57.538 29.630 0.59 0.00 39.86 1.40
2298 3876 8.196771 TCATAAAGAGTCAACTTTGTTGCAATT 58.803 29.630 0.59 0.00 39.86 2.32
2299 3877 7.715657 TCATAAAGAGTCAACTTTGTTGCAAT 58.284 30.769 0.59 0.00 39.86 3.56
2300 3878 7.094508 TCATAAAGAGTCAACTTTGTTGCAA 57.905 32.000 0.00 0.00 39.86 4.08
2301 3879 6.691754 TCATAAAGAGTCAACTTTGTTGCA 57.308 33.333 5.65 0.00 39.86 4.08
2302 3880 7.915397 TCTTTCATAAAGAGTCAACTTTGTTGC 59.085 33.333 5.65 2.18 42.31 4.17
2316 3894 5.957842 ATGTTGCGGTTCTTTCATAAAGA 57.042 34.783 0.00 0.00 45.30 2.52
2317 3895 6.842163 ACTATGTTGCGGTTCTTTCATAAAG 58.158 36.000 0.00 0.00 39.88 1.85
2318 3896 6.811253 ACTATGTTGCGGTTCTTTCATAAA 57.189 33.333 0.00 0.00 0.00 1.40
2319 3897 6.811253 AACTATGTTGCGGTTCTTTCATAA 57.189 33.333 0.00 0.00 0.00 1.90
2320 3898 6.811253 AAACTATGTTGCGGTTCTTTCATA 57.189 33.333 0.00 0.00 0.00 2.15
2321 3899 5.705609 AAACTATGTTGCGGTTCTTTCAT 57.294 34.783 0.00 0.00 0.00 2.57
2322 3900 5.508200 AAAACTATGTTGCGGTTCTTTCA 57.492 34.783 0.00 0.00 0.00 2.69
2342 3920 6.916360 ATGCTGGTTTTATCAGGAGAAAAA 57.084 33.333 3.65 0.00 36.10 1.94
2343 3921 6.916360 AATGCTGGTTTTATCAGGAGAAAA 57.084 33.333 0.00 0.00 36.10 2.29
2344 3922 8.593945 ATTAATGCTGGTTTTATCAGGAGAAA 57.406 30.769 0.00 0.00 36.10 2.52
2345 3923 8.593945 AATTAATGCTGGTTTTATCAGGAGAA 57.406 30.769 0.00 0.00 36.10 2.87
2346 3924 8.593945 AAATTAATGCTGGTTTTATCAGGAGA 57.406 30.769 0.00 0.00 36.10 3.71
2347 3925 9.090692 CAAAATTAATGCTGGTTTTATCAGGAG 57.909 33.333 0.00 0.00 36.10 3.69
2348 3926 8.592809 ACAAAATTAATGCTGGTTTTATCAGGA 58.407 29.630 0.00 0.00 37.02 3.86
2349 3927 8.776376 ACAAAATTAATGCTGGTTTTATCAGG 57.224 30.769 0.00 0.00 33.16 3.86
2351 3929 9.770097 TGAACAAAATTAATGCTGGTTTTATCA 57.230 25.926 0.00 0.00 0.00 2.15
2354 3932 8.997323 CCATGAACAAAATTAATGCTGGTTTTA 58.003 29.630 0.00 0.00 0.00 1.52
2355 3933 7.521910 GCCATGAACAAAATTAATGCTGGTTTT 60.522 33.333 0.00 0.00 0.00 2.43
2356 3934 6.072563 GCCATGAACAAAATTAATGCTGGTTT 60.073 34.615 0.00 0.00 0.00 3.27
2357 3935 5.412286 GCCATGAACAAAATTAATGCTGGTT 59.588 36.000 0.00 0.00 0.00 3.67
2358 3936 4.937015 GCCATGAACAAAATTAATGCTGGT 59.063 37.500 0.00 0.00 0.00 4.00
2359 3937 4.333372 GGCCATGAACAAAATTAATGCTGG 59.667 41.667 0.00 0.00 0.00 4.85
2360 3938 5.180271 AGGCCATGAACAAAATTAATGCTG 58.820 37.500 5.01 0.00 0.00 4.41
2361 3939 5.425196 AGGCCATGAACAAAATTAATGCT 57.575 34.783 5.01 0.00 0.00 3.79
2362 3940 7.790823 AATAGGCCATGAACAAAATTAATGC 57.209 32.000 5.01 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.