Multiple sequence alignment - TraesCS2B01G260300

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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 TraesCS2B01G260300 chr2B 100.000 7582 0 0 1 7582 326674543 326682124 0.000000e+00 14002.0
1 TraesCS2B01G260300 chr2B 100.000 46 0 0 6822 6867 104943311 104943356 1.360000e-12 86.1
2 TraesCS2B01G260300 chr2B 92.453 53 3 1 6815 6866 11036156 11036208 2.930000e-09 75.0
3 TraesCS2B01G260300 chr2D 96.356 4555 123 17 2986 7511 280653253 280648713 0.000000e+00 7452.0
4 TraesCS2B01G260300 chr2D 95.078 2174 66 17 851 3003 280656210 280654057 0.000000e+00 3384.0
5 TraesCS2B01G260300 chr2D 95.385 65 3 0 7518 7582 280648667 280648603 3.740000e-18 104.0
6 TraesCS2B01G260300 chr2A 94.432 2173 80 17 851 3003 334598387 334596236 0.000000e+00 3304.0
7 TraesCS2B01G260300 chr2A 97.224 1657 42 4 5104 6760 334592254 334590602 0.000000e+00 2802.0
8 TraesCS2B01G260300 chr2A 95.081 1240 38 12 2986 4221 334594229 334593009 0.000000e+00 1930.0
9 TraesCS2B01G260300 chr2A 96.359 714 23 2 4262 4972 334593006 334592293 0.000000e+00 1171.0
10 TraesCS2B01G260300 chr2A 84.817 191 12 6 7407 7580 334590602 334590412 7.820000e-40 176.0
11 TraesCS2B01G260300 chr4B 97.773 853 11 6 1 847 640609454 640608604 0.000000e+00 1463.0
12 TraesCS2B01G260300 chr4B 88.235 68 5 1 6821 6885 17498341 17498274 2.270000e-10 78.7
13 TraesCS2B01G260300 chrUn 96.945 851 21 4 1 847 41472687 41473536 0.000000e+00 1423.0
14 TraesCS2B01G260300 chr6B 94.725 853 19 6 1 848 620654175 620653344 0.000000e+00 1303.0
15 TraesCS2B01G260300 chr6B 91.680 625 26 13 233 847 574466346 574466954 0.000000e+00 843.0
16 TraesCS2B01G260300 chr6B 91.814 623 24 16 239 850 690885055 690884449 0.000000e+00 843.0
17 TraesCS2B01G260300 chr6B 88.235 493 29 19 1 475 690885246 690884765 5.140000e-156 562.0
18 TraesCS2B01G260300 chr6B 87.195 492 34 19 1 475 574466162 574466641 4.030000e-147 532.0
19 TraesCS2B01G260300 chr4A 95.504 823 15 10 1 819 651105870 651106674 0.000000e+00 1295.0
20 TraesCS2B01G260300 chr4A 94.595 851 21 6 1 847 563232204 563233033 0.000000e+00 1293.0
21 TraesCS2B01G260300 chr7A 95.238 567 21 5 286 847 19728433 19728998 0.000000e+00 893.0
22 TraesCS2B01G260300 chr7A 87.195 492 34 19 1 475 19728191 19728670 4.030000e-147 532.0
23 TraesCS2B01G260300 chr7A 79.798 99 15 4 7439 7532 35378181 35378083 4.910000e-07 67.6
24 TraesCS2B01G260300 chr3A 91.840 625 28 11 233 848 688304608 688305218 0.000000e+00 850.0
25 TraesCS2B01G260300 chr3A 87.398 492 33 19 1 475 688304424 688304903 8.660000e-149 538.0
26 TraesCS2B01G260300 chr7B 89.406 623 47 13 240 847 393863147 393863765 0.000000e+00 767.0
27 TraesCS2B01G260300 chr7B 85.714 70 5 1 6827 6891 92560532 92560463 1.370000e-07 69.4
28 TraesCS2B01G260300 chr5B 89.246 623 48 14 240 847 242429850 242429232 0.000000e+00 761.0
29 TraesCS2B01G260300 chr3B 90.625 64 5 1 6822 6885 172008075 172008013 4.880000e-12 84.2
30 TraesCS2B01G260300 chr5D 92.982 57 1 1 6832 6885 546080053 546080109 6.310000e-11 80.5
31 TraesCS2B01G260300 chr1D 79.661 118 15 4 7437 7546 76967140 76967024 8.160000e-10 76.8
32 TraesCS2B01G260300 chr1D 89.062 64 2 2 6822 6885 53403108 53403166 2.930000e-09 75.0
33 TraesCS2B01G260300 chr3D 86.765 68 5 1 6822 6885 525535673 525535606 1.060000e-08 73.1
34 TraesCS2B01G260300 chr1B 92.308 39 0 2 7407 7445 491757284 491757249 1.400000e-02 52.8


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 TraesCS2B01G260300 chr2B 326674543 326682124 7581 False 14002.000000 14002 100.000000 1 7582 1 chr2B.!!$F3 7581
1 TraesCS2B01G260300 chr2D 280648603 280656210 7607 True 3646.666667 7452 95.606333 851 7582 3 chr2D.!!$R1 6731
2 TraesCS2B01G260300 chr2A 334590412 334598387 7975 True 1876.600000 3304 93.582600 851 7580 5 chr2A.!!$R1 6729
3 TraesCS2B01G260300 chr4B 640608604 640609454 850 True 1463.000000 1463 97.773000 1 847 1 chr4B.!!$R2 846
4 TraesCS2B01G260300 chrUn 41472687 41473536 849 False 1423.000000 1423 96.945000 1 847 1 chrUn.!!$F1 846
5 TraesCS2B01G260300 chr6B 620653344 620654175 831 True 1303.000000 1303 94.725000 1 848 1 chr6B.!!$R1 847
6 TraesCS2B01G260300 chr6B 690884449 690885246 797 True 702.500000 843 90.024500 1 850 2 chr6B.!!$R2 849
7 TraesCS2B01G260300 chr6B 574466162 574466954 792 False 687.500000 843 89.437500 1 847 2 chr6B.!!$F1 846
8 TraesCS2B01G260300 chr4A 651105870 651106674 804 False 1295.000000 1295 95.504000 1 819 1 chr4A.!!$F2 818
9 TraesCS2B01G260300 chr4A 563232204 563233033 829 False 1293.000000 1293 94.595000 1 847 1 chr4A.!!$F1 846
10 TraesCS2B01G260300 chr7A 19728191 19728998 807 False 712.500000 893 91.216500 1 847 2 chr7A.!!$F1 846
11 TraesCS2B01G260300 chr3A 688304424 688305218 794 False 694.000000 850 89.619000 1 848 2 chr3A.!!$F1 847
12 TraesCS2B01G260300 chr7B 393863147 393863765 618 False 767.000000 767 89.406000 240 847 1 chr7B.!!$F1 607
13 TraesCS2B01G260300 chr5B 242429232 242429850 618 True 761.000000 761 89.246000 240 847 1 chr5B.!!$R1 607

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
871 934 0.540365 CCAGCCACCCAAACACATCT 60.540 55.000 0.00 0.00 0.00 2.90 F
1863 1938 0.320421 GCCTCAAGTGAGTACCGCAA 60.320 55.000 7.51 0.00 40.48 4.85 F
2826 2910 0.318360 TTGCTACTCGTGTCACACCG 60.318 55.000 1.24 0.00 0.00 4.94 F
2945 3029 1.681327 CCTGCTTGCCATGGAGCTT 60.681 57.895 22.22 0.00 39.60 3.74 F
3148 6076 1.930914 TCTGGGCTACTTAGGACTCCT 59.069 52.381 2.31 2.31 37.71 3.69 F
4830 7764 2.093658 TCCTGCGGACCTCTTTATTGTC 60.094 50.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2483 0.178301 TATGCGGGGAATGCGTAACA 59.822 50.000 0.00 0.00 31.22 2.41 R
3586 6515 0.179108 GCCAGGTAGGACAGTAAGCG 60.179 60.000 0.00 0.00 41.22 4.68 R
4795 7727 0.035915 GCAGGAAACAGGGAGAGGAC 60.036 60.000 0.00 0.00 0.00 3.85 R
4830 7764 4.261363 GGAGTGCCTGTGAGAAAGAAAAAG 60.261 45.833 0.00 0.00 0.00 2.27 R
5118 8052 5.876651 AACTCTTTTCTCAAGCCCAAAAT 57.123 34.783 0.00 0.00 0.00 1.82 R
6736 9670 0.102663 TCCACGCGTGTGTCTACAAA 59.897 50.000 34.81 8.42 44.92 2.83 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
426 481 8.164153 CCAAATTCATCATTCACGAACATTTTC 58.836 33.333 0.00 0.00 0.00 2.29
441 496 7.117454 CGAACATTTTCTAAAGTCGCGAATAT 58.883 34.615 12.06 1.56 0.00 1.28
731 793 1.487300 GTTAGAGGGGTCAGGGAGAC 58.513 60.000 0.00 0.00 46.83 3.36
777 840 7.259088 ACTACACTTTAAGGACTTGGATGAT 57.741 36.000 0.00 0.00 0.00 2.45
871 934 0.540365 CCAGCCACCCAAACACATCT 60.540 55.000 0.00 0.00 0.00 2.90
888 951 1.181741 TCTGCCGCTTCTGTCACTCT 61.182 55.000 0.00 0.00 0.00 3.24
897 960 3.876156 GCTTCTGTCACTCTAGTCCTCCT 60.876 52.174 0.00 0.00 0.00 3.69
901 964 4.043561 TCTGTCACTCTAGTCCTCCTTCTT 59.956 45.833 0.00 0.00 0.00 2.52
903 966 3.697542 GTCACTCTAGTCCTCCTTCTTCC 59.302 52.174 0.00 0.00 0.00 3.46
905 968 2.023791 ACTCTAGTCCTCCTTCTTCCCC 60.024 54.545 0.00 0.00 0.00 4.81
1069 1132 1.340248 ACACTGTCGATTCCGTGAAGT 59.660 47.619 11.52 0.00 37.05 3.01
1284 1359 2.084546 CTTGACGATTTGGGGAAGGTC 58.915 52.381 0.00 0.00 0.00 3.85
1367 1442 1.277273 TGTGGCTCATCAGGTCAAGAG 59.723 52.381 0.00 0.00 0.00 2.85
1427 1502 1.380380 CCCAGGGAAATGAGGTGGC 60.380 63.158 0.00 0.00 0.00 5.01
1455 1530 3.462678 GTCGAGGCCCAGGGAGAC 61.463 72.222 10.89 8.84 0.00 3.36
1470 1545 1.174783 GAGACGAGGTGGCTGAGTTA 58.825 55.000 0.00 0.00 0.00 2.24
1617 1692 7.283329 ACAATGGTGGAGATAATAAGAAGGAC 58.717 38.462 0.00 0.00 0.00 3.85
1776 1851 3.118445 AGGCTGAGTTTATCAAGGAGCTC 60.118 47.826 4.71 4.71 37.52 4.09
1862 1937 1.292223 GCCTCAAGTGAGTACCGCA 59.708 57.895 7.51 0.00 40.48 5.69
1863 1938 0.320421 GCCTCAAGTGAGTACCGCAA 60.320 55.000 7.51 0.00 40.48 4.85
1864 1939 1.676014 GCCTCAAGTGAGTACCGCAAT 60.676 52.381 7.51 0.00 40.48 3.56
1883 1958 5.051508 CGCAATGGCTTATCTTTATGTTTGC 60.052 40.000 0.00 0.00 38.10 3.68
1991 2067 5.455326 GGTGGCTATGATCAGGTACTCATTT 60.455 44.000 0.09 0.00 34.60 2.32
2112 2188 5.181009 TGAAGCTGATAAGATCACACTTGG 58.819 41.667 0.00 0.00 33.24 3.61
2113 2189 4.148128 AGCTGATAAGATCACACTTGGG 57.852 45.455 0.00 0.00 35.06 4.12
2114 2190 3.521126 AGCTGATAAGATCACACTTGGGT 59.479 43.478 0.00 0.00 35.06 4.51
2115 2191 4.018960 AGCTGATAAGATCACACTTGGGTT 60.019 41.667 0.00 0.00 35.06 4.11
2117 2193 5.392380 GCTGATAAGATCACACTTGGGTTTG 60.392 44.000 0.00 0.00 35.06 2.93
2119 2195 2.664402 AGATCACACTTGGGTTTGCT 57.336 45.000 0.00 0.00 0.00 3.91
2120 2196 2.949447 AGATCACACTTGGGTTTGCTT 58.051 42.857 0.00 0.00 0.00 3.91
2121 2197 4.098914 AGATCACACTTGGGTTTGCTTA 57.901 40.909 0.00 0.00 0.00 3.09
2122 2198 3.821033 AGATCACACTTGGGTTTGCTTAC 59.179 43.478 0.00 0.00 0.00 2.34
2124 2200 3.626930 TCACACTTGGGTTTGCTTACTT 58.373 40.909 0.00 0.00 0.00 2.24
2125 2201 4.783055 TCACACTTGGGTTTGCTTACTTA 58.217 39.130 0.00 0.00 0.00 2.24
2126 2202 5.194432 TCACACTTGGGTTTGCTTACTTAA 58.806 37.500 0.00 0.00 0.00 1.85
2127 2203 5.830991 TCACACTTGGGTTTGCTTACTTAAT 59.169 36.000 0.00 0.00 0.00 1.40
2128 2204 5.920273 CACACTTGGGTTTGCTTACTTAATG 59.080 40.000 0.00 0.00 0.00 1.90
2176 2258 6.422776 AAATGTTTGTCCGCTTATAGACAG 57.577 37.500 0.00 0.00 43.48 3.51
2202 2284 8.515695 AGATCATTGAAGAGTAAAATGCATCA 57.484 30.769 0.00 0.00 32.50 3.07
2203 2285 8.404000 AGATCATTGAAGAGTAAAATGCATCAC 58.596 33.333 0.00 0.00 32.50 3.06
2204 2286 7.451501 TCATTGAAGAGTAAAATGCATCACA 57.548 32.000 0.00 0.00 32.50 3.58
2205 2287 8.058667 TCATTGAAGAGTAAAATGCATCACAT 57.941 30.769 0.00 0.00 42.30 3.21
2206 2288 7.971722 TCATTGAAGAGTAAAATGCATCACATG 59.028 33.333 0.00 0.00 39.60 3.21
2207 2289 6.822667 TGAAGAGTAAAATGCATCACATGT 57.177 33.333 0.00 0.00 39.60 3.21
2264 2347 4.900635 AACTTCAAAACTGCAGATTCGT 57.099 36.364 23.35 7.79 0.00 3.85
2277 2360 6.874134 ACTGCAGATTCGTGTTCTAAAACTAT 59.126 34.615 23.35 0.00 36.30 2.12
2319 2402 1.404391 CCCAGATCAGCATTGACTTGC 59.596 52.381 0.00 0.00 43.09 4.01
2330 2413 2.238942 TTGACTTGCTCACGTGTCAT 57.761 45.000 16.51 1.18 38.89 3.06
2383 2466 3.973425 AGCCTATTTGCCTTCTGACATT 58.027 40.909 0.00 0.00 0.00 2.71
2399 2482 4.661125 TGACATTGAAATGCATCTTACGC 58.339 39.130 0.00 0.00 40.04 4.42
2400 2483 4.395854 TGACATTGAAATGCATCTTACGCT 59.604 37.500 0.00 0.00 40.04 5.07
2401 2484 4.665212 ACATTGAAATGCATCTTACGCTG 58.335 39.130 0.00 0.00 40.04 5.18
2402 2485 4.156556 ACATTGAAATGCATCTTACGCTGT 59.843 37.500 0.00 0.00 40.04 4.40
2403 2486 4.764679 TTGAAATGCATCTTACGCTGTT 57.235 36.364 0.00 0.00 0.00 3.16
2404 2487 5.871465 TTGAAATGCATCTTACGCTGTTA 57.129 34.783 0.00 0.00 0.00 2.41
2405 2488 5.216566 TGAAATGCATCTTACGCTGTTAC 57.783 39.130 0.00 0.00 0.00 2.50
2406 2489 3.925688 AATGCATCTTACGCTGTTACG 57.074 42.857 0.00 0.00 39.50 3.18
2407 2490 0.996462 TGCATCTTACGCTGTTACGC 59.004 50.000 0.00 0.00 36.19 4.42
2408 2491 0.996462 GCATCTTACGCTGTTACGCA 59.004 50.000 1.04 0.00 36.19 5.24
2433 2516 1.337071 CCGCATAAGTCGGCTTAGAGA 59.663 52.381 15.65 0.00 40.17 3.10
2524 2607 3.341043 CGCGCAACACACTGAGCT 61.341 61.111 8.75 0.00 39.67 4.09
2599 2682 3.181471 TGCAGATTTAGCTCTACTCTGGC 60.181 47.826 14.16 9.22 35.10 4.85
2662 2746 6.365789 CACGATCACCATTTATTTTTGTGCTT 59.634 34.615 0.00 0.00 0.00 3.91
2716 2800 2.990967 CCGCCCTGCACAAATGGT 60.991 61.111 0.00 0.00 0.00 3.55
2760 2844 0.389166 CACGTCTGCTTCTCTGGACC 60.389 60.000 0.00 0.00 0.00 4.46
2769 2853 1.279271 CTTCTCTGGACCGGGTTGAAT 59.721 52.381 6.32 0.00 0.00 2.57
2821 2905 1.324383 TGTCCTTGCTACTCGTGTCA 58.676 50.000 0.00 0.00 0.00 3.58
2826 2910 0.318360 TTGCTACTCGTGTCACACCG 60.318 55.000 1.24 0.00 0.00 4.94
2945 3029 1.681327 CCTGCTTGCCATGGAGCTT 60.681 57.895 22.22 0.00 39.60 3.74
3119 6047 1.937223 CAACAACCACGTGAGCAGTTA 59.063 47.619 19.30 0.00 0.00 2.24
3141 6069 4.608948 AATTCCGATCTGGGCTACTTAG 57.391 45.455 4.16 0.00 38.76 2.18
3148 6076 1.930914 TCTGGGCTACTTAGGACTCCT 59.069 52.381 2.31 2.31 37.71 3.69
3187 6115 2.154462 AGACTTGGATCTGCGGTTTTG 58.846 47.619 0.00 0.00 0.00 2.44
3192 6120 2.582052 TGGATCTGCGGTTTTGAAGTT 58.418 42.857 0.00 0.00 0.00 2.66
3216 6144 3.297736 AGGACTAACTTGATACCCCTCG 58.702 50.000 0.00 0.00 0.00 4.63
3229 6157 6.192773 TGATACCCCTCGAATAGTTATAGGG 58.807 44.000 0.00 0.00 45.57 3.53
3314 6242 9.025020 GTTATGCTATCATACTCATGTAATCCG 57.975 37.037 0.00 0.00 35.07 4.18
3351 6279 2.870035 GCCCAATTTGTTTGCACCCTAC 60.870 50.000 0.00 0.00 33.73 3.18
3352 6280 2.366916 CCCAATTTGTTTGCACCCTACA 59.633 45.455 0.00 0.00 33.73 2.74
3445 6373 5.055812 CCTTTCTCTCTTCCATATGCTGTC 58.944 45.833 0.00 0.00 0.00 3.51
3586 6515 7.881775 ATAGAAATATGACCCAAAACCTCAC 57.118 36.000 0.00 0.00 0.00 3.51
3762 6691 6.948309 AGGTTAACCTTATTGAGCAAATCAGT 59.052 34.615 21.96 0.00 46.09 3.41
3836 6766 2.231215 ACACGAGCCTGAATGATAGC 57.769 50.000 0.00 0.00 0.00 2.97
3932 6862 4.804108 TGCATACACAATTAGCAAACACC 58.196 39.130 0.00 0.00 31.42 4.16
3979 6911 5.825151 AGCTTTGCCCTTGACTTAATATCTC 59.175 40.000 0.00 0.00 0.00 2.75
4006 6938 5.378985 TCTCTCCAGAATAGGGGTAAGGTAT 59.621 44.000 0.00 0.00 0.00 2.73
4126 7058 5.391312 AACCTTTATCAATGTGAGGTTGC 57.609 39.130 5.36 0.00 46.08 4.17
4296 7228 5.565592 TGTAATTGTGCAATGATGGAGTC 57.434 39.130 0.00 0.00 0.00 3.36
4430 7362 5.681494 AGGTACCTCTCTATATTCCCACA 57.319 43.478 9.21 0.00 0.00 4.17
4437 7369 7.713518 ACCTCTCTATATTCCCACAGATGATA 58.286 38.462 0.00 0.00 0.00 2.15
4714 7646 2.172505 TGTTCTCAGCAGGGAAGAAACA 59.827 45.455 0.00 0.00 0.00 2.83
4794 7726 7.691993 AATATAAGTCAGTGTTGATACCCCT 57.308 36.000 0.00 0.00 35.39 4.79
4795 7727 3.703001 AAGTCAGTGTTGATACCCCTG 57.297 47.619 0.00 0.00 35.39 4.45
4830 7764 2.093658 TCCTGCGGACCTCTTTATTGTC 60.094 50.000 0.00 0.00 0.00 3.18
4912 7846 2.357009 CCATGTGGCTGCATCTACTTTC 59.643 50.000 5.63 0.00 0.00 2.62
5058 7992 5.280654 ACAGTGGAAGTTCATTTTTGCAT 57.719 34.783 5.01 0.00 0.00 3.96
5064 7998 8.370182 AGTGGAAGTTCATTTTTGCATCTAAAT 58.630 29.630 5.01 0.00 0.00 1.40
5066 8000 8.991026 TGGAAGTTCATTTTTGCATCTAAATTG 58.009 29.630 5.01 0.00 0.00 2.32
5118 8052 8.408601 GCAGGAATATCTTTTTAGATGAGCAAA 58.591 33.333 0.00 0.00 0.00 3.68
5139 8073 5.876651 AATTTTGGGCTTGAGAAAAGAGT 57.123 34.783 0.00 0.00 0.00 3.24
5140 8074 5.876651 ATTTTGGGCTTGAGAAAAGAGTT 57.123 34.783 0.00 0.00 0.00 3.01
5143 8077 5.675684 TTGGGCTTGAGAAAAGAGTTTTT 57.324 34.783 0.00 0.00 39.16 1.94
5317 8251 8.561738 TTGAAGTCAAAGGTCATTAGTAATCC 57.438 34.615 0.00 0.00 32.11 3.01
5318 8252 6.816640 TGAAGTCAAAGGTCATTAGTAATCCG 59.183 38.462 0.00 0.00 0.00 4.18
5319 8253 5.116882 AGTCAAAGGTCATTAGTAATCCGC 58.883 41.667 0.00 0.00 0.00 5.54
5410 8344 4.635324 ACAAAAATCCAAAAAGCAGTGGTG 59.365 37.500 0.00 0.00 36.23 4.17
5561 8495 5.561679 TCTGAGAAGCTACAGTAACTCTCA 58.438 41.667 9.49 9.49 35.84 3.27
5564 8498 7.177568 TCTGAGAAGCTACAGTAACTCTCATTT 59.822 37.037 10.14 0.00 35.84 2.32
5606 8540 6.110707 CCATCAAATAAATCTTGCAAAGCCT 58.889 36.000 0.00 0.00 45.70 4.58
5623 8557 5.868043 AAGCCTTTTTATTTCATTGCTGC 57.132 34.783 0.00 0.00 0.00 5.25
5627 8561 5.409214 GCCTTTTTATTTCATTGCTGCTGAA 59.591 36.000 0.00 0.24 0.00 3.02
5630 8564 7.799914 CCTTTTTATTTCATTGCTGCTGAAAAC 59.200 33.333 17.40 0.00 43.61 2.43
5704 8638 9.624697 TTCTTTTGCATGTCATAGTTGAATTAC 57.375 29.630 0.00 0.00 32.48 1.89
5708 8642 5.872070 TGCATGTCATAGTTGAATTACGACA 59.128 36.000 0.00 0.00 36.45 4.35
5972 8906 2.278245 ACTGTTTCCCCATGGATCTCA 58.722 47.619 15.22 4.96 41.40 3.27
6000 8934 6.818644 TCCAATAGTTCTCAGTACATTTCTGC 59.181 38.462 0.00 0.00 33.48 4.26
6622 9556 8.681486 AGCAGAATAATACATGTATGCTTTCA 57.319 30.769 18.94 1.82 0.00 2.69
6645 9579 3.213206 TCCAAGAGACACACAGCAATT 57.787 42.857 0.00 0.00 0.00 2.32
6734 9668 9.193806 AGATGCATTATTGAGGAATGTTAGTTT 57.806 29.630 0.00 0.00 36.78 2.66
6797 9731 4.238514 AGCACTAGATTGTTTCACGAGTC 58.761 43.478 0.00 0.00 0.00 3.36
6803 9737 8.162880 CACTAGATTGTTTCACGAGTCATAAAC 58.837 37.037 0.00 5.46 33.46 2.01
6809 9743 2.333926 TCACGAGTCATAAACGGCAAG 58.666 47.619 0.00 0.00 0.00 4.01
6820 9754 6.741358 GTCATAAACGGCAAGACTGAAATAAC 59.259 38.462 0.00 0.00 0.00 1.89
6924 9861 3.557903 CTGGCCTGGTCACAGTGGG 62.558 68.421 3.32 0.00 43.36 4.61
6925 9862 4.351054 GGCCTGGTCACAGTGGGG 62.351 72.222 0.00 0.00 43.36 4.96
6980 9917 5.680619 ACACAGAACACTTATCTTCCAACA 58.319 37.500 0.00 0.00 0.00 3.33
6981 9918 6.299141 ACACAGAACACTTATCTTCCAACAT 58.701 36.000 0.00 0.00 0.00 2.71
6982 9919 6.772716 ACACAGAACACTTATCTTCCAACATT 59.227 34.615 0.00 0.00 0.00 2.71
7062 10017 5.470368 CCTGATCTTTGTTCGTCTAGTTCA 58.530 41.667 0.00 0.00 0.00 3.18
7085 10040 0.803740 CTGCTTCAAGGCTCTTCAGC 59.196 55.000 0.00 0.00 46.06 4.26
7109 10064 4.094887 GGTGCTGTATGTTCTGTGTATTGG 59.905 45.833 0.00 0.00 0.00 3.16
7114 10069 7.094975 TGCTGTATGTTCTGTGTATTGGTTAAC 60.095 37.037 0.00 0.00 0.00 2.01
7173 10129 5.242434 TGTGACATTTAGCGTAAGTTCCAT 58.758 37.500 0.00 0.00 41.68 3.41
7183 10139 2.644676 GTAAGTTCCATCCTCCAAGCC 58.355 52.381 0.00 0.00 0.00 4.35
7237 10193 6.007703 TCATGGTTTATTCGTTCCCTTTTCT 58.992 36.000 0.00 0.00 0.00 2.52
7314 10273 5.147330 ACTTGAGTTTGTCATACATCCGA 57.853 39.130 0.00 0.00 34.17 4.55
7384 10343 1.794512 ACAAAACCATTGCATTCGCC 58.205 45.000 0.00 0.00 37.32 5.54
7397 10356 3.374988 TGCATTCGCCTGACTGAAAATAG 59.625 43.478 0.00 0.00 37.32 1.73
7442 10401 3.786553 TCAAGGTGCTTAGAGAGGGTAA 58.213 45.455 0.00 0.00 0.00 2.85
7445 10404 2.496470 AGGTGCTTAGAGAGGGTAAACG 59.504 50.000 0.00 0.00 0.00 3.60
7461 10420 5.578336 GGGTAAACGCTTAATTAGACGTCTT 59.422 40.000 25.44 8.59 36.22 3.01
7466 10425 8.970691 AAACGCTTAATTAGACGTCTTTACTA 57.029 30.769 25.44 1.28 36.22 1.82
7484 10443 9.778741 TCTTTACTATAGAAATAGGCATTGGTG 57.221 33.333 6.78 0.00 39.63 4.17
7548 10554 4.269523 TGGGCGCTGCTTGGACTT 62.270 61.111 7.64 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
642 703 8.074972 TGTGAACAGTAAAACAACGTTAAGTTT 58.925 29.630 10.10 10.10 42.02 2.66
731 793 0.796312 CGTGTCATTCGGGTCCAAAG 59.204 55.000 0.00 0.00 0.00 2.77
777 840 7.148018 ACGTAGGTCCTCGAACTATGAAAATTA 60.148 37.037 11.89 0.00 40.24 1.40
871 934 0.528017 CTAGAGTGACAGAAGCGGCA 59.472 55.000 1.45 0.00 0.00 5.69
905 968 1.725169 TTTGGGGTGAGGAAGTGGGG 61.725 60.000 0.00 0.00 0.00 4.96
908 971 0.539669 GGGTTTGGGGTGAGGAAGTG 60.540 60.000 0.00 0.00 0.00 3.16
909 972 0.701310 AGGGTTTGGGGTGAGGAAGT 60.701 55.000 0.00 0.00 0.00 3.01
1069 1132 3.202906 CTCTTTCGGGATTTGCCGAATA 58.797 45.455 23.59 15.01 45.59 1.75
1274 1349 3.327404 GGGCTTCGACCTTCCCCA 61.327 66.667 0.00 0.00 35.75 4.96
1284 1359 4.697756 TCCGCACCTTGGGCTTCG 62.698 66.667 0.00 0.00 0.00 3.79
1367 1442 0.394899 CTCATTTCCCTGGGCCTCAC 60.395 60.000 8.22 0.00 0.00 3.51
1427 1502 2.885861 CCTCGACCTTGGTCTCCG 59.114 66.667 16.60 5.75 0.00 4.63
1455 1530 1.275291 TCCTTTAACTCAGCCACCTCG 59.725 52.381 0.00 0.00 0.00 4.63
1460 1535 3.559171 GGTGTCATCCTTTAACTCAGCCA 60.559 47.826 0.00 0.00 0.00 4.75
1470 1545 1.455822 TTCCCTGGGTGTCATCCTTT 58.544 50.000 13.56 0.00 0.00 3.11
1617 1692 1.442526 GCTCATCCTCACCATTGGCG 61.443 60.000 1.54 0.00 0.00 5.69
1695 1770 6.657541 GGGTGTAATCAAACATGAAGGAGTTA 59.342 38.462 0.00 0.00 0.00 2.24
1776 1851 0.448990 TCATCGTGTAGAACCGGTCG 59.551 55.000 8.04 6.09 0.00 4.79
1991 2067 3.953612 GGCATAATGTCACAAAGGGATGA 59.046 43.478 0.00 0.00 0.00 2.92
2080 2156 8.119226 GTGATCTTATCAGCTTCATGTTTGTAC 58.881 37.037 0.00 0.00 40.53 2.90
2145 2227 2.538037 GCGGACAAACATTTCCAAACAC 59.462 45.455 0.00 0.00 0.00 3.32
2176 2258 8.618677 TGATGCATTTTACTCTTCAATGATCTC 58.381 33.333 0.00 0.00 30.66 2.75
2202 2284 7.569111 AGACCCTCTAATATTTGTAGGACATGT 59.431 37.037 0.00 0.00 0.00 3.21
2203 2285 7.967908 AGACCCTCTAATATTTGTAGGACATG 58.032 38.462 13.10 0.00 0.00 3.21
2204 2286 7.789831 TGAGACCCTCTAATATTTGTAGGACAT 59.210 37.037 13.10 3.62 0.00 3.06
2205 2287 7.130099 TGAGACCCTCTAATATTTGTAGGACA 58.870 38.462 13.10 8.56 0.00 4.02
2206 2288 7.598759 TGAGACCCTCTAATATTTGTAGGAC 57.401 40.000 13.10 8.53 0.00 3.85
2207 2289 7.844779 ACTTGAGACCCTCTAATATTTGTAGGA 59.155 37.037 13.10 0.00 0.00 2.94
2264 2347 9.498176 GACTCCCAGTAAAATAGTTTTAGAACA 57.502 33.333 0.00 0.00 38.26 3.18
2277 2360 3.307480 GCTGCTTAGGACTCCCAGTAAAA 60.307 47.826 0.00 0.00 33.88 1.52
2399 2482 1.095228 ATGCGGGGAATGCGTAACAG 61.095 55.000 0.00 0.00 34.24 3.16
2400 2483 0.178301 TATGCGGGGAATGCGTAACA 59.822 50.000 0.00 0.00 31.22 2.41
2401 2484 1.263217 CTTATGCGGGGAATGCGTAAC 59.737 52.381 0.00 0.00 38.52 2.50
2402 2485 1.134340 ACTTATGCGGGGAATGCGTAA 60.134 47.619 0.39 0.39 40.48 3.18
2403 2486 0.466543 ACTTATGCGGGGAATGCGTA 59.533 50.000 0.00 0.00 32.85 4.42
2404 2487 0.814010 GACTTATGCGGGGAATGCGT 60.814 55.000 0.00 0.00 35.38 5.24
2405 2488 1.831389 CGACTTATGCGGGGAATGCG 61.831 60.000 0.00 0.00 34.24 4.73
2406 2489 1.507141 CCGACTTATGCGGGGAATGC 61.507 60.000 0.00 0.00 44.87 3.56
2407 2490 2.616969 CCGACTTATGCGGGGAATG 58.383 57.895 0.00 0.00 44.87 2.67
2433 2516 3.189285 GTGCACAACAAAAAGCTGATGT 58.811 40.909 13.17 0.00 33.04 3.06
2524 2607 2.296190 CCACAGTAGCGGTGCATAGATA 59.704 50.000 5.29 0.00 34.94 1.98
2555 2638 1.867233 GCACCGTGGCTATGATAACTG 59.133 52.381 0.00 0.00 0.00 3.16
2599 2682 0.392595 TTGAGAGCATGCTGAGGCTG 60.393 55.000 28.27 0.00 39.98 4.85
2662 2746 2.263227 CCACGTACCGGCATGACA 59.737 61.111 0.00 0.00 0.00 3.58
2716 2800 1.971505 CTGGGTCTAGCGAATGGGCA 61.972 60.000 0.00 0.00 34.64 5.36
2760 2844 2.817901 CCTAAGACGGTATTCAACCCG 58.182 52.381 0.00 0.00 46.62 5.28
2769 2853 0.542467 TGGTGGTGCCTAAGACGGTA 60.542 55.000 0.00 0.00 38.35 4.02
2821 2905 2.184167 CGGTGCAGTTTTCCGGTGT 61.184 57.895 0.00 0.00 40.49 4.16
2826 2910 4.038080 CCGGCGGTGCAGTTTTCC 62.038 66.667 19.97 0.00 0.00 3.13
3119 6047 3.933861 AAGTAGCCCAGATCGGAATTT 57.066 42.857 5.32 0.00 36.56 1.82
3141 6069 8.041323 TCTATTTAAGTTGTTCATCAGGAGTCC 58.959 37.037 0.00 0.00 0.00 3.85
3148 6076 9.219603 CCAAGTCTCTATTTAAGTTGTTCATCA 57.780 33.333 0.00 0.00 0.00 3.07
3187 6115 7.551974 GGGGTATCAAGTTAGTCCTAAAACTTC 59.448 40.741 0.00 0.00 42.52 3.01
3192 6120 5.361857 CGAGGGGTATCAAGTTAGTCCTAAA 59.638 44.000 0.00 0.00 0.00 1.85
3208 6136 4.347607 GCCCTATAACTATTCGAGGGGTA 58.652 47.826 7.37 0.00 46.11 3.69
3216 6144 7.719871 TGTATCAGAGGCCCTATAACTATTC 57.280 40.000 0.00 0.00 0.00 1.75
3229 6157 8.443953 AAAGATGAGTAAAATGTATCAGAGGC 57.556 34.615 0.00 0.00 0.00 4.70
3314 6242 2.923121 TGGGCAGATGAATAGACAAGC 58.077 47.619 0.00 0.00 0.00 4.01
3351 6279 9.265901 CAGTTAACAGGATCTGATATAAAGGTG 57.734 37.037 8.61 0.00 35.18 4.00
3352 6280 8.432805 CCAGTTAACAGGATCTGATATAAAGGT 58.567 37.037 11.47 0.00 35.18 3.50
3418 6346 6.873076 CAGCATATGGAAGAGAGAAAGGTATC 59.127 42.308 4.56 0.00 0.00 2.24
3432 6360 6.437477 ACGAGGATTATAGACAGCATATGGAA 59.563 38.462 4.56 0.00 0.00 3.53
3586 6515 0.179108 GCCAGGTAGGACAGTAAGCG 60.179 60.000 0.00 0.00 41.22 4.68
3631 6560 7.889600 TGATAATAATGCCAGGCAAGATTATGA 59.110 33.333 31.02 25.16 43.62 2.15
3671 6600 8.220755 TCATATAATTTGCAACCCACTTACTC 57.779 34.615 0.00 0.00 0.00 2.59
3807 6737 3.765026 TCAGGCTCGTGTTTTGTTTTTC 58.235 40.909 0.00 0.00 0.00 2.29
3836 6766 2.082231 CTTCCTCTGCACATGGTCAAG 58.918 52.381 0.00 0.00 0.00 3.02
3884 6814 3.145286 TGCTCGTGGTGAATTTCATCAA 58.855 40.909 13.77 0.00 39.52 2.57
3932 6862 4.389374 TGACTTTCCTCTTAAGCAACCAG 58.611 43.478 0.00 0.00 0.00 4.00
3979 6911 5.071115 CCTTACCCCTATTCTGGAGAGAAAG 59.929 48.000 0.00 0.00 41.64 2.62
3994 6926 6.567260 AGACAGTCTAGATATACCTTACCCCT 59.433 42.308 0.00 0.00 0.00 4.79
4049 6981 9.772973 ATGACAAGTAAAGTAGTAAACACATGA 57.227 29.630 0.00 0.00 0.00 3.07
4063 6995 9.900264 GCAAAAGTTACAAAATGACAAGTAAAG 57.100 29.630 0.00 0.00 0.00 1.85
4126 7058 9.844790 TGTTAATGCAACTCATAAGAAAGAATG 57.155 29.630 0.00 0.00 38.05 2.67
4296 7228 2.739913 ACCACATGTCAATTACGTTCCG 59.260 45.455 0.00 0.00 0.00 4.30
4373 7305 2.076863 CGGAAGGTCCATGAAACAGTC 58.923 52.381 0.00 0.00 35.91 3.51
4437 7369 7.800092 AGTGAGGAGTTATAAGCAATGAGATT 58.200 34.615 0.00 0.00 0.00 2.40
4543 7475 8.339714 TGGTAAAACTTTCAACGAGTTAATCTG 58.660 33.333 0.00 0.00 36.38 2.90
4602 7534 6.655003 TGAACAAGATTACCAATTCTGGAGAC 59.345 38.462 0.00 0.00 46.92 3.36
4714 7646 9.331282 GAGGTTTACAAATATATTGCACTCTCT 57.669 33.333 0.00 0.00 0.00 3.10
4794 7726 1.352083 CAGGAAACAGGGAGAGGACA 58.648 55.000 0.00 0.00 0.00 4.02
4795 7727 0.035915 GCAGGAAACAGGGAGAGGAC 60.036 60.000 0.00 0.00 0.00 3.85
4830 7764 4.261363 GGAGTGCCTGTGAGAAAGAAAAAG 60.261 45.833 0.00 0.00 0.00 2.27
4984 7918 5.971763 ACACATGACTCCTCTCTATTTGAC 58.028 41.667 0.00 0.00 0.00 3.18
5042 7976 8.992073 ACCAATTTAGATGCAAAAATGAACTTC 58.008 29.630 0.00 0.00 0.00 3.01
5047 7981 8.312564 TGATCACCAATTTAGATGCAAAAATGA 58.687 29.630 0.00 0.00 0.00 2.57
5058 7992 9.300681 ACTTCAAAGAATGATCACCAATTTAGA 57.699 29.630 0.00 0.00 38.03 2.10
5064 7998 9.166173 CATACTACTTCAAAGAATGATCACCAA 57.834 33.333 0.00 0.00 38.03 3.67
5066 8000 8.948631 TCATACTACTTCAAAGAATGATCACC 57.051 34.615 0.00 0.00 38.03 4.02
5118 8052 5.876651 AACTCTTTTCTCAAGCCCAAAAT 57.123 34.783 0.00 0.00 0.00 1.82
5140 8074 7.344871 TCCACCCACCTGTAGAAAAATTAAAAA 59.655 33.333 0.00 0.00 0.00 1.94
5143 8077 5.954757 TCCACCCACCTGTAGAAAAATTAA 58.045 37.500 0.00 0.00 0.00 1.40
5317 8251 6.463576 GGATGTTAGTTATACAACAAAACGCG 59.536 38.462 3.53 3.53 38.11 6.01
5318 8252 7.524065 AGGATGTTAGTTATACAACAAAACGC 58.476 34.615 0.00 0.00 38.11 4.84
5410 8344 8.017946 GTCTAACAAATGATGTCCAGAAAAGTC 58.982 37.037 0.00 0.00 42.99 3.01
5519 8453 4.458989 TCAGATTTGTATGGTGTTGCCTTC 59.541 41.667 0.00 0.00 38.35 3.46
5561 8495 9.320295 TGATGGTAATAAAGAGTTGGGAAAAAT 57.680 29.630 0.00 0.00 0.00 1.82
5564 8498 8.713708 TTTGATGGTAATAAAGAGTTGGGAAA 57.286 30.769 0.00 0.00 0.00 3.13
5606 8540 7.281774 TGGTTTTCAGCAGCAATGAAATAAAAA 59.718 29.630 9.89 0.00 43.96 1.94
5623 8557 6.317789 TGCAGAGTTCTTAATGGTTTTCAG 57.682 37.500 0.00 0.00 0.00 3.02
5627 8561 6.655078 ATGTTGCAGAGTTCTTAATGGTTT 57.345 33.333 0.00 0.00 0.00 3.27
5704 8638 2.231478 ACTGGATAGACCTTGTGTGTCG 59.769 50.000 0.00 0.00 37.80 4.35
5708 8642 4.024670 GGTAGACTGGATAGACCTTGTGT 58.975 47.826 0.00 0.00 39.86 3.72
5788 8722 7.798710 TTATTTTCACCCAATCAAACCCATA 57.201 32.000 0.00 0.00 0.00 2.74
6238 9172 1.269726 ACCATTCCAACTTTTGCAGCG 60.270 47.619 0.00 0.00 0.00 5.18
6436 9370 3.684305 TGAGTATCAACAAATCTGGTGCG 59.316 43.478 0.00 0.00 45.97 5.34
6622 9556 3.213206 TGCTGTGTGTCTCTTGGAAAT 57.787 42.857 0.00 0.00 0.00 2.17
6645 9579 8.792633 ACTTTCTGCAAATAAAATAGTACAGCA 58.207 29.630 0.00 0.00 0.00 4.41
6662 9596 9.376075 CTTTCTTAGAGATGATAACTTTCTGCA 57.624 33.333 0.00 0.00 0.00 4.41
6663 9597 9.593134 TCTTTCTTAGAGATGATAACTTTCTGC 57.407 33.333 0.00 0.00 0.00 4.26
6676 9610 8.848474 TTCATTTTCCGTTCTTTCTTAGAGAT 57.152 30.769 0.00 0.00 33.51 2.75
6734 9668 2.030096 TCCACGCGTGTGTCTACAAATA 60.030 45.455 34.81 7.10 44.92 1.40
6736 9670 0.102663 TCCACGCGTGTGTCTACAAA 59.897 50.000 34.81 8.42 44.92 2.83
6797 9731 6.523201 GTGTTATTTCAGTCTTGCCGTTTATG 59.477 38.462 0.00 0.00 0.00 1.90
6803 9737 3.125316 GGAGTGTTATTTCAGTCTTGCCG 59.875 47.826 0.00 0.00 37.75 5.69
6809 9743 4.553330 TGGAGGGAGTGTTATTTCAGTC 57.447 45.455 0.00 0.00 37.13 3.51
6820 9754 6.673978 TCTTATATTATGGGATGGAGGGAGTG 59.326 42.308 0.00 0.00 0.00 3.51
6910 9847 4.351054 GGCCCCACTGTGACCAGG 62.351 72.222 9.86 5.64 43.36 4.45
6924 9861 3.940209 TGAAAATGATGAACACAGGCC 57.060 42.857 0.00 0.00 0.00 5.19
6925 9862 5.390145 GCAAATGAAAATGATGAACACAGGC 60.390 40.000 0.00 0.00 0.00 4.85
6980 9917 2.422276 GCAACCTGCACGAAGAAAAT 57.578 45.000 0.00 0.00 44.26 1.82
6981 9918 3.936585 GCAACCTGCACGAAGAAAA 57.063 47.368 0.00 0.00 44.26 2.29
7062 10017 1.817447 GAAGAGCCTTGAAGCAGCAAT 59.183 47.619 0.00 0.00 34.23 3.56
7085 10040 1.795768 ACACAGAACATACAGCACCG 58.204 50.000 0.00 0.00 0.00 4.94
7129 10085 2.083774 GGCAATGCACAGTACTAAGCA 58.916 47.619 19.78 19.78 41.73 3.91
7173 10129 3.727387 GGCTACAGGCTTGGAGGA 58.273 61.111 10.51 0.00 41.46 3.71
7183 10139 2.224161 GCATCAGGAACCTAGGCTACAG 60.224 54.545 9.30 0.00 0.00 2.74
7256 10212 2.921754 AGCTACAACGCTACAAATCGTC 59.078 45.455 0.00 0.00 38.76 4.20
7258 10214 3.991605 AAGCTACAACGCTACAAATCG 57.008 42.857 0.00 0.00 39.86 3.34
7314 10273 5.240183 CCAGAATTTCATCCGCATCTATGTT 59.760 40.000 0.00 0.00 0.00 2.71
7384 10343 7.361286 GCCTAAAGAACCACTATTTTCAGTCAG 60.361 40.741 0.00 0.00 0.00 3.51
7397 10356 3.746940 TGTACAAGGCCTAAAGAACCAC 58.253 45.455 5.16 0.00 0.00 4.16
7461 10420 7.979444 GCACCAATGCCTATTTCTATAGTAA 57.021 36.000 0.00 0.00 46.97 2.24
7500 10490 9.881529 TCGTACAATGGTGTTTAGAAAAATAAC 57.118 29.630 0.00 0.00 39.30 1.89


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

AutoCloner maintained by Alex Coulton.