Multiple sequence alignment - TraesCS5D01G521000

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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 TraesCS5D01G521000 chr5D 100.000 4421 0 0 1 4421 541989314 541993734 0.000000e+00 8165.0
1 TraesCS5D01G521000 chr5D 86.576 514 57 10 3344 3851 542295696 542296203 1.390000e-154 556.0
2 TraesCS5D01G521000 chr5D 79.108 426 51 19 2593 2985 542097874 542098294 4.390000e-65 259.0
3 TraesCS5D01G521000 chr5D 92.632 95 5 2 3226 3319 513975055 513975148 7.710000e-28 135.0
4 TraesCS5D01G521000 chr5B 93.046 2272 150 5 1 2265 684031044 684033314 0.000000e+00 3314.0
5 TraesCS5D01G521000 chr5B 92.557 2284 150 8 1 2265 684038045 684040327 0.000000e+00 3258.0
6 TraesCS5D01G521000 chr5B 83.473 1549 180 44 925 2450 684049584 684051079 0.000000e+00 1373.0
7 TraesCS5D01G521000 chr5B 93.267 802 31 5 2266 3046 684040365 684041164 0.000000e+00 1160.0
8 TraesCS5D01G521000 chr5B 91.033 881 46 9 3317 4189 684041270 684042125 0.000000e+00 1158.0
9 TraesCS5D01G521000 chr5B 90.899 879 50 6 3317 4189 684034257 684035111 0.000000e+00 1153.0
10 TraesCS5D01G521000 chr5B 92.653 803 34 7 2266 3046 684033352 684034151 0.000000e+00 1133.0
11 TraesCS5D01G521000 chr5B 92.661 218 14 2 4190 4407 684042238 684042453 3.320000e-81 313.0
12 TraesCS5D01G521000 chr5B 84.579 214 25 6 4197 4406 684096769 684096978 5.800000e-49 206.0
13 TraesCS5D01G521000 chr5B 95.283 106 5 0 3132 3237 684034155 684034260 7.600000e-38 169.0
14 TraesCS5D01G521000 chr5B 95.283 106 5 0 3132 3237 684041168 684041273 7.600000e-38 169.0
15 TraesCS5D01G521000 chr4A 91.517 2287 141 28 1 2265 627303151 627300896 0.000000e+00 3099.0
16 TraesCS5D01G521000 chr4A 91.268 2279 148 24 1 2265 627168592 627166351 0.000000e+00 3059.0
17 TraesCS5D01G521000 chr4A 91.224 2279 149 24 1 2265 627088941 627086700 0.000000e+00 3053.0
18 TraesCS5D01G521000 chr4A 91.129 2277 151 25 1 2265 627291791 627289554 0.000000e+00 3038.0
19 TraesCS5D01G521000 chr4A 92.140 2150 142 15 1 2136 627005439 627003303 0.000000e+00 3009.0
20 TraesCS5D01G521000 chr4A 90.663 996 50 13 2269 3237 627300858 627299879 0.000000e+00 1284.0
21 TraesCS5D01G521000 chr4A 92.865 883 46 9 3315 4188 627299885 627299011 0.000000e+00 1266.0
22 TraesCS5D01G521000 chr4A 81.969 1564 196 44 927 2456 626990380 626988869 0.000000e+00 1247.0
23 TraesCS5D01G521000 chr4A 90.136 882 52 19 3317 4189 627283275 627282420 0.000000e+00 1114.0
24 TraesCS5D01G521000 chr4A 89.807 883 53 21 3317 4189 626994593 626993738 0.000000e+00 1098.0
25 TraesCS5D01G521000 chr4A 89.683 882 56 18 3317 4189 627080454 627079599 0.000000e+00 1092.0
26 TraesCS5D01G521000 chr4A 89.683 882 56 18 3317 4189 627160105 627159250 0.000000e+00 1092.0
27 TraesCS5D01G521000 chr4A 91.805 781 40 7 2475 3237 626995364 626994590 0.000000e+00 1066.0
28 TraesCS5D01G521000 chr4A 91.805 781 40 7 2475 3237 627160876 627160102 0.000000e+00 1066.0
29 TraesCS5D01G521000 chr4A 91.421 781 43 7 2475 3237 627081225 627080451 0.000000e+00 1050.0
30 TraesCS5D01G521000 chr4A 91.421 781 43 7 2475 3237 627284046 627283272 0.000000e+00 1050.0
31 TraesCS5D01G521000 chr4A 87.963 540 54 9 3319 3851 626988015 626987480 1.040000e-175 627.0
32 TraesCS5D01G521000 chr4A 94.608 204 10 1 4190 4393 627159135 627158933 9.230000e-82 315.0
33 TraesCS5D01G521000 chr4A 94.608 204 10 1 4190 4393 627282305 627282103 9.230000e-82 315.0
34 TraesCS5D01G521000 chr4A 91.453 234 9 6 2269 2493 627289516 627289285 1.190000e-80 311.0
35 TraesCS5D01G521000 chr4A 94.118 204 11 1 4190 4393 626993623 626993421 4.290000e-80 309.0
36 TraesCS5D01G521000 chr4A 94.118 204 11 1 4190 4393 627079484 627079282 4.290000e-80 309.0
37 TraesCS5D01G521000 chr4A 91.743 218 17 1 4190 4407 627298897 627298681 7.190000e-78 302.0
38 TraesCS5D01G521000 chr4A 77.574 544 69 27 2458 2958 626975980 626975447 3.370000e-71 279.0
39 TraesCS5D01G521000 chr4A 90.367 218 11 5 2269 2478 627000798 627000583 1.210000e-70 278.0
40 TraesCS5D01G521000 chr4A 89.908 218 12 5 2269 2478 627086659 627086444 5.630000e-69 272.0
41 TraesCS5D01G521000 chr4A 89.450 218 13 5 2269 2478 627166310 627166095 2.620000e-67 267.0
42 TraesCS5D01G521000 chr4A 76.829 328 44 20 1939 2266 626976659 626976364 5.920000e-34 156.0
43 TraesCS5D01G521000 chr4A 94.444 90 4 1 3234 3322 712603178 712603267 2.140000e-28 137.0
44 TraesCS5D01G521000 chr4A 94.667 75 4 0 2191 2265 627000913 627000839 2.790000e-22 117.0
45 TraesCS5D01G521000 chr3A 81.481 297 43 11 618 906 675350799 675350507 2.660000e-57 233.0
46 TraesCS5D01G521000 chr3D 80.000 300 50 9 608 901 540275480 540275185 3.460000e-51 213.0
47 TraesCS5D01G521000 chr2B 97.647 85 2 0 3234 3318 132855538 132855622 3.560000e-31 147.0
48 TraesCS5D01G521000 chr2B 94.505 91 5 0 3229 3319 264112896 264112806 1.660000e-29 141.0
49 TraesCS5D01G521000 chr6B 96.512 86 3 0 3237 3322 646750140 646750055 4.610000e-30 143.0
50 TraesCS5D01G521000 chr2D 94.565 92 5 0 3227 3318 29153177 29153268 4.610000e-30 143.0
51 TraesCS5D01G521000 chr2D 96.429 84 3 0 3237 3320 302248094 302248011 5.960000e-29 139.0
52 TraesCS5D01G521000 chr6D 93.478 92 5 1 3234 3325 465044507 465044417 7.710000e-28 135.0
53 TraesCS5D01G521000 chr1A 89.423 104 10 1 3234 3336 558981463 558981566 3.590000e-26 130.0
54 TraesCS5D01G521000 chrUn 100.000 29 0 0 1 29 387317268 387317240 2.000000e-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 TraesCS5D01G521000 chr5D 541989314 541993734 4420 False 8165.000000 8165 100.000000 1 4421 1 chr5D.!!$F2 4420
1 TraesCS5D01G521000 chr5D 542295696 542296203 507 False 556.000000 556 86.576000 3344 3851 1 chr5D.!!$F4 507
2 TraesCS5D01G521000 chr5B 684049584 684051079 1495 False 1373.000000 1373 83.473000 925 2450 1 chr5B.!!$F1 1525
3 TraesCS5D01G521000 chr5B 684031044 684042453 11409 False 1314.111111 3314 92.964667 1 4407 9 chr5B.!!$F3 4406
4 TraesCS5D01G521000 chr4A 627289285 627291791 2506 True 1674.500000 3038 91.291000 1 2493 2 chr4A.!!$R9 2492
5 TraesCS5D01G521000 chr4A 627166095 627168592 2497 True 1663.000000 3059 90.359000 1 2478 2 chr4A.!!$R7 2477
6 TraesCS5D01G521000 chr4A 627086444 627088941 2497 True 1662.500000 3053 90.566000 1 2478 2 chr4A.!!$R5 2477
7 TraesCS5D01G521000 chr4A 627298681 627303151 4470 True 1487.750000 3099 91.697000 1 4407 4 chr4A.!!$R10 4406
8 TraesCS5D01G521000 chr4A 627000583 627005439 4856 True 1134.666667 3009 92.391333 1 2478 3 chr4A.!!$R3 2477
9 TraesCS5D01G521000 chr4A 626987480 626995364 7884 True 869.400000 1247 89.132400 927 4393 5 chr4A.!!$R2 3466
10 TraesCS5D01G521000 chr4A 627282103 627284046 1943 True 826.333333 1114 92.055000 2475 4393 3 chr4A.!!$R8 1918
11 TraesCS5D01G521000 chr4A 627158933 627160876 1943 True 824.333333 1092 92.032000 2475 4393 3 chr4A.!!$R6 1918
12 TraesCS5D01G521000 chr4A 627079282 627081225 1943 True 817.000000 1092 91.740667 2475 4393 3 chr4A.!!$R4 1918
13 TraesCS5D01G521000 chr4A 626975447 626976659 1212 True 217.500000 279 77.201500 1939 2958 2 chr4A.!!$R1 1019

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
223 230 1.237458 GGGCCTGAGGTCCTAGGAT 59.763 63.158 16.57 0.0 45.53 3.24 F
989 5054 1.316706 ACACACACAACCCCCAAACG 61.317 55.000 0.00 0.0 0.00 3.60 F
2048 13168 0.038067 TCGAAGAAACGGATCGGCAA 60.038 50.000 0.00 0.0 37.20 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 5620 0.517755 TCTCAGACGAGAAGACGCAC 59.482 55.0 0.0 0.00 45.47 5.34 R
2309 15912 0.312729 TTCGCTCTCGTGTAGTTGCA 59.687 50.0 0.0 0.00 36.96 4.08 R
3679 17538 1.238439 ACTGCATTGTGGTAGCACAC 58.762 50.0 26.5 15.97 41.68 3.82 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
110 111 4.481930 TTGGTGTTTTCTTATGCTGACG 57.518 40.909 0.00 0.00 0.00 4.35
161 168 5.724328 CACTTAGCCATGAGTGTCTAGAAA 58.276 41.667 0.00 0.00 38.05 2.52
223 230 1.237458 GGGCCTGAGGTCCTAGGAT 59.763 63.158 16.57 0.00 45.53 3.24
246 253 7.172703 GGATAGTATGATTAACCGGTTCTTTGG 59.827 40.741 26.16 0.00 0.00 3.28
277 284 7.599998 AGGTTTTTGACATTTTGCAAGCTATAG 59.400 33.333 0.00 0.00 0.00 1.31
420 427 6.409524 AAATGATGACACCACTCACATTTT 57.590 33.333 0.00 0.00 33.19 1.82
537 545 5.635700 TGGAAGTGTTTTCCGTTTTTCTTTG 59.364 36.000 1.87 0.00 41.43 2.77
547 555 2.781646 CGTTTTTCTTTGTGACGAAGGC 59.218 45.455 12.39 0.00 35.90 4.35
703 729 5.213868 TCTTCATCTACCTTCTTCCTCCT 57.786 43.478 0.00 0.00 0.00 3.69
750 776 3.776781 CATCCACGCACGGGGGTA 61.777 66.667 12.12 0.00 39.67 3.69
949 5008 2.896685 CAGGGCCCAGTTATTTTGTTCA 59.103 45.455 27.56 0.00 0.00 3.18
978 5038 2.115911 GCCCAAACCGACACACACA 61.116 57.895 0.00 0.00 0.00 3.72
979 5039 1.658686 GCCCAAACCGACACACACAA 61.659 55.000 0.00 0.00 0.00 3.33
989 5054 1.316706 ACACACACAACCCCCAAACG 61.317 55.000 0.00 0.00 0.00 3.60
1009 5082 2.124570 CGAACCCCATGGAGGCAG 60.125 66.667 15.22 4.29 35.39 4.85
1536 5620 1.160329 GGGATTTCATCACCTCCGCG 61.160 60.000 0.00 0.00 0.00 6.46
1657 5741 5.248640 ACACAATCTACTTCCTGTTGGATG 58.751 41.667 0.00 0.00 42.81 3.51
1748 5847 5.458126 CCTACGATCAGATTATCATCATGCG 59.542 44.000 0.00 0.00 0.00 4.73
2048 13168 0.038067 TCGAAGAAACGGATCGGCAA 60.038 50.000 0.00 0.00 37.20 4.52
2110 13234 3.275999 ACCGCCAATATTTACAGTGTCC 58.724 45.455 0.00 0.00 0.00 4.02
2111 13235 2.616842 CCGCCAATATTTACAGTGTCCC 59.383 50.000 0.00 0.00 0.00 4.46
2112 13236 3.275143 CGCCAATATTTACAGTGTCCCA 58.725 45.455 0.00 0.00 0.00 4.37
2113 13237 3.312421 CGCCAATATTTACAGTGTCCCAG 59.688 47.826 0.00 0.00 0.00 4.45
2114 13238 4.523083 GCCAATATTTACAGTGTCCCAGA 58.477 43.478 0.00 0.00 0.00 3.86
2115 13239 4.576463 GCCAATATTTACAGTGTCCCAGAG 59.424 45.833 0.00 0.00 0.00 3.35
2116 13240 5.745227 CCAATATTTACAGTGTCCCAGAGT 58.255 41.667 0.00 0.00 0.00 3.24
2117 13241 6.180472 CCAATATTTACAGTGTCCCAGAGTT 58.820 40.000 0.00 0.00 0.00 3.01
2118 13242 6.316390 CCAATATTTACAGTGTCCCAGAGTTC 59.684 42.308 0.00 0.00 0.00 3.01
2119 13243 4.974645 ATTTACAGTGTCCCAGAGTTCA 57.025 40.909 0.00 0.00 0.00 3.18
2120 13244 3.746045 TTACAGTGTCCCAGAGTTCAC 57.254 47.619 0.00 0.00 0.00 3.18
2121 13245 1.496060 ACAGTGTCCCAGAGTTCACA 58.504 50.000 0.00 0.00 33.84 3.58
2122 13246 2.050144 ACAGTGTCCCAGAGTTCACAT 58.950 47.619 0.00 0.00 33.84 3.21
2123 13247 2.439507 ACAGTGTCCCAGAGTTCACATT 59.560 45.455 0.00 0.00 33.84 2.71
2124 13248 3.646162 ACAGTGTCCCAGAGTTCACATTA 59.354 43.478 0.00 0.00 33.84 1.90
2125 13249 4.102524 ACAGTGTCCCAGAGTTCACATTAA 59.897 41.667 0.00 0.00 33.84 1.40
2126 13250 5.221925 ACAGTGTCCCAGAGTTCACATTAAT 60.222 40.000 0.00 0.00 33.84 1.40
2127 13251 5.352569 CAGTGTCCCAGAGTTCACATTAATC 59.647 44.000 0.00 0.00 33.84 1.75
2128 13252 5.249393 AGTGTCCCAGAGTTCACATTAATCT 59.751 40.000 0.00 0.00 33.84 2.40
2129 13253 5.940470 GTGTCCCAGAGTTCACATTAATCTT 59.060 40.000 0.00 0.00 0.00 2.40
2130 13254 6.092807 GTGTCCCAGAGTTCACATTAATCTTC 59.907 42.308 0.00 0.00 0.00 2.87
2131 13255 5.586643 GTCCCAGAGTTCACATTAATCTTCC 59.413 44.000 0.00 0.00 0.00 3.46
2132 13256 5.250543 TCCCAGAGTTCACATTAATCTTCCA 59.749 40.000 0.00 0.00 0.00 3.53
2133 13257 5.945784 CCCAGAGTTCACATTAATCTTCCAA 59.054 40.000 0.00 0.00 0.00 3.53
2134 13258 6.127897 CCCAGAGTTCACATTAATCTTCCAAC 60.128 42.308 0.00 0.00 0.00 3.77
2135 13259 6.656693 CCAGAGTTCACATTAATCTTCCAACT 59.343 38.462 0.00 0.00 0.00 3.16
2218 15728 6.833416 AGCCAGCCATAGTTCATTTACAAATA 59.167 34.615 0.00 0.00 0.00 1.40
2220 15730 7.978975 GCCAGCCATAGTTCATTTACAAATAAA 59.021 33.333 0.00 0.00 34.78 1.40
2267 15840 8.677148 TGAAAGAACTGCTAACTAAATGACTT 57.323 30.769 0.00 0.00 0.00 3.01
2309 15912 7.308589 GCACCAAGTTACTAACAAGTCATTCAT 60.309 37.037 1.79 0.00 0.00 2.57
2364 15968 9.475620 TTTCACAACTAGAAGATGTATAGGAGA 57.524 33.333 0.00 0.00 29.68 3.71
2365 15969 8.684386 TCACAACTAGAAGATGTATAGGAGAG 57.316 38.462 0.00 0.00 29.68 3.20
2530 16296 9.495754 GATCATTGTGTTTATTGCTAGAGTTTC 57.504 33.333 0.00 0.00 0.00 2.78
2580 16349 9.705290 CACCATTAAAAAGTAATTTGCTTACCT 57.295 29.630 0.00 0.00 40.60 3.08
2739 16528 4.990426 ACCAATAGTCTGCATTTTGTTTGC 59.010 37.500 0.00 0.00 40.55 3.68
2877 16692 6.137559 TGTTGGAATTTAGGGTGGTTACTTT 58.862 36.000 0.00 0.00 0.00 2.66
2915 16730 4.828939 TGGTCTGCATTCTTTGTTCTGAAT 59.171 37.500 0.00 0.00 33.69 2.57
2932 16748 8.175069 TGTTCTGAATTGTAGAAAATATGCGTC 58.825 33.333 0.00 0.00 36.06 5.19
2942 16758 4.949856 AGAAAATATGCGTCCATTCTGGTT 59.050 37.500 0.00 0.00 39.03 3.67
2950 16766 3.004315 GCGTCCATTCTGGTTTTCTTTCA 59.996 43.478 0.00 0.00 39.03 2.69
3075 16926 9.681062 TTATCCTTTGTTTTGAGGTAGATTAGG 57.319 33.333 0.00 0.00 34.57 2.69
3078 16929 6.151144 CCTTTGTTTTGAGGTAGATTAGGTGG 59.849 42.308 0.00 0.00 0.00 4.61
3088 16939 4.814771 GGTAGATTAGGTGGTGTACAATGC 59.185 45.833 0.00 0.00 0.00 3.56
3097 16948 3.127548 GTGGTGTACAATGCCTTGATGAG 59.872 47.826 8.84 0.00 36.20 2.90
3104 16955 8.840321 GTGTACAATGCCTTGATGAGTATTTAT 58.160 33.333 8.84 0.00 36.20 1.40
3183 17034 6.207417 AGCAAAAGCTAGTATTTTCTGCAAGA 59.793 34.615 15.50 0.00 44.68 3.02
3237 17088 6.535508 GTGTCACCACCTCTTATCAGTTATTC 59.464 42.308 0.00 0.00 35.44 1.75
3238 17089 6.049790 GTCACCACCTCTTATCAGTTATTCC 58.950 44.000 0.00 0.00 0.00 3.01
3239 17090 5.724370 TCACCACCTCTTATCAGTTATTCCA 59.276 40.000 0.00 0.00 0.00 3.53
3240 17091 6.386927 TCACCACCTCTTATCAGTTATTCCAT 59.613 38.462 0.00 0.00 0.00 3.41
3241 17092 6.708054 CACCACCTCTTATCAGTTATTCCATC 59.292 42.308 0.00 0.00 0.00 3.51
3242 17093 6.617371 ACCACCTCTTATCAGTTATTCCATCT 59.383 38.462 0.00 0.00 0.00 2.90
3243 17094 6.933521 CCACCTCTTATCAGTTATTCCATCTG 59.066 42.308 0.00 0.00 0.00 2.90
3244 17095 7.419518 CCACCTCTTATCAGTTATTCCATCTGT 60.420 40.741 0.00 0.00 0.00 3.41
3245 17096 8.642432 CACCTCTTATCAGTTATTCCATCTGTA 58.358 37.037 0.00 0.00 0.00 2.74
3246 17097 9.213777 ACCTCTTATCAGTTATTCCATCTGTAA 57.786 33.333 0.00 0.00 0.00 2.41
3312 17163 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
3313 17164 7.498443 ACACTCTTATATTTCTTTACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
3314 17165 7.343833 ACACTCTTATATTTCTTTACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
3315 17166 7.868415 CACTCTTATATTTCTTTACGGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
3316 17167 7.564292 ACTCTTATATTTCTTTACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3317 17168 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3318 17169 9.597681 TCTTATATTTCTTTACGGAGGGAGTAT 57.402 33.333 0.00 0.00 0.00 2.12
3403 17255 4.682860 GTGGTGCAAATGATCAAGTTGAAG 59.317 41.667 20.88 0.00 0.00 3.02
3482 17334 5.396772 GGTTGAAGAGGTGATATGACATCCA 60.397 44.000 3.27 0.00 0.00 3.41
3483 17335 5.955961 TGAAGAGGTGATATGACATCCAA 57.044 39.130 3.27 0.00 0.00 3.53
3484 17336 6.312141 TGAAGAGGTGATATGACATCCAAA 57.688 37.500 3.27 0.00 0.00 3.28
3540 17396 4.711399 TGGATCAATATTCTCTGCAGTGG 58.289 43.478 14.67 8.31 0.00 4.00
3614 17470 6.979465 ACTATATCGCCTACTTTGACCTTAC 58.021 40.000 0.00 0.00 0.00 2.34
3648 17507 0.402121 GGAGCTGGGAAACACTCCTT 59.598 55.000 0.00 0.00 44.68 3.36
3679 17538 6.722301 CACAGTTCATAGTTCATTATGCTGG 58.278 40.000 0.00 0.00 31.19 4.85
3713 17572 7.067728 CACAATGCAGTTTATCATATCAGACG 58.932 38.462 0.00 0.00 0.00 4.18
3714 17573 6.986231 ACAATGCAGTTTATCATATCAGACGA 59.014 34.615 0.00 0.00 0.00 4.20
3715 17574 7.042456 ACAATGCAGTTTATCATATCAGACGAC 60.042 37.037 0.00 0.00 0.00 4.34
3861 17729 7.052248 TCATGCTCTCATTGTCACTAATCATT 58.948 34.615 0.00 0.00 0.00 2.57
3961 17832 7.885922 TGTACTAGTTCTCTCTCTGTTGAGATT 59.114 37.037 0.00 0.00 46.93 2.40
3984 17855 3.181475 TGCAAAGAGACGAGAGAACAAGT 60.181 43.478 0.00 0.00 0.00 3.16
4114 17988 3.286751 TGCTGTGCAGGTTTCCGC 61.287 61.111 1.11 0.00 33.32 5.54
4135 18009 1.228245 AGCGGTGAATGTGGCTGTT 60.228 52.632 0.00 0.00 33.81 3.16
4148 18022 8.046708 TGAATGTGGCTGTTAATGAACTACTAT 58.953 33.333 0.00 0.00 36.45 2.12
4246 18234 5.106317 CGTGCTGAACCAATATGTTAGGTTT 60.106 40.000 9.30 0.00 45.15 3.27
4305 18293 3.094484 TCCCCCGCTAAAAATTGTCAT 57.906 42.857 0.00 0.00 0.00 3.06
4372 18360 2.754552 TGCACAAAGTTGAACTCTGCTT 59.245 40.909 17.85 0.39 29.47 3.91
4394 18382 2.624364 GTGTGATGGCATGGCAATATGA 59.376 45.455 27.04 0.45 0.00 2.15
4407 18395 3.686726 GGCAATATGACAGCTGCTATACC 59.313 47.826 15.27 9.93 35.13 2.73
4408 18396 4.564406 GGCAATATGACAGCTGCTATACCT 60.564 45.833 15.27 1.54 35.13 3.08
4409 18397 4.391216 GCAATATGACAGCTGCTATACCTG 59.609 45.833 15.27 13.51 0.00 4.00
4410 18398 4.815533 ATATGACAGCTGCTATACCTGG 57.184 45.455 15.27 0.00 0.00 4.45
4411 18399 1.123077 TGACAGCTGCTATACCTGGG 58.877 55.000 15.27 0.00 0.00 4.45
4412 18400 1.342975 TGACAGCTGCTATACCTGGGA 60.343 52.381 15.27 0.00 0.00 4.37
4413 18401 1.762957 GACAGCTGCTATACCTGGGAA 59.237 52.381 15.27 0.00 0.00 3.97
4414 18402 1.765314 ACAGCTGCTATACCTGGGAAG 59.235 52.381 15.27 0.00 0.00 3.46
4415 18403 1.765314 CAGCTGCTATACCTGGGAAGT 59.235 52.381 0.00 0.00 0.00 3.01
4416 18404 2.965831 CAGCTGCTATACCTGGGAAGTA 59.034 50.000 0.00 0.00 0.00 2.24
4417 18405 3.580458 CAGCTGCTATACCTGGGAAGTAT 59.420 47.826 0.00 0.00 34.79 2.12
4418 18406 4.772624 CAGCTGCTATACCTGGGAAGTATA 59.227 45.833 0.00 0.00 32.71 1.47
4419 18407 5.423610 CAGCTGCTATACCTGGGAAGTATAT 59.576 44.000 0.00 0.00 33.38 0.86
4420 18408 6.607600 CAGCTGCTATACCTGGGAAGTATATA 59.392 42.308 0.00 0.00 33.38 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 168 6.368779 ACACACTATACAAACCCATGTACT 57.631 37.500 0.00 0.00 38.53 2.73
223 230 5.818857 GCCAAAGAACCGGTTAATCATACTA 59.181 40.000 22.33 0.00 0.00 1.82
246 253 4.332268 TGCAAAATGTCAAAAACCTTGAGC 59.668 37.500 0.00 0.00 0.00 4.26
361 368 8.341173 CCTTCATTAATGTTCTCTCAACATAGC 58.659 37.037 14.97 0.00 39.73 2.97
376 383 5.902613 TTCCTCAGCAACCTTCATTAATG 57.097 39.130 9.29 9.29 0.00 1.90
420 427 4.884668 AATCGACTCTAAAGTTGGTGGA 57.115 40.909 0.00 0.00 37.48 4.02
479 486 6.040729 TCACATTGAGAACACATTGACCAATT 59.959 34.615 0.00 0.00 0.00 2.32
537 545 2.434359 CCTTCCGGCCTTCGTCAC 60.434 66.667 0.00 0.00 37.11 3.67
547 555 1.870064 TAAGTTAGACCCCCTTCCGG 58.130 55.000 0.00 0.00 0.00 5.14
596 608 1.302271 GTGACCGGGTGAGGTTTCC 60.302 63.158 3.30 0.00 46.09 3.13
639 651 0.031314 AGGTGCGCGAGATGTATGAG 59.969 55.000 12.10 0.00 0.00 2.90
703 729 4.016666 AGAGAGAAAGAGAGAAGGGGATCA 60.017 45.833 0.00 0.00 0.00 2.92
746 772 4.208686 CGAGGAGCGTGGCTACCC 62.209 72.222 0.00 0.00 41.11 3.69
797 823 2.428925 GGGACCTACGCGGGATCAA 61.429 63.158 12.47 0.00 36.97 2.57
799 825 1.228367 TAGGGACCTACGCGGGATC 60.228 63.158 12.47 0.00 36.97 3.36
838 864 3.793144 GCAGCGGAAGAAGTGCGG 61.793 66.667 0.00 0.00 42.17 5.69
949 5008 2.162681 CGGTTTGGGCTTTGAGAGAAT 58.837 47.619 0.00 0.00 0.00 2.40
978 5038 4.206943 TTCGGGCGTTTGGGGGTT 62.207 61.111 0.00 0.00 0.00 4.11
979 5039 4.960866 GTTCGGGCGTTTGGGGGT 62.961 66.667 0.00 0.00 0.00 4.95
989 5054 4.506255 CCTCCATGGGGTTCGGGC 62.506 72.222 11.67 0.00 34.93 6.13
1267 5342 2.125673 GGACATCGTGACGGTGGG 60.126 66.667 23.08 0.00 42.81 4.61
1274 5349 0.824109 GTCATCTGGGGACATCGTGA 59.176 55.000 0.00 0.00 41.51 4.35
1536 5620 0.517755 TCTCAGACGAGAAGACGCAC 59.482 55.000 0.00 0.00 45.47 5.34
1657 5741 5.725110 ACGAACTCAATGATGCTATTGTC 57.275 39.130 0.00 1.01 38.77 3.18
1748 5847 0.842635 AAGGCATCCATCCTCTGTCC 59.157 55.000 0.00 0.00 32.45 4.02
2110 13234 6.656693 AGTTGGAAGATTAATGTGAACTCTGG 59.343 38.462 0.00 0.00 0.00 3.86
2111 13235 7.388776 TGAGTTGGAAGATTAATGTGAACTCTG 59.611 37.037 21.00 0.00 39.10 3.35
2112 13236 7.453393 TGAGTTGGAAGATTAATGTGAACTCT 58.547 34.615 21.00 6.71 39.10 3.24
2113 13237 7.604164 TCTGAGTTGGAAGATTAATGTGAACTC 59.396 37.037 17.24 17.24 38.90 3.01
2114 13238 7.453393 TCTGAGTTGGAAGATTAATGTGAACT 58.547 34.615 0.00 0.00 0.00 3.01
2115 13239 7.389053 ACTCTGAGTTGGAAGATTAATGTGAAC 59.611 37.037 4.06 0.00 0.00 3.18
2116 13240 7.453393 ACTCTGAGTTGGAAGATTAATGTGAA 58.547 34.615 4.06 0.00 0.00 3.18
2117 13241 7.009179 ACTCTGAGTTGGAAGATTAATGTGA 57.991 36.000 4.06 0.00 0.00 3.58
2118 13242 7.388776 TGAACTCTGAGTTGGAAGATTAATGTG 59.611 37.037 26.47 0.00 38.80 3.21
2119 13243 7.389053 GTGAACTCTGAGTTGGAAGATTAATGT 59.611 37.037 26.47 0.00 38.80 2.71
2120 13244 7.605691 AGTGAACTCTGAGTTGGAAGATTAATG 59.394 37.037 26.47 0.00 38.80 1.90
2121 13245 7.684529 AGTGAACTCTGAGTTGGAAGATTAAT 58.315 34.615 26.47 0.00 38.80 1.40
2122 13246 7.067496 AGTGAACTCTGAGTTGGAAGATTAA 57.933 36.000 26.47 0.00 38.80 1.40
2123 13247 6.672266 AGTGAACTCTGAGTTGGAAGATTA 57.328 37.500 26.47 0.00 38.80 1.75
2124 13248 5.559148 AGTGAACTCTGAGTTGGAAGATT 57.441 39.130 26.47 0.64 38.80 2.40
2125 13249 5.559148 AAGTGAACTCTGAGTTGGAAGAT 57.441 39.130 26.47 1.44 38.80 2.40
2126 13250 5.359194 AAAGTGAACTCTGAGTTGGAAGA 57.641 39.130 26.47 3.68 38.80 2.87
2127 13251 7.659390 AGATTAAAGTGAACTCTGAGTTGGAAG 59.341 37.037 26.47 0.00 38.80 3.46
2128 13252 7.509546 AGATTAAAGTGAACTCTGAGTTGGAA 58.490 34.615 26.47 9.96 38.80 3.53
2129 13253 7.067496 AGATTAAAGTGAACTCTGAGTTGGA 57.933 36.000 26.47 10.78 38.80 3.53
2130 13254 7.736447 AAGATTAAAGTGAACTCTGAGTTGG 57.264 36.000 26.47 0.00 38.80 3.77
2131 13255 8.830580 TGAAAGATTAAAGTGAACTCTGAGTTG 58.169 33.333 26.47 0.00 38.80 3.16
2132 13256 8.964476 TGAAAGATTAAAGTGAACTCTGAGTT 57.036 30.769 22.20 22.20 41.95 3.01
2133 13257 8.831550 GTTGAAAGATTAAAGTGAACTCTGAGT 58.168 33.333 4.06 4.06 0.00 3.41
2134 13258 9.050601 AGTTGAAAGATTAAAGTGAACTCTGAG 57.949 33.333 2.45 2.45 0.00 3.35
2135 13259 8.830580 CAGTTGAAAGATTAAAGTGAACTCTGA 58.169 33.333 0.00 0.00 0.00 3.27
2218 15728 7.823799 TCAAAAGAAGCTCCATGAAAACTTTTT 59.176 29.630 0.00 0.00 35.25 1.94
2220 15730 6.877236 TCAAAAGAAGCTCCATGAAAACTTT 58.123 32.000 0.00 0.00 0.00 2.66
2267 15840 4.901197 TGGTGCAAATCCTACTAGAACA 57.099 40.909 0.00 0.00 0.00 3.18
2309 15912 0.312729 TTCGCTCTCGTGTAGTTGCA 59.687 50.000 0.00 0.00 36.96 4.08
2364 15968 7.075067 GCAAATAACAATGCCAGGACTTCCT 62.075 44.000 0.00 0.00 38.81 3.36
2365 15969 4.747810 CAAATAACAATGCCAGGACTTCC 58.252 43.478 0.00 0.00 0.00 3.46
2530 16296 4.142902 CCACTTGACTAAATGTACAAGCCG 60.143 45.833 0.00 0.00 42.00 5.52
2580 16349 4.350368 TGTTCCTCAAGTGCATCTTACA 57.650 40.909 0.00 0.00 34.66 2.41
2739 16528 5.694816 TGGTTGTTGTTCTATTATGCAACG 58.305 37.500 0.00 0.00 42.71 4.10
2877 16692 5.620206 TGCAGACCAGAGAAATAAGAAACA 58.380 37.500 0.00 0.00 0.00 2.83
2915 16730 7.015226 CAGAATGGACGCATATTTTCTACAA 57.985 36.000 0.00 0.00 0.00 2.41
2942 16758 5.997129 TGTATGCACATGAGAGTGAAAGAAA 59.003 36.000 0.00 0.00 42.05 2.52
2950 16766 7.161404 TCTAAGTTTTGTATGCACATGAGAGT 58.839 34.615 0.00 0.00 33.76 3.24
3046 16893 4.499037 ACCTCAAAACAAAGGATAACGC 57.501 40.909 0.00 0.00 36.46 4.84
3075 16926 3.081061 TCATCAAGGCATTGTACACCAC 58.919 45.455 11.36 0.00 37.68 4.16
3078 16929 6.683974 AATACTCATCAAGGCATTGTACAC 57.316 37.500 11.36 0.00 37.68 2.90
3104 16955 7.013178 TGACATGTACTGCAAGAAATCAAGAAA 59.987 33.333 0.00 0.00 37.43 2.52
3286 17137 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
3287 17138 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
3288 17139 7.343833 TCCCTCCGTAAAGAAATATAAGAGTGT 59.656 37.037 0.00 0.00 0.00 3.55
3289 17140 7.723324 TCCCTCCGTAAAGAAATATAAGAGTG 58.277 38.462 0.00 0.00 0.00 3.51
3290 17141 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
3291 17142 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3292 17143 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3296 17147 9.557061 GAAAATACTCCCTCCGTAAAGAAATAT 57.443 33.333 0.00 0.00 0.00 1.28
3297 17148 8.765517 AGAAAATACTCCCTCCGTAAAGAAATA 58.234 33.333 0.00 0.00 0.00 1.40
3298 17149 7.631007 AGAAAATACTCCCTCCGTAAAGAAAT 58.369 34.615 0.00 0.00 0.00 2.17
3299 17150 7.012661 AGAAAATACTCCCTCCGTAAAGAAA 57.987 36.000 0.00 0.00 0.00 2.52
3300 17151 6.616237 AGAAAATACTCCCTCCGTAAAGAA 57.384 37.500 0.00 0.00 0.00 2.52
3301 17152 6.013984 ACAAGAAAATACTCCCTCCGTAAAGA 60.014 38.462 0.00 0.00 0.00 2.52
3302 17153 6.171213 ACAAGAAAATACTCCCTCCGTAAAG 58.829 40.000 0.00 0.00 0.00 1.85
3303 17154 6.117975 ACAAGAAAATACTCCCTCCGTAAA 57.882 37.500 0.00 0.00 0.00 2.01
3304 17155 5.337813 GGACAAGAAAATACTCCCTCCGTAA 60.338 44.000 0.00 0.00 0.00 3.18
3305 17156 4.161001 GGACAAGAAAATACTCCCTCCGTA 59.839 45.833 0.00 0.00 0.00 4.02
3306 17157 3.055312 GGACAAGAAAATACTCCCTCCGT 60.055 47.826 0.00 0.00 0.00 4.69
3307 17158 3.055385 TGGACAAGAAAATACTCCCTCCG 60.055 47.826 0.00 0.00 0.00 4.63
3308 17159 4.569719 TGGACAAGAAAATACTCCCTCC 57.430 45.455 0.00 0.00 0.00 4.30
3309 17160 5.501156 ACATGGACAAGAAAATACTCCCTC 58.499 41.667 0.00 0.00 0.00 4.30
3310 17161 5.520748 ACATGGACAAGAAAATACTCCCT 57.479 39.130 0.00 0.00 0.00 4.20
3311 17162 6.590234 AAACATGGACAAGAAAATACTCCC 57.410 37.500 0.00 0.00 0.00 4.30
3312 17163 8.141268 TGAAAAACATGGACAAGAAAATACTCC 58.859 33.333 0.00 0.00 0.00 3.85
3313 17164 9.528018 TTGAAAAACATGGACAAGAAAATACTC 57.472 29.630 0.00 0.00 0.00 2.59
3318 17169 9.883142 AAGTATTGAAAAACATGGACAAGAAAA 57.117 25.926 0.00 0.00 0.00 2.29
3448 17300 1.600413 CCTCTTCAACCAACAAAGCGC 60.600 52.381 0.00 0.00 0.00 5.92
3614 17470 2.159234 CAGCTCCAAGAGAAAAAGCGAG 59.841 50.000 0.00 0.00 38.01 5.03
3648 17507 5.151297 TGAACTATGAACTGTGCAGATCA 57.849 39.130 13.18 13.18 42.96 2.92
3679 17538 1.238439 ACTGCATTGTGGTAGCACAC 58.762 50.000 26.50 15.97 41.68 3.82
3861 17729 6.303839 ACTGAAATACTTTTGGCTCAAGGTA 58.696 36.000 2.05 0.00 0.00 3.08
3961 17832 3.452755 TGTTCTCTCGTCTCTTTGCAA 57.547 42.857 0.00 0.00 0.00 4.08
3984 17855 7.832769 AGCAAAACAGTTTCTACCAGTTAAAA 58.167 30.769 0.00 0.00 0.00 1.52
4114 17988 3.499737 GCCACATTCACCGCTCGG 61.500 66.667 6.79 6.79 42.03 4.63
4148 18022 3.067106 GAGCGACACATTTCTCAAGGAA 58.933 45.455 0.00 0.00 0.00 3.36
4327 18315 4.274602 ACACAACATTACGATGGTACCA 57.725 40.909 18.99 18.99 37.60 3.25
4372 18360 2.140839 TATTGCCATGCCATCACACA 57.859 45.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.