Multiple sequence alignment - TraesCS2A01G096100

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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 TraesCS2A01G096100 chr2A 100.000 5034 0 0 1 5034 49928573 49923540 0.000000e+00 9297.0
1 TraesCS2A01G096100 chr2A 85.080 1622 194 28 803 2413 23891512 23893096 0.000000e+00 1611.0
2 TraesCS2A01G096100 chr2A 91.466 1160 73 11 2296 3442 44599002 44597856 0.000000e+00 1570.0
3 TraesCS2A01G096100 chr2A 89.671 1065 104 3 806 1870 44649910 44648852 0.000000e+00 1352.0
4 TraesCS2A01G096100 chr2A 90.810 1012 69 7 1861 2864 44647975 44646980 0.000000e+00 1332.0
5 TraesCS2A01G096100 chr2A 88.931 1057 111 3 814 1870 44626580 44625530 0.000000e+00 1299.0
6 TraesCS2A01G096100 chr2A 79.303 1348 220 47 974 2282 32497139 32498466 0.000000e+00 889.0
7 TraesCS2A01G096100 chr2A 87.585 443 31 16 2495 2926 23893398 23893827 4.530000e-135 492.0
8 TraesCS2A01G096100 chr2A 83.806 494 54 15 3036 3511 23893888 23894373 3.580000e-121 446.0
9 TraesCS2A01G096100 chr2A 90.789 228 18 2 1861 2087 44624657 44624432 8.190000e-78 302.0
10 TraesCS2A01G096100 chr2A 89.266 177 12 1 2622 2791 44645966 44645790 1.100000e-51 215.0
11 TraesCS2A01G096100 chr2B 93.389 4583 216 33 1 4564 73391172 73386658 0.000000e+00 6704.0
12 TraesCS2A01G096100 chr2B 77.905 783 125 31 1522 2282 49987900 49987144 1.290000e-120 444.0
13 TraesCS2A01G096100 chr2B 86.854 426 20 14 4607 5032 73386658 73386269 1.290000e-120 444.0
14 TraesCS2A01G096100 chr2B 75.940 798 126 43 2736 3508 49986451 49985695 2.880000e-92 350.0
15 TraesCS2A01G096100 chr2B 78.176 307 60 6 3599 3901 49979482 49979179 6.650000e-44 189.0
16 TraesCS2A01G096100 chr2D 92.231 3295 187 31 1 3281 46390816 46387577 0.000000e+00 4602.0
17 TraesCS2A01G096100 chr2D 94.235 1700 70 10 3334 5032 46374836 46373164 0.000000e+00 2571.0
18 TraesCS2A01G096100 chr2D 92.468 1009 53 5 1861 2862 38083031 38082039 0.000000e+00 1421.0
19 TraesCS2A01G096100 chr2D 91.584 1010 62 5 1861 2863 40167744 40166751 0.000000e+00 1373.0
20 TraesCS2A01G096100 chr2D 90.063 956 92 1 915 1870 40169570 40168618 0.000000e+00 1236.0
21 TraesCS2A01G096100 chr2D 90.526 665 63 0 1206 1870 38084569 38083905 0.000000e+00 880.0
22 TraesCS2A01G096100 chr2D 90.774 336 28 1 915 1250 38084893 38084561 3.580000e-121 446.0
23 TraesCS2A01G096100 chr2D 80.000 290 56 2 3613 3901 30480754 30481042 3.950000e-51 213.0
24 TraesCS2A01G096100 chr2D 96.970 33 1 0 86 118 431002207 431002239 7.040000e-04 56.5
25 TraesCS2A01G096100 chrUn 87.762 956 81 18 2001 2944 12660826 12661757 0.000000e+00 1085.0
26 TraesCS2A01G096100 chrUn 84.146 410 62 3 3599 4007 331379000 331378593 1.310000e-105 394.0
27 TraesCS2A01G096100 chrUn 88.073 218 15 6 1902 2110 12660602 12660817 1.080000e-61 248.0
28 TraesCS2A01G096100 chrUn 89.000 200 22 0 3946 4145 12662421 12662620 1.080000e-61 248.0
29 TraesCS2A01G096100 chrUn 84.259 108 17 0 3900 4007 342412488 342412595 6.890000e-19 106.0
30 TraesCS2A01G096100 chrUn 84.259 108 17 0 3900 4007 342414971 342415078 6.890000e-19 106.0
31 TraesCS2A01G096100 chr7D 82.779 1173 164 23 1157 2312 153640358 153639207 0.000000e+00 1013.0
32 TraesCS2A01G096100 chr7B 82.420 1132 169 18 1195 2312 115410330 115409215 0.000000e+00 961.0
33 TraesCS2A01G096100 chr7B 82.143 280 42 6 4762 5034 56998396 56998118 3.030000e-57 233.0
34 TraesCS2A01G096100 chr7A 82.014 278 42 6 4762 5032 700288510 700288786 3.920000e-56 230.0
35 TraesCS2A01G096100 chr1A 81.786 280 43 6 4762 5034 586730053 586729775 1.410000e-55 228.0
36 TraesCS2A01G096100 chr1A 78.761 226 45 1 3624 3849 555126123 555126345 1.130000e-31 148.0
37 TraesCS2A01G096100 chr4B 81.655 278 43 6 4762 5032 532723492 532723768 1.820000e-54 224.0
38 TraesCS2A01G096100 chr4B 76.276 333 65 10 4707 5033 87816754 87817078 1.120000e-36 165.0
39 TraesCS2A01G096100 chr4B 81.481 108 16 4 4707 4813 613114610 613114714 8.980000e-13 86.1
40 TraesCS2A01G096100 chr4A 81.588 277 43 6 4763 5032 502363585 502363310 6.560000e-54 222.0
41 TraesCS2A01G096100 chr5B 77.297 185 37 4 4729 4911 112833000 112833181 2.480000e-18 104.0
42 TraesCS2A01G096100 chr6D 83.838 99 15 1 4715 4813 457758267 457758170 5.370000e-15 93.5
43 TraesCS2A01G096100 chr6D 87.838 74 7 1 4698 4771 435937418 435937347 8.980000e-13 86.1


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 TraesCS2A01G096100 chr2A 49923540 49928573 5033 True 9297.000000 9297 100.000000 1 5034 1 chr2A.!!$R2 5033
1 TraesCS2A01G096100 chr2A 44597856 44599002 1146 True 1570.000000 1570 91.466000 2296 3442 1 chr2A.!!$R1 1146
2 TraesCS2A01G096100 chr2A 44645790 44649910 4120 True 966.333333 1352 89.915667 806 2864 3 chr2A.!!$R4 2058
3 TraesCS2A01G096100 chr2A 32497139 32498466 1327 False 889.000000 889 79.303000 974 2282 1 chr2A.!!$F1 1308
4 TraesCS2A01G096100 chr2A 23891512 23894373 2861 False 849.666667 1611 85.490333 803 3511 3 chr2A.!!$F2 2708
5 TraesCS2A01G096100 chr2A 44624432 44626580 2148 True 800.500000 1299 89.860000 814 2087 2 chr2A.!!$R3 1273
6 TraesCS2A01G096100 chr2B 73386269 73391172 4903 True 3574.000000 6704 90.121500 1 5032 2 chr2B.!!$R3 5031
7 TraesCS2A01G096100 chr2B 49985695 49987900 2205 True 397.000000 444 76.922500 1522 3508 2 chr2B.!!$R2 1986
8 TraesCS2A01G096100 chr2D 46387577 46390816 3239 True 4602.000000 4602 92.231000 1 3281 1 chr2D.!!$R2 3280
9 TraesCS2A01G096100 chr2D 46373164 46374836 1672 True 2571.000000 2571 94.235000 3334 5032 1 chr2D.!!$R1 1698
10 TraesCS2A01G096100 chr2D 40166751 40169570 2819 True 1304.500000 1373 90.823500 915 2863 2 chr2D.!!$R4 1948
11 TraesCS2A01G096100 chr2D 38082039 38084893 2854 True 915.666667 1421 91.256000 915 2862 3 chr2D.!!$R3 1947
12 TraesCS2A01G096100 chrUn 12660602 12662620 2018 False 527.000000 1085 88.278333 1902 4145 3 chrUn.!!$F1 2243
13 TraesCS2A01G096100 chr7D 153639207 153640358 1151 True 1013.000000 1013 82.779000 1157 2312 1 chr7D.!!$R1 1155
14 TraesCS2A01G096100 chr7B 115409215 115410330 1115 True 961.000000 961 82.420000 1195 2312 1 chr7B.!!$R2 1117

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
627 628 0.034186 GGACCATCCTCCACATGCAA 60.034 55.000 0.00 0.00 32.53 4.08 F
673 676 1.135575 ACGGGATAAGTGAACGACGTC 60.136 52.381 5.18 5.18 0.00 4.34 F
2024 3147 0.326238 GTACATCCCCTGGTCTCCCA 60.326 60.000 0.00 0.00 38.87 4.37 F
2236 3386 2.154462 CTCAGATGCTTTCCCAACGTT 58.846 47.619 0.00 0.00 0.00 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2867 1.227556 GCACCACGACCAACTCTGT 60.228 57.895 0.0 0.0 0.00 3.41 R
2120 3261 1.470098 CATGGTACTTGTGCTTGCCTC 59.530 52.381 0.0 0.0 0.00 4.70 R
3758 5778 0.768221 TCCAGGAAGCCAACCTCACT 60.768 55.000 0.0 0.0 35.35 3.41 R
4050 6073 0.097325 GCAACGAAAACACGACACCA 59.903 50.000 0.0 0.0 37.03 4.17 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
56 57 3.001086 ACCCTGGAAAATCCTTAACCCT 58.999 45.455 0.00 0.00 37.46 4.34
59 60 5.257816 ACCCTGGAAAATCCTTAACCCTTAT 59.742 40.000 0.00 0.00 37.46 1.73
170 171 4.147321 ACTCCATGCAAATTTCAGAGTGT 58.853 39.130 0.00 3.72 32.16 3.55
192 193 2.908634 GTTCAGCACGACACATTTGAG 58.091 47.619 0.00 0.00 0.00 3.02
278 279 1.620819 ACAAAGATGTCGTCCAGCTCT 59.379 47.619 0.00 0.00 39.37 4.09
293 294 4.785376 TCCAGCTCTCCCTCTTTTAGATTT 59.215 41.667 0.00 0.00 0.00 2.17
310 311 5.841957 AGATTTATGTTCCTCATTGCCAC 57.158 39.130 0.00 0.00 37.91 5.01
327 328 2.772287 CCACTTTCAGTCTTCCAGTCC 58.228 52.381 0.00 0.00 0.00 3.85
357 358 1.840635 ACCTGATGCCTTCTTACCCTC 59.159 52.381 0.00 0.00 0.00 4.30
397 398 2.673833 GATCCCGTCGACACCATTATC 58.326 52.381 17.16 5.59 0.00 1.75
406 407 1.151777 ACACCATTATCGCCGCTTCG 61.152 55.000 0.00 0.00 0.00 3.79
444 445 2.937149 TCTCTCGTCTGATCTTACCACG 59.063 50.000 0.00 0.00 0.00 4.94
553 554 1.271597 GGTGGCAGACAAGACCTCAAT 60.272 52.381 0.00 0.00 0.00 2.57
596 597 1.818363 GCAAACCCTAGCCGCCTAC 60.818 63.158 0.00 0.00 0.00 3.18
608 609 0.515564 CCGCCTACCGTGAAAAACAG 59.484 55.000 0.00 0.00 34.38 3.16
612 613 2.148768 CCTACCGTGAAAAACAGGACC 58.851 52.381 0.00 0.00 36.62 4.46
627 628 0.034186 GGACCATCCTCCACATGCAA 60.034 55.000 0.00 0.00 32.53 4.08
641 642 6.237901 TCCACATGCAAGTACTAAGTGAAAT 58.762 36.000 0.00 0.00 0.00 2.17
673 676 1.135575 ACGGGATAAGTGAACGACGTC 60.136 52.381 5.18 5.18 0.00 4.34
685 688 3.255395 TGAACGACGTCCATACTAAACCA 59.745 43.478 10.58 0.00 0.00 3.67
689 692 4.240096 CGACGTCCATACTAAACCACTTT 58.760 43.478 10.58 0.00 0.00 2.66
723 726 3.504906 TCAAGATGGCTCAGCAAAAGAAG 59.495 43.478 0.00 0.00 0.00 2.85
933 955 2.034879 CCACCATCGCCACACAGTC 61.035 63.158 0.00 0.00 0.00 3.51
934 956 2.034879 CACCATCGCCACACAGTCC 61.035 63.158 0.00 0.00 0.00 3.85
935 957 2.347114 CCATCGCCACACAGTCCA 59.653 61.111 0.00 0.00 0.00 4.02
1837 1916 3.689224 CAAATCTGCAGCTCGGTTG 57.311 52.632 9.47 4.69 0.00 3.77
1892 2867 1.323412 GAGCGGCTTATCCTCTCTGA 58.677 55.000 2.97 0.00 42.18 3.27
1899 2874 3.704061 GGCTTATCCTCTCTGACAGAGTT 59.296 47.826 27.62 15.52 46.85 3.01
1930 2921 2.027745 GCCTTCAGAGTCAGGATTGTCA 60.028 50.000 0.00 0.00 30.81 3.58
2024 3147 0.326238 GTACATCCCCTGGTCTCCCA 60.326 60.000 0.00 0.00 38.87 4.37
2090 3230 8.902540 ACTCAATTAGTTGTGTGATGTTCTTA 57.097 30.769 5.05 0.00 39.73 2.10
2099 3240 8.632679 AGTTGTGTGATGTTCTTATTGAATTGT 58.367 29.630 0.00 0.00 36.99 2.71
2120 3261 3.066760 GTGAAAATTTCAGCCCGGGATAG 59.933 47.826 29.31 13.71 41.01 2.08
2198 3348 3.103911 GGGTTCGCAGTGACGTCG 61.104 66.667 11.62 0.00 0.00 5.12
2236 3386 2.154462 CTCAGATGCTTTCCCAACGTT 58.846 47.619 0.00 0.00 0.00 3.99
2327 3499 7.287810 ACCTGTTATTTACTTCCAAGTCTGTT 58.712 34.615 0.00 0.00 40.37 3.16
2352 3547 9.920133 TTATTATCTGTCATTGTGATAGCTCTC 57.080 33.333 0.00 0.00 35.84 3.20
2389 3584 5.136828 TGGTTTTGTCCACTGTAATGTGAT 58.863 37.500 0.00 0.00 40.12 3.06
2417 3809 9.261180 GATTATAGTGATGCAAGCTAGTGTTTA 57.739 33.333 0.00 0.00 0.00 2.01
2601 4230 4.196971 GAGGCTGTTTCGGTATTGGTAAT 58.803 43.478 0.00 0.00 0.00 1.89
2602 4231 5.362105 AGGCTGTTTCGGTATTGGTAATA 57.638 39.130 0.00 0.00 0.00 0.98
2603 4232 5.121105 AGGCTGTTTCGGTATTGGTAATAC 58.879 41.667 3.67 3.67 42.36 1.89
2604 4233 4.877251 GGCTGTTTCGGTATTGGTAATACA 59.123 41.667 12.26 0.00 44.37 2.29
2605 4234 5.007332 GGCTGTTTCGGTATTGGTAATACAG 59.993 44.000 12.26 9.02 44.37 2.74
2900 4542 6.213677 TGCACTACTAGGCTATTTCGTAATG 58.786 40.000 0.00 0.00 0.00 1.90
3142 4847 3.942829 TCCTGACAGCTAATGGAAACTG 58.057 45.455 0.00 0.00 36.22 3.16
3144 4849 3.076621 CTGACAGCTAATGGAAACTGCA 58.923 45.455 0.00 0.00 33.35 4.41
3222 4942 2.522185 ACTTGTTCCATCTTGCAGCAT 58.478 42.857 0.00 0.00 0.00 3.79
3493 5385 7.614124 AAAATAAGCCAAGCATTACCATTTG 57.386 32.000 0.00 0.00 0.00 2.32
3654 5674 2.159198 GCAAAAGATGCGATCAACCCAT 60.159 45.455 0.00 0.00 46.87 4.00
3758 5778 1.835494 CGAGTTCAGAGGGGACACTA 58.165 55.000 0.00 0.00 0.00 2.74
3856 5876 2.056577 CTTTTCACACCGTACTCGACC 58.943 52.381 0.00 0.00 39.71 4.79
4041 6064 3.195825 GTCTTCCAAGCTTAGCCTCTGTA 59.804 47.826 0.00 0.00 0.00 2.74
4050 6073 3.949113 GCTTAGCCTCTGTAGAGTAGTGT 59.051 47.826 8.02 0.00 40.48 3.55
4056 6079 3.440872 CCTCTGTAGAGTAGTGTGGTGTC 59.559 52.174 8.02 0.00 40.48 3.67
4125 6148 0.179094 CGCGGCCTTATGTTGGTCTA 60.179 55.000 0.00 0.00 0.00 2.59
4146 6169 0.313672 TGAATTTGCGGCTTGGTGTC 59.686 50.000 0.00 0.00 0.00 3.67
4149 6172 0.537143 ATTTGCGGCTTGGTGTCTGA 60.537 50.000 0.00 0.00 0.00 3.27
4206 6229 4.385199 CCATGCTACCAATTTCCCTGTCTA 60.385 45.833 0.00 0.00 0.00 2.59
4207 6230 5.380043 CATGCTACCAATTTCCCTGTCTAT 58.620 41.667 0.00 0.00 0.00 1.98
4208 6231 5.036117 TGCTACCAATTTCCCTGTCTATC 57.964 43.478 0.00 0.00 0.00 2.08
4209 6232 4.721776 TGCTACCAATTTCCCTGTCTATCT 59.278 41.667 0.00 0.00 0.00 1.98
4210 6233 5.903010 TGCTACCAATTTCCCTGTCTATCTA 59.097 40.000 0.00 0.00 0.00 1.98
4211 6234 6.558775 TGCTACCAATTTCCCTGTCTATCTAT 59.441 38.462 0.00 0.00 0.00 1.98
4212 6235 7.100409 GCTACCAATTTCCCTGTCTATCTATC 58.900 42.308 0.00 0.00 0.00 2.08
4213 6236 7.256332 GCTACCAATTTCCCTGTCTATCTATCA 60.256 40.741 0.00 0.00 0.00 2.15
4214 6237 7.451731 ACCAATTTCCCTGTCTATCTATCAA 57.548 36.000 0.00 0.00 0.00 2.57
4286 6310 1.608590 GTTCCATTCCTGGTGTGTGTG 59.391 52.381 0.00 0.00 43.61 3.82
4287 6311 0.843309 TCCATTCCTGGTGTGTGTGT 59.157 50.000 0.00 0.00 43.61 3.72
4288 6312 0.953727 CCATTCCTGGTGTGTGTGTG 59.046 55.000 0.00 0.00 37.79 3.82
4289 6313 1.679139 CATTCCTGGTGTGTGTGTGT 58.321 50.000 0.00 0.00 0.00 3.72
4290 6314 1.334556 CATTCCTGGTGTGTGTGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
4385 6409 6.336842 AGTTGAGGTTCTTTTCAATCATGG 57.663 37.500 0.00 0.00 35.91 3.66
4390 6414 5.397360 AGGTTCTTTTCAATCATGGAAGGT 58.603 37.500 0.00 0.00 0.00 3.50
4518 6542 2.032054 GTGTTGTACATCCATCCATGCG 59.968 50.000 0.00 0.00 0.00 4.73
4563 6587 4.816385 GTGTGTGTATTCAGGGATGGTATG 59.184 45.833 0.00 0.00 0.00 2.39
4564 6588 4.141505 TGTGTGTATTCAGGGATGGTATGG 60.142 45.833 0.00 0.00 0.00 2.74
4565 6589 4.044308 TGTGTATTCAGGGATGGTATGGT 58.956 43.478 0.00 0.00 0.00 3.55
4566 6590 4.476846 TGTGTATTCAGGGATGGTATGGTT 59.523 41.667 0.00 0.00 0.00 3.67
4567 6591 4.821805 GTGTATTCAGGGATGGTATGGTTG 59.178 45.833 0.00 0.00 0.00 3.77
4568 6592 3.600448 ATTCAGGGATGGTATGGTTGG 57.400 47.619 0.00 0.00 0.00 3.77
4569 6593 1.221635 TCAGGGATGGTATGGTTGGG 58.778 55.000 0.00 0.00 0.00 4.12
4570 6594 0.185901 CAGGGATGGTATGGTTGGGG 59.814 60.000 0.00 0.00 0.00 4.96
4571 6595 0.254107 AGGGATGGTATGGTTGGGGT 60.254 55.000 0.00 0.00 0.00 4.95
4572 6596 0.634465 GGGATGGTATGGTTGGGGTT 59.366 55.000 0.00 0.00 0.00 4.11
4573 6597 1.411074 GGGATGGTATGGTTGGGGTTC 60.411 57.143 0.00 0.00 0.00 3.62
4574 6598 1.411074 GGATGGTATGGTTGGGGTTCC 60.411 57.143 0.00 0.00 0.00 3.62
4575 6599 1.569072 GATGGTATGGTTGGGGTTCCT 59.431 52.381 0.00 0.00 0.00 3.36
4576 6600 0.701731 TGGTATGGTTGGGGTTCCTG 59.298 55.000 0.00 0.00 0.00 3.86
4577 6601 0.033503 GGTATGGTTGGGGTTCCTGG 60.034 60.000 0.00 0.00 0.00 4.45
4578 6602 0.033503 GTATGGTTGGGGTTCCTGGG 60.034 60.000 0.00 0.00 0.00 4.45
4579 6603 0.178828 TATGGTTGGGGTTCCTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
4580 6604 0.855400 ATGGTTGGGGTTCCTGGGAT 60.855 55.000 0.00 0.00 0.00 3.85
4581 6605 1.000359 GGTTGGGGTTCCTGGGATG 60.000 63.158 0.00 0.00 0.00 3.51
4582 6606 1.000359 GTTGGGGTTCCTGGGATGG 60.000 63.158 0.00 0.00 0.00 3.51
4583 6607 2.929964 TTGGGGTTCCTGGGATGGC 61.930 63.158 0.00 0.00 0.00 4.40
4584 6608 3.023735 GGGGTTCCTGGGATGGCT 61.024 66.667 0.00 0.00 0.00 4.75
4585 6609 2.597903 GGGTTCCTGGGATGGCTC 59.402 66.667 0.00 0.00 0.00 4.70
4586 6610 2.003548 GGGTTCCTGGGATGGCTCT 61.004 63.158 0.00 0.00 0.00 4.09
4587 6611 1.225704 GGTTCCTGGGATGGCTCTG 59.774 63.158 0.00 0.00 0.00 3.35
4588 6612 1.452833 GTTCCTGGGATGGCTCTGC 60.453 63.158 0.00 0.00 0.00 4.26
4589 6613 1.617536 TTCCTGGGATGGCTCTGCT 60.618 57.895 0.00 0.00 0.00 4.24
4590 6614 1.630126 TTCCTGGGATGGCTCTGCTC 61.630 60.000 0.00 0.00 0.00 4.26
4591 6615 2.372890 CCTGGGATGGCTCTGCTCA 61.373 63.158 0.00 0.00 0.00 4.26
4592 6616 1.605992 CTGGGATGGCTCTGCTCAA 59.394 57.895 0.00 0.00 0.00 3.02
4593 6617 0.034767 CTGGGATGGCTCTGCTCAAA 60.035 55.000 0.00 0.00 0.00 2.69
4594 6618 0.322816 TGGGATGGCTCTGCTCAAAC 60.323 55.000 0.00 0.00 0.00 2.93
4595 6619 1.034292 GGGATGGCTCTGCTCAAACC 61.034 60.000 0.00 0.00 0.00 3.27
4596 6620 1.034292 GGATGGCTCTGCTCAAACCC 61.034 60.000 0.00 0.00 0.00 4.11
4597 6621 0.322816 GATGGCTCTGCTCAAACCCA 60.323 55.000 0.00 0.00 0.00 4.51
4598 6622 0.112995 ATGGCTCTGCTCAAACCCAA 59.887 50.000 0.00 0.00 0.00 4.12
4599 6623 0.112995 TGGCTCTGCTCAAACCCAAT 59.887 50.000 0.00 0.00 0.00 3.16
4600 6624 0.813821 GGCTCTGCTCAAACCCAATC 59.186 55.000 0.00 0.00 0.00 2.67
4601 6625 1.615384 GGCTCTGCTCAAACCCAATCT 60.615 52.381 0.00 0.00 0.00 2.40
4602 6626 1.742268 GCTCTGCTCAAACCCAATCTC 59.258 52.381 0.00 0.00 0.00 2.75
4603 6627 2.877300 GCTCTGCTCAAACCCAATCTCA 60.877 50.000 0.00 0.00 0.00 3.27
4604 6628 2.746362 CTCTGCTCAAACCCAATCTCAC 59.254 50.000 0.00 0.00 0.00 3.51
4605 6629 1.466167 CTGCTCAAACCCAATCTCACG 59.534 52.381 0.00 0.00 0.00 4.35
4632 6699 6.899393 TTTTACATTCTGATTTGCTGGAGT 57.101 33.333 0.00 0.00 0.00 3.85
4655 6722 2.092429 TGTGGAAGCAAAGGAACAGAGT 60.092 45.455 0.00 0.00 0.00 3.24
4768 6938 8.408601 GTTTGATCATGTAATATTGGTTGAGCT 58.591 33.333 0.00 0.00 0.00 4.09
4814 6984 4.647399 TGGTGGTTTCCTTAGTTTCTTTGG 59.353 41.667 0.00 0.00 0.00 3.28
4855 7025 2.091333 ACCTGGTGAACAATGGGAGTTT 60.091 45.455 0.00 0.00 0.00 2.66
4859 7029 0.958091 TGAACAATGGGAGTTTGCCG 59.042 50.000 0.00 0.00 0.00 5.69
4874 7044 1.007849 GCCGCAACCAATCAACGTT 60.008 52.632 0.00 0.00 0.00 3.99
4875 7045 1.274798 GCCGCAACCAATCAACGTTG 61.275 55.000 22.35 22.35 41.84 4.10
4876 7046 0.309302 CCGCAACCAATCAACGTTGA 59.691 50.000 31.41 31.41 41.53 3.18
4877 7047 1.394697 CGCAACCAATCAACGTTGAC 58.605 50.000 31.87 16.57 41.53 3.18
4878 7048 1.394697 GCAACCAATCAACGTTGACG 58.605 50.000 31.87 24.19 41.53 4.35
4879 7049 1.003331 GCAACCAATCAACGTTGACGA 60.003 47.619 31.87 11.96 41.53 4.20
4918 7088 4.441913 CCATTGTGCAAGGACTGAAAAACT 60.442 41.667 0.00 0.00 0.00 2.66
4923 7093 3.214328 GCAAGGACTGAAAAACTCCTGA 58.786 45.455 0.00 0.00 34.46 3.86
4932 7102 6.644347 ACTGAAAAACTCCTGATATCGACAT 58.356 36.000 0.00 0.00 0.00 3.06
5032 7202 5.963865 ACCCCTTTTGATAATATTGCAGGTT 59.036 36.000 0.00 0.00 0.00 3.50
5033 7203 7.129425 ACCCCTTTTGATAATATTGCAGGTTA 58.871 34.615 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.868339 GGTTTGATGGTTTTGATCGAAGAATT 59.132 34.615 0.00 0.00 43.58 2.17
74 75 2.826128 AGATGTCTTGTCTCGGCAACTA 59.174 45.455 0.00 0.00 0.00 2.24
89 90 4.116747 ACCTCTTCGTCATTCAGATGTC 57.883 45.455 0.00 0.00 34.73 3.06
124 125 0.806102 CGCATGAACCGGAGATTCGT 60.806 55.000 9.46 0.00 0.00 3.85
274 275 7.227711 GGAACATAAATCTAAAAGAGGGAGAGC 59.772 40.741 0.00 0.00 0.00 4.09
278 279 8.158025 TGAGGAACATAAATCTAAAAGAGGGA 57.842 34.615 0.00 0.00 0.00 4.20
293 294 4.661222 TGAAAGTGGCAATGAGGAACATA 58.339 39.130 0.00 0.00 38.38 2.29
310 311 2.634940 TGGAGGACTGGAAGACTGAAAG 59.365 50.000 0.00 0.00 37.43 2.62
357 358 1.207329 CGAACTTTAGGGAGGTGGAGG 59.793 57.143 0.00 0.00 0.00 4.30
389 390 0.874607 GTCGAAGCGGCGATAATGGT 60.875 55.000 12.98 0.00 42.82 3.55
394 395 0.596600 GGATTGTCGAAGCGGCGATA 60.597 55.000 12.98 2.22 42.82 2.92
397 398 1.705337 ATTGGATTGTCGAAGCGGCG 61.705 55.000 0.51 0.51 32.50 6.46
406 407 4.322567 GAGAGAGGCCATATTGGATTGTC 58.677 47.826 5.01 0.00 40.96 3.18
444 445 0.955919 CTTCTCGCCCTTGGTGTTCC 60.956 60.000 0.00 0.00 34.40 3.62
483 484 2.743928 CAGACGCTTGGGCTGACC 60.744 66.667 0.00 0.00 40.81 4.02
513 514 2.566746 CTATCCCAATCCCTGCCCTAT 58.433 52.381 0.00 0.00 0.00 2.57
553 554 2.418356 GTCGACGTCCCACCAACA 59.582 61.111 10.58 0.00 0.00 3.33
583 584 3.912907 CACGGTAGGCGGCTAGGG 61.913 72.222 20.35 15.96 0.00 3.53
596 597 1.539827 GGATGGTCCTGTTTTTCACGG 59.460 52.381 0.00 0.00 32.53 4.94
608 609 0.034186 TTGCATGTGGAGGATGGTCC 60.034 55.000 0.00 0.00 36.58 4.46
612 613 3.272574 AGTACTTGCATGTGGAGGATG 57.727 47.619 15.08 0.00 0.00 3.51
685 688 4.002906 TCTTGATCGCCACACTAAAAGT 57.997 40.909 0.00 0.00 0.00 2.66
689 692 2.905075 CCATCTTGATCGCCACACTAA 58.095 47.619 0.00 0.00 0.00 2.24
790 797 4.695455 CACGATTCAGTCACTTATTTGGGT 59.305 41.667 0.00 0.00 0.00 4.51
791 798 4.094887 CCACGATTCAGTCACTTATTTGGG 59.905 45.833 0.00 0.00 0.00 4.12
895 916 3.055963 TGGGCCGTTCGTCTTATAAAAGA 60.056 43.478 0.00 0.00 39.47 2.52
897 918 3.002102 GTGGGCCGTTCGTCTTATAAAA 58.998 45.455 0.00 0.00 0.00 1.52
933 955 3.491598 GACTGGGTGTGGGTGGTGG 62.492 68.421 0.00 0.00 0.00 4.61
934 956 2.113139 GACTGGGTGTGGGTGGTG 59.887 66.667 0.00 0.00 0.00 4.17
935 957 3.556306 CGACTGGGTGTGGGTGGT 61.556 66.667 0.00 0.00 0.00 4.16
1203 1231 4.124943 AGCTCGTCGGGGAGGCTA 62.125 66.667 0.00 0.00 34.56 3.93
1773 1848 2.885861 CGTAGACGCAGCTCCCTT 59.114 61.111 0.00 0.00 0.00 3.95
1837 1916 2.496899 ACCATGGTGATGTTCTCCAC 57.503 50.000 18.99 0.00 42.10 4.02
1892 2867 1.227556 GCACCACGACCAACTCTGT 60.228 57.895 0.00 0.00 0.00 3.41
1899 2874 2.099652 CTCTGAAGGCACCACGACCA 62.100 60.000 0.00 0.00 0.00 4.02
1930 2921 2.999063 GTGCAGCTTGGGGGCATT 60.999 61.111 0.00 0.00 40.05 3.56
2016 3138 8.514363 CTGAACTAACAGAGACATGGGAGACC 62.514 50.000 0.00 0.00 45.17 3.85
2024 3147 6.346477 TGCTAACTGAACTAACAGAGACAT 57.654 37.500 0.00 0.00 40.63 3.06
2090 3230 5.409214 CGGGCTGAAATTTTCACAATTCAAT 59.591 36.000 7.74 0.00 35.46 2.57
2099 3240 2.230130 ATCCCGGGCTGAAATTTTCA 57.770 45.000 18.49 11.19 38.17 2.69
2120 3261 1.470098 CATGGTACTTGTGCTTGCCTC 59.530 52.381 0.00 0.00 0.00 4.70
2236 3386 5.876651 ATACCATAATGTGCAGTCTCTCA 57.123 39.130 0.00 0.00 0.00 3.27
2327 3499 9.306777 AGAGAGCTATCACAATGACAGATAATA 57.693 33.333 11.60 0.00 0.00 0.98
2352 3547 6.072397 TGGACAAAACCAAAACGACCATATAG 60.072 38.462 0.00 0.00 36.96 1.31
2389 3584 6.183361 ACACTAGCTTGCATCACTATAATCCA 60.183 38.462 0.00 0.00 0.00 3.41
2601 4230 8.630037 CATCCATATAGCGATTATGGTACTGTA 58.370 37.037 16.99 3.59 41.04 2.74
2602 4231 7.492524 CATCCATATAGCGATTATGGTACTGT 58.507 38.462 16.99 0.00 41.04 3.55
2603 4232 6.422100 GCATCCATATAGCGATTATGGTACTG 59.578 42.308 16.99 14.40 41.04 2.74
2604 4233 6.325028 AGCATCCATATAGCGATTATGGTACT 59.675 38.462 16.99 12.07 41.04 2.73
2605 4234 6.516718 AGCATCCATATAGCGATTATGGTAC 58.483 40.000 16.99 10.68 41.04 3.34
2673 4302 7.490000 GCTACAACAGCCTCTTTCTATTAGTA 58.510 38.462 0.00 0.00 45.23 1.82
2952 4648 9.520515 AACTAAATGTTGGATCTGATTTGTACT 57.479 29.630 0.00 0.00 37.52 2.73
3072 4773 9.196139 TGGTATTATAATTCCCTTTTTGTGAGG 57.804 33.333 16.11 0.00 0.00 3.86
3185 4905 7.064371 TGGAACAAGTTTTTCAATTGATGTGTG 59.936 33.333 9.40 5.99 31.92 3.82
3222 4942 5.762711 TGAGAACACTGCAAGCAACTAAATA 59.237 36.000 0.00 0.00 37.60 1.40
3493 5385 3.430218 CAGACGACCTGATTGTTGAGAAC 59.570 47.826 0.00 0.00 45.78 3.01
3758 5778 0.768221 TCCAGGAAGCCAACCTCACT 60.768 55.000 0.00 0.00 35.35 3.41
3837 5857 1.408340 TGGTCGAGTACGGTGTGAAAA 59.592 47.619 0.00 0.00 40.21 2.29
3838 5858 1.031235 TGGTCGAGTACGGTGTGAAA 58.969 50.000 0.00 0.00 40.21 2.69
3856 5876 1.672356 CTTGGTGTCCGCCTCCTTG 60.672 63.158 0.00 0.00 0.00 3.61
3890 5910 2.306805 TGGACTCAGATGCCATGTTTCT 59.693 45.455 0.00 0.00 0.00 2.52
3937 5957 3.580319 GCACCCCCTGGTTGTCCT 61.580 66.667 0.00 0.00 44.75 3.85
4041 6064 1.688772 ACACGACACCACACTACTCT 58.311 50.000 0.00 0.00 0.00 3.24
4050 6073 0.097325 GCAACGAAAACACGACACCA 59.903 50.000 0.00 0.00 37.03 4.17
4056 6079 0.524392 TGGCTTGCAACGAAAACACG 60.524 50.000 0.00 0.00 39.31 4.49
4125 6148 1.344114 ACACCAAGCCGCAAATTCAAT 59.656 42.857 0.00 0.00 0.00 2.57
4149 6172 8.571336 GGCAAGTAAAATATCAGTTGATAGCAT 58.429 33.333 7.78 0.17 40.04 3.79
4286 6310 6.457799 CGGCTACCCATTTATCTAAAACACAC 60.458 42.308 0.00 0.00 0.00 3.82
4287 6311 5.587043 CGGCTACCCATTTATCTAAAACACA 59.413 40.000 0.00 0.00 0.00 3.72
4288 6312 5.818857 TCGGCTACCCATTTATCTAAAACAC 59.181 40.000 0.00 0.00 0.00 3.32
4289 6313 5.991861 TCGGCTACCCATTTATCTAAAACA 58.008 37.500 0.00 0.00 0.00 2.83
4290 6314 6.930667 TTCGGCTACCCATTTATCTAAAAC 57.069 37.500 0.00 0.00 0.00 2.43
4385 6409 7.219322 TGTTACCCTAGTTTTTCTACACCTTC 58.781 38.462 0.00 0.00 0.00 3.46
4390 6414 7.381323 GCTACTGTTACCCTAGTTTTTCTACA 58.619 38.462 0.00 0.00 0.00 2.74
4563 6587 1.000359 CATCCCAGGAACCCCAACC 60.000 63.158 0.00 0.00 33.88 3.77
4564 6588 1.000359 CCATCCCAGGAACCCCAAC 60.000 63.158 0.00 0.00 33.88 3.77
4565 6589 2.929964 GCCATCCCAGGAACCCCAA 61.930 63.158 0.00 0.00 33.88 4.12
4566 6590 3.346734 GCCATCCCAGGAACCCCA 61.347 66.667 0.00 0.00 33.88 4.96
4567 6591 3.023735 AGCCATCCCAGGAACCCC 61.024 66.667 0.00 0.00 0.00 4.95
4568 6592 2.003548 AGAGCCATCCCAGGAACCC 61.004 63.158 0.00 0.00 0.00 4.11
4569 6593 1.225704 CAGAGCCATCCCAGGAACC 59.774 63.158 0.00 0.00 0.00 3.62
4570 6594 1.452833 GCAGAGCCATCCCAGGAAC 60.453 63.158 0.00 0.00 0.00 3.62
4571 6595 1.617536 AGCAGAGCCATCCCAGGAA 60.618 57.895 0.00 0.00 0.00 3.36
4572 6596 2.041762 AGCAGAGCCATCCCAGGA 59.958 61.111 0.00 0.00 0.00 3.86
4573 6597 1.918467 TTGAGCAGAGCCATCCCAGG 61.918 60.000 0.00 0.00 0.00 4.45
4574 6598 0.034767 TTTGAGCAGAGCCATCCCAG 60.035 55.000 0.00 0.00 0.00 4.45
4575 6599 0.322816 GTTTGAGCAGAGCCATCCCA 60.323 55.000 0.00 0.00 0.00 4.37
4576 6600 1.034292 GGTTTGAGCAGAGCCATCCC 61.034 60.000 0.00 0.00 0.00 3.85
4577 6601 1.034292 GGGTTTGAGCAGAGCCATCC 61.034 60.000 4.57 0.00 33.73 3.51
4578 6602 0.322816 TGGGTTTGAGCAGAGCCATC 60.323 55.000 7.73 0.00 38.03 3.51
4579 6603 0.112995 TTGGGTTTGAGCAGAGCCAT 59.887 50.000 11.95 0.00 41.73 4.40
4580 6604 0.112995 ATTGGGTTTGAGCAGAGCCA 59.887 50.000 7.73 7.73 40.67 4.75
4581 6605 0.813821 GATTGGGTTTGAGCAGAGCC 59.186 55.000 2.60 2.60 34.09 4.70
4582 6606 1.742268 GAGATTGGGTTTGAGCAGAGC 59.258 52.381 0.00 0.00 0.00 4.09
4583 6607 2.746362 GTGAGATTGGGTTTGAGCAGAG 59.254 50.000 0.00 0.00 0.00 3.35
4584 6608 2.783135 GTGAGATTGGGTTTGAGCAGA 58.217 47.619 0.00 0.00 0.00 4.26
4585 6609 1.466167 CGTGAGATTGGGTTTGAGCAG 59.534 52.381 0.00 0.00 0.00 4.24
4586 6610 1.522668 CGTGAGATTGGGTTTGAGCA 58.477 50.000 0.00 0.00 0.00 4.26
4587 6611 0.804989 CCGTGAGATTGGGTTTGAGC 59.195 55.000 0.00 0.00 0.00 4.26
4588 6612 0.804989 GCCGTGAGATTGGGTTTGAG 59.195 55.000 0.00 0.00 0.00 3.02
4589 6613 0.109532 TGCCGTGAGATTGGGTTTGA 59.890 50.000 0.00 0.00 0.00 2.69
4590 6614 1.176527 ATGCCGTGAGATTGGGTTTG 58.823 50.000 0.00 0.00 0.00 2.93
4591 6615 1.923356 AATGCCGTGAGATTGGGTTT 58.077 45.000 0.00 0.00 0.00 3.27
4592 6616 1.923356 AAATGCCGTGAGATTGGGTT 58.077 45.000 0.00 0.00 0.00 4.11
4593 6617 1.923356 AAAATGCCGTGAGATTGGGT 58.077 45.000 0.00 0.00 0.00 4.51
4594 6618 2.752354 TGTAAAATGCCGTGAGATTGGG 59.248 45.455 0.00 0.00 0.00 4.12
4595 6619 4.637483 ATGTAAAATGCCGTGAGATTGG 57.363 40.909 0.00 0.00 0.00 3.16
4596 6620 5.740569 CAGAATGTAAAATGCCGTGAGATTG 59.259 40.000 0.00 0.00 0.00 2.67
4597 6621 5.647658 TCAGAATGTAAAATGCCGTGAGATT 59.352 36.000 0.00 0.00 37.40 2.40
4598 6622 5.185454 TCAGAATGTAAAATGCCGTGAGAT 58.815 37.500 0.00 0.00 37.40 2.75
4599 6623 4.574892 TCAGAATGTAAAATGCCGTGAGA 58.425 39.130 0.00 0.00 37.40 3.27
4600 6624 4.944962 TCAGAATGTAAAATGCCGTGAG 57.055 40.909 0.00 0.00 37.40 3.51
4601 6625 5.895636 AATCAGAATGTAAAATGCCGTGA 57.104 34.783 0.00 0.00 37.40 4.35
4602 6626 5.220265 GCAAATCAGAATGTAAAATGCCGTG 60.220 40.000 0.00 0.00 37.40 4.94
4603 6627 4.864247 GCAAATCAGAATGTAAAATGCCGT 59.136 37.500 0.00 0.00 37.40 5.68
4604 6628 5.005012 CAGCAAATCAGAATGTAAAATGCCG 59.995 40.000 0.00 0.00 37.40 5.69
4605 6629 5.292589 CCAGCAAATCAGAATGTAAAATGCC 59.707 40.000 0.00 0.00 37.40 4.40
4632 6699 4.202461 ACTCTGTTCCTTTGCTTCCACATA 60.202 41.667 0.00 0.00 0.00 2.29
4768 6938 0.914417 GGGTGAGAATCCACTCCCCA 60.914 60.000 0.00 0.00 42.04 4.96
4814 6984 1.034838 TGTGTGGCTTGGTGTGTTCC 61.035 55.000 0.00 0.00 0.00 3.62
4855 7025 1.729470 AACGTTGATTGGTTGCGGCA 61.729 50.000 0.00 0.00 0.00 5.69
4859 7029 1.003331 TCGTCAACGTTGATTGGTTGC 60.003 47.619 31.81 16.85 42.42 4.17
4874 7044 1.474879 TCACCATTAGCGTCATCGTCA 59.525 47.619 0.00 0.00 39.49 4.35
4875 7045 1.852895 GTCACCATTAGCGTCATCGTC 59.147 52.381 0.00 0.00 39.49 4.20
4876 7046 1.470979 GGTCACCATTAGCGTCATCGT 60.471 52.381 0.00 0.00 39.49 3.73
4877 7047 1.209128 GGTCACCATTAGCGTCATCG 58.791 55.000 0.00 0.00 40.37 3.84
4878 7048 2.309528 TGGTCACCATTAGCGTCATC 57.690 50.000 0.00 0.00 0.00 2.92
4900 7070 3.355626 GGAGTTTTTCAGTCCTTGCAC 57.644 47.619 0.00 0.00 41.51 4.57
4923 7093 4.519350 TCGAAGCTCCTGTTATGTCGATAT 59.481 41.667 0.00 0.00 31.66 1.63
4932 7102 1.629043 ACCAGTCGAAGCTCCTGTTA 58.371 50.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.