Multiple sequence alignment - TraesCS3D01G431200

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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 TraesCS3D01G431200 chr3D 100.000 3026 0 0 1 3026 545179967 545182992 0.000000e+00 5589.0
1 TraesCS3D01G431200 chr3D 85.740 561 64 6 2392 2938 135049416 135049974 2.020000e-161 579.0
2 TraesCS3D01G431200 chr3D 83.871 558 74 11 2387 2935 597283125 597282575 4.470000e-143 518.0
3 TraesCS3D01G431200 chr3D 81.350 563 62 23 2392 2938 281910532 281911067 4.670000e-113 418.0
4 TraesCS3D01G431200 chr3D 81.818 110 19 1 1 110 549278117 549278009 1.160000e-14 91.6
5 TraesCS3D01G431200 chr3A 93.293 2147 120 12 126 2254 681730807 681732947 0.000000e+00 3145.0
6 TraesCS3D01G431200 chr3A 93.370 362 18 2 2392 2747 681739136 681739497 5.740000e-147 531.0
7 TraesCS3D01G431200 chr3A 89.209 417 41 2 2610 3026 681737900 681738312 4.470000e-143 518.0
8 TraesCS3D01G431200 chr3A 82.577 551 57 12 2392 2928 519278962 519278437 1.650000e-122 449.0
9 TraesCS3D01G431200 chr3A 90.345 145 13 1 2254 2397 681738966 681739110 3.980000e-44 189.0
10 TraesCS3D01G431200 chr3A 87.755 49 2 2 198 242 681730919 681730967 2.000000e-03 54.7
11 TraesCS3D01G431200 chr3B 94.375 1280 64 6 980 2254 721070479 721071755 0.000000e+00 1958.0
12 TraesCS3D01G431200 chr3B 87.083 480 53 2 2556 3026 721200084 721200563 4.440000e-148 534.0
13 TraesCS3D01G431200 chr3B 92.991 214 7 3 132 337 721068518 721068731 3.790000e-79 305.0
14 TraesCS3D01G431200 chr3B 87.879 231 10 9 476 699 721069984 721070203 3.870000e-64 255.0
15 TraesCS3D01G431200 chr3B 86.897 145 18 1 2254 2397 721072191 721072335 8.680000e-36 161.0
16 TraesCS3D01G431200 chr3B 78.947 133 24 4 1 131 614911284 614911414 1.490000e-13 87.9
17 TraesCS3D01G431200 chr2D 87.879 561 51 9 2392 2937 95182289 95181731 0.000000e+00 643.0
18 TraesCS3D01G431200 chr2D 80.926 540 86 8 2405 2930 215849812 215849276 7.810000e-111 411.0
19 TraesCS3D01G431200 chr2D 85.135 148 17 5 2252 2397 493083239 493083383 2.430000e-31 147.0
20 TraesCS3D01G431200 chr2D 85.417 144 18 3 2254 2396 606408413 606408272 2.430000e-31 147.0
21 TraesCS3D01G431200 chr4D 84.752 564 63 11 2392 2938 120077899 120078456 7.380000e-151 544.0
22 TraesCS3D01G431200 chr7B 84.276 566 64 12 2392 2938 6777193 6776634 2.070000e-146 529.0
23 TraesCS3D01G431200 chr7B 84.144 555 71 7 2393 2938 388163499 388164045 3.460000e-144 521.0
24 TraesCS3D01G431200 chr7B 86.897 145 18 1 2254 2397 388163327 388163471 8.680000e-36 161.0
25 TraesCS3D01G431200 chr1D 81.994 672 75 14 2392 3026 92094150 92094812 2.070000e-146 529.0
26 TraesCS3D01G431200 chr1D 77.353 340 45 7 2719 3026 299762650 299762311 4.010000e-39 172.0
27 TraesCS3D01G431200 chr1D 81.538 130 22 2 3 131 440709306 440709178 4.130000e-19 106.0
28 TraesCS3D01G431200 chr1D 79.545 132 22 5 1 129 430990433 430990304 4.160000e-14 89.8
29 TraesCS3D01G431200 chr1D 78.788 132 27 1 1 131 463262360 463262229 1.490000e-13 87.9
30 TraesCS3D01G431200 chr5D 84.448 553 66 8 2391 2928 242618301 242618848 7.430000e-146 527.0
31 TraesCS3D01G431200 chr5D 84.233 463 52 9 2583 3024 457284326 457283864 5.990000e-117 431.0
32 TraesCS3D01G431200 chr5D 80.000 130 26 0 1 130 141425348 141425219 2.480000e-16 97.1
33 TraesCS3D01G431200 chr4A 80.952 693 106 18 2254 2928 620183951 620184635 2.670000e-145 525.0
34 TraesCS3D01G431200 chr4A 83.272 544 81 7 2392 2928 742465550 742465010 2.710000e-135 492.0
35 TraesCS3D01G431200 chr2B 83.935 554 74 10 2392 2938 654365454 654364909 1.610000e-142 516.0
36 TraesCS3D01G431200 chr1A 82.624 564 79 7 2393 2938 484295522 484294960 5.870000e-132 481.0
37 TraesCS3D01G431200 chr1A 79.104 134 28 0 1 134 521872931 521872798 3.210000e-15 93.5
38 TraesCS3D01G431200 chr4B 81.047 554 83 10 2384 2928 491089989 491090529 3.610000e-114 422.0
39 TraesCS3D01G431200 chr4B 86.486 74 8 2 1 73 177197249 177197321 2.500000e-11 80.5
40 TraesCS3D01G431200 chr7D 85.616 146 18 3 2254 2397 30828795 30828939 1.880000e-32 150.0
41 TraesCS3D01G431200 chr1B 85.915 142 16 4 2259 2397 557544938 557545078 6.760000e-32 148.0
42 TraesCS3D01G431200 chr7A 84.932 146 19 3 2254 2397 63798543 63798399 8.740000e-31 145.0
43 TraesCS3D01G431200 chr7A 96.154 52 2 0 2975 3026 227439095 227439044 5.380000e-13 86.1
44 TraesCS3D01G431200 chr6D 78.788 132 26 2 1 131 450510010 450510140 1.490000e-13 87.9


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 TraesCS3D01G431200 chr3D 545179967 545182992 3025 False 5589.000000 5589 100.000000 1 3026 1 chr3D.!!$F3 3025
1 TraesCS3D01G431200 chr3D 135049416 135049974 558 False 579.000000 579 85.740000 2392 2938 1 chr3D.!!$F1 546
2 TraesCS3D01G431200 chr3D 597282575 597283125 550 True 518.000000 518 83.871000 2387 2935 1 chr3D.!!$R2 548
3 TraesCS3D01G431200 chr3D 281910532 281911067 535 False 418.000000 418 81.350000 2392 2938 1 chr3D.!!$F2 546
4 TraesCS3D01G431200 chr3A 681730807 681732947 2140 False 1599.850000 3145 90.524000 126 2254 2 chr3A.!!$F1 2128
5 TraesCS3D01G431200 chr3A 519278437 519278962 525 True 449.000000 449 82.577000 2392 2928 1 chr3A.!!$R1 536
6 TraesCS3D01G431200 chr3A 681737900 681739497 1597 False 412.666667 531 90.974667 2254 3026 3 chr3A.!!$F2 772
7 TraesCS3D01G431200 chr3B 721068518 721072335 3817 False 669.750000 1958 90.535500 132 2397 4 chr3B.!!$F3 2265
8 TraesCS3D01G431200 chr2D 95181731 95182289 558 True 643.000000 643 87.879000 2392 2937 1 chr2D.!!$R1 545
9 TraesCS3D01G431200 chr2D 215849276 215849812 536 True 411.000000 411 80.926000 2405 2930 1 chr2D.!!$R2 525
10 TraesCS3D01G431200 chr4D 120077899 120078456 557 False 544.000000 544 84.752000 2392 2938 1 chr4D.!!$F1 546
11 TraesCS3D01G431200 chr7B 6776634 6777193 559 True 529.000000 529 84.276000 2392 2938 1 chr7B.!!$R1 546
12 TraesCS3D01G431200 chr7B 388163327 388164045 718 False 341.000000 521 85.520500 2254 2938 2 chr7B.!!$F1 684
13 TraesCS3D01G431200 chr1D 92094150 92094812 662 False 529.000000 529 81.994000 2392 3026 1 chr1D.!!$F1 634
14 TraesCS3D01G431200 chr5D 242618301 242618848 547 False 527.000000 527 84.448000 2391 2928 1 chr5D.!!$F1 537
15 TraesCS3D01G431200 chr4A 620183951 620184635 684 False 525.000000 525 80.952000 2254 2928 1 chr4A.!!$F1 674
16 TraesCS3D01G431200 chr4A 742465010 742465550 540 True 492.000000 492 83.272000 2392 2928 1 chr4A.!!$R1 536
17 TraesCS3D01G431200 chr2B 654364909 654365454 545 True 516.000000 516 83.935000 2392 2938 1 chr2B.!!$R1 546
18 TraesCS3D01G431200 chr1A 484294960 484295522 562 True 481.000000 481 82.624000 2393 2938 1 chr1A.!!$R1 545
19 TraesCS3D01G431200 chr4B 491089989 491090529 540 False 422.000000 422 81.047000 2384 2928 1 chr4B.!!$F2 544

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
811 2198 0.034896 AAGTTGTGTTCGCCGAGGAT 59.965 50.0 0.0 0.0 0.0 3.24 F
1657 3044 0.320771 AACACTGCGGCTAACTGAGG 60.321 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 3191 0.320374 TTGGCGAGATCAACCTTCGT 59.680 50.000 0.00 0.0 0.00 3.85 R
2782 4824 1.472878 CCTCGTCATCGAAGACCTCAA 59.527 52.381 14.66 0.0 45.61 3.02 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
21 22 2.983592 GGTCAGCCCGGGTGTTTG 60.984 66.667 24.63 15.52 32.43 2.93
23 24 1.966451 GTCAGCCCGGGTGTTTGAG 60.966 63.158 24.63 4.48 32.43 3.02
24 25 2.672996 CAGCCCGGGTGTTTGAGG 60.673 66.667 24.63 0.00 0.00 3.86
25 26 4.660938 AGCCCGGGTGTTTGAGGC 62.661 66.667 24.63 3.52 44.20 4.70
28 29 4.278513 CCGGGTGTTTGAGGCCCA 62.279 66.667 0.00 0.00 42.44 5.36
29 30 2.035626 CGGGTGTTTGAGGCCCAT 59.964 61.111 0.00 0.00 42.44 4.00
30 31 1.606313 CGGGTGTTTGAGGCCCATT 60.606 57.895 0.00 0.00 42.44 3.16
32 33 0.321346 GGGTGTTTGAGGCCCATTTG 59.679 55.000 0.00 0.00 41.93 2.32
33 34 1.337118 GGTGTTTGAGGCCCATTTGA 58.663 50.000 0.00 0.00 0.00 2.69
34 35 1.691434 GGTGTTTGAGGCCCATTTGAA 59.309 47.619 0.00 0.00 0.00 2.69
35 36 2.103941 GGTGTTTGAGGCCCATTTGAAA 59.896 45.455 0.00 0.00 0.00 2.69
36 37 3.130633 GTGTTTGAGGCCCATTTGAAAC 58.869 45.455 0.00 0.00 0.00 2.78
38 39 1.698506 TTGAGGCCCATTTGAAACGT 58.301 45.000 0.00 0.00 0.00 3.99
39 40 1.243902 TGAGGCCCATTTGAAACGTC 58.756 50.000 0.00 0.00 0.00 4.34
41 42 1.211709 GGCCCATTTGAAACGTCCG 59.788 57.895 0.00 0.00 0.00 4.79
42 43 1.211709 GCCCATTTGAAACGTCCGG 59.788 57.895 0.00 0.00 0.00 5.14
44 45 1.241315 CCCATTTGAAACGTCCGGCT 61.241 55.000 0.00 0.00 0.00 5.52
45 46 0.109781 CCATTTGAAACGTCCGGCTG 60.110 55.000 0.00 0.00 0.00 4.85
46 47 0.871722 CATTTGAAACGTCCGGCTGA 59.128 50.000 0.00 0.00 0.00 4.26
47 48 1.265635 CATTTGAAACGTCCGGCTGAA 59.734 47.619 0.00 0.00 0.00 3.02
48 49 1.600023 TTTGAAACGTCCGGCTGAAT 58.400 45.000 0.00 0.00 0.00 2.57
50 51 1.011968 TGAAACGTCCGGCTGAATCG 61.012 55.000 0.00 0.00 0.00 3.34
52 53 0.320073 AAACGTCCGGCTGAATCGAA 60.320 50.000 0.00 0.00 0.00 3.71
53 54 0.320073 AACGTCCGGCTGAATCGAAA 60.320 50.000 0.00 0.00 0.00 3.46
55 56 0.793861 CGTCCGGCTGAATCGAAAAA 59.206 50.000 0.00 0.00 0.00 1.94
71 72 2.346099 AAAAACGTGGCCGATCAATG 57.654 45.000 0.00 0.00 37.88 2.82
72 73 1.529226 AAAACGTGGCCGATCAATGA 58.471 45.000 0.00 0.00 37.88 2.57
73 74 0.802494 AAACGTGGCCGATCAATGAC 59.198 50.000 0.00 0.00 37.88 3.06
74 75 1.024579 AACGTGGCCGATCAATGACC 61.025 55.000 0.00 0.00 37.88 4.02
75 76 1.449423 CGTGGCCGATCAATGACCA 60.449 57.895 0.00 0.00 35.63 4.02
78 79 2.189499 GGCCGATCAATGACCAGGC 61.189 63.158 14.40 14.40 43.47 4.85
79 80 2.189499 GCCGATCAATGACCAGGCC 61.189 63.158 12.47 0.00 38.72 5.19
80 81 1.224315 CCGATCAATGACCAGGCCA 59.776 57.895 5.01 0.00 0.00 5.36
81 82 1.097547 CCGATCAATGACCAGGCCAC 61.098 60.000 5.01 0.00 0.00 5.01
82 83 1.097547 CGATCAATGACCAGGCCACC 61.098 60.000 5.01 0.00 0.00 4.61
83 84 0.753111 GATCAATGACCAGGCCACCC 60.753 60.000 5.01 0.00 0.00 4.61
84 85 2.556840 ATCAATGACCAGGCCACCCG 62.557 60.000 5.01 0.00 35.76 5.28
86 87 3.268103 AATGACCAGGCCACCCGTC 62.268 63.158 5.01 4.98 35.76 4.79
88 89 2.682494 GACCAGGCCACCCGTCTA 60.682 66.667 5.01 0.00 35.76 2.59
90 91 3.470888 CCAGGCCACCCGTCTAGG 61.471 72.222 5.01 0.00 40.63 3.02
95 96 2.496291 GCCACCCGTCTAGGCGTAT 61.496 63.158 16.70 0.00 38.86 3.06
96 97 1.362717 CCACCCGTCTAGGCGTATG 59.637 63.158 16.70 12.79 39.21 2.39
97 98 1.105167 CCACCCGTCTAGGCGTATGA 61.105 60.000 16.70 0.00 39.21 2.15
100 101 0.592148 CCCGTCTAGGCGTATGAGAC 59.408 60.000 16.70 0.00 39.21 3.36
112 113 2.199236 GTATGAGACGGGTTTAAGGCG 58.801 52.381 0.00 0.00 0.00 5.52
114 115 2.046604 AGACGGGTTTAAGGCGCC 60.047 61.111 21.89 21.89 0.00 6.53
129 130 2.823829 CGCCCGGCTGTAAATGCTC 61.824 63.158 8.05 0.00 0.00 4.26
154 155 5.287752 TCATCGATCGTTTACAACTACAAGC 59.712 40.000 15.94 0.00 0.00 4.01
368 1454 1.412710 CACCTATCACGGGCATGTACT 59.587 52.381 0.00 0.00 0.00 2.73
369 1455 1.687123 ACCTATCACGGGCATGTACTC 59.313 52.381 0.00 0.00 0.00 2.59
387 1477 2.430332 ACTCTGGATTGCTACTGCTCTC 59.570 50.000 0.00 0.00 40.48 3.20
390 1480 4.218312 TCTGGATTGCTACTGCTCTCATA 58.782 43.478 0.00 0.00 40.48 2.15
409 1500 3.665675 ATCACGCGCTCCCCACTTC 62.666 63.158 5.73 0.00 0.00 3.01
428 1519 2.192861 CCTTGCTGTTTCACGGGCA 61.193 57.895 0.00 0.00 0.00 5.36
429 1520 1.008538 CTTGCTGTTTCACGGGCAC 60.009 57.895 0.00 0.00 31.42 5.01
463 1559 2.154462 GATTATTGTCCCCAGGCATCG 58.846 52.381 0.00 0.00 0.00 3.84
509 1633 0.244994 AGTCACTCGGTTAGCAGCTG 59.755 55.000 10.11 10.11 0.00 4.24
517 1641 1.433534 GGTTAGCAGCTGTGTCTCAC 58.566 55.000 16.64 5.65 34.56 3.51
573 1697 2.317609 CCAACTGAAGCCGGACACG 61.318 63.158 5.05 0.00 40.55 4.49
645 1776 3.934457 TGCGGATATGCGATTCTCTAA 57.066 42.857 21.62 0.00 37.81 2.10
670 1801 1.527034 TACGCCGCTACCTATCGATT 58.473 50.000 1.71 0.00 0.00 3.34
732 2118 3.584406 ACATCTCACTCATGTTCCTTGGA 59.416 43.478 0.00 0.00 29.75 3.53
752 2138 3.093057 GACCTGGATATCTAGCGGACAT 58.907 50.000 10.49 0.00 0.00 3.06
775 2161 6.052405 TCAAATTTTTAGGCATGGCAGATT 57.948 33.333 22.64 10.27 0.00 2.40
806 2193 0.586319 ATGTCAAGTTGTGTTCGCCG 59.414 50.000 2.11 0.00 0.00 6.46
807 2194 0.460459 TGTCAAGTTGTGTTCGCCGA 60.460 50.000 2.11 0.00 0.00 5.54
811 2198 0.034896 AAGTTGTGTTCGCCGAGGAT 59.965 50.000 0.00 0.00 0.00 3.24
818 2205 1.084370 GTTCGCCGAGGATGTCAAGG 61.084 60.000 0.00 0.00 0.00 3.61
819 2206 2.852495 TTCGCCGAGGATGTCAAGGC 62.852 60.000 0.00 0.00 44.00 4.35
826 2213 2.739932 CGAGGATGTCAAGGCTAGTTGG 60.740 54.545 0.00 0.00 0.00 3.77
835 2222 1.153369 GGCTAGTTGGCGAGCATGA 60.153 57.895 0.00 0.00 43.75 3.07
842 2229 1.470098 GTTGGCGAGCATGACAAATCT 59.530 47.619 0.00 0.00 38.93 2.40
845 2232 0.448990 GCGAGCATGACAAATCTGCA 59.551 50.000 0.00 0.00 38.37 4.41
852 2239 4.945543 AGCATGACAAATCTGCATCAACTA 59.054 37.500 0.00 0.00 38.37 2.24
855 2242 6.755141 GCATGACAAATCTGCATCAACTATTT 59.245 34.615 0.00 0.00 35.96 1.40
859 2246 8.579006 TGACAAATCTGCATCAACTATTTTTCT 58.421 29.630 0.00 0.00 0.00 2.52
881 2268 2.482864 CCAGAAAAATTGCCGTGCTTT 58.517 42.857 0.00 0.00 0.00 3.51
883 2270 3.122297 CAGAAAAATTGCCGTGCTTTCA 58.878 40.909 9.36 0.00 0.00 2.69
884 2271 3.555139 CAGAAAAATTGCCGTGCTTTCAA 59.445 39.130 9.36 0.00 0.00 2.69
917 2304 2.902705 TCCTCGCGCCAATATAAAGT 57.097 45.000 0.00 0.00 0.00 2.66
918 2305 2.479837 TCCTCGCGCCAATATAAAGTG 58.520 47.619 0.00 0.00 0.00 3.16
919 2306 1.069906 CCTCGCGCCAATATAAAGTGC 60.070 52.381 0.00 0.00 0.00 4.40
932 2319 4.846779 ATAAAGTGCCATGAACAACGTT 57.153 36.364 0.00 0.00 0.00 3.99
938 2325 2.292016 TGCCATGAACAACGTTCGATTT 59.708 40.909 0.00 0.00 0.00 2.17
956 2343 5.879777 TCGATTTGCCATGTCTGAAAATCTA 59.120 36.000 10.44 0.48 35.39 1.98
959 2346 6.899393 TTTGCCATGTCTGAAAATCTAACT 57.101 33.333 0.00 0.00 0.00 2.24
972 2359 9.774742 CTGAAAATCTAACTTCGGATTTTTAGG 57.225 33.333 17.37 8.46 45.90 2.69
985 2372 8.795842 TCGGATTTTTAGGCTTTCTGTATTTA 57.204 30.769 0.00 0.00 0.00 1.40
996 2383 7.673926 AGGCTTTCTGTATTTATTTTCAGGGAA 59.326 33.333 0.00 0.00 0.00 3.97
1241 2628 1.740025 GGAGATCAAACAAGCCTTCCG 59.260 52.381 0.00 0.00 0.00 4.30
1242 2629 2.615493 GGAGATCAAACAAGCCTTCCGA 60.615 50.000 0.00 0.00 0.00 4.55
1269 2656 2.082231 CATGACTTGCTCTCCAACCTG 58.918 52.381 0.00 0.00 0.00 4.00
1293 2680 3.121030 CAGCAAGACGAAGGGGCG 61.121 66.667 0.00 0.00 37.29 6.13
1326 2713 3.638627 CCAAAAAGGCCAAGTCTCTCTTT 59.361 43.478 5.01 0.00 33.63 2.52
1488 2875 2.031682 CGTCACAAAGCTTCTTCAAGGG 60.032 50.000 0.00 0.00 0.00 3.95
1602 2989 3.003480 GCTAGGCTTCAAACACGAAGAT 58.997 45.455 4.90 0.00 44.32 2.40
1657 3044 0.320771 AACACTGCGGCTAACTGAGG 60.321 55.000 0.00 0.00 0.00 3.86
1677 3064 1.608590 GGCACGGACATTATTGGGATG 59.391 52.381 0.00 0.00 0.00 3.51
1715 3105 2.076863 GTCACTTCAATCACTTCCCCG 58.923 52.381 0.00 0.00 0.00 5.73
1723 3113 2.798148 ATCACTTCCCCGGTTCACGC 62.798 60.000 0.00 0.00 42.52 5.34
1730 3120 4.636435 CCGGTTCACGCCCTTGGT 62.636 66.667 0.00 0.00 42.52 3.67
1801 3191 0.476338 ACCATGGCCGTGGCAATATA 59.524 50.000 39.01 0.00 43.27 0.86
1890 3280 6.409704 TGGGATCTATTCTTGTGAGAACAAG 58.590 40.000 11.49 11.49 44.27 3.16
1902 3293 0.693049 AGAACAAGGCCGTTCCATCT 59.307 50.000 17.05 6.48 45.27 2.90
1994 3385 4.340617 AGCAGCTCAACTAGAACTAGAGT 58.659 43.478 14.64 1.03 36.97 3.24
2024 3415 6.388689 AGAAACACCCACCCATATCTAATGTA 59.611 38.462 0.00 0.00 0.00 2.29
2051 3442 3.376078 CTGCGCACCCCATTGCTT 61.376 61.111 5.66 0.00 40.62 3.91
2059 3450 1.080569 CCCCATTGCTTGAACGCAC 60.081 57.895 0.00 0.00 40.09 5.34
2231 3622 2.346766 ACCAGCACATCAAACACTCA 57.653 45.000 0.00 0.00 0.00 3.41
2281 4259 0.701310 AAAACACCTCCCACCTCCCT 60.701 55.000 0.00 0.00 0.00 4.20
2293 4273 2.681778 CTCCCTCGTGTGCTCCCT 60.682 66.667 0.00 0.00 0.00 4.20
2825 4870 2.283676 ACCACGATGGAGACGGGT 60.284 61.111 10.46 0.00 40.96 5.28
2827 4872 1.295423 CCACGATGGAGACGGGTTT 59.705 57.895 0.00 0.00 40.96 3.27
2864 4909 4.697756 CCCGCGCCTCCTGTTCAA 62.698 66.667 0.00 0.00 0.00 2.69
2938 4983 4.735132 GCAGCCTACACCGACGCA 62.735 66.667 0.00 0.00 0.00 5.24
2939 4984 2.507102 CAGCCTACACCGACGCAG 60.507 66.667 0.00 0.00 0.00 5.18
2946 5015 1.870055 TACACCGACGCAGGAGGAAC 61.870 60.000 3.59 0.00 34.73 3.62
2958 5027 1.697982 AGGAGGAACAGTGGTACAACC 59.302 52.381 0.00 0.00 44.16 3.77
2969 5038 4.881850 CAGTGGTACAACCTGTTCTTTCTT 59.118 41.667 0.00 0.00 44.16 2.52
2970 5039 6.053005 CAGTGGTACAACCTGTTCTTTCTTA 58.947 40.000 0.00 0.00 44.16 2.10
2972 5041 6.541278 AGTGGTACAACCTGTTCTTTCTTAAC 59.459 38.462 0.00 0.00 44.16 2.01
2982 5051 0.521735 CTTTCTTAACCAGCACCGGC 59.478 55.000 0.00 0.00 41.61 6.13
3013 5082 2.614446 ATATCTACGGCGAGCGCGT 61.614 57.895 16.62 12.14 43.06 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.983592 CAAACACCCGGGCTGACC 60.984 66.667 24.08 0.00 0.00 4.02
5 6 1.966451 CTCAAACACCCGGGCTGAC 60.966 63.158 24.08 0.00 0.00 3.51
6 7 2.429930 CTCAAACACCCGGGCTGA 59.570 61.111 24.08 17.12 0.00 4.26
7 8 2.672996 CCTCAAACACCCGGGCTG 60.673 66.667 24.08 20.40 0.00 4.85
13 14 0.321346 CAAATGGGCCTCAAACACCC 59.679 55.000 4.53 0.00 44.52 4.61
15 16 3.130633 GTTTCAAATGGGCCTCAAACAC 58.869 45.455 4.53 0.00 0.00 3.32
16 17 2.223923 CGTTTCAAATGGGCCTCAAACA 60.224 45.455 4.53 0.00 0.00 2.83
17 18 2.223947 ACGTTTCAAATGGGCCTCAAAC 60.224 45.455 4.53 5.78 0.00 2.93
18 19 2.035321 GACGTTTCAAATGGGCCTCAAA 59.965 45.455 4.53 0.00 0.00 2.69
20 21 1.243902 GACGTTTCAAATGGGCCTCA 58.756 50.000 4.53 0.00 0.00 3.86
21 22 0.526211 GGACGTTTCAAATGGGCCTC 59.474 55.000 4.53 0.00 0.00 4.70
23 24 1.211709 CGGACGTTTCAAATGGGCC 59.788 57.895 0.00 0.00 0.00 5.80
24 25 1.211709 CCGGACGTTTCAAATGGGC 59.788 57.895 0.00 0.00 0.00 5.36
25 26 1.211709 GCCGGACGTTTCAAATGGG 59.788 57.895 5.05 0.00 0.00 4.00
26 27 0.109781 CAGCCGGACGTTTCAAATGG 60.110 55.000 5.05 0.00 0.00 3.16
28 29 1.600023 TTCAGCCGGACGTTTCAAAT 58.400 45.000 5.05 0.00 0.00 2.32
29 30 1.533731 GATTCAGCCGGACGTTTCAAA 59.466 47.619 5.05 0.00 0.00 2.69
30 31 1.153353 GATTCAGCCGGACGTTTCAA 58.847 50.000 5.05 0.00 0.00 2.69
32 33 0.734942 TCGATTCAGCCGGACGTTTC 60.735 55.000 5.05 0.00 0.00 2.78
33 34 0.320073 TTCGATTCAGCCGGACGTTT 60.320 50.000 5.05 0.00 0.00 3.60
34 35 0.320073 TTTCGATTCAGCCGGACGTT 60.320 50.000 5.05 0.00 0.00 3.99
35 36 0.320073 TTTTCGATTCAGCCGGACGT 60.320 50.000 5.05 0.00 0.00 4.34
36 37 0.793861 TTTTTCGATTCAGCCGGACG 59.206 50.000 5.05 0.00 0.00 4.79
52 53 1.883275 TCATTGATCGGCCACGTTTTT 59.117 42.857 2.24 0.00 41.85 1.94
53 54 1.199097 GTCATTGATCGGCCACGTTTT 59.801 47.619 2.24 0.00 41.85 2.43
55 56 1.024579 GGTCATTGATCGGCCACGTT 61.025 55.000 2.24 0.00 41.85 3.99
56 57 1.449601 GGTCATTGATCGGCCACGT 60.450 57.895 2.24 0.00 41.85 4.49
57 58 1.431488 CTGGTCATTGATCGGCCACG 61.431 60.000 2.24 0.00 42.74 4.94
58 59 1.097547 CCTGGTCATTGATCGGCCAC 61.098 60.000 2.24 0.00 0.00 5.01
60 61 2.189499 GCCTGGTCATTGATCGGCC 61.189 63.158 16.92 0.00 30.41 6.13
63 64 1.097547 GGTGGCCTGGTCATTGATCG 61.098 60.000 3.40 0.00 0.00 3.69
65 66 1.307647 GGGTGGCCTGGTCATTGAT 59.692 57.895 3.40 0.00 0.00 2.57
66 67 2.763215 GGGTGGCCTGGTCATTGA 59.237 61.111 3.40 0.00 0.00 2.57
67 68 2.751436 CGGGTGGCCTGGTCATTG 60.751 66.667 3.40 0.00 0.00 2.82
69 70 2.815684 TAGACGGGTGGCCTGGTCAT 62.816 60.000 3.40 0.00 33.40 3.06
70 71 3.533079 TAGACGGGTGGCCTGGTCA 62.533 63.158 3.32 0.00 33.40 4.02
71 72 2.682494 TAGACGGGTGGCCTGGTC 60.682 66.667 3.32 6.12 33.40 4.02
72 73 2.683933 CTAGACGGGTGGCCTGGT 60.684 66.667 3.32 0.00 33.40 4.00
73 74 3.470888 CCTAGACGGGTGGCCTGG 61.471 72.222 3.32 0.00 33.40 4.45
74 75 4.162690 GCCTAGACGGGTGGCCTG 62.163 72.222 3.32 0.00 40.71 4.85
78 79 1.105167 TCATACGCCTAGACGGGTGG 61.105 60.000 2.82 0.00 40.83 4.61
79 80 0.311165 CTCATACGCCTAGACGGGTG 59.689 60.000 2.82 1.27 42.11 4.61
80 81 0.182061 TCTCATACGCCTAGACGGGT 59.818 55.000 2.82 0.00 37.37 5.28
81 82 0.592148 GTCTCATACGCCTAGACGGG 59.408 60.000 2.82 0.00 37.37 5.28
93 94 1.472026 GCGCCTTAAACCCGTCTCATA 60.472 52.381 0.00 0.00 0.00 2.15
95 96 1.375013 GCGCCTTAAACCCGTCTCA 60.375 57.895 0.00 0.00 0.00 3.27
96 97 2.104859 GGCGCCTTAAACCCGTCTC 61.105 63.158 22.15 0.00 0.00 3.36
97 98 2.046604 GGCGCCTTAAACCCGTCT 60.047 61.111 22.15 0.00 0.00 4.18
103 104 3.810896 CAGCCGGGCGCCTTAAAC 61.811 66.667 28.56 8.15 38.78 2.01
104 105 2.466523 TTACAGCCGGGCGCCTTAAA 62.467 55.000 28.56 8.50 38.78 1.52
105 106 2.466523 TTTACAGCCGGGCGCCTTAA 62.467 55.000 28.56 11.16 38.78 1.85
107 108 3.638592 ATTTACAGCCGGGCGCCTT 62.639 57.895 28.56 6.95 38.78 4.35
108 109 4.109675 ATTTACAGCCGGGCGCCT 62.110 61.111 28.56 7.78 38.78 5.52
109 110 3.887868 CATTTACAGCCGGGCGCC 61.888 66.667 21.18 21.18 38.78 6.53
111 112 2.823829 GAGCATTTACAGCCGGGCG 61.824 63.158 14.39 11.21 0.00 6.13
112 113 1.440145 GAGAGCATTTACAGCCGGGC 61.440 60.000 12.11 12.11 0.00 6.13
114 115 1.869767 GATGAGAGCATTTACAGCCGG 59.130 52.381 0.00 0.00 34.11 6.13
116 117 2.826428 TCGATGAGAGCATTTACAGCC 58.174 47.619 0.00 0.00 34.11 4.85
117 118 3.120947 CGATCGATGAGAGCATTTACAGC 59.879 47.826 10.26 0.00 34.30 4.40
118 119 4.294232 ACGATCGATGAGAGCATTTACAG 58.706 43.478 24.34 0.00 34.30 2.74
121 122 6.270064 TGTAAACGATCGATGAGAGCATTTA 58.730 36.000 24.34 9.67 34.30 1.40
122 123 5.109210 TGTAAACGATCGATGAGAGCATTT 58.891 37.500 24.34 10.69 34.30 2.32
123 124 4.682787 TGTAAACGATCGATGAGAGCATT 58.317 39.130 24.34 0.00 34.30 3.56
124 125 4.307443 TGTAAACGATCGATGAGAGCAT 57.693 40.909 24.34 0.00 34.30 3.79
352 371 1.686587 CCAGAGTACATGCCCGTGATA 59.313 52.381 0.00 0.00 0.00 2.15
353 372 0.465705 CCAGAGTACATGCCCGTGAT 59.534 55.000 0.00 0.00 0.00 3.06
368 1454 2.460669 TGAGAGCAGTAGCAATCCAGA 58.539 47.619 0.00 0.00 45.49 3.86
369 1455 2.975732 TGAGAGCAGTAGCAATCCAG 57.024 50.000 0.00 0.00 45.49 3.86
387 1477 1.227527 TGGGGAGCGCGTGATTATG 60.228 57.895 8.43 0.00 0.00 1.90
390 1480 3.254024 AAGTGGGGAGCGCGTGATT 62.254 57.895 8.43 0.00 0.00 2.57
428 1519 9.740710 GGGACAATAATCCTTTGCTTATATAGT 57.259 33.333 0.00 0.00 38.95 2.12
429 1520 9.178758 GGGGACAATAATCCTTTGCTTATATAG 57.821 37.037 0.00 0.00 38.95 1.31
463 1559 1.336795 GCAAATGGGTTGTAGTGTGGC 60.337 52.381 0.00 0.00 39.63 5.01
509 1633 0.175073 GTACGGGATGGGTGAGACAC 59.825 60.000 0.00 0.00 0.00 3.67
517 1641 1.749334 GCAGAGGAGTACGGGATGGG 61.749 65.000 0.00 0.00 0.00 4.00
573 1697 3.133721 AGATGATCACCTTGTCCTAGTGC 59.866 47.826 0.00 0.00 0.00 4.40
645 1776 2.260844 TAGGTAGCGGCGTATACTGT 57.739 50.000 18.95 11.93 0.00 3.55
670 1801 7.610865 TGATGAACGCATGATAGGATGTATAA 58.389 34.615 0.00 0.00 34.11 0.98
732 2118 2.677542 TGTCCGCTAGATATCCAGGT 57.322 50.000 0.00 0.00 0.00 4.00
752 2138 5.680594 ATCTGCCATGCCTAAAAATTTGA 57.319 34.783 0.00 0.00 0.00 2.69
806 2193 2.911484 CCAACTAGCCTTGACATCCTC 58.089 52.381 0.00 0.00 0.00 3.71
807 2194 1.065126 GCCAACTAGCCTTGACATCCT 60.065 52.381 0.00 0.00 0.00 3.24
811 2198 0.037326 CTCGCCAACTAGCCTTGACA 60.037 55.000 0.00 0.00 0.00 3.58
818 2205 0.740868 TGTCATGCTCGCCAACTAGC 60.741 55.000 0.00 0.00 39.25 3.42
819 2206 1.725641 TTGTCATGCTCGCCAACTAG 58.274 50.000 0.00 0.00 0.00 2.57
826 2213 0.448990 TGCAGATTTGTCATGCTCGC 59.551 50.000 0.00 0.00 40.62 5.03
835 2222 7.330208 GCAGAAAAATAGTTGATGCAGATTTGT 59.670 33.333 0.00 0.00 32.58 2.83
842 2229 4.766373 TCTGGCAGAAAAATAGTTGATGCA 59.234 37.500 16.28 0.00 33.94 3.96
855 2242 2.102252 ACGGCAATTTTTCTGGCAGAAA 59.898 40.909 32.85 32.85 42.00 2.52
859 2246 0.599728 GCACGGCAATTTTTCTGGCA 60.600 50.000 0.00 0.00 39.23 4.92
871 2258 1.098869 TTCAGTTTGAAAGCACGGCA 58.901 45.000 0.00 0.00 32.71 5.69
881 2268 4.083324 GCGAGGATGTCAATTTCAGTTTGA 60.083 41.667 0.00 0.00 0.00 2.69
883 2270 3.120199 CGCGAGGATGTCAATTTCAGTTT 60.120 43.478 0.00 0.00 0.00 2.66
884 2271 2.416547 CGCGAGGATGTCAATTTCAGTT 59.583 45.455 0.00 0.00 0.00 3.16
917 2304 1.518325 ATCGAACGTTGTTCATGGCA 58.482 45.000 5.00 0.00 0.00 4.92
918 2305 2.611974 AATCGAACGTTGTTCATGGC 57.388 45.000 5.00 0.00 0.00 4.40
919 2306 2.656422 GCAAATCGAACGTTGTTCATGG 59.344 45.455 5.00 0.00 0.00 3.66
932 2319 4.701651 AGATTTTCAGACATGGCAAATCGA 59.298 37.500 14.08 0.00 39.29 3.59
938 2325 5.122239 CGAAGTTAGATTTTCAGACATGGCA 59.878 40.000 0.00 0.00 0.00 4.92
956 2343 5.535030 ACAGAAAGCCTAAAAATCCGAAGTT 59.465 36.000 0.00 0.00 0.00 2.66
959 2346 7.696992 AATACAGAAAGCCTAAAAATCCGAA 57.303 32.000 0.00 0.00 0.00 4.30
972 2359 9.705290 TTTTCCCTGAAAATAAATACAGAAAGC 57.295 29.630 0.00 0.00 36.73 3.51
996 2383 3.763360 TCTCCGCCATTGTCATCATTTTT 59.237 39.130 0.00 0.00 0.00 1.94
1241 2628 1.066286 AGAGCAAGTCATGGCACTCTC 60.066 52.381 10.66 7.83 28.55 3.20
1242 2629 0.982704 AGAGCAAGTCATGGCACTCT 59.017 50.000 10.66 10.66 0.00 3.24
1269 2656 1.633852 CTTCGTCTTGCTGCAGCTCC 61.634 60.000 36.61 20.66 42.66 4.70
1302 2689 0.969149 GAGACTTGGCCTTTTTGGGG 59.031 55.000 3.32 0.00 36.00 4.96
1410 2797 3.479269 CCGTCCTTCAAGTCGCGC 61.479 66.667 0.00 0.00 0.00 6.86
1488 2875 0.318762 CCTTATACCAGAGCGCCCTC 59.681 60.000 2.29 0.00 38.42 4.30
1657 3044 1.608590 CATCCCAATAATGTCCGTGCC 59.391 52.381 0.00 0.00 0.00 5.01
1715 3105 2.798148 ATCGACCAAGGGCGTGAACC 62.798 60.000 14.90 0.00 0.00 3.62
1723 3113 1.364171 CCGCTAGATCGACCAAGGG 59.636 63.158 0.00 0.00 0.00 3.95
1730 3120 2.593725 CCCCGACCGCTAGATCGA 60.594 66.667 11.69 0.00 40.86 3.59
1801 3191 0.320374 TTGGCGAGATCAACCTTCGT 59.680 50.000 0.00 0.00 0.00 3.85
1835 3225 1.026718 GCAGAATGGGTCTTGACGGG 61.027 60.000 0.00 0.00 32.70 5.28
1890 3280 3.013921 TGTTAATTCAGATGGAACGGCC 58.986 45.455 0.00 0.00 38.60 6.13
1902 3293 8.786826 ATTCTGGAAATCTACGTGTTAATTCA 57.213 30.769 0.00 0.00 0.00 2.57
1994 3385 1.454847 GGGTGGGTGTTTCTGTGCA 60.455 57.895 0.00 0.00 0.00 4.57
2131 3522 5.885912 ACATTTTATACGGCTCATCAGGTTT 59.114 36.000 0.00 0.00 0.00 3.27
2183 3574 8.612619 CAACGACAGGCTTTGATACTATAAATT 58.387 33.333 0.00 0.00 0.00 1.82
2184 3575 7.985184 TCAACGACAGGCTTTGATACTATAAAT 59.015 33.333 0.00 0.00 30.71 1.40
2231 3622 4.158764 CCGGTTTCTCTTATGACACTCTCT 59.841 45.833 0.00 0.00 0.00 3.10
2242 3633 1.128809 TGGTGGGCCGGTTTCTCTTA 61.129 55.000 1.90 0.00 37.67 2.10
2697 4727 2.185350 CGTGCTTCATCTCCGGCT 59.815 61.111 0.00 0.00 0.00 5.52
2782 4824 1.472878 CCTCGTCATCGAAGACCTCAA 59.527 52.381 14.66 0.00 45.61 3.02
2825 4870 4.060038 GGGGCGGAGTCGTCGAAA 62.060 66.667 0.00 0.00 42.74 3.46
2861 4906 1.675310 CATGGTGAAGCCGGCTTGA 60.675 57.895 44.71 35.47 41.21 3.02
2864 4909 3.329889 TCCATGGTGAAGCCGGCT 61.330 61.111 27.08 27.08 41.21 5.52
2938 4983 1.697982 GGTTGTACCACTGTTCCTCCT 59.302 52.381 0.00 0.00 38.42 3.69
2939 4984 1.697982 AGGTTGTACCACTGTTCCTCC 59.302 52.381 0.00 0.00 41.95 4.30
2946 5015 4.451900 AGAAAGAACAGGTTGTACCACTG 58.548 43.478 6.92 6.92 41.95 3.66
2958 5027 3.058914 CGGTGCTGGTTAAGAAAGAACAG 60.059 47.826 0.00 0.00 0.00 3.16
2964 5033 2.636299 GCCGGTGCTGGTTAAGAAA 58.364 52.632 1.90 0.00 33.53 2.52
2996 5065 3.274586 ACGCGCTCGCCGTAGATA 61.275 61.111 5.73 0.00 39.84 1.98


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

AutoCloner maintained by Alex Coulton.