Multiple sequence alignment - TraesCS1D01G156200

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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 TraesCS1D01G156200 chr1D 100.000 5409 0 0 3832 9240 220409867 220415275 0.000000e+00 9989.0
1 TraesCS1D01G156200 chr1D 100.000 3709 0 0 1 3709 220406036 220409744 0.000000e+00 6850.0
2 TraesCS1D01G156200 chr1D 93.750 112 4 3 2699 2808 209519392 209519502 2.060000e-36 165.0
3 TraesCS1D01G156200 chr1D 95.000 40 1 1 9012 9050 220415013 220415052 2.790000e-05 62.1
4 TraesCS1D01G156200 chr1D 95.000 40 1 1 8978 9017 220415047 220415085 2.790000e-05 62.1
5 TraesCS1D01G156200 chr1A 97.099 5171 86 16 3832 8964 284146935 284152079 0.000000e+00 8660.0
6 TraesCS1D01G156200 chr1A 98.695 1762 19 2 1950 3709 284144853 284146612 0.000000e+00 3123.0
7 TraesCS1D01G156200 chr1A 93.895 1638 57 18 289 1909 284143071 284144682 0.000000e+00 2431.0
8 TraesCS1D01G156200 chr1A 88.148 270 27 5 1 267 284142717 284142984 5.390000e-82 316.0
9 TraesCS1D01G156200 chr1A 94.505 91 5 0 9041 9131 284152088 284152178 3.480000e-29 141.0
10 TraesCS1D01G156200 chr1B 96.488 5211 129 23 3832 9007 315532750 315527559 0.000000e+00 8560.0
11 TraesCS1D01G156200 chr1B 94.612 2487 84 17 255 2706 315536281 315533810 0.000000e+00 3805.0
12 TraesCS1D01G156200 chr1B 98.132 910 8 1 2800 3709 315533811 315532911 0.000000e+00 1578.0
13 TraesCS1D01G156200 chr1B 91.034 145 11 1 29 173 315536731 315536589 2.630000e-45 195.0
14 TraesCS1D01G156200 chr1B 88.333 120 10 1 9022 9137 315527578 315527459 3.480000e-29 141.0
15 TraesCS1D01G156200 chr2B 95.041 121 6 0 1191 1311 671889208 671889328 3.410000e-44 191.0
16 TraesCS1D01G156200 chr2B 92.308 78 6 0 9162 9239 470909028 470908951 2.730000e-20 111.0
17 TraesCS1D01G156200 chr2B 89.796 49 4 1 9138 9186 439360161 439360114 2.790000e-05 62.1
18 TraesCS1D01G156200 chr4D 95.455 110 4 1 2701 2809 12354799 12354690 3.430000e-39 174.0
19 TraesCS1D01G156200 chr4D 88.372 129 13 2 2674 2802 258886272 258886398 4.470000e-33 154.0
20 TraesCS1D01G156200 chr4D 80.392 102 18 2 547 647 32418672 32418772 9.950000e-10 76.8
21 TraesCS1D01G156200 chr6D 97.000 100 3 0 2705 2804 361526381 361526282 1.600000e-37 169.0
22 TraesCS1D01G156200 chr6D 83.117 77 11 2 541 617 27481005 27481079 1.660000e-07 69.4
23 TraesCS1D01G156200 chr5B 97.938 97 2 0 2705 2801 316712605 316712701 1.600000e-37 169.0
24 TraesCS1D01G156200 chr5B 95.238 105 4 1 2704 2808 203503150 203503047 2.060000e-36 165.0
25 TraesCS1D01G156200 chr5B 92.308 39 2 1 565 602 610873552 610873590 5.000000e-03 54.7
26 TraesCS1D01G156200 chr3B 96.939 98 3 0 2705 2802 822536280 822536377 2.060000e-36 165.0
27 TraesCS1D01G156200 chr4B 88.372 129 13 2 2674 2802 235358372 235358498 4.470000e-33 154.0
28 TraesCS1D01G156200 chr4B 94.505 91 5 0 9047 9137 500202153 500202243 3.480000e-29 141.0
29 TraesCS1D01G156200 chr4B 90.110 91 9 0 9150 9240 670829589 670829499 1.630000e-22 119.0
30 TraesCS1D01G156200 chr7D 90.476 105 9 1 9033 9137 505372422 505372319 4.500000e-28 137.0
31 TraesCS1D01G156200 chr7D 97.222 72 2 0 9169 9240 238968846 238968775 1.260000e-23 122.0
32 TraesCS1D01G156200 chr7B 89.091 110 10 2 9032 9141 525997480 525997587 1.620000e-27 135.0
33 TraesCS1D01G156200 chr7B 94.186 86 5 0 9046 9131 369418127 369418212 2.090000e-26 132.0
34 TraesCS1D01G156200 chr7B 78.325 203 37 6 456 654 562095446 562095247 3.500000e-24 124.0
35 TraesCS1D01G156200 chr7A 93.407 91 6 0 9047 9137 573027852 573027762 1.620000e-27 135.0
36 TraesCS1D01G156200 chr7A 94.667 75 4 0 9166 9240 515744101 515744175 5.860000e-22 117.0
37 TraesCS1D01G156200 chr6B 91.753 97 8 0 9142 9238 507793280 507793184 1.620000e-27 135.0
38 TraesCS1D01G156200 chr5A 88.182 110 11 2 9032 9141 74077731 74077624 7.530000e-26 130.0
39 TraesCS1D01G156200 chr5A 89.320 103 11 0 9138 9240 652940447 652940345 7.530000e-26 130.0
40 TraesCS1D01G156200 chr3D 89.216 102 10 1 9031 9132 319856679 319856579 9.740000e-25 126.0
41 TraesCS1D01G156200 chr3D 96.000 75 3 0 9166 9240 448273091 448273165 1.260000e-23 122.0
42 TraesCS1D01G156200 chr3D 81.522 92 8 4 9135 9217 303791573 303791664 5.990000e-07 67.6
43 TraesCS1D01G156200 chr3A 87.736 106 13 0 9135 9240 511079638 511079743 3.500000e-24 124.0
44 TraesCS1D01G156200 chr2A 94.872 78 3 1 9163 9240 278468265 278468341 4.530000e-23 121.0
45 TraesCS1D01G156200 chr6A 77.157 197 41 4 454 647 106081571 106081376 2.730000e-20 111.0
46 TraesCS1D01G156200 chr2D 88.372 86 10 0 541 626 361260578 361260663 4.560000e-18 104.0
47 TraesCS1D01G156200 chr2D 90.385 52 4 1 9135 9186 369702524 369702474 5.990000e-07 67.6
48 TraesCS1D01G156200 chr2D 91.667 48 3 1 9140 9187 499230136 499230182 2.150000e-06 65.8


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 TraesCS1D01G156200 chr1D 220406036 220415275 9239 False 4240.8 9989 97.5000 1 9240 4 chr1D.!!$F2 9239
1 TraesCS1D01G156200 chr1A 284142717 284152178 9461 False 2934.2 8660 94.4684 1 9131 5 chr1A.!!$F1 9130
2 TraesCS1D01G156200 chr1B 315527459 315536731 9272 True 2855.8 8560 93.7198 29 9137 5 chr1B.!!$R1 9108

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
329 622 0.108520 CCAATGCTTGTGTGCCATCC 60.109 55.000 0.00 0.0 0.00 3.51 F
820 1141 0.384669 CCCGGGACTCGTATCAACTC 59.615 60.000 18.48 0.0 37.11 3.01 F
1569 1897 1.153469 CCTTCCTCTCGCCTCAAGC 60.153 63.158 0.00 0.0 38.52 4.01 F
2439 2908 2.432444 TGGTATGTTCCAAAGGAAGCG 58.568 47.619 0.00 0.0 42.88 4.68 F
2715 3185 3.388350 GGATTCTGAATTACTCCCTCCGT 59.612 47.826 4.11 0.0 0.00 4.69 F
3173 3643 8.497910 AAGGTACATCATATGTTACATCCTCT 57.502 34.615 0.00 0.0 41.63 3.69 F
4116 4787 0.555769 AGGGACCAACAACACACCAT 59.444 50.000 0.00 0.0 0.00 3.55 F
5012 5707 0.320050 TCACCATTGTACAGCAGCGA 59.680 50.000 0.00 0.0 0.00 4.93 F
6608 7306 6.070596 TGTTCATGATAGAAGACACCATCACT 60.071 38.462 0.00 0.0 30.64 3.41 F
7475 8177 1.903183 AGAGGCTGTAGGAAAGGTGAC 59.097 52.381 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1853 0.251354 ATGCAGCACTCACAGGGTAG 59.749 55.000 0.00 0.0 0.00 3.18 R
1899 2236 1.250840 CCCGGGCTGGAAAAGGAAAG 61.251 60.000 15.75 0.0 42.00 2.62 R
3173 3643 1.892474 GCAACCCATGTTAGGCAAGAA 59.108 47.619 0.00 0.0 32.09 2.52 R
4061 4732 0.671163 GACGGCGGTTCCACACAATA 60.671 55.000 13.24 0.0 34.01 1.90 R
4062 4733 1.964373 GACGGCGGTTCCACACAAT 60.964 57.895 13.24 0.0 34.01 2.71 R
4849 5544 2.586245 CCCAATGAGGCGAGCTCA 59.414 61.111 15.40 0.0 35.39 4.26 R
5701 6397 0.465460 ATCACTGGTGCAACAACCGT 60.465 50.000 5.64 0.0 43.73 4.83 R
6608 7306 3.007614 GCTACTAACCAACCACAGAAGGA 59.992 47.826 0.00 0.0 0.00 3.36 R
8061 8763 3.895656 TGGTAGTACTGACAGAGCTTGTT 59.104 43.478 10.08 0.0 41.05 2.83 R
9014 9739 0.115349 AGGCGTATAGGAGGGCAGAT 59.885 55.000 0.00 0.0 40.80 2.90 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 4.653806 CGACCTTCAAAGAGTCATGAAC 57.346 45.455 0.00 0.00 32.46 3.18
63 64 5.383130 CATGAGCGCATTCATAATCTCTTG 58.617 41.667 11.47 0.00 36.08 3.02
76 77 3.639541 CTCTTGCTCGACAGGCGCT 62.640 63.158 7.64 0.00 40.61 5.92
77 78 2.181777 CTTGCTCGACAGGCGCTA 59.818 61.111 7.64 0.00 40.61 4.26
97 98 6.700020 CGCTACAAGATGTGTGAATCTAAAG 58.300 40.000 0.00 0.00 41.89 1.85
105 106 3.072330 TGTGTGAATCTAAAGCTCCCACA 59.928 43.478 0.00 0.00 0.00 4.17
141 142 1.266718 GTGAAGATGGAAGCGCAAACA 59.733 47.619 11.47 5.10 0.00 2.83
144 145 2.422276 AGATGGAAGCGCAAACAAAC 57.578 45.000 11.47 4.16 0.00 2.93
155 157 2.539274 CGCAAACAAACAACATCCAAGG 59.461 45.455 0.00 0.00 0.00 3.61
184 186 4.789095 AACAATAGTGTTGTGACGACAC 57.211 40.909 24.91 24.91 46.40 3.67
186 188 2.060326 ATAGTGTTGTGACGACACCG 57.940 50.000 27.62 0.00 46.57 4.94
229 232 3.749064 GAGGACGTGCGAGCAGGA 61.749 66.667 22.21 0.00 35.94 3.86
230 233 3.691744 GAGGACGTGCGAGCAGGAG 62.692 68.421 22.21 8.80 35.94 3.69
275 518 2.098680 GAGACGCGAGAGGACGTG 59.901 66.667 15.93 0.00 43.71 4.49
307 600 2.683742 CGATCTATGGCTTGGGTTGGTT 60.684 50.000 0.00 0.00 0.00 3.67
329 622 0.108520 CCAATGCTTGTGTGCCATCC 60.109 55.000 0.00 0.00 0.00 3.51
331 624 0.542467 AATGCTTGTGTGCCATCCCA 60.542 50.000 0.00 0.00 0.00 4.37
333 626 1.902918 GCTTGTGTGCCATCCCACA 60.903 57.895 0.00 0.00 42.99 4.17
359 652 4.335416 GGAGATTTGATGGAAGACACCAA 58.665 43.478 0.00 0.00 43.47 3.67
468 761 4.465305 ACTTGACCCTACTAGTAAATGCGT 59.535 41.667 3.76 0.00 0.00 5.24
615 915 2.306341 AACATGAGGAGTGCTCATCG 57.694 50.000 22.93 19.24 42.72 3.84
616 916 1.478631 ACATGAGGAGTGCTCATCGA 58.521 50.000 22.93 0.00 42.72 3.59
662 971 8.685427 AGATTGACATGATCTAATATCCGAGAG 58.315 37.037 0.00 0.00 32.27 3.20
735 1044 9.802039 AATTAACCTTCTAACCATTGAACTACA 57.198 29.630 0.00 0.00 0.00 2.74
740 1050 9.396022 ACCTTCTAACCATTGAACTACATATTG 57.604 33.333 0.00 0.00 0.00 1.90
778 1088 9.638176 ATTGCATTTTCTTCTCTACCTATGATT 57.362 29.630 0.00 0.00 0.00 2.57
820 1141 0.384669 CCCGGGACTCGTATCAACTC 59.615 60.000 18.48 0.00 37.11 3.01
1176 1500 2.045143 ACCTCGACCTCCTCGTCC 60.045 66.667 0.00 0.00 43.45 4.79
1380 1708 2.959030 TCTCTCTCTCTCTCTCTCTCGG 59.041 54.545 0.00 0.00 0.00 4.63
1525 1853 4.803426 CCCTGTGCTCTCGACGCC 62.803 72.222 0.00 0.00 0.00 5.68
1565 1893 1.380650 ACTCCCTTCCTCTCGCCTC 60.381 63.158 0.00 0.00 0.00 4.70
1569 1897 1.153469 CCTTCCTCTCGCCTCAAGC 60.153 63.158 0.00 0.00 38.52 4.01
1757 2088 7.783090 AATATATCGGAATAAGATGCTGCAG 57.217 36.000 10.11 10.11 0.00 4.41
1899 2236 7.809806 CCTATTTGAGAACACAATTTCCAGTTC 59.190 37.037 0.00 0.00 40.37 3.01
1948 2415 7.325821 GCAAATGAGAGATCTATTAGACACTCG 59.674 40.741 16.83 8.50 36.66 4.18
2066 2533 4.655649 AGGATGTATGCTAATGACCTGACA 59.344 41.667 0.00 0.00 0.00 3.58
2162 2629 7.751732 TCAAATGTCTATGAATTGCTGTGTAC 58.248 34.615 0.00 0.00 0.00 2.90
2353 2822 9.702253 AGTTCCTACATATTCGGATATAGTCAT 57.298 33.333 0.00 0.00 0.00 3.06
2439 2908 2.432444 TGGTATGTTCCAAAGGAAGCG 58.568 47.619 0.00 0.00 42.88 4.68
2472 2941 8.761575 AATTCAAACATATACTGCTGGTTTTG 57.238 30.769 0.00 0.00 29.89 2.44
2549 3019 6.949715 TCCTAACCGTCCATATACACTTTTT 58.050 36.000 0.00 0.00 0.00 1.94
2713 3183 5.638530 AAGGATTCTGAATTACTCCCTCC 57.361 43.478 4.11 0.00 0.00 4.30
2715 3185 3.388350 GGATTCTGAATTACTCCCTCCGT 59.612 47.826 4.11 0.00 0.00 4.69
3173 3643 8.497910 AAGGTACATCATATGTTACATCCTCT 57.502 34.615 0.00 0.00 41.63 3.69
4061 4732 3.429492 TCTGTTGTCTCTCATGAGCTCT 58.571 45.455 18.36 0.00 40.03 4.09
4062 4733 4.593956 TCTGTTGTCTCTCATGAGCTCTA 58.406 43.478 18.36 1.49 40.03 2.43
4116 4787 0.555769 AGGGACCAACAACACACCAT 59.444 50.000 0.00 0.00 0.00 3.55
4697 5386 5.562696 GCAAAAGCTACTGATGTGTGCTTAA 60.563 40.000 0.00 0.00 42.11 1.85
5011 5706 0.723414 CTCACCATTGTACAGCAGCG 59.277 55.000 0.00 0.00 0.00 5.18
5012 5707 0.320050 TCACCATTGTACAGCAGCGA 59.680 50.000 0.00 0.00 0.00 4.93
6608 7306 6.070596 TGTTCATGATAGAAGACACCATCACT 60.071 38.462 0.00 0.00 30.64 3.41
6652 7350 2.618709 AGCAGTACAAGGCAAAACTGTC 59.381 45.455 0.00 4.45 41.11 3.51
6695 7393 4.770874 AATCGGGGCCGTGTTCCG 62.771 66.667 10.81 10.81 44.59 4.30
7161 7859 3.052455 TGTTATCACTCGTGTGCCATT 57.948 42.857 12.66 1.02 43.49 3.16
7240 7939 4.354387 TGGAAGACCCATTTACCCTTTGTA 59.646 41.667 0.00 0.00 40.82 2.41
7244 7943 5.899278 AGACCCATTTACCCTTTGTACATT 58.101 37.500 0.00 0.00 0.00 2.71
7384 8086 2.493278 CCCCTAGTTTGCATTGGACAAG 59.507 50.000 0.00 0.00 0.00 3.16
7475 8177 1.903183 AGAGGCTGTAGGAAAGGTGAC 59.097 52.381 0.00 0.00 0.00 3.67
7638 8340 9.401058 CAGTAAATCCCTCAGTTCAAATATCTT 57.599 33.333 0.00 0.00 0.00 2.40
7641 8343 8.438676 AAATCCCTCAGTTCAAATATCTTACG 57.561 34.615 0.00 0.00 0.00 3.18
7864 8566 4.022416 ACGCATGCTTTTTCAAAGGTCATA 60.022 37.500 17.13 0.00 0.00 2.15
7901 8603 5.445964 AGGTGGTATTTGTGGTTCATATCC 58.554 41.667 0.00 0.00 0.00 2.59
8061 8763 3.242381 CGAAAATGATATGTGCACTGCGA 60.242 43.478 19.41 0.00 0.00 5.10
8066 8768 2.416202 TGATATGTGCACTGCGAACAAG 59.584 45.455 19.41 0.00 0.00 3.16
8360 9062 5.756195 TTCAACCTTGTGTGATTCTCTTG 57.244 39.130 0.00 0.00 0.00 3.02
8460 9162 3.041940 CGTGGCGGTTGTGGACTC 61.042 66.667 0.00 0.00 0.00 3.36
8639 9344 1.400113 CGTATGTGGCTGCTTTGTGTG 60.400 52.381 0.00 0.00 0.00 3.82
8699 9404 6.548622 CCTGGTGTTCTATTGGAATTGATCAT 59.451 38.462 0.00 0.00 36.24 2.45
8816 9529 7.325660 TGCTCCTCAAACTCATAAAATCATC 57.674 36.000 0.00 0.00 0.00 2.92
8881 9605 5.867174 TGAATCATGTCTACGTCGTTGAATT 59.133 36.000 11.06 7.48 0.00 2.17
8882 9606 5.950965 ATCATGTCTACGTCGTTGAATTC 57.049 39.130 11.06 0.00 0.00 2.17
8883 9607 4.171005 TCATGTCTACGTCGTTGAATTCC 58.829 43.478 11.06 0.25 0.00 3.01
8884 9608 3.928727 TGTCTACGTCGTTGAATTCCT 57.071 42.857 11.06 0.00 0.00 3.36
8885 9609 4.247267 TGTCTACGTCGTTGAATTCCTT 57.753 40.909 11.06 0.00 0.00 3.36
8886 9610 3.985279 TGTCTACGTCGTTGAATTCCTTG 59.015 43.478 11.06 0.00 0.00 3.61
8909 9634 3.546616 CGTTTCCACTAACGTTTTGGGAC 60.547 47.826 22.06 19.21 44.28 4.46
8912 9637 3.469739 TCCACTAACGTTTTGGGACTTC 58.530 45.455 22.06 0.00 0.00 3.01
8947 9672 3.574826 AGGATAACTGTTCTCCTATCCGC 59.425 47.826 21.81 0.00 43.09 5.54
8976 9701 1.065854 AGCATCTACAGGTGGACTTGC 60.066 52.381 3.94 3.94 0.00 4.01
8986 9711 2.657297 TGGACTTGCCAAATCTGCC 58.343 52.632 0.00 0.00 45.87 4.85
9007 9732 3.557264 CCCTCCTATACGCCTCAAATTCC 60.557 52.174 0.00 0.00 0.00 3.01
9008 9733 3.557264 CCTCCTATACGCCTCAAATTCCC 60.557 52.174 0.00 0.00 0.00 3.97
9009 9734 3.314693 TCCTATACGCCTCAAATTCCCT 58.685 45.455 0.00 0.00 0.00 4.20
9010 9735 3.714798 TCCTATACGCCTCAAATTCCCTT 59.285 43.478 0.00 0.00 0.00 3.95
9011 9736 4.065789 CCTATACGCCTCAAATTCCCTTC 58.934 47.826 0.00 0.00 0.00 3.46
9012 9737 3.644966 ATACGCCTCAAATTCCCTTCA 57.355 42.857 0.00 0.00 0.00 3.02
9013 9738 2.286365 ACGCCTCAAATTCCCTTCAA 57.714 45.000 0.00 0.00 0.00 2.69
9014 9739 2.593026 ACGCCTCAAATTCCCTTCAAA 58.407 42.857 0.00 0.00 0.00 2.69
9015 9740 3.165071 ACGCCTCAAATTCCCTTCAAAT 58.835 40.909 0.00 0.00 0.00 2.32
9016 9741 3.193479 ACGCCTCAAATTCCCTTCAAATC 59.807 43.478 0.00 0.00 0.00 2.17
9017 9742 3.445096 CGCCTCAAATTCCCTTCAAATCT 59.555 43.478 0.00 0.00 0.00 2.40
9018 9743 4.676196 CGCCTCAAATTCCCTTCAAATCTG 60.676 45.833 0.00 0.00 0.00 2.90
9019 9744 4.752146 CCTCAAATTCCCTTCAAATCTGC 58.248 43.478 0.00 0.00 0.00 4.26
9020 9745 4.382362 CCTCAAATTCCCTTCAAATCTGCC 60.382 45.833 0.00 0.00 0.00 4.85
9021 9746 3.515104 TCAAATTCCCTTCAAATCTGCCC 59.485 43.478 0.00 0.00 0.00 5.36
9022 9747 3.479866 AATTCCCTTCAAATCTGCCCT 57.520 42.857 0.00 0.00 0.00 5.19
9023 9748 2.514458 TTCCCTTCAAATCTGCCCTC 57.486 50.000 0.00 0.00 0.00 4.30
9024 9749 0.625849 TCCCTTCAAATCTGCCCTCC 59.374 55.000 0.00 0.00 0.00 4.30
9025 9750 0.627986 CCCTTCAAATCTGCCCTCCT 59.372 55.000 0.00 0.00 0.00 3.69
9026 9751 1.846439 CCCTTCAAATCTGCCCTCCTA 59.154 52.381 0.00 0.00 0.00 2.94
9027 9752 2.444766 CCCTTCAAATCTGCCCTCCTAT 59.555 50.000 0.00 0.00 0.00 2.57
9028 9753 3.652869 CCCTTCAAATCTGCCCTCCTATA 59.347 47.826 0.00 0.00 0.00 1.31
9029 9754 4.505742 CCCTTCAAATCTGCCCTCCTATAC 60.506 50.000 0.00 0.00 0.00 1.47
9030 9755 4.310769 CTTCAAATCTGCCCTCCTATACG 58.689 47.826 0.00 0.00 0.00 3.06
9031 9756 2.037251 TCAAATCTGCCCTCCTATACGC 59.963 50.000 0.00 0.00 0.00 4.42
9032 9757 0.977395 AATCTGCCCTCCTATACGCC 59.023 55.000 0.00 0.00 0.00 5.68
9033 9758 0.115349 ATCTGCCCTCCTATACGCCT 59.885 55.000 0.00 0.00 0.00 5.52
9034 9759 0.539901 TCTGCCCTCCTATACGCCTC 60.540 60.000 0.00 0.00 0.00 4.70
9035 9760 0.827925 CTGCCCTCCTATACGCCTCA 60.828 60.000 0.00 0.00 0.00 3.86
9036 9761 0.397957 TGCCCTCCTATACGCCTCAA 60.398 55.000 0.00 0.00 0.00 3.02
9037 9762 0.756903 GCCCTCCTATACGCCTCAAA 59.243 55.000 0.00 0.00 0.00 2.69
9038 9763 1.348036 GCCCTCCTATACGCCTCAAAT 59.652 52.381 0.00 0.00 0.00 2.32
9039 9764 2.224548 GCCCTCCTATACGCCTCAAATT 60.225 50.000 0.00 0.00 0.00 1.82
9056 9781 6.536224 CCTCAAATTTCCTTAAATCCATGCAC 59.464 38.462 0.00 0.00 34.12 4.57
9072 9797 3.824414 TGCACGTCGATCATACGATAT 57.176 42.857 20.73 0.11 43.93 1.63
9131 9856 6.403866 AGCAAATCATAGTTCAACAAACCA 57.596 33.333 0.00 0.00 38.76 3.67
9132 9857 6.996509 AGCAAATCATAGTTCAACAAACCAT 58.003 32.000 0.00 0.00 38.76 3.55
9138 9863 9.859427 AATCATAGTTCAACAAACCATACATTG 57.141 29.630 0.00 0.00 38.76 2.82
9146 9871 3.286751 CCATACATTGGCCGGGCG 61.287 66.667 24.45 11.88 39.09 6.13
9147 9872 3.964875 CATACATTGGCCGGGCGC 61.965 66.667 24.45 0.00 0.00 6.53
9174 9899 3.567797 GCGGAATGCGTCCTGCTC 61.568 66.667 12.55 0.00 45.36 4.26
9175 9900 2.892425 CGGAATGCGTCCTGCTCC 60.892 66.667 4.85 0.00 45.36 4.70
9176 9901 2.892425 GGAATGCGTCCTGCTCCG 60.892 66.667 0.00 0.00 46.63 4.63
9183 9908 4.479993 GTCCTGCTCCGCCTGCAT 62.480 66.667 0.00 0.00 39.86 3.96
9184 9909 4.166888 TCCTGCTCCGCCTGCATC 62.167 66.667 0.00 0.00 39.86 3.91
9198 9923 4.247380 CATCCGGGCTGCCTCCTC 62.247 72.222 19.68 0.00 0.00 3.71
9207 9932 4.804420 TGCCTCCTCCGCCTCCAT 62.804 66.667 0.00 0.00 0.00 3.41
9208 9933 3.934962 GCCTCCTCCGCCTCCATC 61.935 72.222 0.00 0.00 0.00 3.51
9209 9934 3.237741 CCTCCTCCGCCTCCATCC 61.238 72.222 0.00 0.00 0.00 3.51
9210 9935 3.610669 CTCCTCCGCCTCCATCCG 61.611 72.222 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.686916 TGGTATTGGTGTCGTTCATGA 57.313 42.857 0.00 0.00 0.00 3.07
21 22 4.514816 TCATGCAATATGGTATTGGTGTCG 59.485 41.667 10.66 0.00 0.00 4.35
63 64 2.126071 TTGTAGCGCCTGTCGAGC 60.126 61.111 2.29 0.00 41.67 5.03
76 77 6.818644 GGAGCTTTAGATTCACACATCTTGTA 59.181 38.462 0.00 0.00 35.67 2.41
77 78 5.645497 GGAGCTTTAGATTCACACATCTTGT 59.355 40.000 0.00 0.00 39.97 3.16
97 98 4.451435 GTGTAAGTAGTCTTTTGTGGGAGC 59.549 45.833 0.00 0.00 35.36 4.70
105 106 6.645415 CCATCTTCACGTGTAAGTAGTCTTTT 59.355 38.462 16.51 0.00 35.36 2.27
141 142 3.450457 TGAACAAGCCTTGGATGTTGTTT 59.550 39.130 9.64 0.00 41.90 2.83
144 145 3.181477 TGTTGAACAAGCCTTGGATGTTG 60.181 43.478 9.64 5.89 37.41 3.33
186 188 4.034258 CCATGATGCGGCATCGGC 62.034 66.667 31.17 14.48 43.14 5.54
240 245 0.471780 TCTCTCCTGTTCACCCTGCA 60.472 55.000 0.00 0.00 0.00 4.41
275 518 1.290203 CATAGATCGTGTGTGGCCAC 58.710 55.000 29.67 29.67 42.19 5.01
329 622 1.019673 CATCAAATCTCCGGCTGTGG 58.980 55.000 0.00 0.00 0.00 4.17
331 624 0.911769 TCCATCAAATCTCCGGCTGT 59.088 50.000 0.00 0.00 0.00 4.40
333 626 1.839994 TCTTCCATCAAATCTCCGGCT 59.160 47.619 0.00 0.00 0.00 5.52
338 631 5.964958 TTTGGTGTCTTCCATCAAATCTC 57.035 39.130 0.00 0.00 46.64 2.75
417 710 5.639506 AGGTTCGATATCTTGTGTGTTTCAG 59.360 40.000 0.34 0.00 0.00 3.02
512 805 8.670521 TGTATCTGATGTCCACCTAATATCAT 57.329 34.615 0.00 0.00 0.00 2.45
732 1041 9.964354 ATGCAATAATAAGAGAGCCAATATGTA 57.036 29.630 0.00 0.00 0.00 2.29
740 1050 8.628280 AGAAGAAAATGCAATAATAAGAGAGCC 58.372 33.333 0.00 0.00 0.00 4.70
777 1087 7.280356 GGTCTAGAATAAGGAAGCCACAATAA 58.720 38.462 0.00 0.00 0.00 1.40
778 1088 6.183361 GGGTCTAGAATAAGGAAGCCACAATA 60.183 42.308 0.00 0.00 0.00 1.90
779 1089 5.398012 GGGTCTAGAATAAGGAAGCCACAAT 60.398 44.000 0.00 0.00 0.00 2.71
861 1182 6.956047 ACGAACTGTGATAGGTTTTCTTTTC 58.044 36.000 0.00 0.00 0.00 2.29
862 1183 6.937436 ACGAACTGTGATAGGTTTTCTTTT 57.063 33.333 0.00 0.00 0.00 2.27
866 1187 5.844396 CGAAAACGAACTGTGATAGGTTTTC 59.156 40.000 14.03 14.03 44.59 2.29
1380 1708 1.333115 GCGTGCCGGAAAACATAAAC 58.667 50.000 5.05 0.00 0.00 2.01
1525 1853 0.251354 ATGCAGCACTCACAGGGTAG 59.749 55.000 0.00 0.00 0.00 3.18
1565 1893 1.473677 TCAATCATTCAAGGGCGCTTG 59.526 47.619 31.65 31.65 35.78 4.01
1569 1897 4.682860 GCAATAATCAATCATTCAAGGGCG 59.317 41.667 0.00 0.00 0.00 6.13
1899 2236 1.250840 CCCGGGCTGGAAAAGGAAAG 61.251 60.000 15.75 0.00 42.00 2.62
1927 2264 5.368989 TGCGAGTGTCTAATAGATCTCTCA 58.631 41.667 0.00 14.06 31.11 3.27
1929 2266 5.767665 ACATGCGAGTGTCTAATAGATCTCT 59.232 40.000 0.00 8.17 31.11 3.10
1930 2267 6.007936 ACATGCGAGTGTCTAATAGATCTC 57.992 41.667 0.00 12.20 0.00 2.75
2066 2533 3.196901 TGCTTCCCGTAGTGTCATTGTAT 59.803 43.478 0.00 0.00 0.00 2.29
2162 2629 3.132160 CAAGCTGAGATGTAGCATCTGG 58.868 50.000 15.35 9.43 43.53 3.86
2439 2908 7.438459 AGCAGTATATGTTTGAATTCCTCGTAC 59.562 37.037 2.27 0.00 0.00 3.67
2713 3183 5.880054 ATTGAGACACTTATTTTGGGACG 57.120 39.130 0.00 0.00 0.00 4.79
3173 3643 1.892474 GCAACCCATGTTAGGCAAGAA 59.108 47.619 0.00 0.00 32.09 2.52
4061 4732 0.671163 GACGGCGGTTCCACACAATA 60.671 55.000 13.24 0.00 34.01 1.90
4062 4733 1.964373 GACGGCGGTTCCACACAAT 60.964 57.895 13.24 0.00 34.01 2.71
4116 4787 2.787473 ATCCTCAATCAAAGGCGTCA 57.213 45.000 0.00 0.00 33.65 4.35
4823 5518 4.500127 TGTTTCGAACTTTCAGTGAGTCA 58.500 39.130 0.00 0.00 0.00 3.41
4849 5544 2.586245 CCCAATGAGGCGAGCTCA 59.414 61.111 15.40 0.00 35.39 4.26
5011 5706 8.476657 GTCAGTACCTTTTTAGTATGACCTTC 57.523 38.462 0.00 0.00 31.79 3.46
5701 6397 0.465460 ATCACTGGTGCAACAACCGT 60.465 50.000 5.64 0.00 43.73 4.83
6391 7088 4.639310 ACATCCTCATTGAGTTGAATCAGC 59.361 41.667 12.54 0.00 0.00 4.26
6608 7306 3.007614 GCTACTAACCAACCACAGAAGGA 59.992 47.826 0.00 0.00 0.00 3.36
6652 7350 3.817084 TCACTTTGATTTCAGTCTGCAGG 59.183 43.478 15.13 0.00 0.00 4.85
6695 7393 8.071368 TCCAAATTCACACTAAATAAACACGAC 58.929 33.333 0.00 0.00 0.00 4.34
7244 7943 8.328758 AGTTAGAAATGTGGAGATAACATTGGA 58.671 33.333 2.78 0.00 45.25 3.53
7864 8566 7.673926 ACAAATACCACCTCTGTTCCAAATTAT 59.326 33.333 0.00 0.00 0.00 1.28
8061 8763 3.895656 TGGTAGTACTGACAGAGCTTGTT 59.104 43.478 10.08 0.00 41.05 2.83
8066 8768 4.202070 GGAAGATGGTAGTACTGACAGAGC 60.202 50.000 10.08 1.14 0.00 4.09
8360 9062 5.424121 AGTTTCAGTGTTACATGAGCAAC 57.576 39.130 0.00 1.11 0.00 4.17
8622 9327 1.364901 GCACACAAAGCAGCCACAT 59.635 52.632 0.00 0.00 0.00 3.21
8639 9344 7.962964 TTAGCATATGTAAGTTCTACATGGC 57.037 36.000 4.29 10.09 38.47 4.40
8699 9404 7.388224 GGACTTATCTCACAGATATAGTCGACA 59.612 40.741 19.50 4.13 40.82 4.35
8881 9605 1.504359 CGTTAGTGGAAACGCAAGGA 58.496 50.000 0.00 0.00 44.83 3.36
8909 9634 8.049721 ACAGTTATCCTCCTTCAAAATAGGAAG 58.950 37.037 0.00 0.00 41.13 3.46
8912 9637 8.049721 AGAACAGTTATCCTCCTTCAAAATAGG 58.950 37.037 0.00 0.00 0.00 2.57
8947 9672 3.034635 ACCTGTAGATGCTCTTAGGTGG 58.965 50.000 14.87 0.00 39.68 4.61
8967 9692 0.244721 GGCAGATTTGGCAAGTCCAC 59.755 55.000 17.82 10.77 46.55 4.02
8976 9701 2.872038 GCGTATAGGAGGGCAGATTTGG 60.872 54.545 0.00 0.00 0.00 3.28
8983 9708 0.397957 TTGAGGCGTATAGGAGGGCA 60.398 55.000 0.00 0.00 40.80 5.36
8984 9709 0.756903 TTTGAGGCGTATAGGAGGGC 59.243 55.000 0.00 0.00 38.72 5.19
8985 9710 3.557264 GGAATTTGAGGCGTATAGGAGGG 60.557 52.174 0.00 0.00 0.00 4.30
8986 9711 3.557264 GGGAATTTGAGGCGTATAGGAGG 60.557 52.174 0.00 0.00 0.00 4.30
9007 9732 3.872459 ATAGGAGGGCAGATTTGAAGG 57.128 47.619 0.00 0.00 0.00 3.46
9008 9733 4.310769 CGTATAGGAGGGCAGATTTGAAG 58.689 47.826 0.00 0.00 0.00 3.02
9009 9734 3.494398 GCGTATAGGAGGGCAGATTTGAA 60.494 47.826 0.00 0.00 0.00 2.69
9010 9735 2.037251 GCGTATAGGAGGGCAGATTTGA 59.963 50.000 0.00 0.00 0.00 2.69
9011 9736 2.417719 GCGTATAGGAGGGCAGATTTG 58.582 52.381 0.00 0.00 0.00 2.32
9012 9737 1.348036 GGCGTATAGGAGGGCAGATTT 59.652 52.381 0.00 0.00 38.33 2.17
9013 9738 0.977395 GGCGTATAGGAGGGCAGATT 59.023 55.000 0.00 0.00 38.33 2.40
9014 9739 0.115349 AGGCGTATAGGAGGGCAGAT 59.885 55.000 0.00 0.00 40.80 2.90
9015 9740 0.539901 GAGGCGTATAGGAGGGCAGA 60.540 60.000 0.00 0.00 40.80 4.26
9016 9741 0.827925 TGAGGCGTATAGGAGGGCAG 60.828 60.000 0.00 0.00 40.80 4.85
9017 9742 0.397957 TTGAGGCGTATAGGAGGGCA 60.398 55.000 0.00 0.00 40.80 5.36
9018 9743 0.756903 TTTGAGGCGTATAGGAGGGC 59.243 55.000 0.00 0.00 38.72 5.19
9019 9744 3.771577 AATTTGAGGCGTATAGGAGGG 57.228 47.619 0.00 0.00 0.00 4.30
9020 9745 4.065789 GGAAATTTGAGGCGTATAGGAGG 58.934 47.826 0.00 0.00 0.00 4.30
9021 9746 4.962155 AGGAAATTTGAGGCGTATAGGAG 58.038 43.478 0.00 0.00 0.00 3.69
9022 9747 5.367945 AAGGAAATTTGAGGCGTATAGGA 57.632 39.130 0.00 0.00 0.00 2.94
9023 9748 7.562454 TTTAAGGAAATTTGAGGCGTATAGG 57.438 36.000 0.00 0.00 0.00 2.57
9024 9749 8.290325 GGATTTAAGGAAATTTGAGGCGTATAG 58.710 37.037 0.00 0.00 35.33 1.31
9025 9750 7.776030 TGGATTTAAGGAAATTTGAGGCGTATA 59.224 33.333 0.00 0.00 35.33 1.47
9026 9751 6.605594 TGGATTTAAGGAAATTTGAGGCGTAT 59.394 34.615 0.00 0.00 35.33 3.06
9027 9752 5.946972 TGGATTTAAGGAAATTTGAGGCGTA 59.053 36.000 0.00 0.00 35.33 4.42
9028 9753 4.770010 TGGATTTAAGGAAATTTGAGGCGT 59.230 37.500 0.00 0.00 35.33 5.68
9029 9754 5.323371 TGGATTTAAGGAAATTTGAGGCG 57.677 39.130 0.00 0.00 35.33 5.52
9030 9755 5.525012 GCATGGATTTAAGGAAATTTGAGGC 59.475 40.000 0.00 0.00 35.33 4.70
9031 9756 6.536224 GTGCATGGATTTAAGGAAATTTGAGG 59.464 38.462 0.00 0.00 35.33 3.86
9032 9757 6.254157 CGTGCATGGATTTAAGGAAATTTGAG 59.746 38.462 0.00 0.00 35.33 3.02
9033 9758 6.098679 CGTGCATGGATTTAAGGAAATTTGA 58.901 36.000 0.00 0.00 35.33 2.69
9034 9759 5.868801 ACGTGCATGGATTTAAGGAAATTTG 59.131 36.000 11.36 0.00 35.33 2.32
9035 9760 6.036577 ACGTGCATGGATTTAAGGAAATTT 57.963 33.333 11.36 0.00 35.33 1.82
9036 9761 5.650543 GACGTGCATGGATTTAAGGAAATT 58.349 37.500 11.36 0.00 35.33 1.82
9037 9762 4.201910 CGACGTGCATGGATTTAAGGAAAT 60.202 41.667 11.36 0.00 38.00 2.17
9038 9763 3.126171 CGACGTGCATGGATTTAAGGAAA 59.874 43.478 11.36 0.00 0.00 3.13
9039 9764 2.675844 CGACGTGCATGGATTTAAGGAA 59.324 45.455 11.36 0.00 0.00 3.36
9056 9781 7.304679 CGGACAATTTATATCGTATGATCGACG 60.305 40.741 12.46 12.46 42.56 5.12
9095 9820 8.212317 ACTATGATTTGCTTTGCTTTGTTTTT 57.788 26.923 0.00 0.00 0.00 1.94
9146 9871 4.537433 ATTCCGCTCGGAGCAGGC 62.537 66.667 27.83 3.83 46.06 4.85
9147 9872 2.587194 CATTCCGCTCGGAGCAGG 60.587 66.667 27.83 26.27 46.06 4.85
9148 9873 3.267860 GCATTCCGCTCGGAGCAG 61.268 66.667 27.83 18.20 46.06 4.24
9151 9876 2.956964 GACGCATTCCGCTCGGAG 60.957 66.667 11.09 0.00 46.06 4.63
9152 9877 4.508128 GGACGCATTCCGCTCGGA 62.508 66.667 6.95 6.95 43.52 4.55
9159 9884 2.892425 CGGAGCAGGACGCATTCC 60.892 66.667 0.00 0.00 46.13 3.01
9181 9906 4.247380 GAGGAGGCAGCCCGGATG 62.247 72.222 8.22 1.84 35.76 3.51
9190 9915 4.804420 ATGGAGGCGGAGGAGGCA 62.804 66.667 0.00 0.00 39.37 4.75
9191 9916 3.934962 GATGGAGGCGGAGGAGGC 61.935 72.222 0.00 0.00 0.00 4.70
9192 9917 3.237741 GGATGGAGGCGGAGGAGG 61.238 72.222 0.00 0.00 0.00 4.30
9193 9918 3.610669 CGGATGGAGGCGGAGGAG 61.611 72.222 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.