Multiple sequence alignment - TraesCS7D01G271800

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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 TraesCS7D01G271800 chr7D 100.000 4413 0 0 1 4413 261864255 261868667 0.000000e+00 8150.0
1 TraesCS7D01G271800 chr7D 92.350 183 12 2 4111 4293 381458560 381458380 4.380000e-65 259.0
2 TraesCS7D01G271800 chr7B 94.805 2310 68 13 1843 4122 242677702 242675415 0.000000e+00 3554.0
3 TraesCS7D01G271800 chr7B 94.192 1429 46 12 429 1843 242679170 242677765 0.000000e+00 2145.0
4 TraesCS7D01G271800 chr7B 92.857 126 9 0 4288 4413 242675423 242675298 2.710000e-42 183.0
5 TraesCS7D01G271800 chr7B 89.583 144 13 2 80 221 242679807 242679664 9.750000e-42 182.0
6 TraesCS7D01G271800 chr7A 92.696 2081 76 25 1843 3877 284760103 284762153 0.000000e+00 2931.0
7 TraesCS7D01G271800 chr7A 95.259 1139 26 7 722 1843 284758912 284760039 0.000000e+00 1779.0
8 TraesCS7D01G271800 chr7A 89.910 446 21 7 237 679 284758491 284758915 1.790000e-153 553.0
9 TraesCS7D01G271800 chr7A 90.114 263 9 5 3874 4122 284776850 284777109 4.260000e-85 326.0
10 TraesCS7D01G271800 chr7A 91.071 224 17 3 1 223 284757700 284757921 2.580000e-77 300.0
11 TraesCS7D01G271800 chr5D 96.386 166 6 0 4121 4286 368995523 368995358 1.560000e-69 274.0
12 TraesCS7D01G271800 chr1D 95.808 167 7 0 4121 4287 81276519 81276353 2.020000e-68 270.0
13 TraesCS7D01G271800 chr1D 93.370 181 9 3 4118 4296 206955705 206955526 9.410000e-67 265.0
14 TraesCS7D01G271800 chr1D 93.333 180 11 1 4114 4293 323833259 323833081 9.410000e-67 265.0
15 TraesCS7D01G271800 chr1D 100.000 28 0 0 428 455 392952272 392952299 8.000000e-03 52.8
16 TraesCS7D01G271800 chr4D 94.253 174 8 2 4112 4285 13359909 13360080 9.410000e-67 265.0
17 TraesCS7D01G271800 chrUn 92.021 188 13 2 4118 4304 74119618 74119432 3.380000e-66 263.0
18 TraesCS7D01G271800 chr6D 94.675 169 9 0 4120 4288 352878325 352878493 3.380000e-66 263.0
19 TraesCS7D01G271800 chr4B 93.785 177 8 3 4116 4291 592024404 592024230 3.380000e-66 263.0
20 TraesCS7D01G271800 chr3B 100.000 35 0 0 428 462 527657156 527657122 1.020000e-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 TraesCS7D01G271800 chr7D 261864255 261868667 4412 False 8150.00 8150 100.00000 1 4413 1 chr7D.!!$F1 4412
1 TraesCS7D01G271800 chr7B 242675298 242679807 4509 True 1516.00 3554 92.85925 80 4413 4 chr7B.!!$R1 4333
2 TraesCS7D01G271800 chr7A 284757700 284762153 4453 False 1390.75 2931 92.23400 1 3877 4 chr7A.!!$F2 3876

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
987 1556 0.032515 TCCGATCCCTAACTGCTCCA 60.033 55.0 0.00 0.0 0.0 3.86 F
1626 2197 0.036294 CGTTTTCTCCCTGTCCCCTC 60.036 60.0 0.00 0.0 0.0 4.30 F
2055 2707 0.108709 TTGCGCCTTCATTCCATTGC 60.109 50.0 4.18 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2788 0.744414 TGCAACGGCTAGGATGCTTC 60.744 55.000 0.0 0.0 41.91 3.86 R
2940 3620 1.082194 AGGAAGAATAGGGGGTGGACA 59.918 52.381 0.0 0.0 0.00 4.02 R
3947 4651 0.555769 AAGCCCCAAACCACTCTGAA 59.444 50.000 0.0 0.0 0.00 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
46 47 9.368674 CACCATCATTTTTGAAGCAATTACATA 57.631 29.630 0.00 0.00 0.00 2.29
86 87 8.732746 TTTGAGACTATTTCTTTAGCATACCC 57.267 34.615 0.00 0.00 33.22 3.69
97 98 1.220749 GCATACCCGAGCCTCACAA 59.779 57.895 0.00 0.00 0.00 3.33
104 105 1.679944 CCCGAGCCTCACAATGACATT 60.680 52.381 0.00 0.00 0.00 2.71
178 179 3.736720 ACTGCATGCACTATACCATCAG 58.263 45.455 18.46 4.87 0.00 2.90
219 498 8.432013 ACATGAGGTGCTGTCTTTATATGATTA 58.568 33.333 0.00 0.00 0.00 1.75
223 502 9.717942 GAGGTGCTGTCTTTATATGATTATCTT 57.282 33.333 0.00 0.00 0.00 2.40
240 799 2.543641 TCTTCATATGCAGCACGAGTG 58.456 47.619 0.00 0.00 0.00 3.51
242 801 0.823460 TCATATGCAGCACGAGTGGA 59.177 50.000 0.00 0.00 0.00 4.02
264 823 6.156775 TGGATCTTAGTTTGAGATGTGGATGA 59.843 38.462 0.00 0.00 34.13 2.92
278 837 7.335627 AGATGTGGATGACCGATTTTAAAGTA 58.664 34.615 0.00 0.00 39.42 2.24
312 871 9.255304 GACTTTTAAATTATGTGGCAAGTTGAA 57.745 29.630 7.16 0.00 0.00 2.69
339 898 9.247861 AGTTGCAATATGGACTTTTCTCTTTAT 57.752 29.630 0.59 0.00 0.00 1.40
410 969 3.983344 AGTCGGTGATTACGTGTTTGTAC 59.017 43.478 0.00 0.00 0.00 2.90
411 970 3.735240 GTCGGTGATTACGTGTTTGTACA 59.265 43.478 0.00 0.00 0.00 2.90
412 971 3.982701 TCGGTGATTACGTGTTTGTACAG 59.017 43.478 0.00 0.00 34.24 2.74
413 972 3.982701 CGGTGATTACGTGTTTGTACAGA 59.017 43.478 0.00 0.00 34.24 3.41
414 973 4.445052 CGGTGATTACGTGTTTGTACAGAA 59.555 41.667 0.00 0.00 34.24 3.02
415 974 5.119588 CGGTGATTACGTGTTTGTACAGAAT 59.880 40.000 0.00 0.00 34.24 2.40
416 975 6.304126 GGTGATTACGTGTTTGTACAGAATG 58.696 40.000 0.00 0.00 46.00 2.67
417 976 6.146510 GGTGATTACGTGTTTGTACAGAATGA 59.853 38.462 0.00 0.00 39.69 2.57
418 977 7.148474 GGTGATTACGTGTTTGTACAGAATGAT 60.148 37.037 0.00 0.00 39.69 2.45
419 978 8.227791 GTGATTACGTGTTTGTACAGAATGATT 58.772 33.333 0.00 0.00 39.69 2.57
420 979 8.779303 TGATTACGTGTTTGTACAGAATGATTT 58.221 29.630 0.00 0.00 39.69 2.17
421 980 9.262472 GATTACGTGTTTGTACAGAATGATTTC 57.738 33.333 0.00 0.00 39.69 2.17
422 981 5.997385 ACGTGTTTGTACAGAATGATTTCC 58.003 37.500 0.00 0.00 39.69 3.13
423 982 5.048991 ACGTGTTTGTACAGAATGATTTCCC 60.049 40.000 0.00 0.00 39.69 3.97
424 983 5.181245 CGTGTTTGTACAGAATGATTTCCCT 59.819 40.000 0.00 0.00 39.69 4.20
425 984 6.293955 CGTGTTTGTACAGAATGATTTCCCTT 60.294 38.462 0.00 0.00 39.69 3.95
426 985 6.863126 GTGTTTGTACAGAATGATTTCCCTTG 59.137 38.462 0.00 0.00 39.69 3.61
427 986 6.549364 TGTTTGTACAGAATGATTTCCCTTGT 59.451 34.615 0.00 0.00 39.69 3.16
428 987 7.721842 TGTTTGTACAGAATGATTTCCCTTGTA 59.278 33.333 0.00 0.00 39.69 2.41
559 1118 5.886960 AAGTCAATAAAGGATGTGACAGC 57.113 39.130 0.00 0.00 42.29 4.40
697 1259 6.964464 AGGAGTACTAGAGACAGAGATTTCA 58.036 40.000 0.00 0.00 0.00 2.69
698 1260 7.054124 AGGAGTACTAGAGACAGAGATTTCAG 58.946 42.308 0.00 0.00 0.00 3.02
707 1269 2.560542 ACAGAGATTTCAGAGCGTGAGT 59.439 45.455 0.00 0.00 36.21 3.41
766 1333 4.385199 CCAACCAGATACCTCCTGCATTTA 60.385 45.833 0.00 0.00 0.00 1.40
767 1334 5.192927 CAACCAGATACCTCCTGCATTTAA 58.807 41.667 0.00 0.00 0.00 1.52
768 1335 5.450818 ACCAGATACCTCCTGCATTTAAA 57.549 39.130 0.00 0.00 0.00 1.52
801 1368 6.759497 AACAGATACCTCATGTTTTAAGGC 57.241 37.500 0.00 0.00 33.49 4.35
951 1520 1.291877 CTGCTTCCTTCCCGTCGTTG 61.292 60.000 0.00 0.00 0.00 4.10
987 1556 0.032515 TCCGATCCCTAACTGCTCCA 60.033 55.000 0.00 0.00 0.00 3.86
1445 2015 3.379445 GACGAGGAGGTGGGCGAA 61.379 66.667 0.00 0.00 0.00 4.70
1618 2189 3.771577 ATTCAGTCACGTTTTCTCCCT 57.228 42.857 0.00 0.00 0.00 4.20
1626 2197 0.036294 CGTTTTCTCCCTGTCCCCTC 60.036 60.000 0.00 0.00 0.00 4.30
1738 2318 6.599244 CAGGTGACAGTACATTCCATTGTTAT 59.401 38.462 0.00 0.00 0.00 1.89
1803 2383 8.389603 GCAGTTTCTCTCTCAAGATTAGATTTG 58.610 37.037 0.00 0.00 0.00 2.32
1913 2560 7.220741 TGCCTTCTACTCATCATCTATGTAC 57.779 40.000 0.00 0.00 36.89 2.90
1978 2630 6.375455 CAGATTCAGTAGTTGGTGGCTAAAAT 59.625 38.462 0.00 0.00 0.00 1.82
1992 2644 5.293079 GTGGCTAAAATCTAGAACTGCTCTG 59.707 44.000 0.00 0.00 35.41 3.35
1996 2648 6.038050 GCTAAAATCTAGAACTGCTCTGCATT 59.962 38.462 0.00 0.00 38.13 3.56
2055 2707 0.108709 TTGCGCCTTCATTCCATTGC 60.109 50.000 4.18 0.00 0.00 3.56
2075 2727 5.705813 TGCCTGTCGTTTGTAAATATACG 57.294 39.130 0.00 0.00 34.60 3.06
2145 2799 1.813102 AGGAAGGGGAAGCATCCTAG 58.187 55.000 8.09 0.00 45.77 3.02
2146 2800 0.109532 GGAAGGGGAAGCATCCTAGC 59.890 60.000 8.09 0.00 45.77 3.42
2147 2801 0.109532 GAAGGGGAAGCATCCTAGCC 59.890 60.000 8.09 0.57 45.77 3.93
2148 2802 1.700042 AAGGGGAAGCATCCTAGCCG 61.700 60.000 8.09 0.00 45.77 5.52
2149 2803 2.444256 GGGGAAGCATCCTAGCCGT 61.444 63.158 8.09 0.00 45.77 5.68
2150 2804 1.527370 GGGAAGCATCCTAGCCGTT 59.473 57.895 8.09 0.00 45.77 4.44
2189 2849 7.345192 CACACAGCCATATCGTTTATTAGAAC 58.655 38.462 0.00 0.00 0.00 3.01
2563 3240 8.519799 TTCTTTTCTGTTAAACCAGACTGAAT 57.480 30.769 3.32 0.00 41.05 2.57
2577 3254 5.474532 CCAGACTGAATTTCAAGATTCACCA 59.525 40.000 3.32 0.00 40.20 4.17
2580 3257 8.086522 CAGACTGAATTTCAAGATTCACCATTT 58.913 33.333 0.00 0.00 40.20 2.32
2584 3262 8.991243 TGAATTTCAAGATTCACCATTTGATC 57.009 30.769 0.00 0.00 40.20 2.92
2711 3390 9.649167 TTAGTAACTTACCAAGCAGAAGATAAC 57.351 33.333 0.00 0.00 0.00 1.89
2940 3620 1.060163 ACAAGGTACAGCCACCACCT 61.060 55.000 0.00 0.00 44.66 4.00
2952 3632 2.124085 CCACCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
3073 3754 8.323140 CCATCAAATGCGATTTCATAAACTTTC 58.677 33.333 0.00 0.00 0.00 2.62
3115 3796 3.201487 TGATGCCAATCCTCATGAAGTCT 59.799 43.478 0.00 0.00 31.15 3.24
3174 3871 6.579666 TTATACACAGTAAGACGTGGACTT 57.420 37.500 0.00 0.00 37.45 3.01
3289 3987 5.891551 AGAGGGAATTTGTTATTAATGGCGT 59.108 36.000 0.00 0.00 0.00 5.68
3317 4015 8.721478 TGATGAAACTGAATACTAGAAAACTGC 58.279 33.333 0.00 0.00 0.00 4.40
3388 4086 1.887344 TACCCCGGGTAACAACGAGC 61.887 60.000 21.85 0.00 34.97 5.03
3698 4399 2.164219 CGCTAGTTGCCCATTGTGATTT 59.836 45.455 0.00 0.00 38.78 2.17
3753 4454 5.122396 GTCATTCTTTTACACTTGATCGCCT 59.878 40.000 0.00 0.00 0.00 5.52
3755 4456 4.002906 TCTTTTACACTTGATCGCCTGT 57.997 40.909 0.00 0.00 0.00 4.00
3813 4514 3.900971 TGCTGAATAATGCTGGATGGAA 58.099 40.909 0.00 0.00 0.00 3.53
3849 4553 4.124970 CCAAGCTCTGAAATGATGATCGA 58.875 43.478 0.00 0.00 0.00 3.59
3880 4584 2.429971 TGCAACATGCCACTCTGAAAAA 59.570 40.909 0.00 0.00 44.23 1.94
3886 4590 5.111293 ACATGCCACTCTGAAAAAGTTTTG 58.889 37.500 0.61 0.00 0.00 2.44
3911 4615 9.349713 TGATATTTTGAACCTTTTAGAGTGTGT 57.650 29.630 0.00 0.00 0.00 3.72
3941 4645 3.228188 TCACTGTGAAAAAGGGATGCT 57.772 42.857 8.27 0.00 18.74 3.79
3947 4651 3.181440 TGTGAAAAAGGGATGCTCAGACT 60.181 43.478 0.00 0.00 0.00 3.24
3956 4660 2.418471 GGATGCTCAGACTTCAGAGTGG 60.418 54.545 1.17 0.00 35.88 4.00
4106 4815 9.255304 CTACTCAAACAATCTAAAGGATAGAGC 57.745 37.037 0.00 0.00 33.71 4.09
4128 4837 9.785982 AGAGCAATTTCTTATAATTACTCCCTC 57.214 33.333 0.00 0.00 38.10 4.30
4129 4838 8.926092 AGCAATTTCTTATAATTACTCCCTCC 57.074 34.615 0.00 0.00 0.00 4.30
4130 4839 7.661847 AGCAATTTCTTATAATTACTCCCTCCG 59.338 37.037 0.00 0.00 0.00 4.63
4131 4840 7.444487 GCAATTTCTTATAATTACTCCCTCCGT 59.556 37.037 0.00 0.00 0.00 4.69
4132 4841 9.338622 CAATTTCTTATAATTACTCCCTCCGTT 57.661 33.333 0.00 0.00 0.00 4.44
4133 4842 9.557061 AATTTCTTATAATTACTCCCTCCGTTC 57.443 33.333 0.00 0.00 0.00 3.95
4134 4843 6.661304 TCTTATAATTACTCCCTCCGTTCC 57.339 41.667 0.00 0.00 0.00 3.62
4135 4844 6.379579 TCTTATAATTACTCCCTCCGTTCCT 58.620 40.000 0.00 0.00 0.00 3.36
4136 4845 7.529555 TCTTATAATTACTCCCTCCGTTCCTA 58.470 38.462 0.00 0.00 0.00 2.94
4137 4846 8.006564 TCTTATAATTACTCCCTCCGTTCCTAA 58.993 37.037 0.00 0.00 0.00 2.69
4138 4847 8.551682 TTATAATTACTCCCTCCGTTCCTAAA 57.448 34.615 0.00 0.00 0.00 1.85
4139 4848 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
4140 4849 8.731591 ATAATTACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
4141 4850 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
4142 4851 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
4143 4852 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4144 4853 8.551682 TTACTCCCTCCGTTCCTAAATATTTA 57.448 34.615 7.66 7.66 0.00 1.40
4145 4854 7.628501 ACTCCCTCCGTTCCTAAATATTTAT 57.371 36.000 8.34 0.00 0.00 1.40
4146 4855 7.677892 ACTCCCTCCGTTCCTAAATATTTATC 58.322 38.462 8.34 0.61 0.00 1.75
4147 4856 7.513091 ACTCCCTCCGTTCCTAAATATTTATCT 59.487 37.037 8.34 0.00 0.00 1.98
4148 4857 8.271398 TCCCTCCGTTCCTAAATATTTATCTT 57.729 34.615 8.34 0.00 0.00 2.40
4149 4858 8.720537 TCCCTCCGTTCCTAAATATTTATCTTT 58.279 33.333 8.34 0.00 0.00 2.52
4150 4859 9.000486 CCCTCCGTTCCTAAATATTTATCTTTC 58.000 37.037 8.34 0.00 0.00 2.62
4151 4860 9.780186 CCTCCGTTCCTAAATATTTATCTTTCT 57.220 33.333 8.34 0.00 0.00 2.52
4171 4880 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
4174 4883 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
4178 4887 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
4179 4888 8.771920 AGATTTCAACAAATGACTACATACGA 57.228 30.769 0.00 0.00 37.92 3.43
4180 4889 9.214957 AGATTTCAACAAATGACTACATACGAA 57.785 29.630 0.00 0.00 37.92 3.85
4181 4890 9.478019 GATTTCAACAAATGACTACATACGAAG 57.522 33.333 0.00 0.00 37.92 3.79
4182 4891 6.403333 TCAACAAATGACTACATACGAAGC 57.597 37.500 0.00 0.00 35.50 3.86
4183 4892 5.929415 TCAACAAATGACTACATACGAAGCA 59.071 36.000 0.00 0.00 35.50 3.91
4184 4893 6.425417 TCAACAAATGACTACATACGAAGCAA 59.575 34.615 0.00 0.00 35.50 3.91
4185 4894 6.795098 ACAAATGACTACATACGAAGCAAA 57.205 33.333 0.00 0.00 35.50 3.68
4186 4895 7.197071 ACAAATGACTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 35.50 2.44
4187 4896 7.816640 ACAAATGACTACATACGAAGCAAAAT 58.183 30.769 0.00 0.00 35.50 1.82
4188 4897 7.750458 ACAAATGACTACATACGAAGCAAAATG 59.250 33.333 0.00 0.00 35.50 2.32
4189 4898 7.609760 AATGACTACATACGAAGCAAAATGA 57.390 32.000 0.00 0.00 35.50 2.57
4190 4899 6.647212 TGACTACATACGAAGCAAAATGAG 57.353 37.500 0.00 0.00 0.00 2.90
4191 4900 6.163476 TGACTACATACGAAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
4192 4901 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4193 4902 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4194 4903 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4195 4904 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
4196 4905 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
4197 4906 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
4198 4907 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
4199 4908 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
4200 4909 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
4201 4910 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
4237 4946 9.511272 TGTCTATATACATCCGTATGTGTTAGT 57.489 33.333 3.56 0.00 45.99 2.24
4243 4952 8.958119 ATACATCCGTATGTGTTAGTTCATTT 57.042 30.769 3.56 0.00 45.99 2.32
4245 4954 8.780846 ACATCCGTATGTGTTAGTTCATTTAA 57.219 30.769 0.00 0.00 44.79 1.52
4246 4955 9.221933 ACATCCGTATGTGTTAGTTCATTTAAA 57.778 29.630 0.00 0.00 44.79 1.52
4280 4989 9.908152 AAAAGACAAATATTTAAGAACGGAAGG 57.092 29.630 0.00 0.00 0.00 3.46
4281 4990 8.857694 AAGACAAATATTTAAGAACGGAAGGA 57.142 30.769 0.00 0.00 0.00 3.36
4282 4991 8.494016 AGACAAATATTTAAGAACGGAAGGAG 57.506 34.615 0.00 0.00 0.00 3.69
4283 4992 8.101419 AGACAAATATTTAAGAACGGAAGGAGT 58.899 33.333 0.00 0.00 0.00 3.85
4284 4993 9.374838 GACAAATATTTAAGAACGGAAGGAGTA 57.625 33.333 0.00 0.00 0.00 2.59
4285 4994 9.379791 ACAAATATTTAAGAACGGAAGGAGTAG 57.620 33.333 0.00 0.00 0.00 2.57
4286 4995 9.379791 CAAATATTTAAGAACGGAAGGAGTAGT 57.620 33.333 0.00 0.00 0.00 2.73
4287 4996 9.955102 AAATATTTAAGAACGGAAGGAGTAGTT 57.045 29.630 0.00 0.00 0.00 2.24
4288 4997 9.955102 AATATTTAAGAACGGAAGGAGTAGTTT 57.045 29.630 0.00 0.00 0.00 2.66
4323 5032 0.310854 AAGTTTGCGGTACTGCTTGC 59.689 50.000 26.36 15.58 35.36 4.01
4333 5042 4.438744 GCGGTACTGCTTGCTTTATTTGAT 60.439 41.667 19.72 0.00 0.00 2.57
4349 5058 9.231297 CTTTATTTGATGGTATCGGAATGGTAT 57.769 33.333 0.00 0.00 0.00 2.73
4356 5065 2.910688 ATCGGAATGGTATCGCAACT 57.089 45.000 0.00 0.00 0.00 3.16
4365 5074 6.349860 GGAATGGTATCGCAACTTTTTAACCT 60.350 38.462 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.100197 GTGGGATTTTTAGAGTGGCCC 58.900 52.381 0.00 0.00 34.67 5.80
10 11 8.845413 TTCAAAAATGATGGTGGGATTTTTAG 57.155 30.769 0.00 0.00 37.24 1.85
18 19 3.681593 TGCTTCAAAAATGATGGTGGG 57.318 42.857 0.00 0.00 0.00 4.61
66 67 5.405873 GCTCGGGTATGCTAAAGAAATAGTC 59.594 44.000 0.00 0.00 0.00 2.59
86 87 3.242091 CGTTAATGTCATTGTGAGGCTCG 60.242 47.826 10.42 0.00 0.00 5.03
97 98 1.730064 GTCGTGGCACGTTAATGTCAT 59.270 47.619 35.65 0.00 43.14 3.06
104 105 0.386476 AAGACTGTCGTGGCACGTTA 59.614 50.000 35.65 24.71 43.14 3.18
115 116 4.741676 CCTTGCAAAACAATGAAGACTGTC 59.258 41.667 0.00 0.00 37.72 3.51
178 179 6.293626 GCACCTCATGTTATAATCATGACCAC 60.294 42.308 18.67 10.31 44.14 4.16
214 493 5.540911 TCGTGCTGCATATGAAGATAATCA 58.459 37.500 15.48 0.00 0.00 2.57
219 498 3.129109 CACTCGTGCTGCATATGAAGAT 58.871 45.455 15.48 0.00 0.00 2.40
223 502 0.823460 TCCACTCGTGCTGCATATGA 59.177 50.000 5.27 3.80 0.00 2.15
226 505 1.114627 AGATCCACTCGTGCTGCATA 58.885 50.000 5.27 0.00 0.00 3.14
232 511 3.585862 TCAAACTAAGATCCACTCGTGC 58.414 45.455 0.00 0.00 0.00 5.34
235 514 5.518128 CACATCTCAAACTAAGATCCACTCG 59.482 44.000 0.00 0.00 31.05 4.18
240 799 6.481644 GTCATCCACATCTCAAACTAAGATCC 59.518 42.308 0.00 0.00 31.05 3.36
242 801 6.352516 GGTCATCCACATCTCAAACTAAGAT 58.647 40.000 0.00 0.00 33.74 2.40
264 823 5.936372 GTCAACCCTCTACTTTAAAATCGGT 59.064 40.000 0.00 0.00 0.00 4.69
278 837 7.309805 GCCACATAATTTAAAAGTCAACCCTCT 60.310 37.037 0.00 0.00 0.00 3.69
297 856 3.382865 TGCAACTTTCAACTTGCCACATA 59.617 39.130 0.00 0.00 41.83 2.29
298 857 2.168106 TGCAACTTTCAACTTGCCACAT 59.832 40.909 0.00 0.00 41.83 3.21
312 871 7.530426 AAGAGAAAAGTCCATATTGCAACTT 57.470 32.000 0.00 0.00 33.53 2.66
373 932 6.105397 TCACCGACTAAAGTACTGGAATTT 57.895 37.500 0.00 0.00 0.00 1.82
410 969 9.740239 CACATTAATACAAGGGAAATCATTCTG 57.260 33.333 0.00 0.00 35.79 3.02
411 970 9.699410 TCACATTAATACAAGGGAAATCATTCT 57.301 29.630 0.00 0.00 35.79 2.40
414 973 8.786898 CGATCACATTAATACAAGGGAAATCAT 58.213 33.333 0.00 0.00 0.00 2.45
415 974 7.773224 ACGATCACATTAATACAAGGGAAATCA 59.227 33.333 0.00 0.00 0.00 2.57
416 975 8.070171 CACGATCACATTAATACAAGGGAAATC 58.930 37.037 0.00 0.00 0.00 2.17
417 976 7.556275 ACACGATCACATTAATACAAGGGAAAT 59.444 33.333 0.00 0.00 0.00 2.17
418 977 6.882140 ACACGATCACATTAATACAAGGGAAA 59.118 34.615 0.00 0.00 0.00 3.13
419 978 6.411376 ACACGATCACATTAATACAAGGGAA 58.589 36.000 0.00 0.00 0.00 3.97
420 979 5.984725 ACACGATCACATTAATACAAGGGA 58.015 37.500 0.00 0.00 0.00 4.20
421 980 7.780008 TTACACGATCACATTAATACAAGGG 57.220 36.000 0.00 0.00 0.00 3.95
559 1118 8.865590 TTTTTCCTTTTTGAAATCCGTCTTAG 57.134 30.769 0.00 0.00 34.41 2.18
697 1259 5.140747 AGATAGAAACAAACTCACGCTCT 57.859 39.130 0.00 0.00 0.00 4.09
698 1260 4.030753 CGAGATAGAAACAAACTCACGCTC 59.969 45.833 0.00 0.00 0.00 5.03
707 1269 5.710567 TCAGGAGACTCGAGATAGAAACAAA 59.289 40.000 21.68 0.00 40.21 2.83
951 1520 0.458260 GGAGACGAGAAGGAGAAGGC 59.542 60.000 0.00 0.00 0.00 4.35
1034 1604 3.284449 GGTTTTGGTCCGCGCTGT 61.284 61.111 5.56 0.00 0.00 4.40
1120 1690 4.525949 GAACGGCCGCCTCCCTAC 62.526 72.222 28.58 3.85 0.00 3.18
1406 1976 0.105658 CATCCCCCTCCTCCTCGTAA 60.106 60.000 0.00 0.00 0.00 3.18
1626 2197 6.263168 ACAAAGAGACTAATCAACAACCCAAG 59.737 38.462 0.00 0.00 0.00 3.61
1632 2203 9.173021 TGAAGAAACAAAGAGACTAATCAACAA 57.827 29.630 0.00 0.00 0.00 2.83
1867 2511 8.426489 AGGCAATAATGAAGATACAATGCAAAT 58.574 29.630 0.00 0.00 33.14 2.32
1978 2630 5.667539 ACTAAATGCAGAGCAGTTCTAGA 57.332 39.130 8.00 0.00 43.31 2.43
1992 2644 9.260002 CCCAATCCACATTATTTTACTAAATGC 57.740 33.333 0.00 0.00 35.61 3.56
2055 2707 6.753279 TCTTCCGTATATTTACAAACGACAGG 59.247 38.462 0.00 0.00 37.53 4.00
2075 2727 7.775561 ACATTCCAAATTCTATACTGGTCTTCC 59.224 37.037 0.00 0.00 0.00 3.46
2121 2773 3.913163 AGGATGCTTCCCCTTCCTTATAG 59.087 47.826 14.77 0.00 43.76 1.31
2134 2788 0.744414 TGCAACGGCTAGGATGCTTC 60.744 55.000 0.00 0.00 41.91 3.86
2145 2799 3.334078 CATTTGAGGATGCAACGGC 57.666 52.632 0.00 0.00 41.68 5.68
2205 2865 8.676401 TCGCAATAAAAAGATCATGATGAAAGA 58.324 29.630 14.30 0.00 0.00 2.52
2258 2918 7.010339 AGATTACTTTCAGCAGTTCCTAGTT 57.990 36.000 0.00 0.00 0.00 2.24
2474 3151 9.280174 CACCCTTTCTTCTAGTACAAAATACAA 57.720 33.333 0.00 0.00 0.00 2.41
2591 3269 5.242838 CAGCTCCTAAAACACCAAAACCATA 59.757 40.000 0.00 0.00 0.00 2.74
2686 3365 8.255905 GGTTATCTTCTGCTTGGTAAGTTACTA 58.744 37.037 12.65 3.88 0.00 1.82
2711 3390 1.955778 TGTTCCATGTTGCTGTCTTGG 59.044 47.619 0.00 0.00 0.00 3.61
2800 3480 4.539870 ACACATCTGCAAAATGAACTTCG 58.460 39.130 14.03 0.00 0.00 3.79
2940 3620 1.082194 AGGAAGAATAGGGGGTGGACA 59.918 52.381 0.00 0.00 0.00 4.02
2952 3632 2.408565 TCCGGCTATGGAAGGAAGAAT 58.591 47.619 0.00 0.00 34.30 2.40
3073 3754 2.503061 CAGGCCGATGGTGGAGAG 59.497 66.667 0.00 0.00 0.00 3.20
3174 3871 7.928103 TGTAACTTAATGTAAGGCGTTTTCAA 58.072 30.769 0.00 0.00 40.08 2.69
3317 4015 2.004583 CAACATGGCAATGGCTGAAG 57.995 50.000 8.59 0.00 40.87 3.02
3753 4454 4.060038 GCATGTAGCTAGGCTAAAGACA 57.940 45.455 0.00 0.18 43.07 3.41
3799 4500 2.290641 ACCAACGTTCCATCCAGCATTA 60.291 45.455 0.00 0.00 0.00 1.90
3813 4514 2.441164 TTGGGCAAGCACCAACGT 60.441 55.556 9.85 0.00 42.75 3.99
3898 4602 3.875134 ACCACGGAAACACACTCTAAAAG 59.125 43.478 0.00 0.00 0.00 2.27
3902 4606 2.431419 TGAACCACGGAAACACACTCTA 59.569 45.455 0.00 0.00 0.00 2.43
3903 4607 1.208535 TGAACCACGGAAACACACTCT 59.791 47.619 0.00 0.00 0.00 3.24
3904 4608 1.329599 GTGAACCACGGAAACACACTC 59.670 52.381 0.00 0.00 0.00 3.51
3905 4609 1.065709 AGTGAACCACGGAAACACACT 60.066 47.619 0.00 0.00 39.64 3.55
3906 4610 1.063469 CAGTGAACCACGGAAACACAC 59.937 52.381 0.00 0.00 39.64 3.82
3907 4611 1.339247 ACAGTGAACCACGGAAACACA 60.339 47.619 0.00 0.00 39.64 3.72
3908 4612 1.063469 CACAGTGAACCACGGAAACAC 59.937 52.381 0.00 0.00 39.64 3.32
3909 4613 1.066071 TCACAGTGAACCACGGAAACA 60.066 47.619 0.00 0.00 39.64 2.83
3910 4614 1.658994 TCACAGTGAACCACGGAAAC 58.341 50.000 0.00 0.00 39.64 2.78
3911 4615 2.404923 TTCACAGTGAACCACGGAAA 57.595 45.000 12.24 0.00 39.64 3.13
3912 4616 2.404923 TTTCACAGTGAACCACGGAA 57.595 45.000 15.93 0.00 39.64 4.30
3913 4617 2.404923 TTTTCACAGTGAACCACGGA 57.595 45.000 15.93 0.00 39.64 4.69
3941 4645 2.104792 CCCAAACCACTCTGAAGTCTGA 59.895 50.000 0.00 0.00 31.71 3.27
3947 4651 0.555769 AAGCCCCAAACCACTCTGAA 59.444 50.000 0.00 0.00 0.00 3.02
3956 4660 4.450976 ACTCAAATTTTCAAGCCCCAAAC 58.549 39.130 0.00 0.00 0.00 2.93
4106 4815 8.904099 ACGGAGGGAGTAATTATAAGAAATTG 57.096 34.615 0.00 0.00 31.63 2.32
4119 4828 7.441903 AAATATTTAGGAACGGAGGGAGTAA 57.558 36.000 0.00 0.00 0.00 2.24
4120 4829 8.731591 ATAAATATTTAGGAACGGAGGGAGTA 57.268 34.615 13.15 0.00 0.00 2.59
4121 4830 5.970501 AAATATTTAGGAACGGAGGGAGT 57.029 39.130 0.00 0.00 0.00 3.85
4122 4831 7.908453 AGATAAATATTTAGGAACGGAGGGAG 58.092 38.462 13.15 0.00 0.00 4.30
4123 4832 7.867160 AGATAAATATTTAGGAACGGAGGGA 57.133 36.000 13.15 0.00 0.00 4.20
4124 4833 8.919777 AAAGATAAATATTTAGGAACGGAGGG 57.080 34.615 13.15 0.00 0.00 4.30
4125 4834 9.780186 AGAAAGATAAATATTTAGGAACGGAGG 57.220 33.333 13.15 0.00 0.00 4.30
4145 4854 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
4148 4857 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
4152 4861 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
4153 4862 8.869897 TCGTATGTAGTCATTTGTTGAAATCTC 58.130 33.333 0.00 0.00 35.70 2.75
4154 4863 8.771920 TCGTATGTAGTCATTTGTTGAAATCT 57.228 30.769 0.00 0.00 35.70 2.40
4155 4864 9.478019 CTTCGTATGTAGTCATTTGTTGAAATC 57.522 33.333 0.00 0.00 35.70 2.17
4156 4865 7.962918 GCTTCGTATGTAGTCATTTGTTGAAAT 59.037 33.333 0.00 0.00 35.70 2.17
4157 4866 7.041712 TGCTTCGTATGTAGTCATTTGTTGAAA 60.042 33.333 0.00 0.00 35.70 2.69
4158 4867 6.425417 TGCTTCGTATGTAGTCATTTGTTGAA 59.575 34.615 0.00 0.00 35.70 2.69
4159 4868 5.929415 TGCTTCGTATGTAGTCATTTGTTGA 59.071 36.000 0.00 0.00 35.70 3.18
4160 4869 6.164408 TGCTTCGTATGTAGTCATTTGTTG 57.836 37.500 0.00 0.00 35.70 3.33
4161 4870 6.795098 TTGCTTCGTATGTAGTCATTTGTT 57.205 33.333 0.00 0.00 35.70 2.83
4162 4871 6.795098 TTTGCTTCGTATGTAGTCATTTGT 57.205 33.333 0.00 0.00 35.70 2.83
4163 4872 7.962373 TCATTTTGCTTCGTATGTAGTCATTTG 59.038 33.333 0.00 0.00 35.70 2.32
4164 4873 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
4165 4874 7.334421 ACTCATTTTGCTTCGTATGTAGTCATT 59.666 33.333 0.00 0.00 35.70 2.57
4166 4875 6.818644 ACTCATTTTGCTTCGTATGTAGTCAT 59.181 34.615 0.00 0.00 38.00 3.06
4167 4876 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4168 4877 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4169 4878 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4170 4879 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4171 4880 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
4172 4881 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
4173 4882 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
4174 4883 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
4175 4884 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
4176 4885 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
4177 4886 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
4178 4887 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
4211 4920 9.511272 ACTAACACATACGGATGTATATAGACA 57.489 33.333 23.23 2.07 44.82 3.41
4218 4927 8.958119 AAATGAACTAACACATACGGATGTAT 57.042 30.769 14.23 8.21 44.82 2.29
4219 4928 9.872721 TTAAATGAACTAACACATACGGATGTA 57.127 29.630 14.23 0.00 44.82 2.29
4254 4963 9.908152 CCTTCCGTTCTTAAATATTTGTCTTTT 57.092 29.630 11.05 0.00 0.00 2.27
4255 4964 9.292195 TCCTTCCGTTCTTAAATATTTGTCTTT 57.708 29.630 11.05 0.00 0.00 2.52
4256 4965 8.857694 TCCTTCCGTTCTTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
4257 4966 8.101419 ACTCCTTCCGTTCTTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
4258 4967 8.265165 ACTCCTTCCGTTCTTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
4259 4968 9.379791 CTACTCCTTCCGTTCTTAAATATTTGT 57.620 33.333 11.05 0.00 0.00 2.83
4260 4969 9.379791 ACTACTCCTTCCGTTCTTAAATATTTG 57.620 33.333 11.05 0.00 0.00 2.32
4261 4970 9.955102 AACTACTCCTTCCGTTCTTAAATATTT 57.045 29.630 5.89 5.89 0.00 1.40
4262 4971 9.955102 AAACTACTCCTTCCGTTCTTAAATATT 57.045 29.630 0.00 0.00 0.00 1.28
4291 5000 8.843262 AGTACCGCAAACTTTTTCTTACTAATT 58.157 29.630 0.00 0.00 0.00 1.40
4292 5001 8.287503 CAGTACCGCAAACTTTTTCTTACTAAT 58.712 33.333 0.00 0.00 0.00 1.73
4323 5032 7.510549 ACCATTCCGATACCATCAAATAAAG 57.489 36.000 0.00 0.00 0.00 1.85
4333 5042 1.964933 TGCGATACCATTCCGATACCA 59.035 47.619 0.00 0.00 0.00 3.25
4349 5058 9.026074 CATAAGAAAAAGGTTAAAAAGTTGCGA 57.974 29.630 0.00 0.00 0.00 5.10
4379 5088 4.568359 CGGACATCCTGACAAGTTCTTATG 59.432 45.833 0.00 0.00 0.00 1.90
4380 5089 4.466370 TCGGACATCCTGACAAGTTCTTAT 59.534 41.667 0.00 0.00 0.00 1.73
4388 5097 2.355716 GGGATTTCGGACATCCTGACAA 60.356 50.000 19.65 0.00 40.32 3.18
4389 5098 1.209504 GGGATTTCGGACATCCTGACA 59.790 52.381 19.65 0.00 40.32 3.58


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

AutoCloner maintained by Alex Coulton.