Multiple sequence alignment - TraesCS7D01G245100

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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 TraesCS7D01G245100 chr7D 100.000 6676 0 0 1 6676 213782503 213789178 0.000000e+00 12329.0
1 TraesCS7D01G245100 chr7D 89.819 884 78 10 74 948 76596432 76597312 0.000000e+00 1123.0
2 TraesCS7D01G245100 chr7D 95.833 120 4 1 2250 2369 120323644 120323526 6.830000e-45 193.0
3 TraesCS7D01G245100 chr7B 96.582 2984 80 7 3367 6343 187782522 187779554 0.000000e+00 4926.0
4 TraesCS7D01G245100 chr7B 96.215 2404 75 7 987 3384 187784933 187782540 0.000000e+00 3921.0
5 TraesCS7D01G245100 chr7B 94.400 125 5 2 2245 2369 78066837 78066959 2.460000e-44 191.0
6 TraesCS7D01G245100 chr7A 91.551 2746 141 36 3485 6166 225630710 225633428 0.000000e+00 3701.0
7 TraesCS7D01G245100 chr7A 96.371 1846 48 7 1048 2879 225615690 225617530 0.000000e+00 3020.0
8 TraesCS7D01G245100 chr7A 96.320 625 20 2 2868 3491 225617627 225618249 0.000000e+00 1024.0
9 TraesCS7D01G245100 chr7A 88.553 463 36 6 6181 6637 225633922 225634373 4.550000e-151 545.0
10 TraesCS7D01G245100 chr7A 96.667 120 4 0 2250 2369 83784823 83784942 4.080000e-47 200.0
11 TraesCS7D01G245100 chr6A 86.743 958 94 18 1 948 555250450 555251384 0.000000e+00 1035.0
12 TraesCS7D01G245100 chr6A 88.235 85 8 1 2698 2782 66388163 66388081 4.260000e-17 100.0
13 TraesCS7D01G245100 chr6B 87.923 886 93 10 74 948 644488832 644489714 0.000000e+00 1031.0
14 TraesCS7D01G245100 chr5A 87.600 871 95 11 90 950 635403751 635404618 0.000000e+00 998.0
15 TraesCS7D01G245100 chr5A 96.694 121 3 1 2250 2369 425456582 425456462 4.080000e-47 200.0
16 TraesCS7D01G245100 chr5A 78.481 316 47 19 6330 6627 510011248 510011560 3.180000e-43 187.0
17 TraesCS7D01G245100 chr5A 85.714 98 10 3 4888 4984 477584858 477584952 4.260000e-17 100.0
18 TraesCS7D01G245100 chr5A 84.706 85 12 1 2699 2783 33929158 33929241 4.290000e-12 84.2
19 TraesCS7D01G245100 chr3B 87.162 888 91 15 74 948 822996939 822996062 0.000000e+00 987.0
20 TraesCS7D01G245100 chr3B 85.246 61 9 0 6402 6462 715256353 715256293 5.590000e-06 63.9
21 TraesCS7D01G245100 chr4A 85.386 958 107 20 1 948 567201406 567200472 0.000000e+00 963.0
22 TraesCS7D01G245100 chr1A 85.386 958 107 16 1 948 572737840 572736906 0.000000e+00 963.0
23 TraesCS7D01G245100 chr1A 85.177 958 109 16 1 948 572734545 572733611 0.000000e+00 952.0
24 TraesCS7D01G245100 chr1A 90.647 139 9 3 2255 2392 550884839 550884974 1.480000e-41 182.0
25 TraesCS7D01G245100 chr1A 83.721 86 14 0 2699 2784 567970009 567969924 1.540000e-11 82.4
26 TraesCS7D01G245100 chr1D 90.309 712 59 8 246 948 38248717 38249427 0.000000e+00 924.0
27 TraesCS7D01G245100 chr1D 83.333 90 14 1 2690 2778 22976627 22976538 1.540000e-11 82.4
28 TraesCS7D01G245100 chr1B 82.031 256 33 9 6403 6645 668003398 668003653 8.780000e-49 206.0
29 TraesCS7D01G245100 chr1B 86.667 90 12 0 2696 2785 411570413 411570502 4.260000e-17 100.0
30 TraesCS7D01G245100 chr1B 83.721 86 14 0 2699 2784 658497513 658497428 1.540000e-11 82.4
31 TraesCS7D01G245100 chr5B 99.091 110 1 0 2260 2369 243411197 243411088 1.470000e-46 198.0
32 TraesCS7D01G245100 chr5B 85.714 98 10 3 4888 4984 450105642 450105736 4.260000e-17 100.0
33 TraesCS7D01G245100 chr4B 95.763 118 3 2 2252 2369 588431006 588430891 8.840000e-44 189.0
34 TraesCS7D01G245100 chr5D 85.714 98 10 3 4888 4984 376937461 376937555 4.260000e-17 100.0
35 TraesCS7D01G245100 chr2D 84.706 85 12 1 2699 2783 234147847 234147930 4.290000e-12 84.2


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 TraesCS7D01G245100 chr7D 213782503 213789178 6675 False 12329.0 12329 100.0000 1 6676 1 chr7D.!!$F2 6675
1 TraesCS7D01G245100 chr7D 76596432 76597312 880 False 1123.0 1123 89.8190 74 948 1 chr7D.!!$F1 874
2 TraesCS7D01G245100 chr7B 187779554 187784933 5379 True 4423.5 4926 96.3985 987 6343 2 chr7B.!!$R1 5356
3 TraesCS7D01G245100 chr7A 225630710 225634373 3663 False 2123.0 3701 90.0520 3485 6637 2 chr7A.!!$F3 3152
4 TraesCS7D01G245100 chr7A 225615690 225618249 2559 False 2022.0 3020 96.3455 1048 3491 2 chr7A.!!$F2 2443
5 TraesCS7D01G245100 chr6A 555250450 555251384 934 False 1035.0 1035 86.7430 1 948 1 chr6A.!!$F1 947
6 TraesCS7D01G245100 chr6B 644488832 644489714 882 False 1031.0 1031 87.9230 74 948 1 chr6B.!!$F1 874
7 TraesCS7D01G245100 chr5A 635403751 635404618 867 False 998.0 998 87.6000 90 950 1 chr5A.!!$F4 860
8 TraesCS7D01G245100 chr3B 822996062 822996939 877 True 987.0 987 87.1620 74 948 1 chr3B.!!$R2 874
9 TraesCS7D01G245100 chr4A 567200472 567201406 934 True 963.0 963 85.3860 1 948 1 chr4A.!!$R1 947
10 TraesCS7D01G245100 chr1A 572733611 572737840 4229 True 957.5 963 85.2815 1 948 2 chr1A.!!$R2 947
11 TraesCS7D01G245100 chr1D 38248717 38249427 710 False 924.0 924 90.3090 246 948 1 chr1D.!!$F1 702

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
250 252 0.035630 AGGTTCTCAGATGCACCAGC 60.036 55.000 0.00 0.0 42.57 4.85 F
491 3789 0.608640 CCTAGTCAGGTTGGCTCGTT 59.391 55.000 0.00 0.0 37.15 3.85 F
854 4160 0.747644 CCGATGGTGTGCATGGCTTA 60.748 55.000 0.00 0.0 0.00 3.09 F
1559 4869 0.565674 GGGAGGAGGAAGAGAGGGAT 59.434 60.000 0.00 0.0 0.00 3.85 F
1771 5081 2.367567 TCACTGAAGAGGTAGCCGTTTT 59.632 45.455 0.00 0.0 0.00 2.43 F
3066 6503 1.961180 CTAGGGCACTGTCCTTCCCG 61.961 65.000 7.71 0.0 43.46 5.14 F
4024 7503 0.743097 GGATCAGCATCCCAGCAAAC 59.257 55.000 0.00 0.0 42.91 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 4628 0.105760 GGCATCCTCCTCTCTCTGGA 60.106 60.000 0.00 0.00 0.00 3.86 R
1553 4863 1.188871 CCTCCCGCTTCCTATCCCTC 61.189 65.000 0.00 0.00 0.00 4.30 R
1795 5105 1.400494 ACAGAACAAAGAACGGTGCAC 59.600 47.619 8.80 8.80 0.00 4.57 R
3048 6485 1.987855 CGGGAAGGACAGTGCCCTA 60.988 63.158 0.00 0.00 38.46 3.53 R
3680 7156 2.160417 GGCTGGAACAAAGAGATGAACG 59.840 50.000 0.00 0.00 38.70 3.95 R
4490 7981 1.173043 CCTGCCTGCCGTTCATTTTA 58.827 50.000 0.00 0.00 0.00 1.52 R
5753 9284 1.110442 TGACCAGGCCTGTTGTTTTG 58.890 50.000 30.63 15.99 0.00 2.44 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
60 61 3.537206 GAGGTGCCTGCCTCGTTGT 62.537 63.158 0.00 0.00 44.64 3.32
110 111 4.514577 CGCCGGATCTCGTTGCCT 62.515 66.667 5.05 0.00 37.11 4.75
165 167 1.377994 CAGAAGCTGGTGGGCTCTT 59.622 57.895 0.00 0.00 42.24 2.85
205 207 0.461548 CATCTCTTGGAGTAGCGGCA 59.538 55.000 1.45 0.00 0.00 5.69
210 212 2.781595 CTTGGAGTAGCGGCACCGTT 62.782 60.000 11.27 7.37 42.09 4.44
225 227 2.591715 GTTCAGCGGCTGTGGTGT 60.592 61.111 27.63 0.00 38.47 4.16
230 232 1.606601 AGCGGCTGTGGTGTAGAGA 60.607 57.895 0.00 0.00 0.00 3.10
250 252 0.035630 AGGTTCTCAGATGCACCAGC 60.036 55.000 0.00 0.00 42.57 4.85
253 255 1.066286 GTTCTCAGATGCACCAGCTCT 60.066 52.381 0.00 0.00 42.74 4.09
266 268 3.461773 GCTCTGGCTCGGCTGGTA 61.462 66.667 0.00 0.00 35.22 3.25
370 373 1.082679 GCTTCGGTTCTAACTCGGCC 61.083 60.000 0.00 0.00 0.00 6.13
407 3705 2.584608 CGGATCCTCGCCCAGTTT 59.415 61.111 10.75 0.00 0.00 2.66
419 3717 2.250939 CCAGTTTTGCGCACGGAGA 61.251 57.895 11.12 0.00 0.00 3.71
421 3719 2.251371 GTTTTGCGCACGGAGACC 59.749 61.111 11.12 0.00 0.00 3.85
441 3739 4.530857 GGACGGCCGGATCTGGTG 62.531 72.222 31.76 16.44 0.00 4.17
451 3749 3.918253 GATCTGGTGTGGCGCCCAA 62.918 63.158 26.77 9.43 34.18 4.12
491 3789 0.608640 CCTAGTCAGGTTGGCTCGTT 59.391 55.000 0.00 0.00 37.15 3.85
623 3927 1.268234 GCTTCGGATGAAAATCCTGCG 60.268 52.381 3.40 0.00 38.57 5.18
648 3952 3.583276 TTGTCAGTGCCGGCGGTAG 62.583 63.158 28.82 12.60 0.00 3.18
713 4017 0.861837 AGCTCGTTTTGCTCTTCGTG 59.138 50.000 0.00 0.00 35.67 4.35
744 4048 1.070105 TGGACTCCGGGTGAAAACG 59.930 57.895 0.00 0.00 0.00 3.60
761 4065 6.147328 GTGAAAACGTAAGATTTGGCTAGTCT 59.853 38.462 0.00 0.00 42.74 3.24
770 4074 1.996798 TTGGCTAGTCTAGATCGGGG 58.003 55.000 11.27 0.00 0.00 5.73
804 4108 6.689561 TGTCCTTAATATCACTCCCTCCTTA 58.310 40.000 0.00 0.00 0.00 2.69
805 4109 7.136885 TGTCCTTAATATCACTCCCTCCTTAA 58.863 38.462 0.00 0.00 0.00 1.85
854 4160 0.747644 CCGATGGTGTGCATGGCTTA 60.748 55.000 0.00 0.00 0.00 3.09
883 4189 1.000993 TTGGGTTTGTGGTGGTGCT 59.999 52.632 0.00 0.00 0.00 4.40
931 4240 1.363807 GCCTTTTGCGGTGCTTTCT 59.636 52.632 0.00 0.00 0.00 2.52
950 4259 4.216411 TCTTTTTCGGAGGGTCCTTATG 57.784 45.455 0.00 0.00 33.30 1.90
951 4260 3.841845 TCTTTTTCGGAGGGTCCTTATGA 59.158 43.478 0.00 0.00 33.30 2.15
952 4261 4.287585 TCTTTTTCGGAGGGTCCTTATGAA 59.712 41.667 0.00 0.00 33.30 2.57
953 4262 4.855298 TTTTCGGAGGGTCCTTATGAAT 57.145 40.909 0.00 0.00 33.30 2.57
954 4263 3.838244 TTCGGAGGGTCCTTATGAATG 57.162 47.619 0.00 0.00 33.30 2.67
955 4264 3.040655 TCGGAGGGTCCTTATGAATGA 57.959 47.619 0.00 0.00 33.30 2.57
956 4265 3.380393 TCGGAGGGTCCTTATGAATGAA 58.620 45.455 0.00 0.00 33.30 2.57
957 4266 3.973973 TCGGAGGGTCCTTATGAATGAAT 59.026 43.478 0.00 0.00 33.30 2.57
958 4267 4.412199 TCGGAGGGTCCTTATGAATGAATT 59.588 41.667 0.00 0.00 33.30 2.17
959 4268 5.104109 TCGGAGGGTCCTTATGAATGAATTT 60.104 40.000 0.00 0.00 33.30 1.82
960 4269 5.239525 CGGAGGGTCCTTATGAATGAATTTC 59.760 44.000 0.00 0.00 33.30 2.17
961 4270 5.239525 GGAGGGTCCTTATGAATGAATTTCG 59.760 44.000 0.00 0.00 33.47 3.46
962 4271 4.580580 AGGGTCCTTATGAATGAATTTCGC 59.419 41.667 0.00 0.00 37.13 4.70
963 4272 4.338118 GGGTCCTTATGAATGAATTTCGCA 59.662 41.667 0.00 0.00 37.13 5.10
964 4273 5.506317 GGGTCCTTATGAATGAATTTCGCAG 60.506 44.000 0.00 0.00 37.13 5.18
965 4274 4.972440 GTCCTTATGAATGAATTTCGCAGC 59.028 41.667 0.00 0.00 37.13 5.25
966 4275 4.883585 TCCTTATGAATGAATTTCGCAGCT 59.116 37.500 0.00 0.00 37.13 4.24
967 4276 5.008019 TCCTTATGAATGAATTTCGCAGCTC 59.992 40.000 0.00 0.00 37.13 4.09
968 4277 5.008415 CCTTATGAATGAATTTCGCAGCTCT 59.992 40.000 0.00 0.00 37.13 4.09
969 4278 6.203530 CCTTATGAATGAATTTCGCAGCTCTA 59.796 38.462 0.00 0.00 37.13 2.43
970 4279 4.864916 TGAATGAATTTCGCAGCTCTAC 57.135 40.909 0.00 0.00 37.13 2.59
971 4280 4.507710 TGAATGAATTTCGCAGCTCTACT 58.492 39.130 0.00 0.00 37.13 2.57
972 4281 4.330894 TGAATGAATTTCGCAGCTCTACTG 59.669 41.667 0.00 0.00 39.67 2.74
979 4288 4.870305 CAGCTCTACTGCGAACGT 57.130 55.556 0.00 0.00 40.19 3.99
980 4289 3.108521 CAGCTCTACTGCGAACGTT 57.891 52.632 0.00 0.00 40.19 3.99
981 4290 2.257974 CAGCTCTACTGCGAACGTTA 57.742 50.000 0.00 0.00 40.19 3.18
982 4291 2.592194 CAGCTCTACTGCGAACGTTAA 58.408 47.619 0.00 0.00 40.19 2.01
983 4292 2.984471 CAGCTCTACTGCGAACGTTAAA 59.016 45.455 0.00 0.00 40.19 1.52
984 4293 3.427528 CAGCTCTACTGCGAACGTTAAAA 59.572 43.478 0.00 0.00 40.19 1.52
985 4294 4.053295 AGCTCTACTGCGAACGTTAAAAA 58.947 39.130 0.00 0.00 38.13 1.94
1011 4320 2.100418 GGAAGTGTATACCGACCTGACC 59.900 54.545 0.00 0.00 0.00 4.02
1023 4332 1.075525 CCTGACCCCACCCGATCTA 60.076 63.158 0.00 0.00 0.00 1.98
1318 4628 2.496817 GCAGGAACGCGAGAGGAT 59.503 61.111 15.93 0.00 0.00 3.24
1553 4863 2.756283 ACGCGGGAGGAGGAAGAG 60.756 66.667 12.47 0.00 0.00 2.85
1559 4869 0.565674 GGGAGGAGGAAGAGAGGGAT 59.434 60.000 0.00 0.00 0.00 3.85
1585 4895 2.447714 GGGAGGAGGAGATGGTGGC 61.448 68.421 0.00 0.00 0.00 5.01
1771 5081 2.367567 TCACTGAAGAGGTAGCCGTTTT 59.632 45.455 0.00 0.00 0.00 2.43
1778 5088 2.367567 AGAGGTAGCCGTTTTTCACTGA 59.632 45.455 0.00 0.00 0.00 3.41
1780 5090 3.074412 AGGTAGCCGTTTTTCACTGATG 58.926 45.455 0.00 0.00 0.00 3.07
2109 5436 5.345741 GCATTTACCACAACACAATGATCAC 59.654 40.000 0.00 0.00 0.00 3.06
2149 5477 7.589395 TGATAATTGTGACAACGTGCTTATTT 58.411 30.769 0.00 0.00 0.00 1.40
2161 5489 7.540745 ACAACGTGCTTATTTGTCCAATATTTC 59.459 33.333 0.00 0.00 0.00 2.17
2214 5542 6.320171 CCTTGAACTCATGATCATTGTGTTC 58.680 40.000 25.84 25.84 34.66 3.18
2388 5716 7.021998 AGGCTCTGAAAGTAAATCCTACTTT 57.978 36.000 9.13 9.13 46.71 2.66
2433 5761 3.490526 CGTTGCCATTTGTTCTTTTCTGG 59.509 43.478 0.00 0.00 0.00 3.86
2608 5937 2.371841 TGGACACAAGCCAACTATCTGT 59.628 45.455 0.00 0.00 31.13 3.41
3066 6503 1.961180 CTAGGGCACTGTCCTTCCCG 61.961 65.000 7.71 0.00 43.46 5.14
3254 6691 4.925646 GTGTACGGTTAACCTTAGTCCTTG 59.074 45.833 22.12 6.00 0.00 3.61
3529 7004 4.000988 CGGCCAAAAGACAGTAGTGTTAT 58.999 43.478 2.24 0.00 36.88 1.89
3641 7116 4.861462 CGAGGGACTATTCATCAATCATCG 59.139 45.833 0.00 0.00 41.55 3.84
3642 7117 5.157940 AGGGACTATTCATCAATCATCGG 57.842 43.478 0.00 0.00 36.02 4.18
3680 7156 4.329545 TCGTGGGAAGGCTGCACC 62.330 66.667 0.50 1.45 39.61 5.01
4024 7503 0.743097 GGATCAGCATCCCAGCAAAC 59.257 55.000 0.00 0.00 42.91 2.93
4082 7562 2.827800 TTCTTGGCAGTCTCTGTCAG 57.172 50.000 4.33 0.00 46.93 3.51
4165 7649 0.801251 CTTTCGGAGCAAAGGAGCTG 59.199 55.000 0.00 0.00 46.75 4.24
4367 7853 3.961182 TCGACAAGCATACCGATACTTC 58.039 45.455 0.00 0.00 0.00 3.01
4522 8013 0.547712 AGGCAGGGGCTTCTTCAGTA 60.548 55.000 0.00 0.00 40.87 2.74
4675 8169 3.650950 GGCCTGTTCCCCTGCAGA 61.651 66.667 17.39 0.00 34.87 4.26
4998 8492 3.314331 CCCTGCGAGACACCCACT 61.314 66.667 0.00 0.00 0.00 4.00
5146 8640 4.554363 CGGTAGCCTGGTCGAGCG 62.554 72.222 10.46 4.87 0.00 5.03
5264 8758 3.678072 CACAAGAGCAAATCAGCAAATGG 59.322 43.478 0.00 0.00 36.85 3.16
5269 8763 4.282703 AGAGCAAATCAGCAAATGGAACTT 59.717 37.500 0.00 0.00 36.85 2.66
5275 8769 1.068333 CAGCAAATGGAACTTGACCGG 60.068 52.381 0.00 0.00 0.00 5.28
5305 8799 1.803555 GTGAGAGCAAGAGAGGCAAAC 59.196 52.381 0.00 0.00 0.00 2.93
5330 8827 0.109597 GTTGCTCACCAAAGGATGCG 60.110 55.000 0.00 0.00 34.68 4.73
5432 8929 1.536766 CAGCTGCGTTTTCCTTGATCA 59.463 47.619 0.00 0.00 0.00 2.92
5488 8985 4.324267 AGCACAGAATTAGTGGTACAACC 58.676 43.478 12.04 0.00 44.95 3.77
5489 8986 3.439129 GCACAGAATTAGTGGTACAACCC 59.561 47.826 11.25 0.00 44.16 4.11
5490 8987 4.806286 GCACAGAATTAGTGGTACAACCCT 60.806 45.833 11.25 0.00 44.16 4.34
5520 9044 6.109359 ACTGAATTTAGCAGTGAGGTATGAC 58.891 40.000 0.00 0.00 44.39 3.06
5577 9102 8.739039 CAAATCTCACAGGGTTTCATTGTATAA 58.261 33.333 0.00 0.00 0.00 0.98
5753 9284 3.924144 TGGGAACAAACAAGCATAATGC 58.076 40.909 0.00 0.00 40.27 3.56
5873 9404 1.064017 GGCCTTCATAATCACACCCCA 60.064 52.381 0.00 0.00 0.00 4.96
5905 9436 1.217942 ACTGGCCCCAGAAAAGAAAGT 59.782 47.619 20.59 0.00 46.30 2.66
6244 10263 3.826157 TGATTGGTAACTGCCCTTTCAAG 59.174 43.478 0.00 0.00 37.61 3.02
6270 10289 5.002840 CGCAAACTCGCAAATTGAAATCTAG 59.997 40.000 0.00 0.00 0.00 2.43
6274 10293 5.931532 ACTCGCAAATTGAAATCTAGTGTG 58.068 37.500 0.00 0.00 0.00 3.82
6279 10298 5.570589 GCAAATTGAAATCTAGTGTGCTGTC 59.429 40.000 0.00 0.00 0.00 3.51
6336 10355 8.557304 ACATTTCTCATCAATATGGGGAAATT 57.443 30.769 12.72 0.00 40.12 1.82
6450 10469 5.652452 AGTAAACTTGACTTCCTTTTGCACT 59.348 36.000 0.00 0.00 0.00 4.40
6471 10490 8.440059 TGCACTAGTATGTAAATTTTCACGAAG 58.560 33.333 0.00 0.00 0.00 3.79
6490 10509 3.746045 AGAAAAGACCAGCGTTGACTA 57.254 42.857 0.00 0.00 0.00 2.59
6491 10510 4.067972 AGAAAAGACCAGCGTTGACTAA 57.932 40.909 0.00 0.00 0.00 2.24
6498 10517 1.234821 CAGCGTTGACTAAAGGGCAA 58.765 50.000 0.00 0.00 41.27 4.52
6499 10518 1.606668 CAGCGTTGACTAAAGGGCAAA 59.393 47.619 0.00 0.00 45.57 3.68
6500 10519 2.034053 CAGCGTTGACTAAAGGGCAAAA 59.966 45.455 0.00 0.00 45.57 2.44
6501 10520 2.691011 AGCGTTGACTAAAGGGCAAAAA 59.309 40.909 0.00 0.00 45.57 1.94
6541 10560 6.699575 ATCACTATTCACACTATTTTGGCC 57.300 37.500 0.00 0.00 0.00 5.36
6585 10610 8.255394 AGAAGTCAATGTGGTTTTTCTTTTTG 57.745 30.769 0.00 0.00 0.00 2.44
6589 10614 7.659390 AGTCAATGTGGTTTTTCTTTTTGTGAA 59.341 29.630 0.00 0.00 0.00 3.18
6630 10655 8.970691 ATGGAAGATCAAGTTTATTTCAAACG 57.029 30.769 0.00 0.00 35.42 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.255379 GAACGTCAGATCGGGCGC 61.255 66.667 19.76 0.00 34.94 6.53
72 73 2.582498 GGAACGTCAGATCGGGCG 60.582 66.667 18.31 18.31 34.94 6.13
83 84 3.352338 GATCCGGCGACTGGAACGT 62.352 63.158 9.30 0.00 36.78 3.99
165 167 1.266718 GGCGTGAACATGCTTGAAAGA 59.733 47.619 16.69 0.00 42.72 2.52
210 212 1.877576 CTCTACACCACAGCCGCTGA 61.878 60.000 27.12 2.07 35.18 4.26
230 232 1.612726 GCTGGTGCATCTGAGAACCTT 60.613 52.381 8.20 0.00 39.41 3.50
250 252 2.055042 AGTACCAGCCGAGCCAGAG 61.055 63.158 0.00 0.00 0.00 3.35
253 255 2.603473 ACAGTACCAGCCGAGCCA 60.603 61.111 0.00 0.00 0.00 4.75
294 296 3.066064 CGAACACCAAATCAAACTGACCA 59.934 43.478 0.00 0.00 0.00 4.02
421 3719 4.271816 CAGATCCGGCCGTCCTCG 62.272 72.222 26.12 8.39 0.00 4.63
427 3725 4.838152 CCACACCAGATCCGGCCG 62.838 72.222 21.04 21.04 0.00 6.13
474 3772 2.762745 GAAAACGAGCCAACCTGACTA 58.237 47.619 0.00 0.00 0.00 2.59
477 3775 1.503818 GCGAAAACGAGCCAACCTGA 61.504 55.000 0.00 0.00 0.00 3.86
521 3820 1.188871 TGCACATACCAGGACGGACA 61.189 55.000 0.00 0.00 38.63 4.02
525 3824 1.439353 GCCATGCACATACCAGGACG 61.439 60.000 0.00 0.00 0.00 4.79
528 3827 0.396139 AAGGCCATGCACATACCAGG 60.396 55.000 5.01 0.00 0.00 4.45
623 3927 1.571460 CGGCACTGACAAGAACAGC 59.429 57.895 0.00 0.00 38.74 4.40
648 3952 2.654404 GACATCCGTAGACGCCGC 60.654 66.667 0.00 0.00 38.18 6.53
669 3973 0.108281 GCGGTACCTCCAAGGAGAAC 60.108 60.000 17.57 13.77 44.53 3.01
671 3975 0.970937 CAGCGGTACCTCCAAGGAGA 60.971 60.000 17.57 0.00 44.53 3.71
729 4033 1.688197 TCTTACGTTTTCACCCGGAGT 59.312 47.619 0.73 0.00 0.00 3.85
744 4048 6.383415 CCGATCTAGACTAGCCAAATCTTAC 58.617 44.000 4.47 0.00 0.00 2.34
761 4065 1.548719 CAACACTGTCACCCCGATCTA 59.451 52.381 0.00 0.00 0.00 1.98
786 4090 5.011738 CGCCTTTAAGGAGGGAGTGATATTA 59.988 44.000 16.18 0.00 37.67 0.98
787 4091 4.202367 CGCCTTTAAGGAGGGAGTGATATT 60.202 45.833 16.18 0.00 37.67 1.28
804 4108 4.035102 GCCTCAGGGGACGCCTTT 62.035 66.667 8.65 0.00 37.23 3.11
854 4160 0.609131 CAAACCCAAGCTCCACCGAT 60.609 55.000 0.00 0.00 0.00 4.18
922 4231 1.269723 CCCTCCGAAAAAGAAAGCACC 59.730 52.381 0.00 0.00 0.00 5.01
931 4240 4.644163 TTCATAAGGACCCTCCGAAAAA 57.356 40.909 0.00 0.00 42.75 1.94
950 4259 4.830912 CAGTAGAGCTGCGAAATTCATTC 58.169 43.478 0.00 0.00 38.52 2.67
951 4260 4.871993 CAGTAGAGCTGCGAAATTCATT 57.128 40.909 0.00 0.00 38.52 2.57
963 4272 3.293311 TTTAACGTTCGCAGTAGAGCT 57.707 42.857 2.82 0.00 0.00 4.09
964 4273 4.379374 TTTTTAACGTTCGCAGTAGAGC 57.621 40.909 2.82 0.00 0.00 4.09
983 4292 4.999311 GGTCGGTATACACTTCCAGTTTTT 59.001 41.667 5.01 0.00 0.00 1.94
984 4293 4.285260 AGGTCGGTATACACTTCCAGTTTT 59.715 41.667 5.01 0.00 0.00 2.43
985 4294 3.836562 AGGTCGGTATACACTTCCAGTTT 59.163 43.478 5.01 0.00 0.00 2.66
1034 4343 2.774687 TTTCCGGCCTGGGGTTAAGC 62.775 60.000 12.77 0.00 38.76 3.09
1035 4344 0.963856 GTTTCCGGCCTGGGGTTAAG 60.964 60.000 12.77 0.00 38.76 1.85
1036 4345 1.075305 GTTTCCGGCCTGGGGTTAA 59.925 57.895 12.77 0.00 38.76 2.01
1038 4347 2.994643 CTTGTTTCCGGCCTGGGGTT 62.995 60.000 12.77 0.00 38.76 4.11
1307 4617 0.817634 CTCTCTGGATCCTCTCGCGT 60.818 60.000 14.23 0.00 0.00 6.01
1318 4628 0.105760 GGCATCCTCCTCTCTCTGGA 60.106 60.000 0.00 0.00 0.00 3.86
1522 4832 2.812499 GCGTCTTGGGCTCCGATA 59.188 61.111 0.00 0.00 0.00 2.92
1553 4863 1.188871 CCTCCCGCTTCCTATCCCTC 61.189 65.000 0.00 0.00 0.00 4.30
1559 4869 1.230497 CTCCTCCTCCCGCTTCCTA 59.770 63.158 0.00 0.00 0.00 2.94
1585 4895 1.999071 CTTCCTCGACCTCAGCTCCG 61.999 65.000 0.00 0.00 0.00 4.63
1676 4986 1.774217 TGGCTCCACCTCCCTGTTT 60.774 57.895 0.00 0.00 40.22 2.83
1778 5088 5.178797 GGTGCACAAGTAAGAGTATCACAT 58.821 41.667 20.43 0.00 37.82 3.21
1780 5090 3.612860 CGGTGCACAAGTAAGAGTATCAC 59.387 47.826 20.43 0.00 37.82 3.06
1795 5105 1.400494 ACAGAACAAAGAACGGTGCAC 59.600 47.619 8.80 8.80 0.00 4.57
2149 5477 7.674471 TGTATGAACAACGAAATATTGGACA 57.326 32.000 0.00 0.00 30.91 4.02
2161 5489 5.102020 TGTGGAAACATGTATGAACAACG 57.898 39.130 0.00 0.00 46.14 4.10
2251 5579 3.599343 GGGCTGCCCTTTTTCTTATTTG 58.401 45.455 30.42 0.00 41.34 2.32
2258 5586 2.600470 ACCGGGCTGCCCTTTTTC 60.600 61.111 33.39 8.22 42.67 2.29
2608 5937 3.969976 AGGTATGAATGCTCTGCCTTCTA 59.030 43.478 8.51 0.00 34.98 2.10
2773 6102 4.345859 ACACTAGAGATCTACTCCCTCG 57.654 50.000 0.00 0.00 45.96 4.63
2894 6331 5.403166 CAGCAAACACACAATGTCTAAATGG 59.597 40.000 0.00 0.00 42.31 3.16
3048 6485 1.987855 CGGGAAGGACAGTGCCCTA 60.988 63.158 0.00 0.00 38.46 3.53
3066 6503 4.928615 GCTCATAGAATCATCACCTGTAGC 59.071 45.833 0.00 0.00 0.00 3.58
3254 6691 3.375299 GGCTATGAACCAGTGATTGTGTC 59.625 47.826 0.00 0.00 0.00 3.67
3385 6857 3.902150 TCTCTGTAGCTTCAAACTGACG 58.098 45.455 0.00 0.00 0.00 4.35
3398 6870 3.390639 AGCTTCCCATTCCATCTCTGTAG 59.609 47.826 0.00 0.00 0.00 2.74
3529 7004 2.899976 TCAACTCGTTTCTTCACAGCA 58.100 42.857 0.00 0.00 0.00 4.41
3641 7116 2.737252 CTCTAACTTCAACTGTTCGGCC 59.263 50.000 0.00 0.00 0.00 6.13
3642 7117 3.391049 ACTCTAACTTCAACTGTTCGGC 58.609 45.455 0.00 0.00 0.00 5.54
3680 7156 2.160417 GGCTGGAACAAAGAGATGAACG 59.840 50.000 0.00 0.00 38.70 3.95
4051 7530 3.763897 ACTGCCAAGAATAATGTGTTCCC 59.236 43.478 0.00 0.00 0.00 3.97
4165 7649 1.743958 AGTGAGATCAAGCAATGCAGC 59.256 47.619 8.35 0.00 0.00 5.25
4367 7853 6.535865 CCCATGTGATGTAAACCATGAATTTG 59.464 38.462 0.00 0.00 37.47 2.32
4490 7981 1.173043 CCTGCCTGCCGTTCATTTTA 58.827 50.000 0.00 0.00 0.00 1.52
4522 8013 4.349503 TGCGCAGGGAAGCATGGT 62.350 61.111 5.66 0.00 38.59 3.55
4998 8492 3.011517 GCCCAGAGCTCCCTCCAA 61.012 66.667 10.93 0.00 38.96 3.53
5029 8523 2.436646 GCATACAGCAGCCACGGT 60.437 61.111 0.00 0.00 44.79 4.83
5264 8758 2.527100 CGATCACTACCGGTCAAGTTC 58.473 52.381 12.40 4.68 0.00 3.01
5275 8769 2.423892 TCTTGCTCTCACCGATCACTAC 59.576 50.000 0.00 0.00 0.00 2.73
5432 8929 2.365293 GTTCCACCAGTTGCCTGAATTT 59.635 45.455 0.00 0.00 41.50 1.82
5488 8985 4.394300 CACTGCTAAATTCAGTTGAGGAGG 59.606 45.833 0.00 0.00 42.38 4.30
5489 8986 5.240891 TCACTGCTAAATTCAGTTGAGGAG 58.759 41.667 0.00 0.00 42.38 3.69
5490 8987 5.227569 TCACTGCTAAATTCAGTTGAGGA 57.772 39.130 0.00 0.00 42.38 3.71
5520 9044 9.632969 CATAACTTTTATTCGGTCATTAACTCG 57.367 33.333 0.00 0.00 0.00 4.18
5612 9137 6.017605 CGTTAGTAGTACCCATCTCGTATTGT 60.018 42.308 0.00 0.00 0.00 2.71
5667 9194 9.950680 GCAGCTTGCTATATCTTTGTTAAATTA 57.049 29.630 0.00 0.00 40.96 1.40
5753 9284 1.110442 TGACCAGGCCTGTTGTTTTG 58.890 50.000 30.63 15.99 0.00 2.44
5873 9404 2.225496 TGGGGCCAGTTTTTCCATGTAT 60.225 45.455 4.39 0.00 0.00 2.29
5905 9436 1.202830 ACATGTACGGTTCCTTTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
6244 10263 2.031037 TCAATTTGCGAGTTTGCGAC 57.969 45.000 0.00 0.00 37.81 5.19
6336 10355 0.923358 ACACCCAGGAACCAAAGTGA 59.077 50.000 11.88 0.00 0.00 3.41
6412 10431 9.668497 AGTCAAGTTTACTCTAAAAACACTTCT 57.332 29.630 2.00 0.00 38.92 2.85
6417 10436 9.457436 AAGGAAGTCAAGTTTACTCTAAAAACA 57.543 29.630 2.00 0.00 38.92 2.83
6440 10459 9.906660 TGAAAATTTACATACTAGTGCAAAAGG 57.093 29.630 5.39 0.00 0.00 3.11
6467 10486 1.864711 TCAACGCTGGTCTTTTCTTCG 59.135 47.619 0.00 0.00 0.00 3.79
6471 10490 4.319549 CCTTTAGTCAACGCTGGTCTTTTC 60.320 45.833 0.00 0.00 0.00 2.29
6476 10495 1.439679 CCCTTTAGTCAACGCTGGTC 58.560 55.000 0.00 0.00 0.00 4.02
6517 10536 6.183360 CGGCCAAAATAGTGTGAATAGTGATT 60.183 38.462 2.24 0.00 0.00 2.57
6555 10580 9.586435 AAGAAAAACCACATTGACTTCTTTTAG 57.414 29.630 0.00 0.00 29.64 1.85
6556 10581 9.936759 AAAGAAAAACCACATTGACTTCTTTTA 57.063 25.926 0.00 0.00 38.04 1.52
6605 10630 8.576442 ACGTTTGAAATAAACTTGATCTTCCAT 58.424 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.