Multiple sequence alignment - TraesCS6B01G147000

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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 TraesCS6B01G147000 chr6B 100.000 6175 0 0 915 7089 147882166 147888340 0.000000e+00 11404.0
1 TraesCS6B01G147000 chr6B 100.000 589 0 0 1 589 147881252 147881840 0.000000e+00 1088.0
2 TraesCS6B01G147000 chr6B 92.733 633 37 4 6461 7089 717738703 717738076 0.000000e+00 905.0
3 TraesCS6B01G147000 chr6B 95.122 41 2 0 4867 4907 143769272 143769312 1.650000e-06 65.8
4 TraesCS6B01G147000 chr6D 95.123 4142 138 18 2358 6460 73521030 73525146 0.000000e+00 6471.0
5 TraesCS6B01G147000 chr6D 95.235 1469 57 8 915 2375 73519553 73521016 0.000000e+00 2313.0
6 TraesCS6B01G147000 chr6D 91.481 540 28 12 6 539 73518727 73519254 0.000000e+00 726.0
7 TraesCS6B01G147000 chr6D 95.122 41 2 0 4867 4907 68863785 68863825 1.650000e-06 65.8
8 TraesCS6B01G147000 chr6A 95.937 1452 49 3 3485 4930 89971152 89972599 0.000000e+00 2346.0
9 TraesCS6B01G147000 chr6A 94.596 1425 45 10 915 2329 89968453 89969855 0.000000e+00 2176.0
10 TraesCS6B01G147000 chr6A 92.082 1566 85 11 4927 6460 89972678 89974236 0.000000e+00 2169.0
11 TraesCS6B01G147000 chr6A 94.838 1143 45 7 2358 3488 89969932 89971072 0.000000e+00 1772.0
12 TraesCS6B01G147000 chr6A 85.390 308 25 11 209 510 89967884 89968177 1.160000e-77 302.0
13 TraesCS6B01G147000 chr6A 92.617 149 5 3 1 148 89967742 89967885 7.210000e-50 209.0
14 TraesCS6B01G147000 chr6A 95.122 41 2 0 4867 4907 86461904 86461944 1.650000e-06 65.8
15 TraesCS6B01G147000 chr3B 95.880 631 25 1 6459 7089 10021848 10022477 0.000000e+00 1020.0
16 TraesCS6B01G147000 chr3B 85.714 210 24 6 6461 6667 225480540 225480746 4.310000e-52 217.0
17 TraesCS6B01G147000 chr4B 93.492 630 37 3 6461 7089 622484162 622484788 0.000000e+00 933.0
18 TraesCS6B01G147000 chr5D 93.333 630 40 2 6461 7089 387250033 387249405 0.000000e+00 929.0
19 TraesCS6B01G147000 chr5B 92.936 637 39 3 6455 7089 659547621 659546989 0.000000e+00 922.0
20 TraesCS6B01G147000 chr2B 93.175 630 39 3 6462 7089 225309448 225310075 0.000000e+00 922.0
21 TraesCS6B01G147000 chr4D 92.744 634 42 4 6460 7089 473869984 473870617 0.000000e+00 913.0
22 TraesCS6B01G147000 chr7B 92.247 632 46 3 6459 7089 36410754 36411383 0.000000e+00 893.0
23 TraesCS6B01G147000 chr7B 84.762 105 16 0 2921 3025 575380013 575380117 9.730000e-19 106.0
24 TraesCS6B01G147000 chr1B 93.542 511 29 2 6582 7089 359212822 359213331 0.000000e+00 758.0
25 TraesCS6B01G147000 chr7D 84.762 105 16 0 2921 3025 535327337 535327441 9.730000e-19 106.0
26 TraesCS6B01G147000 chr7A 84.762 105 16 0 2921 3025 615339168 615339272 9.730000e-19 106.0
27 TraesCS6B01G147000 chr3A 90.566 53 4 1 4866 4918 17624706 17624757 1.280000e-07 69.4
28 TraesCS6B01G147000 chr3A 85.714 63 8 1 4866 4928 221275027 221274966 1.650000e-06 65.8
29 TraesCS6B01G147000 chr1A 91.837 49 2 2 4866 4913 557424107 557424060 4.590000e-07 67.6
30 TraesCS6B01G147000 chr3D 85.714 63 8 1 4866 4928 178651863 178651802 1.650000e-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 TraesCS6B01G147000 chr6B 147881252 147888340 7088 False 6246.000000 11404 100.000000 1 7089 2 chr6B.!!$F2 7088
1 TraesCS6B01G147000 chr6B 717738076 717738703 627 True 905.000000 905 92.733000 6461 7089 1 chr6B.!!$R1 628
2 TraesCS6B01G147000 chr6D 73518727 73525146 6419 False 3170.000000 6471 93.946333 6 6460 3 chr6D.!!$F2 6454
3 TraesCS6B01G147000 chr6A 89967742 89974236 6494 False 1495.666667 2346 92.576667 1 6460 6 chr6A.!!$F2 6459
4 TraesCS6B01G147000 chr3B 10021848 10022477 629 False 1020.000000 1020 95.880000 6459 7089 1 chr3B.!!$F1 630
5 TraesCS6B01G147000 chr4B 622484162 622484788 626 False 933.000000 933 93.492000 6461 7089 1 chr4B.!!$F1 628
6 TraesCS6B01G147000 chr5D 387249405 387250033 628 True 929.000000 929 93.333000 6461 7089 1 chr5D.!!$R1 628
7 TraesCS6B01G147000 chr5B 659546989 659547621 632 True 922.000000 922 92.936000 6455 7089 1 chr5B.!!$R1 634
8 TraesCS6B01G147000 chr2B 225309448 225310075 627 False 922.000000 922 93.175000 6462 7089 1 chr2B.!!$F1 627
9 TraesCS6B01G147000 chr4D 473869984 473870617 633 False 913.000000 913 92.744000 6460 7089 1 chr4D.!!$F1 629
10 TraesCS6B01G147000 chr7B 36410754 36411383 629 False 893.000000 893 92.247000 6459 7089 1 chr7B.!!$F1 630
11 TraesCS6B01G147000 chr1B 359212822 359213331 509 False 758.000000 758 93.542000 6582 7089 1 chr1B.!!$F1 507

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
517 525 1.035139 AAGAGTTTGGTGGCTTGCAG 58.965 50.000 0.00 0.00 0.00 4.41 F
523 531 1.401318 TTGGTGGCTTGCAGTGCATT 61.401 50.000 20.50 0.00 38.76 3.56 F
2004 2024 0.683973 ATAGCTTGGCCTGATCGAGG 59.316 55.000 3.32 6.79 46.13 4.63 F
2270 2295 0.394216 TGTGGGCTATGTGATGGTGC 60.394 55.000 0.00 0.00 0.00 5.01 F
2409 2480 2.803155 TAGCTTGAGCAACTGCCCCG 62.803 60.000 5.70 0.00 45.16 5.73 F
3847 4015 2.043115 GGAAGAGGTCCCCCAAAAGAAT 59.957 50.000 0.00 0.00 41.10 2.40 F
4197 4365 1.464997 GGTTTTCGTCATGTGAGAGCC 59.535 52.381 0.00 0.00 0.00 4.70 F
4208 4376 1.939934 TGTGAGAGCCGACAACAAAAG 59.060 47.619 0.00 0.00 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1970 0.254747 AATCATACCACACACCCCGG 59.745 55.000 0.0 0.0 0.00 5.73 R
2202 2227 0.340208 AACCCCCACAACCCTTTCAA 59.660 50.000 0.0 0.0 0.00 2.69 R
3770 3938 0.109342 CCCAGAGCTTCCACAGTTGT 59.891 55.000 0.0 0.0 0.00 3.32 R
3776 3944 0.329596 ACCATTCCCAGAGCTTCCAC 59.670 55.000 0.0 0.0 0.00 4.02 R
3952 4120 1.108776 CCGACAATACCCTTCTCCGA 58.891 55.000 0.0 0.0 0.00 4.55 R
5369 5664 0.324738 CACCAGGCAGAGGGACTAGA 60.325 60.000 0.0 0.0 41.55 2.43 R
5452 5747 0.803117 CACTCTGCCTGCACTTCATG 59.197 55.000 0.0 0.0 0.00 3.07 R
6118 6413 1.794701 CATTCGCTATGTGGGTCATCG 59.205 52.381 0.0 0.0 37.91 3.84 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 3.181516 GCCATCAGTGATTTTCTCGTGTC 60.182 47.826 1.86 0.00 0.00 3.67
74 76 2.874086 TGTCGAGACGAGAAACAGTACA 59.126 45.455 0.00 0.00 36.23 2.90
75 77 3.224750 GTCGAGACGAGAAACAGTACAC 58.775 50.000 0.00 0.00 36.23 2.90
76 78 2.225019 TCGAGACGAGAAACAGTACACC 59.775 50.000 0.00 0.00 0.00 4.16
77 79 2.031420 CGAGACGAGAAACAGTACACCA 60.031 50.000 0.00 0.00 0.00 4.17
78 80 3.366070 CGAGACGAGAAACAGTACACCAT 60.366 47.826 0.00 0.00 0.00 3.55
79 81 3.914312 AGACGAGAAACAGTACACCATG 58.086 45.455 0.00 0.00 0.00 3.66
107 109 3.869246 GTCATACAATCAGGGGTTACACG 59.131 47.826 0.00 0.00 0.00 4.49
117 119 3.129988 CAGGGGTTACACGGTAAGACTAG 59.870 52.174 0.00 0.00 0.00 2.57
145 147 3.134623 ACCGGATGAAATGTATGCTCTGA 59.865 43.478 9.46 0.00 0.00 3.27
147 149 4.758674 CCGGATGAAATGTATGCTCTGAAT 59.241 41.667 0.00 0.00 0.00 2.57
180 182 1.524961 TGGCACGTTCAGTTCCACT 59.475 52.632 0.00 0.00 41.20 4.00
197 199 6.261826 AGTTCCACTCTTTGATGTTCTTCTTG 59.738 38.462 0.00 0.00 0.00 3.02
204 206 3.319137 TGATGTTCTTCTTGTCCCGAG 57.681 47.619 0.00 0.00 0.00 4.63
233 238 3.365976 GGAGAGCTCTCTGCATGTG 57.634 57.895 36.09 0.00 45.78 3.21
313 319 9.261035 CCCTACATATTATGAGAACTGGTAGAT 57.739 37.037 10.62 0.00 0.00 1.98
370 378 9.905713 AATGGAAGTGACAAATACAGTATACAT 57.094 29.630 5.50 0.00 0.00 2.29
499 507 2.123342 CGCAAATCGTTTTTCTGGCAA 58.877 42.857 0.00 0.00 0.00 4.52
500 508 2.153627 CGCAAATCGTTTTTCTGGCAAG 59.846 45.455 0.00 0.00 0.00 4.01
501 509 3.380142 GCAAATCGTTTTTCTGGCAAGA 58.620 40.909 0.00 0.00 0.00 3.02
517 525 1.035139 AAGAGTTTGGTGGCTTGCAG 58.965 50.000 0.00 0.00 0.00 4.41
523 531 1.401318 TTGGTGGCTTGCAGTGCATT 61.401 50.000 20.50 0.00 38.76 3.56
562 570 8.986477 TTTCTTTTCTTCTTCTTTGTTTGAGG 57.014 30.769 0.00 0.00 0.00 3.86
563 571 7.938140 TCTTTTCTTCTTCTTTGTTTGAGGA 57.062 32.000 0.00 0.00 0.00 3.71
566 574 7.645058 TTTCTTCTTCTTTGTTTGAGGACAT 57.355 32.000 0.00 0.00 0.00 3.06
577 585 4.523558 TGTTTGAGGACATCATTGCATTCA 59.476 37.500 0.00 0.00 37.89 2.57
588 596 4.847198 TCATTGCATTCACTGGTGTCTAT 58.153 39.130 0.00 0.00 0.00 1.98
1967 1987 2.961893 GCCGGGGTGTGTGGTATGA 61.962 63.158 2.18 0.00 0.00 2.15
2004 2024 0.683973 ATAGCTTGGCCTGATCGAGG 59.316 55.000 3.32 6.79 46.13 4.63
2032 2052 1.002430 GTCAGACCTTGCTGATCCACA 59.998 52.381 0.00 0.00 45.75 4.17
2040 2060 2.885135 TGCTGATCCACATTCACCTT 57.115 45.000 0.00 0.00 0.00 3.50
2116 2141 3.211045 TCTTGTGCCCAAAGACTTGTAC 58.789 45.455 0.00 0.00 0.00 2.90
2117 2142 1.588674 TGTGCCCAAAGACTTGTACG 58.411 50.000 0.00 0.00 0.00 3.67
2118 2143 1.134340 TGTGCCCAAAGACTTGTACGT 60.134 47.619 0.00 0.00 0.00 3.57
2119 2144 2.102757 TGTGCCCAAAGACTTGTACGTA 59.897 45.455 0.00 0.00 0.00 3.57
2144 2169 3.144657 TCATGTGTGATTTGGCTGTCT 57.855 42.857 0.00 0.00 0.00 3.41
2185 2210 1.218316 CACTCACCTACGGCCTTCC 59.782 63.158 0.00 0.00 0.00 3.46
2202 2227 0.969149 TCCATCTCAAGCACGTGACT 59.031 50.000 22.23 13.28 0.00 3.41
2232 2257 1.957877 TGTGGGGGTTTAAGCTTTTCG 59.042 47.619 3.20 0.00 0.00 3.46
2258 2283 4.134563 GTTTGATAATCCGTATGTGGGCT 58.865 43.478 0.00 0.00 0.00 5.19
2270 2295 0.394216 TGTGGGCTATGTGATGGTGC 60.394 55.000 0.00 0.00 0.00 5.01
2277 2302 3.270027 GCTATGTGATGGTGCTGTACAA 58.730 45.455 0.00 0.00 0.00 2.41
2409 2480 2.803155 TAGCTTGAGCAACTGCCCCG 62.803 60.000 5.70 0.00 45.16 5.73
2555 2629 4.903049 TCTGTTACTTCTGGGTTTACCTCA 59.097 41.667 0.00 0.00 41.11 3.86
2557 2631 5.370679 TGTTACTTCTGGGTTTACCTCAAC 58.629 41.667 0.00 0.00 41.11 3.18
2558 2632 5.104444 TGTTACTTCTGGGTTTACCTCAACA 60.104 40.000 0.00 0.00 41.11 3.33
2559 2633 4.724279 ACTTCTGGGTTTACCTCAACAT 57.276 40.909 0.00 0.00 41.11 2.71
2560 2634 4.652822 ACTTCTGGGTTTACCTCAACATC 58.347 43.478 0.00 0.00 41.11 3.06
2561 2635 4.351111 ACTTCTGGGTTTACCTCAACATCT 59.649 41.667 0.00 0.00 41.11 2.90
2563 2637 3.009033 TCTGGGTTTACCTCAACATCTGG 59.991 47.826 0.00 0.00 41.11 3.86
2602 2685 8.206325 AGCATGTGAATTAATCTGTTCTACTG 57.794 34.615 0.00 0.00 0.00 2.74
2735 2818 3.219281 GGTGCTTCCAGTAAGGTTCAAA 58.781 45.455 0.00 0.00 39.02 2.69
2832 2915 4.207891 TCCTAAGTTCTCAAGCCATGTC 57.792 45.455 0.00 0.00 0.00 3.06
2897 2980 4.079269 TCCATTTTGAATCCCTGATAGGCA 60.079 41.667 0.00 0.00 32.73 4.75
2992 3075 9.373450 AGTTTATCCTAGCTCTTGAAGATGATA 57.627 33.333 0.00 0.00 0.00 2.15
3070 3153 3.629087 TGAGCTACTGGTACTAGAACCC 58.371 50.000 13.86 0.00 38.90 4.11
3377 3460 8.784043 TCTCTTTCTGAAAATAGTTTGCTTACC 58.216 33.333 4.18 0.00 0.00 2.85
3413 3496 4.201930 GGTACTCCGATCTGTGTTGAGTAG 60.202 50.000 0.00 0.00 38.74 2.57
3425 3508 4.400884 TGTGTTGAGTAGCACCAAAAATGT 59.599 37.500 0.00 0.00 37.24 2.71
3463 3546 8.598924 CATGACTAGATGAAACAGTTGTATGTC 58.401 37.037 0.00 0.00 31.50 3.06
3522 3688 5.650266 TGAGCTTTTCTTGTTGGTAGTTGAA 59.350 36.000 0.00 0.00 0.00 2.69
3692 3860 9.086336 GTGTTACATATATTGCACAATTTTGCT 57.914 29.630 16.97 1.17 43.41 3.91
3710 3878 6.441093 TTTGCTAGTTTTGCTGATATCCTG 57.559 37.500 0.00 0.00 0.00 3.86
3770 3938 3.956199 GGATCAAGCAAATCAGGGAATGA 59.044 43.478 0.00 0.00 43.70 2.57
3776 3944 3.508793 AGCAAATCAGGGAATGACAACTG 59.491 43.478 0.00 0.00 41.91 3.16
3847 4015 2.043115 GGAAGAGGTCCCCCAAAAGAAT 59.957 50.000 0.00 0.00 41.10 2.40
3910 4078 7.170151 TCAGTTCAAAGTATCGACGAATTCAAA 59.830 33.333 0.00 0.00 0.00 2.69
3969 4137 2.758979 TGACTCGGAGAAGGGTATTGTC 59.241 50.000 12.86 0.00 34.09 3.18
4059 4227 3.071023 CAGGGCCTTTAGTCATTATCCGA 59.929 47.826 1.32 0.00 0.00 4.55
4197 4365 1.464997 GGTTTTCGTCATGTGAGAGCC 59.535 52.381 0.00 0.00 0.00 4.70
4208 4376 1.939934 TGTGAGAGCCGACAACAAAAG 59.060 47.619 0.00 0.00 0.00 2.27
4440 4608 3.751479 ACAAAAGTTTTCCATGCTCCC 57.249 42.857 0.00 0.00 0.00 4.30
4595 4763 9.308318 AGCTAAAACAATTTTCAAACGTGTTAT 57.692 25.926 0.00 0.00 32.38 1.89
4596 4764 9.352163 GCTAAAACAATTTTCAAACGTGTTATG 57.648 29.630 0.00 0.00 32.38 1.90
4599 4767 8.696410 AAACAATTTTCAAACGTGTTATGACT 57.304 26.923 0.00 0.00 32.38 3.41
4665 4838 2.877097 TGGAAAGCCAGTTATGCAGA 57.123 45.000 0.00 0.00 39.92 4.26
4778 4952 4.215109 ACAAATTAGGACAGGTGCTGTTT 58.785 39.130 3.52 2.68 45.44 2.83
4797 4971 6.636454 TGTTTGTAGATACTCCCTCCATTT 57.364 37.500 0.00 0.00 0.00 2.32
4838 5012 9.939802 TTATCCTAAGTCAAACTTCCTTAAGTC 57.060 33.333 0.97 0.00 45.37 3.01
4999 5255 7.309438 GGTCAATGTAAAAGAGAAGATTGCCTT 60.309 37.037 0.00 0.00 37.93 4.35
5213 5469 3.483196 CGCCTTCATTGAAATTACATGCG 59.517 43.478 0.01 3.51 0.00 4.73
5261 5517 6.573664 TGATAAAGCTGCAGTGTTACAATT 57.426 33.333 16.64 0.00 0.00 2.32
5369 5664 2.397413 CTGACGCCCCTCCAACAGTT 62.397 60.000 0.00 0.00 0.00 3.16
5452 5747 7.330946 ACTTATTTTCTTTTTATGGAAAGGCGC 59.669 33.333 0.00 0.00 37.27 6.53
5825 6120 6.062434 TGTTTTCATACTTAACCACCAACG 57.938 37.500 0.00 0.00 0.00 4.10
5846 6141 7.219535 CCAACGATTCTTCATTTAGCAGAATTG 59.780 37.037 6.77 6.77 43.17 2.32
5880 6175 3.404899 AGTTTGGCCTCATGCATTTTTG 58.595 40.909 3.32 0.00 43.89 2.44
5886 6181 3.306225 GGCCTCATGCATTTTTGTTGAGA 60.306 43.478 11.83 0.00 43.89 3.27
5887 6182 4.309099 GCCTCATGCATTTTTGTTGAGAA 58.691 39.130 11.83 0.00 40.77 2.87
5888 6183 4.151157 GCCTCATGCATTTTTGTTGAGAAC 59.849 41.667 11.83 1.85 40.77 3.01
5891 6186 5.771469 TCATGCATTTTTGTTGAGAACGAT 58.229 33.333 0.00 0.00 0.00 3.73
5937 6232 3.668447 TCTCACTCTTGTGGAAGCAATC 58.332 45.455 0.00 0.00 43.94 2.67
5995 6290 0.798776 CACTTGTCCGTTCCATGAGC 59.201 55.000 0.00 0.00 0.00 4.26
6011 6306 3.535280 TGAGCATCGCATAACCTGTTA 57.465 42.857 0.00 0.00 38.61 2.41
6118 6413 2.994186 TTTACCCACTCTAATCCGCC 57.006 50.000 0.00 0.00 0.00 6.13
6168 6463 1.519408 AATTACTCGCTGTTGCCGTT 58.481 45.000 0.00 0.00 35.36 4.44
6204 6499 3.445096 CAGACAGGGAATGGGATTTTGTC 59.555 47.826 0.00 0.00 35.04 3.18
6228 6523 1.227234 CTGGCGGACGTATGATGCA 60.227 57.895 0.00 0.00 0.00 3.96
6310 6605 1.526575 CCCGTGCTTGTTGGAATGCT 61.527 55.000 0.00 0.00 0.00 3.79
6311 6606 1.164411 CCGTGCTTGTTGGAATGCTA 58.836 50.000 0.00 0.00 0.00 3.49
6312 6607 1.745087 CCGTGCTTGTTGGAATGCTAT 59.255 47.619 0.00 0.00 0.00 2.97
6326 6621 4.820716 GGAATGCTATGAATCAGAAGCTGT 59.179 41.667 17.54 8.32 35.95 4.40
6327 6622 5.049543 GGAATGCTATGAATCAGAAGCTGTC 60.050 44.000 17.54 14.29 35.95 3.51
6351 6646 1.133884 TCAGTATGATCCGTCCGACCT 60.134 52.381 0.00 0.00 42.56 3.85
6353 6648 0.597072 GTATGATCCGTCCGACCTCC 59.403 60.000 0.00 0.00 0.00 4.30
6355 6650 2.441532 GATCCGTCCGACCTCCCA 60.442 66.667 0.00 0.00 0.00 4.37
6371 6666 3.209410 CTCCCATATTCACAGTTGGAGC 58.791 50.000 0.00 0.00 32.32 4.70
6688 6992 3.607163 CCGTGGCGGTAGGTCTAA 58.393 61.111 0.00 0.00 42.73 2.10
6854 7158 1.144913 CTCCCTCGATCTCCCTCTTCT 59.855 57.143 0.00 0.00 0.00 2.85
6897 7201 4.319133 GGCAAATCGAAGAGGCCA 57.681 55.556 5.01 0.00 46.75 5.36
6919 7223 1.341156 AAGCTCCTCCATTCCCTCCG 61.341 60.000 0.00 0.00 0.00 4.63
6922 7226 1.428869 CTCCTCCATTCCCTCCGATT 58.571 55.000 0.00 0.00 0.00 3.34
6937 7243 4.495844 CCTCCGATTAGTTTTCGAAATGCC 60.496 45.833 12.12 3.15 38.88 4.40
6967 7274 6.601741 TTTTTGAAGCTATTTTTGGCACTG 57.398 33.333 0.00 0.00 0.00 3.66
6971 7278 3.449746 AGCTATTTTTGGCACTGGGTA 57.550 42.857 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 2.031420 TGGTGTACTGTTTCTCGTCTCG 60.031 50.000 0.00 0.00 0.00 4.04
78 80 4.913355 ACCCCTGATTGTATGACCATATCA 59.087 41.667 0.00 0.00 43.13 2.15
79 81 5.505181 ACCCCTGATTGTATGACCATATC 57.495 43.478 0.00 0.00 0.00 1.63
107 109 5.533903 TCATCCGGTAATCACTAGTCTTACC 59.466 44.000 22.96 22.96 40.55 2.85
117 119 5.470098 AGCATACATTTCATCCGGTAATCAC 59.530 40.000 0.00 0.00 0.00 3.06
180 182 4.065088 CGGGACAAGAAGAACATCAAAGA 58.935 43.478 0.00 0.00 0.00 2.52
197 199 1.227205 CTCTGCATGCTCTCGGGAC 60.227 63.158 20.33 0.00 0.00 4.46
204 206 0.249573 GAGCTCTCCTCTGCATGCTC 60.250 60.000 20.33 0.00 39.74 4.26
313 319 0.971386 GAACAGAACACTCCCCGGTA 59.029 55.000 0.00 0.00 0.00 4.02
380 388 1.669265 CACTGTACTCCAGCATGCATG 59.331 52.381 22.70 22.70 45.68 4.06
499 507 0.106519 ACTGCAAGCCACCAAACTCT 60.107 50.000 0.00 0.00 37.60 3.24
500 508 0.031178 CACTGCAAGCCACCAAACTC 59.969 55.000 0.00 0.00 37.60 3.01
501 509 2.019897 GCACTGCAAGCCACCAAACT 62.020 55.000 0.00 0.00 37.60 2.66
538 546 8.244113 GTCCTCAAACAAAGAAGAAGAAAAGAA 58.756 33.333 0.00 0.00 0.00 2.52
539 547 7.393234 TGTCCTCAAACAAAGAAGAAGAAAAGA 59.607 33.333 0.00 0.00 0.00 2.52
540 548 7.538575 TGTCCTCAAACAAAGAAGAAGAAAAG 58.461 34.615 0.00 0.00 0.00 2.27
541 549 7.461182 TGTCCTCAAACAAAGAAGAAGAAAA 57.539 32.000 0.00 0.00 0.00 2.29
542 550 7.339212 TGATGTCCTCAAACAAAGAAGAAGAAA 59.661 33.333 0.00 0.00 31.81 2.52
543 551 6.828273 TGATGTCCTCAAACAAAGAAGAAGAA 59.172 34.615 0.00 0.00 31.81 2.52
544 552 6.356556 TGATGTCCTCAAACAAAGAAGAAGA 58.643 36.000 0.00 0.00 31.81 2.87
545 553 6.624352 TGATGTCCTCAAACAAAGAAGAAG 57.376 37.500 0.00 0.00 31.81 2.85
546 554 7.428020 CAATGATGTCCTCAAACAAAGAAGAA 58.572 34.615 0.00 0.00 37.44 2.52
547 555 6.515531 GCAATGATGTCCTCAAACAAAGAAGA 60.516 38.462 0.00 0.00 37.44 2.87
548 556 5.632347 GCAATGATGTCCTCAAACAAAGAAG 59.368 40.000 0.00 0.00 37.44 2.85
549 557 5.068855 TGCAATGATGTCCTCAAACAAAGAA 59.931 36.000 0.00 0.00 37.44 2.52
550 558 4.583907 TGCAATGATGTCCTCAAACAAAGA 59.416 37.500 0.00 0.00 37.44 2.52
551 559 4.873817 TGCAATGATGTCCTCAAACAAAG 58.126 39.130 0.00 0.00 37.44 2.77
552 560 4.933505 TGCAATGATGTCCTCAAACAAA 57.066 36.364 0.00 0.00 37.44 2.83
553 561 5.010820 TGAATGCAATGATGTCCTCAAACAA 59.989 36.000 0.00 0.00 37.44 2.83
554 562 4.523558 TGAATGCAATGATGTCCTCAAACA 59.476 37.500 0.00 0.00 37.44 2.83
555 563 4.860907 GTGAATGCAATGATGTCCTCAAAC 59.139 41.667 0.00 0.00 37.44 2.93
556 564 4.768448 AGTGAATGCAATGATGTCCTCAAA 59.232 37.500 0.00 0.00 37.44 2.69
557 565 4.157105 CAGTGAATGCAATGATGTCCTCAA 59.843 41.667 0.00 0.00 42.40 3.02
558 566 3.692593 CAGTGAATGCAATGATGTCCTCA 59.307 43.478 0.00 0.00 42.40 3.86
559 567 3.066342 CCAGTGAATGCAATGATGTCCTC 59.934 47.826 1.72 0.00 42.40 3.71
560 568 3.021695 CCAGTGAATGCAATGATGTCCT 58.978 45.455 1.72 0.00 42.40 3.85
561 569 2.756760 ACCAGTGAATGCAATGATGTCC 59.243 45.455 1.72 0.00 42.40 4.02
562 570 3.192001 ACACCAGTGAATGCAATGATGTC 59.808 43.478 1.72 0.00 42.90 3.06
563 571 3.159472 ACACCAGTGAATGCAATGATGT 58.841 40.909 1.72 0.00 41.74 3.06
566 574 3.144657 AGACACCAGTGAATGCAATGA 57.855 42.857 1.72 0.00 42.40 2.57
1434 1452 3.787001 GAGCCAACGAGGGGAGGG 61.787 72.222 0.00 0.00 38.09 4.30
1719 1737 7.064016 CAGAAACACAGAGATTAGCTTAGAACC 59.936 40.741 0.00 0.00 0.00 3.62
1829 1849 2.560542 ACGTGAAAGCTCATCAGAGTCT 59.439 45.455 2.59 0.00 44.00 3.24
1950 1970 0.254747 AATCATACCACACACCCCGG 59.745 55.000 0.00 0.00 0.00 5.73
1951 1971 1.742831 CAAATCATACCACACACCCCG 59.257 52.381 0.00 0.00 0.00 5.73
1952 1972 3.016736 CTCAAATCATACCACACACCCC 58.983 50.000 0.00 0.00 0.00 4.95
1953 1973 3.950397 TCTCAAATCATACCACACACCC 58.050 45.455 0.00 0.00 0.00 4.61
1954 1974 6.258727 CACTATCTCAAATCATACCACACACC 59.741 42.308 0.00 0.00 0.00 4.16
1963 1983 7.757173 GCTATCGCTTCACTATCTCAAATCATA 59.243 37.037 0.00 0.00 0.00 2.15
1964 1984 6.589523 GCTATCGCTTCACTATCTCAAATCAT 59.410 38.462 0.00 0.00 0.00 2.45
1967 1987 6.095432 AGCTATCGCTTCACTATCTCAAAT 57.905 37.500 0.00 0.00 46.47 2.32
2004 2024 1.082690 GCAAGGTCTGACAGCTTAGC 58.917 55.000 10.38 0.00 41.09 3.09
2032 2052 3.575805 ACCCACATGTTTCAAGGTGAAT 58.424 40.909 0.00 0.00 36.11 2.57
2040 2060 5.453057 CCTCAAATCAAACCCACATGTTTCA 60.453 40.000 0.00 0.00 36.33 2.69
2116 2141 5.294306 AGCCAAATCACACATGATAGTTACG 59.706 40.000 0.00 0.00 45.26 3.18
2117 2142 6.094048 ACAGCCAAATCACACATGATAGTTAC 59.906 38.462 0.00 0.00 45.26 2.50
2118 2143 6.179756 ACAGCCAAATCACACATGATAGTTA 58.820 36.000 0.00 0.00 45.26 2.24
2119 2144 5.012239 ACAGCCAAATCACACATGATAGTT 58.988 37.500 0.00 0.00 45.26 2.24
2185 2210 2.407090 TCAAGTCACGTGCTTGAGATG 58.593 47.619 32.59 19.29 44.90 2.90
2202 2227 0.340208 AACCCCCACAACCCTTTCAA 59.660 50.000 0.00 0.00 0.00 2.69
2232 2257 4.514506 CACATACGGATTATCAAACACGC 58.485 43.478 0.00 0.00 0.00 5.34
2258 2283 5.709631 ACAAATTGTACAGCACCATCACATA 59.290 36.000 0.00 0.00 0.00 2.29
2270 2295 3.120060 GGCAGAGCTGACAAATTGTACAG 60.120 47.826 15.99 15.99 38.82 2.74
2277 2302 0.694771 TGAGGGCAGAGCTGACAAAT 59.305 50.000 5.59 0.00 41.42 2.32
2440 2514 1.531578 GACTCCAACTTCTCAAACGCC 59.468 52.381 0.00 0.00 0.00 5.68
2555 2629 7.568349 TGCTTGATACTAAGAATCCAGATGTT 58.432 34.615 0.00 0.00 0.00 2.71
2557 2631 7.660617 ACATGCTTGATACTAAGAATCCAGATG 59.339 37.037 6.60 0.00 0.00 2.90
2558 2632 7.660617 CACATGCTTGATACTAAGAATCCAGAT 59.339 37.037 6.60 0.00 0.00 2.90
2559 2633 6.988580 CACATGCTTGATACTAAGAATCCAGA 59.011 38.462 6.60 0.00 0.00 3.86
2560 2634 6.988580 TCACATGCTTGATACTAAGAATCCAG 59.011 38.462 6.60 0.00 0.00 3.86
2561 2635 6.888105 TCACATGCTTGATACTAAGAATCCA 58.112 36.000 6.60 0.00 0.00 3.41
3070 3153 3.214696 AGGTGGTTCTCAACTGAAAGG 57.785 47.619 0.00 0.00 42.85 3.11
3268 3351 5.843673 TCAACCTGCAATTACAGTCAAAA 57.156 34.783 4.98 0.00 35.83 2.44
3377 3460 3.495377 TCGGAGTACCAAAATTTGTGACG 59.505 43.478 4.92 1.51 35.59 4.35
3413 3496 6.091441 TGAAGTGTTACAAACATTTTTGGTGC 59.909 34.615 9.06 0.00 45.65 5.01
3425 3508 9.554395 TTTCATCTAGTCATGAAGTGTTACAAA 57.446 29.630 0.00 0.00 42.43 2.83
3494 3660 4.376340 ACCAACAAGAAAAGCTCAACTG 57.624 40.909 0.00 0.00 0.00 3.16
3522 3688 4.161565 AGACATGCCAATGATCAGCAAAAT 59.838 37.500 11.63 1.65 40.46 1.82
3692 3860 7.568349 AGACAATCAGGATATCAGCAAAACTA 58.432 34.615 4.83 0.00 0.00 2.24
3710 3878 2.427506 GACCACTGGACCAAGACAATC 58.572 52.381 0.71 0.00 0.00 2.67
3770 3938 0.109342 CCCAGAGCTTCCACAGTTGT 59.891 55.000 0.00 0.00 0.00 3.32
3776 3944 0.329596 ACCATTCCCAGAGCTTCCAC 59.670 55.000 0.00 0.00 0.00 4.02
3847 4015 1.490490 AGCAGTTGAAAGTGGTCCAGA 59.510 47.619 0.00 0.00 35.28 3.86
3910 4078 7.416964 AAGCTAGAGTTTGATCTATGTCAGT 57.583 36.000 0.00 0.00 31.50 3.41
3952 4120 1.108776 CCGACAATACCCTTCTCCGA 58.891 55.000 0.00 0.00 0.00 4.55
3957 4125 4.941873 AGAATGTTTCCGACAATACCCTTC 59.058 41.667 0.00 0.00 42.62 3.46
4059 4227 2.027100 GCCCTTGACAGTAGTTAAGCCT 60.027 50.000 0.00 0.00 39.34 4.58
4197 4365 1.673760 CATCGGCACTTTTGTTGTCG 58.326 50.000 0.00 0.00 32.70 4.35
4208 4376 1.129624 TGATGTTAAACGCATCGGCAC 59.870 47.619 0.00 0.00 44.02 5.01
4416 4584 5.222631 GGAGCATGGAAAACTTTTGTACAG 58.777 41.667 0.00 0.00 0.00 2.74
4420 4588 2.035832 CGGGAGCATGGAAAACTTTTGT 59.964 45.455 0.00 0.00 0.00 2.83
4440 4608 3.885484 AGATGCTTGTGAACAAACTCG 57.115 42.857 0.00 0.00 35.15 4.18
4568 4736 6.988329 ACACGTTTGAAAATTGTTTTAGCTG 58.012 32.000 0.00 0.00 31.94 4.24
4599 4767 8.825745 GCACCAAAAAGAAATTACATGAGAAAA 58.174 29.630 0.00 0.00 0.00 2.29
4665 4838 7.173218 TGCGAAGATTCTTACTTGTTCAGATTT 59.827 33.333 0.00 0.00 0.00 2.17
4752 4926 3.821033 AGCACCTGTCCTAATTTGTTGTC 59.179 43.478 0.00 0.00 0.00 3.18
4778 4952 6.884472 TTTGAAATGGAGGGAGTATCTACA 57.116 37.500 0.00 0.00 33.73 2.74
4999 5255 3.649843 ACTTCAGGTAACCGGATATGGA 58.350 45.455 9.46 0.00 37.17 3.41
5078 5334 9.820229 TTTGCAGAAAGTAATATGTAAACTTCG 57.180 29.630 0.00 0.00 32.42 3.79
5097 5353 8.691797 AGGTACAAGAAATTAAAAGTTTGCAGA 58.308 29.630 0.00 0.00 0.00 4.26
5121 5377 7.770433 TGATGAAACCTGAATACTATCACAAGG 59.230 37.037 0.00 0.00 0.00 3.61
5213 5469 5.300969 TCAATAAACATGACTGCTGCTTC 57.699 39.130 0.00 0.00 0.00 3.86
5261 5517 5.959583 AGGACATGGGGTTTAAACAAAAA 57.040 34.783 19.57 3.07 0.00 1.94
5271 5527 2.376518 CCTGCATATAGGACATGGGGTT 59.623 50.000 0.00 0.00 40.42 4.11
5297 5553 4.471025 TCTGGTATTCTTCTCATTCTGCCA 59.529 41.667 0.00 0.00 0.00 4.92
5369 5664 0.324738 CACCAGGCAGAGGGACTAGA 60.325 60.000 0.00 0.00 41.55 2.43
5444 5739 4.465413 GCACTTCATGCGCCTTTC 57.535 55.556 4.18 0.00 46.55 2.62
5452 5747 0.803117 CACTCTGCCTGCACTTCATG 59.197 55.000 0.00 0.00 0.00 3.07
5586 5881 6.248433 TCAGGCATCAAAGGTTTCTTCTTAT 58.752 36.000 0.00 0.00 31.82 1.73
5796 6091 9.132923 TGGTGGTTAAGTATGAAAACATACAAA 57.867 29.630 18.26 11.29 39.74 2.83
5818 6113 5.122239 TCTGCTAAATGAAGAATCGTTGGTG 59.878 40.000 0.00 0.00 34.99 4.17
5846 6141 3.447944 AGGCCAAACTAGTACAGAGTAGC 59.552 47.826 5.01 2.87 32.49 3.58
5847 6142 4.705507 TGAGGCCAAACTAGTACAGAGTAG 59.294 45.833 5.01 0.00 35.07 2.57
5891 6186 9.702494 GATATACAACAGAGTGATGATGATTCA 57.298 33.333 0.00 0.00 36.00 2.57
5995 6290 4.327357 GGATCGATAACAGGTTATGCGATG 59.673 45.833 25.80 9.47 40.87 3.84
6118 6413 1.794701 CATTCGCTATGTGGGTCATCG 59.205 52.381 0.00 0.00 37.91 3.84
6228 6523 2.228822 GGGTGTTGCAGAAAATGACGAT 59.771 45.455 0.00 0.00 0.00 3.73
6310 6605 7.108194 ACTGATTTGACAGCTTCTGATTCATA 58.892 34.615 0.29 0.00 41.06 2.15
6311 6606 5.944599 ACTGATTTGACAGCTTCTGATTCAT 59.055 36.000 0.29 0.00 41.06 2.57
6312 6607 5.311265 ACTGATTTGACAGCTTCTGATTCA 58.689 37.500 0.29 0.00 41.06 2.57
6326 6621 3.634910 TCGGACGGATCATACTGATTTGA 59.365 43.478 0.00 0.00 37.20 2.69
6327 6622 3.736252 GTCGGACGGATCATACTGATTTG 59.264 47.826 0.00 0.00 37.20 2.32
6343 6638 1.760613 TGTGAATATGGGAGGTCGGAC 59.239 52.381 0.00 0.00 0.00 4.79
6351 6646 2.575735 TGCTCCAACTGTGAATATGGGA 59.424 45.455 0.00 0.00 33.66 4.37
6353 6648 3.317149 CCATGCTCCAACTGTGAATATGG 59.683 47.826 0.00 0.00 0.00 2.74
6355 6650 4.164796 TCTCCATGCTCCAACTGTGAATAT 59.835 41.667 0.00 0.00 0.00 1.28
6371 6666 7.651808 ACAAACAAACATAGAAGTTCTCCATG 58.348 34.615 9.12 11.07 0.00 3.66
6688 6992 1.173444 CGATCTGGCGGTAGGCTACT 61.173 60.000 23.01 2.29 44.18 2.57
6854 7158 0.251916 ATCCGCGAAAATGGTGGAGA 59.748 50.000 8.23 0.00 46.36 3.71
6897 7201 2.403561 GAGGGAATGGAGGAGCTTACT 58.596 52.381 0.00 0.00 0.00 2.24
6967 7274 3.151554 CACCAAAACCTAGGTTGTACCC 58.848 50.000 27.75 0.00 39.75 3.69
6971 7278 3.970842 TCAACACCAAAACCTAGGTTGT 58.029 40.909 27.75 20.19 38.47 3.32


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

AutoCloner maintained by Alex Coulton.