Multiple sequence alignment - TraesCS7A01G550700

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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 TraesCS7A01G550700 chr7A 100.000 6993 0 0 1 6993 724368906 724375898 0.000000e+00 12914.0
1 TraesCS7A01G550700 chr7A 97.542 3051 47 5 804 3837 724263085 724260046 0.000000e+00 5193.0
2 TraesCS7A01G550700 chr7A 97.760 2857 53 7 3891 6744 724260062 724257214 0.000000e+00 4911.0
3 TraesCS7A01G550700 chr7A 99.506 809 1 2 1 808 724264371 724263565 0.000000e+00 1469.0
4 TraesCS7A01G550700 chr7A 93.248 311 20 1 1101 1411 724151820 724152129 2.300000e-124 457.0
5 TraesCS7A01G550700 chr7A 79.276 608 94 18 1747 2336 724189136 724189729 5.080000e-106 396.0
6 TraesCS7A01G550700 chr7A 82.368 397 64 4 1935 2330 724152774 724153165 2.420000e-89 340.0
7 TraesCS7A01G550700 chr7A 91.257 183 14 2 3924 4104 503448861 503449043 1.510000e-61 248.0
8 TraesCS7A01G550700 chr7A 84.259 216 33 1 5829 6043 724225235 724225450 7.110000e-50 209.0
9 TraesCS7A01G550700 chr7A 87.709 179 14 4 5023 5195 724261486 724261310 1.190000e-47 202.0
10 TraesCS7A01G550700 chr7A 87.151 179 16 3 2403 2579 724258931 724258758 5.530000e-46 196.0
11 TraesCS7A01G550700 chr7A 86.813 182 16 4 5020 5195 724371305 724371484 5.530000e-46 196.0
12 TraesCS7A01G550700 chr7A 86.813 182 16 4 2400 2579 724373925 724374100 5.530000e-46 196.0
13 TraesCS7A01G550700 chr7A 79.916 239 35 6 1676 1913 724152495 724152721 5.610000e-36 163.0
14 TraesCS7A01G550700 chrUn 92.221 2211 112 26 4593 6797 87951437 87953593 0.000000e+00 3075.0
15 TraesCS7A01G550700 chrUn 93.312 1540 54 11 1583 3095 87946835 87948352 0.000000e+00 2228.0
16 TraesCS7A01G550700 chrUn 92.368 1140 51 10 3416 4553 87950103 87951208 0.000000e+00 1591.0
17 TraesCS7A01G550700 chrUn 89.594 788 28 21 803 1577 87946038 87946784 0.000000e+00 952.0
18 TraesCS7A01G550700 chrUn 78.730 677 111 20 1674 2336 92813460 92814117 8.390000e-114 422.0
19 TraesCS7A01G550700 chrUn 82.576 396 65 2 1935 2330 92801343 92801734 5.190000e-91 346.0
20 TraesCS7A01G550700 chrUn 82.143 392 66 4 1935 2323 92781432 92781822 4.040000e-87 333.0
21 TraesCS7A01G550700 chrUn 91.837 196 16 0 1215 1410 92800537 92800732 2.490000e-69 274.0
22 TraesCS7A01G550700 chrUn 80.635 315 44 10 1101 1399 333301890 333301577 1.960000e-55 228.0
23 TraesCS7A01G550700 chrUn 98.246 114 2 0 695 808 87944252 87944365 4.280000e-47 200.0
24 TraesCS7A01G550700 chrUn 86.034 179 25 0 5829 6007 92815021 92815199 7.160000e-45 193.0
25 TraesCS7A01G550700 chrUn 91.912 136 9 2 6860 6993 87953607 87953742 9.260000e-44 189.0
26 TraesCS7A01G550700 chrUn 91.304 138 12 0 1241 1378 92780585 92780722 9.260000e-44 189.0
27 TraesCS7A01G550700 chrUn 80.524 267 35 10 1101 1351 377263475 377263740 9.260000e-44 189.0
28 TraesCS7A01G550700 chrUn 86.441 177 17 3 2404 2579 87951836 87952006 3.330000e-43 187.0
29 TraesCS7A01G550700 chrUn 81.667 180 29 4 1222 1399 87936048 87936225 5.650000e-31 147.0
30 TraesCS7A01G550700 chrUn 81.657 169 13 11 3080 3245 87949950 87950103 2.650000e-24 124.0
31 TraesCS7A01G550700 chrUn 94.828 58 3 0 1101 1158 92780463 92780520 2.690000e-14 91.6
32 TraesCS7A01G550700 chr6D 90.148 203 17 2 1 202 375416248 375416448 1.930000e-65 261.0
33 TraesCS7A01G550700 chr6D 92.000 150 10 2 3772 3921 28048760 28048907 7.110000e-50 209.0
34 TraesCS7A01G550700 chr2A 90.426 188 16 2 3922 4108 475164 474978 5.420000e-61 246.0
35 TraesCS7A01G550700 chr2A 84.375 128 14 4 6838 6965 579701219 579701340 3.430000e-23 121.0
36 TraesCS7A01G550700 chr1D 89.055 201 18 3 3924 4121 397084124 397084323 5.420000e-61 246.0
37 TraesCS7A01G550700 chr1D 93.056 144 9 1 3772 3915 103032093 103032235 7.110000e-50 209.0
38 TraesCS7A01G550700 chr1B 89.340 197 18 2 1 196 572881700 572881894 1.950000e-60 244.0
39 TraesCS7A01G550700 chr1B 93.662 142 7 2 3772 3913 658920414 658920275 1.980000e-50 211.0
40 TraesCS7A01G550700 chr2D 91.209 182 11 3 3929 4108 422089737 422089559 7.010000e-60 243.0
41 TraesCS7A01G550700 chr2D 89.894 188 17 2 3922 4108 121960787 121960973 2.520000e-59 241.0
42 TraesCS7A01G550700 chr2D 89.894 188 17 2 3922 4108 181312014 181311828 2.520000e-59 241.0
43 TraesCS7A01G550700 chr5A 89.474 190 18 2 3921 4108 13350262 13350451 9.070000e-59 239.0
44 TraesCS7A01G550700 chr5D 94.444 144 7 1 3772 3915 134471210 134471352 3.280000e-53 220.0
45 TraesCS7A01G550700 chr5D 92.958 142 9 1 3772 3913 315823840 315823980 9.190000e-49 206.0
46 TraesCS7A01G550700 chr4B 93.056 144 9 1 3772 3915 461583285 461583427 7.110000e-50 209.0
47 TraesCS7A01G550700 chr4B 86.719 128 13 3 6838 6965 323869287 323869164 9.460000e-29 139.0
48 TraesCS7A01G550700 chr5B 92.414 145 10 1 3772 3916 69282779 69282636 9.190000e-49 206.0
49 TraesCS7A01G550700 chr5B 92.308 117 6 2 75 191 711341824 711341937 5.610000e-36 163.0
50 TraesCS7A01G550700 chr4D 90.789 152 12 2 3772 3922 76824521 76824371 1.190000e-47 202.0
51 TraesCS7A01G550700 chr7B 85.938 128 14 3 6838 6965 682011928 682012051 4.400000e-27 134.0
52 TraesCS7A01G550700 chr4A 100.000 29 0 0 4125 4153 300463818 300463846 4.000000e-03 54.7


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 TraesCS7A01G550700 chr7A 724368906 724375898 6992 False 12914.000000 12914 100.000000 1 6993 1 chr7A.!!$F4 6992
1 TraesCS7A01G550700 chr7A 724257214 724264371 7157 True 2394.200000 5193 93.933600 1 6744 5 chr7A.!!$R1 6743
2 TraesCS7A01G550700 chr7A 724189136 724189729 593 False 396.000000 396 79.276000 1747 2336 1 chr7A.!!$F2 589
3 TraesCS7A01G550700 chr7A 724151820 724153165 1345 False 320.000000 457 85.177333 1101 2330 3 chr7A.!!$F5 1229
4 TraesCS7A01G550700 chrUn 87944252 87953742 9490 False 1068.250000 3075 90.718875 695 6993 8 chrUn.!!$F3 6298
5 TraesCS7A01G550700 chrUn 92800537 92801734 1197 False 310.000000 346 87.206500 1215 2330 2 chrUn.!!$F5 1115
6 TraesCS7A01G550700 chrUn 92813460 92815199 1739 False 307.500000 422 82.382000 1674 6007 2 chrUn.!!$F6 4333
7 TraesCS7A01G550700 chrUn 92780463 92781822 1359 False 204.533333 333 89.425000 1101 2323 3 chrUn.!!$F4 1222

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
1644 3591 4.853924 ACACACAGAATTCCCATGTTTC 57.146 40.909 0.65 0.00 0.00 2.78 F
2715 4863 0.248661 CATAGGCAGACACGTCCTCG 60.249 60.000 0.00 0.00 43.34 4.63 F
2921 5069 1.133823 TGCCCTATCATCGCCATTGTT 60.134 47.619 0.00 0.00 0.00 2.83 F
4158 7954 1.006758 AGGGTCTGATCCAACCGTCTA 59.993 52.381 10.10 0.00 36.35 2.59 F
4533 8330 0.616111 ATCTGTCGTTGGAGAGGCCT 60.616 55.000 3.86 3.86 34.45 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3045 5193 0.105964 TTGTGGGTCTGACCTTGTCG 59.894 55.000 25.01 0.0 38.64 4.35 R
3661 7456 0.525761 GCCTGGCGCTTCAAATAACA 59.474 50.000 7.64 0.0 0.00 2.41 R
4533 8330 1.152204 TCACCCTTCGGTCTTCCCA 60.152 57.895 0.00 0.0 42.04 4.37 R
5282 9269 1.969923 ACTATCTCAGCAGCCCAGATC 59.030 52.381 6.93 0.0 0.00 2.75 R
6013 10115 3.420893 GTGATGGTGATTTCAACCTCCA 58.579 45.455 0.00 0.0 31.06 3.86 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
1644 3591 4.853924 ACACACAGAATTCCCATGTTTC 57.146 40.909 0.65 0.00 0.00 2.78
1670 3657 4.336713 GCTTTCCTATCCAGATTCAACACC 59.663 45.833 0.00 0.00 0.00 4.16
1806 3812 2.154567 ACCTAACCGCTGAGGACATA 57.845 50.000 3.87 0.00 45.00 2.29
2239 4381 5.177511 GCTCCTTGTTTTGGTATGCTTTTTC 59.822 40.000 0.00 0.00 0.00 2.29
2543 4690 5.937111 TCCCTGGTTTTATTATAGCTGGAC 58.063 41.667 0.00 0.00 34.08 4.02
2715 4863 0.248661 CATAGGCAGACACGTCCTCG 60.249 60.000 0.00 0.00 43.34 4.63
2744 4892 1.260544 GCAAAGGCCCAGTTTGATCT 58.739 50.000 17.63 0.00 37.10 2.75
2775 4923 1.891150 CCAGCAGCATGGAAAGAAACT 59.109 47.619 5.22 0.00 43.57 2.66
2828 4976 5.481105 CATGTGTTTTGGCCTCATACAAAT 58.519 37.500 3.32 0.99 36.57 2.32
2921 5069 1.133823 TGCCCTATCATCGCCATTGTT 60.134 47.619 0.00 0.00 0.00 2.83
3045 5193 1.134670 ACTTGCCTATCAGCTCCGAAC 60.135 52.381 0.00 0.00 0.00 3.95
3097 6858 5.227569 TCTGCAATCCTTTTGTCAGTAGA 57.772 39.130 0.00 0.00 0.00 2.59
3187 6982 5.697473 TCAGCTTATAGTAGCACTGCTAG 57.303 43.478 11.19 1.57 42.11 3.42
3198 6993 2.099921 AGCACTGCTAGTTAGTCATCGG 59.900 50.000 0.21 0.00 36.99 4.18
3200 6995 3.696898 CACTGCTAGTTAGTCATCGGTC 58.303 50.000 0.00 0.00 0.00 4.79
3239 7034 5.746990 AGTTCTGTTCCTTATAGCACTGT 57.253 39.130 0.00 0.00 0.00 3.55
3264 7059 5.004440 CGTGTGGTAATTGATCTAGTGTTCG 59.996 44.000 0.00 0.00 0.00 3.95
3331 7126 6.283694 TGTCTAGCTAAACTCTATTGCCATG 58.716 40.000 0.00 0.00 0.00 3.66
3412 7207 7.168219 TGCACCTAGTACTTTTCATTTGATCT 58.832 34.615 0.00 0.00 0.00 2.75
3676 7471 1.926510 GGCAATGTTATTTGAAGCGCC 59.073 47.619 2.29 0.00 0.00 6.53
3761 7556 3.927142 GCTTAAGCATCTTGTACAGACGT 59.073 43.478 22.59 0.00 41.59 4.34
3762 7557 4.389077 GCTTAAGCATCTTGTACAGACGTT 59.611 41.667 22.59 0.00 41.59 3.99
3838 7633 5.014202 TCTATTTCCTACAAACCAAAGGGC 58.986 41.667 0.00 0.00 37.90 5.19
4024 7820 4.965200 AGGCTTGATTCCTATCCTACAC 57.035 45.455 0.00 0.00 30.79 2.90
4158 7954 1.006758 AGGGTCTGATCCAACCGTCTA 59.993 52.381 10.10 0.00 36.35 2.59
4170 7966 1.330655 ACCGTCTATGCTGGACCCAG 61.331 60.000 11.59 11.59 46.15 4.45
4355 8151 3.297620 GCCAAGCACCACACCCAG 61.298 66.667 0.00 0.00 0.00 4.45
4533 8330 0.616111 ATCTGTCGTTGGAGAGGCCT 60.616 55.000 3.86 3.86 34.45 5.19
4680 8666 1.257750 TGCCGCCAAGCTCTTCTCTA 61.258 55.000 0.00 0.00 0.00 2.43
5066 9052 5.770685 AGAGCCTTACCTTGAGAAGAAAT 57.229 39.130 0.00 0.00 0.00 2.17
5282 9269 1.891150 AGCAGCCCATTGAACAAAGAG 59.109 47.619 0.00 0.00 0.00 2.85
6013 10115 8.548877 ACATAGGATGTGAATTGGTACTAGTTT 58.451 33.333 0.00 0.00 43.01 2.66
6054 10156 3.002656 CACGAGTGATGACATAAATGCCC 59.997 47.826 0.00 0.00 0.00 5.36
6281 10383 2.344025 CCTACAGTTTAGGGCGTTGTC 58.656 52.381 0.00 0.00 0.00 3.18
6360 10462 0.746923 GGGGCGTAATCCTCACCAAC 60.747 60.000 0.00 0.00 0.00 3.77
6454 10557 9.840427 AACAGCACAATATCTTGTTTATGTAAC 57.160 29.630 0.00 0.00 43.05 2.50
6470 10573 9.908152 GTTTATGTAACTGCTTTTTAGTTCCAT 57.092 29.630 0.00 0.00 38.03 3.41
6565 10668 0.785979 GCATGTTTGCTTCCGCTTTG 59.214 50.000 0.00 0.00 45.77 2.77
6633 10738 6.441093 AATAAATGTCAGCATCACGTCATT 57.559 33.333 0.00 0.00 33.50 2.57
6634 10739 3.752412 AATGTCAGCATCACGTCATTG 57.248 42.857 0.00 0.00 33.50 2.82
6656 10767 5.012893 TGAGAGAAGTTCAGCTACATCTCA 58.987 41.667 19.02 15.30 42.43 3.27
6657 10768 5.478332 TGAGAGAAGTTCAGCTACATCTCAA 59.522 40.000 19.02 8.22 42.43 3.02
6658 10769 6.015095 TGAGAGAAGTTCAGCTACATCTCAAA 60.015 38.462 19.02 7.95 42.43 2.69
6659 10770 6.162777 AGAGAAGTTCAGCTACATCTCAAAC 58.837 40.000 19.02 0.00 42.43 2.93
6660 10771 6.014669 AGAGAAGTTCAGCTACATCTCAAACT 60.015 38.462 19.02 1.70 42.43 2.66
6689 10800 6.929625 TCAGTTCACTAGATGGAAGAAAGAG 58.070 40.000 0.00 0.00 0.00 2.85
6745 10856 9.512588 AGATTCCAAATTATGATCTATGTCACC 57.487 33.333 0.00 0.00 0.00 4.02
6746 10857 8.641498 ATTCCAAATTATGATCTATGTCACCC 57.359 34.615 0.00 0.00 0.00 4.61
6771 10882 6.265577 CCAAGGCATTTACTAACATAACTGC 58.734 40.000 0.00 0.00 39.02 4.40
6773 10884 6.436843 AGGCATTTACTAACATAACTGCAC 57.563 37.500 9.24 1.44 40.59 4.57
6793 10904 6.257423 TGCACGAGCTATTTTGTTGATTATG 58.743 36.000 6.36 0.00 42.74 1.90
6797 10908 6.968904 ACGAGCTATTTTGTTGATTATGCAAG 59.031 34.615 0.00 0.00 0.00 4.01
6798 10909 6.075205 CGAGCTATTTTGTTGATTATGCAAGC 60.075 38.462 0.00 0.00 0.00 4.01
6799 10910 6.870769 AGCTATTTTGTTGATTATGCAAGCT 58.129 32.000 0.00 0.00 0.00 3.74
6800 10911 7.325694 AGCTATTTTGTTGATTATGCAAGCTT 58.674 30.769 0.00 0.00 0.00 3.74
6801 10912 7.277098 AGCTATTTTGTTGATTATGCAAGCTTG 59.723 33.333 22.44 22.44 0.00 4.01
6802 10913 7.063780 GCTATTTTGTTGATTATGCAAGCTTGT 59.936 33.333 26.55 11.36 0.00 3.16
6804 10915 8.830201 ATTTTGTTGATTATGCAAGCTTGTTA 57.170 26.923 26.55 16.74 0.00 2.41
6805 10916 8.830201 TTTTGTTGATTATGCAAGCTTGTTAT 57.170 26.923 26.55 21.70 0.00 1.89
6806 10917 9.920133 TTTTGTTGATTATGCAAGCTTGTTATA 57.080 25.926 26.55 20.78 0.00 0.98
6807 10918 9.920133 TTTGTTGATTATGCAAGCTTGTTATAA 57.080 25.926 26.55 26.29 0.00 0.98
6809 10920 7.973388 TGTTGATTATGCAAGCTTGTTATAACC 59.027 33.333 26.31 21.65 0.00 2.85
6810 10921 7.038154 TGATTATGCAAGCTTGTTATAACCC 57.962 36.000 26.31 22.31 0.00 4.11
6811 10922 5.493133 TTATGCAAGCTTGTTATAACCCG 57.507 39.130 26.55 5.19 0.00 5.28
6812 10923 1.470890 TGCAAGCTTGTTATAACCCGC 59.529 47.619 26.55 14.06 0.00 6.13
6813 10924 1.743394 GCAAGCTTGTTATAACCCGCT 59.257 47.619 26.55 17.93 35.74 5.52
6814 10925 2.477863 GCAAGCTTGTTATAACCCGCTG 60.478 50.000 26.55 17.62 34.87 5.18
6815 10926 3.006940 CAAGCTTGTTATAACCCGCTGA 58.993 45.455 21.97 0.00 34.87 4.26
6816 10927 3.560636 AGCTTGTTATAACCCGCTGAT 57.439 42.857 21.11 4.93 33.87 2.90
6817 10928 4.682778 AGCTTGTTATAACCCGCTGATA 57.317 40.909 21.11 0.00 33.87 2.15
6818 10929 4.632153 AGCTTGTTATAACCCGCTGATAG 58.368 43.478 21.11 6.08 33.87 2.08
6819 10930 3.746492 GCTTGTTATAACCCGCTGATAGG 59.254 47.826 13.01 0.00 0.00 2.57
6820 10931 4.502604 GCTTGTTATAACCCGCTGATAGGA 60.503 45.833 13.01 0.00 0.00 2.94
6821 10932 5.607477 CTTGTTATAACCCGCTGATAGGAA 58.393 41.667 13.01 0.00 0.00 3.36
6822 10933 5.617528 TGTTATAACCCGCTGATAGGAAA 57.382 39.130 13.01 0.00 0.00 3.13
6823 10934 5.991861 TGTTATAACCCGCTGATAGGAAAA 58.008 37.500 13.01 0.00 0.00 2.29
6824 10935 5.818857 TGTTATAACCCGCTGATAGGAAAAC 59.181 40.000 13.01 0.00 0.00 2.43
6825 10936 2.871096 AACCCGCTGATAGGAAAACA 57.129 45.000 0.00 0.00 0.00 2.83
6826 10937 3.366052 AACCCGCTGATAGGAAAACAT 57.634 42.857 0.00 0.00 0.00 2.71
6827 10938 4.497291 AACCCGCTGATAGGAAAACATA 57.503 40.909 0.00 0.00 0.00 2.29
6828 10939 4.497291 ACCCGCTGATAGGAAAACATAA 57.503 40.909 0.00 0.00 0.00 1.90
6829 10940 4.850680 ACCCGCTGATAGGAAAACATAAA 58.149 39.130 0.00 0.00 0.00 1.40
6830 10941 4.638865 ACCCGCTGATAGGAAAACATAAAC 59.361 41.667 0.00 0.00 0.00 2.01
6831 10942 4.638421 CCCGCTGATAGGAAAACATAAACA 59.362 41.667 0.00 0.00 0.00 2.83
6832 10943 5.124776 CCCGCTGATAGGAAAACATAAACAA 59.875 40.000 0.00 0.00 0.00 2.83
6833 10944 6.027749 CCGCTGATAGGAAAACATAAACAAC 58.972 40.000 0.00 0.00 0.00 3.32
6834 10945 6.128007 CCGCTGATAGGAAAACATAAACAACT 60.128 38.462 0.00 0.00 0.00 3.16
6835 10946 7.065324 CCGCTGATAGGAAAACATAAACAACTA 59.935 37.037 0.00 0.00 0.00 2.24
6836 10947 8.447833 CGCTGATAGGAAAACATAAACAACTAA 58.552 33.333 0.00 0.00 0.00 2.24
6837 10948 9.556030 GCTGATAGGAAAACATAAACAACTAAC 57.444 33.333 0.00 0.00 0.00 2.34
6839 10950 9.016438 TGATAGGAAAACATAAACAACTAACCC 57.984 33.333 0.00 0.00 0.00 4.11
6840 10951 6.659745 AGGAAAACATAAACAACTAACCCC 57.340 37.500 0.00 0.00 0.00 4.95
6841 10952 6.137559 AGGAAAACATAAACAACTAACCCCA 58.862 36.000 0.00 0.00 0.00 4.96
6842 10953 6.785466 AGGAAAACATAAACAACTAACCCCAT 59.215 34.615 0.00 0.00 0.00 4.00
6843 10954 7.291416 AGGAAAACATAAACAACTAACCCCATT 59.709 33.333 0.00 0.00 0.00 3.16
6844 10955 7.934665 GGAAAACATAAACAACTAACCCCATTT 59.065 33.333 0.00 0.00 0.00 2.32
6845 10956 8.669946 AAAACATAAACAACTAACCCCATTTG 57.330 30.769 0.00 0.00 0.00 2.32
6846 10957 6.353404 ACATAAACAACTAACCCCATTTGG 57.647 37.500 0.00 0.00 0.00 3.28
6847 10958 5.841783 ACATAAACAACTAACCCCATTTGGT 59.158 36.000 0.00 0.00 41.55 3.67
6848 10959 7.011382 ACATAAACAACTAACCCCATTTGGTA 58.989 34.615 0.00 0.00 37.76 3.25
6849 10960 7.177744 ACATAAACAACTAACCCCATTTGGTAG 59.822 37.037 0.00 0.00 37.76 3.18
6850 10961 3.427573 ACAACTAACCCCATTTGGTAGC 58.572 45.455 0.00 0.00 37.76 3.58
6851 10962 3.075432 ACAACTAACCCCATTTGGTAGCT 59.925 43.478 0.00 0.00 37.76 3.32
6852 10963 3.646736 ACTAACCCCATTTGGTAGCTC 57.353 47.619 0.00 0.00 37.76 4.09
6853 10964 2.916934 ACTAACCCCATTTGGTAGCTCA 59.083 45.455 0.00 0.00 37.76 4.26
6854 10965 2.514458 AACCCCATTTGGTAGCTCAG 57.486 50.000 0.00 0.00 37.76 3.35
6855 10966 1.372501 ACCCCATTTGGTAGCTCAGT 58.627 50.000 0.00 0.00 36.67 3.41
6856 10967 1.710809 ACCCCATTTGGTAGCTCAGTT 59.289 47.619 0.00 0.00 36.67 3.16
6857 10968 2.110011 ACCCCATTTGGTAGCTCAGTTT 59.890 45.455 0.00 0.00 36.67 2.66
6947 11058 3.835978 TGGCTGCCACTAGAAACTAGTAA 59.164 43.478 19.30 0.00 0.00 2.24
6979 11090 7.578310 ATGCTGCATTCCATGGTATAATATC 57.422 36.000 12.58 1.12 0.00 1.63
6982 11093 7.121611 TGCTGCATTCCATGGTATAATATCTTG 59.878 37.037 12.58 0.00 0.00 3.02
6985 11096 9.181061 TGCATTCCATGGTATAATATCTTGATG 57.819 33.333 12.58 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
606 608 6.369890 TGTTGCTCTTGTTGTTTGCATTTTAA 59.630 30.769 0.00 0.00 33.50 1.52
1644 3591 3.797039 TGAATCTGGATAGGAAAGCACG 58.203 45.455 0.00 0.00 0.00 5.34
1670 3657 3.002246 CCCATCGACAATTTACATGGACG 59.998 47.826 0.00 0.00 36.84 4.79
2239 4381 7.280876 ACATAATACATAATAAGGCAGGCATCG 59.719 37.037 0.00 0.00 0.00 3.84
2543 4690 2.282462 GGAGGGGCACACCAACAG 60.282 66.667 0.00 0.00 42.91 3.16
2744 4892 1.452651 GCTGCTGGCTTGGCTATCA 60.453 57.895 0.00 0.00 38.06 2.15
2775 4923 3.176411 TCTGCTTTCCTCCTCATCTGAA 58.824 45.455 0.00 0.00 0.00 3.02
2921 5069 1.377202 GGAACCAGCAGCGATTCCA 60.377 57.895 16.41 0.00 40.38 3.53
3045 5193 0.105964 TTGTGGGTCTGACCTTGTCG 59.894 55.000 25.01 0.00 38.64 4.35
3097 6858 1.528309 CCAGCAACGGACAACCCTT 60.528 57.895 0.00 0.00 0.00 3.95
3187 6982 3.800506 CCAAATACCGACCGATGACTAAC 59.199 47.826 0.00 0.00 0.00 2.34
3198 6993 6.750963 CAGAACTAGTACTTCCAAATACCGAC 59.249 42.308 0.00 0.00 0.00 4.79
3200 6995 6.628185 ACAGAACTAGTACTTCCAAATACCG 58.372 40.000 0.00 0.00 0.00 4.02
3239 7034 5.654603 ACACTAGATCAATTACCACACGA 57.345 39.130 0.00 0.00 0.00 4.35
3264 7059 2.508526 ACTTGACCAATTGGCTCAGTC 58.491 47.619 24.79 14.14 39.32 3.51
3331 7126 9.516314 GGTATCATAACTTTAGTTTCAATTGGC 57.484 33.333 5.42 0.00 39.31 4.52
3587 7382 9.620660 CGTGTGTGTGTGTGTGTATATATATAT 57.379 33.333 10.10 10.10 0.00 0.86
3588 7383 8.623030 ACGTGTGTGTGTGTGTGTATATATATA 58.377 33.333 0.00 0.00 0.00 0.86
3589 7384 7.485810 ACGTGTGTGTGTGTGTGTATATATAT 58.514 34.615 0.00 0.00 0.00 0.86
3591 7386 5.716094 ACGTGTGTGTGTGTGTGTATATAT 58.284 37.500 0.00 0.00 0.00 0.86
3593 7388 3.985008 ACGTGTGTGTGTGTGTGTATAT 58.015 40.909 0.00 0.00 0.00 0.86
3595 7390 2.303163 ACGTGTGTGTGTGTGTGTAT 57.697 45.000 0.00 0.00 0.00 2.29
3597 7392 1.930503 CATACGTGTGTGTGTGTGTGT 59.069 47.619 3.83 0.00 33.01 3.72
3598 7393 1.332816 GCATACGTGTGTGTGTGTGTG 60.333 52.381 14.10 0.00 39.23 3.82
3599 7394 0.934496 GCATACGTGTGTGTGTGTGT 59.066 50.000 14.10 0.00 39.23 3.72
3600 7395 0.933796 TGCATACGTGTGTGTGTGTG 59.066 50.000 14.10 0.00 39.23 3.82
3603 7398 1.999735 GCTATGCATACGTGTGTGTGT 59.000 47.619 14.10 0.87 39.23 3.72
3604 7399 1.327460 GGCTATGCATACGTGTGTGTG 59.673 52.381 14.10 3.73 39.93 3.82
3606 7401 1.939974 AGGCTATGCATACGTGTGTG 58.060 50.000 14.10 3.76 0.00 3.82
3607 7402 2.691409 AAGGCTATGCATACGTGTGT 57.309 45.000 14.10 0.00 0.00 3.72
3608 7403 3.494626 CCTTAAGGCTATGCATACGTGTG 59.505 47.826 9.00 8.09 0.00 3.82
3610 7405 3.990092 TCCTTAAGGCTATGCATACGTG 58.010 45.455 17.32 0.00 34.44 4.49
3611 7406 4.377897 GTTCCTTAAGGCTATGCATACGT 58.622 43.478 17.32 0.00 34.44 3.57
3612 7407 3.746492 GGTTCCTTAAGGCTATGCATACG 59.254 47.826 17.32 0.70 34.44 3.06
3661 7456 0.525761 GCCTGGCGCTTCAAATAACA 59.474 50.000 7.64 0.00 0.00 2.41
3693 7488 3.053828 GCACAAAGCAGTGGCCAT 58.946 55.556 9.72 0.00 44.79 4.40
3761 7556 4.000325 CTCCACATTTCATGTCCGTACAA 59.000 43.478 0.00 0.00 42.70 2.41
3762 7557 3.595173 CTCCACATTTCATGTCCGTACA 58.405 45.455 0.00 0.00 42.70 2.90
3876 7672 7.097192 GGTTTGGAGGAATTTTGTAGGAATTC 58.903 38.462 0.00 0.00 40.88 2.17
4038 7834 4.090819 GGGCCTTTTGGTTTGTAGGAATA 58.909 43.478 0.84 0.00 42.99 1.75
4170 7966 3.328505 CATGGATGGGTCAAACAAAAGC 58.671 45.455 0.00 0.00 0.00 3.51
4172 7968 2.971330 AGCATGGATGGGTCAAACAAAA 59.029 40.909 0.00 0.00 0.00 2.44
4355 8151 1.234615 CCGTGTGGTGTGGTCAATCC 61.235 60.000 0.00 0.00 0.00 3.01
4533 8330 1.152204 TCACCCTTCGGTCTTCCCA 60.152 57.895 0.00 0.00 42.04 4.37
4549 8346 4.689549 TCCCCCTTCGCCGTCTCA 62.690 66.667 0.00 0.00 0.00 3.27
4558 8355 2.069430 CCTCAGCTCCTCCCCCTTC 61.069 68.421 0.00 0.00 0.00 3.46
4680 8666 1.815421 GCTCGGGACACATTCGCAT 60.815 57.895 0.00 0.00 36.99 4.73
4888 8874 7.024768 TGAACTAAGCGCCACAAAAATTATAC 58.975 34.615 2.29 0.00 0.00 1.47
5004 8990 2.856222 CCTCAAGGGCCAATCTACATC 58.144 52.381 6.18 0.00 0.00 3.06
5282 9269 1.969923 ACTATCTCAGCAGCCCAGATC 59.030 52.381 6.93 0.00 0.00 2.75
6013 10115 3.420893 GTGATGGTGATTTCAACCTCCA 58.579 45.455 0.00 0.00 31.06 3.86
6281 10383 9.910511 GCATATTTTGATTTCAAACTAGCATTG 57.089 29.630 5.26 3.11 44.56 2.82
6360 10462 4.670221 GCAGAAACATTAGACAAAGGCTCG 60.670 45.833 0.00 0.00 0.00 5.03
6454 10557 5.221422 TGTGGGAAATGGAACTAAAAAGCAG 60.221 40.000 0.00 0.00 0.00 4.24
6459 10562 8.267894 TCAATTTTGTGGGAAATGGAACTAAAA 58.732 29.630 0.00 0.00 28.46 1.52
6565 10668 2.017049 AGGGCAAATCGCTGAATGTAC 58.983 47.619 0.00 0.00 41.91 2.90
6633 10738 5.012893 TGAGATGTAGCTGAACTTCTCTCA 58.987 41.667 23.00 16.78 44.76 3.27
6634 10739 5.574891 TGAGATGTAGCTGAACTTCTCTC 57.425 43.478 23.00 15.17 44.76 3.20
6656 10767 7.963532 TCCATCTAGTGAACTGAGTTTAGTTT 58.036 34.615 0.00 0.00 40.78 2.66
6657 10768 7.540474 TCCATCTAGTGAACTGAGTTTAGTT 57.460 36.000 0.00 0.00 43.24 2.24
6658 10769 7.451877 TCTTCCATCTAGTGAACTGAGTTTAGT 59.548 37.037 0.00 0.40 0.00 2.24
6659 10770 7.831753 TCTTCCATCTAGTGAACTGAGTTTAG 58.168 38.462 0.00 0.00 0.00 1.85
6660 10771 7.776618 TCTTCCATCTAGTGAACTGAGTTTA 57.223 36.000 0.00 0.00 0.00 2.01
6689 10800 9.274206 GGAAACTGTTATCCTATTAATGGAGAC 57.726 37.037 0.00 7.87 36.99 3.36
6745 10856 5.891551 AGTTATGTTAGTAAATGCCTTGGGG 59.108 40.000 0.00 0.00 0.00 4.96
6746 10857 6.680378 GCAGTTATGTTAGTAAATGCCTTGGG 60.680 42.308 7.59 0.00 45.06 4.12
6771 10882 6.257423 TGCATAATCAACAAAATAGCTCGTG 58.743 36.000 0.00 0.00 0.00 4.35
6773 10884 6.075205 GCTTGCATAATCAACAAAATAGCTCG 60.075 38.462 0.00 0.00 0.00 5.03
6793 10904 1.743394 AGCGGGTTATAACAAGCTTGC 59.257 47.619 26.27 8.60 39.12 4.01
6797 10908 3.746492 CCTATCAGCGGGTTATAACAAGC 59.254 47.826 20.23 20.23 34.51 4.01
6798 10909 5.209818 TCCTATCAGCGGGTTATAACAAG 57.790 43.478 17.16 10.83 0.00 3.16
6799 10910 5.617528 TTCCTATCAGCGGGTTATAACAA 57.382 39.130 17.16 0.00 0.00 2.83
6800 10911 5.617528 TTTCCTATCAGCGGGTTATAACA 57.382 39.130 17.16 0.00 0.00 2.41
6801 10912 5.818857 TGTTTTCCTATCAGCGGGTTATAAC 59.181 40.000 7.09 7.09 0.00 1.89
6802 10913 5.991861 TGTTTTCCTATCAGCGGGTTATAA 58.008 37.500 0.00 0.00 0.00 0.98
6804 10915 4.497291 TGTTTTCCTATCAGCGGGTTAT 57.503 40.909 0.00 0.00 0.00 1.89
6805 10916 3.985019 TGTTTTCCTATCAGCGGGTTA 57.015 42.857 0.00 0.00 0.00 2.85
6806 10917 2.871096 TGTTTTCCTATCAGCGGGTT 57.129 45.000 0.00 0.00 0.00 4.11
6807 10918 4.497291 TTATGTTTTCCTATCAGCGGGT 57.503 40.909 0.00 0.00 0.00 5.28
6809 10920 5.811399 TGTTTATGTTTTCCTATCAGCGG 57.189 39.130 0.00 0.00 0.00 5.52
6810 10921 6.842163 AGTTGTTTATGTTTTCCTATCAGCG 58.158 36.000 0.00 0.00 0.00 5.18
6811 10922 9.556030 GTTAGTTGTTTATGTTTTCCTATCAGC 57.444 33.333 0.00 0.00 0.00 4.26
6813 10924 9.016438 GGGTTAGTTGTTTATGTTTTCCTATCA 57.984 33.333 0.00 0.00 0.00 2.15
6814 10925 8.464404 GGGGTTAGTTGTTTATGTTTTCCTATC 58.536 37.037 0.00 0.00 0.00 2.08
6815 10926 7.951245 TGGGGTTAGTTGTTTATGTTTTCCTAT 59.049 33.333 0.00 0.00 0.00 2.57
6816 10927 7.296098 TGGGGTTAGTTGTTTATGTTTTCCTA 58.704 34.615 0.00 0.00 0.00 2.94
6817 10928 6.137559 TGGGGTTAGTTGTTTATGTTTTCCT 58.862 36.000 0.00 0.00 0.00 3.36
6818 10929 6.408107 TGGGGTTAGTTGTTTATGTTTTCC 57.592 37.500 0.00 0.00 0.00 3.13
6819 10930 8.769891 CAAATGGGGTTAGTTGTTTATGTTTTC 58.230 33.333 0.00 0.00 0.00 2.29
6820 10931 7.717436 CCAAATGGGGTTAGTTGTTTATGTTTT 59.283 33.333 0.00 0.00 0.00 2.43
6821 10932 7.147461 ACCAAATGGGGTTAGTTGTTTATGTTT 60.147 33.333 4.17 0.00 42.91 2.83
6822 10933 6.327887 ACCAAATGGGGTTAGTTGTTTATGTT 59.672 34.615 4.17 0.00 42.91 2.71
6823 10934 5.841783 ACCAAATGGGGTTAGTTGTTTATGT 59.158 36.000 4.17 0.00 42.91 2.29
6824 10935 6.353404 ACCAAATGGGGTTAGTTGTTTATG 57.647 37.500 4.17 0.00 42.91 1.90
6825 10936 6.153851 GCTACCAAATGGGGTTAGTTGTTTAT 59.846 38.462 4.17 0.00 42.42 1.40
6826 10937 5.477637 GCTACCAAATGGGGTTAGTTGTTTA 59.522 40.000 4.17 0.00 42.42 2.01
6827 10938 4.282449 GCTACCAAATGGGGTTAGTTGTTT 59.718 41.667 4.17 0.00 42.42 2.83
6828 10939 3.830178 GCTACCAAATGGGGTTAGTTGTT 59.170 43.478 4.17 0.00 42.42 2.83
6829 10940 3.075432 AGCTACCAAATGGGGTTAGTTGT 59.925 43.478 4.17 0.00 42.42 3.32
6830 10941 3.694566 GAGCTACCAAATGGGGTTAGTTG 59.305 47.826 4.17 0.00 42.42 3.16
6831 10942 3.332485 TGAGCTACCAAATGGGGTTAGTT 59.668 43.478 4.17 0.00 42.42 2.24
6832 10943 2.916934 TGAGCTACCAAATGGGGTTAGT 59.083 45.455 4.17 0.00 42.42 2.24
6833 10944 3.054361 ACTGAGCTACCAAATGGGGTTAG 60.054 47.826 4.17 1.91 42.42 2.34
6834 10945 2.916934 ACTGAGCTACCAAATGGGGTTA 59.083 45.455 4.17 0.00 42.42 2.85
6835 10946 1.710809 ACTGAGCTACCAAATGGGGTT 59.289 47.619 4.17 0.00 42.42 4.11
6836 10947 1.372501 ACTGAGCTACCAAATGGGGT 58.627 50.000 4.17 0.00 45.10 4.95
6837 10948 2.514458 AACTGAGCTACCAAATGGGG 57.486 50.000 4.17 0.00 42.91 4.96
6838 10949 4.871933 AAAAACTGAGCTACCAAATGGG 57.128 40.909 4.17 0.00 44.81 4.00
6863 10974 9.924650 AAAACTGTAGTATTCTCACGATACTTT 57.075 29.630 2.51 0.00 33.62 2.66
6896 11007 8.405531 CACCTCATGGTAATTAAAACTATGGTG 58.594 37.037 13.93 11.92 46.60 4.17
6957 11068 7.337689 TCAAGATATTATACCATGGAATGCAGC 59.662 37.037 21.47 1.36 44.97 5.25


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

AutoCloner maintained by Alex Coulton.