Multiple sequence alignment - TraesCS3B01G397700

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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 TraesCS3B01G397700 chr3B 100.000 8117 0 0 1 8117 627926427 627918311 0.000000e+00 14990.0
1 TraesCS3B01G397700 chr3B 87.486 887 91 12 2233 3106 627923919 627923040 0.000000e+00 1005.0
2 TraesCS3B01G397700 chr3B 87.486 887 91 12 2509 3388 627924195 627923322 0.000000e+00 1005.0
3 TraesCS3B01G397700 chr3B 78.560 1236 185 38 2176 3392 627923561 627922387 0.000000e+00 741.0
4 TraesCS3B01G397700 chr3B 79.938 972 125 34 3136 4057 627924254 627923303 0.000000e+00 651.0
5 TraesCS3B01G397700 chr3B 75.799 1376 235 42 2176 3508 627923837 627922517 2.510000e-169 606.0
6 TraesCS3B01G397700 chr3B 75.817 1377 233 41 2591 3911 627924252 627922920 2.510000e-169 606.0
7 TraesCS3B01G397700 chr3B 82.292 672 101 11 2729 3392 627924252 627923591 4.250000e-157 566.0
8 TraesCS3B01G397700 chr3B 82.399 642 89 12 3451 4073 627924195 627923559 9.270000e-149 538.0
9 TraesCS3B01G397700 chr3B 98.953 191 2 0 5285 5475 226085871 226085681 7.800000e-90 342.0
10 TraesCS3B01G397700 chr3B 77.857 560 74 24 3284 3798 627922909 627922355 1.320000e-77 302.0
11 TraesCS3B01G397700 chr3B 100.000 29 0 0 6673 6701 627919698 627919670 4.000000e-03 54.7
12 TraesCS3B01G397700 chr3B 100.000 29 0 0 6730 6758 627919755 627919727 4.000000e-03 54.7
13 TraesCS3B01G397700 chr3A 91.071 2307 105 38 5473 7741 614798790 614796547 0.000000e+00 3025.0
14 TraesCS3B01G397700 chr3A 87.525 1507 158 24 1736 3229 614801683 614800194 0.000000e+00 1714.0
15 TraesCS3B01G397700 chr3A 93.673 1138 48 18 590 1716 614803177 614802053 0.000000e+00 1681.0
16 TraesCS3B01G397700 chr3A 91.468 879 47 4 4078 4930 614799901 614799025 0.000000e+00 1182.0
17 TraesCS3B01G397700 chr3A 84.934 1062 121 16 2452 3485 614801244 614800194 0.000000e+00 1038.0
18 TraesCS3B01G397700 chr3A 82.243 1070 121 32 2729 3748 614801244 614800194 0.000000e+00 859.0
19 TraesCS3B01G397700 chr3A 90.728 604 55 1 1 603 614803795 614803192 0.000000e+00 804.0
20 TraesCS3B01G397700 chr3A 81.663 938 142 26 2169 3091 614801116 614800194 0.000000e+00 752.0
21 TraesCS3B01G397700 chr3A 81.073 951 109 31 3136 4035 614801246 614800316 0.000000e+00 693.0
22 TraesCS3B01G397700 chr3A 78.128 1079 189 32 2314 3373 614801244 614800194 6.870000e-180 641.0
23 TraesCS3B01G397700 chr3A 77.570 1070 173 38 2867 3888 614801244 614800194 1.170000e-162 584.0
24 TraesCS3B01G397700 chr3A 77.243 1081 172 45 2994 4023 614801251 614800194 4.250000e-157 566.0
25 TraesCS3B01G397700 chr3A 81.846 650 88 19 3451 4080 614801186 614800547 3.360000e-143 520.0
26 TraesCS3B01G397700 chr3A 94.052 269 14 2 3825 4091 614800194 614799926 2.730000e-109 407.0
27 TraesCS3B01G397700 chr3A 98.370 184 3 0 4923 5106 642038746 642038929 2.830000e-84 324.0
28 TraesCS3B01G397700 chr3A 95.980 199 3 5 4905 5103 320441042 320440849 1.310000e-82 318.0
29 TraesCS3B01G397700 chr3A 85.113 309 13 8 7814 8089 614796517 614796209 1.330000e-72 285.0
30 TraesCS3B01G397700 chr3A 97.959 147 3 0 5104 5250 614799042 614798896 1.050000e-63 255.0
31 TraesCS3B01G397700 chr3A 100.000 39 0 0 5249 5287 614798821 614798783 1.130000e-08 73.1
32 TraesCS3B01G397700 chr3A 100.000 29 0 0 6730 6758 614797589 614797561 4.000000e-03 54.7
33 TraesCS3B01G397700 chr3D 94.422 1721 75 10 5473 7185 472441891 472440184 0.000000e+00 2627.0
34 TraesCS3B01G397700 chr3D 91.273 1822 101 31 1 1809 472447195 472445419 0.000000e+00 2431.0
35 TraesCS3B01G397700 chr3D 84.786 2123 229 50 1736 3798 472445303 472443215 0.000000e+00 2045.0
36 TraesCS3B01G397700 chr3D 87.798 1680 155 28 2452 4091 472444866 472443197 0.000000e+00 1921.0
37 TraesCS3B01G397700 chr3D 83.157 1229 163 28 2176 3388 472444450 472443250 0.000000e+00 1083.0
38 TraesCS3B01G397700 chr3D 81.129 1399 183 36 2729 4071 472444866 472443493 0.000000e+00 1046.0
39 TraesCS3B01G397700 chr3D 91.586 725 35 7 4231 4930 472442849 472442126 0.000000e+00 977.0
40 TraesCS3B01G397700 chr3D 81.500 1227 193 26 2174 3388 472444730 472443526 0.000000e+00 977.0
41 TraesCS3B01G397700 chr3D 77.146 1689 285 65 2314 3938 472444866 472443215 0.000000e+00 887.0
42 TraesCS3B01G397700 chr3D 84.275 903 120 12 2233 3125 472444121 472443231 0.000000e+00 861.0
43 TraesCS3B01G397700 chr3D 83.816 933 51 36 7204 8089 472438562 472437683 0.000000e+00 795.0
44 TraesCS3B01G397700 chr3D 78.183 1233 221 39 2176 3388 472444589 472443385 0.000000e+00 743.0
45 TraesCS3B01G397700 chr3D 77.699 1269 204 40 2867 4080 472444866 472443622 0.000000e+00 702.0
46 TraesCS3B01G397700 chr3D 80.693 953 110 35 3136 4035 472444868 472443937 0.000000e+00 673.0
47 TraesCS3B01G397700 chr3D 77.542 1131 178 43 2994 4073 472444873 472443768 5.380000e-171 612.0
48 TraesCS3B01G397700 chr3D 83.136 676 100 10 2200 2869 472443882 472443215 9.010000e-169 604.0
49 TraesCS3B01G397700 chr3D 82.462 650 85 20 3451 4080 472444808 472444168 7.170000e-150 542.0
50 TraesCS3B01G397700 chr3D 82.268 485 65 10 182 655 472449400 472448926 4.560000e-107 399.0
51 TraesCS3B01G397700 chr3D 75.858 816 158 30 2591 3388 472444866 472444072 5.950000e-101 379.0
52 TraesCS3B01G397700 chr3D 94.558 147 8 0 5104 5250 472442143 472441997 2.280000e-55 228.0
53 TraesCS3B01G397700 chr3D 89.091 165 9 3 4078 4234 472443172 472443009 6.430000e-46 196.0
54 TraesCS3B01G397700 chr3D 100.000 39 0 0 5249 5287 472441922 472441884 1.130000e-08 73.1
55 TraesCS3B01G397700 chr3D 100.000 29 0 0 6673 6701 472440640 472440612 4.000000e-03 54.7
56 TraesCS3B01G397700 chr3D 100.000 29 0 0 6730 6758 472440697 472440669 4.000000e-03 54.7
57 TraesCS3B01G397700 chr4D 97.525 202 5 0 5277 5478 21754141 21753940 6.030000e-91 346.0
58 TraesCS3B01G397700 chr5D 98.930 187 2 0 5286 5472 236022596 236022782 1.310000e-87 335.0
59 TraesCS3B01G397700 chr5D 98.930 187 2 0 5286 5472 439892985 439893171 1.310000e-87 335.0
60 TraesCS3B01G397700 chr2D 98.930 187 2 0 5286 5472 154547365 154547179 1.310000e-87 335.0
61 TraesCS3B01G397700 chr1D 98.930 187 2 0 5286 5472 488906401 488906587 1.310000e-87 335.0
62 TraesCS3B01G397700 chr7B 98.421 190 2 1 5287 5476 168758381 168758193 4.690000e-87 333.0
63 TraesCS3B01G397700 chr7B 100.000 178 0 0 4929 5106 41525064 41524887 6.070000e-86 329.0
64 TraesCS3B01G397700 chr2A 100.000 180 0 0 4927 5106 286445863 286446042 4.690000e-87 333.0
65 TraesCS3B01G397700 chr1B 100.000 179 0 0 4928 5106 410793827 410793649 1.690000e-86 331.0
66 TraesCS3B01G397700 chr6D 96.500 200 6 1 5276 5475 291261950 291261752 6.070000e-86 329.0
67 TraesCS3B01G397700 chr2B 100.000 178 0 0 4929 5106 402680828 402680651 6.070000e-86 329.0
68 TraesCS3B01G397700 chr6B 96.465 198 7 0 5283 5480 365730046 365729849 2.180000e-85 327.0
69 TraesCS3B01G397700 chr5A 98.907 183 2 0 4924 5106 219371795 219371613 2.180000e-85 327.0
70 TraesCS3B01G397700 chr1A 96.923 195 2 4 4915 5106 582360203 582360010 2.830000e-84 324.0
71 TraesCS3B01G397700 chr4A 98.370 184 2 1 4924 5106 477497849 477497666 1.020000e-83 322.0


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 TraesCS3B01G397700 chr3B 627918311 627926427 8116 True 14990.000000 14990 100.000000 1 8117 1 chr3B.!!$R2 8116
1 TraesCS3B01G397700 chr3B 627919670 627924254 4584 True 557.218182 1005 84.330364 2176 6758 11 chr3B.!!$R3 4582
2 TraesCS3B01G397700 chr3A 614796209 614803795 7586 True 840.766667 3025 87.571611 1 8089 18 chr3A.!!$R2 8088
3 TraesCS3B01G397700 chr3D 472437683 472449400 11717 True 871.270833 2627 85.932417 1 8089 24 chr3D.!!$R1 8088

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
455 2661 0.037882 CTCGAGAGCTTCAGTGGCAA 60.038 55.0 6.58 0.0 0.00 4.52 F
970 3207 0.322816 GGTTTCGGTTACCCCTTCCC 60.323 60.0 0.00 0.0 0.00 3.97 F
1546 3791 0.234106 GATCGATGCTTGATGTGCCG 59.766 55.0 0.54 0.0 0.00 5.69 F
2151 4752 0.887247 TGGCTTACGCAAATGCATGT 59.113 45.0 0.00 0.0 42.21 3.21 F
6988 10093 5.049954 GCAATGTTGTTCCGAACTTGTAGTA 60.050 40.0 12.43 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 3789 0.109272 TCTAGACTGAAGCAACGCGG 60.109 55.000 12.47 0.00 0.00 6.46 R
2102 4703 2.161211 ACCTCGAGAAGTACGTACAAGC 59.839 50.000 26.55 14.93 0.00 4.01 R
6840 9942 8.765488 TCATCTTTCATCACTATCTTCTCTCT 57.235 34.615 0.00 0.00 0.00 3.10 R
7012 10117 0.617413 ATCCAGGCAGGTTCAGACTG 59.383 55.000 0.00 0.00 41.89 3.51 R
8060 12838 0.389166 CTCTCCAACGTGCAGAGGAC 60.389 60.000 9.74 0.00 31.58 3.85 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
74 2280 5.163513 GGACGAGAATTGCATCACAAAAAT 58.836 37.500 0.00 0.00 42.86 1.82
88 2294 7.679400 GCATCACAAAAATATTGTCCTCGATCA 60.679 37.037 0.00 0.00 0.00 2.92
114 2320 3.716195 TGACCTCACGGGCATGGG 61.716 66.667 0.00 0.00 45.79 4.00
275 2481 2.503765 TCTTGCCATTAATCCCTCGACA 59.496 45.455 0.00 0.00 0.00 4.35
281 2487 4.262463 GCCATTAATCCCTCGACATACTCA 60.262 45.833 0.00 0.00 0.00 3.41
308 2514 3.056328 GTGCCGAACAAGGAGCCC 61.056 66.667 0.00 0.00 0.00 5.19
388 2594 0.808755 CACCCTACCAAACCAATCGC 59.191 55.000 0.00 0.00 0.00 4.58
393 2599 0.322322 TACCAAACCAATCGCCGTCT 59.678 50.000 0.00 0.00 0.00 4.18
443 2649 1.652012 CCCTTCGCTAGCTCGAGAG 59.348 63.158 18.75 6.70 39.82 3.20
455 2661 0.037882 CTCGAGAGCTTCAGTGGCAA 60.038 55.000 6.58 0.00 0.00 4.52
484 2690 4.258543 TGCCGAAATGGGAAGTTTACTAG 58.741 43.478 0.00 0.00 38.63 2.57
559 2766 1.377202 ATGATCGCAAACGCCACCT 60.377 52.632 0.00 0.00 39.84 4.00
588 2795 1.017387 CTGCCTATGAAACGCCCTTC 58.983 55.000 0.00 0.00 0.00 3.46
706 2943 6.854496 GGTGCACGATTTATGGTAAGATAA 57.146 37.500 11.45 0.00 0.00 1.75
707 2944 6.888430 GGTGCACGATTTATGGTAAGATAAG 58.112 40.000 11.45 0.00 0.00 1.73
708 2945 6.704493 GGTGCACGATTTATGGTAAGATAAGA 59.296 38.462 11.45 0.00 0.00 2.10
717 2954 3.450904 TGGTAAGATAAGACAGCCTGGT 58.549 45.455 0.00 0.00 0.00 4.00
736 2973 0.465287 TCACAGCAGCAGAGTGACAA 59.535 50.000 10.30 0.00 37.36 3.18
846 3083 0.812549 AACCAACGAACGCCTTTTGT 59.187 45.000 0.00 0.00 32.58 2.83
907 3144 3.230134 ACAGCACTCAAACTCTCTCTCT 58.770 45.455 0.00 0.00 0.00 3.10
912 3149 2.107366 CTCAAACTCTCTCTCTCCCCC 58.893 57.143 0.00 0.00 0.00 5.40
970 3207 0.322816 GGTTTCGGTTACCCCTTCCC 60.323 60.000 0.00 0.00 0.00 3.97
975 3212 1.084273 GGTTACCCCTTCCCCCTCT 59.916 63.158 0.00 0.00 0.00 3.69
977 3214 0.987081 GTTACCCCTTCCCCCTCTCC 60.987 65.000 0.00 0.00 0.00 3.71
982 3219 1.074850 CCTTCCCCCTCTCCCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
983 3220 1.598856 CCTTCCCCCTCTCCCTCTCT 61.599 65.000 0.00 0.00 0.00 3.10
1112 3353 3.535962 GGCAGCGAGAGAGGGAGG 61.536 72.222 0.00 0.00 0.00 4.30
1400 3641 2.103771 TCAGCATCCAGGTAGATTGCTC 59.896 50.000 0.00 0.00 32.14 4.26
1406 3647 1.115467 CAGGTAGATTGCTCTCCCGT 58.885 55.000 0.00 0.00 32.84 5.28
1427 3668 4.202233 CGTCCCTCTTTATTTCCCTAGGTC 60.202 50.000 8.29 0.00 0.00 3.85
1430 3671 5.666265 TCCCTCTTTATTTCCCTAGGTCTTC 59.334 44.000 8.29 0.00 0.00 2.87
1442 3683 2.046280 AGGTCTTCTGCCCTAGGTTT 57.954 50.000 8.29 0.00 0.00 3.27
1456 3700 6.940298 TGCCCTAGGTTTATTATTATGTCTGC 59.060 38.462 8.29 0.00 0.00 4.26
1465 3709 5.950544 ATTATTATGTCTGCCGCCCTATA 57.049 39.130 0.00 0.00 0.00 1.31
1466 3710 3.895232 ATTATGTCTGCCGCCCTATAG 57.105 47.619 0.00 0.00 0.00 1.31
1478 3722 1.692519 GCCCTATAGGTTCGACATGGT 59.307 52.381 17.72 0.00 38.26 3.55
1481 3725 3.386726 CCCTATAGGTTCGACATGGTTCA 59.613 47.826 17.72 0.00 0.00 3.18
1504 3748 3.240606 CTGCGGTTGTCGTGCCTTG 62.241 63.158 0.00 0.00 41.72 3.61
1515 3759 2.227865 GTCGTGCCTTGCAATTTTAGGA 59.772 45.455 5.53 0.00 41.47 2.94
1517 3761 2.415893 CGTGCCTTGCAATTTTAGGAGG 60.416 50.000 5.53 0.00 41.47 4.30
1518 3762 2.562738 GTGCCTTGCAATTTTAGGAGGT 59.437 45.455 5.53 0.00 41.47 3.85
1544 3789 2.207590 TGAGATCGATGCTTGATGTGC 58.792 47.619 0.54 0.00 0.00 4.57
1546 3791 0.234106 GATCGATGCTTGATGTGCCG 59.766 55.000 0.54 0.00 0.00 5.69
1548 3793 2.023741 GATGCTTGATGTGCCGCG 59.976 61.111 0.00 0.00 0.00 6.46
1554 3799 2.462255 CTTGATGTGCCGCGTTGCTT 62.462 55.000 4.92 0.00 0.00 3.91
1572 3817 1.902508 CTTCAGTCTAGAACAGGGCCA 59.097 52.381 6.18 0.00 0.00 5.36
1676 3925 7.604164 CGTCTTGAAATGCATAATCCTACCTAT 59.396 37.037 0.00 0.00 0.00 2.57
1698 3947 3.882888 TGGTGAAGTGATGTTTGGAGTTC 59.117 43.478 0.00 0.00 0.00 3.01
1708 3957 6.431234 GTGATGTTTGGAGTTCTAGGAAATGT 59.569 38.462 0.00 0.00 0.00 2.71
1712 3961 9.838339 ATGTTTGGAGTTCTAGGAAATGTATAG 57.162 33.333 0.00 0.00 0.00 1.31
1716 3965 7.130099 TGGAGTTCTAGGAAATGTATAGTCCA 58.870 38.462 0.00 0.00 33.57 4.02
1717 3966 7.789831 TGGAGTTCTAGGAAATGTATAGTCCAT 59.210 37.037 0.00 0.00 33.57 3.41
1718 3967 8.652290 GGAGTTCTAGGAAATGTATAGTCCATT 58.348 37.037 0.00 0.00 34.07 3.16
1719 3968 9.482627 GAGTTCTAGGAAATGTATAGTCCATTG 57.517 37.037 0.00 0.00 33.01 2.82
1721 3970 9.262358 GTTCTAGGAAATGTATAGTCCATTGTC 57.738 37.037 0.00 0.00 33.01 3.18
1722 3971 8.783660 TCTAGGAAATGTATAGTCCATTGTCT 57.216 34.615 0.00 0.00 33.01 3.41
1723 3972 9.877222 TCTAGGAAATGTATAGTCCATTGTCTA 57.123 33.333 0.00 0.00 33.01 2.59
1754 4101 1.466167 CATGCATAATCCTACCTGCGC 59.534 52.381 0.00 0.00 37.44 6.09
1756 4103 1.140852 TGCATAATCCTACCTGCGCTT 59.859 47.619 9.73 0.00 37.44 4.68
1847 4447 3.330192 TGGAGGCACCACAGTTGT 58.670 55.556 0.00 0.00 44.64 3.32
1848 4448 1.152984 TGGAGGCACCACAGTTGTG 60.153 57.895 0.00 5.28 44.64 3.33
1888 4488 3.617531 CGTAGGTGAAGCCATATCATCCC 60.618 52.174 0.00 0.00 40.61 3.85
1889 4489 1.707427 AGGTGAAGCCATATCATCCCC 59.293 52.381 0.00 0.00 40.61 4.81
1994 4594 5.748670 TGTTAGGCTTGGAGTACAATGTA 57.251 39.130 0.00 0.00 38.65 2.29
2000 4600 7.195374 AGGCTTGGAGTACAATGTATTAAGA 57.805 36.000 0.00 0.00 38.65 2.10
2003 4603 8.736244 GGCTTGGAGTACAATGTATTAAGAAAA 58.264 33.333 0.00 0.00 38.65 2.29
2044 4644 7.840342 TGCTCTTTTTGCATTACTTGAAAAA 57.160 28.000 0.00 0.00 40.44 1.94
2053 4653 6.902341 TGCATTACTTGAAAAAGCTGTCTAG 58.098 36.000 0.00 0.00 0.00 2.43
2064 4664 7.716998 TGAAAAAGCTGTCTAGAGTTGATTCTT 59.283 33.333 0.00 0.00 0.00 2.52
2066 4666 8.770438 AAAAGCTGTCTAGAGTTGATTCTTAG 57.230 34.615 0.00 0.00 0.00 2.18
2091 4692 9.515226 AGGTAGTTGTATTAAAAATGCAAGAGA 57.485 29.630 3.80 0.00 0.00 3.10
2101 4702 9.967346 ATTAAAAATGCAAGAGATCTCATGATG 57.033 29.630 27.63 18.76 32.19 3.07
2102 4703 6.392625 AAAATGCAAGAGATCTCATGATGG 57.607 37.500 27.63 5.98 32.19 3.51
2103 4704 2.847441 TGCAAGAGATCTCATGATGGC 58.153 47.619 27.63 15.46 32.19 4.40
2119 4720 2.624316 TGGCTTGTACGTACTTCTCG 57.376 50.000 25.12 10.61 0.00 4.04
2123 4724 2.161211 GCTTGTACGTACTTCTCGAGGT 59.839 50.000 25.12 6.06 0.00 3.85
2151 4752 0.887247 TGGCTTACGCAAATGCATGT 59.113 45.000 0.00 0.00 42.21 3.21
6988 10093 5.049954 GCAATGTTGTTCCGAACTTGTAGTA 60.050 40.000 12.43 0.00 0.00 1.82
6989 10094 6.590357 CAATGTTGTTCCGAACTTGTAGTAG 58.410 40.000 12.43 0.00 0.00 2.57
6990 10095 5.266733 TGTTGTTCCGAACTTGTAGTAGT 57.733 39.130 12.43 0.00 0.00 2.73
7083 10189 3.935828 GTGGAAACTGCATAGAGACTTCC 59.064 47.826 0.00 0.00 33.06 3.46
7165 10271 9.466497 TGATTTTGATATACTTCCTCTTTTGCT 57.534 29.630 0.00 0.00 0.00 3.91
7362 12092 2.469274 ATCTTGTGTGTCCTGCAGAG 57.531 50.000 17.39 5.49 0.00 3.35
7459 12190 0.389948 ATGGACCAAGAAGACGACGC 60.390 55.000 0.00 0.00 0.00 5.19
7461 12192 1.006571 GACCAAGAAGACGACGCCA 60.007 57.895 0.00 0.00 0.00 5.69
7466 12197 1.192534 CAAGAAGACGACGCCAAAGAC 59.807 52.381 0.00 0.00 0.00 3.01
7500 12231 3.496884 GGTGACGTGCAGTAATTTTGAGA 59.503 43.478 0.00 0.00 0.00 3.27
7504 12235 5.095691 ACGTGCAGTAATTTTGAGAAGTG 57.904 39.130 0.00 0.00 0.00 3.16
7517 12248 1.728971 GAGAAGTGCTCGTTGACATGG 59.271 52.381 0.00 0.00 33.17 3.66
7518 12249 1.344438 AGAAGTGCTCGTTGACATGGA 59.656 47.619 0.00 0.00 0.00 3.41
7520 12251 0.969149 AGTGCTCGTTGACATGGAGA 59.031 50.000 0.00 0.00 0.00 3.71
7521 12252 1.552337 AGTGCTCGTTGACATGGAGAT 59.448 47.619 0.00 0.00 0.00 2.75
7522 12253 1.662629 GTGCTCGTTGACATGGAGATG 59.337 52.381 0.00 0.00 35.49 2.90
7523 12254 1.293924 GCTCGTTGACATGGAGATGG 58.706 55.000 0.00 0.00 33.39 3.51
7524 12255 1.406069 GCTCGTTGACATGGAGATGGT 60.406 52.381 0.00 0.00 33.39 3.55
7525 12256 2.274437 CTCGTTGACATGGAGATGGTG 58.726 52.381 0.00 0.00 33.39 4.17
7526 12257 1.623311 TCGTTGACATGGAGATGGTGT 59.377 47.619 0.00 0.00 33.39 4.16
7527 12258 2.829120 TCGTTGACATGGAGATGGTGTA 59.171 45.455 0.00 0.00 33.39 2.90
7528 12259 2.930040 CGTTGACATGGAGATGGTGTAC 59.070 50.000 0.00 0.00 33.39 2.90
7529 12260 3.270877 GTTGACATGGAGATGGTGTACC 58.729 50.000 0.00 0.00 33.39 3.34
7539 12270 3.006061 TGGTGTACCATGGAGGAGG 57.994 57.895 21.47 0.00 42.01 4.30
7540 12271 0.415830 TGGTGTACCATGGAGGAGGA 59.584 55.000 21.47 0.00 42.01 3.71
7541 12272 1.203376 TGGTGTACCATGGAGGAGGAA 60.203 52.381 21.47 0.00 42.01 3.36
7542 12273 1.486726 GGTGTACCATGGAGGAGGAAG 59.513 57.143 21.47 0.00 41.22 3.46
7543 12274 1.134371 GTGTACCATGGAGGAGGAAGC 60.134 57.143 21.47 0.00 41.22 3.86
7544 12275 1.204146 GTACCATGGAGGAGGAAGCA 58.796 55.000 21.47 0.00 41.22 3.91
7545 12276 1.134371 GTACCATGGAGGAGGAAGCAC 60.134 57.143 21.47 0.00 41.22 4.40
7546 12277 1.225704 CCATGGAGGAGGAAGCACC 59.774 63.158 5.56 0.00 41.22 5.01
7582 12313 1.135972 CGAAGCAACAATTACAGCGCT 60.136 47.619 2.64 2.64 0.00 5.92
7597 12328 1.226575 CGCTTGCACTGCATCATGG 60.227 57.895 4.10 0.00 38.76 3.66
7603 12334 2.441532 ACTGCATCATGGCCTGCC 60.442 61.111 11.81 0.00 37.59 4.85
7670 12409 0.027848 GTCGTGACGAGCTAGCTACC 59.972 60.000 19.38 10.24 36.23 3.18
7742 12481 3.636231 CTCCCAACCTGTCGGGCA 61.636 66.667 0.00 0.00 42.75 5.36
7744 12483 4.263572 CCCAACCTGTCGGGCACA 62.264 66.667 0.00 0.00 39.10 4.57
7745 12484 2.034066 CCAACCTGTCGGGCACAT 59.966 61.111 0.00 0.00 39.10 3.21
7746 12485 2.040544 CCAACCTGTCGGGCACATC 61.041 63.158 0.00 0.00 39.10 3.06
7747 12486 2.047274 AACCTGTCGGGCACATCG 60.047 61.111 0.00 0.00 39.10 3.84
7748 12487 3.605749 AACCTGTCGGGCACATCGG 62.606 63.158 0.00 0.00 39.10 4.18
7749 12488 4.082523 CCTGTCGGGCACATCGGT 62.083 66.667 0.00 0.00 33.23 4.69
7842 12587 1.227263 GCGTGATGTGGCCTCGTAT 60.227 57.895 3.32 0.00 0.00 3.06
7955 12717 2.461986 TAGGTGGGCTCTGGAGTGCT 62.462 60.000 1.09 0.00 35.15 4.40
8072 12850 2.651361 CCTTCGTCCTCTGCACGT 59.349 61.111 0.00 0.00 38.45 4.49
8089 12867 1.412710 ACGTTGGAGAGCAGAGTTCAA 59.587 47.619 0.00 0.00 0.00 2.69
8090 12868 2.064762 CGTTGGAGAGCAGAGTTCAAG 58.935 52.381 0.00 0.00 0.00 3.02
8091 12869 2.421619 GTTGGAGAGCAGAGTTCAAGG 58.578 52.381 0.00 0.00 0.00 3.61
8092 12870 0.979665 TGGAGAGCAGAGTTCAAGGG 59.020 55.000 0.00 0.00 0.00 3.95
8093 12871 0.392327 GGAGAGCAGAGTTCAAGGGC 60.392 60.000 0.00 0.00 0.00 5.19
8094 12872 0.322975 GAGAGCAGAGTTCAAGGGCA 59.677 55.000 0.00 0.00 0.00 5.36
8095 12873 0.324285 AGAGCAGAGTTCAAGGGCAG 59.676 55.000 0.00 0.00 0.00 4.85
8096 12874 0.036022 GAGCAGAGTTCAAGGGCAGT 59.964 55.000 0.00 0.00 0.00 4.40
8097 12875 0.250640 AGCAGAGTTCAAGGGCAGTG 60.251 55.000 0.00 0.00 0.00 3.66
8098 12876 0.250467 GCAGAGTTCAAGGGCAGTGA 60.250 55.000 0.00 0.00 0.00 3.41
8099 12877 1.517242 CAGAGTTCAAGGGCAGTGAC 58.483 55.000 0.00 0.00 0.00 3.67
8100 12878 0.034059 AGAGTTCAAGGGCAGTGACG 59.966 55.000 0.00 0.00 0.00 4.35
8101 12879 1.569479 GAGTTCAAGGGCAGTGACGC 61.569 60.000 0.00 0.00 0.00 5.19
8110 12888 2.661537 CAGTGACGCCGACTGCAA 60.662 61.111 0.00 0.00 41.33 4.08
8111 12889 2.661866 AGTGACGCCGACTGCAAC 60.662 61.111 0.00 0.00 41.33 4.17
8112 12890 2.964925 GTGACGCCGACTGCAACA 60.965 61.111 0.00 0.00 41.33 3.33
8113 12891 2.030412 TGACGCCGACTGCAACAT 59.970 55.556 0.00 0.00 41.33 2.71
8114 12892 2.316867 TGACGCCGACTGCAACATG 61.317 57.895 0.00 0.00 41.33 3.21
8115 12893 2.280797 ACGCCGACTGCAACATGT 60.281 55.556 0.00 0.00 41.33 3.21
8116 12894 2.227968 GACGCCGACTGCAACATGTC 62.228 60.000 0.00 0.00 41.33 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 2280 7.439356 GTCAAGATTGAATGATCGAGGACAATA 59.561 37.037 0.00 0.00 39.21 1.90
114 2320 4.849310 TATGCGGTCGGCTTGGGC 62.849 66.667 3.87 0.00 44.05 5.36
140 2346 2.932614 AGTTCACATAGAGCATGCGTTC 59.067 45.455 13.01 5.33 38.29 3.95
216 2422 8.617809 AGAAGAAGATCTAGACGATGAAGTTAC 58.382 37.037 0.00 0.00 30.84 2.50
275 2481 1.146930 CACGGCTGGGCATGAGTAT 59.853 57.895 0.00 0.00 0.00 2.12
308 2514 0.818938 TAGCATGGCATGGCAAACAG 59.181 50.000 27.04 16.53 0.00 3.16
366 2572 0.411848 ATTGGTTTGGTAGGGTGGGG 59.588 55.000 0.00 0.00 0.00 4.96
388 2594 2.421739 CCGGCCTTGGATAGACGG 59.578 66.667 0.00 0.00 37.68 4.79
393 2599 3.488569 CTGCCCCGGCCTTGGATA 61.489 66.667 11.38 0.00 41.09 2.59
414 2620 1.218316 GCGAAGGGGTGGTCTAGTG 59.782 63.158 0.00 0.00 0.00 2.74
443 2649 1.404391 CATCCATCTTGCCACTGAAGC 59.596 52.381 0.00 0.00 0.00 3.86
455 2661 0.846015 TCCCATTTCGGCATCCATCT 59.154 50.000 0.00 0.00 0.00 2.90
506 2712 7.611855 CCTTTGACTAGGGTTTCATGTTATCTT 59.388 37.037 0.00 0.00 0.00 2.40
539 2745 1.226379 GTGGCGTTTGCGATCATGG 60.226 57.895 0.00 0.00 44.10 3.66
559 2766 0.546507 TCATAGGCAGGACCACCACA 60.547 55.000 6.36 0.00 43.14 4.17
588 2795 7.859377 TCCTTACTCGCTAAGTATTCGTAATTG 59.141 37.037 0.00 0.00 40.18 2.32
691 2928 7.147302 ACCAGGCTGTCTTATCTTACCATAAAT 60.147 37.037 14.43 0.00 0.00 1.40
696 2933 3.450904 ACCAGGCTGTCTTATCTTACCA 58.549 45.455 14.43 0.00 0.00 3.25
699 2936 4.093743 TGTGACCAGGCTGTCTTATCTTA 58.906 43.478 14.43 0.00 36.21 2.10
704 2941 0.321671 GCTGTGACCAGGCTGTCTTA 59.678 55.000 14.43 4.29 39.22 2.10
705 2942 1.072159 GCTGTGACCAGGCTGTCTT 59.928 57.895 14.43 0.00 39.22 3.01
706 2943 2.109517 CTGCTGTGACCAGGCTGTCT 62.110 60.000 14.43 0.00 39.22 3.41
707 2944 1.670406 CTGCTGTGACCAGGCTGTC 60.670 63.158 14.43 11.41 39.22 3.51
708 2945 2.429058 CTGCTGTGACCAGGCTGT 59.571 61.111 14.43 1.17 39.22 4.40
717 2954 0.465287 TTGTCACTCTGCTGCTGTGA 59.535 50.000 14.17 14.90 38.24 3.58
814 3051 3.050354 TTGGTTGCCCACGTGGACT 62.050 57.895 36.07 0.00 41.67 3.85
880 3117 3.356290 AGAGTTTGAGTGCTGTTTGGTT 58.644 40.909 0.00 0.00 0.00 3.67
970 3207 0.998945 AGGGAGAGAGAGGGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
975 3212 2.927007 TCTTGTAAGGGAGAGAGAGGGA 59.073 50.000 0.00 0.00 0.00 4.20
977 3214 4.037446 CGATTCTTGTAAGGGAGAGAGAGG 59.963 50.000 0.00 0.00 0.00 3.69
982 3219 3.712187 GAGCGATTCTTGTAAGGGAGAG 58.288 50.000 0.00 0.00 0.00 3.20
983 3220 2.099263 CGAGCGATTCTTGTAAGGGAGA 59.901 50.000 0.00 0.00 0.00 3.71
1400 3641 2.158798 GGGAAATAAAGAGGGACGGGAG 60.159 54.545 0.00 0.00 0.00 4.30
1406 3647 5.236425 AGACCTAGGGAAATAAAGAGGGA 57.764 43.478 14.81 0.00 0.00 4.20
1427 3668 9.220767 GACATAATAATAAACCTAGGGCAGAAG 57.779 37.037 14.81 0.00 0.00 2.85
1430 3671 7.119846 GCAGACATAATAATAAACCTAGGGCAG 59.880 40.741 14.81 0.00 0.00 4.85
1442 3683 5.950544 ATAGGGCGGCAGACATAATAATA 57.049 39.130 12.47 0.00 0.00 0.98
1456 3700 0.966920 ATGTCGAACCTATAGGGCGG 59.033 55.000 26.18 14.71 40.27 6.13
1465 3709 2.767505 GTCTTGAACCATGTCGAACCT 58.232 47.619 0.00 0.00 0.00 3.50
1492 3736 2.593346 AAAATTGCAAGGCACGACAA 57.407 40.000 4.94 0.00 38.71 3.18
1504 3748 5.048991 TCTCAACGAAACCTCCTAAAATTGC 60.049 40.000 0.00 0.00 0.00 3.56
1515 3759 2.093973 AGCATCGATCTCAACGAAACCT 60.094 45.455 0.00 0.00 42.80 3.50
1517 3761 3.367932 TCAAGCATCGATCTCAACGAAAC 59.632 43.478 0.00 0.00 42.80 2.78
1518 3762 3.584834 TCAAGCATCGATCTCAACGAAA 58.415 40.909 0.00 0.00 42.80 3.46
1544 3789 0.109272 TCTAGACTGAAGCAACGCGG 60.109 55.000 12.47 0.00 0.00 6.46
1546 3791 2.404215 TGTTCTAGACTGAAGCAACGC 58.596 47.619 0.00 0.00 0.00 4.84
1548 3793 3.330267 CCCTGTTCTAGACTGAAGCAAC 58.670 50.000 0.00 0.00 0.00 4.17
1554 3799 2.111384 GATGGCCCTGTTCTAGACTGA 58.889 52.381 0.00 0.00 0.00 3.41
1572 3817 9.700831 ATACAGAATTAACCTAAGGCAAAAGAT 57.299 29.630 0.00 0.00 0.00 2.40
1636 3885 6.443934 TTTCAAGACGGACATCAAAAGAAA 57.556 33.333 0.00 0.00 0.00 2.52
1648 3897 4.780815 AGGATTATGCATTTCAAGACGGA 58.219 39.130 3.54 0.00 0.00 4.69
1676 3925 3.576078 ACTCCAAACATCACTTCACCA 57.424 42.857 0.00 0.00 0.00 4.17
1712 3961 7.254590 GCATGTCAAGACTATTAGACAATGGAC 60.255 40.741 0.00 0.00 43.38 4.02
1716 3965 9.836864 TTATGCATGTCAAGACTATTAGACAAT 57.163 29.630 10.16 0.00 43.38 2.71
1717 3966 9.836864 ATTATGCATGTCAAGACTATTAGACAA 57.163 29.630 10.16 0.00 43.38 3.18
1718 3967 9.481340 GATTATGCATGTCAAGACTATTAGACA 57.519 33.333 10.16 0.00 44.16 3.41
1719 3968 8.930760 GGATTATGCATGTCAAGACTATTAGAC 58.069 37.037 10.16 0.00 0.00 2.59
1722 3971 9.929180 GTAGGATTATGCATGTCAAGACTATTA 57.071 33.333 10.16 0.00 0.00 0.98
1723 3972 7.880195 GGTAGGATTATGCATGTCAAGACTATT 59.120 37.037 10.16 0.00 0.00 1.73
1724 3973 7.236432 AGGTAGGATTATGCATGTCAAGACTAT 59.764 37.037 10.16 0.00 0.00 2.12
1726 3975 5.367937 AGGTAGGATTATGCATGTCAAGACT 59.632 40.000 10.16 1.27 0.00 3.24
1727 3976 5.468072 CAGGTAGGATTATGCATGTCAAGAC 59.532 44.000 10.16 6.52 0.00 3.01
1728 3977 5.614308 CAGGTAGGATTATGCATGTCAAGA 58.386 41.667 10.16 0.00 0.00 3.02
1729 3978 4.214971 GCAGGTAGGATTATGCATGTCAAG 59.785 45.833 10.16 0.00 38.54 3.02
1731 3980 3.743521 GCAGGTAGGATTATGCATGTCA 58.256 45.455 10.16 0.00 38.54 3.58
1734 4081 1.466167 GCGCAGGTAGGATTATGCATG 59.534 52.381 10.16 0.00 38.60 4.06
1790 4137 6.604171 ACACATGGATTATGCATTTCCTAGA 58.396 36.000 22.11 8.77 40.59 2.43
1919 4519 4.197750 GCCAATGGCTAGAGATCCATATG 58.802 47.826 18.47 0.00 46.69 1.78
1961 4561 5.686753 TCCAAGCCTAACAAAGTAACTTCA 58.313 37.500 0.00 0.00 0.00 3.02
1962 4562 5.763698 ACTCCAAGCCTAACAAAGTAACTTC 59.236 40.000 0.00 0.00 0.00 3.01
2007 4607 5.677344 GCAAAAAGAGCAAGCCTATAGGAAC 60.677 44.000 23.61 5.60 37.39 3.62
2044 4644 5.955355 ACCTAAGAATCAACTCTAGACAGCT 59.045 40.000 0.00 0.00 0.00 4.24
2078 4678 6.683110 GCCATCATGAGATCTCTTGCATTTTT 60.683 38.462 26.25 9.58 35.48 1.94
2091 4692 3.827008 ACGTACAAGCCATCATGAGAT 57.173 42.857 0.09 0.00 33.87 2.75
2096 4697 4.683832 GAGAAGTACGTACAAGCCATCAT 58.316 43.478 26.55 0.40 0.00 2.45
2101 4702 2.477525 CCTCGAGAAGTACGTACAAGCC 60.478 54.545 26.55 12.36 0.00 4.35
2102 4703 2.161211 ACCTCGAGAAGTACGTACAAGC 59.839 50.000 26.55 14.93 0.00 4.01
2103 4704 4.416505 AACCTCGAGAAGTACGTACAAG 57.583 45.455 26.55 12.69 0.00 3.16
2119 4720 3.174375 CGTAAGCCAAGTACGTAACCTC 58.826 50.000 0.00 0.00 39.54 3.85
2151 4752 5.859205 ACTACAGATGTATCATGCAGACA 57.141 39.130 0.00 0.00 0.00 3.41
6840 9942 8.765488 TCATCTTTCATCACTATCTTCTCTCT 57.235 34.615 0.00 0.00 0.00 3.10
6868 9970 0.974010 AGCCCGAATGGAACGACCTA 60.974 55.000 0.00 0.00 39.86 3.08
6869 9971 2.267961 GCCCGAATGGAACGACCT 59.732 61.111 0.00 0.00 39.86 3.85
6976 10081 4.615961 CACTCCGAAACTACTACAAGTTCG 59.384 45.833 0.00 0.00 38.76 3.95
7012 10117 0.617413 ATCCAGGCAGGTTCAGACTG 59.383 55.000 0.00 0.00 41.89 3.51
7229 11940 3.785887 AGCATTTCTTCCATACCCCTACA 59.214 43.478 0.00 0.00 0.00 2.74
7230 11941 4.137543 CAGCATTTCTTCCATACCCCTAC 58.862 47.826 0.00 0.00 0.00 3.18
7231 11942 4.044308 TCAGCATTTCTTCCATACCCCTA 58.956 43.478 0.00 0.00 0.00 3.53
7232 11943 2.852449 TCAGCATTTCTTCCATACCCCT 59.148 45.455 0.00 0.00 0.00 4.79
7233 11944 3.297134 TCAGCATTTCTTCCATACCCC 57.703 47.619 0.00 0.00 0.00 4.95
7243 11954 1.146566 GGGATGGGGATCAGCATTTCT 59.853 52.381 0.00 0.00 32.50 2.52
7362 12092 1.212935 ACCATCCAAGCCATACCTGTC 59.787 52.381 0.00 0.00 0.00 3.51
7459 12190 0.443869 CATTGCCTCGTCGTCTTTGG 59.556 55.000 0.00 0.00 0.00 3.28
7461 12192 0.034896 ACCATTGCCTCGTCGTCTTT 59.965 50.000 0.00 0.00 0.00 2.52
7466 12197 2.444624 CGTCACCATTGCCTCGTCG 61.445 63.158 0.00 0.00 0.00 5.12
7500 12231 1.344438 TCTCCATGTCAACGAGCACTT 59.656 47.619 0.00 0.00 0.00 3.16
7504 12235 1.293924 CCATCTCCATGTCAACGAGC 58.706 55.000 0.00 0.00 0.00 5.03
7525 12256 1.134371 GTGCTTCCTCCTCCATGGTAC 60.134 57.143 12.58 0.00 37.07 3.34
7526 12257 1.204146 GTGCTTCCTCCTCCATGGTA 58.796 55.000 12.58 0.00 37.07 3.25
7527 12258 1.566298 GGTGCTTCCTCCTCCATGGT 61.566 60.000 12.58 0.00 37.07 3.55
7528 12259 1.225704 GGTGCTTCCTCCTCCATGG 59.774 63.158 4.97 4.97 37.10 3.66
7529 12260 1.153289 CGGTGCTTCCTCCTCCATG 60.153 63.158 0.00 0.00 0.00 3.66
7530 12261 0.692419 ATCGGTGCTTCCTCCTCCAT 60.692 55.000 0.00 0.00 0.00 3.41
7531 12262 1.306141 ATCGGTGCTTCCTCCTCCA 60.306 57.895 0.00 0.00 0.00 3.86
7532 12263 1.144936 CATCGGTGCTTCCTCCTCC 59.855 63.158 0.00 0.00 0.00 4.30
7533 12264 4.844420 CATCGGTGCTTCCTCCTC 57.156 61.111 0.00 0.00 0.00 3.71
7543 12274 4.147322 GGTTCGTGCGCATCGGTG 62.147 66.667 24.69 10.35 0.00 4.94
7566 12297 0.710017 GCAAGCGCTGTAATTGTTGC 59.290 50.000 12.58 11.19 34.10 4.17
7582 12313 1.304630 AGGCCATGATGCAGTGCAA 60.305 52.632 23.90 6.98 43.62 4.08
7597 12328 1.080298 ACGTACGTACTTGGCAGGC 60.080 57.895 21.41 0.00 0.00 4.85
7603 12334 1.802715 CGGGGCACGTACGTACTTG 60.803 63.158 22.34 23.67 37.93 3.16
7663 12402 3.154473 CGGCAGGGCTGGTAGCTA 61.154 66.667 0.43 0.00 41.99 3.32
7698 12437 4.722855 CCGCGGCCAAAAAGCAGG 62.723 66.667 14.67 0.00 0.00 4.85
7842 12587 2.091541 CCTGGGTTAAGTACGTACGGA 58.908 52.381 21.06 8.59 0.00 4.69
7905 12654 1.260544 GCCAAGGAAAGCATCTGGTT 58.739 50.000 0.00 0.00 37.35 3.67
7955 12717 2.941025 CCCTTCCTTCCCTGCCCA 60.941 66.667 0.00 0.00 0.00 5.36
8056 12834 1.284982 CCAACGTGCAGAGGACGAAG 61.285 60.000 17.52 8.83 39.21 3.79
8058 12836 2.142357 CTCCAACGTGCAGAGGACGA 62.142 60.000 17.52 0.00 39.21 4.20
8060 12838 0.389166 CTCTCCAACGTGCAGAGGAC 60.389 60.000 9.74 0.00 31.58 3.85
8061 12839 1.967535 CTCTCCAACGTGCAGAGGA 59.032 57.895 9.74 0.00 31.58 3.71
8072 12850 1.349026 CCCTTGAACTCTGCTCTCCAA 59.651 52.381 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.