Multiple sequence alignment - TraesCS4B01G284100

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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 TraesCS4B01G284100 chr4B 100.000 2305 0 0 950 3254 567430663 567428359 0.000000e+00 4257.0
1 TraesCS4B01G284100 chr4B 85.262 1547 196 18 1416 2947 567590062 567588533 0.000000e+00 1565.0
2 TraesCS4B01G284100 chr4B 100.000 675 0 0 1 675 567431612 567430938 0.000000e+00 1247.0
3 TraesCS4B01G284100 chr4B 100.000 225 0 0 3697 3921 567427916 567427692 2.180000e-112 416.0
4 TraesCS4B01G284100 chr4B 91.818 110 8 1 90 198 567430195 567430086 6.790000e-33 152.0
5 TraesCS4B01G284100 chr4B 88.034 117 10 3 86 198 567590064 567589948 6.830000e-28 135.0
6 TraesCS4B01G284100 chr4B 78.646 192 27 8 2942 3125 567588497 567588312 8.900000e-22 115.0
7 TraesCS4B01G284100 chr4B 90.741 54 4 1 3860 3913 567587892 567587840 1.950000e-08 71.3
8 TraesCS4B01G284100 chr4A 94.288 2066 99 9 1075 3125 13162875 13164936 0.000000e+00 3144.0
9 TraesCS4B01G284100 chr4A 90.953 1669 130 9 1418 3069 13524969 13526633 0.000000e+00 2226.0
10 TraesCS4B01G284100 chr4A 89.369 1552 148 11 1400 2938 13517976 13519523 0.000000e+00 1936.0
11 TraesCS4B01G284100 chr4A 85.844 1547 188 15 1408 2947 13150691 13152213 0.000000e+00 1615.0
12 TraesCS4B01G284100 chr4A 89.270 466 45 5 18 482 13160644 13161105 2.630000e-161 579.0
13 TraesCS4B01G284100 chr4A 92.045 176 13 1 476 651 13162560 13162734 3.030000e-61 246.0
14 TraesCS4B01G284100 chr4A 93.252 163 10 1 37 198 13524916 13525078 5.060000e-59 239.0
15 TraesCS4B01G284100 chr4A 75.078 321 47 18 2942 3254 13157099 13157394 6.880000e-23 119.0
16 TraesCS4B01G284100 chr4D 88.625 1556 152 15 1408 2947 454991208 454989662 0.000000e+00 1869.0
17 TraesCS4B01G284100 chr4D 94.948 1148 33 10 1075 2204 454835426 454834286 0.000000e+00 1775.0
18 TraesCS4B01G284100 chr4D 84.343 1552 200 20 1408 2947 455090442 455088922 0.000000e+00 1480.0
19 TraesCS4B01G284100 chr4D 89.180 915 85 5 1418 2322 454809771 454808861 0.000000e+00 1129.0
20 TraesCS4B01G284100 chr4D 91.810 757 54 2 2196 2947 454833966 454833213 0.000000e+00 1048.0
21 TraesCS4B01G284100 chr4D 90.368 789 71 5 1665 2452 454839413 454838629 0.000000e+00 1031.0
22 TraesCS4B01G284100 chr4D 89.068 622 55 7 5 613 454836203 454835582 0.000000e+00 760.0
23 TraesCS4B01G284100 chr4D 88.655 238 20 5 1 233 455070113 455069878 2.310000e-72 283.0
24 TraesCS4B01G284100 chr4D 93.252 163 10 1 37 198 454809824 454809662 5.060000e-59 239.0
25 TraesCS4B01G284100 chr4D 88.034 117 10 3 86 198 455090436 455090320 6.830000e-28 135.0
26 TraesCS4B01G284100 chr4D 92.045 88 5 1 2942 3027 455088886 455088799 5.320000e-24 122.0
27 TraesCS4B01G284100 chr4D 78.646 192 27 10 2942 3125 454989626 454989441 8.900000e-22 115.0
28 TraesCS4B01G284100 chr4D 89.773 88 7 2 2942 3027 454833177 454833090 1.150000e-20 111.0
29 TraesCS4B01G284100 chr4D 95.238 42 2 0 3872 3913 455088263 455088222 2.530000e-07 67.6
30 TraesCS4B01G284100 chr4D 78.512 121 11 8 3796 3914 454806160 454806053 9.090000e-07 65.8
31 TraesCS4B01G284100 chr5A 94.771 918 42 1 1075 1992 53220297 53219386 0.000000e+00 1424.0
32 TraesCS4B01G284100 chr5A 91.209 182 16 0 470 651 53220596 53220415 8.410000e-62 248.0
33 TraesCS4B01G284100 chr3D 76.658 754 148 17 1419 2149 435489218 435488470 3.670000e-105 392.0
34 TraesCS4B01G284100 chr3B 80.645 186 30 4 467 651 3890839 3891019 5.280000e-29 139.0
35 TraesCS4B01G284100 chr3B 80.645 186 30 4 467 651 4777759 4777939 5.280000e-29 139.0


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 TraesCS4B01G284100 chr4B 567427692 567431612 3920 True 1518.000000 4257 97.954500 1 3921 4 chr4B.!!$R1 3920
1 TraesCS4B01G284100 chr4B 567587840 567590064 2224 True 471.575000 1565 85.670750 86 3913 4 chr4B.!!$R2 3827
2 TraesCS4B01G284100 chr4A 13517976 13519523 1547 False 1936.000000 1936 89.369000 1400 2938 1 chr4A.!!$F2 1538
3 TraesCS4B01G284100 chr4A 13150691 13152213 1522 False 1615.000000 1615 85.844000 1408 2947 1 chr4A.!!$F1 1539
4 TraesCS4B01G284100 chr4A 13524916 13526633 1717 False 1232.500000 2226 92.102500 37 3069 2 chr4A.!!$F4 3032
5 TraesCS4B01G284100 chr4A 13157099 13164936 7837 False 1022.000000 3144 87.670250 18 3254 4 chr4A.!!$F3 3236
6 TraesCS4B01G284100 chr4D 454989441 454991208 1767 True 992.000000 1869 83.635500 1408 3125 2 chr4D.!!$R4 1717
7 TraesCS4B01G284100 chr4D 454833090 454839413 6323 True 945.000000 1775 91.193400 5 3027 5 chr4D.!!$R3 3022
8 TraesCS4B01G284100 chr4D 454806053 454809824 3771 True 477.933333 1129 86.981333 37 3914 3 chr4D.!!$R2 3877
9 TraesCS4B01G284100 chr4D 455088222 455090442 2220 True 451.150000 1480 89.915000 86 3913 4 chr4D.!!$R5 3827
10 TraesCS4B01G284100 chr5A 53219386 53220596 1210 True 836.000000 1424 92.990000 470 1992 2 chr5A.!!$R1 1522
11 TraesCS4B01G284100 chr3D 435488470 435489218 748 True 392.000000 392 76.658000 1419 2149 1 chr3D.!!$R1 730

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
351 3881 0.177604 CTGGACCTGCCTGTCAGATC 59.822 60.0 0.0 0.0 45.72 2.75 F
1064 4603 0.181587 TGTTTGCTTTCCTCACCCGA 59.818 50.0 0.0 0.0 0.00 5.14 F
1379 4918 0.385390 CTTGCAGCCGAACAAAACCT 59.615 50.0 0.0 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 4930 0.107643 GCAGGCTGGAAGGAGGATAC 59.892 60.0 17.64 0.0 0.0 2.24 R
2902 11228 0.456653 GCATTCGGCGCACTTTTGAT 60.457 50.0 10.83 0.0 0.0 2.57 R
3108 11646 0.976641 TCCATGAGACGCCAAAGAGT 59.023 50.0 0.00 0.0 0.0 3.24 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
121 3650 1.479757 GGATACTTCCTCGCCTCCTCT 60.480 57.143 0.00 0.00 39.14 3.69
143 3672 3.681835 AGCCACCCGTCGTCACTC 61.682 66.667 0.00 0.00 0.00 3.51
145 3674 3.667282 CCACCCGTCGTCACTCGT 61.667 66.667 0.00 0.00 40.80 4.18
151 3680 2.335369 GTCGTCACTCGTGCCAGT 59.665 61.111 0.00 0.00 40.80 4.00
155 3684 3.545574 TCACTCGTGCCAGTGCCA 61.546 61.111 3.26 0.00 43.18 4.92
156 3685 3.046087 CACTCGTGCCAGTGCCAG 61.046 66.667 0.00 0.00 37.58 4.85
228 3758 3.947841 GCGGTTTCAGTGTGCGCA 61.948 61.111 5.66 5.66 0.00 6.09
245 3775 1.230635 GCACGCACAGTCATGAAGGT 61.231 55.000 0.00 0.00 0.00 3.50
248 3778 1.878775 GCACAGTCATGAAGGTGGC 59.121 57.895 22.42 14.26 0.00 5.01
253 3783 1.450312 GTCATGAAGGTGGCGGAGG 60.450 63.158 0.00 0.00 0.00 4.30
282 3812 3.942829 TCTACTAGTTCCCGAGTTTCGA 58.057 45.455 0.00 0.00 43.74 3.71
283 3813 4.521146 TCTACTAGTTCCCGAGTTTCGAT 58.479 43.478 0.00 0.00 43.74 3.59
316 3846 3.391049 GAAGGCGAACAGTCAAGTAACT 58.609 45.455 0.00 0.00 0.00 2.24
343 3873 4.704103 TCCTCGCTGGACCTGCCT 62.704 66.667 16.88 0.00 40.56 4.75
350 3880 1.908340 GCTGGACCTGCCTGTCAGAT 61.908 60.000 12.17 0.00 45.72 2.90
351 3881 0.177604 CTGGACCTGCCTGTCAGATC 59.822 60.000 0.00 0.00 45.72 2.75
353 3883 1.323271 GGACCTGCCTGTCAGATCGA 61.323 60.000 0.00 0.00 45.72 3.59
390 3920 3.050619 GGTGAAGAACTCGGCATATACG 58.949 50.000 0.00 0.00 0.00 3.06
438 3968 3.327172 TGTGGGAATACTTGTTAACCCGA 59.673 43.478 2.48 0.00 40.08 5.14
441 3971 4.225492 TGGGAATACTTGTTAACCCGATGA 59.775 41.667 2.48 0.00 40.08 2.92
443 3973 4.573607 GGAATACTTGTTAACCCGATGACC 59.426 45.833 2.48 0.00 0.00 4.02
446 3976 0.322322 TTGTTAACCCGATGACCGCT 59.678 50.000 2.48 0.00 36.84 5.52
463 3993 2.223971 CCGCTCGAAGTTGGTGGTATAT 60.224 50.000 0.00 0.00 0.00 0.86
465 3995 4.500205 CCGCTCGAAGTTGGTGGTATATAA 60.500 45.833 0.00 0.00 0.00 0.98
466 3996 5.045215 CGCTCGAAGTTGGTGGTATATAAA 58.955 41.667 0.00 0.00 0.00 1.40
468 3998 6.202188 CGCTCGAAGTTGGTGGTATATAAATT 59.798 38.462 0.00 0.00 0.00 1.82
516 4055 4.728102 TTCAATCCGCGCCGTCGT 62.728 61.111 0.00 0.00 38.14 4.34
540 4079 6.202188 GTCACGTAAAACCATGGACATATAGG 59.798 42.308 21.47 11.37 0.00 2.57
586 4125 3.267233 TCCATGCCCAGGCCTTGT 61.267 61.111 0.00 0.00 41.09 3.16
597 4136 4.347453 GCCTTGTGCGCCCAACTG 62.347 66.667 4.18 0.00 0.00 3.16
653 4192 3.591835 CTGGCGTGCGGTTTGGTT 61.592 61.111 0.00 0.00 0.00 3.67
654 4193 3.132481 CTGGCGTGCGGTTTGGTTT 62.132 57.895 0.00 0.00 0.00 3.27
655 4194 2.656973 GGCGTGCGGTTTGGTTTG 60.657 61.111 0.00 0.00 0.00 2.93
659 4198 0.456995 CGTGCGGTTTGGTTTGTTGT 60.457 50.000 0.00 0.00 0.00 3.32
660 4199 1.715993 GTGCGGTTTGGTTTGTTGTT 58.284 45.000 0.00 0.00 0.00 2.83
672 4211 6.301169 TGGTTTGTTGTTGTTTAAATCCCT 57.699 33.333 0.00 0.00 0.00 4.20
674 4213 7.848128 TGGTTTGTTGTTGTTTAAATCCCTAA 58.152 30.769 0.00 0.00 0.00 2.69
967 4506 3.794690 CATTCACGAGACCTGACGT 57.205 52.632 0.00 0.00 43.50 4.34
1044 4583 5.366482 TGCCTAGCCTATATGAACACAAA 57.634 39.130 0.00 0.00 0.00 2.83
1045 4584 5.940617 TGCCTAGCCTATATGAACACAAAT 58.059 37.500 0.00 0.00 0.00 2.32
1046 4585 5.764686 TGCCTAGCCTATATGAACACAAATG 59.235 40.000 0.00 0.00 0.00 2.32
1047 4586 5.765182 GCCTAGCCTATATGAACACAAATGT 59.235 40.000 0.00 0.00 42.46 2.71
1059 4598 4.734398 ACACAAATGTTTGCTTTCCTCA 57.266 36.364 5.44 0.00 41.79 3.86
1060 4599 4.432712 ACACAAATGTTTGCTTTCCTCAC 58.567 39.130 5.44 0.00 41.79 3.51
1061 4600 3.803778 CACAAATGTTTGCTTTCCTCACC 59.196 43.478 5.44 0.00 41.79 4.02
1062 4601 3.181466 ACAAATGTTTGCTTTCCTCACCC 60.181 43.478 5.44 0.00 41.79 4.61
1063 4602 1.247567 ATGTTTGCTTTCCTCACCCG 58.752 50.000 0.00 0.00 0.00 5.28
1064 4603 0.181587 TGTTTGCTTTCCTCACCCGA 59.818 50.000 0.00 0.00 0.00 5.14
1065 4604 1.314730 GTTTGCTTTCCTCACCCGAA 58.685 50.000 0.00 0.00 0.00 4.30
1066 4605 1.679153 GTTTGCTTTCCTCACCCGAAA 59.321 47.619 0.00 0.00 0.00 3.46
1067 4606 2.060050 TTGCTTTCCTCACCCGAAAA 57.940 45.000 0.00 0.00 0.00 2.29
1068 4607 1.604604 TGCTTTCCTCACCCGAAAAG 58.395 50.000 0.00 0.00 33.01 2.27
1069 4608 1.142060 TGCTTTCCTCACCCGAAAAGA 59.858 47.619 0.00 0.00 31.81 2.52
1070 4609 2.227194 GCTTTCCTCACCCGAAAAGAA 58.773 47.619 0.00 0.00 31.81 2.52
1071 4610 2.621526 GCTTTCCTCACCCGAAAAGAAA 59.378 45.455 0.00 0.00 31.81 2.52
1072 4611 3.067601 GCTTTCCTCACCCGAAAAGAAAA 59.932 43.478 0.00 0.00 31.81 2.29
1073 4612 4.440940 GCTTTCCTCACCCGAAAAGAAAAA 60.441 41.667 0.00 0.00 31.81 1.94
1225 4764 8.375493 ACTAATCGGCCTATCCTAATTATTGA 57.625 34.615 0.00 0.00 0.00 2.57
1288 4827 1.407618 GGTCAAAGTGTCAAACCCACC 59.592 52.381 0.00 0.00 33.20 4.61
1317 4856 3.270944 TGGCACAGGATTGGGGTT 58.729 55.556 0.00 0.00 0.00 4.11
1318 4857 1.228831 TGGCACAGGATTGGGGTTG 60.229 57.895 0.00 0.00 0.00 3.77
1319 4858 1.984026 GGCACAGGATTGGGGTTGG 60.984 63.158 0.00 0.00 0.00 3.77
1320 4859 1.984026 GCACAGGATTGGGGTTGGG 60.984 63.158 0.00 0.00 0.00 4.12
1321 4860 1.305213 CACAGGATTGGGGTTGGGG 60.305 63.158 0.00 0.00 0.00 4.96
1322 4861 2.364186 CAGGATTGGGGTTGGGGC 60.364 66.667 0.00 0.00 0.00 5.80
1379 4918 0.385390 CTTGCAGCCGAACAAAACCT 59.615 50.000 0.00 0.00 0.00 3.50
1391 4930 4.156008 CGAACAAAACCTAAAGATCAGGGG 59.844 45.833 0.00 0.00 37.51 4.79
1456 4998 1.684049 CTCGCCTCCTCCTTCCAGT 60.684 63.158 0.00 0.00 0.00 4.00
1458 5000 1.684049 CGCCTCCTCCTTCCAGTCT 60.684 63.158 0.00 0.00 0.00 3.24
1534 7591 2.499205 CCTACTTCGCCATCCGCA 59.501 61.111 0.00 0.00 37.30 5.69
1835 7919 1.507141 CCAGGCACCACAAACTCGTC 61.507 60.000 0.00 0.00 0.00 4.20
2151 8257 1.507140 TCCCGATACCCATGCTTTCT 58.493 50.000 0.00 0.00 0.00 2.52
2178 8284 3.436001 CGAGCAACGGATAAGTGGT 57.564 52.632 0.00 0.00 38.46 4.16
2207 8641 1.274703 ATCCGGGATGTCACCTGCTT 61.275 55.000 9.17 0.00 35.17 3.91
2561 9261 1.923395 CTTGCCCCACCACCCTAGA 60.923 63.158 0.00 0.00 0.00 2.43
2724 11032 2.040939 CTGGAGCTCCTCATCTGTGAT 58.959 52.381 32.28 0.00 36.82 3.06
2859 11185 7.227512 CCAATTCCCTATTTCTACATCTGACAC 59.772 40.741 0.00 0.00 0.00 3.67
2862 11188 7.437713 TCCCTATTTCTACATCTGACACATT 57.562 36.000 0.00 0.00 0.00 2.71
2872 11198 9.554395 TCTACATCTGACACATTTGTTTTCTTA 57.446 29.630 0.00 0.00 35.47 2.10
2873 11199 9.817365 CTACATCTGACACATTTGTTTTCTTAG 57.183 33.333 0.00 0.00 35.47 2.18
2916 11242 0.729140 GTGGAATCAAAAGTGCGCCG 60.729 55.000 4.18 0.00 0.00 6.46
3061 11599 9.292195 CTTTAAGAACCAAACCAACCTCTTATA 57.708 33.333 0.00 0.00 0.00 0.98
3072 11610 7.640597 ACCAACCTCTTATAAAATGGTTAGC 57.359 36.000 12.94 0.00 38.76 3.09
3110 11648 2.957060 TCCATCTGGACGTTCGACT 58.043 52.632 0.00 0.00 39.78 4.18
3111 11649 0.809385 TCCATCTGGACGTTCGACTC 59.191 55.000 0.00 0.00 39.78 3.36
3112 11650 0.811915 CCATCTGGACGTTCGACTCT 59.188 55.000 0.00 0.00 37.39 3.24
3113 11651 1.202582 CCATCTGGACGTTCGACTCTT 59.797 52.381 0.00 0.00 37.39 2.85
3114 11652 2.352814 CCATCTGGACGTTCGACTCTTT 60.353 50.000 0.00 0.00 37.39 2.52
3115 11653 2.417339 TCTGGACGTTCGACTCTTTG 57.583 50.000 0.00 0.00 0.00 2.77
3116 11654 1.000607 TCTGGACGTTCGACTCTTTGG 60.001 52.381 0.00 0.00 0.00 3.28
3117 11655 0.599204 TGGACGTTCGACTCTTTGGC 60.599 55.000 0.00 0.00 0.00 4.52
3123 11661 4.966005 CGACTCTTTGGCGTCTCA 57.034 55.556 0.00 0.00 43.40 3.27
3124 11662 3.425578 CGACTCTTTGGCGTCTCAT 57.574 52.632 0.00 0.00 43.40 2.90
3152 11690 5.639506 CGTTTGACTCTTTGGTGTCTCATAT 59.360 40.000 0.00 0.00 37.02 1.78
3156 11694 7.423844 TGACTCTTTGGTGTCTCATATATGT 57.576 36.000 12.42 0.00 37.02 2.29
3158 11696 7.124147 TGACTCTTTGGTGTCTCATATATGTGA 59.876 37.037 12.42 12.40 37.02 3.58
3161 11699 8.667076 TCTTTGGTGTCTCATATATGTGAATG 57.333 34.615 16.87 6.17 32.81 2.67
3183 11721 6.373005 TGATCCTTTAAGTGGAAGATGACA 57.627 37.500 3.83 0.00 37.13 3.58
3187 11726 7.020827 TCCTTTAAGTGGAAGATGACATTCT 57.979 36.000 0.00 0.00 0.00 2.40
3201 11740 3.618594 TGACATTCTCGTCAATAGCAAGC 59.381 43.478 0.00 0.00 42.82 4.01
3205 11744 1.275010 TCTCGTCAATAGCAAGCCACA 59.725 47.619 0.00 0.00 0.00 4.17
3208 11747 1.535028 CGTCAATAGCAAGCCACACAA 59.465 47.619 0.00 0.00 0.00 3.33
3246 11785 1.412710 TGAAGCTCAACAACTCCGACT 59.587 47.619 0.00 0.00 0.00 4.18
3248 11787 1.040646 AGCTCAACAACTCCGACTCA 58.959 50.000 0.00 0.00 0.00 3.41
3751 12290 4.689612 ACGGATAAGCCTACAATGACAT 57.310 40.909 0.00 0.00 0.00 3.06
3752 12291 5.801531 ACGGATAAGCCTACAATGACATA 57.198 39.130 0.00 0.00 0.00 2.29
3753 12292 5.539048 ACGGATAAGCCTACAATGACATAC 58.461 41.667 0.00 0.00 0.00 2.39
3754 12293 5.304614 ACGGATAAGCCTACAATGACATACT 59.695 40.000 0.00 0.00 0.00 2.12
3755 12294 5.864474 CGGATAAGCCTACAATGACATACTC 59.136 44.000 0.00 0.00 0.00 2.59
3756 12295 6.166982 GGATAAGCCTACAATGACATACTCC 58.833 44.000 0.00 0.00 0.00 3.85
3789 12328 6.494893 TTGAAAATGATACCAAGAACCTCG 57.505 37.500 0.00 0.00 0.00 4.63
3790 12329 4.394920 TGAAAATGATACCAAGAACCTCGC 59.605 41.667 0.00 0.00 0.00 5.03
3791 12330 3.627395 AATGATACCAAGAACCTCGCA 57.373 42.857 0.00 0.00 0.00 5.10
3792 12331 3.627395 ATGATACCAAGAACCTCGCAA 57.373 42.857 0.00 0.00 0.00 4.85
3793 12332 3.410631 TGATACCAAGAACCTCGCAAA 57.589 42.857 0.00 0.00 0.00 3.68
3794 12333 3.745799 TGATACCAAGAACCTCGCAAAA 58.254 40.909 0.00 0.00 0.00 2.44
3830 12474 7.040892 CCAAGAACTGACCATATCCATGTTATG 60.041 40.741 6.10 6.10 0.00 1.90
3834 12478 8.627208 AACTGACCATATCCATGTTATGATTC 57.373 34.615 12.27 9.37 30.16 2.52
3835 12479 7.170965 ACTGACCATATCCATGTTATGATTCC 58.829 38.462 12.27 2.81 30.16 3.01
3838 12482 5.014123 ACCATATCCATGTTATGATTCCGGT 59.986 40.000 0.00 4.10 30.16 5.28
3839 12483 5.355071 CCATATCCATGTTATGATTCCGGTG 59.645 44.000 0.00 0.00 30.16 4.94
3840 12484 3.207265 TCCATGTTATGATTCCGGTGG 57.793 47.619 0.00 0.00 0.00 4.61
3841 12485 2.507886 TCCATGTTATGATTCCGGTGGT 59.492 45.455 0.00 0.00 0.00 4.16
3843 12487 3.433598 CCATGTTATGATTCCGGTGGTCT 60.434 47.826 0.00 0.00 0.00 3.85
3846 12490 4.658063 TGTTATGATTCCGGTGGTCTTTT 58.342 39.130 0.00 0.00 0.00 2.27
3847 12491 4.698304 TGTTATGATTCCGGTGGTCTTTTC 59.302 41.667 0.00 0.00 0.00 2.29
3848 12492 2.940994 TGATTCCGGTGGTCTTTTCA 57.059 45.000 0.00 0.00 0.00 2.69
3849 12493 3.216187 TGATTCCGGTGGTCTTTTCAA 57.784 42.857 0.00 0.00 0.00 2.69
3850 12494 2.882137 TGATTCCGGTGGTCTTTTCAAC 59.118 45.455 0.00 0.00 0.00 3.18
3851 12495 2.421751 TTCCGGTGGTCTTTTCAACA 57.578 45.000 0.00 0.00 0.00 3.33
3852 12496 2.421751 TCCGGTGGTCTTTTCAACAA 57.578 45.000 0.00 0.00 0.00 2.83
3853 12497 2.938838 TCCGGTGGTCTTTTCAACAAT 58.061 42.857 0.00 0.00 0.00 2.71
3854 12498 2.882137 TCCGGTGGTCTTTTCAACAATC 59.118 45.455 0.00 0.00 0.00 2.67
3855 12499 2.621055 CCGGTGGTCTTTTCAACAATCA 59.379 45.455 0.00 0.00 0.00 2.57
3856 12500 3.067461 CCGGTGGTCTTTTCAACAATCAA 59.933 43.478 0.00 0.00 0.00 2.57
3857 12501 4.261994 CCGGTGGTCTTTTCAACAATCAAT 60.262 41.667 0.00 0.00 0.00 2.57
3858 12502 4.917415 CGGTGGTCTTTTCAACAATCAATC 59.083 41.667 0.00 0.00 0.00 2.67
3865 12509 9.044150 GGTCTTTTCAACAATCAATCATCAAAA 57.956 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.853126 ACTGCACGTACCTAATATATAACAGAA 58.147 33.333 0.00 0.00 0.00 3.02
8 9 8.400184 ACTGCACGTACCTAATATATAACAGA 57.600 34.615 0.00 0.00 0.00 3.41
14 15 8.302438 GGAAACTACTGCACGTACCTAATATAT 58.698 37.037 0.00 0.00 0.00 0.86
16 17 6.097270 TGGAAACTACTGCACGTACCTAATAT 59.903 38.462 0.00 0.00 0.00 1.28
29 3558 6.095377 CAGATTGGATTTTGGAAACTACTGC 58.905 40.000 0.00 0.00 0.00 4.40
70 3599 0.170561 CCAGTACTTGCTAGTCGCGT 59.829 55.000 5.77 0.00 43.27 6.01
121 3650 3.524648 GACGACGGGTGGCTGGAAA 62.525 63.158 0.00 0.00 0.00 3.13
143 3672 3.121030 GTAGCTGGCACTGGCACG 61.121 66.667 0.07 0.00 43.71 5.34
228 3758 0.603707 CCACCTTCATGACTGTGCGT 60.604 55.000 15.28 0.00 0.00 5.24
237 3767 2.825836 GCCTCCGCCACCTTCATG 60.826 66.667 0.00 0.00 0.00 3.07
245 3775 1.609635 TAGAACATTCGCCTCCGCCA 61.610 55.000 0.00 0.00 0.00 5.69
248 3778 2.358267 ACTAGTAGAACATTCGCCTCCG 59.642 50.000 3.59 0.00 0.00 4.63
253 3783 3.114065 CGGGAACTAGTAGAACATTCGC 58.886 50.000 3.59 4.90 0.00 4.70
260 3790 4.326826 TCGAAACTCGGGAACTAGTAGAA 58.673 43.478 3.59 0.00 40.88 2.10
282 3812 0.603569 CGCCTTCCTATGCCGAGTAT 59.396 55.000 0.00 0.00 0.00 2.12
283 3813 0.466739 TCGCCTTCCTATGCCGAGTA 60.467 55.000 0.00 0.00 0.00 2.59
294 3824 2.450609 TACTTGACTGTTCGCCTTCC 57.549 50.000 0.00 0.00 0.00 3.46
316 3846 1.299850 CAGCGAGGACGTGTCAACA 60.300 57.895 0.00 0.00 41.98 3.33
339 3869 0.668535 CGGTATCGATCTGACAGGCA 59.331 55.000 0.00 0.00 39.00 4.75
340 3870 0.952280 TCGGTATCGATCTGACAGGC 59.048 55.000 0.00 0.00 40.88 4.85
343 3873 2.640184 ACACTCGGTATCGATCTGACA 58.360 47.619 0.00 0.00 45.04 3.58
350 3880 0.098200 CGCAGAACACTCGGTATCGA 59.902 55.000 0.00 0.00 43.86 3.59
351 3881 0.866061 CCGCAGAACACTCGGTATCG 60.866 60.000 0.00 0.00 38.47 2.92
407 3937 7.784633 AACAAGTATTCCCACAATTTGTTTG 57.215 32.000 0.00 2.46 41.36 2.93
411 3941 6.871492 GGGTTAACAAGTATTCCCACAATTTG 59.129 38.462 8.10 0.00 35.43 2.32
438 3968 0.670546 CACCAACTTCGAGCGGTCAT 60.671 55.000 15.89 0.00 0.00 3.06
441 3971 1.466025 TACCACCAACTTCGAGCGGT 61.466 55.000 0.00 0.00 0.00 5.68
443 3973 2.572191 TATACCACCAACTTCGAGCG 57.428 50.000 0.00 0.00 0.00 5.03
481 4020 6.878389 GGATTGAAATTTCTGGCATTAAACCA 59.122 34.615 18.64 1.05 35.40 3.67
516 4055 6.285224 CCTATATGTCCATGGTTTTACGTGA 58.715 40.000 12.58 0.00 0.00 4.35
540 4079 2.124570 ATGCACGGACATCCAGCC 60.125 61.111 9.20 0.00 36.29 4.85
552 4091 4.722700 ACCGAGGGCCACATGCAC 62.723 66.667 6.18 0.00 46.89 4.57
637 4176 3.141488 AAACCAAACCGCACGCCA 61.141 55.556 0.00 0.00 0.00 5.69
949 4488 3.794690 ACGTCAGGTCTCGTGAATG 57.205 52.632 0.00 0.00 38.85 2.67
964 4503 2.353579 GCCTCATTTTTATACGCCACGT 59.646 45.455 0.00 0.00 44.35 4.49
966 4505 3.691498 GTGCCTCATTTTTATACGCCAC 58.309 45.455 0.00 0.00 0.00 5.01
967 4506 2.353269 CGTGCCTCATTTTTATACGCCA 59.647 45.455 0.00 0.00 0.00 5.69
1005 4544 4.603535 AGCTTTGGGGCGGCTTGT 62.604 61.111 9.56 0.00 37.29 3.16
1006 4545 4.060038 CAGCTTTGGGGCGGCTTG 62.060 66.667 9.56 0.00 37.29 4.01
1011 4550 2.825836 CTAGGCAGCTTTGGGGCG 60.826 66.667 0.00 0.00 37.29 6.13
1012 4551 3.143515 GCTAGGCAGCTTTGGGGC 61.144 66.667 0.00 0.00 44.93 5.80
1037 4576 4.869861 GTGAGGAAAGCAAACATTTGTGTT 59.130 37.500 6.24 1.23 40.24 3.32
1044 4583 1.202879 TCGGGTGAGGAAAGCAAACAT 60.203 47.619 0.00 0.00 0.00 2.71
1045 4584 0.181587 TCGGGTGAGGAAAGCAAACA 59.818 50.000 0.00 0.00 0.00 2.83
1046 4585 1.314730 TTCGGGTGAGGAAAGCAAAC 58.685 50.000 0.00 0.00 0.00 2.93
1047 4586 2.060050 TTTCGGGTGAGGAAAGCAAA 57.940 45.000 0.00 0.00 0.00 3.68
1051 4590 4.911514 TTTTCTTTTCGGGTGAGGAAAG 57.088 40.909 0.00 0.00 35.08 2.62
1071 4610 9.660180 TTAAACTAGGAAAGCAAACATGTTTTT 57.340 25.926 21.10 13.21 0.00 1.94
1072 4611 9.093970 GTTAAACTAGGAAAGCAAACATGTTTT 57.906 29.630 21.10 7.02 0.00 2.43
1073 4612 8.474831 AGTTAAACTAGGAAAGCAAACATGTTT 58.525 29.630 18.13 18.13 0.00 2.83
1190 4729 2.615912 AGGCCGATTAGTAGTACGTGTC 59.384 50.000 0.00 0.00 0.00 3.67
1225 4764 6.540189 GTGATCTATGCTTGGTAATCTTGTGT 59.460 38.462 0.00 0.00 0.00 3.72
1238 4777 5.911752 GGATATGATCCGTGATCTATGCTT 58.088 41.667 12.97 0.00 40.13 3.91
1288 4827 4.394712 GTGCCAGAGTCCCCGTGG 62.395 72.222 0.00 0.00 0.00 4.94
1304 4843 3.190349 CCCCAACCCCAATCCTGT 58.810 61.111 0.00 0.00 0.00 4.00
1368 4907 4.156008 CCCCTGATCTTTAGGTTTTGTTCG 59.844 45.833 0.00 0.00 33.31 3.95
1391 4930 0.107643 GCAGGCTGGAAGGAGGATAC 59.892 60.000 17.64 0.00 0.00 2.24
1456 4998 3.429141 GCGAGTGACGACGGGAGA 61.429 66.667 0.00 0.00 45.77 3.71
1528 7585 3.118454 CGTGGCGTTCTTGCGGAT 61.118 61.111 0.00 0.00 35.06 4.18
1608 7665 3.406595 GAAGTGGGAGATGGCCGGG 62.407 68.421 2.18 0.00 0.00 5.73
1835 7919 2.253452 GCAGGACGCACAAGCTTG 59.747 61.111 24.84 24.84 41.79 4.01
2151 8257 0.669619 TCCGTTGCTCGTCACAGTAA 59.330 50.000 1.89 0.00 37.94 2.24
2207 8641 5.760743 TCGACAAACTTGATGTAACCATTGA 59.239 36.000 0.00 0.00 0.00 2.57
2507 9174 2.586792 GTGCCGATCTTCCAGCCT 59.413 61.111 0.00 0.00 0.00 4.58
2561 9261 0.615331 AACATCCTCGCTGTCCATGT 59.385 50.000 0.00 0.00 0.00 3.21
2724 11032 7.281774 GGAGTTGCATTCAGATATTCAGAGAAA 59.718 37.037 0.00 0.00 0.00 2.52
2862 11188 8.232913 ACCTGAAGCAAATACTAAGAAAACAA 57.767 30.769 0.00 0.00 0.00 2.83
2872 11198 6.375455 CCAATACTTGACCTGAAGCAAATACT 59.625 38.462 0.00 0.00 0.00 2.12
2873 11199 6.151144 ACCAATACTTGACCTGAAGCAAATAC 59.849 38.462 0.00 0.00 0.00 1.89
2902 11228 0.456653 GCATTCGGCGCACTTTTGAT 60.457 50.000 10.83 0.00 0.00 2.57
2916 11242 4.094887 ACATGACAGTTATGTTCCGCATTC 59.905 41.667 5.12 0.00 40.68 2.67
2979 11346 6.300703 AGCACACAGTTAAAATTGTACCCTA 58.699 36.000 0.00 0.00 0.00 3.53
3027 11556 5.826208 TGGTTTGGTTCTTAAAGGAACTCTC 59.174 40.000 7.34 0.00 43.43 3.20
3039 11577 8.541899 TTTTATAAGAGGTTGGTTTGGTTCTT 57.458 30.769 0.00 0.00 0.00 2.52
3061 11599 5.699143 AGCATCATCCTAGCTAACCATTTT 58.301 37.500 0.00 0.00 36.73 1.82
3106 11644 0.994995 CATGAGACGCCAAAGAGTCG 59.005 55.000 0.00 0.00 46.37 4.18
3107 11645 1.066858 TCCATGAGACGCCAAAGAGTC 60.067 52.381 0.00 0.00 42.60 3.36
3108 11646 0.976641 TCCATGAGACGCCAAAGAGT 59.023 50.000 0.00 0.00 0.00 3.24
3109 11647 1.363744 GTCCATGAGACGCCAAAGAG 58.636 55.000 0.00 0.00 35.30 2.85
3110 11648 3.532896 GTCCATGAGACGCCAAAGA 57.467 52.632 0.00 0.00 35.30 2.52
3118 11656 3.305398 AGAGTCAAACGTCCATGAGAC 57.695 47.619 0.00 0.00 42.54 3.36
3119 11657 4.058124 CAAAGAGTCAAACGTCCATGAGA 58.942 43.478 0.00 0.00 0.00 3.27
3120 11658 3.187227 CCAAAGAGTCAAACGTCCATGAG 59.813 47.826 0.00 0.00 0.00 2.90
3121 11659 3.138304 CCAAAGAGTCAAACGTCCATGA 58.862 45.455 0.00 0.00 0.00 3.07
3122 11660 2.878406 ACCAAAGAGTCAAACGTCCATG 59.122 45.455 0.00 0.00 0.00 3.66
3123 11661 2.878406 CACCAAAGAGTCAAACGTCCAT 59.122 45.455 0.00 0.00 0.00 3.41
3124 11662 2.285083 CACCAAAGAGTCAAACGTCCA 58.715 47.619 0.00 0.00 0.00 4.02
3129 11667 8.607459 CATATATGAGACACCAAAGAGTCAAAC 58.393 37.037 6.92 0.00 36.19 2.93
3152 11690 8.548025 TCTTCCACTTAAAGGATCATTCACATA 58.452 33.333 0.00 0.00 34.56 2.29
3156 11694 7.554118 GTCATCTTCCACTTAAAGGATCATTCA 59.446 37.037 0.00 0.00 34.56 2.57
3158 11696 7.405292 TGTCATCTTCCACTTAAAGGATCATT 58.595 34.615 0.00 0.00 34.56 2.57
3161 11699 7.772757 AGAATGTCATCTTCCACTTAAAGGATC 59.227 37.037 0.00 0.00 34.56 3.36
3169 11707 4.021104 TGACGAGAATGTCATCTTCCACTT 60.021 41.667 0.00 0.00 43.62 3.16
3183 11721 2.939103 GTGGCTTGCTATTGACGAGAAT 59.061 45.455 0.00 0.00 0.00 2.40
3187 11726 1.270571 TGTGTGGCTTGCTATTGACGA 60.271 47.619 0.00 0.00 0.00 4.20
3201 11740 1.811965 TGATGAATTCGCCTTGTGTGG 59.188 47.619 0.04 0.00 0.00 4.17
3205 11744 4.278170 TCAAAACTGATGAATTCGCCTTGT 59.722 37.500 0.04 0.00 0.00 3.16
3208 11747 4.616835 GCTTCAAAACTGATGAATTCGCCT 60.617 41.667 0.04 0.00 36.30 5.52
3211 11750 5.692814 TGAGCTTCAAAACTGATGAATTCG 58.307 37.500 0.04 0.00 36.30 3.34
3214 11753 6.395426 TGTTGAGCTTCAAAACTGATGAAT 57.605 33.333 0.00 0.00 38.22 2.57
3696 12235 8.178313 GCAACATTAGTGTATCTCCTTTTTCTC 58.822 37.037 0.00 0.00 37.67 2.87
3697 12236 7.665559 TGCAACATTAGTGTATCTCCTTTTTCT 59.334 33.333 0.00 0.00 37.67 2.52
3698 12237 7.750903 GTGCAACATTAGTGTATCTCCTTTTTC 59.249 37.037 0.00 0.00 37.67 2.29
3699 12238 7.230510 TGTGCAACATTAGTGTATCTCCTTTTT 59.769 33.333 0.00 0.00 45.67 1.94
3700 12239 6.714810 TGTGCAACATTAGTGTATCTCCTTTT 59.285 34.615 0.00 0.00 45.67 2.27
3701 12240 6.237901 TGTGCAACATTAGTGTATCTCCTTT 58.762 36.000 0.00 0.00 45.67 3.11
3702 12241 5.804639 TGTGCAACATTAGTGTATCTCCTT 58.195 37.500 0.00 0.00 45.67 3.36
3703 12242 5.420725 TGTGCAACATTAGTGTATCTCCT 57.579 39.130 0.00 0.00 45.67 3.69
3769 12308 4.331968 TGCGAGGTTCTTGGTATCATTTT 58.668 39.130 0.00 0.00 0.00 1.82
3770 12309 3.950397 TGCGAGGTTCTTGGTATCATTT 58.050 40.909 0.00 0.00 0.00 2.32
3771 12310 3.627395 TGCGAGGTTCTTGGTATCATT 57.373 42.857 0.00 0.00 0.00 2.57
3772 12311 3.627395 TTGCGAGGTTCTTGGTATCAT 57.373 42.857 0.00 0.00 0.00 2.45
3773 12312 3.410631 TTTGCGAGGTTCTTGGTATCA 57.589 42.857 0.00 0.00 0.00 2.15
3774 12313 4.759516 TTTTTGCGAGGTTCTTGGTATC 57.240 40.909 0.00 0.00 0.00 2.24
3794 12333 7.781324 ATGGTCAGTTCTTGGTATCATTTTT 57.219 32.000 0.00 0.00 0.00 1.94
3830 12474 2.882137 TGTTGAAAAGACCACCGGAATC 59.118 45.455 9.46 1.73 0.00 2.52
3834 12478 2.621055 TGATTGTTGAAAAGACCACCGG 59.379 45.455 0.00 0.00 0.00 5.28
3835 12479 3.980646 TGATTGTTGAAAAGACCACCG 57.019 42.857 0.00 0.00 0.00 4.94
3838 12482 7.287512 TGATGATTGATTGTTGAAAAGACCA 57.712 32.000 0.00 0.00 0.00 4.02
3839 12483 8.592105 TTTGATGATTGATTGTTGAAAAGACC 57.408 30.769 0.00 0.00 0.00 3.85
3841 12485 9.263538 CCTTTTGATGATTGATTGTTGAAAAGA 57.736 29.630 0.00 0.00 32.22 2.52
3843 12487 7.444792 CCCCTTTTGATGATTGATTGTTGAAAA 59.555 33.333 0.00 0.00 0.00 2.29
3846 12490 5.779260 TCCCCTTTTGATGATTGATTGTTGA 59.221 36.000 0.00 0.00 0.00 3.18
3847 12491 6.040209 TCCCCTTTTGATGATTGATTGTTG 57.960 37.500 0.00 0.00 0.00 3.33
3848 12492 6.879367 ATCCCCTTTTGATGATTGATTGTT 57.121 33.333 0.00 0.00 0.00 2.83
3849 12493 6.352394 CCAATCCCCTTTTGATGATTGATTGT 60.352 38.462 11.51 0.00 44.24 2.71
3850 12494 6.053005 CCAATCCCCTTTTGATGATTGATTG 58.947 40.000 11.51 0.00 44.24 2.67
3851 12495 5.397109 GCCAATCCCCTTTTGATGATTGATT 60.397 40.000 11.51 0.00 44.24 2.57
3852 12496 4.102054 GCCAATCCCCTTTTGATGATTGAT 59.898 41.667 11.51 0.00 44.24 2.57
3853 12497 3.451902 GCCAATCCCCTTTTGATGATTGA 59.548 43.478 11.51 0.00 44.24 2.57
3854 12498 3.198200 TGCCAATCCCCTTTTGATGATTG 59.802 43.478 0.00 0.00 42.23 2.67
3855 12499 3.452878 TGCCAATCCCCTTTTGATGATT 58.547 40.909 0.00 0.00 0.00 2.57
3856 12500 3.119009 TGCCAATCCCCTTTTGATGAT 57.881 42.857 0.00 0.00 0.00 2.45
3857 12501 2.619697 TGCCAATCCCCTTTTGATGA 57.380 45.000 0.00 0.00 0.00 2.92
3858 12502 3.962718 ACTATGCCAATCCCCTTTTGATG 59.037 43.478 0.00 0.00 0.00 3.07
3865 12509 4.416848 ACTTGAATACTATGCCAATCCCCT 59.583 41.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.