Multiple sequence alignment - TraesCS3B01G365000

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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 TraesCS3B01G365000 chr3B 100.000 5355 0 0 1 5355 576444732 576450086 0.000000e+00 9889.0
1 TraesCS3B01G365000 chr3D 92.297 4375 205 55 492 4784 439673122 439677446 0.000000e+00 6091.0
2 TraesCS3B01G365000 chr3D 95.969 1662 44 7 2113 3771 141540720 141539079 0.000000e+00 2676.0
3 TraesCS3B01G365000 chr3D 95.665 1661 50 10 2113 3771 141546904 141545264 0.000000e+00 2649.0
4 TraesCS3B01G365000 chr3D 96.170 1462 51 4 2312 3771 141563697 141562239 0.000000e+00 2385.0
5 TraesCS3B01G365000 chr3D 95.244 778 36 1 2557 3333 567166932 567166155 0.000000e+00 1230.0
6 TraesCS3B01G365000 chr3D 89.331 478 38 4 4882 5355 439677445 439677913 5.970000e-164 588.0
7 TraesCS3B01G365000 chr3D 91.049 324 16 6 146 457 439672684 439673006 4.960000e-115 425.0
8 TraesCS3B01G365000 chr3D 93.952 248 4 1 1974 2221 567167165 567166929 1.100000e-96 364.0
9 TraesCS3B01G365000 chr3D 96.970 132 4 0 15 146 439672524 439672655 6.980000e-54 222.0
10 TraesCS3B01G365000 chr3A 91.338 2563 145 36 2831 5355 579375210 579377733 0.000000e+00 3432.0
11 TraesCS3B01G365000 chr3A 91.971 2242 93 30 658 2846 579372989 579375196 0.000000e+00 3062.0
12 TraesCS3B01G365000 chr3A 89.014 355 12 8 165 493 579372244 579372597 1.070000e-111 414.0
13 TraesCS3B01G365000 chr3A 90.588 170 11 3 492 660 579372679 579372844 2.510000e-53 220.0
14 TraesCS3B01G365000 chr3A 92.366 131 7 1 16 146 579372061 579372188 3.290000e-42 183.0
15 TraesCS3B01G365000 chr7D 95.422 1660 70 5 2554 4211 141532783 141534438 0.000000e+00 2639.0
16 TraesCS3B01G365000 chr7D 95.432 1007 38 5 3208 4211 141540658 141541659 0.000000e+00 1598.0
17 TraesCS3B01G365000 chr7D 97.630 211 4 1 1974 2184 596365396 596365605 1.420000e-95 361.0
18 TraesCS3B01G365000 chr7D 97.156 211 5 1 1974 2184 141532553 141532762 6.600000e-94 355.0
19 TraesCS3B01G365000 chr5D 96.340 1530 51 4 2554 4081 28019631 28021157 0.000000e+00 2510.0
20 TraesCS3B01G365000 chr5D 97.156 211 5 1 1974 2184 28019401 28019610 6.600000e-94 355.0
21 TraesCS3B01G365000 chr5D 91.558 154 13 0 4058 4211 28021172 28021325 4.200000e-51 213.0
22 TraesCS3B01G365000 chr1D 93.870 1664 57 17 2113 3771 46647748 46646125 0.000000e+00 2466.0
23 TraesCS3B01G365000 chr1D 95.826 1150 43 4 2625 3771 335749814 335748667 0.000000e+00 1853.0
24 TraesCS3B01G365000 chr1D 97.630 211 4 1 1974 2184 288349054 288349263 1.420000e-95 361.0
25 TraesCS3B01G365000 chr1D 98.876 89 1 0 1974 2062 26569548 26569460 5.550000e-35 159.0
26 TraesCS3B01G365000 chr4D 93.735 431 26 1 3781 4211 108899053 108899482 0.000000e+00 645.0
27 TraesCS3B01G365000 chr6D 96.209 211 7 1 1974 2184 56369200 56369409 1.430000e-90 344.0
28 TraesCS3B01G365000 chr6D 94.286 35 1 1 1011 1045 473422593 473422560 1.000000e-02 52.8
29 TraesCS3B01G365000 chr2B 92.308 39 1 2 1011 1048 39428321 39428284 3.000000e-03 54.7
30 TraesCS3B01G365000 chr2A 86.792 53 1 4 994 1042 314683046 314683096 3.000000e-03 54.7
31 TraesCS3B01G365000 chrUn 96.875 32 0 1 1011 1042 304156377 304156407 1.000000e-02 52.8
32 TraesCS3B01G365000 chr4B 96.875 32 0 1 1011 1042 237021404 237021434 1.000000e-02 52.8


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 TraesCS3B01G365000 chr3B 576444732 576450086 5354 False 9889.0 9889 100.00000 1 5355 1 chr3B.!!$F1 5354
1 TraesCS3B01G365000 chr3D 141539079 141540720 1641 True 2676.0 2676 95.96900 2113 3771 1 chr3D.!!$R1 1658
2 TraesCS3B01G365000 chr3D 141545264 141546904 1640 True 2649.0 2649 95.66500 2113 3771 1 chr3D.!!$R2 1658
3 TraesCS3B01G365000 chr3D 141562239 141563697 1458 True 2385.0 2385 96.17000 2312 3771 1 chr3D.!!$R3 1459
4 TraesCS3B01G365000 chr3D 439672524 439677913 5389 False 1831.5 6091 92.41175 15 5355 4 chr3D.!!$F1 5340
5 TraesCS3B01G365000 chr3D 567166155 567167165 1010 True 797.0 1230 94.59800 1974 3333 2 chr3D.!!$R4 1359
6 TraesCS3B01G365000 chr3A 579372061 579377733 5672 False 1462.2 3432 91.05540 16 5355 5 chr3A.!!$F1 5339
7 TraesCS3B01G365000 chr7D 141540658 141541659 1001 False 1598.0 1598 95.43200 3208 4211 1 chr7D.!!$F1 1003
8 TraesCS3B01G365000 chr7D 141532553 141534438 1885 False 1497.0 2639 96.28900 1974 4211 2 chr7D.!!$F3 2237
9 TraesCS3B01G365000 chr5D 28019401 28021325 1924 False 1026.0 2510 95.01800 1974 4211 3 chr5D.!!$F1 2237
10 TraesCS3B01G365000 chr1D 46646125 46647748 1623 True 2466.0 2466 93.87000 2113 3771 1 chr1D.!!$R2 1658
11 TraesCS3B01G365000 chr1D 335748667 335749814 1147 True 1853.0 1853 95.82600 2625 3771 1 chr1D.!!$R3 1146

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
372 428 0.392193 CTGCGGATGCCAAGAAGAGT 60.392 55.0 0.00 0.00 41.78 3.24 F
450 509 0.468226 TTTGTCTGGCACCTTCTCGT 59.532 50.0 0.00 0.00 0.00 4.18 F
1053 1360 0.539518 GCCTCCTCTTCACCCTTCTC 59.460 60.0 0.00 0.00 0.00 2.87 F
2299 2663 0.695347 ACCTCCTCCTTCAAGGCTTG 59.305 55.0 21.17 21.17 36.29 4.01 F
3778 4200 0.616111 AGGAGACCGGCAAGATCACT 60.616 55.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1677 0.326264 AATCTCCCAAACGCAGAGCT 59.674 50.0 0.00 0.0 0.00 4.09 R
1664 2019 0.606673 GGACAGCAAAGGGAGGACAC 60.607 60.0 0.00 0.0 0.00 3.67 R
2976 3393 0.179097 GTTCCCCGATGACTCTCTGC 60.179 60.0 0.00 0.0 0.00 4.26 R
3992 4414 0.036875 CGAAGCTCCTCTTGGGGTTT 59.963 55.0 0.00 0.0 40.10 3.27 R
4772 5274 0.178970 GCCTGGGCTTCATGGATCAT 60.179 55.0 4.12 0.0 38.26 2.45 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
138 139 5.244402 TGAAGATAGTCGTAACCACCTTTGA 59.756 40.000 0.00 0.00 0.00 2.69
274 321 0.629058 GGCCTAAGGTGGGGATCAAA 59.371 55.000 0.00 0.00 0.00 2.69
348 404 6.515531 GCATGTTTGGAATCTTCTTGACAGAA 60.516 38.462 0.00 0.00 36.62 3.02
372 428 0.392193 CTGCGGATGCCAAGAAGAGT 60.392 55.000 0.00 0.00 41.78 3.24
380 436 4.036144 GGATGCCAAGAAGAGTTGCTATTC 59.964 45.833 0.00 0.00 32.58 1.75
446 505 2.087646 GGATCTTTGTCTGGCACCTTC 58.912 52.381 0.00 0.00 0.00 3.46
450 509 0.468226 TTTGTCTGGCACCTTCTCGT 59.532 50.000 0.00 0.00 0.00 4.18
457 516 1.291132 GGCACCTTCTCGTATCAAGC 58.709 55.000 0.00 0.00 0.00 4.01
518 674 1.232119 TATGCAGAAGCGCCATGATG 58.768 50.000 2.29 0.00 46.23 3.07
522 678 2.117156 AGAAGCGCCATGATGCCAC 61.117 57.895 2.29 0.00 0.00 5.01
549 705 4.823989 ACTTGCTGGCCTGTATATGATTTC 59.176 41.667 11.69 0.00 0.00 2.17
598 754 1.460504 CATCTCCTGTGCTGCATGTT 58.539 50.000 5.27 0.00 0.00 2.71
599 755 1.132453 CATCTCCTGTGCTGCATGTTG 59.868 52.381 5.27 0.00 0.00 3.33
734 1038 1.137675 TCCACAGAATCATCGGCTCTG 59.862 52.381 0.00 0.00 41.93 3.35
760 1064 0.596082 CACACCGTGAAAATGACCCC 59.404 55.000 5.28 0.00 35.23 4.95
885 1189 3.064958 TCTGTTAGACAAGATACGCTCCG 59.935 47.826 0.00 0.00 0.00 4.63
929 1233 5.285134 CGTGAAACAAACCAACAAACTAGTG 59.715 40.000 0.00 0.00 35.74 2.74
938 1242 4.134563 CCAACAAACTAGTGCCACTACTT 58.865 43.478 0.00 0.00 32.19 2.24
989 1296 0.846693 AGCAGGAGTTGGAAAGTGGT 59.153 50.000 0.00 0.00 0.00 4.16
994 1301 1.515521 GAGTTGGAAAGTGGTGGCCG 61.516 60.000 0.00 0.00 0.00 6.13
997 1304 2.671963 GGAAAGTGGTGGCCGGAC 60.672 66.667 5.05 0.56 0.00 4.79
1045 1352 3.077556 GCCTCCGCCTCCTCTTCA 61.078 66.667 0.00 0.00 0.00 3.02
1046 1353 2.896443 CCTCCGCCTCCTCTTCAC 59.104 66.667 0.00 0.00 0.00 3.18
1047 1354 2.726351 CCTCCGCCTCCTCTTCACC 61.726 68.421 0.00 0.00 0.00 4.02
1048 1355 2.683933 TCCGCCTCCTCTTCACCC 60.684 66.667 0.00 0.00 0.00 4.61
1049 1356 2.685380 CCGCCTCCTCTTCACCCT 60.685 66.667 0.00 0.00 0.00 4.34
1050 1357 2.294078 CCGCCTCCTCTTCACCCTT 61.294 63.158 0.00 0.00 0.00 3.95
1051 1358 1.219393 CGCCTCCTCTTCACCCTTC 59.781 63.158 0.00 0.00 0.00 3.46
1052 1359 1.261238 CGCCTCCTCTTCACCCTTCT 61.261 60.000 0.00 0.00 0.00 2.85
1053 1360 0.539518 GCCTCCTCTTCACCCTTCTC 59.460 60.000 0.00 0.00 0.00 2.87
1054 1361 0.820871 CCTCCTCTTCACCCTTCTCG 59.179 60.000 0.00 0.00 0.00 4.04
1055 1362 1.551452 CTCCTCTTCACCCTTCTCGT 58.449 55.000 0.00 0.00 0.00 4.18
1056 1363 1.896465 CTCCTCTTCACCCTTCTCGTT 59.104 52.381 0.00 0.00 0.00 3.85
1089 1396 4.760047 GCGTCTCACCCGGCACAT 62.760 66.667 0.00 0.00 0.00 3.21
1175 1484 1.587933 TACGCGGTTGGATTTTGGGC 61.588 55.000 12.47 0.00 0.00 5.36
1359 1677 1.475280 CGAACATCCCGGTGAGTTCTA 59.525 52.381 20.66 0.00 38.50 2.10
1535 1860 1.068264 CGAACTGACACTGCTAGCTCA 60.068 52.381 17.23 10.15 0.00 4.26
1537 1862 1.626686 ACTGACACTGCTAGCTCACT 58.373 50.000 17.23 0.00 0.00 3.41
1577 1904 4.680171 CTTGAAAAGTACCGATGGGAAC 57.320 45.455 0.00 0.00 39.70 3.62
1595 1922 1.136828 ACCTGCAGGGACAGTAAACA 58.863 50.000 35.42 0.00 40.27 2.83
1604 1931 5.122396 GCAGGGACAGTAAACAGTAGATTTG 59.878 44.000 0.00 0.00 0.00 2.32
1630 1957 7.862873 GGACTGTTGACCTTATTTTTCTTTCTG 59.137 37.037 0.00 0.00 0.00 3.02
1661 2016 6.527023 GCATGAAGTGAAATGTTCTGATGAAG 59.473 38.462 0.00 0.00 32.15 3.02
1664 2019 5.852738 AGTGAAATGTTCTGATGAAGTCG 57.147 39.130 0.00 0.00 32.15 4.18
1674 2029 1.187087 GATGAAGTCGTGTCCTCCCT 58.813 55.000 0.00 0.00 0.00 4.20
1698 2054 2.352715 GCTGTCCAACCTTGCCAATTAC 60.353 50.000 0.00 0.00 0.00 1.89
1700 2056 3.153919 TGTCCAACCTTGCCAATTACTC 58.846 45.455 0.00 0.00 0.00 2.59
1735 2096 6.384015 TCTCATATCACTTGTAGGTTGGTGAT 59.616 38.462 11.28 11.28 46.67 3.06
1794 2155 1.134907 CATGCCAGGTGATTTCTTGCC 60.135 52.381 0.00 0.00 0.00 4.52
1808 2172 8.844244 GTGATTTCTTGCCATAGTTCTGAATAT 58.156 33.333 0.00 0.00 0.00 1.28
1809 2173 9.060347 TGATTTCTTGCCATAGTTCTGAATATC 57.940 33.333 0.00 0.00 0.00 1.63
1810 2174 8.985315 ATTTCTTGCCATAGTTCTGAATATCA 57.015 30.769 0.00 0.00 0.00 2.15
1823 2187 8.566260 AGTTCTGAATATCAATAATTCAGCTGC 58.434 33.333 9.47 11.06 46.43 5.25
1828 2192 9.565090 TGAATATCAATAATTCAGCTGCTACTT 57.435 29.630 9.47 2.12 31.50 2.24
1879 2243 5.835280 GGGAAATATCACAGGTGGAATTGAT 59.165 40.000 0.00 0.00 33.31 2.57
1969 2333 4.269523 GCACTGGCTGGTGGGACA 62.270 66.667 11.67 0.00 37.65 4.02
2071 2435 4.853007 AGGCTGCTATGGATTATGGATTC 58.147 43.478 0.00 0.00 0.00 2.52
2189 2553 9.476202 TCTTGGATTATTCTGTTACATATCGTG 57.524 33.333 0.00 0.00 0.00 4.35
2299 2663 0.695347 ACCTCCTCCTTCAAGGCTTG 59.305 55.000 21.17 21.17 36.29 4.01
2467 2831 3.314080 TGTCTTGACGGGTTCATGTTTTC 59.686 43.478 0.00 0.00 32.84 2.29
2632 3003 2.592459 GCAAAATTCGTCAATACACCGC 59.408 45.455 0.00 0.00 0.00 5.68
2701 3072 5.745227 CCAAGGCTAAAAGAGAAGGTATGA 58.255 41.667 0.00 0.00 0.00 2.15
2708 3079 5.441718 AAAAGAGAAGGTATGATGCCTGA 57.558 39.130 1.91 0.00 36.30 3.86
2744 3122 5.534207 ACAAGTTCCTCATCAATGCAAAA 57.466 34.783 0.00 0.00 0.00 2.44
2745 3123 5.535333 ACAAGTTCCTCATCAATGCAAAAG 58.465 37.500 0.00 0.00 0.00 2.27
2792 3171 5.880054 TTACTTTCAGAACATTGGCTAGC 57.120 39.130 6.04 6.04 0.00 3.42
2887 3303 2.651334 CCCATGGGATTGATCATACCCT 59.349 50.000 28.27 15.99 42.49 4.34
2891 3307 5.711976 CCATGGGATTGATCATACCCTAAAC 59.288 44.000 27.02 10.28 42.49 2.01
2976 3393 2.622942 TGTAAGCTCAAACTTTGCAGGG 59.377 45.455 0.00 0.00 0.00 4.45
3114 3531 4.737855 TTATGTAGCTGTGGTTCCTCTC 57.262 45.455 0.00 0.00 0.00 3.20
3116 3533 1.618837 TGTAGCTGTGGTTCCTCTCAC 59.381 52.381 0.00 0.00 34.71 3.51
3179 3596 3.573967 CGGGAAGCAGGGCATAATAAATT 59.426 43.478 0.00 0.00 0.00 1.82
3264 3681 8.290325 CACCTTAATTTCCTAAAGTGTGAAGTC 58.710 37.037 0.00 0.00 0.00 3.01
3274 3691 0.663568 GTGTGAAGTCGTGGAGTCCG 60.664 60.000 4.30 0.00 0.00 4.79
3492 3913 1.532868 CCACTCAGAAAGCTTTCGGTG 59.467 52.381 31.84 31.84 41.92 4.94
3560 3981 2.430694 GGGCTTGAACAAAGGAAACTGT 59.569 45.455 0.00 0.00 42.68 3.55
3561 3982 3.634910 GGGCTTGAACAAAGGAAACTGTA 59.365 43.478 0.00 0.00 42.68 2.74
3571 3992 5.204833 CAAAGGAAACTGTATGTTGTGTCG 58.795 41.667 0.00 0.00 42.68 4.35
3624 4045 6.215431 TCTCTTTTCATTACTTGATCCCAGGA 59.785 38.462 0.00 0.00 33.34 3.86
3715 4137 4.322499 CGTGATGGGTACTAAGTTGGTTCT 60.322 45.833 0.00 0.00 0.00 3.01
3721 4143 5.249852 TGGGTACTAAGTTGGTTCTATTGCT 59.750 40.000 0.00 0.00 0.00 3.91
3778 4200 0.616111 AGGAGACCGGCAAGATCACT 60.616 55.000 0.00 0.00 0.00 3.41
3833 4255 9.330063 CAGAATGGTAGTGCAGAAATTCTATAA 57.670 33.333 0.00 0.00 33.71 0.98
4081 4503 2.039418 GGGCAGAAAAGGAAAGGTTGT 58.961 47.619 0.00 0.00 0.00 3.32
4083 4505 2.035961 GGCAGAAAAGGAAAGGTTGTCC 59.964 50.000 0.00 0.00 35.17 4.02
4089 4511 0.767060 AGGAAAGGTTGTCCCCTCGT 60.767 55.000 0.00 0.00 35.59 4.18
4090 4512 0.109913 GGAAAGGTTGTCCCCTCGTT 59.890 55.000 0.00 0.00 32.13 3.85
4116 4576 6.128391 GCTCACAACTGTTAATCCGACATAAA 60.128 38.462 0.00 0.00 0.00 1.40
4149 4609 4.641396 CAACCTGTGGATGTTTCTGTCTA 58.359 43.478 0.00 0.00 0.00 2.59
4328 4788 0.543410 TTCCCTCCGAGCACCTGTAA 60.543 55.000 0.00 0.00 0.00 2.41
4330 4790 0.970937 CCCTCCGAGCACCTGTAAGA 60.971 60.000 0.00 0.00 34.07 2.10
4358 4826 1.154073 GCTGCTGCTGCTTAACTGC 60.154 57.895 22.10 7.59 43.16 4.40
4359 4827 1.134075 CTGCTGCTGCTTAACTGCG 59.866 57.895 17.00 0.00 45.63 5.18
4393 4861 1.222936 CTCATGGCACCCCTGACTC 59.777 63.158 0.00 0.00 0.00 3.36
4396 4864 1.135094 CATGGCACCCCTGACTCTAT 58.865 55.000 0.00 0.00 0.00 1.98
4505 4974 4.495422 CCTCGTTTATATCCAGATTCGGG 58.505 47.826 0.00 0.00 0.00 5.14
4511 4980 7.830697 TCGTTTATATCCAGATTCGGGTATAGA 59.169 37.037 2.66 0.00 36.25 1.98
4595 5075 5.012871 TCTGATTGGGGAAATTGCAAATTCA 59.987 36.000 24.67 8.23 0.00 2.57
4642 5122 5.596361 TGTCAAATAAGCTTTGGGAGTTTCA 59.404 36.000 3.20 0.00 30.83 2.69
4659 5139 5.670485 AGTTTCACCATATCACGCTGATAA 58.330 37.500 10.39 0.00 42.05 1.75
4725 5219 5.179452 CCACTAAAAAGGGAATGAGGAGA 57.821 43.478 0.00 0.00 0.00 3.71
4749 5246 9.788960 AGAATCACACTTCTTTTTAAACAGTTC 57.211 29.630 1.48 0.00 31.38 3.01
4756 5253 8.798153 CACTTCTTTTTAAACAGTTCATCACAC 58.202 33.333 1.48 0.00 0.00 3.82
4820 5322 0.106819 CTGAAGGGCTTCCTGATGGG 60.107 60.000 0.00 0.00 40.74 4.00
4821 5323 0.846427 TGAAGGGCTTCCTGATGGGT 60.846 55.000 0.00 0.00 40.74 4.51
4822 5324 1.213296 GAAGGGCTTCCTGATGGGTA 58.787 55.000 0.00 0.00 40.74 3.69
4823 5325 0.919710 AAGGGCTTCCTGATGGGTAC 59.080 55.000 0.00 0.00 40.74 3.34
4889 5420 5.594317 ACATGATCCATTAAGTAACTTGGCC 59.406 40.000 0.00 0.00 0.00 5.36
4894 5425 5.014202 TCCATTAAGTAACTTGGCCTTTCC 58.986 41.667 3.32 0.00 0.00 3.13
4936 5467 7.328005 CGATGTCGAGATGTTTATGAATCTGAT 59.672 37.037 0.00 0.00 43.02 2.90
4962 5493 2.432146 TGTCACCTCATCAGGCTGTATC 59.568 50.000 15.27 0.00 45.05 2.24
4974 5505 6.229936 TCAGGCTGTATCGTTTATTTAGGT 57.770 37.500 15.27 0.00 0.00 3.08
5164 5695 7.891498 TTCATCACATGATTCTGATCCAAAT 57.109 32.000 0.00 0.00 39.39 2.32
5180 5711 5.054390 TCCAAATTTCTCGCCAATACAAC 57.946 39.130 0.00 0.00 0.00 3.32
5206 5737 7.496346 ACATTGTGAAGAATCTAGGGAGTAA 57.504 36.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.512588 CCAAATAGGCTTCAATTCTGATATACT 57.487 33.333 0.00 0.00 0.00 2.12
13 14 9.289782 ACCAAATAGGCTTCAATTCTGATATAC 57.710 33.333 0.00 0.00 43.14 1.47
138 139 0.328258 CCCCTTCGTTGGTGGAGAAT 59.672 55.000 0.00 0.00 0.00 2.40
178 221 2.344950 CTCAGCTCATGGAGTGTGTTC 58.655 52.381 0.00 0.00 31.39 3.18
274 321 0.251341 GGAGTGACCCCAAAGCACAT 60.251 55.000 0.00 0.00 35.08 3.21
348 404 1.377725 CTTGGCATCCGCAGAACCT 60.378 57.895 0.00 0.00 41.24 3.50
357 413 1.831580 AGCAACTCTTCTTGGCATCC 58.168 50.000 0.00 0.00 0.00 3.51
392 448 5.694995 AGTACTATACCTTGGCGTAACCTA 58.305 41.667 0.00 0.00 40.22 3.08
433 492 1.476891 GATACGAGAAGGTGCCAGACA 59.523 52.381 0.00 0.00 0.00 3.41
446 505 1.671328 TCTCAGTCGGCTTGATACGAG 59.329 52.381 0.00 0.00 40.09 4.18
450 509 4.220821 AGAACTTTCTCAGTCGGCTTGATA 59.779 41.667 0.00 0.00 32.94 2.15
457 516 3.182572 CGTTGAAGAACTTTCTCAGTCGG 59.817 47.826 0.00 0.00 36.28 4.79
522 678 2.717639 ATACAGGCCAGCAAGTAAGG 57.282 50.000 5.01 0.00 0.00 2.69
598 754 3.957586 CCAGTGGGCAGACAGGCA 61.958 66.667 0.00 0.00 46.44 4.75
760 1064 1.268896 GCACCAATGGCAGATTCATCG 60.269 52.381 0.00 0.00 0.00 3.84
885 1189 1.948144 GCCTTCTCCCTCTTTGACAGC 60.948 57.143 0.00 0.00 0.00 4.40
929 1233 1.080995 CGCAGCAGAGAAGTAGTGGC 61.081 60.000 0.00 0.00 0.00 5.01
938 1242 1.079888 TCGCAAATCGCAGCAGAGA 60.080 52.632 0.00 0.00 42.60 3.10
1029 1336 2.726351 GGTGAAGAGGAGGCGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
1033 1340 1.219393 GAAGGGTGAAGAGGAGGCG 59.781 63.158 0.00 0.00 0.00 5.52
1034 1341 0.539518 GAGAAGGGTGAAGAGGAGGC 59.460 60.000 0.00 0.00 0.00 4.70
1038 1345 1.941668 GCAACGAGAAGGGTGAAGAGG 60.942 57.143 0.00 0.00 0.00 3.69
1042 1349 4.792087 GGCAACGAGAAGGGTGAA 57.208 55.556 0.00 0.00 0.00 3.18
1107 1414 4.992381 ACTAGAAACAAACATGAGACGC 57.008 40.909 0.00 0.00 0.00 5.19
1359 1677 0.326264 AATCTCCCAAACGCAGAGCT 59.674 50.000 0.00 0.00 0.00 4.09
1535 1860 6.987992 TCAAGTTTACCGTGAGATTTTGTAGT 59.012 34.615 0.00 0.00 0.00 2.73
1537 1862 7.789273 TTCAAGTTTACCGTGAGATTTTGTA 57.211 32.000 0.00 0.00 33.01 2.41
1577 1904 1.072331 ACTGTTTACTGTCCCTGCAGG 59.928 52.381 26.87 26.87 40.59 4.85
1595 1922 5.568620 AAGGTCAACAGTCCAAATCTACT 57.431 39.130 0.00 0.00 0.00 2.57
1604 1931 7.862873 CAGAAAGAAAAATAAGGTCAACAGTCC 59.137 37.037 0.00 0.00 0.00 3.85
1630 1957 5.754890 AGAACATTTCACTTCATGCCAAAAC 59.245 36.000 0.00 0.00 0.00 2.43
1661 2016 0.951040 CAGCAAAGGGAGGACACGAC 60.951 60.000 0.00 0.00 0.00 4.34
1664 2019 0.606673 GGACAGCAAAGGGAGGACAC 60.607 60.000 0.00 0.00 0.00 3.67
1674 2029 0.685785 TGGCAAGGTTGGACAGCAAA 60.686 50.000 0.00 0.00 0.00 3.68
1698 2054 8.420222 ACAAGTGATATGAGAACATAAGAGGAG 58.580 37.037 0.00 0.00 41.46 3.69
1700 2056 9.689976 CTACAAGTGATATGAGAACATAAGAGG 57.310 37.037 0.00 0.00 41.46 3.69
1771 2132 1.742761 AGAAATCACCTGGCATGACG 58.257 50.000 0.00 0.00 0.00 4.35
1808 2172 7.452880 AAACAAGTAGCAGCTGAATTATTGA 57.547 32.000 20.43 0.00 0.00 2.57
1809 2173 9.443283 GATAAACAAGTAGCAGCTGAATTATTG 57.557 33.333 20.43 16.24 0.00 1.90
1810 2174 9.177608 TGATAAACAAGTAGCAGCTGAATTATT 57.822 29.630 20.43 1.62 0.00 1.40
1820 2184 7.601073 TGAACTGATGATAAACAAGTAGCAG 57.399 36.000 0.00 0.00 0.00 4.24
1821 2185 7.823799 TGATGAACTGATGATAAACAAGTAGCA 59.176 33.333 0.00 0.00 0.00 3.49
1823 2187 8.824781 CCTGATGAACTGATGATAAACAAGTAG 58.175 37.037 0.00 0.00 0.00 2.57
1828 2192 5.748402 AGCCTGATGAACTGATGATAAACA 58.252 37.500 0.00 0.00 0.00 2.83
1969 2333 3.314913 TGACAAAGTCGATGTGCATTGTT 59.685 39.130 0.00 0.00 34.95 2.83
2071 2435 1.851304 ACTTGGTAATGGCCATGTGG 58.149 50.000 21.63 9.19 42.81 4.17
2186 2550 2.455032 GAGGATCTTCGTCATGTCACG 58.545 52.381 0.69 0.69 41.36 4.35
2494 2865 9.492973 AAGCACAAATTTCATGTTAAAGCTATT 57.507 25.926 0.00 0.00 29.45 1.73
2632 3003 5.122711 TGCTCATCACATGAACAACATACAG 59.877 40.000 0.00 0.00 39.11 2.74
2708 3079 4.469586 AGGAACTTGTTTGAACCAAATGGT 59.530 37.500 0.00 0.00 45.74 3.55
2744 3122 8.814038 ATGTTCATAAAATAACTCTGGCTTCT 57.186 30.769 0.00 0.00 0.00 2.85
2745 3123 9.860898 AAATGTTCATAAAATAACTCTGGCTTC 57.139 29.630 0.00 0.00 0.00 3.86
2949 3366 4.681483 GCAAAGTTTGAGCTTACATCAACC 59.319 41.667 19.82 0.00 36.44 3.77
2976 3393 0.179097 GTTCCCCGATGACTCTCTGC 60.179 60.000 0.00 0.00 0.00 4.26
3114 3531 8.093307 ACATACCTAGAAGCATGATATGAAGTG 58.907 37.037 0.00 0.00 0.00 3.16
3116 3533 8.309656 TCACATACCTAGAAGCATGATATGAAG 58.690 37.037 0.00 0.00 0.00 3.02
3179 3596 4.898320 TGATGAAAGAGCAGCTTGAAGTA 58.102 39.130 0.00 0.00 36.80 2.24
3264 3681 3.241868 CGCTTTATTTTACGGACTCCACG 60.242 47.826 0.00 0.00 37.36 4.94
3492 3913 5.829924 TGGGAATCTTCCTGAAATCATAAGC 59.170 40.000 8.78 0.00 46.72 3.09
3495 3916 6.779049 CCATTGGGAATCTTCCTGAAATCATA 59.221 38.462 8.78 0.00 46.72 2.15
3560 3981 3.565902 TCCATTTGCAACGACACAACATA 59.434 39.130 0.00 0.00 0.00 2.29
3561 3982 2.360483 TCCATTTGCAACGACACAACAT 59.640 40.909 0.00 0.00 0.00 2.71
3571 3992 0.319405 AGCCAGCTTCCATTTGCAAC 59.681 50.000 0.00 0.00 0.00 4.17
3624 4045 9.467258 CAAATTATATGCATCCGTTCTTCAATT 57.533 29.630 0.19 0.00 0.00 2.32
3715 4137 7.665559 AGTCAGAAAACAGAAATACCAGCAATA 59.334 33.333 0.00 0.00 0.00 1.90
3721 4143 8.463930 AATGAAGTCAGAAAACAGAAATACCA 57.536 30.769 0.00 0.00 0.00 3.25
3778 4200 3.761752 TCACTCTCACATAATCGGTGACA 59.238 43.478 0.00 0.00 40.16 3.58
3962 4384 1.870064 TGTCTGCATCAGATCCCTCA 58.130 50.000 0.00 0.00 42.73 3.86
3992 4414 0.036875 CGAAGCTCCTCTTGGGGTTT 59.963 55.000 0.00 0.00 40.10 3.27
4028 4450 2.577059 TCGGACCTCGAATGGTGC 59.423 61.111 0.26 3.12 45.86 5.01
4049 4471 1.812686 TTCTGCCCTCGTACACGCTT 61.813 55.000 0.00 0.00 39.60 4.68
4051 4473 0.947180 TTTTCTGCCCTCGTACACGC 60.947 55.000 0.00 0.00 39.60 5.34
4081 4503 1.070786 GTTGTGAGCAACGAGGGGA 59.929 57.895 0.00 0.00 44.40 4.81
4089 4511 3.496884 GTCGGATTAACAGTTGTGAGCAA 59.503 43.478 0.00 0.00 0.00 3.91
4090 4512 3.064207 GTCGGATTAACAGTTGTGAGCA 58.936 45.455 0.00 0.00 0.00 4.26
4116 4576 2.751166 CACAGGTTGGATCTCGAGTT 57.249 50.000 13.13 3.51 0.00 3.01
4149 4609 4.166144 CCTCTACCATTCCCTACACCAATT 59.834 45.833 0.00 0.00 0.00 2.32
4328 4788 2.919856 AGCAGCCTCACCACGTCT 60.920 61.111 0.00 0.00 0.00 4.18
4330 4790 4.996434 GCAGCAGCCTCACCACGT 62.996 66.667 0.00 0.00 33.58 4.49
4393 4861 8.642935 TCTTGAACCAGATAGGATAGTGATAG 57.357 38.462 0.00 0.00 41.22 2.08
4396 4864 6.667848 TGTTCTTGAACCAGATAGGATAGTGA 59.332 38.462 10.51 0.00 41.22 3.41
4533 5002 8.761575 ATGTTTGCAAGAAAATACTTGTATGG 57.238 30.769 0.00 0.00 45.98 2.74
4553 5033 9.426837 CCAATCAGAAATGTGATTTGTATGTTT 57.573 29.630 3.28 0.00 43.29 2.83
4595 5075 4.529897 TCATGATATGGCAAAGCTTGAGT 58.470 39.130 0.00 0.00 0.00 3.41
4642 5122 5.276461 TCAAGTTATCAGCGTGATATGGT 57.724 39.130 8.03 0.00 38.94 3.55
4659 5139 7.595819 TGGTAGAAAATTTGACCATTCAAGT 57.404 32.000 13.28 0.00 42.79 3.16
4701 5195 3.011257 TCCTCATTCCCTTTTTAGTGGGG 59.989 47.826 0.00 0.00 43.51 4.96
4756 5253 7.389607 TCATGGATCATGCTTCATACACTAATG 59.610 37.037 3.23 0.00 41.18 1.90
4772 5274 0.178970 GCCTGGGCTTCATGGATCAT 60.179 55.000 4.12 0.00 38.26 2.45
4864 5395 6.096846 GGCCAAGTTACTTAATGGATCATGTT 59.903 38.462 5.81 0.00 34.82 2.71
4865 5396 5.594317 GGCCAAGTTACTTAATGGATCATGT 59.406 40.000 5.81 0.00 34.82 3.21
4866 5397 5.829924 AGGCCAAGTTACTTAATGGATCATG 59.170 40.000 5.01 0.00 34.82 3.07
4894 5425 3.318017 ACATCGGTTCTGTTCTTTCGAG 58.682 45.455 0.00 0.00 0.00 4.04
4936 5467 2.840038 AGCCTGATGAGGTGACATGTTA 59.160 45.455 0.00 0.00 42.15 2.41
4974 5505 5.491323 TGTGGACTTGTGGTGTATAATCA 57.509 39.130 0.00 0.00 0.00 2.57
5164 5695 5.218885 CAATGTTGTTGTATTGGCGAGAAA 58.781 37.500 0.00 0.00 32.13 2.52
5180 5711 6.176183 ACTCCCTAGATTCTTCACAATGTTG 58.824 40.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.