Multiple sequence alignment - TraesCS3B01G565600

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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 TraesCS3B01G565600 chr3B 100.000 2237 0 0 1 2237 798231329 798233565 0.000000e+00 4132.0
1 TraesCS3B01G565600 chr3B 73.158 190 44 6 1343 1526 798252291 798252479 6.670000e-06 62.1
2 TraesCS3B01G565600 chr3A 88.067 1257 101 25 22 1253 725555583 725556815 0.000000e+00 1445.0
3 TraesCS3B01G565600 chr3A 88.067 1257 101 25 22 1253 725598131 725599363 0.000000e+00 1445.0
4 TraesCS3B01G565600 chr3A 84.588 1395 124 47 251 1595 725460822 725462175 0.000000e+00 1301.0
5 TraesCS3B01G565600 chr3A 87.445 685 65 7 1251 1922 725556846 725557522 0.000000e+00 769.0
6 TraesCS3B01G565600 chr3A 87.445 685 65 7 1251 1922 725599394 725600070 0.000000e+00 769.0
7 TraesCS3B01G565600 chr3A 85.802 655 51 19 1594 2229 725467516 725468147 0.000000e+00 656.0
8 TraesCS3B01G565600 chr3A 100.000 30 0 0 1 30 725555396 725555425 3.100000e-04 56.5
9 TraesCS3B01G565600 chr3A 100.000 30 0 0 1 30 725597944 725597973 3.100000e-04 56.5
10 TraesCS3B01G565600 chr3D 89.474 912 67 15 1 902 594771340 594772232 0.000000e+00 1125.0
11 TraesCS3B01G565600 chr3D 82.808 634 88 15 274 902 594642764 594643381 4.200000e-152 547.0
12 TraesCS3B01G565600 chr3D 86.667 405 34 13 276 673 594683963 594684354 4.410000e-117 431.0
13 TraesCS3B01G565600 chr3D 88.043 368 39 3 1251 1615 594684994 594685359 4.410000e-117 431.0
14 TraesCS3B01G565600 chr3D 87.688 333 33 4 920 1251 594684636 594684961 4.510000e-102 381.0
15 TraesCS3B01G565600 chr3D 86.527 334 24 7 920 1252 594643370 594643683 4.570000e-92 348.0
16 TraesCS3B01G565600 chr3D 86.527 334 24 7 920 1252 594772221 594772534 4.570000e-92 348.0
17 TraesCS3B01G565600 chr3D 91.905 210 17 0 1042 1251 594772948 594773157 6.040000e-76 294.0
18 TraesCS3B01G565600 chr3D 90.952 210 19 0 1042 1251 594644097 594644306 1.310000e-72 283.0
19 TraesCS3B01G565600 chr3D 88.479 217 22 3 1253 1468 594772570 594772784 2.200000e-65 259.0
20 TraesCS3B01G565600 chr3D 77.350 234 29 10 996 1229 594638827 594639036 1.400000e-22 117.0
21 TraesCS3B01G565600 chr3D 94.872 39 1 1 1463 1501 594643957 594643994 2.400000e-05 60.2
22 TraesCS3B01G565600 chr3D 94.872 39 1 1 1463 1501 594772808 594772845 2.400000e-05 60.2
23 TraesCS3B01G565600 chrUn 90.441 136 12 1 1 136 124668212 124668078 6.350000e-41 178.0
24 TraesCS3B01G565600 chr5D 88.333 60 4 2 1 58 496160709 496160767 3.990000e-08 69.4


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 TraesCS3B01G565600 chr3B 798231329 798233565 2236 False 4132.000000 4132 100.000000 1 2237 1 chr3B.!!$F1 2236
1 TraesCS3B01G565600 chr3A 725460822 725462175 1353 False 1301.000000 1301 84.588000 251 1595 1 chr3A.!!$F1 1344
2 TraesCS3B01G565600 chr3A 725555396 725557522 2126 False 756.833333 1445 91.837333 1 1922 3 chr3A.!!$F3 1921
3 TraesCS3B01G565600 chr3A 725597944 725600070 2126 False 756.833333 1445 91.837333 1 1922 3 chr3A.!!$F4 1921
4 TraesCS3B01G565600 chr3A 725467516 725468147 631 False 656.000000 656 85.802000 1594 2229 1 chr3A.!!$F2 635
5 TraesCS3B01G565600 chr3D 594771340 594773157 1817 False 417.240000 1125 90.251400 1 1501 5 chr3D.!!$F3 1500
6 TraesCS3B01G565600 chr3D 594683963 594685359 1396 False 414.333333 431 87.466000 276 1615 3 chr3D.!!$F2 1339
7 TraesCS3B01G565600 chr3D 594638827 594644306 5479 False 271.040000 547 86.501800 274 1501 5 chr3D.!!$F1 1227

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
789 4549 0.110644 CTGAAAGTTTCGAGCGCCAC 60.111 55.0 2.29 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 5802 0.11714 AGATGGGTGTGAGGAGGTGA 59.883 55.0 0.0 0.0 0.0 4.02 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
96 263 3.498774 ATGTTGTCTCCTTCACTTGCT 57.501 42.857 0.00 0.00 0.00 3.91
119 286 7.929245 TGCTACGATCCAAGCATTAGTATAAAA 59.071 33.333 11.57 0.00 43.56 1.52
176 343 5.757886 TGAGGTGTTAAAAAGAAATGCTCG 58.242 37.500 0.00 0.00 0.00 5.03
192 359 1.542108 GCTCGAAAGCTGGCCTGATAT 60.542 52.381 14.77 0.00 45.55 1.63
233 400 1.277842 CCAAATTTAAGGTGGGTGGCC 59.722 52.381 0.00 0.00 0.00 5.36
249 416 0.249911 GGCCGTAGATGCCCTAACAG 60.250 60.000 0.00 0.00 43.33 3.16
311 3977 0.475044 AAACGGCTTCCACCCACTTA 59.525 50.000 0.00 0.00 0.00 2.24
439 4110 1.900545 GCAACCTCCCCTCTACGCTT 61.901 60.000 0.00 0.00 0.00 4.68
503 4180 4.450053 CAAGGCCAAGGAAAATTCAACAA 58.550 39.130 5.01 0.00 0.00 2.83
505 4182 2.807967 GGCCAAGGAAAATTCAACAAGC 59.192 45.455 0.00 0.00 0.00 4.01
506 4183 2.807967 GCCAAGGAAAATTCAACAAGCC 59.192 45.455 0.00 0.00 0.00 4.35
507 4184 3.743899 GCCAAGGAAAATTCAACAAGCCA 60.744 43.478 0.00 0.00 0.00 4.75
508 4185 3.809279 CCAAGGAAAATTCAACAAGCCAC 59.191 43.478 0.00 0.00 0.00 5.01
509 4186 3.369546 AGGAAAATTCAACAAGCCACG 57.630 42.857 0.00 0.00 0.00 4.94
510 4187 2.955660 AGGAAAATTCAACAAGCCACGA 59.044 40.909 0.00 0.00 0.00 4.35
511 4188 3.004734 AGGAAAATTCAACAAGCCACGAG 59.995 43.478 0.00 0.00 0.00 4.18
512 4189 3.308530 GAAAATTCAACAAGCCACGAGG 58.691 45.455 0.00 0.00 38.23 4.63
531 4214 2.562912 CCACGATGCACAACCAGC 59.437 61.111 0.00 0.00 0.00 4.85
549 4232 1.312371 GCACCACCCACGCAACATAT 61.312 55.000 0.00 0.00 0.00 1.78
550 4233 2.014574 GCACCACCCACGCAACATATA 61.015 52.381 0.00 0.00 0.00 0.86
562 4245 5.230097 CACGCAACATATACACTACAGACTG 59.770 44.000 0.00 0.00 0.00 3.51
657 4350 2.778299 ACATGCGTAACTGTCAATGGT 58.222 42.857 0.00 0.00 0.00 3.55
681 4439 0.992072 CAGATCGTTGTCGTTGCGAT 59.008 50.000 0.00 0.00 46.25 4.58
721 4481 1.996292 TGTGCTCGAATGTGAGTAGC 58.004 50.000 0.00 0.00 38.28 3.58
744 4504 1.372087 GAACCTTCCGATGCCTGCTG 61.372 60.000 0.00 0.00 0.00 4.41
756 4516 1.163554 GCCTGCTGAGAGTTTTGAGG 58.836 55.000 0.00 0.00 0.00 3.86
780 4540 3.850010 GCGAACCTTCAGCTGAAAGTTTC 60.850 47.826 33.23 27.55 38.42 2.78
789 4549 0.110644 CTGAAAGTTTCGAGCGCCAC 60.111 55.000 2.29 0.00 0.00 5.01
809 4574 2.966516 ACGCTCTCCTCCCCTATAAAAG 59.033 50.000 0.00 0.00 0.00 2.27
848 4626 5.277825 TGCTTTTCCAAACAGAAACATACG 58.722 37.500 0.00 0.00 35.53 3.06
853 4631 2.351350 CCAAACAGAAACATACGCACCC 60.351 50.000 0.00 0.00 0.00 4.61
855 4633 0.672401 ACAGAAACATACGCACCCGG 60.672 55.000 0.00 0.00 39.22 5.73
856 4634 0.390603 CAGAAACATACGCACCCGGA 60.391 55.000 0.73 0.00 39.22 5.14
857 4635 0.539986 AGAAACATACGCACCCGGAT 59.460 50.000 0.73 0.00 38.96 4.18
858 4636 0.935196 GAAACATACGCACCCGGATC 59.065 55.000 0.73 0.00 35.34 3.36
859 4637 0.250793 AAACATACGCACCCGGATCA 59.749 50.000 0.73 0.00 35.34 2.92
861 4639 1.956170 CATACGCACCCGGATCAGC 60.956 63.158 0.73 0.00 35.34 4.26
878 4657 2.386660 GCACAGCAGCGGAGAAGAC 61.387 63.158 0.00 0.00 0.00 3.01
888 4671 3.427309 GGAGAAGACCTGCGTTCTC 57.573 57.895 3.90 3.90 45.42 2.87
903 4710 2.333014 GTTCTCCGTGAGCTGAAGAAG 58.667 52.381 0.00 0.00 0.00 2.85
904 4711 0.891373 TCTCCGTGAGCTGAAGAAGG 59.109 55.000 0.00 0.00 0.00 3.46
905 4712 0.891373 CTCCGTGAGCTGAAGAAGGA 59.109 55.000 0.00 0.00 0.00 3.36
906 4713 1.273606 CTCCGTGAGCTGAAGAAGGAA 59.726 52.381 0.00 0.00 0.00 3.36
907 4714 1.000955 TCCGTGAGCTGAAGAAGGAAC 59.999 52.381 0.00 0.00 0.00 3.62
908 4715 1.270305 CCGTGAGCTGAAGAAGGAACA 60.270 52.381 0.00 0.00 0.00 3.18
909 4716 1.795286 CGTGAGCTGAAGAAGGAACAC 59.205 52.381 0.00 0.00 0.00 3.32
910 4717 2.803133 CGTGAGCTGAAGAAGGAACACA 60.803 50.000 0.00 0.00 0.00 3.72
911 4718 3.206150 GTGAGCTGAAGAAGGAACACAA 58.794 45.455 0.00 0.00 0.00 3.33
912 4719 3.249559 GTGAGCTGAAGAAGGAACACAAG 59.750 47.826 0.00 0.00 0.00 3.16
913 4720 3.134623 TGAGCTGAAGAAGGAACACAAGA 59.865 43.478 0.00 0.00 0.00 3.02
914 4721 4.130118 GAGCTGAAGAAGGAACACAAGAA 58.870 43.478 0.00 0.00 0.00 2.52
915 4722 4.723309 AGCTGAAGAAGGAACACAAGAAT 58.277 39.130 0.00 0.00 0.00 2.40
928 4735 5.674052 ACACAAGAATAGAGTGAGCTGAT 57.326 39.130 0.00 0.00 37.05 2.90
930 4737 7.175347 ACACAAGAATAGAGTGAGCTGATAA 57.825 36.000 0.00 0.00 37.05 1.75
976 4783 4.276926 GGGGAAAAGATAGTGCAGCATTAG 59.723 45.833 0.00 0.00 0.00 1.73
977 4784 4.261363 GGGAAAAGATAGTGCAGCATTAGC 60.261 45.833 5.07 5.07 42.56 3.09
994 4801 1.078426 GCTTCGGGCTTTAGCAGGA 60.078 57.895 3.88 0.00 44.36 3.86
1023 4830 1.372087 GATTCTGCTGTGGGCCTTCG 61.372 60.000 4.53 0.00 40.92 3.79
1035 4842 0.322546 GGCCTTCGGATGTCAAGGTT 60.323 55.000 0.00 0.00 41.31 3.50
1038 4845 2.350522 CCTTCGGATGTCAAGGTTCTG 58.649 52.381 0.00 0.00 35.34 3.02
1040 4847 0.976641 TCGGATGTCAAGGTTCTGCT 59.023 50.000 0.00 0.00 0.00 4.24
1041 4848 1.081892 CGGATGTCAAGGTTCTGCTG 58.918 55.000 0.00 0.00 0.00 4.41
1055 4865 2.050144 TCTGCTGAAGAACACCTCCTT 58.950 47.619 0.00 0.00 29.54 3.36
1074 4884 1.026584 TCTTGTCGTCAACGTCCTCA 58.973 50.000 2.09 0.00 40.80 3.86
1120 4930 4.090057 GCGACGGTGGCAAGAAGC 62.090 66.667 10.40 0.00 44.65 3.86
1132 4942 0.386476 CAAGAAGCAGCACCAGCAAA 59.614 50.000 0.00 0.00 45.49 3.68
1134 4944 1.177256 AGAAGCAGCACCAGCAAAGG 61.177 55.000 0.00 0.00 45.49 3.11
1143 4953 1.692411 ACCAGCAAAGGGTGAAGAAC 58.308 50.000 0.00 0.00 45.29 3.01
1185 4995 3.553095 GAGCAACCTTGACCGGGCT 62.553 63.158 9.82 2.28 0.00 5.19
1218 5028 2.679342 CCGCCTCCCCTTCCATTCA 61.679 63.158 0.00 0.00 0.00 2.57
1266 5111 1.329599 GGAACAATTAGCTTACGGCCG 59.670 52.381 26.86 26.86 43.05 6.13
1285 5130 2.483889 CCGAGGTTGGAGCTTAGGATTC 60.484 54.545 0.00 0.00 0.00 2.52
1297 5142 4.345257 AGCTTAGGATTCAATAGCTTCGGA 59.655 41.667 0.00 0.00 38.99 4.55
1303 5148 3.541996 TTCAATAGCTTCGGATGCTCA 57.458 42.857 20.10 8.94 41.46 4.26
1321 5166 6.064846 TGCTCAGTTGAAGTTTTGAGATTC 57.935 37.500 4.65 0.00 39.46 2.52
1338 5183 3.131223 AGATTCCTACTGTCGTCACATGG 59.869 47.826 0.00 0.00 0.00 3.66
1430 5278 4.583871 AGAGATGAAGTTCATTGTCACCC 58.416 43.478 19.19 5.23 37.20 4.61
1460 5308 2.467566 TGTTTCCCTACTTCCTTCGC 57.532 50.000 0.00 0.00 0.00 4.70
1526 5411 4.500545 CGAGCAAGACTAAGCCTACATCAT 60.501 45.833 0.00 0.00 0.00 2.45
1537 5422 5.184892 AGCCTACATCATCCTCAAAAAGT 57.815 39.130 0.00 0.00 0.00 2.66
1701 5633 7.279981 ACCAAACTTTTTCTTATCAACAAAGGC 59.720 33.333 0.00 0.00 0.00 4.35
1709 5641 5.547465 TCTTATCAACAAAGGCGAGAGAAA 58.453 37.500 0.00 0.00 0.00 2.52
1723 5655 4.853743 GCGAGAGAAAAAGCATGGTAAAAG 59.146 41.667 0.00 0.00 0.00 2.27
1734 5666 4.284234 AGCATGGTAAAAGCAAAGGAACAT 59.716 37.500 0.00 0.00 0.00 2.71
1768 5702 1.137872 CTATCCCAGGAGATATGGCGC 59.862 57.143 0.00 0.00 36.43 6.53
1783 5717 1.638467 GCGCGCCTTCATTCTACTG 59.362 57.895 23.24 0.00 0.00 2.74
1806 5741 7.920682 ACTGCACATAAATAAATCGATTTTCCC 59.079 33.333 27.10 7.76 31.51 3.97
1825 5760 1.350019 CCCTTCCCTTAACCAAGACGT 59.650 52.381 0.00 0.00 33.20 4.34
1827 5762 3.369157 CCCTTCCCTTAACCAAGACGTAG 60.369 52.174 0.00 0.00 33.20 3.51
1866 5812 4.609866 TTCTCCTATCTTCACCTCCTCA 57.390 45.455 0.00 0.00 0.00 3.86
1885 5831 1.138859 CACACCCATCTAATGCTCCGA 59.861 52.381 0.00 0.00 0.00 4.55
1886 5832 2.050144 ACACCCATCTAATGCTCCGAT 58.950 47.619 0.00 0.00 0.00 4.18
1935 5881 3.672511 CGTGTTTGACGTGTAGCTAGGAT 60.673 47.826 0.00 0.00 43.50 3.24
1947 5893 5.535406 GTGTAGCTAGGATTAGAGCTTGGTA 59.465 44.000 1.16 0.00 46.99 3.25
1949 5895 5.993748 AGCTAGGATTAGAGCTTGGTATC 57.006 43.478 0.00 0.00 46.99 2.24
1952 5898 5.279056 GCTAGGATTAGAGCTTGGTATCGTT 60.279 44.000 0.00 0.00 35.73 3.85
1958 5904 0.037697 AGCTTGGTATCGTTGCGTCA 60.038 50.000 0.00 0.00 0.00 4.35
1969 5915 1.435577 GTTGCGTCATCGTTTAGGGT 58.564 50.000 0.00 0.00 39.49 4.34
1982 5928 3.227614 GTTTAGGGTTTGATGGTGGTGT 58.772 45.455 0.00 0.00 0.00 4.16
1996 5942 3.761218 TGGTGGTGTTGCATCGAATAATT 59.239 39.130 0.00 0.00 0.00 1.40
2007 5953 2.796557 TCGAATAATTGTTGTGCCCCA 58.203 42.857 0.00 0.00 0.00 4.96
2008 5954 2.752354 TCGAATAATTGTTGTGCCCCAG 59.248 45.455 0.00 0.00 0.00 4.45
2009 5955 2.735126 CGAATAATTGTTGTGCCCCAGC 60.735 50.000 0.00 0.00 40.48 4.85
2010 5956 2.236489 ATAATTGTTGTGCCCCAGCT 57.764 45.000 0.00 0.00 40.80 4.24
2011 5957 2.008242 TAATTGTTGTGCCCCAGCTT 57.992 45.000 0.00 0.00 40.80 3.74
2012 5958 0.681175 AATTGTTGTGCCCCAGCTTC 59.319 50.000 0.00 0.00 40.80 3.86
2013 5959 0.469705 ATTGTTGTGCCCCAGCTTCA 60.470 50.000 0.00 0.00 40.80 3.02
2014 5960 0.685785 TTGTTGTGCCCCAGCTTCAA 60.686 50.000 0.00 0.00 40.80 2.69
2015 5961 1.108727 TGTTGTGCCCCAGCTTCAAG 61.109 55.000 0.00 0.00 40.80 3.02
2016 5962 2.202395 TTGTGCCCCAGCTTCAAGC 61.202 57.895 0.00 0.00 42.84 4.01
2017 5963 3.376918 GTGCCCCAGCTTCAAGCC 61.377 66.667 5.53 0.00 43.77 4.35
2018 5964 4.684134 TGCCCCAGCTTCAAGCCC 62.684 66.667 5.53 0.00 43.77 5.19
2019 5965 4.684134 GCCCCAGCTTCAAGCCCA 62.684 66.667 5.53 0.00 43.77 5.36
2020 5966 2.361771 CCCCAGCTTCAAGCCCAT 59.638 61.111 5.53 0.00 43.77 4.00
2021 5967 1.755783 CCCCAGCTTCAAGCCCATC 60.756 63.158 5.53 0.00 43.77 3.51
2022 5968 1.305623 CCCAGCTTCAAGCCCATCT 59.694 57.895 5.53 0.00 43.77 2.90
2023 5969 0.750911 CCCAGCTTCAAGCCCATCTC 60.751 60.000 5.53 0.00 43.77 2.75
2024 5970 1.094073 CCAGCTTCAAGCCCATCTCG 61.094 60.000 5.53 0.00 43.77 4.04
2025 5971 0.107993 CAGCTTCAAGCCCATCTCGA 60.108 55.000 5.53 0.00 43.77 4.04
2026 5972 0.835941 AGCTTCAAGCCCATCTCGAT 59.164 50.000 5.53 0.00 43.77 3.59
2027 5973 0.942962 GCTTCAAGCCCATCTCGATG 59.057 55.000 0.00 0.00 34.48 3.84
2058 6004 2.610859 ATTGAGGAGCCGGTGGGT 60.611 61.111 1.90 0.00 35.46 4.51
2091 6038 1.523758 GAGCATGTTCTCCACCGTTT 58.476 50.000 1.76 0.00 0.00 3.60
2103 6050 3.972276 CCGTTTGGTGGCGTTGGG 61.972 66.667 0.00 0.00 0.00 4.12
2109 6056 1.668101 TTGGTGGCGTTGGGTTTGTC 61.668 55.000 0.00 0.00 0.00 3.18
2113 6060 1.209127 GGCGTTGGGTTTGTCATCG 59.791 57.895 0.00 0.00 0.00 3.84
2135 6099 2.879462 GCGGTCGTGGCTAGTTCG 60.879 66.667 0.00 0.00 0.00 3.95
2140 6104 1.372499 TCGTGGCTAGTTCGCACAC 60.372 57.895 0.00 0.00 0.00 3.82
2165 6129 1.204704 GTGATCACATCTGGTCCGTCA 59.795 52.381 21.07 0.00 0.00 4.35
2167 6131 1.478510 GATCACATCTGGTCCGTCAGT 59.521 52.381 0.00 0.00 36.25 3.41
2168 6132 1.338107 TCACATCTGGTCCGTCAGTT 58.662 50.000 0.00 0.00 36.25 3.16
2169 6133 2.521126 TCACATCTGGTCCGTCAGTTA 58.479 47.619 0.00 0.00 36.25 2.24
2175 6139 1.069513 CTGGTCCGTCAGTTAACACCA 59.930 52.381 8.61 10.33 32.91 4.17
2180 6144 2.132762 CCGTCAGTTAACACCAGTGAC 58.867 52.381 8.61 11.02 40.07 3.67
2181 6145 2.223971 CCGTCAGTTAACACCAGTGACT 60.224 50.000 17.69 0.00 40.93 3.41
2188 6152 4.021894 AGTTAACACCAGTGACTCTAGCTG 60.022 45.833 8.61 0.00 0.00 4.24
2208 6172 1.901833 GGCCTTGACATTGGTTGGATT 59.098 47.619 0.00 0.00 0.00 3.01
2215 6179 6.381498 TTGACATTGGTTGGATTCCTACTA 57.619 37.500 15.42 8.08 30.42 1.82
2229 6193 7.341256 TGGATTCCTACTAAGACAATAACGAGT 59.659 37.037 3.95 0.00 0.00 4.18
2230 6194 7.861872 GGATTCCTACTAAGACAATAACGAGTC 59.138 40.741 0.00 0.00 35.02 3.36
2231 6195 7.934855 TTCCTACTAAGACAATAACGAGTCT 57.065 36.000 0.00 0.00 46.45 3.24
2232 6196 7.551035 TCCTACTAAGACAATAACGAGTCTC 57.449 40.000 0.00 0.00 43.88 3.36
2233 6197 7.108194 TCCTACTAAGACAATAACGAGTCTCA 58.892 38.462 0.00 0.00 43.88 3.27
2234 6198 7.065563 TCCTACTAAGACAATAACGAGTCTCAC 59.934 40.741 0.00 0.00 43.88 3.51
2235 6199 6.821031 ACTAAGACAATAACGAGTCTCACT 57.179 37.500 0.00 0.00 43.88 3.41
2236 6200 6.844254 ACTAAGACAATAACGAGTCTCACTC 58.156 40.000 0.00 0.00 43.88 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 286 1.337384 TAGCCATCAGGACCGTGCAT 61.337 55.000 0.00 0.00 36.89 3.96
176 343 2.225467 GGACATATCAGGCCAGCTTTC 58.775 52.381 5.01 0.00 0.00 2.62
192 359 1.001974 CTCCTCAAACATCCGTGGACA 59.998 52.381 0.00 0.00 0.00 4.02
233 400 3.823873 AGAGATCTGTTAGGGCATCTACG 59.176 47.826 0.00 0.00 0.00 3.51
249 416 6.763135 TGTGCCACATCTTTTGTATAGAGATC 59.237 38.462 0.00 0.00 36.57 2.75
311 3977 3.202818 TGCCAATCATCTCCTGTAATGGT 59.797 43.478 0.00 0.00 0.00 3.55
439 4110 1.317613 GCAACATTGACCTGTGACCA 58.682 50.000 0.00 0.00 0.00 4.02
506 4183 4.758251 TGCATCGTGGGCCTCGTG 62.758 66.667 25.30 21.78 0.00 4.35
507 4184 4.760047 GTGCATCGTGGGCCTCGT 62.760 66.667 25.30 11.75 0.00 4.18
508 4185 4.758251 TGTGCATCGTGGGCCTCG 62.758 66.667 21.26 21.26 0.00 4.63
509 4186 2.359850 TTGTGCATCGTGGGCCTC 60.360 61.111 4.53 0.00 0.00 4.70
510 4187 2.672996 GTTGTGCATCGTGGGCCT 60.673 61.111 4.53 0.00 0.00 5.19
511 4188 3.747976 GGTTGTGCATCGTGGGCC 61.748 66.667 0.00 0.00 0.00 5.80
512 4189 2.981560 CTGGTTGTGCATCGTGGGC 61.982 63.158 0.00 0.00 0.00 5.36
513 4190 2.981560 GCTGGTTGTGCATCGTGGG 61.982 63.158 0.00 0.00 0.00 4.61
521 4198 3.605664 GGGTGGTGCTGGTTGTGC 61.606 66.667 0.00 0.00 0.00 4.57
531 4214 1.668751 GTATATGTTGCGTGGGTGGTG 59.331 52.381 0.00 0.00 0.00 4.17
543 4226 6.663953 ACCTGTCAGTCTGTAGTGTATATGTT 59.336 38.462 0.00 0.00 0.00 2.71
549 4232 3.154710 CCACCTGTCAGTCTGTAGTGTA 58.845 50.000 0.00 0.00 0.00 2.90
550 4233 1.964223 CCACCTGTCAGTCTGTAGTGT 59.036 52.381 0.00 0.00 0.00 3.55
562 4245 0.107945 GCTCTCATGGTCCACCTGTC 60.108 60.000 0.00 0.00 36.82 3.51
629 4312 2.477375 ACAGTTACGCATGTACGTTTGG 59.523 45.455 3.70 0.00 45.75 3.28
630 4313 3.182772 TGACAGTTACGCATGTACGTTTG 59.817 43.478 3.70 4.16 45.75 2.93
631 4314 3.382855 TGACAGTTACGCATGTACGTTT 58.617 40.909 3.70 0.00 45.75 3.60
632 4315 3.015934 TGACAGTTACGCATGTACGTT 57.984 42.857 3.70 0.00 45.75 3.99
639 4332 2.936498 GCTACCATTGACAGTTACGCAT 59.064 45.455 0.00 0.00 0.00 4.73
657 4350 0.109458 AACGACAACGATCTGCGCTA 60.109 50.000 9.73 0.00 46.04 4.26
721 4481 2.464459 GGCATCGGAAGGTTCGCTG 61.464 63.158 0.00 0.00 0.00 5.18
744 4504 2.070028 GGTTCGCTCCTCAAAACTCTC 58.930 52.381 0.00 0.00 0.00 3.20
756 4516 1.462670 CTTTCAGCTGAAGGTTCGCTC 59.537 52.381 27.02 0.00 35.82 5.03
789 4549 2.300437 CCTTTTATAGGGGAGGAGAGCG 59.700 54.545 0.00 0.00 40.67 5.03
809 4574 4.864334 CAGGGCTCATGGCGACCC 62.864 72.222 4.41 4.95 42.94 4.46
818 4583 1.039856 GTTTGGAAAAGCAGGGCTCA 58.960 50.000 0.00 0.00 38.25 4.26
848 4626 2.821366 CTGTGCTGATCCGGGTGC 60.821 66.667 0.00 0.00 0.00 5.01
853 4631 3.561213 CGCTGCTGTGCTGATCCG 61.561 66.667 0.00 0.00 0.00 4.18
855 4633 2.125391 TCCGCTGCTGTGCTGATC 60.125 61.111 0.00 0.00 0.00 2.92
856 4634 2.125229 CTCCGCTGCTGTGCTGAT 60.125 61.111 0.00 0.00 0.00 2.90
857 4635 2.776670 CTTCTCCGCTGCTGTGCTGA 62.777 60.000 0.00 0.00 0.00 4.26
858 4636 2.357881 TTCTCCGCTGCTGTGCTG 60.358 61.111 0.00 0.00 0.00 4.41
859 4637 2.047465 CTTCTCCGCTGCTGTGCT 60.047 61.111 0.00 0.00 0.00 4.40
861 4639 1.739562 GGTCTTCTCCGCTGCTGTG 60.740 63.158 0.00 0.00 0.00 3.66
886 4665 0.891373 TCCTTCTTCAGCTCACGGAG 59.109 55.000 0.00 0.00 0.00 4.63
888 4671 1.270305 TGTTCCTTCTTCAGCTCACGG 60.270 52.381 0.00 0.00 0.00 4.94
903 4710 4.629200 CAGCTCACTCTATTCTTGTGTTCC 59.371 45.833 0.00 0.00 33.82 3.62
904 4711 5.473931 TCAGCTCACTCTATTCTTGTGTTC 58.526 41.667 0.00 0.00 33.82 3.18
905 4712 5.474578 TCAGCTCACTCTATTCTTGTGTT 57.525 39.130 0.00 0.00 33.82 3.32
906 4713 5.674052 ATCAGCTCACTCTATTCTTGTGT 57.326 39.130 0.00 0.00 33.82 3.72
907 4714 7.254387 GCTTTATCAGCTCACTCTATTCTTGTG 60.254 40.741 0.00 0.00 46.27 3.33
908 4715 6.760770 GCTTTATCAGCTCACTCTATTCTTGT 59.239 38.462 0.00 0.00 46.27 3.16
909 4716 7.176285 GCTTTATCAGCTCACTCTATTCTTG 57.824 40.000 0.00 0.00 46.27 3.02
928 4735 6.187727 TCTTCCTTTCTTTCCTCTGCTTTA 57.812 37.500 0.00 0.00 0.00 1.85
930 4737 4.713792 TCTTCCTTTCTTTCCTCTGCTT 57.286 40.909 0.00 0.00 0.00 3.91
976 4783 1.078426 TCCTGCTAAAGCCCGAAGC 60.078 57.895 0.00 0.00 41.18 3.86
977 4784 0.036388 TGTCCTGCTAAAGCCCGAAG 60.036 55.000 0.00 0.00 41.18 3.79
978 4785 0.036388 CTGTCCTGCTAAAGCCCGAA 60.036 55.000 0.00 0.00 41.18 4.30
979 4786 1.596934 CTGTCCTGCTAAAGCCCGA 59.403 57.895 0.00 0.00 41.18 5.14
980 4787 2.109126 GCTGTCCTGCTAAAGCCCG 61.109 63.158 0.00 0.00 41.18 6.13
981 4788 3.911137 GCTGTCCTGCTAAAGCCC 58.089 61.111 0.00 0.00 41.18 5.19
994 4801 0.395311 CAGCAGAATCCCATGGCTGT 60.395 55.000 6.09 0.00 45.11 4.40
1023 4830 2.479566 TCAGCAGAACCTTGACATCC 57.520 50.000 0.00 0.00 0.00 3.51
1035 4842 1.722034 AGGAGGTGTTCTTCAGCAGA 58.278 50.000 0.00 0.00 45.77 4.26
1038 4845 2.810852 CAAGAAGGAGGTGTTCTTCAGC 59.189 50.000 0.00 0.00 41.37 4.26
1040 4847 3.492656 CGACAAGAAGGAGGTGTTCTTCA 60.493 47.826 0.00 0.00 41.37 3.02
1041 4848 3.060602 CGACAAGAAGGAGGTGTTCTTC 58.939 50.000 0.00 0.00 41.37 2.87
1049 4856 1.269621 ACGTTGACGACAAGAAGGAGG 60.270 52.381 10.87 0.00 43.02 4.30
1050 4857 2.052157 GACGTTGACGACAAGAAGGAG 58.948 52.381 10.87 0.00 43.02 3.69
1051 4858 1.269413 GGACGTTGACGACAAGAAGGA 60.269 52.381 10.87 0.00 43.02 3.36
1055 4865 1.026584 TGAGGACGTTGACGACAAGA 58.973 50.000 10.87 0.00 43.02 3.02
1074 4884 0.961753 TAGCAGGCGATGACGATGAT 59.038 50.000 0.00 0.00 42.66 2.45
1120 4930 3.045142 CACCCTTTGCTGGTGCTG 58.955 61.111 0.00 0.00 46.13 4.41
1125 4935 0.593128 CGTTCTTCACCCTTTGCTGG 59.407 55.000 0.00 0.00 0.00 4.85
1132 4942 1.674057 CCTGCTCGTTCTTCACCCT 59.326 57.895 0.00 0.00 0.00 4.34
1134 4944 1.376037 CCCCTGCTCGTTCTTCACC 60.376 63.158 0.00 0.00 0.00 4.02
1143 4953 2.364317 TTCTCCCTCCCCTGCTCG 60.364 66.667 0.00 0.00 0.00 5.03
1218 5028 1.335132 ATTACATGAGACCGGGCCGT 61.335 55.000 26.32 13.20 0.00 5.68
1266 5111 3.914426 TGAATCCTAAGCTCCAACCTC 57.086 47.619 0.00 0.00 0.00 3.85
1285 5130 2.831333 ACTGAGCATCCGAAGCTATTG 58.169 47.619 0.00 0.00 43.58 1.90
1297 5142 6.294397 GGAATCTCAAAACTTCAACTGAGCAT 60.294 38.462 0.00 0.00 36.15 3.79
1303 5148 7.283329 ACAGTAGGAATCTCAAAACTTCAACT 58.717 34.615 0.00 0.00 0.00 3.16
1321 5166 1.819288 AGACCATGTGACGACAGTAGG 59.181 52.381 0.00 0.00 34.87 3.18
1430 5278 4.451900 AGTAGGGAAACAAATAGCATCCG 58.548 43.478 0.00 0.00 0.00 4.18
1460 5308 6.555360 AGTCAAGTAGGGGAATAGTAATCCAG 59.445 42.308 6.59 0.00 38.80 3.86
1526 5411 8.190326 TGATGTAGACTTAGACTTTTTGAGGA 57.810 34.615 0.00 0.00 0.00 3.71
1537 5422 5.878669 TGCTCGTAGTTGATGTAGACTTAGA 59.121 40.000 0.00 0.00 0.00 2.10
1573 5458 6.334378 TCTATATGGGTTTTGACCAATGGA 57.666 37.500 6.16 0.00 42.17 3.41
1688 5620 6.627395 TTTTTCTCTCGCCTTTGTTGATAA 57.373 33.333 0.00 0.00 0.00 1.75
1701 5633 4.853743 GCTTTTACCATGCTTTTTCTCTCG 59.146 41.667 0.00 0.00 0.00 4.04
1709 5641 4.953940 TCCTTTGCTTTTACCATGCTTT 57.046 36.364 0.00 0.00 0.00 3.51
1723 5655 4.265073 AGTGATGGTAGATGTTCCTTTGC 58.735 43.478 0.00 0.00 0.00 3.68
1734 5666 4.901849 CCTGGGATAGAAAGTGATGGTAGA 59.098 45.833 0.00 0.00 0.00 2.59
1768 5702 1.725641 TGTGCAGTAGAATGAAGGCG 58.274 50.000 0.00 0.00 0.00 5.52
1783 5717 7.433680 AGGGGAAAATCGATTTATTTATGTGC 58.566 34.615 22.99 10.98 0.00 4.57
1806 5741 2.853235 ACGTCTTGGTTAAGGGAAGG 57.147 50.000 0.00 0.00 34.59 3.46
1825 5760 6.719370 GGAGAAATAAGAGATCTGAGAGGCTA 59.281 42.308 0.00 0.00 0.00 3.93
1827 5762 5.539955 AGGAGAAATAAGAGATCTGAGAGGC 59.460 44.000 0.00 0.00 0.00 4.70
1856 5802 0.117140 AGATGGGTGTGAGGAGGTGA 59.883 55.000 0.00 0.00 0.00 4.02
1866 5812 1.496060 TCGGAGCATTAGATGGGTGT 58.504 50.000 0.00 0.00 0.00 4.16
1885 5831 0.119155 TGGTTCTCCTCACCTCCCAT 59.881 55.000 0.00 0.00 35.07 4.00
1886 5832 0.836400 GTGGTTCTCCTCACCTCCCA 60.836 60.000 0.00 0.00 35.07 4.37
1929 5875 5.968528 ACGATACCAAGCTCTAATCCTAG 57.031 43.478 0.00 0.00 0.00 3.02
1935 5881 2.094390 ACGCAACGATACCAAGCTCTAA 60.094 45.455 0.00 0.00 0.00 2.10
1947 5893 1.924524 CCTAAACGATGACGCAACGAT 59.075 47.619 14.21 2.41 43.96 3.73
1949 5895 0.368907 CCCTAAACGATGACGCAACG 59.631 55.000 7.67 7.67 43.96 4.10
1952 5898 1.801771 CAAACCCTAAACGATGACGCA 59.198 47.619 0.00 0.00 43.96 5.24
1958 5904 3.245122 ACCACCATCAAACCCTAAACGAT 60.245 43.478 0.00 0.00 0.00 3.73
1969 5915 1.269174 CGATGCAACACCACCATCAAA 59.731 47.619 0.00 0.00 36.12 2.69
1982 5928 4.172505 GGCACAACAATTATTCGATGCAA 58.827 39.130 0.00 0.00 33.48 4.08
1996 5942 1.076412 TTGAAGCTGGGGCACAACA 60.076 52.632 0.00 0.00 41.70 3.33
2007 5953 0.835941 ATCGAGATGGGCTTGAAGCT 59.164 50.000 17.59 0.00 41.99 3.74
2008 5954 0.942962 CATCGAGATGGGCTTGAAGC 59.057 55.000 9.04 9.04 40.39 3.86
2018 5964 2.865276 ATGTCGACATGCCATCGAGATG 60.865 50.000 29.49 6.12 46.97 2.90
2022 5968 0.459489 TGATGTCGACATGCCATCGA 59.541 50.000 34.48 9.46 45.90 3.59
2023 5969 1.505425 ATGATGTCGACATGCCATCG 58.495 50.000 34.48 0.00 38.22 3.84
2024 5970 2.874086 TCAATGATGTCGACATGCCATC 59.126 45.455 34.48 20.90 36.57 3.51
2025 5971 2.876550 CTCAATGATGTCGACATGCCAT 59.123 45.455 34.48 26.78 36.57 4.40
2026 5972 2.282407 CTCAATGATGTCGACATGCCA 58.718 47.619 34.48 25.83 36.57 4.92
2027 5973 1.600957 CCTCAATGATGTCGACATGCC 59.399 52.381 34.48 21.20 36.57 4.40
2028 5974 2.543012 CTCCTCAATGATGTCGACATGC 59.457 50.000 34.48 23.86 36.57 4.06
2041 5987 2.610859 ACCCACCGGCTCCTCAAT 60.611 61.111 0.00 0.00 0.00 2.57
2058 6004 2.506217 GCTCGACGACGGCAATGA 60.506 61.111 7.55 0.00 40.21 2.57
2059 6005 2.167219 ATGCTCGACGACGGCAATG 61.167 57.895 21.42 0.00 43.95 2.82
2060 6006 2.167219 CATGCTCGACGACGGCAAT 61.167 57.895 21.42 11.27 43.95 3.56
2061 6007 2.809174 CATGCTCGACGACGGCAA 60.809 61.111 21.42 9.91 43.95 4.52
2062 6008 3.567478 AACATGCTCGACGACGGCA 62.567 57.895 20.36 20.36 44.47 5.69
2063 6009 2.789203 GAACATGCTCGACGACGGC 61.789 63.158 7.55 10.25 40.21 5.68
2064 6010 1.134530 GAGAACATGCTCGACGACGG 61.135 60.000 7.55 0.00 40.21 4.79
2091 6038 2.043852 ACAAACCCAACGCCACCA 60.044 55.556 0.00 0.00 0.00 4.17
2103 6050 1.154225 CCGCAAGCCGATGACAAAC 60.154 57.895 0.00 0.00 40.02 2.93
2109 6056 3.853330 CACGACCGCAAGCCGATG 61.853 66.667 0.00 0.00 40.02 3.84
2113 6060 4.752879 TAGCCACGACCGCAAGCC 62.753 66.667 0.00 0.00 0.00 4.35
2165 6129 4.021894 CAGCTAGAGTCACTGGTGTTAACT 60.022 45.833 7.22 0.00 0.00 2.24
2167 6131 3.258372 CCAGCTAGAGTCACTGGTGTTAA 59.742 47.826 15.30 0.00 44.91 2.01
2168 6132 2.826128 CCAGCTAGAGTCACTGGTGTTA 59.174 50.000 15.30 0.00 44.91 2.41
2169 6133 1.620819 CCAGCTAGAGTCACTGGTGTT 59.379 52.381 15.30 0.00 44.91 3.32
2175 6139 0.901124 CAAGGCCAGCTAGAGTCACT 59.099 55.000 5.01 0.00 0.00 3.41
2180 6144 2.286872 CAATGTCAAGGCCAGCTAGAG 58.713 52.381 5.01 0.00 0.00 2.43
2181 6145 1.065199 CCAATGTCAAGGCCAGCTAGA 60.065 52.381 5.01 0.00 0.00 2.43
2188 6152 1.560505 ATCCAACCAATGTCAAGGCC 58.439 50.000 0.00 0.00 0.00 5.19
2208 6172 7.065563 GTGAGACTCGTTATTGTCTTAGTAGGA 59.934 40.741 0.00 0.00 42.79 2.94


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

AutoCloner maintained by Alex Coulton.