Multiple sequence alignment - TraesCS5B01G222000

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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 TraesCS5B01G222000 chr5B 100.000 3841 0 0 1 3841 396620369 396624209 0.000000e+00 7094
1 TraesCS5B01G222000 chr5B 96.667 60 2 0 3415 3474 396623731 396623790 2.440000e-17 100
2 TraesCS5B01G222000 chr5B 96.667 60 2 0 3363 3422 396623783 396623842 2.440000e-17 100
3 TraesCS5B01G222000 chr5D 94.692 1997 71 15 815 2784 337697960 337699948 0.000000e+00 3068
4 TraesCS5B01G222000 chr5D 89.784 509 22 7 2936 3421 337700260 337700761 3.260000e-175 625
5 TraesCS5B01G222000 chr5D 91.964 224 17 1 3618 3841 337700863 337701085 2.880000e-81 313
6 TraesCS5B01G222000 chr5D 93.143 175 10 1 3415 3589 337700703 337700875 4.920000e-64 255
7 TraesCS5B01G222000 chr5D 86.335 161 4 8 2800 2943 337700069 337700228 3.970000e-35 159
8 TraesCS5B01G222000 chr5A 93.232 724 34 8 815 1530 438917756 438918472 0.000000e+00 1051
9 TraesCS5B01G222000 chr5A 95.872 533 17 4 2252 2784 438919373 438919900 0.000000e+00 857
10 TraesCS5B01G222000 chr5A 94.524 420 20 1 1782 2198 438918630 438919049 0.000000e+00 645
11 TraesCS5B01G222000 chr5A 89.279 513 22 6 2937 3421 438920139 438920646 2.540000e-171 612
12 TraesCS5B01G222000 chr5A 93.778 225 13 1 3617 3841 438920747 438920970 1.710000e-88 337
13 TraesCS5B01G222000 chr5A 91.954 174 12 1 3416 3589 438920589 438920760 3.830000e-60 243
14 TraesCS5B01G222000 chr5A 90.441 136 3 4 2808 2943 438919985 438920110 1.830000e-38 171
15 TraesCS5B01G222000 chr6A 85.642 787 103 8 1 780 462210288 462209505 0.000000e+00 819
16 TraesCS5B01G222000 chr7A 84.481 799 116 8 1 794 251822741 251821946 0.000000e+00 782
17 TraesCS5B01G222000 chr7A 80.929 818 131 14 1 804 352810670 352811476 1.170000e-174 623
18 TraesCS5B01G222000 chr4D 84.717 759 104 10 44 796 449964803 449964051 0.000000e+00 749
19 TraesCS5B01G222000 chr4D 84.101 673 98 8 1 668 9339439 9338771 3.240000e-180 641
20 TraesCS5B01G222000 chr7D 81.863 805 128 11 1 797 475074349 475075143 0.000000e+00 662
21 TraesCS5B01G222000 chr2D 82.208 770 112 18 48 804 192792262 192793019 1.160000e-179 640
22 TraesCS5B01G222000 chr6D 83.772 684 92 12 120 795 236207217 236206545 7.000000e-177 630
23 TraesCS5B01G222000 chr4B 82.244 704 111 8 44 742 361417560 361418254 2.550000e-166 595
24 TraesCS5B01G222000 chr7B 77.003 287 48 16 1063 1341 715996631 715996907 8.600000e-32 148


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 TraesCS5B01G222000 chr5B 396620369 396624209 3840 False 2431.333333 7094 97.778000 1 3841 3 chr5B.!!$F1 3840
1 TraesCS5B01G222000 chr5D 337697960 337701085 3125 False 884.000000 3068 91.183600 815 3841 5 chr5D.!!$F1 3026
2 TraesCS5B01G222000 chr5A 438917756 438920970 3214 False 559.428571 1051 92.725714 815 3841 7 chr5A.!!$F1 3026
3 TraesCS5B01G222000 chr6A 462209505 462210288 783 True 819.000000 819 85.642000 1 780 1 chr6A.!!$R1 779
4 TraesCS5B01G222000 chr7A 251821946 251822741 795 True 782.000000 782 84.481000 1 794 1 chr7A.!!$R1 793
5 TraesCS5B01G222000 chr7A 352810670 352811476 806 False 623.000000 623 80.929000 1 804 1 chr7A.!!$F1 803
6 TraesCS5B01G222000 chr4D 449964051 449964803 752 True 749.000000 749 84.717000 44 796 1 chr4D.!!$R2 752
7 TraesCS5B01G222000 chr4D 9338771 9339439 668 True 641.000000 641 84.101000 1 668 1 chr4D.!!$R1 667
8 TraesCS5B01G222000 chr7D 475074349 475075143 794 False 662.000000 662 81.863000 1 797 1 chr7D.!!$F1 796
9 TraesCS5B01G222000 chr2D 192792262 192793019 757 False 640.000000 640 82.208000 48 804 1 chr2D.!!$F1 756
10 TraesCS5B01G222000 chr6D 236206545 236207217 672 True 630.000000 630 83.772000 120 795 1 chr6D.!!$R1 675
11 TraesCS5B01G222000 chr4B 361417560 361418254 694 False 595.000000 595 82.244000 44 742 1 chr4B.!!$F1 698

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
117 118 0.177141 GCCATGGAGTACAACCGCTA 59.823 55.0 18.40 0.0 0.00 4.26 F
1473 1511 0.039256 TTCAGGTTTGCAGCATTCGC 60.039 50.0 0.00 0.0 38.99 4.70 F
1479 1540 0.110419 TTTGCAGCATTCGCGTGTAC 60.110 50.0 5.77 0.0 45.49 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 1937 0.249911 AGAAGGTGACCTGCGTTCAC 60.250 55.0 4.15 4.06 33.44 3.18 R
2718 3128 0.175760 ACGTAGCACGATCATGGCTT 59.824 50.0 14.18 0.00 46.05 4.35 R
3366 3969 1.035139 TACGCTAATCCCCGAACCTC 58.965 55.0 0.00 0.00 0.00 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
38 39 2.046314 CGTGGGTGGCCGAAATCT 60.046 61.111 0.00 0.00 0.00 2.40
40 41 1.299976 GTGGGTGGCCGAAATCTCT 59.700 57.895 0.00 0.00 0.00 3.10
41 42 0.744771 GTGGGTGGCCGAAATCTCTC 60.745 60.000 0.00 0.00 0.00 3.20
42 43 1.153147 GGGTGGCCGAAATCTCTCC 60.153 63.158 0.00 0.00 0.00 3.71
79 80 4.016706 CGGTGGCTCGGGACCTTT 62.017 66.667 0.00 0.00 0.00 3.11
117 118 0.177141 GCCATGGAGTACAACCGCTA 59.823 55.000 18.40 0.00 0.00 4.26
118 119 1.406341 GCCATGGAGTACAACCGCTAA 60.406 52.381 18.40 0.00 0.00 3.09
156 157 1.717348 CGGCGGGTCGGTTAATTTC 59.283 57.895 0.00 0.00 0.00 2.17
214 217 4.899239 CGGGGGTGATGAGCTCGC 62.899 72.222 9.64 4.24 0.00 5.03
321 325 3.062466 CGGAGCTCGTGGAGGTGA 61.062 66.667 7.83 0.00 40.67 4.02
461 479 0.489567 AGTGGAGGAGTGTCTTCCCT 59.510 55.000 2.87 0.00 41.51 4.20
635 658 8.941977 ACTATCTATGTTTATGTTTGAACGCAA 58.058 29.630 0.00 0.00 0.00 4.85
671 694 7.501515 GGTTTAAATTGCTTTGAACTTGATCG 58.498 34.615 6.19 0.00 39.52 3.69
696 720 8.702438 CGAATTGAAGTTTACTCCGTTAAGTTA 58.298 33.333 0.00 0.00 0.00 2.24
715 739 6.600882 AGTTAAAGGGATCGACTAGAAACA 57.399 37.500 0.00 0.00 0.00 2.83
717 741 7.621796 AGTTAAAGGGATCGACTAGAAACAAT 58.378 34.615 0.00 0.00 0.00 2.71
723 747 6.595716 AGGGATCGACTAGAAACAATCAAAAG 59.404 38.462 0.00 0.00 0.00 2.27
781 814 6.880529 ACTCCGTAAATTTTTAGGAAATCGGA 59.119 34.615 0.00 10.41 40.54 4.55
797 830 5.606348 AATCGGATAGAGATGGCCTTATC 57.394 43.478 3.32 4.38 0.00 1.75
800 833 3.511540 CGGATAGAGATGGCCTTATCACA 59.488 47.826 14.98 3.47 0.00 3.58
804 837 4.082665 AGAGATGGCCTTATCACATGTG 57.917 45.455 20.18 20.18 0.00 3.21
805 838 3.457380 AGAGATGGCCTTATCACATGTGT 59.543 43.478 24.63 14.61 0.00 3.72
806 839 3.812053 GAGATGGCCTTATCACATGTGTC 59.188 47.826 24.63 11.80 0.00 3.67
807 840 3.200605 AGATGGCCTTATCACATGTGTCA 59.799 43.478 24.63 11.42 0.00 3.58
808 841 3.650281 TGGCCTTATCACATGTGTCAT 57.350 42.857 24.63 14.56 0.00 3.06
809 842 3.281158 TGGCCTTATCACATGTGTCATG 58.719 45.455 24.63 14.66 0.00 3.07
810 843 3.282021 GGCCTTATCACATGTGTCATGT 58.718 45.455 24.63 9.21 0.00 3.21
812 845 3.065786 GCCTTATCACATGTGTCATGTGG 59.934 47.826 29.73 20.06 46.78 4.17
813 846 4.264253 CCTTATCACATGTGTCATGTGGT 58.736 43.478 29.73 27.41 46.78 4.16
818 851 1.142667 ACATGTGTCATGTGGTGGACA 59.857 47.619 13.47 0.00 41.44 4.02
929 967 5.545658 TCGCAAGAGTTAATCATGGAAAC 57.454 39.130 0.00 0.00 45.01 2.78
934 972 6.624423 CAAGAGTTAATCATGGAAACTTGGG 58.376 40.000 8.86 1.15 33.72 4.12
956 994 1.715019 CCCCCTCACCAAACTCACCA 61.715 60.000 0.00 0.00 0.00 4.17
978 1016 3.101437 TGAGACGCCTATAAAACCCAGA 58.899 45.455 0.00 0.00 0.00 3.86
1032 1070 1.702299 CGCGCTGCACTTACTACAC 59.298 57.895 5.56 0.00 0.00 2.90
1149 1187 1.600638 CAGGAACGGTTACTCCCCC 59.399 63.158 1.69 0.00 31.50 5.40
1465 1503 0.599558 GCTCATGCTTCAGGTTTGCA 59.400 50.000 0.00 0.00 41.13 4.08
1470 1508 1.042229 TGCTTCAGGTTTGCAGCATT 58.958 45.000 0.00 0.00 46.31 3.56
1471 1509 1.000060 TGCTTCAGGTTTGCAGCATTC 60.000 47.619 0.00 0.00 46.31 2.67
1472 1510 1.973138 CTTCAGGTTTGCAGCATTCG 58.027 50.000 0.00 0.00 0.00 3.34
1473 1511 0.039256 TTCAGGTTTGCAGCATTCGC 60.039 50.000 0.00 0.00 38.99 4.70
1474 1512 1.798725 CAGGTTTGCAGCATTCGCG 60.799 57.895 0.00 0.00 45.49 5.87
1475 1513 2.255252 GGTTTGCAGCATTCGCGT 59.745 55.556 5.77 0.00 45.49 6.01
1476 1514 2.082366 GGTTTGCAGCATTCGCGTG 61.082 57.895 5.77 0.00 45.49 5.34
1479 1540 0.110419 TTTGCAGCATTCGCGTGTAC 60.110 50.000 5.77 0.00 45.49 2.90
1492 1553 4.216731 TCGCGTGTACTTAATCGATCATC 58.783 43.478 5.77 0.00 0.00 2.92
1618 1755 1.898574 CACCAACCACACTGGCTCC 60.899 63.158 0.00 0.00 42.67 4.70
1621 1758 1.525995 CAACCACACTGGCTCCGTT 60.526 57.895 0.00 0.00 42.67 4.44
1631 1768 3.057315 CACTGGCTCCGTTTCATTTCATT 60.057 43.478 0.00 0.00 0.00 2.57
1699 1836 4.744570 TCTACAAGTTGATTAGCCTGTCG 58.255 43.478 10.54 0.00 0.00 4.35
1702 1839 5.086104 ACAAGTTGATTAGCCTGTCGTAT 57.914 39.130 10.54 0.00 0.00 3.06
1774 1911 1.084289 GGTTAGCGCACCTAAACTGG 58.916 55.000 11.47 0.00 40.01 4.00
1775 1912 1.609841 GGTTAGCGCACCTAAACTGGT 60.610 52.381 11.47 0.00 40.01 4.00
1776 1913 2.148768 GTTAGCGCACCTAAACTGGTT 58.851 47.619 11.47 0.00 37.75 3.67
2016 2156 2.494918 GACCACAGCCGCGAGTAT 59.505 61.111 8.23 0.00 0.00 2.12
2051 2191 0.179000 GCATCAACCGATCCTCCTGT 59.821 55.000 0.00 0.00 0.00 4.00
2097 2237 4.529219 TACGCCAGCGCCATCCTG 62.529 66.667 12.72 0.00 44.19 3.86
2532 2942 2.027024 TCGCACGACGCTGACTTT 59.973 55.556 0.00 0.00 43.23 2.66
2676 3086 0.902984 TGGCGAGGTTCAAGGAGCTA 60.903 55.000 0.00 0.00 0.00 3.32
2709 3119 2.202987 GCCGCCATGGAGTGAGAG 60.203 66.667 18.40 0.00 42.00 3.20
2710 3120 2.202987 CCGCCATGGAGTGAGAGC 60.203 66.667 18.40 0.00 42.00 4.09
2712 3122 2.729479 CGCCATGGAGTGAGAGCCT 61.729 63.158 18.40 0.00 0.00 4.58
2714 3124 1.440893 CCATGGAGTGAGAGCCTCG 59.559 63.158 5.56 0.00 32.35 4.63
2715 3125 1.227205 CATGGAGTGAGAGCCTCGC 60.227 63.158 7.45 7.45 40.84 5.03
2716 3126 2.430610 ATGGAGTGAGAGCCTCGCC 61.431 63.158 10.86 6.80 41.38 5.54
2717 3127 4.200283 GGAGTGAGAGCCTCGCCG 62.200 72.222 10.86 0.00 41.38 6.46
2718 3128 3.134792 GAGTGAGAGCCTCGCCGA 61.135 66.667 10.86 0.00 41.38 5.54
2773 3183 4.582240 TGTAATGTGAAATGTGCAGGTGAA 59.418 37.500 0.00 0.00 0.00 3.18
2784 3194 8.807948 AAATGTGCAGGTGAAAGTATATAGTT 57.192 30.769 0.00 0.00 0.00 2.24
2785 3195 7.792374 ATGTGCAGGTGAAAGTATATAGTTG 57.208 36.000 3.54 0.00 0.00 3.16
2788 3198 7.979537 TGTGCAGGTGAAAGTATATAGTTGTAG 59.020 37.037 3.54 0.00 0.00 2.74
2837 3356 8.011673 CGTGTATAATCAGAATTTCATGCGAAT 58.988 33.333 0.00 0.00 0.00 3.34
2849 3368 9.252962 GAATTTCATGCGAATAAAGGATCAAAT 57.747 29.630 0.00 0.00 0.00 2.32
2977 3552 2.127496 CAGTTGCGCTGCGAGTTG 60.127 61.111 28.07 13.43 38.52 3.16
3014 3589 2.831742 AACGCGCTATCGGAGGGA 60.832 61.111 5.73 0.00 40.59 4.20
3224 3801 2.895372 CCGCACGGTAATGAGGCC 60.895 66.667 0.00 0.00 32.46 5.19
3339 3937 0.603707 CGTCCCTGACTGCACATTGT 60.604 55.000 0.00 0.00 0.00 2.71
3371 3974 4.617875 CGAATCGCAAGGGAGGTT 57.382 55.556 0.00 0.00 38.47 3.50
3372 3975 2.384203 CGAATCGCAAGGGAGGTTC 58.616 57.895 0.00 0.00 38.47 3.62
3373 3976 1.421410 CGAATCGCAAGGGAGGTTCG 61.421 60.000 7.97 7.97 38.47 3.95
3374 3977 1.078426 AATCGCAAGGGAGGTTCGG 60.078 57.895 0.00 0.00 38.47 4.30
3375 3978 2.536997 AATCGCAAGGGAGGTTCGGG 62.537 60.000 0.00 0.00 38.47 5.14
3376 3979 4.778143 CGCAAGGGAGGTTCGGGG 62.778 72.222 0.00 0.00 0.00 5.73
3377 3980 3.327404 GCAAGGGAGGTTCGGGGA 61.327 66.667 0.00 0.00 0.00 4.81
3378 3981 2.680370 GCAAGGGAGGTTCGGGGAT 61.680 63.158 0.00 0.00 0.00 3.85
3379 3982 1.999346 CAAGGGAGGTTCGGGGATT 59.001 57.895 0.00 0.00 0.00 3.01
3380 3983 1.209621 CAAGGGAGGTTCGGGGATTA 58.790 55.000 0.00 0.00 0.00 1.75
3381 3984 1.141053 CAAGGGAGGTTCGGGGATTAG 59.859 57.143 0.00 0.00 0.00 1.73
3382 3985 1.054978 AGGGAGGTTCGGGGATTAGC 61.055 60.000 0.00 0.00 0.00 3.09
3383 3986 1.069258 GGAGGTTCGGGGATTAGCG 59.931 63.158 0.00 0.00 0.00 4.26
3384 3987 1.683418 GGAGGTTCGGGGATTAGCGT 61.683 60.000 0.00 0.00 0.00 5.07
3385 3988 1.035139 GAGGTTCGGGGATTAGCGTA 58.965 55.000 0.00 0.00 0.00 4.42
3386 3989 1.410153 GAGGTTCGGGGATTAGCGTAA 59.590 52.381 0.00 0.00 0.00 3.18
3387 3990 1.411612 AGGTTCGGGGATTAGCGTAAG 59.588 52.381 0.00 0.00 43.44 2.34
3388 3991 1.410153 GGTTCGGGGATTAGCGTAAGA 59.590 52.381 0.00 0.00 43.02 2.10
3389 3992 2.036862 GGTTCGGGGATTAGCGTAAGAT 59.963 50.000 0.00 0.00 43.02 2.40
3390 3993 3.493873 GGTTCGGGGATTAGCGTAAGATT 60.494 47.826 0.00 0.00 43.02 2.40
3391 3994 3.380479 TCGGGGATTAGCGTAAGATTG 57.620 47.619 0.00 0.00 43.02 2.67
3392 3995 2.696707 TCGGGGATTAGCGTAAGATTGT 59.303 45.455 0.00 0.00 43.02 2.71
3393 3996 3.133362 TCGGGGATTAGCGTAAGATTGTT 59.867 43.478 0.00 0.00 43.02 2.83
3394 3997 3.875134 CGGGGATTAGCGTAAGATTGTTT 59.125 43.478 0.00 0.00 43.02 2.83
3395 3998 4.334481 CGGGGATTAGCGTAAGATTGTTTT 59.666 41.667 0.00 0.00 43.02 2.43
3396 3999 5.578776 GGGGATTAGCGTAAGATTGTTTTG 58.421 41.667 0.00 0.00 43.02 2.44
3397 4000 5.449999 GGGGATTAGCGTAAGATTGTTTTGG 60.450 44.000 0.00 0.00 43.02 3.28
3398 4001 5.124936 GGGATTAGCGTAAGATTGTTTTGGT 59.875 40.000 0.00 0.00 43.02 3.67
3399 4002 6.316890 GGGATTAGCGTAAGATTGTTTTGGTA 59.683 38.462 0.00 0.00 43.02 3.25
3400 4003 7.407337 GGATTAGCGTAAGATTGTTTTGGTAG 58.593 38.462 0.00 0.00 43.02 3.18
3401 4004 7.279313 GGATTAGCGTAAGATTGTTTTGGTAGA 59.721 37.037 0.00 0.00 43.02 2.59
3402 4005 7.591006 TTAGCGTAAGATTGTTTTGGTAGAG 57.409 36.000 0.00 0.00 43.02 2.43
3403 4006 5.548406 AGCGTAAGATTGTTTTGGTAGAGT 58.452 37.500 0.00 0.00 43.02 3.24
3404 4007 5.408604 AGCGTAAGATTGTTTTGGTAGAGTG 59.591 40.000 0.00 0.00 43.02 3.51
3405 4008 5.178809 GCGTAAGATTGTTTTGGTAGAGTGT 59.821 40.000 0.00 0.00 43.02 3.55
3406 4009 6.366877 GCGTAAGATTGTTTTGGTAGAGTGTA 59.633 38.462 0.00 0.00 43.02 2.90
3407 4010 7.620806 GCGTAAGATTGTTTTGGTAGAGTGTAC 60.621 40.741 0.00 0.00 43.02 2.90
3408 4011 7.383029 CGTAAGATTGTTTTGGTAGAGTGTACA 59.617 37.037 0.00 0.00 43.02 2.90
3409 4012 9.048446 GTAAGATTGTTTTGGTAGAGTGTACAA 57.952 33.333 0.00 0.00 0.00 2.41
3410 4013 8.514330 AAGATTGTTTTGGTAGAGTGTACAAA 57.486 30.769 0.00 0.00 0.00 2.83
3411 4014 8.691661 AGATTGTTTTGGTAGAGTGTACAAAT 57.308 30.769 0.00 0.00 33.40 2.32
3412 4015 8.784043 AGATTGTTTTGGTAGAGTGTACAAATC 58.216 33.333 0.00 0.00 33.40 2.17
3413 4016 8.691661 ATTGTTTTGGTAGAGTGTACAAATCT 57.308 30.769 14.43 14.43 33.40 2.40
3414 4017 9.787435 ATTGTTTTGGTAGAGTGTACAAATCTA 57.213 29.630 12.77 12.77 33.40 1.98
3473 4076 7.339721 TGGTAGAGTGTACAAATCTAAGAGAGG 59.660 40.741 16.67 0.00 0.00 3.69
3486 4089 6.744175 TCTAAGAGAGGCAGATGATCATTT 57.256 37.500 10.14 0.28 0.00 2.32
3499 4102 8.559536 GCAGATGATCATTTTCCGATTTAGTTA 58.440 33.333 10.14 0.00 0.00 2.24
3520 4123 7.918076 AGTTATTGTTCACCCTAATTCTCAGA 58.082 34.615 0.00 0.00 0.00 3.27
3584 4187 8.628630 TTCACTGTGATGTAATAATTGGTTCA 57.371 30.769 11.86 0.00 0.00 3.18
3585 4188 8.806429 TCACTGTGATGTAATAATTGGTTCAT 57.194 30.769 6.36 0.00 0.00 2.57
3586 4189 8.892723 TCACTGTGATGTAATAATTGGTTCATC 58.107 33.333 6.36 0.00 34.28 2.92
3587 4190 8.131100 CACTGTGATGTAATAATTGGTTCATCC 58.869 37.037 0.32 0.00 33.20 3.51
3588 4191 8.055181 ACTGTGATGTAATAATTGGTTCATCCT 58.945 33.333 0.00 0.00 37.07 3.24
3589 4192 8.821686 TGTGATGTAATAATTGGTTCATCCTT 57.178 30.769 0.00 0.00 37.07 3.36
3590 4193 9.913310 TGTGATGTAATAATTGGTTCATCCTTA 57.087 29.630 0.00 0.00 37.07 2.69
3592 4195 9.349713 TGATGTAATAATTGGTTCATCCTTACC 57.650 33.333 0.00 0.00 37.07 2.85
3593 4196 8.706322 ATGTAATAATTGGTTCATCCTTACCC 57.294 34.615 0.00 0.00 37.07 3.69
3594 4197 6.768861 TGTAATAATTGGTTCATCCTTACCCG 59.231 38.462 0.00 0.00 37.07 5.28
3595 4198 2.052782 ATTGGTTCATCCTTACCCGC 57.947 50.000 0.00 0.00 37.07 6.13
3596 4199 0.693622 TTGGTTCATCCTTACCCGCA 59.306 50.000 0.00 0.00 37.07 5.69
3597 4200 0.693622 TGGTTCATCCTTACCCGCAA 59.306 50.000 0.00 0.00 37.07 4.85
3598 4201 1.074084 TGGTTCATCCTTACCCGCAAA 59.926 47.619 0.00 0.00 37.07 3.68
3599 4202 2.164338 GGTTCATCCTTACCCGCAAAA 58.836 47.619 0.00 0.00 0.00 2.44
3600 4203 2.758423 GGTTCATCCTTACCCGCAAAAT 59.242 45.455 0.00 0.00 0.00 1.82
3601 4204 3.949113 GGTTCATCCTTACCCGCAAAATA 59.051 43.478 0.00 0.00 0.00 1.40
3602 4205 4.399934 GGTTCATCCTTACCCGCAAAATAA 59.600 41.667 0.00 0.00 0.00 1.40
3603 4206 5.105675 GGTTCATCCTTACCCGCAAAATAAA 60.106 40.000 0.00 0.00 0.00 1.40
3604 4207 6.391537 GTTCATCCTTACCCGCAAAATAAAA 58.608 36.000 0.00 0.00 0.00 1.52
3605 4208 6.591750 TCATCCTTACCCGCAAAATAAAAA 57.408 33.333 0.00 0.00 0.00 1.94
3606 4209 7.176589 TCATCCTTACCCGCAAAATAAAAAT 57.823 32.000 0.00 0.00 0.00 1.82
3607 4210 8.294954 TCATCCTTACCCGCAAAATAAAAATA 57.705 30.769 0.00 0.00 0.00 1.40
3608 4211 8.750298 TCATCCTTACCCGCAAAATAAAAATAA 58.250 29.630 0.00 0.00 0.00 1.40
3609 4212 9.372369 CATCCTTACCCGCAAAATAAAAATAAA 57.628 29.630 0.00 0.00 0.00 1.40
3610 4213 9.945904 ATCCTTACCCGCAAAATAAAAATAAAA 57.054 25.926 0.00 0.00 0.00 1.52
3611 4214 9.774413 TCCTTACCCGCAAAATAAAAATAAAAA 57.226 25.926 0.00 0.00 0.00 1.94
3666 4269 8.660373 GGAATGTAGTATTTGTTCTCAGAGTTG 58.340 37.037 0.00 0.00 0.00 3.16
3727 4330 1.216941 GACGGTTTTCGGCGTCTGAA 61.217 55.000 6.85 0.00 44.45 3.02
3756 4359 5.721232 ACTAAGAAATTCTCCGACGAATGT 58.279 37.500 0.00 0.00 34.07 2.71
3769 4372 4.260212 CCGACGAATGTGAATTAGCGAAAT 60.260 41.667 0.00 0.00 0.00 2.17
3811 4414 1.862201 TCGCTAAACGTTTGTGTCTGG 59.138 47.619 23.46 5.87 44.19 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.810896 GATTTCGGCCACCCACGC 61.811 66.667 2.24 0.00 0.00 5.34
117 118 2.030562 CGTGGAAGCGGACCTGTT 59.969 61.111 0.00 0.00 0.00 3.16
214 217 2.279517 GTCCTCGCGTGCCATAGG 60.280 66.667 5.77 4.14 0.00 2.57
321 325 2.926200 CGTCGACAAAGATCATCTGCTT 59.074 45.455 17.16 0.00 0.00 3.91
439 457 0.109039 GAAGACACTCCTCCACTCGC 60.109 60.000 0.00 0.00 0.00 5.03
579 601 8.159709 GCACAACCGAACATAAAACATAAATTC 58.840 33.333 0.00 0.00 0.00 2.17
631 654 2.611974 AAACCGAAAGTAGCATTGCG 57.388 45.000 2.38 0.00 0.00 4.85
635 658 6.267496 AGCAATTTAAACCGAAAGTAGCAT 57.733 33.333 0.00 0.00 0.00 3.79
696 720 6.049955 TGATTGTTTCTAGTCGATCCCTTT 57.950 37.500 0.00 0.00 0.00 3.11
698 722 5.677319 TTGATTGTTTCTAGTCGATCCCT 57.323 39.130 0.00 0.00 0.00 4.20
781 814 5.309020 ACACATGTGATAAGGCCATCTCTAT 59.691 40.000 31.94 0.06 0.00 1.98
797 830 1.536766 GTCCACCACATGACACATGTG 59.463 52.381 27.39 27.39 46.49 3.21
800 833 2.229792 GTTGTCCACCACATGACACAT 58.770 47.619 0.00 0.00 40.96 3.21
832 865 1.171549 TGGCGCATGCAAAGAAGTGA 61.172 50.000 19.57 0.00 45.35 3.41
833 866 1.005294 GTGGCGCATGCAAAGAAGTG 61.005 55.000 19.57 0.00 45.35 3.16
834 867 1.286880 GTGGCGCATGCAAAGAAGT 59.713 52.632 19.57 0.00 45.35 3.01
840 875 0.179176 GTAAATCGTGGCGCATGCAA 60.179 50.000 19.57 0.00 45.35 4.08
934 972 0.476771 TGAGTTTGGTGAGGGGGTTC 59.523 55.000 0.00 0.00 0.00 3.62
956 994 3.709653 TCTGGGTTTTATAGGCGTCTCAT 59.290 43.478 0.00 0.00 0.00 2.90
978 1016 2.365635 CGACTCCATGGAGGGGGT 60.366 66.667 38.54 23.13 46.94 4.95
1017 1055 2.854777 CGATCTGTGTAGTAAGTGCAGC 59.145 50.000 0.00 0.00 0.00 5.25
1025 1063 1.607148 CGGCCATCGATCTGTGTAGTA 59.393 52.381 2.24 0.00 42.43 1.82
1028 1066 0.384309 GACGGCCATCGATCTGTGTA 59.616 55.000 2.24 0.00 42.43 2.90
1032 1070 0.877649 CTTGGACGGCCATCGATCTG 60.878 60.000 13.08 0.00 45.46 2.90
1140 1178 0.706433 AGTAGACGGTGGGGGAGTAA 59.294 55.000 0.00 0.00 0.00 2.24
1149 1187 1.467713 GCTCGGAAGAAGTAGACGGTG 60.468 57.143 0.00 0.00 41.32 4.94
1465 1503 2.534349 CGATTAAGTACACGCGAATGCT 59.466 45.455 15.93 6.08 39.65 3.79
1470 1508 3.678915 TGATCGATTAAGTACACGCGA 57.321 42.857 15.93 0.00 0.00 5.87
1471 1509 4.219802 AGATGATCGATTAAGTACACGCG 58.780 43.478 3.53 3.53 0.00 6.01
1472 1510 5.117287 GGAAGATGATCGATTAAGTACACGC 59.883 44.000 0.00 0.00 0.00 5.34
1473 1511 6.439599 AGGAAGATGATCGATTAAGTACACG 58.560 40.000 0.00 0.00 0.00 4.49
1474 1512 9.182933 GTAAGGAAGATGATCGATTAAGTACAC 57.817 37.037 0.00 0.00 0.00 2.90
1475 1513 8.074370 CGTAAGGAAGATGATCGATTAAGTACA 58.926 37.037 0.00 0.00 0.00 2.90
1476 1514 8.074972 ACGTAAGGAAGATGATCGATTAAGTAC 58.925 37.037 0.00 0.00 46.39 2.73
1479 1540 6.129062 GCACGTAAGGAAGATGATCGATTAAG 60.129 42.308 0.00 0.00 46.39 1.85
1492 1553 1.019278 ACGCCATGCACGTAAGGAAG 61.019 55.000 9.90 0.00 43.02 3.46
1580 1717 0.600255 CGCTTGACCTTGACCGTCTT 60.600 55.000 0.00 0.00 0.00 3.01
1584 1721 2.664851 TGCGCTTGACCTTGACCG 60.665 61.111 9.73 0.00 0.00 4.79
1618 1755 3.488489 GTCACCGGAATGAAATGAAACG 58.512 45.455 9.46 0.00 0.00 3.60
1621 1758 2.773487 ACGTCACCGGAATGAAATGAA 58.227 42.857 9.46 0.00 38.78 2.57
1631 1768 0.457035 GGTGCTTATACGTCACCGGA 59.543 55.000 9.46 0.00 40.54 5.14
1774 1911 4.085924 CGACACGTCGCCTGTTATAATAAC 60.086 45.833 6.65 0.00 46.50 1.89
1775 1912 4.037021 CGACACGTCGCCTGTTATAATAA 58.963 43.478 6.65 0.00 46.50 1.40
1776 1913 3.620761 CGACACGTCGCCTGTTATAATA 58.379 45.455 6.65 0.00 46.50 0.98
1800 1937 0.249911 AGAAGGTGACCTGCGTTCAC 60.250 55.000 4.15 4.06 33.44 3.18
1987 2127 2.083835 CTGTGGTCGAAGTGGACGGT 62.084 60.000 0.00 0.00 37.82 4.83
2526 2936 3.172106 TCGCCCCACCCAAAGTCA 61.172 61.111 0.00 0.00 0.00 3.41
2676 3086 0.390860 CGGCCATCTCCTCGAAGAAT 59.609 55.000 2.24 0.00 34.09 2.40
2709 3119 4.838152 TCATGGCTTCGGCGAGGC 62.838 66.667 32.49 32.49 42.91 4.70
2710 3120 1.958205 GATCATGGCTTCGGCGAGG 60.958 63.158 15.27 15.27 42.91 4.63
2712 3122 2.279451 CGATCATGGCTTCGGCGA 60.279 61.111 4.99 4.99 42.91 5.54
2714 3124 3.017323 CACGATCATGGCTTCGGC 58.983 61.111 14.89 0.00 39.61 5.54
2715 3125 0.249447 TAGCACGATCATGGCTTCGG 60.249 55.000 14.89 7.62 39.61 4.30
2716 3126 0.855349 GTAGCACGATCATGGCTTCG 59.145 55.000 7.90 10.66 39.01 3.79
2717 3127 0.855349 CGTAGCACGATCATGGCTTC 59.145 55.000 7.90 3.18 46.05 3.86
2718 3128 0.175760 ACGTAGCACGATCATGGCTT 59.824 50.000 14.18 0.00 46.05 4.35
2759 3169 8.677300 CAACTATATACTTTCACCTGCACATTT 58.323 33.333 0.00 0.00 0.00 2.32
2849 3368 4.340666 TCTGGCAGTTCTTTTGCATGTAAA 59.659 37.500 15.27 4.71 43.28 2.01
2896 3426 4.616143 CGGATCACGTTTTCTCTCTCAGAA 60.616 45.833 0.00 0.00 37.28 3.02
2898 3428 3.119814 TCGGATCACGTTTTCTCTCTCAG 60.120 47.826 0.00 0.00 44.69 3.35
2899 3429 2.817844 TCGGATCACGTTTTCTCTCTCA 59.182 45.455 0.00 0.00 44.69 3.27
2900 3430 3.489180 TCGGATCACGTTTTCTCTCTC 57.511 47.619 0.00 0.00 44.69 3.20
2977 3552 1.134694 GTTCGCGAGATTGGTTGCC 59.865 57.895 9.59 0.00 41.60 4.52
3014 3589 4.698625 AGGGGAAGGCGGACTCGT 62.699 66.667 0.00 0.00 38.89 4.18
3233 3810 2.271497 GTCCCGGACGAGAGAGGA 59.729 66.667 0.73 0.00 0.00 3.71
3309 3907 1.734465 GTCAGGGACGAATTTCAGCAG 59.266 52.381 0.00 0.00 0.00 4.24
3312 3910 1.734465 GCAGTCAGGGACGAATTTCAG 59.266 52.381 0.00 0.00 37.67 3.02
3363 3966 1.054978 GCTAATCCCCGAACCTCCCT 61.055 60.000 0.00 0.00 0.00 4.20
3364 3967 1.450642 GCTAATCCCCGAACCTCCC 59.549 63.158 0.00 0.00 0.00 4.30
3365 3968 1.069258 CGCTAATCCCCGAACCTCC 59.931 63.158 0.00 0.00 0.00 4.30
3366 3969 1.035139 TACGCTAATCCCCGAACCTC 58.965 55.000 0.00 0.00 0.00 3.85
3367 3970 1.411612 CTTACGCTAATCCCCGAACCT 59.588 52.381 0.00 0.00 0.00 3.50
3368 3971 1.410153 TCTTACGCTAATCCCCGAACC 59.590 52.381 0.00 0.00 0.00 3.62
3369 3972 2.877043 TCTTACGCTAATCCCCGAAC 57.123 50.000 0.00 0.00 0.00 3.95
3370 3973 3.133362 ACAATCTTACGCTAATCCCCGAA 59.867 43.478 0.00 0.00 0.00 4.30
3371 3974 2.696707 ACAATCTTACGCTAATCCCCGA 59.303 45.455 0.00 0.00 0.00 5.14
3372 3975 3.107642 ACAATCTTACGCTAATCCCCG 57.892 47.619 0.00 0.00 0.00 5.73
3373 3976 5.449999 CCAAAACAATCTTACGCTAATCCCC 60.450 44.000 0.00 0.00 0.00 4.81
3374 3977 5.124936 ACCAAAACAATCTTACGCTAATCCC 59.875 40.000 0.00 0.00 0.00 3.85
3375 3978 6.190954 ACCAAAACAATCTTACGCTAATCC 57.809 37.500 0.00 0.00 0.00 3.01
3376 3979 8.193250 TCTACCAAAACAATCTTACGCTAATC 57.807 34.615 0.00 0.00 0.00 1.75
3377 3980 7.822822 ACTCTACCAAAACAATCTTACGCTAAT 59.177 33.333 0.00 0.00 0.00 1.73
3378 3981 7.117236 CACTCTACCAAAACAATCTTACGCTAA 59.883 37.037 0.00 0.00 0.00 3.09
3379 3982 6.588756 CACTCTACCAAAACAATCTTACGCTA 59.411 38.462 0.00 0.00 0.00 4.26
3380 3983 5.408604 CACTCTACCAAAACAATCTTACGCT 59.591 40.000 0.00 0.00 0.00 5.07
3381 3984 5.178809 ACACTCTACCAAAACAATCTTACGC 59.821 40.000 0.00 0.00 0.00 4.42
3382 3985 6.780706 ACACTCTACCAAAACAATCTTACG 57.219 37.500 0.00 0.00 0.00 3.18
3383 3986 8.597662 TGTACACTCTACCAAAACAATCTTAC 57.402 34.615 0.00 0.00 0.00 2.34
3384 3987 9.616156 TTTGTACACTCTACCAAAACAATCTTA 57.384 29.630 0.00 0.00 0.00 2.10
3385 3988 8.514330 TTTGTACACTCTACCAAAACAATCTT 57.486 30.769 0.00 0.00 0.00 2.40
3386 3989 8.691661 ATTTGTACACTCTACCAAAACAATCT 57.308 30.769 0.00 0.00 0.00 2.40
3387 3990 8.784043 AGATTTGTACACTCTACCAAAACAATC 58.216 33.333 0.00 0.00 0.00 2.67
3388 3991 8.691661 AGATTTGTACACTCTACCAAAACAAT 57.308 30.769 0.00 0.00 0.00 2.71
3389 3992 9.616156 TTAGATTTGTACACTCTACCAAAACAA 57.384 29.630 11.96 0.00 0.00 2.83
3390 3993 9.268268 CTTAGATTTGTACACTCTACCAAAACA 57.732 33.333 11.96 0.00 0.00 2.83
3391 3994 9.485206 TCTTAGATTTGTACACTCTACCAAAAC 57.515 33.333 11.96 0.00 0.00 2.43
3392 3995 9.706691 CTCTTAGATTTGTACACTCTACCAAAA 57.293 33.333 11.96 2.03 0.00 2.44
3393 3996 9.085645 TCTCTTAGATTTGTACACTCTACCAAA 57.914 33.333 11.96 0.00 0.00 3.28
3394 3997 8.645814 TCTCTTAGATTTGTACACTCTACCAA 57.354 34.615 11.96 0.00 0.00 3.67
3395 3998 7.339721 CCTCTCTTAGATTTGTACACTCTACCA 59.660 40.741 11.96 3.94 0.00 3.25
3396 3999 7.339976 ACCTCTCTTAGATTTGTACACTCTACC 59.660 40.741 11.96 0.00 0.00 3.18
3397 4000 8.283699 ACCTCTCTTAGATTTGTACACTCTAC 57.716 38.462 11.96 0.00 0.00 2.59
3398 4001 8.880991 AACCTCTCTTAGATTTGTACACTCTA 57.119 34.615 9.33 9.33 0.00 2.43
3399 4002 7.362229 CGAACCTCTCTTAGATTTGTACACTCT 60.362 40.741 10.97 10.97 0.00 3.24
3400 4003 6.748198 CGAACCTCTCTTAGATTTGTACACTC 59.252 42.308 0.00 0.00 0.00 3.51
3401 4004 6.350277 CCGAACCTCTCTTAGATTTGTACACT 60.350 42.308 0.00 0.00 0.00 3.55
3402 4005 5.805994 CCGAACCTCTCTTAGATTTGTACAC 59.194 44.000 0.00 0.00 0.00 2.90
3403 4006 5.105473 CCCGAACCTCTCTTAGATTTGTACA 60.105 44.000 0.00 0.00 0.00 2.90
3404 4007 5.349809 CCCGAACCTCTCTTAGATTTGTAC 58.650 45.833 0.00 0.00 0.00 2.90
3405 4008 4.404715 CCCCGAACCTCTCTTAGATTTGTA 59.595 45.833 0.00 0.00 0.00 2.41
3406 4009 3.197983 CCCCGAACCTCTCTTAGATTTGT 59.802 47.826 0.00 0.00 0.00 2.83
3407 4010 3.451178 TCCCCGAACCTCTCTTAGATTTG 59.549 47.826 0.00 0.00 0.00 2.32
3408 4011 3.721021 TCCCCGAACCTCTCTTAGATTT 58.279 45.455 0.00 0.00 0.00 2.17
3409 4012 3.399952 TCCCCGAACCTCTCTTAGATT 57.600 47.619 0.00 0.00 0.00 2.40
3410 4013 3.621682 ATCCCCGAACCTCTCTTAGAT 57.378 47.619 0.00 0.00 0.00 1.98
3411 4014 3.399952 AATCCCCGAACCTCTCTTAGA 57.600 47.619 0.00 0.00 0.00 2.10
3412 4015 3.006003 GCTAATCCCCGAACCTCTCTTAG 59.994 52.174 0.00 0.00 0.00 2.18
3413 4016 2.963782 GCTAATCCCCGAACCTCTCTTA 59.036 50.000 0.00 0.00 0.00 2.10
3414 4017 1.763545 GCTAATCCCCGAACCTCTCTT 59.236 52.381 0.00 0.00 0.00 2.85
3473 4076 6.963796 ACTAAATCGGAAAATGATCATCTGC 58.036 36.000 9.06 4.03 0.00 4.26
3486 4089 6.478129 AGGGTGAACAATAACTAAATCGGAA 58.522 36.000 0.00 0.00 0.00 4.30
3499 4102 6.962182 TCATCTGAGAATTAGGGTGAACAAT 58.038 36.000 0.00 0.00 0.00 2.71
3575 4178 2.291282 TGCGGGTAAGGATGAACCAATT 60.291 45.455 0.00 0.00 42.04 2.32
3576 4179 1.283613 TGCGGGTAAGGATGAACCAAT 59.716 47.619 0.00 0.00 42.04 3.16
3577 4180 0.693622 TGCGGGTAAGGATGAACCAA 59.306 50.000 0.00 0.00 42.04 3.67
3578 4181 0.693622 TTGCGGGTAAGGATGAACCA 59.306 50.000 0.00 0.00 42.04 3.67
3579 4182 1.828979 TTTGCGGGTAAGGATGAACC 58.171 50.000 0.00 0.00 39.35 3.62
3580 4183 5.570234 TTATTTTGCGGGTAAGGATGAAC 57.430 39.130 0.00 0.00 0.00 3.18
3581 4184 6.591750 TTTTATTTTGCGGGTAAGGATGAA 57.408 33.333 0.00 0.00 0.00 2.57
3582 4185 6.591750 TTTTTATTTTGCGGGTAAGGATGA 57.408 33.333 0.00 0.00 0.00 2.92
3583 4186 8.934507 TTATTTTTATTTTGCGGGTAAGGATG 57.065 30.769 0.00 0.00 0.00 3.51
3584 4187 9.945904 TTTTATTTTTATTTTGCGGGTAAGGAT 57.054 25.926 0.00 0.00 0.00 3.24
3585 4188 9.774413 TTTTTATTTTTATTTTGCGGGTAAGGA 57.226 25.926 0.00 0.00 0.00 3.36
3606 4209 9.732130 CCCAGGATGAACCAATTTTTATTTTTA 57.268 29.630 0.00 0.00 39.69 1.52
3607 4210 7.176515 GCCCAGGATGAACCAATTTTTATTTTT 59.823 33.333 0.00 0.00 39.69 1.94
3608 4211 6.658816 GCCCAGGATGAACCAATTTTTATTTT 59.341 34.615 0.00 0.00 39.69 1.82
3609 4212 6.179756 GCCCAGGATGAACCAATTTTTATTT 58.820 36.000 0.00 0.00 39.69 1.40
3610 4213 5.250313 TGCCCAGGATGAACCAATTTTTATT 59.750 36.000 0.00 0.00 39.69 1.40
3611 4214 4.782156 TGCCCAGGATGAACCAATTTTTAT 59.218 37.500 0.00 0.00 39.69 1.40
3612 4215 4.163427 TGCCCAGGATGAACCAATTTTTA 58.837 39.130 0.00 0.00 39.69 1.52
3613 4216 2.978278 TGCCCAGGATGAACCAATTTTT 59.022 40.909 0.00 0.00 39.69 1.94
3614 4217 2.618794 TGCCCAGGATGAACCAATTTT 58.381 42.857 0.00 0.00 39.69 1.82
3615 4218 2.323999 TGCCCAGGATGAACCAATTT 57.676 45.000 0.00 0.00 39.69 1.82
3724 4327 7.117812 GTCGGAGAATTTCTTAGTTCACATTCA 59.882 37.037 0.00 0.00 39.69 2.57
3727 4330 5.577164 CGTCGGAGAATTTCTTAGTTCACAT 59.423 40.000 0.00 0.00 39.69 3.21
3791 4394 1.862201 CCAGACACAAACGTTTAGCGA 59.138 47.619 14.20 0.00 44.77 4.93
3799 4402 7.539712 AGATTTATATGTCCAGACACAAACG 57.460 36.000 1.88 0.00 45.05 3.60


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

AutoCloner maintained by Alex Coulton.