Multiple sequence alignment - TraesCS3B01G127300

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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 TraesCS3B01G127300 chr3B 100.000 3034 0 0 1 3034 105464037 105461004 0.000000e+00 5603
1 TraesCS3B01G127300 chr3B 96.108 591 22 1 1 590 105469714 105469124 0.000000e+00 963
2 TraesCS3B01G127300 chr3B 95.270 592 25 3 1 590 159511516 159512106 0.000000e+00 935
3 TraesCS3B01G127300 chr3B 94.595 592 29 3 1 590 159517204 159517794 0.000000e+00 913
4 TraesCS3B01G127300 chr3B 83.171 820 133 5 2214 3032 646281447 646282262 0.000000e+00 745
5 TraesCS3B01G127300 chr3D 93.442 1479 86 6 691 2164 64111299 64109827 0.000000e+00 2183
6 TraesCS3B01G127300 chr3A 91.696 1445 96 8 694 2123 73874548 73873113 0.000000e+00 1982
7 TraesCS3B01G127300 chr2A 90.741 810 74 1 2225 3033 699576658 699577467 0.000000e+00 1079
8 TraesCS3B01G127300 chr2A 74.520 781 175 17 1228 1996 72697318 72696550 4.880000e-83 318
9 TraesCS3B01G127300 chr2A 84.298 121 11 4 1266 1378 81064529 81064649 8.890000e-21 111
10 TraesCS3B01G127300 chr7B 92.443 741 45 8 2215 2954 540808861 540809591 0.000000e+00 1048
11 TraesCS3B01G127300 chr7B 95.262 591 25 3 1 589 402801652 402801063 0.000000e+00 933
12 TraesCS3B01G127300 chr1D 89.133 819 87 2 2215 3032 84705322 84706139 0.000000e+00 1018
13 TraesCS3B01G127300 chr6D 88.293 820 86 6 2215 3034 240115241 240116050 0.000000e+00 974
14 TraesCS3B01G127300 chr5B 95.608 592 23 3 1 590 356259120 356258530 0.000000e+00 946
15 TraesCS3B01G127300 chr5B 95.601 591 23 3 1 589 652852672 652853261 0.000000e+00 944
16 TraesCS3B01G127300 chr5B 95.439 592 24 3 1 590 652846989 652847579 0.000000e+00 941
17 TraesCS3B01G127300 chr5B 94.604 593 29 3 1 592 585497054 585496464 0.000000e+00 915
18 TraesCS3B01G127300 chr5B 94.585 591 29 3 1 590 585501390 585500802 0.000000e+00 911
19 TraesCS3B01G127300 chr5B 83.252 824 131 6 2214 3034 384584370 384583551 0.000000e+00 750
20 TraesCS3B01G127300 chr2B 86.476 806 105 4 1218 2020 110490212 110491016 0.000000e+00 881
21 TraesCS3B01G127300 chr2B 84.044 821 129 2 2214 3034 87532266 87533084 0.000000e+00 789
22 TraesCS3B01G127300 chr2B 75.445 786 155 29 1228 1994 111041575 111040809 6.230000e-92 348
23 TraesCS3B01G127300 chr2B 74.653 793 173 21 1228 2006 111035647 111034869 2.920000e-85 326
24 TraesCS3B01G127300 chr1B 82.460 821 141 3 2215 3032 633623217 633622397 0.000000e+00 715
25 TraesCS3B01G127300 chr7A 88.508 496 55 2 2215 2709 159420775 159420281 1.560000e-167 599
26 TraesCS3B01G127300 chr2D 75.348 791 171 18 1228 2006 73316904 73317682 2.880000e-95 359
27 TraesCS3B01G127300 chr2D 75.000 788 155 36 1228 1994 73268680 73269446 2.920000e-85 326
28 TraesCS3B01G127300 chr6B 88.189 127 15 0 1262 1388 654618271 654618397 5.240000e-33 152


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 TraesCS3B01G127300 chr3B 105461004 105464037 3033 True 5603 5603 100.0000 1 3034 1 chr3B.!!$R1 3033
1 TraesCS3B01G127300 chr3B 105469124 105469714 590 True 963 963 96.1080 1 590 1 chr3B.!!$R2 589
2 TraesCS3B01G127300 chr3B 159511516 159512106 590 False 935 935 95.2700 1 590 1 chr3B.!!$F1 589
3 TraesCS3B01G127300 chr3B 159517204 159517794 590 False 913 913 94.5950 1 590 1 chr3B.!!$F2 589
4 TraesCS3B01G127300 chr3B 646281447 646282262 815 False 745 745 83.1710 2214 3032 1 chr3B.!!$F3 818
5 TraesCS3B01G127300 chr3D 64109827 64111299 1472 True 2183 2183 93.4420 691 2164 1 chr3D.!!$R1 1473
6 TraesCS3B01G127300 chr3A 73873113 73874548 1435 True 1982 1982 91.6960 694 2123 1 chr3A.!!$R1 1429
7 TraesCS3B01G127300 chr2A 699576658 699577467 809 False 1079 1079 90.7410 2225 3033 1 chr2A.!!$F2 808
8 TraesCS3B01G127300 chr2A 72696550 72697318 768 True 318 318 74.5200 1228 1996 1 chr2A.!!$R1 768
9 TraesCS3B01G127300 chr7B 540808861 540809591 730 False 1048 1048 92.4430 2215 2954 1 chr7B.!!$F1 739
10 TraesCS3B01G127300 chr7B 402801063 402801652 589 True 933 933 95.2620 1 589 1 chr7B.!!$R1 588
11 TraesCS3B01G127300 chr1D 84705322 84706139 817 False 1018 1018 89.1330 2215 3032 1 chr1D.!!$F1 817
12 TraesCS3B01G127300 chr6D 240115241 240116050 809 False 974 974 88.2930 2215 3034 1 chr6D.!!$F1 819
13 TraesCS3B01G127300 chr5B 356258530 356259120 590 True 946 946 95.6080 1 590 1 chr5B.!!$R1 589
14 TraesCS3B01G127300 chr5B 652852672 652853261 589 False 944 944 95.6010 1 589 1 chr5B.!!$F2 588
15 TraesCS3B01G127300 chr5B 652846989 652847579 590 False 941 941 95.4390 1 590 1 chr5B.!!$F1 589
16 TraesCS3B01G127300 chr5B 585496464 585501390 4926 True 913 915 94.5945 1 592 2 chr5B.!!$R3 591
17 TraesCS3B01G127300 chr5B 384583551 384584370 819 True 750 750 83.2520 2214 3034 1 chr5B.!!$R2 820
18 TraesCS3B01G127300 chr2B 110490212 110491016 804 False 881 881 86.4760 1218 2020 1 chr2B.!!$F2 802
19 TraesCS3B01G127300 chr2B 87532266 87533084 818 False 789 789 84.0440 2214 3034 1 chr2B.!!$F1 820
20 TraesCS3B01G127300 chr2B 111040809 111041575 766 True 348 348 75.4450 1228 1994 1 chr2B.!!$R2 766
21 TraesCS3B01G127300 chr2B 111034869 111035647 778 True 326 326 74.6530 1228 2006 1 chr2B.!!$R1 778
22 TraesCS3B01G127300 chr1B 633622397 633623217 820 True 715 715 82.4600 2215 3032 1 chr1B.!!$R1 817
23 TraesCS3B01G127300 chr2D 73316904 73317682 778 False 359 359 75.3480 1228 2006 1 chr2D.!!$F2 778
24 TraesCS3B01G127300 chr2D 73268680 73269446 766 False 326 326 75.0000 1228 1994 1 chr2D.!!$F1 766

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
632 4971 0.172578 CCATCACGTCCGCTGAGTAA 59.827 55.0 0.00 0.0 0.00 2.24 F
949 5293 0.242825 TTGTTCCGAAGCTCGATCGT 59.757 50.0 15.94 0.0 43.74 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 5816 0.11714 AGAGGATGTCCAGGTGTCCA 59.883 55.0 1.3 0.0 38.89 4.02 R
2816 7193 0.81401 GGCACGACGGAAGGCAATAT 60.814 55.0 0.0 0.0 41.50 1.28 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
33 34 7.781056 AGGCGGTTGATTTTCATATAACAATT 58.219 30.769 0.00 0.00 0.00 2.32
80 81 3.039011 AGTTACAGCCCGATTAGTGGAT 58.961 45.455 0.00 0.00 0.00 3.41
89 90 3.270027 CCGATTAGTGGATTGCTGTCAA 58.730 45.455 0.00 0.00 36.51 3.18
99 100 3.368739 GGATTGCTGTCAAAAATCTGGGG 60.369 47.826 6.96 0.00 35.56 4.96
224 225 2.816411 TCTTGTACGGGAAGTCCATCT 58.184 47.619 0.00 0.00 37.91 2.90
229 230 1.201429 ACGGGAAGTCCATCTGCCTT 61.201 55.000 0.00 0.00 41.66 4.35
481 4819 0.963962 TCGGGTCTACAAAAGCGTCT 59.036 50.000 0.00 0.00 0.00 4.18
600 4939 3.847037 GTGTGAACACGTACGACAAAT 57.153 42.857 24.41 2.79 37.10 2.32
601 4940 3.528121 GTGTGAACACGTACGACAAATG 58.472 45.455 24.41 11.87 37.10 2.32
602 4941 3.243410 GTGTGAACACGTACGACAAATGA 59.757 43.478 24.41 0.00 37.10 2.57
603 4942 3.864003 TGTGAACACGTACGACAAATGAA 59.136 39.130 24.41 0.00 0.00 2.57
604 4943 4.026393 TGTGAACACGTACGACAAATGAAG 60.026 41.667 24.41 2.52 0.00 3.02
605 4944 4.207635 GTGAACACGTACGACAAATGAAGA 59.792 41.667 24.41 0.00 0.00 2.87
606 4945 4.443063 TGAACACGTACGACAAATGAAGAG 59.557 41.667 24.41 0.00 0.00 2.85
607 4946 3.314553 ACACGTACGACAAATGAAGAGG 58.685 45.455 24.41 0.00 0.00 3.69
608 4947 2.666508 CACGTACGACAAATGAAGAGGG 59.333 50.000 24.41 0.00 0.00 4.30
609 4948 1.659098 CGTACGACAAATGAAGAGGGC 59.341 52.381 10.44 0.00 0.00 5.19
610 4949 2.007608 GTACGACAAATGAAGAGGGCC 58.992 52.381 0.00 0.00 0.00 5.80
611 4950 0.693049 ACGACAAATGAAGAGGGCCT 59.307 50.000 5.25 5.25 0.00 5.19
612 4951 1.073923 ACGACAAATGAAGAGGGCCTT 59.926 47.619 7.89 0.00 37.93 4.35
619 4958 3.485764 GAAGAGGGCCTTCCATCAC 57.514 57.895 11.97 0.00 45.23 3.06
620 4959 0.462759 GAAGAGGGCCTTCCATCACG 60.463 60.000 11.97 0.00 45.23 4.35
621 4960 1.201429 AAGAGGGCCTTCCATCACGT 61.201 55.000 11.97 0.00 45.23 4.49
622 4961 1.153349 GAGGGCCTTCCATCACGTC 60.153 63.158 7.89 0.00 42.49 4.34
623 4962 2.124695 GGGCCTTCCATCACGTCC 60.125 66.667 0.84 0.00 35.00 4.79
624 4963 2.511600 GGCCTTCCATCACGTCCG 60.512 66.667 0.00 0.00 0.00 4.79
625 4964 3.195698 GCCTTCCATCACGTCCGC 61.196 66.667 0.00 0.00 0.00 5.54
626 4965 2.579201 CCTTCCATCACGTCCGCT 59.421 61.111 0.00 0.00 0.00 5.52
627 4966 1.811266 CCTTCCATCACGTCCGCTG 60.811 63.158 0.00 0.00 0.00 5.18
628 4967 1.215382 CTTCCATCACGTCCGCTGA 59.785 57.895 0.00 0.00 0.00 4.26
629 4968 0.803768 CTTCCATCACGTCCGCTGAG 60.804 60.000 0.00 0.00 0.00 3.35
630 4969 1.532604 TTCCATCACGTCCGCTGAGT 61.533 55.000 0.00 0.00 0.00 3.41
631 4970 0.678684 TCCATCACGTCCGCTGAGTA 60.679 55.000 0.00 0.00 0.00 2.59
632 4971 0.172578 CCATCACGTCCGCTGAGTAA 59.827 55.000 0.00 0.00 0.00 2.24
633 4972 1.403647 CCATCACGTCCGCTGAGTAAA 60.404 52.381 0.00 0.00 0.00 2.01
634 4973 1.920574 CATCACGTCCGCTGAGTAAAG 59.079 52.381 0.00 0.00 0.00 1.85
635 4974 0.388134 TCACGTCCGCTGAGTAAAGC 60.388 55.000 0.00 0.00 39.94 3.51
636 4975 0.666274 CACGTCCGCTGAGTAAAGCA 60.666 55.000 0.00 0.00 43.73 3.91
637 4976 0.246635 ACGTCCGCTGAGTAAAGCAT 59.753 50.000 0.00 0.00 43.73 3.79
638 4977 0.924090 CGTCCGCTGAGTAAAGCATC 59.076 55.000 0.00 0.00 43.73 3.91
639 4978 1.735700 CGTCCGCTGAGTAAAGCATCA 60.736 52.381 0.00 0.00 43.73 3.07
640 4979 2.555199 GTCCGCTGAGTAAAGCATCAT 58.445 47.619 0.00 0.00 43.73 2.45
641 4980 2.541762 GTCCGCTGAGTAAAGCATCATC 59.458 50.000 0.00 0.00 43.73 2.92
642 4981 1.524355 CCGCTGAGTAAAGCATCATCG 59.476 52.381 0.00 0.00 43.73 3.84
643 4982 2.196749 CGCTGAGTAAAGCATCATCGT 58.803 47.619 0.00 0.00 43.73 3.73
644 4983 2.604914 CGCTGAGTAAAGCATCATCGTT 59.395 45.455 0.00 0.00 43.73 3.85
645 4984 3.542875 CGCTGAGTAAAGCATCATCGTTG 60.543 47.826 0.00 0.00 43.73 4.10
646 4985 3.242543 GCTGAGTAAAGCATCATCGTTGG 60.243 47.826 0.00 0.00 43.01 3.77
647 4986 4.183865 CTGAGTAAAGCATCATCGTTGGA 58.816 43.478 0.00 0.00 0.00 3.53
648 4987 4.769688 TGAGTAAAGCATCATCGTTGGAT 58.230 39.130 0.00 0.00 0.00 3.41
649 4988 5.185454 TGAGTAAAGCATCATCGTTGGATT 58.815 37.500 0.00 0.00 0.00 3.01
650 4989 6.345298 TGAGTAAAGCATCATCGTTGGATTA 58.655 36.000 0.00 0.00 0.00 1.75
651 4990 6.257849 TGAGTAAAGCATCATCGTTGGATTAC 59.742 38.462 0.00 0.00 0.00 1.89
652 4991 4.900635 AAAGCATCATCGTTGGATTACC 57.099 40.909 0.00 0.00 0.00 2.85
653 4992 3.558931 AGCATCATCGTTGGATTACCA 57.441 42.857 0.00 0.00 45.34 3.25
668 5007 6.755206 TGGATTACCAGTAGTATGGAAATCG 58.245 40.000 0.00 0.00 43.57 3.34
669 5008 6.164176 GGATTACCAGTAGTATGGAAATCGG 58.836 44.000 0.00 0.00 43.57 4.18
670 5009 6.014840 GGATTACCAGTAGTATGGAAATCGGA 60.015 42.308 0.00 0.00 43.57 4.55
671 5010 6.989155 TTACCAGTAGTATGGAAATCGGAT 57.011 37.500 0.00 0.00 43.57 4.18
672 5011 5.470047 ACCAGTAGTATGGAAATCGGATC 57.530 43.478 0.00 0.00 43.57 3.36
673 5012 4.283722 ACCAGTAGTATGGAAATCGGATCC 59.716 45.833 0.00 0.00 43.57 3.36
674 5013 4.528596 CCAGTAGTATGGAAATCGGATCCT 59.471 45.833 10.75 0.00 43.57 3.24
675 5014 5.715279 CCAGTAGTATGGAAATCGGATCCTA 59.285 44.000 10.75 0.00 43.57 2.94
676 5015 6.127591 CCAGTAGTATGGAAATCGGATCCTAG 60.128 46.154 10.75 0.00 43.57 3.02
677 5016 6.434652 CAGTAGTATGGAAATCGGATCCTAGT 59.565 42.308 10.75 0.00 37.85 2.57
678 5017 5.986501 AGTATGGAAATCGGATCCTAGTC 57.013 43.478 10.75 0.76 37.85 2.59
679 5018 5.646215 AGTATGGAAATCGGATCCTAGTCT 58.354 41.667 10.75 0.00 37.85 3.24
680 5019 4.881019 ATGGAAATCGGATCCTAGTCTG 57.119 45.455 10.75 0.00 37.85 3.51
681 5020 3.643237 TGGAAATCGGATCCTAGTCTGT 58.357 45.455 10.75 0.00 37.85 3.41
682 5021 3.637229 TGGAAATCGGATCCTAGTCTGTC 59.363 47.826 10.75 0.00 37.85 3.51
683 5022 3.304794 GGAAATCGGATCCTAGTCTGTCG 60.305 52.174 10.75 0.00 33.98 4.35
684 5023 2.642154 ATCGGATCCTAGTCTGTCGT 57.358 50.000 10.75 0.00 0.00 4.34
685 5024 1.664873 TCGGATCCTAGTCTGTCGTG 58.335 55.000 10.75 0.00 0.00 4.35
686 5025 0.663688 CGGATCCTAGTCTGTCGTGG 59.336 60.000 10.75 0.00 0.00 4.94
687 5026 1.033574 GGATCCTAGTCTGTCGTGGG 58.966 60.000 3.84 0.00 0.00 4.61
688 5027 1.685491 GGATCCTAGTCTGTCGTGGGT 60.685 57.143 3.84 0.00 0.00 4.51
689 5028 2.422519 GGATCCTAGTCTGTCGTGGGTA 60.423 54.545 3.84 0.00 0.00 3.69
699 5038 0.322187 GTCGTGGGTAAATGGCTGGT 60.322 55.000 0.00 0.00 0.00 4.00
750 5089 0.820226 TCTGTAGCAGCGCTCTGAAT 59.180 50.000 7.13 0.00 42.95 2.57
765 5109 4.218635 GCTCTGAATATGTGATCTACCCGA 59.781 45.833 0.00 0.00 0.00 5.14
908 5252 4.100373 AGACCAAGAACTCAAGGCTAGAT 58.900 43.478 0.00 0.00 0.00 1.98
910 5254 4.100373 ACCAAGAACTCAAGGCTAGATCT 58.900 43.478 0.00 0.00 0.00 2.75
928 5272 0.613260 CTGTTACCAGCCACTGCCTA 59.387 55.000 0.00 0.00 38.69 3.93
933 5277 1.376466 CCAGCCACTGCCTAGTTGT 59.624 57.895 0.00 0.00 38.69 3.32
941 5285 1.079503 CTGCCTAGTTGTTCCGAAGC 58.920 55.000 0.00 0.00 0.00 3.86
944 5288 1.630148 CCTAGTTGTTCCGAAGCTCG 58.370 55.000 0.00 0.00 40.07 5.03
946 5290 2.159226 CCTAGTTGTTCCGAAGCTCGAT 60.159 50.000 7.07 0.00 43.74 3.59
947 5291 1.997669 AGTTGTTCCGAAGCTCGATC 58.002 50.000 7.07 0.00 43.74 3.69
949 5293 0.242825 TTGTTCCGAAGCTCGATCGT 59.757 50.000 15.94 0.00 43.74 3.73
955 5299 2.200039 GAAGCTCGATCGTCTTCGC 58.800 57.895 24.96 16.95 38.97 4.70
963 5307 2.564553 GATCGTCTTCGCCACTGCCT 62.565 60.000 0.00 0.00 36.96 4.75
985 5331 1.160137 CCCTGTTGGCGAAGAGAAAG 58.840 55.000 7.21 0.00 0.00 2.62
1027 5373 2.049156 CCGTGCAGCTCGTTCTCA 60.049 61.111 15.31 0.00 0.00 3.27
1047 5393 0.820871 GGGAGACGAGCAGAGTTCAT 59.179 55.000 0.00 0.00 0.00 2.57
1101 5447 1.289066 CACGGCTCCGAACTCTCAA 59.711 57.895 15.95 0.00 42.83 3.02
1164 5520 2.954753 CTCTCCGTTGTTGCGCACC 61.955 63.158 11.12 2.51 0.00 5.01
1170 5526 2.824489 TTGTTGCGCACCGGACAA 60.824 55.556 18.73 18.73 0.00 3.18
1171 5527 2.190170 TTGTTGCGCACCGGACAAT 61.190 52.632 18.73 0.00 0.00 2.71
1172 5528 1.729470 TTGTTGCGCACCGGACAATT 61.729 50.000 18.73 0.00 0.00 2.32
1173 5529 1.007849 GTTGCGCACCGGACAATTT 60.008 52.632 11.12 0.00 0.00 1.82
1174 5530 0.596341 GTTGCGCACCGGACAATTTT 60.596 50.000 11.12 0.00 0.00 1.82
1282 5641 3.064324 GAGCGGCATTGGCAAGGT 61.064 61.111 13.90 0.88 43.71 3.50
1409 5771 2.202440 CGTTGCGACGTCTCCGAT 60.202 61.111 18.62 0.00 44.08 4.18
1484 5846 0.898320 ACATCCTCTACAGCAACGCT 59.102 50.000 0.00 0.00 40.77 5.07
1697 6062 2.716244 CTCGCGTACGCCATCTCT 59.284 61.111 32.64 0.00 39.84 3.10
1712 6077 1.568504 TCTCTAAGGCCACCGTCATT 58.431 50.000 5.01 0.00 0.00 2.57
1817 6182 4.673298 ACGTTGCGGTCGATGGCA 62.673 61.111 9.00 9.00 37.39 4.92
2049 6414 2.127839 TGATCGTGGAGGGATCAGC 58.872 57.895 0.62 0.00 43.87 4.26
2057 6422 2.364842 AGGGATCAGCGAGTGCCT 60.365 61.111 0.00 0.00 44.31 4.75
2124 6489 2.163818 GTGTTCCACACCTCGATTCA 57.836 50.000 0.00 0.00 43.05 2.57
2125 6490 2.069273 GTGTTCCACACCTCGATTCAG 58.931 52.381 0.00 0.00 43.05 3.02
2132 6497 2.492088 CACACCTCGATTCAGTCTACCA 59.508 50.000 0.00 0.00 0.00 3.25
2164 6529 6.407299 GCACCACCCTAATTTCATTTCATCAT 60.407 38.462 0.00 0.00 0.00 2.45
2165 6530 7.558604 CACCACCCTAATTTCATTTCATCATT 58.441 34.615 0.00 0.00 0.00 2.57
2166 6531 8.042515 CACCACCCTAATTTCATTTCATCATTT 58.957 33.333 0.00 0.00 0.00 2.32
2167 6532 8.605065 ACCACCCTAATTTCATTTCATCATTTT 58.395 29.630 0.00 0.00 0.00 1.82
2168 6533 9.452287 CCACCCTAATTTCATTTCATCATTTTT 57.548 29.630 0.00 0.00 0.00 1.94
2313 6679 8.443953 AAAGAGCAAATTTAGCTAGTCTATGG 57.556 34.615 12.96 0.00 43.58 2.74
2333 6699 2.853159 CCTCATAGTTTGCGGCACA 58.147 52.632 0.05 0.00 0.00 4.57
2362 6728 7.916450 CCTCGAAACCAAACTTACAATTAAACA 59.084 33.333 0.00 0.00 0.00 2.83
2412 6778 1.113517 TAGCACCATACCGGCCTCTC 61.114 60.000 0.00 0.00 39.03 3.20
2447 6814 2.682856 TGTCTGAGACAACTTGTTTGCC 59.317 45.455 13.74 0.00 39.78 4.52
2450 6817 4.515191 GTCTGAGACAACTTGTTTGCCATA 59.485 41.667 7.90 0.00 39.01 2.74
2513 6880 1.972660 GCTAAGGCCTCCCGACATGT 61.973 60.000 5.23 0.00 35.76 3.21
2703 7080 3.513225 GCATTAGGCGCCACATGT 58.487 55.556 31.54 10.27 0.00 3.21
2717 7094 3.118408 GCCACATGTGATAACAGTCCCTA 60.118 47.826 27.46 0.00 0.00 3.53
2740 7117 2.369870 GCACGCGTATTGCTACTGT 58.630 52.632 13.44 0.00 43.27 3.55
2790 7167 5.690997 TGTTTATAAACGCATGTGTGGAA 57.309 34.783 20.51 1.76 41.74 3.53
2808 7185 3.152341 GGAATGTGGGCTCTGGAATATG 58.848 50.000 0.00 0.00 0.00 1.78
2816 7193 3.009473 GGGCTCTGGAATATGCCTTCATA 59.991 47.826 0.11 0.00 44.36 2.15
2957 7335 1.855295 TCCATCATTTGCTGCACCAT 58.145 45.000 0.00 0.00 0.00 3.55
2978 7356 1.080230 CACTGTCACTGAGAGCCCG 60.080 63.158 3.09 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.321848 TGCATACGAACTCGGATTAAGATA 57.678 37.500 3.88 0.00 40.60 1.98
80 81 2.676748 ACCCCAGATTTTTGACAGCAA 58.323 42.857 0.00 0.00 0.00 3.91
89 90 1.609210 CCGGCCAACCCCAGATTTT 60.609 57.895 2.24 0.00 0.00 1.82
224 225 7.272978 GTCACCTCTTGTCTATATAAAAGGCA 58.727 38.462 0.00 0.00 0.00 4.75
229 230 5.221382 GGCCGTCACCTCTTGTCTATATAAA 60.221 44.000 0.00 0.00 0.00 1.40
298 299 8.846423 ACAAGGGAGAGAGATAAAGATAAAGA 57.154 34.615 0.00 0.00 0.00 2.52
583 4922 4.361420 TCTTCATTTGTCGTACGTGTTCA 58.639 39.130 16.05 7.97 0.00 3.18
592 4931 0.693049 AGGCCCTCTTCATTTGTCGT 59.307 50.000 0.00 0.00 0.00 4.34
593 4932 1.826385 AAGGCCCTCTTCATTTGTCG 58.174 50.000 0.00 0.00 0.00 4.35
602 4941 1.201429 ACGTGATGGAAGGCCCTCTT 61.201 55.000 0.00 0.00 38.65 2.85
603 4942 1.613630 ACGTGATGGAAGGCCCTCT 60.614 57.895 0.00 0.00 35.38 3.69
604 4943 1.153349 GACGTGATGGAAGGCCCTC 60.153 63.158 0.00 0.00 35.38 4.30
605 4944 2.670148 GGACGTGATGGAAGGCCCT 61.670 63.158 0.00 0.00 35.38 5.19
606 4945 2.124695 GGACGTGATGGAAGGCCC 60.125 66.667 0.00 0.00 0.00 5.80
607 4946 2.511600 CGGACGTGATGGAAGGCC 60.512 66.667 0.00 0.00 0.00 5.19
608 4947 3.195698 GCGGACGTGATGGAAGGC 61.196 66.667 0.00 0.00 0.00 4.35
609 4948 1.811266 CAGCGGACGTGATGGAAGG 60.811 63.158 0.00 0.00 0.00 3.46
610 4949 0.803768 CTCAGCGGACGTGATGGAAG 60.804 60.000 0.00 0.00 0.00 3.46
611 4950 1.215382 CTCAGCGGACGTGATGGAA 59.785 57.895 0.00 0.00 0.00 3.53
612 4951 0.678684 TACTCAGCGGACGTGATGGA 60.679 55.000 0.00 0.00 0.00 3.41
613 4952 0.172578 TTACTCAGCGGACGTGATGG 59.827 55.000 0.00 0.00 0.00 3.51
614 4953 1.920574 CTTTACTCAGCGGACGTGATG 59.079 52.381 0.00 0.00 0.00 3.07
615 4954 1.736032 GCTTTACTCAGCGGACGTGAT 60.736 52.381 0.00 0.00 0.00 3.06
616 4955 0.388134 GCTTTACTCAGCGGACGTGA 60.388 55.000 0.00 0.00 0.00 4.35
617 4956 0.666274 TGCTTTACTCAGCGGACGTG 60.666 55.000 0.00 0.00 43.37 4.49
618 4957 0.246635 ATGCTTTACTCAGCGGACGT 59.753 50.000 0.00 0.00 43.37 4.34
619 4958 0.924090 GATGCTTTACTCAGCGGACG 59.076 55.000 0.00 0.00 43.37 4.79
620 4959 2.010145 TGATGCTTTACTCAGCGGAC 57.990 50.000 0.00 0.00 43.37 4.79
621 4960 2.799562 CGATGATGCTTTACTCAGCGGA 60.800 50.000 2.57 0.00 44.88 5.54
622 4961 1.524355 CGATGATGCTTTACTCAGCGG 59.476 52.381 2.57 0.00 44.88 5.52
623 4962 2.918656 CGATGATGCTTTACTCAGCG 57.081 50.000 0.00 0.00 43.59 5.18
624 4963 3.242543 CCAACGATGATGCTTTACTCAGC 60.243 47.826 0.00 0.00 40.55 4.26
625 4964 4.183865 TCCAACGATGATGCTTTACTCAG 58.816 43.478 0.00 0.00 0.00 3.35
626 4965 4.200838 TCCAACGATGATGCTTTACTCA 57.799 40.909 0.00 0.00 0.00 3.41
627 4966 5.741388 AATCCAACGATGATGCTTTACTC 57.259 39.130 0.00 0.00 0.00 2.59
628 4967 5.527582 GGTAATCCAACGATGATGCTTTACT 59.472 40.000 0.00 0.00 0.00 2.24
629 4968 5.295787 TGGTAATCCAACGATGATGCTTTAC 59.704 40.000 0.00 0.00 41.25 2.01
630 4969 5.432645 TGGTAATCCAACGATGATGCTTTA 58.567 37.500 0.00 0.00 41.25 1.85
631 4970 4.269183 TGGTAATCCAACGATGATGCTTT 58.731 39.130 0.00 0.00 41.25 3.51
632 4971 3.879295 CTGGTAATCCAACGATGATGCTT 59.121 43.478 0.00 0.00 43.81 3.91
633 4972 3.118261 ACTGGTAATCCAACGATGATGCT 60.118 43.478 0.00 0.00 43.81 3.79
634 4973 3.206150 ACTGGTAATCCAACGATGATGC 58.794 45.455 0.00 0.00 43.81 3.91
635 4974 5.601662 ACTACTGGTAATCCAACGATGATG 58.398 41.667 0.00 0.00 43.81 3.07
636 4975 5.871396 ACTACTGGTAATCCAACGATGAT 57.129 39.130 0.00 0.00 43.81 2.45
637 4976 6.239204 CCATACTACTGGTAATCCAACGATGA 60.239 42.308 0.00 0.00 43.81 2.92
638 4977 5.926542 CCATACTACTGGTAATCCAACGATG 59.073 44.000 0.00 0.00 43.81 3.84
639 4978 5.836898 TCCATACTACTGGTAATCCAACGAT 59.163 40.000 0.00 0.00 43.81 3.73
640 4979 5.202765 TCCATACTACTGGTAATCCAACGA 58.797 41.667 0.00 0.00 43.81 3.85
641 4980 5.524971 TCCATACTACTGGTAATCCAACG 57.475 43.478 0.00 0.00 43.81 4.10
642 4981 7.170998 CGATTTCCATACTACTGGTAATCCAAC 59.829 40.741 13.47 0.00 44.19 3.77
643 4982 7.214381 CGATTTCCATACTACTGGTAATCCAA 58.786 38.462 13.47 0.00 44.19 3.53
644 4983 6.239487 CCGATTTCCATACTACTGGTAATCCA 60.239 42.308 13.47 0.00 44.19 3.41
645 4984 6.014840 TCCGATTTCCATACTACTGGTAATCC 60.015 42.308 13.47 0.00 44.19 3.01
646 4985 6.989659 TCCGATTTCCATACTACTGGTAATC 58.010 40.000 10.64 10.64 43.88 1.75
647 4986 6.989155 TCCGATTTCCATACTACTGGTAAT 57.011 37.500 0.00 0.00 38.53 1.89
648 4987 6.014840 GGATCCGATTTCCATACTACTGGTAA 60.015 42.308 0.00 0.00 37.57 2.85
649 4988 5.479375 GGATCCGATTTCCATACTACTGGTA 59.521 44.000 0.00 0.00 37.57 3.25
650 4989 4.283722 GGATCCGATTTCCATACTACTGGT 59.716 45.833 0.00 0.00 37.57 4.00
651 4990 4.528596 AGGATCCGATTTCCATACTACTGG 59.471 45.833 5.98 0.00 35.59 4.00
652 4991 5.730296 AGGATCCGATTTCCATACTACTG 57.270 43.478 5.98 0.00 35.59 2.74
653 4992 6.553857 ACTAGGATCCGATTTCCATACTACT 58.446 40.000 5.98 0.00 35.59 2.57
654 4993 6.660094 AGACTAGGATCCGATTTCCATACTAC 59.340 42.308 5.98 0.00 35.59 2.73
655 4994 6.659668 CAGACTAGGATCCGATTTCCATACTA 59.340 42.308 5.98 0.00 35.59 1.82
656 4995 5.478679 CAGACTAGGATCCGATTTCCATACT 59.521 44.000 5.98 0.00 35.59 2.12
657 4996 5.244178 ACAGACTAGGATCCGATTTCCATAC 59.756 44.000 5.98 0.00 35.59 2.39
658 4997 5.394738 ACAGACTAGGATCCGATTTCCATA 58.605 41.667 5.98 0.00 35.59 2.74
659 4998 4.227197 ACAGACTAGGATCCGATTTCCAT 58.773 43.478 5.98 0.00 35.59 3.41
660 4999 3.637229 GACAGACTAGGATCCGATTTCCA 59.363 47.826 5.98 0.00 35.59 3.53
661 5000 3.304794 CGACAGACTAGGATCCGATTTCC 60.305 52.174 5.98 0.00 0.00 3.13
662 5001 3.315749 ACGACAGACTAGGATCCGATTTC 59.684 47.826 5.98 1.86 0.00 2.17
663 5002 3.066900 CACGACAGACTAGGATCCGATTT 59.933 47.826 5.98 0.00 0.00 2.17
664 5003 2.619177 CACGACAGACTAGGATCCGATT 59.381 50.000 5.98 0.00 0.00 3.34
665 5004 2.222886 CACGACAGACTAGGATCCGAT 58.777 52.381 5.98 0.00 0.00 4.18
666 5005 1.664873 CACGACAGACTAGGATCCGA 58.335 55.000 5.98 0.00 0.00 4.55
667 5006 0.663688 CCACGACAGACTAGGATCCG 59.336 60.000 5.98 0.00 0.00 4.18
668 5007 1.033574 CCCACGACAGACTAGGATCC 58.966 60.000 2.48 2.48 0.00 3.36
669 5008 1.765230 ACCCACGACAGACTAGGATC 58.235 55.000 0.00 0.00 0.00 3.36
670 5009 3.377253 TTACCCACGACAGACTAGGAT 57.623 47.619 0.00 0.00 0.00 3.24
671 5010 2.885135 TTACCCACGACAGACTAGGA 57.115 50.000 0.00 0.00 0.00 2.94
672 5011 3.430374 CCATTTACCCACGACAGACTAGG 60.430 52.174 0.00 0.00 0.00 3.02
673 5012 3.782046 CCATTTACCCACGACAGACTAG 58.218 50.000 0.00 0.00 0.00 2.57
674 5013 2.093869 GCCATTTACCCACGACAGACTA 60.094 50.000 0.00 0.00 0.00 2.59
675 5014 1.338769 GCCATTTACCCACGACAGACT 60.339 52.381 0.00 0.00 0.00 3.24
676 5015 1.084289 GCCATTTACCCACGACAGAC 58.916 55.000 0.00 0.00 0.00 3.51
677 5016 0.981183 AGCCATTTACCCACGACAGA 59.019 50.000 0.00 0.00 0.00 3.41
678 5017 1.086696 CAGCCATTTACCCACGACAG 58.913 55.000 0.00 0.00 0.00 3.51
679 5018 0.322098 CCAGCCATTTACCCACGACA 60.322 55.000 0.00 0.00 0.00 4.35
680 5019 0.322187 ACCAGCCATTTACCCACGAC 60.322 55.000 0.00 0.00 0.00 4.34
681 5020 1.277579 TACCAGCCATTTACCCACGA 58.722 50.000 0.00 0.00 0.00 4.35
682 5021 2.341846 ATACCAGCCATTTACCCACG 57.658 50.000 0.00 0.00 0.00 4.94
683 5022 3.361786 ACAATACCAGCCATTTACCCAC 58.638 45.455 0.00 0.00 0.00 4.61
684 5023 3.748645 ACAATACCAGCCATTTACCCA 57.251 42.857 0.00 0.00 0.00 4.51
685 5024 3.066203 CGAACAATACCAGCCATTTACCC 59.934 47.826 0.00 0.00 0.00 3.69
686 5025 3.692593 ACGAACAATACCAGCCATTTACC 59.307 43.478 0.00 0.00 0.00 2.85
687 5026 4.493545 CGACGAACAATACCAGCCATTTAC 60.494 45.833 0.00 0.00 0.00 2.01
688 5027 3.619483 CGACGAACAATACCAGCCATTTA 59.381 43.478 0.00 0.00 0.00 1.40
689 5028 2.418628 CGACGAACAATACCAGCCATTT 59.581 45.455 0.00 0.00 0.00 2.32
719 5058 4.669453 CGCTGCTACAGATACGATTACGAT 60.669 45.833 0.00 0.00 36.97 3.73
731 5070 0.820226 ATTCAGAGCGCTGCTACAGA 59.180 50.000 18.48 0.00 39.88 3.41
750 5089 4.981812 TCTAAGCTCGGGTAGATCACATA 58.018 43.478 0.00 0.00 0.00 2.29
865 5209 2.438800 TTCGTTTGGGTCTTTGGGAA 57.561 45.000 0.00 0.00 0.00 3.97
910 5254 2.107770 ACTAGGCAGTGGCTGGTAACA 61.108 52.381 30.41 9.05 46.70 2.41
928 5272 1.732732 CGATCGAGCTTCGGAACAACT 60.733 52.381 10.26 0.00 40.88 3.16
933 5277 0.809385 AAGACGATCGAGCTTCGGAA 59.191 50.000 24.34 0.00 40.88 4.30
941 5285 0.863538 CAGTGGCGAAGACGATCGAG 60.864 60.000 24.34 8.37 41.59 4.04
944 5288 2.167861 GGCAGTGGCGAAGACGATC 61.168 63.158 0.00 0.00 41.59 3.69
946 5290 1.529152 TAAGGCAGTGGCGAAGACGA 61.529 55.000 11.51 0.00 41.59 4.20
947 5291 1.080093 TAAGGCAGTGGCGAAGACG 60.080 57.895 11.51 0.00 41.59 4.18
949 5293 1.295423 GGTAAGGCAGTGGCGAAGA 59.705 57.895 11.51 0.00 42.47 2.87
955 5299 0.609131 CCAACAGGGTAAGGCAGTGG 60.609 60.000 0.00 0.00 0.00 4.00
963 5307 1.344065 TCTCTTCGCCAACAGGGTAA 58.656 50.000 0.00 0.00 39.65 2.85
985 5331 2.035193 TGAACATCCTCTGCTCGCTATC 59.965 50.000 0.00 0.00 0.00 2.08
1027 5373 0.251386 TGAACTCTGCTCGTCTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
1047 5393 4.308458 CCTGACGCCGTCAACCCA 62.308 66.667 21.56 0.00 42.26 4.51
1101 5447 6.542821 TGGAAAGATGATGTAGACAAACCTT 58.457 36.000 0.00 0.00 0.00 3.50
1164 5520 3.602390 ACACTCGAACAAAATTGTCCG 57.398 42.857 0.00 0.00 40.44 4.79
1171 5527 9.653287 AGAAGATGATAATACACTCGAACAAAA 57.347 29.630 0.00 0.00 0.00 2.44
1172 5528 9.087424 CAGAAGATGATAATACACTCGAACAAA 57.913 33.333 0.00 0.00 0.00 2.83
1173 5529 7.222805 GCAGAAGATGATAATACACTCGAACAA 59.777 37.037 0.00 0.00 0.00 2.83
1174 5530 6.697455 GCAGAAGATGATAATACACTCGAACA 59.303 38.462 0.00 0.00 0.00 3.18
1185 5541 7.011202 GCATATCATGACGCAGAAGATGATAAT 59.989 37.037 0.00 0.00 39.84 1.28
1282 5641 0.107703 GATGAACTCCATGGCCGTCA 60.108 55.000 6.96 10.08 35.17 4.35
1378 5737 4.078516 AACGGAGGTAGGCCACGC 62.079 66.667 5.01 0.00 39.79 5.34
1381 5740 4.077184 CGCAACGGAGGTAGGCCA 62.077 66.667 5.01 0.00 37.19 5.36
1454 5816 0.117140 AGAGGATGTCCAGGTGTCCA 59.883 55.000 1.30 0.00 38.89 4.02
1692 6057 1.794714 ATGACGGTGGCCTTAGAGAT 58.205 50.000 3.32 0.00 0.00 2.75
1697 6062 1.377987 GGCAATGACGGTGGCCTTA 60.378 57.895 3.32 0.00 43.09 2.69
1803 6168 1.960040 ATCTCTGCCATCGACCGCAA 61.960 55.000 9.32 0.00 33.87 4.85
2049 6414 2.048597 TGGCACGTTAGGCACTCG 60.049 61.111 0.00 0.00 41.75 4.18
2057 6422 4.846551 CCCGATCATGGCACGTTA 57.153 55.556 0.00 0.00 0.00 3.18
2093 6458 2.831685 TGGAACACTACAGCGTCATT 57.168 45.000 0.00 0.00 0.00 2.57
2123 6488 2.300152 TGGTGCTCTCTTTGGTAGACTG 59.700 50.000 0.00 0.00 0.00 3.51
2124 6489 2.300437 GTGGTGCTCTCTTTGGTAGACT 59.700 50.000 0.00 0.00 0.00 3.24
2125 6490 2.613223 GGTGGTGCTCTCTTTGGTAGAC 60.613 54.545 0.00 0.00 0.00 2.59
2132 6497 4.202567 TGAAATTAGGGTGGTGCTCTCTTT 60.203 41.667 0.00 0.00 0.00 2.52
2333 6699 3.888583 TGTAAGTTTGGTTTCGAGGGTT 58.111 40.909 0.00 0.00 0.00 4.11
2362 6728 8.839310 AGCGAAATAAATCTCAATGCTACTAT 57.161 30.769 0.00 0.00 0.00 2.12
2412 6778 1.209504 TCAGACATTTCTAAGGGGGCG 59.790 52.381 0.00 0.00 0.00 6.13
2447 6814 3.873361 ACAGTTCATCATTGCCTCGTATG 59.127 43.478 0.00 0.00 0.00 2.39
2450 6817 2.479566 ACAGTTCATCATTGCCTCGT 57.520 45.000 0.00 0.00 0.00 4.18
2513 6880 3.516300 TCCTACTGTTTTGGAGGCGATTA 59.484 43.478 0.00 0.00 0.00 1.75
2624 6998 1.271856 TGACGCAGGGGTCAGATTTA 58.728 50.000 14.25 0.00 41.76 1.40
2703 7080 3.447586 GTGCTGTCTAGGGACTGTTATCA 59.552 47.826 0.00 0.00 41.52 2.15
2717 7094 3.474806 GCAATACGCGTGCTGTCT 58.525 55.556 24.59 0.00 39.00 3.41
2790 7167 1.202976 GGCATATTCCAGAGCCCACAT 60.203 52.381 0.00 0.00 41.25 3.21
2808 7185 3.412386 ACGGAAGGCAATATATGAAGGC 58.588 45.455 0.00 0.00 0.00 4.35
2816 7193 0.814010 GGCACGACGGAAGGCAATAT 60.814 55.000 0.00 0.00 41.50 1.28
2923 7301 4.993705 TGATGGAAGTTACTGAACCCTT 57.006 40.909 0.00 0.00 36.08 3.95
2957 7335 1.070758 GGGCTCTCAGTGACAGTGAAA 59.929 52.381 13.85 0.11 0.00 2.69
2978 7356 3.056313 GCCGCTTCAAGATGCACCC 62.056 63.158 8.40 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.