Multiple sequence alignment - TraesCS1D01G245600

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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 TraesCS1D01G245600 chr1D 100.000 3684 0 0 1 3684 337216201 337219884 0.000000e+00 6804
1 TraesCS1D01G245600 chr1A 94.232 2826 91 27 887 3684 436421106 436423887 0.000000e+00 4250
2 TraesCS1D01G245600 chr1A 91.787 207 12 4 694 895 436420748 436420954 2.170000e-72 283
3 TraesCS1D01G245600 chr1B 94.297 1964 59 17 882 2824 452571639 452573570 0.000000e+00 2957
4 TraesCS1D01G245600 chr1B 96.526 806 24 4 2879 3684 452573592 452574393 0.000000e+00 1330
5 TraesCS1D01G245600 chr1B 95.652 230 10 0 20 249 452570483 452570712 1.620000e-98 370
6 TraesCS1D01G245600 chr1B 96.111 180 7 0 348 527 452570962 452571141 1.000000e-75 294
7 TraesCS1D01G245600 chr1B 92.233 206 5 4 690 884 452571377 452571582 7.790000e-72 281
8 TraesCS1D01G245600 chr1B 92.157 102 7 1 594 694 61525903 61526004 3.840000e-30 143
9 TraesCS1D01G245600 chr1B 87.129 101 7 4 469 568 452571205 452571300 3.890000e-20 110
10 TraesCS1D01G245600 chr1B 100.000 40 0 0 281 320 452570923 452570962 1.420000e-09 75
11 TraesCS1D01G245600 chr7B 84.175 891 114 20 1032 1910 704664251 704663376 0.000000e+00 839
12 TraesCS1D01G245600 chr7B 83.897 621 72 18 2014 2626 704663321 704662721 5.340000e-158 568
13 TraesCS1D01G245600 chr7A 83.536 905 130 14 1014 1910 705418643 705417750 0.000000e+00 828
14 TraesCS1D01G245600 chr7A 82.989 629 81 15 2011 2632 705417693 705417084 2.500000e-151 545
15 TraesCS1D01G245600 chr7A 80.192 626 112 10 2016 2632 705546542 705545920 3.350000e-125 459
16 TraesCS1D01G245600 chr7A 76.834 518 96 21 2034 2533 706035971 706035460 1.690000e-68 270
17 TraesCS1D01G245600 chr7D 83.203 893 127 16 1028 1910 613694284 613693405 0.000000e+00 797
18 TraesCS1D01G245600 chr7D 83.492 630 76 15 2011 2632 613693352 613692743 2.480000e-156 562
19 TraesCS1D01G245600 chr7D 82.232 439 69 8 2180 2611 613765865 613765429 1.620000e-98 370
20 TraesCS1D01G245600 chr7D 93.204 103 6 1 607 708 519264630 519264528 2.290000e-32 150
21 TraesCS1D01G245600 chr7D 94.737 95 4 1 600 693 226690438 226690344 2.960000e-31 147
22 TraesCS1D01G245600 chr7D 87.826 115 10 4 607 717 169823455 169823341 8.300000e-27 132
23 TraesCS1D01G245600 chr2A 77.493 742 141 17 1118 1846 707957738 707958466 4.400000e-114 422
24 TraesCS1D01G245600 chr2D 77.419 744 138 18 1118 1846 568464416 568465144 2.050000e-112 416
25 TraesCS1D01G245600 chr2D 78.675 483 86 10 1373 1846 568357760 568358234 4.620000e-79 305
26 TraesCS1D01G245600 chr6D 76.421 827 157 30 1104 1909 143092302 143091493 2.650000e-111 412
27 TraesCS1D01G245600 chr6D 77.939 553 101 18 2037 2578 97520597 97520055 3.550000e-85 326
28 TraesCS1D01G245600 chr5A 93.773 273 15 2 1 272 657192201 657191930 3.420000e-110 409
29 TraesCS1D01G245600 chr5A 80.965 373 45 14 214 581 657191924 657191573 4.690000e-69 272
30 TraesCS1D01G245600 chr5B 93.431 274 15 3 1 272 666188621 666188349 1.590000e-108 403
31 TraesCS1D01G245600 chr5B 90.446 157 12 3 214 369 666188343 666188189 1.730000e-48 204
32 TraesCS1D01G245600 chr5D 92.674 273 18 2 1 272 528964950 528964679 3.450000e-105 392
33 TraesCS1D01G245600 chr5D 86.624 157 8 4 214 369 528964673 528964529 1.060000e-35 161
34 TraesCS1D01G245600 chr5D 96.629 89 3 0 607 695 267846681 267846593 8.240000e-32 148
35 TraesCS1D01G245600 chr5D 92.857 98 5 2 594 691 294640224 294640319 1.380000e-29 141
36 TraesCS1D01G245600 chr6A 76.431 751 151 19 1111 1845 188354896 188354156 2.080000e-102 383
37 TraesCS1D01G245600 chr6B 76.299 616 114 19 1105 1713 255211360 255210770 2.150000e-77 300
38 TraesCS1D01G245600 chrUn 77.691 511 99 12 2034 2533 293161515 293161009 7.730000e-77 298
39 TraesCS1D01G245600 chrUn 79.112 383 68 9 2151 2524 409868735 409869114 1.700000e-63 254
40 TraesCS1D01G245600 chr4D 98.824 85 1 0 607 691 124628854 124628770 6.370000e-33 152
41 TraesCS1D01G245600 chr3D 96.703 91 3 0 607 697 526509381 526509291 6.370000e-33 152
42 TraesCS1D01G245600 chr4A 93.000 100 6 1 607 705 556768039 556767940 1.070000e-30 145


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 TraesCS1D01G245600 chr1D 337216201 337219884 3683 False 6804.000000 6804 100.0000 1 3684 1 chr1D.!!$F1 3683
1 TraesCS1D01G245600 chr1A 436420748 436423887 3139 False 2266.500000 4250 93.0095 694 3684 2 chr1A.!!$F1 2990
2 TraesCS1D01G245600 chr1B 452570483 452574393 3910 False 773.857143 2957 94.5640 20 3684 7 chr1B.!!$F2 3664
3 TraesCS1D01G245600 chr7B 704662721 704664251 1530 True 703.500000 839 84.0360 1032 2626 2 chr7B.!!$R1 1594
4 TraesCS1D01G245600 chr7A 705417084 705418643 1559 True 686.500000 828 83.2625 1014 2632 2 chr7A.!!$R3 1618
5 TraesCS1D01G245600 chr7A 705545920 705546542 622 True 459.000000 459 80.1920 2016 2632 1 chr7A.!!$R1 616
6 TraesCS1D01G245600 chr7A 706035460 706035971 511 True 270.000000 270 76.8340 2034 2533 1 chr7A.!!$R2 499
7 TraesCS1D01G245600 chr7D 613692743 613694284 1541 True 679.500000 797 83.3475 1028 2632 2 chr7D.!!$R5 1604
8 TraesCS1D01G245600 chr2A 707957738 707958466 728 False 422.000000 422 77.4930 1118 1846 1 chr2A.!!$F1 728
9 TraesCS1D01G245600 chr2D 568464416 568465144 728 False 416.000000 416 77.4190 1118 1846 1 chr2D.!!$F2 728
10 TraesCS1D01G245600 chr6D 143091493 143092302 809 True 412.000000 412 76.4210 1104 1909 1 chr6D.!!$R2 805
11 TraesCS1D01G245600 chr6D 97520055 97520597 542 True 326.000000 326 77.9390 2037 2578 1 chr6D.!!$R1 541
12 TraesCS1D01G245600 chr5A 657191573 657192201 628 True 340.500000 409 87.3690 1 581 2 chr5A.!!$R1 580
13 TraesCS1D01G245600 chr6A 188354156 188354896 740 True 383.000000 383 76.4310 1111 1845 1 chr6A.!!$R1 734
14 TraesCS1D01G245600 chr6B 255210770 255211360 590 True 300.000000 300 76.2990 1105 1713 1 chr6B.!!$R1 608
15 TraesCS1D01G245600 chrUn 293161009 293161515 506 True 298.000000 298 77.6910 2034 2533 1 chrUn.!!$R1 499

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
918 1438 0.101399 CCTGCTGGTCTACTACGCTG 59.899 60.0 0.51 0.0 0.0 5.18 F
1969 2519 0.179043 TTCAGCACCGTAAGTTGCCA 60.179 50.0 0.00 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2521 0.099082 GTTAGTCTCGCTCCCTCACG 59.901 60.0 0.0 0.0 0.00 4.35 R
2940 3539 1.220529 CAGAAGCAGAACAGCACGAA 58.779 50.0 0.0 0.0 36.85 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
205 206 4.497473 TTCGGATCTTTTCATTTTGCGT 57.503 36.364 0.00 0.00 0.00 5.24
212 213 5.141355 TCTTTTCATTTTGCGTGCTTTTG 57.859 34.783 0.00 0.00 0.00 2.44
256 369 0.814457 ATCAGCGAGAGTGACACCTC 59.186 55.000 0.84 7.85 0.00 3.85
320 501 9.062524 GTAAATATGAATGGTGGTGCTATTGTA 57.937 33.333 0.00 0.00 0.00 2.41
321 502 8.710749 AAATATGAATGGTGGTGCTATTGTAT 57.289 30.769 0.00 0.00 0.00 2.29
322 503 7.692460 ATATGAATGGTGGTGCTATTGTATG 57.308 36.000 0.00 0.00 0.00 2.39
323 504 4.206375 TGAATGGTGGTGCTATTGTATGG 58.794 43.478 0.00 0.00 0.00 2.74
324 505 2.727123 TGGTGGTGCTATTGTATGGG 57.273 50.000 0.00 0.00 0.00 4.00
329 510 4.398319 GTGGTGCTATTGTATGGGCTATT 58.602 43.478 0.00 0.00 0.00 1.73
333 514 6.012945 TGGTGCTATTGTATGGGCTATTATCA 60.013 38.462 0.00 0.00 0.00 2.15
335 516 6.037610 GTGCTATTGTATGGGCTATTATCAGC 59.962 42.308 0.00 0.00 41.02 4.26
342 523 3.990092 TGGGCTATTATCAGCGTGTTAG 58.010 45.455 0.00 0.00 42.76 2.34
343 524 3.244078 TGGGCTATTATCAGCGTGTTAGG 60.244 47.826 0.00 0.00 42.76 2.69
344 525 3.244112 GGGCTATTATCAGCGTGTTAGGT 60.244 47.826 0.00 0.00 42.76 3.08
345 526 4.021719 GGGCTATTATCAGCGTGTTAGGTA 60.022 45.833 0.00 0.00 42.76 3.08
408 595 4.450757 GGTATGACATTACATGTGCGCATA 59.549 41.667 15.91 12.79 45.03 3.14
409 596 5.122239 GGTATGACATTACATGTGCGCATAT 59.878 40.000 15.91 15.11 45.03 1.78
460 647 3.005684 GTGCAGAACCAAATGGATTGTGA 59.994 43.478 6.42 0.00 37.32 3.58
505 692 6.496565 TCCATACTCCAAACATTTGTTGGATT 59.503 34.615 6.36 4.14 38.44 3.01
599 948 1.134401 TCCCTGAGATGCGGATTTGTC 60.134 52.381 0.00 0.00 0.00 3.18
600 949 1.407299 CCCTGAGATGCGGATTTGTCA 60.407 52.381 0.00 0.00 0.00 3.58
601 950 2.358957 CCTGAGATGCGGATTTGTCAA 58.641 47.619 0.00 0.00 0.00 3.18
602 951 2.749076 CCTGAGATGCGGATTTGTCAAA 59.251 45.455 0.00 0.00 0.00 2.69
603 952 3.426695 CCTGAGATGCGGATTTGTCAAAC 60.427 47.826 0.00 0.00 0.00 2.93
604 953 2.159430 TGAGATGCGGATTTGTCAAACG 59.841 45.455 0.00 2.12 0.00 3.60
605 954 2.415168 GAGATGCGGATTTGTCAAACGA 59.585 45.455 11.32 0.00 0.00 3.85
606 955 3.009723 AGATGCGGATTTGTCAAACGAT 58.990 40.909 11.32 3.83 0.00 3.73
607 956 4.188462 AGATGCGGATTTGTCAAACGATA 58.812 39.130 11.32 1.86 0.00 2.92
608 957 3.733024 TGCGGATTTGTCAAACGATAC 57.267 42.857 11.32 0.00 0.00 2.24
609 958 3.331150 TGCGGATTTGTCAAACGATACT 58.669 40.909 11.32 0.00 0.00 2.12
610 959 3.369756 TGCGGATTTGTCAAACGATACTC 59.630 43.478 11.32 0.28 0.00 2.59
611 960 3.242316 GCGGATTTGTCAAACGATACTCC 60.242 47.826 11.32 7.63 0.00 3.85
612 961 3.308866 CGGATTTGTCAAACGATACTCCC 59.691 47.826 0.00 0.00 0.00 4.30
613 962 4.514401 GGATTTGTCAAACGATACTCCCT 58.486 43.478 0.00 0.00 0.00 4.20
614 963 4.571176 GGATTTGTCAAACGATACTCCCTC 59.429 45.833 0.00 0.00 0.00 4.30
615 964 3.604875 TTGTCAAACGATACTCCCTCC 57.395 47.619 0.00 0.00 0.00 4.30
616 965 1.475280 TGTCAAACGATACTCCCTCCG 59.525 52.381 0.00 0.00 0.00 4.63
617 966 1.475682 GTCAAACGATACTCCCTCCGT 59.524 52.381 0.00 0.00 36.77 4.69
618 967 1.747355 TCAAACGATACTCCCTCCGTC 59.253 52.381 0.00 0.00 33.84 4.79
619 968 1.109609 AAACGATACTCCCTCCGTCC 58.890 55.000 0.00 0.00 33.84 4.79
620 969 0.754587 AACGATACTCCCTCCGTCCC 60.755 60.000 0.00 0.00 33.84 4.46
621 970 1.152819 CGATACTCCCTCCGTCCCA 60.153 63.158 0.00 0.00 0.00 4.37
622 971 0.539901 CGATACTCCCTCCGTCCCAT 60.540 60.000 0.00 0.00 0.00 4.00
623 972 1.271762 CGATACTCCCTCCGTCCCATA 60.272 57.143 0.00 0.00 0.00 2.74
624 973 2.816712 CGATACTCCCTCCGTCCCATAA 60.817 54.545 0.00 0.00 0.00 1.90
625 974 3.442076 GATACTCCCTCCGTCCCATAAT 58.558 50.000 0.00 0.00 0.00 1.28
626 975 4.607239 GATACTCCCTCCGTCCCATAATA 58.393 47.826 0.00 0.00 0.00 0.98
627 976 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
628 977 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
629 978 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
630 979 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
631 980 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
632 981 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
633 982 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
634 983 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
635 984 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
636 985 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
637 986 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
638 987 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
639 988 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
640 989 7.385752 CCGTCCCATAATATAAGAGCGTTTTTA 59.614 37.037 0.00 0.00 0.00 1.52
641 990 8.767085 CGTCCCATAATATAAGAGCGTTTTTAA 58.233 33.333 0.00 0.00 0.00 1.52
642 991 9.874215 GTCCCATAATATAAGAGCGTTTTTAAC 57.126 33.333 0.00 0.00 0.00 2.01
643 992 9.616156 TCCCATAATATAAGAGCGTTTTTAACA 57.384 29.630 0.00 0.00 0.00 2.41
644 993 9.659830 CCCATAATATAAGAGCGTTTTTAACAC 57.340 33.333 0.00 0.00 0.00 3.32
650 999 7.958053 ATAAGAGCGTTTTTAACACTACACT 57.042 32.000 0.00 0.00 0.00 3.55
652 1001 7.404139 AAGAGCGTTTTTAACACTACACTAG 57.596 36.000 0.00 0.00 0.00 2.57
653 1002 6.510536 AGAGCGTTTTTAACACTACACTAGT 58.489 36.000 0.00 0.00 40.28 2.57
682 1031 7.647907 AAAACGCTCTTATATTATGGTACGG 57.352 36.000 0.00 0.00 0.00 4.02
683 1032 6.579666 AACGCTCTTATATTATGGTACGGA 57.420 37.500 0.00 0.00 0.00 4.69
684 1033 6.192234 ACGCTCTTATATTATGGTACGGAG 57.808 41.667 0.00 0.00 0.00 4.63
685 1034 5.125097 ACGCTCTTATATTATGGTACGGAGG 59.875 44.000 0.00 0.00 0.00 4.30
686 1035 5.450137 CGCTCTTATATTATGGTACGGAGGG 60.450 48.000 0.00 0.00 0.00 4.30
687 1036 5.655532 GCTCTTATATTATGGTACGGAGGGA 59.344 44.000 0.00 0.00 0.00 4.20
688 1037 6.183360 GCTCTTATATTATGGTACGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
750 1099 2.671963 GGTGGGTTGAACTCCGGC 60.672 66.667 0.00 0.00 0.00 6.13
828 1177 0.109873 GCGTCAGTGTAGCGTACAGT 60.110 55.000 0.00 0.25 42.82 3.55
831 1180 2.414481 CGTCAGTGTAGCGTACAGTAGT 59.586 50.000 0.00 0.00 40.21 2.73
832 1181 3.614176 CGTCAGTGTAGCGTACAGTAGTA 59.386 47.826 0.00 0.00 40.21 1.82
833 1182 4.491602 CGTCAGTGTAGCGTACAGTAGTAC 60.492 50.000 0.00 0.00 45.67 2.73
836 1185 4.033817 CAGTGTAGCGTACAGTAGTACTCC 59.966 50.000 0.00 0.00 46.68 3.85
918 1438 0.101399 CCTGCTGGTCTACTACGCTG 59.899 60.000 0.51 0.00 0.00 5.18
949 1469 2.033407 CACACACAGACAAAGAGAAGCG 60.033 50.000 0.00 0.00 0.00 4.68
950 1470 1.070309 CACACAGACAAAGAGAAGCGC 60.070 52.381 0.00 0.00 0.00 5.92
1079 1599 1.534175 GCTCTACTTCATCCGGTCGTG 60.534 57.143 0.00 0.00 0.00 4.35
1863 2404 2.428085 GGGAGAGGGGAAGCTCGAC 61.428 68.421 0.00 0.00 31.95 4.20
1881 2422 1.995626 CCCTCCCCTCACCAACGAT 60.996 63.158 0.00 0.00 0.00 3.73
1954 2504 7.693969 ACTACAATGGAGGAGAAATTTTCAG 57.306 36.000 11.53 0.00 0.00 3.02
1962 2512 4.394729 AGGAGAAATTTTCAGCACCGTAA 58.605 39.130 11.53 0.00 0.00 3.18
1965 2515 5.278315 GGAGAAATTTTCAGCACCGTAAGTT 60.278 40.000 11.53 0.00 0.00 2.66
1966 2516 5.519722 AGAAATTTTCAGCACCGTAAGTTG 58.480 37.500 11.53 0.00 0.00 3.16
1967 2517 2.766970 TTTTCAGCACCGTAAGTTGC 57.233 45.000 0.00 0.00 0.00 4.17
1968 2518 0.948678 TTTCAGCACCGTAAGTTGCC 59.051 50.000 0.00 0.00 0.00 4.52
1969 2519 0.179043 TTCAGCACCGTAAGTTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
1970 2520 0.882927 TCAGCACCGTAAGTTGCCAC 60.883 55.000 0.00 0.00 0.00 5.01
1971 2521 1.599797 AGCACCGTAAGTTGCCACC 60.600 57.895 0.00 0.00 0.00 4.61
1972 2522 2.961669 GCACCGTAAGTTGCCACCG 61.962 63.158 0.00 0.00 0.00 4.94
1973 2523 1.595929 CACCGTAAGTTGCCACCGT 60.596 57.895 0.00 0.00 0.00 4.83
1974 2524 1.595929 ACCGTAAGTTGCCACCGTG 60.596 57.895 0.00 0.00 0.00 4.94
1975 2525 1.301087 CCGTAAGTTGCCACCGTGA 60.301 57.895 0.00 0.00 0.00 4.35
1976 2526 1.289109 CCGTAAGTTGCCACCGTGAG 61.289 60.000 0.00 0.00 0.00 3.51
1988 2538 4.220413 CGTGAGGGAGCGAGACTA 57.780 61.111 0.00 0.00 0.00 2.59
1989 2539 2.478989 CGTGAGGGAGCGAGACTAA 58.521 57.895 0.00 0.00 0.00 2.24
1990 2540 0.099082 CGTGAGGGAGCGAGACTAAC 59.901 60.000 0.00 0.00 0.00 2.34
1991 2541 1.465794 GTGAGGGAGCGAGACTAACT 58.534 55.000 0.00 0.00 0.00 2.24
1992 2542 1.819903 GTGAGGGAGCGAGACTAACTT 59.180 52.381 0.00 0.00 0.00 2.66
1993 2543 2.093106 TGAGGGAGCGAGACTAACTTC 58.907 52.381 0.00 0.00 0.00 3.01
2386 2947 3.069318 GAGAGGTTCGAGGGCGGT 61.069 66.667 0.00 0.00 38.28 5.68
2689 3261 3.640029 TCGACATTAAGCCTTAGGGTAGG 59.360 47.826 2.41 0.00 38.40 3.18
2694 3266 4.603946 GCCTTAGGGTAGGGCGCG 62.604 72.222 0.00 0.00 41.28 6.86
2695 3267 2.836360 CCTTAGGGTAGGGCGCGA 60.836 66.667 12.10 0.00 34.93 5.87
2696 3268 2.428925 CCTTAGGGTAGGGCGCGAA 61.429 63.158 12.10 0.00 34.93 4.70
2697 3269 1.518774 CTTAGGGTAGGGCGCGAAA 59.481 57.895 12.10 0.00 34.93 3.46
2698 3270 0.808847 CTTAGGGTAGGGCGCGAAAC 60.809 60.000 12.10 0.44 34.93 2.78
2699 3271 1.259840 TTAGGGTAGGGCGCGAAACT 61.260 55.000 12.10 6.58 34.93 2.66
2700 3272 1.259840 TAGGGTAGGGCGCGAAACTT 61.260 55.000 12.10 0.00 34.93 2.66
2709 3281 1.195900 GGCGCGAAACTTACAACATGA 59.804 47.619 12.10 0.00 0.00 3.07
2710 3282 2.350007 GGCGCGAAACTTACAACATGAA 60.350 45.455 12.10 0.00 0.00 2.57
2733 3305 9.740239 TGAAAGATTTATTGCTATTGCTTCATC 57.260 29.630 0.00 0.00 40.48 2.92
2839 3422 4.592485 CAGAACTACTTCTGGACAGTGT 57.408 45.455 0.00 0.00 46.87 3.55
2863 3446 5.579047 ACAACACCTATTCCATTCCATTCA 58.421 37.500 0.00 0.00 0.00 2.57
2865 3448 6.496565 ACAACACCTATTCCATTCCATTCAAA 59.503 34.615 0.00 0.00 0.00 2.69
2866 3449 6.780457 ACACCTATTCCATTCCATTCAAAG 57.220 37.500 0.00 0.00 0.00 2.77
2867 3450 6.256053 ACACCTATTCCATTCCATTCAAAGT 58.744 36.000 0.00 0.00 0.00 2.66
2887 3484 7.775561 TCAAAGTATCAGATACTCAGAGCTACA 59.224 37.037 21.29 0.82 44.94 2.74
2940 3539 1.424302 CCATGGGGCTCTCAAGATGAT 59.576 52.381 2.85 0.00 0.00 2.45
3158 3757 2.689553 TCATCAGCAGTAATGCGGAA 57.310 45.000 21.06 3.89 41.79 4.30
3203 3802 6.596888 TCTGAGCATGTAATCCTTTGAAGAAG 59.403 38.462 0.00 0.00 0.00 2.85
3230 3829 1.909700 TGCCTTCCTTGTTCCACATC 58.090 50.000 0.00 0.00 0.00 3.06
3368 3967 5.685068 TGAAAAATGGCGTCATATAATTGCG 59.315 36.000 1.27 0.00 32.44 4.85
3371 3970 3.388345 TGGCGTCATATAATTGCGGTA 57.612 42.857 0.00 0.00 0.00 4.02
3541 4147 2.805099 CGAGAAAGCAGAAAGAGCAACT 59.195 45.455 0.00 0.00 0.00 3.16
3553 4159 1.065854 AGAGCAACTGGGGAAGAATCG 60.066 52.381 0.00 0.00 0.00 3.34
3632 4238 2.747989 TCAAACACGGTGTACTGCAAAA 59.252 40.909 15.11 0.00 0.00 2.44
3638 4244 2.552315 ACGGTGTACTGCAAAAGATTGG 59.448 45.455 0.00 0.00 37.02 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 1.824230 AGAACACCAGCAACAAAAGCA 59.176 42.857 0.00 0.00 0.00 3.91
212 213 1.569479 GGCTCGAGAACACCAGCAAC 61.569 60.000 18.75 0.00 33.22 4.17
320 501 3.492102 AACACGCTGATAATAGCCCAT 57.508 42.857 0.00 0.00 40.59 4.00
321 502 3.244078 CCTAACACGCTGATAATAGCCCA 60.244 47.826 0.00 0.00 40.59 5.36
322 503 3.244112 ACCTAACACGCTGATAATAGCCC 60.244 47.826 0.00 0.00 40.59 5.19
323 504 3.991367 ACCTAACACGCTGATAATAGCC 58.009 45.455 0.00 0.00 40.59 3.93
324 505 6.645415 ACAATACCTAACACGCTGATAATAGC 59.355 38.462 0.00 0.00 40.29 2.97
329 510 5.585820 TGACAATACCTAACACGCTGATA 57.414 39.130 0.00 0.00 0.00 2.15
333 514 5.106317 CCAAATTGACAATACCTAACACGCT 60.106 40.000 0.00 0.00 0.00 5.07
335 516 6.249035 ACCAAATTGACAATACCTAACACG 57.751 37.500 0.00 0.00 0.00 4.49
342 523 7.404671 AGTTATGGACCAAATTGACAATACC 57.595 36.000 0.00 2.03 0.00 2.73
343 524 8.303876 ACAAGTTATGGACCAAATTGACAATAC 58.696 33.333 12.15 0.00 35.23 1.89
344 525 8.415950 ACAAGTTATGGACCAAATTGACAATA 57.584 30.769 12.15 0.00 35.23 1.90
345 526 7.301868 ACAAGTTATGGACCAAATTGACAAT 57.698 32.000 12.15 0.00 35.23 2.71
408 595 3.301794 TCATTCATACTTGGGCAGCAT 57.698 42.857 0.00 0.00 0.00 3.79
409 596 2.804986 TCATTCATACTTGGGCAGCA 57.195 45.000 0.00 0.00 0.00 4.41
460 647 1.927487 TCCTGAATTTGGCAGCACAT 58.073 45.000 0.00 0.00 32.06 3.21
505 692 3.547214 CCGTCGCTGCTTTGAAACTTTAA 60.547 43.478 0.00 0.00 0.00 1.52
599 948 1.202382 GGACGGAGGGAGTATCGTTTG 60.202 57.143 0.00 0.00 35.91 2.93
600 949 1.109609 GGACGGAGGGAGTATCGTTT 58.890 55.000 0.00 0.00 35.91 3.60
601 950 0.754587 GGGACGGAGGGAGTATCGTT 60.755 60.000 0.00 0.00 35.91 3.85
602 951 1.152798 GGGACGGAGGGAGTATCGT 60.153 63.158 0.00 0.00 38.62 3.73
603 952 0.539901 ATGGGACGGAGGGAGTATCG 60.540 60.000 0.00 0.00 34.37 2.92
604 953 2.599408 TATGGGACGGAGGGAGTATC 57.401 55.000 0.00 0.00 0.00 2.24
605 954 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
606 955 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
607 956 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
608 957 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
609 958 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
610 959 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
611 960 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
612 961 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
613 962 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
614 963 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
615 964 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
616 965 9.874215 GTTAAAAACGCTCTTATATTATGGGAC 57.126 33.333 0.00 0.00 0.00 4.46
617 966 9.616156 TGTTAAAAACGCTCTTATATTATGGGA 57.384 29.630 0.00 0.00 0.00 4.37
618 967 9.659830 GTGTTAAAAACGCTCTTATATTATGGG 57.340 33.333 0.00 0.00 38.81 4.00
643 992 6.510536 AGAGCGTTTTTAACACTAGTGTAGT 58.489 36.000 28.13 16.41 44.13 2.73
644 993 7.404139 AAGAGCGTTTTTAACACTAGTGTAG 57.596 36.000 28.13 14.03 44.13 2.74
656 1005 9.195411 CCGTACCATAATATAAGAGCGTTTTTA 57.805 33.333 0.00 0.00 0.00 1.52
657 1006 7.927629 TCCGTACCATAATATAAGAGCGTTTTT 59.072 33.333 0.00 0.00 0.00 1.94
658 1007 7.436118 TCCGTACCATAATATAAGAGCGTTTT 58.564 34.615 0.00 0.00 0.00 2.43
659 1008 6.985117 TCCGTACCATAATATAAGAGCGTTT 58.015 36.000 0.00 0.00 0.00 3.60
660 1009 6.349944 CCTCCGTACCATAATATAAGAGCGTT 60.350 42.308 0.00 0.00 0.00 4.84
661 1010 5.125097 CCTCCGTACCATAATATAAGAGCGT 59.875 44.000 0.00 0.00 0.00 5.07
662 1011 5.450137 CCCTCCGTACCATAATATAAGAGCG 60.450 48.000 0.00 0.00 0.00 5.03
663 1012 5.655532 TCCCTCCGTACCATAATATAAGAGC 59.344 44.000 0.00 0.00 0.00 4.09
664 1013 6.890814 ACTCCCTCCGTACCATAATATAAGAG 59.109 42.308 0.00 0.00 0.00 2.85
665 1014 6.797707 ACTCCCTCCGTACCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
666 1015 8.763984 ATACTCCCTCCGTACCATAATATAAG 57.236 38.462 0.00 0.00 0.00 1.73
667 1016 9.551339 AAATACTCCCTCCGTACCATAATATAA 57.449 33.333 0.00 0.00 0.00 0.98
668 1017 9.551339 AAAATACTCCCTCCGTACCATAATATA 57.449 33.333 0.00 0.00 0.00 0.86
669 1018 8.445361 AAAATACTCCCTCCGTACCATAATAT 57.555 34.615 0.00 0.00 0.00 1.28
670 1019 7.860649 AAAATACTCCCTCCGTACCATAATA 57.139 36.000 0.00 0.00 0.00 0.98
671 1020 6.758806 AAAATACTCCCTCCGTACCATAAT 57.241 37.500 0.00 0.00 0.00 1.28
672 1021 6.564557 AAAAATACTCCCTCCGTACCATAA 57.435 37.500 0.00 0.00 0.00 1.90
793 1142 2.644992 GCTTTGCCCAACCACTCG 59.355 61.111 0.00 0.00 0.00 4.18
832 1181 9.261035 CTGGTCAATATCCTGTAATATAGGAGT 57.739 37.037 11.38 0.73 46.81 3.85
833 1182 9.480861 TCTGGTCAATATCCTGTAATATAGGAG 57.519 37.037 11.38 0.00 46.81 3.69
1863 2404 1.995626 ATCGTTGGTGAGGGGAGGG 60.996 63.158 0.00 0.00 0.00 4.30
1881 2422 1.276138 ACGATGACTGCCTTGATGTCA 59.724 47.619 0.00 0.00 43.53 3.58
1928 2472 8.561738 TGAAAATTTCTCCTCCATTGTAGTAC 57.438 34.615 7.29 0.00 0.00 2.73
1954 2504 2.951458 GGTGGCAACTTACGGTGC 59.049 61.111 0.00 0.00 37.61 5.01
1962 2512 2.847234 TCCCTCACGGTGGCAACT 60.847 61.111 8.50 0.00 37.61 3.16
1967 2517 4.135153 CTCGCTCCCTCACGGTGG 62.135 72.222 8.50 0.00 0.00 4.61
1968 2518 3.062466 TCTCGCTCCCTCACGGTG 61.062 66.667 0.56 0.56 0.00 4.94
1969 2519 2.194388 TAGTCTCGCTCCCTCACGGT 62.194 60.000 0.00 0.00 0.00 4.83
1970 2520 1.030488 TTAGTCTCGCTCCCTCACGG 61.030 60.000 0.00 0.00 0.00 4.94
1971 2521 0.099082 GTTAGTCTCGCTCCCTCACG 59.901 60.000 0.00 0.00 0.00 4.35
1972 2522 1.465794 AGTTAGTCTCGCTCCCTCAC 58.534 55.000 0.00 0.00 0.00 3.51
1973 2523 2.093106 GAAGTTAGTCTCGCTCCCTCA 58.907 52.381 0.00 0.00 0.00 3.86
1974 2524 1.406180 GGAAGTTAGTCTCGCTCCCTC 59.594 57.143 0.00 0.00 0.00 4.30
1975 2525 1.006162 AGGAAGTTAGTCTCGCTCCCT 59.994 52.381 0.00 0.00 0.00 4.20
1976 2526 1.476477 AGGAAGTTAGTCTCGCTCCC 58.524 55.000 0.00 0.00 0.00 4.30
1977 2527 2.159212 GGAAGGAAGTTAGTCTCGCTCC 60.159 54.545 0.00 0.00 0.00 4.70
1978 2528 2.756207 AGGAAGGAAGTTAGTCTCGCTC 59.244 50.000 0.00 0.00 0.00 5.03
1979 2529 2.756207 GAGGAAGGAAGTTAGTCTCGCT 59.244 50.000 0.00 0.00 0.00 4.93
1980 2530 2.756207 AGAGGAAGGAAGTTAGTCTCGC 59.244 50.000 0.00 0.00 0.00 5.03
1981 2531 3.428316 GCAGAGGAAGGAAGTTAGTCTCG 60.428 52.174 0.00 0.00 0.00 4.04
1982 2532 3.767131 AGCAGAGGAAGGAAGTTAGTCTC 59.233 47.826 0.00 0.00 0.00 3.36
1983 2533 3.785364 AGCAGAGGAAGGAAGTTAGTCT 58.215 45.455 0.00 0.00 0.00 3.24
1984 2534 4.021016 TGAAGCAGAGGAAGGAAGTTAGTC 60.021 45.833 0.00 0.00 0.00 2.59
1985 2535 3.904339 TGAAGCAGAGGAAGGAAGTTAGT 59.096 43.478 0.00 0.00 0.00 2.24
1986 2536 4.543590 TGAAGCAGAGGAAGGAAGTTAG 57.456 45.455 0.00 0.00 0.00 2.34
1987 2537 4.348168 AGTTGAAGCAGAGGAAGGAAGTTA 59.652 41.667 0.00 0.00 0.00 2.24
1988 2538 3.137360 AGTTGAAGCAGAGGAAGGAAGTT 59.863 43.478 0.00 0.00 0.00 2.66
1989 2539 2.708325 AGTTGAAGCAGAGGAAGGAAGT 59.292 45.455 0.00 0.00 0.00 3.01
1990 2540 3.333804 GAGTTGAAGCAGAGGAAGGAAG 58.666 50.000 0.00 0.00 0.00 3.46
1991 2541 2.289072 CGAGTTGAAGCAGAGGAAGGAA 60.289 50.000 0.00 0.00 0.00 3.36
1992 2542 1.273606 CGAGTTGAAGCAGAGGAAGGA 59.726 52.381 0.00 0.00 0.00 3.36
1993 2543 1.674221 CCGAGTTGAAGCAGAGGAAGG 60.674 57.143 0.00 0.00 0.00 3.46
2351 2912 3.132139 CGGCGAGAACTCCTCCGA 61.132 66.667 18.43 0.00 41.60 4.55
2386 2947 2.342279 CCCTTGAAGTCGACGCCA 59.658 61.111 10.46 9.32 0.00 5.69
2689 3261 1.195900 TCATGTTGTAAGTTTCGCGCC 59.804 47.619 0.00 0.00 0.00 6.53
2691 3263 4.768145 TCTTTCATGTTGTAAGTTTCGCG 58.232 39.130 0.00 0.00 0.00 5.87
2692 3264 7.623268 AAATCTTTCATGTTGTAAGTTTCGC 57.377 32.000 0.00 0.00 0.00 4.70
2709 3281 9.962783 GAGATGAAGCAATAGCAATAAATCTTT 57.037 29.630 0.00 0.00 45.49 2.52
2710 3282 8.574737 GGAGATGAAGCAATAGCAATAAATCTT 58.425 33.333 0.00 0.00 45.49 2.40
2732 3304 7.453393 TCTATTCTTTCTTTCTTTGCTGGAGA 58.547 34.615 0.00 0.00 0.00 3.71
2733 3305 7.678947 TCTATTCTTTCTTTCTTTGCTGGAG 57.321 36.000 0.00 0.00 0.00 3.86
2783 3355 3.590630 TGGTCTGGTAGACTGGTAGTACT 59.409 47.826 0.00 0.00 44.46 2.73
2785 3357 3.331591 TGTGGTCTGGTAGACTGGTAGTA 59.668 47.826 8.68 0.00 44.46 1.82
2786 3358 2.109480 TGTGGTCTGGTAGACTGGTAGT 59.891 50.000 8.68 0.00 44.46 2.73
2787 3359 2.803956 TGTGGTCTGGTAGACTGGTAG 58.196 52.381 8.68 0.00 44.46 3.18
2839 3422 6.726379 TGAATGGAATGGAATAGGTGTTGTA 58.274 36.000 0.00 0.00 0.00 2.41
2855 3438 8.981659 TCTGAGTATCTGATACTTTGAATGGAA 58.018 33.333 26.33 7.41 45.64 3.53
2863 3446 7.230510 CCTGTAGCTCTGAGTATCTGATACTTT 59.769 40.741 26.33 9.98 45.64 2.66
2866 3449 6.234920 TCCTGTAGCTCTGAGTATCTGATAC 58.765 44.000 17.97 17.97 42.34 2.24
2867 3450 6.441088 TCCTGTAGCTCTGAGTATCTGATA 57.559 41.667 6.53 0.00 42.34 2.15
2916 3515 1.925255 TCTTGAGAGCCCCATGGAATT 59.075 47.619 15.22 0.00 0.00 2.17
2926 3525 1.596727 GCACGAATCATCTTGAGAGCC 59.403 52.381 0.00 0.00 0.00 4.70
2940 3539 1.220529 CAGAAGCAGAACAGCACGAA 58.779 50.000 0.00 0.00 36.85 3.85
2989 3588 4.738740 GTCTAATCGTCCACTGGTATTTCG 59.261 45.833 0.00 0.00 0.00 3.46
3158 3757 7.362574 GCTCAGATACTAAAGACAGTTCTGAGT 60.363 40.741 25.41 8.89 46.42 3.41
3368 3967 4.131596 TGCCTATAAATTCAACCGCTACC 58.868 43.478 0.00 0.00 0.00 3.18
3371 3970 2.618709 GCTGCCTATAAATTCAACCGCT 59.381 45.455 0.00 0.00 0.00 5.52
3541 4147 2.272146 GCAGGCGATTCTTCCCCA 59.728 61.111 0.00 0.00 0.00 4.96
3553 4159 1.749634 AGAAATGCAGAATCAGCAGGC 59.250 47.619 6.47 0.00 46.36 4.85
3632 4238 9.520515 AGATAACAACTGTTTTATGTCCAATCT 57.479 29.630 0.00 0.00 39.31 2.40
3638 4244 6.736853 GCACGAGATAACAACTGTTTTATGTC 59.263 38.462 0.00 14.93 39.31 3.06


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

AutoCloner maintained by Alex Coulton.