Multiple sequence alignment - TraesCS7A01G297600

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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 TraesCS7A01G297600 chr7A 100.000 2443 0 0 1402 3844 401428496 401426054 0.000000e+00 4512.0
1 TraesCS7A01G297600 chr7A 99.656 1746 6 0 1402 3147 20207201 20205456 0.000000e+00 3192.0
2 TraesCS7A01G297600 chr7A 100.000 1141 0 0 1 1141 401429897 401428757 0.000000e+00 2108.0
3 TraesCS7A01G297600 chr7A 81.612 707 86 25 57 739 65363414 65364100 2.610000e-151 545.0
4 TraesCS7A01G297600 chr7A 83.419 585 83 7 3274 3844 315506695 315506111 7.310000e-147 531.0
5 TraesCS7A01G297600 chr7A 98.400 250 1 2 892 1141 20207520 20207274 1.640000e-118 436.0
6 TraesCS7A01G297600 chr7A 82.873 362 46 8 3377 3734 65378251 65378600 1.040000e-80 311.0
7 TraesCS7A01G297600 chr5B 98.239 1760 16 5 1402 3159 549943475 549941729 0.000000e+00 3064.0
8 TraesCS7A01G297600 chr5B 82.653 588 85 11 3274 3844 50330934 50331521 4.430000e-139 505.0
9 TraesCS7A01G297600 chr5B 82.792 308 42 8 296 599 187093516 187093816 8.190000e-67 265.0
10 TraesCS7A01G297600 chr5B 98.276 58 1 0 1084 1141 549943605 549943548 6.790000e-18 102.0
11 TraesCS7A01G297600 chr5B 81.818 121 18 4 750 869 50330639 50330756 8.790000e-17 99.0
12 TraesCS7A01G297600 chr5B 97.297 37 1 0 884 920 549944088 549944052 3.210000e-06 63.9
13 TraesCS7A01G297600 chr2A 96.625 1748 57 2 1402 3148 24961436 24959690 0.000000e+00 2900.0
14 TraesCS7A01G297600 chr2A 81.805 709 87 22 55 739 46358588 46359278 1.210000e-154 556.0
15 TraesCS7A01G297600 chr2A 82.393 585 89 8 3274 3844 679451677 679451093 7.420000e-137 497.0
16 TraesCS7A01G297600 chr2A 84.255 470 54 6 3274 3734 46359623 46360081 1.270000e-119 440.0
17 TraesCS7A01G297600 chr2A 92.713 247 8 6 895 1141 24961745 24961509 7.900000e-92 348.0
18 TraesCS7A01G297600 chr2B 98.708 1006 13 0 2144 3149 43266043 43265038 0.000000e+00 1786.0
19 TraesCS7A01G297600 chr2B 98.658 745 10 0 1402 2146 43268167 43267423 0.000000e+00 1321.0
20 TraesCS7A01G297600 chr2B 90.608 362 34 0 1893 2254 709858628 709858267 7.470000e-132 481.0
21 TraesCS7A01G297600 chr2B 98.864 88 1 0 1054 1141 43268327 43268240 1.430000e-34 158.0
22 TraesCS7A01G297600 chr2B 88.136 118 13 1 3156 3273 16293298 16293182 5.180000e-29 139.0
23 TraesCS7A01G297600 chr2B 86.667 120 4 1 896 1015 43268825 43268718 5.220000e-24 122.0
24 TraesCS7A01G297600 chr2B 83.065 124 18 2 746 869 16293425 16293305 4.060000e-20 110.0
25 TraesCS7A01G297600 chr7B 96.346 903 33 0 2248 3150 495718727 495719629 0.000000e+00 1485.0
26 TraesCS7A01G297600 chr7D 92.155 905 69 2 2254 3157 169442840 169441937 0.000000e+00 1277.0
27 TraesCS7A01G297600 chr7D 90.707 495 38 4 1404 1891 169443798 169443305 0.000000e+00 652.0
28 TraesCS7A01G297600 chr7D 90.505 495 38 5 1404 1891 109600970 109600478 0.000000e+00 645.0
29 TraesCS7A01G297600 chr7D 91.160 362 32 0 1893 2254 109600446 109600085 3.450000e-135 492.0
30 TraesCS7A01G297600 chr4B 91.750 897 72 2 2254 3149 495131571 495132466 0.000000e+00 1245.0
31 TraesCS7A01G297600 chr4B 91.086 359 28 3 1896 2254 495131145 495131499 2.080000e-132 483.0
32 TraesCS7A01G297600 chr4B 85.079 315 34 10 294 603 587076089 587075783 3.730000e-80 309.0
33 TraesCS7A01G297600 chr2D 91.160 905 71 5 2254 3156 16490644 16489747 0.000000e+00 1219.0
34 TraesCS7A01G297600 chr2D 87.081 209 24 3 397 603 339494311 339494518 2.310000e-57 233.0
35 TraesCS7A01G297600 chr3A 90.022 902 87 3 2254 3153 742794945 742795845 0.000000e+00 1164.0
36 TraesCS7A01G297600 chr6B 90.046 874 63 13 1 873 551053361 551054211 0.000000e+00 1110.0
37 TraesCS7A01G297600 chr6B 93.598 453 27 2 3153 3604 551054210 551054661 0.000000e+00 675.0
38 TraesCS7A01G297600 chr6B 97.101 69 2 0 3776 3844 551054693 551054761 2.430000e-22 117.0
39 TraesCS7A01G297600 chr3B 90.946 497 35 5 1404 1891 64791543 64791048 0.000000e+00 660.0
40 TraesCS7A01G297600 chrUn 90.707 495 38 4 1404 1891 94835250 94834757 0.000000e+00 652.0
41 TraesCS7A01G297600 chrUn 90.909 363 31 2 1893 2254 94834725 94834364 1.610000e-133 486.0
42 TraesCS7A01G297600 chr1D 90.505 495 39 4 1404 1891 464289522 464290015 0.000000e+00 647.0
43 TraesCS7A01G297600 chr1D 90.331 362 35 0 1893 2254 464290047 464290408 3.470000e-130 475.0
44 TraesCS7A01G297600 chr6D 82.436 706 87 24 55 739 135106360 135105671 1.990000e-162 582.0
45 TraesCS7A01G297600 chr6D 84.435 469 54 8 3274 3737 135105328 135104874 9.800000e-121 444.0
46 TraesCS7A01G297600 chr6D 83.940 467 57 6 3274 3734 77673668 77674122 7.630000e-117 431.0
47 TraesCS7A01G297600 chr1B 80.972 741 99 21 19 739 469211688 469210970 2.020000e-152 549.0
48 TraesCS7A01G297600 chr1B 84.295 312 43 6 294 603 393652233 393652540 2.240000e-77 300.0
49 TraesCS7A01G297600 chr1B 85.124 121 15 3 750 869 469210920 469210802 1.880000e-23 121.0
50 TraesCS7A01G297600 chr4D 81.303 706 91 22 55 737 403165735 403166422 5.650000e-148 534.0
51 TraesCS7A01G297600 chr4D 87.081 209 24 3 397 603 330122356 330122563 2.310000e-57 233.0
52 TraesCS7A01G297600 chr3D 83.476 466 61 6 3274 3734 438173210 438173664 1.650000e-113 420.0
53 TraesCS7A01G297600 chr3D 86.603 209 25 3 397 603 547600280 547600487 1.070000e-55 228.0
54 TraesCS7A01G297600 chr5D 88.983 118 13 0 3156 3273 44080004 44080121 3.090000e-31 147.0
55 TraesCS7A01G297600 chr5D 82.677 127 21 1 743 869 44079872 44079997 1.130000e-20 111.0
56 TraesCS7A01G297600 chr1A 88.596 114 13 0 3158 3271 224730769 224730656 5.180000e-29 139.0
57 TraesCS7A01G297600 chr1A 84.921 126 15 3 746 869 224730901 224730778 1.450000e-24 124.0
58 TraesCS7A01G297600 chr6A 85.593 118 17 0 3156 3273 254302534 254302417 1.450000e-24 124.0
59 TraesCS7A01G297600 chr6A 84.874 119 17 1 751 869 254302658 254302541 6.750000e-23 119.0


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 TraesCS7A01G297600 chr7A 401426054 401429897 3843 True 3310.000000 4512 100.000000 1 3844 2 chr7A.!!$R3 3843
1 TraesCS7A01G297600 chr7A 20205456 20207520 2064 True 1814.000000 3192 99.028000 892 3147 2 chr7A.!!$R2 2255
2 TraesCS7A01G297600 chr7A 65363414 65364100 686 False 545.000000 545 81.612000 57 739 1 chr7A.!!$F1 682
3 TraesCS7A01G297600 chr7A 315506111 315506695 584 True 531.000000 531 83.419000 3274 3844 1 chr7A.!!$R1 570
4 TraesCS7A01G297600 chr5B 549941729 549944088 2359 True 1076.633333 3064 97.937333 884 3159 3 chr5B.!!$R1 2275
5 TraesCS7A01G297600 chr5B 50330639 50331521 882 False 302.000000 505 82.235500 750 3844 2 chr5B.!!$F2 3094
6 TraesCS7A01G297600 chr2A 24959690 24961745 2055 True 1624.000000 2900 94.669000 895 3148 2 chr2A.!!$R2 2253
7 TraesCS7A01G297600 chr2A 46358588 46360081 1493 False 498.000000 556 83.030000 55 3734 2 chr2A.!!$F1 3679
8 TraesCS7A01G297600 chr2A 679451093 679451677 584 True 497.000000 497 82.393000 3274 3844 1 chr2A.!!$R1 570
9 TraesCS7A01G297600 chr2B 43265038 43268825 3787 True 846.750000 1786 95.724250 896 3149 4 chr2B.!!$R3 2253
10 TraesCS7A01G297600 chr7B 495718727 495719629 902 False 1485.000000 1485 96.346000 2248 3150 1 chr7B.!!$F1 902
11 TraesCS7A01G297600 chr7D 169441937 169443798 1861 True 964.500000 1277 91.431000 1404 3157 2 chr7D.!!$R2 1753
12 TraesCS7A01G297600 chr7D 109600085 109600970 885 True 568.500000 645 90.832500 1404 2254 2 chr7D.!!$R1 850
13 TraesCS7A01G297600 chr4B 495131145 495132466 1321 False 864.000000 1245 91.418000 1896 3149 2 chr4B.!!$F1 1253
14 TraesCS7A01G297600 chr2D 16489747 16490644 897 True 1219.000000 1219 91.160000 2254 3156 1 chr2D.!!$R1 902
15 TraesCS7A01G297600 chr3A 742794945 742795845 900 False 1164.000000 1164 90.022000 2254 3153 1 chr3A.!!$F1 899
16 TraesCS7A01G297600 chr6B 551053361 551054761 1400 False 634.000000 1110 93.581667 1 3844 3 chr6B.!!$F1 3843
17 TraesCS7A01G297600 chrUn 94834364 94835250 886 True 569.000000 652 90.808000 1404 2254 2 chrUn.!!$R1 850
18 TraesCS7A01G297600 chr1D 464289522 464290408 886 False 561.000000 647 90.418000 1404 2254 2 chr1D.!!$F1 850
19 TraesCS7A01G297600 chr6D 135104874 135106360 1486 True 513.000000 582 83.435500 55 3737 2 chr6D.!!$R1 3682
20 TraesCS7A01G297600 chr1B 469210802 469211688 886 True 335.000000 549 83.048000 19 869 2 chr1B.!!$R1 850
21 TraesCS7A01G297600 chr4D 403165735 403166422 687 False 534.000000 534 81.303000 55 737 1 chr4D.!!$F2 682

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
226 231 1.051556 GGAGGAGCGAGGGGAGAAAT 61.052 60.0 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3196 5456 5.538813 TGGGTCACCATATAGACATGAGTAC 59.461 44.0 0.0 0.0 43.37 2.73 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
17 18 3.007323 GTTCTACGCCCCCAGGGT 61.007 66.667 4.22 0.00 46.51 4.34
80 81 1.614711 GGAGGCATGGTGGATTCCA 59.385 57.895 0.00 0.00 42.01 3.53
98 99 2.170397 TCCAGCTGATTTTGGAGCGATA 59.830 45.455 17.39 0.00 38.53 2.92
135 136 4.396166 CCTCGAACTAAAGAATGCCACAAT 59.604 41.667 0.00 0.00 0.00 2.71
176 177 7.642669 TCAGTGCTTCACTATTTTCTTTCAAG 58.357 34.615 0.00 0.00 43.43 3.02
190 191 1.895020 TTCAAGTCGGCCGCCTATGT 61.895 55.000 23.51 0.00 0.00 2.29
195 196 1.901948 TCGGCCGCCTATGTAGGAG 60.902 63.158 23.51 6.56 46.63 3.69
226 231 1.051556 GGAGGAGCGAGGGGAGAAAT 61.052 60.000 0.00 0.00 0.00 2.17
271 276 2.859538 GTGCAACATCCATATTTTGCGG 59.140 45.455 0.00 0.00 46.96 5.69
280 285 3.383185 TCCATATTTTGCGGGGTTCAATC 59.617 43.478 0.00 0.00 0.00 2.67
293 298 7.600752 TGCGGGGTTCAATCTTTTTATTTAAAG 59.399 33.333 0.00 0.00 36.64 1.85
334 350 8.794335 AAACTAAACATCCTAGAAATCAGGAC 57.206 34.615 0.00 0.00 44.89 3.85
350 366 2.805671 CAGGACGTGACACAATGCTAAA 59.194 45.455 6.37 0.00 0.00 1.85
364 380 7.814107 ACACAATGCTAAAAACATATGAAGTGG 59.186 33.333 10.38 0.00 0.00 4.00
383 400 4.889409 AGTGGCACCCATATCAAATGTAAG 59.111 41.667 15.27 0.00 35.28 2.34
384 401 4.887071 GTGGCACCCATATCAAATGTAAGA 59.113 41.667 6.29 0.00 35.28 2.10
386 403 6.040842 GTGGCACCCATATCAAATGTAAGAAT 59.959 38.462 6.29 0.00 35.28 2.40
388 405 7.782168 TGGCACCCATATCAAATGTAAGAATAA 59.218 33.333 0.00 0.00 0.00 1.40
389 406 8.299570 GGCACCCATATCAAATGTAAGAATAAG 58.700 37.037 0.00 0.00 0.00 1.73
390 407 8.299570 GCACCCATATCAAATGTAAGAATAAGG 58.700 37.037 0.00 0.00 0.00 2.69
511 534 7.339212 TGCTATGTTTTGTAGCACCATTCTATT 59.661 33.333 3.89 0.00 46.92 1.73
550 573 5.978814 TGCTGAGAAATAGGAGTAAGAACC 58.021 41.667 0.00 0.00 0.00 3.62
571 594 6.144078 ACCGAAAAATCAACAAAGCTTAGT 57.856 33.333 0.00 0.00 0.00 2.24
582 605 8.425577 TCAACAAAGCTTAGTAGAAGATATGC 57.574 34.615 0.00 0.00 0.00 3.14
618 643 1.343465 TCAGACCCTCGAGTTGAAACC 59.657 52.381 12.31 0.00 0.00 3.27
675 702 5.885230 TGCCTATCAATGAACTTCTTGTG 57.115 39.130 0.00 0.00 0.00 3.33
677 704 4.702131 GCCTATCAATGAACTTCTTGTGGT 59.298 41.667 0.00 0.00 0.00 4.16
680 707 5.954296 ATCAATGAACTTCTTGTGGTCTG 57.046 39.130 0.00 0.00 0.00 3.51
682 709 5.059161 TCAATGAACTTCTTGTGGTCTGAG 58.941 41.667 0.00 0.00 0.00 3.35
683 710 4.696479 ATGAACTTCTTGTGGTCTGAGT 57.304 40.909 0.00 0.00 0.00 3.41
684 711 3.797039 TGAACTTCTTGTGGTCTGAGTG 58.203 45.455 0.00 0.00 0.00 3.51
685 712 3.197766 TGAACTTCTTGTGGTCTGAGTGT 59.802 43.478 0.00 0.00 0.00 3.55
686 713 3.460857 ACTTCTTGTGGTCTGAGTGTC 57.539 47.619 0.00 0.00 0.00 3.67
687 714 3.034635 ACTTCTTGTGGTCTGAGTGTCT 58.965 45.455 0.00 0.00 0.00 3.41
688 715 3.181471 ACTTCTTGTGGTCTGAGTGTCTG 60.181 47.826 0.00 0.00 0.00 3.51
689 716 2.666317 TCTTGTGGTCTGAGTGTCTGA 58.334 47.619 0.00 0.00 0.00 3.27
690 717 2.362397 TCTTGTGGTCTGAGTGTCTGAC 59.638 50.000 0.00 0.00 42.38 3.51
705 732 4.032217 GTGTCTGACATTGAGAAGCATACG 59.968 45.833 14.37 0.00 0.00 3.06
713 740 6.112734 ACATTGAGAAGCATACGATGGTAAA 58.887 36.000 0.00 0.00 40.65 2.01
714 741 6.258727 ACATTGAGAAGCATACGATGGTAAAG 59.741 38.462 0.00 0.00 40.65 1.85
716 743 3.467803 AGAAGCATACGATGGTAAAGCC 58.532 45.455 10.59 0.34 40.65 4.35
730 757 5.765510 TGGTAAAGCCATTCACCAGATTAT 58.234 37.500 0.00 0.00 43.61 1.28
739 766 6.238759 GCCATTCACCAGATTATCACCTTAAC 60.239 42.308 0.00 0.00 0.00 2.01
740 767 6.017934 CCATTCACCAGATTATCACCTTAACG 60.018 42.308 0.00 0.00 0.00 3.18
744 818 5.989168 CACCAGATTATCACCTTAACGCATA 59.011 40.000 0.00 0.00 0.00 3.14
749 823 6.874134 AGATTATCACCTTAACGCATATCCAC 59.126 38.462 0.00 0.00 0.00 4.02
756 830 5.057149 CCTTAACGCATATCCACTAAAGCT 58.943 41.667 0.00 0.00 0.00 3.74
757 831 5.527582 CCTTAACGCATATCCACTAAAGCTT 59.472 40.000 0.00 0.00 0.00 3.74
763 837 5.266242 GCATATCCACTAAAGCTTTTGTCG 58.734 41.667 21.07 15.92 0.00 4.35
838 912 8.902806 AGATCACTTAAATTCTGTTGTCAAACA 58.097 29.630 0.00 0.00 44.06 2.83
839 913 9.683069 GATCACTTAAATTCTGTTGTCAAACAT 57.317 29.630 0.00 0.00 45.12 2.71
841 915 8.681806 TCACTTAAATTCTGTTGTCAAACATCA 58.318 29.630 0.00 0.00 45.12 3.07
842 916 9.299963 CACTTAAATTCTGTTGTCAAACATCAA 57.700 29.630 0.00 0.00 45.12 2.57
861 935 6.100859 ACATCAATTATGTCTCAGGTCCTCAT 59.899 38.462 0.00 0.00 46.15 2.90
869 943 5.005740 TGTCTCAGGTCCTCATTCAAATTG 58.994 41.667 0.00 0.00 0.00 2.32
870 944 5.006386 GTCTCAGGTCCTCATTCAAATTGT 58.994 41.667 0.00 0.00 0.00 2.71
872 946 6.655003 GTCTCAGGTCCTCATTCAAATTGTAA 59.345 38.462 0.00 0.00 0.00 2.41
873 947 6.655003 TCTCAGGTCCTCATTCAAATTGTAAC 59.345 38.462 0.00 0.00 0.00 2.50
874 948 5.411361 TCAGGTCCTCATTCAAATTGTAACG 59.589 40.000 0.00 0.00 0.00 3.18
879 953 6.801862 GTCCTCATTCAAATTGTAACGGAAAG 59.198 38.462 0.00 0.00 0.00 2.62
880 954 6.072175 TCCTCATTCAAATTGTAACGGAAAGG 60.072 38.462 0.00 0.00 0.00 3.11
881 955 6.019779 TCATTCAAATTGTAACGGAAAGGG 57.980 37.500 0.00 0.00 0.00 3.95
882 956 5.770663 TCATTCAAATTGTAACGGAAAGGGA 59.229 36.000 0.00 0.00 0.00 4.20
3223 5483 4.968719 TCATGTCTATATGGTGACCCAAGT 59.031 41.667 0.00 0.00 46.04 3.16
3234 5494 1.697432 TGACCCAAGTAAGGTGGTGAG 59.303 52.381 0.00 0.00 37.88 3.51
3239 5499 2.613977 CCAAGTAAGGTGGTGAGCAGAG 60.614 54.545 0.00 0.00 0.00 3.35
3248 5508 1.827344 TGGTGAGCAGAGTATGTCAGG 59.173 52.381 0.00 0.00 0.00 3.86
3249 5509 1.137872 GGTGAGCAGAGTATGTCAGGG 59.862 57.143 0.00 0.00 0.00 4.45
3271 5531 8.303876 CAGGGTAACTTTATTTTGTGCTTGTAT 58.696 33.333 0.00 0.00 0.00 2.29
3357 5617 1.300465 CTGCACTGTCGAGCACACT 60.300 57.895 0.00 0.00 36.62 3.55
3384 5644 1.686325 GCTAGGAGGCGGACCATGAA 61.686 60.000 0.00 0.00 39.06 2.57
3391 5651 2.549754 GAGGCGGACCATGAAATATGTG 59.450 50.000 0.00 0.00 39.06 3.21
3412 5672 6.484288 TGTGTAGATGTTTCATCTTCCCAAT 58.516 36.000 15.77 0.00 0.00 3.16
3456 5716 9.856162 ACTATTTTGTGGTTTTCCTAAAGTAGA 57.144 29.630 15.65 0.00 38.13 2.59
3525 5785 4.778534 ATTCCAGAACTTGAAGCATGTG 57.221 40.909 0.00 0.00 0.00 3.21
3568 5828 4.997395 TGAAATAGCTGGAGAAAGACACAC 59.003 41.667 0.00 0.00 0.00 3.82
3624 5884 7.530426 AAATTTCCAGCCATATCATTCCTAC 57.470 36.000 0.00 0.00 0.00 3.18
3626 5886 2.567169 TCCAGCCATATCATTCCTACCG 59.433 50.000 0.00 0.00 0.00 4.02
3650 5910 4.433615 TGACACTTTCAATAGAGATCGGC 58.566 43.478 0.00 0.00 0.00 5.54
3656 5916 0.244994 CAATAGAGATCGGCCGAGGG 59.755 60.000 33.87 11.82 0.00 4.30
3670 5930 1.471119 CGAGGGGCTACAACTGTCTA 58.529 55.000 0.00 0.00 0.00 2.59
3701 5961 1.140375 GCCAGCAGCATAAACAGCC 59.860 57.895 0.00 0.00 42.97 4.85
3702 5962 1.597797 GCCAGCAGCATAAACAGCCA 61.598 55.000 0.00 0.00 42.97 4.75
3719 5979 1.647545 CCAGCACATACCGCCAACAG 61.648 60.000 0.00 0.00 0.00 3.16
3738 5998 2.425668 CAGCAAGATCAATGATGCCACA 59.574 45.455 0.00 0.00 39.59 4.17
3744 6004 2.583024 TCAATGATGCCACACTGGAA 57.417 45.000 0.00 0.00 40.96 3.53
3757 6017 4.549458 CACACTGGAAGCTAATGGTTTTG 58.451 43.478 0.00 0.00 37.60 2.44
3761 6021 2.817258 TGGAAGCTAATGGTTTTGGACG 59.183 45.455 0.00 0.00 33.64 4.79
3766 6037 3.252458 AGCTAATGGTTTTGGACGACAAC 59.748 43.478 0.00 0.00 39.19 3.32
3812 6089 2.758009 ACGCGCTTTCTTGTAGGTTTA 58.242 42.857 5.73 0.00 0.00 2.01
3829 6106 8.871125 TGTAGGTTTAGCCCAAATTTTGAATTA 58.129 29.630 10.72 0.00 38.26 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.594725 TCTCTGACTAACTTGTGAGTTGACT 59.405 40.000 2.25 0.00 45.46 3.41
33 34 5.833082 TCTCTGACTAACTTGTGAGTTGAC 58.167 41.667 2.25 0.00 45.46 3.18
34 35 5.828328 TCTCTCTGACTAACTTGTGAGTTGA 59.172 40.000 2.25 0.00 45.46 3.18
66 67 0.394762 TCAGCTGGAATCCACCATGC 60.395 55.000 15.13 0.00 39.34 4.06
80 81 2.171448 AGGTATCGCTCCAAAATCAGCT 59.829 45.455 0.00 0.00 33.09 4.24
98 99 2.659610 GAGGAGCTTCGTGCAGGT 59.340 61.111 6.26 0.00 45.94 4.00
135 136 3.678072 GCACTGAGTTGATACGTTTGCTA 59.322 43.478 0.00 0.00 0.00 3.49
176 177 2.143594 CTCCTACATAGGCGGCCGAC 62.144 65.000 33.48 30.81 43.31 4.79
190 191 0.042131 TCCCTTTCGCTTCCCTCCTA 59.958 55.000 0.00 0.00 0.00 2.94
195 196 1.222113 CTCCTCCCTTTCGCTTCCC 59.778 63.158 0.00 0.00 0.00 3.97
226 231 8.816144 CACACAGCAAAGCTTTATTTCTTAAAA 58.184 29.630 12.25 0.00 36.40 1.52
271 276 9.502091 AAGCCTTTAAATAAAAAGATTGAACCC 57.498 29.630 0.00 0.00 38.50 4.11
318 334 4.023980 TGTCACGTCCTGATTTCTAGGAT 58.976 43.478 0.00 0.00 45.50 3.24
319 335 3.192844 GTGTCACGTCCTGATTTCTAGGA 59.807 47.826 0.00 0.00 41.91 2.94
334 350 7.020602 TCATATGTTTTTAGCATTGTGTCACG 58.979 34.615 1.90 0.00 0.00 4.35
350 366 3.168035 TGGGTGCCACTTCATATGTTT 57.832 42.857 1.90 0.00 0.00 2.83
364 380 8.299570 CCTTATTCTTACATTTGATATGGGTGC 58.700 37.037 0.00 0.00 0.00 5.01
456 479 1.202580 GGCATCCGTGTCTCATAGCTT 60.203 52.381 0.00 0.00 0.00 3.74
511 534 7.943079 TTCTCAGCATCTCAATTTTGGATAA 57.057 32.000 0.00 0.00 0.00 1.75
550 573 9.107367 CTTCTACTAAGCTTTGTTGATTTTTCG 57.893 33.333 20.97 6.88 0.00 3.46
582 605 6.238648 AGGGTCTGAAATTAGGTAACACTTG 58.761 40.000 0.00 0.00 41.41 3.16
650 677 7.318141 CACAAGAAGTTCATTGATAGGCATTT 58.682 34.615 16.84 0.00 0.00 2.32
653 680 4.701651 CCACAAGAAGTTCATTGATAGGCA 59.298 41.667 16.84 0.00 0.00 4.75
654 681 4.702131 ACCACAAGAAGTTCATTGATAGGC 59.298 41.667 16.84 0.00 0.00 3.93
655 682 6.093219 CAGACCACAAGAAGTTCATTGATAGG 59.907 42.308 16.84 15.94 0.00 2.57
656 683 6.875726 TCAGACCACAAGAAGTTCATTGATAG 59.124 38.462 16.84 9.90 0.00 2.08
657 684 6.768483 TCAGACCACAAGAAGTTCATTGATA 58.232 36.000 16.84 0.00 0.00 2.15
663 690 3.197766 ACACTCAGACCACAAGAAGTTCA 59.802 43.478 5.50 0.00 0.00 3.18
669 696 2.362397 GTCAGACACTCAGACCACAAGA 59.638 50.000 0.00 0.00 28.05 3.02
675 702 3.256879 TCTCAATGTCAGACACTCAGACC 59.743 47.826 5.05 0.00 32.69 3.85
677 704 4.560311 GCTTCTCAATGTCAGACACTCAGA 60.560 45.833 5.05 4.31 0.00 3.27
680 707 3.657634 TGCTTCTCAATGTCAGACACTC 58.342 45.455 5.05 0.00 0.00 3.51
682 709 4.032217 CGTATGCTTCTCAATGTCAGACAC 59.968 45.833 5.05 0.00 0.00 3.67
683 710 4.082245 TCGTATGCTTCTCAATGTCAGACA 60.082 41.667 5.50 5.50 0.00 3.41
684 711 4.424626 TCGTATGCTTCTCAATGTCAGAC 58.575 43.478 0.00 0.00 0.00 3.51
685 712 4.718940 TCGTATGCTTCTCAATGTCAGA 57.281 40.909 0.00 0.00 0.00 3.27
686 713 4.210746 CCATCGTATGCTTCTCAATGTCAG 59.789 45.833 0.00 0.00 0.00 3.51
687 714 4.122046 CCATCGTATGCTTCTCAATGTCA 58.878 43.478 0.00 0.00 0.00 3.58
688 715 4.122776 ACCATCGTATGCTTCTCAATGTC 58.877 43.478 0.00 0.00 0.00 3.06
689 716 4.142609 ACCATCGTATGCTTCTCAATGT 57.857 40.909 0.00 0.00 0.00 2.71
690 717 6.603237 TTTACCATCGTATGCTTCTCAATG 57.397 37.500 0.00 0.00 0.00 2.82
713 740 3.461085 AGGTGATAATCTGGTGAATGGCT 59.539 43.478 0.00 0.00 0.00 4.75
714 741 3.825328 AGGTGATAATCTGGTGAATGGC 58.175 45.455 0.00 0.00 0.00 4.40
716 743 6.511767 GCGTTAAGGTGATAATCTGGTGAATG 60.512 42.308 0.00 0.00 0.00 2.67
730 757 5.601583 TTAGTGGATATGCGTTAAGGTGA 57.398 39.130 0.00 0.00 0.00 4.02
739 766 5.235305 ACAAAAGCTTTAGTGGATATGCG 57.765 39.130 13.10 0.00 0.00 4.73
740 767 5.064707 TCGACAAAAGCTTTAGTGGATATGC 59.935 40.000 13.10 0.79 0.00 3.14
744 818 5.352569 CAGATCGACAAAAGCTTTAGTGGAT 59.647 40.000 13.10 12.84 33.14 3.41
749 823 4.668576 TGCAGATCGACAAAAGCTTTAG 57.331 40.909 13.10 4.94 0.00 1.85
756 830 3.189080 CAGGACATTGCAGATCGACAAAA 59.811 43.478 7.41 0.00 0.00 2.44
757 831 2.743664 CAGGACATTGCAGATCGACAAA 59.256 45.455 7.41 0.00 0.00 2.83
763 837 6.500684 TTCTTAAACAGGACATTGCAGATC 57.499 37.500 0.00 0.00 0.00 2.75
815 889 8.681806 TGATGTTTGACAACAGAATTTAAGTGA 58.318 29.630 0.00 0.00 46.25 3.41
838 912 6.760440 ATGAGGACCTGAGACATAATTGAT 57.240 37.500 0.00 0.00 0.00 2.57
839 913 6.156775 TGAATGAGGACCTGAGACATAATTGA 59.843 38.462 0.00 0.00 0.00 2.57
841 915 6.566079 TGAATGAGGACCTGAGACATAATT 57.434 37.500 0.00 0.00 0.00 1.40
842 916 6.566079 TTGAATGAGGACCTGAGACATAAT 57.434 37.500 0.00 0.00 0.00 1.28
844 918 6.566079 ATTTGAATGAGGACCTGAGACATA 57.434 37.500 0.00 0.00 0.00 2.29
849 923 6.402550 CGTTACAATTTGAATGAGGACCTGAG 60.403 42.308 0.00 0.00 0.00 3.35
861 935 7.832187 AGATATCCCTTTCCGTTACAATTTGAA 59.168 33.333 2.79 0.00 0.00 2.69
869 943 4.268797 GGGAGATATCCCTTTCCGTTAC 57.731 50.000 18.71 0.00 46.39 2.50
880 954 2.695585 AGGTTGACTGGGGAGATATCC 58.304 52.381 0.00 0.00 0.00 2.59
881 955 3.259625 GCTAGGTTGACTGGGGAGATATC 59.740 52.174 0.00 0.00 0.00 1.63
882 956 3.116551 AGCTAGGTTGACTGGGGAGATAT 60.117 47.826 0.00 0.00 0.00 1.63
3196 5456 5.538813 TGGGTCACCATATAGACATGAGTAC 59.461 44.000 0.00 0.00 43.37 2.73
3215 5475 1.610886 GCTCACCACCTTACTTGGGTC 60.611 57.143 0.00 0.00 38.59 4.46
3217 5477 0.400213 TGCTCACCACCTTACTTGGG 59.600 55.000 0.00 0.00 38.59 4.12
3223 5483 3.441101 ACATACTCTGCTCACCACCTTA 58.559 45.455 0.00 0.00 0.00 2.69
3234 5494 4.473477 AAGTTACCCTGACATACTCTGC 57.527 45.455 0.00 0.00 0.00 4.26
3239 5499 7.753580 GCACAAAATAAAGTTACCCTGACATAC 59.246 37.037 0.00 0.00 0.00 2.39
3296 5556 5.079689 TGACATCTCGCAAGTATGGTAAA 57.920 39.130 0.00 0.00 36.55 2.01
3343 5603 2.029666 GCCAGTGTGCTCGACAGT 59.970 61.111 0.00 0.00 38.93 3.55
3357 5617 3.790437 GCCTCCTAGCTGCAGCCA 61.790 66.667 34.39 21.64 43.38 4.75
3384 5644 8.274322 TGGGAAGATGAAACATCTACACATATT 58.726 33.333 13.45 0.00 0.00 1.28
3391 5651 6.382869 CCATTGGGAAGATGAAACATCTAC 57.617 41.667 13.45 10.04 35.59 2.59
3525 5785 1.503800 TAGGGGCTAGGTAAAGGCAC 58.496 55.000 0.00 0.00 45.50 5.01
3531 5791 5.248477 CAGCTATTTCATAGGGGCTAGGTAA 59.752 44.000 0.00 0.00 33.43 2.85
3598 5858 9.247861 GTAGGAATGATATGGCTGGAAATTTAT 57.752 33.333 0.00 0.00 0.00 1.40
3618 5878 3.823281 TGAAAGTGTCAACGGTAGGAA 57.177 42.857 0.00 0.00 31.51 3.36
3650 5910 1.218316 GACAGTTGTAGCCCCTCGG 59.782 63.158 0.00 0.00 0.00 4.63
3656 5916 2.432510 AGCCTGATAGACAGTTGTAGCC 59.567 50.000 0.00 0.00 44.40 3.93
3679 5939 2.089980 CTGTTTATGCTGCTGGCTCTT 58.910 47.619 0.00 0.00 42.39 2.85
3693 5953 1.732941 CGGTATGTGCTGGCTGTTTA 58.267 50.000 0.00 0.00 0.00 2.01
3701 5961 1.796151 CTGTTGGCGGTATGTGCTG 59.204 57.895 0.00 0.00 0.00 4.41
3702 5962 2.040544 GCTGTTGGCGGTATGTGCT 61.041 57.895 0.00 0.00 0.00 4.40
3719 5979 2.426024 AGTGTGGCATCATTGATCTTGC 59.574 45.455 0.00 0.00 0.00 4.01
3738 5998 3.826729 GTCCAAAACCATTAGCTTCCAGT 59.173 43.478 0.00 0.00 0.00 4.00
3744 6004 3.134574 TGTCGTCCAAAACCATTAGCT 57.865 42.857 0.00 0.00 0.00 3.32
3757 6017 3.849911 TGAATCTCTGATGTTGTCGTCC 58.150 45.455 0.00 0.00 0.00 4.79
3812 6089 6.836242 TCTTTGGTAATTCAAAATTTGGGCT 58.164 32.000 5.83 0.00 36.37 5.19


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

AutoCloner maintained by Alex Coulton.