Multiple sequence alignment - TraesCS7D01G529900

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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 TraesCS7D01G529900 chr7D 100.000 3729 0 0 1 3729 625122613 625118885 0.000000e+00 6887.0
1 TraesCS7D01G529900 chr7D 86.088 1222 131 17 1257 2457 625369916 625368713 0.000000e+00 1279.0
2 TraesCS7D01G529900 chr7D 80.272 588 77 23 2463 3041 625368673 625368116 1.250000e-109 407.0
3 TraesCS7D01G529900 chr7D 80.556 144 19 5 3044 3187 625109659 625109525 6.590000e-18 102.0
4 TraesCS7D01G529900 chr7D 95.238 42 2 0 3603 3644 624904878 624904837 2.400000e-07 67.6
5 TraesCS7D01G529900 chr7A 93.584 2182 114 10 887 3049 720953396 720955570 0.000000e+00 3230.0
6 TraesCS7D01G529900 chr7A 84.497 1361 168 27 2063 3403 721023994 721022657 0.000000e+00 1304.0
7 TraesCS7D01G529900 chr7A 81.852 810 90 26 1257 2045 721024719 721023946 2.440000e-176 628.0
8 TraesCS7D01G529900 chr7A 90.716 377 24 6 3113 3485 720955576 720955945 3.350000e-135 492.0
9 TraesCS7D01G529900 chr7A 88.936 235 23 3 3496 3729 721021603 721021371 1.690000e-73 287.0
10 TraesCS7D01G529900 chr7B 91.561 1659 106 7 910 2544 724168293 724169941 0.000000e+00 2257.0
11 TraesCS7D01G529900 chr7B 84.599 1422 158 27 1072 2458 724982806 724981411 0.000000e+00 1356.0
12 TraesCS7D01G529900 chr7B 88.095 924 44 16 1 872 724072618 724073527 0.000000e+00 1037.0
13 TraesCS7D01G529900 chr7B 87.879 924 46 16 1 872 724120532 724121441 0.000000e+00 1026.0
14 TraesCS7D01G529900 chr7B 83.213 971 113 22 1074 2017 724401361 724402308 0.000000e+00 845.0
15 TraesCS7D01G529900 chr7B 82.635 1002 129 23 1072 2045 724791128 724792112 0.000000e+00 845.0
16 TraesCS7D01G529900 chr7B 81.263 998 143 21 1074 2045 724285349 724286328 0.000000e+00 767.0
17 TraesCS7D01G529900 chr7B 84.774 729 68 23 2533 3257 724286762 724287451 0.000000e+00 691.0
18 TraesCS7D01G529900 chr7B 84.341 728 70 21 2533 3257 724792546 724793232 0.000000e+00 673.0
19 TraesCS7D01G529900 chr7B 91.408 419 22 7 2574 2986 724169938 724170348 2.510000e-156 562.0
20 TraesCS7D01G529900 chr7B 83.245 376 44 11 3029 3400 724402886 724403246 9.990000e-86 327.0
21 TraesCS7D01G529900 chr7B 88.333 240 19 8 3496 3729 724288260 724288496 2.840000e-71 279.0
22 TraesCS7D01G529900 chr7B 88.614 202 21 2 3496 3696 724794049 724794249 1.030000e-60 244.0
23 TraesCS7D01G529900 chr7B 80.180 333 53 11 1269 1599 648904800 648905121 1.730000e-58 237.0
24 TraesCS7D01G529900 chr7B 88.889 189 18 3 3496 3683 724969669 724969483 2.900000e-56 230.0
25 TraesCS7D01G529900 chr7B 85.350 157 20 2 2464 2620 723972066 723972219 3.850000e-35 159.0
26 TraesCS7D01G529900 chr7B 78.788 264 37 12 3047 3303 724980797 724980546 3.850000e-35 159.0
27 TraesCS7D01G529900 chr7B 84.277 159 20 3 2463 2619 724981373 724981218 2.320000e-32 150.0
28 TraesCS7D01G529900 chrUn 82.808 1396 183 29 1095 2458 87734020 87735390 0.000000e+00 1195.0
29 TraesCS7D01G529900 chrUn 83.951 972 104 19 1074 2017 93228089 93229036 0.000000e+00 883.0
30 TraesCS7D01G529900 chrUn 93.056 216 15 0 3514 3729 93232520 93232735 2.160000e-82 316.0
31 TraesCS7D01G529900 chrUn 83.871 155 21 2 2463 2616 87735429 87735580 1.080000e-30 145.0
32 TraesCS7D01G529900 chr6A 79.374 543 69 24 2510 3041 493360735 493360225 3.570000e-90 342.0
33 TraesCS7D01G529900 chr1A 78.220 528 76 25 2507 3023 253945380 253945879 6.050000e-78 302.0
34 TraesCS7D01G529900 chr2A 78.671 286 45 11 2537 2819 223888548 223888820 3.830000e-40 176.0


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 TraesCS7D01G529900 chr7D 625118885 625122613 3728 True 6887.000000 6887 100.000000 1 3729 1 chr7D.!!$R3 3728
1 TraesCS7D01G529900 chr7D 625368116 625369916 1800 True 843.000000 1279 83.180000 1257 3041 2 chr7D.!!$R4 1784
2 TraesCS7D01G529900 chr7A 720953396 720955945 2549 False 1861.000000 3230 92.150000 887 3485 2 chr7A.!!$F1 2598
3 TraesCS7D01G529900 chr7A 721021371 721024719 3348 True 739.666667 1304 85.095000 1257 3729 3 chr7A.!!$R1 2472
4 TraesCS7D01G529900 chr7B 724168293 724170348 2055 False 1409.500000 2257 91.484500 910 2986 2 chr7B.!!$F5 2076
5 TraesCS7D01G529900 chr7B 724072618 724073527 909 False 1037.000000 1037 88.095000 1 872 1 chr7B.!!$F3 871
6 TraesCS7D01G529900 chr7B 724120532 724121441 909 False 1026.000000 1026 87.879000 1 872 1 chr7B.!!$F4 871
7 TraesCS7D01G529900 chr7B 724791128 724794249 3121 False 587.333333 845 85.196667 1072 3696 3 chr7B.!!$F8 2624
8 TraesCS7D01G529900 chr7B 724401361 724403246 1885 False 586.000000 845 83.229000 1074 3400 2 chr7B.!!$F7 2326
9 TraesCS7D01G529900 chr7B 724285349 724288496 3147 False 579.000000 767 84.790000 1074 3729 3 chr7B.!!$F6 2655
10 TraesCS7D01G529900 chr7B 724980546 724982806 2260 True 555.000000 1356 82.554667 1072 3303 3 chr7B.!!$R2 2231
11 TraesCS7D01G529900 chrUn 87734020 87735580 1560 False 670.000000 1195 83.339500 1095 2616 2 chrUn.!!$F1 1521
12 TraesCS7D01G529900 chrUn 93228089 93232735 4646 False 599.500000 883 88.503500 1074 3729 2 chrUn.!!$F2 2655
13 TraesCS7D01G529900 chr6A 493360225 493360735 510 True 342.000000 342 79.374000 2510 3041 1 chr6A.!!$R1 531

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
571 617 0.179084 AGTCCACCACACAGACAACG 60.179 55.000 0.00 0.0 32.82 4.10 F
629 675 0.891449 TCGGATCGCCTCTCCTCATC 60.891 60.000 0.00 0.0 0.00 2.92 F
900 953 0.996462 CACAAGTACGCATACCCACG 59.004 55.000 0.00 0.0 30.88 4.94 F
908 961 1.214325 GCATACCCACGGGCAAAAC 59.786 57.895 0.69 0.0 39.32 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2296 1.402968 CCAGACCAAAATCATCAGCCG 59.597 52.381 0.00 0.0 0.0 5.52 R
2514 2778 2.232941 AGCCAAATTCAAGCAGACATGG 59.767 45.455 0.00 0.0 0.0 3.66 R
2543 2807 2.943690 ACATGCATTCATCAGTCAGAGC 59.056 45.455 0.00 0.0 0.0 4.09 R
2828 3109 6.295236 GCTTATAATTCCCATGGCTGCAAATA 60.295 38.462 6.09 0.0 0.0 1.40 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
25 26 2.046892 CAAGCACCACCTCCCTCG 60.047 66.667 0.00 0.00 0.00 4.63
36 37 2.284405 TCCCTCGGACCCTTCACC 60.284 66.667 0.00 0.00 0.00 4.02
42 43 4.097361 GGACCCTTCACCGGAGCC 62.097 72.222 9.46 0.00 0.00 4.70
45 46 3.322466 CCCTTCACCGGAGCCAGT 61.322 66.667 9.46 0.00 0.00 4.00
189 227 2.912295 TCCTCCATCAACACATCCTTCA 59.088 45.455 0.00 0.00 0.00 3.02
192 230 3.534554 TCCATCAACACATCCTTCATCG 58.465 45.455 0.00 0.00 0.00 3.84
216 254 3.173151 TCCTTGTCATTGCACTAGGAGA 58.827 45.455 12.02 0.00 41.61 3.71
223 261 5.188555 TGTCATTGCACTAGGAGAAGATCTT 59.811 40.000 7.95 7.95 0.00 2.40
225 263 3.533606 TGCACTAGGAGAAGATCTTGC 57.466 47.619 14.00 8.76 0.00 4.01
226 264 2.169352 TGCACTAGGAGAAGATCTTGCC 59.831 50.000 14.00 13.78 0.00 4.52
283 321 1.938657 TTCCGCAGCTTCTCCTCTCG 61.939 60.000 0.00 0.00 0.00 4.04
291 329 1.002251 GCTTCTCCTCTCGTATCACCG 60.002 57.143 0.00 0.00 0.00 4.94
328 366 1.587568 TCGTCGCTCGAATTGGGAA 59.412 52.632 0.00 0.00 45.98 3.97
340 378 6.293135 GCTCGAATTGGGAAGAAATGTATCTC 60.293 42.308 0.00 0.00 0.00 2.75
403 448 2.428530 GGGATTTGCTCAACAATCCTCC 59.571 50.000 10.09 2.22 38.31 4.30
412 457 2.501723 TCAACAATCCTCCTGGTAGAGC 59.498 50.000 0.00 0.00 32.17 4.09
429 474 1.559682 GAGCTAATCAACCCCACTCCA 59.440 52.381 0.00 0.00 0.00 3.86
442 487 4.923942 CTCCAGCATCGCCGCCAT 62.924 66.667 0.00 0.00 0.00 4.40
452 497 4.241999 GCCGCCATGTGCATCGAC 62.242 66.667 0.00 0.00 41.33 4.20
571 617 0.179084 AGTCCACCACACAGACAACG 60.179 55.000 0.00 0.00 32.82 4.10
572 618 1.145156 TCCACCACACAGACAACGG 59.855 57.895 0.00 0.00 0.00 4.44
574 620 2.203153 ACCACACAGACAACGGCC 60.203 61.111 0.00 0.00 0.00 6.13
575 621 2.111043 CCACACAGACAACGGCCT 59.889 61.111 0.00 0.00 0.00 5.19
576 622 1.961277 CCACACAGACAACGGCCTC 60.961 63.158 0.00 0.00 0.00 4.70
577 623 1.961277 CACACAGACAACGGCCTCC 60.961 63.158 0.00 0.00 0.00 4.30
609 655 2.278206 CCACGGCGTCTCTGATCG 60.278 66.667 10.85 0.00 0.00 3.69
626 672 2.899044 CGTCGGATCGCCTCTCCTC 61.899 68.421 0.00 0.00 0.00 3.71
627 673 1.824329 GTCGGATCGCCTCTCCTCA 60.824 63.158 0.00 0.00 0.00 3.86
628 674 1.151679 TCGGATCGCCTCTCCTCAT 59.848 57.895 0.00 0.00 0.00 2.90
629 675 0.891449 TCGGATCGCCTCTCCTCATC 60.891 60.000 0.00 0.00 0.00 2.92
630 676 1.175347 CGGATCGCCTCTCCTCATCA 61.175 60.000 0.00 0.00 0.00 3.07
631 677 1.043816 GGATCGCCTCTCCTCATCAA 58.956 55.000 0.00 0.00 0.00 2.57
632 678 1.622811 GGATCGCCTCTCCTCATCAAT 59.377 52.381 0.00 0.00 0.00 2.57
635 681 3.229697 TCGCCTCTCCTCATCAATAGA 57.770 47.619 0.00 0.00 0.00 1.98
640 686 5.418676 GCCTCTCCTCATCAATAGATTAGC 58.581 45.833 0.00 0.00 30.20 3.09
735 781 4.279922 CCTTCCTCCGGTAATTGTTTGTTT 59.720 41.667 0.00 0.00 0.00 2.83
775 821 9.707957 TTTTGTGGGTATGAATATTCATTACCT 57.292 29.630 30.60 13.72 45.13 3.08
819 872 4.399618 TCAATTCTTGTCCGTTGTTTTCCA 59.600 37.500 0.00 0.00 0.00 3.53
823 876 3.118334 TCTTGTCCGTTGTTTTCCAGGTA 60.118 43.478 0.00 0.00 0.00 3.08
826 879 3.816523 TGTCCGTTGTTTTCCAGGTATTC 59.183 43.478 0.00 0.00 0.00 1.75
832 885 5.704053 CGTTGTTTTCCAGGTATTCTTAGGT 59.296 40.000 0.00 0.00 0.00 3.08
840 893 4.501058 CCAGGTATTCTTAGGTAACCTCGC 60.501 50.000 0.00 0.00 38.51 5.03
841 894 3.317430 AGGTATTCTTAGGTAACCTCGCG 59.683 47.826 0.00 0.00 35.67 5.87
842 895 3.316308 GGTATTCTTAGGTAACCTCGCGA 59.684 47.826 9.26 9.26 34.61 5.87
872 925 9.819267 TTTATTTTAAATCCGTTGTTTTCAGGT 57.181 25.926 0.00 0.00 0.00 4.00
875 928 6.563222 TTAAATCCGTTGTTTTCAGGTAGG 57.437 37.500 0.00 0.00 0.00 3.18
876 929 4.360951 AATCCGTTGTTTTCAGGTAGGA 57.639 40.909 0.00 0.00 0.00 2.94
877 930 4.569719 ATCCGTTGTTTTCAGGTAGGAT 57.430 40.909 0.00 0.00 32.91 3.24
878 931 5.687166 ATCCGTTGTTTTCAGGTAGGATA 57.313 39.130 0.00 0.00 35.69 2.59
879 932 5.687166 TCCGTTGTTTTCAGGTAGGATAT 57.313 39.130 0.00 0.00 0.00 1.63
880 933 5.667466 TCCGTTGTTTTCAGGTAGGATATC 58.333 41.667 0.00 0.00 0.00 1.63
881 934 4.814771 CCGTTGTTTTCAGGTAGGATATCC 59.185 45.833 14.41 14.41 0.00 2.59
882 935 5.424757 CGTTGTTTTCAGGTAGGATATCCA 58.575 41.667 23.81 7.13 38.89 3.41
883 936 5.293569 CGTTGTTTTCAGGTAGGATATCCAC 59.706 44.000 23.81 17.65 38.89 4.02
884 937 6.177610 GTTGTTTTCAGGTAGGATATCCACA 58.822 40.000 23.81 12.37 38.89 4.17
885 938 6.381498 TGTTTTCAGGTAGGATATCCACAA 57.619 37.500 23.81 5.97 38.89 3.33
886 939 6.414732 TGTTTTCAGGTAGGATATCCACAAG 58.585 40.000 23.81 14.02 38.89 3.16
887 940 6.012858 TGTTTTCAGGTAGGATATCCACAAGT 60.013 38.462 23.81 5.11 38.89 3.16
888 941 7.181305 TGTTTTCAGGTAGGATATCCACAAGTA 59.819 37.037 23.81 4.08 38.89 2.24
889 942 6.726490 TTCAGGTAGGATATCCACAAGTAC 57.274 41.667 23.81 15.42 38.89 2.73
899 952 1.066716 TCCACAAGTACGCATACCCAC 60.067 52.381 0.00 0.00 30.88 4.61
900 953 0.996462 CACAAGTACGCATACCCACG 59.004 55.000 0.00 0.00 30.88 4.94
908 961 1.214325 GCATACCCACGGGCAAAAC 59.786 57.895 0.69 0.00 39.32 2.43
945 1000 2.353208 CGCTAAGCCCATAGGAGATGTC 60.353 54.545 0.00 0.00 33.47 3.06
946 1001 2.903135 GCTAAGCCCATAGGAGATGTCT 59.097 50.000 0.00 0.00 33.47 3.41
1064 1122 1.894699 AACACTCCCCTAATCCCCTC 58.105 55.000 0.00 0.00 0.00 4.30
1441 1545 1.416813 CTTCTTCTACGGCAGCAGCG 61.417 60.000 0.00 0.00 43.41 5.18
1815 1934 3.793144 GAGCTTTGCGGAGTGGCG 61.793 66.667 0.00 0.00 35.06 5.69
1950 2111 4.245660 ACCTTGAATATCACGACTGTGTG 58.754 43.478 0.00 0.00 46.49 3.82
2111 2335 3.429492 TGGCTCATGGTTTTATTCAGCA 58.571 40.909 0.00 0.00 0.00 4.41
2155 2380 3.511146 TGCCAATTTTCAGAGGGATGAAC 59.489 43.478 0.00 0.00 38.87 3.18
2178 2403 1.402720 GGTGTTGGCATTCGATTGGTG 60.403 52.381 9.21 0.00 0.00 4.17
2494 2758 5.982356 TCTGATCGGAGTCAATTCTTCATT 58.018 37.500 0.00 0.00 0.00 2.57
2543 2807 4.562082 TGCTTGAATTTGGCTCTCATTTG 58.438 39.130 0.00 0.00 0.00 2.32
2719 2991 2.223044 GCATTGCTTAACCTCGTGTAGC 60.223 50.000 0.16 0.00 0.00 3.58
2744 3018 7.011109 GCGTTTGTGTTAAGGTACTATGATCAT 59.989 37.037 13.81 13.81 38.49 2.45
2745 3019 8.879759 CGTTTGTGTTAAGGTACTATGATCATT 58.120 33.333 14.65 0.00 38.49 2.57
2806 3087 1.137675 TCTCGAACATCATGCTGAGGG 59.862 52.381 3.02 0.00 31.56 4.30
2828 3109 9.722184 GAGGGTTAAACTTTTATCTTCTACAGT 57.278 33.333 0.00 0.00 0.00 3.55
2930 3247 5.685954 GTGTGAAATTATGCTGATGATGCAG 59.314 40.000 0.00 0.00 44.04 4.41
2991 3319 3.587797 AATCCTTGCTGCAATCTGTTG 57.412 42.857 16.38 2.77 38.39 3.33
2993 3321 0.389426 CCTTGCTGCAATCTGTTGGC 60.389 55.000 16.38 0.00 35.83 4.52
3002 3330 2.412847 GCAATCTGTTGGCGTAACACTC 60.413 50.000 3.72 0.00 44.07 3.51
3137 3508 2.959507 AAGTGGTCTTTGTTTGTGGC 57.040 45.000 0.00 0.00 0.00 5.01
3150 3521 4.930963 TGTTTGTGGCTATTGTTCAGTTG 58.069 39.130 0.00 0.00 0.00 3.16
3151 3522 4.202101 TGTTTGTGGCTATTGTTCAGTTGG 60.202 41.667 0.00 0.00 0.00 3.77
3153 3524 1.202348 GTGGCTATTGTTCAGTTGGGC 59.798 52.381 0.00 0.00 0.00 5.36
3154 3525 1.202989 TGGCTATTGTTCAGTTGGGCA 60.203 47.619 0.00 0.00 0.00 5.36
3155 3526 1.202348 GGCTATTGTTCAGTTGGGCAC 59.798 52.381 0.00 0.00 0.00 5.01
3156 3527 2.162681 GCTATTGTTCAGTTGGGCACT 58.837 47.619 0.00 0.00 35.35 4.40
3214 3589 2.159653 GCCTTTCATTGTACTCGTGCTG 60.160 50.000 0.00 0.00 0.00 4.41
3215 3590 3.067106 CCTTTCATTGTACTCGTGCTGT 58.933 45.455 0.00 0.00 0.00 4.40
3217 3592 4.024048 CCTTTCATTGTACTCGTGCTGTTT 60.024 41.667 0.00 0.00 0.00 2.83
3290 5076 7.566760 TGAGCTGTTTCTGAATTTTGACTTA 57.433 32.000 0.00 0.00 0.00 2.24
3309 5096 8.589701 TGACTTATTGTGTCCTATAGAACTGA 57.410 34.615 0.00 0.00 33.83 3.41
3335 5123 1.056700 AGGTTCAGGCTCTGTGTGGT 61.057 55.000 2.68 0.00 32.61 4.16
3361 5151 3.822735 TGGTTTCAGCTTCAAATCTCCAG 59.177 43.478 0.00 0.00 0.00 3.86
3387 5179 3.594603 ACTGAAACTATCCCTGTGTCG 57.405 47.619 0.00 0.00 0.00 4.35
3463 5258 3.003480 GCACTGGTGTTTAGGAGCTAAG 58.997 50.000 2.64 0.00 0.00 2.18
3485 5281 4.444056 AGTCGATTTGTTTTTGGCGATTTG 59.556 37.500 0.00 0.00 0.00 2.32
3486 5282 4.208253 GTCGATTTGTTTTTGGCGATTTGT 59.792 37.500 0.00 0.00 0.00 2.83
3487 5283 4.806247 TCGATTTGTTTTTGGCGATTTGTT 59.194 33.333 0.00 0.00 0.00 2.83
3488 5284 5.292101 TCGATTTGTTTTTGGCGATTTGTTT 59.708 32.000 0.00 0.00 0.00 2.83
3489 5285 5.962423 CGATTTGTTTTTGGCGATTTGTTTT 59.038 32.000 0.00 0.00 0.00 2.43
3490 5286 7.010183 TCGATTTGTTTTTGGCGATTTGTTTTA 59.990 29.630 0.00 0.00 0.00 1.52
3491 5287 7.109532 CGATTTGTTTTTGGCGATTTGTTTTAC 59.890 33.333 0.00 0.00 0.00 2.01
3492 5288 6.969828 TTGTTTTTGGCGATTTGTTTTACT 57.030 29.167 0.00 0.00 0.00 2.24
3494 5290 7.452630 TGTTTTTGGCGATTTGTTTTACTAC 57.547 32.000 0.00 0.00 0.00 2.73
3495 5291 7.259161 TGTTTTTGGCGATTTGTTTTACTACT 58.741 30.769 0.00 0.00 0.00 2.57
3496 5292 8.404000 TGTTTTTGGCGATTTGTTTTACTACTA 58.596 29.630 0.00 0.00 0.00 1.82
3497 5293 9.401873 GTTTTTGGCGATTTGTTTTACTACTAT 57.598 29.630 0.00 0.00 0.00 2.12
3501 5297 8.415192 TGGCGATTTGTTTTACTACTATACAG 57.585 34.615 0.00 0.00 0.00 2.74
3529 6378 4.554960 AGTAGTAAAAGCCTGTTCCTCC 57.445 45.455 0.00 0.00 0.00 4.30
3530 6379 2.474410 AGTAAAAGCCTGTTCCTCCG 57.526 50.000 0.00 0.00 0.00 4.63
3533 6382 1.897560 AAAAGCCTGTTCCTCCGAAG 58.102 50.000 0.00 0.00 0.00 3.79
3671 6524 3.099905 TGACGATTCAGATCTCCCTTGT 58.900 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.097361 GGCTCCGGTGAAGGGTCC 62.097 72.222 7.92 0.00 0.00 4.46
36 37 3.760035 ACCGCACTACTGGCTCCG 61.760 66.667 0.00 0.00 0.00 4.63
37 38 2.125512 CACCGCACTACTGGCTCC 60.126 66.667 0.00 0.00 0.00 4.70
42 43 1.076533 CGCTAACCACCGCACTACTG 61.077 60.000 0.00 0.00 0.00 2.74
45 46 1.213537 GTCGCTAACCACCGCACTA 59.786 57.895 0.00 0.00 0.00 2.74
135 152 2.500098 TGTTATTCGGAAGGGAGGAGTG 59.500 50.000 0.00 0.00 0.00 3.51
136 153 2.829023 TGTTATTCGGAAGGGAGGAGT 58.171 47.619 0.00 0.00 0.00 3.85
189 227 0.035152 TGCAATGACAAGGAGGCGAT 60.035 50.000 0.00 0.00 0.00 4.58
192 230 2.012673 CTAGTGCAATGACAAGGAGGC 58.987 52.381 0.00 0.00 0.00 4.70
223 261 2.135581 AAGCTTGCTTGCCTTGGCA 61.136 52.632 10.65 10.65 36.62 4.92
225 263 4.667420 CAAGCTTGCTTGCCTTGG 57.333 55.556 20.22 0.00 0.00 3.61
239 277 1.342496 TCAGGAGGATATGCTCGCAAG 59.658 52.381 16.95 7.60 0.00 4.01
328 366 0.249911 GCCCCGCGAGATACATTTCT 60.250 55.000 8.23 0.00 0.00 2.52
348 386 2.185608 GGCCTCCTCTCTCGCAAC 59.814 66.667 0.00 0.00 0.00 4.17
412 457 1.281867 TGCTGGAGTGGGGTTGATTAG 59.718 52.381 0.00 0.00 0.00 1.73
442 487 2.710902 CCTCCTCGGTCGATGCACA 61.711 63.158 0.00 0.00 0.00 4.57
452 497 0.671251 GCACTATGAGACCTCCTCGG 59.329 60.000 0.00 0.00 44.92 4.63
493 539 2.294233 ACACTTTCATGTCATGTGGCAC 59.706 45.455 11.55 11.55 33.44 5.01
538 584 3.112709 GACTCTCGTGCGGGCAAC 61.113 66.667 0.00 0.00 0.00 4.17
545 591 1.664965 GTGTGGTGGACTCTCGTGC 60.665 63.158 0.00 0.00 0.00 5.34
577 623 2.675423 TGGGTGGTCCTCGTCGAG 60.675 66.667 15.53 15.53 36.20 4.04
593 639 1.583967 GACGATCAGAGACGCCGTG 60.584 63.158 0.00 0.00 33.32 4.94
596 642 1.787057 ATCCGACGATCAGAGACGCC 61.787 60.000 0.00 0.00 0.00 5.68
609 655 1.175983 ATGAGGAGAGGCGATCCGAC 61.176 60.000 5.53 0.00 42.02 4.79
626 672 3.120060 GCAAGCCGGCTAATCTATTGATG 60.120 47.826 33.07 20.88 32.44 3.07
627 673 3.077359 GCAAGCCGGCTAATCTATTGAT 58.923 45.455 33.07 6.78 33.70 2.57
628 674 2.494059 GCAAGCCGGCTAATCTATTGA 58.506 47.619 33.07 0.00 0.00 2.57
629 675 1.537202 GGCAAGCCGGCTAATCTATTG 59.463 52.381 33.07 23.26 37.17 1.90
630 676 1.897560 GGCAAGCCGGCTAATCTATT 58.102 50.000 33.07 9.56 37.17 1.73
631 677 3.633361 GGCAAGCCGGCTAATCTAT 57.367 52.632 33.07 10.49 37.17 1.98
808 856 5.704053 ACCTAAGAATACCTGGAAAACAACG 59.296 40.000 0.00 0.00 0.00 4.10
809 857 8.509690 GTTACCTAAGAATACCTGGAAAACAAC 58.490 37.037 0.00 0.00 0.00 3.32
819 872 3.317430 CGCGAGGTTACCTAAGAATACCT 59.683 47.826 2.88 0.00 41.74 3.08
823 876 3.066481 GTCTCGCGAGGTTACCTAAGAAT 59.934 47.826 33.98 0.00 31.76 2.40
826 879 2.015587 AGTCTCGCGAGGTTACCTAAG 58.984 52.381 33.98 7.32 31.76 2.18
832 885 7.887996 TTTAAAATAAAGTCTCGCGAGGTTA 57.112 32.000 33.98 26.67 0.00 2.85
840 893 8.944212 AACAACGGATTTAAAATAAAGTCTCG 57.056 30.769 0.00 0.00 0.00 4.04
872 925 5.184479 GGTATGCGTACTTGTGGATATCCTA 59.816 44.000 22.35 9.06 36.82 2.94
873 926 4.021368 GGTATGCGTACTTGTGGATATCCT 60.021 45.833 22.35 4.53 36.82 3.24
874 927 4.243270 GGTATGCGTACTTGTGGATATCC 58.757 47.826 15.39 15.39 0.00 2.59
875 928 4.243270 GGGTATGCGTACTTGTGGATATC 58.757 47.826 15.51 0.00 0.00 1.63
876 929 3.644265 TGGGTATGCGTACTTGTGGATAT 59.356 43.478 15.51 0.00 0.00 1.63
877 930 3.032459 TGGGTATGCGTACTTGTGGATA 58.968 45.455 15.51 0.00 0.00 2.59
878 931 1.834896 TGGGTATGCGTACTTGTGGAT 59.165 47.619 15.51 0.00 0.00 3.41
879 932 1.066716 GTGGGTATGCGTACTTGTGGA 60.067 52.381 15.51 0.00 0.00 4.02
880 933 1.365699 GTGGGTATGCGTACTTGTGG 58.634 55.000 15.51 0.00 0.00 4.17
881 934 0.996462 CGTGGGTATGCGTACTTGTG 59.004 55.000 15.51 1.04 0.00 3.33
882 935 0.108520 CCGTGGGTATGCGTACTTGT 60.109 55.000 15.51 0.00 0.00 3.16
883 936 0.808453 CCCGTGGGTATGCGTACTTG 60.808 60.000 15.51 3.78 0.00 3.16
884 937 1.518774 CCCGTGGGTATGCGTACTT 59.481 57.895 15.51 0.00 0.00 2.24
885 938 3.085119 GCCCGTGGGTATGCGTACT 62.085 63.158 15.51 0.00 37.65 2.73
886 939 2.586914 GCCCGTGGGTATGCGTAC 60.587 66.667 7.60 7.60 37.65 3.67
887 940 2.181445 TTTGCCCGTGGGTATGCGTA 62.181 55.000 6.82 0.00 37.65 4.42
888 941 3.554696 TTTGCCCGTGGGTATGCGT 62.555 57.895 6.82 0.00 37.65 5.24
889 942 2.336478 TTTTGCCCGTGGGTATGCG 61.336 57.895 6.82 0.00 37.65 4.73
899 952 1.577421 CCGTTGGTAGTTTTGCCCG 59.423 57.895 0.00 0.00 0.00 6.13
900 953 1.287815 GCCGTTGGTAGTTTTGCCC 59.712 57.895 0.00 0.00 0.00 5.36
908 961 2.469516 GCGAATGGGCCGTTGGTAG 61.470 63.158 17.42 5.65 0.00 3.18
945 1000 5.236478 CCATTAAACGGGCTAACTGTATCAG 59.764 44.000 0.00 0.00 37.84 2.90
946 1001 5.120399 CCATTAAACGGGCTAACTGTATCA 58.880 41.667 0.00 0.00 37.84 2.15
1047 1105 0.030092 TGGAGGGGATTAGGGGAGTG 60.030 60.000 0.00 0.00 0.00 3.51
1323 1427 2.747855 CGGCAGAGTTCCTTGGCC 60.748 66.667 0.00 0.00 41.20 5.36
1348 1452 2.088674 AACCAGTGCTTCGAGACGCT 62.089 55.000 3.35 1.71 0.00 5.07
1660 1773 1.507141 GGCAACACGACCCACTTCTG 61.507 60.000 0.00 0.00 0.00 3.02
1682 1795 2.033141 TGCTGTCCTTGCAGGAGC 59.967 61.111 0.00 0.00 46.90 4.70
1815 1934 1.997606 CCGGTTTCAGACGAATACACC 59.002 52.381 0.00 0.00 0.00 4.16
1922 2083 4.466370 AGTCGTGATATTCAAGGTCAAGGA 59.534 41.667 0.00 0.00 0.00 3.36
1950 2111 2.904866 TTTGTGTCCACCGCAGCC 60.905 61.111 0.00 0.00 34.45 4.85
2072 2296 1.402968 CCAGACCAAAATCATCAGCCG 59.597 52.381 0.00 0.00 0.00 5.52
2155 2380 2.532235 CAATCGAATGCCAACACCATG 58.468 47.619 0.00 0.00 0.00 3.66
2494 2758 2.669133 AAGCACGCTGCCCCATAGA 61.669 57.895 6.39 0.00 46.52 1.98
2514 2778 2.232941 AGCCAAATTCAAGCAGACATGG 59.767 45.455 0.00 0.00 0.00 3.66
2515 2779 3.192844 AGAGCCAAATTCAAGCAGACATG 59.807 43.478 0.00 0.00 0.00 3.21
2543 2807 2.943690 ACATGCATTCATCAGTCAGAGC 59.056 45.455 0.00 0.00 0.00 4.09
2719 2991 7.821595 TGATCATAGTACCTTAACACAAACG 57.178 36.000 0.00 0.00 0.00 3.60
2744 3018 9.337396 GATAACCATTGTCCATGTCTTACATAA 57.663 33.333 0.00 0.00 36.53 1.90
2745 3019 8.490311 TGATAACCATTGTCCATGTCTTACATA 58.510 33.333 0.00 0.00 36.53 2.29
2746 3020 7.345691 TGATAACCATTGTCCATGTCTTACAT 58.654 34.615 0.00 0.00 39.91 2.29
2747 3021 6.716284 TGATAACCATTGTCCATGTCTTACA 58.284 36.000 0.00 0.00 0.00 2.41
2828 3109 6.295236 GCTTATAATTCCCATGGCTGCAAATA 60.295 38.462 6.09 0.00 0.00 1.40
2930 3247 5.047092 TGGCAGGAAAGAAAGGAAAATGATC 60.047 40.000 0.00 0.00 0.00 2.92
2991 3319 1.935933 ATTCATCCGAGTGTTACGCC 58.064 50.000 0.00 0.00 0.00 5.68
2993 3321 5.041287 ACATGTATTCATCCGAGTGTTACG 58.959 41.667 0.00 0.00 31.15 3.18
3033 3361 6.519761 CGTTTGATGATGTTCTAAAAGGAACG 59.480 38.462 0.00 0.00 45.90 3.95
3150 3521 3.676093 ACTCTTTTAAGCTACAGTGCCC 58.324 45.455 0.00 0.00 0.00 5.36
3151 3522 5.238650 TCAAACTCTTTTAAGCTACAGTGCC 59.761 40.000 0.00 0.00 0.00 5.01
3214 3589 4.207841 GGGATCGTGCGTAGTATAACAAAC 59.792 45.833 0.00 0.00 0.00 2.93
3215 3590 4.098349 AGGGATCGTGCGTAGTATAACAAA 59.902 41.667 0.00 0.00 0.00 2.83
3217 3592 3.004002 CAGGGATCGTGCGTAGTATAACA 59.996 47.826 0.00 0.00 0.00 2.41
3266 5052 6.455360 AAGTCAAAATTCAGAAACAGCTCA 57.545 33.333 0.00 0.00 0.00 4.26
3304 5091 4.729868 AGCCTGAACCTTTTGTATCAGTT 58.270 39.130 0.00 0.00 38.06 3.16
3309 5096 4.074970 CACAGAGCCTGAACCTTTTGTAT 58.925 43.478 8.91 0.00 35.18 2.29
3335 5123 4.978099 AGATTTGAAGCTGAAACCAGAGA 58.022 39.130 0.00 0.00 33.56 3.10
3361 5151 5.531287 ACACAGGGATAGTTTCAGTTTGTTC 59.469 40.000 0.00 0.00 0.00 3.18
3387 5179 2.202703 ATAACGACGGGAGCGCAC 60.203 61.111 11.47 1.97 33.77 5.34
3463 5258 4.208253 ACAAATCGCCAAAAACAAATCGAC 59.792 37.500 0.00 0.00 0.00 4.20
3495 5291 8.459394 AGGCTTTTACTACTATACCCCTGTATA 58.541 37.037 0.00 0.00 38.60 1.47
3496 5292 7.234988 CAGGCTTTTACTACTATACCCCTGTAT 59.765 40.741 0.00 0.00 40.72 2.29
3497 5293 6.552350 CAGGCTTTTACTACTATACCCCTGTA 59.448 42.308 0.00 0.00 33.31 2.74
3498 5294 5.365895 CAGGCTTTTACTACTATACCCCTGT 59.634 44.000 0.00 0.00 33.31 4.00
3501 5297 5.883685 ACAGGCTTTTACTACTATACCCC 57.116 43.478 0.00 0.00 0.00 4.95
3507 6356 4.159135 CGGAGGAACAGGCTTTTACTACTA 59.841 45.833 6.30 0.00 0.00 1.82
3511 6360 1.975680 TCGGAGGAACAGGCTTTTACT 59.024 47.619 0.00 0.00 0.00 2.24
3518 6367 1.183549 TACTCTTCGGAGGAACAGGC 58.816 55.000 0.00 0.00 45.78 4.85
3519 6368 3.955650 TTTACTCTTCGGAGGAACAGG 57.044 47.619 0.00 0.00 43.91 4.00
3545 6396 9.331106 GCTTAACTTTTCAAGCTTAATCACTAC 57.669 33.333 0.00 0.00 43.07 2.73
3556 6407 4.275936 TCAGTCAGGCTTAACTTTTCAAGC 59.724 41.667 0.00 0.00 45.15 4.01
3570 6421 2.758736 ATGAGAAGTGTCAGTCAGGC 57.241 50.000 0.00 0.00 0.00 4.85
3671 6524 6.882678 CAGTATGAAATGGCCATCATCAGATA 59.117 38.462 28.09 18.74 39.69 1.98


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

AutoCloner maintained by Alex Coulton.