Multiple sequence alignment - TraesCS2D01G530000

Loading Multiple Alignment...

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 TraesCS2D01G530000 chr2D 100.000 3549 0 0 1 3549 616938721 616935173 0.000000e+00 6554.0
1 TraesCS2D01G530000 chr2A 89.941 1879 101 47 1094 2939 746934253 746932430 0.000000e+00 2342.0
2 TraesCS2D01G530000 chr2A 88.401 638 52 10 2931 3549 746926007 746925373 0.000000e+00 749.0
3 TraesCS2D01G530000 chr2A 85.535 719 51 30 1 689 746935887 746935192 0.000000e+00 702.0
4 TraesCS2D01G530000 chr2A 89.398 415 18 13 704 1097 746934746 746934337 1.900000e-137 499.0
5 TraesCS2D01G530000 chr2A 87.273 55 7 0 667 721 746935188 746935134 2.960000e-06 63.9
6 TraesCS2D01G530000 chr2B 88.557 1005 53 25 1922 2888 752403960 752402980 0.000000e+00 1162.0
7 TraesCS2D01G530000 chr2B 83.447 1178 103 48 1 1097 752406005 752404839 0.000000e+00 1011.0
8 TraesCS2D01G530000 chr2B 92.295 623 23 10 2939 3549 752402982 752402373 0.000000e+00 861.0
9 TraesCS2D01G530000 chr2B 85.943 811 60 23 1094 1891 752404733 752403964 0.000000e+00 817.0
10 TraesCS2D01G530000 chr2B 84.199 462 36 22 167 592 752475877 752475417 7.090000e-112 414.0
11 TraesCS2D01G530000 chr2B 88.000 200 11 6 1 191 752476263 752476068 1.280000e-54 224.0
12 TraesCS2D01G530000 chrUn 87.336 229 19 5 1 220 9574437 9574210 1.640000e-63 254.0
13 TraesCS2D01G530000 chr7D 82.323 198 28 7 3025 3218 439237171 439237365 7.880000e-37 165.0
14 TraesCS2D01G530000 chr1D 85.621 153 19 3 3032 3182 156123362 156123211 1.320000e-34 158.0
15 TraesCS2D01G530000 chr1D 86.555 119 13 3 3094 3210 482224773 482224656 1.030000e-25 128.0
16 TraesCS2D01G530000 chr1D 89.796 98 9 1 1733 1829 16467710 16467807 1.340000e-24 124.0
17 TraesCS2D01G530000 chr7B 88.000 100 12 0 1173 1272 740313306 740313405 6.220000e-23 119.0
18 TraesCS2D01G530000 chr5D 82.222 135 12 9 2994 3125 553862017 553861892 4.850000e-19 106.0
19 TraesCS2D01G530000 chr5D 83.562 73 11 1 3095 3166 266750962 266751034 2.290000e-07 67.6
20 TraesCS2D01G530000 chr4A 79.851 134 15 9 2994 3125 614679435 614679558 1.760000e-13 87.9
21 TraesCS2D01G530000 chr3A 80.189 106 16 4 3031 3133 235809667 235809564 1.370000e-09 75.0
22 TraesCS2D01G530000 chr5B 83.562 73 11 1 3095 3166 300379261 300379333 2.290000e-07 67.6
23 TraesCS2D01G530000 chr6A 100.000 28 0 0 3522 3549 84017352 84017325 6.000000e-03 52.8
24 TraesCS2D01G530000 chr6A 100.000 28 0 0 3522 3549 448472580 448472553 6.000000e-03 52.8
25 TraesCS2D01G530000 chr6A 100.000 28 0 0 3522 3549 537426416 537426389 6.000000e-03 52.8
26 TraesCS2D01G530000 chr4B 100.000 28 0 0 3522 3549 139702011 139702038 6.000000e-03 52.8
27 TraesCS2D01G530000 chr1A 100.000 28 0 0 3522 3549 110996638 110996611 6.000000e-03 52.8
28 TraesCS2D01G530000 chr1A 100.000 28 0 0 3522 3549 305634347 305634374 6.000000e-03 52.8
29 TraesCS2D01G530000 chr1A 100.000 28 0 0 3522 3549 363234499 363234526 6.000000e-03 52.8


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 TraesCS2D01G530000 chr2D 616935173 616938721 3548 True 6554.000 6554 100.00000 1 3549 1 chr2D.!!$R1 3548
1 TraesCS2D01G530000 chr2A 746932430 746935887 3457 True 901.725 2342 88.03675 1 2939 4 chr2A.!!$R2 2938
2 TraesCS2D01G530000 chr2A 746925373 746926007 634 True 749.000 749 88.40100 2931 3549 1 chr2A.!!$R1 618
3 TraesCS2D01G530000 chr2B 752402373 752406005 3632 True 962.750 1162 87.56050 1 3549 4 chr2B.!!$R1 3548
4 TraesCS2D01G530000 chr2B 752475417 752476263 846 True 319.000 414 86.09950 1 592 2 chr2B.!!$R2 591

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
956 1727 0.104986 ATCTCCCATCCCGTCCATCA 60.105 55.0 0.0 0.0 0.0 3.07 F
1528 2436 0.517316 CTTGTACCCAGCGTTTCTGC 59.483 55.0 0.0 0.0 41.5 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 3074 0.105039 ACGCCAAGCCTATACTCTGC 59.895 55.0 0.00 0.0 0.00 4.26 R
3220 4242 0.162082 GCGTTGCAACACGAATCGTA 59.838 50.0 28.01 0.0 43.15 3.43 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
48 49 1.781025 CGTGCCGGAAAAGAACTGCA 61.781 55.000 5.05 0.00 0.00 4.41
52 53 2.102252 TGCCGGAAAAGAACTGCAAAAT 59.898 40.909 5.05 0.00 0.00 1.82
61 62 7.168804 GGAAAAGAACTGCAAAATCAAGAAGAG 59.831 37.037 0.00 0.00 0.00 2.85
63 64 3.930634 ACTGCAAAATCAAGAAGAGGC 57.069 42.857 0.00 0.00 0.00 4.70
245 491 4.712425 CCGCCAAAGTGCTGCAGC 62.712 66.667 31.89 31.89 42.50 5.25
251 497 0.382873 CAAAGTGCTGCAGCTCACAA 59.617 50.000 36.61 16.02 42.66 3.33
282 534 2.507992 CGTCAGCGAGCAGAAGGG 60.508 66.667 0.00 0.00 41.33 3.95
290 542 2.203938 AGCAGAAGGGAACGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
298 559 1.790818 AGGGAACGGGGATAGAGAAC 58.209 55.000 0.00 0.00 0.00 3.01
307 574 0.822532 GGATAGAGAACGAGCGGGGA 60.823 60.000 0.00 0.00 0.00 4.81
595 894 3.555518 GCTTCGGATGTCAAACTGAAAC 58.444 45.455 0.00 0.00 32.20 2.78
609 908 3.671716 ACTGAAACTTTATCCACGGTCC 58.328 45.455 0.00 0.00 0.00 4.46
633 932 2.892425 GCTTCGCCGCTGCAGTAT 60.892 61.111 16.64 0.00 37.32 2.12
641 947 1.202973 CCGCTGCAGTATTCGTCTCG 61.203 60.000 16.64 6.59 0.00 4.04
642 948 0.523546 CGCTGCAGTATTCGTCTCGT 60.524 55.000 16.64 0.00 0.00 4.18
643 949 1.192793 GCTGCAGTATTCGTCTCGTC 58.807 55.000 16.64 0.00 0.00 4.20
644 950 1.202200 GCTGCAGTATTCGTCTCGTCT 60.202 52.381 16.64 0.00 0.00 4.18
645 951 2.710760 CTGCAGTATTCGTCTCGTCTC 58.289 52.381 5.25 0.00 0.00 3.36
646 952 1.400846 TGCAGTATTCGTCTCGTCTCC 59.599 52.381 0.00 0.00 0.00 3.71
647 953 1.268640 GCAGTATTCGTCTCGTCTCCC 60.269 57.143 0.00 0.00 0.00 4.30
648 954 2.014857 CAGTATTCGTCTCGTCTCCCA 58.985 52.381 0.00 0.00 0.00 4.37
649 955 2.015587 AGTATTCGTCTCGTCTCCCAC 58.984 52.381 0.00 0.00 0.00 4.61
650 956 1.065251 GTATTCGTCTCGTCTCCCACC 59.935 57.143 0.00 0.00 0.00 4.61
651 957 0.323542 ATTCGTCTCGTCTCCCACCT 60.324 55.000 0.00 0.00 0.00 4.00
676 982 3.070576 GCCCAATGCACTCCACCC 61.071 66.667 0.00 0.00 40.77 4.61
923 1694 1.086696 CCCCTGCATATAAATCGCCG 58.913 55.000 0.00 0.00 0.00 6.46
948 1719 1.696884 GTCCTCTGAATCTCCCATCCC 59.303 57.143 0.00 0.00 0.00 3.85
949 1720 0.683973 CCTCTGAATCTCCCATCCCG 59.316 60.000 0.00 0.00 0.00 5.14
950 1721 1.418334 CTCTGAATCTCCCATCCCGT 58.582 55.000 0.00 0.00 0.00 5.28
951 1722 1.342819 CTCTGAATCTCCCATCCCGTC 59.657 57.143 0.00 0.00 0.00 4.79
952 1723 0.394565 CTGAATCTCCCATCCCGTCC 59.605 60.000 0.00 0.00 0.00 4.79
953 1724 0.326143 TGAATCTCCCATCCCGTCCA 60.326 55.000 0.00 0.00 0.00 4.02
956 1727 0.104986 ATCTCCCATCCCGTCCATCA 60.105 55.000 0.00 0.00 0.00 3.07
959 1730 2.072487 CCCATCCCGTCCATCAGGT 61.072 63.158 0.00 0.00 35.89 4.00
960 1731 0.762842 CCCATCCCGTCCATCAGGTA 60.763 60.000 0.00 0.00 35.89 3.08
969 1761 1.405821 GTCCATCAGGTACAGAGACCG 59.594 57.143 0.00 0.00 44.88 4.79
987 1783 1.882311 GACATTGGCAATGGCGTCA 59.118 52.632 35.77 0.00 43.21 4.35
992 1788 1.936436 TTGGCAATGGCGTCATCAGC 61.936 55.000 16.40 16.40 42.47 4.26
1292 2197 1.725164 CGCCAGTACGTTTCTTTCCTC 59.275 52.381 0.00 0.00 0.00 3.71
1295 2200 2.729882 CCAGTACGTTTCTTTCCTCACG 59.270 50.000 0.00 0.00 38.62 4.35
1296 2201 2.155155 CAGTACGTTTCTTTCCTCACGC 59.845 50.000 0.00 0.00 36.05 5.34
1297 2202 1.123756 GTACGTTTCTTTCCTCACGCG 59.876 52.381 3.53 3.53 36.05 6.01
1345 2250 9.956720 AAACTCTGTTTGAATTTCTGTATTGAG 57.043 29.630 0.00 0.00 0.00 3.02
1347 2252 9.512588 ACTCTGTTTGAATTTCTGTATTGAGAT 57.487 29.630 0.00 0.00 0.00 2.75
1502 2409 2.907897 AAGCGTCTATGCGAGGGTGC 62.908 60.000 0.00 0.00 38.17 5.01
1528 2436 0.517316 CTTGTACCCAGCGTTTCTGC 59.483 55.000 0.00 0.00 41.50 4.26
1543 2458 2.756840 TCTGCATCACTGTTCTGAGG 57.243 50.000 0.00 0.00 0.00 3.86
1550 2465 4.635223 CATCACTGTTCTGAGGTCTTGAA 58.365 43.478 0.00 0.00 0.00 2.69
1555 2470 3.817084 CTGTTCTGAGGTCTTGAATGCAA 59.183 43.478 0.00 0.00 0.00 4.08
1581 2496 3.427161 GCAAATGCAGATAACCTGACC 57.573 47.619 0.00 0.00 45.78 4.02
1584 2499 2.898729 ATGCAGATAACCTGACCGAG 57.101 50.000 0.00 0.00 45.78 4.63
1657 2577 9.462606 TTTCTTCCTTCTAAAATCTGTAATCCC 57.537 33.333 0.00 0.00 0.00 3.85
1674 2594 7.207383 TGTAATCCCGTGATTATTGTACAGAG 58.793 38.462 3.61 0.00 43.47 3.35
1675 2595 6.479972 AATCCCGTGATTATTGTACAGAGA 57.520 37.500 0.00 0.00 39.44 3.10
1676 2596 6.672266 ATCCCGTGATTATTGTACAGAGAT 57.328 37.500 0.00 0.00 0.00 2.75
1677 2597 6.085555 TCCCGTGATTATTGTACAGAGATC 57.914 41.667 0.00 1.93 0.00 2.75
1678 2598 5.596772 TCCCGTGATTATTGTACAGAGATCA 59.403 40.000 11.01 11.01 0.00 2.92
1679 2599 5.923114 CCCGTGATTATTGTACAGAGATCAG 59.077 44.000 13.90 9.87 0.00 2.90
1680 2600 6.461648 CCCGTGATTATTGTACAGAGATCAGT 60.462 42.308 13.90 0.00 0.00 3.41
1681 2601 6.638873 CCGTGATTATTGTACAGAGATCAGTC 59.361 42.308 13.90 6.32 0.00 3.51
1682 2602 7.421599 CGTGATTATTGTACAGAGATCAGTCT 58.578 38.462 13.90 0.00 37.42 3.24
1700 2620 7.290110 TCAGTCTCTTTGTCTCTGACATAAA 57.710 36.000 1.05 0.00 42.40 1.40
1705 2627 9.818796 GTCTCTTTGTCTCTGACATAAATTTTC 57.181 33.333 0.00 0.00 42.40 2.29
1716 2638 9.190858 TCTGACATAAATTTTCAATTTTGTCCG 57.809 29.630 20.17 17.15 33.43 4.79
1721 2643 6.597262 AAATTTTCAATTTTGTCCGTGGTC 57.403 33.333 0.00 0.00 0.00 4.02
1813 2735 1.620822 AGCACAAATCCAACCTCCAC 58.379 50.000 0.00 0.00 0.00 4.02
1822 2744 3.149005 TCCAACCTCCACCATGTAAAC 57.851 47.619 0.00 0.00 0.00 2.01
1825 2747 3.005367 CCAACCTCCACCATGTAAACAAC 59.995 47.826 0.00 0.00 0.00 3.32
1846 2784 2.146342 CTCCTTGCCTGTAACACACTG 58.854 52.381 0.00 0.00 0.00 3.66
2050 2988 4.180057 GTTGCAAACCAAATGAACTGTCA 58.820 39.130 0.00 0.00 42.21 3.58
2105 3074 5.242393 AGACCAGGAACATGTCTGAAATTTG 59.758 40.000 14.48 1.69 39.40 2.32
2110 3079 5.048224 AGGAACATGTCTGAAATTTGCAGAG 60.048 40.000 7.37 0.00 42.57 3.35
2113 3082 7.362401 GGAACATGTCTGAAATTTGCAGAGTAT 60.362 37.037 7.37 3.25 42.57 2.12
2114 3083 8.565896 AACATGTCTGAAATTTGCAGAGTATA 57.434 30.769 7.37 0.00 42.57 1.47
2115 3084 8.206325 ACATGTCTGAAATTTGCAGAGTATAG 57.794 34.615 7.37 0.15 42.57 1.31
2116 3085 7.281774 ACATGTCTGAAATTTGCAGAGTATAGG 59.718 37.037 7.37 0.35 42.57 2.57
2117 3086 5.586243 TGTCTGAAATTTGCAGAGTATAGGC 59.414 40.000 7.37 0.00 42.57 3.93
2118 3087 5.819901 GTCTGAAATTTGCAGAGTATAGGCT 59.180 40.000 7.37 0.00 42.57 4.58
2120 3089 6.317140 TCTGAAATTTGCAGAGTATAGGCTTG 59.683 38.462 2.73 0.00 37.46 4.01
2121 3090 5.357878 TGAAATTTGCAGAGTATAGGCTTGG 59.642 40.000 0.00 0.00 0.00 3.61
2122 3091 2.332063 TTGCAGAGTATAGGCTTGGC 57.668 50.000 0.00 0.00 0.00 4.52
2123 3092 0.104855 TGCAGAGTATAGGCTTGGCG 59.895 55.000 0.00 0.00 0.00 5.69
2124 3093 0.105039 GCAGAGTATAGGCTTGGCGT 59.895 55.000 0.00 0.00 0.00 5.68
2126 3095 2.474816 CAGAGTATAGGCTTGGCGTTC 58.525 52.381 0.00 0.00 0.00 3.95
2133 3102 6.947464 AGTATAGGCTTGGCGTTCATATAAT 58.053 36.000 0.00 0.00 0.00 1.28
2144 3115 6.037062 TGGCGTTCATATAATTGTCTGTCTTG 59.963 38.462 0.00 0.00 0.00 3.02
2363 3334 0.107508 CCATGCCATTCGTCCTGACT 60.108 55.000 0.00 0.00 0.00 3.41
2374 3345 1.337167 CGTCCTGACTGTGATGCTTCA 60.337 52.381 0.00 0.00 0.00 3.02
2378 3349 3.199289 TCCTGACTGTGATGCTTCATGAT 59.801 43.478 5.49 0.00 33.56 2.45
2469 3440 1.378762 CCATGTTCCTCAACCGGGT 59.621 57.895 6.32 0.00 0.00 5.28
2486 3457 2.828933 GTCTTCGGAGACCACAAGC 58.171 57.895 13.31 0.00 45.34 4.01
2581 3552 2.416547 GTGACAGTCGCTGTATTGCATT 59.583 45.455 11.60 0.00 45.44 3.56
2582 3553 2.416202 TGACAGTCGCTGTATTGCATTG 59.584 45.455 11.60 0.00 45.44 2.82
2583 3554 1.131126 ACAGTCGCTGTATTGCATTGC 59.869 47.619 10.20 0.46 43.46 3.56
2584 3555 1.130938 CAGTCGCTGTATTGCATTGCA 59.869 47.619 7.38 7.38 36.47 4.08
2585 3556 2.019249 AGTCGCTGTATTGCATTGCAT 58.981 42.857 12.95 5.57 38.76 3.96
2591 3562 3.491964 GCTGTATTGCATTGCATCCATGT 60.492 43.478 12.95 0.00 38.76 3.21
2616 3587 1.734465 CTGAAGACTTGGGCACGAATC 59.266 52.381 0.00 0.00 0.00 2.52
2618 3589 1.464997 GAAGACTTGGGCACGAATCAC 59.535 52.381 0.00 0.00 0.00 3.06
2620 3591 0.669318 GACTTGGGCACGAATCACGA 60.669 55.000 0.00 0.00 45.77 4.35
2624 3595 0.177836 TGGGCACGAATCACGATGAT 59.822 50.000 0.00 0.00 45.77 2.45
2627 3598 0.652071 GCACGAATCACGATGATGCA 59.348 50.000 0.00 0.00 45.77 3.96
2718 3693 1.630148 CCAACAGCTAGCGTGTACTC 58.370 55.000 16.73 0.00 0.00 2.59
2719 3694 1.630148 CAACAGCTAGCGTGTACTCC 58.370 55.000 16.73 0.00 0.00 3.85
2791 3773 5.108517 TCTGTTGTCCTTTTGTTTTCATGC 58.891 37.500 0.00 0.00 0.00 4.06
2852 3834 0.749649 ATTTGTCACGGCAAGGCAAA 59.250 45.000 8.14 8.14 34.25 3.68
2870 3852 1.512926 AAATCGTGTCCACACTCTGC 58.487 50.000 8.19 0.00 44.34 4.26
2885 3867 2.568956 ACTCTGCACACATCAGTACCAT 59.431 45.455 0.00 0.00 33.48 3.55
2886 3868 3.008375 ACTCTGCACACATCAGTACCATT 59.992 43.478 0.00 0.00 33.48 3.16
2887 3869 4.005650 CTCTGCACACATCAGTACCATTT 58.994 43.478 0.00 0.00 33.48 2.32
2888 3870 3.752747 TCTGCACACATCAGTACCATTTG 59.247 43.478 0.00 0.00 33.48 2.32
2889 3871 3.485394 TGCACACATCAGTACCATTTGT 58.515 40.909 0.00 0.00 0.00 2.83
2890 3872 3.501828 TGCACACATCAGTACCATTTGTC 59.498 43.478 0.00 0.00 0.00 3.18
2891 3873 3.424829 GCACACATCAGTACCATTTGTCG 60.425 47.826 0.00 0.00 0.00 4.35
2892 3874 3.745975 CACACATCAGTACCATTTGTCGT 59.254 43.478 0.00 0.00 0.00 4.34
2893 3875 3.745975 ACACATCAGTACCATTTGTCGTG 59.254 43.478 0.00 0.00 0.00 4.35
2894 3876 2.742053 ACATCAGTACCATTTGTCGTGC 59.258 45.455 0.00 0.00 0.00 5.34
2895 3877 1.803334 TCAGTACCATTTGTCGTGCC 58.197 50.000 0.00 0.00 0.00 5.01
2896 3878 1.070914 TCAGTACCATTTGTCGTGCCA 59.929 47.619 0.00 0.00 0.00 4.92
2897 3879 2.083774 CAGTACCATTTGTCGTGCCAT 58.916 47.619 0.00 0.00 0.00 4.40
2898 3880 2.083774 AGTACCATTTGTCGTGCCATG 58.916 47.619 0.00 0.00 0.00 3.66
2899 3881 2.080693 GTACCATTTGTCGTGCCATGA 58.919 47.619 0.00 0.00 0.00 3.07
2900 3882 0.881118 ACCATTTGTCGTGCCATGAC 59.119 50.000 10.16 10.16 34.78 3.06
2901 3883 0.880441 CCATTTGTCGTGCCATGACA 59.120 50.000 15.59 15.59 41.94 3.58
2902 3884 1.135603 CCATTTGTCGTGCCATGACAG 60.136 52.381 18.41 8.51 44.09 3.51
2903 3885 1.135603 CATTTGTCGTGCCATGACAGG 60.136 52.381 18.41 9.73 44.09 4.00
2904 3886 0.179032 TTTGTCGTGCCATGACAGGT 60.179 50.000 18.41 0.00 44.09 4.00
2905 3887 0.179032 TTGTCGTGCCATGACAGGTT 60.179 50.000 18.41 0.00 44.09 3.50
2906 3888 0.884259 TGTCGTGCCATGACAGGTTG 60.884 55.000 15.59 0.00 39.05 3.77
2907 3889 1.965930 TCGTGCCATGACAGGTTGC 60.966 57.895 1.60 0.00 0.00 4.17
2908 3890 2.260154 CGTGCCATGACAGGTTGCA 61.260 57.895 0.00 0.00 0.00 4.08
2909 3891 1.588824 CGTGCCATGACAGGTTGCAT 61.589 55.000 0.00 0.00 34.04 3.96
2910 3892 0.171903 GTGCCATGACAGGTTGCATC 59.828 55.000 0.00 0.00 34.04 3.91
2911 3893 0.966875 TGCCATGACAGGTTGCATCC 60.967 55.000 5.61 5.61 0.00 3.51
2912 3894 0.682209 GCCATGACAGGTTGCATCCT 60.682 55.000 10.71 10.71 38.51 3.24
2913 3895 1.843368 CCATGACAGGTTGCATCCTT 58.157 50.000 13.89 5.97 35.37 3.36
2914 3896 1.475280 CCATGACAGGTTGCATCCTTG 59.525 52.381 13.89 9.55 35.37 3.61
2928 3910 4.935885 CATCCTTGCAGTTTGTCTCTAC 57.064 45.455 0.00 0.00 0.00 2.59
2929 3911 4.318332 CATCCTTGCAGTTTGTCTCTACA 58.682 43.478 0.00 0.00 0.00 2.74
2930 3912 4.623932 TCCTTGCAGTTTGTCTCTACAT 57.376 40.909 0.00 0.00 34.97 2.29
2931 3913 4.973168 TCCTTGCAGTTTGTCTCTACATT 58.027 39.130 0.00 0.00 34.97 2.71
2932 3914 5.376625 TCCTTGCAGTTTGTCTCTACATTT 58.623 37.500 0.00 0.00 34.97 2.32
2933 3915 6.530120 TCCTTGCAGTTTGTCTCTACATTTA 58.470 36.000 0.00 0.00 34.97 1.40
2934 3916 6.995686 TCCTTGCAGTTTGTCTCTACATTTAA 59.004 34.615 0.00 0.00 34.97 1.52
2996 4012 3.478857 TGGTGTTTGTATGTTCGTCCT 57.521 42.857 0.00 0.00 0.00 3.85
2999 4015 5.366460 TGGTGTTTGTATGTTCGTCCTAAA 58.634 37.500 0.00 0.00 0.00 1.85
3029 4050 6.708502 TGTCCTTCGTTAACTCAATCAAATCA 59.291 34.615 3.71 0.00 0.00 2.57
3078 4099 8.829612 CAACTAAATCAAAAACATTCCTTGCTT 58.170 29.630 0.00 0.00 0.00 3.91
3124 4146 9.715123 CAAATCAAATTTTACCAAAACCTCAAC 57.285 29.630 0.00 0.00 32.37 3.18
3125 4147 8.445275 AATCAAATTTTACCAAAACCTCAACC 57.555 30.769 0.00 0.00 32.37 3.77
3169 4191 6.395780 TTCCCTACCCATACTCAAATCAAA 57.604 37.500 0.00 0.00 0.00 2.69
3176 4198 7.264373 ACCCATACTCAAATCAAATCGAATC 57.736 36.000 0.00 0.00 0.00 2.52
3204 4226 2.930826 AACTAGAATATGGTGGGCGG 57.069 50.000 0.00 0.00 0.00 6.13
3220 4242 0.674534 GCGGAAGGTATCTGTCGGAT 59.325 55.000 0.00 0.00 36.73 4.18
3253 4275 2.556189 TGCAACGCATGGTCAATTAGTT 59.444 40.909 0.00 0.00 31.71 2.24
3337 4359 3.282831 ACAAACATTAGACCGCTTTGC 57.717 42.857 0.00 0.00 0.00 3.68
3346 4368 0.796927 GACCGCTTTGCACTTACTCC 59.203 55.000 0.00 0.00 0.00 3.85
3478 4511 4.874970 AGGCAATGACATTTTCACTTGTC 58.125 39.130 0.00 0.00 42.05 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.139077 ACGAACGCCTCTTCTTGATTTT 58.861 40.909 0.00 0.00 0.00 1.82
52 53 0.671796 TGACGAACGCCTCTTCTTGA 59.328 50.000 0.00 0.00 0.00 3.02
61 62 2.432628 CTCCCAGTGACGAACGCC 60.433 66.667 0.00 0.00 0.00 5.68
63 64 1.444553 GAGCTCCCAGTGACGAACG 60.445 63.158 0.87 0.00 0.00 3.95
91 113 2.176546 CATTCCGTTGCCGCACTG 59.823 61.111 0.00 0.00 0.00 3.66
230 476 2.257676 GAGCTGCAGCACTTTGGC 59.742 61.111 38.24 12.01 45.16 4.52
245 491 2.908073 GCGGGTGCCTGTTTGTGAG 61.908 63.158 0.00 0.00 33.98 3.51
271 517 2.125512 CCCGTTCCCTTCTGCTCG 60.126 66.667 0.00 0.00 0.00 5.03
278 530 2.117051 GTTCTCTATCCCCGTTCCCTT 58.883 52.381 0.00 0.00 0.00 3.95
282 534 1.269154 GCTCGTTCTCTATCCCCGTTC 60.269 57.143 0.00 0.00 0.00 3.95
290 542 0.824182 CCTCCCCGCTCGTTCTCTAT 60.824 60.000 0.00 0.00 0.00 1.98
298 559 4.824515 AGACCTCCTCCCCGCTCG 62.825 72.222 0.00 0.00 0.00 5.03
307 574 0.324460 CGTAACCCCTCAGACCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
362 629 1.590147 CCTCAACTCCTACCGCGTT 59.410 57.895 4.92 0.00 0.00 4.84
369 636 1.381327 CCCTCGCCCTCAACTCCTA 60.381 63.158 0.00 0.00 0.00 2.94
504 792 2.285368 CACCACCCTGGCCTCCTA 60.285 66.667 3.32 0.00 42.67 2.94
511 799 2.671070 CTACAGCCACCACCCTGG 59.329 66.667 0.00 0.00 45.02 4.45
560 859 4.643387 AAGCCGGTGGGAGTGTGC 62.643 66.667 1.90 0.00 34.06 4.57
573 872 1.808411 TCAGTTTGACATCCGAAGCC 58.192 50.000 0.00 0.00 0.00 4.35
595 894 0.529992 GCCGAGGACCGTGGATAAAG 60.530 60.000 9.05 0.00 36.31 1.85
632 931 0.323542 AGGTGGGAGACGAGACGAAT 60.324 55.000 0.00 0.00 0.00 3.34
633 932 0.325933 TAGGTGGGAGACGAGACGAA 59.674 55.000 0.00 0.00 0.00 3.85
641 947 3.155167 CGGGCCTAGGTGGGAGAC 61.155 72.222 11.31 0.00 36.00 3.36
642 948 4.475444 CCGGGCCTAGGTGGGAGA 62.475 72.222 11.31 0.00 36.00 3.71
689 995 2.760092 GCATCACCCTAAATGCCAGAAA 59.240 45.455 0.00 0.00 41.92 2.52
834 1605 0.951040 GTGGGTTCCTTGCTCGTGAG 60.951 60.000 0.00 0.00 0.00 3.51
835 1606 1.070786 GTGGGTTCCTTGCTCGTGA 59.929 57.895 0.00 0.00 0.00 4.35
836 1607 1.966451 GGTGGGTTCCTTGCTCGTG 60.966 63.158 0.00 0.00 0.00 4.35
837 1608 1.990160 TTGGTGGGTTCCTTGCTCGT 61.990 55.000 0.00 0.00 0.00 4.18
838 1609 0.609131 ATTGGTGGGTTCCTTGCTCG 60.609 55.000 0.00 0.00 0.00 5.03
839 1610 0.890683 CATTGGTGGGTTCCTTGCTC 59.109 55.000 0.00 0.00 0.00 4.26
840 1611 1.187567 GCATTGGTGGGTTCCTTGCT 61.188 55.000 0.00 0.00 35.79 3.91
841 1612 1.293179 GCATTGGTGGGTTCCTTGC 59.707 57.895 0.00 0.00 33.17 4.01
842 1613 0.831288 TGGCATTGGTGGGTTCCTTG 60.831 55.000 0.00 0.00 0.00 3.61
843 1614 0.116940 ATGGCATTGGTGGGTTCCTT 59.883 50.000 0.00 0.00 0.00 3.36
844 1615 0.615544 CATGGCATTGGTGGGTTCCT 60.616 55.000 0.00 0.00 0.00 3.36
845 1616 1.899617 CATGGCATTGGTGGGTTCC 59.100 57.895 0.00 0.00 0.00 3.62
846 1617 1.218854 GCATGGCATTGGTGGGTTC 59.781 57.895 0.00 0.00 0.00 3.62
847 1618 2.648143 CGCATGGCATTGGTGGGTT 61.648 57.895 0.00 0.00 0.00 4.11
848 1619 3.069946 CGCATGGCATTGGTGGGT 61.070 61.111 0.00 0.00 0.00 4.51
849 1620 3.069946 ACGCATGGCATTGGTGGG 61.070 61.111 0.00 0.00 0.00 4.61
896 1667 2.116869 TATATGCAGGGGAGCTGGAA 57.883 50.000 0.00 0.00 34.99 3.53
923 1694 1.760029 GGGAGATTCAGAGGACAGGAC 59.240 57.143 0.00 0.00 0.00 3.85
948 1719 1.405821 GGTCTCTGTACCTGATGGACG 59.594 57.143 0.00 0.00 36.53 4.79
949 1720 1.405821 CGGTCTCTGTACCTGATGGAC 59.594 57.143 0.00 0.00 37.39 4.02
950 1721 1.283905 TCGGTCTCTGTACCTGATGGA 59.716 52.381 0.00 0.00 37.39 3.41
951 1722 1.405821 GTCGGTCTCTGTACCTGATGG 59.594 57.143 0.00 0.00 37.39 3.51
952 1723 2.092323 TGTCGGTCTCTGTACCTGATG 58.908 52.381 0.00 0.00 37.39 3.07
953 1724 2.509166 TGTCGGTCTCTGTACCTGAT 57.491 50.000 0.00 0.00 37.39 2.90
956 1727 1.825474 CCAATGTCGGTCTCTGTACCT 59.175 52.381 0.00 0.00 37.39 3.08
959 1730 1.262417 TGCCAATGTCGGTCTCTGTA 58.738 50.000 0.00 0.00 0.00 2.74
960 1731 0.396435 TTGCCAATGTCGGTCTCTGT 59.604 50.000 0.00 0.00 0.00 3.41
969 1761 0.457035 ATGACGCCATTGCCAATGTC 59.543 50.000 15.83 7.92 37.18 3.06
987 1783 1.945387 CTACCATGAACGCTGCTGAT 58.055 50.000 0.00 0.00 0.00 2.90
992 1788 2.813179 GCCGCTACCATGAACGCTG 61.813 63.158 0.00 0.00 0.00 5.18
1297 2202 4.498520 TACGCTGCTGCTCGCTCC 62.499 66.667 14.03 0.00 40.11 4.70
1339 2244 5.438761 ACACGACGATCATCATCTCAATA 57.561 39.130 0.00 0.00 0.00 1.90
1343 2248 2.656085 GGACACGACGATCATCATCTC 58.344 52.381 0.00 0.00 0.00 2.75
1345 2250 1.002792 TCGGACACGACGATCATCATC 60.003 52.381 0.00 0.00 45.59 2.92
1347 2252 2.473457 TCGGACACGACGATCATCA 58.527 52.632 0.00 0.00 45.59 3.07
1502 2409 3.735237 ACGCTGGGTACAAGATATCAG 57.265 47.619 5.32 0.00 0.00 2.90
1528 2436 4.263018 TCAAGACCTCAGAACAGTGATG 57.737 45.455 0.00 0.00 0.00 3.07
1581 2496 1.070445 CAGGAATAGCAGGGCCTCG 59.930 63.158 0.95 0.00 0.00 4.63
1584 2499 0.464554 GTGACAGGAATAGCAGGGCC 60.465 60.000 0.00 0.00 0.00 5.80
1657 2577 7.421599 AGACTGATCTCTGTACAATAATCACG 58.578 38.462 0.00 3.83 0.00 4.35
1674 2594 5.384063 TGTCAGAGACAAAGAGACTGATC 57.616 43.478 0.00 0.00 39.78 2.92
1675 2595 5.999205 ATGTCAGAGACAAAGAGACTGAT 57.001 39.130 3.74 0.00 45.96 2.90
1676 2596 6.901081 TTATGTCAGAGACAAAGAGACTGA 57.099 37.500 3.74 0.00 45.96 3.41
1677 2597 8.545229 AATTTATGTCAGAGACAAAGAGACTG 57.455 34.615 3.74 0.00 45.96 3.51
1678 2598 9.566432 AAAATTTATGTCAGAGACAAAGAGACT 57.434 29.630 3.74 0.00 45.96 3.24
1679 2599 9.818796 GAAAATTTATGTCAGAGACAAAGAGAC 57.181 33.333 3.74 0.00 45.96 3.36
1680 2600 9.559732 TGAAAATTTATGTCAGAGACAAAGAGA 57.440 29.630 3.74 0.00 45.96 3.10
1700 2620 5.163457 ACAGACCACGGACAAAATTGAAAAT 60.163 36.000 0.00 0.00 0.00 1.82
1705 2627 4.215399 ACATACAGACCACGGACAAAATTG 59.785 41.667 0.00 0.00 0.00 2.32
1716 2638 2.471255 GGCTGCACATACAGACCAC 58.529 57.895 0.50 0.00 40.02 4.16
1813 2735 2.231235 GGCAAGGAGGTTGTTTACATGG 59.769 50.000 0.00 0.00 38.55 3.66
1822 2744 1.880027 GTGTTACAGGCAAGGAGGTTG 59.120 52.381 0.00 0.00 39.41 3.77
1825 2747 1.072331 AGTGTGTTACAGGCAAGGAGG 59.928 52.381 0.00 0.00 0.00 4.30
1856 2794 1.693062 AGCTCTCTGCCTGTGATATGG 59.307 52.381 0.00 0.00 44.23 2.74
1860 2798 2.836981 AGTTAAGCTCTCTGCCTGTGAT 59.163 45.455 0.00 0.00 44.23 3.06
2050 2988 4.357142 CACGTCTGTAACTGTAACTGTGT 58.643 43.478 0.00 0.00 0.00 3.72
2057 2995 3.057736 GGAAGAGCACGTCTGTAACTGTA 60.058 47.826 0.00 0.00 34.84 2.74
2058 2996 2.288273 GGAAGAGCACGTCTGTAACTGT 60.288 50.000 0.00 0.00 34.84 3.55
2061 2999 2.433868 TGGAAGAGCACGTCTGTAAC 57.566 50.000 0.00 0.00 34.84 2.50
2105 3074 0.105039 ACGCCAAGCCTATACTCTGC 59.895 55.000 0.00 0.00 0.00 4.26
2110 3079 7.119262 ACAATTATATGAACGCCAAGCCTATAC 59.881 37.037 0.00 0.00 0.00 1.47
2113 3082 5.373222 ACAATTATATGAACGCCAAGCCTA 58.627 37.500 0.00 0.00 0.00 3.93
2114 3083 4.207165 ACAATTATATGAACGCCAAGCCT 58.793 39.130 0.00 0.00 0.00 4.58
2115 3084 4.275936 AGACAATTATATGAACGCCAAGCC 59.724 41.667 0.00 0.00 0.00 4.35
2116 3085 5.207768 CAGACAATTATATGAACGCCAAGC 58.792 41.667 0.00 0.00 0.00 4.01
2117 3086 6.258727 AGACAGACAATTATATGAACGCCAAG 59.741 38.462 0.00 0.00 0.00 3.61
2118 3087 6.112734 AGACAGACAATTATATGAACGCCAA 58.887 36.000 0.00 0.00 0.00 4.52
2120 3089 6.037172 ACAAGACAGACAATTATATGAACGCC 59.963 38.462 0.00 0.00 0.00 5.68
2121 3090 7.005062 ACAAGACAGACAATTATATGAACGC 57.995 36.000 0.00 0.00 0.00 4.84
2122 3091 8.116753 GGAACAAGACAGACAATTATATGAACG 58.883 37.037 0.00 0.00 0.00 3.95
2123 3092 9.167311 AGGAACAAGACAGACAATTATATGAAC 57.833 33.333 0.00 0.00 0.00 3.18
2124 3093 9.383519 GAGGAACAAGACAGACAATTATATGAA 57.616 33.333 0.00 0.00 0.00 2.57
2126 3095 7.770433 TGGAGGAACAAGACAGACAATTATATG 59.230 37.037 0.00 0.00 0.00 1.78
2133 3102 2.104792 CCTGGAGGAACAAGACAGACAA 59.895 50.000 0.00 0.00 37.39 3.18
2144 3115 2.266055 CACGAGCCCTGGAGGAAC 59.734 66.667 0.00 0.00 38.24 3.62
2310 3281 3.148279 ACGAAGCTAGGCGGGGAG 61.148 66.667 8.17 0.00 0.00 4.30
2311 3282 3.458163 CACGAAGCTAGGCGGGGA 61.458 66.667 8.17 0.00 0.00 4.81
2312 3283 3.310860 AACACGAAGCTAGGCGGGG 62.311 63.158 10.04 4.10 34.70 5.73
2313 3284 1.810030 GAACACGAAGCTAGGCGGG 60.810 63.158 4.50 4.50 36.88 6.13
2363 3334 2.943033 CTGCAGATCATGAAGCATCACA 59.057 45.455 8.42 5.75 38.69 3.58
2374 3345 3.317711 CGAAGTAGTCCTCTGCAGATCAT 59.682 47.826 18.63 6.49 0.00 2.45
2378 3349 1.464734 CCGAAGTAGTCCTCTGCAGA 58.535 55.000 17.19 17.19 0.00 4.26
2437 3408 3.415087 ATGGCCAGCCTCACTCCC 61.415 66.667 13.05 0.00 36.94 4.30
2469 3440 1.671742 GGCTTGTGGTCTCCGAAGA 59.328 57.895 0.00 0.00 0.00 2.87
2581 3552 2.040145 TCTTCAGGTCAACATGGATGCA 59.960 45.455 0.00 0.00 0.00 3.96
2582 3553 2.421424 GTCTTCAGGTCAACATGGATGC 59.579 50.000 0.00 0.00 0.00 3.91
2583 3554 3.947868 AGTCTTCAGGTCAACATGGATG 58.052 45.455 0.00 0.00 0.00 3.51
2584 3555 4.330250 CAAGTCTTCAGGTCAACATGGAT 58.670 43.478 0.00 0.00 0.00 3.41
2585 3556 3.496692 CCAAGTCTTCAGGTCAACATGGA 60.497 47.826 0.00 0.00 33.44 3.41
2591 3562 0.843309 TGCCCAAGTCTTCAGGTCAA 59.157 50.000 1.12 0.00 0.00 3.18
2616 3587 4.217334 AGTCTCCTAGTATGCATCATCGTG 59.783 45.833 0.19 0.00 0.00 4.35
2618 3589 5.645929 AGTAGTCTCCTAGTATGCATCATCG 59.354 44.000 0.19 0.00 0.00 3.84
2619 3590 6.624861 GCAGTAGTCTCCTAGTATGCATCATC 60.625 46.154 0.19 0.00 32.50 2.92
2620 3591 5.184864 GCAGTAGTCTCCTAGTATGCATCAT 59.815 44.000 0.19 0.00 32.50 2.45
2624 3595 4.171878 AGCAGTAGTCTCCTAGTATGCA 57.828 45.455 0.00 0.00 33.70 3.96
2627 3598 6.263617 GCAAGTTAGCAGTAGTCTCCTAGTAT 59.736 42.308 0.00 0.00 0.00 2.12
2718 3693 3.760151 ACATCTTTGGACATGACATGTGG 59.240 43.478 25.45 9.96 45.03 4.17
2719 3694 5.876460 TCTACATCTTTGGACATGACATGTG 59.124 40.000 25.45 10.78 45.03 3.21
2771 3753 5.727515 GCAAGCATGAAAACAAAAGGACAAC 60.728 40.000 0.00 0.00 0.00 3.32
2870 3852 3.745975 ACGACAAATGGTACTGATGTGTG 59.254 43.478 6.10 3.07 0.00 3.82
2885 3867 0.179032 ACCTGTCATGGCACGACAAA 60.179 50.000 17.73 0.00 42.56 2.83
2886 3868 0.179032 AACCTGTCATGGCACGACAA 60.179 50.000 17.73 2.04 42.56 3.18
2887 3869 0.884259 CAACCTGTCATGGCACGACA 60.884 55.000 16.21 16.21 41.00 4.35
2888 3870 1.868997 CAACCTGTCATGGCACGAC 59.131 57.895 6.78 6.78 0.00 4.34
2889 3871 1.965930 GCAACCTGTCATGGCACGA 60.966 57.895 0.00 0.00 0.00 4.35
2890 3872 1.588824 ATGCAACCTGTCATGGCACG 61.589 55.000 0.00 0.00 37.30 5.34
2891 3873 0.171903 GATGCAACCTGTCATGGCAC 59.828 55.000 0.00 0.00 37.30 5.01
2892 3874 0.966875 GGATGCAACCTGTCATGGCA 60.967 55.000 5.61 0.00 39.03 4.92
2893 3875 0.682209 AGGATGCAACCTGTCATGGC 60.682 55.000 15.77 0.00 39.01 4.40
2894 3876 1.475280 CAAGGATGCAACCTGTCATGG 59.525 52.381 17.31 0.00 40.49 3.66
2895 3877 2.933495 CAAGGATGCAACCTGTCATG 57.067 50.000 17.31 7.16 40.49 3.07
2905 3887 7.714467 TGTAGAGACAAACTGCAAGGATGCA 62.714 44.000 3.23 3.23 46.22 3.96
2906 3888 5.336107 TGTAGAGACAAACTGCAAGGATGC 61.336 45.833 0.00 0.00 42.24 3.91
2907 3889 4.318332 TGTAGAGACAAACTGCAAGGATG 58.682 43.478 0.00 0.00 31.95 3.51
2908 3890 4.623932 TGTAGAGACAAACTGCAAGGAT 57.376 40.909 0.00 0.00 31.95 3.24
2909 3891 4.623932 ATGTAGAGACAAACTGCAAGGA 57.376 40.909 0.00 0.00 39.59 3.36
2910 3892 5.695851 AAATGTAGAGACAAACTGCAAGG 57.304 39.130 0.00 0.00 39.59 3.61
2911 3893 9.121517 CATTTAAATGTAGAGACAAACTGCAAG 57.878 33.333 18.32 0.00 39.59 4.01
2996 4012 6.289834 TGAGTTAACGAAGGACATGGTTTTA 58.710 36.000 0.00 0.00 0.00 1.52
2999 4015 4.345859 TGAGTTAACGAAGGACATGGTT 57.654 40.909 0.00 0.00 0.00 3.67
3066 4087 1.202976 AGCAGGTGAAGCAAGGAATGT 60.203 47.619 0.00 0.00 0.00 2.71
3078 4099 2.575735 TGATTTGGGTATGAGCAGGTGA 59.424 45.455 0.00 0.00 0.00 4.02
3176 4198 8.837389 GCCCACCATATTCTAGTTTTTAGTAAG 58.163 37.037 0.00 0.00 0.00 2.34
3181 4203 5.104444 TCCGCCCACCATATTCTAGTTTTTA 60.104 40.000 0.00 0.00 0.00 1.52
3220 4242 0.162082 GCGTTGCAACACGAATCGTA 59.838 50.000 28.01 0.00 43.15 3.43
3227 4249 1.725625 GACCATGCGTTGCAACACG 60.726 57.895 28.01 17.85 43.62 4.49
3253 4275 8.255905 GTGCCTTCCTTCTAAAATACAGTACTA 58.744 37.037 0.00 0.00 0.00 1.82
3316 4338 3.067461 TGCAAAGCGGTCTAATGTTTGTT 59.933 39.130 0.00 0.00 31.96 2.83
3512 4546 6.432783 TCCGTTCCAAAATACTTTGTCATGAT 59.567 34.615 0.00 0.00 40.38 2.45


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

AutoCloner maintained by Alex Coulton.