Multiple sequence alignment - TraesCS6B01G127200

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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 TraesCS6B01G127200 chr6B 100.000 3035 0 0 1 3035 122963627 122966661 0.000000e+00 5605
1 TraesCS6B01G127200 chr6B 89.940 1163 112 3 878 2039 123205948 123204790 0.000000e+00 1495
2 TraesCS6B01G127200 chr6B 84.967 306 28 10 2370 2659 123415474 123415171 8.230000e-76 294
3 TraesCS6B01G127200 chr6B 84.718 301 32 8 2370 2659 123204329 123204032 3.830000e-74 289
4 TraesCS6B01G127200 chr6B 92.347 196 15 0 2135 2330 123229587 123229392 2.300000e-71 279
5 TraesCS6B01G127200 chr6B 84.321 287 36 8 2043 2324 123495705 123495423 3.860000e-69 272
6 TraesCS6B01G127200 chr6B 80.729 192 34 3 2038 2228 123017476 123017287 2.440000e-31 147
7 TraesCS6B01G127200 chr6A 97.591 2159 47 4 878 3035 66423788 66425942 0.000000e+00 3694
8 TraesCS6B01G127200 chr6A 93.465 1163 69 3 878 2039 66379699 66380855 0.000000e+00 1720
9 TraesCS6B01G127200 chr6A 90.714 1163 105 3 878 2039 66373765 66374925 0.000000e+00 1546
10 TraesCS6B01G127200 chr6A 89.013 1165 125 3 878 2041 66821158 66819996 0.000000e+00 1439
11 TraesCS6B01G127200 chr6A 84.431 334 32 12 2370 2689 66992173 66991846 8.170000e-81 311
12 TraesCS6B01G127200 chr6A 83.881 335 35 13 2370 2689 66817562 66817232 4.920000e-78 302
13 TraesCS6B01G127200 chr6A 84.539 304 32 8 2370 2659 66812176 66811874 1.380000e-73 287
14 TraesCS6B01G127200 chr6A 92.424 198 13 1 2135 2330 66994070 66993873 6.410000e-72 281
15 TraesCS6B01G127200 chr6A 92.973 185 11 1 2148 2330 66819467 66819283 4.990000e-68 268
16 TraesCS6B01G127200 chr6A 83.972 287 37 7 2043 2324 67003292 67003010 1.790000e-67 267
17 TraesCS6B01G127200 chr6A 81.818 286 47 5 2042 2324 66380686 66380969 5.060000e-58 235
18 TraesCS6B01G127200 chr6A 88.550 131 15 0 2042 2172 69133865 69133995 3.130000e-35 159
19 TraesCS6B01G127200 chr6A 91.304 115 7 2 2704 2818 66817178 66817067 1.460000e-33 154
20 TraesCS6B01G127200 chr6A 89.565 115 9 2 2704 2818 66991763 66991652 3.150000e-30 143
21 TraesCS6B01G127200 chr6D 93.894 1916 116 1 878 2792 48460048 48458133 0.000000e+00 2889
22 TraesCS6B01G127200 chr6D 91.146 1152 102 0 878 2029 48468514 48467363 0.000000e+00 1563
23 TraesCS6B01G127200 chr6D 89.844 1152 111 4 878 2029 48089502 48090647 0.000000e+00 1474
24 TraesCS6B01G127200 chr6D 88.159 1005 78 22 2042 3034 48467522 48466547 0.000000e+00 1158
25 TraesCS6B01G127200 chr6D 83.993 556 58 17 2494 3035 48464503 48463965 3.490000e-139 505
26 TraesCS6B01G127200 chr6D 96.629 178 3 2 2791 2968 48457974 48457800 2.960000e-75 292
27 TraesCS6B01G127200 chr6D 84.641 306 29 9 2370 2659 48158284 48158587 3.830000e-74 289
28 TraesCS6B01G127200 chr6D 94.048 84 4 1 2952 3035 48455605 48455523 3.180000e-25 126
29 TraesCS6B01G127200 chr7D 90.612 1161 106 1 878 2038 192447852 192449009 0.000000e+00 1537
30 TraesCS6B01G127200 chr7D 95.455 880 38 2 1 880 115267608 115266731 0.000000e+00 1402
31 TraesCS6B01G127200 chr7D 95.336 879 38 3 2 880 11441313 11440438 0.000000e+00 1393
32 TraesCS6B01G127200 chr2D 96.932 880 25 2 1 880 632489768 632490645 0.000000e+00 1474
33 TraesCS6B01G127200 chr2D 96.818 880 26 2 1 880 632495024 632495901 0.000000e+00 1469
34 TraesCS6B01G127200 chr1D 96.818 880 26 2 1 880 209750857 209751734 0.000000e+00 1469
35 TraesCS6B01G127200 chr5B 95.795 880 35 2 1 880 202897500 202896623 0.000000e+00 1419
36 TraesCS6B01G127200 chr7B 95.341 880 39 2 1 880 579798744 579799621 0.000000e+00 1397
37 TraesCS6B01G127200 chr5A 95.341 880 39 2 1 880 104585827 104584950 0.000000e+00 1397
38 TraesCS6B01G127200 chr3B 95.341 880 39 2 1 880 160730131 160731008 0.000000e+00 1397


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 TraesCS6B01G127200 chr6B 122963627 122966661 3034 False 5605.000000 5605 100.000000 1 3035 1 chr6B.!!$F1 3034
1 TraesCS6B01G127200 chr6B 123204032 123205948 1916 True 892.000000 1495 87.329000 878 2659 2 chr6B.!!$R5 1781
2 TraesCS6B01G127200 chr6A 66423788 66425942 2154 False 3694.000000 3694 97.591000 878 3035 1 chr6A.!!$F2 2157
3 TraesCS6B01G127200 chr6A 66373765 66374925 1160 False 1546.000000 1546 90.714000 878 2039 1 chr6A.!!$F1 1161
4 TraesCS6B01G127200 chr6A 66379699 66380969 1270 False 977.500000 1720 87.641500 878 2324 2 chr6A.!!$F4 1446
5 TraesCS6B01G127200 chr6A 66817067 66821158 4091 True 540.750000 1439 89.292750 878 2818 4 chr6A.!!$R3 1940
6 TraesCS6B01G127200 chr6A 66991652 66994070 2418 True 245.000000 311 88.806667 2135 2818 3 chr6A.!!$R4 683
7 TraesCS6B01G127200 chr6D 48089502 48090647 1145 False 1474.000000 1474 89.844000 878 2029 1 chr6D.!!$F1 1151
8 TraesCS6B01G127200 chr6D 48455523 48468514 12991 True 1088.833333 2889 91.311500 878 3035 6 chr6D.!!$R1 2157
9 TraesCS6B01G127200 chr7D 192447852 192449009 1157 False 1537.000000 1537 90.612000 878 2038 1 chr7D.!!$F1 1160
10 TraesCS6B01G127200 chr7D 115266731 115267608 877 True 1402.000000 1402 95.455000 1 880 1 chr7D.!!$R2 879
11 TraesCS6B01G127200 chr7D 11440438 11441313 875 True 1393.000000 1393 95.336000 2 880 1 chr7D.!!$R1 878
12 TraesCS6B01G127200 chr2D 632489768 632490645 877 False 1474.000000 1474 96.932000 1 880 1 chr2D.!!$F1 879
13 TraesCS6B01G127200 chr2D 632495024 632495901 877 False 1469.000000 1469 96.818000 1 880 1 chr2D.!!$F2 879
14 TraesCS6B01G127200 chr1D 209750857 209751734 877 False 1469.000000 1469 96.818000 1 880 1 chr1D.!!$F1 879
15 TraesCS6B01G127200 chr5B 202896623 202897500 877 True 1419.000000 1419 95.795000 1 880 1 chr5B.!!$R1 879
16 TraesCS6B01G127200 chr7B 579798744 579799621 877 False 1397.000000 1397 95.341000 1 880 1 chr7B.!!$F1 879
17 TraesCS6B01G127200 chr5A 104584950 104585827 877 True 1397.000000 1397 95.341000 1 880 1 chr5A.!!$R1 879
18 TraesCS6B01G127200 chr3B 160730131 160731008 877 False 1397.000000 1397 95.341000 1 880 1 chr3B.!!$F1 879

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
398 399 1.771854 TGTTTACTCTTGGAGGTGGCA 59.228 47.619 0.0 0.0 33.35 4.92 F
1858 10335 1.074405 GCAAGATGGGCAGGATGGATA 59.926 52.381 0.0 0.0 35.86 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 10654 0.107214 CCTTCTGCGGCCTATTTGGA 60.107 55.0 0.0 0.0 38.35 3.53 R
2960 14147 1.974265 TGTGATGTCGGGAAAGCAAA 58.026 45.0 0.0 0.0 0.00 3.68 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
204 205 1.940613 GTGAGCAAACTGAGTCGGTTT 59.059 47.619 21.94 21.94 42.78 3.27
295 296 9.869667 ACTATGAACTATGGACTTCACTATACT 57.130 33.333 0.00 0.00 0.00 2.12
398 399 1.771854 TGTTTACTCTTGGAGGTGGCA 59.228 47.619 0.00 0.00 33.35 4.92
477 478 8.796475 AGCAGAATTAACAACATTAGACACATT 58.204 29.630 0.00 0.00 0.00 2.71
671 672 5.177142 GTCAGAAAACTAAGAAACTCCGGAC 59.823 44.000 0.00 0.00 0.00 4.79
755 756 5.106442 TGTCGCGTGTTGTGATAGATAATT 58.894 37.500 5.77 0.00 39.75 1.40
760 761 6.074356 CGCGTGTTGTGATAGATAATTCATCA 60.074 38.462 0.00 0.00 35.96 3.07
876 877 4.381079 GCTAGTGGTTAACTGAGGAGAGTG 60.381 50.000 5.42 0.00 40.26 3.51
1470 9937 5.440610 AGGTTGTTGAAAGTGATGAGAAGT 58.559 37.500 0.00 0.00 0.00 3.01
1802 10279 1.566298 AAGCAGGGGGTGAAGCCTAG 61.566 60.000 0.00 0.00 37.43 3.02
1858 10335 1.074405 GCAAGATGGGCAGGATGGATA 59.926 52.381 0.00 0.00 35.86 2.59
2006 10656 7.840931 ACCAAAATGAAGAACAAGGATATTCC 58.159 34.615 0.00 0.00 36.58 3.01
2007 10657 7.454380 ACCAAAATGAAGAACAAGGATATTCCA 59.546 33.333 0.00 0.00 39.61 3.53
2008 10658 8.313292 CCAAAATGAAGAACAAGGATATTCCAA 58.687 33.333 0.00 0.00 39.61 3.53
2009 10659 9.709495 CAAAATGAAGAACAAGGATATTCCAAA 57.291 29.630 0.00 0.00 39.61 3.28
2013 10663 8.752005 TGAAGAACAAGGATATTCCAAATAGG 57.248 34.615 0.00 0.00 39.61 2.57
2014 10664 7.285401 TGAAGAACAAGGATATTCCAAATAGGC 59.715 37.037 0.00 0.00 39.61 3.93
2015 10665 6.071320 AGAACAAGGATATTCCAAATAGGCC 58.929 40.000 0.00 0.00 39.61 5.19
2016 10666 4.398319 ACAAGGATATTCCAAATAGGCCG 58.602 43.478 0.00 0.00 39.61 6.13
2017 10667 3.073274 AGGATATTCCAAATAGGCCGC 57.927 47.619 0.00 0.00 39.61 6.53
2018 10668 2.375174 AGGATATTCCAAATAGGCCGCA 59.625 45.455 0.00 0.00 39.61 5.69
2019 10669 2.749621 GGATATTCCAAATAGGCCGCAG 59.250 50.000 0.00 0.00 36.28 5.18
2020 10670 3.559171 GGATATTCCAAATAGGCCGCAGA 60.559 47.826 0.00 0.00 36.28 4.26
2021 10671 2.435372 ATTCCAAATAGGCCGCAGAA 57.565 45.000 0.00 0.00 37.29 3.02
2022 10672 1.750193 TTCCAAATAGGCCGCAGAAG 58.250 50.000 0.00 0.00 37.29 2.85
2023 10673 0.107214 TCCAAATAGGCCGCAGAAGG 60.107 55.000 0.00 0.00 37.29 3.46
2024 10674 1.103398 CCAAATAGGCCGCAGAAGGG 61.103 60.000 0.00 0.00 0.00 3.95
2025 10675 0.394352 CAAATAGGCCGCAGAAGGGT 60.394 55.000 0.00 0.00 0.00 4.34
2026 10676 1.134220 CAAATAGGCCGCAGAAGGGTA 60.134 52.381 0.00 0.00 0.00 3.69
2027 10677 1.209621 AATAGGCCGCAGAAGGGTAA 58.790 50.000 0.00 0.00 0.00 2.85
2028 10678 1.435256 ATAGGCCGCAGAAGGGTAAT 58.565 50.000 0.00 0.00 0.00 1.89
2029 10679 1.209621 TAGGCCGCAGAAGGGTAATT 58.790 50.000 0.00 0.00 0.00 1.40
2030 10680 1.209621 AGGCCGCAGAAGGGTAATTA 58.790 50.000 0.00 0.00 0.00 1.40
2031 10681 1.774856 AGGCCGCAGAAGGGTAATTAT 59.225 47.619 0.00 0.00 0.00 1.28
2032 10682 2.174854 AGGCCGCAGAAGGGTAATTATT 59.825 45.455 0.00 0.00 0.00 1.40
2033 10683 2.293399 GGCCGCAGAAGGGTAATTATTG 59.707 50.000 0.00 0.00 0.00 1.90
2034 10684 3.211045 GCCGCAGAAGGGTAATTATTGA 58.789 45.455 0.00 0.00 0.00 2.57
2035 10685 3.630312 GCCGCAGAAGGGTAATTATTGAA 59.370 43.478 0.00 0.00 0.00 2.69
2036 10686 4.497507 GCCGCAGAAGGGTAATTATTGAAC 60.498 45.833 0.00 0.00 0.00 3.18
2037 10687 4.638421 CCGCAGAAGGGTAATTATTGAACA 59.362 41.667 0.00 0.00 0.00 3.18
2038 10688 5.448632 CCGCAGAAGGGTAATTATTGAACAC 60.449 44.000 0.00 0.00 0.00 3.32
2039 10689 5.569413 GCAGAAGGGTAATTATTGAACACG 58.431 41.667 0.00 0.00 0.00 4.49
2040 10690 5.448632 GCAGAAGGGTAATTATTGAACACGG 60.449 44.000 0.00 0.00 0.00 4.94
2041 10691 5.878116 CAGAAGGGTAATTATTGAACACGGA 59.122 40.000 0.00 0.00 0.00 4.69
2042 10692 6.373216 CAGAAGGGTAATTATTGAACACGGAA 59.627 38.462 0.00 0.00 0.00 4.30
2043 10693 6.943718 AGAAGGGTAATTATTGAACACGGAAA 59.056 34.615 0.00 0.00 0.00 3.13
2044 10694 7.449086 AGAAGGGTAATTATTGAACACGGAAAA 59.551 33.333 0.00 0.00 0.00 2.29
2045 10695 7.712204 AGGGTAATTATTGAACACGGAAAAT 57.288 32.000 0.00 0.00 0.00 1.82
2046 10696 8.129496 AGGGTAATTATTGAACACGGAAAATT 57.871 30.769 0.00 0.00 0.00 1.82
2047 10697 8.248253 AGGGTAATTATTGAACACGGAAAATTC 58.752 33.333 0.00 0.00 0.00 2.17
2048 10698 8.030106 GGGTAATTATTGAACACGGAAAATTCA 58.970 33.333 0.00 0.00 0.00 2.57
2049 10699 9.413048 GGTAATTATTGAACACGGAAAATTCAA 57.587 29.630 1.49 1.49 44.18 2.69
2054 10704 6.384258 TTGAACACGGAAAATTCAATGAGA 57.616 33.333 0.00 0.00 37.41 3.27
2055 10705 6.573664 TGAACACGGAAAATTCAATGAGAT 57.426 33.333 0.00 0.00 29.56 2.75
2056 10706 6.380995 TGAACACGGAAAATTCAATGAGATG 58.619 36.000 0.00 0.00 29.56 2.90
2057 10707 6.206438 TGAACACGGAAAATTCAATGAGATGA 59.794 34.615 0.00 0.00 29.56 2.92
2058 10708 6.764308 ACACGGAAAATTCAATGAGATGAT 57.236 33.333 0.00 0.00 0.00 2.45
2059 10709 6.789262 ACACGGAAAATTCAATGAGATGATC 58.211 36.000 0.00 0.00 0.00 2.92
2060 10710 5.905733 CACGGAAAATTCAATGAGATGATCG 59.094 40.000 0.00 0.00 0.00 3.69
2061 10711 5.817296 ACGGAAAATTCAATGAGATGATCGA 59.183 36.000 0.00 0.00 0.00 3.59
2062 10712 6.484643 ACGGAAAATTCAATGAGATGATCGAT 59.515 34.615 0.00 0.00 0.00 3.59
2063 10713 7.657354 ACGGAAAATTCAATGAGATGATCGATA 59.343 33.333 0.00 0.00 0.00 2.92
2064 10714 8.663025 CGGAAAATTCAATGAGATGATCGATAT 58.337 33.333 0.00 0.00 0.00 1.63
2065 10715 9.770503 GGAAAATTCAATGAGATGATCGATATG 57.229 33.333 0.00 0.00 0.00 1.78
2066 10716 9.770503 GAAAATTCAATGAGATGATCGATATGG 57.229 33.333 0.00 0.00 0.00 2.74
2067 10717 7.860918 AATTCAATGAGATGATCGATATGGG 57.139 36.000 0.00 0.00 0.00 4.00
2068 10718 6.610075 TTCAATGAGATGATCGATATGGGA 57.390 37.500 0.00 0.00 0.00 4.37
2069 10719 6.218108 TCAATGAGATGATCGATATGGGAG 57.782 41.667 0.00 0.00 0.00 4.30
2070 10720 5.718607 TCAATGAGATGATCGATATGGGAGT 59.281 40.000 0.00 0.00 0.00 3.85
2071 10721 6.891908 TCAATGAGATGATCGATATGGGAGTA 59.108 38.462 0.00 0.00 0.00 2.59
2072 10722 6.707440 ATGAGATGATCGATATGGGAGTAC 57.293 41.667 0.00 0.00 0.00 2.73
2073 10723 4.950475 TGAGATGATCGATATGGGAGTACC 59.050 45.833 0.00 0.00 40.81 3.34
2083 10733 2.219080 TGGGAGTACCACGTGATACA 57.781 50.000 21.98 0.00 46.80 2.29
2084 10734 2.527497 TGGGAGTACCACGTGATACAA 58.473 47.619 21.98 2.01 46.80 2.41
2085 10735 2.231964 TGGGAGTACCACGTGATACAAC 59.768 50.000 21.98 14.38 46.80 3.32
2086 10736 2.494870 GGGAGTACCACGTGATACAACT 59.505 50.000 21.98 13.91 39.85 3.16
2087 10737 3.508762 GGAGTACCACGTGATACAACTG 58.491 50.000 21.98 2.74 35.97 3.16
2088 10738 3.057033 GGAGTACCACGTGATACAACTGT 60.057 47.826 21.98 8.77 35.97 3.55
2089 10739 4.553323 GAGTACCACGTGATACAACTGTT 58.447 43.478 21.98 0.00 0.00 3.16
2090 10740 4.952460 AGTACCACGTGATACAACTGTTT 58.048 39.130 21.98 0.00 0.00 2.83
2091 10741 6.088016 AGTACCACGTGATACAACTGTTTA 57.912 37.500 21.98 0.00 0.00 2.01
2092 10742 5.922544 AGTACCACGTGATACAACTGTTTAC 59.077 40.000 21.98 3.02 0.00 2.01
2093 10743 4.695396 ACCACGTGATACAACTGTTTACA 58.305 39.130 19.30 0.00 0.00 2.41
2094 10744 5.302360 ACCACGTGATACAACTGTTTACAT 58.698 37.500 19.30 0.00 0.00 2.29
2095 10745 5.178623 ACCACGTGATACAACTGTTTACATG 59.821 40.000 19.30 0.00 0.00 3.21
2096 10746 5.178623 CCACGTGATACAACTGTTTACATGT 59.821 40.000 19.30 2.69 0.00 3.21
2097 10747 6.070829 CACGTGATACAACTGTTTACATGTG 58.929 40.000 10.90 16.19 36.25 3.21
2098 10748 5.079406 CGTGATACAACTGTTTACATGTGC 58.921 41.667 9.11 0.00 0.00 4.57
2099 10749 5.333721 CGTGATACAACTGTTTACATGTGCA 60.334 40.000 9.11 4.08 0.00 4.57
2100 10750 6.611381 GTGATACAACTGTTTACATGTGCAT 58.389 36.000 9.11 0.00 0.00 3.96
2101 10751 6.524239 GTGATACAACTGTTTACATGTGCATG 59.476 38.462 9.11 10.31 44.15 4.06
2102 10752 6.429385 TGATACAACTGTTTACATGTGCATGA 59.571 34.615 17.85 0.60 41.20 3.07
2103 10753 5.710513 ACAACTGTTTACATGTGCATGAT 57.289 34.783 17.85 5.98 41.20 2.45
2104 10754 6.088016 ACAACTGTTTACATGTGCATGATT 57.912 33.333 17.85 0.45 41.20 2.57
2105 10755 5.921976 ACAACTGTTTACATGTGCATGATTG 59.078 36.000 17.85 9.04 41.20 2.67
2106 10756 5.963176 ACTGTTTACATGTGCATGATTGA 57.037 34.783 17.85 0.04 41.20 2.57
2107 10757 5.946298 ACTGTTTACATGTGCATGATTGAG 58.054 37.500 17.85 9.30 41.20 3.02
2108 10758 5.106038 ACTGTTTACATGTGCATGATTGAGG 60.106 40.000 17.85 7.10 41.20 3.86
2109 10759 4.158209 TGTTTACATGTGCATGATTGAGGG 59.842 41.667 17.85 0.00 41.20 4.30
2110 10760 2.519771 ACATGTGCATGATTGAGGGT 57.480 45.000 17.85 0.00 41.20 4.34
2111 10761 2.811410 ACATGTGCATGATTGAGGGTT 58.189 42.857 17.85 0.00 41.20 4.11
2112 10762 3.966979 ACATGTGCATGATTGAGGGTTA 58.033 40.909 17.85 0.00 41.20 2.85
2113 10763 4.539726 ACATGTGCATGATTGAGGGTTAT 58.460 39.130 17.85 0.00 41.20 1.89
2114 10764 4.957954 ACATGTGCATGATTGAGGGTTATT 59.042 37.500 17.85 0.00 41.20 1.40
2115 10765 5.422970 ACATGTGCATGATTGAGGGTTATTT 59.577 36.000 17.85 0.00 41.20 1.40
2116 10766 5.327616 TGTGCATGATTGAGGGTTATTTG 57.672 39.130 0.00 0.00 0.00 2.32
2117 10767 5.015515 TGTGCATGATTGAGGGTTATTTGA 58.984 37.500 0.00 0.00 0.00 2.69
2118 10768 5.479724 TGTGCATGATTGAGGGTTATTTGAA 59.520 36.000 0.00 0.00 0.00 2.69
2119 10769 6.154877 TGTGCATGATTGAGGGTTATTTGAAT 59.845 34.615 0.00 0.00 0.00 2.57
2120 10770 6.698766 GTGCATGATTGAGGGTTATTTGAATC 59.301 38.462 0.00 0.00 0.00 2.52
2121 10771 6.380560 TGCATGATTGAGGGTTATTTGAATCA 59.619 34.615 0.00 0.00 35.06 2.57
2173 10823 8.099364 TGATTACTGAAATGAAGAACAAGGAC 57.901 34.615 0.00 0.00 0.00 3.85
2382 13322 4.080356 TCATGGTCATTCTTTCGAAGGGAT 60.080 41.667 7.49 0.64 32.11 3.85
2668 13624 1.000955 AGGACAACATGACCAGTCGAC 59.999 52.381 7.70 7.70 34.63 4.20
2669 13625 1.270094 GGACAACATGACCAGTCGACA 60.270 52.381 19.50 0.00 32.46 4.35
2774 13798 6.071728 GGATATGCCATTTTATCCTGGAGTTG 60.072 42.308 1.52 0.00 40.42 3.16
2775 13799 2.760092 TGCCATTTTATCCTGGAGTTGC 59.240 45.455 1.52 0.00 34.24 4.17
2776 13800 3.026694 GCCATTTTATCCTGGAGTTGCT 58.973 45.455 1.52 0.00 34.24 3.91
2960 14147 7.725251 TCTTTTCTGTTTGCATGAAATAACCT 58.275 30.769 0.00 0.00 31.08 3.50
2984 16381 1.081556 TTTCCCGACATCACATCGCG 61.082 55.000 0.00 0.00 38.27 5.87
3023 16420 3.068732 TCAATCTCTGCAAGGAGGTATCG 59.931 47.826 3.36 0.00 34.39 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.404923 TCCAAAACGACTCAACACCA 57.595 45.000 0.00 0.00 0.00 4.17
204 205 2.761208 ACATCACCCGGTTTTGAAACAA 59.239 40.909 0.00 0.00 40.63 2.83
398 399 2.092429 TGCAAGACTTCCAGGAAACAGT 60.092 45.455 2.72 0.00 0.00 3.55
442 443 7.517614 TGTTGTTAATTCTGCTTCCATTGTA 57.482 32.000 0.00 0.00 0.00 2.41
477 478 0.321564 CCATCCTGCTTCGACACCAA 60.322 55.000 0.00 0.00 0.00 3.67
671 672 3.643763 GGACATACTCCAACGCTATCAG 58.356 50.000 0.00 0.00 39.21 2.90
731 732 2.425578 TCTATCACAACACGCGACAA 57.574 45.000 15.93 0.00 0.00 3.18
733 734 5.231357 TGAATTATCTATCACAACACGCGAC 59.769 40.000 15.93 0.00 0.00 5.19
755 756 3.906218 CTCATACCCATCTCCCTTGATGA 59.094 47.826 6.12 0.00 44.71 2.92
760 761 2.695585 GGTCTCATACCCATCTCCCTT 58.304 52.381 0.00 0.00 43.16 3.95
805 806 2.890808 TCTCCGATCACATAGGTTGC 57.109 50.000 0.00 0.00 0.00 4.17
1470 9937 1.164411 CGCTTGGCATAACACCTTGA 58.836 50.000 0.00 0.00 0.00 3.02
2003 10653 1.681780 CCTTCTGCGGCCTATTTGGAA 60.682 52.381 0.00 0.00 38.35 3.53
2004 10654 0.107214 CCTTCTGCGGCCTATTTGGA 60.107 55.000 0.00 0.00 38.35 3.53
2005 10655 1.103398 CCCTTCTGCGGCCTATTTGG 61.103 60.000 0.00 0.00 39.35 3.28
2006 10656 0.394352 ACCCTTCTGCGGCCTATTTG 60.394 55.000 0.00 0.00 0.00 2.32
2007 10657 1.209621 TACCCTTCTGCGGCCTATTT 58.790 50.000 0.00 0.00 0.00 1.40
2008 10658 1.209621 TTACCCTTCTGCGGCCTATT 58.790 50.000 0.00 0.00 0.00 1.73
2009 10659 1.435256 ATTACCCTTCTGCGGCCTAT 58.565 50.000 0.00 0.00 0.00 2.57
2010 10660 1.209621 AATTACCCTTCTGCGGCCTA 58.790 50.000 0.00 0.00 0.00 3.93
2011 10661 1.209621 TAATTACCCTTCTGCGGCCT 58.790 50.000 0.00 0.00 0.00 5.19
2012 10662 2.271944 ATAATTACCCTTCTGCGGCC 57.728 50.000 0.00 0.00 0.00 6.13
2013 10663 3.211045 TCAATAATTACCCTTCTGCGGC 58.789 45.455 0.00 0.00 0.00 6.53
2014 10664 4.638421 TGTTCAATAATTACCCTTCTGCGG 59.362 41.667 0.00 0.00 0.00 5.69
2015 10665 5.569413 GTGTTCAATAATTACCCTTCTGCG 58.431 41.667 0.00 0.00 0.00 5.18
2016 10666 5.448632 CCGTGTTCAATAATTACCCTTCTGC 60.449 44.000 0.00 0.00 0.00 4.26
2017 10667 5.878116 TCCGTGTTCAATAATTACCCTTCTG 59.122 40.000 0.00 0.00 0.00 3.02
2018 10668 6.057321 TCCGTGTTCAATAATTACCCTTCT 57.943 37.500 0.00 0.00 0.00 2.85
2019 10669 6.746745 TTCCGTGTTCAATAATTACCCTTC 57.253 37.500 0.00 0.00 0.00 3.46
2020 10670 7.527568 TTTTCCGTGTTCAATAATTACCCTT 57.472 32.000 0.00 0.00 0.00 3.95
2021 10671 7.712204 ATTTTCCGTGTTCAATAATTACCCT 57.288 32.000 0.00 0.00 0.00 4.34
2022 10672 8.030106 TGAATTTTCCGTGTTCAATAATTACCC 58.970 33.333 0.00 0.00 0.00 3.69
2023 10673 8.973835 TGAATTTTCCGTGTTCAATAATTACC 57.026 30.769 0.00 0.00 0.00 2.85
2026 10676 9.703892 TCATTGAATTTTCCGTGTTCAATAATT 57.296 25.926 10.98 0.00 45.64 1.40
2027 10677 9.357652 CTCATTGAATTTTCCGTGTTCAATAAT 57.642 29.630 10.98 0.00 45.64 1.28
2028 10678 8.572185 TCTCATTGAATTTTCCGTGTTCAATAA 58.428 29.630 10.98 0.00 45.64 1.40
2029 10679 8.105097 TCTCATTGAATTTTCCGTGTTCAATA 57.895 30.769 10.98 0.00 45.64 1.90
2031 10681 6.384258 TCTCATTGAATTTTCCGTGTTCAA 57.616 33.333 2.71 2.71 43.51 2.69
2032 10682 6.206438 TCATCTCATTGAATTTTCCGTGTTCA 59.794 34.615 0.00 0.00 0.00 3.18
2033 10683 6.611381 TCATCTCATTGAATTTTCCGTGTTC 58.389 36.000 0.00 0.00 0.00 3.18
2034 10684 6.573664 TCATCTCATTGAATTTTCCGTGTT 57.426 33.333 0.00 0.00 0.00 3.32
2035 10685 6.457392 CGATCATCTCATTGAATTTTCCGTGT 60.457 38.462 0.00 0.00 0.00 4.49
2036 10686 5.905733 CGATCATCTCATTGAATTTTCCGTG 59.094 40.000 0.00 0.00 0.00 4.94
2037 10687 5.817296 TCGATCATCTCATTGAATTTTCCGT 59.183 36.000 0.00 0.00 0.00 4.69
2038 10688 6.291067 TCGATCATCTCATTGAATTTTCCG 57.709 37.500 0.00 0.00 0.00 4.30
2039 10689 9.770503 CATATCGATCATCTCATTGAATTTTCC 57.229 33.333 0.00 0.00 0.00 3.13
2040 10690 9.770503 CCATATCGATCATCTCATTGAATTTTC 57.229 33.333 0.00 0.00 0.00 2.29
2041 10691 8.737175 CCCATATCGATCATCTCATTGAATTTT 58.263 33.333 0.00 0.00 0.00 1.82
2042 10692 8.105197 TCCCATATCGATCATCTCATTGAATTT 58.895 33.333 0.00 0.00 0.00 1.82
2043 10693 7.627311 TCCCATATCGATCATCTCATTGAATT 58.373 34.615 0.00 0.00 0.00 2.17
2044 10694 7.092979 ACTCCCATATCGATCATCTCATTGAAT 60.093 37.037 0.00 0.00 0.00 2.57
2045 10695 6.212187 ACTCCCATATCGATCATCTCATTGAA 59.788 38.462 0.00 0.00 0.00 2.69
2046 10696 5.718607 ACTCCCATATCGATCATCTCATTGA 59.281 40.000 0.00 0.00 0.00 2.57
2047 10697 5.975282 ACTCCCATATCGATCATCTCATTG 58.025 41.667 0.00 0.00 0.00 2.82
2048 10698 6.097554 GGTACTCCCATATCGATCATCTCATT 59.902 42.308 0.00 0.00 0.00 2.57
2049 10699 5.596361 GGTACTCCCATATCGATCATCTCAT 59.404 44.000 0.00 0.00 0.00 2.90
2050 10700 4.950475 GGTACTCCCATATCGATCATCTCA 59.050 45.833 0.00 0.00 0.00 3.27
2051 10701 4.950475 TGGTACTCCCATATCGATCATCTC 59.050 45.833 0.00 0.00 38.72 2.75
2052 10702 4.935578 TGGTACTCCCATATCGATCATCT 58.064 43.478 0.00 0.00 38.72 2.90
2064 10714 2.219080 TGTATCACGTGGTACTCCCA 57.781 50.000 32.66 15.19 42.51 4.37
2065 10715 2.494870 AGTTGTATCACGTGGTACTCCC 59.505 50.000 32.66 21.84 0.00 4.30
2066 10716 3.057033 ACAGTTGTATCACGTGGTACTCC 60.057 47.826 32.66 23.89 0.00 3.85
2067 10717 4.170292 ACAGTTGTATCACGTGGTACTC 57.830 45.455 32.66 25.41 0.00 2.59
2068 10718 4.595762 AACAGTTGTATCACGTGGTACT 57.404 40.909 32.66 17.26 0.00 2.73
2069 10719 5.691305 TGTAAACAGTTGTATCACGTGGTAC 59.309 40.000 28.24 28.24 0.00 3.34
2070 10720 5.840715 TGTAAACAGTTGTATCACGTGGTA 58.159 37.500 17.00 10.73 0.00 3.25
2071 10721 4.695396 TGTAAACAGTTGTATCACGTGGT 58.305 39.130 17.00 12.05 0.00 4.16
2072 10722 5.178623 ACATGTAAACAGTTGTATCACGTGG 59.821 40.000 17.00 0.00 0.00 4.94
2073 10723 6.070829 CACATGTAAACAGTTGTATCACGTG 58.929 40.000 9.94 9.94 0.00 4.49
2074 10724 5.333798 GCACATGTAAACAGTTGTATCACGT 60.334 40.000 0.00 0.00 0.00 4.49
2075 10725 5.079406 GCACATGTAAACAGTTGTATCACG 58.921 41.667 0.00 0.00 0.00 4.35
2076 10726 5.996219 TGCACATGTAAACAGTTGTATCAC 58.004 37.500 0.00 0.00 0.00 3.06
2077 10727 6.429385 TCATGCACATGTAAACAGTTGTATCA 59.571 34.615 10.27 0.00 39.72 2.15
2078 10728 6.841119 TCATGCACATGTAAACAGTTGTATC 58.159 36.000 10.27 0.00 39.72 2.24
2079 10729 6.816134 TCATGCACATGTAAACAGTTGTAT 57.184 33.333 10.27 0.00 39.72 2.29
2080 10730 6.816134 ATCATGCACATGTAAACAGTTGTA 57.184 33.333 10.27 0.00 39.72 2.41
2081 10731 5.710513 ATCATGCACATGTAAACAGTTGT 57.289 34.783 10.27 0.00 39.72 3.32
2082 10732 6.151004 TCAATCATGCACATGTAAACAGTTG 58.849 36.000 10.27 1.12 39.72 3.16
2083 10733 6.330004 TCAATCATGCACATGTAAACAGTT 57.670 33.333 10.27 0.00 39.72 3.16
2084 10734 5.106038 CCTCAATCATGCACATGTAAACAGT 60.106 40.000 10.27 0.00 39.72 3.55
2085 10735 5.337554 CCTCAATCATGCACATGTAAACAG 58.662 41.667 10.27 2.58 39.72 3.16
2086 10736 4.158209 CCCTCAATCATGCACATGTAAACA 59.842 41.667 10.27 0.00 39.72 2.83
2087 10737 4.158394 ACCCTCAATCATGCACATGTAAAC 59.842 41.667 10.27 0.00 39.72 2.01
2088 10738 4.343231 ACCCTCAATCATGCACATGTAAA 58.657 39.130 10.27 0.00 39.72 2.01
2089 10739 3.966979 ACCCTCAATCATGCACATGTAA 58.033 40.909 10.27 0.00 39.72 2.41
2090 10740 3.650281 ACCCTCAATCATGCACATGTA 57.350 42.857 10.27 0.00 39.72 2.29
2091 10741 2.519771 ACCCTCAATCATGCACATGT 57.480 45.000 10.27 0.00 39.72 3.21
2092 10742 5.524971 AATAACCCTCAATCATGCACATG 57.475 39.130 4.18 4.18 40.09 3.21
2093 10743 5.657745 TCAAATAACCCTCAATCATGCACAT 59.342 36.000 0.00 0.00 0.00 3.21
2094 10744 5.015515 TCAAATAACCCTCAATCATGCACA 58.984 37.500 0.00 0.00 0.00 4.57
2095 10745 5.581126 TCAAATAACCCTCAATCATGCAC 57.419 39.130 0.00 0.00 0.00 4.57
2096 10746 6.380560 TGATTCAAATAACCCTCAATCATGCA 59.619 34.615 0.00 0.00 0.00 3.96
2097 10747 6.698766 GTGATTCAAATAACCCTCAATCATGC 59.301 38.462 0.00 0.00 33.89 4.06
2098 10748 6.914215 CGTGATTCAAATAACCCTCAATCATG 59.086 38.462 0.00 0.00 33.89 3.07
2099 10749 6.039717 CCGTGATTCAAATAACCCTCAATCAT 59.960 38.462 0.00 0.00 33.89 2.45
2100 10750 5.356751 CCGTGATTCAAATAACCCTCAATCA 59.643 40.000 0.00 0.00 0.00 2.57
2101 10751 5.357032 ACCGTGATTCAAATAACCCTCAATC 59.643 40.000 0.00 0.00 0.00 2.67
2102 10752 5.125417 CACCGTGATTCAAATAACCCTCAAT 59.875 40.000 0.00 0.00 0.00 2.57
2103 10753 4.457603 CACCGTGATTCAAATAACCCTCAA 59.542 41.667 0.00 0.00 0.00 3.02
2104 10754 4.006989 CACCGTGATTCAAATAACCCTCA 58.993 43.478 0.00 0.00 0.00 3.86
2105 10755 4.094442 GTCACCGTGATTCAAATAACCCTC 59.906 45.833 4.13 0.00 0.00 4.30
2106 10756 4.007659 GTCACCGTGATTCAAATAACCCT 58.992 43.478 4.13 0.00 0.00 4.34
2107 10757 4.007659 AGTCACCGTGATTCAAATAACCC 58.992 43.478 4.13 0.00 0.00 4.11
2108 10758 4.094442 GGAGTCACCGTGATTCAAATAACC 59.906 45.833 21.55 3.77 35.16 2.85
2109 10759 4.693566 TGGAGTCACCGTGATTCAAATAAC 59.306 41.667 21.55 7.34 42.61 1.89
2110 10760 4.900684 TGGAGTCACCGTGATTCAAATAA 58.099 39.130 21.55 3.45 42.61 1.40
2111 10761 4.545208 TGGAGTCACCGTGATTCAAATA 57.455 40.909 21.55 6.07 42.61 1.40
2112 10762 3.417069 TGGAGTCACCGTGATTCAAAT 57.583 42.857 21.55 0.00 42.61 2.32
2113 10763 2.920724 TGGAGTCACCGTGATTCAAA 57.079 45.000 21.55 9.59 42.61 2.69
2121 10771 0.670546 CGCTTTCATGGAGTCACCGT 60.671 55.000 0.00 0.00 42.61 4.83
2173 10823 0.249447 TCTGCGGCCTATGACGAATG 60.249 55.000 0.00 0.00 0.00 2.67
2382 13322 7.993183 AGGAAAGTGAAATTGTTCTGTTCTCTA 59.007 33.333 0.00 0.00 34.60 2.43
2960 14147 1.974265 TGTGATGTCGGGAAAGCAAA 58.026 45.000 0.00 0.00 0.00 3.68
2984 16381 6.481644 AGAGATTGAAGAACTTGACAAGTCAC 59.518 38.462 20.81 16.77 41.91 3.67


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

AutoCloner maintained by Alex Coulton.