Multiple sequence alignment - TraesCS2D01G586000

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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 TraesCS2D01G586000 chr2D 100.000 3909 0 0 1 3909 644717514 644721422 0.000000e+00 7219
1 TraesCS2D01G586000 chr2D 79.348 460 79 10 2607 3053 644518777 644519233 3.790000e-80 309
2 TraesCS2D01G586000 chr2A 92.596 3836 166 39 111 3909 770008868 770012622 0.000000e+00 5402
3 TraesCS2D01G586000 chr2A 87.241 870 92 15 1205 2059 770005166 770006031 0.000000e+00 974
4 TraesCS2D01G586000 chr2A 86.108 871 77 23 109 960 769982904 769983749 0.000000e+00 898
5 TraesCS2D01G586000 chr2A 80.750 1174 165 35 1047 2198 769983747 769984881 0.000000e+00 859
6 TraesCS2D01G586000 chr2A 80.078 773 136 14 1437 2202 769489119 769489880 3.410000e-155 558
7 TraesCS2D01G586000 chr2A 77.208 917 143 40 1827 2724 757870074 757870943 3.530000e-130 475
8 TraesCS2D01G586000 chr2A 84.667 450 44 11 190 630 770000306 770000739 3.610000e-115 425
9 TraesCS2D01G586000 chr2A 82.436 427 59 8 718 1133 770004716 770005137 3.710000e-95 359
10 TraesCS2D01G586000 chr2A 81.892 370 60 5 1429 1797 757869716 757870079 4.910000e-79 305
11 TraesCS2D01G586000 chr2A 82.301 226 36 2 2535 2758 769985220 769985443 3.990000e-45 193
12 TraesCS2D01G586000 chr2A 82.301 226 34 3 2535 2758 770006506 770006727 1.430000e-44 191
13 TraesCS2D01G586000 chr2B 92.396 3827 189 41 110 3909 790756388 790752637 0.000000e+00 5361
14 TraesCS2D01G586000 chr2B 85.937 1735 208 20 715 2424 790863337 790861614 0.000000e+00 1820
15 TraesCS2D01G586000 chr2B 83.834 1231 162 25 993 2198 790858324 790857106 0.000000e+00 1136
16 TraesCS2D01G586000 chr2B 91.816 782 50 10 2529 3310 790861374 790860607 0.000000e+00 1077
17 TraesCS2D01G586000 chr2B 82.640 553 55 18 105 630 790863908 790863370 5.960000e-123 451
18 TraesCS2D01G586000 chr2B 88.793 348 29 2 112 459 790859206 790858869 6.040000e-113 418
19 TraesCS2D01G586000 chr2B 82.734 417 35 21 3060 3455 17482371 17481971 1.740000e-88 337
20 TraesCS2D01G586000 chr2B 83.486 218 34 2 2541 2758 790856760 790856545 6.620000e-48 202
21 TraesCS2D01G586000 chr2B 93.000 100 7 0 2659 2758 790775780 790775681 3.150000e-31 147
22 TraesCS2D01G586000 chr3D 88.255 1524 128 22 1778 3282 588315854 588317345 0.000000e+00 1775
23 TraesCS2D01G586000 chr3D 78.324 752 82 41 3221 3909 588317343 588318076 1.010000e-110 411
24 TraesCS2D01G586000 chr3A 81.363 1218 109 54 2753 3909 718351467 718352627 0.000000e+00 883
25 TraesCS2D01G586000 chr3A 89.181 342 30 5 2407 2747 718350867 718351202 1.680000e-113 420
26 TraesCS2D01G586000 chr3B 82.426 882 70 43 2830 3660 786723154 786724001 0.000000e+00 691
27 TraesCS2D01G586000 chr3B 82.507 383 29 19 3085 3446 168989660 168990025 6.350000e-78 302
28 TraesCS2D01G586000 chr3B 99.038 104 0 1 6 108 655449635 655449738 6.670000e-43 185
29 TraesCS2D01G586000 chr3B 90.090 111 10 1 2669 2779 786723046 786723155 4.070000e-30 143
30 TraesCS2D01G586000 chr4B 83.455 411 31 20 3057 3446 76501458 76501852 8.040000e-92 348
31 TraesCS2D01G586000 chr4B 83.088 408 32 20 3057 3443 592372657 592373048 1.740000e-88 337
32 TraesCS2D01G586000 chr7B 83.538 407 30 23 3061 3446 571234882 571235272 2.890000e-91 346
33 TraesCS2D01G586000 chr7B 95.455 110 4 1 1 109 293132813 293132922 1.440000e-39 174
34 TraesCS2D01G586000 chr5B 83.212 411 32 23 3057 3446 685680387 685680781 3.740000e-90 342
35 TraesCS2D01G586000 chr5B 82.968 411 33 22 3057 3446 534293000 534293394 1.740000e-88 337
36 TraesCS2D01G586000 chr1B 82.974 417 34 23 3060 3455 10526642 10526242 3.740000e-90 342
37 TraesCS2D01G586000 chr1A 83.212 411 32 23 3057 3446 575301618 575302012 3.740000e-90 342
38 TraesCS2D01G586000 chrUn 82.014 417 38 21 3060 3455 34685341 34684941 1.750000e-83 320
39 TraesCS2D01G586000 chr4A 84.211 247 16 12 3229 3455 655273432 655273189 6.580000e-53 219


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 TraesCS2D01G586000 chr2D 644717514 644721422 3908 False 7219.000000 7219 100.000000 1 3909 1 chr2D.!!$F2 3908
1 TraesCS2D01G586000 chr2A 770000306 770012622 12316 False 1470.200000 5402 85.848200 111 3909 5 chr2A.!!$F4 3798
2 TraesCS2D01G586000 chr2A 769982904 769985443 2539 False 650.000000 898 83.053000 109 2758 3 chr2A.!!$F3 2649
3 TraesCS2D01G586000 chr2A 769489119 769489880 761 False 558.000000 558 80.078000 1437 2202 1 chr2A.!!$F1 765
4 TraesCS2D01G586000 chr2A 757869716 757870943 1227 False 390.000000 475 79.550000 1429 2724 2 chr2A.!!$F2 1295
5 TraesCS2D01G586000 chr2B 790752637 790756388 3751 True 5361.000000 5361 92.396000 110 3909 1 chr2B.!!$R2 3799
6 TraesCS2D01G586000 chr2B 790856545 790863908 7363 True 850.666667 1820 86.084333 105 3310 6 chr2B.!!$R4 3205
7 TraesCS2D01G586000 chr3D 588315854 588318076 2222 False 1093.000000 1775 83.289500 1778 3909 2 chr3D.!!$F1 2131
8 TraesCS2D01G586000 chr3A 718350867 718352627 1760 False 651.500000 883 85.272000 2407 3909 2 chr3A.!!$F1 1502
9 TraesCS2D01G586000 chr3B 786723046 786724001 955 False 417.000000 691 86.258000 2669 3660 2 chr3B.!!$F3 991

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
657 9149 0.036388 TGATGTTCCTTCAGGCCGAC 60.036 55.0 0.00 0.0 34.44 4.79 F
858 9373 0.545646 TGGCGGGATTCATGATCACA 59.454 50.0 0.00 0.0 38.11 3.58 F
2145 10717 0.321122 CACCGAGCTTGCTCTTCCTT 60.321 55.0 18.75 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 10345 4.201744 ACACCGTTTTTAGTGTGAGTTTCG 60.202 41.667 0.0 0.0 45.24 3.46 R
2811 11858 2.332117 GGTAATGGTCCCCCTCGATAA 58.668 52.381 0.0 0.0 0.00 1.75 R
3614 12866 1.004745 TGGCTCTGTCCCCTCATTTTC 59.995 52.381 0.0 0.0 0.00 2.29 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 2.338620 TCTGGACGACCAACAGCG 59.661 61.111 8.23 0.00 46.32 5.18
18 19 2.738521 CTGGACGACCAACAGCGG 60.739 66.667 8.23 0.00 46.32 5.52
19 20 3.515316 CTGGACGACCAACAGCGGT 62.515 63.158 8.23 0.00 46.32 5.68
20 21 2.149803 CTGGACGACCAACAGCGGTA 62.150 60.000 8.23 0.00 46.32 4.02
21 22 1.445582 GGACGACCAACAGCGGTAG 60.446 63.158 0.00 0.00 40.22 3.18
22 23 1.288127 GACGACCAACAGCGGTAGT 59.712 57.895 0.00 0.00 46.20 2.73
23 24 0.523072 GACGACCAACAGCGGTAGTA 59.477 55.000 0.00 0.00 43.93 1.82
24 25 1.133790 GACGACCAACAGCGGTAGTAT 59.866 52.381 0.00 0.00 43.93 2.12
25 26 2.355756 GACGACCAACAGCGGTAGTATA 59.644 50.000 0.00 0.00 43.93 1.47
27 28 3.193267 ACGACCAACAGCGGTAGTATAAA 59.807 43.478 0.00 0.00 42.35 1.40
28 29 4.175516 CGACCAACAGCGGTAGTATAAAA 58.824 43.478 0.00 0.00 40.22 1.52
30 31 5.978919 CGACCAACAGCGGTAGTATAAAATA 59.021 40.000 0.00 0.00 40.22 1.40
31 32 6.476380 CGACCAACAGCGGTAGTATAAAATAA 59.524 38.462 0.00 0.00 40.22 1.40
32 33 7.170320 CGACCAACAGCGGTAGTATAAAATAAT 59.830 37.037 0.00 0.00 40.22 1.28
33 34 8.374327 ACCAACAGCGGTAGTATAAAATAATC 57.626 34.615 0.00 0.00 37.57 1.75
34 35 7.170320 ACCAACAGCGGTAGTATAAAATAATCG 59.830 37.037 0.00 0.00 37.57 3.34
35 36 6.701432 ACAGCGGTAGTATAAAATAATCGC 57.299 37.500 0.00 0.00 40.75 4.58
36 37 6.218019 ACAGCGGTAGTATAAAATAATCGCA 58.782 36.000 0.00 0.00 42.53 5.10
37 38 6.145048 ACAGCGGTAGTATAAAATAATCGCAC 59.855 38.462 0.00 0.00 42.53 5.34
39 40 6.145048 AGCGGTAGTATAAAATAATCGCACAC 59.855 38.462 0.00 0.00 42.53 3.82
42 43 8.160342 CGGTAGTATAAAATAATCGCACACATC 58.840 37.037 0.00 0.00 0.00 3.06
43 44 8.440833 GGTAGTATAAAATAATCGCACACATCC 58.559 37.037 0.00 0.00 0.00 3.51
44 45 8.984764 GTAGTATAAAATAATCGCACACATCCA 58.015 33.333 0.00 0.00 0.00 3.41
45 46 8.621532 AGTATAAAATAATCGCACACATCCAT 57.378 30.769 0.00 0.00 0.00 3.41
46 47 9.719355 AGTATAAAATAATCGCACACATCCATA 57.281 29.630 0.00 0.00 0.00 2.74
48 49 5.947228 AAATAATCGCACACATCCATAGG 57.053 39.130 0.00 0.00 0.00 2.57
50 51 0.601046 ATCGCACACATCCATAGGCG 60.601 55.000 0.00 0.00 45.24 5.52
51 52 2.885676 CGCACACATCCATAGGCGC 61.886 63.158 0.00 0.00 37.96 6.53
52 53 2.546494 GCACACATCCATAGGCGCC 61.546 63.158 21.89 21.89 0.00 6.53
54 55 1.146930 ACACATCCATAGGCGCCAG 59.853 57.895 31.54 17.91 0.00 4.85
55 56 2.111878 ACATCCATAGGCGCCAGC 59.888 61.111 31.54 0.33 44.18 4.85
77 78 1.557099 ACCTGTGGATAACGAGAGCA 58.443 50.000 0.00 0.00 0.00 4.26
78 79 2.111384 ACCTGTGGATAACGAGAGCAT 58.889 47.619 0.00 0.00 0.00 3.79
79 80 2.501723 ACCTGTGGATAACGAGAGCATT 59.498 45.455 0.00 0.00 0.00 3.56
80 81 3.055094 ACCTGTGGATAACGAGAGCATTT 60.055 43.478 0.00 0.00 0.00 2.32
81 82 3.310774 CCTGTGGATAACGAGAGCATTTG 59.689 47.826 0.00 0.00 0.00 2.32
82 83 4.183865 CTGTGGATAACGAGAGCATTTGA 58.816 43.478 0.00 0.00 0.00 2.69
83 84 4.183865 TGTGGATAACGAGAGCATTTGAG 58.816 43.478 0.00 0.00 0.00 3.02
91 92 4.384599 AGCATTTGAGCTCGTGCA 57.615 50.000 28.69 5.18 42.18 4.57
93 94 0.886043 AGCATTTGAGCTCGTGCACA 60.886 50.000 28.69 8.95 42.18 4.57
94 95 0.453950 GCATTTGAGCTCGTGCACAG 60.454 55.000 24.81 14.03 40.57 3.66
95 96 0.870393 CATTTGAGCTCGTGCACAGT 59.130 50.000 18.64 0.00 40.57 3.55
96 97 1.265095 CATTTGAGCTCGTGCACAGTT 59.735 47.619 18.64 11.18 40.57 3.16
97 98 2.232756 TTTGAGCTCGTGCACAGTTA 57.767 45.000 18.64 0.00 40.57 2.24
98 99 1.497991 TTGAGCTCGTGCACAGTTAC 58.502 50.000 18.64 5.57 40.57 2.50
100 101 1.335964 TGAGCTCGTGCACAGTTACTC 60.336 52.381 18.64 15.04 42.74 2.59
101 102 0.038159 AGCTCGTGCACAGTTACTCC 60.038 55.000 18.64 0.30 42.74 3.85
102 103 1.344942 GCTCGTGCACAGTTACTCCG 61.345 60.000 18.64 0.00 39.41 4.63
103 104 1.344942 CTCGTGCACAGTTACTCCGC 61.345 60.000 18.64 0.00 0.00 5.54
108 109 1.287815 CACAGTTACTCCGCGTCCA 59.712 57.895 4.92 0.00 0.00 4.02
442 8920 2.202878 GGCGCCGCTACTCAATCA 60.203 61.111 12.58 0.00 0.00 2.57
482 8960 5.506317 CGAATCCCTGTTAAGAATTGATGGC 60.506 44.000 0.00 0.00 0.00 4.40
500 8978 1.305930 GCCGCGTTCCTCAATTCCTT 61.306 55.000 4.92 0.00 0.00 3.36
501 8979 0.447801 CCGCGTTCCTCAATTCCTTG 59.552 55.000 4.92 0.00 0.00 3.61
512 8990 5.536161 TCCTCAATTCCTTGGAGAAAAACAG 59.464 40.000 0.00 0.00 32.95 3.16
515 8993 5.890985 TCAATTCCTTGGAGAAAAACAGTCA 59.109 36.000 0.00 0.00 32.95 3.41
546 9024 2.130193 TGCTGAATGGAGGCTAGGATT 58.870 47.619 0.00 0.00 0.00 3.01
579 9071 3.371034 TCCAGTTCCAATCCTACGATCA 58.629 45.455 0.00 0.00 0.00 2.92
612 9104 9.480538 CAAAATTTTGAATTTTCATATGAGCGG 57.519 29.630 23.72 0.00 40.55 5.52
630 9122 2.038557 GCGGATCCCCATTGTAGTGTAT 59.961 50.000 6.06 0.00 0.00 2.29
631 9123 3.259876 GCGGATCCCCATTGTAGTGTATA 59.740 47.826 6.06 0.00 0.00 1.47
632 9124 4.262721 GCGGATCCCCATTGTAGTGTATAA 60.263 45.833 6.06 0.00 0.00 0.98
633 9125 5.570844 GCGGATCCCCATTGTAGTGTATAAT 60.571 44.000 6.06 0.00 0.00 1.28
634 9126 5.874810 CGGATCCCCATTGTAGTGTATAATG 59.125 44.000 6.06 0.00 37.12 1.90
635 9127 6.520061 CGGATCCCCATTGTAGTGTATAATGT 60.520 42.308 6.06 0.00 36.07 2.71
636 9128 7.310175 CGGATCCCCATTGTAGTGTATAATGTA 60.310 40.741 6.06 0.00 36.07 2.29
637 9129 7.822822 GGATCCCCATTGTAGTGTATAATGTAC 59.177 40.741 0.00 0.00 36.07 2.90
638 9130 7.924358 TCCCCATTGTAGTGTATAATGTACT 57.076 36.000 0.00 0.00 36.07 2.73
639 9131 7.732025 TCCCCATTGTAGTGTATAATGTACTG 58.268 38.462 0.00 0.00 36.07 2.74
657 9149 0.036388 TGATGTTCCTTCAGGCCGAC 60.036 55.000 0.00 0.00 34.44 4.79
664 9156 3.713826 TCCTTCAGGCCGACTTTAAAT 57.286 42.857 0.00 0.00 34.44 1.40
735 9235 7.110043 AGGCTAGTAACCTGTAATGTAAGTC 57.890 40.000 0.00 0.00 35.72 3.01
770 9283 9.693739 AAAAATAAAAAGGGAAAAATCCTGTGT 57.306 25.926 0.00 0.00 34.34 3.72
787 9300 7.914427 TCCTGTGTTGTAAGATACCTGATAT 57.086 36.000 0.00 0.00 0.00 1.63
858 9373 0.545646 TGGCGGGATTCATGATCACA 59.454 50.000 0.00 0.00 38.11 3.58
876 9398 3.817084 TCACAATTGCTCTCTGAAACCAG 59.183 43.478 5.05 0.00 0.00 4.00
893 9415 3.894759 ACCAGTGATAATGATGCTTGCT 58.105 40.909 0.00 0.00 0.00 3.91
908 9430 5.063180 TGCTTGCTGAAACCAATGATAAG 57.937 39.130 0.00 0.00 0.00 1.73
911 9433 5.163478 GCTTGCTGAAACCAATGATAAGGAT 60.163 40.000 0.00 0.00 0.00 3.24
1070 9596 3.181448 GGTTTCAGTAGGGTGGAGAAACA 60.181 47.826 15.47 0.00 45.90 2.83
1075 9601 2.303311 AGTAGGGTGGAGAAACAGAAGC 59.697 50.000 0.00 0.00 0.00 3.86
1187 9722 1.476845 TTAGCAAGGGGAGCGTGACA 61.477 55.000 0.00 0.00 37.01 3.58
1188 9723 1.264749 TAGCAAGGGGAGCGTGACAT 61.265 55.000 0.00 0.00 37.01 3.06
1196 9731 2.231235 GGGGAGCGTGACATTTGAATTT 59.769 45.455 0.00 0.00 0.00 1.82
1211 9746 7.714377 ACATTTGAATTTATGCCACAACTTGAA 59.286 29.630 0.00 0.00 0.00 2.69
1216 9751 8.149647 TGAATTTATGCCACAACTTGAATTCTT 58.850 29.630 7.05 0.00 34.00 2.52
1546 10105 4.487714 TTGCTATCGAATTTGGTCTCCT 57.512 40.909 0.00 0.00 0.00 3.69
1786 10345 3.592059 TCTGCGGTATCACAAACCTTAC 58.408 45.455 0.00 0.00 34.66 2.34
2007 10573 7.504924 AATCTTACCAAATTTGAGTTCGACA 57.495 32.000 19.86 0.00 0.00 4.35
2145 10717 0.321122 CACCGAGCTTGCTCTTCCTT 60.321 55.000 18.75 0.00 0.00 3.36
2932 11989 0.475475 CAATGCTGGGGCTGGAGATA 59.525 55.000 0.00 0.00 39.59 1.98
3052 12109 4.591202 CATTCATGTACAAGCCGAATGAC 58.409 43.478 23.05 0.00 43.55 3.06
3106 12164 4.739716 GTGTTGTCTGCATTTTGGTTGTAG 59.260 41.667 0.00 0.00 0.00 2.74
3127 12185 4.504858 AGTCTGGGTTAACTATGCTTTCG 58.495 43.478 5.42 0.00 0.00 3.46
3128 12186 3.621715 GTCTGGGTTAACTATGCTTTCGG 59.378 47.826 5.42 0.00 0.00 4.30
3129 12187 3.262405 TCTGGGTTAACTATGCTTTCGGT 59.738 43.478 5.42 0.00 0.00 4.69
3130 12188 3.602483 TGGGTTAACTATGCTTTCGGTC 58.398 45.455 5.42 0.00 0.00 4.79
3132 12190 4.467082 TGGGTTAACTATGCTTTCGGTCTA 59.533 41.667 5.42 0.00 0.00 2.59
3133 12191 5.046448 TGGGTTAACTATGCTTTCGGTCTAA 60.046 40.000 5.42 0.00 0.00 2.10
3134 12192 5.522824 GGGTTAACTATGCTTTCGGTCTAAG 59.477 44.000 5.42 0.00 0.00 2.18
3135 12193 6.104665 GGTTAACTATGCTTTCGGTCTAAGT 58.895 40.000 5.42 0.00 0.00 2.24
3136 12194 6.592994 GGTTAACTATGCTTTCGGTCTAAGTT 59.407 38.462 5.42 0.00 0.00 2.66
3137 12195 7.118825 GGTTAACTATGCTTTCGGTCTAAGTTT 59.881 37.037 5.42 0.00 0.00 2.66
3138 12196 8.501580 GTTAACTATGCTTTCGGTCTAAGTTTT 58.498 33.333 0.00 0.00 0.00 2.43
3139 12197 7.506328 AACTATGCTTTCGGTCTAAGTTTTT 57.494 32.000 0.00 0.00 0.00 1.94
3140 12198 6.899114 ACTATGCTTTCGGTCTAAGTTTTTG 58.101 36.000 0.00 0.00 0.00 2.44
3141 12199 5.767816 ATGCTTTCGGTCTAAGTTTTTGT 57.232 34.783 0.00 0.00 0.00 2.83
3142 12200 4.915704 TGCTTTCGGTCTAAGTTTTTGTG 58.084 39.130 0.00 0.00 0.00 3.33
3143 12201 4.396790 TGCTTTCGGTCTAAGTTTTTGTGT 59.603 37.500 0.00 0.00 0.00 3.72
3144 12202 4.733405 GCTTTCGGTCTAAGTTTTTGTGTG 59.267 41.667 0.00 0.00 0.00 3.82
3175 12233 7.864108 TGCTATTATGAACATAAGCAGTTGT 57.136 32.000 13.67 0.70 36.79 3.32
3184 12242 7.083858 TGAACATAAGCAGTTGTTAGCAATTC 58.916 34.615 0.00 0.00 36.25 2.17
3187 12245 7.978982 ACATAAGCAGTTGTTAGCAATTCTAG 58.021 34.615 0.00 0.00 36.92 2.43
3188 12246 7.824289 ACATAAGCAGTTGTTAGCAATTCTAGA 59.176 33.333 0.00 0.00 36.92 2.43
3189 12247 6.734104 AAGCAGTTGTTAGCAATTCTAGAG 57.266 37.500 0.00 0.00 36.92 2.43
3190 12248 5.799213 AGCAGTTGTTAGCAATTCTAGAGT 58.201 37.500 0.00 0.00 36.92 3.24
3192 12250 7.386851 AGCAGTTGTTAGCAATTCTAGAGTAA 58.613 34.615 0.00 0.00 36.92 2.24
3193 12251 7.332182 AGCAGTTGTTAGCAATTCTAGAGTAAC 59.668 37.037 0.00 0.00 36.92 2.50
3195 12253 8.651588 CAGTTGTTAGCAATTCTAGAGTAACTG 58.348 37.037 9.19 9.19 36.92 3.16
3196 12254 8.585881 AGTTGTTAGCAATTCTAGAGTAACTGA 58.414 33.333 0.00 0.00 36.92 3.41
3197 12255 9.372369 GTTGTTAGCAATTCTAGAGTAACTGAT 57.628 33.333 0.00 0.00 36.92 2.90
3217 12275 7.205992 ACTGATATAATGTGCTACACTGTCAG 58.794 38.462 0.00 0.00 35.11 3.51
3248 12365 8.941995 AAATCATGGAATCATTCATCTCATCT 57.058 30.769 0.00 0.00 0.00 2.90
3343 12485 7.556844 TCCTTCACAATACTACATTCTTCTCC 58.443 38.462 0.00 0.00 0.00 3.71
3351 12501 4.822026 ACTACATTCTTCTCCGAACCAAG 58.178 43.478 0.00 0.00 0.00 3.61
3458 12679 6.521151 AATTAACTGCAAAAGGGATCTCAG 57.479 37.500 0.00 0.00 0.00 3.35
3521 12745 4.829492 GGAGTTCTGCATATTTTGGCCTAT 59.171 41.667 3.32 0.00 0.00 2.57
3523 12747 6.490040 GGAGTTCTGCATATTTTGGCCTATAA 59.510 38.462 3.32 0.00 0.00 0.98
3524 12748 7.014230 GGAGTTCTGCATATTTTGGCCTATAAA 59.986 37.037 3.32 2.28 0.00 1.40
3530 12754 7.940850 TGCATATTTTGGCCTATAAAGAGTTC 58.059 34.615 3.32 0.00 0.00 3.01
3531 12755 7.559533 TGCATATTTTGGCCTATAAAGAGTTCA 59.440 33.333 3.32 0.00 0.00 3.18
3806 16238 1.160137 CAAAAGGAGAGGGAACTGCG 58.840 55.000 0.00 0.00 44.43 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.338620 CGCTGTTGGTCGTCCAGA 59.661 61.111 0.74 0.00 45.22 3.86
1 2 2.149803 TACCGCTGTTGGTCGTCCAG 62.150 60.000 0.74 0.00 45.22 3.86
2 3 2.149803 CTACCGCTGTTGGTCGTCCA 62.150 60.000 0.00 0.00 42.62 4.02
3 4 1.445582 CTACCGCTGTTGGTCGTCC 60.446 63.158 0.00 0.00 42.62 4.79
6 7 3.425577 TTATACTACCGCTGTTGGTCG 57.574 47.619 0.00 0.00 42.62 4.79
8 9 7.170320 CGATTATTTTATACTACCGCTGTTGGT 59.830 37.037 0.00 0.00 46.26 3.67
9 10 7.507304 CGATTATTTTATACTACCGCTGTTGG 58.493 38.462 0.00 0.00 0.00 3.77
10 11 7.007697 GCGATTATTTTATACTACCGCTGTTG 58.992 38.462 0.00 0.00 37.51 3.33
11 12 6.702723 TGCGATTATTTTATACTACCGCTGTT 59.297 34.615 0.00 0.00 40.59 3.16
12 13 6.145048 GTGCGATTATTTTATACTACCGCTGT 59.855 38.462 0.00 0.00 40.59 4.40
13 14 6.144886 TGTGCGATTATTTTATACTACCGCTG 59.855 38.462 0.00 0.00 40.59 5.18
16 17 7.397512 TGTGTGCGATTATTTTATACTACCG 57.602 36.000 0.00 0.00 0.00 4.02
17 18 8.440833 GGATGTGTGCGATTATTTTATACTACC 58.559 37.037 0.00 0.00 0.00 3.18
18 19 8.984764 TGGATGTGTGCGATTATTTTATACTAC 58.015 33.333 0.00 0.00 0.00 2.73
19 20 9.719355 ATGGATGTGTGCGATTATTTTATACTA 57.281 29.630 0.00 0.00 0.00 1.82
20 21 8.621532 ATGGATGTGTGCGATTATTTTATACT 57.378 30.769 0.00 0.00 0.00 2.12
21 22 9.973246 CTATGGATGTGTGCGATTATTTTATAC 57.027 33.333 0.00 0.00 0.00 1.47
22 23 9.161629 CCTATGGATGTGTGCGATTATTTTATA 57.838 33.333 0.00 0.00 0.00 0.98
23 24 7.362056 GCCTATGGATGTGTGCGATTATTTTAT 60.362 37.037 0.00 0.00 0.00 1.40
24 25 6.072728 GCCTATGGATGTGTGCGATTATTTTA 60.073 38.462 0.00 0.00 0.00 1.52
25 26 5.278463 GCCTATGGATGTGTGCGATTATTTT 60.278 40.000 0.00 0.00 0.00 1.82
27 28 3.753272 GCCTATGGATGTGTGCGATTATT 59.247 43.478 0.00 0.00 0.00 1.40
28 29 3.338249 GCCTATGGATGTGTGCGATTAT 58.662 45.455 0.00 0.00 0.00 1.28
30 31 1.597742 GCCTATGGATGTGTGCGATT 58.402 50.000 0.00 0.00 0.00 3.34
31 32 0.601046 CGCCTATGGATGTGTGCGAT 60.601 55.000 0.00 0.00 44.32 4.58
32 33 1.227234 CGCCTATGGATGTGTGCGA 60.227 57.895 0.00 0.00 44.32 5.10
33 34 2.885676 GCGCCTATGGATGTGTGCG 61.886 63.158 0.00 0.00 44.38 5.34
34 35 2.546494 GGCGCCTATGGATGTGTGC 61.546 63.158 22.15 0.00 0.00 4.57
35 36 1.153188 TGGCGCCTATGGATGTGTG 60.153 57.895 29.70 0.00 0.00 3.82
36 37 1.146930 CTGGCGCCTATGGATGTGT 59.853 57.895 29.70 0.00 0.00 3.72
37 38 2.256591 GCTGGCGCCTATGGATGTG 61.257 63.158 29.70 7.23 0.00 3.21
50 51 0.323360 TTATCCACAGGTTGGCTGGC 60.323 55.000 0.00 0.00 46.47 4.85
51 52 1.463674 GTTATCCACAGGTTGGCTGG 58.536 55.000 0.00 0.00 46.47 4.85
52 53 1.086696 CGTTATCCACAGGTTGGCTG 58.913 55.000 0.00 0.00 46.47 4.85
54 55 1.066430 TCTCGTTATCCACAGGTTGGC 60.066 52.381 0.00 0.00 46.47 4.52
56 57 2.271800 GCTCTCGTTATCCACAGGTTG 58.728 52.381 0.00 0.00 0.00 3.77
58 59 1.557099 TGCTCTCGTTATCCACAGGT 58.443 50.000 0.00 0.00 0.00 4.00
60 61 4.183865 TCAAATGCTCTCGTTATCCACAG 58.816 43.478 0.00 0.00 0.00 3.66
61 62 4.183865 CTCAAATGCTCTCGTTATCCACA 58.816 43.478 0.00 0.00 0.00 4.17
62 63 3.001736 GCTCAAATGCTCTCGTTATCCAC 59.998 47.826 0.00 0.00 0.00 4.02
63 64 3.118629 AGCTCAAATGCTCTCGTTATCCA 60.119 43.478 0.00 0.00 39.34 3.41
64 65 3.462021 AGCTCAAATGCTCTCGTTATCC 58.538 45.455 0.00 0.00 39.34 2.59
75 76 0.453950 CTGTGCACGAGCTCAAATGC 60.454 55.000 21.74 21.74 42.95 3.56
77 78 1.597742 AACTGTGCACGAGCTCAAAT 58.402 45.000 15.40 0.00 42.95 2.32
78 79 1.864711 GTAACTGTGCACGAGCTCAAA 59.135 47.619 15.40 0.00 42.95 2.69
79 80 1.068588 AGTAACTGTGCACGAGCTCAA 59.931 47.619 15.40 0.00 42.95 3.02
80 81 0.673985 AGTAACTGTGCACGAGCTCA 59.326 50.000 15.40 7.93 41.52 4.26
81 82 1.341606 GAGTAACTGTGCACGAGCTC 58.658 55.000 13.13 2.73 42.74 4.09
82 83 0.038159 GGAGTAACTGTGCACGAGCT 60.038 55.000 13.13 5.67 42.74 4.09
83 84 1.344942 CGGAGTAACTGTGCACGAGC 61.345 60.000 13.13 0.00 42.57 5.03
85 86 1.372499 GCGGAGTAACTGTGCACGA 60.372 57.895 13.13 0.33 0.00 4.35
86 87 2.716828 CGCGGAGTAACTGTGCACG 61.717 63.158 13.13 9.67 0.00 5.34
87 88 1.615107 GACGCGGAGTAACTGTGCAC 61.615 60.000 12.47 10.75 38.80 4.57
88 89 1.372499 GACGCGGAGTAACTGTGCA 60.372 57.895 12.47 0.00 38.80 4.57
89 90 2.092882 GGACGCGGAGTAACTGTGC 61.093 63.158 12.47 0.00 38.80 4.57
91 92 0.390124 TTTGGACGCGGAGTAACTGT 59.610 50.000 12.47 0.00 0.00 3.55
93 94 2.243602 TTTTTGGACGCGGAGTAACT 57.756 45.000 12.47 0.00 0.00 2.24
310 8788 1.168714 GCCATTAATCGCCTGGATCC 58.831 55.000 4.20 4.20 33.02 3.36
364 8842 1.298859 CTCGCCGGAACAAGGGAAAG 61.299 60.000 5.05 0.00 0.00 2.62
400 8878 2.367202 GGGAGCACGAATGGGGAGA 61.367 63.158 0.00 0.00 0.00 3.71
438 8916 6.540438 TTCGAACTGAGGTACCTATTGATT 57.460 37.500 16.29 5.24 0.00 2.57
442 8920 4.344390 GGGATTCGAACTGAGGTACCTATT 59.656 45.833 16.29 9.88 0.00 1.73
482 8960 0.447801 CAAGGAATTGAGGAACGCGG 59.552 55.000 12.47 0.00 0.00 6.46
500 8978 2.484770 CCCTCGTGACTGTTTTTCTCCA 60.485 50.000 0.00 0.00 0.00 3.86
501 8979 2.143925 CCCTCGTGACTGTTTTTCTCC 58.856 52.381 0.00 0.00 0.00 3.71
515 8993 1.679944 CCATTCAGCAATCACCCTCGT 60.680 52.381 0.00 0.00 0.00 4.18
527 9005 2.947127 AATCCTAGCCTCCATTCAGC 57.053 50.000 0.00 0.00 0.00 4.26
546 9024 7.898636 AGGATTGGAACTGGATAATTAACCAAA 59.101 33.333 14.68 7.02 39.12 3.28
612 9104 8.594550 AGTACATTATACACTACAATGGGGATC 58.405 37.037 0.00 0.00 34.63 3.36
638 9130 0.036388 GTCGGCCTGAAGGAACATCA 60.036 55.000 0.00 0.00 37.39 3.07
639 9131 0.250513 AGTCGGCCTGAAGGAACATC 59.749 55.000 0.00 0.00 37.39 3.06
683 9178 7.032377 CTGGGAGAAGAATAAATAAACCAGC 57.968 40.000 0.00 0.00 35.84 4.85
750 9263 6.061022 ACAACACAGGATTTTTCCCTTTTT 57.939 33.333 0.00 0.00 0.00 1.94
858 9373 4.090761 TCACTGGTTTCAGAGAGCAATT 57.909 40.909 0.00 0.00 43.49 2.32
876 9398 5.039333 GGTTTCAGCAAGCATCATTATCAC 58.961 41.667 0.00 0.00 32.66 3.06
893 9415 6.632909 CAAGCAATCCTTATCATTGGTTTCA 58.367 36.000 7.02 0.00 45.32 2.69
908 9430 2.927553 ATCGTTTCAGCAAGCAATCC 57.072 45.000 0.00 0.00 0.00 3.01
911 9433 2.998772 GTGAATCGTTTCAGCAAGCAA 58.001 42.857 9.14 0.00 42.41 3.91
1070 9596 2.305343 AGTTGAATCTCTGCCAGCTTCT 59.695 45.455 0.00 0.00 29.81 2.85
1075 9601 4.070716 AGTTGAAGTTGAATCTCTGCCAG 58.929 43.478 0.00 0.00 0.00 4.85
1089 9615 6.958192 TCCTTACATAGGGTAGAAGTTGAAGT 59.042 38.462 0.00 0.00 44.86 3.01
1119 9645 7.065443 GGTAATACCCGACATAAATAAGGCATC 59.935 40.741 0.00 0.00 30.04 3.91
1187 9722 8.851541 ATTCAAGTTGTGGCATAAATTCAAAT 57.148 26.923 6.70 7.39 0.00 2.32
1188 9723 8.674263 AATTCAAGTTGTGGCATAAATTCAAA 57.326 26.923 6.70 5.54 0.00 2.69
1196 9731 9.109393 GAGTATAAGAATTCAAGTTGTGGCATA 57.891 33.333 8.44 0.00 0.00 3.14
1211 9746 9.886132 AAAACGTCCTGTAATGAGTATAAGAAT 57.114 29.630 0.00 0.00 0.00 2.40
1216 9751 5.517411 CGCAAAACGTCCTGTAATGAGTATA 59.483 40.000 0.00 0.00 36.87 1.47
1219 9754 2.478894 CGCAAAACGTCCTGTAATGAGT 59.521 45.455 0.00 0.00 36.87 3.41
1315 9850 1.983691 CCAGATCTGGGTGGCATATCT 59.016 52.381 31.14 0.00 46.81 1.98
1546 10105 8.969260 ATCAATGTGATACTTATGCTTTCTGA 57.031 30.769 0.00 0.00 34.88 3.27
1786 10345 4.201744 ACACCGTTTTTAGTGTGAGTTTCG 60.202 41.667 0.00 0.00 45.24 3.46
2064 10630 7.009179 ACTCTTGAGTCCTCATGTTTGATAA 57.991 36.000 9.27 0.00 39.64 1.75
2811 11858 2.332117 GGTAATGGTCCCCCTCGATAA 58.668 52.381 0.00 0.00 0.00 1.75
3052 12109 1.081892 GCACACACTACTGCATCCAG 58.918 55.000 0.00 0.00 44.80 3.86
3106 12164 3.621715 CCGAAAGCATAGTTAACCCAGAC 59.378 47.826 0.88 0.00 0.00 3.51
3127 12185 3.380320 AGCCACACACAAAAACTTAGACC 59.620 43.478 0.00 0.00 0.00 3.85
3128 12186 4.632538 AGCCACACACAAAAACTTAGAC 57.367 40.909 0.00 0.00 0.00 2.59
3129 12187 5.406649 CAAAGCCACACACAAAAACTTAGA 58.593 37.500 0.00 0.00 0.00 2.10
3130 12188 4.032786 GCAAAGCCACACACAAAAACTTAG 59.967 41.667 0.00 0.00 0.00 2.18
3132 12190 2.741517 GCAAAGCCACACACAAAAACTT 59.258 40.909 0.00 0.00 0.00 2.66
3133 12191 2.028203 AGCAAAGCCACACACAAAAACT 60.028 40.909 0.00 0.00 0.00 2.66
3134 12192 2.345876 AGCAAAGCCACACACAAAAAC 58.654 42.857 0.00 0.00 0.00 2.43
3135 12193 2.758736 AGCAAAGCCACACACAAAAA 57.241 40.000 0.00 0.00 0.00 1.94
3136 12194 4.399004 AATAGCAAAGCCACACACAAAA 57.601 36.364 0.00 0.00 0.00 2.44
3137 12195 5.242615 TCATAATAGCAAAGCCACACACAAA 59.757 36.000 0.00 0.00 0.00 2.83
3138 12196 4.764308 TCATAATAGCAAAGCCACACACAA 59.236 37.500 0.00 0.00 0.00 3.33
3139 12197 4.331108 TCATAATAGCAAAGCCACACACA 58.669 39.130 0.00 0.00 0.00 3.72
3140 12198 4.963276 TCATAATAGCAAAGCCACACAC 57.037 40.909 0.00 0.00 0.00 3.82
3141 12199 4.764308 TGTTCATAATAGCAAAGCCACACA 59.236 37.500 0.00 0.00 0.00 3.72
3142 12200 5.309323 TGTTCATAATAGCAAAGCCACAC 57.691 39.130 0.00 0.00 0.00 3.82
3143 12201 7.637631 TTATGTTCATAATAGCAAAGCCACA 57.362 32.000 1.68 0.00 0.00 4.17
3144 12202 6.638468 GCTTATGTTCATAATAGCAAAGCCAC 59.362 38.462 5.83 0.00 32.65 5.01
3187 12245 9.186323 CAGTGTAGCACATTATATCAGTTACTC 57.814 37.037 2.01 0.00 36.74 2.59
3188 12246 8.696374 ACAGTGTAGCACATTATATCAGTTACT 58.304 33.333 0.00 0.00 36.74 2.24
3189 12247 8.873215 ACAGTGTAGCACATTATATCAGTTAC 57.127 34.615 0.00 0.00 36.74 2.50
3190 12248 8.691797 TGACAGTGTAGCACATTATATCAGTTA 58.308 33.333 0.00 0.00 36.74 2.24
3192 12250 7.112452 TGACAGTGTAGCACATTATATCAGT 57.888 36.000 0.00 0.00 36.74 3.41
3193 12251 7.205992 ACTGACAGTGTAGCACATTATATCAG 58.794 38.462 7.47 0.00 36.74 2.90
3195 12253 9.698309 ATTACTGACAGTGTAGCACATTATATC 57.302 33.333 18.58 0.00 36.74 1.63
3198 12256 9.884636 TTTATTACTGACAGTGTAGCACATTAT 57.115 29.630 18.58 0.00 36.74 1.28
3199 12257 9.713713 TTTTATTACTGACAGTGTAGCACATTA 57.286 29.630 18.58 0.00 36.74 1.90
3200 12258 8.615878 TTTTATTACTGACAGTGTAGCACATT 57.384 30.769 18.58 0.00 36.74 2.71
3206 12264 9.599866 TCCATGATTTTATTACTGACAGTGTAG 57.400 33.333 18.58 0.00 0.00 2.74
3248 12365 3.910568 TCATACACAGACCATGCATGA 57.089 42.857 28.31 5.54 0.00 3.07
3343 12485 5.388890 CGACTTCTCTGATTTTCTTGGTTCG 60.389 44.000 0.00 0.00 0.00 3.95
3351 12501 3.855858 AGGAGCGACTTCTCTGATTTTC 58.144 45.455 0.00 0.00 33.70 2.29
3458 12679 6.402222 TCTCCTCTCACTAAAATTTCTCTGC 58.598 40.000 0.00 0.00 0.00 4.26
3538 12762 3.814842 TCTGCGATTCTTTCAAGCAAGAA 59.185 39.130 0.00 0.00 44.90 2.52
3579 12812 6.814146 ACCGACAAGAAAATATTCTGAGACTC 59.186 38.462 0.00 0.00 45.19 3.36
3581 12814 6.969828 ACCGACAAGAAAATATTCTGAGAC 57.030 37.500 0.00 0.00 45.19 3.36
3614 12866 1.004745 TGGCTCTGTCCCCTCATTTTC 59.995 52.381 0.00 0.00 0.00 2.29
3806 16238 2.151881 TGTTCATGGTTGCATTGCAC 57.848 45.000 11.66 6.75 38.71 4.57


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

AutoCloner maintained by Alex Coulton.