Multiple sequence alignment - TraesCS3B01G308100

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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 TraesCS3B01G308100 chr3B 100.000 4730 0 0 1 4730 495155022 495150293 0.000000e+00 8735.0
1 TraesCS3B01G308100 chr3B 100.000 224 0 0 5151 5374 495149872 495149649 1.080000e-111 414.0
2 TraesCS3B01G308100 chr3B 93.119 218 14 1 4514 4730 561000862 561000645 8.690000e-83 318.0
3 TraesCS3B01G308100 chr3B 92.093 215 15 2 4517 4730 420653725 420653512 8.750000e-78 302.0
4 TraesCS3B01G308100 chr3B 97.744 133 3 0 5242 5374 561000123 560999991 4.190000e-56 230.0
5 TraesCS3B01G308100 chr3A 94.356 3880 164 34 657 4516 503755487 503751643 0.000000e+00 5901.0
6 TraesCS3B01G308100 chr3A 92.166 217 12 3 4517 4730 170244833 170244619 8.750000e-78 302.0
7 TraesCS3B01G308100 chr3A 90.000 160 15 1 5215 5374 739970029 739969871 7.060000e-49 206.0
8 TraesCS3B01G308100 chr3D 93.859 3843 151 37 705 4516 379539895 379536107 0.000000e+00 5710.0
9 TraesCS3B01G308100 chr3D 86.529 1017 75 29 786 1801 150824933 150823978 0.000000e+00 1062.0
10 TraesCS3B01G308100 chr3D 89.120 625 50 6 3 625 379605293 379604685 0.000000e+00 761.0
11 TraesCS3B01G308100 chr1B 87.993 1166 131 7 998 2157 583210886 583209724 0.000000e+00 1369.0
12 TraesCS3B01G308100 chr1B 82.708 960 111 26 1157 2098 684276905 684277827 0.000000e+00 802.0
13 TraesCS3B01G308100 chr1D 87.918 1167 132 7 997 2157 431829517 431828354 0.000000e+00 1365.0
14 TraesCS3B01G308100 chr1D 84.653 202 27 1 1797 1994 491900768 491900969 1.180000e-46 198.0
15 TraesCS3B01G308100 chr1D 97.674 43 1 0 1738 1780 491900733 491900775 2.080000e-09 75.0
16 TraesCS3B01G308100 chr1A 87.511 1177 136 8 987 2157 530260434 530259263 0.000000e+00 1349.0
17 TraesCS3B01G308100 chr4B 84.987 1179 153 11 999 2153 667726378 667727556 0.000000e+00 1175.0
18 TraesCS3B01G308100 chr4B 98.496 133 2 0 5242 5374 667904611 667904743 9.000000e-58 235.0
19 TraesCS3B01G308100 chr7D 88.551 428 35 7 2081 2500 38229535 38229956 1.730000e-139 507.0
20 TraesCS3B01G308100 chr7D 84.167 240 28 5 2495 2732 38229990 38230221 1.950000e-54 224.0
21 TraesCS3B01G308100 chr4A 86.946 429 41 8 2081 2500 642907978 642907556 8.150000e-128 468.0
22 TraesCS3B01G308100 chr2A 92.727 220 12 2 4514 4730 1315796 1316014 1.120000e-81 315.0
23 TraesCS3B01G308100 chr2A 92.991 214 14 1 4517 4730 755764979 755764767 1.450000e-80 311.0
24 TraesCS3B01G308100 chr2A 91.364 220 14 3 4515 4730 50063491 50063709 4.070000e-76 296.0
25 TraesCS3B01G308100 chr2A 86.316 190 18 6 5185 5374 508024344 508024525 3.280000e-47 200.0
26 TraesCS3B01G308100 chr6B 92.958 213 14 1 4517 4729 125611419 125611208 5.230000e-80 309.0
27 TraesCS3B01G308100 chr6B 97.727 132 3 0 5243 5374 125610328 125610197 1.510000e-55 228.0
28 TraesCS3B01G308100 chr5B 91.071 224 18 2 4506 4729 595120773 595120552 8.750000e-78 302.0
29 TraesCS3B01G308100 chr5B 88.235 51 4 2 538 587 534226674 534226625 5.810000e-05 60.2
30 TraesCS3B01G308100 chr7B 91.549 213 17 1 4517 4729 563660353 563660564 5.260000e-75 292.0
31 TraesCS3B01G308100 chr7B 97.727 132 3 0 5243 5374 563660825 563660956 1.510000e-55 228.0
32 TraesCS3B01G308100 chr2B 89.320 206 13 5 5170 5374 5298618 5298421 3.210000e-62 250.0
33 TraesCS3B01G308100 chrUn 90.000 160 15 1 5215 5374 300571446 300571288 7.060000e-49 206.0
34 TraesCS3B01G308100 chr7A 90.000 160 15 1 5215 5374 106430406 106430564 7.060000e-49 206.0
35 TraesCS3B01G308100 chr6D 90.566 53 5 0 74 126 338413586 338413534 2.690000e-08 71.3


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 TraesCS3B01G308100 chr3B 495149649 495155022 5373 True 4574.5 8735 100.0000 1 5374 2 chr3B.!!$R2 5373
1 TraesCS3B01G308100 chr3B 560999991 561000862 871 True 274.0 318 95.4315 4514 5374 2 chr3B.!!$R3 860
2 TraesCS3B01G308100 chr3A 503751643 503755487 3844 True 5901.0 5901 94.3560 657 4516 1 chr3A.!!$R2 3859
3 TraesCS3B01G308100 chr3D 379536107 379539895 3788 True 5710.0 5710 93.8590 705 4516 1 chr3D.!!$R2 3811
4 TraesCS3B01G308100 chr3D 150823978 150824933 955 True 1062.0 1062 86.5290 786 1801 1 chr3D.!!$R1 1015
5 TraesCS3B01G308100 chr3D 379604685 379605293 608 True 761.0 761 89.1200 3 625 1 chr3D.!!$R3 622
6 TraesCS3B01G308100 chr1B 583209724 583210886 1162 True 1369.0 1369 87.9930 998 2157 1 chr1B.!!$R1 1159
7 TraesCS3B01G308100 chr1B 684276905 684277827 922 False 802.0 802 82.7080 1157 2098 1 chr1B.!!$F1 941
8 TraesCS3B01G308100 chr1D 431828354 431829517 1163 True 1365.0 1365 87.9180 997 2157 1 chr1D.!!$R1 1160
9 TraesCS3B01G308100 chr1A 530259263 530260434 1171 True 1349.0 1349 87.5110 987 2157 1 chr1A.!!$R1 1170
10 TraesCS3B01G308100 chr4B 667726378 667727556 1178 False 1175.0 1175 84.9870 999 2153 1 chr4B.!!$F1 1154
11 TraesCS3B01G308100 chr7D 38229535 38230221 686 False 365.5 507 86.3590 2081 2732 2 chr7D.!!$F1 651
12 TraesCS3B01G308100 chr6B 125610197 125611419 1222 True 268.5 309 95.3425 4517 5374 2 chr6B.!!$R1 857
13 TraesCS3B01G308100 chr7B 563660353 563660956 603 False 260.0 292 94.6380 4517 5374 2 chr7B.!!$F1 857

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
526 527 0.030501 ACTCCCCCGTCCCATAATCA 60.031 55.000 0.00 0.00 0.00 2.57 F
528 529 1.072331 CTCCCCCGTCCCATAATCAAG 59.928 57.143 0.00 0.00 0.00 3.02 F
2222 2301 0.743688 TGCACGGTCAATTTTGCAGT 59.256 45.000 0.00 0.00 40.01 4.40 F
2788 2915 0.035630 GTGCTCTGCAGGAGGTTGAT 60.036 55.000 15.13 0.00 40.08 2.57 F
2797 2924 0.106819 AGGAGGTTGATGCTGCCATC 60.107 55.000 0.00 1.23 46.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1474 1.751162 CCGGAGCTTCTCGACCTCT 60.751 63.158 0.00 0.0 0.00 3.69 R
2237 2316 3.242969 CGTCGATTTAAGACCGGAGATCA 60.243 47.826 9.46 0.0 35.33 2.92 R
3638 3767 0.302890 GATCGCGAGCAACCTTCATG 59.697 55.000 21.13 0.0 0.00 3.07 R
3856 3994 0.677731 CTTTCATCTGAAGCCGGGCA 60.678 55.000 23.09 0.0 35.21 5.36 R
4378 4517 0.868406 GGGATCAATCGATGCGGTTC 59.132 55.000 0.00 0.0 40.71 3.62 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
21 22 3.343941 TGCCTACGCCTTTACAAATCT 57.656 42.857 0.00 0.00 0.00 2.40
68 69 1.747355 CCTAGACGTAAAGAGGCCGAA 59.253 52.381 0.00 0.00 0.00 4.30
70 71 0.109412 AGACGTAAAGAGGCCGAACG 60.109 55.000 14.05 14.05 39.37 3.95
75 76 2.414559 CGTAAAGAGGCCGAACGAGTTA 60.415 50.000 11.30 0.00 35.66 2.24
78 79 0.179108 AGAGGCCGAACGAGTTATGC 60.179 55.000 0.00 0.00 0.00 3.14
83 84 2.264813 GCCGAACGAGTTATGCTTGTA 58.735 47.619 0.00 0.00 40.85 2.41
91 92 6.422776 ACGAGTTATGCTTGTATTCCTTTG 57.577 37.500 0.00 0.00 39.96 2.77
97 98 3.342719 TGCTTGTATTCCTTTGATGCGA 58.657 40.909 0.00 0.00 0.00 5.10
103 104 7.566760 TTGTATTCCTTTGATGCGACATTAT 57.433 32.000 0.00 0.00 0.00 1.28
104 105 6.958255 TGTATTCCTTTGATGCGACATTATG 58.042 36.000 0.00 0.00 0.00 1.90
106 107 6.698008 ATTCCTTTGATGCGACATTATGAA 57.302 33.333 0.00 0.00 0.00 2.57
183 184 9.653516 AGAGAGAGAAGAATGAGGTATTTCATA 57.346 33.333 0.00 0.00 36.81 2.15
210 211 9.483062 TTTTTCAAGTTTCATTACATTTTTGCG 57.517 25.926 0.00 0.00 0.00 4.85
215 216 5.630680 AGTTTCATTACATTTTTGCGAGCTG 59.369 36.000 0.00 0.00 0.00 4.24
218 219 2.900122 TACATTTTTGCGAGCTGAGC 57.100 45.000 0.00 0.00 0.00 4.26
243 244 8.586570 CGTAGCTCAGATGATTAGATTTCTTT 57.413 34.615 0.00 0.00 0.00 2.52
309 310 2.418976 GGTTAGGTTTCTGGCGATGTTC 59.581 50.000 0.00 0.00 0.00 3.18
321 322 1.260206 CGATGTTCGTTCAGTCGGAG 58.740 55.000 0.00 0.00 34.72 4.63
326 327 1.473278 GTTCGTTCAGTCGGAGGAGAT 59.527 52.381 0.00 0.00 0.00 2.75
361 362 7.361201 CGACTATGAAATGATTGTGGTGACTTT 60.361 37.037 0.00 0.00 0.00 2.66
389 390 5.386958 TCTTATAAGATATTGCGCCGACT 57.613 39.130 11.24 0.00 0.00 4.18
391 392 2.046283 TAAGATATTGCGCCGACTCG 57.954 50.000 4.18 0.00 0.00 4.18
423 424 6.932400 TCAAGGTATACGTGCATTAATAAGGG 59.068 38.462 0.00 0.00 0.00 3.95
424 425 5.243207 AGGTATACGTGCATTAATAAGGGC 58.757 41.667 0.00 0.00 0.00 5.19
425 426 5.012768 AGGTATACGTGCATTAATAAGGGCT 59.987 40.000 0.00 0.00 0.00 5.19
426 427 6.211986 AGGTATACGTGCATTAATAAGGGCTA 59.788 38.462 0.00 0.00 0.00 3.93
442 443 3.134081 AGGGCTAGTATATGTGCGTGTTT 59.866 43.478 0.00 0.00 0.00 2.83
443 444 3.247648 GGGCTAGTATATGTGCGTGTTTG 59.752 47.826 0.00 0.00 0.00 2.93
472 473 6.692681 GCATCTGCGATTGTAATGTGTTAAAT 59.307 34.615 0.00 0.00 0.00 1.40
525 526 2.019807 TACTCCCCCGTCCCATAATC 57.980 55.000 0.00 0.00 0.00 1.75
526 527 0.030501 ACTCCCCCGTCCCATAATCA 60.031 55.000 0.00 0.00 0.00 2.57
528 529 1.072331 CTCCCCCGTCCCATAATCAAG 59.928 57.143 0.00 0.00 0.00 3.02
529 530 1.136828 CCCCCGTCCCATAATCAAGA 58.863 55.000 0.00 0.00 0.00 3.02
530 531 1.202770 CCCCCGTCCCATAATCAAGAC 60.203 57.143 0.00 0.00 0.00 3.01
536 539 4.096382 CCGTCCCATAATCAAGACCTTTTG 59.904 45.833 0.00 0.00 0.00 2.44
629 632 9.461312 TTTAGGAATTTCATGTACATAGTTGCT 57.539 29.630 8.32 10.05 0.00 3.91
630 633 7.325660 AGGAATTTCATGTACATAGTTGCTG 57.674 36.000 8.32 0.00 0.00 4.41
631 634 6.319658 AGGAATTTCATGTACATAGTTGCTGG 59.680 38.462 8.32 0.00 0.00 4.85
632 635 6.455360 AATTTCATGTACATAGTTGCTGGG 57.545 37.500 8.32 0.00 0.00 4.45
633 636 2.917933 TCATGTACATAGTTGCTGGGC 58.082 47.619 8.32 0.00 0.00 5.36
634 637 2.238395 TCATGTACATAGTTGCTGGGCA 59.762 45.455 8.32 0.00 36.47 5.36
635 638 2.107950 TGTACATAGTTGCTGGGCAC 57.892 50.000 0.00 0.00 38.71 5.01
636 639 1.349357 TGTACATAGTTGCTGGGCACA 59.651 47.619 0.00 0.00 38.71 4.57
684 687 1.202663 TGAAATCGGAACCAACGGTCA 60.203 47.619 0.00 0.00 33.12 4.02
718 721 8.274939 GTCTCGTGTGATAGTAGATACAGTAAC 58.725 40.741 0.00 0.00 0.00 2.50
737 740 2.250190 CGCACGGTTCCGGTTTTC 59.750 61.111 15.66 0.00 0.00 2.29
2222 2301 0.743688 TGCACGGTCAATTTTGCAGT 59.256 45.000 0.00 0.00 40.01 4.40
2242 2321 5.407387 GCAGTGTTTTTGCATTGATTGATCT 59.593 36.000 0.00 0.00 41.17 2.75
2262 2341 4.129380 TCTCCGGTCTTAAATCGACGATA 58.871 43.478 11.42 0.00 32.24 2.92
2268 2347 7.043192 TCCGGTCTTAAATCGACGATATTTTTC 60.043 37.037 11.42 1.62 32.24 2.29
2472 2554 3.119245 TCGGCTAGTTGATGTGAGTAACC 60.119 47.826 0.00 0.00 0.00 2.85
2477 2559 2.631062 AGTTGATGTGAGTAACCGGTGA 59.369 45.455 8.52 0.00 0.00 4.02
2479 2561 3.973206 TGATGTGAGTAACCGGTGAAT 57.027 42.857 8.52 0.00 0.00 2.57
2503 2585 9.865321 AATTTGGTGATCTTGATTTTATCAGTG 57.135 29.630 0.00 0.00 40.94 3.66
2507 2629 7.280876 TGGTGATCTTGATTTTATCAGTGTAGC 59.719 37.037 0.00 0.00 40.94 3.58
2521 2643 4.727507 AGTGTAGCTGATTCGTTCTGAT 57.272 40.909 0.00 0.00 0.00 2.90
2788 2915 0.035630 GTGCTCTGCAGGAGGTTGAT 60.036 55.000 15.13 0.00 40.08 2.57
2797 2924 0.106819 AGGAGGTTGATGCTGCCATC 60.107 55.000 0.00 1.23 46.46 3.51
2828 2955 2.126031 GTGAGACCGGCGAGAACC 60.126 66.667 9.30 0.00 0.00 3.62
2888 3015 3.059188 CGAGGTAAGTTCGTTGTTGCAAT 60.059 43.478 0.59 0.00 33.57 3.56
2904 3031 7.187244 TGTTGCAATCAATTTTATGGTGTTG 57.813 32.000 0.59 0.00 34.29 3.33
2941 3068 6.533723 GGTATGAACGATGTTGTATTGAGACA 59.466 38.462 0.00 0.00 0.00 3.41
2998 3125 1.661341 GCATTCCTGTCACTAGGCTG 58.339 55.000 0.00 0.00 37.76 4.85
3016 3143 0.620556 TGGGACAGAATGAGAAGGCC 59.379 55.000 0.00 0.00 39.69 5.19
3028 3155 3.011517 AAGGCCAGGCTGATCGGT 61.012 61.111 17.94 0.00 0.00 4.69
3160 3287 1.134371 GGTTCATTCCTCTTCCTCGGG 60.134 57.143 0.00 0.00 0.00 5.14
3241 3368 1.741770 GAACCTGCTCGTCCGCATT 60.742 57.895 0.00 0.00 39.52 3.56
3245 3372 2.434185 TGCTCGTCCGCATTGACC 60.434 61.111 0.00 0.00 34.44 4.02
3312 3439 1.843368 CCACCTGGGTAAGTACTCGA 58.157 55.000 0.00 0.00 0.00 4.04
3313 3440 1.749634 CCACCTGGGTAAGTACTCGAG 59.250 57.143 11.84 11.84 0.00 4.04
3314 3441 2.444421 CACCTGGGTAAGTACTCGAGT 58.556 52.381 23.66 23.66 0.00 4.18
3331 3459 5.358442 ACTCGAGTAATTCTGTATGCTCACT 59.642 40.000 18.46 0.00 0.00 3.41
3333 3461 7.229707 ACTCGAGTAATTCTGTATGCTCACTAT 59.770 37.037 18.46 0.00 0.00 2.12
3334 3462 7.363431 TCGAGTAATTCTGTATGCTCACTATG 58.637 38.462 0.00 0.00 0.00 2.23
3335 3463 6.584184 CGAGTAATTCTGTATGCTCACTATGG 59.416 42.308 0.00 0.00 0.00 2.74
3336 3464 7.522236 CGAGTAATTCTGTATGCTCACTATGGA 60.522 40.741 0.00 0.00 0.00 3.41
3337 3465 8.200024 AGTAATTCTGTATGCTCACTATGGAT 57.800 34.615 0.00 0.00 0.00 3.41
3338 3466 8.310382 AGTAATTCTGTATGCTCACTATGGATC 58.690 37.037 0.00 0.00 0.00 3.36
3346 3475 2.806818 GCTCACTATGGATCTGTGCATG 59.193 50.000 0.00 0.00 36.99 4.06
3347 3476 3.743584 GCTCACTATGGATCTGTGCATGT 60.744 47.826 0.00 0.00 36.99 3.21
3367 3496 7.201106 CATGTTATGCGATTTCTGAGTTTTG 57.799 36.000 0.00 0.00 0.00 2.44
3368 3497 6.552859 TGTTATGCGATTTCTGAGTTTTGA 57.447 33.333 0.00 0.00 0.00 2.69
3369 3498 6.370593 TGTTATGCGATTTCTGAGTTTTGAC 58.629 36.000 0.00 0.00 0.00 3.18
3370 3499 6.017523 TGTTATGCGATTTCTGAGTTTTGACA 60.018 34.615 0.00 0.00 0.00 3.58
3371 3500 5.633830 ATGCGATTTCTGAGTTTTGACAT 57.366 34.783 0.00 0.00 0.00 3.06
3372 3501 5.034554 TGCGATTTCTGAGTTTTGACATC 57.965 39.130 0.00 0.00 0.00 3.06
3428 3557 2.596851 GGAAGGAGGGCAGCTGACA 61.597 63.158 23.90 0.00 0.00 3.58
3485 3614 1.176619 TCGACGAGGTTGAGAAGGCA 61.177 55.000 0.00 0.00 0.00 4.75
3506 3635 1.132262 CATGTGGCGGTATTCAACACC 59.868 52.381 0.00 0.00 0.00 4.16
3578 3707 2.225727 GGTTGATTTCAGGAACACCGTC 59.774 50.000 0.00 0.00 0.00 4.79
3638 3767 2.046285 CGGAATGGTGGGCAACTCC 61.046 63.158 0.00 0.00 0.00 3.85
3692 3821 5.758784 GGAGGTATGTACTACTGAATTTGCC 59.241 44.000 0.00 0.00 0.00 4.52
3696 3825 3.950397 TGTACTACTGAATTTGCCCCTG 58.050 45.455 0.00 0.00 0.00 4.45
3703 3832 0.749049 GAATTTGCCCCTGATCTGCC 59.251 55.000 0.00 0.00 0.00 4.85
3712 3841 1.470098 CCCTGATCTGCCTTTTGTTCG 59.530 52.381 0.00 0.00 0.00 3.95
3729 3862 3.163594 GTTCGGAATCAATCAGTTTGCG 58.836 45.455 0.00 0.00 40.66 4.85
3751 3888 2.541762 GTCTGATGCCTAATGCGAGAAC 59.458 50.000 0.00 0.00 45.60 3.01
3886 4024 4.824479 TCAGATGAAAGATGTGGCAGTA 57.176 40.909 0.00 0.00 0.00 2.74
3922 4060 2.904866 GTTGCCTTGGCCGTCACA 60.905 61.111 9.35 0.00 0.00 3.58
3958 4096 4.787551 ACGTCATCCTCTCACTCTCTTAT 58.212 43.478 0.00 0.00 0.00 1.73
4003 4141 8.640091 TCGAATCTCATTCTTCACTAATCAAG 57.360 34.615 0.00 0.00 37.13 3.02
4006 4144 6.974932 TCTCATTCTTCACTAATCAAGCAC 57.025 37.500 0.00 0.00 0.00 4.40
4007 4145 6.705302 TCTCATTCTTCACTAATCAAGCACT 58.295 36.000 0.00 0.00 0.00 4.40
4008 4146 6.592994 TCTCATTCTTCACTAATCAAGCACTG 59.407 38.462 0.00 0.00 0.00 3.66
4009 4147 6.466812 TCATTCTTCACTAATCAAGCACTGA 58.533 36.000 0.00 0.00 38.81 3.41
4011 4149 6.974932 TTCTTCACTAATCAAGCACTGATC 57.025 37.500 2.14 0.00 44.43 2.92
4012 4150 6.041423 TCTTCACTAATCAAGCACTGATCA 57.959 37.500 0.00 0.00 44.43 2.92
4015 4153 5.181009 TCACTAATCAAGCACTGATCAAGG 58.819 41.667 0.00 0.00 44.43 3.61
4016 4154 5.046376 TCACTAATCAAGCACTGATCAAGGA 60.046 40.000 0.00 0.00 44.43 3.36
4017 4155 5.293814 CACTAATCAAGCACTGATCAAGGAG 59.706 44.000 0.00 0.00 44.43 3.69
4020 4158 5.627182 ATCAAGCACTGATCAAGGAGTAT 57.373 39.130 0.00 0.00 41.13 2.12
4021 4159 5.016051 TCAAGCACTGATCAAGGAGTATC 57.984 43.478 0.00 0.00 0.00 2.24
4022 4160 4.713814 TCAAGCACTGATCAAGGAGTATCT 59.286 41.667 0.00 0.00 33.73 1.98
4023 4161 5.188555 TCAAGCACTGATCAAGGAGTATCTT 59.811 40.000 0.00 0.00 33.73 2.40
4024 4162 5.275067 AGCACTGATCAAGGAGTATCTTC 57.725 43.478 0.00 0.00 33.73 2.87
4025 4163 4.961730 AGCACTGATCAAGGAGTATCTTCT 59.038 41.667 0.00 0.00 33.73 2.85
4026 4164 5.049167 GCACTGATCAAGGAGTATCTTCTG 58.951 45.833 0.00 0.00 33.73 3.02
4027 4165 5.599732 CACTGATCAAGGAGTATCTTCTGG 58.400 45.833 0.00 0.00 33.73 3.86
4028 4166 5.362143 CACTGATCAAGGAGTATCTTCTGGA 59.638 44.000 0.00 0.00 33.73 3.86
4059 4198 5.995282 TCTAACTCGGTGACATTTCAATTGT 59.005 36.000 5.13 0.00 31.90 2.71
4124 4263 2.445682 AGAGGATAGTGACGGAGCTT 57.554 50.000 0.00 0.00 0.00 3.74
4378 4517 3.312890 ACATGGAGGAAGAGTAGATGGG 58.687 50.000 0.00 0.00 0.00 4.00
4416 4557 3.578716 TCCCTTTCTGACTGTAGTTCCAG 59.421 47.826 0.00 0.00 38.45 3.86
4585 4726 6.928348 TCTGTTTTCCCTGTATAGTTGAGA 57.072 37.500 0.00 0.00 0.00 3.27
4592 4733 5.030147 TCCCTGTATAGTTGAGATTGTGGT 58.970 41.667 0.00 0.00 0.00 4.16
4596 4737 6.367374 TGTATAGTTGAGATTGTGGTCCAA 57.633 37.500 0.00 0.00 37.49 3.53
4599 4740 4.974645 AGTTGAGATTGTGGTCCAACTA 57.025 40.909 0.00 0.00 43.65 2.24
4662 4803 1.267806 CGATTGCACAGCCCATAATCC 59.732 52.381 0.00 0.00 0.00 3.01
5235 5708 3.390521 ACCGCTTCCGCTCCATCA 61.391 61.111 0.00 0.00 0.00 3.07
5236 5709 2.892425 CCGCTTCCGCTCCATCAC 60.892 66.667 0.00 0.00 0.00 3.06
5237 5710 2.185350 CGCTTCCGCTCCATCACT 59.815 61.111 0.00 0.00 0.00 3.41
5347 5867 3.518998 ACCCTCGTCCGCGATCTG 61.519 66.667 8.23 0.00 46.80 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.264020 GATGCGCAGAGACAACAACAA 59.736 47.619 18.32 0.00 0.00 2.83
36 37 0.317436 CGTCTAGGATGCGCAGAGAC 60.317 60.000 23.93 23.93 34.48 3.36
37 38 0.748367 ACGTCTAGGATGCGCAGAGA 60.748 55.000 18.32 12.88 0.00 3.10
43 44 2.859032 GCCTCTTTACGTCTAGGATGCG 60.859 54.545 0.00 0.00 0.00 4.73
68 69 6.170506 TCAAAGGAATACAAGCATAACTCGT 58.829 36.000 0.00 0.00 0.00 4.18
70 71 6.914757 GCATCAAAGGAATACAAGCATAACTC 59.085 38.462 0.00 0.00 0.00 3.01
75 76 3.947196 TCGCATCAAAGGAATACAAGCAT 59.053 39.130 0.00 0.00 0.00 3.79
78 79 4.944962 TGTCGCATCAAAGGAATACAAG 57.055 40.909 0.00 0.00 0.00 3.16
83 84 6.698008 TTCATAATGTCGCATCAAAGGAAT 57.302 33.333 0.00 0.00 0.00 3.01
91 92 9.449550 TGTTTTATTGATTCATAATGTCGCATC 57.550 29.630 0.00 0.00 0.00 3.91
202 203 1.394917 CTACGCTCAGCTCGCAAAAAT 59.605 47.619 0.00 0.00 0.00 1.82
218 219 8.586570 AAAGAAATCTAATCATCTGAGCTACG 57.413 34.615 0.00 0.00 0.00 3.51
309 310 0.811915 ACATCTCCTCCGACTGAACG 59.188 55.000 0.00 0.00 0.00 3.95
361 362 8.194769 TCGGCGCAATATCTTATAAGATTGATA 58.805 33.333 28.39 14.16 42.96 2.15
398 399 6.932400 CCCTTATTAATGCACGTATACCTTGA 59.068 38.462 0.00 0.00 0.00 3.02
399 400 6.348213 GCCCTTATTAATGCACGTATACCTTG 60.348 42.308 0.00 0.00 0.00 3.61
407 408 4.417426 ACTAGCCCTTATTAATGCACGT 57.583 40.909 0.00 0.00 0.00 4.49
409 410 8.883731 CACATATACTAGCCCTTATTAATGCAC 58.116 37.037 0.00 0.00 0.00 4.57
423 424 4.565166 TCACAAACACGCACATATACTAGC 59.435 41.667 0.00 0.00 0.00 3.42
424 425 5.276395 GCTCACAAACACGCACATATACTAG 60.276 44.000 0.00 0.00 0.00 2.57
425 426 4.565166 GCTCACAAACACGCACATATACTA 59.435 41.667 0.00 0.00 0.00 1.82
426 427 3.370978 GCTCACAAACACGCACATATACT 59.629 43.478 0.00 0.00 0.00 2.12
442 443 2.671130 TACAATCGCAGATGCTCACA 57.329 45.000 2.95 0.00 45.12 3.58
443 444 3.310774 ACATTACAATCGCAGATGCTCAC 59.689 43.478 2.95 0.00 45.12 3.51
487 488 8.873144 GGGGAGTAATTTTTAAAGGGTAAAAGT 58.127 33.333 0.00 0.00 0.00 2.66
488 489 8.316214 GGGGGAGTAATTTTTAAAGGGTAAAAG 58.684 37.037 0.00 0.00 0.00 2.27
489 490 7.039152 CGGGGGAGTAATTTTTAAAGGGTAAAA 60.039 37.037 0.00 0.00 0.00 1.52
490 491 6.436847 CGGGGGAGTAATTTTTAAAGGGTAAA 59.563 38.462 0.00 0.00 0.00 2.01
491 492 5.951148 CGGGGGAGTAATTTTTAAAGGGTAA 59.049 40.000 0.00 0.00 0.00 2.85
501 502 1.374572 TGGGACGGGGGAGTAATTTT 58.625 50.000 0.00 0.00 0.00 1.82
525 526 7.837863 TCTAGTATAGTGTCCAAAAGGTCTTG 58.162 38.462 0.00 0.00 40.38 3.02
526 527 7.674772 ACTCTAGTATAGTGTCCAAAAGGTCTT 59.325 37.037 0.00 0.00 41.11 3.01
528 529 7.407393 ACTCTAGTATAGTGTCCAAAAGGTC 57.593 40.000 0.00 0.00 41.11 3.85
529 530 8.890410 TTACTCTAGTATAGTGTCCAAAAGGT 57.110 34.615 0.00 0.00 41.11 3.50
571 574 5.642165 TGGACAGTATACTTCCTCTATCCC 58.358 45.833 23.24 9.33 0.00 3.85
576 579 8.611051 AAAACTATGGACAGTATACTTCCTCT 57.389 34.615 23.24 16.84 0.00 3.69
604 607 8.892723 CAGCAACTATGTACATGAAATTCCTAA 58.107 33.333 18.81 0.00 0.00 2.69
605 608 7.498900 CCAGCAACTATGTACATGAAATTCCTA 59.501 37.037 18.81 0.00 0.00 2.94
609 612 5.163519 GCCCAGCAACTATGTACATGAAATT 60.164 40.000 18.81 4.49 0.00 1.82
619 622 0.692476 TCTGTGCCCAGCAACTATGT 59.308 50.000 0.00 0.00 41.47 2.29
625 628 2.956799 TTTCGCTCTGTGCCCAGCAA 62.957 55.000 0.00 0.00 41.47 3.91
626 629 2.956799 TTTTCGCTCTGTGCCCAGCA 62.957 55.000 0.00 0.00 38.66 4.41
627 630 1.795170 TTTTTCGCTCTGTGCCCAGC 61.795 55.000 0.00 0.00 38.66 4.85
628 631 2.330254 TTTTTCGCTCTGTGCCCAG 58.670 52.632 0.00 0.00 40.25 4.45
629 632 4.569279 TTTTTCGCTCTGTGCCCA 57.431 50.000 0.00 0.00 38.78 5.36
648 651 1.710816 TTCATGCCTTCCCCGTTTTT 58.289 45.000 0.00 0.00 0.00 1.94
649 652 1.710816 TTTCATGCCTTCCCCGTTTT 58.289 45.000 0.00 0.00 0.00 2.43
650 653 1.824852 GATTTCATGCCTTCCCCGTTT 59.175 47.619 0.00 0.00 0.00 3.60
651 654 1.474330 GATTTCATGCCTTCCCCGTT 58.526 50.000 0.00 0.00 0.00 4.44
652 655 0.748005 CGATTTCATGCCTTCCCCGT 60.748 55.000 0.00 0.00 0.00 5.28
653 656 1.447317 CCGATTTCATGCCTTCCCCG 61.447 60.000 0.00 0.00 0.00 5.73
654 657 0.106719 TCCGATTTCATGCCTTCCCC 60.107 55.000 0.00 0.00 0.00 4.81
655 658 1.405463 GTTCCGATTTCATGCCTTCCC 59.595 52.381 0.00 0.00 0.00 3.97
684 687 4.783055 ACTATCACACGAGACAGTATCCT 58.217 43.478 0.00 0.00 0.00 3.24
700 703 4.512571 TGCGCGTTACTGTATCTACTATCA 59.487 41.667 8.43 0.00 0.00 2.15
733 736 5.105064 TGTGGAACCGTTTTATTTGGGAAAA 60.105 36.000 0.00 0.00 34.36 2.29
737 740 3.319689 AGTGTGGAACCGTTTTATTTGGG 59.680 43.478 0.00 0.00 34.36 4.12
888 891 3.988517 GTCTTCTTCTCGTCGGAAATTGT 59.011 43.478 0.00 0.00 0.00 2.71
945 948 1.545582 CGGAACTGGCAATGGTGATTT 59.454 47.619 0.00 0.00 0.00 2.17
1266 1312 3.876589 GACGGCCTTGACCAGCGAA 62.877 63.158 0.00 0.00 0.00 4.70
1368 1414 3.114647 GAGCGCGTCGGAGATCTGT 62.115 63.158 8.43 0.00 40.67 3.41
1422 1474 1.751162 CCGGAGCTTCTCGACCTCT 60.751 63.158 0.00 0.00 0.00 3.69
2222 2301 5.162794 CGGAGATCAATCAATGCAAAAACA 58.837 37.500 0.00 0.00 0.00 2.83
2231 2310 6.425114 CGATTTAAGACCGGAGATCAATCAAT 59.575 38.462 9.46 0.00 0.00 2.57
2234 2313 5.402867 GTCGATTTAAGACCGGAGATCAATC 59.597 44.000 9.46 9.25 32.78 2.67
2235 2314 5.290386 GTCGATTTAAGACCGGAGATCAAT 58.710 41.667 9.46 0.00 32.78 2.57
2237 2316 3.242969 CGTCGATTTAAGACCGGAGATCA 60.243 47.826 9.46 0.00 35.33 2.92
2242 2321 5.443185 AATATCGTCGATTTAAGACCGGA 57.557 39.130 13.91 0.00 35.33 5.14
2262 2341 6.095720 TGACGACCTGTAACAAAAGGAAAAAT 59.904 34.615 0.00 0.00 37.01 1.82
2268 2347 4.152402 CAGATGACGACCTGTAACAAAAGG 59.848 45.833 0.00 0.00 39.65 3.11
2472 2554 4.970662 ATCAAGATCACCAAATTCACCG 57.029 40.909 0.00 0.00 0.00 4.94
2477 2559 9.865321 CACTGATAAAATCAAGATCACCAAATT 57.135 29.630 0.00 0.00 39.11 1.82
2479 2561 8.408043 ACACTGATAAAATCAAGATCACCAAA 57.592 30.769 0.00 0.00 39.11 3.28
2503 2585 6.563010 GCACATTATCAGAACGAATCAGCTAC 60.563 42.308 0.00 0.00 0.00 3.58
2507 2629 5.723492 TGCACATTATCAGAACGAATCAG 57.277 39.130 0.00 0.00 0.00 2.90
2543 2670 1.467734 CATTGTCAGAACAGAGCAGGC 59.532 52.381 0.00 0.00 36.57 4.85
2788 2915 1.816679 CAGCTTAGCGATGGCAGCA 60.817 57.895 13.27 0.00 39.84 4.41
2797 2924 1.142748 CTCACCCTCCAGCTTAGCG 59.857 63.158 0.00 0.00 0.00 4.26
2828 2955 4.169508 CCGACAGTCTCTGTTAACATCAG 58.830 47.826 9.13 8.42 45.44 2.90
2904 3031 4.806330 TCGTTCATACCTGAAGAGTGAAC 58.194 43.478 6.50 6.50 41.96 3.18
2992 3119 2.550277 TCTCATTCTGTCCCAGCCTA 57.450 50.000 0.00 0.00 0.00 3.93
2998 3125 0.620556 TGGCCTTCTCATTCTGTCCC 59.379 55.000 3.32 0.00 0.00 4.46
3016 3143 2.202987 GCCAGACCGATCAGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
3028 3155 2.364647 CTGATGCAGTCTATCAGCCAGA 59.635 50.000 1.51 0.00 43.38 3.86
3160 3287 3.534054 TTTACCCACACCGGTCGGC 62.534 63.158 2.59 0.00 37.34 5.54
3241 3368 3.118629 GCTCCATGTATTCAGACAGGTCA 60.119 47.826 1.84 0.00 31.51 4.02
3245 3372 2.871022 GCTGCTCCATGTATTCAGACAG 59.129 50.000 0.00 0.00 31.51 3.51
3311 3438 7.661968 TCCATAGTGAGCATACAGAATTACTC 58.338 38.462 0.00 0.00 0.00 2.59
3312 3439 7.603180 TCCATAGTGAGCATACAGAATTACT 57.397 36.000 0.00 0.00 0.00 2.24
3313 3440 8.310382 AGATCCATAGTGAGCATACAGAATTAC 58.690 37.037 0.00 0.00 0.00 1.89
3314 3441 8.309656 CAGATCCATAGTGAGCATACAGAATTA 58.690 37.037 0.00 0.00 0.00 1.40
3346 3475 6.370593 TGTCAAAACTCAGAAATCGCATAAC 58.629 36.000 0.00 0.00 0.00 1.89
3347 3476 6.552859 TGTCAAAACTCAGAAATCGCATAA 57.447 33.333 0.00 0.00 0.00 1.90
3362 3491 6.321717 TCACAACAAGTTCAGATGTCAAAAC 58.678 36.000 0.00 0.00 0.00 2.43
3365 3494 6.698008 ATTCACAACAAGTTCAGATGTCAA 57.302 33.333 0.00 0.00 0.00 3.18
3366 3495 6.698008 AATTCACAACAAGTTCAGATGTCA 57.302 33.333 0.00 0.00 0.00 3.58
3367 3496 6.074676 GCAAATTCACAACAAGTTCAGATGTC 60.075 38.462 0.00 0.00 0.00 3.06
3368 3497 5.750067 GCAAATTCACAACAAGTTCAGATGT 59.250 36.000 0.00 0.00 0.00 3.06
3369 3498 5.749588 TGCAAATTCACAACAAGTTCAGATG 59.250 36.000 0.00 0.00 0.00 2.90
3370 3499 5.904941 TGCAAATTCACAACAAGTTCAGAT 58.095 33.333 0.00 0.00 0.00 2.90
3371 3500 5.105797 ACTGCAAATTCACAACAAGTTCAGA 60.106 36.000 0.00 0.00 0.00 3.27
3372 3501 5.104374 ACTGCAAATTCACAACAAGTTCAG 58.896 37.500 0.00 0.00 0.00 3.02
3428 3557 1.264045 GCCTCCTCCTCACTTGCTCT 61.264 60.000 0.00 0.00 0.00 4.09
3485 3614 1.810151 GTGTTGAATACCGCCACATGT 59.190 47.619 0.00 0.00 0.00 3.21
3578 3707 3.465742 AGGTTCGAGGTCATGATGATG 57.534 47.619 0.00 0.00 0.00 3.07
3638 3767 0.302890 GATCGCGAGCAACCTTCATG 59.697 55.000 21.13 0.00 0.00 3.07
3692 3821 1.470098 CGAACAAAAGGCAGATCAGGG 59.530 52.381 0.00 0.00 0.00 4.45
3696 3825 3.440173 TGATTCCGAACAAAAGGCAGATC 59.560 43.478 0.00 0.00 0.00 2.75
3703 3832 6.346040 GCAAACTGATTGATTCCGAACAAAAG 60.346 38.462 1.49 0.00 41.85 2.27
3712 3841 2.749621 AGACCGCAAACTGATTGATTCC 59.250 45.455 1.49 0.00 41.85 3.01
3729 3862 1.069204 TCTCGCATTAGGCATCAGACC 59.931 52.381 0.00 0.00 45.17 3.85
3856 3994 0.677731 CTTTCATCTGAAGCCGGGCA 60.678 55.000 23.09 0.00 35.21 5.36
3886 4024 3.382832 CCCCTCTCCGCAAGACGT 61.383 66.667 0.00 0.00 41.42 4.34
3958 4096 2.127271 TACTTCCACGTACCGGATCA 57.873 50.000 9.46 0.00 30.99 2.92
4003 4141 5.049167 CAGAAGATACTCCTTGATCAGTGC 58.951 45.833 0.00 0.00 0.00 4.40
4006 4144 5.598005 ACTCCAGAAGATACTCCTTGATCAG 59.402 44.000 0.00 0.00 0.00 2.90
4007 4145 5.523588 ACTCCAGAAGATACTCCTTGATCA 58.476 41.667 0.00 0.00 0.00 2.92
4008 4146 7.001674 TCTACTCCAGAAGATACTCCTTGATC 58.998 42.308 0.00 0.00 0.00 2.92
4009 4147 6.916909 TCTACTCCAGAAGATACTCCTTGAT 58.083 40.000 0.00 0.00 0.00 2.57
4011 4149 7.505585 AGAATCTACTCCAGAAGATACTCCTTG 59.494 40.741 0.00 0.00 36.67 3.61
4012 4150 7.591821 AGAATCTACTCCAGAAGATACTCCTT 58.408 38.462 0.00 0.00 36.67 3.36
4015 4153 9.569122 AGTTAGAATCTACTCCAGAAGATACTC 57.431 37.037 0.00 0.00 36.67 2.59
4016 4154 9.569122 GAGTTAGAATCTACTCCAGAAGATACT 57.431 37.037 7.97 0.00 36.67 2.12
4017 4155 8.500773 CGAGTTAGAATCTACTCCAGAAGATAC 58.499 40.741 11.49 0.00 37.98 2.24
4020 4158 5.823570 CCGAGTTAGAATCTACTCCAGAAGA 59.176 44.000 11.49 0.00 37.98 2.87
4021 4159 5.591067 ACCGAGTTAGAATCTACTCCAGAAG 59.409 44.000 11.49 2.16 37.98 2.85
4022 4160 5.357314 CACCGAGTTAGAATCTACTCCAGAA 59.643 44.000 11.49 0.00 37.98 3.02
4023 4161 4.882427 CACCGAGTTAGAATCTACTCCAGA 59.118 45.833 11.49 0.00 37.98 3.86
4024 4162 4.882427 TCACCGAGTTAGAATCTACTCCAG 59.118 45.833 11.49 7.84 37.98 3.86
4025 4163 4.639310 GTCACCGAGTTAGAATCTACTCCA 59.361 45.833 11.49 0.00 37.98 3.86
4026 4164 4.639310 TGTCACCGAGTTAGAATCTACTCC 59.361 45.833 11.49 2.61 37.98 3.85
4027 4165 5.814764 TGTCACCGAGTTAGAATCTACTC 57.185 43.478 8.73 8.73 37.90 2.59
4028 4166 6.777213 AATGTCACCGAGTTAGAATCTACT 57.223 37.500 0.00 0.00 0.00 2.57
4059 4198 2.281208 GCCGTACACCTGTTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
4124 4263 1.066502 TCGCGGATCAACATCTTGGAA 60.067 47.619 6.13 0.00 0.00 3.53
4378 4517 0.868406 GGGATCAATCGATGCGGTTC 59.132 55.000 0.00 0.00 40.71 3.62
4435 4576 6.756074 CCAAAAACAAAAACAGAGCTCATACA 59.244 34.615 17.77 0.00 0.00 2.29
4508 4649 9.755064 GTACACAATATACTCAACACATTTCAC 57.245 33.333 0.00 0.00 0.00 3.18
4509 4650 8.652463 CGTACACAATATACTCAACACATTTCA 58.348 33.333 0.00 0.00 0.00 2.69
4510 4651 8.653338 ACGTACACAATATACTCAACACATTTC 58.347 33.333 0.00 0.00 0.00 2.17
4562 4703 6.928348 TCTCAACTATACAGGGAAAACAGA 57.072 37.500 0.00 0.00 0.00 3.41
4599 4740 7.987458 GCACCAGGCACATATATATAAGTACAT 59.013 37.037 0.49 0.00 43.97 2.29
4662 4803 4.142795 CGATAGATACCATGTGGAGAGACG 60.143 50.000 5.96 0.00 37.29 4.18
5222 5695 1.144936 GGGAGTGATGGAGCGGAAG 59.855 63.158 0.00 0.00 0.00 3.46
5223 5696 1.198094 TTGGGAGTGATGGAGCGGAA 61.198 55.000 0.00 0.00 0.00 4.30
5224 5697 1.612146 TTGGGAGTGATGGAGCGGA 60.612 57.895 0.00 0.00 0.00 5.54
5225 5698 1.450312 GTTGGGAGTGATGGAGCGG 60.450 63.158 0.00 0.00 0.00 5.52
5227 5700 1.077429 GGGTTGGGAGTGATGGAGC 60.077 63.158 0.00 0.00 0.00 4.70
5232 5705 4.778143 GCGCGGGTTGGGAGTGAT 62.778 66.667 8.83 0.00 0.00 3.06
5347 5867 1.638467 GACGCGCTCATGGATGTTC 59.362 57.895 5.73 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.