Multiple sequence alignment - TraesCS3B01G212900

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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 TraesCS3B01G212900 chr3B 100.000 9510 0 0 1 9510 252597146 252587637 0.000000e+00 17562.0
1 TraesCS3B01G212900 chr3B 94.094 254 12 1 3467 3717 820413613 820413866 5.390000e-102 383.0
2 TraesCS3B01G212900 chr3B 90.000 110 8 2 8741 8847 470032281 470032390 1.290000e-28 139.0
3 TraesCS3B01G212900 chr3D 96.402 4502 85 20 7 4474 173716623 173712165 0.000000e+00 7345.0
4 TraesCS3B01G212900 chr3D 97.017 4191 82 6 4565 8741 173712164 173708003 0.000000e+00 7007.0
5 TraesCS3B01G212900 chr3D 93.695 793 34 9 8730 9510 444722666 444721878 0.000000e+00 1173.0
6 TraesCS3B01G212900 chr3D 89.750 400 31 5 9119 9510 550742016 550741619 3.960000e-138 503.0
7 TraesCS3B01G212900 chr3D 94.583 240 13 0 3476 3715 216472102 216471863 1.170000e-98 372.0
8 TraesCS3B01G212900 chr3D 85.220 318 33 10 8736 9040 550742597 550742281 1.990000e-81 315.0
9 TraesCS3B01G212900 chr3D 78.908 403 58 12 1379 1762 501271450 501271056 2.050000e-61 248.0
10 TraesCS3B01G212900 chr3D 93.671 158 8 2 8736 8893 596661730 596661885 1.600000e-57 235.0
11 TraesCS3B01G212900 chr3D 84.404 109 15 1 8735 8843 299900398 299900504 1.310000e-18 106.0
12 TraesCS3B01G212900 chr3A 93.746 3502 120 29 7 3452 212133056 212129598 0.000000e+00 5162.0
13 TraesCS3B01G212900 chr3A 96.694 2571 63 7 6178 8741 212115022 212112467 0.000000e+00 4257.0
14 TraesCS3B01G212900 chr3A 89.925 1062 70 15 5132 6192 212122662 212121637 0.000000e+00 1334.0
15 TraesCS3B01G212900 chr3A 90.000 170 11 3 4967 5130 212129578 212129409 2.080000e-51 215.0
16 TraesCS3B01G212900 chr3A 85.789 190 22 5 3118 3305 447004 446818 7.530000e-46 196.0
17 TraesCS3B01G212900 chr7D 92.206 1206 83 10 3727 4928 43373353 43372155 0.000000e+00 1696.0
18 TraesCS3B01G212900 chr7D 90.137 1166 104 9 3767 4928 69078646 69077488 0.000000e+00 1506.0
19 TraesCS3B01G212900 chr7D 89.367 1185 114 9 3749 4927 563462395 563463573 0.000000e+00 1480.0
20 TraesCS3B01G212900 chr7D 94.620 539 23 1 8978 9510 51462627 51462089 0.000000e+00 830.0
21 TraesCS3B01G212900 chr7D 95.181 249 11 1 3467 3715 204017343 204017590 8.950000e-105 392.0
22 TraesCS3B01G212900 chr7D 93.976 249 15 0 3467 3715 72121052 72120804 2.510000e-100 377.0
23 TraesCS3B01G212900 chr7D 91.506 259 17 3 8742 8997 51462926 51462670 1.520000e-92 351.0
24 TraesCS3B01G212900 chr7D 80.225 445 70 12 4936 5371 295340718 295340283 1.540000e-82 318.0
25 TraesCS3B01G212900 chr7D 96.875 32 1 0 5098 5129 183791554 183791585 5.000000e-03 54.7
26 TraesCS3B01G212900 chr2D 91.016 1191 97 7 3743 4927 19606254 19607440 0.000000e+00 1598.0
27 TraesCS3B01G212900 chr2D 89.390 1197 113 13 3741 4932 186330661 186331848 0.000000e+00 1495.0
28 TraesCS3B01G212900 chr2D 89.447 1175 115 8 3757 4926 18611511 18610341 0.000000e+00 1474.0
29 TraesCS3B01G212900 chr2D 77.976 504 93 12 4934 5426 284495983 284496479 5.580000e-77 300.0
30 TraesCS3B01G212900 chr2D 80.387 362 60 8 4936 5289 271510482 271510840 2.040000e-66 265.0
31 TraesCS3B01G212900 chr2D 77.966 118 20 6 5054 5167 112182612 112182727 1.710000e-07 69.4
32 TraesCS3B01G212900 chr5B 89.592 1201 111 10 3741 4936 440566638 440565447 0.000000e+00 1513.0
33 TraesCS3B01G212900 chr5B 89.160 1190 116 11 3744 4928 637015143 637013962 0.000000e+00 1471.0
34 TraesCS3B01G212900 chr5B 76.755 641 124 18 4944 5577 687755978 687756600 1.530000e-87 335.0
35 TraesCS3B01G212900 chr5B 94.118 204 9 3 8734 8935 8996404 8996202 3.340000e-79 307.0
36 TraesCS3B01G212900 chr5D 89.513 1192 107 13 3741 4928 371288179 371287002 0.000000e+00 1493.0
37 TraesCS3B01G212900 chr5D 92.190 781 45 7 8740 9510 43184572 43183798 0.000000e+00 1090.0
38 TraesCS3B01G212900 chr5D 75.064 393 76 18 4930 5311 80444443 80444824 7.640000e-36 163.0
39 TraesCS3B01G212900 chr4A 93.014 773 43 4 8741 9504 685838819 685839589 0.000000e+00 1118.0
40 TraesCS3B01G212900 chr4A 81.250 272 39 10 3118 3389 687390364 687390623 9.680000e-50 209.0
41 TraesCS3B01G212900 chr4A 85.437 103 13 1 8741 8843 59232112 59232212 1.310000e-18 106.0
42 TraesCS3B01G212900 chr5A 87.633 938 88 18 7597 8509 688141621 688142555 0.000000e+00 1064.0
43 TraesCS3B01G212900 chr5A 86.800 750 66 27 6464 7189 688140224 688140964 0.000000e+00 806.0
44 TraesCS3B01G212900 chr5A 88.528 462 53 0 2517 2978 688139659 688140120 2.320000e-155 560.0
45 TraesCS3B01G212900 chr5A 87.901 405 39 6 7189 7585 688141004 688141406 1.450000e-127 468.0
46 TraesCS3B01G212900 chr5A 95.902 244 10 0 3467 3710 36245026 36244783 6.920000e-106 396.0
47 TraesCS3B01G212900 chr5A 83.217 286 26 8 2193 2466 688139255 688139530 9.540000e-60 243.0
48 TraesCS3B01G212900 chr5A 94.595 37 1 1 5141 5176 708089649 708089685 1.000000e-03 56.5
49 TraesCS3B01G212900 chr4D 87.866 923 91 16 7607 8511 503620805 503621724 0.000000e+00 1064.0
50 TraesCS3B01G212900 chr4D 86.933 750 66 23 6468 7189 503619111 503619856 0.000000e+00 813.0
51 TraesCS3B01G212900 chr4D 88.936 470 50 2 2517 2985 503618556 503619024 6.400000e-161 579.0
52 TraesCS3B01G212900 chr4D 88.480 408 38 6 7185 7585 503619891 503620296 1.440000e-132 484.0
53 TraesCS3B01G212900 chr4D 85.563 284 21 11 2193 2466 503618096 503618369 7.270000e-71 279.0
54 TraesCS3B01G212900 chr4D 87.302 189 19 4 3120 3305 449206908 449206722 2.690000e-50 211.0
55 TraesCS3B01G212900 chr4B 87.218 931 94 18 7597 8509 649474195 649475118 0.000000e+00 1037.0
56 TraesCS3B01G212900 chr4B 84.671 835 81 29 6381 7187 649472740 649473555 0.000000e+00 789.0
57 TraesCS3B01G212900 chr4B 88.106 454 54 0 2525 2978 649472253 649472706 3.020000e-149 540.0
58 TraesCS3B01G212900 chr4B 87.864 412 35 8 7187 7585 649473600 649474009 4.020000e-128 470.0
59 TraesCS3B01G212900 chr4B 86.071 280 19 11 2193 2466 649471850 649472115 5.620000e-72 283.0
60 TraesCS3B01G212900 chr6D 80.324 803 106 35 8741 9510 122928429 122929212 2.320000e-155 560.0
61 TraesCS3B01G212900 chr6D 79.777 806 114 35 8741 9502 441655891 441656691 3.020000e-149 540.0
62 TraesCS3B01G212900 chr6D 94.355 248 14 0 3467 3714 436684214 436683967 1.940000e-101 381.0
63 TraesCS3B01G212900 chr1B 95.547 247 8 3 3471 3716 497800841 497801085 8.950000e-105 392.0
64 TraesCS3B01G212900 chr1B 85.455 55 5 3 5120 5172 549732036 549731983 5.000000e-03 54.7
65 TraesCS3B01G212900 chr7A 93.676 253 15 1 3467 3718 445250743 445250491 2.510000e-100 377.0
66 TraesCS3B01G212900 chr7A 84.532 278 31 6 3118 3394 398906417 398906683 2.040000e-66 265.0
67 TraesCS3B01G212900 chr7A 79.666 359 42 12 3118 3459 490278214 490277870 7.430000e-56 230.0
68 TraesCS3B01G212900 chr7A 87.931 58 7 0 4953 5010 43012276 43012333 1.710000e-07 69.4
69 TraesCS3B01G212900 chr7B 82.167 443 71 6 4936 5372 339219105 339218665 3.240000e-99 374.0
70 TraesCS3B01G212900 chr7B 79.722 360 43 10 3118 3459 354288692 354288345 5.740000e-57 233.0
71 TraesCS3B01G212900 chr2B 80.324 432 67 14 4936 5358 342301062 342300640 2.580000e-80 311.0
72 TraesCS3B01G212900 chr2B 87.435 191 24 0 3119 3309 245657198 245657388 4.470000e-53 220.0
73 TraesCS3B01G212900 chr6B 78.060 433 68 13 1378 1791 535442727 535443151 2.050000e-61 248.0
74 TraesCS3B01G212900 chr6B 80.537 298 52 4 4939 5230 681237417 681237120 3.460000e-54 224.0
75 TraesCS3B01G212900 chr6A 93.478 46 3 0 8696 8741 299319213 299319258 1.710000e-07 69.4
76 TraesCS3B01G212900 chr1A 84.848 66 10 0 5107 5172 504417455 504417390 6.160000e-07 67.6


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 TraesCS3B01G212900 chr3B 252587637 252597146 9509 True 17562.0 17562 100.0000 1 9510 1 chr3B.!!$R1 9509
1 TraesCS3B01G212900 chr3D 173708003 173716623 8620 True 7176.0 7345 96.7095 7 8741 2 chr3D.!!$R4 8734
2 TraesCS3B01G212900 chr3D 444721878 444722666 788 True 1173.0 1173 93.6950 8730 9510 1 chr3D.!!$R2 780
3 TraesCS3B01G212900 chr3D 550741619 550742597 978 True 409.0 503 87.4850 8736 9510 2 chr3D.!!$R5 774
4 TraesCS3B01G212900 chr3A 212112467 212115022 2555 True 4257.0 4257 96.6940 6178 8741 1 chr3A.!!$R2 2563
5 TraesCS3B01G212900 chr3A 212129409 212133056 3647 True 2688.5 5162 91.8730 7 5130 2 chr3A.!!$R4 5123
6 TraesCS3B01G212900 chr3A 212121637 212122662 1025 True 1334.0 1334 89.9250 5132 6192 1 chr3A.!!$R3 1060
7 TraesCS3B01G212900 chr7D 43372155 43373353 1198 True 1696.0 1696 92.2060 3727 4928 1 chr7D.!!$R1 1201
8 TraesCS3B01G212900 chr7D 69077488 69078646 1158 True 1506.0 1506 90.1370 3767 4928 1 chr7D.!!$R2 1161
9 TraesCS3B01G212900 chr7D 563462395 563463573 1178 False 1480.0 1480 89.3670 3749 4927 1 chr7D.!!$F3 1178
10 TraesCS3B01G212900 chr7D 51462089 51462926 837 True 590.5 830 93.0630 8742 9510 2 chr7D.!!$R5 768
11 TraesCS3B01G212900 chr2D 19606254 19607440 1186 False 1598.0 1598 91.0160 3743 4927 1 chr2D.!!$F1 1184
12 TraesCS3B01G212900 chr2D 186330661 186331848 1187 False 1495.0 1495 89.3900 3741 4932 1 chr2D.!!$F3 1191
13 TraesCS3B01G212900 chr2D 18610341 18611511 1170 True 1474.0 1474 89.4470 3757 4926 1 chr2D.!!$R1 1169
14 TraesCS3B01G212900 chr5B 440565447 440566638 1191 True 1513.0 1513 89.5920 3741 4936 1 chr5B.!!$R2 1195
15 TraesCS3B01G212900 chr5B 637013962 637015143 1181 True 1471.0 1471 89.1600 3744 4928 1 chr5B.!!$R3 1184
16 TraesCS3B01G212900 chr5B 687755978 687756600 622 False 335.0 335 76.7550 4944 5577 1 chr5B.!!$F1 633
17 TraesCS3B01G212900 chr5D 371287002 371288179 1177 True 1493.0 1493 89.5130 3741 4928 1 chr5D.!!$R2 1187
18 TraesCS3B01G212900 chr5D 43183798 43184572 774 True 1090.0 1090 92.1900 8740 9510 1 chr5D.!!$R1 770
19 TraesCS3B01G212900 chr4A 685838819 685839589 770 False 1118.0 1118 93.0140 8741 9504 1 chr4A.!!$F2 763
20 TraesCS3B01G212900 chr5A 688139255 688142555 3300 False 628.2 1064 86.8158 2193 8509 5 chr5A.!!$F2 6316
21 TraesCS3B01G212900 chr4D 503618096 503621724 3628 False 643.8 1064 87.5556 2193 8511 5 chr4D.!!$F1 6318
22 TraesCS3B01G212900 chr4B 649471850 649475118 3268 False 623.8 1037 86.7860 2193 8509 5 chr4B.!!$F1 6316
23 TraesCS3B01G212900 chr6D 122928429 122929212 783 False 560.0 560 80.3240 8741 9510 1 chr6D.!!$F1 769
24 TraesCS3B01G212900 chr6D 441655891 441656691 800 False 540.0 540 79.7770 8741 9502 1 chr6D.!!$F2 761

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
410 418 1.202651 CGGTGTCTGTTTGGTTCTCCT 60.203 52.381 0.00 0.00 34.23 3.69 F
1231 1251 1.262417 TGTCAGGCCAGTTGACGATA 58.738 50.000 16.38 0.00 46.14 2.92 F
1314 1334 1.001706 TCGAAACTGAGACAGGTGACG 60.002 52.381 0.00 0.00 35.51 4.35 F
3258 3452 1.843368 AGTTTGATGATGTGCCCTGG 58.157 50.000 0.00 0.00 0.00 4.45 F
3620 3845 0.384669 GACTAGGCTCGGTGCGTAAT 59.615 55.000 0.00 0.00 44.05 1.89 F
4293 4530 0.536006 GACCCACTTGTGCTGCTCTT 60.536 55.000 0.00 0.00 0.00 2.85 F
5603 5866 0.107459 GTCCCTCTAGGCAAGCCAAG 60.107 60.000 14.40 7.44 38.92 3.61 F
5607 5870 1.079127 TCTAGGCAAGCCAAGCGAC 60.079 57.895 14.40 0.00 38.92 5.19 F
5690 5953 1.133761 CCACCTCTAGGGATGACGAGA 60.134 57.143 0.20 0.00 40.27 4.04 F
5819 6094 1.823250 GCACTTTTGATGTCCCCCACT 60.823 52.381 0.00 0.00 0.00 4.00 F
7694 8554 1.637553 AGGGGAATCACTGACAGCAAT 59.362 47.619 1.25 0.00 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1334 0.389426 TCGTCAGCTTTAGCCCGTTC 60.389 55.000 0.00 0.00 43.38 3.95 R
2869 3051 1.919240 TACGGCAGACAGGAAGAAGA 58.081 50.000 0.00 0.00 0.00 2.87 R
3305 3499 2.280524 CGTTGGACGGCTTGGTGA 60.281 61.111 0.00 0.00 38.08 4.02 R
4282 4519 0.473755 TTTCCCTCAAGAGCAGCACA 59.526 50.000 0.00 0.00 0.00 4.57 R
4928 5175 0.811616 CAAGGTGGTGGCGCTATCTC 60.812 60.000 7.64 1.45 0.00 2.75 R
5691 5954 1.018840 TCTTCCATCCTCCCCTCTCA 58.981 55.000 0.00 0.00 0.00 3.27 R
6928 7224 5.359756 TGTACATCCATGTCTGATAACAGC 58.640 41.667 0.00 0.00 43.17 4.40 R
7048 7344 6.791867 AAGGAAAAACTATATGAAAGGGGC 57.208 37.500 0.00 0.00 0.00 5.80 R
7694 8554 3.631250 AGAAGTTCCTTTTCACCTTGCA 58.369 40.909 0.00 0.00 0.00 4.08 R
7775 8642 7.151999 TCTTGTACATGTCAAACAAAGTTGT 57.848 32.000 12.47 0.00 44.72 3.32 R
9105 10113 0.108424 AGAGATCGTGTGGAAGCTGC 60.108 55.000 0.00 0.00 0.00 5.25 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
108 112 1.474143 GCATTGGAGGAGTAGGAGCAC 60.474 57.143 0.00 0.00 0.00 4.40
150 154 2.126951 CAGGCAAAAGCCACCTGTT 58.873 52.632 9.42 0.00 44.91 3.16
249 254 2.026014 CGCCTGCGCAGTTTGTTT 59.974 55.556 33.75 0.00 34.03 2.83
373 381 3.004419 CCCCTCCGAGTTTTCAAAAGAAC 59.996 47.826 0.00 0.00 0.00 3.01
410 418 1.202651 CGGTGTCTGTTTGGTTCTCCT 60.203 52.381 0.00 0.00 34.23 3.69
512 520 4.166187 GGAATGTTCCTCTGTTTCTTGC 57.834 45.455 4.53 0.00 44.11 4.01
533 541 4.711355 TGCCCATTTTTCTATCTCCCTTTG 59.289 41.667 0.00 0.00 0.00 2.77
591 610 2.093341 GGCTTCGGTGTTAATCCCAGTA 60.093 50.000 0.00 0.00 0.00 2.74
592 611 3.195661 GCTTCGGTGTTAATCCCAGTAG 58.804 50.000 0.00 0.00 0.00 2.57
696 716 4.518970 AGTGTGCCGTCAATTTCTTGTTAT 59.481 37.500 0.00 0.00 33.87 1.89
697 717 5.703592 AGTGTGCCGTCAATTTCTTGTTATA 59.296 36.000 0.00 0.00 33.87 0.98
698 718 6.021596 GTGTGCCGTCAATTTCTTGTTATAG 58.978 40.000 0.00 0.00 33.87 1.31
699 719 5.935206 TGTGCCGTCAATTTCTTGTTATAGA 59.065 36.000 0.00 0.00 33.87 1.98
700 720 6.428465 TGTGCCGTCAATTTCTTGTTATAGAA 59.572 34.615 0.00 0.00 33.87 2.10
701 721 7.041030 TGTGCCGTCAATTTCTTGTTATAGAAA 60.041 33.333 0.00 0.00 45.35 2.52
702 722 7.481798 GTGCCGTCAATTTCTTGTTATAGAAAG 59.518 37.037 0.00 0.00 44.72 2.62
742 762 9.830186 TCTGCTCTCCTCTTTTAGGTTATATAT 57.170 33.333 0.00 0.00 46.62 0.86
813 833 2.432146 TCAGTCTGTCTGAGCAAACTGT 59.568 45.455 9.15 0.00 46.77 3.55
864 884 6.498304 GCTGATTTGTATCCATCACGATTTT 58.502 36.000 0.00 0.00 0.00 1.82
865 885 6.974622 GCTGATTTGTATCCATCACGATTTTT 59.025 34.615 0.00 0.00 0.00 1.94
866 886 7.166473 GCTGATTTGTATCCATCACGATTTTTC 59.834 37.037 0.00 0.00 0.00 2.29
867 887 8.279970 TGATTTGTATCCATCACGATTTTTCT 57.720 30.769 0.00 0.00 0.00 2.52
1152 1172 1.961793 CCACCAGGTTCAAAGACGAA 58.038 50.000 0.00 0.00 0.00 3.85
1231 1251 1.262417 TGTCAGGCCAGTTGACGATA 58.738 50.000 16.38 0.00 46.14 2.92
1314 1334 1.001706 TCGAAACTGAGACAGGTGACG 60.002 52.381 0.00 0.00 35.51 4.35
1357 1377 2.594592 GCAAGAAGGTGCCACCGT 60.595 61.111 8.52 4.76 44.90 4.83
2324 2370 6.667414 TCAGGGTGTAAATTTGAGGCATTAAT 59.333 34.615 0.00 0.00 0.00 1.40
2325 2371 7.180051 TCAGGGTGTAAATTTGAGGCATTAATT 59.820 33.333 0.00 0.00 0.00 1.40
2490 2664 8.149973 TGTCCAATAAACTAACAGTTGAGAAC 57.850 34.615 0.00 0.00 38.66 3.01
2869 3051 4.360889 TGAAATTCAATATGGCCCTGGTT 58.639 39.130 0.00 0.00 0.00 3.67
3005 3187 5.703592 TGTACCTGTTCTTATGTGCGAAAAT 59.296 36.000 0.00 0.00 0.00 1.82
3021 3203 6.364706 GTGCGAAAATCTCTCGATCTGATATT 59.635 38.462 0.00 0.00 38.61 1.28
3258 3452 1.843368 AGTTTGATGATGTGCCCTGG 58.157 50.000 0.00 0.00 0.00 4.45
3307 3501 4.329545 GGCCTCACCAAGCCGTCA 62.330 66.667 0.00 0.00 39.87 4.35
3308 3502 3.050275 GCCTCACCAAGCCGTCAC 61.050 66.667 0.00 0.00 0.00 3.67
3309 3503 2.358737 CCTCACCAAGCCGTCACC 60.359 66.667 0.00 0.00 0.00 4.02
3360 3554 1.342674 ACTGGTATAGCGGACCCTCAA 60.343 52.381 17.51 0.00 35.99 3.02
3368 3562 2.426023 GGACCCTCAACGTGCACT 59.574 61.111 16.19 0.00 0.00 4.40
3438 3663 3.944250 ATTGACCTTGGCAGGCCCG 62.944 63.158 8.02 0.00 45.56 6.13
3511 3736 2.224917 GGGAGTGGATGTACAAACCCAA 60.225 50.000 14.17 0.00 37.68 4.12
3532 3757 4.675063 ACACCTGGGTTTAAATCCTCAT 57.325 40.909 18.31 0.95 0.00 2.90
3553 3778 2.307686 TGGAGGCGAATTTAGGTTCCTT 59.692 45.455 0.00 0.00 0.00 3.36
3554 3779 3.520317 TGGAGGCGAATTTAGGTTCCTTA 59.480 43.478 0.00 0.00 0.00 2.69
3610 3835 3.743396 CGCATTTATTGAGGACTAGGCTC 59.257 47.826 0.00 0.00 0.00 4.70
3620 3845 0.384669 GACTAGGCTCGGTGCGTAAT 59.615 55.000 0.00 0.00 44.05 1.89
3621 3846 0.822164 ACTAGGCTCGGTGCGTAATT 59.178 50.000 0.00 0.00 44.05 1.40
3663 3888 4.814771 ACTCATACTTAAAAGGCCGTATGC 59.185 41.667 16.90 0.00 39.17 3.14
4039 4273 1.549203 GATGTGGCCATGGTTGACTT 58.451 50.000 9.72 5.88 0.00 3.01
4168 4402 1.609635 TTCGCCATCTAGTTCCGGCA 61.610 55.000 0.00 0.00 45.14 5.69
4282 4519 3.005155 GTGTAACTACTGTCGACCCACTT 59.995 47.826 14.12 0.68 0.00 3.16
4292 4529 1.072159 GACCCACTTGTGCTGCTCT 59.928 57.895 0.00 0.00 0.00 4.09
4293 4530 0.536006 GACCCACTTGTGCTGCTCTT 60.536 55.000 0.00 0.00 0.00 2.85
4380 4617 2.601240 TGGGAGCATCATTTGTGGAA 57.399 45.000 0.00 0.00 36.25 3.53
4381 4618 3.104519 TGGGAGCATCATTTGTGGAAT 57.895 42.857 0.00 0.00 36.25 3.01
4464 4701 1.303561 GTCAAGTCATGCCTGGCCA 60.304 57.895 17.53 4.71 0.00 5.36
5052 5300 3.536917 CCGCGCCACCTCCTGATA 61.537 66.667 0.00 0.00 0.00 2.15
5072 5320 1.003355 AGATCACCGCCAACACCAG 60.003 57.895 0.00 0.00 0.00 4.00
5233 5487 5.046591 TGAACGTATCCATGGAGAAAAGACT 60.047 40.000 21.33 2.81 0.00 3.24
5311 5574 1.071385 GATCTGAATCGCCACCTCCAT 59.929 52.381 0.00 0.00 0.00 3.41
5395 5658 1.773391 CTCCTGGCCCATCATCCCT 60.773 63.158 0.00 0.00 0.00 4.20
5399 5662 1.619057 TGGCCCATCATCCCTGACA 60.619 57.895 0.00 0.00 33.22 3.58
5467 5730 1.070601 TGCATGGTAGATCACATCCCG 59.929 52.381 0.00 0.00 0.00 5.14
5585 5848 2.513026 CTAGGCAGCCAAGCGACAGT 62.513 60.000 15.80 0.00 34.64 3.55
5586 5849 2.507110 TAGGCAGCCAAGCGACAGTC 62.507 60.000 15.80 0.00 34.64 3.51
5587 5850 3.426568 GCAGCCAAGCGACAGTCC 61.427 66.667 0.00 0.00 0.00 3.85
5588 5851 2.743928 CAGCCAAGCGACAGTCCC 60.744 66.667 0.00 0.00 0.00 4.46
5589 5852 2.925170 AGCCAAGCGACAGTCCCT 60.925 61.111 0.00 0.00 0.00 4.20
5590 5853 2.435059 GCCAAGCGACAGTCCCTC 60.435 66.667 0.00 0.00 0.00 4.30
5591 5854 2.948720 GCCAAGCGACAGTCCCTCT 61.949 63.158 0.00 0.00 0.00 3.69
5592 5855 1.605058 GCCAAGCGACAGTCCCTCTA 61.605 60.000 0.00 0.00 0.00 2.43
5593 5856 0.457851 CCAAGCGACAGTCCCTCTAG 59.542 60.000 0.00 0.00 0.00 2.43
5594 5857 0.457851 CAAGCGACAGTCCCTCTAGG 59.542 60.000 0.00 0.00 0.00 3.02
5595 5858 1.324005 AAGCGACAGTCCCTCTAGGC 61.324 60.000 0.00 0.00 34.51 3.93
5596 5859 2.052690 GCGACAGTCCCTCTAGGCA 61.053 63.158 0.00 0.00 34.51 4.75
5597 5860 1.605058 GCGACAGTCCCTCTAGGCAA 61.605 60.000 0.00 0.00 34.51 4.52
5598 5861 0.457851 CGACAGTCCCTCTAGGCAAG 59.542 60.000 0.00 0.00 34.51 4.01
5599 5862 0.176910 GACAGTCCCTCTAGGCAAGC 59.823 60.000 0.00 0.00 34.51 4.01
5600 5863 1.268283 ACAGTCCCTCTAGGCAAGCC 61.268 60.000 2.02 2.02 34.51 4.35
5601 5864 1.081092 AGTCCCTCTAGGCAAGCCA 59.919 57.895 14.40 0.00 38.92 4.75
5602 5865 0.547712 AGTCCCTCTAGGCAAGCCAA 60.548 55.000 14.40 0.00 38.92 4.52
5603 5866 0.107459 GTCCCTCTAGGCAAGCCAAG 60.107 60.000 14.40 7.44 38.92 3.61
5604 5867 1.452833 CCCTCTAGGCAAGCCAAGC 60.453 63.158 14.40 0.00 38.92 4.01
5605 5868 1.817099 CCTCTAGGCAAGCCAAGCG 60.817 63.158 14.40 0.00 38.92 4.68
5606 5869 1.219124 CTCTAGGCAAGCCAAGCGA 59.781 57.895 14.40 3.03 38.92 4.93
5607 5870 1.079127 TCTAGGCAAGCCAAGCGAC 60.079 57.895 14.40 0.00 38.92 5.19
5608 5871 2.046314 TAGGCAAGCCAAGCGACC 60.046 61.111 14.40 0.00 38.92 4.79
5609 5872 3.950794 TAGGCAAGCCAAGCGACCG 62.951 63.158 14.40 0.00 38.92 4.79
5690 5953 1.133761 CCACCTCTAGGGATGACGAGA 60.134 57.143 0.20 0.00 40.27 4.04
5691 5954 2.489985 CCACCTCTAGGGATGACGAGAT 60.490 54.545 0.20 0.00 40.27 2.75
5819 6094 1.823250 GCACTTTTGATGTCCCCCACT 60.823 52.381 0.00 0.00 0.00 4.00
5865 6140 6.679327 TCATGATGAGAGAAGATTTTGCAG 57.321 37.500 0.00 0.00 0.00 4.41
6350 6627 1.997606 GTGAAGCTTTCCATTGCATGC 59.002 47.619 11.82 11.82 0.00 4.06
7048 7344 9.099454 GATTCAGAAGGTACCACTATTAAACAG 57.901 37.037 15.94 0.00 0.00 3.16
7072 7369 7.559897 CAGCCCCTTTCATATAGTTTTTCCTTA 59.440 37.037 0.00 0.00 0.00 2.69
7694 8554 1.637553 AGGGGAATCACTGACAGCAAT 59.362 47.619 1.25 0.00 0.00 3.56
7775 8642 3.496160 GCAAACTCCTGTCTGACCCTAAA 60.496 47.826 5.17 0.00 0.00 1.85
7776 8643 4.065789 CAAACTCCTGTCTGACCCTAAAC 58.934 47.826 5.17 0.00 0.00 2.01
7777 8644 2.972348 ACTCCTGTCTGACCCTAAACA 58.028 47.619 5.17 0.00 0.00 2.83
8231 9102 3.104512 TGATATCTTGTCCGGAACCAGT 58.895 45.455 5.23 0.00 0.00 4.00
8250 9121 1.604278 GTGTCAAGACTCACTTTGCCC 59.396 52.381 1.53 0.00 36.61 5.36
8252 9123 0.756294 TCAAGACTCACTTTGCCCGA 59.244 50.000 0.00 0.00 36.61 5.14
8343 9220 3.103447 TCCATTCTCACATCGATCTGC 57.897 47.619 0.00 0.00 0.00 4.26
8554 9444 3.135167 TGTCTATGCCATGCTTCATCAGA 59.865 43.478 0.00 0.00 0.00 3.27
8671 9564 9.182214 ACTCTATGTTGTTAAGGAGTATACGAA 57.818 33.333 0.00 0.00 33.13 3.85
8728 9621 4.072839 CCTTTCCTTGTACCCAAGTCTTC 58.927 47.826 2.17 0.00 45.49 2.87
8872 9769 0.322456 TAAAGAGCAACATGCCCGCT 60.322 50.000 3.95 3.95 46.52 5.52
8873 9770 1.870055 AAAGAGCAACATGCCCGCTG 61.870 55.000 8.68 0.00 46.52 5.18
8896 9801 2.167075 GGAAAACTCCCCTCGACGATAA 59.833 50.000 0.00 0.00 0.00 1.75
8897 9802 3.368739 GGAAAACTCCCCTCGACGATAAA 60.369 47.826 0.00 0.00 0.00 1.40
8943 9848 3.100671 AGATAAAACAGGACGGAGCTCT 58.899 45.455 14.64 0.00 0.00 4.09
8961 9898 0.824759 CTAGCCCTTAGTCGCCACTT 59.175 55.000 0.00 0.00 33.62 3.16
9031 10037 1.959985 GATCAGATCGCTCCCAGAGAA 59.040 52.381 0.00 0.00 0.00 2.87
9057 10065 1.004745 CCCCATATCTTCCCCCAATCG 59.995 57.143 0.00 0.00 0.00 3.34
9081 10089 0.178891 GGATCTGGCCATAGGAGGGA 60.179 60.000 5.51 0.00 0.00 4.20
9105 10113 1.608801 GGGGTTTCTTGCCATTTGCTG 60.609 52.381 0.00 0.00 42.00 4.41
9114 10306 1.969085 CCATTTGCTGCAGCTTCCA 59.031 52.632 36.61 16.43 42.66 3.53
9215 10407 1.070601 CGATCACCTGCATACCCATCA 59.929 52.381 0.00 0.00 0.00 3.07
9235 10427 7.273381 CCCATCAAAGTCAATCGATTAAAACAC 59.727 37.037 10.97 3.16 0.00 3.32
9434 10634 4.083590 GGCAAGAAGACTCATGTTCAGAAC 60.084 45.833 6.32 6.32 30.40 3.01
9487 10690 4.100963 TGTCTCTTGCAAAGGTTGTCTCTA 59.899 41.667 0.00 0.00 46.24 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.370049 CAGCAAGGATGATGAGTCTGTAG 58.630 47.826 0.00 0.00 45.81 2.74
1 2 3.431346 GCAGCAAGGATGATGAGTCTGTA 60.431 47.826 0.00 0.00 45.81 2.74
2 3 2.680221 GCAGCAAGGATGATGAGTCTGT 60.680 50.000 0.00 0.00 45.81 3.41
3 4 1.941294 GCAGCAAGGATGATGAGTCTG 59.059 52.381 0.00 0.00 45.81 3.51
150 154 1.006337 GGCAACCAATCTTGCGCAA 60.006 52.632 23.48 23.48 46.43 4.85
153 157 2.476534 AAGCGGCAACCAATCTTGCG 62.477 55.000 1.45 0.00 46.43 4.85
249 254 1.048601 AGAAAAGAGAGTCCACCGCA 58.951 50.000 0.00 0.00 0.00 5.69
373 381 0.994995 CCGAGAATCAAGCACACTCG 59.005 55.000 0.00 0.00 46.20 4.18
410 418 3.133003 TGAACCGGAAATTTGCCAGAAAA 59.867 39.130 9.46 0.00 0.00 2.29
512 520 5.127682 CCACAAAGGGAGATAGAAAAATGGG 59.872 44.000 0.00 0.00 0.00 4.00
533 541 3.624861 CAGATCTAGAAACCATGTGCCAC 59.375 47.826 0.00 0.00 0.00 5.01
591 610 5.805728 ACCAATCAGACGAAATAACTTCCT 58.194 37.500 0.00 0.00 0.00 3.36
592 611 6.496338 AACCAATCAGACGAAATAACTTCC 57.504 37.500 0.00 0.00 0.00 3.46
594 613 6.348213 CGGAAACCAATCAGACGAAATAACTT 60.348 38.462 0.00 0.00 0.00 2.66
696 716 5.622460 GCAGAACGTTGGATCTCTCTTTCTA 60.622 44.000 5.00 0.00 0.00 2.10
697 717 4.815269 CAGAACGTTGGATCTCTCTTTCT 58.185 43.478 5.00 0.00 0.00 2.52
698 718 3.369451 GCAGAACGTTGGATCTCTCTTTC 59.631 47.826 5.00 0.00 0.00 2.62
699 719 3.007398 AGCAGAACGTTGGATCTCTCTTT 59.993 43.478 5.00 0.00 0.00 2.52
700 720 2.564947 AGCAGAACGTTGGATCTCTCTT 59.435 45.455 5.00 0.00 0.00 2.85
701 721 2.165437 GAGCAGAACGTTGGATCTCTCT 59.835 50.000 5.00 0.00 0.00 3.10
702 722 2.165437 AGAGCAGAACGTTGGATCTCTC 59.835 50.000 5.00 6.01 0.00 3.20
813 833 7.176690 GGGAAGGAAAGTAAAATCACAGATTCA 59.823 37.037 0.00 0.00 0.00 2.57
912 932 4.205588 CCTTTTTCGGCGAAACAAACTTAC 59.794 41.667 32.32 0.00 30.83 2.34
914 934 3.183754 CCTTTTTCGGCGAAACAAACTT 58.816 40.909 32.32 0.00 30.83 2.66
1152 1172 1.111116 TCTCAACAACCCCGTCGTCT 61.111 55.000 0.00 0.00 0.00 4.18
1231 1251 2.281345 GCTGTGTGCTGAGCCACT 60.281 61.111 20.93 0.00 38.95 4.00
1314 1334 0.389426 TCGTCAGCTTTAGCCCGTTC 60.389 55.000 0.00 0.00 43.38 3.95
1366 1386 0.456995 CTCTTCCTCACGGTCTTCGC 60.457 60.000 0.00 0.00 43.89 4.70
1368 1388 4.580995 TCATATCTCTTCCTCACGGTCTTC 59.419 45.833 0.00 0.00 0.00 2.87
1473 1493 2.096417 GTGATTGAACCGTTTCTCCACG 60.096 50.000 0.00 0.00 40.02 4.94
2869 3051 1.919240 TACGGCAGACAGGAAGAAGA 58.081 50.000 0.00 0.00 0.00 2.87
3021 3203 6.381133 ACCACATCTCACATTCTCACTATACA 59.619 38.462 0.00 0.00 0.00 2.29
3258 3452 4.024143 TGTGCGTTGATGCGTGGC 62.024 61.111 0.00 0.00 37.81 5.01
3304 3498 2.604174 CGTTGGACGGCTTGGTGAC 61.604 63.158 0.00 0.00 38.08 3.67
3305 3499 2.280524 CGTTGGACGGCTTGGTGA 60.281 61.111 0.00 0.00 38.08 4.02
3374 3568 1.820906 GCGGATTCTGGAGCATGCA 60.821 57.895 21.98 0.00 33.07 3.96
3511 3736 4.344104 CATGAGGATTTAAACCCAGGTGT 58.656 43.478 0.21 0.00 0.00 4.16
3532 3757 1.913419 AGGAACCTAAATTCGCCTCCA 59.087 47.619 0.00 0.00 0.00 3.86
3553 3778 5.975988 AAGCCTGGTCCTCAAGAATAATA 57.024 39.130 0.00 0.00 0.00 0.98
3554 3779 4.870021 AAGCCTGGTCCTCAAGAATAAT 57.130 40.909 0.00 0.00 0.00 1.28
3610 3835 6.033091 GGATTTTTAAACTCAATTACGCACCG 59.967 38.462 0.00 0.00 0.00 4.94
3663 3888 1.134280 CCTCTGCACCAACTAGGGATG 60.134 57.143 0.00 0.00 43.89 3.51
3729 3954 1.327303 GGGAGCGATCAGATCTGAGT 58.673 55.000 28.26 17.19 43.61 3.41
3990 4222 1.281925 ATCCGCCCTTCCCATGAAGT 61.282 55.000 0.00 0.00 45.45 3.01
4139 4373 3.823873 ACTAGATGGCGAATCTCGAGATT 59.176 43.478 34.89 34.89 42.27 2.40
4168 4402 1.025812 CTATGTCTTCCCGACTCGCT 58.974 55.000 0.00 0.00 43.25 4.93
4282 4519 0.473755 TTTCCCTCAAGAGCAGCACA 59.526 50.000 0.00 0.00 0.00 4.57
4347 4584 2.303022 TGCTCCCAAGAGAGAAAACGAT 59.697 45.455 0.00 0.00 43.39 3.73
4380 4617 2.038659 GCCTCTGTCTTCCAGCTCTAT 58.961 52.381 0.00 0.00 41.25 1.98
4381 4618 1.272704 TGCCTCTGTCTTCCAGCTCTA 60.273 52.381 0.00 0.00 41.25 2.43
4513 4751 3.632604 AGACGCGAAGATTCTGGAAGATA 59.367 43.478 15.93 0.00 46.36 1.98
4601 4842 2.036992 GAGAGATCCGCATCATCCTTGT 59.963 50.000 0.00 0.00 0.00 3.16
4928 5175 0.811616 CAAGGTGGTGGCGCTATCTC 60.812 60.000 7.64 1.45 0.00 2.75
5052 5300 1.302511 GGTGTTGGCGGTGATCTGT 60.303 57.895 0.00 0.00 0.00 3.41
5072 5320 2.203337 TTGGCTGGTGGACACTGC 60.203 61.111 2.13 7.30 29.21 4.40
5301 5564 1.595093 CGGTTGGAAATGGAGGTGGC 61.595 60.000 0.00 0.00 0.00 5.01
5311 5574 1.205417 GGTCCTCGATACGGTTGGAAA 59.795 52.381 0.00 0.00 0.00 3.13
5395 5658 2.280552 GGTGGTAGCCCGTCTGTCA 61.281 63.158 0.00 0.00 0.00 3.58
5467 5730 4.222847 GGGATGACGGACTCGGCC 62.223 72.222 0.00 0.00 45.49 6.13
5536 5799 2.509336 CGGTGGCGCGAGATCTTT 60.509 61.111 12.10 0.00 0.00 2.52
5585 5848 1.915078 GCTTGGCTTGCCTAGAGGGA 61.915 60.000 23.19 0.00 37.23 4.20
5586 5849 1.452833 GCTTGGCTTGCCTAGAGGG 60.453 63.158 23.19 2.18 35.18 4.30
5587 5850 1.817099 CGCTTGGCTTGCCTAGAGG 60.817 63.158 23.19 12.06 38.53 3.69
5588 5851 1.086634 GTCGCTTGGCTTGCCTAGAG 61.087 60.000 23.19 20.11 0.00 2.43
5589 5852 1.079127 GTCGCTTGGCTTGCCTAGA 60.079 57.895 23.19 10.09 0.00 2.43
5590 5853 2.109126 GGTCGCTTGGCTTGCCTAG 61.109 63.158 16.60 16.60 0.00 3.02
5591 5854 2.046314 GGTCGCTTGGCTTGCCTA 60.046 61.111 13.18 4.37 0.00 3.93
5594 5857 4.090057 GACGGTCGCTTGGCTTGC 62.090 66.667 0.00 0.00 0.00 4.01
5595 5858 3.777925 CGACGGTCGCTTGGCTTG 61.778 66.667 18.36 0.00 31.14 4.01
5609 5872 2.278013 GATCTCACGTCCCGCGAC 60.278 66.667 8.23 0.00 44.77 5.19
5620 5883 2.282446 GGGACGGAGGGGATCTCA 59.718 66.667 0.00 0.00 44.19 3.27
5690 5953 1.582624 TCTTCCATCCTCCCCTCTCAT 59.417 52.381 0.00 0.00 0.00 2.90
5691 5954 1.018840 TCTTCCATCCTCCCCTCTCA 58.981 55.000 0.00 0.00 0.00 3.27
5819 6094 8.168790 TGAACATTTCATCATGTTTCTCTTCA 57.831 30.769 0.81 0.00 45.55 3.02
5865 6140 4.436852 CGTATGTAAGGCAAATGTGTGACC 60.437 45.833 0.00 0.00 0.00 4.02
6324 6601 0.729116 ATGGAAAGCTTCACGATGCG 59.271 50.000 0.00 0.00 36.69 4.73
6350 6627 7.375280 GCTCATTGATAAGAAATTGTGTGATCG 59.625 37.037 0.00 0.00 0.00 3.69
6928 7224 5.359756 TGTACATCCATGTCTGATAACAGC 58.640 41.667 0.00 0.00 43.17 4.40
7048 7344 6.791867 AAGGAAAAACTATATGAAAGGGGC 57.208 37.500 0.00 0.00 0.00 5.80
7694 8554 3.631250 AGAAGTTCCTTTTCACCTTGCA 58.369 40.909 0.00 0.00 0.00 4.08
7775 8642 7.151999 TCTTGTACATGTCAAACAAAGTTGT 57.848 32.000 12.47 0.00 44.72 3.32
7776 8643 8.633075 AATCTTGTACATGTCAAACAAAGTTG 57.367 30.769 12.47 3.38 33.05 3.16
7777 8644 7.920682 GGAATCTTGTACATGTCAAACAAAGTT 59.079 33.333 12.47 10.14 33.05 2.66
8117 8988 1.202639 ACACTCGAGCAATGGTTGTGA 60.203 47.619 13.61 3.07 0.00 3.58
8231 9102 1.810031 CGGGCAAAGTGAGTCTTGACA 60.810 52.381 3.49 0.00 36.40 3.58
8250 9121 1.082117 ACGCTTCGCCAATTAGGTCG 61.082 55.000 0.00 0.00 40.61 4.79
8252 9123 0.249398 AGACGCTTCGCCAATTAGGT 59.751 50.000 0.00 0.00 40.61 3.08
8343 9220 8.974060 ATGGTAATTACCCACATTTGTAGTAG 57.026 34.615 28.00 0.00 45.87 2.57
8519 9409 8.026341 CATGGCATAGACATGTTCTTATACAG 57.974 38.462 0.00 0.00 43.48 2.74
8877 9774 3.967332 TTTATCGTCGAGGGGAGTTTT 57.033 42.857 5.12 0.00 0.00 2.43
8896 9801 6.878317 AGCTTCTTTCAGTTTTAGCCTTTTT 58.122 32.000 0.00 0.00 0.00 1.94
8897 9802 6.471233 AGCTTCTTTCAGTTTTAGCCTTTT 57.529 33.333 0.00 0.00 0.00 2.27
8943 9848 0.822164 GAAGTGGCGACTAAGGGCTA 59.178 55.000 0.30 0.00 0.00 3.93
9031 10037 2.648838 GGGGAAGATATGGGGGAGAAT 58.351 52.381 0.00 0.00 0.00 2.40
9057 10065 0.689623 CCTATGGCCAGATCCAGGTC 59.310 60.000 13.05 0.00 39.89 3.85
9105 10113 0.108424 AGAGATCGTGTGGAAGCTGC 60.108 55.000 0.00 0.00 0.00 5.25
9114 10306 2.159226 CCGGAGCTAAAAGAGATCGTGT 60.159 50.000 0.00 0.00 41.83 4.49
9215 10407 8.349245 TGACATGTGTTTTAATCGATTGACTTT 58.651 29.630 20.87 0.00 0.00 2.66
9235 10427 3.760151 TCTGGAAAAGCAGGAATGACATG 59.240 43.478 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.