Multiple sequence alignment - TraesCS6A01G050900

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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 TraesCS6A01G050900 chr6A 100.000 4458 0 0 1 4458 26564036 26568493 0.000000e+00 8233
1 TraesCS6A01G050900 chrUn 91.323 2593 170 35 445 3008 95005250 95007816 0.000000e+00 3491
2 TraesCS6A01G050900 chrUn 92.577 714 43 4 3004 3707 95015365 95016078 0.000000e+00 1016
3 TraesCS6A01G050900 chrUn 87.290 417 39 9 53 468 95004013 95004416 8.730000e-127 464
4 TraesCS6A01G050900 chr6B 90.557 1938 120 28 1115 3029 45548156 45550053 0.000000e+00 2507
5 TraesCS6A01G050900 chr6B 86.943 988 83 16 2 982 45546781 45547729 0.000000e+00 1068
6 TraesCS6A01G050900 chr6B 92.297 688 48 4 3022 3707 45550973 45551657 0.000000e+00 972
7 TraesCS6A01G050900 chr2D 80.534 786 112 30 3698 4455 375838321 375839093 2.330000e-157 566
8 TraesCS6A01G050900 chr2D 83.846 260 38 4 6 263 7129417 7129674 1.240000e-60 244
9 TraesCS6A01G050900 chr5D 80.375 800 90 38 3701 4456 107410046 107409270 3.030000e-151 545
10 TraesCS6A01G050900 chr5D 80.628 733 108 28 3742 4456 540205102 540204386 1.820000e-148 536
11 TraesCS6A01G050900 chr7D 79.468 789 115 32 3701 4454 45737606 45738382 2.380000e-142 516
12 TraesCS6A01G050900 chr7D 77.905 525 69 26 3800 4286 564146344 564145829 2.620000e-72 283
13 TraesCS6A01G050900 chr1D 78.238 749 124 25 3700 4424 465215746 465216479 1.140000e-120 444
14 TraesCS6A01G050900 chr1D 74.607 764 127 44 3710 4436 11847854 11848587 1.580000e-69 274
15 TraesCS6A01G050900 chr4D 78.158 760 109 39 3701 4431 390674116 390674847 8.860000e-117 431
16 TraesCS6A01G050900 chr4D 77.339 759 125 32 3701 4431 166991720 166992459 5.370000e-109 405
17 TraesCS6A01G050900 chr3D 77.919 788 101 47 3703 4456 551221900 551222648 1.480000e-114 424
18 TraesCS6A01G050900 chr3D 88.346 266 29 2 1 266 319844133 319843870 7.200000e-83 318
19 TraesCS6A01G050900 chr3D 84.354 294 40 6 3701 3990 269758103 269757812 2.620000e-72 283
20 TraesCS6A01G050900 chr3D 83.895 267 40 3 1 266 382501105 382501369 7.400000e-63 252
21 TraesCS6A01G050900 chr3B 79.589 632 76 26 3797 4390 788251311 788251927 1.930000e-108 403
22 TraesCS6A01G050900 chr3B 83.270 263 37 4 1 263 531792183 531792438 7.450000e-58 235
23 TraesCS6A01G050900 chr3B 84.932 219 31 2 46 263 19965000 19964783 2.090000e-53 220
24 TraesCS6A01G050900 chr7B 77.305 564 74 37 3932 4456 652056798 652056250 2.620000e-72 283
25 TraesCS6A01G050900 chr3A 85.171 263 35 1 1 263 223531325 223531583 2.640000e-67 267
26 TraesCS6A01G050900 chr6D 83.019 265 42 1 2 263 166772773 166773037 2.070000e-58 237
27 TraesCS6A01G050900 chr6D 82.129 263 47 0 1 263 441826559 441826821 4.490000e-55 226


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 TraesCS6A01G050900 chr6A 26564036 26568493 4457 False 8233.000000 8233 100.000000 1 4458 1 chr6A.!!$F1 4457
1 TraesCS6A01G050900 chrUn 95004013 95007816 3803 False 1977.500000 3491 89.306500 53 3008 2 chrUn.!!$F2 2955
2 TraesCS6A01G050900 chrUn 95015365 95016078 713 False 1016.000000 1016 92.577000 3004 3707 1 chrUn.!!$F1 703
3 TraesCS6A01G050900 chr6B 45546781 45551657 4876 False 1515.666667 2507 89.932333 2 3707 3 chr6B.!!$F1 3705
4 TraesCS6A01G050900 chr2D 375838321 375839093 772 False 566.000000 566 80.534000 3698 4455 1 chr2D.!!$F2 757
5 TraesCS6A01G050900 chr5D 107409270 107410046 776 True 545.000000 545 80.375000 3701 4456 1 chr5D.!!$R1 755
6 TraesCS6A01G050900 chr5D 540204386 540205102 716 True 536.000000 536 80.628000 3742 4456 1 chr5D.!!$R2 714
7 TraesCS6A01G050900 chr7D 45737606 45738382 776 False 516.000000 516 79.468000 3701 4454 1 chr7D.!!$F1 753
8 TraesCS6A01G050900 chr7D 564145829 564146344 515 True 283.000000 283 77.905000 3800 4286 1 chr7D.!!$R1 486
9 TraesCS6A01G050900 chr1D 465215746 465216479 733 False 444.000000 444 78.238000 3700 4424 1 chr1D.!!$F2 724
10 TraesCS6A01G050900 chr1D 11847854 11848587 733 False 274.000000 274 74.607000 3710 4436 1 chr1D.!!$F1 726
11 TraesCS6A01G050900 chr4D 390674116 390674847 731 False 431.000000 431 78.158000 3701 4431 1 chr4D.!!$F2 730
12 TraesCS6A01G050900 chr4D 166991720 166992459 739 False 405.000000 405 77.339000 3701 4431 1 chr4D.!!$F1 730
13 TraesCS6A01G050900 chr3D 551221900 551222648 748 False 424.000000 424 77.919000 3703 4456 1 chr3D.!!$F2 753
14 TraesCS6A01G050900 chr3B 788251311 788251927 616 False 403.000000 403 79.589000 3797 4390 1 chr3B.!!$F2 593
15 TraesCS6A01G050900 chr7B 652056250 652056798 548 True 283.000000 283 77.305000 3932 4456 1 chr7B.!!$R1 524

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
34 35 0.186386 TGACCCGGACCCAACAATTT 59.814 50.0 0.73 0.00 0.00 1.82 F
233 235 0.245266 TGGCTGCATGCATTGTCTTG 59.755 50.0 22.97 8.76 45.15 3.02 F
245 247 0.401356 TTGTCTTGATGCAGAGGCCA 59.599 50.0 5.01 0.00 40.13 5.36 F
1778 2948 0.530744 TCGAGGGTGTAGTCACATGC 59.469 55.0 0.00 0.00 45.45 4.06 F
2852 4037 0.393537 CAATCACTCCAGGAGGCACC 60.394 60.0 21.31 0.00 33.35 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2930 0.246360 TGCATGTGACTACACCCTCG 59.754 55.00 0.00 0.00 45.4 4.63 R
2107 3281 1.173043 CCATGGCACCGTACAATGTT 58.827 50.00 0.00 0.00 0.0 2.71 R
2227 3401 5.703978 TCCATCCAACTTGTACAACATTG 57.296 39.13 16.15 16.15 0.0 2.82 R
3217 5331 0.324552 TAGTGTAGCCGCCCCAAGTA 60.325 55.00 0.00 0.00 0.0 2.24 R
3748 5873 0.745128 AGTGTTTTCGGCGGTGAACA 60.745 50.00 7.21 12.81 0.0 3.18 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 2.663852 GGACCGTTGTGTGACCCG 60.664 66.667 0.00 0.00 0.00 5.28
27 28 2.768769 TTGTGTGACCCGGACCCA 60.769 61.111 0.73 0.00 0.00 4.51
34 35 0.186386 TGACCCGGACCCAACAATTT 59.814 50.000 0.73 0.00 0.00 1.82
44 45 4.202315 GGACCCAACAATTTAGCTTGGTTT 60.202 41.667 0.00 0.00 33.78 3.27
51 52 1.627864 TTTAGCTTGGTTTGGGCCTC 58.372 50.000 4.53 0.00 0.00 4.70
90 91 3.197983 GCTTTAGTGTGAGGTCTGGGTAT 59.802 47.826 0.00 0.00 0.00 2.73
91 92 4.404715 GCTTTAGTGTGAGGTCTGGGTATA 59.595 45.833 0.00 0.00 0.00 1.47
137 138 6.407412 CCTTCATCAAGTGGATAAGAGTAGCA 60.407 42.308 0.00 0.00 33.95 3.49
156 157 2.349590 CAACAGATGTCGCCAAGATGA 58.650 47.619 0.00 0.00 0.00 2.92
158 159 2.558378 ACAGATGTCGCCAAGATGATG 58.442 47.619 0.00 0.00 0.00 3.07
173 174 7.254727 GCCAAGATGATGACTTCAGACTTATTC 60.255 40.741 10.77 0.00 37.89 1.75
227 229 7.811117 AATTAATAAAATGGCTGCATGCATT 57.189 28.000 22.97 13.89 45.15 3.56
231 233 1.191535 AATGGCTGCATGCATTGTCT 58.808 45.000 22.97 3.23 45.15 3.41
233 235 0.245266 TGGCTGCATGCATTGTCTTG 59.755 50.000 22.97 8.76 45.15 3.02
245 247 0.401356 TTGTCTTGATGCAGAGGCCA 59.599 50.000 5.01 0.00 40.13 5.36
248 250 0.911045 TCTTGATGCAGAGGCCAGGA 60.911 55.000 5.01 0.00 40.13 3.86
304 306 4.924305 TGGAAGCAATGATAGCATTTCC 57.076 40.909 13.63 13.63 41.87 3.13
341 343 4.773323 GCTTCATGTTAAAGCAGGACTT 57.227 40.909 11.61 0.00 46.63 3.01
352 354 1.089920 GCAGGACTTGGTACATGCAG 58.910 55.000 0.00 0.00 39.30 4.41
360 362 5.334879 GGACTTGGTACATGCAGTTTAGTTG 60.335 44.000 0.00 0.00 39.30 3.16
361 363 4.023193 ACTTGGTACATGCAGTTTAGTTGC 60.023 41.667 0.00 0.00 39.30 4.17
367 370 2.928801 TGCAGTTTAGTTGCTCCTCA 57.071 45.000 0.00 0.00 42.02 3.86
376 379 1.746220 AGTTGCTCCTCAGTACTAGCG 59.254 52.381 10.09 0.00 37.80 4.26
392 395 7.898309 CAGTACTAGCGTTATGTTCAATTTGAC 59.102 37.037 0.00 0.00 0.00 3.18
395 398 3.119990 AGCGTTATGTTCAATTTGACCCG 60.120 43.478 0.00 0.00 0.00 5.28
495 1355 7.378995 CCTATCTACGCAACAGTGTAATCTAAC 59.621 40.741 0.00 0.00 0.00 2.34
499 1359 4.684703 ACGCAACAGTGTAATCTAACTGAC 59.315 41.667 9.63 0.00 45.43 3.51
520 1380 4.770795 ACGGAATTAAGTTGAGAGGGATG 58.229 43.478 0.00 0.00 0.00 3.51
548 1408 5.302360 TCCCACTGCGTAAATATATTGGTC 58.698 41.667 0.00 0.00 0.00 4.02
584 1444 6.646240 CCATTTATTTTCAAGGTGTCAGTTGG 59.354 38.462 0.00 0.00 0.00 3.77
596 1456 2.757314 TGTCAGTTGGATTGTTGTTGCA 59.243 40.909 0.00 0.00 0.00 4.08
612 1472 8.865420 TGTTGTTGCAAATATTAGGTAGGTAA 57.135 30.769 0.00 0.00 0.00 2.85
637 1497 1.471287 GCGTGGGATTTAACTTGGTCC 59.529 52.381 0.00 0.00 0.00 4.46
777 1639 6.126863 TGACACTTCTGGGTCTATGAATTT 57.873 37.500 0.12 0.00 35.11 1.82
886 1748 5.163426 CCATAAGGAGCACAATAAATGCCAA 60.163 40.000 0.00 0.00 44.53 4.52
910 1772 4.987912 ACATATTTGTTTCTTTTGTGGCCG 59.012 37.500 0.00 0.00 29.55 6.13
919 1781 1.679153 CTTTTGTGGCCGTTTACACCT 59.321 47.619 0.00 0.00 36.80 4.00
920 1782 2.634815 TTTGTGGCCGTTTACACCTA 57.365 45.000 0.00 0.00 36.80 3.08
991 1857 4.883585 GTGCAAATATTCACATCTCCCTCA 59.116 41.667 0.00 0.00 33.63 3.86
1036 1902 8.378172 TGTCTACATTTTCTTGGTACTCTTTG 57.622 34.615 0.00 0.00 0.00 2.77
1049 1915 4.816925 GGTACTCTTTGCCTTATGCTTAGG 59.183 45.833 0.00 0.00 42.00 2.69
1061 1927 9.101325 TGCCTTATGCTTAGGTAAAGTATCTAT 57.899 33.333 0.00 0.00 39.47 1.98
1153 2313 8.538701 AGAGAATAATATCGATTGAGGCTGAAT 58.461 33.333 1.71 0.00 0.00 2.57
1160 2320 2.421073 CGATTGAGGCTGAATTGCAAGA 59.579 45.455 4.94 0.00 34.04 3.02
1165 2325 1.514553 GCTGAATTGCAAGAGGGCC 59.485 57.895 4.94 0.00 0.00 5.80
1170 2330 3.439154 TGAATTGCAAGAGGGCCAAATA 58.561 40.909 6.18 0.00 0.00 1.40
1201 2361 6.815641 ACATGTAAGTTCATGCTTCTAGACAG 59.184 38.462 0.00 0.00 46.15 3.51
1291 2452 9.705290 TTAAATAAGAGCCCAATTGAGTTTTTC 57.295 29.630 7.12 0.00 0.00 2.29
1293 2454 5.876651 AAGAGCCCAATTGAGTTTTTCTT 57.123 34.783 7.12 4.70 0.00 2.52
1294 2455 6.976934 AAGAGCCCAATTGAGTTTTTCTTA 57.023 33.333 7.12 0.00 0.00 2.10
1295 2456 7.544804 AAGAGCCCAATTGAGTTTTTCTTAT 57.455 32.000 7.12 0.00 0.00 1.73
1296 2457 7.544804 AGAGCCCAATTGAGTTTTTCTTATT 57.455 32.000 7.12 0.00 0.00 1.40
1297 2458 7.381323 AGAGCCCAATTGAGTTTTTCTTATTG 58.619 34.615 7.12 0.00 32.89 1.90
1298 2459 7.233348 AGAGCCCAATTGAGTTTTTCTTATTGA 59.767 33.333 7.12 0.00 33.91 2.57
1299 2460 7.910584 AGCCCAATTGAGTTTTTCTTATTGAT 58.089 30.769 7.12 0.00 33.91 2.57
1357 2518 9.787532 AACAAAAGTCCATATTCATATCAAACG 57.212 29.630 0.00 0.00 0.00 3.60
1362 2523 8.964476 AGTCCATATTCATATCAAACGTTTCT 57.036 30.769 11.37 4.20 0.00 2.52
1374 2535 2.496899 ACGTTTCTCCCGTACTCCTA 57.503 50.000 0.00 0.00 36.65 2.94
1380 2541 1.493446 TCTCCCGTACTCCTAGCATGA 59.507 52.381 0.00 0.00 0.00 3.07
1383 2545 4.079970 CTCCCGTACTCCTAGCATGAATA 58.920 47.826 0.00 0.00 0.00 1.75
1394 2556 8.680903 ACTCCTAGCATGAATATTTTTGAGTTG 58.319 33.333 0.00 0.00 0.00 3.16
1411 2573 1.351430 TTGCGCTCCATCGTTCGAAG 61.351 55.000 9.73 0.00 0.00 3.79
1433 2595 1.075601 AAGCCACTCCCTTTGATCCA 58.924 50.000 0.00 0.00 0.00 3.41
1434 2596 1.075601 AGCCACTCCCTTTGATCCAA 58.924 50.000 0.00 0.00 0.00 3.53
1470 2632 9.581289 TTCATCTTCCTTTCCTTGTTTTGTATA 57.419 29.630 0.00 0.00 0.00 1.47
1483 2645 8.522830 CCTTGTTTTGTATAATGTCCATCAACT 58.477 33.333 0.00 0.00 0.00 3.16
1511 2673 8.919145 AGAGTTCTGGTCTACAATAGGATTTAG 58.081 37.037 0.00 0.00 0.00 1.85
1572 2734 5.712004 CAACAATGTCAAGGATGTGCATAA 58.288 37.500 0.00 0.00 0.00 1.90
1616 2784 2.368655 AGGCAAACATTTTGGATCGC 57.631 45.000 1.07 0.00 0.00 4.58
1619 2787 3.119495 AGGCAAACATTTTGGATCGCTAC 60.119 43.478 1.07 0.00 0.00 3.58
1632 2800 1.939974 TCGCTACAGGATGACATTGC 58.060 50.000 0.00 0.00 39.69 3.56
1758 2928 2.650322 TGAAGTGTGAAACCTTGGGAC 58.350 47.619 0.00 0.00 34.36 4.46
1760 2930 2.640316 AGTGTGAAACCTTGGGACTC 57.360 50.000 0.00 0.00 34.36 3.36
1778 2948 0.530744 TCGAGGGTGTAGTCACATGC 59.469 55.000 0.00 0.00 45.45 4.06
1787 2957 2.039613 TGTAGTCACATGCATTGGACCA 59.960 45.455 19.01 11.15 0.00 4.02
1791 2961 1.744522 TCACATGCATTGGACCAATCG 59.255 47.619 17.16 13.21 31.05 3.34
1825 2997 6.493116 ACATACCGAGACTACATACGAAAAG 58.507 40.000 0.00 0.00 0.00 2.27
1834 3006 7.971455 AGACTACATACGAAAAGTAAAATGGC 58.029 34.615 0.00 0.00 39.04 4.40
1869 3041 7.872113 TGTCAACCTTTTGCCATTTTAAATT 57.128 28.000 0.00 0.00 32.17 1.82
1893 3065 7.593875 TTTCATTTAAATTTCCATTGCTCCG 57.406 32.000 0.00 0.00 0.00 4.63
1926 3099 5.978322 GGTTAAAATTTCGCAACTTACCACA 59.022 36.000 0.00 0.00 0.00 4.17
1936 3109 6.890558 TCGCAACTTACCACAATTAGTTTAC 58.109 36.000 0.00 0.00 0.00 2.01
1958 3131 3.316308 CACTTGCTACTTGCTTTTGTCCT 59.684 43.478 0.00 0.00 43.37 3.85
1988 3161 6.048732 TCTTTATCTAATGCACTGTGTGGA 57.951 37.500 9.86 0.00 38.41 4.02
2012 3186 7.148069 GGAAGACAACCTATAAAAATGTCCCTG 60.148 40.741 0.00 0.00 40.92 4.45
2028 3202 4.202556 TGTCCCTGTTTCATTCAATCCTCA 60.203 41.667 0.00 0.00 0.00 3.86
2090 3264 3.552684 GCAGATTGCAGCTTACCAAACAA 60.553 43.478 0.00 0.00 44.26 2.83
2107 3281 6.102663 CCAAACAACACCAAATTCTACAACA 58.897 36.000 0.00 0.00 0.00 3.33
2179 3353 3.452990 TCAAGGCGGGACAAATAGTATCA 59.547 43.478 0.00 0.00 0.00 2.15
2251 3425 6.493115 TCAATGTTGTACAAGTTGGATGGAAT 59.507 34.615 23.25 0.00 0.00 3.01
2554 3739 7.926018 GGTTTGACATCTTGTTAACCAAAAGAT 59.074 33.333 11.84 11.84 41.23 2.40
2569 3754 6.576185 ACCAAAAGATGATAATGTTGATGGC 58.424 36.000 5.38 0.00 0.00 4.40
2786 3971 3.717842 TGGAAACAAGACGAAGGGG 57.282 52.632 0.00 0.00 37.44 4.79
2852 4037 0.393537 CAATCACTCCAGGAGGCACC 60.394 60.000 21.31 0.00 33.35 5.01
2913 4098 3.246936 GGTGTGACGTCAACTTTCTTACC 59.753 47.826 21.95 13.73 0.00 2.85
3217 5331 5.833406 TGTCCGATCATGCAAATTATGTT 57.167 34.783 0.00 0.00 0.00 2.71
3325 5440 7.690637 GCTTCATTTCAAAATGTGCAATATGTG 59.309 33.333 20.13 0.00 44.66 3.21
3504 5619 7.865707 ACTATCATCAATAAATGCGAGTTTCC 58.134 34.615 0.00 0.00 0.00 3.13
3521 5636 9.909644 GCGAGTTTCCTCTTTACTATATCATTA 57.090 33.333 0.00 0.00 35.43 1.90
3565 5681 4.582240 TGTCATACACTTGCATTTGAACCA 59.418 37.500 2.21 0.00 0.00 3.67
3625 5748 9.442062 TGTTTATCAAATATACTACTCCCTCCA 57.558 33.333 0.00 0.00 0.00 3.86
3642 5765 8.435982 ACTCCCTCCATTCTCTTTTATAAGATG 58.564 37.037 0.00 0.00 39.58 2.90
3683 5806 4.439016 GGTTTTGAACTGTTTTGGACGCTA 60.439 41.667 0.00 0.00 0.00 4.26
3732 5855 8.354426 ACCTACTAATAAAACAATGTGCGTTTT 58.646 29.630 6.30 6.30 45.78 2.43
3740 5864 3.305110 ACAATGTGCGTTTTTCCGATTC 58.695 40.909 0.00 0.00 0.00 2.52
3746 5871 3.420904 GTGCGTTTTTCCGATTCTTTCAC 59.579 43.478 0.00 0.00 0.00 3.18
3748 5873 3.304458 GCGTTTTTCCGATTCTTTCACCT 60.304 43.478 0.00 0.00 0.00 4.00
3764 5889 1.281656 CCTGTTCACCGCCGAAAAC 59.718 57.895 0.00 0.00 0.00 2.43
3766 5891 0.316689 CTGTTCACCGCCGAAAACAC 60.317 55.000 0.00 0.00 0.00 3.32
3783 5909 9.083080 CCGAAAACACTTTTCTTTTATTTGAGT 57.917 29.630 6.03 0.00 45.23 3.41
3817 5946 1.774639 TTGCGTCCGTCTGTTAGAAC 58.225 50.000 0.00 0.00 0.00 3.01
3851 5980 6.540914 GGTTTGTCCAGAATTTCGTATATGGA 59.459 38.462 1.31 1.31 34.54 3.41
3860 5989 1.395635 TCGTATATGGACCACACGCT 58.604 50.000 16.45 0.00 32.85 5.07
3884 6015 2.357836 CCCAGTGAAGCCAGCCAT 59.642 61.111 0.00 0.00 0.00 4.40
3895 6026 6.889722 AGTGAAGCCAGCCATTTAATTTACTA 59.110 34.615 0.00 0.00 0.00 1.82
3953 6092 1.338200 CGGCATATAGTCAGGCCTTCC 60.338 57.143 0.00 0.00 44.23 3.46
3965 6104 1.074775 GCCTTCCCACATGACACCA 59.925 57.895 0.00 0.00 0.00 4.17
3973 6112 1.072173 CCACATGACACCAAGGACTGA 59.928 52.381 0.00 0.00 0.00 3.41
3989 6128 1.203100 ACTGAGCTGGCCCATTTTCTT 60.203 47.619 0.00 0.00 0.00 2.52
3990 6129 2.041620 ACTGAGCTGGCCCATTTTCTTA 59.958 45.455 0.00 0.00 0.00 2.10
3993 6132 3.448301 TGAGCTGGCCCATTTTCTTATTG 59.552 43.478 0.00 0.00 0.00 1.90
4274 6478 9.933723 AAATCAAGGTTCAGAAAATATTCTTGG 57.066 29.630 8.54 0.00 43.43 3.61
4317 6521 6.626199 ATTGAAAATAATGTTCGCGTTTCC 57.374 33.333 5.77 0.00 0.00 3.13
4456 6671 5.586643 GCTTCGGTTTCAAATTATCTCTCCT 59.413 40.000 0.00 0.00 0.00 3.69
4457 6672 6.457528 GCTTCGGTTTCAAATTATCTCTCCTG 60.458 42.308 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.953868 TCACACAACGGTCCGGCG 62.954 66.667 17.28 8.48 0.00 6.46
1 2 3.343421 GTCACACAACGGTCCGGC 61.343 66.667 17.28 0.00 0.00 6.13
3 4 2.663852 GGGTCACACAACGGTCCG 60.664 66.667 10.48 10.48 0.00 4.79
5 6 2.663852 CCGGGTCACACAACGGTC 60.664 66.667 0.00 0.00 41.34 4.79
6 7 3.155861 TCCGGGTCACACAACGGT 61.156 61.111 0.00 0.00 46.06 4.83
8 9 2.663852 GGTCCGGGTCACACAACG 60.664 66.667 0.00 0.00 0.00 4.10
10 11 2.376165 TTGGGTCCGGGTCACACAA 61.376 57.895 5.39 5.39 34.70 3.33
21 22 2.897326 ACCAAGCTAAATTGTTGGGTCC 59.103 45.455 11.69 0.00 44.37 4.46
27 28 3.495983 GGCCCAAACCAAGCTAAATTGTT 60.496 43.478 0.00 0.00 0.00 2.83
34 35 1.382629 GGAGGCCCAAACCAAGCTA 59.617 57.895 0.00 0.00 0.00 3.32
51 52 0.394352 AGCCCAACATCTAAAGCCGG 60.394 55.000 0.00 0.00 0.00 6.13
90 91 2.639065 GTGCAGATTTTCGGGTCCATA 58.361 47.619 0.00 0.00 0.00 2.74
91 92 1.463674 GTGCAGATTTTCGGGTCCAT 58.536 50.000 0.00 0.00 0.00 3.41
101 102 2.905415 TGATGAAGGGGTGCAGATTT 57.095 45.000 0.00 0.00 0.00 2.17
137 138 2.768253 TCATCTTGGCGACATCTGTT 57.232 45.000 0.00 0.00 42.32 3.16
173 174 9.689075 CGTCAAGTCATTACAAAGTAATACATG 57.311 33.333 2.40 0.00 0.00 3.21
198 200 8.164153 GCATGCAGCCATTTTATTAATTATTCG 58.836 33.333 14.21 0.00 37.23 3.34
227 229 0.035725 CTGGCCTCTGCATCAAGACA 60.036 55.000 3.32 0.00 40.13 3.41
231 233 1.203441 ACTCCTGGCCTCTGCATCAA 61.203 55.000 3.32 0.00 40.13 2.57
233 235 1.145819 GACTCCTGGCCTCTGCATC 59.854 63.158 3.32 0.00 40.13 3.91
281 283 5.187381 TGGAAATGCTATCATTGCTTCCAAA 59.813 36.000 10.94 0.00 41.00 3.28
304 306 6.040247 ACATGAAGCATGATTGTTATTGCTG 58.960 36.000 13.79 0.00 44.26 4.41
340 342 4.141287 AGCAACTAAACTGCATGTACCAA 58.859 39.130 0.00 0.00 42.48 3.67
341 343 3.750371 AGCAACTAAACTGCATGTACCA 58.250 40.909 0.00 0.00 42.48 3.25
352 354 5.103687 GCTAGTACTGAGGAGCAACTAAAC 58.896 45.833 5.39 0.00 34.96 2.01
360 362 3.315749 ACATAACGCTAGTACTGAGGAGC 59.684 47.826 5.39 5.42 0.00 4.70
361 363 5.066117 TGAACATAACGCTAGTACTGAGGAG 59.934 44.000 5.39 0.00 0.00 3.69
367 370 7.064253 GGTCAAATTGAACATAACGCTAGTACT 59.936 37.037 6.09 0.00 33.38 2.73
376 379 6.189677 TCATCGGGTCAAATTGAACATAAC 57.810 37.500 13.49 0.00 35.30 1.89
392 395 6.764560 TGATTCTCATATGCATATTCATCGGG 59.235 38.462 16.71 5.56 0.00 5.14
395 398 8.943002 TGTGTGATTCTCATATGCATATTCATC 58.057 33.333 16.71 14.33 0.00 2.92
477 1337 4.201494 CGTCAGTTAGATTACACTGTTGCG 60.201 45.833 0.00 0.00 41.16 4.85
495 1355 4.081642 TCCCTCTCAACTTAATTCCGTCAG 60.082 45.833 0.00 0.00 0.00 3.51
499 1359 4.572389 CACATCCCTCTCAACTTAATTCCG 59.428 45.833 0.00 0.00 0.00 4.30
555 1415 7.942341 ACTGACACCTTGAAAATAAATGGTAGA 59.058 33.333 0.00 0.00 0.00 2.59
556 1416 8.110860 ACTGACACCTTGAAAATAAATGGTAG 57.889 34.615 0.00 0.00 0.00 3.18
557 1417 8.356657 CAACTGACACCTTGAAAATAAATGGTA 58.643 33.333 0.00 0.00 0.00 3.25
558 1418 6.976934 ACTGACACCTTGAAAATAAATGGT 57.023 33.333 0.00 0.00 0.00 3.55
559 1419 6.646240 CCAACTGACACCTTGAAAATAAATGG 59.354 38.462 0.00 0.00 0.00 3.16
561 1421 7.595819 TCCAACTGACACCTTGAAAATAAAT 57.404 32.000 0.00 0.00 0.00 1.40
562 1422 7.595819 ATCCAACTGACACCTTGAAAATAAA 57.404 32.000 0.00 0.00 0.00 1.40
578 1438 7.424227 AATATTTGCAACAACAATCCAACTG 57.576 32.000 0.00 0.00 0.00 3.16
584 1444 8.466798 ACCTACCTAATATTTGCAACAACAATC 58.533 33.333 0.00 0.00 0.00 2.67
596 1456 5.367644 ACGCCCAGTTACCTACCTAATATTT 59.632 40.000 0.00 0.00 0.00 1.40
612 1472 0.696501 AGTTAAATCCCACGCCCAGT 59.303 50.000 0.00 0.00 0.00 4.00
741 1602 6.403636 CCCAGAAGTGTCATTAATGTTAGTGC 60.404 42.308 14.97 7.23 0.00 4.40
850 1712 6.096705 TGTGCTCCTTATGGTGGAAATTAATG 59.903 38.462 0.00 0.00 32.61 1.90
859 1721 5.737063 GCATTTATTGTGCTCCTTATGGTGG 60.737 44.000 0.00 0.00 39.45 4.61
860 1722 5.284079 GCATTTATTGTGCTCCTTATGGTG 58.716 41.667 0.00 0.00 39.45 4.17
861 1723 4.342092 GGCATTTATTGTGCTCCTTATGGT 59.658 41.667 0.00 0.00 42.16 3.55
905 1767 8.370266 AGAATATATATAGGTGTAAACGGCCA 57.630 34.615 2.24 0.00 0.00 5.36
991 1857 4.419282 ACATGTTTCATCATCTTTGGGGT 58.581 39.130 0.00 0.00 0.00 4.95
1036 1902 9.372369 CATAGATACTTTACCTAAGCATAAGGC 57.628 37.037 0.00 0.00 45.30 4.35
1076 1942 4.878397 GCTTGTGCCTTCTTAGATATGTGT 59.122 41.667 0.00 0.00 0.00 3.72
1078 1944 5.102953 TGCTTGTGCCTTCTTAGATATGT 57.897 39.130 0.00 0.00 38.71 2.29
1083 1949 5.804639 TCTAATTGCTTGTGCCTTCTTAGA 58.195 37.500 0.00 0.00 38.71 2.10
1153 2313 2.446435 GACTATTTGGCCCTCTTGCAA 58.554 47.619 0.00 0.00 0.00 4.08
1160 2320 2.026262 ACATGTTCGACTATTTGGCCCT 60.026 45.455 0.00 0.00 0.00 5.19
1165 2325 7.426456 GCATGAACTTACATGTTCGACTATTTG 59.574 37.037 2.30 0.00 46.59 2.32
1170 2330 4.569943 AGCATGAACTTACATGTTCGACT 58.430 39.130 2.30 0.00 46.59 4.18
1337 2498 8.964476 AGAAACGTTTGATATGAATATGGACT 57.036 30.769 20.10 0.00 0.00 3.85
1339 2500 7.444183 GGGAGAAACGTTTGATATGAATATGGA 59.556 37.037 20.10 0.00 0.00 3.41
1357 2518 2.097825 TGCTAGGAGTACGGGAGAAAC 58.902 52.381 0.00 0.00 0.00 2.78
1362 2523 2.447408 TTCATGCTAGGAGTACGGGA 57.553 50.000 0.00 0.00 0.00 5.14
1374 2535 4.563976 GCGCAACTCAAAAATATTCATGCT 59.436 37.500 0.30 0.00 0.00 3.79
1394 2556 1.743855 GACTTCGAACGATGGAGCGC 61.744 60.000 0.00 0.00 33.86 5.92
1411 2573 2.087646 GATCAAAGGGAGTGGCTTGAC 58.912 52.381 0.00 0.00 31.00 3.18
1470 2632 6.176183 CCAGAACTCTTAGTTGATGGACATT 58.824 40.000 12.27 0.00 41.06 2.71
1483 2645 8.840200 AATCCTATTGTAGACCAGAACTCTTA 57.160 34.615 0.00 0.00 0.00 2.10
1511 2673 1.000506 TCACGCCAGAGTCCACTAAAC 59.999 52.381 0.00 0.00 0.00 2.01
1583 2750 9.620259 AAAATGTTTGCCTAAAATCCTAAAACA 57.380 25.926 0.00 0.00 39.52 2.83
1596 2763 3.088532 AGCGATCCAAAATGTTTGCCTA 58.911 40.909 0.00 0.00 0.00 3.93
1616 2784 7.228108 ACATTATTCTGCAATGTCATCCTGTAG 59.772 37.037 0.00 0.00 41.61 2.74
1619 2787 6.387041 ACATTATTCTGCAATGTCATCCTG 57.613 37.500 0.00 0.00 41.61 3.86
1758 2928 1.469940 GCATGTGACTACACCCTCGAG 60.470 57.143 5.13 5.13 45.40 4.04
1760 2930 0.246360 TGCATGTGACTACACCCTCG 59.754 55.000 0.00 0.00 45.40 4.63
1834 3006 5.234972 GCAAAAGGTTGACAAGGAAATGAAG 59.765 40.000 0.00 0.00 36.83 3.02
1869 3041 7.158021 ACGGAGCAATGGAAATTTAAATGAAA 58.842 30.769 0.39 0.00 0.00 2.69
1988 3161 7.238710 ACAGGGACATTTTTATAGGTTGTCTT 58.761 34.615 0.00 0.00 37.45 3.01
2090 3264 6.872920 ACAATGTTGTTGTAGAATTTGGTGT 58.127 32.000 0.00 0.00 38.47 4.16
2107 3281 1.173043 CCATGGCACCGTACAATGTT 58.827 50.000 0.00 0.00 0.00 2.71
2131 3305 7.044181 CAGCCAGAGACTCATAAACATCTAAA 58.956 38.462 5.02 0.00 0.00 1.85
2179 3353 5.707066 AATTCTCTACCCAGATTTCAGCT 57.293 39.130 0.00 0.00 0.00 4.24
2227 3401 5.703978 TCCATCCAACTTGTACAACATTG 57.296 39.130 16.15 16.15 0.00 2.82
2297 3471 7.994911 TCAGATTTATCAAGCAATATGGACACT 59.005 33.333 0.00 0.00 0.00 3.55
2298 3472 8.158169 TCAGATTTATCAAGCAATATGGACAC 57.842 34.615 0.00 0.00 0.00 3.67
2460 3644 8.924303 ACATAGGAGTGTGCACTTAATATTCTA 58.076 33.333 19.41 9.06 42.66 2.10
2554 3739 1.675483 GCCACGCCATCAACATTATCA 59.325 47.619 0.00 0.00 0.00 2.15
2569 3754 3.628989 TGAGTATCAGGGGCCACG 58.371 61.111 4.39 0.00 42.56 4.94
2583 3768 5.852738 ATGACTGAGTTGTTTCGATTGAG 57.147 39.130 0.00 0.00 0.00 3.02
2786 3971 5.404968 TCCATCGCATTTCAAATCAAAACAC 59.595 36.000 0.00 0.00 0.00 3.32
2852 4037 7.142995 AGATATCTTAGTTTTCCCCTCAAGG 57.857 40.000 0.00 0.00 0.00 3.61
2898 4083 4.389077 GGAGACATGGTAAGAAAGTTGACG 59.611 45.833 0.00 0.00 0.00 4.35
2942 4129 7.054491 ACACATAGGCCAATAAATCCAATTC 57.946 36.000 5.01 0.00 0.00 2.17
3108 5222 3.694566 GTGTAACCACCAATCTCCATTCC 59.305 47.826 0.00 0.00 35.44 3.01
3217 5331 0.324552 TAGTGTAGCCGCCCCAAGTA 60.325 55.000 0.00 0.00 0.00 2.24
3265 5379 2.519063 CAGCGCCCATTGCCCATA 60.519 61.111 2.29 0.00 36.24 2.74
3325 5440 0.887933 AACCATGCCCGTCATTGTTC 59.112 50.000 0.00 0.00 36.62 3.18
3334 5449 2.051334 TTGGAAGATAACCATGCCCG 57.949 50.000 0.00 0.00 37.26 6.13
3534 5649 9.838975 CAAATGCAAGTGTATGACATTACTTAA 57.161 29.630 13.99 8.68 32.53 1.85
3538 5653 7.273381 GGTTCAAATGCAAGTGTATGACATTAC 59.727 37.037 0.00 0.00 31.47 1.89
3553 5669 4.603989 ATGTCATGTTGGTTCAAATGCA 57.396 36.364 0.00 0.00 0.00 3.96
3559 5675 4.886489 TGACTGAAATGTCATGTTGGTTCA 59.114 37.500 0.00 0.00 41.43 3.18
3642 5765 6.816140 TCAAAACCAAGTTTCCAAAATGTCTC 59.184 34.615 0.00 0.00 34.43 3.36
3655 5778 5.699001 GTCCAAAACAGTTCAAAACCAAGTT 59.301 36.000 0.00 0.00 0.00 2.66
3657 5780 4.326009 CGTCCAAAACAGTTCAAAACCAAG 59.674 41.667 0.00 0.00 0.00 3.61
3719 5842 3.004315 AGAATCGGAAAAACGCACATTGT 59.996 39.130 0.00 0.00 0.00 2.71
3723 5846 3.065510 TGAAAGAATCGGAAAAACGCACA 59.934 39.130 0.00 0.00 0.00 4.57
3732 5855 3.813166 GTGAACAGGTGAAAGAATCGGAA 59.187 43.478 0.00 0.00 0.00 4.30
3740 5864 1.841663 CGGCGGTGAACAGGTGAAAG 61.842 60.000 0.00 0.00 0.00 2.62
3746 5871 1.281656 GTTTTCGGCGGTGAACAGG 59.718 57.895 7.21 0.00 0.00 4.00
3748 5873 0.745128 AGTGTTTTCGGCGGTGAACA 60.745 50.000 7.21 12.81 0.00 3.18
3851 5980 4.008933 GGCCAGAGAGCGTGTGGT 62.009 66.667 0.00 0.00 41.96 4.16
3860 5989 2.596851 GGCTTCACTGGGCCAGAGA 61.597 63.158 38.99 32.74 46.84 3.10
3953 6092 1.072173 TCAGTCCTTGGTGTCATGTGG 59.928 52.381 0.00 0.00 0.00 4.17
3965 6104 1.504275 AATGGGCCAGCTCAGTCCTT 61.504 55.000 13.78 0.00 0.00 3.36
3973 6112 3.444029 ACAATAAGAAAATGGGCCAGCT 58.556 40.909 13.78 3.62 0.00 4.24
4317 6521 9.419737 CGGAACAATTTTAGAAAATGTGTTTTG 57.580 29.630 18.51 10.07 38.35 2.44
4357 6563 7.372451 TGTGATGGTTTCTAAAATAGGAACG 57.628 36.000 3.18 0.00 43.76 3.95


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

AutoCloner maintained by Alex Coulton.