Multiple sequence alignment - TraesCS7A01G309100

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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 TraesCS7A01G309100 chr7A 100.000 5512 0 0 1 5512 437061182 437066693 0.000000e+00 10179.0
1 TraesCS7A01G309100 chr7A 83.089 615 84 14 3 599 409256348 409255736 4.860000e-150 542.0
2 TraesCS7A01G309100 chr7D 95.125 3241 88 22 1959 5154 387212595 387215810 0.000000e+00 5046.0
3 TraesCS7A01G309100 chr7D 94.607 1335 45 16 640 1954 387211222 387212549 0.000000e+00 2041.0
4 TraesCS7A01G309100 chr7D 88.636 616 55 8 1 602 386922812 386923426 0.000000e+00 736.0
5 TraesCS7A01G309100 chr7D 79.843 511 83 16 101 601 12900254 12899754 6.790000e-94 355.0
6 TraesCS7A01G309100 chr7D 86.307 241 22 7 5149 5380 387218784 387219022 9.170000e-63 252.0
7 TraesCS7A01G309100 chr7D 96.875 32 0 1 617 647 386923862 386923893 1.000000e-02 52.8
8 TraesCS7A01G309100 chr7B 95.196 2685 76 14 2372 5023 382272718 382275382 0.000000e+00 4194.0
9 TraesCS7A01G309100 chr7B 95.870 799 26 3 612 1410 382271023 382271814 0.000000e+00 1286.0
10 TraesCS7A01G309100 chr7B 95.582 498 16 1 1463 1954 382271817 382272314 0.000000e+00 793.0
11 TraesCS7A01G309100 chr7B 93.207 368 21 2 1959 2326 382272357 382272720 6.280000e-149 538.0
12 TraesCS7A01G309100 chr7B 82.820 617 81 21 1 602 382269951 382270557 3.780000e-146 529.0
13 TraesCS7A01G309100 chr7B 83.977 518 51 17 5020 5512 382275686 382276196 8.360000e-128 468.0
14 TraesCS7A01G309100 chr7B 79.868 606 104 9 3 602 584187098 584187691 1.420000e-115 427.0
15 TraesCS7A01G309100 chr5D 80.782 614 96 18 3 602 464621767 464621162 1.400000e-125 460.0
16 TraesCS7A01G309100 chr5D 76.417 441 87 13 174 602 384344944 384345379 7.190000e-54 222.0
17 TraesCS7A01G309100 chr1D 79.968 624 104 14 1 607 446474860 446475479 1.820000e-119 440.0
18 TraesCS7A01G309100 chr5A 79.479 614 104 14 3 602 585071960 585071355 3.070000e-112 416.0
19 TraesCS7A01G309100 chr2D 79.206 529 84 14 3 512 53654647 53654126 1.470000e-90 344.0
20 TraesCS7A01G309100 chr3A 80.841 428 72 7 5 425 458924253 458924677 1.480000e-85 327.0
21 TraesCS7A01G309100 chr4D 88.211 246 25 2 2350 2592 367800771 367800527 1.940000e-74 291.0
22 TraesCS7A01G309100 chr3B 73.754 301 62 12 305 602 825430712 825430998 9.770000e-18 102.0
23 TraesCS7A01G309100 chr2B 84.286 70 10 1 533 602 181612445 181612513 3.560000e-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 TraesCS7A01G309100 chr7A 437061182 437066693 5511 False 10179.000000 10179 100.000000 1 5512 1 chr7A.!!$F1 5511
1 TraesCS7A01G309100 chr7A 409255736 409256348 612 True 542.000000 542 83.089000 3 599 1 chr7A.!!$R1 596
2 TraesCS7A01G309100 chr7D 387211222 387219022 7800 False 2446.333333 5046 92.013000 640 5380 3 chr7D.!!$F2 4740
3 TraesCS7A01G309100 chr7D 386922812 386923893 1081 False 394.400000 736 92.755500 1 647 2 chr7D.!!$F1 646
4 TraesCS7A01G309100 chr7D 12899754 12900254 500 True 355.000000 355 79.843000 101 601 1 chr7D.!!$R1 500
5 TraesCS7A01G309100 chr7B 382269951 382276196 6245 False 1301.333333 4194 91.108667 1 5512 6 chr7B.!!$F2 5511
6 TraesCS7A01G309100 chr7B 584187098 584187691 593 False 427.000000 427 79.868000 3 602 1 chr7B.!!$F1 599
7 TraesCS7A01G309100 chr5D 464621162 464621767 605 True 460.000000 460 80.782000 3 602 1 chr5D.!!$R1 599
8 TraesCS7A01G309100 chr1D 446474860 446475479 619 False 440.000000 440 79.968000 1 607 1 chr1D.!!$F1 606
9 TraesCS7A01G309100 chr5A 585071355 585071960 605 True 416.000000 416 79.479000 3 602 1 chr5A.!!$R1 599
10 TraesCS7A01G309100 chr2D 53654126 53654647 521 True 344.000000 344 79.206000 3 512 1 chr2D.!!$R1 509

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
287 306 0.742990 CGAGGCCGAACCAAGCATTA 60.743 55.000 0.00 0.0 43.14 1.90 F
758 1251 1.433534 CCAAGTTCTGACTTCGCCTC 58.566 55.000 0.00 0.0 44.14 4.70 F
1421 1924 1.336887 CGAGACGGATGTGTTTCCAGT 60.337 52.381 0.00 0.0 35.34 4.00 F
1931 2443 1.144708 TCATGGAGGTCTTTTGCACCA 59.855 47.619 0.00 0.0 36.23 4.17 F
2448 3004 2.370519 TCCAGTGGCACTAACTTTGCTA 59.629 45.455 21.59 0.0 40.07 3.49 F
2817 3377 2.627515 TAATGCCTGTCTCTCCATGC 57.372 50.000 0.00 0.0 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1924 0.321210 TTCGAATCCAGCGCCAGAAA 60.321 50.000 2.29 0.0 0.0 2.52 R
1747 2259 1.300080 CAACCCAAGCAAGCAACGG 60.300 57.895 0.00 0.0 0.0 4.44 R
2807 3367 1.194218 TCGGTTCATGCATGGAGAGA 58.806 50.000 25.97 16.3 0.0 3.10 R
3672 4261 2.118679 CCCATCTGATACACCACTCCA 58.881 52.381 0.00 0.0 0.0 3.86 R
4022 4611 1.669115 CAGTGCACTTGTCCGGGAG 60.669 63.158 18.94 0.0 0.0 4.30 R
4600 5194 1.695242 ACCAACCGTCAGTATGTTCCA 59.305 47.619 0.00 0.0 37.4 3.53 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
89 99 2.224209 CCCAAACACTTGTCCGTCTAGT 60.224 50.000 0.00 0.00 32.81 2.57
139 154 1.227853 GGGTGACAACGCAGGAACT 60.228 57.895 0.00 0.00 43.88 3.01
233 251 4.062293 CACAATGACTCCAACGAGGTAAA 58.938 43.478 0.00 0.00 40.77 2.01
284 303 4.697756 CCGAGGCCGAACCAAGCA 62.698 66.667 0.00 0.00 43.14 3.91
287 306 0.742990 CGAGGCCGAACCAAGCATTA 60.743 55.000 0.00 0.00 43.14 1.90
418 440 3.365265 GCAACCCGGAACTGCCAG 61.365 66.667 0.73 0.00 35.94 4.85
429 451 4.943252 CTGCCAGCCCGCCCATAG 62.943 72.222 0.00 0.00 0.00 2.23
431 453 4.937431 GCCAGCCCGCCCATAGAC 62.937 72.222 0.00 0.00 0.00 2.59
432 454 4.256180 CCAGCCCGCCCATAGACC 62.256 72.222 0.00 0.00 0.00 3.85
437 469 2.727392 CCCGCCCATAGACCGTGAA 61.727 63.158 0.00 0.00 0.00 3.18
514 546 1.596934 GGATCTCCACCGCAACTGA 59.403 57.895 0.00 0.00 35.64 3.41
614 1107 2.265904 GCGAGGGAAGGCCGTTTTT 61.266 57.895 0.00 0.00 33.83 1.94
708 1201 2.683362 CTCCGCCTAAAATTTGACCTCC 59.317 50.000 0.00 0.00 0.00 4.30
758 1251 1.433534 CCAAGTTCTGACTTCGCCTC 58.566 55.000 0.00 0.00 44.14 4.70
766 1260 2.668550 ACTTCGCCTCGCCAAACC 60.669 61.111 0.00 0.00 0.00 3.27
967 1464 3.664223 GACCGACGGCGAGACAGAC 62.664 68.421 15.16 0.00 40.82 3.51
1389 1892 2.739996 CCGATTGCTGCTCTCCCCT 61.740 63.158 0.00 0.00 0.00 4.79
1394 1897 4.087892 GCTGCTCTCCCCTTGCGA 62.088 66.667 0.00 0.00 0.00 5.10
1395 1898 2.906458 CTGCTCTCCCCTTGCGAT 59.094 61.111 0.00 0.00 0.00 4.58
1421 1924 1.336887 CGAGACGGATGTGTTTCCAGT 60.337 52.381 0.00 0.00 35.34 4.00
1537 2048 2.147958 GAGGGTGTGATTGTAAACGCA 58.852 47.619 0.00 0.00 0.00 5.24
1686 2197 8.632679 TGAATAGCCAGATTATGTCCAAAATTC 58.367 33.333 0.00 0.00 0.00 2.17
1719 2231 3.440522 GGGTACATTTTTCTGCCTCTGAC 59.559 47.826 0.00 0.00 0.00 3.51
1747 2259 4.953940 AGCTTGAGATCTGGGAATAGTC 57.046 45.455 0.00 0.00 0.00 2.59
1794 2306 3.611025 ACTTGGACCCCTTTTTCATGA 57.389 42.857 0.00 0.00 0.00 3.07
1833 2345 7.655328 CAGGTTCTCTTGTCATAACTCATATCC 59.345 40.741 0.00 0.00 0.00 2.59
1931 2443 1.144708 TCATGGAGGTCTTTTGCACCA 59.855 47.619 0.00 0.00 36.23 4.17
1954 2466 6.208599 CCAAGTTCCATTAGCTTTAAGTGGAA 59.791 38.462 7.64 7.64 44.30 3.53
1957 2469 5.514500 TCCATTAGCTTTAAGTGGAACCT 57.486 39.130 0.00 0.00 37.80 3.50
2017 2570 6.889722 CCTATCTTTTTGGACCAACTGGATAA 59.110 38.462 6.36 0.00 38.94 1.75
2147 2702 3.131709 ACACTCCAAGAGATTGTGGTG 57.868 47.619 0.00 0.00 37.03 4.17
2235 2790 4.214310 TGCTTCAGAAGATTGAAAACCCA 58.786 39.130 14.86 0.00 36.69 4.51
2300 2855 7.762615 AGTGCTTTCATAATTTCATTCATGTGG 59.237 33.333 0.00 0.00 0.00 4.17
2448 3004 2.370519 TCCAGTGGCACTAACTTTGCTA 59.629 45.455 21.59 0.00 40.07 3.49
2481 3037 5.604758 TCTCATCTGTAGTATGCTTTGCT 57.395 39.130 0.00 0.00 0.00 3.91
2530 3086 6.232692 AGCATCAAATTTTTACATGGTTGCT 58.767 32.000 0.00 0.00 32.02 3.91
2807 3367 6.604171 TGATTAAGACATCCATAATGCCTGT 58.396 36.000 0.00 0.00 39.12 4.00
2817 3377 2.627515 TAATGCCTGTCTCTCCATGC 57.372 50.000 0.00 0.00 0.00 4.06
2842 3402 8.075574 GCATGAACCGATATGAATAATTTGTGA 58.924 33.333 0.00 0.00 0.00 3.58
2916 3478 7.806680 AACACCACCCCTTCATTTTAAATAT 57.193 32.000 0.00 0.00 0.00 1.28
3092 3681 3.657015 AGTCTAGCATGATGGTCATCG 57.343 47.619 0.00 0.00 40.63 3.84
3184 3773 7.876936 AAGTCAATACTCGATACCACTCTTA 57.123 36.000 0.00 0.00 33.75 2.10
3458 4047 4.872691 GCAATAAGTATGTGCACTCTCTGT 59.127 41.667 19.41 1.67 38.19 3.41
3672 4261 4.220602 GGTGAAATTACAATCAGCTGGGTT 59.779 41.667 15.13 6.66 40.11 4.11
3838 4427 5.067023 CAGCTCCCCAGATTAATTCTTGAAC 59.933 44.000 0.00 0.00 29.93 3.18
3960 4549 3.320610 TTTCATGGAACTTCCCACCAA 57.679 42.857 5.30 0.00 39.34 3.67
4022 4611 6.566197 AATCTGTCAGTTTTCCTTGTCATC 57.434 37.500 0.00 0.00 0.00 2.92
4231 4820 3.399440 TGGGCACATTTTTGGCTAAAG 57.601 42.857 0.00 0.00 41.74 1.85
4475 5069 0.036010 CAGGAAGCCCTCGACATGTT 60.036 55.000 0.00 0.00 42.02 2.71
4636 5230 4.236935 GGTTGGTGCATTTACTGTTGATG 58.763 43.478 0.00 0.00 0.00 3.07
4687 5281 2.987596 TTGGCCAGCTCTCCATGGG 61.988 63.158 13.02 2.57 37.05 4.00
4784 5378 4.974368 TTTGTATTATTGTTGCCCGGAG 57.026 40.909 0.73 0.00 0.00 4.63
4840 5434 6.751514 TGTGTAGATGTGTTTGTTGTCTTT 57.248 33.333 0.00 0.00 0.00 2.52
4841 5435 7.851387 TGTGTAGATGTGTTTGTTGTCTTTA 57.149 32.000 0.00 0.00 0.00 1.85
4842 5436 8.270080 TGTGTAGATGTGTTTGTTGTCTTTAA 57.730 30.769 0.00 0.00 0.00 1.52
4843 5437 8.394877 TGTGTAGATGTGTTTGTTGTCTTTAAG 58.605 33.333 0.00 0.00 0.00 1.85
4844 5438 7.855904 GTGTAGATGTGTTTGTTGTCTTTAAGG 59.144 37.037 0.00 0.00 0.00 2.69
4845 5439 7.554835 TGTAGATGTGTTTGTTGTCTTTAAGGT 59.445 33.333 0.00 0.00 0.00 3.50
4846 5440 6.795399 AGATGTGTTTGTTGTCTTTAAGGTG 58.205 36.000 0.00 0.00 0.00 4.00
4847 5441 4.739195 TGTGTTTGTTGTCTTTAAGGTGC 58.261 39.130 0.00 0.00 0.00 5.01
4848 5442 4.461081 TGTGTTTGTTGTCTTTAAGGTGCT 59.539 37.500 0.00 0.00 0.00 4.40
4849 5443 4.798387 GTGTTTGTTGTCTTTAAGGTGCTG 59.202 41.667 0.00 0.00 0.00 4.41
4850 5444 4.461081 TGTTTGTTGTCTTTAAGGTGCTGT 59.539 37.500 0.00 0.00 0.00 4.40
4886 5480 1.180029 CTCCCAAAGATGCAACCTGG 58.820 55.000 5.88 5.88 0.00 4.45
4960 5568 5.063944 CCTGTCTGTATGCACATTGTACTTC 59.936 44.000 0.00 0.00 33.14 3.01
4961 5569 5.546526 TGTCTGTATGCACATTGTACTTCA 58.453 37.500 0.00 0.00 33.14 3.02
4962 5570 5.994668 TGTCTGTATGCACATTGTACTTCAA 59.005 36.000 0.00 0.00 40.53 2.69
4963 5571 6.484977 TGTCTGTATGCACATTGTACTTCAAA 59.515 34.615 0.00 0.00 39.62 2.69
4964 5572 6.797033 GTCTGTATGCACATTGTACTTCAAAC 59.203 38.462 0.00 0.00 39.62 2.93
4965 5573 6.484977 TCTGTATGCACATTGTACTTCAAACA 59.515 34.615 0.00 0.00 39.62 2.83
4966 5574 7.174772 TCTGTATGCACATTGTACTTCAAACAT 59.825 33.333 0.00 0.00 39.62 2.71
4967 5575 8.329203 TGTATGCACATTGTACTTCAAACATA 57.671 30.769 0.00 0.00 39.62 2.29
4968 5576 8.787852 TGTATGCACATTGTACTTCAAACATAA 58.212 29.630 0.00 0.00 39.62 1.90
4969 5577 9.619316 GTATGCACATTGTACTTCAAACATAAA 57.381 29.630 0.00 0.00 39.62 1.40
4971 5579 8.572828 TGCACATTGTACTTCAAACATAAAAG 57.427 30.769 0.00 0.00 39.62 2.27
4972 5580 8.409371 TGCACATTGTACTTCAAACATAAAAGA 58.591 29.630 0.00 0.00 39.62 2.52
4973 5581 9.243637 GCACATTGTACTTCAAACATAAAAGAA 57.756 29.630 0.00 0.00 39.62 2.52
5043 5959 0.309302 TTGCACGTTTTCCATGTCCG 59.691 50.000 0.00 0.00 0.00 4.79
5051 5967 4.162812 CGTTTTCCATGTCCGTTTATTGG 58.837 43.478 0.00 0.00 0.00 3.16
5055 5971 2.026729 TCCATGTCCGTTTATTGGCTCA 60.027 45.455 0.00 0.00 0.00 4.26
5133 6056 7.746475 CGAATGAAGTTGTTAAGATCCTGTTTC 59.254 37.037 0.00 0.00 0.00 2.78
5154 9056 4.566004 TCGAAGGCGGATATATTTCTTGG 58.434 43.478 0.00 0.00 38.28 3.61
5155 9057 3.125316 CGAAGGCGGATATATTTCTTGGC 59.875 47.826 0.00 5.08 0.00 4.52
5158 9060 2.673368 GGCGGATATATTTCTTGGCTCG 59.327 50.000 0.00 0.00 0.00 5.03
5159 9061 2.094417 GCGGATATATTTCTTGGCTCGC 59.906 50.000 0.00 0.00 0.00 5.03
5172 9074 0.097150 GGCTCGCGAGGAAATTGAAC 59.903 55.000 35.10 16.12 0.00 3.18
5179 9081 2.095212 GCGAGGAAATTGAACTGTTCCC 60.095 50.000 17.26 10.70 41.55 3.97
5186 9088 6.265422 AGGAAATTGAACTGTTCCCTGTAAAG 59.735 38.462 17.26 0.00 41.55 1.85
5220 9122 2.365635 GCCTCCAGACAGGGCCTA 60.366 66.667 5.28 0.00 39.96 3.93
5228 9132 1.224592 GACAGGGCCTATGTGGTGG 59.775 63.158 17.31 0.00 38.35 4.61
5231 9135 2.275418 GGGCCTATGTGGTGGTGG 59.725 66.667 0.84 0.00 38.35 4.61
5253 9158 1.265905 GTTACTTGTGCGGGAAGTTGG 59.734 52.381 0.00 0.00 35.30 3.77
5258 9163 1.966451 GTGCGGGAAGTTGGTGGAG 60.966 63.158 0.00 0.00 0.00 3.86
5270 9175 0.618458 TGGTGGAGATGTACTTGCCC 59.382 55.000 0.00 0.00 0.00 5.36
5271 9176 0.462047 GGTGGAGATGTACTTGCCCG 60.462 60.000 0.00 0.00 0.00 6.13
5273 9178 1.523938 GGAGATGTACTTGCCCGCC 60.524 63.158 0.00 0.00 0.00 6.13
5274 9179 1.220749 GAGATGTACTTGCCCGCCA 59.779 57.895 0.00 0.00 0.00 5.69
5276 9181 1.819632 GATGTACTTGCCCGCCAGG 60.820 63.158 0.00 0.00 39.47 4.45
5325 9230 3.565764 TGGCCATATGTTTCTCCTCAG 57.434 47.619 0.00 0.00 0.00 3.35
5327 9232 2.421952 GGCCATATGTTTCTCCTCAGCA 60.422 50.000 0.00 0.00 0.00 4.41
5328 9233 2.877168 GCCATATGTTTCTCCTCAGCAG 59.123 50.000 1.24 0.00 0.00 4.24
5329 9234 3.474600 CCATATGTTTCTCCTCAGCAGG 58.525 50.000 1.24 0.00 42.01 4.85
5350 9260 0.314935 ATTGTTTGCGTTGCCTCTGG 59.685 50.000 0.00 0.00 0.00 3.86
5380 9290 5.686397 GCTGCTCAAGATAATTCAAGCAATC 59.314 40.000 0.00 0.00 39.08 2.67
5381 9291 6.459848 GCTGCTCAAGATAATTCAAGCAATCT 60.460 38.462 0.00 0.00 39.08 2.40
5382 9292 6.792326 TGCTCAAGATAATTCAAGCAATCTG 58.208 36.000 0.00 0.00 36.86 2.90
5383 9293 6.600427 TGCTCAAGATAATTCAAGCAATCTGA 59.400 34.615 0.00 0.00 36.86 3.27
5384 9294 7.284716 TGCTCAAGATAATTCAAGCAATCTGAT 59.715 33.333 0.00 0.00 36.86 2.90
5387 9297 9.797556 TCAAGATAATTCAAGCAATCTGATTTG 57.202 29.630 0.00 0.00 0.00 2.32
5388 9298 9.582431 CAAGATAATTCAAGCAATCTGATTTGT 57.418 29.630 0.00 0.00 0.00 2.83
5389 9299 9.798994 AAGATAATTCAAGCAATCTGATTTGTC 57.201 29.630 0.00 0.00 0.00 3.18
5390 9300 9.186837 AGATAATTCAAGCAATCTGATTTGTCT 57.813 29.630 0.00 0.00 0.00 3.41
5391 9301 9.448294 GATAATTCAAGCAATCTGATTTGTCTC 57.552 33.333 0.00 0.00 0.00 3.36
5394 9305 6.492007 TCAAGCAATCTGATTTGTCTCTTC 57.508 37.500 0.00 0.00 0.00 2.87
5432 9343 5.478407 TCGTGCTTTATTGATCAAGAGACA 58.522 37.500 14.54 6.04 0.00 3.41
5433 9344 5.578336 TCGTGCTTTATTGATCAAGAGACAG 59.422 40.000 14.54 7.76 0.00 3.51
5434 9345 5.349817 CGTGCTTTATTGATCAAGAGACAGT 59.650 40.000 14.54 0.00 0.00 3.55
5435 9346 6.541086 GTGCTTTATTGATCAAGAGACAGTG 58.459 40.000 14.54 0.00 0.00 3.66
5436 9347 5.122869 TGCTTTATTGATCAAGAGACAGTGC 59.877 40.000 14.54 5.14 0.00 4.40
5437 9348 5.726138 GCTTTATTGATCAAGAGACAGTGCG 60.726 44.000 14.54 0.00 0.00 5.34
5477 9401 7.916552 ACGAATTTATACATGACTAAACCAGC 58.083 34.615 0.00 0.00 0.00 4.85
5478 9402 7.063456 CGAATTTATACATGACTAAACCAGCG 58.937 38.462 0.00 2.47 0.00 5.18
5479 9403 7.042992 CGAATTTATACATGACTAAACCAGCGA 60.043 37.037 0.00 0.00 0.00 4.93
5483 9407 2.478894 ACATGACTAAACCAGCGAAACG 59.521 45.455 0.00 0.00 0.00 3.60
5498 9422 2.802057 CGAAACGGACTCTCTGGTTTGT 60.802 50.000 0.00 0.00 31.73 2.83
5500 9424 3.277142 AACGGACTCTCTGGTTTGTTT 57.723 42.857 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 154 4.385358 TTTCGGATCAGATGATGACGAA 57.615 40.909 19.59 19.59 42.92 3.85
218 236 1.622312 GGGTCTTTACCTCGTTGGAGT 59.378 52.381 4.38 0.00 45.95 3.85
284 303 2.949644 GGGTACGAATTTGCCAGCTAAT 59.050 45.455 0.00 0.00 0.00 1.73
287 306 0.037590 TGGGTACGAATTTGCCAGCT 59.962 50.000 0.00 0.00 0.00 4.24
331 350 0.749649 GTGCTCGATGATGGAGGAGT 59.250 55.000 6.59 0.00 32.26 3.85
418 440 4.910585 CACGGTCTATGGGCGGGC 62.911 72.222 0.00 0.00 0.00 6.13
425 447 0.469917 ATGGCCCTTCACGGTCTATG 59.530 55.000 0.00 0.00 0.00 2.23
427 449 0.616395 TGATGGCCCTTCACGGTCTA 60.616 55.000 0.00 0.00 0.00 2.59
429 451 1.450312 CTGATGGCCCTTCACGGTC 60.450 63.158 0.00 0.00 0.00 4.79
430 452 2.671070 CTGATGGCCCTTCACGGT 59.329 61.111 0.00 0.00 0.00 4.83
431 453 2.825836 GCTGATGGCCCTTCACGG 60.826 66.667 0.00 0.00 34.27 4.94
432 454 2.930385 ATCGCTGATGGCCCTTCACG 62.930 60.000 0.00 10.24 37.74 4.35
434 456 1.153107 CATCGCTGATGGCCCTTCA 60.153 57.895 0.00 2.29 36.51 3.02
437 469 3.800833 TGCATCGCTGATGGCCCT 61.801 61.111 16.56 0.00 40.10 5.19
470 502 1.735571 GGTGTCTTTGACGTGTGTGTT 59.264 47.619 0.00 0.00 34.95 3.32
473 505 0.808453 CGGGTGTCTTTGACGTGTGT 60.808 55.000 0.00 0.00 34.95 3.72
602 635 1.611491 TGGACATCAAAAACGGCCTTC 59.389 47.619 0.00 0.00 0.00 3.46
603 636 1.698506 TGGACATCAAAAACGGCCTT 58.301 45.000 0.00 0.00 0.00 4.35
607 640 6.393990 TGGATTATTTGGACATCAAAAACGG 58.606 36.000 0.00 0.00 46.93 4.44
608 641 7.881643 TTGGATTATTTGGACATCAAAAACG 57.118 32.000 0.00 0.00 46.93 3.60
647 1140 4.165779 CACACAGGATCGGCAATTTTTAC 58.834 43.478 0.00 0.00 0.00 2.01
651 1144 1.812571 GACACACAGGATCGGCAATTT 59.187 47.619 0.00 0.00 0.00 1.82
652 1145 1.453155 GACACACAGGATCGGCAATT 58.547 50.000 0.00 0.00 0.00 2.32
758 1251 3.757745 ACGATATCAAAAGGTTTGGCG 57.242 42.857 3.12 0.00 0.00 5.69
766 1260 8.926710 AGTCAGTGTCTTTAACGATATCAAAAG 58.073 33.333 3.12 9.17 0.00 2.27
967 1464 1.403687 GGGGGAATGGAGACGGAGAG 61.404 65.000 0.00 0.00 0.00 3.20
1355 1858 3.753294 ATCGGATCAGCCTACGAATTT 57.247 42.857 0.00 0.00 38.94 1.82
1389 1892 1.136774 CGTCTCGTCTCCATCGCAA 59.863 57.895 0.00 0.00 0.00 4.85
1394 1897 0.741326 CACATCCGTCTCGTCTCCAT 59.259 55.000 0.00 0.00 0.00 3.41
1395 1898 0.608308 ACACATCCGTCTCGTCTCCA 60.608 55.000 0.00 0.00 0.00 3.86
1421 1924 0.321210 TTCGAATCCAGCGCCAGAAA 60.321 50.000 2.29 0.00 0.00 2.52
1537 2048 0.678048 GCTCAAAATCGCCTCCCTGT 60.678 55.000 0.00 0.00 0.00 4.00
1747 2259 1.300080 CAACCCAAGCAAGCAACGG 60.300 57.895 0.00 0.00 0.00 4.44
1833 2345 5.805728 AGTCCAGTTACTTGTTATGGAAGG 58.194 41.667 0.00 0.00 41.52 3.46
1898 2410 1.683385 CTCCATGAGCCTCACGTATCA 59.317 52.381 0.00 0.00 0.00 2.15
2147 2702 7.019774 TGTCAGCATCACTATTTCTATTTGC 57.980 36.000 0.00 0.00 0.00 3.68
2235 2790 7.057894 TCCCAAATAGAAGTGTGTTACAAAGT 58.942 34.615 0.00 0.00 0.00 2.66
2304 2859 8.233190 CACAGAAAAAGAATCCATCAGTACTTC 58.767 37.037 0.00 0.00 0.00 3.01
2365 2921 6.127479 TGCAAATCAGGACAAACAAAGTACTT 60.127 34.615 1.12 1.12 0.00 2.24
2367 2923 5.587289 TGCAAATCAGGACAAACAAAGTAC 58.413 37.500 0.00 0.00 0.00 2.73
2369 2925 4.685924 CTGCAAATCAGGACAAACAAAGT 58.314 39.130 0.00 0.00 39.15 2.66
2448 3004 6.975196 ACTACAGATGAGAAGAGCATATGT 57.025 37.500 4.29 8.59 46.35 2.29
2481 3037 6.303839 AGGTACCTTGAAAATCTTTGTAGCA 58.696 36.000 9.21 0.00 0.00 3.49
2807 3367 1.194218 TCGGTTCATGCATGGAGAGA 58.806 50.000 25.97 16.30 0.00 3.10
2817 3377 9.949174 TTCACAAATTATTCATATCGGTTCATG 57.051 29.630 0.00 0.00 0.00 3.07
2916 3478 4.792068 AGTCTGATGAAAACCAACCTCAA 58.208 39.130 0.00 0.00 0.00 3.02
3070 3659 3.986572 CGATGACCATCATGCTAGACTTC 59.013 47.826 10.24 0.00 37.20 3.01
3184 3773 5.690464 AGACCAGCATATTTCTTCTCACT 57.310 39.130 0.00 0.00 0.00 3.41
3291 3880 9.685828 GGTGAGCTAGTTAGAGAAATAATACAG 57.314 37.037 0.00 0.00 0.00 2.74
3458 4047 7.739498 ACGCTTTACCTTCTCAATCTAAAAA 57.261 32.000 0.00 0.00 0.00 1.94
3672 4261 2.118679 CCCATCTGATACACCACTCCA 58.881 52.381 0.00 0.00 0.00 3.86
3838 4427 9.968743 GATTAAATTACGAGAACAAACAGTAGG 57.031 33.333 0.00 0.00 0.00 3.18
3960 4549 7.329226 GCACATGCAGTTTAAGAACAATGTAAT 59.671 33.333 0.00 0.00 41.59 1.89
4022 4611 1.669115 CAGTGCACTTGTCCGGGAG 60.669 63.158 18.94 0.00 0.00 4.30
4231 4820 7.420800 CAGAAAATATCAGGTGCAGGTAATTC 58.579 38.462 0.00 0.00 0.00 2.17
4475 5069 8.593679 TCTTTTGTAGAGTTCAATGGTATCTCA 58.406 33.333 0.00 0.00 0.00 3.27
4600 5194 1.695242 ACCAACCGTCAGTATGTTCCA 59.305 47.619 0.00 0.00 37.40 3.53
4636 5230 2.983229 TCAAGAGCTCAATTCTCCTGC 58.017 47.619 17.77 0.00 0.00 4.85
4687 5281 8.616076 CCTGTTGATTTGTAGGAAGAATGTATC 58.384 37.037 0.00 0.00 0.00 2.24
4784 5378 3.772853 TATGATGTGCCCGCCCTGC 62.773 63.158 0.00 0.00 0.00 4.85
4840 5434 5.396772 CCTGATGGATTTCTACAGCACCTTA 60.397 44.000 0.00 0.00 34.57 2.69
4841 5435 4.521146 CTGATGGATTTCTACAGCACCTT 58.479 43.478 0.00 0.00 0.00 3.50
4842 5436 3.118112 CCTGATGGATTTCTACAGCACCT 60.118 47.826 0.00 0.00 34.57 4.00
4843 5437 3.209410 CCTGATGGATTTCTACAGCACC 58.791 50.000 0.00 0.00 34.57 5.01
4844 5438 3.624861 CACCTGATGGATTTCTACAGCAC 59.375 47.826 0.00 0.00 37.04 4.40
4845 5439 3.877559 CACCTGATGGATTTCTACAGCA 58.122 45.455 0.00 0.00 37.04 4.41
4846 5440 2.615912 GCACCTGATGGATTTCTACAGC 59.384 50.000 0.00 0.00 37.04 4.40
4847 5441 4.125703 GAGCACCTGATGGATTTCTACAG 58.874 47.826 0.00 0.00 37.04 2.74
4848 5442 3.118261 GGAGCACCTGATGGATTTCTACA 60.118 47.826 0.00 0.00 37.04 2.74
4849 5443 3.471680 GGAGCACCTGATGGATTTCTAC 58.528 50.000 0.00 0.00 37.04 2.59
4850 5444 2.439507 GGGAGCACCTGATGGATTTCTA 59.560 50.000 0.00 0.00 37.04 2.10
4886 5480 7.880059 AAGTAACGAAGTATACCAACAGAAC 57.120 36.000 0.00 0.00 45.00 3.01
5133 6056 3.125316 GCCAAGAAATATATCCGCCTTCG 59.875 47.826 0.00 0.00 0.00 3.79
5154 9056 1.079503 AGTTCAATTTCCTCGCGAGC 58.920 50.000 30.49 13.20 0.00 5.03
5155 9057 2.069273 ACAGTTCAATTTCCTCGCGAG 58.931 47.619 29.06 29.06 0.00 5.03
5158 9060 2.095212 GGGAACAGTTCAATTTCCTCGC 60.095 50.000 15.36 0.00 39.11 5.03
5159 9061 3.189287 CAGGGAACAGTTCAATTTCCTCG 59.811 47.826 15.36 3.91 39.11 4.63
5179 9081 6.638468 GCAAGAATTTCACCTGAACTTTACAG 59.362 38.462 0.00 0.00 33.13 2.74
5186 9088 3.057245 GGAGGCAAGAATTTCACCTGAAC 60.057 47.826 9.57 0.00 33.13 3.18
5190 9092 2.376518 TCTGGAGGCAAGAATTTCACCT 59.623 45.455 5.60 5.60 0.00 4.00
5220 9122 2.092103 ACAAGTAACACCACCACCACAT 60.092 45.455 0.00 0.00 0.00 3.21
5228 9132 0.533308 TCCCGCACAAGTAACACCAC 60.533 55.000 0.00 0.00 0.00 4.16
5231 9135 1.589803 ACTTCCCGCACAAGTAACAC 58.410 50.000 0.00 0.00 32.08 3.32
5253 9158 1.090052 GCGGGCAAGTACATCTCCAC 61.090 60.000 0.00 0.00 0.00 4.02
5258 9163 1.819632 CCTGGCGGGCAAGTACATC 60.820 63.158 5.54 0.00 0.00 3.06
5270 9175 2.042259 ACATCATGTGTGCCTGGCG 61.042 57.895 14.98 0.00 40.28 5.69
5271 9176 4.007457 ACATCATGTGTGCCTGGC 57.993 55.556 12.87 12.87 40.28 4.85
5289 9194 3.401182 TGGCCAAAATTTCTGCATGAAC 58.599 40.909 0.61 0.00 33.88 3.18
5325 9230 0.508213 GCAACGCAAACAATTCCTGC 59.492 50.000 0.00 0.00 0.00 4.85
5327 9232 1.000274 GAGGCAACGCAAACAATTCCT 60.000 47.619 0.00 0.00 46.39 3.36
5328 9233 1.000274 AGAGGCAACGCAAACAATTCC 60.000 47.619 0.00 0.00 46.39 3.01
5329 9234 2.053627 CAGAGGCAACGCAAACAATTC 58.946 47.619 0.00 0.00 46.39 2.17
5334 9244 1.008538 CACCAGAGGCAACGCAAAC 60.009 57.895 0.00 0.00 46.39 2.93
5350 9260 4.154737 TGAATTATCTTGAGCAGCACACAC 59.845 41.667 0.00 0.00 0.00 3.82
5400 9311 8.661352 TGATCAATAAAGCACGATATTTCTCA 57.339 30.769 0.00 0.00 0.00 3.27
5412 9323 5.122869 GCACTGTCTCTTGATCAATAAAGCA 59.877 40.000 8.96 8.46 0.00 3.91
5415 9326 4.631377 CCGCACTGTCTCTTGATCAATAAA 59.369 41.667 8.96 0.00 0.00 1.40
5432 9343 2.809601 GTCGAATGTCGCCGCACT 60.810 61.111 0.00 0.00 40.21 4.40
5433 9344 2.165362 TTTGTCGAATGTCGCCGCAC 62.165 55.000 0.00 0.00 40.21 5.34
5434 9345 1.956678 TTTGTCGAATGTCGCCGCA 60.957 52.632 0.00 0.00 40.21 5.69
5435 9346 1.509162 GTTTGTCGAATGTCGCCGC 60.509 57.895 0.00 0.00 40.21 6.53
5436 9347 1.225368 CGTTTGTCGAATGTCGCCG 60.225 57.895 0.00 0.00 40.21 6.46
5437 9348 2.146954 TCGTTTGTCGAATGTCGCC 58.853 52.632 0.00 0.00 45.98 5.54
5451 9362 8.395633 GCTGGTTTAGTCATGTATAAATTCGTT 58.604 33.333 7.89 0.00 0.00 3.85
5454 9365 8.138365 TCGCTGGTTTAGTCATGTATAAATTC 57.862 34.615 7.89 5.65 0.00 2.17
5459 9370 5.517411 CGTTTCGCTGGTTTAGTCATGTATA 59.483 40.000 0.00 0.00 0.00 1.47
5460 9371 4.328983 CGTTTCGCTGGTTTAGTCATGTAT 59.671 41.667 0.00 0.00 0.00 2.29
5473 9397 0.734253 CAGAGAGTCCGTTTCGCTGG 60.734 60.000 4.61 0.00 38.37 4.85
5475 9399 1.179814 ACCAGAGAGTCCGTTTCGCT 61.180 55.000 0.00 0.00 0.00 4.93
5476 9400 0.319641 AACCAGAGAGTCCGTTTCGC 60.320 55.000 0.00 0.00 0.00 4.70
5477 9401 1.792949 CAAACCAGAGAGTCCGTTTCG 59.207 52.381 0.00 0.00 0.00 3.46
5478 9402 2.835027 ACAAACCAGAGAGTCCGTTTC 58.165 47.619 0.00 0.00 0.00 2.78
5479 9403 3.277142 AACAAACCAGAGAGTCCGTTT 57.723 42.857 0.00 0.00 0.00 3.60
5483 9407 3.809905 ACTCAAACAAACCAGAGAGTCC 58.190 45.455 0.00 0.00 31.19 3.85


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

AutoCloner maintained by Alex Coulton.