Multiple sequence alignment - TraesCS7B01G281900

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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 TraesCS7B01G281900 chr7B 100.000 5542 0 0 1 5542 516446737 516441196 0.000000e+00 10235
1 TraesCS7B01G281900 chr7B 84.565 1542 216 14 3283 4808 514255146 514256681 0.000000e+00 1509
2 TraesCS7B01G281900 chr7B 85.274 1039 141 10 1393 2424 514249848 514250881 0.000000e+00 1061
3 TraesCS7B01G281900 chr7B 87.871 371 32 5 3 372 514247964 514248322 1.850000e-114 424
4 TraesCS7B01G281900 chr7B 75.730 890 173 27 1061 1937 513771577 513770718 1.860000e-109 407
5 TraesCS7B01G281900 chr7B 84.314 204 29 2 2418 2620 514253501 514253702 4.380000e-46 196
6 TraesCS7B01G281900 chr7D 92.544 4694 297 32 3 4668 486732188 486727520 0.000000e+00 6680
7 TraesCS7B01G281900 chr7D 87.047 2262 256 18 369 2615 486306302 486308541 0.000000e+00 2519
8 TraesCS7B01G281900 chr7D 85.594 1541 204 10 3283 4808 486308911 486310448 0.000000e+00 1600
9 TraesCS7B01G281900 chr7D 92.276 738 33 10 4807 5542 486676151 486675436 0.000000e+00 1026
10 TraesCS7B01G281900 chr7D 87.588 427 52 1 3283 3708 119753476 119753902 1.390000e-135 494
11 TraesCS7B01G281900 chr7D 87.354 427 53 1 3283 3708 581698496 581698922 6.450000e-134 488
12 TraesCS7B01G281900 chr7D 89.488 371 26 3 3 372 486305891 486306249 1.820000e-124 457
13 TraesCS7B01G281900 chr7D 75.661 908 162 32 1061 1939 486107947 486107070 1.120000e-106 398
14 TraesCS7B01G281900 chr7A 92.227 2470 175 9 2350 4808 555624080 555621617 0.000000e+00 3482
15 TraesCS7B01G281900 chr7A 91.767 1919 148 9 369 2286 555625991 555624082 0.000000e+00 2660
16 TraesCS7B01G281900 chr7A 87.003 2262 255 21 369 2619 555437202 555439435 0.000000e+00 2512
17 TraesCS7B01G281900 chr7A 85.425 1434 191 11 3390 4808 555439929 555441359 0.000000e+00 1474
18 TraesCS7B01G281900 chr7A 91.796 646 46 7 4901 5542 555539497 555538855 0.000000e+00 893
19 TraesCS7B01G281900 chr7A 94.293 368 17 1 5 372 555626406 555626043 1.350000e-155 560
20 TraesCS7B01G281900 chr7A 79.245 742 131 16 4807 5533 555442061 555442794 3.860000e-136 496
21 TraesCS7B01G281900 chr7A 89.488 371 33 4 5 372 555436782 555437149 1.090000e-126 464
22 TraesCS7B01G281900 chr7A 76.185 886 178 22 1061 1937 554491547 554490686 2.370000e-118 436
23 TraesCS7B01G281900 chr7A 73.552 518 105 23 3733 4229 555467469 555466963 9.550000e-38 169
24 TraesCS7B01G281900 chr7A 72.805 467 104 17 3727 4175 555474766 555474305 2.690000e-28 137
25 TraesCS7B01G281900 chr5D 87.119 427 54 1 3283 3708 173558908 173559334 3.000000e-132 483
26 TraesCS7B01G281900 chr4D 87.119 427 54 1 3283 3708 150602362 150602788 3.000000e-132 483
27 TraesCS7B01G281900 chr4D 95.745 47 1 1 767 813 426689524 426689569 2.140000e-09 75
28 TraesCS7B01G281900 chr5A 81.628 430 64 6 2192 2620 566147264 566147679 5.320000e-90 342
29 TraesCS7B01G281900 chr6D 84.024 169 23 4 1078 1243 380565585 380565752 5.750000e-35 159
30 TraesCS7B01G281900 chr6D 92.453 53 3 1 1095 1146 349760455 349760507 2.140000e-09 75
31 TraesCS7B01G281900 chr6A 75.637 353 64 13 1078 1426 522044504 522044838 7.430000e-34 156
32 TraesCS7B01G281900 chr6B 83.432 169 24 4 1078 1243 567844228 567844395 2.670000e-33 154


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 TraesCS7B01G281900 chr7B 516441196 516446737 5541 True 10235.000000 10235 100.000000 1 5542 1 chr7B.!!$R2 5541
1 TraesCS7B01G281900 chr7B 514247964 514256681 8717 False 797.500000 1509 85.506000 3 4808 4 chr7B.!!$F1 4805
2 TraesCS7B01G281900 chr7B 513770718 513771577 859 True 407.000000 407 75.730000 1061 1937 1 chr7B.!!$R1 876
3 TraesCS7B01G281900 chr7D 486727520 486732188 4668 True 6680.000000 6680 92.544000 3 4668 1 chr7D.!!$R3 4665
4 TraesCS7B01G281900 chr7D 486305891 486310448 4557 False 1525.333333 2519 87.376333 3 4808 3 chr7D.!!$F3 4805
5 TraesCS7B01G281900 chr7D 486675436 486676151 715 True 1026.000000 1026 92.276000 4807 5542 1 chr7D.!!$R2 735
6 TraesCS7B01G281900 chr7D 486107070 486107947 877 True 398.000000 398 75.661000 1061 1939 1 chr7D.!!$R1 878
7 TraesCS7B01G281900 chr7A 555621617 555626406 4789 True 2234.000000 3482 92.762333 5 4808 3 chr7A.!!$R5 4803
8 TraesCS7B01G281900 chr7A 555436782 555442794 6012 False 1236.500000 2512 85.290250 5 5533 4 chr7A.!!$F1 5528
9 TraesCS7B01G281900 chr7A 555538855 555539497 642 True 893.000000 893 91.796000 4901 5542 1 chr7A.!!$R4 641
10 TraesCS7B01G281900 chr7A 554490686 554491547 861 True 436.000000 436 76.185000 1061 1937 1 chr7A.!!$R1 876

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
365 377 0.462375 ACACTGGTCACGTGTGCTAA 59.538 50.0 16.51 0.0 43.44 3.09 F
491 559 0.610174 TGGCGCATCTCTTTGAGAGT 59.390 50.0 10.83 0.0 42.26 3.24 F
1625 2184 0.690762 ACCAGTACATCCACCGCTTT 59.309 50.0 0.00 0.0 0.00 3.51 F
2491 5707 0.603707 CCTTGCAGCTCCTGAAACGA 60.604 55.0 0.00 0.0 32.44 3.85 F
2949 7591 0.889186 AACAGCCTACAAAGCCCACG 60.889 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1442 0.550914 ACTCTGGGAGCTCGAGATCT 59.449 55.0 28.08 11.42 32.04 2.75 R
1979 2562 0.925558 TTATGAATGGAGCCAGGGCA 59.074 50.0 13.63 0.00 44.88 5.36 R
3225 7869 1.177401 GGGCCTTGAACCTGATCAAC 58.823 55.0 0.84 0.00 35.55 3.18 R
4206 8902 0.684535 TCATTCACCTCGTCTGCCAA 59.315 50.0 0.00 0.00 0.00 4.52 R
4889 10308 0.788391 CTCGTAGTGGGTGTTTTCGC 59.212 55.0 0.00 0.00 0.00 4.70 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
142 143 3.535561 CAGCTGGTCGTTTCTATTGGAT 58.464 45.455 5.57 0.00 0.00 3.41
143 144 3.941483 CAGCTGGTCGTTTCTATTGGATT 59.059 43.478 5.57 0.00 0.00 3.01
203 215 5.549742 AATGGATTCTCTCTGGATGTCTC 57.450 43.478 0.00 0.00 0.00 3.36
205 217 4.214310 TGGATTCTCTCTGGATGTCTCTC 58.786 47.826 0.00 0.00 0.00 3.20
259 271 4.348168 TCCTTGGCTTATATCCAGTTCCTC 59.652 45.833 0.00 0.00 34.66 3.71
268 280 1.352083 TCCAGTTCCTCCAACCTCAG 58.648 55.000 0.00 0.00 35.28 3.35
300 312 3.717576 TGTGAGATCAATCAGAGGTCCT 58.282 45.455 0.00 0.00 0.00 3.85
301 313 4.871822 TGTGAGATCAATCAGAGGTCCTA 58.128 43.478 0.00 0.00 0.00 2.94
313 325 6.187727 TCAGAGGTCCTATGTTTGTCTTTT 57.812 37.500 13.21 0.00 0.00 2.27
331 343 9.444600 TTGTCTTTTATGTACCCTTTCATAGTC 57.555 33.333 0.00 0.00 0.00 2.59
365 377 0.462375 ACACTGGTCACGTGTGCTAA 59.538 50.000 16.51 0.00 43.44 3.09
395 463 7.064866 AGATTTGCCTCATCTTTATCAATGGA 58.935 34.615 0.00 0.00 0.00 3.41
397 465 4.139786 TGCCTCATCTTTATCAATGGAGC 58.860 43.478 0.00 0.00 0.00 4.70
437 505 1.961793 TAGTGTGTTGCCAAGTGGAC 58.038 50.000 0.18 0.00 37.39 4.02
440 508 0.751277 TGTGTTGCCAAGTGGACAGG 60.751 55.000 0.18 0.00 37.39 4.00
485 553 1.674441 CATCACATGGCGCATCTCTTT 59.326 47.619 10.83 0.00 0.00 2.52
491 559 0.610174 TGGCGCATCTCTTTGAGAGT 59.390 50.000 10.83 0.00 42.26 3.24
520 588 0.836606 TATCTTCATCAAGGGCGGCA 59.163 50.000 12.47 0.00 0.00 5.69
705 773 6.192970 AGGGTATATGGAAAGAGAACATGG 57.807 41.667 0.00 0.00 0.00 3.66
782 853 9.912634 TTTGCTTCTTCTTCTACAAAAATATGG 57.087 29.630 0.00 0.00 0.00 2.74
841 914 4.527038 TGTTAGGGTTTTCTCGATGACTCT 59.473 41.667 0.00 0.00 0.00 3.24
919 994 5.663456 ACGACTTTGGTTAGTTAGTCAACA 58.337 37.500 0.00 0.00 37.46 3.33
921 996 5.521010 CGACTTTGGTTAGTTAGTCAACACA 59.479 40.000 0.00 0.00 37.46 3.72
948 1023 3.320541 AGAGATAGTGCCAGTGTGCTATC 59.679 47.826 13.52 13.52 39.77 2.08
1029 1104 4.850680 TCACACTTGTTTTCCCAACTAGT 58.149 39.130 0.00 0.00 36.85 2.57
1039 1114 6.043938 TGTTTTCCCAACTAGTAGATCCACTT 59.956 38.462 3.59 0.00 0.00 3.16
1041 1116 7.801893 TTTCCCAACTAGTAGATCCACTTTA 57.198 36.000 3.59 0.00 0.00 1.85
1280 1358 3.842923 CTCTCCGAGGCCACGCAT 61.843 66.667 17.90 0.00 0.00 4.73
1408 1961 4.020617 CCTCCTCGCCACCAAGCA 62.021 66.667 0.00 0.00 0.00 3.91
1445 2001 2.151502 TCCAGAACAAGCAAACCCAA 57.848 45.000 0.00 0.00 0.00 4.12
1625 2184 0.690762 ACCAGTACATCCACCGCTTT 59.309 50.000 0.00 0.00 0.00 3.51
1630 2189 1.135199 GTACATCCACCGCTTTCTCGA 60.135 52.381 0.00 0.00 0.00 4.04
1658 2217 2.196595 CCCATTCTGGAGTACCTTGGA 58.803 52.381 0.00 0.00 40.96 3.53
1710 2269 1.303155 GTCTGCAGCCAAAGCCTCT 60.303 57.895 9.47 0.00 41.25 3.69
1938 2516 1.352687 GGTTGCCTTTCCTTCTCTCCT 59.647 52.381 0.00 0.00 0.00 3.69
2022 2609 3.085443 AGAAACGATATGGCTCGAGTG 57.915 47.619 15.13 0.00 41.12 3.51
2311 2899 6.935240 TCCTTCTCCTCTTGATGTTTAAGA 57.065 37.500 0.00 0.00 33.44 2.10
2370 2958 1.750399 CCACCGCTTCCTTCCATGG 60.750 63.158 4.97 4.97 0.00 3.66
2476 5692 5.825151 GGAAATCCATTAAGTCTCCTCCTTG 59.175 44.000 0.00 0.00 35.64 3.61
2491 5707 0.603707 CCTTGCAGCTCCTGAAACGA 60.604 55.000 0.00 0.00 32.44 3.85
2500 5716 2.095212 GCTCCTGAAACGATTTTGTCCC 60.095 50.000 0.00 0.00 0.00 4.46
2547 5763 0.984230 TAGCACCTGTTTCAGAGGGG 59.016 55.000 0.00 0.00 37.03 4.79
2601 5818 3.916349 TCTAAGGTTCCATATCCCCCATG 59.084 47.826 0.00 0.00 0.00 3.66
2704 7344 5.717119 TCTCTAAAAGGTGTAAGCCTAACG 58.283 41.667 0.00 0.00 38.03 3.18
2744 7384 6.747414 ACCATTACACCATTAGCTCATCTA 57.253 37.500 0.00 0.00 0.00 1.98
2796 7436 1.283029 ACCACCATCCCACAGATCAAG 59.717 52.381 0.00 0.00 30.59 3.02
2846 7486 9.396022 CTAAAGAATACATGTCCCAGTATGTTT 57.604 33.333 0.00 0.00 38.41 2.83
2901 7543 9.771534 CTTCCCAAAATTTAATTTGACTACCAA 57.228 29.630 3.51 0.00 41.73 3.67
2949 7591 0.889186 AACAGCCTACAAAGCCCACG 60.889 55.000 0.00 0.00 0.00 4.94
2977 7619 4.505039 GCTTTTCCAGAACTGAGAAGGGTA 60.505 45.833 3.19 0.00 0.00 3.69
2978 7620 5.621193 CTTTTCCAGAACTGAGAAGGGTAA 58.379 41.667 3.19 0.00 0.00 2.85
2993 7635 2.766828 AGGGTAACTGTCCTGATAGCAC 59.233 50.000 0.00 0.00 31.11 4.40
2995 7637 3.134804 GGGTAACTGTCCTGATAGCACAT 59.865 47.826 0.00 0.00 0.00 3.21
2998 7640 4.767578 AACTGTCCTGATAGCACATGAT 57.232 40.909 0.00 0.00 0.00 2.45
3019 7661 6.306199 TGATGTTGGGATTCCTGGTATTATG 58.694 40.000 2.01 0.00 0.00 1.90
3030 7674 8.627208 ATTCCTGGTATTATGCTTATTGTCAG 57.373 34.615 0.00 0.00 0.00 3.51
3041 7685 9.618890 TTATGCTTATTGTCAGCTATCTTCTTT 57.381 29.630 0.00 0.00 38.19 2.52
3055 7699 8.332487 AGCTATCTTCTTTCATAAGGAACCTTT 58.668 33.333 11.44 0.00 37.47 3.11
3113 7757 9.807649 ATTAAACAAATGTTCATATCTTGGAGC 57.192 29.630 0.00 0.00 37.25 4.70
3144 7788 3.277664 CCTATCCCCCATATCCCCTCTTA 59.722 52.174 0.00 0.00 0.00 2.10
3148 7792 5.601370 TCCCCCATATCCCCTCTTAATAT 57.399 43.478 0.00 0.00 0.00 1.28
3188 7832 3.734902 GCTAGATGAATTTTGTTGGCCCG 60.735 47.826 0.00 0.00 0.00 6.13
3225 7869 3.005050 ACAGACAATTTGCCATGTGTGAG 59.995 43.478 9.61 0.00 41.79 3.51
3300 7944 1.337118 GATGCTAGCTAGGCAGGACT 58.663 55.000 22.10 5.92 43.15 3.85
3301 7945 1.000731 GATGCTAGCTAGGCAGGACTG 59.999 57.143 22.10 0.00 43.15 3.51
3339 7985 8.956533 TTTTCCCAAATAAGAAAGAAGTTTGG 57.043 30.769 7.93 7.93 45.17 3.28
3357 8003 2.477245 TGGCTCTCCAACCAGCTATTA 58.523 47.619 0.00 0.00 39.99 0.98
3385 8031 9.430623 GGCTAAAAATTTACCAATCAAAGCTAA 57.569 29.630 0.00 0.00 0.00 3.09
3398 8044 7.984050 CCAATCAAAGCTAACAGATCTTCTCTA 59.016 37.037 0.00 0.00 31.13 2.43
3499 8195 7.989741 CACAAAGGGAGTGAGATCATTAACTAT 59.010 37.037 0.00 0.00 39.30 2.12
3500 8196 8.207545 ACAAAGGGAGTGAGATCATTAACTATC 58.792 37.037 0.00 0.00 0.00 2.08
3501 8197 6.582677 AGGGAGTGAGATCATTAACTATCG 57.417 41.667 0.00 0.00 0.00 2.92
3502 8198 6.307776 AGGGAGTGAGATCATTAACTATCGA 58.692 40.000 0.00 0.00 0.00 3.59
3503 8199 6.432783 AGGGAGTGAGATCATTAACTATCGAG 59.567 42.308 0.00 0.00 0.00 4.04
3504 8200 6.207810 GGGAGTGAGATCATTAACTATCGAGT 59.792 42.308 0.00 0.00 37.59 4.18
3506 8202 8.784994 GGAGTGAGATCATTAACTATCGAGTTA 58.215 37.037 0.00 0.00 44.36 2.24
3553 8249 1.754226 GCTAATTGGCATCCCCGAAAA 59.246 47.619 9.17 0.00 35.87 2.29
3559 8255 1.274728 TGGCATCCCCGAAAATTGTTG 59.725 47.619 0.00 0.00 35.87 3.33
3603 8299 3.194062 GGATTCAGAGCAACTCTAGCAC 58.806 50.000 0.00 0.00 38.99 4.40
3691 8387 4.689612 ACTGTTCTGTGACCAGTTACAT 57.310 40.909 0.00 0.00 39.82 2.29
3693 8389 5.539048 ACTGTTCTGTGACCAGTTACATAC 58.461 41.667 0.00 0.00 39.82 2.39
3725 8421 6.629515 GCATGTTCTAATGGTCCACTGTACTA 60.630 42.308 0.00 0.00 0.00 1.82
3974 8670 4.256110 CTCATTGGTATGAACTGCAGTCA 58.744 43.478 21.95 19.20 40.17 3.41
4027 8723 1.746615 CCACCGAAGAGCACCATGG 60.747 63.158 11.19 11.19 0.00 3.66
4180 8876 2.247790 GAGCATTGCTGGTCGTGTT 58.752 52.632 17.51 0.00 39.88 3.32
4279 8975 0.467384 CCATGGACTGCTAGAGGGTG 59.533 60.000 5.56 0.00 0.00 4.61
4326 9022 8.186821 GCAATGTTTTGATCTCTGCTAAAGTAT 58.813 33.333 0.00 0.00 34.60 2.12
4333 9029 7.423844 TGATCTCTGCTAAAGTATCCTTTCA 57.576 36.000 0.00 0.00 41.18 2.69
4352 9048 2.154462 CACAGTGTCCATGACCCTTTC 58.846 52.381 0.00 0.00 0.00 2.62
4426 9124 5.591472 TGGGAATCATTGAATGCTCTACTTG 59.409 40.000 0.00 0.00 0.00 3.16
4474 9172 6.377080 AGGTGTGTGATCTCCTAAGATATGA 58.623 40.000 0.00 0.00 42.46 2.15
4495 9193 5.630121 TGACAGGTTTCAACTTACCATGAT 58.370 37.500 0.00 0.00 36.87 2.45
4554 9257 8.883731 CGATTTTCAACTATACAGAACATCCTT 58.116 33.333 0.00 0.00 29.20 3.36
4566 9270 6.735556 ACAGAACATCCTTGAAAATAGGGAT 58.264 36.000 0.00 0.00 38.92 3.85
4620 9324 1.066587 AATCTCTAGCACGAGCCGC 59.933 57.895 0.00 0.00 43.56 6.53
4676 9380 6.371548 TCACATAGCCAAACTATCTTGTGAAC 59.628 38.462 0.00 0.00 41.83 3.18
4706 9410 0.523968 CCACAATGAAAGATGGCGCG 60.524 55.000 0.00 0.00 0.00 6.86
4713 9417 0.102481 GAAAGATGGCGCGGAGACTA 59.898 55.000 8.83 0.00 0.00 2.59
4717 9421 2.088674 GATGGCGCGGAGACTATGGT 62.089 60.000 8.83 0.00 0.00 3.55
4720 9424 0.318784 GGCGCGGAGACTATGGTTAG 60.319 60.000 8.83 0.00 0.00 2.34
4740 9456 0.820871 GACGGAGAAGGAGCACAGAT 59.179 55.000 0.00 0.00 0.00 2.90
4798 9514 4.195416 CAAGGAGAGAATAAAGAGGCCAC 58.805 47.826 5.01 0.00 0.00 5.01
4803 9519 1.134788 AGAATAAAGAGGCCACGGTCG 60.135 52.381 5.01 0.00 0.00 4.79
4812 10231 1.301165 GCCACGGTCGTGTTTAGGT 60.301 57.895 19.94 0.00 44.02 3.08
4889 10308 6.893958 AACTAGAACATCTACAGCAAATCG 57.106 37.500 0.00 0.00 0.00 3.34
4911 10332 2.800629 CGAAAACACCCACTACGAGTGT 60.801 50.000 12.10 0.00 44.50 3.55
5023 10446 1.070601 CACATGAGCCCCACATATCGA 59.929 52.381 0.00 0.00 0.00 3.59
5032 10455 3.096852 CCCCACATATCGATGGCTACTA 58.903 50.000 8.54 0.00 37.39 1.82
5177 10603 1.638467 GCGTCTCGGTGATCAATGC 59.362 57.895 0.00 0.00 0.00 3.56
5186 10612 2.803133 CGGTGATCAATGCCATAGACGT 60.803 50.000 0.00 0.00 0.00 4.34
5188 10614 3.457234 GTGATCAATGCCATAGACGTGA 58.543 45.455 0.00 0.00 0.00 4.35
5233 10659 3.373830 CACCAACATGGATGGGGTTATT 58.626 45.455 20.14 0.03 40.96 1.40
5252 10679 7.069455 GGGTTATTAGAAAATATGCAACCCTGT 59.931 37.037 11.12 0.00 42.25 4.00
5423 10875 8.641498 CTAATTATAGCTCATCCCCAAAACAT 57.359 34.615 0.00 0.00 0.00 2.71
5424 10876 7.530426 AATTATAGCTCATCCCCAAAACATC 57.470 36.000 0.00 0.00 0.00 3.06
5425 10877 2.905415 AGCTCATCCCCAAAACATCA 57.095 45.000 0.00 0.00 0.00 3.07
5427 10879 3.716431 AGCTCATCCCCAAAACATCAAT 58.284 40.909 0.00 0.00 0.00 2.57
5429 10881 4.161001 AGCTCATCCCCAAAACATCAATTC 59.839 41.667 0.00 0.00 0.00 2.17
5431 10883 3.774216 TCATCCCCAAAACATCAATTCCC 59.226 43.478 0.00 0.00 0.00 3.97
5432 10884 2.175202 TCCCCAAAACATCAATTCCCG 58.825 47.619 0.00 0.00 0.00 5.14
5476 10928 1.052124 TATCCCAGCCACCTAACCCG 61.052 60.000 0.00 0.00 0.00 5.28
5522 10974 4.007659 CTCAGTAAATTTGGGTTAGCGGT 58.992 43.478 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.515028 ATTGCATGAGATGGAAAGGAGA 57.485 40.909 0.00 0.00 43.81 3.71
1 2 5.618236 TCTATTGCATGAGATGGAAAGGAG 58.382 41.667 0.00 0.00 43.81 3.69
142 143 6.212388 TCTCCAAAAATAGGCCAAGCATTTAA 59.788 34.615 5.01 0.00 0.00 1.52
143 144 5.719085 TCTCCAAAAATAGGCCAAGCATTTA 59.281 36.000 5.01 0.00 0.00 1.40
203 215 7.297391 TGTGTTTATGTTTCAACATCATCGAG 58.703 34.615 8.46 0.00 46.10 4.04
205 217 7.148983 GGTTGTGTTTATGTTTCAACATCATCG 60.149 37.037 8.46 0.00 46.10 3.84
259 271 3.264450 ACAATAGGAGAACCTGAGGTTGG 59.736 47.826 23.60 0.00 46.95 3.77
268 280 6.586344 TGATTGATCTCACAATAGGAGAACC 58.414 40.000 0.00 0.00 44.01 3.62
300 312 9.575868 TGAAAGGGTACATAAAAGACAAACATA 57.424 29.630 0.00 0.00 0.00 2.29
301 313 8.472007 TGAAAGGGTACATAAAAGACAAACAT 57.528 30.769 0.00 0.00 0.00 2.71
313 325 6.293790 CGTCATCGACTATGAAAGGGTACATA 60.294 42.308 0.00 0.00 46.17 2.29
331 343 1.322637 CAGTGTGCATCTTCGTCATCG 59.677 52.381 0.00 0.00 38.55 3.84
365 377 3.902881 AAGATGAGGCAAATCTCTCGT 57.097 42.857 2.84 0.00 33.17 4.18
425 493 0.754957 CAACCCTGTCCACTTGGCAA 60.755 55.000 0.00 0.00 34.44 4.52
440 508 0.325577 ATTTCCCTGGGGATGCAACC 60.326 55.000 14.00 4.00 44.74 3.77
631 699 5.066593 TGTATTGTTGTGCATTACTGGTCA 58.933 37.500 0.00 0.00 35.85 4.02
737 807 8.806177 AAGCAAAACGGGTTATTAAAACTTAG 57.194 30.769 0.00 0.00 0.00 2.18
745 815 6.713450 AGAAGAAGAAGCAAAACGGGTTATTA 59.287 34.615 0.00 0.00 30.74 0.98
749 819 3.288092 AGAAGAAGAAGCAAAACGGGTT 58.712 40.909 0.00 0.00 0.00 4.11
751 821 3.813166 TGTAGAAGAAGAAGCAAAACGGG 59.187 43.478 0.00 0.00 0.00 5.28
753 823 7.734538 TTTTTGTAGAAGAAGAAGCAAAACG 57.265 32.000 0.00 0.00 36.14 3.60
841 914 8.313944 TGATTAGTTGTTGGCTAGTAATCCTA 57.686 34.615 0.00 0.00 39.63 2.94
919 994 3.446873 CACTGGCACTATCTCTCTCTTGT 59.553 47.826 0.00 0.00 0.00 3.16
921 996 3.446873 CACACTGGCACTATCTCTCTCTT 59.553 47.826 0.00 0.00 0.00 2.85
948 1023 2.155194 GTCTAGTGCACGCTGCTCG 61.155 63.158 12.01 0.00 45.31 5.03
967 1042 2.650778 GGGCCCGAAAGCTTTGTG 59.349 61.111 18.30 8.74 0.00 3.33
1029 1104 5.697633 GTGTTTTGACCGTAAAGTGGATCTA 59.302 40.000 0.00 0.00 0.00 1.98
1039 1114 3.243975 GGAGAGGAGTGTTTTGACCGTAA 60.244 47.826 0.00 0.00 0.00 3.18
1041 1116 1.070289 GGAGAGGAGTGTTTTGACCGT 59.930 52.381 0.00 0.00 0.00 4.83
1098 1176 2.260434 GTCCTCGCCGTTGTAGCA 59.740 61.111 0.00 0.00 0.00 3.49
1364 1442 0.550914 ACTCTGGGAGCTCGAGATCT 59.449 55.000 28.08 11.42 32.04 2.75
1408 1961 2.104170 GGAAGGAGAGGTTCTCGATGT 58.896 52.381 0.41 0.00 44.28 3.06
1445 2001 2.516888 CGACAAGGTGGTCTGGGGT 61.517 63.158 0.00 0.00 35.63 4.95
1550 2109 3.521765 ATTGGGGAAGGCGTTGGCA 62.522 57.895 0.00 0.00 42.47 4.92
1625 2184 2.329539 GAATGGGGCAGGCATCGAGA 62.330 60.000 0.00 0.00 0.00 4.04
1658 2217 1.676014 GGCTTACCATTGAGCACGAGT 60.676 52.381 0.00 0.00 40.63 4.18
1710 2269 2.115910 CCCAAGGAGCAAGCACCA 59.884 61.111 11.05 0.00 0.00 4.17
1770 2347 3.711086 TGAAGAAGATGATGCGCTCTAC 58.289 45.455 9.73 0.00 0.00 2.59
1772 2349 2.975732 TGAAGAAGATGATGCGCTCT 57.024 45.000 9.73 0.00 0.00 4.09
1979 2562 0.925558 TTATGAATGGAGCCAGGGCA 59.074 50.000 13.63 0.00 44.88 5.36
2022 2609 9.486857 GATCTTAGAAAGTTTGTAATAAACGGC 57.513 33.333 5.74 0.00 35.42 5.68
2188 2776 8.669243 CCCATGTAAGAGTTTGAAAGTAGAATC 58.331 37.037 0.00 0.00 0.00 2.52
2311 2899 4.322953 GGAAGAACCACAATTGAATGCCAT 60.323 41.667 13.59 0.00 38.79 4.40
2370 2958 3.072944 AGAGAAGCAAGTGAGACAATGC 58.927 45.455 0.00 0.00 39.06 3.56
2476 5692 2.030805 ACAAAATCGTTTCAGGAGCTGC 60.031 45.455 0.00 0.00 0.00 5.25
2491 5707 5.523916 CGATATTTGAGAGACGGGACAAAAT 59.476 40.000 0.00 0.00 36.19 1.82
2500 5716 3.891324 GTCTCCCGATATTTGAGAGACG 58.109 50.000 3.00 0.00 42.73 4.18
2601 5818 6.014156 ACCTCTATAGTTACATCTGCAATCCC 60.014 42.308 0.00 0.00 0.00 3.85
2833 7473 6.412214 TCCTTTAGCTAAAACATACTGGGAC 58.588 40.000 19.10 0.00 0.00 4.46
2894 7536 5.466127 AATGGTATGTTGGGATTGGTAGT 57.534 39.130 0.00 0.00 0.00 2.73
2901 7543 6.538209 TGGGTATAAATGGTATGTTGGGAT 57.462 37.500 0.00 0.00 0.00 3.85
2949 7591 6.293680 CCTTCTCAGTTCTGGAAAAGCTTTAC 60.294 42.308 13.10 9.39 0.00 2.01
2993 7635 3.022557 ACCAGGAATCCCAACATCATG 57.977 47.619 0.00 0.00 33.88 3.07
2995 7637 4.879295 AATACCAGGAATCCCAACATCA 57.121 40.909 0.00 0.00 33.88 3.07
2998 7640 4.167892 AGCATAATACCAGGAATCCCAACA 59.832 41.667 0.00 0.00 33.88 3.33
3019 7661 7.545362 TGAAAGAAGATAGCTGACAATAAGC 57.455 36.000 0.00 0.00 41.15 3.09
3030 7674 8.401709 CAAAGGTTCCTTATGAAAGAAGATAGC 58.598 37.037 4.43 0.00 34.37 2.97
3041 7685 2.041620 AGCTGGCAAAGGTTCCTTATGA 59.958 45.455 4.43 0.00 30.45 2.15
3055 7699 4.040461 GGGTTAAGAGATACATAGCTGGCA 59.960 45.833 0.00 0.00 0.00 4.92
3113 7757 5.281037 GGATATGGGGGATAGGGTGTTAAAG 60.281 48.000 0.00 0.00 0.00 1.85
3162 7806 4.627035 GCCAACAAAATTCATCTAGCCAAC 59.373 41.667 0.00 0.00 0.00 3.77
3188 7832 7.891183 AATTGTCTGTGTAGTGATAGTGAAC 57.109 36.000 0.00 0.00 0.00 3.18
3225 7869 1.177401 GGGCCTTGAACCTGATCAAC 58.823 55.000 0.84 0.00 35.55 3.18
3339 7985 3.406764 CCATAATAGCTGGTTGGAGAGC 58.593 50.000 0.00 0.00 35.28 4.09
3357 8003 8.102676 AGCTTTGATTGGTAAATTTTTAGCCAT 58.897 29.630 0.00 4.66 39.66 4.40
3385 8031 4.530161 ACAAGCTTGGTAGAGAAGATCTGT 59.470 41.667 29.18 0.83 39.20 3.41
3398 8044 3.540314 TTGCATTTTGACAAGCTTGGT 57.460 38.095 29.18 15.37 0.00 3.67
3499 8195 8.219178 AGAGTTCTCTTATCCCTATTAACTCGA 58.781 37.037 0.00 0.00 43.86 4.04
3500 8196 8.398878 AGAGTTCTCTTATCCCTATTAACTCG 57.601 38.462 0.00 0.00 43.86 4.18
3534 8230 4.141959 ACAATTTTCGGGGATGCCAATTAG 60.142 41.667 5.30 1.17 0.00 1.73
3581 8277 2.833943 TGCTAGAGTTGCTCTGAATCCA 59.166 45.455 8.75 0.00 41.37 3.41
3691 8387 8.655901 TGGACCATTAGAACATGCATATTAGTA 58.344 33.333 0.00 0.00 0.00 1.82
3693 8389 7.663081 AGTGGACCATTAGAACATGCATATTAG 59.337 37.037 0.00 0.00 0.00 1.73
3725 8421 1.968017 CGCCATTGTGTCAGGCTGT 60.968 57.895 15.27 0.00 46.14 4.40
4027 8723 1.222113 GCCTCCTGCCAGAACCTAC 59.778 63.158 0.00 0.00 0.00 3.18
4134 8830 2.176546 CGCATTCAAGGCCACGTG 59.823 61.111 9.08 9.08 0.00 4.49
4160 8856 2.029288 CACGACCAGCAATGCTCGT 61.029 57.895 13.91 13.91 37.16 4.18
4206 8902 0.684535 TCATTCACCTCGTCTGCCAA 59.315 50.000 0.00 0.00 0.00 4.52
4326 9022 2.224523 GGTCATGGACACTGTGAAAGGA 60.225 50.000 15.86 3.79 33.68 3.36
4333 9029 1.073923 GGAAAGGGTCATGGACACTGT 59.926 52.381 1.28 0.00 46.54 3.55
4352 9048 1.178534 AACCATTGGTTCACCAGCGG 61.179 55.000 15.48 12.22 43.05 5.52
4426 9124 5.830000 ACAAACTAAACAACCTGACCTTC 57.170 39.130 0.00 0.00 0.00 3.46
4474 9172 9.920946 ATATAATCATGGTAAGTTGAAACCTGT 57.079 29.630 0.00 0.00 36.67 4.00
4528 9231 8.425577 AGGATGTTCTGTATAGTTGAAAATCG 57.574 34.615 0.00 0.00 36.06 3.34
4566 9270 9.955102 TGGCTCTTCGAGTATCTAGTTATAATA 57.045 33.333 0.00 0.00 31.39 0.98
4620 9324 1.561542 ACACAAGGCTTCTAGGATGGG 59.438 52.381 0.00 0.00 0.00 4.00
4676 9380 4.803088 TCTTTCATTGTGGCAAAAGTTTCG 59.197 37.500 8.10 0.00 32.03 3.46
4706 9410 2.885894 CTCCGTCCTAACCATAGTCTCC 59.114 54.545 0.00 0.00 0.00 3.71
4713 9417 2.389715 CTCCTTCTCCGTCCTAACCAT 58.610 52.381 0.00 0.00 0.00 3.55
4717 9421 1.183549 GTGCTCCTTCTCCGTCCTAA 58.816 55.000 0.00 0.00 0.00 2.69
4720 9424 1.216710 CTGTGCTCCTTCTCCGTCC 59.783 63.158 0.00 0.00 0.00 4.79
4798 9514 1.200716 TCAGCTACCTAAACACGACCG 59.799 52.381 0.00 0.00 0.00 4.79
4803 9519 8.494016 AGATGTTAATTCAGCTACCTAAACAC 57.506 34.615 5.55 2.19 32.10 3.32
4889 10308 0.788391 CTCGTAGTGGGTGTTTTCGC 59.212 55.000 0.00 0.00 0.00 4.70
5023 10446 2.043801 GAGAGAGGGGGATAGTAGCCAT 59.956 54.545 6.80 0.00 0.00 4.40
5032 10455 0.326904 TGCACATGAGAGAGGGGGAT 60.327 55.000 0.00 0.00 0.00 3.85
5126 10552 1.065102 GCATCATTGATTGCTCGCACT 59.935 47.619 0.00 0.00 0.00 4.40
5132 10558 1.737816 GCCCGCATCATTGATTGCT 59.262 52.632 14.72 0.00 0.00 3.91
5155 10581 1.107945 TTGATCACCGAGACGCCATA 58.892 50.000 0.00 0.00 0.00 2.74
5177 10603 4.392921 AGGAAACTCATCACGTCTATGG 57.607 45.455 7.40 2.40 32.90 2.74
5186 10612 7.557719 GGGAATGAAGAAATAGGAAACTCATCA 59.442 37.037 0.00 0.00 43.67 3.07
5188 10614 7.340487 GTGGGAATGAAGAAATAGGAAACTCAT 59.660 37.037 0.00 0.00 43.67 2.90
5252 10679 9.922477 AAACACCCAAAATTCCCTTTTATAAAA 57.078 25.926 10.16 10.16 35.27 1.52
5318 10753 6.531948 GCTATAGATGCCCTAATACTTCAACG 59.468 42.308 3.21 0.00 0.00 4.10
5416 10868 6.843069 AAGTTTTCGGGAATTGATGTTTTG 57.157 33.333 0.00 0.00 0.00 2.44
5417 10869 8.822855 GTTAAAGTTTTCGGGAATTGATGTTTT 58.177 29.630 0.00 0.00 0.00 2.43
5421 10873 8.587952 AAAGTTAAAGTTTTCGGGAATTGATG 57.412 30.769 0.00 0.00 0.00 3.07
5423 10875 8.251721 TGAAAAGTTAAAGTTTTCGGGAATTGA 58.748 29.630 14.86 0.00 45.70 2.57
5424 10876 8.413899 TGAAAAGTTAAAGTTTTCGGGAATTG 57.586 30.769 14.86 0.00 45.70 2.32
5425 10877 9.607988 ATTGAAAAGTTAAAGTTTTCGGGAATT 57.392 25.926 14.86 0.00 45.70 2.17
5427 10879 7.707464 GGATTGAAAAGTTAAAGTTTTCGGGAA 59.293 33.333 14.86 8.03 45.70 3.97
5429 10881 6.422701 GGGATTGAAAAGTTAAAGTTTTCGGG 59.577 38.462 14.86 0.00 45.70 5.14
5431 10883 6.981559 TGGGGATTGAAAAGTTAAAGTTTTCG 59.018 34.615 14.86 0.00 45.70 3.46
5432 10884 8.902540 ATGGGGATTGAAAAGTTAAAGTTTTC 57.097 30.769 13.71 13.71 44.01 2.29
5522 10974 3.068691 CGCCAAGAGGGAGGTCGA 61.069 66.667 0.00 0.00 40.01 4.20


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

AutoCloner maintained by Alex Coulton.