Multiple sequence alignment - TraesCS6D01G166700

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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 TraesCS6D01G166700 chr6D 100.000 5499 0 0 1 5499 148764140 148769638 0.000000e+00 10155
1 TraesCS6D01G166700 chr6D 80.751 639 74 26 4819 5448 84289798 84289200 2.340000e-123 453
2 TraesCS6D01G166700 chr6D 75.806 682 113 41 4792 5447 13088682 13088027 1.160000e-76 298
3 TraesCS6D01G166700 chr6A 95.649 2988 68 30 1584 4538 198367240 198364282 0.000000e+00 4741
4 TraesCS6D01G166700 chr6A 94.654 767 20 7 718 1467 198368006 198367244 0.000000e+00 1170
5 TraesCS6D01G166700 chr6A 79.826 689 100 27 4772 5450 617061524 617062183 3.000000e-127 466
6 TraesCS6D01G166700 chr6A 87.948 307 11 8 4451 4752 198364286 198364001 6.820000e-89 339
7 TraesCS6D01G166700 chr6A 95.804 143 4 1 1341 1483 9429244 9429104 4.280000e-56 230
8 TraesCS6D01G166700 chr6A 90.625 128 5 5 1737 1861 198367194 198367071 4.410000e-36 163
9 TraesCS6D01G166700 chr6B 95.777 2652 76 21 2138 4774 261528775 261531405 0.000000e+00 4244
10 TraesCS6D01G166700 chr6B 91.446 1286 41 28 659 1887 261527191 261528464 0.000000e+00 1701
11 TraesCS6D01G166700 chr6B 89.371 668 62 6 1 662 261510575 261511239 0.000000e+00 832
12 TraesCS6D01G166700 chr6B 94.318 264 12 1 1889 2152 261528499 261528759 8.580000e-108 401
13 TraesCS6D01G166700 chr7A 81.340 627 91 22 2477 3085 545949185 545949803 2.300000e-133 486
14 TraesCS6D01G166700 chr7A 79.661 472 73 19 5036 5499 79146707 79146251 8.890000e-83 318
15 TraesCS6D01G166700 chr7A 79.536 474 63 24 4978 5450 54585049 54584609 1.920000e-79 307
16 TraesCS6D01G166700 chr7A 79.739 306 51 10 3433 3737 545950112 545950407 1.550000e-50 211
17 TraesCS6D01G166700 chr7A 84.332 217 17 10 1001 1201 545947896 545948111 4.350000e-46 196
18 TraesCS6D01G166700 chr7A 78.322 286 44 15 4772 5053 577489750 577489479 9.470000e-38 169
19 TraesCS6D01G166700 chr2B 78.695 751 109 37 4768 5499 603191629 603192347 2.340000e-123 453
20 TraesCS6D01G166700 chr3D 79.007 705 103 28 4771 5450 580329775 580329091 1.820000e-119 440
21 TraesCS6D01G166700 chr1A 80.346 636 78 23 4819 5448 115556689 115556095 6.540000e-119 438
22 TraesCS6D01G166700 chr1A 80.251 638 74 31 4819 5448 137935093 137935686 3.040000e-117 433
23 TraesCS6D01G166700 chr7B 79.375 640 80 31 4819 5448 677706270 677705673 2.390000e-108 403
24 TraesCS6D01G166700 chr7B 77.097 620 107 26 4796 5408 59074656 59075247 5.310000e-85 326
25 TraesCS6D01G166700 chr7B 85.253 217 15 10 1001 1201 468854435 468854220 2.010000e-49 207
26 TraesCS6D01G166700 chr2A 80.961 541 69 27 4973 5499 459472823 459472303 1.110000e-106 398
27 TraesCS6D01G166700 chr2A 79.036 477 74 18 4982 5447 749658393 749658854 2.490000e-78 303
28 TraesCS6D01G166700 chr2A 76.154 650 107 35 4833 5450 712965647 712965014 1.160000e-76 298
29 TraesCS6D01G166700 chr5B 77.681 690 107 33 4770 5450 548523350 548522699 1.450000e-100 377
30 TraesCS6D01G166700 chr5B 78.929 280 41 14 4772 5047 248655258 248655523 2.040000e-39 174
31 TraesCS6D01G166700 chr5A 78.685 502 70 29 4765 5256 43252153 43251679 3.220000e-77 300
32 TraesCS6D01G166700 chr7D 90.909 176 16 0 1 176 267762398 267762223 2.560000e-58 237
33 TraesCS6D01G166700 chr7D 84.793 217 16 10 1001 1201 451051619 451051404 9.340000e-48 202
34 TraesCS6D01G166700 chr4A 74.806 516 95 22 4771 5276 614420924 614421414 3.360000e-47 200
35 TraesCS6D01G166700 chr5D 79.612 206 29 7 4766 4966 420632947 420633144 9.610000e-28 135


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 TraesCS6D01G166700 chr6D 148764140 148769638 5498 False 10155.000000 10155 100.000000 1 5499 1 chr6D.!!$F1 5498
1 TraesCS6D01G166700 chr6D 84289200 84289798 598 True 453.000000 453 80.751000 4819 5448 1 chr6D.!!$R2 629
2 TraesCS6D01G166700 chr6D 13088027 13088682 655 True 298.000000 298 75.806000 4792 5447 1 chr6D.!!$R1 655
3 TraesCS6D01G166700 chr6A 198364001 198368006 4005 True 1603.250000 4741 92.219000 718 4752 4 chr6A.!!$R2 4034
4 TraesCS6D01G166700 chr6A 617061524 617062183 659 False 466.000000 466 79.826000 4772 5450 1 chr6A.!!$F1 678
5 TraesCS6D01G166700 chr6B 261527191 261531405 4214 False 2115.333333 4244 93.847000 659 4774 3 chr6B.!!$F2 4115
6 TraesCS6D01G166700 chr6B 261510575 261511239 664 False 832.000000 832 89.371000 1 662 1 chr6B.!!$F1 661
7 TraesCS6D01G166700 chr7A 545947896 545950407 2511 False 297.666667 486 81.803667 1001 3737 3 chr7A.!!$F1 2736
8 TraesCS6D01G166700 chr2B 603191629 603192347 718 False 453.000000 453 78.695000 4768 5499 1 chr2B.!!$F1 731
9 TraesCS6D01G166700 chr3D 580329091 580329775 684 True 440.000000 440 79.007000 4771 5450 1 chr3D.!!$R1 679
10 TraesCS6D01G166700 chr1A 115556095 115556689 594 True 438.000000 438 80.346000 4819 5448 1 chr1A.!!$R1 629
11 TraesCS6D01G166700 chr1A 137935093 137935686 593 False 433.000000 433 80.251000 4819 5448 1 chr1A.!!$F1 629
12 TraesCS6D01G166700 chr7B 677705673 677706270 597 True 403.000000 403 79.375000 4819 5448 1 chr7B.!!$R2 629
13 TraesCS6D01G166700 chr7B 59074656 59075247 591 False 326.000000 326 77.097000 4796 5408 1 chr7B.!!$F1 612
14 TraesCS6D01G166700 chr2A 459472303 459472823 520 True 398.000000 398 80.961000 4973 5499 1 chr2A.!!$R1 526
15 TraesCS6D01G166700 chr2A 712965014 712965647 633 True 298.000000 298 76.154000 4833 5450 1 chr2A.!!$R2 617
16 TraesCS6D01G166700 chr5B 548522699 548523350 651 True 377.000000 377 77.681000 4770 5450 1 chr5B.!!$R1 680

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
609 611 0.175760 GGTCATGCGAGCTTAGGACA 59.824 55.000 11.58 0.0 36.68 4.02 F
1368 1432 0.039256 CAACCGGTGATTGGCTGTTG 60.039 55.000 8.52 0.0 0.00 3.33 F
1586 1651 1.000052 TGTGTTGCATGCCATGAACAG 60.000 47.619 18.50 0.0 33.90 3.16 F
3269 3727 0.610232 AGTCTGGAACTGGCAATGGC 60.610 55.000 0.00 0.0 36.65 4.40 F
3948 4415 0.463620 GTCTCCTCCTGCTGATCCAC 59.536 60.000 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1640 1.234821 GTTCCGTTCTGTTCATGGCA 58.765 50.000 0.00 0.0 0.00 4.92 R
2964 3362 1.154338 GTGATGAGCAACTGCACGC 60.154 57.895 4.22 0.0 45.16 5.34 R
3427 3893 1.236616 TTGCCATCAGAACCTGCACG 61.237 55.000 0.00 0.0 0.00 5.34 R
4247 4719 1.608590 AGCCGTGAACAAGGAAATGTG 59.391 47.619 10.64 0.0 32.81 3.21 R
5047 5704 2.420022 AGAAATGTTCGCCGATTCAAGG 59.580 45.455 1.56 0.0 34.02 3.61 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
25 26 4.083862 GGTCAGGGTGCTCGGGAC 62.084 72.222 0.00 0.00 0.00 4.46
27 28 2.284625 TCAGGGTGCTCGGGACAT 60.285 61.111 0.00 0.00 0.00 3.06
30 31 0.179073 CAGGGTGCTCGGGACATAAG 60.179 60.000 0.00 0.00 0.00 1.73
34 35 1.207329 GGTGCTCGGGACATAAGTTCT 59.793 52.381 0.00 0.00 0.00 3.01
59 60 4.086457 TCTTGGATAAAACAGGGAAAGGC 58.914 43.478 0.00 0.00 0.00 4.35
64 65 5.479027 TGGATAAAACAGGGAAAGGCTTTAC 59.521 40.000 14.03 14.03 0.00 2.01
87 88 1.037493 TGAAGATGGTCGTATCCCCG 58.963 55.000 0.00 0.00 0.00 5.73
95 96 2.838225 CGTATCCCCGGCAGGTCT 60.838 66.667 1.11 0.00 35.12 3.85
114 115 1.610038 CTGCAGTGATGGCAACTTTGA 59.390 47.619 5.25 0.00 41.39 2.69
186 187 2.165437 AGCTCCTCGTCTTGTTCATCTC 59.835 50.000 0.00 0.00 0.00 2.75
191 192 3.506810 CTCGTCTTGTTCATCTCAGGTC 58.493 50.000 0.00 0.00 0.00 3.85
197 198 4.838423 TCTTGTTCATCTCAGGTCCTAACA 59.162 41.667 0.00 0.00 0.00 2.41
199 200 3.901222 TGTTCATCTCAGGTCCTAACACA 59.099 43.478 0.00 0.00 0.00 3.72
210 211 1.169661 CCTAACACACGCCCAAGCAA 61.170 55.000 0.00 0.00 39.83 3.91
253 254 0.532640 CATTGCCACATCGATCGGGA 60.533 55.000 16.41 8.09 0.00 5.14
256 257 2.498941 GCCACATCGATCGGGAGGA 61.499 63.158 21.46 2.54 0.00 3.71
257 258 1.364171 CCACATCGATCGGGAGGAC 59.636 63.158 16.41 0.00 0.00 3.85
258 259 1.364171 CACATCGATCGGGAGGACC 59.636 63.158 16.41 0.00 0.00 4.46
278 279 4.227197 ACCCACCATGGTGTGAAATTTTA 58.773 39.130 36.62 0.00 44.02 1.52
287 288 7.360269 CCATGGTGTGAAATTTTACAAATGAGC 60.360 37.037 25.87 13.37 30.53 4.26
303 304 8.986477 ACAAATGAGCCATTTATAAGTGTTTC 57.014 30.769 11.32 5.08 41.40 2.78
345 346 1.805428 GCTTTCCCGGCACAACATGT 61.805 55.000 0.00 0.00 0.00 3.21
392 393 3.426568 GGCCGTGAGCTGCAAGAC 61.427 66.667 1.02 0.00 43.05 3.01
468 470 2.060980 CCCTCCCCCTCTCTTGTCG 61.061 68.421 0.00 0.00 0.00 4.35
471 473 1.618888 CCTCCCCCTCTCTTGTCGTAA 60.619 57.143 0.00 0.00 0.00 3.18
474 476 2.764572 TCCCCCTCTCTTGTCGTAAATC 59.235 50.000 0.00 0.00 0.00 2.17
475 477 2.158943 CCCCCTCTCTTGTCGTAAATCC 60.159 54.545 0.00 0.00 0.00 3.01
485 487 4.718858 TGTCGTAAATCCGTTTGTGAAG 57.281 40.909 0.00 0.00 0.00 3.02
495 497 3.256136 TCCGTTTGTGAAGGTTGTTGTTT 59.744 39.130 0.00 0.00 0.00 2.83
497 499 3.366422 CGTTTGTGAAGGTTGTTGTTTGG 59.634 43.478 0.00 0.00 0.00 3.28
501 503 1.205893 TGAAGGTTGTTGTTTGGGCAC 59.794 47.619 0.00 0.00 0.00 5.01
518 520 0.792640 CACGAGCACAACCTCATCAC 59.207 55.000 0.00 0.00 0.00 3.06
521 523 1.639298 GAGCACAACCTCATCACGCC 61.639 60.000 0.00 0.00 0.00 5.68
557 559 1.061546 TGTGGGTCCCTTAGGTCAAC 58.938 55.000 10.00 0.00 0.00 3.18
582 584 4.616592 CGATACGCGTCAGCAGAT 57.383 55.556 18.63 1.03 45.49 2.90
583 585 2.414950 CGATACGCGTCAGCAGATC 58.585 57.895 18.63 11.51 45.49 2.75
584 586 1.323827 CGATACGCGTCAGCAGATCG 61.324 60.000 18.63 20.18 45.00 3.69
585 587 1.601147 GATACGCGTCAGCAGATCGC 61.601 60.000 18.63 13.28 45.49 4.58
586 588 3.751401 TACGCGTCAGCAGATCGCC 62.751 63.158 18.63 4.18 45.85 5.54
609 611 0.175760 GGTCATGCGAGCTTAGGACA 59.824 55.000 11.58 0.00 36.68 4.02
611 613 1.863454 GTCATGCGAGCTTAGGACATG 59.137 52.381 6.52 7.44 39.53 3.21
623 625 6.529220 AGCTTAGGACATGAGATGAATAACC 58.471 40.000 0.00 0.00 0.00 2.85
627 629 8.547481 TTAGGACATGAGATGAATAACCTACA 57.453 34.615 0.00 0.00 0.00 2.74
633 639 9.685276 ACATGAGATGAATAACCTACATTTGAA 57.315 29.630 0.00 0.00 0.00 2.69
716 726 9.924650 TTCATAGTTTCAGGACTTAGTTTACTC 57.075 33.333 0.00 0.00 0.00 2.59
1244 1298 4.123545 CCGCCCCCAAACCCTAGG 62.124 72.222 0.06 0.06 0.00 3.02
1367 1431 1.805428 GCAACCGGTGATTGGCTGTT 61.805 55.000 8.52 0.00 0.00 3.16
1368 1432 0.039256 CAACCGGTGATTGGCTGTTG 60.039 55.000 8.52 0.00 0.00 3.33
1377 1441 3.016031 TGATTGGCTGTTGCGATATGTT 58.984 40.909 0.00 0.00 40.82 2.71
1501 1566 2.826428 GCGAATTGCTCATACTCTGGA 58.174 47.619 0.00 0.00 41.73 3.86
1503 1568 2.791560 CGAATTGCTCATACTCTGGACG 59.208 50.000 0.00 0.00 0.00 4.79
1527 1592 2.345244 CTCTGGGCTGACTGCGTT 59.655 61.111 0.00 0.00 44.05 4.84
1531 1596 3.423154 GGGCTGACTGCGTTTCGG 61.423 66.667 0.00 0.00 44.05 4.30
1557 1622 3.782656 AGTGGTTTCCCGTATTTCTGT 57.217 42.857 0.00 0.00 0.00 3.41
1573 1638 9.158364 CGTATTTCTGTAATGATATTGTGTTGC 57.842 33.333 0.00 0.00 0.00 4.17
1577 1642 6.497437 TCTGTAATGATATTGTGTTGCATGC 58.503 36.000 11.82 11.82 0.00 4.06
1578 1643 5.590145 TGTAATGATATTGTGTTGCATGCC 58.410 37.500 16.68 0.28 0.00 4.40
1581 1646 4.048241 TGATATTGTGTTGCATGCCATG 57.952 40.909 16.68 0.00 0.00 3.66
1583 1648 4.159879 TGATATTGTGTTGCATGCCATGAA 59.840 37.500 16.68 0.00 0.00 2.57
1584 1649 2.151881 TTGTGTTGCATGCCATGAAC 57.848 45.000 16.68 13.21 0.00 3.18
1586 1651 1.000052 TGTGTTGCATGCCATGAACAG 60.000 47.619 18.50 0.00 33.90 3.16
1587 1652 1.270274 GTGTTGCATGCCATGAACAGA 59.730 47.619 18.50 0.00 33.90 3.41
1589 1654 2.288334 TGTTGCATGCCATGAACAGAAC 60.288 45.455 16.68 9.86 31.52 3.01
1651 1721 6.493115 TCTCTTCAATAGCTAGATTCTCCCAG 59.507 42.308 0.00 0.00 0.00 4.45
1729 1820 5.971763 TGGTACCAATAATCCAAAACATGC 58.028 37.500 13.60 0.00 0.00 4.06
1831 1923 6.749139 TGTTACTCTCATGCATACATACTCC 58.251 40.000 0.00 0.00 33.67 3.85
1873 1965 6.515272 ACATGACTTTTCTTGAACAACTGT 57.485 33.333 0.00 0.00 32.42 3.55
1994 2119 5.699915 TCTTTGCATGAGCTATTCATCTAGC 59.300 40.000 0.00 0.00 44.76 3.42
2010 2135 5.069119 TCATCTAGCGCTTCCTCTAAATTGA 59.931 40.000 18.68 2.13 0.00 2.57
2017 2142 4.442733 CGCTTCCTCTAAATTGACTCGATC 59.557 45.833 0.00 0.00 0.00 3.69
2207 2486 6.913873 TGACAAAGGTACAAGTTGTAAGAC 57.086 37.500 17.16 7.99 35.67 3.01
2964 3362 1.269448 ACAGGCAAAACATTACTGGCG 59.731 47.619 0.00 0.00 40.36 5.69
3221 3679 9.053840 GCACCATCTATTATATTCATGGATGAG 57.946 37.037 16.47 11.81 37.93 2.90
3269 3727 0.610232 AGTCTGGAACTGGCAATGGC 60.610 55.000 0.00 0.00 36.65 4.40
3427 3893 2.418368 TGATGCCCTGTATGTGTTCC 57.582 50.000 0.00 0.00 0.00 3.62
3698 4164 7.095270 GTGGAATTGATCTGAAAAAGATTGCT 58.905 34.615 0.00 0.00 46.12 3.91
3802 4268 7.759433 ACGTCATGTTTCAGTTTTCTCAATTTT 59.241 29.630 0.00 0.00 0.00 1.82
3885 4352 8.587608 TCTCTTCCAAAAATTGAATATTGCACT 58.412 29.630 0.00 0.00 0.00 4.40
3910 4377 3.562505 CACTTGAGCTTTGATTGCTGAC 58.437 45.455 0.00 0.00 41.30 3.51
3948 4415 0.463620 GTCTCCTCCTGCTGATCCAC 59.536 60.000 0.00 0.00 0.00 4.02
4064 4532 1.281419 TATGGTTTCGAGGGCCTGAA 58.719 50.000 12.95 12.65 0.00 3.02
4077 4545 4.600062 AGGGCCTGAAATAGTTGGTTAAG 58.400 43.478 4.50 0.00 0.00 1.85
4105 4573 6.019779 TGTTGTTAGCTGTTTGTTGAGTTT 57.980 33.333 0.00 0.00 0.00 2.66
4215 4686 5.012664 TGCAGAAGTATGGTAAGACTTTCCA 59.987 40.000 15.09 15.09 37.96 3.53
4217 4688 6.464222 CAGAAGTATGGTAAGACTTTCCACA 58.536 40.000 15.06 1.55 37.96 4.17
4228 4699 3.063485 GACTTTCCACACTCTTCTGCTC 58.937 50.000 0.00 0.00 0.00 4.26
4247 4719 6.910433 TCTGCTCGAAAACACTTACATTTTTC 59.090 34.615 0.00 0.00 36.36 2.29
4248 4720 6.556212 TGCTCGAAAACACTTACATTTTTCA 58.444 32.000 6.79 0.00 38.57 2.69
4275 4747 1.603802 CTTGTTCACGGCTGACAACAT 59.396 47.619 12.76 0.00 0.00 2.71
4301 4773 0.607489 GTGCACAACATCCCTGCTCT 60.607 55.000 13.17 0.00 0.00 4.09
4303 4775 1.251251 GCACAACATCCCTGCTCTTT 58.749 50.000 0.00 0.00 0.00 2.52
4304 4776 1.615392 GCACAACATCCCTGCTCTTTT 59.385 47.619 0.00 0.00 0.00 2.27
4305 4777 2.352127 GCACAACATCCCTGCTCTTTTC 60.352 50.000 0.00 0.00 0.00 2.29
4306 4778 2.886523 CACAACATCCCTGCTCTTTTCA 59.113 45.455 0.00 0.00 0.00 2.69
4307 4779 2.887152 ACAACATCCCTGCTCTTTTCAC 59.113 45.455 0.00 0.00 0.00 3.18
4308 4780 2.206576 ACATCCCTGCTCTTTTCACC 57.793 50.000 0.00 0.00 0.00 4.02
4309 4781 1.707427 ACATCCCTGCTCTTTTCACCT 59.293 47.619 0.00 0.00 0.00 4.00
4310 4782 2.108952 ACATCCCTGCTCTTTTCACCTT 59.891 45.455 0.00 0.00 0.00 3.50
4311 4783 2.276732 TCCCTGCTCTTTTCACCTTG 57.723 50.000 0.00 0.00 0.00 3.61
4312 4784 1.774254 TCCCTGCTCTTTTCACCTTGA 59.226 47.619 0.00 0.00 0.00 3.02
4313 4785 2.157738 CCCTGCTCTTTTCACCTTGAG 58.842 52.381 0.00 0.00 0.00 3.02
4320 4792 5.470098 TGCTCTTTTCACCTTGAGTTCATAC 59.530 40.000 0.00 0.00 0.00 2.39
4334 4806 6.741109 TGAGTTCATACGAAGTTGTTCACTA 58.259 36.000 0.00 0.00 37.78 2.74
4562 5102 0.748005 ACTGCACGTTGCTGGACTTT 60.748 50.000 16.59 0.00 45.06 2.66
4670 5211 4.859629 AATCGAACTCGTTGAATTAGCC 57.140 40.909 0.00 0.00 40.80 3.93
4672 5213 3.857052 TCGAACTCGTTGAATTAGCCAT 58.143 40.909 0.00 0.00 40.80 4.40
4684 5225 1.683943 TTAGCCATGCAATCTGCCTC 58.316 50.000 0.00 0.00 44.23 4.70
4794 5339 9.555727 TTTACTAGCAAAAGAGTCTGTATGTTT 57.444 29.630 0.00 0.00 0.00 2.83
4800 5345 6.715464 CAAAAGAGTCTGTATGTTTCAACGT 58.285 36.000 0.00 0.00 0.00 3.99
4831 5379 9.921637 AAAAATAAATCGTAATCTCAAAAGGCA 57.078 25.926 0.00 0.00 0.00 4.75
5083 5740 7.427606 GCGAACATTTCTAGAATTGATGAACAG 59.572 37.037 26.35 13.51 0.00 3.16
5161 5821 5.356882 AACGAACATTGTGTCGATTCAAT 57.643 34.783 20.43 10.71 35.08 2.57
5280 5963 9.984190 TTCATTCATGAACATTTTCTGAATTGA 57.016 25.926 11.07 2.91 41.51 2.57
5307 5990 9.658799 TGAAATTTTGTTCAGTTTCATTAACCA 57.341 25.926 0.00 0.00 36.11 3.67
5318 6001 9.619316 TCAGTTTCATTAACCATTTTGAATACG 57.381 29.630 0.00 0.00 37.46 3.06
5326 6010 4.719040 ACCATTTTGAATACGCGAACTTC 58.281 39.130 15.93 12.84 0.00 3.01
5379 6073 9.547753 TCCCGAACATTTATTTTCAAATTTTCA 57.452 25.926 7.72 0.00 35.65 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.449719 TTTTATCCAAGAAGAGAACTTATGTCC 57.550 33.333 0.00 0.00 36.39 4.02
27 28 7.883311 CCCTGTTTTATCCAAGAAGAGAACTTA 59.117 37.037 0.00 0.00 36.39 2.24
30 31 6.238648 TCCCTGTTTTATCCAAGAAGAGAAC 58.761 40.000 0.00 0.00 0.00 3.01
34 35 6.010219 CCTTTCCCTGTTTTATCCAAGAAGA 58.990 40.000 0.00 0.00 0.00 2.87
59 60 3.782046 ACGACCATCTTCATCGGTAAAG 58.218 45.455 0.00 0.00 40.16 1.85
64 65 2.352814 GGGATACGACCATCTTCATCGG 60.353 54.545 0.00 0.00 40.16 4.18
68 69 1.037493 CGGGGATACGACCATCTTCA 58.963 55.000 0.00 0.00 35.47 3.02
95 96 1.689984 TCAAAGTTGCCATCACTGCA 58.310 45.000 0.00 0.00 36.84 4.41
97 98 2.608752 GGCTTCAAAGTTGCCATCACTG 60.609 50.000 0.00 0.00 45.46 3.66
186 187 1.375523 GGGCGTGTGTTAGGACCTG 60.376 63.158 3.53 0.00 39.36 4.00
191 192 1.169661 TTGCTTGGGCGTGTGTTAGG 61.170 55.000 0.00 0.00 42.25 2.69
197 198 2.186826 GTCAGTTGCTTGGGCGTGT 61.187 57.895 0.00 0.00 42.25 4.49
199 200 2.594592 GGTCAGTTGCTTGGGCGT 60.595 61.111 0.00 0.00 42.25 5.68
210 211 1.069823 CAAGTGAGTCAGCAGGTCAGT 59.930 52.381 0.00 0.00 0.00 3.41
220 221 1.545428 GGCAATGGTCCAAGTGAGTCA 60.545 52.381 9.58 0.00 0.00 3.41
221 222 1.168714 GGCAATGGTCCAAGTGAGTC 58.831 55.000 9.58 0.00 0.00 3.36
278 279 8.034804 GGAAACACTTATAAATGGCTCATTTGT 58.965 33.333 18.02 15.04 42.91 2.83
287 288 5.955355 TGGGAAGGGAAACACTTATAAATGG 59.045 40.000 0.00 0.00 0.00 3.16
296 297 2.838637 TTGTTGGGAAGGGAAACACT 57.161 45.000 0.00 0.00 33.73 3.55
303 304 0.251742 TGGAGCATTGTTGGGAAGGG 60.252 55.000 0.00 0.00 0.00 3.95
345 346 2.492090 GGCGTGTTGGTTGCAACA 59.508 55.556 29.55 13.95 42.10 3.33
350 351 3.601685 GGGTGGGCGTGTTGGTTG 61.602 66.667 0.00 0.00 0.00 3.77
351 352 4.906537 GGGGTGGGCGTGTTGGTT 62.907 66.667 0.00 0.00 0.00 3.67
370 371 4.687215 GCAGCTCACGGCCACAGA 62.687 66.667 2.24 0.00 43.05 3.41
371 372 4.994471 TGCAGCTCACGGCCACAG 62.994 66.667 2.24 0.00 43.05 3.66
408 410 1.412710 GGATGGCGTCCTCTATGTTGA 59.587 52.381 18.69 0.00 44.16 3.18
428 430 2.271800 GTTGACGAGGAAGGTAGCATG 58.728 52.381 0.00 0.00 0.00 4.06
468 470 5.177725 ACAACCTTCACAAACGGATTTAC 57.822 39.130 0.00 0.00 0.00 2.01
471 473 3.445805 ACAACAACCTTCACAAACGGATT 59.554 39.130 0.00 0.00 0.00 3.01
474 476 2.931512 ACAACAACCTTCACAAACGG 57.068 45.000 0.00 0.00 0.00 4.44
475 477 3.366422 CCAAACAACAACCTTCACAAACG 59.634 43.478 0.00 0.00 0.00 3.60
485 487 0.248866 CTCGTGCCCAAACAACAACC 60.249 55.000 0.00 0.00 0.00 3.77
495 497 3.825160 GAGGTTGTGCTCGTGCCCA 62.825 63.158 7.05 0.00 38.71 5.36
497 499 1.639298 GATGAGGTTGTGCTCGTGCC 61.639 60.000 7.05 0.00 38.71 5.01
501 503 1.959899 GCGTGATGAGGTTGTGCTCG 61.960 60.000 0.00 0.00 0.00 5.03
521 523 1.730064 CACAAGGTTAACCGATGACCG 59.270 52.381 29.06 17.60 42.08 4.79
538 540 1.061546 GTTGACCTAAGGGACCCACA 58.938 55.000 14.60 0.00 36.25 4.17
568 570 2.277949 GCGATCTGCTGACGCGTA 60.278 61.111 13.97 0.00 42.65 4.42
577 579 4.819761 TGACCAGCGGCGATCTGC 62.820 66.667 12.98 0.00 44.91 4.26
578 580 2.107750 ATGACCAGCGGCGATCTG 59.892 61.111 12.98 9.57 0.00 2.90
580 582 3.643978 GCATGACCAGCGGCGATC 61.644 66.667 12.98 2.13 0.00 3.69
587 589 1.156645 CCTAAGCTCGCATGACCAGC 61.157 60.000 0.00 0.00 0.00 4.85
588 590 0.461548 TCCTAAGCTCGCATGACCAG 59.538 55.000 0.00 0.00 0.00 4.00
611 613 9.178758 AGGTTTCAAATGTAGGTTATTCATCTC 57.821 33.333 0.00 0.00 0.00 2.75
669 675 7.581213 TGAAACTATTGAAGGTGTGTCAATT 57.419 32.000 5.08 0.00 41.82 2.32
674 684 8.691661 AAACTATGAAACTATTGAAGGTGTGT 57.308 30.769 0.00 0.00 0.00 3.72
709 719 6.085849 CACGCGGTAAAATCAAAAGAGTAAAC 59.914 38.462 12.47 0.00 0.00 2.01
710 720 6.137415 CACGCGGTAAAATCAAAAGAGTAAA 58.863 36.000 12.47 0.00 0.00 2.01
711 721 5.236911 ACACGCGGTAAAATCAAAAGAGTAA 59.763 36.000 12.47 0.00 0.00 2.24
712 722 4.751098 ACACGCGGTAAAATCAAAAGAGTA 59.249 37.500 12.47 0.00 0.00 2.59
713 723 3.562557 ACACGCGGTAAAATCAAAAGAGT 59.437 39.130 12.47 0.00 0.00 3.24
714 724 4.141855 ACACGCGGTAAAATCAAAAGAG 57.858 40.909 12.47 0.00 0.00 2.85
715 725 4.751098 AGTACACGCGGTAAAATCAAAAGA 59.249 37.500 12.47 0.00 32.72 2.52
716 726 4.843984 CAGTACACGCGGTAAAATCAAAAG 59.156 41.667 12.47 0.00 32.72 2.27
808 830 2.892425 CGGTTCCTGCGAGGATGC 60.892 66.667 5.83 3.32 45.34 3.91
1244 1298 1.082104 CACGAAAAAGCCGCTGTCC 60.082 57.895 0.00 0.00 0.00 4.02
1557 1622 5.848833 TGGCATGCAACACAATATCATTA 57.151 34.783 21.36 0.00 0.00 1.90
1573 1638 1.452110 TCCGTTCTGTTCATGGCATG 58.548 50.000 21.42 21.42 0.00 4.06
1574 1639 1.812571 GTTCCGTTCTGTTCATGGCAT 59.187 47.619 0.00 0.00 0.00 4.40
1575 1640 1.234821 GTTCCGTTCTGTTCATGGCA 58.765 50.000 0.00 0.00 0.00 4.92
1577 1642 2.766313 TCTGTTCCGTTCTGTTCATGG 58.234 47.619 0.00 0.00 0.00 3.66
1578 1643 3.559655 TGTTCTGTTCCGTTCTGTTCATG 59.440 43.478 0.00 0.00 0.00 3.07
1581 1646 3.001330 CAGTGTTCTGTTCCGTTCTGTTC 59.999 47.826 0.00 0.00 36.97 3.18
1583 1648 2.550978 CAGTGTTCTGTTCCGTTCTGT 58.449 47.619 0.00 0.00 36.97 3.41
1685 1755 5.658634 ACCAAGAGTATGCATTAGAGACTCA 59.341 40.000 22.43 0.00 39.20 3.41
1687 1757 6.041069 GGTACCAAGAGTATGCATTAGAGACT 59.959 42.308 3.54 0.61 32.28 3.24
1729 1820 9.225436 GGGAGAATCTAGCTATTGAAAAATAGG 57.775 37.037 0.00 0.00 32.72 2.57
1831 1923 6.974622 GTCATGTTTTGGATTATTGCTACCAG 59.025 38.462 0.00 0.00 33.85 4.00
1873 1965 2.749076 GTCATGGCTCAATTGCACAGTA 59.251 45.455 0.00 0.00 34.04 2.74
1994 2119 3.770666 TCGAGTCAATTTAGAGGAAGCG 58.229 45.455 0.00 0.00 0.00 4.68
2207 2486 7.066284 CCCAACTAATAAAGAACACTGATGAGG 59.934 40.741 0.00 0.00 0.00 3.86
2386 2770 1.693627 TAAACCCAAAAGAGCGGCAA 58.306 45.000 1.45 0.00 0.00 4.52
2387 2771 1.917872 ATAAACCCAAAAGAGCGGCA 58.082 45.000 1.45 0.00 0.00 5.69
2964 3362 1.154338 GTGATGAGCAACTGCACGC 60.154 57.895 4.22 0.00 45.16 5.34
3102 3560 8.988934 CGTATCAAAGGCAAATAATTCTAGCTA 58.011 33.333 0.00 0.00 0.00 3.32
3127 3585 3.546020 GGATGCACGTGGAACATATTTCG 60.546 47.826 15.51 0.00 44.52 3.46
3221 3679 4.888326 AGCAGATCCAATGGAGTCTATC 57.112 45.455 8.40 0.00 34.05 2.08
3269 3727 1.654105 GTCCGTTGCACTTCACTATCG 59.346 52.381 0.00 0.00 0.00 2.92
3427 3893 1.236616 TTGCCATCAGAACCTGCACG 61.237 55.000 0.00 0.00 0.00 5.34
3698 4164 1.745087 GAAGCGCCATTCATCTTTCCA 59.255 47.619 2.29 0.00 0.00 3.53
3802 4268 1.953686 GCAAAGGCACTAAACAGACCA 59.046 47.619 0.00 0.00 38.49 4.02
3885 4352 3.760151 AGCAATCAAAGCTCAAGTGCATA 59.240 39.130 14.92 0.00 38.01 3.14
3910 4377 4.115516 AGACTATAACGTGAGCATGCTTG 58.884 43.478 23.61 16.95 0.00 4.01
3948 4415 6.088016 TCATTCATGAACAGGTTCCAAAAG 57.912 37.500 11.07 0.15 38.77 2.27
4038 4506 3.376234 GGCCCTCGAAACCATAACTAAAC 59.624 47.826 0.00 0.00 0.00 2.01
4043 4511 1.065709 TCAGGCCCTCGAAACCATAAC 60.066 52.381 0.00 0.00 0.00 1.89
4077 4545 6.491394 TCAACAAACAGCTAACAACATACAC 58.509 36.000 0.00 0.00 0.00 2.90
4154 4622 2.943033 GTTGCTAACCAGATAATGCGGT 59.057 45.455 0.00 0.00 33.32 5.68
4215 4686 2.866762 GTGTTTTCGAGCAGAAGAGTGT 59.133 45.455 0.00 0.00 40.40 3.55
4217 4688 3.460857 AGTGTTTTCGAGCAGAAGAGT 57.539 42.857 0.00 0.00 40.40 3.24
4228 4699 9.618410 GAAATGTGAAAAATGTAAGTGTTTTCG 57.382 29.630 0.00 0.00 41.86 3.46
4247 4719 1.608590 AGCCGTGAACAAGGAAATGTG 59.391 47.619 10.64 0.00 32.81 3.21
4248 4720 1.608590 CAGCCGTGAACAAGGAAATGT 59.391 47.619 10.64 0.00 34.24 2.71
4275 4747 2.093890 GGGATGTTGTGCACATGATGA 58.906 47.619 22.39 1.34 46.96 2.92
4301 4773 6.053005 ACTTCGTATGAACTCAAGGTGAAAA 58.947 36.000 0.00 0.00 0.00 2.29
4303 4775 5.209818 ACTTCGTATGAACTCAAGGTGAA 57.790 39.130 0.00 0.00 0.00 3.18
4304 4776 4.866508 ACTTCGTATGAACTCAAGGTGA 57.133 40.909 0.00 0.00 0.00 4.02
4305 4777 4.750098 ACAACTTCGTATGAACTCAAGGTG 59.250 41.667 0.00 0.00 37.11 4.00
4306 4778 4.957296 ACAACTTCGTATGAACTCAAGGT 58.043 39.130 0.00 0.00 0.00 3.50
4307 4779 5.465390 TGAACAACTTCGTATGAACTCAAGG 59.535 40.000 0.00 0.00 0.00 3.61
4308 4780 6.201044 AGTGAACAACTTCGTATGAACTCAAG 59.799 38.462 0.00 0.00 34.57 3.02
4309 4781 6.046593 AGTGAACAACTTCGTATGAACTCAA 58.953 36.000 0.00 0.00 34.57 3.02
4310 4782 5.597806 AGTGAACAACTTCGTATGAACTCA 58.402 37.500 0.00 0.00 34.57 3.41
4311 4783 7.201444 CCATAGTGAACAACTTCGTATGAACTC 60.201 40.741 0.00 0.00 40.56 3.01
4312 4784 6.590292 CCATAGTGAACAACTTCGTATGAACT 59.410 38.462 0.00 0.00 40.56 3.01
4313 4785 6.367969 ACCATAGTGAACAACTTCGTATGAAC 59.632 38.462 0.00 0.00 40.56 3.18
4320 4792 5.236478 ACAGAAACCATAGTGAACAACTTCG 59.764 40.000 0.00 0.00 40.56 3.79
4334 4806 6.294731 GCCTGAATAACAAAGACAGAAACCAT 60.295 38.462 0.00 0.00 0.00 3.55
4562 5102 9.093970 CATGGAACGACATAAGTTAAGAATACA 57.906 33.333 0.00 0.00 31.14 2.29
4831 5379 5.353938 GTGATGCAGCAAAATATGGTCATT 58.646 37.500 6.05 0.00 37.77 2.57
4962 5569 9.364989 TGAATTCAGAAAACGTTCTCAATTTTT 57.635 25.926 3.38 0.00 42.58 1.94
4969 5577 5.792468 GCTCATGAATTCAGAAAACGTTCTC 59.208 40.000 14.54 0.00 42.45 2.87
5034 5668 6.310224 CGCCGATTCAAGGAAATTGTTTAAAT 59.690 34.615 0.00 0.00 40.05 1.40
5047 5704 2.420022 AGAAATGTTCGCCGATTCAAGG 59.580 45.455 1.56 0.00 34.02 3.61
5133 5792 5.908916 TCGACACAATGTTCGTTAAATCA 57.091 34.783 14.13 0.00 0.00 2.57
5134 5793 7.012943 TGAATCGACACAATGTTCGTTAAATC 58.987 34.615 14.13 9.16 0.00 2.17
5135 5794 6.893759 TGAATCGACACAATGTTCGTTAAAT 58.106 32.000 14.13 2.77 0.00 1.40
5136 5795 6.288426 TGAATCGACACAATGTTCGTTAAA 57.712 33.333 14.13 1.02 0.00 1.52
5137 5796 5.908916 TGAATCGACACAATGTTCGTTAA 57.091 34.783 14.13 1.28 0.00 2.01
5138 5797 5.908916 TTGAATCGACACAATGTTCGTTA 57.091 34.783 14.13 1.81 0.00 3.18
5139 5798 4.804608 TTGAATCGACACAATGTTCGTT 57.195 36.364 14.13 9.74 0.00 3.85
5140 5799 4.711721 CATTGAATCGACACAATGTTCGT 58.288 39.130 25.26 0.00 44.43 3.85
5146 5805 8.592105 AAAAATGTTCATTGAATCGACACAAT 57.408 26.923 11.48 11.48 37.22 2.71
5204 5869 7.811653 TGTTCGTGACTTGCAAAATATATTCA 58.188 30.769 0.00 0.00 0.00 2.57
5205 5870 8.667987 TTGTTCGTGACTTGCAAAATATATTC 57.332 30.769 0.00 0.00 0.00 1.75
5206 5871 9.638239 AATTGTTCGTGACTTGCAAAATATATT 57.362 25.926 0.00 0.00 0.00 1.28
5207 5872 9.638239 AAATTGTTCGTGACTTGCAAAATATAT 57.362 25.926 0.00 0.00 0.00 0.86
5295 5978 7.271653 TCGCGTATTCAAAATGGTTAATGAAAC 59.728 33.333 5.77 0.00 35.62 2.78
5306 5989 8.429739 TTTAAGAAGTTCGCGTATTCAAAATG 57.570 30.769 5.77 0.00 0.00 2.32
5307 5990 9.620660 ATTTTAAGAAGTTCGCGTATTCAAAAT 57.379 25.926 5.77 13.51 0.00 1.82
5318 6001 9.722056 ATGTTCATGATATTTTAAGAAGTTCGC 57.278 29.630 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.