Multiple sequence alignment - TraesCS3B01G254600

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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 TraesCS3B01G254600 chr3B 100.000 4421 0 0 1 4421 410591970 410587550 0.000000e+00 8165.0
1 TraesCS3B01G254600 chr3B 81.226 261 33 7 3868 4114 1383272 1383530 3.490000e-46 196.0
2 TraesCS3B01G254600 chr3D 95.263 2660 64 9 582 3220 310707675 310710293 0.000000e+00 4157.0
3 TraesCS3B01G254600 chr3D 91.777 1204 64 12 3217 4420 310710451 310711619 0.000000e+00 1642.0
4 TraesCS3B01G254600 chr3D 77.749 382 66 13 3873 4237 374969001 374968622 2.680000e-52 217.0
5 TraesCS3B01G254600 chr3D 92.857 70 0 2 463 527 310707588 310707657 3.640000e-16 97.1
6 TraesCS3B01G254600 chr3A 94.621 2138 111 4 2081 4216 421675228 421673093 0.000000e+00 3308.0
7 TraesCS3B01G254600 chr3A 94.075 1654 50 12 463 2112 421677260 421675651 0.000000e+00 2468.0
8 TraesCS3B01G254600 chr3A 85.830 247 28 3 1 245 421678591 421678350 5.670000e-64 255.0
9 TraesCS3B01G254600 chr3A 96.850 127 4 0 249 375 421677388 421677262 3.460000e-51 213.0
10 TraesCS3B01G254600 chr3A 80.000 90 10 5 44 127 26582729 26582816 4.780000e-05 60.2
11 TraesCS3B01G254600 chr7D 78.697 568 90 21 3873 4420 135940747 135940191 2.530000e-92 350.0
12 TraesCS3B01G254600 chr7D 91.089 101 2 1 735 835 78265532 78265625 3.590000e-26 130.0
13 TraesCS3B01G254600 chr7D 90.099 101 3 1 735 835 78265332 78265425 1.670000e-24 124.0
14 TraesCS3B01G254600 chr6B 83.565 359 53 6 4062 4418 256448926 256449280 9.170000e-87 331.0
15 TraesCS3B01G254600 chr6B 97.531 81 2 0 378 458 132118059 132118139 5.960000e-29 139.0
16 TraesCS3B01G254600 chr6B 98.276 58 1 0 778 835 707282713 707282656 7.820000e-18 102.0
17 TraesCS3B01G254600 chr2B 77.807 383 59 21 3873 4237 2360416 2360042 3.460000e-51 213.0
18 TraesCS3B01G254600 chr2B 93.827 81 5 0 378 458 683157832 683157752 6.000000e-24 122.0
19 TraesCS3B01G254600 chr6D 97.500 80 2 0 379 458 443841351 443841272 2.140000e-28 137.0
20 TraesCS3B01G254600 chr6D 90.123 81 8 0 380 460 428986724 428986804 6.050000e-19 106.0
21 TraesCS3B01G254600 chr5B 97.500 80 2 0 379 458 688975018 688974939 2.140000e-28 137.0
22 TraesCS3B01G254600 chr5B 95.349 86 2 2 375 458 546101060 546101145 7.710000e-28 135.0
23 TraesCS3B01G254600 chr5B 93.671 79 5 0 380 458 522620764 522620842 7.770000e-23 119.0
24 TraesCS3B01G254600 chr1D 81.915 188 11 11 3873 4056 338540604 338540772 2.140000e-28 137.0
25 TraesCS3B01G254600 chr5A 93.902 82 4 1 378 458 545863154 545863235 6.000000e-24 122.0
26 TraesCS3B01G254600 chr1B 98.276 58 1 0 778 835 511441392 511441335 7.820000e-18 102.0
27 TraesCS3B01G254600 chr2D 92.647 68 5 0 381 448 170610983 170610916 1.010000e-16 99.0
28 TraesCS3B01G254600 chr2A 96.552 58 2 0 778 835 652295532 652295589 3.640000e-16 97.1
29 TraesCS3B01G254600 chr7A 96.429 56 2 0 780 835 701879678 701879733 4.710000e-15 93.5
30 TraesCS3B01G254600 chr4A 90.698 43 3 1 49 91 45374290 45374249 6.180000e-04 56.5


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 TraesCS3B01G254600 chr3B 410587550 410591970 4420 True 8165.000000 8165 100.000 1 4421 1 chr3B.!!$R1 4420
1 TraesCS3B01G254600 chr3D 310707588 310711619 4031 False 1965.366667 4157 93.299 463 4420 3 chr3D.!!$F1 3957
2 TraesCS3B01G254600 chr3A 421673093 421678591 5498 True 1561.000000 3308 92.844 1 4216 4 chr3A.!!$R1 4215
3 TraesCS3B01G254600 chr7D 135940191 135940747 556 True 350.000000 350 78.697 3873 4420 1 chr7D.!!$R1 547

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
409 1370 0.044855 ACCATCCAGGACTAGCCCTT 59.955 55.0 0.00 0.00 41.22 3.95 F
413 1374 0.325671 TCCAGGACTAGCCCTTGGAG 60.326 60.0 10.74 0.00 37.37 3.86 F
453 1414 0.543410 TTCTCTAAGCACCCGGGTCA 60.543 55.0 27.51 8.48 0.00 4.02 F
2108 3550 0.380378 GCGTGCTGGACAACTTGAAA 59.620 50.0 0.00 0.00 0.00 2.69 F
2566 4008 0.508641 CAGACGCCGAGTTTGACTTG 59.491 55.0 0.00 0.00 37.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 2378 0.454452 GAAATTGCGACCGAGTTGCC 60.454 55.000 12.07 0.0 41.86 4.52 R
2108 3550 0.533755 GCGCCCTGACAGCATAATCT 60.534 55.000 0.00 0.0 0.00 2.40 R
2426 3868 8.614469 TGAGAAATACATGTTTGTATCACACA 57.386 30.769 2.30 0.0 46.10 3.72 R
3313 4918 0.400213 TGGATTTGACGCCCTCTTGT 59.600 50.000 0.00 0.0 0.00 3.16 R
4116 5734 0.178981 GCACCATGGATGCCACCTAT 60.179 55.000 21.47 0.0 35.80 2.57 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
78 79 4.120331 GGCATGCAACTGGCCGAC 62.120 66.667 21.36 0.00 43.89 4.79
83 84 3.670377 GCAACTGGCCGACAACCC 61.670 66.667 0.00 0.00 36.11 4.11
84 85 2.983592 CAACTGGCCGACAACCCC 60.984 66.667 0.00 0.00 0.00 4.95
85 86 4.280019 AACTGGCCGACAACCCCC 62.280 66.667 0.00 0.00 0.00 5.40
102 103 2.203351 CCTCCCGGCCCTAATTGC 60.203 66.667 0.00 0.00 0.00 3.56
106 107 1.823899 CCCGGCCCTAATTGCAGTC 60.824 63.158 0.00 0.00 0.00 3.51
108 109 0.394352 CCGGCCCTAATTGCAGTCTT 60.394 55.000 0.00 0.00 0.00 3.01
114 115 4.213482 GGCCCTAATTGCAGTCTTATTACG 59.787 45.833 0.00 0.00 0.00 3.18
117 118 5.454187 CCCTAATTGCAGTCTTATTACGGGA 60.454 44.000 12.61 0.00 31.20 5.14
121 122 3.202906 TGCAGTCTTATTACGGGAATGC 58.797 45.455 7.50 7.50 46.63 3.56
127 128 4.634443 GTCTTATTACGGGAATGCAGTTGT 59.366 41.667 0.00 0.00 0.00 3.32
128 129 4.634004 TCTTATTACGGGAATGCAGTTGTG 59.366 41.667 0.00 0.00 0.00 3.33
130 131 1.803334 TACGGGAATGCAGTTGTGTC 58.197 50.000 0.00 0.00 0.00 3.67
133 136 1.135603 CGGGAATGCAGTTGTGTCATG 60.136 52.381 0.00 0.00 0.00 3.07
137 140 1.999648 ATGCAGTTGTGTCATGGGTT 58.000 45.000 0.00 0.00 0.00 4.11
170 173 4.459337 CAGAGACAAAAATAGGTTGGACCC 59.541 45.833 0.00 0.00 39.75 4.46
184 187 3.417069 TGGACCCAGTTACATGTTGAG 57.583 47.619 2.30 0.00 0.00 3.02
199 202 1.067060 GTTGAGGGTGAAGTTGCAACC 59.933 52.381 25.62 11.10 46.24 3.77
236 239 0.107848 CGGTCCCCAGTTGTGTATCC 60.108 60.000 0.00 0.00 0.00 2.59
239 242 1.906574 GTCCCCAGTTGTGTATCCTGA 59.093 52.381 0.00 0.00 0.00 3.86
301 1262 4.720046 TGTCAAGGCCATAACTTGTTACA 58.280 39.130 5.01 0.00 44.29 2.41
355 1316 1.068816 GGTACCAACGCACCAAACATC 60.069 52.381 7.15 0.00 34.77 3.06
357 1318 0.951558 ACCAACGCACCAAACATCTC 59.048 50.000 0.00 0.00 0.00 2.75
375 1336 0.528017 TCGCAACCAAACAGCAACAA 59.472 45.000 0.00 0.00 0.00 2.83
376 1337 0.644843 CGCAACCAAACAGCAACAAC 59.355 50.000 0.00 0.00 0.00 3.32
377 1338 1.719600 GCAACCAAACAGCAACAACA 58.280 45.000 0.00 0.00 0.00 3.33
378 1339 2.072298 GCAACCAAACAGCAACAACAA 58.928 42.857 0.00 0.00 0.00 2.83
379 1340 2.481952 GCAACCAAACAGCAACAACAAA 59.518 40.909 0.00 0.00 0.00 2.83
380 1341 3.058639 GCAACCAAACAGCAACAACAAAA 60.059 39.130 0.00 0.00 0.00 2.44
381 1342 4.555511 GCAACCAAACAGCAACAACAAAAA 60.556 37.500 0.00 0.00 0.00 1.94
402 1363 4.664688 AAAAATGAGACCATCCAGGACT 57.335 40.909 0.00 0.00 45.32 3.85
403 1364 5.779241 AAAAATGAGACCATCCAGGACTA 57.221 39.130 0.00 0.00 42.62 2.59
404 1365 5.365021 AAAATGAGACCATCCAGGACTAG 57.635 43.478 0.00 0.00 42.62 2.57
405 1366 1.781786 TGAGACCATCCAGGACTAGC 58.218 55.000 0.00 0.00 42.62 3.42
406 1367 1.044611 GAGACCATCCAGGACTAGCC 58.955 60.000 0.00 0.00 42.62 3.93
407 1368 0.399233 AGACCATCCAGGACTAGCCC 60.399 60.000 0.00 0.00 40.73 5.19
408 1369 0.399233 GACCATCCAGGACTAGCCCT 60.399 60.000 0.00 0.00 41.22 5.19
409 1370 0.044855 ACCATCCAGGACTAGCCCTT 59.955 55.000 0.00 0.00 41.22 3.95
410 1371 0.471617 CCATCCAGGACTAGCCCTTG 59.528 60.000 0.00 0.00 41.22 3.61
411 1372 0.471617 CATCCAGGACTAGCCCTTGG 59.528 60.000 0.00 1.00 37.37 3.61
412 1373 0.343372 ATCCAGGACTAGCCCTTGGA 59.657 55.000 15.20 15.20 37.66 3.53
413 1374 0.325671 TCCAGGACTAGCCCTTGGAG 60.326 60.000 10.74 0.00 37.37 3.86
414 1375 1.341156 CCAGGACTAGCCCTTGGAGG 61.341 65.000 0.00 0.00 37.37 4.30
415 1376 0.618968 CAGGACTAGCCCTTGGAGGT 60.619 60.000 0.00 0.00 37.37 3.85
416 1377 1.016415 AGGACTAGCCCTTGGAGGTA 58.984 55.000 0.00 0.00 37.37 3.08
417 1378 1.581149 AGGACTAGCCCTTGGAGGTAT 59.419 52.381 0.00 0.00 37.37 2.73
418 1379 2.795960 AGGACTAGCCCTTGGAGGTATA 59.204 50.000 0.00 0.00 37.37 1.47
419 1380 3.406498 AGGACTAGCCCTTGGAGGTATAT 59.594 47.826 0.00 0.00 37.37 0.86
420 1381 4.140423 AGGACTAGCCCTTGGAGGTATATT 60.140 45.833 0.00 0.00 37.37 1.28
421 1382 4.597940 GGACTAGCCCTTGGAGGTATATTT 59.402 45.833 0.00 0.00 31.93 1.40
422 1383 5.073280 GGACTAGCCCTTGGAGGTATATTTT 59.927 44.000 0.00 0.00 31.93 1.82
423 1384 6.410504 GGACTAGCCCTTGGAGGTATATTTTT 60.411 42.308 0.00 0.00 31.93 1.94
424 1385 7.202158 GGACTAGCCCTTGGAGGTATATTTTTA 60.202 40.741 0.00 0.00 31.93 1.52
425 1386 7.515586 ACTAGCCCTTGGAGGTATATTTTTAC 58.484 38.462 0.00 0.00 31.93 2.01
426 1387 6.335781 AGCCCTTGGAGGTATATTTTTACA 57.664 37.500 0.00 0.00 31.93 2.41
427 1388 6.365520 AGCCCTTGGAGGTATATTTTTACAG 58.634 40.000 0.00 0.00 31.93 2.74
428 1389 6.159751 AGCCCTTGGAGGTATATTTTTACAGA 59.840 38.462 0.00 0.00 31.93 3.41
429 1390 6.831868 GCCCTTGGAGGTATATTTTTACAGAA 59.168 38.462 0.00 0.00 31.93 3.02
430 1391 7.013369 GCCCTTGGAGGTATATTTTTACAGAAG 59.987 40.741 0.00 0.00 31.93 2.85
431 1392 8.272173 CCCTTGGAGGTATATTTTTACAGAAGA 58.728 37.037 0.00 0.00 31.93 2.87
432 1393 9.681062 CCTTGGAGGTATATTTTTACAGAAGAA 57.319 33.333 0.00 0.00 0.00 2.52
446 1407 7.907214 TTACAGAAGAAATTCTCTAAGCACC 57.093 36.000 0.00 0.00 32.46 5.01
447 1408 5.249420 ACAGAAGAAATTCTCTAAGCACCC 58.751 41.667 0.00 0.00 32.46 4.61
448 1409 4.331168 CAGAAGAAATTCTCTAAGCACCCG 59.669 45.833 0.00 0.00 32.46 5.28
449 1410 3.268023 AGAAATTCTCTAAGCACCCGG 57.732 47.619 0.00 0.00 30.22 5.73
450 1411 2.092914 AGAAATTCTCTAAGCACCCGGG 60.093 50.000 22.25 22.25 30.22 5.73
451 1412 1.286248 AATTCTCTAAGCACCCGGGT 58.714 50.000 24.16 24.16 0.00 5.28
452 1413 0.831307 ATTCTCTAAGCACCCGGGTC 59.169 55.000 27.51 18.95 0.00 4.46
453 1414 0.543410 TTCTCTAAGCACCCGGGTCA 60.543 55.000 27.51 8.48 0.00 4.02
454 1415 1.218316 CTCTAAGCACCCGGGTCAC 59.782 63.158 27.51 19.85 0.00 3.67
455 1416 2.240162 CTCTAAGCACCCGGGTCACC 62.240 65.000 27.51 15.54 0.00 4.02
456 1417 2.203877 TAAGCACCCGGGTCACCT 60.204 61.111 27.51 17.78 33.28 4.00
457 1418 2.240162 CTAAGCACCCGGGTCACCTC 62.240 65.000 27.51 10.70 33.28 3.85
458 1419 2.741878 TAAGCACCCGGGTCACCTCT 62.742 60.000 27.51 12.98 33.28 3.69
459 1420 4.394712 GCACCCGGGTCACCTCTG 62.395 72.222 27.51 12.49 33.28 3.35
460 1421 2.603473 CACCCGGGTCACCTCTGA 60.603 66.667 27.51 0.00 33.28 3.27
461 1422 2.203182 ACCCGGGTCACCTCTGAA 59.797 61.111 24.16 0.00 33.28 3.02
566 1532 3.290948 ACTAGCTCCCACAAAACACAA 57.709 42.857 0.00 0.00 0.00 3.33
579 1545 4.881850 ACAAAACACAACCGAGAGAGATTT 59.118 37.500 0.00 0.00 0.00 2.17
726 1693 2.892334 CGACTGGCAACCAACACGG 61.892 63.158 0.00 0.00 42.50 4.94
770 1737 2.681778 CACCCTCACCTCCTCGCT 60.682 66.667 0.00 0.00 0.00 4.93
771 1738 2.363147 ACCCTCACCTCCTCGCTC 60.363 66.667 0.00 0.00 0.00 5.03
772 1739 3.522731 CCCTCACCTCCTCGCTCG 61.523 72.222 0.00 0.00 0.00 5.03
773 1740 4.200283 CCTCACCTCCTCGCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
774 1741 3.137459 CTCACCTCCTCGCTCGCT 61.137 66.667 0.00 0.00 0.00 4.93
775 1742 3.408501 CTCACCTCCTCGCTCGCTG 62.409 68.421 0.00 0.00 0.00 5.18
776 1743 4.504916 CACCTCCTCGCTCGCTGG 62.505 72.222 0.00 0.00 0.00 4.85
1361 2328 5.120519 GCAGAAGCATATGTGAGCTATTCTC 59.879 44.000 4.29 0.00 40.90 2.87
1399 2366 5.338632 TCCCAGTTCTACCACTCAATTCTA 58.661 41.667 0.00 0.00 0.00 2.10
1490 2457 1.544724 TTACTTGATGTTGCCAGCCC 58.455 50.000 0.00 0.00 0.00 5.19
1603 2590 1.895020 TTTGCGCCCATCTACCGACT 61.895 55.000 4.18 0.00 0.00 4.18
1671 2658 1.355720 AGGTGTGGAGGCTTAAATGCT 59.644 47.619 0.00 0.00 0.00 3.79
1820 2807 3.496884 TCCAAATTGTGCAACTACTCGAC 59.503 43.478 0.00 0.00 38.04 4.20
1863 2853 1.537135 GCTCAGAATCGTCCACCTAGC 60.537 57.143 0.00 0.00 0.00 3.42
1882 2872 7.121168 CACCTAGCAATAAGAATTTCTTGGTCA 59.879 37.037 19.60 2.28 40.46 4.02
1929 2919 6.529829 TGTTAATTTTAGTTGAATGGATGCGC 59.470 34.615 0.00 0.00 0.00 6.09
1998 2988 7.669722 TCTGTAAATATGGAAGAACAAAAGGCT 59.330 33.333 0.00 0.00 0.00 4.58
2017 3007 2.477525 GCTGCATCAAGTTTCTGCTAGC 60.478 50.000 8.10 8.10 36.84 3.42
2027 3017 3.260380 AGTTTCTGCTAGCTGATCACTGT 59.740 43.478 24.51 10.89 0.00 3.55
2028 3018 2.955477 TCTGCTAGCTGATCACTGTG 57.045 50.000 19.26 0.17 0.00 3.66
2047 3037 3.070018 GTGCAGAAGTAGAACATGCAGT 58.930 45.455 0.00 0.00 46.63 4.40
2108 3550 0.380378 GCGTGCTGGACAACTTGAAA 59.620 50.000 0.00 0.00 0.00 2.69
2426 3868 7.120923 ACATTACATCGTACCAAGTAAGGAT 57.879 36.000 7.15 0.00 33.80 3.24
2479 3921 7.915397 CCCAAGAAACGATTATCACCTAATTTG 59.085 37.037 0.00 0.00 29.93 2.32
2506 3948 6.249035 TGTTAAATTTTCCCTGAACTAGCG 57.751 37.500 0.00 0.00 0.00 4.26
2566 4008 0.508641 CAGACGCCGAGTTTGACTTG 59.491 55.000 0.00 0.00 37.14 3.16
2622 4064 1.200716 CTTCTGTGCGCACATTTGGAT 59.799 47.619 40.50 0.00 41.01 3.41
2623 4065 1.246649 TCTGTGCGCACATTTGGATT 58.753 45.000 40.50 0.00 41.01 3.01
2665 4107 7.851822 AGTGTACTAATGCAAAATGTTTTCG 57.148 32.000 0.00 0.00 0.00 3.46
2780 4222 4.202367 ACGTCCATTTTTCTCCACTCTTCT 60.202 41.667 0.00 0.00 0.00 2.85
2841 4283 2.490509 CCATGGGGAAACGAAAACTACC 59.509 50.000 2.85 0.00 35.59 3.18
2859 4301 0.749454 CCAAGCCTACATCCAGTGGC 60.749 60.000 3.51 0.00 41.68 5.01
2928 4370 6.276847 CCCAGTTGTGTGTTTTGCTTTTATA 58.723 36.000 0.00 0.00 0.00 0.98
3313 4918 4.584327 TCATTCAGTTCTCTCGACAACA 57.416 40.909 0.00 0.00 0.00 3.33
3435 5040 2.548057 TCGTTGATCAACTGCAAACCTC 59.452 45.455 30.45 6.22 39.08 3.85
3483 5088 5.168526 TGAAGTACATGCAACAAACTCAC 57.831 39.130 0.00 0.00 0.00 3.51
3491 5096 3.023119 TGCAACAAACTCACTCCACATT 58.977 40.909 0.00 0.00 0.00 2.71
3691 5296 3.156293 TGCATATGGGTATGTCAATGGC 58.844 45.455 4.56 0.00 39.90 4.40
3739 5344 6.462073 TCATAAAGCGTGTCTGTAAAGAAC 57.538 37.500 0.00 0.00 0.00 3.01
3780 5385 5.868454 TCTCCTTGAATGAATGTTCACAGA 58.132 37.500 0.00 0.00 40.49 3.41
3789 5394 8.415553 TGAATGAATGTTCACAGATCTTTTTGT 58.584 29.630 0.00 0.00 40.49 2.83
3802 5407 8.352942 ACAGATCTTTTTGTGTGGAAAACTATC 58.647 33.333 0.00 0.00 0.00 2.08
3811 5416 1.339631 TGGAAAACTATCGCCACTGGG 60.340 52.381 0.00 0.00 37.18 4.45
3830 5435 3.153919 GGGTTTTCAGGCATACTCACAA 58.846 45.455 0.00 0.00 0.00 3.33
3952 5567 1.262640 GCCTTCCTCCCACTTACCGA 61.263 60.000 0.00 0.00 0.00 4.69
3955 5570 0.115745 TTCCTCCCACTTACCGACCT 59.884 55.000 0.00 0.00 0.00 3.85
3956 5571 0.115745 TCCTCCCACTTACCGACCTT 59.884 55.000 0.00 0.00 0.00 3.50
3961 5576 1.290955 CACTTACCGACCTTGCCGA 59.709 57.895 0.00 0.00 0.00 5.54
3972 5587 3.925630 CTTGCCGATGCCACAGGGT 62.926 63.158 0.00 0.00 36.33 4.34
4129 5747 0.908910 ACGACAATAGGTGGCATCCA 59.091 50.000 0.00 0.00 33.13 3.41
4140 5758 0.615261 TGGCATCCATGGTGCATTGT 60.615 50.000 28.69 3.28 44.25 2.71
4142 5760 0.533491 GCATCCATGGTGCATTGTGT 59.467 50.000 25.24 0.00 42.08 3.72
4176 5794 3.437795 GTGCTTGCCGCTGCTCAT 61.438 61.111 0.70 0.00 40.11 2.90
4185 5803 0.813184 CCGCTGCTCATGACCAAATT 59.187 50.000 0.00 0.00 0.00 1.82
4256 5874 3.141488 CGCTGCGGGTCCTAGACT 61.141 66.667 15.40 0.00 32.47 3.24
4343 5961 3.246880 GTCCCGGGAAGGTGGTGT 61.247 66.667 28.84 0.00 38.74 4.16
4371 5989 2.435938 TGGCGGCGATGAACCTTC 60.436 61.111 12.98 0.00 0.00 3.46
4420 6038 4.492160 GACTCATGGGCGACGCGA 62.492 66.667 15.93 4.30 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.265467 GACTGCAATTAGGGCCGGGA 62.265 60.000 2.18 0.00 0.00 5.14
92 93 4.213482 CCGTAATAAGACTGCAATTAGGGC 59.787 45.833 11.77 0.00 35.52 5.19
95 96 7.576236 CATTCCCGTAATAAGACTGCAATTAG 58.424 38.462 0.00 0.00 0.00 1.73
98 99 4.275936 GCATTCCCGTAATAAGACTGCAAT 59.724 41.667 0.00 0.00 36.52 3.56
102 103 4.442706 ACTGCATTCCCGTAATAAGACTG 58.557 43.478 0.00 0.00 0.00 3.51
106 107 4.394920 ACACAACTGCATTCCCGTAATAAG 59.605 41.667 0.00 0.00 0.00 1.73
108 109 3.936453 GACACAACTGCATTCCCGTAATA 59.064 43.478 0.00 0.00 0.00 0.98
114 115 1.203052 CCATGACACAACTGCATTCCC 59.797 52.381 0.00 0.00 0.00 3.97
117 118 1.999648 ACCCATGACACAACTGCATT 58.000 45.000 0.00 0.00 0.00 3.56
130 131 4.023707 GTCTCTGTTTCAAGTCAACCCATG 60.024 45.833 0.00 0.00 0.00 3.66
133 136 3.541632 TGTCTCTGTTTCAAGTCAACCC 58.458 45.455 0.00 0.00 0.00 4.11
137 140 7.556275 ACCTATTTTTGTCTCTGTTTCAAGTCA 59.444 33.333 0.00 0.00 0.00 3.41
148 151 4.105697 TGGGTCCAACCTATTTTTGTCTCT 59.894 41.667 0.00 0.00 38.64 3.10
170 173 4.389374 ACTTCACCCTCAACATGTAACTG 58.611 43.478 0.00 0.00 0.00 3.16
184 187 2.561037 CCCGGTTGCAACTTCACCC 61.561 63.158 27.64 10.34 0.00 4.61
258 1219 8.718102 TGACATGTACTAAAAGGAGAATTAGC 57.282 34.615 0.00 0.00 33.39 3.09
301 1262 4.319139 TGCTGTACATTGCAATTTGTGT 57.681 36.364 9.83 8.97 36.15 3.72
355 1316 0.100325 TGTTGCTGTTTGGTTGCGAG 59.900 50.000 0.00 0.00 0.00 5.03
357 1318 0.644843 GTTGTTGCTGTTTGGTTGCG 59.355 50.000 0.00 0.00 0.00 4.85
381 1342 4.664688 AGTCCTGGATGGTCTCATTTTT 57.335 40.909 0.00 0.00 37.07 1.94
382 1343 4.384647 GCTAGTCCTGGATGGTCTCATTTT 60.385 45.833 0.00 0.00 35.81 1.82
383 1344 3.135530 GCTAGTCCTGGATGGTCTCATTT 59.864 47.826 0.00 0.00 35.81 2.32
384 1345 2.703007 GCTAGTCCTGGATGGTCTCATT 59.297 50.000 0.00 0.00 35.81 2.57
385 1346 2.324541 GCTAGTCCTGGATGGTCTCAT 58.675 52.381 0.00 0.00 35.81 2.90
386 1347 1.689575 GGCTAGTCCTGGATGGTCTCA 60.690 57.143 0.00 0.00 35.81 3.27
387 1348 1.044611 GGCTAGTCCTGGATGGTCTC 58.955 60.000 0.00 0.00 35.81 3.36
388 1349 0.399233 GGGCTAGTCCTGGATGGTCT 60.399 60.000 5.99 0.00 37.87 3.85
389 1350 0.399233 AGGGCTAGTCCTGGATGGTC 60.399 60.000 17.14 0.00 35.47 4.02
390 1351 0.044855 AAGGGCTAGTCCTGGATGGT 59.955 55.000 18.80 0.00 37.20 3.55
391 1352 0.471617 CAAGGGCTAGTCCTGGATGG 59.528 60.000 18.80 0.60 37.20 3.51
392 1353 0.471617 CCAAGGGCTAGTCCTGGATG 59.528 60.000 20.22 12.81 37.20 3.51
393 1354 0.343372 TCCAAGGGCTAGTCCTGGAT 59.657 55.000 20.22 0.00 37.20 3.41
394 1355 0.325671 CTCCAAGGGCTAGTCCTGGA 60.326 60.000 20.22 22.84 37.20 3.86
395 1356 1.341156 CCTCCAAGGGCTAGTCCTGG 61.341 65.000 18.80 19.59 37.20 4.45
396 1357 0.618968 ACCTCCAAGGGCTAGTCCTG 60.619 60.000 18.80 11.09 40.58 3.86
397 1358 1.016415 TACCTCCAAGGGCTAGTCCT 58.984 55.000 11.08 11.08 40.58 3.85
398 1359 2.104669 ATACCTCCAAGGGCTAGTCC 57.895 55.000 4.79 4.79 40.58 3.85
399 1360 5.827326 AAATATACCTCCAAGGGCTAGTC 57.173 43.478 0.00 0.00 40.58 2.59
400 1361 6.592207 AAAAATATACCTCCAAGGGCTAGT 57.408 37.500 0.00 0.00 40.58 2.57
401 1362 7.514721 TGTAAAAATATACCTCCAAGGGCTAG 58.485 38.462 0.00 0.00 40.58 3.42
402 1363 7.348801 TCTGTAAAAATATACCTCCAAGGGCTA 59.651 37.037 0.00 0.00 40.58 3.93
403 1364 6.159751 TCTGTAAAAATATACCTCCAAGGGCT 59.840 38.462 0.00 0.00 40.58 5.19
404 1365 6.362248 TCTGTAAAAATATACCTCCAAGGGC 58.638 40.000 0.00 0.00 40.58 5.19
405 1366 8.272173 TCTTCTGTAAAAATATACCTCCAAGGG 58.728 37.037 0.00 0.00 40.58 3.95
406 1367 9.681062 TTCTTCTGTAAAAATATACCTCCAAGG 57.319 33.333 0.00 0.00 42.49 3.61
420 1381 8.784043 GGTGCTTAGAGAATTTCTTCTGTAAAA 58.216 33.333 0.00 0.00 43.02 1.52
421 1382 7.390718 GGGTGCTTAGAGAATTTCTTCTGTAAA 59.609 37.037 0.00 0.00 43.02 2.01
422 1383 6.879458 GGGTGCTTAGAGAATTTCTTCTGTAA 59.121 38.462 0.00 5.26 42.05 2.41
423 1384 6.407202 GGGTGCTTAGAGAATTTCTTCTGTA 58.593 40.000 0.00 0.00 41.87 2.74
424 1385 5.249420 GGGTGCTTAGAGAATTTCTTCTGT 58.751 41.667 0.00 0.00 41.87 3.41
425 1386 4.331168 CGGGTGCTTAGAGAATTTCTTCTG 59.669 45.833 0.00 0.00 41.87 3.02
426 1387 4.508662 CGGGTGCTTAGAGAATTTCTTCT 58.491 43.478 0.00 2.61 44.53 2.85
427 1388 3.623510 CCGGGTGCTTAGAGAATTTCTTC 59.376 47.826 0.00 0.00 37.36 2.87
428 1389 3.610911 CCGGGTGCTTAGAGAATTTCTT 58.389 45.455 0.00 0.00 37.36 2.52
429 1390 2.092914 CCCGGGTGCTTAGAGAATTTCT 60.093 50.000 14.18 0.00 40.06 2.52
430 1391 2.289565 CCCGGGTGCTTAGAGAATTTC 58.710 52.381 14.18 0.00 0.00 2.17
431 1392 1.633945 ACCCGGGTGCTTAGAGAATTT 59.366 47.619 29.69 0.00 0.00 1.82
432 1393 1.209747 GACCCGGGTGCTTAGAGAATT 59.790 52.381 36.01 0.00 0.00 2.17
433 1394 0.831307 GACCCGGGTGCTTAGAGAAT 59.169 55.000 36.01 0.00 0.00 2.40
434 1395 0.543410 TGACCCGGGTGCTTAGAGAA 60.543 55.000 36.01 1.36 0.00 2.87
435 1396 1.077805 TGACCCGGGTGCTTAGAGA 59.922 57.895 36.01 2.55 0.00 3.10
436 1397 1.218316 GTGACCCGGGTGCTTAGAG 59.782 63.158 36.01 0.00 0.00 2.43
437 1398 2.288025 GGTGACCCGGGTGCTTAGA 61.288 63.158 36.01 4.20 0.00 2.10
438 1399 2.240162 GAGGTGACCCGGGTGCTTAG 62.240 65.000 36.01 0.00 35.12 2.18
439 1400 2.203877 AGGTGACCCGGGTGCTTA 60.204 61.111 36.01 12.00 35.12 3.09
440 1401 3.637273 GAGGTGACCCGGGTGCTT 61.637 66.667 36.01 20.37 35.12 3.91
441 1402 4.640690 AGAGGTGACCCGGGTGCT 62.641 66.667 36.01 16.96 35.12 4.40
442 1403 4.394712 CAGAGGTGACCCGGGTGC 62.395 72.222 36.01 23.41 35.12 5.01
443 1404 2.214216 TTCAGAGGTGACCCGGGTG 61.214 63.158 36.01 15.64 35.12 4.61
444 1405 2.203182 TTCAGAGGTGACCCGGGT 59.797 61.111 30.81 30.81 35.12 5.28
445 1406 2.663196 GTTCAGAGGTGACCCGGG 59.337 66.667 22.25 22.25 35.12 5.73
446 1407 1.764571 TTGGTTCAGAGGTGACCCGG 61.765 60.000 0.00 0.00 38.11 5.73
447 1408 0.320771 CTTGGTTCAGAGGTGACCCG 60.321 60.000 0.00 0.00 38.11 5.28
448 1409 0.765510 ACTTGGTTCAGAGGTGACCC 59.234 55.000 0.00 0.00 35.78 4.46
449 1410 1.884235 CACTTGGTTCAGAGGTGACC 58.116 55.000 0.00 0.00 30.10 4.02
450 1411 1.230324 GCACTTGGTTCAGAGGTGAC 58.770 55.000 0.00 0.00 30.10 3.67
451 1412 0.836606 TGCACTTGGTTCAGAGGTGA 59.163 50.000 0.00 0.00 0.00 4.02
452 1413 1.202687 TCTGCACTTGGTTCAGAGGTG 60.203 52.381 0.00 0.00 31.60 4.00
453 1414 1.071385 CTCTGCACTTGGTTCAGAGGT 59.929 52.381 15.76 0.00 45.34 3.85
454 1415 1.805869 CTCTGCACTTGGTTCAGAGG 58.194 55.000 15.76 2.57 45.34 3.69
456 1417 1.070758 GTCCTCTGCACTTGGTTCAGA 59.929 52.381 0.86 0.86 33.88 3.27
457 1418 1.517242 GTCCTCTGCACTTGGTTCAG 58.483 55.000 0.00 0.00 0.00 3.02
458 1419 0.249868 CGTCCTCTGCACTTGGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
459 1420 0.033504 TCGTCCTCTGCACTTGGTTC 59.966 55.000 0.00 0.00 0.00 3.62
460 1421 0.034059 CTCGTCCTCTGCACTTGGTT 59.966 55.000 0.00 0.00 0.00 3.67
461 1422 1.668294 CTCGTCCTCTGCACTTGGT 59.332 57.895 0.00 0.00 0.00 3.67
566 1532 1.817209 GCGGGAAATCTCTCTCGGT 59.183 57.895 0.00 0.00 0.00 4.69
579 1545 0.321298 CCTCTTTTTCCTTCGCGGGA 60.321 55.000 6.13 2.32 0.00 5.14
959 1926 4.430765 CGTCGGTGGGAACGGGAG 62.431 72.222 0.00 0.00 0.00 4.30
1361 2328 1.519455 GGGAATCGCAGTGGAGACG 60.519 63.158 0.00 0.00 0.00 4.18
1411 2378 0.454452 GAAATTGCGACCGAGTTGCC 60.454 55.000 12.07 0.00 41.86 4.52
1589 2576 2.557490 CCTAGTTAGTCGGTAGATGGGC 59.443 54.545 0.00 0.00 0.00 5.36
1603 2590 7.180229 TGTCCTTGATTTGTCTGATCCTAGTTA 59.820 37.037 0.00 0.00 0.00 2.24
1671 2658 7.718334 TGATTAATTCTCTAGTGGTGTCTCA 57.282 36.000 0.00 0.00 0.00 3.27
1766 2753 2.933906 CTCAGGCGACGGCTTAAAATAA 59.066 45.455 22.67 0.79 35.88 1.40
1925 2915 1.820906 GATGCAGAAGATGGGCGCA 60.821 57.895 10.83 5.70 36.95 6.09
1929 2919 2.562635 CAGTCAGATGCAGAAGATGGG 58.437 52.381 0.00 0.00 0.00 4.00
1998 2988 2.745821 CAGCTAGCAGAAACTTGATGCA 59.254 45.455 18.83 0.00 42.45 3.96
2017 3007 4.446994 TCTACTTCTGCACAGTGATCAG 57.553 45.455 4.15 3.17 0.00 2.90
2027 3017 3.069289 CACTGCATGTTCTACTTCTGCA 58.931 45.455 0.00 0.00 40.29 4.41
2028 3018 3.329386 TCACTGCATGTTCTACTTCTGC 58.671 45.455 0.00 0.00 0.00 4.26
2047 3037 5.409520 CGAAAAATGATCAGACAACCTCTCA 59.590 40.000 0.09 0.00 0.00 3.27
2108 3550 0.533755 GCGCCCTGACAGCATAATCT 60.534 55.000 0.00 0.00 0.00 2.40
2426 3868 8.614469 TGAGAAATACATGTTTGTATCACACA 57.386 30.769 2.30 0.00 46.10 3.72
2479 3921 7.808381 GCTAGTTCAGGGAAAATTTAACAAGTC 59.192 37.037 0.00 0.00 0.00 3.01
2495 3937 2.515996 TTTCCCGCCGCTAGTTCAGG 62.516 60.000 0.00 0.00 0.00 3.86
2506 3948 1.270041 TGCATTCTTTTGTTTCCCGCC 60.270 47.619 0.00 0.00 0.00 6.13
2566 4008 4.445019 CCTGAGGGATAAGGTTTAGGCTTC 60.445 50.000 0.00 0.00 33.58 3.86
2622 4064 9.073475 AGTACACTAAGTATTTGGCATCAAAAA 57.927 29.630 0.00 0.00 44.83 1.94
2623 4065 8.630054 AGTACACTAAGTATTTGGCATCAAAA 57.370 30.769 0.00 0.00 44.83 2.44
2780 4222 7.072263 ACAACAAATCAAATACCCCATTTCA 57.928 32.000 0.00 0.00 34.49 2.69
2841 4283 1.091771 CGCCACTGGATGTAGGCTTG 61.092 60.000 0.00 0.00 39.24 4.01
2941 4383 8.128322 TGCAAAAATCTGCCTAAATAGGTAAA 57.872 30.769 8.24 0.00 45.42 2.01
3313 4918 0.400213 TGGATTTGACGCCCTCTTGT 59.600 50.000 0.00 0.00 0.00 3.16
3435 5040 2.335712 GCGGGAAGGAGCAAACTGG 61.336 63.158 0.00 0.00 0.00 4.00
3448 5053 3.727258 CTTCATGGTGGGGCGGGA 61.727 66.667 0.00 0.00 0.00 5.14
3491 5096 8.887036 ACACGATGCAAATAGTCATATAAGAA 57.113 30.769 0.00 0.00 0.00 2.52
3513 5118 8.776470 GTCTATCTCTAGACCACTAACATACAC 58.224 40.741 2.06 0.00 45.51 2.90
3548 5153 9.419297 CATCAATTTATAGATGAAAAGGGCATG 57.581 33.333 0.00 0.00 43.28 4.06
3739 5344 5.178797 AGGAGATACAAATCTTCGGTTGTG 58.821 41.667 0.00 0.00 41.99 3.33
3780 5385 6.149633 GCGATAGTTTTCCACACAAAAAGAT 58.850 36.000 0.00 0.00 39.35 2.40
3802 5407 2.919494 GCCTGAAAACCCAGTGGCG 61.919 63.158 2.61 0.00 33.59 5.69
3811 5416 5.689383 TCTTTGTGAGTATGCCTGAAAAC 57.311 39.130 0.00 0.00 0.00 2.43
3830 5435 7.168302 CGTCGCTCTCAACTGAATAATAATCTT 59.832 37.037 0.00 0.00 0.00 2.40
3900 5505 1.309006 GTTCCCTCCCCGTCTCCTA 59.691 63.158 0.00 0.00 0.00 2.94
3952 5567 2.360350 CTGTGGCATCGGCAAGGT 60.360 61.111 0.00 0.00 43.71 3.50
3955 5570 3.965258 ACCCTGTGGCATCGGCAA 61.965 61.111 0.00 0.00 43.71 4.52
3956 5571 4.720902 CACCCTGTGGCATCGGCA 62.721 66.667 0.00 0.00 43.71 5.69
4116 5734 0.178981 GCACCATGGATGCCACCTAT 60.179 55.000 21.47 0.00 35.80 2.57
4140 5758 2.115910 CCCCTCCAGCAAGCAACA 59.884 61.111 0.00 0.00 0.00 3.33
4185 5803 1.302383 CCAAATACACTCCGCGCCAA 61.302 55.000 0.00 0.00 0.00 4.52
4194 5812 3.496131 CGCGCCGCCAAATACACT 61.496 61.111 2.28 0.00 0.00 3.55
4256 5874 4.920112 CGACCAACCGCCACCACA 62.920 66.667 0.00 0.00 0.00 4.17
4305 5923 2.723746 CAACAGTGGCCAGCACAC 59.276 61.111 5.11 0.00 39.10 3.82
4315 5933 1.377202 CCCGGGACATCCAACAGTG 60.377 63.158 18.48 0.00 37.91 3.66
4316 5934 1.131303 TTCCCGGGACATCCAACAGT 61.131 55.000 26.87 0.00 37.91 3.55
4320 5938 1.540367 ACCTTCCCGGGACATCCAA 60.540 57.895 26.87 6.37 37.91 3.53
4371 5989 4.320456 CCCCCGATGCAGATCCGG 62.320 72.222 11.23 11.23 42.64 5.14


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

AutoCloner maintained by Alex Coulton.