Multiple sequence alignment - TraesCS4D01G132600

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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 TraesCS4D01G132600 chr4D 100.000 6584 0 0 1 6584 119411913 119405330 0.000000e+00 12159.0
1 TraesCS4D01G132600 chr4A 97.371 2206 43 6 2298 4489 449817724 449815520 0.000000e+00 3738.0
2 TraesCS4D01G132600 chr4A 95.652 2116 47 13 4485 6583 449815438 449813351 0.000000e+00 3356.0
3 TraesCS4D01G132600 chr4A 92.662 1608 56 28 711 2294 449819414 449817845 0.000000e+00 2259.0
4 TraesCS4D01G132600 chr4A 100.000 129 0 0 588 716 449820276 449820148 8.530000e-59 239.0
5 TraesCS4D01G132600 chr4A 79.848 263 16 13 1 259 449889787 449889558 2.460000e-34 158.0
6 TraesCS4D01G132600 chr4A 90.526 95 9 0 363 457 449889465 449889371 6.930000e-25 126.0
7 TraesCS4D01G132600 chr4A 88.158 76 2 5 258 333 449889526 449889458 4.230000e-12 84.2
8 TraesCS4D01G132600 chr4B 97.591 2159 39 6 2342 4489 181690178 181688022 0.000000e+00 3687.0
9 TraesCS4D01G132600 chr4B 96.056 2003 33 13 4485 6483 181687940 181685980 0.000000e+00 3219.0
10 TraesCS4D01G132600 chr4B 95.312 1728 39 11 583 2294 181692021 181690320 0.000000e+00 2704.0
11 TraesCS4D01G132600 chr4B 92.116 482 15 7 1 471 181692825 181692356 0.000000e+00 658.0
12 TraesCS4D01G132600 chr4B 97.368 38 1 0 2297 2334 181690203 181690240 1.530000e-06 65.8
13 TraesCS4D01G132600 chr3A 82.663 646 100 9 5435 6076 186846071 186845434 4.460000e-156 562.0
14 TraesCS4D01G132600 chr3A 85.742 519 68 5 2365 2880 186848732 186848217 1.610000e-150 544.0
15 TraesCS4D01G132600 chr3A 91.324 219 19 0 3028 3246 186848218 186848000 3.860000e-77 300.0
16 TraesCS4D01G132600 chr3A 86.466 266 25 7 4613 4877 186846664 186846409 1.400000e-71 281.0
17 TraesCS4D01G132600 chr3B 82.481 645 103 8 5435 6076 237292012 237291375 2.070000e-154 556.0
18 TraesCS4D01G132600 chr3B 85.192 520 70 6 2364 2880 237294685 237294170 1.630000e-145 527.0
19 TraesCS4D01G132600 chr3B 86.525 282 24 7 4613 4893 237292607 237292339 1.390000e-76 298.0
20 TraesCS4D01G132600 chr3B 90.868 219 20 0 3028 3246 237294171 237293953 1.800000e-75 294.0
21 TraesCS4D01G132600 chr3D 82.353 646 102 9 5435 6076 160613209 160612572 9.650000e-153 551.0
22 TraesCS4D01G132600 chr3D 85.207 507 67 7 2378 2880 160615856 160615354 1.270000e-141 514.0
23 TraesCS4D01G132600 chr3D 91.324 219 19 0 3028 3246 160615355 160615137 3.860000e-77 300.0
24 TraesCS4D01G132600 chr3D 86.466 266 25 7 4613 4877 160613802 160613547 1.400000e-71 281.0
25 TraesCS4D01G132600 chr1A 87.446 231 17 3 5865 6093 566584952 566584732 8.470000e-64 255.0
26 TraesCS4D01G132600 chr1A 89.820 167 7 8 6165 6327 566584728 566584568 8.650000e-49 206.0
27 TraesCS4D01G132600 chr1B 88.679 212 9 9 6088 6294 657280588 657280387 1.830000e-60 244.0
28 TraesCS4D01G132600 chrUn 100.000 28 0 0 2307 2334 94184206 94184179 1.200000e-02 52.8


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 TraesCS4D01G132600 chr4D 119405330 119411913 6583 True 12159.00 12159 100.00000 1 6584 1 chr4D.!!$R1 6583
1 TraesCS4D01G132600 chr4A 449813351 449820276 6925 True 2398.00 3738 96.42125 588 6583 4 chr4A.!!$R1 5995
2 TraesCS4D01G132600 chr4B 181685980 181692825 6845 True 2567.00 3687 95.26875 1 6483 4 chr4B.!!$R1 6482
3 TraesCS4D01G132600 chr3A 186845434 186848732 3298 True 421.75 562 86.54875 2365 6076 4 chr3A.!!$R1 3711
4 TraesCS4D01G132600 chr3B 237291375 237294685 3310 True 418.75 556 86.26650 2364 6076 4 chr3B.!!$R1 3712
5 TraesCS4D01G132600 chr3D 160612572 160615856 3284 True 411.50 551 86.33750 2378 6076 4 chr3D.!!$R1 3698


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
556 568 0.038166 TGCTGAAGACCACCATTCCC 59.962 55.000 0.00 0.0 0.00 3.97 F
561 573 0.178975 AAGACCACCATTCCCGCAAA 60.179 50.000 0.00 0.0 0.00 3.68 F
826 1800 0.193069 CCTCAGATCCAGATCCCCCT 59.807 60.000 4.01 0.0 38.58 4.79 F
1100 2087 0.381089 CCGTGCGCTTAGTAGTAGCT 59.619 55.000 9.73 0.0 36.49 3.32 F
1527 2519 0.893270 CCACCAACAATCCCTTCGCA 60.893 55.000 0.00 0.0 0.00 5.10 F
1925 2917 0.899019 AACTTTGGCGGTGGTTTGTT 59.101 45.000 0.00 0.0 0.00 2.83 F
2340 3459 1.042229 TATTATGGGACGGTCGTGGG 58.958 55.000 0.00 0.0 0.00 4.61 F
3963 5102 1.015609 TCACTGGAGGTGGAGGGATA 58.984 55.000 0.00 0.0 45.38 2.59 F
5001 6445 3.304257 CCGAGCAGAACATTATCAATGGC 60.304 47.826 4.09 0.0 43.21 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2955 2.808244 ACAAATGTGTTCCAAGTTGCG 58.192 42.857 0.0 0.0 32.58 4.85 R
2335 3454 3.429207 ACGAAACAAAACAAAAACCCACG 59.571 39.130 0.0 0.0 0.00 4.94 R
2338 3457 4.142859 GGGAACGAAACAAAACAAAAACCC 60.143 41.667 0.0 0.0 0.00 4.11 R
2861 3988 3.933332 CCTACCGAATGGAGAAGTTTGTC 59.067 47.826 0.0 0.0 39.21 3.18 R
3439 4566 4.555262 ACAAGCAACAAAATAATGGGACG 58.445 39.130 0.0 0.0 0.00 4.79 R
3652 4779 0.446616 GATGAAAACGGGTTCGGAGC 59.553 55.000 0.0 0.0 41.39 4.70 R
4130 5273 2.093869 CAGGGGCAGATTGTTGAAATGG 60.094 50.000 0.0 0.0 0.00 3.16 R
5559 7004 1.442769 CACCCATCTTCTCAACGGTG 58.557 55.000 0.0 0.0 35.24 4.94 R
6134 7586 0.389948 CAGACCAGCTACCGACCAAC 60.390 60.000 0.0 0.0 0.00 3.77 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
33 34 3.988976 AGCTAGATTGGCAGAAAGTCA 57.011 42.857 0.00 0.00 0.00 3.41
35 36 4.260170 AGCTAGATTGGCAGAAAGTCAAG 58.740 43.478 0.00 0.00 46.51 3.02
41 42 1.214175 TGGCAGAAAGTCAAGGGTTGA 59.786 47.619 0.00 0.00 37.33 3.18
84 85 2.557924 TCCATGTGTTTGATGTTCTGCC 59.442 45.455 0.00 0.00 0.00 4.85
101 102 3.119459 TCTGCCGCTAACAAACAAACAAA 60.119 39.130 0.00 0.00 0.00 2.83
102 103 3.585862 TGCCGCTAACAAACAAACAAAA 58.414 36.364 0.00 0.00 0.00 2.44
103 104 3.368236 TGCCGCTAACAAACAAACAAAAC 59.632 39.130 0.00 0.00 0.00 2.43
104 105 3.368236 GCCGCTAACAAACAAACAAAACA 59.632 39.130 0.00 0.00 0.00 2.83
105 106 4.143094 GCCGCTAACAAACAAACAAAACAA 60.143 37.500 0.00 0.00 0.00 2.83
106 107 5.546434 CCGCTAACAAACAAACAAAACAAG 58.454 37.500 0.00 0.00 0.00 3.16
107 108 5.012613 CGCTAACAAACAAACAAAACAAGC 58.987 37.500 0.00 0.00 0.00 4.01
108 109 5.388890 CGCTAACAAACAAACAAAACAAGCA 60.389 36.000 0.00 0.00 0.00 3.91
109 110 6.014898 GCTAACAAACAAACAAAACAAGCAG 58.985 36.000 0.00 0.00 0.00 4.24
113 114 2.620242 ACAAACAAAACAAGCAGGCAG 58.380 42.857 0.00 0.00 0.00 4.85
186 187 5.509832 AAGGATTTAAGGGTTACCGTTCT 57.490 39.130 12.88 1.13 43.47 3.01
187 188 5.509832 AGGATTTAAGGGTTACCGTTCTT 57.490 39.130 12.88 4.71 43.47 2.52
188 189 5.494724 AGGATTTAAGGGTTACCGTTCTTC 58.505 41.667 12.88 8.42 43.47 2.87
249 250 1.153549 GCTACAGCTTAGGCGCACT 60.154 57.895 10.83 6.69 44.37 4.40
263 264 3.569210 CACTGCCACCCTCCACCA 61.569 66.667 0.00 0.00 0.00 4.17
264 265 2.776526 ACTGCCACCCTCCACCAA 60.777 61.111 0.00 0.00 0.00 3.67
266 267 3.099841 TGCCACCCTCCACCAACA 61.100 61.111 0.00 0.00 0.00 3.33
268 269 2.281484 CCACCCTCCACCAACACG 60.281 66.667 0.00 0.00 0.00 4.49
366 378 1.751351 TGAAGCACTCCTCTATGTCCG 59.249 52.381 0.00 0.00 0.00 4.79
482 494 2.629763 GCGACGGCGTTCAGTTTT 59.370 55.556 16.19 0.00 40.36 2.43
483 495 1.010462 GCGACGGCGTTCAGTTTTT 60.010 52.632 16.19 0.00 40.36 1.94
503 515 4.563404 TTTTTGAGGGAACGGCGT 57.437 50.000 6.77 6.77 0.00 5.68
504 516 2.796500 TTTTTGAGGGAACGGCGTT 58.204 47.368 27.15 27.15 0.00 4.84
505 517 0.664224 TTTTTGAGGGAACGGCGTTC 59.336 50.000 37.30 37.30 41.32 3.95
506 518 0.464013 TTTTGAGGGAACGGCGTTCA 60.464 50.000 42.13 27.24 43.54 3.18
507 519 0.882927 TTTGAGGGAACGGCGTTCAG 60.883 55.000 42.13 4.88 43.54 3.02
508 520 2.434359 GAGGGAACGGCGTTCAGG 60.434 66.667 42.13 4.09 43.54 3.86
509 521 3.236003 GAGGGAACGGCGTTCAGGT 62.236 63.158 42.13 29.91 43.54 4.00
510 522 1.880819 GAGGGAACGGCGTTCAGGTA 61.881 60.000 42.13 0.00 43.54 3.08
511 523 1.004679 GGGAACGGCGTTCAGGTAA 60.005 57.895 42.13 0.00 43.54 2.85
512 524 1.293963 GGGAACGGCGTTCAGGTAAC 61.294 60.000 42.13 28.08 43.54 2.50
528 540 2.488153 GGTAACTGAAGACCACCAATGC 59.512 50.000 0.00 0.00 35.65 3.56
529 541 2.664402 AACTGAAGACCACCAATGCT 57.336 45.000 0.00 0.00 0.00 3.79
530 542 3.788227 AACTGAAGACCACCAATGCTA 57.212 42.857 0.00 0.00 0.00 3.49
531 543 3.788227 ACTGAAGACCACCAATGCTAA 57.212 42.857 0.00 0.00 0.00 3.09
532 544 4.307032 ACTGAAGACCACCAATGCTAAT 57.693 40.909 0.00 0.00 0.00 1.73
533 545 4.012374 ACTGAAGACCACCAATGCTAATG 58.988 43.478 0.00 0.00 0.00 1.90
534 546 2.754552 TGAAGACCACCAATGCTAATGC 59.245 45.455 0.00 0.00 40.20 3.56
535 547 2.814805 AGACCACCAATGCTAATGCT 57.185 45.000 0.00 0.00 40.48 3.79
536 548 2.372264 AGACCACCAATGCTAATGCTG 58.628 47.619 0.00 0.00 40.48 4.41
537 549 2.094675 GACCACCAATGCTAATGCTGT 58.905 47.619 0.00 0.00 40.48 4.40
538 550 1.820519 ACCACCAATGCTAATGCTGTG 59.179 47.619 0.00 0.00 40.48 3.66
539 551 1.470285 CCACCAATGCTAATGCTGTGC 60.470 52.381 0.00 0.00 40.48 4.57
540 552 1.475280 CACCAATGCTAATGCTGTGCT 59.525 47.619 0.00 0.00 40.48 4.40
541 553 1.475280 ACCAATGCTAATGCTGTGCTG 59.525 47.619 0.00 0.00 40.48 4.41
542 554 1.746787 CCAATGCTAATGCTGTGCTGA 59.253 47.619 0.00 0.00 40.48 4.26
543 555 2.164827 CCAATGCTAATGCTGTGCTGAA 59.835 45.455 0.00 0.00 40.48 3.02
544 556 3.435566 CAATGCTAATGCTGTGCTGAAG 58.564 45.455 0.00 0.00 40.48 3.02
545 557 2.477845 TGCTAATGCTGTGCTGAAGA 57.522 45.000 0.00 0.00 40.48 2.87
546 558 2.079158 TGCTAATGCTGTGCTGAAGAC 58.921 47.619 0.00 0.00 40.48 3.01
547 559 1.399791 GCTAATGCTGTGCTGAAGACC 59.600 52.381 0.00 0.00 36.03 3.85
548 560 2.703416 CTAATGCTGTGCTGAAGACCA 58.297 47.619 0.00 0.00 0.00 4.02
549 561 1.242076 AATGCTGTGCTGAAGACCAC 58.758 50.000 0.00 0.00 0.00 4.16
550 562 0.607489 ATGCTGTGCTGAAGACCACC 60.607 55.000 0.00 0.00 0.00 4.61
551 563 1.227943 GCTGTGCTGAAGACCACCA 60.228 57.895 0.00 0.00 0.00 4.17
552 564 0.607489 GCTGTGCTGAAGACCACCAT 60.607 55.000 0.00 0.00 0.00 3.55
553 565 1.901591 CTGTGCTGAAGACCACCATT 58.098 50.000 0.00 0.00 0.00 3.16
554 566 1.808945 CTGTGCTGAAGACCACCATTC 59.191 52.381 0.00 0.00 0.00 2.67
555 567 1.168714 GTGCTGAAGACCACCATTCC 58.831 55.000 0.00 0.00 0.00 3.01
556 568 0.038166 TGCTGAAGACCACCATTCCC 59.962 55.000 0.00 0.00 0.00 3.97
557 569 1.026718 GCTGAAGACCACCATTCCCG 61.027 60.000 0.00 0.00 0.00 5.14
558 570 1.002624 TGAAGACCACCATTCCCGC 60.003 57.895 0.00 0.00 0.00 6.13
559 571 1.002624 GAAGACCACCATTCCCGCA 60.003 57.895 0.00 0.00 0.00 5.69
560 572 0.608035 GAAGACCACCATTCCCGCAA 60.608 55.000 0.00 0.00 0.00 4.85
561 573 0.178975 AAGACCACCATTCCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
562 574 0.893727 AGACCACCATTCCCGCAAAC 60.894 55.000 0.00 0.00 0.00 2.93
563 575 1.873270 GACCACCATTCCCGCAAACC 61.873 60.000 0.00 0.00 0.00 3.27
564 576 2.566010 CACCATTCCCGCAAACCG 59.434 61.111 0.00 0.00 0.00 4.44
565 577 2.114411 ACCATTCCCGCAAACCGT 59.886 55.556 0.00 0.00 34.38 4.83
566 578 2.265182 ACCATTCCCGCAAACCGTG 61.265 57.895 0.00 0.00 34.38 4.94
577 589 2.331809 CAAACCGTGCTTTTAGGAGC 57.668 50.000 0.00 0.00 43.00 4.70
578 590 1.068541 CAAACCGTGCTTTTAGGAGCC 60.069 52.381 0.00 0.00 42.01 4.70
579 591 0.608308 AACCGTGCTTTTAGGAGCCC 60.608 55.000 0.00 0.00 42.01 5.19
580 592 1.002624 CCGTGCTTTTAGGAGCCCA 60.003 57.895 0.00 0.00 42.01 5.36
581 593 1.026718 CCGTGCTTTTAGGAGCCCAG 61.027 60.000 0.00 0.00 42.01 4.45
822 1796 0.686224 CCAGCCTCAGATCCAGATCC 59.314 60.000 4.01 0.00 38.58 3.36
823 1797 0.686224 CAGCCTCAGATCCAGATCCC 59.314 60.000 4.01 0.00 38.58 3.85
824 1798 0.473501 AGCCTCAGATCCAGATCCCC 60.474 60.000 4.01 0.00 38.58 4.81
825 1799 1.487850 GCCTCAGATCCAGATCCCCC 61.488 65.000 4.01 0.00 38.58 5.40
826 1800 0.193069 CCTCAGATCCAGATCCCCCT 59.807 60.000 4.01 0.00 38.58 4.79
864 1838 4.845387 TCGATTATCTTTTCGTCTCCTCG 58.155 43.478 0.00 0.00 36.74 4.63
877 1851 1.000060 TCTCCTCGTAAACCAACACCG 60.000 52.381 0.00 0.00 0.00 4.94
1100 2087 0.381089 CCGTGCGCTTAGTAGTAGCT 59.619 55.000 9.73 0.00 36.49 3.32
1217 2208 6.144854 CCCATTTGATGATGCGTTACTAATG 58.855 40.000 0.00 0.00 0.00 1.90
1241 2232 1.282248 TGCTTTCGCGCTACAGTGTC 61.282 55.000 5.56 0.00 39.65 3.67
1242 2233 1.009389 GCTTTCGCGCTACAGTGTCT 61.009 55.000 5.56 0.00 0.00 3.41
1258 2249 6.957631 ACAGTGTCTATAAACCATCCATCAA 58.042 36.000 0.00 0.00 0.00 2.57
1259 2250 7.402054 ACAGTGTCTATAAACCATCCATCAAA 58.598 34.615 0.00 0.00 0.00 2.69
1260 2251 7.888021 ACAGTGTCTATAAACCATCCATCAAAA 59.112 33.333 0.00 0.00 0.00 2.44
1261 2252 8.739039 CAGTGTCTATAAACCATCCATCAAAAA 58.261 33.333 0.00 0.00 0.00 1.94
1333 2324 4.621034 GCGGATTTCAGTTACCATTGTTTG 59.379 41.667 0.00 0.00 0.00 2.93
1337 2328 7.375053 GGATTTCAGTTACCATTGTTTGCTTA 58.625 34.615 0.00 0.00 0.00 3.09
1338 2329 8.034804 GGATTTCAGTTACCATTGTTTGCTTAT 58.965 33.333 0.00 0.00 0.00 1.73
1361 2352 9.998106 TTATATACTCTTCCAGTTTTGCCTATC 57.002 33.333 0.00 0.00 36.43 2.08
1527 2519 0.893270 CCACCAACAATCCCTTCGCA 60.893 55.000 0.00 0.00 0.00 5.10
1809 2801 2.676121 TTTGGCCAGCCATCCACG 60.676 61.111 13.10 0.00 46.64 4.94
1925 2917 0.899019 AACTTTGGCGGTGGTTTGTT 59.101 45.000 0.00 0.00 0.00 2.83
1926 2918 0.899019 ACTTTGGCGGTGGTTTGTTT 59.101 45.000 0.00 0.00 0.00 2.83
1963 2955 7.820648 TCTCAGCATTTAATTTCTGTTCTTCC 58.179 34.615 0.00 0.00 0.00 3.46
2148 3140 8.997621 TTTTAGGTTGTGTTATCTAGCACTAG 57.002 34.615 5.90 0.00 38.12 2.57
2294 3296 8.993424 AGACTTGAAATACTGTCACCCTATAAT 58.007 33.333 0.00 0.00 32.41 1.28
2296 3298 8.768397 ACTTGAAATACTGTCACCCTATAATCA 58.232 33.333 0.00 0.00 0.00 2.57
2334 3453 7.989947 ATAACATCCTATATTATGGGACGGT 57.010 36.000 10.65 4.54 43.12 4.83
2335 3454 5.934402 ACATCCTATATTATGGGACGGTC 57.066 43.478 10.65 0.00 43.12 4.79
2337 3456 4.038271 TCCTATATTATGGGACGGTCGT 57.962 45.455 4.74 0.00 34.71 4.34
2338 3457 3.760151 TCCTATATTATGGGACGGTCGTG 59.240 47.826 4.74 0.00 34.71 4.35
2340 3459 1.042229 TATTATGGGACGGTCGTGGG 58.958 55.000 0.00 0.00 0.00 4.61
2359 3483 5.375717 GTGGGTTTTTGTTTTGTTTCGTTC 58.624 37.500 0.00 0.00 0.00 3.95
2861 3988 2.364972 ACAACTTCACCCTTTGGAGG 57.635 50.000 0.00 0.00 43.15 4.30
3011 4138 9.534565 TGTAACTGCAGATTATCTTATCAGTTC 57.465 33.333 23.35 18.96 38.60 3.01
3343 4470 9.753674 AATGGTTCTTATTTTCTATGAACTGGA 57.246 29.630 0.00 0.00 37.66 3.86
3963 5102 1.015609 TCACTGGAGGTGGAGGGATA 58.984 55.000 0.00 0.00 45.38 2.59
4130 5273 8.694394 GTTGATCTTTGCTCATTTTTAAGTCAC 58.306 33.333 0.00 0.00 0.00 3.67
4205 5351 5.892119 CCTCAGACTCAACCAGGTTAGTATA 59.108 44.000 3.89 0.00 0.00 1.47
4239 5556 9.077885 ACTTAATGCTTCCTTCTCATTAACAAA 57.922 29.630 0.00 0.00 37.59 2.83
4811 6255 7.066645 GCCGGTTAGTATTTTCTTTACCATCTT 59.933 37.037 1.90 0.00 0.00 2.40
4812 6256 8.953313 CCGGTTAGTATTTTCTTTACCATCTTT 58.047 33.333 0.00 0.00 0.00 2.52
4880 6324 6.302269 AGATGAGCAAGGAGGGTATTATTTG 58.698 40.000 0.00 0.00 0.00 2.32
5001 6445 3.304257 CCGAGCAGAACATTATCAATGGC 60.304 47.826 4.09 0.00 43.21 4.40
5380 6825 9.832445 TGTTTAGAACTGTCTGTATTCTTTCTT 57.168 29.630 0.00 0.00 34.55 2.52
5559 7004 1.996786 CTCGGCATGTGAATGGTGCC 61.997 60.000 5.57 5.57 41.84 5.01
5574 7019 0.798776 GTGCCACCGTTGAGAAGATG 59.201 55.000 0.00 0.00 0.00 2.90
6080 7525 2.488153 GCCGATTCCTTGTAGCTTTGTT 59.512 45.455 0.00 0.00 0.00 2.83
6084 7536 5.584649 CCGATTCCTTGTAGCTTTGTTGATA 59.415 40.000 0.00 0.00 0.00 2.15
6085 7537 6.238211 CCGATTCCTTGTAGCTTTGTTGATAG 60.238 42.308 0.00 0.00 0.00 2.08
6086 7538 6.238211 CGATTCCTTGTAGCTTTGTTGATAGG 60.238 42.308 0.00 0.00 0.00 2.57
6087 7539 5.499004 TCCTTGTAGCTTTGTTGATAGGT 57.501 39.130 0.00 0.00 0.00 3.08
6088 7540 5.245531 TCCTTGTAGCTTTGTTGATAGGTG 58.754 41.667 0.00 0.00 0.00 4.00
6089 7541 4.142600 CCTTGTAGCTTTGTTGATAGGTGC 60.143 45.833 0.00 0.00 0.00 5.01
6090 7542 4.286297 TGTAGCTTTGTTGATAGGTGCT 57.714 40.909 0.00 0.00 0.00 4.40
6134 7586 2.120232 GACACTCGATTCCATGTAGCG 58.880 52.381 0.00 0.00 0.00 4.26
6228 7692 7.056635 CCTTCCCATGTTCTTCTGTACATATT 58.943 38.462 0.00 0.00 33.41 1.28
6366 7830 3.036091 CCTGGATGGAATGCATCCTTTT 58.964 45.455 29.35 0.00 46.12 2.27
6367 7831 3.181469 CCTGGATGGAATGCATCCTTTTG 60.181 47.826 29.35 17.90 46.12 2.44
6368 7832 3.181469 CTGGATGGAATGCATCCTTTTGG 60.181 47.826 29.35 13.54 46.12 3.28
6369 7833 6.772769 CTGGATGGAATGCATCCTTTTGGC 62.773 50.000 29.35 6.64 46.12 4.52
6371 7835 2.304751 GGAATGCATCCTTTTGGCAG 57.695 50.000 0.00 0.00 45.56 4.85
6372 7836 1.551883 GGAATGCATCCTTTTGGCAGT 59.448 47.619 0.00 0.00 45.56 4.40
6373 7837 2.027837 GGAATGCATCCTTTTGGCAGTT 60.028 45.455 0.00 0.00 45.56 3.16
6374 7838 3.557686 GGAATGCATCCTTTTGGCAGTTT 60.558 43.478 0.00 0.00 45.56 2.66
6375 7839 4.322650 GGAATGCATCCTTTTGGCAGTTTA 60.323 41.667 0.00 0.00 45.56 2.01
6457 7933 4.635765 TGATTAGCCAAGTGTCATAACAGC 59.364 41.667 0.00 0.00 35.64 4.40
6519 7995 4.192317 ACCTCTGCTCGGAATTAATTGTC 58.808 43.478 5.17 0.00 0.00 3.18
6528 8004 3.778718 CGGAATTAATTGTCGCTCAAACG 59.221 43.478 5.17 0.00 39.62 3.60
6534 8010 2.661504 TTGTCGCTCAAACGAATGTG 57.338 45.000 0.00 0.00 44.93 3.21
6583 8059 3.056322 GGCATTTCTGGCATTTCACTCTT 60.056 43.478 0.00 0.00 46.77 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.751806 ACTTTCTGCCAATCTAGCTTGC 59.248 45.455 0.59 0.00 0.00 4.01
11 12 4.005650 TGACTTTCTGCCAATCTAGCTTG 58.994 43.478 0.00 0.00 0.00 4.01
14 15 3.376546 CCTTGACTTTCTGCCAATCTAGC 59.623 47.826 0.00 0.00 0.00 3.42
22 23 1.981256 TCAACCCTTGACTTTCTGCC 58.019 50.000 0.00 0.00 34.08 4.85
26 27 6.151648 TGAATCATGATCAACCCTTGACTTTC 59.848 38.462 9.06 1.52 43.48 2.62
84 85 5.012613 GCTTGTTTTGTTTGTTTGTTAGCG 58.987 37.500 0.00 0.00 0.00 4.26
101 102 0.319405 GAATTGCCTGCCTGCTTGTT 59.681 50.000 0.00 0.00 0.00 2.83
102 103 0.828762 TGAATTGCCTGCCTGCTTGT 60.829 50.000 0.00 0.00 0.00 3.16
103 104 0.108804 CTGAATTGCCTGCCTGCTTG 60.109 55.000 0.00 0.00 0.00 4.01
104 105 0.541296 ACTGAATTGCCTGCCTGCTT 60.541 50.000 0.00 0.00 0.00 3.91
105 106 0.541296 AACTGAATTGCCTGCCTGCT 60.541 50.000 0.00 0.00 0.00 4.24
106 107 0.319405 AAACTGAATTGCCTGCCTGC 59.681 50.000 0.00 0.00 0.00 4.85
107 108 1.401931 CGAAACTGAATTGCCTGCCTG 60.402 52.381 0.00 0.00 0.00 4.85
108 109 0.883833 CGAAACTGAATTGCCTGCCT 59.116 50.000 0.00 0.00 0.00 4.75
109 110 0.598065 ACGAAACTGAATTGCCTGCC 59.402 50.000 0.00 0.00 0.00 4.85
113 114 3.049912 GTCCAAACGAAACTGAATTGCC 58.950 45.455 0.00 0.00 0.00 4.52
159 160 4.397103 CGGTAACCCTTAAATCCTTTGACC 59.603 45.833 0.00 0.00 0.00 4.02
249 250 3.099841 TGTTGGTGGAGGGTGGCA 61.100 61.111 0.00 0.00 0.00 4.92
260 261 2.031163 GGAGAGCTGCGTGTTGGT 59.969 61.111 0.00 0.00 0.00 3.67
261 262 1.739562 GAGGAGAGCTGCGTGTTGG 60.740 63.158 0.00 0.00 0.00 3.77
263 264 1.882989 GAGGAGGAGAGCTGCGTGTT 61.883 60.000 0.00 0.00 0.00 3.32
264 265 2.283532 AGGAGGAGAGCTGCGTGT 60.284 61.111 0.00 0.00 0.00 4.49
266 267 1.752694 GAGAGGAGGAGAGCTGCGT 60.753 63.158 0.00 0.00 0.00 5.24
268 269 1.076044 AGGAGAGGAGGAGAGCTGC 60.076 63.158 0.00 0.00 0.00 5.25
389 401 2.825836 GGGCTCTGATTGGTGCCG 60.826 66.667 0.00 0.00 45.75 5.69
486 498 0.664224 GAACGCCGTTCCCTCAAAAA 59.336 50.000 18.88 0.00 36.65 1.94
487 499 0.464013 TGAACGCCGTTCCCTCAAAA 60.464 50.000 25.56 3.70 41.35 2.44
488 500 0.882927 CTGAACGCCGTTCCCTCAAA 60.883 55.000 25.56 6.40 41.35 2.69
489 501 1.301401 CTGAACGCCGTTCCCTCAA 60.301 57.895 25.56 7.12 41.35 3.02
490 502 2.342279 CTGAACGCCGTTCCCTCA 59.658 61.111 25.56 8.30 41.35 3.86
491 503 1.880819 TACCTGAACGCCGTTCCCTC 61.881 60.000 25.56 3.50 41.35 4.30
492 504 1.474332 TTACCTGAACGCCGTTCCCT 61.474 55.000 25.56 11.19 41.35 4.20
493 505 1.004679 TTACCTGAACGCCGTTCCC 60.005 57.895 25.56 4.60 41.35 3.97
494 506 0.320160 AGTTACCTGAACGCCGTTCC 60.320 55.000 25.56 10.16 43.37 3.62
495 507 0.788391 CAGTTACCTGAACGCCGTTC 59.212 55.000 22.39 22.39 43.37 3.95
496 508 0.390124 TCAGTTACCTGAACGCCGTT 59.610 50.000 0.16 0.16 44.67 4.44
497 509 2.043625 TCAGTTACCTGAACGCCGT 58.956 52.632 0.00 0.00 44.67 5.68
498 510 4.979204 TCAGTTACCTGAACGCCG 57.021 55.556 0.00 0.00 44.67 6.46
504 516 2.684943 TGGTGGTCTTCAGTTACCTGA 58.315 47.619 0.00 0.00 45.95 3.86
505 517 3.485463 TTGGTGGTCTTCAGTTACCTG 57.515 47.619 0.00 0.00 40.25 4.00
506 518 3.810743 GCATTGGTGGTCTTCAGTTACCT 60.811 47.826 0.00 0.00 36.67 3.08
507 519 2.488153 GCATTGGTGGTCTTCAGTTACC 59.512 50.000 0.00 0.00 36.24 2.85
508 520 3.412386 AGCATTGGTGGTCTTCAGTTAC 58.588 45.455 0.00 0.00 0.00 2.50
509 521 3.788227 AGCATTGGTGGTCTTCAGTTA 57.212 42.857 0.00 0.00 0.00 2.24
510 522 2.664402 AGCATTGGTGGTCTTCAGTT 57.336 45.000 0.00 0.00 0.00 3.16
511 523 3.788227 TTAGCATTGGTGGTCTTCAGT 57.212 42.857 0.00 0.00 37.28 3.41
512 524 3.181493 GCATTAGCATTGGTGGTCTTCAG 60.181 47.826 0.00 0.00 41.58 3.02
513 525 2.754552 GCATTAGCATTGGTGGTCTTCA 59.245 45.455 0.00 0.00 41.58 3.02
514 526 3.019564 AGCATTAGCATTGGTGGTCTTC 58.980 45.455 0.00 0.00 45.49 2.87
515 527 2.756760 CAGCATTAGCATTGGTGGTCTT 59.243 45.455 0.00 0.00 45.49 3.01
516 528 2.291153 ACAGCATTAGCATTGGTGGTCT 60.291 45.455 14.48 0.00 44.70 3.85
517 529 2.094675 ACAGCATTAGCATTGGTGGTC 58.905 47.619 14.48 0.00 44.70 4.02
518 530 1.820519 CACAGCATTAGCATTGGTGGT 59.179 47.619 14.48 0.00 44.70 4.16
519 531 1.470285 GCACAGCATTAGCATTGGTGG 60.470 52.381 14.48 7.06 44.70 4.61
520 532 1.475280 AGCACAGCATTAGCATTGGTG 59.525 47.619 10.11 10.11 45.62 4.17
521 533 1.475280 CAGCACAGCATTAGCATTGGT 59.525 47.619 0.00 0.00 45.49 3.67
522 534 1.746787 TCAGCACAGCATTAGCATTGG 59.253 47.619 0.00 0.00 45.49 3.16
523 535 3.128068 TCTTCAGCACAGCATTAGCATTG 59.872 43.478 0.00 0.00 45.49 2.82
524 536 3.128242 GTCTTCAGCACAGCATTAGCATT 59.872 43.478 0.00 0.00 45.49 3.56
525 537 2.681848 GTCTTCAGCACAGCATTAGCAT 59.318 45.455 0.00 0.00 45.49 3.79
526 538 2.079158 GTCTTCAGCACAGCATTAGCA 58.921 47.619 0.00 0.00 45.49 3.49
527 539 1.399791 GGTCTTCAGCACAGCATTAGC 59.600 52.381 0.00 0.00 42.56 3.09
528 540 2.703416 TGGTCTTCAGCACAGCATTAG 58.297 47.619 0.00 0.00 0.00 1.73
529 541 2.857186 TGGTCTTCAGCACAGCATTA 57.143 45.000 0.00 0.00 0.00 1.90
530 542 3.731716 TGGTCTTCAGCACAGCATT 57.268 47.368 0.00 0.00 0.00 3.56
538 550 1.026718 CGGGAATGGTGGTCTTCAGC 61.027 60.000 0.00 0.00 43.68 4.26
539 551 1.026718 GCGGGAATGGTGGTCTTCAG 61.027 60.000 0.00 0.00 0.00 3.02
540 552 1.002624 GCGGGAATGGTGGTCTTCA 60.003 57.895 0.00 0.00 0.00 3.02
541 553 0.608035 TTGCGGGAATGGTGGTCTTC 60.608 55.000 0.00 0.00 0.00 2.87
542 554 0.178975 TTTGCGGGAATGGTGGTCTT 60.179 50.000 0.00 0.00 0.00 3.01
543 555 0.893727 GTTTGCGGGAATGGTGGTCT 60.894 55.000 0.00 0.00 0.00 3.85
544 556 1.584495 GTTTGCGGGAATGGTGGTC 59.416 57.895 0.00 0.00 0.00 4.02
545 557 1.906333 GGTTTGCGGGAATGGTGGT 60.906 57.895 0.00 0.00 0.00 4.16
546 558 2.969827 GGTTTGCGGGAATGGTGG 59.030 61.111 0.00 0.00 0.00 4.61
547 559 2.265182 ACGGTTTGCGGGAATGGTG 61.265 57.895 0.00 0.00 0.00 4.17
548 560 2.114411 ACGGTTTGCGGGAATGGT 59.886 55.556 0.00 0.00 0.00 3.55
549 561 2.566010 CACGGTTTGCGGGAATGG 59.434 61.111 0.00 0.00 0.00 3.16
550 562 2.126502 GCACGGTTTGCGGGAATG 60.127 61.111 0.00 0.00 42.79 2.67
558 570 1.068541 GGCTCCTAAAAGCACGGTTTG 60.069 52.381 0.00 0.00 44.35 2.93
559 571 1.244816 GGCTCCTAAAAGCACGGTTT 58.755 50.000 0.00 0.00 44.35 3.27
560 572 0.608308 GGGCTCCTAAAAGCACGGTT 60.608 55.000 0.00 0.00 44.35 4.44
561 573 1.002502 GGGCTCCTAAAAGCACGGT 60.003 57.895 0.00 0.00 44.35 4.83
562 574 3.905249 GGGCTCCTAAAAGCACGG 58.095 61.111 0.00 0.00 44.35 4.94
564 576 0.322906 AGCTGGGCTCCTAAAAGCAC 60.323 55.000 0.00 0.00 46.26 4.40
565 577 2.078452 AGCTGGGCTCCTAAAAGCA 58.922 52.632 0.00 0.00 44.35 3.91
575 587 2.270205 CGTGAATGGAGCTGGGCT 59.730 61.111 0.00 0.00 43.88 5.19
576 588 2.045926 ACGTGAATGGAGCTGGGC 60.046 61.111 0.00 0.00 0.00 5.36
577 589 0.249120 TACACGTGAATGGAGCTGGG 59.751 55.000 25.01 0.00 0.00 4.45
578 590 1.337728 TGTACACGTGAATGGAGCTGG 60.338 52.381 25.01 0.00 0.00 4.85
579 591 2.078849 TGTACACGTGAATGGAGCTG 57.921 50.000 25.01 0.00 0.00 4.24
580 592 2.621338 CATGTACACGTGAATGGAGCT 58.379 47.619 25.01 0.00 34.90 4.09
581 593 1.665679 CCATGTACACGTGAATGGAGC 59.334 52.381 29.40 12.17 41.84 4.70
824 1798 4.806339 AAGGCGGAGGAGGGGAGG 62.806 72.222 0.00 0.00 0.00 4.30
825 1799 2.689034 AAAGGCGGAGGAGGGGAG 60.689 66.667 0.00 0.00 0.00 4.30
826 1800 2.687566 GAAAGGCGGAGGAGGGGA 60.688 66.667 0.00 0.00 0.00 4.81
864 1838 1.331447 GTGGTGTCGGTGTTGGTTTAC 59.669 52.381 0.00 0.00 0.00 2.01
877 1851 1.550065 CTGTCGATCGATGTGGTGTC 58.450 55.000 22.50 6.11 0.00 3.67
990 1970 3.277133 CCGAACATGGCTGGTTGG 58.723 61.111 0.00 0.00 37.29 3.77
1100 2087 1.438651 CGACAGCAATCGAGGGAAAA 58.561 50.000 3.71 0.00 45.13 2.29
1258 2249 2.917933 GCCCAGGCAGAAAAACTTTTT 58.082 42.857 3.12 0.00 41.49 1.94
1259 2250 2.620251 GCCCAGGCAGAAAAACTTTT 57.380 45.000 3.12 0.00 41.49 2.27
1333 2324 6.768381 AGGCAAAACTGGAAGAGTATATAAGC 59.232 38.462 0.00 0.00 37.43 3.09
1337 2328 8.034313 TGATAGGCAAAACTGGAAGAGTATAT 57.966 34.615 0.00 0.00 37.43 0.86
1338 2329 7.432148 TGATAGGCAAAACTGGAAGAGTATA 57.568 36.000 0.00 0.00 37.43 1.47
1339 2330 6.313519 TGATAGGCAAAACTGGAAGAGTAT 57.686 37.500 0.00 0.00 37.43 2.12
1361 2352 3.840890 TGGCGGCAATAACTAACTTTG 57.159 42.857 10.22 0.00 0.00 2.77
1925 2917 6.829229 AAATGCTGAGATTGTGAGAATGAA 57.171 33.333 0.00 0.00 0.00 2.57
1926 2918 7.926674 TTAAATGCTGAGATTGTGAGAATGA 57.073 32.000 0.00 0.00 0.00 2.57
1963 2955 2.808244 ACAAATGTGTTCCAAGTTGCG 58.192 42.857 0.00 0.00 32.58 4.85
2334 3453 3.673809 CGAAACAAAACAAAAACCCACGA 59.326 39.130 0.00 0.00 0.00 4.35
2335 3454 3.429207 ACGAAACAAAACAAAAACCCACG 59.571 39.130 0.00 0.00 0.00 4.94
2337 3456 4.451435 GGAACGAAACAAAACAAAAACCCA 59.549 37.500 0.00 0.00 0.00 4.51
2338 3457 4.142859 GGGAACGAAACAAAACAAAAACCC 60.143 41.667 0.00 0.00 0.00 4.11
2340 3459 5.849357 AGGGAACGAAACAAAACAAAAAC 57.151 34.783 0.00 0.00 0.00 2.43
2359 3483 6.349033 CCACAAAACTATCGGTCTAAAAAGGG 60.349 42.308 0.00 0.00 0.00 3.95
2861 3988 3.933332 CCTACCGAATGGAGAAGTTTGTC 59.067 47.826 0.00 0.00 39.21 3.18
2990 4117 8.674263 AAAGGAACTGATAAGATAATCTGCAG 57.326 34.615 7.63 7.63 40.86 4.41
3236 4363 5.534654 CCAGACATTTCCTTTACCTTTGTCA 59.465 40.000 0.00 0.00 35.60 3.58
3343 4470 8.664079 ACCAGAAGCCAGAACATAATATCTATT 58.336 33.333 0.00 0.00 0.00 1.73
3439 4566 4.555262 ACAAGCAACAAAATAATGGGACG 58.445 39.130 0.00 0.00 0.00 4.79
3652 4779 0.446616 GATGAAAACGGGTTCGGAGC 59.553 55.000 0.00 0.00 41.39 4.70
3963 5102 3.299503 AGGTGAAGAAGTGTTGCCAAAT 58.700 40.909 0.00 0.00 0.00 2.32
3975 5114 6.151985 TGCTTACTGTTTGAAAAGGTGAAGAA 59.848 34.615 0.00 0.00 0.00 2.52
4130 5273 2.093869 CAGGGGCAGATTGTTGAAATGG 60.094 50.000 0.00 0.00 0.00 3.16
4205 5351 7.127339 TGAGAAGGAAGCATTAAGTATTAGGGT 59.873 37.037 0.00 0.00 0.00 4.34
4246 5563 2.472695 TGGCATACACACAGAACCTC 57.527 50.000 0.00 0.00 0.00 3.85
4373 5710 6.839657 TGTACTTCCACCCATAAAAAGGAAAA 59.160 34.615 0.00 0.00 37.86 2.29
4610 6052 6.313744 ACAGGCTGTTACAAACTTACAATC 57.686 37.500 15.88 0.00 0.00 2.67
4837 6281 6.916909 TCATCTCTACTATCCTTCCACTCTT 58.083 40.000 0.00 0.00 0.00 2.85
4901 6345 3.482436 CTTCCTCGTGGCTCTAGATACT 58.518 50.000 0.00 0.00 0.00 2.12
5001 6445 1.737793 GTGACAAATGCCTAGGAACCG 59.262 52.381 14.75 0.00 0.00 4.44
5108 6552 5.059404 ACGGCTTTCATAAAACTCCAATG 57.941 39.130 0.00 0.00 0.00 2.82
5380 6825 5.362430 ACAAACAATTTTGCAAGTCTAGGGA 59.638 36.000 0.00 0.00 45.32 4.20
5559 7004 1.442769 CACCCATCTTCTCAACGGTG 58.557 55.000 0.00 0.00 35.24 4.94
5574 7019 3.164977 GGGAGAGCCTAGGCACCC 61.165 72.222 32.59 32.59 44.88 4.61
5822 7267 1.962144 CAGCTTTGTTCAGGCCCTG 59.038 57.895 3.69 3.69 0.00 4.45
6080 7525 5.596361 TCCAAAAGAAAACAAGCACCTATCA 59.404 36.000 0.00 0.00 0.00 2.15
6084 7536 4.405358 TCATCCAAAAGAAAACAAGCACCT 59.595 37.500 0.00 0.00 0.00 4.00
6085 7537 4.692228 TCATCCAAAAGAAAACAAGCACC 58.308 39.130 0.00 0.00 0.00 5.01
6086 7538 5.276348 CGTTCATCCAAAAGAAAACAAGCAC 60.276 40.000 0.00 0.00 0.00 4.40
6087 7539 4.803088 CGTTCATCCAAAAGAAAACAAGCA 59.197 37.500 0.00 0.00 0.00 3.91
6088 7540 4.209080 CCGTTCATCCAAAAGAAAACAAGC 59.791 41.667 0.00 0.00 0.00 4.01
6089 7541 5.231991 CACCGTTCATCCAAAAGAAAACAAG 59.768 40.000 0.00 0.00 0.00 3.16
6090 7542 5.105752 CACCGTTCATCCAAAAGAAAACAA 58.894 37.500 0.00 0.00 0.00 2.83
6134 7586 0.389948 CAGACCAGCTACCGACCAAC 60.390 60.000 0.00 0.00 0.00 3.77
6368 7832 2.540361 CGCAGGCATCAAGATAAACTGC 60.540 50.000 16.34 16.34 44.52 4.40
6369 7833 2.032550 CCGCAGGCATCAAGATAAACTG 59.967 50.000 0.00 0.00 46.14 3.16
6370 7834 2.292267 CCGCAGGCATCAAGATAAACT 58.708 47.619 0.00 0.00 46.14 2.66
6371 7835 2.763249 CCGCAGGCATCAAGATAAAC 57.237 50.000 0.00 0.00 46.14 2.01
6457 7933 8.888579 AGGGAATATAATGTAAGTTCTTCGTG 57.111 34.615 0.00 0.00 0.00 4.35
6488 7964 2.093106 CCGAGCAGAGGTAGTACAACT 58.907 52.381 2.06 0.00 0.00 3.16
6489 7965 2.089980 TCCGAGCAGAGGTAGTACAAC 58.910 52.381 2.06 0.00 0.00 3.32
6519 7995 2.286125 TGTGAACACATTCGTTTGAGCG 60.286 45.455 3.39 0.00 37.69 5.03
6548 8024 1.678101 GAAATGCCTCATAGCCACACC 59.322 52.381 0.00 0.00 0.00 4.16
6549 8025 2.357009 CAGAAATGCCTCATAGCCACAC 59.643 50.000 0.00 0.00 0.00 3.82
6550 8026 2.646930 CAGAAATGCCTCATAGCCACA 58.353 47.619 0.00 0.00 0.00 4.17
6557 8033 3.101437 TGAAATGCCAGAAATGCCTCAT 58.899 40.909 0.00 0.00 0.00 2.90



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

AutoCloner maintained by Alex Coulton.