Multiple sequence alignment - TraesCS2A01G168600

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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 TraesCS2A01G168600 chr2A 100.000 9794 0 0 1 9794 122015765 122005972 0.000000e+00 18087
1 TraesCS2A01G168600 chr2D 95.428 9668 276 58 1 9572 119669171 119659574 0.000000e+00 15252
2 TraesCS2A01G168600 chr2D 96.035 227 7 2 9569 9794 119659508 119659283 1.550000e-97 368
3 TraesCS2A01G168600 chr2B 96.520 4742 125 18 3745 8479 172000955 171996247 0.000000e+00 7806
4 TraesCS2A01G168600 chr2B 87.792 3678 272 85 132 3744 172004572 172001007 0.000000e+00 4141
5 TraesCS2A01G168600 chr2B 93.388 726 26 9 8461 9180 171996234 171995525 0.000000e+00 1055
6 TraesCS2A01G168600 chr2B 88.070 285 26 4 1 281 172004775 172004495 2.040000e-86 331
7 TraesCS2A01G168600 chr2B 96.479 142 5 0 9653 9794 171995027 171994886 1.640000e-57 235
8 TraesCS2A01G168600 chr2B 93.277 119 8 0 9179 9297 171995401 171995283 1.010000e-39 176
9 TraesCS2A01G168600 chr2B 97.938 97 2 0 9569 9665 171995139 171995043 1.690000e-37 169
10 TraesCS2A01G168600 chr1D 80.818 391 63 8 2773 3155 411173218 411172832 7.440000e-76 296
11 TraesCS2A01G168600 chr4D 82.547 212 24 9 1394 1599 3860429 3860633 3.640000e-39 174


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 TraesCS2A01G168600 chr2A 122005972 122015765 9793 True 18087.000000 18087 100.0000 1 9794 1 chr2A.!!$R1 9793
1 TraesCS2A01G168600 chr2D 119659283 119669171 9888 True 7810.000000 15252 95.7315 1 9794 2 chr2D.!!$R1 9793
2 TraesCS2A01G168600 chr2B 171994886 172004775 9889 True 1987.571429 7806 93.3520 1 9794 7 chr2B.!!$R1 9793

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
110 112 0.109153 CTAGGCATAGCATGGGCACA 59.891 55.000 0.00 0.00 44.61 4.57 F
699 803 0.393808 TATCCCGAAAAGCCAGCCAC 60.394 55.000 0.00 0.00 0.00 5.01 F
1712 1838 0.249447 TGCTGGAGATGGCGAATACG 60.249 55.000 0.00 0.00 42.93 3.06 F
2429 2564 1.180907 TTTGCCAAGTCTTGCACACA 58.819 45.000 7.09 0.02 37.18 3.72 F
3610 3765 1.211457 GAGATGCTGGATGGTGGAAGT 59.789 52.381 0.00 0.00 0.00 3.01 F
5129 5342 0.810648 GCCACATCCAATTCTCGCAA 59.189 50.000 0.00 0.00 0.00 4.85 F
5873 6086 0.034186 ATGCGGGCCAAATTCTCTCA 60.034 50.000 4.39 0.00 0.00 3.27 F
6332 6551 0.107508 ATCCGTTGCTCCTGTCCATG 60.108 55.000 0.00 0.00 0.00 3.66 F
6684 6903 1.102978 AACACCCATAAATCTGGCGC 58.897 50.000 0.00 0.00 34.77 6.53 F
6994 7213 2.290960 GGAGGCATCCAGTACCAAGTTT 60.291 50.000 13.69 0.00 45.87 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1838 1.128507 TGCGACATTTCTGCATCGAAC 59.871 47.619 9.20 0.0 36.70 3.95 R
1874 2001 1.143684 ACATTAGGGCATACCAGCTGG 59.856 52.381 31.60 31.6 43.89 4.85 R
3369 3524 0.913934 TGCTGATGGGGGCTCACTTA 60.914 55.000 0.00 0.0 0.00 2.24 R
3876 4086 1.438651 GACGCTGGCAAAGTGACATA 58.561 50.000 6.24 0.0 33.12 2.29 R
5408 5621 1.894756 CCCTTTGCCGGTTTCGTCA 60.895 57.895 1.90 0.0 33.95 4.35 R
6971 7190 0.253160 TTGGTACTGGATGCCTCCCT 60.253 55.000 5.49 0.0 41.29 4.20 R
7360 7579 2.026915 CCGGCCATCTTCCATATCATCA 60.027 50.000 2.24 0.0 0.00 3.07 R
8019 8261 0.954452 GTGCAAAGAGGTGGGTGAAG 59.046 55.000 0.00 0.0 0.00 3.02 R
8497 8770 1.069668 ACAGTCACCTTCACGGGTTAC 59.930 52.381 0.00 0.0 37.52 2.50 R
8824 9098 2.939460 AGCAAACAACAACAGTGGAC 57.061 45.000 0.00 0.0 0.00 4.02 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
27 28 9.880157 GATCCTATAGAACGACTAGACTAGAAT 57.120 37.037 16.55 0.00 34.35 2.40
62 63 0.255890 AACCACTGTTCACTGTGCCT 59.744 50.000 10.61 0.00 42.25 4.75
108 110 1.763120 CCTAGGCATAGCATGGGCA 59.237 57.895 0.00 0.00 44.61 5.36
110 112 0.109153 CTAGGCATAGCATGGGCACA 59.891 55.000 0.00 0.00 44.61 4.57
149 151 1.128507 CAGTACATCAACGCGCAATGT 59.871 47.619 20.61 20.61 37.40 2.71
154 156 2.168384 CATCAACGCGCAATGTGTAAG 58.832 47.619 5.73 0.00 41.44 2.34
202 204 8.876790 AGATATGTAAACGTTAACCAAACTAGC 58.123 33.333 0.00 0.00 35.81 3.42
203 205 6.864360 ATGTAAACGTTAACCAAACTAGCA 57.136 33.333 0.00 0.00 35.81 3.49
204 206 6.674694 TGTAAACGTTAACCAAACTAGCAA 57.325 33.333 0.00 0.00 35.81 3.91
206 208 7.354257 TGTAAACGTTAACCAAACTAGCAATC 58.646 34.615 0.00 0.00 35.81 2.67
208 210 6.380095 AACGTTAACCAAACTAGCAATCAA 57.620 33.333 0.00 0.00 35.81 2.57
210 212 4.843984 CGTTAACCAAACTAGCAATCAACG 59.156 41.667 0.00 0.00 35.81 4.10
212 288 2.504367 ACCAAACTAGCAATCAACGCT 58.496 42.857 0.00 0.00 43.62 5.07
219 295 3.689161 ACTAGCAATCAACGCTAAATGCA 59.311 39.130 0.00 0.00 41.27 3.96
310 386 1.821936 CCCTTGCTGCAACCAAACA 59.178 52.632 11.69 0.00 0.00 2.83
312 388 1.406614 CCCTTGCTGCAACCAAACAAA 60.407 47.619 11.69 0.00 0.00 2.83
323 399 4.756135 GCAACCAAACAAATTCATCATGGT 59.244 37.500 0.00 0.00 41.23 3.55
328 404 3.615224 ACAAATTCATCATGGTTGGCC 57.385 42.857 0.00 0.00 0.00 5.36
351 433 4.909305 CACGTCGTAGTTTTCATGCAAAAT 59.091 37.500 0.00 0.00 36.35 1.82
378 467 8.462589 AAAAAGATAAAACAAAATGCCCACAT 57.537 26.923 0.00 0.00 38.49 3.21
379 468 7.671495 AAAGATAAAACAAAATGCCCACATC 57.329 32.000 0.00 0.00 34.62 3.06
380 469 5.410067 AGATAAAACAAAATGCCCACATCG 58.590 37.500 0.00 0.00 34.62 3.84
381 470 3.467374 AAAACAAAATGCCCACATCGT 57.533 38.095 0.00 0.00 34.62 3.73
382 471 2.723124 AACAAAATGCCCACATCGTC 57.277 45.000 0.00 0.00 34.62 4.20
386 476 1.909700 AAATGCCCACATCGTCACTT 58.090 45.000 0.00 0.00 34.62 3.16
391 481 0.603707 CCCACATCGTCACTTGCTGT 60.604 55.000 0.00 0.00 0.00 4.40
395 485 1.010935 CATCGTCACTTGCTGTCGCT 61.011 55.000 0.00 0.00 36.97 4.93
403 493 1.802960 ACTTGCTGTCGCTGAAAGATG 59.197 47.619 10.08 0.00 34.07 2.90
408 498 2.736721 GCTGTCGCTGAAAGATGTGTTA 59.263 45.455 0.64 0.00 34.07 2.41
409 499 3.372206 GCTGTCGCTGAAAGATGTGTTAT 59.628 43.478 0.64 0.00 34.07 1.89
410 500 4.566759 GCTGTCGCTGAAAGATGTGTTATA 59.433 41.667 0.64 0.00 34.07 0.98
411 501 5.276584 GCTGTCGCTGAAAGATGTGTTATAG 60.277 44.000 0.64 0.00 34.07 1.31
420 518 9.741168 CTGAAAGATGTGTTATAGTAACGTTTG 57.259 33.333 5.91 0.00 34.07 2.93
438 536 2.279584 TTTCCAGTTGTCGCGCGA 60.280 55.556 31.40 31.40 0.00 5.87
449 550 1.666553 TCGCGCGAAAGATTGGTGT 60.667 52.632 32.97 0.00 0.00 4.16
455 556 1.336795 GCGAAAGATTGGTGTTTGGGG 60.337 52.381 0.00 0.00 0.00 4.96
479 580 8.172484 GGGTTACAAATTGACAAAACAGAAAAC 58.828 33.333 0.00 0.00 0.00 2.43
481 582 9.523730 GTTACAAATTGACAAAACAGAAAACAC 57.476 29.630 0.00 0.00 0.00 3.32
587 689 2.396590 TTCGAAAAATCCCTCCTCCG 57.603 50.000 0.00 0.00 0.00 4.63
598 700 3.418047 TCCCTCCTCCGAAATTCAAAAC 58.582 45.455 0.00 0.00 0.00 2.43
641 745 3.492482 CGTTTTCTGTTGAGGGGCAAAAT 60.492 43.478 0.00 0.00 38.44 1.82
699 803 0.393808 TATCCCGAAAAGCCAGCCAC 60.394 55.000 0.00 0.00 0.00 5.01
714 823 2.404789 CACCGCCGCATAAAGCAG 59.595 61.111 0.00 0.00 46.13 4.24
716 825 1.815421 ACCGCCGCATAAAGCAGAG 60.815 57.895 0.00 0.00 46.13 3.35
721 830 2.519963 GCCGCATAAAGCAGAGAAAAC 58.480 47.619 0.00 0.00 46.13 2.43
797 911 4.530857 CACGCCTAAGCTCCCCCG 62.531 72.222 0.00 0.00 36.60 5.73
849 963 2.035155 CACCCCCGGAAGTTTCCC 59.965 66.667 0.73 0.00 44.67 3.97
898 1012 2.481104 GCATTTCTCACGGAGGAGAGAG 60.481 54.545 4.32 0.00 44.23 3.20
899 1013 2.881111 TTTCTCACGGAGGAGAGAGA 57.119 50.000 4.32 0.00 44.23 3.10
900 1014 2.411628 TTCTCACGGAGGAGAGAGAG 57.588 55.000 4.32 0.00 44.23 3.20
902 1016 0.465460 CTCACGGAGGAGAGAGAGGG 60.465 65.000 0.00 0.00 37.05 4.30
903 1017 2.124693 CACGGAGGAGAGAGAGGGC 61.125 68.421 0.00 0.00 0.00 5.19
904 1018 2.904866 CGGAGGAGAGAGAGGGCG 60.905 72.222 0.00 0.00 0.00 6.13
905 1019 2.277404 GGAGGAGAGAGAGGGCGT 59.723 66.667 0.00 0.00 0.00 5.68
1428 1554 1.716826 GGACGGAGAAGATCGCGTCT 61.717 60.000 5.77 5.63 44.34 4.18
1570 1696 1.649664 CCTCGAGAGGTTTGCTGATG 58.350 55.000 15.71 0.00 43.61 3.07
1712 1838 0.249447 TGCTGGAGATGGCGAATACG 60.249 55.000 0.00 0.00 42.93 3.06
1899 2026 3.433598 GCTGGTATGCCCTAATGTCTTGA 60.434 47.826 0.00 0.00 0.00 3.02
1944 2071 6.873605 AGTTCATTAACACTCGTTCATCATGA 59.126 34.615 0.00 0.00 38.12 3.07
1951 2078 3.372206 CACTCGTTCATCATGAGAAACCC 59.628 47.826 14.19 2.51 40.67 4.11
1998 2125 4.803329 ATGGGAGCTGATAAAATCCAGT 57.197 40.909 0.00 0.00 33.24 4.00
2151 2278 8.746052 TGAACCTCCATTAATAAGGTAACATG 57.254 34.615 17.69 0.00 42.58 3.21
2286 2413 5.180117 CAGCTGCAGACATTACAAAGTAAGT 59.820 40.000 20.43 0.00 0.00 2.24
2429 2564 1.180907 TTTGCCAAGTCTTGCACACA 58.819 45.000 7.09 0.02 37.18 3.72
2486 2621 2.380084 TGTTCCCATCGTGTTAGCTC 57.620 50.000 0.00 0.00 0.00 4.09
2501 2636 6.817140 CGTGTTAGCTCCTTTCTATAACCTTT 59.183 38.462 0.00 0.00 0.00 3.11
2547 2682 2.804647 TGTAGCATGTGGACGATAACG 58.195 47.619 0.00 0.00 45.75 3.18
2621 2757 4.754618 TGTGATTACATCTCGTGCACTTTT 59.245 37.500 16.19 0.00 0.00 2.27
2622 2758 5.238432 TGTGATTACATCTCGTGCACTTTTT 59.762 36.000 16.19 0.00 0.00 1.94
2638 2774 8.121305 TGCACTTTTTGTGGATATATTTCTGT 57.879 30.769 0.00 0.00 46.27 3.41
2852 2996 7.197703 TGATTGATATGCATTCATGTGACAAC 58.802 34.615 3.54 0.00 33.31 3.32
2879 3023 5.673337 TGTGCTGTGAGTTTTTGATAGAC 57.327 39.130 0.00 0.00 0.00 2.59
2920 3066 5.438761 AATTTTTGTCTGTAGGCTGTGTC 57.561 39.130 0.00 0.00 0.00 3.67
2945 3091 9.275398 TCGTGGTATCAAGTAATTTACAGTTTT 57.725 29.630 9.15 0.00 0.00 2.43
3319 3472 5.897377 AAGCACATTAAGGTACAATCCAC 57.103 39.130 0.00 0.00 0.00 4.02
3369 3524 5.909621 AAGTTGATGTGCAGATTTAGCAT 57.090 34.783 0.00 0.00 44.79 3.79
3424 3579 6.803807 GTGCTCAAGTTATCCTTTTTGACATC 59.196 38.462 0.00 0.00 0.00 3.06
3484 3639 6.902341 TGCAGCTGTAAAGAGAAAGTTTATG 58.098 36.000 16.64 0.00 0.00 1.90
3537 3692 4.113354 CGTCAACTTAGTTCTATGCTCCC 58.887 47.826 0.00 0.00 0.00 4.30
3610 3765 1.211457 GAGATGCTGGATGGTGGAAGT 59.789 52.381 0.00 0.00 0.00 3.01
3622 3781 6.177610 GGATGGTGGAAGTTGTATAGAAACA 58.822 40.000 2.07 0.00 0.00 2.83
3623 3782 6.657541 GGATGGTGGAAGTTGTATAGAAACAA 59.342 38.462 2.07 0.00 37.03 2.83
3734 3893 1.285280 TAGGAGGGTGGGTCATGTTG 58.715 55.000 0.00 0.00 0.00 3.33
3951 4164 3.777106 TCATCACACTGGAAGAGCTTT 57.223 42.857 0.00 0.00 37.43 3.51
4058 4271 1.815757 ACAAGTTGGGGTAGTGTCCT 58.184 50.000 7.96 0.00 0.00 3.85
4065 4278 1.273609 TGGGGTAGTGTCCTGCATACT 60.274 52.381 0.00 0.00 0.00 2.12
4117 4330 1.489481 TGTTCCATCAGGATCGAGCT 58.511 50.000 0.00 0.00 45.26 4.09
4433 4646 4.335594 GGGTAACAATGATAACAGTGGCTC 59.664 45.833 5.42 0.00 44.83 4.70
4743 4956 4.095782 GCCTCTAGTACTGAGAGTGAGTTG 59.904 50.000 18.34 8.91 39.09 3.16
5011 5224 1.093159 TAGAGGTTCTCGCCTTCGTC 58.907 55.000 0.00 0.00 39.34 4.20
5129 5342 0.810648 GCCACATCCAATTCTCGCAA 59.189 50.000 0.00 0.00 0.00 4.85
5167 5380 2.187163 GTAGGGACGAAGCTGGCC 59.813 66.667 0.00 0.00 0.00 5.36
5245 5458 1.561643 AGAGGATGTGCGGAGAAAGA 58.438 50.000 0.00 0.00 0.00 2.52
5365 5578 6.075315 AGTTTGCTGGGAGGTAAAGTTAAAT 58.925 36.000 0.00 0.00 0.00 1.40
5408 5621 0.618968 CCCTTGGAGCAGACTAGGGT 60.619 60.000 11.69 0.00 40.58 4.34
5655 5868 3.014623 TGCCAATGAGCTTCTGAAGATG 58.985 45.455 21.06 10.14 0.00 2.90
5814 6027 8.182881 CAGAAAGAAGAGAAGGAAGCAATATTG 58.817 37.037 11.27 11.27 0.00 1.90
5873 6086 0.034186 ATGCGGGCCAAATTCTCTCA 60.034 50.000 4.39 0.00 0.00 3.27
6046 6265 9.850198 TTTACTAAAGGTAAAAGGCTAGTTCAA 57.150 29.630 0.00 0.00 44.43 2.69
6065 6284 5.356882 TCAATTTTTCTGCGAAGTACTGG 57.643 39.130 0.00 0.00 0.00 4.00
6232 6451 7.397221 TGGTAGAAGATGAAATGAACAGTGAT 58.603 34.615 0.00 0.00 0.00 3.06
6317 6536 5.108385 AGCTTACACACAAAAGAAATCCG 57.892 39.130 0.00 0.00 0.00 4.18
6332 6551 0.107508 ATCCGTTGCTCCTGTCCATG 60.108 55.000 0.00 0.00 0.00 3.66
6334 6553 1.296392 CGTTGCTCCTGTCCATGGA 59.704 57.895 11.44 11.44 0.00 3.41
6362 6581 3.868077 GCATTCGTCAAGAGCTGTAAGAT 59.132 43.478 0.00 0.00 34.07 2.40
6584 6803 4.263331 GGGGGTCACAGTCTATGAGAAAAA 60.263 45.833 0.00 0.00 29.77 1.94
6643 6862 7.390440 TCAGTGAACAAGGATATTTACAACTGG 59.610 37.037 0.00 0.00 0.00 4.00
6684 6903 1.102978 AACACCCATAAATCTGGCGC 58.897 50.000 0.00 0.00 34.77 6.53
6720 6939 4.597507 TGTTAGGAAAGACAATGGGACTCT 59.402 41.667 0.00 0.00 0.00 3.24
6971 7190 4.599047 AATGGCGATGTTTCTTTTCCAA 57.401 36.364 0.00 0.00 0.00 3.53
6976 7195 3.366374 GCGATGTTTCTTTTCCAAGGGAG 60.366 47.826 0.00 0.00 31.21 4.30
6994 7213 2.290960 GGAGGCATCCAGTACCAAGTTT 60.291 50.000 13.69 0.00 45.87 2.66
7321 7540 5.373812 AGAATAGGGGTGATGGTTTAGTG 57.626 43.478 0.00 0.00 0.00 2.74
7360 7579 3.708403 TCAACTGCCTCAGAATGTGAT 57.292 42.857 0.29 0.00 37.40 3.06
7581 7801 8.570068 TTTAACCCATTTGAAGTATAGTGTCC 57.430 34.615 0.00 0.00 0.00 4.02
7594 7814 9.523168 GAAGTATAGTGTCCTGACCTAGATTAT 57.477 37.037 0.00 0.00 0.00 1.28
7693 7913 8.691661 TTAGATCAGAATAAAACCAATAGGGC 57.308 34.615 0.00 0.00 42.05 5.19
7713 7933 4.402474 GGGCAAGCCTTCATTTTAGTACAT 59.598 41.667 11.40 0.00 36.10 2.29
7875 8095 7.610305 ACCAGATAAATTAAAGTGACGGTGAAT 59.390 33.333 0.00 0.00 0.00 2.57
7876 8096 7.910162 CCAGATAAATTAAAGTGACGGTGAATG 59.090 37.037 0.00 0.00 0.00 2.67
7897 8117 7.334421 TGAATGAGTTACTTTATCCTTGCTGAC 59.666 37.037 0.00 0.00 0.00 3.51
7950 8170 8.850156 ACATATACTAACCTTGGAATCAATTGC 58.150 33.333 0.00 0.00 31.75 3.56
8019 8261 6.133356 TGGTGACAAATATTAAATCCCCTCC 58.867 40.000 0.00 0.00 37.44 4.30
8161 8403 7.093333 CCAAAACTAGAATCCAAAAATAGGGCT 60.093 37.037 0.00 0.00 0.00 5.19
8190 8432 4.275196 AGATCATGTGCATGCAGTATTGAC 59.725 41.667 23.41 8.03 38.65 3.18
8202 8444 4.222114 GCAGTATTGACAGAGTTTTGTGC 58.778 43.478 0.00 0.00 0.00 4.57
8224 8466 7.086376 GTGCATGGGAATGATACATTTACATC 58.914 38.462 0.00 0.00 0.00 3.06
8274 8516 2.942710 TGAGTCTTAAGCTGTACGTGC 58.057 47.619 0.00 0.00 0.00 5.34
8329 8571 6.488006 GCTCTTCATTTCTTTCCCTGCATATA 59.512 38.462 0.00 0.00 0.00 0.86
8331 8573 6.772716 TCTTCATTTCTTTCCCTGCATATACC 59.227 38.462 0.00 0.00 0.00 2.73
8497 8770 5.530519 TGTTAAGCTGCTCAATTAGAACG 57.469 39.130 1.00 0.00 0.00 3.95
8504 8777 3.255725 TGCTCAATTAGAACGTAACCCG 58.744 45.455 0.00 0.00 44.03 5.28
8566 8839 7.016153 ACCTGTTCTGTCATTGGTAATCTTA 57.984 36.000 0.00 0.00 0.00 2.10
8567 8840 7.458397 ACCTGTTCTGTCATTGGTAATCTTAA 58.542 34.615 0.00 0.00 0.00 1.85
8684 8957 1.451936 GTGACCCTCAAGCACCAGT 59.548 57.895 0.00 0.00 0.00 4.00
8824 9098 1.438651 TAAGCTGCCAGTTAAGCGTG 58.561 50.000 0.00 0.00 44.34 5.34
9319 9754 3.126686 GGTGAATTGCTCTGCTCTTCTTC 59.873 47.826 0.00 0.00 0.00 2.87
9323 9758 2.398252 TGCTCTGCTCTTCTTCCATG 57.602 50.000 0.00 0.00 0.00 3.66
9393 9831 1.946768 CCAGTCCGTGCTCTTTCAAAA 59.053 47.619 0.00 0.00 0.00 2.44
9400 9838 2.354510 CGTGCTCTTTCAAAAGACCACA 59.645 45.455 21.80 10.74 45.39 4.17
9429 9867 3.435327 TCAAAATTGTGACGGGATTCTCG 59.565 43.478 3.95 3.95 0.00 4.04
9442 9880 4.459685 CGGGATTCTCGGTTCAGATATACT 59.540 45.833 0.00 0.00 0.00 2.12
9443 9881 5.392165 CGGGATTCTCGGTTCAGATATACTC 60.392 48.000 0.00 0.00 0.00 2.59
9464 9916 2.440409 CCCCAGGTTCAGTCTTTGATG 58.560 52.381 0.00 0.00 35.27 3.07
9527 9979 3.515104 CACAACCATAGGGGAAATGCTTT 59.485 43.478 0.00 0.00 41.15 3.51
9528 9980 4.020307 CACAACCATAGGGGAAATGCTTTT 60.020 41.667 0.00 0.00 41.15 2.27
9542 9994 0.881118 GCTTTTTGCATCTGGACGGA 59.119 50.000 0.00 0.00 42.31 4.69
9556 10008 0.868406 GACGGAAAGTGCAAGGACAG 59.132 55.000 0.00 0.00 0.00 3.51
9587 10108 1.099295 ACAGGATCCATGTGCATGCG 61.099 55.000 15.82 0.00 37.49 4.73
9621 10142 1.004918 ACTCGGGTGTAGCAGTTGC 60.005 57.895 0.00 0.00 42.49 4.17
9756 10305 1.219124 CGTGCTACATCCTGCCACT 59.781 57.895 0.00 0.00 0.00 4.00
9777 10326 2.288666 GTCCATGCACACCAATCGTAT 58.711 47.619 0.00 0.00 0.00 3.06
9784 10333 3.244078 TGCACACCAATCGTATATCTCCC 60.244 47.826 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.389757 GTGGTTAAGCGCCCCAAAAA 59.610 50.000 2.29 0.00 0.00 1.94
32 33 1.602323 CAGTGGTTAAGCGCCCCAA 60.602 57.895 14.28 0.00 0.00 4.12
33 34 2.033448 CAGTGGTTAAGCGCCCCA 59.967 61.111 14.28 2.09 0.00 4.96
34 35 1.583495 GAACAGTGGTTAAGCGCCCC 61.583 60.000 14.28 0.00 37.36 5.80
35 36 0.887387 TGAACAGTGGTTAAGCGCCC 60.887 55.000 14.28 0.00 37.36 6.13
108 110 3.829601 TGGTTGGAGTTCACTTTTTGTGT 59.170 39.130 0.00 0.00 46.27 3.72
110 112 4.086457 ACTGGTTGGAGTTCACTTTTTGT 58.914 39.130 0.00 0.00 0.00 2.83
149 151 6.398234 TTTTTGATTAGTTGCTGCCTTACA 57.602 33.333 0.00 0.00 0.00 2.41
154 156 6.158598 TCTTGATTTTTGATTAGTTGCTGCC 58.841 36.000 0.00 0.00 0.00 4.85
190 192 4.069304 AGCGTTGATTGCTAGTTTGGTTA 58.931 39.130 0.00 0.00 41.87 2.85
286 362 3.061752 TTGCAGCAAGGGCAATGG 58.938 55.556 2.83 0.00 45.57 3.16
323 399 1.219646 GAAAACTACGACGTGGCCAA 58.780 50.000 7.24 0.00 0.00 4.52
328 404 3.513462 TTGCATGAAAACTACGACGTG 57.487 42.857 11.56 3.29 0.00 4.49
358 447 5.167845 ACGATGTGGGCATTTTGTTTTATC 58.832 37.500 0.00 0.00 35.07 1.75
363 452 1.959985 TGACGATGTGGGCATTTTGTT 59.040 42.857 0.00 0.00 35.07 2.83
365 454 1.541147 AGTGACGATGTGGGCATTTTG 59.459 47.619 0.00 0.00 35.07 2.44
366 455 1.909700 AGTGACGATGTGGGCATTTT 58.090 45.000 0.00 0.00 35.07 1.82
368 457 1.167851 CAAGTGACGATGTGGGCATT 58.832 50.000 0.00 0.00 35.07 3.56
369 458 1.308069 GCAAGTGACGATGTGGGCAT 61.308 55.000 0.00 0.00 38.18 4.40
370 459 1.965930 GCAAGTGACGATGTGGGCA 60.966 57.895 0.00 0.00 0.00 5.36
371 460 1.672356 AGCAAGTGACGATGTGGGC 60.672 57.895 0.00 0.00 0.00 5.36
372 461 0.603707 ACAGCAAGTGACGATGTGGG 60.604 55.000 0.00 0.00 0.00 4.61
373 462 0.792640 GACAGCAAGTGACGATGTGG 59.207 55.000 0.00 0.00 0.00 4.17
375 464 1.284982 GCGACAGCAAGTGACGATGT 61.285 55.000 1.18 0.00 45.67 3.06
376 465 1.010935 AGCGACAGCAAGTGACGATG 61.011 55.000 1.18 0.00 45.67 3.84
378 467 1.661509 CAGCGACAGCAAGTGACGA 60.662 57.895 1.18 0.00 45.67 4.20
391 481 6.471198 CGTTACTATAACACATCTTTCAGCGA 59.529 38.462 0.00 0.00 0.00 4.93
395 485 9.263538 ACAAACGTTACTATAACACATCTTTCA 57.736 29.630 0.00 0.00 0.00 2.69
403 493 7.854534 ACTGGAAACAAACGTTACTATAACAC 58.145 34.615 0.00 0.00 42.06 3.32
408 498 6.292488 CGACAACTGGAAACAAACGTTACTAT 60.292 38.462 0.00 0.00 42.06 2.12
409 499 5.005586 CGACAACTGGAAACAAACGTTACTA 59.994 40.000 0.00 0.00 42.06 1.82
410 500 4.201744 CGACAACTGGAAACAAACGTTACT 60.202 41.667 0.00 0.00 42.06 2.24
411 501 4.023783 CGACAACTGGAAACAAACGTTAC 58.976 43.478 0.00 0.00 42.06 2.50
420 518 2.096481 TTCGCGCGACAACTGGAAAC 62.096 55.000 35.02 0.00 0.00 2.78
438 536 4.290942 TGTAACCCCAAACACCAATCTTT 58.709 39.130 0.00 0.00 0.00 2.52
449 550 6.472887 TGTTTTGTCAATTTGTAACCCCAAA 58.527 32.000 0.00 0.00 38.58 3.28
455 556 9.523730 GTGTTTTCTGTTTTGTCAATTTGTAAC 57.476 29.630 0.00 0.00 0.00 2.50
479 580 1.705256 ATGTACTGCAACGTACCGTG 58.295 50.000 12.29 0.00 39.99 4.94
481 582 3.799137 AAAATGTACTGCAACGTACCG 57.201 42.857 12.29 0.00 39.14 4.02
511 612 2.948979 TGGGTGTGTAGCTTTTGTCTTG 59.051 45.455 0.00 0.00 0.00 3.02
523 624 0.543410 ACGAGGATGGTGGGTGTGTA 60.543 55.000 0.00 0.00 0.00 2.90
587 689 2.899900 AGGGGCTCTGGTTTTGAATTTC 59.100 45.455 0.00 0.00 0.00 2.17
598 700 1.277580 AACTGGATGAGGGGCTCTGG 61.278 60.000 0.00 0.00 0.00 3.86
641 745 3.164977 TTGGTGCGGGTCTGACCA 61.165 61.111 26.94 5.18 41.02 4.02
797 911 0.462759 CGGCCCTGATCTGGAGTTTC 60.463 60.000 19.59 3.84 0.00 2.78
849 963 0.932399 AAACGGACGAAGGTGAAACG 59.068 50.000 0.00 0.00 38.12 3.60
898 1012 2.794028 GGTACTGCCCTACGCCCTC 61.794 68.421 0.00 0.00 36.24 4.30
899 1013 2.762875 GGTACTGCCCTACGCCCT 60.763 66.667 0.00 0.00 36.24 5.19
900 1014 3.078836 TGGTACTGCCCTACGCCC 61.079 66.667 0.00 0.00 36.24 6.13
902 1016 1.141234 GACTGGTACTGCCCTACGC 59.859 63.158 0.00 0.00 36.04 4.42
903 1017 0.739561 GAGACTGGTACTGCCCTACG 59.260 60.000 0.00 0.00 36.04 3.51
904 1018 1.112950 GGAGACTGGTACTGCCCTAC 58.887 60.000 0.00 0.00 36.04 3.18
905 1019 0.708209 TGGAGACTGGTACTGCCCTA 59.292 55.000 0.00 0.00 36.04 3.53
1245 1367 1.226717 CTGGAAGAGCGCGTAGTCC 60.227 63.158 8.43 10.51 34.07 3.85
1570 1696 3.876198 CACCGCCGCATAAGCCAC 61.876 66.667 0.00 0.00 37.52 5.01
1616 1742 3.484407 CACCCATCAGAATCCAATCTCC 58.516 50.000 0.00 0.00 0.00 3.71
1712 1838 1.128507 TGCGACATTTCTGCATCGAAC 59.871 47.619 9.20 0.00 36.70 3.95
1874 2001 1.143684 ACATTAGGGCATACCAGCTGG 59.856 52.381 31.60 31.60 43.89 4.85
1899 2026 7.907389 TGAACTGTATGAGGTATGAAAAGACT 58.093 34.615 0.00 0.00 0.00 3.24
1944 2071 4.911390 CAGTTAAGATGGACTGGGTTTCT 58.089 43.478 0.00 0.00 39.60 2.52
1951 2078 6.071334 TGAGTAACTCCAGTTAAGATGGACTG 60.071 42.308 5.41 0.00 41.96 3.51
2286 2413 4.036734 GCGGCAATTGAAATAAGAGATGGA 59.963 41.667 10.34 0.00 0.00 3.41
2477 2612 7.010275 CGAAAGGTTATAGAAAGGAGCTAACAC 59.990 40.741 0.00 0.00 0.00 3.32
2486 2621 8.757164 AATTTTTGCGAAAGGTTATAGAAAGG 57.243 30.769 0.00 0.00 0.00 3.11
2501 2636 2.877786 TCTGCACTCTGAATTTTTGCGA 59.122 40.909 0.00 0.00 35.90 5.10
2547 2682 5.874895 AAAGAAACTAACTTCATACGGGC 57.125 39.130 0.00 0.00 0.00 6.13
2621 2757 9.753674 AAAAGGAAGACAGAAATATATCCACAA 57.246 29.630 0.00 0.00 0.00 3.33
2622 2758 9.753674 AAAAAGGAAGACAGAAATATATCCACA 57.246 29.630 0.00 0.00 0.00 4.17
2945 3091 6.926630 ATTTCAGGTTGCATTAAAAGGGTA 57.073 33.333 0.00 0.00 0.00 3.69
2977 3123 5.534914 AGCCAGGGCATAAATTATGGATA 57.465 39.130 13.63 0.00 44.88 2.59
3093 3240 2.308570 ACTATCATGGTTGAACCCTGCA 59.691 45.455 12.53 3.40 37.50 4.41
3111 3258 3.441500 TGGAGAAGCTCAGAGACACTA 57.558 47.619 0.00 0.00 31.08 2.74
3310 3463 3.222173 AGTTGTTGCTGGTGGATTGTA 57.778 42.857 0.00 0.00 0.00 2.41
3319 3472 6.823689 AGATATACCAAAGTAGTTGTTGCTGG 59.176 38.462 0.00 0.00 35.23 4.85
3369 3524 0.913934 TGCTGATGGGGGCTCACTTA 60.914 55.000 0.00 0.00 0.00 2.24
3424 3579 6.748333 TCCTCAATTAGATCTGCTTGTTTG 57.252 37.500 5.18 0.79 0.00 2.93
3492 3647 9.973246 GACGTGTATTATAATGGCATTTGATAG 57.027 33.333 19.21 4.44 0.00 2.08
3706 3865 3.391626 GACCCACCCTCCTAATTCCTAAG 59.608 52.174 0.00 0.00 0.00 2.18
3734 3893 4.453478 TCATATCTCAATGCGCTCCAATTC 59.547 41.667 9.73 0.00 0.00 2.17
3801 4011 8.868522 ATCTAAACACCATTCATCAAGAAAGA 57.131 30.769 0.00 0.00 40.22 2.52
3876 4086 1.438651 GACGCTGGCAAAGTGACATA 58.561 50.000 6.24 0.00 33.12 2.29
4058 4271 7.012327 GGTTGTTGCTTAATCTATCAGTATGCA 59.988 37.037 0.00 0.00 34.76 3.96
4065 4278 7.701539 ATGTTGGTTGTTGCTTAATCTATCA 57.298 32.000 0.00 0.00 0.00 2.15
4117 4330 3.701205 TGGCTTAGATTGCTGTTCAGA 57.299 42.857 3.84 0.00 0.00 3.27
4433 4646 9.185192 GAGTTCCATTTTCACTTTTGTCATTAG 57.815 33.333 0.00 0.00 0.00 1.73
4692 4905 3.432749 CCATGTCATCTCCCGAACAAGAT 60.433 47.826 0.00 0.00 32.44 2.40
5011 5224 2.097036 TCCAGCATGCATCTCTTTTGG 58.903 47.619 21.98 15.79 31.97 3.28
5037 5250 2.037121 TCGATCCTTCTTCACAACTGCA 59.963 45.455 0.00 0.00 0.00 4.41
5129 5342 5.994416 ACCAGATGAACCCCTAACATTAT 57.006 39.130 0.00 0.00 0.00 1.28
5167 5380 6.018098 GCATCATGAACTTCAGATTCTGTAGG 60.018 42.308 20.32 11.51 34.03 3.18
5245 5458 4.460382 CAGTATTTCAGACCCAACAGCAAT 59.540 41.667 0.00 0.00 0.00 3.56
5365 5578 7.428020 GGAATAGCATTTGCATCATTTACTGA 58.572 34.615 5.20 0.00 45.16 3.41
5408 5621 1.894756 CCCTTTGCCGGTTTCGTCA 60.895 57.895 1.90 0.00 33.95 4.35
5600 5813 3.809832 ACTCTCCATCACAGTTTGTTTCG 59.190 43.478 0.00 0.00 0.00 3.46
5604 5817 5.290493 TGTTACTCTCCATCACAGTTTGT 57.710 39.130 0.00 0.00 0.00 2.83
5655 5868 3.264947 GTTATACCCTTCGTTGTCCACC 58.735 50.000 0.00 0.00 0.00 4.61
5814 6027 3.863142 AGACTTTCATGCATTGCCTTC 57.137 42.857 6.12 0.00 0.00 3.46
5991 6207 5.190925 ACAGAGTACAGCATTTGGGGTATAA 59.809 40.000 0.00 0.00 0.00 0.98
6044 6263 5.356882 TCCAGTACTTCGCAGAAAAATTG 57.643 39.130 0.00 0.00 45.90 2.32
6046 6265 5.063880 ACTTCCAGTACTTCGCAGAAAAAT 58.936 37.500 0.00 0.00 45.90 1.82
6099 6318 9.681692 GCAATATGTCAAATGATTGTAGCATTA 57.318 29.630 0.00 0.00 35.06 1.90
6176 6395 2.057830 CCCCCTGGAAAAGGCAAAC 58.942 57.895 0.00 0.00 45.89 2.93
6232 6451 7.581464 CTGGAAGAACAATCACCAGATAGGTAA 60.581 40.741 0.00 0.00 44.24 2.85
6317 6536 2.859992 GTCCATGGACAGGAGCAAC 58.140 57.895 35.21 9.26 44.02 4.17
6332 6551 3.001736 GCTCTTGACGAATGCTTATGTCC 59.998 47.826 0.00 0.00 0.00 4.02
6334 6553 3.620374 CAGCTCTTGACGAATGCTTATGT 59.380 43.478 0.00 0.00 0.00 2.29
6584 6803 8.957466 GTCCCTTAATTCACTAGCATTTAAGTT 58.043 33.333 11.82 0.00 31.17 2.66
6627 6846 3.138468 GGGAGCCCAGTTGTAAATATCCT 59.862 47.826 0.00 0.00 35.81 3.24
6643 6862 2.774809 ACTAGAAATTCCTGAGGGAGCC 59.225 50.000 0.00 0.00 43.29 4.70
6684 6903 5.526111 TCTTTCCTAACAAAAGACTTCGGTG 59.474 40.000 0.00 0.00 37.72 4.94
6971 7190 0.253160 TTGGTACTGGATGCCTCCCT 60.253 55.000 5.49 0.00 41.29 4.20
6976 7195 4.440112 GCATTAAACTTGGTACTGGATGCC 60.440 45.833 0.00 0.00 33.23 4.40
6994 7213 3.995705 GCATGTTTCCTGCAAAAGCATTA 59.004 39.130 7.75 0.00 39.46 1.90
7007 7226 4.160252 ACCAGGTAAATCATGCATGTTTCC 59.840 41.667 25.43 19.65 0.00 3.13
7056 7275 2.717639 AGGCAATAGGTGTGGATGAC 57.282 50.000 0.00 0.00 0.00 3.06
7321 7540 3.149196 TGAAGCAGAAACCCAGTCATTC 58.851 45.455 0.00 0.00 0.00 2.67
7360 7579 2.026915 CCGGCCATCTTCCATATCATCA 60.027 50.000 2.24 0.00 0.00 3.07
7581 7801 4.503991 GGGGACAAGCATAATCTAGGTCAG 60.504 50.000 0.00 0.00 0.00 3.51
7594 7814 3.586543 TGTCATGGGGGACAAGCA 58.413 55.556 0.00 0.00 44.34 3.91
7693 7913 6.913170 ACACATGTACTAAAATGAAGGCTTG 58.087 36.000 3.46 0.00 0.00 4.01
7713 7933 2.123589 TGAAGGACCCTGAAAGACACA 58.876 47.619 0.00 0.00 34.07 3.72
7875 8095 6.109156 TGTCAGCAAGGATAAAGTAACTCA 57.891 37.500 0.00 0.00 0.00 3.41
7876 8096 7.066374 CTTGTCAGCAAGGATAAAGTAACTC 57.934 40.000 0.00 0.00 46.17 3.01
7897 8117 9.553064 AACATGTAAAGAGAGGATATTAGCTTG 57.447 33.333 0.00 0.00 0.00 4.01
7950 8170 9.127006 CGATACATTCATGTCAAGAGATAGAAG 57.873 37.037 0.00 0.00 41.97 2.85
7999 8241 7.014326 GGTGAAGGAGGGGATTTAATATTTGTC 59.986 40.741 0.00 0.00 0.00 3.18
8019 8261 0.954452 GTGCAAAGAGGTGGGTGAAG 59.046 55.000 0.00 0.00 0.00 3.02
8161 8403 3.881089 CTGCATGCACATGATCTAGGAAA 59.119 43.478 18.46 0.00 41.20 3.13
8190 8432 3.256383 TCATTCCCATGCACAAAACTCTG 59.744 43.478 0.00 0.00 0.00 3.35
8202 8444 8.294577 CACTGATGTAAATGTATCATTCCCATG 58.705 37.037 9.74 0.00 33.25 3.66
8224 8466 7.010923 GTCAGAAGTCTAAGCAAATATCCACTG 59.989 40.741 0.00 0.00 0.00 3.66
8274 8516 3.744660 ACAGTAACTGAAGCCTGAAAGG 58.255 45.455 0.00 0.00 46.02 3.11
8319 8561 3.764237 AAGTAACCGGTATATGCAGGG 57.236 47.619 8.00 6.74 0.00 4.45
8329 8571 6.093633 GCAAATTCAGATCTTAAGTAACCGGT 59.906 38.462 0.00 0.00 0.00 5.28
8331 8573 7.064609 TCTGCAAATTCAGATCTTAAGTAACCG 59.935 37.037 1.63 0.00 38.11 4.44
8468 8741 8.883731 TCTAATTGAGCAGCTTAACATAAGAAC 58.116 33.333 0.87 0.00 0.00 3.01
8497 8770 1.069668 ACAGTCACCTTCACGGGTTAC 59.930 52.381 0.00 0.00 37.52 2.50
8504 8777 6.650807 TGATAAAGATGAACAGTCACCTTCAC 59.349 38.462 0.00 0.00 36.51 3.18
8544 8817 7.390440 TGGTTAAGATTACCAATGACAGAACAG 59.610 37.037 0.00 0.00 42.50 3.16
8566 8839 8.557029 CGTGAAGATAGTTTTAGACTTTTGGTT 58.443 33.333 0.00 0.00 39.86 3.67
8567 8840 7.307811 GCGTGAAGATAGTTTTAGACTTTTGGT 60.308 37.037 0.00 0.00 39.86 3.67
8684 8957 7.121168 CCAGAAGAAACTTTATACAATCCAGCA 59.879 37.037 0.00 0.00 0.00 4.41
8797 9071 6.433766 GCTTAACTGGCAGCTTATAAGAATG 58.566 40.000 23.03 13.86 32.87 2.67
8824 9098 2.939460 AGCAAACAACAACAGTGGAC 57.061 45.000 0.00 0.00 0.00 4.02
8873 9150 8.967552 AAAATCTAGAAGTACAACTCTACACG 57.032 34.615 0.00 0.00 0.00 4.49
9099 9381 1.929169 CATCACATGTCGCCTGTACAG 59.071 52.381 16.34 16.34 0.00 2.74
9183 9590 5.527026 TTTGGCCCCAAATATTCCAAATT 57.473 34.783 12.10 0.00 40.60 1.82
9393 9831 5.184479 CACAATTTTGATGGAGATGTGGTCT 59.816 40.000 0.00 0.00 40.81 3.85
9429 9867 2.907042 CCTGGGGGAGTATATCTGAACC 59.093 54.545 0.00 0.00 33.58 3.62
9442 9880 0.771127 CAAAGACTGAACCTGGGGGA 59.229 55.000 0.00 0.00 36.25 4.81
9443 9881 0.771127 TCAAAGACTGAACCTGGGGG 59.229 55.000 0.00 0.00 38.88 5.40
9464 9916 9.855021 ACTAAATATTTGCACAAGAAATACACC 57.145 29.630 11.05 0.00 30.08 4.16
9493 9945 6.887545 CCCCTATGGTTGTGATTTGTAAGTAA 59.112 38.462 0.00 0.00 0.00 2.24
9499 9951 4.396357 TTCCCCTATGGTTGTGATTTGT 57.604 40.909 0.00 0.00 34.77 2.83
9527 9979 1.879380 CACTTTCCGTCCAGATGCAAA 59.121 47.619 0.00 0.00 0.00 3.68
9528 9980 1.522668 CACTTTCCGTCCAGATGCAA 58.477 50.000 0.00 0.00 0.00 4.08
9537 9989 0.868406 CTGTCCTTGCACTTTCCGTC 59.132 55.000 0.00 0.00 0.00 4.79
9542 9994 4.685924 CAAATTGACTGTCCTTGCACTTT 58.314 39.130 5.17 0.00 0.00 2.66
9552 10004 4.305989 TCCTGTTTGCAAATTGACTGTC 57.694 40.909 16.21 0.00 0.00 3.51
9556 10008 4.255833 TGGATCCTGTTTGCAAATTGAC 57.744 40.909 16.21 3.36 0.00 3.18
9587 10108 3.495753 CCCGAGTGGTGTAAACTTGTAAC 59.504 47.826 0.00 0.00 0.00 2.50
9621 10142 0.529773 ACACACACAGTAGCCACACG 60.530 55.000 0.00 0.00 0.00 4.49
9756 10305 0.250684 ACGATTGGTGTGCATGGACA 60.251 50.000 16.89 16.89 0.00 4.02


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

AutoCloner maintained by Alex Coulton.