Multiple sequence alignment - TraesCS6B01G273900

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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 TraesCS6B01G273900 chr6B 100.000 5224 0 0 1 5224 494423200 494428423 0.000000e+00 9648.0
1 TraesCS6B01G273900 chr6B 75.159 314 55 15 398 691 142987226 142986916 5.490000e-25 126.0
2 TraesCS6B01G273900 chr6A 92.934 5279 259 45 1 5218 465938794 465933569 0.000000e+00 7577.0
3 TraesCS6B01G273900 chr6D 93.381 4925 206 47 326 5218 327210383 327205547 0.000000e+00 7179.0
4 TraesCS6B01G273900 chr6D 74.888 223 42 10 395 607 3918417 3918635 7.210000e-14 89.8
5 TraesCS6B01G273900 chr6D 79.389 131 22 4 395 521 324780764 324780635 2.590000e-13 87.9
6 TraesCS6B01G273900 chr1B 74.847 326 52 16 395 696 7037457 7037776 2.560000e-23 121.0
7 TraesCS6B01G273900 chr1B 75.732 239 42 11 394 619 10273092 10272857 7.150000e-19 106.0
8 TraesCS6B01G273900 chr1D 76.136 264 39 16 394 641 8005692 8005437 3.310000e-22 117.0
9 TraesCS6B01G273900 chr2B 75.665 263 44 12 394 641 776989051 776989308 4.280000e-21 113.0
10 TraesCS6B01G273900 chr7D 78.295 129 20 7 463 584 53702795 53702922 5.610000e-10 76.8
11 TraesCS6B01G273900 chr7D 95.000 40 1 1 657 696 634141229 634141267 1.570000e-05 62.1
12 TraesCS6B01G273900 chr7B 77.027 148 22 8 559 696 24122661 24122516 2.020000e-09 75.0
13 TraesCS6B01G273900 chr3D 93.617 47 3 0 650 696 603152915 603152869 2.610000e-08 71.3
14 TraesCS6B01G273900 chr2A 93.333 45 3 0 652 696 735556717 735556761 3.380000e-07 67.6
15 TraesCS6B01G273900 chr1A 91.489 47 4 0 650 696 32540008 32539962 1.210000e-06 65.8
16 TraesCS6B01G273900 chr5D 95.000 40 1 1 657 696 327210937 327210899 1.570000e-05 62.1
17 TraesCS6B01G273900 chrUn 94.872 39 1 1 658 696 42486786 42486823 5.650000e-05 60.2
18 TraesCS6B01G273900 chr4D 94.872 39 1 1 658 696 495094073 495094110 5.650000e-05 60.2


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 TraesCS6B01G273900 chr6B 494423200 494428423 5223 False 9648 9648 100.000 1 5224 1 chr6B.!!$F1 5223
1 TraesCS6B01G273900 chr6A 465933569 465938794 5225 True 7577 7577 92.934 1 5218 1 chr6A.!!$R1 5217
2 TraesCS6B01G273900 chr6D 327205547 327210383 4836 True 7179 7179 93.381 326 5218 1 chr6D.!!$R2 4892

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
697 708 0.032416 AGGCCGGGTATGTACTCACT 60.032 55.0 2.18 0.0 0.00 3.41 F
698 709 0.104304 GGCCGGGTATGTACTCACTG 59.896 60.0 2.18 0.0 0.00 3.66 F
700 711 0.248907 CCGGGTATGTACTCACTGCG 60.249 60.0 0.00 0.0 0.00 5.18 F
701 712 0.736636 CGGGTATGTACTCACTGCGA 59.263 55.0 0.00 0.0 0.00 5.10 F
2471 2522 1.028905 TTTCCCTTGCAGAAACCGTG 58.971 50.0 0.00 0.0 0.00 4.94 F
2741 2792 1.708993 AAGGCTGTGAAGGTCTGGCA 61.709 55.0 0.00 0.0 33.29 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2445 1.616367 ATGGACATGGCCATCAGCA 59.384 52.632 28.49 0.15 45.36 4.41 R
2423 2473 3.005897 GCAAGAAAAGAGGGGAGAAAACC 59.994 47.826 0.00 0.00 0.00 3.27 R
2612 2663 5.126222 TGCAACAAGTTCCTGATTAACAACA 59.874 36.000 0.00 0.00 0.00 3.33 R
2741 2792 6.042093 TGACAGATTCTACCAGAACTGTTCTT 59.958 38.462 19.89 9.84 41.75 2.52 R
3954 4011 1.336755 CAAACTAAAGTGGGCGCAAGT 59.663 47.619 10.83 2.01 41.68 3.16 R
4560 4621 1.061411 CATCATGCGCACAAGGTCG 59.939 57.895 14.90 0.00 0.00 4.79 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
36 37 8.834004 TGAGAACCACATACTATAGTAAGGTT 57.166 34.615 29.15 29.15 41.99 3.50
55 56 7.735326 AAGGTTAGTGTGATAGGTCAAGTAT 57.265 36.000 0.00 0.00 35.80 2.12
57 58 6.895756 AGGTTAGTGTGATAGGTCAAGTATGA 59.104 38.462 0.00 0.00 35.80 2.15
72 73 8.669243 GGTCAAGTATGAAGTTTATCTTTGGAG 58.331 37.037 5.01 0.00 37.30 3.86
92 93 5.774690 TGGAGGATACAATTTGATAATGGGC 59.225 40.000 2.79 0.00 41.41 5.36
99 100 1.109609 TTTGATAATGGGCGCATGCA 58.890 45.000 17.93 12.79 45.35 3.96
103 104 0.386476 ATAATGGGCGCATGCAACAG 59.614 50.000 17.93 1.75 45.35 3.16
123 124 7.252708 CAACAGTGCATGTGACATATTTGTAT 58.747 34.615 0.00 0.00 43.00 2.29
125 126 5.684184 CAGTGCATGTGACATATTTGTATGC 59.316 40.000 12.79 12.79 42.09 3.14
155 156 7.894376 AGGAATATTTCAAATGCAACACAAG 57.106 32.000 0.00 0.00 0.00 3.16
163 164 4.513318 TCAAATGCAACACAAGTATCACGA 59.487 37.500 0.00 0.00 0.00 4.35
179 180 1.066303 CACGAGAGGTGCAGATCCTAC 59.934 57.143 0.00 0.00 40.33 3.18
180 181 1.341089 ACGAGAGGTGCAGATCCTACA 60.341 52.381 0.00 0.00 35.20 2.74
225 226 5.750067 ACGCATGCCATGATTAAGAAAAATC 59.250 36.000 13.15 0.00 36.57 2.17
244 245 9.788960 GAAAAATCTAAACTGCAAAGGTATAGG 57.211 33.333 0.00 0.00 0.00 2.57
310 311 8.898792 GTCAAACCTTACACGATTAATTTTGTC 58.101 33.333 6.24 0.00 0.00 3.18
315 316 7.960738 ACCTTACACGATTAATTTTGTCATTCG 59.039 33.333 6.24 0.00 0.00 3.34
318 319 7.775729 ACACGATTAATTTTGTCATTCGTTC 57.224 32.000 0.00 0.00 36.33 3.95
319 320 6.799925 ACACGATTAATTTTGTCATTCGTTCC 59.200 34.615 0.00 0.00 36.33 3.62
323 324 6.885952 TTAATTTTGTCATTCGTTCCTGGA 57.114 33.333 0.00 0.00 0.00 3.86
344 345 4.403453 GAAGGCATCATGTAACGTTGTTC 58.597 43.478 11.99 2.07 0.00 3.18
379 380 5.859205 AGCTGATGTTCTTTGAAAAAGGT 57.141 34.783 0.00 0.00 0.00 3.50
380 381 6.959639 AGCTGATGTTCTTTGAAAAAGGTA 57.040 33.333 0.00 0.00 0.00 3.08
381 382 7.530426 AGCTGATGTTCTTTGAAAAAGGTAT 57.470 32.000 0.00 0.00 0.00 2.73
382 383 8.635765 AGCTGATGTTCTTTGAAAAAGGTATA 57.364 30.769 0.00 0.00 0.00 1.47
383 384 9.247861 AGCTGATGTTCTTTGAAAAAGGTATAT 57.752 29.630 0.00 0.00 0.00 0.86
392 395 8.167392 TCTTTGAAAAAGGTATATCTTGGACCA 58.833 33.333 0.00 0.00 35.56 4.02
393 396 7.938140 TTGAAAAAGGTATATCTTGGACCAG 57.062 36.000 0.00 0.00 35.56 4.00
423 426 8.380742 TCAGGGTGAAAATCTAGAATCTTACT 57.619 34.615 0.00 0.00 0.00 2.24
439 442 3.053544 TCTTACTTTTGGTGGTTGGGTCA 60.054 43.478 0.00 0.00 0.00 4.02
440 443 2.239681 ACTTTTGGTGGTTGGGTCAA 57.760 45.000 0.00 0.00 0.00 3.18
451 454 0.179067 TTGGGTCAAGTGACGGTGAC 60.179 55.000 12.25 12.25 45.65 3.67
471 474 1.134367 CCGAGCGTCACTCCATTCTTA 59.866 52.381 0.00 0.00 43.01 2.10
495 498 5.444663 AGGCTTTGTTGTTGAAGAATCTC 57.555 39.130 0.00 0.00 0.00 2.75
505 508 4.511454 TGTTGAAGAATCTCGTTGTCCTTG 59.489 41.667 0.00 0.00 0.00 3.61
526 529 2.357009 GTGGTGTCATGAGATGAATGGC 59.643 50.000 0.00 0.00 41.69 4.40
527 530 2.026075 TGGTGTCATGAGATGAATGGCA 60.026 45.455 0.00 0.00 41.69 4.92
530 533 3.630769 GTGTCATGAGATGAATGGCATGT 59.369 43.478 0.00 0.00 41.37 3.21
554 557 7.822334 TGTCCATACTTTTAGTTTGTCGATCAT 59.178 33.333 0.00 0.00 0.00 2.45
634 645 1.651987 ATGAGTATTTGTCGGCGTGG 58.348 50.000 6.85 0.00 0.00 4.94
662 673 5.966636 TCATGTCGATGTTAGTTGTATGC 57.033 39.130 0.00 0.00 0.00 3.14
669 680 6.700081 GTCGATGTTAGTTGTATGCATCCTAA 59.300 38.462 0.19 3.33 34.21 2.69
687 698 1.136828 AATTATGCAGAGGCCGGGTA 58.863 50.000 2.18 0.00 40.13 3.69
696 707 0.388294 GAGGCCGGGTATGTACTCAC 59.612 60.000 2.18 0.00 0.00 3.51
697 708 0.032416 AGGCCGGGTATGTACTCACT 60.032 55.000 2.18 0.00 0.00 3.41
698 709 0.104304 GGCCGGGTATGTACTCACTG 59.896 60.000 2.18 0.00 0.00 3.66
699 710 0.529992 GCCGGGTATGTACTCACTGC 60.530 60.000 2.18 0.00 0.00 4.40
700 711 0.248907 CCGGGTATGTACTCACTGCG 60.249 60.000 0.00 0.00 0.00 5.18
701 712 0.736636 CGGGTATGTACTCACTGCGA 59.263 55.000 0.00 0.00 0.00 5.10
703 714 2.022195 GGGTATGTACTCACTGCGAGA 58.978 52.381 0.00 0.00 45.45 4.04
704 715 2.623889 GGGTATGTACTCACTGCGAGAT 59.376 50.000 0.00 0.00 45.45 2.75
705 716 3.551046 GGGTATGTACTCACTGCGAGATG 60.551 52.174 0.00 0.00 45.45 2.90
706 717 3.066900 GGTATGTACTCACTGCGAGATGT 59.933 47.826 0.00 0.00 45.45 3.06
707 718 2.636768 TGTACTCACTGCGAGATGTG 57.363 50.000 0.00 0.00 45.45 3.21
708 719 1.886542 TGTACTCACTGCGAGATGTGT 59.113 47.619 0.00 0.00 45.45 3.72
709 720 3.078837 TGTACTCACTGCGAGATGTGTA 58.921 45.455 0.00 0.00 45.45 2.90
710 721 2.638556 ACTCACTGCGAGATGTGTAC 57.361 50.000 0.00 0.00 45.45 2.90
711 722 2.163509 ACTCACTGCGAGATGTGTACT 58.836 47.619 0.00 0.00 45.45 2.73
712 723 2.162608 ACTCACTGCGAGATGTGTACTC 59.837 50.000 0.00 0.00 45.45 2.59
823 853 2.485426 CTGACATGCCGTTGTTTCATCT 59.515 45.455 0.00 0.00 0.00 2.90
935 966 2.794910 CTCTCTCGTCGCAGTTTCAAAA 59.205 45.455 0.00 0.00 0.00 2.44
1155 1186 1.265454 ACCCTAACAGCCTTCTCCCG 61.265 60.000 0.00 0.00 0.00 5.14
1552 1590 5.723672 ATGGTAAGACATGATACGGGTAG 57.276 43.478 0.00 0.00 0.00 3.18
1553 1591 3.319972 TGGTAAGACATGATACGGGTAGC 59.680 47.826 0.00 0.00 0.00 3.58
1554 1592 2.795175 AAGACATGATACGGGTAGCG 57.205 50.000 0.00 0.00 0.00 4.26
1577 1615 2.351726 CCTGTTTATTCTTTCGAGCGGG 59.648 50.000 0.00 0.00 0.00 6.13
1663 1701 2.302157 GGTACAGTACAGGTCAGGCTTT 59.698 50.000 12.89 0.00 0.00 3.51
1669 1707 4.631813 CAGTACAGGTCAGGCTTTGTTATC 59.368 45.833 0.00 0.00 0.00 1.75
1747 1791 1.888512 TCCTTCTTGTGCAAATGGAGC 59.111 47.619 0.00 0.00 0.00 4.70
1806 1850 8.738645 ATAAGTCAATAACTGGAATCCTCAAC 57.261 34.615 0.00 0.00 38.58 3.18
1911 1957 3.554934 ACACTTTGTTGAAGGAGATGCA 58.445 40.909 0.00 0.00 39.79 3.96
1920 1966 2.093288 TGAAGGAGATGCAAGCAGTAGG 60.093 50.000 0.00 0.00 0.00 3.18
1949 1995 4.160252 AGGTGCTTCAGTTGTTTTGTCATT 59.840 37.500 0.00 0.00 0.00 2.57
2045 2091 8.057623 AGATTGGATGACCAGACATCTAAAAAT 58.942 33.333 11.45 6.72 45.52 1.82
2101 2147 6.633500 TTGTTCTTTTGTCTATCAAGTGGG 57.367 37.500 0.00 0.00 37.35 4.61
2142 2188 5.130975 TGGAAGATGATTGGCTAGCTCTTTA 59.869 40.000 15.72 5.52 0.00 1.85
2148 2194 5.529791 TGATTGGCTAGCTCTTTATACGTC 58.470 41.667 15.72 0.00 0.00 4.34
2287 2333 4.652421 TCGTTTGCCAAATATGCATGAT 57.348 36.364 10.16 0.00 38.76 2.45
2299 2345 8.447833 CCAAATATGCATGATATTCCAAATTGC 58.552 33.333 10.16 0.00 36.39 3.56
2302 2348 8.771920 ATATGCATGATATTCCAAATTGCAAG 57.228 30.769 10.16 0.00 41.38 4.01
2350 2396 8.813643 ACTATGTGTCAGTGTTTTAGTAAGAC 57.186 34.615 0.00 0.00 0.00 3.01
2395 2445 4.895297 CCATACTTTTGGCCTATGGAATGT 59.105 41.667 18.88 9.80 39.52 2.71
2398 2448 2.530460 TTTGGCCTATGGAATGTGCT 57.470 45.000 3.32 0.00 0.00 4.40
2423 2473 1.410153 GCCATGTCCATTTAAGGCTGG 59.590 52.381 0.00 0.00 39.02 4.85
2468 2519 2.166459 GCCTATTTCCCTTGCAGAAACC 59.834 50.000 2.07 0.00 36.13 3.27
2471 2522 1.028905 TTTCCCTTGCAGAAACCGTG 58.971 50.000 0.00 0.00 0.00 4.94
2741 2792 1.708993 AAGGCTGTGAAGGTCTGGCA 61.709 55.000 0.00 0.00 33.29 4.92
2807 2858 3.933332 GGTGTGCTTGGTTAGAGATACAC 59.067 47.826 0.00 0.00 35.16 2.90
3050 3101 6.263168 TGATTTTTGAAGAACTCCTCAGAACC 59.737 38.462 0.00 0.00 0.00 3.62
3398 3449 4.848357 CTTGGTATGGTCTTGGTCAGATT 58.152 43.478 0.00 0.00 32.60 2.40
3566 3617 2.355010 ATGAGAGGGCTGCAAATACC 57.645 50.000 0.50 0.00 0.00 2.73
3597 3648 4.072131 TGAAGGAATAGCACTTCACCAAC 58.928 43.478 3.23 0.00 45.76 3.77
3686 3737 5.545723 AGAGAGAATGGAAGTTGAGGAAAGA 59.454 40.000 0.00 0.00 0.00 2.52
3728 3779 2.159114 AGCCTTGCTTTTTCTTGCGAAA 60.159 40.909 0.00 0.00 33.89 3.46
3797 3848 4.348168 ACAAGACTCTTGGATTACACTGGT 59.652 41.667 20.58 0.00 0.00 4.00
3800 3851 3.515901 GACTCTTGGATTACACTGGTCCT 59.484 47.826 0.00 0.00 33.15 3.85
3812 3863 9.880157 GATTACACTGGTCCTGTAAGTTATTTA 57.120 33.333 9.03 0.00 37.48 1.40
3816 3867 7.977853 ACACTGGTCCTGTAAGTTATTTATACG 59.022 37.037 0.37 0.00 0.00 3.06
3829 3880 8.154649 AGTTATTTATACGCTTTGCTTAGCAT 57.845 30.769 8.05 0.00 41.28 3.79
3859 3910 9.551734 AATTGAAAAGAAAAAGAGATGAAAGGG 57.448 29.630 0.00 0.00 0.00 3.95
3883 3934 6.642540 GGAACAAAATGGTGAAATCTTGAGAC 59.357 38.462 0.00 0.00 0.00 3.36
3884 3935 6.966534 ACAAAATGGTGAAATCTTGAGACT 57.033 33.333 0.00 0.00 0.00 3.24
3885 3936 8.463930 AACAAAATGGTGAAATCTTGAGACTA 57.536 30.769 0.00 0.00 0.00 2.59
3887 3938 7.721399 ACAAAATGGTGAAATCTTGAGACTAGT 59.279 33.333 0.00 0.00 0.00 2.57
3895 3946 7.062839 GTGAAATCTTGAGACTAGTGTTAGCAG 59.937 40.741 0.00 0.00 0.00 4.24
3953 4010 7.763985 CAGTTCAAACCAACTTCAACCTAATTT 59.236 33.333 0.00 0.00 34.17 1.82
3954 4011 8.973182 AGTTCAAACCAACTTCAACCTAATTTA 58.027 29.630 0.00 0.00 32.34 1.40
3955 4012 9.027129 GTTCAAACCAACTTCAACCTAATTTAC 57.973 33.333 0.00 0.00 0.00 2.01
3960 4017 5.856455 CCAACTTCAACCTAATTTACTTGCG 59.144 40.000 0.00 0.00 0.00 4.85
3985 4042 7.115236 CGCCCACTTTAGTTTGTTTTATTAACC 59.885 37.037 0.00 0.00 0.00 2.85
4013 4070 6.068473 GCATATTTGCTCAGATCAATCACA 57.932 37.500 0.35 0.00 45.77 3.58
4014 4071 5.913514 GCATATTTGCTCAGATCAATCACAC 59.086 40.000 0.35 0.00 45.77 3.82
4015 4072 6.238676 GCATATTTGCTCAGATCAATCACACT 60.239 38.462 0.35 0.00 45.77 3.55
4018 4075 3.340928 TGCTCAGATCAATCACACTTGG 58.659 45.455 0.00 0.00 0.00 3.61
4039 4099 6.817765 TGGGTTTGCTAGTGAAAAATAGAG 57.182 37.500 0.00 0.00 0.00 2.43
4040 4100 6.539173 TGGGTTTGCTAGTGAAAAATAGAGA 58.461 36.000 0.00 0.00 0.00 3.10
4041 4101 7.001674 TGGGTTTGCTAGTGAAAAATAGAGAA 58.998 34.615 0.00 0.00 0.00 2.87
4042 4102 7.669722 TGGGTTTGCTAGTGAAAAATAGAGAAT 59.330 33.333 0.00 0.00 0.00 2.40
4043 4103 9.174166 GGGTTTGCTAGTGAAAAATAGAGAATA 57.826 33.333 0.00 0.00 0.00 1.75
4089 4149 2.582728 TGCTTTGCTGTGTTTTCCTG 57.417 45.000 0.00 0.00 0.00 3.86
4090 4150 2.098614 TGCTTTGCTGTGTTTTCCTGA 58.901 42.857 0.00 0.00 0.00 3.86
4102 4162 7.149569 TGTGTTTTCCTGATGATTCTGATTC 57.850 36.000 0.00 0.00 0.00 2.52
4114 4174 6.662414 TGATTCTGATTCGGTACAATTGTC 57.338 37.500 15.85 6.91 0.00 3.18
4117 4177 7.390440 TGATTCTGATTCGGTACAATTGTCTTT 59.610 33.333 15.85 0.00 0.00 2.52
4119 4179 7.504924 TCTGATTCGGTACAATTGTCTTTTT 57.495 32.000 15.85 0.00 0.00 1.94
4157 4217 6.551227 AGGAAAAGGAGACTGCAAAAAGTATT 59.449 34.615 0.00 0.00 42.68 1.89
4196 4256 1.545428 GCACAGTCTGGATTTCCACCA 60.545 52.381 4.53 0.00 42.01 4.17
4232 4293 5.689514 TCATTTTGCGTTGTAAATTGACCTG 59.310 36.000 0.00 0.00 28.48 4.00
4303 4364 4.946478 AGAGAGTAGTGTCACTTGCTTT 57.054 40.909 11.54 5.50 0.00 3.51
4308 4369 5.525378 AGAGTAGTGTCACTTGCTTTCTTTG 59.475 40.000 11.54 0.00 0.00 2.77
4331 4392 5.528690 TGTTTATCTCCATCTTACATGCAGC 59.471 40.000 0.00 0.00 0.00 5.25
4361 4422 8.141268 GGACAATACATTTGGTTTCAAGAGAAA 58.859 33.333 0.00 0.00 41.26 2.52
4413 4474 2.838202 GAGTTATTCACCCCACTCCAGA 59.162 50.000 0.00 0.00 31.16 3.86
4560 4621 0.036388 TCCAAATGGCTGGAGACGAC 60.036 55.000 0.00 0.00 40.71 4.34
4582 4643 1.374343 CCTTGTGCGCATGATGCTCT 61.374 55.000 15.91 0.00 42.25 4.09
4704 4765 4.005650 TCAGCATTGTTGGTTGATCTCTC 58.994 43.478 0.40 0.00 0.00 3.20
4818 4884 2.278854 GCATCTCTGGAAGACTTGCTC 58.721 52.381 8.27 0.00 38.67 4.26
4819 4885 2.903798 CATCTCTGGAAGACTTGCTCC 58.096 52.381 8.27 0.00 38.67 4.70
4822 4888 0.318441 TCTGGAAGACTTGCTCCGTG 59.682 55.000 8.27 0.00 38.67 4.94
4952 5018 4.370049 CCTTTGCATGTGTTGATGTTTCA 58.630 39.130 0.00 0.00 0.00 2.69
4961 5027 2.042297 TGTTGATGTTTCATAGGCCCCA 59.958 45.455 0.00 0.00 0.00 4.96
5038 5104 7.252995 CGTGATGCGACTTTAGCTTTAATTTTC 60.253 37.037 0.00 0.00 44.77 2.29
5040 5106 5.705902 TGCGACTTTAGCTTTAATTTTCCC 58.294 37.500 0.00 0.00 35.28 3.97
5041 5107 5.241949 TGCGACTTTAGCTTTAATTTTCCCA 59.758 36.000 0.00 0.00 35.28 4.37
5042 5108 5.800438 GCGACTTTAGCTTTAATTTTCCCAG 59.200 40.000 0.00 0.00 0.00 4.45
5068 5134 9.309796 GTTAGTACTAATACGTGCAAAAACAAG 57.690 33.333 18.03 0.00 36.33 3.16
5079 5146 2.419990 GCAAAAACAAGTCCTTGGCCTT 60.420 45.455 3.32 0.00 44.45 4.35
5092 5159 3.575687 CCTTGGCCTTCAAAGATTCTGTT 59.424 43.478 3.32 0.00 34.56 3.16
5097 5164 6.690530 TGGCCTTCAAAGATTCTGTTATTTG 58.309 36.000 3.32 0.00 34.66 2.32
5151 5219 4.581409 TCACGTTTTTCCCTTTCCCTTTAG 59.419 41.667 0.00 0.00 0.00 1.85
5153 5221 5.068067 CACGTTTTTCCCTTTCCCTTTAGAA 59.932 40.000 0.00 0.00 0.00 2.10
5218 5286 5.300969 CACACCAGTGTTAATCATTGAGG 57.699 43.478 0.00 0.00 42.83 3.86
5219 5287 3.758554 ACACCAGTGTTAATCATTGAGGC 59.241 43.478 0.00 0.00 41.83 4.70
5220 5288 3.009723 ACCAGTGTTAATCATTGAGGCG 58.990 45.455 0.00 0.00 36.12 5.52
5221 5289 3.009723 CCAGTGTTAATCATTGAGGCGT 58.990 45.455 0.00 0.00 36.12 5.68
5222 5290 3.181507 CCAGTGTTAATCATTGAGGCGTG 60.182 47.826 0.00 0.00 36.12 5.34
5223 5291 2.420022 AGTGTTAATCATTGAGGCGTGC 59.580 45.455 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.956328 ACTTCATACTTGACCTATCACACTA 57.044 36.000 0.00 0.00 33.38 2.74
44 45 9.667107 CCAAAGATAAACTTCATACTTGACCTA 57.333 33.333 0.00 0.00 37.93 3.08
46 47 8.561738 TCCAAAGATAAACTTCATACTTGACC 57.438 34.615 0.00 0.00 37.93 4.02
48 49 8.602424 TCCTCCAAAGATAAACTTCATACTTGA 58.398 33.333 0.00 0.00 37.93 3.02
55 56 9.753674 AATTGTATCCTCCAAAGATAAACTTCA 57.246 29.630 0.00 0.00 37.93 3.02
72 73 4.022416 TGCGCCCATTATCAAATTGTATCC 60.022 41.667 4.18 0.00 0.00 2.59
99 100 5.710513 ACAAATATGTCACATGCACTGTT 57.289 34.783 0.00 0.00 33.41 3.16
103 104 5.580661 TGCATACAAATATGTCACATGCAC 58.419 37.500 11.71 0.00 46.41 4.57
131 132 7.444299 ACTTGTGTTGCATTTGAAATATTCCT 58.556 30.769 0.00 0.00 0.00 3.36
138 139 5.685068 CGTGATACTTGTGTTGCATTTGAAA 59.315 36.000 0.00 0.00 0.00 2.69
140 141 4.513318 TCGTGATACTTGTGTTGCATTTGA 59.487 37.500 0.00 0.00 0.00 2.69
155 156 2.287909 GGATCTGCACCTCTCGTGATAC 60.288 54.545 0.00 0.00 46.20 2.24
163 164 5.898120 AGTATATGTAGGATCTGCACCTCT 58.102 41.667 0.00 0.00 38.76 3.69
194 195 6.917477 TCTTAATCATGGCATGCGTAAAATTC 59.083 34.615 22.56 0.00 0.00 2.17
200 201 5.826601 TTTTCTTAATCATGGCATGCGTA 57.173 34.783 22.56 13.31 0.00 4.42
202 203 5.981315 AGATTTTTCTTAATCATGGCATGCG 59.019 36.000 22.56 8.14 37.06 4.73
225 226 5.497474 ACCACCTATACCTTTGCAGTTTAG 58.503 41.667 0.00 0.00 0.00 1.85
283 284 8.626526 ACAAAATTAATCGTGTAAGGTTTGACT 58.373 29.630 16.98 0.00 32.03 3.41
298 299 7.535139 TCCAGGAACGAATGACAAAATTAATC 58.465 34.615 0.00 0.00 0.00 1.75
299 300 7.461182 TCCAGGAACGAATGACAAAATTAAT 57.539 32.000 0.00 0.00 0.00 1.40
303 304 4.218417 CCTTCCAGGAACGAATGACAAAAT 59.782 41.667 0.00 0.00 37.67 1.82
310 311 1.672881 GATGCCTTCCAGGAACGAATG 59.327 52.381 0.00 0.00 37.67 2.67
315 316 2.134789 ACATGATGCCTTCCAGGAAC 57.865 50.000 0.00 0.00 37.67 3.62
318 319 1.942657 CGTTACATGATGCCTTCCAGG 59.057 52.381 0.00 0.00 38.80 4.45
319 320 2.632377 ACGTTACATGATGCCTTCCAG 58.368 47.619 0.00 0.00 0.00 3.86
323 324 3.818210 TGAACAACGTTACATGATGCCTT 59.182 39.130 0.00 0.00 0.00 4.35
333 334 9.047871 GCTTTATTAATCACTGAACAACGTTAC 57.952 33.333 0.00 0.00 0.00 2.50
377 378 6.235231 TGAAGAACTGGTCCAAGATATACC 57.765 41.667 0.00 0.00 0.00 2.73
379 380 5.366768 CCCTGAAGAACTGGTCCAAGATATA 59.633 44.000 0.00 0.00 36.11 0.86
380 381 4.164988 CCCTGAAGAACTGGTCCAAGATAT 59.835 45.833 0.00 0.00 36.11 1.63
381 382 3.519510 CCCTGAAGAACTGGTCCAAGATA 59.480 47.826 0.00 0.00 36.11 1.98
382 383 2.307098 CCCTGAAGAACTGGTCCAAGAT 59.693 50.000 0.00 0.00 36.11 2.40
383 384 1.699634 CCCTGAAGAACTGGTCCAAGA 59.300 52.381 0.00 0.00 36.11 3.02
392 395 6.688073 TCTAGATTTTCACCCTGAAGAACT 57.312 37.500 0.00 0.00 37.70 3.01
393 396 7.826744 AGATTCTAGATTTTCACCCTGAAGAAC 59.173 37.037 0.00 0.00 37.70 3.01
423 426 1.827969 CACTTGACCCAACCACCAAAA 59.172 47.619 0.00 0.00 0.00 2.44
429 432 1.147376 CCGTCACTTGACCCAACCA 59.853 57.895 3.77 0.00 41.86 3.67
451 454 0.108615 AAGAATGGAGTGACGCTCGG 60.109 55.000 9.84 0.00 45.03 4.63
452 455 2.561733 TAAGAATGGAGTGACGCTCG 57.438 50.000 9.84 0.00 45.03 5.03
471 474 6.225981 AGATTCTTCAACAACAAAGCCTTT 57.774 33.333 0.00 0.00 0.00 3.11
495 498 1.264020 CATGACACCACAAGGACAACG 59.736 52.381 0.00 0.00 38.69 4.10
505 508 2.357009 GCCATTCATCTCATGACACCAC 59.643 50.000 0.00 0.00 39.39 4.16
526 529 7.359262 TCGACAAACTAAAAGTATGGACATG 57.641 36.000 0.00 0.00 0.00 3.21
527 530 7.822334 TGATCGACAAACTAAAAGTATGGACAT 59.178 33.333 0.00 0.00 0.00 3.06
530 533 9.878667 TTATGATCGACAAACTAAAAGTATGGA 57.121 29.630 0.00 0.00 0.00 3.41
619 625 2.691984 AAAACCACGCCGACAAATAC 57.308 45.000 0.00 0.00 0.00 1.89
662 673 3.005554 CGGCCTCTGCATAATTAGGATG 58.994 50.000 0.00 0.00 40.13 3.51
669 680 1.003580 CATACCCGGCCTCTGCATAAT 59.996 52.381 0.00 0.00 40.13 1.28
675 686 0.674534 GAGTACATACCCGGCCTCTG 59.325 60.000 0.00 0.00 0.00 3.35
687 698 2.493675 ACACATCTCGCAGTGAGTACAT 59.506 45.455 10.85 0.00 45.46 2.29
700 711 2.638556 ACACAGCGAGTACACATCTC 57.361 50.000 0.00 0.00 0.00 2.75
701 712 3.059884 CAAACACAGCGAGTACACATCT 58.940 45.455 0.00 0.00 0.00 2.90
702 713 2.800544 ACAAACACAGCGAGTACACATC 59.199 45.455 0.00 0.00 0.00 3.06
703 714 2.833794 ACAAACACAGCGAGTACACAT 58.166 42.857 0.00 0.00 0.00 3.21
704 715 2.303163 ACAAACACAGCGAGTACACA 57.697 45.000 0.00 0.00 0.00 3.72
705 716 3.367025 GGATACAAACACAGCGAGTACAC 59.633 47.826 0.00 0.00 0.00 2.90
706 717 3.581755 GGATACAAACACAGCGAGTACA 58.418 45.455 0.00 0.00 0.00 2.90
777 788 3.945640 TCTTTAGCCATTTCCCCTACC 57.054 47.619 0.00 0.00 0.00 3.18
778 789 5.048846 TCATCTTTAGCCATTTCCCCTAC 57.951 43.478 0.00 0.00 0.00 3.18
823 853 2.602676 GGCTGGTTGGGCCTGAGTA 61.603 63.158 4.53 0.00 45.57 2.59
935 966 0.308993 GCAGTGAGAGCGCAAACTTT 59.691 50.000 11.47 0.00 0.00 2.66
1548 1586 4.032558 CGAAAGAATAAACAGGACGCTACC 59.967 45.833 0.00 0.00 0.00 3.18
1549 1587 4.860907 TCGAAAGAATAAACAGGACGCTAC 59.139 41.667 0.00 0.00 37.03 3.58
1550 1588 5.063180 TCGAAAGAATAAACAGGACGCTA 57.937 39.130 0.00 0.00 37.03 4.26
1551 1589 3.921677 TCGAAAGAATAAACAGGACGCT 58.078 40.909 0.00 0.00 37.03 5.07
1552 1590 3.483738 GCTCGAAAGAATAAACAGGACGC 60.484 47.826 0.00 0.00 41.32 5.19
1553 1591 3.241678 CGCTCGAAAGAATAAACAGGACG 60.242 47.826 0.00 0.00 41.32 4.79
1554 1592 3.062234 CCGCTCGAAAGAATAAACAGGAC 59.938 47.826 0.00 0.00 41.32 3.85
1577 1615 3.720193 CTGCACACTGGCACGAGC 61.720 66.667 0.00 0.00 39.25 5.03
1651 1689 2.699954 ACGATAACAAAGCCTGACCTG 58.300 47.619 0.00 0.00 0.00 4.00
1663 1701 6.708502 TCAATTGGAAACTCAGAACGATAACA 59.291 34.615 5.42 0.00 0.00 2.41
1669 1707 4.065088 TCCTCAATTGGAAACTCAGAACG 58.935 43.478 5.42 0.00 32.39 3.95
1703 1741 4.320870 CCCTAACGAGCAAAACTTCCTAA 58.679 43.478 0.00 0.00 0.00 2.69
1747 1791 8.971073 ACCAAAATCCAGGTAAATCTTCTATTG 58.029 33.333 0.00 0.00 36.07 1.90
1806 1850 7.837202 AATTCACCATCAATAACAGCAAATG 57.163 32.000 0.00 0.00 0.00 2.32
1896 1940 2.156917 CTGCTTGCATCTCCTTCAACA 58.843 47.619 0.00 0.00 0.00 3.33
1920 1966 5.629079 AAACAACTGAAGCACCTAATAGC 57.371 39.130 0.00 0.00 0.00 2.97
1924 1970 4.702612 TGACAAAACAACTGAAGCACCTAA 59.297 37.500 0.00 0.00 0.00 2.69
1949 1995 9.421806 CACAATTTATTCCAGCTTCATTAAACA 57.578 29.630 0.00 0.00 0.00 2.83
2101 2147 6.937436 TCTTCCAAACACCTAGAGAAAAAC 57.063 37.500 0.00 0.00 0.00 2.43
2142 2188 4.754372 TCACAACGAGTACTTGACGTAT 57.246 40.909 17.37 2.27 39.31 3.06
2148 2194 8.346300 AGTATCTATCATCACAACGAGTACTTG 58.654 37.037 8.69 8.69 0.00 3.16
2280 2326 5.128991 TCCTTGCAATTTGGAATATCATGCA 59.871 36.000 0.00 0.00 40.22 3.96
2287 2333 7.098477 CACATTTCTCCTTGCAATTTGGAATA 58.902 34.615 0.00 0.00 0.00 1.75
2395 2445 1.616367 ATGGACATGGCCATCAGCA 59.384 52.632 28.49 0.15 45.36 4.41
2423 2473 3.005897 GCAAGAAAAGAGGGGAGAAAACC 59.994 47.826 0.00 0.00 0.00 3.27
2612 2663 5.126222 TGCAACAAGTTCCTGATTAACAACA 59.874 36.000 0.00 0.00 0.00 3.33
2741 2792 6.042093 TGACAGATTCTACCAGAACTGTTCTT 59.958 38.462 19.89 9.84 41.75 2.52
2807 2858 2.478134 GTCACTGCTAGTGCACAAAGAG 59.522 50.000 21.04 15.53 45.54 2.85
3050 3101 1.463444 GAATCCACACGAAAAGGGTCG 59.537 52.381 0.00 0.00 46.54 4.79
3398 3449 4.727792 TGGCATTCCCATCATCTCATAA 57.272 40.909 0.00 0.00 39.18 1.90
3566 3617 4.940046 AGTGCTATTCCTTCAGTGTCATTG 59.060 41.667 0.00 0.00 0.00 2.82
3665 3716 5.308825 TGTCTTTCCTCAACTTCCATTCTC 58.691 41.667 0.00 0.00 0.00 2.87
3686 3737 2.676748 TCAACAAAATTCTGGCCCTGT 58.323 42.857 0.00 0.00 0.00 4.00
3749 3800 5.105997 GCAATAGTGTTCTGCTTCCTCAAAT 60.106 40.000 0.00 0.00 33.20 2.32
3797 3848 7.767198 AGCAAAGCGTATAAATAACTTACAGGA 59.233 33.333 0.00 0.00 0.00 3.86
3812 3863 3.199880 AGGATGCTAAGCAAAGCGTAT 57.800 42.857 5.13 0.00 45.85 3.06
3816 3867 5.505173 TCAATTAGGATGCTAAGCAAAGC 57.495 39.130 12.50 3.50 43.62 3.51
3825 3876 9.082313 TCTCTTTTTCTTTTCAATTAGGATGCT 57.918 29.630 0.00 0.00 0.00 3.79
3826 3877 9.866798 ATCTCTTTTTCTTTTCAATTAGGATGC 57.133 29.630 0.00 0.00 0.00 3.91
3848 3899 5.243730 TCACCATTTTGTTCCCTTTCATCTC 59.756 40.000 0.00 0.00 0.00 2.75
3859 3910 7.428826 AGTCTCAAGATTTCACCATTTTGTTC 58.571 34.615 0.00 0.00 0.00 3.18
3883 3934 7.979115 GAGTTAACTCATCTGCTAACACTAG 57.021 40.000 27.12 0.00 42.42 2.57
3929 3986 9.027129 GTAAATTAGGTTGAAGTTGGTTTGAAC 57.973 33.333 0.00 0.00 0.00 3.18
3932 3989 9.030301 CAAGTAAATTAGGTTGAAGTTGGTTTG 57.970 33.333 0.00 0.00 0.00 2.93
3953 4010 2.550606 CAAACTAAAGTGGGCGCAAGTA 59.449 45.455 10.83 0.00 41.68 2.24
3954 4011 1.336755 CAAACTAAAGTGGGCGCAAGT 59.663 47.619 10.83 2.01 41.68 3.16
3955 4012 1.336755 ACAAACTAAAGTGGGCGCAAG 59.663 47.619 10.83 1.26 43.44 4.01
3960 4017 8.145767 AGGTTAATAAAACAAACTAAAGTGGGC 58.854 33.333 0.00 0.00 0.00 5.36
4008 4065 3.149196 CACTAGCAAACCCAAGTGTGAT 58.851 45.455 0.00 0.00 32.34 3.06
4009 4066 2.171659 TCACTAGCAAACCCAAGTGTGA 59.828 45.455 0.00 0.00 40.18 3.58
4011 4068 3.290948 TTCACTAGCAAACCCAAGTGT 57.709 42.857 0.00 0.00 40.18 3.55
4012 4069 4.647424 TTTTCACTAGCAAACCCAAGTG 57.353 40.909 0.00 0.00 40.54 3.16
4013 4070 5.869649 ATTTTTCACTAGCAAACCCAAGT 57.130 34.783 0.00 0.00 0.00 3.16
4014 4071 7.174946 TCTCTATTTTTCACTAGCAAACCCAAG 59.825 37.037 0.00 0.00 0.00 3.61
4015 4072 7.001674 TCTCTATTTTTCACTAGCAAACCCAA 58.998 34.615 0.00 0.00 0.00 4.12
4073 4133 5.302568 AGAATCATCAGGAAAACACAGCAAA 59.697 36.000 0.00 0.00 0.00 3.68
4089 4149 7.225538 AGACAATTGTACCGAATCAGAATCATC 59.774 37.037 11.95 0.00 0.00 2.92
4090 4150 7.050377 AGACAATTGTACCGAATCAGAATCAT 58.950 34.615 11.95 0.00 0.00 2.45
4119 4179 6.772716 GTCTCCTTTTCCTGCATATATTGGAA 59.227 38.462 0.00 0.00 36.87 3.53
4121 4181 6.206243 CAGTCTCCTTTTCCTGCATATATTGG 59.794 42.308 0.00 0.00 0.00 3.16
4157 4217 3.251487 GTGCTCGTTTTAGCCCTTGTAAA 59.749 43.478 0.00 0.00 42.05 2.01
4196 4256 5.947228 ACGCAAAATGATCGATATCCATT 57.053 34.783 0.00 1.06 0.00 3.16
4303 4364 7.828717 TGCATGTAAGATGGAGATAAACAAAGA 59.171 33.333 0.00 0.00 0.00 2.52
4308 4369 5.333645 CGCTGCATGTAAGATGGAGATAAAC 60.334 44.000 9.18 0.00 39.43 2.01
4331 4392 4.457603 TGAAACCAAATGTATTGTCCCTCG 59.542 41.667 0.00 0.00 0.00 4.63
4379 4440 7.054124 GGGTGAATAACTCATCTTGTCCATAA 58.946 38.462 0.00 0.00 35.28 1.90
4390 4451 3.189606 TGGAGTGGGGTGAATAACTCAT 58.810 45.455 4.27 0.00 40.67 2.90
4391 4452 2.571653 CTGGAGTGGGGTGAATAACTCA 59.428 50.000 4.27 0.00 40.67 3.41
4397 4458 1.566298 GCCTCTGGAGTGGGGTGAAT 61.566 60.000 0.00 0.00 0.00 2.57
4413 4474 2.097825 CTTGCTAGCATTTCCTTGCCT 58.902 47.619 20.13 0.00 43.83 4.75
4491 4552 2.031157 CGTCACATTGTGAAGGAAACCC 60.031 50.000 20.57 5.52 44.49 4.11
4536 4597 1.377202 TCCAGCCATTTGGAGTCGC 60.377 57.895 0.00 0.00 42.24 5.19
4547 4608 3.371063 GGTCGTCGTCTCCAGCCA 61.371 66.667 0.00 0.00 0.00 4.75
4560 4621 1.061411 CATCATGCGCACAAGGTCG 59.939 57.895 14.90 0.00 0.00 4.79
4582 4643 1.130054 AACCTCCAGCAGCTGAAGGA 61.130 55.000 33.11 21.26 32.44 3.36
4704 4765 4.202090 GCCATAGAATTTCAGAAGCCAAGG 60.202 45.833 0.00 0.00 0.00 3.61
4794 4860 0.540923 AGTCTTCCAGAGATGCCTGC 59.459 55.000 0.00 0.00 36.61 4.85
4818 4884 2.435938 CACCCGGAATCCACACGG 60.436 66.667 0.73 0.00 46.79 4.94
4819 4885 3.124921 GCACCCGGAATCCACACG 61.125 66.667 0.73 0.00 0.00 4.49
4822 4888 2.851263 TATATGCACCCGGAATCCAC 57.149 50.000 0.73 0.00 0.00 4.02
4863 4929 2.762535 AATAGTGCACCGCAACTAGT 57.237 45.000 14.63 0.00 41.47 2.57
4864 4930 3.782046 AGTAATAGTGCACCGCAACTAG 58.218 45.455 14.63 0.00 41.47 2.57
4865 4931 3.880047 AGTAATAGTGCACCGCAACTA 57.120 42.857 14.63 0.00 41.47 2.24
4961 5027 0.681564 TGCCAACGGTCACAAAAGGT 60.682 50.000 0.00 0.00 0.00 3.50
5038 5104 5.252969 TGCACGTATTAGTACTAACTGGG 57.747 43.478 17.45 11.96 36.36 4.45
5040 5106 8.489559 TGTTTTTGCACGTATTAGTACTAACTG 58.510 33.333 17.45 12.14 36.36 3.16
5041 5107 8.592105 TGTTTTTGCACGTATTAGTACTAACT 57.408 30.769 17.45 9.52 39.91 2.24
5042 5108 9.309796 CTTGTTTTTGCACGTATTAGTACTAAC 57.690 33.333 17.45 6.10 0.00 2.34
5054 5120 2.416701 CCAAGGACTTGTTTTTGCACGT 60.417 45.455 10.81 0.00 38.85 4.49
5068 5134 3.192212 CAGAATCTTTGAAGGCCAAGGAC 59.808 47.826 5.01 0.00 42.52 3.85
5079 5146 4.764823 ACCGGCAAATAACAGAATCTTTGA 59.235 37.500 0.00 0.00 31.76 2.69
5097 5164 8.230486 CACTCAGATGATAATAATTAAACCGGC 58.770 37.037 0.00 0.00 0.00 6.13
5151 5219 6.574350 ACTAGTAACATCACAGCCACTATTC 58.426 40.000 0.00 0.00 0.00 1.75
5153 5221 7.841282 ATACTAGTAACATCACAGCCACTAT 57.159 36.000 6.70 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.