Multiple sequence alignment - TraesCS7A01G256700

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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 TraesCS7A01G256700 chr7A 100.000 5149 0 0 1 5149 245828234 245833382 0.000000e+00 9509.0
1 TraesCS7A01G256700 chr7A 93.023 129 9 0 4606 4734 706262846 706262718 6.810000e-44 189.0
2 TraesCS7A01G256700 chr7A 87.879 66 7 1 96 160 170686389 170686454 5.530000e-10 76.8
3 TraesCS7A01G256700 chr7B 95.719 4485 136 16 160 4604 204103896 204099428 0.000000e+00 7167.0
4 TraesCS7A01G256700 chr7B 90.435 115 8 2 1 112 480630005 480629891 1.160000e-31 148.0
5 TraesCS7A01G256700 chr7D 95.733 4476 131 17 160 4604 233050970 233046524 0.000000e+00 7153.0
6 TraesCS7A01G256700 chr7D 86.842 76 8 2 96 169 117208536 117208611 3.300000e-12 84.2
7 TraesCS7A01G256700 chr6B 88.562 577 33 8 4606 5149 412282831 412283407 0.000000e+00 669.0
8 TraesCS7A01G256700 chr6B 87.522 577 39 5 4606 5149 708042012 708042588 2.020000e-178 636.0
9 TraesCS7A01G256700 chr6B 85.269 577 42 18 4606 5149 197230020 197230586 5.830000e-154 555.0
10 TraesCS7A01G256700 chr6B 95.050 101 4 1 9 109 714187787 714187688 1.920000e-34 158.0
11 TraesCS7A01G256700 chr6B 88.406 69 6 1 106 174 423782522 423782588 1.190000e-11 82.4
12 TraesCS7A01G256700 chr6B 86.111 72 9 1 96 166 476814432 476814361 5.530000e-10 76.8
13 TraesCS7A01G256700 chr1B 88.408 578 33 9 4605 5149 550681389 550680813 0.000000e+00 665.0
14 TraesCS7A01G256700 chr1B 87.716 578 36 9 4606 5149 61320145 61319569 4.350000e-180 641.0
15 TraesCS7A01G256700 chr1B 94.949 99 5 0 9 107 279500416 279500318 6.900000e-34 156.0
16 TraesCS7A01G256700 chr3A 87.674 576 38 5 4606 5148 11779789 11779214 1.560000e-179 640.0
17 TraesCS7A01G256700 chr3A 93.701 127 8 0 4606 4732 544196790 544196916 1.890000e-44 191.0
18 TraesCS7A01G256700 chr3A 94.949 99 5 0 9 107 272766728 272766630 6.900000e-34 156.0
19 TraesCS7A01G256700 chr1A 87.304 575 42 15 4606 5149 373761023 373760449 3.380000e-176 628.0
20 TraesCS7A01G256700 chr1A 92.857 56 4 0 104 159 534529288 534529233 1.190000e-11 82.4
21 TraesCS7A01G256700 chr2B 86.851 578 42 17 4606 5149 383361587 383361010 2.630000e-172 616.0
22 TraesCS7A01G256700 chr2B 91.473 129 10 1 4606 4734 609079654 609079781 5.300000e-40 176.0
23 TraesCS7A01G256700 chr2B 94.949 99 5 0 9 107 703576482 703576384 6.900000e-34 156.0
24 TraesCS7A01G256700 chr2A 85.095 577 50 18 4606 5149 671341821 671342394 1.620000e-154 556.0
25 TraesCS7A01G256700 chr2A 94.495 109 6 0 1 109 17819977 17820085 8.870000e-38 169.0
26 TraesCS7A01G256700 chr2A 91.667 60 5 0 106 165 208749773 208749832 3.300000e-12 84.2
27 TraesCS7A01G256700 chr2A 85.915 71 10 0 105 175 62220536 62220466 5.530000e-10 76.8
28 TraesCS7A01G256700 chr4A 93.023 129 6 3 4607 4734 21048163 21048289 8.800000e-43 185.0
29 TraesCS7A01G256700 chr4A 89.394 66 6 1 96 160 624923518 624923583 1.190000e-11 82.4
30 TraesCS7A01G256700 chr4B 92.248 129 10 0 4606 4734 646926507 646926379 3.170000e-42 183.0
31 TraesCS7A01G256700 chr4B 91.071 112 9 1 1 112 642090774 642090664 3.210000e-32 150.0
32 TraesCS7A01G256700 chr5B 94.059 101 6 0 9 109 641044635 641044535 2.480000e-33 154.0
33 TraesCS7A01G256700 chr3B 92.593 108 5 3 9 113 194766616 194766509 8.930000e-33 152.0
34 TraesCS7A01G256700 chr3B 86.667 75 8 2 96 168 23166030 23166104 1.190000e-11 82.4


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 TraesCS7A01G256700 chr7A 245828234 245833382 5148 False 9509 9509 100.000 1 5149 1 chr7A.!!$F2 5148
1 TraesCS7A01G256700 chr7B 204099428 204103896 4468 True 7167 7167 95.719 160 4604 1 chr7B.!!$R1 4444
2 TraesCS7A01G256700 chr7D 233046524 233050970 4446 True 7153 7153 95.733 160 4604 1 chr7D.!!$R1 4444
3 TraesCS7A01G256700 chr6B 412282831 412283407 576 False 669 669 88.562 4606 5149 1 chr6B.!!$F2 543
4 TraesCS7A01G256700 chr6B 708042012 708042588 576 False 636 636 87.522 4606 5149 1 chr6B.!!$F4 543
5 TraesCS7A01G256700 chr6B 197230020 197230586 566 False 555 555 85.269 4606 5149 1 chr6B.!!$F1 543
6 TraesCS7A01G256700 chr1B 550680813 550681389 576 True 665 665 88.408 4605 5149 1 chr1B.!!$R3 544
7 TraesCS7A01G256700 chr1B 61319569 61320145 576 True 641 641 87.716 4606 5149 1 chr1B.!!$R1 543
8 TraesCS7A01G256700 chr3A 11779214 11779789 575 True 640 640 87.674 4606 5148 1 chr3A.!!$R1 542
9 TraesCS7A01G256700 chr1A 373760449 373761023 574 True 628 628 87.304 4606 5149 1 chr1A.!!$R1 543
10 TraesCS7A01G256700 chr2B 383361010 383361587 577 True 616 616 86.851 4606 5149 1 chr2B.!!$R1 543
11 TraesCS7A01G256700 chr2A 671341821 671342394 573 False 556 556 85.095 4606 5149 1 chr2A.!!$F3 543

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
447 455 0.338814 AGAATCCACCTCTACCGGGT 59.661 55.000 6.32 4.46 37.59 5.28 F
816 824 1.139654 TGCTTGCCGATCAGAGCTTAT 59.860 47.619 0.00 0.00 36.16 1.73 F
870 878 1.179174 GGTGGTTTTGGGGAGCAGTC 61.179 60.000 0.00 0.00 0.00 3.51 F
1274 1283 1.539388 TGCTGTTTGCGGGTTAAGATG 59.461 47.619 0.00 0.00 46.63 2.90 F
1275 1284 1.539827 GCTGTTTGCGGGTTAAGATGT 59.460 47.619 0.00 0.00 0.00 3.06 F
1737 1748 1.554617 GTTGGGAATTTGGGATGGGTG 59.445 52.381 0.00 0.00 0.00 4.61 F
2684 2706 3.356529 AAAGATGAGTTGGCTACCCAG 57.643 47.619 0.00 0.00 43.37 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1787 1.115467 CGTGAGGATAGGCTGTCCTT 58.885 55.000 30.36 16.32 45.93 3.36 R
2684 2706 1.003580 TGACCTTCTTGGCCTGTGATC 59.996 52.381 3.32 0.00 40.22 2.92 R
2799 2821 5.250543 TGGATTTCCCATTCACTCTACTGAA 59.749 40.000 0.00 0.00 40.82 3.02 R
2891 2913 1.242076 CTGACCCAAGTTGAAGGCTG 58.758 55.000 3.87 0.00 0.00 4.85 R
3143 3165 2.242926 TGAAAATTGTCGGCATTCCCA 58.757 42.857 0.00 0.00 0.00 4.37 R
3557 3579 2.086610 AAAATCAGCCCCGCCATAAT 57.913 45.000 0.00 0.00 0.00 1.28 R
4383 4428 0.107017 ACAGCAGGAGCAACACTTGT 60.107 50.000 0.00 0.00 45.49 3.16 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
35 36 8.617290 ACTTATAAGTCCCTGTAAACAAACAG 57.383 34.615 12.50 0.00 39.86 3.16
44 45 4.969484 CTGTAAACAAACAGGTAGGGACT 58.031 43.478 0.00 0.00 42.63 3.85
45 46 5.374071 CTGTAAACAAACAGGTAGGGACTT 58.626 41.667 0.00 0.00 42.63 3.01
46 47 6.497624 TGTAAACAAACAGGTAGGGACTTA 57.502 37.500 0.00 0.00 41.75 2.24
47 48 7.081857 TGTAAACAAACAGGTAGGGACTTAT 57.918 36.000 0.00 0.00 41.75 1.73
48 49 6.938030 TGTAAACAAACAGGTAGGGACTTATG 59.062 38.462 0.00 0.00 41.75 1.90
49 50 5.836024 AACAAACAGGTAGGGACTTATGA 57.164 39.130 0.00 0.00 41.75 2.15
50 51 5.161943 ACAAACAGGTAGGGACTTATGAC 57.838 43.478 0.00 0.00 41.75 3.06
51 52 4.844655 ACAAACAGGTAGGGACTTATGACT 59.155 41.667 0.00 0.00 41.75 3.41
52 53 5.309806 ACAAACAGGTAGGGACTTATGACTT 59.690 40.000 0.00 0.00 41.75 3.01
53 54 6.499350 ACAAACAGGTAGGGACTTATGACTTA 59.501 38.462 0.00 0.00 41.75 2.24
54 55 7.182206 ACAAACAGGTAGGGACTTATGACTTAT 59.818 37.037 0.00 0.00 41.75 1.73
55 56 8.701895 CAAACAGGTAGGGACTTATGACTTATA 58.298 37.037 0.00 0.00 41.75 0.98
56 57 8.849543 AACAGGTAGGGACTTATGACTTATAA 57.150 34.615 0.00 0.00 41.75 0.98
99 100 9.110502 GTCCTAAGACTTATGAAACAAATAGGG 57.889 37.037 2.20 0.00 40.10 3.53
100 101 7.773690 TCCTAAGACTTATGAAACAAATAGGGC 59.226 37.037 0.00 0.00 0.00 5.19
101 102 7.556275 CCTAAGACTTATGAAACAAATAGGGCA 59.444 37.037 0.00 0.00 0.00 5.36
102 103 7.961326 AAGACTTATGAAACAAATAGGGCAT 57.039 32.000 0.00 0.00 0.00 4.40
104 105 9.474313 AAGACTTATGAAACAAATAGGGCATAA 57.526 29.630 0.00 0.00 0.00 1.90
105 106 9.125026 AGACTTATGAAACAAATAGGGCATAAG 57.875 33.333 15.09 15.09 45.13 1.73
106 107 9.120538 GACTTATGAAACAAATAGGGCATAAGA 57.879 33.333 20.69 0.00 43.64 2.10
107 108 8.903820 ACTTATGAAACAAATAGGGCATAAGAC 58.096 33.333 20.69 0.00 43.64 3.01
108 109 9.125026 CTTATGAAACAAATAGGGCATAAGACT 57.875 33.333 12.58 0.00 43.64 3.24
109 110 7.961326 ATGAAACAAATAGGGCATAAGACTT 57.039 32.000 0.00 0.00 0.00 3.01
110 111 7.775053 TGAAACAAATAGGGCATAAGACTTT 57.225 32.000 0.00 0.00 0.00 2.66
111 112 8.189119 TGAAACAAATAGGGCATAAGACTTTT 57.811 30.769 0.00 0.00 0.00 2.27
112 113 8.646900 TGAAACAAATAGGGCATAAGACTTTTT 58.353 29.630 0.00 0.00 0.00 1.94
115 116 8.879427 ACAAATAGGGCATAAGACTTTTTAGT 57.121 30.769 0.00 0.00 0.00 2.24
116 117 9.309224 ACAAATAGGGCATAAGACTTTTTAGTT 57.691 29.630 0.00 0.00 0.00 2.24
117 118 9.573133 CAAATAGGGCATAAGACTTTTTAGTTG 57.427 33.333 0.00 0.00 0.00 3.16
118 119 9.528489 AAATAGGGCATAAGACTTTTTAGTTGA 57.472 29.630 0.00 0.00 0.00 3.18
119 120 8.738645 ATAGGGCATAAGACTTTTTAGTTGAG 57.261 34.615 0.00 0.00 0.00 3.02
120 121 6.779860 AGGGCATAAGACTTTTTAGTTGAGA 58.220 36.000 0.00 0.00 0.00 3.27
121 122 6.655425 AGGGCATAAGACTTTTTAGTTGAGAC 59.345 38.462 0.00 0.00 0.00 3.36
122 123 6.655425 GGGCATAAGACTTTTTAGTTGAGACT 59.345 38.462 0.00 0.00 39.97 3.24
123 124 7.822822 GGGCATAAGACTTTTTAGTTGAGACTA 59.177 37.037 0.00 0.00 37.33 2.59
124 125 8.874816 GGCATAAGACTTTTTAGTTGAGACTAG 58.125 37.037 0.00 0.00 39.43 2.57
125 126 9.640963 GCATAAGACTTTTTAGTTGAGACTAGA 57.359 33.333 0.00 0.00 39.43 2.43
154 155 7.681125 GTCGTAGGACTTATACATCAAACAG 57.319 40.000 8.31 0.00 40.15 3.16
155 156 6.696148 GTCGTAGGACTTATACATCAAACAGG 59.304 42.308 8.31 0.00 40.15 4.00
156 157 5.983720 CGTAGGACTTATACATCAAACAGGG 59.016 44.000 0.00 0.00 0.00 4.45
157 158 4.781934 AGGACTTATACATCAAACAGGGC 58.218 43.478 0.00 0.00 0.00 5.19
158 159 3.883489 GGACTTATACATCAAACAGGGCC 59.117 47.826 0.00 0.00 0.00 5.80
437 445 2.508439 TTCGCGCGAGAATCCACC 60.508 61.111 32.74 0.00 0.00 4.61
447 455 0.338814 AGAATCCACCTCTACCGGGT 59.661 55.000 6.32 4.46 37.59 5.28
745 753 8.431910 TGGAAGAGGACTGTACTTTACTATTT 57.568 34.615 0.00 0.00 0.00 1.40
816 824 1.139654 TGCTTGCCGATCAGAGCTTAT 59.860 47.619 0.00 0.00 36.16 1.73
825 833 4.279671 CCGATCAGAGCTTATAGTGGTCTT 59.720 45.833 6.75 0.00 39.84 3.01
832 840 3.510360 AGCTTATAGTGGTCTTGTCGTGT 59.490 43.478 0.00 0.00 0.00 4.49
870 878 1.179174 GGTGGTTTTGGGGAGCAGTC 61.179 60.000 0.00 0.00 0.00 3.51
944 952 3.431626 CCAGTCTGTGTGTGGTAACTTGA 60.432 47.826 0.00 0.00 37.61 3.02
1206 1215 4.096190 AGGCGGTGCTAGACTAACTATA 57.904 45.455 0.00 0.00 0.00 1.31
1271 1280 3.773117 CTGCTGTTTGCGGGTTAAG 57.227 52.632 0.00 0.00 46.63 1.85
1274 1283 1.539388 TGCTGTTTGCGGGTTAAGATG 59.461 47.619 0.00 0.00 46.63 2.90
1275 1284 1.539827 GCTGTTTGCGGGTTAAGATGT 59.460 47.619 0.00 0.00 0.00 3.06
1529 1540 6.986250 CATGATACTATGGAACTAGCTCACA 58.014 40.000 0.00 0.00 0.00 3.58
1654 1665 7.781056 ACATGTTCCTTTTACTGTCACAAAAT 58.219 30.769 0.00 0.00 0.00 1.82
1737 1748 1.554617 GTTGGGAATTTGGGATGGGTG 59.445 52.381 0.00 0.00 0.00 4.61
1773 1787 4.019321 AGCAACACTATTTCCTGCCTTAGA 60.019 41.667 0.00 0.00 33.41 2.10
1774 1788 4.700213 GCAACACTATTTCCTGCCTTAGAA 59.300 41.667 0.00 0.00 0.00 2.10
1775 1789 5.163713 GCAACACTATTTCCTGCCTTAGAAG 60.164 44.000 0.00 0.00 0.00 2.85
1879 1893 6.018180 GTGAATCCGTGATCTACAAAATACCC 60.018 42.308 0.00 0.00 0.00 3.69
2258 2276 7.523293 ACATGATGGTGTTTGATAGAAAACA 57.477 32.000 0.00 0.00 45.38 2.83
2283 2301 8.680903 CAGCAGTGAGGTCTTGATTTTATTATT 58.319 33.333 0.00 0.00 0.00 1.40
2284 2302 8.680903 AGCAGTGAGGTCTTGATTTTATTATTG 58.319 33.333 0.00 0.00 0.00 1.90
2479 2501 5.763088 AGAAAGAAAAGAAAAGGATCGTGC 58.237 37.500 0.00 0.00 0.00 5.34
2627 2649 5.997746 TCTTGACAATAGAAGACCCAAACAG 59.002 40.000 0.00 0.00 0.00 3.16
2629 2651 5.305585 TGACAATAGAAGACCCAAACAGAC 58.694 41.667 0.00 0.00 0.00 3.51
2684 2706 3.356529 AAAGATGAGTTGGCTACCCAG 57.643 47.619 0.00 0.00 43.37 4.45
2790 2812 7.171167 GTGTTGTAGGTTCTAAAGAGAAGGAAC 59.829 40.741 0.00 0.00 42.46 3.62
2874 2896 7.653311 CCAGTGAAAAGGGAAAGAATAAAACTG 59.347 37.037 0.00 0.00 0.00 3.16
2891 2913 3.983044 ACTGGAATCTTGAGTGGTACC 57.017 47.619 4.43 4.43 0.00 3.34
3023 3045 4.686091 TCTCAACAGAAGTGCAGAATTACG 59.314 41.667 0.00 0.00 0.00 3.18
3143 3165 6.127253 CCAAGTGGATGGCAGAGAATAAAAAT 60.127 38.462 0.00 0.00 37.39 1.82
3310 3332 8.617809 TGTAAATCAGAAGGTTGTTAAAGACAC 58.382 33.333 0.00 0.00 38.18 3.67
3331 3353 7.710044 AGACACAGATAGAGATTGCAATGTAAG 59.290 37.037 18.59 2.64 0.00 2.34
3395 3417 7.126421 AGGGAGAAAAGAAGTGCTATAGATGAA 59.874 37.037 3.21 0.00 0.00 2.57
3498 3520 5.474876 GGGAACAAGTTCACTTCTGATGATT 59.525 40.000 14.25 0.00 39.79 2.57
3589 3611 5.127031 GGGGCTGATTTTATATGTGTGTGTT 59.873 40.000 0.00 0.00 0.00 3.32
3626 3648 7.201478 GCATACGCTTAGATTTAGATAGCCTTG 60.201 40.741 0.00 0.00 34.30 3.61
3683 3705 5.447757 TCCATAATGTTGGCAGATCATCAA 58.552 37.500 0.00 0.00 36.66 2.57
3773 3795 1.446907 AGCATTCTCAAGGAACTGCG 58.553 50.000 0.00 0.00 40.86 5.18
3864 3886 3.785859 GCATGACCGGCCTCCTCA 61.786 66.667 0.00 0.00 0.00 3.86
3962 3984 4.285517 CCTGATACCAAGTATCTGAGCCAT 59.714 45.833 17.99 0.00 43.56 4.40
4068 4090 3.126879 CGATGCTTGAGGCCGCAA 61.127 61.111 21.34 21.34 39.89 4.85
4272 4316 2.656947 TTTCTGGCCACTAAACTGCT 57.343 45.000 0.00 0.00 0.00 4.24
4337 4382 1.328279 ATCAGATGATACGACGGCCA 58.672 50.000 2.24 0.00 32.01 5.36
4370 4415 4.456280 TGAGATTCTGTACATGAAGCGT 57.544 40.909 0.00 6.43 35.31 5.07
4373 4418 5.700832 TGAGATTCTGTACATGAAGCGTTTT 59.299 36.000 0.00 2.13 35.31 2.43
4383 4428 2.594529 GAAGCGTTTTGATTCAGCGA 57.405 45.000 10.18 0.00 42.56 4.93
4416 4461 1.004918 GCTGTACCGCCAGACAGTT 60.005 57.895 0.00 0.00 44.10 3.16
4466 4511 2.970609 CAGTTTTGGCGTTGTATTCGTG 59.029 45.455 0.00 0.00 0.00 4.35
4469 4514 4.023536 AGTTTTGGCGTTGTATTCGTGAAT 60.024 37.500 0.22 0.22 34.93 2.57
4470 4515 3.733024 TTGGCGTTGTATTCGTGAATC 57.267 42.857 0.00 0.00 32.50 2.52
4539 4584 8.558973 AAAAATGAAGTGTCTCTAAGATCCTG 57.441 34.615 0.00 0.00 0.00 3.86
4604 4650 4.876679 TGTGTTTGTTTGAGTATCCGTTCA 59.123 37.500 0.00 0.00 0.00 3.18
4674 4720 7.509659 TGAGAGAGAAGTTTTAGAGGTTAAGGT 59.490 37.037 0.00 0.00 0.00 3.50
4675 4721 7.672240 AGAGAGAAGTTTTAGAGGTTAAGGTG 58.328 38.462 0.00 0.00 0.00 4.00
4676 4722 6.231951 AGAGAAGTTTTAGAGGTTAAGGTGC 58.768 40.000 0.00 0.00 0.00 5.01
4682 4728 1.068121 AGAGGTTAAGGTGCAAGGCT 58.932 50.000 0.00 0.00 0.00 4.58
4729 4802 6.680055 GCATTATGTTATTCAAATGCCTCG 57.320 37.500 7.48 0.00 40.39 4.63
4732 4805 4.558538 ATGTTATTCAAATGCCTCGCTC 57.441 40.909 0.00 0.00 0.00 5.03
4750 4823 2.872858 GCTCCTTTAATCCTAGCAACGG 59.127 50.000 0.00 0.00 33.38 4.44
4767 4846 2.511600 GCGACTCCCACCGGATTG 60.512 66.667 9.46 0.00 37.60 2.67
4797 4876 4.583871 AGATTCGTGCATTCCTCTCTTTT 58.416 39.130 0.00 0.00 0.00 2.27
4815 4894 7.334090 TCTCTTTTCATAACTCCCAAGAGATG 58.666 38.462 5.51 0.00 43.39 2.90
4910 4989 2.290260 TGGAAGTCGCATCACTCCAATT 60.290 45.455 0.00 0.00 0.00 2.32
4994 5075 4.974645 ATCGGCATTGGAATAGAAGGTA 57.025 40.909 0.00 0.00 0.00 3.08
4997 5078 3.181454 CGGCATTGGAATAGAAGGTAGGT 60.181 47.826 0.00 0.00 0.00 3.08
5000 5081 5.193679 GCATTGGAATAGAAGGTAGGTTGT 58.806 41.667 0.00 0.00 0.00 3.32
5034 5115 3.138884 TGCTTGCATAGTGGACAAAGA 57.861 42.857 0.00 0.00 0.00 2.52
5044 5125 7.230510 TGCATAGTGGACAAAGATTACAGTTTT 59.769 33.333 0.00 0.00 0.00 2.43
5082 5163 1.648467 GCCTGTCTGCCGTCCAAATC 61.648 60.000 0.00 0.00 0.00 2.17
5126 5207 3.684788 GCGAAGAACTTGCATTTAGGAGA 59.315 43.478 0.00 0.00 0.00 3.71
5127 5208 4.333926 GCGAAGAACTTGCATTTAGGAGAT 59.666 41.667 0.00 0.00 0.00 2.75
5144 5226 3.118992 GGAGATGCCCAAATCTTCCAAAC 60.119 47.826 0.00 0.00 37.03 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.718734 CTGTTTGTTTACAGGGACTTATAAGTC 58.281 37.037 29.84 29.84 43.68 3.01
10 11 8.617290 CTGTTTGTTTACAGGGACTTATAAGT 57.383 34.615 18.05 18.05 41.43 2.24
22 23 4.969484 AGTCCCTACCTGTTTGTTTACAG 58.031 43.478 0.00 0.00 44.07 2.74
23 24 5.376756 AAGTCCCTACCTGTTTGTTTACA 57.623 39.130 0.00 0.00 0.00 2.41
24 25 7.118825 GTCATAAGTCCCTACCTGTTTGTTTAC 59.881 40.741 0.00 0.00 0.00 2.01
25 26 7.016858 AGTCATAAGTCCCTACCTGTTTGTTTA 59.983 37.037 0.00 0.00 0.00 2.01
26 27 6.002082 GTCATAAGTCCCTACCTGTTTGTTT 58.998 40.000 0.00 0.00 0.00 2.83
27 28 5.309806 AGTCATAAGTCCCTACCTGTTTGTT 59.690 40.000 0.00 0.00 0.00 2.83
28 29 4.844655 AGTCATAAGTCCCTACCTGTTTGT 59.155 41.667 0.00 0.00 0.00 2.83
29 30 5.422214 AGTCATAAGTCCCTACCTGTTTG 57.578 43.478 0.00 0.00 0.00 2.93
30 31 7.750947 ATAAGTCATAAGTCCCTACCTGTTT 57.249 36.000 0.00 0.00 0.00 2.83
31 32 8.849543 TTATAAGTCATAAGTCCCTACCTGTT 57.150 34.615 0.00 0.00 0.00 3.16
32 33 8.480133 CTTATAAGTCATAAGTCCCTACCTGT 57.520 38.462 4.18 0.00 40.84 4.00
73 74 9.110502 CCCTATTTGTTTCATAAGTCTTAGGAC 57.889 37.037 6.47 0.00 42.41 3.85
74 75 7.773690 GCCCTATTTGTTTCATAAGTCTTAGGA 59.226 37.037 2.85 2.85 0.00 2.94
75 76 7.556275 TGCCCTATTTGTTTCATAAGTCTTAGG 59.444 37.037 0.00 0.00 0.00 2.69
76 77 8.506168 TGCCCTATTTGTTTCATAAGTCTTAG 57.494 34.615 0.00 0.00 0.00 2.18
78 79 7.961326 ATGCCCTATTTGTTTCATAAGTCTT 57.039 32.000 0.00 0.00 0.00 3.01
79 80 9.125026 CTTATGCCCTATTTGTTTCATAAGTCT 57.875 33.333 10.12 0.00 38.60 3.24
80 81 9.120538 TCTTATGCCCTATTTGTTTCATAAGTC 57.879 33.333 15.20 0.00 41.54 3.01
81 82 8.903820 GTCTTATGCCCTATTTGTTTCATAAGT 58.096 33.333 15.20 0.00 41.54 2.24
82 83 9.125026 AGTCTTATGCCCTATTTGTTTCATAAG 57.875 33.333 11.46 11.46 41.87 1.73
83 84 9.474313 AAGTCTTATGCCCTATTTGTTTCATAA 57.526 29.630 0.00 0.00 0.00 1.90
84 85 9.474313 AAAGTCTTATGCCCTATTTGTTTCATA 57.526 29.630 0.00 0.00 0.00 2.15
85 86 7.961326 AAGTCTTATGCCCTATTTGTTTCAT 57.039 32.000 0.00 0.00 0.00 2.57
86 87 7.775053 AAAGTCTTATGCCCTATTTGTTTCA 57.225 32.000 0.00 0.00 0.00 2.69
89 90 9.309224 ACTAAAAAGTCTTATGCCCTATTTGTT 57.691 29.630 0.00 0.00 0.00 2.83
90 91 8.879427 ACTAAAAAGTCTTATGCCCTATTTGT 57.121 30.769 0.00 0.00 0.00 2.83
91 92 9.573133 CAACTAAAAAGTCTTATGCCCTATTTG 57.427 33.333 0.00 0.00 0.00 2.32
92 93 9.528489 TCAACTAAAAAGTCTTATGCCCTATTT 57.472 29.630 0.00 0.00 0.00 1.40
93 94 9.178758 CTCAACTAAAAAGTCTTATGCCCTATT 57.821 33.333 0.00 0.00 0.00 1.73
94 95 8.548877 TCTCAACTAAAAAGTCTTATGCCCTAT 58.451 33.333 0.00 0.00 0.00 2.57
95 96 7.822822 GTCTCAACTAAAAAGTCTTATGCCCTA 59.177 37.037 0.00 0.00 0.00 3.53
96 97 6.655425 GTCTCAACTAAAAAGTCTTATGCCCT 59.345 38.462 0.00 0.00 0.00 5.19
97 98 6.655425 AGTCTCAACTAAAAAGTCTTATGCCC 59.345 38.462 0.00 0.00 32.59 5.36
98 99 7.674471 AGTCTCAACTAAAAAGTCTTATGCC 57.326 36.000 0.00 0.00 32.59 4.40
99 100 9.640963 TCTAGTCTCAACTAAAAAGTCTTATGC 57.359 33.333 0.00 0.00 37.53 3.14
107 108 9.851043 CGACTTTTTCTAGTCTCAACTAAAAAG 57.149 33.333 16.94 16.94 45.72 2.27
108 109 9.374838 ACGACTTTTTCTAGTCTCAACTAAAAA 57.625 29.630 0.00 0.00 41.89 1.94
109 110 8.937634 ACGACTTTTTCTAGTCTCAACTAAAA 57.062 30.769 0.00 0.00 41.89 1.52
110 111 9.674824 CTACGACTTTTTCTAGTCTCAACTAAA 57.325 33.333 0.00 0.00 41.89 1.85
111 112 8.295288 CCTACGACTTTTTCTAGTCTCAACTAA 58.705 37.037 0.00 0.00 41.89 2.24
112 113 7.663081 TCCTACGACTTTTTCTAGTCTCAACTA 59.337 37.037 0.00 0.00 41.89 2.24
113 114 6.489361 TCCTACGACTTTTTCTAGTCTCAACT 59.511 38.462 0.00 0.00 41.89 3.16
114 115 6.581919 GTCCTACGACTTTTTCTAGTCTCAAC 59.418 42.308 0.00 0.00 41.89 3.18
115 116 6.675987 GTCCTACGACTTTTTCTAGTCTCAA 58.324 40.000 0.00 0.00 41.89 3.02
116 117 6.251655 GTCCTACGACTTTTTCTAGTCTCA 57.748 41.667 0.00 0.00 41.89 3.27
130 131 6.696148 CCTGTTTGATGTATAAGTCCTACGAC 59.304 42.308 0.00 0.00 39.50 4.34
131 132 6.183360 CCCTGTTTGATGTATAAGTCCTACGA 60.183 42.308 0.00 0.00 0.00 3.43
132 133 5.983720 CCCTGTTTGATGTATAAGTCCTACG 59.016 44.000 0.00 0.00 0.00 3.51
133 134 5.758784 GCCCTGTTTGATGTATAAGTCCTAC 59.241 44.000 0.00 0.00 0.00 3.18
134 135 5.163237 GGCCCTGTTTGATGTATAAGTCCTA 60.163 44.000 0.00 0.00 0.00 2.94
135 136 4.385310 GGCCCTGTTTGATGTATAAGTCCT 60.385 45.833 0.00 0.00 0.00 3.85
136 137 3.883489 GGCCCTGTTTGATGTATAAGTCC 59.117 47.826 0.00 0.00 0.00 3.85
137 138 4.576463 CAGGCCCTGTTTGATGTATAAGTC 59.424 45.833 1.39 0.00 0.00 3.01
138 139 4.227300 TCAGGCCCTGTTTGATGTATAAGT 59.773 41.667 11.27 0.00 32.61 2.24
139 140 4.780815 TCAGGCCCTGTTTGATGTATAAG 58.219 43.478 11.27 0.00 32.61 1.73
140 141 4.853468 TCAGGCCCTGTTTGATGTATAA 57.147 40.909 11.27 0.00 32.61 0.98
141 142 4.853468 TTCAGGCCCTGTTTGATGTATA 57.147 40.909 11.27 0.00 32.61 1.47
142 143 3.737559 TTCAGGCCCTGTTTGATGTAT 57.262 42.857 11.27 0.00 32.61 2.29
143 144 3.737559 ATTCAGGCCCTGTTTGATGTA 57.262 42.857 11.27 0.00 32.61 2.29
144 145 2.610438 ATTCAGGCCCTGTTTGATGT 57.390 45.000 11.27 0.00 32.61 3.06
145 146 3.129287 GTGTATTCAGGCCCTGTTTGATG 59.871 47.826 11.27 0.00 32.61 3.07
146 147 3.010584 AGTGTATTCAGGCCCTGTTTGAT 59.989 43.478 11.27 4.05 32.61 2.57
147 148 2.375174 AGTGTATTCAGGCCCTGTTTGA 59.625 45.455 11.27 0.00 32.61 2.69
148 149 2.795329 AGTGTATTCAGGCCCTGTTTG 58.205 47.619 11.27 0.00 32.61 2.93
149 150 3.157087 CAAGTGTATTCAGGCCCTGTTT 58.843 45.455 11.27 1.97 32.61 2.83
150 151 2.108250 ACAAGTGTATTCAGGCCCTGTT 59.892 45.455 11.27 2.35 32.61 3.16
151 152 1.705186 ACAAGTGTATTCAGGCCCTGT 59.295 47.619 11.27 0.00 32.61 4.00
152 153 2.489329 CAACAAGTGTATTCAGGCCCTG 59.511 50.000 3.69 3.69 0.00 4.45
153 154 2.795329 CAACAAGTGTATTCAGGCCCT 58.205 47.619 0.00 0.00 0.00 5.19
154 155 1.202348 GCAACAAGTGTATTCAGGCCC 59.798 52.381 0.00 0.00 0.00 5.80
155 156 1.202348 GGCAACAAGTGTATTCAGGCC 59.798 52.381 0.00 0.00 0.00 5.19
156 157 1.202348 GGGCAACAAGTGTATTCAGGC 59.798 52.381 0.00 0.00 39.74 4.85
157 158 2.513753 TGGGCAACAAGTGTATTCAGG 58.486 47.619 0.00 0.00 39.74 3.86
158 159 4.278170 TCTTTGGGCAACAAGTGTATTCAG 59.722 41.667 0.00 0.00 40.82 3.02
204 205 1.717194 TCACTTCCGATTGCGTAACC 58.283 50.000 0.00 0.00 35.23 2.85
275 276 1.038130 TCCGTCCTCCTCTTGCTAGC 61.038 60.000 8.10 8.10 0.00 3.42
437 445 1.655329 GATCGCAGACCCGGTAGAG 59.345 63.158 0.00 0.00 42.51 2.43
557 565 3.411351 CAACCCCGAACGCGACAG 61.411 66.667 15.93 2.31 40.82 3.51
609 617 3.282745 GAAGCACCAGTCTCGCCGA 62.283 63.158 0.00 0.00 0.00 5.54
745 753 2.343101 CGAAATCCAAGTGGTAGCGAA 58.657 47.619 0.00 0.00 36.34 4.70
816 824 1.601162 GCGAACACGACAAGACCACTA 60.601 52.381 0.00 0.00 0.00 2.74
832 840 2.879233 AAGAACCTGCTCCGGCGAA 61.879 57.895 9.30 0.00 42.25 4.70
1206 1215 1.546476 GTTCATCCTCTCACCGACTGT 59.454 52.381 0.00 0.00 0.00 3.55
1274 1283 8.599055 TGCAATAGATGAAGATGATTCAGTAC 57.401 34.615 0.00 0.00 0.00 2.73
1275 1284 9.617523 TTTGCAATAGATGAAGATGATTCAGTA 57.382 29.630 0.00 0.00 0.00 2.74
1294 1303 6.182627 TCAACATCCACTCTCTATTTGCAAT 58.817 36.000 0.00 0.00 0.00 3.56
1451 1462 2.916934 ACTTATGGCCACCTTCCTTGTA 59.083 45.455 8.16 0.00 0.00 2.41
1529 1540 5.329035 AGCCTCGAACATTTTGCAAATAT 57.671 34.783 13.65 6.85 0.00 1.28
1654 1665 5.014202 GGGCTGGTCTTTTCCTGTTTTATA 58.986 41.667 0.00 0.00 0.00 0.98
1773 1787 1.115467 CGTGAGGATAGGCTGTCCTT 58.885 55.000 30.36 16.32 45.93 3.36
1775 1789 1.333177 ATCGTGAGGATAGGCTGTCC 58.667 55.000 21.57 21.57 32.17 4.02
1852 1866 2.863401 TGTAGATCACGGATTCACGG 57.137 50.000 0.00 0.00 38.39 4.94
1853 1867 5.718649 ATTTTGTAGATCACGGATTCACG 57.281 39.130 0.00 0.00 40.31 4.35
1854 1868 6.018180 GGGTATTTTGTAGATCACGGATTCAC 60.018 42.308 0.00 0.00 0.00 3.18
1855 1869 6.053005 GGGTATTTTGTAGATCACGGATTCA 58.947 40.000 0.00 0.00 0.00 2.57
1856 1870 6.053005 TGGGTATTTTGTAGATCACGGATTC 58.947 40.000 0.00 0.00 0.00 2.52
1857 1871 5.996644 TGGGTATTTTGTAGATCACGGATT 58.003 37.500 0.00 0.00 0.00 3.01
1858 1872 5.623956 TGGGTATTTTGTAGATCACGGAT 57.376 39.130 0.00 0.00 0.00 4.18
1879 1893 6.819649 AGGGCAACATGAAATTTGAACATATG 59.180 34.615 0.00 0.00 39.74 1.78
2017 2031 5.086104 ACAAGAATAGTAGGAACGTGCAT 57.914 39.130 0.00 0.00 0.00 3.96
2146 2160 6.357367 TGATCTAAGCCAGGATTTAAGTTCC 58.643 40.000 0.00 0.00 0.00 3.62
2258 2276 8.680903 CAATAATAAAATCAAGACCTCACTGCT 58.319 33.333 0.00 0.00 0.00 4.24
2479 2501 9.823647 TCTTCTTGTGCTTATCTTTCCTATAAG 57.176 33.333 0.00 0.00 39.10 1.73
2627 2649 3.686241 TGACTGCTTCATTATGCACTGTC 59.314 43.478 0.00 0.00 35.96 3.51
2629 2651 4.690184 TTGACTGCTTCATTATGCACTG 57.310 40.909 0.00 0.00 35.20 3.66
2684 2706 1.003580 TGACCTTCTTGGCCTGTGATC 59.996 52.381 3.32 0.00 40.22 2.92
2790 2812 6.090088 CCATTCACTCTACTGAAAGAAGTTCG 59.910 42.308 0.00 0.00 39.30 3.95
2799 2821 5.250543 TGGATTTCCCATTCACTCTACTGAA 59.749 40.000 0.00 0.00 40.82 3.02
2874 2896 2.633488 GCTGGTACCACTCAAGATTCC 58.367 52.381 11.60 0.00 0.00 3.01
2891 2913 1.242076 CTGACCCAAGTTGAAGGCTG 58.758 55.000 3.87 0.00 0.00 4.85
3143 3165 2.242926 TGAAAATTGTCGGCATTCCCA 58.757 42.857 0.00 0.00 0.00 4.37
3310 3332 8.442632 TTTCCTTACATTGCAATCTCTATCTG 57.557 34.615 9.53 0.00 0.00 2.90
3331 3353 5.984695 ACCATCTTTAGCCTTTCTTTTCC 57.015 39.130 0.00 0.00 0.00 3.13
3395 3417 3.462021 GTCAAGCTCTCTGTGTTTCTGT 58.538 45.455 0.00 0.00 0.00 3.41
3498 3520 6.270064 CGTTTAAGCCTTTCCTTTTCTTGAA 58.730 36.000 0.00 0.00 0.00 2.69
3557 3579 2.086610 AAAATCAGCCCCGCCATAAT 57.913 45.000 0.00 0.00 0.00 1.28
3562 3584 2.228822 CACATATAAAATCAGCCCCGCC 59.771 50.000 0.00 0.00 0.00 6.13
3564 3586 3.882888 ACACACATATAAAATCAGCCCCG 59.117 43.478 0.00 0.00 0.00 5.73
3589 3611 3.760693 GCGTATGCTTCCAAGGAGA 57.239 52.632 0.00 0.00 38.39 3.71
3661 3683 5.777850 TTGATGATCTGCCAACATTATGG 57.222 39.130 0.00 0.00 43.70 2.74
3683 3705 4.823989 GGCATCTTAGTCATTGGCATACTT 59.176 41.667 3.43 0.00 35.00 2.24
3764 3786 1.134491 GGTAATGTAGGCGCAGTTCCT 60.134 52.381 10.83 0.00 37.72 3.36
3773 3795 0.254747 TGCCCACTGGTAATGTAGGC 59.745 55.000 0.00 0.00 41.43 3.93
3864 3886 4.202461 TGCAGAATTGTGTTCCTCTAGGTT 60.202 41.667 4.33 0.00 36.34 3.50
3929 3951 1.147153 GGTATCAGGGTGAGCTGGC 59.853 63.158 0.00 0.00 0.00 4.85
3991 4013 6.041511 CAGTCTTGATCAATGTACTCTGAGG 58.958 44.000 8.96 0.00 0.00 3.86
4068 4090 2.846532 CCAGACCTGGGGTGCTTT 59.153 61.111 8.17 0.00 46.81 3.51
4272 4316 8.426489 ACAATAAAACCTCAACTAGTGTCACTA 58.574 33.333 12.16 12.16 0.00 2.74
4281 4325 8.434392 ACCTTACAGACAATAAAACCTCAACTA 58.566 33.333 0.00 0.00 0.00 2.24
4294 4339 2.554032 GCAGCACAACCTTACAGACAAT 59.446 45.455 0.00 0.00 0.00 2.71
4337 4382 1.072331 AGAATCTCAAGTGTGCCCGTT 59.928 47.619 0.00 0.00 0.00 4.44
4370 4415 4.350346 CAACACTTGTCGCTGAATCAAAA 58.650 39.130 0.00 0.00 0.00 2.44
4373 4418 1.264020 GCAACACTTGTCGCTGAATCA 59.736 47.619 0.00 0.00 0.00 2.57
4383 4428 0.107017 ACAGCAGGAGCAACACTTGT 60.107 50.000 0.00 0.00 45.49 3.16
4416 4461 3.061429 CGCAAAAGAAAGAAAAACGCCAA 59.939 39.130 0.00 0.00 0.00 4.52
4443 4488 3.223157 CGAATACAACGCCAAAACTGTC 58.777 45.455 0.00 0.00 0.00 3.51
4470 4515 6.578919 GCCTCTAAACATTTCTTTCGTGAAAG 59.421 38.462 14.70 14.70 46.82 2.62
4539 4584 5.113502 AGCTCTTGTTCAAGCACAATAAC 57.886 39.130 7.58 0.00 41.06 1.89
4649 4695 7.815549 CACCTTAACCTCTAAAACTTCTCTCTC 59.184 40.741 0.00 0.00 0.00 3.20
4674 4720 4.280425 TGATTGTTGTAATTCAGCCTTGCA 59.720 37.500 0.00 0.00 0.00 4.08
4675 4721 4.622740 GTGATTGTTGTAATTCAGCCTTGC 59.377 41.667 0.00 0.00 0.00 4.01
4676 4722 6.017400 AGTGATTGTTGTAATTCAGCCTTG 57.983 37.500 0.00 0.00 0.00 3.61
4682 4728 4.091365 CGCGAGAGTGATTGTTGTAATTCA 59.909 41.667 0.00 0.00 46.66 2.57
4729 4802 2.872858 CCGTTGCTAGGATTAAAGGAGC 59.127 50.000 0.00 0.00 0.00 4.70
4732 4805 1.597663 CGCCGTTGCTAGGATTAAAGG 59.402 52.381 0.00 0.00 34.43 3.11
4797 4876 4.033009 TGCTCATCTCTTGGGAGTTATGA 58.967 43.478 0.00 0.00 40.29 2.15
4815 4894 2.864968 CTTGCTTTCTTGATGCTGCTC 58.135 47.619 0.00 0.00 0.00 4.26
4887 4966 2.107366 TGGAGTGATGCGACTTCCATA 58.893 47.619 0.00 0.00 0.00 2.74
4889 4968 0.684535 TTGGAGTGATGCGACTTCCA 59.315 50.000 0.00 0.00 0.00 3.53
4910 4989 1.565288 TCCATGATGTGCATCCTTCCA 59.435 47.619 9.39 0.00 37.02 3.53
4994 5075 3.545703 CAAGTTCAGGAGTCAACAACCT 58.454 45.455 0.00 0.00 34.02 3.50
4997 5078 3.281727 AGCAAGTTCAGGAGTCAACAA 57.718 42.857 0.00 0.00 0.00 2.83
5000 5081 1.949525 GCAAGCAAGTTCAGGAGTCAA 59.050 47.619 0.00 0.00 0.00 3.18
5034 5115 1.611491 CGTGGGTGGCAAAACTGTAAT 59.389 47.619 0.00 0.00 0.00 1.89
5082 5163 2.101783 TGGCTGGCAATCAACAATAGG 58.898 47.619 0.00 0.00 0.00 2.57
5126 5207 1.550072 CCGTTTGGAAGATTTGGGCAT 59.450 47.619 0.00 0.00 37.49 4.40
5127 5208 0.965439 CCGTTTGGAAGATTTGGGCA 59.035 50.000 0.00 0.00 37.49 5.36


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

AutoCloner maintained by Alex Coulton.