Multiple sequence alignment - TraesCS7D01G399400

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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 TraesCS7D01G399400 chr7D 100.000 6486 0 0 998 7483 515475821 515469336 0.000000e+00 11978
1 TraesCS7D01G399400 chr7D 100.000 806 0 0 1 806 515476818 515476013 0.000000e+00 1489
2 TraesCS7D01G399400 chr7D 95.256 780 29 3 1 780 636607509 636606738 0.000000e+00 1229
3 TraesCS7D01G399400 chr7A 95.661 4494 163 21 1221 5694 589141252 589136771 0.000000e+00 7190
4 TraesCS7D01G399400 chr7A 92.628 1587 51 28 5940 7477 589135834 589134265 0.000000e+00 2222
5 TraesCS7D01G399400 chr7A 91.165 249 12 3 5705 5946 589136166 589135921 5.600000e-86 329
6 TraesCS7D01G399400 chr7B 93.518 2530 120 26 3434 5946 546020630 546018128 0.000000e+00 3723
7 TraesCS7D01G399400 chr7B 95.253 2296 85 10 1024 3314 546023329 546021053 0.000000e+00 3615
8 TraesCS7D01G399400 chr7B 90.965 1129 49 21 6394 7483 546017561 546016447 0.000000e+00 1471
9 TraesCS7D01G399400 chr7B 91.814 794 41 10 1 788 44268185 44267410 0.000000e+00 1085
10 TraesCS7D01G399400 chr7B 95.652 437 16 1 5935 6371 546018051 546017618 0.000000e+00 699
11 TraesCS7D01G399400 chr2D 95.369 799 17 3 1 780 425476496 425475699 0.000000e+00 1253
12 TraesCS7D01G399400 chr2D 94.677 789 21 3 1 770 298847844 298847058 0.000000e+00 1205
13 TraesCS7D01G399400 chr3D 94.081 811 22 10 1 789 559263268 559264074 0.000000e+00 1208
14 TraesCS7D01G399400 chr3D 86.134 238 23 7 543 775 10658110 10658342 1.610000e-61 248
15 TraesCS7D01G399400 chr1D 94.250 800 25 4 1 780 296613912 296613114 0.000000e+00 1203
16 TraesCS7D01G399400 chr4B 91.779 815 40 10 1 789 569760994 569761807 0.000000e+00 1109
17 TraesCS7D01G399400 chr6D 96.508 630 21 1 1 629 203757817 203757188 0.000000e+00 1040
18 TraesCS7D01G399400 chr6D 92.213 244 12 6 543 780 203757242 203757000 9.300000e-89 339
19 TraesCS7D01G399400 chr4A 95.382 628 27 2 1 626 733390517 733391144 0.000000e+00 998
20 TraesCS7D01G399400 chr2A 93.620 627 38 2 1 626 747163406 747164031 0.000000e+00 935
21 TraesCS7D01G399400 chr2A 86.719 256 27 6 532 780 747163969 747164224 2.060000e-70 278
22 TraesCS7D01G399400 chr2B 88.608 237 19 7 532 762 451119521 451119287 1.590000e-71 281


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 TraesCS7D01G399400 chr7D 515469336 515476818 7482 True 6733.5 11978 100.000000 1 7483 2 chr7D.!!$R2 7482
1 TraesCS7D01G399400 chr7D 636606738 636607509 771 True 1229.0 1229 95.256000 1 780 1 chr7D.!!$R1 779
2 TraesCS7D01G399400 chr7A 589134265 589141252 6987 True 3247.0 7190 93.151333 1221 7477 3 chr7A.!!$R1 6256
3 TraesCS7D01G399400 chr7B 546016447 546023329 6882 True 2377.0 3723 93.847000 1024 7483 4 chr7B.!!$R2 6459
4 TraesCS7D01G399400 chr7B 44267410 44268185 775 True 1085.0 1085 91.814000 1 788 1 chr7B.!!$R1 787
5 TraesCS7D01G399400 chr2D 425475699 425476496 797 True 1253.0 1253 95.369000 1 780 1 chr2D.!!$R2 779
6 TraesCS7D01G399400 chr2D 298847058 298847844 786 True 1205.0 1205 94.677000 1 770 1 chr2D.!!$R1 769
7 TraesCS7D01G399400 chr3D 559263268 559264074 806 False 1208.0 1208 94.081000 1 789 1 chr3D.!!$F2 788
8 TraesCS7D01G399400 chr1D 296613114 296613912 798 True 1203.0 1203 94.250000 1 780 1 chr1D.!!$R1 779
9 TraesCS7D01G399400 chr4B 569760994 569761807 813 False 1109.0 1109 91.779000 1 789 1 chr4B.!!$F1 788
10 TraesCS7D01G399400 chr6D 203757000 203757817 817 True 689.5 1040 94.360500 1 780 2 chr6D.!!$R1 779
11 TraesCS7D01G399400 chr4A 733390517 733391144 627 False 998.0 998 95.382000 1 626 1 chr4A.!!$F1 625
12 TraesCS7D01G399400 chr2A 747163406 747164224 818 False 606.5 935 90.169500 1 780 2 chr2A.!!$F1 779

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
803 875 0.037877 TTTTATTCCGAACCCCCGCA 59.962 50.000 0.00 0.0 0.00 5.69 F
804 876 0.677414 TTTATTCCGAACCCCCGCAC 60.677 55.000 0.00 0.0 0.00 5.34 F
1575 1653 0.800012 GGTAATTTTGGCGCAGTCGA 59.200 50.000 10.83 0.0 38.10 4.20 F
3226 3311 0.102844 TGCTTTGCACAAGAACTGGC 59.897 50.000 11.34 0.0 31.71 4.85 F
3950 4340 1.001706 GTGGAGGAACGGCAACTTTTC 60.002 52.381 0.00 0.0 0.00 2.29 F
5420 5818 0.108992 TTCGACCTGACACGTATGGC 60.109 55.000 0.00 0.0 0.00 4.40 F
5702 6106 0.108472 CAGTCTTGCAGATCTCCGCA 60.108 55.000 3.70 3.7 36.05 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1843 0.615331 ATTCATCTGCTGACCCACGT 59.385 50.000 0.00 0.00 32.17 4.49 R
1803 1881 3.297134 TCAAGAAATGGTGATAGGCCC 57.703 47.619 0.00 0.00 0.00 5.80 R
3550 3939 1.002366 GTGCAACCTATCACTCTGCG 58.998 55.000 0.00 0.00 35.76 5.18 R
4384 4777 0.105593 ATGCTAGCATCCACCTGTCG 59.894 55.000 24.67 0.00 29.42 4.35 R
5445 5843 0.251209 TCTCCGGACTACTGCACAGT 60.251 55.000 0.00 8.57 45.02 3.55 R
6371 7471 1.016130 ACATCGTCGCAGCTTTGAGG 61.016 55.000 0.00 0.00 0.00 3.86 R
7359 8540 1.666599 GCGTGCATTGCATTCTCAACA 60.667 47.619 15.49 0.00 41.91 3.33 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
41 43 5.683681 ACCAAAATGCTTCAAACCAAGATT 58.316 33.333 0.00 0.00 0.00 2.40
278 285 6.803154 AAAGAAAGCTACAACCATACACTC 57.197 37.500 0.00 0.00 0.00 3.51
374 381 2.031919 ACCGAGCCGCAATCACAA 59.968 55.556 0.00 0.00 0.00 3.33
411 420 0.935831 TCGTCGACGCAATTTCGTGT 60.936 50.000 32.19 0.00 43.42 4.49
802 874 1.175654 TTTTTATTCCGAACCCCCGC 58.824 50.000 0.00 0.00 0.00 6.13
803 875 0.037877 TTTTATTCCGAACCCCCGCA 59.962 50.000 0.00 0.00 0.00 5.69
804 876 0.677414 TTTATTCCGAACCCCCGCAC 60.677 55.000 0.00 0.00 0.00 5.34
805 877 1.555477 TTATTCCGAACCCCCGCACT 61.555 55.000 0.00 0.00 0.00 4.40
1014 1086 4.426313 CCCCTTTGACTCCGCCCC 62.426 72.222 0.00 0.00 0.00 5.80
1015 1087 3.330720 CCCTTTGACTCCGCCCCT 61.331 66.667 0.00 0.00 0.00 4.79
1016 1088 2.269241 CCTTTGACTCCGCCCCTC 59.731 66.667 0.00 0.00 0.00 4.30
1017 1089 2.269241 CTTTGACTCCGCCCCTCC 59.731 66.667 0.00 0.00 0.00 4.30
1018 1090 3.327404 TTTGACTCCGCCCCTCCC 61.327 66.667 0.00 0.00 0.00 4.30
1046 1118 3.327757 TCTCTCTCTATCTCTCTCCTGGC 59.672 52.174 0.00 0.00 0.00 4.85
1049 1121 0.847373 TCTATCTCTCTCCTGGCGGT 59.153 55.000 0.00 0.00 0.00 5.68
1296 1370 2.040606 GACTAGGGGTCAGGGGCA 59.959 66.667 0.00 0.00 43.94 5.36
1321 1395 1.351080 TTGGTCCCGTGGGTGGTTTA 61.351 55.000 4.53 0.00 36.47 2.01
1327 1401 1.816224 CCCGTGGGTGGTTTATTTCTG 59.184 52.381 0.00 0.00 0.00 3.02
1378 1452 1.202915 GGGAGGGTTTTGTCGGGTTTA 60.203 52.381 0.00 0.00 0.00 2.01
1474 1551 1.000938 CTGTTTGCAACTCTGAAGGGC 60.001 52.381 0.00 0.00 0.00 5.19
1575 1653 0.800012 GGTAATTTTGGCGCAGTCGA 59.200 50.000 10.83 0.00 38.10 4.20
1576 1654 1.198178 GGTAATTTTGGCGCAGTCGAA 59.802 47.619 10.83 0.00 38.10 3.71
1596 1674 4.150627 CGAATGTTGGAATAGCTCGTATGG 59.849 45.833 0.00 0.00 0.00 2.74
1803 1881 4.585581 TGAATGTATCAGAATGGCCCATTG 59.414 41.667 15.10 0.63 36.16 2.82
1981 2059 7.547019 TCTGCTTTCAGAGTATCACAACAATAG 59.453 37.037 0.00 0.00 43.95 1.73
2092 2174 4.981806 TTTTCTTCTGTTTGGGTGTGAG 57.018 40.909 0.00 0.00 0.00 3.51
2094 2176 3.194005 TCTTCTGTTTGGGTGTGAGAC 57.806 47.619 0.00 0.00 0.00 3.36
2097 2179 4.346709 TCTTCTGTTTGGGTGTGAGACATA 59.653 41.667 0.00 0.00 0.00 2.29
2222 2304 7.799784 TGAAATCTTGTATATGCATGATCACG 58.200 34.615 18.27 0.00 33.80 4.35
2367 2450 8.854117 CCCTCCCTCTTAAGAATTATCATTTTG 58.146 37.037 6.63 0.00 0.00 2.44
2388 2471 5.097742 TGTTCCTCACACTTTTTGAGAGA 57.902 39.130 0.83 0.00 43.64 3.10
2429 2512 5.167121 CAACACAAACACCATTTCAACTCA 58.833 37.500 0.00 0.00 0.00 3.41
2476 2559 9.499479 CATATCATGTTTAAGCAGGAAGATACT 57.501 33.333 10.68 0.00 32.80 2.12
2582 2665 2.836981 ACTTCAGCTAGAGCAGGAATGT 59.163 45.455 4.01 5.21 45.16 2.71
2627 2710 3.713003 TGATCAGGCTTCTAGTTCCAGA 58.287 45.455 0.00 0.00 0.00 3.86
2775 2859 7.390027 CCATCTCAACCTAGGTCCTTTATATG 58.610 42.308 16.64 7.28 0.00 1.78
3226 3311 0.102844 TGCTTTGCACAAGAACTGGC 59.897 50.000 11.34 0.00 31.71 4.85
3550 3939 9.860898 AATGGCACTCTTAATTTCTTTTGTATC 57.139 29.630 0.00 0.00 0.00 2.24
3664 4053 4.036518 ACTGAAGTTCATCCTAGCCTCAT 58.963 43.478 5.91 0.00 0.00 2.90
3779 4168 6.747414 AAGAGGCTTGGAAAGGTAAATTTT 57.253 33.333 0.00 0.00 46.35 1.82
3831 4221 7.708752 CCTCTCTTTAGGTGTCTTTGATATCAC 59.291 40.741 4.48 0.00 31.46 3.06
3859 4249 7.541091 TCGTATGTGATCTTGTTTCTGACTAAC 59.459 37.037 0.00 0.00 0.00 2.34
3950 4340 1.001706 GTGGAGGAACGGCAACTTTTC 60.002 52.381 0.00 0.00 0.00 2.29
3956 4346 2.571206 GAACGGCAACTTTTCGATCAC 58.429 47.619 0.00 0.00 0.00 3.06
3992 4382 5.344743 TGTCCTCAACATTGGATAGAGTC 57.655 43.478 0.00 0.00 34.58 3.36
4057 4447 5.938438 AAGATGTGTTTTCTTCTCTCAGC 57.062 39.130 0.00 0.00 0.00 4.26
4075 4465 3.684305 TCAGCGAGTTTGGTGTATTGATG 59.316 43.478 0.00 0.00 38.47 3.07
4076 4466 3.436704 CAGCGAGTTTGGTGTATTGATGT 59.563 43.478 0.00 0.00 32.82 3.06
4100 4492 2.919228 AGTCCTTGTTGTTCACCTGTC 58.081 47.619 0.00 0.00 0.00 3.51
4345 4738 6.655003 TGGAGAACCAGATACTTAAAGCAAAG 59.345 38.462 0.00 0.00 41.77 2.77
4384 4777 5.819901 CAGAAAGGACATATTGGAGAAGGTC 59.180 44.000 0.00 0.00 0.00 3.85
4442 4835 3.552478 GCTTGAAGACTATAGCCGGGTAC 60.552 52.174 17.09 2.92 0.00 3.34
4585 4978 4.531854 TCCATGAAGTTGAAACCACTTGA 58.468 39.130 0.00 0.00 0.00 3.02
4622 5015 8.316946 ACTCTCACATTGATGTTCTCTTATTGA 58.683 33.333 0.00 0.00 39.39 2.57
4643 5036 5.847304 TGACAGGATGATAACAGATACAGC 58.153 41.667 0.00 0.00 39.69 4.40
4679 5072 1.016130 ATCTGAACCTCAAGCGTGCG 61.016 55.000 0.00 0.00 0.00 5.34
4793 5186 3.689649 GGCTTGGGGCTCATTATATTACG 59.310 47.826 0.00 0.00 41.46 3.18
4821 5216 3.187227 GCATGATATGTGATGGGAACGTC 59.813 47.826 0.00 0.00 46.97 4.34
4944 5339 1.153628 AGCATTCACCTACGACGGC 60.154 57.895 0.00 0.00 0.00 5.68
4981 5376 4.626042 GATGCTGGACGAATACAGAATCT 58.374 43.478 5.59 0.00 45.73 2.40
5022 5417 2.093764 AGAGAAGCGAAGAATGAGGGTG 60.094 50.000 0.00 0.00 0.00 4.61
5050 5445 3.056465 TCTTTTGTGCCGTTCCTTTTTGT 60.056 39.130 0.00 0.00 0.00 2.83
5084 5479 2.540265 ATGTCCAGCGAATCATCTCC 57.460 50.000 0.00 0.00 0.00 3.71
5414 5812 2.081212 GCGTCTTCGACCTGACACG 61.081 63.158 11.33 3.80 39.71 4.49
5416 5814 0.514255 CGTCTTCGACCTGACACGTA 59.486 55.000 11.33 0.00 39.71 3.57
5417 5815 1.129998 CGTCTTCGACCTGACACGTAT 59.870 52.381 11.33 0.00 39.71 3.06
5418 5816 2.516923 GTCTTCGACCTGACACGTATG 58.483 52.381 7.31 0.00 33.75 2.39
5419 5817 1.471287 TCTTCGACCTGACACGTATGG 59.529 52.381 0.00 0.00 0.00 2.74
5420 5818 0.108992 TTCGACCTGACACGTATGGC 60.109 55.000 0.00 0.00 0.00 4.40
5421 5819 0.963856 TCGACCTGACACGTATGGCT 60.964 55.000 0.00 0.00 33.48 4.75
5422 5820 0.802222 CGACCTGACACGTATGGCTG 60.802 60.000 0.00 0.00 33.48 4.85
5423 5821 4.521075 CCTGACACGTATGGCTGG 57.479 61.111 0.00 0.00 45.68 4.85
5424 5822 1.596934 CCTGACACGTATGGCTGGT 59.403 57.895 0.00 0.00 45.78 4.00
5426 5824 1.361668 CTGACACGTATGGCTGGTGC 61.362 60.000 0.00 0.00 33.48 5.01
5445 5843 3.093814 TGCCAGTGTCGGAGAAGTATAA 58.906 45.455 0.00 0.00 39.69 0.98
5459 5857 6.210287 AGAAGTATAACTGTGCAGTAGTCC 57.790 41.667 5.18 0.00 41.58 3.85
5471 5871 4.519730 GTGCAGTAGTCCGGAGATTATAGT 59.480 45.833 3.06 0.00 0.00 2.12
5477 5877 5.968528 AGTCCGGAGATTATAGTGCTTAG 57.031 43.478 3.06 0.00 0.00 2.18
5478 5878 4.218852 AGTCCGGAGATTATAGTGCTTAGC 59.781 45.833 3.06 0.00 0.00 3.09
5479 5879 4.218852 GTCCGGAGATTATAGTGCTTAGCT 59.781 45.833 3.06 0.00 0.00 3.32
5480 5880 4.833380 TCCGGAGATTATAGTGCTTAGCTT 59.167 41.667 0.00 0.00 0.00 3.74
5507 5907 0.901124 CTCAGCTAGGTGGAGCAAGT 59.099 55.000 21.22 0.00 45.43 3.16
5508 5908 1.277557 CTCAGCTAGGTGGAGCAAGTT 59.722 52.381 21.22 0.00 45.43 2.66
5509 5909 1.002430 TCAGCTAGGTGGAGCAAGTTG 59.998 52.381 21.22 0.00 45.43 3.16
5510 5910 0.326264 AGCTAGGTGGAGCAAGTTGG 59.674 55.000 4.75 0.00 45.43 3.77
5511 5911 0.324943 GCTAGGTGGAGCAAGTTGGA 59.675 55.000 4.75 0.00 42.36 3.53
5512 5912 1.065126 GCTAGGTGGAGCAAGTTGGAT 60.065 52.381 4.75 0.00 42.36 3.41
5513 5913 2.636830 CTAGGTGGAGCAAGTTGGATG 58.363 52.381 4.75 0.00 0.00 3.51
5516 5916 1.545428 GGTGGAGCAAGTTGGATGTGA 60.545 52.381 4.75 0.00 0.00 3.58
5517 5917 2.440409 GTGGAGCAAGTTGGATGTGAT 58.560 47.619 4.75 0.00 0.00 3.06
5533 5936 2.562738 TGTGATATAGTCATGGCGGGAG 59.437 50.000 0.00 0.00 39.48 4.30
5621 6025 6.874664 TGCTATGAATAACCGACACTTTTACA 59.125 34.615 0.00 0.00 0.00 2.41
5636 6040 6.983890 ACACTTTTACAAATGTTTCATCACCC 59.016 34.615 0.00 0.00 0.00 4.61
5694 6098 1.269778 CCGACTTGTCAGTCTTGCAGA 60.270 52.381 1.59 0.00 46.67 4.26
5696 6100 2.665537 CGACTTGTCAGTCTTGCAGATC 59.334 50.000 1.59 0.00 46.67 2.75
5697 6101 3.613671 CGACTTGTCAGTCTTGCAGATCT 60.614 47.826 0.00 0.00 46.67 2.75
5698 6102 3.924144 ACTTGTCAGTCTTGCAGATCTC 58.076 45.455 0.00 0.00 0.00 2.75
5699 6103 3.260740 CTTGTCAGTCTTGCAGATCTCC 58.739 50.000 0.00 0.00 0.00 3.71
5700 6104 1.203287 TGTCAGTCTTGCAGATCTCCG 59.797 52.381 0.00 0.00 0.00 4.63
5701 6105 0.174389 TCAGTCTTGCAGATCTCCGC 59.826 55.000 0.00 0.00 0.00 5.54
5702 6106 0.108472 CAGTCTTGCAGATCTCCGCA 60.108 55.000 3.70 3.70 36.05 5.69
5724 6722 5.007039 GCACTTAAATCAGCTCGAATCATCA 59.993 40.000 0.00 0.00 0.00 3.07
5803 6801 2.983229 ACACAGCAATCAGGATCTGAC 58.017 47.619 0.00 0.00 43.63 3.51
5824 6823 4.299155 ACGAAGCTATGTACATCATTCCG 58.701 43.478 12.68 13.70 37.91 4.30
5901 6906 2.864946 CGACTTGATGATCCTTCTGCAG 59.135 50.000 7.63 7.63 0.00 4.41
5902 6907 2.613133 GACTTGATGATCCTTCTGCAGC 59.387 50.000 9.47 0.00 0.00 5.25
5903 6908 2.239150 ACTTGATGATCCTTCTGCAGCT 59.761 45.455 9.47 0.00 0.00 4.24
5923 6928 0.975040 GCTGCTTCTCCTCCCTCTGA 60.975 60.000 0.00 0.00 0.00 3.27
5954 7052 1.425066 TGCTCACCTTGTGGGATCTTT 59.575 47.619 0.00 0.00 35.82 2.52
5964 7062 0.322456 TGGGATCTTTGTTGGAGCCG 60.322 55.000 0.00 0.00 39.85 5.52
5965 7063 1.032114 GGGATCTTTGTTGGAGCCGG 61.032 60.000 0.00 0.00 39.85 6.13
5966 7064 0.322546 GGATCTTTGTTGGAGCCGGT 60.323 55.000 1.90 0.00 29.47 5.28
6052 7150 4.537433 CCGGGCCTGTAGCAGCTC 62.537 72.222 11.58 0.00 46.50 4.09
6359 7459 0.994995 CTGCCGATCAAGACGAGTTG 59.005 55.000 0.00 0.00 0.00 3.16
6371 7471 3.078837 AGACGAGTTGAGAAGAGACTCC 58.921 50.000 0.00 0.00 37.17 3.85
6373 7473 2.224917 ACGAGTTGAGAAGAGACTCCCT 60.225 50.000 0.00 0.00 37.17 4.20
6378 7478 4.283212 AGTTGAGAAGAGACTCCCTCAAAG 59.717 45.833 26.44 0.00 44.24 2.77
6379 7479 2.564947 TGAGAAGAGACTCCCTCAAAGC 59.435 50.000 17.82 0.00 44.40 3.51
6380 7480 2.831526 GAGAAGAGACTCCCTCAAAGCT 59.168 50.000 14.31 0.00 44.40 3.74
6381 7481 2.566724 AGAAGAGACTCCCTCAAAGCTG 59.433 50.000 0.00 0.00 44.40 4.24
6382 7482 0.612744 AGAGACTCCCTCAAAGCTGC 59.387 55.000 0.00 0.00 44.40 5.25
6385 7510 1.004440 ACTCCCTCAAAGCTGCGAC 60.004 57.895 0.00 0.00 0.00 5.19
6532 7666 6.600822 CACTCCTCCTGAAACATCACATTTAT 59.399 38.462 0.00 0.00 0.00 1.40
6533 7667 7.770433 CACTCCTCCTGAAACATCACATTTATA 59.230 37.037 0.00 0.00 0.00 0.98
6583 7720 4.760715 TGCCAAATTAAGCCGTAACACTAA 59.239 37.500 0.00 0.00 0.00 2.24
6631 7768 1.620819 AGTCAAGTCCCTGTGTGCTAG 59.379 52.381 0.00 0.00 0.00 3.42
6632 7769 1.344763 GTCAAGTCCCTGTGTGCTAGT 59.655 52.381 0.00 0.00 0.00 2.57
6811 7974 3.393970 CCGAGGCAGGGCTCTTGA 61.394 66.667 18.95 0.00 0.00 3.02
6920 8083 3.564644 GCACCATGATCTTCATTCAGGAG 59.435 47.826 0.00 0.00 34.28 3.69
7170 8333 2.181777 GTCATCGCGCAGGTCTCA 59.818 61.111 8.75 0.00 0.00 3.27
7247 8410 3.470567 GTTCTCGTCGCCGCACAG 61.471 66.667 0.00 0.00 0.00 3.66
7248 8411 4.717629 TTCTCGTCGCCGCACAGG 62.718 66.667 0.00 0.00 44.97 4.00
7275 8438 2.686835 AGCCTCAGAGAGCCCCAC 60.687 66.667 0.00 0.00 0.00 4.61
7293 8456 2.125912 CTCCTCTTGTGGTCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
7325 8506 3.006859 TCCTGCGAAGAAGAAGAATGTCA 59.993 43.478 0.00 0.00 0.00 3.58
7359 8540 0.525761 GACTGAACTCTCGAGCTGCT 59.474 55.000 7.81 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 285 4.675146 CGGATGCAACTTTTCTGGTTATGG 60.675 45.833 0.00 0.00 0.00 2.74
305 312 5.726138 GCACATACGATTGAAGCTTTCTCTG 60.726 44.000 0.00 0.00 0.00 3.35
411 420 0.875908 GCCGTTGATGCTCATCGCTA 60.876 55.000 5.51 0.00 40.63 4.26
606 672 3.234730 CCGCGCCTCCTATCCCTT 61.235 66.667 0.00 0.00 0.00 3.95
788 860 3.327404 AGTGCGGGGGTTCGGAAT 61.327 61.111 0.00 0.00 31.23 3.01
997 1069 4.426313 GGGGCGGAGTCAAAGGGG 62.426 72.222 0.00 0.00 0.00 4.79
998 1070 3.330720 AGGGGCGGAGTCAAAGGG 61.331 66.667 0.00 0.00 0.00 3.95
999 1071 2.269241 GAGGGGCGGAGTCAAAGG 59.731 66.667 0.00 0.00 0.00 3.11
1000 1072 2.269241 GGAGGGGCGGAGTCAAAG 59.731 66.667 0.00 0.00 0.00 2.77
1001 1073 3.327404 GGGAGGGGCGGAGTCAAA 61.327 66.667 0.00 0.00 0.00 2.69
1011 1083 3.700350 AGAGAGGTGGGGGAGGGG 61.700 72.222 0.00 0.00 0.00 4.79
1012 1084 2.041405 GAGAGAGGTGGGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1013 1085 1.075600 GAGAGAGAGGTGGGGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
1014 1086 1.227249 TAGAGAGAGAGGTGGGGGAG 58.773 60.000 0.00 0.00 0.00 4.30
1015 1087 1.783979 GATAGAGAGAGAGGTGGGGGA 59.216 57.143 0.00 0.00 0.00 4.81
1016 1088 1.786441 AGATAGAGAGAGAGGTGGGGG 59.214 57.143 0.00 0.00 0.00 5.40
1017 1089 2.716424 AGAGATAGAGAGAGAGGTGGGG 59.284 54.545 0.00 0.00 0.00 4.96
1018 1090 3.652869 AGAGAGATAGAGAGAGAGGTGGG 59.347 52.174 0.00 0.00 0.00 4.61
1019 1091 4.263068 GGAGAGAGATAGAGAGAGAGGTGG 60.263 54.167 0.00 0.00 0.00 4.61
1020 1092 4.594920 AGGAGAGAGATAGAGAGAGAGGTG 59.405 50.000 0.00 0.00 0.00 4.00
1021 1093 4.594920 CAGGAGAGAGATAGAGAGAGAGGT 59.405 50.000 0.00 0.00 0.00 3.85
1022 1094 4.019860 CCAGGAGAGAGATAGAGAGAGAGG 60.020 54.167 0.00 0.00 0.00 3.69
1049 1121 4.994201 GTGCGCGTGAGGTGACGA 62.994 66.667 8.43 0.00 42.10 4.20
1113 1185 2.419436 GCTAGGGTTCTTGCTTCCTCTC 60.419 54.545 0.00 0.00 38.42 3.20
1144 1216 3.322466 AGGCGTCCTCACCTTGGG 61.322 66.667 0.00 0.00 29.74 4.12
1296 1370 1.350310 ACCCACGGGACCAAGAAACT 61.350 55.000 9.72 0.00 38.96 2.66
1321 1395 3.526019 TCCGGAGTAAAATCCCCAGAAAT 59.474 43.478 0.00 0.00 35.82 2.17
1327 1401 2.809299 CGGAATCCGGAGTAAAATCCCC 60.809 54.545 14.91 1.40 44.15 4.81
1410 1487 2.077155 CGAAATCGCTGAAATGACCG 57.923 50.000 0.00 0.00 0.00 4.79
1430 1507 3.470567 GGACGCGCGAGAACACAG 61.471 66.667 39.36 3.76 0.00 3.66
1529 1607 7.467403 CGATTCTGTTAAAGCTCCTAAATTCCC 60.467 40.741 0.00 0.00 0.00 3.97
1575 1653 3.815401 GCCATACGAGCTATTCCAACATT 59.185 43.478 0.00 0.00 0.00 2.71
1576 1654 3.071602 AGCCATACGAGCTATTCCAACAT 59.928 43.478 0.00 0.00 39.29 2.71
1596 1674 4.254492 ACGACCTTCTTGGAATTTCTAGC 58.746 43.478 0.00 0.00 39.71 3.42
1752 1830 2.695055 CACGTATGCCTTGCGTCG 59.305 61.111 0.00 0.00 45.31 5.12
1765 1843 0.615331 ATTCATCTGCTGACCCACGT 59.385 50.000 0.00 0.00 32.17 4.49
1803 1881 3.297134 TCAAGAAATGGTGATAGGCCC 57.703 47.619 0.00 0.00 0.00 5.80
1807 1885 6.094603 CCCAGACTTTCAAGAAATGGTGATAG 59.905 42.308 10.91 0.00 0.00 2.08
2097 2179 7.809331 CACACATTACACAAACAATGAAGCTAT 59.191 33.333 1.58 0.00 36.00 2.97
2222 2304 6.019318 GTCAAAATCTGCAATGATGGCAATAC 60.019 38.462 0.00 0.00 41.39 1.89
2367 2450 7.730364 TTATCTCTCAAAAAGTGTGAGGAAC 57.270 36.000 1.85 0.00 44.55 3.62
2388 2471 7.798596 TGTGTTGCCATTGTTTTCAATTTAT 57.201 28.000 0.00 0.00 46.94 1.40
2476 2559 7.994334 ACACAGACCAGTTACAAATAAAACCTA 59.006 33.333 0.00 0.00 0.00 3.08
2487 2570 5.468746 GCTGAAATAACACAGACCAGTTACA 59.531 40.000 0.00 0.00 36.38 2.41
2497 2580 6.057533 TCCCATATCAGCTGAAATAACACAG 58.942 40.000 22.50 3.96 37.22 3.66
2582 2665 8.215050 TCAACCTTTCTCCTGTAAACATCTAAA 58.785 33.333 0.00 0.00 0.00 1.85
2627 2710 3.460857 AGTTGTTGAAGAAGACGAGCT 57.539 42.857 0.00 0.00 0.00 4.09
2840 2924 3.269178 ACTCTAGCAGAAATGCAGAAGC 58.731 45.455 2.73 0.00 42.57 3.86
2900 2984 6.347061 AAATCAGGAGAAAGGGGACATATT 57.653 37.500 0.00 0.00 0.00 1.28
3316 3401 9.474920 TGGATTTGAGAAACACATAAAACATTC 57.525 29.630 0.00 0.00 0.00 2.67
3369 3454 5.694995 ACATCAAGGGGGTAATGATTACTG 58.305 41.667 14.34 5.44 36.39 2.74
3550 3939 1.002366 GTGCAACCTATCACTCTGCG 58.998 55.000 0.00 0.00 35.76 5.18
3664 4053 0.106708 GTGAGCACCCACAGAGTCAA 59.893 55.000 0.00 0.00 37.04 3.18
3779 4168 3.008375 AGCAATAACAAGAGGCTCACTGA 59.992 43.478 18.26 0.00 0.00 3.41
3831 4221 6.587990 AGTCAGAAACAAGATCACATACGAAG 59.412 38.462 0.00 0.00 0.00 3.79
3847 4237 5.415221 AGAGCATAGCAGTTAGTCAGAAAC 58.585 41.667 0.00 0.00 0.00 2.78
3859 4249 5.406175 GCTTGAATCTAAGAGAGCATAGCAG 59.594 44.000 0.00 0.00 0.00 4.24
3950 4340 3.245990 ACATATTGCATGTGACGTGATCG 59.754 43.478 9.33 0.00 43.34 3.69
3956 4346 3.197265 TGAGGACATATTGCATGTGACG 58.803 45.455 0.00 0.00 31.52 4.35
3992 4382 2.753865 GCCAAAGCTCCAGGAACTGTG 61.754 57.143 3.17 3.17 46.20 3.66
4057 4447 7.033791 ACTACTACATCAATACACCAAACTCG 58.966 38.462 0.00 0.00 0.00 4.18
4075 4465 4.989168 CAGGTGAACAACAAGGACTACTAC 59.011 45.833 0.00 0.00 0.00 2.73
4076 4466 4.652421 ACAGGTGAACAACAAGGACTACTA 59.348 41.667 0.00 0.00 0.00 1.82
4100 4492 8.984891 TTTAGAATGCAAAAATATGTCAGGTG 57.015 30.769 0.00 0.00 0.00 4.00
4315 4708 8.150945 GCTTTAAGTATCTGGTTCTCCATATCA 58.849 37.037 0.00 0.00 43.43 2.15
4384 4777 0.105593 ATGCTAGCATCCACCTGTCG 59.894 55.000 24.67 0.00 29.42 4.35
4442 4835 4.555262 AGGGTAACATGACAAATTTTGCG 58.445 39.130 9.04 0.00 39.74 4.85
4533 4926 0.109597 GGAAGAACAATGCTGGTGCG 60.110 55.000 0.00 0.00 43.34 5.34
4585 4978 1.059098 TGTGAGAGTCCACAGCCAAT 58.941 50.000 9.55 0.00 41.63 3.16
4622 5015 4.797604 GCGCTGTATCTGTTATCATCCTGT 60.798 45.833 0.00 0.00 0.00 4.00
4679 5072 3.159353 ACCAAAACACGAGCTTTTTCC 57.841 42.857 0.00 0.00 0.00 3.13
4776 5169 5.350640 GCAAGTACGTAATATAATGAGCCCC 59.649 44.000 0.00 0.00 0.00 5.80
4793 5186 5.308014 TCCCATCACATATCATGCAAGTAC 58.692 41.667 0.00 0.00 0.00 2.73
4821 5216 2.166664 GGTCAGGTTAGGACTAGCACTG 59.833 54.545 0.00 0.00 35.61 3.66
4911 5306 2.497107 ATGCTGTGTTGTGTTCTTGC 57.503 45.000 0.00 0.00 0.00 4.01
4981 5376 3.169099 CTTCCTCCTTCTCCTGTCTCAA 58.831 50.000 0.00 0.00 0.00 3.02
5022 5417 2.479275 GGAACGGCACAAAAGAGTACTC 59.521 50.000 15.41 15.41 0.00 2.59
5050 5445 1.134521 GGACATAGCCGTTGGACATGA 60.135 52.381 0.00 0.00 0.00 3.07
5084 5479 1.851021 TTGAGCAAACATGGGACGCG 61.851 55.000 3.53 3.53 0.00 6.01
5251 5649 2.046700 TTCGGCGTCCCATTCACC 60.047 61.111 6.85 0.00 0.00 4.02
5254 5652 3.192922 CGGTTCGGCGTCCCATTC 61.193 66.667 6.85 0.00 0.00 2.67
5421 5819 2.099652 CTTCTCCGACACTGGCACCA 62.100 60.000 0.00 0.00 0.00 4.17
5422 5820 1.374758 CTTCTCCGACACTGGCACC 60.375 63.158 0.00 0.00 0.00 5.01
5423 5821 0.601558 TACTTCTCCGACACTGGCAC 59.398 55.000 0.00 0.00 0.00 5.01
5424 5822 1.557099 ATACTTCTCCGACACTGGCA 58.443 50.000 0.00 0.00 0.00 4.92
5426 5824 4.158025 ACAGTTATACTTCTCCGACACTGG 59.842 45.833 0.00 0.00 35.69 4.00
5427 5825 5.096169 CACAGTTATACTTCTCCGACACTG 58.904 45.833 0.00 0.00 37.11 3.66
5428 5826 4.380655 GCACAGTTATACTTCTCCGACACT 60.381 45.833 0.00 0.00 0.00 3.55
5429 5827 3.858238 GCACAGTTATACTTCTCCGACAC 59.142 47.826 0.00 0.00 0.00 3.67
5430 5828 3.508402 TGCACAGTTATACTTCTCCGACA 59.492 43.478 0.00 0.00 0.00 4.35
5445 5843 0.251209 TCTCCGGACTACTGCACAGT 60.251 55.000 0.00 8.57 45.02 3.55
5459 5857 5.802956 GCTAAGCTAAGCACTATAATCTCCG 59.197 44.000 0.00 0.00 42.30 4.63
5490 5890 1.446907 CAACTTGCTCCACCTAGCTG 58.553 55.000 0.00 0.00 43.19 4.24
5504 5904 6.000219 GCCATGACTATATCACATCCAACTT 59.000 40.000 0.00 0.00 41.24 2.66
5507 5907 4.563374 CCGCCATGACTATATCACATCCAA 60.563 45.833 0.00 0.00 41.24 3.53
5508 5908 3.055891 CCGCCATGACTATATCACATCCA 60.056 47.826 0.00 0.00 41.24 3.41
5509 5909 3.525537 CCGCCATGACTATATCACATCC 58.474 50.000 0.00 0.00 41.24 3.51
5510 5910 3.195610 TCCCGCCATGACTATATCACATC 59.804 47.826 0.00 0.00 41.24 3.06
5511 5911 3.173151 TCCCGCCATGACTATATCACAT 58.827 45.455 0.00 0.00 41.24 3.21
5512 5912 2.562738 CTCCCGCCATGACTATATCACA 59.437 50.000 0.00 0.00 41.24 3.58
5513 5913 2.563179 ACTCCCGCCATGACTATATCAC 59.437 50.000 0.00 0.00 41.24 3.06
5516 5916 1.819288 CGACTCCCGCCATGACTATAT 59.181 52.381 0.00 0.00 0.00 0.86
5517 5917 1.244816 CGACTCCCGCCATGACTATA 58.755 55.000 0.00 0.00 0.00 1.31
5533 5936 1.737793 CCATCCAGTTACAAAGGCGAC 59.262 52.381 0.00 0.00 0.00 5.19
5540 5943 5.103982 ACATCCATGATCCATCCAGTTACAA 60.104 40.000 0.00 0.00 0.00 2.41
5609 6013 7.096640 GGTGATGAAACATTTGTAAAAGTGTCG 60.097 37.037 0.00 0.00 28.90 4.35
5621 6025 1.243902 ACGCGGGTGATGAAACATTT 58.756 45.000 12.47 0.00 0.00 2.32
5636 6040 3.301379 TCACTAAATAAAGTACGCACGCG 59.699 43.478 10.36 10.36 46.03 6.01
5694 6098 3.462021 GAGCTGATTTAAGTGCGGAGAT 58.538 45.455 0.00 0.00 0.00 2.75
5696 6100 1.590238 CGAGCTGATTTAAGTGCGGAG 59.410 52.381 0.00 0.00 0.00 4.63
5697 6101 1.203758 TCGAGCTGATTTAAGTGCGGA 59.796 47.619 0.00 0.00 0.00 5.54
5698 6102 1.640428 TCGAGCTGATTTAAGTGCGG 58.360 50.000 0.00 0.00 0.00 5.69
5699 6103 3.306973 TGATTCGAGCTGATTTAAGTGCG 59.693 43.478 0.00 0.00 0.00 5.34
5700 6104 4.864916 TGATTCGAGCTGATTTAAGTGC 57.135 40.909 0.00 0.00 0.00 4.40
5701 6105 6.594284 TGATGATTCGAGCTGATTTAAGTG 57.406 37.500 0.00 0.00 0.00 3.16
5702 6106 7.119699 TGTTTGATGATTCGAGCTGATTTAAGT 59.880 33.333 0.00 0.00 0.00 2.24
5724 6722 1.473258 TGCTTGGTGCTGAAGTGTTT 58.527 45.000 0.00 0.00 43.37 2.83
5781 6779 3.126514 GTCAGATCCTGATTGCTGTGTTG 59.873 47.826 0.00 0.00 42.73 3.33
5803 6801 4.299155 ACGGAATGATGTACATAGCTTCG 58.701 43.478 8.71 12.52 38.38 3.79
5824 6823 3.367025 CGGATTACTGAAACCGAGACAAC 59.633 47.826 0.00 0.00 46.94 3.32
5901 6906 2.124778 GGGAGGAGAAGCAGCAGC 60.125 66.667 0.00 0.00 42.56 5.25
5902 6907 0.977108 AGAGGGAGGAGAAGCAGCAG 60.977 60.000 0.00 0.00 0.00 4.24
5903 6908 1.079987 AGAGGGAGGAGAAGCAGCA 59.920 57.895 0.00 0.00 0.00 4.41
5923 6928 3.044305 GTGAGCAAGAAGGCGCGT 61.044 61.111 8.43 0.00 39.27 6.01
5954 7052 4.263572 CCACCACCGGCTCCAACA 62.264 66.667 0.00 0.00 0.00 3.33
5964 7062 4.712425 CGTCGTCGGACCACCACC 62.712 72.222 1.91 0.00 40.17 4.61
6153 7251 4.660938 GGGTGGTGGTGGTGAGGC 62.661 72.222 0.00 0.00 0.00 4.70
6359 7459 2.831526 AGCTTTGAGGGAGTCTCTTCTC 59.168 50.000 0.00 13.33 42.86 2.87
6371 7471 1.016130 ACATCGTCGCAGCTTTGAGG 61.016 55.000 0.00 0.00 0.00 3.86
6373 7473 1.900585 GCACATCGTCGCAGCTTTGA 61.901 55.000 0.00 0.00 0.00 2.69
6385 7510 2.506217 AGGTACGCACGCACATCG 60.506 61.111 0.00 0.00 45.38 3.84
6583 7720 4.344679 TGGCATCACTTTGGTCAAGAAAAT 59.655 37.500 0.00 0.00 36.21 1.82
6631 7768 4.516365 AGGTACTGTTGCTACACTGTAC 57.484 45.455 16.89 16.89 44.95 2.90
6632 7769 4.262292 CCAAGGTACTGTTGCTACACTGTA 60.262 45.833 0.00 0.00 40.86 2.74
6644 7781 2.300437 GTCTTCAGAGCCAAGGTACTGT 59.700 50.000 11.88 0.00 40.86 3.55
6811 7974 2.125912 CTGCTACGGTGAAGCGCT 60.126 61.111 2.64 2.64 43.11 5.92
6920 8083 3.732788 GCGTCTAGCTAGCTACGTC 57.267 57.895 30.47 22.15 44.04 4.34
7170 8333 2.665603 GTCTCGGCCAGGAGCTTT 59.334 61.111 2.24 0.00 43.05 3.51
7275 8438 2.266055 GGCGACCACAAGAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
7293 8456 3.268103 TTCGCAGGAAAGGAGCCCC 62.268 63.158 0.00 0.00 0.00 5.80
7325 8506 3.737172 GTCTGCCGCCGCAATGTT 61.737 61.111 0.47 0.00 46.66 2.71
7359 8540 1.666599 GCGTGCATTGCATTCTCAACA 60.667 47.619 15.49 0.00 41.91 3.33


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

AutoCloner maintained by Alex Coulton.