Multiple sequence alignment - TraesCS3A01G457200

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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 TraesCS3A01G457200 chr3A 100.000 3242 0 0 1 3242 694947405 694950646 0.000000e+00 5987
1 TraesCS3A01G457200 chr2A 93.955 1803 108 1 1441 3242 60112520 60114322 0.000000e+00 2724
2 TraesCS3A01G457200 chr2A 95.053 950 45 1 494 1443 60102836 60103783 0.000000e+00 1493
3 TraesCS3A01G457200 chr2A 90.489 368 28 3 127 494 60102521 60102881 2.260000e-131 479
4 TraesCS3A01G457200 chr6A 93.475 1502 81 10 1742 3242 554866854 554865369 0.000000e+00 2215
5 TraesCS3A01G457200 chr7A 98.630 73 1 0 1 73 69307698 69307626 2.620000e-26 130
6 TraesCS3A01G457200 chr6D 95.122 82 4 0 1 82 360605687 360605606 2.620000e-26 130
7 TraesCS3A01G457200 chr3D 95.122 82 4 0 1 82 41540056 41539975 2.620000e-26 130
8 TraesCS3A01G457200 chr2D 95.122 82 4 0 1 82 474644888 474644969 2.620000e-26 130
9 TraesCS3A01G457200 chr2D 95.122 82 4 0 1 82 603821418 603821499 2.620000e-26 130
10 TraesCS3A01G457200 chr5B 92.683 82 6 0 1 82 551811274 551811355 5.680000e-23 119


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 TraesCS3A01G457200 chr3A 694947405 694950646 3241 False 5987 5987 100.000 1 3242 1 chr3A.!!$F1 3241
1 TraesCS3A01G457200 chr2A 60112520 60114322 1802 False 2724 2724 93.955 1441 3242 1 chr2A.!!$F1 1801
2 TraesCS3A01G457200 chr2A 60102521 60103783 1262 False 986 1493 92.771 127 1443 2 chr2A.!!$F2 1316
3 TraesCS3A01G457200 chr6A 554865369 554866854 1485 True 2215 2215 93.475 1742 3242 1 chr6A.!!$R1 1500

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
86 87 0.032912 TCACTATCCCGGCACACCTA 60.033 55.0 0.00 0.00 0.00 3.08 F
288 289 0.464013 CTCCTCTGGCCATTCTGCAG 60.464 60.0 5.51 7.63 0.00 4.41 F
1395 1396 0.104855 TCTGCATCGAAGGAATCCCG 59.895 55.0 0.00 0.00 37.58 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1012 0.106708 TTGAAGCAGCGTCTCCAAGT 59.893 50.000 9.88 0.0 0.00 3.16 R
1616 1617 1.211212 CCTCATGCAGGTCCAGATGAA 59.789 52.381 0.00 0.0 37.53 2.57 R
2505 2507 0.251341 AATGGCCTTGCGTCTTCCTT 60.251 50.000 3.32 0.0 0.00 3.36 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
44 45 8.430801 TTTTTCTTTGTTTATGAACCATGGTG 57.569 30.769 20.60 0.58 34.80 4.17
45 46 6.723298 TTCTTTGTTTATGAACCATGGTGT 57.277 33.333 20.60 10.50 34.80 4.16
46 47 6.723298 TCTTTGTTTATGAACCATGGTGTT 57.277 33.333 20.60 2.64 34.80 3.32
47 48 6.511416 TCTTTGTTTATGAACCATGGTGTTG 58.489 36.000 20.60 0.00 34.80 3.33
48 49 6.322456 TCTTTGTTTATGAACCATGGTGTTGA 59.678 34.615 20.60 0.00 34.80 3.18
49 50 6.471233 TTGTTTATGAACCATGGTGTTGAA 57.529 33.333 20.60 8.28 34.80 2.69
50 51 6.083098 TGTTTATGAACCATGGTGTTGAAG 57.917 37.500 20.60 0.00 34.80 3.02
51 52 5.010516 TGTTTATGAACCATGGTGTTGAAGG 59.989 40.000 20.60 0.00 34.80 3.46
52 53 2.746279 TGAACCATGGTGTTGAAGGT 57.254 45.000 20.60 0.00 0.00 3.50
53 54 3.025322 TGAACCATGGTGTTGAAGGTT 57.975 42.857 20.60 0.00 44.69 3.50
55 56 2.746279 ACCATGGTGTTGAAGGTTCA 57.254 45.000 18.99 0.00 34.92 3.18
56 57 3.025322 ACCATGGTGTTGAAGGTTCAA 57.975 42.857 18.99 0.87 44.31 2.69
64 65 2.470057 TTGAAGGTTCAAAGGGGCTT 57.530 45.000 2.59 0.00 43.62 4.35
65 66 3.603965 TTGAAGGTTCAAAGGGGCTTA 57.396 42.857 2.59 0.00 43.62 3.09
66 67 3.603965 TGAAGGTTCAAAGGGGCTTAA 57.396 42.857 0.00 0.00 33.55 1.85
67 68 4.126520 TGAAGGTTCAAAGGGGCTTAAT 57.873 40.909 0.00 0.00 33.55 1.40
68 69 4.086457 TGAAGGTTCAAAGGGGCTTAATC 58.914 43.478 0.00 0.00 33.55 1.75
69 70 3.825908 AGGTTCAAAGGGGCTTAATCA 57.174 42.857 0.00 0.00 0.00 2.57
70 71 3.431415 AGGTTCAAAGGGGCTTAATCAC 58.569 45.455 0.00 0.00 0.00 3.06
71 72 3.076032 AGGTTCAAAGGGGCTTAATCACT 59.924 43.478 0.00 0.00 0.00 3.41
72 73 4.291249 AGGTTCAAAGGGGCTTAATCACTA 59.709 41.667 0.00 0.00 0.00 2.74
73 74 5.044105 AGGTTCAAAGGGGCTTAATCACTAT 60.044 40.000 0.00 0.00 0.00 2.12
74 75 5.299531 GGTTCAAAGGGGCTTAATCACTATC 59.700 44.000 0.00 0.00 0.00 2.08
75 76 5.048846 TCAAAGGGGCTTAATCACTATCC 57.951 43.478 0.00 0.00 0.00 2.59
76 77 4.141251 TCAAAGGGGCTTAATCACTATCCC 60.141 45.833 0.00 0.00 0.00 3.85
77 78 1.978580 AGGGGCTTAATCACTATCCCG 59.021 52.381 0.00 0.00 37.98 5.14
78 79 1.003233 GGGGCTTAATCACTATCCCGG 59.997 57.143 0.00 0.00 34.63 5.73
79 80 1.610886 GGGCTTAATCACTATCCCGGC 60.611 57.143 0.00 0.00 0.00 6.13
80 81 1.071699 GGCTTAATCACTATCCCGGCA 59.928 52.381 0.00 0.00 0.00 5.69
81 82 2.143925 GCTTAATCACTATCCCGGCAC 58.856 52.381 0.00 0.00 0.00 5.01
82 83 2.484770 GCTTAATCACTATCCCGGCACA 60.485 50.000 0.00 0.00 0.00 4.57
83 84 2.902705 TAATCACTATCCCGGCACAC 57.097 50.000 0.00 0.00 0.00 3.82
84 85 0.180406 AATCACTATCCCGGCACACC 59.820 55.000 0.00 0.00 0.00 4.16
85 86 0.691078 ATCACTATCCCGGCACACCT 60.691 55.000 0.00 0.00 0.00 4.00
86 87 0.032912 TCACTATCCCGGCACACCTA 60.033 55.000 0.00 0.00 0.00 3.08
87 88 0.828022 CACTATCCCGGCACACCTAA 59.172 55.000 0.00 0.00 0.00 2.69
88 89 1.208535 CACTATCCCGGCACACCTAAA 59.791 52.381 0.00 0.00 0.00 1.85
89 90 2.124411 ACTATCCCGGCACACCTAAAT 58.876 47.619 0.00 0.00 0.00 1.40
90 91 3.070446 CACTATCCCGGCACACCTAAATA 59.930 47.826 0.00 0.00 0.00 1.40
91 92 3.908103 ACTATCCCGGCACACCTAAATAT 59.092 43.478 0.00 0.00 0.00 1.28
92 93 2.922740 TCCCGGCACACCTAAATATC 57.077 50.000 0.00 0.00 0.00 1.63
93 94 2.404559 TCCCGGCACACCTAAATATCT 58.595 47.619 0.00 0.00 0.00 1.98
94 95 2.367567 TCCCGGCACACCTAAATATCTC 59.632 50.000 0.00 0.00 0.00 2.75
95 96 2.368875 CCCGGCACACCTAAATATCTCT 59.631 50.000 0.00 0.00 0.00 3.10
96 97 3.576982 CCCGGCACACCTAAATATCTCTA 59.423 47.826 0.00 0.00 0.00 2.43
97 98 4.039973 CCCGGCACACCTAAATATCTCTAA 59.960 45.833 0.00 0.00 0.00 2.10
98 99 5.230942 CCGGCACACCTAAATATCTCTAAG 58.769 45.833 0.00 0.00 0.00 2.18
99 100 5.010719 CCGGCACACCTAAATATCTCTAAGA 59.989 44.000 0.00 0.00 0.00 2.10
100 101 5.921408 CGGCACACCTAAATATCTCTAAGAC 59.079 44.000 0.00 0.00 0.00 3.01
101 102 6.461092 CGGCACACCTAAATATCTCTAAGACA 60.461 42.308 0.00 0.00 0.00 3.41
102 103 7.445945 GGCACACCTAAATATCTCTAAGACAT 58.554 38.462 0.00 0.00 0.00 3.06
103 104 8.585881 GGCACACCTAAATATCTCTAAGACATA 58.414 37.037 0.00 0.00 0.00 2.29
104 105 9.982651 GCACACCTAAATATCTCTAAGACATAA 57.017 33.333 0.00 0.00 0.00 1.90
116 117 8.134202 TCTCTAAGACATAACAATTGTCCTCA 57.866 34.615 12.39 0.00 43.62 3.86
117 118 8.253810 TCTCTAAGACATAACAATTGTCCTCAG 58.746 37.037 12.39 3.48 43.62 3.35
118 119 8.134202 TCTAAGACATAACAATTGTCCTCAGA 57.866 34.615 12.39 3.14 43.62 3.27
119 120 8.593679 TCTAAGACATAACAATTGTCCTCAGAA 58.406 33.333 12.39 0.00 43.62 3.02
120 121 7.440523 AAGACATAACAATTGTCCTCAGAAC 57.559 36.000 12.39 0.00 43.62 3.01
121 122 6.533730 AGACATAACAATTGTCCTCAGAACA 58.466 36.000 12.39 0.00 43.62 3.18
122 123 6.998074 AGACATAACAATTGTCCTCAGAACAA 59.002 34.615 12.39 0.00 43.62 2.83
123 124 7.173907 AGACATAACAATTGTCCTCAGAACAAG 59.826 37.037 12.39 0.00 43.62 3.16
124 125 6.998074 ACATAACAATTGTCCTCAGAACAAGA 59.002 34.615 12.39 0.00 39.78 3.02
125 126 7.502226 ACATAACAATTGTCCTCAGAACAAGAA 59.498 33.333 12.39 0.00 39.78 2.52
133 134 5.425217 TGTCCTCAGAACAAGAATATGCCTA 59.575 40.000 0.00 0.00 0.00 3.93
140 141 2.700897 ACAAGAATATGCCTACCGCTCT 59.299 45.455 0.00 0.00 38.78 4.09
144 145 1.051812 ATATGCCTACCGCTCTGCTT 58.948 50.000 0.00 0.00 38.78 3.91
155 156 2.203983 TCTGCTTCCCCCTGCTCA 60.204 61.111 0.00 0.00 0.00 4.26
225 226 4.746309 GCCTGCTGGTCCATGCCA 62.746 66.667 11.69 0.00 36.97 4.92
268 269 1.565390 TAAGTGGCCAGCTGCTCCAT 61.565 55.000 23.18 13.99 40.92 3.41
274 275 1.446791 CCAGCTGCTCCATCTCCTC 59.553 63.158 8.66 0.00 0.00 3.71
288 289 0.464013 CTCCTCTGGCCATTCTGCAG 60.464 60.000 5.51 7.63 0.00 4.41
323 324 3.157252 GCCATCCCTCGGCTCAGA 61.157 66.667 0.00 0.00 46.56 3.27
337 338 2.356793 CAGATCTGGATCCGCCGC 60.357 66.667 15.38 0.00 40.66 6.53
403 404 2.925170 AGGTGGCTGCTTCTCCGT 60.925 61.111 0.00 0.00 0.00 4.69
486 487 1.454479 CCAGGGCATTCAAGGCGAT 60.454 57.895 0.00 0.00 34.40 4.58
487 488 1.731433 CCAGGGCATTCAAGGCGATG 61.731 60.000 0.00 0.00 34.40 3.84
488 489 2.123428 AGGGCATTCAAGGCGATGC 61.123 57.895 8.85 8.85 39.15 3.91
489 490 2.025156 GGCATTCAAGGCGATGCG 59.975 61.111 10.43 0.00 40.65 4.73
490 491 2.025156 GCATTCAAGGCGATGCGG 59.975 61.111 0.00 0.00 0.00 5.69
491 492 2.717485 CATTCAAGGCGATGCGGG 59.283 61.111 0.00 0.00 0.00 6.13
492 493 3.211963 ATTCAAGGCGATGCGGGC 61.212 61.111 0.00 0.00 0.00 6.13
493 494 3.704231 ATTCAAGGCGATGCGGGCT 62.704 57.895 0.00 0.00 45.86 5.19
494 495 4.838152 TCAAGGCGATGCGGGCTC 62.838 66.667 0.00 0.00 42.70 4.70
507 508 3.191539 GGCTCCTCGCGCTCTTTG 61.192 66.667 5.56 0.00 40.44 2.77
508 509 3.858989 GCTCCTCGCGCTCTTTGC 61.859 66.667 5.56 0.28 38.57 3.68
509 510 2.125753 CTCCTCGCGCTCTTTGCT 60.126 61.111 5.56 0.00 40.11 3.91
510 511 1.739562 CTCCTCGCGCTCTTTGCTT 60.740 57.895 5.56 0.00 40.11 3.91
511 512 1.964290 CTCCTCGCGCTCTTTGCTTG 61.964 60.000 5.56 0.00 40.11 4.01
512 513 2.202272 CTCGCGCTCTTTGCTTGC 60.202 61.111 5.56 0.00 40.11 4.01
513 514 3.657835 CTCGCGCTCTTTGCTTGCC 62.658 63.158 5.56 0.00 40.11 4.52
514 515 4.766088 CGCGCTCTTTGCTTGCCC 62.766 66.667 5.56 0.00 40.11 5.36
515 516 3.673484 GCGCTCTTTGCTTGCCCA 61.673 61.111 0.00 0.00 40.11 5.36
516 517 2.564975 CGCTCTTTGCTTGCCCAG 59.435 61.111 0.00 0.00 40.11 4.45
517 518 2.968206 GCTCTTTGCTTGCCCAGG 59.032 61.111 0.00 0.00 38.95 4.45
518 519 2.643232 GCTCTTTGCTTGCCCAGGG 61.643 63.158 0.00 0.00 38.95 4.45
529 530 3.142838 CCCAGGGCATTCAAGGCG 61.143 66.667 0.00 0.00 34.40 5.52
530 531 2.045045 CCAGGGCATTCAAGGCGA 60.045 61.111 0.00 0.00 34.40 5.54
534 535 3.880846 GGCATTCAAGGCGAGGCG 61.881 66.667 0.00 0.00 0.00 5.52
637 638 3.138798 GCTGGTAGCTCGTCCGGA 61.139 66.667 0.00 0.00 38.45 5.14
765 766 2.813042 GCTGCAGACTGCCGAGAC 60.813 66.667 24.33 8.76 44.23 3.36
783 784 4.457496 CCCATCCGCTGCACTCGT 62.457 66.667 0.00 0.00 0.00 4.18
800 801 1.150536 GTTGCCTGGAGAACCACCA 59.849 57.895 0.00 0.00 41.77 4.17
805 806 4.308458 TGGAGAACCACCACCGCG 62.308 66.667 0.00 0.00 41.77 6.46
864 865 3.474570 GCCCACCTCATCGCTCCT 61.475 66.667 0.00 0.00 0.00 3.69
866 867 1.760086 CCCACCTCATCGCTCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
870 871 2.027314 CTCATCGCTCCTCTGCCG 59.973 66.667 0.00 0.00 0.00 5.69
873 874 2.519541 ATCGCTCCTCTGCCGCTA 60.520 61.111 0.00 0.00 0.00 4.26
890 891 1.530013 CTACCCCGTCCTGTTGTCGT 61.530 60.000 0.00 0.00 0.00 4.34
921 922 1.909781 CACTGCCCCATGCTTTGGT 60.910 57.895 5.67 0.00 44.83 3.67
927 928 2.990967 CCATGCTTTGGTGCGGGT 60.991 61.111 0.00 0.00 40.99 5.28
930 931 3.545124 ATGCTTTGGTGCGGGTCGA 62.545 57.895 0.00 0.00 35.36 4.20
1011 1012 4.802051 GCTCCAATGGCCCGCAGA 62.802 66.667 0.00 0.00 0.00 4.26
1026 1027 1.291588 CAGACTTGGAGACGCTGCT 59.708 57.895 0.00 0.00 0.00 4.24
1054 1055 0.111832 AGAGGTGGACTACGTGGTCA 59.888 55.000 29.76 15.41 37.91 4.02
1060 1061 1.436336 GACTACGTGGTCATCCCGG 59.564 63.158 25.18 0.00 36.35 5.73
1083 1084 1.626356 CCCCGAAGATGCAGGAGGAA 61.626 60.000 0.00 0.00 0.00 3.36
1087 1088 1.871408 CGAAGATGCAGGAGGAATCGG 60.871 57.143 0.00 0.00 0.00 4.18
1088 1089 0.179034 AAGATGCAGGAGGAATCGGC 60.179 55.000 0.00 0.00 0.00 5.54
1230 1231 2.494918 CGCCACTACCCCGAGAAG 59.505 66.667 0.00 0.00 0.00 2.85
1240 1241 2.047830 ACCCCGAGAAGTTCTTTGTCT 58.952 47.619 6.88 0.00 0.00 3.41
1368 1369 2.730934 ATGAAGACCAGCTGCATCAT 57.269 45.000 8.66 11.47 38.61 2.45
1392 1393 1.224965 GCCTCTGCATCGAAGGAATC 58.775 55.000 4.23 0.00 37.47 2.52
1395 1396 0.104855 TCTGCATCGAAGGAATCCCG 59.895 55.000 0.00 0.00 37.58 5.14
1424 1425 0.319083 TGGAACAACTACGTCGCCAT 59.681 50.000 0.00 0.00 31.92 4.40
1434 1435 1.076533 ACGTCGCCATGTTCGTCATC 61.077 55.000 0.00 0.00 34.09 2.92
1439 1440 2.525248 CCATGTTCGTCATCGGGCG 61.525 63.158 0.00 0.00 37.69 6.13
1473 1474 2.753452 GGACTACATCGAGAACAGGTCA 59.247 50.000 0.00 0.00 0.00 4.02
1543 1544 3.564027 CCGACGCGATCCCAAAGC 61.564 66.667 15.93 0.00 0.00 3.51
1632 1633 2.748798 GCTCATTCATCTGGACCTGCAT 60.749 50.000 0.00 0.00 0.00 3.96
1659 1660 3.000080 CTCCAACGCACGCGAAGAC 62.000 63.158 19.66 0.00 42.83 3.01
1661 1662 4.409588 CAACGCACGCGAAGACGG 62.410 66.667 19.66 0.00 42.83 4.79
1662 1663 4.936823 AACGCACGCGAAGACGGT 62.937 61.111 19.66 6.30 42.83 4.83
1668 1669 1.947642 ACGCGAAGACGGTGACAAC 60.948 57.895 15.93 0.00 40.15 3.32
1675 1676 3.584868 GACGGTGACAACCCTCCCG 62.585 68.421 0.00 0.00 44.42 5.14
1709 1710 6.704394 GAACGAGTTCATCTGGTACCCAGG 62.704 54.167 10.07 0.00 43.70 4.45
1717 1718 2.106332 GGTACCCAGGCATCGTCG 59.894 66.667 0.00 0.00 0.00 5.12
1830 1831 3.224324 GGCCGCGGTAGAGATGGA 61.224 66.667 28.70 0.00 0.00 3.41
1841 1842 3.254657 GGTAGAGATGGATCAAGAGGTCG 59.745 52.174 0.00 0.00 0.00 4.79
1887 1888 2.989253 TCTCTCTCCCGCAACGCA 60.989 61.111 0.00 0.00 0.00 5.24
1967 1968 2.027605 CCACGATGTCGCGCCTAT 59.972 61.111 0.00 0.00 44.43 2.57
2010 2011 3.602030 AGGGACGAGGTCAGGGGT 61.602 66.667 0.00 0.00 33.68 4.95
2048 2049 3.298958 GTCTCCACGATCTGGCCA 58.701 61.111 4.71 4.71 40.39 5.36
2056 2057 2.105128 GATCTGGCCACCGTCTCG 59.895 66.667 0.00 0.00 0.00 4.04
2204 2205 2.363147 GGCTCACCTCGTCTCCCT 60.363 66.667 0.00 0.00 0.00 4.20
2263 2265 3.633609 ATCCCCGACCTCGACGACA 62.634 63.158 0.00 0.00 43.02 4.35
2265 2267 2.707849 CCCCGACCTCGACGACAAT 61.708 63.158 0.00 0.00 43.02 2.71
2380 2382 0.529833 CTGAGCCTATCATCGCGGAT 59.470 55.000 6.13 4.46 37.28 4.18
2479 2481 1.300233 CGGTGGCCTATCTCTTCGC 60.300 63.158 3.32 0.00 0.00 4.70
2503 2505 2.125912 AGTGCTCGGCTACGCAAG 60.126 61.111 0.00 0.00 40.69 4.01
2505 2507 3.378602 TGCTCGGCTACGCAAGGA 61.379 61.111 0.00 0.00 46.39 3.36
2512 2514 0.249398 GGCTACGCAAGGAAGGAAGA 59.751 55.000 0.00 0.00 46.39 2.87
2644 2646 2.034687 TTCAAGGAGCAGCTGCCC 59.965 61.111 34.39 31.14 43.38 5.36
2772 2774 0.749649 GAGATGGTCTCTGGCGATGT 59.250 55.000 0.00 0.00 40.30 3.06
2783 2785 3.945434 GCGATGTGGCGAGGCATG 61.945 66.667 1.94 0.00 0.00 4.06
2826 2829 0.742281 CAGCTCTACGCCTGTGCAAT 60.742 55.000 0.00 0.00 40.39 3.56
2874 2877 1.003839 TTAGCTTGTGTGCTCCCCG 60.004 57.895 0.00 0.00 42.97 5.73
2875 2878 1.476845 TTAGCTTGTGTGCTCCCCGA 61.477 55.000 0.00 0.00 42.97 5.14
2912 2915 1.227674 GGCATGTCCATCGAGGGTC 60.228 63.158 16.92 11.49 38.24 4.46
2987 2990 1.210234 TGCCTATGTGTCTCCATGGTG 59.790 52.381 12.58 9.91 0.00 4.17
3029 3032 3.072330 TGTGAACATCCTAAGCTGGAACA 59.928 43.478 0.00 0.00 39.85 3.18
3038 3041 0.622665 AAGCTGGAACATCAGGGGAG 59.377 55.000 0.00 0.00 38.20 4.30
3172 3175 2.442413 CTGGGAGGGCAAAGGCTT 59.558 61.111 0.00 0.00 40.87 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.054922 CACCATGGTTCATAAACAAAGAAAAAT 57.945 29.630 16.84 0.00 37.10 1.82
19 20 8.043710 ACACCATGGTTCATAAACAAAGAAAAA 58.956 29.630 16.84 0.00 37.10 1.94
20 21 7.560368 ACACCATGGTTCATAAACAAAGAAAA 58.440 30.769 16.84 0.00 37.10 2.29
21 22 7.118496 ACACCATGGTTCATAAACAAAGAAA 57.882 32.000 16.84 0.00 37.10 2.52
22 23 6.723298 ACACCATGGTTCATAAACAAAGAA 57.277 33.333 16.84 0.00 37.10 2.52
23 24 6.322456 TCAACACCATGGTTCATAAACAAAGA 59.678 34.615 16.84 0.00 37.10 2.52
24 25 6.511416 TCAACACCATGGTTCATAAACAAAG 58.489 36.000 16.84 1.33 37.10 2.77
25 26 6.471233 TCAACACCATGGTTCATAAACAAA 57.529 33.333 16.84 0.00 37.10 2.83
26 27 6.462207 CCTTCAACACCATGGTTCATAAACAA 60.462 38.462 16.84 0.00 37.10 2.83
27 28 5.010516 CCTTCAACACCATGGTTCATAAACA 59.989 40.000 16.84 0.00 37.10 2.83
28 29 5.010617 ACCTTCAACACCATGGTTCATAAAC 59.989 40.000 16.84 0.00 34.46 2.01
29 30 5.144100 ACCTTCAACACCATGGTTCATAAA 58.856 37.500 16.84 5.52 0.00 1.40
30 31 4.735369 ACCTTCAACACCATGGTTCATAA 58.265 39.130 16.84 6.97 0.00 1.90
31 32 4.380843 ACCTTCAACACCATGGTTCATA 57.619 40.909 16.84 0.00 0.00 2.15
32 33 3.243359 ACCTTCAACACCATGGTTCAT 57.757 42.857 16.84 0.04 0.00 2.57
33 34 2.746279 ACCTTCAACACCATGGTTCA 57.254 45.000 16.84 0.00 0.00 3.18
34 35 3.643159 GAACCTTCAACACCATGGTTC 57.357 47.619 16.84 2.81 46.16 3.62
35 36 3.025322 TGAACCTTCAACACCATGGTT 57.975 42.857 16.84 4.03 42.85 3.67
36 37 2.746279 TGAACCTTCAACACCATGGT 57.254 45.000 13.00 13.00 33.55 3.55
37 38 3.243839 CCTTTGAACCTTCAACACCATGG 60.244 47.826 11.19 11.19 45.99 3.66
38 39 3.243839 CCCTTTGAACCTTCAACACCATG 60.244 47.826 0.00 0.00 45.99 3.66
39 40 2.965147 CCCTTTGAACCTTCAACACCAT 59.035 45.455 0.00 0.00 45.99 3.55
40 41 2.383855 CCCTTTGAACCTTCAACACCA 58.616 47.619 0.00 0.00 45.99 4.17
41 42 1.686587 CCCCTTTGAACCTTCAACACC 59.313 52.381 0.00 0.00 45.99 4.16
42 43 1.068588 GCCCCTTTGAACCTTCAACAC 59.931 52.381 0.00 0.00 45.99 3.32
43 44 1.063266 AGCCCCTTTGAACCTTCAACA 60.063 47.619 0.00 0.00 45.99 3.33
44 45 1.704641 AGCCCCTTTGAACCTTCAAC 58.295 50.000 0.00 0.00 45.99 3.18
45 46 2.470057 AAGCCCCTTTGAACCTTCAA 57.530 45.000 0.00 0.00 44.78 2.69
46 47 3.603965 TTAAGCCCCTTTGAACCTTCA 57.396 42.857 0.00 0.00 34.92 3.02
47 48 4.082190 GTGATTAAGCCCCTTTGAACCTTC 60.082 45.833 0.00 0.00 0.00 3.46
48 49 3.832490 GTGATTAAGCCCCTTTGAACCTT 59.168 43.478 0.00 0.00 0.00 3.50
49 50 3.076032 AGTGATTAAGCCCCTTTGAACCT 59.924 43.478 0.00 0.00 0.00 3.50
50 51 3.431415 AGTGATTAAGCCCCTTTGAACC 58.569 45.455 0.00 0.00 0.00 3.62
51 52 5.299531 GGATAGTGATTAAGCCCCTTTGAAC 59.700 44.000 0.00 0.00 0.00 3.18
52 53 5.445964 GGATAGTGATTAAGCCCCTTTGAA 58.554 41.667 0.00 0.00 0.00 2.69
53 54 4.141251 GGGATAGTGATTAAGCCCCTTTGA 60.141 45.833 0.00 0.00 0.00 2.69
54 55 4.145052 GGGATAGTGATTAAGCCCCTTTG 58.855 47.826 0.00 0.00 0.00 2.77
55 56 3.181443 CGGGATAGTGATTAAGCCCCTTT 60.181 47.826 0.00 0.00 31.81 3.11
56 57 2.372172 CGGGATAGTGATTAAGCCCCTT 59.628 50.000 0.00 0.00 31.81 3.95
57 58 1.978580 CGGGATAGTGATTAAGCCCCT 59.021 52.381 0.00 0.00 31.81 4.79
58 59 1.003233 CCGGGATAGTGATTAAGCCCC 59.997 57.143 0.00 0.00 31.81 5.80
59 60 1.610886 GCCGGGATAGTGATTAAGCCC 60.611 57.143 2.18 0.00 0.00 5.19
60 61 1.071699 TGCCGGGATAGTGATTAAGCC 59.928 52.381 2.18 0.00 0.00 4.35
61 62 2.143925 GTGCCGGGATAGTGATTAAGC 58.856 52.381 2.18 0.00 0.00 3.09
62 63 3.131396 GTGTGCCGGGATAGTGATTAAG 58.869 50.000 2.18 0.00 0.00 1.85
63 64 2.158871 GGTGTGCCGGGATAGTGATTAA 60.159 50.000 2.18 0.00 0.00 1.40
64 65 1.414919 GGTGTGCCGGGATAGTGATTA 59.585 52.381 2.18 0.00 0.00 1.75
65 66 0.180406 GGTGTGCCGGGATAGTGATT 59.820 55.000 2.18 0.00 0.00 2.57
66 67 0.691078 AGGTGTGCCGGGATAGTGAT 60.691 55.000 2.18 0.00 40.50 3.06
67 68 0.032912 TAGGTGTGCCGGGATAGTGA 60.033 55.000 2.18 0.00 40.50 3.41
68 69 0.828022 TTAGGTGTGCCGGGATAGTG 59.172 55.000 2.18 0.00 40.50 2.74
69 70 1.575419 TTTAGGTGTGCCGGGATAGT 58.425 50.000 2.18 0.00 40.50 2.12
70 71 2.930826 ATTTAGGTGTGCCGGGATAG 57.069 50.000 2.18 0.00 40.50 2.08
71 72 4.164981 AGATATTTAGGTGTGCCGGGATA 58.835 43.478 2.18 0.00 40.50 2.59
72 73 2.979678 AGATATTTAGGTGTGCCGGGAT 59.020 45.455 2.18 0.00 40.50 3.85
73 74 2.367567 GAGATATTTAGGTGTGCCGGGA 59.632 50.000 2.18 0.00 40.50 5.14
74 75 2.368875 AGAGATATTTAGGTGTGCCGGG 59.631 50.000 2.18 0.00 40.50 5.73
75 76 3.753294 AGAGATATTTAGGTGTGCCGG 57.247 47.619 0.00 0.00 40.50 6.13
76 77 5.921408 GTCTTAGAGATATTTAGGTGTGCCG 59.079 44.000 0.00 0.00 40.50 5.69
77 78 6.817184 TGTCTTAGAGATATTTAGGTGTGCC 58.183 40.000 0.00 0.00 0.00 5.01
78 79 9.982651 TTATGTCTTAGAGATATTTAGGTGTGC 57.017 33.333 0.00 0.00 28.74 4.57
90 91 8.762645 TGAGGACAATTGTTATGTCTTAGAGAT 58.237 33.333 13.36 0.00 45.13 2.75
91 92 8.134202 TGAGGACAATTGTTATGTCTTAGAGA 57.866 34.615 13.36 0.00 45.13 3.10
92 93 8.253810 TCTGAGGACAATTGTTATGTCTTAGAG 58.746 37.037 13.36 1.96 45.13 2.43
93 94 8.134202 TCTGAGGACAATTGTTATGTCTTAGA 57.866 34.615 13.36 12.79 45.13 2.10
94 95 8.660373 GTTCTGAGGACAATTGTTATGTCTTAG 58.340 37.037 13.36 11.02 45.13 2.18
95 96 8.154203 TGTTCTGAGGACAATTGTTATGTCTTA 58.846 33.333 13.36 2.65 45.13 2.10
96 97 6.998074 TGTTCTGAGGACAATTGTTATGTCTT 59.002 34.615 13.36 0.00 45.13 3.01
97 98 6.533730 TGTTCTGAGGACAATTGTTATGTCT 58.466 36.000 13.36 5.88 45.13 3.41
98 99 6.801539 TGTTCTGAGGACAATTGTTATGTC 57.198 37.500 13.36 7.83 45.08 3.06
99 100 6.998074 TCTTGTTCTGAGGACAATTGTTATGT 59.002 34.615 13.36 0.00 0.00 2.29
100 101 7.439157 TCTTGTTCTGAGGACAATTGTTATG 57.561 36.000 13.36 2.52 0.00 1.90
101 102 8.641498 ATTCTTGTTCTGAGGACAATTGTTAT 57.359 30.769 13.36 4.28 0.00 1.89
102 103 9.739276 ATATTCTTGTTCTGAGGACAATTGTTA 57.261 29.630 13.36 0.00 0.00 2.41
103 104 6.966534 ATTCTTGTTCTGAGGACAATTGTT 57.033 33.333 13.36 0.00 0.00 2.83
104 105 7.362401 GCATATTCTTGTTCTGAGGACAATTGT 60.362 37.037 11.78 11.78 0.00 2.71
105 106 6.971184 GCATATTCTTGTTCTGAGGACAATTG 59.029 38.462 6.79 3.24 0.00 2.32
106 107 6.096001 GGCATATTCTTGTTCTGAGGACAATT 59.904 38.462 6.79 0.00 0.00 2.32
107 108 5.591877 GGCATATTCTTGTTCTGAGGACAAT 59.408 40.000 6.79 0.00 0.00 2.71
108 109 4.943705 GGCATATTCTTGTTCTGAGGACAA 59.056 41.667 6.11 6.11 0.00 3.18
109 110 4.225942 AGGCATATTCTTGTTCTGAGGACA 59.774 41.667 0.00 0.00 0.00 4.02
110 111 4.775236 AGGCATATTCTTGTTCTGAGGAC 58.225 43.478 0.00 0.00 0.00 3.85
111 112 5.163301 GGTAGGCATATTCTTGTTCTGAGGA 60.163 44.000 0.00 0.00 0.00 3.71
112 113 5.059833 GGTAGGCATATTCTTGTTCTGAGG 58.940 45.833 0.00 0.00 0.00 3.86
113 114 4.747108 CGGTAGGCATATTCTTGTTCTGAG 59.253 45.833 0.00 0.00 0.00 3.35
114 115 4.693283 CGGTAGGCATATTCTTGTTCTGA 58.307 43.478 0.00 0.00 0.00 3.27
115 116 3.248602 GCGGTAGGCATATTCTTGTTCTG 59.751 47.826 0.00 0.00 42.87 3.02
116 117 3.467803 GCGGTAGGCATATTCTTGTTCT 58.532 45.455 0.00 0.00 42.87 3.01
117 118 3.879932 GCGGTAGGCATATTCTTGTTC 57.120 47.619 0.00 0.00 42.87 3.18
140 141 3.333219 CCTGAGCAGGGGGAAGCA 61.333 66.667 8.69 0.00 44.87 3.91
191 192 4.069232 CGAGGAAGGAGCCACGCA 62.069 66.667 0.00 0.00 35.38 5.24
248 249 1.451028 GGAGCAGCTGGCCACTTAG 60.451 63.158 17.12 0.00 46.50 2.18
268 269 0.911045 TGCAGAATGGCCAGAGGAGA 60.911 55.000 13.05 0.00 35.86 3.71
274 275 3.515286 CCGCTGCAGAATGGCCAG 61.515 66.667 20.43 0.00 35.86 4.85
309 310 0.831288 CCAGATCTGAGCCGAGGGAT 60.831 60.000 24.62 0.00 0.00 3.85
315 316 1.288439 CGGATCCAGATCTGAGCCG 59.712 63.158 26.03 26.03 44.92 5.52
378 379 4.154347 GCAGCCACCTCCTCCTCG 62.154 72.222 0.00 0.00 0.00 4.63
379 380 2.250741 GAAGCAGCCACCTCCTCCTC 62.251 65.000 0.00 0.00 0.00 3.71
380 381 2.204059 AAGCAGCCACCTCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
381 382 2.250741 GAGAAGCAGCCACCTCCTCC 62.251 65.000 0.00 0.00 0.00 4.30
437 438 2.430921 GCGAGGACTCACACACCG 60.431 66.667 0.00 0.00 0.00 4.94
440 441 3.268965 GAGCGCGAGGACTCACACA 62.269 63.158 12.10 0.00 32.98 3.72
456 457 2.271497 CCCTGGGCAAGCAGAGAG 59.729 66.667 0.00 0.00 0.00 3.20
489 490 4.459089 AAAGAGCGCGAGGAGCCC 62.459 66.667 12.10 0.00 44.76 5.19
490 491 3.191539 CAAAGAGCGCGAGGAGCC 61.192 66.667 12.10 0.00 44.76 4.70
491 492 3.858989 GCAAAGAGCGCGAGGAGC 61.859 66.667 12.10 0.88 43.95 4.70
500 501 2.643232 CCCTGGGCAAGCAAAGAGC 61.643 63.158 0.00 0.00 46.19 4.09
501 502 3.690745 CCCTGGGCAAGCAAAGAG 58.309 61.111 0.00 0.00 0.00 2.85
512 513 3.142838 CGCCTTGAATGCCCTGGG 61.143 66.667 8.86 8.86 0.00 4.45
513 514 2.045045 TCGCCTTGAATGCCCTGG 60.045 61.111 0.00 0.00 0.00 4.45
514 515 2.117156 CCTCGCCTTGAATGCCCTG 61.117 63.158 0.00 0.00 0.00 4.45
515 516 2.273449 CCTCGCCTTGAATGCCCT 59.727 61.111 0.00 0.00 0.00 5.19
516 517 3.521796 GCCTCGCCTTGAATGCCC 61.522 66.667 0.00 0.00 0.00 5.36
517 518 3.880846 CGCCTCGCCTTGAATGCC 61.881 66.667 0.00 0.00 0.00 4.40
518 519 3.880846 CCGCCTCGCCTTGAATGC 61.881 66.667 0.00 0.00 0.00 3.56
519 520 3.204827 CCCGCCTCGCCTTGAATG 61.205 66.667 0.00 0.00 0.00 2.67
592 593 2.841988 ATCAGCCTCCTCCTCGCC 60.842 66.667 0.00 0.00 0.00 5.54
606 607 4.758251 CAGCCGCCGGTCACATCA 62.758 66.667 4.45 0.00 0.00 3.07
625 626 3.807538 GCGTGTCCGGACGAGCTA 61.808 66.667 33.26 15.60 42.10 3.32
673 674 2.941964 GAATGCGCCTTGAATGCCGG 62.942 60.000 4.18 0.00 0.00 6.13
783 784 1.150536 GTGGTGGTTCTCCAGGCAA 59.849 57.895 0.00 0.00 45.24 4.52
870 871 1.079336 GACAACAGGACGGGGTAGC 60.079 63.158 0.00 0.00 0.00 3.58
873 874 2.841044 ACGACAACAGGACGGGGT 60.841 61.111 0.00 0.00 38.99 4.95
913 914 4.243008 TCGACCCGCACCAAAGCA 62.243 61.111 0.00 0.00 0.00 3.91
1011 1012 0.106708 TTGAAGCAGCGTCTCCAAGT 59.893 50.000 9.88 0.00 0.00 3.16
1026 1027 0.768221 AGTCCACCTCTGGCCTTGAA 60.768 55.000 3.32 0.00 37.49 2.69
1060 1061 2.825836 CTGCATCTTCGGGGTGGC 60.826 66.667 0.00 0.00 0.00 5.01
1066 1067 1.871408 CGATTCCTCCTGCATCTTCGG 60.871 57.143 0.00 0.00 0.00 4.30
1069 1070 0.179034 GCCGATTCCTCCTGCATCTT 60.179 55.000 0.00 0.00 0.00 2.40
1083 1084 3.222855 CTGGAGAGGAGCGCCGAT 61.223 66.667 2.29 0.00 39.67 4.18
1087 1088 2.817396 GTTGCTGGAGAGGAGCGC 60.817 66.667 0.00 0.00 39.47 5.92
1088 1089 2.507992 CGTTGCTGGAGAGGAGCG 60.508 66.667 0.00 0.00 39.47 5.03
1228 1229 5.531287 GGTACATGAACCAGACAAAGAACTT 59.469 40.000 0.00 0.00 39.50 2.66
1230 1231 4.819630 TGGTACATGAACCAGACAAAGAAC 59.180 41.667 0.00 0.00 44.68 3.01
1368 1369 3.588057 TTCGATGCAGAGGCGCACA 62.588 57.895 10.83 0.00 46.56 4.57
1439 1440 2.418910 TAGTCCAGAGAGCAGCCGC 61.419 63.158 0.00 0.00 38.99 6.53
1473 1474 2.932234 CGTGTCCTCCCTTCGCAGT 61.932 63.158 0.00 0.00 0.00 4.40
1476 1477 2.182030 CTCGTGTCCTCCCTTCGC 59.818 66.667 0.00 0.00 0.00 4.70
1538 1539 1.602311 AGTGAGCCACTTGAGCTTTG 58.398 50.000 2.38 0.00 42.59 2.77
1609 1610 2.748798 GCAGGTCCAGATGAATGAGCAT 60.749 50.000 0.00 0.00 0.00 3.79
1616 1617 1.211212 CCTCATGCAGGTCCAGATGAA 59.789 52.381 0.00 0.00 37.53 2.57
1632 1633 2.137528 TGCGTTGGAGTGGTCCTCA 61.138 57.895 0.00 0.00 44.30 3.86
1661 1662 4.717313 GGGCGGGAGGGTTGTCAC 62.717 72.222 0.00 0.00 0.00 3.67
1675 1676 2.432628 CTCGTTCACGTCTGGGGC 60.433 66.667 0.00 0.00 40.80 5.80
1830 1831 2.058595 CCCCGTCCGACCTCTTGAT 61.059 63.158 0.00 0.00 0.00 2.57
1909 1910 3.239253 ACGGGAGCGGTCCTTGTT 61.239 61.111 31.09 11.70 43.36 2.83
1912 1913 2.683933 ATCACGGGAGCGGTCCTT 60.684 61.111 31.09 17.00 43.36 3.36
1965 1966 4.473643 GCCGCAAGCATACCCATA 57.526 55.556 0.00 0.00 42.97 2.74
2056 2057 3.041940 CGTGAGGTTGTCGTGGGC 61.042 66.667 0.00 0.00 0.00 5.36
2204 2205 2.751436 GGGAAAGCGATGGCAGCA 60.751 61.111 2.73 0.00 43.41 4.41
2425 2427 2.123208 TCCATCCCCGCCATCGTA 60.123 61.111 0.00 0.00 0.00 3.43
2467 2469 1.287503 GGAGCGGCGAAGAGATAGG 59.712 63.158 12.98 0.00 0.00 2.57
2503 2505 2.041115 GGCCTTGCGTCTTCCTTCC 61.041 63.158 0.00 0.00 0.00 3.46
2505 2507 0.251341 AATGGCCTTGCGTCTTCCTT 60.251 50.000 3.32 0.00 0.00 3.36
2558 2560 0.774276 TGGACAATGCCCAGGTTACA 59.226 50.000 0.00 0.00 0.00 2.41
2584 2586 0.898320 CCCGTTCAGTGACATCCTCT 59.102 55.000 0.00 0.00 0.00 3.69
2756 2758 1.524002 CCACATCGCCAGAGACCAT 59.476 57.895 0.00 0.00 0.00 3.55
2782 2784 4.951715 AGCATCAATTATTCTTCTGGTGCA 59.048 37.500 8.69 0.00 46.19 4.57
2783 2785 5.506982 GGAGCATCAATTATTCTTCTGGTGC 60.507 44.000 0.00 0.00 44.53 5.01
2874 2877 2.943033 CCCATCCGAGGTAACAAACATC 59.057 50.000 0.00 0.00 41.41 3.06
2875 2878 2.944094 GCCCATCCGAGGTAACAAACAT 60.944 50.000 0.00 0.00 41.41 2.71
2912 2915 1.060713 CAACCACGAACAGAGTAGCG 58.939 55.000 0.00 0.00 0.00 4.26
2987 2990 3.947834 ACAGGTTGCTCTAACATATTGGC 59.052 43.478 0.00 0.00 41.18 4.52
3029 3032 4.570926 TCTGGATCATTTACTCCCCTGAT 58.429 43.478 0.00 0.00 0.00 2.90
3038 3041 3.318017 CCCGACGATCTGGATCATTTAC 58.682 50.000 10.62 0.00 37.69 2.01
3172 3175 3.386402 CAGGTCTTTGGGCAAACCTTTTA 59.614 43.478 0.00 0.00 41.11 1.52


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

AutoCloner maintained by Alex Coulton.