Multiple sequence alignment - TraesCS7A01G024300

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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 TraesCS7A01G024300 chr7A 100.000 2810 0 0 1 2810 9684373 9681564 0.000000e+00 5190.0
1 TraesCS7A01G024300 chr7A 91.885 1528 84 16 694 2215 9363816 9365309 0.000000e+00 2098.0
2 TraesCS7A01G024300 chr7A 91.169 385 26 2 2229 2606 9365292 9365675 1.490000e-142 516.0
3 TraesCS7A01G024300 chr7A 91.566 249 14 4 115 358 9361853 9362099 1.250000e-88 337.0
4 TraesCS7A01G024300 chr7A 84.770 348 27 6 359 705 9362154 9362476 2.700000e-85 326.0
5 TraesCS7A01G024300 chr7A 92.473 186 14 0 359 544 9508147 9508332 1.660000e-67 267.0
6 TraesCS7A01G024300 chr7A 94.512 164 9 0 2641 2804 9365678 9365841 1.290000e-63 254.0
7 TraesCS7A01G024300 chr7A 90.141 71 6 1 1 70 9336139 9336209 1.070000e-14 91.6
8 TraesCS7A01G024300 chr4A 89.608 2040 182 18 178 2215 729653695 729655706 0.000000e+00 2566.0
9 TraesCS7A01G024300 chr4A 89.612 1906 166 16 178 2083 729798053 729799926 0.000000e+00 2394.0
10 TraesCS7A01G024300 chr4A 90.991 1776 137 16 418 2190 729151968 729153723 0.000000e+00 2372.0
11 TraesCS7A01G024300 chr4A 89.022 1339 118 17 578 1913 729213130 729214442 0.000000e+00 1631.0
12 TraesCS7A01G024300 chr4A 93.078 939 55 7 1281 2215 729120520 729119588 0.000000e+00 1365.0
13 TraesCS7A01G024300 chr4A 91.274 722 55 7 1496 2215 729921293 729922008 0.000000e+00 977.0
14 TraesCS7A01G024300 chr4A 91.166 566 46 4 2248 2810 729657063 729657627 0.000000e+00 765.0
15 TraesCS7A01G024300 chr4A 89.555 584 38 10 2229 2810 729921991 729922553 0.000000e+00 719.0
16 TraesCS7A01G024300 chr4A 88.494 591 48 6 2233 2810 729153720 729154303 0.000000e+00 697.0
17 TraesCS7A01G024300 chr4A 87.931 580 42 8 2229 2807 729215051 729215603 0.000000e+00 658.0
18 TraesCS7A01G024300 chr4A 86.786 613 51 15 628 1218 729920318 729920922 0.000000e+00 656.0
19 TraesCS7A01G024300 chr4A 88.857 350 35 4 2229 2577 729119605 729119259 7.190000e-116 427.0
20 TraesCS7A01G024300 chr4A 91.549 284 24 0 359 642 729904240 729904523 2.620000e-105 392.0
21 TraesCS7A01G024300 chr4A 88.065 310 17 7 1908 2213 729214773 729215066 1.600000e-92 350.0
22 TraesCS7A01G024300 chr4A 79.264 299 40 14 1803 2089 728834113 728834401 3.700000e-44 189.0
23 TraesCS7A01G024300 chr4A 78.610 187 23 10 178 358 730914566 730914741 1.060000e-19 108.0
24 TraesCS7A01G024300 chr4A 91.781 73 5 1 1 72 729077230 729077158 1.780000e-17 100.0
25 TraesCS7A01G024300 chr4A 77.778 180 29 6 178 357 729904015 729904183 1.780000e-17 100.0
26 TraesCS7A01G024300 chr4A 96.875 32 0 1 117 147 729653600 729653631 5.000000e-03 52.8
27 TraesCS7A01G024300 chr7D 89.734 1958 154 21 178 2135 10056219 10058129 0.000000e+00 2459.0
28 TraesCS7A01G024300 chr7D 96.875 32 0 1 117 147 10056124 10056155 5.000000e-03 52.8
29 TraesCS7A01G024300 chr2D 81.909 1006 148 25 805 1796 564438222 564439207 0.000000e+00 819.0
30 TraesCS7A01G024300 chr2D 79.087 1205 191 41 605 1796 564475911 564477067 0.000000e+00 773.0
31 TraesCS7A01G024300 chr2D 76.618 1313 243 40 506 1796 564418201 564419471 0.000000e+00 665.0
32 TraesCS7A01G024300 chr2B 75.665 1315 264 41 506 1796 675524363 675525645 3.100000e-169 604.0


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 TraesCS7A01G024300 chr7A 9681564 9684373 2809 True 5190.000000 5190 100.000000 1 2810 1 chr7A.!!$R1 2809
1 TraesCS7A01G024300 chr7A 9361853 9365841 3988 False 706.200000 2098 90.780400 115 2804 5 chr7A.!!$F3 2689
2 TraesCS7A01G024300 chr4A 729798053 729799926 1873 False 2394.000000 2394 89.612000 178 2083 1 chr4A.!!$F2 1905
3 TraesCS7A01G024300 chr4A 729151968 729154303 2335 False 1534.500000 2372 89.742500 418 2810 2 chr4A.!!$F4 2392
4 TraesCS7A01G024300 chr4A 729653600 729657627 4027 False 1127.933333 2566 92.549667 117 2810 3 chr4A.!!$F6 2693
5 TraesCS7A01G024300 chr4A 729119259 729120520 1261 True 896.000000 1365 90.967500 1281 2577 2 chr4A.!!$R2 1296
6 TraesCS7A01G024300 chr4A 729213130 729215603 2473 False 879.666667 1631 88.339333 578 2807 3 chr4A.!!$F5 2229
7 TraesCS7A01G024300 chr4A 729920318 729922553 2235 False 784.000000 977 89.205000 628 2810 3 chr4A.!!$F8 2182
8 TraesCS7A01G024300 chr4A 729904015 729904523 508 False 246.000000 392 84.663500 178 642 2 chr4A.!!$F7 464
9 TraesCS7A01G024300 chr7D 10056124 10058129 2005 False 1255.900000 2459 93.304500 117 2135 2 chr7D.!!$F1 2018
10 TraesCS7A01G024300 chr2D 564438222 564439207 985 False 819.000000 819 81.909000 805 1796 1 chr2D.!!$F2 991
11 TraesCS7A01G024300 chr2D 564475911 564477067 1156 False 773.000000 773 79.087000 605 1796 1 chr2D.!!$F3 1191
12 TraesCS7A01G024300 chr2D 564418201 564419471 1270 False 665.000000 665 76.618000 506 1796 1 chr2D.!!$F1 1290
13 TraesCS7A01G024300 chr2B 675524363 675525645 1282 False 604.000000 604 75.665000 506 1796 1 chr2B.!!$F1 1290

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
91 92 0.031178 CAGTGTTGTCCCAAGCAAGC 59.969 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 3486 0.951558 GAAGGCCAAAGAAACGCAGA 59.048 50.0 5.01 0.0 0.0 4.26 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
25 26 7.202526 TGTGAACAAGAACATCTCATTTTTCC 58.797 34.615 0.00 0.00 0.00 3.13
26 27 7.147932 TGTGAACAAGAACATCTCATTTTTCCA 60.148 33.333 0.00 0.00 0.00 3.53
27 28 7.869429 GTGAACAAGAACATCTCATTTTTCCAT 59.131 33.333 0.00 0.00 0.00 3.41
28 29 8.423349 TGAACAAGAACATCTCATTTTTCCATT 58.577 29.630 0.00 0.00 0.00 3.16
29 30 8.822652 AACAAGAACATCTCATTTTTCCATTC 57.177 30.769 0.00 0.00 0.00 2.67
30 31 7.954835 ACAAGAACATCTCATTTTTCCATTCA 58.045 30.769 0.00 0.00 0.00 2.57
31 32 7.869429 ACAAGAACATCTCATTTTTCCATTCAC 59.131 33.333 0.00 0.00 0.00 3.18
32 33 7.771927 AGAACATCTCATTTTTCCATTCACT 57.228 32.000 0.00 0.00 0.00 3.41
33 34 8.186709 AGAACATCTCATTTTTCCATTCACTT 57.813 30.769 0.00 0.00 0.00 3.16
34 35 8.086522 AGAACATCTCATTTTTCCATTCACTTG 58.913 33.333 0.00 0.00 0.00 3.16
35 36 6.694447 ACATCTCATTTTTCCATTCACTTGG 58.306 36.000 0.00 0.00 38.18 3.61
36 37 5.726980 TCTCATTTTTCCATTCACTTGGG 57.273 39.130 0.00 0.00 37.37 4.12
37 38 5.147032 TCTCATTTTTCCATTCACTTGGGT 58.853 37.500 0.00 0.00 37.37 4.51
38 39 5.010922 TCTCATTTTTCCATTCACTTGGGTG 59.989 40.000 0.00 0.00 44.23 4.61
48 49 3.374042 TCACTTGGGTGACTGGAAAAA 57.626 42.857 0.00 0.00 46.19 1.94
49 50 3.020984 TCACTTGGGTGACTGGAAAAAC 58.979 45.455 0.00 0.00 46.19 2.43
50 51 2.757868 CACTTGGGTGACTGGAAAAACA 59.242 45.455 0.00 0.00 45.61 2.83
51 52 3.023832 ACTTGGGTGACTGGAAAAACAG 58.976 45.455 0.00 0.00 44.03 3.16
59 60 2.405892 CTGGAAAAACAGTTGAGGCG 57.594 50.000 0.00 0.00 33.81 5.52
60 61 1.001378 CTGGAAAAACAGTTGAGGCGG 60.001 52.381 0.00 0.00 33.81 6.13
61 62 1.314730 GGAAAAACAGTTGAGGCGGA 58.685 50.000 0.00 0.00 0.00 5.54
62 63 1.001706 GGAAAAACAGTTGAGGCGGAC 60.002 52.381 0.00 0.00 0.00 4.79
63 64 1.673920 GAAAAACAGTTGAGGCGGACA 59.326 47.619 0.00 0.00 0.00 4.02
64 65 1.308998 AAAACAGTTGAGGCGGACAG 58.691 50.000 0.00 0.00 0.00 3.51
65 66 0.468226 AAACAGTTGAGGCGGACAGA 59.532 50.000 0.00 0.00 0.00 3.41
66 67 0.034059 AACAGTTGAGGCGGACAGAG 59.966 55.000 0.00 0.00 0.00 3.35
67 68 0.827925 ACAGTTGAGGCGGACAGAGA 60.828 55.000 0.00 0.00 0.00 3.10
68 69 0.534412 CAGTTGAGGCGGACAGAGAT 59.466 55.000 0.00 0.00 0.00 2.75
69 70 1.751351 CAGTTGAGGCGGACAGAGATA 59.249 52.381 0.00 0.00 0.00 1.98
70 71 1.751924 AGTTGAGGCGGACAGAGATAC 59.248 52.381 0.00 0.00 0.00 2.24
71 72 1.112113 TTGAGGCGGACAGAGATACC 58.888 55.000 0.00 0.00 0.00 2.73
72 73 0.755698 TGAGGCGGACAGAGATACCC 60.756 60.000 0.00 0.00 0.00 3.69
73 74 0.755698 GAGGCGGACAGAGATACCCA 60.756 60.000 0.00 0.00 0.00 4.51
74 75 0.757188 AGGCGGACAGAGATACCCAG 60.757 60.000 0.00 0.00 0.00 4.45
75 76 1.043673 GGCGGACAGAGATACCCAGT 61.044 60.000 0.00 0.00 0.00 4.00
76 77 0.103208 GCGGACAGAGATACCCAGTG 59.897 60.000 0.00 0.00 0.00 3.66
77 78 1.475403 CGGACAGAGATACCCAGTGT 58.525 55.000 0.00 0.00 0.00 3.55
78 79 1.825474 CGGACAGAGATACCCAGTGTT 59.175 52.381 0.00 0.00 0.00 3.32
79 80 2.417379 CGGACAGAGATACCCAGTGTTG 60.417 54.545 0.00 0.00 0.00 3.33
80 81 2.567615 GGACAGAGATACCCAGTGTTGT 59.432 50.000 0.00 0.00 0.00 3.32
81 82 3.368531 GGACAGAGATACCCAGTGTTGTC 60.369 52.174 0.00 0.00 34.48 3.18
82 83 2.567615 ACAGAGATACCCAGTGTTGTCC 59.432 50.000 0.00 0.00 0.00 4.02
83 84 2.093447 CAGAGATACCCAGTGTTGTCCC 60.093 54.545 0.00 0.00 0.00 4.46
84 85 1.906574 GAGATACCCAGTGTTGTCCCA 59.093 52.381 0.00 0.00 0.00 4.37
85 86 2.304761 GAGATACCCAGTGTTGTCCCAA 59.695 50.000 0.00 0.00 0.00 4.12
86 87 2.305927 AGATACCCAGTGTTGTCCCAAG 59.694 50.000 0.00 0.00 0.00 3.61
87 88 0.109723 TACCCAGTGTTGTCCCAAGC 59.890 55.000 0.00 0.00 0.00 4.01
88 89 1.152777 CCCAGTGTTGTCCCAAGCA 60.153 57.895 0.00 0.00 0.00 3.91
89 90 0.754957 CCCAGTGTTGTCCCAAGCAA 60.755 55.000 0.00 0.00 0.00 3.91
90 91 0.670162 CCAGTGTTGTCCCAAGCAAG 59.330 55.000 0.00 0.00 0.00 4.01
91 92 0.031178 CAGTGTTGTCCCAAGCAAGC 59.969 55.000 0.00 0.00 0.00 4.01
92 93 0.395586 AGTGTTGTCCCAAGCAAGCA 60.396 50.000 0.00 0.00 0.00 3.91
93 94 0.031178 GTGTTGTCCCAAGCAAGCAG 59.969 55.000 0.00 0.00 0.00 4.24
94 95 1.108727 TGTTGTCCCAAGCAAGCAGG 61.109 55.000 0.00 0.00 0.00 4.85
95 96 1.109323 GTTGTCCCAAGCAAGCAGGT 61.109 55.000 0.00 0.00 0.00 4.00
96 97 1.108727 TTGTCCCAAGCAAGCAGGTG 61.109 55.000 0.00 0.00 0.00 4.00
97 98 1.228245 GTCCCAAGCAAGCAGGTGA 60.228 57.895 0.00 0.00 0.00 4.02
98 99 0.823356 GTCCCAAGCAAGCAGGTGAA 60.823 55.000 0.00 0.00 0.00 3.18
99 100 0.112995 TCCCAAGCAAGCAGGTGAAT 59.887 50.000 0.00 0.00 0.00 2.57
100 101 0.245539 CCCAAGCAAGCAGGTGAATG 59.754 55.000 0.00 0.00 0.00 2.67
101 102 1.250328 CCAAGCAAGCAGGTGAATGA 58.750 50.000 0.00 0.00 0.00 2.57
102 103 1.614903 CCAAGCAAGCAGGTGAATGAA 59.385 47.619 0.00 0.00 0.00 2.57
103 104 2.608752 CCAAGCAAGCAGGTGAATGAAC 60.609 50.000 0.00 0.00 0.00 3.18
104 105 1.251251 AGCAAGCAGGTGAATGAACC 58.749 50.000 0.00 0.00 40.85 3.62
105 106 0.961019 GCAAGCAGGTGAATGAACCA 59.039 50.000 0.24 0.00 43.20 3.67
106 107 1.068055 GCAAGCAGGTGAATGAACCAG 60.068 52.381 0.24 0.00 43.20 4.00
107 108 2.507484 CAAGCAGGTGAATGAACCAGA 58.493 47.619 0.24 0.00 43.20 3.86
108 109 2.486472 AGCAGGTGAATGAACCAGAG 57.514 50.000 0.24 0.00 43.20 3.35
109 110 1.701847 AGCAGGTGAATGAACCAGAGT 59.298 47.619 0.24 0.00 43.20 3.24
110 111 2.107204 AGCAGGTGAATGAACCAGAGTT 59.893 45.455 0.24 0.00 43.20 3.01
119 120 2.640346 GAACCAGAGTTCGGAGAGAC 57.360 55.000 0.00 0.00 42.85 3.36
151 152 4.451629 ACGTTCCACAGTATTACTCCTG 57.548 45.455 0.00 0.00 34.82 3.86
192 232 3.632145 ACTGTTTCCATCAAGTTGTCACC 59.368 43.478 2.11 0.00 0.00 4.02
215 255 6.436532 ACCGATCAGTTTCTTCTACCTCTTAA 59.563 38.462 0.00 0.00 0.00 1.85
216 256 7.124448 ACCGATCAGTTTCTTCTACCTCTTAAT 59.876 37.037 0.00 0.00 0.00 1.40
257 297 1.989706 TTACTTGTTCAACAGCCCCC 58.010 50.000 0.00 0.00 0.00 5.40
263 303 3.252554 TGTTCAACAGCCCCCTTATTT 57.747 42.857 0.00 0.00 0.00 1.40
283 323 4.553330 TTCTACTGTAAGCCCCTCTTTG 57.447 45.455 0.00 0.00 37.60 2.77
336 381 5.078411 AGAGATGATTGCGTAGTCAAACT 57.922 39.130 2.35 5.89 0.00 2.66
345 390 7.752239 TGATTGCGTAGTCAAACTTACTACTAC 59.248 37.037 10.64 0.00 44.65 2.73
355 458 9.577003 GTCAAACTTACTACTACGAACATTTTG 57.423 33.333 0.00 0.00 0.00 2.44
356 459 9.316730 TCAAACTTACTACTACGAACATTTTGT 57.683 29.630 0.00 0.00 0.00 2.83
357 460 9.577003 CAAACTTACTACTACGAACATTTTGTC 57.423 33.333 0.00 0.00 0.00 3.18
385 488 3.326747 GGCTGTATATGACGATTCCCAC 58.673 50.000 0.00 0.00 0.00 4.61
470 573 7.566760 TGTTTTCTTTGACTACATCATGTGT 57.433 32.000 0.00 0.00 44.95 3.72
533 636 2.358957 TCTGCATTGACAAGGAATCCG 58.641 47.619 3.57 0.00 0.00 4.18
569 672 9.942526 ATTATTGAATGAAAGGGATTTCTACCT 57.057 29.630 2.75 0.00 39.21 3.08
582 685 7.849904 AGGGATTTCTACCTAAGTCCTTCATAA 59.150 37.037 0.00 0.00 35.97 1.90
667 774 5.446143 TGTCATTGTTCCGCTTGTTAAAT 57.554 34.783 0.00 0.00 0.00 1.40
721 2179 9.377312 CTCTTTTCATCCCTCTCTAGTAAAAAG 57.623 37.037 0.00 0.00 34.25 2.27
727 2185 9.101325 TCATCCCTCTCTAGTAAAAAGAAAAGA 57.899 33.333 0.00 0.00 0.00 2.52
775 2233 2.234908 GTTGGTGAGTAGCATCTGTCCT 59.765 50.000 0.00 0.00 33.73 3.85
787 2245 3.731867 GCATCTGTCCTAACATTTTGCCG 60.732 47.826 0.00 0.00 34.13 5.69
814 2287 5.123227 CCGCTTCTTATTCTAACAATGGGA 58.877 41.667 0.00 0.00 0.00 4.37
841 2315 7.175641 AGTTTCTCTACAGCTGCACAAATATTT 59.824 33.333 15.27 0.00 0.00 1.40
936 2416 4.045104 CGTAATGAGAAGCAGCGAAGTAT 58.955 43.478 0.00 0.00 0.00 2.12
1003 2497 5.564550 AGCTATAGGAACCATTTAGCATGG 58.435 41.667 16.12 0.07 44.54 3.66
1038 2532 4.523943 ACCAATAGCATGTTGAGCTTTTCA 59.476 37.500 0.00 0.00 43.25 2.69
1316 2982 3.245016 ACAGATTTCCTGCTCAACATCCA 60.245 43.478 0.00 0.00 46.81 3.41
1317 2983 3.760151 CAGATTTCCTGCTCAACATCCAA 59.240 43.478 0.00 0.00 35.89 3.53
1473 3142 0.040692 CCGTCGAGTTTGACACGAGA 60.041 55.000 0.00 0.00 41.47 4.04
1542 3211 8.267620 ACATCAACAACATCAAATCTATTCGA 57.732 30.769 0.00 0.00 0.00 3.71
1584 3253 1.487976 TCCATCATCCTCTCAAGTGGC 59.512 52.381 0.00 0.00 0.00 5.01
1831 3507 0.667993 CTGCGTTTCTTTGGCCTTCA 59.332 50.000 3.32 0.00 0.00 3.02
1885 3561 2.430367 GGGTTGCTCTTCACGGGT 59.570 61.111 0.00 0.00 0.00 5.28
1906 3918 1.279840 GGCTCGACAACACAACAGC 59.720 57.895 0.00 0.00 0.00 4.40
1966 3979 7.730364 AAGTGAGTATTGTGGAAAGTTGTAG 57.270 36.000 0.00 0.00 0.00 2.74
2144 4163 8.713971 TCTTATGATTTCTTAGCATGTCCCTTA 58.286 33.333 0.00 0.00 0.00 2.69
2148 4167 8.593945 TGATTTCTTAGCATGTCCCTTATTTT 57.406 30.769 0.00 0.00 0.00 1.82
2149 4168 8.686334 TGATTTCTTAGCATGTCCCTTATTTTC 58.314 33.333 0.00 0.00 0.00 2.29
2150 4169 8.829373 ATTTCTTAGCATGTCCCTTATTTTCT 57.171 30.769 0.00 0.00 0.00 2.52
2151 4170 8.650143 TTTCTTAGCATGTCCCTTATTTTCTT 57.350 30.769 0.00 0.00 0.00 2.52
2154 4173 5.921962 AGCATGTCCCTTATTTTCTTTCC 57.078 39.130 0.00 0.00 0.00 3.13
2176 4200 5.298276 TCCTTTTTAGCCCGCTATACATTTG 59.702 40.000 0.00 0.00 0.00 2.32
2207 4231 7.219484 ACCAAAACAGACTCAGATAAAATGG 57.781 36.000 0.00 0.00 0.00 3.16
2208 4232 7.004086 ACCAAAACAGACTCAGATAAAATGGA 58.996 34.615 0.00 0.00 0.00 3.41
2209 4233 7.505585 ACCAAAACAGACTCAGATAAAATGGAA 59.494 33.333 0.00 0.00 0.00 3.53
2210 4234 8.025445 CCAAAACAGACTCAGATAAAATGGAAG 58.975 37.037 0.00 0.00 0.00 3.46
2211 4235 8.786898 CAAAACAGACTCAGATAAAATGGAAGA 58.213 33.333 0.00 0.00 0.00 2.87
2212 4236 7.913674 AACAGACTCAGATAAAATGGAAGAC 57.086 36.000 0.00 0.00 0.00 3.01
2213 4237 7.009179 ACAGACTCAGATAAAATGGAAGACA 57.991 36.000 0.00 0.00 0.00 3.41
2214 4238 7.628234 ACAGACTCAGATAAAATGGAAGACAT 58.372 34.615 0.00 0.00 43.07 3.06
2373 5760 8.417176 GTGCGATTCAACTAAAAATTGTTAGTG 58.583 33.333 19.57 13.95 42.25 2.74
2437 5824 2.004583 CGTGTATTTTCTGGCTCCGA 57.995 50.000 0.00 0.00 0.00 4.55
2537 5938 0.734889 GTGGCTGTCATCGGAAATGG 59.265 55.000 0.00 0.00 0.00 3.16
2554 5955 2.035442 GGGTGAAGCTTCTGACGGC 61.035 63.158 26.09 9.80 0.00 5.68
2556 5957 1.294659 GGTGAAGCTTCTGACGGCAG 61.295 60.000 26.09 13.65 43.67 4.85
2628 6029 1.485480 TCGTACACCTTGTTCCACCAA 59.515 47.619 0.00 0.00 0.00 3.67
2636 6037 4.582656 CACCTTGTTCCACCAATGTTCTTA 59.417 41.667 0.00 0.00 0.00 2.10
2761 6162 1.614317 GCTATTGACACCCAACCTGCT 60.614 52.381 0.00 0.00 37.63 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.147932 TGGAAAAATGAGATGTTCTTGTTCACA 60.148 33.333 0.00 0.00 0.00 3.58
4 5 8.423349 TGAATGGAAAAATGAGATGTTCTTGTT 58.577 29.630 0.00 0.00 0.00 2.83
6 7 8.086522 AGTGAATGGAAAAATGAGATGTTCTTG 58.913 33.333 0.00 0.00 0.00 3.02
7 8 8.186709 AGTGAATGGAAAAATGAGATGTTCTT 57.813 30.769 0.00 0.00 0.00 2.52
8 9 7.771927 AGTGAATGGAAAAATGAGATGTTCT 57.228 32.000 0.00 0.00 0.00 3.01
9 10 7.330208 CCAAGTGAATGGAAAAATGAGATGTTC 59.670 37.037 0.00 0.00 43.54 3.18
10 11 7.156673 CCAAGTGAATGGAAAAATGAGATGTT 58.843 34.615 0.00 0.00 43.54 2.71
11 12 6.295462 CCCAAGTGAATGGAAAAATGAGATGT 60.295 38.462 0.00 0.00 43.54 3.06
12 13 6.103997 CCCAAGTGAATGGAAAAATGAGATG 58.896 40.000 0.00 0.00 43.54 2.90
13 14 5.781818 ACCCAAGTGAATGGAAAAATGAGAT 59.218 36.000 0.00 0.00 43.54 2.75
14 15 5.147032 ACCCAAGTGAATGGAAAAATGAGA 58.853 37.500 0.00 0.00 43.54 3.27
15 16 5.473066 ACCCAAGTGAATGGAAAAATGAG 57.527 39.130 0.00 0.00 43.54 2.90
28 29 7.796075 ACTGTTTTTCCAGTCACCCAAGTGA 62.796 44.000 0.00 0.00 41.84 3.41
29 30 2.757868 TGTTTTTCCAGTCACCCAAGTG 59.242 45.455 0.00 0.00 46.00 3.16
30 31 3.023832 CTGTTTTTCCAGTCACCCAAGT 58.976 45.455 0.00 0.00 0.00 3.16
31 32 3.023832 ACTGTTTTTCCAGTCACCCAAG 58.976 45.455 0.00 0.00 41.84 3.61
32 33 3.094484 ACTGTTTTTCCAGTCACCCAA 57.906 42.857 0.00 0.00 41.84 4.12
33 34 2.757868 CAACTGTTTTTCCAGTCACCCA 59.242 45.455 0.00 0.00 44.74 4.51
34 35 3.020984 TCAACTGTTTTTCCAGTCACCC 58.979 45.455 0.00 0.00 44.74 4.61
35 36 3.066760 CCTCAACTGTTTTTCCAGTCACC 59.933 47.826 0.00 0.00 44.74 4.02
36 37 3.489229 GCCTCAACTGTTTTTCCAGTCAC 60.489 47.826 0.00 0.00 44.74 3.67
37 38 2.687935 GCCTCAACTGTTTTTCCAGTCA 59.312 45.455 0.00 0.00 44.74 3.41
38 39 2.287009 CGCCTCAACTGTTTTTCCAGTC 60.287 50.000 0.00 0.00 44.74 3.51
40 41 1.001378 CCGCCTCAACTGTTTTTCCAG 60.001 52.381 0.00 0.00 38.45 3.86
41 42 1.028905 CCGCCTCAACTGTTTTTCCA 58.971 50.000 0.00 0.00 0.00 3.53
42 43 1.001706 GTCCGCCTCAACTGTTTTTCC 60.002 52.381 0.00 0.00 0.00 3.13
43 44 1.673920 TGTCCGCCTCAACTGTTTTTC 59.326 47.619 0.00 0.00 0.00 2.29
44 45 1.676006 CTGTCCGCCTCAACTGTTTTT 59.324 47.619 0.00 0.00 0.00 1.94
45 46 1.134220 TCTGTCCGCCTCAACTGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
46 47 0.468226 TCTGTCCGCCTCAACTGTTT 59.532 50.000 0.00 0.00 0.00 2.83
47 48 0.034059 CTCTGTCCGCCTCAACTGTT 59.966 55.000 0.00 0.00 0.00 3.16
48 49 0.827925 TCTCTGTCCGCCTCAACTGT 60.828 55.000 0.00 0.00 0.00 3.55
49 50 0.534412 ATCTCTGTCCGCCTCAACTG 59.466 55.000 0.00 0.00 0.00 3.16
50 51 1.751924 GTATCTCTGTCCGCCTCAACT 59.248 52.381 0.00 0.00 0.00 3.16
51 52 1.202428 GGTATCTCTGTCCGCCTCAAC 60.202 57.143 0.00 0.00 0.00 3.18
52 53 1.112113 GGTATCTCTGTCCGCCTCAA 58.888 55.000 0.00 0.00 0.00 3.02
53 54 0.755698 GGGTATCTCTGTCCGCCTCA 60.756 60.000 0.00 0.00 0.00 3.86
54 55 0.755698 TGGGTATCTCTGTCCGCCTC 60.756 60.000 0.00 0.00 0.00 4.70
55 56 0.757188 CTGGGTATCTCTGTCCGCCT 60.757 60.000 0.00 0.00 0.00 5.52
56 57 1.043673 ACTGGGTATCTCTGTCCGCC 61.044 60.000 0.00 0.00 0.00 6.13
57 58 0.103208 CACTGGGTATCTCTGTCCGC 59.897 60.000 0.00 0.00 0.00 5.54
58 59 1.475403 ACACTGGGTATCTCTGTCCG 58.525 55.000 0.00 0.00 0.00 4.79
59 60 2.567615 ACAACACTGGGTATCTCTGTCC 59.432 50.000 0.00 0.00 0.00 4.02
60 61 3.368531 GGACAACACTGGGTATCTCTGTC 60.369 52.174 3.74 3.74 32.94 3.51
61 62 2.567615 GGACAACACTGGGTATCTCTGT 59.432 50.000 0.00 0.00 0.00 3.41
62 63 2.093447 GGGACAACACTGGGTATCTCTG 60.093 54.545 0.00 0.00 0.00 3.35
63 64 2.188817 GGGACAACACTGGGTATCTCT 58.811 52.381 0.00 0.00 0.00 3.10
64 65 1.906574 TGGGACAACACTGGGTATCTC 59.093 52.381 0.00 0.00 31.92 2.75
65 66 2.038863 TGGGACAACACTGGGTATCT 57.961 50.000 0.00 0.00 31.92 1.98
78 79 1.529010 CACCTGCTTGCTTGGGACA 60.529 57.895 9.18 0.00 0.00 4.02
79 80 0.823356 TTCACCTGCTTGCTTGGGAC 60.823 55.000 9.18 0.00 0.00 4.46
80 81 0.112995 ATTCACCTGCTTGCTTGGGA 59.887 50.000 9.18 0.00 0.00 4.37
81 82 0.245539 CATTCACCTGCTTGCTTGGG 59.754 55.000 9.18 4.86 0.00 4.12
82 83 1.250328 TCATTCACCTGCTTGCTTGG 58.750 50.000 0.00 0.00 0.00 3.61
83 84 2.608752 GGTTCATTCACCTGCTTGCTTG 60.609 50.000 0.00 0.00 33.50 4.01
84 85 1.615392 GGTTCATTCACCTGCTTGCTT 59.385 47.619 0.00 0.00 33.50 3.91
85 86 1.251251 GGTTCATTCACCTGCTTGCT 58.749 50.000 0.00 0.00 33.50 3.91
86 87 0.961019 TGGTTCATTCACCTGCTTGC 59.039 50.000 0.00 0.00 37.75 4.01
87 88 2.486982 CTCTGGTTCATTCACCTGCTTG 59.513 50.000 0.00 0.00 37.75 4.01
88 89 2.107204 ACTCTGGTTCATTCACCTGCTT 59.893 45.455 0.00 0.00 37.75 3.91
89 90 1.701847 ACTCTGGTTCATTCACCTGCT 59.298 47.619 0.00 0.00 37.75 4.24
90 91 2.191128 ACTCTGGTTCATTCACCTGC 57.809 50.000 0.00 0.00 37.75 4.85
100 101 1.887198 TGTCTCTCCGAACTCTGGTTC 59.113 52.381 0.00 0.00 45.91 3.62
101 102 1.996798 TGTCTCTCCGAACTCTGGTT 58.003 50.000 0.00 0.00 38.52 3.67
102 103 2.096248 GATGTCTCTCCGAACTCTGGT 58.904 52.381 0.00 0.00 0.00 4.00
103 104 2.095461 TGATGTCTCTCCGAACTCTGG 58.905 52.381 0.00 0.00 0.00 3.86
104 105 3.192422 ACTTGATGTCTCTCCGAACTCTG 59.808 47.826 0.00 0.00 0.00 3.35
105 106 3.426615 ACTTGATGTCTCTCCGAACTCT 58.573 45.455 0.00 0.00 0.00 3.24
106 107 3.859411 ACTTGATGTCTCTCCGAACTC 57.141 47.619 0.00 0.00 0.00 3.01
107 108 3.574396 TGAACTTGATGTCTCTCCGAACT 59.426 43.478 0.00 0.00 0.00 3.01
108 109 3.914312 TGAACTTGATGTCTCTCCGAAC 58.086 45.455 0.00 0.00 0.00 3.95
109 110 4.307432 GTTGAACTTGATGTCTCTCCGAA 58.693 43.478 0.00 0.00 0.00 4.30
110 111 3.611766 CGTTGAACTTGATGTCTCTCCGA 60.612 47.826 0.00 0.00 0.00 4.55
111 112 2.663602 CGTTGAACTTGATGTCTCTCCG 59.336 50.000 0.00 0.00 0.00 4.63
112 113 3.654414 ACGTTGAACTTGATGTCTCTCC 58.346 45.455 0.00 0.00 0.00 3.71
113 114 4.150804 GGAACGTTGAACTTGATGTCTCTC 59.849 45.833 5.00 0.00 0.00 3.20
114 115 4.058817 GGAACGTTGAACTTGATGTCTCT 58.941 43.478 5.00 0.00 0.00 3.10
115 116 3.807622 TGGAACGTTGAACTTGATGTCTC 59.192 43.478 5.00 0.00 0.00 3.36
116 117 3.560068 GTGGAACGTTGAACTTGATGTCT 59.440 43.478 5.00 0.00 0.00 3.41
117 118 3.311322 TGTGGAACGTTGAACTTGATGTC 59.689 43.478 5.00 0.00 42.39 3.06
118 119 3.275143 TGTGGAACGTTGAACTTGATGT 58.725 40.909 5.00 0.00 42.39 3.06
119 120 3.312421 ACTGTGGAACGTTGAACTTGATG 59.688 43.478 5.00 0.00 42.39 3.07
151 152 2.558359 AGTGTAGTTTCCATTGGCTTGC 59.442 45.455 0.00 0.00 0.00 4.01
192 232 7.976734 ACATTAAGAGGTAGAAGAAACTGATCG 59.023 37.037 0.00 0.00 0.00 3.69
257 297 6.487299 AGAGGGGCTTACAGTAGAAATAAG 57.513 41.667 0.00 0.00 0.00 1.73
263 303 3.786553 TCAAAGAGGGGCTTACAGTAGA 58.213 45.455 0.00 0.00 35.24 2.59
283 323 7.777095 TCTTTCTAGACTCTAGAGGCAAATTC 58.223 38.462 27.48 12.46 39.50 2.17
336 381 7.567409 GCAACGACAAAATGTTCGTAGTAGTAA 60.567 37.037 0.00 0.00 34.73 2.24
385 488 8.855110 AGTTATACTTGGATGAGACATAGTCAG 58.145 37.037 0.00 0.00 34.60 3.51
427 530 3.624726 CAAGCATTGTAACTCGACTCG 57.375 47.619 0.00 0.00 42.34 4.18
550 653 7.184753 AGGACTTAGGTAGAAATCCCTTTCATT 59.815 37.037 1.40 0.00 42.71 2.57
569 672 6.382859 TGATAGTGCCAGTTATGAAGGACTTA 59.617 38.462 0.00 0.00 0.00 2.24
582 685 3.338249 GTCACAACATGATAGTGCCAGT 58.662 45.455 0.00 0.00 40.28 4.00
667 774 4.935578 TCTGAGAGGATCAACAAGGTCTA 58.064 43.478 0.00 0.00 37.52 2.59
721 2179 4.636249 ACTATGCGATCTCCCATCTTTTC 58.364 43.478 0.00 0.00 0.00 2.29
727 2185 3.134623 TGTTTGACTATGCGATCTCCCAT 59.865 43.478 0.00 0.00 0.00 4.00
775 2233 1.581954 CGGTGCCGGCAAAATGTTA 59.418 52.632 34.66 1.55 35.56 2.41
787 2245 3.267483 TGTTAGAATAAGAAGCGGTGCC 58.733 45.455 0.00 0.00 0.00 5.01
814 2287 3.475566 TGTGCAGCTGTAGAGAAACTT 57.524 42.857 16.64 0.00 0.00 2.66
864 2341 3.455910 TGGAAGAGACATAGTCAATGGGG 59.544 47.826 0.00 0.00 40.16 4.96
970 2458 5.278061 TGGTTCCTATAGCTTCCTACAACT 58.722 41.667 0.00 0.00 0.00 3.16
1003 2497 2.364970 TGCTATTGGTATTGGGCATTGC 59.635 45.455 0.00 0.00 0.00 3.56
1316 2982 3.087065 CCCCATTCTGACCGGGTT 58.913 61.111 6.32 0.00 38.40 4.11
1317 2983 3.728373 GCCCCATTCTGACCGGGT 61.728 66.667 6.32 0.00 38.40 5.28
1437 3106 1.597797 CGGCTACAACTGGGTCCGTA 61.598 60.000 0.00 0.00 32.93 4.02
1473 3142 4.718774 TCAAGGTCATCCTCATAGCTCTTT 59.281 41.667 0.00 0.00 44.35 2.52
1542 3211 4.813750 AACATTACTAAGCGGGTACTGT 57.186 40.909 0.00 4.80 35.56 3.55
1584 3253 5.047448 CCTGATACTGACCCATACATCAGAG 60.047 48.000 8.18 0.00 44.32 3.35
1811 3486 0.951558 GAAGGCCAAAGAAACGCAGA 59.048 50.000 5.01 0.00 0.00 4.26
1831 3507 4.794648 TGCCGCTAATTGCCGCCT 62.795 61.111 9.36 0.00 43.52 5.52
1847 3523 2.092995 CGACGTCCGATAGCTCTATCTG 59.907 54.545 10.58 8.20 39.72 2.90
1852 3528 1.892862 CCCGACGTCCGATAGCTCT 60.893 63.158 10.58 0.00 41.76 4.09
1885 3561 1.525077 GTTGTGTTGTCGAGCCCCA 60.525 57.895 0.00 0.00 0.00 4.96
1906 3918 3.030291 AGTAGAGGTCATGGAGCAGAAG 58.970 50.000 0.00 0.00 31.89 2.85
1939 3951 7.480810 ACAACTTTCCACAATACTCACTTTTC 58.519 34.615 0.00 0.00 0.00 2.29
1940 3952 7.404671 ACAACTTTCCACAATACTCACTTTT 57.595 32.000 0.00 0.00 0.00 2.27
1966 3979 7.891183 ACACTCAACACTCTCAATACAATAC 57.109 36.000 0.00 0.00 0.00 1.89
2144 4163 4.283467 AGCGGGCTAAAAAGGAAAGAAAAT 59.717 37.500 0.00 0.00 0.00 1.82
2148 4167 2.579410 AGCGGGCTAAAAAGGAAAGA 57.421 45.000 0.00 0.00 0.00 2.52
2149 4168 4.879545 TGTATAGCGGGCTAAAAAGGAAAG 59.120 41.667 4.26 0.00 31.73 2.62
2150 4169 4.846040 TGTATAGCGGGCTAAAAAGGAAA 58.154 39.130 4.26 0.00 31.73 3.13
2151 4170 4.490899 TGTATAGCGGGCTAAAAAGGAA 57.509 40.909 4.26 0.00 31.73 3.36
2154 4173 6.131544 ACAAATGTATAGCGGGCTAAAAAG 57.868 37.500 4.26 0.00 31.73 2.27
2193 4217 7.337942 GGTGAATGTCTTCCATTTTATCTGAGT 59.662 37.037 0.00 0.00 43.87 3.41
2194 4218 7.555554 AGGTGAATGTCTTCCATTTTATCTGAG 59.444 37.037 0.00 0.00 43.87 3.35
2195 4219 7.405292 AGGTGAATGTCTTCCATTTTATCTGA 58.595 34.615 0.00 0.00 43.87 3.27
2196 4220 7.636150 AGGTGAATGTCTTCCATTTTATCTG 57.364 36.000 0.00 0.00 43.87 2.90
2197 4221 9.753674 TTTAGGTGAATGTCTTCCATTTTATCT 57.246 29.630 0.00 0.00 43.87 1.98
2253 4277 8.791327 TTAATGTAGATCAACAAGCAATCTCA 57.209 30.769 0.00 0.00 32.25 3.27
2288 5667 4.683781 GCTTCTGTCTAGAATCCTATTGCG 59.316 45.833 0.00 0.00 41.83 4.85
2373 5760 6.183360 GCACAACAAATTGAATGATGGTCATC 60.183 38.462 0.00 4.13 36.27 2.92
2537 5938 1.294659 CTGCCGTCAGAAGCTTCACC 61.295 60.000 27.57 13.51 42.95 4.02
2554 5955 3.562973 TGAAAAGCTTCAGACTTCAGCTG 59.437 43.478 7.63 7.63 43.28 4.24
2556 5957 4.558538 TTGAAAAGCTTCAGACTTCAGC 57.441 40.909 0.00 0.00 42.48 4.26
2608 6009 1.121378 TGGTGGAACAAGGTGTACGA 58.879 50.000 0.00 0.00 44.16 3.43
2628 6029 8.852135 TCGAACCCTTTATTTGTTTAAGAACAT 58.148 29.630 0.00 0.00 44.71 2.71
2636 6037 8.301720 GGTATTTCTCGAACCCTTTATTTGTTT 58.698 33.333 0.00 0.00 0.00 2.83
2737 6138 2.644798 AGGTTGGGTGTCAATAGCTTCT 59.355 45.455 0.00 0.00 37.73 2.85
2771 6172 1.145377 GAGACGGTGTGGTGGTGTT 59.855 57.895 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.