Multiple sequence alignment - TraesCS4D01G063600

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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 TraesCS4D01G063600 chr4D 100.000 2697 0 0 613 3309 39356421 39359117 0.000000e+00 4981.0
1 TraesCS4D01G063600 chr4D 100.000 202 0 0 1 202 39355809 39356010 1.120000e-99 374.0
2 TraesCS4D01G063600 chr4B 95.754 2426 59 17 750 3137 57796569 57794150 0.000000e+00 3869.0
3 TraesCS4D01G063600 chr4B 96.748 123 4 0 627 749 57796845 57796723 4.330000e-49 206.0
4 TraesCS4D01G063600 chr4B 92.500 120 8 1 3190 3309 57793795 57793677 1.580000e-38 171.0
5 TraesCS4D01G063600 chr4B 83.908 87 13 1 1 87 568348436 568348521 7.610000e-12 82.4
6 TraesCS4D01G063600 chr4A 93.951 1620 62 12 846 2457 560970325 560971916 0.000000e+00 2416.0
7 TraesCS4D01G063600 chr4A 93.960 149 9 0 3161 3309 560971913 560972061 3.320000e-55 226.0
8 TraesCS4D01G063600 chr4A 80.488 287 40 9 2886 3168 668318209 668317935 4.330000e-49 206.0
9 TraesCS4D01G063600 chr4A 96.154 78 3 0 628 705 560970079 560970156 9.640000e-26 128.0
10 TraesCS4D01G063600 chr7B 85.431 1565 200 16 1242 2787 748802144 748800589 0.000000e+00 1602.0
11 TraesCS4D01G063600 chr7B 83.465 1772 236 30 903 2647 747890587 747892328 0.000000e+00 1596.0
12 TraesCS4D01G063600 chr7B 85.507 276 35 3 1828 2103 744704708 744704978 1.940000e-72 283.0
13 TraesCS4D01G063600 chr7B 78.478 381 69 7 1487 1866 745217992 745217624 1.530000e-58 237.0
14 TraesCS4D01G063600 chr7B 88.690 168 19 0 2570 2737 744707162 744707329 4.330000e-49 206.0
15 TraesCS4D01G063600 chr7B 69.885 1222 302 43 1146 2322 748608099 748609299 1.230000e-34 158.0
16 TraesCS4D01G063600 chr7B 88.889 72 4 1 767 834 748856532 748856461 5.880000e-13 86.1
17 TraesCS4D01G063600 chr7D 84.843 1115 136 15 1767 2854 633127293 633128401 0.000000e+00 1092.0
18 TraesCS4D01G063600 chr7D 75.866 779 161 20 1291 2059 632733274 632732513 4.030000e-99 372.0
19 TraesCS4D01G063600 chr7D 82.979 94 15 1 1 93 523431341 523431248 2.120000e-12 84.2
20 TraesCS4D01G063600 chr3B 97.600 125 3 0 1 125 778375470 778375346 7.190000e-52 215.0
21 TraesCS4D01G063600 chr7A 95.200 125 6 0 1 125 670677268 670677392 7.240000e-47 198.0
22 TraesCS4D01G063600 chr7A 82.949 217 36 1 2886 3102 56836136 56835921 9.370000e-46 195.0
23 TraesCS4D01G063600 chr7A 70.139 1219 298 41 1149 2322 734890274 734889077 1.220000e-39 174.0
24 TraesCS4D01G063600 chr7A 84.444 90 12 2 1 90 438023345 438023258 1.640000e-13 87.9
25 TraesCS4D01G063600 chr1A 92.000 125 10 0 1 125 428993612 428993736 3.390000e-40 176.0
26 TraesCS4D01G063600 chr2A 92.771 83 6 0 2885 2967 564614212 564614130 1.610000e-23 121.0
27 TraesCS4D01G063600 chrUn 88.750 80 9 0 2886 2965 69783975 69783896 7.560000e-17 99.0
28 TraesCS4D01G063600 chr1B 88.312 77 8 1 1 77 338611414 338611489 1.260000e-14 91.6
29 TraesCS4D01G063600 chr1B 83.908 87 13 1 1 87 629068158 629068243 7.610000e-12 82.4
30 TraesCS4D01G063600 chr5A 85.057 87 12 1 1 87 493628030 493628115 1.640000e-13 87.9


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 TraesCS4D01G063600 chr4D 39355809 39359117 3308 False 2677.500000 4981 100.000000 1 3309 2 chr4D.!!$F1 3308
1 TraesCS4D01G063600 chr4B 57793677 57796845 3168 True 1415.333333 3869 95.000667 627 3309 3 chr4B.!!$R1 2682
2 TraesCS4D01G063600 chr4A 560970079 560972061 1982 False 923.333333 2416 94.688333 628 3309 3 chr4A.!!$F1 2681
3 TraesCS4D01G063600 chr7B 748800589 748802144 1555 True 1602.000000 1602 85.431000 1242 2787 1 chr7B.!!$R2 1545
4 TraesCS4D01G063600 chr7B 747890587 747892328 1741 False 1596.000000 1596 83.465000 903 2647 1 chr7B.!!$F1 1744
5 TraesCS4D01G063600 chr7B 744704708 744707329 2621 False 244.500000 283 87.098500 1828 2737 2 chr7B.!!$F3 909
6 TraesCS4D01G063600 chr7D 633127293 633128401 1108 False 1092.000000 1092 84.843000 1767 2854 1 chr7D.!!$F1 1087
7 TraesCS4D01G063600 chr7D 632732513 632733274 761 True 372.000000 372 75.866000 1291 2059 1 chr7D.!!$R2 768

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
121 122 0.394938 TAGTGAAGCGAACAAGCCCA 59.605 50.000 0.00 0.00 38.01 5.36 F
122 123 0.465460 AGTGAAGCGAACAAGCCCAA 60.465 50.000 0.00 0.00 38.01 4.12 F
123 124 0.598065 GTGAAGCGAACAAGCCCAAT 59.402 50.000 0.00 0.00 38.01 3.16 F
124 125 0.881118 TGAAGCGAACAAGCCCAATC 59.119 50.000 0.00 0.00 38.01 2.67 F
655 656 1.136305 GCAACTTCATGCATGCCATCT 59.864 47.619 22.25 2.21 45.70 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1540 0.460311 GCATAGCCGAGTACACCAGT 59.540 55.000 0.0 0.0 0.00 4.00 R
1445 1668 3.189910 CCATGTGTTCATGTTGAGGACAG 59.810 47.826 7.3 0.0 46.99 3.51 R
1545 1768 4.218312 TGCTACTATCAGCTTCATCAGGA 58.782 43.478 0.0 0.0 42.30 3.86 R
2050 2276 5.772825 CCAACATGGATATTTGGGTACAG 57.227 43.478 0.0 0.0 40.96 2.74 R
2511 2779 1.549170 ACCGACAAGTACTGATCACCC 59.451 52.381 0.0 0.0 0.00 4.61 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
24 25 6.840780 TGTGTAGACATGAAGATGAAGAGA 57.159 37.500 0.00 0.00 33.36 3.10
25 26 6.861144 TGTGTAGACATGAAGATGAAGAGAG 58.139 40.000 0.00 0.00 33.36 3.20
26 27 6.660949 TGTGTAGACATGAAGATGAAGAGAGA 59.339 38.462 0.00 0.00 33.36 3.10
27 28 7.341512 TGTGTAGACATGAAGATGAAGAGAGAT 59.658 37.037 0.00 0.00 33.36 2.75
28 29 7.648908 GTGTAGACATGAAGATGAAGAGAGATG 59.351 40.741 0.00 0.00 33.36 2.90
29 30 7.559170 TGTAGACATGAAGATGAAGAGAGATGA 59.441 37.037 0.00 0.00 33.36 2.92
30 31 7.421087 AGACATGAAGATGAAGAGAGATGAA 57.579 36.000 0.00 0.00 33.36 2.57
31 32 8.025270 AGACATGAAGATGAAGAGAGATGAAT 57.975 34.615 0.00 0.00 33.36 2.57
32 33 8.145767 AGACATGAAGATGAAGAGAGATGAATC 58.854 37.037 0.00 0.00 33.36 2.52
33 34 6.924612 ACATGAAGATGAAGAGAGATGAATCG 59.075 38.462 0.00 0.00 33.36 3.34
34 35 6.705863 TGAAGATGAAGAGAGATGAATCGA 57.294 37.500 0.00 0.00 0.00 3.59
35 36 7.287512 TGAAGATGAAGAGAGATGAATCGAT 57.712 36.000 0.00 0.00 0.00 3.59
36 37 7.724287 TGAAGATGAAGAGAGATGAATCGATT 58.276 34.615 11.20 11.20 0.00 3.34
37 38 7.866898 TGAAGATGAAGAGAGATGAATCGATTC 59.133 37.037 27.59 27.59 37.31 2.52
38 39 6.380995 AGATGAAGAGAGATGAATCGATTCG 58.619 40.000 28.07 0.00 39.62 3.34
39 40 5.506686 TGAAGAGAGATGAATCGATTCGT 57.493 39.130 28.51 28.51 39.62 3.85
40 41 5.895928 TGAAGAGAGATGAATCGATTCGTT 58.104 37.500 28.69 20.31 39.62 3.85
41 42 7.027778 TGAAGAGAGATGAATCGATTCGTTA 57.972 36.000 28.69 15.22 39.62 3.18
42 43 7.652727 TGAAGAGAGATGAATCGATTCGTTAT 58.347 34.615 28.69 21.50 39.62 1.89
43 44 8.138074 TGAAGAGAGATGAATCGATTCGTTATT 58.862 33.333 28.69 18.49 39.62 1.40
44 45 8.879342 AAGAGAGATGAATCGATTCGTTATTT 57.121 30.769 28.69 17.78 39.62 1.40
45 46 8.879342 AGAGAGATGAATCGATTCGTTATTTT 57.121 30.769 28.69 15.41 39.62 1.82
46 47 9.319143 AGAGAGATGAATCGATTCGTTATTTTT 57.681 29.630 28.69 14.41 39.62 1.94
73 74 2.291741 CCAGTTGGTTCAAGTTCTCAGC 59.708 50.000 0.00 0.00 0.00 4.26
74 75 2.291741 CAGTTGGTTCAAGTTCTCAGCC 59.708 50.000 0.00 0.00 0.00 4.85
75 76 2.092429 AGTTGGTTCAAGTTCTCAGCCA 60.092 45.455 0.00 0.00 0.00 4.75
76 77 2.887152 GTTGGTTCAAGTTCTCAGCCAT 59.113 45.455 0.00 0.00 0.00 4.40
77 78 2.783135 TGGTTCAAGTTCTCAGCCATC 58.217 47.619 0.00 0.00 0.00 3.51
78 79 2.106338 TGGTTCAAGTTCTCAGCCATCA 59.894 45.455 0.00 0.00 0.00 3.07
79 80 2.746362 GGTTCAAGTTCTCAGCCATCAG 59.254 50.000 0.00 0.00 0.00 2.90
80 81 3.557898 GGTTCAAGTTCTCAGCCATCAGA 60.558 47.826 0.00 0.00 0.00 3.27
81 82 4.067896 GTTCAAGTTCTCAGCCATCAGAA 58.932 43.478 0.00 0.00 0.00 3.02
82 83 4.356405 TCAAGTTCTCAGCCATCAGAAA 57.644 40.909 0.00 0.00 30.38 2.52
83 84 4.717877 TCAAGTTCTCAGCCATCAGAAAA 58.282 39.130 0.00 0.00 30.38 2.29
84 85 5.319453 TCAAGTTCTCAGCCATCAGAAAAT 58.681 37.500 0.00 0.00 30.38 1.82
85 86 5.182570 TCAAGTTCTCAGCCATCAGAAAATG 59.817 40.000 0.00 0.00 30.38 2.32
86 87 4.914983 AGTTCTCAGCCATCAGAAAATGA 58.085 39.130 0.00 0.00 43.70 2.57
87 88 4.699257 AGTTCTCAGCCATCAGAAAATGAC 59.301 41.667 0.00 0.00 41.91 3.06
88 89 3.264947 TCTCAGCCATCAGAAAATGACG 58.735 45.455 0.00 0.00 41.91 4.35
89 90 1.739466 TCAGCCATCAGAAAATGACGC 59.261 47.619 0.00 0.00 41.91 5.19
90 91 1.741706 CAGCCATCAGAAAATGACGCT 59.258 47.619 0.00 0.00 44.06 5.07
91 92 2.938451 CAGCCATCAGAAAATGACGCTA 59.062 45.455 2.10 0.00 42.30 4.26
92 93 2.939103 AGCCATCAGAAAATGACGCTAC 59.061 45.455 0.73 0.00 42.35 3.58
93 94 2.939103 GCCATCAGAAAATGACGCTACT 59.061 45.455 0.00 0.00 41.91 2.57
94 95 3.242543 GCCATCAGAAAATGACGCTACTG 60.243 47.826 0.00 0.00 41.91 2.74
95 96 3.935203 CCATCAGAAAATGACGCTACTGT 59.065 43.478 0.00 0.00 41.91 3.55
96 97 4.201753 CCATCAGAAAATGACGCTACTGTG 60.202 45.833 0.00 0.00 41.91 3.66
97 98 2.736721 TCAGAAAATGACGCTACTGTGC 59.263 45.455 0.00 0.00 31.12 4.57
98 99 2.480037 CAGAAAATGACGCTACTGTGCA 59.520 45.455 0.00 0.00 0.00 4.57
99 100 3.058983 CAGAAAATGACGCTACTGTGCAA 60.059 43.478 0.00 0.00 0.00 4.08
100 101 3.753272 AGAAAATGACGCTACTGTGCAAT 59.247 39.130 0.00 0.00 0.00 3.56
101 102 3.747099 AAATGACGCTACTGTGCAATC 57.253 42.857 0.00 0.00 0.00 2.67
102 103 2.680312 ATGACGCTACTGTGCAATCT 57.320 45.000 0.00 0.00 0.00 2.40
103 104 3.801114 ATGACGCTACTGTGCAATCTA 57.199 42.857 0.00 0.00 0.00 1.98
104 105 3.150848 TGACGCTACTGTGCAATCTAG 57.849 47.619 0.00 0.00 0.00 2.43
105 106 2.492088 TGACGCTACTGTGCAATCTAGT 59.508 45.455 0.00 0.00 0.00 2.57
106 107 2.854777 GACGCTACTGTGCAATCTAGTG 59.145 50.000 0.00 0.00 0.00 2.74
107 108 2.492088 ACGCTACTGTGCAATCTAGTGA 59.508 45.455 11.41 0.00 0.00 3.41
108 109 3.056821 ACGCTACTGTGCAATCTAGTGAA 60.057 43.478 11.41 0.00 0.00 3.18
109 110 3.549471 CGCTACTGTGCAATCTAGTGAAG 59.451 47.826 0.00 0.00 0.00 3.02
110 111 3.308323 GCTACTGTGCAATCTAGTGAAGC 59.692 47.826 0.00 0.00 0.00 3.86
111 112 2.341257 ACTGTGCAATCTAGTGAAGCG 58.659 47.619 0.00 0.00 32.33 4.68
112 113 2.029020 ACTGTGCAATCTAGTGAAGCGA 60.029 45.455 0.00 0.00 32.33 4.93
113 114 2.995939 CTGTGCAATCTAGTGAAGCGAA 59.004 45.455 0.00 0.00 32.33 4.70
114 115 2.736721 TGTGCAATCTAGTGAAGCGAAC 59.263 45.455 0.00 0.00 32.33 3.95
115 116 2.736721 GTGCAATCTAGTGAAGCGAACA 59.263 45.455 0.00 0.00 32.33 3.18
116 117 3.186409 GTGCAATCTAGTGAAGCGAACAA 59.814 43.478 0.00 0.00 32.33 2.83
117 118 3.433274 TGCAATCTAGTGAAGCGAACAAG 59.567 43.478 0.00 0.00 32.33 3.16
118 119 3.726190 GCAATCTAGTGAAGCGAACAAGC 60.726 47.826 0.00 0.00 37.41 4.01
119 120 2.080286 TCTAGTGAAGCGAACAAGCC 57.920 50.000 0.00 0.00 38.01 4.35
120 121 1.079503 CTAGTGAAGCGAACAAGCCC 58.920 55.000 0.00 0.00 38.01 5.19
121 122 0.394938 TAGTGAAGCGAACAAGCCCA 59.605 50.000 0.00 0.00 38.01 5.36
122 123 0.465460 AGTGAAGCGAACAAGCCCAA 60.465 50.000 0.00 0.00 38.01 4.12
123 124 0.598065 GTGAAGCGAACAAGCCCAAT 59.402 50.000 0.00 0.00 38.01 3.16
124 125 0.881118 TGAAGCGAACAAGCCCAATC 59.119 50.000 0.00 0.00 38.01 2.67
125 126 1.168714 GAAGCGAACAAGCCCAATCT 58.831 50.000 0.00 0.00 38.01 2.40
126 127 2.290008 TGAAGCGAACAAGCCCAATCTA 60.290 45.455 0.00 0.00 38.01 1.98
127 128 2.029838 AGCGAACAAGCCCAATCTAG 57.970 50.000 0.00 0.00 38.01 2.43
128 129 1.279271 AGCGAACAAGCCCAATCTAGT 59.721 47.619 0.00 0.00 38.01 2.57
129 130 1.398390 GCGAACAAGCCCAATCTAGTG 59.602 52.381 0.00 0.00 0.00 2.74
130 131 2.935238 GCGAACAAGCCCAATCTAGTGA 60.935 50.000 0.00 0.00 0.00 3.41
131 132 3.334691 CGAACAAGCCCAATCTAGTGAA 58.665 45.455 0.00 0.00 0.00 3.18
132 133 3.372206 CGAACAAGCCCAATCTAGTGAAG 59.628 47.826 0.00 0.00 0.00 3.02
133 134 2.716217 ACAAGCCCAATCTAGTGAAGC 58.284 47.619 0.00 0.00 0.00 3.86
134 135 1.667724 CAAGCCCAATCTAGTGAAGCG 59.332 52.381 0.00 0.00 0.00 4.68
135 136 1.195115 AGCCCAATCTAGTGAAGCGA 58.805 50.000 0.00 0.00 0.00 4.93
136 137 1.555075 AGCCCAATCTAGTGAAGCGAA 59.445 47.619 0.00 0.00 0.00 4.70
137 138 1.666189 GCCCAATCTAGTGAAGCGAAC 59.334 52.381 0.00 0.00 0.00 3.95
138 139 2.935238 GCCCAATCTAGTGAAGCGAACA 60.935 50.000 0.00 0.00 0.00 3.18
139 140 3.334691 CCCAATCTAGTGAAGCGAACAA 58.665 45.455 0.00 0.00 0.00 2.83
140 141 3.372206 CCCAATCTAGTGAAGCGAACAAG 59.628 47.826 0.00 0.00 0.00 3.16
141 142 3.181516 CCAATCTAGTGAAGCGAACAAGC 60.182 47.826 0.00 0.00 37.41 4.01
142 143 2.812358 TCTAGTGAAGCGAACAAGCA 57.188 45.000 0.00 0.00 40.15 3.91
143 144 3.319137 TCTAGTGAAGCGAACAAGCAT 57.681 42.857 0.00 0.00 40.15 3.79
144 145 2.995939 TCTAGTGAAGCGAACAAGCATG 59.004 45.455 0.00 0.00 40.15 4.06
145 146 1.597742 AGTGAAGCGAACAAGCATGT 58.402 45.000 0.00 0.00 43.14 3.21
179 180 6.496338 AAGAACTTATTAGTGAAAAGCGGG 57.504 37.500 0.00 0.00 34.01 6.13
180 181 5.557866 AGAACTTATTAGTGAAAAGCGGGT 58.442 37.500 0.00 0.00 34.01 5.28
181 182 6.002082 AGAACTTATTAGTGAAAAGCGGGTT 58.998 36.000 0.00 0.00 34.01 4.11
182 183 7.163441 AGAACTTATTAGTGAAAAGCGGGTTA 58.837 34.615 0.00 0.00 34.01 2.85
183 184 7.662669 AGAACTTATTAGTGAAAAGCGGGTTAA 59.337 33.333 0.00 0.00 34.01 2.01
184 185 7.137490 ACTTATTAGTGAAAAGCGGGTTAAC 57.863 36.000 0.00 0.00 31.99 2.01
185 186 6.149973 ACTTATTAGTGAAAAGCGGGTTAACC 59.850 38.462 16.85 16.85 31.99 2.85
186 187 2.651382 AGTGAAAAGCGGGTTAACCT 57.349 45.000 23.69 2.85 36.97 3.50
187 188 3.775261 AGTGAAAAGCGGGTTAACCTA 57.225 42.857 23.69 0.00 36.97 3.08
188 189 4.089408 AGTGAAAAGCGGGTTAACCTAA 57.911 40.909 23.69 0.00 36.97 2.69
189 190 4.463070 AGTGAAAAGCGGGTTAACCTAAA 58.537 39.130 23.69 0.00 36.97 1.85
190 191 4.517832 AGTGAAAAGCGGGTTAACCTAAAG 59.482 41.667 23.69 13.58 36.97 1.85
191 192 4.516321 GTGAAAAGCGGGTTAACCTAAAGA 59.484 41.667 23.69 0.00 36.97 2.52
192 193 5.008911 GTGAAAAGCGGGTTAACCTAAAGAA 59.991 40.000 23.69 1.50 36.97 2.52
193 194 5.239963 TGAAAAGCGGGTTAACCTAAAGAAG 59.760 40.000 23.69 8.21 36.97 2.85
194 195 4.628963 AAGCGGGTTAACCTAAAGAAGA 57.371 40.909 23.69 0.00 36.97 2.87
195 196 4.628963 AGCGGGTTAACCTAAAGAAGAA 57.371 40.909 23.69 0.00 36.97 2.52
196 197 4.976864 AGCGGGTTAACCTAAAGAAGAAA 58.023 39.130 23.69 0.00 36.97 2.52
197 198 5.379187 AGCGGGTTAACCTAAAGAAGAAAA 58.621 37.500 23.69 0.00 36.97 2.29
198 199 5.829391 AGCGGGTTAACCTAAAGAAGAAAAA 59.171 36.000 23.69 0.00 36.97 1.94
655 656 1.136305 GCAACTTCATGCATGCCATCT 59.864 47.619 22.25 2.21 45.70 2.90
718 719 3.966979 TCCAATTCCATGTATGTGCAGT 58.033 40.909 0.00 0.00 0.00 4.40
779 954 1.389609 GCCTGATGCACATGGGGAAG 61.390 60.000 0.00 0.00 40.77 3.46
814 989 1.526686 CAGGTCAGTGGCAGCACAA 60.527 57.895 0.00 0.00 0.00 3.33
1094 1312 2.943033 GCCAGCGAAGTACCAACATATT 59.057 45.455 0.00 0.00 0.00 1.28
1317 1540 1.287815 CGCCACGAGACCACTAACA 59.712 57.895 0.00 0.00 0.00 2.41
1543 1766 2.155279 GCACCTTCCTCTCAAAACCTC 58.845 52.381 0.00 0.00 0.00 3.85
1544 1767 2.784347 CACCTTCCTCTCAAAACCTCC 58.216 52.381 0.00 0.00 0.00 4.30
1545 1768 2.373502 CACCTTCCTCTCAAAACCTCCT 59.626 50.000 0.00 0.00 0.00 3.69
1560 1783 2.048601 CCTCCTCCTGATGAAGCTGAT 58.951 52.381 0.00 0.00 0.00 2.90
2050 2276 7.231722 TGGACATAGAGGAGAAGCTACTATTTC 59.768 40.741 0.00 0.00 0.00 2.17
2331 2564 8.439971 TGAATTCTACCATCTTGGCTGTAATAT 58.560 33.333 7.05 0.00 42.67 1.28
2361 2602 8.929827 TTTTGTACTTCATAATTCATGCCATG 57.070 30.769 0.00 0.00 34.35 3.66
2965 4978 2.356313 CTATGCCGCACCTAGCCG 60.356 66.667 0.00 0.00 41.38 5.52
3058 5071 0.462047 AGGCGGCCGAGTAAAATCTG 60.462 55.000 33.48 0.00 0.00 2.90
3072 5085 0.985490 AATCTGTGGCCTCTCCCTCC 60.985 60.000 3.32 0.00 0.00 4.30
3137 5150 2.821366 CTGATGACCACCGGCAGC 60.821 66.667 0.00 0.00 0.00 5.25
3138 5151 4.408821 TGATGACCACCGGCAGCC 62.409 66.667 0.00 0.00 0.00 4.85
3139 5152 4.101448 GATGACCACCGGCAGCCT 62.101 66.667 10.54 0.00 0.00 4.58
3140 5153 3.628646 GATGACCACCGGCAGCCTT 62.629 63.158 10.54 0.00 0.00 4.35
3141 5154 3.925630 ATGACCACCGGCAGCCTTG 62.926 63.158 10.54 6.40 0.00 3.61
3175 5188 4.129737 CGACATCGCCGGTGACCT 62.130 66.667 22.26 8.04 0.00 3.85
3176 5189 2.264794 GACATCGCCGGTGACCTT 59.735 61.111 22.26 7.25 0.00 3.50
3177 5190 2.047274 ACATCGCCGGTGACCTTG 60.047 61.111 22.26 17.51 0.00 3.61
3178 5191 3.499737 CATCGCCGGTGACCTTGC 61.500 66.667 22.26 1.04 0.00 4.01
3179 5192 4.778143 ATCGCCGGTGACCTTGCC 62.778 66.667 22.26 0.00 0.00 4.52
3200 5515 0.686769 CCCCCACTAGCTACGTTCCT 60.687 60.000 0.00 0.00 0.00 3.36
3206 5521 0.753262 CTAGCTACGTTCCTGGCCAT 59.247 55.000 5.51 0.00 0.00 4.40
3285 5600 2.127758 GTTCGACAGCAAACGCGG 60.128 61.111 12.47 0.00 0.00 6.46
3296 5611 2.879233 AAACGCGGCCTCTCCTTGA 61.879 57.895 12.47 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.177392 TCTCTCTTCATCTTCATGTCTACACAA 59.823 37.037 0.00 0.00 35.64 3.33
1 2 6.660949 TCTCTCTTCATCTTCATGTCTACACA 59.339 38.462 0.00 0.00 36.78 3.72
2 3 7.094508 TCTCTCTTCATCTTCATGTCTACAC 57.905 40.000 0.00 0.00 0.00 2.90
3 4 7.559170 TCATCTCTCTTCATCTTCATGTCTACA 59.441 37.037 0.00 0.00 0.00 2.74
4 5 7.939782 TCATCTCTCTTCATCTTCATGTCTAC 58.060 38.462 0.00 0.00 0.00 2.59
5 6 8.530804 TTCATCTCTCTTCATCTTCATGTCTA 57.469 34.615 0.00 0.00 0.00 2.59
6 7 7.421087 TTCATCTCTCTTCATCTTCATGTCT 57.579 36.000 0.00 0.00 0.00 3.41
7 8 7.115236 CGATTCATCTCTCTTCATCTTCATGTC 59.885 40.741 0.00 0.00 0.00 3.06
8 9 6.924612 CGATTCATCTCTCTTCATCTTCATGT 59.075 38.462 0.00 0.00 0.00 3.21
9 10 7.146648 TCGATTCATCTCTCTTCATCTTCATG 58.853 38.462 0.00 0.00 0.00 3.07
10 11 7.287512 TCGATTCATCTCTCTTCATCTTCAT 57.712 36.000 0.00 0.00 0.00 2.57
11 12 6.705863 TCGATTCATCTCTCTTCATCTTCA 57.294 37.500 0.00 0.00 0.00 3.02
12 13 7.060979 CGAATCGATTCATCTCTCTTCATCTTC 59.939 40.741 31.57 5.90 36.61 2.87
13 14 6.862608 CGAATCGATTCATCTCTCTTCATCTT 59.137 38.462 31.57 0.00 36.61 2.40
14 15 6.016360 ACGAATCGATTCATCTCTCTTCATCT 60.016 38.462 31.57 0.00 36.61 2.90
15 16 6.148948 ACGAATCGATTCATCTCTCTTCATC 58.851 40.000 31.57 6.45 36.61 2.92
16 17 6.083098 ACGAATCGATTCATCTCTCTTCAT 57.917 37.500 31.57 0.00 36.61 2.57
17 18 5.506686 ACGAATCGATTCATCTCTCTTCA 57.493 39.130 31.57 0.00 36.61 3.02
18 19 8.514136 AATAACGAATCGATTCATCTCTCTTC 57.486 34.615 31.57 8.25 36.61 2.87
19 20 8.879342 AAATAACGAATCGATTCATCTCTCTT 57.121 30.769 31.57 15.68 36.61 2.85
20 21 8.879342 AAAATAACGAATCGATTCATCTCTCT 57.121 30.769 31.57 9.37 36.61 3.10
52 53 2.291741 GCTGAGAACTTGAACCAACTGG 59.708 50.000 0.00 0.00 42.17 4.00
53 54 2.291741 GGCTGAGAACTTGAACCAACTG 59.708 50.000 0.00 0.00 0.00 3.16
54 55 2.092429 TGGCTGAGAACTTGAACCAACT 60.092 45.455 0.00 0.00 0.00 3.16
55 56 2.297701 TGGCTGAGAACTTGAACCAAC 58.702 47.619 0.00 0.00 0.00 3.77
56 57 2.727123 TGGCTGAGAACTTGAACCAA 57.273 45.000 0.00 0.00 0.00 3.67
57 58 2.106338 TGATGGCTGAGAACTTGAACCA 59.894 45.455 0.00 0.00 0.00 3.67
58 59 2.746362 CTGATGGCTGAGAACTTGAACC 59.254 50.000 0.00 0.00 0.00 3.62
59 60 3.668447 TCTGATGGCTGAGAACTTGAAC 58.332 45.455 0.00 0.00 0.00 3.18
60 61 4.356405 TTCTGATGGCTGAGAACTTGAA 57.644 40.909 0.00 0.00 0.00 2.69
61 62 4.356405 TTTCTGATGGCTGAGAACTTGA 57.644 40.909 0.00 0.00 0.00 3.02
62 63 5.182570 TCATTTTCTGATGGCTGAGAACTTG 59.817 40.000 0.00 0.00 0.00 3.16
63 64 5.182760 GTCATTTTCTGATGGCTGAGAACTT 59.817 40.000 0.00 0.00 35.97 2.66
64 65 4.699257 GTCATTTTCTGATGGCTGAGAACT 59.301 41.667 0.00 0.00 35.97 3.01
65 66 4.436584 CGTCATTTTCTGATGGCTGAGAAC 60.437 45.833 0.00 0.00 37.26 3.01
66 67 3.686241 CGTCATTTTCTGATGGCTGAGAA 59.314 43.478 0.00 0.00 37.26 2.87
67 68 3.264947 CGTCATTTTCTGATGGCTGAGA 58.735 45.455 0.00 0.00 37.26 3.27
68 69 2.223203 GCGTCATTTTCTGATGGCTGAG 60.223 50.000 0.00 0.00 40.64 3.35
69 70 1.739466 GCGTCATTTTCTGATGGCTGA 59.261 47.619 0.00 0.00 40.64 4.26
70 71 1.741706 AGCGTCATTTTCTGATGGCTG 59.258 47.619 3.84 0.00 41.88 4.85
71 72 2.119801 AGCGTCATTTTCTGATGGCT 57.880 45.000 0.00 0.00 40.64 4.75
72 73 2.939103 AGTAGCGTCATTTTCTGATGGC 59.061 45.455 0.00 0.00 40.64 4.40
73 74 3.935203 ACAGTAGCGTCATTTTCTGATGG 59.065 43.478 0.00 0.00 40.64 3.51
74 75 4.726021 GCACAGTAGCGTCATTTTCTGATG 60.726 45.833 0.00 0.00 42.79 3.07
75 76 3.372206 GCACAGTAGCGTCATTTTCTGAT 59.628 43.478 0.00 0.00 35.97 2.90
76 77 2.736721 GCACAGTAGCGTCATTTTCTGA 59.263 45.455 0.00 0.00 0.00 3.27
77 78 2.480037 TGCACAGTAGCGTCATTTTCTG 59.520 45.455 0.00 0.00 37.31 3.02
78 79 2.766313 TGCACAGTAGCGTCATTTTCT 58.234 42.857 0.00 0.00 37.31 2.52
79 80 3.536158 TTGCACAGTAGCGTCATTTTC 57.464 42.857 0.00 0.00 37.31 2.29
80 81 3.753272 AGATTGCACAGTAGCGTCATTTT 59.247 39.130 0.00 0.00 37.31 1.82
81 82 3.338249 AGATTGCACAGTAGCGTCATTT 58.662 40.909 0.00 0.00 37.31 2.32
82 83 2.977914 AGATTGCACAGTAGCGTCATT 58.022 42.857 0.00 0.00 37.31 2.57
83 84 2.680312 AGATTGCACAGTAGCGTCAT 57.320 45.000 0.00 0.00 37.31 3.06
84 85 2.492088 ACTAGATTGCACAGTAGCGTCA 59.508 45.455 0.00 0.00 37.31 4.35
85 86 2.854777 CACTAGATTGCACAGTAGCGTC 59.145 50.000 0.00 0.00 37.31 5.19
86 87 2.492088 TCACTAGATTGCACAGTAGCGT 59.508 45.455 0.00 0.00 37.31 5.07
87 88 3.150848 TCACTAGATTGCACAGTAGCG 57.849 47.619 0.00 0.00 37.31 4.26
88 89 3.308323 GCTTCACTAGATTGCACAGTAGC 59.692 47.826 0.00 0.00 0.00 3.58
89 90 3.549471 CGCTTCACTAGATTGCACAGTAG 59.451 47.826 0.00 0.00 0.00 2.57
90 91 3.192633 TCGCTTCACTAGATTGCACAGTA 59.807 43.478 0.00 0.00 0.00 2.74
91 92 2.029020 TCGCTTCACTAGATTGCACAGT 60.029 45.455 0.00 0.00 0.00 3.55
92 93 2.610433 TCGCTTCACTAGATTGCACAG 58.390 47.619 0.00 0.00 0.00 3.66
93 94 2.736721 GTTCGCTTCACTAGATTGCACA 59.263 45.455 0.00 0.00 0.00 4.57
94 95 2.736721 TGTTCGCTTCACTAGATTGCAC 59.263 45.455 0.00 0.00 0.00 4.57
95 96 3.038788 TGTTCGCTTCACTAGATTGCA 57.961 42.857 0.00 0.00 0.00 4.08
96 97 3.726190 GCTTGTTCGCTTCACTAGATTGC 60.726 47.826 0.00 0.00 0.00 3.56
97 98 3.181516 GGCTTGTTCGCTTCACTAGATTG 60.182 47.826 0.00 0.00 0.00 2.67
98 99 3.003480 GGCTTGTTCGCTTCACTAGATT 58.997 45.455 0.00 0.00 0.00 2.40
99 100 2.622436 GGCTTGTTCGCTTCACTAGAT 58.378 47.619 0.00 0.00 0.00 1.98
100 101 1.337823 GGGCTTGTTCGCTTCACTAGA 60.338 52.381 0.00 0.00 0.00 2.43
101 102 1.079503 GGGCTTGTTCGCTTCACTAG 58.920 55.000 0.00 0.00 0.00 2.57
102 103 0.394938 TGGGCTTGTTCGCTTCACTA 59.605 50.000 0.00 0.00 0.00 2.74
103 104 0.465460 TTGGGCTTGTTCGCTTCACT 60.465 50.000 0.00 0.00 0.00 3.41
104 105 0.598065 ATTGGGCTTGTTCGCTTCAC 59.402 50.000 0.00 0.00 0.00 3.18
105 106 0.881118 GATTGGGCTTGTTCGCTTCA 59.119 50.000 0.00 0.00 0.00 3.02
106 107 1.168714 AGATTGGGCTTGTTCGCTTC 58.831 50.000 0.00 0.00 0.00 3.86
107 108 2.290323 ACTAGATTGGGCTTGTTCGCTT 60.290 45.455 0.00 0.00 0.00 4.68
108 109 1.279271 ACTAGATTGGGCTTGTTCGCT 59.721 47.619 0.00 0.00 0.00 4.93
109 110 1.398390 CACTAGATTGGGCTTGTTCGC 59.602 52.381 0.00 0.00 0.00 4.70
110 111 2.972625 TCACTAGATTGGGCTTGTTCG 58.027 47.619 0.00 0.00 0.00 3.95
111 112 3.127721 GCTTCACTAGATTGGGCTTGTTC 59.872 47.826 0.00 0.00 0.00 3.18
112 113 3.084786 GCTTCACTAGATTGGGCTTGTT 58.915 45.455 0.00 0.00 0.00 2.83
113 114 2.716217 GCTTCACTAGATTGGGCTTGT 58.284 47.619 0.00 0.00 0.00 3.16
114 115 1.667724 CGCTTCACTAGATTGGGCTTG 59.332 52.381 0.00 0.00 0.00 4.01
115 116 1.555075 TCGCTTCACTAGATTGGGCTT 59.445 47.619 0.00 0.00 0.00 4.35
116 117 1.195115 TCGCTTCACTAGATTGGGCT 58.805 50.000 0.00 0.00 0.00 5.19
117 118 1.666189 GTTCGCTTCACTAGATTGGGC 59.334 52.381 0.00 0.00 0.00 5.36
118 119 2.972625 TGTTCGCTTCACTAGATTGGG 58.027 47.619 0.00 0.00 0.00 4.12
119 120 3.181516 GCTTGTTCGCTTCACTAGATTGG 60.182 47.826 0.00 0.00 0.00 3.16
120 121 3.433274 TGCTTGTTCGCTTCACTAGATTG 59.567 43.478 0.00 0.00 0.00 2.67
121 122 3.664107 TGCTTGTTCGCTTCACTAGATT 58.336 40.909 0.00 0.00 0.00 2.40
122 123 3.319137 TGCTTGTTCGCTTCACTAGAT 57.681 42.857 0.00 0.00 0.00 1.98
123 124 2.812358 TGCTTGTTCGCTTCACTAGA 57.188 45.000 0.00 0.00 0.00 2.43
124 125 2.738846 ACATGCTTGTTCGCTTCACTAG 59.261 45.455 0.00 0.00 29.55 2.57
125 126 2.766313 ACATGCTTGTTCGCTTCACTA 58.234 42.857 0.00 0.00 29.55 2.74
126 127 1.597742 ACATGCTTGTTCGCTTCACT 58.402 45.000 0.00 0.00 29.55 3.41
127 128 2.405892 AACATGCTTGTTCGCTTCAC 57.594 45.000 11.92 0.00 42.43 3.18
128 129 4.764679 ATTAACATGCTTGTTCGCTTCA 57.235 36.364 20.08 0.60 42.43 3.02
129 130 5.393962 AGAATTAACATGCTTGTTCGCTTC 58.606 37.500 20.08 18.55 42.43 3.86
130 131 5.376854 AGAATTAACATGCTTGTTCGCTT 57.623 34.783 20.08 12.38 42.43 4.68
131 132 6.683974 ATAGAATTAACATGCTTGTTCGCT 57.316 33.333 20.08 14.75 42.43 4.93
132 133 8.835467 TTAATAGAATTAACATGCTTGTTCGC 57.165 30.769 20.08 9.23 42.43 4.70
153 154 8.674607 CCCGCTTTTCACTAATAAGTTCTTAAT 58.325 33.333 0.00 0.00 31.97 1.40
154 155 7.662669 ACCCGCTTTTCACTAATAAGTTCTTAA 59.337 33.333 0.00 0.00 31.97 1.85
155 156 7.163441 ACCCGCTTTTCACTAATAAGTTCTTA 58.837 34.615 0.00 0.00 31.97 2.10
156 157 6.002082 ACCCGCTTTTCACTAATAAGTTCTT 58.998 36.000 0.00 0.00 31.97 2.52
157 158 5.557866 ACCCGCTTTTCACTAATAAGTTCT 58.442 37.500 0.00 0.00 31.97 3.01
158 159 5.874895 ACCCGCTTTTCACTAATAAGTTC 57.125 39.130 0.00 0.00 31.97 3.01
159 160 7.308770 GGTTAACCCGCTTTTCACTAATAAGTT 60.309 37.037 14.16 0.00 31.97 2.66
160 161 6.149973 GGTTAACCCGCTTTTCACTAATAAGT 59.850 38.462 14.16 0.00 35.91 2.24
161 162 6.373495 AGGTTAACCCGCTTTTCACTAATAAG 59.627 38.462 21.30 0.00 38.74 1.73
162 163 6.240145 AGGTTAACCCGCTTTTCACTAATAA 58.760 36.000 21.30 0.00 38.74 1.40
163 164 5.807909 AGGTTAACCCGCTTTTCACTAATA 58.192 37.500 21.30 0.00 38.74 0.98
164 165 4.659115 AGGTTAACCCGCTTTTCACTAAT 58.341 39.130 21.30 0.00 38.74 1.73
165 166 4.089408 AGGTTAACCCGCTTTTCACTAA 57.911 40.909 21.30 0.00 38.74 2.24
166 167 3.775261 AGGTTAACCCGCTTTTCACTA 57.225 42.857 21.30 0.00 38.74 2.74
167 168 2.651382 AGGTTAACCCGCTTTTCACT 57.349 45.000 21.30 0.00 38.74 3.41
168 169 4.516321 TCTTTAGGTTAACCCGCTTTTCAC 59.484 41.667 21.30 0.00 38.74 3.18
169 170 4.716794 TCTTTAGGTTAACCCGCTTTTCA 58.283 39.130 21.30 0.00 38.74 2.69
170 171 5.471116 TCTTCTTTAGGTTAACCCGCTTTTC 59.529 40.000 21.30 0.00 38.74 2.29
171 172 5.379187 TCTTCTTTAGGTTAACCCGCTTTT 58.621 37.500 21.30 4.00 38.74 2.27
172 173 4.976864 TCTTCTTTAGGTTAACCCGCTTT 58.023 39.130 21.30 4.76 38.74 3.51
173 174 4.628963 TCTTCTTTAGGTTAACCCGCTT 57.371 40.909 21.30 5.16 38.74 4.68
174 175 4.628963 TTCTTCTTTAGGTTAACCCGCT 57.371 40.909 21.30 5.54 38.74 5.52
175 176 5.694231 TTTTCTTCTTTAGGTTAACCCGC 57.306 39.130 21.30 0.00 38.74 6.13
621 622 4.980702 TTGCACAGCTGGCCAGGG 62.981 66.667 33.46 12.01 0.00 4.45
622 623 3.677648 GTTGCACAGCTGGCCAGG 61.678 66.667 33.46 20.34 0.00 4.45
623 624 2.138656 GAAGTTGCACAGCTGGCCAG 62.139 60.000 29.34 29.34 0.00 4.85
624 625 2.123769 AAGTTGCACAGCTGGCCA 60.124 55.556 19.93 4.71 0.00 5.36
625 626 1.530013 ATGAAGTTGCACAGCTGGCC 61.530 55.000 19.93 8.82 0.00 5.36
814 989 2.932234 CGAGACGACCCAAGGTGCT 61.932 63.158 0.00 0.00 35.25 4.40
854 1029 1.751351 TCTGAATCACAGGCCTAGACG 59.249 52.381 3.98 0.00 45.76 4.18
1317 1540 0.460311 GCATAGCCGAGTACACCAGT 59.540 55.000 0.00 0.00 0.00 4.00
1445 1668 3.189910 CCATGTGTTCATGTTGAGGACAG 59.810 47.826 7.30 0.00 46.99 3.51
1543 1766 4.321899 GCTACTATCAGCTTCATCAGGAGG 60.322 50.000 0.00 0.00 38.57 4.30
1544 1767 4.280425 TGCTACTATCAGCTTCATCAGGAG 59.720 45.833 0.00 0.00 42.30 3.69
1545 1768 4.218312 TGCTACTATCAGCTTCATCAGGA 58.782 43.478 0.00 0.00 42.30 3.86
2050 2276 5.772825 CCAACATGGATATTTGGGTACAG 57.227 43.478 0.00 0.00 40.96 2.74
2511 2779 1.549170 ACCGACAAGTACTGATCACCC 59.451 52.381 0.00 0.00 0.00 4.61
2894 4907 5.727630 AGCTAGATAGGGGATTGGTTAGAA 58.272 41.667 0.00 0.00 0.00 2.10
3058 5071 2.683933 TTCGGAGGGAGAGGCCAC 60.684 66.667 5.01 0.00 38.95 5.01
3072 5085 3.124921 GTGGGGATGGCACGTTCG 61.125 66.667 0.00 0.00 0.00 3.95
3121 5134 4.408821 GGCTGCCGGTGGTCATCA 62.409 66.667 1.35 0.00 0.00 3.07
3158 5171 3.642778 AAGGTCACCGGCGATGTCG 62.643 63.158 9.30 0.00 43.27 4.35
3159 5172 2.100631 CAAGGTCACCGGCGATGTC 61.101 63.158 9.30 0.00 0.00 3.06
3160 5173 2.047274 CAAGGTCACCGGCGATGT 60.047 61.111 9.30 0.00 0.00 3.06
3161 5174 3.499737 GCAAGGTCACCGGCGATG 61.500 66.667 9.30 0.00 0.00 3.84
3162 5175 4.778143 GGCAAGGTCACCGGCGAT 62.778 66.667 9.30 0.00 31.33 4.58
3173 5186 4.489771 CTAGTGGGGGCGGCAAGG 62.490 72.222 12.47 0.00 0.00 3.61
3176 5189 4.789173 TAGCTAGTGGGGGCGGCA 62.789 66.667 12.47 0.00 0.00 5.69
3177 5190 4.237207 GTAGCTAGTGGGGGCGGC 62.237 72.222 0.00 0.00 0.00 6.53
3178 5191 3.912907 CGTAGCTAGTGGGGGCGG 61.913 72.222 0.00 0.00 0.00 6.13
3179 5192 2.624437 GAACGTAGCTAGTGGGGGCG 62.624 65.000 0.00 0.00 0.00 6.13
3180 5193 1.143401 GAACGTAGCTAGTGGGGGC 59.857 63.158 0.00 0.00 0.00 5.80
3181 5194 0.686769 AGGAACGTAGCTAGTGGGGG 60.687 60.000 0.00 0.00 0.00 5.40
3182 5195 0.460311 CAGGAACGTAGCTAGTGGGG 59.540 60.000 0.00 0.00 0.00 4.96
3183 5196 0.460311 CCAGGAACGTAGCTAGTGGG 59.540 60.000 0.00 0.00 0.00 4.61
3184 5197 0.179108 GCCAGGAACGTAGCTAGTGG 60.179 60.000 0.00 0.00 0.00 4.00
3185 5198 0.179108 GGCCAGGAACGTAGCTAGTG 60.179 60.000 0.00 0.00 0.00 2.74
3186 5199 0.613853 TGGCCAGGAACGTAGCTAGT 60.614 55.000 0.00 0.00 0.00 2.57
3187 5200 0.753262 ATGGCCAGGAACGTAGCTAG 59.247 55.000 13.05 0.00 0.00 3.42
3188 5201 0.750850 GATGGCCAGGAACGTAGCTA 59.249 55.000 13.05 0.00 0.00 3.32
3192 5507 2.185867 GCGATGGCCAGGAACGTA 59.814 61.111 13.05 0.00 0.00 3.57


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

AutoCloner maintained by Alex Coulton.