Multiple sequence alignment - TraesCS2B01G348300

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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 TraesCS2B01G348300 chr2B 100.000 2288 0 0 1 2288 495053721 495056008 0.000000e+00 4226.0
1 TraesCS2B01G348300 chr2B 92.005 1526 115 6 204 1724 713704542 713703019 0.000000e+00 2135.0
2 TraesCS2B01G348300 chr3A 92.308 1534 111 3 198 1725 418765469 418763937 0.000000e+00 2172.0
3 TraesCS2B01G348300 chr5A 91.992 1536 115 5 204 1734 604231863 604230331 0.000000e+00 2148.0
4 TraesCS2B01G348300 chr4D 92.071 1526 106 7 206 1724 116524358 116522841 0.000000e+00 2134.0
5 TraesCS2B01G348300 chr4D 91.934 1525 114 6 204 1722 421048439 421046918 0.000000e+00 2126.0
6 TraesCS2B01G348300 chr4D 91.542 1537 112 8 198 1724 493970918 493969390 0.000000e+00 2102.0
7 TraesCS2B01G348300 chr4D 89.404 151 15 1 46 196 414224947 414225096 3.000000e-44 189.0
8 TraesCS2B01G348300 chr7D 91.563 1529 120 5 202 1724 432740348 432738823 0.000000e+00 2100.0
9 TraesCS2B01G348300 chr7D 88.742 151 16 1 48 197 2075765 2075615 1.400000e-42 183.0
10 TraesCS2B01G348300 chr1B 91.580 1532 114 8 202 1726 192469915 192468392 0.000000e+00 2100.0
11 TraesCS2B01G348300 chr1B 87.195 164 18 2 45 206 623939397 623939235 1.400000e-42 183.0
12 TraesCS2B01G348300 chr2A 91.401 1535 119 8 198 1724 456462325 456460796 0.000000e+00 2091.0
13 TraesCS2B01G348300 chr2A 84.193 601 49 31 1725 2286 569006750 569007343 2.000000e-150 542.0
14 TraesCS2B01G348300 chr2D 83.709 577 52 25 1725 2286 422621832 422622381 7.290000e-140 507.0
15 TraesCS2B01G348300 chr2D 100.000 39 0 0 1 39 422621787 422621825 3.150000e-09 73.1
16 TraesCS2B01G348300 chr7A 88.415 164 16 2 48 209 141313240 141313078 6.450000e-46 195.0
17 TraesCS2B01G348300 chr4A 90.000 150 15 0 47 196 19186586 19186437 6.450000e-46 195.0
18 TraesCS2B01G348300 chr4A 88.608 158 17 1 50 206 60890964 60891121 8.340000e-45 191.0
19 TraesCS2B01G348300 chr3D 88.679 159 15 2 50 206 449745976 449746133 8.340000e-45 191.0
20 TraesCS2B01G348300 chr3D 88.742 151 17 0 46 196 81832691 81832841 3.880000e-43 185.0
21 TraesCS2B01G348300 chrUn 86.905 168 19 2 41 206 405156026 405156192 3.880000e-43 185.0


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 TraesCS2B01G348300 chr2B 495053721 495056008 2287 False 4226.00 4226 100.0000 1 2288 1 chr2B.!!$F1 2287
1 TraesCS2B01G348300 chr2B 713703019 713704542 1523 True 2135.00 2135 92.0050 204 1724 1 chr2B.!!$R1 1520
2 TraesCS2B01G348300 chr3A 418763937 418765469 1532 True 2172.00 2172 92.3080 198 1725 1 chr3A.!!$R1 1527
3 TraesCS2B01G348300 chr5A 604230331 604231863 1532 True 2148.00 2148 91.9920 204 1734 1 chr5A.!!$R1 1530
4 TraesCS2B01G348300 chr4D 116522841 116524358 1517 True 2134.00 2134 92.0710 206 1724 1 chr4D.!!$R1 1518
5 TraesCS2B01G348300 chr4D 421046918 421048439 1521 True 2126.00 2126 91.9340 204 1722 1 chr4D.!!$R2 1518
6 TraesCS2B01G348300 chr4D 493969390 493970918 1528 True 2102.00 2102 91.5420 198 1724 1 chr4D.!!$R3 1526
7 TraesCS2B01G348300 chr7D 432738823 432740348 1525 True 2100.00 2100 91.5630 202 1724 1 chr7D.!!$R2 1522
8 TraesCS2B01G348300 chr1B 192468392 192469915 1523 True 2100.00 2100 91.5800 202 1726 1 chr1B.!!$R1 1524
9 TraesCS2B01G348300 chr2A 456460796 456462325 1529 True 2091.00 2091 91.4010 198 1724 1 chr2A.!!$R1 1526
10 TraesCS2B01G348300 chr2A 569006750 569007343 593 False 542.00 542 84.1930 1725 2286 1 chr2A.!!$F1 561
11 TraesCS2B01G348300 chr2D 422621787 422622381 594 False 290.05 507 91.8545 1 2286 2 chr2D.!!$F1 2285

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
75 76 0.037975 GTTTGGTTGCCTGCATGAGG 60.038 55.0 0.00 1.51 46.13 3.86 F
116 117 0.041663 CGCAAACGTGTCGATTGGTT 60.042 50.0 12.35 0.00 39.40 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1232 0.038166 ACCACCTCAATGCCATCGTT 59.962 50.0 0.0 0.0 0.00 3.85 R
1578 1589 0.538057 CATGGGCAGAACCACACTGT 60.538 55.0 0.0 0.0 44.72 3.55 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
39 40 1.175983 CGGGCAGGCAAAACAGGTTA 61.176 55.000 0.00 0.00 0.00 2.85
41 42 0.038251 GGCAGGCAAAACAGGTTAGC 60.038 55.000 0.00 2.10 0.00 3.09
42 43 0.961753 GCAGGCAAAACAGGTTAGCT 59.038 50.000 0.00 0.00 0.00 3.32
43 44 1.068264 GCAGGCAAAACAGGTTAGCTC 60.068 52.381 0.00 0.00 0.00 4.09
44 45 1.541588 CAGGCAAAACAGGTTAGCTCC 59.458 52.381 0.00 0.00 0.00 4.70
45 46 1.144913 AGGCAAAACAGGTTAGCTCCA 59.855 47.619 0.00 0.00 0.00 3.86
46 47 2.171003 GGCAAAACAGGTTAGCTCCAT 58.829 47.619 0.00 0.00 0.00 3.41
47 48 2.164422 GGCAAAACAGGTTAGCTCCATC 59.836 50.000 0.00 0.00 0.00 3.51
48 49 3.084786 GCAAAACAGGTTAGCTCCATCT 58.915 45.455 0.00 0.00 0.00 2.90
49 50 4.261801 GCAAAACAGGTTAGCTCCATCTA 58.738 43.478 0.00 0.00 0.00 1.98
50 51 4.333926 GCAAAACAGGTTAGCTCCATCTAG 59.666 45.833 0.00 0.00 0.00 2.43
51 52 4.762289 AAACAGGTTAGCTCCATCTAGG 57.238 45.455 0.00 0.00 39.47 3.02
52 53 2.683768 ACAGGTTAGCTCCATCTAGGG 58.316 52.381 0.00 0.00 38.24 3.53
53 54 1.346068 CAGGTTAGCTCCATCTAGGGC 59.654 57.143 0.00 0.00 38.24 5.19
54 55 1.062121 AGGTTAGCTCCATCTAGGGCA 60.062 52.381 0.00 0.00 36.41 5.36
55 56 1.981495 GGTTAGCTCCATCTAGGGCAT 59.019 52.381 0.00 0.00 36.41 4.40
56 57 2.289945 GGTTAGCTCCATCTAGGGCATG 60.290 54.545 0.00 0.00 36.41 4.06
57 58 2.370189 GTTAGCTCCATCTAGGGCATGT 59.630 50.000 0.00 0.00 36.41 3.21
58 59 1.516110 AGCTCCATCTAGGGCATGTT 58.484 50.000 0.00 0.00 36.41 2.71
59 60 1.849039 AGCTCCATCTAGGGCATGTTT 59.151 47.619 0.00 0.00 36.41 2.83
60 61 1.952296 GCTCCATCTAGGGCATGTTTG 59.048 52.381 0.00 0.00 38.24 2.93
61 62 2.579873 CTCCATCTAGGGCATGTTTGG 58.420 52.381 0.00 0.00 38.24 3.28
62 63 1.922447 TCCATCTAGGGCATGTTTGGT 59.078 47.619 0.00 0.00 38.24 3.67
63 64 2.311542 TCCATCTAGGGCATGTTTGGTT 59.688 45.455 0.00 0.00 38.24 3.67
64 65 2.428171 CCATCTAGGGCATGTTTGGTTG 59.572 50.000 0.00 0.00 0.00 3.77
65 66 1.544724 TCTAGGGCATGTTTGGTTGC 58.455 50.000 0.00 0.00 38.14 4.17
69 70 3.955775 GCATGTTTGGTTGCCTGC 58.044 55.556 0.00 0.00 32.66 4.85
70 71 1.069427 GCATGTTTGGTTGCCTGCA 59.931 52.632 0.00 0.00 32.66 4.41
71 72 0.320946 GCATGTTTGGTTGCCTGCAT 60.321 50.000 0.00 0.00 32.66 3.96
72 73 1.434555 CATGTTTGGTTGCCTGCATG 58.565 50.000 0.00 0.00 0.00 4.06
73 74 1.001068 CATGTTTGGTTGCCTGCATGA 59.999 47.619 0.00 0.00 36.71 3.07
74 75 0.675083 TGTTTGGTTGCCTGCATGAG 59.325 50.000 0.00 0.00 0.00 2.90
75 76 0.037975 GTTTGGTTGCCTGCATGAGG 60.038 55.000 0.00 1.51 46.13 3.86
86 87 4.864334 CATGAGGCCCGCCCTGAC 62.864 72.222 0.00 0.00 46.60 3.51
97 98 4.436998 CCCTGACTCGTGCGGGAC 62.437 72.222 0.00 0.00 39.08 4.46
114 115 4.415490 CGCAAACGTGTCGATTGG 57.585 55.556 12.35 1.98 39.40 3.16
115 116 1.567537 CGCAAACGTGTCGATTGGT 59.432 52.632 12.35 0.00 39.40 3.67
116 117 0.041663 CGCAAACGTGTCGATTGGTT 60.042 50.000 12.35 0.00 39.40 3.67
117 118 1.394697 GCAAACGTGTCGATTGGTTG 58.605 50.000 12.35 7.63 39.40 3.77
118 119 1.394697 CAAACGTGTCGATTGGTTGC 58.605 50.000 0.00 0.00 36.32 4.17
119 120 0.309612 AAACGTGTCGATTGGTTGCC 59.690 50.000 0.00 0.00 0.00 4.52
120 121 0.534203 AACGTGTCGATTGGTTGCCT 60.534 50.000 0.00 0.00 0.00 4.75
121 122 1.227999 ACGTGTCGATTGGTTGCCTG 61.228 55.000 0.00 0.00 0.00 4.85
122 123 1.227999 CGTGTCGATTGGTTGCCTGT 61.228 55.000 0.00 0.00 0.00 4.00
123 124 0.951558 GTGTCGATTGGTTGCCTGTT 59.048 50.000 0.00 0.00 0.00 3.16
124 125 1.336755 GTGTCGATTGGTTGCCTGTTT 59.663 47.619 0.00 0.00 0.00 2.83
125 126 2.028130 TGTCGATTGGTTGCCTGTTTT 58.972 42.857 0.00 0.00 0.00 2.43
126 127 2.428890 TGTCGATTGGTTGCCTGTTTTT 59.571 40.909 0.00 0.00 0.00 1.94
127 128 3.632604 TGTCGATTGGTTGCCTGTTTTTA 59.367 39.130 0.00 0.00 0.00 1.52
128 129 3.978855 GTCGATTGGTTGCCTGTTTTTAC 59.021 43.478 0.00 0.00 0.00 2.01
129 130 3.886505 TCGATTGGTTGCCTGTTTTTACT 59.113 39.130 0.00 0.00 0.00 2.24
130 131 3.980775 CGATTGGTTGCCTGTTTTTACTG 59.019 43.478 0.00 0.00 0.00 2.74
131 132 4.499019 CGATTGGTTGCCTGTTTTTACTGT 60.499 41.667 0.00 0.00 0.00 3.55
132 133 4.810191 TTGGTTGCCTGTTTTTACTGTT 57.190 36.364 0.00 0.00 0.00 3.16
133 134 4.810191 TGGTTGCCTGTTTTTACTGTTT 57.190 36.364 0.00 0.00 0.00 2.83
134 135 5.916661 TGGTTGCCTGTTTTTACTGTTTA 57.083 34.783 0.00 0.00 0.00 2.01
135 136 5.897050 TGGTTGCCTGTTTTTACTGTTTAG 58.103 37.500 0.00 0.00 0.00 1.85
136 137 4.743151 GGTTGCCTGTTTTTACTGTTTAGC 59.257 41.667 0.00 0.00 0.00 3.09
137 138 4.577834 TGCCTGTTTTTACTGTTTAGCC 57.422 40.909 0.00 0.00 0.00 3.93
138 139 3.319689 TGCCTGTTTTTACTGTTTAGCCC 59.680 43.478 0.00 0.00 0.00 5.19
139 140 3.610821 GCCTGTTTTTACTGTTTAGCCCG 60.611 47.826 0.00 0.00 0.00 6.13
140 141 3.561503 CTGTTTTTACTGTTTAGCCCGC 58.438 45.455 0.00 0.00 0.00 6.13
141 142 2.950309 TGTTTTTACTGTTTAGCCCGCA 59.050 40.909 0.00 0.00 0.00 5.69
142 143 3.570550 TGTTTTTACTGTTTAGCCCGCAT 59.429 39.130 0.00 0.00 0.00 4.73
143 144 3.840890 TTTTACTGTTTAGCCCGCATG 57.159 42.857 0.00 0.00 0.00 4.06
144 145 1.745232 TTACTGTTTAGCCCGCATGG 58.255 50.000 0.00 0.00 37.09 3.66
154 155 3.055719 CCGCATGGCACGAACCTT 61.056 61.111 0.00 0.00 0.00 3.50
155 156 1.743623 CCGCATGGCACGAACCTTA 60.744 57.895 0.00 0.00 0.00 2.69
156 157 1.302383 CCGCATGGCACGAACCTTAA 61.302 55.000 0.00 0.00 0.00 1.85
157 158 0.519519 CGCATGGCACGAACCTTAAA 59.480 50.000 0.00 0.00 0.00 1.52
158 159 1.465689 CGCATGGCACGAACCTTAAAG 60.466 52.381 0.00 0.00 0.00 1.85
159 160 1.732405 GCATGGCACGAACCTTAAAGC 60.732 52.381 0.00 0.00 0.00 3.51
160 161 1.539388 CATGGCACGAACCTTAAAGCA 59.461 47.619 0.00 0.00 0.00 3.91
161 162 0.948678 TGGCACGAACCTTAAAGCAC 59.051 50.000 0.00 0.00 0.00 4.40
162 163 1.235724 GGCACGAACCTTAAAGCACT 58.764 50.000 0.00 0.00 0.00 4.40
163 164 1.197036 GGCACGAACCTTAAAGCACTC 59.803 52.381 0.00 0.00 0.00 3.51
164 165 1.197036 GCACGAACCTTAAAGCACTCC 59.803 52.381 0.00 0.00 0.00 3.85
165 166 2.767505 CACGAACCTTAAAGCACTCCT 58.232 47.619 0.00 0.00 0.00 3.69
166 167 3.863400 GCACGAACCTTAAAGCACTCCTA 60.863 47.826 0.00 0.00 0.00 2.94
167 168 3.927142 CACGAACCTTAAAGCACTCCTAG 59.073 47.826 0.00 0.00 0.00 3.02
168 169 3.056035 ACGAACCTTAAAGCACTCCTAGG 60.056 47.826 0.82 0.82 0.00 3.02
169 170 3.271729 GAACCTTAAAGCACTCCTAGGC 58.728 50.000 2.96 0.00 0.00 3.93
170 171 1.560146 ACCTTAAAGCACTCCTAGGCC 59.440 52.381 2.96 0.00 0.00 5.19
171 172 1.840635 CCTTAAAGCACTCCTAGGCCT 59.159 52.381 11.78 11.78 0.00 5.19
172 173 2.420687 CCTTAAAGCACTCCTAGGCCTG 60.421 54.545 17.99 5.26 0.00 4.85
173 174 1.204146 TAAAGCACTCCTAGGCCTGG 58.796 55.000 17.99 13.68 0.00 4.45
174 175 2.203549 AAAGCACTCCTAGGCCTGGC 62.204 60.000 17.99 11.05 0.00 4.85
175 176 3.086600 GCACTCCTAGGCCTGGCT 61.087 66.667 17.99 5.31 0.00 4.75
176 177 3.100503 GCACTCCTAGGCCTGGCTC 62.101 68.421 17.99 8.86 0.00 4.70
177 178 2.041405 ACTCCTAGGCCTGGCTCC 60.041 66.667 17.99 2.28 0.00 4.70
178 179 2.285180 CTCCTAGGCCTGGCTCCT 59.715 66.667 17.99 10.66 37.72 3.69
179 180 1.383803 CTCCTAGGCCTGGCTCCTT 60.384 63.158 17.99 4.80 35.21 3.36
180 181 1.690633 TCCTAGGCCTGGCTCCTTG 60.691 63.158 17.99 8.86 35.21 3.61
181 182 2.750657 CCTAGGCCTGGCTCCTTGG 61.751 68.421 17.99 14.04 39.53 3.61
182 183 2.692368 TAGGCCTGGCTCCTTGGG 60.692 66.667 17.99 0.00 35.21 4.12
183 184 3.267177 TAGGCCTGGCTCCTTGGGA 62.267 63.158 17.99 0.00 35.21 4.37
184 185 2.781258 TAGGCCTGGCTCCTTGGGAA 62.781 60.000 17.99 0.00 35.21 3.97
185 186 2.361737 GCCTGGCTCCTTGGGAAC 60.362 66.667 12.43 0.00 0.00 3.62
186 187 2.045926 CCTGGCTCCTTGGGAACG 60.046 66.667 0.00 0.00 0.00 3.95
187 188 2.747855 CTGGCTCCTTGGGAACGC 60.748 66.667 0.00 0.00 0.00 4.84
188 189 3.249189 TGGCTCCTTGGGAACGCT 61.249 61.111 0.00 0.00 0.00 5.07
189 190 2.436824 GGCTCCTTGGGAACGCTC 60.437 66.667 0.00 0.00 0.00 5.03
190 191 2.815647 GCTCCTTGGGAACGCTCG 60.816 66.667 0.00 0.00 0.00 5.03
191 192 2.970639 CTCCTTGGGAACGCTCGA 59.029 61.111 0.00 0.00 0.00 4.04
192 193 1.292223 CTCCTTGGGAACGCTCGAA 59.708 57.895 0.00 0.00 0.00 3.71
193 194 0.108138 CTCCTTGGGAACGCTCGAAT 60.108 55.000 0.00 0.00 0.00 3.34
194 195 0.108329 TCCTTGGGAACGCTCGAATC 60.108 55.000 0.00 0.00 0.00 2.52
195 196 1.421410 CCTTGGGAACGCTCGAATCG 61.421 60.000 0.00 0.00 0.00 3.34
196 197 1.421410 CTTGGGAACGCTCGAATCGG 61.421 60.000 1.76 0.00 0.00 4.18
200 201 1.139095 GAACGCTCGAATCGGGTCT 59.861 57.895 3.87 0.00 0.00 3.85
219 220 1.541310 TTCTCCCAGTACACTGCGGG 61.541 60.000 13.56 7.47 42.47 6.13
271 272 4.485875 TGTACTTGGACCACTTCTTCCTA 58.514 43.478 0.00 0.00 32.55 2.94
278 279 5.801380 TGGACCACTTCTTCCTATGTTTAC 58.199 41.667 0.00 0.00 32.55 2.01
467 468 4.136796 CTCCATGGTGTTCTCAAACTTGA 58.863 43.478 12.58 0.00 36.30 3.02
499 500 1.669440 CGACCACCCGAGGAAGAAA 59.331 57.895 0.00 0.00 0.00 2.52
619 624 1.648116 GTGGGTAAGTAGTGGTGGGA 58.352 55.000 0.00 0.00 0.00 4.37
671 679 1.973515 AGGAAGAGTGACAGTCATGCA 59.026 47.619 6.51 0.00 0.00 3.96
672 680 2.369860 AGGAAGAGTGACAGTCATGCAA 59.630 45.455 6.51 0.00 0.00 4.08
694 702 6.578919 GCAAGTTTTAACTACATGCTCTTCAC 59.421 38.462 9.43 0.00 38.57 3.18
704 712 2.408271 TGCTCTTCACTAAGCCATGG 57.592 50.000 7.63 7.63 37.73 3.66
708 716 3.133003 GCTCTTCACTAAGCCATGGACTA 59.867 47.826 18.40 4.38 32.36 2.59
741 749 4.081862 CCTGACTCCATGAATTGTTTGCAT 60.082 41.667 0.00 0.00 0.00 3.96
834 842 1.614051 CCAATGCCTGAGGTTGTGCTA 60.614 52.381 0.00 0.00 0.00 3.49
835 843 2.372264 CAATGCCTGAGGTTGTGCTAT 58.628 47.619 0.00 0.00 0.00 2.97
838 846 0.108138 GCCTGAGGTTGTGCTATCGT 60.108 55.000 0.00 0.00 0.00 3.73
839 847 1.136305 GCCTGAGGTTGTGCTATCGTA 59.864 52.381 0.00 0.00 0.00 3.43
1110 1120 1.216064 AGCTGATGAATGGCAGGGTA 58.784 50.000 0.00 0.00 32.83 3.69
1150 1160 2.159296 TCCACCTATGACGTCGTTCATG 60.159 50.000 16.79 11.10 36.84 3.07
1182 1192 2.147958 GGCTACATGGTGACGTTCAAA 58.852 47.619 0.00 0.00 0.00 2.69
1194 1204 2.036089 GACGTTCAAACTCCTCACTCCT 59.964 50.000 0.00 0.00 0.00 3.69
1222 1232 2.493675 CTCAAGGTCATCCTCTTCGACA 59.506 50.000 0.00 0.00 44.35 4.35
1318 1328 4.894114 GCACCTCCTTCCTAAGTACTATCA 59.106 45.833 0.00 0.00 0.00 2.15
1504 1514 4.567747 CCAACTAGCCAAAGAGGTTACCAT 60.568 45.833 3.51 0.00 40.61 3.55
1568 1579 2.230992 GTCCATTAACATGCAGGCAACA 59.769 45.455 0.00 0.00 41.41 3.33
1578 1589 2.649190 TGCAGGCAACAAAACACTAGA 58.351 42.857 0.00 0.00 41.41 2.43
1752 1768 0.031994 GCACCTTGCGGACAAATTGT 59.968 50.000 0.00 0.00 34.74 2.71
1807 1825 4.022068 CCCAACATTAACACAAGCATCAGT 60.022 41.667 0.00 0.00 0.00 3.41
1810 1828 6.479660 CCAACATTAACACAAGCATCAGTTTT 59.520 34.615 0.00 0.00 0.00 2.43
1885 1903 3.568538 CGTCAAATTGAGGAGCTTTTGG 58.431 45.455 9.84 0.00 34.44 3.28
1894 1912 0.315251 GGAGCTTTTGGTGAAGGCAC 59.685 55.000 0.00 0.00 42.38 5.01
1910 1928 2.596046 ACGTGCGAAATGGGCCAA 60.596 55.556 11.89 0.00 0.00 4.52
1928 1947 1.200020 CAACCCATTCTTTGGCGAGTC 59.800 52.381 0.00 0.00 44.97 3.36
1948 1967 4.753107 AGTCGCTTTTCTTATTTTGGTCGA 59.247 37.500 0.00 0.00 0.00 4.20
2025 2049 8.925161 TTGAAAGTGAACAAATTTCGAAGATT 57.075 26.923 0.00 0.00 36.04 2.40
2033 2057 9.144747 TGAACAAATTTCGAAGATTTGAACAAA 57.855 25.926 30.57 18.30 43.71 2.83
2205 2268 6.978024 TGTGAACACATATTTAAAACGTGC 57.022 33.333 12.40 2.30 36.21 5.34
2221 2284 2.033299 ACGTGCACAATTCCTGAAAGTG 59.967 45.455 18.64 9.95 38.87 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.516110 AACATGCCCTAGATGGAGCT 58.484 50.000 0.00 0.00 38.35 4.09
41 42 2.092212 ACCAAACATGCCCTAGATGGAG 60.092 50.000 0.00 0.00 38.35 3.86
42 43 1.922447 ACCAAACATGCCCTAGATGGA 59.078 47.619 0.00 0.00 38.35 3.41
43 44 2.428171 CAACCAAACATGCCCTAGATGG 59.572 50.000 0.00 0.00 0.00 3.51
44 45 2.159198 GCAACCAAACATGCCCTAGATG 60.159 50.000 0.00 0.00 36.56 2.90
45 46 2.102578 GCAACCAAACATGCCCTAGAT 58.897 47.619 0.00 0.00 36.56 1.98
46 47 1.544724 GCAACCAAACATGCCCTAGA 58.455 50.000 0.00 0.00 36.56 2.43
52 53 0.320946 ATGCAGGCAACCAAACATGC 60.321 50.000 0.00 0.00 41.82 4.06
53 54 1.001068 TCATGCAGGCAACCAAACATG 59.999 47.619 0.00 0.00 34.16 3.21
54 55 1.274167 CTCATGCAGGCAACCAAACAT 59.726 47.619 0.00 0.00 37.17 2.71
55 56 0.675083 CTCATGCAGGCAACCAAACA 59.325 50.000 0.00 0.00 37.17 2.83
56 57 0.037975 CCTCATGCAGGCAACCAAAC 60.038 55.000 0.00 0.00 34.56 2.93
57 58 2.353858 CCTCATGCAGGCAACCAAA 58.646 52.632 0.00 0.00 34.56 3.28
58 59 4.100479 CCTCATGCAGGCAACCAA 57.900 55.556 0.00 0.00 34.56 3.67
69 70 4.864334 GTCAGGGCGGGCCTCATG 62.864 72.222 21.75 11.12 36.10 3.07
80 81 4.436998 GTCCCGCACGAGTCAGGG 62.437 72.222 6.28 6.28 45.10 4.45
97 98 0.041663 AACCAATCGACACGTTTGCG 60.042 50.000 8.73 0.00 44.93 4.85
98 99 1.394697 CAACCAATCGACACGTTTGC 58.605 50.000 8.73 0.00 35.89 3.68
99 100 1.394697 GCAACCAATCGACACGTTTG 58.605 50.000 0.00 0.00 36.64 2.93
100 101 0.309612 GGCAACCAATCGACACGTTT 59.690 50.000 0.00 0.00 0.00 3.60
101 102 0.534203 AGGCAACCAATCGACACGTT 60.534 50.000 0.00 0.00 37.17 3.99
102 103 1.070786 AGGCAACCAATCGACACGT 59.929 52.632 0.00 0.00 37.17 4.49
103 104 1.227999 ACAGGCAACCAATCGACACG 61.228 55.000 0.00 0.00 37.17 4.49
104 105 0.951558 AACAGGCAACCAATCGACAC 59.048 50.000 0.00 0.00 37.17 3.67
105 106 1.686355 AAACAGGCAACCAATCGACA 58.314 45.000 0.00 0.00 37.17 4.35
106 107 2.793278 AAAACAGGCAACCAATCGAC 57.207 45.000 0.00 0.00 37.17 4.20
107 108 3.886505 AGTAAAAACAGGCAACCAATCGA 59.113 39.130 0.00 0.00 37.17 3.59
108 109 3.980775 CAGTAAAAACAGGCAACCAATCG 59.019 43.478 0.00 0.00 37.17 3.34
109 110 4.944048 ACAGTAAAAACAGGCAACCAATC 58.056 39.130 0.00 0.00 37.17 2.67
110 111 5.351948 AACAGTAAAAACAGGCAACCAAT 57.648 34.783 0.00 0.00 37.17 3.16
111 112 4.810191 AACAGTAAAAACAGGCAACCAA 57.190 36.364 0.00 0.00 37.17 3.67
112 113 4.810191 AAACAGTAAAAACAGGCAACCA 57.190 36.364 0.00 0.00 37.17 3.67
113 114 4.743151 GCTAAACAGTAAAAACAGGCAACC 59.257 41.667 0.00 0.00 37.17 3.77
114 115 4.743151 GGCTAAACAGTAAAAACAGGCAAC 59.257 41.667 0.00 0.00 0.00 4.17
115 116 4.202172 GGGCTAAACAGTAAAAACAGGCAA 60.202 41.667 0.00 0.00 0.00 4.52
116 117 3.319689 GGGCTAAACAGTAAAAACAGGCA 59.680 43.478 0.00 0.00 0.00 4.75
117 118 3.610821 CGGGCTAAACAGTAAAAACAGGC 60.611 47.826 0.00 0.00 0.00 4.85
118 119 3.610821 GCGGGCTAAACAGTAAAAACAGG 60.611 47.826 0.00 0.00 0.00 4.00
119 120 3.003897 TGCGGGCTAAACAGTAAAAACAG 59.996 43.478 0.00 0.00 0.00 3.16
120 121 2.950309 TGCGGGCTAAACAGTAAAAACA 59.050 40.909 0.00 0.00 0.00 2.83
121 122 3.629438 TGCGGGCTAAACAGTAAAAAC 57.371 42.857 0.00 0.00 0.00 2.43
122 123 3.057174 CCATGCGGGCTAAACAGTAAAAA 60.057 43.478 0.00 0.00 0.00 1.94
123 124 2.490115 CCATGCGGGCTAAACAGTAAAA 59.510 45.455 0.00 0.00 0.00 1.52
124 125 2.088423 CCATGCGGGCTAAACAGTAAA 58.912 47.619 0.00 0.00 0.00 2.01
125 126 1.745232 CCATGCGGGCTAAACAGTAA 58.255 50.000 0.00 0.00 0.00 2.24
126 127 3.469564 CCATGCGGGCTAAACAGTA 57.530 52.632 0.00 0.00 0.00 2.74
127 128 4.319133 CCATGCGGGCTAAACAGT 57.681 55.556 0.00 0.00 0.00 3.55
137 138 1.302383 TTAAGGTTCGTGCCATGCGG 61.302 55.000 0.00 0.00 0.00 5.69
138 139 0.519519 TTTAAGGTTCGTGCCATGCG 59.480 50.000 0.00 0.00 0.00 4.73
139 140 1.732405 GCTTTAAGGTTCGTGCCATGC 60.732 52.381 0.00 0.00 0.00 4.06
140 141 1.539388 TGCTTTAAGGTTCGTGCCATG 59.461 47.619 0.00 0.00 0.00 3.66
141 142 1.539827 GTGCTTTAAGGTTCGTGCCAT 59.460 47.619 0.00 0.00 0.00 4.40
142 143 0.948678 GTGCTTTAAGGTTCGTGCCA 59.051 50.000 0.00 0.00 0.00 4.92
143 144 1.197036 GAGTGCTTTAAGGTTCGTGCC 59.803 52.381 0.00 0.00 0.00 5.01
144 145 1.197036 GGAGTGCTTTAAGGTTCGTGC 59.803 52.381 0.00 0.00 0.00 5.34
145 146 2.767505 AGGAGTGCTTTAAGGTTCGTG 58.232 47.619 0.00 0.00 0.00 4.35
146 147 3.056035 CCTAGGAGTGCTTTAAGGTTCGT 60.056 47.826 1.05 0.00 0.00 3.85
147 148 3.522553 CCTAGGAGTGCTTTAAGGTTCG 58.477 50.000 1.05 0.00 0.00 3.95
148 149 3.271729 GCCTAGGAGTGCTTTAAGGTTC 58.728 50.000 14.75 0.00 0.00 3.62
149 150 2.026169 GGCCTAGGAGTGCTTTAAGGTT 60.026 50.000 14.75 0.00 0.00 3.50
150 151 1.560146 GGCCTAGGAGTGCTTTAAGGT 59.440 52.381 14.75 0.00 0.00 3.50
151 152 1.840635 AGGCCTAGGAGTGCTTTAAGG 59.159 52.381 14.75 0.00 0.00 2.69
152 153 2.420687 CCAGGCCTAGGAGTGCTTTAAG 60.421 54.545 14.75 0.00 0.00 1.85
153 154 1.559682 CCAGGCCTAGGAGTGCTTTAA 59.440 52.381 14.75 0.00 0.00 1.52
154 155 1.204146 CCAGGCCTAGGAGTGCTTTA 58.796 55.000 14.75 0.00 0.00 1.85
155 156 1.994463 CCAGGCCTAGGAGTGCTTT 59.006 57.895 14.75 0.00 0.00 3.51
156 157 2.674220 GCCAGGCCTAGGAGTGCTT 61.674 63.158 21.37 0.00 0.00 3.91
157 158 3.086600 GCCAGGCCTAGGAGTGCT 61.087 66.667 21.37 0.00 0.00 4.40
158 159 3.086600 AGCCAGGCCTAGGAGTGC 61.087 66.667 21.37 8.92 0.00 4.40
159 160 2.439104 GGAGCCAGGCCTAGGAGTG 61.439 68.421 21.37 8.46 0.00 3.51
160 161 2.041405 GGAGCCAGGCCTAGGAGT 60.041 66.667 21.37 9.90 0.00 3.85
161 162 1.383803 AAGGAGCCAGGCCTAGGAG 60.384 63.158 21.37 3.22 33.76 3.69
162 163 1.690633 CAAGGAGCCAGGCCTAGGA 60.691 63.158 21.37 0.00 33.76 2.94
163 164 2.750657 CCAAGGAGCCAGGCCTAGG 61.751 68.421 3.98 11.19 33.76 3.02
164 165 2.750657 CCCAAGGAGCCAGGCCTAG 61.751 68.421 3.98 0.00 33.76 3.02
165 166 2.692368 CCCAAGGAGCCAGGCCTA 60.692 66.667 3.98 0.00 33.76 3.93
166 167 4.682714 TCCCAAGGAGCCAGGCCT 62.683 66.667 8.22 0.00 37.35 5.19
167 168 3.661648 TTCCCAAGGAGCCAGGCC 61.662 66.667 8.22 0.00 31.21 5.19
168 169 2.361737 GTTCCCAAGGAGCCAGGC 60.362 66.667 1.84 1.84 31.21 4.85
169 170 2.045926 CGTTCCCAAGGAGCCAGG 60.046 66.667 0.00 0.00 31.21 4.45
170 171 2.747855 GCGTTCCCAAGGAGCCAG 60.748 66.667 0.00 0.00 31.21 4.85
171 172 3.249189 AGCGTTCCCAAGGAGCCA 61.249 61.111 0.00 0.00 31.21 4.75
172 173 2.436824 GAGCGTTCCCAAGGAGCC 60.437 66.667 0.00 0.00 31.21 4.70
173 174 2.781595 TTCGAGCGTTCCCAAGGAGC 62.782 60.000 0.00 0.00 31.21 4.70
174 175 0.108138 ATTCGAGCGTTCCCAAGGAG 60.108 55.000 0.00 0.00 31.21 3.69
175 176 0.108329 GATTCGAGCGTTCCCAAGGA 60.108 55.000 0.00 0.00 0.00 3.36
176 177 1.421410 CGATTCGAGCGTTCCCAAGG 61.421 60.000 0.00 0.00 0.00 3.61
177 178 1.421410 CCGATTCGAGCGTTCCCAAG 61.421 60.000 7.83 0.00 0.00 3.61
178 179 1.447140 CCGATTCGAGCGTTCCCAA 60.447 57.895 7.83 0.00 0.00 4.12
179 180 2.183300 CCGATTCGAGCGTTCCCA 59.817 61.111 7.83 0.00 0.00 4.37
180 181 2.585247 CCCGATTCGAGCGTTCCC 60.585 66.667 7.83 0.00 0.00 3.97
181 182 1.877165 GACCCGATTCGAGCGTTCC 60.877 63.158 7.83 0.00 0.00 3.62
182 183 0.458025 AAGACCCGATTCGAGCGTTC 60.458 55.000 7.83 0.00 0.00 3.95
183 184 0.458025 GAAGACCCGATTCGAGCGTT 60.458 55.000 7.83 0.00 0.00 4.84
184 185 1.139095 GAAGACCCGATTCGAGCGT 59.861 57.895 7.83 0.29 0.00 5.07
185 186 0.592754 GAGAAGACCCGATTCGAGCG 60.593 60.000 7.83 3.14 0.00 5.03
186 187 0.249114 GGAGAAGACCCGATTCGAGC 60.249 60.000 7.83 0.00 0.00 5.03
187 188 0.386113 GGGAGAAGACCCGATTCGAG 59.614 60.000 7.83 0.00 40.49 4.04
188 189 2.501492 GGGAGAAGACCCGATTCGA 58.499 57.895 7.83 0.00 40.49 3.71
196 197 1.066787 GCAGTGTACTGGGAGAAGACC 60.067 57.143 13.41 0.00 43.94 3.85
219 220 0.248949 GGCTCCTAATGACCGTCGTC 60.249 60.000 0.00 0.00 39.66 4.20
293 294 0.749091 CGCTGGGCCATGAATCAAGA 60.749 55.000 6.72 0.00 0.00 3.02
295 296 0.323269 TTCGCTGGGCCATGAATCAA 60.323 50.000 6.72 0.00 0.00 2.57
460 461 3.007635 GGCTAGTAACCGCATCAAGTTT 58.992 45.455 0.00 0.00 0.00 2.66
499 500 2.386935 GGGTATTGGCTGGAGGGCT 61.387 63.158 0.00 0.00 41.48 5.19
556 557 0.482887 TCCTCCTCTCCATCGCCATA 59.517 55.000 0.00 0.00 0.00 2.74
619 624 4.277672 TCGCGCCTATATTTACTCACTCTT 59.722 41.667 0.00 0.00 0.00 2.85
671 679 9.555727 TTAGTGAAGAGCATGTAGTTAAAACTT 57.444 29.630 0.00 0.00 40.37 2.66
672 680 9.209175 CTTAGTGAAGAGCATGTAGTTAAAACT 57.791 33.333 0.39 0.39 37.69 2.66
694 702 4.333649 CACAACACATAGTCCATGGCTTAG 59.666 45.833 6.96 6.46 39.13 2.18
704 712 2.996621 GAGTCAGGCACAACACATAGTC 59.003 50.000 0.00 0.00 0.00 2.59
708 716 0.473755 TGGAGTCAGGCACAACACAT 59.526 50.000 0.00 0.00 0.00 3.21
741 749 4.041321 CCCATCTCATTGCTCTCCTTGATA 59.959 45.833 0.00 0.00 0.00 2.15
834 842 2.753043 ACCTCGGCGGTGTACGAT 60.753 61.111 7.21 0.00 46.80 3.73
851 859 0.387622 CGTTGGCGTCTTCGGTTCTA 60.388 55.000 0.00 0.00 37.56 2.10
921 929 2.358267 CTCCTCATGGTAGTGGTCGTAC 59.642 54.545 0.00 0.00 34.23 3.67
1139 1149 3.850122 TCTTGATCTCATGAACGACGT 57.150 42.857 0.00 0.00 0.00 4.34
1150 1160 3.006323 ACCATGTAGCCGATCTTGATCTC 59.994 47.826 8.70 1.59 0.00 2.75
1182 1192 0.543174 GGGTGTCAGGAGTGAGGAGT 60.543 60.000 0.00 0.00 31.53 3.85
1222 1232 0.038166 ACCACCTCAATGCCATCGTT 59.962 50.000 0.00 0.00 0.00 3.85
1318 1328 6.780457 ATGCATAAACCATAAAGCAGACTT 57.220 33.333 0.00 0.00 37.90 3.01
1402 1412 6.018913 CAGAGCATAAACAGAGCATCAACTAG 60.019 42.308 0.00 0.00 37.82 2.57
1504 1514 2.171341 TGTATGCAACGCTTGGTGTA 57.829 45.000 0.00 0.00 0.00 2.90
1530 1540 2.107378 TGGACAAACTCAAGGCATGGTA 59.893 45.455 0.00 0.00 0.00 3.25
1578 1589 0.538057 CATGGGCAGAACCACACTGT 60.538 55.000 0.00 0.00 44.72 3.55
1807 1825 8.158132 TGAACCTATATGACTGTACCAACAAAA 58.842 33.333 0.00 0.00 34.49 2.44
1810 1828 6.860790 TGAACCTATATGACTGTACCAACA 57.139 37.500 0.00 0.00 0.00 3.33
1885 1903 0.725784 CATTTCGCACGTGCCTTCAC 60.726 55.000 33.23 6.74 39.78 3.18
1894 1912 2.126502 GTTGGCCCATTTCGCACG 60.127 61.111 0.00 0.00 0.00 5.34
1928 1947 6.927933 AAATCGACCAAAATAAGAAAAGCG 57.072 33.333 0.00 0.00 0.00 4.68
1999 2023 7.969387 TCTTCGAAATTTGTTCACTTTCAAG 57.031 32.000 0.00 0.00 0.00 3.02
2193 2256 5.837437 TCAGGAATTGTGCACGTTTTAAAT 58.163 33.333 13.13 1.99 0.00 1.40
2197 2260 3.791973 TTCAGGAATTGTGCACGTTTT 57.208 38.095 13.13 5.37 0.00 2.43
2205 2268 5.036737 GTGTTCACACTTTCAGGAATTGTG 58.963 41.667 5.69 5.69 43.25 3.33


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

AutoCloner maintained by Alex Coulton.