Multiple sequence alignment - TraesCS3B01G322200

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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 TraesCS3B01G322200 chr3B 100.000 2828 0 0 1 2828 521687091 521689918 0.000000e+00 5223.0
1 TraesCS3B01G322200 chr3B 95.445 1361 42 4 711 2064 521475953 521477300 0.000000e+00 2152.0
2 TraesCS3B01G322200 chr3B 96.259 1203 27 6 711 1911 521609393 521610579 0.000000e+00 1956.0
3 TraesCS3B01G322200 chr3B 93.957 1175 57 11 710 1875 521216850 521218019 0.000000e+00 1764.0
4 TraesCS3B01G322200 chr3B 94.411 984 45 6 711 1688 521405027 521406006 0.000000e+00 1504.0
5 TraesCS3B01G322200 chr3B 94.864 623 28 4 2207 2828 755707434 755706815 0.000000e+00 970.0
6 TraesCS3B01G322200 chr3B 95.900 439 17 1 273 711 592646949 592646512 0.000000e+00 710.0
7 TraesCS3B01G322200 chr3B 89.770 391 25 7 1678 2064 521413619 521413998 1.180000e-133 486.0
8 TraesCS3B01G322200 chr3B 95.902 122 3 2 2065 2185 593930590 593930710 2.220000e-46 196.0
9 TraesCS3B01G322200 chr3B 92.126 127 7 3 2054 2178 520613546 520613421 2.900000e-40 176.0
10 TraesCS3B01G322200 chr3B 85.714 63 8 1 133 195 582410038 582409977 6.540000e-07 65.8
11 TraesCS3B01G322200 chr3D 95.004 1361 56 8 711 2064 396204877 396206232 0.000000e+00 2126.0
12 TraesCS3B01G322200 chr3D 92.438 1362 60 8 709 2056 395837076 395838408 0.000000e+00 1905.0
13 TraesCS3B01G322200 chr3D 91.114 1328 64 17 711 2024 395832703 395833990 0.000000e+00 1749.0
14 TraesCS3B01G322200 chr3D 92.879 660 38 9 2172 2828 435694193 435693540 0.000000e+00 950.0
15 TraesCS3B01G322200 chr3D 89.394 66 7 0 646 711 569467675 569467610 1.810000e-12 84.2
16 TraesCS3B01G322200 chr3D 84.810 79 11 1 643 721 479744804 479744881 8.400000e-11 78.7
17 TraesCS3B01G322200 chr3A 93.180 1305 69 16 779 2064 515860969 515862272 0.000000e+00 1899.0
18 TraesCS3B01G322200 chr3A 91.234 559 36 12 2274 2828 569621658 569621109 0.000000e+00 749.0
19 TraesCS3B01G322200 chr4B 99.476 763 4 0 2066 2828 567194853 567194091 0.000000e+00 1387.0
20 TraesCS3B01G322200 chr4B 99.517 207 1 0 2066 2272 567195280 567195074 7.400000e-101 377.0
21 TraesCS3B01G322200 chr6B 95.170 766 34 3 2065 2828 46266935 46267699 0.000000e+00 1206.0
22 TraesCS3B01G322200 chr6B 92.424 528 34 6 2303 2828 420773850 420773327 0.000000e+00 749.0
23 TraesCS3B01G322200 chr6B 90.703 441 38 3 273 711 2730255 2730694 4.060000e-163 584.0
24 TraesCS3B01G322200 chr6B 88.333 60 6 1 137 195 96678965 96679024 1.410000e-08 71.3
25 TraesCS3B01G322200 chr2A 94.634 764 39 2 2065 2828 761906050 761905289 0.000000e+00 1182.0
26 TraesCS3B01G322200 chr6D 86.321 636 73 11 2176 2808 459268963 459269587 0.000000e+00 680.0
27 TraesCS3B01G322200 chr6D 95.041 121 5 1 2062 2181 140222444 140222564 3.720000e-44 189.0
28 TraesCS3B01G322200 chr5B 85.243 637 80 14 2176 2809 98499953 98499328 0.000000e+00 643.0
29 TraesCS3B01G322200 chr5B 90.000 40 4 0 156 195 696579068 696579029 5.000000e-03 52.8
30 TraesCS3B01G322200 chr2B 95.679 324 14 0 273 596 539367401 539367078 3.230000e-144 521.0
31 TraesCS3B01G322200 chr2B 90.488 389 26 4 273 658 22694333 22693953 1.170000e-138 503.0
32 TraesCS3B01G322200 chr2B 97.970 197 3 1 519 715 539366820 539366625 9.700000e-90 340.0
33 TraesCS3B01G322200 chr2B 92.982 114 8 0 407 520 539367091 539366978 1.740000e-37 167.0
34 TraesCS3B01G322200 chr7B 96.203 158 6 0 99 256 427707145 427706988 2.790000e-65 259.0
35 TraesCS3B01G322200 chr7B 93.814 97 6 0 1 97 427707405 427707309 2.270000e-31 147.0
36 TraesCS3B01G322200 chr7B 90.476 42 4 0 142 183 565561222 565561263 3.940000e-04 56.5
37 TraesCS3B01G322200 chr7A 95.935 123 3 2 2061 2181 125920625 125920503 6.180000e-47 198.0
38 TraesCS3B01G322200 chr7A 88.976 127 11 2 588 711 37240744 37240618 1.360000e-33 154.0
39 TraesCS3B01G322200 chr5D 95.000 120 5 1 2065 2184 385963165 385963047 1.340000e-43 187.0
40 TraesCS3B01G322200 chr5D 90.840 131 5 5 559 689 522603044 522602921 4.850000e-38 169.0
41 TraesCS3B01G322200 chr5D 89.855 69 7 0 643 711 335792475 335792543 3.880000e-14 89.8
42 TraesCS3B01G322200 chr4D 89.552 67 5 2 646 711 145592973 145592908 1.810000e-12 84.2


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 TraesCS3B01G322200 chr3B 521687091 521689918 2827 False 5223.000000 5223 100.000000 1 2828 1 chr3B.!!$F6 2827
1 TraesCS3B01G322200 chr3B 521475953 521477300 1347 False 2152.000000 2152 95.445000 711 2064 1 chr3B.!!$F4 1353
2 TraesCS3B01G322200 chr3B 521609393 521610579 1186 False 1956.000000 1956 96.259000 711 1911 1 chr3B.!!$F5 1200
3 TraesCS3B01G322200 chr3B 521216850 521218019 1169 False 1764.000000 1764 93.957000 710 1875 1 chr3B.!!$F1 1165
4 TraesCS3B01G322200 chr3B 521405027 521406006 979 False 1504.000000 1504 94.411000 711 1688 1 chr3B.!!$F2 977
5 TraesCS3B01G322200 chr3B 755706815 755707434 619 True 970.000000 970 94.864000 2207 2828 1 chr3B.!!$R4 621
6 TraesCS3B01G322200 chr3D 396204877 396206232 1355 False 2126.000000 2126 95.004000 711 2064 1 chr3D.!!$F1 1353
7 TraesCS3B01G322200 chr3D 395832703 395838408 5705 False 1827.000000 1905 91.776000 709 2056 2 chr3D.!!$F3 1347
8 TraesCS3B01G322200 chr3D 435693540 435694193 653 True 950.000000 950 92.879000 2172 2828 1 chr3D.!!$R1 656
9 TraesCS3B01G322200 chr3A 515860969 515862272 1303 False 1899.000000 1899 93.180000 779 2064 1 chr3A.!!$F1 1285
10 TraesCS3B01G322200 chr3A 569621109 569621658 549 True 749.000000 749 91.234000 2274 2828 1 chr3A.!!$R1 554
11 TraesCS3B01G322200 chr4B 567194091 567195280 1189 True 882.000000 1387 99.496500 2066 2828 2 chr4B.!!$R1 762
12 TraesCS3B01G322200 chr6B 46266935 46267699 764 False 1206.000000 1206 95.170000 2065 2828 1 chr6B.!!$F2 763
13 TraesCS3B01G322200 chr6B 420773327 420773850 523 True 749.000000 749 92.424000 2303 2828 1 chr6B.!!$R1 525
14 TraesCS3B01G322200 chr2A 761905289 761906050 761 True 1182.000000 1182 94.634000 2065 2828 1 chr2A.!!$R1 763
15 TraesCS3B01G322200 chr6D 459268963 459269587 624 False 680.000000 680 86.321000 2176 2808 1 chr6D.!!$F2 632
16 TraesCS3B01G322200 chr5B 98499328 98499953 625 True 643.000000 643 85.243000 2176 2809 1 chr5B.!!$R1 633
17 TraesCS3B01G322200 chr2B 539366625 539367401 776 True 342.666667 521 95.543667 273 715 3 chr2B.!!$R2 442

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
24 25 0.031857 TGTTGGCGGCATTGTTTCTG 59.968 50.0 14.32 0.00 0.00 3.02 F
216 217 0.034896 TTGAAGGGAGACGCTCAACC 59.965 55.0 8.71 2.72 31.08 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 6549 0.108615 ATCAGTTCTTGACGCCGAGG 60.109 55.0 0.00 0.00 38.99 4.63 R
1929 6679 1.082117 AATTAGCTTCCACCGACGCG 61.082 55.0 3.53 3.53 38.28 6.01 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
20 21 3.608316 AATTATGTTGGCGGCATTGTT 57.392 38.095 14.32 0.65 0.00 2.83
21 22 3.608316 ATTATGTTGGCGGCATTGTTT 57.392 38.095 14.32 0.00 0.00 2.83
22 23 2.645730 TATGTTGGCGGCATTGTTTC 57.354 45.000 14.32 0.34 0.00 2.78
23 24 0.968405 ATGTTGGCGGCATTGTTTCT 59.032 45.000 14.32 0.00 0.00 2.52
24 25 0.031857 TGTTGGCGGCATTGTTTCTG 59.968 50.000 14.32 0.00 0.00 3.02
25 26 1.006337 TTGGCGGCATTGTTTCTGC 60.006 52.632 14.32 0.00 38.93 4.26
26 27 1.742324 TTGGCGGCATTGTTTCTGCA 61.742 50.000 14.32 0.00 41.47 4.41
27 28 1.006337 GGCGGCATTGTTTCTGCAA 60.006 52.632 3.07 0.00 41.47 4.08
28 29 1.284297 GGCGGCATTGTTTCTGCAAC 61.284 55.000 3.07 0.00 41.47 4.17
29 30 0.597118 GCGGCATTGTTTCTGCAACA 60.597 50.000 0.00 0.00 44.11 3.33
30 31 1.130955 CGGCATTGTTTCTGCAACAC 58.869 50.000 0.00 0.00 45.54 3.32
31 32 1.501169 GGCATTGTTTCTGCAACACC 58.499 50.000 0.00 0.00 45.54 4.16
32 33 1.130955 GCATTGTTTCTGCAACACCG 58.869 50.000 0.00 0.00 45.54 4.94
33 34 1.535860 GCATTGTTTCTGCAACACCGT 60.536 47.619 0.00 0.00 45.54 4.83
34 35 2.384382 CATTGTTTCTGCAACACCGTC 58.616 47.619 0.00 0.00 45.54 4.79
35 36 1.745232 TTGTTTCTGCAACACCGTCT 58.255 45.000 0.00 0.00 45.54 4.18
36 37 2.605837 TGTTTCTGCAACACCGTCTA 57.394 45.000 0.00 0.00 40.71 2.59
37 38 2.206750 TGTTTCTGCAACACCGTCTAC 58.793 47.619 0.00 0.00 40.71 2.59
38 39 1.191647 GTTTCTGCAACACCGTCTACG 59.808 52.381 0.00 0.00 35.18 3.51
39 40 0.386476 TTCTGCAACACCGTCTACGT 59.614 50.000 1.41 0.00 37.74 3.57
40 41 0.386476 TCTGCAACACCGTCTACGTT 59.614 50.000 0.00 0.00 37.74 3.99
41 42 0.506932 CTGCAACACCGTCTACGTTG 59.493 55.000 0.00 0.00 42.29 4.10
43 44 2.595707 CAACACCGTCTACGTTGCA 58.404 52.632 0.00 0.00 35.06 4.08
44 45 0.931702 CAACACCGTCTACGTTGCAA 59.068 50.000 0.00 0.00 35.06 4.08
45 46 1.328069 CAACACCGTCTACGTTGCAAA 59.672 47.619 0.00 0.00 35.06 3.68
46 47 1.654317 ACACCGTCTACGTTGCAAAA 58.346 45.000 0.00 0.00 35.06 2.44
47 48 2.008329 ACACCGTCTACGTTGCAAAAA 58.992 42.857 0.00 0.00 35.06 1.94
69 70 6.741992 AAAAATTATGTGACATGCTCTCGA 57.258 33.333 8.61 0.00 0.00 4.04
70 71 6.932356 AAAATTATGTGACATGCTCTCGAT 57.068 33.333 8.61 0.00 0.00 3.59
71 72 6.932356 AAATTATGTGACATGCTCTCGATT 57.068 33.333 8.61 0.00 0.00 3.34
72 73 5.919272 ATTATGTGACATGCTCTCGATTG 57.081 39.130 8.61 0.00 0.00 2.67
73 74 1.362768 TGTGACATGCTCTCGATTGC 58.637 50.000 0.00 3.24 0.00 3.56
74 75 1.338011 TGTGACATGCTCTCGATTGCA 60.338 47.619 13.51 13.51 43.67 4.08
75 76 1.733912 GTGACATGCTCTCGATTGCAA 59.266 47.619 14.80 0.00 42.74 4.08
76 77 2.160219 GTGACATGCTCTCGATTGCAAA 59.840 45.455 14.80 0.00 42.74 3.68
77 78 2.813172 TGACATGCTCTCGATTGCAAAA 59.187 40.909 14.80 0.00 42.74 2.44
78 79 3.252944 TGACATGCTCTCGATTGCAAAAA 59.747 39.130 14.80 0.00 42.74 1.94
117 118 9.878667 ATGATCAATATTGAAAATGTTTCTGCA 57.121 25.926 21.50 6.58 41.13 4.41
118 119 9.708092 TGATCAATATTGAAAATGTTTCTGCAA 57.292 25.926 21.50 0.00 41.13 4.08
119 120 9.962759 GATCAATATTGAAAATGTTTCTGCAAC 57.037 29.630 21.50 0.00 41.13 4.17
120 121 8.883954 TCAATATTGAAAATGTTTCTGCAACA 57.116 26.923 15.82 0.00 41.03 3.33
121 122 9.491675 TCAATATTGAAAATGTTTCTGCAACAT 57.508 25.926 15.82 0.00 44.77 2.71
132 133 6.567959 TGTTTCTGCAACATAATTTGTGTCA 58.432 32.000 0.00 0.00 40.71 3.58
133 134 6.475076 TGTTTCTGCAACATAATTTGTGTCAC 59.525 34.615 0.00 0.00 40.71 3.67
134 135 5.764487 TCTGCAACATAATTTGTGTCACA 57.236 34.783 0.18 0.18 38.99 3.58
135 136 6.141560 TCTGCAACATAATTTGTGTCACAA 57.858 33.333 14.48 14.48 38.99 3.33
160 161 8.682936 AAAAAGTTCTACAACATGATCTCTGT 57.317 30.769 0.00 0.00 34.60 3.41
161 162 8.682936 AAAAGTTCTACAACATGATCTCTGTT 57.317 30.769 0.00 8.01 37.31 3.16
169 170 5.466819 CAACATGATCTCTGTTGCAAATGT 58.533 37.500 20.98 1.60 44.78 2.71
170 171 5.717078 ACATGATCTCTGTTGCAAATGTT 57.283 34.783 0.00 0.00 0.00 2.71
171 172 6.092955 ACATGATCTCTGTTGCAAATGTTT 57.907 33.333 0.00 0.00 0.00 2.83
172 173 6.154445 ACATGATCTCTGTTGCAAATGTTTC 58.846 36.000 0.00 0.00 0.00 2.78
173 174 6.015688 ACATGATCTCTGTTGCAAATGTTTCT 60.016 34.615 0.00 0.00 0.00 2.52
174 175 5.765176 TGATCTCTGTTGCAAATGTTTCTG 58.235 37.500 0.00 0.00 0.00 3.02
175 176 3.968649 TCTCTGTTGCAAATGTTTCTGC 58.031 40.909 0.00 0.00 39.09 4.26
176 177 3.380954 TCTCTGTTGCAAATGTTTCTGCA 59.619 39.130 0.00 0.00 46.50 4.41
187 188 3.213206 TGTTTCTGCAACATGACCTCT 57.787 42.857 0.00 0.00 40.71 3.69
188 189 2.880268 TGTTTCTGCAACATGACCTCTG 59.120 45.455 0.00 0.00 40.71 3.35
189 190 2.880890 GTTTCTGCAACATGACCTCTGT 59.119 45.455 0.00 0.00 35.18 3.41
190 191 2.936919 TCTGCAACATGACCTCTGTT 57.063 45.000 0.00 0.00 37.31 3.16
195 196 3.928727 CAACATGACCTCTGTTGCAAT 57.071 42.857 0.59 0.00 44.78 3.56
197 198 5.571784 CAACATGACCTCTGTTGCAATAT 57.428 39.130 0.59 0.00 44.78 1.28
198 199 5.957798 CAACATGACCTCTGTTGCAATATT 58.042 37.500 0.59 0.00 44.78 1.28
199 200 5.571784 ACATGACCTCTGTTGCAATATTG 57.428 39.130 11.27 11.27 0.00 1.90
200 201 5.255687 ACATGACCTCTGTTGCAATATTGA 58.744 37.500 19.73 1.75 0.00 2.57
201 202 5.711506 ACATGACCTCTGTTGCAATATTGAA 59.288 36.000 19.73 5.71 0.00 2.69
202 203 5.885230 TGACCTCTGTTGCAATATTGAAG 57.115 39.130 19.73 9.94 0.00 3.02
203 204 4.701651 TGACCTCTGTTGCAATATTGAAGG 59.298 41.667 19.73 14.99 0.00 3.46
204 205 4.019174 ACCTCTGTTGCAATATTGAAGGG 58.981 43.478 19.73 9.62 0.00 3.95
205 206 4.263905 ACCTCTGTTGCAATATTGAAGGGA 60.264 41.667 19.73 7.16 0.00 4.20
206 207 4.337555 CCTCTGTTGCAATATTGAAGGGAG 59.662 45.833 19.73 14.92 0.00 4.30
207 208 5.178096 TCTGTTGCAATATTGAAGGGAGA 57.822 39.130 19.73 8.09 0.00 3.71
208 209 4.943705 TCTGTTGCAATATTGAAGGGAGAC 59.056 41.667 19.73 4.04 0.00 3.36
209 210 3.689161 TGTTGCAATATTGAAGGGAGACG 59.311 43.478 19.73 0.00 0.00 4.18
210 211 2.288666 TGCAATATTGAAGGGAGACGC 58.711 47.619 19.73 0.00 0.00 5.19
211 212 2.092968 TGCAATATTGAAGGGAGACGCT 60.093 45.455 19.73 0.00 0.00 5.07
212 213 2.545946 GCAATATTGAAGGGAGACGCTC 59.454 50.000 19.73 0.00 0.00 5.03
213 214 3.797039 CAATATTGAAGGGAGACGCTCA 58.203 45.455 10.04 0.00 31.08 4.26
214 215 4.191544 CAATATTGAAGGGAGACGCTCAA 58.808 43.478 10.04 0.00 31.08 3.02
215 216 2.100605 ATTGAAGGGAGACGCTCAAC 57.899 50.000 8.71 2.22 31.08 3.18
216 217 0.034896 TTGAAGGGAGACGCTCAACC 59.965 55.000 8.71 2.72 31.08 3.77
217 218 1.446272 GAAGGGAGACGCTCAACCG 60.446 63.158 8.71 0.00 31.08 4.44
218 219 3.591254 AAGGGAGACGCTCAACCGC 62.591 63.158 8.71 0.00 31.08 5.68
219 220 4.070552 GGGAGACGCTCAACCGCT 62.071 66.667 8.71 0.00 31.08 5.52
220 221 2.507324 GGAGACGCTCAACCGCTC 60.507 66.667 8.71 0.00 33.63 5.03
221 222 2.876645 GAGACGCTCAACCGCTCG 60.877 66.667 2.53 0.00 0.00 5.03
239 240 4.689484 CTGGCGCCAGATCTATGG 57.311 61.111 46.72 21.90 46.30 2.74
245 246 4.567435 CCAGATCTATGGCTCGCG 57.433 61.111 0.00 0.00 32.48 5.87
246 247 1.959848 CCAGATCTATGGCTCGCGA 59.040 57.895 9.26 9.26 32.48 5.87
247 248 0.387878 CCAGATCTATGGCTCGCGAC 60.388 60.000 3.71 1.87 32.48 5.19
248 249 0.387878 CAGATCTATGGCTCGCGACC 60.388 60.000 3.71 12.86 0.00 4.79
249 250 1.080434 GATCTATGGCTCGCGACCC 60.080 63.158 13.71 13.71 0.00 4.46
250 251 2.804368 GATCTATGGCTCGCGACCCG 62.804 65.000 15.44 2.57 38.61 5.28
251 252 4.647615 CTATGGCTCGCGACCCGG 62.648 72.222 15.44 2.18 37.59 5.73
257 258 4.933064 CTCGCGACCCGGCTGATC 62.933 72.222 3.71 0.00 37.59 2.92
261 262 4.129737 CGACCCGGCTGATCACGT 62.130 66.667 0.00 0.00 0.00 4.49
262 263 2.767445 CGACCCGGCTGATCACGTA 61.767 63.158 0.00 0.00 0.00 3.57
263 264 1.065928 GACCCGGCTGATCACGTAG 59.934 63.158 0.00 0.00 0.00 3.51
264 265 1.379443 ACCCGGCTGATCACGTAGA 60.379 57.895 0.00 0.00 0.00 2.59
265 266 1.360551 CCCGGCTGATCACGTAGAG 59.639 63.158 0.00 0.00 0.00 2.43
266 267 1.299468 CCGGCTGATCACGTAGAGC 60.299 63.158 0.00 0.00 0.00 4.09
267 268 1.433471 CGGCTGATCACGTAGAGCA 59.567 57.895 4.94 7.44 41.05 4.26
271 272 1.816537 TGATCACGTAGAGCAGCCC 59.183 57.895 0.00 0.00 37.82 5.19
355 356 4.459390 TCAATTTTCCATGCCATGTCTG 57.541 40.909 3.63 0.00 0.00 3.51
503 680 7.484975 ACCAAAACAATTGACGTAATTTCTGA 58.515 30.769 13.59 0.00 36.87 3.27
507 684 7.623268 AACAATTGACGTAATTTCTGAAAGC 57.377 32.000 13.59 1.35 36.87 3.51
517 694 9.216117 ACGTAATTTCTGAAAGCAGTTAGTTAT 57.784 29.630 8.95 0.00 42.84 1.89
551 887 2.277008 AGGAATGGTGGAGAGGTCAT 57.723 50.000 0.00 0.00 0.00 3.06
680 1016 1.168714 GTGGTCTGATGGGAAGCAAC 58.831 55.000 0.00 0.00 0.00 4.17
717 1053 1.427753 CCCTAGTGGTTCCCCAAAACT 59.572 52.381 0.00 0.00 44.15 2.66
725 1061 2.631062 GGTTCCCCAAAACTAAACCTGG 59.369 50.000 0.00 0.00 37.10 4.45
736 1072 2.152297 TAAACCTGGTTCGCCGCGTA 62.152 55.000 13.36 0.00 41.18 4.42
1774 6514 1.210413 GACTGCAAGCTCGAGTCGA 59.790 57.895 15.64 15.64 37.60 4.20
1843 6583 2.388890 CTGATCCATCCGTCCCTGCC 62.389 65.000 0.00 0.00 0.00 4.85
1882 6627 7.621006 TTGGGGATCGATACCTTATTTTCTA 57.379 36.000 25.97 1.87 0.00 2.10
1929 6679 2.738013 AGTGTACGAGTTTGGGTAGC 57.262 50.000 0.00 0.00 0.00 3.58
1958 6708 4.517075 GGTGGAAGCTAATTAAGGATGAGC 59.483 45.833 0.00 0.00 0.00 4.26
1966 6716 5.698545 GCTAATTAAGGATGAGCAGTTCGAT 59.301 40.000 0.00 0.00 0.00 3.59
2045 6814 0.957395 CTGGCAATGGTGAAGCTCGT 60.957 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.195396 AGAAACAATGCCGCCAACATAAT 59.805 39.130 0.00 0.00 0.00 1.28
5 6 0.031857 CAGAAACAATGCCGCCAACA 59.968 50.000 0.00 0.00 0.00 3.33
6 7 1.284297 GCAGAAACAATGCCGCCAAC 61.284 55.000 0.00 0.00 37.73 3.77
7 8 1.006337 GCAGAAACAATGCCGCCAA 60.006 52.632 0.00 0.00 37.73 4.52
9 10 1.006337 TTGCAGAAACAATGCCGCC 60.006 52.632 0.00 0.00 43.18 6.13
10 11 0.597118 TGTTGCAGAAACAATGCCGC 60.597 50.000 0.00 0.00 45.85 6.53
11 12 3.566273 TGTTGCAGAAACAATGCCG 57.434 47.368 0.00 0.00 45.85 5.69
17 18 2.206750 GTAGACGGTGTTGCAGAAACA 58.793 47.619 0.00 0.00 46.66 2.83
18 19 1.191647 CGTAGACGGTGTTGCAGAAAC 59.808 52.381 0.00 0.00 36.07 2.78
19 20 1.202440 ACGTAGACGGTGTTGCAGAAA 60.202 47.619 7.04 0.00 44.95 2.52
20 21 0.386476 ACGTAGACGGTGTTGCAGAA 59.614 50.000 7.04 0.00 44.95 3.02
21 22 0.386476 AACGTAGACGGTGTTGCAGA 59.614 50.000 7.04 0.00 44.95 4.26
22 23 2.895039 AACGTAGACGGTGTTGCAG 58.105 52.632 7.04 0.00 44.95 4.41
46 47 6.741992 TCGAGAGCATGTCACATAATTTTT 57.258 33.333 0.00 0.00 0.00 1.94
47 48 6.932356 ATCGAGAGCATGTCACATAATTTT 57.068 33.333 0.00 0.00 0.00 1.82
48 49 6.722301 CAATCGAGAGCATGTCACATAATTT 58.278 36.000 0.00 0.00 0.00 1.82
49 50 5.277683 GCAATCGAGAGCATGTCACATAATT 60.278 40.000 6.97 0.00 0.00 1.40
50 51 4.212847 GCAATCGAGAGCATGTCACATAAT 59.787 41.667 6.97 0.00 0.00 1.28
51 52 3.557185 GCAATCGAGAGCATGTCACATAA 59.443 43.478 6.97 0.00 0.00 1.90
52 53 3.126073 GCAATCGAGAGCATGTCACATA 58.874 45.455 6.97 0.00 0.00 2.29
53 54 1.938577 GCAATCGAGAGCATGTCACAT 59.061 47.619 6.97 0.00 0.00 3.21
54 55 1.338011 TGCAATCGAGAGCATGTCACA 60.338 47.619 10.16 0.00 35.51 3.58
55 56 1.362768 TGCAATCGAGAGCATGTCAC 58.637 50.000 10.16 0.00 35.51 3.67
56 57 2.097680 TTGCAATCGAGAGCATGTCA 57.902 45.000 14.31 0.00 40.94 3.58
57 58 3.476295 TTTTGCAATCGAGAGCATGTC 57.524 42.857 14.31 0.00 40.94 3.06
58 59 3.921119 TTTTTGCAATCGAGAGCATGT 57.079 38.095 14.31 0.00 40.94 3.21
91 92 9.878667 TGCAGAAACATTTTCAATATTGATCAT 57.121 25.926 18.61 10.78 37.00 2.45
92 93 9.708092 TTGCAGAAACATTTTCAATATTGATCA 57.292 25.926 18.61 8.98 37.00 2.92
93 94 9.962759 GTTGCAGAAACATTTTCAATATTGATC 57.037 29.630 18.61 11.16 38.75 2.92
94 95 9.491675 TGTTGCAGAAACATTTTCAATATTGAT 57.508 25.926 18.61 2.10 43.96 2.57
95 96 8.883954 TGTTGCAGAAACATTTTCAATATTGA 57.116 26.923 14.23 14.23 43.96 2.57
109 110 6.475076 TGTGACACAAATTATGTTGCAGAAAC 59.525 34.615 5.62 0.00 41.46 2.78
110 111 6.567959 TGTGACACAAATTATGTTGCAGAAA 58.432 32.000 5.62 0.00 41.46 2.52
111 112 6.141560 TGTGACACAAATTATGTTGCAGAA 57.858 33.333 5.62 0.00 41.46 3.02
112 113 5.764487 TGTGACACAAATTATGTTGCAGA 57.236 34.783 5.62 0.00 41.46 4.26
113 114 6.825284 TTTGTGACACAAATTATGTTGCAG 57.175 33.333 26.08 0.00 42.55 4.41
114 115 7.601073 TTTTTGTGACACAAATTATGTTGCA 57.399 28.000 29.19 12.20 46.17 4.08
135 136 8.682936 ACAGAGATCATGTTGTAGAACTTTTT 57.317 30.769 4.21 0.00 32.79 1.94
136 137 8.682936 AACAGAGATCATGTTGTAGAACTTTT 57.317 30.769 13.68 0.00 39.36 2.27
147 148 5.717078 ACATTTGCAACAGAGATCATGTT 57.283 34.783 0.00 9.77 41.47 2.71
148 149 5.717078 AACATTTGCAACAGAGATCATGT 57.283 34.783 0.00 0.40 0.00 3.21
149 150 6.308041 CAGAAACATTTGCAACAGAGATCATG 59.692 38.462 0.00 0.00 0.00 3.07
150 151 6.387465 CAGAAACATTTGCAACAGAGATCAT 58.613 36.000 0.00 0.00 0.00 2.45
151 152 5.765176 CAGAAACATTTGCAACAGAGATCA 58.235 37.500 0.00 0.00 0.00 2.92
152 153 4.620184 GCAGAAACATTTGCAACAGAGATC 59.380 41.667 0.00 0.00 40.02 2.75
153 154 4.038282 TGCAGAAACATTTGCAACAGAGAT 59.962 37.500 0.00 0.00 46.42 2.75
154 155 3.380954 TGCAGAAACATTTGCAACAGAGA 59.619 39.130 0.00 0.00 46.42 3.10
155 156 3.708890 TGCAGAAACATTTGCAACAGAG 58.291 40.909 0.00 0.00 46.42 3.35
156 157 3.797451 TGCAGAAACATTTGCAACAGA 57.203 38.095 0.00 0.00 46.42 3.41
168 169 2.880890 ACAGAGGTCATGTTGCAGAAAC 59.119 45.455 0.00 0.00 39.41 2.78
169 170 3.213206 ACAGAGGTCATGTTGCAGAAA 57.787 42.857 0.00 0.00 0.00 2.52
170 171 2.936919 ACAGAGGTCATGTTGCAGAA 57.063 45.000 0.00 0.00 0.00 3.02
171 172 2.936919 AACAGAGGTCATGTTGCAGA 57.063 45.000 0.00 0.00 39.36 4.26
176 177 5.711506 TCAATATTGCAACAGAGGTCATGTT 59.288 36.000 10.76 0.00 41.47 2.71
177 178 5.255687 TCAATATTGCAACAGAGGTCATGT 58.744 37.500 10.76 0.00 0.00 3.21
178 179 5.823209 TCAATATTGCAACAGAGGTCATG 57.177 39.130 10.76 0.00 0.00 3.07
179 180 5.359009 CCTTCAATATTGCAACAGAGGTCAT 59.641 40.000 10.76 0.00 0.00 3.06
180 181 4.701651 CCTTCAATATTGCAACAGAGGTCA 59.298 41.667 10.76 0.00 0.00 4.02
181 182 4.096984 CCCTTCAATATTGCAACAGAGGTC 59.903 45.833 10.76 0.00 0.00 3.85
182 183 4.019174 CCCTTCAATATTGCAACAGAGGT 58.981 43.478 10.76 0.00 0.00 3.85
183 184 4.272489 TCCCTTCAATATTGCAACAGAGG 58.728 43.478 10.76 9.72 0.00 3.69
184 185 5.065731 GTCTCCCTTCAATATTGCAACAGAG 59.934 44.000 10.76 11.79 0.00 3.35
185 186 4.943705 GTCTCCCTTCAATATTGCAACAGA 59.056 41.667 10.76 5.44 0.00 3.41
186 187 4.201851 CGTCTCCCTTCAATATTGCAACAG 60.202 45.833 10.76 4.12 0.00 3.16
187 188 3.689161 CGTCTCCCTTCAATATTGCAACA 59.311 43.478 10.76 0.00 0.00 3.33
188 189 3.487544 GCGTCTCCCTTCAATATTGCAAC 60.488 47.826 10.76 0.00 0.00 4.17
189 190 2.682856 GCGTCTCCCTTCAATATTGCAA 59.317 45.455 10.76 0.00 0.00 4.08
190 191 2.092968 AGCGTCTCCCTTCAATATTGCA 60.093 45.455 10.76 0.00 0.00 4.08
191 192 2.545946 GAGCGTCTCCCTTCAATATTGC 59.454 50.000 10.76 0.00 0.00 3.56
192 193 3.797039 TGAGCGTCTCCCTTCAATATTG 58.203 45.455 9.29 9.29 0.00 1.90
193 194 4.192317 GTTGAGCGTCTCCCTTCAATATT 58.808 43.478 4.73 0.00 32.76 1.28
194 195 3.432326 GGTTGAGCGTCTCCCTTCAATAT 60.432 47.826 4.73 0.00 32.76 1.28
195 196 2.093658 GGTTGAGCGTCTCCCTTCAATA 60.094 50.000 4.73 0.00 32.76 1.90
196 197 1.339151 GGTTGAGCGTCTCCCTTCAAT 60.339 52.381 4.73 0.00 32.76 2.57
197 198 0.034896 GGTTGAGCGTCTCCCTTCAA 59.965 55.000 4.73 0.00 0.00 2.69
198 199 1.671742 GGTTGAGCGTCTCCCTTCA 59.328 57.895 4.73 0.00 0.00 3.02
199 200 1.446272 CGGTTGAGCGTCTCCCTTC 60.446 63.158 4.73 0.00 0.00 3.46
200 201 2.657237 CGGTTGAGCGTCTCCCTT 59.343 61.111 4.73 0.00 0.00 3.95
201 202 4.070552 GCGGTTGAGCGTCTCCCT 62.071 66.667 4.45 0.00 0.00 4.20
202 203 3.991536 GAGCGGTTGAGCGTCTCCC 62.992 68.421 12.59 0.00 43.00 4.30
203 204 2.507324 GAGCGGTTGAGCGTCTCC 60.507 66.667 12.59 0.00 43.00 3.71
204 205 2.876645 CGAGCGGTTGAGCGTCTC 60.877 66.667 0.00 13.21 43.00 3.36
219 220 2.203082 ATAGATCTGGCGCCAGCGA 61.203 57.895 44.77 32.52 46.35 4.93
220 221 2.025969 CATAGATCTGGCGCCAGCG 61.026 63.158 44.77 28.52 46.35 5.18
221 222 1.670406 CCATAGATCTGGCGCCAGC 60.670 63.158 44.77 33.28 43.31 4.85
222 223 4.689484 CCATAGATCTGGCGCCAG 57.311 61.111 44.24 44.24 44.86 4.85
228 229 0.387878 GTCGCGAGCCATAGATCTGG 60.388 60.000 10.24 0.31 39.45 3.86
229 230 0.387878 GGTCGCGAGCCATAGATCTG 60.388 60.000 27.12 0.00 0.00 2.90
230 231 1.960612 GGTCGCGAGCCATAGATCT 59.039 57.895 27.12 0.00 0.00 2.75
231 232 4.561731 GGTCGCGAGCCATAGATC 57.438 61.111 27.12 2.77 0.00 2.75
240 241 4.933064 GATCAGCCGGGTCGCGAG 62.933 72.222 10.24 0.00 0.00 5.03
244 245 2.663630 CTACGTGATCAGCCGGGTCG 62.664 65.000 1.27 6.67 0.00 4.79
245 246 1.065928 CTACGTGATCAGCCGGGTC 59.934 63.158 1.27 0.00 0.00 4.46
246 247 1.379443 TCTACGTGATCAGCCGGGT 60.379 57.895 0.00 0.00 0.00 5.28
247 248 1.360551 CTCTACGTGATCAGCCGGG 59.639 63.158 2.18 0.00 0.00 5.73
248 249 1.299468 GCTCTACGTGATCAGCCGG 60.299 63.158 10.11 0.00 0.00 6.13
249 250 0.593518 CTGCTCTACGTGATCAGCCG 60.594 60.000 0.00 0.00 33.03 5.52
250 251 3.264666 CTGCTCTACGTGATCAGCC 57.735 57.895 0.00 0.00 33.03 4.85
252 253 0.249238 GGGCTGCTCTACGTGATCAG 60.249 60.000 0.00 6.42 40.72 2.90
253 254 0.970427 TGGGCTGCTCTACGTGATCA 60.970 55.000 0.00 0.00 0.00 2.92
254 255 0.390860 ATGGGCTGCTCTACGTGATC 59.609 55.000 0.00 0.00 0.00 2.92
255 256 0.833287 AATGGGCTGCTCTACGTGAT 59.167 50.000 0.00 0.00 0.00 3.06
256 257 0.613260 AAATGGGCTGCTCTACGTGA 59.387 50.000 0.00 0.00 0.00 4.35
257 258 1.131126 CAAAATGGGCTGCTCTACGTG 59.869 52.381 0.00 0.00 0.00 4.49
258 259 1.271379 ACAAAATGGGCTGCTCTACGT 60.271 47.619 0.00 0.00 0.00 3.57
259 260 1.453155 ACAAAATGGGCTGCTCTACG 58.547 50.000 0.00 0.00 0.00 3.51
260 261 4.217550 TGTTTACAAAATGGGCTGCTCTAC 59.782 41.667 0.00 0.00 0.00 2.59
261 262 4.402829 TGTTTACAAAATGGGCTGCTCTA 58.597 39.130 0.00 0.00 0.00 2.43
262 263 3.230134 TGTTTACAAAATGGGCTGCTCT 58.770 40.909 0.00 0.00 0.00 4.09
263 264 3.005791 ACTGTTTACAAAATGGGCTGCTC 59.994 43.478 0.00 0.00 0.00 4.26
264 265 2.965147 ACTGTTTACAAAATGGGCTGCT 59.035 40.909 0.00 0.00 0.00 4.24
265 266 3.385193 ACTGTTTACAAAATGGGCTGC 57.615 42.857 0.00 0.00 0.00 5.25
266 267 6.676237 AAAAACTGTTTACAAAATGGGCTG 57.324 33.333 6.16 0.00 0.00 4.85
355 356 1.981533 GATGTTCTCTTTTTGCAGCGC 59.018 47.619 0.00 0.00 0.00 5.92
458 635 6.839124 TGGTAATCTGTGATTGCTTTCAAT 57.161 33.333 7.95 0.00 45.04 2.57
462 639 6.815089 TGTTTTGGTAATCTGTGATTGCTTT 58.185 32.000 7.95 0.00 0.00 3.51
475 652 9.974980 AGAAATTACGTCAATTGTTTTGGTAAT 57.025 25.926 5.13 9.90 36.93 1.89
517 694 7.292356 TCCACCATTCCTTATCTATGCTTCTAA 59.708 37.037 0.00 0.00 0.00 2.10
551 887 3.042682 TGCTTCCATAATAACCTCCCGA 58.957 45.455 0.00 0.00 0.00 5.14
586 922 2.237392 AGGCGCTGAGTTATTTCCTTCT 59.763 45.455 7.64 0.00 0.00 2.85
717 1053 2.152297 TACGCGGCGAACCAGGTTTA 62.152 55.000 30.94 4.29 34.57 2.01
725 1061 3.184003 GGAAGGTACGCGGCGAAC 61.184 66.667 30.94 17.47 0.00 3.95
1809 6549 0.108615 ATCAGTTCTTGACGCCGAGG 60.109 55.000 0.00 0.00 38.99 4.63
1843 6583 4.927978 TCCCCAAATTAATGGTAATGCG 57.072 40.909 0.00 0.00 38.91 4.73
1882 6627 3.181469 CCAGCATATCAGGCAAGCAAATT 60.181 43.478 0.00 0.00 0.00 1.82
1929 6679 1.082117 AATTAGCTTCCACCGACGCG 61.082 55.000 3.53 3.53 38.28 6.01
1958 6708 1.353103 GCCATTGGCGATCGAACTG 59.647 57.895 21.57 10.18 39.62 3.16


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

AutoCloner maintained by Alex Coulton.