Multiple sequence alignment - TraesCS2A01G405400

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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 TraesCS2A01G405400 chr2A 100.000 2602 0 0 1 2602 661226103 661228704 0.000000e+00 4806.0
1 TraesCS2A01G405400 chr2A 90.650 1401 119 11 1 1401 661241178 661242566 0.000000e+00 1851.0
2 TraesCS2A01G405400 chr2A 90.457 1226 97 4 1397 2602 661244143 661245368 0.000000e+00 1598.0
3 TraesCS2A01G405400 chr2A 84.359 569 64 19 2054 2602 239251707 239252270 3.810000e-148 534.0
4 TraesCS2A01G405400 chr2A 83.082 597 65 19 2027 2602 331522225 331521644 6.420000e-141 510.0
5 TraesCS2A01G405400 chr2A 83.480 569 69 21 2054 2602 239049373 239049936 8.310000e-140 507.0
6 TraesCS2A01G405400 chr2A 82.014 556 80 12 1 549 375979830 375980372 3.050000e-124 455.0
7 TraesCS2A01G405400 chr2A 83.624 287 30 12 1 285 279066520 279066249 1.200000e-63 254.0
8 TraesCS2A01G405400 chr2A 91.837 49 4 0 1209 1257 364642699 364642651 4.650000e-08 69.4
9 TraesCS2A01G405400 chr3A 85.460 1011 121 23 1 1003 325472688 325471696 0.000000e+00 1029.0
10 TraesCS2A01G405400 chr3A 81.503 865 121 30 1 846 496508622 496507778 0.000000e+00 675.0
11 TraesCS2A01G405400 chr3A 78.596 570 89 19 2053 2602 495425312 495424756 1.920000e-91 346.0
12 TraesCS2A01G405400 chr3A 88.333 120 14 0 1102 1221 258713307 258713426 7.500000e-31 145.0
13 TraesCS2A01G405400 chr3A 87.395 119 15 0 1106 1224 321872228 321872346 1.260000e-28 137.0
14 TraesCS2A01G405400 chr3A 85.000 120 18 0 1102 1221 258770696 258770815 3.520000e-24 122.0
15 TraesCS2A01G405400 chr3D 84.286 980 113 37 1 967 405795841 405796792 0.000000e+00 918.0
16 TraesCS2A01G405400 chr3D 84.049 978 115 37 1 967 474143154 474142207 0.000000e+00 904.0
17 TraesCS2A01G405400 chr3D 83.776 980 119 36 1 967 581953438 581952486 0.000000e+00 893.0
18 TraesCS2A01G405400 chr3D 80.936 1133 145 55 1 1104 254211406 254210316 0.000000e+00 830.0
19 TraesCS2A01G405400 chr3D 82.653 294 39 8 1 294 190060267 190060548 1.550000e-62 250.0
20 TraesCS2A01G405400 chr3D 89.362 94 9 1 1307 1399 386622928 386623021 1.640000e-22 117.0
21 TraesCS2A01G405400 chr4D 84.135 977 116 33 1 967 191601746 191600799 0.000000e+00 909.0
22 TraesCS2A01G405400 chr4D 83.947 978 117 36 1 967 191609498 191608550 0.000000e+00 900.0
23 TraesCS2A01G405400 chr4D 86.784 227 28 2 1305 1530 331533444 331533669 4.300000e-63 252.0
24 TraesCS2A01G405400 chr4D 88.125 160 18 1 1241 1399 98351374 98351533 3.420000e-44 189.0
25 TraesCS2A01G405400 chr2D 83.930 977 111 39 9 967 395191193 395192141 0.000000e+00 893.0
26 TraesCS2A01G405400 chr2D 83.611 360 38 8 2261 2602 230414702 230414346 4.180000e-83 318.0
27 TraesCS2A01G405400 chr2D 85.833 120 14 3 1407 1526 233149222 233149106 9.780000e-25 124.0
28 TraesCS2A01G405400 chr2D 91.860 86 7 0 1089 1174 249848908 249848823 1.260000e-23 121.0
29 TraesCS2A01G405400 chr2D 91.860 86 7 0 1089 1174 285360050 285360135 1.260000e-23 121.0
30 TraesCS2A01G405400 chr2D 91.860 86 7 0 1089 1174 581276306 581276391 1.260000e-23 121.0
31 TraesCS2A01G405400 chr2D 90.698 86 8 0 1089 1174 249864721 249864636 5.880000e-22 115.0
32 TraesCS2A01G405400 chr2D 89.535 86 9 0 1089 1174 249856803 249856718 2.740000e-20 110.0
33 TraesCS2A01G405400 chr6D 82.929 1031 126 39 1 1009 173283238 173282236 0.000000e+00 883.0
34 TraesCS2A01G405400 chr6D 86.869 99 11 2 1089 1186 121005908 121005811 2.740000e-20 110.0
35 TraesCS2A01G405400 chr6D 93.056 72 5 0 1103 1174 167563288 167563359 3.540000e-19 106.0
36 TraesCS2A01G405400 chr6D 93.056 72 5 0 1103 1174 275035392 275035463 3.540000e-19 106.0
37 TraesCS2A01G405400 chr6D 93.056 72 5 0 1103 1174 334163980 334164051 3.540000e-19 106.0
38 TraesCS2A01G405400 chr6D 88.506 87 8 2 1089 1174 239674281 239674366 1.270000e-18 104.0
39 TraesCS2A01G405400 chr6D 91.667 72 6 0 1103 1174 251044668 251044739 1.650000e-17 100.0
40 TraesCS2A01G405400 chr6D 90.769 65 6 0 1110 1174 235646626 235646690 1.280000e-13 87.9
41 TraesCS2A01G405400 chr6D 87.500 72 9 0 1103 1174 192593698 192593769 1.660000e-12 84.2
42 TraesCS2A01G405400 chr7D 83.129 978 127 33 1 967 241480709 241479759 0.000000e+00 857.0
43 TraesCS2A01G405400 chr7D 81.608 995 122 40 1 978 287780901 287781851 0.000000e+00 767.0
44 TraesCS2A01G405400 chr7D 87.981 208 23 1 1325 1530 274827031 274827238 7.190000e-61 244.0
45 TraesCS2A01G405400 chr7D 87.560 209 22 3 1325 1530 274848136 274848343 3.350000e-59 239.0
46 TraesCS2A01G405400 chr7D 87.019 208 25 1 1325 1530 274836324 274836531 1.560000e-57 233.0
47 TraesCS2A01G405400 chr7D 79.725 291 47 8 2263 2546 359242253 359241968 1.580000e-47 200.0
48 TraesCS2A01G405400 chr7D 91.860 86 7 0 1089 1174 492005171 492005256 1.260000e-23 121.0
49 TraesCS2A01G405400 chr7D 92.958 71 5 0 1104 1174 291643493 291643423 1.270000e-18 104.0
50 TraesCS2A01G405400 chr5A 85.448 591 57 15 2030 2602 354563199 354563778 2.880000e-164 588.0
51 TraesCS2A01G405400 chr5A 84.422 199 25 4 1238 1433 312157513 312157708 9.500000e-45 191.0
52 TraesCS2A01G405400 chr5A 84.103 195 25 4 1242 1433 312165396 312165587 1.590000e-42 183.0
53 TraesCS2A01G405400 chr5A 90.000 120 9 1 1407 1526 362570094 362570210 4.480000e-33 152.0
54 TraesCS2A01G405400 chr5A 88.462 52 6 0 1204 1255 481594480 481594531 2.160000e-06 63.9
55 TraesCS2A01G405400 chr5D 86.232 552 60 11 1 549 130691169 130691707 3.730000e-163 584.0
56 TraesCS2A01G405400 chr5D 85.583 326 45 2 1242 1565 380370229 380370554 8.920000e-90 340.0
57 TraesCS2A01G405400 chr5D 96.479 142 5 0 1 142 139502082 139501941 4.330000e-58 235.0
58 TraesCS2A01G405400 chr5D 88.750 160 17 1 1241 1399 477825248 477825407 7.350000e-46 195.0
59 TraesCS2A01G405400 chr7A 85.662 544 60 12 8 549 291923350 291922823 8.130000e-155 556.0
60 TraesCS2A01G405400 chr5B 88.184 347 41 0 1089 1435 93681166 93680820 5.180000e-112 414.0
61 TraesCS2A01G405400 chr5B 85.873 361 33 5 2258 2602 145810399 145810757 4.090000e-98 368.0
62 TraesCS2A01G405400 chr5B 85.596 361 34 5 2258 2602 281371285 281371643 1.900000e-96 363.0
63 TraesCS2A01G405400 chr4A 80.680 559 75 24 2053 2602 248257599 248257065 1.120000e-108 403.0
64 TraesCS2A01G405400 chr4A 80.000 540 74 19 2056 2576 409751100 409750576 4.090000e-98 368.0
65 TraesCS2A01G405400 chr4A 79.630 540 75 19 2056 2576 409743269 409742746 3.180000e-94 355.0
66 TraesCS2A01G405400 chr4A 84.184 196 27 2 1248 1442 556966800 556966608 1.230000e-43 187.0
67 TraesCS2A01G405400 chr4A 87.402 127 12 2 1407 1533 512728304 512728182 2.700000e-30 143.0
68 TraesCS2A01G405400 chr4A 83.942 137 19 2 1407 1543 238458513 238458380 7.560000e-26 128.0
69 TraesCS2A01G405400 chr7B 86.275 357 32 5 2261 2602 627346029 627345675 3.160000e-99 372.0
70 TraesCS2A01G405400 chr7B 85.994 357 33 5 2261 2602 627389315 627388961 1.470000e-97 366.0
71 TraesCS2A01G405400 chr7B 84.416 154 11 5 1855 1996 254514238 254514390 3.490000e-29 139.0
72 TraesCS2A01G405400 chr7B 83.969 131 9 9 1855 1973 277879222 277879092 5.880000e-22 115.0
73 TraesCS2A01G405400 chr7B 80.233 172 17 13 1855 2012 277886330 277886162 2.120000e-21 113.0
74 TraesCS2A01G405400 chr7B 86.111 108 7 6 1855 1954 184319784 184319891 2.740000e-20 110.0
75 TraesCS2A01G405400 chr7B 83.206 131 10 9 1855 1973 277894438 277894308 2.740000e-20 110.0
76 TraesCS2A01G405400 chr3B 86.819 349 27 7 2269 2602 139062847 139062503 3.160000e-99 372.0
77 TraesCS2A01G405400 chr3B 80.612 196 30 7 2263 2454 286922384 286922575 7.500000e-31 145.0
78 TraesCS2A01G405400 chr6B 86.034 358 32 4 2261 2602 332448551 332448196 4.090000e-98 368.0
79 TraesCS2A01G405400 chr1D 82.019 317 43 10 2263 2576 69536305 69536610 9.240000e-65 257.0
80 TraesCS2A01G405400 chr1D 88.750 160 17 1 1241 1399 356008041 356008200 7.350000e-46 195.0
81 TraesCS2A01G405400 chr1D 93.056 72 5 0 1103 1174 458687446 458687517 3.540000e-19 106.0
82 TraesCS2A01G405400 chr1D 93.056 72 5 0 1103 1174 458695639 458695710 3.540000e-19 106.0
83 TraesCS2A01G405400 chr1D 91.667 72 6 0 1103 1174 170728635 170728706 1.650000e-17 100.0
84 TraesCS2A01G405400 chr1D 89.091 55 6 0 1050 1104 116568327 116568381 4.650000e-08 69.4
85 TraesCS2A01G405400 chr1A 81.884 276 38 4 1794 2057 177532979 177532704 3.370000e-54 222.0
86 TraesCS2A01G405400 chr2B 86.432 199 14 8 1854 2039 482584725 482584923 3.390000e-49 206.0
87 TraesCS2A01G405400 chr2B 81.452 124 18 3 913 1034 206308107 206307987 2.130000e-16 97.1
88 TraesCS2A01G405400 chr4B 81.579 228 37 5 1305 1530 409817053 409816829 1.590000e-42 183.0
89 TraesCS2A01G405400 chr1B 84.530 181 14 9 1855 2021 258501559 258501739 1.600000e-37 167.0


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 TraesCS2A01G405400 chr2A 661226103 661228704 2601 False 4806.0 4806 100.0000 1 2602 1 chr2A.!!$F4 2601
1 TraesCS2A01G405400 chr2A 661241178 661245368 4190 False 1724.5 1851 90.5535 1 2602 2 chr2A.!!$F5 2601
2 TraesCS2A01G405400 chr2A 239251707 239252270 563 False 534.0 534 84.3590 2054 2602 1 chr2A.!!$F2 548
3 TraesCS2A01G405400 chr2A 331521644 331522225 581 True 510.0 510 83.0820 2027 2602 1 chr2A.!!$R2 575
4 TraesCS2A01G405400 chr2A 239049373 239049936 563 False 507.0 507 83.4800 2054 2602 1 chr2A.!!$F1 548
5 TraesCS2A01G405400 chr2A 375979830 375980372 542 False 455.0 455 82.0140 1 549 1 chr2A.!!$F3 548
6 TraesCS2A01G405400 chr3A 325471696 325472688 992 True 1029.0 1029 85.4600 1 1003 1 chr3A.!!$R1 1002
7 TraesCS2A01G405400 chr3A 496507778 496508622 844 True 675.0 675 81.5030 1 846 1 chr3A.!!$R3 845
8 TraesCS2A01G405400 chr3A 495424756 495425312 556 True 346.0 346 78.5960 2053 2602 1 chr3A.!!$R2 549
9 TraesCS2A01G405400 chr3D 405795841 405796792 951 False 918.0 918 84.2860 1 967 1 chr3D.!!$F3 966
10 TraesCS2A01G405400 chr3D 474142207 474143154 947 True 904.0 904 84.0490 1 967 1 chr3D.!!$R2 966
11 TraesCS2A01G405400 chr3D 581952486 581953438 952 True 893.0 893 83.7760 1 967 1 chr3D.!!$R3 966
12 TraesCS2A01G405400 chr3D 254210316 254211406 1090 True 830.0 830 80.9360 1 1104 1 chr3D.!!$R1 1103
13 TraesCS2A01G405400 chr4D 191600799 191601746 947 True 909.0 909 84.1350 1 967 1 chr4D.!!$R1 966
14 TraesCS2A01G405400 chr4D 191608550 191609498 948 True 900.0 900 83.9470 1 967 1 chr4D.!!$R2 966
15 TraesCS2A01G405400 chr2D 395191193 395192141 948 False 893.0 893 83.9300 9 967 1 chr2D.!!$F2 958
16 TraesCS2A01G405400 chr6D 173282236 173283238 1002 True 883.0 883 82.9290 1 1009 1 chr6D.!!$R2 1008
17 TraesCS2A01G405400 chr7D 241479759 241480709 950 True 857.0 857 83.1290 1 967 1 chr7D.!!$R1 966
18 TraesCS2A01G405400 chr7D 287780901 287781851 950 False 767.0 767 81.6080 1 978 1 chr7D.!!$F4 977
19 TraesCS2A01G405400 chr5A 354563199 354563778 579 False 588.0 588 85.4480 2030 2602 1 chr5A.!!$F3 572
20 TraesCS2A01G405400 chr5D 130691169 130691707 538 False 584.0 584 86.2320 1 549 1 chr5D.!!$F1 548
21 TraesCS2A01G405400 chr7A 291922823 291923350 527 True 556.0 556 85.6620 8 549 1 chr7A.!!$R1 541
22 TraesCS2A01G405400 chr4A 248257065 248257599 534 True 403.0 403 80.6800 2053 2602 1 chr4A.!!$R2 549
23 TraesCS2A01G405400 chr4A 409750576 409751100 524 True 368.0 368 80.0000 2056 2576 1 chr4A.!!$R4 520
24 TraesCS2A01G405400 chr4A 409742746 409743269 523 True 355.0 355 79.6300 2056 2576 1 chr4A.!!$R3 520

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
153 155 0.747283 AGTAGACGGGTCAGCGTAGG 60.747 60.000 1.17 0.0 0.00 3.18 F
980 1031 1.079888 GTGCATTTTTCGGGGCAGG 60.080 57.895 0.00 0.0 36.86 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1279 0.030908 GTTCGGAGCCCTCAGATACG 59.969 60.0 0.0 0.0 34.02 3.06 R
1967 3605 0.034960 CTCTCGTCCTCCCACTCTCA 60.035 60.0 0.0 0.0 0.00 3.27 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
66 68 4.266502 CGAGACAACTAGCATAGCAAAGAC 59.733 45.833 0.00 0.00 44.39 3.01
129 131 3.004839 CCGCTAGGAAGAAGATCGAATCA 59.995 47.826 0.00 0.00 41.02 2.57
144 146 3.446161 TCGAATCAATGAAGTAGACGGGT 59.554 43.478 0.00 0.00 0.00 5.28
153 155 0.747283 AGTAGACGGGTCAGCGTAGG 60.747 60.000 1.17 0.00 0.00 3.18
167 169 4.189639 AGCGTAGGTGAAAAGGTTAGAG 57.810 45.455 0.00 0.00 36.17 2.43
168 170 3.056035 AGCGTAGGTGAAAAGGTTAGAGG 60.056 47.826 0.00 0.00 36.17 3.69
169 171 3.259902 CGTAGGTGAAAAGGTTAGAGGC 58.740 50.000 0.00 0.00 0.00 4.70
171 173 4.159135 CGTAGGTGAAAAGGTTAGAGGCTA 59.841 45.833 0.00 0.00 0.00 3.93
174 176 4.783227 AGGTGAAAAGGTTAGAGGCTATCA 59.217 41.667 0.00 0.00 0.00 2.15
175 177 5.250774 AGGTGAAAAGGTTAGAGGCTATCAA 59.749 40.000 0.00 0.00 0.00 2.57
176 178 6.069381 AGGTGAAAAGGTTAGAGGCTATCAAT 60.069 38.462 0.00 0.00 0.00 2.57
177 179 6.038714 GGTGAAAAGGTTAGAGGCTATCAATG 59.961 42.308 0.00 0.00 0.00 2.82
179 181 7.336931 GTGAAAAGGTTAGAGGCTATCAATGAA 59.663 37.037 0.00 0.00 0.00 2.57
183 185 7.863901 AGGTTAGAGGCTATCAATGAAGTAT 57.136 36.000 0.00 0.00 0.00 2.12
184 186 7.675062 AGGTTAGAGGCTATCAATGAAGTATG 58.325 38.462 0.00 0.00 0.00 2.39
185 187 6.370166 GGTTAGAGGCTATCAATGAAGTATGC 59.630 42.308 0.00 0.00 0.00 3.14
186 188 4.904241 AGAGGCTATCAATGAAGTATGCC 58.096 43.478 0.00 0.00 39.40 4.40
187 189 4.349048 AGAGGCTATCAATGAAGTATGCCA 59.651 41.667 14.10 0.00 41.33 4.92
188 190 5.013913 AGAGGCTATCAATGAAGTATGCCAT 59.986 40.000 14.10 0.00 41.33 4.40
189 191 5.008331 AGGCTATCAATGAAGTATGCCATG 58.992 41.667 14.10 0.00 41.33 3.66
190 192 4.763793 GGCTATCAATGAAGTATGCCATGT 59.236 41.667 0.00 0.00 38.99 3.21
191 193 5.242393 GGCTATCAATGAAGTATGCCATGTT 59.758 40.000 0.00 0.00 38.99 2.71
192 194 6.239120 GGCTATCAATGAAGTATGCCATGTTT 60.239 38.462 0.00 0.00 38.99 2.83
365 381 5.679734 AATTAAGTGGAGCTCAATATGCG 57.320 39.130 17.19 0.00 35.28 4.73
459 481 4.519540 ATGTGGTTAAACATGGCAAGAC 57.480 40.909 0.00 0.00 39.32 3.01
461 483 1.268352 TGGTTAAACATGGCAAGACGC 59.732 47.619 0.00 0.00 41.28 5.19
535 559 4.813697 ACCAAACAACAATTCCGGAAAATG 59.186 37.500 23.08 23.77 0.00 2.32
657 686 9.571810 TTATGAAAATGTTACATCAGCATGTTC 57.428 29.630 0.00 0.00 40.66 3.18
690 723 2.176798 TCACCATGGTGGAAAGAAAGGT 59.823 45.455 38.12 0.54 45.43 3.50
803 843 1.722751 CGAAACATGCAAGAGTGACGC 60.723 52.381 0.00 0.00 0.00 5.19
840 880 2.049433 GGTGTCCCACGTGTCGAG 60.049 66.667 15.65 0.00 34.83 4.04
843 883 1.605451 TGTCCCACGTGTCGAGGAT 60.605 57.895 15.65 0.00 39.84 3.24
873 914 1.717645 CGAGGGAACAACTAACGTTCG 59.282 52.381 2.82 0.00 43.00 3.95
978 1029 2.647875 CGTGCATTTTTCGGGGCA 59.352 55.556 0.00 0.00 0.00 5.36
980 1031 1.079888 GTGCATTTTTCGGGGCAGG 60.080 57.895 0.00 0.00 36.86 4.85
1004 1055 2.205074 GTTCGATGCGATGGAGATGTT 58.795 47.619 0.00 0.00 35.23 2.71
1016 1067 2.765699 TGGAGATGTTCACGGATCATCA 59.234 45.455 18.77 5.13 39.71 3.07
1112 1169 3.192844 AGTTGTACACAGTCCGTAGATGG 59.807 47.826 0.00 0.00 0.00 3.51
1160 1217 1.913762 ACAGGGTCTTGGAGGGTCG 60.914 63.158 0.00 0.00 0.00 4.79
1194 1251 2.544277 CCCACGTCGTTGTGAAAGTAGA 60.544 50.000 10.61 0.00 42.55 2.59
1197 1254 1.719780 CGTCGTTGTGAAAGTAGAGGC 59.280 52.381 0.00 0.00 0.00 4.70
1206 1263 2.432146 TGAAAGTAGAGGCTCATGCGAT 59.568 45.455 18.26 0.00 40.82 4.58
1207 1264 2.522836 AAGTAGAGGCTCATGCGATG 57.477 50.000 18.26 0.00 40.82 3.84
1222 1279 1.918609 GCGATGGTAGTCGAACTTGAC 59.081 52.381 0.00 0.00 44.06 3.18
1228 1285 4.005650 TGGTAGTCGAACTTGACGTATCT 58.994 43.478 0.00 0.00 43.70 1.98
1233 1290 2.422479 TCGAACTTGACGTATCTGAGGG 59.578 50.000 0.00 0.00 0.00 4.30
1237 1294 1.067821 CTTGACGTATCTGAGGGCTCC 59.932 57.143 0.00 0.00 0.00 4.70
1239 1296 0.818445 GACGTATCTGAGGGCTCCGA 60.818 60.000 0.00 0.00 0.00 4.55
1240 1297 0.395311 ACGTATCTGAGGGCTCCGAA 60.395 55.000 0.00 0.00 0.00 4.30
1245 1302 2.599281 TGAGGGCTCCGAACGTCA 60.599 61.111 0.00 0.00 0.00 4.35
1254 1311 2.259618 CTCCGAACGTCATGGTACTTG 58.740 52.381 0.00 0.00 0.00 3.16
1257 1314 1.084289 GAACGTCATGGTACTTGGCC 58.916 55.000 0.00 0.00 0.00 5.36
1282 1339 2.670148 GCCATTCCAGAGACGGGGT 61.670 63.158 0.00 0.00 0.00 4.95
1285 1342 0.105039 CATTCCAGAGACGGGGTAGC 59.895 60.000 0.00 0.00 0.00 3.58
1295 1352 1.140375 CGGGGTAGCGGTACTTGAC 59.860 63.158 22.84 11.52 0.00 3.18
1296 1353 1.597797 CGGGGTAGCGGTACTTGACA 61.598 60.000 22.84 0.00 0.00 3.58
1298 1355 0.604578 GGGTAGCGGTACTTGACACA 59.395 55.000 22.84 0.00 0.00 3.72
1302 1359 2.080286 AGCGGTACTTGACACATCAC 57.920 50.000 0.00 0.00 33.38 3.06
1303 1360 1.076332 GCGGTACTTGACACATCACC 58.924 55.000 0.00 0.00 33.38 4.02
1304 1361 1.606994 GCGGTACTTGACACATCACCA 60.607 52.381 0.00 0.00 33.38 4.17
1307 1364 3.674997 GGTACTTGACACATCACCATGT 58.325 45.455 0.00 0.00 44.72 3.21
1310 1367 4.623932 ACTTGACACATCACCATGTAGT 57.376 40.909 0.00 0.00 41.69 2.73
1312 1369 3.230743 TGACACATCACCATGTAGTCG 57.769 47.619 0.00 0.00 41.69 4.18
1323 1380 1.386748 CATGTAGTCGTGCACTTGTCG 59.613 52.381 16.19 0.55 36.43 4.35
1324 1381 0.664224 TGTAGTCGTGCACTTGTCGA 59.336 50.000 16.19 3.45 36.43 4.20
1387 1444 1.147376 CGGGTCTTGGTGGTCAACA 59.853 57.895 0.00 0.00 0.00 3.33
1401 1458 2.034221 AACAAAGAGAGGCGGCCC 59.966 61.111 17.02 7.43 0.00 5.80
1402 1459 2.529744 AACAAAGAGAGGCGGCCCT 61.530 57.895 17.02 12.67 46.74 5.19
1403 1460 2.437359 CAAAGAGAGGCGGCCCTG 60.437 66.667 17.02 0.00 43.12 4.45
1404 1461 3.721706 AAAGAGAGGCGGCCCTGG 61.722 66.667 17.02 0.00 43.12 4.45
1406 1463 4.488911 AGAGAGGCGGCCCTGGAT 62.489 66.667 17.02 0.00 43.12 3.41
1414 1471 3.415087 GGCCCTGGATGGAGCTGT 61.415 66.667 0.00 0.00 38.35 4.40
1418 3056 1.270414 CCCTGGATGGAGCTGTGAGT 61.270 60.000 0.00 0.00 38.35 3.41
1420 3058 1.411977 CCTGGATGGAGCTGTGAGTAG 59.588 57.143 0.00 0.00 38.35 2.57
1431 3069 3.006323 AGCTGTGAGTAGAGGACAAACAG 59.994 47.826 0.00 0.00 42.46 3.16
1473 3111 2.798689 CGATTGACGAGGAGGCGA 59.201 61.111 0.00 0.00 45.77 5.54
1482 3120 1.068921 GAGGAGGCGAAGATGGAGC 59.931 63.158 0.00 0.00 0.00 4.70
1529 3167 2.037136 CAGAGCAGGGAACTTGGCG 61.037 63.158 0.00 0.00 40.21 5.69
1549 3187 4.643387 GCGGTGGCCTGTCCTTGT 62.643 66.667 3.32 0.00 35.26 3.16
1565 3203 0.039180 TTGTAGAGGAGGTCGAGGCA 59.961 55.000 0.00 0.00 0.00 4.75
1609 3247 0.912486 ACTTGGCGCTAAGGAAGGAT 59.088 50.000 32.87 11.90 31.94 3.24
1614 3252 0.178068 GCGCTAAGGAAGGATGTCCA 59.822 55.000 0.00 0.00 40.48 4.02
1616 3254 1.482593 CGCTAAGGAAGGATGTCCAGT 59.517 52.381 1.30 0.00 40.48 4.00
1649 3287 1.221840 GCCAGATCAAAGCGGAGGA 59.778 57.895 0.00 0.00 0.00 3.71
1653 3291 0.325671 AGATCAAAGCGGAGGAGGGA 60.326 55.000 0.00 0.00 0.00 4.20
1660 3298 2.995574 CGGAGGAGGGACAACGGT 60.996 66.667 0.00 0.00 0.00 4.83
1671 3309 1.006102 ACAACGGTCTTGGAGCTCG 60.006 57.895 7.83 0.00 0.00 5.03
1673 3311 2.207924 AACGGTCTTGGAGCTCGGT 61.208 57.895 7.83 0.00 0.00 4.69
1674 3312 2.156051 AACGGTCTTGGAGCTCGGTC 62.156 60.000 7.83 0.00 0.00 4.79
1676 3314 1.901085 GGTCTTGGAGCTCGGTCAT 59.099 57.895 7.83 0.00 0.00 3.06
1677 3315 0.250513 GGTCTTGGAGCTCGGTCATT 59.749 55.000 7.83 0.00 0.00 2.57
1683 3321 1.476891 TGGAGCTCGGTCATTAGTCAC 59.523 52.381 7.83 0.00 0.00 3.67
1693 3331 1.768275 TCATTAGTCACCCATGGCGAT 59.232 47.619 6.09 0.00 34.75 4.58
1729 3367 3.851128 TGGCGTTGGTCGTGGTCA 61.851 61.111 0.00 0.00 42.13 4.02
1797 3435 4.357947 GTCGGACAGCAGCGGTCA 62.358 66.667 24.65 4.91 37.00 4.02
1804 3442 4.521062 AGCAGCGGTCATCGGAGC 62.521 66.667 0.00 0.00 39.69 4.70
1829 3467 3.122323 GGTGGCGCCGAATCGAAA 61.122 61.111 23.90 0.00 0.00 3.46
1833 3471 2.277310 GCGCCGAATCGAAAAGGC 60.277 61.111 15.63 15.63 45.67 4.35
1841 3479 0.114364 AATCGAAAAGGCCCAAGGGT 59.886 50.000 7.05 0.00 37.65 4.34
1859 3497 4.070552 GCGAGAAGGGGTGCGAGT 62.071 66.667 0.00 0.00 0.00 4.18
1860 3498 2.125912 CGAGAAGGGGTGCGAGTG 60.126 66.667 0.00 0.00 0.00 3.51
1937 3575 3.547249 CTGGCGCTGGCTTTGTGTG 62.547 63.158 7.64 0.00 39.81 3.82
1943 3581 2.043551 TGGCTTTGTGTGGTGGCA 60.044 55.556 0.00 0.00 0.00 4.92
1967 3605 1.539869 CAGGGATGGGGATCGGGAT 60.540 63.158 0.00 0.00 0.00 3.85
2388 4040 7.255277 GGAAAAGAATTATAGGCAAGGCTACAG 60.255 40.741 5.43 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 3.428180 CGTCACCTTGGATCTCACTACTG 60.428 52.174 0.00 0.00 0.00 2.74
129 131 1.135083 CGCTGACCCGTCTACTTCATT 60.135 52.381 0.00 0.00 0.00 2.57
144 146 2.922740 AACCTTTTCACCTACGCTGA 57.077 45.000 0.00 0.00 0.00 4.26
153 155 6.823689 TCATTGATAGCCTCTAACCTTTTCAC 59.176 38.462 0.00 0.00 0.00 3.18
158 160 6.567602 ACTTCATTGATAGCCTCTAACCTT 57.432 37.500 0.00 0.00 0.00 3.50
161 163 6.370166 GGCATACTTCATTGATAGCCTCTAAC 59.630 42.308 0.00 0.00 37.89 2.34
163 165 5.543790 TGGCATACTTCATTGATAGCCTCTA 59.456 40.000 0.00 0.00 41.33 2.43
164 166 4.349048 TGGCATACTTCATTGATAGCCTCT 59.651 41.667 0.00 0.00 41.33 3.69
165 167 4.645535 TGGCATACTTCATTGATAGCCTC 58.354 43.478 0.00 0.00 41.33 4.70
167 169 4.763793 ACATGGCATACTTCATTGATAGCC 59.236 41.667 0.00 0.00 41.15 3.93
168 170 5.954296 ACATGGCATACTTCATTGATAGC 57.046 39.130 0.00 0.00 0.00 2.97
169 171 8.292448 GGTAAACATGGCATACTTCATTGATAG 58.708 37.037 0.00 0.00 0.00 2.08
171 173 6.238731 CGGTAAACATGGCATACTTCATTGAT 60.239 38.462 0.00 0.00 0.00 2.57
174 176 5.189928 TCGGTAAACATGGCATACTTCATT 58.810 37.500 0.00 0.00 0.00 2.57
175 177 4.776349 TCGGTAAACATGGCATACTTCAT 58.224 39.130 0.00 0.00 0.00 2.57
176 178 4.209307 TCGGTAAACATGGCATACTTCA 57.791 40.909 0.00 0.00 0.00 3.02
177 179 4.873827 TCTTCGGTAAACATGGCATACTTC 59.126 41.667 0.00 0.00 0.00 3.01
179 181 4.481368 TCTTCGGTAAACATGGCATACT 57.519 40.909 0.00 0.00 0.00 2.12
183 185 5.029807 TGATATCTTCGGTAAACATGGCA 57.970 39.130 3.98 0.00 0.00 4.92
184 186 5.049405 CCTTGATATCTTCGGTAAACATGGC 60.049 44.000 3.98 0.00 0.00 4.40
185 187 6.288294 TCCTTGATATCTTCGGTAAACATGG 58.712 40.000 3.98 0.00 0.00 3.66
186 188 7.210174 TCTCCTTGATATCTTCGGTAAACATG 58.790 38.462 3.98 0.00 0.00 3.21
187 189 7.361457 TCTCCTTGATATCTTCGGTAAACAT 57.639 36.000 3.98 0.00 0.00 2.71
188 190 6.785337 TCTCCTTGATATCTTCGGTAAACA 57.215 37.500 3.98 0.00 0.00 2.83
189 191 6.201234 GCTTCTCCTTGATATCTTCGGTAAAC 59.799 42.308 3.98 0.00 0.00 2.01
190 192 6.281405 GCTTCTCCTTGATATCTTCGGTAAA 58.719 40.000 3.98 1.40 0.00 2.01
191 193 5.507482 CGCTTCTCCTTGATATCTTCGGTAA 60.507 44.000 3.98 1.66 0.00 2.85
192 194 4.023107 CGCTTCTCCTTGATATCTTCGGTA 60.023 45.833 3.98 0.00 0.00 4.02
365 381 6.648725 AGTTTCGTCAATATGCAACTAGTC 57.351 37.500 0.00 0.00 0.00 2.59
648 677 3.909430 ACAAATGCTTCAGAACATGCTG 58.091 40.909 0.00 0.00 37.24 4.41
803 843 1.440476 GGTAACCGGGATCACTCCG 59.560 63.158 6.32 2.21 43.11 4.63
840 880 2.046285 CCCTCGTTTGGCACCATCC 61.046 63.158 0.00 0.00 0.00 3.51
843 883 1.527380 GTTCCCTCGTTTGGCACCA 60.527 57.895 0.00 0.00 0.00 4.17
873 914 1.368641 TGGATGTTGTATCTGCACGC 58.631 50.000 0.00 0.00 0.00 5.34
879 920 5.889853 AGATGCATGTTTGGATGTTGTATCT 59.110 36.000 2.46 0.00 35.71 1.98
978 1029 3.849951 ATCGCATCGAACCCGCCT 61.850 61.111 0.00 0.00 39.99 5.52
980 1031 3.640000 CCATCGCATCGAACCCGC 61.640 66.667 0.00 0.00 39.99 6.13
1004 1055 3.960755 ACTACTTCCATGATGATCCGTGA 59.039 43.478 0.00 0.00 0.00 4.35
1036 1093 0.389391 CATTACCGCCATCGAGGACT 59.611 55.000 0.00 0.00 41.22 3.85
1072 1129 1.865788 CTACCGACGACCCCGAACAA 61.866 60.000 0.00 0.00 39.50 2.83
1112 1169 0.391597 TTCCTTGTCGTGACCCTGAC 59.608 55.000 0.00 0.00 35.67 3.51
1144 1201 1.609794 GTCGACCCTCCAAGACCCT 60.610 63.158 3.51 0.00 0.00 4.34
1178 1235 2.987821 GAGCCTCTACTTTCACAACGAC 59.012 50.000 0.00 0.00 0.00 4.34
1181 1238 3.126000 GCATGAGCCTCTACTTTCACAAC 59.874 47.826 0.00 0.00 33.58 3.32
1194 1251 0.390860 GACTACCATCGCATGAGCCT 59.609 55.000 0.00 0.00 37.52 4.58
1197 1254 2.120232 GTTCGACTACCATCGCATGAG 58.880 52.381 0.00 0.00 41.97 2.90
1206 1263 4.005650 AGATACGTCAAGTTCGACTACCA 58.994 43.478 0.00 0.00 33.54 3.25
1207 1264 4.093998 TCAGATACGTCAAGTTCGACTACC 59.906 45.833 0.00 0.00 33.54 3.18
1222 1279 0.030908 GTTCGGAGCCCTCAGATACG 59.969 60.000 0.00 0.00 34.02 3.06
1228 1285 1.982395 ATGACGTTCGGAGCCCTCA 60.982 57.895 0.00 0.00 0.00 3.86
1233 1290 0.172803 AGTACCATGACGTTCGGAGC 59.827 55.000 5.92 0.00 0.00 4.70
1237 1294 0.719465 GCCAAGTACCATGACGTTCG 59.281 55.000 0.00 0.00 0.00 3.95
1239 1296 0.690762 AGGCCAAGTACCATGACGTT 59.309 50.000 5.01 0.00 0.00 3.99
1240 1297 0.690762 AAGGCCAAGTACCATGACGT 59.309 50.000 5.01 0.00 0.00 4.34
1245 1302 2.514458 CCAAGAAGGCCAAGTACCAT 57.486 50.000 5.01 0.00 0.00 3.55
1282 1339 2.094390 GGTGATGTGTCAAGTACCGCTA 60.094 50.000 0.00 0.00 35.80 4.26
1285 1342 2.448926 TGGTGATGTGTCAAGTACCG 57.551 50.000 0.00 0.00 35.80 4.02
1295 1352 1.660607 GCACGACTACATGGTGATGTG 59.339 52.381 0.00 1.46 43.03 3.21
1296 1353 1.275010 TGCACGACTACATGGTGATGT 59.725 47.619 0.00 0.00 45.24 3.06
1298 1355 1.550524 AGTGCACGACTACATGGTGAT 59.449 47.619 12.01 0.00 39.28 3.06
1302 1359 1.726791 GACAAGTGCACGACTACATGG 59.273 52.381 12.01 0.00 33.09 3.66
1303 1360 1.386748 CGACAAGTGCACGACTACATG 59.613 52.381 12.01 5.91 33.09 3.21
1304 1361 1.268625 TCGACAAGTGCACGACTACAT 59.731 47.619 12.01 0.00 33.09 2.29
1307 1364 1.605232 TCTTCGACAAGTGCACGACTA 59.395 47.619 12.01 0.00 35.82 2.59
1310 1367 0.318699 CCTCTTCGACAAGTGCACGA 60.319 55.000 12.01 1.00 0.00 4.35
1312 1369 1.996191 GATCCTCTTCGACAAGTGCAC 59.004 52.381 9.40 9.40 0.00 4.57
1323 1380 1.224965 GATGCGCCAAGATCCTCTTC 58.775 55.000 4.18 0.00 33.78 2.87
1324 1381 0.179034 GGATGCGCCAAGATCCTCTT 60.179 55.000 15.35 0.00 37.14 2.85
1348 1405 0.463620 GGCCCTTTTGTGTTGCTTCA 59.536 50.000 0.00 0.00 0.00 3.02
1387 1444 3.721706 CCAGGGCCGCCTCTCTTT 61.722 66.667 9.86 0.00 0.00 2.52
1401 1458 2.361757 CTCTACTCACAGCTCCATCCAG 59.638 54.545 0.00 0.00 0.00 3.86
1402 1459 2.382882 CTCTACTCACAGCTCCATCCA 58.617 52.381 0.00 0.00 0.00 3.41
1403 1460 1.686052 CCTCTACTCACAGCTCCATCC 59.314 57.143 0.00 0.00 0.00 3.51
1404 1461 2.360801 GTCCTCTACTCACAGCTCCATC 59.639 54.545 0.00 0.00 0.00 3.51
1406 1463 1.075536 TGTCCTCTACTCACAGCTCCA 59.924 52.381 0.00 0.00 0.00 3.86
1408 1465 3.005897 TGTTTGTCCTCTACTCACAGCTC 59.994 47.826 0.00 0.00 0.00 4.09
1409 1466 2.965831 TGTTTGTCCTCTACTCACAGCT 59.034 45.455 0.00 0.00 0.00 4.24
1410 1467 3.321497 CTGTTTGTCCTCTACTCACAGC 58.679 50.000 0.00 0.00 34.28 4.40
1412 1469 2.632996 CCCTGTTTGTCCTCTACTCACA 59.367 50.000 0.00 0.00 0.00 3.58
1414 1471 2.897969 GTCCCTGTTTGTCCTCTACTCA 59.102 50.000 0.00 0.00 0.00 3.41
1418 3056 2.637872 CCAAGTCCCTGTTTGTCCTCTA 59.362 50.000 0.00 0.00 0.00 2.43
1420 3058 1.897560 CCAAGTCCCTGTTTGTCCTC 58.102 55.000 0.00 0.00 0.00 3.71
1455 3093 2.884087 TTCGCCTCCTCGTCAATCGC 62.884 60.000 0.00 0.00 39.67 4.58
1456 3094 0.867753 CTTCGCCTCCTCGTCAATCG 60.868 60.000 0.00 0.00 41.41 3.34
1460 3098 1.667154 CCATCTTCGCCTCCTCGTCA 61.667 60.000 0.00 0.00 0.00 4.35
1473 3111 3.036429 GCCGGACCTGCTCCATCTT 62.036 63.158 5.05 0.00 39.39 2.40
1482 3120 4.101448 CTCCCCTTGCCGGACCTG 62.101 72.222 5.05 0.00 33.16 4.00
1489 3127 4.748144 CCTGCACCTCCCCTTGCC 62.748 72.222 0.00 0.00 38.00 4.52
1549 3187 0.181587 CTCTGCCTCGACCTCCTCTA 59.818 60.000 0.00 0.00 0.00 2.43
1565 3203 4.101448 GCGCCATGTCCCACCTCT 62.101 66.667 0.00 0.00 0.00 3.69
1587 3225 0.744771 CTTCCTTAGCGCCAAGTCCC 60.745 60.000 14.47 0.00 0.00 4.46
1614 3252 3.402681 CAGGATCGGTGCCCCACT 61.403 66.667 0.00 0.00 34.40 4.00
1626 3264 0.465097 CCGCTTTGATCTGGCAGGAT 60.465 55.000 15.73 6.90 0.00 3.24
1631 3269 0.813210 CTCCTCCGCTTTGATCTGGC 60.813 60.000 0.00 0.00 0.00 4.85
1635 3273 0.179070 GTCCCTCCTCCGCTTTGATC 60.179 60.000 0.00 0.00 0.00 2.92
1649 3287 2.058675 CTCCAAGACCGTTGTCCCT 58.941 57.895 0.00 0.00 42.81 4.20
1653 3291 1.006102 CGAGCTCCAAGACCGTTGT 60.006 57.895 8.47 0.00 0.00 3.32
1660 3298 2.427453 GACTAATGACCGAGCTCCAAGA 59.573 50.000 8.47 0.00 0.00 3.02
1671 3309 1.680338 GCCATGGGTGACTAATGACC 58.320 55.000 15.13 0.00 0.00 4.02
1673 3311 1.199615 TCGCCATGGGTGACTAATGA 58.800 50.000 15.13 0.00 37.29 2.57
1674 3312 1.875514 CATCGCCATGGGTGACTAATG 59.124 52.381 15.13 0.09 45.43 1.90
1676 3314 0.463654 GCATCGCCATGGGTGACTAA 60.464 55.000 15.13 0.00 45.43 2.24
1677 3315 1.146041 GCATCGCCATGGGTGACTA 59.854 57.895 15.13 0.00 45.43 2.59
1712 3350 3.851128 TGACCACGACCAACGCCA 61.851 61.111 0.00 0.00 46.94 5.69
1715 3353 1.954146 CTGGTGACCACGACCAACG 60.954 63.158 0.00 0.00 43.02 4.10
1717 3355 2.110213 GCTGGTGACCACGACCAA 59.890 61.111 0.00 0.00 43.02 3.67
1742 3380 2.202570 CATCCCGTCGTCACGTCC 60.203 66.667 0.00 0.00 45.17 4.79
1747 3385 3.822192 CTCGCCATCCCGTCGTCA 61.822 66.667 0.00 0.00 0.00 4.35
1753 3391 4.598894 CTCTGCCTCGCCATCCCG 62.599 72.222 0.00 0.00 0.00 5.14
1755 3393 4.166888 TGCTCTGCCTCGCCATCC 62.167 66.667 0.00 0.00 0.00 3.51
1781 3419 3.356639 GATGACCGCTGCTGTCCGA 62.357 63.158 19.32 4.47 31.60 4.55
1818 3456 1.591504 TTGGGCCTTTTCGATTCGGC 61.592 55.000 4.53 10.01 41.75 5.54
1822 3460 0.114364 ACCCTTGGGCCTTTTCGATT 59.886 50.000 4.53 0.00 0.00 3.34
1827 3465 2.917227 CGCACCCTTGGGCCTTTT 60.917 61.111 4.53 0.00 0.00 2.27
1829 3467 4.351054 CTCGCACCCTTGGGCCTT 62.351 66.667 4.53 0.00 35.63 4.35
1833 3471 2.045926 CCTTCTCGCACCCTTGGG 60.046 66.667 3.77 3.77 37.01 4.12
1841 3479 4.069232 CTCGCACCCCTTCTCGCA 62.069 66.667 0.00 0.00 0.00 5.10
1856 3494 2.124403 CCTCTGGCCATGGCACTC 60.124 66.667 36.56 20.78 44.11 3.51
1859 3497 3.414193 CTCCCTCTGGCCATGGCA 61.414 66.667 36.56 21.67 44.11 4.92
1860 3498 3.092511 TCTCCCTCTGGCCATGGC 61.093 66.667 29.47 29.47 41.06 4.40
1866 3504 2.364842 TCAGCCTCTCCCTCTGGC 60.365 66.667 0.00 0.00 46.42 4.85
1954 3592 0.192064 ACTCTCATCCCGATCCCCAT 59.808 55.000 0.00 0.00 0.00 4.00
1967 3605 0.034960 CTCTCGTCCTCCCACTCTCA 60.035 60.000 0.00 0.00 0.00 3.27
2139 3788 9.331282 CTCTCTTTCTTTTCTCCAAAGTTCTAA 57.669 33.333 0.00 0.00 42.47 2.10
2388 4040 6.422100 GCCTTTCCTTCTTCAAGTTTTGATTC 59.578 38.462 0.00 0.00 39.84 2.52
2490 4173 8.946085 TCACATGGTGATTTCTCTTTATAACAC 58.054 33.333 0.00 0.00 37.67 3.32


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

AutoCloner maintained by Alex Coulton.