Multiple sequence alignment - TraesCS1D01G144700

Loading Multiple Alignment...

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 TraesCS1D01G144700 chr1D 100.000 4075 0 0 1 4075 199873314 199869240 0.000000e+00 7526.0
1 TraesCS1D01G144700 chr1D 100.000 2233 0 0 4268 6500 199869047 199866815 0.000000e+00 4124.0
2 TraesCS1D01G144700 chr1D 89.362 329 26 5 447 768 194536156 194535830 7.850000e-109 405.0
3 TraesCS1D01G144700 chr1D 96.970 165 5 0 6313 6477 356185773 356185937 1.780000e-70 278.0
4 TraesCS1D01G144700 chr1D 94.382 178 9 1 6310 6486 466603287 466603464 8.300000e-69 272.0
5 TraesCS1D01G144700 chr1D 90.805 87 7 1 5742 5827 320589945 320590031 1.480000e-21 115.0
6 TraesCS1D01G144700 chr1D 90.385 52 2 3 3988 4038 405082767 405082816 1.510000e-06 65.8
7 TraesCS1D01G144700 chr1D 100.000 31 0 0 3983 4013 323463627 323463597 2.530000e-04 58.4
8 TraesCS1D01G144700 chr1D 100.000 28 0 0 3668 3695 108104660 108104633 1.200000e-02 52.8
9 TraesCS1D01G144700 chr1B 97.081 4111 78 12 1 4074 286714978 286710873 0.000000e+00 6889.0
10 TraesCS1D01G144700 chr1B 98.792 2236 14 3 4269 6499 286710594 286708367 0.000000e+00 3967.0
11 TraesCS1D01G144700 chr1B 96.085 281 10 1 1818 2098 478710593 478710872 2.140000e-124 457.0
12 TraesCS1D01G144700 chr1B 91.935 62 4 1 3976 4037 60129220 60129160 1.160000e-12 86.1
13 TraesCS1D01G144700 chr1B 91.935 62 4 1 3976 4037 60275527 60275587 1.160000e-12 86.1
14 TraesCS1D01G144700 chr1B 91.935 62 2 3 3978 4038 614503617 614503558 4.180000e-12 84.2
15 TraesCS1D01G144700 chr1B 92.727 55 4 0 3984 4038 675450456 675450402 5.400000e-11 80.5
16 TraesCS1D01G144700 chr1A 96.225 2013 54 11 4314 6314 252504883 252502881 0.000000e+00 3277.0
17 TraesCS1D01G144700 chr1A 95.690 1972 56 13 2093 4043 252513761 252511798 0.000000e+00 3144.0
18 TraesCS1D01G144700 chr1A 92.632 950 42 14 820 1756 252518200 252517266 0.000000e+00 1341.0
19 TraesCS1D01G144700 chr1A 97.633 169 4 0 6309 6477 586112581 586112413 2.290000e-74 291.0
20 TraesCS1D01G144700 chr1A 74.468 329 58 13 3656 3973 287525881 287525568 1.140000e-22 119.0
21 TraesCS1D01G144700 chr1A 89.024 82 7 2 5743 5822 287311441 287311522 4.150000e-17 100.0
22 TraesCS1D01G144700 chr6B 96.466 283 9 1 1818 2100 64197583 64197864 3.550000e-127 466.0
23 TraesCS1D01G144700 chr6B 95.402 174 8 0 6305 6478 701379936 701380109 1.780000e-70 278.0
24 TraesCS1D01G144700 chr6B 93.011 186 10 2 6313 6498 603896890 603896708 1.070000e-67 268.0
25 TraesCS1D01G144700 chr6B 91.860 86 6 1 5743 5827 512188589 512188504 1.140000e-22 119.0
26 TraesCS1D01G144700 chr6B 90.588 85 6 2 5748 5830 618944027 618944111 1.920000e-20 111.0
27 TraesCS1D01G144700 chr2D 96.763 278 8 1 1818 2095 241688382 241688106 4.590000e-126 462.0
28 TraesCS1D01G144700 chr2D 90.090 333 26 4 445 771 251930727 251930396 6.020000e-115 425.0
29 TraesCS1D01G144700 chr7D 94.631 298 15 1 1818 2115 429475592 429475888 1.650000e-125 460.0
30 TraesCS1D01G144700 chr7D 89.297 327 28 4 445 765 114378476 114378151 2.820000e-108 403.0
31 TraesCS1D01G144700 chr7D 98.788 165 2 0 6313 6477 52255649 52255813 1.770000e-75 294.0
32 TraesCS1D01G144700 chr7D 92.473 186 14 0 6313 6498 565469662 565469477 3.860000e-67 267.0
33 TraesCS1D01G144700 chr7D 90.588 85 7 1 5746 5829 612833392 612833308 1.920000e-20 111.0
34 TraesCS1D01G144700 chr7D 90.909 55 4 1 3984 4038 28398702 28398755 9.040000e-09 73.1
35 TraesCS1D01G144700 chr7D 88.333 60 6 1 3979 4038 380924652 380924594 3.250000e-08 71.3
36 TraesCS1D01G144700 chr5B 96.403 278 9 1 1818 2095 342871819 342872095 2.140000e-124 457.0
37 TraesCS1D01G144700 chr5B 95.156 289 11 3 1818 2106 313138993 313139278 2.760000e-123 453.0
38 TraesCS1D01G144700 chr5B 93.878 294 17 1 1818 2111 692693342 692693050 5.980000e-120 442.0
39 TraesCS1D01G144700 chr5B 91.379 58 5 0 3979 4036 306437662 306437605 5.400000e-11 80.5
40 TraesCS1D01G144700 chr3D 95.423 284 12 1 1818 2101 263802734 263802452 9.940000e-123 451.0
41 TraesCS1D01G144700 chr3D 96.450 169 6 0 6309 6477 545912165 545912333 4.960000e-71 279.0
42 TraesCS1D01G144700 chr3D 88.506 87 9 1 5743 5828 48851074 48850988 3.210000e-18 104.0
43 TraesCS1D01G144700 chr3D 87.640 89 9 2 5745 5832 399377765 399377852 1.150000e-17 102.0
44 TraesCS1D01G144700 chr3D 92.857 56 4 0 3984 4039 433564296 433564241 1.500000e-11 82.4
45 TraesCS1D01G144700 chr3D 90.909 55 5 0 3984 4038 24872046 24871992 2.510000e-09 75.0
46 TraesCS1D01G144700 chr3A 89.254 335 29 4 438 765 408946481 408946147 4.690000e-111 412.0
47 TraesCS1D01G144700 chr5D 89.362 329 28 3 444 765 306485047 306484719 2.180000e-109 407.0
48 TraesCS1D01G144700 chr5D 88.922 334 28 6 445 771 181704011 181704342 2.820000e-108 403.0
49 TraesCS1D01G144700 chr5D 98.246 171 3 0 6310 6480 117350446 117350616 3.810000e-77 300.0
50 TraesCS1D01G144700 chr5D 97.006 167 5 0 6313 6479 386859292 386859458 1.380000e-71 281.0
51 TraesCS1D01G144700 chr5D 96.988 166 5 0 6313 6478 48668966 48669131 4.960000e-71 279.0
52 TraesCS1D01G144700 chr5D 93.956 182 9 2 6298 6478 339108901 339108721 2.310000e-69 274.0
53 TraesCS1D01G144700 chr5D 82.979 282 34 7 3671 3942 276311338 276311615 6.510000e-60 243.0
54 TraesCS1D01G144700 chr5D 88.889 54 4 2 3986 4038 343098806 343098858 1.510000e-06 65.8
55 TraesCS1D01G144700 chr4D 89.091 330 31 3 441 765 401027808 401027479 7.850000e-109 405.0
56 TraesCS1D01G144700 chr4D 95.906 171 7 0 6309 6479 93336852 93336682 1.780000e-70 278.0
57 TraesCS1D01G144700 chr4D 94.886 176 8 1 6309 6484 3370913 3371087 2.310000e-69 274.0
58 TraesCS1D01G144700 chr4D 95.858 169 7 0 6309 6477 243613268 243613436 2.310000e-69 274.0
59 TraesCS1D01G144700 chr4D 94.857 175 9 0 6313 6487 457481051 457481225 2.310000e-69 274.0
60 TraesCS1D01G144700 chr4D 95.833 168 7 0 6310 6477 23005227 23005394 8.300000e-69 272.0
61 TraesCS1D01G144700 chr4D 94.828 174 9 0 6304 6477 62120462 62120635 8.300000e-69 272.0
62 TraesCS1D01G144700 chr4D 94.798 173 9 0 6312 6484 423909747 423909575 2.990000e-68 270.0
63 TraesCS1D01G144700 chr4D 93.333 180 10 2 6301 6478 475146205 475146384 1.390000e-66 265.0
64 TraesCS1D01G144700 chr4D 79.747 316 53 5 3656 3961 323918624 323918938 1.100000e-52 219.0
65 TraesCS1D01G144700 chr4D 89.247 93 8 2 5740 5830 34699231 34699139 1.480000e-21 115.0
66 TraesCS1D01G144700 chr4D 90.698 86 7 1 5743 5827 459425898 459425983 5.330000e-21 113.0
67 TraesCS1D01G144700 chr4D 90.000 80 5 2 5744 5822 230473164 230473087 4.150000e-17 100.0
68 TraesCS1D01G144700 chr4A 89.297 327 28 4 445 765 329318257 329317932 2.820000e-108 403.0
69 TraesCS1D01G144700 chr4A 88.421 95 7 4 5740 5830 567678251 567678345 1.920000e-20 111.0
70 TraesCS1D01G144700 chr4A 94.643 56 3 0 3982 4037 346858293 346858238 3.230000e-13 87.9
71 TraesCS1D01G144700 chr6D 97.076 171 5 0 6308 6478 446533395 446533225 8.250000e-74 289.0
72 TraesCS1D01G144700 chr6D 97.576 165 4 0 6313 6477 305359627 305359791 3.840000e-72 283.0
73 TraesCS1D01G144700 chr6D 95.858 169 7 0 6310 6478 109240485 109240317 2.310000e-69 274.0
74 TraesCS1D01G144700 chr6D 96.386 166 6 0 6312 6477 218407375 218407210 2.310000e-69 274.0
75 TraesCS1D01G144700 chr6D 96.364 165 6 0 6313 6477 318765119 318764955 8.300000e-69 272.0
76 TraesCS1D01G144700 chr6D 96.914 162 5 0 6316 6477 460864658 460864497 8.300000e-69 272.0
77 TraesCS1D01G144700 chr6D 95.808 167 7 0 6313 6479 104041162 104041328 2.990000e-68 270.0
78 TraesCS1D01G144700 chr6D 91.099 191 13 4 6287 6477 463528888 463528702 8.360000e-64 255.0
79 TraesCS1D01G144700 chr6D 88.889 72 5 3 5744 5813 384535005 384535075 1.160000e-12 86.1
80 TraesCS1D01G144700 chr6D 87.500 72 7 2 5749 5818 2894264 2894335 1.500000e-11 82.4
81 TraesCS1D01G144700 chr6D 87.324 71 5 4 3970 4038 90441875 90441807 1.940000e-10 78.7
82 TraesCS1D01G144700 chr6D 87.500 56 5 2 3984 4038 141388867 141388813 5.440000e-06 63.9
83 TraesCS1D01G144700 chr6D 88.462 52 3 3 3988 4038 165527323 165527274 7.040000e-05 60.2
84 TraesCS1D01G144700 chr6D 100.000 31 0 0 3983 4013 33545668 33545698 2.530000e-04 58.4
85 TraesCS1D01G144700 chr4B 95.930 172 6 1 6307 6477 618189795 618189966 1.780000e-70 278.0
86 TraesCS1D01G144700 chr4B 77.709 323 54 10 3656 3961 404461728 404462049 1.440000e-41 182.0
87 TraesCS1D01G144700 chr2B 94.413 179 10 0 6306 6484 134045918 134045740 6.420000e-70 276.0
88 TraesCS1D01G144700 chr2B 92.941 85 5 1 5744 5827 754008534 754008450 8.850000e-24 122.0
89 TraesCS1D01G144700 chr5A 93.048 187 11 2 6312 6497 526657790 526657975 8.300000e-69 272.0
90 TraesCS1D01G144700 chrUn 95.266 169 8 0 6309 6477 112299385 112299217 1.070000e-67 268.0
91 TraesCS1D01G144700 chrUn 93.785 177 10 1 6308 6483 24831244 24831420 1.390000e-66 265.0
92 TraesCS1D01G144700 chrUn 93.785 177 10 1 6308 6483 24833762 24833938 1.390000e-66 265.0
93 TraesCS1D01G144700 chrUn 93.785 177 10 1 6308 6483 212860725 212860901 1.390000e-66 265.0
94 TraesCS1D01G144700 chrUn 95.181 166 8 0 6312 6477 92483865 92483700 5.000000e-66 263.0
95 TraesCS1D01G144700 chrUn 94.611 167 9 0 6311 6477 407971349 407971183 6.470000e-65 259.0
96 TraesCS1D01G144700 chrUn 94.545 165 9 0 6313 6477 105244422 105244586 8.360000e-64 255.0
97 TraesCS1D01G144700 chrUn 94.012 167 10 0 6311 6477 70231882 70231716 3.010000e-63 254.0
98 TraesCS1D01G144700 chrUn 93.064 173 12 0 6305 6477 178722331 178722503 3.010000e-63 254.0
99 TraesCS1D01G144700 chrUn 94.012 167 10 0 6311 6477 196159519 196159353 3.010000e-63 254.0
100 TraesCS1D01G144700 chrUn 93.064 173 12 0 6305 6477 315745862 315746034 3.010000e-63 254.0
101 TraesCS1D01G144700 chrUn 92.090 177 13 1 6311 6486 92777895 92777719 1.400000e-61 248.0
102 TraesCS1D01G144700 chrUn 90.811 185 15 1 6299 6483 309082373 309082555 5.030000e-61 246.0
103 TraesCS1D01G144700 chrUn 74.487 341 59 15 3656 3984 69338069 69337745 8.850000e-24 122.0
104 TraesCS1D01G144700 chrUn 75.281 267 57 5 3658 3922 306349245 306349504 1.140000e-22 119.0
105 TraesCS1D01G144700 chrUn 75.281 267 57 5 3658 3922 337028578 337028837 1.140000e-22 119.0
106 TraesCS1D01G144700 chrUn 74.194 341 60 15 3656 3984 69355654 69355330 4.120000e-22 117.0
107 TraesCS1D01G144700 chrUn 86.813 91 10 2 5743 5831 39577913 39577823 4.150000e-17 100.0
108 TraesCS1D01G144700 chrUn 90.698 43 4 0 3995 4037 450225570 450225528 2.530000e-04 58.4
109 TraesCS1D01G144700 chr6A 91.860 86 6 1 5743 5827 64260789 64260704 1.140000e-22 119.0
110 TraesCS1D01G144700 chr6A 88.000 75 7 2 5744 5816 529049093 529049167 3.230000e-13 87.9
111 TraesCS1D01G144700 chr6A 88.525 61 3 4 3979 4038 68625737 68625680 3.250000e-08 71.3
112 TraesCS1D01G144700 chr6A 90.196 51 3 2 3984 4033 262302450 262302499 1.510000e-06 65.8


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 TraesCS1D01G144700 chr1D 199866815 199873314 6499 True 5825.0 7526 100.0000 1 6500 2 chr1D.!!$R4 6499
1 TraesCS1D01G144700 chr1B 286708367 286714978 6611 True 5428.0 6889 97.9365 1 6499 2 chr1B.!!$R4 6498
2 TraesCS1D01G144700 chr1A 252502881 252504883 2002 True 3277.0 3277 96.2250 4314 6314 1 chr1A.!!$R1 2000
3 TraesCS1D01G144700 chr1A 252511798 252518200 6402 True 2242.5 3144 94.1610 820 4043 2 chr1A.!!$R4 3223
4 TraesCS1D01G144700 chrUn 24831244 24833938 2694 False 265.0 265 93.7850 6308 6483 2 chrUn.!!$F8 175

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
900 909 0.889306 ACCAGTTCGGCTACAGAGAC 59.111 55.000 0.0 0.0 39.03 3.36 F
1871 5004 4.044065 TGGGTTTCATATCCAAAGGACTGT 59.956 41.667 0.0 0.0 32.98 3.55 F
2038 5171 0.613260 TCGCCAAGCCTATCACAACT 59.387 50.000 0.0 0.0 0.00 3.16 F
2040 5173 1.383523 GCCAAGCCTATCACAACTCC 58.616 55.000 0.0 0.0 0.00 3.85 F
4074 7439 2.844946 TGATACAGGGTTGTGTGTGTG 58.155 47.619 0.0 0.0 38.23 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 5171 2.041596 CCCGGGTAAAGGAGGGGA 59.958 66.667 14.18 0.0 40.51 4.81 R
3743 7108 2.139917 CTACAGCGCAACTACCAAACA 58.860 47.619 11.47 0.0 0.00 2.83 R
4043 7408 5.127031 ACAACCCTGTATCATTTTGGCATAC 59.873 40.000 0.00 0.0 32.54 2.39 R
4267 7632 1.066908 CGGCTCTCCAAAAGCACAAAA 59.933 47.619 0.00 0.0 41.66 2.44 R
6145 9603 2.684881 CTGCAGTTCAACAAGTGTTCCT 59.315 45.455 5.25 0.0 35.83 3.36 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
33 34 2.123180 TTGGACTAGGCGGGGGAA 59.877 61.111 0.00 0.00 0.00 3.97
67 68 5.737290 CACGTGTTTGACTTTTCTTTACAGG 59.263 40.000 7.58 0.00 0.00 4.00
132 133 2.648454 GTGCGACCGGCCAAAATT 59.352 55.556 0.00 0.00 42.61 1.82
136 137 1.154112 CGACCGGCCAAAATTTCGG 60.154 57.895 12.95 12.95 46.95 4.30
147 148 1.247419 AAATTTCGGCCGATGCACCA 61.247 50.000 31.56 10.33 40.13 4.17
223 225 3.644335 AGAAAGATAGGTAGAAGGCGGT 58.356 45.455 0.00 0.00 0.00 5.68
229 231 6.496144 AGATAGGTAGAAGGCGGTTAAAAT 57.504 37.500 0.00 0.00 0.00 1.82
236 238 4.003648 AGAAGGCGGTTAAAATCAGTCAG 58.996 43.478 0.00 0.00 0.00 3.51
246 248 7.305993 CGGTTAAAATCAGTCAGTTTTCTTTGC 60.306 37.037 0.00 0.00 0.00 3.68
322 324 3.052455 TCTTAGATCGTTTGGCAGCAA 57.948 42.857 0.00 0.00 0.00 3.91
326 328 3.221964 AGATCGTTTGGCAGCAAAATC 57.778 42.857 0.00 0.00 0.00 2.17
328 330 2.132740 TCGTTTGGCAGCAAAATCAC 57.867 45.000 0.00 0.00 0.00 3.06
329 331 1.406898 TCGTTTGGCAGCAAAATCACA 59.593 42.857 0.00 0.00 0.00 3.58
359 363 1.336125 TGATTGCATTGCACACGAACA 59.664 42.857 11.66 0.00 38.71 3.18
360 364 1.715519 GATTGCATTGCACACGAACAC 59.284 47.619 11.66 0.00 38.71 3.32
425 429 2.425143 ATGTGCTAGGTGGTCCAATG 57.575 50.000 0.00 0.00 35.89 2.82
488 492 5.138125 TGGCTCAATTCAAAAATCTCACC 57.862 39.130 0.00 0.00 0.00 4.02
501 505 7.890127 TCAAAAATCTCACCAACCAAGATAGAT 59.110 33.333 0.00 0.00 0.00 1.98
505 509 5.922053 TCTCACCAACCAAGATAGATGATG 58.078 41.667 0.00 0.00 0.00 3.07
516 520 6.259608 CCAAGATAGATGATGAGTGGTGAAAC 59.740 42.308 0.00 0.00 0.00 2.78
518 522 7.134362 AGATAGATGATGAGTGGTGAAACAT 57.866 36.000 0.00 0.00 39.98 2.71
626 635 9.849166 CATGCATGCATAAAATACATCTATTGA 57.151 29.630 31.73 0.00 34.91 2.57
749 758 7.775053 AAAATTGAGATAAGCCCTGTAAACA 57.225 32.000 0.00 0.00 0.00 2.83
798 807 2.945008 ACGTTGTAGGATTATCGGACGA 59.055 45.455 0.00 0.00 33.86 4.20
900 909 0.889306 ACCAGTTCGGCTACAGAGAC 59.111 55.000 0.00 0.00 39.03 3.36
1796 1828 4.278170 CCAACTCTAGCCATGTTCAAACAA 59.722 41.667 0.00 0.00 43.03 2.83
1871 5004 4.044065 TGGGTTTCATATCCAAAGGACTGT 59.956 41.667 0.00 0.00 32.98 3.55
2038 5171 0.613260 TCGCCAAGCCTATCACAACT 59.387 50.000 0.00 0.00 0.00 3.16
2040 5173 1.383523 GCCAAGCCTATCACAACTCC 58.616 55.000 0.00 0.00 0.00 3.85
2209 5542 3.389002 AGGCAGCCAAAGAAAAAGAACAT 59.611 39.130 15.80 0.00 0.00 2.71
2405 5755 5.101628 TCATTTATTTCATTCGCAGGTTGC 58.898 37.500 0.00 0.00 40.69 4.17
3485 6836 7.038587 AGGTAATGTATCTGGTCTGTTAACACA 60.039 37.037 3.59 0.52 0.00 3.72
3521 6872 9.433153 TGCATGTTTAAATTCATTATCTGCAAA 57.567 25.926 0.00 0.00 0.00 3.68
3638 6989 8.807667 ACATTTCTCAAAAATACTTCTGCTTG 57.192 30.769 0.00 0.00 0.00 4.01
3743 7108 3.118531 AGATTGGAGCCAAGATACAGGT 58.881 45.455 8.09 0.00 39.47 4.00
4043 7408 2.951642 TCTCAAGTCAAACTTTGGCCAG 59.048 45.455 5.11 0.00 36.03 4.85
4074 7439 2.844946 TGATACAGGGTTGTGTGTGTG 58.155 47.619 0.00 0.00 38.23 3.82
4748 8202 4.735369 TGGGAATTTCACCACATTACAGT 58.265 39.130 0.00 0.00 0.00 3.55
6145 9603 1.358402 GTGCCGTGTGTTGCAATCA 59.642 52.632 0.59 2.54 39.57 2.57
6232 9693 9.797556 ACATTTGTTTAAGACTTTAAGTTCACC 57.202 29.630 0.00 0.00 30.84 4.02
6318 9779 8.573035 TGACATTTAAACTTTTCATGTACTCCC 58.427 33.333 0.00 0.00 29.28 4.30
6319 9780 8.706322 ACATTTAAACTTTTCATGTACTCCCT 57.294 30.769 0.00 0.00 0.00 4.20
6320 9781 8.793592 ACATTTAAACTTTTCATGTACTCCCTC 58.206 33.333 0.00 0.00 0.00 4.30
6321 9782 7.754851 TTTAAACTTTTCATGTACTCCCTCC 57.245 36.000 0.00 0.00 0.00 4.30
6435 9896 3.119602 TGCTCCGTATGTAGTCACTTGTC 60.120 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.100087 GTCAAACACGTGTTCCCCAATT 59.900 45.455 32.36 13.74 37.25 2.32
67 68 1.750682 GCCATTGGATAGGTGGTCCAC 60.751 57.143 14.13 14.13 45.05 4.02
127 128 0.108851 GGTGCATCGGCCGAAATTTT 60.109 50.000 34.66 13.09 40.13 1.82
141 142 2.438254 CTAATGGGCGCTGGTGCA 60.438 61.111 7.64 0.00 39.64 4.57
195 197 7.561251 GCCTTCTACCTATCTTTCTTCTCTTT 58.439 38.462 0.00 0.00 0.00 2.52
223 225 9.033481 CATGCAAAGAAAACTGACTGATTTTAA 57.967 29.630 0.00 0.00 0.00 1.52
229 231 4.639755 TCACATGCAAAGAAAACTGACTGA 59.360 37.500 0.00 0.00 0.00 3.41
246 248 7.967854 TCGCCAAAAAGAGTTATTTATCACATG 59.032 33.333 0.00 0.00 0.00 3.21
305 307 3.755905 TGATTTTGCTGCCAAACGATCTA 59.244 39.130 0.59 0.00 40.45 1.98
307 309 2.663119 GTGATTTTGCTGCCAAACGATC 59.337 45.455 0.59 0.00 40.45 3.69
322 324 5.653330 TGCAATCATGTAGGTGATGTGATTT 59.347 36.000 0.00 0.00 38.76 2.17
326 328 5.278604 CAATGCAATCATGTAGGTGATGTG 58.721 41.667 0.00 0.00 38.76 3.21
328 330 4.202070 TGCAATGCAATCATGTAGGTGATG 60.202 41.667 5.01 0.00 38.76 3.07
329 331 3.955551 TGCAATGCAATCATGTAGGTGAT 59.044 39.130 5.01 0.00 40.44 3.06
359 363 2.163810 TAGGTGTAGCATTACCCCGT 57.836 50.000 0.00 0.00 37.70 5.28
360 364 2.367567 ACATAGGTGTAGCATTACCCCG 59.632 50.000 0.00 0.00 36.63 5.73
412 416 5.016173 CCTCAAATTTCATTGGACCACCTA 58.984 41.667 0.00 0.00 37.04 3.08
452 456 9.434420 TTGAATTGAGCCATATAAACCAAAAAG 57.566 29.630 0.00 0.00 0.00 2.27
469 473 6.514947 TGGTTGGTGAGATTTTTGAATTGAG 58.485 36.000 0.00 0.00 0.00 3.02
488 492 5.526479 CACCACTCATCATCTATCTTGGTTG 59.474 44.000 0.00 0.00 33.77 3.77
725 734 7.775053 TGTTTACAGGGCTTATCTCAATTTT 57.225 32.000 0.00 0.00 0.00 1.82
742 751 3.323775 ACTCCCTCCTTTCCTGTTTACA 58.676 45.455 0.00 0.00 0.00 2.41
749 758 3.601537 TCCTAACTACTCCCTCCTTTCCT 59.398 47.826 0.00 0.00 0.00 3.36
829 838 2.546789 GTCTCAAATTCGTGTCGGGTTT 59.453 45.455 0.00 0.00 0.00 3.27
1796 1828 4.699735 TGATGCGATACCAACAACTCATTT 59.300 37.500 0.00 0.00 0.00 2.32
1810 1842 3.239449 ACTAGGATTGGGTGATGCGATA 58.761 45.455 0.00 0.00 0.00 2.92
1813 1845 2.365617 AGTACTAGGATTGGGTGATGCG 59.634 50.000 0.00 0.00 0.00 4.73
1871 5004 2.733026 GCGAGCCAACGTAAAAACTAGA 59.267 45.455 0.00 0.00 35.59 2.43
2038 5171 2.041596 CCCGGGTAAAGGAGGGGA 59.958 66.667 14.18 0.00 40.51 4.81
2040 5173 2.306384 AAGCCCGGGTAAAGGAGGG 61.306 63.158 24.63 0.00 46.44 4.30
3743 7108 2.139917 CTACAGCGCAACTACCAAACA 58.860 47.619 11.47 0.00 0.00 2.83
4043 7408 5.127031 ACAACCCTGTATCATTTTGGCATAC 59.873 40.000 0.00 0.00 32.54 2.39
4267 7632 1.066908 CGGCTCTCCAAAAGCACAAAA 59.933 47.619 0.00 0.00 41.66 2.44
5245 8699 4.035208 GGAAACACACTGGAGTACACAAAG 59.965 45.833 0.00 0.00 0.00 2.77
6145 9603 2.684881 CTGCAGTTCAACAAGTGTTCCT 59.315 45.455 5.25 0.00 35.83 3.36


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

AutoCloner maintained by Alex Coulton.