Multiple sequence alignment - TraesCS1D01G096000

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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 TraesCS1D01G096000 chr1D 100.000 2856 0 0 2928 5783 81286443 81289298 0.000000e+00 5275.0
1 TraesCS1D01G096000 chr1D 100.000 2444 0 0 1 2444 81283516 81285959 0.000000e+00 4514.0
2 TraesCS1D01G096000 chr1D 91.404 2350 124 27 2929 5229 81176931 81179251 0.000000e+00 3149.0
3 TraesCS1D01G096000 chr1D 90.189 795 65 8 1641 2428 81175980 81176768 0.000000e+00 1024.0
4 TraesCS1D01G096000 chr1D 94.758 496 18 7 203 695 81174407 81174897 0.000000e+00 765.0
5 TraesCS1D01G096000 chr1D 91.667 540 29 6 4695 5229 81185020 81185548 0.000000e+00 734.0
6 TraesCS1D01G096000 chr1D 90.943 541 26 7 4691 5229 81182488 81183007 0.000000e+00 706.0
7 TraesCS1D01G096000 chr1D 93.722 446 14 3 698 1141 81175329 81175762 0.000000e+00 656.0
8 TraesCS1D01G096000 chr1D 92.287 363 15 7 5230 5591 36869838 36870188 2.410000e-138 503.0
9 TraesCS1D01G096000 chr1D 87.963 324 25 11 5226 5542 303332927 303332611 2.550000e-98 370.0
10 TraesCS1D01G096000 chr1D 76.439 747 105 30 2929 3643 157720242 157719535 7.180000e-89 339.0
11 TraesCS1D01G096000 chr1D 93.600 125 6 1 80 204 386156705 386156827 9.900000e-43 185.0
12 TraesCS1D01G096000 chr1D 83.978 181 29 0 3690 3870 474900612 474900432 2.140000e-39 174.0
13 TraesCS1D01G096000 chr1D 77.689 251 52 3 3640 3886 474883726 474883476 3.610000e-32 150.0
14 TraesCS1D01G096000 chr1D 84.536 97 14 1 3329 3425 323672331 323672236 1.720000e-15 95.3
15 TraesCS1D01G096000 chr1D 84.211 95 15 0 4613 4707 469811279 469811373 6.170000e-15 93.5
16 TraesCS1D01G096000 chr1D 72.238 353 79 10 4442 4783 18079325 18078981 2.220000e-14 91.6
17 TraesCS1D01G096000 chr1B 97.714 2231 41 7 203 2430 134642470 134644693 0.000000e+00 3829.0
18 TraesCS1D01G096000 chr1B 98.984 2066 20 1 3164 5229 134574333 134576397 0.000000e+00 3698.0
19 TraesCS1D01G096000 chr1B 97.888 1989 39 3 447 2433 134572007 134573994 0.000000e+00 3437.0
20 TraesCS1D01G096000 chr1B 94.147 1999 88 10 3234 5229 134436387 134438359 0.000000e+00 3016.0
21 TraesCS1D01G096000 chr1B 98.452 1227 7 1 4000 5226 134645377 134646591 0.000000e+00 2150.0
22 TraesCS1D01G096000 chr1B 90.977 809 62 8 1624 2428 134435091 134435892 0.000000e+00 1079.0
23 TraesCS1D01G096000 chr1B 94.019 535 18 6 4695 5229 134450213 134450733 0.000000e+00 798.0
24 TraesCS1D01G096000 chr1B 93.952 496 21 8 203 695 134430385 134430874 0.000000e+00 741.0
25 TraesCS1D01G096000 chr1B 90.058 513 29 6 4718 5229 134452391 134452882 0.000000e+00 645.0
26 TraesCS1D01G096000 chr1B 96.875 288 7 1 2928 3213 134645090 134645377 1.130000e-131 481.0
27 TraesCS1D01G096000 chr1B 91.667 348 15 2 796 1141 134434755 134435090 2.440000e-128 470.0
28 TraesCS1D01G096000 chr1B 98.473 262 2 2 203 464 134571686 134571945 1.470000e-125 460.0
29 TraesCS1D01G096000 chr1B 96.591 176 4 1 2928 3101 134574165 134574340 2.040000e-74 291.0
30 TraesCS1D01G096000 chr1B 100.000 98 0 0 2 99 134642374 134642471 1.280000e-41 182.0
31 TraesCS1D01G096000 chr1B 98.980 98 1 0 2 99 134571590 134571687 5.960000e-40 176.0
32 TraesCS1D01G096000 chr1B 80.591 237 39 5 3739 3973 660013012 660012781 5.960000e-40 176.0
33 TraesCS1D01G096000 chr1B 96.907 97 2 1 709 804 134433114 134433210 1.670000e-35 161.0
34 TraesCS1D01G096000 chr1A 91.521 2347 124 29 2929 5229 99904605 99906922 0.000000e+00 3162.0
35 TraesCS1D01G096000 chr1A 90.447 806 66 7 1628 2428 99903655 99904454 0.000000e+00 1051.0
36 TraesCS1D01G096000 chr1A 92.377 446 20 3 698 1141 99903217 99903650 1.770000e-174 623.0
37 TraesCS1D01G096000 chr1A 94.464 289 10 5 203 489 99897137 99897421 1.910000e-119 440.0
38 TraesCS1D01G096000 chr1A 94.393 214 9 3 484 695 99900285 99900497 5.590000e-85 326.0
39 TraesCS1D01G096000 chr1A 82.967 182 31 0 3690 3871 570423265 570423084 1.290000e-36 165.0
40 TraesCS1D01G096000 chr1A 72.709 491 108 18 4312 4783 20237080 20236597 2.170000e-29 141.0
41 TraesCS1D01G096000 chr1A 72.653 490 105 21 4313 4783 20245269 20244790 1.010000e-27 135.0
42 TraesCS1D01G096000 chr1A 88.776 98 10 1 3303 3400 380993455 380993551 1.020000e-22 119.0
43 TraesCS1D01G096000 chr7B 82.196 674 90 10 3915 4583 33012333 33011685 2.350000e-153 553.0
44 TraesCS1D01G096000 chr7B 85.630 341 36 9 1096 1435 33066112 33065784 4.290000e-91 346.0
45 TraesCS1D01G096000 chr7B 83.333 288 39 5 3640 3919 33065379 33065093 2.070000e-64 257.0
46 TraesCS1D01G096000 chr7B 85.417 192 24 4 797 987 33066615 33066427 4.570000e-46 196.0
47 TraesCS1D01G096000 chr7B 81.034 174 33 0 1693 1866 33065545 33065372 7.810000e-29 139.0
48 TraesCS1D01G096000 chr4D 96.165 339 10 2 5230 5568 119893018 119893353 8.470000e-153 551.0
49 TraesCS1D01G096000 chr4D 87.597 387 15 25 5226 5611 83868775 83869129 8.960000e-113 418.0
50 TraesCS1D01G096000 chr4D 91.582 297 15 6 5230 5517 329872842 329872547 9.030000e-108 401.0
51 TraesCS1D01G096000 chr4D 84.375 416 54 9 3231 3642 442885535 442885943 1.170000e-106 398.0
52 TraesCS1D01G096000 chr4D 83.894 416 56 7 3231 3642 442876248 442875840 2.530000e-103 387.0
53 TraesCS1D01G096000 chr4D 85.714 371 33 18 5230 5591 119907049 119906690 1.970000e-99 374.0
54 TraesCS1D01G096000 chr4D 78.967 271 52 3 2936 3206 442876602 442876337 4.600000e-41 180.0
55 TraesCS1D01G096000 chr4D 91.603 131 8 3 86 216 57472579 57472706 1.660000e-40 178.0
56 TraesCS1D01G096000 chr4D 97.619 84 2 0 5700 5783 119893690 119893773 1.680000e-30 145.0
57 TraesCS1D01G096000 chr2D 86.719 384 18 16 5228 5611 328345845 328346195 4.200000e-106 396.0
58 TraesCS1D01G096000 chr2D 95.798 238 7 3 5230 5466 353273796 353273561 1.180000e-101 381.0
59 TraesCS1D01G096000 chr6D 85.838 346 28 12 5230 5567 266792010 266791678 1.190000e-91 348.0
60 TraesCS1D01G096000 chr6D 88.525 122 9 4 3325 3441 430039856 430039977 6.040000e-30 143.0
61 TraesCS1D01G096000 chr7A 85.061 328 41 5 707 1028 85200727 85200402 1.550000e-85 327.0
62 TraesCS1D01G096000 chr7A 87.045 247 25 5 1096 1341 85199834 85199594 7.380000e-69 272.0
63 TraesCS1D01G096000 chr7A 97.345 113 2 1 95 206 645027110 645027222 2.130000e-44 191.0
64 TraesCS1D01G096000 chr7A 94.958 119 5 1 88 206 381253914 381254031 9.900000e-43 185.0
65 TraesCS1D01G096000 chr7A 80.328 122 17 5 3522 3642 287488788 287488903 1.030000e-12 86.1
66 TraesCS1D01G096000 chrUn 79.643 280 51 4 2929 3206 471727356 471727081 4.570000e-46 196.0
67 TraesCS1D01G096000 chr6A 96.522 115 3 1 91 204 190598830 190598716 7.650000e-44 189.0
68 TraesCS1D01G096000 chr2A 95.726 117 4 1 92 208 78333703 78333818 2.750000e-43 187.0
69 TraesCS1D01G096000 chr2A 85.000 120 9 6 3525 3642 475364886 475364998 4.740000e-21 113.0
70 TraesCS1D01G096000 chr3B 93.600 125 6 2 91 213 217773282 217773158 9.900000e-43 185.0
71 TraesCS1D01G096000 chr4A 94.118 119 6 1 98 216 628491116 628490999 4.600000e-41 180.0
72 TraesCS1D01G096000 chr4A 82.609 92 11 3 3554 3641 207290692 207290782 6.210000e-10 76.8
73 TraesCS1D01G096000 chr3D 92.742 124 8 1 88 210 572130993 572131116 1.660000e-40 178.0
74 TraesCS1D01G096000 chr5B 78.689 122 18 6 3522 3641 357112582 357112697 2.230000e-09 75.0


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 TraesCS1D01G096000 chr1D 81283516 81289298 5782 False 4894.500000 5275 100.000000 1 5783 2 chr1D.!!$F5 5782
1 TraesCS1D01G096000 chr1D 81174407 81185548 11141 False 1172.333333 3149 92.113833 203 5229 6 chr1D.!!$F4 5026
2 TraesCS1D01G096000 chr1D 157719535 157720242 707 True 339.000000 339 76.439000 2929 3643 1 chr1D.!!$R2 714
3 TraesCS1D01G096000 chr1B 134642374 134646591 4217 False 1660.500000 3829 98.260250 2 5226 4 chr1B.!!$F4 5224
4 TraesCS1D01G096000 chr1B 134571590 134576397 4807 False 1612.400000 3698 98.183200 2 5229 5 chr1B.!!$F3 5227
5 TraesCS1D01G096000 chr1B 134430385 134438359 7974 False 1093.400000 3016 93.530000 203 5229 5 chr1B.!!$F1 5026
6 TraesCS1D01G096000 chr1B 134450213 134452882 2669 False 721.500000 798 92.038500 4695 5229 2 chr1B.!!$F2 534
7 TraesCS1D01G096000 chr1A 99897137 99906922 9785 False 1120.400000 3162 92.640400 203 5229 5 chr1A.!!$F2 5026
8 TraesCS1D01G096000 chr7B 33011685 33012333 648 True 553.000000 553 82.196000 3915 4583 1 chr7B.!!$R1 668
9 TraesCS1D01G096000 chr7B 33065093 33066615 1522 True 234.500000 346 83.853500 797 3919 4 chr7B.!!$R2 3122
10 TraesCS1D01G096000 chr4D 119893018 119893773 755 False 348.000000 551 96.892000 5230 5783 2 chr4D.!!$F4 553
11 TraesCS1D01G096000 chr4D 442875840 442876602 762 True 283.500000 387 81.430500 2936 3642 2 chr4D.!!$R3 706
12 TraesCS1D01G096000 chr7A 85199594 85200727 1133 True 299.500000 327 86.053000 707 1341 2 chr7A.!!$R1 634

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
137 138 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06 F
191 192 1.206132 ACATGCGACAGGTAATTCGGA 59.794 47.619 0.00 0.00 40.02 4.55 F
1992 10137 1.228552 GTGGCTGATTGGGTGGTGT 60.229 57.895 0.00 0.00 0.00 4.16 F
2366 10515 0.392461 GCGTCTGGCCATTGGTAAGA 60.392 55.000 5.51 5.06 34.80 2.10 F
2443 10592 1.454976 CTCCCATCCCTGCCAGATG 59.545 63.158 0.00 0.00 40.71 2.90 F
3265 11485 1.673009 TGGACGTCGCCATTTTCCC 60.673 57.895 9.92 0.00 31.66 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 9516 0.551624 TCTAGGGTTTGGGAAGGGGG 60.552 60.000 0.00 0.0 0.00 5.40 R
2267 10415 1.000521 CATCACAGCCCACACCCAT 60.001 57.895 0.00 0.0 0.00 4.00 R
2934 11083 1.448717 GAGAAGAGGTGAAGCGGGC 60.449 63.158 0.00 0.0 0.00 6.13 R
3374 11595 1.817099 CCGTGAGCTCCAAGATGGC 60.817 63.158 12.15 0.0 37.47 4.40 R
3790 12036 3.343972 GCACTTGAAGCGGCAGAA 58.656 55.556 1.45 0.0 0.00 3.02 R
5195 13450 2.644676 CTCGAAAAATCCTCTTCCCCC 58.355 52.381 0.00 0.0 0.00 5.40 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
107 108 7.729116 TGGTTTACTAAATTATACTCCCTCCG 58.271 38.462 0.00 0.00 0.00 4.63
108 109 7.345392 TGGTTTACTAAATTATACTCCCTCCGT 59.655 37.037 0.00 0.00 0.00 4.69
109 110 8.206867 GGTTTACTAAATTATACTCCCTCCGTT 58.793 37.037 0.00 0.00 0.00 4.44
110 111 9.254133 GTTTACTAAATTATACTCCCTCCGTTC 57.746 37.037 0.00 0.00 0.00 3.95
111 112 8.773033 TTACTAAATTATACTCCCTCCGTTCT 57.227 34.615 0.00 0.00 0.00 3.01
112 113 9.866655 TTACTAAATTATACTCCCTCCGTTCTA 57.133 33.333 0.00 0.00 0.00 2.10
113 114 8.773033 ACTAAATTATACTCCCTCCGTTCTAA 57.227 34.615 0.00 0.00 0.00 2.10
114 115 9.205513 ACTAAATTATACTCCCTCCGTTCTAAA 57.794 33.333 0.00 0.00 0.00 1.85
118 119 9.993454 AATTATACTCCCTCCGTTCTAAATTAC 57.007 33.333 0.00 0.00 0.00 1.89
119 120 8.773033 TTATACTCCCTCCGTTCTAAATTACT 57.227 34.615 0.00 0.00 0.00 2.24
120 121 5.595257 ACTCCCTCCGTTCTAAATTACTC 57.405 43.478 0.00 0.00 0.00 2.59
121 122 4.097589 ACTCCCTCCGTTCTAAATTACTCG 59.902 45.833 0.00 0.00 0.00 4.18
122 123 4.019174 TCCCTCCGTTCTAAATTACTCGT 58.981 43.478 0.00 0.00 0.00 4.18
123 124 4.096984 TCCCTCCGTTCTAAATTACTCGTC 59.903 45.833 0.00 0.00 0.00 4.20
124 125 4.033684 CCTCCGTTCTAAATTACTCGTCG 58.966 47.826 0.00 0.00 0.00 5.12
125 126 3.429085 TCCGTTCTAAATTACTCGTCGC 58.571 45.455 0.00 0.00 0.00 5.19
126 127 3.119884 TCCGTTCTAAATTACTCGTCGCA 60.120 43.478 0.00 0.00 0.00 5.10
127 128 3.239941 CCGTTCTAAATTACTCGTCGCAG 59.760 47.826 0.00 0.00 0.00 5.18
128 129 4.093514 CGTTCTAAATTACTCGTCGCAGA 58.906 43.478 0.00 0.00 0.00 4.26
129 130 4.556135 CGTTCTAAATTACTCGTCGCAGAA 59.444 41.667 0.00 0.00 39.69 3.02
130 131 5.060077 CGTTCTAAATTACTCGTCGCAGAAA 59.940 40.000 0.00 0.00 39.69 2.52
131 132 6.237490 CGTTCTAAATTACTCGTCGCAGAAAT 60.237 38.462 0.00 0.00 39.69 2.17
132 133 6.569228 TCTAAATTACTCGTCGCAGAAATG 57.431 37.500 0.00 0.00 39.69 2.32
133 134 4.600012 AAATTACTCGTCGCAGAAATGG 57.400 40.909 0.00 0.00 39.69 3.16
134 135 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
135 136 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
136 137 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
137 138 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
138 139 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
139 140 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
140 141 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
141 142 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
142 143 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
143 144 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
144 145 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
145 146 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
146 147 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
147 148 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
148 149 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
149 150 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
150 151 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
177 178 9.741647 ATACATCTAGATACATTCATACATGCG 57.258 33.333 4.54 0.00 0.00 4.73
178 179 7.830739 ACATCTAGATACATTCATACATGCGA 58.169 34.615 4.54 0.00 0.00 5.10
179 180 7.757173 ACATCTAGATACATTCATACATGCGAC 59.243 37.037 4.54 0.00 0.00 5.19
180 181 7.214467 TCTAGATACATTCATACATGCGACA 57.786 36.000 0.00 0.00 0.00 4.35
181 182 7.308435 TCTAGATACATTCATACATGCGACAG 58.692 38.462 0.00 0.00 0.00 3.51
182 183 5.233225 AGATACATTCATACATGCGACAGG 58.767 41.667 0.00 0.00 0.00 4.00
183 184 3.266510 ACATTCATACATGCGACAGGT 57.733 42.857 0.00 2.98 31.84 4.00
184 185 4.400529 ACATTCATACATGCGACAGGTA 57.599 40.909 6.78 6.78 35.17 3.08
185 186 4.765273 ACATTCATACATGCGACAGGTAA 58.235 39.130 8.07 0.00 34.39 2.85
186 187 5.368145 ACATTCATACATGCGACAGGTAAT 58.632 37.500 8.07 0.00 34.39 1.89
187 188 5.822519 ACATTCATACATGCGACAGGTAATT 59.177 36.000 8.07 0.00 34.39 1.40
188 189 5.984233 TTCATACATGCGACAGGTAATTC 57.016 39.130 8.07 0.00 34.39 2.17
189 190 4.048504 TCATACATGCGACAGGTAATTCG 58.951 43.478 8.07 0.00 34.39 3.34
190 191 1.651987 ACATGCGACAGGTAATTCGG 58.348 50.000 0.00 0.00 35.73 4.30
191 192 1.206132 ACATGCGACAGGTAATTCGGA 59.794 47.619 0.00 0.00 40.02 4.55
192 193 2.276201 CATGCGACAGGTAATTCGGAA 58.724 47.619 0.00 0.00 39.13 4.30
193 194 1.717194 TGCGACAGGTAATTCGGAAC 58.283 50.000 0.00 0.00 35.73 3.62
310 312 7.243604 TGCAATTAAGAAGGATGTTGGATTT 57.756 32.000 0.00 0.00 0.00 2.17
661 3615 2.032178 GGCATGTACTGGCGAAGAATTC 59.968 50.000 0.00 0.00 41.02 2.17
932 8177 7.389330 TCAGTCGTAATCAATTCCTGCTTTTTA 59.611 33.333 0.00 0.00 0.00 1.52
1631 9516 3.793144 CACAGCCGCCGCTCTTTC 61.793 66.667 0.00 0.00 43.95 2.62
1826 9970 4.559704 CGTAGCTTCTGAGGTTTGTTCTCT 60.560 45.833 0.00 0.00 34.88 3.10
1992 10137 1.228552 GTGGCTGATTGGGTGGTGT 60.229 57.895 0.00 0.00 0.00 4.16
2036 10182 2.110899 ACATCCCTCGGATCTAGGTCAT 59.889 50.000 5.14 3.45 40.98 3.06
2366 10515 0.392461 GCGTCTGGCCATTGGTAAGA 60.392 55.000 5.51 5.06 34.80 2.10
2437 10586 4.512914 GGCACCTCCCATCCCTGC 62.513 72.222 0.00 0.00 0.00 4.85
2438 10587 4.512914 GCACCTCCCATCCCTGCC 62.513 72.222 0.00 0.00 0.00 4.85
2439 10588 3.016971 CACCTCCCATCCCTGCCA 61.017 66.667 0.00 0.00 0.00 4.92
2441 10590 2.367377 CCTCCCATCCCTGCCAGA 60.367 66.667 0.00 0.00 0.00 3.86
2442 10591 1.773391 CCTCCCATCCCTGCCAGAT 60.773 63.158 0.00 0.00 0.00 2.90
2443 10592 1.454976 CTCCCATCCCTGCCAGATG 59.545 63.158 0.00 0.00 40.71 2.90
3147 11302 4.687215 GCTCAGGTGCAGGCGACA 62.687 66.667 0.00 0.00 0.00 4.35
3265 11485 1.673009 TGGACGTCGCCATTTTCCC 60.673 57.895 9.92 0.00 31.66 3.97
3306 11527 2.668212 TTTCCCTTCGCCGTGCTG 60.668 61.111 0.00 0.00 0.00 4.41
3790 12036 0.035439 CCGGGTGCCTTACAAGTCAT 60.035 55.000 0.00 0.00 0.00 3.06
5151 13406 3.942829 TGTTAAAGACTGGAGATGCCTG 58.057 45.455 0.00 0.00 41.12 4.85
5169 13424 4.688879 TGCCTGTCTCTTGTACGTTTATTG 59.311 41.667 0.00 0.00 0.00 1.90
5229 13484 5.710409 TTTTTCGAGGGGAGGAGAATAAT 57.290 39.130 0.00 0.00 0.00 1.28
5230 13485 4.689612 TTTCGAGGGGAGGAGAATAATG 57.310 45.455 0.00 0.00 0.00 1.90
5232 13487 3.654273 TCGAGGGGAGGAGAATAATGTT 58.346 45.455 0.00 0.00 0.00 2.71
5234 13489 5.213519 TCGAGGGGAGGAGAATAATGTTAA 58.786 41.667 0.00 0.00 0.00 2.01
5311 13682 4.261801 GTTTCCTGCATATGTACCACACT 58.738 43.478 4.29 0.00 0.00 3.55
5427 18338 1.215382 CAACTCGTGCTCGATCCCA 59.785 57.895 11.75 0.00 45.21 4.37
5717 20445 2.587473 GCTAGGCGCTGCTTCTCC 60.587 66.667 7.64 0.00 35.14 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 5.297776 CGAGTAATTTAGAACGGAGGGAGTA 59.702 44.000 0.00 0.00 0.00 2.59
98 99 4.097589 CGAGTAATTTAGAACGGAGGGAGT 59.902 45.833 0.00 0.00 0.00 3.85
99 100 4.097589 ACGAGTAATTTAGAACGGAGGGAG 59.902 45.833 0.00 0.00 0.00 4.30
100 101 4.019174 ACGAGTAATTTAGAACGGAGGGA 58.981 43.478 0.00 0.00 0.00 4.20
101 102 4.357996 GACGAGTAATTTAGAACGGAGGG 58.642 47.826 0.00 0.00 0.00 4.30
102 103 4.033684 CGACGAGTAATTTAGAACGGAGG 58.966 47.826 0.00 0.00 0.00 4.30
103 104 3.481388 GCGACGAGTAATTTAGAACGGAG 59.519 47.826 0.00 0.00 0.00 4.63
104 105 3.119884 TGCGACGAGTAATTTAGAACGGA 60.120 43.478 0.00 0.00 0.00 4.69
105 106 3.173599 TGCGACGAGTAATTTAGAACGG 58.826 45.455 0.00 0.00 0.00 4.44
106 107 4.093514 TCTGCGACGAGTAATTTAGAACG 58.906 43.478 0.00 0.00 0.00 3.95
107 108 6.385537 TTTCTGCGACGAGTAATTTAGAAC 57.614 37.500 0.00 0.00 0.00 3.01
108 109 6.035650 CCATTTCTGCGACGAGTAATTTAGAA 59.964 38.462 0.00 0.00 0.00 2.10
109 110 5.518847 CCATTTCTGCGACGAGTAATTTAGA 59.481 40.000 0.00 0.00 0.00 2.10
110 111 5.518847 TCCATTTCTGCGACGAGTAATTTAG 59.481 40.000 0.00 0.00 0.00 1.85
111 112 5.412640 TCCATTTCTGCGACGAGTAATTTA 58.587 37.500 0.00 0.00 0.00 1.40
112 113 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
113 114 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
114 115 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
115 116 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
116 117 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
117 118 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
118 119 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
119 120 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
120 121 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
121 122 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
122 123 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
123 124 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
124 125 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
151 152 9.741647 CGCATGTATGAATGTATCTAGATGTAT 57.258 33.333 15.79 6.61 0.00 2.29
152 153 8.956426 TCGCATGTATGAATGTATCTAGATGTA 58.044 33.333 15.79 4.44 0.00 2.29
153 154 7.757173 GTCGCATGTATGAATGTATCTAGATGT 59.243 37.037 15.79 0.00 0.00 3.06
154 155 7.756722 TGTCGCATGTATGAATGTATCTAGATG 59.243 37.037 15.79 0.00 0.00 2.90
155 156 7.830739 TGTCGCATGTATGAATGTATCTAGAT 58.169 34.615 10.73 10.73 0.00 1.98
156 157 7.214467 TGTCGCATGTATGAATGTATCTAGA 57.786 36.000 0.00 0.00 0.00 2.43
157 158 6.529477 CCTGTCGCATGTATGAATGTATCTAG 59.471 42.308 0.00 0.00 0.00 2.43
158 159 6.015434 ACCTGTCGCATGTATGAATGTATCTA 60.015 38.462 0.00 0.00 0.00 1.98
159 160 5.221521 ACCTGTCGCATGTATGAATGTATCT 60.222 40.000 0.00 0.00 0.00 1.98
160 161 4.991056 ACCTGTCGCATGTATGAATGTATC 59.009 41.667 0.00 0.00 0.00 2.24
161 162 4.960938 ACCTGTCGCATGTATGAATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
162 163 4.400529 ACCTGTCGCATGTATGAATGTA 57.599 40.909 0.00 0.00 0.00 2.29
163 164 3.266510 ACCTGTCGCATGTATGAATGT 57.733 42.857 0.00 0.00 0.00 2.71
164 165 5.929697 ATTACCTGTCGCATGTATGAATG 57.070 39.130 0.00 0.00 0.00 2.67
165 166 5.177511 CGAATTACCTGTCGCATGTATGAAT 59.822 40.000 0.00 0.00 0.00 2.57
166 167 4.506288 CGAATTACCTGTCGCATGTATGAA 59.494 41.667 0.00 0.00 0.00 2.57
167 168 4.048504 CGAATTACCTGTCGCATGTATGA 58.951 43.478 0.00 0.00 0.00 2.15
168 169 3.184379 CCGAATTACCTGTCGCATGTATG 59.816 47.826 0.00 0.00 35.93 2.39
169 170 3.069016 TCCGAATTACCTGTCGCATGTAT 59.931 43.478 0.00 0.00 35.93 2.29
170 171 2.427812 TCCGAATTACCTGTCGCATGTA 59.572 45.455 0.00 0.00 35.93 2.29
171 172 1.206132 TCCGAATTACCTGTCGCATGT 59.794 47.619 0.00 0.00 35.93 3.21
172 173 1.934589 TCCGAATTACCTGTCGCATG 58.065 50.000 0.00 0.00 35.93 4.06
173 174 2.277084 GTTCCGAATTACCTGTCGCAT 58.723 47.619 0.00 0.00 35.93 4.73
174 175 1.717194 GTTCCGAATTACCTGTCGCA 58.283 50.000 0.00 0.00 35.93 5.10
175 176 0.643820 CGTTCCGAATTACCTGTCGC 59.356 55.000 0.00 0.00 35.93 5.19
176 177 1.135315 TCCGTTCCGAATTACCTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
177 178 2.537401 CTCCGTTCCGAATTACCTGTC 58.463 52.381 0.00 0.00 0.00 3.51
178 179 1.206371 CCTCCGTTCCGAATTACCTGT 59.794 52.381 0.00 0.00 0.00 4.00
179 180 1.472728 CCCTCCGTTCCGAATTACCTG 60.473 57.143 0.00 0.00 0.00 4.00
180 181 0.828677 CCCTCCGTTCCGAATTACCT 59.171 55.000 0.00 0.00 0.00 3.08
181 182 0.826062 TCCCTCCGTTCCGAATTACC 59.174 55.000 0.00 0.00 0.00 2.85
182 183 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
183 184 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
184 185 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
185 186 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
186 187 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
187 188 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
188 189 1.978454 ATACTACTCCCTCCGTTCCG 58.022 55.000 0.00 0.00 0.00 4.30
189 190 3.450096 ACAAATACTACTCCCTCCGTTCC 59.550 47.826 0.00 0.00 0.00 3.62
190 191 4.732672 ACAAATACTACTCCCTCCGTTC 57.267 45.455 0.00 0.00 0.00 3.95
191 192 4.776308 AGAACAAATACTACTCCCTCCGTT 59.224 41.667 0.00 0.00 0.00 4.44
192 193 4.351127 AGAACAAATACTACTCCCTCCGT 58.649 43.478 0.00 0.00 0.00 4.69
193 194 4.401519 TGAGAACAAATACTACTCCCTCCG 59.598 45.833 0.00 0.00 0.00 4.63
194 195 5.682730 GCTGAGAACAAATACTACTCCCTCC 60.683 48.000 0.00 0.00 0.00 4.30
195 196 5.105310 TGCTGAGAACAAATACTACTCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
196 197 4.777896 TGCTGAGAACAAATACTACTCCCT 59.222 41.667 0.00 0.00 0.00 4.20
197 198 5.086104 TGCTGAGAACAAATACTACTCCC 57.914 43.478 0.00 0.00 0.00 4.30
198 199 5.578727 CACTGCTGAGAACAAATACTACTCC 59.421 44.000 0.00 0.00 0.00 3.85
199 200 5.062809 GCACTGCTGAGAACAAATACTACTC 59.937 44.000 0.00 0.00 0.00 2.59
200 201 4.932200 GCACTGCTGAGAACAAATACTACT 59.068 41.667 0.00 0.00 0.00 2.57
201 202 4.690748 TGCACTGCTGAGAACAAATACTAC 59.309 41.667 1.98 0.00 0.00 2.73
435 439 6.594788 ACAAAAGGATCACATTTGCTGTAT 57.405 33.333 13.72 0.00 37.52 2.29
956 8201 1.064758 AGTTGGCCGATAATGCTTCCA 60.065 47.619 0.00 0.00 0.00 3.53
1631 9516 0.551624 TCTAGGGTTTGGGAAGGGGG 60.552 60.000 0.00 0.00 0.00 5.40
2267 10415 1.000521 CATCACAGCCCACACCCAT 60.001 57.895 0.00 0.00 0.00 4.00
2357 10506 8.998662 GGACCTCCACAAGAGTATCTTACCAAT 61.999 44.444 0.00 0.00 44.95 3.16
2366 10515 2.950990 AGGGACCTCCACAAGAGTAT 57.049 50.000 0.00 0.00 41.47 2.12
2932 11081 4.394712 AAGAGGTGAAGCGGGCGG 62.395 66.667 0.00 0.00 0.00 6.13
2933 11082 2.815647 GAAGAGGTGAAGCGGGCG 60.816 66.667 0.00 0.00 0.00 6.13
2934 11083 1.448717 GAGAAGAGGTGAAGCGGGC 60.449 63.158 0.00 0.00 0.00 6.13
3265 11485 2.056577 GTAACCACAACGGAGACTTCG 58.943 52.381 0.28 0.28 38.63 3.79
3306 11527 4.499696 CCAATGGTCCAGATTTTTATCCGC 60.500 45.833 0.00 0.00 0.00 5.54
3374 11595 1.817099 CCGTGAGCTCCAAGATGGC 60.817 63.158 12.15 0.00 37.47 4.40
3790 12036 3.343972 GCACTTGAAGCGGCAGAA 58.656 55.556 1.45 0.00 0.00 3.02
5151 13406 7.170320 TGGAAGAACAATAAACGTACAAGAGAC 59.830 37.037 0.00 0.00 0.00 3.36
5195 13450 2.644676 CTCGAAAAATCCTCTTCCCCC 58.355 52.381 0.00 0.00 0.00 5.40
5254 13509 7.012661 ACGGGATAAATACAAAGGGGTATAG 57.987 40.000 0.00 0.00 32.95 1.31
5335 13943 4.354987 ACTTGTATTCCCATGAGGCCATAT 59.645 41.667 5.01 0.00 34.51 1.78
5701 20429 2.107953 GGGAGAAGCAGCGCCTAG 59.892 66.667 2.29 0.00 0.00 3.02
5702 20430 3.838271 CGGGAGAAGCAGCGCCTA 61.838 66.667 2.29 0.00 0.00 3.93
5727 20455 4.681978 GACAGGAACGGCGGCACT 62.682 66.667 13.24 2.29 0.00 4.40


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

AutoCloner maintained by Alex Coulton.