Multiple sequence alignment - TraesCS7B01G426900

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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 TraesCS7B01G426900 chr7B 100.000 3845 0 0 1001 4845 696145894 696142050 0.000000e+00 7101
1 TraesCS7B01G426900 chr7B 90.897 2889 189 40 1008 3845 694364992 694362127 0.000000e+00 3810
2 TraesCS7B01G426900 chr7B 90.731 2902 196 30 1001 3845 699145975 699143090 0.000000e+00 3801
3 TraesCS7B01G426900 chr7B 90.627 2902 199 30 1001 3845 698655665 698652780 0.000000e+00 3784
4 TraesCS7B01G426900 chr7B 93.697 2110 101 18 1747 3845 699182425 699180337 0.000000e+00 3131
5 TraesCS7B01G426900 chr7B 92.287 2191 116 23 1670 3845 699141571 699139419 0.000000e+00 3061
6 TraesCS7B01G426900 chr7B 100.000 835 0 0 1 835 696146894 696146060 0.000000e+00 1543
7 TraesCS7B01G426900 chr7B 87.124 1196 116 20 1426 2612 693314885 693316051 0.000000e+00 1321
8 TraesCS7B01G426900 chr7B 84.708 1079 116 23 1286 2348 697024502 697025547 0.000000e+00 1033
9 TraesCS7B01G426900 chr7B 82.751 858 93 21 4014 4839 694362131 694361297 0.000000e+00 713
10 TraesCS7B01G426900 chr7B 85.902 610 42 14 4014 4580 699139423 699138815 1.150000e-170 610
11 TraesCS7B01G426900 chr7B 84.007 594 58 13 4014 4577 698652784 698652198 1.980000e-148 536
12 TraesCS7B01G426900 chr7B 86.920 474 53 6 4014 4481 693620287 693619817 1.550000e-144 523
13 TraesCS7B01G426900 chr7B 89.349 338 25 7 1080 1408 699183216 699182881 9.700000e-112 414
14 TraesCS7B01G426900 chr7B 86.631 374 33 13 1040 1408 694189286 694189647 9.770000e-107 398
15 TraesCS7B01G426900 chr7B 90.698 301 21 3 1040 1339 693313254 693313548 1.260000e-105 394
16 TraesCS7B01G426900 chr7B 85.640 383 38 10 1040 1408 699142638 699142259 2.120000e-103 387
17 TraesCS7B01G426900 chr7B 91.241 274 22 2 4014 4286 699180341 699180069 5.920000e-99 372
18 TraesCS7B01G426900 chr7B 83.251 406 45 14 4014 4408 636073782 636073389 7.720000e-93 351
19 TraesCS7B01G426900 chr7B 88.889 261 29 0 4585 4845 698652149 698651889 6.050000e-84 322
20 TraesCS7B01G426900 chr7B 88.506 261 30 0 4585 4845 693619665 693619405 2.810000e-82 316
21 TraesCS7B01G426900 chr7B 88.506 261 28 1 4585 4845 699138770 699138512 1.010000e-81 315
22 TraesCS7B01G426900 chr7B 87.795 254 25 2 4585 4838 699179651 699179404 4.740000e-75 292
23 TraesCS7B01G426900 chr7B 91.489 94 8 0 4392 4485 699180021 699179928 3.940000e-26 130
24 TraesCS7B01G426900 chr7D 90.692 2847 173 35 1040 3845 608199850 608197055 0.000000e+00 3705
25 TraesCS7B01G426900 chr7D 89.159 2057 143 31 2844 4845 610533556 610535587 0.000000e+00 2490
26 TraesCS7B01G426900 chr7D 90.775 1496 110 9 2289 3764 514749009 514747522 0.000000e+00 1973
27 TraesCS7B01G426900 chr7D 89.524 1470 113 21 2844 4290 600234103 600235554 0.000000e+00 1823
28 TraesCS7B01G426900 chr7D 88.693 1194 108 11 1670 2849 600232886 600234066 0.000000e+00 1432
29 TraesCS7B01G426900 chr7D 90.198 1061 87 11 1671 2723 610532296 610533347 0.000000e+00 1367
30 TraesCS7B01G426900 chr7D 87.719 855 61 20 4014 4845 514746956 514746123 0.000000e+00 957
31 TraesCS7B01G426900 chr7D 83.442 1075 116 27 1294 2348 609861941 609862973 0.000000e+00 942
32 TraesCS7B01G426900 chr7D 86.846 631 41 15 211 821 575662273 575661665 0.000000e+00 667
33 TraesCS7B01G426900 chr7D 88.911 514 28 4 4356 4845 600235585 600236093 1.490000e-169 606
34 TraesCS7B01G426900 chr7D 91.328 369 28 3 1040 1408 610531534 610531898 7.240000e-138 501
35 TraesCS7B01G426900 chr7D 84.120 466 45 15 4014 4478 608197059 608196622 1.610000e-114 424
36 TraesCS7B01G426900 chr7D 91.870 246 17 2 3 246 575662444 575662200 1.670000e-89 340
37 TraesCS7B01G426900 chr7A 87.105 1613 136 47 2284 3845 700504900 700506491 0.000000e+00 1760
38 TraesCS7B01G426900 chr7A 83.041 1256 151 40 1001 2221 700503631 700504859 0.000000e+00 1083
39 TraesCS7B01G426900 chr7A 83.624 861 58 29 4011 4812 700506484 700507320 0.000000e+00 732
40 TraesCS7B01G426900 chr7A 85.902 610 38 12 4014 4579 700207091 700206486 1.490000e-169 606
41 TraesCS7B01G426900 chr7A 92.337 261 20 0 4585 4845 700206439 700206179 5.920000e-99 372
42 TraesCS7B01G426900 chr4A 95.521 1094 47 2 2536 3628 661823500 661822408 0.000000e+00 1748
43 TraesCS7B01G426900 chr4A 96.145 830 32 0 1709 2538 661826027 661825198 0.000000e+00 1356
44 TraesCS7B01G426900 chr4A 83.498 606 43 18 4014 4580 661822251 661821664 3.340000e-141 512
45 TraesCS7B01G426900 chr4A 87.546 273 27 4 1051 1319 661826296 661826027 4.710000e-80 309
46 TraesCS7B01G426900 chr4A 87.500 168 16 3 3680 3845 661822411 661822247 6.400000e-44 189
47 TraesCS7B01G426900 chr3B 98.173 821 14 1 1 821 823102727 823103546 0.000000e+00 1432
48 TraesCS7B01G426900 chr3B 96.715 822 25 2 1 822 365282218 365281399 0.000000e+00 1367
49 TraesCS7B01G426900 chrUn 83.489 1072 115 27 1297 2348 209380914 209379885 0.000000e+00 942
50 TraesCS7B01G426900 chr5A 91.623 573 42 3 252 822 224187831 224187263 0.000000e+00 787
51 TraesCS7B01G426900 chr5A 92.574 202 15 0 1 202 224188032 224187831 1.710000e-74 291
52 TraesCS7B01G426900 chr2A 87.937 630 52 11 211 822 769614517 769615140 0.000000e+00 721
53 TraesCS7B01G426900 chr2A 85.375 253 22 6 1 246 769614346 769614590 1.040000e-61 248
54 TraesCS7B01G426900 chr6D 93.168 483 21 7 344 821 298156353 298156828 0.000000e+00 699
55 TraesCS7B01G426900 chr6D 90.090 222 8 2 1 222 298156318 298156111 4.780000e-70 276
56 TraesCS7B01G426900 chr6D 89.498 219 9 1 1 219 298155900 298156104 1.030000e-66 265
57 TraesCS7B01G426900 chr2B 86.854 639 51 10 211 821 383524945 383524312 0.000000e+00 684
58 TraesCS7B01G426900 chr2B 93.249 237 11 2 3635 3869 134440290 134440523 1.290000e-90 344
59 TraesCS7B01G426900 chr2B 81.931 404 54 11 4014 4408 135994633 135995026 1.680000e-84 324
60 TraesCS7B01G426900 chr1D 86.529 631 40 17 211 821 121661278 121661883 0.000000e+00 652
61 TraesCS7B01G426900 chr1D 89.802 353 23 5 479 821 454522242 454522591 1.600000e-119 440
62 TraesCS7B01G426900 chr1D 91.057 246 19 2 3 246 121661107 121661351 3.620000e-86 329
63 TraesCS7B01G426900 chr1D 87.179 273 22 9 211 477 454514999 454515264 1.020000e-76 298
64 TraesCS7B01G426900 chr3A 85.215 629 65 13 211 821 575145039 575144421 5.330000e-174 621


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 TraesCS7B01G426900 chr7B 696142050 696146894 4844 True 4322.000000 7101 100.000000 1 4845 2 chr7B.!!$R4 4844
1 TraesCS7B01G426900 chr7B 694361297 694364992 3695 True 2261.500000 3810 86.824000 1008 4839 2 chr7B.!!$R3 3831
2 TraesCS7B01G426900 chr7B 699138512 699145975 7463 True 1634.800000 3801 88.613200 1001 4845 5 chr7B.!!$R6 3844
3 TraesCS7B01G426900 chr7B 698651889 698655665 3776 True 1547.333333 3784 87.841000 1001 4845 3 chr7B.!!$R5 3844
4 TraesCS7B01G426900 chr7B 697024502 697025547 1045 False 1033.000000 1033 84.708000 1286 2348 1 chr7B.!!$F2 1062
5 TraesCS7B01G426900 chr7B 699179404 699183216 3812 True 867.800000 3131 90.714200 1080 4838 5 chr7B.!!$R7 3758
6 TraesCS7B01G426900 chr7B 693313254 693316051 2797 False 857.500000 1321 88.911000 1040 2612 2 chr7B.!!$F3 1572
7 TraesCS7B01G426900 chr7B 693619405 693620287 882 True 419.500000 523 87.713000 4014 4845 2 chr7B.!!$R2 831
8 TraesCS7B01G426900 chr7D 608196622 608199850 3228 True 2064.500000 3705 87.406000 1040 4478 2 chr7D.!!$R3 3438
9 TraesCS7B01G426900 chr7D 514746123 514749009 2886 True 1465.000000 1973 89.247000 2289 4845 2 chr7D.!!$R1 2556
10 TraesCS7B01G426900 chr7D 610531534 610535587 4053 False 1452.666667 2490 90.228333 1040 4845 3 chr7D.!!$F3 3805
11 TraesCS7B01G426900 chr7D 600232886 600236093 3207 False 1287.000000 1823 89.042667 1670 4845 3 chr7D.!!$F2 3175
12 TraesCS7B01G426900 chr7D 609861941 609862973 1032 False 942.000000 942 83.442000 1294 2348 1 chr7D.!!$F1 1054
13 TraesCS7B01G426900 chr7D 575661665 575662444 779 True 503.500000 667 89.358000 3 821 2 chr7D.!!$R2 818
14 TraesCS7B01G426900 chr7A 700503631 700507320 3689 False 1191.666667 1760 84.590000 1001 4812 3 chr7A.!!$F1 3811
15 TraesCS7B01G426900 chr7A 700206179 700207091 912 True 489.000000 606 89.119500 4014 4845 2 chr7A.!!$R1 831
16 TraesCS7B01G426900 chr4A 661821664 661826296 4632 True 822.800000 1748 90.042000 1051 4580 5 chr4A.!!$R1 3529
17 TraesCS7B01G426900 chr3B 823102727 823103546 819 False 1432.000000 1432 98.173000 1 821 1 chr3B.!!$F1 820
18 TraesCS7B01G426900 chr3B 365281399 365282218 819 True 1367.000000 1367 96.715000 1 822 1 chr3B.!!$R1 821
19 TraesCS7B01G426900 chrUn 209379885 209380914 1029 True 942.000000 942 83.489000 1297 2348 1 chrUn.!!$R1 1051
20 TraesCS7B01G426900 chr5A 224187263 224188032 769 True 539.000000 787 92.098500 1 822 2 chr5A.!!$R1 821
21 TraesCS7B01G426900 chr2A 769614346 769615140 794 False 484.500000 721 86.656000 1 822 2 chr2A.!!$F1 821
22 TraesCS7B01G426900 chr6D 298155900 298156828 928 False 482.000000 699 91.333000 1 821 2 chr6D.!!$F1 820
23 TraesCS7B01G426900 chr2B 383524312 383524945 633 True 684.000000 684 86.854000 211 821 1 chr2B.!!$R1 610
24 TraesCS7B01G426900 chr1D 121661107 121661883 776 False 490.500000 652 88.793000 3 821 2 chr1D.!!$F3 818
25 TraesCS7B01G426900 chr3A 575144421 575145039 618 True 621.000000 621 85.215000 211 821 1 chr3A.!!$R1 610

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
189 199 0.032678 AGCGGCAATGATCTAGTCCG 59.967 55.0 1.45 11.0 39.81 4.79 F
202 212 0.032952 TAGTCCGCAAACGCTGAAGT 59.967 50.0 0.00 0.0 38.22 3.01 F
205 215 0.315886 TCCGCAAACGCTGAAGTCTA 59.684 50.0 0.00 0.0 38.22 2.59 F
1249 1558 0.627986 CTCAGGGAAGGCAAGGGAAT 59.372 55.0 0.00 0.0 0.00 3.01 F
1259 1568 0.878416 GCAAGGGAATGCGTTGTGTA 59.122 50.0 8.81 0.0 36.45 2.90 F
2450 4235 0.036105 TCATTGATGTCAGCTGCGGT 60.036 50.0 9.47 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1512 0.461548 TGAGAATCAGCTAGTGGCGG 59.538 55.000 0.00 0.00 42.56 6.13 R
1701 3456 0.505655 GCGTCAGTTTCACACGGTAC 59.494 55.000 0.00 0.00 34.04 3.34 R
1936 3705 1.347707 CCTATAAATCGCTGGCCTGGA 59.652 52.381 12.06 7.45 0.00 3.86 R
2225 4000 1.493022 ACAGGCCAGGTGTGTAAGAAA 59.507 47.619 5.01 0.00 0.00 2.52 R
2869 6449 1.672356 CAAGGTTCCTGCAGGACCG 60.672 63.158 35.26 20.77 45.39 4.79 R
4274 12082 0.970937 TCAGCCGGTACTCTCTTGGG 60.971 60.000 1.90 0.00 0.00 4.12 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
171 181 1.830279 TGCCTTTGCAGATCCTTCAG 58.170 50.000 0.00 0.00 44.23 3.02
172 182 0.455005 GCCTTTGCAGATCCTTCAGC 59.545 55.000 0.00 0.00 37.47 4.26
173 183 0.731417 CCTTTGCAGATCCTTCAGCG 59.269 55.000 0.00 0.00 37.20 5.18
174 184 0.731417 CTTTGCAGATCCTTCAGCGG 59.269 55.000 0.00 0.00 37.20 5.52
175 185 1.308069 TTTGCAGATCCTTCAGCGGC 61.308 55.000 0.00 0.00 37.20 6.53
176 186 2.124983 GCAGATCCTTCAGCGGCA 60.125 61.111 1.45 0.00 0.00 5.69
177 187 1.746615 GCAGATCCTTCAGCGGCAA 60.747 57.895 1.45 0.00 0.00 4.52
178 188 1.099879 GCAGATCCTTCAGCGGCAAT 61.100 55.000 1.45 0.00 0.00 3.56
179 189 0.661552 CAGATCCTTCAGCGGCAATG 59.338 55.000 1.45 0.00 0.00 2.82
180 190 0.543277 AGATCCTTCAGCGGCAATGA 59.457 50.000 1.45 0.00 0.00 2.57
181 191 1.142465 AGATCCTTCAGCGGCAATGAT 59.858 47.619 1.45 0.00 0.00 2.45
182 192 1.534595 GATCCTTCAGCGGCAATGATC 59.465 52.381 1.45 2.94 0.00 2.92
183 193 0.543277 TCCTTCAGCGGCAATGATCT 59.457 50.000 1.45 0.00 0.00 2.75
184 194 1.762370 TCCTTCAGCGGCAATGATCTA 59.238 47.619 1.45 0.00 0.00 1.98
185 195 2.141517 CCTTCAGCGGCAATGATCTAG 58.858 52.381 1.45 0.00 0.00 2.43
186 196 2.484417 CCTTCAGCGGCAATGATCTAGT 60.484 50.000 1.45 0.00 0.00 2.57
187 197 2.515926 TCAGCGGCAATGATCTAGTC 57.484 50.000 1.45 0.00 0.00 2.59
188 198 1.069204 TCAGCGGCAATGATCTAGTCC 59.931 52.381 1.45 0.00 0.00 3.85
189 199 0.032678 AGCGGCAATGATCTAGTCCG 59.967 55.000 1.45 11.00 39.81 4.79
190 200 2.522060 CGGCAATGATCTAGTCCGC 58.478 57.895 0.00 0.00 0.00 5.54
191 201 0.249447 CGGCAATGATCTAGTCCGCA 60.249 55.000 0.00 0.00 0.00 5.69
192 202 1.806247 CGGCAATGATCTAGTCCGCAA 60.806 52.381 0.00 0.00 0.00 4.85
193 203 2.288666 GGCAATGATCTAGTCCGCAAA 58.711 47.619 0.00 0.00 0.00 3.68
194 204 2.032178 GGCAATGATCTAGTCCGCAAAC 59.968 50.000 0.00 0.00 0.00 2.93
195 205 2.285834 GCAATGATCTAGTCCGCAAACG 60.286 50.000 0.00 0.00 39.67 3.60
196 206 1.571919 ATGATCTAGTCCGCAAACGC 58.428 50.000 0.00 0.00 38.22 4.84
197 207 0.530744 TGATCTAGTCCGCAAACGCT 59.469 50.000 0.00 0.00 38.22 5.07
198 208 0.924090 GATCTAGTCCGCAAACGCTG 59.076 55.000 0.00 0.00 38.22 5.18
199 209 0.530744 ATCTAGTCCGCAAACGCTGA 59.469 50.000 0.00 0.00 38.22 4.26
200 210 0.315886 TCTAGTCCGCAAACGCTGAA 59.684 50.000 0.00 0.00 38.22 3.02
201 211 0.716108 CTAGTCCGCAAACGCTGAAG 59.284 55.000 0.00 0.00 38.22 3.02
202 212 0.032952 TAGTCCGCAAACGCTGAAGT 59.967 50.000 0.00 0.00 38.22 3.01
203 213 1.204312 GTCCGCAAACGCTGAAGTC 59.796 57.895 0.00 0.00 38.22 3.01
204 214 1.069090 TCCGCAAACGCTGAAGTCT 59.931 52.632 0.00 0.00 38.22 3.24
205 215 0.315886 TCCGCAAACGCTGAAGTCTA 59.684 50.000 0.00 0.00 38.22 2.59
206 216 1.144969 CCGCAAACGCTGAAGTCTAA 58.855 50.000 0.00 0.00 38.22 2.10
207 217 1.732259 CCGCAAACGCTGAAGTCTAAT 59.268 47.619 0.00 0.00 38.22 1.73
208 218 2.222819 CCGCAAACGCTGAAGTCTAATC 60.223 50.000 0.00 0.00 38.22 1.75
209 219 2.222819 CGCAAACGCTGAAGTCTAATCC 60.223 50.000 0.00 0.00 0.00 3.01
397 662 1.261619 CATACGGGAGATTTTGCTCGC 59.738 52.381 0.00 0.00 42.48 5.03
832 1124 4.641645 CCCCTGCCAACACAGCGA 62.642 66.667 0.00 0.00 36.29 4.93
833 1125 3.357079 CCCTGCCAACACAGCGAC 61.357 66.667 0.00 0.00 36.29 5.19
834 1126 3.716006 CCTGCCAACACAGCGACG 61.716 66.667 0.00 0.00 36.29 5.12
1029 1321 2.496828 AATTGCTTTGCTGCTCCGCC 62.497 55.000 0.00 0.00 0.00 6.13
1249 1558 0.627986 CTCAGGGAAGGCAAGGGAAT 59.372 55.000 0.00 0.00 0.00 3.01
1259 1568 0.878416 GCAAGGGAATGCGTTGTGTA 59.122 50.000 8.81 0.00 36.45 2.90
1320 1635 8.461898 CAAATGTTTGGTGTTATGCCTAGGCA 62.462 42.308 37.53 37.53 43.67 4.75
1358 1684 3.698040 CCAAGCTCTGTATTTGCTCCAAT 59.302 43.478 0.00 0.00 35.85 3.16
1362 1688 5.749462 AGCTCTGTATTTGCTCCAATAGTT 58.251 37.500 0.00 0.00 30.41 2.24
1377 1703 6.436261 TCCAATAGTTATCAATCGAGTCGAC 58.564 40.000 19.16 7.70 39.18 4.20
1396 2939 3.861113 CGACATAGGCGTAAGTTTAGCAA 59.139 43.478 0.00 0.00 41.68 3.91
1442 3018 3.439129 TGCTGTCAGATGCAAAGATTGAG 59.561 43.478 3.32 0.00 36.15 3.02
1447 3023 3.014623 CAGATGCAAAGATTGAGCCTCA 58.985 45.455 0.00 0.00 0.00 3.86
1468 3044 6.041409 CCTCACATGGTAGATTAGTGACTCAT 59.959 42.308 0.00 0.00 35.57 2.90
1505 3090 2.749280 TATGGCTGCTGATATCCGTG 57.251 50.000 0.00 0.00 0.00 4.94
1528 3113 5.418524 TGTTTCTGTTGCCTTACATGCATAT 59.581 36.000 0.00 0.00 38.76 1.78
1535 3120 6.072342 TGTTGCCTTACATGCATATGATGATC 60.072 38.462 6.97 0.00 38.76 2.92
1536 3121 5.562635 TGCCTTACATGCATATGATGATCA 58.437 37.500 6.97 0.00 37.73 2.92
1538 3123 5.878669 GCCTTACATGCATATGATGATCAGA 59.121 40.000 6.97 0.00 37.73 3.27
1575 3275 7.856415 AGCTTCCACTATTTAACTCTGAAGAT 58.144 34.615 0.00 0.00 31.85 2.40
1701 3456 2.869233 CCAAGGTTGGCCATTATTCG 57.131 50.000 6.09 0.00 42.21 3.34
1813 3574 1.398390 CCTGTTTGCTATGAACCGCTC 59.602 52.381 0.00 0.00 0.00 5.03
1931 3700 6.621316 TTTATGTTGTTTTGGCTTCTACGA 57.379 33.333 0.00 0.00 0.00 3.43
1936 3705 3.537580 TGTTTTGGCTTCTACGAGTGTT 58.462 40.909 0.00 0.00 0.00 3.32
2028 3797 4.021544 GTCTTCTTGGATCTCACTGTCACT 60.022 45.833 0.00 0.00 0.00 3.41
2225 4000 5.182001 CCTTAAGTTGTTGCTGCTCACTAAT 59.818 40.000 0.00 0.00 0.00 1.73
2380 4165 2.977914 TCTGATGTACTGCTGGCTTTC 58.022 47.619 0.00 0.00 0.00 2.62
2417 4202 6.070251 TGGCTCAAGACTATTTCCAATCAGTA 60.070 38.462 0.00 0.00 0.00 2.74
2450 4235 0.036105 TCATTGATGTCAGCTGCGGT 60.036 50.000 9.47 0.00 0.00 5.68
2834 6372 7.559897 ACCTCAGAATGTTCCTTTTGTTCTAAA 59.440 33.333 0.00 0.00 37.40 1.85
2869 6449 8.074370 AGCAATTACTTACCGTTTTCTTCTTTC 58.926 33.333 0.00 0.00 0.00 2.62
3058 6665 5.243207 ACTATTAAAACTGGTGTCTTCGGG 58.757 41.667 0.00 0.00 0.00 5.14
3244 6852 2.480073 GCTTTCAACAGCTTTGTGCAGA 60.480 45.455 0.00 0.00 45.94 4.26
3273 6889 3.243907 GCATCTGACCTGTGTACCTATCC 60.244 52.174 0.00 0.00 0.00 2.59
3310 6926 9.631257 TGAACTTATTCATCACCATGACATATT 57.369 29.630 0.00 0.00 40.01 1.28
3445 7065 1.448540 CGCACTAAGGCCACTGAGG 60.449 63.158 5.01 0.00 41.84 3.86
3474 7094 2.891112 AGAAGTCGTCGATCGTCTAGT 58.109 47.619 15.94 1.45 36.99 2.57
3481 7102 2.347753 CGTCGATCGTCTAGTGCTACTG 60.348 54.545 15.94 0.00 34.52 2.74
3722 7347 0.657840 CTTTGTATAGCCAGCCACGC 59.342 55.000 0.00 0.00 0.00 5.34
3795 7917 2.368655 AAATCAGGTGGCGAAAATGC 57.631 45.000 0.00 0.00 0.00 3.56
3905 8029 6.794158 GTCGCGTCGTACTATCACTTAATATT 59.206 38.462 5.77 0.00 0.00 1.28
3964 8088 6.573434 ACAATGCTCTGACGAGATGTTAATA 58.427 36.000 0.00 0.00 39.74 0.98
3989 8113 2.749076 GTGAAGTTCATGCATGCCTGTA 59.251 45.455 22.25 10.21 0.00 2.74
3990 8114 3.191162 GTGAAGTTCATGCATGCCTGTAA 59.809 43.478 22.25 7.74 0.00 2.41
3991 8115 3.441222 TGAAGTTCATGCATGCCTGTAAG 59.559 43.478 22.25 0.00 0.00 2.34
3992 8116 1.747355 AGTTCATGCATGCCTGTAAGC 59.253 47.619 22.25 5.71 0.00 3.09
4033 8158 5.453903 CCCCACTCTGATGAACAATAGTAGG 60.454 48.000 0.00 0.00 0.00 3.18
4077 8202 6.463995 TGAGCAAAAGTTTTACACCTGAAT 57.536 33.333 0.00 0.00 0.00 2.57
4155 8280 9.100197 ACAAACCTTTTATGGTATCCATTTCTT 57.900 29.630 6.59 0.00 42.23 2.52
4204 12001 8.259049 TGTCTATTAAAATGTTCAAGGGTACG 57.741 34.615 0.00 0.00 0.00 3.67
4266 12074 4.522789 TCCTGGCTCCAATTTTTACAGAAC 59.477 41.667 0.00 0.00 0.00 3.01
4269 12077 3.366985 GGCTCCAATTTTTACAGAACGGG 60.367 47.826 0.00 0.00 0.00 5.28
4274 12082 4.979815 CCAATTTTTACAGAACGGGTGAAC 59.020 41.667 0.00 0.00 0.00 3.18
4294 12121 0.895530 CCAAGAGAGTACCGGCTGAA 59.104 55.000 0.00 0.00 0.00 3.02
4298 12125 1.751924 AGAGAGTACCGGCTGAATGAC 59.248 52.381 0.00 0.00 0.00 3.06
4303 12130 1.204941 GTACCGGCTGAATGACTGACT 59.795 52.381 0.00 0.00 0.00 3.41
4323 12150 5.097742 ACTGGATATCGTCATCAACCAAA 57.902 39.130 0.00 0.00 0.00 3.28
4326 12153 6.603201 ACTGGATATCGTCATCAACCAAAATT 59.397 34.615 0.00 0.00 0.00 1.82
4385 12242 5.295540 CAGCAAGAAAGAAAGTATCCTAGCC 59.704 44.000 0.00 0.00 0.00 3.93
4398 12259 1.850998 TCCTAGCCACTACTCAGCCTA 59.149 52.381 0.00 0.00 0.00 3.93
4478 12339 2.972713 AGCAGAGTGGTGAAGAAACCTA 59.027 45.455 0.00 0.00 41.16 3.08
4481 12342 4.743955 GCAGAGTGGTGAAGAAACCTACTT 60.744 45.833 0.00 0.00 41.16 2.24
4620 12667 5.925969 CCATGGTGTTAAATGAAAGGTCAAC 59.074 40.000 2.57 0.00 37.30 3.18
4656 12703 2.855514 GCAAAACCGGCAAGCCAGA 61.856 57.895 12.19 0.00 35.37 3.86
4762 12815 4.931002 ACTCTCTACTCTCGACACACTTAC 59.069 45.833 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 178 1.069204 GGACTAGATCATTGCCGCTGA 59.931 52.381 0.00 0.00 0.00 4.26
171 181 2.522060 CGGACTAGATCATTGCCGC 58.478 57.895 0.00 0.00 31.80 6.53
172 182 0.249447 TGCGGACTAGATCATTGCCG 60.249 55.000 11.28 11.28 41.51 5.69
173 183 1.953559 TTGCGGACTAGATCATTGCC 58.046 50.000 0.00 0.00 0.00 4.52
174 184 2.285834 CGTTTGCGGACTAGATCATTGC 60.286 50.000 0.00 0.00 0.00 3.56
175 185 2.285834 GCGTTTGCGGACTAGATCATTG 60.286 50.000 0.00 0.00 38.78 2.82
176 186 1.933853 GCGTTTGCGGACTAGATCATT 59.066 47.619 0.00 0.00 38.78 2.57
177 187 1.571919 GCGTTTGCGGACTAGATCAT 58.428 50.000 0.00 0.00 38.78 2.45
178 188 3.044809 GCGTTTGCGGACTAGATCA 57.955 52.632 0.00 0.00 38.78 2.92
179 189 2.989276 TTCAGCGTTTGCGGACTAGATC 60.989 50.000 0.00 0.00 45.12 2.75
180 190 1.067142 TTCAGCGTTTGCGGACTAGAT 60.067 47.619 0.00 0.00 45.12 1.98
181 191 0.315886 TTCAGCGTTTGCGGACTAGA 59.684 50.000 0.00 0.00 45.12 2.43
182 192 0.716108 CTTCAGCGTTTGCGGACTAG 59.284 55.000 0.00 0.00 45.12 2.57
183 193 0.032952 ACTTCAGCGTTTGCGGACTA 59.967 50.000 0.00 0.00 45.12 2.59
184 194 1.222115 GACTTCAGCGTTTGCGGACT 61.222 55.000 0.00 0.00 45.12 3.85
185 195 1.204312 GACTTCAGCGTTTGCGGAC 59.796 57.895 0.00 0.00 45.12 4.79
189 199 2.222819 CGGATTAGACTTCAGCGTTTGC 60.223 50.000 0.00 0.00 43.24 3.68
190 200 2.222819 GCGGATTAGACTTCAGCGTTTG 60.223 50.000 0.00 0.00 0.00 2.93
191 201 2.000447 GCGGATTAGACTTCAGCGTTT 59.000 47.619 0.00 0.00 0.00 3.60
192 202 1.641577 GCGGATTAGACTTCAGCGTT 58.358 50.000 0.00 0.00 0.00 4.84
193 203 3.347411 GCGGATTAGACTTCAGCGT 57.653 52.632 0.00 0.00 0.00 5.07
195 205 1.491505 GCCGCGGATTAGACTTCAGC 61.492 60.000 33.48 3.97 0.00 4.26
196 206 0.179111 TGCCGCGGATTAGACTTCAG 60.179 55.000 33.48 0.00 0.00 3.02
197 207 0.248012 TTGCCGCGGATTAGACTTCA 59.752 50.000 33.48 11.24 0.00 3.02
198 208 1.261619 CATTGCCGCGGATTAGACTTC 59.738 52.381 33.48 8.18 0.00 3.01
199 209 1.134521 TCATTGCCGCGGATTAGACTT 60.135 47.619 33.48 0.02 0.00 3.01
200 210 0.464036 TCATTGCCGCGGATTAGACT 59.536 50.000 33.48 1.65 0.00 3.24
201 211 1.461127 GATCATTGCCGCGGATTAGAC 59.539 52.381 33.48 10.79 0.00 2.59
202 212 1.344438 AGATCATTGCCGCGGATTAGA 59.656 47.619 33.48 20.86 0.00 2.10
203 213 1.800805 AGATCATTGCCGCGGATTAG 58.199 50.000 33.48 15.75 0.00 1.73
204 214 2.299013 ACTAGATCATTGCCGCGGATTA 59.701 45.455 33.48 13.60 0.00 1.75
205 215 1.070758 ACTAGATCATTGCCGCGGATT 59.929 47.619 33.48 9.58 0.00 3.01
206 216 0.681733 ACTAGATCATTGCCGCGGAT 59.318 50.000 33.48 13.68 0.00 4.18
207 217 0.032130 GACTAGATCATTGCCGCGGA 59.968 55.000 33.48 9.86 0.00 5.54
208 218 0.032678 AGACTAGATCATTGCCGCGG 59.967 55.000 24.05 24.05 0.00 6.46
209 219 1.135046 CAGACTAGATCATTGCCGCG 58.865 55.000 0.00 0.00 0.00 6.46
397 662 7.095187 GGAGGAAACAACAGTTAAGATGTACTG 60.095 40.741 0.00 0.00 45.61 2.74
541 808 7.383102 TCTCAACTTTGGAGCTATTCATTTC 57.617 36.000 0.00 0.00 32.38 2.17
1070 1362 1.616628 GGGGAGGAGGAGCAGGAAA 60.617 63.158 0.00 0.00 0.00 3.13
1209 1512 0.461548 TGAGAATCAGCTAGTGGCGG 59.538 55.000 0.00 0.00 42.56 6.13
1249 1558 2.734276 TCTAGCACATACACAACGCA 57.266 45.000 0.00 0.00 0.00 5.24
1320 1635 2.118294 GGTTCCTGCCAAAGCCCT 59.882 61.111 0.00 0.00 38.69 5.19
1358 1684 6.348295 GCCTATGTCGACTCGATTGATAACTA 60.348 42.308 17.92 0.00 38.42 2.24
1362 1688 3.120304 CGCCTATGTCGACTCGATTGATA 60.120 47.826 17.92 3.35 38.42 2.15
1377 1703 4.332819 AGCTTTGCTAAACTTACGCCTATG 59.667 41.667 0.00 0.00 36.99 2.23
1396 2939 1.891150 CAGGCCATGACTGAAAAGCTT 59.109 47.619 5.01 0.00 42.14 3.74
1442 3018 4.100189 AGTCACTAATCTACCATGTGAGGC 59.900 45.833 0.00 0.00 38.16 4.70
1447 3023 8.768501 TTAGATGAGTCACTAATCTACCATGT 57.231 34.615 11.13 0.00 34.62 3.21
1528 3113 5.509332 GCTAGATTGCAGAGTCTGATCATCA 60.509 44.000 24.55 8.75 32.44 3.07
1535 3120 3.118847 TGGAAGCTAGATTGCAGAGTCTG 60.119 47.826 16.21 16.21 34.99 3.51
1536 3121 3.102972 TGGAAGCTAGATTGCAGAGTCT 58.897 45.455 11.15 4.17 34.99 3.24
1538 3123 2.836981 AGTGGAAGCTAGATTGCAGAGT 59.163 45.455 15.65 0.62 30.60 3.24
1575 3275 5.215903 CGATCGCTTGCTAGAAAGATTAGA 58.784 41.667 15.22 7.60 0.00 2.10
1584 3284 2.858646 GCATACACGATCGCTTGCTAGA 60.859 50.000 16.60 0.00 0.00 2.43
1701 3456 0.505655 GCGTCAGTTTCACACGGTAC 59.494 55.000 0.00 0.00 34.04 3.34
1813 3574 2.203209 GGCGGCCCTGTCCTTATG 60.203 66.667 8.12 0.00 0.00 1.90
1931 3700 2.129555 AATCGCTGGCCTGGAACACT 62.130 55.000 12.06 0.00 0.00 3.55
1936 3705 1.347707 CCTATAAATCGCTGGCCTGGA 59.652 52.381 12.06 7.45 0.00 3.86
2028 3797 7.939039 AGTTCACTGTATTCTTTCATTCCTGAA 59.061 33.333 0.00 0.00 39.62 3.02
2225 4000 1.493022 ACAGGCCAGGTGTGTAAGAAA 59.507 47.619 5.01 0.00 0.00 2.52
2372 4157 3.057033 CCATTTGGAACTGAGAAAGCCAG 60.057 47.826 0.00 0.00 37.39 4.85
2380 4165 3.190118 GTCTTGAGCCATTTGGAACTGAG 59.810 47.826 0.00 0.00 37.39 3.35
2417 4202 4.410228 ACATCAATGAGTATACCACCAGCT 59.590 41.667 0.00 0.00 0.00 4.24
2450 4235 4.532834 ACTTCCTTGAAAACAAGCCACTA 58.467 39.130 0.00 0.00 0.00 2.74
2834 6372 6.870769 ACGGTAAGTAATTGCTGTACTGTAT 58.129 36.000 19.02 5.83 33.55 2.29
2856 6436 2.349532 GCAGGACCGAAAGAAGAAAACG 60.350 50.000 0.00 0.00 0.00 3.60
2869 6449 1.672356 CAAGGTTCCTGCAGGACCG 60.672 63.158 35.26 20.77 45.39 4.79
3058 6665 7.656137 TGGACTCTGGCGAATAAAATAGTAATC 59.344 37.037 0.00 0.00 0.00 1.75
3244 6852 3.658398 CAGGTCAGATGCCCTGTTT 57.342 52.632 1.70 0.00 42.72 2.83
3308 6924 3.450457 TGGTTTTCAAACAGCAGTGGAAT 59.550 39.130 4.85 0.00 40.63 3.01
3310 6926 2.426738 CTGGTTTTCAAACAGCAGTGGA 59.573 45.455 4.85 0.00 40.63 4.02
3445 7065 2.669364 TCGACGACTTCTTTTACCTGC 58.331 47.619 0.00 0.00 0.00 4.85
3474 7094 4.096833 CCATGCAGAAAATAAGCAGTAGCA 59.903 41.667 0.00 0.00 45.49 3.49
3504 7129 3.577848 AGAAGATGCATCAGGCTAGGTAG 59.422 47.826 27.81 0.00 45.15 3.18
3768 7890 1.662122 CGCCACCTGATTTAACCGTAC 59.338 52.381 0.00 0.00 0.00 3.67
3795 7917 3.498082 GGCCTAATGCGTGTTTAAGTTG 58.502 45.455 0.00 0.00 42.61 3.16
3905 8029 4.009675 GGAGTGAAATACTGGCATGTCAA 58.990 43.478 0.00 0.00 40.53 3.18
3964 8088 1.542915 GCATGCATGAACTTCACCAGT 59.457 47.619 30.64 0.00 37.30 4.00
3989 8113 2.224548 GGTGGAGTACTTCAACAGGCTT 60.225 50.000 14.76 0.00 30.67 4.35
3990 8114 1.348036 GGTGGAGTACTTCAACAGGCT 59.652 52.381 14.76 0.00 30.67 4.58
3991 8115 1.610886 GGGTGGAGTACTTCAACAGGC 60.611 57.143 20.96 0.00 30.67 4.85
3992 8116 1.003233 GGGGTGGAGTACTTCAACAGG 59.997 57.143 20.96 0.00 30.67 4.00
4033 8158 4.460382 TCAATGCCTGAACCTGAAGAAATC 59.540 41.667 0.00 0.00 0.00 2.17
4077 8202 4.991153 TGGTGCAGAAACAACACAATTA 57.009 36.364 0.00 0.00 36.00 1.40
4122 8247 7.550196 GGATACCATAAAAGGTTTGTAGTTCGA 59.450 37.037 0.00 0.00 43.08 3.71
4123 8248 7.334921 TGGATACCATAAAAGGTTTGTAGTTCG 59.665 37.037 0.00 0.00 43.08 3.95
4155 8280 7.985184 ACATTCAGGTCGTTATCAAGCTTAATA 59.015 33.333 0.00 0.00 0.00 0.98
4192 8317 2.825861 TTCAGTCCGTACCCTTGAAC 57.174 50.000 0.00 0.00 0.00 3.18
4204 12001 7.176589 TCTTCTCTAGAAAGGAATTCAGTCC 57.823 40.000 7.93 0.00 40.72 3.85
4269 12077 1.067071 CCGGTACTCTCTTGGGTTCAC 60.067 57.143 0.00 0.00 0.00 3.18
4274 12082 0.970937 TCAGCCGGTACTCTCTTGGG 60.971 60.000 1.90 0.00 0.00 4.12
4277 12085 2.166664 GTCATTCAGCCGGTACTCTCTT 59.833 50.000 1.90 0.00 0.00 2.85
4279 12087 1.751924 AGTCATTCAGCCGGTACTCTC 59.248 52.381 1.90 0.00 0.00 3.20
4280 12088 1.478510 CAGTCATTCAGCCGGTACTCT 59.521 52.381 1.90 0.00 0.00 3.24
4281 12089 1.476891 TCAGTCATTCAGCCGGTACTC 59.523 52.381 1.90 0.00 0.00 2.59
4282 12090 1.204941 GTCAGTCATTCAGCCGGTACT 59.795 52.381 1.90 0.00 0.00 2.73
4283 12091 1.204941 AGTCAGTCATTCAGCCGGTAC 59.795 52.381 1.90 0.00 0.00 3.34
4303 12130 8.690203 ATAATTTTGGTTGATGACGATATCCA 57.310 30.769 0.00 0.00 0.00 3.41
4323 12150 5.205517 TGTTGTGGATCCTGGGAATAATT 57.794 39.130 14.23 0.00 0.00 1.40
4326 12153 4.340617 GTTTGTTGTGGATCCTGGGAATA 58.659 43.478 14.23 0.00 0.00 1.75
4398 12259 1.538876 TACCTTGAGGCCAGCCAGT 60.539 57.895 12.03 0.00 39.32 4.00
4445 12306 2.613977 CCACTCTGCTTGTACCTTGAGG 60.614 54.545 0.00 0.00 42.17 3.86
4481 12342 0.603569 GACACGCCTCTTCCTGAAGA 59.396 55.000 9.14 9.14 44.47 2.87
4489 12376 1.069765 CACCTGTGACACGCCTCTT 59.930 57.895 0.22 0.00 0.00 2.85
4490 12377 2.737180 CACCTGTGACACGCCTCT 59.263 61.111 0.22 0.00 0.00 3.69
4620 12667 6.314784 GTTTTGCTACAGTGCTGTAATTAGG 58.685 40.000 12.41 3.16 44.47 2.69
4656 12703 2.035940 ACTCGCTCCTCCGACCTT 59.964 61.111 0.00 0.00 33.12 3.50
4781 12834 9.965824 ATAGTTATGTTGTTTTTCAAGAAGTGG 57.034 29.630 0.00 0.00 36.66 4.00


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

AutoCloner maintained by Alex Coulton.