Multiple sequence alignment - TraesCS7B01G204200

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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 TraesCS7B01G204200 chr7B 100.000 3080 0 0 1 3080 374557629 374560708 0.000000e+00 5688.0
1 TraesCS7B01G204200 chr7B 79.221 154 28 3 187 340 64780101 64780250 1.510000e-18 104.0
2 TraesCS7B01G204200 chr7B 100.000 31 0 0 2570 2600 259789058 259789028 1.190000e-04 58.4
3 TraesCS7B01G204200 chr7A 93.167 2078 77 24 399 2434 427611424 427613478 0.000000e+00 2990.0
4 TraesCS7B01G204200 chr7A 97.924 289 6 0 2792 3080 427614729 427615017 4.590000e-138 501.0
5 TraesCS7B01G204200 chr7A 90.777 206 18 1 1 205 427611162 427611367 1.090000e-69 274.0
6 TraesCS7B01G204200 chr7A 90.066 151 13 2 191 340 208247500 208247351 8.710000e-46 195.0
7 TraesCS7B01G204200 chr7D 92.975 1452 54 20 899 2321 379246139 379247571 0.000000e+00 2073.0
8 TraesCS7B01G204200 chr7D 97.551 245 5 1 2792 3036 379311789 379312032 4.750000e-113 418.0
9 TraesCS7B01G204200 chr7D 77.020 396 44 22 501 864 379245259 379245639 1.890000e-42 183.0
10 TraesCS7B01G204200 chr7D 94.737 114 5 1 2320 2433 379289232 379289344 3.160000e-40 176.0
11 TraesCS7B01G204200 chr7D 95.370 108 4 1 2973 3080 379312095 379312201 1.470000e-38 171.0
12 TraesCS7B01G204200 chr7D 94.231 104 6 0 399 502 379245125 379245228 3.180000e-35 159.0
13 TraesCS7B01G204200 chr7D 89.076 119 5 4 97 215 379244971 379245081 1.150000e-29 141.0
14 TraesCS7B01G204200 chr7D 98.438 64 1 0 2973 3036 379312032 379312095 2.510000e-21 113.0
15 TraesCS7B01G204200 chr7D 80.576 139 22 4 1 135 231400072 231399935 5.430000e-18 102.0
16 TraesCS7B01G204200 chr7D 98.039 51 1 0 2744 2794 379311713 379311763 4.230000e-14 89.8
17 TraesCS7B01G204200 chr6B 80.144 418 78 3 1215 1628 84848905 84848489 1.070000e-79 307.0
18 TraesCS7B01G204200 chr6B 82.394 142 20 5 1 139 637986780 637986641 5.400000e-23 119.0
19 TraesCS7B01G204200 chr6B 85.294 102 14 1 2571 2672 681025887 681025987 1.510000e-18 104.0
20 TraesCS7B01G204200 chr6D 78.066 424 80 6 1215 1627 36581793 36581372 3.940000e-64 255.0
21 TraesCS7B01G204200 chr6D 92.308 156 12 0 1929 2084 36581148 36580993 4.000000e-54 222.0
22 TraesCS7B01G204200 chr6D 89.172 157 14 3 188 344 450652881 450653034 3.130000e-45 193.0
23 TraesCS7B01G204200 chr5A 97.744 133 2 1 212 344 331398977 331399108 8.590000e-56 228.0
24 TraesCS7B01G204200 chr5A 97.656 128 3 0 213 340 642505178 642505305 1.440000e-53 220.0
25 TraesCS7B01G204200 chr5A 85.714 112 13 3 21 130 318761459 318761349 6.980000e-22 115.0
26 TraesCS7B01G204200 chr6A 98.438 128 2 0 212 339 133757560 133757433 3.090000e-55 226.0
27 TraesCS7B01G204200 chr3B 97.656 128 3 0 212 339 167260415 167260288 1.440000e-53 220.0
28 TraesCS7B01G204200 chr3B 92.466 146 8 3 212 355 182379431 182379287 4.030000e-49 206.0
29 TraesCS7B01G204200 chr3B 84.615 65 9 1 2678 2741 492568133 492568197 2.560000e-06 63.9
30 TraesCS7B01G204200 chr2B 97.656 128 3 0 213 340 667413376 667413249 1.440000e-53 220.0
31 TraesCS7B01G204200 chr1B 96.124 129 5 0 212 340 409879936 409879808 8.650000e-51 211.0
32 TraesCS7B01G204200 chr1B 93.182 132 8 1 208 339 543038772 543038902 3.130000e-45 193.0
33 TraesCS7B01G204200 chr1B 82.443 131 16 6 1 127 678344038 678344165 1.170000e-19 108.0
34 TraesCS7B01G204200 chr1B 81.301 123 20 3 10 130 58778200 58778321 2.530000e-16 97.1
35 TraesCS7B01G204200 chr1B 91.892 37 3 0 2636 2672 69196995 69197031 6.000000e-03 52.8
36 TraesCS7B01G204200 chr1D 93.056 144 7 3 203 343 178459500 178459643 1.120000e-49 207.0
37 TraesCS7B01G204200 chr3D 85.246 122 14 4 4 123 575216827 575216708 4.170000e-24 122.0
38 TraesCS7B01G204200 chr3D 85.938 64 9 0 2678 2741 378024929 378024992 5.510000e-08 69.4
39 TraesCS7B01G204200 chr5D 82.576 132 20 3 1 130 442630034 442629904 2.510000e-21 113.0
40 TraesCS7B01G204200 chr4A 83.193 119 17 3 14 130 418135788 418135671 4.200000e-19 106.0
41 TraesCS7B01G204200 chr3A 85.938 64 9 0 2678 2741 502097959 502098022 5.510000e-08 69.4
42 TraesCS7B01G204200 chr3A 77.119 118 15 5 2555 2671 663189049 663189155 1.190000e-04 58.4
43 TraesCS7B01G204200 chr4B 93.478 46 2 1 2555 2600 69613221 69613177 1.980000e-07 67.6
44 TraesCS7B01G204200 chr4B 91.304 46 4 0 2555 2600 427914240 427914285 2.560000e-06 63.9
45 TraesCS7B01G204200 chr1A 89.362 47 4 1 2547 2593 451286191 451286146 1.190000e-04 58.4
46 TraesCS7B01G204200 chr2D 100.000 29 0 0 2647 2675 78576582 78576610 2.000000e-03 54.7


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 TraesCS7B01G204200 chr7B 374557629 374560708 3079 False 5688.0 5688 100.0000 1 3080 1 chr7B.!!$F2 3079
1 TraesCS7B01G204200 chr7A 427611162 427615017 3855 False 1255.0 2990 93.9560 1 3080 3 chr7A.!!$F1 3079
2 TraesCS7B01G204200 chr7D 379244971 379247571 2600 False 639.0 2073 88.3255 97 2321 4 chr7D.!!$F2 2224
3 TraesCS7B01G204200 chr6D 36580993 36581793 800 True 238.5 255 85.1870 1215 2084 2 chr6D.!!$R1 869

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
363 369 0.037605 ATTCGGTTGGTCACGTCCTC 60.038 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2939 0.108963 ATGTTCCCGGGAAACGTCAA 59.891 50.0 37.18 18.2 42.24 3.18 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
52 53 5.871524 TCTCTGTTAGATTGCATGACTTGTC 59.128 40.000 0.00 0.00 0.00 3.18
56 58 8.043113 TCTGTTAGATTGCATGACTTGTCTATT 58.957 33.333 0.00 0.00 0.00 1.73
215 221 1.663702 GCCGCACTTGTGACGTACT 60.664 57.895 4.79 0.00 0.00 2.73
216 222 1.615107 GCCGCACTTGTGACGTACTC 61.615 60.000 4.79 0.00 0.00 2.59
217 223 1.007336 CCGCACTTGTGACGTACTCC 61.007 60.000 4.79 0.00 0.00 3.85
218 224 1.007336 CGCACTTGTGACGTACTCCC 61.007 60.000 4.79 0.00 0.00 4.30
219 225 0.317479 GCACTTGTGACGTACTCCCT 59.683 55.000 4.79 0.00 0.00 4.20
220 226 1.669211 GCACTTGTGACGTACTCCCTC 60.669 57.143 4.79 0.00 0.00 4.30
221 227 1.067776 CACTTGTGACGTACTCCCTCC 60.068 57.143 0.00 0.00 0.00 4.30
222 228 0.170561 CTTGTGACGTACTCCCTCCG 59.829 60.000 0.00 0.00 0.00 4.63
223 229 0.538057 TTGTGACGTACTCCCTCCGT 60.538 55.000 0.00 0.00 37.56 4.69
225 231 3.507290 GACGTACTCCCTCCGTCC 58.493 66.667 0.00 0.00 43.77 4.79
226 232 2.437359 ACGTACTCCCTCCGTCCG 60.437 66.667 0.00 0.00 0.00 4.79
227 233 2.124983 CGTACTCCCTCCGTCCGA 60.125 66.667 0.00 0.00 0.00 4.55
228 234 1.746615 CGTACTCCCTCCGTCCGAA 60.747 63.158 0.00 0.00 0.00 4.30
229 235 1.308069 CGTACTCCCTCCGTCCGAAA 61.308 60.000 0.00 0.00 0.00 3.46
230 236 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
231 237 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
232 238 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
233 239 1.755380 ACTCCCTCCGTCCGAAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
234 240 1.755380 CTCCCTCCGTCCGAAAATAGT 59.245 52.381 0.00 0.00 0.00 2.12
235 241 2.167900 CTCCCTCCGTCCGAAAATAGTT 59.832 50.000 0.00 0.00 0.00 2.24
236 242 2.093869 TCCCTCCGTCCGAAAATAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
237 243 2.354403 CCCTCCGTCCGAAAATAGTTGT 60.354 50.000 0.00 0.00 0.00 3.32
238 244 2.928116 CCTCCGTCCGAAAATAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
239 245 3.581755 CTCCGTCCGAAAATAGTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
240 246 4.181578 CTCCGTCCGAAAATAGTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
241 247 4.178540 TCCGTCCGAAAATAGTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
242 248 3.930229 CCGTCCGAAAATAGTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
243 249 4.390603 CCGTCCGAAAATAGTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
244 250 5.106869 CCGTCCGAAAATAGTTGTCATCAAA 60.107 40.000 0.00 0.00 35.20 2.69
245 251 6.367421 CGTCCGAAAATAGTTGTCATCAAAA 58.633 36.000 0.00 0.00 35.20 2.44
246 252 6.853872 CGTCCGAAAATAGTTGTCATCAAAAA 59.146 34.615 0.00 0.00 35.20 1.94
247 253 7.059488 CGTCCGAAAATAGTTGTCATCAAAAAG 59.941 37.037 0.00 0.00 35.20 2.27
248 254 8.073768 GTCCGAAAATAGTTGTCATCAAAAAGA 58.926 33.333 0.00 0.00 35.20 2.52
249 255 8.625651 TCCGAAAATAGTTGTCATCAAAAAGAA 58.374 29.630 0.00 0.00 35.20 2.52
250 256 9.410556 CCGAAAATAGTTGTCATCAAAAAGAAT 57.589 29.630 0.00 0.00 35.20 2.40
258 264 8.923270 AGTTGTCATCAAAAAGAATAAAAGGGA 58.077 29.630 0.00 0.00 35.20 4.20
259 265 9.541143 GTTGTCATCAAAAAGAATAAAAGGGAA 57.459 29.630 0.00 0.00 35.20 3.97
261 267 9.709495 TGTCATCAAAAAGAATAAAAGGGAATG 57.291 29.630 0.00 0.00 0.00 2.67
262 268 9.710900 GTCATCAAAAAGAATAAAAGGGAATGT 57.289 29.630 0.00 0.00 0.00 2.71
304 310 9.206690 AGTTCTAGATACATCTCTTTTCATCCA 57.793 33.333 0.00 0.00 38.32 3.41
305 311 9.995003 GTTCTAGATACATCTCTTTTCATCCAT 57.005 33.333 0.00 0.00 38.32 3.41
310 316 8.910944 AGATACATCTCTTTTCATCCATTTTGG 58.089 33.333 0.00 0.00 32.96 3.28
311 317 6.923199 ACATCTCTTTTCATCCATTTTGGT 57.077 33.333 0.00 0.00 39.03 3.67
312 318 6.694447 ACATCTCTTTTCATCCATTTTGGTG 58.306 36.000 0.00 0.00 39.03 4.17
313 319 6.494491 ACATCTCTTTTCATCCATTTTGGTGA 59.506 34.615 0.00 0.00 39.03 4.02
314 320 6.331369 TCTCTTTTCATCCATTTTGGTGAC 57.669 37.500 0.00 0.00 39.03 3.67
315 321 5.832595 TCTCTTTTCATCCATTTTGGTGACA 59.167 36.000 0.00 0.00 39.03 3.58
329 335 3.061322 TGGTGACAAGTATTTTCGGACG 58.939 45.455 0.00 0.00 37.44 4.79
330 336 2.414138 GGTGACAAGTATTTTCGGACGG 59.586 50.000 0.00 0.00 0.00 4.79
331 337 3.319755 GTGACAAGTATTTTCGGACGGA 58.680 45.455 0.00 0.00 0.00 4.69
332 338 3.367025 GTGACAAGTATTTTCGGACGGAG 59.633 47.826 0.00 0.00 0.00 4.63
333 339 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
334 340 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
335 341 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
336 342 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
337 343 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
338 344 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
339 345 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
360 366 1.504359 TTCATTCGGTTGGTCACGTC 58.496 50.000 0.00 0.00 0.00 4.34
361 367 0.320073 TCATTCGGTTGGTCACGTCC 60.320 55.000 0.00 0.00 0.00 4.79
363 369 0.037605 ATTCGGTTGGTCACGTCCTC 60.038 55.000 0.00 0.00 0.00 3.71
395 401 8.413309 TTTTGAAAGGACAATCATCATTCTCT 57.587 30.769 0.00 0.00 0.00 3.10
396 402 7.621428 TTGAAAGGACAATCATCATTCTCTC 57.379 36.000 0.00 0.00 0.00 3.20
397 403 5.814188 TGAAAGGACAATCATCATTCTCTCG 59.186 40.000 0.00 0.00 0.00 4.04
408 414 7.277174 TCATCATTCTCTCGTTAGCTGATAA 57.723 36.000 0.00 0.00 0.00 1.75
453 459 5.348451 CAGGTAACAGCCAAATAAAATGTGC 59.652 40.000 0.00 0.00 41.41 4.57
478 484 6.013898 CCCATCATTCTCTCTGCTCCTTATTA 60.014 42.308 0.00 0.00 0.00 0.98
543 581 3.490348 CAACATATGGCCTCCCCTAAAG 58.510 50.000 3.32 0.00 0.00 1.85
545 583 1.425066 CATATGGCCTCCCCTAAAGCA 59.575 52.381 3.32 0.00 0.00 3.91
546 584 0.843984 TATGGCCTCCCCTAAAGCAC 59.156 55.000 3.32 0.00 0.00 4.40
565 603 2.025981 CACCCTCCCATCATCAGAAACA 60.026 50.000 0.00 0.00 0.00 2.83
650 700 4.517453 TGACCAAGTAAAACGGGAATGAAG 59.483 41.667 0.00 0.00 0.00 3.02
736 808 4.040829 TGAATCAATCATAGGCTCATCGGT 59.959 41.667 0.00 0.00 31.50 4.69
742 814 1.683385 CATAGGCTCATCGGTCAGTGA 59.317 52.381 0.00 0.00 0.00 3.41
758 830 2.032550 CAGTGATTTGCAGCTAATCGGG 59.967 50.000 20.28 11.08 35.29 5.14
766 838 1.556564 CAGCTAATCGGGTGTGTACG 58.443 55.000 0.00 0.00 0.00 3.67
768 840 2.097954 CAGCTAATCGGGTGTGTACGTA 59.902 50.000 0.00 0.00 0.00 3.57
769 841 2.098117 AGCTAATCGGGTGTGTACGTAC 59.902 50.000 18.90 18.90 0.00 3.67
855 928 1.280421 CAGGCCTGCCTTCTCTACTTT 59.720 52.381 22.33 0.00 45.70 2.66
862 935 3.550820 TGCCTTCTCTACTTTTGTTGCA 58.449 40.909 0.00 0.00 0.00 4.08
863 936 4.144297 TGCCTTCTCTACTTTTGTTGCAT 58.856 39.130 0.00 0.00 0.00 3.96
864 937 5.312895 TGCCTTCTCTACTTTTGTTGCATA 58.687 37.500 0.00 0.00 0.00 3.14
865 938 5.945784 TGCCTTCTCTACTTTTGTTGCATAT 59.054 36.000 0.00 0.00 0.00 1.78
888 1415 5.871396 ATATATATACACCTCCCCAAGCG 57.129 43.478 0.00 0.00 0.00 4.68
946 1488 4.398358 CCCTTCGCTCGATCAGGTATATAA 59.602 45.833 8.63 0.00 0.00 0.98
947 1489 5.449314 CCCTTCGCTCGATCAGGTATATAAG 60.449 48.000 8.63 0.00 0.00 1.73
948 1490 5.124138 CCTTCGCTCGATCAGGTATATAAGT 59.876 44.000 0.00 0.00 0.00 2.24
949 1491 6.315642 CCTTCGCTCGATCAGGTATATAAGTA 59.684 42.308 0.00 0.00 0.00 2.24
970 1512 7.033530 AGTAGATAGATAGTCTGTGTTGTGC 57.966 40.000 0.00 0.00 0.00 4.57
1258 1809 4.819761 TGCTGTCGGCGCTGATCC 62.820 66.667 24.03 11.25 45.43 3.36
1558 2118 0.389817 CACCGCCGAGACATTCTTGA 60.390 55.000 0.00 0.00 29.08 3.02
1605 2165 0.742505 TCTTCGTAATCGTCGCCCAT 59.257 50.000 0.00 0.00 38.33 4.00
1658 2244 0.904649 TGCCCATCGATCTCACTTGT 59.095 50.000 0.00 0.00 0.00 3.16
1670 2275 6.039829 TCGATCTCACTTGTTCAGCTATATGT 59.960 38.462 0.00 0.00 0.00 2.29
1671 2276 6.362016 CGATCTCACTTGTTCAGCTATATGTC 59.638 42.308 0.00 0.00 0.00 3.06
1682 2287 8.924303 TGTTCAGCTATATGTCCTACTATTGTT 58.076 33.333 0.00 0.00 0.00 2.83
1849 2462 6.486657 CCATCCACGGTTAAATGAATCTGTAT 59.513 38.462 0.00 0.00 0.00 2.29
1876 2492 7.552687 TCAAACTGATTTTACCTGGCTAGTATG 59.447 37.037 0.00 0.00 0.00 2.39
1890 2506 9.871238 CCTGGCTAGTATGATAAATTACGTATT 57.129 33.333 0.00 0.00 0.00 1.89
2108 2724 1.342555 CCATCAATGCTTGCACGTTG 58.657 50.000 0.00 3.45 37.80 4.10
2159 2775 8.947115 GCTGCTAGGTCTAAATTTCTAAAGAAA 58.053 33.333 7.56 7.56 46.60 2.52
2201 2817 4.082274 TGCTGATTCATGCAACTAAACG 57.918 40.909 0.00 0.00 36.15 3.60
2202 2818 3.119884 TGCTGATTCATGCAACTAAACGG 60.120 43.478 0.00 0.00 36.15 4.44
2206 2822 1.529226 TCATGCAACTAAACGGGGTG 58.471 50.000 0.00 0.00 0.00 4.61
2323 2939 0.034186 TCCATTTCGGCAATCTGGCT 60.034 50.000 0.00 0.00 41.25 4.75
2411 3027 2.303022 TCTTGGAGCAAACTCGATTCCT 59.697 45.455 0.00 0.00 44.48 3.36
2422 3038 6.737070 GCAAACTCGATTCCTCATCAGATCTA 60.737 42.308 0.00 0.00 0.00 1.98
2423 3039 7.377398 CAAACTCGATTCCTCATCAGATCTAT 58.623 38.462 0.00 0.00 0.00 1.98
2434 3050 7.989741 TCCTCATCAGATCTATGAAAACTTTCC 59.010 37.037 0.00 0.00 36.36 3.13
2435 3051 7.228308 CCTCATCAGATCTATGAAAACTTTCCC 59.772 40.741 0.00 0.00 36.36 3.97
2436 3052 7.632861 TCATCAGATCTATGAAAACTTTCCCA 58.367 34.615 0.00 0.00 36.36 4.37
2437 3053 7.554118 TCATCAGATCTATGAAAACTTTCCCAC 59.446 37.037 0.00 0.00 36.36 4.61
2438 3054 7.020827 TCAGATCTATGAAAACTTTCCCACT 57.979 36.000 0.00 0.00 36.36 4.00
2439 3055 6.881065 TCAGATCTATGAAAACTTTCCCACTG 59.119 38.462 0.00 0.00 36.36 3.66
2440 3056 5.649831 AGATCTATGAAAACTTTCCCACTGC 59.350 40.000 0.00 0.00 36.36 4.40
2441 3057 3.751175 TCTATGAAAACTTTCCCACTGCG 59.249 43.478 0.00 0.00 36.36 5.18
2442 3058 1.757682 TGAAAACTTTCCCACTGCGT 58.242 45.000 0.00 0.00 36.36 5.24
2443 3059 2.920524 TGAAAACTTTCCCACTGCGTA 58.079 42.857 0.00 0.00 36.36 4.42
2444 3060 2.614983 TGAAAACTTTCCCACTGCGTAC 59.385 45.455 0.00 0.00 36.36 3.67
2445 3061 2.335316 AAACTTTCCCACTGCGTACA 57.665 45.000 0.00 0.00 0.00 2.90
2446 3062 5.744968 TGAAAACTTTCCCACTGCGTACAG 61.745 45.833 0.00 0.00 41.90 2.74
2447 3063 9.993598 TATGAAAACTTTCCCACTGCGTACAGT 62.994 40.741 0.00 0.00 46.00 3.55
2454 3070 2.507102 CTGCGTACAGTCCCAGCG 60.507 66.667 0.00 0.00 39.22 5.18
2455 3071 2.986979 TGCGTACAGTCCCAGCGA 60.987 61.111 0.00 0.00 0.00 4.93
2456 3072 2.260434 GCGTACAGTCCCAGCGAA 59.740 61.111 0.00 0.00 0.00 4.70
2457 3073 2.092882 GCGTACAGTCCCAGCGAAC 61.093 63.158 0.00 0.00 0.00 3.95
2458 3074 1.800315 CGTACAGTCCCAGCGAACG 60.800 63.158 0.00 0.00 0.00 3.95
2459 3075 2.092882 GTACAGTCCCAGCGAACGC 61.093 63.158 11.31 11.31 42.33 4.84
2460 3076 2.566570 TACAGTCCCAGCGAACGCA 61.567 57.895 20.66 0.00 44.88 5.24
2461 3077 1.884075 TACAGTCCCAGCGAACGCAT 61.884 55.000 20.66 3.91 44.88 4.73
2481 3097 4.282957 GCATCATCTCACCTCTCCTTATCA 59.717 45.833 0.00 0.00 0.00 2.15
2486 3102 6.612863 TCATCTCACCTCTCCTTATCAATTCA 59.387 38.462 0.00 0.00 0.00 2.57
2487 3103 6.477053 TCTCACCTCTCCTTATCAATTCAG 57.523 41.667 0.00 0.00 0.00 3.02
2490 3106 5.046529 CACCTCTCCTTATCAATTCAGTCG 58.953 45.833 0.00 0.00 0.00 4.18
2491 3107 4.054671 CCTCTCCTTATCAATTCAGTCGC 58.945 47.826 0.00 0.00 0.00 5.19
2492 3108 4.202202 CCTCTCCTTATCAATTCAGTCGCT 60.202 45.833 0.00 0.00 0.00 4.93
2493 3109 5.344743 TCTCCTTATCAATTCAGTCGCTT 57.655 39.130 0.00 0.00 0.00 4.68
2497 3113 4.260538 CCTTATCAATTCAGTCGCTTGCTC 60.261 45.833 0.00 0.00 0.00 4.26
2498 3114 2.462456 TCAATTCAGTCGCTTGCTCT 57.538 45.000 0.00 0.00 0.00 4.09
2499 3115 3.592898 TCAATTCAGTCGCTTGCTCTA 57.407 42.857 0.00 0.00 0.00 2.43
2500 3116 4.128925 TCAATTCAGTCGCTTGCTCTAT 57.871 40.909 0.00 0.00 0.00 1.98
2501 3117 3.867493 TCAATTCAGTCGCTTGCTCTATG 59.133 43.478 0.00 0.00 0.00 2.23
2502 3118 1.645034 TTCAGTCGCTTGCTCTATGC 58.355 50.000 0.00 0.00 43.25 3.14
2504 3120 0.460811 CAGTCGCTTGCTCTATGCCA 60.461 55.000 0.00 0.00 42.00 4.92
2506 3122 1.153369 TCGCTTGCTCTATGCCACC 60.153 57.895 0.00 0.00 42.00 4.61
2508 3124 1.156645 CGCTTGCTCTATGCCACCTC 61.157 60.000 0.00 0.00 42.00 3.85
2511 3127 1.971505 TTGCTCTATGCCACCTCCGG 61.972 60.000 0.00 0.00 42.00 5.14
2525 3141 4.595538 CCGGCCGCGGTAATGCTA 62.596 66.667 28.70 0.00 0.00 3.49
2526 3142 2.357034 CGGCCGCGGTAATGCTAT 60.357 61.111 28.70 0.00 0.00 2.97
2527 3143 1.959226 CGGCCGCGGTAATGCTATT 60.959 57.895 28.70 0.00 0.00 1.73
2528 3144 1.503818 CGGCCGCGGTAATGCTATTT 61.504 55.000 28.70 0.00 0.00 1.40
2529 3145 1.515081 GGCCGCGGTAATGCTATTTA 58.485 50.000 28.70 0.00 0.00 1.40
2530 3146 1.463444 GGCCGCGGTAATGCTATTTAG 59.537 52.381 28.70 0.00 0.00 1.85
2531 3147 2.140717 GCCGCGGTAATGCTATTTAGT 58.859 47.619 28.70 0.00 0.00 2.24
2532 3148 2.546789 GCCGCGGTAATGCTATTTAGTT 59.453 45.455 28.70 0.00 0.00 2.24
2533 3149 3.606153 GCCGCGGTAATGCTATTTAGTTG 60.606 47.826 28.70 0.00 0.00 3.16
2534 3150 3.805422 CCGCGGTAATGCTATTTAGTTGA 59.195 43.478 19.50 0.00 0.00 3.18
2535 3151 4.318546 CCGCGGTAATGCTATTTAGTTGAC 60.319 45.833 19.50 0.00 0.00 3.18
2536 3152 4.605354 CGCGGTAATGCTATTTAGTTGACG 60.605 45.833 0.00 0.00 0.00 4.35
2537 3153 4.269363 GCGGTAATGCTATTTAGTTGACGT 59.731 41.667 0.00 0.00 0.00 4.34
2538 3154 5.220529 GCGGTAATGCTATTTAGTTGACGTT 60.221 40.000 0.00 0.00 0.00 3.99
2539 3155 6.673796 GCGGTAATGCTATTTAGTTGACGTTT 60.674 38.462 0.00 0.00 0.00 3.60
2569 3185 2.761208 AGATGGTACTCCTTTCGTCCAG 59.239 50.000 0.00 0.00 34.23 3.86
2576 3192 5.105432 GGTACTCCTTTCGTCCAGAATTACT 60.105 44.000 0.00 0.00 38.86 2.24
2581 3197 4.994852 CCTTTCGTCCAGAATTACTTGTCA 59.005 41.667 0.00 0.00 38.86 3.58
2584 3200 4.951254 TCGTCCAGAATTACTTGTCACAA 58.049 39.130 0.00 0.00 0.00 3.33
2590 3206 7.920682 GTCCAGAATTACTTGTCACAAAAATGT 59.079 33.333 0.00 0.00 0.00 2.71
2661 4138 9.407514 CATTTTTGTGACAAGTAATTTGAAACG 57.592 29.630 0.00 0.00 39.21 3.60
2662 4139 8.744008 TTTTTGTGACAAGTAATTTGAAACGA 57.256 26.923 0.00 0.00 39.21 3.85
2664 4141 7.962934 TTGTGACAAGTAATTTGAAACGAAG 57.037 32.000 0.00 0.00 39.21 3.79
2680 4157 1.459592 CGAAGGGAGTACTTGCAAACG 59.540 52.381 0.00 0.00 0.00 3.60
2711 4188 6.055231 TGGCAATTTATATTGTCACGCTAC 57.945 37.500 8.85 0.00 46.43 3.58
2712 4189 5.008217 TGGCAATTTATATTGTCACGCTACC 59.992 40.000 8.85 0.06 46.43 3.18
2721 4198 3.300852 TGTCACGCTACCGACAATTTA 57.699 42.857 0.00 0.00 39.14 1.40
2734 4211 4.685628 CCGACAATTTAAGTTTGCAAGCAT 59.314 37.500 16.04 6.14 0.00 3.79
2735 4212 5.388682 CCGACAATTTAAGTTTGCAAGCATG 60.389 40.000 16.04 6.82 0.00 4.06
2736 4213 5.388682 CGACAATTTAAGTTTGCAAGCATGG 60.389 40.000 16.04 0.43 0.00 3.66
2760 4281 6.473455 GGCAAATTCTAAAATTGTCATCCTCG 59.527 38.462 0.00 0.00 35.27 4.63
2787 4308 6.033831 CGTCAAAATCATTAACAGTTGCCATC 59.966 38.462 0.00 0.00 0.00 3.51
2811 4360 5.167121 CCGCCAAAATTGTTCATCATACAA 58.833 37.500 0.00 0.00 39.58 2.41
2850 4399 0.337428 AGGATGGGCCAGAAAATGCT 59.663 50.000 13.78 1.58 40.02 3.79
2872 4421 1.102222 GGGTGCCAAAACGGTGTGTA 61.102 55.000 0.00 0.00 36.97 2.90
2895 4444 9.066892 TGTATATCTTTCATCACCTATTTTGGC 57.933 33.333 0.00 0.00 0.00 4.52
2915 4464 6.132791 TGGCGATTTTGTGTACTTGTTTAA 57.867 33.333 0.00 0.00 0.00 1.52
3006 4555 3.119955 GGACTTCGGGTACAATTTGAAGC 60.120 47.826 2.79 0.00 39.64 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.471456 ACAGAGAGAAGGCAAGTAACATTTG 59.529 40.000 0.00 0.00 0.00 2.32
12 13 5.234466 ACAGAGAGAAGGCAAGTAACATT 57.766 39.130 0.00 0.00 0.00 2.71
19 20 4.332268 GCAATCTAACAGAGAGAAGGCAAG 59.668 45.833 0.00 0.00 37.70 4.01
23 24 5.523188 GTCATGCAATCTAACAGAGAGAAGG 59.477 44.000 0.00 0.00 37.70 3.46
123 125 6.378280 GGTTCAAATGATGTACTCCTTGGAAT 59.622 38.462 0.00 0.00 28.12 3.01
130 132 4.202050 GCCATGGTTCAAATGATGTACTCC 60.202 45.833 14.67 0.00 30.66 3.85
131 133 4.202050 GGCCATGGTTCAAATGATGTACTC 60.202 45.833 14.67 0.00 30.66 2.59
164 166 7.171678 AGGCTTATCGACAAAATATAAGACAGC 59.828 37.037 7.97 0.00 41.67 4.40
215 221 1.856629 ACTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
216 222 2.277084 CAACTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
217 223 2.928116 GACAACTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
218 224 3.581755 TGACAACTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
219 225 3.663995 TGACAACTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
220 226 3.930229 TGATGACAACTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
221 227 5.524511 TTGATGACAACTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
222 228 8.073768 TCTTTTTGATGACAACTATTTTCGGAC 58.926 33.333 0.00 0.00 35.63 4.79
223 229 8.160521 TCTTTTTGATGACAACTATTTTCGGA 57.839 30.769 0.00 0.00 35.63 4.55
224 230 8.795786 TTCTTTTTGATGACAACTATTTTCGG 57.204 30.769 0.00 0.00 35.63 4.30
232 238 8.923270 TCCCTTTTATTCTTTTTGATGACAACT 58.077 29.630 0.00 0.00 35.63 3.16
233 239 9.541143 TTCCCTTTTATTCTTTTTGATGACAAC 57.459 29.630 0.00 0.00 35.63 3.32
235 241 9.709495 CATTCCCTTTTATTCTTTTTGATGACA 57.291 29.630 0.00 0.00 0.00 3.58
236 242 9.710900 ACATTCCCTTTTATTCTTTTTGATGAC 57.289 29.630 0.00 0.00 0.00 3.06
278 284 9.206690 TGGATGAAAAGAGATGTATCTAGAACT 57.793 33.333 0.00 0.00 37.25 3.01
279 285 9.995003 ATGGATGAAAAGAGATGTATCTAGAAC 57.005 33.333 0.00 0.00 37.25 3.01
284 290 8.910944 CCAAAATGGATGAAAAGAGATGTATCT 58.089 33.333 0.00 0.00 40.96 1.98
285 291 8.689972 ACCAAAATGGATGAAAAGAGATGTATC 58.310 33.333 2.85 0.00 40.96 2.24
286 292 8.472413 CACCAAAATGGATGAAAAGAGATGTAT 58.528 33.333 2.85 0.00 40.96 2.29
287 293 7.669304 TCACCAAAATGGATGAAAAGAGATGTA 59.331 33.333 2.85 0.00 40.96 2.29
288 294 6.494491 TCACCAAAATGGATGAAAAGAGATGT 59.506 34.615 2.85 0.00 40.96 3.06
289 295 6.810182 GTCACCAAAATGGATGAAAAGAGATG 59.190 38.462 2.85 0.00 40.96 2.90
290 296 6.494491 TGTCACCAAAATGGATGAAAAGAGAT 59.506 34.615 2.85 0.00 40.96 2.75
291 297 5.832595 TGTCACCAAAATGGATGAAAAGAGA 59.167 36.000 2.85 0.00 40.96 3.10
292 298 6.088016 TGTCACCAAAATGGATGAAAAGAG 57.912 37.500 2.85 0.00 40.96 2.85
293 299 6.098124 ACTTGTCACCAAAATGGATGAAAAGA 59.902 34.615 23.67 4.78 40.96 2.52
294 300 6.282930 ACTTGTCACCAAAATGGATGAAAAG 58.717 36.000 19.37 19.37 40.96 2.27
295 301 6.232581 ACTTGTCACCAAAATGGATGAAAA 57.767 33.333 2.85 4.39 40.96 2.29
296 302 5.867903 ACTTGTCACCAAAATGGATGAAA 57.132 34.783 2.85 0.00 40.96 2.69
297 303 7.537596 AATACTTGTCACCAAAATGGATGAA 57.462 32.000 2.85 0.00 40.96 2.57
298 304 7.537596 AAATACTTGTCACCAAAATGGATGA 57.462 32.000 2.85 0.97 40.96 2.92
299 305 7.062138 CGAAAATACTTGTCACCAAAATGGATG 59.938 37.037 2.85 0.00 40.96 3.51
300 306 7.090173 CGAAAATACTTGTCACCAAAATGGAT 58.910 34.615 2.85 0.00 40.96 3.41
301 307 6.442952 CGAAAATACTTGTCACCAAAATGGA 58.557 36.000 2.85 0.00 40.96 3.41
302 308 5.633182 CCGAAAATACTTGTCACCAAAATGG 59.367 40.000 0.00 0.00 45.02 3.16
303 309 6.362283 GTCCGAAAATACTTGTCACCAAAATG 59.638 38.462 0.00 0.00 0.00 2.32
304 310 6.443792 GTCCGAAAATACTTGTCACCAAAAT 58.556 36.000 0.00 0.00 0.00 1.82
305 311 5.504337 CGTCCGAAAATACTTGTCACCAAAA 60.504 40.000 0.00 0.00 0.00 2.44
306 312 4.024725 CGTCCGAAAATACTTGTCACCAAA 60.025 41.667 0.00 0.00 0.00 3.28
307 313 3.495377 CGTCCGAAAATACTTGTCACCAA 59.505 43.478 0.00 0.00 0.00 3.67
308 314 3.061322 CGTCCGAAAATACTTGTCACCA 58.939 45.455 0.00 0.00 0.00 4.17
309 315 2.414138 CCGTCCGAAAATACTTGTCACC 59.586 50.000 0.00 0.00 0.00 4.02
310 316 3.319755 TCCGTCCGAAAATACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
311 317 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
312 318 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
313 319 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
314 320 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
315 321 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
316 322 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
317 323 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
318 324 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
319 325 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
320 326 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
321 327 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
322 328 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
323 329 0.033796 AATGTACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
324 330 0.384669 GAATGTACTCCCTCCGTCCG 59.615 60.000 0.00 0.00 0.00 4.79
325 331 1.481871 TGAATGTACTCCCTCCGTCC 58.518 55.000 0.00 0.00 0.00 4.79
326 332 3.718815 GAATGAATGTACTCCCTCCGTC 58.281 50.000 0.00 0.00 0.00 4.79
327 333 2.100916 CGAATGAATGTACTCCCTCCGT 59.899 50.000 0.00 0.00 0.00 4.69
328 334 2.545952 CCGAATGAATGTACTCCCTCCG 60.546 54.545 0.00 0.00 0.00 4.63
329 335 2.434702 ACCGAATGAATGTACTCCCTCC 59.565 50.000 0.00 0.00 0.00 4.30
330 336 3.821421 ACCGAATGAATGTACTCCCTC 57.179 47.619 0.00 0.00 0.00 4.30
331 337 3.370527 CCAACCGAATGAATGTACTCCCT 60.371 47.826 0.00 0.00 0.00 4.20
332 338 2.943033 CCAACCGAATGAATGTACTCCC 59.057 50.000 0.00 0.00 0.00 4.30
333 339 3.606687 ACCAACCGAATGAATGTACTCC 58.393 45.455 0.00 0.00 0.00 3.85
334 340 4.092968 GTGACCAACCGAATGAATGTACTC 59.907 45.833 0.00 0.00 0.00 2.59
335 341 4.000988 GTGACCAACCGAATGAATGTACT 58.999 43.478 0.00 0.00 0.00 2.73
336 342 3.181524 CGTGACCAACCGAATGAATGTAC 60.182 47.826 0.00 0.00 0.00 2.90
337 343 2.997303 CGTGACCAACCGAATGAATGTA 59.003 45.455 0.00 0.00 0.00 2.29
338 344 1.804151 CGTGACCAACCGAATGAATGT 59.196 47.619 0.00 0.00 0.00 2.71
339 345 1.804151 ACGTGACCAACCGAATGAATG 59.196 47.619 0.00 0.00 0.00 2.67
369 375 8.863086 AGAGAATGATGATTGTCCTTTCAAAAA 58.137 29.630 0.00 0.00 33.25 1.94
371 377 7.148356 CGAGAGAATGATGATTGTCCTTTCAAA 60.148 37.037 0.00 0.00 33.25 2.69
372 378 6.314648 CGAGAGAATGATGATTGTCCTTTCAA 59.685 38.462 0.00 0.00 33.25 2.69
373 379 5.814188 CGAGAGAATGATGATTGTCCTTTCA 59.186 40.000 0.00 0.00 33.25 2.69
374 380 5.814705 ACGAGAGAATGATGATTGTCCTTTC 59.185 40.000 0.00 0.00 33.25 2.62
375 381 5.738909 ACGAGAGAATGATGATTGTCCTTT 58.261 37.500 0.00 0.00 33.25 3.11
376 382 5.350504 ACGAGAGAATGATGATTGTCCTT 57.649 39.130 0.00 0.00 33.25 3.36
377 383 5.350504 AACGAGAGAATGATGATTGTCCT 57.649 39.130 0.00 0.00 33.25 3.85
378 384 5.176590 GCTAACGAGAGAATGATGATTGTCC 59.823 44.000 0.00 0.00 33.25 4.02
379 385 5.982516 AGCTAACGAGAGAATGATGATTGTC 59.017 40.000 0.00 0.00 33.02 3.18
383 389 5.781210 TCAGCTAACGAGAGAATGATGAT 57.219 39.130 0.00 0.00 0.00 2.45
384 390 5.781210 ATCAGCTAACGAGAGAATGATGA 57.219 39.130 0.00 0.00 0.00 2.92
385 391 7.651304 ACTTTATCAGCTAACGAGAGAATGATG 59.349 37.037 14.02 0.00 31.03 3.07
386 392 7.721402 ACTTTATCAGCTAACGAGAGAATGAT 58.279 34.615 0.00 2.50 32.40 2.45
387 393 7.101652 ACTTTATCAGCTAACGAGAGAATGA 57.898 36.000 0.00 0.00 0.00 2.57
388 394 7.276658 ACAACTTTATCAGCTAACGAGAGAATG 59.723 37.037 0.00 0.00 0.00 2.67
389 395 7.324178 ACAACTTTATCAGCTAACGAGAGAAT 58.676 34.615 0.00 0.00 0.00 2.40
390 396 6.688578 ACAACTTTATCAGCTAACGAGAGAA 58.311 36.000 0.00 0.00 0.00 2.87
391 397 6.072119 TGACAACTTTATCAGCTAACGAGAGA 60.072 38.462 0.00 0.00 0.00 3.10
392 398 6.093404 TGACAACTTTATCAGCTAACGAGAG 58.907 40.000 0.00 0.00 0.00 3.20
393 399 6.020971 TGACAACTTTATCAGCTAACGAGA 57.979 37.500 0.00 0.00 0.00 4.04
394 400 6.366332 ACTTGACAACTTTATCAGCTAACGAG 59.634 38.462 0.00 0.00 0.00 4.18
395 401 6.220930 ACTTGACAACTTTATCAGCTAACGA 58.779 36.000 0.00 0.00 0.00 3.85
396 402 6.467723 ACTTGACAACTTTATCAGCTAACG 57.532 37.500 0.00 0.00 0.00 3.18
397 403 8.989980 ACTTACTTGACAACTTTATCAGCTAAC 58.010 33.333 0.00 0.00 0.00 2.34
408 414 5.031066 TGGCTGTACTTACTTGACAACTT 57.969 39.130 0.00 0.00 0.00 2.66
453 459 2.048601 AGGAGCAGAGAGAATGATGGG 58.951 52.381 0.00 0.00 0.00 4.00
478 484 5.986501 TTTATACGGCAAACATTCCCTTT 57.013 34.783 0.00 0.00 0.00 3.11
494 500 7.210873 ACGAGGGAATGTTCTCAGATTTATAC 58.789 38.462 0.00 0.00 0.00 1.47
543 581 0.548031 TTCTGATGATGGGAGGGTGC 59.452 55.000 0.00 0.00 0.00 5.01
545 583 2.278245 TGTTTCTGATGATGGGAGGGT 58.722 47.619 0.00 0.00 0.00 4.34
546 584 3.370840 TTGTTTCTGATGATGGGAGGG 57.629 47.619 0.00 0.00 0.00 4.30
565 603 5.991606 TGACGTCTGAATTCTCTCATGTTTT 59.008 36.000 17.92 0.00 0.00 2.43
650 700 1.078759 CCTTGTCGATGTCTGGCGTC 61.079 60.000 0.00 0.00 0.00 5.19
736 808 2.938451 CCGATTAGCTGCAAATCACTGA 59.062 45.455 1.02 0.00 33.75 3.41
742 814 1.745087 CACACCCGATTAGCTGCAAAT 59.255 47.619 1.02 0.00 0.00 2.32
758 830 5.695816 TCCATACAAAAAGGTACGTACACAC 59.304 40.000 26.02 9.95 0.00 3.82
766 838 5.766174 TGTCCTTGTCCATACAAAAAGGTAC 59.234 40.000 0.00 0.00 44.79 3.34
768 840 4.798882 TGTCCTTGTCCATACAAAAAGGT 58.201 39.130 0.00 0.00 44.79 3.50
769 841 5.782893 TTGTCCTTGTCCATACAAAAAGG 57.217 39.130 0.00 0.00 44.79 3.11
862 935 9.256228 CGCTTGGGGAGGTGTATATATATATAT 57.744 37.037 17.37 17.37 33.68 0.86
863 936 8.229605 ACGCTTGGGGAGGTGTATATATATATA 58.770 37.037 8.16 8.16 0.00 0.86
864 937 7.073854 ACGCTTGGGGAGGTGTATATATATAT 58.926 38.462 10.10 10.10 0.00 0.86
865 938 6.437755 ACGCTTGGGGAGGTGTATATATATA 58.562 40.000 0.00 0.00 0.00 0.86
888 1415 2.743636 TCGAGGTGAGTTCCAATGAC 57.256 50.000 0.00 0.00 0.00 3.06
946 1488 6.831353 AGCACAACACAGACTATCTATCTACT 59.169 38.462 0.00 0.00 0.00 2.57
947 1489 6.915300 CAGCACAACACAGACTATCTATCTAC 59.085 42.308 0.00 0.00 0.00 2.59
948 1490 6.039829 CCAGCACAACACAGACTATCTATCTA 59.960 42.308 0.00 0.00 0.00 1.98
949 1491 5.163468 CCAGCACAACACAGACTATCTATCT 60.163 44.000 0.00 0.00 0.00 1.98
970 1512 9.314321 CTGGTTAGTGATTAGTAATTGTACCAG 57.686 37.037 18.62 18.62 30.81 4.00
1068 1610 4.778415 CTCCTGTCGGTGCCGTCG 62.778 72.222 10.60 2.38 40.74 5.12
1190 1741 3.121030 CCGCCAGCACCTTCTTCG 61.121 66.667 0.00 0.00 0.00 3.79
1258 1809 3.103911 GTCGTGGGTCGCGTTCAG 61.104 66.667 5.77 0.00 38.57 3.02
1326 1877 4.961511 AGCGACGCCACGAGCAAA 62.962 61.111 17.79 0.00 44.04 3.68
1467 2018 2.747855 GCCTTGGCCACGAAGGAG 60.748 66.667 23.76 9.42 42.44 3.69
1545 2105 3.794028 GGAACTCGATCAAGAATGTCTCG 59.206 47.826 0.00 0.00 35.56 4.04
1605 2165 4.424711 GCCTTGGGATCGGTGGCA 62.425 66.667 11.18 0.00 42.79 4.92
1670 2275 6.015772 GGACAAAAGGCAAAACAATAGTAGGA 60.016 38.462 0.00 0.00 0.00 2.94
1671 2276 6.156519 GGACAAAAGGCAAAACAATAGTAGG 58.843 40.000 0.00 0.00 0.00 3.18
1682 2287 0.463620 GCTGGTGGACAAAAGGCAAA 59.536 50.000 0.00 0.00 0.00 3.68
1849 2462 6.303839 ACTAGCCAGGTAAAATCAGTTTGAA 58.696 36.000 0.00 0.00 0.00 2.69
1852 2465 7.630082 TCATACTAGCCAGGTAAAATCAGTTT 58.370 34.615 0.00 0.00 0.00 2.66
1890 2506 7.163441 ACATGCATGCATTATGTCAGATAGTA 58.837 34.615 30.32 0.00 39.08 1.82
1891 2507 6.002082 ACATGCATGCATTATGTCAGATAGT 58.998 36.000 30.32 16.89 39.08 2.12
1892 2508 6.496338 ACATGCATGCATTATGTCAGATAG 57.504 37.500 30.32 16.25 39.08 2.08
2108 2724 5.422214 TCTCTGGTAGAGTTTTTCATCCC 57.578 43.478 5.81 0.00 42.83 3.85
2165 2781 8.717821 CATGAATCAGCAAATTCACAATTTCTT 58.282 29.630 13.91 0.00 45.68 2.52
2201 2817 1.677217 GCACTGATCACTCTTCACCCC 60.677 57.143 0.00 0.00 0.00 4.95
2202 2818 1.002430 TGCACTGATCACTCTTCACCC 59.998 52.381 0.00 0.00 0.00 4.61
2323 2939 0.108963 ATGTTCCCGGGAAACGTCAA 59.891 50.000 37.18 18.20 42.24 3.18
2328 2944 2.736144 GGAAAATGTTCCCGGGAAAC 57.264 50.000 37.18 28.18 46.84 2.78
2411 3027 7.554118 GTGGGAAAGTTTTCATAGATCTGATGA 59.446 37.037 5.18 7.97 38.92 2.92
2422 3038 2.306847 ACGCAGTGGGAAAGTTTTCAT 58.693 42.857 14.98 0.00 42.51 2.57
2423 3039 1.757682 ACGCAGTGGGAAAGTTTTCA 58.242 45.000 14.98 0.00 42.51 2.69
2438 3054 2.566570 TTCGCTGGGACTGTACGCA 61.567 57.895 0.00 0.00 0.00 5.24
2439 3055 2.092882 GTTCGCTGGGACTGTACGC 61.093 63.158 0.00 0.00 0.00 4.42
2440 3056 1.800315 CGTTCGCTGGGACTGTACG 60.800 63.158 0.00 0.00 0.00 3.67
2441 3057 2.092882 GCGTTCGCTGGGACTGTAC 61.093 63.158 9.99 0.00 0.00 2.90
2442 3058 1.884075 ATGCGTTCGCTGGGACTGTA 61.884 55.000 17.63 0.00 0.00 2.74
2443 3059 3.240134 ATGCGTTCGCTGGGACTGT 62.240 57.895 17.63 0.00 0.00 3.55
2444 3060 2.434884 ATGCGTTCGCTGGGACTG 60.435 61.111 17.63 0.00 0.00 3.51
2445 3061 2.125512 GATGCGTTCGCTGGGACT 60.126 61.111 17.63 0.00 0.00 3.85
2446 3062 1.766143 GATGATGCGTTCGCTGGGAC 61.766 60.000 17.63 5.92 0.00 4.46
2447 3063 1.521457 GATGATGCGTTCGCTGGGA 60.521 57.895 17.63 0.00 0.00 4.37
2448 3064 1.493950 GAGATGATGCGTTCGCTGGG 61.494 60.000 17.63 0.00 0.00 4.45
2449 3065 0.807275 TGAGATGATGCGTTCGCTGG 60.807 55.000 17.63 0.00 0.00 4.85
2450 3066 0.299895 GTGAGATGATGCGTTCGCTG 59.700 55.000 17.63 0.00 0.00 5.18
2451 3067 0.807667 GGTGAGATGATGCGTTCGCT 60.808 55.000 17.63 4.07 0.00 4.93
2452 3068 0.807667 AGGTGAGATGATGCGTTCGC 60.808 55.000 10.34 10.34 0.00 4.70
2453 3069 1.202348 AGAGGTGAGATGATGCGTTCG 60.202 52.381 0.00 0.00 0.00 3.95
2454 3070 2.468831 GAGAGGTGAGATGATGCGTTC 58.531 52.381 0.00 0.00 0.00 3.95
2455 3071 1.137872 GGAGAGGTGAGATGATGCGTT 59.862 52.381 0.00 0.00 0.00 4.84
2456 3072 0.749649 GGAGAGGTGAGATGATGCGT 59.250 55.000 0.00 0.00 0.00 5.24
2457 3073 1.039068 AGGAGAGGTGAGATGATGCG 58.961 55.000 0.00 0.00 0.00 4.73
2458 3074 4.282957 TGATAAGGAGAGGTGAGATGATGC 59.717 45.833 0.00 0.00 0.00 3.91
2459 3075 6.416631 TTGATAAGGAGAGGTGAGATGATG 57.583 41.667 0.00 0.00 0.00 3.07
2460 3076 7.291885 TGAATTGATAAGGAGAGGTGAGATGAT 59.708 37.037 0.00 0.00 0.00 2.45
2461 3077 6.612863 TGAATTGATAAGGAGAGGTGAGATGA 59.387 38.462 0.00 0.00 0.00 2.92
2481 3097 2.611292 GCATAGAGCAAGCGACTGAATT 59.389 45.455 0.00 0.00 44.79 2.17
2491 3107 3.836871 CCGGAGGTGGCATAGAGCAAG 62.837 61.905 0.00 0.00 45.69 4.01
2492 3108 1.971505 CCGGAGGTGGCATAGAGCAA 61.972 60.000 0.00 0.00 45.69 3.91
2493 3109 2.434843 CCGGAGGTGGCATAGAGCA 61.435 63.158 0.00 0.00 45.69 4.26
2511 3127 2.140717 ACTAAATAGCATTACCGCGGC 58.859 47.619 28.58 11.19 36.85 6.53
2514 3130 4.269363 ACGTCAACTAAATAGCATTACCGC 59.731 41.667 0.00 0.00 0.00 5.68
2515 3131 5.961395 ACGTCAACTAAATAGCATTACCG 57.039 39.130 0.00 0.00 0.00 4.02
2517 3133 7.216317 CAGCAAACGTCAACTAAATAGCATTAC 59.784 37.037 0.00 0.00 0.00 1.89
2519 3135 6.086222 CAGCAAACGTCAACTAAATAGCATT 58.914 36.000 0.00 0.00 0.00 3.56
2521 3137 4.083537 CCAGCAAACGTCAACTAAATAGCA 60.084 41.667 0.00 0.00 0.00 3.49
2522 3138 4.403453 CCAGCAAACGTCAACTAAATAGC 58.597 43.478 0.00 0.00 0.00 2.97
2523 3139 4.693566 TCCCAGCAAACGTCAACTAAATAG 59.306 41.667 0.00 0.00 0.00 1.73
2524 3140 4.643463 TCCCAGCAAACGTCAACTAAATA 58.357 39.130 0.00 0.00 0.00 1.40
2525 3141 3.482436 TCCCAGCAAACGTCAACTAAAT 58.518 40.909 0.00 0.00 0.00 1.40
2526 3142 2.875933 CTCCCAGCAAACGTCAACTAAA 59.124 45.455 0.00 0.00 0.00 1.85
2527 3143 2.103432 TCTCCCAGCAAACGTCAACTAA 59.897 45.455 0.00 0.00 0.00 2.24
2528 3144 1.689813 TCTCCCAGCAAACGTCAACTA 59.310 47.619 0.00 0.00 0.00 2.24
2529 3145 0.468226 TCTCCCAGCAAACGTCAACT 59.532 50.000 0.00 0.00 0.00 3.16
2530 3146 0.868406 CTCTCCCAGCAAACGTCAAC 59.132 55.000 0.00 0.00 0.00 3.18
2531 3147 0.756294 TCTCTCCCAGCAAACGTCAA 59.244 50.000 0.00 0.00 0.00 3.18
2532 3148 0.976641 ATCTCTCCCAGCAAACGTCA 59.023 50.000 0.00 0.00 0.00 4.35
2533 3149 1.363744 CATCTCTCCCAGCAAACGTC 58.636 55.000 0.00 0.00 0.00 4.34
2534 3150 0.036010 CCATCTCTCCCAGCAAACGT 60.036 55.000 0.00 0.00 0.00 3.99
2535 3151 0.036010 ACCATCTCTCCCAGCAAACG 60.036 55.000 0.00 0.00 0.00 3.60
2536 3152 2.237392 AGTACCATCTCTCCCAGCAAAC 59.763 50.000 0.00 0.00 0.00 2.93
2537 3153 2.501723 GAGTACCATCTCTCCCAGCAAA 59.498 50.000 0.00 0.00 0.00 3.68
2538 3154 2.111384 GAGTACCATCTCTCCCAGCAA 58.889 52.381 0.00 0.00 0.00 3.91
2539 3155 1.689575 GGAGTACCATCTCTCCCAGCA 60.690 57.143 0.00 0.00 42.96 4.41
2560 3176 5.361427 TGTGACAAGTAATTCTGGACGAAA 58.639 37.500 0.00 0.00 34.79 3.46
2661 4138 2.490991 ACGTTTGCAAGTACTCCCTTC 58.509 47.619 0.00 0.00 0.00 3.46
2662 4139 2.632987 ACGTTTGCAAGTACTCCCTT 57.367 45.000 0.00 0.00 0.00 3.95
2664 4141 3.703286 AAAACGTTTGCAAGTACTCCC 57.297 42.857 15.46 0.00 0.00 4.30
2703 4180 3.916761 ACTTAAATTGTCGGTAGCGTGA 58.083 40.909 14.79 1.97 0.00 4.35
2705 4182 4.612033 GCAAACTTAAATTGTCGGTAGCGT 60.612 41.667 14.79 0.00 0.00 5.07
2711 4188 4.047822 TGCTTGCAAACTTAAATTGTCGG 58.952 39.130 0.00 0.00 0.00 4.79
2712 4189 5.388682 CCATGCTTGCAAACTTAAATTGTCG 60.389 40.000 0.00 0.00 0.00 4.35
2734 4211 7.243604 AGGATGACAATTTTAGAATTTGCCA 57.756 32.000 0.00 0.00 33.25 4.92
2735 4212 6.473455 CGAGGATGACAATTTTAGAATTTGCC 59.527 38.462 0.00 0.00 33.25 4.52
2736 4213 6.473455 CCGAGGATGACAATTTTAGAATTTGC 59.527 38.462 0.00 0.00 33.25 3.68
2760 4281 4.089923 GCAACTGTTAATGATTTTGACGCC 59.910 41.667 0.00 0.00 0.00 5.68
2787 4308 2.739885 TGATGAACAATTTTGGCGGG 57.260 45.000 0.00 0.00 0.00 6.13
2850 4399 1.826054 CACCGTTTTGGCACCCTCA 60.826 57.895 0.00 0.00 43.94 3.86
2872 4421 6.998074 TCGCCAAAATAGGTGATGAAAGATAT 59.002 34.615 0.00 0.00 42.94 1.63


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

AutoCloner maintained by Alex Coulton.