Multiple sequence alignment - TraesCS5A01G334900

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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 TraesCS5A01G334900 chr5A 100.000 6259 0 0 1 6259 544243133 544249391 0.000000e+00 11559
1 TraesCS5A01G334900 chr5A 86.227 2062 269 12 3214 5271 544454304 544456354 0.000000e+00 2220
2 TraesCS5A01G334900 chr5A 85.536 2081 273 16 3215 5278 544503770 544505839 0.000000e+00 2150
3 TraesCS5A01G334900 chr5A 87.906 1695 200 3 3638 5327 544463367 544465061 0.000000e+00 1989
4 TraesCS5A01G334900 chr5A 83.215 1412 200 22 997 2392 544158548 544159938 0.000000e+00 1260
5 TraesCS5A01G334900 chr5A 82.309 1464 221 23 961 2399 544452859 544454309 0.000000e+00 1234
6 TraesCS5A01G334900 chr5A 81.909 1404 221 22 1023 2398 544502375 544503773 0.000000e+00 1155
7 TraesCS5A01G334900 chr5D 98.066 2120 39 1 3213 5330 428594377 428596496 0.000000e+00 3687
8 TraesCS5A01G334900 chr5D 95.290 2017 66 14 386 2400 428592395 428594384 0.000000e+00 3171
9 TraesCS5A01G334900 chr5D 88.669 2074 218 12 3222 5287 428513610 428515674 0.000000e+00 2512
10 TraesCS5A01G334900 chr5D 87.500 2096 247 10 3217 5303 428566912 428569001 0.000000e+00 2405
11 TraesCS5A01G334900 chr5D 86.119 2118 277 14 3214 5326 428672041 428674146 0.000000e+00 2266
12 TraesCS5A01G334900 chr5D 82.370 1747 234 44 687 2392 428511887 428513600 0.000000e+00 1452
13 TraesCS5A01G334900 chr5D 90.568 933 82 4 5330 6259 458781371 458782300 0.000000e+00 1230
14 TraesCS5A01G334900 chr5D 83.236 1372 197 22 1033 2393 428565559 428566908 0.000000e+00 1229
15 TraesCS5A01G334900 chr5D 90.247 933 85 6 5330 6259 387991283 387992212 0.000000e+00 1214
16 TraesCS5A01G334900 chr5D 82.121 1443 222 21 981 2399 428670616 428672046 0.000000e+00 1203
17 TraesCS5A01G334900 chr5D 92.975 242 16 1 23 263 428592163 428592404 9.980000e-93 351
18 TraesCS5A01G334900 chr5D 82.192 146 18 7 688 830 428520417 428520557 1.100000e-22 119
19 TraesCS5A01G334900 chr5B 97.972 2120 41 1 3213 5330 517776305 517778424 0.000000e+00 3675
20 TraesCS5A01G334900 chr5B 95.259 2025 77 9 386 2400 517774297 517776312 0.000000e+00 3190
21 TraesCS5A01G334900 chr5B 86.106 2116 277 12 3216 5326 517799107 517801210 0.000000e+00 2263
22 TraesCS5A01G334900 chr5B 85.111 2109 280 20 3214 5300 517695767 517697863 0.000000e+00 2124
23 TraesCS5A01G334900 chr5B 82.488 1439 227 13 981 2399 517797677 517799110 0.000000e+00 1238
24 TraesCS5A01G334900 chr5B 90.299 938 82 5 5329 6259 566046713 566047648 0.000000e+00 1219
25 TraesCS5A01G334900 chr5B 89.574 940 83 13 5330 6259 692300872 692301806 0.000000e+00 1179
26 TraesCS5A01G334900 chr5B 80.579 1416 231 33 997 2399 517694388 517695772 0.000000e+00 1051
27 TraesCS5A01G334900 chr5B 87.129 202 24 1 2393 2594 183380909 183381108 1.760000e-55 228
28 TraesCS5A01G334900 chr5B 86.869 198 22 4 2399 2593 127194560 127194364 1.060000e-52 219
29 TraesCS5A01G334900 chr5B 97.600 125 3 0 262 386 397406953 397407077 1.370000e-51 215
30 TraesCS5A01G334900 chr5B 81.712 257 27 13 23 263 517774054 517774306 4.950000e-46 196
31 TraesCS5A01G334900 chr4B 98.773 815 9 1 2400 3213 172751994 172752808 0.000000e+00 1448
32 TraesCS5A01G334900 chr4B 87.245 196 21 4 2401 2593 653083169 653083363 2.940000e-53 220
33 TraesCS5A01G334900 chr4B 84.746 177 20 7 3043 3216 653083833 653084005 3.000000e-38 171
34 TraesCS5A01G334900 chrUn 90.548 931 83 5 5330 6259 310745234 310746160 0.000000e+00 1227
35 TraesCS5A01G334900 chr2D 90.743 929 71 10 5330 6253 596031652 596032570 0.000000e+00 1225
36 TraesCS5A01G334900 chr3A 90.343 932 86 4 5330 6259 257086774 257085845 0.000000e+00 1219
37 TraesCS5A01G334900 chr3A 97.581 124 3 0 262 385 38291816 38291693 4.920000e-51 213
38 TraesCS5A01G334900 chr1D 90.257 934 87 4 5328 6259 201774971 201774040 0.000000e+00 1218
39 TraesCS5A01G334900 chr7A 90.129 932 86 6 5330 6259 287819616 287818689 0.000000e+00 1206
40 TraesCS5A01G334900 chr7A 98.387 124 2 0 262 385 607549733 607549856 1.060000e-52 219
41 TraesCS5A01G334900 chr7D 91.220 205 16 1 2397 2599 549360497 549360701 1.720000e-70 278
42 TraesCS5A01G334900 chr1A 90.860 186 17 0 3027 3212 48582695 48582510 3.750000e-62 250
43 TraesCS5A01G334900 chr1A 97.638 127 2 1 259 385 335996453 335996328 3.800000e-52 217
44 TraesCS5A01G334900 chr6A 87.113 194 23 1 2401 2594 151519832 151519641 1.060000e-52 219
45 TraesCS5A01G334900 chr6A 86.364 198 25 1 2400 2597 322014930 322014735 1.370000e-51 215
46 TraesCS5A01G334900 chr6A 97.581 124 3 0 262 385 107177406 107177529 4.920000e-51 213
47 TraesCS5A01G334900 chr7B 98.374 123 2 0 263 385 607428327 607428449 3.800000e-52 217
48 TraesCS5A01G334900 chr4D 86.567 201 21 4 2400 2598 293520124 293520320 3.800000e-52 217
49 TraesCS5A01G334900 chr6B 86.802 197 21 4 2399 2594 696500032 696500224 1.370000e-51 215
50 TraesCS5A01G334900 chr4A 97.600 125 3 0 262 386 615120066 615119942 1.370000e-51 215
51 TraesCS5A01G334900 chr1B 97.561 123 3 0 263 385 648709628 648709750 1.770000e-50 211
52 TraesCS5A01G334900 chr2A 96.094 128 5 0 258 385 544155094 544155221 6.360000e-50 209
53 TraesCS5A01G334900 chr3D 78.947 171 21 9 3050 3217 400667029 400667187 1.110000e-17 102


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 TraesCS5A01G334900 chr5A 544243133 544249391 6258 False 11559.000000 11559 100.000000 1 6259 1 chr5A.!!$F2 6258
1 TraesCS5A01G334900 chr5A 544463367 544465061 1694 False 1989.000000 1989 87.906000 3638 5327 1 chr5A.!!$F3 1689
2 TraesCS5A01G334900 chr5A 544452859 544456354 3495 False 1727.000000 2220 84.268000 961 5271 2 chr5A.!!$F4 4310
3 TraesCS5A01G334900 chr5A 544502375 544505839 3464 False 1652.500000 2150 83.722500 1023 5278 2 chr5A.!!$F5 4255
4 TraesCS5A01G334900 chr5A 544158548 544159938 1390 False 1260.000000 1260 83.215000 997 2392 1 chr5A.!!$F1 1395
5 TraesCS5A01G334900 chr5D 428592163 428596496 4333 False 2403.000000 3687 95.443667 23 5330 3 chr5D.!!$F6 5307
6 TraesCS5A01G334900 chr5D 428511887 428515674 3787 False 1982.000000 2512 85.519500 687 5287 2 chr5D.!!$F4 4600
7 TraesCS5A01G334900 chr5D 428565559 428569001 3442 False 1817.000000 2405 85.368000 1033 5303 2 chr5D.!!$F5 4270
8 TraesCS5A01G334900 chr5D 428670616 428674146 3530 False 1734.500000 2266 84.120000 981 5326 2 chr5D.!!$F7 4345
9 TraesCS5A01G334900 chr5D 458781371 458782300 929 False 1230.000000 1230 90.568000 5330 6259 1 chr5D.!!$F3 929
10 TraesCS5A01G334900 chr5D 387991283 387992212 929 False 1214.000000 1214 90.247000 5330 6259 1 chr5D.!!$F1 929
11 TraesCS5A01G334900 chr5B 517774054 517778424 4370 False 2353.666667 3675 91.647667 23 5330 3 chr5B.!!$F6 5307
12 TraesCS5A01G334900 chr5B 517797677 517801210 3533 False 1750.500000 2263 84.297000 981 5326 2 chr5B.!!$F7 4345
13 TraesCS5A01G334900 chr5B 517694388 517697863 3475 False 1587.500000 2124 82.845000 997 5300 2 chr5B.!!$F5 4303
14 TraesCS5A01G334900 chr5B 566046713 566047648 935 False 1219.000000 1219 90.299000 5329 6259 1 chr5B.!!$F3 930
15 TraesCS5A01G334900 chr5B 692300872 692301806 934 False 1179.000000 1179 89.574000 5330 6259 1 chr5B.!!$F4 929
16 TraesCS5A01G334900 chr4B 172751994 172752808 814 False 1448.000000 1448 98.773000 2400 3213 1 chr4B.!!$F1 813
17 TraesCS5A01G334900 chrUn 310745234 310746160 926 False 1227.000000 1227 90.548000 5330 6259 1 chrUn.!!$F1 929
18 TraesCS5A01G334900 chr2D 596031652 596032570 918 False 1225.000000 1225 90.743000 5330 6253 1 chr2D.!!$F1 923
19 TraesCS5A01G334900 chr3A 257085845 257086774 929 True 1219.000000 1219 90.343000 5330 6259 1 chr3A.!!$R2 929
20 TraesCS5A01G334900 chr1D 201774040 201774971 931 True 1218.000000 1218 90.257000 5328 6259 1 chr1D.!!$R1 931
21 TraesCS5A01G334900 chr7A 287818689 287819616 927 True 1206.000000 1206 90.129000 5330 6259 1 chr7A.!!$R1 929

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
690 709 0.026803 GACCGCATCAATCGCAGAAC 59.973 55.000 0.0 0.0 43.58 3.01 F
1046 1103 0.456221 CTACATCGCCTGGTTCTCGT 59.544 55.000 0.0 0.0 0.00 4.18 F
2000 2093 1.128809 TTGACCGGCCCTGTTCCTTA 61.129 55.000 0.0 0.0 0.00 2.69 F
3215 3309 0.321564 CCGATTGCCAGGTTGAGTCA 60.322 55.000 0.0 0.0 0.00 3.41 F
4289 4396 1.442520 CGTGCGCAAAAGGGATGTG 60.443 57.895 14.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2011 1.613255 CCCAAACTCTGCCGGTATTGT 60.613 52.381 1.90 0.0 0.00 2.71 R
2937 3031 1.734465 CTTGAATCTCACCGAGTTGGC 59.266 52.381 0.00 0.0 43.94 4.52 R
3819 3921 1.074889 GGCCCAAACTACCAGGAAGAA 59.925 52.381 0.00 0.0 0.00 2.52 R
5153 5268 1.889829 CACCGTCTCACTTCTTCCTCT 59.110 52.381 0.00 0.0 0.00 3.69 R
6192 6339 0.905357 CCTTGAGACTTGACCGGGAT 59.095 55.000 6.32 0.0 0.00 3.85 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
109 114 6.865834 AGATAGATCAACAGTTGGAGAAGT 57.134 37.500 13.52 0.00 0.00 3.01
160 165 2.242965 TCCCCTTAGTGACGGTCATAGA 59.757 50.000 14.78 0.00 0.00 1.98
164 172 5.290386 CCCTTAGTGACGGTCATAGAAATC 58.710 45.833 14.78 0.00 0.00 2.17
170 178 4.209288 GTGACGGTCATAGAAATCGATTGG 59.791 45.833 14.78 0.00 0.00 3.16
175 183 4.511826 GGTCATAGAAATCGATTGGTGGAC 59.488 45.833 12.25 14.64 0.00 4.02
254 270 6.789457 TCATTTCAGACCATCCTCTACCATAT 59.211 38.462 0.00 0.00 0.00 1.78
255 271 7.293299 TCATTTCAGACCATCCTCTACCATATT 59.707 37.037 0.00 0.00 0.00 1.28
256 272 6.672266 TTCAGACCATCCTCTACCATATTC 57.328 41.667 0.00 0.00 0.00 1.75
257 273 5.087323 TCAGACCATCCTCTACCATATTCC 58.913 45.833 0.00 0.00 0.00 3.01
258 274 4.840680 CAGACCATCCTCTACCATATTCCA 59.159 45.833 0.00 0.00 0.00 3.53
259 275 5.307976 CAGACCATCCTCTACCATATTCCAA 59.692 44.000 0.00 0.00 0.00 3.53
260 276 5.911178 AGACCATCCTCTACCATATTCCAAA 59.089 40.000 0.00 0.00 0.00 3.28
261 277 5.941788 ACCATCCTCTACCATATTCCAAAC 58.058 41.667 0.00 0.00 0.00 2.93
262 278 4.997395 CCATCCTCTACCATATTCCAAACG 59.003 45.833 0.00 0.00 0.00 3.60
263 279 4.682778 TCCTCTACCATATTCCAAACGG 57.317 45.455 0.00 0.00 0.00 4.44
264 280 4.291792 TCCTCTACCATATTCCAAACGGA 58.708 43.478 0.00 0.00 0.00 4.69
265 281 4.100498 TCCTCTACCATATTCCAAACGGAC 59.900 45.833 0.00 0.00 30.04 4.79
266 282 4.049186 CTCTACCATATTCCAAACGGACG 58.951 47.826 0.00 0.00 30.04 4.79
267 283 3.700539 TCTACCATATTCCAAACGGACGA 59.299 43.478 0.00 0.00 30.04 4.20
268 284 2.901249 ACCATATTCCAAACGGACGAG 58.099 47.619 0.00 0.00 30.04 4.18
269 285 2.210116 CCATATTCCAAACGGACGAGG 58.790 52.381 0.00 0.00 30.04 4.63
270 286 2.159014 CCATATTCCAAACGGACGAGGA 60.159 50.000 0.00 0.01 30.04 3.71
271 287 3.494398 CCATATTCCAAACGGACGAGGAT 60.494 47.826 0.00 0.00 30.04 3.24
272 288 2.311124 ATTCCAAACGGACGAGGATC 57.689 50.000 0.00 0.00 30.04 3.36
273 289 0.248289 TTCCAAACGGACGAGGATCC 59.752 55.000 2.48 2.48 35.16 3.36
274 290 0.613853 TCCAAACGGACGAGGATCCT 60.614 55.000 16.13 16.13 36.52 3.24
275 291 0.179108 CCAAACGGACGAGGATCCTC 60.179 60.000 29.15 29.15 36.52 3.71
276 292 0.818296 CAAACGGACGAGGATCCTCT 59.182 55.000 33.70 22.77 40.69 3.69
277 293 0.818296 AAACGGACGAGGATCCTCTG 59.182 55.000 33.70 28.14 40.69 3.35
278 294 0.034380 AACGGACGAGGATCCTCTGA 60.034 55.000 33.70 0.00 40.69 3.27
279 295 0.183971 ACGGACGAGGATCCTCTGAT 59.816 55.000 33.70 21.61 40.69 2.90
280 296 0.595588 CGGACGAGGATCCTCTGATG 59.404 60.000 33.70 22.60 40.69 3.07
281 297 1.698506 GGACGAGGATCCTCTGATGT 58.301 55.000 33.70 25.33 40.69 3.06
282 298 2.810767 CGGACGAGGATCCTCTGATGTA 60.811 54.545 33.70 0.00 40.69 2.29
283 299 2.554893 GGACGAGGATCCTCTGATGTAC 59.445 54.545 33.70 22.91 40.69 2.90
284 300 2.222886 ACGAGGATCCTCTGATGTACG 58.777 52.381 33.70 22.92 40.69 3.67
285 301 1.537638 CGAGGATCCTCTGATGTACGG 59.462 57.143 33.70 15.09 40.69 4.02
286 302 1.271102 GAGGATCCTCTGATGTACGGC 59.729 57.143 31.11 3.75 39.80 5.68
287 303 1.040646 GGATCCTCTGATGTACGGCA 58.959 55.000 3.84 0.00 0.00 5.69
288 304 1.000283 GGATCCTCTGATGTACGGCAG 60.000 57.143 3.84 8.12 0.00 4.85
289 305 0.390860 ATCCTCTGATGTACGGCAGC 59.609 55.000 9.28 0.00 32.27 5.25
290 306 1.227380 CCTCTGATGTACGGCAGCC 60.227 63.158 0.00 0.00 31.34 4.85
291 307 1.680522 CCTCTGATGTACGGCAGCCT 61.681 60.000 10.54 0.00 31.34 4.58
292 308 0.529337 CTCTGATGTACGGCAGCCTG 60.529 60.000 10.54 5.77 31.34 4.85
293 309 2.125147 TGATGTACGGCAGCCTGC 60.125 61.111 8.55 8.55 44.08 4.85
302 318 3.426568 GCAGCCTGCCGTTCTGTC 61.427 66.667 5.06 0.00 37.42 3.51
303 319 2.031012 CAGCCTGCCGTTCTGTCA 59.969 61.111 0.00 0.00 0.00 3.58
304 320 2.031163 AGCCTGCCGTTCTGTCAC 59.969 61.111 0.00 0.00 0.00 3.67
305 321 2.031163 GCCTGCCGTTCTGTCACT 59.969 61.111 0.00 0.00 0.00 3.41
306 322 2.320587 GCCTGCCGTTCTGTCACTG 61.321 63.158 0.00 0.00 0.00 3.66
307 323 1.367471 CCTGCCGTTCTGTCACTGA 59.633 57.895 0.00 0.00 0.00 3.41
308 324 0.946221 CCTGCCGTTCTGTCACTGAC 60.946 60.000 1.86 1.86 0.00 3.51
309 325 0.249447 CTGCCGTTCTGTCACTGACA 60.249 55.000 11.44 11.44 40.50 3.58
310 326 0.392706 TGCCGTTCTGTCACTGACAT 59.607 50.000 12.34 0.00 41.94 3.06
311 327 0.792640 GCCGTTCTGTCACTGACATG 59.207 55.000 12.34 7.20 41.94 3.21
312 328 1.873903 GCCGTTCTGTCACTGACATGT 60.874 52.381 12.34 0.00 41.94 3.21
313 329 1.794701 CCGTTCTGTCACTGACATGTG 59.205 52.381 12.34 1.75 41.94 3.21
314 330 1.794701 CGTTCTGTCACTGACATGTGG 59.205 52.381 12.34 1.40 41.94 4.17
315 331 2.146342 GTTCTGTCACTGACATGTGGG 58.854 52.381 12.34 1.04 41.94 4.61
316 332 0.035317 TCTGTCACTGACATGTGGGC 59.965 55.000 12.34 0.00 41.94 5.36
317 333 0.957395 CTGTCACTGACATGTGGGCC 60.957 60.000 12.34 0.00 41.94 5.80
318 334 1.376466 GTCACTGACATGTGGGCCT 59.624 57.895 1.15 0.00 38.40 5.19
319 335 0.250901 GTCACTGACATGTGGGCCTT 60.251 55.000 1.15 0.00 38.40 4.35
320 336 0.478072 TCACTGACATGTGGGCCTTT 59.522 50.000 1.15 0.00 38.40 3.11
321 337 1.133513 TCACTGACATGTGGGCCTTTT 60.134 47.619 1.15 0.00 38.40 2.27
322 338 1.000060 CACTGACATGTGGGCCTTTTG 60.000 52.381 1.15 1.57 34.56 2.44
323 339 0.604578 CTGACATGTGGGCCTTTTGG 59.395 55.000 1.15 0.00 44.18 3.28
324 340 0.831288 TGACATGTGGGCCTTTTGGG 60.831 55.000 1.15 0.00 40.82 4.12
325 341 0.541764 GACATGTGGGCCTTTTGGGA 60.542 55.000 1.15 0.00 40.82 4.37
326 342 0.105246 ACATGTGGGCCTTTTGGGAA 60.105 50.000 4.53 0.00 40.82 3.97
327 343 0.321346 CATGTGGGCCTTTTGGGAAC 59.679 55.000 4.53 0.00 40.82 3.62
340 356 2.440599 GGAACCTGGCCCACATGT 59.559 61.111 0.00 0.00 0.00 3.21
341 357 1.678970 GGAACCTGGCCCACATGTC 60.679 63.158 0.00 0.00 0.00 3.06
342 358 1.074775 GAACCTGGCCCACATGTCA 59.925 57.895 0.00 0.00 0.00 3.58
343 359 0.962356 GAACCTGGCCCACATGTCAG 60.962 60.000 0.00 0.00 0.00 3.51
344 360 1.719063 AACCTGGCCCACATGTCAGT 61.719 55.000 0.00 0.00 0.00 3.41
345 361 1.676635 CCTGGCCCACATGTCAGTG 60.677 63.158 0.00 0.00 39.21 3.66
351 367 4.498346 CACATGTCAGTGGCCCAA 57.502 55.556 0.00 0.00 35.88 4.12
352 368 1.959085 CACATGTCAGTGGCCCAAC 59.041 57.895 0.00 0.00 35.88 3.77
353 369 1.600636 ACATGTCAGTGGCCCAACG 60.601 57.895 0.00 0.00 0.00 4.10
354 370 2.034066 ATGTCAGTGGCCCAACGG 59.966 61.111 0.00 0.00 0.00 4.44
381 397 4.803426 CACGGCAGAGGAGCGTCC 62.803 72.222 0.00 0.00 36.58 4.79
492 510 6.762702 TGAAGATATGTCATTTGCACACAT 57.237 33.333 0.00 0.00 35.00 3.21
502 520 5.115472 GTCATTTGCACACATAAACGTCAAG 59.885 40.000 0.00 0.00 0.00 3.02
537 556 7.910162 GTCGAATACAGTCAACAATGCAATTAT 59.090 33.333 0.00 0.00 32.46 1.28
666 685 6.207417 AGTCACAATGATCTGAAACCGAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
690 709 0.026803 GACCGCATCAATCGCAGAAC 59.973 55.000 0.00 0.00 43.58 3.01
728 747 0.603569 GACTCAGCCAAGGTCTTCGA 59.396 55.000 0.00 0.00 0.00 3.71
749 768 1.071987 CAGGTGAGAGGCAAGTGCA 59.928 57.895 5.52 0.00 44.36 4.57
754 773 1.065854 GTGAGAGGCAAGTGCATAGGT 60.066 52.381 5.52 0.00 44.36 3.08
769 788 2.762535 TAGGTGTGTTAGGCTGCTTC 57.237 50.000 0.00 0.00 0.00 3.86
839 878 2.852075 ACACCACCATCACCGGGT 60.852 61.111 6.32 0.00 39.88 5.28
842 881 0.825840 CACCACCATCACCGGGTTTT 60.826 55.000 6.32 0.00 36.19 2.43
858 897 0.944386 TTTTGGCGTTCTGCTCTCAC 59.056 50.000 0.00 0.00 45.43 3.51
863 902 1.560860 GCGTTCTGCTCTCACACACC 61.561 60.000 0.00 0.00 41.73 4.16
864 903 1.278172 CGTTCTGCTCTCACACACCG 61.278 60.000 0.00 0.00 0.00 4.94
921 968 1.745232 TTTCGCCTGTGTGTGTCTTT 58.255 45.000 0.00 0.00 0.00 2.52
978 1025 1.945394 CACTTGGCCTATGCAGTCATC 59.055 52.381 3.32 0.00 40.13 2.92
989 1042 6.517362 GCCTATGCAGTCATCTTCATAGTACA 60.517 42.308 11.54 0.00 42.26 2.90
1046 1103 0.456221 CTACATCGCCTGGTTCTCGT 59.544 55.000 0.00 0.00 0.00 4.18
1069 1129 3.683966 CTCCTCCTGCTGCTGCCTG 62.684 68.421 13.47 5.96 38.71 4.85
1188 1260 3.797256 GGAAATCATCCGTCAAGTACTCG 59.203 47.826 0.00 0.00 38.79 4.18
1289 1374 1.746615 CACGCAGAGGAACCATGGG 60.747 63.158 18.09 0.00 0.00 4.00
1392 1485 2.232452 CCTTGTCAACCTCGATCTCAGT 59.768 50.000 0.00 0.00 0.00 3.41
2000 2093 1.128809 TTGACCGGCCCTGTTCCTTA 61.129 55.000 0.00 0.00 0.00 2.69
2398 2491 6.737254 ACCTTACCAATTTAGTCGTCATTG 57.263 37.500 0.00 0.00 0.00 2.82
2550 2644 1.813753 CATAGGTTCGTGCCCGTGG 60.814 63.158 0.00 0.00 35.01 4.94
2937 3031 5.166398 CAAGGTAGTTTTAGTACCACCTCG 58.834 45.833 12.05 0.00 44.76 4.63
3100 3194 1.306056 ATGGGTTTGGGCATGGGTC 60.306 57.895 0.00 0.00 0.00 4.46
3166 3260 3.888930 CGATTAGTATTTGGGCATGGGTT 59.111 43.478 0.00 0.00 0.00 4.11
3180 3274 2.754946 TGGGTTTGGTAGATGTCGAC 57.245 50.000 9.11 9.11 0.00 4.20
3213 3307 1.002134 CCCGATTGCCAGGTTGAGT 60.002 57.895 0.00 0.00 0.00 3.41
3214 3308 1.026718 CCCGATTGCCAGGTTGAGTC 61.027 60.000 0.00 0.00 0.00 3.36
3215 3309 0.321564 CCGATTGCCAGGTTGAGTCA 60.322 55.000 0.00 0.00 0.00 3.41
3216 3310 1.679944 CCGATTGCCAGGTTGAGTCAT 60.680 52.381 0.00 0.00 0.00 3.06
3217 3311 2.086869 CGATTGCCAGGTTGAGTCATT 58.913 47.619 0.00 0.00 0.00 2.57
3241 3335 2.719739 CTGGATGACAACCAGCTGATT 58.280 47.619 17.79 0.00 46.30 2.57
3543 3637 5.661312 TGATACAAGGCAGTATACCTTCTGT 59.339 40.000 0.00 0.41 44.35 3.41
3793 3887 5.577835 TGTTTGAAACTGCAGTCATTACAC 58.422 37.500 21.95 12.34 0.00 2.90
3819 3921 6.245408 TGAATAACAACAGCCTTAGTGGAAT 58.755 36.000 0.00 0.00 38.35 3.01
4275 4382 3.684788 ACCTCAAAATACTGATGTCGTGC 59.315 43.478 0.00 0.00 0.00 5.34
4289 4396 1.442520 CGTGCGCAAAAGGGATGTG 60.443 57.895 14.00 0.00 0.00 3.21
4995 5110 5.570844 GCAGAATGTTCCTACACTTCCCTAA 60.571 44.000 0.00 0.00 39.31 2.69
5153 5268 1.701031 TTCCACAACCCGAAGCTGGA 61.701 55.000 0.00 0.00 0.00 3.86
5307 5435 7.177832 TGTAGCATCTTAGCCTTGTTTAGTA 57.822 36.000 0.00 0.00 34.23 1.82
5354 5484 4.974645 AGAATAAATCCGAGGCATACCA 57.025 40.909 0.00 0.00 39.06 3.25
5429 5560 2.231478 CGAGGTTCACCGATATGGCTAT 59.769 50.000 0.00 0.00 43.94 2.97
5434 5565 4.406003 GGTTCACCGATATGGCTATATCCT 59.594 45.833 20.67 6.76 41.32 3.24
5437 5568 3.883489 CACCGATATGGCTATATCCTCGA 59.117 47.826 20.67 0.00 41.32 4.04
5438 5569 4.338400 CACCGATATGGCTATATCCTCGAA 59.662 45.833 20.67 0.00 41.32 3.71
5444 5575 2.289072 TGGCTATATCCTCGAAGCTTGC 60.289 50.000 2.10 0.00 35.30 4.01
5608 5742 3.052490 AGAGGCCTAGGATACAAGTGTCT 60.052 47.826 14.75 0.00 41.41 3.41
5633 5767 4.651503 ACTTGGACACTACTCCATATCCTG 59.348 45.833 0.00 0.00 40.18 3.86
5638 5772 5.474189 GGACACTACTCCATATCCTGTCTAC 59.526 48.000 0.00 0.00 0.00 2.59
5643 5777 3.961408 ACTCCATATCCTGTCTACACACC 59.039 47.826 0.00 0.00 0.00 4.16
5644 5778 2.956333 TCCATATCCTGTCTACACACCG 59.044 50.000 0.00 0.00 0.00 4.94
5648 5782 1.159285 TCCTGTCTACACACCGTACG 58.841 55.000 8.69 8.69 0.00 3.67
5656 5790 0.746063 ACACACCGTACGACTCCAAA 59.254 50.000 18.76 0.00 0.00 3.28
5672 5806 6.195600 ACTCCAAATCCAACTGTAACCTAA 57.804 37.500 0.00 0.00 0.00 2.69
5681 5815 6.887013 TCCAACTGTAACCTAACTTGTACAA 58.113 36.000 8.28 8.28 0.00 2.41
5748 5882 0.796312 CACCACCTTGAATTCGTCCG 59.204 55.000 0.04 0.00 0.00 4.79
5759 5893 1.562575 ATTCGTCCGTGCGTCAAACC 61.563 55.000 0.00 0.00 0.00 3.27
5763 5897 1.952133 TCCGTGCGTCAAACCTTCG 60.952 57.895 0.00 0.00 0.00 3.79
5853 5996 4.092116 AGTCCCTTCTTTTCTTGACCAG 57.908 45.455 0.00 0.00 0.00 4.00
5877 6022 6.780706 AGTCAACACTCGAACGAAATTAAT 57.219 33.333 0.00 0.00 0.00 1.40
5880 6025 8.126700 AGTCAACACTCGAACGAAATTAATTTT 58.873 29.630 14.45 0.00 0.00 1.82
5902 6047 4.566004 TCACATTACTCTAGTTTGCGCTT 58.434 39.130 9.73 0.00 0.00 4.68
6024 6170 2.550830 ACTCAACATCACCGCTCTTT 57.449 45.000 0.00 0.00 0.00 2.52
6144 6290 0.898320 CCTGGTCCGTCTTCATGTCT 59.102 55.000 0.00 0.00 0.00 3.41
6176 6323 1.324740 ACGCCTCACCGCTATTACCA 61.325 55.000 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.881751 GGAACCTACAATGTAGGAGTACTTTTT 59.118 37.037 37.71 22.31 38.09 1.94
12 13 6.944096 GGAACCTACAATGTAGGAGTACTTT 58.056 40.000 37.71 23.56 38.09 2.66
13 14 6.541934 GGAACCTACAATGTAGGAGTACTT 57.458 41.667 37.71 24.19 38.09 2.24
78 83 9.421399 TCCAACTGTTGATCTATCTATCTTGTA 57.579 33.333 21.49 0.00 0.00 2.41
89 94 6.174720 ACAACTTCTCCAACTGTTGATCTA 57.825 37.500 21.49 3.81 41.35 1.98
93 98 5.741011 AGTAACAACTTCTCCAACTGTTGA 58.259 37.500 21.49 7.21 41.35 3.18
109 114 2.554893 GCAACCCCATTCGAAGTAACAA 59.445 45.455 3.35 0.00 0.00 2.83
160 165 1.750778 GGCATGTCCACCAATCGATTT 59.249 47.619 8.21 0.00 34.01 2.17
164 172 0.180171 TAGGGCATGTCCACCAATCG 59.820 55.000 20.74 0.00 36.21 3.34
170 178 2.938956 ATAGCTTAGGGCATGTCCAC 57.061 50.000 20.74 4.78 44.79 4.02
254 270 4.045103 GAGGATCCTCGTCCGTTTGGAA 62.045 54.545 25.78 0.00 43.27 3.53
255 271 0.613853 AGGATCCTCGTCCGTTTGGA 60.614 55.000 9.02 0.00 43.27 3.53
256 272 0.179108 GAGGATCCTCGTCCGTTTGG 60.179 60.000 25.78 0.00 43.27 3.28
257 273 0.818296 AGAGGATCCTCGTCCGTTTG 59.182 55.000 31.51 0.00 46.90 2.93
258 274 0.818296 CAGAGGATCCTCGTCCGTTT 59.182 55.000 31.51 13.24 46.90 3.60
259 275 0.034380 TCAGAGGATCCTCGTCCGTT 60.034 55.000 31.51 13.95 46.90 4.44
260 276 0.183971 ATCAGAGGATCCTCGTCCGT 59.816 55.000 31.51 14.67 46.90 4.69
261 277 0.595588 CATCAGAGGATCCTCGTCCG 59.404 60.000 31.51 21.97 46.90 4.79
262 278 1.698506 ACATCAGAGGATCCTCGTCC 58.301 55.000 31.51 12.72 46.90 4.79
263 279 2.224549 CGTACATCAGAGGATCCTCGTC 59.775 54.545 31.51 13.31 46.90 4.20
264 280 2.222886 CGTACATCAGAGGATCCTCGT 58.777 52.381 31.51 25.16 46.90 4.18
265 281 1.537638 CCGTACATCAGAGGATCCTCG 59.462 57.143 31.51 25.65 46.90 4.63
266 282 1.271102 GCCGTACATCAGAGGATCCTC 59.729 57.143 31.27 31.27 43.03 3.71
267 283 1.333177 GCCGTACATCAGAGGATCCT 58.667 55.000 16.13 16.13 33.66 3.24
268 284 1.000283 CTGCCGTACATCAGAGGATCC 60.000 57.143 2.48 2.48 33.66 3.36
269 285 1.604185 GCTGCCGTACATCAGAGGATC 60.604 57.143 13.66 0.00 32.26 3.36
270 286 0.390860 GCTGCCGTACATCAGAGGAT 59.609 55.000 13.66 0.00 32.26 3.24
271 287 1.676678 GGCTGCCGTACATCAGAGGA 61.677 60.000 1.35 0.00 32.26 3.71
272 288 1.227380 GGCTGCCGTACATCAGAGG 60.227 63.158 1.35 0.00 32.26 3.69
273 289 0.529337 CAGGCTGCCGTACATCAGAG 60.529 60.000 13.96 1.71 32.26 3.35
274 290 1.517361 CAGGCTGCCGTACATCAGA 59.483 57.895 13.96 0.00 32.26 3.27
275 291 2.176273 GCAGGCTGCCGTACATCAG 61.176 63.158 28.87 6.92 37.42 2.90
276 292 2.125147 GCAGGCTGCCGTACATCA 60.125 61.111 28.87 0.00 37.42 3.07
285 301 3.426568 GACAGAACGGCAGGCTGC 61.427 66.667 30.93 30.93 44.08 5.25
286 302 2.031012 TGACAGAACGGCAGGCTG 59.969 61.111 10.94 10.94 35.81 4.85
287 303 2.031163 GTGACAGAACGGCAGGCT 59.969 61.111 0.00 0.00 0.00 4.58
288 304 2.031163 AGTGACAGAACGGCAGGC 59.969 61.111 0.00 0.00 0.00 4.85
289 305 0.946221 GTCAGTGACAGAACGGCAGG 60.946 60.000 18.54 0.00 32.09 4.85
290 306 0.249447 TGTCAGTGACAGAACGGCAG 60.249 55.000 22.06 0.00 37.67 4.85
291 307 0.392706 ATGTCAGTGACAGAACGGCA 59.607 50.000 28.54 5.24 46.04 5.69
292 308 0.792640 CATGTCAGTGACAGAACGGC 59.207 55.000 28.54 0.00 46.04 5.68
293 309 1.794701 CACATGTCAGTGACAGAACGG 59.205 52.381 28.54 17.59 46.04 4.44
294 310 1.794701 CCACATGTCAGTGACAGAACG 59.205 52.381 28.54 19.00 46.04 3.95
295 311 2.146342 CCCACATGTCAGTGACAGAAC 58.854 52.381 28.54 1.97 46.04 3.01
296 312 1.543208 GCCCACATGTCAGTGACAGAA 60.543 52.381 28.54 8.14 46.04 3.02
297 313 0.035317 GCCCACATGTCAGTGACAGA 59.965 55.000 28.54 8.89 46.04 3.41
298 314 0.957395 GGCCCACATGTCAGTGACAG 60.957 60.000 28.54 21.75 46.04 3.51
299 315 1.073025 GGCCCACATGTCAGTGACA 59.927 57.895 27.35 27.35 46.90 3.58
300 316 0.250901 AAGGCCCACATGTCAGTGAC 60.251 55.000 16.68 16.68 42.05 3.67
301 317 0.478072 AAAGGCCCACATGTCAGTGA 59.522 50.000 0.00 0.00 42.05 3.41
302 318 1.000060 CAAAAGGCCCACATGTCAGTG 60.000 52.381 0.00 0.00 39.21 3.66
303 319 1.331214 CAAAAGGCCCACATGTCAGT 58.669 50.000 0.00 0.00 0.00 3.41
304 320 0.604578 CCAAAAGGCCCACATGTCAG 59.395 55.000 0.00 0.00 0.00 3.51
305 321 0.831288 CCCAAAAGGCCCACATGTCA 60.831 55.000 0.00 0.00 0.00 3.58
306 322 0.541764 TCCCAAAAGGCCCACATGTC 60.542 55.000 0.00 0.00 34.51 3.06
307 323 0.105246 TTCCCAAAAGGCCCACATGT 60.105 50.000 0.00 0.00 34.51 3.21
308 324 0.321346 GTTCCCAAAAGGCCCACATG 59.679 55.000 0.00 0.00 34.51 3.21
309 325 0.835971 GGTTCCCAAAAGGCCCACAT 60.836 55.000 0.00 0.00 34.51 3.21
310 326 1.458588 GGTTCCCAAAAGGCCCACA 60.459 57.895 0.00 0.00 34.51 4.17
311 327 1.152333 AGGTTCCCAAAAGGCCCAC 60.152 57.895 0.00 0.00 34.51 4.61
312 328 1.152355 CAGGTTCCCAAAAGGCCCA 60.152 57.895 0.00 0.00 34.51 5.36
313 329 1.913262 CCAGGTTCCCAAAAGGCCC 60.913 63.158 0.00 0.00 34.51 5.80
314 330 2.583441 GCCAGGTTCCCAAAAGGCC 61.583 63.158 0.00 0.00 36.17 5.19
315 331 2.583441 GGCCAGGTTCCCAAAAGGC 61.583 63.158 0.00 0.00 41.29 4.35
316 332 1.913262 GGGCCAGGTTCCCAAAAGG 60.913 63.158 4.39 0.00 43.37 3.11
317 333 3.791640 GGGCCAGGTTCCCAAAAG 58.208 61.111 4.39 0.00 43.37 2.27
322 338 2.362889 CATGTGGGCCAGGTTCCC 60.363 66.667 6.40 0.00 44.17 3.97
323 339 1.678970 GACATGTGGGCCAGGTTCC 60.679 63.158 6.40 0.00 38.40 3.62
324 340 0.962356 CTGACATGTGGGCCAGGTTC 60.962 60.000 6.40 1.46 38.40 3.62
325 341 1.075482 CTGACATGTGGGCCAGGTT 59.925 57.895 6.40 0.00 38.40 3.50
326 342 2.156098 ACTGACATGTGGGCCAGGT 61.156 57.895 6.40 5.66 41.63 4.00
327 343 1.676635 CACTGACATGTGGGCCAGG 60.677 63.158 6.40 1.59 34.56 4.45
328 344 3.991999 CACTGACATGTGGGCCAG 58.008 61.111 6.40 6.93 34.56 4.85
334 350 1.855213 CGTTGGGCCACTGACATGTG 61.855 60.000 5.23 0.00 37.66 3.21
335 351 1.600636 CGTTGGGCCACTGACATGT 60.601 57.895 5.23 0.00 0.00 3.21
336 352 2.334946 CCGTTGGGCCACTGACATG 61.335 63.158 5.23 0.00 0.00 3.21
337 353 2.034066 CCGTTGGGCCACTGACAT 59.966 61.111 5.23 0.00 0.00 3.06
349 365 4.424430 GTGCGCTACGTGCCGTTG 62.424 66.667 9.73 5.36 41.54 4.10
358 374 4.129737 TCCTCTGCCGTGCGCTAC 62.130 66.667 9.73 4.27 38.78 3.58
359 375 3.826754 CTCCTCTGCCGTGCGCTA 61.827 66.667 9.73 0.00 38.78 4.26
364 380 4.803426 GGACGCTCCTCTGCCGTG 62.803 72.222 0.00 0.00 32.53 4.94
373 389 0.035439 TTTGGAATGGAGGACGCTCC 60.035 55.000 2.35 2.35 43.60 4.70
374 390 1.087501 GTTTGGAATGGAGGACGCTC 58.912 55.000 0.00 0.00 0.00 5.03
375 391 0.673644 CGTTTGGAATGGAGGACGCT 60.674 55.000 0.00 0.00 0.00 5.07
376 392 0.672401 TCGTTTGGAATGGAGGACGC 60.672 55.000 0.00 0.00 0.00 5.19
377 393 1.803334 TTCGTTTGGAATGGAGGACG 58.197 50.000 0.00 0.00 0.00 4.79
385 401 6.001460 TCCAGAAGTTACATTCGTTTGGAAT 58.999 36.000 0.00 0.00 46.29 3.01
451 467 1.139095 AACGGCTAGCTACGCTGAC 59.861 57.895 22.78 2.80 40.10 3.51
492 510 3.064207 GACATGGACAGCTTGACGTTTA 58.936 45.455 0.00 0.00 0.00 2.01
502 520 2.860735 GACTGTATTCGACATGGACAGC 59.139 50.000 0.00 0.00 40.97 4.40
537 556 1.295792 GCGTCAACAGGAAGTGAACA 58.704 50.000 0.00 0.00 0.00 3.18
621 640 3.584406 ACTGGTTCTCTGTGATGATTCCA 59.416 43.478 0.00 0.00 0.00 3.53
666 685 1.136110 TGCGATTGATGCGGTCTAAGA 59.864 47.619 0.00 0.00 34.24 2.10
690 709 2.295349 GTCCAATCTGGCTGGCATAATG 59.705 50.000 3.74 0.73 37.47 1.90
728 747 0.322277 CACTTGCCTCTCACCTGCAT 60.322 55.000 0.00 0.00 34.51 3.96
749 768 2.571653 TGAAGCAGCCTAACACACCTAT 59.428 45.455 0.00 0.00 0.00 2.57
754 773 3.004629 CACATTTGAAGCAGCCTAACACA 59.995 43.478 0.00 0.00 0.00 3.72
769 788 6.435904 TCTCCAGGGGTTTATAAACACATTTG 59.564 38.462 27.40 21.10 44.04 2.32
839 878 0.944386 GTGAGAGCAGAACGCCAAAA 59.056 50.000 0.00 0.00 44.04 2.44
842 881 1.300931 GTGTGAGAGCAGAACGCCA 60.301 57.895 0.00 0.00 44.04 5.69
863 902 0.318275 GAGAGAATAGCGCACCTCCG 60.318 60.000 11.47 0.00 0.00 4.63
864 903 1.036707 AGAGAGAATAGCGCACCTCC 58.963 55.000 11.47 4.76 0.00 4.30
921 968 0.764369 AGTCCCACAAGTCTGGCAGA 60.764 55.000 14.43 14.43 0.00 4.26
978 1025 6.805760 CCATGATCTCACGATGTACTATGAAG 59.194 42.308 0.00 0.00 0.00 3.02
989 1042 2.827800 ATTCGCCATGATCTCACGAT 57.172 45.000 0.00 0.00 32.13 3.73
1046 1103 2.033141 GCAGCAGGAGGAGCAACA 59.967 61.111 0.00 0.00 0.00 3.33
1069 1129 0.738975 GCTTGCCCGGAATTAAGGAC 59.261 55.000 0.73 0.00 0.00 3.85
1289 1374 3.696548 GGAAATTCCTGTGATGACCTTCC 59.303 47.826 4.46 0.00 32.53 3.46
1392 1485 2.100197 CCGGAGAGATGGTAGTTGTCA 58.900 52.381 0.00 0.00 0.00 3.58
1918 2011 1.613255 CCCAAACTCTGCCGGTATTGT 60.613 52.381 1.90 0.00 0.00 2.71
1957 2050 3.327757 TGGTTATCTGACAAGTCCAAGCT 59.672 43.478 0.00 0.00 0.00 3.74
1959 2052 6.430925 TCAAATGGTTATCTGACAAGTCCAAG 59.569 38.462 0.00 0.00 0.00 3.61
2000 2093 7.168219 TGAAGTAAGATTTCCAGCAACACTAT 58.832 34.615 0.00 0.00 0.00 2.12
2368 2461 5.470777 CGACTAAATTGGTAAGGTTGGACAA 59.529 40.000 0.00 0.00 0.00 3.18
2398 2491 1.896660 TCAAACTGCCGGGTTGAGC 60.897 57.895 2.18 0.00 45.57 4.26
2457 2550 2.071778 TACCGTGACCCATACCCTAC 57.928 55.000 0.00 0.00 0.00 3.18
2670 2764 9.994957 TGCTTAGAAGGCATGGTGATATCACAG 62.995 44.444 31.51 22.37 40.44 3.66
2937 3031 1.734465 CTTGAATCTCACCGAGTTGGC 59.266 52.381 0.00 0.00 43.94 4.52
3166 3260 3.269578 TCGGGTCGACATCTACCAA 57.730 52.632 18.91 0.00 37.51 3.67
3213 3307 2.161855 GGTTGTCATCCAGTGCAATGA 58.838 47.619 17.16 5.09 0.00 2.57
3214 3308 1.887854 TGGTTGTCATCCAGTGCAATG 59.112 47.619 7.29 7.29 0.00 2.82
3215 3309 2.165167 CTGGTTGTCATCCAGTGCAAT 58.835 47.619 18.42 0.00 45.09 3.56
3216 3310 1.608055 CTGGTTGTCATCCAGTGCAA 58.392 50.000 18.42 0.00 45.09 4.08
3217 3311 3.327600 CTGGTTGTCATCCAGTGCA 57.672 52.632 18.42 0.00 45.09 4.57
3241 3335 1.955778 CACAAATCTGGCAAGTGTCCA 59.044 47.619 0.00 0.00 0.00 4.02
3524 3618 3.055094 ACCACAGAAGGTATACTGCCTTG 60.055 47.826 2.25 0.00 45.51 3.61
3793 3887 5.647658 TCCACTAAGGCTGTTGTTATTCATG 59.352 40.000 0.00 0.00 37.29 3.07
3819 3921 1.074889 GGCCCAAACTACCAGGAAGAA 59.925 52.381 0.00 0.00 0.00 2.52
3884 3986 2.168521 CTGACGGTATTGGTCCACTGAT 59.831 50.000 0.00 0.00 33.46 2.90
4275 4382 2.095567 CAGAGAACACATCCCTTTTGCG 60.096 50.000 0.00 0.00 0.00 4.85
4289 4396 4.574013 CCATCAAAGCTCCATACAGAGAAC 59.426 45.833 0.00 0.00 35.82 3.01
4786 4894 3.410631 TTCTTGCAATACCGAAGTCCA 57.589 42.857 0.00 0.00 0.00 4.02
5153 5268 1.889829 CACCGTCTCACTTCTTCCTCT 59.110 52.381 0.00 0.00 0.00 3.69
5307 5435 8.919777 AACAGTTAGCCTAAGTTTTATTCAGT 57.080 30.769 0.00 0.00 0.00 3.41
5354 5484 2.486191 GCTTGGTCCTCGGATGATCAAT 60.486 50.000 9.02 0.00 0.00 2.57
5429 5560 1.337071 CGTAGGCAAGCTTCGAGGATA 59.663 52.381 0.00 0.00 0.00 2.59
5620 5754 5.138276 GGTGTGTAGACAGGATATGGAGTA 58.862 45.833 0.00 0.00 30.74 2.59
5633 5767 1.129437 GGAGTCGTACGGTGTGTAGAC 59.871 57.143 16.52 3.27 34.31 2.59
5638 5772 1.990563 GATTTGGAGTCGTACGGTGTG 59.009 52.381 16.52 0.00 0.00 3.82
5643 5777 2.666508 CAGTTGGATTTGGAGTCGTACG 59.333 50.000 9.53 9.53 0.00 3.67
5644 5778 3.660865 ACAGTTGGATTTGGAGTCGTAC 58.339 45.455 0.00 0.00 0.00 3.67
5648 5782 4.652822 AGGTTACAGTTGGATTTGGAGTC 58.347 43.478 0.00 0.00 0.00 3.36
5656 5790 7.069877 TGTACAAGTTAGGTTACAGTTGGAT 57.930 36.000 0.00 0.00 0.00 3.41
5672 5806 9.431887 AGTTGTGTCGAATATTATTGTACAAGT 57.568 29.630 14.65 5.42 0.00 3.16
5699 5833 4.139859 TCGTCAAGGTGGAGTTTGTTAA 57.860 40.909 0.00 0.00 0.00 2.01
5748 5882 1.071041 GTACACGAAGGTTTGACGCAC 60.071 52.381 0.00 0.00 0.00 5.34
5759 5893 3.123621 GCTCAAGTCCAATGTACACGAAG 59.876 47.826 0.00 0.00 0.00 3.79
5763 5897 5.294552 GGATAAGCTCAAGTCCAATGTACAC 59.705 44.000 0.00 0.00 0.00 2.90
5853 5996 4.710528 AATTTCGTTCGAGTGTTGACTC 57.289 40.909 0.00 0.00 44.70 3.36
5877 6022 5.468746 AGCGCAAACTAGAGTAATGTGAAAA 59.531 36.000 11.47 0.00 31.32 2.29
5880 6025 4.188247 AGCGCAAACTAGAGTAATGTGA 57.812 40.909 11.47 0.00 31.32 3.58
5902 6047 4.838423 TGGACTGATACTCTGAAAGTTGGA 59.162 41.667 0.00 0.00 39.55 3.53
6192 6339 0.905357 CCTTGAGACTTGACCGGGAT 59.095 55.000 6.32 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.