Multiple sequence alignment - TraesCS2B01G143300

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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 TraesCS2B01G143300 chr2B 100.000 2210 0 0 1 2210 109974101 109971892 0.000000e+00 4082.0
1 TraesCS2B01G143300 chr2B 93.103 812 43 3 488 1288 124615556 124614747 0.000000e+00 1177.0
2 TraesCS2B01G143300 chr2B 93.878 784 35 3 515 1288 24318503 24319283 0.000000e+00 1170.0
3 TraesCS2B01G143300 chr2B 96.785 622 17 1 1332 1953 109929549 109928931 0.000000e+00 1035.0
4 TraesCS2B01G143300 chr2B 83.468 248 32 6 1964 2207 103799313 103799555 2.860000e-54 222.0
5 TraesCS2B01G143300 chr5B 94.212 812 34 3 488 1288 693630313 693631122 0.000000e+00 1227.0
6 TraesCS2B01G143300 chr5B 91.453 351 7 8 195 525 17740889 17741236 5.560000e-126 460.0
7 TraesCS2B01G143300 chr5B 91.691 337 19 5 195 528 182615016 182614686 2.000000e-125 459.0
8 TraesCS2B01G143300 chr1B 92.883 843 41 7 462 1288 108095008 108095847 0.000000e+00 1206.0
9 TraesCS2B01G143300 chr1B 93.264 772 31 6 528 1288 121454178 121454939 0.000000e+00 1118.0
10 TraesCS2B01G143300 chr1B 89.637 193 15 4 2021 2210 3970108 3970298 7.880000e-60 241.0
11 TraesCS2B01G143300 chr3B 93.218 811 41 4 489 1288 817401925 817401118 0.000000e+00 1181.0
12 TraesCS2B01G143300 chr3B 85.965 228 25 4 1986 2210 436758658 436758435 1.020000e-58 237.0
13 TraesCS2B01G143300 chr3B 86.222 225 22 6 1990 2210 436759495 436759276 3.670000e-58 235.0
14 TraesCS2B01G143300 chr3B 100.000 30 0 0 1306 1335 804667199 804667228 3.070000e-04 56.5
15 TraesCS2B01G143300 chrUn 96.769 619 16 2 1332 1950 261755263 261755877 0.000000e+00 1029.0
16 TraesCS2B01G143300 chrUn 96.769 619 16 2 1332 1950 271486844 271487458 0.000000e+00 1029.0
17 TraesCS2B01G143300 chrUn 93.376 619 40 1 1333 1951 289660487 289659870 0.000000e+00 915.0
18 TraesCS2B01G143300 chrUn 93.215 619 38 3 1333 1951 235544083 235544697 0.000000e+00 907.0
19 TraesCS2B01G143300 chrUn 86.735 196 25 1 1 195 261752594 261752789 1.330000e-52 217.0
20 TraesCS2B01G143300 chr2D 93.538 619 39 1 1333 1951 72373972 72373355 0.000000e+00 920.0
21 TraesCS2B01G143300 chr2D 93.376 619 40 1 1333 1951 72654453 72653836 0.000000e+00 915.0
22 TraesCS2B01G143300 chr2A 93.258 623 36 2 1332 1953 71153931 71153314 0.000000e+00 913.0
23 TraesCS2B01G143300 chr2A 93.215 619 41 1 1333 1951 71212121 71211504 0.000000e+00 909.0
24 TraesCS2B01G143300 chr2A 93.548 124 7 1 54 177 71209994 71209872 1.350000e-42 183.0
25 TraesCS2B01G143300 chr2A 93.548 124 7 1 54 177 71262624 71262502 1.350000e-42 183.0
26 TraesCS2B01G143300 chr6B 95.625 480 19 1 809 1288 268614755 268614278 0.000000e+00 769.0
27 TraesCS2B01G143300 chr6B 85.965 171 13 2 488 647 268623994 268623824 2.920000e-39 172.0
28 TraesCS2B01G143300 chr6B 93.396 106 7 0 1944 2049 37774086 37774191 8.170000e-35 158.0
29 TraesCS2B01G143300 chr6D 93.777 466 18 2 515 969 31276641 31277106 0.000000e+00 689.0
30 TraesCS2B01G143300 chr6D 93.709 461 21 4 515 969 128400289 128400747 0.000000e+00 684.0
31 TraesCS2B01G143300 chr5D 92.593 486 22 5 496 969 43780939 43780456 0.000000e+00 686.0
32 TraesCS2B01G143300 chr5D 96.636 327 9 1 962 1288 43780421 43780097 1.930000e-150 542.0
33 TraesCS2B01G143300 chr6A 92.275 466 22 3 515 969 571152956 571152494 0.000000e+00 649.0
34 TraesCS2B01G143300 chr6A 92.560 336 11 6 195 528 185312989 185312666 9.240000e-129 470.0
35 TraesCS2B01G143300 chr6A 92.035 339 14 10 195 528 583924940 583924610 4.300000e-127 464.0
36 TraesCS2B01G143300 chr6A 88.451 355 14 12 198 531 3793166 3792818 9.500000e-109 403.0
37 TraesCS2B01G143300 chr3A 91.202 466 27 8 515 969 15883582 15884044 2.410000e-174 621.0
38 TraesCS2B01G143300 chr3A 100.000 30 0 0 1306 1335 727990535 727990564 3.070000e-04 56.5
39 TraesCS2B01G143300 chr1A 90.987 466 30 4 515 969 471679196 471679660 3.120000e-173 617.0
40 TraesCS2B01G143300 chr1A 93.093 333 16 5 195 525 220259692 220260019 4.270000e-132 481.0
41 TraesCS2B01G143300 chr1A 83.577 274 27 10 1940 2207 63044309 63044570 7.880000e-60 241.0
42 TraesCS2B01G143300 chr1A 88.372 129 11 1 2079 2207 580028454 580028578 3.800000e-33 152.0
43 TraesCS2B01G143300 chr7D 96.636 327 9 1 962 1288 556904265 556904589 1.930000e-150 542.0
44 TraesCS2B01G143300 chr7D 91.592 333 12 10 195 525 116131735 116132053 1.560000e-121 446.0
45 TraesCS2B01G143300 chr5A 90.113 354 13 8 195 528 498306682 498306331 7.240000e-120 440.0
46 TraesCS2B01G143300 chr5A 90.909 110 7 2 1944 2052 386703849 386703742 6.360000e-31 145.0
47 TraesCS2B01G143300 chr1D 89.296 355 17 8 195 528 475036909 475036555 2.030000e-115 425.0
48 TraesCS2B01G143300 chr7B 88.889 351 13 11 195 525 25967015 25967359 2.040000e-110 409.0
49 TraesCS2B01G143300 chr7B 89.189 111 12 0 2100 2210 553186954 553186844 2.960000e-29 139.0
50 TraesCS2B01G143300 chr4A 90.282 319 17 8 195 512 732223581 732223276 2.640000e-109 405.0
51 TraesCS2B01G143300 chr3D 83.395 271 31 11 1944 2207 130949937 130949674 2.840000e-59 239.0
52 TraesCS2B01G143300 chr3D 83.471 242 27 7 1973 2207 20538223 20537988 1.720000e-51 213.0
53 TraesCS2B01G143300 chr3D 100.000 30 0 0 1306 1335 598010617 598010646 3.070000e-04 56.5
54 TraesCS2B01G143300 chr4B 91.597 119 8 2 411 528 134172530 134172413 1.760000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G143300 chr2B 109971892 109974101 2209 True 4082 4082 100.0000 1 2210 1 chr2B.!!$R2 2209
1 TraesCS2B01G143300 chr2B 124614747 124615556 809 True 1177 1177 93.1030 488 1288 1 chr2B.!!$R3 800
2 TraesCS2B01G143300 chr2B 24318503 24319283 780 False 1170 1170 93.8780 515 1288 1 chr2B.!!$F1 773
3 TraesCS2B01G143300 chr2B 109928931 109929549 618 True 1035 1035 96.7850 1332 1953 1 chr2B.!!$R1 621
4 TraesCS2B01G143300 chr5B 693630313 693631122 809 False 1227 1227 94.2120 488 1288 1 chr5B.!!$F2 800
5 TraesCS2B01G143300 chr1B 108095008 108095847 839 False 1206 1206 92.8830 462 1288 1 chr1B.!!$F2 826
6 TraesCS2B01G143300 chr1B 121454178 121454939 761 False 1118 1118 93.2640 528 1288 1 chr1B.!!$F3 760
7 TraesCS2B01G143300 chr3B 817401118 817401925 807 True 1181 1181 93.2180 489 1288 1 chr3B.!!$R1 799
8 TraesCS2B01G143300 chr3B 436758435 436759495 1060 True 236 237 86.0935 1986 2210 2 chr3B.!!$R2 224
9 TraesCS2B01G143300 chrUn 271486844 271487458 614 False 1029 1029 96.7690 1332 1950 1 chrUn.!!$F2 618
10 TraesCS2B01G143300 chrUn 289659870 289660487 617 True 915 915 93.3760 1333 1951 1 chrUn.!!$R1 618
11 TraesCS2B01G143300 chrUn 235544083 235544697 614 False 907 907 93.2150 1333 1951 1 chrUn.!!$F1 618
12 TraesCS2B01G143300 chrUn 261752594 261755877 3283 False 623 1029 91.7520 1 1950 2 chrUn.!!$F3 1949
13 TraesCS2B01G143300 chr2D 72373355 72373972 617 True 920 920 93.5380 1333 1951 1 chr2D.!!$R1 618
14 TraesCS2B01G143300 chr2D 72653836 72654453 617 True 915 915 93.3760 1333 1951 1 chr2D.!!$R2 618
15 TraesCS2B01G143300 chr2A 71153314 71153931 617 True 913 913 93.2580 1332 1953 1 chr2A.!!$R1 621
16 TraesCS2B01G143300 chr2A 71209872 71212121 2249 True 546 909 93.3815 54 1951 2 chr2A.!!$R3 1897
17 TraesCS2B01G143300 chr5D 43780097 43780939 842 True 614 686 94.6145 496 1288 2 chr5D.!!$R1 792

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
387 389 0.036164 TAGTGCGCCTGTCCAAACAT 59.964 50.0 4.18 0.0 34.13 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 2129 0.672401 AACATACCCACCACGAAGCG 60.672 55.0 0.0 0.0 0.0 4.68 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
21 22 4.133526 CCAGATGGAAGTATCCTCCCTA 57.866 50.000 0.00 0.00 46.70 3.53
28 29 1.326055 AGTATCCTCCCTACCCACCA 58.674 55.000 0.00 0.00 0.00 4.17
32 33 2.068831 TCCTCCCTACCCACCAAATT 57.931 50.000 0.00 0.00 0.00 1.82
37 38 1.618616 CCCTACCCACCAAATTGGACC 60.619 57.143 20.25 0.00 40.96 4.46
94 95 6.323203 CCCATGGCAAATCTAATTCTAGTG 57.677 41.667 6.09 0.00 0.00 2.74
95 96 5.242393 CCCATGGCAAATCTAATTCTAGTGG 59.758 44.000 6.09 0.00 0.00 4.00
97 98 6.016777 CCATGGCAAATCTAATTCTAGTGGTC 60.017 42.308 0.00 0.00 0.00 4.02
103 104 5.599999 ATCTAATTCTAGTGGTCGCTTGT 57.400 39.130 0.00 0.00 0.00 3.16
105 106 2.279582 ATTCTAGTGGTCGCTTGTCG 57.720 50.000 0.00 0.00 40.15 4.35
189 191 2.106566 ACCAAACATGGTGCAGTCAAA 58.893 42.857 0.00 0.00 41.33 2.69
195 197 4.019792 ACATGGTGCAGTCAAATGAGTA 57.980 40.909 0.00 0.00 0.00 2.59
196 198 3.753272 ACATGGTGCAGTCAAATGAGTAC 59.247 43.478 0.00 0.00 0.00 2.73
197 199 3.769739 TGGTGCAGTCAAATGAGTACT 57.230 42.857 0.00 0.00 0.00 2.73
198 200 4.882842 TGGTGCAGTCAAATGAGTACTA 57.117 40.909 0.00 0.00 0.00 1.82
200 202 4.526650 TGGTGCAGTCAAATGAGTACTAGA 59.473 41.667 0.00 0.00 0.00 2.43
201 203 5.011635 TGGTGCAGTCAAATGAGTACTAGAA 59.988 40.000 0.00 0.00 0.00 2.10
202 204 5.932303 GGTGCAGTCAAATGAGTACTAGAAA 59.068 40.000 0.00 0.00 0.00 2.52
203 205 6.426937 GGTGCAGTCAAATGAGTACTAGAAAA 59.573 38.462 0.00 0.00 0.00 2.29
204 206 7.041372 GGTGCAGTCAAATGAGTACTAGAAAAA 60.041 37.037 0.00 0.00 0.00 1.94
205 207 8.012241 GTGCAGTCAAATGAGTACTAGAAAAAG 58.988 37.037 0.00 0.00 0.00 2.27
206 208 7.173218 TGCAGTCAAATGAGTACTAGAAAAAGG 59.827 37.037 0.00 0.00 0.00 3.11
208 210 8.713271 CAGTCAAATGAGTACTAGAAAAAGGAC 58.287 37.037 0.00 0.00 0.00 3.85
209 211 8.652290 AGTCAAATGAGTACTAGAAAAAGGACT 58.348 33.333 0.00 0.00 43.66 3.85
210 212 9.924650 GTCAAATGAGTACTAGAAAAAGGACTA 57.075 33.333 0.00 0.00 40.92 2.59
219 221 9.364653 GTACTAGAAAAAGGACTATAGATGGGA 57.635 37.037 6.78 0.00 0.00 4.37
221 223 9.453830 ACTAGAAAAAGGACTATAGATGGGATT 57.546 33.333 6.78 0.00 0.00 3.01
222 224 9.717942 CTAGAAAAAGGACTATAGATGGGATTG 57.282 37.037 6.78 0.00 0.00 2.67
223 225 8.337118 AGAAAAAGGACTATAGATGGGATTGA 57.663 34.615 6.78 0.00 0.00 2.57
226 228 6.426646 AAGGACTATAGATGGGATTGACAC 57.573 41.667 6.78 0.00 0.00 3.67
228 230 6.864421 AGGACTATAGATGGGATTGACACTA 58.136 40.000 6.78 0.00 0.00 2.74
229 231 7.306013 AGGACTATAGATGGGATTGACACTAA 58.694 38.462 6.78 0.00 0.00 2.24
232 234 7.911651 ACTATAGATGGGATTGACACTAATGG 58.088 38.462 6.78 0.00 0.00 3.16
234 236 2.036958 TGGGATTGACACTAATGGCG 57.963 50.000 0.00 0.00 36.14 5.69
235 237 0.663153 GGGATTGACACTAATGGCGC 59.337 55.000 0.00 0.00 36.14 6.53
236 238 1.378531 GGATTGACACTAATGGCGCA 58.621 50.000 10.83 0.00 36.14 6.09
237 239 1.949525 GGATTGACACTAATGGCGCAT 59.050 47.619 10.83 0.00 36.14 4.73
238 240 2.031682 GGATTGACACTAATGGCGCATC 60.032 50.000 10.83 0.00 36.14 3.91
239 241 2.106477 TTGACACTAATGGCGCATCA 57.894 45.000 10.83 0.00 36.14 3.07
241 243 1.206849 TGACACTAATGGCGCATCAGA 59.793 47.619 10.83 0.00 36.14 3.27
242 244 1.594862 GACACTAATGGCGCATCAGAC 59.405 52.381 10.83 0.00 0.00 3.51
243 245 1.066215 ACACTAATGGCGCATCAGACA 60.066 47.619 10.83 0.00 0.00 3.41
244 246 2.009051 CACTAATGGCGCATCAGACAA 58.991 47.619 10.83 0.00 30.05 3.18
245 247 2.031314 CACTAATGGCGCATCAGACAAG 59.969 50.000 10.83 0.00 30.05 3.16
246 248 1.003116 CTAATGGCGCATCAGACAAGC 60.003 52.381 10.83 0.00 30.05 4.01
251 253 2.482374 GCATCAGACAAGCGGTGC 59.518 61.111 0.00 0.00 0.00 5.01
267 269 4.106029 CGGTGCGCCATTAGTATATACT 57.894 45.455 19.07 19.07 36.14 2.12
268 270 5.239359 CGGTGCGCCATTAGTATATACTA 57.761 43.478 18.18 17.03 34.75 1.82
279 281 6.593268 TTAGTATATACTAATGGCGCACCA 57.407 37.500 25.06 0.00 42.34 4.17
280 282 4.817517 AGTATATACTAATGGCGCACCAC 58.182 43.478 13.88 0.00 41.40 4.16
281 283 4.322499 AGTATATACTAATGGCGCACCACC 60.322 45.833 13.88 0.00 41.40 4.61
282 284 6.510790 AGTATATACTAATGGCGCACCACCT 61.511 44.000 13.88 0.00 41.40 4.00
283 285 7.929446 AGTATATACTAATGGCGCACCACCTT 61.929 42.308 13.88 0.00 41.40 3.50
284 286 9.615037 AGTATATACTAATGGCGCACCACCTTC 62.615 44.444 13.88 0.00 41.40 3.46
287 289 3.555324 TGGCGCACCACCTTCTGA 61.555 61.111 10.83 0.00 42.67 3.27
288 290 2.045926 GGCGCACCACCTTCTGAT 60.046 61.111 10.83 0.00 35.26 2.90
289 291 1.220749 GGCGCACCACCTTCTGATA 59.779 57.895 10.83 0.00 35.26 2.15
290 292 1.090052 GGCGCACCACCTTCTGATAC 61.090 60.000 10.83 0.00 35.26 2.24
291 293 1.421410 GCGCACCACCTTCTGATACG 61.421 60.000 0.30 0.00 0.00 3.06
292 294 1.421410 CGCACCACCTTCTGATACGC 61.421 60.000 0.00 0.00 0.00 4.42
293 295 1.090052 GCACCACCTTCTGATACGCC 61.090 60.000 0.00 0.00 0.00 5.68
294 296 0.249120 CACCACCTTCTGATACGCCA 59.751 55.000 0.00 0.00 0.00 5.69
295 297 1.134401 CACCACCTTCTGATACGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
296 298 1.559682 ACCACCTTCTGATACGCCATT 59.440 47.619 0.00 0.00 0.00 3.16
297 299 2.769663 ACCACCTTCTGATACGCCATTA 59.230 45.455 0.00 0.00 0.00 1.90
298 300 3.181465 ACCACCTTCTGATACGCCATTAG 60.181 47.826 0.00 0.00 0.00 1.73
299 301 3.069586 CCACCTTCTGATACGCCATTAGA 59.930 47.826 0.00 0.00 0.00 2.10
300 302 4.302455 CACCTTCTGATACGCCATTAGAG 58.698 47.826 0.00 0.00 31.43 2.43
301 303 3.961408 ACCTTCTGATACGCCATTAGAGT 59.039 43.478 0.00 0.00 31.43 3.24
302 304 4.406003 ACCTTCTGATACGCCATTAGAGTT 59.594 41.667 0.00 0.00 31.43 3.01
303 305 4.747108 CCTTCTGATACGCCATTAGAGTTG 59.253 45.833 0.00 0.00 31.43 3.16
304 306 5.451937 CCTTCTGATACGCCATTAGAGTTGA 60.452 44.000 0.00 0.00 31.43 3.18
305 307 5.592104 TCTGATACGCCATTAGAGTTGAA 57.408 39.130 0.00 0.00 0.00 2.69
306 308 5.972935 TCTGATACGCCATTAGAGTTGAAA 58.027 37.500 0.00 0.00 0.00 2.69
307 309 5.810587 TCTGATACGCCATTAGAGTTGAAAC 59.189 40.000 0.00 0.00 0.00 2.78
308 310 5.730550 TGATACGCCATTAGAGTTGAAACT 58.269 37.500 0.00 0.00 43.16 2.66
309 311 6.869695 TGATACGCCATTAGAGTTGAAACTA 58.130 36.000 0.00 0.00 39.88 2.24
310 312 6.755141 TGATACGCCATTAGAGTTGAAACTAC 59.245 38.462 0.00 0.00 39.88 2.73
311 313 5.148651 ACGCCATTAGAGTTGAAACTACT 57.851 39.130 0.00 0.00 39.88 2.57
312 314 6.276832 ACGCCATTAGAGTTGAAACTACTA 57.723 37.500 0.00 0.00 39.88 1.82
313 315 6.694447 ACGCCATTAGAGTTGAAACTACTAA 58.306 36.000 12.97 12.97 39.88 2.24
314 316 7.328737 ACGCCATTAGAGTTGAAACTACTAAT 58.671 34.615 15.03 15.03 39.88 1.73
315 317 7.277981 ACGCCATTAGAGTTGAAACTACTAATG 59.722 37.037 25.60 25.60 44.21 1.90
318 320 8.492673 CATTAGAGTTGAAACTACTAATGGCA 57.507 34.615 25.29 0.00 43.04 4.92
319 321 7.900782 TTAGAGTTGAAACTACTAATGGCAC 57.099 36.000 0.00 0.00 39.88 5.01
320 322 5.865085 AGAGTTGAAACTACTAATGGCACA 58.135 37.500 0.00 0.00 41.24 4.57
321 323 5.701290 AGAGTTGAAACTACTAATGGCACAC 59.299 40.000 0.00 0.00 40.05 3.82
322 324 4.760204 AGTTGAAACTACTAATGGCACACC 59.240 41.667 0.00 0.00 38.49 4.16
323 325 5.456186 AGTTGAAACTACTAATGGCACACCT 60.456 40.000 0.00 0.00 38.49 4.00
324 326 7.462844 AGTTGAAACTACTAATGGCACACCTG 61.463 42.308 0.00 0.00 38.49 4.00
342 344 2.753849 GCCCAAGGTGCGCCATTA 60.754 61.111 20.59 0.00 37.19 1.90
343 345 2.774799 GCCCAAGGTGCGCCATTAG 61.775 63.158 20.59 5.54 37.19 1.73
344 346 1.378514 CCCAAGGTGCGCCATTAGT 60.379 57.895 20.59 0.00 37.19 2.24
345 347 0.107410 CCCAAGGTGCGCCATTAGTA 60.107 55.000 20.59 0.00 37.19 1.82
346 348 1.476833 CCCAAGGTGCGCCATTAGTAT 60.477 52.381 20.59 0.00 37.19 2.12
347 349 1.873591 CCAAGGTGCGCCATTAGTATC 59.126 52.381 20.59 0.00 37.19 2.24
348 350 2.560504 CAAGGTGCGCCATTAGTATCA 58.439 47.619 20.59 0.00 37.19 2.15
349 351 2.942376 CAAGGTGCGCCATTAGTATCAA 59.058 45.455 20.59 0.00 37.19 2.57
350 352 3.275617 AGGTGCGCCATTAGTATCAAA 57.724 42.857 20.59 0.00 37.19 2.69
382 384 0.970640 TAAACTAGTGCGCCTGTCCA 59.029 50.000 4.18 0.00 0.00 4.02
383 385 0.107831 AAACTAGTGCGCCTGTCCAA 59.892 50.000 4.18 0.00 0.00 3.53
384 386 0.107831 AACTAGTGCGCCTGTCCAAA 59.892 50.000 4.18 0.00 0.00 3.28
385 387 0.602905 ACTAGTGCGCCTGTCCAAAC 60.603 55.000 4.18 0.00 0.00 2.93
386 388 0.602638 CTAGTGCGCCTGTCCAAACA 60.603 55.000 4.18 0.00 0.00 2.83
387 389 0.036164 TAGTGCGCCTGTCCAAACAT 59.964 50.000 4.18 0.00 34.13 2.71
390 392 0.036164 TGCGCCTGTCCAAACATACT 59.964 50.000 4.18 0.00 34.13 2.12
392 394 2.289756 TGCGCCTGTCCAAACATACTAA 60.290 45.455 4.18 0.00 34.13 2.24
394 396 3.242739 GCGCCTGTCCAAACATACTAATG 60.243 47.826 0.00 0.00 39.17 1.90
395 397 3.312421 CGCCTGTCCAAACATACTAATGG 59.688 47.826 0.00 0.00 37.43 3.16
396 398 3.066760 GCCTGTCCAAACATACTAATGGC 59.933 47.826 0.00 0.00 37.43 4.40
397 399 3.312421 CCTGTCCAAACATACTAATGGCG 59.688 47.826 0.00 0.00 37.43 5.69
399 401 2.680841 GTCCAAACATACTAATGGCGCA 59.319 45.455 10.83 0.00 37.43 6.09
401 403 3.563808 TCCAAACATACTAATGGCGCATC 59.436 43.478 10.83 0.00 37.43 3.91
412 414 1.812922 GGCGCATCCAGACTCAGTG 60.813 63.158 10.83 0.00 34.01 3.66
413 415 2.459442 GCGCATCCAGACTCAGTGC 61.459 63.158 0.30 0.00 0.00 4.40
414 416 3.791539 GCATCCAGACTCAGTGCG 58.208 61.111 0.00 0.00 0.00 5.34
417 419 2.285773 ATCCAGACTCAGTGCGCCA 61.286 57.895 4.18 0.00 0.00 5.69
418 420 1.620739 ATCCAGACTCAGTGCGCCAT 61.621 55.000 4.18 0.00 0.00 4.40
419 421 1.376424 CCAGACTCAGTGCGCCATT 60.376 57.895 4.18 0.00 0.00 3.16
421 423 1.002366 CAGACTCAGTGCGCCATTAC 58.998 55.000 4.18 0.00 0.00 1.89
422 424 0.898320 AGACTCAGTGCGCCATTACT 59.102 50.000 4.18 0.00 0.00 2.24
423 425 2.100197 AGACTCAGTGCGCCATTACTA 58.900 47.619 4.18 0.00 0.00 1.82
424 426 2.099921 AGACTCAGTGCGCCATTACTAG 59.900 50.000 4.18 3.14 0.00 2.57
425 427 1.825474 ACTCAGTGCGCCATTACTAGT 59.175 47.619 4.18 0.00 0.00 2.57
427 429 3.262420 CTCAGTGCGCCATTACTAGTTT 58.738 45.455 4.18 0.00 0.00 2.66
428 430 3.670625 TCAGTGCGCCATTACTAGTTTT 58.329 40.909 4.18 0.00 0.00 2.43
429 431 3.435327 TCAGTGCGCCATTACTAGTTTTG 59.565 43.478 4.18 0.00 0.00 2.44
430 432 2.747446 AGTGCGCCATTACTAGTTTTGG 59.253 45.455 15.92 15.92 0.00 3.28
431 433 2.745281 GTGCGCCATTACTAGTTTTGGA 59.255 45.455 21.78 4.45 0.00 3.53
432 434 3.189702 GTGCGCCATTACTAGTTTTGGAA 59.810 43.478 21.78 3.13 0.00 3.53
436 438 5.390613 CGCCATTACTAGTTTTGGAAAGTG 58.609 41.667 21.78 2.41 0.00 3.16
437 439 5.161358 GCCATTACTAGTTTTGGAAAGTGC 58.839 41.667 21.78 5.24 0.00 4.40
438 440 5.390613 CCATTACTAGTTTTGGAAAGTGCG 58.609 41.667 15.40 0.00 0.00 5.34
439 441 5.390613 CATTACTAGTTTTGGAAAGTGCGG 58.609 41.667 0.00 0.00 0.00 5.69
441 443 0.589223 TAGTTTTGGAAAGTGCGGCG 59.411 50.000 0.51 0.51 0.00 6.46
447 449 2.740826 GAAAGTGCGGCGCCACTA 60.741 61.111 30.82 7.64 44.86 2.74
448 450 2.281208 AAAGTGCGGCGCCACTAA 60.281 55.556 30.82 7.18 44.86 2.24
449 451 1.644786 GAAAGTGCGGCGCCACTAAT 61.645 55.000 30.82 21.65 44.86 1.73
450 452 1.922135 AAAGTGCGGCGCCACTAATG 61.922 55.000 30.82 10.13 44.86 1.90
451 453 3.124921 GTGCGGCGCCACTAATGT 61.125 61.111 30.82 0.00 33.02 2.71
452 454 2.359354 TGCGGCGCCACTAATGTT 60.359 55.556 30.82 0.00 0.00 2.71
453 455 2.100216 GCGGCGCCACTAATGTTG 59.900 61.111 28.98 7.61 0.00 3.33
454 456 2.686816 GCGGCGCCACTAATGTTGT 61.687 57.895 28.98 0.00 0.00 3.32
455 457 1.873165 CGGCGCCACTAATGTTGTT 59.127 52.632 28.98 0.00 0.00 2.83
456 458 0.239879 CGGCGCCACTAATGTTGTTT 59.760 50.000 28.98 0.00 0.00 2.83
457 459 1.335506 CGGCGCCACTAATGTTGTTTT 60.336 47.619 28.98 0.00 0.00 2.43
458 460 2.749776 GGCGCCACTAATGTTGTTTTT 58.250 42.857 24.80 0.00 0.00 1.94
505 507 2.161609 GCAAAACTACTAATGGCGCACT 59.838 45.455 10.83 0.00 0.00 4.40
513 516 0.958382 TAATGGCGCACTGTTCCACC 60.958 55.000 10.83 0.00 31.94 4.61
524 531 2.036006 GTTCCACCGTGCGCCATTA 61.036 57.895 4.18 0.00 0.00 1.90
525 532 1.743623 TTCCACCGTGCGCCATTAG 60.744 57.895 4.18 0.00 0.00 1.73
591 756 4.996113 AAGCAACACAACGCTTCG 57.004 50.000 0.00 0.00 45.10 3.79
664 1021 0.122021 CCTCCTATCCCCATCCCCAT 59.878 60.000 0.00 0.00 0.00 4.00
748 1168 2.456840 CCCTCACCCTCTCCCCTT 59.543 66.667 0.00 0.00 0.00 3.95
751 1171 0.252927 CCTCACCCTCTCCCCTTTCT 60.253 60.000 0.00 0.00 0.00 2.52
834 1255 0.252742 CCTACTCCTTCCACCCCACT 60.253 60.000 0.00 0.00 0.00 4.00
974 1438 4.196778 TTCAGCGCCCCCACAACA 62.197 61.111 2.29 0.00 0.00 3.33
1051 1515 2.520536 AAGCAGGCGTGGAAGGAGT 61.521 57.895 8.72 0.00 0.00 3.85
1149 1628 0.526524 GCGTCCACAAGATCCTCGAG 60.527 60.000 5.13 5.13 0.00 4.04
1223 2024 1.381928 CCGTAAGCAGTCGCCTCCTA 61.382 60.000 0.00 0.00 39.83 2.94
1224 2025 0.029567 CGTAAGCAGTCGCCTCCTAG 59.970 60.000 0.00 0.00 39.83 3.02
1244 2045 2.124996 CCCTTCCTCTCACCCCCA 59.875 66.667 0.00 0.00 0.00 4.96
1288 2089 0.324460 CCGTCTCCTTCCCTACACCT 60.324 60.000 0.00 0.00 0.00 4.00
1290 2091 1.196012 GTCTCCTTCCCTACACCTGG 58.804 60.000 0.00 0.00 0.00 4.45
1292 2093 1.151413 TCTCCTTCCCTACACCTGGTT 59.849 52.381 0.00 0.00 0.00 3.67
1293 2094 1.279271 CTCCTTCCCTACACCTGGTTG 59.721 57.143 0.00 0.00 0.00 3.77
1294 2095 1.064825 CCTTCCCTACACCTGGTTGT 58.935 55.000 0.00 1.72 0.00 3.32
1296 2097 0.768622 TTCCCTACACCTGGTTGTGG 59.231 55.000 0.00 1.25 40.62 4.17
1297 2098 1.131303 TCCCTACACCTGGTTGTGGG 61.131 60.000 18.33 18.33 45.47 4.61
1299 2100 1.303317 CTACACCTGGTTGTGGGCC 60.303 63.158 0.00 0.00 40.62 5.80
1300 2101 2.764637 CTACACCTGGTTGTGGGCCC 62.765 65.000 17.59 17.59 40.62 5.80
1301 2102 3.902112 CACCTGGTTGTGGGCCCT 61.902 66.667 25.70 0.00 32.50 5.19
1302 2103 3.110031 ACCTGGTTGTGGGCCCTT 61.110 61.111 25.70 0.00 0.00 3.95
1304 2105 2.520458 CTGGTTGTGGGCCCTTGA 59.480 61.111 25.70 5.26 0.00 3.02
1305 2106 1.903404 CTGGTTGTGGGCCCTTGAC 60.903 63.158 25.70 17.58 0.00 3.18
1307 2108 2.197324 GTTGTGGGCCCTTGACCA 59.803 61.111 25.70 8.94 0.00 4.02
1308 2109 1.456705 GTTGTGGGCCCTTGACCAA 60.457 57.895 25.70 14.50 38.73 3.67
1309 2110 1.152567 TTGTGGGCCCTTGACCAAG 60.153 57.895 25.70 2.89 38.73 3.61
1310 2111 2.991540 GTGGGCCCTTGACCAAGC 60.992 66.667 25.70 0.00 38.73 4.01
1311 2112 3.506743 TGGGCCCTTGACCAAGCA 61.507 61.111 25.70 0.00 37.11 3.91
1312 2113 2.677875 GGGCCCTTGACCAAGCAG 60.678 66.667 17.04 0.00 37.11 4.24
1313 2114 2.677875 GGCCCTTGACCAAGCAGG 60.678 66.667 4.31 3.05 45.67 4.85
1314 2115 3.376918 GCCCTTGACCAAGCAGGC 61.377 66.667 12.12 12.12 43.14 4.85
1315 2116 3.058160 CCCTTGACCAAGCAGGCG 61.058 66.667 4.31 0.00 43.14 5.52
1316 2117 3.741476 CCTTGACCAAGCAGGCGC 61.741 66.667 0.00 0.00 43.14 6.53
1445 3195 8.891671 ATGTTTATTTGCTGAACACTCATTTT 57.108 26.923 0.00 0.00 36.31 1.82
1517 3267 1.440618 TTGGCAACCTGAAGACCCTA 58.559 50.000 0.00 0.00 0.00 3.53
1575 3325 4.885413 TGCATTAATTTTCTTGCTGCAGT 58.115 34.783 16.64 0.00 36.10 4.40
1691 3441 4.882842 TGAGTACCTGAACACATGCTTA 57.117 40.909 0.00 0.00 0.00 3.09
1692 3442 4.820897 TGAGTACCTGAACACATGCTTAG 58.179 43.478 0.00 0.00 0.00 2.18
1693 3443 3.600388 AGTACCTGAACACATGCTTAGC 58.400 45.455 0.00 0.00 0.00 3.09
1734 3489 6.738114 TGCAAAAGAACTTCAATACCAGAAG 58.262 36.000 0.00 0.00 46.08 2.85
1801 3556 3.609409 GCAAAGACCTTCGAATGGTGAAC 60.609 47.826 19.69 8.99 38.03 3.18
1835 3590 2.336891 AGGATGATGGGAGAGTCCATG 58.663 52.381 0.64 0.00 46.67 3.66
1935 3691 7.836685 TGAGTCATACCTTCTCTTCAGATAACT 59.163 37.037 0.00 0.00 0.00 2.24
1967 3723 3.477210 TTTTTGAATTTTCACCGGGGG 57.523 42.857 2.42 0.00 36.83 5.40
1988 3744 3.404773 GGAGAACTCCCCCACCTG 58.595 66.667 9.50 0.00 43.94 4.00
1989 3745 1.229529 GGAGAACTCCCCCACCTGA 60.230 63.158 9.50 0.00 43.94 3.86
1991 3747 1.290134 GAGAACTCCCCCACCTGAAT 58.710 55.000 0.00 0.00 0.00 2.57
1992 3748 2.478292 GAGAACTCCCCCACCTGAATA 58.522 52.381 0.00 0.00 0.00 1.75
2007 3955 6.017109 CCACCTGAATATATTTCTCAAACCCG 60.017 42.308 0.00 0.00 0.00 5.28
2011 3959 7.254795 CCTGAATATATTTCTCAAACCCGACAC 60.255 40.741 0.00 0.00 0.00 3.67
2013 3961 1.519408 ATTTCTCAAACCCGACACCG 58.481 50.000 0.00 0.00 0.00 4.94
2020 4317 0.971386 AAACCCGACACCGAGTACAT 59.029 50.000 0.00 0.00 38.22 2.29
2026 4323 2.479049 CCGACACCGAGTACATTGGTAG 60.479 54.545 3.71 2.62 44.72 3.18
2037 4334 1.283613 ACATTGGTAGAAATGCCGGGA 59.716 47.619 2.18 0.00 40.54 5.14
2052 4508 2.588989 GGAAGGCAGCAGAGAGGG 59.411 66.667 0.00 0.00 0.00 4.30
2054 4510 3.013932 AAGGCAGCAGAGAGGGGG 61.014 66.667 0.00 0.00 0.00 5.40
2109 4695 4.481930 TGCAGTTTTTGTGTTCTATCCG 57.518 40.909 0.00 0.00 0.00 4.18
2110 4696 3.234386 GCAGTTTTTGTGTTCTATCCGC 58.766 45.455 0.00 0.00 0.00 5.54
2187 5614 2.710902 CCAGAGGATGGCGTCGTCA 61.711 63.158 26.03 0.14 43.83 4.35
2207 5634 1.531602 GGCAGGCCTTCAAAGTGGT 60.532 57.895 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.228737 CGGGTCCAATTTGGTGGGT 60.229 57.895 14.98 0.00 39.03 4.51
71 72 5.242393 CCACTAGAATTAGATTTGCCATGGG 59.758 44.000 15.13 0.00 0.00 4.00
73 74 6.293081 CGACCACTAGAATTAGATTTGCCATG 60.293 42.308 0.00 0.00 0.00 3.66
78 79 6.313905 ACAAGCGACCACTAGAATTAGATTTG 59.686 38.462 0.00 0.00 0.00 2.32
86 87 1.736032 GCGACAAGCGACCACTAGAAT 60.736 52.381 0.00 0.00 44.57 2.40
89 90 3.768632 GCGACAAGCGACCACTAG 58.231 61.111 0.00 0.00 44.57 2.57
103 104 1.269448 GCAAAGATGAACAAAGGGCGA 59.731 47.619 0.00 0.00 0.00 5.54
105 106 1.338105 GGGCAAAGATGAACAAAGGGC 60.338 52.381 0.00 0.00 0.00 5.19
138 140 0.676782 GCCAAACCCACTCTATGCGT 60.677 55.000 0.00 0.00 0.00 5.24
155 157 2.102252 TGTTTGGTGATTTGGTCAAGCC 59.898 45.455 0.00 0.00 38.90 4.35
195 197 9.453830 AATCCCATCTATAGTCCTTTTTCTAGT 57.546 33.333 0.00 0.00 0.00 2.57
196 198 9.717942 CAATCCCATCTATAGTCCTTTTTCTAG 57.282 37.037 0.00 0.00 0.00 2.43
197 199 9.447279 TCAATCCCATCTATAGTCCTTTTTCTA 57.553 33.333 0.00 0.00 0.00 2.10
198 200 8.214364 GTCAATCCCATCTATAGTCCTTTTTCT 58.786 37.037 0.00 0.00 0.00 2.52
200 202 7.775561 GTGTCAATCCCATCTATAGTCCTTTTT 59.224 37.037 0.00 0.00 0.00 1.94
201 203 7.127955 AGTGTCAATCCCATCTATAGTCCTTTT 59.872 37.037 0.00 0.00 0.00 2.27
202 204 6.617371 AGTGTCAATCCCATCTATAGTCCTTT 59.383 38.462 0.00 0.00 0.00 3.11
203 205 6.146760 AGTGTCAATCCCATCTATAGTCCTT 58.853 40.000 0.00 0.00 0.00 3.36
204 206 5.721225 AGTGTCAATCCCATCTATAGTCCT 58.279 41.667 0.00 0.00 0.00 3.85
205 207 7.540474 TTAGTGTCAATCCCATCTATAGTCC 57.460 40.000 0.00 0.00 0.00 3.85
206 208 8.037758 CCATTAGTGTCAATCCCATCTATAGTC 58.962 40.741 0.00 0.00 0.00 2.59
208 210 6.820656 GCCATTAGTGTCAATCCCATCTATAG 59.179 42.308 0.00 0.00 0.00 1.31
209 211 6.574269 CGCCATTAGTGTCAATCCCATCTATA 60.574 42.308 0.00 0.00 0.00 1.31
210 212 5.564550 GCCATTAGTGTCAATCCCATCTAT 58.435 41.667 0.00 0.00 0.00 1.98
211 213 4.503123 CGCCATTAGTGTCAATCCCATCTA 60.503 45.833 0.00 0.00 0.00 1.98
212 214 3.745480 CGCCATTAGTGTCAATCCCATCT 60.745 47.826 0.00 0.00 0.00 2.90
213 215 2.549754 CGCCATTAGTGTCAATCCCATC 59.450 50.000 0.00 0.00 0.00 3.51
214 216 2.575532 CGCCATTAGTGTCAATCCCAT 58.424 47.619 0.00 0.00 0.00 4.00
216 218 0.663153 GCGCCATTAGTGTCAATCCC 59.337 55.000 0.00 0.00 0.00 3.85
217 219 1.378531 TGCGCCATTAGTGTCAATCC 58.621 50.000 4.18 0.00 0.00 3.01
219 221 2.615447 CTGATGCGCCATTAGTGTCAAT 59.385 45.455 4.18 0.00 0.00 2.57
221 223 1.206849 TCTGATGCGCCATTAGTGTCA 59.793 47.619 4.18 0.00 30.87 3.58
222 224 1.594862 GTCTGATGCGCCATTAGTGTC 59.405 52.381 4.18 0.00 30.87 3.67
223 225 1.066215 TGTCTGATGCGCCATTAGTGT 60.066 47.619 4.18 0.00 30.87 3.55
226 228 1.003116 GCTTGTCTGATGCGCCATTAG 60.003 52.381 4.18 5.13 0.00 1.73
228 230 1.805254 GCTTGTCTGATGCGCCATT 59.195 52.632 4.18 0.00 0.00 3.16
229 231 2.466982 CGCTTGTCTGATGCGCCAT 61.467 57.895 4.18 0.00 40.83 4.40
232 234 3.121030 ACCGCTTGTCTGATGCGC 61.121 61.111 0.00 0.00 44.70 6.09
234 236 2.482374 GCACCGCTTGTCTGATGC 59.518 61.111 0.00 0.00 0.00 3.91
235 237 2.780643 CGCACCGCTTGTCTGATG 59.219 61.111 0.00 0.00 0.00 3.07
242 244 9.900090 TAGTATATACTAATGGCGCACCGCTTG 62.900 44.444 18.36 0.00 42.82 4.01
243 245 7.298323 AGTATATACTAATGGCGCACCGCTT 62.298 44.000 13.88 0.00 43.06 4.68
244 246 5.884255 AGTATATACTAATGGCGCACCGCT 61.884 45.833 13.88 0.00 43.06 5.52
245 247 3.675228 AGTATATACTAATGGCGCACCGC 60.675 47.826 13.88 0.24 42.89 5.68
246 248 4.106029 AGTATATACTAATGGCGCACCG 57.894 45.455 13.88 0.00 34.69 4.94
270 272 1.549243 TATCAGAAGGTGGTGCGCCA 61.549 55.000 16.89 16.89 43.73 5.69
271 273 1.090052 GTATCAGAAGGTGGTGCGCC 61.090 60.000 10.11 10.11 0.00 6.53
272 274 1.421410 CGTATCAGAAGGTGGTGCGC 61.421 60.000 0.00 0.00 38.61 6.09
273 275 2.665777 CGTATCAGAAGGTGGTGCG 58.334 57.895 0.00 0.00 39.12 5.34
274 276 1.090052 GGCGTATCAGAAGGTGGTGC 61.090 60.000 0.00 0.00 0.00 5.01
275 277 0.249120 TGGCGTATCAGAAGGTGGTG 59.751 55.000 0.00 0.00 0.00 4.17
276 278 1.204146 ATGGCGTATCAGAAGGTGGT 58.796 50.000 0.00 0.00 0.00 4.16
277 279 2.332063 AATGGCGTATCAGAAGGTGG 57.668 50.000 0.00 0.00 0.00 4.61
278 280 4.202161 ACTCTAATGGCGTATCAGAAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
279 281 3.961408 ACTCTAATGGCGTATCAGAAGGT 59.039 43.478 0.00 0.00 0.00 3.50
280 282 4.592485 ACTCTAATGGCGTATCAGAAGG 57.408 45.455 0.00 0.00 0.00 3.46
281 283 5.592054 TCAACTCTAATGGCGTATCAGAAG 58.408 41.667 0.00 0.00 0.00 2.85
282 284 5.592104 TCAACTCTAATGGCGTATCAGAA 57.408 39.130 0.00 0.00 0.00 3.02
283 285 5.592104 TTCAACTCTAATGGCGTATCAGA 57.408 39.130 0.00 0.00 0.00 3.27
284 286 5.812642 AGTTTCAACTCTAATGGCGTATCAG 59.187 40.000 0.00 0.00 32.86 2.90
285 287 5.730550 AGTTTCAACTCTAATGGCGTATCA 58.269 37.500 0.00 0.00 32.86 2.15
286 288 6.979238 AGTAGTTTCAACTCTAATGGCGTATC 59.021 38.462 0.00 0.00 40.37 2.24
287 289 6.875076 AGTAGTTTCAACTCTAATGGCGTAT 58.125 36.000 0.00 0.00 40.37 3.06
288 290 6.276832 AGTAGTTTCAACTCTAATGGCGTA 57.723 37.500 0.00 0.00 40.37 4.42
289 291 5.148651 AGTAGTTTCAACTCTAATGGCGT 57.851 39.130 0.00 0.00 40.37 5.68
290 292 7.621991 CATTAGTAGTTTCAACTCTAATGGCG 58.378 38.462 24.00 12.58 43.04 5.69
293 295 8.391106 GTGCCATTAGTAGTTTCAACTCTAATG 58.609 37.037 24.33 24.33 44.21 1.90
294 296 8.100791 TGTGCCATTAGTAGTTTCAACTCTAAT 58.899 33.333 13.27 13.27 40.37 1.73
295 297 7.386848 GTGTGCCATTAGTAGTTTCAACTCTAA 59.613 37.037 0.00 5.13 40.37 2.10
296 298 6.872020 GTGTGCCATTAGTAGTTTCAACTCTA 59.128 38.462 0.00 0.00 40.37 2.43
297 299 5.701290 GTGTGCCATTAGTAGTTTCAACTCT 59.299 40.000 0.00 0.00 40.37 3.24
298 300 5.106673 GGTGTGCCATTAGTAGTTTCAACTC 60.107 44.000 0.00 0.00 36.21 3.01
299 301 4.760204 GGTGTGCCATTAGTAGTTTCAACT 59.240 41.667 0.00 0.00 37.61 3.16
300 302 4.760204 AGGTGTGCCATTAGTAGTTTCAAC 59.240 41.667 0.00 0.00 37.19 3.18
301 303 4.759693 CAGGTGTGCCATTAGTAGTTTCAA 59.240 41.667 0.00 0.00 37.19 2.69
302 304 4.323417 CAGGTGTGCCATTAGTAGTTTCA 58.677 43.478 0.00 0.00 37.19 2.69
303 305 3.689649 CCAGGTGTGCCATTAGTAGTTTC 59.310 47.826 0.00 0.00 37.19 2.78
304 306 3.686016 CCAGGTGTGCCATTAGTAGTTT 58.314 45.455 0.00 0.00 37.19 2.66
305 307 2.618045 GCCAGGTGTGCCATTAGTAGTT 60.618 50.000 0.00 0.00 37.19 2.24
306 308 1.065418 GCCAGGTGTGCCATTAGTAGT 60.065 52.381 0.00 0.00 37.19 2.73
307 309 1.668419 GCCAGGTGTGCCATTAGTAG 58.332 55.000 0.00 0.00 37.19 2.57
308 310 3.873781 GCCAGGTGTGCCATTAGTA 57.126 52.632 0.00 0.00 37.19 1.82
309 311 4.743018 GCCAGGTGTGCCATTAGT 57.257 55.556 0.00 0.00 37.19 2.24
316 318 4.603535 ACCTTGGGCCAGGTGTGC 62.604 66.667 21.94 0.00 46.22 4.57
326 328 0.107410 TACTAATGGCGCACCTTGGG 60.107 55.000 10.83 0.04 36.63 4.12
327 329 1.873591 GATACTAATGGCGCACCTTGG 59.126 52.381 10.83 3.59 36.63 3.61
328 330 2.560504 TGATACTAATGGCGCACCTTG 58.439 47.619 10.83 0.00 36.63 3.61
329 331 3.275617 TTGATACTAATGGCGCACCTT 57.724 42.857 10.83 1.13 36.63 3.50
330 332 3.275617 TTTGATACTAATGGCGCACCT 57.724 42.857 10.83 0.00 36.63 4.00
331 333 4.364415 TTTTTGATACTAATGGCGCACC 57.636 40.909 10.83 0.00 0.00 5.01
360 362 2.809696 GGACAGGCGCACTAGTTTAAAA 59.190 45.455 10.83 0.00 0.00 1.52
361 363 2.224329 TGGACAGGCGCACTAGTTTAAA 60.224 45.455 10.83 0.00 0.00 1.52
362 364 1.345089 TGGACAGGCGCACTAGTTTAA 59.655 47.619 10.83 0.00 0.00 1.52
363 365 0.970640 TGGACAGGCGCACTAGTTTA 59.029 50.000 10.83 0.00 0.00 2.01
364 366 0.107831 TTGGACAGGCGCACTAGTTT 59.892 50.000 10.83 0.00 0.00 2.66
365 367 0.107831 TTTGGACAGGCGCACTAGTT 59.892 50.000 10.83 0.00 0.00 2.24
366 368 0.602905 GTTTGGACAGGCGCACTAGT 60.603 55.000 10.83 0.47 0.00 2.57
367 369 0.602638 TGTTTGGACAGGCGCACTAG 60.603 55.000 10.83 0.00 0.00 2.57
368 370 0.036164 ATGTTTGGACAGGCGCACTA 59.964 50.000 10.83 0.00 39.58 2.74
369 371 0.036164 TATGTTTGGACAGGCGCACT 59.964 50.000 10.83 0.02 39.58 4.40
371 373 0.036164 AGTATGTTTGGACAGGCGCA 59.964 50.000 10.83 0.00 39.58 6.09
372 374 2.018542 TAGTATGTTTGGACAGGCGC 57.981 50.000 0.00 0.00 39.58 6.53
373 375 3.312421 CCATTAGTATGTTTGGACAGGCG 59.688 47.826 0.00 0.00 39.58 5.52
375 377 3.312421 CGCCATTAGTATGTTTGGACAGG 59.688 47.826 0.00 0.00 39.58 4.00
376 378 3.242739 GCGCCATTAGTATGTTTGGACAG 60.243 47.826 0.00 0.00 39.58 3.51
377 379 2.680841 GCGCCATTAGTATGTTTGGACA 59.319 45.455 0.00 0.00 40.71 4.02
379 381 2.992593 TGCGCCATTAGTATGTTTGGA 58.007 42.857 4.18 0.00 0.00 3.53
382 384 3.550820 TGGATGCGCCATTAGTATGTTT 58.449 40.909 4.18 0.00 43.33 2.83
383 385 3.207265 TGGATGCGCCATTAGTATGTT 57.793 42.857 4.18 0.00 43.33 2.71
384 386 2.928801 TGGATGCGCCATTAGTATGT 57.071 45.000 4.18 0.00 43.33 2.29
394 396 1.812922 CACTGAGTCTGGATGCGCC 60.813 63.158 4.18 0.00 37.10 6.53
395 397 2.459442 GCACTGAGTCTGGATGCGC 61.459 63.158 0.00 0.00 0.00 6.09
396 398 3.791539 GCACTGAGTCTGGATGCG 58.208 61.111 1.82 0.00 0.00 4.73
397 399 2.459442 GCGCACTGAGTCTGGATGC 61.459 63.158 0.30 2.71 0.00 3.91
399 401 1.620739 ATGGCGCACTGAGTCTGGAT 61.621 55.000 10.83 0.00 0.00 3.41
401 403 0.108186 TAATGGCGCACTGAGTCTGG 60.108 55.000 10.83 0.00 0.00 3.86
403 405 0.898320 AGTAATGGCGCACTGAGTCT 59.102 50.000 10.83 0.00 0.00 3.24
405 407 1.825474 ACTAGTAATGGCGCACTGAGT 59.175 47.619 10.83 5.92 0.00 3.41
406 408 2.586258 ACTAGTAATGGCGCACTGAG 57.414 50.000 10.83 5.32 0.00 3.35
408 410 3.426159 CCAAAACTAGTAATGGCGCACTG 60.426 47.826 10.83 1.89 0.00 3.66
409 411 2.747446 CCAAAACTAGTAATGGCGCACT 59.253 45.455 10.83 6.53 0.00 4.40
412 414 4.082949 ACTTTCCAAAACTAGTAATGGCGC 60.083 41.667 17.92 0.00 32.87 6.53
413 415 5.390613 CACTTTCCAAAACTAGTAATGGCG 58.609 41.667 17.92 12.42 32.87 5.69
414 416 5.161358 GCACTTTCCAAAACTAGTAATGGC 58.839 41.667 17.92 5.70 32.87 4.40
417 419 4.082949 GCCGCACTTTCCAAAACTAGTAAT 60.083 41.667 0.00 0.00 0.00 1.89
418 420 3.251487 GCCGCACTTTCCAAAACTAGTAA 59.749 43.478 0.00 0.00 0.00 2.24
419 421 2.809696 GCCGCACTTTCCAAAACTAGTA 59.190 45.455 0.00 0.00 0.00 1.82
421 423 1.399727 CGCCGCACTTTCCAAAACTAG 60.400 52.381 0.00 0.00 0.00 2.57
422 424 0.589223 CGCCGCACTTTCCAAAACTA 59.411 50.000 0.00 0.00 0.00 2.24
423 425 1.358759 CGCCGCACTTTCCAAAACT 59.641 52.632 0.00 0.00 0.00 2.66
424 426 2.300066 GCGCCGCACTTTCCAAAAC 61.300 57.895 3.15 0.00 0.00 2.43
425 427 2.026879 GCGCCGCACTTTCCAAAA 59.973 55.556 3.15 0.00 0.00 2.44
430 432 1.644786 ATTAGTGGCGCCGCACTTTC 61.645 55.000 39.02 14.86 33.26 2.62
431 433 1.674322 ATTAGTGGCGCCGCACTTT 60.674 52.632 39.02 22.52 33.26 2.66
432 434 2.046314 ATTAGTGGCGCCGCACTT 60.046 55.556 39.02 22.90 33.26 3.16
436 438 2.100216 CAACATTAGTGGCGCCGC 59.900 61.111 32.51 32.51 0.00 6.53
437 439 0.239879 AAACAACATTAGTGGCGCCG 59.760 50.000 23.90 8.78 0.00 6.46
438 440 2.432206 AAAACAACATTAGTGGCGCC 57.568 45.000 22.73 22.73 0.00 6.53
484 486 2.161609 AGTGCGCCATTAGTAGTTTTGC 59.838 45.455 4.18 0.00 0.00 3.68
505 507 2.733319 TAATGGCGCACGGTGGAACA 62.733 55.000 10.83 0.00 39.98 3.18
513 516 0.042188 GCACATACTAATGGCGCACG 60.042 55.000 10.83 0.00 37.43 5.34
524 531 1.079127 GGTCGGTGCAGCACATACT 60.079 57.895 26.78 0.00 35.86 2.12
525 532 2.452813 CGGTCGGTGCAGCACATAC 61.453 63.158 26.78 21.43 35.86 2.39
591 756 0.105913 ATTCGAGGGGAGAGGAGGAC 60.106 60.000 0.00 0.00 0.00 3.85
641 998 0.905337 GGATGGGGATAGGAGGTCCG 60.905 65.000 0.00 0.00 42.08 4.79
664 1021 2.359602 AGGAGACGAGAACGCCGA 60.360 61.111 0.00 0.00 43.96 5.54
734 1154 0.193574 ACAGAAAGGGGAGAGGGTGA 59.806 55.000 0.00 0.00 0.00 4.02
748 1168 2.927007 TCCCTCCTAGGAAGAGACAGAA 59.073 50.000 13.77 0.00 37.67 3.02
751 1171 1.063567 GCTCCCTCCTAGGAAGAGACA 60.064 57.143 30.07 3.68 37.67 3.41
974 1438 0.998945 CTCCTCTCCCCTCCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1098 1577 0.888619 ATGAGTTGAAGTCGCCGAGA 59.111 50.000 0.00 0.00 0.00 4.04
1223 2024 1.306568 GGGTGAGAGGAAGGGAGCT 60.307 63.158 0.00 0.00 0.00 4.09
1224 2025 2.371259 GGGGTGAGAGGAAGGGAGC 61.371 68.421 0.00 0.00 0.00 4.70
1244 2045 1.277557 GTGAGTTCAGAGATGCAGGGT 59.722 52.381 0.00 0.00 0.00 4.34
1288 2089 2.197324 GTCAAGGGCCCACAACCA 59.803 61.111 27.56 0.00 0.00 3.67
1290 2091 1.456705 TTGGTCAAGGGCCCACAAC 60.457 57.895 27.56 17.93 0.00 3.32
1292 2093 2.520458 CTTGGTCAAGGGCCCACA 59.480 61.111 27.56 11.86 34.87 4.17
1293 2094 2.991540 GCTTGGTCAAGGGCCCAC 60.992 66.667 27.56 14.09 38.80 4.61
1294 2095 3.506743 TGCTTGGTCAAGGGCCCA 61.507 61.111 27.56 0.00 38.80 5.36
1296 2097 2.677875 CCTGCTTGGTCAAGGGCC 60.678 66.667 12.02 0.00 38.80 5.80
1297 2098 3.376918 GCCTGCTTGGTCAAGGGC 61.377 66.667 12.02 12.40 38.14 5.19
1299 2100 3.741476 GCGCCTGCTTGGTCAAGG 61.741 66.667 12.02 0.00 38.80 3.61
1315 2116 4.755614 AAGCGGACGACGTCGAGC 62.756 66.667 41.52 36.14 46.52 5.03
1316 2117 2.573689 GAAGCGGACGACGTCGAG 60.574 66.667 41.52 29.95 46.52 4.04
1317 2118 4.434938 CGAAGCGGACGACGTCGA 62.435 66.667 41.52 0.00 46.52 4.20
1318 2119 4.731503 ACGAAGCGGACGACGTCG 62.732 66.667 34.58 34.58 46.52 5.12
1319 2120 3.164011 CACGAAGCGGACGACGTC 61.164 66.667 19.70 19.70 46.52 4.34
1322 2123 3.103911 CACCACGAAGCGGACGAC 61.104 66.667 7.16 0.00 31.69 4.34
1323 2124 4.351938 CCACCACGAAGCGGACGA 62.352 66.667 7.16 0.00 31.69 4.20
1325 2126 2.234913 ATACCCACCACGAAGCGGAC 62.235 60.000 0.00 0.00 31.69 4.79
1326 2127 1.985662 ATACCCACCACGAAGCGGA 60.986 57.895 0.00 0.00 31.69 5.54
1327 2128 1.813753 CATACCCACCACGAAGCGG 60.814 63.158 0.00 0.00 34.73 5.52
1328 2129 0.672401 AACATACCCACCACGAAGCG 60.672 55.000 0.00 0.00 0.00 4.68
1329 2130 1.199097 CAAACATACCCACCACGAAGC 59.801 52.381 0.00 0.00 0.00 3.86
1330 2131 2.500229 ACAAACATACCCACCACGAAG 58.500 47.619 0.00 0.00 0.00 3.79
1445 3195 3.712016 ACCACCTACACATTGCACATA 57.288 42.857 0.00 0.00 0.00 2.29
1517 3267 0.916086 TACACCATTCGCCAAGGGAT 59.084 50.000 0.56 0.00 36.89 3.85
1575 3325 8.998277 AAGAGCTTCTGTATATTAGGTGAGTA 57.002 34.615 0.00 0.00 0.00 2.59
1691 3441 3.633525 TGCAGATCAAGAAAGTTGTTGCT 59.366 39.130 0.00 0.00 32.09 3.91
1692 3442 3.968649 TGCAGATCAAGAAAGTTGTTGC 58.031 40.909 0.00 0.00 32.09 4.17
1693 3443 6.753279 TCTTTTGCAGATCAAGAAAGTTGTTG 59.247 34.615 0.00 0.00 35.84 3.33
1734 3489 3.281727 TGATACCTGTTTCTGATGCCC 57.718 47.619 0.00 0.00 0.00 5.36
1801 3556 5.278808 CCCATCATCCTTTGAGCATGTAATG 60.279 44.000 0.00 0.00 41.31 1.90
1835 3590 3.745975 GCCCTAAACAAATTTGCCAACTC 59.254 43.478 18.12 0.00 0.00 3.01
1972 3728 1.290134 ATTCAGGTGGGGGAGTTCTC 58.710 55.000 0.00 0.00 0.00 2.87
1973 3729 2.661176 TATTCAGGTGGGGGAGTTCT 57.339 50.000 0.00 0.00 0.00 3.01
1974 3730 5.584551 AATATATTCAGGTGGGGGAGTTC 57.415 43.478 0.00 0.00 0.00 3.01
1975 3731 5.676811 AGAAATATATTCAGGTGGGGGAGTT 59.323 40.000 0.00 0.00 0.00 3.01
1976 3732 5.235534 AGAAATATATTCAGGTGGGGGAGT 58.764 41.667 0.00 0.00 0.00 3.85
1977 3733 5.310594 TGAGAAATATATTCAGGTGGGGGAG 59.689 44.000 0.00 0.00 0.00 4.30
1979 3735 5.582950 TGAGAAATATATTCAGGTGGGGG 57.417 43.478 0.00 0.00 0.00 5.40
1980 3736 6.265422 GGTTTGAGAAATATATTCAGGTGGGG 59.735 42.308 0.00 0.00 0.00 4.96
1981 3737 6.265422 GGGTTTGAGAAATATATTCAGGTGGG 59.735 42.308 0.00 0.00 0.00 4.61
1983 3739 6.765989 TCGGGTTTGAGAAATATATTCAGGTG 59.234 38.462 0.00 0.00 0.00 4.00
1984 3740 6.766467 GTCGGGTTTGAGAAATATATTCAGGT 59.234 38.462 0.00 0.00 0.00 4.00
1985 3741 6.765989 TGTCGGGTTTGAGAAATATATTCAGG 59.234 38.462 0.00 0.00 0.00 3.86
1986 3742 7.254795 GGTGTCGGGTTTGAGAAATATATTCAG 60.255 40.741 0.00 0.00 0.00 3.02
1987 3743 6.540914 GGTGTCGGGTTTGAGAAATATATTCA 59.459 38.462 0.00 0.00 0.00 2.57
1988 3744 6.292703 CGGTGTCGGGTTTGAGAAATATATTC 60.293 42.308 0.00 0.00 0.00 1.75
1989 3745 5.526111 CGGTGTCGGGTTTGAGAAATATATT 59.474 40.000 0.00 0.00 0.00 1.28
1991 3747 4.160065 TCGGTGTCGGGTTTGAGAAATATA 59.840 41.667 0.00 0.00 36.95 0.86
1992 3748 3.055675 TCGGTGTCGGGTTTGAGAAATAT 60.056 43.478 0.00 0.00 36.95 1.28
2007 3955 4.445452 TTCTACCAATGTACTCGGTGTC 57.555 45.455 10.54 0.00 34.12 3.67
2011 3959 3.560068 GGCATTTCTACCAATGTACTCGG 59.440 47.826 0.00 0.00 36.63 4.63
2013 3961 3.560068 CCGGCATTTCTACCAATGTACTC 59.440 47.826 0.00 0.00 36.63 2.59
2020 4317 1.340600 CCTTCCCGGCATTTCTACCAA 60.341 52.381 0.00 0.00 0.00 3.67
2037 4334 3.013932 CCCCCTCTCTGCTGCCTT 61.014 66.667 0.00 0.00 0.00 4.35
2061 4520 2.987431 TAGTGGGGTTGGGGGTTCGT 62.987 60.000 0.00 0.00 0.00 3.85
2071 4530 3.010138 ACTGCATGTAACATAGTGGGGTT 59.990 43.478 0.00 0.00 0.00 4.11
2074 4660 5.643379 AAAACTGCATGTAACATAGTGGG 57.357 39.130 0.00 0.00 0.00 4.61
2139 4725 1.028330 TTCGCTCTACGGATCGTGGT 61.028 55.000 3.03 0.00 41.39 4.16
2187 5614 1.898574 CACTTTGAAGGCCTGCCGT 60.899 57.895 5.69 0.00 41.95 5.68


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

AutoCloner maintained by Alex Coulton.