Multiple sequence alignment - TraesCS1A01G005000

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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 TraesCS1A01G005000 chr1A 100.000 3581 0 0 1 3581 2974187 2977767 0.000000e+00 6613.0
1 TraesCS1A01G005000 chr1A 89.463 2572 258 8 1017 3581 3453535 3450970 0.000000e+00 3236.0
2 TraesCS1A01G005000 chr1A 89.283 2566 249 11 1017 3578 3680247 3677704 0.000000e+00 3192.0
3 TraesCS1A01G005000 chr1A 97.920 673 13 1 349 1020 535839096 535838424 0.000000e+00 1164.0
4 TraesCS1A01G005000 chr1A 87.162 148 10 6 3434 3578 3488366 3488225 3.700000e-35 159.0
5 TraesCS1A01G005000 chr1A 85.714 147 11 6 3434 3578 3669098 3668960 2.880000e-31 147.0
6 TraesCS1A01G005000 chr1A 88.889 117 9 3 3434 3547 2986018 2986133 1.340000e-29 141.0
7 TraesCS1A01G005000 chr1D 90.237 2571 235 9 1017 3578 619957 617394 0.000000e+00 3343.0
8 TraesCS1A01G005000 chr1D 86.401 2581 291 38 1017 3578 448366 450905 0.000000e+00 2767.0
9 TraesCS1A01G005000 chr1D 86.277 2514 310 21 1073 3581 696761 694278 0.000000e+00 2699.0
10 TraesCS1A01G005000 chr1D 93.333 45 2 1 3511 3554 220062149 220062105 8.300000e-07 65.8
11 TraesCS1A01G005000 chr1B 90.459 2547 216 16 1017 3551 4115719 4118250 0.000000e+00 3332.0
12 TraesCS1A01G005000 chr1B 89.014 2576 258 17 1017 3578 4560458 4557894 0.000000e+00 3166.0
13 TraesCS1A01G005000 chr1B 89.315 2527 252 10 1017 3532 4482487 4479968 0.000000e+00 3155.0
14 TraesCS1A01G005000 chr1B 88.167 2324 260 12 1017 3337 3943565 3945876 0.000000e+00 2754.0
15 TraesCS1A01G005000 chr1B 99.429 350 1 1 1 350 531563504 531563852 5.040000e-178 634.0
16 TraesCS1A01G005000 chr1B 86.486 148 12 5 3434 3578 4759007 4758865 4.790000e-34 156.0
17 TraesCS1A01G005000 chr3D 87.854 2363 267 13 1017 3371 560056929 560054579 0.000000e+00 2756.0
18 TraesCS1A01G005000 chr4A 98.514 673 9 1 349 1020 93069943 93069271 0.000000e+00 1186.0
19 TraesCS1A01G005000 chr4A 97.920 673 13 1 349 1020 75167373 75168045 0.000000e+00 1164.0
20 TraesCS1A01G005000 chr2A 98.217 673 11 1 349 1020 687106249 687105577 0.000000e+00 1175.0
21 TraesCS1A01G005000 chr2A 98.071 674 11 2 349 1020 625806705 625807378 0.000000e+00 1171.0
22 TraesCS1A01G005000 chr6A 98.071 674 12 1 348 1020 185345591 185344918 0.000000e+00 1171.0
23 TraesCS1A01G005000 chr6A 99.425 348 2 0 1 348 531033783 531034130 1.810000e-177 632.0
24 TraesCS1A01G005000 chr7A 97.920 673 13 1 349 1020 83118098 83118770 0.000000e+00 1164.0
25 TraesCS1A01G005000 chr5A 97.920 673 13 1 349 1020 578804903 578804231 0.000000e+00 1164.0
26 TraesCS1A01G005000 chr3A 97.920 673 13 1 349 1020 503079541 503080213 0.000000e+00 1164.0
27 TraesCS1A01G005000 chr5B 99.716 352 1 0 1 352 563088099 563088450 0.000000e+00 645.0
28 TraesCS1A01G005000 chrUn 99.715 351 1 0 1 351 350702171 350701821 0.000000e+00 643.0
29 TraesCS1A01G005000 chrUn 100.000 348 0 0 1 348 469750225 469750572 0.000000e+00 643.0
30 TraesCS1A01G005000 chrUn 99.713 349 0 1 1 349 231150810 231151157 3.900000e-179 638.0
31 TraesCS1A01G005000 chrUn 99.713 348 0 1 1 348 430750063 430749717 1.400000e-178 636.0
32 TraesCS1A01G005000 chr7B 98.886 359 2 2 1 358 218539861 218539504 1.080000e-179 640.0
33 TraesCS1A01G005000 chr4B 99.713 348 0 1 1 348 310959218 310958872 1.400000e-178 636.0


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 TraesCS1A01G005000 chr1A 2974187 2977767 3580 False 6613 6613 100.000 1 3581 1 chr1A.!!$F1 3580
1 TraesCS1A01G005000 chr1A 3450970 3453535 2565 True 3236 3236 89.463 1017 3581 1 chr1A.!!$R1 2564
2 TraesCS1A01G005000 chr1A 3677704 3680247 2543 True 3192 3192 89.283 1017 3578 1 chr1A.!!$R4 2561
3 TraesCS1A01G005000 chr1A 535838424 535839096 672 True 1164 1164 97.920 349 1020 1 chr1A.!!$R5 671
4 TraesCS1A01G005000 chr1D 617394 619957 2563 True 3343 3343 90.237 1017 3578 1 chr1D.!!$R1 2561
5 TraesCS1A01G005000 chr1D 448366 450905 2539 False 2767 2767 86.401 1017 3578 1 chr1D.!!$F1 2561
6 TraesCS1A01G005000 chr1D 694278 696761 2483 True 2699 2699 86.277 1073 3581 1 chr1D.!!$R2 2508
7 TraesCS1A01G005000 chr1B 4115719 4118250 2531 False 3332 3332 90.459 1017 3551 1 chr1B.!!$F2 2534
8 TraesCS1A01G005000 chr1B 4557894 4560458 2564 True 3166 3166 89.014 1017 3578 1 chr1B.!!$R2 2561
9 TraesCS1A01G005000 chr1B 4479968 4482487 2519 True 3155 3155 89.315 1017 3532 1 chr1B.!!$R1 2515
10 TraesCS1A01G005000 chr1B 3943565 3945876 2311 False 2754 2754 88.167 1017 3337 1 chr1B.!!$F1 2320
11 TraesCS1A01G005000 chr3D 560054579 560056929 2350 True 2756 2756 87.854 1017 3371 1 chr3D.!!$R1 2354
12 TraesCS1A01G005000 chr4A 93069271 93069943 672 True 1186 1186 98.514 349 1020 1 chr4A.!!$R1 671
13 TraesCS1A01G005000 chr4A 75167373 75168045 672 False 1164 1164 97.920 349 1020 1 chr4A.!!$F1 671
14 TraesCS1A01G005000 chr2A 687105577 687106249 672 True 1175 1175 98.217 349 1020 1 chr2A.!!$R1 671
15 TraesCS1A01G005000 chr2A 625806705 625807378 673 False 1171 1171 98.071 349 1020 1 chr2A.!!$F1 671
16 TraesCS1A01G005000 chr6A 185344918 185345591 673 True 1171 1171 98.071 348 1020 1 chr6A.!!$R1 672
17 TraesCS1A01G005000 chr7A 83118098 83118770 672 False 1164 1164 97.920 349 1020 1 chr7A.!!$F1 671
18 TraesCS1A01G005000 chr5A 578804231 578804903 672 True 1164 1164 97.920 349 1020 1 chr5A.!!$R1 671
19 TraesCS1A01G005000 chr3A 503079541 503080213 672 False 1164 1164 97.920 349 1020 1 chr3A.!!$F1 671

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
345 346 0.034337 GCCTAATTATCCGGGCGTCA 59.966 55.000 0.00 0.0 35.08 4.35 F
346 347 1.792006 CCTAATTATCCGGGCGTCAC 58.208 55.000 0.00 0.0 0.00 3.67 F
1584 1587 1.754621 TCTCAGCGGCGAGATTCCT 60.755 57.895 12.98 0.0 37.12 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1401 0.109532 TTCGTTGACAAGCCCATCCA 59.890 50.000 0.00 0.0 0.00 3.41 R
1772 1775 1.067821 TCCCGTTGAATTGGTTGTTGC 59.932 47.619 0.00 0.0 0.00 4.17 R
3251 3259 0.662619 CGCTGAAAGGCACAGAACAA 59.337 50.000 9.76 0.0 37.54 2.83 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
22 23 5.782677 AACACAATATACCCTACCACCAA 57.217 39.130 0.00 0.00 0.00 3.67
23 24 5.782677 ACACAATATACCCTACCACCAAA 57.217 39.130 0.00 0.00 0.00 3.28
24 25 6.142259 ACACAATATACCCTACCACCAAAA 57.858 37.500 0.00 0.00 0.00 2.44
25 26 6.553857 ACACAATATACCCTACCACCAAAAA 58.446 36.000 0.00 0.00 0.00 1.94
26 27 6.434965 ACACAATATACCCTACCACCAAAAAC 59.565 38.462 0.00 0.00 0.00 2.43
27 28 6.661805 CACAATATACCCTACCACCAAAAACT 59.338 38.462 0.00 0.00 0.00 2.66
28 29 7.830201 CACAATATACCCTACCACCAAAAACTA 59.170 37.037 0.00 0.00 0.00 2.24
29 30 8.050930 ACAATATACCCTACCACCAAAAACTAG 58.949 37.037 0.00 0.00 0.00 2.57
30 31 7.760400 ATATACCCTACCACCAAAAACTAGT 57.240 36.000 0.00 0.00 0.00 2.57
31 32 4.801521 ACCCTACCACCAAAAACTAGTT 57.198 40.909 1.12 1.12 0.00 2.24
32 33 5.133383 ACCCTACCACCAAAAACTAGTTT 57.867 39.130 15.22 15.22 0.00 2.66
33 34 4.891168 ACCCTACCACCAAAAACTAGTTTG 59.109 41.667 21.22 10.68 38.07 2.93
50 51 9.762381 AACTAGTTTGGGGTAATTATCATTTCA 57.238 29.630 1.12 0.00 0.00 2.69
51 52 9.936329 ACTAGTTTGGGGTAATTATCATTTCAT 57.064 29.630 0.00 0.00 0.00 2.57
99 100 9.923143 AAAGGTTAGTAAATAATGTTTTCAGCC 57.077 29.630 0.00 0.00 0.00 4.85
100 101 8.644374 AGGTTAGTAAATAATGTTTTCAGCCA 57.356 30.769 0.00 0.00 0.00 4.75
101 102 8.520351 AGGTTAGTAAATAATGTTTTCAGCCAC 58.480 33.333 0.00 0.00 0.00 5.01
102 103 8.520351 GGTTAGTAAATAATGTTTTCAGCCACT 58.480 33.333 0.00 0.00 0.00 4.00
103 104 9.341899 GTTAGTAAATAATGTTTTCAGCCACTG 57.658 33.333 0.00 0.00 0.00 3.66
104 105 7.524717 AGTAAATAATGTTTTCAGCCACTGT 57.475 32.000 0.00 0.00 32.61 3.55
105 106 7.951591 AGTAAATAATGTTTTCAGCCACTGTT 58.048 30.769 0.00 0.00 32.61 3.16
106 107 8.421002 AGTAAATAATGTTTTCAGCCACTGTTT 58.579 29.630 0.00 0.00 32.61 2.83
107 108 7.481275 AAATAATGTTTTCAGCCACTGTTTG 57.519 32.000 0.00 0.00 32.61 2.93
108 109 4.734398 AATGTTTTCAGCCACTGTTTGA 57.266 36.364 0.00 0.00 32.61 2.69
109 110 3.781079 TGTTTTCAGCCACTGTTTGAG 57.219 42.857 0.00 0.00 32.61 3.02
110 111 2.426738 TGTTTTCAGCCACTGTTTGAGG 59.573 45.455 0.00 0.00 32.61 3.86
111 112 2.427095 GTTTTCAGCCACTGTTTGAGGT 59.573 45.455 0.00 0.00 32.61 3.85
112 113 2.435372 TTCAGCCACTGTTTGAGGTT 57.565 45.000 0.00 0.00 32.61 3.50
113 114 1.679139 TCAGCCACTGTTTGAGGTTG 58.321 50.000 0.00 0.00 38.55 3.77
114 115 1.064758 TCAGCCACTGTTTGAGGTTGT 60.065 47.619 0.00 0.00 38.40 3.32
115 116 1.750778 CAGCCACTGTTTGAGGTTGTT 59.249 47.619 0.00 0.00 34.12 2.83
116 117 2.166254 CAGCCACTGTTTGAGGTTGTTT 59.834 45.455 0.00 0.00 34.12 2.83
117 118 3.380004 CAGCCACTGTTTGAGGTTGTTTA 59.620 43.478 0.00 0.00 34.12 2.01
118 119 4.020543 AGCCACTGTTTGAGGTTGTTTAA 58.979 39.130 0.00 0.00 0.00 1.52
119 120 4.097892 AGCCACTGTTTGAGGTTGTTTAAG 59.902 41.667 0.00 0.00 0.00 1.85
120 121 4.142249 GCCACTGTTTGAGGTTGTTTAAGT 60.142 41.667 0.00 0.00 0.00 2.24
121 122 5.578776 CCACTGTTTGAGGTTGTTTAAGTC 58.421 41.667 0.00 0.00 0.00 3.01
122 123 5.124776 CCACTGTTTGAGGTTGTTTAAGTCA 59.875 40.000 0.00 0.00 0.00 3.41
123 124 6.027749 CACTGTTTGAGGTTGTTTAAGTCAC 58.972 40.000 0.00 0.00 0.00 3.67
124 125 5.944007 ACTGTTTGAGGTTGTTTAAGTCACT 59.056 36.000 0.00 0.00 0.00 3.41
125 126 6.433093 ACTGTTTGAGGTTGTTTAAGTCACTT 59.567 34.615 0.00 0.00 0.00 3.16
126 127 7.608761 ACTGTTTGAGGTTGTTTAAGTCACTTA 59.391 33.333 0.00 0.00 0.00 2.24
127 128 8.514330 TGTTTGAGGTTGTTTAAGTCACTTAT 57.486 30.769 0.00 0.00 0.00 1.73
128 129 8.617809 TGTTTGAGGTTGTTTAAGTCACTTATC 58.382 33.333 0.00 0.00 0.00 1.75
129 130 8.617809 GTTTGAGGTTGTTTAAGTCACTTATCA 58.382 33.333 0.00 0.00 0.00 2.15
130 131 8.740123 TTGAGGTTGTTTAAGTCACTTATCAA 57.260 30.769 0.00 5.06 0.00 2.57
131 132 8.740123 TGAGGTTGTTTAAGTCACTTATCAAA 57.260 30.769 13.69 0.00 29.67 2.69
132 133 9.349713 TGAGGTTGTTTAAGTCACTTATCAAAT 57.650 29.630 13.69 8.42 29.67 2.32
170 171 9.679661 TGTTTACAATTTTATCATAGCCTCTGA 57.320 29.630 0.00 0.00 0.00 3.27
257 258 9.270640 TGATTTTGATTTTGAATTTGAATCGGT 57.729 25.926 0.00 0.00 33.55 4.69
260 261 9.928236 TTTTGATTTTGAATTTGAATCGGTTTC 57.072 25.926 0.00 0.00 33.55 2.78
261 262 7.332003 TGATTTTGAATTTGAATCGGTTTCG 57.668 32.000 0.00 0.00 37.13 3.46
270 271 4.157817 TCGGTTTCGAGCTAACGC 57.842 55.556 0.00 0.00 40.88 4.84
271 272 1.798725 TCGGTTTCGAGCTAACGCG 60.799 57.895 3.53 3.53 40.88 6.01
272 273 1.798725 CGGTTTCGAGCTAACGCGA 60.799 57.895 15.93 0.00 46.70 5.87
278 279 2.380102 TCGAGCTAACGCGAGATTAC 57.620 50.000 15.93 0.00 43.42 1.89
279 280 1.938577 TCGAGCTAACGCGAGATTACT 59.061 47.619 15.93 1.35 43.42 2.24
280 281 3.126073 TCGAGCTAACGCGAGATTACTA 58.874 45.455 15.93 0.00 43.42 1.82
281 282 3.557185 TCGAGCTAACGCGAGATTACTAA 59.443 43.478 15.93 0.00 43.42 2.24
282 283 3.658533 CGAGCTAACGCGAGATTACTAAC 59.341 47.826 15.93 0.00 42.18 2.34
283 284 4.595116 GAGCTAACGCGAGATTACTAACA 58.405 43.478 15.93 0.00 42.32 2.41
284 285 4.599047 AGCTAACGCGAGATTACTAACAG 58.401 43.478 15.93 0.00 42.32 3.16
285 286 4.096081 AGCTAACGCGAGATTACTAACAGT 59.904 41.667 15.93 0.00 42.32 3.55
286 287 5.295292 AGCTAACGCGAGATTACTAACAGTA 59.705 40.000 15.93 0.00 42.32 2.74
287 288 5.967674 GCTAACGCGAGATTACTAACAGTAA 59.032 40.000 15.93 1.51 43.95 2.24
288 289 7.468357 AGCTAACGCGAGATTACTAACAGTAAT 60.468 37.037 15.93 10.55 45.75 1.89
300 301 6.764877 ACTAACAGTAATCAAAGTGACGTG 57.235 37.500 0.00 0.00 0.00 4.49
301 302 5.694910 ACTAACAGTAATCAAAGTGACGTGG 59.305 40.000 0.00 0.00 0.00 4.94
302 303 2.806244 ACAGTAATCAAAGTGACGTGGC 59.194 45.455 0.00 0.00 0.00 5.01
303 304 2.805671 CAGTAATCAAAGTGACGTGGCA 59.194 45.455 0.00 0.00 0.00 4.92
304 305 3.436704 CAGTAATCAAAGTGACGTGGCAT 59.563 43.478 0.00 0.00 0.00 4.40
305 306 3.684788 AGTAATCAAAGTGACGTGGCATC 59.315 43.478 0.00 0.00 0.00 3.91
306 307 1.078709 ATCAAAGTGACGTGGCATCG 58.921 50.000 0.00 7.71 0.00 3.84
307 308 0.249699 TCAAAGTGACGTGGCATCGT 60.250 50.000 13.44 13.44 46.88 3.73
308 309 0.586319 CAAAGTGACGTGGCATCGTT 59.414 50.000 14.43 0.00 44.21 3.85
309 310 1.795872 CAAAGTGACGTGGCATCGTTA 59.204 47.619 14.43 9.12 44.21 3.18
310 311 2.157834 AAGTGACGTGGCATCGTTAA 57.842 45.000 14.43 5.94 44.21 2.01
311 312 1.425412 AGTGACGTGGCATCGTTAAC 58.575 50.000 14.43 14.72 44.21 2.01
312 313 0.092351 GTGACGTGGCATCGTTAACG 59.908 55.000 21.85 21.85 44.21 3.18
313 314 4.659480 ACGTGGCATCGTTAACGT 57.341 50.000 25.98 11.94 43.87 3.99
314 315 2.146954 ACGTGGCATCGTTAACGTG 58.853 52.632 25.98 22.24 46.58 4.49
315 316 1.286354 ACGTGGCATCGTTAACGTGG 61.286 55.000 25.98 19.51 46.58 4.94
316 317 1.791662 GTGGCATCGTTAACGTGGG 59.208 57.895 25.98 17.27 40.80 4.61
317 318 0.671163 GTGGCATCGTTAACGTGGGA 60.671 55.000 25.98 8.70 40.80 4.37
318 319 0.250793 TGGCATCGTTAACGTGGGAT 59.749 50.000 25.98 10.69 40.80 3.85
319 320 1.339247 TGGCATCGTTAACGTGGGATT 60.339 47.619 25.98 4.55 40.80 3.01
320 321 2.093606 TGGCATCGTTAACGTGGGATTA 60.094 45.455 25.98 6.82 40.80 1.75
321 322 2.286025 GGCATCGTTAACGTGGGATTAC 59.714 50.000 25.98 7.95 40.80 1.89
322 323 3.192466 GCATCGTTAACGTGGGATTACT 58.808 45.455 25.98 0.57 40.80 2.24
323 324 3.000925 GCATCGTTAACGTGGGATTACTG 59.999 47.826 25.98 11.92 40.80 2.74
324 325 3.940209 TCGTTAACGTGGGATTACTGT 57.060 42.857 25.98 0.00 40.80 3.55
325 326 5.342433 CATCGTTAACGTGGGATTACTGTA 58.658 41.667 25.98 3.87 40.80 2.74
326 327 4.985413 TCGTTAACGTGGGATTACTGTAG 58.015 43.478 25.98 0.00 40.80 2.74
327 328 3.549070 CGTTAACGTGGGATTACTGTAGC 59.451 47.826 19.75 0.00 34.11 3.58
328 329 2.685850 AACGTGGGATTACTGTAGCC 57.314 50.000 0.00 1.45 0.00 3.93
329 330 1.861982 ACGTGGGATTACTGTAGCCT 58.138 50.000 0.00 0.00 0.00 4.58
330 331 3.022557 ACGTGGGATTACTGTAGCCTA 57.977 47.619 0.00 1.19 0.00 3.93
331 332 3.368248 ACGTGGGATTACTGTAGCCTAA 58.632 45.455 0.00 0.00 0.00 2.69
332 333 3.965347 ACGTGGGATTACTGTAGCCTAAT 59.035 43.478 0.00 0.00 0.00 1.73
333 334 4.407945 ACGTGGGATTACTGTAGCCTAATT 59.592 41.667 0.00 0.00 0.00 1.40
334 335 5.599656 ACGTGGGATTACTGTAGCCTAATTA 59.400 40.000 0.00 0.00 0.00 1.40
335 336 6.269307 ACGTGGGATTACTGTAGCCTAATTAT 59.731 38.462 0.00 0.00 0.00 1.28
336 337 6.812160 CGTGGGATTACTGTAGCCTAATTATC 59.188 42.308 8.19 0.00 0.00 1.75
337 338 7.104290 GTGGGATTACTGTAGCCTAATTATCC 58.896 42.308 8.19 5.83 0.00 2.59
338 339 6.070995 TGGGATTACTGTAGCCTAATTATCCG 60.071 42.308 8.19 0.00 31.87 4.18
339 340 6.338937 GGATTACTGTAGCCTAATTATCCGG 58.661 44.000 0.00 0.00 0.00 5.14
340 341 5.733620 TTACTGTAGCCTAATTATCCGGG 57.266 43.478 0.00 0.00 0.00 5.73
341 342 2.302157 ACTGTAGCCTAATTATCCGGGC 59.698 50.000 0.00 5.52 44.38 6.13
344 345 2.836944 GCCTAATTATCCGGGCGTC 58.163 57.895 0.00 0.00 35.08 5.19
345 346 0.034337 GCCTAATTATCCGGGCGTCA 59.966 55.000 0.00 0.00 35.08 4.35
346 347 1.792006 CCTAATTATCCGGGCGTCAC 58.208 55.000 0.00 0.00 0.00 3.67
732 734 6.018913 GCGAATAGCTCAAGGATCATCATATG 60.019 42.308 0.00 0.00 44.04 1.78
815 817 5.538053 GGAGAACCATCACTATCTCATCTGA 59.462 44.000 4.27 0.00 40.02 3.27
1015 1017 4.022464 TCTGCGATGTTTCAAAAACGTT 57.978 36.364 0.00 0.00 0.00 3.99
1023 1025 4.773510 TGTTTCAAAAACGTTTTGGCAAC 58.226 34.783 26.76 26.76 0.00 4.17
1029 1031 4.657436 AAAACGTTTTGGCAACCTGATA 57.343 36.364 24.68 0.00 0.00 2.15
1056 1058 8.189119 ACCTCAAATATTTAGCCTTGTTTCAA 57.811 30.769 0.00 0.00 0.00 2.69
1113 1115 3.546616 GCAAGTTGCAAAGCATCCAAAAC 60.547 43.478 22.90 0.00 44.26 2.43
1245 1247 6.186957 ACCTGCAAATATATGTTCAAGTGGA 58.813 36.000 0.00 0.00 0.00 4.02
1262 1264 3.131400 AGTGGAGGACTAAAATCTCTCGC 59.869 47.826 0.00 0.00 30.86 5.03
1264 1266 4.338682 GTGGAGGACTAAAATCTCTCGCTA 59.661 45.833 0.00 0.00 0.00 4.26
1290 1292 4.584325 GCTTCTAATATGTTCAATGGCCCA 59.416 41.667 0.00 0.00 0.00 5.36
1414 1416 3.202818 ACTCATATGGATGGGCTTGTCAA 59.797 43.478 2.13 0.00 36.99 3.18
1445 1447 2.699321 TCTCTGGGCAGATCTCATCAAG 59.301 50.000 0.00 0.00 36.76 3.02
1584 1587 1.754621 TCTCAGCGGCGAGATTCCT 60.755 57.895 12.98 0.00 37.12 3.36
1681 1684 9.534565 CTACACAGATAGAAAAGCTAAGCAATA 57.465 33.333 0.00 0.00 31.66 1.90
1771 1774 5.715070 AGAAACTACAGTCCTTGAAGATCG 58.285 41.667 0.00 0.00 0.00 3.69
1772 1775 4.457834 AACTACAGTCCTTGAAGATCGG 57.542 45.455 0.00 0.00 0.00 4.18
1780 1783 1.200020 CCTTGAAGATCGGCAACAACC 59.800 52.381 0.00 0.00 0.00 3.77
1782 1785 1.974265 TGAAGATCGGCAACAACCAA 58.026 45.000 0.00 0.00 0.00 3.67
1788 1791 2.500509 TCGGCAACAACCAATTCAAC 57.499 45.000 0.00 0.00 0.00 3.18
1902 1905 2.089980 CTTGGGAAGTTGGAGATGCTG 58.910 52.381 0.00 0.00 0.00 4.41
1907 1910 2.948315 GGAAGTTGGAGATGCTGGAATC 59.052 50.000 0.00 0.00 0.00 2.52
1938 1941 9.685276 AATTTATCACATAATCAGTTCAGTGGA 57.315 29.630 0.00 0.00 0.00 4.02
1961 1964 2.168936 GCATTCCATCCTCCATTGCAAA 59.831 45.455 1.71 0.00 0.00 3.68
1966 1969 2.546778 CATCCTCCATTGCAAACATGC 58.453 47.619 1.71 0.00 0.00 4.06
2076 2079 5.321927 TGGTTTCTTCCCAATAAAGGTCTC 58.678 41.667 0.00 0.00 0.00 3.36
2095 2098 1.203187 TCTGTGGTAACCTCTCTGGCT 60.203 52.381 0.00 0.00 40.22 4.75
2161 2164 5.221441 GGGAAGATACTTGGTTTGCTTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
2163 2166 5.453567 AGATACTTGGTTTGCTTTTGTCC 57.546 39.130 0.00 0.00 0.00 4.02
2284 2287 3.198853 AGCAAGGGACCTATTCTCTGTTC 59.801 47.826 0.00 0.00 34.05 3.18
2578 2584 4.502016 TCTCGTCTACGACTACATTCAGT 58.498 43.478 0.14 0.00 44.22 3.41
2619 2625 7.148340 GGAATATTGGAAAATGAGGAGCTATCG 60.148 40.741 0.00 0.00 0.00 2.92
3039 3047 0.396139 GATGGGCAAGCATCCAAGGA 60.396 55.000 0.00 0.00 36.54 3.36
3159 3167 4.550076 AACTTAGCTCTGCTCATCAAGT 57.450 40.909 0.00 0.00 40.44 3.16
3214 3222 2.036256 GCCAACCATGCAGGAGGT 59.964 61.111 0.00 0.31 41.22 3.85
3251 3259 2.428890 CCAGCGACCATCTTCTAGTTCT 59.571 50.000 0.00 0.00 0.00 3.01
3255 3263 4.021016 AGCGACCATCTTCTAGTTCTTGTT 60.021 41.667 0.00 0.00 0.00 2.83
3257 3265 5.715070 CGACCATCTTCTAGTTCTTGTTCT 58.285 41.667 0.00 0.00 0.00 3.01
3272 3280 2.606961 TTCTGTGCCTTTCAGCGCG 61.607 57.895 0.00 0.00 46.35 6.86
3277 3285 1.745115 TGCCTTTCAGCGCGCTTAT 60.745 52.632 34.58 8.62 34.65 1.73
3337 3350 2.234908 CCTAGTGAGAAACCAGGGTCTG 59.765 54.545 0.00 0.00 0.00 3.51
3578 3608 5.063944 CAGTCCCGTGTTCTTGATATTTCTG 59.936 44.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.782677 TTGGTGGTAGGGTATATTGTGTT 57.217 39.130 0.00 0.00 0.00 3.32
1 2 5.782677 TTTGGTGGTAGGGTATATTGTGT 57.217 39.130 0.00 0.00 0.00 3.72
2 3 6.661805 AGTTTTTGGTGGTAGGGTATATTGTG 59.338 38.462 0.00 0.00 0.00 3.33
3 4 6.796648 AGTTTTTGGTGGTAGGGTATATTGT 58.203 36.000 0.00 0.00 0.00 2.71
4 5 8.050930 ACTAGTTTTTGGTGGTAGGGTATATTG 58.949 37.037 0.00 0.00 0.00 1.90
5 6 8.166479 ACTAGTTTTTGGTGGTAGGGTATATT 57.834 34.615 0.00 0.00 0.00 1.28
6 7 7.760400 ACTAGTTTTTGGTGGTAGGGTATAT 57.240 36.000 0.00 0.00 0.00 0.86
7 8 7.572546 AACTAGTTTTTGGTGGTAGGGTATA 57.427 36.000 1.12 0.00 0.00 1.47
8 9 6.458630 AACTAGTTTTTGGTGGTAGGGTAT 57.541 37.500 1.12 0.00 0.00 2.73
9 10 5.910355 AACTAGTTTTTGGTGGTAGGGTA 57.090 39.130 1.12 0.00 0.00 3.69
10 11 4.801521 AACTAGTTTTTGGTGGTAGGGT 57.198 40.909 1.12 0.00 0.00 4.34
11 12 5.447624 CAAACTAGTTTTTGGTGGTAGGG 57.552 43.478 18.25 0.00 33.53 3.53
24 25 9.762381 TGAAATGATAATTACCCCAAACTAGTT 57.238 29.630 1.12 1.12 0.00 2.24
25 26 9.936329 ATGAAATGATAATTACCCCAAACTAGT 57.064 29.630 0.00 0.00 0.00 2.57
73 74 9.923143 GGCTGAAAACATTATTTACTAACCTTT 57.077 29.630 0.00 0.00 0.00 3.11
74 75 9.084533 TGGCTGAAAACATTATTTACTAACCTT 57.915 29.630 0.00 0.00 0.00 3.50
75 76 8.520351 GTGGCTGAAAACATTATTTACTAACCT 58.480 33.333 0.00 0.00 0.00 3.50
76 77 8.520351 AGTGGCTGAAAACATTATTTACTAACC 58.480 33.333 0.00 0.00 0.00 2.85
77 78 9.341899 CAGTGGCTGAAAACATTATTTACTAAC 57.658 33.333 0.00 0.00 32.44 2.34
78 79 9.073475 ACAGTGGCTGAAAACATTATTTACTAA 57.927 29.630 2.91 0.00 35.18 2.24
79 80 8.630054 ACAGTGGCTGAAAACATTATTTACTA 57.370 30.769 2.91 0.00 35.18 1.82
80 81 7.524717 ACAGTGGCTGAAAACATTATTTACT 57.475 32.000 2.91 0.00 35.18 2.24
81 82 8.487176 CAAACAGTGGCTGAAAACATTATTTAC 58.513 33.333 2.91 0.00 35.18 2.01
82 83 8.417106 TCAAACAGTGGCTGAAAACATTATTTA 58.583 29.630 2.91 0.00 35.18 1.40
83 84 7.271511 TCAAACAGTGGCTGAAAACATTATTT 58.728 30.769 2.91 0.00 35.18 1.40
84 85 6.815089 TCAAACAGTGGCTGAAAACATTATT 58.185 32.000 2.91 0.00 35.18 1.40
85 86 6.403866 TCAAACAGTGGCTGAAAACATTAT 57.596 33.333 2.91 0.00 35.18 1.28
86 87 5.221224 CCTCAAACAGTGGCTGAAAACATTA 60.221 40.000 2.91 0.00 35.18 1.90
87 88 4.441913 CCTCAAACAGTGGCTGAAAACATT 60.442 41.667 2.91 0.00 35.18 2.71
88 89 3.068590 CCTCAAACAGTGGCTGAAAACAT 59.931 43.478 2.91 0.00 35.18 2.71
89 90 2.426738 CCTCAAACAGTGGCTGAAAACA 59.573 45.455 2.91 0.00 35.18 2.83
90 91 2.427095 ACCTCAAACAGTGGCTGAAAAC 59.573 45.455 2.91 0.00 35.18 2.43
91 92 2.733956 ACCTCAAACAGTGGCTGAAAA 58.266 42.857 2.91 0.00 35.18 2.29
92 93 2.426738 CAACCTCAAACAGTGGCTGAAA 59.573 45.455 2.91 0.00 35.18 2.69
93 94 2.023673 CAACCTCAAACAGTGGCTGAA 58.976 47.619 2.91 0.00 35.18 3.02
94 95 1.064758 ACAACCTCAAACAGTGGCTGA 60.065 47.619 2.91 0.00 35.18 4.26
95 96 1.392589 ACAACCTCAAACAGTGGCTG 58.607 50.000 0.00 0.00 37.52 4.85
96 97 2.143876 AACAACCTCAAACAGTGGCT 57.856 45.000 0.00 0.00 34.14 4.75
97 98 2.959507 AAACAACCTCAAACAGTGGC 57.040 45.000 0.00 0.00 34.14 5.01
98 99 5.124776 TGACTTAAACAACCTCAAACAGTGG 59.875 40.000 0.00 0.00 36.93 4.00
99 100 6.027749 GTGACTTAAACAACCTCAAACAGTG 58.972 40.000 0.00 0.00 0.00 3.66
100 101 5.944007 AGTGACTTAAACAACCTCAAACAGT 59.056 36.000 0.00 0.00 0.00 3.55
101 102 6.436843 AGTGACTTAAACAACCTCAAACAG 57.563 37.500 0.00 0.00 0.00 3.16
102 103 6.827586 AAGTGACTTAAACAACCTCAAACA 57.172 33.333 0.00 0.00 0.00 2.83
103 104 8.617809 TGATAAGTGACTTAAACAACCTCAAAC 58.382 33.333 9.35 0.00 29.35 2.93
104 105 8.740123 TGATAAGTGACTTAAACAACCTCAAA 57.260 30.769 9.35 0.00 29.35 2.69
105 106 8.740123 TTGATAAGTGACTTAAACAACCTCAA 57.260 30.769 9.35 9.64 29.35 3.02
106 107 8.740123 TTTGATAAGTGACTTAAACAACCTCA 57.260 30.769 19.76 11.21 31.72 3.86
144 145 9.679661 TCAGAGGCTATGATAAAATTGTAAACA 57.320 29.630 7.93 0.00 0.00 2.83
231 232 9.270640 ACCGATTCAAATTCAAAATCAAAATCA 57.729 25.926 7.67 0.00 31.25 2.57
234 235 9.928236 GAAACCGATTCAAATTCAAAATCAAAA 57.072 25.926 7.67 0.00 37.99 2.44
235 236 8.272176 CGAAACCGATTCAAATTCAAAATCAAA 58.728 29.630 7.67 0.00 37.96 2.69
236 237 7.649705 TCGAAACCGATTCAAATTCAAAATCAA 59.350 29.630 7.67 0.00 37.96 2.57
237 238 7.142021 TCGAAACCGATTCAAATTCAAAATCA 58.858 30.769 7.67 0.00 37.96 2.57
238 239 7.561237 TCGAAACCGATTCAAATTCAAAATC 57.439 32.000 0.00 0.00 37.96 2.17
239 240 6.089417 GCTCGAAACCGATTCAAATTCAAAAT 59.911 34.615 0.00 0.00 37.96 1.82
240 241 5.401079 GCTCGAAACCGATTCAAATTCAAAA 59.599 36.000 0.00 0.00 37.96 2.44
241 242 4.915085 GCTCGAAACCGATTCAAATTCAAA 59.085 37.500 0.00 0.00 37.96 2.69
242 243 4.215399 AGCTCGAAACCGATTCAAATTCAA 59.785 37.500 0.00 0.00 37.96 2.69
243 244 3.751175 AGCTCGAAACCGATTCAAATTCA 59.249 39.130 0.00 0.00 37.96 2.57
244 245 4.342352 AGCTCGAAACCGATTCAAATTC 57.658 40.909 0.00 0.00 37.96 2.17
245 246 5.628134 GTTAGCTCGAAACCGATTCAAATT 58.372 37.500 0.00 0.00 37.96 1.82
246 247 4.201685 CGTTAGCTCGAAACCGATTCAAAT 60.202 41.667 0.00 0.00 37.96 2.32
247 248 3.122278 CGTTAGCTCGAAACCGATTCAAA 59.878 43.478 0.00 0.00 37.96 2.69
248 249 2.664568 CGTTAGCTCGAAACCGATTCAA 59.335 45.455 0.00 0.00 37.96 2.69
249 250 2.256174 CGTTAGCTCGAAACCGATTCA 58.744 47.619 0.00 0.00 37.96 2.57
250 251 1.006287 GCGTTAGCTCGAAACCGATTC 60.006 52.381 0.00 0.00 41.01 2.52
251 252 0.997196 GCGTTAGCTCGAAACCGATT 59.003 50.000 0.00 0.00 41.01 3.34
252 253 1.138047 CGCGTTAGCTCGAAACCGAT 61.138 55.000 0.00 0.00 42.32 4.18
253 254 1.798725 CGCGTTAGCTCGAAACCGA 60.799 57.895 0.00 0.00 42.32 4.69
254 255 1.730593 CTCGCGTTAGCTCGAAACCG 61.731 60.000 5.77 0.00 42.32 4.44
255 256 0.455633 TCTCGCGTTAGCTCGAAACC 60.456 55.000 5.77 0.00 42.32 3.27
256 257 1.546834 ATCTCGCGTTAGCTCGAAAC 58.453 50.000 5.77 0.00 42.32 2.78
257 258 2.273370 AATCTCGCGTTAGCTCGAAA 57.727 45.000 5.77 0.00 42.32 3.46
258 259 2.353889 AGTAATCTCGCGTTAGCTCGAA 59.646 45.455 5.77 0.00 42.32 3.71
259 260 1.938577 AGTAATCTCGCGTTAGCTCGA 59.061 47.619 5.77 0.00 42.32 4.04
260 261 2.386501 AGTAATCTCGCGTTAGCTCG 57.613 50.000 5.77 0.00 42.32 5.03
261 262 4.595116 TGTTAGTAATCTCGCGTTAGCTC 58.405 43.478 5.77 0.00 42.32 4.09
262 263 4.096081 ACTGTTAGTAATCTCGCGTTAGCT 59.904 41.667 5.77 0.00 42.32 3.32
263 264 4.349501 ACTGTTAGTAATCTCGCGTTAGC 58.650 43.478 5.77 0.00 40.74 3.09
275 276 7.383029 CCACGTCACTTTGATTACTGTTAGTAA 59.617 37.037 4.12 4.12 43.95 2.24
276 277 6.864685 CCACGTCACTTTGATTACTGTTAGTA 59.135 38.462 0.00 0.00 0.00 1.82
277 278 5.694910 CCACGTCACTTTGATTACTGTTAGT 59.305 40.000 0.00 0.00 0.00 2.24
278 279 5.389516 GCCACGTCACTTTGATTACTGTTAG 60.390 44.000 0.00 0.00 0.00 2.34
279 280 4.449743 GCCACGTCACTTTGATTACTGTTA 59.550 41.667 0.00 0.00 0.00 2.41
280 281 3.250040 GCCACGTCACTTTGATTACTGTT 59.750 43.478 0.00 0.00 0.00 3.16
281 282 2.806244 GCCACGTCACTTTGATTACTGT 59.194 45.455 0.00 0.00 0.00 3.55
282 283 2.805671 TGCCACGTCACTTTGATTACTG 59.194 45.455 0.00 0.00 0.00 2.74
283 284 3.120321 TGCCACGTCACTTTGATTACT 57.880 42.857 0.00 0.00 0.00 2.24
284 285 3.483574 CGATGCCACGTCACTTTGATTAC 60.484 47.826 0.00 0.00 0.00 1.89
285 286 2.670905 CGATGCCACGTCACTTTGATTA 59.329 45.455 0.00 0.00 0.00 1.75
286 287 1.464608 CGATGCCACGTCACTTTGATT 59.535 47.619 0.00 0.00 0.00 2.57
287 288 1.078709 CGATGCCACGTCACTTTGAT 58.921 50.000 0.00 0.00 0.00 2.57
288 289 0.249699 ACGATGCCACGTCACTTTGA 60.250 50.000 0.00 0.00 43.02 2.69
289 290 0.586319 AACGATGCCACGTCACTTTG 59.414 50.000 5.80 0.00 45.83 2.77
290 291 2.157834 TAACGATGCCACGTCACTTT 57.842 45.000 5.80 0.00 45.83 2.66
291 292 1.796459 GTTAACGATGCCACGTCACTT 59.204 47.619 5.80 0.00 45.83 3.16
292 293 1.425412 GTTAACGATGCCACGTCACT 58.575 50.000 5.80 0.00 45.83 3.41
293 294 0.092351 CGTTAACGATGCCACGTCAC 59.908 55.000 23.35 5.66 45.83 3.67
294 295 0.318869 ACGTTAACGATGCCACGTCA 60.319 50.000 33.06 0.00 41.97 4.35
295 296 0.092351 CACGTTAACGATGCCACGTC 59.908 55.000 33.06 0.00 43.79 4.34
296 297 1.286354 CCACGTTAACGATGCCACGT 61.286 55.000 33.06 7.10 46.45 4.49
297 298 1.418367 CCACGTTAACGATGCCACG 59.582 57.895 33.06 6.38 43.02 4.94
298 299 0.671163 TCCCACGTTAACGATGCCAC 60.671 55.000 33.06 0.00 43.02 5.01
299 300 0.250793 ATCCCACGTTAACGATGCCA 59.749 50.000 33.06 15.53 43.02 4.92
300 301 1.375551 AATCCCACGTTAACGATGCC 58.624 50.000 33.06 0.00 43.02 4.40
301 302 3.000925 CAGTAATCCCACGTTAACGATGC 59.999 47.826 33.06 14.45 43.02 3.91
302 303 4.178540 ACAGTAATCCCACGTTAACGATG 58.821 43.478 33.06 24.21 43.02 3.84
303 304 4.460948 ACAGTAATCCCACGTTAACGAT 57.539 40.909 33.06 14.09 43.02 3.73
304 305 3.940209 ACAGTAATCCCACGTTAACGA 57.060 42.857 33.06 12.27 43.02 3.85
305 306 3.549070 GCTACAGTAATCCCACGTTAACG 59.451 47.826 25.68 25.68 46.33 3.18
306 307 3.867493 GGCTACAGTAATCCCACGTTAAC 59.133 47.826 0.00 0.00 0.00 2.01
307 308 3.770933 AGGCTACAGTAATCCCACGTTAA 59.229 43.478 0.00 0.00 0.00 2.01
308 309 3.368248 AGGCTACAGTAATCCCACGTTA 58.632 45.455 0.00 0.00 0.00 3.18
309 310 2.185387 AGGCTACAGTAATCCCACGTT 58.815 47.619 0.00 0.00 0.00 3.99
310 311 1.861982 AGGCTACAGTAATCCCACGT 58.138 50.000 0.00 0.00 0.00 4.49
311 312 4.602340 ATTAGGCTACAGTAATCCCACG 57.398 45.455 0.00 0.00 0.00 4.94
312 313 7.104290 GGATAATTAGGCTACAGTAATCCCAC 58.896 42.308 0.00 0.00 0.00 4.61
313 314 6.070995 CGGATAATTAGGCTACAGTAATCCCA 60.071 42.308 0.00 0.00 0.00 4.37
314 315 6.338937 CGGATAATTAGGCTACAGTAATCCC 58.661 44.000 0.00 0.00 0.00 3.85
315 316 6.338937 CCGGATAATTAGGCTACAGTAATCC 58.661 44.000 0.00 2.50 0.00 3.01
316 317 6.338937 CCCGGATAATTAGGCTACAGTAATC 58.661 44.000 0.73 0.00 0.00 1.75
317 318 5.338137 GCCCGGATAATTAGGCTACAGTAAT 60.338 44.000 0.73 0.00 42.34 1.89
318 319 4.020839 GCCCGGATAATTAGGCTACAGTAA 60.021 45.833 0.73 0.00 42.34 2.24
319 320 3.512724 GCCCGGATAATTAGGCTACAGTA 59.487 47.826 0.73 0.00 42.34 2.74
320 321 2.302157 GCCCGGATAATTAGGCTACAGT 59.698 50.000 0.73 0.00 42.34 3.55
321 322 2.674177 CGCCCGGATAATTAGGCTACAG 60.674 54.545 0.73 0.00 43.48 2.74
322 323 1.274167 CGCCCGGATAATTAGGCTACA 59.726 52.381 0.73 0.00 43.48 2.74
323 324 1.274447 ACGCCCGGATAATTAGGCTAC 59.726 52.381 0.73 0.00 43.48 3.58
324 325 1.547372 GACGCCCGGATAATTAGGCTA 59.453 52.381 0.73 0.00 43.48 3.93
325 326 0.320697 GACGCCCGGATAATTAGGCT 59.679 55.000 0.73 0.00 43.48 4.58
326 327 0.034337 TGACGCCCGGATAATTAGGC 59.966 55.000 0.73 3.86 42.18 3.93
327 328 1.069513 TGTGACGCCCGGATAATTAGG 59.930 52.381 0.73 0.00 0.00 2.69
328 329 2.132762 GTGTGACGCCCGGATAATTAG 58.867 52.381 0.73 0.00 0.00 1.73
329 330 1.758280 AGTGTGACGCCCGGATAATTA 59.242 47.619 0.73 0.00 0.00 1.40
330 331 0.539986 AGTGTGACGCCCGGATAATT 59.460 50.000 0.73 0.00 0.00 1.40
331 332 0.539986 AAGTGTGACGCCCGGATAAT 59.460 50.000 0.73 0.00 0.00 1.28
332 333 0.322322 AAAGTGTGACGCCCGGATAA 59.678 50.000 0.73 0.00 0.00 1.75
333 334 0.108520 GAAAGTGTGACGCCCGGATA 60.109 55.000 0.73 0.00 0.00 2.59
334 335 1.375523 GAAAGTGTGACGCCCGGAT 60.376 57.895 0.73 0.00 0.00 4.18
335 336 2.029964 GAAAGTGTGACGCCCGGA 59.970 61.111 0.73 0.00 0.00 5.14
336 337 1.234615 AATGAAAGTGTGACGCCCGG 61.235 55.000 0.00 0.00 0.00 5.73
337 338 0.591170 AAATGAAAGTGTGACGCCCG 59.409 50.000 0.00 0.00 0.00 6.13
338 339 2.034053 TCAAAATGAAAGTGTGACGCCC 59.966 45.455 0.00 0.00 0.00 6.13
339 340 3.243068 ACTCAAAATGAAAGTGTGACGCC 60.243 43.478 0.00 0.00 0.00 5.68
340 341 3.952535 ACTCAAAATGAAAGTGTGACGC 58.047 40.909 0.00 0.00 0.00 5.19
341 342 5.907391 GGTAACTCAAAATGAAAGTGTGACG 59.093 40.000 0.00 0.00 0.00 4.35
342 343 6.791303 TGGTAACTCAAAATGAAAGTGTGAC 58.209 36.000 0.00 0.00 37.61 3.67
343 344 7.094162 TGTTGGTAACTCAAAATGAAAGTGTGA 60.094 33.333 0.00 0.00 37.61 3.58
344 345 7.009174 GTGTTGGTAACTCAAAATGAAAGTGTG 59.991 37.037 0.00 0.00 37.61 3.82
345 346 7.033185 GTGTTGGTAACTCAAAATGAAAGTGT 58.967 34.615 0.00 0.00 37.61 3.55
346 347 7.257722 AGTGTTGGTAACTCAAAATGAAAGTG 58.742 34.615 0.00 0.00 37.61 3.16
566 567 4.134563 TGCTCTAGTGAAGAAACCCAAAC 58.865 43.478 0.00 0.00 32.46 2.93
815 817 4.020218 TGAATCGAGTGGGAGTTGATCTTT 60.020 41.667 0.00 0.00 0.00 2.52
1015 1017 3.838565 TGAGGTTTATCAGGTTGCCAAA 58.161 40.909 0.00 0.00 0.00 3.28
1023 1025 8.697507 AGGCTAAATATTTGAGGTTTATCAGG 57.302 34.615 11.05 0.00 0.00 3.86
1029 1031 8.646900 TGAAACAAGGCTAAATATTTGAGGTTT 58.353 29.630 11.05 11.32 0.00 3.27
1056 1058 5.482175 TGGTATTGATCCCGAAATTTGGTTT 59.518 36.000 0.00 0.00 0.00 3.27
1092 1094 3.622163 TGTTTTGGATGCTTTGCAACTTG 59.378 39.130 0.00 0.00 43.62 3.16
1128 1130 7.391554 TGAGGAAGAGAACCTGATAATTTGTTG 59.608 37.037 0.00 0.00 37.93 3.33
1245 1247 5.365403 CGATAGCGAGAGATTTTAGTCCT 57.635 43.478 0.00 0.00 40.82 3.85
1262 1264 7.413438 GGCCATTGAACATATTAGAAGCGATAG 60.413 40.741 0.00 0.00 0.00 2.08
1264 1266 5.182001 GGCCATTGAACATATTAGAAGCGAT 59.818 40.000 0.00 0.00 0.00 4.58
1290 1292 7.839680 ACATGTCTTTAAACTCCTTGGAATT 57.160 32.000 0.00 0.00 0.00 2.17
1399 1401 0.109532 TTCGTTGACAAGCCCATCCA 59.890 50.000 0.00 0.00 0.00 3.41
1405 1407 3.851098 AGAGTCTATTCGTTGACAAGCC 58.149 45.455 0.00 0.00 35.81 4.35
1414 1416 2.028130 CTGCCCAGAGAGTCTATTCGT 58.972 52.381 0.00 0.00 0.00 3.85
1445 1447 3.873910 AGTTGGGTACATGCACATAGAC 58.126 45.455 0.00 0.00 0.00 2.59
1620 1623 7.910162 CCAAATAACTGGTTCGATGATAAGTTG 59.090 37.037 8.76 0.00 0.00 3.16
1771 1774 1.496934 CCGTTGAATTGGTTGTTGCC 58.503 50.000 0.00 0.00 0.00 4.52
1772 1775 1.067821 TCCCGTTGAATTGGTTGTTGC 59.932 47.619 0.00 0.00 0.00 4.17
1780 1783 1.613437 AGGCAAACTCCCGTTGAATTG 59.387 47.619 0.00 0.00 32.65 2.32
1782 1785 1.247567 CAGGCAAACTCCCGTTGAAT 58.752 50.000 0.00 0.00 32.65 2.57
1788 1791 2.113139 ACACCAGGCAAACTCCCG 59.887 61.111 0.00 0.00 0.00 5.14
1911 1914 9.726232 CCACTGAACTGATTATGTGATAAATTG 57.274 33.333 0.00 0.00 0.00 2.32
1938 1941 2.037144 GCAATGGAGGATGGAATGCTT 58.963 47.619 0.00 0.00 45.52 3.91
1961 1964 1.610522 GTGTTGAAAGGCTCAGCATGT 59.389 47.619 0.00 0.00 45.67 3.21
1966 1969 3.567164 ACATCAAGTGTTGAAAGGCTCAG 59.433 43.478 0.00 0.00 43.95 3.35
2076 2079 1.270907 AGCCAGAGAGGTTACCACAG 58.729 55.000 3.51 0.00 40.61 3.66
2095 2098 2.630580 GGGTTGAATAACAAGGTGGCAA 59.369 45.455 0.00 0.00 39.30 4.52
2161 2164 1.355381 ACCCATCACAAGAGCAATGGA 59.645 47.619 1.85 0.00 40.98 3.41
2163 2166 3.671433 CGAAACCCATCACAAGAGCAATG 60.671 47.826 0.00 0.00 0.00 2.82
2284 2287 2.159627 CCAGTCTTCCGTCAAAATTCCG 59.840 50.000 0.00 0.00 0.00 4.30
2578 2584 2.212752 ATTCCATGGAGGCTTCCCTA 57.787 50.000 15.53 0.00 43.12 3.53
2619 2625 9.625747 ATTCTCTTCTTCCAATCTAATTCCTTC 57.374 33.333 0.00 0.00 0.00 3.46
2689 2695 5.645497 GGATTATAGGTGGACTGCATTCATC 59.355 44.000 6.38 0.00 0.00 2.92
2691 2697 4.411869 TGGATTATAGGTGGACTGCATTCA 59.588 41.667 6.38 0.00 0.00 2.57
2865 2871 9.364989 CTTCTGATGTGAAAAACAAGGTTAAAA 57.635 29.630 0.00 0.00 43.61 1.52
2867 2873 6.978080 GCTTCTGATGTGAAAAACAAGGTTAA 59.022 34.615 0.00 0.00 43.61 2.01
3159 3167 5.332743 AGATTCCAAACAAGATAAGGCCAA 58.667 37.500 5.01 0.00 0.00 4.52
3214 3222 3.449377 TCGCTGGATGAGTGTTTGGTATA 59.551 43.478 0.00 0.00 33.51 1.47
3251 3259 0.662619 CGCTGAAAGGCACAGAACAA 59.337 50.000 9.76 0.00 37.54 2.83
3255 3263 3.043713 CGCGCTGAAAGGCACAGA 61.044 61.111 5.56 0.00 37.54 3.41
3298 3310 8.642935 TCACTAGGATTCAGACCTTATATCAG 57.357 38.462 0.00 0.00 38.76 2.90
3337 3350 0.729690 GAATCGGCCTCTGCTTTGAC 59.270 55.000 0.00 0.00 37.74 3.18
3409 3431 3.580904 GCATGGCATGGCATACAAG 57.419 52.632 31.77 21.00 0.00 3.16
3417 3444 2.717044 CCTGTGTGGCATGGCATGG 61.717 63.158 26.07 19.44 0.00 3.66


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

AutoCloner maintained by Alex Coulton.