Multiple sequence alignment - TraesCS5B01G374900

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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 TraesCS5B01G374900 chr5B 100.000 5109 0 0 1 5109 552298203 552293095 0.000000e+00 9435.0
1 TraesCS5B01G374900 chr5B 87.730 163 16 4 993 1152 603954030 603954191 2.430000e-43 187.0
2 TraesCS5B01G374900 chr5D 95.386 2644 90 18 2481 5109 452219190 452216564 0.000000e+00 4178.0
3 TraesCS5B01G374900 chr5D 91.085 1862 99 34 426 2242 452221422 452219583 0.000000e+00 2457.0
4 TraesCS5B01G374900 chr5D 73.847 1258 250 61 2897 4115 489775835 489777052 1.310000e-115 427.0
5 TraesCS5B01G374900 chr5D 83.000 300 43 5 2 295 452222427 452222130 1.090000e-66 265.0
6 TraesCS5B01G374900 chr5D 90.116 172 12 3 2309 2475 452219397 452219226 8.610000e-53 219.0
7 TraesCS5B01G374900 chr5D 87.117 163 17 4 993 1152 489774790 489774951 1.130000e-41 182.0
8 TraesCS5B01G374900 chr5A 90.269 2672 151 48 2481 5109 570939715 570937110 0.000000e+00 3393.0
9 TraesCS5B01G374900 chr5A 91.404 1780 105 19 505 2244 570941793 570940022 0.000000e+00 2396.0
10 TraesCS5B01G374900 chr5A 74.324 1258 246 67 2897 4115 611340628 611341847 3.600000e-126 462.0
11 TraesCS5B01G374900 chr5A 88.776 196 13 7 2276 2466 570939951 570939760 1.110000e-56 231.0
12 TraesCS5B01G374900 chr5A 87.730 163 16 4 993 1152 611339333 611339494 2.430000e-43 187.0
13 TraesCS5B01G374900 chr5A 74.222 225 40 10 154 373 345133521 345133310 1.530000e-10 78.7
14 TraesCS5B01G374900 chr1D 79.828 233 42 5 143 372 237913685 237913915 1.140000e-36 165.0
15 TraesCS5B01G374900 chr1B 91.667 84 7 0 158 241 336615592 336615509 3.230000e-22 117.0
16 TraesCS5B01G374900 chr1B 87.719 57 7 0 317 373 2065981 2065925 3.300000e-07 67.6
17 TraesCS5B01G374900 chr4B 79.452 146 28 2 172 316 517564664 517564808 9.050000e-18 102.0
18 TraesCS5B01G374900 chr4B 76.866 134 26 4 223 353 659590520 659590651 2.550000e-08 71.3
19 TraesCS5B01G374900 chr2D 80.315 127 23 2 229 354 74764335 74764210 1.510000e-15 95.3
20 TraesCS5B01G374900 chr2D 77.852 149 29 4 228 373 645935139 645935286 7.050000e-14 89.8
21 TraesCS5B01G374900 chr6B 90.741 54 5 0 320 373 34443968 34444021 7.100000e-09 73.1
22 TraesCS5B01G374900 chr7B 73.707 232 40 13 148 373 340938690 340938906 2.550000e-08 71.3
23 TraesCS5B01G374900 chr6D 77.236 123 26 2 228 349 406198603 406198724 2.550000e-08 71.3
24 TraesCS5B01G374900 chr6D 82.857 70 11 1 145 213 335558355 335558286 1.540000e-05 62.1
25 TraesCS5B01G374900 chr6D 85.000 60 9 0 154 213 415617504 415617445 1.540000e-05 62.1
26 TraesCS5B01G374900 chr7D 73.148 216 49 8 226 436 474264757 474264546 9.180000e-08 69.4
27 TraesCS5B01G374900 chr3A 73.214 224 43 9 154 373 273305277 273305067 1.190000e-06 65.8
28 TraesCS5B01G374900 chr7A 75.893 112 27 0 262 373 85621889 85621778 1.990000e-04 58.4
29 TraesCS5B01G374900 chr2B 96.970 33 1 0 5061 5093 171013339 171013371 7.150000e-04 56.5


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 TraesCS5B01G374900 chr5B 552293095 552298203 5108 True 9435.000000 9435 100.000000 1 5109 1 chr5B.!!$R1 5108
1 TraesCS5B01G374900 chr5D 452216564 452222427 5863 True 1779.750000 4178 89.896750 2 5109 4 chr5D.!!$R1 5107
2 TraesCS5B01G374900 chr5D 489774790 489777052 2262 False 304.500000 427 80.482000 993 4115 2 chr5D.!!$F1 3122
3 TraesCS5B01G374900 chr5A 570937110 570941793 4683 True 2006.666667 3393 90.149667 505 5109 3 chr5A.!!$R2 4604
4 TraesCS5B01G374900 chr5A 611339333 611341847 2514 False 324.500000 462 81.027000 993 4115 2 chr5A.!!$F1 3122

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
244 250 0.240945 CCGGTGCTCGCATTTTCTTT 59.759 50.0 0.00 0.0 37.59 2.52 F
733 1365 0.323725 CAGGTCCAACAATCCAGGGG 60.324 60.0 0.00 0.0 0.00 4.79 F
1355 2086 0.789383 GCGAGTTTTGCGTGGATTCG 60.789 55.0 0.00 0.0 0.00 3.34 F
1585 2321 0.112412 AAAGTTTCCCTGGGCGTGAT 59.888 50.0 8.22 0.0 0.00 3.06 F
2731 3870 0.178831 AAGGAATGGGTGGAGGAGGT 60.179 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 2023 0.174845 CCTACGCGAATTGACTCCCA 59.825 55.0 15.93 0.0 0.0 4.37 R
1539 2275 0.813210 GCATCAGTAGCCAGCACTCC 60.813 60.0 0.00 0.0 0.0 3.85 R
2217 3166 0.820871 GTCCAAACAAACTGCCCACA 59.179 50.0 0.00 0.0 0.0 4.17 R
3549 4717 0.310854 CGCCCTTTCGCTTGAACTTT 59.689 50.0 0.00 0.0 0.0 2.66 R
4167 5343 0.033601 AACACCACCAAAGCACCAGA 60.034 50.0 0.00 0.0 0.0 3.86 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
60 64 8.407832 ACCAAACACACAAAATAGTTAACTACC 58.592 33.333 17.45 0.00 0.00 3.18
82 86 7.483580 ACCTTGTACTGTATTTTCTCTAGCT 57.516 36.000 0.00 0.00 0.00 3.32
96 100 6.472686 TTCTCTAGCTAAGGGACATTTCTC 57.527 41.667 0.00 0.00 33.06 2.87
100 104 5.958380 TCTAGCTAAGGGACATTTCTCTGAA 59.042 40.000 0.00 0.00 30.45 3.02
111 115 8.023706 GGGACATTTCTCTGAATTGAGTTTAAC 58.976 37.037 8.55 0.00 35.68 2.01
128 132 1.388547 AACAACATGGAAGCACGTGT 58.611 45.000 18.38 0.00 42.10 4.49
130 134 2.778299 ACAACATGGAAGCACGTGTAT 58.222 42.857 18.38 6.14 39.55 2.29
137 141 6.321717 ACATGGAAGCACGTGTATAAAAATG 58.678 36.000 18.38 14.05 38.74 2.32
156 160 3.648339 TGAGCCTTTCAGCAAATCAAC 57.352 42.857 0.00 0.00 34.23 3.18
157 161 2.957680 TGAGCCTTTCAGCAAATCAACA 59.042 40.909 0.00 0.00 34.23 3.33
162 166 3.991773 CCTTTCAGCAAATCAACATGTGG 59.008 43.478 0.00 0.00 0.00 4.17
165 169 5.781210 TTCAGCAAATCAACATGTGGTTA 57.219 34.783 0.00 0.00 37.72 2.85
175 179 5.496556 TCAACATGTGGTTAGATGGTTAGG 58.503 41.667 0.00 0.00 37.72 2.69
177 181 5.359194 ACATGTGGTTAGATGGTTAGGAG 57.641 43.478 0.00 0.00 32.16 3.69
178 182 4.164221 ACATGTGGTTAGATGGTTAGGAGG 59.836 45.833 0.00 0.00 32.16 4.30
182 186 4.224370 GTGGTTAGATGGTTAGGAGGACAA 59.776 45.833 0.00 0.00 0.00 3.18
183 187 4.469945 TGGTTAGATGGTTAGGAGGACAAG 59.530 45.833 0.00 0.00 0.00 3.16
186 190 2.197465 GATGGTTAGGAGGACAAGGGT 58.803 52.381 0.00 0.00 0.00 4.34
190 194 2.704596 GGTTAGGAGGACAAGGGTATCC 59.295 54.545 0.00 0.00 34.60 2.59
191 195 2.704596 GTTAGGAGGACAAGGGTATCCC 59.295 54.545 0.00 0.00 45.90 3.85
216 221 5.814705 CAGCCCATGAGAGTTTAAGTCTTAG 59.185 44.000 3.63 0.00 0.00 2.18
234 239 0.456221 AGACTTGATACCGGTGCTCG 59.544 55.000 19.93 4.20 38.88 5.03
241 246 1.003866 GATACCGGTGCTCGCATTTTC 60.004 52.381 19.93 0.00 37.59 2.29
244 250 0.240945 CCGGTGCTCGCATTTTCTTT 59.759 50.000 0.00 0.00 37.59 2.52
246 252 2.097466 CCGGTGCTCGCATTTTCTTTAT 59.903 45.455 0.00 0.00 37.59 1.40
249 255 5.328691 CGGTGCTCGCATTTTCTTTATTTA 58.671 37.500 0.00 0.00 0.00 1.40
256 262 9.289303 GCTCGCATTTTCTTTATTTATTTCAGA 57.711 29.630 0.00 0.00 0.00 3.27
281 287 5.278907 CCTTTTGGTGATGTGCATTTAGTGA 60.279 40.000 0.00 0.00 34.07 3.41
289 295 4.193826 TGTGCATTTAGTGAGAGGAGAC 57.806 45.455 0.00 0.00 0.00 3.36
292 298 3.119459 TGCATTTAGTGAGAGGAGACGTC 60.119 47.826 7.70 7.70 0.00 4.34
295 301 1.287217 TAGTGAGAGGAGACGTCCCT 58.713 55.000 21.20 21.20 45.26 4.20
296 302 1.287217 AGTGAGAGGAGACGTCCCTA 58.713 55.000 21.12 7.51 45.26 3.53
298 304 3.047115 AGTGAGAGGAGACGTCCCTATA 58.953 50.000 21.12 10.73 45.26 1.31
300 306 3.071312 GTGAGAGGAGACGTCCCTATAGA 59.929 52.174 21.12 9.21 45.26 1.98
301 307 3.071312 TGAGAGGAGACGTCCCTATAGAC 59.929 52.174 21.12 11.32 45.26 2.59
302 308 3.320129 AGAGGAGACGTCCCTATAGACT 58.680 50.000 21.12 12.97 45.26 3.24
303 309 4.491675 AGAGGAGACGTCCCTATAGACTA 58.508 47.826 21.12 0.00 45.26 2.59
304 310 4.284234 AGAGGAGACGTCCCTATAGACTAC 59.716 50.000 21.12 9.64 45.26 2.73
305 311 3.972638 AGGAGACGTCCCTATAGACTACA 59.027 47.826 20.10 0.00 45.26 2.74
306 312 4.411540 AGGAGACGTCCCTATAGACTACAA 59.588 45.833 20.10 0.00 45.26 2.41
307 313 5.104193 AGGAGACGTCCCTATAGACTACAAA 60.104 44.000 20.10 0.00 45.26 2.83
308 314 5.769162 GGAGACGTCCCTATAGACTACAAAT 59.231 44.000 13.01 0.00 36.76 2.32
309 315 6.264970 GGAGACGTCCCTATAGACTACAAATT 59.735 42.308 13.01 0.00 36.76 1.82
310 316 7.274603 AGACGTCCCTATAGACTACAAATTC 57.725 40.000 13.01 0.00 34.46 2.17
311 317 6.017275 AGACGTCCCTATAGACTACAAATTCG 60.017 42.308 13.01 0.00 34.46 3.34
312 318 5.591877 ACGTCCCTATAGACTACAAATTCGT 59.408 40.000 0.00 0.00 34.46 3.85
313 319 6.141462 CGTCCCTATAGACTACAAATTCGTC 58.859 44.000 0.00 0.00 34.46 4.20
314 320 6.017275 CGTCCCTATAGACTACAAATTCGTCT 60.017 42.308 0.00 0.00 40.74 4.18
315 321 7.468357 CGTCCCTATAGACTACAAATTCGTCTT 60.468 40.741 0.00 0.00 38.77 3.01
316 322 8.196103 GTCCCTATAGACTACAAATTCGTCTTT 58.804 37.037 0.00 0.00 38.77 2.52
317 323 8.195436 TCCCTATAGACTACAAATTCGTCTTTG 58.805 37.037 0.00 9.76 41.02 2.77
318 324 7.438459 CCCTATAGACTACAAATTCGTCTTTGG 59.562 40.741 0.00 0.00 39.83 3.28
319 325 7.980099 CCTATAGACTACAAATTCGTCTTTGGT 59.020 37.037 0.00 6.01 39.83 3.67
320 326 5.924475 AGACTACAAATTCGTCTTTGGTG 57.076 39.130 14.02 9.64 39.83 4.17
321 327 5.607477 AGACTACAAATTCGTCTTTGGTGA 58.393 37.500 14.02 2.58 39.83 4.02
322 328 5.465724 AGACTACAAATTCGTCTTTGGTGAC 59.534 40.000 14.02 8.29 39.83 3.67
323 329 5.365619 ACTACAAATTCGTCTTTGGTGACT 58.634 37.500 14.02 0.21 39.83 3.41
324 330 5.820947 ACTACAAATTCGTCTTTGGTGACTT 59.179 36.000 14.02 0.00 39.83 3.01
325 331 5.169836 ACAAATTCGTCTTTGGTGACTTC 57.830 39.130 14.02 0.00 39.83 3.01
326 332 4.211389 CAAATTCGTCTTTGGTGACTTCG 58.789 43.478 5.05 0.00 35.00 3.79
327 333 2.589798 TTCGTCTTTGGTGACTTCGT 57.410 45.000 0.00 0.00 35.00 3.85
328 334 2.129823 TCGTCTTTGGTGACTTCGTC 57.870 50.000 0.00 0.00 35.00 4.20
329 335 1.406180 TCGTCTTTGGTGACTTCGTCA 59.594 47.619 0.00 0.00 40.50 4.35
330 336 2.159212 TCGTCTTTGGTGACTTCGTCAA 60.159 45.455 0.00 0.00 44.49 3.18
331 337 2.800544 CGTCTTTGGTGACTTCGTCAAT 59.199 45.455 0.00 0.00 44.49 2.57
332 338 3.120991 CGTCTTTGGTGACTTCGTCAATC 60.121 47.826 0.00 0.00 44.49 2.67
333 339 4.058817 GTCTTTGGTGACTTCGTCAATCT 58.941 43.478 0.00 0.00 44.49 2.40
334 340 4.150804 GTCTTTGGTGACTTCGTCAATCTC 59.849 45.833 0.00 0.00 44.49 2.75
335 341 3.744238 TTGGTGACTTCGTCAATCTCA 57.256 42.857 0.00 0.00 44.49 3.27
336 342 3.744238 TGGTGACTTCGTCAATCTCAA 57.256 42.857 0.00 0.00 44.49 3.02
337 343 4.066646 TGGTGACTTCGTCAATCTCAAA 57.933 40.909 0.00 0.00 44.49 2.69
343 349 7.064609 GGTGACTTCGTCAATCTCAAAATGATA 59.935 37.037 0.00 0.00 44.49 2.15
349 355 4.913924 GTCAATCTCAAAATGATATGCCGC 59.086 41.667 0.00 0.00 0.00 6.53
354 360 3.286353 TCAAAATGATATGCCGCCTCAA 58.714 40.909 0.00 0.00 0.00 3.02
356 362 4.341806 TCAAAATGATATGCCGCCTCAATT 59.658 37.500 0.00 0.00 0.00 2.32
358 364 4.510038 AATGATATGCCGCCTCAATTTC 57.490 40.909 0.00 0.00 0.00 2.17
365 371 1.406069 GCCGCCTCAATTTCTCAGAGA 60.406 52.381 0.00 0.00 0.00 3.10
368 374 2.287373 CGCCTCAATTTCTCAGAGATGC 59.713 50.000 0.00 0.00 0.00 3.91
373 379 5.237561 CCTCAATTTCTCAGAGATGCTCATG 59.762 44.000 0.00 0.00 32.06 3.07
374 380 5.742063 TCAATTTCTCAGAGATGCTCATGT 58.258 37.500 0.00 0.00 32.06 3.21
405 411 9.516546 AGGATAGACACGTATACATTCATAAGA 57.483 33.333 3.32 0.00 0.00 2.10
434 1055 8.528917 AATGTATATGCGTATGTATGAACGTT 57.471 30.769 8.77 0.00 41.10 3.99
436 1057 9.628746 ATGTATATGCGTATGTATGAACGTTTA 57.371 29.630 8.77 0.00 41.10 2.01
444 1065 4.833469 TGTATGAACGTTTACATCTGCG 57.167 40.909 0.46 0.00 0.00 5.18
451 1072 0.996462 GTTTACATCTGCGCTGCGTA 59.004 50.000 24.04 18.70 0.00 4.42
454 1075 1.277326 TACATCTGCGCTGCGTAAAG 58.723 50.000 24.04 17.69 0.00 1.85
455 1076 0.389817 ACATCTGCGCTGCGTAAAGA 60.390 50.000 24.04 21.90 0.00 2.52
461 1082 1.050009 GCGCTGCGTAAAGAAAAACC 58.950 50.000 24.04 0.00 0.00 3.27
462 1083 1.314581 CGCTGCGTAAAGAAAAACCG 58.685 50.000 14.93 0.00 0.00 4.44
563 1190 1.153005 CTCCTGCCAGAATCAGCCC 60.153 63.158 0.00 0.00 0.00 5.19
568 1195 4.161295 CCAGAATCAGCCCGCGGA 62.161 66.667 30.73 6.75 0.00 5.54
593 1220 2.360852 ATGCAGAGCAGCCACCAC 60.361 61.111 0.00 0.00 43.65 4.16
616 1243 3.343326 TGGGCCCGGGTGCTAAAT 61.343 61.111 24.63 0.00 0.00 1.40
699 1331 3.434167 GCTCATTTGGGCTGGAATCTCTA 60.434 47.826 0.00 0.00 0.00 2.43
700 1332 4.749166 GCTCATTTGGGCTGGAATCTCTAT 60.749 45.833 0.00 0.00 0.00 1.98
713 1345 1.982660 TCTCTATCCAGCGACCGAAT 58.017 50.000 0.00 0.00 0.00 3.34
733 1365 0.323725 CAGGTCCAACAATCCAGGGG 60.324 60.000 0.00 0.00 0.00 4.79
734 1366 1.000359 GGTCCAACAATCCAGGGGG 60.000 63.158 0.00 0.00 0.00 5.40
1235 1879 2.240500 GCGCGATCTGGTGTGATCC 61.241 63.158 12.10 0.00 39.57 3.36
1293 2023 4.681978 GGAAGTCCGTGCGGTGCT 62.682 66.667 10.60 7.46 36.47 4.40
1340 2071 4.827087 ATGTGGCCGAGCTGCGAG 62.827 66.667 0.00 0.00 44.57 5.03
1346 2077 2.174349 CCGAGCTGCGAGTTTTGC 59.826 61.111 0.00 0.00 44.57 3.68
1355 2086 0.789383 GCGAGTTTTGCGTGGATTCG 60.789 55.000 0.00 0.00 0.00 3.34
1359 2090 2.151202 AGTTTTGCGTGGATTCGTGAT 58.849 42.857 0.00 0.00 0.00 3.06
1453 2186 1.353694 AGAAGAGGATTGCTGTGGCTT 59.646 47.619 0.00 0.00 39.59 4.35
1539 2275 1.062525 GCGGGTATTGCTTTCTGCG 59.937 57.895 0.00 0.00 46.63 5.18
1557 2293 0.529337 CGGAGTGCTGGCTACTGATG 60.529 60.000 3.30 0.00 0.00 3.07
1585 2321 0.112412 AAAGTTTCCCTGGGCGTGAT 59.888 50.000 8.22 0.00 0.00 3.06
1703 2439 3.967332 AAAAATGCTCCTGGTTGGATG 57.033 42.857 0.00 0.00 45.16 3.51
1711 2447 1.906574 TCCTGGTTGGATGGTACTCAC 59.093 52.381 0.00 0.00 40.56 3.51
1757 2528 6.903883 TGCATATTTCTAGACGTCTTTTCC 57.096 37.500 25.44 3.81 0.00 3.13
1876 2671 1.587054 CACCCCTCGACAGTGACTC 59.413 63.158 0.00 0.00 33.21 3.36
1974 2922 3.993081 CCCATCTTTCAGCTAGCTTATCG 59.007 47.826 16.46 3.65 0.00 2.92
2049 2997 3.329225 TGTGTATGGGAGTGTCAAATCCA 59.671 43.478 7.47 0.77 37.33 3.41
2061 3009 1.406180 TCAAATCCAATGCTGATGGCG 59.594 47.619 0.00 0.00 45.43 5.69
2068 3017 2.361757 CCAATGCTGATGGCGGAAAATA 59.638 45.455 0.00 0.00 45.43 1.40
2112 3061 6.078456 TCATACCAAGGATCATTCACCTTT 57.922 37.500 0.00 0.00 43.54 3.11
2132 3081 9.161629 CACCTTTTCTGTTTTTGGACTTTTATT 57.838 29.630 0.00 0.00 0.00 1.40
2189 3138 0.623723 TCCTACAGCACCCCCATTTC 59.376 55.000 0.00 0.00 0.00 2.17
2191 3140 1.463674 CTACAGCACCCCCATTTCAC 58.536 55.000 0.00 0.00 0.00 3.18
2202 3151 2.449464 CCCATTTCACCTCTGATGCAA 58.551 47.619 0.00 0.00 0.00 4.08
2217 3166 7.286316 CCTCTGATGCAAATTCCCTTACTAAAT 59.714 37.037 0.00 0.00 0.00 1.40
2222 3171 5.186797 TGCAAATTCCCTTACTAAATGTGGG 59.813 40.000 0.00 0.00 39.22 4.61
2258 3273 5.956642 ACAATGTTCGCCGGTTTATTTATT 58.043 33.333 1.90 0.00 0.00 1.40
2259 3274 7.086230 ACAATGTTCGCCGGTTTATTTATTA 57.914 32.000 1.90 0.00 0.00 0.98
2260 3275 7.708998 ACAATGTTCGCCGGTTTATTTATTAT 58.291 30.769 1.90 0.00 0.00 1.28
2261 3276 8.838365 ACAATGTTCGCCGGTTTATTTATTATA 58.162 29.630 1.90 0.00 0.00 0.98
2262 3277 9.834628 CAATGTTCGCCGGTTTATTTATTATAT 57.165 29.630 1.90 0.00 0.00 0.86
2263 3278 9.834628 AATGTTCGCCGGTTTATTTATTATATG 57.165 29.630 1.90 0.00 0.00 1.78
2264 3279 8.604640 TGTTCGCCGGTTTATTTATTATATGA 57.395 30.769 1.90 0.00 0.00 2.15
2265 3280 9.053840 TGTTCGCCGGTTTATTTATTATATGAA 57.946 29.630 1.90 0.00 0.00 2.57
2268 3283 9.221933 TCGCCGGTTTATTTATTATATGAATGT 57.778 29.630 1.90 0.00 0.00 2.71
2269 3284 9.834628 CGCCGGTTTATTTATTATATGAATGTT 57.165 29.630 1.90 0.00 0.00 2.71
2276 3291 7.681939 ATTTATTATATGAATGTTCGCCGGT 57.318 32.000 1.90 0.00 0.00 5.28
2277 3292 7.499321 TTTATTATATGAATGTTCGCCGGTT 57.501 32.000 1.90 0.00 0.00 4.44
2278 3293 7.499321 TTATTATATGAATGTTCGCCGGTTT 57.501 32.000 1.90 0.00 0.00 3.27
2279 3294 8.604640 TTATTATATGAATGTTCGCCGGTTTA 57.395 30.769 1.90 0.00 0.00 2.01
2280 3295 7.681939 ATTATATGAATGTTCGCCGGTTTAT 57.318 32.000 1.90 0.00 0.00 1.40
2281 3296 7.499321 TTATATGAATGTTCGCCGGTTTATT 57.501 32.000 1.90 0.00 0.00 1.40
2282 3297 4.712122 ATGAATGTTCGCCGGTTTATTT 57.288 36.364 1.90 0.00 0.00 1.40
2283 3298 5.821516 ATGAATGTTCGCCGGTTTATTTA 57.178 34.783 1.90 0.00 0.00 1.40
2284 3299 5.821516 TGAATGTTCGCCGGTTTATTTAT 57.178 34.783 1.90 0.00 0.00 1.40
2285 3300 6.197364 TGAATGTTCGCCGGTTTATTTATT 57.803 33.333 1.90 0.00 0.00 1.40
2286 3301 7.317842 TGAATGTTCGCCGGTTTATTTATTA 57.682 32.000 1.90 0.00 0.00 0.98
2369 3467 7.503902 TCTCTTTATTCTGCTATACTCTGCTGA 59.496 37.037 0.00 0.00 35.83 4.26
2379 3477 1.709578 ACTCTGCTGAAGTGGAGTGA 58.290 50.000 0.00 0.00 37.60 3.41
2385 3483 4.223700 TCTGCTGAAGTGGAGTGATACAAT 59.776 41.667 0.00 0.00 0.00 2.71
2386 3484 4.910195 TGCTGAAGTGGAGTGATACAATT 58.090 39.130 0.00 0.00 0.00 2.32
2580 3719 6.358991 TGATTTACCATGATCTGCAGAATGA 58.641 36.000 24.00 11.52 39.69 2.57
2680 3819 2.025155 GACCCTGAGAAGCGTGAGATA 58.975 52.381 0.00 0.00 0.00 1.98
2731 3870 0.178831 AAGGAATGGGTGGAGGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
2826 3974 4.794169 CAACCTATTTTCCTGTTTGACCG 58.206 43.478 0.00 0.00 0.00 4.79
3285 4440 4.441217 GGGGAGAGTATTAACGACAAGGAC 60.441 50.000 0.00 0.00 0.00 3.85
3345 4500 5.513962 GGAGAAGAAAGTTCTGGAGGTTCAT 60.514 44.000 0.00 0.00 37.65 2.57
3467 4635 8.839310 ATTATTATAGCTTTGCTTCGATGTCT 57.161 30.769 0.00 0.00 40.44 3.41
3549 4717 1.059584 TCCAGCAGAAGGAACACCCA 61.060 55.000 0.00 0.00 37.41 4.51
3712 4880 2.307768 CTGGTAAGGCCTCGTAGATCA 58.692 52.381 5.23 0.00 38.35 2.92
3720 4888 1.018148 CCTCGTAGATCACAGCGACT 58.982 55.000 0.00 0.00 33.89 4.18
3738 4906 6.197282 CAGCGACTAATCTGTGTACTTATGTG 59.803 42.308 0.00 0.00 0.00 3.21
3739 4907 5.051641 GCGACTAATCTGTGTACTTATGTGC 60.052 44.000 0.00 0.00 0.00 4.57
4145 5321 2.688477 AGCATTTTTGGGACCCAAGAA 58.312 42.857 26.73 26.73 44.84 2.52
4167 5343 3.397613 GATGCCTGCCCGCTCTCTT 62.398 63.158 0.00 0.00 0.00 2.85
4168 5344 3.397613 ATGCCTGCCCGCTCTCTTC 62.398 63.158 0.00 0.00 0.00 2.87
4169 5345 3.780173 GCCTGCCCGCTCTCTTCT 61.780 66.667 0.00 0.00 0.00 2.85
4171 5347 2.186384 CTGCCCGCTCTCTTCTGG 59.814 66.667 0.00 0.00 0.00 3.86
4172 5348 2.604686 TGCCCGCTCTCTTCTGGT 60.605 61.111 0.00 0.00 0.00 4.00
4173 5349 2.125350 GCCCGCTCTCTTCTGGTG 60.125 66.667 0.00 0.00 0.00 4.17
4174 5350 2.125350 CCCGCTCTCTTCTGGTGC 60.125 66.667 0.00 0.00 0.00 5.01
4228 5404 2.442458 TATGGCGCCGGGACTGTA 60.442 61.111 23.90 0.49 0.00 2.74
4229 5405 1.835267 TATGGCGCCGGGACTGTAT 60.835 57.895 23.90 9.54 0.00 2.29
4230 5406 1.812686 TATGGCGCCGGGACTGTATC 61.813 60.000 23.90 0.00 0.00 2.24
4250 5430 8.365060 TGTATCCATCCATGTCTTTTGAAAAT 57.635 30.769 0.00 0.00 0.00 1.82
4266 5446 4.069304 TGAAAATTGCTACGTGGCTACTT 58.931 39.130 24.82 10.93 0.00 2.24
4267 5447 4.153475 TGAAAATTGCTACGTGGCTACTTC 59.847 41.667 24.82 20.68 0.00 3.01
4269 5449 2.363788 TTGCTACGTGGCTACTTCTG 57.636 50.000 24.82 0.00 0.00 3.02
4281 5461 4.082190 TGGCTACTTCTGATGTAGTGTGAC 60.082 45.833 23.55 11.93 39.47 3.67
4298 5478 5.756347 AGTGTGACACTCGTATAAAAGCAAA 59.244 36.000 13.33 0.00 41.21 3.68
4299 5479 6.259167 AGTGTGACACTCGTATAAAAGCAAAA 59.741 34.615 13.33 0.00 41.21 2.44
4305 5485 7.519002 ACACTCGTATAAAAGCAAAATCTGTC 58.481 34.615 0.00 0.00 0.00 3.51
4306 5486 6.961554 CACTCGTATAAAAGCAAAATCTGTCC 59.038 38.462 0.00 0.00 0.00 4.02
4326 5506 1.717429 CGTGAAAACTAACGCACGCTC 60.717 52.381 0.00 0.00 45.81 5.03
4328 5508 2.033151 GTGAAAACTAACGCACGCTCTT 60.033 45.455 0.00 0.00 0.00 2.85
4361 5541 4.744570 TCTGAATACGTTGTCTAAGCAGG 58.255 43.478 0.00 0.00 0.00 4.85
4372 5552 0.108615 CTAAGCAGGACCGTGGACAG 60.109 60.000 0.00 0.00 0.00 3.51
4380 5560 0.307760 GACCGTGGACAGTTTTGCAG 59.692 55.000 0.00 0.00 0.00 4.41
4394 5574 0.032403 TTGCAGAGCATGTTTGTGGC 59.968 50.000 0.00 0.00 38.76 5.01
4479 5659 6.238211 GCACTTGCATTATTGTCGATCTAAGT 60.238 38.462 0.00 0.00 41.59 2.24
4492 5672 8.867112 TGTCGATCTAAGTACAATTCCATTAC 57.133 34.615 0.00 0.00 0.00 1.89
4530 5713 9.998106 ACTAGAAGAAAATAGTAGCAGTTGAAA 57.002 29.630 0.00 0.00 30.50 2.69
4532 5715 8.329203 AGAAGAAAATAGTAGCAGTTGAAAGG 57.671 34.615 0.00 0.00 0.00 3.11
4553 5739 4.407296 AGGAGGAGTTTATTACTGCAGAGG 59.593 45.833 23.35 0.00 46.76 3.69
4567 5753 2.217038 AGAGGTTGCAGGGCGAGAA 61.217 57.895 0.00 0.00 0.00 2.87
4569 5755 2.747855 GGTTGCAGGGCGAGAAGG 60.748 66.667 0.00 0.00 0.00 3.46
4576 5762 2.358737 GGGCGAGAAGGTGTGTGG 60.359 66.667 0.00 0.00 0.00 4.17
4603 5793 0.965866 TGCTGGACCTGGACGTAGAG 60.966 60.000 0.00 0.00 0.00 2.43
4629 5819 1.517832 CCGAGGGAGCAGTAGTTGG 59.482 63.158 0.00 0.00 0.00 3.77
4649 5839 1.468565 GCGATGGTGCAGACGTAGTAA 60.469 52.381 0.00 0.00 35.97 2.24
4665 5855 1.079875 GTAATTGGCGTCGGCGAAGA 61.080 55.000 26.37 6.08 40.30 2.87
4666 5856 0.804544 TAATTGGCGTCGGCGAAGAG 60.805 55.000 26.37 14.72 40.30 2.85
4703 5893 1.676384 GCTGCTCTTGAGGGTGTCT 59.324 57.895 0.00 0.00 0.00 3.41
4790 5980 2.654912 CGCGTCGAACCTGAACACC 61.655 63.158 0.00 0.00 0.00 4.16
5066 6273 4.530857 CAGGGACCGGATCGCCAC 62.531 72.222 9.46 0.00 41.22 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 63 9.522804 CTTAGCTAGAGAAAATACAGTACAAGG 57.477 37.037 0.00 0.00 0.00 3.61
60 64 9.522804 CCTTAGCTAGAGAAAATACAGTACAAG 57.477 37.037 0.00 0.00 0.00 3.16
66 70 7.113658 TGTCCCTTAGCTAGAGAAAATACAG 57.886 40.000 0.00 0.00 0.00 2.74
75 79 5.596361 TCAGAGAAATGTCCCTTAGCTAGAG 59.404 44.000 0.00 0.00 0.00 2.43
82 86 7.020827 ACTCAATTCAGAGAAATGTCCCTTA 57.979 36.000 0.07 0.00 38.98 2.69
96 100 7.115378 GCTTCCATGTTGTTAAACTCAATTCAG 59.885 37.037 0.00 0.00 37.19 3.02
100 104 6.215845 GTGCTTCCATGTTGTTAAACTCAAT 58.784 36.000 0.00 0.00 37.19 2.57
111 115 4.937696 TTATACACGTGCTTCCATGTTG 57.062 40.909 17.22 0.00 39.12 3.33
128 132 8.530311 TGATTTGCTGAAAGGCTCATTTTTATA 58.470 29.630 0.00 0.00 32.14 0.98
130 134 6.757237 TGATTTGCTGAAAGGCTCATTTTTA 58.243 32.000 0.00 0.00 32.14 1.52
137 141 3.648339 TGTTGATTTGCTGAAAGGCTC 57.352 42.857 0.00 0.00 0.00 4.70
156 160 4.408921 TCCTCCTAACCATCTAACCACATG 59.591 45.833 0.00 0.00 0.00 3.21
157 161 4.409247 GTCCTCCTAACCATCTAACCACAT 59.591 45.833 0.00 0.00 0.00 3.21
162 166 4.141688 CCCTTGTCCTCCTAACCATCTAAC 60.142 50.000 0.00 0.00 0.00 2.34
165 169 2.225908 ACCCTTGTCCTCCTAACCATCT 60.226 50.000 0.00 0.00 0.00 2.90
186 190 0.268869 ACTCTCATGGGCTGGGGATA 59.731 55.000 0.00 0.00 0.00 2.59
190 194 2.025887 ACTTAAACTCTCATGGGCTGGG 60.026 50.000 0.00 0.00 0.00 4.45
191 195 3.054802 AGACTTAAACTCTCATGGGCTGG 60.055 47.826 0.00 0.00 0.00 4.85
195 199 7.176589 AGTCTAAGACTTAAACTCTCATGGG 57.823 40.000 0.00 0.00 40.28 4.00
216 221 1.146358 GCGAGCACCGGTATCAAGTC 61.146 60.000 6.87 0.00 39.04 3.01
223 228 0.036765 AGAAAATGCGAGCACCGGTA 60.037 50.000 6.87 0.00 39.04 4.02
225 230 0.240945 AAAGAAAATGCGAGCACCGG 59.759 50.000 0.00 0.00 39.04 5.28
226 231 2.892373 TAAAGAAAATGCGAGCACCG 57.108 45.000 0.00 0.00 42.21 4.94
244 250 9.308000 ACATCACCAAAAGGTCTGAAATAAATA 57.692 29.630 0.00 0.00 0.00 1.40
246 252 7.432869 CACATCACCAAAAGGTCTGAAATAAA 58.567 34.615 0.00 0.00 0.00 1.40
249 255 4.262164 GCACATCACCAAAAGGTCTGAAAT 60.262 41.667 0.00 0.00 0.00 2.17
256 262 4.588528 ACTAAATGCACATCACCAAAAGGT 59.411 37.500 0.00 0.00 0.00 3.50
261 267 4.650734 TCTCACTAAATGCACATCACCAA 58.349 39.130 0.00 0.00 0.00 3.67
262 268 4.256110 CTCTCACTAAATGCACATCACCA 58.744 43.478 0.00 0.00 0.00 4.17
265 271 4.467438 TCTCCTCTCACTAAATGCACATCA 59.533 41.667 0.00 0.00 0.00 3.07
271 277 3.440228 GACGTCTCCTCTCACTAAATGC 58.560 50.000 8.70 0.00 0.00 3.56
272 278 3.181485 GGGACGTCTCCTCTCACTAAATG 60.181 52.174 16.46 0.00 36.68 2.32
275 281 1.634459 AGGGACGTCTCCTCTCACTAA 59.366 52.381 12.98 0.00 36.68 2.24
281 287 3.320129 AGTCTATAGGGACGTCTCCTCT 58.680 50.000 23.59 17.99 40.76 3.69
289 295 6.017275 AGACGAATTTGTAGTCTATAGGGACG 60.017 42.308 0.00 0.00 42.71 4.79
292 298 7.438459 CCAAAGACGAATTTGTAGTCTATAGGG 59.562 40.741 0.00 0.58 43.60 3.53
295 301 8.525316 TCACCAAAGACGAATTTGTAGTCTATA 58.475 33.333 0.00 0.00 43.60 1.31
296 302 7.331193 GTCACCAAAGACGAATTTGTAGTCTAT 59.669 37.037 0.00 0.00 43.60 1.98
298 304 5.465724 GTCACCAAAGACGAATTTGTAGTCT 59.534 40.000 0.00 0.04 46.01 3.24
300 306 5.365619 AGTCACCAAAGACGAATTTGTAGT 58.634 37.500 0.00 5.33 43.24 2.73
301 307 5.924475 AGTCACCAAAGACGAATTTGTAG 57.076 39.130 0.00 7.54 43.24 2.74
302 308 5.050634 CGAAGTCACCAAAGACGAATTTGTA 60.051 40.000 0.00 0.67 43.24 2.41
303 309 4.260620 CGAAGTCACCAAAGACGAATTTGT 60.261 41.667 0.00 0.00 43.24 2.83
304 310 4.211389 CGAAGTCACCAAAGACGAATTTG 58.789 43.478 9.25 9.25 43.24 2.32
305 311 3.875134 ACGAAGTCACCAAAGACGAATTT 59.125 39.130 0.00 0.00 43.24 1.82
306 312 3.463944 ACGAAGTCACCAAAGACGAATT 58.536 40.909 0.00 0.00 43.24 2.17
307 313 3.107642 ACGAAGTCACCAAAGACGAAT 57.892 42.857 0.00 0.00 43.24 3.34
308 314 2.589798 ACGAAGTCACCAAAGACGAA 57.410 45.000 0.00 0.00 43.24 3.85
322 328 6.854892 GGCATATCATTTTGAGATTGACGAAG 59.145 38.462 0.00 0.00 0.00 3.79
323 329 6.511605 CGGCATATCATTTTGAGATTGACGAA 60.512 38.462 6.54 0.00 37.28 3.85
324 330 5.050159 CGGCATATCATTTTGAGATTGACGA 60.050 40.000 6.54 0.00 37.28 4.20
325 331 5.142265 CGGCATATCATTTTGAGATTGACG 58.858 41.667 0.00 0.00 32.82 4.35
326 332 4.913924 GCGGCATATCATTTTGAGATTGAC 59.086 41.667 0.00 0.00 0.00 3.18
327 333 4.022935 GGCGGCATATCATTTTGAGATTGA 60.023 41.667 3.07 0.00 0.00 2.57
328 334 4.022589 AGGCGGCATATCATTTTGAGATTG 60.023 41.667 13.08 0.00 0.00 2.67
329 335 4.147321 AGGCGGCATATCATTTTGAGATT 58.853 39.130 13.08 0.00 0.00 2.40
330 336 3.755378 GAGGCGGCATATCATTTTGAGAT 59.245 43.478 13.08 0.00 0.00 2.75
331 337 3.141398 GAGGCGGCATATCATTTTGAGA 58.859 45.455 13.08 0.00 0.00 3.27
332 338 2.880268 TGAGGCGGCATATCATTTTGAG 59.120 45.455 13.08 0.00 0.00 3.02
333 339 2.929641 TGAGGCGGCATATCATTTTGA 58.070 42.857 13.08 0.00 0.00 2.69
334 340 3.713858 TTGAGGCGGCATATCATTTTG 57.286 42.857 13.08 0.00 0.00 2.44
335 341 4.942761 AATTGAGGCGGCATATCATTTT 57.057 36.364 13.08 1.04 0.00 1.82
336 342 4.586001 AGAAATTGAGGCGGCATATCATTT 59.414 37.500 13.08 7.95 0.00 2.32
337 343 4.147321 AGAAATTGAGGCGGCATATCATT 58.853 39.130 13.08 0.00 0.00 2.57
343 349 1.065199 TCTGAGAAATTGAGGCGGCAT 60.065 47.619 13.08 0.00 0.00 4.40
349 355 4.767478 TGAGCATCTCTGAGAAATTGAGG 58.233 43.478 12.00 0.00 34.92 3.86
354 360 6.550481 TCTCTACATGAGCATCTCTGAGAAAT 59.450 38.462 12.00 0.34 42.38 2.17
356 362 5.444176 TCTCTACATGAGCATCTCTGAGAA 58.556 41.667 12.00 0.00 42.38 2.87
358 364 4.216902 CCTCTCTACATGAGCATCTCTGAG 59.783 50.000 0.00 0.00 42.38 3.35
365 371 5.476599 GTGTCTATCCTCTCTACATGAGCAT 59.523 44.000 0.00 0.00 42.38 3.79
368 374 5.060506 ACGTGTCTATCCTCTCTACATGAG 58.939 45.833 0.00 0.00 43.96 2.90
373 379 8.550710 AATGTATACGTGTCTATCCTCTCTAC 57.449 38.462 0.00 0.00 0.00 2.59
374 380 8.373220 TGAATGTATACGTGTCTATCCTCTCTA 58.627 37.037 0.00 0.00 0.00 2.43
378 384 9.776158 CTTATGAATGTATACGTGTCTATCCTC 57.224 37.037 0.00 0.00 0.00 3.71
410 416 8.528917 AAACGTTCATACATACGCATATACAT 57.471 30.769 0.00 0.00 41.24 2.29
412 418 8.904712 TGTAAACGTTCATACATACGCATATAC 58.095 33.333 0.00 0.00 41.24 1.47
418 424 6.344800 CAGATGTAAACGTTCATACATACGC 58.655 40.000 20.26 11.61 41.53 4.42
419 425 6.344800 GCAGATGTAAACGTTCATACATACG 58.655 40.000 20.26 16.01 41.53 3.06
421 427 5.051307 GCGCAGATGTAAACGTTCATACATA 60.051 40.000 20.26 0.00 41.53 2.29
422 428 4.260212 GCGCAGATGTAAACGTTCATACAT 60.260 41.667 20.32 20.32 43.52 2.29
424 430 3.306166 AGCGCAGATGTAAACGTTCATAC 59.694 43.478 11.47 1.84 0.00 2.39
425 431 3.305897 CAGCGCAGATGTAAACGTTCATA 59.694 43.478 11.47 0.00 40.13 2.15
426 432 2.094258 CAGCGCAGATGTAAACGTTCAT 59.906 45.455 11.47 0.95 40.13 2.57
427 433 1.459209 CAGCGCAGATGTAAACGTTCA 59.541 47.619 11.47 0.00 40.13 3.18
428 434 2.145053 CAGCGCAGATGTAAACGTTC 57.855 50.000 11.47 0.00 40.13 3.95
444 1065 2.394545 ACGGTTTTTCTTTACGCAGC 57.605 45.000 0.00 0.00 0.00 5.25
454 1075 9.563898 TTTTCTAGAAGAAAGAAACGGTTTTTC 57.436 29.630 7.65 8.51 44.14 2.29
455 1076 9.917129 TTTTTCTAGAAGAAAGAAACGGTTTTT 57.083 25.926 7.65 0.00 44.14 1.94
490 1113 1.296392 CAACGACCCCTCTGCATCA 59.704 57.895 0.00 0.00 0.00 3.07
495 1118 0.537371 AAAAGCCAACGACCCCTCTG 60.537 55.000 0.00 0.00 0.00 3.35
534 1158 4.792804 GCAGGAGGCCAGCTGGAC 62.793 72.222 37.21 35.11 46.16 4.02
553 1180 2.759973 TCTCCGCGGGCTGATTCT 60.760 61.111 27.83 0.00 0.00 2.40
563 1190 2.125952 TGCATCTGTGTCTCCGCG 60.126 61.111 0.00 0.00 0.00 6.46
568 1195 0.391395 GCTGCTCTGCATCTGTGTCT 60.391 55.000 0.00 0.00 38.13 3.41
606 1233 1.702491 GCCGTGACGATTTAGCACCC 61.702 60.000 6.54 0.00 0.00 4.61
634 1261 2.815503 TCTTTGATCGGTCAGTGTCGTA 59.184 45.455 0.00 0.00 35.39 3.43
699 1331 1.330655 ACCTGATTCGGTCGCTGGAT 61.331 55.000 0.00 0.00 29.14 3.41
700 1332 1.945354 GACCTGATTCGGTCGCTGGA 61.945 60.000 10.48 0.00 43.56 3.86
713 1345 0.698238 CCCTGGATTGTTGGACCTGA 59.302 55.000 0.00 0.00 0.00 3.86
740 1372 1.549170 GTTTACTGCTCTCGAGGGGAA 59.451 52.381 15.59 0.00 0.00 3.97
792 1424 2.420043 GGCTGCGGAGGCGTATTA 59.580 61.111 16.05 0.00 44.10 0.98
824 1456 1.070914 GCCAGGGCTAATGTAGAGACC 59.929 57.143 2.30 0.00 43.23 3.85
825 1457 1.269831 CGCCAGGGCTAATGTAGAGAC 60.270 57.143 8.91 0.00 39.32 3.36
1163 1806 1.748329 CGATGATCGCAGGGGAGGAA 61.748 60.000 0.41 0.00 31.14 3.36
1185 1829 3.557595 CCCGAAAAGTAGCAGCTAAGATG 59.442 47.826 2.87 0.00 0.00 2.90
1186 1830 3.197983 ACCCGAAAAGTAGCAGCTAAGAT 59.802 43.478 2.87 0.00 0.00 2.40
1293 2023 0.174845 CCTACGCGAATTGACTCCCA 59.825 55.000 15.93 0.00 0.00 4.37
1340 2071 2.095969 TCATCACGAATCCACGCAAAAC 60.096 45.455 0.00 0.00 36.70 2.43
1346 2077 1.524355 GCAGATCATCACGAATCCACG 59.476 52.381 0.00 0.00 39.31 4.94
1355 2086 1.941294 CCAGCAGAAGCAGATCATCAC 59.059 52.381 0.00 0.00 45.49 3.06
1359 2090 1.203441 ACCCCAGCAGAAGCAGATCA 61.203 55.000 0.00 0.00 45.49 2.92
1453 2186 2.431683 GGCAAGCACTCCCTGACA 59.568 61.111 0.00 0.00 0.00 3.58
1539 2275 0.813210 GCATCAGTAGCCAGCACTCC 60.813 60.000 0.00 0.00 0.00 3.85
1585 2321 2.040545 TGTTCCCCGAATCTAGCCAAAA 59.959 45.455 0.00 0.00 0.00 2.44
1635 2371 2.739609 GCAGATGCAAAATAACTGGCCC 60.740 50.000 0.00 0.00 41.59 5.80
1703 2439 4.872691 CAGATGAATCACCAAGTGAGTACC 59.127 45.833 3.56 0.00 46.04 3.34
1711 2447 3.589951 ATCCCCAGATGAATCACCAAG 57.410 47.619 0.00 0.00 0.00 3.61
1757 2528 6.338937 GGTTGTCCACCTTATAACTAGACTG 58.661 44.000 0.00 0.00 43.29 3.51
1876 2671 3.754323 TCCTAACAAATAACAACGGGCAG 59.246 43.478 0.00 0.00 0.00 4.85
1881 2677 5.351233 TGCACTCCTAACAAATAACAACG 57.649 39.130 0.00 0.00 0.00 4.10
1974 2922 2.890945 GGAATGTATAACCACCCCATGC 59.109 50.000 0.00 0.00 0.00 4.06
2049 2997 4.942761 ATTATTTTCCGCCATCAGCATT 57.057 36.364 0.00 0.00 44.04 3.56
2061 3009 7.948278 ACAGACTAGACGCATATTATTTTCC 57.052 36.000 0.00 0.00 0.00 3.13
2157 3106 5.147162 GTGCTGTAGGAAATCAAAAGTTCG 58.853 41.667 0.00 0.00 30.24 3.95
2164 3113 1.005450 GGGGGTGCTGTAGGAAATCAA 59.995 52.381 0.00 0.00 0.00 2.57
2189 3138 2.731572 AGGGAATTTGCATCAGAGGTG 58.268 47.619 0.00 0.00 0.00 4.00
2191 3140 4.530875 AGTAAGGGAATTTGCATCAGAGG 58.469 43.478 0.00 0.00 0.00 3.69
2202 3151 4.941713 TGCCCACATTTAGTAAGGGAATT 58.058 39.130 8.75 0.00 42.25 2.17
2217 3166 0.820871 GTCCAAACAAACTGCCCACA 59.179 50.000 0.00 0.00 0.00 4.17
2258 3273 7.499321 AAATAAACCGGCGAACATTCATATA 57.501 32.000 9.30 0.00 0.00 0.86
2259 3274 6.385649 AAATAAACCGGCGAACATTCATAT 57.614 33.333 9.30 0.00 0.00 1.78
2260 3275 5.821516 AAATAAACCGGCGAACATTCATA 57.178 34.783 9.30 0.00 0.00 2.15
2261 3276 4.712122 AAATAAACCGGCGAACATTCAT 57.288 36.364 9.30 0.00 0.00 2.57
2262 3277 5.821516 ATAAATAAACCGGCGAACATTCA 57.178 34.783 9.30 0.00 0.00 2.57
2264 3279 9.834628 CATATAATAAATAAACCGGCGAACATT 57.165 29.630 9.30 0.00 0.00 2.71
2265 3280 7.966204 GCATATAATAAATAAACCGGCGAACAT 59.034 33.333 9.30 0.00 0.00 2.71
2266 3281 7.173562 AGCATATAATAAATAAACCGGCGAACA 59.826 33.333 9.30 0.00 0.00 3.18
2267 3282 7.524065 AGCATATAATAAATAAACCGGCGAAC 58.476 34.615 9.30 0.00 0.00 3.95
2268 3283 7.675962 AGCATATAATAAATAAACCGGCGAA 57.324 32.000 9.30 0.00 0.00 4.70
2269 3284 7.604927 AGAAGCATATAATAAATAAACCGGCGA 59.395 33.333 9.30 0.00 0.00 5.54
2270 3285 7.748847 AGAAGCATATAATAAATAAACCGGCG 58.251 34.615 0.00 0.00 0.00 6.46
2271 3286 9.341899 CAAGAAGCATATAATAAATAAACCGGC 57.658 33.333 0.00 0.00 0.00 6.13
2272 3287 9.341899 GCAAGAAGCATATAATAAATAAACCGG 57.658 33.333 0.00 0.00 44.79 5.28
2455 3560 7.999679 TCAATGAGTTCTTGAACAGTTGAAAT 58.000 30.769 14.80 0.00 29.96 2.17
2459 3564 7.703621 ACATTTCAATGAGTTCTTGAACAGTTG 59.296 33.333 14.80 14.25 41.10 3.16
2475 3580 5.234972 TGCGCTCACTAGATACATTTCAATG 59.765 40.000 9.73 0.00 42.10 2.82
2549 3688 5.334957 GCAGATCATGGTAAATCAGCAGATG 60.335 44.000 0.00 0.00 38.24 2.90
2580 3719 6.485171 ACAGATACACCTGAAATAAGCCTTT 58.515 36.000 0.00 0.00 37.59 3.11
2680 3819 5.105023 AGCATCTTCGCCATACTGATCATAT 60.105 40.000 0.00 0.00 0.00 1.78
2758 3897 3.519107 AGGGCCCGAAAAATGATGAAAAT 59.481 39.130 18.44 0.00 0.00 1.82
2761 3900 2.099405 GAGGGCCCGAAAAATGATGAA 58.901 47.619 18.44 0.00 0.00 2.57
3345 4500 1.144708 TGTTGCATCCCCTTCTCAACA 59.855 47.619 0.00 0.00 42.95 3.33
3467 4635 9.182933 GAAAACAAAACACACTGTTAGTTTGTA 57.817 29.630 14.34 0.00 42.48 2.41
3549 4717 0.310854 CGCCCTTTCGCTTGAACTTT 59.689 50.000 0.00 0.00 0.00 2.66
3705 4873 5.176407 ACAGATTAGTCGCTGTGATCTAC 57.824 43.478 0.00 0.00 43.26 2.59
3712 4880 4.785511 AAGTACACAGATTAGTCGCTGT 57.214 40.909 0.00 0.00 45.62 4.40
3720 4888 9.838975 CAATTTTGCACATAAGTACACAGATTA 57.161 29.630 0.00 0.00 0.00 1.75
3728 4896 9.458374 AACAAGTACAATTTTGCACATAAGTAC 57.542 29.630 0.00 8.93 0.00 2.73
3738 4906 9.848172 CAAAGTTATCAACAAGTACAATTTTGC 57.152 29.630 0.00 0.00 0.00 3.68
3779 4955 4.097437 GCTGATTGCCTTGAATGAATCTGA 59.903 41.667 0.00 0.00 35.15 3.27
4128 5304 4.294347 TCTTGTTCTTGGGTCCCAAAAAT 58.706 39.130 23.89 0.00 43.44 1.82
4145 5321 3.984193 GAGCGGGCAGGCATCTTGT 62.984 63.158 0.00 0.00 34.64 3.16
4167 5343 0.033601 AACACCACCAAAGCACCAGA 60.034 50.000 0.00 0.00 0.00 3.86
4168 5344 1.686355 TAACACCACCAAAGCACCAG 58.314 50.000 0.00 0.00 0.00 4.00
4169 5345 2.235016 GATAACACCACCAAAGCACCA 58.765 47.619 0.00 0.00 0.00 4.17
4171 5347 2.147958 TCGATAACACCACCAAAGCAC 58.852 47.619 0.00 0.00 0.00 4.40
4172 5348 2.552599 TCGATAACACCACCAAAGCA 57.447 45.000 0.00 0.00 0.00 3.91
4173 5349 3.006940 TCATCGATAACACCACCAAAGC 58.993 45.455 0.00 0.00 0.00 3.51
4174 5350 4.437390 GCTTCATCGATAACACCACCAAAG 60.437 45.833 0.00 0.00 0.00 2.77
4228 5404 6.596497 GCAATTTTCAAAAGACATGGATGGAT 59.404 34.615 0.00 0.00 0.00 3.41
4229 5405 5.933463 GCAATTTTCAAAAGACATGGATGGA 59.067 36.000 0.00 0.00 0.00 3.41
4230 5406 5.935789 AGCAATTTTCAAAAGACATGGATGG 59.064 36.000 0.00 0.00 0.00 3.51
4231 5407 7.201376 CGTAGCAATTTTCAAAAGACATGGATG 60.201 37.037 0.00 0.00 0.00 3.51
4250 5430 1.890489 TCAGAAGTAGCCACGTAGCAA 59.110 47.619 9.06 0.00 34.23 3.91
4266 5446 3.146847 ACGAGTGTCACACTACATCAGA 58.853 45.455 11.42 0.00 45.44 3.27
4267 5447 3.560902 ACGAGTGTCACACTACATCAG 57.439 47.619 11.42 1.21 45.44 2.90
4269 5449 7.253684 GCTTTTATACGAGTGTCACACTACATC 60.254 40.741 11.42 0.00 45.44 3.06
4281 5461 6.961554 GGACAGATTTTGCTTTTATACGAGTG 59.038 38.462 0.00 0.00 0.00 3.51
4298 5478 3.185797 GCGTTAGTTTTCACGGACAGATT 59.814 43.478 0.00 0.00 36.88 2.40
4299 5479 2.735134 GCGTTAGTTTTCACGGACAGAT 59.265 45.455 0.00 0.00 36.88 2.90
4305 5485 3.338603 CGTGCGTTAGTTTTCACGG 57.661 52.632 5.80 0.00 45.76 4.94
4326 5506 5.704888 ACGTATTCAGAGAGACAGACAAAG 58.295 41.667 0.00 0.00 0.00 2.77
4328 5508 5.009710 ACAACGTATTCAGAGAGACAGACAA 59.990 40.000 0.00 0.00 0.00 3.18
4361 5541 0.307760 CTGCAAAACTGTCCACGGTC 59.692 55.000 0.00 0.00 33.61 4.79
4372 5552 2.540931 CCACAAACATGCTCTGCAAAAC 59.459 45.455 0.00 0.00 43.62 2.43
4380 5560 5.229423 TGATTAAAAGCCACAAACATGCTC 58.771 37.500 0.00 0.00 33.36 4.26
4394 5574 5.473039 CCAGCCAGAAAACCTGATTAAAAG 58.527 41.667 0.00 0.00 45.78 2.27
4454 5634 4.542662 AGATCGACAATAATGCAAGTGC 57.457 40.909 0.00 0.00 42.50 4.40
4479 5659 9.826574 GTATGTTACTCCAGTAATGGAATTGTA 57.173 33.333 13.78 9.30 41.85 2.41
4515 5697 5.026790 ACTCCTCCTTTCAACTGCTACTAT 58.973 41.667 0.00 0.00 0.00 2.12
4522 5705 7.361286 GCAGTAATAAACTCCTCCTTTCAACTG 60.361 40.741 0.00 0.00 35.76 3.16
4526 5709 6.013725 TCTGCAGTAATAAACTCCTCCTTTCA 60.014 38.462 14.67 0.00 35.76 2.69
4528 5711 6.374417 TCTGCAGTAATAAACTCCTCCTTT 57.626 37.500 14.67 0.00 35.76 3.11
4530 5713 4.407296 CCTCTGCAGTAATAAACTCCTCCT 59.593 45.833 14.67 0.00 35.76 3.69
4531 5714 4.162509 ACCTCTGCAGTAATAAACTCCTCC 59.837 45.833 14.67 0.00 35.76 4.30
4532 5715 5.346181 ACCTCTGCAGTAATAAACTCCTC 57.654 43.478 14.67 0.00 35.76 3.71
4553 5739 2.032681 ACCTTCTCGCCCTGCAAC 59.967 61.111 0.00 0.00 0.00 4.17
4567 5753 1.761174 CAGGCCTAACCACACACCT 59.239 57.895 3.98 0.00 43.14 4.00
4569 5755 1.073199 AGCAGGCCTAACCACACAC 59.927 57.895 3.98 0.00 43.14 3.82
4576 5762 1.078143 CAGGTCCAGCAGGCCTAAC 60.078 63.158 3.98 0.00 38.76 2.34
4629 5819 0.099968 TACTACGTCTGCACCATCGC 59.900 55.000 0.00 0.00 0.00 4.58
4649 5839 2.509336 CTCTTCGCCGACGCCAAT 60.509 61.111 0.00 0.00 39.84 3.16
4665 5855 4.003788 CGCCGTGTTCCACCTCCT 62.004 66.667 0.00 0.00 0.00 3.69
4872 6079 2.047179 GACAACCTCGGTGAGCCC 60.047 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.