Multiple sequence alignment - TraesCS7D01G001300

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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 TraesCS7D01G001300 chr7D 100.000 3664 0 0 1 3664 1188458 1184795 0.000000e+00 6767.0
1 TraesCS7D01G001300 chrUn 93.478 2484 114 16 831 3306 269322147 269324590 0.000000e+00 3646.0
2 TraesCS7D01G001300 chrUn 93.371 2489 113 16 825 3306 245963231 245965674 0.000000e+00 3635.0
3 TraesCS7D01G001300 chrUn 93.857 2230 105 12 831 3050 316654691 316652484 0.000000e+00 3330.0
4 TraesCS7D01G001300 chrUn 93.809 2229 106 12 832 3050 51485698 51487904 0.000000e+00 3323.0
5 TraesCS7D01G001300 chrUn 96.098 615 22 2 2692 3306 351031718 351031106 0.000000e+00 1002.0
6 TraesCS7D01G001300 chrUn 92.174 345 20 5 3321 3662 51488220 51488560 7.120000e-132 481.0
7 TraesCS7D01G001300 chrUn 89.174 351 38 0 477 827 316655080 316654730 4.340000e-119 438.0
8 TraesCS7D01G001300 chrUn 88.034 351 40 1 477 827 269321760 269322108 7.320000e-112 414.0
9 TraesCS7D01G001300 chrUn 92.281 285 17 4 3321 3604 316652168 316651888 2.050000e-107 399.0
10 TraesCS7D01G001300 chrUn 93.237 207 12 2 3100 3305 51487901 51488106 1.650000e-78 303.0
11 TraesCS7D01G001300 chrUn 93.237 207 12 2 3100 3305 316652487 316652282 1.650000e-78 303.0
12 TraesCS7D01G001300 chrUn 83.630 281 22 9 2 281 269321509 269321766 3.660000e-60 243.0
13 TraesCS7D01G001300 chrUn 82.979 282 22 10 2 281 316655331 316655074 7.910000e-57 231.0
14 TraesCS7D01G001300 chrUn 88.827 179 15 5 2 178 366019325 366019150 7.970000e-52 215.0
15 TraesCS7D01G001300 chrUn 90.196 153 9 2 3326 3477 351030963 351030816 1.040000e-45 195.0
16 TraesCS7D01G001300 chrUn 88.889 153 10 2 3326 3477 245965817 245965963 8.080000e-42 182.0
17 TraesCS7D01G001300 chrUn 96.364 55 2 0 195 249 366019153 366019099 1.400000e-14 91.6
18 TraesCS7D01G001300 chr4A 92.906 2185 117 10 477 2655 742790840 742788688 0.000000e+00 3142.0
19 TraesCS7D01G001300 chr4A 92.718 412 24 6 2654 3063 742788526 742788119 1.130000e-164 590.0
20 TraesCS7D01G001300 chr4A 81.424 576 96 9 1872 2438 469245735 469246308 9.270000e-126 460.0
21 TraesCS7D01G001300 chr4A 90.871 241 14 1 41 281 742791066 742790834 2.120000e-82 316.0
22 TraesCS7D01G001300 chr4A 79.167 240 37 6 1543 1782 469245374 469245600 1.760000e-33 154.0
23 TraesCS7D01G001300 chr4A 96.296 54 2 0 3252 3305 744314883 744314830 5.040000e-14 89.8
24 TraesCS7D01G001300 chr4A 89.091 55 3 2 3251 3305 743687814 743687763 8.490000e-07 65.8
25 TraesCS7D01G001300 chr4B 77.482 826 141 30 1872 2674 169937304 169938107 1.550000e-123 453.0
26 TraesCS7D01G001300 chr4B 94.231 208 12 0 274 481 211717067 211716860 5.900000e-83 318.0
27 TraesCS7D01G001300 chr4B 93.365 211 13 1 272 482 560463372 560463163 9.880000e-81 311.0
28 TraesCS7D01G001300 chr4B 79.167 240 37 6 1543 1782 169936943 169937169 1.760000e-33 154.0
29 TraesCS7D01G001300 chr4D 77.212 825 144 31 1872 2674 106679342 106678540 3.360000e-120 442.0
30 TraesCS7D01G001300 chr4D 95.122 205 10 0 276 480 442784285 442784489 1.270000e-84 324.0
31 TraesCS7D01G001300 chr4D 95.122 205 10 0 276 480 453483379 453483175 1.270000e-84 324.0
32 TraesCS7D01G001300 chr4D 95.122 205 10 0 276 480 460837687 460837891 1.270000e-84 324.0
33 TraesCS7D01G001300 chr4D 79.646 226 37 3 1557 1782 106679693 106679477 1.760000e-33 154.0
34 TraesCS7D01G001300 chr6B 94.634 205 11 0 278 482 447685133 447685337 5.900000e-83 318.0
35 TraesCS7D01G001300 chr6B 94.175 206 12 0 277 482 439350239 439350034 7.640000e-82 315.0
36 TraesCS7D01G001300 chr6B 94.146 205 12 0 278 482 205275986 205275782 2.750000e-81 313.0
37 TraesCS7D01G001300 chr5D 94.608 204 11 0 276 479 538136893 538137096 2.120000e-82 316.0
38 TraesCS7D01G001300 chr3B 79.245 212 38 5 28 239 816551696 816551491 3.810000e-30 143.0
39 TraesCS7D01G001300 chr3A 78.302 212 41 4 28 239 739554969 739554763 8.260000e-27 132.0
40 TraesCS7D01G001300 chr6D 77.376 221 43 7 6 224 218426408 218426623 1.380000e-24 124.0
41 TraesCS7D01G001300 chr7B 85.135 74 8 2 2130 2200 744232274 744232347 5.080000e-09 73.1
42 TraesCS7D01G001300 chr5B 80.412 97 17 2 79 174 1418476 1418381 5.080000e-09 73.1
43 TraesCS7D01G001300 chr2B 81.319 91 12 5 2916 3003 623370883 623370795 6.570000e-08 69.4
44 TraesCS7D01G001300 chr2B 80.899 89 7 9 2900 2983 37572377 37572460 1.100000e-05 62.1
45 TraesCS7D01G001300 chr2B 80.899 89 7 9 2900 2983 38397743 38397826 1.100000e-05 62.1


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 TraesCS7D01G001300 chr7D 1184795 1188458 3663 True 6767.000000 6767 100.000000 1 3664 1 chr7D.!!$R1 3663
1 TraesCS7D01G001300 chrUn 245963231 245965963 2732 False 1908.500000 3635 91.130000 825 3477 2 chrUn.!!$F2 2652
2 TraesCS7D01G001300 chrUn 269321509 269324590 3081 False 1434.333333 3646 88.380667 2 3306 3 chrUn.!!$F3 3304
3 TraesCS7D01G001300 chrUn 51485698 51488560 2862 False 1369.000000 3323 93.073333 832 3662 3 chrUn.!!$F1 2830
4 TraesCS7D01G001300 chrUn 316651888 316655331 3443 True 940.200000 3330 90.305600 2 3604 5 chrUn.!!$R1 3602
5 TraesCS7D01G001300 chrUn 351030816 351031718 902 True 598.500000 1002 93.147000 2692 3477 2 chrUn.!!$R2 785
6 TraesCS7D01G001300 chr4A 742788119 742791066 2947 True 1349.333333 3142 92.165000 41 3063 3 chr4A.!!$R3 3022
7 TraesCS7D01G001300 chr4A 469245374 469246308 934 False 307.000000 460 80.295500 1543 2438 2 chr4A.!!$F1 895
8 TraesCS7D01G001300 chr4B 169936943 169938107 1164 False 303.500000 453 78.324500 1543 2674 2 chr4B.!!$F1 1131
9 TraesCS7D01G001300 chr4D 106678540 106679693 1153 True 298.000000 442 78.429000 1557 2674 2 chr4D.!!$R2 1117

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
412 413 0.032515 TCCCGGTGGAGAGATGCTTA 60.033 55.0 0.00 0.0 35.03 3.09 F
1304 1347 0.178068 ACCGTGTATGATGGTCCTGC 59.822 55.0 0.00 0.0 40.26 4.85 F
1907 1998 0.323908 TCGGCCCTTGGGGTAAAATG 60.324 55.0 7.91 0.0 46.51 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2038 0.249447 CGGATGGTGATGCGCTCTAA 60.249 55.000 9.73 0.0 36.56 2.10 R
2442 2540 1.453015 TGTGACACAACACCCAGGC 60.453 57.895 5.62 0.0 39.69 4.85 R
3169 3449 2.061848 TGATGAACCAAGGGTCCTGAA 58.938 47.619 0.93 0.0 33.12 3.02 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
25 26 6.095377 GGTTTCTTTGATTCGCATGATTCTT 58.905 36.000 0.00 0.00 0.00 2.52
59 60 3.674528 AGAGTGTCATGTCCTCTTGTG 57.325 47.619 0.00 0.00 31.64 3.33
70 71 7.920682 GTCATGTCCTCTTGTGTTTTGTAAAAT 59.079 33.333 0.00 0.00 0.00 1.82
75 76 9.145865 GTCCTCTTGTGTTTTGTAAAATGAAAA 57.854 29.630 0.00 0.00 0.00 2.29
77 78 9.971744 CCTCTTGTGTTTTGTAAAATGAAAAAG 57.028 29.630 0.00 0.00 0.00 2.27
283 284 9.836864 ATAATCAAAAAGAAAAATCTATGGCCC 57.163 29.630 0.00 0.00 0.00 5.80
284 285 6.933514 TCAAAAAGAAAAATCTATGGCCCT 57.066 33.333 0.00 0.00 0.00 5.19
285 286 6.700352 TCAAAAAGAAAAATCTATGGCCCTG 58.300 36.000 0.00 0.00 0.00 4.45
286 287 6.269769 TCAAAAAGAAAAATCTATGGCCCTGT 59.730 34.615 0.00 0.00 0.00 4.00
287 288 6.686484 AAAAGAAAAATCTATGGCCCTGTT 57.314 33.333 0.00 0.00 0.00 3.16
288 289 6.686484 AAAGAAAAATCTATGGCCCTGTTT 57.314 33.333 0.00 0.00 0.00 2.83
289 290 5.665916 AGAAAAATCTATGGCCCTGTTTG 57.334 39.130 0.00 0.00 0.00 2.93
290 291 4.467438 AGAAAAATCTATGGCCCTGTTTGG 59.533 41.667 0.00 0.00 0.00 3.28
291 292 3.756082 AAATCTATGGCCCTGTTTGGA 57.244 42.857 0.00 0.00 38.35 3.53
292 293 3.979501 AATCTATGGCCCTGTTTGGAT 57.020 42.857 0.00 0.00 38.35 3.41
293 294 3.515602 ATCTATGGCCCTGTTTGGATC 57.484 47.619 0.00 0.00 38.35 3.36
294 295 2.204463 TCTATGGCCCTGTTTGGATCA 58.796 47.619 0.00 0.00 38.35 2.92
295 296 2.092429 TCTATGGCCCTGTTTGGATCAC 60.092 50.000 0.00 0.00 38.35 3.06
296 297 0.409092 ATGGCCCTGTTTGGATCACA 59.591 50.000 0.00 0.00 38.35 3.58
297 298 0.251297 TGGCCCTGTTTGGATCACAG 60.251 55.000 0.00 4.98 41.29 3.66
298 299 0.038166 GGCCCTGTTTGGATCACAGA 59.962 55.000 12.10 0.00 43.90 3.41
299 300 1.457346 GCCCTGTTTGGATCACAGAG 58.543 55.000 12.10 1.74 43.90 3.35
300 301 1.271597 GCCCTGTTTGGATCACAGAGT 60.272 52.381 12.10 0.00 43.90 3.24
301 302 2.815589 GCCCTGTTTGGATCACAGAGTT 60.816 50.000 12.10 0.00 43.90 3.01
302 303 3.559171 GCCCTGTTTGGATCACAGAGTTA 60.559 47.826 12.10 0.00 43.90 2.24
303 304 4.256920 CCCTGTTTGGATCACAGAGTTAG 58.743 47.826 12.10 0.00 43.90 2.34
304 305 4.020218 CCCTGTTTGGATCACAGAGTTAGA 60.020 45.833 12.10 0.00 43.90 2.10
305 306 5.174395 CCTGTTTGGATCACAGAGTTAGAG 58.826 45.833 12.10 0.00 43.90 2.43
306 307 4.569943 TGTTTGGATCACAGAGTTAGAGC 58.430 43.478 0.00 0.00 0.00 4.09
307 308 4.284490 TGTTTGGATCACAGAGTTAGAGCT 59.716 41.667 0.00 0.00 0.00 4.09
308 309 5.480422 TGTTTGGATCACAGAGTTAGAGCTA 59.520 40.000 0.00 0.00 0.00 3.32
309 310 5.843673 TTGGATCACAGAGTTAGAGCTAG 57.156 43.478 0.00 0.00 0.00 3.42
310 311 4.861196 TGGATCACAGAGTTAGAGCTAGT 58.139 43.478 0.00 0.00 0.00 2.57
311 312 5.265191 TGGATCACAGAGTTAGAGCTAGTT 58.735 41.667 0.00 0.00 0.00 2.24
312 313 5.717178 TGGATCACAGAGTTAGAGCTAGTTT 59.283 40.000 0.00 0.00 0.00 2.66
313 314 6.039616 GGATCACAGAGTTAGAGCTAGTTTG 58.960 44.000 0.00 0.00 0.00 2.93
314 315 5.392767 TCACAGAGTTAGAGCTAGTTTGG 57.607 43.478 0.00 0.00 0.00 3.28
315 316 4.220821 TCACAGAGTTAGAGCTAGTTTGGG 59.779 45.833 0.00 0.00 0.00 4.12
316 317 4.021016 CACAGAGTTAGAGCTAGTTTGGGT 60.021 45.833 0.00 0.00 0.00 4.51
317 318 4.593634 ACAGAGTTAGAGCTAGTTTGGGTT 59.406 41.667 0.00 0.00 0.00 4.11
318 319 5.778750 ACAGAGTTAGAGCTAGTTTGGGTTA 59.221 40.000 0.00 0.00 0.00 2.85
319 320 6.071278 ACAGAGTTAGAGCTAGTTTGGGTTAG 60.071 42.308 0.00 0.00 0.00 2.34
320 321 6.017830 AGAGTTAGAGCTAGTTTGGGTTAGT 58.982 40.000 0.00 0.00 0.00 2.24
321 322 6.497606 AGAGTTAGAGCTAGTTTGGGTTAGTT 59.502 38.462 0.00 0.00 0.00 2.24
322 323 6.465084 AGTTAGAGCTAGTTTGGGTTAGTTG 58.535 40.000 0.00 0.00 0.00 3.16
323 324 4.287766 AGAGCTAGTTTGGGTTAGTTGG 57.712 45.455 0.00 0.00 0.00 3.77
324 325 3.009143 AGAGCTAGTTTGGGTTAGTTGGG 59.991 47.826 0.00 0.00 0.00 4.12
325 326 2.041216 AGCTAGTTTGGGTTAGTTGGGG 59.959 50.000 0.00 0.00 0.00 4.96
326 327 2.882643 GCTAGTTTGGGTTAGTTGGGGG 60.883 54.545 0.00 0.00 0.00 5.40
327 328 0.178944 AGTTTGGGTTAGTTGGGGGC 60.179 55.000 0.00 0.00 0.00 5.80
328 329 0.178944 GTTTGGGTTAGTTGGGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
329 330 0.113580 TTTGGGTTAGTTGGGGGCTC 59.886 55.000 0.00 0.00 0.00 4.70
330 331 1.068943 TTGGGTTAGTTGGGGGCTCA 61.069 55.000 0.00 0.00 0.00 4.26
331 332 1.068943 TGGGTTAGTTGGGGGCTCAA 61.069 55.000 0.00 0.00 0.00 3.02
332 333 0.113580 GGGTTAGTTGGGGGCTCAAA 59.886 55.000 0.00 0.00 0.00 2.69
333 334 1.273041 GGGTTAGTTGGGGGCTCAAAT 60.273 52.381 0.00 0.00 0.00 2.32
334 335 2.024751 GGGTTAGTTGGGGGCTCAAATA 60.025 50.000 0.00 0.00 0.00 1.40
335 336 3.564790 GGGTTAGTTGGGGGCTCAAATAA 60.565 47.826 8.87 8.87 35.65 1.40
336 337 4.713824 GTTAGTTGGGGGCTCAAATAAC 57.286 45.455 19.46 19.46 44.78 1.89
337 338 2.231716 AGTTGGGGGCTCAAATAACC 57.768 50.000 0.00 0.00 0.00 2.85
338 339 1.191535 GTTGGGGGCTCAAATAACCC 58.808 55.000 0.00 0.00 43.44 4.11
340 341 3.701800 GGGGGCTCAAATAACCCAA 57.298 52.632 0.00 0.00 46.21 4.12
341 342 1.945580 GGGGGCTCAAATAACCCAAA 58.054 50.000 0.00 0.00 46.21 3.28
342 343 2.261729 GGGGGCTCAAATAACCCAAAA 58.738 47.619 0.00 0.00 46.21 2.44
343 344 2.236146 GGGGGCTCAAATAACCCAAAAG 59.764 50.000 0.00 0.00 46.21 2.27
344 345 2.903784 GGGGCTCAAATAACCCAAAAGT 59.096 45.455 0.00 0.00 46.21 2.66
345 346 4.090819 GGGGCTCAAATAACCCAAAAGTA 58.909 43.478 0.00 0.00 46.21 2.24
346 347 4.714802 GGGGCTCAAATAACCCAAAAGTAT 59.285 41.667 0.00 0.00 46.21 2.12
347 348 5.163447 GGGGCTCAAATAACCCAAAAGTATC 60.163 44.000 0.00 0.00 46.21 2.24
348 349 5.163447 GGGCTCAAATAACCCAAAAGTATCC 60.163 44.000 0.00 0.00 43.64 2.59
349 350 5.420739 GGCTCAAATAACCCAAAAGTATCCA 59.579 40.000 0.00 0.00 0.00 3.41
350 351 6.071051 GGCTCAAATAACCCAAAAGTATCCAA 60.071 38.462 0.00 0.00 0.00 3.53
351 352 7.382898 GCTCAAATAACCCAAAAGTATCCAAA 58.617 34.615 0.00 0.00 0.00 3.28
352 353 7.330946 GCTCAAATAACCCAAAAGTATCCAAAC 59.669 37.037 0.00 0.00 0.00 2.93
353 354 8.251383 TCAAATAACCCAAAAGTATCCAAACA 57.749 30.769 0.00 0.00 0.00 2.83
354 355 8.364142 TCAAATAACCCAAAAGTATCCAAACAG 58.636 33.333 0.00 0.00 0.00 3.16
355 356 6.850752 ATAACCCAAAAGTATCCAAACAGG 57.149 37.500 0.00 0.00 39.47 4.00
356 357 3.506398 ACCCAAAAGTATCCAAACAGGG 58.494 45.455 0.00 0.00 39.66 4.45
357 358 3.141272 ACCCAAAAGTATCCAAACAGGGA 59.859 43.478 0.00 0.00 42.21 4.20
358 359 3.763897 CCCAAAAGTATCCAAACAGGGAG 59.236 47.826 0.00 0.00 41.08 4.30
359 360 3.763897 CCAAAAGTATCCAAACAGGGAGG 59.236 47.826 0.00 0.00 41.08 4.30
360 361 3.739401 AAAGTATCCAAACAGGGAGGG 57.261 47.619 0.00 0.00 41.08 4.30
361 362 2.361085 AGTATCCAAACAGGGAGGGT 57.639 50.000 0.00 0.00 41.08 4.34
362 363 2.644151 AGTATCCAAACAGGGAGGGTT 58.356 47.619 0.00 0.00 41.08 4.11
363 364 3.810623 AGTATCCAAACAGGGAGGGTTA 58.189 45.455 0.00 0.00 41.08 2.85
364 365 3.780850 AGTATCCAAACAGGGAGGGTTAG 59.219 47.826 0.00 0.00 41.08 2.34
365 366 2.426431 TCCAAACAGGGAGGGTTAGA 57.574 50.000 0.00 0.00 38.24 2.10
366 367 2.266279 TCCAAACAGGGAGGGTTAGAG 58.734 52.381 0.00 0.00 38.24 2.43
367 368 1.985895 CCAAACAGGGAGGGTTAGAGT 59.014 52.381 0.00 0.00 0.00 3.24
368 369 2.290323 CCAAACAGGGAGGGTTAGAGTG 60.290 54.545 0.00 0.00 0.00 3.51
369 370 1.657804 AACAGGGAGGGTTAGAGTGG 58.342 55.000 0.00 0.00 0.00 4.00
370 371 0.252742 ACAGGGAGGGTTAGAGTGGG 60.253 60.000 0.00 0.00 0.00 4.61
371 372 0.252742 CAGGGAGGGTTAGAGTGGGT 60.253 60.000 0.00 0.00 0.00 4.51
372 373 0.496841 AGGGAGGGTTAGAGTGGGTT 59.503 55.000 0.00 0.00 0.00 4.11
373 374 1.726352 AGGGAGGGTTAGAGTGGGTTA 59.274 52.381 0.00 0.00 0.00 2.85
374 375 2.117051 GGGAGGGTTAGAGTGGGTTAG 58.883 57.143 0.00 0.00 0.00 2.34
375 376 2.561526 GGGAGGGTTAGAGTGGGTTAGT 60.562 54.545 0.00 0.00 0.00 2.24
376 377 3.179685 GGAGGGTTAGAGTGGGTTAGTT 58.820 50.000 0.00 0.00 0.00 2.24
377 378 3.197333 GGAGGGTTAGAGTGGGTTAGTTC 59.803 52.174 0.00 0.00 0.00 3.01
378 379 3.179685 AGGGTTAGAGTGGGTTAGTTCC 58.820 50.000 0.00 0.00 0.00 3.62
379 380 2.908351 GGGTTAGAGTGGGTTAGTTCCA 59.092 50.000 0.00 0.00 0.00 3.53
380 381 3.522343 GGGTTAGAGTGGGTTAGTTCCAT 59.478 47.826 0.00 0.00 36.58 3.41
381 382 4.383880 GGGTTAGAGTGGGTTAGTTCCATC 60.384 50.000 0.00 0.00 36.58 3.51
382 383 4.470304 GGTTAGAGTGGGTTAGTTCCATCT 59.530 45.833 0.00 0.00 36.58 2.90
383 384 5.659971 GGTTAGAGTGGGTTAGTTCCATCTA 59.340 44.000 0.00 0.00 36.58 1.98
384 385 6.155737 GGTTAGAGTGGGTTAGTTCCATCTAA 59.844 42.308 0.00 0.00 36.58 2.10
385 386 5.678955 AGAGTGGGTTAGTTCCATCTAAC 57.321 43.478 7.74 7.74 45.03 2.34
395 396 5.632034 AGTTCCATCTAACCCAACTATCC 57.368 43.478 0.00 0.00 0.00 2.59
396 397 4.412528 AGTTCCATCTAACCCAACTATCCC 59.587 45.833 0.00 0.00 0.00 3.85
397 398 2.969950 TCCATCTAACCCAACTATCCCG 59.030 50.000 0.00 0.00 0.00 5.14
398 399 2.038557 CCATCTAACCCAACTATCCCGG 59.961 54.545 0.00 0.00 0.00 5.73
399 400 2.555732 TCTAACCCAACTATCCCGGT 57.444 50.000 0.00 0.00 0.00 5.28
400 401 2.112998 TCTAACCCAACTATCCCGGTG 58.887 52.381 0.00 0.00 0.00 4.94
401 402 1.140252 CTAACCCAACTATCCCGGTGG 59.860 57.143 0.00 0.00 0.00 4.61
403 404 0.981277 ACCCAACTATCCCGGTGGAG 60.981 60.000 8.06 0.31 46.08 3.86
404 405 0.689745 CCCAACTATCCCGGTGGAGA 60.690 60.000 8.06 0.00 46.08 3.71
409 410 2.746697 TATCCCGGTGGAGAGATGC 58.253 57.895 0.00 0.00 46.08 3.91
410 411 0.188587 TATCCCGGTGGAGAGATGCT 59.811 55.000 0.00 0.00 46.08 3.79
411 412 0.692419 ATCCCGGTGGAGAGATGCTT 60.692 55.000 0.00 0.00 46.08 3.91
412 413 0.032515 TCCCGGTGGAGAGATGCTTA 60.033 55.000 0.00 0.00 35.03 3.09
413 414 1.051812 CCCGGTGGAGAGATGCTTAT 58.948 55.000 0.00 0.00 0.00 1.73
414 415 1.417890 CCCGGTGGAGAGATGCTTATT 59.582 52.381 0.00 0.00 0.00 1.40
415 416 2.158755 CCCGGTGGAGAGATGCTTATTT 60.159 50.000 0.00 0.00 0.00 1.40
416 417 2.874701 CCGGTGGAGAGATGCTTATTTG 59.125 50.000 0.00 0.00 0.00 2.32
417 418 2.874701 CGGTGGAGAGATGCTTATTTGG 59.125 50.000 0.00 0.00 0.00 3.28
418 419 3.217626 GGTGGAGAGATGCTTATTTGGG 58.782 50.000 0.00 0.00 0.00 4.12
419 420 3.372025 GGTGGAGAGATGCTTATTTGGGT 60.372 47.826 0.00 0.00 0.00 4.51
420 421 4.273318 GTGGAGAGATGCTTATTTGGGTT 58.727 43.478 0.00 0.00 0.00 4.11
421 422 5.437060 GTGGAGAGATGCTTATTTGGGTTA 58.563 41.667 0.00 0.00 0.00 2.85
422 423 5.529060 GTGGAGAGATGCTTATTTGGGTTAG 59.471 44.000 0.00 0.00 0.00 2.34
423 424 5.428457 TGGAGAGATGCTTATTTGGGTTAGA 59.572 40.000 0.00 0.00 0.00 2.10
424 425 5.994668 GGAGAGATGCTTATTTGGGTTAGAG 59.005 44.000 0.00 0.00 0.00 2.43
425 426 6.408662 GGAGAGATGCTTATTTGGGTTAGAGT 60.409 42.308 0.00 0.00 0.00 3.24
426 427 6.352516 AGAGATGCTTATTTGGGTTAGAGTG 58.647 40.000 0.00 0.00 0.00 3.51
427 428 5.440610 AGATGCTTATTTGGGTTAGAGTGG 58.559 41.667 0.00 0.00 0.00 4.00
428 429 3.963129 TGCTTATTTGGGTTAGAGTGGG 58.037 45.455 0.00 0.00 0.00 4.61
429 430 3.332485 TGCTTATTTGGGTTAGAGTGGGT 59.668 43.478 0.00 0.00 0.00 4.51
430 431 4.202631 TGCTTATTTGGGTTAGAGTGGGTT 60.203 41.667 0.00 0.00 0.00 4.11
431 432 5.014333 TGCTTATTTGGGTTAGAGTGGGTTA 59.986 40.000 0.00 0.00 0.00 2.85
432 433 5.947566 GCTTATTTGGGTTAGAGTGGGTTAA 59.052 40.000 0.00 0.00 0.00 2.01
433 434 6.434965 GCTTATTTGGGTTAGAGTGGGTTAAA 59.565 38.462 0.00 0.00 0.00 1.52
434 435 7.039574 GCTTATTTGGGTTAGAGTGGGTTAAAA 60.040 37.037 0.00 0.00 0.00 1.52
435 436 8.779096 TTATTTGGGTTAGAGTGGGTTAAAAA 57.221 30.769 0.00 0.00 0.00 1.94
467 468 8.921205 TCTAACATTAACTGGGTTAGAGTATCC 58.079 37.037 8.85 0.00 44.68 2.59
468 469 7.504926 AACATTAACTGGGTTAGAGTATCCA 57.495 36.000 0.00 0.00 33.66 3.41
469 470 7.504926 ACATTAACTGGGTTAGAGTATCCAA 57.495 36.000 0.00 0.00 33.66 3.53
470 471 7.924541 ACATTAACTGGGTTAGAGTATCCAAA 58.075 34.615 0.00 0.00 33.66 3.28
471 472 8.557450 ACATTAACTGGGTTAGAGTATCCAAAT 58.443 33.333 0.00 0.00 33.66 2.32
474 475 6.749036 ACTGGGTTAGAGTATCCAAATAGG 57.251 41.667 0.00 0.00 33.66 2.57
475 476 5.607171 ACTGGGTTAGAGTATCCAAATAGGG 59.393 44.000 0.00 0.00 38.24 3.53
488 489 4.669768 TCCAAATAGGGCCTATGGAATTCT 59.330 41.667 26.58 9.23 38.24 2.40
534 535 4.427312 GTCGACGAGTATTGGTTATGGTT 58.573 43.478 0.00 0.00 0.00 3.67
543 544 7.238486 AGTATTGGTTATGGTTTTTGATGCA 57.762 32.000 0.00 0.00 0.00 3.96
563 564 2.127708 AGAGGTGGGTGGGTGATATTC 58.872 52.381 0.00 0.00 0.00 1.75
639 640 2.202295 ATGTTGTTCACACCGTTTGC 57.798 45.000 0.00 0.00 38.61 3.68
642 643 1.062294 GTTGTTCACACCGTTTGCGTA 59.938 47.619 0.00 0.00 36.15 4.42
652 653 0.656205 CGTTTGCGTAGTTGGCACAC 60.656 55.000 0.00 0.00 40.71 3.82
653 654 0.317519 GTTTGCGTAGTTGGCACACC 60.318 55.000 0.00 0.00 40.71 4.16
748 749 5.348164 TGACGTCATCAACACCATATAGTG 58.652 41.667 15.76 0.00 36.71 2.74
791 792 5.347620 TTGCCGGTCATAATGTACTACTT 57.652 39.130 1.90 0.00 0.00 2.24
796 797 5.278858 CCGGTCATAATGTACTACTTCCTCC 60.279 48.000 0.00 0.00 0.00 4.30
797 798 5.301045 CGGTCATAATGTACTACTTCCTCCA 59.699 44.000 0.00 0.00 0.00 3.86
854 890 6.458342 GGCGAAAACTAATATGAAACAGAGGG 60.458 42.308 0.00 0.00 0.00 4.30
894 930 2.350676 GCGTGATTCATGAGTGCACAAA 60.351 45.455 21.04 6.80 0.00 2.83
1111 1154 2.360852 CTGCTGCCAAGGGGTCAG 60.361 66.667 0.00 0.00 39.70 3.51
1242 1285 2.534298 CAGGCAGTCATAGTTGAGTCG 58.466 52.381 0.00 0.00 33.07 4.18
1293 1336 2.764010 TGCTAATGACTGGACCGTGTAT 59.236 45.455 0.00 0.00 0.00 2.29
1304 1347 0.178068 ACCGTGTATGATGGTCCTGC 59.822 55.000 0.00 0.00 40.26 4.85
1402 1445 3.536570 TGTTTCAACATGGTCTTCGTCA 58.463 40.909 0.00 0.00 33.17 4.35
1465 1508 8.330466 TCTCTCTTTGAAATTTTACCGCATTA 57.670 30.769 0.00 0.00 0.00 1.90
1498 1542 2.570302 ACTGGAGCCATAGTACGGTTTT 59.430 45.455 0.00 0.00 0.00 2.43
1610 1654 0.995024 AGGTGATGGGGGACTTTCAG 59.005 55.000 0.00 0.00 0.00 3.02
1907 1998 0.323908 TCGGCCCTTGGGGTAAAATG 60.324 55.000 7.91 0.00 46.51 2.32
2083 2174 2.370849 ACAAGGACACGGTAGGTTCATT 59.629 45.455 0.00 0.00 0.00 2.57
2084 2175 2.742053 CAAGGACACGGTAGGTTCATTG 59.258 50.000 0.00 0.00 0.00 2.82
2154 2252 7.013274 TCCTACATGCAATTCTATTAACTTGGC 59.987 37.037 0.00 0.00 0.00 4.52
2288 2386 2.489985 CCCTCACCATTACCACAAACCA 60.490 50.000 0.00 0.00 0.00 3.67
2400 2498 1.134491 GCTGGTAAATACGTGGAGGCT 60.134 52.381 0.00 0.00 0.00 4.58
2442 2540 2.288395 ACCCGTTTCAACCTAGTACGTG 60.288 50.000 0.00 0.00 0.00 4.49
2514 2612 5.472137 TGGCAATAAGGAAGAAGTGTGTTAC 59.528 40.000 0.00 0.00 0.00 2.50
2574 2680 5.940192 TGTTGGTTTACTTATCAGCACAG 57.060 39.130 0.00 0.00 0.00 3.66
2688 2966 9.661563 AATAGTGATGCATGAATTGTTTTTGAT 57.338 25.926 2.46 0.00 0.00 2.57
2690 2968 6.370442 AGTGATGCATGAATTGTTTTTGATGG 59.630 34.615 2.46 0.00 0.00 3.51
3064 3344 1.389609 CCCTCCTTAGCGGCGTTCTA 61.390 60.000 9.37 0.00 0.00 2.10
3190 3470 2.061848 TCAGGACCCTTGGTTCATCAA 58.938 47.619 0.00 0.00 35.25 2.57
3249 3529 3.861276 CGATAGTTGGTGGTGAGTACA 57.139 47.619 0.00 0.00 0.00 2.90
3349 3753 8.839914 CAACAACAACTCGTAATCAAATGTATG 58.160 33.333 0.00 0.00 0.00 2.39
3463 3867 0.866906 CAAACAACACAGCAGCACCG 60.867 55.000 0.00 0.00 0.00 4.94
3464 3868 2.003658 AAACAACACAGCAGCACCGG 62.004 55.000 0.00 0.00 0.00 5.28
3487 3891 4.264543 CAATCTGGTTGTTAGCTAAGCG 57.735 45.455 6.38 0.00 33.01 4.68
3501 3905 5.689383 AGCTAAGCGTTGAATTGAAGAAA 57.311 34.783 0.00 0.00 0.00 2.52
3505 3909 2.622942 AGCGTTGAATTGAAGAAAGGCA 59.377 40.909 0.00 0.00 36.23 4.75
3541 3945 7.493971 CAGATAAAACCCTCACTCATAGAACAG 59.506 40.741 0.00 0.00 0.00 3.16
3604 4008 6.373495 CCCTGCTAAAACTCCGTAAATAAACT 59.627 38.462 0.00 0.00 0.00 2.66
3662 4068 4.855715 TGACGAATCTCTTCACTTGACT 57.144 40.909 0.00 0.00 0.00 3.41
3663 4069 5.201713 TGACGAATCTCTTCACTTGACTT 57.798 39.130 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.183713 AGAATCATGCGAATCAAAGAAACCA 59.816 36.000 0.00 0.00 0.00 3.67
2 3 6.803320 TCAAGAATCATGCGAATCAAAGAAAC 59.197 34.615 0.00 0.00 0.00 2.78
5 6 6.499234 TTCAAGAATCATGCGAATCAAAGA 57.501 33.333 0.00 0.00 0.00 2.52
6 7 6.237123 CGTTTCAAGAATCATGCGAATCAAAG 60.237 38.462 0.00 0.00 0.00 2.77
25 26 5.743026 TGACACTCTATTTTTGCGTTTCA 57.257 34.783 0.00 0.00 0.00 2.69
79 80 9.981460 ACTCTTCCATCTAAATTCCTGTATTTT 57.019 29.630 0.00 0.00 0.00 1.82
260 261 7.038088 ACAGGGCCATAGATTTTTCTTTTTGAT 60.038 33.333 6.18 0.00 0.00 2.57
274 275 2.092429 GTGATCCAAACAGGGCCATAGA 60.092 50.000 6.18 0.00 38.24 1.98
275 276 2.301346 GTGATCCAAACAGGGCCATAG 58.699 52.381 6.18 0.00 38.24 2.23
276 277 1.638070 TGTGATCCAAACAGGGCCATA 59.362 47.619 6.18 0.00 38.24 2.74
277 278 0.409092 TGTGATCCAAACAGGGCCAT 59.591 50.000 6.18 0.00 38.24 4.40
278 279 0.251297 CTGTGATCCAAACAGGGCCA 60.251 55.000 6.18 0.00 41.13 5.36
279 280 0.038166 TCTGTGATCCAAACAGGGCC 59.962 55.000 10.77 0.00 44.26 5.80
280 281 1.457346 CTCTGTGATCCAAACAGGGC 58.543 55.000 10.77 0.00 44.26 5.19
282 283 5.152623 TCTAACTCTGTGATCCAAACAGG 57.847 43.478 10.77 5.60 44.26 4.00
283 284 4.629200 GCTCTAACTCTGTGATCCAAACAG 59.371 45.833 5.51 5.51 45.26 3.16
284 285 4.284490 AGCTCTAACTCTGTGATCCAAACA 59.716 41.667 0.00 0.00 0.00 2.83
285 286 4.826556 AGCTCTAACTCTGTGATCCAAAC 58.173 43.478 0.00 0.00 0.00 2.93
286 287 5.717178 ACTAGCTCTAACTCTGTGATCCAAA 59.283 40.000 0.00 0.00 0.00 3.28
287 288 5.265191 ACTAGCTCTAACTCTGTGATCCAA 58.735 41.667 0.00 0.00 0.00 3.53
288 289 4.861196 ACTAGCTCTAACTCTGTGATCCA 58.139 43.478 0.00 0.00 0.00 3.41
289 290 5.845391 AACTAGCTCTAACTCTGTGATCC 57.155 43.478 0.00 0.00 0.00 3.36
290 291 6.039616 CCAAACTAGCTCTAACTCTGTGATC 58.960 44.000 0.00 0.00 0.00 2.92
291 292 5.105146 CCCAAACTAGCTCTAACTCTGTGAT 60.105 44.000 0.00 0.00 0.00 3.06
292 293 4.220821 CCCAAACTAGCTCTAACTCTGTGA 59.779 45.833 0.00 0.00 0.00 3.58
293 294 4.021016 ACCCAAACTAGCTCTAACTCTGTG 60.021 45.833 0.00 0.00 0.00 3.66
294 295 4.161102 ACCCAAACTAGCTCTAACTCTGT 58.839 43.478 0.00 0.00 0.00 3.41
295 296 4.810191 ACCCAAACTAGCTCTAACTCTG 57.190 45.455 0.00 0.00 0.00 3.35
296 297 6.017830 ACTAACCCAAACTAGCTCTAACTCT 58.982 40.000 0.00 0.00 0.00 3.24
297 298 6.283544 ACTAACCCAAACTAGCTCTAACTC 57.716 41.667 0.00 0.00 0.00 3.01
298 299 6.465084 CAACTAACCCAAACTAGCTCTAACT 58.535 40.000 0.00 0.00 0.00 2.24
299 300 5.642491 CCAACTAACCCAAACTAGCTCTAAC 59.358 44.000 0.00 0.00 0.00 2.34
300 301 5.280317 CCCAACTAACCCAAACTAGCTCTAA 60.280 44.000 0.00 0.00 0.00 2.10
301 302 4.224370 CCCAACTAACCCAAACTAGCTCTA 59.776 45.833 0.00 0.00 0.00 2.43
302 303 3.009143 CCCAACTAACCCAAACTAGCTCT 59.991 47.826 0.00 0.00 0.00 4.09
303 304 3.344515 CCCAACTAACCCAAACTAGCTC 58.655 50.000 0.00 0.00 0.00 4.09
304 305 2.041216 CCCCAACTAACCCAAACTAGCT 59.959 50.000 0.00 0.00 0.00 3.32
305 306 2.443416 CCCCAACTAACCCAAACTAGC 58.557 52.381 0.00 0.00 0.00 3.42
306 307 2.882643 GCCCCCAACTAACCCAAACTAG 60.883 54.545 0.00 0.00 0.00 2.57
307 308 1.075861 GCCCCCAACTAACCCAAACTA 59.924 52.381 0.00 0.00 0.00 2.24
308 309 0.178944 GCCCCCAACTAACCCAAACT 60.179 55.000 0.00 0.00 0.00 2.66
309 310 0.178944 AGCCCCCAACTAACCCAAAC 60.179 55.000 0.00 0.00 0.00 2.93
310 311 0.113580 GAGCCCCCAACTAACCCAAA 59.886 55.000 0.00 0.00 0.00 3.28
311 312 1.068943 TGAGCCCCCAACTAACCCAA 61.069 55.000 0.00 0.00 0.00 4.12
312 313 1.068943 TTGAGCCCCCAACTAACCCA 61.069 55.000 0.00 0.00 0.00 4.51
313 314 0.113580 TTTGAGCCCCCAACTAACCC 59.886 55.000 0.00 0.00 0.00 4.11
314 315 2.231716 ATTTGAGCCCCCAACTAACC 57.768 50.000 0.00 0.00 0.00 2.85
315 316 3.446161 GGTTATTTGAGCCCCCAACTAAC 59.554 47.826 12.05 12.05 39.43 2.34
316 317 3.564790 GGGTTATTTGAGCCCCCAACTAA 60.565 47.826 0.00 0.00 36.46 2.24
317 318 2.024751 GGGTTATTTGAGCCCCCAACTA 60.025 50.000 0.00 0.00 36.46 2.24
318 319 1.273041 GGGTTATTTGAGCCCCCAACT 60.273 52.381 0.00 0.00 36.46 3.16
319 320 1.191535 GGGTTATTTGAGCCCCCAAC 58.808 55.000 0.00 0.00 36.46 3.77
320 321 0.787084 TGGGTTATTTGAGCCCCCAA 59.213 50.000 0.00 0.00 42.30 4.12
321 322 0.787084 TTGGGTTATTTGAGCCCCCA 59.213 50.000 0.00 0.00 43.54 4.96
322 323 1.945580 TTTGGGTTATTTGAGCCCCC 58.054 50.000 0.00 0.00 41.66 5.40
323 324 2.903784 ACTTTTGGGTTATTTGAGCCCC 59.096 45.455 0.00 0.00 41.66 5.80
324 325 5.163447 GGATACTTTTGGGTTATTTGAGCCC 60.163 44.000 0.00 0.00 42.64 5.19
325 326 5.420739 TGGATACTTTTGGGTTATTTGAGCC 59.579 40.000 0.00 0.00 35.98 4.70
326 327 6.524101 TGGATACTTTTGGGTTATTTGAGC 57.476 37.500 0.00 0.00 37.61 4.26
327 328 8.364142 TGTTTGGATACTTTTGGGTTATTTGAG 58.636 33.333 0.00 0.00 37.61 3.02
328 329 8.251383 TGTTTGGATACTTTTGGGTTATTTGA 57.749 30.769 0.00 0.00 37.61 2.69
329 330 7.602265 CCTGTTTGGATACTTTTGGGTTATTTG 59.398 37.037 0.00 0.00 38.35 2.32
330 331 7.256511 CCCTGTTTGGATACTTTTGGGTTATTT 60.257 37.037 0.00 0.00 38.35 1.40
331 332 6.212589 CCCTGTTTGGATACTTTTGGGTTATT 59.787 38.462 0.00 0.00 38.35 1.40
332 333 5.719563 CCCTGTTTGGATACTTTTGGGTTAT 59.280 40.000 0.00 0.00 38.35 1.89
333 334 5.081032 CCCTGTTTGGATACTTTTGGGTTA 58.919 41.667 0.00 0.00 38.35 2.85
334 335 3.901222 CCCTGTTTGGATACTTTTGGGTT 59.099 43.478 0.00 0.00 38.35 4.11
335 336 3.141272 TCCCTGTTTGGATACTTTTGGGT 59.859 43.478 0.00 0.00 38.35 4.51
336 337 3.763897 CTCCCTGTTTGGATACTTTTGGG 59.236 47.826 0.00 0.00 38.35 4.12
337 338 3.763897 CCTCCCTGTTTGGATACTTTTGG 59.236 47.826 0.00 0.00 38.35 3.28
338 339 3.763897 CCCTCCCTGTTTGGATACTTTTG 59.236 47.826 0.00 0.00 38.35 2.44
339 340 3.401342 ACCCTCCCTGTTTGGATACTTTT 59.599 43.478 0.00 0.00 38.35 2.27
340 341 2.993863 ACCCTCCCTGTTTGGATACTTT 59.006 45.455 0.00 0.00 38.35 2.66
341 342 2.644151 ACCCTCCCTGTTTGGATACTT 58.356 47.619 0.00 0.00 38.35 2.24
342 343 2.361085 ACCCTCCCTGTTTGGATACT 57.639 50.000 0.00 0.00 38.35 2.12
343 344 3.778629 TCTAACCCTCCCTGTTTGGATAC 59.221 47.826 0.00 0.00 38.35 2.24
344 345 4.037927 CTCTAACCCTCCCTGTTTGGATA 58.962 47.826 0.00 0.00 38.35 2.59
345 346 2.846827 CTCTAACCCTCCCTGTTTGGAT 59.153 50.000 0.00 0.00 38.35 3.41
346 347 2.266279 CTCTAACCCTCCCTGTTTGGA 58.734 52.381 0.00 0.00 38.35 3.53
347 348 1.985895 ACTCTAACCCTCCCTGTTTGG 59.014 52.381 0.00 0.00 0.00 3.28
348 349 2.290323 CCACTCTAACCCTCCCTGTTTG 60.290 54.545 0.00 0.00 0.00 2.93
349 350 1.985895 CCACTCTAACCCTCCCTGTTT 59.014 52.381 0.00 0.00 0.00 2.83
350 351 1.657804 CCACTCTAACCCTCCCTGTT 58.342 55.000 0.00 0.00 0.00 3.16
351 352 0.252742 CCCACTCTAACCCTCCCTGT 60.253 60.000 0.00 0.00 0.00 4.00
352 353 0.252742 ACCCACTCTAACCCTCCCTG 60.253 60.000 0.00 0.00 0.00 4.45
353 354 0.496841 AACCCACTCTAACCCTCCCT 59.503 55.000 0.00 0.00 0.00 4.20
354 355 2.117051 CTAACCCACTCTAACCCTCCC 58.883 57.143 0.00 0.00 0.00 4.30
355 356 2.830293 ACTAACCCACTCTAACCCTCC 58.170 52.381 0.00 0.00 0.00 4.30
356 357 3.197333 GGAACTAACCCACTCTAACCCTC 59.803 52.174 0.00 0.00 0.00 4.30
357 358 3.179685 GGAACTAACCCACTCTAACCCT 58.820 50.000 0.00 0.00 0.00 4.34
358 359 2.908351 TGGAACTAACCCACTCTAACCC 59.092 50.000 0.00 0.00 0.00 4.11
359 360 4.470304 AGATGGAACTAACCCACTCTAACC 59.530 45.833 0.00 0.00 36.36 2.85
360 361 5.678955 AGATGGAACTAACCCACTCTAAC 57.321 43.478 0.00 0.00 36.36 2.34
361 362 7.179076 GTTAGATGGAACTAACCCACTCTAA 57.821 40.000 0.00 0.00 43.43 2.10
362 363 6.786967 GTTAGATGGAACTAACCCACTCTA 57.213 41.667 0.00 0.00 43.43 2.43
363 364 5.678955 GTTAGATGGAACTAACCCACTCT 57.321 43.478 0.00 0.00 43.43 3.24
370 371 6.990939 GGATAGTTGGGTTAGATGGAACTAAC 59.009 42.308 0.00 0.00 46.41 2.34
371 372 6.100714 GGGATAGTTGGGTTAGATGGAACTAA 59.899 42.308 0.00 0.00 33.90 2.24
372 373 5.605488 GGGATAGTTGGGTTAGATGGAACTA 59.395 44.000 0.00 0.00 34.51 2.24
373 374 4.412528 GGGATAGTTGGGTTAGATGGAACT 59.587 45.833 0.00 0.00 0.00 3.01
374 375 4.715713 GGGATAGTTGGGTTAGATGGAAC 58.284 47.826 0.00 0.00 0.00 3.62
375 376 3.389983 CGGGATAGTTGGGTTAGATGGAA 59.610 47.826 0.00 0.00 0.00 3.53
376 377 2.969950 CGGGATAGTTGGGTTAGATGGA 59.030 50.000 0.00 0.00 0.00 3.41
377 378 2.038557 CCGGGATAGTTGGGTTAGATGG 59.961 54.545 0.00 0.00 0.00 3.51
378 379 2.704065 ACCGGGATAGTTGGGTTAGATG 59.296 50.000 6.32 0.00 0.00 2.90
379 380 2.704065 CACCGGGATAGTTGGGTTAGAT 59.296 50.000 6.32 0.00 0.00 1.98
380 381 2.112998 CACCGGGATAGTTGGGTTAGA 58.887 52.381 6.32 0.00 0.00 2.10
381 382 1.140252 CCACCGGGATAGTTGGGTTAG 59.860 57.143 6.32 0.00 35.59 2.34
382 383 1.205966 CCACCGGGATAGTTGGGTTA 58.794 55.000 6.32 0.00 35.59 2.85
383 384 0.548197 TCCACCGGGATAGTTGGGTT 60.548 55.000 6.32 0.00 38.64 4.11
384 385 0.981277 CTCCACCGGGATAGTTGGGT 60.981 60.000 6.32 0.00 43.91 4.51
385 386 0.689745 TCTCCACCGGGATAGTTGGG 60.690 60.000 6.32 0.00 43.91 4.12
386 387 0.753262 CTCTCCACCGGGATAGTTGG 59.247 60.000 6.32 2.68 43.91 3.77
387 388 1.776662 TCTCTCCACCGGGATAGTTG 58.223 55.000 6.32 0.00 43.91 3.16
388 389 2.320781 CATCTCTCCACCGGGATAGTT 58.679 52.381 6.32 0.00 43.91 2.24
389 390 2.002505 CATCTCTCCACCGGGATAGT 57.997 55.000 6.32 0.00 43.91 2.12
390 391 0.605589 GCATCTCTCCACCGGGATAG 59.394 60.000 6.32 0.00 43.91 2.08
391 392 0.188587 AGCATCTCTCCACCGGGATA 59.811 55.000 6.32 0.00 43.91 2.59
392 393 0.692419 AAGCATCTCTCCACCGGGAT 60.692 55.000 6.32 0.00 43.91 3.85
393 394 0.032515 TAAGCATCTCTCCACCGGGA 60.033 55.000 6.32 0.00 42.29 5.14
394 395 1.051812 ATAAGCATCTCTCCACCGGG 58.948 55.000 6.32 0.00 0.00 5.73
395 396 2.874701 CAAATAAGCATCTCTCCACCGG 59.125 50.000 0.00 0.00 0.00 5.28
396 397 2.874701 CCAAATAAGCATCTCTCCACCG 59.125 50.000 0.00 0.00 0.00 4.94
397 398 3.217626 CCCAAATAAGCATCTCTCCACC 58.782 50.000 0.00 0.00 0.00 4.61
398 399 3.891049 ACCCAAATAAGCATCTCTCCAC 58.109 45.455 0.00 0.00 0.00 4.02
399 400 4.591321 AACCCAAATAAGCATCTCTCCA 57.409 40.909 0.00 0.00 0.00 3.86
400 401 5.930135 TCTAACCCAAATAAGCATCTCTCC 58.070 41.667 0.00 0.00 0.00 3.71
401 402 6.481644 CACTCTAACCCAAATAAGCATCTCTC 59.518 42.308 0.00 0.00 0.00 3.20
402 403 6.352516 CACTCTAACCCAAATAAGCATCTCT 58.647 40.000 0.00 0.00 0.00 3.10
403 404 5.529060 CCACTCTAACCCAAATAAGCATCTC 59.471 44.000 0.00 0.00 0.00 2.75
404 405 5.440610 CCACTCTAACCCAAATAAGCATCT 58.559 41.667 0.00 0.00 0.00 2.90
405 406 4.580580 CCCACTCTAACCCAAATAAGCATC 59.419 45.833 0.00 0.00 0.00 3.91
406 407 4.017499 ACCCACTCTAACCCAAATAAGCAT 60.017 41.667 0.00 0.00 0.00 3.79
407 408 3.332485 ACCCACTCTAACCCAAATAAGCA 59.668 43.478 0.00 0.00 0.00 3.91
408 409 3.964411 ACCCACTCTAACCCAAATAAGC 58.036 45.455 0.00 0.00 0.00 3.09
409 410 8.411991 TTTTAACCCACTCTAACCCAAATAAG 57.588 34.615 0.00 0.00 0.00 1.73
410 411 8.779096 TTTTTAACCCACTCTAACCCAAATAA 57.221 30.769 0.00 0.00 0.00 1.40
441 442 8.921205 GGATACTCTAACCCAGTTAATGTTAGA 58.079 37.037 10.03 10.03 44.84 2.10
442 443 8.701895 TGGATACTCTAACCCAGTTAATGTTAG 58.298 37.037 0.00 0.00 41.66 2.34
443 444 8.612486 TGGATACTCTAACCCAGTTAATGTTA 57.388 34.615 0.00 0.00 37.61 2.41
444 445 7.504926 TGGATACTCTAACCCAGTTAATGTT 57.495 36.000 0.00 0.00 37.61 2.71
445 446 7.504926 TTGGATACTCTAACCCAGTTAATGT 57.495 36.000 0.00 0.00 37.61 2.71
446 447 8.980481 ATTTGGATACTCTAACCCAGTTAATG 57.020 34.615 0.00 0.00 37.61 1.90
448 449 8.711170 CCTATTTGGATACTCTAACCCAGTTAA 58.289 37.037 0.00 0.00 38.35 2.01
449 450 7.291651 CCCTATTTGGATACTCTAACCCAGTTA 59.708 40.741 0.00 0.00 38.35 2.24
450 451 6.101296 CCCTATTTGGATACTCTAACCCAGTT 59.899 42.308 0.00 0.00 38.35 3.16
451 452 5.607171 CCCTATTTGGATACTCTAACCCAGT 59.393 44.000 0.00 0.00 38.35 4.00
452 453 5.513267 GCCCTATTTGGATACTCTAACCCAG 60.513 48.000 0.00 0.00 38.35 4.45
453 454 4.349930 GCCCTATTTGGATACTCTAACCCA 59.650 45.833 0.00 0.00 38.35 4.51
454 455 4.263374 GGCCCTATTTGGATACTCTAACCC 60.263 50.000 0.00 0.00 38.35 4.11
455 456 4.597940 AGGCCCTATTTGGATACTCTAACC 59.402 45.833 0.00 0.00 38.35 2.85
456 457 5.827326 AGGCCCTATTTGGATACTCTAAC 57.173 43.478 0.00 0.00 38.35 2.34
457 458 6.443849 CCATAGGCCCTATTTGGATACTCTAA 59.556 42.308 4.61 0.00 38.35 2.10
458 459 5.964477 CCATAGGCCCTATTTGGATACTCTA 59.036 44.000 4.61 0.00 38.35 2.43
459 460 4.785376 CCATAGGCCCTATTTGGATACTCT 59.215 45.833 4.61 0.00 38.35 3.24
460 461 4.783227 TCCATAGGCCCTATTTGGATACTC 59.217 45.833 8.75 0.00 38.35 2.59
461 462 4.774779 TCCATAGGCCCTATTTGGATACT 58.225 43.478 8.75 0.00 38.35 2.12
462 463 5.514500 TTCCATAGGCCCTATTTGGATAC 57.486 43.478 12.82 0.00 38.35 2.24
463 464 6.508920 AGAATTCCATAGGCCCTATTTGGATA 59.491 38.462 12.82 6.04 38.35 2.59
464 465 5.316992 AGAATTCCATAGGCCCTATTTGGAT 59.683 40.000 12.82 0.90 38.35 3.41
465 466 4.669768 AGAATTCCATAGGCCCTATTTGGA 59.330 41.667 8.75 8.75 38.35 3.53
466 467 4.768968 CAGAATTCCATAGGCCCTATTTGG 59.231 45.833 0.00 1.98 0.00 3.28
467 468 5.388654 ACAGAATTCCATAGGCCCTATTTG 58.611 41.667 0.00 0.00 0.00 2.32
468 469 5.669798 ACAGAATTCCATAGGCCCTATTT 57.330 39.130 0.00 0.00 0.00 1.40
469 470 5.134339 TCAACAGAATTCCATAGGCCCTATT 59.866 40.000 0.00 0.00 0.00 1.73
470 471 4.665009 TCAACAGAATTCCATAGGCCCTAT 59.335 41.667 0.00 0.00 0.00 2.57
471 472 4.044308 TCAACAGAATTCCATAGGCCCTA 58.956 43.478 0.00 0.00 0.00 3.53
472 473 2.852449 TCAACAGAATTCCATAGGCCCT 59.148 45.455 0.00 0.00 0.00 5.19
473 474 3.297134 TCAACAGAATTCCATAGGCCC 57.703 47.619 0.00 0.00 0.00 5.80
474 475 4.889409 TGATTCAACAGAATTCCATAGGCC 59.111 41.667 0.65 0.00 32.32 5.19
475 476 6.455360 TTGATTCAACAGAATTCCATAGGC 57.545 37.500 0.65 0.00 32.32 3.93
488 489 2.158593 TCGGGGTTCCTTTGATTCAACA 60.159 45.455 0.00 0.00 0.00 3.33
534 535 1.619654 CACCCACCTCTGCATCAAAA 58.380 50.000 0.00 0.00 0.00 2.44
543 544 2.127708 GAATATCACCCACCCACCTCT 58.872 52.381 0.00 0.00 0.00 3.69
563 564 7.630026 TCGAGCAACTAATAATTAAGTGCATG 58.370 34.615 0.00 0.00 0.00 4.06
639 640 1.999048 TAATCGGTGTGCCAACTACG 58.001 50.000 0.00 0.00 34.09 3.51
642 643 1.153353 CGTTAATCGGTGTGCCAACT 58.847 50.000 0.00 0.00 35.71 3.16
652 653 4.112634 TGAGAGCTTCAATCGTTAATCGG 58.887 43.478 0.00 0.00 34.84 4.18
653 654 5.896922 ATGAGAGCTTCAATCGTTAATCG 57.103 39.130 0.00 0.00 39.77 3.34
740 741 4.616953 TGGTGCACGTACATCACTATATG 58.383 43.478 11.45 0.00 0.00 1.78
748 749 4.277239 TGCTGGTGCACGTACATC 57.723 55.556 11.45 0.00 45.31 3.06
765 766 4.973168 AGTACATTATGACCGGCAATGAT 58.027 39.130 19.60 6.95 34.48 2.45
774 775 6.726490 TGGAGGAAGTAGTACATTATGACC 57.274 41.667 2.52 0.00 0.00 4.02
791 792 7.054124 AGCGAAAACTAATATGAAATGGAGGA 58.946 34.615 0.00 0.00 0.00 3.71
829 865 6.458342 CCCTCTGTTTCATATTAGTTTTCGCC 60.458 42.308 0.00 0.00 0.00 5.54
854 890 3.061429 ACGCTCGTACGTTTCTAGTACTC 59.939 47.826 16.05 0.00 45.75 2.59
894 930 2.185004 AAGTACGCACATGGCTTTCT 57.815 45.000 0.00 0.00 41.67 2.52
908 944 9.362539 TCTCAAAATTAATCACCGACTAAGTAC 57.637 33.333 0.00 0.00 0.00 2.73
1108 1151 3.269592 TTGGAAGTAGGAAGGGTCTGA 57.730 47.619 0.00 0.00 0.00 3.27
1111 1154 2.158943 CGGATTGGAAGTAGGAAGGGTC 60.159 54.545 0.00 0.00 0.00 4.46
1242 1285 2.668550 AAACACTCGGGGCGCTTC 60.669 61.111 7.64 0.00 0.00 3.86
1293 1336 0.323633 CATTGTGGGCAGGACCATCA 60.324 55.000 0.00 0.00 43.59 3.07
1437 1480 7.748847 TGCGGTAAAATTTCAAAGAGAGATAC 58.251 34.615 0.00 0.00 0.00 2.24
1465 1508 3.230134 TGGCTCCAGTGCAAACTTAATT 58.770 40.909 0.00 0.00 34.04 1.40
1498 1542 5.250235 TCTTTACGGTGTTTGAATTGCAA 57.750 34.783 0.00 0.00 33.88 4.08
1539 1583 7.808381 CCAAGTATATAGACATAGTTGACACGG 59.192 40.741 10.75 0.00 41.40 4.94
1907 1998 3.065648 GGATGTCGAGTAACTCTCCACTC 59.934 52.174 0.00 0.00 39.84 3.51
1947 2038 0.249447 CGGATGGTGATGCGCTCTAA 60.249 55.000 9.73 0.00 36.56 2.10
2050 2141 1.276989 TGTCCTTGTTATCCCCACGTC 59.723 52.381 0.00 0.00 0.00 4.34
2154 2252 3.373130 TCTGCATGCAAGAAAAGAGATCG 59.627 43.478 22.88 5.10 0.00 3.69
2227 2325 4.318332 TCGACATTGTCTTCTGCAAAGAT 58.682 39.130 14.54 0.15 0.00 2.40
2400 2498 2.086251 AACGCACGTAAACCCCGAGA 62.086 55.000 0.00 0.00 0.00 4.04
2442 2540 1.453015 TGTGACACAACACCCAGGC 60.453 57.895 5.62 0.00 39.69 4.85
2688 2966 7.880160 TTCTTGATGAAAGTCTTCTTTTCCA 57.120 32.000 0.00 0.00 42.99 3.53
2887 3165 6.482524 AGGAAGTTTAGTCTTAACCCCATTC 58.517 40.000 11.16 4.26 0.00 2.67
2973 3252 5.862678 GGCCTAGCCCATTTATTGTTTAA 57.137 39.130 0.00 0.00 44.06 1.52
3064 3344 8.543774 AGATGTTCCATTACTAGATGTTCAACT 58.456 33.333 0.00 0.00 0.00 3.16
3169 3449 2.061848 TGATGAACCAAGGGTCCTGAA 58.938 47.619 0.93 0.00 33.12 3.02
3171 3451 2.584835 TTGATGAACCAAGGGTCCTG 57.415 50.000 0.93 0.00 33.12 3.86
3172 3452 3.140144 TCTTTTGATGAACCAAGGGTCCT 59.860 43.478 0.93 0.00 33.12 3.85
3177 3457 5.772825 TCTTGTCTTTTGATGAACCAAGG 57.227 39.130 0.00 0.00 0.00 3.61
3190 3470 6.708054 ACAAAGATCGAGTGATTCTTGTCTTT 59.292 34.615 0.00 0.00 36.05 2.52
3389 3793 6.816140 TGAGTTCAAAAGAATGTTTGGGAAAC 59.184 34.615 0.00 0.00 38.72 2.78
3446 3850 2.480610 CCGGTGCTGCTGTGTTGTT 61.481 57.895 0.00 0.00 0.00 2.83
3629 4035 4.040461 AGAGATTCGTCAAGACCCTGAAAA 59.960 41.667 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.