Multiple sequence alignment - TraesCS7A01G036100

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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 TraesCS7A01G036100 chr7A 100.000 2913 0 0 1 2913 16165708 16162796 0.000000e+00 5380.0
1 TraesCS7A01G036100 chr7A 76.983 517 58 34 2448 2913 278807561 278808067 3.750000e-59 239.0
2 TraesCS7A01G036100 chr7A 94.815 135 7 0 338 472 686164086 686164220 8.180000e-51 211.0
3 TraesCS7A01G036100 chr7A 88.202 178 7 3 345 510 24861278 24861453 1.770000e-47 200.0
4 TraesCS7A01G036100 chr7D 92.841 1746 70 27 696 2410 16912913 16911192 0.000000e+00 2481.0
5 TraesCS7A01G036100 chr7D 81.017 295 35 11 2637 2913 135401230 135400939 6.320000e-52 215.0
6 TraesCS7A01G036100 chr7D 83.420 193 20 6 42 224 16914284 16914094 4.990000e-38 169.0
7 TraesCS7A01G036100 chr4A 90.367 1879 100 44 600 2427 717725235 717723387 0.000000e+00 2392.0
8 TraesCS7A01G036100 chr4A 77.872 235 30 12 2679 2913 736207767 736207555 3.050000e-25 126.0
9 TraesCS7A01G036100 chr1B 82.160 1065 82 52 1340 2384 665294303 665295279 0.000000e+00 815.0
10 TraesCS7A01G036100 chr1B 75.904 498 53 30 2446 2902 539942124 539942595 2.960000e-45 193.0
11 TraesCS7A01G036100 chr1B 85.405 185 25 2 1494 1677 499896494 499896677 1.070000e-44 191.0
12 TraesCS7A01G036100 chr1B 84.713 157 20 2 1142 1295 665294169 665294324 1.400000e-33 154.0
13 TraesCS7A01G036100 chr3B 85.343 423 20 18 1271 1686 766032144 766031757 1.630000e-107 399.0
14 TraesCS7A01G036100 chr3B 79.880 502 59 22 2443 2913 223510913 223510423 2.160000e-86 329.0
15 TraesCS7A01G036100 chr3B 82.443 131 12 4 1866 1985 766031651 766031521 1.430000e-18 104.0
16 TraesCS7A01G036100 chr3B 82.243 107 6 7 951 1054 766032320 766032224 2.410000e-11 80.5
17 TraesCS7A01G036100 chr3B 97.500 40 1 0 1146 1185 766032187 766032148 5.210000e-08 69.4
18 TraesCS7A01G036100 chr5D 83.114 456 47 16 2473 2910 45488846 45489289 3.520000e-104 388.0
19 TraesCS7A01G036100 chr5D 77.326 516 53 31 2447 2913 219538616 219539116 2.240000e-61 246.0
20 TraesCS7A01G036100 chr5D 84.390 205 20 8 327 520 116576062 116575859 1.070000e-44 191.0
21 TraesCS7A01G036100 chr5D 91.176 136 11 1 338 473 344567244 344567378 1.780000e-42 183.0
22 TraesCS7A01G036100 chr5D 90.441 136 12 1 338 473 353654544 353654678 8.300000e-41 178.0
23 TraesCS7A01G036100 chr6D 79.615 520 53 25 2436 2913 1947134 1946626 1.010000e-84 324.0
24 TraesCS7A01G036100 chr3D 77.973 513 56 34 2448 2913 224689480 224688978 4.780000e-68 268.0
25 TraesCS7A01G036100 chr7B 79.903 413 34 18 2518 2913 297212714 297213094 1.040000e-64 257.0
26 TraesCS7A01G036100 chr7B 83.396 265 16 10 2670 2913 728990077 728990334 1.360000e-53 220.0
27 TraesCS7A01G036100 chr3A 81.908 304 19 15 2644 2913 294133589 294133288 1.050000e-54 224.0
28 TraesCS7A01G036100 chr3A 82.383 193 29 4 1488 1676 616492652 616492461 2.320000e-36 163.0
29 TraesCS7A01G036100 chr1A 80.756 291 40 11 2637 2913 295456143 295456431 2.270000e-51 213.0
30 TraesCS7A01G036100 chr1A 80.851 282 24 12 2653 2913 545912707 545912435 8.240000e-46 195.0
31 TraesCS7A01G036100 chr1A 83.957 187 28 2 1492 1677 474450729 474450544 8.300000e-41 178.0
32 TraesCS7A01G036100 chr2A 86.096 187 18 6 330 509 15643354 15643539 8.240000e-46 195.0
33 TraesCS7A01G036100 chr2A 83.889 180 29 0 1491 1670 759456107 759456286 3.860000e-39 172.0
34 TraesCS7A01G036100 chr1D 85.561 187 25 2 1492 1677 375646699 375646514 8.240000e-46 195.0
35 TraesCS7A01G036100 chr2D 85.864 191 13 10 338 515 522752394 522752205 1.070000e-44 191.0
36 TraesCS7A01G036100 chr2D 91.176 136 11 1 338 473 414295114 414295248 1.780000e-42 183.0
37 TraesCS7A01G036100 chr5A 79.344 305 35 15 2637 2913 708301139 708301443 3.830000e-44 189.0
38 TraesCS7A01G036100 chr6A 88.079 151 14 4 334 481 421528017 421527868 2.980000e-40 176.0
39 TraesCS7A01G036100 chr2B 83.978 181 27 2 1491 1670 776213602 776213781 3.860000e-39 172.0


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 TraesCS7A01G036100 chr7A 16162796 16165708 2912 True 5380.0 5380 100.0000 1 2913 1 chr7A.!!$R1 2912
1 TraesCS7A01G036100 chr7A 278807561 278808067 506 False 239.0 239 76.9830 2448 2913 1 chr7A.!!$F2 465
2 TraesCS7A01G036100 chr7D 16911192 16914284 3092 True 1325.0 2481 88.1305 42 2410 2 chr7D.!!$R2 2368
3 TraesCS7A01G036100 chr4A 717723387 717725235 1848 True 2392.0 2392 90.3670 600 2427 1 chr4A.!!$R1 1827
4 TraesCS7A01G036100 chr1B 665294169 665295279 1110 False 484.5 815 83.4365 1142 2384 2 chr1B.!!$F3 1242
5 TraesCS7A01G036100 chr5D 219538616 219539116 500 False 246.0 246 77.3260 2447 2913 1 chr5D.!!$F2 466
6 TraesCS7A01G036100 chr6D 1946626 1947134 508 True 324.0 324 79.6150 2436 2913 1 chr6D.!!$R1 477
7 TraesCS7A01G036100 chr3D 224688978 224689480 502 True 268.0 268 77.9730 2448 2913 1 chr3D.!!$R1 465

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
596 1526 0.032813 CCTGCATCCAAATCCCTGGT 60.033 55.0 0.0 0.0 37.74 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 3247 0.03496 AGTCTCCAGTCGCAGCTCTA 60.035 55.0 0.0 0.0 0.0 2.43 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
26 27 7.617041 AGGCAATGTCAACTTTAACTCTATC 57.383 36.000 0.00 0.00 0.00 2.08
27 28 7.398024 AGGCAATGTCAACTTTAACTCTATCT 58.602 34.615 0.00 0.00 0.00 1.98
28 29 8.540388 AGGCAATGTCAACTTTAACTCTATCTA 58.460 33.333 0.00 0.00 0.00 1.98
29 30 9.331282 GGCAATGTCAACTTTAACTCTATCTAT 57.669 33.333 0.00 0.00 0.00 1.98
96 97 6.176975 TGCGTGTCAAAAATATTAGTCAGG 57.823 37.500 0.00 0.00 0.00 3.86
102 103 9.556030 GTGTCAAAAATATTAGTCAGGTTTAGC 57.444 33.333 0.00 0.00 0.00 3.09
119 126 7.604164 CAGGTTTAGCTTCTTTAGATTGTCTGA 59.396 37.037 0.00 0.00 0.00 3.27
135 142 6.426980 TTGTCTGACATGTGATGCTAATTC 57.573 37.500 11.86 0.00 0.00 2.17
136 143 5.490159 TGTCTGACATGTGATGCTAATTCA 58.510 37.500 1.15 0.00 0.00 2.57
144 151 6.538021 ACATGTGATGCTAATTCAGAGACTTC 59.462 38.462 0.00 0.00 0.00 3.01
159 170 5.804979 CAGAGACTTCTAGTTTAGCAGCTTC 59.195 44.000 0.00 0.00 30.73 3.86
193 204 4.318760 CGTCGCCAAACAACATATAGATGG 60.319 45.833 1.85 0.00 37.39 3.51
197 208 6.545666 TCGCCAAACAACATATAGATGGATTT 59.454 34.615 1.85 0.00 37.39 2.17
198 209 7.717436 TCGCCAAACAACATATAGATGGATTTA 59.283 33.333 1.85 0.00 37.39 1.40
226 237 8.776680 TTTTAAGCACGTTACTTTGAATTCTC 57.223 30.769 7.05 0.00 0.00 2.87
227 238 4.647291 AGCACGTTACTTTGAATTCTCG 57.353 40.909 7.05 3.40 0.00 4.04
229 240 4.929808 AGCACGTTACTTTGAATTCTCGAT 59.070 37.500 7.05 0.00 0.00 3.59
230 241 5.015733 GCACGTTACTTTGAATTCTCGATG 58.984 41.667 7.05 0.00 0.00 3.84
231 242 5.389516 GCACGTTACTTTGAATTCTCGATGT 60.390 40.000 7.05 4.39 0.00 3.06
234 245 7.893236 CACGTTACTTTGAATTCTCGATGTAAG 59.107 37.037 7.05 8.05 36.75 2.34
235 246 7.811236 ACGTTACTTTGAATTCTCGATGTAAGA 59.189 33.333 7.05 0.00 36.75 2.10
236 247 8.808529 CGTTACTTTGAATTCTCGATGTAAGAT 58.191 33.333 7.05 0.00 36.75 2.40
237 248 9.907576 GTTACTTTGAATTCTCGATGTAAGATG 57.092 33.333 7.05 0.00 36.75 2.90
239 250 6.540189 ACTTTGAATTCTCGATGTAAGATGGG 59.460 38.462 7.05 0.00 0.00 4.00
266 741 6.408858 TGAGAAAGAAAATTAGCAGCTACG 57.591 37.500 0.00 0.00 0.00 3.51
279 754 2.289002 GCAGCTACGATCCCTTTTGATG 59.711 50.000 0.00 0.00 0.00 3.07
283 758 5.297776 CAGCTACGATCCCTTTTGATGAAAT 59.702 40.000 0.00 0.00 0.00 2.17
285 760 7.012327 CAGCTACGATCCCTTTTGATGAAATAA 59.988 37.037 0.00 0.00 0.00 1.40
291 766 7.702348 CGATCCCTTTTGATGAAATAAAAGTCC 59.298 37.037 0.00 0.00 40.52 3.85
293 768 8.122472 TCCCTTTTGATGAAATAAAAGTCCTC 57.878 34.615 0.00 0.00 40.52 3.71
294 769 7.029563 CCCTTTTGATGAAATAAAAGTCCTCG 58.970 38.462 0.00 0.00 40.52 4.63
299 774 9.443323 TTTGATGAAATAAAAGTCCTCGTATGA 57.557 29.630 0.00 0.00 0.00 2.15
301 776 9.443323 TGATGAAATAAAAGTCCTCGTATGAAA 57.557 29.630 0.00 0.00 0.00 2.69
310 785 4.811557 AGTCCTCGTATGAAAATTAGCAGC 59.188 41.667 0.00 0.00 0.00 5.25
315 1245 6.257849 CCTCGTATGAAAATTAGCAGCTACAA 59.742 38.462 0.00 0.00 0.00 2.41
325 1255 8.947055 AAATTAGCAGCTACAAATTTAATGGG 57.053 30.769 11.23 0.00 31.55 4.00
326 1256 7.660030 ATTAGCAGCTACAAATTTAATGGGT 57.340 32.000 0.00 0.00 0.00 4.51
327 1257 7.475137 TTAGCAGCTACAAATTTAATGGGTT 57.525 32.000 0.00 0.00 0.00 4.11
328 1258 6.358974 AGCAGCTACAAATTTAATGGGTTT 57.641 33.333 0.00 0.00 0.00 3.27
329 1259 6.768483 AGCAGCTACAAATTTAATGGGTTTT 58.232 32.000 0.00 0.00 0.00 2.43
330 1260 7.223584 AGCAGCTACAAATTTAATGGGTTTTT 58.776 30.769 0.00 0.00 0.00 1.94
355 1285 9.998106 TTTCTTATAGTTTTGCTAAGTCTCAGT 57.002 29.630 0.00 0.00 32.72 3.41
356 1286 9.640963 TTCTTATAGTTTTGCTAAGTCTCAGTC 57.359 33.333 0.00 0.00 32.72 3.51
357 1287 7.968956 TCTTATAGTTTTGCTAAGTCTCAGTCG 59.031 37.037 0.00 0.00 32.72 4.18
358 1288 4.585955 AGTTTTGCTAAGTCTCAGTCGA 57.414 40.909 0.00 0.00 0.00 4.20
359 1289 4.299978 AGTTTTGCTAAGTCTCAGTCGAC 58.700 43.478 7.70 7.70 0.00 4.20
360 1290 4.038162 AGTTTTGCTAAGTCTCAGTCGACT 59.962 41.667 13.58 13.58 45.73 4.18
378 1308 7.901874 GTCGACTTAGACTTCATTATGTCTC 57.098 40.000 8.70 0.00 41.92 3.36
379 1309 7.473366 GTCGACTTAGACTTCATTATGTCTCA 58.527 38.462 8.70 0.00 41.92 3.27
380 1310 7.642194 GTCGACTTAGACTTCATTATGTCTCAG 59.358 40.741 8.70 0.00 41.92 3.35
381 1311 7.337184 TCGACTTAGACTTCATTATGTCTCAGT 59.663 37.037 8.67 8.67 45.06 3.41
383 1313 7.476667 ACTTAGACTTCATTATGTCTCAGTCG 58.523 38.462 4.68 0.00 41.23 4.18
384 1314 7.337184 ACTTAGACTTCATTATGTCTCAGTCGA 59.663 37.037 4.68 0.00 41.23 4.20
385 1315 6.707440 AGACTTCATTATGTCTCAGTCGAT 57.293 37.500 0.00 0.00 39.04 3.59
386 1316 6.502652 AGACTTCATTATGTCTCAGTCGATG 58.497 40.000 0.00 0.00 39.04 3.84
387 1317 6.096141 AGACTTCATTATGTCTCAGTCGATGT 59.904 38.462 0.00 0.00 39.04 3.06
388 1318 6.634805 ACTTCATTATGTCTCAGTCGATGTT 58.365 36.000 0.00 0.00 0.00 2.71
389 1319 6.533012 ACTTCATTATGTCTCAGTCGATGTTG 59.467 38.462 0.00 0.00 0.00 3.33
390 1320 5.965922 TCATTATGTCTCAGTCGATGTTGT 58.034 37.500 0.00 0.00 0.00 3.32
391 1321 7.095695 TCATTATGTCTCAGTCGATGTTGTA 57.904 36.000 0.00 0.00 0.00 2.41
392 1322 7.716612 TCATTATGTCTCAGTCGATGTTGTAT 58.283 34.615 0.00 0.00 0.00 2.29
393 1323 8.197439 TCATTATGTCTCAGTCGATGTTGTATT 58.803 33.333 0.00 0.00 0.00 1.89
394 1324 7.987268 TTATGTCTCAGTCGATGTTGTATTC 57.013 36.000 0.00 0.00 0.00 1.75
395 1325 5.644977 TGTCTCAGTCGATGTTGTATTCT 57.355 39.130 0.00 0.00 0.00 2.40
396 1326 6.753107 TGTCTCAGTCGATGTTGTATTCTA 57.247 37.500 0.00 0.00 0.00 2.10
397 1327 7.334844 TGTCTCAGTCGATGTTGTATTCTAT 57.665 36.000 0.00 0.00 0.00 1.98
398 1328 7.772166 TGTCTCAGTCGATGTTGTATTCTATT 58.228 34.615 0.00 0.00 0.00 1.73
399 1329 7.702348 TGTCTCAGTCGATGTTGTATTCTATTG 59.298 37.037 0.00 0.00 0.00 1.90
400 1330 7.915923 GTCTCAGTCGATGTTGTATTCTATTGA 59.084 37.037 0.00 0.00 0.00 2.57
401 1331 8.633561 TCTCAGTCGATGTTGTATTCTATTGAT 58.366 33.333 0.00 0.00 0.00 2.57
402 1332 8.803201 TCAGTCGATGTTGTATTCTATTGATC 57.197 34.615 0.00 0.00 0.00 2.92
403 1333 8.633561 TCAGTCGATGTTGTATTCTATTGATCT 58.366 33.333 0.00 0.00 0.00 2.75
404 1334 9.254133 CAGTCGATGTTGTATTCTATTGATCTT 57.746 33.333 0.00 0.00 0.00 2.40
405 1335 9.254133 AGTCGATGTTGTATTCTATTGATCTTG 57.746 33.333 0.00 0.00 0.00 3.02
406 1336 8.006590 GTCGATGTTGTATTCTATTGATCTTGC 58.993 37.037 0.00 0.00 0.00 4.01
407 1337 7.710475 TCGATGTTGTATTCTATTGATCTTGCA 59.290 33.333 0.00 0.00 0.00 4.08
408 1338 8.501580 CGATGTTGTATTCTATTGATCTTGCAT 58.498 33.333 0.00 0.00 0.00 3.96
410 1340 9.961265 ATGTTGTATTCTATTGATCTTGCATTG 57.039 29.630 0.00 0.00 0.00 2.82
411 1341 9.176460 TGTTGTATTCTATTGATCTTGCATTGA 57.824 29.630 0.00 0.00 0.00 2.57
412 1342 9.661187 GTTGTATTCTATTGATCTTGCATTGAG 57.339 33.333 0.00 0.00 0.00 3.02
413 1343 9.617523 TTGTATTCTATTGATCTTGCATTGAGA 57.382 29.630 0.00 0.00 0.00 3.27
414 1344 9.788889 TGTATTCTATTGATCTTGCATTGAGAT 57.211 29.630 0.00 0.00 36.60 2.75
417 1347 7.417496 TCTATTGATCTTGCATTGAGATTCG 57.583 36.000 1.03 0.00 34.13 3.34
418 1348 6.988580 TCTATTGATCTTGCATTGAGATTCGT 59.011 34.615 1.03 0.00 34.13 3.85
419 1349 8.143835 TCTATTGATCTTGCATTGAGATTCGTA 58.856 33.333 1.03 0.00 34.13 3.43
420 1350 5.973651 TGATCTTGCATTGAGATTCGTAC 57.026 39.130 1.03 0.00 34.13 3.67
421 1351 5.418676 TGATCTTGCATTGAGATTCGTACA 58.581 37.500 1.03 0.00 34.13 2.90
422 1352 5.874261 TGATCTTGCATTGAGATTCGTACAA 59.126 36.000 1.03 0.00 34.13 2.41
423 1353 6.371271 TGATCTTGCATTGAGATTCGTACAAA 59.629 34.615 1.03 0.00 34.13 2.83
424 1354 6.552859 TCTTGCATTGAGATTCGTACAAAA 57.447 33.333 0.00 0.00 0.00 2.44
425 1355 6.964908 TCTTGCATTGAGATTCGTACAAAAA 58.035 32.000 0.00 0.00 0.00 1.94
472 1402 9.613428 TTTTCTTCCCATATACACTATCACTTG 57.387 33.333 0.00 0.00 0.00 3.16
473 1403 7.914427 TCTTCCCATATACACTATCACTTGT 57.086 36.000 0.00 0.00 0.00 3.16
474 1404 8.319057 TCTTCCCATATACACTATCACTTGTT 57.681 34.615 0.00 0.00 0.00 2.83
475 1405 9.429109 TCTTCCCATATACACTATCACTTGTTA 57.571 33.333 0.00 0.00 0.00 2.41
478 1408 9.209048 TCCCATATACACTATCACTTGTTAAGT 57.791 33.333 0.00 0.00 44.06 2.24
479 1409 9.477484 CCCATATACACTATCACTTGTTAAGTC 57.523 37.037 0.00 0.00 40.46 3.01
484 1414 7.291411 ACACTATCACTTGTTAAGTCTCAGT 57.709 36.000 0.00 0.00 40.46 3.41
485 1415 7.371936 ACACTATCACTTGTTAAGTCTCAGTC 58.628 38.462 0.00 0.00 40.46 3.51
486 1416 6.524933 CACTATCACTTGTTAAGTCTCAGTCG 59.475 42.308 0.00 0.00 40.46 4.18
487 1417 5.707242 ATCACTTGTTAAGTCTCAGTCGA 57.293 39.130 0.00 0.00 40.46 4.20
488 1418 4.856664 TCACTTGTTAAGTCTCAGTCGAC 58.143 43.478 7.70 7.70 40.46 4.20
489 1419 4.579340 TCACTTGTTAAGTCTCAGTCGACT 59.421 41.667 13.58 13.58 45.73 4.18
490 1420 5.761726 TCACTTGTTAAGTCTCAGTCGACTA 59.238 40.000 19.57 0.00 43.14 2.59
491 1421 6.261603 TCACTTGTTAAGTCTCAGTCGACTAA 59.738 38.462 19.57 1.94 43.14 2.24
492 1422 6.360148 CACTTGTTAAGTCTCAGTCGACTAAC 59.640 42.308 19.57 16.82 43.14 2.34
493 1423 6.039047 ACTTGTTAAGTCTCAGTCGACTAACA 59.961 38.462 19.57 19.19 43.14 2.41
494 1424 5.755813 TGTTAAGTCTCAGTCGACTAACAC 58.244 41.667 19.57 14.07 43.14 3.32
495 1425 5.297527 TGTTAAGTCTCAGTCGACTAACACA 59.702 40.000 19.57 13.36 43.14 3.72
496 1426 6.016527 TGTTAAGTCTCAGTCGACTAACACAT 60.017 38.462 19.57 9.93 43.14 3.21
497 1427 7.173735 TGTTAAGTCTCAGTCGACTAACACATA 59.826 37.037 19.57 8.97 43.14 2.29
498 1428 5.804692 AGTCTCAGTCGACTAACACATAG 57.195 43.478 19.57 3.12 42.19 2.23
499 1429 5.489249 AGTCTCAGTCGACTAACACATAGA 58.511 41.667 19.57 7.76 42.19 1.98
500 1430 5.352016 AGTCTCAGTCGACTAACACATAGAC 59.648 44.000 19.57 18.94 42.19 2.59
501 1431 5.121925 GTCTCAGTCGACTAACACATAGACA 59.878 44.000 19.57 0.00 35.47 3.41
502 1432 5.121925 TCTCAGTCGACTAACACATAGACAC 59.878 44.000 19.57 0.00 35.47 3.67
503 1433 4.758165 TCAGTCGACTAACACATAGACACA 59.242 41.667 19.57 0.00 35.47 3.72
504 1434 4.852104 CAGTCGACTAACACATAGACACAC 59.148 45.833 19.57 0.00 35.47 3.82
505 1435 4.082895 AGTCGACTAACACATAGACACACC 60.083 45.833 18.46 0.00 35.47 4.16
506 1436 3.192001 TCGACTAACACATAGACACACCC 59.808 47.826 0.00 0.00 35.47 4.61
523 1453 7.123547 AGACACACCCTTTTTCTTAATGTGAAA 59.876 33.333 8.35 0.00 38.56 2.69
525 1455 6.198216 CACACCCTTTTTCTTAATGTGAAACG 59.802 38.462 0.00 0.00 42.39 3.60
528 1458 6.097129 ACCCTTTTTCTTAATGTGAAACGGAA 59.903 34.615 0.00 0.00 42.39 4.30
535 1465 9.893634 TTTCTTAATGTGAAACGGAATATAGGA 57.106 29.630 0.00 0.00 42.39 2.94
536 1466 9.542462 TTCTTAATGTGAAACGGAATATAGGAG 57.458 33.333 0.00 0.00 42.39 3.69
538 1468 9.976511 CTTAATGTGAAACGGAATATAGGAGTA 57.023 33.333 0.00 0.00 42.39 2.59
541 1471 8.833231 ATGTGAAACGGAATATAGGAGTAATG 57.167 34.615 0.00 0.00 42.39 1.90
542 1472 7.788026 TGTGAAACGGAATATAGGAGTAATGT 58.212 34.615 0.00 0.00 42.39 2.71
546 1476 9.931210 GAAACGGAATATAGGAGTAATGTTTTG 57.069 33.333 0.00 0.00 0.00 2.44
557 1487 3.763897 AGTAATGTTTTGGGCACTGGATC 59.236 43.478 0.00 0.00 0.00 3.36
558 1488 2.610438 ATGTTTTGGGCACTGGATCT 57.390 45.000 0.00 0.00 0.00 2.75
571 1501 4.268884 GCACTGGATCTTTTTACTAGCTCG 59.731 45.833 0.00 0.00 0.00 5.03
591 1521 4.282881 CCCCCTGCATCCAAATCC 57.717 61.111 0.00 0.00 0.00 3.01
592 1522 1.458209 CCCCCTGCATCCAAATCCC 60.458 63.158 0.00 0.00 0.00 3.85
593 1523 1.622499 CCCCTGCATCCAAATCCCT 59.378 57.895 0.00 0.00 0.00 4.20
594 1524 0.757935 CCCCTGCATCCAAATCCCTG 60.758 60.000 0.00 0.00 0.00 4.45
595 1525 0.757935 CCCTGCATCCAAATCCCTGG 60.758 60.000 0.00 0.00 37.87 4.45
596 1526 0.032813 CCTGCATCCAAATCCCTGGT 60.033 55.000 0.00 0.00 37.74 4.00
597 1527 1.396653 CTGCATCCAAATCCCTGGTC 58.603 55.000 0.00 0.00 37.74 4.02
598 1528 0.033208 TGCATCCAAATCCCTGGTCC 60.033 55.000 0.00 0.00 37.74 4.46
599 1529 1.103398 GCATCCAAATCCCTGGTCCG 61.103 60.000 0.00 0.00 37.74 4.79
600 1530 1.103398 CATCCAAATCCCTGGTCCGC 61.103 60.000 0.00 0.00 37.74 5.54
601 1531 2.284515 ATCCAAATCCCTGGTCCGCC 62.285 60.000 0.00 0.00 37.74 6.13
602 1532 2.440247 CAAATCCCTGGTCCGCCC 60.440 66.667 0.00 0.00 0.00 6.13
603 1533 3.739613 AAATCCCTGGTCCGCCCC 61.740 66.667 0.00 0.00 0.00 5.80
604 1534 4.760220 AATCCCTGGTCCGCCCCT 62.760 66.667 0.00 0.00 0.00 4.79
608 1538 3.966543 CCTGGTCCGCCCCTGTTT 61.967 66.667 0.00 0.00 0.00 2.83
609 1539 2.359975 CTGGTCCGCCCCTGTTTC 60.360 66.667 0.00 0.00 0.00 2.78
610 1540 4.323477 TGGTCCGCCCCTGTTTCG 62.323 66.667 0.00 0.00 0.00 3.46
680 1610 1.743252 AACTAGCCTTGCAGCGCTC 60.743 57.895 7.13 2.98 36.53 5.03
804 1777 1.068921 TTTTTGGCGGGCAAAGCTC 59.931 52.632 25.55 0.00 34.52 4.09
882 1865 2.139484 TGGCCAACAGCAAAAGGGG 61.139 57.895 0.61 0.00 46.50 4.79
955 1938 0.912486 CGATTCCCACCTCCTTCCTT 59.088 55.000 0.00 0.00 0.00 3.36
969 1952 1.139853 CTTCCTTGCGGATAAGCCTCT 59.860 52.381 0.00 0.00 39.58 3.69
1012 2007 2.659063 CCCACGATGGCCACTCAGA 61.659 63.158 8.16 0.00 35.79 3.27
1017 2012 1.903294 GATGGCCACTCAGAGAGCA 59.097 57.895 8.16 5.95 32.04 4.26
1399 2403 3.212685 GAGGAGCACAGGTACGTACTAT 58.787 50.000 24.07 11.40 0.00 2.12
1400 2404 4.384056 GAGGAGCACAGGTACGTACTATA 58.616 47.826 24.07 0.00 0.00 1.31
1462 2472 2.553086 CAGAGGAAGCTCTGCATCTTC 58.447 52.381 12.43 12.43 43.39 2.87
1516 2526 1.676967 GTTCTTGCTGGGGCTGGAG 60.677 63.158 0.00 0.00 39.59 3.86
1969 2999 4.246206 CGCCGGCATGCATGTCAG 62.246 66.667 29.36 20.45 31.41 3.51
1979 3009 2.107750 CATGTCAGGCGCCTCGAT 59.892 61.111 30.29 15.95 0.00 3.59
2023 3057 7.822161 TCCTTGTTCTTTCTTGATTGATTCA 57.178 32.000 0.00 0.00 0.00 2.57
2053 3087 1.320344 CCGTCCGTTCCTCATCCTCA 61.320 60.000 0.00 0.00 0.00 3.86
2054 3088 0.747255 CGTCCGTTCCTCATCCTCAT 59.253 55.000 0.00 0.00 0.00 2.90
2055 3089 1.269309 CGTCCGTTCCTCATCCTCATC 60.269 57.143 0.00 0.00 0.00 2.92
2059 3093 2.632028 CCGTTCCTCATCCTCATCTGAT 59.368 50.000 0.00 0.00 0.00 2.90
2071 3105 1.144298 TCATCTGATTGCAGGGATGGG 59.856 52.381 15.18 0.00 42.53 4.00
2119 3160 4.631813 ACTGTTGCAAGTGCTAGCTTATAC 59.368 41.667 17.23 5.48 42.66 1.47
2120 3161 4.832248 TGTTGCAAGTGCTAGCTTATACT 58.168 39.130 17.23 7.99 42.66 2.12
2122 3163 4.060038 TGCAAGTGCTAGCTTATACTCC 57.940 45.455 17.23 6.46 42.66 3.85
2150 3191 0.889186 CACAGACCCGGGAAAGGTTG 60.889 60.000 32.02 17.03 37.88 3.77
2172 3213 7.988028 GGTTGAGAGAGGTAAATGTAATTAGCT 59.012 37.037 0.00 0.00 44.05 3.32
2205 3247 2.849942 TGTGTAGCTGTTCATGCTTGT 58.150 42.857 0.00 0.00 41.46 3.16
2289 3331 8.948853 ACTTTGACGTGAATAAATTACACATG 57.051 30.769 0.00 0.00 34.69 3.21
2290 3332 7.537306 ACTTTGACGTGAATAAATTACACATGC 59.463 33.333 0.00 0.00 34.69 4.06
2291 3333 6.487689 TGACGTGAATAAATTACACATGCA 57.512 33.333 0.00 0.00 34.69 3.96
2292 3334 7.082700 TGACGTGAATAAATTACACATGCAT 57.917 32.000 0.00 0.00 34.69 3.96
2293 3335 7.186128 TGACGTGAATAAATTACACATGCATC 58.814 34.615 0.00 0.00 34.69 3.91
2294 3336 7.082700 ACGTGAATAAATTACACATGCATCA 57.917 32.000 0.00 0.00 34.69 3.07
2295 3337 7.534282 ACGTGAATAAATTACACATGCATCAA 58.466 30.769 0.00 0.00 34.69 2.57
2413 3455 0.804933 GCCGTACCGAGACATGAACC 60.805 60.000 0.00 0.00 0.00 3.62
2417 3459 2.858344 CGTACCGAGACATGAACCATTC 59.142 50.000 0.00 0.00 0.00 2.67
2419 3461 4.201980 CGTACCGAGACATGAACCATTCTA 60.202 45.833 0.00 0.00 0.00 2.10
2420 3462 5.507482 CGTACCGAGACATGAACCATTCTAT 60.507 44.000 0.00 0.00 0.00 1.98
2421 3463 6.293790 CGTACCGAGACATGAACCATTCTATA 60.294 42.308 0.00 0.00 0.00 1.31
2423 3465 6.692486 ACCGAGACATGAACCATTCTATATC 58.308 40.000 0.00 0.00 0.00 1.63
2424 3466 6.495181 ACCGAGACATGAACCATTCTATATCT 59.505 38.462 0.00 0.00 0.00 1.98
2425 3467 7.670140 ACCGAGACATGAACCATTCTATATCTA 59.330 37.037 0.00 0.00 0.00 1.98
2426 3468 8.690884 CCGAGACATGAACCATTCTATATCTAT 58.309 37.037 0.00 0.00 0.00 1.98
2519 3562 6.973474 TCCATCAATGTTTTTCGTACGTTTTT 59.027 30.769 16.05 0.00 0.00 1.94
2589 3641 0.032952 CTGAAACGGACTCGAACCCA 59.967 55.000 3.98 0.00 40.11 4.51
2595 3648 1.002624 GGACTCGAACCCATGCCAA 60.003 57.895 0.00 0.00 0.00 4.52
2602 3655 2.948979 TCGAACCCATGCCAATTATGTC 59.051 45.455 0.00 0.00 0.00 3.06
2604 3657 1.691196 ACCCATGCCAATTATGTCCG 58.309 50.000 0.00 0.00 0.00 4.79
2626 3679 2.930455 GCCGCAATGCAATAACCAAAGT 60.930 45.455 5.91 0.00 0.00 2.66
2627 3680 2.667481 CCGCAATGCAATAACCAAAGTG 59.333 45.455 5.91 0.00 0.00 3.16
2628 3681 3.316283 CGCAATGCAATAACCAAAGTGT 58.684 40.909 5.91 0.00 0.00 3.55
2633 3698 6.201806 GCAATGCAATAACCAAAGTGTTTGTA 59.798 34.615 0.00 0.00 38.98 2.41
2634 3699 7.254590 GCAATGCAATAACCAAAGTGTTTGTAA 60.255 33.333 0.00 0.00 38.98 2.41
2635 3700 8.607459 CAATGCAATAACCAAAGTGTTTGTAAA 58.393 29.630 0.00 0.00 38.98 2.01
2685 3752 1.901948 CACTCCCTCGCGCCCTATA 60.902 63.158 0.00 0.00 0.00 1.31
2833 3928 1.045407 CCGTGCACCCTATTAGGCTA 58.955 55.000 12.15 0.00 32.73 3.93
2872 3967 4.456566 GGGACGCCACTGTTTTCTTATTTA 59.543 41.667 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.540388 AGATAGAGTTAAAGTTGACATTGCCTA 58.460 33.333 0.00 0.00 0.00 3.93
2 3 7.398024 AGATAGAGTTAAAGTTGACATTGCCT 58.602 34.615 0.00 0.00 0.00 4.75
3 4 7.617041 AGATAGAGTTAAAGTTGACATTGCC 57.383 36.000 0.00 0.00 0.00 4.52
45 46 9.529325 GGTCAAAATTGGGAAATATTTACTAGC 57.471 33.333 10.27 0.00 0.00 3.42
48 49 9.942850 CAAGGTCAAAATTGGGAAATATTTACT 57.057 29.630 10.27 0.00 0.00 2.24
49 50 8.664798 GCAAGGTCAAAATTGGGAAATATTTAC 58.335 33.333 1.35 1.35 0.00 2.01
50 51 7.547370 CGCAAGGTCAAAATTGGGAAATATTTA 59.453 33.333 0.00 0.00 40.65 1.40
51 52 6.371271 CGCAAGGTCAAAATTGGGAAATATTT 59.629 34.615 0.00 0.00 40.65 1.40
52 53 5.874261 CGCAAGGTCAAAATTGGGAAATATT 59.126 36.000 0.00 0.00 40.65 1.28
53 54 5.046663 ACGCAAGGTCAAAATTGGGAAATAT 60.047 36.000 8.68 0.00 40.65 1.28
54 55 4.282195 ACGCAAGGTCAAAATTGGGAAATA 59.718 37.500 8.68 0.00 40.65 1.40
55 56 3.070878 ACGCAAGGTCAAAATTGGGAAAT 59.929 39.130 8.68 0.00 40.65 2.17
56 57 2.432510 ACGCAAGGTCAAAATTGGGAAA 59.567 40.909 8.68 0.00 40.65 3.13
57 58 2.035632 ACGCAAGGTCAAAATTGGGAA 58.964 42.857 8.68 0.00 40.65 3.97
58 59 1.339610 CACGCAAGGTCAAAATTGGGA 59.660 47.619 8.68 0.00 40.65 4.37
59 60 1.068434 ACACGCAAGGTCAAAATTGGG 59.932 47.619 0.00 0.00 42.99 4.12
60 61 2.223688 TGACACGCAAGGTCAAAATTGG 60.224 45.455 0.11 0.00 42.05 3.16
70 71 6.607689 TGACTAATATTTTTGACACGCAAGG 58.392 36.000 0.00 0.00 46.39 3.61
72 73 6.205853 ACCTGACTAATATTTTTGACACGCAA 59.794 34.615 0.00 0.00 33.88 4.85
96 97 8.311650 TGTCAGACAATCTAAAGAAGCTAAAC 57.688 34.615 0.00 0.00 0.00 2.01
102 103 7.895975 TCACATGTCAGACAATCTAAAGAAG 57.104 36.000 7.50 0.00 0.00 2.85
104 105 6.314648 GCATCACATGTCAGACAATCTAAAGA 59.685 38.462 7.50 0.00 0.00 2.52
109 110 4.217836 AGCATCACATGTCAGACAATCT 57.782 40.909 7.50 0.00 0.00 2.40
111 112 6.600427 TGAATTAGCATCACATGTCAGACAAT 59.400 34.615 7.50 0.00 0.00 2.71
119 126 5.987098 AGTCTCTGAATTAGCATCACATGT 58.013 37.500 0.00 0.00 0.00 3.21
135 142 5.323371 AGCTGCTAAACTAGAAGTCTCTG 57.677 43.478 0.00 0.00 33.71 3.35
136 143 5.478679 TGAAGCTGCTAAACTAGAAGTCTCT 59.521 40.000 0.90 0.00 33.71 3.10
144 151 6.545504 TTTCTGTTGAAGCTGCTAAACTAG 57.454 37.500 21.53 17.60 33.28 2.57
159 170 0.028770 TTGGCGACGCTTTTCTGTTG 59.971 50.000 20.77 0.00 0.00 3.33
207 218 4.640805 TCGAGAATTCAAAGTAACGTGC 57.359 40.909 8.44 0.00 0.00 5.34
214 225 6.540189 CCCATCTTACATCGAGAATTCAAAGT 59.460 38.462 8.44 1.68 0.00 2.66
221 232 5.777223 TCATCTCCCATCTTACATCGAGAAT 59.223 40.000 0.00 0.00 30.70 2.40
224 235 4.764308 TCTCATCTCCCATCTTACATCGAG 59.236 45.833 0.00 0.00 0.00 4.04
226 237 5.459536 TTCTCATCTCCCATCTTACATCG 57.540 43.478 0.00 0.00 0.00 3.84
227 238 7.060383 TCTTTCTCATCTCCCATCTTACATC 57.940 40.000 0.00 0.00 0.00 3.06
229 240 6.874278 TTCTTTCTCATCTCCCATCTTACA 57.126 37.500 0.00 0.00 0.00 2.41
230 241 8.744568 ATTTTCTTTCTCATCTCCCATCTTAC 57.255 34.615 0.00 0.00 0.00 2.34
234 245 7.284034 TGCTAATTTTCTTTCTCATCTCCCATC 59.716 37.037 0.00 0.00 0.00 3.51
235 246 7.121382 TGCTAATTTTCTTTCTCATCTCCCAT 58.879 34.615 0.00 0.00 0.00 4.00
236 247 6.484288 TGCTAATTTTCTTTCTCATCTCCCA 58.516 36.000 0.00 0.00 0.00 4.37
237 248 6.459435 GCTGCTAATTTTCTTTCTCATCTCCC 60.459 42.308 0.00 0.00 0.00 4.30
239 250 7.319142 AGCTGCTAATTTTCTTTCTCATCTC 57.681 36.000 0.00 0.00 0.00 2.75
266 741 8.753133 AGGACTTTTATTTCATCAAAAGGGATC 58.247 33.333 10.53 0.00 43.10 3.36
283 758 8.780846 TGCTAATTTTCATACGAGGACTTTTA 57.219 30.769 0.00 0.00 0.00 1.52
285 760 6.183360 GCTGCTAATTTTCATACGAGGACTTT 60.183 38.462 0.00 0.00 0.00 2.66
291 766 6.828502 TGTAGCTGCTAATTTTCATACGAG 57.171 37.500 11.57 0.00 0.00 4.18
293 768 8.841444 AATTTGTAGCTGCTAATTTTCATACG 57.159 30.769 16.03 0.00 0.00 3.06
299 774 9.382275 CCCATTAAATTTGTAGCTGCTAATTTT 57.618 29.630 29.98 17.45 36.10 1.82
301 776 8.078060 ACCCATTAAATTTGTAGCTGCTAATT 57.922 30.769 16.03 16.03 0.00 1.40
302 777 7.660030 ACCCATTAAATTTGTAGCTGCTAAT 57.340 32.000 11.57 5.71 0.00 1.73
303 778 7.475137 AACCCATTAAATTTGTAGCTGCTAA 57.525 32.000 11.57 1.71 0.00 3.09
305 780 6.358974 AAACCCATTAAATTTGTAGCTGCT 57.641 33.333 7.57 7.57 0.00 4.24
329 1259 9.998106 ACTGAGACTTAGCAAAACTATAAGAAA 57.002 29.630 0.00 0.00 32.16 2.52
330 1260 9.640963 GACTGAGACTTAGCAAAACTATAAGAA 57.359 33.333 0.00 0.00 32.16 2.52
331 1261 7.968956 CGACTGAGACTTAGCAAAACTATAAGA 59.031 37.037 0.00 0.00 32.16 2.10
332 1262 7.968956 TCGACTGAGACTTAGCAAAACTATAAG 59.031 37.037 0.00 0.00 33.63 1.73
333 1263 7.754027 GTCGACTGAGACTTAGCAAAACTATAA 59.246 37.037 8.70 0.00 38.09 0.98
334 1264 7.249147 GTCGACTGAGACTTAGCAAAACTATA 58.751 38.462 8.70 0.00 38.09 1.31
335 1265 6.094061 GTCGACTGAGACTTAGCAAAACTAT 58.906 40.000 8.70 0.00 38.09 2.12
336 1266 5.458891 GTCGACTGAGACTTAGCAAAACTA 58.541 41.667 8.70 0.00 38.09 2.24
337 1267 4.299978 GTCGACTGAGACTTAGCAAAACT 58.700 43.478 8.70 0.00 38.09 2.66
338 1268 4.632740 GTCGACTGAGACTTAGCAAAAC 57.367 45.455 8.70 0.00 38.09 2.43
349 1279 7.337184 ACATAATGAAGTCTAAGTCGACTGAGA 59.663 37.037 26.12 26.12 43.14 3.27
350 1280 7.476667 ACATAATGAAGTCTAAGTCGACTGAG 58.523 38.462 22.32 22.32 43.14 3.35
351 1281 7.337184 AGACATAATGAAGTCTAAGTCGACTGA 59.663 37.037 20.85 11.31 43.14 3.41
352 1282 7.476667 AGACATAATGAAGTCTAAGTCGACTG 58.523 38.462 20.85 7.79 43.14 3.51
353 1283 7.337184 TGAGACATAATGAAGTCTAAGTCGACT 59.663 37.037 13.58 13.58 44.61 4.18
354 1284 7.473366 TGAGACATAATGAAGTCTAAGTCGAC 58.527 38.462 7.70 7.70 44.61 4.20
355 1285 7.625828 TGAGACATAATGAAGTCTAAGTCGA 57.374 36.000 0.00 0.00 44.61 4.20
356 1286 7.906611 CTGAGACATAATGAAGTCTAAGTCG 57.093 40.000 0.00 0.00 44.61 4.18
359 1289 7.698628 TCGACTGAGACATAATGAAGTCTAAG 58.301 38.462 5.59 5.59 45.20 2.18
360 1290 7.625828 TCGACTGAGACATAATGAAGTCTAA 57.374 36.000 0.00 0.00 44.61 2.10
361 1291 7.283354 ACATCGACTGAGACATAATGAAGTCTA 59.717 37.037 0.00 0.00 44.61 2.59
363 1293 6.269315 ACATCGACTGAGACATAATGAAGTC 58.731 40.000 0.00 0.00 35.02 3.01
364 1294 6.214191 ACATCGACTGAGACATAATGAAGT 57.786 37.500 0.00 0.00 0.00 3.01
365 1295 6.533012 ACAACATCGACTGAGACATAATGAAG 59.467 38.462 0.00 0.00 0.00 3.02
366 1296 6.398095 ACAACATCGACTGAGACATAATGAA 58.602 36.000 0.00 0.00 0.00 2.57
367 1297 5.965922 ACAACATCGACTGAGACATAATGA 58.034 37.500 0.00 0.00 0.00 2.57
368 1298 7.936950 ATACAACATCGACTGAGACATAATG 57.063 36.000 0.00 0.00 0.00 1.90
369 1299 8.417106 AGAATACAACATCGACTGAGACATAAT 58.583 33.333 0.00 0.00 0.00 1.28
370 1300 7.772166 AGAATACAACATCGACTGAGACATAA 58.228 34.615 0.00 0.00 0.00 1.90
371 1301 7.334844 AGAATACAACATCGACTGAGACATA 57.665 36.000 0.00 0.00 0.00 2.29
372 1302 6.214191 AGAATACAACATCGACTGAGACAT 57.786 37.500 0.00 0.00 0.00 3.06
373 1303 5.644977 AGAATACAACATCGACTGAGACA 57.355 39.130 0.00 0.00 0.00 3.41
374 1304 7.915923 TCAATAGAATACAACATCGACTGAGAC 59.084 37.037 0.00 0.00 0.00 3.36
375 1305 7.996385 TCAATAGAATACAACATCGACTGAGA 58.004 34.615 0.00 0.00 0.00 3.27
376 1306 8.809159 ATCAATAGAATACAACATCGACTGAG 57.191 34.615 0.00 0.00 0.00 3.35
377 1307 8.633561 AGATCAATAGAATACAACATCGACTGA 58.366 33.333 0.00 0.00 0.00 3.41
378 1308 8.809159 AGATCAATAGAATACAACATCGACTG 57.191 34.615 0.00 0.00 0.00 3.51
379 1309 9.254133 CAAGATCAATAGAATACAACATCGACT 57.746 33.333 0.00 0.00 0.00 4.18
380 1310 8.006590 GCAAGATCAATAGAATACAACATCGAC 58.993 37.037 0.00 0.00 0.00 4.20
381 1311 7.710475 TGCAAGATCAATAGAATACAACATCGA 59.290 33.333 0.00 0.00 0.00 3.59
382 1312 7.854534 TGCAAGATCAATAGAATACAACATCG 58.145 34.615 0.00 0.00 0.00 3.84
384 1314 9.961265 CAATGCAAGATCAATAGAATACAACAT 57.039 29.630 0.00 0.00 0.00 2.71
385 1315 9.176460 TCAATGCAAGATCAATAGAATACAACA 57.824 29.630 0.00 0.00 0.00 3.33
386 1316 9.661187 CTCAATGCAAGATCAATAGAATACAAC 57.339 33.333 0.00 0.00 0.00 3.32
387 1317 9.617523 TCTCAATGCAAGATCAATAGAATACAA 57.382 29.630 0.00 0.00 0.00 2.41
388 1318 9.788889 ATCTCAATGCAAGATCAATAGAATACA 57.211 29.630 0.00 0.00 0.00 2.29
391 1321 8.504815 CGAATCTCAATGCAAGATCAATAGAAT 58.495 33.333 0.00 0.00 32.29 2.40
392 1322 7.496920 ACGAATCTCAATGCAAGATCAATAGAA 59.503 33.333 0.00 0.00 32.29 2.10
393 1323 6.988580 ACGAATCTCAATGCAAGATCAATAGA 59.011 34.615 0.00 0.00 32.29 1.98
394 1324 7.187244 ACGAATCTCAATGCAAGATCAATAG 57.813 36.000 0.00 0.00 32.29 1.73
395 1325 7.710475 TGTACGAATCTCAATGCAAGATCAATA 59.290 33.333 0.00 0.00 32.29 1.90
396 1326 6.539826 TGTACGAATCTCAATGCAAGATCAAT 59.460 34.615 0.00 0.00 32.29 2.57
397 1327 5.874261 TGTACGAATCTCAATGCAAGATCAA 59.126 36.000 0.00 0.00 32.29 2.57
398 1328 5.418676 TGTACGAATCTCAATGCAAGATCA 58.581 37.500 0.00 0.00 32.29 2.92
399 1329 5.973651 TGTACGAATCTCAATGCAAGATC 57.026 39.130 0.00 0.00 32.29 2.75
400 1330 6.741992 TTTGTACGAATCTCAATGCAAGAT 57.258 33.333 0.00 0.00 34.96 2.40
401 1331 6.552859 TTTTGTACGAATCTCAATGCAAGA 57.447 33.333 0.00 0.00 0.00 3.02
446 1376 9.613428 CAAGTGATAGTGTATATGGGAAGAAAA 57.387 33.333 0.00 0.00 0.00 2.29
447 1377 8.768397 ACAAGTGATAGTGTATATGGGAAGAAA 58.232 33.333 0.00 0.00 0.00 2.52
448 1378 8.319057 ACAAGTGATAGTGTATATGGGAAGAA 57.681 34.615 0.00 0.00 0.00 2.52
449 1379 7.914427 ACAAGTGATAGTGTATATGGGAAGA 57.086 36.000 0.00 0.00 0.00 2.87
452 1382 9.209048 ACTTAACAAGTGATAGTGTATATGGGA 57.791 33.333 0.00 0.00 41.01 4.37
453 1383 9.477484 GACTTAACAAGTGATAGTGTATATGGG 57.523 37.037 0.00 0.00 43.03 4.00
458 1388 9.026121 ACTGAGACTTAACAAGTGATAGTGTAT 57.974 33.333 0.00 0.00 43.03 2.29
459 1389 8.405418 ACTGAGACTTAACAAGTGATAGTGTA 57.595 34.615 0.00 0.00 43.03 2.90
460 1390 7.291411 ACTGAGACTTAACAAGTGATAGTGT 57.709 36.000 0.00 0.00 43.03 3.55
461 1391 6.524933 CGACTGAGACTTAACAAGTGATAGTG 59.475 42.308 0.00 0.00 43.03 2.74
462 1392 6.430308 TCGACTGAGACTTAACAAGTGATAGT 59.570 38.462 0.00 0.00 43.03 2.12
463 1393 6.743627 GTCGACTGAGACTTAACAAGTGATAG 59.256 42.308 8.70 0.00 43.03 2.08
464 1394 6.609533 GTCGACTGAGACTTAACAAGTGATA 58.390 40.000 8.70 0.00 43.03 2.15
465 1395 5.462405 GTCGACTGAGACTTAACAAGTGAT 58.538 41.667 8.70 0.00 43.03 3.06
466 1396 4.856664 GTCGACTGAGACTTAACAAGTGA 58.143 43.478 8.70 0.00 43.03 3.41
477 1407 5.121925 TGTCTATGTGTTAGTCGACTGAGAC 59.878 44.000 28.12 26.43 41.23 3.36
478 1408 5.121925 GTGTCTATGTGTTAGTCGACTGAGA 59.878 44.000 28.12 15.99 0.00 3.27
479 1409 5.106673 TGTGTCTATGTGTTAGTCGACTGAG 60.107 44.000 28.12 12.44 0.00 3.35
480 1410 4.758165 TGTGTCTATGTGTTAGTCGACTGA 59.242 41.667 28.12 17.78 0.00 3.41
481 1411 4.852104 GTGTGTCTATGTGTTAGTCGACTG 59.148 45.833 28.12 8.61 0.00 3.51
482 1412 4.082895 GGTGTGTCTATGTGTTAGTCGACT 60.083 45.833 23.66 23.66 0.00 4.18
483 1413 4.164294 GGTGTGTCTATGTGTTAGTCGAC 58.836 47.826 7.70 7.70 0.00 4.20
484 1414 3.192001 GGGTGTGTCTATGTGTTAGTCGA 59.808 47.826 0.00 0.00 0.00 4.20
485 1415 3.192844 AGGGTGTGTCTATGTGTTAGTCG 59.807 47.826 0.00 0.00 0.00 4.18
486 1416 4.803098 AGGGTGTGTCTATGTGTTAGTC 57.197 45.455 0.00 0.00 0.00 2.59
487 1417 5.562298 AAAGGGTGTGTCTATGTGTTAGT 57.438 39.130 0.00 0.00 0.00 2.24
488 1418 6.710744 AGAAAAAGGGTGTGTCTATGTGTTAG 59.289 38.462 0.00 0.00 0.00 2.34
489 1419 6.597562 AGAAAAAGGGTGTGTCTATGTGTTA 58.402 36.000 0.00 0.00 0.00 2.41
490 1420 5.445964 AGAAAAAGGGTGTGTCTATGTGTT 58.554 37.500 0.00 0.00 0.00 3.32
491 1421 5.048846 AGAAAAAGGGTGTGTCTATGTGT 57.951 39.130 0.00 0.00 0.00 3.72
492 1422 7.504924 TTAAGAAAAAGGGTGTGTCTATGTG 57.495 36.000 0.00 0.00 0.00 3.21
493 1423 7.724061 ACATTAAGAAAAAGGGTGTGTCTATGT 59.276 33.333 0.00 0.00 0.00 2.29
494 1424 8.023128 CACATTAAGAAAAAGGGTGTGTCTATG 58.977 37.037 0.00 0.00 32.92 2.23
495 1425 7.942341 TCACATTAAGAAAAAGGGTGTGTCTAT 59.058 33.333 0.00 0.00 37.38 1.98
496 1426 7.284074 TCACATTAAGAAAAAGGGTGTGTCTA 58.716 34.615 0.00 0.00 37.38 2.59
497 1427 6.126409 TCACATTAAGAAAAAGGGTGTGTCT 58.874 36.000 0.00 0.00 37.38 3.41
498 1428 6.385649 TCACATTAAGAAAAAGGGTGTGTC 57.614 37.500 0.00 0.00 37.38 3.67
499 1429 6.783708 TTCACATTAAGAAAAAGGGTGTGT 57.216 33.333 0.00 0.00 37.38 3.72
500 1430 6.198216 CGTTTCACATTAAGAAAAAGGGTGTG 59.802 38.462 0.00 0.00 36.80 3.82
501 1431 6.270064 CGTTTCACATTAAGAAAAAGGGTGT 58.730 36.000 0.00 0.00 36.80 4.16
502 1432 5.689961 CCGTTTCACATTAAGAAAAAGGGTG 59.310 40.000 0.00 0.00 36.80 4.61
503 1433 5.595133 TCCGTTTCACATTAAGAAAAAGGGT 59.405 36.000 0.00 0.00 36.80 4.34
504 1434 6.079424 TCCGTTTCACATTAAGAAAAAGGG 57.921 37.500 0.00 0.00 36.80 3.95
505 1435 9.855021 ATATTCCGTTTCACATTAAGAAAAAGG 57.145 29.630 0.00 0.00 36.80 3.11
523 1453 6.996282 CCCAAAACATTACTCCTATATTCCGT 59.004 38.462 0.00 0.00 0.00 4.69
525 1455 6.775629 TGCCCAAAACATTACTCCTATATTCC 59.224 38.462 0.00 0.00 0.00 3.01
528 1458 6.772716 CAGTGCCCAAAACATTACTCCTATAT 59.227 38.462 0.00 0.00 0.00 0.86
532 1462 3.157087 CAGTGCCCAAAACATTACTCCT 58.843 45.455 0.00 0.00 0.00 3.69
533 1463 2.231235 CCAGTGCCCAAAACATTACTCC 59.769 50.000 0.00 0.00 0.00 3.85
534 1464 3.153919 TCCAGTGCCCAAAACATTACTC 58.846 45.455 0.00 0.00 0.00 2.59
535 1465 3.237268 TCCAGTGCCCAAAACATTACT 57.763 42.857 0.00 0.00 0.00 2.24
536 1466 3.763897 AGATCCAGTGCCCAAAACATTAC 59.236 43.478 0.00 0.00 0.00 1.89
538 1468 2.893424 AGATCCAGTGCCCAAAACATT 58.107 42.857 0.00 0.00 0.00 2.71
539 1469 2.610438 AGATCCAGTGCCCAAAACAT 57.390 45.000 0.00 0.00 0.00 2.71
540 1470 2.380064 AAGATCCAGTGCCCAAAACA 57.620 45.000 0.00 0.00 0.00 2.83
541 1471 3.751479 AAAAGATCCAGTGCCCAAAAC 57.249 42.857 0.00 0.00 0.00 2.43
542 1472 4.898861 AGTAAAAAGATCCAGTGCCCAAAA 59.101 37.500 0.00 0.00 0.00 2.44
546 1476 3.628032 GCTAGTAAAAAGATCCAGTGCCC 59.372 47.826 0.00 0.00 0.00 5.36
557 1487 1.664873 GGGGCCGAGCTAGTAAAAAG 58.335 55.000 0.00 0.00 0.00 2.27
558 1488 0.253894 GGGGGCCGAGCTAGTAAAAA 59.746 55.000 0.00 0.00 0.00 1.94
578 1508 1.396653 GACCAGGGATTTGGATGCAG 58.603 55.000 0.00 0.00 40.87 4.41
579 1509 0.033208 GGACCAGGGATTTGGATGCA 60.033 55.000 0.00 0.00 40.87 3.96
580 1510 1.103398 CGGACCAGGGATTTGGATGC 61.103 60.000 0.00 0.00 40.87 3.91
581 1511 1.103398 GCGGACCAGGGATTTGGATG 61.103 60.000 0.00 0.00 40.87 3.51
582 1512 1.227383 GCGGACCAGGGATTTGGAT 59.773 57.895 0.00 0.00 40.87 3.41
583 1513 2.674754 GCGGACCAGGGATTTGGA 59.325 61.111 0.00 0.00 40.87 3.53
584 1514 2.440247 GGCGGACCAGGGATTTGG 60.440 66.667 0.00 0.00 44.09 3.28
585 1515 2.440247 GGGCGGACCAGGGATTTG 60.440 66.667 0.00 0.00 39.85 2.32
586 1516 3.739613 GGGGCGGACCAGGGATTT 61.740 66.667 0.36 0.00 42.91 2.17
587 1517 4.760220 AGGGGCGGACCAGGGATT 62.760 66.667 0.36 0.00 42.91 3.01
591 1521 3.920093 GAAACAGGGGCGGACCAGG 62.920 68.421 0.36 0.00 42.91 4.45
592 1522 2.359975 GAAACAGGGGCGGACCAG 60.360 66.667 0.36 0.00 42.91 4.00
593 1523 4.323477 CGAAACAGGGGCGGACCA 62.323 66.667 0.36 0.00 42.91 4.02
594 1524 3.952628 CTCGAAACAGGGGCGGACC 62.953 68.421 0.00 0.00 39.11 4.46
595 1525 2.434359 CTCGAAACAGGGGCGGAC 60.434 66.667 0.00 0.00 0.00 4.79
596 1526 4.388499 GCTCGAAACAGGGGCGGA 62.388 66.667 0.00 0.00 0.00 5.54
597 1527 3.976701 ATGCTCGAAACAGGGGCGG 62.977 63.158 0.00 0.00 0.00 6.13
598 1528 2.436646 ATGCTCGAAACAGGGGCG 60.437 61.111 0.00 0.00 0.00 6.13
599 1529 2.409870 CCATGCTCGAAACAGGGGC 61.410 63.158 10.20 0.00 35.35 5.80
600 1530 1.002134 ACCATGCTCGAAACAGGGG 60.002 57.895 19.39 12.94 43.21 4.79
601 1531 0.606401 ACACCATGCTCGAAACAGGG 60.606 55.000 15.15 15.15 44.45 4.45
602 1532 0.798776 GACACCATGCTCGAAACAGG 59.201 55.000 0.00 0.00 0.00 4.00
603 1533 1.462283 CAGACACCATGCTCGAAACAG 59.538 52.381 0.00 0.00 0.00 3.16
604 1534 1.511850 CAGACACCATGCTCGAAACA 58.488 50.000 0.00 0.00 0.00 2.83
605 1535 0.166814 GCAGACACCATGCTCGAAAC 59.833 55.000 0.00 0.00 40.59 2.78
606 1536 1.291184 CGCAGACACCATGCTCGAAA 61.291 55.000 0.00 0.00 41.61 3.46
607 1537 1.737735 CGCAGACACCATGCTCGAA 60.738 57.895 0.00 0.00 41.61 3.71
608 1538 2.125952 CGCAGACACCATGCTCGA 60.126 61.111 0.00 0.00 41.61 4.04
609 1539 1.568612 AAACGCAGACACCATGCTCG 61.569 55.000 0.00 0.00 41.61 5.03
610 1540 0.110056 CAAACGCAGACACCATGCTC 60.110 55.000 0.00 0.00 41.61 4.26
650 1580 4.166011 CTAGTTGCCGCAAGCCGC 62.166 66.667 5.91 0.00 42.71 6.53
680 1610 1.154672 CATGAACACAACGACGGCG 60.155 57.895 10.39 10.39 44.79 6.46
684 1614 0.517316 GCCTCCATGAACACAACGAC 59.483 55.000 0.00 0.00 0.00 4.34
714 1676 1.282570 GCAGCTCTCCGATCTCTCG 59.717 63.158 0.00 0.00 44.62 4.04
763 1730 1.831106 TCTCTCTCGCTCTCTGTCTCT 59.169 52.381 0.00 0.00 0.00 3.10
764 1731 2.309528 TCTCTCTCGCTCTCTGTCTC 57.690 55.000 0.00 0.00 0.00 3.36
765 1732 2.092968 ACATCTCTCTCGCTCTCTGTCT 60.093 50.000 0.00 0.00 0.00 3.41
766 1733 2.288666 ACATCTCTCTCGCTCTCTGTC 58.711 52.381 0.00 0.00 0.00 3.51
767 1734 2.418368 ACATCTCTCTCGCTCTCTGT 57.582 50.000 0.00 0.00 0.00 3.41
768 1735 3.781079 AAACATCTCTCTCGCTCTCTG 57.219 47.619 0.00 0.00 0.00 3.35
804 1777 1.915266 TCCACAGGCTCTGGTGGAG 60.915 63.158 18.36 0.00 44.49 3.86
815 1794 2.170607 ACCTTATCCATTCGTCCACAGG 59.829 50.000 0.00 0.00 0.00 4.00
955 1938 2.505982 GGCAGAGGCTTATCCGCA 59.494 61.111 0.00 0.00 40.77 5.69
994 1989 2.124983 CTGAGTGGCCATCGTGGG 60.125 66.667 9.72 0.00 38.19 4.61
997 1992 1.954362 GCTCTCTGAGTGGCCATCGT 61.954 60.000 9.72 0.00 31.39 3.73
1006 2001 2.644212 CCGTGGCTGCTCTCTGAGT 61.644 63.158 4.32 0.00 31.39 3.41
1296 2300 1.645704 CGGAGTCGAAGCTCTTCCGA 61.646 60.000 15.13 7.25 39.00 4.55
1323 2327 3.066814 GCCTTGGAGCAGCCCTTG 61.067 66.667 0.00 0.00 34.97 3.61
1399 2403 7.808381 CGATCCGAGCTTTCTTTCTTGTATATA 59.192 37.037 0.00 0.00 0.00 0.86
1400 2404 6.642950 CGATCCGAGCTTTCTTTCTTGTATAT 59.357 38.462 0.00 0.00 0.00 0.86
1462 2472 1.153369 ACGCACCCCGATCATCAAG 60.153 57.895 0.00 0.00 41.02 3.02
1516 2526 2.358247 TCGCCCTTGCCGAACTTC 60.358 61.111 0.00 0.00 0.00 3.01
1768 2786 4.910585 GCCCCTCCGTACATGCCG 62.911 72.222 0.00 0.00 0.00 5.69
1900 2918 2.713770 CATGCTCACTGATGCGGC 59.286 61.111 0.00 0.00 0.00 6.53
1979 3009 1.317613 AGAAATGCTTGTGCGGTTCA 58.682 45.000 0.00 0.00 43.34 3.18
2053 3087 0.178970 GCCCATCCCTGCAATCAGAT 60.179 55.000 0.00 0.00 42.95 2.90
2054 3088 1.228228 GCCCATCCCTGCAATCAGA 59.772 57.895 0.00 0.00 42.95 3.27
2055 3089 2.191513 CGCCCATCCCTGCAATCAG 61.192 63.158 0.00 0.00 40.02 2.90
2071 3105 4.025145 AGCAAATACTTACTTATTCGCCGC 60.025 41.667 0.00 0.00 0.00 6.53
2119 3160 3.445450 CCGGGTCTGTGATCATATAGGAG 59.555 52.174 0.00 0.00 0.00 3.69
2120 3161 3.431415 CCGGGTCTGTGATCATATAGGA 58.569 50.000 0.00 0.00 0.00 2.94
2122 3163 3.431415 TCCCGGGTCTGTGATCATATAG 58.569 50.000 22.86 0.00 0.00 1.31
2150 3191 6.144724 CGCAGCTAATTACATTTACCTCTCTC 59.855 42.308 0.00 0.00 0.00 3.20
2205 3247 0.034960 AGTCTCCAGTCGCAGCTCTA 60.035 55.000 0.00 0.00 0.00 2.43
2519 3562 9.388346 CGTAAAATAGCAACAGATAAAACACAA 57.612 29.630 0.00 0.00 0.00 3.33
2563 3615 2.135933 CGAGTCCGTTTCAGAGCTTTT 58.864 47.619 0.00 0.00 0.00 2.27
2564 3616 1.340248 TCGAGTCCGTTTCAGAGCTTT 59.660 47.619 0.00 0.00 37.05 3.51
2565 3617 0.959553 TCGAGTCCGTTTCAGAGCTT 59.040 50.000 0.00 0.00 37.05 3.74
2566 3618 0.959553 TTCGAGTCCGTTTCAGAGCT 59.040 50.000 0.00 0.00 37.05 4.09
2567 3619 1.061485 GTTCGAGTCCGTTTCAGAGC 58.939 55.000 0.00 0.00 37.05 4.09
2569 3621 0.316204 GGGTTCGAGTCCGTTTCAGA 59.684 55.000 3.30 0.00 37.05 3.27
2571 3623 0.682852 ATGGGTTCGAGTCCGTTTCA 59.317 50.000 3.30 0.00 37.05 2.69
2572 3624 1.076332 CATGGGTTCGAGTCCGTTTC 58.924 55.000 0.00 0.00 37.05 2.78
2574 3626 1.375523 GCATGGGTTCGAGTCCGTT 60.376 57.895 0.00 0.00 37.05 4.44
2595 3648 1.795170 GCATTGCGGCCGGACATAAT 61.795 55.000 29.38 12.03 0.00 1.28
2602 3655 1.588667 GTTATTGCATTGCGGCCGG 60.589 57.895 29.38 11.47 0.00 6.13
2604 3657 0.108424 TTGGTTATTGCATTGCGGCC 60.108 50.000 3.84 0.00 0.00 6.13
2650 3715 9.137459 CGAGGGAGTGATGTATATATAAGGATT 57.863 37.037 0.00 0.00 0.00 3.01
2653 3718 6.513556 CGCGAGGGAGTGATGTATATATAAGG 60.514 46.154 0.00 0.00 0.00 2.69
2654 3719 6.431278 CGCGAGGGAGTGATGTATATATAAG 58.569 44.000 0.00 0.00 0.00 1.73
2656 3721 4.275196 GCGCGAGGGAGTGATGTATATATA 59.725 45.833 12.10 0.00 0.00 0.86
2657 3722 3.066900 GCGCGAGGGAGTGATGTATATAT 59.933 47.826 12.10 0.00 0.00 0.86
2665 3730 3.622532 TATAGGGCGCGAGGGAGTGAT 62.623 57.143 12.10 0.00 0.00 3.06
2813 3908 1.892391 GCCTAATAGGGTGCACGGC 60.892 63.158 11.45 12.26 35.37 5.68


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

AutoCloner maintained by Alex Coulton.