Multiple sequence alignment - TraesCS5A01G278300

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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 TraesCS5A01G278300 chr5A 100.000 2270 0 0 1 2270 487919645 487917376 0.000000e+00 4193.0
1 TraesCS5A01G278300 chr5A 88.754 907 57 22 854 1742 487925069 487924190 0.000000e+00 1068.0
2 TraesCS5A01G278300 chr5A 86.536 765 64 10 648 1406 487949305 487948574 0.000000e+00 806.0
3 TraesCS5A01G278300 chr5A 82.831 862 68 29 590 1433 487941214 487940415 0.000000e+00 699.0
4 TraesCS5A01G278300 chr5A 94.253 348 16 3 992 1338 488008883 488008539 1.540000e-146 529.0
5 TraesCS5A01G278300 chr5A 83.424 549 57 18 1427 1961 487940195 487939667 1.580000e-131 479.0
6 TraesCS5A01G278300 chr5A 84.314 510 50 15 1475 1961 488008081 488007579 2.640000e-129 472.0
7 TraesCS5A01G278300 chr5A 89.298 299 20 5 298 589 488016754 488017047 4.610000e-97 364.0
8 TraesCS5A01G278300 chr5A 92.641 231 16 1 298 528 487943210 487942981 4.670000e-87 331.0
9 TraesCS5A01G278300 chr5A 86.667 285 28 2 672 946 488009185 488008901 7.880000e-80 307.0
10 TraesCS5A01G278300 chr5A 86.842 266 21 6 1 253 488016484 488016748 3.690000e-73 285.0
11 TraesCS5A01G278300 chr5A 90.385 156 12 2 298 453 487985367 487985215 3.820000e-48 202.0
12 TraesCS5A01G278300 chr5A 84.091 220 17 7 595 808 487925288 487925081 1.780000e-46 196.0
13 TraesCS5A01G278300 chr5A 83.085 201 18 7 56 253 487943403 487943216 3.880000e-38 169.0
14 TraesCS5A01G278300 chr5D 85.027 1683 117 57 328 1966 385979192 385977601 0.000000e+00 1587.0
15 TraesCS5A01G278300 chr5D 84.593 1363 93 58 298 1618 386036553 386035266 0.000000e+00 1245.0
16 TraesCS5A01G278300 chr5D 88.296 675 49 15 672 1338 386067700 386067048 0.000000e+00 782.0
17 TraesCS5A01G278300 chr5D 85.714 679 51 30 771 1433 386058317 386057669 0.000000e+00 675.0
18 TraesCS5A01G278300 chr5D 84.375 512 48 13 1475 1961 386066615 386066111 7.340000e-130 473.0
19 TraesCS5A01G278300 chr5D 86.631 374 32 10 1602 1962 386035243 386034875 4.540000e-107 398.0
20 TraesCS5A01G278300 chr5D 94.298 228 12 1 298 525 386100535 386100761 4.640000e-92 348.0
21 TraesCS5A01G278300 chr5D 88.550 262 18 5 1 250 386100265 386100526 7.880000e-80 307.0
22 TraesCS5A01G278300 chr5D 87.912 273 13 8 1 253 386036831 386036559 1.020000e-78 303.0
23 TraesCS5A01G278300 chr5D 92.308 195 9 2 298 487 386046517 386046324 2.870000e-69 272.0
24 TraesCS5A01G278300 chr5D 86.207 174 15 5 68 232 385979568 385979395 1.790000e-41 180.0
25 TraesCS5A01G278300 chr5D 86.813 91 8 2 2180 2270 385977596 385977510 5.160000e-17 99.0
26 TraesCS5A01G278300 chr5D 100.000 35 0 0 298 332 385979363 385979329 5.230000e-07 65.8
27 TraesCS5A01G278300 chr5B 87.040 1412 105 40 595 1961 463919093 463917715 0.000000e+00 1522.0
28 TraesCS5A01G278300 chr5B 83.210 1078 58 55 405 1445 463912936 463911945 0.000000e+00 874.0
29 TraesCS5A01G278300 chr5B 88.789 669 49 12 672 1338 463945395 463944751 0.000000e+00 797.0
30 TraesCS5A01G278300 chr5B 90.000 550 26 5 1429 1966 463911922 463911390 0.000000e+00 684.0
31 TraesCS5A01G278300 chr5B 87.063 572 45 13 771 1338 463937932 463937386 8.910000e-174 619.0
32 TraesCS5A01G278300 chr5B 85.507 483 45 15 1497 1961 463937376 463936901 4.390000e-132 481.0
33 TraesCS5A01G278300 chr5B 85.714 462 44 10 1475 1919 463944300 463943844 3.410000e-128 468.0
34 TraesCS5A01G278300 chr5B 92.576 229 17 0 297 525 463970114 463970342 1.680000e-86 329.0
35 TraesCS5A01G278300 chr5B 87.597 258 19 6 1 246 463969846 463970102 1.030000e-73 287.0
36 TraesCS5A01G278300 chr5B 90.909 121 9 1 300 420 463920720 463920602 6.490000e-36 161.0
37 TraesCS5A01G278300 chr5B 93.103 58 4 0 418 475 463919274 463919217 4.020000e-13 86.1
38 TraesCS5A01G278300 chr6D 93.642 173 7 3 1967 2136 365597697 365597868 2.890000e-64 255.0
39 TraesCS5A01G278300 chr6D 97.143 35 0 1 2146 2180 365598283 365598316 8.760000e-05 58.4
40 TraesCS5A01G278300 chr6A 93.567 171 9 2 1967 2136 25769026 25769195 1.040000e-63 254.0
41 TraesCS5A01G278300 chr6A 97.143 35 0 1 2146 2180 25769271 25769304 8.760000e-05 58.4
42 TraesCS5A01G278300 chrUn 91.758 182 11 4 1958 2136 61742704 61742524 1.350000e-62 250.0
43 TraesCS5A01G278300 chrUn 97.143 35 0 1 2146 2180 94876894 94876927 8.760000e-05 58.4
44 TraesCS5A01G278300 chr4D 91.758 182 11 4 1958 2136 499897811 499897991 1.350000e-62 250.0
45 TraesCS5A01G278300 chr3D 82.373 295 39 8 299 589 334636850 334637135 6.260000e-61 244.0
46 TraesCS5A01G278300 chr3D 97.143 35 0 1 2146 2180 510649601 510649634 8.760000e-05 58.4
47 TraesCS5A01G278300 chr7A 91.860 172 12 2 1967 2136 692893557 692893386 2.910000e-59 239.0
48 TraesCS5A01G278300 chr4A 91.860 172 11 2 1966 2136 43690484 43690315 1.050000e-58 237.0
49 TraesCS5A01G278300 chr4A 97.143 35 0 1 2146 2180 43690248 43690215 8.760000e-05 58.4
50 TraesCS5A01G278300 chr4A 97.143 35 0 1 2146 2180 514414938 514414905 8.760000e-05 58.4
51 TraesCS5A01G278300 chr4A 97.143 35 0 1 2146 2180 595874351 595874384 8.760000e-05 58.4
52 TraesCS5A01G278300 chr7D 91.228 171 12 2 1967 2136 600897602 600897434 1.750000e-56 230.0
53 TraesCS5A01G278300 chr1D 90.698 172 15 1 1965 2135 471297883 471298054 6.310000e-56 228.0
54 TraesCS5A01G278300 chr1A 90.698 172 15 1 1966 2136 589892756 589892585 6.310000e-56 228.0
55 TraesCS5A01G278300 chr7B 94.286 35 1 1 2146 2180 71072489 71072522 4.000000e-03 52.8


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 TraesCS5A01G278300 chr5A 487917376 487919645 2269 True 4193.000000 4193 100.000000 1 2270 1 chr5A.!!$R1 2269
1 TraesCS5A01G278300 chr5A 487948574 487949305 731 True 806.000000 806 86.536000 648 1406 1 chr5A.!!$R2 758
2 TraesCS5A01G278300 chr5A 487924190 487925288 1098 True 632.000000 1068 86.422500 595 1742 2 chr5A.!!$R4 1147
3 TraesCS5A01G278300 chr5A 488007579 488009185 1606 True 436.000000 529 88.411333 672 1961 3 chr5A.!!$R6 1289
4 TraesCS5A01G278300 chr5A 487939667 487943403 3736 True 419.500000 699 85.495250 56 1961 4 chr5A.!!$R5 1905
5 TraesCS5A01G278300 chr5A 488016484 488017047 563 False 324.500000 364 88.070000 1 589 2 chr5A.!!$F1 588
6 TraesCS5A01G278300 chr5D 386057669 386058317 648 True 675.000000 675 85.714000 771 1433 1 chr5D.!!$R2 662
7 TraesCS5A01G278300 chr5D 386034875 386036831 1956 True 648.666667 1245 86.378667 1 1962 3 chr5D.!!$R4 1961
8 TraesCS5A01G278300 chr5D 386066111 386067700 1589 True 627.500000 782 86.335500 672 1961 2 chr5D.!!$R5 1289
9 TraesCS5A01G278300 chr5D 385977510 385979568 2058 True 482.950000 1587 89.511750 68 2270 4 chr5D.!!$R3 2202
10 TraesCS5A01G278300 chr5B 463911390 463912936 1546 True 779.000000 874 86.605000 405 1966 2 chr5B.!!$R1 1561
11 TraesCS5A01G278300 chr5B 463943844 463945395 1551 True 632.500000 797 87.251500 672 1919 2 chr5B.!!$R4 1247
12 TraesCS5A01G278300 chr5B 463917715 463920720 3005 True 589.700000 1522 90.350667 300 1961 3 chr5B.!!$R2 1661
13 TraesCS5A01G278300 chr5B 463936901 463937932 1031 True 550.000000 619 86.285000 771 1961 2 chr5B.!!$R3 1190

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
276 309 0.034283 TACCCAATTAACCCGCCACC 60.034 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 4710 0.107312 AGGCTAGAACCTGCATGCTG 60.107 55.0 20.33 18.55 39.13 4.41 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
51 52 2.107178 GAGATTACTACCGCGAACGTG 58.893 52.381 8.23 0.62 37.70 4.49
54 55 0.109179 TTACTACCGCGAACGTGCAT 60.109 50.000 8.23 0.00 37.70 3.96
98 103 6.078456 ACATCAAACTGGATCCCAAATCTA 57.922 37.500 9.90 0.00 30.80 1.98
135 140 1.340889 GATTCCAAGCACCAACTTGCA 59.659 47.619 0.00 0.00 45.62 4.08
147 152 3.094572 CCAACTTGCAGGATTGGAATCT 58.905 45.455 18.82 0.00 44.84 2.40
167 186 0.684479 AGGCGGTCTCTACATCAGCA 60.684 55.000 0.00 0.00 0.00 4.41
169 188 0.528684 GCGGTCTCTACATCAGCACC 60.529 60.000 0.00 0.00 0.00 5.01
170 189 0.817654 CGGTCTCTACATCAGCACCA 59.182 55.000 0.00 0.00 30.66 4.17
171 190 1.202348 CGGTCTCTACATCAGCACCAG 60.202 57.143 0.00 0.00 30.66 4.00
226 254 2.484062 CCCAATCCTGATGTGCCGC 61.484 63.158 0.00 0.00 0.00 6.53
246 279 1.731257 GATTCTCTCGGCGCGATCC 60.731 63.158 12.10 0.01 34.61 3.36
253 286 2.049985 CGGCGCGATCCTTCCTAG 60.050 66.667 12.10 0.00 0.00 3.02
254 287 2.356433 GGCGCGATCCTTCCTAGC 60.356 66.667 12.10 0.00 0.00 3.42
255 288 2.731374 GCGCGATCCTTCCTAGCT 59.269 61.111 12.10 0.00 0.00 3.32
256 289 1.524863 GGCGCGATCCTTCCTAGCTA 61.525 60.000 12.10 0.00 0.00 3.32
257 290 0.528470 GCGCGATCCTTCCTAGCTAT 59.472 55.000 12.10 0.00 0.00 2.97
258 291 1.743958 GCGCGATCCTTCCTAGCTATA 59.256 52.381 12.10 0.00 0.00 1.31
259 292 2.478200 GCGCGATCCTTCCTAGCTATAC 60.478 54.545 12.10 0.00 0.00 1.47
260 293 2.097791 CGCGATCCTTCCTAGCTATACC 59.902 54.545 0.00 0.00 0.00 2.73
261 294 2.427812 GCGATCCTTCCTAGCTATACCC 59.572 54.545 0.00 0.00 0.00 3.69
262 295 3.698289 CGATCCTTCCTAGCTATACCCA 58.302 50.000 0.00 0.00 0.00 4.51
263 296 4.087182 CGATCCTTCCTAGCTATACCCAA 58.913 47.826 0.00 0.00 0.00 4.12
264 297 4.712337 CGATCCTTCCTAGCTATACCCAAT 59.288 45.833 0.00 0.00 0.00 3.16
265 298 5.187967 CGATCCTTCCTAGCTATACCCAATT 59.812 44.000 0.00 0.00 0.00 2.32
266 299 6.380274 CGATCCTTCCTAGCTATACCCAATTA 59.620 42.308 0.00 0.00 0.00 1.40
267 300 7.093465 CGATCCTTCCTAGCTATACCCAATTAA 60.093 40.741 0.00 0.00 0.00 1.40
268 301 7.312415 TCCTTCCTAGCTATACCCAATTAAC 57.688 40.000 0.00 0.00 0.00 2.01
269 302 6.271624 TCCTTCCTAGCTATACCCAATTAACC 59.728 42.308 0.00 0.00 0.00 2.85
270 303 6.443995 TTCCTAGCTATACCCAATTAACCC 57.556 41.667 0.00 0.00 0.00 4.11
271 304 4.529377 TCCTAGCTATACCCAATTAACCCG 59.471 45.833 0.00 0.00 0.00 5.28
272 305 3.136009 AGCTATACCCAATTAACCCGC 57.864 47.619 0.00 0.00 0.00 6.13
273 306 2.156917 GCTATACCCAATTAACCCGCC 58.843 52.381 0.00 0.00 0.00 6.13
274 307 2.487625 GCTATACCCAATTAACCCGCCA 60.488 50.000 0.00 0.00 0.00 5.69
275 308 2.061509 ATACCCAATTAACCCGCCAC 57.938 50.000 0.00 0.00 0.00 5.01
276 309 0.034283 TACCCAATTAACCCGCCACC 60.034 55.000 0.00 0.00 0.00 4.61
277 310 2.055633 CCCAATTAACCCGCCACCC 61.056 63.158 0.00 0.00 0.00 4.61
278 311 1.000145 CCAATTAACCCGCCACCCT 60.000 57.895 0.00 0.00 0.00 4.34
279 312 0.613572 CCAATTAACCCGCCACCCTT 60.614 55.000 0.00 0.00 0.00 3.95
280 313 0.530288 CAATTAACCCGCCACCCTTG 59.470 55.000 0.00 0.00 0.00 3.61
281 314 0.113580 AATTAACCCGCCACCCTTGT 59.886 50.000 0.00 0.00 0.00 3.16
282 315 0.323087 ATTAACCCGCCACCCTTGTC 60.323 55.000 0.00 0.00 0.00 3.18
283 316 1.420532 TTAACCCGCCACCCTTGTCT 61.421 55.000 0.00 0.00 0.00 3.41
284 317 1.833787 TAACCCGCCACCCTTGTCTC 61.834 60.000 0.00 0.00 0.00 3.36
285 318 3.636231 CCCGCCACCCTTGTCTCA 61.636 66.667 0.00 0.00 0.00 3.27
286 319 2.429930 CCGCCACCCTTGTCTCAA 59.570 61.111 0.00 0.00 0.00 3.02
287 320 1.228124 CCGCCACCCTTGTCTCAAA 60.228 57.895 0.00 0.00 0.00 2.69
288 321 0.821711 CCGCCACCCTTGTCTCAAAA 60.822 55.000 0.00 0.00 0.00 2.44
289 322 1.028905 CGCCACCCTTGTCTCAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
350 528 5.919755 TCTAGTATCTCGCTCGATCCATAT 58.080 41.667 0.00 0.00 0.00 1.78
376 554 0.512952 CACCGACAAGAAAGGCGAAG 59.487 55.000 0.00 0.00 0.00 3.79
572 3802 3.505464 ACGCTAGCTGTTCGACTTTAT 57.495 42.857 13.93 0.00 0.00 1.40
573 3803 3.846360 ACGCTAGCTGTTCGACTTTATT 58.154 40.909 13.93 0.00 0.00 1.40
574 3804 4.243270 ACGCTAGCTGTTCGACTTTATTT 58.757 39.130 13.93 0.00 0.00 1.40
600 3876 2.756760 TCTTATCGCACCCGTAGAAACT 59.243 45.455 0.00 0.00 35.54 2.66
694 3988 6.037172 GTGGATCAACAAATTATGCGTACTCT 59.963 38.462 0.00 0.00 0.00 3.24
749 4045 3.071874 TCGACATTCCAAAGGAAGCAT 57.928 42.857 4.65 0.00 45.48 3.79
759 4055 2.393271 AAGGAAGCATCTTCGTCCAG 57.607 50.000 2.78 0.00 37.13 3.86
802 4111 2.040278 CCTCACTGACCTTTCAATCCCA 59.960 50.000 0.00 0.00 0.00 4.37
847 4167 4.704833 GAGCGACAAGGCCTGGCA 62.705 66.667 22.05 0.00 28.94 4.92
1193 4538 2.353889 GCCACTACGAGATACTTGACGA 59.646 50.000 0.00 0.00 0.00 4.20
1282 4639 6.392354 GCTTGGAACTGATTCATCAATCAAA 58.608 36.000 0.00 0.00 46.35 2.69
1311 4671 0.324943 AACCCAACCTGATCCTCGTG 59.675 55.000 0.00 0.00 0.00 4.35
1341 4711 9.990360 TGTCTACAATTTATAAGTGTGAAGTCA 57.010 29.630 12.01 5.93 40.31 3.41
1343 4713 9.151471 TCTACAATTTATAAGTGTGAAGTCAGC 57.849 33.333 12.01 0.00 40.31 4.26
1344 4714 7.744087 ACAATTTATAAGTGTGAAGTCAGCA 57.256 32.000 3.73 0.00 38.42 4.41
1345 4715 8.340618 ACAATTTATAAGTGTGAAGTCAGCAT 57.659 30.769 3.73 0.00 38.42 3.79
1352 4724 1.242076 GTGAAGTCAGCATGCAGGTT 58.758 50.000 21.98 9.31 34.76 3.50
1358 4730 0.107508 TCAGCATGCAGGTTCTAGCC 60.108 55.000 21.98 0.00 34.76 3.93
1359 4731 0.107312 CAGCATGCAGGTTCTAGCCT 60.107 55.000 21.98 0.00 39.99 4.58
1403 4799 9.545105 GATCTCAACTCAATCACTTCTCATAAT 57.455 33.333 0.00 0.00 0.00 1.28
1449 5473 6.496338 AGCCTAGCATTTACACAAAACTAC 57.504 37.500 0.00 0.00 0.00 2.73
1469 5493 0.677414 CCAAACAAATGGGGGCATGC 60.677 55.000 9.90 9.90 36.79 4.06
1470 5494 0.036448 CAAACAAATGGGGGCATGCA 59.964 50.000 21.36 0.00 0.00 3.96
1471 5495 0.325602 AAACAAATGGGGGCATGCAG 59.674 50.000 21.36 0.84 0.00 4.41
1472 5496 0.544833 AACAAATGGGGGCATGCAGA 60.545 50.000 21.36 0.00 0.00 4.26
1473 5497 0.325860 ACAAATGGGGGCATGCAGAT 60.326 50.000 21.36 1.98 0.00 2.90
1474 5498 0.105964 CAAATGGGGGCATGCAGATG 59.894 55.000 21.36 4.36 0.00 2.90
1501 5529 8.927721 CATGTTTCTCACATTGAAATGCAAATA 58.072 29.630 2.92 0.00 44.40 1.40
1764 5887 9.538508 GTGTACATAATACTAGGTTTGTAAGGG 57.461 37.037 0.00 0.00 0.00 3.95
1775 5898 3.161866 GTTTGTAAGGGAATCAAGGGCA 58.838 45.455 0.00 0.00 0.00 5.36
1780 5903 1.376649 AGGGAATCAAGGGCACTTCT 58.623 50.000 0.00 0.00 33.81 2.85
1794 5917 2.594321 CACTTCTTCTCTCAGACGCTG 58.406 52.381 1.02 1.02 0.00 5.18
1913 6047 6.939730 TGAACTTGTGCTTGGTAGAATATTCA 59.060 34.615 17.56 1.25 0.00 2.57
1966 6108 7.644551 TGTTTACGGTTGCACTTTACAATTTAG 59.355 33.333 0.00 0.00 0.00 1.85
1967 6109 7.493743 TTACGGTTGCACTTTACAATTTAGA 57.506 32.000 0.00 0.00 0.00 2.10
1968 6110 5.997385 ACGGTTGCACTTTACAATTTAGAG 58.003 37.500 0.00 0.00 0.00 2.43
1969 6111 5.761234 ACGGTTGCACTTTACAATTTAGAGA 59.239 36.000 0.00 0.00 0.00 3.10
1970 6112 6.073222 ACGGTTGCACTTTACAATTTAGAGAG 60.073 38.462 0.00 0.00 0.00 3.20
1971 6113 6.073222 CGGTTGCACTTTACAATTTAGAGAGT 60.073 38.462 0.00 0.00 0.00 3.24
1972 6114 7.078228 GGTTGCACTTTACAATTTAGAGAGTG 58.922 38.462 0.00 0.00 36.88 3.51
1973 6115 6.801539 TGCACTTTACAATTTAGAGAGTGG 57.198 37.500 0.00 0.00 34.98 4.00
1974 6116 6.296026 TGCACTTTACAATTTAGAGAGTGGT 58.704 36.000 0.00 0.00 34.98 4.16
1975 6117 6.770785 TGCACTTTACAATTTAGAGAGTGGTT 59.229 34.615 0.00 0.00 34.98 3.67
1976 6118 7.284489 TGCACTTTACAATTTAGAGAGTGGTTT 59.716 33.333 0.00 0.00 34.98 3.27
1977 6119 8.135529 GCACTTTACAATTTAGAGAGTGGTTTT 58.864 33.333 0.00 0.00 34.98 2.43
1983 6125 8.974060 ACAATTTAGAGAGTGGTTTTTCTACA 57.026 30.769 0.00 0.00 0.00 2.74
1984 6126 8.837389 ACAATTTAGAGAGTGGTTTTTCTACAC 58.163 33.333 0.00 0.00 35.43 2.90
1985 6127 7.981102 ATTTAGAGAGTGGTTTTTCTACACC 57.019 36.000 0.00 0.00 35.79 4.16
1986 6128 4.353383 AGAGAGTGGTTTTTCTACACCC 57.647 45.455 0.00 0.00 35.79 4.61
1987 6129 3.714798 AGAGAGTGGTTTTTCTACACCCA 59.285 43.478 0.00 0.00 35.79 4.51
1988 6130 3.813724 GAGAGTGGTTTTTCTACACCCAC 59.186 47.826 0.00 0.00 44.69 4.61
1989 6131 2.882761 GAGTGGTTTTTCTACACCCACC 59.117 50.000 0.00 0.00 45.31 4.61
1990 6132 1.958579 GTGGTTTTTCTACACCCACCC 59.041 52.381 0.00 0.00 39.71 4.61
1991 6133 1.854280 TGGTTTTTCTACACCCACCCT 59.146 47.619 0.00 0.00 31.24 4.34
1992 6134 2.245287 TGGTTTTTCTACACCCACCCTT 59.755 45.455 0.00 0.00 31.24 3.95
1993 6135 2.626266 GGTTTTTCTACACCCACCCTTG 59.374 50.000 0.00 0.00 0.00 3.61
1994 6136 2.626266 GTTTTTCTACACCCACCCTTGG 59.374 50.000 0.00 0.00 43.50 3.61
1995 6137 1.525175 TTTCTACACCCACCCTTGGT 58.475 50.000 0.00 0.00 42.10 3.67
2014 6156 1.189752 TGCACCCAAGCAAGAAAACA 58.810 45.000 0.00 0.00 42.46 2.83
2015 6157 1.761784 TGCACCCAAGCAAGAAAACAT 59.238 42.857 0.00 0.00 42.46 2.71
2016 6158 2.961741 TGCACCCAAGCAAGAAAACATA 59.038 40.909 0.00 0.00 42.46 2.29
2017 6159 3.243704 TGCACCCAAGCAAGAAAACATAC 60.244 43.478 0.00 0.00 42.46 2.39
2018 6160 3.860754 GCACCCAAGCAAGAAAACATACC 60.861 47.826 0.00 0.00 0.00 2.73
2019 6161 3.320541 CACCCAAGCAAGAAAACATACCA 59.679 43.478 0.00 0.00 0.00 3.25
2020 6162 3.964031 ACCCAAGCAAGAAAACATACCAA 59.036 39.130 0.00 0.00 0.00 3.67
2021 6163 4.407296 ACCCAAGCAAGAAAACATACCAAA 59.593 37.500 0.00 0.00 0.00 3.28
2022 6164 5.104735 ACCCAAGCAAGAAAACATACCAAAA 60.105 36.000 0.00 0.00 0.00 2.44
2023 6165 5.236263 CCCAAGCAAGAAAACATACCAAAAC 59.764 40.000 0.00 0.00 0.00 2.43
2024 6166 5.814705 CCAAGCAAGAAAACATACCAAAACA 59.185 36.000 0.00 0.00 0.00 2.83
2025 6167 6.482973 CCAAGCAAGAAAACATACCAAAACAT 59.517 34.615 0.00 0.00 0.00 2.71
2026 6168 7.012232 CCAAGCAAGAAAACATACCAAAACATT 59.988 33.333 0.00 0.00 0.00 2.71
2027 6169 8.397148 CAAGCAAGAAAACATACCAAAACATTT 58.603 29.630 0.00 0.00 0.00 2.32
2028 6170 8.504812 AGCAAGAAAACATACCAAAACATTTT 57.495 26.923 0.00 0.00 0.00 1.82
2029 6171 8.397148 AGCAAGAAAACATACCAAAACATTTTG 58.603 29.630 9.66 9.66 45.34 2.44
2053 6195 5.612725 AAAAATCTGAAGCTTTGTGGGAA 57.387 34.783 0.00 0.00 0.00 3.97
2054 6196 5.813513 AAAATCTGAAGCTTTGTGGGAAT 57.186 34.783 0.00 0.00 0.00 3.01
2055 6197 4.796038 AATCTGAAGCTTTGTGGGAATG 57.204 40.909 0.00 0.00 0.00 2.67
2056 6198 3.507162 TCTGAAGCTTTGTGGGAATGA 57.493 42.857 0.00 0.00 0.00 2.57
2057 6199 4.038271 TCTGAAGCTTTGTGGGAATGAT 57.962 40.909 0.00 0.00 0.00 2.45
2058 6200 4.012374 TCTGAAGCTTTGTGGGAATGATC 58.988 43.478 0.00 0.00 0.00 2.92
2059 6201 3.760151 CTGAAGCTTTGTGGGAATGATCA 59.240 43.478 0.00 0.00 0.00 2.92
2060 6202 4.346730 TGAAGCTTTGTGGGAATGATCAT 58.653 39.130 1.18 1.18 0.00 2.45
2061 6203 4.400251 TGAAGCTTTGTGGGAATGATCATC 59.600 41.667 9.06 2.77 0.00 2.92
2062 6204 4.246712 AGCTTTGTGGGAATGATCATCT 57.753 40.909 9.06 0.00 0.00 2.90
2063 6205 5.378230 AGCTTTGTGGGAATGATCATCTA 57.622 39.130 9.06 0.00 0.00 1.98
2064 6206 5.128919 AGCTTTGTGGGAATGATCATCTAC 58.871 41.667 9.06 6.32 0.00 2.59
2065 6207 4.883585 GCTTTGTGGGAATGATCATCTACA 59.116 41.667 9.06 8.93 0.00 2.74
2066 6208 5.357878 GCTTTGTGGGAATGATCATCTACAA 59.642 40.000 17.16 17.16 0.00 2.41
2067 6209 6.040166 GCTTTGTGGGAATGATCATCTACAAT 59.960 38.462 19.99 1.83 0.00 2.71
2068 6210 6.947644 TTGTGGGAATGATCATCTACAATG 57.052 37.500 17.16 0.00 0.00 2.82
2069 6211 6.005066 TGTGGGAATGATCATCTACAATGT 57.995 37.500 9.06 0.00 0.00 2.71
2070 6212 6.425735 TGTGGGAATGATCATCTACAATGTT 58.574 36.000 9.06 0.00 0.00 2.71
2071 6213 7.572814 TGTGGGAATGATCATCTACAATGTTA 58.427 34.615 9.06 0.00 0.00 2.41
2072 6214 7.716560 TGTGGGAATGATCATCTACAATGTTAG 59.283 37.037 9.06 0.00 0.00 2.34
2073 6215 7.933577 GTGGGAATGATCATCTACAATGTTAGA 59.066 37.037 9.06 0.00 0.00 2.10
2074 6216 8.152898 TGGGAATGATCATCTACAATGTTAGAG 58.847 37.037 9.06 0.00 0.00 2.43
2075 6217 8.370940 GGGAATGATCATCTACAATGTTAGAGA 58.629 37.037 9.06 0.00 0.00 3.10
2076 6218 9.421806 GGAATGATCATCTACAATGTTAGAGAG 57.578 37.037 9.06 0.00 0.00 3.20
2077 6219 9.421806 GAATGATCATCTACAATGTTAGAGAGG 57.578 37.037 9.06 0.00 0.00 3.69
2078 6220 6.753180 TGATCATCTACAATGTTAGAGAGGC 58.247 40.000 0.00 0.00 0.00 4.70
2079 6221 6.552725 TGATCATCTACAATGTTAGAGAGGCT 59.447 38.462 0.00 0.00 0.00 4.58
2080 6222 6.798427 TCATCTACAATGTTAGAGAGGCTT 57.202 37.500 0.00 0.00 0.00 4.35
2081 6223 6.577103 TCATCTACAATGTTAGAGAGGCTTG 58.423 40.000 0.00 0.00 0.00 4.01
2082 6224 4.759782 TCTACAATGTTAGAGAGGCTTGC 58.240 43.478 0.00 0.00 0.00 4.01
2083 6225 3.423539 ACAATGTTAGAGAGGCTTGCA 57.576 42.857 0.00 0.00 0.00 4.08
2084 6226 3.754965 ACAATGTTAGAGAGGCTTGCAA 58.245 40.909 0.00 0.00 0.00 4.08
2085 6227 4.144297 ACAATGTTAGAGAGGCTTGCAAA 58.856 39.130 0.00 0.00 0.00 3.68
2086 6228 4.768968 ACAATGTTAGAGAGGCTTGCAAAT 59.231 37.500 0.00 0.00 0.00 2.32
2087 6229 5.244626 ACAATGTTAGAGAGGCTTGCAAATT 59.755 36.000 0.00 0.00 0.00 1.82
2088 6230 5.990120 ATGTTAGAGAGGCTTGCAAATTT 57.010 34.783 0.00 0.00 0.00 1.82
2089 6231 5.789643 TGTTAGAGAGGCTTGCAAATTTT 57.210 34.783 0.00 0.00 0.00 1.82
2090 6232 5.772521 TGTTAGAGAGGCTTGCAAATTTTC 58.227 37.500 0.00 0.00 0.00 2.29
2091 6233 3.565905 AGAGAGGCTTGCAAATTTTCG 57.434 42.857 0.00 0.00 0.00 3.46
2092 6234 2.887152 AGAGAGGCTTGCAAATTTTCGT 59.113 40.909 0.00 0.00 0.00 3.85
2093 6235 2.982470 GAGAGGCTTGCAAATTTTCGTG 59.018 45.455 0.00 0.00 0.00 4.35
2094 6236 2.061028 GAGGCTTGCAAATTTTCGTGG 58.939 47.619 0.00 0.00 0.00 4.94
2095 6237 1.412343 AGGCTTGCAAATTTTCGTGGT 59.588 42.857 0.00 0.00 0.00 4.16
2096 6238 1.792367 GGCTTGCAAATTTTCGTGGTC 59.208 47.619 0.00 0.00 0.00 4.02
2097 6239 2.468831 GCTTGCAAATTTTCGTGGTCA 58.531 42.857 0.00 0.00 0.00 4.02
2098 6240 2.863137 GCTTGCAAATTTTCGTGGTCAA 59.137 40.909 0.00 0.00 0.00 3.18
2099 6241 3.308323 GCTTGCAAATTTTCGTGGTCAAA 59.692 39.130 0.00 0.00 0.00 2.69
2100 6242 4.024977 GCTTGCAAATTTTCGTGGTCAAAT 60.025 37.500 0.00 0.00 0.00 2.32
2101 6243 5.401033 TTGCAAATTTTCGTGGTCAAATG 57.599 34.783 0.00 0.00 0.00 2.32
2102 6244 4.686972 TGCAAATTTTCGTGGTCAAATGA 58.313 34.783 0.00 0.00 0.00 2.57
2103 6245 4.505922 TGCAAATTTTCGTGGTCAAATGAC 59.494 37.500 4.96 4.96 44.04 3.06
2104 6246 4.505922 GCAAATTTTCGTGGTCAAATGACA 59.494 37.500 14.93 0.00 46.47 3.58
2105 6247 5.177327 GCAAATTTTCGTGGTCAAATGACAT 59.823 36.000 14.93 0.00 46.47 3.06
2106 6248 6.616260 GCAAATTTTCGTGGTCAAATGACATC 60.616 38.462 14.93 6.53 46.47 3.06
2107 6249 4.497473 TTTTCGTGGTCAAATGACATCC 57.503 40.909 14.93 0.00 46.47 3.51
2108 6250 1.720805 TCGTGGTCAAATGACATCCG 58.279 50.000 14.93 12.41 46.47 4.18
2109 6251 1.273886 TCGTGGTCAAATGACATCCGA 59.726 47.619 14.93 14.19 46.47 4.55
2110 6252 1.660607 CGTGGTCAAATGACATCCGAG 59.339 52.381 14.93 0.00 46.47 4.63
2111 6253 2.009774 GTGGTCAAATGACATCCGAGG 58.990 52.381 14.93 0.00 46.47 4.63
2112 6254 1.905894 TGGTCAAATGACATCCGAGGA 59.094 47.619 14.93 0.00 46.47 3.71
2113 6255 2.093500 TGGTCAAATGACATCCGAGGAG 60.093 50.000 14.93 0.00 46.47 3.69
2114 6256 1.936547 GTCAAATGACATCCGAGGAGC 59.063 52.381 8.63 0.00 44.18 4.70
2115 6257 1.833630 TCAAATGACATCCGAGGAGCT 59.166 47.619 0.00 0.00 0.00 4.09
2116 6258 2.159043 TCAAATGACATCCGAGGAGCTC 60.159 50.000 4.71 4.71 0.00 4.09
2117 6259 1.786937 AATGACATCCGAGGAGCTCT 58.213 50.000 14.64 0.00 0.00 4.09
2118 6260 2.666272 ATGACATCCGAGGAGCTCTA 57.334 50.000 14.64 0.00 0.00 2.43
2119 6261 2.666272 TGACATCCGAGGAGCTCTAT 57.334 50.000 14.64 2.26 0.00 1.98
2120 6262 3.790089 TGACATCCGAGGAGCTCTATA 57.210 47.619 14.64 0.00 0.00 1.31
2121 6263 4.308526 TGACATCCGAGGAGCTCTATAT 57.691 45.455 14.64 0.00 0.00 0.86
2122 6264 5.437191 TGACATCCGAGGAGCTCTATATA 57.563 43.478 14.64 0.00 0.00 0.86
2123 6265 5.816682 TGACATCCGAGGAGCTCTATATAA 58.183 41.667 14.64 0.00 0.00 0.98
2124 6266 6.246163 TGACATCCGAGGAGCTCTATATAAA 58.754 40.000 14.64 0.00 0.00 1.40
2125 6267 6.719829 TGACATCCGAGGAGCTCTATATAAAA 59.280 38.462 14.64 0.00 0.00 1.52
2126 6268 7.232737 TGACATCCGAGGAGCTCTATATAAAAA 59.767 37.037 14.64 0.00 0.00 1.94
2156 6298 5.885449 ATGAAATTTTCTTTGGACCACCA 57.115 34.783 10.33 0.00 45.34 4.17
2157 6299 6.657875 AATGAAATTTTCTTTGGACCACCAA 58.342 32.000 10.33 0.00 43.97 3.67
2159 6301 7.066887 AATGAAATTTTCTTTGGACCACCAAAC 59.933 33.333 9.88 0.57 46.65 2.93
2172 6314 2.737503 CCAAACTTGGCAAGCCTCT 58.262 52.632 26.45 4.61 42.21 3.69
2173 6315 0.600057 CCAAACTTGGCAAGCCTCTC 59.400 55.000 26.45 0.00 42.21 3.20
2174 6316 1.613836 CAAACTTGGCAAGCCTCTCT 58.386 50.000 26.45 3.41 36.94 3.10
2175 6317 2.553028 CCAAACTTGGCAAGCCTCTCTA 60.553 50.000 26.45 0.00 42.21 2.43
2176 6318 3.149196 CAAACTTGGCAAGCCTCTCTAA 58.851 45.455 26.45 0.00 36.94 2.10
2177 6319 2.481289 ACTTGGCAAGCCTCTCTAAC 57.519 50.000 26.45 0.00 36.94 2.34
2178 6320 1.699634 ACTTGGCAAGCCTCTCTAACA 59.300 47.619 26.45 0.00 36.94 2.41
2195 6337 6.209589 TCTCTAACATATCGATCCCTTTGGAG 59.790 42.308 0.00 8.35 46.08 3.86
2196 6338 6.075315 TCTAACATATCGATCCCTTTGGAGA 58.925 40.000 0.00 0.00 46.08 3.71
2201 6343 6.043706 ACATATCGATCCCTTTGGAGAAAGAT 59.956 38.462 0.00 0.00 46.08 2.40
2209 6351 4.195416 CCTTTGGAGAAAGATGGAGTAGC 58.805 47.826 0.00 0.00 41.12 3.58
2211 6353 5.129485 CCTTTGGAGAAAGATGGAGTAGCTA 59.871 44.000 0.00 0.00 41.12 3.32
2212 6354 5.860941 TTGGAGAAAGATGGAGTAGCTAG 57.139 43.478 0.00 0.00 0.00 3.42
2213 6355 3.639094 TGGAGAAAGATGGAGTAGCTAGC 59.361 47.826 6.62 6.62 0.00 3.42
2214 6356 3.895041 GGAGAAAGATGGAGTAGCTAGCT 59.105 47.826 23.12 23.12 0.00 3.32
2215 6357 5.074115 GGAGAAAGATGGAGTAGCTAGCTA 58.926 45.833 20.67 20.67 0.00 3.32
2216 6358 5.183140 GGAGAAAGATGGAGTAGCTAGCTAG 59.817 48.000 24.78 16.84 0.00 3.42
2225 6367 4.939439 GGAGTAGCTAGCTAGGAGTATGAC 59.061 50.000 24.78 12.19 0.00 3.06
2254 6396 5.187772 TGGCATCTGATAACTTGTGTACTCT 59.812 40.000 0.00 0.00 0.00 3.24
2257 6399 7.038659 GCATCTGATAACTTGTGTACTCTCTT 58.961 38.462 0.00 0.00 0.00 2.85
2259 6401 7.761038 TCTGATAACTTGTGTACTCTCTTCA 57.239 36.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 103 3.054065 GGAATCTGAGAGGTTCCATTGGT 60.054 47.826 10.26 0.00 40.82 3.67
122 127 0.963962 CAATCCTGCAAGTTGGTGCT 59.036 50.000 4.75 0.00 45.17 4.40
135 140 1.694696 GACCGCCTAGATTCCAATCCT 59.305 52.381 0.00 0.00 36.04 3.24
147 152 1.319541 GCTGATGTAGAGACCGCCTA 58.680 55.000 0.00 0.00 0.00 3.93
167 186 5.357032 CGGAAAAGGAGTAAATATTGCTGGT 59.643 40.000 0.00 0.00 0.00 4.00
169 188 5.163663 TGCGGAAAAGGAGTAAATATTGCTG 60.164 40.000 0.00 0.00 0.00 4.41
170 189 4.947388 TGCGGAAAAGGAGTAAATATTGCT 59.053 37.500 0.00 0.00 0.00 3.91
171 190 5.243426 TGCGGAAAAGGAGTAAATATTGC 57.757 39.130 0.00 0.00 0.00 3.56
240 273 2.427812 GGGTATAGCTAGGAAGGATCGC 59.572 54.545 0.00 0.00 0.00 4.58
246 279 6.473758 GGGTTAATTGGGTATAGCTAGGAAG 58.526 44.000 0.00 0.00 0.00 3.46
253 286 2.156917 GGCGGGTTAATTGGGTATAGC 58.843 52.381 0.00 0.00 0.00 2.97
254 287 3.143728 GTGGCGGGTTAATTGGGTATAG 58.856 50.000 0.00 0.00 0.00 1.31
255 288 2.158638 GGTGGCGGGTTAATTGGGTATA 60.159 50.000 0.00 0.00 0.00 1.47
256 289 1.410507 GGTGGCGGGTTAATTGGGTAT 60.411 52.381 0.00 0.00 0.00 2.73
257 290 0.034283 GGTGGCGGGTTAATTGGGTA 60.034 55.000 0.00 0.00 0.00 3.69
258 291 1.304630 GGTGGCGGGTTAATTGGGT 60.305 57.895 0.00 0.00 0.00 4.51
259 292 2.055633 GGGTGGCGGGTTAATTGGG 61.056 63.158 0.00 0.00 0.00 4.12
260 293 0.613572 AAGGGTGGCGGGTTAATTGG 60.614 55.000 0.00 0.00 0.00 3.16
261 294 0.530288 CAAGGGTGGCGGGTTAATTG 59.470 55.000 0.00 0.00 0.00 2.32
262 295 0.113580 ACAAGGGTGGCGGGTTAATT 59.886 50.000 0.00 0.00 0.00 1.40
263 296 0.323087 GACAAGGGTGGCGGGTTAAT 60.323 55.000 0.00 0.00 0.00 1.40
264 297 1.073548 GACAAGGGTGGCGGGTTAA 59.926 57.895 0.00 0.00 0.00 2.01
265 298 1.833787 GAGACAAGGGTGGCGGGTTA 61.834 60.000 0.00 0.00 38.10 2.85
266 299 3.175710 AGACAAGGGTGGCGGGTT 61.176 61.111 0.00 0.00 38.10 4.11
267 300 3.637273 GAGACAAGGGTGGCGGGT 61.637 66.667 0.00 0.00 38.10 5.28
268 301 2.690653 TTTGAGACAAGGGTGGCGGG 62.691 60.000 0.00 0.00 38.10 6.13
269 302 0.821711 TTTTGAGACAAGGGTGGCGG 60.822 55.000 0.00 0.00 38.10 6.13
270 303 1.028905 TTTTTGAGACAAGGGTGGCG 58.971 50.000 0.00 0.00 38.10 5.69
293 326 1.605451 GCTAGGGTGGCGGGTTTTT 60.605 57.895 0.00 0.00 0.00 1.94
294 327 1.202769 TAGCTAGGGTGGCGGGTTTT 61.203 55.000 0.00 0.00 34.52 2.43
295 328 1.614226 TAGCTAGGGTGGCGGGTTT 60.614 57.895 0.00 0.00 34.52 3.27
296 329 2.039951 TAGCTAGGGTGGCGGGTT 59.960 61.111 0.00 0.00 34.52 4.11
376 554 0.682209 ATCAGGGCCACATGCAGAAC 60.682 55.000 6.18 0.00 43.89 3.01
534 2049 1.227823 TTTGGCCACTCACCAGTCG 60.228 57.895 3.88 0.00 38.73 4.18
572 3802 3.340034 ACGGGTGCGATAAGATTCAAAA 58.660 40.909 0.00 0.00 0.00 2.44
573 3803 2.980568 ACGGGTGCGATAAGATTCAAA 58.019 42.857 0.00 0.00 0.00 2.69
574 3804 2.684001 ACGGGTGCGATAAGATTCAA 57.316 45.000 0.00 0.00 0.00 2.69
600 3876 3.016031 TGAACTTGCAGCAAAGAGTCAA 58.984 40.909 9.65 0.00 0.00 3.18
694 3988 1.017177 GCGCTTGGGACGACACATAA 61.017 55.000 0.00 0.00 0.00 1.90
731 4027 4.437930 CGAAGATGCTTCCTTTGGAATGTC 60.438 45.833 0.00 0.00 41.23 3.06
749 4045 4.665833 TCTGAACTTTTCTGGACGAAGA 57.334 40.909 0.00 0.00 32.21 2.87
759 4055 9.167311 TGAGGCTAATTAGATTCTGAACTTTTC 57.833 33.333 16.85 0.00 0.00 2.29
1116 4461 2.429930 CGGGACACCTTGAGCCAA 59.570 61.111 0.00 0.00 33.28 4.52
1146 4491 1.592400 CCTCGTCAGCCGTCTTGGTA 61.592 60.000 0.00 0.00 41.21 3.25
1193 4538 1.474478 ACTCGATCAGCTTGATGTCGT 59.526 47.619 3.76 0.00 37.20 4.34
1282 4639 2.245287 TCAGGTTGGGTTTTGGTTACCT 59.755 45.455 2.07 0.00 36.47 3.08
1340 4710 0.107312 AGGCTAGAACCTGCATGCTG 60.107 55.000 20.33 18.55 39.13 4.41
1341 4711 1.500474 TAGGCTAGAACCTGCATGCT 58.500 50.000 20.33 0.00 41.34 3.79
1342 4712 2.332063 TTAGGCTAGAACCTGCATGC 57.668 50.000 11.82 11.82 41.34 4.06
1343 4713 2.615912 GCTTTAGGCTAGAACCTGCATG 59.384 50.000 0.00 0.00 41.34 4.06
1344 4714 2.924421 GCTTTAGGCTAGAACCTGCAT 58.076 47.619 0.00 0.00 41.34 3.96
1345 4715 2.403252 GCTTTAGGCTAGAACCTGCA 57.597 50.000 0.00 0.00 41.34 4.41
1403 4799 5.362105 AGGGCATGGTCTAACGTTATTAA 57.638 39.130 8.76 0.00 0.00 1.40
1477 5501 9.142515 GATATTTGCATTTCAATGTGAGAAACA 57.857 29.630 1.59 0.00 44.79 2.83
1478 5502 9.142515 TGATATTTGCATTTCAATGTGAGAAAC 57.857 29.630 1.59 0.00 37.76 2.78
1501 5529 7.615365 TCAAATTTAGAACTGGGCTACATTGAT 59.385 33.333 0.00 0.00 0.00 2.57
1623 5715 6.206243 CAGCCAAGGATTAGATTATCAACAGG 59.794 42.308 0.00 0.00 0.00 4.00
1638 5743 1.838611 ATATGGTCCCAGCCAAGGAT 58.161 50.000 0.00 0.00 42.48 3.24
1764 5887 3.938334 GAGAGAAGAAGTGCCCTTGATTC 59.062 47.826 0.00 0.00 0.00 2.52
1775 5898 1.543802 CCAGCGTCTGAGAGAAGAAGT 59.456 52.381 8.20 0.00 32.44 3.01
1780 5903 0.108472 CATGCCAGCGTCTGAGAGAA 60.108 55.000 8.20 0.00 32.44 2.87
1794 5917 8.243426 TGAGTTACAGAATGAAAAATACATGCC 58.757 33.333 0.00 0.00 39.69 4.40
1858 5988 2.912956 ACACACAAGTACAGGGGATGAT 59.087 45.455 0.00 0.00 0.00 2.45
1859 5989 2.334977 ACACACAAGTACAGGGGATGA 58.665 47.619 0.00 0.00 0.00 2.92
1860 5990 2.859165 ACACACAAGTACAGGGGATG 57.141 50.000 0.00 0.00 0.00 3.51
1913 6047 7.824289 TCCGAATCTTGAAGATAGACAAAACAT 59.176 33.333 8.30 0.00 32.89 2.71
1966 6108 3.813724 GTGGGTGTAGAAAAACCACTCTC 59.186 47.826 3.37 0.00 46.12 3.20
1967 6109 3.816994 GTGGGTGTAGAAAAACCACTCT 58.183 45.455 3.37 0.00 46.12 3.24
1971 6113 1.854280 AGGGTGGGTGTAGAAAAACCA 59.146 47.619 0.00 0.00 38.27 3.67
1972 6114 2.626266 CAAGGGTGGGTGTAGAAAAACC 59.374 50.000 0.00 0.00 35.59 3.27
1973 6115 2.626266 CCAAGGGTGGGTGTAGAAAAAC 59.374 50.000 0.00 0.00 41.77 2.43
1974 6116 2.952116 CCAAGGGTGGGTGTAGAAAAA 58.048 47.619 0.00 0.00 41.77 1.94
1975 6117 2.668144 CCAAGGGTGGGTGTAGAAAA 57.332 50.000 0.00 0.00 41.77 2.29
1993 6135 0.463620 TTTTCTTGCTTGGGTGCACC 59.536 50.000 28.57 28.57 43.20 5.01
1994 6136 1.134848 TGTTTTCTTGCTTGGGTGCAC 60.135 47.619 8.80 8.80 43.20 4.57
1995 6137 1.189752 TGTTTTCTTGCTTGGGTGCA 58.810 45.000 0.00 0.00 41.65 4.57
1996 6138 2.531522 ATGTTTTCTTGCTTGGGTGC 57.468 45.000 0.00 0.00 0.00 5.01
1997 6139 3.320541 TGGTATGTTTTCTTGCTTGGGTG 59.679 43.478 0.00 0.00 0.00 4.61
1998 6140 3.571590 TGGTATGTTTTCTTGCTTGGGT 58.428 40.909 0.00 0.00 0.00 4.51
1999 6141 4.599047 TTGGTATGTTTTCTTGCTTGGG 57.401 40.909 0.00 0.00 0.00 4.12
2000 6142 5.814705 TGTTTTGGTATGTTTTCTTGCTTGG 59.185 36.000 0.00 0.00 0.00 3.61
2001 6143 6.900568 TGTTTTGGTATGTTTTCTTGCTTG 57.099 33.333 0.00 0.00 0.00 4.01
2002 6144 8.504812 AAATGTTTTGGTATGTTTTCTTGCTT 57.495 26.923 0.00 0.00 0.00 3.91
2003 6145 8.397148 CAAAATGTTTTGGTATGTTTTCTTGCT 58.603 29.630 9.75 0.00 42.81 3.91
2004 6146 8.394121 TCAAAATGTTTTGGTATGTTTTCTTGC 58.606 29.630 15.84 0.00 45.68 4.01
2031 6173 5.612725 TTCCCACAAAGCTTCAGATTTTT 57.387 34.783 0.00 0.00 30.39 1.94
2032 6174 5.305128 TCATTCCCACAAAGCTTCAGATTTT 59.695 36.000 0.00 0.00 30.39 1.82
2033 6175 4.834496 TCATTCCCACAAAGCTTCAGATTT 59.166 37.500 0.00 0.00 33.44 2.17
2034 6176 4.410099 TCATTCCCACAAAGCTTCAGATT 58.590 39.130 0.00 0.00 0.00 2.40
2035 6177 4.038271 TCATTCCCACAAAGCTTCAGAT 57.962 40.909 0.00 0.00 0.00 2.90
2036 6178 3.507162 TCATTCCCACAAAGCTTCAGA 57.493 42.857 0.00 0.00 0.00 3.27
2037 6179 3.760151 TGATCATTCCCACAAAGCTTCAG 59.240 43.478 0.00 0.00 0.00 3.02
2038 6180 3.765381 TGATCATTCCCACAAAGCTTCA 58.235 40.909 0.00 0.00 0.00 3.02
2039 6181 4.643784 AGATGATCATTCCCACAAAGCTTC 59.356 41.667 10.14 0.00 0.00 3.86
2040 6182 4.607239 AGATGATCATTCCCACAAAGCTT 58.393 39.130 10.14 0.00 0.00 3.74
2041 6183 4.246712 AGATGATCATTCCCACAAAGCT 57.753 40.909 10.14 0.00 0.00 3.74
2042 6184 4.883585 TGTAGATGATCATTCCCACAAAGC 59.116 41.667 10.14 0.00 0.00 3.51
2043 6185 7.067859 ACATTGTAGATGATCATTCCCACAAAG 59.932 37.037 19.92 18.48 0.00 2.77
2044 6186 6.891361 ACATTGTAGATGATCATTCCCACAAA 59.109 34.615 19.92 8.17 0.00 2.83
2045 6187 6.425735 ACATTGTAGATGATCATTCCCACAA 58.574 36.000 10.14 16.06 0.00 3.33
2046 6188 6.005066 ACATTGTAGATGATCATTCCCACA 57.995 37.500 10.14 8.75 0.00 4.17
2047 6189 6.949352 AACATTGTAGATGATCATTCCCAC 57.051 37.500 10.14 6.35 0.00 4.61
2048 6190 8.033178 TCTAACATTGTAGATGATCATTCCCA 57.967 34.615 10.14 3.99 0.00 4.37
2049 6191 8.370940 TCTCTAACATTGTAGATGATCATTCCC 58.629 37.037 10.14 0.00 29.78 3.97
2050 6192 9.421806 CTCTCTAACATTGTAGATGATCATTCC 57.578 37.037 10.14 0.00 29.78 3.01
2051 6193 9.421806 CCTCTCTAACATTGTAGATGATCATTC 57.578 37.037 10.14 3.48 29.78 2.67
2052 6194 7.877097 GCCTCTCTAACATTGTAGATGATCATT 59.123 37.037 10.14 2.85 29.78 2.57
2053 6195 7.235193 AGCCTCTCTAACATTGTAGATGATCAT 59.765 37.037 8.25 8.25 29.78 2.45
2054 6196 6.552725 AGCCTCTCTAACATTGTAGATGATCA 59.447 38.462 0.00 0.00 29.78 2.92
2055 6197 6.991938 AGCCTCTCTAACATTGTAGATGATC 58.008 40.000 0.00 0.00 29.78 2.92
2056 6198 6.992664 AGCCTCTCTAACATTGTAGATGAT 57.007 37.500 0.00 0.00 29.78 2.45
2057 6199 6.577103 CAAGCCTCTCTAACATTGTAGATGA 58.423 40.000 0.00 0.00 29.78 2.92
2058 6200 5.236047 GCAAGCCTCTCTAACATTGTAGATG 59.764 44.000 0.00 0.00 29.78 2.90
2059 6201 5.104776 TGCAAGCCTCTCTAACATTGTAGAT 60.105 40.000 0.00 0.00 29.78 1.98
2060 6202 4.222810 TGCAAGCCTCTCTAACATTGTAGA 59.777 41.667 0.00 0.00 0.00 2.59
2061 6203 4.507710 TGCAAGCCTCTCTAACATTGTAG 58.492 43.478 0.00 0.00 0.00 2.74
2062 6204 4.551702 TGCAAGCCTCTCTAACATTGTA 57.448 40.909 0.00 0.00 0.00 2.41
2063 6205 3.423539 TGCAAGCCTCTCTAACATTGT 57.576 42.857 0.00 0.00 0.00 2.71
2064 6206 4.771590 TTTGCAAGCCTCTCTAACATTG 57.228 40.909 0.00 0.00 0.00 2.82
2065 6207 5.990120 AATTTGCAAGCCTCTCTAACATT 57.010 34.783 0.00 0.00 0.00 2.71
2066 6208 5.990120 AAATTTGCAAGCCTCTCTAACAT 57.010 34.783 0.00 0.00 0.00 2.71
2067 6209 5.562696 CGAAAATTTGCAAGCCTCTCTAACA 60.563 40.000 0.00 0.00 0.00 2.41
2068 6210 4.853743 CGAAAATTTGCAAGCCTCTCTAAC 59.146 41.667 0.00 0.00 0.00 2.34
2069 6211 4.518970 ACGAAAATTTGCAAGCCTCTCTAA 59.481 37.500 0.00 0.00 0.00 2.10
2070 6212 4.072131 ACGAAAATTTGCAAGCCTCTCTA 58.928 39.130 0.00 0.00 0.00 2.43
2071 6213 2.887152 ACGAAAATTTGCAAGCCTCTCT 59.113 40.909 0.00 0.00 0.00 3.10
2072 6214 2.982470 CACGAAAATTTGCAAGCCTCTC 59.018 45.455 0.00 0.00 0.00 3.20
2073 6215 2.288395 CCACGAAAATTTGCAAGCCTCT 60.288 45.455 0.00 0.00 0.00 3.69
2074 6216 2.061028 CCACGAAAATTTGCAAGCCTC 58.939 47.619 0.00 0.00 0.00 4.70
2075 6217 1.412343 ACCACGAAAATTTGCAAGCCT 59.588 42.857 0.00 0.00 0.00 4.58
2076 6218 1.792367 GACCACGAAAATTTGCAAGCC 59.208 47.619 0.00 0.00 0.00 4.35
2077 6219 2.468831 TGACCACGAAAATTTGCAAGC 58.531 42.857 0.00 0.00 0.00 4.01
2078 6220 5.233902 TCATTTGACCACGAAAATTTGCAAG 59.766 36.000 0.00 0.00 0.00 4.01
2079 6221 5.006165 GTCATTTGACCACGAAAATTTGCAA 59.994 36.000 0.00 0.00 39.07 4.08
2080 6222 4.505922 GTCATTTGACCACGAAAATTTGCA 59.494 37.500 0.00 0.00 39.07 4.08
2081 6223 4.505922 TGTCATTTGACCACGAAAATTTGC 59.494 37.500 8.16 0.00 44.15 3.68
2082 6224 6.128849 GGATGTCATTTGACCACGAAAATTTG 60.129 38.462 8.16 0.00 44.15 2.32
2083 6225 5.925969 GGATGTCATTTGACCACGAAAATTT 59.074 36.000 8.16 0.00 44.15 1.82
2084 6226 5.469479 GGATGTCATTTGACCACGAAAATT 58.531 37.500 8.16 0.00 44.15 1.82
2085 6227 4.379394 CGGATGTCATTTGACCACGAAAAT 60.379 41.667 8.16 0.00 44.15 1.82
2086 6228 3.058570 CGGATGTCATTTGACCACGAAAA 60.059 43.478 8.16 0.00 44.15 2.29
2087 6229 2.482336 CGGATGTCATTTGACCACGAAA 59.518 45.455 8.16 0.00 44.15 3.46
2088 6230 2.073056 CGGATGTCATTTGACCACGAA 58.927 47.619 8.16 0.00 44.15 3.85
2089 6231 1.273886 TCGGATGTCATTTGACCACGA 59.726 47.619 8.16 11.41 44.15 4.35
2090 6232 1.660607 CTCGGATGTCATTTGACCACG 59.339 52.381 8.16 9.55 44.15 4.94
2091 6233 2.009774 CCTCGGATGTCATTTGACCAC 58.990 52.381 8.16 2.70 44.15 4.16
2092 6234 1.905894 TCCTCGGATGTCATTTGACCA 59.094 47.619 8.16 0.00 44.15 4.02
2093 6235 2.555199 CTCCTCGGATGTCATTTGACC 58.445 52.381 8.16 0.00 44.15 4.02
2094 6236 1.936547 GCTCCTCGGATGTCATTTGAC 59.063 52.381 3.72 3.72 44.97 3.18
2095 6237 1.833630 AGCTCCTCGGATGTCATTTGA 59.166 47.619 0.00 0.00 0.00 2.69
2096 6238 2.158986 AGAGCTCCTCGGATGTCATTTG 60.159 50.000 10.93 0.00 35.36 2.32
2097 6239 2.114616 AGAGCTCCTCGGATGTCATTT 58.885 47.619 10.93 0.00 35.36 2.32
2098 6240 1.786937 AGAGCTCCTCGGATGTCATT 58.213 50.000 10.93 0.00 35.36 2.57
2099 6241 2.666272 TAGAGCTCCTCGGATGTCAT 57.334 50.000 10.93 0.00 35.36 3.06
2100 6242 2.666272 ATAGAGCTCCTCGGATGTCA 57.334 50.000 10.93 0.00 35.36 3.58
2101 6243 6.761099 TTTATATAGAGCTCCTCGGATGTC 57.239 41.667 10.93 0.00 35.36 3.06
2102 6244 7.540474 TTTTTATATAGAGCTCCTCGGATGT 57.460 36.000 10.93 0.00 35.36 3.06
2126 6268 8.892723 GGTCCAAAGAAAATTTCATTTTGTCTT 58.107 29.630 8.55 7.04 42.15 3.01
2127 6269 8.046107 TGGTCCAAAGAAAATTTCATTTTGTCT 58.954 29.630 8.55 2.32 42.15 3.41
2128 6270 8.122330 GTGGTCCAAAGAAAATTTCATTTTGTC 58.878 33.333 8.55 6.47 42.15 3.18
2129 6271 7.066887 GGTGGTCCAAAGAAAATTTCATTTTGT 59.933 33.333 8.55 0.00 42.15 2.83
2130 6272 7.066766 TGGTGGTCCAAAGAAAATTTCATTTTG 59.933 33.333 8.55 10.20 40.42 2.44
2131 6273 7.115414 TGGTGGTCCAAAGAAAATTTCATTTT 58.885 30.769 8.55 0.00 41.74 1.82
2132 6274 6.657875 TGGTGGTCCAAAGAAAATTTCATTT 58.342 32.000 8.55 3.45 41.25 2.32
2133 6275 6.245890 TGGTGGTCCAAAGAAAATTTCATT 57.754 33.333 8.55 0.00 41.25 2.57
2134 6276 5.885449 TGGTGGTCCAAAGAAAATTTCAT 57.115 34.783 8.55 0.00 41.25 2.57
2155 6297 1.613836 AGAGAGGCTTGCCAAGTTTG 58.386 50.000 14.54 0.00 0.00 2.93
2156 6298 3.149981 GTTAGAGAGGCTTGCCAAGTTT 58.850 45.455 14.54 0.00 0.00 2.66
2157 6299 2.106511 TGTTAGAGAGGCTTGCCAAGTT 59.893 45.455 14.54 0.00 0.00 2.66
2158 6300 1.699634 TGTTAGAGAGGCTTGCCAAGT 59.300 47.619 14.54 0.00 0.00 3.16
2159 6301 2.479566 TGTTAGAGAGGCTTGCCAAG 57.520 50.000 14.54 0.00 0.00 3.61
2160 6302 4.708177 GATATGTTAGAGAGGCTTGCCAA 58.292 43.478 14.54 0.00 0.00 4.52
2161 6303 3.243873 CGATATGTTAGAGAGGCTTGCCA 60.244 47.826 14.54 0.00 0.00 4.92
2162 6304 3.005897 TCGATATGTTAGAGAGGCTTGCC 59.994 47.826 2.97 2.97 0.00 4.52
2163 6305 4.244425 TCGATATGTTAGAGAGGCTTGC 57.756 45.455 0.00 0.00 0.00 4.01
2164 6306 5.406649 GGATCGATATGTTAGAGAGGCTTG 58.593 45.833 0.00 0.00 0.00 4.01
2165 6307 4.464597 GGGATCGATATGTTAGAGAGGCTT 59.535 45.833 0.00 0.00 0.00 4.35
2166 6308 4.020543 GGGATCGATATGTTAGAGAGGCT 58.979 47.826 0.00 0.00 0.00 4.58
2167 6309 4.020543 AGGGATCGATATGTTAGAGAGGC 58.979 47.826 0.00 0.00 0.00 4.70
2168 6310 6.393990 CAAAGGGATCGATATGTTAGAGAGG 58.606 44.000 0.00 0.00 0.00 3.69
2169 6311 6.209589 TCCAAAGGGATCGATATGTTAGAGAG 59.790 42.308 0.00 0.00 38.64 3.20
2170 6312 6.075315 TCCAAAGGGATCGATATGTTAGAGA 58.925 40.000 0.00 0.00 38.64 3.10
2171 6313 6.209589 TCTCCAAAGGGATCGATATGTTAGAG 59.790 42.308 0.00 0.25 43.91 2.43
2172 6314 6.075315 TCTCCAAAGGGATCGATATGTTAGA 58.925 40.000 0.00 0.00 43.91 2.10
2173 6315 6.346477 TCTCCAAAGGGATCGATATGTTAG 57.654 41.667 0.00 0.00 43.91 2.34
2174 6316 6.740944 TTCTCCAAAGGGATCGATATGTTA 57.259 37.500 0.00 0.00 43.91 2.41
2175 6317 5.630415 TTCTCCAAAGGGATCGATATGTT 57.370 39.130 0.00 0.00 43.91 2.71
2176 6318 5.366768 TCTTTCTCCAAAGGGATCGATATGT 59.633 40.000 0.00 0.00 43.91 2.29
2177 6319 5.858381 TCTTTCTCCAAAGGGATCGATATG 58.142 41.667 0.00 0.00 43.91 1.78
2178 6320 6.471146 CATCTTTCTCCAAAGGGATCGATAT 58.529 40.000 0.00 0.00 43.91 1.63
2195 6337 5.074115 TCCTAGCTAGCTACTCCATCTTTC 58.926 45.833 20.67 0.00 0.00 2.62
2196 6338 5.068215 TCCTAGCTAGCTACTCCATCTTT 57.932 43.478 20.67 0.00 0.00 2.52
2201 6343 4.597940 TCATACTCCTAGCTAGCTACTCCA 59.402 45.833 20.67 1.82 0.00 3.86
2209 6351 5.124776 GCCACATAGTCATACTCCTAGCTAG 59.875 48.000 14.20 14.20 0.00 3.42
2211 6353 3.829601 GCCACATAGTCATACTCCTAGCT 59.170 47.826 0.00 0.00 0.00 3.32
2212 6354 3.574396 TGCCACATAGTCATACTCCTAGC 59.426 47.826 0.00 0.00 0.00 3.42
2213 6355 5.714333 AGATGCCACATAGTCATACTCCTAG 59.286 44.000 0.00 0.00 0.00 3.02
2214 6356 5.478332 CAGATGCCACATAGTCATACTCCTA 59.522 44.000 0.00 0.00 0.00 2.94
2215 6357 4.282957 CAGATGCCACATAGTCATACTCCT 59.717 45.833 0.00 0.00 0.00 3.69
2216 6358 4.281941 TCAGATGCCACATAGTCATACTCC 59.718 45.833 0.00 0.00 0.00 3.85
2225 6367 5.819379 ACACAAGTTATCAGATGCCACATAG 59.181 40.000 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.