Multiple sequence alignment - TraesCS6B01G203800

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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 TraesCS6B01G203800 chr6B 100.000 2687 0 0 1 2687 250794561 250791875 0.000000e+00 4963.0
1 TraesCS6B01G203800 chr6B 99.396 331 2 0 1 331 250802337 250802007 3.830000e-168 601.0
2 TraesCS6B01G203800 chr6B 93.789 322 18 2 331 651 250818290 250817970 1.450000e-132 483.0
3 TraesCS6B01G203800 chr6B 84.921 126 19 0 2562 2687 563143112 563142987 7.810000e-26 128.0
4 TraesCS6B01G203800 chr2B 97.811 1599 21 1 668 2252 127146874 127145276 0.000000e+00 2747.0
5 TraesCS6B01G203800 chr2B 99.094 331 3 0 1 331 325649211 325648881 1.780000e-166 595.0
6 TraesCS6B01G203800 chr2B 99.094 331 3 0 1 331 472917149 472917479 1.780000e-166 595.0
7 TraesCS6B01G203800 chr2B 98.489 331 5 0 1 331 402284268 402284598 3.850000e-163 584.0
8 TraesCS6B01G203800 chr2B 98.198 333 6 0 1 333 472920847 472921179 1.390000e-162 582.0
9 TraesCS6B01G203800 chr2B 94.545 330 2 2 2348 2661 127144863 127144534 1.860000e-136 496.0
10 TraesCS6B01G203800 chr2B 90.236 297 26 2 995 1288 753324775 753325071 4.200000e-103 385.0
11 TraesCS6B01G203800 chr2B 85.714 224 23 6 2100 2322 90577456 90577241 7.480000e-56 228.0
12 TraesCS6B01G203800 chr2B 79.832 238 37 6 2461 2687 140248471 140248234 2.140000e-36 163.0
13 TraesCS6B01G203800 chr2B 88.889 126 14 0 668 793 188448389 188448264 3.580000e-34 156.0
14 TraesCS6B01G203800 chr2B 93.878 98 6 0 668 765 771168357 771168260 5.990000e-32 148.0
15 TraesCS6B01G203800 chr7B 98.815 1434 15 1 840 2271 122839512 122840945 0.000000e+00 2553.0
16 TraesCS6B01G203800 chr7B 88.596 342 30 8 1 338 279807747 279808083 8.960000e-110 407.0
17 TraesCS6B01G203800 chr7B 88.338 343 28 12 1 338 288820469 288820134 4.170000e-108 401.0
18 TraesCS6B01G203800 chr7B 87.234 282 36 0 331 612 418691360 418691641 3.340000e-84 322.0
19 TraesCS6B01G203800 chr7B 97.849 186 3 1 676 861 122839318 122839502 1.200000e-83 320.0
20 TraesCS6B01G203800 chr5B 99.094 331 3 0 1 331 130050545 130050215 1.780000e-166 595.0
21 TraesCS6B01G203800 chr5B 98.802 334 4 0 1 334 231225014 231225347 1.780000e-166 595.0
22 TraesCS6B01G203800 chr5B 98.507 335 5 0 1 335 194103496 194103162 2.300000e-165 592.0
23 TraesCS6B01G203800 chr5B 98.209 335 5 1 1 335 177557580 177557913 3.850000e-163 584.0
24 TraesCS6B01G203800 chr5B 96.165 339 11 1 1 337 242683941 242683603 1.090000e-153 553.0
25 TraesCS6B01G203800 chr1B 89.254 335 29 6 2 332 297755537 297755868 1.920000e-111 412.0
26 TraesCS6B01G203800 chr1B 77.638 398 55 13 2323 2687 66934461 66934065 7.540000e-51 211.0
27 TraesCS6B01G203800 chr1B 84.080 201 26 6 2101 2300 447176802 447176607 3.530000e-44 189.0
28 TraesCS6B01G203800 chr1B 84.000 200 27 5 2101 2300 644722487 644722681 1.270000e-43 187.0
29 TraesCS6B01G203800 chr1B 89.683 126 13 0 668 793 65544632 65544507 7.700000e-36 161.0
30 TraesCS6B01G203800 chr1B 87.654 81 10 0 2570 2650 633731514 633731434 7.920000e-16 95.3
31 TraesCS6B01G203800 chr2A 90.541 296 25 2 995 1287 747623287 747623582 3.240000e-104 388.0
32 TraesCS6B01G203800 chr2A 89.600 125 13 0 669 793 214069241 214069117 2.770000e-35 159.0
33 TraesCS6B01G203800 chr3B 90.444 293 22 6 48 338 339333734 339333446 5.430000e-102 381.0
34 TraesCS6B01G203800 chr2D 89.899 297 27 2 995 1288 617405915 617406211 1.950000e-101 379.0
35 TraesCS6B01G203800 chr2D 77.487 382 39 33 1621 1968 235508073 235507705 4.570000e-43 185.0
36 TraesCS6B01G203800 chr1D 93.644 236 12 3 104 337 182686703 182686469 1.530000e-92 350.0
37 TraesCS6B01G203800 chr1D 82.906 117 16 3 1311 1424 482245625 482245510 4.730000e-18 102.0
38 TraesCS6B01G203800 chr7D 92.672 232 13 4 106 336 329812397 329812169 5.540000e-87 331.0
39 TraesCS6B01G203800 chr7D 83.019 318 48 6 334 648 446529110 446528796 1.570000e-72 283.0
40 TraesCS6B01G203800 chr7D 93.333 75 4 1 2235 2309 538287521 538287594 2.830000e-20 110.0
41 TraesCS6B01G203800 chr7A 82.071 396 37 11 2321 2687 217700060 217699670 9.340000e-80 307.0
42 TraesCS6B01G203800 chr7A 78.730 315 36 14 2011 2322 217700447 217700161 5.910000e-42 182.0
43 TraesCS6B01G203800 chr7A 76.453 327 40 25 1665 1968 53174273 53174585 2.790000e-30 143.0
44 TraesCS6B01G203800 chr6D 86.691 278 34 3 356 632 289712781 289713056 3.360000e-79 305.0
45 TraesCS6B01G203800 chr6D 85.870 276 36 3 362 635 78309156 78308882 9.410000e-75 291.0
46 TraesCS6B01G203800 chr6D 84.783 138 19 2 2550 2687 376943042 376942907 1.300000e-28 137.0
47 TraesCS6B01G203800 chr6D 85.075 134 20 0 2554 2687 376971929 376971796 1.300000e-28 137.0
48 TraesCS6B01G203800 chr6A 84.691 307 44 3 331 635 298374062 298373757 1.210000e-78 303.0
49 TraesCS6B01G203800 chr6A 87.407 135 16 1 2554 2687 518547313 518547179 1.290000e-33 154.0
50 TraesCS6B01G203800 chr6A 93.878 98 6 0 668 765 317609295 317609198 5.990000e-32 148.0
51 TraesCS6B01G203800 chr6A 85.714 126 18 0 2562 2687 518595439 518595314 1.680000e-27 134.0
52 TraesCS6B01G203800 chr4B 84.459 296 44 2 331 625 427685549 427685843 9.410000e-75 291.0
53 TraesCS6B01G203800 chr5D 84.281 299 44 3 331 628 86847205 86846909 3.380000e-74 289.0
54 TraesCS6B01G203800 chr5D 84.175 297 43 4 334 628 202565185 202565479 4.380000e-73 285.0
55 TraesCS6B01G203800 chr5D 78.689 244 35 9 2458 2687 447249277 447249517 2.160000e-31 147.0
56 TraesCS6B01G203800 chr5D 79.167 168 17 11 1735 1895 49670294 49670450 1.700000e-17 100.0
57 TraesCS6B01G203800 chr5D 82.051 117 17 3 2203 2317 431537944 431538058 2.200000e-16 97.1
58 TraesCS6B01G203800 chr3D 82.972 323 51 4 331 651 186177879 186177559 3.380000e-74 289.0
59 TraesCS6B01G203800 chr3D 90.000 60 6 0 1506 1565 87625893 87625952 7.980000e-11 78.7
60 TraesCS6B01G203800 chr5A 82.243 321 51 6 331 648 113714792 113715109 3.410000e-69 272.0
61 TraesCS6B01G203800 chr5A 77.778 396 56 12 2323 2687 512084503 512084897 5.830000e-52 215.0
62 TraesCS6B01G203800 chr5A 77.778 234 40 8 2458 2687 457255031 457255256 1.680000e-27 134.0
63 TraesCS6B01G203800 chr3A 79.188 394 41 14 2321 2687 165100378 165100757 4.470000e-58 235.0
64 TraesCS6B01G203800 chr3A 78.405 301 33 9 2416 2687 327830806 327830509 1.650000e-37 167.0
65 TraesCS6B01G203800 chr3A 90.000 60 6 0 2345 2404 327830970 327830911 7.980000e-11 78.7
66 TraesCS6B01G203800 chrUn 81.720 186 31 3 2139 2323 64338034 64338217 4.630000e-33 152.0
67 TraesCS6B01G203800 chr4A 93.878 98 6 0 668 765 650405049 650404952 5.990000e-32 148.0
68 TraesCS6B01G203800 chr1A 93.878 98 6 0 668 765 74755118 74755021 5.990000e-32 148.0
69 TraesCS6B01G203800 chr1A 92.857 98 7 0 668 765 446716997 446716900 2.790000e-30 143.0


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 TraesCS6B01G203800 chr6B 250791875 250794561 2686 True 4963.0 4963 100.0000 1 2687 1 chr6B.!!$R1 2686
1 TraesCS6B01G203800 chr2B 127144534 127146874 2340 True 1621.5 2747 96.1780 668 2661 2 chr2B.!!$R6 1993
2 TraesCS6B01G203800 chr2B 472917149 472921179 4030 False 588.5 595 98.6460 1 333 2 chr2B.!!$F3 332
3 TraesCS6B01G203800 chr7B 122839318 122840945 1627 False 1436.5 2553 98.3320 676 2271 2 chr7B.!!$F3 1595
4 TraesCS6B01G203800 chr7A 217699670 217700447 777 True 244.5 307 80.4005 2011 2687 2 chr7A.!!$R1 676

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
405 406 0.030369 CAGGGCTACACGATACCGAC 59.970 60.0 0.00 0.00 39.50 4.79 F
711 1763 0.039798 GTGCTTCTGGTCGTACGTCA 60.040 55.0 16.05 13.58 0.00 4.35 F
1043 4173 0.250858 TACGTCTTCCTCCACGTCCA 60.251 55.0 0.00 0.00 46.04 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1273 4638 0.666577 CGTTCGTCGGCCTTCTTCTT 60.667 55.000 0.0 0.0 35.71 2.52 R
1626 4991 1.079127 CGACCAACAGCCTCGGATT 60.079 57.895 0.0 0.0 0.00 3.01 R
2290 5659 1.421485 GTCGTGCAAGGCGAATCAG 59.579 57.895 0.0 0.0 40.19 2.90 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
58 59 2.169978 CTCCATGTGAGAAGATCCTGCA 59.830 50.000 5.53 0.00 44.42 4.41
257 258 0.768997 TTTCTCCCCGTTCTTCCCCA 60.769 55.000 0.00 0.00 0.00 4.96
305 306 3.057019 CACTCCAAACGTGAAAGATCGA 58.943 45.455 0.00 0.00 34.35 3.59
334 335 2.711542 GGTTCCACCCTACATCACAAG 58.288 52.381 0.00 0.00 30.04 3.16
335 336 2.039879 GGTTCCACCCTACATCACAAGT 59.960 50.000 0.00 0.00 30.04 3.16
337 338 1.003118 TCCACCCTACATCACAAGTGC 59.997 52.381 0.00 0.00 0.00 4.40
339 340 2.503331 CACCCTACATCACAAGTGCAA 58.497 47.619 0.00 0.00 0.00 4.08
340 341 3.084039 CACCCTACATCACAAGTGCAAT 58.916 45.455 0.00 0.00 0.00 3.56
342 343 4.094887 CACCCTACATCACAAGTGCAATAC 59.905 45.833 0.00 0.00 0.00 1.89
343 344 4.019321 ACCCTACATCACAAGTGCAATACT 60.019 41.667 0.00 0.00 42.89 2.12
344 345 5.188948 ACCCTACATCACAAGTGCAATACTA 59.811 40.000 0.00 0.00 39.18 1.82
345 346 6.112734 CCCTACATCACAAGTGCAATACTAA 58.887 40.000 0.00 0.00 39.18 2.24
346 347 6.258727 CCCTACATCACAAGTGCAATACTAAG 59.741 42.308 0.00 0.00 39.18 2.18
347 348 5.551760 ACATCACAAGTGCAATACTAAGC 57.448 39.130 0.00 0.00 39.18 3.09
356 357 3.000041 TGCAATACTAAGCACGACAAGG 59.000 45.455 0.00 0.00 35.51 3.61
357 358 3.000727 GCAATACTAAGCACGACAAGGT 58.999 45.455 0.00 0.00 0.00 3.50
358 359 4.178540 GCAATACTAAGCACGACAAGGTA 58.821 43.478 0.00 0.00 0.00 3.08
359 360 4.628333 GCAATACTAAGCACGACAAGGTAA 59.372 41.667 0.00 0.00 0.00 2.85
360 361 5.445540 GCAATACTAAGCACGACAAGGTAAC 60.446 44.000 0.00 0.00 0.00 2.50
361 362 3.738830 ACTAAGCACGACAAGGTAACA 57.261 42.857 0.00 0.00 41.41 2.41
362 363 4.062677 ACTAAGCACGACAAGGTAACAA 57.937 40.909 0.00 0.00 41.41 2.83
363 364 4.056050 ACTAAGCACGACAAGGTAACAAG 58.944 43.478 0.00 0.00 41.41 3.16
364 365 2.902705 AGCACGACAAGGTAACAAGA 57.097 45.000 0.00 0.00 41.41 3.02
365 366 3.188159 AGCACGACAAGGTAACAAGAA 57.812 42.857 0.00 0.00 41.41 2.52
366 367 3.131396 AGCACGACAAGGTAACAAGAAG 58.869 45.455 0.00 0.00 41.41 2.85
367 368 2.349532 GCACGACAAGGTAACAAGAAGC 60.350 50.000 0.00 0.00 41.41 3.86
368 369 2.869801 CACGACAAGGTAACAAGAAGCA 59.130 45.455 0.00 0.00 41.41 3.91
370 371 3.131396 CGACAAGGTAACAAGAAGCACT 58.869 45.455 0.00 0.00 41.41 4.40
371 372 4.202182 ACGACAAGGTAACAAGAAGCACTA 60.202 41.667 0.00 0.00 41.41 2.74
372 373 4.386049 CGACAAGGTAACAAGAAGCACTAG 59.614 45.833 0.00 0.00 41.41 2.57
373 374 4.642429 ACAAGGTAACAAGAAGCACTAGG 58.358 43.478 0.00 0.00 41.41 3.02
374 375 3.983044 AGGTAACAAGAAGCACTAGGG 57.017 47.619 0.00 0.00 41.41 3.53
375 376 2.572104 AGGTAACAAGAAGCACTAGGGG 59.428 50.000 0.00 0.00 41.41 4.79
376 377 2.305052 GGTAACAAGAAGCACTAGGGGT 59.695 50.000 0.00 0.00 0.00 4.95
377 378 6.087123 AGGTAACAAGAAGCACTAGGGGTG 62.087 50.000 0.00 0.00 44.35 4.61
378 379 1.435256 ACAAGAAGCACTAGGGGTGT 58.565 50.000 0.00 0.00 46.86 4.16
379 380 1.774856 ACAAGAAGCACTAGGGGTGTT 59.225 47.619 0.00 0.00 46.86 3.32
380 381 2.224548 ACAAGAAGCACTAGGGGTGTTC 60.225 50.000 0.00 0.00 46.86 3.18
381 382 2.031495 AGAAGCACTAGGGGTGTTCT 57.969 50.000 0.00 0.00 46.86 3.01
382 383 3.185880 AGAAGCACTAGGGGTGTTCTA 57.814 47.619 0.00 0.00 46.86 2.10
383 384 3.725634 AGAAGCACTAGGGGTGTTCTAT 58.274 45.455 0.00 0.00 46.86 1.98
384 385 3.707102 AGAAGCACTAGGGGTGTTCTATC 59.293 47.826 0.00 0.00 46.86 2.08
385 386 2.032620 AGCACTAGGGGTGTTCTATCG 58.967 52.381 0.00 0.00 46.86 2.92
386 387 1.538419 GCACTAGGGGTGTTCTATCGC 60.538 57.143 0.00 0.00 46.86 4.58
387 388 1.754803 CACTAGGGGTGTTCTATCGCA 59.245 52.381 0.00 0.00 40.79 5.10
388 389 2.032620 ACTAGGGGTGTTCTATCGCAG 58.967 52.381 0.00 0.00 0.00 5.18
389 390 1.341531 CTAGGGGTGTTCTATCGCAGG 59.658 57.143 0.00 0.00 0.00 4.85
390 391 1.146263 GGGGTGTTCTATCGCAGGG 59.854 63.158 0.00 0.00 0.00 4.45
391 392 1.523938 GGGTGTTCTATCGCAGGGC 60.524 63.158 0.00 0.00 0.00 5.19
392 393 1.522569 GGTGTTCTATCGCAGGGCT 59.477 57.895 0.00 0.00 0.00 5.19
393 394 0.750850 GGTGTTCTATCGCAGGGCTA 59.249 55.000 0.00 0.00 0.00 3.93
394 395 1.538419 GGTGTTCTATCGCAGGGCTAC 60.538 57.143 0.00 0.00 0.00 3.58
395 396 1.136305 GTGTTCTATCGCAGGGCTACA 59.864 52.381 0.00 0.00 0.00 2.74
396 397 1.136305 TGTTCTATCGCAGGGCTACAC 59.864 52.381 0.00 0.00 0.00 2.90
397 398 0.384309 TTCTATCGCAGGGCTACACG 59.616 55.000 0.00 0.00 0.00 4.49
398 399 0.464916 TCTATCGCAGGGCTACACGA 60.465 55.000 0.00 0.00 39.11 4.35
399 400 0.598562 CTATCGCAGGGCTACACGAT 59.401 55.000 9.45 9.45 46.18 3.73
400 401 1.810755 CTATCGCAGGGCTACACGATA 59.189 52.381 10.43 10.43 42.96 2.92
401 402 0.314302 ATCGCAGGGCTACACGATAC 59.686 55.000 0.00 0.00 42.96 2.24
402 403 1.299926 CGCAGGGCTACACGATACC 60.300 63.158 0.00 0.00 0.00 2.73
403 404 1.299926 GCAGGGCTACACGATACCG 60.300 63.158 0.00 0.00 42.50 4.02
404 405 1.731433 GCAGGGCTACACGATACCGA 61.731 60.000 0.00 0.00 39.50 4.69
405 406 0.030369 CAGGGCTACACGATACCGAC 59.970 60.000 0.00 0.00 39.50 4.79
406 407 1.009222 GGGCTACACGATACCGACG 60.009 63.158 0.00 0.00 39.50 5.12
407 408 1.439353 GGGCTACACGATACCGACGA 61.439 60.000 0.00 0.00 39.50 4.20
408 409 0.378257 GGCTACACGATACCGACGAA 59.622 55.000 0.00 0.00 39.50 3.85
409 410 1.596464 GGCTACACGATACCGACGAAG 60.596 57.143 0.00 0.00 39.50 3.79
410 411 1.596464 GCTACACGATACCGACGAAGG 60.596 57.143 0.00 0.00 39.50 3.46
411 412 1.935873 CTACACGATACCGACGAAGGA 59.064 52.381 7.84 0.00 39.50 3.36
412 413 1.167851 ACACGATACCGACGAAGGAA 58.832 50.000 7.84 0.00 39.50 3.36
413 414 1.131883 ACACGATACCGACGAAGGAAG 59.868 52.381 7.84 0.00 39.50 3.46
414 415 1.399440 CACGATACCGACGAAGGAAGA 59.601 52.381 7.84 0.00 39.50 2.87
415 416 2.033049 CACGATACCGACGAAGGAAGAT 59.967 50.000 7.84 0.00 39.50 2.40
416 417 3.249320 CACGATACCGACGAAGGAAGATA 59.751 47.826 7.84 0.00 39.50 1.98
417 418 3.879295 ACGATACCGACGAAGGAAGATAA 59.121 43.478 7.84 0.00 39.50 1.75
418 419 4.217497 CGATACCGACGAAGGAAGATAAC 58.783 47.826 7.84 0.00 38.22 1.89
419 420 4.260907 CGATACCGACGAAGGAAGATAACA 60.261 45.833 7.84 0.00 38.22 2.41
420 421 5.562307 CGATACCGACGAAGGAAGATAACAT 60.562 44.000 7.84 0.00 38.22 2.71
421 422 4.043037 ACCGACGAAGGAAGATAACATC 57.957 45.455 7.84 0.00 34.73 3.06
422 423 3.181478 ACCGACGAAGGAAGATAACATCC 60.181 47.826 7.84 0.00 34.50 3.51
423 424 3.043586 CGACGAAGGAAGATAACATCCG 58.956 50.000 0.00 0.00 38.71 4.18
424 425 3.242969 CGACGAAGGAAGATAACATCCGA 60.243 47.826 0.00 0.00 38.71 4.55
425 426 4.291783 GACGAAGGAAGATAACATCCGAG 58.708 47.826 0.00 0.00 38.71 4.63
426 427 3.952323 ACGAAGGAAGATAACATCCGAGA 59.048 43.478 0.00 0.00 38.71 4.04
427 428 4.401519 ACGAAGGAAGATAACATCCGAGAA 59.598 41.667 0.00 0.00 38.71 2.87
428 429 5.069251 ACGAAGGAAGATAACATCCGAGAAT 59.931 40.000 0.00 0.00 38.71 2.40
429 430 5.403766 CGAAGGAAGATAACATCCGAGAATG 59.596 44.000 0.00 0.00 38.71 2.67
430 431 5.878406 AGGAAGATAACATCCGAGAATGT 57.122 39.130 0.00 0.00 41.60 2.71
432 433 6.653989 AGGAAGATAACATCCGAGAATGTTT 58.346 36.000 13.48 5.12 45.29 2.83
433 434 7.112779 AGGAAGATAACATCCGAGAATGTTTT 58.887 34.615 13.48 7.97 45.29 2.43
434 435 7.281100 AGGAAGATAACATCCGAGAATGTTTTC 59.719 37.037 13.48 14.12 45.29 2.29
435 436 6.927294 AGATAACATCCGAGAATGTTTTCC 57.073 37.500 13.48 6.30 45.29 3.13
436 437 5.823045 AGATAACATCCGAGAATGTTTTCCC 59.177 40.000 13.48 4.60 45.29 3.97
437 438 2.356135 ACATCCGAGAATGTTTTCCCG 58.644 47.619 0.00 0.00 36.47 5.14
438 439 2.027561 ACATCCGAGAATGTTTTCCCGA 60.028 45.455 0.00 0.00 35.32 5.14
439 440 2.843401 TCCGAGAATGTTTTCCCGAA 57.157 45.000 0.00 0.00 35.32 4.30
440 441 2.695359 TCCGAGAATGTTTTCCCGAAG 58.305 47.619 0.00 0.00 35.32 3.79
441 442 2.038033 TCCGAGAATGTTTTCCCGAAGT 59.962 45.455 0.00 0.00 35.32 3.01
442 443 2.812011 CCGAGAATGTTTTCCCGAAGTT 59.188 45.455 0.00 0.00 35.32 2.66
443 444 3.252458 CCGAGAATGTTTTCCCGAAGTTT 59.748 43.478 0.00 0.00 35.32 2.66
444 445 4.219033 CGAGAATGTTTTCCCGAAGTTTG 58.781 43.478 0.00 0.00 35.32 2.93
445 446 4.546570 GAGAATGTTTTCCCGAAGTTTGG 58.453 43.478 1.59 1.59 31.84 3.28
446 447 2.812358 ATGTTTTCCCGAAGTTTGGC 57.188 45.000 3.24 0.00 0.00 4.52
447 448 1.475403 TGTTTTCCCGAAGTTTGGCA 58.525 45.000 3.24 0.00 0.00 4.92
448 449 2.035632 TGTTTTCCCGAAGTTTGGCAT 58.964 42.857 3.24 0.00 0.00 4.40
449 450 2.432510 TGTTTTCCCGAAGTTTGGCATT 59.567 40.909 3.24 0.00 0.00 3.56
450 451 3.118592 TGTTTTCCCGAAGTTTGGCATTT 60.119 39.130 3.24 0.00 0.00 2.32
451 452 3.378911 TTTCCCGAAGTTTGGCATTTC 57.621 42.857 3.24 0.00 0.00 2.17
452 453 1.253100 TCCCGAAGTTTGGCATTTCC 58.747 50.000 3.24 0.00 0.00 3.13
453 454 0.109319 CCCGAAGTTTGGCATTTCCG 60.109 55.000 3.24 0.00 37.80 4.30
454 455 0.109319 CCGAAGTTTGGCATTTCCGG 60.109 55.000 0.00 0.00 37.80 5.14
455 456 0.878416 CGAAGTTTGGCATTTCCGGA 59.122 50.000 0.00 0.00 37.80 5.14
456 457 1.401018 CGAAGTTTGGCATTTCCGGAC 60.401 52.381 1.83 0.00 37.80 4.79
457 458 1.611491 GAAGTTTGGCATTTCCGGACA 59.389 47.619 1.83 0.00 37.80 4.02
458 459 1.247567 AGTTTGGCATTTCCGGACAG 58.752 50.000 1.83 0.00 37.80 3.51
459 460 0.243636 GTTTGGCATTTCCGGACAGG 59.756 55.000 1.83 0.00 42.97 4.00
460 461 1.531739 TTTGGCATTTCCGGACAGGC 61.532 55.000 18.57 18.57 40.77 4.85
461 462 3.508840 GGCATTTCCGGACAGGCG 61.509 66.667 19.85 0.91 40.77 5.52
462 463 2.435938 GCATTTCCGGACAGGCGA 60.436 61.111 11.93 0.00 40.77 5.54
463 464 2.038269 GCATTTCCGGACAGGCGAA 61.038 57.895 11.93 0.00 40.77 4.70
464 465 1.582610 GCATTTCCGGACAGGCGAAA 61.583 55.000 11.93 0.00 40.77 3.46
465 466 0.168128 CATTTCCGGACAGGCGAAAC 59.832 55.000 1.83 0.00 40.77 2.78
466 467 1.296056 ATTTCCGGACAGGCGAAACG 61.296 55.000 1.83 0.00 40.77 3.60
467 468 3.869473 TTCCGGACAGGCGAAACGG 62.869 63.158 1.83 7.28 45.52 4.44
469 470 2.809601 CGGACAGGCGAAACGGAG 60.810 66.667 0.00 0.00 0.00 4.63
470 471 2.434359 GGACAGGCGAAACGGAGG 60.434 66.667 0.00 0.00 0.00 4.30
471 472 2.434359 GACAGGCGAAACGGAGGG 60.434 66.667 0.00 0.00 0.00 4.30
472 473 3.952628 GACAGGCGAAACGGAGGGG 62.953 68.421 0.00 0.00 0.00 4.79
473 474 3.702048 CAGGCGAAACGGAGGGGA 61.702 66.667 0.00 0.00 0.00 4.81
474 475 2.926242 AGGCGAAACGGAGGGGAA 60.926 61.111 0.00 0.00 0.00 3.97
475 476 2.032987 GGCGAAACGGAGGGGAAA 59.967 61.111 0.00 0.00 0.00 3.13
476 477 2.038837 GGCGAAACGGAGGGGAAAG 61.039 63.158 0.00 0.00 0.00 2.62
477 478 2.038837 GCGAAACGGAGGGGAAAGG 61.039 63.158 0.00 0.00 0.00 3.11
478 479 1.373812 CGAAACGGAGGGGAAAGGT 59.626 57.895 0.00 0.00 0.00 3.50
479 480 0.250597 CGAAACGGAGGGGAAAGGTT 60.251 55.000 0.00 0.00 0.00 3.50
480 481 1.244816 GAAACGGAGGGGAAAGGTTG 58.755 55.000 0.00 0.00 0.00 3.77
481 482 0.826256 AAACGGAGGGGAAAGGTTGC 60.826 55.000 0.00 0.00 0.00 4.17
482 483 2.002018 AACGGAGGGGAAAGGTTGCA 62.002 55.000 0.00 0.00 0.00 4.08
483 484 1.000896 CGGAGGGGAAAGGTTGCAT 60.001 57.895 0.00 0.00 0.00 3.96
484 485 1.315257 CGGAGGGGAAAGGTTGCATG 61.315 60.000 0.00 0.00 0.00 4.06
485 486 0.251787 GGAGGGGAAAGGTTGCATGT 60.252 55.000 0.00 0.00 0.00 3.21
486 487 1.632589 GAGGGGAAAGGTTGCATGTT 58.367 50.000 0.00 0.00 0.00 2.71
487 488 1.970640 GAGGGGAAAGGTTGCATGTTT 59.029 47.619 0.00 0.00 0.00 2.83
488 489 1.693606 AGGGGAAAGGTTGCATGTTTG 59.306 47.619 0.00 0.00 0.00 2.93
500 501 1.610522 GCATGTTTGCTATGCTAGGGG 59.389 52.381 0.00 0.00 45.64 4.79
501 502 1.610522 CATGTTTGCTATGCTAGGGGC 59.389 52.381 0.00 0.00 42.22 5.80
502 503 0.463654 TGTTTGCTATGCTAGGGGCG 60.464 55.000 0.00 0.00 45.43 6.13
503 504 0.463833 GTTTGCTATGCTAGGGGCGT 60.464 55.000 0.00 0.00 45.43 5.68
504 505 0.463654 TTTGCTATGCTAGGGGCGTG 60.464 55.000 0.00 0.00 45.43 5.34
505 506 1.622607 TTGCTATGCTAGGGGCGTGT 61.623 55.000 0.00 0.00 45.43 4.49
506 507 1.595382 GCTATGCTAGGGGCGTGTG 60.595 63.158 0.00 0.00 45.43 3.82
507 508 1.069765 CTATGCTAGGGGCGTGTGG 59.930 63.158 0.00 0.00 45.43 4.17
508 509 2.996168 CTATGCTAGGGGCGTGTGGC 62.996 65.000 0.00 0.00 45.43 5.01
517 518 4.147322 GCGTGTGGCGGACGAATG 62.147 66.667 11.77 0.00 39.21 2.67
518 519 3.487202 CGTGTGGCGGACGAATGG 61.487 66.667 2.18 0.00 39.21 3.16
519 520 3.124921 GTGTGGCGGACGAATGGG 61.125 66.667 0.00 0.00 0.00 4.00
526 527 4.517815 GGACGAATGGGCCGCGTA 62.518 66.667 16.91 0.00 38.51 4.42
527 528 2.279918 GACGAATGGGCCGCGTAT 60.280 61.111 16.91 0.00 38.51 3.06
528 529 1.885850 GACGAATGGGCCGCGTATT 60.886 57.895 16.91 2.79 38.51 1.89
529 530 1.433837 GACGAATGGGCCGCGTATTT 61.434 55.000 16.91 0.00 38.51 1.40
530 531 1.010125 CGAATGGGCCGCGTATTTG 60.010 57.895 4.92 0.64 0.00 2.32
531 532 1.358759 GAATGGGCCGCGTATTTGG 59.641 57.895 4.92 0.00 0.00 3.28
532 533 1.077357 AATGGGCCGCGTATTTGGA 60.077 52.632 4.92 0.00 0.00 3.53
533 534 0.467290 AATGGGCCGCGTATTTGGAT 60.467 50.000 4.92 0.00 0.00 3.41
534 535 0.467290 ATGGGCCGCGTATTTGGATT 60.467 50.000 4.92 0.00 0.00 3.01
535 536 1.098712 TGGGCCGCGTATTTGGATTC 61.099 55.000 4.92 0.00 0.00 2.52
536 537 1.278637 GGCCGCGTATTTGGATTCG 59.721 57.895 4.92 0.00 0.00 3.34
537 538 1.433837 GGCCGCGTATTTGGATTCGT 61.434 55.000 4.92 0.00 0.00 3.85
538 539 0.042448 GCCGCGTATTTGGATTCGTC 60.042 55.000 4.92 0.00 0.00 4.20
539 540 1.567504 CCGCGTATTTGGATTCGTCT 58.432 50.000 4.92 0.00 0.00 4.18
540 541 1.931172 CCGCGTATTTGGATTCGTCTT 59.069 47.619 4.92 0.00 0.00 3.01
541 542 2.285602 CCGCGTATTTGGATTCGTCTTG 60.286 50.000 4.92 0.00 0.00 3.02
542 543 2.347452 CGCGTATTTGGATTCGTCTTGT 59.653 45.455 0.00 0.00 0.00 3.16
543 544 3.181524 CGCGTATTTGGATTCGTCTTGTT 60.182 43.478 0.00 0.00 0.00 2.83
544 545 4.088648 GCGTATTTGGATTCGTCTTGTTG 58.911 43.478 0.00 0.00 0.00 3.33
545 546 4.378046 GCGTATTTGGATTCGTCTTGTTGT 60.378 41.667 0.00 0.00 0.00 3.32
546 547 5.685841 CGTATTTGGATTCGTCTTGTTGTT 58.314 37.500 0.00 0.00 0.00 2.83
547 548 5.788531 CGTATTTGGATTCGTCTTGTTGTTC 59.211 40.000 0.00 0.00 0.00 3.18
548 549 6.347402 CGTATTTGGATTCGTCTTGTTGTTCT 60.347 38.462 0.00 0.00 0.00 3.01
549 550 4.811555 TTGGATTCGTCTTGTTGTTCTG 57.188 40.909 0.00 0.00 0.00 3.02
550 551 4.066646 TGGATTCGTCTTGTTGTTCTGA 57.933 40.909 0.00 0.00 0.00 3.27
551 552 4.058124 TGGATTCGTCTTGTTGTTCTGAG 58.942 43.478 0.00 0.00 0.00 3.35
552 553 3.120511 GGATTCGTCTTGTTGTTCTGAGC 60.121 47.826 0.00 0.00 0.00 4.26
553 554 2.595124 TCGTCTTGTTGTTCTGAGCA 57.405 45.000 0.00 0.00 0.00 4.26
554 555 2.899976 TCGTCTTGTTGTTCTGAGCAA 58.100 42.857 2.62 2.62 0.00 3.91
555 556 2.607635 TCGTCTTGTTGTTCTGAGCAAC 59.392 45.455 24.74 24.74 44.50 4.17
556 557 2.609459 CGTCTTGTTGTTCTGAGCAACT 59.391 45.455 29.04 0.00 44.54 3.16
557 558 3.063997 CGTCTTGTTGTTCTGAGCAACTT 59.936 43.478 29.04 0.00 44.54 2.66
558 559 4.437390 CGTCTTGTTGTTCTGAGCAACTTT 60.437 41.667 29.04 0.00 44.54 2.66
559 560 5.030936 GTCTTGTTGTTCTGAGCAACTTTC 58.969 41.667 29.04 17.06 44.54 2.62
560 561 4.699735 TCTTGTTGTTCTGAGCAACTTTCA 59.300 37.500 29.04 13.06 44.54 2.69
561 562 5.357878 TCTTGTTGTTCTGAGCAACTTTCAT 59.642 36.000 29.04 0.00 44.54 2.57
562 563 4.923893 TGTTGTTCTGAGCAACTTTCATG 58.076 39.130 29.04 0.00 44.54 3.07
563 564 4.398988 TGTTGTTCTGAGCAACTTTCATGT 59.601 37.500 29.04 0.00 44.54 3.21
564 565 5.588246 TGTTGTTCTGAGCAACTTTCATGTA 59.412 36.000 29.04 10.94 44.54 2.29
565 566 5.929697 TGTTCTGAGCAACTTTCATGTAG 57.070 39.130 0.00 0.00 0.00 2.74
566 567 5.610398 TGTTCTGAGCAACTTTCATGTAGA 58.390 37.500 0.00 0.00 0.00 2.59
567 568 6.054941 TGTTCTGAGCAACTTTCATGTAGAA 58.945 36.000 0.00 0.00 0.00 2.10
568 569 6.542005 TGTTCTGAGCAACTTTCATGTAGAAA 59.458 34.615 0.00 0.00 43.71 2.52
569 570 7.066887 TGTTCTGAGCAACTTTCATGTAGAAAA 59.933 33.333 0.00 0.00 45.11 2.29
570 571 6.959361 TCTGAGCAACTTTCATGTAGAAAAC 58.041 36.000 0.00 0.00 45.11 2.43
571 572 6.542005 TCTGAGCAACTTTCATGTAGAAAACA 59.458 34.615 0.00 0.00 45.11 2.83
585 586 7.504924 TGTAGAAAACATTTTCATCCGAGTT 57.495 32.000 17.12 0.00 46.81 3.01
586 587 8.610248 TGTAGAAAACATTTTCATCCGAGTTA 57.390 30.769 17.12 0.00 46.81 2.24
587 588 8.500773 TGTAGAAAACATTTTCATCCGAGTTAC 58.499 33.333 17.12 9.62 46.81 2.50
588 589 7.504924 AGAAAACATTTTCATCCGAGTTACA 57.495 32.000 17.12 0.00 46.81 2.41
589 590 7.584987 AGAAAACATTTTCATCCGAGTTACAG 58.415 34.615 17.12 0.00 46.81 2.74
590 591 7.444183 AGAAAACATTTTCATCCGAGTTACAGA 59.556 33.333 17.12 0.00 46.81 3.41
591 592 7.687941 AAACATTTTCATCCGAGTTACAGAT 57.312 32.000 0.00 0.00 0.00 2.90
592 593 7.687941 AACATTTTCATCCGAGTTACAGATT 57.312 32.000 0.00 0.00 0.00 2.40
593 594 8.786826 AACATTTTCATCCGAGTTACAGATTA 57.213 30.769 0.00 0.00 0.00 1.75
594 595 8.786826 ACATTTTCATCCGAGTTACAGATTAA 57.213 30.769 0.00 0.00 0.00 1.40
595 596 9.396022 ACATTTTCATCCGAGTTACAGATTAAT 57.604 29.630 0.00 0.00 0.00 1.40
711 1763 0.039798 GTGCTTCTGGTCGTACGTCA 60.040 55.000 16.05 13.58 0.00 4.35
899 4029 2.203337 ACGCAGCACCACCACAAT 60.203 55.556 0.00 0.00 0.00 2.71
1014 4144 1.384191 GGCCATGGACCAGGTCTTT 59.616 57.895 18.40 4.32 32.47 2.52
1043 4173 0.250858 TACGTCTTCCTCCACGTCCA 60.251 55.000 0.00 0.00 46.04 4.02
1129 4494 2.168521 GAGGCCAAGTACTATGCTGACA 59.831 50.000 5.01 0.00 0.00 3.58
1198 4563 4.497984 AGCACCACCGCAACCACA 62.498 61.111 0.00 0.00 0.00 4.17
1273 4638 3.755628 CGACTTCCCCTTCGCCGA 61.756 66.667 0.00 0.00 0.00 5.54
1309 4674 0.603569 ACGCGAAGTCTCCAATCACT 59.396 50.000 15.93 0.00 0.00 3.41
1770 5135 0.853530 GGGGTTGCTTCCCTGGATAT 59.146 55.000 14.53 0.00 46.27 1.63
2290 5659 2.815211 TGCATCTTGCTCGCGTCC 60.815 61.111 5.77 0.00 45.31 4.79
2293 5662 1.153765 CATCTTGCTCGCGTCCTGA 60.154 57.895 5.77 0.00 0.00 3.86
2309 5678 2.283780 CTGATTCGCCTTGCACGACG 62.284 60.000 0.00 0.00 39.67 5.12
2316 5685 3.726517 CTTGCACGACGGCTTGGG 61.727 66.667 0.00 0.00 34.04 4.12
2341 5811 2.103263 GGAGGGTGTGCTCCTAATACTG 59.897 54.545 0.00 0.00 36.84 2.74
2345 5815 1.136305 GTGTGCTCCTAATACTGGCGA 59.864 52.381 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.663298 AGGGGGTCTTGATGATATCCT 57.337 47.619 0.00 0.00 0.00 3.24
257 258 3.254060 CCTCGAAGAACACGATGAACAT 58.746 45.455 0.00 0.00 39.02 2.71
335 336 3.000041 CCTTGTCGTGCTTAGTATTGCA 59.000 45.455 0.00 0.00 36.79 4.08
337 338 5.636121 TGTTACCTTGTCGTGCTTAGTATTG 59.364 40.000 0.00 0.00 0.00 1.90
339 340 5.395682 TGTTACCTTGTCGTGCTTAGTAT 57.604 39.130 0.00 0.00 0.00 2.12
340 341 4.852134 TGTTACCTTGTCGTGCTTAGTA 57.148 40.909 0.00 0.00 0.00 1.82
342 343 4.304110 TCTTGTTACCTTGTCGTGCTTAG 58.696 43.478 0.00 0.00 0.00 2.18
343 344 4.325028 TCTTGTTACCTTGTCGTGCTTA 57.675 40.909 0.00 0.00 0.00 3.09
344 345 3.188159 TCTTGTTACCTTGTCGTGCTT 57.812 42.857 0.00 0.00 0.00 3.91
345 346 2.902705 TCTTGTTACCTTGTCGTGCT 57.097 45.000 0.00 0.00 0.00 4.40
346 347 2.349532 GCTTCTTGTTACCTTGTCGTGC 60.350 50.000 0.00 0.00 0.00 5.34
347 348 2.869801 TGCTTCTTGTTACCTTGTCGTG 59.130 45.455 0.00 0.00 0.00 4.35
349 350 3.131396 AGTGCTTCTTGTTACCTTGTCG 58.869 45.455 0.00 0.00 0.00 4.35
350 351 4.691216 CCTAGTGCTTCTTGTTACCTTGTC 59.309 45.833 0.00 0.00 0.00 3.18
351 352 4.505039 CCCTAGTGCTTCTTGTTACCTTGT 60.505 45.833 0.00 0.00 0.00 3.16
352 353 4.003648 CCCTAGTGCTTCTTGTTACCTTG 58.996 47.826 0.00 0.00 0.00 3.61
354 355 2.572104 CCCCTAGTGCTTCTTGTTACCT 59.428 50.000 0.00 0.00 0.00 3.08
355 356 2.305052 ACCCCTAGTGCTTCTTGTTACC 59.695 50.000 0.00 0.00 0.00 2.85
356 357 3.335579 CACCCCTAGTGCTTCTTGTTAC 58.664 50.000 0.00 0.00 40.28 2.50
357 358 3.695830 CACCCCTAGTGCTTCTTGTTA 57.304 47.619 0.00 0.00 40.28 2.41
358 359 2.568623 CACCCCTAGTGCTTCTTGTT 57.431 50.000 0.00 0.00 40.28 2.83
361 362 7.131302 CGATAGAACACCCCTAGTGCTTCTT 62.131 48.000 12.50 5.23 46.01 2.52
362 363 5.708981 CGATAGAACACCCCTAGTGCTTCT 61.709 50.000 12.14 12.14 46.01 2.85
363 364 3.491104 CGATAGAACACCCCTAGTGCTTC 60.491 52.174 0.00 0.00 46.01 3.86
364 365 2.431057 CGATAGAACACCCCTAGTGCTT 59.569 50.000 0.00 0.00 46.01 3.91
365 366 2.032620 CGATAGAACACCCCTAGTGCT 58.967 52.381 0.00 0.00 46.01 4.40
366 367 1.538419 GCGATAGAACACCCCTAGTGC 60.538 57.143 0.00 0.00 46.01 4.40
368 369 2.032620 CTGCGATAGAACACCCCTAGT 58.967 52.381 0.00 0.00 39.76 2.57
370 371 1.410004 CCTGCGATAGAACACCCCTA 58.590 55.000 0.00 0.00 39.76 3.53
371 372 1.338136 CCCTGCGATAGAACACCCCT 61.338 60.000 0.00 0.00 39.76 4.79
372 373 1.146263 CCCTGCGATAGAACACCCC 59.854 63.158 0.00 0.00 39.76 4.95
373 374 1.523938 GCCCTGCGATAGAACACCC 60.524 63.158 0.00 0.00 39.76 4.61
374 375 0.750850 TAGCCCTGCGATAGAACACC 59.249 55.000 0.00 0.00 39.76 4.16
375 376 1.136305 TGTAGCCCTGCGATAGAACAC 59.864 52.381 0.00 0.00 39.76 3.32
376 377 1.136305 GTGTAGCCCTGCGATAGAACA 59.864 52.381 0.00 0.00 39.76 3.18
377 378 1.854227 GTGTAGCCCTGCGATAGAAC 58.146 55.000 0.00 0.00 39.76 3.01
378 379 0.384309 CGTGTAGCCCTGCGATAGAA 59.616 55.000 0.00 0.00 39.76 2.10
379 380 0.464916 TCGTGTAGCCCTGCGATAGA 60.465 55.000 0.00 0.00 39.76 1.98
380 381 0.598562 ATCGTGTAGCCCTGCGATAG 59.401 55.000 0.00 0.00 41.46 2.08
381 382 1.538512 GTATCGTGTAGCCCTGCGATA 59.461 52.381 0.00 0.00 42.84 2.92
382 383 0.314302 GTATCGTGTAGCCCTGCGAT 59.686 55.000 8.47 8.47 44.67 4.58
383 384 1.731433 GGTATCGTGTAGCCCTGCGA 61.731 60.000 0.00 0.00 37.76 5.10
384 385 1.299926 GGTATCGTGTAGCCCTGCG 60.300 63.158 0.00 0.00 0.00 5.18
385 386 1.299926 CGGTATCGTGTAGCCCTGC 60.300 63.158 0.00 0.00 0.00 4.85
386 387 0.030369 GTCGGTATCGTGTAGCCCTG 59.970 60.000 0.00 0.00 37.69 4.45
387 388 1.442526 CGTCGGTATCGTGTAGCCCT 61.443 60.000 0.00 0.00 37.69 5.19
388 389 1.009222 CGTCGGTATCGTGTAGCCC 60.009 63.158 0.00 0.00 37.69 5.19
389 390 0.378257 TTCGTCGGTATCGTGTAGCC 59.622 55.000 0.00 0.00 37.69 3.93
390 391 1.596464 CCTTCGTCGGTATCGTGTAGC 60.596 57.143 0.00 0.00 37.69 3.58
391 392 1.935873 TCCTTCGTCGGTATCGTGTAG 59.064 52.381 0.00 0.00 37.69 2.74
392 393 2.022764 TCCTTCGTCGGTATCGTGTA 57.977 50.000 0.00 0.00 37.69 2.90
393 394 1.131883 CTTCCTTCGTCGGTATCGTGT 59.868 52.381 0.00 0.00 37.69 4.49
394 395 1.399440 TCTTCCTTCGTCGGTATCGTG 59.601 52.381 0.00 0.00 37.69 4.35
395 396 1.742761 TCTTCCTTCGTCGGTATCGT 58.257 50.000 0.00 0.00 37.69 3.73
396 397 4.217497 GTTATCTTCCTTCGTCGGTATCG 58.783 47.826 0.00 0.00 37.82 2.92
397 398 5.179045 TGTTATCTTCCTTCGTCGGTATC 57.821 43.478 0.00 0.00 0.00 2.24
398 399 5.278858 GGATGTTATCTTCCTTCGTCGGTAT 60.279 44.000 0.00 0.00 35.71 2.73
399 400 4.037208 GGATGTTATCTTCCTTCGTCGGTA 59.963 45.833 0.00 0.00 35.71 4.02
400 401 3.181478 GGATGTTATCTTCCTTCGTCGGT 60.181 47.826 0.00 0.00 35.71 4.69
401 402 3.381949 GGATGTTATCTTCCTTCGTCGG 58.618 50.000 0.00 0.00 35.71 4.79
402 403 3.043586 CGGATGTTATCTTCCTTCGTCG 58.956 50.000 4.67 0.00 36.23 5.12
403 404 4.036498 TCTCGGATGTTATCTTCCTTCGTC 59.964 45.833 4.67 0.00 36.23 4.20
404 405 3.952323 TCTCGGATGTTATCTTCCTTCGT 59.048 43.478 4.67 0.00 36.23 3.85
405 406 4.569761 TCTCGGATGTTATCTTCCTTCG 57.430 45.455 4.67 0.00 36.23 3.79
406 407 6.284459 ACATTCTCGGATGTTATCTTCCTTC 58.716 40.000 4.67 0.00 36.92 3.46
407 408 6.240549 ACATTCTCGGATGTTATCTTCCTT 57.759 37.500 4.67 0.00 36.92 3.36
408 409 5.878406 ACATTCTCGGATGTTATCTTCCT 57.122 39.130 4.67 0.00 36.92 3.36
409 410 6.927294 AAACATTCTCGGATGTTATCTTCC 57.073 37.500 4.10 0.00 46.53 3.46
410 411 7.410485 GGAAAACATTCTCGGATGTTATCTTC 58.590 38.462 4.10 5.12 46.53 2.87
411 412 6.318900 GGGAAAACATTCTCGGATGTTATCTT 59.681 38.462 4.10 0.00 46.53 2.40
412 413 5.823045 GGGAAAACATTCTCGGATGTTATCT 59.177 40.000 4.10 0.00 46.53 1.98
413 414 5.277345 CGGGAAAACATTCTCGGATGTTATC 60.277 44.000 4.10 0.00 46.53 1.75
414 415 4.574828 CGGGAAAACATTCTCGGATGTTAT 59.425 41.667 4.10 0.00 46.53 1.89
415 416 3.936453 CGGGAAAACATTCTCGGATGTTA 59.064 43.478 4.10 0.00 46.53 2.41
417 418 2.027561 TCGGGAAAACATTCTCGGATGT 60.028 45.455 10.57 0.00 44.53 3.06
418 419 2.627945 TCGGGAAAACATTCTCGGATG 58.372 47.619 10.57 0.00 44.53 3.51
419 420 3.270877 CTTCGGGAAAACATTCTCGGAT 58.729 45.455 10.57 0.00 44.53 4.18
420 421 2.038033 ACTTCGGGAAAACATTCTCGGA 59.962 45.455 10.57 1.44 44.53 4.55
421 422 2.423577 ACTTCGGGAAAACATTCTCGG 58.576 47.619 10.57 0.00 44.53 4.63
422 423 4.219033 CAAACTTCGGGAAAACATTCTCG 58.781 43.478 4.53 4.53 45.70 4.04
423 424 4.546570 CCAAACTTCGGGAAAACATTCTC 58.453 43.478 0.00 0.00 0.00 2.87
424 425 3.243737 GCCAAACTTCGGGAAAACATTCT 60.244 43.478 0.00 0.00 0.00 2.40
425 426 3.057019 GCCAAACTTCGGGAAAACATTC 58.943 45.455 0.00 0.00 0.00 2.67
426 427 2.432510 TGCCAAACTTCGGGAAAACATT 59.567 40.909 0.00 0.00 0.00 2.71
427 428 2.035632 TGCCAAACTTCGGGAAAACAT 58.964 42.857 0.00 0.00 0.00 2.71
428 429 1.475403 TGCCAAACTTCGGGAAAACA 58.525 45.000 0.00 0.00 0.00 2.83
429 430 2.812358 ATGCCAAACTTCGGGAAAAC 57.188 45.000 0.00 0.00 0.00 2.43
430 431 3.493524 GGAAATGCCAAACTTCGGGAAAA 60.494 43.478 0.00 0.00 36.34 2.29
431 432 2.036604 GGAAATGCCAAACTTCGGGAAA 59.963 45.455 0.00 0.00 36.34 3.13
432 433 1.616374 GGAAATGCCAAACTTCGGGAA 59.384 47.619 0.00 0.00 36.34 3.97
433 434 1.253100 GGAAATGCCAAACTTCGGGA 58.747 50.000 0.00 0.00 36.34 5.14
434 435 0.109319 CGGAAATGCCAAACTTCGGG 60.109 55.000 0.00 0.00 35.94 5.14
435 436 0.109319 CCGGAAATGCCAAACTTCGG 60.109 55.000 0.00 0.00 35.94 4.30
436 437 0.878416 TCCGGAAATGCCAAACTTCG 59.122 50.000 0.00 0.00 35.94 3.79
437 438 1.611491 TGTCCGGAAATGCCAAACTTC 59.389 47.619 5.23 0.00 35.94 3.01
438 439 1.613437 CTGTCCGGAAATGCCAAACTT 59.387 47.619 5.23 0.00 35.94 2.66
439 440 1.247567 CTGTCCGGAAATGCCAAACT 58.752 50.000 5.23 0.00 35.94 2.66
440 441 0.243636 CCTGTCCGGAAATGCCAAAC 59.756 55.000 5.23 0.00 35.94 2.93
441 442 1.531739 GCCTGTCCGGAAATGCCAAA 61.532 55.000 5.23 0.00 35.94 3.28
442 443 1.976474 GCCTGTCCGGAAATGCCAA 60.976 57.895 5.23 0.00 35.94 4.52
443 444 2.361104 GCCTGTCCGGAAATGCCA 60.361 61.111 5.23 0.00 35.94 4.92
444 445 3.508840 CGCCTGTCCGGAAATGCC 61.509 66.667 15.45 0.00 33.16 4.40
445 446 1.582610 TTTCGCCTGTCCGGAAATGC 61.583 55.000 5.23 9.19 33.16 3.56
446 447 0.168128 GTTTCGCCTGTCCGGAAATG 59.832 55.000 5.23 0.00 33.16 2.32
447 448 1.296056 CGTTTCGCCTGTCCGGAAAT 61.296 55.000 5.23 0.00 33.16 2.17
448 449 1.957186 CGTTTCGCCTGTCCGGAAA 60.957 57.895 5.23 0.00 33.16 3.13
449 450 2.356553 CGTTTCGCCTGTCCGGAA 60.357 61.111 5.23 0.00 33.16 4.30
450 451 4.367023 CCGTTTCGCCTGTCCGGA 62.367 66.667 0.00 0.00 41.08 5.14
451 452 4.367023 TCCGTTTCGCCTGTCCGG 62.367 66.667 0.00 0.00 39.98 5.14
452 453 2.809601 CTCCGTTTCGCCTGTCCG 60.810 66.667 0.00 0.00 0.00 4.79
453 454 2.434359 CCTCCGTTTCGCCTGTCC 60.434 66.667 0.00 0.00 0.00 4.02
454 455 2.434359 CCCTCCGTTTCGCCTGTC 60.434 66.667 0.00 0.00 0.00 3.51
455 456 4.016706 CCCCTCCGTTTCGCCTGT 62.017 66.667 0.00 0.00 0.00 4.00
456 457 2.741486 TTTCCCCTCCGTTTCGCCTG 62.741 60.000 0.00 0.00 0.00 4.85
457 458 2.465055 CTTTCCCCTCCGTTTCGCCT 62.465 60.000 0.00 0.00 0.00 5.52
458 459 2.032987 TTTCCCCTCCGTTTCGCC 59.967 61.111 0.00 0.00 0.00 5.54
459 460 2.038837 CCTTTCCCCTCCGTTTCGC 61.039 63.158 0.00 0.00 0.00 4.70
460 461 0.250597 AACCTTTCCCCTCCGTTTCG 60.251 55.000 0.00 0.00 0.00 3.46
461 462 1.244816 CAACCTTTCCCCTCCGTTTC 58.755 55.000 0.00 0.00 0.00 2.78
462 463 0.826256 GCAACCTTTCCCCTCCGTTT 60.826 55.000 0.00 0.00 0.00 3.60
463 464 1.228459 GCAACCTTTCCCCTCCGTT 60.228 57.895 0.00 0.00 0.00 4.44
464 465 1.789576 ATGCAACCTTTCCCCTCCGT 61.790 55.000 0.00 0.00 0.00 4.69
465 466 1.000896 ATGCAACCTTTCCCCTCCG 60.001 57.895 0.00 0.00 0.00 4.63
466 467 0.251787 ACATGCAACCTTTCCCCTCC 60.252 55.000 0.00 0.00 0.00 4.30
467 468 1.632589 AACATGCAACCTTTCCCCTC 58.367 50.000 0.00 0.00 0.00 4.30
468 469 1.693606 CAAACATGCAACCTTTCCCCT 59.306 47.619 0.00 0.00 0.00 4.79
469 470 1.877680 GCAAACATGCAACCTTTCCCC 60.878 52.381 0.00 0.00 34.41 4.81
470 471 1.070601 AGCAAACATGCAACCTTTCCC 59.929 47.619 3.41 0.00 37.25 3.97
471 472 2.531522 AGCAAACATGCAACCTTTCC 57.468 45.000 3.41 0.00 37.25 3.13
472 473 3.368843 GCATAGCAAACATGCAACCTTTC 59.631 43.478 3.41 0.00 46.47 2.62
473 474 3.328505 GCATAGCAAACATGCAACCTTT 58.671 40.909 3.41 0.00 46.47 3.11
474 475 2.963432 GCATAGCAAACATGCAACCTT 58.037 42.857 3.41 0.00 46.47 3.50
475 476 2.660189 GCATAGCAAACATGCAACCT 57.340 45.000 3.41 0.00 46.47 3.50
481 482 1.610522 GCCCCTAGCATAGCAAACATG 59.389 52.381 0.00 0.00 42.97 3.21
482 483 1.815408 CGCCCCTAGCATAGCAAACAT 60.815 52.381 0.00 0.00 44.04 2.71
483 484 0.463654 CGCCCCTAGCATAGCAAACA 60.464 55.000 0.00 0.00 44.04 2.83
484 485 0.463833 ACGCCCCTAGCATAGCAAAC 60.464 55.000 0.00 0.00 44.04 2.93
485 486 0.463654 CACGCCCCTAGCATAGCAAA 60.464 55.000 0.00 0.00 44.04 3.68
486 487 1.146041 CACGCCCCTAGCATAGCAA 59.854 57.895 0.00 0.00 44.04 3.91
487 488 2.063979 ACACGCCCCTAGCATAGCA 61.064 57.895 0.00 0.00 44.04 3.49
488 489 1.595382 CACACGCCCCTAGCATAGC 60.595 63.158 0.00 0.00 44.04 2.97
489 490 1.069765 CCACACGCCCCTAGCATAG 59.930 63.158 0.00 0.00 44.04 2.23
490 491 3.101796 GCCACACGCCCCTAGCATA 62.102 63.158 0.00 0.00 44.04 3.14
491 492 4.489771 GCCACACGCCCCTAGCAT 62.490 66.667 0.00 0.00 44.04 3.79
500 501 4.147322 CATTCGTCCGCCACACGC 62.147 66.667 0.00 0.00 41.76 5.34
501 502 3.487202 CCATTCGTCCGCCACACG 61.487 66.667 0.00 0.00 43.15 4.49
502 503 3.124921 CCCATTCGTCCGCCACAC 61.125 66.667 0.00 0.00 0.00 3.82
509 510 3.802418 ATACGCGGCCCATTCGTCC 62.802 63.158 12.47 0.00 37.61 4.79
510 511 1.433837 AAATACGCGGCCCATTCGTC 61.434 55.000 12.47 0.00 37.61 4.20
511 512 1.450669 AAATACGCGGCCCATTCGT 60.451 52.632 12.47 4.62 39.88 3.85
512 513 1.010125 CAAATACGCGGCCCATTCG 60.010 57.895 12.47 0.00 0.00 3.34
513 514 1.098712 TCCAAATACGCGGCCCATTC 61.099 55.000 12.47 0.00 0.00 2.67
514 515 0.467290 ATCCAAATACGCGGCCCATT 60.467 50.000 12.47 1.04 0.00 3.16
515 516 0.467290 AATCCAAATACGCGGCCCAT 60.467 50.000 12.47 0.00 0.00 4.00
516 517 1.077357 AATCCAAATACGCGGCCCA 60.077 52.632 12.47 0.00 0.00 5.36
517 518 1.652563 GAATCCAAATACGCGGCCC 59.347 57.895 12.47 0.00 0.00 5.80
518 519 1.278637 CGAATCCAAATACGCGGCC 59.721 57.895 12.47 0.00 0.00 6.13
519 520 0.042448 GACGAATCCAAATACGCGGC 60.042 55.000 12.47 0.00 0.00 6.53
520 521 1.567504 AGACGAATCCAAATACGCGG 58.432 50.000 12.47 0.00 0.00 6.46
521 522 2.347452 ACAAGACGAATCCAAATACGCG 59.653 45.455 3.53 3.53 0.00 6.01
522 523 4.088648 CAACAAGACGAATCCAAATACGC 58.911 43.478 0.00 0.00 0.00 4.42
523 524 5.277601 ACAACAAGACGAATCCAAATACG 57.722 39.130 0.00 0.00 0.00 3.06
524 525 6.797033 CAGAACAACAAGACGAATCCAAATAC 59.203 38.462 0.00 0.00 0.00 1.89
525 526 6.708502 TCAGAACAACAAGACGAATCCAAATA 59.291 34.615 0.00 0.00 0.00 1.40
526 527 5.530915 TCAGAACAACAAGACGAATCCAAAT 59.469 36.000 0.00 0.00 0.00 2.32
527 528 4.878971 TCAGAACAACAAGACGAATCCAAA 59.121 37.500 0.00 0.00 0.00 3.28
528 529 4.447290 TCAGAACAACAAGACGAATCCAA 58.553 39.130 0.00 0.00 0.00 3.53
529 530 4.058124 CTCAGAACAACAAGACGAATCCA 58.942 43.478 0.00 0.00 0.00 3.41
530 531 3.120511 GCTCAGAACAACAAGACGAATCC 60.121 47.826 0.00 0.00 0.00 3.01
531 532 3.494626 TGCTCAGAACAACAAGACGAATC 59.505 43.478 0.00 0.00 0.00 2.52
532 533 3.466836 TGCTCAGAACAACAAGACGAAT 58.533 40.909 0.00 0.00 0.00 3.34
533 534 2.899976 TGCTCAGAACAACAAGACGAA 58.100 42.857 0.00 0.00 0.00 3.85
534 535 2.595124 TGCTCAGAACAACAAGACGA 57.405 45.000 0.00 0.00 0.00 4.20
535 536 2.974165 GTTGCTCAGAACAACAAGACG 58.026 47.619 11.19 0.00 45.35 4.18
541 542 4.925068 ACATGAAAGTTGCTCAGAACAAC 58.075 39.130 8.44 8.44 46.18 3.32
542 543 6.054941 TCTACATGAAAGTTGCTCAGAACAA 58.945 36.000 0.00 0.00 0.00 2.83
543 544 5.610398 TCTACATGAAAGTTGCTCAGAACA 58.390 37.500 0.00 0.00 0.00 3.18
544 545 6.545504 TTCTACATGAAAGTTGCTCAGAAC 57.454 37.500 0.00 0.00 0.00 3.01
545 546 7.066887 TGTTTTCTACATGAAAGTTGCTCAGAA 59.933 33.333 0.00 0.00 44.40 3.02
546 547 6.542005 TGTTTTCTACATGAAAGTTGCTCAGA 59.458 34.615 0.00 0.00 44.40 3.27
547 548 6.728200 TGTTTTCTACATGAAAGTTGCTCAG 58.272 36.000 0.00 0.00 44.40 3.35
548 549 6.691754 TGTTTTCTACATGAAAGTTGCTCA 57.308 33.333 0.00 0.00 44.40 4.26
549 550 8.579682 AAATGTTTTCTACATGAAAGTTGCTC 57.420 30.769 0.00 0.00 46.75 4.26
550 551 8.947055 AAAATGTTTTCTACATGAAAGTTGCT 57.053 26.923 0.00 0.00 46.75 3.91
551 552 8.816144 TGAAAATGTTTTCTACATGAAAGTTGC 58.184 29.630 16.53 0.00 46.75 4.17
554 555 9.696917 GGATGAAAATGTTTTCTACATGAAAGT 57.303 29.630 16.53 0.00 46.75 2.66
555 556 8.853345 CGGATGAAAATGTTTTCTACATGAAAG 58.147 33.333 16.53 0.00 46.75 2.62
556 557 8.572185 TCGGATGAAAATGTTTTCTACATGAAA 58.428 29.630 16.53 0.00 46.75 2.69
557 558 8.105097 TCGGATGAAAATGTTTTCTACATGAA 57.895 30.769 16.53 0.00 46.75 2.57
558 559 7.390440 ACTCGGATGAAAATGTTTTCTACATGA 59.610 33.333 16.53 11.32 46.75 3.07
559 560 7.530010 ACTCGGATGAAAATGTTTTCTACATG 58.470 34.615 16.53 0.00 46.75 3.21
561 562 7.504924 AACTCGGATGAAAATGTTTTCTACA 57.495 32.000 16.53 1.36 45.14 2.74
562 563 8.500773 TGTAACTCGGATGAAAATGTTTTCTAC 58.499 33.333 16.53 11.11 45.14 2.59
563 564 8.610248 TGTAACTCGGATGAAAATGTTTTCTA 57.390 30.769 16.53 6.38 45.14 2.10
564 565 7.444183 TCTGTAACTCGGATGAAAATGTTTTCT 59.556 33.333 16.53 5.27 45.14 2.52
565 566 7.581476 TCTGTAACTCGGATGAAAATGTTTTC 58.419 34.615 10.49 10.49 45.13 2.29
566 567 7.504924 TCTGTAACTCGGATGAAAATGTTTT 57.495 32.000 0.00 0.00 0.00 2.43
567 568 7.687941 ATCTGTAACTCGGATGAAAATGTTT 57.312 32.000 0.00 0.00 40.30 2.83
568 569 7.687941 AATCTGTAACTCGGATGAAAATGTT 57.312 32.000 0.00 0.00 40.87 2.71
569 570 8.786826 TTAATCTGTAACTCGGATGAAAATGT 57.213 30.769 0.00 0.00 40.87 2.71
665 666 6.596497 CCGTGCTTTATTAGTAGGGAAAGAAA 59.404 38.462 0.00 0.00 44.42 2.52
899 4029 2.895680 GAGATGTGGCTGGCTCGA 59.104 61.111 2.00 0.00 0.00 4.04
995 4125 2.484287 AAAGACCTGGTCCATGGCCG 62.484 60.000 22.81 8.20 32.18 6.13
1273 4638 0.666577 CGTTCGTCGGCCTTCTTCTT 60.667 55.000 0.00 0.00 35.71 2.52
1626 4991 1.079127 CGACCAACAGCCTCGGATT 60.079 57.895 0.00 0.00 0.00 3.01
1770 5135 6.405953 CCGATGCTCTACCTTCTTTTCTTCTA 60.406 42.308 0.00 0.00 0.00 2.10
2290 5659 1.421485 GTCGTGCAAGGCGAATCAG 59.579 57.895 0.00 0.00 40.19 2.90
2293 5662 3.118454 CCGTCGTGCAAGGCGAAT 61.118 61.111 27.87 0.00 40.19 3.34
2298 5667 3.726517 CCAAGCCGTCGTGCAAGG 61.727 66.667 0.00 0.00 0.00 3.61
2331 5801 3.196901 ACATGTTGTCGCCAGTATTAGGA 59.803 43.478 0.00 0.00 0.00 2.94
2332 5802 3.531538 ACATGTTGTCGCCAGTATTAGG 58.468 45.455 0.00 0.00 0.00 2.69
2333 5803 4.778842 GACATGTTGTCGCCAGTATTAG 57.221 45.455 0.00 0.00 37.67 1.73
2345 5815 2.033299 CGCTCTTTGGTTGACATGTTGT 59.967 45.455 0.00 0.00 0.00 3.32
2540 6239 9.632638 AGCCTGCATAGAAAGAATTATAGAAAA 57.367 29.630 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.