Multiple sequence alignment - TraesCS2D01G430100

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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 TraesCS2D01G430100 chr2D 100.000 2198 0 0 1 2198 542327812 542330009 0.000000e+00 4060.0
1 TraesCS2D01G430100 chr2D 86.684 1149 82 34 937 2068 542710517 542711611 0.000000e+00 1208.0
2 TraesCS2D01G430100 chr2D 87.646 858 55 16 717 1542 542543683 542544521 0.000000e+00 950.0
3 TraesCS2D01G430100 chr2D 95.131 267 12 1 318 583 647763092 647763358 9.380000e-114 420.0
4 TraesCS2D01G430100 chr2D 88.056 360 24 7 858 1198 542777861 542778220 2.030000e-110 409.0
5 TraesCS2D01G430100 chr2D 94.677 263 12 2 327 588 406639784 406640045 7.310000e-110 407.0
6 TraesCS2D01G430100 chr2D 90.584 308 15 8 1526 1832 542544477 542544771 1.580000e-106 396.0
7 TraesCS2D01G430100 chr2D 93.243 148 7 1 1864 2011 542544768 542544912 4.750000e-52 215.0
8 TraesCS2D01G430100 chr2D 94.382 89 5 0 2110 2198 542711701 542711789 1.060000e-28 137.0
9 TraesCS2D01G430100 chr2D 96.970 33 1 0 1 33 542687616 542687648 3.050000e-04 56.5
10 TraesCS2D01G430100 chr2B 86.018 894 70 32 708 1571 647450780 647451648 0.000000e+00 907.0
11 TraesCS2D01G430100 chr2B 88.315 736 40 22 1278 1984 647539440 647540158 0.000000e+00 841.0
12 TraesCS2D01G430100 chr2B 85.082 610 33 20 1499 2100 647451607 647452166 8.810000e-159 569.0
13 TraesCS2D01G430100 chr2B 87.750 400 29 16 871 1255 647538951 647539345 1.200000e-122 449.0
14 TraesCS2D01G430100 chr2B 84.490 245 29 8 6 248 647538275 647538512 1.310000e-57 233.0
15 TraesCS2D01G430100 chr2B 85.616 146 8 8 1969 2114 647540595 647540727 8.180000e-30 141.0
16 TraesCS2D01G430100 chr2A 84.528 795 59 24 716 1478 685373379 685374141 0.000000e+00 728.0
17 TraesCS2D01G430100 chr2A 81.989 744 64 32 715 1449 685380371 685381053 3.170000e-158 568.0
18 TraesCS2D01G430100 chr2A 83.304 563 52 22 815 1338 685491357 685491916 4.240000e-132 481.0
19 TraesCS2D01G430100 chr2A 88.020 409 24 13 815 1198 685410477 685410885 5.530000e-126 460.0
20 TraesCS2D01G430100 chr2A 87.532 385 15 16 1495 1867 685381048 685381411 4.370000e-112 414.0
21 TraesCS2D01G430100 chr2A 80.600 567 39 28 1586 2114 685374188 685374721 2.670000e-99 372.0
22 TraesCS2D01G430100 chr2A 97.333 75 2 0 2124 2198 685381740 685381814 6.370000e-26 128.0
23 TraesCS2D01G430100 chr2A 89.873 79 3 3 1876 1954 685381464 685381537 1.800000e-16 97.1
24 TraesCS2D01G430100 chr2A 92.424 66 5 0 2000 2065 685381551 685381616 6.460000e-16 95.3
25 TraesCS2D01G430100 chr2A 97.297 37 1 0 1302 1338 685410968 685411004 1.820000e-06 63.9
26 TraesCS2D01G430100 chr6D 94.757 267 13 1 321 587 203349392 203349127 4.370000e-112 414.0
27 TraesCS2D01G430100 chr7D 94.717 265 13 1 324 588 96378914 96378651 5.650000e-111 411.0
28 TraesCS2D01G430100 chr7D 94.656 262 14 0 322 583 78042677 78042416 7.310000e-110 407.0
29 TraesCS2D01G430100 chr5B 94.697 264 13 1 325 588 273258509 273258247 2.030000e-110 409.0
30 TraesCS2D01G430100 chr1D 95.000 260 13 0 324 583 442997876 442998135 2.030000e-110 409.0
31 TraesCS2D01G430100 chr5D 94.007 267 16 0 317 583 301682386 301682120 2.630000e-109 405.0
32 TraesCS2D01G430100 chr1A 93.431 274 16 1 322 593 333917871 333918144 2.630000e-109 405.0


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 TraesCS2D01G430100 chr2D 542327812 542330009 2197 False 4060.000000 4060 100.00000 1 2198 1 chr2D.!!$F2 2197
1 TraesCS2D01G430100 chr2D 542710517 542711789 1272 False 672.500000 1208 90.53300 937 2198 2 chr2D.!!$F7 1261
2 TraesCS2D01G430100 chr2D 542543683 542544912 1229 False 520.333333 950 90.49100 717 2011 3 chr2D.!!$F6 1294
3 TraesCS2D01G430100 chr2B 647450780 647452166 1386 False 738.000000 907 85.55000 708 2100 2 chr2B.!!$F1 1392
4 TraesCS2D01G430100 chr2B 647538275 647540727 2452 False 416.000000 841 86.54275 6 2114 4 chr2B.!!$F2 2108
5 TraesCS2D01G430100 chr2A 685373379 685374721 1342 False 550.000000 728 82.56400 716 2114 2 chr2A.!!$F2 1398
6 TraesCS2D01G430100 chr2A 685491357 685491916 559 False 481.000000 481 83.30400 815 1338 1 chr2A.!!$F1 523
7 TraesCS2D01G430100 chr2A 685410477 685411004 527 False 261.950000 460 92.65850 815 1338 2 chr2A.!!$F4 523
8 TraesCS2D01G430100 chr2A 685380371 685381814 1443 False 260.480000 568 89.83020 715 2198 5 chr2A.!!$F3 1483

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
314 480 0.099968 TGTACACTAGCGCCGCTAAG 59.9 55.0 20.5 17.03 40.82 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1789 0.397941 TTGACAGAGAGGTTGCTGGG 59.602 55.0 0.0 0.0 36.47 4.45 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
42 43 5.750067 GGCAACATATACAAAGGAATTGCTG 59.250 40.000 0.00 0.00 43.13 4.41
46 47 1.555967 TACAAAGGAATTGCTGGGGC 58.444 50.000 0.00 0.00 43.13 5.80
64 65 1.137086 GGCATGGTGTATCGAGACAGT 59.863 52.381 14.18 0.00 0.00 3.55
83 84 7.051623 AGACAGTCGAGAGAACAACTATATCT 58.948 38.462 0.00 0.00 45.01 1.98
121 122 2.359975 GTAGGCCCTGTTGCGCTT 60.360 61.111 9.73 0.00 0.00 4.68
123 124 0.675522 GTAGGCCCTGTTGCGCTTAA 60.676 55.000 9.73 0.00 0.00 1.85
124 125 0.254747 TAGGCCCTGTTGCGCTTAAT 59.745 50.000 9.73 0.00 0.00 1.40
127 128 0.179163 GCCCTGTTGCGCTTAATGTC 60.179 55.000 9.73 0.00 0.00 3.06
128 129 1.453155 CCCTGTTGCGCTTAATGTCT 58.547 50.000 9.73 0.00 0.00 3.41
129 130 2.627945 CCCTGTTGCGCTTAATGTCTA 58.372 47.619 9.73 0.00 0.00 2.59
130 131 3.206150 CCCTGTTGCGCTTAATGTCTAT 58.794 45.455 9.73 0.00 0.00 1.98
131 132 4.377021 CCCTGTTGCGCTTAATGTCTATA 58.623 43.478 9.73 0.00 0.00 1.31
136 137 6.802608 TGTTGCGCTTAATGTCTATACTAGT 58.197 36.000 9.73 0.00 0.00 2.57
174 176 9.507329 AAACTTTATCTTATCATGGATGCGTAT 57.493 29.630 0.00 0.00 0.00 3.06
176 178 8.314021 ACTTTATCTTATCATGGATGCGTATGA 58.686 33.333 0.00 0.00 37.68 2.15
205 207 2.953001 ATGGGCACACGCATGCATAAG 61.953 52.381 19.57 3.36 46.76 1.73
210 212 2.598589 CACACGCATGCATAAGCTTTT 58.401 42.857 19.57 0.00 42.74 2.27
211 213 2.988493 CACACGCATGCATAAGCTTTTT 59.012 40.909 19.57 0.00 42.74 1.94
212 214 4.165036 CACACGCATGCATAAGCTTTTTA 58.835 39.130 19.57 0.00 42.74 1.52
213 215 4.799949 CACACGCATGCATAAGCTTTTTAT 59.200 37.500 19.57 0.00 42.74 1.40
215 217 6.471841 CACACGCATGCATAAGCTTTTTATTA 59.528 34.615 19.57 0.00 42.74 0.98
218 220 9.345517 CACGCATGCATAAGCTTTTTATTATAT 57.654 29.630 19.57 0.00 42.74 0.86
251 258 8.908678 ACAAATATACACGTATAGTAATGCACG 58.091 33.333 0.00 0.00 40.15 5.34
256 263 4.563976 ACACGTATAGTAATGCACGAAACC 59.436 41.667 5.56 0.00 37.80 3.27
261 268 3.974871 AGTAATGCACGAAACCGTTTT 57.025 38.095 0.00 0.00 38.35 2.43
273 434 4.273235 CGAAACCGTTTTTGTAGTAAGGGT 59.727 41.667 0.00 0.00 42.52 4.34
274 435 5.465056 CGAAACCGTTTTTGTAGTAAGGGTA 59.535 40.000 0.00 0.00 40.53 3.69
279 440 8.361169 ACCGTTTTTGTAGTAAGGGTATAGTA 57.639 34.615 0.00 0.00 39.86 1.82
314 480 0.099968 TGTACACTAGCGCCGCTAAG 59.900 55.000 20.50 17.03 40.82 2.18
326 493 4.024302 AGCGCCGCTAAGGAAAAATAATAC 60.024 41.667 11.29 0.00 45.00 1.89
328 495 5.676953 CGCCGCTAAGGAAAAATAATACTC 58.323 41.667 0.00 0.00 45.00 2.59
329 496 5.333875 CGCCGCTAAGGAAAAATAATACTCC 60.334 44.000 0.00 0.00 45.00 3.85
330 497 5.333875 GCCGCTAAGGAAAAATAATACTCCG 60.334 44.000 0.00 0.00 45.00 4.63
331 498 5.756833 CCGCTAAGGAAAAATAATACTCCGT 59.243 40.000 0.00 0.00 45.00 4.69
332 499 6.073927 CCGCTAAGGAAAAATAATACTCCGTC 60.074 42.308 0.00 0.00 45.00 4.79
333 500 6.073927 CGCTAAGGAAAAATAATACTCCGTCC 60.074 42.308 0.00 0.00 32.91 4.79
334 501 6.073927 GCTAAGGAAAAATAATACTCCGTCCG 60.074 42.308 0.00 0.00 32.91 4.79
335 502 5.349061 AGGAAAAATAATACTCCGTCCGT 57.651 39.130 0.00 0.00 32.91 4.69
336 503 5.737860 AGGAAAAATAATACTCCGTCCGTT 58.262 37.500 0.00 0.00 32.91 4.44
337 504 5.814188 AGGAAAAATAATACTCCGTCCGTTC 59.186 40.000 0.00 0.00 32.91 3.95
338 505 5.007039 GGAAAAATAATACTCCGTCCGTTCC 59.993 44.000 0.00 0.00 0.00 3.62
340 507 4.950205 AATAATACTCCGTCCGTTCCAT 57.050 40.909 0.00 0.00 0.00 3.41
341 508 6.409524 AAATAATACTCCGTCCGTTCCATA 57.590 37.500 0.00 0.00 0.00 2.74
343 510 4.950205 AATACTCCGTCCGTTCCATAAT 57.050 40.909 0.00 0.00 0.00 1.28
344 511 2.596904 ACTCCGTCCGTTCCATAATG 57.403 50.000 0.00 0.00 0.00 1.90
345 512 1.829222 ACTCCGTCCGTTCCATAATGT 59.171 47.619 0.00 0.00 0.00 2.71
346 513 3.025978 ACTCCGTCCGTTCCATAATGTA 58.974 45.455 0.00 0.00 0.00 2.29
347 514 3.067742 ACTCCGTCCGTTCCATAATGTAG 59.932 47.826 0.00 0.00 0.00 2.74
348 515 3.025978 TCCGTCCGTTCCATAATGTAGT 58.974 45.455 0.00 0.00 0.00 2.73
349 516 3.120792 CCGTCCGTTCCATAATGTAGTG 58.879 50.000 0.00 0.00 0.00 2.74
350 517 3.429822 CCGTCCGTTCCATAATGTAGTGT 60.430 47.826 0.00 0.00 0.00 3.55
351 518 3.795101 CGTCCGTTCCATAATGTAGTGTC 59.205 47.826 0.00 0.00 0.00 3.67
352 519 4.439700 CGTCCGTTCCATAATGTAGTGTCT 60.440 45.833 0.00 0.00 0.00 3.41
353 520 5.220912 CGTCCGTTCCATAATGTAGTGTCTA 60.221 44.000 0.00 0.00 0.00 2.59
354 521 6.514541 CGTCCGTTCCATAATGTAGTGTCTAT 60.515 42.308 0.00 0.00 0.00 1.98
355 522 7.308169 CGTCCGTTCCATAATGTAGTGTCTATA 60.308 40.741 0.00 0.00 0.00 1.31
356 523 8.021973 GTCCGTTCCATAATGTAGTGTCTATAG 58.978 40.741 0.00 0.00 0.00 1.31
357 524 7.940688 TCCGTTCCATAATGTAGTGTCTATAGA 59.059 37.037 0.00 0.00 0.00 1.98
358 525 8.740906 CCGTTCCATAATGTAGTGTCTATAGAT 58.259 37.037 5.57 0.00 0.00 1.98
384 551 6.704512 TTTGAGAAGTCAAACTTTGCAAAC 57.295 33.333 8.05 0.00 45.82 2.93
385 552 4.411327 TGAGAAGTCAAACTTTGCAAACG 58.589 39.130 8.05 7.39 38.80 3.60
386 553 3.179048 AGAAGTCAAACTTTGCAAACGC 58.821 40.909 8.05 0.00 38.80 4.84
387 554 2.939460 AGTCAAACTTTGCAAACGCT 57.061 40.000 8.05 0.00 0.00 5.07
388 555 2.529151 AGTCAAACTTTGCAAACGCTG 58.471 42.857 8.05 5.61 0.00 5.18
389 556 2.163412 AGTCAAACTTTGCAAACGCTGA 59.837 40.909 8.05 7.89 0.00 4.26
390 557 2.278875 GTCAAACTTTGCAAACGCTGAC 59.721 45.455 19.21 19.21 0.00 3.51
391 558 1.587946 CAAACTTTGCAAACGCTGACC 59.412 47.619 8.05 0.00 0.00 4.02
392 559 0.814457 AACTTTGCAAACGCTGACCA 59.186 45.000 8.05 0.00 0.00 4.02
393 560 0.814457 ACTTTGCAAACGCTGACCAA 59.186 45.000 8.05 0.00 0.00 3.67
394 561 1.202290 ACTTTGCAAACGCTGACCAAG 60.202 47.619 8.05 0.00 0.00 3.61
395 562 0.814457 TTTGCAAACGCTGACCAAGT 59.186 45.000 8.05 0.00 0.00 3.16
396 563 0.814457 TTGCAAACGCTGACCAAGTT 59.186 45.000 0.00 0.00 0.00 2.66
397 564 0.814457 TGCAAACGCTGACCAAGTTT 59.186 45.000 0.00 0.00 38.46 2.66
399 566 2.559998 CAAACGCTGACCAAGTTTGT 57.440 45.000 16.00 0.00 45.49 2.83
400 567 3.684103 CAAACGCTGACCAAGTTTGTA 57.316 42.857 16.00 0.00 45.49 2.41
401 568 3.617669 CAAACGCTGACCAAGTTTGTAG 58.382 45.455 16.00 0.00 45.49 2.74
402 569 2.902705 ACGCTGACCAAGTTTGTAGA 57.097 45.000 0.00 0.00 0.00 2.59
403 570 2.755650 ACGCTGACCAAGTTTGTAGAG 58.244 47.619 0.00 0.00 0.00 2.43
404 571 2.364324 ACGCTGACCAAGTTTGTAGAGA 59.636 45.455 0.00 0.00 0.00 3.10
405 572 3.181469 ACGCTGACCAAGTTTGTAGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
406 573 3.807622 CGCTGACCAAGTTTGTAGAGAAA 59.192 43.478 0.00 0.00 0.00 2.52
407 574 4.272504 CGCTGACCAAGTTTGTAGAGAAAA 59.727 41.667 0.00 0.00 0.00 2.29
408 575 5.220777 CGCTGACCAAGTTTGTAGAGAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
409 576 6.513393 CGCTGACCAAGTTTGTAGAGAAAAAT 60.513 38.462 0.00 0.00 0.00 1.82
410 577 7.307751 CGCTGACCAAGTTTGTAGAGAAAAATA 60.308 37.037 0.00 0.00 0.00 1.40
411 578 7.803659 GCTGACCAAGTTTGTAGAGAAAAATAC 59.196 37.037 0.00 0.00 0.00 1.89
412 579 8.974060 TGACCAAGTTTGTAGAGAAAAATACT 57.026 30.769 0.00 0.00 0.00 2.12
413 580 9.403583 TGACCAAGTTTGTAGAGAAAAATACTT 57.596 29.630 0.00 0.00 0.00 2.24
518 685 9.703892 TGTAAATATTTTTCTCCACAAACATGG 57.296 29.630 5.91 0.00 41.57 3.66
519 686 9.705290 GTAAATATTTTTCTCCACAAACATGGT 57.295 29.630 5.91 0.00 40.95 3.55
520 687 8.831715 AAATATTTTTCTCCACAAACATGGTC 57.168 30.769 0.00 0.00 40.95 4.02
521 688 5.867903 ATTTTTCTCCACAAACATGGTCA 57.132 34.783 0.00 0.00 40.95 4.02
522 689 5.667539 TTTTTCTCCACAAACATGGTCAA 57.332 34.783 0.00 0.00 40.95 3.18
523 690 5.667539 TTTTCTCCACAAACATGGTCAAA 57.332 34.783 0.00 0.00 40.95 2.69
524 691 4.916983 TTCTCCACAAACATGGTCAAAG 57.083 40.909 0.00 0.00 40.95 2.77
525 692 3.897239 TCTCCACAAACATGGTCAAAGT 58.103 40.909 0.00 0.00 40.95 2.66
526 693 4.277476 TCTCCACAAACATGGTCAAAGTT 58.723 39.130 0.00 0.00 40.95 2.66
527 694 4.709397 TCTCCACAAACATGGTCAAAGTTT 59.291 37.500 0.00 0.00 40.95 2.66
532 699 5.954434 CAAACATGGTCAAAGTTTGTGAG 57.046 39.130 15.08 5.40 44.18 3.51
533 700 4.654091 AACATGGTCAAAGTTTGTGAGG 57.346 40.909 15.08 5.22 0.00 3.86
534 701 3.631250 ACATGGTCAAAGTTTGTGAGGT 58.369 40.909 15.08 5.79 0.00 3.85
535 702 4.023291 ACATGGTCAAAGTTTGTGAGGTT 58.977 39.130 15.08 0.00 0.00 3.50
536 703 4.466015 ACATGGTCAAAGTTTGTGAGGTTT 59.534 37.500 15.08 0.00 0.00 3.27
537 704 4.448537 TGGTCAAAGTTTGTGAGGTTTG 57.551 40.909 15.08 0.00 0.00 2.93
538 705 4.082845 TGGTCAAAGTTTGTGAGGTTTGA 58.917 39.130 15.08 0.00 36.74 2.69
541 708 5.975693 TCAAAGTTTGTGAGGTTTGACTT 57.024 34.783 15.08 0.00 34.72 3.01
542 709 6.339587 TCAAAGTTTGTGAGGTTTGACTTT 57.660 33.333 15.08 0.00 37.70 2.66
543 710 6.754193 TCAAAGTTTGTGAGGTTTGACTTTT 58.246 32.000 15.08 0.00 35.75 2.27
544 711 6.866248 TCAAAGTTTGTGAGGTTTGACTTTTC 59.134 34.615 15.08 0.00 35.75 2.29
545 712 5.975693 AGTTTGTGAGGTTTGACTTTTCA 57.024 34.783 0.00 0.00 0.00 2.69
546 713 6.339587 AGTTTGTGAGGTTTGACTTTTCAA 57.660 33.333 0.00 0.00 40.14 2.69
576 743 3.194005 AGGCACTACATTATGGAACGG 57.806 47.619 0.00 0.00 36.02 4.44
577 744 2.769663 AGGCACTACATTATGGAACGGA 59.230 45.455 0.00 0.00 36.02 4.69
578 745 3.131396 GGCACTACATTATGGAACGGAG 58.869 50.000 0.00 0.00 0.00 4.63
579 746 3.131396 GCACTACATTATGGAACGGAGG 58.869 50.000 0.00 0.00 0.00 4.30
580 747 3.728845 CACTACATTATGGAACGGAGGG 58.271 50.000 0.00 0.00 0.00 4.30
581 748 3.386726 CACTACATTATGGAACGGAGGGA 59.613 47.826 0.00 0.00 0.00 4.20
605 772 1.004511 ACTGTAGCGTGTACTCCTCCT 59.995 52.381 0.00 0.00 0.00 3.69
608 775 2.502947 TGTAGCGTGTACTCCTCCTCTA 59.497 50.000 0.00 0.00 0.00 2.43
610 777 1.560611 AGCGTGTACTCCTCCTCTAGT 59.439 52.381 0.00 0.00 0.00 2.57
611 778 2.026075 AGCGTGTACTCCTCCTCTAGTT 60.026 50.000 0.00 0.00 0.00 2.24
613 780 4.136051 GCGTGTACTCCTCCTCTAGTTAT 58.864 47.826 0.00 0.00 0.00 1.89
614 781 4.579753 GCGTGTACTCCTCCTCTAGTTATT 59.420 45.833 0.00 0.00 0.00 1.40
615 782 5.067544 GCGTGTACTCCTCCTCTAGTTATTT 59.932 44.000 0.00 0.00 0.00 1.40
616 783 6.405619 GCGTGTACTCCTCCTCTAGTTATTTT 60.406 42.308 0.00 0.00 0.00 1.82
617 784 7.201767 GCGTGTACTCCTCCTCTAGTTATTTTA 60.202 40.741 0.00 0.00 0.00 1.52
618 785 8.344098 CGTGTACTCCTCCTCTAGTTATTTTAG 58.656 40.741 0.00 0.00 0.00 1.85
619 786 8.631797 GTGTACTCCTCCTCTAGTTATTTTAGG 58.368 40.741 0.00 0.00 0.00 2.69
620 787 6.734502 ACTCCTCCTCTAGTTATTTTAGGC 57.265 41.667 0.00 0.00 0.00 3.93
621 788 6.203072 ACTCCTCCTCTAGTTATTTTAGGCA 58.797 40.000 0.00 0.00 0.00 4.75
622 789 6.672657 ACTCCTCCTCTAGTTATTTTAGGCAA 59.327 38.462 0.00 0.00 0.00 4.52
623 790 7.182206 ACTCCTCCTCTAGTTATTTTAGGCAAA 59.818 37.037 0.00 0.00 0.00 3.68
624 791 7.336396 TCCTCCTCTAGTTATTTTAGGCAAAC 58.664 38.462 0.00 0.00 0.00 2.93
625 792 7.182206 TCCTCCTCTAGTTATTTTAGGCAAACT 59.818 37.037 0.00 0.00 36.26 2.66
626 793 7.496263 CCTCCTCTAGTTATTTTAGGCAAACTC 59.504 40.741 0.00 0.00 34.23 3.01
627 794 7.336396 TCCTCTAGTTATTTTAGGCAAACTCC 58.664 38.462 0.00 0.00 34.23 3.85
628 795 7.182206 TCCTCTAGTTATTTTAGGCAAACTCCT 59.818 37.037 0.00 0.00 40.21 3.69
629 796 7.496263 CCTCTAGTTATTTTAGGCAAACTCCTC 59.504 40.741 0.00 0.00 37.66 3.71
630 797 7.336396 TCTAGTTATTTTAGGCAAACTCCTCC 58.664 38.462 0.00 0.00 37.66 4.30
631 798 5.887754 AGTTATTTTAGGCAAACTCCTCCA 58.112 37.500 0.00 0.00 37.66 3.86
632 799 5.710567 AGTTATTTTAGGCAAACTCCTCCAC 59.289 40.000 0.00 0.00 37.66 4.02
633 800 3.876309 TTTTAGGCAAACTCCTCCACT 57.124 42.857 0.00 0.00 37.66 4.00
634 801 4.986054 TTTTAGGCAAACTCCTCCACTA 57.014 40.909 0.00 0.00 37.66 2.74
635 802 4.553330 TTTAGGCAAACTCCTCCACTAG 57.447 45.455 0.00 0.00 37.66 2.57
636 803 2.031495 AGGCAAACTCCTCCACTAGT 57.969 50.000 0.00 0.00 0.00 2.57
637 804 3.185880 AGGCAAACTCCTCCACTAGTA 57.814 47.619 0.00 0.00 0.00 1.82
638 805 3.517612 AGGCAAACTCCTCCACTAGTAA 58.482 45.455 0.00 0.00 0.00 2.24
639 806 4.104831 AGGCAAACTCCTCCACTAGTAAT 58.895 43.478 0.00 0.00 0.00 1.89
640 807 4.536489 AGGCAAACTCCTCCACTAGTAATT 59.464 41.667 0.00 0.00 0.00 1.40
641 808 5.014228 AGGCAAACTCCTCCACTAGTAATTT 59.986 40.000 0.00 0.00 0.00 1.82
642 809 5.710567 GGCAAACTCCTCCACTAGTAATTTT 59.289 40.000 0.00 0.00 0.00 1.82
643 810 6.208797 GGCAAACTCCTCCACTAGTAATTTTT 59.791 38.462 0.00 0.00 0.00 1.94
661 828 1.665137 TTTTCAGGGGTACTCCTCCC 58.335 55.000 12.80 3.71 43.90 4.30
666 833 3.535574 GGGGTACTCCTCCCTAGTG 57.464 63.158 3.84 0.00 44.07 2.74
667 834 0.635555 GGGGTACTCCTCCCTAGTGT 59.364 60.000 3.84 0.00 44.07 3.55
668 835 1.008084 GGGGTACTCCTCCCTAGTGTT 59.992 57.143 3.84 0.00 44.07 3.32
669 836 2.561526 GGGGTACTCCTCCCTAGTGTTT 60.562 54.545 3.84 0.00 44.07 2.83
670 837 3.179685 GGGTACTCCTCCCTAGTGTTTT 58.820 50.000 0.00 0.00 41.58 2.43
671 838 3.586174 GGGTACTCCTCCCTAGTGTTTTT 59.414 47.826 0.00 0.00 41.58 1.94
757 932 4.389992 GGTCGTATATCCATCGAGACGTAA 59.610 45.833 0.00 0.00 34.33 3.18
760 935 3.851976 ATATCCATCGAGACGTAAGCC 57.148 47.619 0.00 0.00 45.62 4.35
768 943 0.456312 GAGACGTAAGCCAGTCGGTG 60.456 60.000 0.00 0.00 41.86 4.94
799 987 4.789075 AACGCGCGCAGGTCGTAT 62.789 61.111 32.58 3.21 41.07 3.06
846 1040 0.395311 CTCGCCCCCTCCGCTATATA 60.395 60.000 0.00 0.00 0.00 0.86
847 1041 0.260816 TCGCCCCCTCCGCTATATAT 59.739 55.000 0.00 0.00 0.00 0.86
851 1045 1.424638 CCCCTCCGCTATATATGGGG 58.575 60.000 7.94 7.94 46.89 4.96
855 1049 0.830648 TCCGCTATATATGGGGCTGC 59.169 55.000 7.53 0.00 37.43 5.25
869 1077 4.511246 CTGCCATGCCATCCCGGT 62.511 66.667 0.00 0.00 36.97 5.28
900 1109 5.754890 CACAAAAATCCCCAGACTTTTGAAG 59.245 40.000 14.45 5.20 46.92 3.02
1192 1429 1.058438 CGACTCGTCACCGTCTACG 59.942 63.158 0.00 0.00 40.40 3.51
1213 1451 2.486370 GGCTAGAAGAATCCAAGCCTCC 60.486 54.545 4.44 0.00 45.40 4.30
1235 1481 3.736433 CGCTCCTATCAATCGATCCATCC 60.736 52.174 0.00 0.00 32.73 3.51
1251 1497 1.154205 ATCCATCAACTAGCGTGCGC 61.154 55.000 8.67 8.67 42.33 6.09
1255 1501 0.172578 ATCAACTAGCGTGCGCAGTA 59.827 50.000 12.22 1.51 44.88 2.74
1281 1629 1.430992 TCCCCGAGTTCTTTGGTTCT 58.569 50.000 0.00 0.00 0.00 3.01
1282 1630 1.772453 TCCCCGAGTTCTTTGGTTCTT 59.228 47.619 0.00 0.00 0.00 2.52
1283 1631 1.880027 CCCCGAGTTCTTTGGTTCTTG 59.120 52.381 0.00 0.00 0.00 3.02
1392 1755 2.274948 ATCTGGTGGGCGTGCATCAT 62.275 55.000 0.00 0.00 0.00 2.45
1411 1789 1.032014 TGTGAAGGGCTGCAAAACTC 58.968 50.000 0.50 0.00 0.00 3.01
1412 1790 0.315251 GTGAAGGGCTGCAAAACTCC 59.685 55.000 0.50 0.00 0.00 3.85
1433 1828 2.289882 CCAGCAACCTCTCTGTCAATGA 60.290 50.000 0.00 0.00 0.00 2.57
1617 2049 2.203209 GGGACCGACCATCATGGC 60.203 66.667 2.52 0.00 42.67 4.40
1624 2056 1.005804 CGACCATCATGGCGATCGAG 61.006 60.000 21.57 5.10 42.67 4.04
1625 2057 0.032678 GACCATCATGGCGATCGAGT 59.967 55.000 21.57 0.00 42.67 4.18
1626 2058 0.249615 ACCATCATGGCGATCGAGTG 60.250 55.000 21.57 13.44 42.67 3.51
1627 2059 0.032540 CCATCATGGCGATCGAGTGA 59.967 55.000 21.57 18.25 29.21 3.41
1670 2102 0.968901 CCCAGTGACTAGCGTACCCA 60.969 60.000 0.00 0.00 0.00 4.51
1756 2191 5.163509 ACCTGAGCTGTTTTCTTTCCTTTTC 60.164 40.000 0.00 0.00 0.00 2.29
1758 2193 5.894807 TGAGCTGTTTTCTTTCCTTTTCTG 58.105 37.500 0.00 0.00 0.00 3.02
1875 2327 3.989787 CGCCCACAGGTTTTGGCC 61.990 66.667 0.00 0.00 40.87 5.36
1954 2455 2.495366 TTCGCGGGCAATCACGTACT 62.495 55.000 6.13 0.00 0.00 2.73
1995 2947 1.878522 GCGATTCGATCTGCACGGT 60.879 57.895 10.88 0.00 0.00 4.83
2039 2993 0.179215 GTCCAATCTGAACGCGCAAG 60.179 55.000 5.73 0.56 43.44 4.01
2103 3057 6.018098 GGAGTCTGTCATGACAATTCATCATC 60.018 42.308 27.63 16.05 40.79 2.92
2114 3068 5.475719 ACAATTCATCATCAGTTGCCAAAG 58.524 37.500 0.00 0.00 0.00 2.77
2134 3196 2.158234 AGGGGGAAGGTTAATTTGTGCA 60.158 45.455 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.594725 TGTTGCCAACAAACAATACTAGGAA 59.405 36.000 8.02 0.00 38.72 3.36
3 4 9.716507 GTATATGTTGCCAACAAACAATACTAG 57.283 33.333 15.17 0.00 45.86 2.57
15 16 6.035975 GCAATTCCTTTGTATATGTTGCCAAC 59.964 38.462 0.00 0.00 37.65 3.77
17 18 5.421693 AGCAATTCCTTTGTATATGTTGCCA 59.578 36.000 0.00 0.00 41.00 4.92
42 43 0.249911 GTCTCGATACACCATGCCCC 60.250 60.000 0.00 0.00 0.00 5.80
46 47 2.354821 TCGACTGTCTCGATACACCATG 59.645 50.000 6.21 0.00 46.75 3.66
83 84 5.401531 ACGGCTGAAGACATCTTAGTTTA 57.598 39.130 0.00 0.00 36.11 2.01
111 112 6.918569 ACTAGTATAGACATTAAGCGCAACAG 59.081 38.462 11.47 0.00 42.77 3.16
113 114 6.362820 GGACTAGTATAGACATTAAGCGCAAC 59.637 42.308 11.47 0.00 42.77 4.17
115 116 5.533528 TGGACTAGTATAGACATTAAGCGCA 59.466 40.000 11.47 0.00 42.77 6.09
121 122 9.483489 TGGTCTTTTGGACTAGTATAGACATTA 57.517 33.333 17.07 6.76 42.77 1.90
123 124 7.973048 TGGTCTTTTGGACTAGTATAGACAT 57.027 36.000 17.07 0.00 42.77 3.06
124 125 7.786046 TTGGTCTTTTGGACTAGTATAGACA 57.214 36.000 17.07 3.42 42.77 3.41
127 128 9.503399 AAGTTTTGGTCTTTTGGACTAGTATAG 57.497 33.333 0.00 0.00 46.50 1.31
128 129 9.856162 AAAGTTTTGGTCTTTTGGACTAGTATA 57.144 29.630 0.00 0.00 43.97 1.47
129 130 8.762481 AAAGTTTTGGTCTTTTGGACTAGTAT 57.238 30.769 0.00 0.00 43.97 2.12
130 131 9.856162 ATAAAGTTTTGGTCTTTTGGACTAGTA 57.144 29.630 0.00 0.00 43.97 1.82
131 132 8.762481 ATAAAGTTTTGGTCTTTTGGACTAGT 57.238 30.769 0.00 0.00 43.97 2.57
154 156 9.154847 CTTTTCATACGCATCCATGATAAGATA 57.845 33.333 0.00 0.00 40.08 1.98
174 176 1.340889 GTGTGCCCATCTTGCTTTTCA 59.659 47.619 0.00 0.00 0.00 2.69
176 178 0.314935 CGTGTGCCCATCTTGCTTTT 59.685 50.000 0.00 0.00 0.00 2.27
232 234 5.743398 GGTTTCGTGCATTACTATACGTGTA 59.257 40.000 0.00 0.00 37.74 2.90
251 258 5.756195 ACCCTTACTACAAAAACGGTTTC 57.244 39.130 6.57 0.00 0.00 2.78
293 454 0.309922 TAGCGGCGCTAGTGTACATC 59.690 55.000 35.39 0.57 40.44 3.06
326 493 2.596904 ACATTATGGAACGGACGGAG 57.403 50.000 0.00 0.00 0.00 4.63
328 495 3.120792 CACTACATTATGGAACGGACGG 58.879 50.000 0.00 0.00 0.00 4.79
329 496 3.777478 ACACTACATTATGGAACGGACG 58.223 45.455 0.00 0.00 0.00 4.79
330 497 5.007385 AGACACTACATTATGGAACGGAC 57.993 43.478 0.00 0.00 0.00 4.79
331 498 6.971726 ATAGACACTACATTATGGAACGGA 57.028 37.500 0.00 0.00 0.00 4.69
332 499 8.107399 TCTATAGACACTACATTATGGAACGG 57.893 38.462 0.00 0.00 0.00 4.44
359 526 7.568497 CGTTTGCAAAGTTTGACTTCTCAAAAA 60.568 33.333 19.82 3.43 45.89 1.94
360 527 6.128956 CGTTTGCAAAGTTTGACTTCTCAAAA 60.129 34.615 19.82 4.02 45.89 2.44
361 528 5.344665 CGTTTGCAAAGTTTGACTTCTCAAA 59.655 36.000 19.82 14.41 42.93 2.69
362 529 4.856487 CGTTTGCAAAGTTTGACTTCTCAA 59.144 37.500 19.82 9.48 37.47 3.02
363 530 4.411327 CGTTTGCAAAGTTTGACTTCTCA 58.589 39.130 19.82 3.64 37.47 3.27
364 531 3.240631 GCGTTTGCAAAGTTTGACTTCTC 59.759 43.478 19.82 0.92 37.47 2.87
365 532 3.119495 AGCGTTTGCAAAGTTTGACTTCT 60.119 39.130 19.82 5.93 46.23 2.85
366 533 3.000773 CAGCGTTTGCAAAGTTTGACTTC 60.001 43.478 19.82 2.02 46.23 3.01
367 534 2.923020 CAGCGTTTGCAAAGTTTGACTT 59.077 40.909 19.82 0.00 46.23 3.01
368 535 2.163412 TCAGCGTTTGCAAAGTTTGACT 59.837 40.909 19.82 1.11 46.23 3.41
369 536 2.278875 GTCAGCGTTTGCAAAGTTTGAC 59.721 45.455 23.05 23.05 46.23 3.18
370 537 2.525055 GTCAGCGTTTGCAAAGTTTGA 58.475 42.857 19.82 12.94 46.23 2.69
371 538 1.587946 GGTCAGCGTTTGCAAAGTTTG 59.412 47.619 13.26 11.41 46.23 2.93
372 539 1.203523 TGGTCAGCGTTTGCAAAGTTT 59.796 42.857 13.26 0.00 46.23 2.66
373 540 0.814457 TGGTCAGCGTTTGCAAAGTT 59.186 45.000 13.26 2.22 46.23 2.66
374 541 0.814457 TTGGTCAGCGTTTGCAAAGT 59.186 45.000 13.26 0.00 46.23 2.66
375 542 1.202290 ACTTGGTCAGCGTTTGCAAAG 60.202 47.619 13.26 8.11 46.23 2.77
376 543 0.814457 ACTTGGTCAGCGTTTGCAAA 59.186 45.000 8.05 8.05 46.23 3.68
377 544 0.814457 AACTTGGTCAGCGTTTGCAA 59.186 45.000 0.00 0.00 46.23 4.08
378 545 0.814457 AAACTTGGTCAGCGTTTGCA 59.186 45.000 0.00 0.00 46.23 4.08
379 546 1.199624 CAAACTTGGTCAGCGTTTGC 58.800 50.000 11.83 0.00 40.41 3.68
381 548 3.537580 TCTACAAACTTGGTCAGCGTTT 58.462 40.909 0.00 0.00 0.00 3.60
382 549 3.131396 CTCTACAAACTTGGTCAGCGTT 58.869 45.455 0.00 0.00 0.00 4.84
383 550 2.364324 TCTCTACAAACTTGGTCAGCGT 59.636 45.455 0.00 0.00 0.00 5.07
384 551 3.026630 TCTCTACAAACTTGGTCAGCG 57.973 47.619 0.00 0.00 0.00 5.18
385 552 5.751243 TTTTCTCTACAAACTTGGTCAGC 57.249 39.130 0.00 0.00 0.00 4.26
386 553 9.057089 AGTATTTTTCTCTACAAACTTGGTCAG 57.943 33.333 0.00 0.00 0.00 3.51
387 554 8.974060 AGTATTTTTCTCTACAAACTTGGTCA 57.026 30.769 0.00 0.00 0.00 4.02
492 659 9.703892 CCATGTTTGTGGAGAAAAATATTTACA 57.296 29.630 0.01 0.00 42.02 2.41
493 660 9.705290 ACCATGTTTGTGGAGAAAAATATTTAC 57.295 29.630 0.01 0.00 42.02 2.01
494 661 9.921637 GACCATGTTTGTGGAGAAAAATATTTA 57.078 29.630 0.01 0.00 42.02 1.40
495 662 8.428063 TGACCATGTTTGTGGAGAAAAATATTT 58.572 29.630 0.00 0.00 42.02 1.40
496 663 7.961351 TGACCATGTTTGTGGAGAAAAATATT 58.039 30.769 0.00 0.00 42.02 1.28
497 664 7.537596 TGACCATGTTTGTGGAGAAAAATAT 57.462 32.000 0.00 0.00 42.02 1.28
498 665 6.968263 TGACCATGTTTGTGGAGAAAAATA 57.032 33.333 0.00 0.00 42.02 1.40
499 666 5.867903 TGACCATGTTTGTGGAGAAAAAT 57.132 34.783 0.00 0.00 42.02 1.82
500 667 5.667539 TTGACCATGTTTGTGGAGAAAAA 57.332 34.783 0.00 0.00 42.02 1.94
501 668 5.186797 ACTTTGACCATGTTTGTGGAGAAAA 59.813 36.000 0.00 0.00 42.02 2.29
502 669 4.709397 ACTTTGACCATGTTTGTGGAGAAA 59.291 37.500 0.00 0.00 42.02 2.52
503 670 4.277476 ACTTTGACCATGTTTGTGGAGAA 58.723 39.130 0.00 0.00 42.02 2.87
504 671 3.897239 ACTTTGACCATGTTTGTGGAGA 58.103 40.909 0.00 0.00 42.02 3.71
505 672 4.654091 AACTTTGACCATGTTTGTGGAG 57.346 40.909 0.00 0.00 42.02 3.86
506 673 4.753233 CAAACTTTGACCATGTTTGTGGA 58.247 39.130 14.89 0.00 42.96 4.02
511 678 4.466015 ACCTCACAAACTTTGACCATGTTT 59.534 37.500 8.55 0.00 34.69 2.83
512 679 4.023291 ACCTCACAAACTTTGACCATGTT 58.977 39.130 8.55 0.00 0.00 2.71
513 680 3.631250 ACCTCACAAACTTTGACCATGT 58.369 40.909 8.55 0.00 0.00 3.21
514 681 4.654091 AACCTCACAAACTTTGACCATG 57.346 40.909 8.55 0.00 0.00 3.66
515 682 4.709397 TCAAACCTCACAAACTTTGACCAT 59.291 37.500 8.55 0.00 29.66 3.55
516 683 4.082463 GTCAAACCTCACAAACTTTGACCA 60.082 41.667 8.55 0.00 43.35 4.02
517 684 4.421058 GTCAAACCTCACAAACTTTGACC 58.579 43.478 8.55 0.00 43.35 4.02
518 685 5.310720 AGTCAAACCTCACAAACTTTGAC 57.689 39.130 8.55 12.19 46.84 3.18
519 686 5.975693 AAGTCAAACCTCACAAACTTTGA 57.024 34.783 8.55 0.00 31.68 2.69
520 687 6.644592 TGAAAAGTCAAACCTCACAAACTTTG 59.355 34.615 0.00 0.00 37.12 2.77
521 688 6.754193 TGAAAAGTCAAACCTCACAAACTTT 58.246 32.000 0.00 0.00 38.27 2.66
522 689 6.339587 TGAAAAGTCAAACCTCACAAACTT 57.660 33.333 0.00 0.00 0.00 2.66
523 690 5.975693 TGAAAAGTCAAACCTCACAAACT 57.024 34.783 0.00 0.00 0.00 2.66
548 715 9.726438 GTTCCATAATGTAGTGCCTATAGATTT 57.274 33.333 0.00 0.00 0.00 2.17
549 716 8.035394 CGTTCCATAATGTAGTGCCTATAGATT 58.965 37.037 0.00 0.00 0.00 2.40
550 717 7.363880 CCGTTCCATAATGTAGTGCCTATAGAT 60.364 40.741 0.00 0.00 0.00 1.98
551 718 6.071560 CCGTTCCATAATGTAGTGCCTATAGA 60.072 42.308 0.00 0.00 0.00 1.98
552 719 6.071560 TCCGTTCCATAATGTAGTGCCTATAG 60.072 42.308 0.00 0.00 0.00 1.31
553 720 5.776208 TCCGTTCCATAATGTAGTGCCTATA 59.224 40.000 0.00 0.00 0.00 1.31
554 721 4.591498 TCCGTTCCATAATGTAGTGCCTAT 59.409 41.667 0.00 0.00 0.00 2.57
555 722 3.962063 TCCGTTCCATAATGTAGTGCCTA 59.038 43.478 0.00 0.00 0.00 3.93
556 723 2.769663 TCCGTTCCATAATGTAGTGCCT 59.230 45.455 0.00 0.00 0.00 4.75
557 724 3.131396 CTCCGTTCCATAATGTAGTGCC 58.869 50.000 0.00 0.00 0.00 5.01
558 725 3.131396 CCTCCGTTCCATAATGTAGTGC 58.869 50.000 0.00 0.00 0.00 4.40
559 726 3.386726 TCCCTCCGTTCCATAATGTAGTG 59.613 47.826 0.00 0.00 0.00 2.74
560 727 3.641906 CTCCCTCCGTTCCATAATGTAGT 59.358 47.826 0.00 0.00 0.00 2.73
561 728 3.555168 GCTCCCTCCGTTCCATAATGTAG 60.555 52.174 0.00 0.00 0.00 2.74
562 729 2.367567 GCTCCCTCCGTTCCATAATGTA 59.632 50.000 0.00 0.00 0.00 2.29
563 730 1.141053 GCTCCCTCCGTTCCATAATGT 59.859 52.381 0.00 0.00 0.00 2.71
564 731 1.417890 AGCTCCCTCCGTTCCATAATG 59.582 52.381 0.00 0.00 0.00 1.90
565 732 1.807814 AGCTCCCTCCGTTCCATAAT 58.192 50.000 0.00 0.00 0.00 1.28
566 733 2.037144 GTAGCTCCCTCCGTTCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
567 734 1.217183 AGTAGCTCCCTCCGTTCCATA 59.783 52.381 0.00 0.00 0.00 2.74
568 735 0.032017 AGTAGCTCCCTCCGTTCCAT 60.032 55.000 0.00 0.00 0.00 3.41
569 736 0.970937 CAGTAGCTCCCTCCGTTCCA 60.971 60.000 0.00 0.00 0.00 3.53
570 737 0.971447 ACAGTAGCTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
571 738 1.677052 CTACAGTAGCTCCCTCCGTTC 59.323 57.143 0.00 0.00 0.00 3.95
572 739 1.765230 CTACAGTAGCTCCCTCCGTT 58.235 55.000 0.00 0.00 0.00 4.44
573 740 3.498502 CTACAGTAGCTCCCTCCGT 57.501 57.895 0.00 0.00 0.00 4.69
605 772 7.037873 TGGAGGAGTTTGCCTAAAATAACTAGA 60.038 37.037 0.00 0.00 38.73 2.43
608 775 5.710567 GTGGAGGAGTTTGCCTAAAATAACT 59.289 40.000 0.00 0.00 38.73 2.24
610 777 5.887754 AGTGGAGGAGTTTGCCTAAAATAA 58.112 37.500 0.00 0.00 38.73 1.40
611 778 5.514500 AGTGGAGGAGTTTGCCTAAAATA 57.486 39.130 0.00 0.00 38.73 1.40
613 780 3.876309 AGTGGAGGAGTTTGCCTAAAA 57.124 42.857 0.00 0.00 38.73 1.52
614 781 3.908103 ACTAGTGGAGGAGTTTGCCTAAA 59.092 43.478 0.00 0.00 38.73 1.85
615 782 3.517612 ACTAGTGGAGGAGTTTGCCTAA 58.482 45.455 0.00 0.00 38.73 2.69
616 783 3.185880 ACTAGTGGAGGAGTTTGCCTA 57.814 47.619 0.00 0.00 38.73 3.93
617 784 2.031495 ACTAGTGGAGGAGTTTGCCT 57.969 50.000 0.00 0.00 42.17 4.75
618 785 3.975168 TTACTAGTGGAGGAGTTTGCC 57.025 47.619 5.39 0.00 0.00 4.52
619 786 6.819397 AAAATTACTAGTGGAGGAGTTTGC 57.181 37.500 5.39 0.00 28.69 3.68
641 808 1.990327 GGGAGGAGTACCCCTGAAAAA 59.010 52.381 0.00 0.00 41.38 1.94
642 809 1.665137 GGGAGGAGTACCCCTGAAAA 58.335 55.000 0.00 0.00 41.38 2.29
643 810 3.411875 GGGAGGAGTACCCCTGAAA 57.588 57.895 0.00 0.00 41.38 2.69
650 817 4.904895 AAAAACACTAGGGAGGAGTACC 57.095 45.455 0.00 0.00 0.00 3.34
689 856 2.551504 GGAGTACCTCCTTCGCCAAAAA 60.552 50.000 2.98 0.00 46.41 1.94
690 857 1.002773 GGAGTACCTCCTTCGCCAAAA 59.997 52.381 2.98 0.00 46.41 2.44
691 858 0.611714 GGAGTACCTCCTTCGCCAAA 59.388 55.000 2.98 0.00 46.41 3.28
692 859 2.283824 GGAGTACCTCCTTCGCCAA 58.716 57.895 2.98 0.00 46.41 4.52
693 860 4.029472 GGAGTACCTCCTTCGCCA 57.971 61.111 2.98 0.00 46.41 5.69
703 870 2.064581 ATGTGCGGGGAGGAGTACC 61.065 63.158 0.00 0.00 0.00 3.34
704 871 1.144057 CATGTGCGGGGAGGAGTAC 59.856 63.158 0.00 0.00 0.00 2.73
705 872 2.063979 CCATGTGCGGGGAGGAGTA 61.064 63.158 0.00 0.00 0.00 2.59
706 873 3.402681 CCATGTGCGGGGAGGAGT 61.403 66.667 0.00 0.00 0.00 3.85
757 932 2.876550 GTTTTACTTTCACCGACTGGCT 59.123 45.455 0.00 0.00 39.70 4.75
760 935 3.207778 TGGGTTTTACTTTCACCGACTG 58.792 45.455 0.00 0.00 0.00 3.51
768 943 1.782569 GCGCGTTTGGGTTTTACTTTC 59.217 47.619 8.43 0.00 0.00 2.62
795 983 0.687354 AAGCAGGGGCAGGATATACG 59.313 55.000 0.00 0.00 44.61 3.06
796 984 1.003696 GGAAGCAGGGGCAGGATATAC 59.996 57.143 0.00 0.00 44.61 1.47
797 985 1.362224 GGAAGCAGGGGCAGGATATA 58.638 55.000 0.00 0.00 44.61 0.86
799 987 2.078665 GGGAAGCAGGGGCAGGATA 61.079 63.158 0.00 0.00 44.61 2.59
855 1049 2.113139 GGTACCGGGATGGCATGG 59.887 66.667 3.81 2.12 43.94 3.66
869 1077 0.612453 GGGGATTTTTGTGGCCGGTA 60.612 55.000 1.90 0.00 0.00 4.02
897 1106 0.673985 GAGTTGGTGGTTTGGCCTTC 59.326 55.000 3.32 0.00 38.35 3.46
900 1109 2.207229 GGGAGTTGGTGGTTTGGCC 61.207 63.158 0.00 0.00 37.90 5.36
923 1136 0.243907 CGCACGAGAGGAGGAAGAAA 59.756 55.000 0.00 0.00 0.00 2.52
965 1202 3.940640 CGCCCATTGTCGCCATCG 61.941 66.667 0.00 0.00 0.00 3.84
1192 1429 2.486370 GGAGGCTTGGATTCTTCTAGCC 60.486 54.545 0.00 0.00 43.77 3.93
1198 1435 4.645809 GCGGAGGCTTGGATTCTT 57.354 55.556 0.00 0.00 35.83 2.52
1213 1451 3.443037 GATGGATCGATTGATAGGAGCG 58.557 50.000 0.00 0.00 34.09 5.03
1219 1461 6.364568 AGTTGATGGATGGATCGATTGATA 57.635 37.500 0.00 0.00 34.09 2.15
1223 1469 4.573900 GCTAGTTGATGGATGGATCGATT 58.426 43.478 0.00 0.00 0.00 3.34
1235 1481 1.346197 CTGCGCACGCTAGTTGATG 59.654 57.895 16.77 0.00 42.51 3.07
1251 1497 3.195825 AGAACTCGGGGATTGTTCTACTG 59.804 47.826 5.90 0.00 45.61 2.74
1281 1629 2.220313 GTAACCACGGCCAACTAACAA 58.780 47.619 2.24 0.00 0.00 2.83
1282 1630 1.873069 CGTAACCACGGCCAACTAACA 60.873 52.381 2.24 0.00 44.59 2.41
1283 1631 0.792031 CGTAACCACGGCCAACTAAC 59.208 55.000 2.24 0.00 44.59 2.34
1392 1755 1.032014 GAGTTTTGCAGCCCTTCACA 58.968 50.000 0.00 0.00 0.00 3.58
1411 1789 0.397941 TTGACAGAGAGGTTGCTGGG 59.602 55.000 0.00 0.00 36.47 4.45
1412 1790 2.082231 CATTGACAGAGAGGTTGCTGG 58.918 52.381 0.00 0.00 36.47 4.85
1617 2049 4.084849 GGACTGCATTTTATCACTCGATCG 60.085 45.833 9.36 9.36 32.73 3.69
1624 2056 1.065551 GCCGGGACTGCATTTTATCAC 59.934 52.381 2.18 0.00 38.81 3.06
1625 2057 1.388547 GCCGGGACTGCATTTTATCA 58.611 50.000 2.18 0.00 38.81 2.15
1626 2058 0.668535 GGCCGGGACTGCATTTTATC 59.331 55.000 2.18 0.00 41.47 1.75
1627 2059 0.755327 GGGCCGGGACTGCATTTTAT 60.755 55.000 2.18 0.00 41.47 1.40
1954 2455 3.130340 GGGGATTTTACTCGTACCACGTA 59.870 47.826 0.00 0.00 43.14 3.57
2039 2993 4.844420 CAGAAGGGTCTGGATCGC 57.156 61.111 0.00 0.00 46.55 4.58
2103 3057 1.187567 CCTTCCCCCTTTGGCAACTG 61.188 60.000 0.00 0.00 37.61 3.16
2114 3068 2.252714 TGCACAAATTAACCTTCCCCC 58.747 47.619 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.