Multiple sequence alignment - TraesCS2D01G246700

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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 TraesCS2D01G246700 chr2D 100.000 5406 0 0 1 5406 288616836 288611431 0.000000e+00 9984.0
1 TraesCS2D01G246700 chr2D 95.172 145 7 0 73 217 288616913 288616769 4.210000e-56 230.0
2 TraesCS2D01G246700 chr2D 95.588 68 3 0 1 68 288616687 288616620 5.720000e-20 110.0
3 TraesCS2D01G246700 chr2D 96.226 53 2 0 5258 5310 288611523 288611471 2.680000e-13 87.9
4 TraesCS2D01G246700 chr2D 96.226 53 2 0 5314 5366 288611579 288611527 2.680000e-13 87.9
5 TraesCS2D01G246700 chr2A 97.910 4162 66 13 579 4727 348093877 348089724 0.000000e+00 7184.0
6 TraesCS2D01G246700 chr2A 96.830 347 9 2 4713 5057 348089221 348088875 3.630000e-161 579.0
7 TraesCS2D01G246700 chr2A 95.070 284 14 0 1 284 348119053 348118770 1.070000e-121 448.0
8 TraesCS2D01G246700 chr2A 87.023 262 32 2 322 581 265273263 265273524 1.470000e-75 294.0
9 TraesCS2D01G246700 chr2A 84.912 285 36 7 304 585 310452836 310453116 1.150000e-71 281.0
10 TraesCS2D01G246700 chr2A 95.105 143 7 0 75 217 348119128 348118986 5.450000e-55 226.0
11 TraesCS2D01G246700 chr2B 95.659 3755 115 12 1546 5264 316051518 316047776 0.000000e+00 5987.0
12 TraesCS2D01G246700 chr2B 96.372 882 23 5 619 1498 316052495 316051621 0.000000e+00 1443.0
13 TraesCS2D01G246700 chr2B 89.602 327 32 2 1 326 316052945 316052620 1.080000e-111 414.0
14 TraesCS2D01G246700 chr2B 78.571 322 55 11 5092 5406 794888571 794888885 3.300000e-47 200.0
15 TraesCS2D01G246700 chr2B 90.604 149 12 2 73 220 316053021 316052874 4.270000e-46 196.0
16 TraesCS2D01G246700 chr3A 89.354 263 25 2 321 580 27037745 27037483 1.450000e-85 327.0
17 TraesCS2D01G246700 chr3A 80.473 169 19 13 5103 5263 551760522 551760684 3.420000e-22 117.0
18 TraesCS2D01G246700 chr5B 87.692 260 30 2 321 578 18065448 18065189 8.800000e-78 302.0
19 TraesCS2D01G246700 chr5B 84.431 167 23 2 1023 1189 534365519 534365356 1.560000e-35 161.0
20 TraesCS2D01G246700 chr7A 86.891 267 31 4 322 585 706650673 706650938 4.090000e-76 296.0
21 TraesCS2D01G246700 chr3B 86.617 269 32 4 315 580 734588570 734588303 1.470000e-75 294.0
22 TraesCS2D01G246700 chr3B 88.312 77 9 0 5330 5406 703845872 703845796 5.770000e-15 93.5
23 TraesCS2D01G246700 chr4B 86.742 264 31 4 321 581 624043270 624043532 1.900000e-74 291.0
24 TraesCS2D01G246700 chr4B 79.000 300 51 10 5109 5404 10403232 10402941 1.540000e-45 195.0
25 TraesCS2D01G246700 chr4B 100.000 34 0 0 5373 5406 515138397 515138364 4.520000e-06 63.9
26 TraesCS2D01G246700 chr1B 86.567 268 31 5 317 581 302759808 302760073 1.900000e-74 291.0
27 TraesCS2D01G246700 chr5A 86.692 263 31 4 322 581 10553771 10553510 6.850000e-74 289.0
28 TraesCS2D01G246700 chr5A 85.030 167 25 0 1023 1189 555568264 555568098 2.590000e-38 171.0
29 TraesCS2D01G246700 chr7D 80.495 323 50 11 5059 5378 205499462 205499774 9.050000e-58 235.0
30 TraesCS2D01G246700 chr7D 74.528 212 37 15 5059 5264 55010497 55010297 5.810000e-10 76.8
31 TraesCS2D01G246700 chr7D 84.615 65 4 4 5200 5264 55005531 55005473 5.850000e-05 60.2
32 TraesCS2D01G246700 chr5D 83.951 162 23 2 1028 1189 439678252 439678094 9.380000e-33 152.0


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 TraesCS2D01G246700 chr2D 288611431 288616836 5405 True 9984.0 9984 100.00000 1 5406 1 chr2D.!!$R1 5405
1 TraesCS2D01G246700 chr2A 348088875 348093877 5002 True 3881.5 7184 97.37000 579 5057 2 chr2A.!!$R1 4478
2 TraesCS2D01G246700 chr2B 316047776 316053021 5245 True 2010.0 5987 93.05925 1 5264 4 chr2B.!!$R1 5263

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
883 964 0.111253 CAACTTGGAGCCTCCCTGTT 59.889 55.000 8.62 10.22 35.03 3.16 F
994 1080 0.251165 GATCTCGGGAGGAGGAGGAG 60.251 65.000 0.00 0.00 43.34 3.69 F
1643 1794 1.343069 GGTGGTTTTACATGGCCCAA 58.657 50.000 0.00 0.00 0.00 4.12 F
2726 2877 3.005791 GCATTAACCTAACCCATGATGCC 59.994 47.826 0.00 0.00 34.21 4.40 F
2763 2914 3.667087 GCCTTCAATCACGTGGCA 58.333 55.556 17.00 0.00 42.79 4.92 F
3069 3220 5.806654 ATTAGTTGGCATTTTTCTGTGGT 57.193 34.783 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2726 2877 7.652909 TGAAGGCAATTCAAAAGACAACATAAG 59.347 33.333 1.40 0.0 45.00 1.73 R
2908 3059 6.554334 TTTTGTTATCTGAAAGGACTTCCG 57.446 37.500 0.00 0.0 42.08 4.30 R
3469 3622 2.267174 ATTCCCGAGCATCTGATTGG 57.733 50.000 0.00 0.0 34.78 3.16 R
3817 3970 3.010420 GTGGGGCTTTACATCAGAGTTC 58.990 50.000 0.00 0.0 0.00 3.01 R
4304 4457 3.128242 GGCTTTGAATCTGTGTCATCCTG 59.872 47.826 0.00 0.0 0.00 3.86 R
4997 5678 2.035576 ACAGTTCTCGCGACTAAAAGGT 59.964 45.455 3.71 0.0 0.00 3.50 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
21 98 1.268079 GCTCCAACAAGTCCTTCAAGC 59.732 52.381 0.00 0.00 0.00 4.01
25 102 1.267806 CAACAAGTCCTTCAAGCGCAT 59.732 47.619 11.47 0.00 0.00 4.73
27 104 0.449388 CAAGTCCTTCAAGCGCATCC 59.551 55.000 11.47 0.00 0.00 3.51
38 115 2.383527 GCGCATCCGGATCGAATCC 61.384 63.158 28.70 14.30 46.22 3.01
74 151 6.233434 TCAACTTGACATATCCATATCAGCC 58.767 40.000 0.00 0.00 0.00 4.85
89 166 0.570734 CAGCCGTAAACGCATCGTAG 59.429 55.000 0.00 0.00 39.99 3.51
97 174 4.431214 CGTAAACGCATCGTAGCATATGTC 60.431 45.833 4.29 0.00 39.99 3.06
100 177 3.052745 ACGCATCGTAGCATATGTCAAG 58.947 45.455 4.29 0.00 38.73 3.02
101 178 3.052745 CGCATCGTAGCATATGTCAAGT 58.947 45.455 4.29 0.00 0.00 3.16
112 189 7.054491 AGCATATGTCAAGTTTTTCCTTTGT 57.946 32.000 4.29 0.00 0.00 2.83
117 194 4.928615 TGTCAAGTTTTTCCTTTGTTGCAG 59.071 37.500 0.00 0.00 0.00 4.41
128 205 4.400884 TCCTTTGTTGCAGCAAGAAAGTTA 59.599 37.500 36.89 27.92 46.36 2.24
130 207 4.981806 TTGTTGCAGCAAGAAAGTTACT 57.018 36.364 15.07 0.00 0.00 2.24
141 218 8.386606 CAGCAAGAAAGTTACTATTGTGATCTC 58.613 37.037 0.00 0.00 0.00 2.75
171 248 0.319555 TCCGACAAGTCCTTCAAGCG 60.320 55.000 0.00 0.00 0.00 4.68
177 254 1.021390 AAGTCCTTCAAGCGCATCCG 61.021 55.000 11.47 0.00 37.57 4.18
179 256 3.204827 CCTTCAAGCGCATCCGGG 61.205 66.667 11.47 1.78 34.32 5.73
182 259 3.247056 TTCAAGCGCATCCGGGTCA 62.247 57.895 11.47 0.00 34.32 4.02
201 278 4.883585 GGTCAAATCCTGCATCTACATTCA 59.116 41.667 0.00 0.00 0.00 2.57
221 298 7.121168 ACATTCAACTTGACATATCCATTCGTT 59.879 33.333 0.00 0.00 0.00 3.85
225 302 2.571212 TGACATATCCATTCGTTGGCC 58.429 47.619 0.00 0.00 46.01 5.36
231 308 2.046285 CCATTCGTTGGCCTGGTCC 61.046 63.158 3.32 0.00 39.09 4.46
248 325 4.427637 TGGTCCAACCACCTACTTGTATA 58.572 43.478 0.00 0.00 44.79 1.47
250 327 6.203813 TGGTCCAACCACCTACTTGTATATA 58.796 40.000 0.00 0.00 44.79 0.86
251 328 6.098695 TGGTCCAACCACCTACTTGTATATAC 59.901 42.308 5.89 5.89 44.79 1.47
256 333 5.945310 ACCACCTACTTGTATATACGGAGA 58.055 41.667 17.95 1.60 0.00 3.71
277 354 5.464168 AGAACATGCAGTAATGAAGTTTGC 58.536 37.500 0.00 0.00 35.42 3.68
285 362 5.514204 GCAGTAATGAAGTTTGCAGCTAATG 59.486 40.000 0.00 0.00 34.99 1.90
286 363 6.615088 CAGTAATGAAGTTTGCAGCTAATGT 58.385 36.000 0.00 0.00 0.00 2.71
291 368 6.875948 TGAAGTTTGCAGCTAATGTTCTTA 57.124 33.333 12.59 0.00 0.00 2.10
323 400 7.434897 TCAAGAAAGACATGTGTTTTGCAATAC 59.565 33.333 20.63 12.51 0.00 1.89
324 401 7.042797 AGAAAGACATGTGTTTTGCAATACT 57.957 32.000 20.63 9.51 0.00 2.12
325 402 7.141363 AGAAAGACATGTGTTTTGCAATACTC 58.859 34.615 20.63 15.89 0.00 2.59
327 404 4.218417 AGACATGTGTTTTGCAATACTCCC 59.782 41.667 18.84 9.00 0.00 4.30
328 405 4.151883 ACATGTGTTTTGCAATACTCCCT 58.848 39.130 18.84 5.37 0.00 4.20
330 407 3.153919 TGTGTTTTGCAATACTCCCTCC 58.846 45.455 18.84 3.58 0.00 4.30
331 408 2.161609 GTGTTTTGCAATACTCCCTCCG 59.838 50.000 18.84 0.00 0.00 4.63
332 409 2.224670 TGTTTTGCAATACTCCCTCCGT 60.225 45.455 18.84 0.00 0.00 4.69
334 411 2.396590 TTGCAATACTCCCTCCGTTC 57.603 50.000 0.00 0.00 0.00 3.95
335 412 0.539986 TGCAATACTCCCTCCGTTCC 59.460 55.000 0.00 0.00 0.00 3.62
337 414 1.141053 GCAATACTCCCTCCGTTCCAT 59.859 52.381 0.00 0.00 0.00 3.41
339 416 3.181458 GCAATACTCCCTCCGTTCCATAA 60.181 47.826 0.00 0.00 0.00 1.90
340 417 4.505039 GCAATACTCCCTCCGTTCCATAAT 60.505 45.833 0.00 0.00 0.00 1.28
341 418 4.891992 ATACTCCCTCCGTTCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
342 419 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
343 420 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
344 421 3.641906 ACTCCCTCCGTTCCATAATGTAG 59.358 47.826 0.00 0.00 0.00 2.74
345 422 2.367567 TCCCTCCGTTCCATAATGTAGC 59.632 50.000 0.00 0.00 0.00 3.58
346 423 2.404215 CCTCCGTTCCATAATGTAGCG 58.596 52.381 0.00 0.00 0.00 4.26
347 424 1.792949 CTCCGTTCCATAATGTAGCGC 59.207 52.381 0.00 0.00 0.00 5.92
348 425 1.137282 TCCGTTCCATAATGTAGCGCA 59.863 47.619 11.47 0.00 0.00 6.09
349 426 2.143122 CCGTTCCATAATGTAGCGCAT 58.857 47.619 11.47 0.00 40.03 4.73
350 427 3.006003 TCCGTTCCATAATGTAGCGCATA 59.994 43.478 11.47 0.00 36.67 3.14
352 429 5.105675 TCCGTTCCATAATGTAGCGCATATA 60.106 40.000 11.47 0.00 36.67 0.86
353 430 5.232202 CCGTTCCATAATGTAGCGCATATAG 59.768 44.000 11.47 0.00 36.67 1.31
354 431 6.033966 CGTTCCATAATGTAGCGCATATAGA 58.966 40.000 11.47 0.00 36.67 1.98
355 432 6.697455 CGTTCCATAATGTAGCGCATATAGAT 59.303 38.462 11.47 0.00 36.67 1.98
360 437 9.102757 CCATAATGTAGCGCATATAGATTTTCT 57.897 33.333 11.47 0.00 36.67 2.52
361 438 9.911980 CATAATGTAGCGCATATAGATTTTCTG 57.088 33.333 11.47 0.00 36.67 3.02
362 439 6.974932 ATGTAGCGCATATAGATTTTCTGG 57.025 37.500 11.47 0.00 35.74 3.86
363 440 6.096673 TGTAGCGCATATAGATTTTCTGGA 57.903 37.500 11.47 0.00 0.00 3.86
364 441 6.521162 TGTAGCGCATATAGATTTTCTGGAA 58.479 36.000 11.47 0.00 0.00 3.53
365 442 6.989759 TGTAGCGCATATAGATTTTCTGGAAA 59.010 34.615 11.47 0.00 0.00 3.13
366 443 6.942532 AGCGCATATAGATTTTCTGGAAAA 57.057 33.333 11.47 10.33 43.48 2.29
382 459 9.936759 TTTCTGGAAAATCAAACTTTACAAACT 57.063 25.926 0.00 0.00 0.00 2.66
383 460 9.936759 TTCTGGAAAATCAAACTTTACAAACTT 57.063 25.926 0.00 0.00 0.00 2.66
385 462 9.971744 CTGGAAAATCAAACTTTACAAACTTTG 57.028 29.630 0.00 0.00 0.00 2.77
386 463 9.712305 TGGAAAATCAAACTTTACAAACTTTGA 57.288 25.926 8.55 10.11 36.16 2.69
387 464 9.967245 GGAAAATCAAACTTTACAAACTTTGAC 57.033 29.630 8.55 1.87 35.26 3.18
388 465 9.967245 GAAAATCAAACTTTACAAACTTTGACC 57.033 29.630 8.55 1.49 35.26 4.02
389 466 9.495572 AAAATCAAACTTTACAAACTTTGACCA 57.504 25.926 8.55 0.00 35.26 4.02
390 467 9.495572 AAATCAAACTTTACAAACTTTGACCAA 57.504 25.926 8.55 0.00 35.26 3.67
391 468 8.702163 ATCAAACTTTACAAACTTTGACCAAG 57.298 30.769 8.55 8.83 35.26 3.61
394 471 7.462571 AACTTTACAAACTTTGACCAAGTCT 57.537 32.000 8.55 2.98 45.77 3.24
397 474 9.841295 ACTTTACAAACTTTGACCAAGTCTATA 57.159 29.630 8.55 0.00 45.77 1.31
462 539 8.743085 ATGAAAGTACATCTTGTAATGCATCT 57.257 30.769 0.00 0.00 34.21 2.90
463 540 9.836864 ATGAAAGTACATCTTGTAATGCATCTA 57.163 29.630 0.00 0.00 34.21 1.98
464 541 9.665719 TGAAAGTACATCTTGTAATGCATCTAA 57.334 29.630 0.00 0.00 34.21 2.10
467 544 9.836864 AAGTACATCTTGTAATGCATCTAATGA 57.163 29.630 0.00 0.00 34.21 2.57
514 591 9.019656 TGCATATATTTTGTCTACAAACTTGGT 57.980 29.630 7.75 0.00 44.56 3.67
515 592 9.503427 GCATATATTTTGTCTACAAACTTGGTC 57.497 33.333 7.75 0.00 44.56 4.02
519 596 7.639113 ATTTTGTCTACAAACTTGGTCAAGA 57.361 32.000 16.55 0.00 44.56 3.02
520 597 7.639113 TTTTGTCTACAAACTTGGTCAAGAT 57.361 32.000 16.55 2.82 44.56 2.40
521 598 7.639113 TTTGTCTACAAACTTGGTCAAGATT 57.361 32.000 16.55 8.77 40.55 2.40
522 599 7.639113 TTGTCTACAAACTTGGTCAAGATTT 57.361 32.000 16.55 10.31 41.42 2.17
523 600 7.026631 TGTCTACAAACTTGGTCAAGATTTG 57.973 36.000 22.11 22.11 40.79 2.32
524 601 6.601613 TGTCTACAAACTTGGTCAAGATTTGT 59.398 34.615 26.76 26.76 44.55 2.83
525 602 7.771361 TGTCTACAAACTTGGTCAAGATTTGTA 59.229 33.333 26.43 26.43 42.94 2.41
526 603 8.617809 GTCTACAAACTTGGTCAAGATTTGTAA 58.382 33.333 27.06 21.32 43.61 2.41
527 604 9.179909 TCTACAAACTTGGTCAAGATTTGTAAA 57.820 29.630 27.06 20.99 43.61 2.01
528 605 9.450807 CTACAAACTTGGTCAAGATTTGTAAAG 57.549 33.333 27.06 21.70 43.61 1.85
529 606 7.836842 ACAAACTTGGTCAAGATTTGTAAAGT 58.163 30.769 24.86 11.28 42.94 2.66
530 607 8.311109 ACAAACTTGGTCAAGATTTGTAAAGTT 58.689 29.630 24.86 12.12 42.94 2.66
531 608 9.150348 CAAACTTGGTCAAGATTTGTAAAGTTT 57.850 29.630 16.55 16.60 42.27 2.66
532 609 8.702163 AACTTGGTCAAGATTTGTAAAGTTTG 57.298 30.769 16.55 0.00 40.79 2.93
533 610 8.062065 ACTTGGTCAAGATTTGTAAAGTTTGA 57.938 30.769 16.55 0.00 40.79 2.69
534 611 8.695456 ACTTGGTCAAGATTTGTAAAGTTTGAT 58.305 29.630 16.55 0.00 40.79 2.57
535 612 9.533253 CTTGGTCAAGATTTGTAAAGTTTGATT 57.467 29.630 4.82 0.00 40.79 2.57
536 613 9.883142 TTGGTCAAGATTTGTAAAGTTTGATTT 57.117 25.926 0.00 0.00 31.42 2.17
537 614 9.883142 TGGTCAAGATTTGTAAAGTTTGATTTT 57.117 25.926 0.00 0.00 31.42 1.82
570 647 9.667107 AATCTATATGGGTTACATTATGGAACG 57.333 33.333 13.45 0.00 42.08 3.95
571 648 7.617225 TCTATATGGGTTACATTATGGAACGG 58.383 38.462 13.45 0.00 42.08 4.44
572 649 4.781775 ATGGGTTACATTATGGAACGGA 57.218 40.909 13.45 3.66 42.08 4.69
573 650 4.145365 TGGGTTACATTATGGAACGGAG 57.855 45.455 13.45 0.00 42.08 4.63
574 651 3.775866 TGGGTTACATTATGGAACGGAGA 59.224 43.478 13.45 0.00 42.08 3.71
575 652 4.141801 TGGGTTACATTATGGAACGGAGAG 60.142 45.833 13.45 0.00 42.08 3.20
576 653 4.100498 GGGTTACATTATGGAACGGAGAGA 59.900 45.833 13.45 0.00 42.08 3.10
577 654 5.290386 GGTTACATTATGGAACGGAGAGAG 58.710 45.833 13.45 0.00 42.08 3.20
593 670 6.591834 ACGGAGAGAGTATGATGTTTCAAAAG 59.408 38.462 0.00 0.00 34.96 2.27
882 963 1.763770 CAACTTGGAGCCTCCCTGT 59.236 57.895 8.62 4.03 35.03 4.00
883 964 0.111253 CAACTTGGAGCCTCCCTGTT 59.889 55.000 8.62 10.22 35.03 3.16
884 965 0.402121 AACTTGGAGCCTCCCTGTTC 59.598 55.000 8.62 0.00 35.03 3.18
889 970 1.078823 TGGAGCCTCCCTGTTCTTCTA 59.921 52.381 8.62 0.00 35.03 2.10
992 1078 1.228737 GGATCTCGGGAGGAGGAGG 60.229 68.421 0.00 0.00 43.34 4.30
993 1079 1.721093 GGATCTCGGGAGGAGGAGGA 61.721 65.000 0.00 0.00 43.34 3.71
994 1080 0.251165 GATCTCGGGAGGAGGAGGAG 60.251 65.000 0.00 0.00 43.34 3.69
1194 1283 4.462417 CTCGCCTTCGACGTCGCT 62.462 66.667 32.19 0.00 40.21 4.93
1259 1349 1.807742 CCGACCGAGATCCTATCTGAC 59.192 57.143 0.00 0.00 40.38 3.51
1498 1593 4.184629 GGTGGCTGCATGTAGTATATAGC 58.815 47.826 12.66 0.00 0.00 2.97
1502 1597 4.872691 GGCTGCATGTAGTATATAGCCTTG 59.127 45.833 12.66 0.00 44.33 3.61
1503 1598 4.872691 GCTGCATGTAGTATATAGCCTTGG 59.127 45.833 12.66 0.00 0.00 3.61
1504 1599 5.420725 TGCATGTAGTATATAGCCTTGGG 57.579 43.478 0.00 0.00 0.00 4.12
1643 1794 1.343069 GGTGGTTTTACATGGCCCAA 58.657 50.000 0.00 0.00 0.00 4.12
2726 2877 3.005791 GCATTAACCTAACCCATGATGCC 59.994 47.826 0.00 0.00 34.21 4.40
2763 2914 3.667087 GCCTTCAATCACGTGGCA 58.333 55.556 17.00 0.00 42.79 4.92
3022 3173 9.030452 AGAAGATGAGACTAATGTACAGTTCTT 57.970 33.333 0.00 2.41 0.00 2.52
3069 3220 5.806654 ATTAGTTGGCATTTTTCTGTGGT 57.193 34.783 0.00 0.00 0.00 4.16
3330 3483 9.098355 GATACAATCAACAAACTCAGCAGTATA 57.902 33.333 0.00 0.00 30.14 1.47
3817 3970 8.571336 GGAACAATCATGTATAAGGATGGAAAG 58.429 37.037 0.00 0.00 39.40 2.62
4384 4537 2.548875 GAGAGCAGCATGAGTAAGGTG 58.451 52.381 0.00 0.00 39.69 4.00
4449 4602 5.762825 TCTTCATCAAAGCTTGGATATGC 57.237 39.130 16.14 0.00 34.76 3.14
4467 4620 2.646930 TGCTTATTGTGGAGAGGCATG 58.353 47.619 0.00 0.00 0.00 4.06
4585 4749 7.826252 CACCAGCTGGCACTTTATATATCTATT 59.174 37.037 33.06 3.07 39.32 1.73
4768 5449 8.593945 ACATTTTCCACTGGAATGTATGTAAT 57.406 30.769 21.10 11.41 41.71 1.89
4859 5540 2.874648 TAATCTGGCTGGCCGCACAG 62.875 60.000 18.87 19.99 41.67 3.66
4997 5678 3.365472 TGTAAGGCATCTCTAGCAGACA 58.635 45.455 0.00 0.00 32.26 3.41
5029 5710 1.128692 CGAGAACTGTCAAAATCCGGC 59.871 52.381 0.00 0.00 0.00 6.13
5045 5726 1.485032 CGGCGACTATACGGGTTTGC 61.485 60.000 0.00 0.00 0.00 3.68
5075 5778 3.917300 TGGGGCCCGTAAATGATTTTAT 58.083 40.909 19.83 0.00 30.34 1.40
5076 5779 3.639094 TGGGGCCCGTAAATGATTTTATG 59.361 43.478 19.83 0.00 35.12 1.90
5077 5780 3.892588 GGGGCCCGTAAATGATTTTATGA 59.107 43.478 17.79 0.00 36.73 2.15
5082 5785 5.469479 CCCGTAAATGATTTTATGATGGCC 58.531 41.667 0.00 0.00 36.73 5.36
5083 5786 5.469479 CCGTAAATGATTTTATGATGGCCC 58.531 41.667 0.00 0.00 36.73 5.80
5084 5787 5.010516 CCGTAAATGATTTTATGATGGCCCA 59.989 40.000 0.00 0.00 36.73 5.36
5091 5794 1.468985 TTATGATGGCCCACAAACCG 58.531 50.000 0.00 0.00 0.00 4.44
5093 5796 4.114997 GATGGCCCACAAACCGCG 62.115 66.667 0.00 0.00 0.00 6.46
5131 5835 2.203800 TATCTACAGGTTTGCGCGAG 57.796 50.000 12.10 0.00 0.00 5.03
5134 5838 1.270274 TCTACAGGTTTGCGCGAGTAA 59.730 47.619 12.10 0.00 0.00 2.24
5136 5840 1.519408 ACAGGTTTGCGCGAGTAAAT 58.481 45.000 12.10 0.00 46.89 1.40
5141 5845 1.928706 TTTGCGCGAGTAAATGGGGC 61.929 55.000 12.10 0.00 40.76 5.80
5158 5862 2.110420 CGAAACCCTATCCCCCGC 59.890 66.667 0.00 0.00 0.00 6.13
5159 5863 2.514395 GAAACCCTATCCCCCGCC 59.486 66.667 0.00 0.00 0.00 6.13
5183 5888 3.850454 GATTTCCCAATCCCCTCCC 57.150 57.895 0.00 0.00 33.74 4.30
5185 5890 0.254784 ATTTCCCAATCCCCTCCCCT 60.255 55.000 0.00 0.00 0.00 4.79
5193 5898 3.207549 CCAATCCCCTCCCCTATTTTCTT 59.792 47.826 0.00 0.00 0.00 2.52
5195 5900 1.569072 TCCCCTCCCCTATTTTCTTGC 59.431 52.381 0.00 0.00 0.00 4.01
5214 5919 1.153449 CGCCGGTGAGCTAAATCCA 60.153 57.895 10.20 0.00 0.00 3.41
5225 5930 3.352990 TAAATCCACCGCCCCTGCC 62.353 63.158 0.00 0.00 0.00 4.85
5280 5985 4.120331 GCAAGCGCTCGGCCAAAT 62.120 61.111 19.97 0.00 45.17 2.32
5281 5986 2.202518 CAAGCGCTCGGCCAAATG 60.203 61.111 12.06 0.00 45.17 2.32
5282 5987 4.120331 AAGCGCTCGGCCAAATGC 62.120 61.111 12.06 0.35 45.17 3.56
5284 5989 3.202001 GCGCTCGGCCAAATGCTA 61.202 61.111 2.24 0.00 40.92 3.49
5285 5990 2.709475 CGCTCGGCCAAATGCTAC 59.291 61.111 2.24 0.00 40.92 3.58
5286 5991 2.106074 CGCTCGGCCAAATGCTACA 61.106 57.895 2.24 0.00 40.92 2.74
5287 5992 1.429423 GCTCGGCCAAATGCTACAC 59.571 57.895 2.24 0.00 40.92 2.90
5288 5993 1.993369 GCTCGGCCAAATGCTACACC 61.993 60.000 2.24 0.00 40.92 4.16
5289 5994 0.676466 CTCGGCCAAATGCTACACCA 60.676 55.000 2.24 0.00 40.92 4.17
5290 5995 0.250945 TCGGCCAAATGCTACACCAA 60.251 50.000 2.24 0.00 40.92 3.67
5291 5996 0.109319 CGGCCAAATGCTACACCAAC 60.109 55.000 2.24 0.00 40.92 3.77
5292 5997 1.256812 GGCCAAATGCTACACCAACT 58.743 50.000 0.00 0.00 40.92 3.16
5293 5998 2.442413 GGCCAAATGCTACACCAACTA 58.558 47.619 0.00 0.00 40.92 2.24
5294 5999 3.023832 GGCCAAATGCTACACCAACTAT 58.976 45.455 0.00 0.00 40.92 2.12
5295 6000 3.181487 GGCCAAATGCTACACCAACTATG 60.181 47.826 0.00 0.00 40.92 2.23
5296 6001 3.181487 GCCAAATGCTACACCAACTATGG 60.181 47.826 0.00 0.00 44.53 2.74
5297 6002 6.232513 GCCAAATGCTACACCAACTATGGG 62.233 50.000 0.00 0.00 43.78 4.00
5305 6010 4.483243 CAACTATGGGCGCCCGGT 62.483 66.667 39.00 31.72 39.42 5.28
5306 6011 4.483243 AACTATGGGCGCCCGGTG 62.483 66.667 39.00 30.54 39.42 4.94
5336 6041 4.120331 GCAAGCGCTCGGCCAAAT 62.120 61.111 19.97 0.00 45.17 2.32
5337 6042 2.202518 CAAGCGCTCGGCCAAATG 60.203 61.111 12.06 0.00 45.17 2.32
5338 6043 4.120331 AAGCGCTCGGCCAAATGC 62.120 61.111 12.06 0.35 45.17 3.56
5340 6045 3.202001 GCGCTCGGCCAAATGCTA 61.202 61.111 2.24 0.00 40.92 3.49
5341 6046 2.709475 CGCTCGGCCAAATGCTAC 59.291 61.111 2.24 0.00 40.92 3.58
5342 6047 2.106074 CGCTCGGCCAAATGCTACA 61.106 57.895 2.24 0.00 40.92 2.74
5343 6048 1.429423 GCTCGGCCAAATGCTACAC 59.571 57.895 2.24 0.00 40.92 2.90
5344 6049 1.993369 GCTCGGCCAAATGCTACACC 61.993 60.000 2.24 0.00 40.92 4.16
5345 6050 0.676466 CTCGGCCAAATGCTACACCA 60.676 55.000 2.24 0.00 40.92 4.17
5346 6051 0.250945 TCGGCCAAATGCTACACCAA 60.251 50.000 2.24 0.00 40.92 3.67
5347 6052 0.109319 CGGCCAAATGCTACACCAAC 60.109 55.000 2.24 0.00 40.92 3.77
5348 6053 1.256812 GGCCAAATGCTACACCAACT 58.743 50.000 0.00 0.00 40.92 3.16
5349 6054 2.442413 GGCCAAATGCTACACCAACTA 58.558 47.619 0.00 0.00 40.92 2.24
5350 6055 2.163613 GGCCAAATGCTACACCAACTAC 59.836 50.000 0.00 0.00 40.92 2.73
5351 6056 2.159572 GCCAAATGCTACACCAACTACG 60.160 50.000 0.00 0.00 36.87 3.51
5352 6057 2.418628 CCAAATGCTACACCAACTACGG 59.581 50.000 0.00 0.00 0.00 4.02
5353 6058 2.396590 AATGCTACACCAACTACGGG 57.603 50.000 0.00 0.00 0.00 5.28
5354 6059 0.107848 ATGCTACACCAACTACGGGC 60.108 55.000 0.00 0.00 0.00 6.13
5355 6060 1.189524 TGCTACACCAACTACGGGCT 61.190 55.000 0.00 0.00 0.00 5.19
5356 6061 0.459759 GCTACACCAACTACGGGCTC 60.460 60.000 0.00 0.00 0.00 4.70
5357 6062 0.175073 CTACACCAACTACGGGCTCC 59.825 60.000 0.00 0.00 0.00 4.70
5358 6063 1.259840 TACACCAACTACGGGCTCCC 61.260 60.000 0.00 0.00 0.00 4.30
5388 6093 4.200283 CCTCCTCTGCCGCGAGAC 62.200 72.222 8.23 0.00 32.74 3.36
5389 6094 4.544689 CTCCTCTGCCGCGAGACG 62.545 72.222 8.23 0.00 43.15 4.18
5401 6106 2.108178 GCGAGACGAAGGAGTATGAC 57.892 55.000 0.00 0.00 0.00 3.06
5402 6107 1.268640 GCGAGACGAAGGAGTATGACC 60.269 57.143 0.00 0.00 0.00 4.02
5403 6108 1.003759 CGAGACGAAGGAGTATGACCG 60.004 57.143 0.00 0.00 0.00 4.79
5404 6109 0.739561 AGACGAAGGAGTATGACCGC 59.260 55.000 0.00 0.00 0.00 5.68
5405 6110 0.248949 GACGAAGGAGTATGACCGCC 60.249 60.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.856222 CTTGAAGGACTTGTTGGAGCT 58.144 47.619 0.00 0.00 0.00 4.09
1 2 1.268079 GCTTGAAGGACTTGTTGGAGC 59.732 52.381 0.00 0.00 0.00 4.70
3 4 1.593196 CGCTTGAAGGACTTGTTGGA 58.407 50.000 0.00 0.00 0.00 3.53
4 5 0.040067 GCGCTTGAAGGACTTGTTGG 60.040 55.000 0.00 0.00 0.00 3.77
5 6 0.662619 TGCGCTTGAAGGACTTGTTG 59.337 50.000 9.73 0.00 0.00 3.33
9 10 1.021390 CGGATGCGCTTGAAGGACTT 61.021 55.000 9.73 0.00 0.00 3.01
10 11 1.448540 CGGATGCGCTTGAAGGACT 60.449 57.895 9.73 0.00 0.00 3.85
21 98 3.862124 GGATTCGATCCGGATGCG 58.138 61.111 24.82 23.30 40.13 4.73
38 115 5.868043 TGTCAAGTTGAATGTAGATGCAG 57.132 39.130 7.25 0.00 0.00 4.41
71 148 1.143969 GCTACGATGCGTTTACGGCT 61.144 55.000 4.29 0.00 41.54 5.52
74 151 3.424198 ACATATGCTACGATGCGTTTACG 59.576 43.478 1.58 0.00 41.54 3.18
89 166 7.566709 CAACAAAGGAAAAACTTGACATATGC 58.433 34.615 1.58 0.00 0.00 3.14
97 174 3.683822 TGCTGCAACAAAGGAAAAACTTG 59.316 39.130 0.00 0.00 0.00 3.16
100 177 3.932089 TCTTGCTGCAACAAAGGAAAAAC 59.068 39.130 11.69 0.00 0.00 2.43
101 178 4.199432 TCTTGCTGCAACAAAGGAAAAA 57.801 36.364 11.69 0.00 0.00 1.94
112 189 6.262049 TCACAATAGTAACTTTCTTGCTGCAA 59.738 34.615 15.16 15.16 0.00 4.08
117 194 8.386606 CAGAGATCACAATAGTAACTTTCTTGC 58.613 37.037 0.00 0.00 0.00 4.01
128 205 7.358770 AGCTGTTATCAGAGATCACAATAGT 57.641 36.000 4.94 0.00 43.76 2.12
130 207 6.515696 CGGAGCTGTTATCAGAGATCACAATA 60.516 42.308 4.94 0.00 43.76 1.90
141 218 3.182967 GACTTGTCGGAGCTGTTATCAG 58.817 50.000 0.00 0.00 43.87 2.90
171 248 1.728490 GCAGGATTTGACCCGGATGC 61.728 60.000 0.73 0.00 0.00 3.91
177 254 3.281727 TGTAGATGCAGGATTTGACCC 57.718 47.619 0.00 0.00 0.00 4.46
179 256 6.094603 AGTTGAATGTAGATGCAGGATTTGAC 59.905 38.462 0.00 0.00 0.00 3.18
182 259 6.660521 TCAAGTTGAATGTAGATGCAGGATTT 59.339 34.615 2.20 0.00 0.00 2.17
231 308 6.263842 TCTCCGTATATACAAGTAGGTGGTTG 59.736 42.308 13.22 2.57 0.00 3.77
248 325 5.276461 TCATTACTGCATGTTCTCCGTAT 57.724 39.130 0.00 0.00 0.00 3.06
250 327 3.610040 TCATTACTGCATGTTCTCCGT 57.390 42.857 0.00 0.00 0.00 4.69
251 328 3.935203 ACTTCATTACTGCATGTTCTCCG 59.065 43.478 0.00 0.00 0.00 4.63
256 333 5.199024 TGCAAACTTCATTACTGCATGTT 57.801 34.783 0.00 0.00 38.06 2.71
277 354 8.988064 TCTTGAACTAGTAAGAACATTAGCTG 57.012 34.615 5.75 0.00 30.49 4.24
285 362 9.262358 ACATGTCTTTCTTGAACTAGTAAGAAC 57.738 33.333 16.86 9.76 41.23 3.01
286 363 9.261180 CACATGTCTTTCTTGAACTAGTAAGAA 57.739 33.333 14.26 14.26 40.17 2.52
291 368 7.865706 AAACACATGTCTTTCTTGAACTAGT 57.134 32.000 0.00 0.00 0.00 2.57
323 400 3.555168 GCTACATTATGGAACGGAGGGAG 60.555 52.174 0.00 0.00 0.00 4.30
324 401 2.367567 GCTACATTATGGAACGGAGGGA 59.632 50.000 0.00 0.00 0.00 4.20
325 402 2.767505 GCTACATTATGGAACGGAGGG 58.232 52.381 0.00 0.00 0.00 4.30
327 404 1.792949 GCGCTACATTATGGAACGGAG 59.207 52.381 0.00 0.00 0.00 4.63
328 405 1.137282 TGCGCTACATTATGGAACGGA 59.863 47.619 9.73 0.00 0.00 4.69
330 407 6.033966 TCTATATGCGCTACATTATGGAACG 58.966 40.000 9.73 0.00 40.38 3.95
331 408 8.425577 AATCTATATGCGCTACATTATGGAAC 57.574 34.615 9.73 0.00 40.38 3.62
332 409 9.448438 AAAATCTATATGCGCTACATTATGGAA 57.552 29.630 9.73 0.00 40.38 3.53
334 411 9.102757 AGAAAATCTATATGCGCTACATTATGG 57.897 33.333 9.73 0.89 40.38 2.74
335 412 9.911980 CAGAAAATCTATATGCGCTACATTATG 57.088 33.333 9.73 0.00 40.38 1.90
337 414 8.311109 TCCAGAAAATCTATATGCGCTACATTA 58.689 33.333 9.73 0.00 40.38 1.90
339 416 6.701340 TCCAGAAAATCTATATGCGCTACAT 58.299 36.000 9.73 1.21 43.18 2.29
340 417 6.096673 TCCAGAAAATCTATATGCGCTACA 57.903 37.500 9.73 0.00 0.00 2.74
341 418 7.421530 TTTCCAGAAAATCTATATGCGCTAC 57.578 36.000 9.73 0.00 0.00 3.58
342 419 8.621532 ATTTTCCAGAAAATCTATATGCGCTA 57.378 30.769 9.73 0.00 44.98 4.26
343 420 6.942532 TTTTCCAGAAAATCTATATGCGCT 57.057 33.333 9.73 0.00 35.57 5.92
436 513 9.836864 AGATGCATTACAAGATGTACTTTCATA 57.163 29.630 0.00 0.00 36.61 2.15
488 565 9.019656 ACCAAGTTTGTAGACAAAATATATGCA 57.980 29.630 9.33 0.00 46.08 3.96
489 566 9.503427 GACCAAGTTTGTAGACAAAATATATGC 57.497 33.333 9.33 0.00 46.08 3.14
493 570 9.349713 TCTTGACCAAGTTTGTAGACAAAATAT 57.650 29.630 9.33 0.00 46.08 1.28
494 571 8.740123 TCTTGACCAAGTTTGTAGACAAAATA 57.260 30.769 9.33 0.00 46.08 1.40
495 572 7.639113 TCTTGACCAAGTTTGTAGACAAAAT 57.361 32.000 9.33 5.86 46.08 1.82
496 573 7.639113 ATCTTGACCAAGTTTGTAGACAAAA 57.361 32.000 9.33 0.00 46.08 2.44
497 574 7.639113 AATCTTGACCAAGTTTGTAGACAAA 57.361 32.000 9.31 3.71 38.94 2.83
498 575 7.122055 ACAAATCTTGACCAAGTTTGTAGACAA 59.878 33.333 24.54 0.00 42.94 3.18
499 576 6.601613 ACAAATCTTGACCAAGTTTGTAGACA 59.398 34.615 24.54 4.20 42.94 3.41
500 577 7.027778 ACAAATCTTGACCAAGTTTGTAGAC 57.972 36.000 24.54 0.00 42.94 2.59
501 578 8.740123 TTACAAATCTTGACCAAGTTTGTAGA 57.260 30.769 26.23 20.75 44.10 2.59
502 579 9.450807 CTTTACAAATCTTGACCAAGTTTGTAG 57.549 33.333 26.23 21.10 44.10 2.74
503 580 8.962679 ACTTTACAAATCTTGACCAAGTTTGTA 58.037 29.630 25.33 25.33 42.94 2.41
504 581 7.836842 ACTTTACAAATCTTGACCAAGTTTGT 58.163 30.769 26.47 26.47 44.55 2.83
505 582 8.702163 AACTTTACAAATCTTGACCAAGTTTG 57.298 30.769 21.77 21.77 40.71 2.93
506 583 9.150348 CAAACTTTACAAATCTTGACCAAGTTT 57.850 29.630 9.31 14.89 41.96 2.66
507 584 8.527810 TCAAACTTTACAAATCTTGACCAAGTT 58.472 29.630 9.31 0.00 38.29 2.66
508 585 8.062065 TCAAACTTTACAAATCTTGACCAAGT 57.938 30.769 9.31 0.00 39.38 3.16
509 586 9.533253 AATCAAACTTTACAAATCTTGACCAAG 57.467 29.630 3.47 3.47 39.71 3.61
510 587 9.883142 AAATCAAACTTTACAAATCTTGACCAA 57.117 25.926 0.00 0.00 0.00 3.67
511 588 9.883142 AAAATCAAACTTTACAAATCTTGACCA 57.117 25.926 0.00 0.00 0.00 4.02
544 621 9.667107 CGTTCCATAATGTAACCCATATAGATT 57.333 33.333 0.00 0.00 31.97 2.40
545 622 8.265055 CCGTTCCATAATGTAACCCATATAGAT 58.735 37.037 0.00 0.00 31.97 1.98
546 623 7.455323 TCCGTTCCATAATGTAACCCATATAGA 59.545 37.037 0.00 0.00 31.97 1.98
547 624 7.617225 TCCGTTCCATAATGTAACCCATATAG 58.383 38.462 0.00 0.00 31.97 1.31
548 625 7.455323 TCTCCGTTCCATAATGTAACCCATATA 59.545 37.037 0.00 0.00 31.97 0.86
549 626 6.271391 TCTCCGTTCCATAATGTAACCCATAT 59.729 38.462 0.00 0.00 31.97 1.78
550 627 5.603395 TCTCCGTTCCATAATGTAACCCATA 59.397 40.000 0.00 0.00 31.97 2.74
551 628 4.410883 TCTCCGTTCCATAATGTAACCCAT 59.589 41.667 0.00 0.00 34.36 4.00
552 629 3.775866 TCTCCGTTCCATAATGTAACCCA 59.224 43.478 0.00 0.00 0.00 4.51
553 630 4.100498 TCTCTCCGTTCCATAATGTAACCC 59.900 45.833 0.00 0.00 0.00 4.11
554 631 5.163437 ACTCTCTCCGTTCCATAATGTAACC 60.163 44.000 0.00 0.00 0.00 2.85
555 632 5.903810 ACTCTCTCCGTTCCATAATGTAAC 58.096 41.667 0.00 0.00 0.00 2.50
556 633 7.504574 TCATACTCTCTCCGTTCCATAATGTAA 59.495 37.037 0.00 0.00 0.00 2.41
557 634 7.002276 TCATACTCTCTCCGTTCCATAATGTA 58.998 38.462 0.00 0.00 0.00 2.29
558 635 5.833667 TCATACTCTCTCCGTTCCATAATGT 59.166 40.000 0.00 0.00 0.00 2.71
559 636 6.332735 TCATACTCTCTCCGTTCCATAATG 57.667 41.667 0.00 0.00 0.00 1.90
560 637 6.495181 ACATCATACTCTCTCCGTTCCATAAT 59.505 38.462 0.00 0.00 0.00 1.28
561 638 5.833667 ACATCATACTCTCTCCGTTCCATAA 59.166 40.000 0.00 0.00 0.00 1.90
562 639 5.386060 ACATCATACTCTCTCCGTTCCATA 58.614 41.667 0.00 0.00 0.00 2.74
563 640 4.219115 ACATCATACTCTCTCCGTTCCAT 58.781 43.478 0.00 0.00 0.00 3.41
564 641 3.632333 ACATCATACTCTCTCCGTTCCA 58.368 45.455 0.00 0.00 0.00 3.53
565 642 4.657436 AACATCATACTCTCTCCGTTCC 57.343 45.455 0.00 0.00 0.00 3.62
566 643 5.651530 TGAAACATCATACTCTCTCCGTTC 58.348 41.667 0.00 0.00 0.00 3.95
567 644 5.661056 TGAAACATCATACTCTCTCCGTT 57.339 39.130 0.00 0.00 0.00 4.44
568 645 5.661056 TTGAAACATCATACTCTCTCCGT 57.339 39.130 0.00 0.00 0.00 4.69
569 646 6.456181 GCTTTTGAAACATCATACTCTCTCCG 60.456 42.308 0.00 0.00 0.00 4.63
570 647 6.597280 AGCTTTTGAAACATCATACTCTCTCC 59.403 38.462 0.00 0.00 0.00 3.71
571 648 7.413877 CCAGCTTTTGAAACATCATACTCTCTC 60.414 40.741 0.00 0.00 0.00 3.20
572 649 6.373774 CCAGCTTTTGAAACATCATACTCTCT 59.626 38.462 0.00 0.00 0.00 3.10
573 650 6.372659 TCCAGCTTTTGAAACATCATACTCTC 59.627 38.462 0.00 0.00 0.00 3.20
574 651 6.240894 TCCAGCTTTTGAAACATCATACTCT 58.759 36.000 0.00 0.00 0.00 3.24
575 652 6.372659 TCTCCAGCTTTTGAAACATCATACTC 59.627 38.462 0.00 0.00 0.00 2.59
576 653 6.240894 TCTCCAGCTTTTGAAACATCATACT 58.759 36.000 0.00 0.00 0.00 2.12
577 654 6.500684 TCTCCAGCTTTTGAAACATCATAC 57.499 37.500 0.00 0.00 0.00 2.39
593 670 1.336755 TGTTTCGCCTTTTTCTCCAGC 59.663 47.619 0.00 0.00 0.00 4.85
992 1078 2.892425 CCCGCGACATTGCTCCTC 60.892 66.667 8.23 0.00 0.00 3.71
1259 1349 4.426313 GTTCGGGGGCTGGAAGGG 62.426 72.222 0.00 0.00 0.00 3.95
1498 1593 4.369182 CGCACTCTAGTAAATACCCAAGG 58.631 47.826 0.00 0.00 0.00 3.61
1499 1594 4.098960 TCCGCACTCTAGTAAATACCCAAG 59.901 45.833 0.00 0.00 0.00 3.61
1502 1597 4.868314 ATCCGCACTCTAGTAAATACCC 57.132 45.455 0.00 0.00 0.00 3.69
1503 1598 7.432059 ACTAAATCCGCACTCTAGTAAATACC 58.568 38.462 0.00 0.00 0.00 2.73
1504 1599 8.868635 AACTAAATCCGCACTCTAGTAAATAC 57.131 34.615 0.00 0.00 0.00 1.89
1643 1794 7.221450 TCTACGGCATAATTGGCTATTTAACT 58.779 34.615 0.00 0.00 45.85 2.24
2726 2877 7.652909 TGAAGGCAATTCAAAAGACAACATAAG 59.347 33.333 1.40 0.00 45.00 1.73
2763 2914 7.669427 TCAAATTCAATCTACCTTGCAAATGT 58.331 30.769 0.00 3.43 0.00 2.71
2908 3059 6.554334 TTTTGTTATCTGAAAGGACTTCCG 57.446 37.500 0.00 0.00 42.08 4.30
3022 3173 6.179756 ACAGTATAATGCTGTGACATTTCCA 58.820 36.000 0.00 0.00 44.52 3.53
3469 3622 2.267174 ATTCCCGAGCATCTGATTGG 57.733 50.000 0.00 0.00 34.78 3.16
3775 3928 3.142951 TGTTCCAGTGTTGGGATTTACG 58.857 45.455 0.00 0.00 45.10 3.18
3817 3970 3.010420 GTGGGGCTTTACATCAGAGTTC 58.990 50.000 0.00 0.00 0.00 3.01
4304 4457 3.128242 GGCTTTGAATCTGTGTCATCCTG 59.872 47.826 0.00 0.00 0.00 3.86
4384 4537 3.849911 TCATCGATATCTCCCGATTTGC 58.150 45.455 0.00 0.00 42.79 3.68
4449 4602 4.521146 AGAACATGCCTCTCCACAATAAG 58.479 43.478 0.00 0.00 0.00 1.73
4768 5449 3.580895 TCCTTGGTCTGTACAGCACATAA 59.419 43.478 18.45 13.33 36.29 1.90
4997 5678 2.035576 ACAGTTCTCGCGACTAAAAGGT 59.964 45.455 3.71 0.00 0.00 3.50
5075 5778 2.988684 GCGGTTTGTGGGCCATCA 60.989 61.111 10.70 7.15 0.00 3.07
5076 5779 4.114997 CGCGGTTTGTGGGCCATC 62.115 66.667 10.70 4.10 0.00 3.51
5094 5797 2.608745 TATACCACGTGGGGGAGGGG 62.609 65.000 36.47 11.22 42.91 4.79
5096 5799 0.974383 GATATACCACGTGGGGGAGG 59.026 60.000 36.47 12.81 42.91 4.30
5107 5810 3.724374 GCGCAAACCTGTAGATATACCA 58.276 45.455 0.30 0.00 0.00 3.25
5141 5845 2.110420 GCGGGGGATAGGGTTTCG 59.890 66.667 0.00 0.00 0.00 3.46
5164 5869 0.188587 GGGAGGGGATTGGGAAATCC 59.811 60.000 8.67 8.67 46.27 3.01
5168 5873 0.659133 ATAGGGGAGGGGATTGGGAA 59.341 55.000 0.00 0.00 0.00 3.97
5169 5874 0.659133 AATAGGGGAGGGGATTGGGA 59.341 55.000 0.00 0.00 0.00 4.37
5170 5875 1.545931 AAATAGGGGAGGGGATTGGG 58.454 55.000 0.00 0.00 0.00 4.12
5182 5887 1.724582 CCGGCGGCAAGAAAATAGGG 61.725 60.000 15.42 0.00 0.00 3.53
5183 5888 1.029947 ACCGGCGGCAAGAAAATAGG 61.030 55.000 28.71 0.43 0.00 2.57
5185 5890 0.321741 TCACCGGCGGCAAGAAAATA 60.322 50.000 28.71 0.00 0.00 1.40
5193 5898 3.323758 ATTTAGCTCACCGGCGGCA 62.324 57.895 28.71 12.45 37.29 5.69
5195 5900 1.887707 GGATTTAGCTCACCGGCGG 60.888 63.158 27.06 27.06 37.29 6.13
5225 5930 3.138930 ATCGTCGCAGATCCGGTGG 62.139 63.158 0.00 0.00 40.67 4.61
5230 5935 0.596083 CTCCACATCGTCGCAGATCC 60.596 60.000 0.00 0.00 40.67 3.36
5264 5969 2.202518 CATTTGGCCGAGCGCTTG 60.203 61.111 18.28 18.28 37.74 4.01
5265 5970 4.120331 GCATTTGGCCGAGCGCTT 62.120 61.111 13.26 0.00 37.74 4.68
5266 5971 3.680620 TAGCATTTGGCCGAGCGCT 62.681 57.895 11.27 11.27 46.50 5.92
5267 5972 3.202001 TAGCATTTGGCCGAGCGC 61.202 61.111 0.00 0.00 46.50 5.92
5268 5973 2.106074 TGTAGCATTTGGCCGAGCG 61.106 57.895 0.00 0.00 46.50 5.03
5269 5974 1.429423 GTGTAGCATTTGGCCGAGC 59.571 57.895 0.00 0.00 46.50 5.03
5270 5975 0.676466 TGGTGTAGCATTTGGCCGAG 60.676 55.000 0.00 0.00 46.50 4.63
5271 5976 0.250945 TTGGTGTAGCATTTGGCCGA 60.251 50.000 0.00 0.00 46.50 5.54
5272 5977 0.109319 GTTGGTGTAGCATTTGGCCG 60.109 55.000 0.00 0.00 46.50 6.13
5273 5978 1.256812 AGTTGGTGTAGCATTTGGCC 58.743 50.000 0.00 0.00 46.50 5.36
5274 5979 3.181487 CCATAGTTGGTGTAGCATTTGGC 60.181 47.826 0.00 0.00 39.65 4.52
5275 5980 3.381272 CCCATAGTTGGTGTAGCATTTGG 59.619 47.826 0.00 0.00 41.91 3.28
5276 5981 3.181487 GCCCATAGTTGGTGTAGCATTTG 60.181 47.826 0.00 0.00 41.91 2.32
5277 5982 3.023832 GCCCATAGTTGGTGTAGCATTT 58.976 45.455 0.00 0.00 41.91 2.32
5278 5983 2.654863 GCCCATAGTTGGTGTAGCATT 58.345 47.619 0.00 0.00 41.91 3.56
5279 5984 1.475034 CGCCCATAGTTGGTGTAGCAT 60.475 52.381 0.00 0.00 41.91 3.79
5280 5985 0.107897 CGCCCATAGTTGGTGTAGCA 60.108 55.000 0.00 0.00 41.91 3.49
5281 5986 1.436983 GCGCCCATAGTTGGTGTAGC 61.437 60.000 0.00 0.00 41.91 3.58
5282 5987 0.814010 GGCGCCCATAGTTGGTGTAG 60.814 60.000 18.11 0.00 41.91 2.74
5283 5988 1.222387 GGCGCCCATAGTTGGTGTA 59.778 57.895 18.11 0.00 41.91 2.90
5284 5989 2.045340 GGCGCCCATAGTTGGTGT 60.045 61.111 18.11 0.00 41.91 4.16
5285 5990 2.828549 GGGCGCCCATAGTTGGTG 60.829 66.667 40.73 0.00 41.91 4.17
5286 5991 4.483243 CGGGCGCCCATAGTTGGT 62.483 66.667 42.78 0.00 41.91 3.67
5288 5993 4.483243 ACCGGGCGCCCATAGTTG 62.483 66.667 42.78 25.99 35.37 3.16
5289 5994 4.483243 CACCGGGCGCCCATAGTT 62.483 66.667 42.78 20.10 35.37 2.24
5319 6024 4.120331 ATTTGGCCGAGCGCTTGC 62.120 61.111 19.81 20.37 37.74 4.01
5320 6025 2.202518 CATTTGGCCGAGCGCTTG 60.203 61.111 18.28 18.28 37.74 4.01
5321 6026 4.120331 GCATTTGGCCGAGCGCTT 62.120 61.111 13.26 0.00 37.74 4.68
5322 6027 3.680620 TAGCATTTGGCCGAGCGCT 62.681 57.895 11.27 11.27 46.50 5.92
5323 6028 3.202001 TAGCATTTGGCCGAGCGC 61.202 61.111 0.00 0.00 46.50 5.92
5324 6029 2.106074 TGTAGCATTTGGCCGAGCG 61.106 57.895 0.00 0.00 46.50 5.03
5325 6030 1.429423 GTGTAGCATTTGGCCGAGC 59.571 57.895 0.00 0.00 46.50 5.03
5326 6031 0.676466 TGGTGTAGCATTTGGCCGAG 60.676 55.000 0.00 0.00 46.50 4.63
5327 6032 0.250945 TTGGTGTAGCATTTGGCCGA 60.251 50.000 0.00 0.00 46.50 5.54
5328 6033 0.109319 GTTGGTGTAGCATTTGGCCG 60.109 55.000 0.00 0.00 46.50 6.13
5329 6034 1.256812 AGTTGGTGTAGCATTTGGCC 58.743 50.000 0.00 0.00 46.50 5.36
5330 6035 2.159572 CGTAGTTGGTGTAGCATTTGGC 60.160 50.000 0.00 0.00 45.30 4.52
5331 6036 2.418628 CCGTAGTTGGTGTAGCATTTGG 59.581 50.000 0.00 0.00 0.00 3.28
5332 6037 2.418628 CCCGTAGTTGGTGTAGCATTTG 59.581 50.000 0.00 0.00 0.00 2.32
5333 6038 2.706890 CCCGTAGTTGGTGTAGCATTT 58.293 47.619 0.00 0.00 0.00 2.32
5334 6039 1.677820 GCCCGTAGTTGGTGTAGCATT 60.678 52.381 0.00 0.00 0.00 3.56
5335 6040 0.107848 GCCCGTAGTTGGTGTAGCAT 60.108 55.000 0.00 0.00 0.00 3.79
5336 6041 1.189524 AGCCCGTAGTTGGTGTAGCA 61.190 55.000 0.00 0.00 0.00 3.49
5337 6042 0.459759 GAGCCCGTAGTTGGTGTAGC 60.460 60.000 0.00 0.00 0.00 3.58
5338 6043 0.175073 GGAGCCCGTAGTTGGTGTAG 59.825 60.000 0.00 0.00 0.00 2.74
5339 6044 1.259840 GGGAGCCCGTAGTTGGTGTA 61.260 60.000 0.00 0.00 0.00 2.90
5340 6045 2.590114 GGGAGCCCGTAGTTGGTGT 61.590 63.158 0.00 0.00 0.00 4.16
5341 6046 2.267961 GGGAGCCCGTAGTTGGTG 59.732 66.667 0.00 0.00 0.00 4.17
5371 6076 4.200283 GTCTCGCGGCAGAGGAGG 62.200 72.222 6.13 0.00 38.71 4.30
5372 6077 4.544689 CGTCTCGCGGCAGAGGAG 62.545 72.222 6.13 8.62 38.71 3.69
5374 6079 4.116328 TTCGTCTCGCGGCAGAGG 62.116 66.667 6.13 8.79 41.72 3.69
5375 6080 2.578178 CTTCGTCTCGCGGCAGAG 60.578 66.667 6.13 13.26 41.72 3.35
5376 6081 4.116328 CCTTCGTCTCGCGGCAGA 62.116 66.667 6.13 0.00 41.72 4.26
5377 6082 4.116328 TCCTTCGTCTCGCGGCAG 62.116 66.667 6.13 0.00 41.72 4.85
5378 6083 4.116328 CTCCTTCGTCTCGCGGCA 62.116 66.667 6.13 0.00 41.72 5.69
5379 6084 2.061182 ATACTCCTTCGTCTCGCGGC 62.061 60.000 6.13 0.00 41.72 6.53
5380 6085 0.317103 CATACTCCTTCGTCTCGCGG 60.317 60.000 6.13 0.00 41.72 6.46
5381 6086 0.656259 TCATACTCCTTCGTCTCGCG 59.344 55.000 0.00 0.00 43.01 5.87
5382 6087 1.268640 GGTCATACTCCTTCGTCTCGC 60.269 57.143 0.00 0.00 0.00 5.03
5383 6088 1.003759 CGGTCATACTCCTTCGTCTCG 60.004 57.143 0.00 0.00 0.00 4.04
5384 6089 1.268640 GCGGTCATACTCCTTCGTCTC 60.269 57.143 0.00 0.00 0.00 3.36
5385 6090 0.739561 GCGGTCATACTCCTTCGTCT 59.260 55.000 0.00 0.00 0.00 4.18
5386 6091 0.248949 GGCGGTCATACTCCTTCGTC 60.249 60.000 0.00 0.00 0.00 4.20
5387 6092 1.814527 GGCGGTCATACTCCTTCGT 59.185 57.895 0.00 0.00 0.00 3.85
5388 6093 4.732106 GGCGGTCATACTCCTTCG 57.268 61.111 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.