Multiple sequence alignment - TraesCS4D01G244000

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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 TraesCS4D01G244000 chr4D 100.000 6005 0 0 1 6005 408789320 408795324 0.000000e+00 11090.0
1 TraesCS4D01G244000 chr4B 95.321 4168 154 24 1846 6003 507249553 507245417 0.000000e+00 6578.0
2 TraesCS4D01G244000 chr4B 91.914 1212 35 21 593 1775 507250905 507249728 0.000000e+00 1637.0
3 TraesCS4D01G244000 chr4B 98.485 66 1 0 1780 1845 507249682 507249617 3.800000e-22 117.0
4 TraesCS4D01G244000 chr4A 96.815 2072 66 0 3115 5186 80167104 80169175 0.000000e+00 3461.0
5 TraesCS4D01G244000 chr4A 92.564 1560 65 22 1593 3118 80165402 80166944 0.000000e+00 2191.0
6 TraesCS4D01G244000 chr4A 91.725 1148 42 18 475 1598 80163960 80165078 0.000000e+00 1544.0
7 TraesCS4D01G244000 chr4A 96.388 886 28 1 5122 6003 80169173 80170058 0.000000e+00 1456.0
8 TraesCS4D01G244000 chr4A 84.768 151 22 1 2 152 80163273 80163422 3.750000e-32 150.0
9 TraesCS4D01G244000 chr4A 92.308 65 5 0 5122 5186 80169142 80169206 6.410000e-15 93.5
10 TraesCS4D01G244000 chr4A 97.368 38 0 1 394 430 482158359 482158322 5.020000e-06 63.9
11 TraesCS4D01G244000 chr1D 97.778 45 1 0 386 430 41583136 41583180 1.790000e-10 78.7
12 TraesCS4D01G244000 chr5B 95.745 47 2 0 386 432 228272250 228272296 6.450000e-10 76.8
13 TraesCS4D01G244000 chr1B 95.745 47 2 0 384 430 104479465 104479511 6.450000e-10 76.8
14 TraesCS4D01G244000 chr6D 93.878 49 1 1 384 430 319002194 319002146 8.350000e-09 73.1
15 TraesCS4D01G244000 chr2D 93.750 48 2 1 384 430 73133256 73133303 3.000000e-08 71.3
16 TraesCS4D01G244000 chr3D 90.385 52 3 1 385 434 127334719 127334668 3.880000e-07 67.6
17 TraesCS4D01G244000 chr2A 93.478 46 2 1 383 427 718456917 718456872 3.880000e-07 67.6
18 TraesCS4D01G244000 chr5A 90.385 52 2 1 386 434 477394360 477394309 1.400000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G244000 chr4D 408789320 408795324 6004 False 11090.000000 11090 100.000 1 6005 1 chr4D.!!$F1 6004
1 TraesCS4D01G244000 chr4B 507245417 507250905 5488 True 2777.333333 6578 95.240 593 6003 3 chr4B.!!$R1 5410
2 TraesCS4D01G244000 chr4A 80163273 80170058 6785 False 1482.583333 3461 92.428 2 6003 6 chr4A.!!$F1 6001

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
397 532 0.471591 ACCCCCTACCACGTAACACA 60.472 55.000 0.00 0.0 0.00 3.72 F
449 584 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
453 588 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
455 590 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
457 592 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 F
1376 1685 1.007963 TCCTGGGATCGGAGTAGGTTT 59.992 52.381 0.00 0.0 0.00 3.27 F
2786 3536 2.036556 CGATGCTGCACTTCGTTTTT 57.963 45.000 15.43 0.0 40.16 1.94 F
4339 5265 0.459585 GCGTGACTATCCCGAGCAAA 60.460 55.000 0.00 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1650 1.073199 AGGAGGGTTTCGCCAACAG 59.927 57.895 0.00 0.0 37.84 3.16 R
2072 2817 1.323412 ACCAACCGCAAGCATGTTAA 58.677 45.000 0.00 0.0 0.00 2.01 R
2204 2951 1.961277 GTCGGCACAAGTGACTGGG 60.961 63.158 4.04 0.0 36.16 4.45 R
2274 3022 8.115490 AGAAAAGCAACAAGATTACTTAGCAT 57.885 30.769 0.00 0.0 34.70 3.79 R
2463 3211 8.190784 AGTACTATTTATTGCAAGTTTGGCATC 58.809 33.333 4.94 0.0 41.58 3.91 R
3066 3829 0.179051 CTTCTCCAGGATGCTCAGCC 60.179 60.000 0.00 0.0 37.08 4.85 R
4740 5666 1.045407 TACTTCTTGTCGCCCACAGT 58.955 50.000 0.00 0.0 35.97 3.55 R
5287 6277 2.401583 TTACCATGCTGCACCTGTAG 57.598 50.000 3.57 0.0 0.00 2.74 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
29 30 9.906660 TTTTACACTTACACCATGAAATTCATC 57.093 29.630 5.36 0.00 34.28 2.92
42 43 8.405418 CATGAAATTCATCCATGGTCTCTAAT 57.595 34.615 12.58 3.47 34.28 1.73
81 82 3.000819 TGACCACGGGCCACCTAG 61.001 66.667 4.39 0.00 33.28 3.02
137 138 7.582435 TGCGAAAGTTTTGAAATTTTGTGTA 57.418 28.000 7.05 0.00 29.53 2.90
158 159 9.995003 TGTGTAGATATGCATCATGTTATAACA 57.005 29.630 20.14 20.14 44.06 2.41
178 179 6.603940 AACATGTACCTATGCAATTTTGGT 57.396 33.333 0.00 0.00 35.05 3.67
179 180 6.603940 ACATGTACCTATGCAATTTTGGTT 57.396 33.333 0.00 0.00 32.74 3.67
180 181 7.710676 ACATGTACCTATGCAATTTTGGTTA 57.289 32.000 0.00 0.00 32.74 2.85
181 182 8.128322 ACATGTACCTATGCAATTTTGGTTAA 57.872 30.769 0.00 0.00 32.74 2.01
182 183 8.589338 ACATGTACCTATGCAATTTTGGTTAAA 58.411 29.630 0.00 0.00 32.74 1.52
183 184 9.429359 CATGTACCTATGCAATTTTGGTTAAAA 57.571 29.630 0.00 0.00 39.86 1.52
184 185 8.819643 TGTACCTATGCAATTTTGGTTAAAAC 57.180 30.769 0.00 0.00 38.50 2.43
185 186 8.421784 TGTACCTATGCAATTTTGGTTAAAACA 58.578 29.630 0.00 0.00 38.50 2.83
186 187 9.262358 GTACCTATGCAATTTTGGTTAAAACAA 57.738 29.630 0.00 0.00 38.50 2.83
187 188 8.738645 ACCTATGCAATTTTGGTTAAAACAAA 57.261 26.923 0.00 0.00 38.50 2.83
188 189 9.348476 ACCTATGCAATTTTGGTTAAAACAAAT 57.652 25.926 1.23 0.00 38.50 2.32
193 194 9.490663 TGCAATTTTGGTTAAAACAAATAAACG 57.509 25.926 1.23 0.00 38.50 3.60
194 195 9.704098 GCAATTTTGGTTAAAACAAATAAACGA 57.296 25.926 1.23 0.00 38.50 3.85
242 244 2.178580 TCATCTTGAAAACCCCATGCC 58.821 47.619 0.00 0.00 0.00 4.40
243 245 2.181975 CATCTTGAAAACCCCATGCCT 58.818 47.619 0.00 0.00 0.00 4.75
246 248 1.693606 CTTGAAAACCCCATGCCTTGT 59.306 47.619 0.00 0.00 0.00 3.16
257 259 0.478072 ATGCCTTGTGGGTTGTGAGA 59.522 50.000 0.00 0.00 37.43 3.27
261 263 1.949525 CCTTGTGGGTTGTGAGACTTG 59.050 52.381 0.00 0.00 0.00 3.16
268 270 2.158813 GGGTTGTGAGACTTGAGACCAA 60.159 50.000 0.00 0.00 0.00 3.67
269 271 3.496870 GGGTTGTGAGACTTGAGACCAAT 60.497 47.826 0.00 0.00 0.00 3.16
284 286 6.479006 TGAGACCAATGATGAACTTCATTCT 58.521 36.000 5.73 3.83 42.90 2.40
285 287 6.596888 TGAGACCAATGATGAACTTCATTCTC 59.403 38.462 15.88 15.88 42.90 2.87
291 293 9.136952 CCAATGATGAACTTCATTCTCTTTTTC 57.863 33.333 5.73 0.00 42.90 2.29
292 294 9.909644 CAATGATGAACTTCATTCTCTTTTTCT 57.090 29.630 5.73 0.00 42.90 2.52
309 311 8.271312 TCTTTTTCTTTTTCTTGTAGAACCGA 57.729 30.769 0.00 0.00 33.26 4.69
322 457 5.361427 TGTAGAACCGAATGAACTGAAACA 58.639 37.500 0.00 0.00 0.00 2.83
332 467 3.760738 TGAACTGAAACACATGGCCATA 58.239 40.909 20.30 0.00 0.00 2.74
333 468 3.758023 TGAACTGAAACACATGGCCATAG 59.242 43.478 20.30 16.63 0.00 2.23
334 469 3.719268 ACTGAAACACATGGCCATAGA 57.281 42.857 20.30 0.00 0.00 1.98
335 470 4.240881 ACTGAAACACATGGCCATAGAT 57.759 40.909 20.30 6.09 0.00 1.98
336 471 5.372343 ACTGAAACACATGGCCATAGATA 57.628 39.130 20.30 0.51 0.00 1.98
337 472 5.126067 ACTGAAACACATGGCCATAGATAC 58.874 41.667 20.30 9.26 0.00 2.24
338 473 5.109500 TGAAACACATGGCCATAGATACA 57.891 39.130 20.30 11.76 0.00 2.29
339 474 4.881273 TGAAACACATGGCCATAGATACAC 59.119 41.667 20.30 8.28 0.00 2.90
340 475 3.492102 ACACATGGCCATAGATACACC 57.508 47.619 20.30 0.00 0.00 4.16
341 476 2.224281 ACACATGGCCATAGATACACCG 60.224 50.000 20.30 5.04 0.00 4.94
342 477 2.047061 ACATGGCCATAGATACACCGT 58.953 47.619 20.30 5.77 0.00 4.83
343 478 2.037251 ACATGGCCATAGATACACCGTC 59.963 50.000 20.30 0.00 0.00 4.79
344 479 1.045407 TGGCCATAGATACACCGTCC 58.955 55.000 0.00 0.00 0.00 4.79
345 480 1.045407 GGCCATAGATACACCGTCCA 58.955 55.000 0.00 0.00 0.00 4.02
346 481 1.414919 GGCCATAGATACACCGTCCAA 59.585 52.381 0.00 0.00 0.00 3.53
347 482 2.158871 GGCCATAGATACACCGTCCAAA 60.159 50.000 0.00 0.00 0.00 3.28
348 483 3.131396 GCCATAGATACACCGTCCAAAG 58.869 50.000 0.00 0.00 0.00 2.77
349 484 3.181469 GCCATAGATACACCGTCCAAAGA 60.181 47.826 0.00 0.00 0.00 2.52
350 485 4.682320 GCCATAGATACACCGTCCAAAGAA 60.682 45.833 0.00 0.00 0.00 2.52
351 486 5.424757 CCATAGATACACCGTCCAAAGAAA 58.575 41.667 0.00 0.00 0.00 2.52
352 487 5.878116 CCATAGATACACCGTCCAAAGAAAA 59.122 40.000 0.00 0.00 0.00 2.29
353 488 6.373216 CCATAGATACACCGTCCAAAGAAAAA 59.627 38.462 0.00 0.00 0.00 1.94
354 489 5.684550 AGATACACCGTCCAAAGAAAAAC 57.315 39.130 0.00 0.00 0.00 2.43
355 490 5.127491 AGATACACCGTCCAAAGAAAAACA 58.873 37.500 0.00 0.00 0.00 2.83
356 491 5.768164 AGATACACCGTCCAAAGAAAAACAT 59.232 36.000 0.00 0.00 0.00 2.71
357 492 4.729227 ACACCGTCCAAAGAAAAACATT 57.271 36.364 0.00 0.00 0.00 2.71
358 493 5.079689 ACACCGTCCAAAGAAAAACATTT 57.920 34.783 0.00 0.00 0.00 2.32
359 494 5.483811 ACACCGTCCAAAGAAAAACATTTT 58.516 33.333 0.00 0.00 0.00 1.82
360 495 5.579119 ACACCGTCCAAAGAAAAACATTTTC 59.421 36.000 7.34 7.34 0.00 2.29
361 496 5.578727 CACCGTCCAAAGAAAAACATTTTCA 59.421 36.000 15.59 0.00 0.00 2.69
362 497 5.579119 ACCGTCCAAAGAAAAACATTTTCAC 59.421 36.000 15.59 5.89 0.00 3.18
363 498 5.578727 CCGTCCAAAGAAAAACATTTTCACA 59.421 36.000 15.59 0.00 0.00 3.58
364 499 6.091441 CCGTCCAAAGAAAAACATTTTCACAA 59.909 34.615 15.59 0.00 0.00 3.33
365 500 6.953189 CGTCCAAAGAAAAACATTTTCACAAC 59.047 34.615 15.59 7.16 0.00 3.32
366 501 7.359598 CGTCCAAAGAAAAACATTTTCACAACA 60.360 33.333 15.59 0.00 0.00 3.33
367 502 8.450180 GTCCAAAGAAAAACATTTTCACAACAT 58.550 29.630 15.59 0.00 0.00 2.71
368 503 8.663911 TCCAAAGAAAAACATTTTCACAACATC 58.336 29.630 15.59 0.00 0.00 3.06
369 504 7.635587 CCAAAGAAAAACATTTTCACAACATCG 59.364 33.333 15.59 0.00 0.00 3.84
370 505 8.379161 CAAAGAAAAACATTTTCACAACATCGA 58.621 29.630 15.59 0.00 0.00 3.59
371 506 8.647143 AAGAAAAACATTTTCACAACATCGAT 57.353 26.923 15.59 0.00 0.00 3.59
372 507 9.743057 AAGAAAAACATTTTCACAACATCGATA 57.257 25.926 15.59 0.00 0.00 2.92
373 508 9.180678 AGAAAAACATTTTCACAACATCGATAC 57.819 29.630 15.59 0.00 0.00 2.24
374 509 8.864069 AAAAACATTTTCACAACATCGATACA 57.136 26.923 0.00 0.00 0.00 2.29
375 510 9.474920 AAAAACATTTTCACAACATCGATACAT 57.525 25.926 0.00 0.00 0.00 2.29
376 511 9.474920 AAAACATTTTCACAACATCGATACATT 57.525 25.926 0.00 0.00 0.00 2.71
377 512 9.474920 AAACATTTTCACAACATCGATACATTT 57.525 25.926 0.00 0.00 0.00 2.32
379 514 9.554724 ACATTTTCACAACATCGATACATTTAC 57.445 29.630 0.00 0.00 0.00 2.01
380 515 9.009327 CATTTTCACAACATCGATACATTTACC 57.991 33.333 0.00 0.00 0.00 2.85
381 516 6.671614 TTCACAACATCGATACATTTACCC 57.328 37.500 0.00 0.00 0.00 3.69
382 517 5.120399 TCACAACATCGATACATTTACCCC 58.880 41.667 0.00 0.00 0.00 4.95
383 518 4.274950 CACAACATCGATACATTTACCCCC 59.725 45.833 0.00 0.00 0.00 5.40
384 519 4.165372 ACAACATCGATACATTTACCCCCT 59.835 41.667 0.00 0.00 0.00 4.79
385 520 5.367352 ACAACATCGATACATTTACCCCCTA 59.633 40.000 0.00 0.00 0.00 3.53
386 521 5.479124 ACATCGATACATTTACCCCCTAC 57.521 43.478 0.00 0.00 0.00 3.18
387 522 4.285260 ACATCGATACATTTACCCCCTACC 59.715 45.833 0.00 0.00 0.00 3.18
388 523 3.926198 TCGATACATTTACCCCCTACCA 58.074 45.455 0.00 0.00 0.00 3.25
389 524 3.642848 TCGATACATTTACCCCCTACCAC 59.357 47.826 0.00 0.00 0.00 4.16
390 525 3.553508 CGATACATTTACCCCCTACCACG 60.554 52.174 0.00 0.00 0.00 4.94
391 526 1.660242 ACATTTACCCCCTACCACGT 58.340 50.000 0.00 0.00 0.00 4.49
392 527 2.831565 ACATTTACCCCCTACCACGTA 58.168 47.619 0.00 0.00 0.00 3.57
393 528 3.180507 ACATTTACCCCCTACCACGTAA 58.819 45.455 0.00 0.00 0.00 3.18
394 529 3.055167 ACATTTACCCCCTACCACGTAAC 60.055 47.826 0.00 0.00 0.00 2.50
395 530 2.317371 TTACCCCCTACCACGTAACA 57.683 50.000 0.00 0.00 0.00 2.41
396 531 1.555967 TACCCCCTACCACGTAACAC 58.444 55.000 0.00 0.00 0.00 3.32
397 532 0.471591 ACCCCCTACCACGTAACACA 60.472 55.000 0.00 0.00 0.00 3.72
398 533 0.906775 CCCCCTACCACGTAACACAT 59.093 55.000 0.00 0.00 0.00 3.21
399 534 1.406341 CCCCCTACCACGTAACACATG 60.406 57.143 0.00 0.00 0.00 3.21
400 535 1.276989 CCCCTACCACGTAACACATGT 59.723 52.381 0.00 0.00 0.00 3.21
401 536 2.343101 CCCTACCACGTAACACATGTG 58.657 52.381 24.25 24.25 42.84 3.21
407 542 3.449322 CACGTAACACATGTGGTAAGC 57.551 47.619 29.36 16.63 40.02 3.09
408 543 2.803386 CACGTAACACATGTGGTAAGCA 59.197 45.455 29.36 8.28 40.02 3.91
409 544 3.248841 CACGTAACACATGTGGTAAGCAA 59.751 43.478 29.36 7.91 40.02 3.91
410 545 4.069304 ACGTAACACATGTGGTAAGCAAT 58.931 39.130 29.36 13.13 36.01 3.56
411 546 4.517453 ACGTAACACATGTGGTAAGCAATT 59.483 37.500 29.36 15.59 36.01 2.32
412 547 5.086058 CGTAACACATGTGGTAAGCAATTC 58.914 41.667 24.79 9.92 34.09 2.17
413 548 5.334491 CGTAACACATGTGGTAAGCAATTCA 60.334 40.000 24.79 0.00 34.09 2.57
414 549 5.528043 AACACATGTGGTAAGCAATTCAA 57.472 34.783 28.64 0.00 34.19 2.69
415 550 5.528043 ACACATGTGGTAAGCAATTCAAA 57.472 34.783 28.64 0.00 34.19 2.69
416 551 5.288804 ACACATGTGGTAAGCAATTCAAAC 58.711 37.500 28.64 0.00 34.19 2.93
417 552 5.163468 ACACATGTGGTAAGCAATTCAAACA 60.163 36.000 28.64 0.00 34.19 2.83
418 553 5.752472 CACATGTGGTAAGCAATTCAAACAA 59.248 36.000 18.51 0.00 0.00 2.83
419 554 6.424509 CACATGTGGTAAGCAATTCAAACAAT 59.575 34.615 18.51 0.00 0.00 2.71
420 555 6.991531 ACATGTGGTAAGCAATTCAAACAATT 59.008 30.769 0.00 0.00 0.00 2.32
421 556 8.147058 ACATGTGGTAAGCAATTCAAACAATTA 58.853 29.630 0.00 0.00 0.00 1.40
422 557 8.986847 CATGTGGTAAGCAATTCAAACAATTAA 58.013 29.630 0.00 0.00 0.00 1.40
423 558 8.948631 TGTGGTAAGCAATTCAAACAATTAAA 57.051 26.923 0.00 0.00 0.00 1.52
424 559 9.383519 TGTGGTAAGCAATTCAAACAATTAAAA 57.616 25.926 0.00 0.00 0.00 1.52
445 580 3.717400 AAAAACACACACACACACACA 57.283 38.095 0.00 0.00 0.00 3.72
446 581 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
447 582 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
448 583 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
449 584 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
450 585 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
451 586 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
452 587 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
453 588 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
454 589 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
455 590 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
456 591 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
457 592 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
458 593 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
459 594 1.468127 ACACACACACACACACACATG 59.532 47.619 0.00 0.00 0.00 3.21
460 595 1.468127 CACACACACACACACACATGT 59.532 47.619 0.00 0.00 40.80 3.21
481 745 4.202192 TGTGAACCAAACTATGCAATGCAA 60.202 37.500 13.45 0.73 43.62 4.08
495 759 3.331150 CAATGCAATGCAACAGTTGGAT 58.669 40.909 13.45 14.22 43.62 3.41
548 819 1.885850 ACCAGAAACGTGTGTCGCC 60.886 57.895 0.00 0.00 44.19 5.54
591 864 3.081409 GGTAAGCCGGCTCCAGGA 61.081 66.667 32.93 10.26 0.00 3.86
789 1073 3.099141 AGCACCATAAATCCCAACCAAG 58.901 45.455 0.00 0.00 0.00 3.61
873 1161 2.412112 CCGGCAGTACGTAGGCTC 59.588 66.667 16.16 7.86 0.00 4.70
874 1162 2.024305 CGGCAGTACGTAGGCTCG 59.976 66.667 16.16 13.99 0.00 5.03
875 1163 2.278661 GGCAGTACGTAGGCTCGC 60.279 66.667 16.16 8.38 0.00 5.03
985 1284 3.005261 CCGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
986 1285 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
987 1286 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
988 1287 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
989 1288 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
990 1289 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
991 1290 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
992 1291 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
993 1292 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
994 1293 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
995 1294 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
996 1295 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
997 1296 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
998 1297 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1179 1482 2.263741 GCACCACACAAGGCTGAGG 61.264 63.158 0.00 0.00 0.00 3.86
1341 1650 4.082571 AGAGGCATGCAAGTGTTGTATTTC 60.083 41.667 21.36 0.00 33.54 2.17
1376 1685 1.007963 TCCTGGGATCGGAGTAGGTTT 59.992 52.381 0.00 0.00 0.00 3.27
2043 2788 7.486407 ACAAGAAATTTGCCCAGATTCTAAT 57.514 32.000 0.00 0.00 0.00 1.73
2067 2812 6.817765 ATACAGGTGTGACAAAACAATAGG 57.182 37.500 0.00 0.00 0.00 2.57
2070 2815 5.473504 ACAGGTGTGACAAAACAATAGGATC 59.526 40.000 0.00 0.00 0.00 3.36
2072 2817 6.207417 CAGGTGTGACAAAACAATAGGATCTT 59.793 38.462 0.00 0.00 0.00 2.40
2204 2951 8.184192 CAGGTTAATTGTCACCAGATATTCAAC 58.816 37.037 6.18 0.00 35.25 3.18
2463 3211 7.962918 CACCTAACATGTTTCTTAAGGAATTCG 59.037 37.037 24.69 8.71 33.53 3.34
2786 3536 2.036556 CGATGCTGCACTTCGTTTTT 57.963 45.000 15.43 0.00 40.16 1.94
2971 3721 5.529014 CTCTGTTTCTTCTGAGCTTAAGC 57.471 43.478 20.09 20.09 42.49 3.09
3012 3775 3.012518 CTGGATGCAACCTGGACTTAAG 58.987 50.000 14.77 0.00 0.00 1.85
3031 3794 2.688507 AGTTTACCTGACGTCTGCATG 58.311 47.619 17.92 6.39 0.00 4.06
3066 3829 2.029470 AGCTGAAGAAACAGGACGAGAG 60.029 50.000 0.00 0.00 38.22 3.20
3094 3857 0.612229 TCCTGGAGAAGCAGCTTGAG 59.388 55.000 13.91 2.87 0.00 3.02
3119 4045 4.998033 AGAAGGTTGCTTAGTGCTTACTTC 59.002 41.667 0.00 0.00 43.37 3.01
3196 4122 3.000523 CGGTTACATGACGGGTAAATTCG 59.999 47.826 0.00 0.00 32.94 3.34
3229 4155 5.221904 TGACAGAATCTGGATGTGAAAAGGA 60.222 40.000 15.38 0.00 35.51 3.36
3312 4238 0.678366 TCCACTCGGCTCAGAGAGAC 60.678 60.000 0.00 0.00 40.57 3.36
3384 4310 5.738619 TCAAGAAGTACAAGCATGAGGTA 57.261 39.130 0.00 0.00 0.00 3.08
3427 4353 1.881973 GCACCATTTGAGCAGAGTGAA 59.118 47.619 0.00 0.00 0.00 3.18
3473 4399 1.303643 GGCTTACCTGTGGCTGCTT 60.304 57.895 0.00 0.00 0.00 3.91
3612 4538 1.407258 AGAGCGCTGATTGTAGAGGAC 59.593 52.381 18.48 0.00 0.00 3.85
3633 4559 5.160607 ACGTCCAGAACCAGAATATTGAA 57.839 39.130 0.00 0.00 0.00 2.69
3918 4844 1.201429 ACCAGAACCAGGCTACCAGG 61.201 60.000 0.00 0.00 36.18 4.45
3981 4907 4.120589 GGTCGATCCCATTCTAGTTTGTC 58.879 47.826 0.00 0.00 0.00 3.18
4145 5071 1.270305 TGGCTGGAAGAACGAAGACTG 60.270 52.381 0.00 0.00 34.07 3.51
4203 5129 1.360192 GCCGCTGCAATCCCATTAC 59.640 57.895 0.00 0.00 37.47 1.89
4339 5265 0.459585 GCGTGACTATCCCGAGCAAA 60.460 55.000 0.00 0.00 0.00 3.68
4466 5392 3.304911 TGGAAAATCCAACACACCTGA 57.695 42.857 0.00 0.00 45.00 3.86
4740 5666 2.612972 GGAGCGTCCTGTGAGAAATCAA 60.613 50.000 0.00 0.00 32.53 2.57
4821 5747 4.433186 TCCAAATTACAAGCCACATTCG 57.567 40.909 0.00 0.00 0.00 3.34
5228 6218 8.723365 TGTAAGATTATGGTTCAAGGGATACAT 58.277 33.333 0.00 0.00 39.74 2.29
5241 6231 5.584551 AGGGATACATAGGACCCAAAATC 57.415 43.478 0.00 0.00 44.25 2.17
5287 6277 9.458374 TCTAAAATCGTTCATTTCTTTGTTTCC 57.542 29.630 0.00 0.00 33.16 3.13
5629 6619 9.713684 TCCATCCCTTTATTCATGTAAAAGATT 57.286 29.630 14.54 2.24 33.05 2.40
5791 6785 5.482175 TCTTTCTTTTTGTTCCACCAAAGGA 59.518 36.000 0.00 0.00 35.85 3.36
5866 6860 4.572389 AGCGAGCATAGGAAACATGTAAAG 59.428 41.667 0.00 0.00 0.00 1.85
6003 6999 1.815003 GGCTCTCTGGTGACAAAATGG 59.185 52.381 0.00 0.00 42.06 3.16
6004 7000 1.815003 GCTCTCTGGTGACAAAATGGG 59.185 52.381 0.00 0.00 42.06 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.688747 AGAATTAGAGACCATGGATGAATTTC 57.311 34.615 21.47 12.35 0.00 2.17
27 28 5.848369 TGATGGAGAATTAGAGACCATGGAT 59.152 40.000 21.47 6.30 40.74 3.41
29 30 5.163269 TGTGATGGAGAATTAGAGACCATGG 60.163 44.000 11.19 11.19 40.74 3.66
39 40 7.825761 CAGCCATATATGTGTGATGGAGAATTA 59.174 37.037 11.73 0.00 42.41 1.40
42 43 5.307716 TCAGCCATATATGTGTGATGGAGAA 59.692 40.000 11.73 0.00 42.41 2.87
110 111 8.825745 ACACAAAATTTCAAAACTTTCGCATAT 58.174 25.926 0.00 0.00 0.00 1.78
111 112 8.190888 ACACAAAATTTCAAAACTTTCGCATA 57.809 26.923 0.00 0.00 0.00 3.14
112 113 7.071014 ACACAAAATTTCAAAACTTTCGCAT 57.929 28.000 0.00 0.00 0.00 4.73
113 114 6.473397 ACACAAAATTTCAAAACTTTCGCA 57.527 29.167 0.00 0.00 0.00 5.10
114 115 7.890763 TCTACACAAAATTTCAAAACTTTCGC 58.109 30.769 0.00 0.00 0.00 4.70
119 120 9.979578 TGCATATCTACACAAAATTTCAAAACT 57.020 25.926 0.00 0.00 0.00 2.66
152 153 9.415008 ACCAAAATTGCATAGGTACATGTTATA 57.585 29.630 2.30 0.00 0.00 0.98
153 154 8.305046 ACCAAAATTGCATAGGTACATGTTAT 57.695 30.769 2.30 0.00 0.00 1.89
154 155 7.710676 ACCAAAATTGCATAGGTACATGTTA 57.289 32.000 2.30 0.00 0.00 2.41
155 156 6.603940 ACCAAAATTGCATAGGTACATGTT 57.396 33.333 2.30 0.00 0.00 2.71
156 157 6.603940 AACCAAAATTGCATAGGTACATGT 57.396 33.333 2.69 2.69 31.10 3.21
157 158 8.994429 TTTAACCAAAATTGCATAGGTACATG 57.006 30.769 0.00 0.00 31.10 3.21
158 159 9.430623 GTTTTAACCAAAATTGCATAGGTACAT 57.569 29.630 0.00 0.00 36.10 2.29
159 160 8.421784 TGTTTTAACCAAAATTGCATAGGTACA 58.578 29.630 0.00 0.00 36.10 2.90
160 161 8.819643 TGTTTTAACCAAAATTGCATAGGTAC 57.180 30.769 0.00 0.00 36.10 3.34
161 162 9.832445 TTTGTTTTAACCAAAATTGCATAGGTA 57.168 25.926 0.00 0.00 36.10 3.08
162 163 8.738645 TTTGTTTTAACCAAAATTGCATAGGT 57.261 26.923 0.00 0.00 36.10 3.08
167 168 9.490663 CGTTTATTTGTTTTAACCAAAATTGCA 57.509 25.926 4.18 0.00 36.10 4.08
168 169 9.704098 TCGTTTATTTGTTTTAACCAAAATTGC 57.296 25.926 4.18 0.00 36.10 3.56
173 174 9.367444 ACACATCGTTTATTTGTTTTAACCAAA 57.633 25.926 2.84 2.84 0.00 3.28
174 175 8.928270 ACACATCGTTTATTTGTTTTAACCAA 57.072 26.923 0.00 0.00 0.00 3.67
175 176 8.188799 TGACACATCGTTTATTTGTTTTAACCA 58.811 29.630 0.00 0.00 28.49 3.67
176 177 8.563289 TGACACATCGTTTATTTGTTTTAACC 57.437 30.769 0.00 0.00 28.49 2.85
177 178 9.987901 CATGACACATCGTTTATTTGTTTTAAC 57.012 29.630 0.00 0.00 28.49 2.01
178 179 9.952188 TCATGACACATCGTTTATTTGTTTTAA 57.048 25.926 0.00 0.00 28.49 1.52
179 180 9.952188 TTCATGACACATCGTTTATTTGTTTTA 57.048 25.926 0.00 0.00 28.49 1.52
180 181 8.864069 TTCATGACACATCGTTTATTTGTTTT 57.136 26.923 0.00 0.00 28.49 2.43
181 182 8.864069 TTTCATGACACATCGTTTATTTGTTT 57.136 26.923 0.00 0.00 28.49 2.83
182 183 8.864069 TTTTCATGACACATCGTTTATTTGTT 57.136 26.923 0.00 0.00 28.49 2.83
183 184 8.864069 TTTTTCATGACACATCGTTTATTTGT 57.136 26.923 0.00 0.00 31.05 2.83
209 210 5.486735 TTCAAGATGAACCAATTGGCATT 57.513 34.783 24.79 12.26 39.32 3.56
211 212 4.952071 TTTCAAGATGAACCAATTGGCA 57.048 36.364 24.79 15.39 35.89 4.92
212 213 4.452114 GGTTTTCAAGATGAACCAATTGGC 59.548 41.667 24.79 9.75 41.86 4.52
213 214 4.996758 GGGTTTTCAAGATGAACCAATTGG 59.003 41.667 23.31 23.31 43.59 3.16
214 215 4.996758 GGGGTTTTCAAGATGAACCAATTG 59.003 41.667 14.10 0.00 43.59 2.32
215 216 4.657969 TGGGGTTTTCAAGATGAACCAATT 59.342 37.500 14.10 0.00 43.59 2.32
216 217 4.230455 TGGGGTTTTCAAGATGAACCAAT 58.770 39.130 14.10 0.00 43.59 3.16
242 244 2.874701 CTCAAGTCTCACAACCCACAAG 59.125 50.000 0.00 0.00 0.00 3.16
243 245 2.503765 TCTCAAGTCTCACAACCCACAA 59.496 45.455 0.00 0.00 0.00 3.33
246 248 1.416401 GGTCTCAAGTCTCACAACCCA 59.584 52.381 0.00 0.00 0.00 4.51
257 259 5.624159 TGAAGTTCATCATTGGTCTCAAGT 58.376 37.500 0.08 0.00 36.19 3.16
284 286 8.271312 TCGGTTCTACAAGAAAAAGAAAAAGA 57.729 30.769 0.00 0.00 35.75 2.52
285 287 8.905103 TTCGGTTCTACAAGAAAAAGAAAAAG 57.095 30.769 0.00 0.00 35.75 2.27
291 293 7.587757 CAGTTCATTCGGTTCTACAAGAAAAAG 59.412 37.037 0.00 0.00 35.75 2.27
292 294 7.281324 TCAGTTCATTCGGTTCTACAAGAAAAA 59.719 33.333 0.00 0.00 35.75 1.94
293 295 6.764085 TCAGTTCATTCGGTTCTACAAGAAAA 59.236 34.615 0.00 0.00 35.75 2.29
301 303 5.361427 TGTGTTTCAGTTCATTCGGTTCTA 58.639 37.500 0.00 0.00 0.00 2.10
309 311 2.964464 TGGCCATGTGTTTCAGTTCATT 59.036 40.909 0.00 0.00 0.00 2.57
322 457 2.037251 GACGGTGTATCTATGGCCATGT 59.963 50.000 29.04 13.81 0.00 3.21
332 467 5.127491 TGTTTTTCTTTGGACGGTGTATCT 58.873 37.500 0.00 0.00 0.00 1.98
333 468 5.427036 TGTTTTTCTTTGGACGGTGTATC 57.573 39.130 0.00 0.00 0.00 2.24
334 469 6.399639 AATGTTTTTCTTTGGACGGTGTAT 57.600 33.333 0.00 0.00 0.00 2.29
335 470 5.838531 AATGTTTTTCTTTGGACGGTGTA 57.161 34.783 0.00 0.00 0.00 2.90
336 471 4.729227 AATGTTTTTCTTTGGACGGTGT 57.271 36.364 0.00 0.00 0.00 4.16
337 472 5.578727 TGAAAATGTTTTTCTTTGGACGGTG 59.421 36.000 12.44 0.00 0.00 4.94
338 473 5.579119 GTGAAAATGTTTTTCTTTGGACGGT 59.421 36.000 12.44 0.00 0.00 4.83
339 474 5.578727 TGTGAAAATGTTTTTCTTTGGACGG 59.421 36.000 12.44 0.00 0.00 4.79
340 475 6.639671 TGTGAAAATGTTTTTCTTTGGACG 57.360 33.333 12.44 0.00 0.00 4.79
341 476 7.801752 TGTTGTGAAAATGTTTTTCTTTGGAC 58.198 30.769 12.44 4.50 0.00 4.02
342 477 7.969536 TGTTGTGAAAATGTTTTTCTTTGGA 57.030 28.000 12.44 0.00 0.00 3.53
343 478 7.635587 CGATGTTGTGAAAATGTTTTTCTTTGG 59.364 33.333 12.44 0.00 0.00 3.28
344 479 8.379161 TCGATGTTGTGAAAATGTTTTTCTTTG 58.621 29.630 12.44 0.00 0.00 2.77
345 480 8.472683 TCGATGTTGTGAAAATGTTTTTCTTT 57.527 26.923 12.44 0.00 0.00 2.52
346 481 8.647143 ATCGATGTTGTGAAAATGTTTTTCTT 57.353 26.923 12.44 0.00 0.00 2.52
347 482 9.180678 GTATCGATGTTGTGAAAATGTTTTTCT 57.819 29.630 8.54 0.00 0.00 2.52
348 483 8.963130 TGTATCGATGTTGTGAAAATGTTTTTC 58.037 29.630 8.54 5.90 0.00 2.29
349 484 8.864069 TGTATCGATGTTGTGAAAATGTTTTT 57.136 26.923 8.54 0.00 0.00 1.94
350 485 9.474920 AATGTATCGATGTTGTGAAAATGTTTT 57.525 25.926 8.54 0.00 0.00 2.43
351 486 9.474920 AAATGTATCGATGTTGTGAAAATGTTT 57.525 25.926 8.54 0.00 0.00 2.83
353 488 9.554724 GTAAATGTATCGATGTTGTGAAAATGT 57.445 29.630 8.54 0.00 0.00 2.71
354 489 9.009327 GGTAAATGTATCGATGTTGTGAAAATG 57.991 33.333 8.54 0.00 0.00 2.32
355 490 8.188139 GGGTAAATGTATCGATGTTGTGAAAAT 58.812 33.333 8.54 0.00 0.00 1.82
356 491 7.362229 GGGGTAAATGTATCGATGTTGTGAAAA 60.362 37.037 8.54 0.00 0.00 2.29
357 492 6.094325 GGGGTAAATGTATCGATGTTGTGAAA 59.906 38.462 8.54 0.00 0.00 2.69
358 493 5.587043 GGGGTAAATGTATCGATGTTGTGAA 59.413 40.000 8.54 0.00 0.00 3.18
359 494 5.120399 GGGGTAAATGTATCGATGTTGTGA 58.880 41.667 8.54 0.00 0.00 3.58
360 495 4.274950 GGGGGTAAATGTATCGATGTTGTG 59.725 45.833 8.54 0.00 0.00 3.33
361 496 4.165372 AGGGGGTAAATGTATCGATGTTGT 59.835 41.667 8.54 0.00 0.00 3.32
362 497 4.714632 AGGGGGTAAATGTATCGATGTTG 58.285 43.478 8.54 0.00 0.00 3.33
363 498 5.221783 GGTAGGGGGTAAATGTATCGATGTT 60.222 44.000 8.54 0.00 0.00 2.71
364 499 4.285260 GGTAGGGGGTAAATGTATCGATGT 59.715 45.833 8.54 0.00 0.00 3.06
365 500 4.285003 TGGTAGGGGGTAAATGTATCGATG 59.715 45.833 8.54 0.00 0.00 3.84
366 501 4.285260 GTGGTAGGGGGTAAATGTATCGAT 59.715 45.833 2.16 2.16 0.00 3.59
367 502 3.642848 GTGGTAGGGGGTAAATGTATCGA 59.357 47.826 0.00 0.00 0.00 3.59
368 503 3.553508 CGTGGTAGGGGGTAAATGTATCG 60.554 52.174 0.00 0.00 0.00 2.92
369 504 3.389002 ACGTGGTAGGGGGTAAATGTATC 59.611 47.826 0.00 0.00 0.00 2.24
370 505 3.387012 ACGTGGTAGGGGGTAAATGTAT 58.613 45.455 0.00 0.00 0.00 2.29
371 506 2.831565 ACGTGGTAGGGGGTAAATGTA 58.168 47.619 0.00 0.00 0.00 2.29
372 507 1.660242 ACGTGGTAGGGGGTAAATGT 58.340 50.000 0.00 0.00 0.00 2.71
373 508 3.055240 TGTTACGTGGTAGGGGGTAAATG 60.055 47.826 0.00 0.00 0.00 2.32
374 509 3.055167 GTGTTACGTGGTAGGGGGTAAAT 60.055 47.826 0.00 0.00 0.00 1.40
375 510 2.301583 GTGTTACGTGGTAGGGGGTAAA 59.698 50.000 0.00 0.00 0.00 2.01
376 511 1.899142 GTGTTACGTGGTAGGGGGTAA 59.101 52.381 0.00 0.00 0.00 2.85
377 512 1.203112 TGTGTTACGTGGTAGGGGGTA 60.203 52.381 0.00 0.00 0.00 3.69
378 513 0.471591 TGTGTTACGTGGTAGGGGGT 60.472 55.000 0.00 0.00 0.00 4.95
379 514 0.906775 ATGTGTTACGTGGTAGGGGG 59.093 55.000 0.00 0.00 0.00 5.40
380 515 1.276989 ACATGTGTTACGTGGTAGGGG 59.723 52.381 0.00 0.00 39.36 4.79
381 516 2.343101 CACATGTGTTACGTGGTAGGG 58.657 52.381 18.03 0.00 39.36 3.53
382 517 2.343101 CCACATGTGTTACGTGGTAGG 58.657 52.381 23.79 0.50 44.27 3.18
387 522 2.803386 TGCTTACCACATGTGTTACGTG 59.197 45.455 23.79 10.21 40.80 4.49
388 523 3.114668 TGCTTACCACATGTGTTACGT 57.885 42.857 23.79 16.29 0.00 3.57
389 524 4.678509 ATTGCTTACCACATGTGTTACG 57.321 40.909 23.79 13.21 0.00 3.18
390 525 6.007936 TGAATTGCTTACCACATGTGTTAC 57.992 37.500 23.79 9.40 0.00 2.50
391 526 6.641169 TTGAATTGCTTACCACATGTGTTA 57.359 33.333 23.79 12.19 0.00 2.41
392 527 5.528043 TTGAATTGCTTACCACATGTGTT 57.472 34.783 23.79 13.33 0.00 3.32
393 528 5.163468 TGTTTGAATTGCTTACCACATGTGT 60.163 36.000 23.79 14.29 0.00 3.72
394 529 5.288015 TGTTTGAATTGCTTACCACATGTG 58.712 37.500 19.31 19.31 0.00 3.21
395 530 5.528043 TGTTTGAATTGCTTACCACATGT 57.472 34.783 0.00 0.00 0.00 3.21
396 531 7.424227 AATTGTTTGAATTGCTTACCACATG 57.576 32.000 0.00 0.00 0.00 3.21
397 532 9.553064 TTTAATTGTTTGAATTGCTTACCACAT 57.447 25.926 0.00 0.00 0.00 3.21
398 533 8.948631 TTTAATTGTTTGAATTGCTTACCACA 57.051 26.923 0.00 0.00 0.00 4.17
425 560 3.181486 TGTGTGTGTGTGTGTGTGTTTTT 60.181 39.130 0.00 0.00 0.00 1.94
426 561 2.359214 TGTGTGTGTGTGTGTGTGTTTT 59.641 40.909 0.00 0.00 0.00 2.43
427 562 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
428 563 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
429 564 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
430 565 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
431 566 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
432 567 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
433 568 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
434 569 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
435 570 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
436 571 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
437 572 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
438 573 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
439 574 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
440 575 1.468127 ACATGTGTGTGTGTGTGTGTG 59.532 47.619 0.00 0.00 37.14 3.82
441 576 1.819928 ACATGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 37.14 3.72
451 586 4.261572 GCATAGTTTGGTTCACATGTGTGT 60.262 41.667 24.63 0.00 45.76 3.72
452 587 4.229096 GCATAGTTTGGTTCACATGTGTG 58.771 43.478 24.63 12.66 46.91 3.82
453 588 3.888323 TGCATAGTTTGGTTCACATGTGT 59.112 39.130 24.63 6.17 0.00 3.72
454 589 4.502171 TGCATAGTTTGGTTCACATGTG 57.498 40.909 20.18 20.18 0.00 3.21
455 590 5.472148 CATTGCATAGTTTGGTTCACATGT 58.528 37.500 0.00 0.00 0.00 3.21
456 591 4.327898 GCATTGCATAGTTTGGTTCACATG 59.672 41.667 3.15 0.00 0.00 3.21
457 592 4.021280 TGCATTGCATAGTTTGGTTCACAT 60.021 37.500 7.38 0.00 31.71 3.21
458 593 3.320256 TGCATTGCATAGTTTGGTTCACA 59.680 39.130 7.38 0.00 31.71 3.58
459 594 3.911868 TGCATTGCATAGTTTGGTTCAC 58.088 40.909 7.38 0.00 31.71 3.18
460 595 4.597404 TTGCATTGCATAGTTTGGTTCA 57.403 36.364 12.95 0.00 38.76 3.18
461 596 4.201744 GCATTGCATTGCATAGTTTGGTTC 60.202 41.667 24.71 0.00 42.31 3.62
462 597 3.685756 GCATTGCATTGCATAGTTTGGTT 59.314 39.130 24.71 0.00 42.31 3.67
463 598 3.264104 GCATTGCATTGCATAGTTTGGT 58.736 40.909 24.71 0.00 42.31 3.67
464 599 3.936902 GCATTGCATTGCATAGTTTGG 57.063 42.857 24.71 0.00 42.31 3.28
473 608 1.195900 CCAACTGTTGCATTGCATTGC 59.804 47.619 23.33 23.33 38.76 3.56
481 745 3.090210 TGATGGATCCAACTGTTGCAT 57.910 42.857 20.67 12.12 0.00 3.96
495 759 3.047280 GTGCACGCGGTTGATGGA 61.047 61.111 12.47 0.00 0.00 3.41
515 779 2.185310 CTGGTGACCCTTTCCTCCCG 62.185 65.000 0.00 0.00 0.00 5.14
516 780 0.840722 TCTGGTGACCCTTTCCTCCC 60.841 60.000 0.00 0.00 0.00 4.30
517 781 1.064825 TTCTGGTGACCCTTTCCTCC 58.935 55.000 0.00 0.00 0.00 4.30
518 782 2.505405 GTTTCTGGTGACCCTTTCCTC 58.495 52.381 0.00 0.00 0.00 3.71
519 783 1.202770 CGTTTCTGGTGACCCTTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
530 801 1.885850 GGCGACACACGTTTCTGGT 60.886 57.895 0.00 0.00 44.60 4.00
591 864 3.649277 GAGACACATGGAGCCGCGT 62.649 63.158 4.92 0.00 0.00 6.01
789 1073 1.218316 CGAAGAGTAGTGGGTGGGC 59.782 63.158 0.00 0.00 0.00 5.36
873 1161 1.142778 GAGAGGCTAGCAGTTTCGCG 61.143 60.000 18.24 0.00 36.85 5.87
874 1162 0.808060 GGAGAGGCTAGCAGTTTCGC 60.808 60.000 18.24 9.60 0.00 4.70
875 1163 0.526524 CGGAGAGGCTAGCAGTTTCG 60.527 60.000 18.24 10.53 0.00 3.46
916 1215 1.854126 GTACGTACACACACACACACC 59.146 52.381 20.67 0.00 0.00 4.16
950 1249 0.395036 CTCTCGGCCCTCTCTCTTGA 60.395 60.000 0.00 0.00 0.00 3.02
985 1284 3.297134 ACCCATGTCTCTCTCTCTCTC 57.703 52.381 0.00 0.00 0.00 3.20
986 1285 3.435026 GCTACCCATGTCTCTCTCTCTCT 60.435 52.174 0.00 0.00 0.00 3.10
987 1286 2.884639 GCTACCCATGTCTCTCTCTCTC 59.115 54.545 0.00 0.00 0.00 3.20
988 1287 2.513738 AGCTACCCATGTCTCTCTCTCT 59.486 50.000 0.00 0.00 0.00 3.10
989 1288 2.944129 AGCTACCCATGTCTCTCTCTC 58.056 52.381 0.00 0.00 0.00 3.20
990 1289 3.030291 CAAGCTACCCATGTCTCTCTCT 58.970 50.000 0.00 0.00 0.00 3.10
991 1290 2.102252 CCAAGCTACCCATGTCTCTCTC 59.898 54.545 0.00 0.00 0.00 3.20
992 1291 2.114616 CCAAGCTACCCATGTCTCTCT 58.885 52.381 0.00 0.00 0.00 3.10
993 1292 1.139853 CCCAAGCTACCCATGTCTCTC 59.860 57.143 0.00 0.00 0.00 3.20
994 1293 1.207791 CCCAAGCTACCCATGTCTCT 58.792 55.000 0.00 0.00 0.00 3.10
995 1294 1.204146 TCCCAAGCTACCCATGTCTC 58.796 55.000 0.00 0.00 0.00 3.36
996 1295 1.771255 GATCCCAAGCTACCCATGTCT 59.229 52.381 0.00 0.00 0.00 3.41
997 1296 1.541233 CGATCCCAAGCTACCCATGTC 60.541 57.143 0.00 0.00 0.00 3.06
998 1297 0.469917 CGATCCCAAGCTACCCATGT 59.530 55.000 0.00 0.00 0.00 3.21
1072 1371 2.031516 CCAGCCTGTTGAGCTCGTG 61.032 63.158 9.64 0.00 38.95 4.35
1179 1482 2.558313 GTTGCACTTCGAGCTGGC 59.442 61.111 0.00 0.00 0.00 4.85
1341 1650 1.073199 AGGAGGGTTTCGCCAACAG 59.927 57.895 0.00 0.00 37.84 3.16
1495 1804 1.643292 CTCACACACAACCACGCAG 59.357 57.895 0.00 0.00 0.00 5.18
1498 1807 1.577468 TTAGCTCACACACAACCACG 58.423 50.000 0.00 0.00 0.00 4.94
1554 1863 7.481642 TCTCGGATTAGATACTTGAAAGTGAC 58.518 38.462 5.95 0.59 40.07 3.67
1763 2401 4.178540 GCAGCATTGTCACAAAGCAATAT 58.821 39.130 19.34 0.00 34.01 1.28
1778 2442 7.241738 TAAAACCATTTTCAGCATGCAGCATT 61.242 34.615 21.98 0.00 38.77 3.56
1867 2608 7.306749 CCTGCTTTGCTGTTAATTTGTAAAGTG 60.307 37.037 13.03 8.91 36.35 3.16
2043 2788 7.681679 TCCTATTGTTTTGTCACACCTGTATA 58.318 34.615 0.00 0.00 0.00 1.47
2067 2812 3.764885 ACCGCAAGCATGTTAAAGATC 57.235 42.857 0.00 0.00 0.00 2.75
2070 2815 2.288152 ACCAACCGCAAGCATGTTAAAG 60.288 45.455 0.00 0.00 0.00 1.85
2072 2817 1.323412 ACCAACCGCAAGCATGTTAA 58.677 45.000 0.00 0.00 0.00 2.01
2187 2934 3.587061 ACTGGGTTGAATATCTGGTGACA 59.413 43.478 0.00 0.00 39.59 3.58
2204 2951 1.961277 GTCGGCACAAGTGACTGGG 60.961 63.158 4.04 0.00 36.16 4.45
2274 3022 8.115490 AGAAAAGCAACAAGATTACTTAGCAT 57.885 30.769 0.00 0.00 34.70 3.79
2463 3211 8.190784 AGTACTATTTATTGCAAGTTTGGCATC 58.809 33.333 4.94 0.00 41.58 3.91
2695 3445 6.785466 AGTATTTTGGTGGAAAACATTAGGGT 59.215 34.615 0.00 0.00 36.35 4.34
2767 3517 2.036556 AAAAACGAAGTGCAGCATCG 57.963 45.000 15.38 15.38 45.00 3.84
2786 3536 5.136828 TCTGCAGGAAATGACCAAAGTTTA 58.863 37.500 15.13 0.00 0.00 2.01
2971 3721 6.220930 TCCAGTTAGCAGTGTACAAAGTTAG 58.779 40.000 0.00 0.00 0.00 2.34
2976 3739 3.751175 GCATCCAGTTAGCAGTGTACAAA 59.249 43.478 0.00 0.00 0.00 2.83
3012 3775 1.128692 GCATGCAGACGTCAGGTAAAC 59.871 52.381 19.50 2.25 0.00 2.01
3066 3829 0.179051 CTTCTCCAGGATGCTCAGCC 60.179 60.000 0.00 0.00 37.08 4.85
3111 3874 4.770795 TCAAATGAGCTAGGGAAGTAAGC 58.229 43.478 0.00 0.00 36.48 3.09
3119 4045 5.591472 TGATGTCAAATCAAATGAGCTAGGG 59.409 40.000 0.00 0.00 0.00 3.53
3157 4083 6.771573 TGTAACCGGAAAAGGAAGAAGAATA 58.228 36.000 9.46 0.00 34.73 1.75
3196 4122 8.504815 CACATCCAGATTCTGTCATATCAAATC 58.495 37.037 12.54 0.00 0.00 2.17
3229 4155 1.971481 TCCTTGCGCTCATTGCATAT 58.029 45.000 9.73 0.00 42.84 1.78
3303 4229 1.074084 ACCACTTCCTCGTCTCTCTGA 59.926 52.381 0.00 0.00 0.00 3.27
3395 4321 2.723124 AATGGTGCCGAATTGAACAC 57.277 45.000 0.00 0.00 0.00 3.32
3455 4381 1.303643 AAGCAGCCACAGGTAAGCC 60.304 57.895 0.00 0.00 0.00 4.35
3473 4399 3.243035 CGCAATCTGACAAGAACCAAACA 60.243 43.478 0.00 0.00 35.59 2.83
3612 4538 5.063944 CAGTTCAATATTCTGGTTCTGGACG 59.936 44.000 0.00 0.00 0.00 4.79
3633 4559 6.127196 GGTAGATCTCCATCTGTTTCTTCAGT 60.127 42.308 0.00 0.00 39.90 3.41
3918 4844 6.893958 ACATCGATCTCACTTACATTCAAC 57.106 37.500 0.00 0.00 0.00 3.18
3981 4907 9.239002 CTCCTACAAGTTAAAGATCGTTATGAG 57.761 37.037 1.81 0.00 0.00 2.90
4032 4958 2.159421 CGTAGACTTTAGCTCGAGCCAA 60.159 50.000 32.94 24.02 43.38 4.52
4339 5265 5.171339 AGGTAAGAATTGAGTGCTCATGT 57.829 39.130 2.47 0.00 39.64 3.21
4466 5392 2.025887 CCTTTCCTATTGGCCTCACTGT 60.026 50.000 3.32 0.00 0.00 3.55
4635 5561 3.540211 AGGCTCGGTGTCTGAATTG 57.460 52.632 0.00 0.00 0.00 2.32
4740 5666 1.045407 TACTTCTTGTCGCCCACAGT 58.955 50.000 0.00 0.00 35.97 3.55
4868 5794 4.813161 AGTCTCCATTCGCATCAAATACTG 59.187 41.667 0.00 0.00 0.00 2.74
5228 6218 2.983192 TCAGGTGTGATTTTGGGTCCTA 59.017 45.455 0.00 0.00 0.00 2.94
5241 6231 4.841422 AGATCCAAAGAATCTCAGGTGTG 58.159 43.478 0.00 0.00 0.00 3.82
5287 6277 2.401583 TTACCATGCTGCACCTGTAG 57.598 50.000 3.57 0.00 0.00 2.74
5629 6619 4.649674 GTCATAAGGGACAGTGATGGACTA 59.350 45.833 0.00 0.00 37.73 2.59
5765 6759 6.652900 CCTTTGGTGGAACAAAAAGAAAGAAA 59.347 34.615 0.00 0.00 39.72 2.52
5781 6775 3.243068 CGAAGTTTTCACTCCTTTGGTGG 60.243 47.826 0.00 0.00 35.61 4.61
5791 6785 7.812669 ACTTTTCATTTTCACGAAGTTTTCACT 59.187 29.630 0.00 0.00 41.61 3.41


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

AutoCloner maintained by Alex Coulton.