Multiple sequence alignment - TraesCS5A01G179800

Loading Multiple Alignment...

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 TraesCS5A01G179800 chr5A 100.000 3187 0 0 1 3187 378273863 378270677 0.000000e+00 5886.0
1 TraesCS5A01G179800 chr5D 92.427 2641 105 33 604 3187 285840977 285838375 0.000000e+00 3681.0
2 TraesCS5A01G179800 chr5B 90.959 2168 103 36 1082 3187 324249405 324247269 0.000000e+00 2832.0
3 TraesCS5A01G179800 chr5B 97.133 279 4 1 693 971 324249911 324249637 4.810000e-128 468.0
4 TraesCS5A01G179800 chr5B 90.370 270 18 4 1 262 324251607 324251338 6.540000e-92 348.0
5 TraesCS5A01G179800 chr5B 90.000 250 24 1 258 506 348868792 348869041 3.970000e-84 322.0
6 TraesCS5A01G179800 chr1D 85.934 391 48 7 1673 2060 372360599 372360985 8.230000e-111 411.0
7 TraesCS5A01G179800 chr1B 85.751 386 49 6 1673 2055 497274562 497274944 1.380000e-108 403.0
8 TraesCS5A01G179800 chr1B 89.683 252 23 2 258 506 534113557 534113808 5.130000e-83 318.0
9 TraesCS5A01G179800 chr1A 85.864 382 48 6 1673 2051 471730050 471730428 4.950000e-108 401.0
10 TraesCS5A01G179800 chr7B 83.805 389 40 10 1673 2060 544481052 544480686 6.540000e-92 348.0
11 TraesCS5A01G179800 chr7B 86.513 304 38 3 1758 2059 193310900 193311202 6.590000e-87 331.0
12 TraesCS5A01G179800 chr7D 83.290 389 42 10 1673 2060 512747071 512746705 1.420000e-88 337.0
13 TraesCS5A01G179800 chr7D 90.244 41 3 1 599 638 58767938 58767978 6.000000e-03 52.8
14 TraesCS5A01G179800 chr3B 87.500 288 34 2 1769 2055 638357176 638356890 6.590000e-87 331.0
15 TraesCS5A01G179800 chr7A 90.400 250 23 1 258 506 423098118 423097869 8.520000e-86 327.0
16 TraesCS5A01G179800 chr4B 90.361 249 23 1 258 505 196378879 196379127 3.070000e-85 326.0
17 TraesCS5A01G179800 chr4B 90.040 251 24 1 258 507 628956798 628957048 1.100000e-84 324.0
18 TraesCS5A01G179800 chr4B 89.960 249 24 1 258 505 225134350 225134102 1.430000e-83 320.0
19 TraesCS5A01G179800 chr3A 89.960 249 24 1 258 505 717202544 717202296 1.430000e-83 320.0
20 TraesCS5A01G179800 chr6A 89.641 251 24 2 258 506 504320622 504320372 5.130000e-83 318.0
21 TraesCS5A01G179800 chr2B 88.846 260 27 2 258 515 590440483 590440742 5.130000e-83 318.0


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 TraesCS5A01G179800 chr5A 378270677 378273863 3186 True 5886 5886 100.000000 1 3187 1 chr5A.!!$R1 3186
1 TraesCS5A01G179800 chr5D 285838375 285840977 2602 True 3681 3681 92.427000 604 3187 1 chr5D.!!$R1 2583
2 TraesCS5A01G179800 chr5B 324247269 324251607 4338 True 1216 2832 92.820667 1 3187 3 chr5B.!!$R1 3186

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
587 640 0.093026 GTGAGCACGCGATGTTACAC 59.907 55.0 15.93 11.29 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 3597 1.066908 GTGCAGGCAACAAAGCTAACA 59.933 47.619 0.0 0.0 41.41 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.816640 TCATAGGCAAGTTAACAAGTCAAATC 58.183 34.615 8.61 0.00 0.00 2.17
44 45 9.014297 CAAGTTAACAAGTCAAATCCTAATCCT 57.986 33.333 8.61 0.00 0.00 3.24
47 48 8.601476 GTTAACAAGTCAAATCCTAATCCTACG 58.399 37.037 0.00 0.00 0.00 3.51
50 51 7.210873 ACAAGTCAAATCCTAATCCTACGATC 58.789 38.462 0.00 0.00 0.00 3.69
84 85 6.713762 TTATAGGGAATTTTGATGCCACTG 57.286 37.500 0.00 0.00 0.00 3.66
159 165 9.901172 AACTAACTATTCCCTTCGATACAATTT 57.099 29.630 0.00 0.00 0.00 1.82
164 170 9.765795 ACTATTCCCTTCGATACAATTTTAGAG 57.234 33.333 0.00 0.00 0.00 2.43
220 229 3.192422 CGGATGGAGTATTTGTTTTGGCA 59.808 43.478 0.00 0.00 0.00 4.92
223 232 2.896685 TGGAGTATTTGTTTTGGCAGGG 59.103 45.455 0.00 0.00 0.00 4.45
247 256 9.682465 GGGAAGAAAAATACACTAACTAGGAAT 57.318 33.333 0.00 0.00 0.00 3.01
268 277 9.377238 AGGAATACTCGGATACTTAATTAAGGT 57.623 33.333 25.25 15.35 37.62 3.50
270 279 9.978044 GAATACTCGGATACTTAATTAAGGTGT 57.022 33.333 25.25 16.37 37.62 4.16
324 333 4.258935 GTGTATTACATTGCACCACTCG 57.741 45.455 0.00 0.00 0.00 4.18
325 334 3.682858 GTGTATTACATTGCACCACTCGT 59.317 43.478 0.00 0.00 0.00 4.18
326 335 3.930229 TGTATTACATTGCACCACTCGTC 59.070 43.478 0.00 0.00 0.00 4.20
327 336 2.831685 TTACATTGCACCACTCGTCT 57.168 45.000 0.00 0.00 0.00 4.18
328 337 2.078849 TACATTGCACCACTCGTCTG 57.921 50.000 0.00 0.00 0.00 3.51
329 338 0.603707 ACATTGCACCACTCGTCTGG 60.604 55.000 0.00 0.22 37.33 3.86
330 339 0.320683 CATTGCACCACTCGTCTGGA 60.321 55.000 7.95 0.00 35.04 3.86
331 340 0.615331 ATTGCACCACTCGTCTGGAT 59.385 50.000 7.95 0.00 35.04 3.41
332 341 1.262417 TTGCACCACTCGTCTGGATA 58.738 50.000 7.95 0.00 35.04 2.59
333 342 1.262417 TGCACCACTCGTCTGGATAA 58.738 50.000 7.95 0.00 35.04 1.75
334 343 1.831106 TGCACCACTCGTCTGGATAAT 59.169 47.619 7.95 0.00 35.04 1.28
335 344 2.205074 GCACCACTCGTCTGGATAATG 58.795 52.381 7.95 0.00 35.04 1.90
336 345 2.418746 GCACCACTCGTCTGGATAATGT 60.419 50.000 7.95 0.00 35.04 2.71
337 346 3.861840 CACCACTCGTCTGGATAATGTT 58.138 45.455 7.95 0.00 35.04 2.71
338 347 4.253685 CACCACTCGTCTGGATAATGTTT 58.746 43.478 7.95 0.00 35.04 2.83
339 348 4.695455 CACCACTCGTCTGGATAATGTTTT 59.305 41.667 7.95 0.00 35.04 2.43
340 349 5.181245 CACCACTCGTCTGGATAATGTTTTT 59.819 40.000 7.95 0.00 35.04 1.94
341 350 6.370442 CACCACTCGTCTGGATAATGTTTTTA 59.630 38.462 7.95 0.00 35.04 1.52
342 351 6.594159 ACCACTCGTCTGGATAATGTTTTTAG 59.406 38.462 7.95 0.00 35.04 1.85
343 352 6.037172 CCACTCGTCTGGATAATGTTTTTAGG 59.963 42.308 0.00 0.00 32.30 2.69
344 353 6.037172 CACTCGTCTGGATAATGTTTTTAGGG 59.963 42.308 0.00 0.00 0.00 3.53
345 354 6.070424 ACTCGTCTGGATAATGTTTTTAGGGA 60.070 38.462 0.00 0.00 0.00 4.20
346 355 6.895782 TCGTCTGGATAATGTTTTTAGGGAT 58.104 36.000 0.00 0.00 0.00 3.85
347 356 7.343357 TCGTCTGGATAATGTTTTTAGGGATT 58.657 34.615 0.00 0.00 0.00 3.01
348 357 7.832187 TCGTCTGGATAATGTTTTTAGGGATTT 59.168 33.333 0.00 0.00 0.00 2.17
349 358 7.915397 CGTCTGGATAATGTTTTTAGGGATTTG 59.085 37.037 0.00 0.00 0.00 2.32
350 359 8.966868 GTCTGGATAATGTTTTTAGGGATTTGA 58.033 33.333 0.00 0.00 0.00 2.69
351 360 9.713684 TCTGGATAATGTTTTTAGGGATTTGAT 57.286 29.630 0.00 0.00 0.00 2.57
393 402 7.318893 AGGAAAGCTTCTTTATTTTCTCATGC 58.681 34.615 0.00 0.00 31.83 4.06
394 403 6.533012 GGAAAGCTTCTTTATTTTCTCATGCC 59.467 38.462 0.00 0.00 31.83 4.40
395 404 6.594788 AAGCTTCTTTATTTTCTCATGCCA 57.405 33.333 0.00 0.00 0.00 4.92
396 405 6.594788 AGCTTCTTTATTTTCTCATGCCAA 57.405 33.333 0.00 0.00 0.00 4.52
397 406 7.179076 AGCTTCTTTATTTTCTCATGCCAAT 57.821 32.000 0.00 0.00 0.00 3.16
398 407 7.618137 AGCTTCTTTATTTTCTCATGCCAATT 58.382 30.769 0.00 0.00 0.00 2.32
399 408 8.752187 AGCTTCTTTATTTTCTCATGCCAATTA 58.248 29.630 0.00 0.00 0.00 1.40
400 409 9.028185 GCTTCTTTATTTTCTCATGCCAATTAG 57.972 33.333 0.00 0.00 0.00 1.73
403 412 9.241919 TCTTTATTTTCTCATGCCAATTAGTCA 57.758 29.630 0.00 0.00 0.00 3.41
404 413 9.512435 CTTTATTTTCTCATGCCAATTAGTCAG 57.488 33.333 0.00 0.00 0.00 3.51
405 414 5.902613 TTTTCTCATGCCAATTAGTCAGG 57.097 39.130 0.00 0.00 0.00 3.86
406 415 4.842531 TTCTCATGCCAATTAGTCAGGA 57.157 40.909 0.00 0.00 0.00 3.86
407 416 4.842531 TCTCATGCCAATTAGTCAGGAA 57.157 40.909 0.00 0.00 0.00 3.36
408 417 5.378230 TCTCATGCCAATTAGTCAGGAAT 57.622 39.130 0.00 0.00 0.00 3.01
409 418 6.499106 TCTCATGCCAATTAGTCAGGAATA 57.501 37.500 0.00 0.00 0.00 1.75
410 419 6.899089 TCTCATGCCAATTAGTCAGGAATAA 58.101 36.000 0.00 0.00 0.00 1.40
411 420 7.520798 TCTCATGCCAATTAGTCAGGAATAAT 58.479 34.615 0.00 0.00 33.58 1.28
412 421 7.663081 TCTCATGCCAATTAGTCAGGAATAATC 59.337 37.037 2.86 0.00 31.30 1.75
413 422 7.520798 TCATGCCAATTAGTCAGGAATAATCT 58.479 34.615 2.86 0.00 31.30 2.40
414 423 7.663081 TCATGCCAATTAGTCAGGAATAATCTC 59.337 37.037 2.86 0.00 31.30 2.75
415 424 5.991606 TGCCAATTAGTCAGGAATAATCTCG 59.008 40.000 2.86 0.00 31.30 4.04
416 425 5.106908 GCCAATTAGTCAGGAATAATCTCGC 60.107 44.000 2.86 2.42 31.30 5.03
417 426 5.409826 CCAATTAGTCAGGAATAATCTCGCC 59.590 44.000 2.86 0.00 31.30 5.54
418 427 6.226787 CAATTAGTCAGGAATAATCTCGCCT 58.773 40.000 2.86 0.00 31.30 5.52
419 428 7.378966 CAATTAGTCAGGAATAATCTCGCCTA 58.621 38.462 2.86 0.00 31.30 3.93
420 429 6.971726 TTAGTCAGGAATAATCTCGCCTAA 57.028 37.500 0.00 0.00 0.00 2.69
421 430 5.871396 AGTCAGGAATAATCTCGCCTAAA 57.129 39.130 0.00 0.00 0.00 1.85
422 431 6.235231 AGTCAGGAATAATCTCGCCTAAAA 57.765 37.500 0.00 0.00 0.00 1.52
423 432 6.049790 AGTCAGGAATAATCTCGCCTAAAAC 58.950 40.000 0.00 0.00 0.00 2.43
424 433 6.049790 GTCAGGAATAATCTCGCCTAAAACT 58.950 40.000 0.00 0.00 0.00 2.66
425 434 6.539103 GTCAGGAATAATCTCGCCTAAAACTT 59.461 38.462 0.00 0.00 0.00 2.66
426 435 7.709613 GTCAGGAATAATCTCGCCTAAAACTTA 59.290 37.037 0.00 0.00 0.00 2.24
427 436 8.429641 TCAGGAATAATCTCGCCTAAAACTTAT 58.570 33.333 0.00 0.00 0.00 1.73
428 437 8.499162 CAGGAATAATCTCGCCTAAAACTTATG 58.501 37.037 0.00 0.00 0.00 1.90
429 438 8.211629 AGGAATAATCTCGCCTAAAACTTATGT 58.788 33.333 0.00 0.00 0.00 2.29
430 439 9.485206 GGAATAATCTCGCCTAAAACTTATGTA 57.515 33.333 0.00 0.00 0.00 2.29
437 446 8.671028 TCTCGCCTAAAACTTATGTAATTTTCC 58.329 33.333 0.00 0.00 0.00 3.13
438 447 7.764331 TCGCCTAAAACTTATGTAATTTTCCC 58.236 34.615 0.00 0.00 0.00 3.97
439 448 7.612633 TCGCCTAAAACTTATGTAATTTTCCCT 59.387 33.333 0.00 0.00 0.00 4.20
440 449 7.913821 CGCCTAAAACTTATGTAATTTTCCCTC 59.086 37.037 0.00 0.00 0.00 4.30
441 450 8.195436 GCCTAAAACTTATGTAATTTTCCCTCC 58.805 37.037 0.00 0.00 0.00 4.30
442 451 9.250246 CCTAAAACTTATGTAATTTTCCCTCCA 57.750 33.333 0.00 0.00 0.00 3.86
444 453 6.753107 AACTTATGTAATTTTCCCTCCACG 57.247 37.500 0.00 0.00 0.00 4.94
445 454 5.812286 ACTTATGTAATTTTCCCTCCACGT 58.188 37.500 0.00 0.00 0.00 4.49
446 455 5.646360 ACTTATGTAATTTTCCCTCCACGTG 59.354 40.000 9.08 9.08 0.00 4.49
447 456 3.495434 TGTAATTTTCCCTCCACGTGT 57.505 42.857 15.65 0.00 0.00 4.49
448 457 3.142951 TGTAATTTTCCCTCCACGTGTG 58.857 45.455 15.65 6.24 0.00 3.82
449 458 2.358322 AATTTTCCCTCCACGTGTGT 57.642 45.000 15.65 0.00 0.00 3.72
450 459 2.358322 ATTTTCCCTCCACGTGTGTT 57.642 45.000 15.65 0.00 0.00 3.32
451 460 1.670791 TTTTCCCTCCACGTGTGTTC 58.329 50.000 15.65 0.00 0.00 3.18
452 461 0.834612 TTTCCCTCCACGTGTGTTCT 59.165 50.000 15.65 0.00 0.00 3.01
453 462 0.834612 TTCCCTCCACGTGTGTTCTT 59.165 50.000 15.65 0.00 0.00 2.52
454 463 0.834612 TCCCTCCACGTGTGTTCTTT 59.165 50.000 15.65 0.00 0.00 2.52
455 464 2.040939 TCCCTCCACGTGTGTTCTTTA 58.959 47.619 15.65 0.00 0.00 1.85
456 465 2.435069 TCCCTCCACGTGTGTTCTTTAA 59.565 45.455 15.65 0.00 0.00 1.52
457 466 3.071892 TCCCTCCACGTGTGTTCTTTAAT 59.928 43.478 15.65 0.00 0.00 1.40
458 467 3.818773 CCCTCCACGTGTGTTCTTTAATT 59.181 43.478 15.65 0.00 0.00 1.40
459 468 4.277423 CCCTCCACGTGTGTTCTTTAATTT 59.723 41.667 15.65 0.00 0.00 1.82
460 469 5.221165 CCCTCCACGTGTGTTCTTTAATTTT 60.221 40.000 15.65 0.00 0.00 1.82
461 470 5.912955 CCTCCACGTGTGTTCTTTAATTTTC 59.087 40.000 15.65 0.00 0.00 2.29
462 471 5.503498 TCCACGTGTGTTCTTTAATTTTCG 58.497 37.500 15.65 0.00 0.00 3.46
463 472 5.064962 TCCACGTGTGTTCTTTAATTTTCGT 59.935 36.000 15.65 0.00 0.00 3.85
464 473 5.170625 CCACGTGTGTTCTTTAATTTTCGTG 59.829 40.000 15.65 0.00 42.48 4.35
465 474 4.731480 ACGTGTGTTCTTTAATTTTCGTGC 59.269 37.500 0.00 0.00 0.00 5.34
466 475 4.145756 CGTGTGTTCTTTAATTTTCGTGCC 59.854 41.667 0.00 0.00 0.00 5.01
467 476 5.038033 GTGTGTTCTTTAATTTTCGTGCCA 58.962 37.500 0.00 0.00 0.00 4.92
468 477 5.517054 GTGTGTTCTTTAATTTTCGTGCCAA 59.483 36.000 0.00 0.00 0.00 4.52
469 478 6.035112 GTGTGTTCTTTAATTTTCGTGCCAAA 59.965 34.615 0.00 0.00 0.00 3.28
470 479 6.590292 TGTGTTCTTTAATTTTCGTGCCAAAA 59.410 30.769 0.00 0.00 0.00 2.44
471 480 7.117812 TGTGTTCTTTAATTTTCGTGCCAAAAA 59.882 29.630 0.00 0.00 0.00 1.94
472 481 7.424167 GTGTTCTTTAATTTTCGTGCCAAAAAC 59.576 33.333 0.00 0.00 0.00 2.43
473 482 7.332182 TGTTCTTTAATTTTCGTGCCAAAAACT 59.668 29.630 0.00 0.00 0.00 2.66
474 483 8.809478 GTTCTTTAATTTTCGTGCCAAAAACTA 58.191 29.630 0.00 0.00 0.00 2.24
475 484 9.535878 TTCTTTAATTTTCGTGCCAAAAACTAT 57.464 25.926 0.00 0.00 0.00 2.12
478 487 9.745880 TTTAATTTTCGTGCCAAAAACTATACA 57.254 25.926 0.00 0.00 0.00 2.29
479 488 7.631915 AATTTTCGTGCCAAAAACTATACAC 57.368 32.000 0.00 0.00 0.00 2.90
480 489 4.752661 TTCGTGCCAAAAACTATACACC 57.247 40.909 0.00 0.00 0.00 4.16
481 490 4.010667 TCGTGCCAAAAACTATACACCT 57.989 40.909 0.00 0.00 0.00 4.00
482 491 4.391155 TCGTGCCAAAAACTATACACCTT 58.609 39.130 0.00 0.00 0.00 3.50
483 492 5.549347 TCGTGCCAAAAACTATACACCTTA 58.451 37.500 0.00 0.00 0.00 2.69
484 493 6.174760 TCGTGCCAAAAACTATACACCTTAT 58.825 36.000 0.00 0.00 0.00 1.73
485 494 7.329499 TCGTGCCAAAAACTATACACCTTATA 58.671 34.615 0.00 0.00 0.00 0.98
486 495 7.988599 TCGTGCCAAAAACTATACACCTTATAT 59.011 33.333 0.00 0.00 0.00 0.86
487 496 8.617809 CGTGCCAAAAACTATACACCTTATATT 58.382 33.333 0.00 0.00 0.00 1.28
497 506 9.592196 ACTATACACCTTATATTAAGGAACGGA 57.408 33.333 17.93 5.30 39.81 4.69
499 508 6.170846 ACACCTTATATTAAGGAACGGAGG 57.829 41.667 17.93 0.00 39.81 4.30
500 509 5.071384 ACACCTTATATTAAGGAACGGAGGG 59.929 44.000 17.93 0.00 39.81 4.30
501 510 5.306160 CACCTTATATTAAGGAACGGAGGGA 59.694 44.000 17.93 0.00 39.81 4.20
502 511 5.543020 ACCTTATATTAAGGAACGGAGGGAG 59.457 44.000 17.93 0.00 39.81 4.30
503 512 5.543020 CCTTATATTAAGGAACGGAGGGAGT 59.457 44.000 7.42 0.00 39.81 3.85
504 513 6.723052 CCTTATATTAAGGAACGGAGGGAGTA 59.277 42.308 7.42 0.00 39.81 2.59
505 514 7.399478 CCTTATATTAAGGAACGGAGGGAGTAT 59.601 40.741 7.42 0.00 39.81 2.12
506 515 4.957684 ATTAAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
507 516 2.249309 AAGGAACGGAGGGAGTATGT 57.751 50.000 0.00 0.00 0.00 2.29
508 517 2.249309 AGGAACGGAGGGAGTATGTT 57.751 50.000 0.00 0.00 0.00 2.71
509 518 3.393426 AGGAACGGAGGGAGTATGTTA 57.607 47.619 0.00 0.00 0.00 2.41
534 543 1.557832 GGTAGTGGGTCAGTGGCATAA 59.442 52.381 0.00 0.00 0.00 1.90
538 547 2.843730 AGTGGGTCAGTGGCATAACATA 59.156 45.455 0.00 0.00 0.00 2.29
580 633 1.396996 GGTATTTTGTGAGCACGCGAT 59.603 47.619 15.93 0.00 0.00 4.58
586 639 0.319125 TGTGAGCACGCGATGTTACA 60.319 50.000 15.93 9.68 0.00 2.41
587 640 0.093026 GTGAGCACGCGATGTTACAC 59.907 55.000 15.93 11.29 0.00 2.90
588 641 1.011968 TGAGCACGCGATGTTACACC 61.012 55.000 15.93 0.00 0.00 4.16
589 642 2.009625 GAGCACGCGATGTTACACCG 62.010 60.000 15.93 0.00 0.00 4.94
590 643 2.377310 GCACGCGATGTTACACCGT 61.377 57.895 15.93 1.39 0.00 4.83
591 644 1.700029 CACGCGATGTTACACCGTC 59.300 57.895 15.93 0.00 0.00 4.79
592 645 1.798725 ACGCGATGTTACACCGTCG 60.799 57.895 15.93 12.66 44.62 5.12
593 646 1.512522 CGCGATGTTACACCGTCGA 60.513 57.895 0.00 0.00 44.60 4.20
595 648 1.274596 GCGATGTTACACCGTCGATT 58.725 50.000 10.48 0.00 44.60 3.34
596 649 2.453080 GCGATGTTACACCGTCGATTA 58.547 47.619 10.48 0.00 44.60 1.75
597 650 2.214914 GCGATGTTACACCGTCGATTAC 59.785 50.000 10.48 0.00 44.60 1.89
598 651 2.785477 CGATGTTACACCGTCGATTACC 59.215 50.000 1.12 0.00 44.60 2.85
599 652 2.652941 TGTTACACCGTCGATTACCC 57.347 50.000 0.00 0.00 0.00 3.69
600 653 2.170166 TGTTACACCGTCGATTACCCT 58.830 47.619 0.00 0.00 0.00 4.34
601 654 3.351740 TGTTACACCGTCGATTACCCTA 58.648 45.455 0.00 0.00 0.00 3.53
602 655 3.761218 TGTTACACCGTCGATTACCCTAA 59.239 43.478 0.00 0.00 0.00 2.69
651 1639 8.673711 TCCAAAATTCATAAGTTCCTACATTCG 58.326 33.333 0.00 0.00 0.00 3.34
664 1652 5.205821 TCCTACATTCGAGTCCCTTAATCA 58.794 41.667 0.00 0.00 0.00 2.57
665 1653 5.659525 TCCTACATTCGAGTCCCTTAATCAA 59.340 40.000 0.00 0.00 0.00 2.57
815 2067 1.457823 TATATATAGCGCCCGGCCGG 61.458 60.000 37.99 37.99 45.17 6.13
858 2110 1.135915 ACCAGCAATCAGACGAGCTAG 59.864 52.381 0.00 0.00 35.19 3.42
1532 2917 1.206072 GCGCAGTCTGCAACAAGAG 59.794 57.895 24.13 7.39 45.36 2.85
1587 2972 4.789629 CGATGATCTTTGTCGTACGTACAA 59.210 41.667 24.50 21.33 35.12 2.41
1601 2986 5.949787 CGTACGTACAACATTTAATGCACTC 59.050 40.000 24.50 0.00 0.00 3.51
1602 2987 5.291293 ACGTACAACATTTAATGCACTCC 57.709 39.130 4.68 0.00 0.00 3.85
1622 3011 2.677003 GGTGCGGATCAACGTGTGG 61.677 63.158 0.00 0.00 35.98 4.17
1623 3012 1.666553 GTGCGGATCAACGTGTGGA 60.667 57.895 0.00 0.00 35.98 4.02
1624 3013 1.374125 TGCGGATCAACGTGTGGAG 60.374 57.895 0.00 0.00 35.98 3.86
1625 3014 1.374252 GCGGATCAACGTGTGGAGT 60.374 57.895 0.00 0.00 35.98 3.85
1626 3015 0.108992 GCGGATCAACGTGTGGAGTA 60.109 55.000 0.00 0.00 35.98 2.59
1820 3211 1.906333 GGGGTGCCGGAACAACATT 60.906 57.895 16.38 0.00 0.00 2.71
2069 3460 4.164664 CACGCGCCGCACATCATT 62.165 61.111 10.75 0.00 0.00 2.57
2079 3470 1.725641 GCACATCATTGAGTCCGTGA 58.274 50.000 10.67 0.00 0.00 4.35
2093 3484 2.747822 CGTGACCGTCGACGAGGAT 61.748 63.158 37.65 20.09 43.02 3.24
2114 3505 2.202324 GACGAGGACGACGAGCAC 60.202 66.667 0.00 0.00 42.66 4.40
2141 3532 0.249073 GCGACCTGCATCTGTACGAT 60.249 55.000 0.00 0.00 45.45 3.73
2193 3584 3.944055 TGGTCTTGCTCTAGACAACTC 57.056 47.619 12.14 0.00 45.07 3.01
2199 3590 3.176924 TGCTCTAGACAACTCCTCCTT 57.823 47.619 0.00 0.00 0.00 3.36
2201 3592 3.245443 TGCTCTAGACAACTCCTCCTTCT 60.245 47.826 0.00 0.00 0.00 2.85
2202 3593 3.767131 GCTCTAGACAACTCCTCCTTCTT 59.233 47.826 0.00 0.00 0.00 2.52
2203 3594 4.142249 GCTCTAGACAACTCCTCCTTCTTC 60.142 50.000 0.00 0.00 0.00 2.87
2204 3595 4.011023 TCTAGACAACTCCTCCTTCTTCG 58.989 47.826 0.00 0.00 0.00 3.79
2205 3596 2.599677 AGACAACTCCTCCTTCTTCGT 58.400 47.619 0.00 0.00 0.00 3.85
2206 3597 2.966516 AGACAACTCCTCCTTCTTCGTT 59.033 45.455 0.00 0.00 0.00 3.85
2207 3598 3.060602 GACAACTCCTCCTTCTTCGTTG 58.939 50.000 0.00 0.00 38.10 4.10
2224 3615 2.127251 GTTGTTAGCTTTGTTGCCTGC 58.873 47.619 0.00 0.00 0.00 4.85
2281 3678 6.749578 GGTACGTAGCTTCTAGGTTTAGTTTC 59.250 42.308 17.27 0.00 0.00 2.78
2373 3775 8.175716 CCTAGTGCAAGCTTAATTAACTACAAC 58.824 37.037 0.00 0.00 0.00 3.32
2394 3796 3.891977 ACTGTATGTCTGTGTGTCTGTCT 59.108 43.478 0.00 0.00 0.00 3.41
2515 3917 3.556365 GGTCTTTATCTGCGTCTAAAGCC 59.444 47.826 6.78 7.56 35.74 4.35
2624 4030 1.333177 ACTGGGTTTATTTTGGCGCA 58.667 45.000 10.83 0.00 0.00 6.09
2633 4039 4.846779 TTATTTTGGCGCAGAAAAGAGT 57.153 36.364 10.83 1.99 0.00 3.24
2851 4258 7.331934 GCAAACTCAACTACTCATCATCAACTA 59.668 37.037 0.00 0.00 0.00 2.24
2861 4268 6.644347 ACTCATCATCAACTAGGGTAACAAG 58.356 40.000 0.00 0.00 39.74 3.16
2895 4302 2.964209 TCCGCCTCTCCAGATAGAAAT 58.036 47.619 0.00 0.00 0.00 2.17
2896 4303 2.894126 TCCGCCTCTCCAGATAGAAATC 59.106 50.000 0.00 0.00 0.00 2.17
2897 4304 2.896685 CCGCCTCTCCAGATAGAAATCT 59.103 50.000 0.00 0.00 43.54 2.40
2938 4363 6.483385 CAGCATGTGATCCATCTATTTCTC 57.517 41.667 0.00 0.00 0.00 2.87
2940 4365 6.369340 CAGCATGTGATCCATCTATTTCTCTC 59.631 42.308 0.00 0.00 0.00 3.20
3002 4430 0.107410 ACTGAACCGACACTTTGGCA 60.107 50.000 0.00 0.00 0.00 4.92
3007 4437 3.726517 CGACACTTTGGCAGGGCG 61.727 66.667 0.00 0.00 0.00 6.13
3016 4446 0.467844 TTGGCAGGGCGCATTATGAT 60.468 50.000 10.83 0.00 45.17 2.45
3129 4565 8.691661 AAATAGGTATGTTGGAATATGACACC 57.308 34.615 0.00 0.00 0.00 4.16
3140 4576 7.624360 TGGAATATGACACCAACTTTATGTC 57.376 36.000 0.00 0.00 42.54 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.714810 TGACTTGTTAACTTGCCTATGAATGT 59.285 34.615 7.22 0.00 0.00 2.71
36 37 7.989416 AGTCTCTTTAGATCGTAGGATTAGG 57.011 40.000 0.00 0.00 33.30 2.69
44 45 9.857656 TTCCCTATAAAGTCTCTTTAGATCGTA 57.142 33.333 7.76 0.00 33.30 3.43
45 46 8.763984 TTCCCTATAAAGTCTCTTTAGATCGT 57.236 34.615 7.76 0.00 33.30 3.73
66 67 2.562298 TGACAGTGGCATCAAAATTCCC 59.438 45.455 0.00 0.00 0.00 3.97
131 137 9.901172 ATTGTATCGAAGGGAATAGTTAGTTTT 57.099 29.630 0.00 0.00 0.00 2.43
142 148 7.848128 ACTCTCTAAAATTGTATCGAAGGGAA 58.152 34.615 0.00 0.00 0.00 3.97
159 165 8.733458 TGACGCTACTTTAATACAACTCTCTAA 58.267 33.333 0.00 0.00 0.00 2.10
163 169 8.773404 AATTGACGCTACTTTAATACAACTCT 57.227 30.769 0.00 0.00 0.00 3.24
193 202 6.765989 CCAAAACAAATACTCCATCCGATCTA 59.234 38.462 0.00 0.00 0.00 1.98
199 208 4.381932 CCTGCCAAAACAAATACTCCATCC 60.382 45.833 0.00 0.00 0.00 3.51
220 229 8.445361 TCCTAGTTAGTGTATTTTTCTTCCCT 57.555 34.615 0.00 0.00 0.00 4.20
303 312 3.682858 ACGAGTGGTGCAATGTAATACAC 59.317 43.478 0.00 0.00 33.96 2.90
304 313 3.930229 GACGAGTGGTGCAATGTAATACA 59.070 43.478 0.00 0.00 0.00 2.29
305 314 4.032900 CAGACGAGTGGTGCAATGTAATAC 59.967 45.833 0.00 0.00 0.00 1.89
306 315 4.180817 CAGACGAGTGGTGCAATGTAATA 58.819 43.478 0.00 0.00 0.00 0.98
307 316 3.002791 CAGACGAGTGGTGCAATGTAAT 58.997 45.455 0.00 0.00 0.00 1.89
308 317 2.412870 CAGACGAGTGGTGCAATGTAA 58.587 47.619 0.00 0.00 0.00 2.41
309 318 1.337728 CCAGACGAGTGGTGCAATGTA 60.338 52.381 0.00 0.00 32.32 2.29
310 319 0.603707 CCAGACGAGTGGTGCAATGT 60.604 55.000 0.00 0.00 32.32 2.71
311 320 0.320683 TCCAGACGAGTGGTGCAATG 60.321 55.000 7.53 0.00 38.88 2.82
312 321 0.615331 ATCCAGACGAGTGGTGCAAT 59.385 50.000 7.53 0.00 38.88 3.56
313 322 1.262417 TATCCAGACGAGTGGTGCAA 58.738 50.000 7.53 0.00 38.88 4.08
314 323 1.262417 TTATCCAGACGAGTGGTGCA 58.738 50.000 7.53 0.00 38.88 4.57
315 324 2.205074 CATTATCCAGACGAGTGGTGC 58.795 52.381 7.53 0.00 38.88 5.01
316 325 3.526931 ACATTATCCAGACGAGTGGTG 57.473 47.619 7.53 2.31 38.88 4.17
317 326 4.553330 AAACATTATCCAGACGAGTGGT 57.447 40.909 7.53 0.00 38.88 4.16
318 327 5.880054 AAAAACATTATCCAGACGAGTGG 57.120 39.130 0.00 0.00 39.19 4.00
319 328 6.037172 CCCTAAAAACATTATCCAGACGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
320 329 6.070424 TCCCTAAAAACATTATCCAGACGAGT 60.070 38.462 0.00 0.00 0.00 4.18
321 330 6.346096 TCCCTAAAAACATTATCCAGACGAG 58.654 40.000 0.00 0.00 0.00 4.18
322 331 6.302535 TCCCTAAAAACATTATCCAGACGA 57.697 37.500 0.00 0.00 0.00 4.20
323 332 7.568199 AATCCCTAAAAACATTATCCAGACG 57.432 36.000 0.00 0.00 0.00 4.18
324 333 8.966868 TCAAATCCCTAAAAACATTATCCAGAC 58.033 33.333 0.00 0.00 0.00 3.51
325 334 9.713684 ATCAAATCCCTAAAAACATTATCCAGA 57.286 29.630 0.00 0.00 0.00 3.86
367 376 8.462016 GCATGAGAAAATAAAGAAGCTTTCCTA 58.538 33.333 0.00 0.00 0.00 2.94
368 377 7.318893 GCATGAGAAAATAAAGAAGCTTTCCT 58.681 34.615 0.00 0.00 0.00 3.36
369 378 6.533012 GGCATGAGAAAATAAAGAAGCTTTCC 59.467 38.462 0.00 0.00 0.00 3.13
370 379 7.092716 TGGCATGAGAAAATAAAGAAGCTTTC 58.907 34.615 0.00 0.00 0.00 2.62
371 380 6.996509 TGGCATGAGAAAATAAAGAAGCTTT 58.003 32.000 0.00 0.00 0.00 3.51
372 381 6.594788 TGGCATGAGAAAATAAAGAAGCTT 57.405 33.333 0.00 0.00 0.00 3.74
373 382 6.594788 TTGGCATGAGAAAATAAAGAAGCT 57.405 33.333 0.00 0.00 0.00 3.74
374 383 7.838771 AATTGGCATGAGAAAATAAAGAAGC 57.161 32.000 0.00 0.00 0.00 3.86
377 386 9.241919 TGACTAATTGGCATGAGAAAATAAAGA 57.758 29.630 0.00 0.00 0.00 2.52
378 387 9.512435 CTGACTAATTGGCATGAGAAAATAAAG 57.488 33.333 0.00 0.00 30.31 1.85
379 388 8.469200 CCTGACTAATTGGCATGAGAAAATAAA 58.531 33.333 0.00 0.00 30.31 1.40
380 389 7.833682 TCCTGACTAATTGGCATGAGAAAATAA 59.166 33.333 0.00 0.00 30.31 1.40
381 390 7.345691 TCCTGACTAATTGGCATGAGAAAATA 58.654 34.615 0.00 0.00 30.31 1.40
382 391 6.189859 TCCTGACTAATTGGCATGAGAAAAT 58.810 36.000 0.00 0.00 30.31 1.82
383 392 5.569355 TCCTGACTAATTGGCATGAGAAAA 58.431 37.500 0.00 0.00 30.31 2.29
384 393 5.178096 TCCTGACTAATTGGCATGAGAAA 57.822 39.130 0.00 0.00 30.31 2.52
385 394 4.842531 TCCTGACTAATTGGCATGAGAA 57.157 40.909 0.00 0.00 30.31 2.87
386 395 4.842531 TTCCTGACTAATTGGCATGAGA 57.157 40.909 0.00 0.00 30.12 3.27
387 396 7.664731 AGATTATTCCTGACTAATTGGCATGAG 59.335 37.037 0.00 0.00 30.12 2.90
388 397 7.520798 AGATTATTCCTGACTAATTGGCATGA 58.479 34.615 0.00 0.00 30.31 3.07
389 398 7.360691 CGAGATTATTCCTGACTAATTGGCATG 60.361 40.741 0.00 0.00 30.31 4.06
390 399 6.652481 CGAGATTATTCCTGACTAATTGGCAT 59.348 38.462 0.00 0.00 30.31 4.40
391 400 5.991606 CGAGATTATTCCTGACTAATTGGCA 59.008 40.000 0.00 0.00 0.00 4.92
392 401 5.106908 GCGAGATTATTCCTGACTAATTGGC 60.107 44.000 0.00 0.00 0.00 4.52
393 402 5.409826 GGCGAGATTATTCCTGACTAATTGG 59.590 44.000 0.00 0.00 0.00 3.16
394 403 6.226787 AGGCGAGATTATTCCTGACTAATTG 58.773 40.000 0.00 0.00 0.00 2.32
395 404 6.426646 AGGCGAGATTATTCCTGACTAATT 57.573 37.500 0.00 0.00 0.00 1.40
396 405 7.540474 TTAGGCGAGATTATTCCTGACTAAT 57.460 36.000 0.00 0.00 27.71 1.73
397 406 6.971726 TTAGGCGAGATTATTCCTGACTAA 57.028 37.500 0.00 0.29 29.30 2.24
398 407 6.971726 TTTAGGCGAGATTATTCCTGACTA 57.028 37.500 0.00 0.00 0.00 2.59
399 408 5.871396 TTTAGGCGAGATTATTCCTGACT 57.129 39.130 0.00 0.00 0.00 3.41
400 409 6.049790 AGTTTTAGGCGAGATTATTCCTGAC 58.950 40.000 0.00 0.00 0.00 3.51
401 410 6.235231 AGTTTTAGGCGAGATTATTCCTGA 57.765 37.500 0.00 0.00 0.00 3.86
402 411 6.927294 AAGTTTTAGGCGAGATTATTCCTG 57.073 37.500 0.00 0.00 0.00 3.86
403 412 8.211629 ACATAAGTTTTAGGCGAGATTATTCCT 58.788 33.333 0.00 0.00 0.00 3.36
404 413 8.379457 ACATAAGTTTTAGGCGAGATTATTCC 57.621 34.615 0.00 0.00 0.00 3.01
411 420 8.671028 GGAAAATTACATAAGTTTTAGGCGAGA 58.329 33.333 0.00 0.00 34.16 4.04
412 421 7.913821 GGGAAAATTACATAAGTTTTAGGCGAG 59.086 37.037 0.00 0.00 34.16 5.03
413 422 7.612633 AGGGAAAATTACATAAGTTTTAGGCGA 59.387 33.333 0.00 0.00 34.16 5.54
414 423 7.768240 AGGGAAAATTACATAAGTTTTAGGCG 58.232 34.615 0.00 0.00 34.16 5.52
415 424 8.195436 GGAGGGAAAATTACATAAGTTTTAGGC 58.805 37.037 0.00 0.00 34.16 3.93
416 425 9.250246 TGGAGGGAAAATTACATAAGTTTTAGG 57.750 33.333 0.00 0.00 34.16 2.69
418 427 8.732531 CGTGGAGGGAAAATTACATAAGTTTTA 58.267 33.333 0.00 0.00 34.16 1.52
419 428 7.231925 ACGTGGAGGGAAAATTACATAAGTTTT 59.768 33.333 0.00 0.00 34.16 2.43
420 429 6.717997 ACGTGGAGGGAAAATTACATAAGTTT 59.282 34.615 0.00 0.00 36.35 2.66
421 430 6.150474 CACGTGGAGGGAAAATTACATAAGTT 59.850 38.462 7.95 0.00 0.00 2.66
422 431 5.646360 CACGTGGAGGGAAAATTACATAAGT 59.354 40.000 7.95 0.00 0.00 2.24
423 432 5.646360 ACACGTGGAGGGAAAATTACATAAG 59.354 40.000 21.57 0.00 0.00 1.73
424 433 5.413213 CACACGTGGAGGGAAAATTACATAA 59.587 40.000 21.57 0.00 0.00 1.90
425 434 4.938832 CACACGTGGAGGGAAAATTACATA 59.061 41.667 21.57 0.00 0.00 2.29
426 435 3.756434 CACACGTGGAGGGAAAATTACAT 59.244 43.478 21.57 0.00 0.00 2.29
427 436 3.142951 CACACGTGGAGGGAAAATTACA 58.857 45.455 21.57 0.00 0.00 2.41
428 437 3.143728 ACACACGTGGAGGGAAAATTAC 58.856 45.455 21.57 0.00 34.19 1.89
429 438 3.495434 ACACACGTGGAGGGAAAATTA 57.505 42.857 21.57 0.00 34.19 1.40
430 439 2.358322 ACACACGTGGAGGGAAAATT 57.642 45.000 21.57 0.00 34.19 1.82
431 440 2.158667 AGAACACACGTGGAGGGAAAAT 60.159 45.455 21.57 0.00 34.19 1.82
432 441 1.210967 AGAACACACGTGGAGGGAAAA 59.789 47.619 21.57 0.00 34.19 2.29
433 442 0.834612 AGAACACACGTGGAGGGAAA 59.165 50.000 21.57 0.00 34.19 3.13
434 443 0.834612 AAGAACACACGTGGAGGGAA 59.165 50.000 21.57 0.00 34.19 3.97
435 444 0.834612 AAAGAACACACGTGGAGGGA 59.165 50.000 21.57 0.00 34.19 4.20
436 445 2.536761 TAAAGAACACACGTGGAGGG 57.463 50.000 21.57 8.78 34.19 4.30
437 446 5.432885 AAATTAAAGAACACACGTGGAGG 57.567 39.130 21.57 11.40 34.19 4.30
438 447 5.619607 CGAAAATTAAAGAACACACGTGGAG 59.380 40.000 21.57 14.41 34.19 3.86
439 448 5.064962 ACGAAAATTAAAGAACACACGTGGA 59.935 36.000 21.57 0.00 34.19 4.02
440 449 5.170625 CACGAAAATTAAAGAACACACGTGG 59.829 40.000 21.57 11.39 41.86 4.94
441 450 5.330498 GCACGAAAATTAAAGAACACACGTG 60.330 40.000 15.48 15.48 46.00 4.49
442 451 4.731480 GCACGAAAATTAAAGAACACACGT 59.269 37.500 0.00 0.00 0.00 4.49
443 452 4.145756 GGCACGAAAATTAAAGAACACACG 59.854 41.667 0.00 0.00 0.00 4.49
444 453 5.038033 TGGCACGAAAATTAAAGAACACAC 58.962 37.500 0.00 0.00 0.00 3.82
445 454 5.250235 TGGCACGAAAATTAAAGAACACA 57.750 34.783 0.00 0.00 0.00 3.72
446 455 6.576551 TTTGGCACGAAAATTAAAGAACAC 57.423 33.333 0.00 0.00 0.00 3.32
447 456 7.332182 AGTTTTTGGCACGAAAATTAAAGAACA 59.668 29.630 0.84 0.00 0.00 3.18
448 457 7.680982 AGTTTTTGGCACGAAAATTAAAGAAC 58.319 30.769 0.84 0.00 0.00 3.01
449 458 7.835634 AGTTTTTGGCACGAAAATTAAAGAA 57.164 28.000 0.84 0.00 0.00 2.52
452 461 9.745880 TGTATAGTTTTTGGCACGAAAATTAAA 57.254 25.926 0.84 0.00 0.00 1.52
453 462 9.182933 GTGTATAGTTTTTGGCACGAAAATTAA 57.817 29.630 0.84 0.00 0.00 1.40
454 463 7.808856 GGTGTATAGTTTTTGGCACGAAAATTA 59.191 33.333 0.84 2.13 0.00 1.40
455 464 6.643360 GGTGTATAGTTTTTGGCACGAAAATT 59.357 34.615 0.84 0.06 0.00 1.82
456 465 6.015772 AGGTGTATAGTTTTTGGCACGAAAAT 60.016 34.615 0.84 1.41 0.00 1.82
457 466 5.299782 AGGTGTATAGTTTTTGGCACGAAAA 59.700 36.000 0.00 0.00 0.00 2.29
458 467 4.822896 AGGTGTATAGTTTTTGGCACGAAA 59.177 37.500 0.00 0.00 0.00 3.46
459 468 4.391155 AGGTGTATAGTTTTTGGCACGAA 58.609 39.130 0.00 0.00 0.00 3.85
460 469 4.010667 AGGTGTATAGTTTTTGGCACGA 57.989 40.909 0.00 0.00 0.00 4.35
461 470 4.759516 AAGGTGTATAGTTTTTGGCACG 57.240 40.909 0.00 0.00 0.00 5.34
471 480 9.592196 TCCGTTCCTTAATATAAGGTGTATAGT 57.408 33.333 14.18 0.00 38.55 2.12
473 482 9.028284 CCTCCGTTCCTTAATATAAGGTGTATA 57.972 37.037 14.18 0.00 38.55 1.47
474 483 7.038516 CCCTCCGTTCCTTAATATAAGGTGTAT 60.039 40.741 14.18 0.00 38.55 2.29
475 484 6.268387 CCCTCCGTTCCTTAATATAAGGTGTA 59.732 42.308 14.18 1.67 38.55 2.90
476 485 5.071384 CCCTCCGTTCCTTAATATAAGGTGT 59.929 44.000 14.18 0.00 38.55 4.16
477 486 5.306160 TCCCTCCGTTCCTTAATATAAGGTG 59.694 44.000 14.18 7.21 38.55 4.00
478 487 5.470501 TCCCTCCGTTCCTTAATATAAGGT 58.529 41.667 14.18 0.00 38.55 3.50
479 488 5.543020 ACTCCCTCCGTTCCTTAATATAAGG 59.457 44.000 9.44 9.44 38.78 2.69
480 489 6.667558 ACTCCCTCCGTTCCTTAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
481 490 7.731688 ACATACTCCCTCCGTTCCTTAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
482 491 7.243824 ACATACTCCCTCCGTTCCTTAATATA 58.756 38.462 0.00 0.00 0.00 0.86
483 492 6.082707 ACATACTCCCTCCGTTCCTTAATAT 58.917 40.000 0.00 0.00 0.00 1.28
484 493 5.461327 ACATACTCCCTCCGTTCCTTAATA 58.539 41.667 0.00 0.00 0.00 0.98
485 494 4.296056 ACATACTCCCTCCGTTCCTTAAT 58.704 43.478 0.00 0.00 0.00 1.40
486 495 3.716431 ACATACTCCCTCCGTTCCTTAA 58.284 45.455 0.00 0.00 0.00 1.85
487 496 3.393426 ACATACTCCCTCCGTTCCTTA 57.607 47.619 0.00 0.00 0.00 2.69
488 497 2.249309 ACATACTCCCTCCGTTCCTT 57.751 50.000 0.00 0.00 0.00 3.36
489 498 2.249309 AACATACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
490 499 4.141779 ACAATAACATACTCCCTCCGTTCC 60.142 45.833 0.00 0.00 0.00 3.62
491 500 4.809426 CACAATAACATACTCCCTCCGTTC 59.191 45.833 0.00 0.00 0.00 3.95
492 501 4.383770 CCACAATAACATACTCCCTCCGTT 60.384 45.833 0.00 0.00 0.00 4.44
493 502 3.134081 CCACAATAACATACTCCCTCCGT 59.866 47.826 0.00 0.00 0.00 4.69
494 503 3.134081 ACCACAATAACATACTCCCTCCG 59.866 47.826 0.00 0.00 0.00 4.63
495 504 4.772886 ACCACAATAACATACTCCCTCC 57.227 45.455 0.00 0.00 0.00 4.30
496 505 6.281405 CACTACCACAATAACATACTCCCTC 58.719 44.000 0.00 0.00 0.00 4.30
497 506 5.130477 CCACTACCACAATAACATACTCCCT 59.870 44.000 0.00 0.00 0.00 4.20
498 507 5.365619 CCACTACCACAATAACATACTCCC 58.634 45.833 0.00 0.00 0.00 4.30
499 508 5.104652 ACCCACTACCACAATAACATACTCC 60.105 44.000 0.00 0.00 0.00 3.85
500 509 5.985911 ACCCACTACCACAATAACATACTC 58.014 41.667 0.00 0.00 0.00 2.59
501 510 5.486063 TGACCCACTACCACAATAACATACT 59.514 40.000 0.00 0.00 0.00 2.12
502 511 5.736813 TGACCCACTACCACAATAACATAC 58.263 41.667 0.00 0.00 0.00 2.39
503 512 5.486063 ACTGACCCACTACCACAATAACATA 59.514 40.000 0.00 0.00 0.00 2.29
504 513 4.288626 ACTGACCCACTACCACAATAACAT 59.711 41.667 0.00 0.00 0.00 2.71
505 514 3.649023 ACTGACCCACTACCACAATAACA 59.351 43.478 0.00 0.00 0.00 2.41
506 515 4.000988 CACTGACCCACTACCACAATAAC 58.999 47.826 0.00 0.00 0.00 1.89
507 516 3.008594 CCACTGACCCACTACCACAATAA 59.991 47.826 0.00 0.00 0.00 1.40
508 517 2.569853 CCACTGACCCACTACCACAATA 59.430 50.000 0.00 0.00 0.00 1.90
509 518 1.351017 CCACTGACCCACTACCACAAT 59.649 52.381 0.00 0.00 0.00 2.71
549 558 8.548721 GTGCTCACAAAATACCACTGTATATAC 58.451 37.037 5.89 5.89 36.65 1.47
551 560 6.257849 CGTGCTCACAAAATACCACTGTATAT 59.742 38.462 0.69 0.00 36.65 0.86
553 562 4.391830 CGTGCTCACAAAATACCACTGTAT 59.608 41.667 0.69 0.00 39.39 2.29
555 564 2.548057 CGTGCTCACAAAATACCACTGT 59.452 45.455 0.69 0.00 0.00 3.55
556 565 2.665519 GCGTGCTCACAAAATACCACTG 60.666 50.000 0.69 0.00 0.00 3.66
558 567 1.724654 CGCGTGCTCACAAAATACCAC 60.725 52.381 0.00 0.00 0.00 4.16
559 568 0.515127 CGCGTGCTCACAAAATACCA 59.485 50.000 0.00 0.00 0.00 3.25
560 569 0.793861 TCGCGTGCTCACAAAATACC 59.206 50.000 5.77 0.00 0.00 2.73
561 570 2.159707 ACATCGCGTGCTCACAAAATAC 60.160 45.455 5.77 0.00 0.00 1.89
569 622 1.011968 GGTGTAACATCGCGTGCTCA 61.012 55.000 5.77 2.04 39.98 4.26
580 633 2.170166 AGGGTAATCGACGGTGTAACA 58.830 47.619 0.00 0.00 39.98 2.41
586 639 5.796424 ACATTATTAGGGTAATCGACGGT 57.204 39.130 0.00 0.00 0.00 4.83
587 640 6.218019 TCAACATTATTAGGGTAATCGACGG 58.782 40.000 0.00 0.00 0.00 4.79
588 641 7.095774 CCTTCAACATTATTAGGGTAATCGACG 60.096 40.741 0.00 0.00 0.00 5.12
589 642 7.929785 TCCTTCAACATTATTAGGGTAATCGAC 59.070 37.037 0.00 0.00 0.00 4.20
590 643 8.025270 TCCTTCAACATTATTAGGGTAATCGA 57.975 34.615 0.00 0.00 0.00 3.59
591 644 8.848474 ATCCTTCAACATTATTAGGGTAATCG 57.152 34.615 0.00 0.00 0.00 3.34
636 689 4.607239 AGGGACTCGAATGTAGGAACTTA 58.393 43.478 0.00 0.00 41.75 2.24
640 693 5.659525 TGATTAAGGGACTCGAATGTAGGAA 59.340 40.000 0.00 0.00 38.49 3.36
651 1639 3.309954 GCATGTCGTTGATTAAGGGACTC 59.690 47.826 0.00 0.00 38.49 3.36
664 1652 3.058293 CCTTAACACACATGCATGTCGTT 60.058 43.478 31.54 31.54 39.39 3.85
665 1653 2.483877 CCTTAACACACATGCATGTCGT 59.516 45.455 29.23 24.30 39.39 4.34
1063 2315 1.075482 CACCACTGGCCATCTTGGT 59.925 57.895 22.42 22.42 43.39 3.67
1094 2467 2.284798 CTGGTCGTCATCCTCGGTGG 62.285 65.000 0.00 0.00 37.10 4.61
1341 2714 2.444895 GGAGGGGCGATGGAGAGT 60.445 66.667 0.00 0.00 0.00 3.24
1532 2917 1.202245 TGTTGTTGAAGCGGTTGAAGC 60.202 47.619 3.70 0.00 0.00 3.86
1579 2964 6.091577 CAGGAGTGCATTAAATGTTGTACGTA 59.908 38.462 0.00 0.00 34.20 3.57
1601 2986 2.047274 ACGTTGATCCGCACCAGG 60.047 61.111 0.00 0.00 0.00 4.45
1602 2987 1.667830 ACACGTTGATCCGCACCAG 60.668 57.895 0.00 0.00 0.00 4.00
1609 2994 2.930040 CACATACTCCACACGTTGATCC 59.070 50.000 0.00 0.00 0.00 3.36
1622 3011 7.421530 ACACATGTACTTTGAACACATACTC 57.578 36.000 0.00 0.00 31.81 2.59
1623 3012 7.497579 TCAACACATGTACTTTGAACACATACT 59.502 33.333 12.14 0.00 31.81 2.12
1624 3013 7.635423 TCAACACATGTACTTTGAACACATAC 58.365 34.615 12.14 0.00 31.81 2.39
1625 3014 7.519809 GCTCAACACATGTACTTTGAACACATA 60.520 37.037 14.36 0.00 31.81 2.29
1626 3015 6.691754 TCAACACATGTACTTTGAACACAT 57.308 33.333 12.14 0.00 33.22 3.21
2069 3460 2.281002 TCGACGGTCACGGACTCA 60.281 61.111 9.10 0.00 46.48 3.41
2079 3470 2.113433 CCTCATCCTCGTCGACGGT 61.113 63.158 35.05 17.43 40.29 4.83
2093 3484 1.740664 CTCGTCGTCCTCGTCCTCA 60.741 63.158 0.00 0.00 38.33 3.86
2132 3523 1.170442 TGCCGTTCTCATCGTACAGA 58.830 50.000 0.00 0.00 0.00 3.41
2162 3553 1.672030 CAAGACCATGTCGCTGCCA 60.672 57.895 0.00 0.00 37.67 4.92
2193 3584 3.320673 AGCTAACAACGAAGAAGGAGG 57.679 47.619 0.00 0.00 0.00 4.30
2199 3590 3.242936 GGCAACAAAGCTAACAACGAAGA 60.243 43.478 0.00 0.00 34.17 2.87
2201 3592 2.685897 AGGCAACAAAGCTAACAACGAA 59.314 40.909 0.00 0.00 41.41 3.85
2202 3593 2.032799 CAGGCAACAAAGCTAACAACGA 59.967 45.455 0.00 0.00 41.41 3.85
2203 3594 2.384382 CAGGCAACAAAGCTAACAACG 58.616 47.619 0.00 0.00 41.41 4.10
2204 3595 2.127251 GCAGGCAACAAAGCTAACAAC 58.873 47.619 0.00 0.00 41.41 3.32
2205 3596 1.753649 TGCAGGCAACAAAGCTAACAA 59.246 42.857 0.00 0.00 41.41 2.83
2206 3597 1.066908 GTGCAGGCAACAAAGCTAACA 59.933 47.619 0.00 0.00 41.41 2.41
2207 3598 1.770957 GTGCAGGCAACAAAGCTAAC 58.229 50.000 0.00 0.00 41.41 2.34
2224 3615 8.121708 GGACTAGTACTAACTAAAGACATCGTG 58.878 40.741 3.76 0.00 37.75 4.35
2281 3678 1.444895 GCACTTGGGAAGCAATGCG 60.445 57.895 0.00 0.00 0.00 4.73
2373 3775 4.022849 TGAGACAGACACACAGACATACAG 60.023 45.833 0.00 0.00 0.00 2.74
2394 3796 4.142752 CGTACTACGACACTTCTTCCATGA 60.143 45.833 2.17 0.00 46.05 3.07
2515 3917 3.074412 GACACCATGAAACAGTGGTAGG 58.926 50.000 0.00 0.00 46.62 3.18
2624 4030 6.451064 CCACAGTGGTAAAAACTCTTTTCT 57.549 37.500 11.99 0.00 36.20 2.52
2895 4302 2.642311 TGTTGCATTGGAGGTCCTTAGA 59.358 45.455 0.00 0.00 36.82 2.10
2896 4303 3.012518 CTGTTGCATTGGAGGTCCTTAG 58.987 50.000 0.00 0.00 36.82 2.18
2897 4304 2.879756 GCTGTTGCATTGGAGGTCCTTA 60.880 50.000 0.00 0.00 39.41 2.69
2992 4420 4.892965 TGCGCCCTGCCAAAGTGT 62.893 61.111 4.18 0.00 45.60 3.55
2995 4423 0.249155 CATAATGCGCCCTGCCAAAG 60.249 55.000 4.18 0.00 45.60 2.77
3002 4430 6.596888 GCATATATATCATCATAATGCGCCCT 59.403 38.462 4.18 0.00 32.58 5.19
3039 4469 5.415701 TGTTGGTCAAAGGCTTCTCATAATC 59.584 40.000 0.00 0.00 0.00 1.75
3040 4470 5.183904 GTGTTGGTCAAAGGCTTCTCATAAT 59.816 40.000 0.00 0.00 0.00 1.28
3044 4474 2.092429 AGTGTTGGTCAAAGGCTTCTCA 60.092 45.455 0.00 0.00 0.00 3.27
3126 4562 8.948631 ATATACTCTGTGACATAAAGTTGGTG 57.051 34.615 1.62 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.