Multiple sequence alignment - TraesCS3B01G440000

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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 TraesCS3B01G440000 chr3B 100.000 3013 0 0 1 3013 679625233 679622221 0.000000e+00 5565.0
1 TraesCS3B01G440000 chr3B 93.522 494 25 4 1 493 724045057 724044570 0.000000e+00 728.0
2 TraesCS3B01G440000 chr3B 79.531 938 129 28 1279 2167 678711023 678711946 7.140000e-171 610.0
3 TraesCS3B01G440000 chr3B 81.818 165 20 7 1070 1225 678710861 678711024 2.440000e-26 130.0
4 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45768529 45768406 6.870000e-17 99.0
5 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45838670 45838547 6.870000e-17 99.0
6 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45875951 45875828 6.870000e-17 99.0
7 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45890045 45889922 6.870000e-17 99.0
8 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45933757 45933634 6.870000e-17 99.0
9 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 45983727 45983604 6.870000e-17 99.0
10 TraesCS3B01G440000 chr3B 80.952 126 22 1 2647 2772 46022563 46022440 6.870000e-17 99.0
11 TraesCS3B01G440000 chr3A 87.922 2045 178 31 496 2501 651502808 651500794 0.000000e+00 2344.0
12 TraesCS3B01G440000 chr3A 80.947 866 118 18 1319 2167 650195340 650196175 2.530000e-180 641.0
13 TraesCS3B01G440000 chr3A 95.086 407 18 2 2608 3012 651500793 651500387 9.110000e-180 640.0
14 TraesCS3B01G440000 chr3A 79.667 300 57 3 572 869 37632490 37632193 2.350000e-51 213.0
15 TraesCS3B01G440000 chr3A 79.734 301 53 6 572 868 37591795 37591499 8.460000e-51 211.0
16 TraesCS3B01G440000 chr3D 91.267 1042 60 16 496 1520 516194756 516193729 0.000000e+00 1391.0
17 TraesCS3B01G440000 chr3D 90.964 664 54 4 1505 2167 516193712 516193054 0.000000e+00 889.0
18 TraesCS3B01G440000 chr3D 92.446 556 13 3 2460 3013 516192834 516192306 0.000000e+00 767.0
19 TraesCS3B01G440000 chr3D 81.309 947 116 31 1265 2167 515818982 515819911 0.000000e+00 712.0
20 TraesCS3B01G440000 chr3D 96.234 239 8 1 2184 2421 516193069 516192831 1.010000e-104 390.0
21 TraesCS3B01G440000 chr7D 94.141 495 25 4 1 493 509902550 509902058 0.000000e+00 750.0
22 TraesCS3B01G440000 chr7D 92.929 495 32 3 1 494 174792582 174792090 0.000000e+00 717.0
23 TraesCS3B01G440000 chr7B 93.964 497 27 3 1 496 374712460 374711966 0.000000e+00 749.0
24 TraesCS3B01G440000 chr7B 92.475 505 36 2 1 503 716137387 716136883 0.000000e+00 721.0
25 TraesCS3B01G440000 chr7A 94.118 493 24 5 1 490 510570389 510570879 0.000000e+00 745.0
26 TraesCS3B01G440000 chr7A 100.000 29 0 0 1676 1704 303967860 303967832 2.000000e-03 54.7
27 TraesCS3B01G440000 chrUn 93.279 491 29 3 1 490 18055134 18054647 0.000000e+00 721.0
28 TraesCS3B01G440000 chr6B 92.800 500 32 3 1 498 526740145 526740642 0.000000e+00 721.0
29 TraesCS3B01G440000 chr5B 92.430 502 34 3 1 501 523906524 523906026 0.000000e+00 713.0
30 TraesCS3B01G440000 chr5A 100.000 28 0 0 1680 1707 275080756 275080783 5.000000e-03 52.8


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 TraesCS3B01G440000 chr3B 679622221 679625233 3012 True 5565.00 5565 100.00000 1 3013 1 chr3B.!!$R8 3012
1 TraesCS3B01G440000 chr3B 678710861 678711946 1085 False 370.00 610 80.67450 1070 2167 2 chr3B.!!$F1 1097
2 TraesCS3B01G440000 chr3A 651500387 651502808 2421 True 1492.00 2344 91.50400 496 3012 2 chr3A.!!$R3 2516
3 TraesCS3B01G440000 chr3A 650195340 650196175 835 False 641.00 641 80.94700 1319 2167 1 chr3A.!!$F1 848
4 TraesCS3B01G440000 chr3D 516192306 516194756 2450 True 859.25 1391 92.72775 496 3013 4 chr3D.!!$R1 2517
5 TraesCS3B01G440000 chr3D 515818982 515819911 929 False 712.00 712 81.30900 1265 2167 1 chr3D.!!$F1 902
6 TraesCS3B01G440000 chr7B 716136883 716137387 504 True 721.00 721 92.47500 1 503 1 chr7B.!!$R2 502

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
422 425 0.315625 CATGCATGCGATGACGTGAC 60.316 55.0 14.93 0.0 41.98 3.67 F
1183 1210 0.370273 CGATTCTGTTGGTAGTGCGC 59.630 55.0 0.00 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1693 0.318445 CTTGCACTGCCAGTTTCTGC 60.318 55.0 0.00 0.0 0.0 4.26 R
2544 2702 2.634815 ATGGCATGGCAGTCTTCTAG 57.365 50.0 27.02 0.0 0.0 2.43 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
35 36 6.953101 TGGCAATTCTAGTACTTTGACCATA 58.047 36.000 0.00 0.00 0.00 2.74
110 113 5.474578 TTTAGTTTATGGTGCATGGCAAA 57.525 34.783 0.00 0.00 41.47 3.68
198 201 6.624423 AGTTGAAACATATCATGGCAACTTC 58.376 36.000 13.64 0.00 42.74 3.01
209 212 6.494893 TCATGGCAACTTCAGTGTAAATAC 57.505 37.500 0.00 0.00 37.61 1.89
218 221 5.951747 ACTTCAGTGTAAATACCATGGCAAT 59.048 36.000 13.04 2.51 0.00 3.56
249 252 6.155827 GCAATAGACATGGCAACTTTTAACA 58.844 36.000 0.00 0.00 30.66 2.41
250 253 6.644592 GCAATAGACATGGCAACTTTTAACAA 59.355 34.615 0.00 0.00 30.66 2.83
329 332 4.082463 GCGAGGGATTTAATGGTGAAAACA 60.082 41.667 0.00 0.00 0.00 2.83
330 333 5.640732 CGAGGGATTTAATGGTGAAAACAG 58.359 41.667 0.00 0.00 0.00 3.16
331 334 5.414454 CGAGGGATTTAATGGTGAAAACAGA 59.586 40.000 0.00 0.00 0.00 3.41
332 335 6.095440 CGAGGGATTTAATGGTGAAAACAGAT 59.905 38.462 0.00 0.00 0.00 2.90
333 336 7.410120 AGGGATTTAATGGTGAAAACAGATC 57.590 36.000 0.00 0.00 0.00 2.75
334 337 7.184862 AGGGATTTAATGGTGAAAACAGATCT 58.815 34.615 0.00 0.00 0.00 2.75
335 338 7.675619 AGGGATTTAATGGTGAAAACAGATCTT 59.324 33.333 0.00 0.00 0.00 2.40
336 339 7.976175 GGGATTTAATGGTGAAAACAGATCTTC 59.024 37.037 0.00 0.00 0.00 2.87
337 340 8.522830 GGATTTAATGGTGAAAACAGATCTTCA 58.477 33.333 0.00 0.00 0.00 3.02
338 341 9.912634 GATTTAATGGTGAAAACAGATCTTCAA 57.087 29.630 0.00 0.00 33.52 2.69
340 343 9.912634 TTTAATGGTGAAAACAGATCTTCAATC 57.087 29.630 0.00 0.00 33.52 2.67
341 344 7.528996 AATGGTGAAAACAGATCTTCAATCA 57.471 32.000 0.00 0.00 33.52 2.57
342 345 6.564709 TGGTGAAAACAGATCTTCAATCAG 57.435 37.500 0.00 0.00 33.52 2.90
343 346 6.298361 TGGTGAAAACAGATCTTCAATCAGA 58.702 36.000 0.00 0.00 33.52 3.27
344 347 6.944290 TGGTGAAAACAGATCTTCAATCAGAT 59.056 34.615 0.00 0.00 36.12 2.90
345 348 7.449395 TGGTGAAAACAGATCTTCAATCAGATT 59.551 33.333 0.00 0.00 33.36 2.40
346 349 8.302438 GGTGAAAACAGATCTTCAATCAGATTT 58.698 33.333 0.00 0.00 33.36 2.17
347 350 9.688592 GTGAAAACAGATCTTCAATCAGATTTT 57.311 29.630 0.00 0.00 33.36 1.82
398 401 8.950403 AAACTAAAAATCCGAAAAGATTCTCG 57.050 30.769 0.00 0.00 35.40 4.04
399 402 6.543736 ACTAAAAATCCGAAAAGATTCTCGC 58.456 36.000 0.00 0.00 35.40 5.03
400 403 5.371115 AAAAATCCGAAAAGATTCTCGCA 57.629 34.783 0.00 0.00 35.40 5.10
401 404 5.567138 AAAATCCGAAAAGATTCTCGCAT 57.433 34.783 0.00 0.00 35.40 4.73
402 405 6.677781 AAAATCCGAAAAGATTCTCGCATA 57.322 33.333 0.00 0.00 35.40 3.14
403 406 5.659048 AATCCGAAAAGATTCTCGCATAC 57.341 39.130 0.00 0.00 30.51 2.39
404 407 4.118093 TCCGAAAAGATTCTCGCATACA 57.882 40.909 0.00 0.00 33.70 2.29
405 408 4.693283 TCCGAAAAGATTCTCGCATACAT 58.307 39.130 0.00 0.00 33.70 2.29
406 409 4.507756 TCCGAAAAGATTCTCGCATACATG 59.492 41.667 0.00 0.00 33.70 3.21
407 410 4.206843 CGAAAAGATTCTCGCATACATGC 58.793 43.478 4.04 4.04 40.63 4.06
408 411 4.260334 CGAAAAGATTCTCGCATACATGCA 60.260 41.667 14.18 0.00 42.39 3.96
409 412 5.559608 CGAAAAGATTCTCGCATACATGCAT 60.560 40.000 14.18 0.00 42.39 3.96
410 413 5.624081 GAAAAGATTCTCGCATACATGCATG 59.376 40.000 25.09 25.09 41.84 4.06
411 414 7.749573 GAAAAGATTCTCGCATACATGCATGC 61.750 42.308 26.53 19.26 41.84 4.06
418 421 2.221799 CATACATGCATGCGATGACG 57.778 50.000 26.85 15.10 42.93 4.35
419 422 1.528161 CATACATGCATGCGATGACGT 59.472 47.619 26.85 14.63 41.98 4.34
420 423 0.929615 TACATGCATGCGATGACGTG 59.070 50.000 26.53 14.04 41.98 4.49
421 424 0.740516 ACATGCATGCGATGACGTGA 60.741 50.000 26.53 4.39 41.98 4.35
422 425 0.315625 CATGCATGCGATGACGTGAC 60.316 55.000 14.93 0.00 41.98 3.67
423 426 0.740516 ATGCATGCGATGACGTGACA 60.741 50.000 14.09 0.00 41.98 3.58
424 427 0.948141 TGCATGCGATGACGTGACAA 60.948 50.000 14.09 0.00 41.98 3.18
425 428 0.374758 GCATGCGATGACGTGACAAT 59.625 50.000 0.00 0.00 41.98 2.71
426 429 1.593070 GCATGCGATGACGTGACAATC 60.593 52.381 0.00 0.00 41.98 2.67
427 430 1.929169 CATGCGATGACGTGACAATCT 59.071 47.619 0.00 0.00 41.98 2.40
428 431 2.931512 TGCGATGACGTGACAATCTA 57.068 45.000 0.00 0.00 41.98 1.98
429 432 3.436700 TGCGATGACGTGACAATCTAT 57.563 42.857 0.00 0.00 41.98 1.98
430 433 3.780902 TGCGATGACGTGACAATCTATT 58.219 40.909 0.00 0.00 41.98 1.73
431 434 4.180817 TGCGATGACGTGACAATCTATTT 58.819 39.130 0.00 0.00 41.98 1.40
432 435 4.032786 TGCGATGACGTGACAATCTATTTG 59.967 41.667 0.00 0.00 41.98 2.32
433 436 4.508971 CGATGACGTGACAATCTATTTGC 58.491 43.478 0.00 0.00 35.32 3.68
434 437 4.032786 CGATGACGTGACAATCTATTTGCA 59.967 41.667 0.00 0.00 35.32 4.08
435 438 5.277011 CGATGACGTGACAATCTATTTGCAT 60.277 40.000 0.00 0.00 35.32 3.96
436 439 5.878332 TGACGTGACAATCTATTTGCATT 57.122 34.783 0.00 0.00 39.03 3.56
437 440 6.976636 TGACGTGACAATCTATTTGCATTA 57.023 33.333 0.00 0.00 39.03 1.90
438 441 7.003939 TGACGTGACAATCTATTTGCATTAG 57.996 36.000 0.00 0.00 39.03 1.73
439 442 6.816140 TGACGTGACAATCTATTTGCATTAGA 59.184 34.615 0.00 8.79 39.03 2.10
440 443 7.010460 TGACGTGACAATCTATTTGCATTAGAG 59.990 37.037 0.00 0.09 39.03 2.43
441 444 7.041721 ACGTGACAATCTATTTGCATTAGAGA 58.958 34.615 11.30 4.99 39.03 3.10
442 445 7.010552 ACGTGACAATCTATTTGCATTAGAGAC 59.989 37.037 11.30 2.81 39.03 3.36
443 446 7.010460 CGTGACAATCTATTTGCATTAGAGACA 59.990 37.037 11.30 4.70 39.03 3.41
444 447 8.834465 GTGACAATCTATTTGCATTAGAGACAT 58.166 33.333 11.30 0.40 39.03 3.06
445 448 8.833493 TGACAATCTATTTGCATTAGAGACATG 58.167 33.333 11.30 8.89 39.03 3.21
446 449 8.743085 ACAATCTATTTGCATTAGAGACATGT 57.257 30.769 0.00 0.00 39.03 3.21
447 450 8.618677 ACAATCTATTTGCATTAGAGACATGTG 58.381 33.333 1.15 0.00 39.03 3.21
448 451 7.741027 ATCTATTTGCATTAGAGACATGTGG 57.259 36.000 1.15 0.00 0.00 4.17
449 452 6.653020 TCTATTTGCATTAGAGACATGTGGT 58.347 36.000 1.15 0.00 0.00 4.16
450 453 5.571784 ATTTGCATTAGAGACATGTGGTG 57.428 39.130 1.15 0.00 0.00 4.17
451 454 2.358957 TGCATTAGAGACATGTGGTGC 58.641 47.619 1.15 5.00 0.00 5.01
452 455 1.328680 GCATTAGAGACATGTGGTGCG 59.671 52.381 1.15 0.00 0.00 5.34
453 456 2.621338 CATTAGAGACATGTGGTGCGT 58.379 47.619 1.15 0.00 0.00 5.24
454 457 3.780902 CATTAGAGACATGTGGTGCGTA 58.219 45.455 1.15 0.00 0.00 4.42
455 458 4.371786 CATTAGAGACATGTGGTGCGTAT 58.628 43.478 1.15 0.00 0.00 3.06
456 459 2.586258 AGAGACATGTGGTGCGTATC 57.414 50.000 1.15 0.00 0.00 2.24
457 460 1.137086 AGAGACATGTGGTGCGTATCC 59.863 52.381 1.15 0.00 0.00 2.59
458 461 1.137086 GAGACATGTGGTGCGTATCCT 59.863 52.381 1.15 0.00 0.00 3.24
459 462 1.555075 AGACATGTGGTGCGTATCCTT 59.445 47.619 1.15 0.00 0.00 3.36
460 463 2.027192 AGACATGTGGTGCGTATCCTTT 60.027 45.455 1.15 0.00 0.00 3.11
461 464 2.351726 GACATGTGGTGCGTATCCTTTC 59.648 50.000 1.15 0.00 0.00 2.62
462 465 1.670811 CATGTGGTGCGTATCCTTTCC 59.329 52.381 0.00 0.00 0.00 3.13
463 466 0.981183 TGTGGTGCGTATCCTTTCCT 59.019 50.000 0.00 0.00 0.00 3.36
464 467 1.338674 TGTGGTGCGTATCCTTTCCTG 60.339 52.381 0.00 0.00 0.00 3.86
465 468 0.981183 TGGTGCGTATCCTTTCCTGT 59.019 50.000 0.00 0.00 0.00 4.00
466 469 1.066430 TGGTGCGTATCCTTTCCTGTC 60.066 52.381 0.00 0.00 0.00 3.51
467 470 1.066430 GGTGCGTATCCTTTCCTGTCA 60.066 52.381 0.00 0.00 0.00 3.58
468 471 2.000447 GTGCGTATCCTTTCCTGTCAC 59.000 52.381 0.00 0.00 0.00 3.67
469 472 1.621317 TGCGTATCCTTTCCTGTCACA 59.379 47.619 0.00 0.00 0.00 3.58
470 473 2.000447 GCGTATCCTTTCCTGTCACAC 59.000 52.381 0.00 0.00 0.00 3.82
471 474 2.259618 CGTATCCTTTCCTGTCACACG 58.740 52.381 0.00 0.00 0.00 4.49
472 475 2.352421 CGTATCCTTTCCTGTCACACGT 60.352 50.000 0.00 0.00 0.00 4.49
473 476 2.169832 ATCCTTTCCTGTCACACGTG 57.830 50.000 15.48 15.48 0.00 4.49
474 477 0.828022 TCCTTTCCTGTCACACGTGT 59.172 50.000 17.22 17.22 0.00 4.49
475 478 0.937304 CCTTTCCTGTCACACGTGTG 59.063 55.000 37.04 37.04 46.91 3.82
488 491 2.792674 ACACGTGTGACAGTTATTGACG 59.207 45.455 22.71 0.00 31.72 4.35
489 492 2.792674 CACGTGTGACAGTTATTGACGT 59.207 45.455 7.58 0.00 37.10 4.34
490 493 3.244345 CACGTGTGACAGTTATTGACGTT 59.756 43.478 7.58 0.00 35.23 3.99
491 494 3.488310 ACGTGTGACAGTTATTGACGTTC 59.512 43.478 0.00 0.00 34.16 3.95
492 495 3.734231 CGTGTGACAGTTATTGACGTTCT 59.266 43.478 0.00 0.00 0.00 3.01
493 496 4.208460 CGTGTGACAGTTATTGACGTTCTT 59.792 41.667 0.00 0.00 0.00 2.52
494 497 5.276678 CGTGTGACAGTTATTGACGTTCTTT 60.277 40.000 0.00 0.00 0.00 2.52
495 498 6.074729 CGTGTGACAGTTATTGACGTTCTTTA 60.075 38.462 0.00 0.00 0.00 1.85
496 499 7.358931 CGTGTGACAGTTATTGACGTTCTTTAT 60.359 37.037 0.00 0.00 0.00 1.40
497 500 8.280497 GTGTGACAGTTATTGACGTTCTTTATT 58.720 33.333 0.00 0.00 0.00 1.40
498 501 8.832521 TGTGACAGTTATTGACGTTCTTTATTT 58.167 29.630 0.00 0.00 0.00 1.40
499 502 9.659830 GTGACAGTTATTGACGTTCTTTATTTT 57.340 29.630 0.00 0.00 0.00 1.82
528 532 6.707161 ACGAAAAATACCACTGTAAGCACTTA 59.293 34.615 0.00 0.00 37.60 2.24
643 650 6.736123 TCTGTAGAAGTAGCCGTTGATAATC 58.264 40.000 0.00 0.00 0.00 1.75
657 664 5.385198 GTTGATAATCCCAGGCAGGAAATA 58.615 41.667 0.00 0.00 40.04 1.40
676 683 8.793592 AGGAAATAAAAGCTTACCACAAGTTAG 58.206 33.333 0.00 0.00 0.00 2.34
711 718 6.381481 TCTGTACGTAGAAAGAAACACAGA 57.619 37.500 6.42 6.42 38.95 3.41
722 729 1.697772 AAACACAGACGCGCGAACAA 61.698 50.000 39.36 0.00 0.00 2.83
739 746 6.560166 GCGAACAAATTTAGAAGAAAACACG 58.440 36.000 0.00 0.00 0.00 4.49
812 819 4.335416 TGGGACTTTAAAAGGAGATGCTG 58.665 43.478 0.00 0.00 0.00 4.41
894 901 3.737774 GCTTTCTGTTCAGGTTGCAAATC 59.262 43.478 0.00 0.00 0.00 2.17
904 911 2.641815 AGGTTGCAAATCTGTCTCCTCT 59.358 45.455 0.00 0.00 34.70 3.69
905 912 2.746362 GGTTGCAAATCTGTCTCCTCTG 59.254 50.000 0.00 0.00 0.00 3.35
926 933 3.579586 TGTATCTTTCGTTGGGTAGTGGT 59.420 43.478 0.00 0.00 0.00 4.16
934 941 2.774687 GTTGGGTAGTGGTTAGTGGTG 58.225 52.381 0.00 0.00 0.00 4.17
943 950 5.261040 AGTGGTTAGTGGTGGTAGTAGTA 57.739 43.478 0.00 0.00 0.00 1.82
948 955 6.015180 TGGTTAGTGGTGGTAGTAGTAACAAG 60.015 42.308 0.00 0.00 33.82 3.16
952 959 5.837438 AGTGGTGGTAGTAGTAACAAGTTCT 59.163 40.000 0.00 0.00 0.00 3.01
975 982 3.675348 TGGATTTGATGCAGGATCCTT 57.325 42.857 13.00 0.00 39.03 3.36
1035 1042 3.204382 AGAACAACAAGGGGAAGGAGAAA 59.796 43.478 0.00 0.00 0.00 2.52
1080 1093 3.487042 CCGACGATTCAGATTCAGTACGT 60.487 47.826 0.00 0.00 35.53 3.57
1135 1148 4.162690 CCCCGGAGCAGCAGGTAC 62.163 72.222 0.73 0.00 0.00 3.34
1183 1210 0.370273 CGATTCTGTTGGTAGTGCGC 59.630 55.000 0.00 0.00 0.00 6.09
1215 1242 3.438434 TGCGTTGCAATTCTGTGCTAATA 59.562 39.130 0.59 0.00 45.17 0.98
1230 1258 8.336987 TCTGTGCTAATAGATTCTAGGGCTATA 58.663 37.037 12.94 3.74 0.00 1.31
1258 1286 6.732531 TGTGTGATGTTTCTTGAGATGATC 57.267 37.500 0.00 0.00 0.00 2.92
1260 1288 6.370718 TGTGTGATGTTTCTTGAGATGATCTG 59.629 38.462 0.00 0.00 0.00 2.90
1270 1298 5.246883 TCTTGAGATGATCTGTTGTTCTGGA 59.753 40.000 0.00 0.00 0.00 3.86
1281 1309 2.655090 TGTTCTGGACAAATCTGGCA 57.345 45.000 0.00 0.00 34.69 4.92
1394 1428 5.068198 CGTGAATTTCATCCAATCCCTGAAT 59.932 40.000 1.78 0.00 0.00 2.57
1433 1467 4.390603 GGGAAAACAACTCACAAAACCAAC 59.609 41.667 0.00 0.00 0.00 3.77
1451 1485 3.105203 CAACAGACAAAAATCGCGTGTT 58.895 40.909 5.77 2.74 0.00 3.32
1452 1486 4.275662 CAACAGACAAAAATCGCGTGTTA 58.724 39.130 5.77 0.00 0.00 2.41
1453 1487 4.128554 ACAGACAAAAATCGCGTGTTAG 57.871 40.909 5.77 2.16 0.00 2.34
1454 1488 3.558418 ACAGACAAAAATCGCGTGTTAGT 59.442 39.130 5.77 2.79 0.00 2.24
1455 1489 4.141680 CAGACAAAAATCGCGTGTTAGTC 58.858 43.478 5.77 12.55 0.00 2.59
1456 1490 4.056050 AGACAAAAATCGCGTGTTAGTCT 58.944 39.130 5.77 14.36 0.00 3.24
1457 1491 4.510340 AGACAAAAATCGCGTGTTAGTCTT 59.490 37.500 5.77 2.40 30.32 3.01
1458 1492 5.007332 AGACAAAAATCGCGTGTTAGTCTTT 59.993 36.000 5.77 0.00 30.32 2.52
1459 1493 4.967575 ACAAAAATCGCGTGTTAGTCTTTG 59.032 37.500 5.77 11.85 0.00 2.77
1469 1503 3.883489 GTGTTAGTCTTTGGCTCCAACTT 59.117 43.478 0.00 0.00 35.46 2.66
1488 1522 7.068839 TCCAACTTTTGCATGGTAGTCTTTTTA 59.931 33.333 3.30 0.00 35.66 1.52
1500 1534 6.153000 TGGTAGTCTTTTTAAGGTTGCAACAA 59.847 34.615 29.55 13.82 0.00 2.83
1507 1573 8.257306 TCTTTTTAAGGTTGCAACAAAGAGAAT 58.743 29.630 29.55 9.33 0.00 2.40
1527 1593 6.284459 AGAATCTGATCCGATCTGTAAAACC 58.716 40.000 9.78 0.00 0.00 3.27
1532 1598 6.549736 TCTGATCCGATCTGTAAAACCATCTA 59.450 38.462 9.78 0.00 0.00 1.98
1533 1599 7.233553 TCTGATCCGATCTGTAAAACCATCTAT 59.766 37.037 9.78 0.00 0.00 1.98
1541 1607 8.873215 ATCTGTAAAACCATCTATAACACTCG 57.127 34.615 0.00 0.00 0.00 4.18
1547 1613 7.772332 AAACCATCTATAACACTCGTGAATC 57.228 36.000 3.74 0.00 0.00 2.52
1574 1640 2.671177 CGCACAAGGTCCGCTGAAG 61.671 63.158 1.37 0.00 0.00 3.02
1621 1693 3.260475 TGGTACCATCATTGACGGAAG 57.740 47.619 11.60 0.00 0.00 3.46
1655 1727 1.032114 GCAAGTACTGCCCCATGGTC 61.032 60.000 11.73 2.42 46.13 4.02
1720 1792 2.677228 CAGCACCAGGGTAAGGGG 59.323 66.667 0.00 0.00 0.00 4.79
1742 1814 1.387737 CCCATCTGCCCCCAAAGAA 59.612 57.895 0.00 0.00 0.00 2.52
1749 1821 1.000771 GCCCCCAAAGAAGTCTCCC 60.001 63.158 0.00 0.00 0.00 4.30
1750 1822 1.299976 CCCCCAAAGAAGTCTCCCG 59.700 63.158 0.00 0.00 0.00 5.14
1770 1846 3.049912 CGTGAGATGAGACGTTTGTTGA 58.950 45.455 0.00 0.00 0.00 3.18
1775 1851 3.248602 AGATGAGACGTTTGTTGAACAGC 59.751 43.478 0.00 0.00 38.18 4.40
1805 1884 1.101049 AACCAAAGTGGACTGCACGG 61.101 55.000 0.18 0.00 40.96 4.94
1822 1903 1.841663 CGGAAAGGGACTGTTGTGCG 61.842 60.000 0.00 0.00 40.86 5.34
1913 2023 4.856801 CGTGCATTCCCCTCCCCG 62.857 72.222 0.00 0.00 0.00 5.73
1975 2088 4.222353 AGAGGTGCTGAGCAAGGA 57.778 55.556 9.51 0.00 41.47 3.36
1976 2089 1.981636 AGAGGTGCTGAGCAAGGAG 59.018 57.895 9.51 0.00 41.47 3.69
1977 2090 1.078567 GAGGTGCTGAGCAAGGAGG 60.079 63.158 9.51 0.00 41.47 4.30
2047 2168 6.790319 AGATTGGTGGAGGTGTAAAAGTAAT 58.210 36.000 0.00 0.00 0.00 1.89
2055 2178 9.836076 GTGGAGGTGTAAAAGTAATAATTTGTC 57.164 33.333 0.00 0.00 0.00 3.18
2117 2245 8.051901 ACTTGTTAATGTAACTTTAGGATGCC 57.948 34.615 0.31 0.00 39.38 4.40
2154 2284 1.093159 CTTGGGAGAATGCTGTCAGC 58.907 55.000 18.32 18.32 42.82 4.26
2155 2285 0.694771 TTGGGAGAATGCTGTCAGCT 59.305 50.000 24.76 6.33 42.97 4.24
2156 2286 0.694771 TGGGAGAATGCTGTCAGCTT 59.305 50.000 24.76 16.37 42.97 3.74
2157 2287 1.908619 TGGGAGAATGCTGTCAGCTTA 59.091 47.619 24.76 6.86 42.97 3.09
2158 2288 2.305635 TGGGAGAATGCTGTCAGCTTAA 59.694 45.455 24.76 6.09 42.97 1.85
2159 2289 2.941720 GGGAGAATGCTGTCAGCTTAAG 59.058 50.000 24.76 0.00 42.97 1.85
2160 2290 3.604582 GGAGAATGCTGTCAGCTTAAGT 58.395 45.455 24.76 4.82 42.97 2.24
2161 2291 4.383118 GGGAGAATGCTGTCAGCTTAAGTA 60.383 45.833 24.76 4.55 42.97 2.24
2162 2292 5.178797 GGAGAATGCTGTCAGCTTAAGTAA 58.821 41.667 24.76 3.79 42.97 2.24
2163 2293 5.643777 GGAGAATGCTGTCAGCTTAAGTAAA 59.356 40.000 24.76 3.03 42.97 2.01
2164 2294 6.183360 GGAGAATGCTGTCAGCTTAAGTAAAG 60.183 42.308 24.76 0.00 42.97 1.85
2165 2295 6.234177 AGAATGCTGTCAGCTTAAGTAAAGT 58.766 36.000 24.76 1.76 42.97 2.66
2166 2296 6.712547 AGAATGCTGTCAGCTTAAGTAAAGTT 59.287 34.615 24.76 1.25 42.97 2.66
2167 2297 6.884280 ATGCTGTCAGCTTAAGTAAAGTTT 57.116 33.333 24.76 0.00 42.97 2.66
2168 2298 6.060028 TGCTGTCAGCTTAAGTAAAGTTTG 57.940 37.500 24.76 0.00 42.97 2.93
2169 2299 5.588648 TGCTGTCAGCTTAAGTAAAGTTTGT 59.411 36.000 24.76 0.00 42.97 2.83
2170 2300 6.094881 TGCTGTCAGCTTAAGTAAAGTTTGTT 59.905 34.615 24.76 0.00 42.97 2.83
2171 2301 6.972901 GCTGTCAGCTTAAGTAAAGTTTGTTT 59.027 34.615 17.89 0.00 38.45 2.83
2172 2302 7.488150 GCTGTCAGCTTAAGTAAAGTTTGTTTT 59.512 33.333 17.89 0.00 38.45 2.43
2173 2303 9.353999 CTGTCAGCTTAAGTAAAGTTTGTTTTT 57.646 29.630 4.02 0.00 37.53 1.94
2323 2481 1.050204 ATGATCTCTCCTCTGCCTGC 58.950 55.000 0.00 0.00 0.00 4.85
2371 2529 2.954316 TGTGAATGTACACGCCACTAG 58.046 47.619 18.72 0.00 42.86 2.57
2442 2600 7.951706 TTGTAAACAGTACAAGCGTTTTTAC 57.048 32.000 0.54 0.54 34.78 2.01
2443 2601 7.069852 TGTAAACAGTACAAGCGTTTTTACA 57.930 32.000 10.35 5.39 36.24 2.41
2444 2602 7.695820 TGTAAACAGTACAAGCGTTTTTACAT 58.304 30.769 10.35 0.00 34.60 2.29
2445 2603 8.824781 TGTAAACAGTACAAGCGTTTTTACATA 58.175 29.630 10.35 0.00 34.60 2.29
2446 2604 9.815936 GTAAACAGTACAAGCGTTTTTACATAT 57.184 29.630 10.35 0.00 34.78 1.78
2455 2613 8.324567 ACAAGCGTTTTTACATATGTTTTTGTG 58.675 29.630 14.77 2.32 0.00 3.33
2456 2614 7.401484 AGCGTTTTTACATATGTTTTTGTGG 57.599 32.000 14.77 0.29 0.00 4.17
2482 2640 5.900339 TTTACTTAGCCGATTCATAAGCG 57.100 39.130 0.00 0.00 40.52 4.68
2515 2673 7.382110 GGCCATGGACTATATATATGCTACAG 58.618 42.308 18.40 0.00 0.00 2.74
2544 2702 9.794719 AGTTAATTACTTATCTAGCCCCAAATC 57.205 33.333 0.00 0.00 31.29 2.17
2597 2755 4.818546 AGAGTGAGTGGAAAGTTCAACATG 59.181 41.667 1.52 0.00 33.44 3.21
2763 2921 4.156008 CAGAAAATGAAGGAGGTTTACCCG 59.844 45.833 0.00 0.00 38.74 5.28
2783 2941 5.012354 ACCCGAAACAATTTAGTCCTACTGA 59.988 40.000 0.00 0.00 0.00 3.41
2959 3134 5.163364 TGTGTTTTTCTAATTGGGTGCACAT 60.163 36.000 20.43 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 7.488792 TGTCATGATACATGCACTTAAAATTGC 59.511 33.333 0.00 0.00 39.33 3.56
84 86 5.046735 TGCCATGCACCATAAACTAAAATGT 60.047 36.000 0.00 0.00 31.71 2.71
198 201 6.206395 TGAATTGCCATGGTATTTACACTG 57.794 37.500 14.67 0.00 0.00 3.66
209 212 2.388310 TTGCACATGAATTGCCATGG 57.612 45.000 7.63 7.63 46.06 3.66
289 292 1.983605 TCGCGACGAGATCTTCAAAAC 59.016 47.619 3.71 0.00 0.00 2.43
372 375 9.394477 CGAGAATCTTTTCGGATTTTTAGTTTT 57.606 29.630 0.00 0.00 36.24 2.43
373 376 7.537649 GCGAGAATCTTTTCGGATTTTTAGTTT 59.462 33.333 5.22 0.00 36.24 2.66
374 377 7.021790 GCGAGAATCTTTTCGGATTTTTAGTT 58.978 34.615 5.22 0.00 36.24 2.24
375 378 6.148811 TGCGAGAATCTTTTCGGATTTTTAGT 59.851 34.615 5.22 0.00 36.24 2.24
376 379 6.542852 TGCGAGAATCTTTTCGGATTTTTAG 58.457 36.000 5.22 0.00 36.24 1.85
377 380 6.489127 TGCGAGAATCTTTTCGGATTTTTA 57.511 33.333 5.22 0.00 36.24 1.52
378 381 5.371115 TGCGAGAATCTTTTCGGATTTTT 57.629 34.783 5.22 0.00 36.24 1.94
379 382 5.567138 ATGCGAGAATCTTTTCGGATTTT 57.433 34.783 4.43 0.00 43.79 1.82
380 383 5.584649 TGTATGCGAGAATCTTTTCGGATTT 59.415 36.000 13.41 0.00 43.79 2.17
381 384 5.116180 TGTATGCGAGAATCTTTTCGGATT 58.884 37.500 13.41 0.00 43.79 3.01
382 385 4.693283 TGTATGCGAGAATCTTTTCGGAT 58.307 39.130 12.91 12.91 46.93 4.18
383 386 4.118093 TGTATGCGAGAATCTTTTCGGA 57.882 40.909 5.22 2.71 41.27 4.55
384 387 4.766007 CATGTATGCGAGAATCTTTTCGG 58.234 43.478 5.22 0.00 36.93 4.30
385 388 4.206843 GCATGTATGCGAGAATCTTTTCG 58.793 43.478 0.53 0.00 44.67 3.46
399 402 1.528161 ACGTCATCGCATGCATGTATG 59.472 47.619 26.79 26.26 41.18 2.39
400 403 1.528161 CACGTCATCGCATGCATGTAT 59.472 47.619 26.79 17.72 41.18 2.29
401 404 0.929615 CACGTCATCGCATGCATGTA 59.070 50.000 26.79 16.27 41.18 2.29
402 405 0.740516 TCACGTCATCGCATGCATGT 60.741 50.000 26.79 6.64 41.18 3.21
403 406 0.315625 GTCACGTCATCGCATGCATG 60.316 55.000 22.70 22.70 41.18 4.06
404 407 0.740516 TGTCACGTCATCGCATGCAT 60.741 50.000 19.57 7.64 41.18 3.96
405 408 0.948141 TTGTCACGTCATCGCATGCA 60.948 50.000 19.57 5.34 41.18 3.96
406 409 0.374758 ATTGTCACGTCATCGCATGC 59.625 50.000 7.91 7.91 41.18 4.06
407 410 1.929169 AGATTGTCACGTCATCGCATG 59.071 47.619 0.00 0.00 41.18 4.06
408 411 2.299993 AGATTGTCACGTCATCGCAT 57.700 45.000 0.00 0.00 41.18 4.73
409 412 2.931512 TAGATTGTCACGTCATCGCA 57.068 45.000 0.00 0.00 41.18 5.10
410 413 4.508971 CAAATAGATTGTCACGTCATCGC 58.491 43.478 0.00 0.00 36.00 4.58
411 414 4.032786 TGCAAATAGATTGTCACGTCATCG 59.967 41.667 0.00 0.00 41.32 3.84
412 415 5.469373 TGCAAATAGATTGTCACGTCATC 57.531 39.130 0.00 0.00 41.32 2.92
413 416 6.441093 AATGCAAATAGATTGTCACGTCAT 57.559 33.333 0.00 0.00 41.32 3.06
414 417 5.878332 AATGCAAATAGATTGTCACGTCA 57.122 34.783 0.00 0.00 41.32 4.35
415 418 7.222805 TCTCTAATGCAAATAGATTGTCACGTC 59.777 37.037 11.67 0.00 41.32 4.34
416 419 7.010552 GTCTCTAATGCAAATAGATTGTCACGT 59.989 37.037 11.67 0.00 41.32 4.49
417 420 7.010460 TGTCTCTAATGCAAATAGATTGTCACG 59.990 37.037 11.67 1.62 41.32 4.35
418 421 8.201554 TGTCTCTAATGCAAATAGATTGTCAC 57.798 34.615 11.67 6.28 41.32 3.67
419 422 8.833493 CATGTCTCTAATGCAAATAGATTGTCA 58.167 33.333 11.67 7.08 41.32 3.58
420 423 8.834465 ACATGTCTCTAATGCAAATAGATTGTC 58.166 33.333 11.67 2.84 41.32 3.18
421 424 8.618677 CACATGTCTCTAATGCAAATAGATTGT 58.381 33.333 11.67 10.42 41.32 2.71
422 425 8.074370 CCACATGTCTCTAATGCAAATAGATTG 58.926 37.037 11.67 9.97 42.21 2.67
423 426 7.776969 ACCACATGTCTCTAATGCAAATAGATT 59.223 33.333 11.67 0.00 0.00 2.40
424 427 7.228108 CACCACATGTCTCTAATGCAAATAGAT 59.772 37.037 11.67 0.00 0.00 1.98
425 428 6.539826 CACCACATGTCTCTAATGCAAATAGA 59.460 38.462 10.98 10.98 0.00 1.98
426 429 6.722301 CACCACATGTCTCTAATGCAAATAG 58.278 40.000 0.00 0.00 0.00 1.73
427 430 5.066375 GCACCACATGTCTCTAATGCAAATA 59.934 40.000 0.00 0.00 0.00 1.40
428 431 4.142315 GCACCACATGTCTCTAATGCAAAT 60.142 41.667 0.00 0.00 0.00 2.32
429 432 3.191162 GCACCACATGTCTCTAATGCAAA 59.809 43.478 0.00 0.00 0.00 3.68
430 433 2.749076 GCACCACATGTCTCTAATGCAA 59.251 45.455 0.00 0.00 0.00 4.08
431 434 2.358957 GCACCACATGTCTCTAATGCA 58.641 47.619 0.00 0.00 0.00 3.96
432 435 1.328680 CGCACCACATGTCTCTAATGC 59.671 52.381 0.00 0.00 0.00 3.56
433 436 2.621338 ACGCACCACATGTCTCTAATG 58.379 47.619 0.00 0.00 0.00 1.90
434 437 4.501571 GGATACGCACCACATGTCTCTAAT 60.502 45.833 0.00 0.00 0.00 1.73
435 438 3.181479 GGATACGCACCACATGTCTCTAA 60.181 47.826 0.00 0.00 0.00 2.10
436 439 2.361119 GGATACGCACCACATGTCTCTA 59.639 50.000 0.00 0.00 0.00 2.43
437 440 1.137086 GGATACGCACCACATGTCTCT 59.863 52.381 0.00 0.00 0.00 3.10
438 441 1.137086 AGGATACGCACCACATGTCTC 59.863 52.381 0.00 0.00 46.39 3.36
439 442 1.195115 AGGATACGCACCACATGTCT 58.805 50.000 0.00 0.00 46.39 3.41
440 443 2.024176 AAGGATACGCACCACATGTC 57.976 50.000 0.00 0.00 46.39 3.06
441 444 2.356135 GAAAGGATACGCACCACATGT 58.644 47.619 0.00 0.00 46.39 3.21
442 445 1.670811 GGAAAGGATACGCACCACATG 59.329 52.381 0.00 0.00 46.39 3.21
443 446 1.559682 AGGAAAGGATACGCACCACAT 59.440 47.619 0.00 0.00 46.39 3.21
444 447 0.981183 AGGAAAGGATACGCACCACA 59.019 50.000 0.00 0.00 46.39 4.17
445 448 1.338769 ACAGGAAAGGATACGCACCAC 60.339 52.381 0.00 0.00 46.39 4.16
446 449 0.981183 ACAGGAAAGGATACGCACCA 59.019 50.000 0.00 0.00 46.39 4.17
447 450 1.066430 TGACAGGAAAGGATACGCACC 60.066 52.381 0.00 0.00 46.39 5.01
448 451 2.000447 GTGACAGGAAAGGATACGCAC 59.000 52.381 0.00 0.00 46.39 5.34
449 452 1.621317 TGTGACAGGAAAGGATACGCA 59.379 47.619 0.00 0.00 46.39 5.24
450 453 2.000447 GTGTGACAGGAAAGGATACGC 59.000 52.381 0.00 0.00 46.39 4.42
451 454 2.259618 CGTGTGACAGGAAAGGATACG 58.740 52.381 0.00 0.00 46.39 3.06
452 455 2.993899 CACGTGTGACAGGAAAGGATAC 59.006 50.000 12.67 0.00 0.00 2.24
453 456 2.631062 ACACGTGTGACAGGAAAGGATA 59.369 45.455 22.71 0.00 0.00 2.59
454 457 1.416401 ACACGTGTGACAGGAAAGGAT 59.584 47.619 22.71 0.00 0.00 3.24
455 458 0.828022 ACACGTGTGACAGGAAAGGA 59.172 50.000 22.71 0.00 0.00 3.36
456 459 3.379650 ACACGTGTGACAGGAAAGG 57.620 52.632 22.71 1.51 0.00 3.11
466 469 3.361627 CGTCAATAACTGTCACACGTGTG 60.362 47.826 37.04 37.04 46.91 3.82
467 470 2.792674 CGTCAATAACTGTCACACGTGT 59.207 45.455 17.22 17.22 0.00 4.49
468 471 2.792674 ACGTCAATAACTGTCACACGTG 59.207 45.455 15.48 15.48 34.53 4.49
469 472 3.088194 ACGTCAATAACTGTCACACGT 57.912 42.857 0.00 0.00 31.88 4.49
470 473 3.734231 AGAACGTCAATAACTGTCACACG 59.266 43.478 0.00 0.00 0.00 4.49
471 474 5.652744 AAGAACGTCAATAACTGTCACAC 57.347 39.130 0.00 0.00 0.00 3.82
472 475 7.956420 ATAAAGAACGTCAATAACTGTCACA 57.044 32.000 0.00 0.00 0.00 3.58
473 476 9.659830 AAAATAAAGAACGTCAATAACTGTCAC 57.340 29.630 0.00 0.00 0.00 3.67
497 500 9.235537 GCTTACAGTGGTATTTTTCGTTAAAAA 57.764 29.630 0.00 0.00 45.89 1.94
498 501 8.404000 TGCTTACAGTGGTATTTTTCGTTAAAA 58.596 29.630 0.00 1.81 39.88 1.52
499 502 7.856894 GTGCTTACAGTGGTATTTTTCGTTAAA 59.143 33.333 0.00 0.00 0.00 1.52
500 503 7.227116 AGTGCTTACAGTGGTATTTTTCGTTAA 59.773 33.333 0.00 0.00 0.00 2.01
501 504 6.707161 AGTGCTTACAGTGGTATTTTTCGTTA 59.293 34.615 0.00 0.00 0.00 3.18
502 505 5.529800 AGTGCTTACAGTGGTATTTTTCGTT 59.470 36.000 0.00 0.00 0.00 3.85
528 532 0.763652 TACGCTCTCCCTCCGTATCT 59.236 55.000 0.00 0.00 36.51 1.98
581 587 5.995282 TGACGTGGACAAGTTATCTTTTCAT 59.005 36.000 0.00 0.00 33.51 2.57
643 650 2.460669 AGCTTTTATTTCCTGCCTGGG 58.539 47.619 0.00 0.00 36.20 4.45
657 664 5.763698 GTCCTCTAACTTGTGGTAAGCTTTT 59.236 40.000 3.20 0.00 0.00 2.27
676 683 4.815308 TCTACGTACAGATTAGCAGTCCTC 59.185 45.833 0.00 0.00 0.00 3.71
711 718 2.477375 TCTTCTAAATTTGTTCGCGCGT 59.523 40.909 30.98 10.38 0.00 6.01
722 729 5.560183 CGCCAGACGTGTTTTCTTCTAAATT 60.560 40.000 0.00 0.00 36.87 1.82
780 787 6.045106 TCCTTTTAAAGTCCCAGGAGTATTGT 59.955 38.462 3.91 0.00 0.00 2.71
812 819 2.335011 GTGACAAACTTGGCGCCC 59.665 61.111 26.77 5.97 40.79 6.13
894 901 4.974368 ACGAAAGATACAGAGGAGACAG 57.026 45.455 0.00 0.00 0.00 3.51
900 907 3.611766 ACCCAACGAAAGATACAGAGG 57.388 47.619 0.00 0.00 0.00 3.69
904 911 3.579586 ACCACTACCCAACGAAAGATACA 59.420 43.478 0.00 0.00 0.00 2.29
905 912 4.198028 ACCACTACCCAACGAAAGATAC 57.802 45.455 0.00 0.00 0.00 2.24
926 933 7.506938 AGAACTTGTTACTACTACCACCACTAA 59.493 37.037 0.00 0.00 0.00 2.24
948 955 3.507233 TCCTGCATCAAATCCAACAGAAC 59.493 43.478 0.00 0.00 0.00 3.01
952 959 3.025978 GGATCCTGCATCAAATCCAACA 58.974 45.455 3.84 0.00 38.05 3.33
1035 1042 2.510238 GACTCCGAGCAGCGCATT 60.510 61.111 11.47 0.00 39.11 3.56
1135 1148 4.329489 CAAGCGAGAATTCAACAGAATCG 58.671 43.478 8.44 7.38 30.96 3.34
1139 1152 2.481568 CTGCAAGCGAGAATTCAACAGA 59.518 45.455 8.44 0.00 0.00 3.41
1183 1210 5.510674 CAGAATTGCAACGCAGAAGATAAAG 59.489 40.000 0.00 0.00 40.61 1.85
1215 1242 8.494433 TCACACAAAAATATAGCCCTAGAATCT 58.506 33.333 0.00 0.00 0.00 2.40
1230 1258 8.415553 TCATCTCAAGAAACATCACACAAAAAT 58.584 29.630 0.00 0.00 0.00 1.82
1236 1264 6.370994 ACAGATCATCTCAAGAAACATCACAC 59.629 38.462 0.00 0.00 0.00 3.82
1433 1467 4.084537 AGACTAACACGCGATTTTTGTCTG 60.085 41.667 23.17 12.86 35.10 3.51
1451 1485 3.317993 GCAAAAGTTGGAGCCAAAGACTA 59.682 43.478 3.05 0.00 37.70 2.59
1452 1486 2.101415 GCAAAAGTTGGAGCCAAAGACT 59.899 45.455 3.05 0.00 37.70 3.24
1453 1487 2.159114 TGCAAAAGTTGGAGCCAAAGAC 60.159 45.455 3.05 0.00 37.70 3.01
1454 1488 2.106566 TGCAAAAGTTGGAGCCAAAGA 58.893 42.857 3.05 0.00 37.70 2.52
1455 1489 2.600470 TGCAAAAGTTGGAGCCAAAG 57.400 45.000 3.05 0.00 37.70 2.77
1456 1490 2.485124 CCATGCAAAAGTTGGAGCCAAA 60.485 45.455 3.05 0.00 37.70 3.28
1457 1491 1.070445 CCATGCAAAAGTTGGAGCCAA 59.930 47.619 0.00 0.00 33.40 4.52
1458 1492 0.680618 CCATGCAAAAGTTGGAGCCA 59.319 50.000 0.00 0.00 33.40 4.75
1459 1493 0.681175 ACCATGCAAAAGTTGGAGCC 59.319 50.000 10.25 0.00 33.40 4.70
1469 1503 6.969993 ACCTTAAAAAGACTACCATGCAAA 57.030 33.333 0.00 0.00 0.00 3.68
1488 1522 4.889409 TCAGATTCTCTTTGTTGCAACCTT 59.111 37.500 26.14 2.63 0.00 3.50
1500 1534 6.968263 TTACAGATCGGATCAGATTCTCTT 57.032 37.500 19.47 0.00 0.00 2.85
1507 1573 5.363868 AGATGGTTTTACAGATCGGATCAGA 59.636 40.000 19.47 0.00 0.00 3.27
1523 1589 7.556844 AGATTCACGAGTGTTATAGATGGTTT 58.443 34.615 2.97 0.00 0.00 3.27
1527 1593 6.476706 TGCAAGATTCACGAGTGTTATAGATG 59.523 38.462 2.97 0.00 0.00 2.90
1532 1598 4.820897 TCTGCAAGATTCACGAGTGTTAT 58.179 39.130 2.97 0.00 38.67 1.89
1533 1599 4.237724 CTCTGCAAGATTCACGAGTGTTA 58.762 43.478 2.97 0.00 45.62 2.41
1566 1632 0.319383 CGATCCCTGATCTTCAGCGG 60.319 60.000 0.00 3.05 42.98 5.52
1574 1640 2.289945 CCATCCCTTTCGATCCCTGATC 60.290 54.545 0.00 0.00 35.88 2.92
1621 1693 0.318445 CTTGCACTGCCAGTTTCTGC 60.318 55.000 0.00 0.00 0.00 4.26
1670 1742 1.001641 ATGCTTGAGGCTGGTGACC 60.002 57.895 0.00 0.00 42.39 4.02
1733 1805 0.321653 CACGGGAGACTTCTTTGGGG 60.322 60.000 0.00 0.00 0.00 4.96
1749 1821 3.049912 TCAACAAACGTCTCATCTCACG 58.950 45.455 0.00 0.00 41.90 4.35
1750 1822 4.270084 TGTTCAACAAACGTCTCATCTCAC 59.730 41.667 0.00 0.00 41.02 3.51
1770 1846 1.600916 GTTTCCGCCTCCTGCTGTT 60.601 57.895 0.00 0.00 38.05 3.16
1775 1851 0.537371 ACTTTGGTTTCCGCCTCCTG 60.537 55.000 0.00 0.00 0.00 3.86
1805 1884 1.949257 CCGCACAACAGTCCCTTTC 59.051 57.895 0.00 0.00 0.00 2.62
1896 2006 4.856801 CGGGGAGGGGAATGCACG 62.857 72.222 0.00 0.00 0.00 5.34
1913 2023 2.283298 AGACGTGTCATGAATGATGCC 58.717 47.619 0.00 0.00 39.30 4.40
1975 2088 3.013932 CCTTGGCCTGCTCCTCCT 61.014 66.667 3.32 0.00 0.00 3.69
1976 2089 3.011517 TCCTTGGCCTGCTCCTCC 61.012 66.667 3.32 0.00 0.00 4.30
1977 2090 2.250741 GAGTCCTTGGCCTGCTCCTC 62.251 65.000 3.32 0.05 0.00 3.71
2047 2168 4.693566 CGCAGAGGTTAAGGTGACAAATTA 59.306 41.667 0.00 0.00 0.00 1.40
2109 2237 6.558775 AGGAAAATACTGTATGAGGCATCCTA 59.441 38.462 0.22 0.00 31.76 2.94
2117 2245 6.889198 TCCCAAGAGGAAAATACTGTATGAG 58.111 40.000 0.22 0.00 43.78 2.90
2171 2301 9.651913 ACTTTTCTTGAGACTAATTTGCAAAAA 57.348 25.926 17.19 6.69 0.00 1.94
2172 2302 9.651913 AACTTTTCTTGAGACTAATTTGCAAAA 57.348 25.926 17.19 0.00 0.00 2.44
2173 2303 9.086336 CAACTTTTCTTGAGACTAATTTGCAAA 57.914 29.630 15.44 15.44 0.00 3.68
2174 2304 7.222611 GCAACTTTTCTTGAGACTAATTTGCAA 59.777 33.333 16.55 0.00 36.13 4.08
2175 2305 6.697019 GCAACTTTTCTTGAGACTAATTTGCA 59.303 34.615 16.55 0.00 36.13 4.08
2176 2306 6.697019 TGCAACTTTTCTTGAGACTAATTTGC 59.303 34.615 15.55 15.55 36.35 3.68
2177 2307 8.807667 ATGCAACTTTTCTTGAGACTAATTTG 57.192 30.769 0.00 0.00 0.00 2.32
2179 2309 9.899226 GTAATGCAACTTTTCTTGAGACTAATT 57.101 29.630 0.00 0.00 0.00 1.40
2180 2310 8.515414 GGTAATGCAACTTTTCTTGAGACTAAT 58.485 33.333 0.00 0.00 0.00 1.73
2181 2311 7.500892 TGGTAATGCAACTTTTCTTGAGACTAA 59.499 33.333 0.00 0.00 0.00 2.24
2182 2312 6.995686 TGGTAATGCAACTTTTCTTGAGACTA 59.004 34.615 0.00 0.00 0.00 2.59
2183 2313 5.827797 TGGTAATGCAACTTTTCTTGAGACT 59.172 36.000 0.00 0.00 0.00 3.24
2184 2314 6.072112 TGGTAATGCAACTTTTCTTGAGAC 57.928 37.500 0.00 0.00 0.00 3.36
2188 2318 9.474920 TTCTAAATGGTAATGCAACTTTTCTTG 57.525 29.630 0.00 0.00 0.00 3.02
2264 2422 3.888934 ACGTGCAACTTTTAGCATTCAG 58.111 40.909 0.00 0.00 43.44 3.02
2323 2481 2.820059 TATGCGCCAGTAGATTGAGG 57.180 50.000 4.18 0.00 0.00 3.86
2445 2603 7.810759 CGGCTAAGTAAATAACCACAAAAACAT 59.189 33.333 0.00 0.00 0.00 2.71
2446 2604 7.013083 TCGGCTAAGTAAATAACCACAAAAACA 59.987 33.333 0.00 0.00 0.00 2.83
2455 2613 8.228464 GCTTATGAATCGGCTAAGTAAATAACC 58.772 37.037 0.00 0.00 0.00 2.85
2456 2614 7.950496 CGCTTATGAATCGGCTAAGTAAATAAC 59.050 37.037 0.00 0.00 0.00 1.89
2482 2640 3.508845 ATAGTCCATGGCCCATAACAC 57.491 47.619 6.96 0.00 0.00 3.32
2515 2673 9.623000 TTGGGGCTAGATAAGTAATTAACTTTC 57.377 33.333 0.00 0.00 46.61 2.62
2525 2683 8.232412 TCTTCTAGATTTGGGGCTAGATAAGTA 58.768 37.037 0.00 0.00 41.78 2.24
2544 2702 2.634815 ATGGCATGGCAGTCTTCTAG 57.365 50.000 27.02 0.00 0.00 2.43
2763 2921 8.837389 ACACTTTCAGTAGGACTAAATTGTTTC 58.163 33.333 0.00 0.00 0.00 2.78
2783 2941 7.201522 GCTTGCTTTTAACAGCTAAAACACTTT 60.202 33.333 14.37 0.00 40.79 2.66
2829 2987 9.703892 CTGATGGTTTCCATAATTTGTTAAACA 57.296 29.630 0.99 0.00 45.26 2.83
2959 3134 2.824936 CACCCATGGTTTCTATGCAACA 59.175 45.455 11.73 0.00 31.02 3.33


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

AutoCloner maintained by Alex Coulton.