Multiple sequence alignment - TraesCS7D01G121300

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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 TraesCS7D01G121300 chr7D 100.000 4355 0 0 1 4355 75338143 75342497 0.000000e+00 8043.0
1 TraesCS7D01G121300 chr7D 98.093 2465 44 3 1894 4355 530113858 530116322 0.000000e+00 4289.0
2 TraesCS7D01G121300 chr7D 84.615 78 7 5 3280 3355 197692394 197692468 6.040000e-09 73.1
3 TraesCS7D01G121300 chr4B 94.866 2941 128 4 1415 4354 450853747 450856665 0.000000e+00 4573.0
4 TraesCS7D01G121300 chr4B 94.672 807 43 0 605 1411 450852812 450853618 0.000000e+00 1253.0
5 TraesCS7D01G121300 chr3D 98.097 2260 40 3 2097 4355 608043765 608041508 0.000000e+00 3932.0
6 TraesCS7D01G121300 chr5A 83.995 3805 530 54 592 4354 601481176 601477409 0.000000e+00 3579.0
7 TraesCS7D01G121300 chr2B 95.206 2211 100 5 2145 4354 95858571 95856366 0.000000e+00 3491.0
8 TraesCS7D01G121300 chr1A 83.403 3808 554 56 588 4354 484280345 484276575 0.000000e+00 3459.0
9 TraesCS7D01G121300 chr5B 87.968 881 100 6 3478 4354 299625926 299626804 0.000000e+00 1035.0
10 TraesCS7D01G121300 chr5B 80.412 97 15 4 3286 3380 483852843 483852749 2.170000e-08 71.3
11 TraesCS7D01G121300 chr4A 96.192 604 22 1 3752 4354 674428258 674428861 0.000000e+00 987.0
12 TraesCS7D01G121300 chr7A 87.696 447 40 10 109 543 79634199 79634642 1.400000e-139 507.0
13 TraesCS7D01G121300 chr7B 82.639 576 55 31 1 557 21658315 21658864 6.590000e-128 468.0
14 TraesCS7D01G121300 chr2D 82.400 125 19 3 438 561 357287866 357287744 5.960000e-19 106.0
15 TraesCS7D01G121300 chr6A 79.381 97 16 4 3286 3380 13688875 13688781 1.010000e-06 65.8
16 TraesCS7D01G121300 chr4D 100.000 28 0 0 569 596 63222066 63222093 8.000000e-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 TraesCS7D01G121300 chr7D 75338143 75342497 4354 False 8043 8043 100.000 1 4355 1 chr7D.!!$F1 4354
1 TraesCS7D01G121300 chr7D 530113858 530116322 2464 False 4289 4289 98.093 1894 4355 1 chr7D.!!$F3 2461
2 TraesCS7D01G121300 chr4B 450852812 450856665 3853 False 2913 4573 94.769 605 4354 2 chr4B.!!$F1 3749
3 TraesCS7D01G121300 chr3D 608041508 608043765 2257 True 3932 3932 98.097 2097 4355 1 chr3D.!!$R1 2258
4 TraesCS7D01G121300 chr5A 601477409 601481176 3767 True 3579 3579 83.995 592 4354 1 chr5A.!!$R1 3762
5 TraesCS7D01G121300 chr2B 95856366 95858571 2205 True 3491 3491 95.206 2145 4354 1 chr2B.!!$R1 2209
6 TraesCS7D01G121300 chr1A 484276575 484280345 3770 True 3459 3459 83.403 588 4354 1 chr1A.!!$R1 3766
7 TraesCS7D01G121300 chr5B 299625926 299626804 878 False 1035 1035 87.968 3478 4354 1 chr5B.!!$F1 876
8 TraesCS7D01G121300 chr4A 674428258 674428861 603 False 987 987 96.192 3752 4354 1 chr4A.!!$F1 602
9 TraesCS7D01G121300 chr7B 21658315 21658864 549 False 468 468 82.639 1 557 1 chr7B.!!$F1 556

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
969 1003 0.035458 AGGACAAAGAAGAGGCACCG 59.965 55.000 0.0 0.0 0.00 4.94 F
970 1004 0.250338 GGACAAAGAAGAGGCACCGT 60.250 55.000 0.0 0.0 0.00 4.83 F
1751 1934 0.885879 TGTAAGTGGCTCATCGTCGT 59.114 50.000 0.0 0.0 0.00 4.34 F
2342 2525 1.142097 GGTTCTCTACGGAGCAGCC 59.858 63.158 0.0 0.0 39.31 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2003 0.392863 TTCTGTCATGTCCCCATGCG 60.393 55.000 0.00 0.0 46.64 4.73 R
2342 2525 1.224075 CATCTTGTATGGCGAGGCAG 58.776 55.000 5.43 0.0 0.00 4.85 R
2586 2769 1.649664 CCTTGAGATTCTCCACAGCG 58.350 55.000 11.12 0.0 0.00 5.18 R
3732 3917 2.432300 ATGGTCCCGGCGAGGTTAG 61.432 63.158 9.30 0.0 38.74 2.34 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
101 102 1.136336 GCGTCGGAATCGGCATTTATC 60.136 52.381 0.00 0.00 41.75 1.75
117 121 2.154854 TATCCCGTACGTACTCTCCG 57.845 55.000 22.55 9.62 0.00 4.63
170 178 2.228343 CGTCTCCAGGACTTTCGTACTT 59.772 50.000 0.00 0.00 42.44 2.24
179 190 3.061697 GGACTTTCGTACTTGCCGTATTG 59.938 47.826 0.00 0.00 0.00 1.90
184 195 6.202570 ACTTTCGTACTTGCCGTATTGTTTTA 59.797 34.615 0.00 0.00 0.00 1.52
185 196 6.724694 TTCGTACTTGCCGTATTGTTTTAT 57.275 33.333 0.00 0.00 0.00 1.40
205 216 9.660180 GTTTTATTTTATTATGGTGGGAAAGCA 57.340 29.630 0.00 0.00 41.41 3.91
207 218 4.974368 TTTATTATGGTGGGAAAGCACG 57.026 40.909 0.00 0.00 39.59 5.34
208 219 2.507407 ATTATGGTGGGAAAGCACGT 57.493 45.000 0.00 0.00 39.59 4.49
209 220 3.637911 ATTATGGTGGGAAAGCACGTA 57.362 42.857 0.00 0.00 39.59 3.57
244 256 8.845648 CGTTTTCTTGCATATTTTATTGTCGAA 58.154 29.630 0.00 0.00 0.00 3.71
264 280 0.314302 AAAGAGCGAGCACGTACTGT 59.686 50.000 5.23 0.00 41.98 3.55
267 283 2.558378 AGAGCGAGCACGTACTGTATA 58.442 47.619 5.23 0.00 41.98 1.47
268 284 2.544686 AGAGCGAGCACGTACTGTATAG 59.455 50.000 5.23 0.00 41.98 1.31
272 288 2.537214 CGAGCACGTACTGTATAGACGA 59.463 50.000 14.75 0.00 39.81 4.20
279 295 3.545624 CGTACTGTATAGACGACACTGGC 60.546 52.174 0.00 0.00 38.88 4.85
280 296 1.749634 ACTGTATAGACGACACTGGCC 59.250 52.381 0.00 0.00 0.00 5.36
282 298 1.341679 TGTATAGACGACACTGGCCCT 60.342 52.381 0.00 0.00 0.00 5.19
289 305 0.752658 CGACACTGGCCCTCATGATA 59.247 55.000 0.00 0.00 0.00 2.15
330 346 2.508663 GTGGCGCGTCTCCTAACC 60.509 66.667 13.81 0.00 0.00 2.85
331 347 2.992689 TGGCGCGTCTCCTAACCA 60.993 61.111 13.81 2.44 0.00 3.67
345 361 4.733165 TCCTAACCACACACTACTACACT 58.267 43.478 0.00 0.00 0.00 3.55
354 370 4.159879 ACACACTACTACACTAGAATGGCC 59.840 45.833 0.00 0.00 0.00 5.36
360 376 4.097418 ACTACACTAGAATGGCCAAGACT 58.903 43.478 10.96 12.23 0.00 3.24
362 378 2.906389 ACACTAGAATGGCCAAGACTGA 59.094 45.455 10.96 0.00 0.00 3.41
363 379 3.055530 ACACTAGAATGGCCAAGACTGAG 60.056 47.826 10.96 5.31 0.00 3.35
370 386 1.576421 GCCAAGACTGAGGTTTGCG 59.424 57.895 0.00 0.00 0.00 4.85
382 398 4.922719 TGAGGTTTGCGTAAAATTTTCGT 58.077 34.783 6.72 0.00 0.00 3.85
390 406 7.784790 TTGCGTAAAATTTTCGTTCTATTCC 57.215 32.000 6.72 0.00 0.00 3.01
391 407 6.900189 TGCGTAAAATTTTCGTTCTATTCCA 58.100 32.000 6.72 0.47 0.00 3.53
392 408 7.531716 TGCGTAAAATTTTCGTTCTATTCCAT 58.468 30.769 6.72 0.00 0.00 3.41
393 409 8.024285 TGCGTAAAATTTTCGTTCTATTCCATT 58.976 29.630 6.72 0.00 0.00 3.16
394 410 8.311120 GCGTAAAATTTTCGTTCTATTCCATTG 58.689 33.333 6.72 0.00 0.00 2.82
395 411 9.549509 CGTAAAATTTTCGTTCTATTCCATTGA 57.450 29.630 6.72 0.00 0.00 2.57
400 416 9.740239 AATTTTCGTTCTATTCCATTGATCATG 57.260 29.630 0.00 0.00 0.00 3.07
401 417 8.504812 TTTTCGTTCTATTCCATTGATCATGA 57.495 30.769 0.00 0.00 34.31 3.07
402 418 7.482654 TTCGTTCTATTCCATTGATCATGAC 57.517 36.000 0.00 0.00 34.31 3.06
403 419 6.581712 TCGTTCTATTCCATTGATCATGACA 58.418 36.000 0.00 0.00 34.31 3.58
404 420 6.479990 TCGTTCTATTCCATTGATCATGACAC 59.520 38.462 0.00 0.00 34.31 3.67
405 421 6.258507 CGTTCTATTCCATTGATCATGACACA 59.741 38.462 0.00 0.00 34.31 3.72
406 422 7.517893 CGTTCTATTCCATTGATCATGACACAG 60.518 40.741 0.00 0.00 34.31 3.66
407 423 4.913335 ATTCCATTGATCATGACACAGC 57.087 40.909 0.00 0.00 34.31 4.40
408 424 2.282407 TCCATTGATCATGACACAGCG 58.718 47.619 0.00 0.00 34.31 5.18
409 425 2.093553 TCCATTGATCATGACACAGCGA 60.094 45.455 0.00 0.00 34.31 4.93
410 426 2.287103 CCATTGATCATGACACAGCGAG 59.713 50.000 0.00 0.00 34.31 5.03
411 427 3.192466 CATTGATCATGACACAGCGAGA 58.808 45.455 0.00 0.00 34.31 4.04
412 428 2.284263 TGATCATGACACAGCGAGAC 57.716 50.000 0.00 0.00 0.00 3.36
413 429 1.545582 TGATCATGACACAGCGAGACA 59.454 47.619 0.00 0.00 0.00 3.41
414 430 2.029110 TGATCATGACACAGCGAGACAA 60.029 45.455 0.00 0.00 0.00 3.18
415 431 2.524569 TCATGACACAGCGAGACAAA 57.475 45.000 0.00 0.00 0.00 2.83
416 432 2.832563 TCATGACACAGCGAGACAAAA 58.167 42.857 0.00 0.00 0.00 2.44
417 433 3.202097 TCATGACACAGCGAGACAAAAA 58.798 40.909 0.00 0.00 0.00 1.94
452 468 8.839310 ATTACATTCATAGACCATCTAGCAAC 57.161 34.615 0.00 0.00 31.67 4.17
453 469 5.292765 ACATTCATAGACCATCTAGCAACG 58.707 41.667 0.00 0.00 31.67 4.10
454 470 5.069119 ACATTCATAGACCATCTAGCAACGA 59.931 40.000 0.00 0.00 31.67 3.85
455 471 4.569761 TCATAGACCATCTAGCAACGAC 57.430 45.455 0.00 0.00 31.67 4.34
456 472 4.207955 TCATAGACCATCTAGCAACGACT 58.792 43.478 0.00 0.00 31.67 4.18
457 473 5.374071 TCATAGACCATCTAGCAACGACTA 58.626 41.667 0.00 0.00 31.67 2.59
458 474 6.004574 TCATAGACCATCTAGCAACGACTAT 58.995 40.000 0.00 0.00 31.67 2.12
459 475 7.166167 TCATAGACCATCTAGCAACGACTATA 58.834 38.462 0.00 0.00 31.67 1.31
460 476 7.664318 TCATAGACCATCTAGCAACGACTATAA 59.336 37.037 0.00 0.00 31.67 0.98
461 477 6.710597 AGACCATCTAGCAACGACTATAAA 57.289 37.500 0.00 0.00 0.00 1.40
462 478 7.291411 AGACCATCTAGCAACGACTATAAAT 57.709 36.000 0.00 0.00 0.00 1.40
463 479 8.405418 AGACCATCTAGCAACGACTATAAATA 57.595 34.615 0.00 0.00 0.00 1.40
464 480 8.298140 AGACCATCTAGCAACGACTATAAATAC 58.702 37.037 0.00 0.00 0.00 1.89
465 481 8.179509 ACCATCTAGCAACGACTATAAATACT 57.820 34.615 0.00 0.00 0.00 2.12
466 482 8.082852 ACCATCTAGCAACGACTATAAATACTG 58.917 37.037 0.00 0.00 0.00 2.74
467 483 8.297426 CCATCTAGCAACGACTATAAATACTGA 58.703 37.037 0.00 0.00 0.00 3.41
468 484 9.678941 CATCTAGCAACGACTATAAATACTGAA 57.321 33.333 0.00 0.00 0.00 3.02
469 485 9.900710 ATCTAGCAACGACTATAAATACTGAAG 57.099 33.333 0.00 0.00 0.00 3.02
470 486 6.830114 AGCAACGACTATAAATACTGAAGC 57.170 37.500 0.00 0.00 0.00 3.86
471 487 6.338146 AGCAACGACTATAAATACTGAAGCA 58.662 36.000 0.00 0.00 0.00 3.91
472 488 6.816640 AGCAACGACTATAAATACTGAAGCAA 59.183 34.615 0.00 0.00 0.00 3.91
473 489 7.010552 AGCAACGACTATAAATACTGAAGCAAG 59.989 37.037 0.00 0.00 0.00 4.01
474 490 6.830114 ACGACTATAAATACTGAAGCAAGC 57.170 37.500 0.00 0.00 0.00 4.01
475 491 5.753921 ACGACTATAAATACTGAAGCAAGCC 59.246 40.000 0.00 0.00 0.00 4.35
476 492 5.107837 CGACTATAAATACTGAAGCAAGCCG 60.108 44.000 0.00 0.00 0.00 5.52
477 493 5.914033 ACTATAAATACTGAAGCAAGCCGA 58.086 37.500 0.00 0.00 0.00 5.54
478 494 6.346096 ACTATAAATACTGAAGCAAGCCGAA 58.654 36.000 0.00 0.00 0.00 4.30
479 495 5.741388 ATAAATACTGAAGCAAGCCGAAG 57.259 39.130 0.00 0.00 0.00 3.79
496 512 2.410469 GGCAATGCCGCTGTCATC 59.590 61.111 9.14 0.00 39.62 2.92
497 513 2.409055 GGCAATGCCGCTGTCATCA 61.409 57.895 9.14 0.00 39.62 3.07
498 514 1.226491 GCAATGCCGCTGTCATCAC 60.226 57.895 0.00 0.00 0.00 3.06
499 515 1.925415 GCAATGCCGCTGTCATCACA 61.925 55.000 0.00 0.00 0.00 3.58
500 516 0.179181 CAATGCCGCTGTCATCACAC 60.179 55.000 0.00 0.00 0.00 3.82
501 517 1.308069 AATGCCGCTGTCATCACACC 61.308 55.000 0.00 0.00 0.00 4.16
502 518 2.046892 GCCGCTGTCATCACACCT 60.047 61.111 0.00 0.00 0.00 4.00
503 519 2.103042 GCCGCTGTCATCACACCTC 61.103 63.158 0.00 0.00 0.00 3.85
504 520 1.448540 CCGCTGTCATCACACCTCC 60.449 63.158 0.00 0.00 0.00 4.30
505 521 1.448540 CGCTGTCATCACACCTCCC 60.449 63.158 0.00 0.00 0.00 4.30
506 522 1.892819 CGCTGTCATCACACCTCCCT 61.893 60.000 0.00 0.00 0.00 4.20
507 523 0.107945 GCTGTCATCACACCTCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
508 524 0.174389 CTGTCATCACACCTCCCTCG 59.826 60.000 0.00 0.00 0.00 4.63
509 525 1.153549 GTCATCACACCTCCCTCGC 60.154 63.158 0.00 0.00 0.00 5.03
510 526 1.305297 TCATCACACCTCCCTCGCT 60.305 57.895 0.00 0.00 0.00 4.93
511 527 1.153489 CATCACACCTCCCTCGCTG 60.153 63.158 0.00 0.00 0.00 5.18
512 528 2.362369 ATCACACCTCCCTCGCTGG 61.362 63.158 0.00 0.00 0.00 4.85
513 529 2.805313 ATCACACCTCCCTCGCTGGA 62.805 60.000 0.00 0.00 38.35 3.86
526 542 4.394712 CTGGAGCCGGGCGAAACT 62.395 66.667 14.39 0.00 0.00 2.66
527 543 3.901797 CTGGAGCCGGGCGAAACTT 62.902 63.158 14.39 0.00 0.00 2.66
528 544 3.431725 GGAGCCGGGCGAAACTTG 61.432 66.667 14.39 0.00 0.00 3.16
529 545 2.668550 GAGCCGGGCGAAACTTGT 60.669 61.111 14.39 0.00 0.00 3.16
530 546 2.203294 AGCCGGGCGAAACTTGTT 60.203 55.556 14.39 0.00 0.00 2.83
531 547 2.183858 GAGCCGGGCGAAACTTGTTC 62.184 60.000 14.39 0.00 0.00 3.18
532 548 2.258726 GCCGGGCGAAACTTGTTCT 61.259 57.895 1.81 0.00 0.00 3.01
533 549 0.952010 GCCGGGCGAAACTTGTTCTA 60.952 55.000 1.81 0.00 0.00 2.10
534 550 1.515081 CCGGGCGAAACTTGTTCTAA 58.485 50.000 0.00 0.00 0.00 2.10
535 551 2.081462 CCGGGCGAAACTTGTTCTAAT 58.919 47.619 0.00 0.00 0.00 1.73
536 552 2.486592 CCGGGCGAAACTTGTTCTAATT 59.513 45.455 0.00 0.00 0.00 1.40
537 553 3.488489 CGGGCGAAACTTGTTCTAATTG 58.512 45.455 0.00 0.00 0.00 2.32
538 554 3.187637 CGGGCGAAACTTGTTCTAATTGA 59.812 43.478 0.00 0.00 0.00 2.57
539 555 4.473199 GGGCGAAACTTGTTCTAATTGAC 58.527 43.478 0.00 0.00 0.00 3.18
540 556 4.023536 GGGCGAAACTTGTTCTAATTGACA 60.024 41.667 0.00 0.00 0.00 3.58
541 557 5.147162 GGCGAAACTTGTTCTAATTGACAG 58.853 41.667 0.00 0.00 0.00 3.51
542 558 5.277828 GGCGAAACTTGTTCTAATTGACAGT 60.278 40.000 0.00 0.00 0.00 3.55
543 559 6.199393 GCGAAACTTGTTCTAATTGACAGTT 58.801 36.000 0.00 0.00 0.00 3.16
544 560 7.349711 GCGAAACTTGTTCTAATTGACAGTTA 58.650 34.615 0.00 0.00 0.00 2.24
545 561 7.853929 GCGAAACTTGTTCTAATTGACAGTTAA 59.146 33.333 0.00 0.00 0.00 2.01
546 562 9.370126 CGAAACTTGTTCTAATTGACAGTTAAG 57.630 33.333 0.00 0.00 0.00 1.85
550 566 9.614792 ACTTGTTCTAATTGACAGTTAAGAAGT 57.385 29.630 4.07 4.07 0.00 3.01
552 568 8.294341 TGTTCTAATTGACAGTTAAGAAGTCG 57.706 34.615 0.00 0.00 35.09 4.18
553 569 7.924412 TGTTCTAATTGACAGTTAAGAAGTCGT 59.076 33.333 0.00 0.00 35.09 4.34
554 570 8.426251 GTTCTAATTGACAGTTAAGAAGTCGTC 58.574 37.037 0.00 0.00 35.09 4.20
555 571 5.824243 AATTGACAGTTAAGAAGTCGTCG 57.176 39.130 0.00 0.00 35.09 5.12
556 572 3.976793 TGACAGTTAAGAAGTCGTCGT 57.023 42.857 0.00 0.00 35.09 4.34
557 573 3.624900 TGACAGTTAAGAAGTCGTCGTG 58.375 45.455 0.00 0.00 35.09 4.35
558 574 2.391879 ACAGTTAAGAAGTCGTCGTGC 58.608 47.619 0.00 0.00 0.00 5.34
559 575 2.034305 ACAGTTAAGAAGTCGTCGTGCT 59.966 45.455 0.00 0.00 0.00 4.40
560 576 3.251729 ACAGTTAAGAAGTCGTCGTGCTA 59.748 43.478 0.00 0.00 0.00 3.49
561 577 4.082895 ACAGTTAAGAAGTCGTCGTGCTAT 60.083 41.667 0.00 0.00 0.00 2.97
562 578 4.263209 CAGTTAAGAAGTCGTCGTGCTATG 59.737 45.833 0.00 0.00 0.00 2.23
563 579 4.155462 AGTTAAGAAGTCGTCGTGCTATGA 59.845 41.667 0.00 0.00 0.00 2.15
564 580 3.570926 AAGAAGTCGTCGTGCTATGAA 57.429 42.857 0.00 0.00 0.00 2.57
565 581 3.570926 AGAAGTCGTCGTGCTATGAAA 57.429 42.857 0.00 0.00 0.00 2.69
566 582 4.111375 AGAAGTCGTCGTGCTATGAAAT 57.889 40.909 0.00 0.00 0.00 2.17
567 583 4.495422 AGAAGTCGTCGTGCTATGAAATT 58.505 39.130 0.00 0.00 0.00 1.82
568 584 5.647589 AGAAGTCGTCGTGCTATGAAATTA 58.352 37.500 0.00 0.00 0.00 1.40
569 585 6.097356 AGAAGTCGTCGTGCTATGAAATTAA 58.903 36.000 0.00 0.00 0.00 1.40
570 586 6.757010 AGAAGTCGTCGTGCTATGAAATTAAT 59.243 34.615 0.00 0.00 0.00 1.40
571 587 6.903883 AGTCGTCGTGCTATGAAATTAATT 57.096 33.333 0.00 0.00 0.00 1.40
572 588 7.997107 AGTCGTCGTGCTATGAAATTAATTA 57.003 32.000 0.01 0.00 0.00 1.40
573 589 7.838498 AGTCGTCGTGCTATGAAATTAATTAC 58.162 34.615 0.01 0.00 0.00 1.89
574 590 7.490079 AGTCGTCGTGCTATGAAATTAATTACA 59.510 33.333 0.01 0.00 0.00 2.41
575 591 8.111836 GTCGTCGTGCTATGAAATTAATTACAA 58.888 33.333 0.01 0.00 0.00 2.41
576 592 8.822855 TCGTCGTGCTATGAAATTAATTACAAT 58.177 29.630 0.01 0.00 0.00 2.71
577 593 9.092322 CGTCGTGCTATGAAATTAATTACAATC 57.908 33.333 0.01 0.00 0.00 2.67
578 594 9.929722 GTCGTGCTATGAAATTAATTACAATCA 57.070 29.630 0.01 2.04 0.00 2.57
599 615 9.301153 CAATCAAATCCTAAACGAAAATTAGGG 57.699 33.333 11.34 0.00 46.23 3.53
600 616 7.399245 TCAAATCCTAAACGAAAATTAGGGG 57.601 36.000 11.34 1.94 46.23 4.79
601 617 7.176490 TCAAATCCTAAACGAAAATTAGGGGA 58.824 34.615 11.34 0.00 46.23 4.81
602 618 7.338449 TCAAATCCTAAACGAAAATTAGGGGAG 59.662 37.037 11.34 2.23 46.23 4.30
603 619 6.570654 ATCCTAAACGAAAATTAGGGGAGA 57.429 37.500 11.34 0.00 46.23 3.71
625 641 0.249911 CGAAATTAGGGGAGAGGCGG 60.250 60.000 0.00 0.00 0.00 6.13
809 843 3.814577 CGAAAGCGAGGAAGGAAGA 57.185 52.632 0.00 0.00 40.82 2.87
864 898 1.648467 GCAAGTTGGAGCCGATGGTC 61.648 60.000 4.75 0.00 38.29 4.02
879 913 3.726607 GATGGTCGCAGATCTGAAGAAT 58.273 45.455 27.04 14.42 39.28 2.40
885 919 3.070015 TCGCAGATCTGAAGAATATGGCA 59.930 43.478 27.04 0.00 0.00 4.92
887 921 5.047092 TCGCAGATCTGAAGAATATGGCATA 60.047 40.000 27.04 10.07 0.00 3.14
893 927 6.352016 TCTGAAGAATATGGCATAGGAGAC 57.648 41.667 13.39 5.33 0.00 3.36
907 941 3.978571 GAGACCCTTGAAGGCGGGC 62.979 68.421 5.50 0.00 44.63 6.13
916 950 3.662117 GAAGGCGGGCTGGGGAATT 62.662 63.158 4.27 0.00 0.00 2.17
921 955 2.679342 CGGGCTGGGGAATTGGAGA 61.679 63.158 0.00 0.00 0.00 3.71
955 989 0.042731 ATCCCCGGAGAAAGAGGACA 59.957 55.000 0.73 0.00 0.00 4.02
969 1003 0.035458 AGGACAAAGAAGAGGCACCG 59.965 55.000 0.00 0.00 0.00 4.94
970 1004 0.250338 GGACAAAGAAGAGGCACCGT 60.250 55.000 0.00 0.00 0.00 4.83
1001 1035 3.668821 TCCAGACCATCCCTGTGATTAT 58.331 45.455 0.00 0.00 0.00 1.28
1094 1128 6.696411 TGTTTGCCATTCCTAAAATTGTAGG 58.304 36.000 14.87 14.87 41.93 3.18
1122 1156 3.003173 TGGAAGGCCACCGGAGAG 61.003 66.667 9.46 0.00 39.92 3.20
1175 1209 1.377856 GGAAAGAGACCAGGCCTGC 60.378 63.158 28.39 14.93 0.00 4.85
1198 1232 4.008074 AGTTTCCTTTCTCAGCGATCAA 57.992 40.909 0.00 0.00 0.00 2.57
1218 1252 4.076394 CAACGGAAGATTTTTGGGAGGTA 58.924 43.478 0.00 0.00 0.00 3.08
1467 1629 3.693807 TCCAAAGAAGAATGCTGCTGAT 58.306 40.909 0.00 0.00 27.48 2.90
1500 1662 2.284995 AGGAGCTGTGGAGGGGAC 60.285 66.667 0.00 0.00 0.00 4.46
1751 1934 0.885879 TGTAAGTGGCTCATCGTCGT 59.114 50.000 0.00 0.00 0.00 4.34
1767 1950 3.189702 TCGTCGTTGTGTATCTGACATCA 59.810 43.478 0.00 0.00 41.14 3.07
1936 2119 1.671556 CGTGGATCCATGACAACGACA 60.672 52.381 27.27 0.00 35.09 4.35
2207 2390 1.672881 GATTGAAGGCACGGATGGAAG 59.327 52.381 0.00 0.00 0.00 3.46
2240 2423 3.455910 AGATGCCCTGTAAAGTATGAGCA 59.544 43.478 0.00 0.00 0.00 4.26
2342 2525 1.142097 GGTTCTCTACGGAGCAGCC 59.858 63.158 0.00 0.00 39.31 4.85
2529 2712 2.038387 ATATGAAGGCCACCGACAAC 57.962 50.000 5.01 0.00 0.00 3.32
2586 2769 2.561037 CGTGAAAGGGGTGGTTGCC 61.561 63.158 0.00 0.00 0.00 4.52
2644 2827 2.426024 GCGGACAGAGTACACAGGATAA 59.574 50.000 0.00 0.00 0.00 1.75
2818 3001 2.913501 CTGCAGCTATCAGGGCCA 59.086 61.111 6.18 0.00 0.00 5.36
3010 3193 2.541547 TACTGATGGGCCAGTGCAGC 62.542 60.000 24.97 0.00 46.00 5.25
3098 3281 1.542328 CGGTCCAGATGACACCAACAA 60.542 52.381 0.00 0.00 46.38 2.83
3732 3917 7.222031 GGGATCTAATGCGTAAAATGAAAAACC 59.778 37.037 0.00 0.00 0.00 3.27
4090 4278 2.035449 TCCAGTCAGTCAACAACGTAGG 59.965 50.000 0.00 0.00 0.00 3.18
4224 4412 4.760204 TGTGATGAGTTCTCTTCACGACTA 59.240 41.667 27.47 16.53 43.45 2.59
4273 4461 8.477419 TCACAAAGAAAATAAAGGACCTTCAT 57.523 30.769 7.34 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.025401 CAGTTCACGCGTTGGCCC 62.025 66.667 10.22 0.00 35.02 5.80
58 59 4.683334 GCAGTTCACGCGTTGGCC 62.683 66.667 10.22 0.00 35.02 5.36
80 81 0.460459 TAAATGCCGATTCCGACGCA 60.460 50.000 0.00 0.00 37.37 5.24
101 102 2.828128 GCCGGAGAGTACGTACGGG 61.828 68.421 21.06 16.41 44.39 5.28
179 190 9.660180 TGCTTTCCCACCATAATAAAATAAAAC 57.340 29.630 0.00 0.00 0.00 2.43
184 195 5.420739 ACGTGCTTTCCCACCATAATAAAAT 59.579 36.000 0.00 0.00 32.10 1.82
185 196 4.767928 ACGTGCTTTCCCACCATAATAAAA 59.232 37.500 0.00 0.00 32.10 1.52
192 203 0.981183 TCTACGTGCTTTCCCACCAT 59.019 50.000 0.00 0.00 32.10 3.55
193 204 0.034337 GTCTACGTGCTTTCCCACCA 59.966 55.000 0.00 0.00 32.10 4.17
194 205 1.012486 CGTCTACGTGCTTTCCCACC 61.012 60.000 0.00 0.00 32.10 4.61
244 256 1.269621 ACAGTACGTGCTCGCTCTTTT 60.270 47.619 2.06 0.00 41.18 2.27
246 258 1.162698 TACAGTACGTGCTCGCTCTT 58.837 50.000 2.06 0.00 41.18 2.85
247 259 1.380524 ATACAGTACGTGCTCGCTCT 58.619 50.000 2.06 4.08 41.18 4.09
264 280 1.064240 TGAGGGCCAGTGTCGTCTATA 60.064 52.381 6.18 0.00 32.33 1.31
267 283 1.610673 ATGAGGGCCAGTGTCGTCT 60.611 57.895 6.18 0.00 32.33 4.18
268 284 1.448540 CATGAGGGCCAGTGTCGTC 60.449 63.158 6.18 0.00 0.00 4.20
272 288 0.465705 CGTATCATGAGGGCCAGTGT 59.534 55.000 6.18 0.00 0.00 3.55
279 295 1.596603 TGCATTGCGTATCATGAGGG 58.403 50.000 0.09 0.00 0.00 4.30
280 296 3.181527 CGTATGCATTGCGTATCATGAGG 60.182 47.826 13.41 0.00 32.46 3.86
282 298 3.184178 CACGTATGCATTGCGTATCATGA 59.816 43.478 22.41 0.00 37.07 3.07
289 305 1.136085 GTGAACACGTATGCATTGCGT 60.136 47.619 18.91 18.91 39.59 5.24
330 346 5.103000 GCCATTCTAGTGTAGTAGTGTGTG 58.897 45.833 0.00 0.00 0.00 3.82
331 347 4.159879 GGCCATTCTAGTGTAGTAGTGTGT 59.840 45.833 0.00 0.00 0.00 3.72
345 361 2.551270 ACCTCAGTCTTGGCCATTCTA 58.449 47.619 6.09 0.00 0.00 2.10
354 370 4.545823 TTTTACGCAAACCTCAGTCTTG 57.454 40.909 0.00 0.00 0.00 3.02
360 376 4.922719 ACGAAAATTTTACGCAAACCTCA 58.077 34.783 17.09 0.00 0.00 3.86
362 378 5.584442 AGAACGAAAATTTTACGCAAACCT 58.416 33.333 17.09 8.57 0.00 3.50
363 379 5.876576 AGAACGAAAATTTTACGCAAACC 57.123 34.783 17.09 0.00 0.00 3.27
382 398 6.261603 GCTGTGTCATGATCAATGGAATAGAA 59.738 38.462 0.00 0.00 36.86 2.10
390 406 3.001026 GTCTCGCTGTGTCATGATCAATG 59.999 47.826 0.00 0.00 37.66 2.82
391 407 3.193263 GTCTCGCTGTGTCATGATCAAT 58.807 45.455 0.00 0.00 0.00 2.57
392 408 2.029110 TGTCTCGCTGTGTCATGATCAA 60.029 45.455 0.00 0.00 0.00 2.57
393 409 1.545582 TGTCTCGCTGTGTCATGATCA 59.454 47.619 0.00 0.00 0.00 2.92
394 410 2.284263 TGTCTCGCTGTGTCATGATC 57.716 50.000 0.00 0.00 0.00 2.92
395 411 2.749280 TTGTCTCGCTGTGTCATGAT 57.251 45.000 0.00 0.00 0.00 2.45
396 412 2.524569 TTTGTCTCGCTGTGTCATGA 57.475 45.000 0.00 0.00 0.00 3.07
397 413 3.607422 TTTTTGTCTCGCTGTGTCATG 57.393 42.857 0.00 0.00 0.00 3.07
426 442 9.929180 GTTGCTAGATGGTCTATGAATGTAATA 57.071 33.333 0.00 0.00 0.00 0.98
427 443 7.600375 CGTTGCTAGATGGTCTATGAATGTAAT 59.400 37.037 0.00 0.00 0.00 1.89
428 444 6.923508 CGTTGCTAGATGGTCTATGAATGTAA 59.076 38.462 0.00 0.00 0.00 2.41
429 445 6.264518 TCGTTGCTAGATGGTCTATGAATGTA 59.735 38.462 0.00 0.00 0.00 2.29
430 446 5.069119 TCGTTGCTAGATGGTCTATGAATGT 59.931 40.000 0.00 0.00 0.00 2.71
431 447 5.403766 GTCGTTGCTAGATGGTCTATGAATG 59.596 44.000 0.00 0.00 0.00 2.67
432 448 5.303078 AGTCGTTGCTAGATGGTCTATGAAT 59.697 40.000 0.00 0.00 0.00 2.57
433 449 4.645136 AGTCGTTGCTAGATGGTCTATGAA 59.355 41.667 0.00 0.00 0.00 2.57
434 450 4.207955 AGTCGTTGCTAGATGGTCTATGA 58.792 43.478 0.00 0.00 0.00 2.15
435 451 4.576216 AGTCGTTGCTAGATGGTCTATG 57.424 45.455 0.00 0.00 0.00 2.23
436 452 7.997773 TTATAGTCGTTGCTAGATGGTCTAT 57.002 36.000 0.00 0.00 0.00 1.98
437 453 7.812690 TTTATAGTCGTTGCTAGATGGTCTA 57.187 36.000 0.00 0.00 0.00 2.59
438 454 6.710597 TTTATAGTCGTTGCTAGATGGTCT 57.289 37.500 0.00 0.00 0.00 3.85
439 455 8.298140 AGTATTTATAGTCGTTGCTAGATGGTC 58.702 37.037 0.00 0.00 0.00 4.02
440 456 8.082852 CAGTATTTATAGTCGTTGCTAGATGGT 58.917 37.037 0.00 0.00 0.00 3.55
441 457 8.297426 TCAGTATTTATAGTCGTTGCTAGATGG 58.703 37.037 0.00 0.00 0.00 3.51
442 458 9.678941 TTCAGTATTTATAGTCGTTGCTAGATG 57.321 33.333 0.00 0.00 0.00 2.90
443 459 9.900710 CTTCAGTATTTATAGTCGTTGCTAGAT 57.099 33.333 0.00 0.00 0.00 1.98
444 460 7.861372 GCTTCAGTATTTATAGTCGTTGCTAGA 59.139 37.037 0.00 0.00 0.00 2.43
445 461 7.648112 TGCTTCAGTATTTATAGTCGTTGCTAG 59.352 37.037 0.00 0.00 0.00 3.42
446 462 7.485810 TGCTTCAGTATTTATAGTCGTTGCTA 58.514 34.615 0.00 0.00 0.00 3.49
447 463 6.338146 TGCTTCAGTATTTATAGTCGTTGCT 58.662 36.000 0.00 0.00 0.00 3.91
448 464 6.583912 TGCTTCAGTATTTATAGTCGTTGC 57.416 37.500 0.00 0.00 0.00 4.17
449 465 7.119997 GCTTGCTTCAGTATTTATAGTCGTTG 58.880 38.462 0.00 0.00 0.00 4.10
450 466 6.258068 GGCTTGCTTCAGTATTTATAGTCGTT 59.742 38.462 0.00 0.00 0.00 3.85
451 467 5.753921 GGCTTGCTTCAGTATTTATAGTCGT 59.246 40.000 0.00 0.00 0.00 4.34
452 468 5.107837 CGGCTTGCTTCAGTATTTATAGTCG 60.108 44.000 0.00 0.00 0.00 4.18
453 469 5.983720 TCGGCTTGCTTCAGTATTTATAGTC 59.016 40.000 0.00 0.00 0.00 2.59
454 470 5.914033 TCGGCTTGCTTCAGTATTTATAGT 58.086 37.500 0.00 0.00 0.00 2.12
455 471 6.073548 CCTTCGGCTTGCTTCAGTATTTATAG 60.074 42.308 0.00 0.00 0.00 1.31
456 472 5.758296 CCTTCGGCTTGCTTCAGTATTTATA 59.242 40.000 0.00 0.00 0.00 0.98
457 473 4.576463 CCTTCGGCTTGCTTCAGTATTTAT 59.424 41.667 0.00 0.00 0.00 1.40
458 474 3.938963 CCTTCGGCTTGCTTCAGTATTTA 59.061 43.478 0.00 0.00 0.00 1.40
459 475 2.749621 CCTTCGGCTTGCTTCAGTATTT 59.250 45.455 0.00 0.00 0.00 1.40
460 476 2.359900 CCTTCGGCTTGCTTCAGTATT 58.640 47.619 0.00 0.00 0.00 1.89
461 477 2.014068 GCCTTCGGCTTGCTTCAGTAT 61.014 52.381 0.00 0.00 46.69 2.12
462 478 0.673644 GCCTTCGGCTTGCTTCAGTA 60.674 55.000 0.00 0.00 46.69 2.74
463 479 1.968540 GCCTTCGGCTTGCTTCAGT 60.969 57.895 0.00 0.00 46.69 3.41
464 480 2.873288 GCCTTCGGCTTGCTTCAG 59.127 61.111 0.00 0.00 46.69 3.02
479 495 2.409055 TGATGACAGCGGCATTGCC 61.409 57.895 18.10 18.10 46.75 4.52
480 496 1.226491 GTGATGACAGCGGCATTGC 60.226 57.895 1.45 0.00 0.00 3.56
481 497 0.179181 GTGTGATGACAGCGGCATTG 60.179 55.000 1.45 0.00 30.74 2.82
482 498 1.308069 GGTGTGATGACAGCGGCATT 61.308 55.000 1.45 0.00 40.59 3.56
483 499 1.746615 GGTGTGATGACAGCGGCAT 60.747 57.895 1.45 0.00 40.59 4.40
484 500 2.358615 GGTGTGATGACAGCGGCA 60.359 61.111 1.45 0.00 40.59 5.69
489 505 0.174389 CGAGGGAGGTGTGATGACAG 59.826 60.000 0.00 0.00 30.74 3.51
490 506 1.888436 GCGAGGGAGGTGTGATGACA 61.888 60.000 0.00 0.00 0.00 3.58
491 507 1.153549 GCGAGGGAGGTGTGATGAC 60.154 63.158 0.00 0.00 0.00 3.06
492 508 1.305297 AGCGAGGGAGGTGTGATGA 60.305 57.895 0.00 0.00 0.00 2.92
493 509 1.153489 CAGCGAGGGAGGTGTGATG 60.153 63.158 0.00 0.00 35.15 3.07
494 510 2.362369 CCAGCGAGGGAGGTGTGAT 61.362 63.158 0.00 0.00 37.88 3.06
495 511 2.997315 CCAGCGAGGGAGGTGTGA 60.997 66.667 0.00 0.00 37.88 3.58
496 512 2.997315 TCCAGCGAGGGAGGTGTG 60.997 66.667 0.00 0.00 37.88 3.82
509 525 3.901797 AAGTTTCGCCCGGCTCCAG 62.902 63.158 8.05 0.00 0.00 3.86
510 526 3.948719 AAGTTTCGCCCGGCTCCA 61.949 61.111 8.05 0.00 0.00 3.86
511 527 3.431725 CAAGTTTCGCCCGGCTCC 61.432 66.667 8.05 0.00 0.00 4.70
512 528 2.183858 GAACAAGTTTCGCCCGGCTC 62.184 60.000 8.05 0.00 0.00 4.70
513 529 2.203294 AACAAGTTTCGCCCGGCT 60.203 55.556 8.05 0.00 0.00 5.52
514 530 0.952010 TAGAACAAGTTTCGCCCGGC 60.952 55.000 0.00 0.00 0.00 6.13
515 531 1.515081 TTAGAACAAGTTTCGCCCGG 58.485 50.000 0.00 0.00 0.00 5.73
516 532 3.187637 TCAATTAGAACAAGTTTCGCCCG 59.812 43.478 0.00 0.00 0.00 6.13
517 533 4.023536 TGTCAATTAGAACAAGTTTCGCCC 60.024 41.667 0.00 0.00 0.00 6.13
518 534 5.103290 TGTCAATTAGAACAAGTTTCGCC 57.897 39.130 0.00 0.00 0.00 5.54
519 535 5.748592 ACTGTCAATTAGAACAAGTTTCGC 58.251 37.500 0.00 0.00 0.00 4.70
520 536 9.370126 CTTAACTGTCAATTAGAACAAGTTTCG 57.630 33.333 0.00 0.00 0.00 3.46
524 540 9.614792 ACTTCTTAACTGTCAATTAGAACAAGT 57.385 29.630 0.00 0.00 0.00 3.16
526 542 8.761497 CGACTTCTTAACTGTCAATTAGAACAA 58.239 33.333 0.00 0.00 0.00 2.83
527 543 7.924412 ACGACTTCTTAACTGTCAATTAGAACA 59.076 33.333 0.00 0.00 0.00 3.18
528 544 8.295569 ACGACTTCTTAACTGTCAATTAGAAC 57.704 34.615 0.00 0.00 0.00 3.01
529 545 7.325338 CGACGACTTCTTAACTGTCAATTAGAA 59.675 37.037 0.00 0.00 0.00 2.10
530 546 6.800408 CGACGACTTCTTAACTGTCAATTAGA 59.200 38.462 0.00 0.00 0.00 2.10
531 547 6.581542 ACGACGACTTCTTAACTGTCAATTAG 59.418 38.462 0.00 0.00 0.00 1.73
532 548 6.361481 CACGACGACTTCTTAACTGTCAATTA 59.639 38.462 0.00 0.00 0.00 1.40
533 549 5.175126 CACGACGACTTCTTAACTGTCAATT 59.825 40.000 0.00 0.00 0.00 2.32
534 550 4.680110 CACGACGACTTCTTAACTGTCAAT 59.320 41.667 0.00 0.00 0.00 2.57
535 551 4.039703 CACGACGACTTCTTAACTGTCAA 58.960 43.478 0.00 0.00 0.00 3.18
536 552 3.624900 CACGACGACTTCTTAACTGTCA 58.375 45.455 0.00 0.00 0.00 3.58
537 553 2.404361 GCACGACGACTTCTTAACTGTC 59.596 50.000 0.00 0.00 0.00 3.51
538 554 2.034305 AGCACGACGACTTCTTAACTGT 59.966 45.455 0.00 0.00 0.00 3.55
539 555 2.662700 AGCACGACGACTTCTTAACTG 58.337 47.619 0.00 0.00 0.00 3.16
540 556 4.155462 TCATAGCACGACGACTTCTTAACT 59.845 41.667 0.00 0.00 0.00 2.24
541 557 4.409570 TCATAGCACGACGACTTCTTAAC 58.590 43.478 0.00 0.00 0.00 2.01
542 558 4.690184 TCATAGCACGACGACTTCTTAA 57.310 40.909 0.00 0.00 0.00 1.85
543 559 4.690184 TTCATAGCACGACGACTTCTTA 57.310 40.909 0.00 0.00 0.00 2.10
544 560 3.570926 TTCATAGCACGACGACTTCTT 57.429 42.857 0.00 0.00 0.00 2.52
545 561 3.570926 TTTCATAGCACGACGACTTCT 57.429 42.857 0.00 0.00 0.00 2.85
546 562 4.842139 AATTTCATAGCACGACGACTTC 57.158 40.909 0.00 0.00 0.00 3.01
547 563 6.903883 ATTAATTTCATAGCACGACGACTT 57.096 33.333 0.00 0.00 0.00 3.01
548 564 6.903883 AATTAATTTCATAGCACGACGACT 57.096 33.333 0.00 0.59 0.00 4.18
549 565 7.614908 TGTAATTAATTTCATAGCACGACGAC 58.385 34.615 5.91 0.00 0.00 4.34
550 566 7.758613 TGTAATTAATTTCATAGCACGACGA 57.241 32.000 5.91 0.00 0.00 4.20
551 567 8.987599 ATTGTAATTAATTTCATAGCACGACG 57.012 30.769 5.91 0.00 0.00 5.12
552 568 9.929722 TGATTGTAATTAATTTCATAGCACGAC 57.070 29.630 5.91 0.00 0.00 4.34
572 588 9.855021 CCTAATTTTCGTTTAGGATTTGATTGT 57.145 29.630 3.86 0.00 45.76 2.71
573 589 9.301153 CCCTAATTTTCGTTTAGGATTTGATTG 57.699 33.333 10.36 0.00 45.76 2.67
574 590 8.474831 CCCCTAATTTTCGTTTAGGATTTGATT 58.525 33.333 10.36 0.00 45.76 2.57
575 591 7.837187 TCCCCTAATTTTCGTTTAGGATTTGAT 59.163 33.333 10.36 0.00 45.76 2.57
576 592 7.176490 TCCCCTAATTTTCGTTTAGGATTTGA 58.824 34.615 10.36 0.93 45.76 2.69
577 593 7.338449 TCTCCCCTAATTTTCGTTTAGGATTTG 59.662 37.037 10.36 0.46 45.76 2.32
578 594 7.407729 TCTCCCCTAATTTTCGTTTAGGATTT 58.592 34.615 10.36 0.00 45.76 2.17
579 595 6.965607 TCTCCCCTAATTTTCGTTTAGGATT 58.034 36.000 10.36 0.00 45.76 3.01
580 596 6.409349 CCTCTCCCCTAATTTTCGTTTAGGAT 60.409 42.308 10.36 0.00 45.76 3.24
581 597 5.104652 CCTCTCCCCTAATTTTCGTTTAGGA 60.105 44.000 10.36 0.00 45.76 2.94
582 598 5.123936 CCTCTCCCCTAATTTTCGTTTAGG 58.876 45.833 3.05 3.05 43.56 2.69
583 599 4.575236 GCCTCTCCCCTAATTTTCGTTTAG 59.425 45.833 0.00 0.00 0.00 1.85
584 600 4.520179 GCCTCTCCCCTAATTTTCGTTTA 58.480 43.478 0.00 0.00 0.00 2.01
585 601 3.353557 GCCTCTCCCCTAATTTTCGTTT 58.646 45.455 0.00 0.00 0.00 3.60
586 602 2.679930 CGCCTCTCCCCTAATTTTCGTT 60.680 50.000 0.00 0.00 0.00 3.85
587 603 1.134491 CGCCTCTCCCCTAATTTTCGT 60.134 52.381 0.00 0.00 0.00 3.85
588 604 1.138266 TCGCCTCTCCCCTAATTTTCG 59.862 52.381 0.00 0.00 0.00 3.46
589 605 3.277142 TTCGCCTCTCCCCTAATTTTC 57.723 47.619 0.00 0.00 0.00 2.29
590 606 3.732048 TTTCGCCTCTCCCCTAATTTT 57.268 42.857 0.00 0.00 0.00 1.82
591 607 3.953542 ATTTCGCCTCTCCCCTAATTT 57.046 42.857 0.00 0.00 0.00 1.82
592 608 3.953542 AATTTCGCCTCTCCCCTAATT 57.046 42.857 0.00 0.00 0.00 1.40
593 609 3.328050 CCTAATTTCGCCTCTCCCCTAAT 59.672 47.826 0.00 0.00 0.00 1.73
594 610 2.704065 CCTAATTTCGCCTCTCCCCTAA 59.296 50.000 0.00 0.00 0.00 2.69
595 611 2.326428 CCTAATTTCGCCTCTCCCCTA 58.674 52.381 0.00 0.00 0.00 3.53
596 612 1.132500 CCTAATTTCGCCTCTCCCCT 58.868 55.000 0.00 0.00 0.00 4.79
597 613 0.108774 CCCTAATTTCGCCTCTCCCC 59.891 60.000 0.00 0.00 0.00 4.81
598 614 0.108774 CCCCTAATTTCGCCTCTCCC 59.891 60.000 0.00 0.00 0.00 4.30
599 615 1.070914 CTCCCCTAATTTCGCCTCTCC 59.929 57.143 0.00 0.00 0.00 3.71
600 616 2.036604 CTCTCCCCTAATTTCGCCTCTC 59.963 54.545 0.00 0.00 0.00 3.20
601 617 2.043227 CTCTCCCCTAATTTCGCCTCT 58.957 52.381 0.00 0.00 0.00 3.69
602 618 1.070914 CCTCTCCCCTAATTTCGCCTC 59.929 57.143 0.00 0.00 0.00 4.70
603 619 1.132500 CCTCTCCCCTAATTTCGCCT 58.868 55.000 0.00 0.00 0.00 5.52
809 843 0.756294 TGGTCGCCGGAATATCACAT 59.244 50.000 5.05 0.00 0.00 3.21
836 870 2.504367 GCTCCAACTTGCCTTCTACAA 58.496 47.619 0.00 0.00 0.00 2.41
850 884 3.664025 CTGCGACCATCGGCTCCAA 62.664 63.158 0.00 0.00 40.84 3.53
864 898 3.396560 TGCCATATTCTTCAGATCTGCG 58.603 45.455 18.36 11.23 0.00 5.18
879 913 3.344535 TCAAGGGTCTCCTATGCCATA 57.655 47.619 0.00 0.00 44.07 2.74
885 919 1.123928 CGCCTTCAAGGGTCTCCTAT 58.876 55.000 5.33 0.00 44.07 2.57
907 941 2.357569 CCTCCTTTCTCCAATTCCCCAG 60.358 54.545 0.00 0.00 0.00 4.45
916 950 1.437149 TCTCCCTTCCTCCTTTCTCCA 59.563 52.381 0.00 0.00 0.00 3.86
948 982 1.349357 GGTGCCTCTTCTTTGTCCTCT 59.651 52.381 0.00 0.00 0.00 3.69
955 989 2.158813 TCTTCAACGGTGCCTCTTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
969 1003 4.195416 GGATGGTCTGGATCTTCTTCAAC 58.805 47.826 0.00 0.00 0.00 3.18
970 1004 3.200825 GGGATGGTCTGGATCTTCTTCAA 59.799 47.826 0.00 0.00 0.00 2.69
1020 1054 1.826024 CTCGCAGGGCTCCATTACT 59.174 57.895 0.00 0.00 0.00 2.24
1094 1128 1.153147 GCCTTCCATCCCCGACTTC 60.153 63.158 0.00 0.00 0.00 3.01
1175 1209 4.748892 TGATCGCTGAGAAAGGAAACTAG 58.251 43.478 0.00 0.00 42.68 2.57
1198 1232 2.971901 ACCTCCCAAAAATCTTCCGT 57.028 45.000 0.00 0.00 0.00 4.69
1218 1252 0.043940 ATCCCTCCCTGCTCTCTGTT 59.956 55.000 0.00 0.00 0.00 3.16
1467 1629 2.296792 CTCCTGATCTCGCTCTTCTCA 58.703 52.381 0.00 0.00 0.00 3.27
1500 1662 2.297033 CTGAACAAAGGGGGTGATGTTG 59.703 50.000 0.00 0.00 36.22 3.33
1544 1706 2.362889 CAACACCATGCCCCTCCC 60.363 66.667 0.00 0.00 0.00 4.30
1584 1746 0.459489 CAGCTTCTTCTCTCTCCCGG 59.541 60.000 0.00 0.00 0.00 5.73
1751 1934 4.041567 ACACCCTTGATGTCAGATACACAA 59.958 41.667 0.00 0.00 42.09 3.33
1820 2003 0.392863 TTCTGTCATGTCCCCATGCG 60.393 55.000 0.00 0.00 46.64 4.73
1823 2006 2.450476 GCTTTTCTGTCATGTCCCCAT 58.550 47.619 0.00 0.00 0.00 4.00
2172 2355 5.760131 CCTTCAATCTTTATCCACCTCCTT 58.240 41.667 0.00 0.00 0.00 3.36
2207 2390 3.549794 ACAGGGCATCTTTTAGCATCTC 58.450 45.455 0.00 0.00 0.00 2.75
2240 2423 6.824196 ACAATAAAAACAAAAATGGGGAACGT 59.176 30.769 0.00 0.00 0.00 3.99
2342 2525 1.224075 CATCTTGTATGGCGAGGCAG 58.776 55.000 5.43 0.00 0.00 4.85
2529 2712 2.497092 CGTTGTCGTCCGCTCATCG 61.497 63.158 0.00 0.00 38.08 3.84
2586 2769 1.649664 CCTTGAGATTCTCCACAGCG 58.350 55.000 11.12 0.00 0.00 5.18
2818 3001 3.869623 CAGTATGCTTGGCCACTCT 57.130 52.632 3.88 0.00 0.00 3.24
3010 3193 4.162690 GGAGTAGGCCACCGCTGG 62.163 72.222 5.01 0.00 41.13 4.85
3732 3917 2.432300 ATGGTCCCGGCGAGGTTAG 61.432 63.158 9.30 0.00 38.74 2.34
3834 4021 8.560903 ACAGTGGGATAGGATTTCTCTAAAATT 58.439 33.333 0.00 0.00 0.00 1.82
4090 4278 5.010282 TCCTTTTCCCAGAAAGCTTCATAC 58.990 41.667 0.00 0.00 35.73 2.39
4224 4412 3.636764 AGAACCAAAATTCCGTTTGCTCT 59.363 39.130 0.00 0.00 37.20 4.09
4273 4461 7.441157 CGGTGACTGATAGCCTGAATTTTATTA 59.559 37.037 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.