Multiple sequence alignment - TraesCS4D01G085200

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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 TraesCS4D01G085200 chr4D 100.000 2392 0 0 1 2392 59642031 59644422 0.000000e+00 4418.0
1 TraesCS4D01G085200 chr4D 100.000 1851 0 0 2823 4673 59644853 59646703 0.000000e+00 3419.0
2 TraesCS4D01G085200 chr4D 77.698 278 57 5 4155 4428 474919592 474919868 1.040000e-36 165.0
3 TraesCS4D01G085200 chr4B 92.063 1575 73 21 2828 4364 89057124 89058684 0.000000e+00 2169.0
4 TraesCS4D01G085200 chr4B 91.171 1563 54 27 543 2037 89054905 89056451 0.000000e+00 2045.0
5 TraesCS4D01G085200 chr4B 94.169 343 18 2 46 387 89054584 89054925 5.360000e-144 521.0
6 TraesCS4D01G085200 chr4B 88.268 358 17 8 2036 2392 89056775 89057108 5.630000e-109 405.0
7 TraesCS4D01G085200 chr4B 89.441 161 13 3 387 546 618535134 618534977 2.850000e-47 200.0
8 TraesCS4D01G085200 chr4A 93.555 1024 40 6 3106 4124 536771269 536770267 0.000000e+00 1502.0
9 TraesCS4D01G085200 chr4A 92.463 544 25 10 4133 4673 536767084 536766554 0.000000e+00 763.0
10 TraesCS4D01G085200 chr4A 89.769 606 29 9 930 1509 536772840 536772242 0.000000e+00 745.0
11 TraesCS4D01G085200 chr4A 96.183 393 11 2 543 933 536773257 536772867 1.420000e-179 640.0
12 TraesCS4D01G085200 chr4A 94.161 411 12 4 1648 2053 536772083 536771680 2.390000e-172 616.0
13 TraesCS4D01G085200 chr4A 92.677 396 20 2 1 387 536773632 536773237 3.160000e-156 562.0
14 TraesCS4D01G085200 chr4A 92.642 299 12 7 2828 3120 536771580 536771286 5.590000e-114 422.0
15 TraesCS4D01G085200 chr4A 93.651 63 1 3 2272 2334 536771667 536771608 1.790000e-14 91.6
16 TraesCS4D01G085200 chr5D 91.358 162 12 1 385 546 558037185 558037026 2.190000e-53 220.0
17 TraesCS4D01G085200 chr5D 77.580 281 57 6 4155 4430 505928236 505927957 1.040000e-36 165.0
18 TraesCS4D01G085200 chr1A 90.506 158 13 1 389 546 591086063 591086218 1.700000e-49 207.0
19 TraesCS4D01G085200 chr7D 90.062 161 13 2 386 546 403062425 403062582 6.130000e-49 206.0
20 TraesCS4D01G085200 chr7D 89.441 161 14 2 387 546 633166180 633166338 2.850000e-47 200.0
21 TraesCS4D01G085200 chr6B 89.441 161 15 1 386 546 513607091 513607249 7.930000e-48 202.0
22 TraesCS4D01G085200 chr7B 88.889 162 14 3 387 546 718846876 718846717 3.690000e-46 196.0
23 TraesCS4D01G085200 chr7B 87.647 170 16 4 380 546 143261163 143260996 4.770000e-45 193.0
24 TraesCS4D01G085200 chr5B 89.172 157 15 1 388 544 590558297 590558451 1.330000e-45 195.0
25 TraesCS4D01G085200 chr1D 79.286 280 51 6 4155 4430 211630087 211629811 6.170000e-44 189.0
26 TraesCS4D01G085200 chr5A 77.660 282 40 15 4155 4429 489685610 489685875 2.910000e-32 150.0
27 TraesCS4D01G085200 chr5A 76.531 294 56 10 4155 4441 513965880 513966167 1.050000e-31 148.0
28 TraesCS4D01G085200 chrUn 76.596 282 50 14 4165 4441 93141080 93140810 1.750000e-29 141.0
29 TraesCS4D01G085200 chr3B 75.000 288 58 9 4156 4436 685066013 685065733 2.280000e-23 121.0


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 TraesCS4D01G085200 chr4D 59642031 59646703 4672 False 3918.5 4418 100.000000 1 4673 2 chr4D.!!$F2 4672
1 TraesCS4D01G085200 chr4B 89054584 89058684 4100 False 1285.0 2169 91.417750 46 4364 4 chr4B.!!$F1 4318
2 TraesCS4D01G085200 chr4A 536766554 536773632 7078 True 667.7 1502 93.137625 1 4673 8 chr4A.!!$R1 4672

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
446 456 0.107268 TGGACGATGCATGCAGCTAT 59.893 50.0 31.04 20.3 45.94 2.97 F
530 540 0.109226 GCGACACCTGTCACTACTCC 60.109 60.0 6.27 0.0 44.99 3.85 F
1133 1181 0.320334 TAGATGGGTGTGTGCGTGTG 60.320 55.0 0.00 0.0 0.00 3.82 F
2154 2615 0.394762 GGAGCCACATGCATCTTCCA 60.395 55.0 0.00 0.0 44.83 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2528 0.172578 CGACTGCCACCGAGTAATCA 59.827 55.000 0.00 0.0 0.00 2.57 R
2321 2783 2.599082 CGTCTGTCCTACGCATTTTCTC 59.401 50.000 0.00 0.0 33.04 2.87 R
2916 3378 3.906846 AGCTCAATCTACCAGATTAGGGG 59.093 47.826 1.26 0.0 42.67 4.79 R
3994 4526 0.033781 TTGCTGCATTTTGTGAGCCC 59.966 50.000 1.84 0.0 33.07 5.19 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
58 59 3.413105 AGCAATCCTCTAACCTCTCCT 57.587 47.619 0.00 0.00 0.00 3.69
60 61 3.709141 AGCAATCCTCTAACCTCTCCTTC 59.291 47.826 0.00 0.00 0.00 3.46
63 64 5.364157 GCAATCCTCTAACCTCTCCTTCTAA 59.636 44.000 0.00 0.00 0.00 2.10
181 182 0.917333 AACCTTCCCCCGGCATCTAA 60.917 55.000 0.00 0.00 0.00 2.10
217 218 7.270779 TCATCTCTTTATTGTGTGATCTCCAG 58.729 38.462 0.00 0.00 0.00 3.86
243 247 7.612677 AGGAAAAGCATATATCCTTACTACCG 58.387 38.462 0.00 0.00 39.23 4.02
309 313 5.677091 GCATGCAACCACTAAATCACCTTAG 60.677 44.000 14.21 0.00 35.40 2.18
310 314 4.331968 TGCAACCACTAAATCACCTTAGG 58.668 43.478 0.00 0.00 33.85 2.69
336 340 3.944087 ACTCTGGTGCAAATTAGGTCTC 58.056 45.455 0.00 0.00 0.00 3.36
389 399 5.485662 GCACTAGGCGAATTAGTGATTTT 57.514 39.130 19.26 0.00 46.98 1.82
390 400 5.880341 GCACTAGGCGAATTAGTGATTTTT 58.120 37.500 19.26 0.00 46.98 1.94
411 421 5.612725 TTTTTGGAAAAGGAGCATTGACT 57.387 34.783 0.00 0.00 0.00 3.41
412 422 4.853924 TTTGGAAAAGGAGCATTGACTC 57.146 40.909 0.00 0.00 35.86 3.36
413 423 2.426522 TGGAAAAGGAGCATTGACTCG 58.573 47.619 0.00 0.00 37.57 4.18
414 424 1.740025 GGAAAAGGAGCATTGACTCGG 59.260 52.381 0.00 0.00 37.57 4.63
415 425 1.131315 GAAAAGGAGCATTGACTCGGC 59.869 52.381 0.00 0.00 37.57 5.54
416 426 0.678048 AAAGGAGCATTGACTCGGCC 60.678 55.000 0.00 0.00 37.57 6.13
417 427 1.557269 AAGGAGCATTGACTCGGCCT 61.557 55.000 0.00 0.00 37.57 5.19
418 428 1.522580 GGAGCATTGACTCGGCCTC 60.523 63.158 0.00 0.00 37.57 4.70
419 429 1.519719 GAGCATTGACTCGGCCTCT 59.480 57.895 0.00 0.00 0.00 3.69
420 430 0.809241 GAGCATTGACTCGGCCTCTG 60.809 60.000 0.00 0.00 0.00 3.35
421 431 2.467826 GCATTGACTCGGCCTCTGC 61.468 63.158 0.00 0.00 0.00 4.26
422 432 2.169789 CATTGACTCGGCCTCTGCG 61.170 63.158 0.00 0.00 38.85 5.18
423 433 4.742201 TTGACTCGGCCTCTGCGC 62.742 66.667 0.00 0.00 38.85 6.09
425 435 4.521062 GACTCGGCCTCTGCGCAT 62.521 66.667 12.24 0.00 38.85 4.73
426 436 4.521062 ACTCGGCCTCTGCGCATC 62.521 66.667 12.24 0.00 38.85 3.91
427 437 4.218578 CTCGGCCTCTGCGCATCT 62.219 66.667 12.24 0.00 38.85 2.90
428 438 4.519437 TCGGCCTCTGCGCATCTG 62.519 66.667 12.24 6.06 38.85 2.90
430 440 4.166888 GGCCTCTGCGCATCTGGA 62.167 66.667 22.18 11.46 38.85 3.86
431 441 2.894387 GCCTCTGCGCATCTGGAC 60.894 66.667 22.18 12.38 0.00 4.02
432 442 2.584418 CCTCTGCGCATCTGGACG 60.584 66.667 12.24 0.00 0.00 4.79
433 443 2.491621 CTCTGCGCATCTGGACGA 59.508 61.111 12.24 0.97 0.00 4.20
434 444 1.067084 CTCTGCGCATCTGGACGAT 59.933 57.895 12.24 0.00 0.00 3.73
441 451 2.697819 CATCTGGACGATGCATGCA 58.302 52.632 25.04 25.04 42.75 3.96
442 452 0.586802 CATCTGGACGATGCATGCAG 59.413 55.000 26.69 15.79 42.75 4.41
443 453 1.164662 ATCTGGACGATGCATGCAGC 61.165 55.000 25.69 25.69 45.96 5.25
444 454 1.818363 CTGGACGATGCATGCAGCT 60.818 57.895 31.04 19.15 45.94 4.24
445 455 0.531311 CTGGACGATGCATGCAGCTA 60.531 55.000 31.04 14.91 45.94 3.32
446 456 0.107268 TGGACGATGCATGCAGCTAT 59.893 50.000 31.04 20.30 45.94 2.97
447 457 1.233019 GGACGATGCATGCAGCTATT 58.767 50.000 31.04 16.70 45.94 1.73
448 458 1.605710 GGACGATGCATGCAGCTATTT 59.394 47.619 31.04 11.78 45.94 1.40
449 459 2.033801 GGACGATGCATGCAGCTATTTT 59.966 45.455 31.04 10.99 45.94 1.82
450 460 3.250762 GGACGATGCATGCAGCTATTTTA 59.749 43.478 31.04 2.45 45.94 1.52
451 461 4.083110 GGACGATGCATGCAGCTATTTTAT 60.083 41.667 31.04 9.41 45.94 1.40
452 462 5.443185 ACGATGCATGCAGCTATTTTATT 57.557 34.783 31.04 8.62 45.94 1.40
453 463 6.348458 GGACGATGCATGCAGCTATTTTATTA 60.348 38.462 31.04 0.86 45.94 0.98
454 464 6.969366 ACGATGCATGCAGCTATTTTATTAA 58.031 32.000 31.04 0.38 45.94 1.40
455 465 7.596494 ACGATGCATGCAGCTATTTTATTAAT 58.404 30.769 31.04 7.38 45.94 1.40
456 466 8.084073 ACGATGCATGCAGCTATTTTATTAATT 58.916 29.630 31.04 6.69 45.94 1.40
457 467 9.558648 CGATGCATGCAGCTATTTTATTAATTA 57.441 29.630 31.04 0.00 45.94 1.40
483 493 9.771534 ATTCTCAGAGACCTTATAAAGCATTAC 57.228 33.333 0.00 0.00 0.00 1.89
484 494 8.306313 TCTCAGAGACCTTATAAAGCATTACA 57.694 34.615 0.00 0.00 0.00 2.41
485 495 8.928448 TCTCAGAGACCTTATAAAGCATTACAT 58.072 33.333 0.00 0.00 0.00 2.29
486 496 9.202273 CTCAGAGACCTTATAAAGCATTACATC 57.798 37.037 0.00 0.00 0.00 3.06
487 497 8.704668 TCAGAGACCTTATAAAGCATTACATCA 58.295 33.333 0.00 0.00 0.00 3.07
488 498 8.986847 CAGAGACCTTATAAAGCATTACATCAG 58.013 37.037 0.00 0.00 0.00 2.90
489 499 8.709308 AGAGACCTTATAAAGCATTACATCAGT 58.291 33.333 0.00 0.00 0.00 3.41
490 500 9.982651 GAGACCTTATAAAGCATTACATCAGTA 57.017 33.333 0.00 0.00 0.00 2.74
507 517 4.766404 CAGTAAACCTGAAACCACCATC 57.234 45.455 0.00 0.00 44.49 3.51
508 518 4.398319 CAGTAAACCTGAAACCACCATCT 58.602 43.478 0.00 0.00 44.49 2.90
509 519 4.827284 CAGTAAACCTGAAACCACCATCTT 59.173 41.667 0.00 0.00 44.49 2.40
510 520 6.001460 CAGTAAACCTGAAACCACCATCTTA 58.999 40.000 0.00 0.00 44.49 2.10
511 521 6.149474 CAGTAAACCTGAAACCACCATCTTAG 59.851 42.308 0.00 0.00 44.49 2.18
512 522 3.073274 ACCTGAAACCACCATCTTAGC 57.927 47.619 0.00 0.00 0.00 3.09
513 523 2.009774 CCTGAAACCACCATCTTAGCG 58.990 52.381 0.00 0.00 0.00 4.26
514 524 2.354704 CCTGAAACCACCATCTTAGCGA 60.355 50.000 0.00 0.00 0.00 4.93
515 525 2.673368 CTGAAACCACCATCTTAGCGAC 59.327 50.000 0.00 0.00 0.00 5.19
516 526 2.037902 TGAAACCACCATCTTAGCGACA 59.962 45.455 0.00 0.00 0.00 4.35
517 527 2.094762 AACCACCATCTTAGCGACAC 57.905 50.000 0.00 0.00 0.00 3.67
518 528 0.249398 ACCACCATCTTAGCGACACC 59.751 55.000 0.00 0.00 0.00 4.16
519 529 0.537188 CCACCATCTTAGCGACACCT 59.463 55.000 0.00 0.00 0.00 4.00
520 530 1.645034 CACCATCTTAGCGACACCTG 58.355 55.000 0.00 0.00 0.00 4.00
521 531 1.066858 CACCATCTTAGCGACACCTGT 60.067 52.381 0.00 0.00 0.00 4.00
522 532 1.204941 ACCATCTTAGCGACACCTGTC 59.795 52.381 0.00 0.00 41.47 3.51
523 533 1.204704 CCATCTTAGCGACACCTGTCA 59.795 52.381 6.27 0.00 44.99 3.58
524 534 2.263077 CATCTTAGCGACACCTGTCAC 58.737 52.381 6.27 0.00 44.99 3.67
525 535 1.617322 TCTTAGCGACACCTGTCACT 58.383 50.000 6.27 3.97 44.99 3.41
526 536 2.786777 TCTTAGCGACACCTGTCACTA 58.213 47.619 6.27 3.02 44.99 2.74
527 537 2.486982 TCTTAGCGACACCTGTCACTAC 59.513 50.000 6.27 0.00 44.99 2.73
528 538 2.195741 TAGCGACACCTGTCACTACT 57.804 50.000 6.27 0.65 44.99 2.57
529 539 0.882474 AGCGACACCTGTCACTACTC 59.118 55.000 6.27 0.00 44.99 2.59
530 540 0.109226 GCGACACCTGTCACTACTCC 60.109 60.000 6.27 0.00 44.99 3.85
531 541 1.535833 CGACACCTGTCACTACTCCT 58.464 55.000 6.27 0.00 44.99 3.69
532 542 2.708051 CGACACCTGTCACTACTCCTA 58.292 52.381 6.27 0.00 44.99 2.94
533 543 3.280295 CGACACCTGTCACTACTCCTAT 58.720 50.000 6.27 0.00 44.99 2.57
534 544 3.312973 CGACACCTGTCACTACTCCTATC 59.687 52.174 6.27 0.00 44.99 2.08
535 545 3.633065 GACACCTGTCACTACTCCTATCC 59.367 52.174 0.31 0.00 44.18 2.59
536 546 2.959707 CACCTGTCACTACTCCTATCCC 59.040 54.545 0.00 0.00 0.00 3.85
537 547 2.091222 ACCTGTCACTACTCCTATCCCC 60.091 54.545 0.00 0.00 0.00 4.81
538 548 2.178106 CCTGTCACTACTCCTATCCCCT 59.822 54.545 0.00 0.00 0.00 4.79
539 549 3.374318 CCTGTCACTACTCCTATCCCCTT 60.374 52.174 0.00 0.00 0.00 3.95
540 550 3.639094 CTGTCACTACTCCTATCCCCTTG 59.361 52.174 0.00 0.00 0.00 3.61
541 551 3.271225 TGTCACTACTCCTATCCCCTTGA 59.729 47.826 0.00 0.00 0.00 3.02
542 552 4.078571 TGTCACTACTCCTATCCCCTTGAT 60.079 45.833 0.00 0.00 37.49 2.57
543 553 4.282195 GTCACTACTCCTATCCCCTTGATG 59.718 50.000 0.00 0.00 34.76 3.07
544 554 3.007398 CACTACTCCTATCCCCTTGATGC 59.993 52.174 0.00 0.00 34.76 3.91
545 555 2.196742 ACTCCTATCCCCTTGATGCA 57.803 50.000 0.00 0.00 34.76 3.96
546 556 1.771255 ACTCCTATCCCCTTGATGCAC 59.229 52.381 0.00 0.00 34.76 4.57
547 557 2.053244 CTCCTATCCCCTTGATGCACT 58.947 52.381 0.00 0.00 34.76 4.40
548 558 3.242867 CTCCTATCCCCTTGATGCACTA 58.757 50.000 0.00 0.00 34.76 2.74
549 559 3.242867 TCCTATCCCCTTGATGCACTAG 58.757 50.000 0.00 0.00 34.76 2.57
550 560 2.304180 CCTATCCCCTTGATGCACTAGG 59.696 54.545 0.00 0.00 40.33 3.02
551 561 0.475906 ATCCCCTTGATGCACTAGGC 59.524 55.000 9.92 0.00 39.54 3.93
622 632 2.838813 AGTTCCAAGTTCCTAGGTAGCC 59.161 50.000 9.08 0.00 0.00 3.93
639 649 5.071250 AGGTAGCCGAACAAATACCATCATA 59.929 40.000 3.31 0.00 40.16 2.15
654 667 6.299805 ACCATCATAGAGAGCAAAGTACAA 57.700 37.500 0.00 0.00 0.00 2.41
655 668 6.711277 ACCATCATAGAGAGCAAAGTACAAA 58.289 36.000 0.00 0.00 0.00 2.83
656 669 7.168219 ACCATCATAGAGAGCAAAGTACAAAA 58.832 34.615 0.00 0.00 0.00 2.44
1056 1104 0.900182 TCTGCTCGAGGTCATGGTGT 60.900 55.000 15.58 0.00 0.00 4.16
1060 1108 1.005037 TCGAGGTCATGGTGTGTGC 60.005 57.895 0.00 0.00 0.00 4.57
1073 1121 1.002468 GTGTGTGCTTGCTAACCAGTG 60.002 52.381 0.00 0.00 0.00 3.66
1081 1129 3.561725 GCTTGCTAACCAGTGGACATATC 59.438 47.826 18.40 2.51 0.00 1.63
1097 1145 3.962718 ACATATCCCCCATTTTGCTTCTG 59.037 43.478 0.00 0.00 0.00 3.02
1103 1151 5.090139 TCCCCCATTTTGCTTCTGAATTTA 58.910 37.500 0.00 0.00 0.00 1.40
1122 1170 6.959606 ATTTATCAGCCTGTATAGATGGGT 57.040 37.500 0.00 0.00 0.00 4.51
1128 1176 2.838736 CCTGTATAGATGGGTGTGTGC 58.161 52.381 0.00 0.00 0.00 4.57
1132 1180 0.613260 ATAGATGGGTGTGTGCGTGT 59.387 50.000 0.00 0.00 0.00 4.49
1133 1181 0.320334 TAGATGGGTGTGTGCGTGTG 60.320 55.000 0.00 0.00 0.00 3.82
1134 1182 1.596752 GATGGGTGTGTGCGTGTGA 60.597 57.895 0.00 0.00 0.00 3.58
1178 1253 6.858993 GCCTGATCGTGTTTGTAATTTGTTTA 59.141 34.615 0.00 0.00 0.00 2.01
1251 1326 1.820056 CTGCATCCAGGAGCTGCTG 60.820 63.158 26.95 26.95 36.84 4.41
1446 1521 3.853330 CAGTTCATGGCCGTCGCG 61.853 66.667 0.00 0.00 35.02 5.87
1512 1587 9.844257 TCATTTCTTCTTCTTCTTCTTCTTCTT 57.156 29.630 0.00 0.00 0.00 2.52
1515 1590 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
1516 1591 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1517 1592 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1625 1752 9.768662 ATTTTTGCCAATAATGATGGATTAGTC 57.231 29.630 0.00 0.00 40.56 2.59
1629 1756 7.397221 TGCCAATAATGATGGATTAGTCTAGG 58.603 38.462 0.00 0.00 40.56 3.02
1630 1757 7.017551 TGCCAATAATGATGGATTAGTCTAGGT 59.982 37.037 0.00 0.00 40.56 3.08
1631 1758 8.540388 GCCAATAATGATGGATTAGTCTAGGTA 58.460 37.037 0.00 0.00 40.56 3.08
1881 2015 4.608170 AATTGATTCTGTGGGTGGGTAT 57.392 40.909 0.00 0.00 0.00 2.73
1883 2017 5.725551 ATTGATTCTGTGGGTGGGTATTA 57.274 39.130 0.00 0.00 0.00 0.98
1884 2018 5.725551 TTGATTCTGTGGGTGGGTATTAT 57.274 39.130 0.00 0.00 0.00 1.28
1885 2019 5.725551 TGATTCTGTGGGTGGGTATTATT 57.274 39.130 0.00 0.00 0.00 1.40
1886 2020 6.833346 TGATTCTGTGGGTGGGTATTATTA 57.167 37.500 0.00 0.00 0.00 0.98
2010 2146 1.065491 AGAGCGAGAAGAGAGCAGAGA 60.065 52.381 0.00 0.00 0.00 3.10
2119 2580 3.884774 TGGCCGCCCCATATGACC 61.885 66.667 7.03 0.00 39.18 4.02
2120 2581 3.570212 GGCCGCCCCATATGACCT 61.570 66.667 3.65 0.00 0.00 3.85
2121 2582 2.281761 GCCGCCCCATATGACCTG 60.282 66.667 3.65 0.00 0.00 4.00
2122 2583 2.431683 CCGCCCCATATGACCTGG 59.568 66.667 3.65 0.00 0.00 4.45
2154 2615 0.394762 GGAGCCACATGCATCTTCCA 60.395 55.000 0.00 0.00 44.83 3.53
2155 2616 1.466856 GAGCCACATGCATCTTCCAA 58.533 50.000 0.00 0.00 44.83 3.53
2193 2654 9.289303 CTGAACGAATAAAATGGGATTAAACAG 57.711 33.333 0.00 0.00 0.00 3.16
2197 2658 9.801873 ACGAATAAAATGGGATTAAACAGAATG 57.198 29.630 0.00 0.00 46.00 2.67
2206 2667 8.303780 TGGGATTAAACAGAATGCATATGAAA 57.696 30.769 16.46 9.08 42.53 2.69
2207 2668 8.926374 TGGGATTAAACAGAATGCATATGAAAT 58.074 29.630 16.46 12.33 42.53 2.17
2252 2713 7.373493 AGTTCCAATAGAATGCTTTTGAAGTG 58.627 34.615 5.50 0.00 35.78 3.16
2262 2723 6.715347 ATGCTTTTGAAGTGACCTAGTTTT 57.285 33.333 0.00 0.00 0.00 2.43
2263 2724 6.524101 TGCTTTTGAAGTGACCTAGTTTTT 57.476 33.333 0.00 0.00 0.00 1.94
2264 2725 7.633193 TGCTTTTGAAGTGACCTAGTTTTTA 57.367 32.000 0.00 0.00 0.00 1.52
2265 2726 8.232913 TGCTTTTGAAGTGACCTAGTTTTTAT 57.767 30.769 0.00 0.00 0.00 1.40
2266 2727 8.691797 TGCTTTTGAAGTGACCTAGTTTTTATT 58.308 29.630 0.00 0.00 0.00 1.40
2267 2728 9.181805 GCTTTTGAAGTGACCTAGTTTTTATTC 57.818 33.333 0.00 0.00 0.00 1.75
2268 2729 9.678941 CTTTTGAAGTGACCTAGTTTTTATTCC 57.321 33.333 0.00 0.00 0.00 3.01
2269 2730 8.754991 TTTGAAGTGACCTAGTTTTTATTCCA 57.245 30.769 0.00 0.00 0.00 3.53
2270 2731 7.979444 TGAAGTGACCTAGTTTTTATTCCAG 57.021 36.000 0.00 0.00 0.00 3.86
2316 2777 2.346099 AAACCGTGAATTTGATGCGG 57.654 45.000 0.00 0.00 46.83 5.69
2321 2783 1.650153 CGTGAATTTGATGCGGCAAAG 59.350 47.619 6.82 0.00 40.68 2.77
2370 2832 4.067896 GCAGTTCTCCATTCTTTGACTCA 58.932 43.478 0.00 0.00 0.00 3.41
2374 2836 7.137426 CAGTTCTCCATTCTTTGACTCAAAAG 58.863 38.462 5.72 0.02 38.31 2.27
2869 3331 4.941609 ACCACTCGGTGATCATGC 57.058 55.556 0.00 0.00 46.79 4.06
2916 3378 2.369394 GATGGTCCATTGGTCCTGTTC 58.631 52.381 18.11 9.85 32.23 3.18
2992 3454 6.934048 ATATTCCTCACAAGAAAAGCTAGC 57.066 37.500 6.62 6.62 0.00 3.42
2996 3458 2.746362 CTCACAAGAAAAGCTAGCCCAG 59.254 50.000 12.13 0.00 0.00 4.45
3047 3512 8.432805 ACTAGTTATGCTTAGCTGGAATAATGT 58.567 33.333 12.39 0.60 0.00 2.71
3048 3513 9.929180 CTAGTTATGCTTAGCTGGAATAATGTA 57.071 33.333 5.60 0.00 0.00 2.29
3049 3514 8.608844 AGTTATGCTTAGCTGGAATAATGTAC 57.391 34.615 5.60 0.00 0.00 2.90
3186 3695 2.395988 ATCACGTGCAGCAGTGGGAA 62.396 55.000 11.67 6.35 38.77 3.97
3526 4035 3.555324 TGGTGCAGCTTGACCCGA 61.555 61.111 18.08 0.00 0.00 5.14
3668 4177 1.122019 AGTTGCAACTCCGAGGAGGT 61.122 55.000 26.36 13.97 45.88 3.85
3675 4184 0.684805 ACTCCGAGGAGGTGTGATCC 60.685 60.000 21.79 0.00 44.36 3.36
3677 4186 0.684479 TCCGAGGAGGTGTGATCCAG 60.684 60.000 0.00 0.00 39.47 3.86
3686 4195 4.202305 GGAGGTGTGATCCAGGAGAATTAG 60.202 50.000 0.00 0.00 36.79 1.73
3709 4218 3.732169 GCATCTGAATTCTCTCGTGACGA 60.732 47.826 7.70 7.70 0.00 4.20
3710 4219 4.415735 CATCTGAATTCTCTCGTGACGAA 58.584 43.478 9.64 0.00 34.74 3.85
3717 4230 2.981898 TCTCTCGTGACGAATACCAGA 58.018 47.619 9.64 0.35 34.74 3.86
3719 4232 3.754850 TCTCTCGTGACGAATACCAGAAA 59.245 43.478 9.64 0.00 34.74 2.52
3896 4417 6.128282 GCTCAAAAATAGCTGCAGTGTACTAA 60.128 38.462 16.64 0.00 37.01 2.24
3905 4426 7.829378 AGCTGCAGTGTACTAAAGTATAAAC 57.171 36.000 16.64 0.00 32.54 2.01
3908 4429 8.169268 GCTGCAGTGTACTAAAGTATAAACAAG 58.831 37.037 16.64 0.00 32.54 3.16
3940 4472 4.121317 ACAATTTTGCCATGTCACAGTTG 58.879 39.130 0.00 0.00 0.00 3.16
3994 4526 7.554118 ACCAACATAGTTCATTAATCCTGACAG 59.446 37.037 0.00 0.00 0.00 3.51
4126 4658 2.427245 CACGTTGTGCATGCCGTG 60.427 61.111 25.33 25.33 43.70 4.94
4182 7888 2.860735 GTCGATGAAGATTTCACCTCCG 59.139 50.000 0.00 0.00 43.48 4.63
4200 7906 5.636543 ACCTCCGTAAAGAATCAAACTAACG 59.363 40.000 0.00 0.00 0.00 3.18
4238 7944 6.882678 ACACTAACATAAACTAATCACACCCC 59.117 38.462 0.00 0.00 0.00 4.95
4287 7993 2.560981 TCTCTAACTTCATGACACCGCA 59.439 45.455 0.00 0.00 0.00 5.69
4436 8144 0.603065 ACCAAAATTTCTCTGGCGGC 59.397 50.000 0.00 0.00 33.19 6.53
4454 8162 1.205064 CGGCGTCTGCAGTTCTTTG 59.795 57.895 14.67 0.00 45.35 2.77
4473 8181 4.345337 GGGCATGTAGCTCGCTAC 57.655 61.111 19.39 19.39 46.56 3.58
4475 8183 0.105039 GGGCATGTAGCTCGCTACTT 59.895 55.000 24.52 17.74 46.53 2.24
4491 8202 3.366374 GCTACTTGGGAGTCACAAAATGC 60.366 47.826 9.55 9.34 37.33 3.56
4533 8244 1.600916 GCTATGGGACGGGCCAATC 60.601 63.158 4.39 0.00 38.95 2.67
4542 8253 4.838152 GGGCCAATCGCTCGCTCA 62.838 66.667 4.39 0.00 37.74 4.26
4586 8297 3.062774 GTGGCGCTCACTCTAGAAAAATC 59.937 47.826 18.16 0.00 42.86 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 8.918202 TGGTTAAGTGAGATTAAAGTTGTGAT 57.082 30.769 0.00 0.00 0.00 3.06
160 161 2.037208 ATGCCGGGGGAAGGTTTG 59.963 61.111 2.18 0.00 0.00 2.93
181 182 8.295288 CACAATAAAGAGATGAAGAAGCAAAGT 58.705 33.333 0.00 0.00 0.00 2.66
217 218 7.760340 CGGTAGTAAGGATATATGCTTTTCCTC 59.240 40.741 22.56 10.61 39.29 3.71
309 313 3.733443 AATTTGCACCAGAGTTGTTCC 57.267 42.857 0.00 0.00 0.00 3.62
310 314 4.278419 ACCTAATTTGCACCAGAGTTGTTC 59.722 41.667 0.00 0.00 0.00 3.18
336 340 7.447374 TGGAGTACATACAATGTCAAAAAGG 57.553 36.000 0.00 0.00 43.67 3.11
389 399 5.600696 GAGTCAATGCTCCTTTTCCAAAAA 58.399 37.500 0.00 0.00 0.00 1.94
390 400 4.261572 CGAGTCAATGCTCCTTTTCCAAAA 60.262 41.667 0.00 0.00 32.11 2.44
391 401 3.253188 CGAGTCAATGCTCCTTTTCCAAA 59.747 43.478 0.00 0.00 32.11 3.28
392 402 2.813754 CGAGTCAATGCTCCTTTTCCAA 59.186 45.455 0.00 0.00 32.11 3.53
393 403 2.426522 CGAGTCAATGCTCCTTTTCCA 58.573 47.619 0.00 0.00 32.11 3.53
394 404 1.740025 CCGAGTCAATGCTCCTTTTCC 59.260 52.381 0.00 0.00 32.11 3.13
395 405 1.131315 GCCGAGTCAATGCTCCTTTTC 59.869 52.381 0.00 0.00 32.11 2.29
396 406 1.168714 GCCGAGTCAATGCTCCTTTT 58.831 50.000 0.00 0.00 32.11 2.27
397 407 0.678048 GGCCGAGTCAATGCTCCTTT 60.678 55.000 0.00 0.00 32.11 3.11
398 408 1.078143 GGCCGAGTCAATGCTCCTT 60.078 57.895 0.00 0.00 32.11 3.36
399 409 1.965754 GAGGCCGAGTCAATGCTCCT 61.966 60.000 0.00 0.00 32.11 3.69
400 410 1.522580 GAGGCCGAGTCAATGCTCC 60.523 63.158 0.00 0.00 32.11 4.70
401 411 0.809241 CAGAGGCCGAGTCAATGCTC 60.809 60.000 0.00 0.00 0.00 4.26
402 412 1.220206 CAGAGGCCGAGTCAATGCT 59.780 57.895 0.00 0.00 0.00 3.79
403 413 2.467826 GCAGAGGCCGAGTCAATGC 61.468 63.158 0.00 0.00 0.00 3.56
404 414 2.169789 CGCAGAGGCCGAGTCAATG 61.170 63.158 0.00 0.00 36.38 2.82
405 415 2.185350 CGCAGAGGCCGAGTCAAT 59.815 61.111 0.00 0.00 36.38 2.57
406 416 4.742201 GCGCAGAGGCCGAGTCAA 62.742 66.667 0.30 0.00 36.38 3.18
408 418 4.521062 ATGCGCAGAGGCCGAGTC 62.521 66.667 18.32 0.00 36.38 3.36
409 419 4.521062 GATGCGCAGAGGCCGAGT 62.521 66.667 18.32 0.00 36.38 4.18
410 420 4.218578 AGATGCGCAGAGGCCGAG 62.219 66.667 18.32 0.00 36.38 4.63
411 421 4.519437 CAGATGCGCAGAGGCCGA 62.519 66.667 18.32 0.00 36.38 5.54
413 423 4.166888 TCCAGATGCGCAGAGGCC 62.167 66.667 18.32 0.00 36.38 5.19
414 424 2.894387 GTCCAGATGCGCAGAGGC 60.894 66.667 18.32 9.78 0.00 4.70
415 425 2.360949 ATCGTCCAGATGCGCAGAGG 62.361 60.000 18.32 17.41 38.36 3.69
416 426 1.067084 ATCGTCCAGATGCGCAGAG 59.933 57.895 18.32 7.96 38.36 3.35
417 427 3.210302 ATCGTCCAGATGCGCAGA 58.790 55.556 18.32 5.90 38.36 4.26
424 434 1.164662 GCTGCATGCATCGTCCAGAT 61.165 55.000 22.97 0.00 42.31 2.90
425 435 1.816679 GCTGCATGCATCGTCCAGA 60.817 57.895 22.97 0.00 42.31 3.86
426 436 0.531311 TAGCTGCATGCATCGTCCAG 60.531 55.000 22.97 8.76 45.94 3.86
427 437 0.107268 ATAGCTGCATGCATCGTCCA 59.893 50.000 22.97 5.77 45.94 4.02
428 438 1.233019 AATAGCTGCATGCATCGTCC 58.767 50.000 22.97 7.52 45.94 4.79
429 439 3.344904 AAAATAGCTGCATGCATCGTC 57.655 42.857 22.97 10.78 45.94 4.20
430 440 5.443185 AATAAAATAGCTGCATGCATCGT 57.557 34.783 22.97 11.21 45.94 3.73
431 441 8.456904 AATTAATAAAATAGCTGCATGCATCG 57.543 30.769 22.97 12.00 45.94 3.84
457 467 9.771534 GTAATGCTTTATAAGGTCTCTGAGAAT 57.228 33.333 9.31 1.91 0.00 2.40
458 468 8.758829 TGTAATGCTTTATAAGGTCTCTGAGAA 58.241 33.333 9.31 0.00 0.00 2.87
459 469 8.306313 TGTAATGCTTTATAAGGTCTCTGAGA 57.694 34.615 2.58 2.58 0.00 3.27
460 470 9.202273 GATGTAATGCTTTATAAGGTCTCTGAG 57.798 37.037 0.00 0.00 0.00 3.35
461 471 8.704668 TGATGTAATGCTTTATAAGGTCTCTGA 58.295 33.333 0.00 0.00 0.00 3.27
462 472 8.893219 TGATGTAATGCTTTATAAGGTCTCTG 57.107 34.615 0.00 0.00 0.00 3.35
463 473 8.709308 ACTGATGTAATGCTTTATAAGGTCTCT 58.291 33.333 0.00 0.00 0.00 3.10
464 474 8.894768 ACTGATGTAATGCTTTATAAGGTCTC 57.105 34.615 0.00 0.00 0.00 3.36
487 497 4.724279 AGATGGTGGTTTCAGGTTTACT 57.276 40.909 0.00 0.00 0.00 2.24
488 498 5.106277 GCTAAGATGGTGGTTTCAGGTTTAC 60.106 44.000 0.00 0.00 0.00 2.01
489 499 5.007682 GCTAAGATGGTGGTTTCAGGTTTA 58.992 41.667 0.00 0.00 0.00 2.01
490 500 3.826729 GCTAAGATGGTGGTTTCAGGTTT 59.173 43.478 0.00 0.00 0.00 3.27
491 501 3.421844 GCTAAGATGGTGGTTTCAGGTT 58.578 45.455 0.00 0.00 0.00 3.50
492 502 2.615493 CGCTAAGATGGTGGTTTCAGGT 60.615 50.000 0.00 0.00 0.00 4.00
493 503 2.009774 CGCTAAGATGGTGGTTTCAGG 58.990 52.381 0.00 0.00 0.00 3.86
494 504 2.673368 GTCGCTAAGATGGTGGTTTCAG 59.327 50.000 0.00 0.00 0.00 3.02
495 505 2.037902 TGTCGCTAAGATGGTGGTTTCA 59.962 45.455 0.00 0.00 0.00 2.69
496 506 2.415512 GTGTCGCTAAGATGGTGGTTTC 59.584 50.000 0.00 0.00 0.00 2.78
497 507 2.423577 GTGTCGCTAAGATGGTGGTTT 58.576 47.619 0.00 0.00 0.00 3.27
498 508 1.338769 GGTGTCGCTAAGATGGTGGTT 60.339 52.381 0.00 0.00 0.00 3.67
499 509 0.249398 GGTGTCGCTAAGATGGTGGT 59.751 55.000 0.00 0.00 0.00 4.16
500 510 0.537188 AGGTGTCGCTAAGATGGTGG 59.463 55.000 0.00 0.00 0.00 4.61
501 511 1.066858 ACAGGTGTCGCTAAGATGGTG 60.067 52.381 0.00 0.00 0.00 4.17
502 512 1.204941 GACAGGTGTCGCTAAGATGGT 59.795 52.381 0.00 0.00 35.12 3.55
503 513 1.927895 GACAGGTGTCGCTAAGATGG 58.072 55.000 0.00 0.00 35.12 3.51
513 523 3.633065 GGATAGGAGTAGTGACAGGTGTC 59.367 52.174 2.99 2.99 44.97 3.67
514 524 3.627747 GGGATAGGAGTAGTGACAGGTGT 60.628 52.174 0.00 0.00 0.00 4.16
515 525 2.959707 GGGATAGGAGTAGTGACAGGTG 59.040 54.545 0.00 0.00 0.00 4.00
516 526 2.091222 GGGGATAGGAGTAGTGACAGGT 60.091 54.545 0.00 0.00 0.00 4.00
517 527 2.178106 AGGGGATAGGAGTAGTGACAGG 59.822 54.545 0.00 0.00 0.00 4.00
518 528 3.603965 AGGGGATAGGAGTAGTGACAG 57.396 52.381 0.00 0.00 0.00 3.51
519 529 3.271225 TCAAGGGGATAGGAGTAGTGACA 59.729 47.826 0.00 0.00 0.00 3.58
520 530 3.912248 TCAAGGGGATAGGAGTAGTGAC 58.088 50.000 0.00 0.00 0.00 3.67
521 531 4.483950 CATCAAGGGGATAGGAGTAGTGA 58.516 47.826 0.00 0.00 33.95 3.41
522 532 3.007398 GCATCAAGGGGATAGGAGTAGTG 59.993 52.174 0.00 0.00 33.95 2.74
523 533 3.243724 GCATCAAGGGGATAGGAGTAGT 58.756 50.000 0.00 0.00 33.95 2.73
524 534 3.007398 GTGCATCAAGGGGATAGGAGTAG 59.993 52.174 0.00 0.00 33.95 2.57
525 535 2.972713 GTGCATCAAGGGGATAGGAGTA 59.027 50.000 0.00 0.00 33.95 2.59
526 536 1.771255 GTGCATCAAGGGGATAGGAGT 59.229 52.381 0.00 0.00 33.95 3.85
527 537 2.053244 AGTGCATCAAGGGGATAGGAG 58.947 52.381 0.00 0.00 33.95 3.69
528 538 2.196742 AGTGCATCAAGGGGATAGGA 57.803 50.000 0.00 0.00 33.95 2.94
529 539 2.304180 CCTAGTGCATCAAGGGGATAGG 59.696 54.545 0.00 0.00 33.95 2.57
530 540 2.289945 GCCTAGTGCATCAAGGGGATAG 60.290 54.545 12.32 0.00 40.77 2.08
531 541 1.699634 GCCTAGTGCATCAAGGGGATA 59.300 52.381 12.32 0.00 40.77 2.59
532 542 0.475906 GCCTAGTGCATCAAGGGGAT 59.524 55.000 12.32 0.00 40.77 3.85
533 543 1.915228 GCCTAGTGCATCAAGGGGA 59.085 57.895 12.32 0.00 40.77 4.81
534 544 1.524621 CGCCTAGTGCATCAAGGGG 60.525 63.158 12.48 12.48 41.33 4.79
535 545 0.107703 TTCGCCTAGTGCATCAAGGG 60.108 55.000 12.32 2.83 41.33 3.95
536 546 1.959042 ATTCGCCTAGTGCATCAAGG 58.041 50.000 7.41 7.41 41.33 3.61
537 547 4.025396 CACTAATTCGCCTAGTGCATCAAG 60.025 45.833 0.00 0.00 39.75 3.02
538 548 3.871006 CACTAATTCGCCTAGTGCATCAA 59.129 43.478 0.00 0.00 39.75 2.57
539 549 3.132111 TCACTAATTCGCCTAGTGCATCA 59.868 43.478 11.39 0.00 43.94 3.07
540 550 3.717707 TCACTAATTCGCCTAGTGCATC 58.282 45.455 11.39 0.00 43.94 3.91
541 551 3.819564 TCACTAATTCGCCTAGTGCAT 57.180 42.857 11.39 0.00 43.94 3.96
542 552 3.118775 ACATCACTAATTCGCCTAGTGCA 60.119 43.478 11.39 0.00 43.94 4.57
543 553 3.458189 ACATCACTAATTCGCCTAGTGC 58.542 45.455 11.39 0.00 43.94 4.40
544 554 5.588240 TGTACATCACTAATTCGCCTAGTG 58.412 41.667 10.44 10.44 45.09 2.74
545 555 5.847111 TGTACATCACTAATTCGCCTAGT 57.153 39.130 0.00 0.00 0.00 2.57
546 556 5.119279 GCATGTACATCACTAATTCGCCTAG 59.881 44.000 5.07 0.00 0.00 3.02
547 557 4.988540 GCATGTACATCACTAATTCGCCTA 59.011 41.667 5.07 0.00 0.00 3.93
548 558 3.809832 GCATGTACATCACTAATTCGCCT 59.190 43.478 5.07 0.00 0.00 5.52
549 559 3.559655 TGCATGTACATCACTAATTCGCC 59.440 43.478 5.07 0.00 0.00 5.54
550 560 4.794248 TGCATGTACATCACTAATTCGC 57.206 40.909 5.07 3.76 0.00 4.70
551 561 6.105657 TGTTGCATGTACATCACTAATTCG 57.894 37.500 5.07 0.00 0.00 3.34
552 562 7.530010 AGTTGTTGCATGTACATCACTAATTC 58.470 34.615 5.07 0.00 0.00 2.17
553 563 7.391554 AGAGTTGTTGCATGTACATCACTAATT 59.608 33.333 5.07 2.94 0.00 1.40
554 564 6.881065 AGAGTTGTTGCATGTACATCACTAAT 59.119 34.615 5.07 0.00 0.00 1.73
555 565 6.230472 AGAGTTGTTGCATGTACATCACTAA 58.770 36.000 5.07 3.17 0.00 2.24
556 566 5.793817 AGAGTTGTTGCATGTACATCACTA 58.206 37.500 5.07 0.00 0.00 2.74
557 567 4.645535 AGAGTTGTTGCATGTACATCACT 58.354 39.130 5.07 1.62 0.00 3.41
558 568 5.049474 TGAAGAGTTGTTGCATGTACATCAC 60.049 40.000 5.07 4.01 0.00 3.06
559 569 5.062528 TGAAGAGTTGTTGCATGTACATCA 58.937 37.500 5.07 4.71 0.00 3.07
622 632 5.985530 TGCTCTCTATGATGGTATTTGTTCG 59.014 40.000 0.00 0.00 0.00 3.95
655 668 8.729756 GGGCACTAGAAAAATGCAAATATTTTT 58.270 29.630 7.94 7.94 46.97 1.94
656 669 8.102676 AGGGCACTAGAAAAATGCAAATATTTT 58.897 29.630 0.00 0.00 40.84 1.82
912 925 1.198637 GATGAAATGGCCGAGCTATGC 59.801 52.381 0.00 0.00 28.30 3.14
1056 1104 0.472044 TCCACTGGTTAGCAAGCACA 59.528 50.000 0.00 0.00 34.75 4.57
1060 1108 4.130118 GGATATGTCCACTGGTTAGCAAG 58.870 47.826 3.16 0.00 44.42 4.01
1073 1121 2.962859 AGCAAAATGGGGGATATGTCC 58.037 47.619 0.00 0.00 44.29 4.02
1081 1129 3.986996 AATTCAGAAGCAAAATGGGGG 57.013 42.857 0.00 0.00 0.00 5.40
1097 1145 7.335422 CACCCATCTATACAGGCTGATAAATTC 59.665 40.741 23.66 0.00 0.00 2.17
1103 1151 3.326006 CACACCCATCTATACAGGCTGAT 59.674 47.826 23.66 12.61 0.00 2.90
1122 1170 1.217001 GTGAAGATCACACGCACACA 58.783 50.000 5.65 0.00 46.22 3.72
1178 1253 7.348274 TCAAAGAATCCTCACTTATGGACCTAT 59.652 37.037 0.00 0.00 34.90 2.57
1377 1452 2.819595 CGGAACATCTGCCCCGTG 60.820 66.667 0.00 0.00 37.40 4.94
1524 1599 7.764443 TCAGACACCTCTACAGCAAATTATTAC 59.236 37.037 0.00 0.00 0.00 1.89
1526 1601 6.711277 TCAGACACCTCTACAGCAAATTATT 58.289 36.000 0.00 0.00 0.00 1.40
1527 1602 6.299805 TCAGACACCTCTACAGCAAATTAT 57.700 37.500 0.00 0.00 0.00 1.28
1625 1752 2.512896 TCCCAGTGGTACTCCTACCTAG 59.487 54.545 8.74 0.00 42.94 3.02
1629 1756 1.006878 ACCTCCCAGTGGTACTCCTAC 59.993 57.143 8.74 0.00 35.80 3.18
1630 1757 1.390287 ACCTCCCAGTGGTACTCCTA 58.610 55.000 8.74 0.00 35.80 2.94
1631 1758 0.492276 AACCTCCCAGTGGTACTCCT 59.508 55.000 8.74 0.00 36.69 3.69
1632 1759 2.108970 CTAACCTCCCAGTGGTACTCC 58.891 57.143 8.74 0.00 36.69 3.85
1633 1760 2.759535 GACTAACCTCCCAGTGGTACTC 59.240 54.545 8.74 0.00 36.69 2.59
1634 1761 2.382649 AGACTAACCTCCCAGTGGTACT 59.617 50.000 8.74 0.00 36.69 2.73
1684 1811 0.999406 CGGTCATAACTTGTCCAGCG 59.001 55.000 0.00 0.00 33.59 5.18
1855 1986 3.129287 CCACCCACAGAATCAATTACTGC 59.871 47.826 0.00 0.00 35.38 4.40
1884 2018 9.109393 GCTCCATGTCAGATAAAATAAGTGTAA 57.891 33.333 0.00 0.00 0.00 2.41
1885 2019 8.264347 TGCTCCATGTCAGATAAAATAAGTGTA 58.736 33.333 0.00 0.00 0.00 2.90
1886 2020 7.112122 TGCTCCATGTCAGATAAAATAAGTGT 58.888 34.615 0.00 0.00 0.00 3.55
1935 2070 1.447838 CGTACTTGTGGGCTCGCAT 60.448 57.895 0.00 0.00 32.95 4.73
2010 2146 0.459899 TCATCCTCGTATTGCGTGCT 59.540 50.000 0.00 0.00 42.13 4.40
2067 2528 0.172578 CGACTGCCACCGAGTAATCA 59.827 55.000 0.00 0.00 0.00 2.57
2216 2677 8.037166 GCATTCTATTGGAACTTTCAAGGATTT 58.963 33.333 0.00 0.00 36.70 2.17
2217 2678 7.398332 AGCATTCTATTGGAACTTTCAAGGATT 59.602 33.333 0.00 0.00 36.70 3.01
2218 2679 6.894103 AGCATTCTATTGGAACTTTCAAGGAT 59.106 34.615 0.00 0.00 36.70 3.24
2219 2680 6.248433 AGCATTCTATTGGAACTTTCAAGGA 58.752 36.000 0.00 0.00 36.70 3.36
2252 2713 9.457436 TGGAATAACTGGAATAAAAACTAGGTC 57.543 33.333 0.00 0.00 0.00 3.85
2316 2777 3.188460 TGTCCTACGCATTTTCTCTTTGC 59.812 43.478 0.00 0.00 0.00 3.68
2321 2783 2.599082 CGTCTGTCCTACGCATTTTCTC 59.401 50.000 0.00 0.00 33.04 2.87
2353 2815 8.786898 CATAACTTTTGAGTCAAAGAATGGAGA 58.213 33.333 17.36 0.82 34.72 3.71
2354 2816 8.571336 ACATAACTTTTGAGTCAAAGAATGGAG 58.429 33.333 17.36 13.29 34.72 3.86
2822 3284 5.648330 AAGAGGTTAGGTATTGATTCCCC 57.352 43.478 0.00 0.00 0.00 4.81
2823 3285 8.272889 ACTTAAAGAGGTTAGGTATTGATTCCC 58.727 37.037 0.00 0.00 30.62 3.97
2916 3378 3.906846 AGCTCAATCTACCAGATTAGGGG 59.093 47.826 1.26 0.00 42.67 4.79
2992 3454 5.833131 AGGGTTATAATGCAATGTTACTGGG 59.167 40.000 0.00 0.00 0.00 4.45
2996 3458 5.068460 TGGCAGGGTTATAATGCAATGTTAC 59.932 40.000 10.78 0.00 41.78 2.50
3186 3695 2.792599 GCGTCGACGAGGTCAGAT 59.207 61.111 39.74 0.00 43.02 2.90
3207 3716 0.811616 CGCCCAGCTCCTTGATGTAC 60.812 60.000 0.00 0.00 0.00 2.90
3668 4177 3.114606 TGCCTAATTCTCCTGGATCACA 58.885 45.455 0.00 0.00 0.00 3.58
3675 4184 6.297582 AGAATTCAGATGCCTAATTCTCCTG 58.702 40.000 8.44 0.00 43.18 3.86
3686 4195 2.863137 GTCACGAGAGAATTCAGATGCC 59.137 50.000 8.44 0.00 0.00 4.40
3752 4270 5.227908 TCTCAAGTTACGAGACACCATTTC 58.772 41.667 0.00 0.00 34.59 2.17
3905 4426 5.048083 TGGCAAAATTGTAGCTACCTTCTTG 60.048 40.000 21.01 17.92 0.00 3.02
3908 4429 5.105756 ACATGGCAAAATTGTAGCTACCTTC 60.106 40.000 21.01 4.14 0.00 3.46
3940 4472 2.103263 ACTCTGAAACACTGGAGACACC 59.897 50.000 0.00 0.00 35.60 4.16
3994 4526 0.033781 TTGCTGCATTTTGTGAGCCC 59.966 50.000 1.84 0.00 33.07 5.19
4040 4572 5.016051 TCTATCCTTGCACTGATCTGTTC 57.984 43.478 1.95 0.00 0.00 3.18
4094 4626 1.153901 CGTGTATCTTCACCGCGGT 60.154 57.895 28.70 28.70 35.18 5.68
4126 4658 1.408453 ATCCCCGGCCAAGTAGCTAC 61.408 60.000 16.43 16.43 0.00 3.58
4238 7944 4.930405 TGTGCATCATACAGCCAATTTTTG 59.070 37.500 0.00 0.00 0.00 2.44
4256 7962 6.017934 GTCATGAAGTTAGAGAGTTTTGTGCA 60.018 38.462 0.00 0.00 0.00 4.57
4405 8113 2.814913 ATTTTGGTCCCGTCGCCTCC 62.815 60.000 0.00 0.00 0.00 4.30
4413 8121 1.202348 GCCAGAGAAATTTTGGTCCCG 59.798 52.381 8.76 0.00 34.43 5.14
4436 8144 1.205064 CAAAGAACTGCAGACGCCG 59.795 57.895 23.35 0.00 37.32 6.46
4454 8162 2.507854 TAGCGAGCTACATGCCCCC 61.508 63.158 0.00 0.00 44.23 5.40
4473 8181 2.361757 TGTGCATTTTGTGACTCCCAAG 59.638 45.455 0.00 0.00 0.00 3.61
4475 8183 1.955778 CTGTGCATTTTGTGACTCCCA 59.044 47.619 0.00 0.00 0.00 4.37
4476 8184 1.336240 GCTGTGCATTTTGTGACTCCC 60.336 52.381 0.00 0.00 0.00 4.30
4514 8225 3.476031 ATTGGCCCGTCCCATAGCG 62.476 63.158 0.00 0.00 34.21 4.26
4533 8244 2.278206 ACAGCGTATGAGCGAGCG 60.278 61.111 0.00 0.00 43.00 5.03
4586 8297 1.086696 CTGTTAGCCACCATCCGTTG 58.913 55.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.