Multiple sequence alignment - TraesCS7D01G400300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G400300 chr7D 100.000 2375 0 0 1 2375 517217899 517220273 0.000000e+00 4386.0
1 TraesCS7D01G400300 chr7A 89.495 1742 94 27 668 2370 592045872 592047563 0.000000e+00 2121.0
2 TraesCS7D01G400300 chr7B 93.757 849 29 10 801 1638 550030437 550031272 0.000000e+00 1253.0
3 TraesCS7D01G400300 chr7B 90.821 414 27 5 1961 2373 550031521 550031924 5.770000e-151 544.0
4 TraesCS7D01G400300 chr7B 87.500 344 41 2 31 372 550028803 550029146 1.710000e-106 396.0
5 TraesCS7D01G400300 chr7B 98.246 57 1 0 668 724 550029263 550029319 1.500000e-17 100.0
6 TraesCS7D01G400300 chr7B 92.063 63 5 0 1689 1751 550031267 550031329 3.250000e-14 89.8
7 TraesCS7D01G400300 chr3B 81.712 514 62 13 1001 1485 172958849 172958339 1.320000e-107 399.0
8 TraesCS7D01G400300 chr2B 89.617 183 14 4 488 668 653840744 653840923 6.600000e-56 228.0
9 TraesCS7D01G400300 chr2B 100.000 29 0 0 7 35 704762425 704762453 1.000000e-03 54.7
10 TraesCS7D01G400300 chr2D 87.432 183 19 4 488 668 547601925 547602105 8.600000e-50 207.0
11 TraesCS7D01G400300 chr1D 100.000 32 0 0 1 32 471795137 471795106 2.550000e-05 60.2
12 TraesCS7D01G400300 chr6B 100.000 29 0 0 3 31 679742017 679742045 1.000000e-03 54.7
13 TraesCS7D01G400300 chr6B 100.000 28 0 0 7 34 649628580 649628607 4.000000e-03 52.8
14 TraesCS7D01G400300 chr3D 100.000 29 0 0 3 31 606579049 606579077 1.000000e-03 54.7
15 TraesCS7D01G400300 chr6D 100.000 28 0 0 3 30 76048119 76048092 4.000000e-03 52.8
16 TraesCS7D01G400300 chr6D 100.000 28 0 0 3 30 76048695 76048668 4.000000e-03 52.8
17 TraesCS7D01G400300 chr6D 100.000 28 0 0 3 30 99548115 99548142 4.000000e-03 52.8
18 TraesCS7D01G400300 chr6D 100.000 28 0 0 3 30 413817079 413817052 4.000000e-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 TraesCS7D01G400300 chr7D 517217899 517220273 2374 False 4386.00 4386 100.0000 1 2375 1 chr7D.!!$F1 2374
1 TraesCS7D01G400300 chr7A 592045872 592047563 1691 False 2121.00 2121 89.4950 668 2370 1 chr7A.!!$F1 1702
2 TraesCS7D01G400300 chr7B 550028803 550031924 3121 False 476.56 1253 92.4774 31 2373 5 chr7B.!!$F1 2342
3 TraesCS7D01G400300 chr3B 172958339 172958849 510 True 399.00 399 81.7120 1001 1485 1 chr3B.!!$R1 484

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
475 503 0.173255 CATTTGGCCGGCCTGTAAAG 59.827 55.0 43.34 26.56 36.94 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 3074 0.034863 TAATTCCACCACCTTCCGCC 60.035 55.0 0.0 0.0 0.0 6.13 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
45 46 2.304761 TCAACAGTACCTTCCCACCATC 59.695 50.000 0.00 0.00 0.00 3.51
66 67 6.352516 CATCAGGTACAATTAGCTCTTCCTT 58.647 40.000 0.00 0.00 33.58 3.36
72 73 5.096443 ACAATTAGCTCTTCCTTCTCCTG 57.904 43.478 0.00 0.00 0.00 3.86
107 108 5.244402 TCAGGTTCATGTCAAAATTCTGCAT 59.756 36.000 0.00 0.00 0.00 3.96
117 118 5.630680 GTCAAAATTCTGCATCATCGTGTTT 59.369 36.000 0.00 0.00 0.00 2.83
120 121 3.541071 TTCTGCATCATCGTGTTTGTG 57.459 42.857 0.00 0.00 0.00 3.33
123 124 1.197492 TGCATCATCGTGTTTGTGAGC 59.803 47.619 0.00 0.00 0.00 4.26
133 134 2.480037 GTGTTTGTGAGCGATGACATCA 59.520 45.455 15.58 0.00 0.00 3.07
136 137 5.007039 GTGTTTGTGAGCGATGACATCATAT 59.993 40.000 15.58 0.27 36.57 1.78
140 141 5.544650 TGTGAGCGATGACATCATATCATT 58.455 37.500 15.58 0.00 36.92 2.57
141 142 6.690530 TGTGAGCGATGACATCATATCATTA 58.309 36.000 15.58 6.75 36.92 1.90
165 166 2.549754 CAAGTGCTCGTTCAATGGAGTT 59.450 45.455 0.00 0.00 32.83 3.01
171 172 3.773117 GTTCAATGGAGTTGCACGG 57.227 52.632 0.00 0.00 37.74 4.94
190 191 1.407989 GGATGCTTCTGCTGCTACCTT 60.408 52.381 0.00 0.00 40.48 3.50
214 215 5.874892 GAAGATTTGGACTATCTTCGTCG 57.125 43.478 9.15 0.00 44.56 5.12
215 216 4.308899 AGATTTGGACTATCTTCGTCGG 57.691 45.455 0.00 0.00 32.24 4.79
219 220 0.739561 GGACTATCTTCGTCGGCAGT 59.260 55.000 0.00 0.00 32.24 4.40
229 230 1.227002 GTCGGCAGTTCCCTCGATC 60.227 63.158 0.00 0.00 34.13 3.69
262 264 1.842381 AAGCCGGTTCTGAAGGAGGG 61.842 60.000 1.90 0.00 0.00 4.30
265 267 2.677848 GGTTCTGAAGGAGGGGGC 59.322 66.667 0.00 0.00 0.00 5.80
270 272 0.846427 TCTGAAGGAGGGGGCATTGT 60.846 55.000 0.00 0.00 0.00 2.71
277 279 3.076916 GGGGGCATTGTCAAGGGC 61.077 66.667 14.80 14.80 36.98 5.19
279 281 2.361104 GGGCATTGTCAAGGGCGA 60.361 61.111 16.33 0.00 38.77 5.54
280 282 2.700773 GGGCATTGTCAAGGGCGAC 61.701 63.158 16.33 1.48 38.77 5.19
284 286 1.943968 GCATTGTCAAGGGCGACAGTA 60.944 52.381 0.00 0.00 46.14 2.74
290 292 1.202371 TCAAGGGCGACAGTATTAGCG 60.202 52.381 0.00 0.00 0.00 4.26
302 304 5.445964 ACAGTATTAGCGGGAATCCAAATT 58.554 37.500 0.09 0.00 0.00 1.82
307 309 2.807676 AGCGGGAATCCAAATTCAAGT 58.192 42.857 0.09 0.00 42.66 3.16
314 316 5.359756 GGAATCCAAATTCAAGTAATGGGC 58.640 41.667 0.00 0.00 42.66 5.36
315 317 5.357742 AATCCAAATTCAAGTAATGGGCC 57.642 39.130 0.00 0.00 0.00 5.80
316 318 3.784178 TCCAAATTCAAGTAATGGGCCA 58.216 40.909 9.61 9.61 0.00 5.36
320 322 2.214376 TTCAAGTAATGGGCCAGTGG 57.786 50.000 18.22 4.20 0.00 4.00
339 342 2.391389 CGCGACCCAGAAAAGAGGC 61.391 63.158 0.00 0.00 0.00 4.70
342 345 1.302511 GACCCAGAAAAGAGGCGCA 60.303 57.895 10.83 0.00 0.00 6.09
348 351 1.876156 CAGAAAAGAGGCGCAACTTCT 59.124 47.619 10.83 6.69 0.00 2.85
349 352 3.067106 CAGAAAAGAGGCGCAACTTCTA 58.933 45.455 10.83 0.00 0.00 2.10
350 353 3.124297 CAGAAAAGAGGCGCAACTTCTAG 59.876 47.826 10.83 2.08 0.00 2.43
364 367 2.045926 CTAGCCGGCTTGCAGGTT 60.046 61.111 37.74 10.55 0.00 3.50
374 385 2.295909 GGCTTGCAGGTTGTGAATTACA 59.704 45.455 0.00 0.00 37.56 2.41
446 474 1.826385 ACTTGGCGAGGAAGAAATGG 58.174 50.000 6.71 0.00 0.00 3.16
447 475 1.098050 CTTGGCGAGGAAGAAATGGG 58.902 55.000 0.00 0.00 0.00 4.00
448 476 0.965363 TTGGCGAGGAAGAAATGGGC 60.965 55.000 0.00 0.00 0.00 5.36
449 477 1.378514 GGCGAGGAAGAAATGGGCA 60.379 57.895 0.00 0.00 0.00 5.36
450 478 0.965363 GGCGAGGAAGAAATGGGCAA 60.965 55.000 0.00 0.00 0.00 4.52
451 479 0.887933 GCGAGGAAGAAATGGGCAAA 59.112 50.000 0.00 0.00 0.00 3.68
452 480 1.478105 GCGAGGAAGAAATGGGCAAAT 59.522 47.619 0.00 0.00 0.00 2.32
453 481 2.736400 GCGAGGAAGAAATGGGCAAATG 60.736 50.000 0.00 0.00 0.00 2.32
472 500 2.044451 CCATTTGGCCGGCCTGTA 60.044 61.111 43.34 28.75 36.94 2.74
473 501 1.680651 CCATTTGGCCGGCCTGTAA 60.681 57.895 43.34 32.47 36.94 2.41
474 502 1.254284 CCATTTGGCCGGCCTGTAAA 61.254 55.000 43.34 34.20 36.94 2.01
475 503 0.173255 CATTTGGCCGGCCTGTAAAG 59.827 55.000 43.34 26.56 36.94 1.85
476 504 0.251608 ATTTGGCCGGCCTGTAAAGT 60.252 50.000 43.34 24.50 36.94 2.66
477 505 0.468400 TTTGGCCGGCCTGTAAAGTT 60.468 50.000 43.34 0.00 36.94 2.66
478 506 1.175983 TTGGCCGGCCTGTAAAGTTG 61.176 55.000 43.34 0.00 36.94 3.16
479 507 1.602605 GGCCGGCCTGTAAAGTTGT 60.603 57.895 38.76 0.00 0.00 3.32
480 508 0.321830 GGCCGGCCTGTAAAGTTGTA 60.322 55.000 38.76 0.00 0.00 2.41
481 509 1.525941 GCCGGCCTGTAAAGTTGTAA 58.474 50.000 18.11 0.00 0.00 2.41
482 510 2.089201 GCCGGCCTGTAAAGTTGTAAT 58.911 47.619 18.11 0.00 0.00 1.89
483 511 2.490509 GCCGGCCTGTAAAGTTGTAATT 59.509 45.455 18.11 0.00 0.00 1.40
484 512 3.057104 GCCGGCCTGTAAAGTTGTAATTT 60.057 43.478 18.11 0.00 0.00 1.82
485 513 4.559906 GCCGGCCTGTAAAGTTGTAATTTT 60.560 41.667 18.11 0.00 0.00 1.82
486 514 4.920927 CCGGCCTGTAAAGTTGTAATTTTG 59.079 41.667 0.00 0.00 0.00 2.44
487 515 5.278561 CCGGCCTGTAAAGTTGTAATTTTGA 60.279 40.000 0.00 0.00 0.00 2.69
488 516 6.210078 CGGCCTGTAAAGTTGTAATTTTGAA 58.790 36.000 0.00 0.00 0.00 2.69
489 517 6.866248 CGGCCTGTAAAGTTGTAATTTTGAAT 59.134 34.615 0.00 0.00 0.00 2.57
490 518 7.061789 CGGCCTGTAAAGTTGTAATTTTGAATC 59.938 37.037 0.00 0.00 0.00 2.52
491 519 7.870445 GGCCTGTAAAGTTGTAATTTTGAATCA 59.130 33.333 0.00 0.00 0.00 2.57
492 520 9.255304 GCCTGTAAAGTTGTAATTTTGAATCAA 57.745 29.630 0.00 0.00 0.00 2.57
506 534 9.504708 AATTTTGAATCAAAAATGCTACATCCA 57.495 25.926 22.76 0.00 44.68 3.41
507 535 7.887996 TTTGAATCAAAAATGCTACATCCAC 57.112 32.000 5.87 0.00 29.89 4.02
508 536 5.639757 TGAATCAAAAATGCTACATCCACG 58.360 37.500 0.00 0.00 0.00 4.94
509 537 5.182950 TGAATCAAAAATGCTACATCCACGT 59.817 36.000 0.00 0.00 0.00 4.49
510 538 6.372937 TGAATCAAAAATGCTACATCCACGTA 59.627 34.615 0.00 0.00 0.00 3.57
511 539 6.751514 ATCAAAAATGCTACATCCACGTAA 57.248 33.333 0.00 0.00 0.00 3.18
512 540 6.561737 TCAAAAATGCTACATCCACGTAAA 57.438 33.333 0.00 0.00 0.00 2.01
513 541 6.375377 TCAAAAATGCTACATCCACGTAAAC 58.625 36.000 0.00 0.00 0.00 2.01
514 542 4.957759 AAATGCTACATCCACGTAAACC 57.042 40.909 0.00 0.00 0.00 3.27
515 543 3.906720 ATGCTACATCCACGTAAACCT 57.093 42.857 0.00 0.00 0.00 3.50
516 544 5.347620 AATGCTACATCCACGTAAACCTA 57.652 39.130 0.00 0.00 0.00 3.08
517 545 4.114058 TGCTACATCCACGTAAACCTAC 57.886 45.455 0.00 0.00 0.00 3.18
542 570 9.508567 ACGAAAGTCTTACGTAATATTCCTAAC 57.491 33.333 8.76 0.00 44.19 2.34
543 571 9.727627 CGAAAGTCTTACGTAATATTCCTAACT 57.272 33.333 8.76 0.77 0.00 2.24
557 585 6.563037 ATTCCTAACTAACTCTTCTTCCCC 57.437 41.667 0.00 0.00 0.00 4.81
558 586 4.359996 TCCTAACTAACTCTTCTTCCCCC 58.640 47.826 0.00 0.00 0.00 5.40
579 607 2.022718 TTGATTTTCAAGGGGGTGGG 57.977 50.000 0.00 0.00 31.83 4.61
580 608 0.544120 TGATTTTCAAGGGGGTGGGC 60.544 55.000 0.00 0.00 0.00 5.36
581 609 0.252239 GATTTTCAAGGGGGTGGGCT 60.252 55.000 0.00 0.00 0.00 5.19
582 610 0.252239 ATTTTCAAGGGGGTGGGCTC 60.252 55.000 0.00 0.00 0.00 4.70
583 611 2.380571 TTTTCAAGGGGGTGGGCTCC 62.381 60.000 0.00 0.00 0.00 4.70
584 612 3.829311 TTCAAGGGGGTGGGCTCCT 62.829 63.158 0.00 0.00 34.96 3.69
585 613 3.268032 CAAGGGGGTGGGCTCCTT 61.268 66.667 0.00 0.00 41.15 3.36
586 614 2.941583 AAGGGGGTGGGCTCCTTC 60.942 66.667 0.00 0.00 36.22 3.46
589 617 3.412408 GGGGTGGGCTCCTTCCTC 61.412 72.222 0.00 0.00 30.72 3.71
590 618 3.412408 GGGTGGGCTCCTTCCTCC 61.412 72.222 0.00 0.00 37.25 4.30
591 619 3.412408 GGTGGGCTCCTTCCTCCC 61.412 72.222 0.00 0.00 40.47 4.30
592 620 3.412408 GTGGGCTCCTTCCTCCCC 61.412 72.222 0.00 0.00 39.30 4.81
593 621 3.626596 TGGGCTCCTTCCTCCCCT 61.627 66.667 0.00 0.00 39.30 4.79
594 622 2.261293 TGGGCTCCTTCCTCCCCTA 61.261 63.158 0.00 0.00 39.30 3.53
595 623 1.004361 GGGCTCCTTCCTCCCCTAA 59.996 63.158 0.00 0.00 34.59 2.69
596 624 0.402126 GGGCTCCTTCCTCCCCTAAT 60.402 60.000 0.00 0.00 34.59 1.73
597 625 1.060729 GGCTCCTTCCTCCCCTAATC 58.939 60.000 0.00 0.00 0.00 1.75
598 626 1.415273 GGCTCCTTCCTCCCCTAATCT 60.415 57.143 0.00 0.00 0.00 2.40
599 627 2.413601 GCTCCTTCCTCCCCTAATCTT 58.586 52.381 0.00 0.00 0.00 2.40
600 628 2.370519 GCTCCTTCCTCCCCTAATCTTC 59.629 54.545 0.00 0.00 0.00 2.87
601 629 3.658725 CTCCTTCCTCCCCTAATCTTCA 58.341 50.000 0.00 0.00 0.00 3.02
602 630 4.040755 CTCCTTCCTCCCCTAATCTTCAA 58.959 47.826 0.00 0.00 0.00 2.69
603 631 4.646157 TCCTTCCTCCCCTAATCTTCAAT 58.354 43.478 0.00 0.00 0.00 2.57
604 632 4.660771 TCCTTCCTCCCCTAATCTTCAATC 59.339 45.833 0.00 0.00 0.00 2.67
605 633 4.202514 CCTTCCTCCCCTAATCTTCAATCC 60.203 50.000 0.00 0.00 0.00 3.01
606 634 4.302004 TCCTCCCCTAATCTTCAATCCT 57.698 45.455 0.00 0.00 0.00 3.24
607 635 5.434003 TCCTCCCCTAATCTTCAATCCTA 57.566 43.478 0.00 0.00 0.00 2.94
608 636 5.799536 TCCTCCCCTAATCTTCAATCCTAA 58.200 41.667 0.00 0.00 0.00 2.69
609 637 6.402442 TCCTCCCCTAATCTTCAATCCTAAT 58.598 40.000 0.00 0.00 0.00 1.73
610 638 6.502158 TCCTCCCCTAATCTTCAATCCTAATC 59.498 42.308 0.00 0.00 0.00 1.75
611 639 6.296720 CCTCCCCTAATCTTCAATCCTAATCC 60.297 46.154 0.00 0.00 0.00 3.01
612 640 6.402442 TCCCCTAATCTTCAATCCTAATCCT 58.598 40.000 0.00 0.00 0.00 3.24
613 641 6.502158 TCCCCTAATCTTCAATCCTAATCCTC 59.498 42.308 0.00 0.00 0.00 3.71
614 642 6.296720 CCCCTAATCTTCAATCCTAATCCTCC 60.297 46.154 0.00 0.00 0.00 4.30
615 643 6.273260 CCCTAATCTTCAATCCTAATCCTCCA 59.727 42.308 0.00 0.00 0.00 3.86
616 644 7.164803 CCTAATCTTCAATCCTAATCCTCCAC 58.835 42.308 0.00 0.00 0.00 4.02
617 645 5.574970 ATCTTCAATCCTAATCCTCCACC 57.425 43.478 0.00 0.00 0.00 4.61
618 646 4.635473 TCTTCAATCCTAATCCTCCACCT 58.365 43.478 0.00 0.00 0.00 4.00
619 647 4.410228 TCTTCAATCCTAATCCTCCACCTG 59.590 45.833 0.00 0.00 0.00 4.00
620 648 3.048600 TCAATCCTAATCCTCCACCTGG 58.951 50.000 0.00 0.00 0.00 4.45
621 649 2.780010 CAATCCTAATCCTCCACCTGGT 59.220 50.000 0.00 0.00 36.34 4.00
622 650 3.973973 CAATCCTAATCCTCCACCTGGTA 59.026 47.826 0.00 0.00 36.34 3.25
623 651 3.788116 TCCTAATCCTCCACCTGGTAA 57.212 47.619 0.00 0.00 36.34 2.85
624 652 4.295905 TCCTAATCCTCCACCTGGTAAT 57.704 45.455 0.00 0.00 36.34 1.89
625 653 4.641868 TCCTAATCCTCCACCTGGTAATT 58.358 43.478 0.00 0.00 36.34 1.40
626 654 5.795079 TCCTAATCCTCCACCTGGTAATTA 58.205 41.667 0.00 0.00 36.34 1.40
627 655 5.605488 TCCTAATCCTCCACCTGGTAATTAC 59.395 44.000 7.09 7.09 36.34 1.89
628 656 4.417426 AATCCTCCACCTGGTAATTACG 57.583 45.455 9.46 0.00 36.34 3.18
629 657 2.823959 TCCTCCACCTGGTAATTACGT 58.176 47.619 9.46 0.00 36.34 3.57
630 658 3.175594 TCCTCCACCTGGTAATTACGTT 58.824 45.455 9.46 0.00 36.34 3.99
631 659 4.352009 TCCTCCACCTGGTAATTACGTTA 58.648 43.478 9.46 0.00 36.34 3.18
632 660 4.776837 TCCTCCACCTGGTAATTACGTTAA 59.223 41.667 9.46 0.00 36.34 2.01
633 661 5.426185 TCCTCCACCTGGTAATTACGTTAAT 59.574 40.000 9.46 0.00 36.34 1.40
634 662 5.756833 CCTCCACCTGGTAATTACGTTAATC 59.243 44.000 9.46 0.00 36.34 1.75
635 663 6.297080 TCCACCTGGTAATTACGTTAATCA 57.703 37.500 9.46 0.34 36.34 2.57
636 664 6.342906 TCCACCTGGTAATTACGTTAATCAG 58.657 40.000 9.46 9.31 36.34 2.90
637 665 5.526111 CCACCTGGTAATTACGTTAATCAGG 59.474 44.000 23.75 23.75 43.91 3.86
638 666 6.303903 ACCTGGTAATTACGTTAATCAGGT 57.696 37.500 24.67 24.67 45.01 4.00
639 667 7.267128 CACCTGGTAATTACGTTAATCAGGTA 58.733 38.462 27.40 0.00 46.37 3.08
640 668 7.765360 CACCTGGTAATTACGTTAATCAGGTAA 59.235 37.037 27.40 1.90 46.37 2.85
641 669 8.320617 ACCTGGTAATTACGTTAATCAGGTAAA 58.679 33.333 27.05 0.00 46.31 2.01
642 670 8.606602 CCTGGTAATTACGTTAATCAGGTAAAC 58.393 37.037 20.00 1.20 38.81 2.01
643 671 9.153721 CTGGTAATTACGTTAATCAGGTAAACA 57.846 33.333 9.46 0.00 38.81 2.83
644 672 9.499479 TGGTAATTACGTTAATCAGGTAAACAA 57.501 29.630 9.46 0.00 38.81 2.83
652 680 9.974980 ACGTTAATCAGGTAAACAAATTTTCAT 57.025 25.926 0.00 0.00 0.00 2.57
745 774 1.656652 ACTTCGGCCATGAATTCGAG 58.343 50.000 2.24 0.00 33.11 4.04
761 790 1.884579 TCGAGCTTCGTGGTCTAGTTT 59.115 47.619 0.00 0.00 41.35 2.66
767 796 2.433868 TCGTGGTCTAGTTTGTGCTC 57.566 50.000 0.00 0.00 0.00 4.26
781 1183 1.377202 TGCTCCAAATGAGGACGGC 60.377 57.895 0.00 0.00 41.73 5.68
782 1184 2.464459 GCTCCAAATGAGGACGGCG 61.464 63.158 4.80 4.80 41.73 6.46
783 1185 2.435938 TCCAAATGAGGACGGCGC 60.436 61.111 6.90 0.00 31.23 6.53
784 1186 2.436646 CCAAATGAGGACGGCGCT 60.437 61.111 6.90 0.00 0.00 5.92
785 1187 2.753966 CCAAATGAGGACGGCGCTG 61.754 63.158 16.39 16.39 0.00 5.18
786 1188 1.741401 CAAATGAGGACGGCGCTGA 60.741 57.895 25.98 0.00 0.00 4.26
787 1189 1.741770 AAATGAGGACGGCGCTGAC 60.742 57.895 25.98 17.79 0.00 3.51
788 1190 2.449031 AAATGAGGACGGCGCTGACA 62.449 55.000 25.98 16.61 0.00 3.58
789 1191 2.842394 AATGAGGACGGCGCTGACAG 62.842 60.000 25.98 0.00 0.00 3.51
801 1203 1.527433 GCTGACAGTTTTGCCCTCCC 61.527 60.000 3.99 0.00 0.00 4.30
803 1205 1.360393 TGACAGTTTTGCCCTCCCCT 61.360 55.000 0.00 0.00 0.00 4.79
919 2008 1.334689 GCACGGCTTAAGTTTCACCAC 60.335 52.381 4.02 0.00 0.00 4.16
1017 2106 4.304413 ATGGCACCCCAGCAGCAA 62.304 61.111 0.00 0.00 46.24 3.91
1128 2223 3.529533 TCCGTTCTTCTACTACTCTCCG 58.470 50.000 0.00 0.00 0.00 4.63
1371 2484 2.612972 CGCACTTCTTCTATGGTGGTGT 60.613 50.000 0.00 0.00 0.00 4.16
1375 2488 4.631813 CACTTCTTCTATGGTGGTGTTAGC 59.368 45.833 0.00 0.00 0.00 3.09
1493 2617 8.764524 AGATTTCTGCGAGGATTATATTGTAC 57.235 34.615 0.00 0.00 0.00 2.90
1494 2618 8.589338 AGATTTCTGCGAGGATTATATTGTACT 58.411 33.333 0.00 0.00 0.00 2.73
1495 2619 9.856488 GATTTCTGCGAGGATTATATTGTACTA 57.144 33.333 0.00 0.00 0.00 1.82
1524 2652 2.730090 GCAGTGCACTCAAATTCCGATG 60.730 50.000 18.64 2.94 0.00 3.84
1525 2653 2.485426 CAGTGCACTCAAATTCCGATGT 59.515 45.455 18.64 0.00 0.00 3.06
1544 2672 4.402056 TGTGGGTTCGATTAATCTCTCC 57.598 45.455 13.45 11.21 0.00 3.71
1671 2799 1.079875 GTGGCCTGCATTTTCGCATG 61.080 55.000 3.32 0.00 42.06 4.06
1733 2861 6.591834 CCTTTGTATGAAGAACACCACTAGAG 59.408 42.308 0.00 0.00 0.00 2.43
1741 2869 1.982395 CACCACTAGAGCACCCGGA 60.982 63.158 0.73 0.00 0.00 5.14
1766 2894 3.508840 GCATCCGCCCGGTTCTTG 61.509 66.667 6.61 2.67 36.47 3.02
1814 2942 3.445096 GCTTGAGGCTTCAATGGTGTTAT 59.555 43.478 12.10 0.00 42.19 1.89
1832 2960 5.007682 TGTTATAAGCTTGGGGTCTTGTTC 58.992 41.667 9.86 0.00 0.00 3.18
1833 2961 5.222048 TGTTATAAGCTTGGGGTCTTGTTCT 60.222 40.000 9.86 0.00 0.00 3.01
1834 2962 1.986882 AAGCTTGGGGTCTTGTTCTG 58.013 50.000 0.00 0.00 0.00 3.02
1835 2963 0.111253 AGCTTGGGGTCTTGTTCTGG 59.889 55.000 0.00 0.00 0.00 3.86
1836 2964 0.178990 GCTTGGGGTCTTGTTCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
1837 2965 1.754201 GCTTGGGGTCTTGTTCTGGTT 60.754 52.381 0.00 0.00 0.00 3.67
1838 2966 2.230660 CTTGGGGTCTTGTTCTGGTTC 58.769 52.381 0.00 0.00 0.00 3.62
1839 2967 1.217916 TGGGGTCTTGTTCTGGTTCA 58.782 50.000 0.00 0.00 0.00 3.18
1872 3000 7.426929 AACTTTACTGCTGTATTTCAGTCTG 57.573 36.000 4.12 0.00 45.23 3.51
1886 3014 1.808945 CAGTCTGGATGTGTTCTTGCC 59.191 52.381 0.00 0.00 0.00 4.52
1901 3029 1.269448 CTTGCCGTGCCTGTAAAATGT 59.731 47.619 0.00 0.00 0.00 2.71
1910 3038 6.075280 CGTGCCTGTAAAATGTACTGTTAAC 58.925 40.000 0.00 0.00 0.00 2.01
1912 3040 7.572353 CGTGCCTGTAAAATGTACTGTTAACAT 60.572 37.037 9.13 2.49 39.22 2.71
1914 3042 8.079203 TGCCTGTAAAATGTACTGTTAACATTG 58.921 33.333 9.13 0.68 44.66 2.82
1935 3077 9.285153 ACATTGTATTAATGTTAAGCCCTGGCG 62.285 40.741 1.84 0.00 40.84 5.69
1958 3100 1.065418 AGGTGGTGGAATTAAGCCGAG 60.065 52.381 0.00 0.00 0.00 4.63
1959 3101 1.339727 GGTGGTGGAATTAAGCCGAGT 60.340 52.381 0.00 0.00 0.00 4.18
1968 3146 1.975660 TTAAGCCGAGTTGTGCCTTT 58.024 45.000 0.00 0.00 0.00 3.11
1973 3151 0.673644 CCGAGTTGTGCCTTTCCGAT 60.674 55.000 0.00 0.00 0.00 4.18
1982 3161 3.191162 TGTGCCTTTCCGATTGAATGAAG 59.809 43.478 0.00 0.00 31.67 3.02
1983 3162 2.754552 TGCCTTTCCGATTGAATGAAGG 59.245 45.455 0.00 0.00 33.38 3.46
1984 3163 2.099756 GCCTTTCCGATTGAATGAAGGG 59.900 50.000 3.08 3.08 38.05 3.95
2001 3185 4.166725 TGAAGGGGAAATATCTGATGTGCT 59.833 41.667 0.00 0.00 0.00 4.40
2065 3249 2.804527 TCGACCTCGTATCGATAAGGTG 59.195 50.000 26.40 19.28 43.38 4.00
2066 3250 2.547211 CGACCTCGTATCGATAAGGTGT 59.453 50.000 26.40 18.61 42.25 4.16
2067 3251 3.606384 CGACCTCGTATCGATAAGGTGTG 60.606 52.174 26.40 17.19 42.25 3.82
2068 3252 3.285484 ACCTCGTATCGATAAGGTGTGT 58.715 45.455 22.50 10.85 32.23 3.72
2082 3266 3.039011 AGGTGTGTGTCTACAAGGAAGT 58.961 45.455 0.00 0.00 38.82 3.01
2086 3270 2.047061 TGTGTCTACAAGGAAGTGGCT 58.953 47.619 0.00 0.00 32.88 4.75
2120 3304 3.039526 CCTCCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
2121 3305 2.612251 CTCCCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
2122 3306 3.036959 TCCCCCTCCTCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
2154 3338 1.330655 ACCGACTACCAGCCATCCAG 61.331 60.000 0.00 0.00 0.00 3.86
2177 3361 1.688884 GGCTCAGCTCCTCCCTCTT 60.689 63.158 0.00 0.00 0.00 2.85
2226 3410 3.125607 CGACGCCAGGTAGCCATA 58.874 61.111 0.00 0.00 0.00 2.74
2231 3415 0.249489 CGCCAGGTAGCCATACTCAC 60.249 60.000 0.00 0.00 32.12 3.51
2241 3425 0.671251 CCATACTCACTCGCCTCTCC 59.329 60.000 0.00 0.00 0.00 3.71
2294 3481 5.208463 TCCTGGCACAAAAATCCTTTTAC 57.792 39.130 0.00 0.00 38.70 2.01
2302 3489 1.900245 AAATCCTTTTACCCGCGTGT 58.100 45.000 4.92 0.99 0.00 4.49
2303 3490 1.900245 AATCCTTTTACCCGCGTGTT 58.100 45.000 4.92 0.00 0.00 3.32
2361 3548 0.774908 GAGCTAGCTCCCTCTCCCTA 59.225 60.000 30.89 0.00 37.11 3.53
2373 3560 2.501723 CCTCTCCCTAACTAGCTTTGCA 59.498 50.000 0.00 0.00 0.00 4.08
2374 3561 3.055094 CCTCTCCCTAACTAGCTTTGCAA 60.055 47.826 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.590451 CTGTTGAAAATATGAGCAATTTACCAT 57.410 29.630 0.00 0.00 0.00 3.55
5 6 8.584157 ACTGTTGAAAATATGAGCAATTTACCA 58.416 29.630 0.00 0.00 0.00 3.25
6 7 8.986477 ACTGTTGAAAATATGAGCAATTTACC 57.014 30.769 0.00 0.00 0.00 2.85
9 10 8.806146 AGGTACTGTTGAAAATATGAGCAATTT 58.194 29.630 0.00 0.00 37.18 1.82
10 11 8.353423 AGGTACTGTTGAAAATATGAGCAATT 57.647 30.769 0.00 0.00 37.18 2.32
11 12 7.944729 AGGTACTGTTGAAAATATGAGCAAT 57.055 32.000 0.00 0.00 37.18 3.56
12 13 7.094377 GGAAGGTACTGTTGAAAATATGAGCAA 60.094 37.037 0.00 0.00 40.86 3.91
13 14 6.374333 GGAAGGTACTGTTGAAAATATGAGCA 59.626 38.462 0.00 0.00 40.86 4.26
14 15 6.183360 GGGAAGGTACTGTTGAAAATATGAGC 60.183 42.308 0.00 0.00 40.86 4.26
15 16 6.884295 TGGGAAGGTACTGTTGAAAATATGAG 59.116 38.462 0.00 0.00 40.86 2.90
16 17 6.657541 GTGGGAAGGTACTGTTGAAAATATGA 59.342 38.462 0.00 0.00 40.86 2.15
17 18 6.127730 GGTGGGAAGGTACTGTTGAAAATATG 60.128 42.308 0.00 0.00 40.86 1.78
18 19 5.949952 GGTGGGAAGGTACTGTTGAAAATAT 59.050 40.000 0.00 0.00 40.86 1.28
19 20 5.163077 TGGTGGGAAGGTACTGTTGAAAATA 60.163 40.000 0.00 0.00 40.86 1.40
20 21 4.149598 GGTGGGAAGGTACTGTTGAAAAT 58.850 43.478 0.00 0.00 40.86 1.82
21 22 3.053544 TGGTGGGAAGGTACTGTTGAAAA 60.054 43.478 0.00 0.00 40.86 2.29
22 23 2.510382 TGGTGGGAAGGTACTGTTGAAA 59.490 45.455 0.00 0.00 40.86 2.69
23 24 2.128535 TGGTGGGAAGGTACTGTTGAA 58.871 47.619 0.00 0.00 40.86 2.69
24 25 1.809133 TGGTGGGAAGGTACTGTTGA 58.191 50.000 0.00 0.00 40.86 3.18
25 26 2.039746 TGATGGTGGGAAGGTACTGTTG 59.960 50.000 0.00 0.00 40.86 3.33
26 27 2.305927 CTGATGGTGGGAAGGTACTGTT 59.694 50.000 0.00 0.00 40.86 3.16
27 28 1.909302 CTGATGGTGGGAAGGTACTGT 59.091 52.381 0.00 0.00 40.86 3.55
28 29 1.210478 CCTGATGGTGGGAAGGTACTG 59.790 57.143 0.00 0.00 40.86 2.74
29 30 1.203440 ACCTGATGGTGGGAAGGTACT 60.203 52.381 0.00 0.00 46.51 2.73
45 46 5.983540 AGAAGGAAGAGCTAATTGTACCTG 58.016 41.667 0.00 0.00 0.00 4.00
55 56 2.697751 GCATCAGGAGAAGGAAGAGCTA 59.302 50.000 0.00 0.00 0.00 3.32
72 73 4.260170 ACATGAACCTGAAGAAGAGCATC 58.740 43.478 0.00 0.00 0.00 3.91
107 108 2.078849 ATCGCTCACAAACACGATGA 57.921 45.000 0.00 0.00 43.13 2.92
117 118 4.589216 TGATATGATGTCATCGCTCACA 57.411 40.909 8.29 2.68 37.76 3.58
120 121 6.257193 TGCATAATGATATGATGTCATCGCTC 59.743 38.462 16.24 5.48 41.25 5.03
123 124 7.903431 CACTTGCATAATGATATGATGTCATCG 59.097 37.037 5.12 0.00 41.25 3.84
133 134 5.759763 TGAACGAGCACTTGCATAATGATAT 59.240 36.000 3.62 0.00 45.16 1.63
136 137 3.333804 TGAACGAGCACTTGCATAATGA 58.666 40.909 3.62 0.00 45.16 2.57
140 141 2.419673 CCATTGAACGAGCACTTGCATA 59.580 45.455 3.62 0.00 45.16 3.14
141 142 1.200716 CCATTGAACGAGCACTTGCAT 59.799 47.619 3.62 0.00 45.16 3.96
171 172 1.669779 CAAGGTAGCAGCAGAAGCATC 59.330 52.381 0.00 0.00 45.49 3.91
181 182 3.691609 GTCCAAATCTTCCAAGGTAGCAG 59.308 47.826 0.00 0.00 0.00 4.24
214 215 0.460987 CACTGATCGAGGGAACTGCC 60.461 60.000 0.00 0.00 44.43 4.85
215 216 0.460987 CCACTGATCGAGGGAACTGC 60.461 60.000 0.00 0.00 44.43 4.40
219 220 0.250234 CAAGCCACTGATCGAGGGAA 59.750 55.000 0.00 0.00 0.00 3.97
262 264 2.361104 TCGCCCTTGACAATGCCC 60.361 61.111 4.73 0.00 0.00 5.36
270 272 1.202371 CGCTAATACTGTCGCCCTTGA 60.202 52.381 0.00 0.00 0.00 3.02
277 279 2.035449 TGGATTCCCGCTAATACTGTCG 59.965 50.000 0.00 0.00 34.29 4.35
279 281 4.497291 TTTGGATTCCCGCTAATACTGT 57.503 40.909 0.00 0.00 34.29 3.55
280 282 5.530915 TGAATTTGGATTCCCGCTAATACTG 59.469 40.000 0.00 0.00 40.79 2.74
284 286 4.956075 ACTTGAATTTGGATTCCCGCTAAT 59.044 37.500 0.00 0.00 40.79 1.73
290 292 5.684813 GCCCATTACTTGAATTTGGATTCCC 60.685 44.000 0.00 0.00 40.79 3.97
302 304 0.323360 GCCACTGGCCCATTACTTGA 60.323 55.000 9.13 0.00 44.06 3.02
315 317 4.680237 TTCTGGGTCGCGCCACTG 62.680 66.667 18.87 5.92 39.65 3.66
316 318 3.469863 TTTTCTGGGTCGCGCCACT 62.470 57.895 18.87 0.00 39.65 4.00
320 322 2.391389 CCTCTTTTCTGGGTCGCGC 61.391 63.158 0.00 0.00 0.00 6.86
322 324 2.391389 CGCCTCTTTTCTGGGTCGC 61.391 63.158 0.00 0.00 0.00 5.19
339 342 1.741770 AAGCCGGCTAGAAGTTGCG 60.742 57.895 33.07 0.00 0.00 4.85
342 345 0.674895 CTGCAAGCCGGCTAGAAGTT 60.675 55.000 33.07 10.49 34.04 2.66
348 351 2.359850 CAACCTGCAAGCCGGCTA 60.360 61.111 33.07 14.25 34.04 3.93
349 352 4.586235 ACAACCTGCAAGCCGGCT 62.586 61.111 27.08 27.08 34.04 5.52
350 353 4.347453 CACAACCTGCAAGCCGGC 62.347 66.667 21.89 21.89 0.00 6.13
413 441 1.951602 GCCAAGTTTCAAACCCTACGT 59.048 47.619 0.00 0.00 0.00 3.57
419 447 1.314730 TCCTCGCCAAGTTTCAAACC 58.685 50.000 0.00 0.00 0.00 3.27
420 448 2.616842 TCTTCCTCGCCAAGTTTCAAAC 59.383 45.455 0.00 0.00 0.00 2.93
464 492 5.764131 TCAAAATTACAACTTTACAGGCCG 58.236 37.500 0.00 0.00 0.00 6.13
465 493 7.870445 TGATTCAAAATTACAACTTTACAGGCC 59.130 33.333 0.00 0.00 0.00 5.19
480 508 9.504708 TGGATGTAGCATTTTTGATTCAAAATT 57.495 25.926 21.75 16.40 41.89 1.82
481 509 8.938906 GTGGATGTAGCATTTTTGATTCAAAAT 58.061 29.630 21.75 11.71 41.89 1.82
482 510 7.116090 CGTGGATGTAGCATTTTTGATTCAAAA 59.884 33.333 18.29 18.29 40.85 2.44
483 511 6.585702 CGTGGATGTAGCATTTTTGATTCAAA 59.414 34.615 7.74 7.74 0.00 2.69
484 512 6.092092 CGTGGATGTAGCATTTTTGATTCAA 58.908 36.000 0.00 0.00 0.00 2.69
485 513 5.182950 ACGTGGATGTAGCATTTTTGATTCA 59.817 36.000 0.00 0.00 0.00 2.57
486 514 5.640732 ACGTGGATGTAGCATTTTTGATTC 58.359 37.500 0.00 0.00 0.00 2.52
487 515 5.643379 ACGTGGATGTAGCATTTTTGATT 57.357 34.783 0.00 0.00 0.00 2.57
488 516 6.751514 TTACGTGGATGTAGCATTTTTGAT 57.248 33.333 0.00 0.00 0.00 2.57
489 517 6.375377 GTTTACGTGGATGTAGCATTTTTGA 58.625 36.000 0.00 0.00 0.00 2.69
490 518 5.571357 GGTTTACGTGGATGTAGCATTTTTG 59.429 40.000 0.00 0.00 0.00 2.44
491 519 5.475564 AGGTTTACGTGGATGTAGCATTTTT 59.524 36.000 0.00 0.00 0.00 1.94
492 520 5.007682 AGGTTTACGTGGATGTAGCATTTT 58.992 37.500 0.00 0.00 0.00 1.82
493 521 4.585879 AGGTTTACGTGGATGTAGCATTT 58.414 39.130 0.00 0.00 0.00 2.32
494 522 4.216411 AGGTTTACGTGGATGTAGCATT 57.784 40.909 0.00 0.00 0.00 3.56
495 523 3.906720 AGGTTTACGTGGATGTAGCAT 57.093 42.857 0.00 0.00 0.00 3.79
496 524 3.427909 CGTAGGTTTACGTGGATGTAGCA 60.428 47.826 0.00 0.00 45.79 3.49
497 525 3.111098 CGTAGGTTTACGTGGATGTAGC 58.889 50.000 0.00 0.00 45.79 3.58
503 531 9.825369 CGTAAGACTTTCGTAGGTTTACGTGGA 62.825 44.444 18.34 0.00 46.61 4.02
504 532 7.798347 CGTAAGACTTTCGTAGGTTTACGTGG 61.798 46.154 18.34 2.49 46.61 4.94
505 533 5.058492 CGTAAGACTTTCGTAGGTTTACGTG 59.942 44.000 18.34 2.76 46.61 4.49
506 534 5.147162 CGTAAGACTTTCGTAGGTTTACGT 58.853 41.667 18.34 0.00 46.61 3.57
508 536 8.675040 ATTACGTAAGACTTTCGTAGGTTTAC 57.325 34.615 21.26 0.00 40.26 2.01
510 538 9.860898 AATATTACGTAAGACTTTCGTAGGTTT 57.139 29.630 21.26 14.85 40.26 3.27
511 539 9.508567 GAATATTACGTAAGACTTTCGTAGGTT 57.491 33.333 21.26 17.51 40.26 3.50
512 540 8.131731 GGAATATTACGTAAGACTTTCGTAGGT 58.868 37.037 21.26 17.37 40.26 3.08
513 541 8.348507 AGGAATATTACGTAAGACTTTCGTAGG 58.651 37.037 21.26 1.49 40.26 3.18
516 544 9.508567 GTTAGGAATATTACGTAAGACTTTCGT 57.491 33.333 21.14 21.14 43.62 3.85
517 545 9.727627 AGTTAGGAATATTACGTAAGACTTTCG 57.272 33.333 14.25 12.07 43.62 3.46
531 559 8.715842 GGGGAAGAAGAGTTAGTTAGGAATATT 58.284 37.037 0.00 0.00 0.00 1.28
532 560 7.292827 GGGGGAAGAAGAGTTAGTTAGGAATAT 59.707 40.741 0.00 0.00 0.00 1.28
533 561 6.614496 GGGGGAAGAAGAGTTAGTTAGGAATA 59.386 42.308 0.00 0.00 0.00 1.75
534 562 5.429109 GGGGGAAGAAGAGTTAGTTAGGAAT 59.571 44.000 0.00 0.00 0.00 3.01
535 563 4.781621 GGGGGAAGAAGAGTTAGTTAGGAA 59.218 45.833 0.00 0.00 0.00 3.36
536 564 4.359996 GGGGGAAGAAGAGTTAGTTAGGA 58.640 47.826 0.00 0.00 0.00 2.94
537 565 4.757019 GGGGGAAGAAGAGTTAGTTAGG 57.243 50.000 0.00 0.00 0.00 2.69
560 588 2.022718 CCCACCCCCTTGAAAATCAA 57.977 50.000 0.00 0.00 34.79 2.57
561 589 0.544120 GCCCACCCCCTTGAAAATCA 60.544 55.000 0.00 0.00 0.00 2.57
562 590 0.252239 AGCCCACCCCCTTGAAAATC 60.252 55.000 0.00 0.00 0.00 2.17
563 591 0.252239 GAGCCCACCCCCTTGAAAAT 60.252 55.000 0.00 0.00 0.00 1.82
564 592 1.155155 GAGCCCACCCCCTTGAAAA 59.845 57.895 0.00 0.00 0.00 2.29
565 593 2.851045 GAGCCCACCCCCTTGAAA 59.149 61.111 0.00 0.00 0.00 2.69
566 594 3.264845 GGAGCCCACCCCCTTGAA 61.265 66.667 0.00 0.00 0.00 2.69
567 595 3.829311 AAGGAGCCCACCCCCTTGA 62.829 63.158 0.00 0.00 38.74 3.02
568 596 3.268032 AAGGAGCCCACCCCCTTG 61.268 66.667 0.00 0.00 38.74 3.61
569 597 2.941583 GAAGGAGCCCACCCCCTT 60.942 66.667 0.00 0.00 42.53 3.95
572 600 3.412408 GAGGAAGGAGCCCACCCC 61.412 72.222 0.00 0.00 0.00 4.95
573 601 3.412408 GGAGGAAGGAGCCCACCC 61.412 72.222 0.00 0.00 0.00 4.61
574 602 3.412408 GGGAGGAAGGAGCCCACC 61.412 72.222 0.00 0.00 41.64 4.61
575 603 2.547123 TAGGGGAGGAAGGAGCCCAC 62.547 65.000 0.00 0.00 43.89 4.61
576 604 1.833055 TTAGGGGAGGAAGGAGCCCA 61.833 60.000 0.00 0.00 43.89 5.36
577 605 0.402126 ATTAGGGGAGGAAGGAGCCC 60.402 60.000 0.00 0.00 41.28 5.19
578 606 1.060729 GATTAGGGGAGGAAGGAGCC 58.939 60.000 0.00 0.00 0.00 4.70
579 607 2.110753 AGATTAGGGGAGGAAGGAGC 57.889 55.000 0.00 0.00 0.00 4.70
580 608 3.658725 TGAAGATTAGGGGAGGAAGGAG 58.341 50.000 0.00 0.00 0.00 3.69
581 609 3.795755 TGAAGATTAGGGGAGGAAGGA 57.204 47.619 0.00 0.00 0.00 3.36
582 610 4.202514 GGATTGAAGATTAGGGGAGGAAGG 60.203 50.000 0.00 0.00 0.00 3.46
583 611 4.662650 AGGATTGAAGATTAGGGGAGGAAG 59.337 45.833 0.00 0.00 0.00 3.46
584 612 4.646157 AGGATTGAAGATTAGGGGAGGAA 58.354 43.478 0.00 0.00 0.00 3.36
585 613 4.302004 AGGATTGAAGATTAGGGGAGGA 57.698 45.455 0.00 0.00 0.00 3.71
586 614 6.296720 GGATTAGGATTGAAGATTAGGGGAGG 60.297 46.154 0.00 0.00 0.00 4.30
587 615 6.503570 AGGATTAGGATTGAAGATTAGGGGAG 59.496 42.308 0.00 0.00 0.00 4.30
588 616 6.402442 AGGATTAGGATTGAAGATTAGGGGA 58.598 40.000 0.00 0.00 0.00 4.81
589 617 6.296720 GGAGGATTAGGATTGAAGATTAGGGG 60.297 46.154 0.00 0.00 0.00 4.79
590 618 6.273260 TGGAGGATTAGGATTGAAGATTAGGG 59.727 42.308 0.00 0.00 0.00 3.53
591 619 7.164803 GTGGAGGATTAGGATTGAAGATTAGG 58.835 42.308 0.00 0.00 0.00 2.69
592 620 7.017056 AGGTGGAGGATTAGGATTGAAGATTAG 59.983 40.741 0.00 0.00 0.00 1.73
593 621 6.851836 AGGTGGAGGATTAGGATTGAAGATTA 59.148 38.462 0.00 0.00 0.00 1.75
594 622 5.674035 AGGTGGAGGATTAGGATTGAAGATT 59.326 40.000 0.00 0.00 0.00 2.40
595 623 5.072872 CAGGTGGAGGATTAGGATTGAAGAT 59.927 44.000 0.00 0.00 0.00 2.40
596 624 4.410228 CAGGTGGAGGATTAGGATTGAAGA 59.590 45.833 0.00 0.00 0.00 2.87
597 625 4.445448 CCAGGTGGAGGATTAGGATTGAAG 60.445 50.000 0.00 0.00 37.39 3.02
598 626 3.459598 CCAGGTGGAGGATTAGGATTGAA 59.540 47.826 0.00 0.00 37.39 2.69
599 627 3.048600 CCAGGTGGAGGATTAGGATTGA 58.951 50.000 0.00 0.00 37.39 2.57
600 628 2.780010 ACCAGGTGGAGGATTAGGATTG 59.220 50.000 2.10 0.00 38.94 2.67
601 629 3.151542 ACCAGGTGGAGGATTAGGATT 57.848 47.619 2.10 0.00 38.94 3.01
602 630 2.897823 ACCAGGTGGAGGATTAGGAT 57.102 50.000 2.10 0.00 38.94 3.24
603 631 3.788116 TTACCAGGTGGAGGATTAGGA 57.212 47.619 0.76 0.00 38.94 2.94
604 632 5.510861 CGTAATTACCAGGTGGAGGATTAGG 60.511 48.000 10.01 6.18 38.94 2.69
605 633 5.070047 ACGTAATTACCAGGTGGAGGATTAG 59.930 44.000 10.01 2.51 38.94 1.73
606 634 4.964262 ACGTAATTACCAGGTGGAGGATTA 59.036 41.667 10.01 1.93 38.94 1.75
607 635 3.778629 ACGTAATTACCAGGTGGAGGATT 59.221 43.478 10.01 2.82 38.94 3.01
608 636 3.381335 ACGTAATTACCAGGTGGAGGAT 58.619 45.455 10.01 0.00 38.94 3.24
609 637 2.823959 ACGTAATTACCAGGTGGAGGA 58.176 47.619 10.01 0.00 38.94 3.71
610 638 3.622166 AACGTAATTACCAGGTGGAGG 57.378 47.619 10.01 0.00 38.94 4.30
611 639 6.342906 TGATTAACGTAATTACCAGGTGGAG 58.657 40.000 10.01 0.00 38.94 3.86
612 640 6.297080 TGATTAACGTAATTACCAGGTGGA 57.703 37.500 10.01 0.00 38.94 4.02
613 641 5.526111 CCTGATTAACGTAATTACCAGGTGG 59.474 44.000 20.00 6.36 42.17 4.61
614 642 6.598753 CCTGATTAACGTAATTACCAGGTG 57.401 41.667 20.00 6.93 36.20 4.00
615 643 6.303903 ACCTGATTAACGTAATTACCAGGT 57.696 37.500 24.67 24.67 45.70 4.00
616 644 8.606602 GTTTACCTGATTAACGTAATTACCAGG 58.393 37.037 23.75 23.75 43.94 4.45
617 645 9.153721 TGTTTACCTGATTAACGTAATTACCAG 57.846 33.333 10.01 9.54 0.00 4.00
618 646 9.499479 TTGTTTACCTGATTAACGTAATTACCA 57.501 29.630 10.01 0.52 0.00 3.25
626 654 9.974980 ATGAAAATTTGTTTACCTGATTAACGT 57.025 25.926 0.00 0.00 0.00 3.99
745 774 1.194772 GCACAAACTAGACCACGAAGC 59.805 52.381 0.00 0.00 0.00 3.86
761 790 0.321564 CCGTCCTCATTTGGAGCACA 60.322 55.000 0.00 0.00 42.62 4.57
767 796 2.436646 AGCGCCGTCCTCATTTGG 60.437 61.111 2.29 0.00 0.00 3.28
778 1180 2.427410 GCAAAACTGTCAGCGCCG 60.427 61.111 2.29 0.00 0.00 6.46
779 1181 2.050077 GGCAAAACTGTCAGCGCC 60.050 61.111 2.29 3.66 0.00 6.53
780 1182 2.050077 GGGCAAAACTGTCAGCGC 60.050 61.111 0.00 0.00 0.00 5.92
781 1183 1.576421 GAGGGCAAAACTGTCAGCG 59.424 57.895 0.00 0.00 0.00 5.18
782 1184 1.527433 GGGAGGGCAAAACTGTCAGC 61.527 60.000 0.00 0.00 0.00 4.26
783 1185 0.895559 GGGGAGGGCAAAACTGTCAG 60.896 60.000 0.00 0.00 0.00 3.51
784 1186 1.152830 GGGGAGGGCAAAACTGTCA 59.847 57.895 0.00 0.00 0.00 3.58
785 1187 0.178961 AAGGGGAGGGCAAAACTGTC 60.179 55.000 0.00 0.00 0.00 3.51
786 1188 0.178961 GAAGGGGAGGGCAAAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
787 1189 0.113190 AGAAGGGGAGGGCAAAACTG 59.887 55.000 0.00 0.00 0.00 3.16
788 1190 0.860457 AAGAAGGGGAGGGCAAAACT 59.140 50.000 0.00 0.00 0.00 2.66
789 1191 1.257743 GAAGAAGGGGAGGGCAAAAC 58.742 55.000 0.00 0.00 0.00 2.43
801 1203 3.440522 GTCGGATGGAAAAAGGAAGAAGG 59.559 47.826 0.00 0.00 0.00 3.46
803 1205 4.072131 CTGTCGGATGGAAAAAGGAAGAA 58.928 43.478 0.00 0.00 0.00 2.52
893 1977 0.817634 AACTTAAGCCGTGCACTGCA 60.818 50.000 30.93 12.15 35.60 4.41
894 1978 0.310854 AAACTTAAGCCGTGCACTGC 59.689 50.000 23.93 23.93 0.00 4.40
895 1979 1.601903 TGAAACTTAAGCCGTGCACTG 59.398 47.619 16.19 9.93 0.00 3.66
896 1980 1.602377 GTGAAACTTAAGCCGTGCACT 59.398 47.619 16.19 0.00 0.00 4.40
897 1981 1.334689 GGTGAAACTTAAGCCGTGCAC 60.335 52.381 6.82 6.82 36.74 4.57
1017 2106 1.685421 GAGGAGCAGCAGGAGGAGT 60.685 63.158 0.00 0.00 0.00 3.85
1278 2385 4.191015 GACCCGGAATGGAGCCCC 62.191 72.222 0.73 0.00 42.00 5.80
1375 2488 4.994471 TGGCACAGCAGCGAGTGG 62.994 66.667 18.80 5.16 36.29 4.00
1493 2617 3.069289 TGAGTGCACTGCAAGAACATAG 58.931 45.455 27.27 0.00 41.47 2.23
1494 2618 3.124578 TGAGTGCACTGCAAGAACATA 57.875 42.857 27.27 0.00 41.47 2.29
1495 2619 1.971481 TGAGTGCACTGCAAGAACAT 58.029 45.000 27.27 0.00 41.47 2.71
1496 2620 1.748950 TTGAGTGCACTGCAAGAACA 58.251 45.000 27.27 11.32 41.47 3.18
1524 2652 3.381949 CGGAGAGATTAATCGAACCCAC 58.618 50.000 9.78 0.00 0.00 4.61
1525 2653 2.223971 GCGGAGAGATTAATCGAACCCA 60.224 50.000 9.78 0.00 0.00 4.51
1586 2714 6.126863 ACACCCTCTTCAGTCATCAAATTA 57.873 37.500 0.00 0.00 0.00 1.40
1589 2717 4.136796 CAACACCCTCTTCAGTCATCAAA 58.863 43.478 0.00 0.00 0.00 2.69
1630 2758 6.816140 CCACCTTTTACAAACACAAAGTTGAT 59.184 34.615 0.00 0.00 41.19 2.57
1671 2799 1.389784 GTTGTAACCATGCATTTGCGC 59.610 47.619 0.00 0.00 45.83 6.09
1672 2800 2.945278 AGTTGTAACCATGCATTTGCG 58.055 42.857 0.00 0.00 45.83 4.85
1757 2885 1.203523 CTCTCTGTCTCCAAGAACCGG 59.796 57.143 0.00 0.00 0.00 5.28
1761 2889 5.815233 AACAATCTCTCTGTCTCCAAGAA 57.185 39.130 0.00 0.00 0.00 2.52
1766 2894 3.006247 GCCAAACAATCTCTCTGTCTCC 58.994 50.000 0.00 0.00 0.00 3.71
1797 2925 4.860022 AGCTTATAACACCATTGAAGCCT 58.140 39.130 0.00 0.00 40.07 4.58
1814 2942 2.224769 CCAGAACAAGACCCCAAGCTTA 60.225 50.000 0.00 0.00 0.00 3.09
1832 2960 5.820947 AGTAAAGTTACAACCAGTGAACCAG 59.179 40.000 4.14 0.00 36.12 4.00
1833 2961 5.587043 CAGTAAAGTTACAACCAGTGAACCA 59.413 40.000 4.14 0.00 36.12 3.67
1834 2962 5.505159 GCAGTAAAGTTACAACCAGTGAACC 60.505 44.000 4.14 0.00 36.12 3.62
1835 2963 5.296035 AGCAGTAAAGTTACAACCAGTGAAC 59.704 40.000 4.14 0.00 36.12 3.18
1836 2964 5.295787 CAGCAGTAAAGTTACAACCAGTGAA 59.704 40.000 4.14 0.00 36.12 3.18
1837 2965 4.814234 CAGCAGTAAAGTTACAACCAGTGA 59.186 41.667 4.14 0.00 36.12 3.41
1838 2966 4.574828 ACAGCAGTAAAGTTACAACCAGTG 59.425 41.667 4.14 0.00 36.12 3.66
1839 2967 4.777463 ACAGCAGTAAAGTTACAACCAGT 58.223 39.130 4.14 0.00 36.12 4.00
1872 3000 1.210155 GCACGGCAAGAACACATCC 59.790 57.895 0.00 0.00 0.00 3.51
1886 3014 4.742438 AACAGTACATTTTACAGGCACG 57.258 40.909 0.00 0.00 0.00 5.34
1910 3038 6.215845 GCCAGGGCTTAACATTAATACAATG 58.784 40.000 2.30 0.00 38.26 2.82
1912 3040 4.336993 CGCCAGGGCTTAACATTAATACAA 59.663 41.667 8.91 0.00 39.32 2.41
1914 3042 3.252458 CCGCCAGGGCTTAACATTAATAC 59.748 47.826 8.91 0.00 39.32 1.89
1919 3061 0.039035 TTCCGCCAGGGCTTAACATT 59.961 50.000 8.91 0.00 39.32 2.71
1928 3070 4.722700 CACCACCTTCCGCCAGGG 62.723 72.222 3.38 0.00 38.42 4.45
1930 3072 2.484287 ATTCCACCACCTTCCGCCAG 62.484 60.000 0.00 0.00 0.00 4.85
1932 3074 0.034863 TAATTCCACCACCTTCCGCC 60.035 55.000 0.00 0.00 0.00 6.13
1935 3077 2.100197 GGCTTAATTCCACCACCTTCC 58.900 52.381 0.00 0.00 0.00 3.46
1958 3100 3.057596 TCATTCAATCGGAAAGGCACAAC 60.058 43.478 0.00 0.00 39.39 3.32
1959 3101 3.153130 TCATTCAATCGGAAAGGCACAA 58.847 40.909 0.00 0.00 39.39 3.33
1968 3146 3.730215 TTTCCCCTTCATTCAATCGGA 57.270 42.857 0.00 0.00 0.00 4.55
1973 3151 7.286087 CACATCAGATATTTCCCCTTCATTCAA 59.714 37.037 0.00 0.00 0.00 2.69
1982 3161 6.261826 GCATATAGCACATCAGATATTTCCCC 59.738 42.308 0.00 0.00 44.79 4.81
1983 3162 7.256756 GCATATAGCACATCAGATATTTCCC 57.743 40.000 0.00 0.00 44.79 3.97
2001 3185 0.109153 CAGTGCCTGGCCTGCATATA 59.891 55.000 20.92 0.00 41.46 0.86
2039 3223 1.148157 TCGATACGAGGTCGACCGAC 61.148 60.000 28.26 23.38 42.57 4.79
2048 3232 3.066342 ACACACACCTTATCGATACGAGG 59.934 47.826 17.94 17.94 39.91 4.63
2065 3249 2.143925 GCCACTTCCTTGTAGACACAC 58.856 52.381 0.00 0.00 33.30 3.82
2066 3250 2.047061 AGCCACTTCCTTGTAGACACA 58.953 47.619 0.00 0.00 0.00 3.72
2067 3251 2.841442 AGCCACTTCCTTGTAGACAC 57.159 50.000 0.00 0.00 0.00 3.67
2068 3252 4.157246 TCTAAGCCACTTCCTTGTAGACA 58.843 43.478 0.00 0.00 0.00 3.41
2086 3270 2.383855 GAGGAGAGGAGCAGCTTCTAA 58.616 52.381 2.00 0.00 32.36 2.10
2120 3304 2.204090 GGTGAGGTGGGGAAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
2121 3305 3.717294 CGGTGAGGTGGGGAAGGG 61.717 72.222 0.00 0.00 0.00 3.95
2122 3306 2.606519 TCGGTGAGGTGGGGAAGG 60.607 66.667 0.00 0.00 0.00 3.46
2154 3338 2.203181 GAGGAGCTGAGCCATGGC 60.203 66.667 30.12 30.12 42.33 4.40
2177 3361 3.393970 CTGGGAGCAGCGGAGGAA 61.394 66.667 0.00 0.00 0.00 3.36
2226 3410 0.543174 AAAGGGAGAGGCGAGTGAGT 60.543 55.000 0.00 0.00 0.00 3.41
2231 3415 0.459489 CAGAGAAAGGGAGAGGCGAG 59.541 60.000 0.00 0.00 0.00 5.03
2294 3481 1.440938 TTCAGTTTCCAACACGCGGG 61.441 55.000 6.92 6.92 0.00 6.13
2302 3489 2.223876 ACGACGCTACTTCAGTTTCCAA 60.224 45.455 0.00 0.00 0.00 3.53
2303 3490 1.338973 ACGACGCTACTTCAGTTTCCA 59.661 47.619 0.00 0.00 0.00 3.53
2309 3496 2.665052 GGGTTTTACGACGCTACTTCAG 59.335 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.