Multiple sequence alignment - TraesCS7D01G263400

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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 TraesCS7D01G263400 chr7D 100.000 2663 0 0 1 2663 243806745 243809407 0.000000e+00 4918.0
1 TraesCS7D01G263400 chr7A 92.143 1960 60 26 709 2655 258823787 258825665 0.000000e+00 2680.0
2 TraesCS7D01G263400 chr7A 89.080 348 28 6 1 344 258823189 258823530 8.810000e-115 424.0
3 TraesCS7D01G263400 chr7B 90.412 1189 70 17 712 1887 218976753 218975596 0.000000e+00 1524.0
4 TraesCS7D01G263400 chr7B 89.809 157 12 3 2320 2475 218975078 218974925 5.810000e-47 198.0
5 TraesCS7D01G263400 chr5A 90.625 288 27 0 1310 1597 453519495 453519782 1.500000e-102 383.0
6 TraesCS7D01G263400 chr5D 90.526 285 27 0 1313 1597 352454408 352454124 6.960000e-101 377.0
7 TraesCS7D01G263400 chr3A 90.526 285 27 0 1313 1597 398879801 398879517 6.960000e-101 377.0
8 TraesCS7D01G263400 chr3A 83.636 165 24 3 1404 1567 599326205 599326367 4.590000e-33 152.0
9 TraesCS7D01G263400 chr6A 90.175 285 28 0 1313 1597 116813216 116812932 3.240000e-99 372.0
10 TraesCS7D01G263400 chr6A 84.746 59 6 3 546 603 148436675 148436619 3.700000e-04 56.5
11 TraesCS7D01G263400 chr5B 90.175 285 28 0 1313 1597 415127717 415127433 3.240000e-99 372.0
12 TraesCS7D01G263400 chr5B 85.965 171 21 3 469 637 508063625 508063794 2.110000e-41 180.0
13 TraesCS7D01G263400 chr4B 91.620 179 14 1 469 646 657307228 657307050 2.050000e-61 246.0
14 TraesCS7D01G263400 chr4B 86.010 193 21 2 460 646 659667060 659667252 4.490000e-48 202.0
15 TraesCS7D01G263400 chr4B 86.667 180 22 2 469 647 661671202 661671024 5.810000e-47 198.0
16 TraesCS7D01G263400 chr2B 90.556 180 15 2 469 647 542756803 542756625 1.230000e-58 237.0
17 TraesCS7D01G263400 chr1B 90.960 177 13 2 469 644 686821590 686821764 4.430000e-58 235.0
18 TraesCS7D01G263400 chr1A 86.598 194 9 4 469 646 539315153 539315345 5.810000e-47 198.0
19 TraesCS7D01G263400 chr1A 75.556 315 55 19 79 374 8208045 8207734 4.620000e-28 135.0
20 TraesCS7D01G263400 chr1A 76.384 271 42 19 123 374 8177594 8177327 2.780000e-25 126.0
21 TraesCS7D01G263400 chr3D 83.030 165 25 3 1404 1567 456534480 456534642 2.140000e-31 147.0
22 TraesCS7D01G263400 chr3D 84.746 59 6 3 546 603 476347908 476347964 3.700000e-04 56.5
23 TraesCS7D01G263400 chr4D 84.746 59 6 3 546 603 76129925 76129869 3.700000e-04 56.5


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 TraesCS7D01G263400 chr7D 243806745 243809407 2662 False 4918 4918 100.0000 1 2663 1 chr7D.!!$F1 2662
1 TraesCS7D01G263400 chr7A 258823189 258825665 2476 False 1552 2680 90.6115 1 2655 2 chr7A.!!$F1 2654
2 TraesCS7D01G263400 chr7B 218974925 218976753 1828 True 861 1524 90.1105 712 2475 2 chr7B.!!$R1 1763

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
578 676 0.040204 ACCCCAGCTGAAAATCAGGG 59.96 55.0 17.39 17.47 44.43 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1882 1.083401 CTATCAACGCGCGCATTCC 60.083 57.895 32.58 0.27 0.0 3.01 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
41 42 4.954970 CCACAACCAGCACCGCCT 62.955 66.667 0.00 0.00 0.00 5.52
71 72 3.238497 CCGAGGTCACCACCACCA 61.238 66.667 0.00 0.00 46.68 4.17
72 73 2.813726 CCGAGGTCACCACCACCAA 61.814 63.158 0.00 0.00 46.68 3.67
73 74 1.597027 CGAGGTCACCACCACCAAC 60.597 63.158 0.00 0.00 46.68 3.77
74 75 1.228154 GAGGTCACCACCACCAACC 60.228 63.158 0.00 0.00 46.68 3.77
75 76 2.203437 GGTCACCACCACCAACCC 60.203 66.667 0.00 0.00 43.17 4.11
121 122 2.200092 ACCCGCCCCAATTTGTGT 59.800 55.556 0.00 0.00 0.00 3.72
125 126 2.048316 GCCCCAATTTGTGTGCCG 60.048 61.111 0.00 0.00 0.00 5.69
145 146 2.603776 ACCCCACCTCTGGACGTC 60.604 66.667 7.13 7.13 40.55 4.34
166 167 1.033574 CCTCCCTACATCGACCTCAC 58.966 60.000 0.00 0.00 0.00 3.51
171 172 0.100682 CTACATCGACCTCACCACGG 59.899 60.000 0.00 0.00 0.00 4.94
172 173 0.322726 TACATCGACCTCACCACGGA 60.323 55.000 0.00 0.00 0.00 4.69
173 174 1.153823 CATCGACCTCACCACGGAC 60.154 63.158 0.00 0.00 0.00 4.79
175 176 3.359523 CGACCTCACCACGGACGA 61.360 66.667 0.00 0.00 41.10 4.20
208 209 1.228657 GGTGACGCCTGAAGACAACC 61.229 60.000 0.00 0.00 0.00 3.77
210 211 0.396435 TGACGCCTGAAGACAACCAT 59.604 50.000 0.00 0.00 0.00 3.55
212 213 0.396435 ACGCCTGAAGACAACCATGA 59.604 50.000 0.00 0.00 0.00 3.07
213 214 1.003580 ACGCCTGAAGACAACCATGAT 59.996 47.619 0.00 0.00 0.00 2.45
219 220 1.315257 AAGACAACCATGATGGCGGC 61.315 55.000 12.25 5.18 42.67 6.53
220 221 3.112126 GACAACCATGATGGCGGCG 62.112 63.158 12.25 0.51 42.67 6.46
221 222 3.891400 CAACCATGATGGCGGCGG 61.891 66.667 12.25 0.68 42.67 6.13
243 244 5.357032 CGGGCAGATCTACCTTTTATGTTTT 59.643 40.000 11.90 0.00 0.00 2.43
273 275 2.629051 ACTTAAGTTCTATGTGCGGCC 58.371 47.619 1.12 0.00 0.00 6.13
349 447 7.701539 AATTATTTTCCAATGCCTTTTTCCC 57.298 32.000 0.00 0.00 0.00 3.97
375 473 7.692908 TTTTTCGATCAAACAGACAAAATCC 57.307 32.000 0.00 0.00 0.00 3.01
376 474 4.661993 TCGATCAAACAGACAAAATCCG 57.338 40.909 0.00 0.00 0.00 4.18
377 475 3.435327 TCGATCAAACAGACAAAATCCGG 59.565 43.478 0.00 0.00 0.00 5.14
378 476 3.435327 CGATCAAACAGACAAAATCCGGA 59.565 43.478 6.61 6.61 0.00 5.14
380 478 5.293324 CGATCAAACAGACAAAATCCGGATA 59.707 40.000 19.48 0.00 0.00 2.59
381 479 6.183360 CGATCAAACAGACAAAATCCGGATAA 60.183 38.462 19.48 0.00 0.00 1.75
382 480 6.494893 TCAAACAGACAAAATCCGGATAAG 57.505 37.500 19.48 12.98 0.00 1.73
383 481 4.965119 AACAGACAAAATCCGGATAAGC 57.035 40.909 19.48 6.01 0.00 3.09
384 482 3.279434 ACAGACAAAATCCGGATAAGCC 58.721 45.455 19.48 6.52 0.00 4.35
396 494 1.202290 GGATAAGCCGACGTCCGTTTA 60.202 52.381 10.58 12.39 36.31 2.01
397 495 2.529151 GATAAGCCGACGTCCGTTTAA 58.471 47.619 14.77 2.63 36.31 1.52
406 504 2.163211 GACGTCCGTTTAAGGTCTAGCT 59.837 50.000 3.51 0.00 0.00 3.32
408 506 3.177487 CGTCCGTTTAAGGTCTAGCTTC 58.823 50.000 0.00 0.00 0.00 3.86
410 508 3.084039 TCCGTTTAAGGTCTAGCTTCGA 58.916 45.455 0.00 0.00 0.00 3.71
457 555 2.053627 GCGTGGATTGTTTTCAGCAAG 58.946 47.619 0.00 0.00 0.00 4.01
471 569 2.030007 TCAGCAAGCTTTTCCCGAAATG 60.030 45.455 0.00 0.00 0.00 2.32
472 570 1.070821 GCAAGCTTTTCCCGAAATGC 58.929 50.000 16.26 16.26 45.90 3.56
477 575 2.863739 GCTTTTCCCGAAATGCTACAC 58.136 47.619 16.57 0.00 43.71 2.90
479 577 3.821841 CTTTTCCCGAAATGCTACACAC 58.178 45.455 0.00 0.00 0.00 3.82
480 578 2.552599 TTCCCGAAATGCTACACACA 57.447 45.000 0.00 0.00 0.00 3.72
481 579 1.803334 TCCCGAAATGCTACACACAC 58.197 50.000 0.00 0.00 0.00 3.82
483 581 0.442310 CCGAAATGCTACACACACGG 59.558 55.000 0.00 0.00 36.04 4.94
484 582 0.442310 CGAAATGCTACACACACGGG 59.558 55.000 0.00 0.00 0.00 5.28
485 583 0.168128 GAAATGCTACACACACGGGC 59.832 55.000 0.00 0.00 0.00 6.13
486 584 0.536233 AAATGCTACACACACGGGCA 60.536 50.000 0.00 0.00 37.32 5.36
487 585 0.322456 AATGCTACACACACGGGCAT 60.322 50.000 0.00 0.00 44.09 4.40
488 586 0.744414 ATGCTACACACACGGGCATC 60.744 55.000 0.00 0.00 39.02 3.91
489 587 1.375396 GCTACACACACGGGCATCA 60.375 57.895 0.00 0.00 0.00 3.07
490 588 0.953471 GCTACACACACGGGCATCAA 60.953 55.000 0.00 0.00 0.00 2.57
491 589 1.737838 CTACACACACGGGCATCAAT 58.262 50.000 0.00 0.00 0.00 2.57
492 590 2.083774 CTACACACACGGGCATCAATT 58.916 47.619 0.00 0.00 0.00 2.32
493 591 1.327303 ACACACACGGGCATCAATTT 58.673 45.000 0.00 0.00 0.00 1.82
494 592 1.686052 ACACACACGGGCATCAATTTT 59.314 42.857 0.00 0.00 0.00 1.82
495 593 2.887783 ACACACACGGGCATCAATTTTA 59.112 40.909 0.00 0.00 0.00 1.52
496 594 3.241701 CACACACGGGCATCAATTTTAC 58.758 45.455 0.00 0.00 0.00 2.01
497 595 2.095466 ACACACGGGCATCAATTTTACG 60.095 45.455 0.00 0.00 0.00 3.18
498 596 1.470890 ACACGGGCATCAATTTTACGG 59.529 47.619 0.00 0.00 0.00 4.02
499 597 1.099689 ACGGGCATCAATTTTACGGG 58.900 50.000 0.00 0.00 0.00 5.28
500 598 0.383949 CGGGCATCAATTTTACGGGG 59.616 55.000 0.00 0.00 0.00 5.73
501 599 1.480789 GGGCATCAATTTTACGGGGT 58.519 50.000 0.00 0.00 0.00 4.95
502 600 1.828595 GGGCATCAATTTTACGGGGTT 59.171 47.619 0.00 0.00 0.00 4.11
503 601 2.159156 GGGCATCAATTTTACGGGGTTC 60.159 50.000 0.00 0.00 0.00 3.62
504 602 2.494073 GGCATCAATTTTACGGGGTTCA 59.506 45.455 0.00 0.00 0.00 3.18
505 603 3.507786 GCATCAATTTTACGGGGTTCAC 58.492 45.455 0.00 0.00 0.00 3.18
506 604 3.753842 CATCAATTTTACGGGGTTCACG 58.246 45.455 0.00 0.00 37.36 4.35
507 605 2.152830 TCAATTTTACGGGGTTCACGG 58.847 47.619 0.00 0.00 35.23 4.94
508 606 2.152830 CAATTTTACGGGGTTCACGGA 58.847 47.619 0.00 0.00 35.23 4.69
509 607 2.103537 ATTTTACGGGGTTCACGGAG 57.896 50.000 0.00 0.00 35.23 4.63
510 608 1.047002 TTTTACGGGGTTCACGGAGA 58.953 50.000 0.00 0.00 35.23 3.71
511 609 0.604578 TTTACGGGGTTCACGGAGAG 59.395 55.000 0.00 0.00 35.23 3.20
512 610 1.252904 TTACGGGGTTCACGGAGAGG 61.253 60.000 0.00 0.00 35.23 3.69
513 611 4.452733 CGGGGTTCACGGAGAGGC 62.453 72.222 0.00 0.00 0.00 4.70
514 612 3.003763 GGGGTTCACGGAGAGGCT 61.004 66.667 0.00 0.00 0.00 4.58
515 613 2.266055 GGGTTCACGGAGAGGCTG 59.734 66.667 0.00 0.00 0.00 4.85
516 614 2.283529 GGGTTCACGGAGAGGCTGA 61.284 63.158 0.00 0.00 0.00 4.26
517 615 1.216710 GGTTCACGGAGAGGCTGAG 59.783 63.158 0.00 0.00 0.00 3.35
518 616 1.216710 GTTCACGGAGAGGCTGAGG 59.783 63.158 0.00 0.00 0.00 3.86
519 617 1.228894 TTCACGGAGAGGCTGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
520 618 1.536073 TTCACGGAGAGGCTGAGGTG 61.536 60.000 0.00 0.00 0.00 4.00
521 619 2.681778 ACGGAGAGGCTGAGGTGG 60.682 66.667 0.00 0.00 0.00 4.61
522 620 3.465403 CGGAGAGGCTGAGGTGGG 61.465 72.222 0.00 0.00 0.00 4.61
523 621 2.284995 GGAGAGGCTGAGGTGGGT 60.285 66.667 0.00 0.00 0.00 4.51
524 622 1.920835 GGAGAGGCTGAGGTGGGTT 60.921 63.158 0.00 0.00 0.00 4.11
525 623 1.492993 GGAGAGGCTGAGGTGGGTTT 61.493 60.000 0.00 0.00 0.00 3.27
526 624 0.402121 GAGAGGCTGAGGTGGGTTTT 59.598 55.000 0.00 0.00 0.00 2.43
527 625 0.853530 AGAGGCTGAGGTGGGTTTTT 59.146 50.000 0.00 0.00 0.00 1.94
548 646 5.815233 TTTTAATTGGGTGCAAATCAGGA 57.185 34.783 0.00 0.00 0.00 3.86
549 647 6.371595 TTTTAATTGGGTGCAAATCAGGAT 57.628 33.333 0.00 0.00 0.00 3.24
550 648 7.487822 TTTTAATTGGGTGCAAATCAGGATA 57.512 32.000 0.00 0.00 0.00 2.59
551 649 7.487822 TTTAATTGGGTGCAAATCAGGATAA 57.512 32.000 0.00 0.00 0.00 1.75
552 650 5.603170 AATTGGGTGCAAATCAGGATAAG 57.397 39.130 0.00 0.00 0.00 1.73
553 651 3.017048 TGGGTGCAAATCAGGATAAGG 57.983 47.619 0.00 0.00 0.00 2.69
554 652 2.310538 GGGTGCAAATCAGGATAAGGG 58.689 52.381 0.00 0.00 0.00 3.95
555 653 1.683385 GGTGCAAATCAGGATAAGGGC 59.317 52.381 0.00 0.00 0.00 5.19
556 654 1.683385 GTGCAAATCAGGATAAGGGCC 59.317 52.381 0.00 0.00 0.00 5.80
557 655 1.332195 GCAAATCAGGATAAGGGCCC 58.668 55.000 16.46 16.46 0.00 5.80
558 656 2.001076 CAAATCAGGATAAGGGCCCC 57.999 55.000 21.43 1.70 0.00 5.80
559 657 1.217689 CAAATCAGGATAAGGGCCCCA 59.782 52.381 21.43 7.28 0.00 4.96
560 658 0.853530 AATCAGGATAAGGGCCCCAC 59.146 55.000 21.43 7.41 0.00 4.61
561 659 1.068352 ATCAGGATAAGGGCCCCACC 61.068 60.000 21.43 16.82 37.93 4.61
571 669 4.299796 GCCCCACCCCAGCTGAAA 62.300 66.667 17.39 0.00 0.00 2.69
572 670 2.525592 CCCCACCCCAGCTGAAAA 59.474 61.111 17.39 0.00 0.00 2.29
573 671 1.079073 CCCCACCCCAGCTGAAAAT 59.921 57.895 17.39 0.00 0.00 1.82
574 672 0.972471 CCCCACCCCAGCTGAAAATC 60.972 60.000 17.39 0.00 0.00 2.17
575 673 0.251742 CCCACCCCAGCTGAAAATCA 60.252 55.000 17.39 0.00 0.00 2.57
576 674 1.180029 CCACCCCAGCTGAAAATCAG 58.820 55.000 17.39 3.00 46.90 2.90
577 675 1.180029 CACCCCAGCTGAAAATCAGG 58.820 55.000 17.39 5.54 44.43 3.86
578 676 0.040204 ACCCCAGCTGAAAATCAGGG 59.960 55.000 17.39 17.47 44.43 4.45
579 677 0.685458 CCCCAGCTGAAAATCAGGGG 60.685 60.000 17.39 11.05 44.43 4.79
580 678 0.685458 CCCAGCTGAAAATCAGGGGG 60.685 60.000 17.39 0.00 44.43 5.40
598 696 3.296854 GGGGGCAAGTTTAATTAGGAGG 58.703 50.000 0.00 0.00 0.00 4.30
599 697 3.053170 GGGGGCAAGTTTAATTAGGAGGA 60.053 47.826 0.00 0.00 0.00 3.71
600 698 4.571148 GGGGGCAAGTTTAATTAGGAGGAA 60.571 45.833 0.00 0.00 0.00 3.36
601 699 5.020795 GGGGCAAGTTTAATTAGGAGGAAA 58.979 41.667 0.00 0.00 0.00 3.13
602 700 5.127194 GGGGCAAGTTTAATTAGGAGGAAAG 59.873 44.000 0.00 0.00 0.00 2.62
603 701 5.949952 GGGCAAGTTTAATTAGGAGGAAAGA 59.050 40.000 0.00 0.00 0.00 2.52
604 702 6.095580 GGGCAAGTTTAATTAGGAGGAAAGAG 59.904 42.308 0.00 0.00 0.00 2.85
605 703 6.404844 GGCAAGTTTAATTAGGAGGAAAGAGC 60.405 42.308 0.00 0.00 0.00 4.09
606 704 6.404844 GCAAGTTTAATTAGGAGGAAAGAGCC 60.405 42.308 0.00 0.00 0.00 4.70
607 705 5.756918 AGTTTAATTAGGAGGAAAGAGCCC 58.243 41.667 0.00 0.00 0.00 5.19
608 706 5.253096 AGTTTAATTAGGAGGAAAGAGCCCA 59.747 40.000 0.00 0.00 0.00 5.36
609 707 5.994416 TTAATTAGGAGGAAAGAGCCCAT 57.006 39.130 0.00 0.00 0.00 4.00
610 708 7.128883 AGTTTAATTAGGAGGAAAGAGCCCATA 59.871 37.037 0.00 0.00 0.00 2.74
611 709 7.648177 TTAATTAGGAGGAAAGAGCCCATAT 57.352 36.000 0.00 0.00 0.00 1.78
612 710 6.536684 AATTAGGAGGAAAGAGCCCATATT 57.463 37.500 0.00 0.00 0.00 1.28
613 711 7.648177 AATTAGGAGGAAAGAGCCCATATTA 57.352 36.000 0.00 0.00 0.00 0.98
614 712 6.688073 TTAGGAGGAAAGAGCCCATATTAG 57.312 41.667 0.00 0.00 0.00 1.73
615 713 3.329225 AGGAGGAAAGAGCCCATATTAGC 59.671 47.826 0.00 0.00 0.00 3.09
616 714 3.073062 GGAGGAAAGAGCCCATATTAGCA 59.927 47.826 0.00 0.00 0.00 3.49
617 715 4.263683 GGAGGAAAGAGCCCATATTAGCAT 60.264 45.833 0.00 0.00 0.00 3.79
618 716 4.660168 AGGAAAGAGCCCATATTAGCATG 58.340 43.478 0.00 0.00 0.00 4.06
619 717 4.105377 AGGAAAGAGCCCATATTAGCATGT 59.895 41.667 0.00 0.00 0.00 3.21
620 718 5.310594 AGGAAAGAGCCCATATTAGCATGTA 59.689 40.000 0.00 0.00 0.00 2.29
621 719 6.003950 GGAAAGAGCCCATATTAGCATGTAA 58.996 40.000 0.00 0.00 0.00 2.41
622 720 6.150140 GGAAAGAGCCCATATTAGCATGTAAG 59.850 42.308 0.00 0.00 0.00 2.34
623 721 6.439636 AAGAGCCCATATTAGCATGTAAGA 57.560 37.500 0.00 0.00 0.00 2.10
624 722 6.047511 AGAGCCCATATTAGCATGTAAGAG 57.952 41.667 0.00 0.00 0.00 2.85
625 723 5.545723 AGAGCCCATATTAGCATGTAAGAGT 59.454 40.000 0.00 0.00 0.00 3.24
626 724 5.799213 AGCCCATATTAGCATGTAAGAGTC 58.201 41.667 0.00 0.00 0.00 3.36
627 725 5.545723 AGCCCATATTAGCATGTAAGAGTCT 59.454 40.000 0.00 0.00 0.00 3.24
628 726 5.641209 GCCCATATTAGCATGTAAGAGTCTG 59.359 44.000 0.00 0.00 0.00 3.51
629 727 6.742644 GCCCATATTAGCATGTAAGAGTCTGT 60.743 42.308 0.00 0.00 0.00 3.41
630 728 6.648310 CCCATATTAGCATGTAAGAGTCTGTG 59.352 42.308 0.00 0.00 0.00 3.66
631 729 7.436933 CCATATTAGCATGTAAGAGTCTGTGA 58.563 38.462 0.00 0.00 0.00 3.58
632 730 7.598118 CCATATTAGCATGTAAGAGTCTGTGAG 59.402 40.741 0.00 0.00 0.00 3.51
633 731 5.984695 TTAGCATGTAAGAGTCTGTGAGT 57.015 39.130 0.00 0.00 0.00 3.41
634 732 4.448537 AGCATGTAAGAGTCTGTGAGTC 57.551 45.455 0.00 0.00 32.62 3.36
635 733 4.085733 AGCATGTAAGAGTCTGTGAGTCT 58.914 43.478 0.00 0.00 43.32 3.24
636 734 5.257262 AGCATGTAAGAGTCTGTGAGTCTA 58.743 41.667 5.48 0.00 40.95 2.59
637 735 5.356751 AGCATGTAAGAGTCTGTGAGTCTAG 59.643 44.000 5.48 0.00 40.95 2.43
638 736 5.124776 GCATGTAAGAGTCTGTGAGTCTAGT 59.875 44.000 5.48 0.00 40.95 2.57
639 737 6.316640 GCATGTAAGAGTCTGTGAGTCTAGTA 59.683 42.308 5.48 0.00 40.95 1.82
640 738 7.012894 GCATGTAAGAGTCTGTGAGTCTAGTAT 59.987 40.741 5.48 0.00 40.95 2.12
641 739 8.898761 CATGTAAGAGTCTGTGAGTCTAGTATT 58.101 37.037 5.48 0.00 40.95 1.89
642 740 8.865420 TGTAAGAGTCTGTGAGTCTAGTATTT 57.135 34.615 5.48 0.00 40.95 1.40
643 741 9.298250 TGTAAGAGTCTGTGAGTCTAGTATTTT 57.702 33.333 5.48 0.00 40.95 1.82
644 742 9.777575 GTAAGAGTCTGTGAGTCTAGTATTTTC 57.222 37.037 5.48 0.00 40.95 2.29
645 743 7.079182 AGAGTCTGTGAGTCTAGTATTTTCG 57.921 40.000 3.36 0.00 40.15 3.46
646 744 5.642686 AGTCTGTGAGTCTAGTATTTTCGC 58.357 41.667 0.00 0.00 0.00 4.70
668 766 8.818141 TCGCACAAAAATTATACCATGAAAAA 57.182 26.923 0.00 0.00 0.00 1.94
684 782 9.835389 ACCATGAAAAATCTTCTTCAAATCAAA 57.165 25.926 0.00 0.00 35.31 2.69
836 935 0.695803 CCCTAGACCCTGCCCATTCT 60.696 60.000 0.00 0.00 0.00 2.40
850 949 4.020218 TGCCCATTCTCTATAAATAGCGCT 60.020 41.667 17.26 17.26 0.00 5.92
908 1009 1.197430 ACCTGTGCTCTGGCTAGCTT 61.197 55.000 15.72 0.00 43.19 3.74
955 1056 4.292643 TCTCTCATCATCCACATCTTCCA 58.707 43.478 0.00 0.00 0.00 3.53
962 1063 6.267242 TCATCATCCACATCTTCCAAAACAAA 59.733 34.615 0.00 0.00 0.00 2.83
963 1064 5.841810 TCATCCACATCTTCCAAAACAAAC 58.158 37.500 0.00 0.00 0.00 2.93
972 1073 5.474825 TCTTCCAAAACAAACCAAGTTGTC 58.525 37.500 1.45 0.00 40.86 3.18
1149 1250 1.213013 CCCTCGTCACCAGTTCTCG 59.787 63.158 0.00 0.00 0.00 4.04
1485 1589 4.087892 ATCCTGCAGCGCCTCGTT 62.088 61.111 8.66 0.00 0.00 3.85
1695 1799 2.749839 GCCACCCGCATGTGCTTA 60.750 61.111 0.00 0.00 39.32 3.09
1873 1986 5.055812 AGTATGAGCACGAGTACTAGTACC 58.944 45.833 25.97 17.27 36.75 3.34
1967 2115 4.478206 ACTCTTACTACTGCATGCATGT 57.522 40.909 26.79 21.81 0.00 3.21
1986 2134 6.997239 CATGTATGCATGCACCTATCTTAT 57.003 37.500 25.37 6.17 44.87 1.73
1987 2135 6.782150 CATGTATGCATGCACCTATCTTATG 58.218 40.000 25.37 14.26 44.87 1.90
1988 2136 6.112927 TGTATGCATGCACCTATCTTATGA 57.887 37.500 25.37 0.00 0.00 2.15
1989 2137 6.168389 TGTATGCATGCACCTATCTTATGAG 58.832 40.000 25.37 0.00 0.00 2.90
1990 2138 4.694760 TGCATGCACCTATCTTATGAGT 57.305 40.909 18.46 0.00 0.00 3.41
1991 2139 5.806654 TGCATGCACCTATCTTATGAGTA 57.193 39.130 18.46 0.00 0.00 2.59
1992 2140 6.173427 TGCATGCACCTATCTTATGAGTAA 57.827 37.500 18.46 0.00 0.00 2.24
1993 2141 6.226052 TGCATGCACCTATCTTATGAGTAAG 58.774 40.000 18.46 0.00 38.93 2.34
1994 2142 6.183361 TGCATGCACCTATCTTATGAGTAAGT 60.183 38.462 18.46 0.00 38.72 2.24
1995 2143 6.708054 GCATGCACCTATCTTATGAGTAAGTT 59.292 38.462 14.21 0.00 38.72 2.66
1996 2144 7.227512 GCATGCACCTATCTTATGAGTAAGTTT 59.772 37.037 14.21 0.00 38.72 2.66
1997 2145 9.113838 CATGCACCTATCTTATGAGTAAGTTTT 57.886 33.333 0.00 0.00 38.72 2.43
1998 2146 9.686683 ATGCACCTATCTTATGAGTAAGTTTTT 57.313 29.630 0.00 0.00 38.72 1.94
2074 2254 9.906660 CATTAAATAGTTTGTCCTTGCAACTTA 57.093 29.630 0.00 0.00 0.00 2.24
2088 2268 6.128795 CCTTGCAACTTAGAACTACGAAGAAG 60.129 42.308 0.00 0.00 35.66 2.85
2093 2273 7.541437 GCAACTTAGAACTACGAAGAAGTACAT 59.459 37.037 0.00 0.00 35.66 2.29
2103 2283 5.274718 ACGAAGAAGTACATCTTAGATGCG 58.725 41.667 22.39 17.93 39.70 4.73
2159 2350 3.733443 ACATGCCCTTTGTTCTTGAAC 57.267 42.857 6.56 6.56 0.00 3.18
2160 2351 3.299503 ACATGCCCTTTGTTCTTGAACT 58.700 40.909 13.65 0.00 0.00 3.01
2181 2372 4.708421 ACTACGCTGTAGGTCCAGATTAAA 59.292 41.667 16.42 0.00 34.23 1.52
2195 2386 7.013369 GGTCCAGATTAAAAGAGAACACAAAGT 59.987 37.037 0.00 0.00 0.00 2.66
2207 2399 4.099881 AGAACACAAAGTGGAAACATGCAT 59.900 37.500 0.00 0.00 46.14 3.96
2216 2408 4.114794 GTGGAAACATGCATATTGAAGGC 58.885 43.478 0.00 0.00 46.14 4.35
2237 2429 1.017387 AGGCTAGTTTGCTATTGCGC 58.983 50.000 0.00 0.00 43.34 6.09
2238 2430 0.316196 GGCTAGTTTGCTATTGCGCG 60.316 55.000 0.00 0.00 43.34 6.86
2239 2431 0.925721 GCTAGTTTGCTATTGCGCGC 60.926 55.000 27.26 27.26 43.34 6.86
2240 2432 0.651610 CTAGTTTGCTATTGCGCGCG 60.652 55.000 28.44 28.44 43.34 6.86
2244 2440 2.450960 TTTGCTATTGCGCGCGTTGT 62.451 50.000 32.35 18.88 43.34 3.32
2302 2564 8.596271 ACTTCTCTAAAAAGCTGTAGAAGAAC 57.404 34.615 17.48 0.00 41.46 3.01
2303 2565 8.204836 ACTTCTCTAAAAAGCTGTAGAAGAACA 58.795 33.333 17.48 0.00 41.46 3.18
2311 2573 3.685139 CTGTAGAAGAACAGCTGGGAA 57.315 47.619 19.93 0.00 40.40 3.97
2312 2574 4.008074 CTGTAGAAGAACAGCTGGGAAA 57.992 45.455 19.93 0.00 40.40 3.13
2313 2575 3.999663 CTGTAGAAGAACAGCTGGGAAAG 59.000 47.826 19.93 0.00 40.40 2.62
2392 2654 2.613026 TTGTGATGTCAACCACGTCT 57.387 45.000 0.00 0.00 41.19 4.18
2447 2710 2.305928 TGTGCTGCACTTGTTTATGGT 58.694 42.857 30.43 0.00 35.11 3.55
2514 2777 8.022550 AGTTAATTAACCAAACGGTAAAATCGG 58.977 33.333 21.92 0.00 34.92 4.18
2620 2883 7.784790 AAAAAGTAAACACGTTACAACACAG 57.215 32.000 0.00 0.00 44.03 3.66
2641 2904 7.275779 ACACAGTTATAAATCACTACTTGCTCG 59.724 37.037 0.00 0.00 0.00 5.03
2655 2918 1.377202 GCTCGGCACTTTGGATGGA 60.377 57.895 0.00 0.00 0.00 3.41
2656 2919 1.372087 GCTCGGCACTTTGGATGGAG 61.372 60.000 0.00 0.00 0.00 3.86
2657 2920 0.036010 CTCGGCACTTTGGATGGAGT 60.036 55.000 0.00 0.00 0.00 3.85
2658 2921 1.207089 CTCGGCACTTTGGATGGAGTA 59.793 52.381 0.00 0.00 0.00 2.59
2659 2922 1.207089 TCGGCACTTTGGATGGAGTAG 59.793 52.381 0.00 0.00 0.00 2.57
2660 2923 1.207089 CGGCACTTTGGATGGAGTAGA 59.793 52.381 0.00 0.00 0.00 2.59
2661 2924 2.158900 CGGCACTTTGGATGGAGTAGAT 60.159 50.000 0.00 0.00 0.00 1.98
2662 2925 3.209410 GGCACTTTGGATGGAGTAGATG 58.791 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.763645 GGGTTGGTGGTGGTGACCT 61.764 63.158 2.11 0.00 43.58 3.85
111 112 1.664333 GTGGCGGCACACAAATTGG 60.664 57.895 34.40 0.00 40.99 3.16
114 115 3.302344 GGGTGGCGGCACACAAAT 61.302 61.111 38.28 0.00 43.08 2.32
125 126 4.035102 GTCCAGAGGTGGGGTGGC 62.035 72.222 0.00 0.00 45.11 5.01
145 146 1.797211 GAGGTCGATGTAGGGAGGCG 61.797 65.000 0.00 0.00 0.00 5.52
171 172 3.808656 GTCCTCGTCCCCGTCGTC 61.809 72.222 0.00 0.00 35.01 4.20
178 179 4.112341 CGTCACCGTCCTCGTCCC 62.112 72.222 0.00 0.00 35.01 4.46
180 181 4.773117 GGCGTCACCGTCCTCGTC 62.773 72.222 0.00 0.00 36.15 4.20
183 184 2.820767 CTTCAGGCGTCACCGTCCTC 62.821 65.000 0.00 0.00 46.52 3.71
193 194 0.396435 TCATGGTTGTCTTCAGGCGT 59.604 50.000 0.00 0.00 0.00 5.68
219 220 4.073293 ACATAAAAGGTAGATCTGCCCG 57.927 45.455 24.61 10.06 35.84 6.13
220 221 6.775594 AAAACATAAAAGGTAGATCTGCCC 57.224 37.500 24.61 14.68 35.84 5.36
313 315 9.786105 CATTGGAAAATAATTTAAAATGGGCAC 57.214 29.630 0.00 0.00 32.74 5.01
356 454 3.435327 TCCGGATTTTGTCTGTTTGATCG 59.565 43.478 0.00 0.00 0.00 3.69
357 455 5.567138 ATCCGGATTTTGTCTGTTTGATC 57.433 39.130 12.38 0.00 0.00 2.92
358 456 6.404734 GCTTATCCGGATTTTGTCTGTTTGAT 60.405 38.462 24.71 0.00 0.00 2.57
359 457 5.106317 GCTTATCCGGATTTTGTCTGTTTGA 60.106 40.000 24.71 0.00 0.00 2.69
376 474 0.459063 AAACGGACGTCGGCTTATCC 60.459 55.000 21.60 0.00 44.45 2.59
377 475 2.193306 TAAACGGACGTCGGCTTATC 57.807 50.000 21.60 0.00 44.45 1.75
378 476 2.533266 CTTAAACGGACGTCGGCTTAT 58.467 47.619 21.60 8.92 44.45 1.73
380 478 0.668401 CCTTAAACGGACGTCGGCTT 60.668 55.000 21.60 18.02 44.45 4.35
381 479 1.080298 CCTTAAACGGACGTCGGCT 60.080 57.895 21.60 8.13 44.45 5.52
382 480 1.347097 GACCTTAAACGGACGTCGGC 61.347 60.000 21.60 2.31 44.45 5.54
383 481 0.242017 AGACCTTAAACGGACGTCGG 59.758 55.000 20.28 20.28 44.45 4.79
384 482 2.778659 CTAGACCTTAAACGGACGTCG 58.221 52.381 9.92 7.64 45.88 5.12
385 483 2.163211 AGCTAGACCTTAAACGGACGTC 59.837 50.000 7.13 7.13 0.00 4.34
386 484 2.165998 AGCTAGACCTTAAACGGACGT 58.834 47.619 0.00 0.00 0.00 4.34
387 485 2.935481 AGCTAGACCTTAAACGGACG 57.065 50.000 0.00 0.00 0.00 4.79
388 486 3.119708 TCGAAGCTAGACCTTAAACGGAC 60.120 47.826 0.00 0.00 0.00 4.79
389 487 3.084039 TCGAAGCTAGACCTTAAACGGA 58.916 45.455 0.00 0.00 0.00 4.69
390 488 3.498927 TCGAAGCTAGACCTTAAACGG 57.501 47.619 0.00 0.00 0.00 4.44
391 489 4.483311 ACTTCGAAGCTAGACCTTAAACG 58.517 43.478 24.86 0.00 0.00 3.60
392 490 5.120363 CCAACTTCGAAGCTAGACCTTAAAC 59.880 44.000 24.86 0.00 0.00 2.01
396 494 2.613223 GCCAACTTCGAAGCTAGACCTT 60.613 50.000 24.86 7.08 0.00 3.50
397 495 1.066787 GCCAACTTCGAAGCTAGACCT 60.067 52.381 24.86 0.31 0.00 3.85
406 504 3.818773 CCTCTTTTAAGGCCAACTTCGAA 59.181 43.478 5.01 0.00 40.64 3.71
408 506 3.831715 CCTCTTTTAAGGCCAACTTCG 57.168 47.619 5.01 0.00 40.64 3.79
433 531 1.443702 GAAAACAATCCACGCGCCC 60.444 57.895 5.73 0.00 0.00 6.13
442 540 4.212004 GGGAAAAGCTTGCTGAAAACAATC 59.788 41.667 0.00 0.00 0.00 2.67
457 555 2.227865 TGTGTAGCATTTCGGGAAAAGC 59.772 45.455 12.08 12.08 43.09 3.51
471 569 0.953471 TTGATGCCCGTGTGTGTAGC 60.953 55.000 0.00 0.00 0.00 3.58
472 570 1.737838 ATTGATGCCCGTGTGTGTAG 58.262 50.000 0.00 0.00 0.00 2.74
473 571 2.192664 AATTGATGCCCGTGTGTGTA 57.807 45.000 0.00 0.00 0.00 2.90
475 573 2.437200 AAAATTGATGCCCGTGTGTG 57.563 45.000 0.00 0.00 0.00 3.82
476 574 2.095466 CGTAAAATTGATGCCCGTGTGT 60.095 45.455 0.00 0.00 0.00 3.72
477 575 2.514902 CGTAAAATTGATGCCCGTGTG 58.485 47.619 0.00 0.00 0.00 3.82
479 577 1.202245 CCCGTAAAATTGATGCCCGTG 60.202 52.381 0.00 0.00 0.00 4.94
480 578 1.099689 CCCGTAAAATTGATGCCCGT 58.900 50.000 0.00 0.00 0.00 5.28
481 579 0.383949 CCCCGTAAAATTGATGCCCG 59.616 55.000 0.00 0.00 0.00 6.13
483 581 2.494073 TGAACCCCGTAAAATTGATGCC 59.506 45.455 0.00 0.00 0.00 4.40
484 582 3.507786 GTGAACCCCGTAAAATTGATGC 58.492 45.455 0.00 0.00 0.00 3.91
485 583 3.426963 CCGTGAACCCCGTAAAATTGATG 60.427 47.826 0.00 0.00 0.00 3.07
486 584 2.750712 CCGTGAACCCCGTAAAATTGAT 59.249 45.455 0.00 0.00 0.00 2.57
487 585 2.152830 CCGTGAACCCCGTAAAATTGA 58.847 47.619 0.00 0.00 0.00 2.57
488 586 2.152830 TCCGTGAACCCCGTAAAATTG 58.847 47.619 0.00 0.00 0.00 2.32
489 587 2.038820 TCTCCGTGAACCCCGTAAAATT 59.961 45.455 0.00 0.00 0.00 1.82
490 588 1.624813 TCTCCGTGAACCCCGTAAAAT 59.375 47.619 0.00 0.00 0.00 1.82
491 589 1.001181 CTCTCCGTGAACCCCGTAAAA 59.999 52.381 0.00 0.00 0.00 1.52
492 590 0.604578 CTCTCCGTGAACCCCGTAAA 59.395 55.000 0.00 0.00 0.00 2.01
493 591 1.252904 CCTCTCCGTGAACCCCGTAA 61.253 60.000 0.00 0.00 0.00 3.18
494 592 1.679977 CCTCTCCGTGAACCCCGTA 60.680 63.158 0.00 0.00 0.00 4.02
495 593 2.995574 CCTCTCCGTGAACCCCGT 60.996 66.667 0.00 0.00 0.00 5.28
496 594 4.452733 GCCTCTCCGTGAACCCCG 62.453 72.222 0.00 0.00 0.00 5.73
497 595 3.003763 AGCCTCTCCGTGAACCCC 61.004 66.667 0.00 0.00 0.00 4.95
498 596 2.232298 CTCAGCCTCTCCGTGAACCC 62.232 65.000 0.00 0.00 0.00 4.11
499 597 1.216710 CTCAGCCTCTCCGTGAACC 59.783 63.158 0.00 0.00 0.00 3.62
500 598 1.216710 CCTCAGCCTCTCCGTGAAC 59.783 63.158 0.00 0.00 0.00 3.18
501 599 1.228894 ACCTCAGCCTCTCCGTGAA 60.229 57.895 0.00 0.00 0.00 3.18
502 600 1.979155 CACCTCAGCCTCTCCGTGA 60.979 63.158 0.00 0.00 0.00 4.35
503 601 2.575993 CACCTCAGCCTCTCCGTG 59.424 66.667 0.00 0.00 0.00 4.94
504 602 2.681778 CCACCTCAGCCTCTCCGT 60.682 66.667 0.00 0.00 0.00 4.69
505 603 3.465403 CCCACCTCAGCCTCTCCG 61.465 72.222 0.00 0.00 0.00 4.63
506 604 1.492993 AAACCCACCTCAGCCTCTCC 61.493 60.000 0.00 0.00 0.00 3.71
507 605 0.402121 AAAACCCACCTCAGCCTCTC 59.598 55.000 0.00 0.00 0.00 3.20
508 606 0.853530 AAAAACCCACCTCAGCCTCT 59.146 50.000 0.00 0.00 0.00 3.69
509 607 3.439440 AAAAACCCACCTCAGCCTC 57.561 52.632 0.00 0.00 0.00 4.70
525 623 6.179906 TCCTGATTTGCACCCAATTAAAAA 57.820 33.333 0.00 0.00 0.00 1.94
526 624 5.815233 TCCTGATTTGCACCCAATTAAAA 57.185 34.783 0.00 0.00 0.00 1.52
527 625 7.364585 CCTTATCCTGATTTGCACCCAATTAAA 60.365 37.037 0.00 0.00 0.00 1.52
528 626 6.098124 CCTTATCCTGATTTGCACCCAATTAA 59.902 38.462 0.00 0.00 0.00 1.40
529 627 5.598005 CCTTATCCTGATTTGCACCCAATTA 59.402 40.000 0.00 0.00 0.00 1.40
530 628 4.406649 CCTTATCCTGATTTGCACCCAATT 59.593 41.667 0.00 0.00 0.00 2.32
531 629 3.962718 CCTTATCCTGATTTGCACCCAAT 59.037 43.478 0.00 0.00 0.00 3.16
532 630 3.364549 CCTTATCCTGATTTGCACCCAA 58.635 45.455 0.00 0.00 0.00 4.12
533 631 2.358090 CCCTTATCCTGATTTGCACCCA 60.358 50.000 0.00 0.00 0.00 4.51
534 632 2.310538 CCCTTATCCTGATTTGCACCC 58.689 52.381 0.00 0.00 0.00 4.61
535 633 1.683385 GCCCTTATCCTGATTTGCACC 59.317 52.381 0.00 0.00 0.00 5.01
536 634 1.683385 GGCCCTTATCCTGATTTGCAC 59.317 52.381 0.00 0.00 0.00 4.57
537 635 1.411501 GGGCCCTTATCCTGATTTGCA 60.412 52.381 17.04 0.00 0.00 4.08
538 636 1.332195 GGGCCCTTATCCTGATTTGC 58.668 55.000 17.04 0.00 0.00 3.68
539 637 1.217689 TGGGGCCCTTATCCTGATTTG 59.782 52.381 25.93 0.00 0.00 2.32
540 638 1.217942 GTGGGGCCCTTATCCTGATTT 59.782 52.381 25.93 0.00 0.00 2.17
541 639 0.853530 GTGGGGCCCTTATCCTGATT 59.146 55.000 25.93 0.00 0.00 2.57
542 640 1.068352 GGTGGGGCCCTTATCCTGAT 61.068 60.000 25.93 0.00 0.00 2.90
543 641 1.696314 GGTGGGGCCCTTATCCTGA 60.696 63.158 25.93 0.00 0.00 3.86
544 642 2.927056 GGTGGGGCCCTTATCCTG 59.073 66.667 25.93 0.00 0.00 3.86
554 652 3.826265 TTTTCAGCTGGGGTGGGGC 62.826 63.158 15.13 0.00 0.00 5.80
555 653 0.972471 GATTTTCAGCTGGGGTGGGG 60.972 60.000 15.13 0.00 0.00 4.96
556 654 0.251742 TGATTTTCAGCTGGGGTGGG 60.252 55.000 15.13 0.00 0.00 4.61
557 655 1.180029 CTGATTTTCAGCTGGGGTGG 58.820 55.000 15.13 0.00 37.72 4.61
558 656 1.180029 CCTGATTTTCAGCTGGGGTG 58.820 55.000 15.13 0.00 42.98 4.61
559 657 0.040204 CCCTGATTTTCAGCTGGGGT 59.960 55.000 15.13 0.00 42.98 4.95
560 658 2.892025 CCCTGATTTTCAGCTGGGG 58.108 57.895 15.13 10.78 42.98 4.96
561 659 0.685458 CCCCCTGATTTTCAGCTGGG 60.685 60.000 15.13 3.97 43.70 4.45
562 660 2.892025 CCCCCTGATTTTCAGCTGG 58.108 57.895 15.13 0.00 42.98 4.85
577 675 3.053170 TCCTCCTAATTAAACTTGCCCCC 60.053 47.826 0.00 0.00 0.00 5.40
578 676 4.245251 TCCTCCTAATTAAACTTGCCCC 57.755 45.455 0.00 0.00 0.00 5.80
579 677 5.949952 TCTTTCCTCCTAATTAAACTTGCCC 59.050 40.000 0.00 0.00 0.00 5.36
580 678 6.404844 GCTCTTTCCTCCTAATTAAACTTGCC 60.405 42.308 0.00 0.00 0.00 4.52
581 679 6.404844 GGCTCTTTCCTCCTAATTAAACTTGC 60.405 42.308 0.00 0.00 0.00 4.01
582 680 6.095580 GGGCTCTTTCCTCCTAATTAAACTTG 59.904 42.308 0.00 0.00 0.00 3.16
583 681 6.188407 GGGCTCTTTCCTCCTAATTAAACTT 58.812 40.000 0.00 0.00 0.00 2.66
584 682 5.253096 TGGGCTCTTTCCTCCTAATTAAACT 59.747 40.000 0.00 0.00 0.00 2.66
585 683 5.506708 TGGGCTCTTTCCTCCTAATTAAAC 58.493 41.667 0.00 0.00 0.00 2.01
586 684 5.789574 TGGGCTCTTTCCTCCTAATTAAA 57.210 39.130 0.00 0.00 0.00 1.52
587 685 5.994416 ATGGGCTCTTTCCTCCTAATTAA 57.006 39.130 0.00 0.00 0.00 1.40
588 686 7.648177 AATATGGGCTCTTTCCTCCTAATTA 57.352 36.000 0.00 0.00 0.00 1.40
589 687 6.536684 AATATGGGCTCTTTCCTCCTAATT 57.463 37.500 0.00 0.00 0.00 1.40
590 688 6.296720 GCTAATATGGGCTCTTTCCTCCTAAT 60.297 42.308 0.00 0.00 0.00 1.73
591 689 5.013183 GCTAATATGGGCTCTTTCCTCCTAA 59.987 44.000 0.00 0.00 0.00 2.69
592 690 4.532521 GCTAATATGGGCTCTTTCCTCCTA 59.467 45.833 0.00 0.00 0.00 2.94
593 691 3.329225 GCTAATATGGGCTCTTTCCTCCT 59.671 47.826 0.00 0.00 0.00 3.69
594 692 3.073062 TGCTAATATGGGCTCTTTCCTCC 59.927 47.826 0.00 0.00 0.00 4.30
595 693 4.357918 TGCTAATATGGGCTCTTTCCTC 57.642 45.455 0.00 0.00 0.00 3.71
596 694 4.105377 ACATGCTAATATGGGCTCTTTCCT 59.895 41.667 0.00 0.00 32.32 3.36
597 695 4.401925 ACATGCTAATATGGGCTCTTTCC 58.598 43.478 0.00 0.00 32.32 3.13
598 696 6.936900 TCTTACATGCTAATATGGGCTCTTTC 59.063 38.462 0.00 0.00 32.32 2.62
599 697 6.841601 TCTTACATGCTAATATGGGCTCTTT 58.158 36.000 0.00 0.00 32.32 2.52
600 698 6.043706 ACTCTTACATGCTAATATGGGCTCTT 59.956 38.462 0.00 0.00 32.32 2.85
601 699 5.545723 ACTCTTACATGCTAATATGGGCTCT 59.454 40.000 0.00 0.00 32.32 4.09
602 700 5.799213 ACTCTTACATGCTAATATGGGCTC 58.201 41.667 0.00 0.00 32.32 4.70
603 701 5.545723 AGACTCTTACATGCTAATATGGGCT 59.454 40.000 0.00 0.00 32.32 5.19
604 702 5.641209 CAGACTCTTACATGCTAATATGGGC 59.359 44.000 0.00 0.00 32.32 5.36
605 703 6.648310 CACAGACTCTTACATGCTAATATGGG 59.352 42.308 0.00 0.00 32.32 4.00
606 704 7.436933 TCACAGACTCTTACATGCTAATATGG 58.563 38.462 0.00 0.00 32.32 2.74
607 705 8.140628 ACTCACAGACTCTTACATGCTAATATG 58.859 37.037 0.00 0.00 0.00 1.78
608 706 8.243961 ACTCACAGACTCTTACATGCTAATAT 57.756 34.615 0.00 0.00 0.00 1.28
609 707 7.558081 AGACTCACAGACTCTTACATGCTAATA 59.442 37.037 0.00 0.00 0.00 0.98
610 708 6.379703 AGACTCACAGACTCTTACATGCTAAT 59.620 38.462 0.00 0.00 0.00 1.73
611 709 5.712446 AGACTCACAGACTCTTACATGCTAA 59.288 40.000 0.00 0.00 0.00 3.09
612 710 5.257262 AGACTCACAGACTCTTACATGCTA 58.743 41.667 0.00 0.00 0.00 3.49
613 711 4.085733 AGACTCACAGACTCTTACATGCT 58.914 43.478 0.00 0.00 0.00 3.79
614 712 4.448537 AGACTCACAGACTCTTACATGC 57.551 45.455 0.00 0.00 0.00 4.06
615 713 6.751514 ACTAGACTCACAGACTCTTACATG 57.248 41.667 0.00 0.00 0.00 3.21
616 714 9.469097 AAATACTAGACTCACAGACTCTTACAT 57.531 33.333 0.00 0.00 0.00 2.29
617 715 8.865420 AAATACTAGACTCACAGACTCTTACA 57.135 34.615 0.00 0.00 0.00 2.41
618 716 9.777575 GAAAATACTAGACTCACAGACTCTTAC 57.222 37.037 0.00 0.00 0.00 2.34
619 717 8.666573 CGAAAATACTAGACTCACAGACTCTTA 58.333 37.037 0.00 0.00 0.00 2.10
620 718 7.531716 CGAAAATACTAGACTCACAGACTCTT 58.468 38.462 0.00 0.00 0.00 2.85
621 719 6.403855 GCGAAAATACTAGACTCACAGACTCT 60.404 42.308 0.00 0.00 0.00 3.24
622 720 5.740099 GCGAAAATACTAGACTCACAGACTC 59.260 44.000 0.00 0.00 0.00 3.36
623 721 5.183331 TGCGAAAATACTAGACTCACAGACT 59.817 40.000 0.00 0.00 0.00 3.24
624 722 5.286558 GTGCGAAAATACTAGACTCACAGAC 59.713 44.000 0.00 0.00 0.00 3.51
625 723 5.048294 TGTGCGAAAATACTAGACTCACAGA 60.048 40.000 0.00 0.00 0.00 3.41
626 724 5.161358 TGTGCGAAAATACTAGACTCACAG 58.839 41.667 0.00 0.00 0.00 3.66
627 725 5.128992 TGTGCGAAAATACTAGACTCACA 57.871 39.130 0.00 0.00 0.00 3.58
628 726 6.462073 TTTGTGCGAAAATACTAGACTCAC 57.538 37.500 0.00 0.00 0.00 3.51
629 727 7.485418 TTTTTGTGCGAAAATACTAGACTCA 57.515 32.000 0.00 0.00 0.00 3.41
630 728 8.950403 AATTTTTGTGCGAAAATACTAGACTC 57.050 30.769 9.72 0.00 38.04 3.36
639 737 8.994429 TCATGGTATAATTTTTGTGCGAAAAT 57.006 26.923 4.72 4.72 40.06 1.82
640 738 8.818141 TTCATGGTATAATTTTTGTGCGAAAA 57.182 26.923 0.00 0.43 33.46 2.29
641 739 8.818141 TTTCATGGTATAATTTTTGTGCGAAA 57.182 26.923 0.00 0.00 0.00 3.46
642 740 8.818141 TTTTCATGGTATAATTTTTGTGCGAA 57.182 26.923 0.00 0.00 0.00 4.70
643 741 8.818141 TTTTTCATGGTATAATTTTTGTGCGA 57.182 26.923 0.00 0.00 0.00 5.10
644 742 9.687717 GATTTTTCATGGTATAATTTTTGTGCG 57.312 29.630 0.00 0.00 0.00 5.34
703 801 8.842280 CCAAGGTATAGGTAATTTTATTCGCAA 58.158 33.333 0.00 0.00 0.00 4.85
704 802 7.994334 ACCAAGGTATAGGTAATTTTATTCGCA 59.006 33.333 0.00 0.00 36.07 5.10
705 803 8.287503 CACCAAGGTATAGGTAATTTTATTCGC 58.712 37.037 0.00 0.00 36.07 4.70
706 804 8.780249 CCACCAAGGTATAGGTAATTTTATTCG 58.220 37.037 0.00 0.00 36.07 3.34
707 805 8.573885 GCCACCAAGGTATAGGTAATTTTATTC 58.426 37.037 0.00 0.00 40.61 1.75
726 824 2.149383 AGTGAGGAGCTGCCACCAA 61.149 57.895 18.47 1.72 40.02 3.67
850 949 1.593196 AGCTAGTTGCACGCAGAAAA 58.407 45.000 0.00 0.00 45.94 2.29
908 1009 0.617820 AAAGGGGCGAGGAAGCTAGA 60.618 55.000 0.00 0.00 37.29 2.43
955 1056 7.164230 TCTGTATGACAACTTGGTTTGTTTT 57.836 32.000 0.00 0.00 39.88 2.43
962 1063 4.220821 ACTCGATCTGTATGACAACTTGGT 59.779 41.667 0.00 0.00 0.00 3.67
963 1064 4.564372 CACTCGATCTGTATGACAACTTGG 59.436 45.833 0.00 0.00 0.00 3.61
972 1073 2.584492 TGTGCCACTCGATCTGTATG 57.416 50.000 0.00 0.00 0.00 2.39
1778 1882 1.083401 CTATCAACGCGCGCATTCC 60.083 57.895 32.58 0.27 0.00 3.01
1873 1986 1.135689 GTTCAGTAACAAGCATGCCCG 60.136 52.381 15.66 8.37 35.56 6.13
1967 2115 6.364568 ACTCATAAGATAGGTGCATGCATA 57.635 37.500 25.64 13.81 0.00 3.14
2001 2149 9.824216 ACAATACTTACTCATAAGATAGCCCTA 57.176 33.333 1.17 0.00 40.38 3.53
2002 2150 8.728596 ACAATACTTACTCATAAGATAGCCCT 57.271 34.615 1.17 0.00 40.38 5.19
2004 2152 9.575783 GCTACAATACTTACTCATAAGATAGCC 57.424 37.037 1.17 0.00 40.38 3.93
2074 2254 8.789825 TCTAAGATGTACTTCTTCGTAGTTCT 57.210 34.615 23.11 3.78 39.72 3.01
2088 2268 9.503427 AAAAATAAAAGCGCATCTAAGATGTAC 57.497 29.630 11.47 0.00 0.00 2.90
2129 2313 1.668419 AAGGGCATGTAAGATGACGC 58.332 50.000 0.00 0.00 0.00 5.19
2159 2350 4.913335 TTAATCTGGACCTACAGCGTAG 57.087 45.455 8.25 8.25 38.36 3.51
2160 2351 5.419788 TCTTTTAATCTGGACCTACAGCGTA 59.580 40.000 0.00 0.00 38.36 4.42
2181 2372 5.679638 GCATGTTTCCACTTTGTGTTCTCTT 60.680 40.000 0.00 0.00 0.00 2.85
2195 2386 4.025360 AGCCTTCAATATGCATGTTTCCA 58.975 39.130 10.16 0.00 0.00 3.53
2207 2399 4.164221 AGCAAACTAGCCTAGCCTTCAATA 59.836 41.667 0.00 0.00 34.23 1.90
2216 2408 2.221981 GCGCAATAGCAAACTAGCCTAG 59.778 50.000 0.30 0.00 42.27 3.02
2237 2429 3.277481 GAAGTAACTTCAACACAACGCG 58.723 45.455 3.53 3.53 39.95 6.01
2238 2430 3.547413 GGGAAGTAACTTCAACACAACGC 60.547 47.826 0.00 0.00 41.77 4.84
2239 2431 3.875134 AGGGAAGTAACTTCAACACAACG 59.125 43.478 0.00 0.00 41.77 4.10
2240 2432 4.879545 TCAGGGAAGTAACTTCAACACAAC 59.120 41.667 0.00 0.00 41.77 3.32
2244 2440 4.282449 TCGATCAGGGAAGTAACTTCAACA 59.718 41.667 0.00 0.00 41.77 3.33
2306 2568 5.549742 ATCAACTTTTTCATGCTTTCCCA 57.450 34.783 0.00 0.00 0.00 4.37
2310 2572 6.523840 TGGCTAATCAACTTTTTCATGCTTT 58.476 32.000 0.00 0.00 0.00 3.51
2311 2573 6.100404 TGGCTAATCAACTTTTTCATGCTT 57.900 33.333 0.00 0.00 0.00 3.91
2312 2574 5.726980 TGGCTAATCAACTTTTTCATGCT 57.273 34.783 0.00 0.00 0.00 3.79
2313 2575 6.783892 TTTGGCTAATCAACTTTTTCATGC 57.216 33.333 0.00 0.00 0.00 4.06
2314 2576 8.537049 TCATTTGGCTAATCAACTTTTTCATG 57.463 30.769 0.00 0.00 0.00 3.07
2316 2578 9.859427 CTATCATTTGGCTAATCAACTTTTTCA 57.141 29.630 0.00 0.00 0.00 2.69
2392 2654 2.324215 GCAGCAGCTGACAACTGAA 58.676 52.632 27.39 0.00 37.32 3.02
2447 2710 4.975502 CGTGTCTATTTTTCTGCTGCAAAA 59.024 37.500 3.02 1.82 0.00 2.44
2613 2876 8.721478 AGCAAGTAGTGATTTATAACTGTGTTG 58.279 33.333 0.00 0.00 0.00 3.33
2620 2883 5.522460 TGCCGAGCAAGTAGTGATTTATAAC 59.478 40.000 0.00 0.00 34.76 1.89
2637 2900 1.372087 CTCCATCCAAAGTGCCGAGC 61.372 60.000 0.00 0.00 0.00 5.03
2641 2904 3.209410 CATCTACTCCATCCAAAGTGCC 58.791 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.