Multiple sequence alignment - TraesCS5D01G248800

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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 TraesCS5D01G248800 chr5D 100.000 4415 0 0 1 4415 355740723 355736309 0.000000e+00 8154.0
1 TraesCS5D01G248800 chr5A 96.590 3372 87 15 914 4264 457519871 457523235 0.000000e+00 5565.0
2 TraesCS5D01G248800 chr5A 87.140 521 62 3 1 520 457519304 457519820 1.770000e-163 586.0
3 TraesCS5D01G248800 chr5A 92.437 119 9 0 4297 4415 457523229 457523347 2.110000e-38 171.0
4 TraesCS5D01G248800 chr5B 95.604 2775 87 13 883 3628 420471869 420469101 0.000000e+00 4416.0
5 TraesCS5D01G248800 chr5B 91.755 849 55 6 3571 4415 420469080 420468243 0.000000e+00 1166.0
6 TraesCS5D01G248800 chr5B 100.000 43 0 0 857 899 420471927 420471885 3.660000e-11 80.5
7 TraesCS5D01G248800 chr5B 88.710 62 7 0 4081 4142 420459007 420458946 4.740000e-10 76.8
8 TraesCS5D01G248800 chr6D 89.610 308 21 8 553 856 368061159 368061459 8.960000e-102 381.0
9 TraesCS5D01G248800 chr6D 89.610 308 21 8 553 856 368145039 368145339 8.960000e-102 381.0
10 TraesCS5D01G248800 chr4D 87.869 305 28 6 554 856 454771204 454770907 2.530000e-92 350.0


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 TraesCS5D01G248800 chr5D 355736309 355740723 4414 True 8154.000000 8154 100.000000 1 4415 1 chr5D.!!$R1 4414
1 TraesCS5D01G248800 chr5A 457519304 457523347 4043 False 2107.333333 5565 92.055667 1 4415 3 chr5A.!!$F1 4414
2 TraesCS5D01G248800 chr5B 420468243 420471927 3684 True 1887.500000 4416 95.786333 857 4415 3 chr5B.!!$R2 3558

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
56 57 0.035820 CGGGGAAAGAAACGGGATCA 60.036 55.0 0.00 0.0 0.00 2.92 F
669 671 0.115152 CCAAGGGGGAGGAAAAAGCT 59.885 55.0 0.00 0.0 40.01 3.74 F
803 805 0.251474 TTGCTTCCTGCTGCCAGATT 60.251 50.0 0.00 0.0 41.77 2.40 F
2150 2208 0.596600 ACACCGTGACTTACAGTGCG 60.597 55.0 5.28 0.0 30.86 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1797 0.955428 CACTGACCCCAACATCGGTG 60.955 60.000 0.00 0.0 43.75 4.94 R
1955 2013 4.340381 GCCTTACTGATCATCTTGGCATTT 59.660 41.667 18.76 0.0 38.99 2.32 R
2693 2751 0.673437 CCGTCCTGTTGGTTTTGCAT 59.327 50.000 0.00 0.0 34.23 3.96 R
3771 3913 0.316442 CAGGAATTGTAGCATGCGCG 60.316 55.000 13.01 0.0 45.49 6.86 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
18 19 1.079127 GACGGTGTGACCCAGATGG 60.079 63.158 0.00 0.00 33.75 3.51
32 33 3.246301 CCAGATGGTACCCAGAGATGAT 58.754 50.000 10.07 0.00 36.75 2.45
35 36 5.328565 CAGATGGTACCCAGAGATGATAGA 58.671 45.833 10.07 0.00 36.75 1.98
37 38 5.777732 AGATGGTACCCAGAGATGATAGAAC 59.222 44.000 10.07 0.00 36.75 3.01
39 40 3.256136 GGTACCCAGAGATGATAGAACGG 59.744 52.174 0.00 0.00 0.00 4.44
56 57 0.035820 CGGGGAAAGAAACGGGATCA 60.036 55.000 0.00 0.00 0.00 2.92
58 59 1.816835 GGGGAAAGAAACGGGATCAAC 59.183 52.381 0.00 0.00 0.00 3.18
70 71 1.174712 GGATCAACCATGATGCCGGG 61.175 60.000 2.18 0.00 46.30 5.73
90 91 3.312697 GGGATGAAAGGATGAAAGTACGC 59.687 47.826 0.00 0.00 0.00 4.42
102 103 2.372148 AAGTACGCGGTTTTGAAACG 57.628 45.000 12.47 0.00 39.77 3.60
109 110 1.873295 CGGTTTTGAAACGCGATACC 58.127 50.000 15.93 3.79 39.77 2.73
164 165 3.622060 TACTGGAAGCCTTGGCGCC 62.622 63.158 22.73 22.73 37.60 6.53
177 178 4.838152 GCGCCGGAGAAGCCATGA 62.838 66.667 10.31 0.00 35.94 3.07
241 242 3.697747 CGACGTGGGGGTGGCTAA 61.698 66.667 0.00 0.00 0.00 3.09
261 262 1.073923 ACCTAGGTTGGGCTTGAAGTG 59.926 52.381 9.21 0.00 0.00 3.16
264 265 1.832167 GGTTGGGCTTGAAGTGGCA 60.832 57.895 0.00 0.00 0.00 4.92
265 266 1.662044 GTTGGGCTTGAAGTGGCAG 59.338 57.895 0.00 0.00 0.00 4.85
266 267 2.202395 TTGGGCTTGAAGTGGCAGC 61.202 57.895 0.00 0.00 0.00 5.25
270 271 0.606401 GGCTTGAAGTGGCAGCTGTA 60.606 55.000 16.64 1.73 0.00 2.74
271 272 0.801251 GCTTGAAGTGGCAGCTGTAG 59.199 55.000 16.64 1.87 0.00 2.74
304 305 1.403972 GACGGAAGCTCGCGTGTTAG 61.404 60.000 5.77 0.00 0.00 2.34
305 306 2.789203 CGGAAGCTCGCGTGTTAGC 61.789 63.158 5.77 7.86 39.08 3.09
333 334 2.504274 GCGGGGTCGGTCATCCATA 61.504 63.158 0.00 0.00 36.79 2.74
341 342 3.243401 GGTCGGTCATCCATATTTTTGGC 60.243 47.826 0.00 0.00 36.66 4.52
345 346 3.321968 GGTCATCCATATTTTTGGCTCCC 59.678 47.826 0.00 0.00 36.66 4.30
361 362 3.391296 GGCTCCCCTACTATGATGTGAAA 59.609 47.826 0.00 0.00 0.00 2.69
367 368 6.268617 TCCCCTACTATGATGTGAAATCTGAG 59.731 42.308 0.00 0.00 0.00 3.35
368 369 6.042552 CCCCTACTATGATGTGAAATCTGAGT 59.957 42.308 0.00 0.00 0.00 3.41
371 372 8.081633 CCTACTATGATGTGAAATCTGAGTCTC 58.918 40.741 0.00 0.00 0.00 3.36
373 374 7.490840 ACTATGATGTGAAATCTGAGTCTCAG 58.509 38.462 21.95 21.95 45.59 3.35
409 410 6.359804 TCTGCTAGGCTTTATTGATCAACAT 58.640 36.000 11.07 0.00 0.00 2.71
410 411 7.508687 TCTGCTAGGCTTTATTGATCAACATA 58.491 34.615 11.07 0.00 0.00 2.29
446 447 6.486657 GCTATAACAAGTGGATCATTAGGCAA 59.513 38.462 0.00 0.00 0.00 4.52
447 448 7.013274 GCTATAACAAGTGGATCATTAGGCAAA 59.987 37.037 0.00 0.00 0.00 3.68
460 461 0.539518 AGGCAAACCCAACCACAAAC 59.460 50.000 0.00 0.00 36.11 2.93
463 464 1.735018 GCAAACCCAACCACAAACAAC 59.265 47.619 0.00 0.00 0.00 3.32
470 471 1.408702 CAACCACAAACAACTCCCCTG 59.591 52.381 0.00 0.00 0.00 4.45
487 488 7.357471 ACTCCCCTGATTTAAAGATAAAGCAT 58.643 34.615 0.42 0.00 44.01 3.79
522 524 9.971922 AATTATTATTTTAGTTGAGCATGCCTC 57.028 29.630 15.66 11.86 41.15 4.70
524 526 6.683974 TTATTTTAGTTGAGCATGCCTCTC 57.316 37.500 15.66 6.25 41.35 3.20
526 528 3.533606 TTAGTTGAGCATGCCTCTCTC 57.466 47.619 15.66 5.41 41.35 3.20
527 529 1.570803 AGTTGAGCATGCCTCTCTCT 58.429 50.000 15.66 6.05 41.35 3.10
528 530 1.481772 AGTTGAGCATGCCTCTCTCTC 59.518 52.381 15.66 3.79 41.35 3.20
530 532 1.401761 TGAGCATGCCTCTCTCTCTC 58.598 55.000 15.66 2.17 41.35 3.20
531 533 1.063792 TGAGCATGCCTCTCTCTCTCT 60.064 52.381 15.66 0.00 41.35 3.10
532 534 1.610522 GAGCATGCCTCTCTCTCTCTC 59.389 57.143 15.66 0.00 37.60 3.20
534 536 1.610522 GCATGCCTCTCTCTCTCTCTC 59.389 57.143 6.36 0.00 0.00 3.20
535 537 2.750807 GCATGCCTCTCTCTCTCTCTCT 60.751 54.545 6.36 0.00 0.00 3.10
536 538 3.559069 CATGCCTCTCTCTCTCTCTCTT 58.441 50.000 0.00 0.00 0.00 2.85
537 539 3.737559 TGCCTCTCTCTCTCTCTCTTT 57.262 47.619 0.00 0.00 0.00 2.52
538 540 4.046286 TGCCTCTCTCTCTCTCTCTTTT 57.954 45.455 0.00 0.00 0.00 2.27
540 542 4.016444 GCCTCTCTCTCTCTCTCTTTTGA 58.984 47.826 0.00 0.00 0.00 2.69
541 543 4.142381 GCCTCTCTCTCTCTCTCTTTTGAC 60.142 50.000 0.00 0.00 0.00 3.18
542 544 5.256474 CCTCTCTCTCTCTCTCTTTTGACT 58.744 45.833 0.00 0.00 0.00 3.41
543 545 5.711976 CCTCTCTCTCTCTCTCTTTTGACTT 59.288 44.000 0.00 0.00 0.00 3.01
544 546 6.349611 CCTCTCTCTCTCTCTCTTTTGACTTG 60.350 46.154 0.00 0.00 0.00 3.16
545 547 6.303054 TCTCTCTCTCTCTCTTTTGACTTGA 58.697 40.000 0.00 0.00 0.00 3.02
546 548 6.430925 TCTCTCTCTCTCTCTTTTGACTTGAG 59.569 42.308 0.00 0.00 0.00 3.02
547 549 5.048083 TCTCTCTCTCTCTTTTGACTTGAGC 60.048 44.000 0.00 0.00 0.00 4.26
549 551 5.245751 TCTCTCTCTCTTTTGACTTGAGCAT 59.754 40.000 0.00 0.00 0.00 3.79
550 552 5.236282 TCTCTCTCTTTTGACTTGAGCATG 58.764 41.667 0.00 0.00 0.00 4.06
551 553 3.750130 TCTCTCTTTTGACTTGAGCATGC 59.250 43.478 10.51 10.51 0.00 4.06
552 554 2.816087 TCTCTTTTGACTTGAGCATGCC 59.184 45.455 15.66 6.65 0.00 4.40
554 556 3.225104 TCTTTTGACTTGAGCATGCCTT 58.775 40.909 15.66 0.00 0.00 4.35
556 558 4.099881 TCTTTTGACTTGAGCATGCCTTTT 59.900 37.500 15.66 0.00 0.00 2.27
557 559 4.405116 TTTGACTTGAGCATGCCTTTTT 57.595 36.364 15.66 0.00 0.00 1.94
589 591 5.044428 GAGCATCTAGGCTTTATTGCATG 57.956 43.478 12.01 0.00 45.99 4.06
590 592 4.467769 AGCATCTAGGCTTTATTGCATGT 58.532 39.130 12.01 0.00 42.71 3.21
591 593 4.891756 AGCATCTAGGCTTTATTGCATGTT 59.108 37.500 12.01 0.00 42.71 2.71
592 594 4.980434 GCATCTAGGCTTTATTGCATGTTG 59.020 41.667 0.00 0.00 34.04 3.33
593 595 5.450965 GCATCTAGGCTTTATTGCATGTTGT 60.451 40.000 0.00 0.00 34.04 3.32
594 596 6.238731 GCATCTAGGCTTTATTGCATGTTGTA 60.239 38.462 0.00 0.00 34.04 2.41
595 597 7.681782 GCATCTAGGCTTTATTGCATGTTGTAA 60.682 37.037 0.00 0.00 34.04 2.41
596 598 7.695480 TCTAGGCTTTATTGCATGTTGTAAA 57.305 32.000 0.00 0.00 34.04 2.01
597 599 8.292444 TCTAGGCTTTATTGCATGTTGTAAAT 57.708 30.769 0.00 0.00 34.04 1.40
598 600 8.190122 TCTAGGCTTTATTGCATGTTGTAAATG 58.810 33.333 0.00 0.00 34.04 2.32
599 601 6.700352 AGGCTTTATTGCATGTTGTAAATGT 58.300 32.000 0.00 0.00 34.04 2.71
600 602 7.160726 AGGCTTTATTGCATGTTGTAAATGTT 58.839 30.769 0.00 0.00 34.04 2.71
601 603 7.661027 AGGCTTTATTGCATGTTGTAAATGTTT 59.339 29.630 0.00 0.00 34.04 2.83
602 604 8.930760 GGCTTTATTGCATGTTGTAAATGTTTA 58.069 29.630 0.00 0.00 34.04 2.01
603 605 9.739786 GCTTTATTGCATGTTGTAAATGTTTAC 57.260 29.630 8.36 8.36 42.51 2.01
619 621 8.464770 AAATGTTTACATGAATGGATTTCACG 57.535 30.769 0.00 0.00 46.80 4.35
620 622 6.567687 TGTTTACATGAATGGATTTCACGT 57.432 33.333 0.00 0.00 46.80 4.49
621 623 6.976088 TGTTTACATGAATGGATTTCACGTT 58.024 32.000 0.00 0.00 46.80 3.99
622 624 8.100508 TGTTTACATGAATGGATTTCACGTTA 57.899 30.769 0.00 0.00 46.80 3.18
623 625 8.735315 TGTTTACATGAATGGATTTCACGTTAT 58.265 29.630 0.00 0.00 46.80 1.89
624 626 9.009327 GTTTACATGAATGGATTTCACGTTATG 57.991 33.333 0.00 0.00 46.80 1.90
625 627 6.757897 ACATGAATGGATTTCACGTTATGT 57.242 33.333 0.00 0.00 46.80 2.29
626 628 6.554419 ACATGAATGGATTTCACGTTATGTG 58.446 36.000 0.00 0.00 46.80 3.21
636 638 2.851263 ACGTTATGTGAAGCTCCCAA 57.149 45.000 0.00 0.00 0.00 4.12
637 639 2.423577 ACGTTATGTGAAGCTCCCAAC 58.576 47.619 0.00 0.00 0.00 3.77
638 640 1.737793 CGTTATGTGAAGCTCCCAACC 59.262 52.381 0.00 0.00 0.00 3.77
639 641 2.790433 GTTATGTGAAGCTCCCAACCA 58.210 47.619 0.00 0.00 0.00 3.67
640 642 3.356290 GTTATGTGAAGCTCCCAACCAT 58.644 45.455 0.00 0.00 0.00 3.55
641 643 4.523083 GTTATGTGAAGCTCCCAACCATA 58.477 43.478 0.00 0.00 0.00 2.74
642 644 3.737559 ATGTGAAGCTCCCAACCATAA 57.262 42.857 0.00 0.00 0.00 1.90
643 645 3.071874 TGTGAAGCTCCCAACCATAAG 57.928 47.619 0.00 0.00 0.00 1.73
644 646 2.375174 TGTGAAGCTCCCAACCATAAGT 59.625 45.455 0.00 0.00 0.00 2.24
645 647 2.749621 GTGAAGCTCCCAACCATAAGTG 59.250 50.000 0.00 0.00 0.00 3.16
646 648 2.375174 TGAAGCTCCCAACCATAAGTGT 59.625 45.455 0.00 0.00 0.00 3.55
647 649 2.789409 AGCTCCCAACCATAAGTGTC 57.211 50.000 0.00 0.00 0.00 3.67
648 650 2.269940 AGCTCCCAACCATAAGTGTCT 58.730 47.619 0.00 0.00 0.00 3.41
649 651 3.450904 AGCTCCCAACCATAAGTGTCTA 58.549 45.455 0.00 0.00 0.00 2.59
650 652 3.197983 AGCTCCCAACCATAAGTGTCTAC 59.802 47.826 0.00 0.00 0.00 2.59
651 653 3.681874 GCTCCCAACCATAAGTGTCTACC 60.682 52.174 0.00 0.00 0.00 3.18
652 654 3.517901 CTCCCAACCATAAGTGTCTACCA 59.482 47.826 0.00 0.00 0.00 3.25
653 655 3.911260 TCCCAACCATAAGTGTCTACCAA 59.089 43.478 0.00 0.00 0.00 3.67
654 656 4.019681 TCCCAACCATAAGTGTCTACCAAG 60.020 45.833 0.00 0.00 0.00 3.61
655 657 4.261801 CCAACCATAAGTGTCTACCAAGG 58.738 47.826 0.00 0.00 0.00 3.61
656 658 4.261801 CAACCATAAGTGTCTACCAAGGG 58.738 47.826 0.00 0.00 0.00 3.95
657 659 2.844348 ACCATAAGTGTCTACCAAGGGG 59.156 50.000 0.00 0.00 41.29 4.79
658 660 2.172717 CCATAAGTGTCTACCAAGGGGG 59.827 54.545 0.00 0.00 44.81 5.40
659 661 3.112263 CATAAGTGTCTACCAAGGGGGA 58.888 50.000 0.00 0.00 41.15 4.81
661 663 0.252742 AGTGTCTACCAAGGGGGAGG 60.253 60.000 0.00 0.00 46.21 4.30
662 664 0.252558 GTGTCTACCAAGGGGGAGGA 60.253 60.000 0.00 0.00 46.21 3.71
663 665 0.494551 TGTCTACCAAGGGGGAGGAA 59.505 55.000 0.00 0.00 46.21 3.36
664 666 1.132332 TGTCTACCAAGGGGGAGGAAA 60.132 52.381 0.00 0.00 46.21 3.13
665 667 1.990327 GTCTACCAAGGGGGAGGAAAA 59.010 52.381 0.00 0.00 46.21 2.29
666 668 2.377531 GTCTACCAAGGGGGAGGAAAAA 59.622 50.000 0.00 0.00 46.21 1.94
667 669 2.647802 TCTACCAAGGGGGAGGAAAAAG 59.352 50.000 0.00 0.00 46.21 2.27
668 670 0.178932 ACCAAGGGGGAGGAAAAAGC 60.179 55.000 0.00 0.00 41.15 3.51
669 671 0.115152 CCAAGGGGGAGGAAAAAGCT 59.885 55.000 0.00 0.00 40.01 3.74
670 672 1.357761 CCAAGGGGGAGGAAAAAGCTA 59.642 52.381 0.00 0.00 40.01 3.32
671 673 2.225267 CCAAGGGGGAGGAAAAAGCTAA 60.225 50.000 0.00 0.00 40.01 3.09
672 674 3.506398 CAAGGGGGAGGAAAAAGCTAAA 58.494 45.455 0.00 0.00 0.00 1.85
673 675 4.096681 CAAGGGGGAGGAAAAAGCTAAAT 58.903 43.478 0.00 0.00 0.00 1.40
674 676 3.982516 AGGGGGAGGAAAAAGCTAAATC 58.017 45.455 0.00 0.00 0.00 2.17
675 677 3.598324 AGGGGGAGGAAAAAGCTAAATCT 59.402 43.478 0.00 0.00 0.00 2.40
676 678 4.794067 AGGGGGAGGAAAAAGCTAAATCTA 59.206 41.667 0.00 0.00 0.00 1.98
677 679 5.436709 AGGGGGAGGAAAAAGCTAAATCTAT 59.563 40.000 0.00 0.00 0.00 1.98
678 680 6.624021 AGGGGGAGGAAAAAGCTAAATCTATA 59.376 38.462 0.00 0.00 0.00 1.31
679 681 6.715718 GGGGGAGGAAAAAGCTAAATCTATAC 59.284 42.308 0.00 0.00 0.00 1.47
680 682 7.421499 GGGGGAGGAAAAAGCTAAATCTATACT 60.421 40.741 0.00 0.00 0.00 2.12
681 683 8.657712 GGGGAGGAAAAAGCTAAATCTATACTA 58.342 37.037 0.00 0.00 0.00 1.82
716 718 5.208624 TCGAAATTCGAAGCTCTTGATTG 57.791 39.130 16.25 0.00 46.90 2.67
717 719 4.929211 TCGAAATTCGAAGCTCTTGATTGA 59.071 37.500 16.25 0.00 46.90 2.57
718 720 5.408299 TCGAAATTCGAAGCTCTTGATTGAA 59.592 36.000 16.25 0.00 46.90 2.69
719 721 6.073276 TCGAAATTCGAAGCTCTTGATTGAAA 60.073 34.615 16.25 0.00 46.90 2.69
720 722 6.578545 CGAAATTCGAAGCTCTTGATTGAAAA 59.421 34.615 10.18 0.00 43.74 2.29
721 723 7.272084 CGAAATTCGAAGCTCTTGATTGAAAAT 59.728 33.333 10.18 0.00 43.74 1.82
722 724 8.822652 AAATTCGAAGCTCTTGATTGAAAATT 57.177 26.923 3.35 0.00 0.00 1.82
723 725 9.912634 AAATTCGAAGCTCTTGATTGAAAATTA 57.087 25.926 3.35 0.00 0.00 1.40
724 726 9.912634 AATTCGAAGCTCTTGATTGAAAATTAA 57.087 25.926 3.35 0.00 0.00 1.40
725 727 9.912634 ATTCGAAGCTCTTGATTGAAAATTAAA 57.087 25.926 3.35 0.00 0.00 1.52
726 728 9.743057 TTCGAAGCTCTTGATTGAAAATTAAAA 57.257 25.926 0.00 0.00 0.00 1.52
727 729 9.743057 TCGAAGCTCTTGATTGAAAATTAAAAA 57.257 25.926 0.00 0.00 0.00 1.94
728 730 9.783425 CGAAGCTCTTGATTGAAAATTAAAAAC 57.217 29.630 0.00 0.00 0.00 2.43
731 733 9.598517 AGCTCTTGATTGAAAATTAAAAACACA 57.401 25.926 0.00 0.00 0.00 3.72
778 780 6.923012 TCTCTGATCTCTCTAATTATGCTGC 58.077 40.000 0.00 0.00 0.00 5.25
779 781 6.035368 TCTGATCTCTCTAATTATGCTGCC 57.965 41.667 0.00 0.00 0.00 4.85
780 782 4.814147 TGATCTCTCTAATTATGCTGCCG 58.186 43.478 0.00 0.00 0.00 5.69
781 783 4.281941 TGATCTCTCTAATTATGCTGCCGT 59.718 41.667 0.00 0.00 0.00 5.68
782 784 5.476945 TGATCTCTCTAATTATGCTGCCGTA 59.523 40.000 0.00 0.00 0.00 4.02
783 785 5.378292 TCTCTCTAATTATGCTGCCGTAG 57.622 43.478 0.00 0.00 0.00 3.51
784 786 4.827835 TCTCTCTAATTATGCTGCCGTAGT 59.172 41.667 0.00 0.00 0.00 2.73
785 787 5.302059 TCTCTCTAATTATGCTGCCGTAGTT 59.698 40.000 0.00 0.00 0.00 2.24
786 788 5.289595 TCTCTAATTATGCTGCCGTAGTTG 58.710 41.667 0.00 0.00 0.00 3.16
787 789 3.807622 TCTAATTATGCTGCCGTAGTTGC 59.192 43.478 0.00 0.00 0.00 4.17
788 790 2.332063 ATTATGCTGCCGTAGTTGCT 57.668 45.000 0.00 0.00 0.00 3.91
789 791 2.107950 TTATGCTGCCGTAGTTGCTT 57.892 45.000 0.00 0.00 0.00 3.91
790 792 1.651987 TATGCTGCCGTAGTTGCTTC 58.348 50.000 0.00 0.00 0.00 3.86
791 793 1.026718 ATGCTGCCGTAGTTGCTTCC 61.027 55.000 0.00 0.00 0.00 3.46
792 794 1.376037 GCTGCCGTAGTTGCTTCCT 60.376 57.895 0.00 0.00 0.00 3.36
793 795 1.639298 GCTGCCGTAGTTGCTTCCTG 61.639 60.000 0.00 0.00 0.00 3.86
794 796 1.639298 CTGCCGTAGTTGCTTCCTGC 61.639 60.000 0.00 0.00 43.25 4.85
795 797 1.376037 GCCGTAGTTGCTTCCTGCT 60.376 57.895 0.00 0.00 43.37 4.24
796 798 1.639298 GCCGTAGTTGCTTCCTGCTG 61.639 60.000 0.00 0.00 43.37 4.41
797 799 1.639298 CCGTAGTTGCTTCCTGCTGC 61.639 60.000 0.00 0.00 43.37 5.25
798 800 1.639298 CGTAGTTGCTTCCTGCTGCC 61.639 60.000 0.00 0.00 43.37 4.85
799 801 0.606401 GTAGTTGCTTCCTGCTGCCA 60.606 55.000 0.00 0.00 43.37 4.92
800 802 0.321919 TAGTTGCTTCCTGCTGCCAG 60.322 55.000 0.00 0.00 43.37 4.85
801 803 1.601759 GTTGCTTCCTGCTGCCAGA 60.602 57.895 0.00 0.00 41.77 3.86
802 804 0.964358 GTTGCTTCCTGCTGCCAGAT 60.964 55.000 0.00 0.00 41.77 2.90
803 805 0.251474 TTGCTTCCTGCTGCCAGATT 60.251 50.000 0.00 0.00 41.77 2.40
804 806 0.963856 TGCTTCCTGCTGCCAGATTG 60.964 55.000 0.00 0.00 41.77 2.67
805 807 0.679002 GCTTCCTGCTGCCAGATTGA 60.679 55.000 0.00 0.00 41.77 2.57
806 808 2.022754 GCTTCCTGCTGCCAGATTGAT 61.023 52.381 0.00 0.00 41.77 2.57
807 809 1.676529 CTTCCTGCTGCCAGATTGATG 59.323 52.381 0.00 0.00 41.77 3.07
808 810 0.622136 TCCTGCTGCCAGATTGATGT 59.378 50.000 0.00 0.00 41.77 3.06
809 811 0.738975 CCTGCTGCCAGATTGATGTG 59.261 55.000 0.00 0.00 41.77 3.21
810 812 1.680860 CCTGCTGCCAGATTGATGTGA 60.681 52.381 0.00 0.00 41.77 3.58
811 813 2.298610 CTGCTGCCAGATTGATGTGAT 58.701 47.619 0.00 0.00 41.77 3.06
812 814 2.688446 CTGCTGCCAGATTGATGTGATT 59.312 45.455 0.00 0.00 41.77 2.57
813 815 3.881089 CTGCTGCCAGATTGATGTGATTA 59.119 43.478 0.00 0.00 41.77 1.75
814 816 4.271661 TGCTGCCAGATTGATGTGATTAA 58.728 39.130 0.00 0.00 0.00 1.40
815 817 4.096833 TGCTGCCAGATTGATGTGATTAAC 59.903 41.667 0.00 0.00 0.00 2.01
816 818 4.498682 GCTGCCAGATTGATGTGATTAACC 60.499 45.833 0.00 0.00 0.00 2.85
817 819 4.598022 TGCCAGATTGATGTGATTAACCA 58.402 39.130 0.00 0.00 0.00 3.67
818 820 4.398988 TGCCAGATTGATGTGATTAACCAC 59.601 41.667 0.00 0.00 37.55 4.16
819 821 4.641989 GCCAGATTGATGTGATTAACCACT 59.358 41.667 0.71 0.00 37.89 4.00
820 822 5.126061 GCCAGATTGATGTGATTAACCACTT 59.874 40.000 0.71 0.00 37.89 3.16
821 823 6.558009 CCAGATTGATGTGATTAACCACTTG 58.442 40.000 0.71 0.00 37.89 3.16
822 824 6.032094 CAGATTGATGTGATTAACCACTTGC 58.968 40.000 0.71 0.00 37.89 4.01
823 825 5.948162 AGATTGATGTGATTAACCACTTGCT 59.052 36.000 0.71 0.00 37.89 3.91
824 826 6.435277 AGATTGATGTGATTAACCACTTGCTT 59.565 34.615 0.71 0.00 37.89 3.91
825 827 7.611467 AGATTGATGTGATTAACCACTTGCTTA 59.389 33.333 0.71 0.00 37.89 3.09
826 828 6.494893 TGATGTGATTAACCACTTGCTTAC 57.505 37.500 0.71 0.00 37.89 2.34
827 829 6.000840 TGATGTGATTAACCACTTGCTTACA 58.999 36.000 0.71 0.00 37.89 2.41
828 830 5.940192 TGTGATTAACCACTTGCTTACAG 57.060 39.130 0.71 0.00 37.89 2.74
829 831 5.373222 TGTGATTAACCACTTGCTTACAGT 58.627 37.500 0.71 0.00 37.89 3.55
830 832 5.468746 TGTGATTAACCACTTGCTTACAGTC 59.531 40.000 0.71 0.00 37.89 3.51
831 833 5.468746 GTGATTAACCACTTGCTTACAGTCA 59.531 40.000 0.00 0.00 34.38 3.41
832 834 5.700832 TGATTAACCACTTGCTTACAGTCAG 59.299 40.000 0.00 0.00 0.00 3.51
833 835 3.838244 AACCACTTGCTTACAGTCAGA 57.162 42.857 0.00 0.00 0.00 3.27
834 836 3.113260 ACCACTTGCTTACAGTCAGAC 57.887 47.619 0.00 0.00 0.00 3.51
835 837 2.224305 ACCACTTGCTTACAGTCAGACC 60.224 50.000 0.00 0.00 0.00 3.85
836 838 2.417719 CACTTGCTTACAGTCAGACCC 58.582 52.381 0.00 0.00 0.00 4.46
837 839 2.047061 ACTTGCTTACAGTCAGACCCA 58.953 47.619 0.00 0.00 0.00 4.51
838 840 2.438021 ACTTGCTTACAGTCAGACCCAA 59.562 45.455 0.00 0.00 0.00 4.12
839 841 3.073062 ACTTGCTTACAGTCAGACCCAAT 59.927 43.478 0.00 0.00 0.00 3.16
840 842 3.057969 TGCTTACAGTCAGACCCAATG 57.942 47.619 0.00 0.00 0.00 2.82
841 843 2.290260 TGCTTACAGTCAGACCCAATGG 60.290 50.000 0.00 0.00 37.80 3.16
842 844 2.027192 GCTTACAGTCAGACCCAATGGA 60.027 50.000 0.00 0.00 34.81 3.41
843 845 3.370953 GCTTACAGTCAGACCCAATGGAT 60.371 47.826 0.00 0.00 34.81 3.41
844 846 4.141711 GCTTACAGTCAGACCCAATGGATA 60.142 45.833 0.00 0.00 34.81 2.59
845 847 5.605534 CTTACAGTCAGACCCAATGGATAG 58.394 45.833 0.00 0.00 34.81 2.08
846 848 2.774234 ACAGTCAGACCCAATGGATAGG 59.226 50.000 0.00 0.00 34.81 2.57
847 849 3.041211 CAGTCAGACCCAATGGATAGGA 58.959 50.000 0.00 0.00 34.81 2.94
848 850 3.455910 CAGTCAGACCCAATGGATAGGAA 59.544 47.826 0.00 0.00 34.81 3.36
849 851 4.103785 CAGTCAGACCCAATGGATAGGAAT 59.896 45.833 0.00 0.00 34.81 3.01
850 852 4.728860 AGTCAGACCCAATGGATAGGAATT 59.271 41.667 0.00 0.00 34.81 2.17
851 853 4.823989 GTCAGACCCAATGGATAGGAATTG 59.176 45.833 0.00 0.00 34.26 2.32
852 854 3.571401 CAGACCCAATGGATAGGAATTGC 59.429 47.826 0.00 0.00 33.34 3.56
853 855 3.205056 AGACCCAATGGATAGGAATTGCA 59.795 43.478 0.00 0.00 33.34 4.08
854 856 4.140853 AGACCCAATGGATAGGAATTGCAT 60.141 41.667 0.00 0.00 33.34 3.96
855 857 3.899360 ACCCAATGGATAGGAATTGCATG 59.101 43.478 0.00 0.00 33.34 4.06
905 939 0.784778 GAGCTCGTCAACAAACTCGG 59.215 55.000 0.00 0.00 0.00 4.63
909 943 1.649171 CTCGTCAACAAACTCGGATCG 59.351 52.381 0.00 0.00 0.00 3.69
920 954 1.455773 TCGGATCGAGTGATGCCCT 60.456 57.895 0.00 0.00 39.59 5.19
1325 1364 8.655651 ATCAGCTTTCTTTATACTGCTAACTC 57.344 34.615 0.00 0.00 0.00 3.01
1354 1393 2.294979 TCATGTTCTGATGCAGCCATC 58.705 47.619 0.00 0.00 46.46 3.51
1365 1404 2.153645 TGCAGCCATCTGTAACAGTTG 58.846 47.619 0.00 0.00 42.29 3.16
1373 1412 4.393062 CCATCTGTAACAGTTGCCTTAGTG 59.607 45.833 0.00 0.00 31.91 2.74
1443 1482 9.221775 GCTGGATTAGATTGTTGTTTTAATACG 57.778 33.333 0.00 0.00 0.00 3.06
1466 1522 5.521372 CGATCTCTGTTGCTGTATGAAATGA 59.479 40.000 0.00 0.00 0.00 2.57
1554 1612 3.054875 TGAGATTGTCCAGATGTTCCAGG 60.055 47.826 0.00 0.00 0.00 4.45
1558 1616 1.541118 TCCAGATGTTCCAGGCCCA 60.541 57.895 0.00 0.00 0.00 5.36
1607 1665 0.762418 CCACTGGACCAAGGTACACA 59.238 55.000 0.00 0.00 33.38 3.72
1617 1675 5.249780 ACCAAGGTACACACATTCCATAA 57.750 39.130 0.00 0.00 0.00 1.90
1739 1797 5.801380 TGGTTGGTAAGAGAGGTTATGAAC 58.199 41.667 0.00 0.00 0.00 3.18
1838 1896 3.303990 CCACTTACATGGCATTGATACGC 60.304 47.826 0.00 0.00 31.52 4.42
1955 2013 1.756665 CATCATCCGGATGCTGGGA 59.243 57.895 35.16 20.72 46.35 4.37
2150 2208 0.596600 ACACCGTGACTTACAGTGCG 60.597 55.000 5.28 0.00 30.86 5.34
2498 2556 1.302993 GGGCAAGGCTGGTCGTTTA 60.303 57.895 0.00 0.00 0.00 2.01
2693 2751 8.717717 ACCTACTCAATCTTGATTGATGGATTA 58.282 33.333 26.90 15.19 39.52 1.75
3203 3261 6.159293 ACCAGATGCTGTGTCATATAATACG 58.841 40.000 0.00 0.00 0.00 3.06
3474 3532 2.674852 AGCACTGCAACTGTTCGATATG 59.325 45.455 3.30 0.00 0.00 1.78
3483 3541 5.858581 GCAACTGTTCGATATGAAAAGCTTT 59.141 36.000 5.69 5.69 44.57 3.51
3484 3542 6.363357 GCAACTGTTCGATATGAAAAGCTTTT 59.637 34.615 24.08 24.08 44.57 2.27
3485 3543 7.096065 GCAACTGTTCGATATGAAAAGCTTTTT 60.096 33.333 24.58 12.98 44.57 1.94
3543 3601 1.117994 CATGGAGGACAGCAGCTAGA 58.882 55.000 0.00 0.00 0.00 2.43
3579 3720 6.494893 GTGTGTATTTCACCTAGCAAATGA 57.505 37.500 0.00 0.00 45.61 2.57
3643 3784 4.753516 TCTGCAGCTGCCTAAATACTTA 57.246 40.909 34.64 11.92 41.18 2.24
3673 3814 4.994852 TGGTTTCAGAATCACTTTACTCCG 59.005 41.667 0.00 0.00 0.00 4.63
3674 3815 4.142881 GGTTTCAGAATCACTTTACTCCGC 60.143 45.833 0.00 0.00 0.00 5.54
3681 3822 6.758886 CAGAATCACTTTACTCCGCTAAGATT 59.241 38.462 0.00 0.00 0.00 2.40
3693 3834 2.633488 GCTAAGATTCGAGGGCTGTTT 58.367 47.619 0.00 0.00 0.00 2.83
3715 3857 5.772825 TCTGAAAAGTTGAGACCATTTGG 57.227 39.130 0.00 0.00 42.17 3.28
3771 3913 2.045926 AGCAATCACCGGTGGAGC 60.046 61.111 33.40 30.15 0.00 4.70
3829 3971 2.860582 GCCGTGTTTGTGTGGGTAAATG 60.861 50.000 0.00 0.00 0.00 2.32
3908 4050 1.342672 TAGCCGTCCCCATTTCTCCC 61.343 60.000 0.00 0.00 0.00 4.30
3913 4055 1.299939 GTCCCCATTTCTCCCCTCTT 58.700 55.000 0.00 0.00 0.00 2.85
4004 4146 7.450074 GTGAAAACATTTTCTTATTTCCCCCT 58.550 34.615 16.01 0.00 45.14 4.79
4050 4192 7.063308 GCATTTTTCACACTTTTCTCTTTCACA 59.937 33.333 0.00 0.00 0.00 3.58
4077 4219 5.080337 ACTCTGTGGATTCTGACACTAAGA 58.920 41.667 0.00 0.00 38.39 2.10
4159 4301 0.838554 TGTGCACAGGGGCTTACCTA 60.839 55.000 17.42 0.00 39.34 3.08
4205 4348 1.947456 GTGTTTGAGCCTTCCGAAACT 59.053 47.619 0.00 0.00 31.03 2.66
4217 4360 3.478857 TCCGAAACTAGCAAAGAACCA 57.521 42.857 0.00 0.00 0.00 3.67
4253 4399 1.138859 CATGGTAGGCGTCCAGAATCA 59.861 52.381 9.26 0.00 38.42 2.57
4260 4406 4.696479 AGGCGTCCAGAATCAAGATATT 57.304 40.909 0.00 0.00 0.00 1.28
4290 4436 2.731976 GACCAACTCAGAACTAACAGCG 59.268 50.000 0.00 0.00 0.00 5.18
4291 4437 2.102588 ACCAACTCAGAACTAACAGCGT 59.897 45.455 0.00 0.00 0.00 5.07
4327 4473 4.355437 TGGCGTCTGTAAAATTTGTGTTG 58.645 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.256136 CCCGTTCTATCATCTCTGGGTAC 59.744 52.174 0.00 0.00 0.00 3.34
20 21 2.320781 CCCGTTCTATCATCTCTGGGT 58.679 52.381 0.00 0.00 0.00 4.51
27 28 4.270325 CGTTTCTTTCCCCGTTCTATCATC 59.730 45.833 0.00 0.00 0.00 2.92
32 33 1.002315 CCCGTTTCTTTCCCCGTTCTA 59.998 52.381 0.00 0.00 0.00 2.10
35 36 0.402887 ATCCCGTTTCTTTCCCCGTT 59.597 50.000 0.00 0.00 0.00 4.44
37 38 0.035820 TGATCCCGTTTCTTTCCCCG 60.036 55.000 0.00 0.00 0.00 5.73
39 40 1.816835 GGTTGATCCCGTTTCTTTCCC 59.183 52.381 0.00 0.00 0.00 3.97
56 57 0.258484 TTCATCCCGGCATCATGGTT 59.742 50.000 0.00 0.00 0.00 3.67
58 59 0.956633 CTTTCATCCCGGCATCATGG 59.043 55.000 0.00 0.00 0.00 3.66
64 65 0.623194 TTCATCCTTTCATCCCGGCA 59.377 50.000 0.00 0.00 0.00 5.69
70 71 3.001330 CCGCGTACTTTCATCCTTTCATC 59.999 47.826 4.92 0.00 0.00 2.92
90 91 1.461897 AGGTATCGCGTTTCAAAACCG 59.538 47.619 5.77 5.41 35.51 4.44
102 103 0.759436 TCCTTCTCCCCAGGTATCGC 60.759 60.000 0.00 0.00 32.59 4.58
109 110 0.554792 ATTGCCATCCTTCTCCCCAG 59.445 55.000 0.00 0.00 0.00 4.45
135 136 0.522180 CTTCCAGTAGCACGTCGACT 59.478 55.000 14.70 0.00 0.00 4.18
164 165 1.227089 CGACCTCATGGCTTCTCCG 60.227 63.158 0.00 0.00 37.80 4.63
166 167 4.844420 CCGACCTCATGGCTTCTC 57.156 61.111 0.00 0.00 36.63 2.87
241 242 1.073923 CACTTCAAGCCCAACCTAGGT 59.926 52.381 9.21 9.21 0.00 3.08
278 279 4.856607 GAGCTTCCGTCCGGCGAG 62.857 72.222 17.96 10.28 44.77 5.03
321 322 3.882888 GAGCCAAAAATATGGATGACCGA 59.117 43.478 0.00 0.00 39.71 4.69
331 332 6.780198 TCATAGTAGGGGAGCCAAAAATAT 57.220 37.500 0.00 0.00 0.00 1.28
333 334 5.103515 ACATCATAGTAGGGGAGCCAAAAAT 60.104 40.000 0.00 0.00 0.00 1.82
341 342 6.268617 TCAGATTTCACATCATAGTAGGGGAG 59.731 42.308 0.00 0.00 0.00 4.30
345 346 7.950512 AGACTCAGATTTCACATCATAGTAGG 58.049 38.462 0.00 0.00 0.00 3.18
382 383 7.176515 TGTTGATCAATAAAGCCTAGCAGAAAA 59.823 33.333 12.12 0.00 0.00 2.29
384 385 6.179756 TGTTGATCAATAAAGCCTAGCAGAA 58.820 36.000 12.12 0.00 0.00 3.02
385 386 5.744171 TGTTGATCAATAAAGCCTAGCAGA 58.256 37.500 12.12 0.00 0.00 4.26
386 387 6.630444 ATGTTGATCAATAAAGCCTAGCAG 57.370 37.500 12.12 0.00 0.00 4.24
446 447 1.828595 GGAGTTGTTTGTGGTTGGGTT 59.171 47.619 0.00 0.00 0.00 4.11
447 448 1.480789 GGAGTTGTTTGTGGTTGGGT 58.519 50.000 0.00 0.00 0.00 4.51
460 461 7.122650 TGCTTTATCTTTAAATCAGGGGAGTTG 59.877 37.037 0.00 0.00 32.82 3.16
463 464 7.655490 CATGCTTTATCTTTAAATCAGGGGAG 58.345 38.462 0.00 0.00 29.66 4.30
503 505 4.853007 AGAGAGGCATGCTCAACTAAAAT 58.147 39.130 18.92 0.00 34.85 1.82
507 509 2.692557 GAGAGAGAGGCATGCTCAACTA 59.307 50.000 18.92 0.00 34.85 2.24
520 522 6.430925 TCAAGTCAAAAGAGAGAGAGAGAGAG 59.569 42.308 0.00 0.00 0.00 3.20
522 524 6.573664 TCAAGTCAAAAGAGAGAGAGAGAG 57.426 41.667 0.00 0.00 0.00 3.20
524 526 5.163513 GCTCAAGTCAAAAGAGAGAGAGAG 58.836 45.833 0.00 0.00 0.00 3.20
526 528 4.880759 TGCTCAAGTCAAAAGAGAGAGAG 58.119 43.478 0.00 0.00 0.00 3.20
527 529 4.944619 TGCTCAAGTCAAAAGAGAGAGA 57.055 40.909 0.00 0.00 0.00 3.10
528 530 4.142859 GCATGCTCAAGTCAAAAGAGAGAG 60.143 45.833 11.37 0.00 0.00 3.20
530 532 3.119919 GGCATGCTCAAGTCAAAAGAGAG 60.120 47.826 18.92 0.00 0.00 3.20
531 533 2.816087 GGCATGCTCAAGTCAAAAGAGA 59.184 45.455 18.92 0.00 0.00 3.10
532 534 2.818432 AGGCATGCTCAAGTCAAAAGAG 59.182 45.455 18.92 0.00 0.00 2.85
534 536 3.655276 AAGGCATGCTCAAGTCAAAAG 57.345 42.857 18.92 0.00 0.00 2.27
535 537 4.405116 AAAAGGCATGCTCAAGTCAAAA 57.595 36.364 18.92 0.00 0.00 2.44
536 538 4.405116 AAAAAGGCATGCTCAAGTCAAA 57.595 36.364 18.92 0.00 0.00 2.69
556 558 4.475016 AGCCTAGATGCTCTTTCCCTAAAA 59.525 41.667 0.00 0.00 36.75 1.52
557 559 4.040755 AGCCTAGATGCTCTTTCCCTAAA 58.959 43.478 0.00 0.00 36.75 1.85
558 560 3.658725 AGCCTAGATGCTCTTTCCCTAA 58.341 45.455 0.00 0.00 36.75 2.69
560 562 2.188818 AGCCTAGATGCTCTTTCCCT 57.811 50.000 0.00 0.00 36.75 4.20
561 563 3.289407 AAAGCCTAGATGCTCTTTCCC 57.711 47.619 0.00 0.00 41.80 3.97
562 564 5.278218 GCAATAAAGCCTAGATGCTCTTTCC 60.278 44.000 0.00 0.00 41.80 3.13
563 565 5.297776 TGCAATAAAGCCTAGATGCTCTTTC 59.702 40.000 0.00 0.00 41.80 2.62
564 566 5.195940 TGCAATAAAGCCTAGATGCTCTTT 58.804 37.500 0.00 0.00 41.80 2.52
565 567 4.785301 TGCAATAAAGCCTAGATGCTCTT 58.215 39.130 0.00 0.00 41.80 2.85
566 568 4.428294 TGCAATAAAGCCTAGATGCTCT 57.572 40.909 0.00 0.00 41.80 4.09
567 569 4.518211 ACATGCAATAAAGCCTAGATGCTC 59.482 41.667 0.00 0.00 41.80 4.26
569 571 4.843220 ACATGCAATAAAGCCTAGATGC 57.157 40.909 0.00 0.00 0.00 3.91
570 572 6.140303 ACAACATGCAATAAAGCCTAGATG 57.860 37.500 0.00 0.00 0.00 2.90
571 573 7.880160 TTACAACATGCAATAAAGCCTAGAT 57.120 32.000 0.00 0.00 0.00 1.98
572 574 7.695480 TTTACAACATGCAATAAAGCCTAGA 57.305 32.000 0.00 0.00 0.00 2.43
573 575 7.975616 ACATTTACAACATGCAATAAAGCCTAG 59.024 33.333 0.00 0.00 0.00 3.02
574 576 7.835822 ACATTTACAACATGCAATAAAGCCTA 58.164 30.769 0.00 0.00 0.00 3.93
575 577 6.700352 ACATTTACAACATGCAATAAAGCCT 58.300 32.000 0.00 0.00 0.00 4.58
576 578 6.966435 ACATTTACAACATGCAATAAAGCC 57.034 33.333 0.00 0.00 0.00 4.35
577 579 9.739786 GTAAACATTTACAACATGCAATAAAGC 57.260 29.630 9.20 0.00 41.93 3.51
617 619 2.423577 GTTGGGAGCTTCACATAACGT 58.576 47.619 0.00 0.00 24.99 3.99
618 620 1.737793 GGTTGGGAGCTTCACATAACG 59.262 52.381 0.00 0.00 24.99 3.18
619 621 2.790433 TGGTTGGGAGCTTCACATAAC 58.210 47.619 0.00 0.00 24.99 1.89
620 622 3.737559 ATGGTTGGGAGCTTCACATAA 57.262 42.857 0.00 0.00 24.99 1.90
621 623 4.227300 ACTTATGGTTGGGAGCTTCACATA 59.773 41.667 0.00 0.00 24.99 2.29
622 624 3.010584 ACTTATGGTTGGGAGCTTCACAT 59.989 43.478 0.00 0.00 24.99 3.21
623 625 2.375174 ACTTATGGTTGGGAGCTTCACA 59.625 45.455 0.00 0.00 0.00 3.58
624 626 2.749621 CACTTATGGTTGGGAGCTTCAC 59.250 50.000 0.00 0.00 0.00 3.18
625 627 2.375174 ACACTTATGGTTGGGAGCTTCA 59.625 45.455 0.00 0.00 0.00 3.02
626 628 3.010420 GACACTTATGGTTGGGAGCTTC 58.990 50.000 0.00 0.00 0.00 3.86
627 629 2.644798 AGACACTTATGGTTGGGAGCTT 59.355 45.455 0.00 0.00 0.00 3.74
628 630 2.269940 AGACACTTATGGTTGGGAGCT 58.730 47.619 0.00 0.00 0.00 4.09
629 631 2.789409 AGACACTTATGGTTGGGAGC 57.211 50.000 0.00 0.00 0.00 4.70
630 632 3.517901 TGGTAGACACTTATGGTTGGGAG 59.482 47.826 0.00 0.00 0.00 4.30
631 633 3.522759 TGGTAGACACTTATGGTTGGGA 58.477 45.455 0.00 0.00 0.00 4.37
632 634 3.992943 TGGTAGACACTTATGGTTGGG 57.007 47.619 0.00 0.00 0.00 4.12
633 635 4.261801 CCTTGGTAGACACTTATGGTTGG 58.738 47.826 0.00 0.00 0.00 3.77
634 636 4.261801 CCCTTGGTAGACACTTATGGTTG 58.738 47.826 0.00 0.00 0.00 3.77
635 637 3.265995 CCCCTTGGTAGACACTTATGGTT 59.734 47.826 0.00 0.00 0.00 3.67
636 638 2.844348 CCCCTTGGTAGACACTTATGGT 59.156 50.000 0.00 0.00 0.00 3.55
637 639 2.172717 CCCCCTTGGTAGACACTTATGG 59.827 54.545 0.00 0.00 0.00 2.74
638 640 3.112263 TCCCCCTTGGTAGACACTTATG 58.888 50.000 0.00 0.00 34.77 1.90
639 641 3.385115 CTCCCCCTTGGTAGACACTTAT 58.615 50.000 0.00 0.00 34.77 1.73
640 642 2.561297 CCTCCCCCTTGGTAGACACTTA 60.561 54.545 0.00 0.00 34.77 2.24
641 643 1.657804 CTCCCCCTTGGTAGACACTT 58.342 55.000 0.00 0.00 34.77 3.16
642 644 0.252742 CCTCCCCCTTGGTAGACACT 60.253 60.000 0.00 0.00 34.77 3.55
643 645 0.252558 TCCTCCCCCTTGGTAGACAC 60.253 60.000 0.00 0.00 34.77 3.67
644 646 0.494551 TTCCTCCCCCTTGGTAGACA 59.505 55.000 0.00 0.00 34.77 3.41
645 647 1.665137 TTTCCTCCCCCTTGGTAGAC 58.335 55.000 0.00 0.00 34.77 2.59
646 648 2.444033 TTTTCCTCCCCCTTGGTAGA 57.556 50.000 0.00 0.00 34.77 2.59
647 649 2.884304 GCTTTTTCCTCCCCCTTGGTAG 60.884 54.545 0.00 0.00 34.77 3.18
648 650 1.076513 GCTTTTTCCTCCCCCTTGGTA 59.923 52.381 0.00 0.00 34.77 3.25
649 651 0.178932 GCTTTTTCCTCCCCCTTGGT 60.179 55.000 0.00 0.00 34.77 3.67
650 652 0.115152 AGCTTTTTCCTCCCCCTTGG 59.885 55.000 0.00 0.00 0.00 3.61
651 653 2.899303 TAGCTTTTTCCTCCCCCTTG 57.101 50.000 0.00 0.00 0.00 3.61
652 654 3.915346 TTTAGCTTTTTCCTCCCCCTT 57.085 42.857 0.00 0.00 0.00 3.95
653 655 3.598324 AGATTTAGCTTTTTCCTCCCCCT 59.402 43.478 0.00 0.00 0.00 4.79
654 656 3.982516 AGATTTAGCTTTTTCCTCCCCC 58.017 45.455 0.00 0.00 0.00 5.40
655 657 7.519057 AGTATAGATTTAGCTTTTTCCTCCCC 58.481 38.462 0.00 0.00 0.00 4.81
695 697 5.208624 TCAATCAAGAGCTTCGAATTTCG 57.791 39.130 12.54 12.54 42.10 3.46
696 698 7.858052 TTTTCAATCAAGAGCTTCGAATTTC 57.142 32.000 0.00 0.00 0.00 2.17
697 699 8.822652 AATTTTCAATCAAGAGCTTCGAATTT 57.177 26.923 0.00 0.00 0.00 1.82
698 700 9.912634 TTAATTTTCAATCAAGAGCTTCGAATT 57.087 25.926 0.00 0.00 0.00 2.17
699 701 9.912634 TTTAATTTTCAATCAAGAGCTTCGAAT 57.087 25.926 0.00 0.00 0.00 3.34
700 702 9.743057 TTTTAATTTTCAATCAAGAGCTTCGAA 57.257 25.926 0.00 0.00 0.00 3.71
701 703 9.743057 TTTTTAATTTTCAATCAAGAGCTTCGA 57.257 25.926 0.00 0.00 0.00 3.71
702 704 9.783425 GTTTTTAATTTTCAATCAAGAGCTTCG 57.217 29.630 0.00 0.00 0.00 3.79
705 707 9.598517 TGTGTTTTTAATTTTCAATCAAGAGCT 57.401 25.926 0.00 0.00 0.00 4.09
752 754 8.036575 GCAGCATAATTAGAGAGATCAGAGATT 58.963 37.037 0.00 0.00 0.00 2.40
753 755 7.364056 GGCAGCATAATTAGAGAGATCAGAGAT 60.364 40.741 0.00 0.00 0.00 2.75
754 756 6.071447 GGCAGCATAATTAGAGAGATCAGAGA 60.071 42.308 0.00 0.00 0.00 3.10
755 757 6.101332 GGCAGCATAATTAGAGAGATCAGAG 58.899 44.000 0.00 0.00 0.00 3.35
756 758 5.336293 CGGCAGCATAATTAGAGAGATCAGA 60.336 44.000 0.00 0.00 0.00 3.27
757 759 4.863689 CGGCAGCATAATTAGAGAGATCAG 59.136 45.833 0.00 0.00 0.00 2.90
758 760 4.281941 ACGGCAGCATAATTAGAGAGATCA 59.718 41.667 0.00 0.00 0.00 2.92
759 761 4.815269 ACGGCAGCATAATTAGAGAGATC 58.185 43.478 0.00 0.00 0.00 2.75
760 762 4.881019 ACGGCAGCATAATTAGAGAGAT 57.119 40.909 0.00 0.00 0.00 2.75
761 763 4.827835 ACTACGGCAGCATAATTAGAGAGA 59.172 41.667 0.00 0.00 0.00 3.10
762 764 5.127693 ACTACGGCAGCATAATTAGAGAG 57.872 43.478 0.00 0.00 0.00 3.20
763 765 5.289595 CAACTACGGCAGCATAATTAGAGA 58.710 41.667 0.00 0.00 0.00 3.10
764 766 4.084328 GCAACTACGGCAGCATAATTAGAG 60.084 45.833 0.00 0.00 0.00 2.43
765 767 3.807622 GCAACTACGGCAGCATAATTAGA 59.192 43.478 0.00 0.00 0.00 2.10
766 768 3.809832 AGCAACTACGGCAGCATAATTAG 59.190 43.478 0.00 0.00 0.00 1.73
767 769 3.804036 AGCAACTACGGCAGCATAATTA 58.196 40.909 0.00 0.00 0.00 1.40
768 770 2.643551 AGCAACTACGGCAGCATAATT 58.356 42.857 0.00 0.00 0.00 1.40
769 771 2.332063 AGCAACTACGGCAGCATAAT 57.668 45.000 0.00 0.00 0.00 1.28
770 772 2.006888 GAAGCAACTACGGCAGCATAA 58.993 47.619 0.00 0.00 0.00 1.90
771 773 1.651987 GAAGCAACTACGGCAGCATA 58.348 50.000 0.00 0.00 0.00 3.14
772 774 1.026718 GGAAGCAACTACGGCAGCAT 61.027 55.000 0.00 0.00 0.00 3.79
773 775 1.671054 GGAAGCAACTACGGCAGCA 60.671 57.895 0.00 0.00 0.00 4.41
774 776 1.376037 AGGAAGCAACTACGGCAGC 60.376 57.895 0.00 0.00 0.00 5.25
775 777 1.639298 GCAGGAAGCAACTACGGCAG 61.639 60.000 0.00 0.00 44.79 4.85
776 778 1.671054 GCAGGAAGCAACTACGGCA 60.671 57.895 0.00 0.00 44.79 5.69
777 779 3.178539 GCAGGAAGCAACTACGGC 58.821 61.111 0.00 0.00 44.79 5.68
786 788 0.679002 TCAATCTGGCAGCAGGAAGC 60.679 55.000 10.34 0.00 46.19 3.86
787 789 1.676529 CATCAATCTGGCAGCAGGAAG 59.323 52.381 10.34 0.00 0.00 3.46
788 790 1.005097 ACATCAATCTGGCAGCAGGAA 59.995 47.619 10.34 0.00 0.00 3.36
789 791 0.622136 ACATCAATCTGGCAGCAGGA 59.378 50.000 10.34 6.95 0.00 3.86
790 792 0.738975 CACATCAATCTGGCAGCAGG 59.261 55.000 10.34 0.98 0.00 4.85
791 793 1.746470 TCACATCAATCTGGCAGCAG 58.254 50.000 10.34 1.80 0.00 4.24
792 794 2.430248 ATCACATCAATCTGGCAGCA 57.570 45.000 10.34 0.00 0.00 4.41
793 795 4.498682 GGTTAATCACATCAATCTGGCAGC 60.499 45.833 10.34 0.00 0.00 5.25
794 796 4.641541 TGGTTAATCACATCAATCTGGCAG 59.358 41.667 8.58 8.58 0.00 4.85
795 797 4.398988 GTGGTTAATCACATCAATCTGGCA 59.601 41.667 14.10 0.00 37.57 4.92
796 798 4.641989 AGTGGTTAATCACATCAATCTGGC 59.358 41.667 20.65 0.00 39.93 4.85
797 799 6.558009 CAAGTGGTTAATCACATCAATCTGG 58.442 40.000 20.65 0.00 39.93 3.86
798 800 6.032094 GCAAGTGGTTAATCACATCAATCTG 58.968 40.000 20.65 7.13 39.93 2.90
799 801 5.948162 AGCAAGTGGTTAATCACATCAATCT 59.052 36.000 20.65 6.06 39.93 2.40
800 802 6.199937 AGCAAGTGGTTAATCACATCAATC 57.800 37.500 20.65 4.02 39.93 2.67
801 803 6.594788 AAGCAAGTGGTTAATCACATCAAT 57.405 33.333 20.65 1.54 39.93 2.57
802 804 6.488344 TGTAAGCAAGTGGTTAATCACATCAA 59.512 34.615 20.65 0.00 39.36 2.57
803 805 6.000840 TGTAAGCAAGTGGTTAATCACATCA 58.999 36.000 20.65 0.35 39.36 3.07
804 806 6.149474 ACTGTAAGCAAGTGGTTAATCACATC 59.851 38.462 20.65 8.90 39.36 3.06
805 807 6.003950 ACTGTAAGCAAGTGGTTAATCACAT 58.996 36.000 20.65 6.18 39.36 3.21
806 808 5.373222 ACTGTAAGCAAGTGGTTAATCACA 58.627 37.500 20.65 0.00 39.36 3.58
807 809 5.468746 TGACTGTAAGCAAGTGGTTAATCAC 59.531 40.000 11.06 11.06 39.36 3.06
808 810 5.616270 TGACTGTAAGCAAGTGGTTAATCA 58.384 37.500 4.61 6.74 39.36 2.57
809 811 5.932303 TCTGACTGTAAGCAAGTGGTTAATC 59.068 40.000 4.61 4.61 39.36 1.75
810 812 5.701290 GTCTGACTGTAAGCAAGTGGTTAAT 59.299 40.000 4.61 0.00 39.36 1.40
811 813 5.054477 GTCTGACTGTAAGCAAGTGGTTAA 58.946 41.667 4.61 0.00 39.36 2.01
812 814 4.502604 GGTCTGACTGTAAGCAAGTGGTTA 60.503 45.833 7.85 0.00 37.60 2.85
813 815 3.467803 GTCTGACTGTAAGCAAGTGGTT 58.532 45.455 0.00 0.91 37.60 3.67
814 816 2.224305 GGTCTGACTGTAAGCAAGTGGT 60.224 50.000 7.85 0.00 37.60 4.16
815 817 2.417719 GGTCTGACTGTAAGCAAGTGG 58.582 52.381 7.85 0.00 37.60 4.00
816 818 2.224281 TGGGTCTGACTGTAAGCAAGTG 60.224 50.000 7.85 0.00 37.60 3.16
817 819 2.047061 TGGGTCTGACTGTAAGCAAGT 58.953 47.619 7.85 0.00 37.60 3.16
818 820 2.839486 TGGGTCTGACTGTAAGCAAG 57.161 50.000 7.85 0.00 37.60 4.01
819 821 3.411446 CATTGGGTCTGACTGTAAGCAA 58.589 45.455 7.85 0.00 37.60 3.91
820 822 2.290260 CCATTGGGTCTGACTGTAAGCA 60.290 50.000 7.85 0.00 37.60 3.91
821 823 2.027192 TCCATTGGGTCTGACTGTAAGC 60.027 50.000 7.85 0.00 33.72 3.09
822 824 3.981071 TCCATTGGGTCTGACTGTAAG 57.019 47.619 7.85 0.00 35.95 2.34
823 825 4.408921 CCTATCCATTGGGTCTGACTGTAA 59.591 45.833 7.85 1.56 34.93 2.41
824 826 3.967326 CCTATCCATTGGGTCTGACTGTA 59.033 47.826 7.85 0.00 34.93 2.74
825 827 2.774234 CCTATCCATTGGGTCTGACTGT 59.226 50.000 7.85 0.00 34.93 3.55
826 828 3.041211 TCCTATCCATTGGGTCTGACTG 58.959 50.000 7.85 0.00 34.93 3.51
827 829 3.421394 TCCTATCCATTGGGTCTGACT 57.579 47.619 7.85 0.00 34.93 3.41
828 830 4.713792 ATTCCTATCCATTGGGTCTGAC 57.286 45.455 2.09 0.00 34.93 3.51
829 831 4.689705 GCAATTCCTATCCATTGGGTCTGA 60.690 45.833 2.09 0.00 31.97 3.27
830 832 3.571401 GCAATTCCTATCCATTGGGTCTG 59.429 47.826 2.09 0.00 31.97 3.51
831 833 3.205056 TGCAATTCCTATCCATTGGGTCT 59.795 43.478 2.09 0.00 31.97 3.85
832 834 3.565307 TGCAATTCCTATCCATTGGGTC 58.435 45.455 2.09 0.00 31.97 4.46
833 835 3.686227 TGCAATTCCTATCCATTGGGT 57.314 42.857 2.09 0.00 31.97 4.51
834 836 4.154176 TCATGCAATTCCTATCCATTGGG 58.846 43.478 2.09 0.00 31.97 4.12
835 837 4.321750 GCTCATGCAATTCCTATCCATTGG 60.322 45.833 0.00 0.00 39.41 3.16
836 838 4.806330 GCTCATGCAATTCCTATCCATTG 58.194 43.478 0.00 0.00 39.41 2.82
852 854 5.975344 CACAATTTAACTAGGCATGCTCATG 59.025 40.000 18.92 8.19 41.60 3.07
853 855 5.887598 TCACAATTTAACTAGGCATGCTCAT 59.112 36.000 18.92 6.74 0.00 2.90
854 856 5.252547 TCACAATTTAACTAGGCATGCTCA 58.747 37.500 18.92 4.56 0.00 4.26
855 857 5.818136 TCACAATTTAACTAGGCATGCTC 57.182 39.130 18.92 7.89 0.00 4.26
905 939 0.179000 AACCAGGGCATCACTCGATC 59.821 55.000 0.00 0.00 0.00 3.69
909 943 4.326255 CCAACCAGGGCATCACTC 57.674 61.111 0.00 0.00 0.00 3.51
1007 1041 4.214327 GCGGCGAGGAAGAGGAGG 62.214 72.222 12.98 0.00 0.00 4.30
1159 1198 2.089201 CCGAAATAAAGGGGAAGCGTT 58.911 47.619 0.00 0.00 0.00 4.84
1325 1364 4.093850 TGCATCAGAACATGATTTCACTCG 59.906 41.667 0.00 0.00 46.97 4.18
1389 1428 6.441924 ACATGAGGACTAATCTCAGAAGGAAA 59.558 38.462 0.00 0.00 43.45 3.13
1441 1480 4.456280 TTCATACAGCAACAGAGATCGT 57.544 40.909 0.00 0.00 0.00 3.73
1442 1481 5.521372 TCATTTCATACAGCAACAGAGATCG 59.479 40.000 0.00 0.00 0.00 3.69
1443 1482 6.314648 TGTCATTTCATACAGCAACAGAGATC 59.685 38.462 0.00 0.00 0.00 2.75
1446 1485 5.868043 TGTCATTTCATACAGCAACAGAG 57.132 39.130 0.00 0.00 0.00 3.35
1448 1487 7.878477 AAAATGTCATTTCATACAGCAACAG 57.122 32.000 11.19 0.00 0.00 3.16
1525 1583 5.672503 ACATCTGGACAATCTCATTCTCTG 58.327 41.667 0.00 0.00 0.00 3.35
1526 1584 5.954153 ACATCTGGACAATCTCATTCTCT 57.046 39.130 0.00 0.00 0.00 3.10
1554 1612 1.374758 CACTCTGACGAACCTGGGC 60.375 63.158 0.00 0.00 0.00 5.36
1558 1616 1.540267 CTCCTCACTCTGACGAACCT 58.460 55.000 0.00 0.00 0.00 3.50
1617 1675 3.717576 TGAACCTCTCATCCATGACTCT 58.282 45.455 0.00 0.00 32.50 3.24
1739 1797 0.955428 CACTGACCCCAACATCGGTG 60.955 60.000 0.00 0.00 43.75 4.94
1838 1896 7.255312 CCATACTGCTCTACTACCTCTAAACAG 60.255 44.444 0.00 0.00 0.00 3.16
1955 2013 4.340381 GCCTTACTGATCATCTTGGCATTT 59.660 41.667 18.76 0.00 38.99 2.32
2498 2556 6.318144 CCTCAAACAACTTCATAGCATCATCT 59.682 38.462 0.00 0.00 0.00 2.90
2693 2751 0.673437 CCGTCCTGTTGGTTTTGCAT 59.327 50.000 0.00 0.00 34.23 3.96
3203 3261 1.239347 GACTCAAGGCACCAAGAACC 58.761 55.000 0.00 0.00 0.00 3.62
3394 3452 5.899299 AGCTTGGATCAAGATGTTTTATGC 58.101 37.500 11.35 0.00 43.42 3.14
3486 3544 3.509575 AGTTCACTTGAGTGGCACAAAAA 59.490 39.130 21.41 9.71 44.16 1.94
3543 3601 6.050432 TGAAATACACACCTTCTACGTTTGT 58.950 36.000 0.00 0.00 0.00 2.83
3579 3720 4.325972 ACGGAACATAACGGTATTTTGGT 58.674 39.130 0.00 0.00 0.00 3.67
3668 3809 1.033574 CCCTCGAATCTTAGCGGAGT 58.966 55.000 0.00 0.00 0.00 3.85
3673 3814 2.317530 AACAGCCCTCGAATCTTAGC 57.682 50.000 0.00 0.00 0.00 3.09
3674 3815 3.868077 CAGAAACAGCCCTCGAATCTTAG 59.132 47.826 0.00 0.00 0.00 2.18
3681 3822 2.158813 ACTTTTCAGAAACAGCCCTCGA 60.159 45.455 0.00 0.00 0.00 4.04
3693 3834 5.772825 CCAAATGGTCTCAACTTTTCAGA 57.227 39.130 0.00 0.00 0.00 3.27
3771 3913 0.316442 CAGGAATTGTAGCATGCGCG 60.316 55.000 13.01 0.00 45.49 6.86
3908 4050 2.540101 CGGAAAGCTACGCATAAAGAGG 59.460 50.000 0.00 0.00 0.00 3.69
3913 4055 3.241067 AGTTCGGAAAGCTACGCATAA 57.759 42.857 0.00 0.00 0.00 1.90
4004 4146 2.159310 GCTGCCAAACTACAACACACAA 60.159 45.455 0.00 0.00 0.00 3.33
4050 4192 3.007398 GTGTCAGAATCCACAGAGTTCCT 59.993 47.826 0.00 0.00 0.00 3.36
4077 4219 5.488262 AATTTGGAAGCCTGCAAGTATTT 57.512 34.783 0.00 0.00 34.03 1.40
4205 4348 2.237643 TGCATTGCTGGTTCTTTGCTA 58.762 42.857 10.49 0.00 0.00 3.49
4217 4360 6.108015 CCTACCATGTTTTTATTGCATTGCT 58.892 36.000 10.49 0.00 0.00 3.91
4290 4436 1.333619 ACGCCAAAGACACATTCACAC 59.666 47.619 0.00 0.00 0.00 3.82
4291 4437 1.601903 GACGCCAAAGACACATTCACA 59.398 47.619 0.00 0.00 0.00 3.58
4339 4485 4.093850 ACCATTTCTTACAAACGCCGTATC 59.906 41.667 0.00 0.00 0.00 2.24
4340 4486 4.004982 ACCATTTCTTACAAACGCCGTAT 58.995 39.130 0.00 0.00 0.00 3.06
4343 4489 2.031508 ACACCATTTCTTACAAACGCCG 60.032 45.455 0.00 0.00 0.00 6.46
4379 4525 1.141657 AGCTGAGAGCAAAGACCACAA 59.858 47.619 0.00 0.00 45.56 3.33


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

AutoCloner maintained by Alex Coulton.