Multiple sequence alignment - TraesCS3B01G360700

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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 TraesCS3B01G360700 chr3B 100.000 3844 0 0 394 4237 572671256 572667413 0.000000e+00 7099.0
1 TraesCS3B01G360700 chr3B 100.000 70 0 0 1 70 572671649 572671580 3.440000e-26 130.0
2 TraesCS3B01G360700 chr3B 83.495 103 16 1 459 561 40239400 40239299 1.250000e-15 95.3
3 TraesCS3B01G360700 chr3A 93.693 3393 148 26 886 4237 575411497 575408130 0.000000e+00 5020.0
4 TraesCS3B01G360700 chr3D 92.427 1294 78 8 2958 4237 437356391 437355104 0.000000e+00 1829.0
5 TraesCS3B01G360700 chr3D 92.254 994 49 17 886 1876 437358692 437357724 0.000000e+00 1384.0
6 TraesCS3B01G360700 chr3D 85.747 877 94 20 1862 2718 437357642 437356777 0.000000e+00 898.0
7 TraesCS3B01G360700 chr3D 100.000 29 0 0 1034 1062 264521596 264521624 2.000000e-03 54.7
8 TraesCS3B01G360700 chr3D 100.000 29 0 0 1034 1062 264528824 264528852 2.000000e-03 54.7
9 TraesCS3B01G360700 chr5A 88.442 199 19 4 2314 2510 34717294 34717490 1.970000e-58 237.0
10 TraesCS3B01G360700 chr5A 86.458 96 12 1 467 561 344534569 344534474 2.080000e-18 104.0
11 TraesCS3B01G360700 chr5A 97.619 42 1 0 2467 2508 34717558 34717599 5.880000e-09 73.1
12 TraesCS3B01G360700 chr4B 87.356 87 11 0 480 566 366930220 366930306 2.700000e-17 100.0
13 TraesCS3B01G360700 chr4B 89.231 65 5 1 1 65 626057718 626057656 3.510000e-11 80.5
14 TraesCS3B01G360700 chr2B 88.889 81 9 0 480 560 209085265 209085345 2.700000e-17 100.0
15 TraesCS3B01G360700 chr2B 84.694 98 13 2 467 563 175630218 175630314 3.490000e-16 97.1
16 TraesCS3B01G360700 chr2B 84.211 95 13 1 467 561 306886152 306886060 1.620000e-14 91.6
17 TraesCS3B01G360700 chr2B 89.231 65 6 1 1 65 104072162 104072225 3.510000e-11 80.5
18 TraesCS3B01G360700 chr5B 84.848 99 13 2 467 565 405715992 405716088 9.700000e-17 99.0
19 TraesCS3B01G360700 chr2D 85.000 100 12 3 467 563 122864170 122864269 9.700000e-17 99.0
20 TraesCS3B01G360700 chr2D 89.231 65 6 1 1 65 557141633 557141570 3.510000e-11 80.5
21 TraesCS3B01G360700 chr1D 84.375 96 13 2 467 561 137418356 137418450 4.510000e-15 93.5
22 TraesCS3B01G360700 chr1D 89.231 65 5 1 1 65 448650882 448650944 3.510000e-11 80.5
23 TraesCS3B01G360700 chr7D 90.000 70 6 1 1 70 497975113 497975181 5.840000e-14 89.8
24 TraesCS3B01G360700 chr7D 88.571 70 6 1 1 70 425725664 425725597 2.710000e-12 84.2
25 TraesCS3B01G360700 chr6B 89.231 65 5 2 1 65 719230901 719230963 3.510000e-11 80.5
26 TraesCS3B01G360700 chr1B 89.231 65 5 1 1 65 176289651 176289589 3.510000e-11 80.5
27 TraesCS3B01G360700 chr5D 87.143 70 7 2 1 70 481732840 481732907 1.260000e-10 78.7
28 TraesCS3B01G360700 chr5D 96.970 33 1 0 564 596 356332496 356332528 5.920000e-04 56.5
29 TraesCS3B01G360700 chr4A 96.970 33 1 0 564 596 609945271 609945303 5.920000e-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 TraesCS3B01G360700 chr3B 572667413 572671649 4236 True 3614.500000 7099 100.000000 1 4237 2 chr3B.!!$R2 4236
1 TraesCS3B01G360700 chr3A 575408130 575411497 3367 True 5020.000000 5020 93.693000 886 4237 1 chr3A.!!$R1 3351
2 TraesCS3B01G360700 chr3D 437355104 437358692 3588 True 1370.333333 1829 90.142667 886 4237 3 chr3D.!!$R1 3351

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
777 778 0.234884 AAGTAAAACACGAGCGCTGC 59.765 50.000 18.48 5.6 0.00 5.25 F
862 863 0.239879 GACGCATTCCGAGCCAAAAA 59.760 50.000 0.00 0.0 41.02 1.94 F
904 905 0.323629 TTAGACGGGCCTGGAAACTG 59.676 55.000 18.00 0.0 0.00 3.16 F
947 949 1.422161 CCCACCCCATCTCCTCCATC 61.422 65.000 0.00 0.0 0.00 3.51 F
1312 1314 2.283388 AAGGGAGGGCGTACGTCA 60.283 61.111 22.92 0.0 35.71 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1884 1.961394 CCTAGGATTGCCGTGCTACTA 59.039 52.381 1.05 0.00 39.96 1.82 R
1912 2015 2.289072 ACACCCAGTTCAGTCTCAATCG 60.289 50.000 0.00 0.00 0.00 3.34 R
2745 2869 2.897326 TCTGCTGCAGGAGTTTGTACTA 59.103 45.455 31.17 9.83 33.84 1.82 R
2909 3147 1.344763 AGAACTTGACAGGAACGGAGG 59.655 52.381 0.00 0.00 0.00 4.30 R
3237 3523 2.911926 GCAGAGGGGCCTTTCCTGT 61.912 63.158 0.84 0.00 34.21 4.00 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
422 423 9.639563 TTGTGGGTGATATATATGTTTTGATGT 57.360 29.630 0.00 0.00 0.00 3.06
423 424 9.639563 TGTGGGTGATATATATGTTTTGATGTT 57.360 29.630 0.00 0.00 0.00 2.71
433 434 7.881775 ATATGTTTTGATGTTTACTCCCTCC 57.118 36.000 0.00 0.00 0.00 4.30
434 435 4.069304 TGTTTTGATGTTTACTCCCTCCG 58.931 43.478 0.00 0.00 0.00 4.63
435 436 4.070009 GTTTTGATGTTTACTCCCTCCGT 58.930 43.478 0.00 0.00 0.00 4.69
436 437 4.360951 TTTGATGTTTACTCCCTCCGTT 57.639 40.909 0.00 0.00 0.00 4.44
437 438 3.604875 TGATGTTTACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
438 439 2.901192 TGATGTTTACTCCCTCCGTTCA 59.099 45.455 0.00 0.00 0.00 3.18
439 440 2.825861 TGTTTACTCCCTCCGTTCAC 57.174 50.000 0.00 0.00 0.00 3.18
440 441 2.040939 TGTTTACTCCCTCCGTTCACA 58.959 47.619 0.00 0.00 0.00 3.58
441 442 2.435069 TGTTTACTCCCTCCGTTCACAA 59.565 45.455 0.00 0.00 0.00 3.33
442 443 3.071892 TGTTTACTCCCTCCGTTCACAAT 59.928 43.478 0.00 0.00 0.00 2.71
443 444 4.070009 GTTTACTCCCTCCGTTCACAATT 58.930 43.478 0.00 0.00 0.00 2.32
444 445 5.221682 TGTTTACTCCCTCCGTTCACAATTA 60.222 40.000 0.00 0.00 0.00 1.40
445 446 5.687166 TTACTCCCTCCGTTCACAATTAT 57.313 39.130 0.00 0.00 0.00 1.28
446 447 6.795144 TTACTCCCTCCGTTCACAATTATA 57.205 37.500 0.00 0.00 0.00 0.98
447 448 5.687166 ACTCCCTCCGTTCACAATTATAA 57.313 39.130 0.00 0.00 0.00 0.98
448 449 5.671493 ACTCCCTCCGTTCACAATTATAAG 58.329 41.667 0.00 0.00 0.00 1.73
449 450 5.189145 ACTCCCTCCGTTCACAATTATAAGT 59.811 40.000 0.00 0.00 0.00 2.24
450 451 6.057321 TCCCTCCGTTCACAATTATAAGTT 57.943 37.500 0.00 0.00 0.00 2.66
451 452 6.478129 TCCCTCCGTTCACAATTATAAGTTT 58.522 36.000 0.00 0.00 0.00 2.66
452 453 6.943718 TCCCTCCGTTCACAATTATAAGTTTT 59.056 34.615 0.00 0.00 0.00 2.43
453 454 7.449086 TCCCTCCGTTCACAATTATAAGTTTTT 59.551 33.333 0.00 0.00 0.00 1.94
520 521 8.127150 TGTGTCTATATACATCTGATTCAGGG 57.873 38.462 13.59 8.88 31.51 4.45
521 522 7.950124 TGTGTCTATATACATCTGATTCAGGGA 59.050 37.037 13.59 0.00 31.51 4.20
522 523 8.807118 GTGTCTATATACATCTGATTCAGGGAA 58.193 37.037 13.59 0.00 31.51 3.97
523 524 9.379770 TGTCTATATACATCTGATTCAGGGAAA 57.620 33.333 13.59 0.00 31.51 3.13
530 531 9.753674 ATACATCTGATTCAGGGAAAAGTTAAA 57.246 29.630 13.59 0.00 31.51 1.52
531 532 8.477419 ACATCTGATTCAGGGAAAAGTTAAAA 57.523 30.769 13.59 0.00 31.51 1.52
532 533 8.360390 ACATCTGATTCAGGGAAAAGTTAAAAC 58.640 33.333 13.59 0.00 31.51 2.43
533 534 7.889873 TCTGATTCAGGGAAAAGTTAAAACA 57.110 32.000 13.59 0.00 31.51 2.83
534 535 8.477419 TCTGATTCAGGGAAAAGTTAAAACAT 57.523 30.769 13.59 0.00 31.51 2.71
535 536 8.576442 TCTGATTCAGGGAAAAGTTAAAACATC 58.424 33.333 13.59 0.00 31.51 3.06
536 537 8.477419 TGATTCAGGGAAAAGTTAAAACATCT 57.523 30.769 0.00 0.00 0.00 2.90
537 538 8.923270 TGATTCAGGGAAAAGTTAAAACATCTT 58.077 29.630 0.00 0.00 0.00 2.40
564 565 7.741554 AATAGTGAATGAAGGGAGTACTCTT 57.258 36.000 21.88 9.83 39.83 2.85
565 566 7.741554 ATAGTGAATGAAGGGAGTACTCTTT 57.258 36.000 21.88 16.03 36.91 2.52
566 567 6.441088 AGTGAATGAAGGGAGTACTCTTTT 57.559 37.500 21.88 15.70 36.91 2.27
567 568 6.468543 AGTGAATGAAGGGAGTACTCTTTTC 58.531 40.000 21.88 22.11 36.91 2.29
568 569 6.043243 AGTGAATGAAGGGAGTACTCTTTTCA 59.957 38.462 28.32 28.32 36.91 2.69
569 570 6.881602 GTGAATGAAGGGAGTACTCTTTTCAT 59.118 38.462 29.40 29.40 40.58 2.57
570 571 8.041323 GTGAATGAAGGGAGTACTCTTTTCATA 58.959 37.037 32.00 23.46 39.36 2.15
571 572 8.041323 TGAATGAAGGGAGTACTCTTTTCATAC 58.959 37.037 32.00 18.42 39.36 2.39
572 573 6.928348 TGAAGGGAGTACTCTTTTCATACA 57.072 37.500 25.30 12.82 36.91 2.29
573 574 7.496346 TGAAGGGAGTACTCTTTTCATACAT 57.504 36.000 25.30 5.90 36.91 2.29
574 575 7.331026 TGAAGGGAGTACTCTTTTCATACATG 58.669 38.462 25.30 0.00 36.91 3.21
575 576 6.875972 AGGGAGTACTCTTTTCATACATGT 57.124 37.500 21.88 2.69 0.00 3.21
576 577 7.259088 AGGGAGTACTCTTTTCATACATGTT 57.741 36.000 21.88 0.00 0.00 2.71
577 578 7.106239 AGGGAGTACTCTTTTCATACATGTTG 58.894 38.462 21.88 2.55 0.00 3.33
578 579 6.879458 GGGAGTACTCTTTTCATACATGTTGT 59.121 38.462 21.88 0.00 0.00 3.32
579 580 8.038944 GGGAGTACTCTTTTCATACATGTTGTA 58.961 37.037 21.88 0.00 37.24 2.41
580 581 8.870879 GGAGTACTCTTTTCATACATGTTGTAC 58.129 37.037 21.88 4.61 35.42 2.90
581 582 9.419297 GAGTACTCTTTTCATACATGTTGTACA 57.581 33.333 15.91 0.00 35.42 2.90
582 583 9.944376 AGTACTCTTTTCATACATGTTGTACAT 57.056 29.630 2.30 0.00 39.91 2.29
589 590 9.737427 TTTTCATACATGTTGTACATTTTTCGT 57.263 25.926 2.30 0.00 36.53 3.85
596 597 9.982291 ACATGTTGTACATTTTTCGTATACATC 57.018 29.630 3.32 0.00 36.53 3.06
597 598 9.980780 CATGTTGTACATTTTTCGTATACATCA 57.019 29.630 3.32 0.00 36.53 3.07
599 600 9.425577 TGTTGTACATTTTTCGTATACATCAGA 57.574 29.630 3.32 0.00 0.00 3.27
617 618 8.094798 ACATCAGATACAATTTTTACACACGT 57.905 30.769 0.00 0.00 0.00 4.49
618 619 8.564574 ACATCAGATACAATTTTTACACACGTT 58.435 29.630 0.00 0.00 0.00 3.99
619 620 9.393249 CATCAGATACAATTTTTACACACGTTT 57.607 29.630 0.00 0.00 0.00 3.60
620 621 8.996988 TCAGATACAATTTTTACACACGTTTC 57.003 30.769 0.00 0.00 0.00 2.78
621 622 8.613482 TCAGATACAATTTTTACACACGTTTCA 58.387 29.630 0.00 0.00 0.00 2.69
622 623 8.678510 CAGATACAATTTTTACACACGTTTCAC 58.321 33.333 0.00 0.00 0.00 3.18
623 624 8.399425 AGATACAATTTTTACACACGTTTCACA 58.601 29.630 0.00 0.00 0.00 3.58
624 625 9.176181 GATACAATTTTTACACACGTTTCACAT 57.824 29.630 0.00 0.00 0.00 3.21
625 626 7.820044 ACAATTTTTACACACGTTTCACATT 57.180 28.000 0.00 0.00 0.00 2.71
626 627 8.245701 ACAATTTTTACACACGTTTCACATTT 57.754 26.923 0.00 0.00 0.00 2.32
627 628 8.713271 ACAATTTTTACACACGTTTCACATTTT 58.287 25.926 0.00 0.00 0.00 1.82
628 629 9.535270 CAATTTTTACACACGTTTCACATTTTT 57.465 25.926 0.00 0.00 0.00 1.94
629 630 9.748100 AATTTTTACACACGTTTCACATTTTTC 57.252 25.926 0.00 0.00 0.00 2.29
630 631 7.869016 TTTTACACACGTTTCACATTTTTCA 57.131 28.000 0.00 0.00 0.00 2.69
631 632 7.869016 TTTACACACGTTTCACATTTTTCAA 57.131 28.000 0.00 0.00 0.00 2.69
632 633 7.869016 TTACACACGTTTCACATTTTTCAAA 57.131 28.000 0.00 0.00 0.00 2.69
633 634 6.959671 ACACACGTTTCACATTTTTCAAAT 57.040 29.167 0.00 0.00 0.00 2.32
634 635 7.357951 ACACACGTTTCACATTTTTCAAATT 57.642 28.000 0.00 0.00 0.00 1.82
635 636 7.452231 ACACACGTTTCACATTTTTCAAATTC 58.548 30.769 0.00 0.00 0.00 2.17
636 637 7.116948 ACACACGTTTCACATTTTTCAAATTCA 59.883 29.630 0.00 0.00 0.00 2.57
637 638 8.115520 CACACGTTTCACATTTTTCAAATTCAT 58.884 29.630 0.00 0.00 0.00 2.57
638 639 9.307121 ACACGTTTCACATTTTTCAAATTCATA 57.693 25.926 0.00 0.00 0.00 2.15
729 730 7.404671 AAACAAAGGTAAAGAAGAAGAAGCA 57.595 32.000 0.00 0.00 0.00 3.91
730 731 7.404671 AACAAAGGTAAAGAAGAAGAAGCAA 57.595 32.000 0.00 0.00 0.00 3.91
731 732 7.404671 ACAAAGGTAAAGAAGAAGAAGCAAA 57.595 32.000 0.00 0.00 0.00 3.68
732 733 7.836842 ACAAAGGTAAAGAAGAAGAAGCAAAA 58.163 30.769 0.00 0.00 0.00 2.44
733 734 8.311109 ACAAAGGTAAAGAAGAAGAAGCAAAAA 58.689 29.630 0.00 0.00 0.00 1.94
734 735 8.595533 CAAAGGTAAAGAAGAAGAAGCAAAAAC 58.404 33.333 0.00 0.00 0.00 2.43
735 736 6.806751 AGGTAAAGAAGAAGAAGCAAAAACC 58.193 36.000 0.00 0.00 0.00 3.27
736 737 5.685954 GGTAAAGAAGAAGAAGCAAAAACCG 59.314 40.000 0.00 0.00 0.00 4.44
737 738 5.576447 AAAGAAGAAGAAGCAAAAACCGA 57.424 34.783 0.00 0.00 0.00 4.69
738 739 5.576447 AAGAAGAAGAAGCAAAAACCGAA 57.424 34.783 0.00 0.00 0.00 4.30
739 740 5.576447 AGAAGAAGAAGCAAAAACCGAAA 57.424 34.783 0.00 0.00 0.00 3.46
740 741 5.961272 AGAAGAAGAAGCAAAAACCGAAAA 58.039 33.333 0.00 0.00 0.00 2.29
741 742 5.805486 AGAAGAAGAAGCAAAAACCGAAAAC 59.195 36.000 0.00 0.00 0.00 2.43
742 743 4.102649 AGAAGAAGCAAAAACCGAAAACG 58.897 39.130 0.00 0.00 0.00 3.60
743 744 3.768468 AGAAGCAAAAACCGAAAACGA 57.232 38.095 0.00 0.00 0.00 3.85
744 745 4.099380 AGAAGCAAAAACCGAAAACGAA 57.901 36.364 0.00 0.00 0.00 3.85
745 746 4.487019 AGAAGCAAAAACCGAAAACGAAA 58.513 34.783 0.00 0.00 0.00 3.46
746 747 5.106442 AGAAGCAAAAACCGAAAACGAAAT 58.894 33.333 0.00 0.00 0.00 2.17
747 748 4.770351 AGCAAAAACCGAAAACGAAATG 57.230 36.364 0.00 0.00 0.00 2.32
748 749 3.000825 AGCAAAAACCGAAAACGAAATGC 59.999 39.130 0.00 0.00 0.00 3.56
749 750 3.843153 GCAAAAACCGAAAACGAAATGCC 60.843 43.478 0.00 0.00 0.00 4.40
750 751 2.873133 AAACCGAAAACGAAATGCCA 57.127 40.000 0.00 0.00 0.00 4.92
751 752 2.873133 AACCGAAAACGAAATGCCAA 57.127 40.000 0.00 0.00 0.00 4.52
752 753 2.873133 ACCGAAAACGAAATGCCAAA 57.127 40.000 0.00 0.00 0.00 3.28
753 754 3.166489 ACCGAAAACGAAATGCCAAAA 57.834 38.095 0.00 0.00 0.00 2.44
754 755 3.522553 ACCGAAAACGAAATGCCAAAAA 58.477 36.364 0.00 0.00 0.00 1.94
773 774 3.872560 AAAGGAAGTAAAACACGAGCG 57.127 42.857 0.00 0.00 0.00 5.03
774 775 1.145803 AGGAAGTAAAACACGAGCGC 58.854 50.000 0.00 0.00 0.00 5.92
775 776 1.145803 GGAAGTAAAACACGAGCGCT 58.854 50.000 11.27 11.27 0.00 5.92
776 777 1.136336 GGAAGTAAAACACGAGCGCTG 60.136 52.381 18.48 10.31 0.00 5.18
777 778 0.234884 AAGTAAAACACGAGCGCTGC 59.765 50.000 18.48 5.60 0.00 5.25
778 779 0.600255 AGTAAAACACGAGCGCTGCT 60.600 50.000 18.48 0.00 43.88 4.24
801 802 4.740822 GCACTGGGCCCGTCCATT 62.741 66.667 19.37 0.00 36.05 3.16
802 803 2.035626 CACTGGGCCCGTCCATTT 59.964 61.111 19.37 0.00 36.05 2.32
803 804 2.035626 ACTGGGCCCGTCCATTTG 59.964 61.111 19.37 1.87 36.05 2.32
804 805 2.035626 CTGGGCCCGTCCATTTGT 59.964 61.111 19.37 0.00 36.05 2.83
805 806 1.606313 CTGGGCCCGTCCATTTGTT 60.606 57.895 19.37 0.00 36.05 2.83
806 807 1.876497 CTGGGCCCGTCCATTTGTTG 61.876 60.000 19.37 0.00 36.05 3.33
807 808 2.261361 GGCCCGTCCATTTGTTGC 59.739 61.111 0.00 0.00 34.01 4.17
808 809 2.569354 GGCCCGTCCATTTGTTGCA 61.569 57.895 0.00 0.00 34.01 4.08
809 810 1.080569 GCCCGTCCATTTGTTGCAG 60.081 57.895 0.00 0.00 0.00 4.41
810 811 1.080569 CCCGTCCATTTGTTGCAGC 60.081 57.895 0.00 0.00 0.00 5.25
811 812 1.080569 CCGTCCATTTGTTGCAGCC 60.081 57.895 0.00 0.00 0.00 4.85
812 813 1.442520 CGTCCATTTGTTGCAGCCG 60.443 57.895 0.00 0.00 0.00 5.52
813 814 1.734117 GTCCATTTGTTGCAGCCGC 60.734 57.895 0.00 0.00 39.24 6.53
814 815 2.806198 CCATTTGTTGCAGCCGCG 60.806 61.111 0.00 0.00 42.97 6.46
815 816 3.472298 CATTTGTTGCAGCCGCGC 61.472 61.111 0.00 0.00 42.97 6.86
816 817 3.976000 ATTTGTTGCAGCCGCGCA 61.976 55.556 8.75 5.90 42.97 6.09
817 818 4.921847 TTTGTTGCAGCCGCGCAC 62.922 61.111 8.75 0.00 42.87 5.34
827 828 2.421314 CCGCGCACTGGATGGATA 59.579 61.111 8.75 0.00 0.00 2.59
828 829 1.004560 CCGCGCACTGGATGGATAT 60.005 57.895 8.75 0.00 0.00 1.63
829 830 0.246360 CCGCGCACTGGATGGATATA 59.754 55.000 8.75 0.00 0.00 0.86
830 831 1.633561 CGCGCACTGGATGGATATAG 58.366 55.000 8.75 0.00 0.00 1.31
831 832 1.363744 GCGCACTGGATGGATATAGC 58.636 55.000 0.30 0.00 0.00 2.97
832 833 1.633561 CGCACTGGATGGATATAGCG 58.366 55.000 0.00 0.00 37.91 4.26
833 834 1.363744 GCACTGGATGGATATAGCGC 58.636 55.000 0.00 0.00 0.00 5.92
834 835 1.066573 GCACTGGATGGATATAGCGCT 60.067 52.381 17.26 17.26 0.00 5.92
835 836 2.614779 CACTGGATGGATATAGCGCTG 58.385 52.381 22.90 0.00 0.00 5.18
836 837 1.066573 ACTGGATGGATATAGCGCTGC 60.067 52.381 22.90 6.51 0.00 5.25
837 838 0.250234 TGGATGGATATAGCGCTGCC 59.750 55.000 22.90 16.17 0.00 4.85
838 839 0.462759 GGATGGATATAGCGCTGCCC 60.463 60.000 22.90 15.49 0.00 5.36
839 840 0.807667 GATGGATATAGCGCTGCCCG 60.808 60.000 22.90 0.00 40.75 6.13
850 851 3.434319 CTGCCCGCTTGACGCATT 61.434 61.111 0.00 0.00 41.76 3.56
851 852 3.386867 CTGCCCGCTTGACGCATTC 62.387 63.158 0.00 0.00 41.76 2.67
852 853 4.179579 GCCCGCTTGACGCATTCC 62.180 66.667 0.00 0.00 41.76 3.01
853 854 3.864686 CCCGCTTGACGCATTCCG 61.865 66.667 0.00 0.00 41.76 4.30
854 855 2.813474 CCGCTTGACGCATTCCGA 60.813 61.111 0.00 0.00 41.76 4.55
855 856 2.697425 CGCTTGACGCATTCCGAG 59.303 61.111 0.00 0.00 41.02 4.63
856 857 2.401195 GCTTGACGCATTCCGAGC 59.599 61.111 0.00 0.00 41.02 5.03
857 858 3.093278 CTTGACGCATTCCGAGCC 58.907 61.111 0.00 0.00 41.02 4.70
858 859 1.741401 CTTGACGCATTCCGAGCCA 60.741 57.895 0.00 0.00 41.02 4.75
859 860 1.298157 CTTGACGCATTCCGAGCCAA 61.298 55.000 0.00 0.00 41.02 4.52
860 861 0.886938 TTGACGCATTCCGAGCCAAA 60.887 50.000 0.00 0.00 41.02 3.28
861 862 0.886938 TGACGCATTCCGAGCCAAAA 60.887 50.000 0.00 0.00 41.02 2.44
862 863 0.239879 GACGCATTCCGAGCCAAAAA 59.760 50.000 0.00 0.00 41.02 1.94
863 864 0.887933 ACGCATTCCGAGCCAAAAAT 59.112 45.000 0.00 0.00 41.02 1.82
864 865 2.088423 ACGCATTCCGAGCCAAAAATA 58.912 42.857 0.00 0.00 41.02 1.40
865 866 2.490115 ACGCATTCCGAGCCAAAAATAA 59.510 40.909 0.00 0.00 41.02 1.40
866 867 3.057174 ACGCATTCCGAGCCAAAAATAAA 60.057 39.130 0.00 0.00 41.02 1.40
867 868 3.923461 CGCATTCCGAGCCAAAAATAAAA 59.077 39.130 0.00 0.00 40.02 1.52
868 869 4.387256 CGCATTCCGAGCCAAAAATAAAAA 59.613 37.500 0.00 0.00 40.02 1.94
904 905 0.323629 TTAGACGGGCCTGGAAACTG 59.676 55.000 18.00 0.00 0.00 3.16
947 949 1.422161 CCCACCCCATCTCCTCCATC 61.422 65.000 0.00 0.00 0.00 3.51
958 960 3.437213 TCTCCTCCATCGAAACCAAGTA 58.563 45.455 0.00 0.00 0.00 2.24
970 972 2.902705 ACCAAGTAAAGTGAGTGCGA 57.097 45.000 0.00 0.00 0.00 5.10
1098 1100 3.522731 CTCCGCTCCCTCTCCACG 61.523 72.222 0.00 0.00 0.00 4.94
1312 1314 2.283388 AAGGGAGGGCGTACGTCA 60.283 61.111 22.92 0.00 35.71 4.35
1443 1445 3.636231 CACAAGGAGGACCCCGCA 61.636 66.667 0.00 0.00 36.73 5.69
1631 1635 8.800370 AAGAGATCCTTTATTTCCTTCAGTTC 57.200 34.615 0.00 0.00 0.00 3.01
1683 1687 7.067981 TCGGAGTAAAAAGATCTAGGGTTCTAC 59.932 40.741 0.00 0.00 0.00 2.59
1684 1688 7.068470 CGGAGTAAAAAGATCTAGGGTTCTACT 59.932 40.741 0.00 0.00 0.00 2.57
1685 1689 8.198778 GGAGTAAAAAGATCTAGGGTTCTACTG 58.801 40.741 0.00 0.00 0.00 2.74
1686 1690 8.667592 AGTAAAAAGATCTAGGGTTCTACTGT 57.332 34.615 0.00 0.00 0.00 3.55
1687 1691 9.765295 AGTAAAAAGATCTAGGGTTCTACTGTA 57.235 33.333 0.00 0.00 0.00 2.74
1700 1704 6.127786 GGGTTCTACTGTAGTTCGTAAGTCAT 60.128 42.308 14.11 0.00 39.48 3.06
1702 1706 7.361542 GGTTCTACTGTAGTTCGTAAGTCATGA 60.362 40.741 14.11 0.00 39.48 3.07
1823 1827 4.437682 ACTGGGTCTCTTGAATTGTTGA 57.562 40.909 0.00 0.00 0.00 3.18
1880 1884 3.285484 GCTCTGGATCATGACAATTGGT 58.715 45.455 10.83 0.00 0.00 3.67
1888 1892 5.237344 GGATCATGACAATTGGTAGTAGCAC 59.763 44.000 10.83 0.00 0.00 4.40
2102 2210 3.117512 AGTTGTTCCAGGATGAAGTTGGT 60.118 43.478 0.00 0.00 39.69 3.67
2121 2229 9.606631 AAGTTGGTTTAATGTTATTTTGCAAGA 57.393 25.926 0.00 0.00 0.00 3.02
2132 2240 6.372659 TGTTATTTTGCAAGAAAAACAGGCAA 59.627 30.769 13.80 0.00 42.15 4.52
2136 2244 3.871485 TGCAAGAAAAACAGGCAATTGT 58.129 36.364 7.40 0.00 0.00 2.71
2231 2345 5.198116 TCAACATTACACGCATAAAGTCG 57.802 39.130 0.00 0.00 0.00 4.18
2402 2522 6.312487 TCTCGTGAGTAGTGAGAATAAAACG 58.688 40.000 0.00 0.00 35.91 3.60
2422 2542 4.708177 ACGATGAGATTGGAAGGTTATGG 58.292 43.478 0.00 0.00 0.00 2.74
2612 2734 9.117183 TGTATGAGATTTCAATGAAGGAAGATG 57.883 33.333 0.00 0.00 36.78 2.90
2613 2735 6.446781 TGAGATTTCAATGAAGGAAGATGC 57.553 37.500 0.00 0.00 0.00 3.91
2671 2793 5.705609 TCAACAAGAAAAAGGTAGGCATC 57.294 39.130 0.00 0.00 0.00 3.91
2673 2795 6.539173 TCAACAAGAAAAAGGTAGGCATCTA 58.461 36.000 0.00 0.00 0.00 1.98
2682 2806 9.574458 GAAAAAGGTAGGCATCTAATTTTCTTC 57.426 33.333 0.00 0.00 35.19 2.87
2826 2973 3.077359 AGTACAAATTCCTGCAGTCTGC 58.923 45.455 18.32 18.32 45.29 4.26
2909 3147 3.821033 ACTGGAGTTTGTGCATAGGAAAC 59.179 43.478 0.00 0.00 0.00 2.78
2913 3151 3.421844 AGTTTGTGCATAGGAAACCTCC 58.578 45.455 0.00 0.00 42.81 4.30
3237 3523 6.721318 AGGATCATTGCTCCTTACAAGTAAA 58.279 36.000 3.15 0.00 40.29 2.01
3269 3556 3.557898 CCCCTCTGCTCGTTATAATGCAT 60.558 47.826 0.00 0.00 34.79 3.96
3283 3570 7.043656 CGTTATAATGCATGAGTTCTACGAACA 60.044 37.037 0.00 0.00 0.00 3.18
3285 3572 7.792374 ATAATGCATGAGTTCTACGAACAAT 57.208 32.000 0.00 0.56 0.00 2.71
3373 3665 3.286751 TTGCAGCGCCACCAGAAC 61.287 61.111 2.29 0.00 0.00 3.01
3498 3791 1.210413 CGTGTCTCCGTCTCCACAG 59.790 63.158 0.00 0.00 0.00 3.66
3566 3862 8.239314 ACACTTTGCACTCAACATTTCATATAG 58.761 33.333 0.00 0.00 30.75 1.31
3572 3868 6.514048 GCACTCAACATTTCATATAGCCTTCC 60.514 42.308 0.00 0.00 0.00 3.46
3605 3901 5.643348 TGCTTACAATGAGTACTTGGACATG 59.357 40.000 0.00 0.00 30.91 3.21
3644 3940 1.345422 TGGACTGGAGGCCCAATAGAT 60.345 52.381 0.00 0.00 42.98 1.98
3657 3953 7.300658 AGGCCCAATAGATTATTTCTGATGTT 58.699 34.615 0.00 0.00 35.79 2.71
3685 3987 4.701651 TGTATGATTTCCTTTCCTGCTGTG 59.298 41.667 0.00 0.00 0.00 3.66
3688 3990 1.999648 TTTCCTTTCCTGCTGTGCAT 58.000 45.000 0.00 0.00 38.13 3.96
3793 4095 7.926018 TCAATAAGCTTATTTCGCAGTCATCTA 59.074 33.333 25.71 0.00 31.28 1.98
3865 4167 1.237285 GCTCACCTGTCCGCATGTTT 61.237 55.000 0.00 0.00 0.00 2.83
3867 4169 2.422597 CTCACCTGTCCGCATGTTTAA 58.577 47.619 0.00 0.00 0.00 1.52
3869 4171 1.199097 CACCTGTCCGCATGTTTAACC 59.801 52.381 0.00 0.00 0.00 2.85
3870 4172 0.446222 CCTGTCCGCATGTTTAACCG 59.554 55.000 0.00 0.00 0.00 4.44
3871 4173 1.153353 CTGTCCGCATGTTTAACCGT 58.847 50.000 0.00 0.00 0.00 4.83
3872 4174 0.869068 TGTCCGCATGTTTAACCGTG 59.131 50.000 0.00 0.00 0.00 4.94
3873 4175 0.453782 GTCCGCATGTTTAACCGTGC 60.454 55.000 7.11 7.11 42.62 5.34
3921 4225 4.256110 CCACTGACTTGCTTGATGATGTA 58.744 43.478 0.00 0.00 0.00 2.29
3922 4226 4.696877 CCACTGACTTGCTTGATGATGTAA 59.303 41.667 0.00 0.00 0.00 2.41
3989 4293 3.296709 ATCCACCGTGCGGACTGTC 62.297 63.158 18.16 0.00 38.96 3.51
3997 4301 4.194720 GCGGACTGTCGATCGGCT 62.195 66.667 21.85 0.13 38.85 5.52
4067 4372 3.632145 ACAACAAAACTAACCCAGCAGAG 59.368 43.478 0.00 0.00 0.00 3.35
4071 4376 3.409026 AAACTAACCCAGCAGAGAGTG 57.591 47.619 0.00 0.00 0.00 3.51
4098 4403 5.229921 TGAAACGACACTTCTTTTCTTGG 57.770 39.130 0.00 0.00 39.57 3.61
4119 4424 2.351726 GACTTAATCATGACACGCCACC 59.648 50.000 0.00 0.00 0.00 4.61
4120 4425 1.670811 CTTAATCATGACACGCCACCC 59.329 52.381 0.00 0.00 0.00 4.61
4170 4475 1.542915 AGACGCGTAAAGGCTGAAGTA 59.457 47.619 13.97 0.00 0.00 2.24
4175 4480 2.159037 GCGTAAAGGCTGAAGTAACCAC 59.841 50.000 0.00 0.00 0.00 4.16
4177 4482 4.813027 CGTAAAGGCTGAAGTAACCACTA 58.187 43.478 0.00 0.00 33.48 2.74
4197 4502 1.429148 CCATGTTTAGCGCCCGTCTC 61.429 60.000 2.29 0.00 0.00 3.36
4208 4513 0.530870 GCCCGTCTCCTATCAGTTGC 60.531 60.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
396 397 9.639563 ACATCAAAACATATATATCACCCACAA 57.360 29.630 0.00 0.00 0.00 3.33
397 398 9.639563 AACATCAAAACATATATATCACCCACA 57.360 29.630 0.00 0.00 0.00 4.17
407 408 9.574516 GGAGGGAGTAAACATCAAAACATATAT 57.425 33.333 0.00 0.00 0.00 0.86
408 409 7.713507 CGGAGGGAGTAAACATCAAAACATATA 59.286 37.037 0.00 0.00 0.00 0.86
409 410 6.542370 CGGAGGGAGTAAACATCAAAACATAT 59.458 38.462 0.00 0.00 0.00 1.78
410 411 5.878116 CGGAGGGAGTAAACATCAAAACATA 59.122 40.000 0.00 0.00 0.00 2.29
411 412 4.700213 CGGAGGGAGTAAACATCAAAACAT 59.300 41.667 0.00 0.00 0.00 2.71
412 413 4.069304 CGGAGGGAGTAAACATCAAAACA 58.931 43.478 0.00 0.00 0.00 2.83
413 414 4.070009 ACGGAGGGAGTAAACATCAAAAC 58.930 43.478 0.00 0.00 0.00 2.43
414 415 4.360951 ACGGAGGGAGTAAACATCAAAA 57.639 40.909 0.00 0.00 0.00 2.44
415 416 4.202377 TGAACGGAGGGAGTAAACATCAAA 60.202 41.667 0.00 0.00 0.00 2.69
416 417 3.325425 TGAACGGAGGGAGTAAACATCAA 59.675 43.478 0.00 0.00 0.00 2.57
417 418 2.901192 TGAACGGAGGGAGTAAACATCA 59.099 45.455 0.00 0.00 0.00 3.07
418 419 3.259902 GTGAACGGAGGGAGTAAACATC 58.740 50.000 0.00 0.00 0.00 3.06
419 420 2.635915 TGTGAACGGAGGGAGTAAACAT 59.364 45.455 0.00 0.00 0.00 2.71
420 421 2.040939 TGTGAACGGAGGGAGTAAACA 58.959 47.619 0.00 0.00 0.00 2.83
421 422 2.825861 TGTGAACGGAGGGAGTAAAC 57.174 50.000 0.00 0.00 0.00 2.01
422 423 4.360951 AATTGTGAACGGAGGGAGTAAA 57.639 40.909 0.00 0.00 0.00 2.01
423 424 5.687166 ATAATTGTGAACGGAGGGAGTAA 57.313 39.130 0.00 0.00 0.00 2.24
424 425 6.381994 ACTTATAATTGTGAACGGAGGGAGTA 59.618 38.462 0.00 0.00 0.00 2.59
425 426 5.189145 ACTTATAATTGTGAACGGAGGGAGT 59.811 40.000 0.00 0.00 0.00 3.85
426 427 5.671493 ACTTATAATTGTGAACGGAGGGAG 58.329 41.667 0.00 0.00 0.00 4.30
427 428 5.687166 ACTTATAATTGTGAACGGAGGGA 57.313 39.130 0.00 0.00 0.00 4.20
428 429 6.753107 AAACTTATAATTGTGAACGGAGGG 57.247 37.500 0.00 0.00 0.00 4.30
494 495 8.756927 CCCTGAATCAGATGTATATAGACACAT 58.243 37.037 12.53 0.00 38.08 3.21
495 496 7.950124 TCCCTGAATCAGATGTATATAGACACA 59.050 37.037 12.53 0.00 32.44 3.72
496 497 8.354711 TCCCTGAATCAGATGTATATAGACAC 57.645 38.462 12.53 0.00 32.44 3.67
497 498 8.956446 TTCCCTGAATCAGATGTATATAGACA 57.044 34.615 12.53 2.07 32.44 3.41
504 505 9.753674 TTTAACTTTTCCCTGAATCAGATGTAT 57.246 29.630 12.53 0.00 32.44 2.29
505 506 9.581289 TTTTAACTTTTCCCTGAATCAGATGTA 57.419 29.630 12.53 0.00 32.44 2.29
506 507 8.360390 GTTTTAACTTTTCCCTGAATCAGATGT 58.640 33.333 12.53 0.00 32.44 3.06
507 508 8.359642 TGTTTTAACTTTTCCCTGAATCAGATG 58.640 33.333 12.53 2.62 32.44 2.90
508 509 8.477419 TGTTTTAACTTTTCCCTGAATCAGAT 57.523 30.769 12.53 0.00 32.44 2.90
509 510 7.889873 TGTTTTAACTTTTCCCTGAATCAGA 57.110 32.000 12.53 0.00 32.44 3.27
510 511 8.579863 AGATGTTTTAACTTTTCCCTGAATCAG 58.420 33.333 2.68 2.68 0.00 2.90
511 512 8.477419 AGATGTTTTAACTTTTCCCTGAATCA 57.523 30.769 0.00 0.00 0.00 2.57
538 539 9.440761 AAGAGTACTCCCTTCATTCACTATTAT 57.559 33.333 19.38 0.00 0.00 1.28
539 540 8.840200 AAGAGTACTCCCTTCATTCACTATTA 57.160 34.615 19.38 0.00 0.00 0.98
540 541 7.741554 AAGAGTACTCCCTTCATTCACTATT 57.258 36.000 19.38 0.00 0.00 1.73
541 542 7.741554 AAAGAGTACTCCCTTCATTCACTAT 57.258 36.000 19.38 0.00 0.00 2.12
542 543 7.234782 TGAAAAGAGTACTCCCTTCATTCACTA 59.765 37.037 23.63 8.06 30.47 2.74
543 544 6.043243 TGAAAAGAGTACTCCCTTCATTCACT 59.957 38.462 23.63 4.06 30.47 3.41
544 545 6.231211 TGAAAAGAGTACTCCCTTCATTCAC 58.769 40.000 23.63 9.71 30.47 3.18
545 546 6.433847 TGAAAAGAGTACTCCCTTCATTCA 57.566 37.500 23.63 18.56 30.47 2.57
546 547 8.041323 TGTATGAAAAGAGTACTCCCTTCATTC 58.959 37.037 33.41 29.99 39.75 2.67
547 548 7.918076 TGTATGAAAAGAGTACTCCCTTCATT 58.082 34.615 33.41 24.04 39.75 2.57
548 549 7.496346 TGTATGAAAAGAGTACTCCCTTCAT 57.504 36.000 32.13 32.13 40.94 2.57
549 550 6.928348 TGTATGAAAAGAGTACTCCCTTCA 57.072 37.500 27.00 27.00 36.08 3.02
550 551 7.331791 ACATGTATGAAAAGAGTACTCCCTTC 58.668 38.462 19.38 19.92 0.00 3.46
551 552 7.259088 ACATGTATGAAAAGAGTACTCCCTT 57.741 36.000 19.38 12.51 0.00 3.95
552 553 6.875972 ACATGTATGAAAAGAGTACTCCCT 57.124 37.500 19.38 4.21 0.00 4.20
553 554 6.879458 ACAACATGTATGAAAAGAGTACTCCC 59.121 38.462 19.38 7.17 0.00 4.30
554 555 7.907214 ACAACATGTATGAAAAGAGTACTCC 57.093 36.000 19.38 4.63 0.00 3.85
555 556 9.419297 TGTACAACATGTATGAAAAGAGTACTC 57.581 33.333 15.41 15.41 35.05 2.59
556 557 9.944376 ATGTACAACATGTATGAAAAGAGTACT 57.056 29.630 0.00 0.00 37.45 2.73
563 564 9.737427 ACGAAAAATGTACAACATGTATGAAAA 57.263 25.926 0.00 0.00 37.97 2.29
570 571 9.982291 GATGTATACGAAAAATGTACAACATGT 57.018 29.630 0.00 0.00 37.97 3.21
571 572 9.980780 TGATGTATACGAAAAATGTACAACATG 57.019 29.630 0.00 0.00 37.97 3.21
573 574 9.425577 TCTGATGTATACGAAAAATGTACAACA 57.574 29.630 0.00 0.00 29.91 3.33
591 592 9.210329 ACGTGTGTAAAAATTGTATCTGATGTA 57.790 29.630 0.00 0.00 0.00 2.29
592 593 8.094798 ACGTGTGTAAAAATTGTATCTGATGT 57.905 30.769 0.00 0.00 0.00 3.06
593 594 8.948853 AACGTGTGTAAAAATTGTATCTGATG 57.051 30.769 0.00 0.00 0.00 3.07
594 595 9.607285 GAAACGTGTGTAAAAATTGTATCTGAT 57.393 29.630 0.00 0.00 0.00 2.90
595 596 8.613482 TGAAACGTGTGTAAAAATTGTATCTGA 58.387 29.630 0.00 0.00 0.00 3.27
596 597 8.678510 GTGAAACGTGTGTAAAAATTGTATCTG 58.321 33.333 0.00 0.00 0.00 2.90
597 598 8.399425 TGTGAAACGTGTGTAAAAATTGTATCT 58.601 29.630 0.00 0.00 42.39 1.98
598 599 8.549777 TGTGAAACGTGTGTAAAAATTGTATC 57.450 30.769 0.00 0.00 42.39 2.24
599 600 9.522804 AATGTGAAACGTGTGTAAAAATTGTAT 57.477 25.926 0.00 0.00 42.39 2.29
600 601 8.912787 AATGTGAAACGTGTGTAAAAATTGTA 57.087 26.923 0.00 0.00 42.39 2.41
601 602 7.820044 AATGTGAAACGTGTGTAAAAATTGT 57.180 28.000 0.00 0.00 42.39 2.71
602 603 9.535270 AAAAATGTGAAACGTGTGTAAAAATTG 57.465 25.926 0.00 0.00 42.39 2.32
603 604 9.748100 GAAAAATGTGAAACGTGTGTAAAAATT 57.252 25.926 0.00 0.00 42.39 1.82
604 605 8.926710 TGAAAAATGTGAAACGTGTGTAAAAAT 58.073 25.926 0.00 0.00 42.39 1.82
605 606 8.294341 TGAAAAATGTGAAACGTGTGTAAAAA 57.706 26.923 0.00 0.00 42.39 1.94
606 607 7.869016 TGAAAAATGTGAAACGTGTGTAAAA 57.131 28.000 0.00 0.00 42.39 1.52
607 608 7.869016 TTGAAAAATGTGAAACGTGTGTAAA 57.131 28.000 0.00 0.00 42.39 2.01
608 609 7.869016 TTTGAAAAATGTGAAACGTGTGTAA 57.131 28.000 0.00 0.00 42.39 2.41
609 610 8.467402 AATTTGAAAAATGTGAAACGTGTGTA 57.533 26.923 0.00 0.00 42.39 2.90
610 611 6.959671 ATTTGAAAAATGTGAAACGTGTGT 57.040 29.167 0.00 0.00 42.39 3.72
611 612 7.451429 TGAATTTGAAAAATGTGAAACGTGTG 58.549 30.769 0.00 0.00 42.39 3.82
612 613 7.588143 TGAATTTGAAAAATGTGAAACGTGT 57.412 28.000 0.00 0.00 42.39 4.49
703 704 9.131791 TGCTTCTTCTTCTTTACCTTTGTTTAT 57.868 29.630 0.00 0.00 0.00 1.40
704 705 8.514330 TGCTTCTTCTTCTTTACCTTTGTTTA 57.486 30.769 0.00 0.00 0.00 2.01
705 706 7.404671 TGCTTCTTCTTCTTTACCTTTGTTT 57.595 32.000 0.00 0.00 0.00 2.83
706 707 7.404671 TTGCTTCTTCTTCTTTACCTTTGTT 57.595 32.000 0.00 0.00 0.00 2.83
707 708 7.404671 TTTGCTTCTTCTTCTTTACCTTTGT 57.595 32.000 0.00 0.00 0.00 2.83
708 709 8.595533 GTTTTTGCTTCTTCTTCTTTACCTTTG 58.404 33.333 0.00 0.00 0.00 2.77
709 710 7.764443 GGTTTTTGCTTCTTCTTCTTTACCTTT 59.236 33.333 0.00 0.00 0.00 3.11
710 711 7.265673 GGTTTTTGCTTCTTCTTCTTTACCTT 58.734 34.615 0.00 0.00 0.00 3.50
711 712 6.459710 CGGTTTTTGCTTCTTCTTCTTTACCT 60.460 38.462 0.00 0.00 0.00 3.08
712 713 5.685954 CGGTTTTTGCTTCTTCTTCTTTACC 59.314 40.000 0.00 0.00 0.00 2.85
713 714 6.492254 TCGGTTTTTGCTTCTTCTTCTTTAC 58.508 36.000 0.00 0.00 0.00 2.01
714 715 6.687081 TCGGTTTTTGCTTCTTCTTCTTTA 57.313 33.333 0.00 0.00 0.00 1.85
715 716 5.576447 TCGGTTTTTGCTTCTTCTTCTTT 57.424 34.783 0.00 0.00 0.00 2.52
716 717 5.576447 TTCGGTTTTTGCTTCTTCTTCTT 57.424 34.783 0.00 0.00 0.00 2.52
717 718 5.576447 TTTCGGTTTTTGCTTCTTCTTCT 57.424 34.783 0.00 0.00 0.00 2.85
718 719 5.275741 CGTTTTCGGTTTTTGCTTCTTCTTC 60.276 40.000 0.00 0.00 39.94 2.87
719 720 4.561213 CGTTTTCGGTTTTTGCTTCTTCTT 59.439 37.500 0.00 0.00 39.94 2.52
720 721 4.102649 CGTTTTCGGTTTTTGCTTCTTCT 58.897 39.130 0.00 0.00 39.94 2.85
721 722 4.099824 TCGTTTTCGGTTTTTGCTTCTTC 58.900 39.130 0.00 0.00 44.25 2.87
722 723 4.099380 TCGTTTTCGGTTTTTGCTTCTT 57.901 36.364 0.00 0.00 44.25 2.52
723 724 3.768468 TCGTTTTCGGTTTTTGCTTCT 57.232 38.095 0.00 0.00 44.25 2.85
724 725 4.826569 TTTCGTTTTCGGTTTTTGCTTC 57.173 36.364 0.00 0.00 44.25 3.86
725 726 4.493382 GCATTTCGTTTTCGGTTTTTGCTT 60.493 37.500 0.00 0.00 44.25 3.91
726 727 3.000825 GCATTTCGTTTTCGGTTTTTGCT 59.999 39.130 0.00 0.00 44.25 3.91
727 728 3.276660 GCATTTCGTTTTCGGTTTTTGC 58.723 40.909 0.00 0.00 44.25 3.68
728 729 3.307242 TGGCATTTCGTTTTCGGTTTTTG 59.693 39.130 0.00 0.00 44.25 2.44
729 730 3.522553 TGGCATTTCGTTTTCGGTTTTT 58.477 36.364 0.00 0.00 44.25 1.94
730 731 3.166489 TGGCATTTCGTTTTCGGTTTT 57.834 38.095 0.00 0.00 44.25 2.43
731 732 2.873133 TGGCATTTCGTTTTCGGTTT 57.127 40.000 0.00 0.00 44.25 3.27
732 733 2.873133 TTGGCATTTCGTTTTCGGTT 57.127 40.000 0.00 0.00 44.25 4.44
733 734 2.873133 TTTGGCATTTCGTTTTCGGT 57.127 40.000 0.00 0.00 44.25 4.69
751 752 4.594136 CGCTCGTGTTTTACTTCCTTTTT 58.406 39.130 0.00 0.00 0.00 1.94
752 753 3.547413 GCGCTCGTGTTTTACTTCCTTTT 60.547 43.478 0.00 0.00 0.00 2.27
753 754 2.032290 GCGCTCGTGTTTTACTTCCTTT 60.032 45.455 0.00 0.00 0.00 3.11
754 755 1.529865 GCGCTCGTGTTTTACTTCCTT 59.470 47.619 0.00 0.00 0.00 3.36
755 756 1.145803 GCGCTCGTGTTTTACTTCCT 58.854 50.000 0.00 0.00 0.00 3.36
756 757 1.136336 CAGCGCTCGTGTTTTACTTCC 60.136 52.381 7.13 0.00 0.00 3.46
757 758 1.721804 GCAGCGCTCGTGTTTTACTTC 60.722 52.381 7.13 0.00 0.00 3.01
758 759 0.234884 GCAGCGCTCGTGTTTTACTT 59.765 50.000 7.13 0.00 0.00 2.24
759 760 0.600255 AGCAGCGCTCGTGTTTTACT 60.600 50.000 7.13 0.00 30.62 2.24
760 761 0.179248 GAGCAGCGCTCGTGTTTTAC 60.179 55.000 7.13 0.00 45.85 2.01
761 762 2.150424 GAGCAGCGCTCGTGTTTTA 58.850 52.632 7.13 0.00 45.85 1.52
762 763 2.939022 GAGCAGCGCTCGTGTTTT 59.061 55.556 7.13 0.00 45.85 2.43
784 785 4.740822 AATGGACGGGCCCAGTGC 62.741 66.667 24.92 24.53 39.97 4.40
785 786 2.035626 AAATGGACGGGCCCAGTG 59.964 61.111 24.92 8.33 39.97 3.66
786 787 2.035626 CAAATGGACGGGCCCAGT 59.964 61.111 24.92 20.78 39.97 4.00
787 788 1.606313 AACAAATGGACGGGCCCAG 60.606 57.895 24.92 17.36 39.97 4.45
788 789 1.905843 CAACAAATGGACGGGCCCA 60.906 57.895 24.92 1.02 41.05 5.36
789 790 2.969827 CAACAAATGGACGGGCCC 59.030 61.111 13.57 13.57 34.97 5.80
790 791 2.261361 GCAACAAATGGACGGGCC 59.739 61.111 0.00 0.00 37.10 5.80
791 792 1.080569 CTGCAACAAATGGACGGGC 60.081 57.895 0.00 0.00 0.00 6.13
792 793 1.080569 GCTGCAACAAATGGACGGG 60.081 57.895 0.00 0.00 0.00 5.28
793 794 1.080569 GGCTGCAACAAATGGACGG 60.081 57.895 0.50 0.00 0.00 4.79
794 795 1.442520 CGGCTGCAACAAATGGACG 60.443 57.895 0.50 0.00 0.00 4.79
795 796 1.734117 GCGGCTGCAACAAATGGAC 60.734 57.895 14.08 0.00 42.15 4.02
796 797 2.650196 GCGGCTGCAACAAATGGA 59.350 55.556 14.08 0.00 42.15 3.41
797 798 2.806198 CGCGGCTGCAACAAATGG 60.806 61.111 19.50 0.00 42.97 3.16
798 799 3.472298 GCGCGGCTGCAACAAATG 61.472 61.111 19.50 0.00 42.97 2.32
799 800 3.976000 TGCGCGGCTGCAACAAAT 61.976 55.556 19.50 0.00 43.02 2.32
809 810 3.693128 TATATCCATCCAGTGCGCGGC 62.693 57.143 8.83 0.00 0.00 6.53
810 811 0.246360 TATATCCATCCAGTGCGCGG 59.754 55.000 8.83 0.00 0.00 6.46
811 812 1.633561 CTATATCCATCCAGTGCGCG 58.366 55.000 0.00 0.00 0.00 6.86
812 813 1.363744 GCTATATCCATCCAGTGCGC 58.636 55.000 0.00 0.00 0.00 6.09
813 814 1.633561 CGCTATATCCATCCAGTGCG 58.366 55.000 0.00 0.00 36.41 5.34
814 815 1.066573 AGCGCTATATCCATCCAGTGC 60.067 52.381 8.99 0.00 43.23 4.40
815 816 2.614779 CAGCGCTATATCCATCCAGTG 58.385 52.381 10.99 0.00 0.00 3.66
816 817 1.066573 GCAGCGCTATATCCATCCAGT 60.067 52.381 10.99 0.00 0.00 4.00
817 818 1.649664 GCAGCGCTATATCCATCCAG 58.350 55.000 10.99 0.00 0.00 3.86
818 819 0.250234 GGCAGCGCTATATCCATCCA 59.750 55.000 10.99 0.00 0.00 3.41
819 820 0.462759 GGGCAGCGCTATATCCATCC 60.463 60.000 10.99 1.10 0.00 3.51
820 821 0.807667 CGGGCAGCGCTATATCCATC 60.808 60.000 10.99 0.00 0.00 3.51
821 822 1.219124 CGGGCAGCGCTATATCCAT 59.781 57.895 10.99 0.00 0.00 3.41
822 823 2.656646 CGGGCAGCGCTATATCCA 59.343 61.111 10.99 0.00 0.00 3.41
823 824 2.815647 GCGGGCAGCGCTATATCC 60.816 66.667 10.99 9.19 35.41 2.59
840 841 1.298157 TTGGCTCGGAATGCGTCAAG 61.298 55.000 0.00 0.00 0.00 3.02
841 842 0.886938 TTTGGCTCGGAATGCGTCAA 60.887 50.000 0.00 0.00 0.00 3.18
842 843 0.886938 TTTTGGCTCGGAATGCGTCA 60.887 50.000 0.00 0.00 0.00 4.35
843 844 0.239879 TTTTTGGCTCGGAATGCGTC 59.760 50.000 0.00 0.00 0.00 5.19
844 845 0.887933 ATTTTTGGCTCGGAATGCGT 59.112 45.000 0.00 0.00 0.00 5.24
845 846 2.842208 TATTTTTGGCTCGGAATGCG 57.158 45.000 0.00 0.00 0.00 4.73
846 847 5.854431 TTTTTATTTTTGGCTCGGAATGC 57.146 34.783 0.00 0.00 0.00 3.56
872 873 3.275999 CCCGTCTAAATTAACCCAGTGG 58.724 50.000 0.63 0.63 37.80 4.00
873 874 2.681344 GCCCGTCTAAATTAACCCAGTG 59.319 50.000 0.00 0.00 0.00 3.66
874 875 2.356432 GGCCCGTCTAAATTAACCCAGT 60.356 50.000 0.00 0.00 0.00 4.00
875 876 2.092592 AGGCCCGTCTAAATTAACCCAG 60.093 50.000 0.00 0.00 0.00 4.45
876 877 1.917568 AGGCCCGTCTAAATTAACCCA 59.082 47.619 0.00 0.00 0.00 4.51
877 878 2.294979 CAGGCCCGTCTAAATTAACCC 58.705 52.381 0.00 0.00 0.00 4.11
878 879 2.092807 TCCAGGCCCGTCTAAATTAACC 60.093 50.000 0.00 0.00 0.00 2.85
879 880 3.271055 TCCAGGCCCGTCTAAATTAAC 57.729 47.619 0.00 0.00 0.00 2.01
880 881 4.011698 GTTTCCAGGCCCGTCTAAATTAA 58.988 43.478 0.00 0.00 0.00 1.40
881 882 3.264964 AGTTTCCAGGCCCGTCTAAATTA 59.735 43.478 0.00 0.00 0.00 1.40
882 883 2.041216 AGTTTCCAGGCCCGTCTAAATT 59.959 45.455 0.00 0.00 0.00 1.82
883 884 1.633945 AGTTTCCAGGCCCGTCTAAAT 59.366 47.619 0.00 0.00 0.00 1.40
884 885 1.061546 AGTTTCCAGGCCCGTCTAAA 58.938 50.000 0.00 0.00 0.00 1.85
890 891 2.747855 GCTCAGTTTCCAGGCCCG 60.748 66.667 0.00 0.00 0.00 6.13
934 936 1.486310 TGGTTTCGATGGAGGAGATGG 59.514 52.381 0.00 0.00 0.00 3.51
947 949 3.603857 CGCACTCACTTTACTTGGTTTCG 60.604 47.826 0.00 0.00 0.00 3.46
958 960 1.598130 GGGCTGTCGCACTCACTTT 60.598 57.895 0.00 0.00 36.36 2.66
970 972 0.957395 CGCTCTTGTGATTGGGCTGT 60.957 55.000 0.00 0.00 0.00 4.40
1312 1314 0.463116 AAACGCTTGTCCCACGAGTT 60.463 50.000 0.00 0.00 32.12 3.01
1380 1382 3.458163 TCCTTGAGGTAGGCGCCG 61.458 66.667 23.20 3.36 35.15 6.46
1631 1635 8.950210 ACTCATGACCTAATTATTTCAACACAG 58.050 33.333 0.00 0.00 0.00 3.66
1683 1687 4.421948 GGGTCATGACTTACGAACTACAG 58.578 47.826 24.50 0.00 0.00 2.74
1684 1688 3.194116 GGGGTCATGACTTACGAACTACA 59.806 47.826 24.50 0.00 0.00 2.74
1685 1689 3.446516 AGGGGTCATGACTTACGAACTAC 59.553 47.826 24.50 4.49 0.00 2.73
1686 1690 3.446161 CAGGGGTCATGACTTACGAACTA 59.554 47.826 24.50 0.00 0.00 2.24
1687 1691 2.233922 CAGGGGTCATGACTTACGAACT 59.766 50.000 24.50 9.91 0.00 3.01
1700 1704 7.291566 TGTTCTCTTAAATAAAACAGGGGTCA 58.708 34.615 0.00 0.00 0.00 4.02
1702 1706 8.721133 AATGTTCTCTTAAATAAAACAGGGGT 57.279 30.769 0.00 0.00 33.74 4.95
1836 1840 8.137745 AGCATTGGAAATTTCTATTCAGGAAA 57.862 30.769 17.42 0.00 37.15 3.13
1880 1884 1.961394 CCTAGGATTGCCGTGCTACTA 59.039 52.381 1.05 0.00 39.96 1.82
1888 1892 2.835027 GGTTCTAACCTAGGATTGCCG 58.165 52.381 17.98 0.00 45.75 5.69
1912 2015 2.289072 ACACCCAGTTCAGTCTCAATCG 60.289 50.000 0.00 0.00 0.00 3.34
1991 2098 7.014615 TCCTCGACTCATATCATTTCATGAAGA 59.985 37.037 8.41 4.03 43.50 2.87
1995 2102 7.902387 ATTCCTCGACTCATATCATTTCATG 57.098 36.000 0.00 0.00 0.00 3.07
2121 2229 6.205270 GGATTTGATGACAATTGCCTGTTTTT 59.795 34.615 5.05 0.00 35.85 1.94
2129 2237 5.957798 TCTCAAGGATTTGATGACAATTGC 58.042 37.500 5.05 0.00 42.19 3.56
2132 2240 7.832685 TGAATCTCTCAAGGATTTGATGACAAT 59.167 33.333 0.00 0.00 42.19 2.71
2136 2244 7.803131 AGATGAATCTCTCAAGGATTTGATGA 58.197 34.615 0.00 0.00 42.19 2.92
2196 2310 7.391786 CGTGTAATGTTGAGCTAATCAGTAAC 58.608 38.462 0.00 0.00 39.68 2.50
2231 2345 6.183360 CCCACTATTTACCAATTTCCACCATC 60.183 42.308 0.00 0.00 0.00 3.51
2402 2522 5.300286 CCAACCATAACCTTCCAATCTCATC 59.700 44.000 0.00 0.00 0.00 2.92
2422 2542 5.001232 TGGAGTAGTAAGTGCAATTCCAAC 58.999 41.667 1.02 0.00 31.02 3.77
2612 2734 7.639039 TGAACAAATTCCTCATATAACATCGC 58.361 34.615 0.00 0.00 33.49 4.58
2613 2735 9.438291 GTTGAACAAATTCCTCATATAACATCG 57.562 33.333 0.00 0.00 33.49 3.84
2671 2793 7.985476 TCATAAAAGGGAGCGAAGAAAATTAG 58.015 34.615 0.00 0.00 0.00 1.73
2673 2795 6.834168 TCATAAAAGGGAGCGAAGAAAATT 57.166 33.333 0.00 0.00 0.00 1.82
2682 2806 5.239306 TCAGCAAATATCATAAAAGGGAGCG 59.761 40.000 0.00 0.00 0.00 5.03
2744 2868 3.323691 TCTGCTGCAGGAGTTTGTACTAA 59.676 43.478 31.17 9.10 33.84 2.24
2745 2869 2.897326 TCTGCTGCAGGAGTTTGTACTA 59.103 45.455 31.17 9.83 33.84 1.82
2788 2913 9.959721 AATTTGTACTAGATCACAACCATACTT 57.040 29.630 0.00 0.00 34.52 2.24
2826 2973 4.039973 TGGGGTCTTACAAGTCACTACAAG 59.960 45.833 0.00 0.00 0.00 3.16
2909 3147 1.344763 AGAACTTGACAGGAACGGAGG 59.655 52.381 0.00 0.00 0.00 4.30
2913 3151 3.927142 GTCCATAGAACTTGACAGGAACG 59.073 47.826 0.00 0.00 0.00 3.95
2964 3250 4.072131 GCAGATGACCAGTGGAAAACTTA 58.928 43.478 18.40 0.00 36.83 2.24
3237 3523 2.911926 GCAGAGGGGCCTTTCCTGT 61.912 63.158 0.84 0.00 34.21 4.00
3283 3570 4.124238 TGGAGAACGACAAAAGAACGATT 58.876 39.130 0.00 0.00 0.00 3.34
3285 3572 3.120792 CTGGAGAACGACAAAAGAACGA 58.879 45.455 0.00 0.00 0.00 3.85
3348 3635 0.875474 GTGGCGCTGCAACAAAACAT 60.875 50.000 7.64 0.00 31.84 2.71
3373 3665 2.325761 GCTGCAGCAAAACAAGATGAG 58.674 47.619 33.36 0.00 41.59 2.90
3498 3791 1.212751 GTGACTTGCCCGGAAATGC 59.787 57.895 0.73 0.00 0.00 3.56
3550 3846 7.756395 ATGGAAGGCTATATGAAATGTTGAG 57.244 36.000 0.00 0.00 0.00 3.02
3590 3886 6.542821 AGGAAATTTCATGTCCAAGTACTCA 58.457 36.000 19.49 0.00 33.57 3.41
3605 3901 7.764901 CCAGTCCAACTAGTAGTAGGAAATTTC 59.235 40.741 9.83 9.83 0.00 2.17
3657 3953 5.824624 GCAGGAAAGGAAATCATACATCTCA 59.175 40.000 0.00 0.00 0.00 3.27
3685 3987 1.312815 GGGCACAACAGGAGATATGC 58.687 55.000 0.00 0.00 0.00 3.14
3688 3990 2.575735 TGATTGGGCACAACAGGAGATA 59.424 45.455 1.86 0.00 39.87 1.98
3752 4054 7.934855 AGCTTATTGAATCACATTTGTCTCT 57.065 32.000 0.00 0.00 0.00 3.10
3793 4095 4.331168 GCAAGAAGATTCGCAGTTAGTCAT 59.669 41.667 0.00 0.00 0.00 3.06
3870 4172 3.782244 CTGCTGCCTCGTTCGCAC 61.782 66.667 0.00 0.00 31.61 5.34
3871 4173 4.299547 ACTGCTGCCTCGTTCGCA 62.300 61.111 0.00 0.00 34.41 5.10
3872 4174 3.782244 CACTGCTGCCTCGTTCGC 61.782 66.667 0.00 0.00 0.00 4.70
3873 4175 3.114616 CCACTGCTGCCTCGTTCG 61.115 66.667 0.00 0.00 0.00 3.95
3921 4225 4.676471 CGATGCACATTAAAGCGCATTATT 59.324 37.500 11.47 1.50 44.77 1.40
3922 4226 4.221342 CGATGCACATTAAAGCGCATTAT 58.779 39.130 11.47 0.00 44.77 1.28
3989 4293 0.933097 CAAAGGACATCAGCCGATCG 59.067 55.000 8.51 8.51 0.00 3.69
3997 4301 1.383799 CCAGGGCCAAAGGACATCA 59.616 57.895 6.18 0.00 27.52 3.07
4022 4326 1.084018 AGGTGGTTGGTGGATTGGAT 58.916 50.000 0.00 0.00 0.00 3.41
4023 4327 1.353022 GTAGGTGGTTGGTGGATTGGA 59.647 52.381 0.00 0.00 0.00 3.53
4024 4328 1.354368 AGTAGGTGGTTGGTGGATTGG 59.646 52.381 0.00 0.00 0.00 3.16
4025 4329 2.879103 AGTAGGTGGTTGGTGGATTG 57.121 50.000 0.00 0.00 0.00 2.67
4026 4330 3.253220 TGTAGTAGGTGGTTGGTGGATT 58.747 45.455 0.00 0.00 0.00 3.01
4067 4372 4.926238 AGAAGTGTCGTTTCATGATCACTC 59.074 41.667 0.00 2.81 35.53 3.51
4098 4403 2.351726 GGTGGCGTGTCATGATTAAGTC 59.648 50.000 0.00 0.00 0.00 3.01
4120 4425 3.869272 CCGACGTACCGAGGACCG 61.869 72.222 0.00 0.00 38.18 4.79
4129 4434 3.040409 GTCATTGGACCCGACGTAC 57.960 57.895 0.00 0.00 38.12 3.67
4144 4449 1.290955 CCTTTACGCGTCTGGGTCA 59.709 57.895 18.63 0.00 42.00 4.02
4167 4472 4.501071 CGCTAAACATGGTAGTGGTTACT 58.499 43.478 10.06 0.00 40.99 2.24
4170 4475 2.081462 GCGCTAAACATGGTAGTGGTT 58.919 47.619 16.51 0.00 32.84 3.67
4175 4480 0.461339 ACGGGCGCTAAACATGGTAG 60.461 55.000 7.64 0.00 0.00 3.18
4177 4482 1.743995 GACGGGCGCTAAACATGGT 60.744 57.895 7.64 0.00 0.00 3.55
4197 4502 6.474427 TCGTAAATTCGTAAGCAACTGATAGG 59.526 38.462 0.00 0.00 37.18 2.57
4208 4513 6.822073 TCACCATCATCGTAAATTCGTAAG 57.178 37.500 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.