Multiple sequence alignment - TraesCS6A01G346000

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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 TraesCS6A01G346000 chr6A 100.000 3748 0 0 1 3748 579148910 579145163 0.000000e+00 6922.0
1 TraesCS6A01G346000 chr6A 77.809 356 48 17 2509 2847 579767116 579767457 1.370000e-44 191.0
2 TraesCS6A01G346000 chr6A 90.071 141 13 1 573 713 536437864 536437725 8.270000e-42 182.0
3 TraesCS6A01G346000 chr6D 97.043 2469 55 8 697 3162 433287631 433285178 0.000000e+00 4139.0
4 TraesCS6A01G346000 chr6D 96.464 1103 21 8 1863 2955 433164329 433163235 0.000000e+00 1805.0
5 TraesCS6A01G346000 chr6D 97.842 417 8 1 177 593 433288044 433287629 0.000000e+00 719.0
6 TraesCS6A01G346000 chr6D 95.110 409 12 4 1476 1876 433206658 433206250 4.080000e-179 638.0
7 TraesCS6A01G346000 chr6D 91.627 418 19 6 1478 1887 432963623 432963214 7.030000e-157 564.0
8 TraesCS6A01G346000 chr6D 87.119 427 26 9 2947 3368 433162024 433161622 1.230000e-124 457.0
9 TraesCS6A01G346000 chr6D 82.479 468 66 9 2291 2752 433036170 433035713 2.710000e-106 396.0
10 TraesCS6A01G346000 chr6D 93.802 242 14 1 3507 3748 433282935 433282695 2.750000e-96 363.0
11 TraesCS6A01G346000 chr6D 92.486 173 13 0 3575 3747 433157527 433157355 8.040000e-62 248.0
12 TraesCS6A01G346000 chr6D 95.484 155 7 0 3303 3457 433285097 433284943 8.040000e-62 248.0
13 TraesCS6A01G346000 chr6D 94.531 128 7 0 52 179 433288347 433288220 8.210000e-47 198.0
14 TraesCS6A01G346000 chr6D 100.000 47 0 0 3507 3553 433157573 433157527 1.850000e-13 87.9
15 TraesCS6A01G346000 chr6B 94.996 2398 84 16 696 3070 653884485 653882101 0.000000e+00 3731.0
16 TraesCS6A01G346000 chr6B 95.957 1113 32 4 962 2061 653221446 653222558 0.000000e+00 1794.0
17 TraesCS6A01G346000 chr6B 93.482 1028 50 8 2130 3152 653222553 653223568 0.000000e+00 1511.0
18 TraesCS6A01G346000 chr6B 94.984 638 27 2 1909 2544 653220813 653221447 0.000000e+00 996.0
19 TraesCS6A01G346000 chr6B 93.913 345 15 2 252 593 653884823 653884482 2.000000e-142 516.0
20 TraesCS6A01G346000 chr6B 94.215 242 14 0 3507 3748 653228767 653229008 1.640000e-98 370.0
21 TraesCS6A01G346000 chr6B 93.004 243 16 1 3507 3748 653874843 653874601 1.660000e-93 353.0
22 TraesCS6A01G346000 chr6B 83.923 311 18 6 3148 3458 653223794 653224072 6.170000e-68 268.0
23 TraesCS6A01G346000 chr6B 77.995 409 53 20 2456 2845 655070489 655070879 4.870000e-54 222.0
24 TraesCS6A01G346000 chr6B 96.610 118 4 0 582 699 287011691 287011808 2.950000e-46 196.0
25 TraesCS6A01G346000 chr6B 95.122 82 4 0 3376 3457 653881447 653881366 3.040000e-26 130.0
26 TraesCS6A01G346000 chr1A 82.645 242 38 4 3507 3747 580991446 580991208 1.050000e-50 211.0
27 TraesCS6A01G346000 chr2B 99.130 115 1 0 587 701 672018320 672018434 1.360000e-49 207.0
28 TraesCS6A01G346000 chr7A 99.115 113 0 1 592 704 685837622 685837733 6.350000e-48 202.0
29 TraesCS6A01G346000 chr7A 95.690 116 4 1 585 699 188030220 188030335 6.390000e-43 185.0
30 TraesCS6A01G346000 chr7A 91.729 133 11 0 567 699 457210630 457210498 6.390000e-43 185.0
31 TraesCS6A01G346000 chr2D 99.107 112 1 0 588 699 326217473 326217584 6.350000e-48 202.0
32 TraesCS6A01G346000 chrUn 94.615 130 5 2 571 699 94014638 94014510 2.280000e-47 200.0
33 TraesCS6A01G346000 chr4A 96.639 119 2 2 585 703 537443301 537443417 2.950000e-46 196.0
34 TraesCS6A01G346000 chr4A 83.333 84 13 1 3665 3747 608507672 608507589 4.010000e-10 76.8
35 TraesCS6A01G346000 chr5B 80.861 209 36 4 3541 3747 449712257 449712051 1.080000e-35 161.0
36 TraesCS6A01G346000 chr5B 79.500 200 36 5 3550 3747 449715142 449714946 1.820000e-28 137.0
37 TraesCS6A01G346000 chr3B 88.889 108 10 2 1955 2061 126001521 126001415 8.450000e-27 132.0
38 TraesCS6A01G346000 chr3A 88.889 108 10 2 1955 2061 93895168 93895062 8.450000e-27 132.0


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 TraesCS6A01G346000 chr6A 579145163 579148910 3747 True 6922.00 6922 100.0000 1 3748 1 chr6A.!!$R2 3747
1 TraesCS6A01G346000 chr6D 433282695 433288347 5652 True 1133.40 4139 95.7404 52 3748 5 chr6D.!!$R6 3696
2 TraesCS6A01G346000 chr6D 433161622 433164329 2707 True 1131.00 1805 91.7915 1863 3368 2 chr6D.!!$R5 1505
3 TraesCS6A01G346000 chr6B 653881366 653884823 3457 True 1459.00 3731 94.6770 252 3457 3 chr6B.!!$R2 3205
4 TraesCS6A01G346000 chr6B 653220813 653224072 3259 False 1142.25 1794 92.0865 962 3458 4 chr6B.!!$F4 2496

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
37 38 0.390472 GTCTACCACCAGCTGCAGTC 60.390 60.000 16.64 7.83 0.00 3.51 F
39 40 0.390866 CTACCACCAGCTGCAGTCTG 60.391 60.000 23.26 23.26 0.00 3.51 F
43 44 0.740164 CACCAGCTGCAGTCTGCTAG 60.740 60.000 24.76 19.61 45.31 3.42 F
44 45 1.190833 ACCAGCTGCAGTCTGCTAGT 61.191 55.000 24.76 17.07 45.31 2.57 F
45 46 0.740164 CCAGCTGCAGTCTGCTAGTG 60.740 60.000 24.76 17.32 45.31 2.74 F
612 794 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83 F
2679 2901 1.146637 GATAGCAAGCTCATCTGGCG 58.853 55.000 0.00 0.00 46.61 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1565 0.458260 AAGTGGCAAAACAACCGACC 59.542 50.000 0.0 0.0 0.00 4.79 R
1817 2012 2.279517 GTAGATGCGTGGAGGGCG 60.280 66.667 0.0 0.0 0.00 6.13 R
2036 2246 4.460382 CCTGTACAAGTTTGGAGCATCAAT 59.540 41.667 0.0 0.0 36.25 2.57 R
2078 2288 7.630242 AAGAAACATAACATCACATCCGAAT 57.370 32.000 0.0 0.0 0.00 3.34 R
2679 2901 1.797046 CATGTGGCGAGTATCAGATGC 59.203 52.381 0.0 0.0 30.05 3.91 R
2710 2941 0.099259 CTGCGTCGGTATTGTCGGTA 59.901 55.000 0.0 0.0 0.00 4.02 R
3491 5575 0.037697 TGATTTAGCCTGTGCGACGT 60.038 50.000 0.0 0.0 44.33 4.34 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
20 21 1.829849 GGTGGTAACCCAGTAGAGGTC 59.170 57.143 0.00 0.00 42.94 3.85
21 22 2.559252 GGTGGTAACCCAGTAGAGGTCT 60.559 54.545 0.00 0.00 42.94 3.85
22 23 3.309410 GGTGGTAACCCAGTAGAGGTCTA 60.309 52.174 0.00 0.00 42.94 2.59
23 24 3.698539 GTGGTAACCCAGTAGAGGTCTAC 59.301 52.174 8.84 8.84 46.93 2.59
35 36 1.078848 GGTCTACCACCAGCTGCAG 60.079 63.158 10.11 10.11 45.98 4.41
37 38 0.390472 GTCTACCACCAGCTGCAGTC 60.390 60.000 16.64 7.83 0.00 3.51
39 40 0.390866 CTACCACCAGCTGCAGTCTG 60.391 60.000 23.26 23.26 0.00 3.51
40 41 2.454832 TACCACCAGCTGCAGTCTGC 62.455 60.000 24.24 18.32 45.29 4.26
41 42 2.032223 CACCAGCTGCAGTCTGCT 59.968 61.111 24.76 11.66 45.31 4.24
43 44 0.740164 CACCAGCTGCAGTCTGCTAG 60.740 60.000 24.76 19.61 45.31 3.42
44 45 1.190833 ACCAGCTGCAGTCTGCTAGT 61.191 55.000 24.76 17.07 45.31 2.57
45 46 0.740164 CCAGCTGCAGTCTGCTAGTG 60.740 60.000 24.76 17.32 45.31 2.74
88 89 5.173774 TCTCTTGAGTTTGATGTTGTTGC 57.826 39.130 0.00 0.00 0.00 4.17
174 175 4.681074 TCATTGTACTGTGAACCTGTGA 57.319 40.909 0.00 0.00 0.00 3.58
265 444 4.916358 AGCTTTGCTGCTCCTTGT 57.084 50.000 0.00 0.00 39.34 3.16
413 592 4.143333 AGCCGGATCCCGTTGTCG 62.143 66.667 5.05 0.00 46.80 4.35
604 786 9.993454 ATATTAATTTTAGTACTCCCTCCGTTC 57.007 33.333 0.00 0.00 0.00 3.95
605 787 5.750352 AATTTTAGTACTCCCTCCGTTCA 57.250 39.130 0.00 0.00 0.00 3.18
606 788 4.525912 TTTTAGTACTCCCTCCGTTCAC 57.474 45.455 0.00 0.00 0.00 3.18
607 789 3.446442 TTAGTACTCCCTCCGTTCACT 57.554 47.619 0.00 0.00 0.00 3.41
608 790 2.305858 AGTACTCCCTCCGTTCACTT 57.694 50.000 0.00 0.00 0.00 3.16
609 791 2.606378 AGTACTCCCTCCGTTCACTTT 58.394 47.619 0.00 0.00 0.00 2.66
610 792 2.970640 AGTACTCCCTCCGTTCACTTTT 59.029 45.455 0.00 0.00 0.00 2.27
611 793 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
612 794 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
613 795 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
614 796 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
615 797 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
616 798 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
617 799 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
618 800 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
619 801 4.755123 CCTCCGTTCACTTTTGTAAGTCAT 59.245 41.667 0.00 0.00 42.67 3.06
620 802 5.238650 CCTCCGTTCACTTTTGTAAGTCATT 59.761 40.000 0.00 0.00 42.67 2.57
621 803 6.238648 CCTCCGTTCACTTTTGTAAGTCATTT 60.239 38.462 0.00 0.00 42.67 2.32
622 804 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
623 805 6.316640 TCCGTTCACTTTTGTAAGTCATTTCA 59.683 34.615 0.00 0.00 42.67 2.69
624 806 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
625 807 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
626 808 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
627 809 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
628 810 8.275015 TCACTTTTGTAAGTCATTTCAGACAA 57.725 30.769 0.00 0.00 42.67 3.18
629 811 8.181573 TCACTTTTGTAAGTCATTTCAGACAAC 58.818 33.333 0.00 0.00 42.67 3.32
630 812 8.184192 CACTTTTGTAAGTCATTTCAGACAACT 58.816 33.333 0.00 0.00 42.67 3.16
631 813 8.398665 ACTTTTGTAAGTCATTTCAGACAACTC 58.601 33.333 0.00 0.00 40.60 3.01
632 814 7.857734 TTTGTAAGTCATTTCAGACAACTCA 57.142 32.000 0.00 0.00 40.98 3.41
633 815 7.857734 TTGTAAGTCATTTCAGACAACTCAA 57.142 32.000 0.00 0.00 40.98 3.02
634 816 7.857734 TGTAAGTCATTTCAGACAACTCAAA 57.142 32.000 0.00 0.00 40.98 2.69
635 817 8.275015 TGTAAGTCATTTCAGACAACTCAAAA 57.725 30.769 0.00 0.00 40.98 2.44
636 818 8.902806 TGTAAGTCATTTCAGACAACTCAAAAT 58.097 29.630 0.00 0.00 40.98 1.82
637 819 9.173939 GTAAGTCATTTCAGACAACTCAAAATG 57.826 33.333 0.00 0.00 40.98 2.32
638 820 6.742109 AGTCATTTCAGACAACTCAAAATGG 58.258 36.000 0.00 0.00 40.98 3.16
639 821 5.922544 GTCATTTCAGACAACTCAAAATGGG 59.077 40.000 0.00 0.00 37.16 4.00
640 822 4.320608 TTTCAGACAACTCAAAATGGGC 57.679 40.909 0.00 0.00 0.00 5.36
641 823 3.228188 TCAGACAACTCAAAATGGGCT 57.772 42.857 0.00 0.00 0.00 5.19
642 824 2.886523 TCAGACAACTCAAAATGGGCTG 59.113 45.455 0.00 0.00 0.00 4.85
643 825 2.624838 CAGACAACTCAAAATGGGCTGT 59.375 45.455 0.00 0.00 0.00 4.40
644 826 3.068590 CAGACAACTCAAAATGGGCTGTT 59.931 43.478 0.00 0.00 0.00 3.16
645 827 3.706086 AGACAACTCAAAATGGGCTGTTT 59.294 39.130 0.00 0.00 0.00 2.83
646 828 4.162131 AGACAACTCAAAATGGGCTGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
647 829 4.190772 ACAACTCAAAATGGGCTGTTTTG 58.809 39.130 16.38 16.38 44.10 2.44
648 830 4.190772 CAACTCAAAATGGGCTGTTTTGT 58.809 39.130 19.52 6.52 43.52 2.83
649 831 5.105146 ACAACTCAAAATGGGCTGTTTTGTA 60.105 36.000 19.52 10.81 43.52 2.41
650 832 4.944048 ACTCAAAATGGGCTGTTTTGTAC 58.056 39.130 19.52 0.00 43.52 2.90
651 833 4.404073 ACTCAAAATGGGCTGTTTTGTACA 59.596 37.500 19.52 0.00 43.52 2.90
652 834 5.070313 ACTCAAAATGGGCTGTTTTGTACAT 59.930 36.000 19.52 7.99 43.52 2.29
653 835 5.923204 TCAAAATGGGCTGTTTTGTACATT 58.077 33.333 19.52 0.00 43.52 2.71
654 836 5.757320 TCAAAATGGGCTGTTTTGTACATTG 59.243 36.000 19.52 0.00 43.52 2.82
655 837 4.953940 AATGGGCTGTTTTGTACATTGT 57.046 36.364 0.00 0.00 35.85 2.71
656 838 4.519540 ATGGGCTGTTTTGTACATTGTC 57.480 40.909 0.00 0.00 35.85 3.18
657 839 3.561143 TGGGCTGTTTTGTACATTGTCT 58.439 40.909 0.00 0.00 35.85 3.41
658 840 3.317711 TGGGCTGTTTTGTACATTGTCTG 59.682 43.478 0.00 0.00 35.85 3.51
659 841 3.568007 GGGCTGTTTTGTACATTGTCTGA 59.432 43.478 0.00 0.00 35.85 3.27
660 842 4.037446 GGGCTGTTTTGTACATTGTCTGAA 59.963 41.667 0.00 0.00 35.85 3.02
661 843 5.451242 GGGCTGTTTTGTACATTGTCTGAAA 60.451 40.000 0.00 0.00 35.85 2.69
662 844 6.215845 GGCTGTTTTGTACATTGTCTGAAAT 58.784 36.000 0.00 0.00 35.85 2.17
663 845 6.144402 GGCTGTTTTGTACATTGTCTGAAATG 59.856 38.462 0.00 9.50 42.21 2.32
665 847 7.096477 GCTGTTTTGTACATTGTCTGAAATGTC 60.096 37.037 16.13 11.24 45.47 3.06
666 848 7.995289 TGTTTTGTACATTGTCTGAAATGTCT 58.005 30.769 16.13 3.09 45.47 3.41
667 849 8.465999 TGTTTTGTACATTGTCTGAAATGTCTT 58.534 29.630 16.13 2.61 45.47 3.01
668 850 8.958043 GTTTTGTACATTGTCTGAAATGTCTTC 58.042 33.333 16.13 11.26 45.47 2.87
669 851 7.800155 TTGTACATTGTCTGAAATGTCTTCA 57.200 32.000 16.13 12.76 45.47 3.02
670 852 7.800155 TGTACATTGTCTGAAATGTCTTCAA 57.200 32.000 16.13 0.18 45.47 2.69
671 853 7.864686 TGTACATTGTCTGAAATGTCTTCAAG 58.135 34.615 16.13 0.00 45.47 3.02
672 854 6.323203 ACATTGTCTGAAATGTCTTCAAGG 57.677 37.500 10.41 0.00 45.47 3.61
673 855 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
674 856 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
675 857 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
676 858 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
677 859 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
678 860 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
679 861 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
680 862 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
686 868 9.793259 AATGTCTTCAAGGTCTTATAAAAGTGA 57.207 29.630 0.00 0.00 34.13 3.41
687 869 9.793259 ATGTCTTCAAGGTCTTATAAAAGTGAA 57.207 29.630 0.00 0.00 34.13 3.18
688 870 9.052759 TGTCTTCAAGGTCTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 34.13 3.18
689 871 9.052759 GTCTTCAAGGTCTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 34.13 3.18
690 872 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
691 873 9.273016 CTTCAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
692 874 8.833231 TCAAGGTCTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 34.13 3.35
693 875 7.878127 TCAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
694 876 6.712276 AGGTCTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 34.13 4.30
733 915 7.936496 TTCATTATGTTTGAAGATGGTGCTA 57.064 32.000 0.00 0.00 0.00 3.49
777 959 6.874664 TGACACACTAATGCGTTTTTCCTATA 59.125 34.615 0.00 0.00 0.00 1.31
778 960 7.064134 TGACACACTAATGCGTTTTTCCTATAG 59.936 37.037 0.00 0.00 0.00 1.31
989 1171 7.377766 TCAAAATTCAAGGTCATACTGCTAC 57.622 36.000 0.00 0.00 0.00 3.58
1109 1291 4.020218 TGTTGGTAGAGAGAACCATGAAGG 60.020 45.833 0.00 0.00 46.16 3.46
1383 1565 2.494471 TGAGTGGGTCATAGGTTACACG 59.506 50.000 0.00 0.00 34.28 4.49
1817 2012 2.959465 ATGGGAGCTAGTTTATGCCC 57.041 50.000 0.00 0.00 36.11 5.36
2397 2607 2.266055 GGGACTGACAAGGAGCGG 59.734 66.667 0.00 0.00 0.00 5.52
2679 2901 1.146637 GATAGCAAGCTCATCTGGCG 58.853 55.000 0.00 0.00 46.61 5.69
2699 2921 1.797046 GCATCTGATACTCGCCACATG 59.203 52.381 0.00 0.00 0.00 3.21
2710 2941 0.677731 CGCCACATGGACCATTCAGT 60.678 55.000 3.52 0.00 37.39 3.41
2711 2942 1.406751 CGCCACATGGACCATTCAGTA 60.407 52.381 3.52 0.00 37.39 2.74
2712 2943 2.017049 GCCACATGGACCATTCAGTAC 58.983 52.381 3.52 0.00 37.39 2.73
2713 2944 2.643551 CCACATGGACCATTCAGTACC 58.356 52.381 3.52 0.00 37.39 3.34
2714 2945 2.279741 CACATGGACCATTCAGTACCG 58.720 52.381 3.52 0.00 0.00 4.02
2715 2946 2.093711 CACATGGACCATTCAGTACCGA 60.094 50.000 3.52 0.00 0.00 4.69
2716 2947 2.093658 ACATGGACCATTCAGTACCGAC 60.094 50.000 3.52 0.00 0.00 4.79
2717 2948 1.634960 TGGACCATTCAGTACCGACA 58.365 50.000 0.00 0.00 0.00 4.35
2718 2949 1.972075 TGGACCATTCAGTACCGACAA 59.028 47.619 0.00 0.00 0.00 3.18
2907 3142 8.691661 TTTTAATCTTGGAGAAGTTACAGCTT 57.308 30.769 0.00 0.00 0.00 3.74
2965 4419 5.732647 CAGTATTGTTTCTATTTGGCGTTCG 59.267 40.000 0.00 0.00 0.00 3.95
3018 4475 6.318900 GCCCAGGTATATATATGTTGCCTTTC 59.681 42.308 5.44 0.00 0.00 2.62
3169 5119 1.161563 ACACGCACGTAACCTTTGGG 61.162 55.000 0.00 0.00 38.88 4.12
3194 5144 3.051392 GCATGCTGGTGTAACGGCC 62.051 63.158 11.37 0.00 38.12 6.13
3204 5154 1.227060 GTAACGGCCGCGTAGGATT 60.227 57.895 28.58 12.96 45.00 3.01
3223 5173 6.054295 AGGATTGTCTATCAGAAATGAGCAC 58.946 40.000 0.00 0.00 34.77 4.40
3224 5174 5.238214 GGATTGTCTATCAGAAATGAGCACC 59.762 44.000 0.00 0.00 34.77 5.01
3225 5175 4.824479 TGTCTATCAGAAATGAGCACCA 57.176 40.909 0.00 0.00 0.00 4.17
3226 5176 4.763073 TGTCTATCAGAAATGAGCACCAG 58.237 43.478 0.00 0.00 0.00 4.00
3227 5177 4.467438 TGTCTATCAGAAATGAGCACCAGA 59.533 41.667 0.00 0.00 0.00 3.86
3228 5178 4.808364 GTCTATCAGAAATGAGCACCAGAC 59.192 45.833 0.00 0.00 0.00 3.51
3229 5179 3.996921 ATCAGAAATGAGCACCAGACT 57.003 42.857 0.00 0.00 0.00 3.24
3242 5192 1.761784 ACCAGACTCCAGAGATCATGC 59.238 52.381 0.70 0.00 0.00 4.06
3257 5207 4.589798 AGATCATGCTGAGCAGAGTAGATT 59.410 41.667 14.36 0.00 43.65 2.40
3265 5215 1.297664 GCAGAGTAGATTGCTGGCTG 58.702 55.000 0.00 0.00 37.35 4.85
3279 5229 4.329545 GCTGGGGGACTCGCACAA 62.330 66.667 0.00 0.00 34.47 3.33
3284 5234 1.896660 GGGGACTCGCACAAGCAAA 60.897 57.895 0.00 0.00 42.27 3.68
3293 5243 1.255859 CGCACAAGCAAACAACATGTG 59.744 47.619 0.00 0.00 43.17 3.21
3295 5245 3.443037 GCACAAGCAAACAACATGTGTA 58.557 40.909 0.00 0.00 42.48 2.90
3298 5248 5.522456 CACAAGCAAACAACATGTGTAGAT 58.478 37.500 0.00 0.00 40.60 1.98
3299 5249 5.400188 CACAAGCAAACAACATGTGTAGATG 59.600 40.000 0.00 0.00 40.60 2.90
3300 5250 5.067674 ACAAGCAAACAACATGTGTAGATGT 59.932 36.000 0.00 0.00 40.60 3.06
3301 5251 5.772825 AGCAAACAACATGTGTAGATGTT 57.227 34.783 0.00 2.72 45.51 2.71
3421 5489 0.534877 TTGTTCAGCTGTGTGCCGAT 60.535 50.000 14.67 0.00 44.23 4.18
3423 5491 1.270571 TGTTCAGCTGTGTGCCGATTA 60.271 47.619 14.67 0.00 44.23 1.75
3464 5548 4.708421 AGCATACGGAGAGTAAAACCACTA 59.292 41.667 0.00 0.00 39.04 2.74
3465 5549 4.802563 GCATACGGAGAGTAAAACCACTAC 59.197 45.833 0.00 0.00 39.04 2.73
3472 5556 5.695363 GGAGAGTAAAACCACTACTCAACAC 59.305 44.000 11.46 2.20 45.18 3.32
3474 5558 5.365895 AGAGTAAAACCACTACTCAACACCT 59.634 40.000 11.46 0.00 45.18 4.00
3476 5560 2.814280 AACCACTACTCAACACCTCG 57.186 50.000 0.00 0.00 0.00 4.63
3477 5561 1.700955 ACCACTACTCAACACCTCGT 58.299 50.000 0.00 0.00 0.00 4.18
3478 5562 1.340248 ACCACTACTCAACACCTCGTG 59.660 52.381 0.00 0.00 39.75 4.35
3486 5570 3.420943 ACACCTCGTGTTGCTTGC 58.579 55.556 0.00 0.00 45.08 4.01
3487 5571 2.249309 CACCTCGTGTTGCTTGCG 59.751 61.111 0.00 0.00 0.00 4.85
3488 5572 3.649986 ACCTCGTGTTGCTTGCGC 61.650 61.111 0.00 0.00 0.00 6.09
3489 5573 4.389576 CCTCGTGTTGCTTGCGCC 62.390 66.667 4.18 0.00 34.43 6.53
3490 5574 4.724697 CTCGTGTTGCTTGCGCCG 62.725 66.667 4.18 0.00 34.43 6.46
3495 5579 4.719616 GTTGCTTGCGCCGACGTC 62.720 66.667 4.18 5.18 42.83 4.34
3505 5589 4.111016 CCGACGTCGCACAGGCTA 62.111 66.667 31.73 0.00 38.10 3.93
3547 7573 7.512402 TCTGACACCCATATTGATTCCTACATA 59.488 37.037 0.00 0.00 0.00 2.29
3553 7579 6.368791 CCCATATTGATTCCTACATACACACG 59.631 42.308 0.00 0.00 0.00 4.49
3586 7612 2.394708 GAGGAAACCTTCTTTTTGCGC 58.605 47.619 0.00 0.00 31.76 6.09
3597 7623 2.100584 TCTTTTTGCGCACACAATTCCT 59.899 40.909 11.12 0.00 0.00 3.36
3637 7663 2.814336 ACAAAATCCAAGGCGAGACTTC 59.186 45.455 0.00 0.00 0.00 3.01
3648 7674 2.685897 GGCGAGACTTCTGTCAGTATCT 59.314 50.000 0.00 1.69 45.20 1.98
3651 7677 4.560819 GCGAGACTTCTGTCAGTATCTTTG 59.439 45.833 0.00 1.18 45.20 2.77
3657 7683 8.153550 AGACTTCTGTCAGTATCTTTGTGAATT 58.846 33.333 0.00 0.00 45.20 2.17
3689 7715 9.529325 TTTGATCACAATACTAAGTTATCCTCG 57.471 33.333 0.00 0.00 35.85 4.63
3693 7719 9.962783 ATCACAATACTAAGTTATCCTCGTTAC 57.037 33.333 0.00 0.00 0.00 2.50
3712 7738 3.938778 ACGGTTTTGTTCTCGTTTCTC 57.061 42.857 0.00 0.00 31.38 2.87
3718 7744 4.525411 TTTGTTCTCGTTTCTCGTTTCC 57.475 40.909 0.00 0.00 40.80 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.817665 AGACCTCTACTGGGTTACCAC 58.182 52.381 2.98 0.00 43.37 4.16
4 5 3.698539 GTGGTAGACCTCTACTGGGTTAC 59.301 52.174 11.41 0.86 46.06 2.50
5 6 3.309410 GGTGGTAGACCTCTACTGGGTTA 60.309 52.174 11.41 0.00 46.06 2.85
6 7 2.559252 GGTGGTAGACCTCTACTGGGTT 60.559 54.545 11.41 0.00 46.06 4.11
7 8 1.006878 GGTGGTAGACCTCTACTGGGT 59.993 57.143 11.41 0.00 46.06 4.51
8 9 1.006758 TGGTGGTAGACCTCTACTGGG 59.993 57.143 11.41 0.00 46.32 4.45
9 10 2.379972 CTGGTGGTAGACCTCTACTGG 58.620 57.143 11.41 0.00 46.32 4.00
10 11 1.751924 GCTGGTGGTAGACCTCTACTG 59.248 57.143 11.41 1.15 46.32 2.74
11 12 1.641714 AGCTGGTGGTAGACCTCTACT 59.358 52.381 11.41 0.00 46.32 2.57
12 13 1.751924 CAGCTGGTGGTAGACCTCTAC 59.248 57.143 5.57 4.14 46.32 2.59
13 14 1.960471 GCAGCTGGTGGTAGACCTCTA 60.960 57.143 17.12 0.00 46.32 2.43
14 15 1.261238 GCAGCTGGTGGTAGACCTCT 61.261 60.000 17.12 0.00 46.32 3.69
15 16 1.219393 GCAGCTGGTGGTAGACCTC 59.781 63.158 17.12 0.00 46.32 3.85
16 17 1.536418 TGCAGCTGGTGGTAGACCT 60.536 57.895 17.12 0.00 46.32 3.85
18 19 0.390472 GACTGCAGCTGGTGGTAGAC 60.390 60.000 17.12 0.00 0.00 2.59
20 21 0.390866 CAGACTGCAGCTGGTGGTAG 60.391 60.000 22.77 0.04 0.00 3.18
21 22 1.673477 CAGACTGCAGCTGGTGGTA 59.327 57.895 22.77 0.00 0.00 3.25
22 23 2.429058 CAGACTGCAGCTGGTGGT 59.571 61.111 22.77 1.59 0.00 4.16
23 24 3.054503 GCAGACTGCAGCTGGTGG 61.055 66.667 27.90 12.09 44.26 4.61
29 30 7.846707 TAGTAAAGCACTAGCAGACTGCAGC 62.847 48.000 28.43 23.46 41.54 5.25
30 31 4.380973 TAGTAAAGCACTAGCAGACTGCAG 60.381 45.833 28.43 23.06 41.54 4.41
35 36 7.596749 TCAAAATAGTAAAGCACTAGCAGAC 57.403 36.000 0.00 0.00 43.01 3.51
88 89 5.693769 TCCTCAAGGACAAGGTTAATAGG 57.306 43.478 0.00 0.00 39.78 2.57
161 162 2.002586 CGCCTTATCACAGGTTCACAG 58.997 52.381 0.00 0.00 36.15 3.66
163 164 1.338769 ACCGCCTTATCACAGGTTCAC 60.339 52.381 0.00 0.00 36.15 3.18
174 175 4.460263 TCTAATTTGCATCACCGCCTTAT 58.540 39.130 0.00 0.00 0.00 1.73
265 444 3.877559 CATATGGGTGAAGTGAGCAAGA 58.122 45.455 0.00 0.00 0.00 3.02
413 592 6.913873 TGAAGCACGGGTTATAGAAATAAC 57.086 37.500 0.00 0.60 44.55 1.89
546 728 5.830457 TCATATGTATCCGGAATTTTTGCCA 59.170 36.000 9.01 0.00 0.00 4.92
589 771 2.305858 AAGTGAACGGAGGGAGTACT 57.694 50.000 0.00 0.00 0.00 2.73
590 772 3.064931 CAAAAGTGAACGGAGGGAGTAC 58.935 50.000 0.00 0.00 0.00 2.73
591 773 2.701951 ACAAAAGTGAACGGAGGGAGTA 59.298 45.455 0.00 0.00 0.00 2.59
592 774 1.489230 ACAAAAGTGAACGGAGGGAGT 59.511 47.619 0.00 0.00 0.00 3.85
593 775 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
594 776 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
595 777 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
596 778 4.124238 TGACTTACAAAAGTGAACGGAGG 58.876 43.478 0.00 0.00 46.09 4.30
597 779 5.924475 ATGACTTACAAAAGTGAACGGAG 57.076 39.130 0.00 0.00 46.09 4.63
598 780 6.316640 TGAAATGACTTACAAAAGTGAACGGA 59.683 34.615 0.00 0.00 46.09 4.69
599 781 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
600 782 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
601 783 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
602 784 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
603 785 7.857734 TGTCTGAAATGACTTACAAAAGTGA 57.142 32.000 0.00 0.00 46.09 3.41
604 786 8.184192 AGTTGTCTGAAATGACTTACAAAAGTG 58.816 33.333 0.00 0.00 46.09 3.16
606 788 8.397906 TGAGTTGTCTGAAATGACTTACAAAAG 58.602 33.333 0.00 0.00 37.79 2.27
607 789 8.275015 TGAGTTGTCTGAAATGACTTACAAAA 57.725 30.769 0.00 0.00 37.79 2.44
608 790 7.857734 TGAGTTGTCTGAAATGACTTACAAA 57.142 32.000 0.00 0.00 37.79 2.83
609 791 7.857734 TTGAGTTGTCTGAAATGACTTACAA 57.142 32.000 0.00 0.00 37.79 2.41
610 792 7.857734 TTTGAGTTGTCTGAAATGACTTACA 57.142 32.000 0.00 0.00 37.79 2.41
611 793 9.173939 CATTTTGAGTTGTCTGAAATGACTTAC 57.826 33.333 0.00 0.00 38.18 2.34
612 794 8.352201 CCATTTTGAGTTGTCTGAAATGACTTA 58.648 33.333 8.27 0.00 38.18 2.24
613 795 7.205297 CCATTTTGAGTTGTCTGAAATGACTT 58.795 34.615 8.27 0.00 38.18 3.01
614 796 6.239120 CCCATTTTGAGTTGTCTGAAATGACT 60.239 38.462 8.27 0.00 38.18 3.41
615 797 5.922544 CCCATTTTGAGTTGTCTGAAATGAC 59.077 40.000 8.27 0.00 38.18 3.06
616 798 5.509501 GCCCATTTTGAGTTGTCTGAAATGA 60.510 40.000 8.27 0.00 38.18 2.57
617 799 4.687483 GCCCATTTTGAGTTGTCTGAAATG 59.313 41.667 0.00 0.00 37.04 2.32
618 800 4.590222 AGCCCATTTTGAGTTGTCTGAAAT 59.410 37.500 0.00 0.00 0.00 2.17
619 801 3.960102 AGCCCATTTTGAGTTGTCTGAAA 59.040 39.130 0.00 0.00 0.00 2.69
620 802 3.318839 CAGCCCATTTTGAGTTGTCTGAA 59.681 43.478 0.00 0.00 0.00 3.02
621 803 2.886523 CAGCCCATTTTGAGTTGTCTGA 59.113 45.455 0.00 0.00 0.00 3.27
622 804 2.624838 ACAGCCCATTTTGAGTTGTCTG 59.375 45.455 0.00 0.00 0.00 3.51
623 805 2.949447 ACAGCCCATTTTGAGTTGTCT 58.051 42.857 0.00 0.00 0.00 3.41
624 806 3.733443 AACAGCCCATTTTGAGTTGTC 57.267 42.857 0.00 0.00 0.00 3.18
625 807 4.190772 CAAAACAGCCCATTTTGAGTTGT 58.809 39.130 10.61 0.00 45.75 3.32
626 808 4.190772 ACAAAACAGCCCATTTTGAGTTG 58.809 39.130 19.09 6.15 45.75 3.16
627 809 4.486125 ACAAAACAGCCCATTTTGAGTT 57.514 36.364 19.09 0.99 45.75 3.01
628 810 4.404073 TGTACAAAACAGCCCATTTTGAGT 59.596 37.500 19.09 5.72 45.75 3.41
629 811 4.942852 TGTACAAAACAGCCCATTTTGAG 58.057 39.130 19.09 1.00 45.75 3.02
630 812 5.543507 ATGTACAAAACAGCCCATTTTGA 57.456 34.783 19.09 3.50 45.75 2.69
632 814 5.679601 ACAATGTACAAAACAGCCCATTTT 58.320 33.333 0.00 0.00 42.70 1.82
633 815 5.070313 AGACAATGTACAAAACAGCCCATTT 59.930 36.000 0.00 0.00 42.70 2.32
634 816 4.588528 AGACAATGTACAAAACAGCCCATT 59.411 37.500 0.00 0.00 42.70 3.16
635 817 4.022068 CAGACAATGTACAAAACAGCCCAT 60.022 41.667 0.00 0.00 42.70 4.00
636 818 3.317711 CAGACAATGTACAAAACAGCCCA 59.682 43.478 0.00 0.00 42.70 5.36
637 819 3.568007 TCAGACAATGTACAAAACAGCCC 59.432 43.478 0.00 0.00 42.70 5.19
638 820 4.829064 TCAGACAATGTACAAAACAGCC 57.171 40.909 0.00 0.00 42.70 4.85
639 821 6.697019 ACATTTCAGACAATGTACAAAACAGC 59.303 34.615 0.00 0.00 44.08 4.40
640 822 8.131100 AGACATTTCAGACAATGTACAAAACAG 58.869 33.333 0.00 0.00 45.55 3.16
641 823 7.995289 AGACATTTCAGACAATGTACAAAACA 58.005 30.769 0.00 0.00 45.55 2.83
642 824 8.856490 AAGACATTTCAGACAATGTACAAAAC 57.144 30.769 0.00 0.00 45.55 2.43
643 825 8.681806 TGAAGACATTTCAGACAATGTACAAAA 58.318 29.630 0.00 0.00 45.55 2.44
644 826 8.219546 TGAAGACATTTCAGACAATGTACAAA 57.780 30.769 0.00 0.00 45.55 2.83
645 827 7.800155 TGAAGACATTTCAGACAATGTACAA 57.200 32.000 0.00 0.00 45.55 2.41
646 828 7.041167 CCTTGAAGACATTTCAGACAATGTACA 60.041 37.037 0.00 0.00 45.55 2.90
647 829 7.041098 ACCTTGAAGACATTTCAGACAATGTAC 60.041 37.037 9.58 0.00 45.55 2.90
648 830 6.998074 ACCTTGAAGACATTTCAGACAATGTA 59.002 34.615 9.58 0.00 45.55 2.29
650 832 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
651 833 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
652 834 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
653 835 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
654 836 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
660 842 9.793259 TCACTTTTATAAGACCTTGAAGACATT 57.207 29.630 0.00 0.00 35.30 2.71
661 843 9.793259 TTCACTTTTATAAGACCTTGAAGACAT 57.207 29.630 0.00 0.00 35.30 3.06
662 844 9.052759 GTTCACTTTTATAAGACCTTGAAGACA 57.947 33.333 0.00 0.00 35.30 3.41
663 845 9.052759 TGTTCACTTTTATAAGACCTTGAAGAC 57.947 33.333 0.00 0.00 35.30 3.01
664 846 9.273016 CTGTTCACTTTTATAAGACCTTGAAGA 57.727 33.333 0.00 0.00 35.30 2.87
665 847 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
666 848 9.273016 CTCTGTTCACTTTTATAAGACCTTGAA 57.727 33.333 0.00 0.00 35.30 2.69
667 849 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
668 850 7.119846 CCCTCTGTTCACTTTTATAAGACCTTG 59.880 40.741 0.00 0.00 35.30 3.61
669 851 7.017254 TCCCTCTGTTCACTTTTATAAGACCTT 59.983 37.037 0.00 0.00 35.30 3.50
670 852 6.500751 TCCCTCTGTTCACTTTTATAAGACCT 59.499 38.462 0.00 0.00 35.30 3.85
671 853 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
672 854 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
673 855 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
674 856 7.492994 GCTACTCCCTCTGTTCACTTTTATAAG 59.507 40.741 0.00 0.00 37.40 1.73
675 857 7.180408 AGCTACTCCCTCTGTTCACTTTTATAA 59.820 37.037 0.00 0.00 0.00 0.98
676 858 6.668283 AGCTACTCCCTCTGTTCACTTTTATA 59.332 38.462 0.00 0.00 0.00 0.98
677 859 5.485708 AGCTACTCCCTCTGTTCACTTTTAT 59.514 40.000 0.00 0.00 0.00 1.40
678 860 4.838986 AGCTACTCCCTCTGTTCACTTTTA 59.161 41.667 0.00 0.00 0.00 1.52
679 861 3.648545 AGCTACTCCCTCTGTTCACTTTT 59.351 43.478 0.00 0.00 0.00 2.27
680 862 3.243724 AGCTACTCCCTCTGTTCACTTT 58.756 45.455 0.00 0.00 0.00 2.66
681 863 2.896039 AGCTACTCCCTCTGTTCACTT 58.104 47.619 0.00 0.00 0.00 3.16
682 864 2.614134 AGCTACTCCCTCTGTTCACT 57.386 50.000 0.00 0.00 0.00 3.41
683 865 5.112686 CAATAAGCTACTCCCTCTGTTCAC 58.887 45.833 0.00 0.00 0.00 3.18
684 866 4.162320 CCAATAAGCTACTCCCTCTGTTCA 59.838 45.833 0.00 0.00 0.00 3.18
685 867 4.162509 ACCAATAAGCTACTCCCTCTGTTC 59.837 45.833 0.00 0.00 0.00 3.18
686 868 4.104831 ACCAATAAGCTACTCCCTCTGTT 58.895 43.478 0.00 0.00 0.00 3.16
687 869 3.725634 ACCAATAAGCTACTCCCTCTGT 58.274 45.455 0.00 0.00 0.00 3.41
688 870 4.762289 AACCAATAAGCTACTCCCTCTG 57.238 45.455 0.00 0.00 0.00 3.35
689 871 4.783227 TGAAACCAATAAGCTACTCCCTCT 59.217 41.667 0.00 0.00 0.00 3.69
690 872 5.099042 TGAAACCAATAAGCTACTCCCTC 57.901 43.478 0.00 0.00 0.00 4.30
691 873 5.717119 ATGAAACCAATAAGCTACTCCCT 57.283 39.130 0.00 0.00 0.00 4.20
692 874 7.502561 ACATAATGAAACCAATAAGCTACTCCC 59.497 37.037 0.00 0.00 0.00 4.30
693 875 8.451908 ACATAATGAAACCAATAAGCTACTCC 57.548 34.615 0.00 0.00 0.00 3.85
733 915 2.360483 TCACCATTTGCACACACGAAAT 59.640 40.909 0.00 0.00 0.00 2.17
989 1171 3.244976 GTTTGTTCCATTCCAGATTGCG 58.755 45.455 0.00 0.00 0.00 4.85
1109 1291 2.576615 GCCTATCCACAGGATTCAACC 58.423 52.381 3.55 0.00 39.79 3.77
1383 1565 0.458260 AAGTGGCAAAACAACCGACC 59.542 50.000 0.00 0.00 0.00 4.79
1817 2012 2.279517 GTAGATGCGTGGAGGGCG 60.280 66.667 0.00 0.00 0.00 6.13
1857 2067 8.778059 ACCCATCCATAACAGAAAAGAACTATA 58.222 33.333 0.00 0.00 0.00 1.31
1866 2076 7.659799 CGTATTATGACCCATCCATAACAGAAA 59.340 37.037 0.00 0.00 38.74 2.52
2036 2246 4.460382 CCTGTACAAGTTTGGAGCATCAAT 59.540 41.667 0.00 0.00 36.25 2.57
2078 2288 7.630242 AAGAAACATAACATCACATCCGAAT 57.370 32.000 0.00 0.00 0.00 3.34
2679 2901 1.797046 CATGTGGCGAGTATCAGATGC 59.203 52.381 0.00 0.00 30.05 3.91
2699 2921 2.754946 TTGTCGGTACTGAATGGTCC 57.245 50.000 5.82 0.00 0.00 4.46
2710 2941 0.099259 CTGCGTCGGTATTGTCGGTA 59.901 55.000 0.00 0.00 0.00 4.02
2711 2942 1.153901 CTGCGTCGGTATTGTCGGT 60.154 57.895 0.00 0.00 0.00 4.69
2712 2943 1.876714 CCTGCGTCGGTATTGTCGG 60.877 63.158 0.00 0.00 0.00 4.79
2713 2944 0.866061 CTCCTGCGTCGGTATTGTCG 60.866 60.000 0.00 0.00 0.00 4.35
2714 2945 0.454600 TCTCCTGCGTCGGTATTGTC 59.545 55.000 0.00 0.00 0.00 3.18
2715 2946 1.112113 ATCTCCTGCGTCGGTATTGT 58.888 50.000 0.00 0.00 0.00 2.71
2716 2947 1.860950 CAATCTCCTGCGTCGGTATTG 59.139 52.381 0.00 0.00 0.00 1.90
2717 2948 1.754803 TCAATCTCCTGCGTCGGTATT 59.245 47.619 0.00 0.00 0.00 1.89
2718 2949 1.399714 TCAATCTCCTGCGTCGGTAT 58.600 50.000 0.00 0.00 0.00 2.73
2907 3142 2.866156 CAAGAGTGTTGACAGCGAGAAA 59.134 45.455 0.00 0.00 0.00 2.52
2965 4419 0.247460 GCATTTCCCCAAGTTCAGCC 59.753 55.000 0.00 0.00 0.00 4.85
3018 4475 0.179084 CATAGGCCGTACCACAGTGG 60.179 60.000 18.93 18.93 45.02 4.00
3129 4849 1.210931 CAACCCAGCAATCACGCAG 59.789 57.895 0.00 0.00 0.00 5.18
3169 5119 1.097232 TACACCAGCATGCAAGATGC 58.903 50.000 21.98 1.66 45.29 3.91
3194 5144 3.898517 TCTGATAGACAATCCTACGCG 57.101 47.619 3.53 3.53 33.22 6.01
3204 5154 4.467438 TCTGGTGCTCATTTCTGATAGACA 59.533 41.667 0.00 0.00 0.00 3.41
3223 5173 2.040939 AGCATGATCTCTGGAGTCTGG 58.959 52.381 0.00 0.00 0.00 3.86
3224 5174 2.694109 TCAGCATGATCTCTGGAGTCTG 59.306 50.000 0.00 0.00 42.56 3.51
3225 5175 3.029483 TCAGCATGATCTCTGGAGTCT 57.971 47.619 0.00 0.00 42.56 3.24
3242 5192 2.823984 CCAGCAATCTACTCTGCTCAG 58.176 52.381 0.00 0.00 45.79 3.35
3265 5215 3.842925 TTGCTTGTGCGAGTCCCCC 62.843 63.158 0.00 0.00 43.34 5.40
3279 5229 5.772825 AACATCTACACATGTTGTTTGCT 57.227 34.783 6.97 0.00 43.88 3.91
3374 5377 4.091509 GCAACGACAGTATTTCCTGTAGTG 59.908 45.833 7.64 4.58 46.32 2.74
3421 5489 5.979993 TGCTGAGTACCCGTGAATTTATAA 58.020 37.500 0.00 0.00 0.00 0.98
3423 5491 4.481368 TGCTGAGTACCCGTGAATTTAT 57.519 40.909 0.00 0.00 0.00 1.40
3488 5572 3.620300 TTAGCCTGTGCGACGTCGG 62.620 63.158 36.13 21.44 44.33 4.79
3489 5573 1.076533 ATTTAGCCTGTGCGACGTCG 61.077 55.000 32.57 32.57 44.33 5.12
3490 5574 0.645868 GATTTAGCCTGTGCGACGTC 59.354 55.000 5.18 5.18 44.33 4.34
3491 5575 0.037697 TGATTTAGCCTGTGCGACGT 60.038 50.000 0.00 0.00 44.33 4.34
3493 5577 3.871594 ACTATTGATTTAGCCTGTGCGAC 59.128 43.478 0.00 0.00 44.33 5.19
3494 5578 3.871006 CACTATTGATTTAGCCTGTGCGA 59.129 43.478 0.00 0.00 44.33 5.10
3495 5579 3.623060 ACACTATTGATTTAGCCTGTGCG 59.377 43.478 0.00 0.00 44.33 5.34
3496 5580 4.635765 TCACACTATTGATTTAGCCTGTGC 59.364 41.667 0.00 0.00 31.33 4.57
3497 5581 6.932356 ATCACACTATTGATTTAGCCTGTG 57.068 37.500 0.00 0.00 31.87 3.66
3499 5583 7.496920 TCAGAATCACACTATTGATTTAGCCTG 59.503 37.037 0.15 3.72 44.59 4.85
3501 5585 7.280876 TGTCAGAATCACACTATTGATTTAGCC 59.719 37.037 0.15 0.00 44.59 3.93
3503 5587 8.607459 GGTGTCAGAATCACACTATTGATTTAG 58.393 37.037 4.27 0.00 44.59 1.85
3504 5588 7.552687 GGGTGTCAGAATCACACTATTGATTTA 59.447 37.037 4.27 0.00 44.59 1.40
3505 5589 6.375455 GGGTGTCAGAATCACACTATTGATTT 59.625 38.462 4.27 0.00 44.59 2.17
3547 7573 8.975439 GTTTCCTCGATAAATATATTCGTGTGT 58.025 33.333 0.00 0.00 0.00 3.72
3580 7606 2.593346 AAAGGAATTGTGTGCGCAAA 57.407 40.000 14.00 2.45 31.63 3.68
3586 7612 5.291178 TCATGAAGCAAAAGGAATTGTGTG 58.709 37.500 0.00 0.00 32.80 3.82
3623 7649 0.318441 TGACAGAAGTCTCGCCTTGG 59.682 55.000 0.00 0.00 45.20 3.61
3689 7715 5.147767 AGAAACGAGAACAAAACCGTAAC 57.852 39.130 0.00 0.00 34.60 2.50
3693 7719 2.283351 ACGAGAAACGAGAACAAAACCG 59.717 45.455 0.00 0.00 45.77 4.44
3718 7744 4.215613 TGATCACGAGGATACAAGGATACG 59.784 45.833 0.00 0.00 37.95 3.06


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

AutoCloner maintained by Alex Coulton.