Multiple sequence alignment - TraesCS6D01G282000

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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 TraesCS6D01G282000 chr6D 100.000 3180 0 0 1 3180 389599466 389596287 0.000000e+00 5873.0
1 TraesCS6D01G282000 chr6A 92.961 1520 65 26 800 2295 535991829 535990328 0.000000e+00 2176.0
2 TraesCS6D01G282000 chr6A 89.567 393 25 8 2293 2672 535990286 535989897 4.770000e-133 484.0
3 TraesCS6D01G282000 chr6A 89.726 292 29 1 2806 3097 535989763 535989473 3.870000e-99 372.0
4 TraesCS6D01G282000 chr6B 89.130 1150 64 38 864 1985 583052477 583051361 0.000000e+00 1375.0
5 TraesCS6D01G282000 chr6B 90.096 626 60 2 175 800 508533461 508532838 0.000000e+00 811.0
6 TraesCS6D01G282000 chr6B 92.063 315 18 4 1984 2294 583051202 583050891 1.350000e-118 436.0
7 TraesCS6D01G282000 chr6B 86.800 250 20 5 2388 2631 583050773 583050531 1.880000e-67 267.0
8 TraesCS6D01G282000 chr6B 88.889 90 10 0 1 90 583052628 583052539 9.320000e-21 111.0
9 TraesCS6D01G282000 chr7D 92.473 651 47 2 150 800 133886907 133887555 0.000000e+00 929.0
10 TraesCS6D01G282000 chr7D 91.250 640 55 1 163 801 251355465 251354826 0.000000e+00 870.0
11 TraesCS6D01G282000 chr7D 86.433 656 84 5 149 800 136414265 136414919 0.000000e+00 713.0
12 TraesCS6D01G282000 chr7A 90.967 631 56 1 169 799 393325121 393325750 0.000000e+00 848.0
13 TraesCS6D01G282000 chr4D 90.741 594 49 4 208 801 421546002 421546589 0.000000e+00 787.0
14 TraesCS6D01G282000 chr4D 87.635 647 75 3 152 798 51845548 51844907 0.000000e+00 747.0
15 TraesCS6D01G282000 chr4A 88.308 650 76 0 151 800 688766267 688766916 0.000000e+00 780.0
16 TraesCS6D01G282000 chr1B 87.309 654 75 3 150 798 678869139 678868489 0.000000e+00 741.0
17 TraesCS6D01G282000 chr5D 89.796 49 4 1 3 51 8011165 8011118 9.520000e-06 62.1
18 TraesCS6D01G282000 chr1D 88.889 45 5 0 2 46 24095240 24095196 4.430000e-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 TraesCS6D01G282000 chr6D 389596287 389599466 3179 True 5873.000000 5873 100.000000 1 3180 1 chr6D.!!$R1 3179
1 TraesCS6D01G282000 chr6A 535989473 535991829 2356 True 1010.666667 2176 90.751333 800 3097 3 chr6A.!!$R1 2297
2 TraesCS6D01G282000 chr6B 508532838 508533461 623 True 811.000000 811 90.096000 175 800 1 chr6B.!!$R1 625
3 TraesCS6D01G282000 chr6B 583050531 583052628 2097 True 547.250000 1375 89.220500 1 2631 4 chr6B.!!$R2 2630
4 TraesCS6D01G282000 chr7D 133886907 133887555 648 False 929.000000 929 92.473000 150 800 1 chr7D.!!$F1 650
5 TraesCS6D01G282000 chr7D 251354826 251355465 639 True 870.000000 870 91.250000 163 801 1 chr7D.!!$R1 638
6 TraesCS6D01G282000 chr7D 136414265 136414919 654 False 713.000000 713 86.433000 149 800 1 chr7D.!!$F2 651
7 TraesCS6D01G282000 chr7A 393325121 393325750 629 False 848.000000 848 90.967000 169 799 1 chr7A.!!$F1 630
8 TraesCS6D01G282000 chr4D 421546002 421546589 587 False 787.000000 787 90.741000 208 801 1 chr4D.!!$F1 593
9 TraesCS6D01G282000 chr4D 51844907 51845548 641 True 747.000000 747 87.635000 152 798 1 chr4D.!!$R1 646
10 TraesCS6D01G282000 chr4A 688766267 688766916 649 False 780.000000 780 88.308000 151 800 1 chr4A.!!$F1 649
11 TraesCS6D01G282000 chr1B 678868489 678869139 650 True 741.000000 741 87.309000 150 798 1 chr1B.!!$R1 648

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
699 708 1.154016 CAGTGCCTGTAGTCGTCGG 60.154 63.158 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2621 0.108804 TTCGCCGCCTGAAGAACTAG 60.109 55.0 0.0 0.0 0.0 2.57 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
44 45 7.932491 TCCACAAATGTCATTTCATCACAAAAT 59.068 29.630 7.87 0.00 0.00 1.82
506 513 3.089982 GTCGTTCGTCTACATTCGTCTC 58.910 50.000 0.00 0.00 0.00 3.36
542 549 3.311871 TCCTTTCGATCTACGCTACACTC 59.688 47.826 0.00 0.00 42.26 3.51
570 577 1.993369 GCGGTTGCTATTCTGGTGCC 61.993 60.000 0.00 0.00 38.39 5.01
661 670 3.838271 GGAGAGGCGACGATGGCA 61.838 66.667 0.00 0.00 36.77 4.92
687 696 4.742201 TCGGCTCGCTTCAGTGCC 62.742 66.667 0.00 0.00 44.68 5.01
699 708 1.154016 CAGTGCCTGTAGTCGTCGG 60.154 63.158 0.00 0.00 0.00 4.79
701 710 1.443872 GTGCCTGTAGTCGTCGGTG 60.444 63.158 0.00 0.00 0.00 4.94
727 736 6.015688 GGTGGTCTACGAATCTGGATGTAATA 60.016 42.308 0.00 0.00 0.00 0.98
728 737 7.431249 GTGGTCTACGAATCTGGATGTAATAA 58.569 38.462 0.00 0.00 0.00 1.40
828 838 2.358957 CATGTGAGCTCGGGATCAAAA 58.641 47.619 3.99 0.00 39.68 2.44
830 840 3.071874 TGTGAGCTCGGGATCAAAAAT 57.928 42.857 3.99 0.00 39.68 1.82
831 841 2.749076 TGTGAGCTCGGGATCAAAAATG 59.251 45.455 3.99 0.00 39.68 2.32
832 842 1.745087 TGAGCTCGGGATCAAAAATGC 59.255 47.619 0.00 0.00 34.74 3.56
833 843 2.019984 GAGCTCGGGATCAAAAATGCT 58.980 47.619 0.00 0.00 0.00 3.79
877 893 9.663904 TTTTGAATGAATAAAGAACTCTGTTCG 57.336 29.630 5.02 0.00 0.00 3.95
893 909 6.320418 ACTCTGTTCGGGTAAAAGAAAAACAT 59.680 34.615 0.00 0.00 0.00 2.71
908 924 3.923017 AAACATTTTTCGAGAGCCCAG 57.077 42.857 0.00 0.00 0.00 4.45
932 948 3.950794 CTAGGCGCGGCAAACCAGA 62.951 63.158 34.94 9.20 34.57 3.86
933 949 3.950794 TAGGCGCGGCAAACCAGAG 62.951 63.158 34.94 0.00 34.57 3.35
952 968 2.351823 TCGCGTAAAACGACCATCG 58.648 52.632 5.77 0.00 46.05 3.84
1122 1139 4.717629 TGCAACTCCTCGGCGTCG 62.718 66.667 1.15 1.15 37.82 5.12
1431 1477 1.222936 CCCTGCTGGCTTCACCTAG 59.777 63.158 3.63 0.00 40.22 3.02
1432 1478 1.267574 CCCTGCTGGCTTCACCTAGA 61.268 60.000 3.63 0.00 40.22 2.43
1433 1479 0.835941 CCTGCTGGCTTCACCTAGAT 59.164 55.000 0.00 0.00 40.22 1.98
1434 1480 1.474677 CCTGCTGGCTTCACCTAGATG 60.475 57.143 0.00 0.00 40.22 2.90
1515 1561 2.601067 TACACGGCGAGGTTCCCA 60.601 61.111 16.62 0.00 0.00 4.37
1615 1665 2.703416 TCGCTCACTGAAAGATGCAAT 58.297 42.857 0.00 0.00 37.43 3.56
1616 1666 2.417586 TCGCTCACTGAAAGATGCAATG 59.582 45.455 0.00 0.00 37.43 2.82
1617 1667 2.527100 GCTCACTGAAAGATGCAATGC 58.473 47.619 0.00 0.00 37.43 3.56
1618 1668 2.163815 GCTCACTGAAAGATGCAATGCT 59.836 45.455 6.82 0.00 37.43 3.79
1619 1669 3.367087 GCTCACTGAAAGATGCAATGCTT 60.367 43.478 6.82 0.00 37.43 3.91
1638 1694 3.216800 CTTATTATTGCAGCCAGGCAGA 58.783 45.455 15.80 0.00 45.88 4.26
1639 1695 1.688772 ATTATTGCAGCCAGGCAGAG 58.311 50.000 15.80 4.00 45.88 3.35
1640 1696 0.329261 TTATTGCAGCCAGGCAGAGT 59.671 50.000 15.80 0.00 45.88 3.24
1641 1697 0.329261 TATTGCAGCCAGGCAGAGTT 59.671 50.000 15.80 0.00 45.88 3.01
1642 1698 0.541296 ATTGCAGCCAGGCAGAGTTT 60.541 50.000 15.80 0.00 45.88 2.66
1643 1699 0.756442 TTGCAGCCAGGCAGAGTTTT 60.756 50.000 15.80 0.00 45.88 2.43
1644 1700 1.174712 TGCAGCCAGGCAGAGTTTTC 61.175 55.000 15.80 0.00 39.25 2.29
1647 1703 1.268899 CAGCCAGGCAGAGTTTTCTTG 59.731 52.381 15.80 0.00 0.00 3.02
1671 1731 1.741770 GTGTGTGATCGTCTGGGCC 60.742 63.158 0.00 0.00 0.00 5.80
1690 1750 3.506455 GGCCTAAACCCTTCTGTCTTTTC 59.494 47.826 0.00 0.00 0.00 2.29
1704 1764 5.771666 TCTGTCTTTTCTCCATTTGCAGATT 59.228 36.000 0.00 0.00 0.00 2.40
1792 1852 2.770802 AGACTTCAGCAGCCATCTGTAT 59.229 45.455 0.00 0.00 42.29 2.29
1831 1891 6.640907 GCATTTCGTTCCAAACAAACTCTTAT 59.359 34.615 0.00 0.00 0.00 1.73
1834 1894 6.539649 TCGTTCCAAACAAACTCTTATCTG 57.460 37.500 0.00 0.00 0.00 2.90
1838 1898 7.700656 CGTTCCAAACAAACTCTTATCTGTTTT 59.299 33.333 0.00 0.00 39.37 2.43
1839 1899 9.020813 GTTCCAAACAAACTCTTATCTGTTTTC 57.979 33.333 0.00 0.00 39.37 2.29
1840 1900 8.519799 TCCAAACAAACTCTTATCTGTTTTCT 57.480 30.769 0.00 0.00 39.37 2.52
1841 1901 8.405531 TCCAAACAAACTCTTATCTGTTTTCTG 58.594 33.333 0.00 0.00 39.37 3.02
1843 1903 9.787532 CAAACAAACTCTTATCTGTTTTCTGAA 57.212 29.630 0.00 0.00 39.37 3.02
1844 1904 9.788960 AAACAAACTCTTATCTGTTTTCTGAAC 57.211 29.630 0.00 0.00 38.51 3.18
1845 1905 8.738645 ACAAACTCTTATCTGTTTTCTGAACT 57.261 30.769 0.00 0.00 34.60 3.01
1846 1906 8.616076 ACAAACTCTTATCTGTTTTCTGAACTG 58.384 33.333 0.00 0.00 34.60 3.16
1847 1907 6.793492 ACTCTTATCTGTTTTCTGAACTGC 57.207 37.500 0.00 0.00 0.00 4.40
1909 1969 3.136443 TGATGATACCTCCGATTTTGGCT 59.864 43.478 0.00 0.00 0.00 4.75
1952 2016 2.708861 TGCTTCTCAGGTACCAAAAGGA 59.291 45.455 15.94 9.82 0.00 3.36
1994 2220 6.829849 TGAGGAAATGTACTATGATGCATCA 58.170 36.000 30.47 30.47 41.70 3.07
2001 2227 4.350520 TGTACTATGATGCATCAATCCCCA 59.649 41.667 31.79 21.58 40.69 4.96
2006 2232 0.105862 ATGCATCAATCCCCACCTGG 60.106 55.000 0.00 0.00 0.00 4.45
2055 2281 2.306847 GACTTGGCTTGTTTTCTCCCA 58.693 47.619 0.00 0.00 0.00 4.37
2089 2315 3.154710 CCCATGCATGCATATTCAGACT 58.845 45.455 31.73 5.79 34.91 3.24
2158 2384 5.311265 TCCACGATACTATACGACATCCTT 58.689 41.667 0.00 0.00 0.00 3.36
2201 2427 1.226575 TCTGACGGCAGCGAATACG 60.227 57.895 15.33 0.00 42.01 3.06
2202 2428 1.516386 CTGACGGCAGCGAATACGT 60.516 57.895 4.70 0.00 42.88 3.57
2203 2429 3.296584 GACGGCAGCGAATACGTC 58.703 61.111 5.54 5.54 46.89 4.34
2204 2430 2.202703 ACGGCAGCGAATACGTCC 60.203 61.111 0.00 0.00 41.98 4.79
2205 2431 2.202690 CGGCAGCGAATACGTCCA 60.203 61.111 0.00 0.00 41.98 4.02
2206 2432 2.514013 CGGCAGCGAATACGTCCAC 61.514 63.158 0.00 0.00 41.98 4.02
2240 2470 5.681695 GCATAGGTCCAGTACAAGGTAGAAC 60.682 48.000 0.00 0.00 0.00 3.01
2257 2487 2.363359 AGAACCCTTTTTCTTGCAGCAG 59.637 45.455 0.00 0.00 31.39 4.24
2338 2621 3.425492 GGCAGACGAAGAGAAAGATTTGC 60.425 47.826 0.00 0.00 0.00 3.68
2351 2643 5.414144 AGAAAGATTTGCTAGTTCTTCAGGC 59.586 40.000 0.00 0.00 0.00 4.85
2369 2661 2.598632 CGGCGAAATCGGATGCTCC 61.599 63.158 0.00 0.00 40.23 4.70
2374 2666 2.325393 GAAATCGGATGCTCCCCGGT 62.325 60.000 0.00 2.59 46.47 5.28
2572 2870 2.435059 GCTTGACTCGGTGAGGGC 60.435 66.667 0.00 0.00 33.35 5.19
2573 2871 2.266055 CTTGACTCGGTGAGGGCC 59.734 66.667 0.00 0.00 33.35 5.80
2631 2929 0.798776 GTCGCACCCTCTTGTTGATG 59.201 55.000 0.00 0.00 0.00 3.07
2637 2935 3.119708 GCACCCTCTTGTTGATGACATTC 60.120 47.826 0.00 0.00 38.26 2.67
2662 2960 5.782893 TTGTCAGGGGTTCTTGTTATTTG 57.217 39.130 0.00 0.00 0.00 2.32
2664 2962 4.149598 GTCAGGGGTTCTTGTTATTTGGT 58.850 43.478 0.00 0.00 0.00 3.67
2684 3016 4.141344 TGGTTTACAGCCTGGAGTTTAGTT 60.141 41.667 0.00 0.00 0.00 2.24
2686 3018 4.967084 TTACAGCCTGGAGTTTAGTTGA 57.033 40.909 0.00 0.00 0.00 3.18
2692 3024 4.580580 AGCCTGGAGTTTAGTTGACTTTTG 59.419 41.667 0.00 0.00 0.00 2.44
2705 3037 2.306847 GACTTTTGTCCCTCCAAGCAA 58.693 47.619 0.00 0.00 43.37 3.91
2706 3038 2.693074 GACTTTTGTCCCTCCAAGCAAA 59.307 45.455 0.00 0.00 43.37 3.68
2713 3045 2.629656 CCTCCAAGCAAAGGCCGTG 61.630 63.158 0.00 0.04 42.56 4.94
2714 3046 1.898574 CTCCAAGCAAAGGCCGTGT 60.899 57.895 10.70 0.00 42.56 4.49
2730 3062 2.480416 CCGTGTCTGAGAACTAGATGCC 60.480 54.545 0.00 0.00 0.00 4.40
2741 3073 4.716784 AGAACTAGATGCCCAGTTATGACA 59.283 41.667 0.00 0.00 35.17 3.58
2742 3074 5.189736 AGAACTAGATGCCCAGTTATGACAA 59.810 40.000 0.00 0.00 35.17 3.18
2743 3075 5.435686 ACTAGATGCCCAGTTATGACAAA 57.564 39.130 0.00 0.00 0.00 2.83
2777 3109 3.893720 GAGCATCTTCAACCACACTTTG 58.106 45.455 0.00 0.00 0.00 2.77
2778 3110 3.554934 AGCATCTTCAACCACACTTTGA 58.445 40.909 0.00 0.00 0.00 2.69
2779 3111 3.316308 AGCATCTTCAACCACACTTTGAC 59.684 43.478 0.00 0.00 32.65 3.18
2780 3112 3.316308 GCATCTTCAACCACACTTTGACT 59.684 43.478 0.00 0.00 32.65 3.41
2781 3113 4.515191 GCATCTTCAACCACACTTTGACTA 59.485 41.667 0.00 0.00 32.65 2.59
2782 3114 5.008613 GCATCTTCAACCACACTTTGACTAA 59.991 40.000 0.00 0.00 32.65 2.24
2783 3115 6.294176 GCATCTTCAACCACACTTTGACTAAT 60.294 38.462 0.00 0.00 32.65 1.73
2784 3116 7.651808 CATCTTCAACCACACTTTGACTAATT 58.348 34.615 0.00 0.00 32.65 1.40
2785 3117 7.259290 TCTTCAACCACACTTTGACTAATTC 57.741 36.000 0.00 0.00 32.65 2.17
2786 3118 5.666969 TCAACCACACTTTGACTAATTCG 57.333 39.130 0.00 0.00 0.00 3.34
2787 3119 4.513692 TCAACCACACTTTGACTAATTCGG 59.486 41.667 0.00 0.00 0.00 4.30
2788 3120 4.081322 ACCACACTTTGACTAATTCGGT 57.919 40.909 0.00 0.00 0.00 4.69
2789 3121 4.062991 ACCACACTTTGACTAATTCGGTC 58.937 43.478 4.99 4.99 0.00 4.79
2790 3122 3.435671 CCACACTTTGACTAATTCGGTCC 59.564 47.826 8.41 0.00 33.22 4.46
2791 3123 4.062293 CACACTTTGACTAATTCGGTCCA 58.938 43.478 8.41 0.00 33.22 4.02
2792 3124 4.695455 CACACTTTGACTAATTCGGTCCAT 59.305 41.667 8.41 0.00 33.22 3.41
2793 3125 5.181245 CACACTTTGACTAATTCGGTCCATT 59.819 40.000 8.41 0.00 33.22 3.16
2794 3126 6.370442 CACACTTTGACTAATTCGGTCCATTA 59.630 38.462 8.41 0.00 33.22 1.90
2795 3127 7.065803 CACACTTTGACTAATTCGGTCCATTAT 59.934 37.037 8.41 0.00 33.22 1.28
2796 3128 8.262227 ACACTTTGACTAATTCGGTCCATTATA 58.738 33.333 8.41 0.00 33.22 0.98
2797 3129 9.273016 CACTTTGACTAATTCGGTCCATTATAT 57.727 33.333 8.41 0.00 33.22 0.86
2798 3130 9.273016 ACTTTGACTAATTCGGTCCATTATATG 57.727 33.333 8.41 0.00 33.22 1.78
2799 3131 9.273016 CTTTGACTAATTCGGTCCATTATATGT 57.727 33.333 8.41 0.00 33.22 2.29
2800 3132 8.827177 TTGACTAATTCGGTCCATTATATGTC 57.173 34.615 8.41 0.00 33.22 3.06
2801 3133 7.383687 TGACTAATTCGGTCCATTATATGTCC 58.616 38.462 8.41 0.00 33.22 4.02
2802 3134 7.015779 TGACTAATTCGGTCCATTATATGTCCA 59.984 37.037 8.41 0.00 33.22 4.02
2803 3135 7.159372 ACTAATTCGGTCCATTATATGTCCAC 58.841 38.462 0.00 0.00 0.00 4.02
2804 3136 3.653539 TCGGTCCATTATATGTCCACG 57.346 47.619 0.00 0.00 0.00 4.94
2820 3152 1.014044 CACGGACATGTTCGGGACAG 61.014 60.000 29.26 10.55 42.62 3.51
2827 3159 3.119096 GTTCGGGACAGAAGCCGC 61.119 66.667 0.00 0.00 0.00 6.53
2837 3169 3.706373 GAAGCCGCCTGTCTCCCA 61.706 66.667 0.00 0.00 0.00 4.37
2848 3180 2.648059 CTGTCTCCCATTTGTCCATCC 58.352 52.381 0.00 0.00 0.00 3.51
2858 3190 0.605319 TTGTCCATCCGAGCAACCAC 60.605 55.000 0.00 0.00 0.00 4.16
2859 3191 1.003839 GTCCATCCGAGCAACCACA 60.004 57.895 0.00 0.00 0.00 4.17
2869 3201 1.454847 GCAACCACACCCCTCACAA 60.455 57.895 0.00 0.00 0.00 3.33
2875 3207 1.613437 CCACACCCCTCACAATGAAAC 59.387 52.381 0.00 0.00 0.00 2.78
2876 3208 2.586425 CACACCCCTCACAATGAAACT 58.414 47.619 0.00 0.00 0.00 2.66
2893 3225 9.132521 CAATGAAACTCTCAAATCCATACAAAC 57.867 33.333 0.00 0.00 37.67 2.93
2906 3238 3.309682 CCATACAAACTCATGCACGTAGG 59.690 47.826 0.00 0.00 0.00 3.18
2908 3240 2.846193 ACAAACTCATGCACGTAGGTT 58.154 42.857 0.00 0.00 0.00 3.50
2912 3244 5.472137 ACAAACTCATGCACGTAGGTTATTT 59.528 36.000 0.00 0.00 0.00 1.40
2913 3245 5.796350 AACTCATGCACGTAGGTTATTTC 57.204 39.130 0.00 0.00 0.00 2.17
2916 3248 5.581085 ACTCATGCACGTAGGTTATTTCTTC 59.419 40.000 0.00 0.00 0.00 2.87
3006 3338 5.527951 GCTACACAAATGAATGAAACACCA 58.472 37.500 0.00 0.00 0.00 4.17
3023 3355 2.558359 CACCATTGGTTTCCTCCTTGAC 59.442 50.000 5.34 0.00 31.02 3.18
3024 3356 2.171003 CCATTGGTTTCCTCCTTGACC 58.829 52.381 0.00 0.00 0.00 4.02
3071 3403 7.227711 TCACTTCTTGATTTTGTTATCCACGAA 59.772 33.333 0.00 0.00 0.00 3.85
3080 3412 4.119442 TGTTATCCACGAACCTAGCTTC 57.881 45.455 0.00 0.00 0.00 3.86
3097 3429 2.224161 GCTTCGGCTAACATGATCCTCT 60.224 50.000 0.00 0.00 38.08 3.69
3098 3430 3.742640 GCTTCGGCTAACATGATCCTCTT 60.743 47.826 0.00 0.00 38.08 2.85
3099 3431 4.446371 CTTCGGCTAACATGATCCTCTTT 58.554 43.478 0.00 0.00 0.00 2.52
3100 3432 4.487714 TCGGCTAACATGATCCTCTTTT 57.512 40.909 0.00 0.00 0.00 2.27
3101 3433 4.843728 TCGGCTAACATGATCCTCTTTTT 58.156 39.130 0.00 0.00 0.00 1.94
3124 3456 8.648698 TTTTTGTCATTTATCCATCTTCTCCA 57.351 30.769 0.00 0.00 0.00 3.86
3125 3457 8.827832 TTTTGTCATTTATCCATCTTCTCCAT 57.172 30.769 0.00 0.00 0.00 3.41
3126 3458 7.812690 TTGTCATTTATCCATCTTCTCCATG 57.187 36.000 0.00 0.00 0.00 3.66
3127 3459 6.903516 TGTCATTTATCCATCTTCTCCATGT 58.096 36.000 0.00 0.00 0.00 3.21
3128 3460 6.994496 TGTCATTTATCCATCTTCTCCATGTC 59.006 38.462 0.00 0.00 0.00 3.06
3129 3461 7.147426 TGTCATTTATCCATCTTCTCCATGTCT 60.147 37.037 0.00 0.00 0.00 3.41
3130 3462 8.370940 GTCATTTATCCATCTTCTCCATGTCTA 58.629 37.037 0.00 0.00 0.00 2.59
3131 3463 9.109246 TCATTTATCCATCTTCTCCATGTCTAT 57.891 33.333 0.00 0.00 0.00 1.98
3132 3464 9.381033 CATTTATCCATCTTCTCCATGTCTATC 57.619 37.037 0.00 0.00 0.00 2.08
3133 3465 8.496534 TTTATCCATCTTCTCCATGTCTATCA 57.503 34.615 0.00 0.00 0.00 2.15
3134 3466 8.676397 TTATCCATCTTCTCCATGTCTATCAT 57.324 34.615 0.00 0.00 37.22 2.45
3135 3467 6.602410 TCCATCTTCTCCATGTCTATCATC 57.398 41.667 0.00 0.00 34.09 2.92
3136 3468 5.483231 TCCATCTTCTCCATGTCTATCATCC 59.517 44.000 0.00 0.00 34.09 3.51
3137 3469 5.338219 CCATCTTCTCCATGTCTATCATCCC 60.338 48.000 0.00 0.00 34.09 3.85
3138 3470 4.163427 TCTTCTCCATGTCTATCATCCCC 58.837 47.826 0.00 0.00 34.09 4.81
3139 3471 2.907892 TCTCCATGTCTATCATCCCCC 58.092 52.381 0.00 0.00 34.09 5.40
3140 3472 2.456340 TCTCCATGTCTATCATCCCCCT 59.544 50.000 0.00 0.00 34.09 4.79
3141 3473 2.836981 CTCCATGTCTATCATCCCCCTC 59.163 54.545 0.00 0.00 34.09 4.30
3142 3474 2.456340 TCCATGTCTATCATCCCCCTCT 59.544 50.000 0.00 0.00 34.09 3.69
3143 3475 2.836981 CCATGTCTATCATCCCCCTCTC 59.163 54.545 0.00 0.00 34.09 3.20
3144 3476 3.514539 CATGTCTATCATCCCCCTCTCA 58.485 50.000 0.00 0.00 34.09 3.27
3145 3477 3.706389 TGTCTATCATCCCCCTCTCAA 57.294 47.619 0.00 0.00 0.00 3.02
3146 3478 4.219392 TGTCTATCATCCCCCTCTCAAT 57.781 45.455 0.00 0.00 0.00 2.57
3147 3479 3.906218 TGTCTATCATCCCCCTCTCAATG 59.094 47.826 0.00 0.00 0.00 2.82
3148 3480 3.262915 GTCTATCATCCCCCTCTCAATGG 59.737 52.174 0.00 0.00 0.00 3.16
3149 3481 0.776176 ATCATCCCCCTCTCAATGGC 59.224 55.000 0.00 0.00 0.00 4.40
3150 3482 0.624206 TCATCCCCCTCTCAATGGCA 60.624 55.000 0.00 0.00 0.00 4.92
3151 3483 0.481567 CATCCCCCTCTCAATGGCAT 59.518 55.000 0.00 0.00 0.00 4.40
3152 3484 0.776176 ATCCCCCTCTCAATGGCATC 59.224 55.000 0.00 0.00 0.00 3.91
3153 3485 1.152368 CCCCCTCTCAATGGCATCC 59.848 63.158 0.00 0.00 0.00 3.51
3154 3486 1.358830 CCCCCTCTCAATGGCATCCT 61.359 60.000 0.00 0.00 0.00 3.24
3155 3487 0.110104 CCCCTCTCAATGGCATCCTC 59.890 60.000 0.00 0.00 0.00 3.71
3156 3488 0.110104 CCCTCTCAATGGCATCCTCC 59.890 60.000 0.00 0.00 0.00 4.30
3157 3489 0.110104 CCTCTCAATGGCATCCTCCC 59.890 60.000 0.00 0.00 0.00 4.30
3158 3490 1.138568 CTCTCAATGGCATCCTCCCT 58.861 55.000 0.00 0.00 0.00 4.20
3159 3491 1.072015 CTCTCAATGGCATCCTCCCTC 59.928 57.143 0.00 0.00 0.00 4.30
3160 3492 0.250209 CTCAATGGCATCCTCCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
3161 3493 0.690744 TCAATGGCATCCTCCCTCGA 60.691 55.000 0.00 0.00 0.00 4.04
3162 3494 0.399454 CAATGGCATCCTCCCTCGAT 59.601 55.000 0.00 0.00 0.00 3.59
3163 3495 0.689623 AATGGCATCCTCCCTCGATC 59.310 55.000 0.00 0.00 0.00 3.69
3164 3496 1.539560 ATGGCATCCTCCCTCGATCG 61.540 60.000 9.36 9.36 0.00 3.69
3165 3497 1.903890 GGCATCCTCCCTCGATCGA 60.904 63.158 18.32 18.32 0.00 3.59
3166 3498 1.464376 GGCATCCTCCCTCGATCGAA 61.464 60.000 19.92 3.02 0.00 3.71
3167 3499 0.319125 GCATCCTCCCTCGATCGAAC 60.319 60.000 19.92 0.00 0.00 3.95
3168 3500 1.323412 CATCCTCCCTCGATCGAACT 58.677 55.000 19.92 0.00 0.00 3.01
3169 3501 1.000827 CATCCTCCCTCGATCGAACTG 60.001 57.143 19.92 10.27 0.00 3.16
3170 3502 1.066587 CCTCCCTCGATCGAACTGC 59.933 63.158 19.92 0.00 0.00 4.40
3171 3503 1.667154 CCTCCCTCGATCGAACTGCA 61.667 60.000 19.92 0.76 0.00 4.41
3172 3504 0.387202 CTCCCTCGATCGAACTGCAT 59.613 55.000 19.92 0.00 0.00 3.96
3173 3505 0.385751 TCCCTCGATCGAACTGCATC 59.614 55.000 19.92 0.00 0.00 3.91
3174 3506 0.598680 CCCTCGATCGAACTGCATCC 60.599 60.000 19.92 0.00 0.00 3.51
3175 3507 0.387202 CCTCGATCGAACTGCATCCT 59.613 55.000 19.92 0.00 0.00 3.24
3176 3508 1.601663 CCTCGATCGAACTGCATCCTC 60.602 57.143 19.92 0.00 0.00 3.71
3177 3509 1.336440 CTCGATCGAACTGCATCCTCT 59.664 52.381 19.92 0.00 0.00 3.69
3178 3510 1.335182 TCGATCGAACTGCATCCTCTC 59.665 52.381 16.99 0.00 0.00 3.20
3179 3511 1.601663 CGATCGAACTGCATCCTCTCC 60.602 57.143 10.26 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.056607 ACATTTGTGGAAGCCTATGCAAC 60.057 43.478 0.00 0.00 41.13 4.17
11 12 5.716228 TGAAATGACATTTGTGGAAGCCTAT 59.284 36.000 18.00 0.00 31.47 2.57
15 16 5.346822 GTGATGAAATGACATTTGTGGAAGC 59.653 40.000 18.00 2.75 27.82 3.86
122 123 9.462174 CACATGCTCTTTGATAAACAGTAAAAA 57.538 29.630 0.00 0.00 0.00 1.94
129 130 3.193267 GGCCACATGCTCTTTGATAAACA 59.807 43.478 0.00 0.00 40.92 2.83
135 136 0.322816 GGAGGCCACATGCTCTTTGA 60.323 55.000 5.01 0.00 40.92 2.69
290 292 8.926715 ACAAAACTCAAAGAACCATCTAAAAC 57.073 30.769 0.00 0.00 33.77 2.43
448 455 4.039730 CAGATCCACCAAAGATAGATCCGT 59.960 45.833 0.00 0.00 35.08 4.69
506 513 4.072131 TCGAAAGGATCCAACCTGAAAAG 58.928 43.478 15.82 0.00 40.49 2.27
687 696 1.211969 CACCCACCGACGACTACAG 59.788 63.158 0.00 0.00 0.00 2.74
699 708 1.134788 CCAGATTCGTAGACCACCCAC 60.135 57.143 0.00 0.00 34.32 4.61
701 710 1.481871 TCCAGATTCGTAGACCACCC 58.518 55.000 0.00 0.00 34.32 4.61
814 824 2.019984 GAGCATTTTTGATCCCGAGCT 58.980 47.619 0.00 0.00 0.00 4.09
828 838 1.368641 TTTGCGATACAGCGAGCATT 58.631 45.000 0.00 0.00 39.50 3.56
830 840 1.062440 CATTTTGCGATACAGCGAGCA 59.938 47.619 0.00 0.00 40.67 4.26
831 841 1.062587 ACATTTTGCGATACAGCGAGC 59.937 47.619 0.00 0.00 40.67 5.03
832 842 3.389687 AACATTTTGCGATACAGCGAG 57.610 42.857 0.00 0.00 40.67 5.03
833 843 3.822594 AAACATTTTGCGATACAGCGA 57.177 38.095 0.00 0.00 40.67 4.93
893 909 1.671054 CCGCTGGGCTCTCGAAAAA 60.671 57.895 0.41 0.00 0.00 1.94
1414 1460 0.835941 ATCTAGGTGAAGCCAGCAGG 59.164 55.000 0.00 0.00 42.91 4.85
1431 1477 4.669700 TGAAATCCATCCATCCATCCATC 58.330 43.478 0.00 0.00 0.00 3.51
1432 1478 4.752621 TGAAATCCATCCATCCATCCAT 57.247 40.909 0.00 0.00 0.00 3.41
1433 1479 4.079038 ACTTGAAATCCATCCATCCATCCA 60.079 41.667 0.00 0.00 0.00 3.41
1434 1480 4.477249 ACTTGAAATCCATCCATCCATCC 58.523 43.478 0.00 0.00 0.00 3.51
1515 1561 2.595463 TCGAACACCGTCCCGTCT 60.595 61.111 0.00 0.00 39.75 4.18
1524 1570 0.319555 TGTAGCTGCTGTCGAACACC 60.320 55.000 13.43 0.00 0.00 4.16
1615 1665 1.682854 GCCTGGCTGCAATAATAAGCA 59.317 47.619 12.43 0.00 38.73 3.91
1616 1666 1.682854 TGCCTGGCTGCAATAATAAGC 59.317 47.619 21.03 0.00 38.56 3.09
1617 1667 3.216800 TCTGCCTGGCTGCAATAATAAG 58.783 45.455 21.03 4.60 41.51 1.73
1618 1668 3.216800 CTCTGCCTGGCTGCAATAATAA 58.783 45.455 21.03 0.00 41.51 1.40
1619 1669 2.173356 ACTCTGCCTGGCTGCAATAATA 59.827 45.455 21.03 0.52 41.51 0.98
1630 1686 2.485814 GCTACAAGAAAACTCTGCCTGG 59.514 50.000 0.00 0.00 0.00 4.45
1638 1694 4.513442 TCACACACTGCTACAAGAAAACT 58.487 39.130 0.00 0.00 0.00 2.66
1639 1695 4.875544 TCACACACTGCTACAAGAAAAC 57.124 40.909 0.00 0.00 0.00 2.43
1640 1696 4.211164 CGATCACACACTGCTACAAGAAAA 59.789 41.667 0.00 0.00 0.00 2.29
1641 1697 3.740832 CGATCACACACTGCTACAAGAAA 59.259 43.478 0.00 0.00 0.00 2.52
1642 1698 3.243737 ACGATCACACACTGCTACAAGAA 60.244 43.478 0.00 0.00 0.00 2.52
1643 1699 2.296190 ACGATCACACACTGCTACAAGA 59.704 45.455 0.00 0.00 0.00 3.02
1644 1700 2.663602 GACGATCACACACTGCTACAAG 59.336 50.000 0.00 0.00 0.00 3.16
1647 1703 2.254459 CAGACGATCACACACTGCTAC 58.746 52.381 0.00 0.00 0.00 3.58
1671 1731 5.621193 TGGAGAAAAGACAGAAGGGTTTAG 58.379 41.667 0.00 0.00 0.00 1.85
1685 1745 5.648572 GGAGAATCTGCAAATGGAGAAAAG 58.351 41.667 8.73 0.00 45.49 2.27
1690 1750 2.871022 CTCGGAGAATCTGCAAATGGAG 59.129 50.000 0.00 0.00 42.67 3.86
1704 1764 1.544825 CCTGTTGAAGCCCTCGGAGA 61.545 60.000 6.58 0.00 0.00 3.71
1792 1852 3.874543 ACGAAATGCCGATGCTTGTAATA 59.125 39.130 0.00 0.00 38.71 0.98
1831 1891 2.899976 TCACGCAGTTCAGAAAACAGA 58.100 42.857 0.00 0.00 41.61 3.41
1834 1894 3.248602 AGACATCACGCAGTTCAGAAAAC 59.751 43.478 0.00 0.00 41.61 2.43
1838 1898 2.035832 TCAAGACATCACGCAGTTCAGA 59.964 45.455 0.00 0.00 41.61 3.27
1839 1899 2.407090 TCAAGACATCACGCAGTTCAG 58.593 47.619 0.00 0.00 41.61 3.02
1840 1900 2.524569 TCAAGACATCACGCAGTTCA 57.475 45.000 0.00 0.00 41.61 3.18
1841 1901 3.248602 AGTTTCAAGACATCACGCAGTTC 59.751 43.478 0.00 0.00 41.61 3.01
1844 1904 2.663879 GCAGTTTCAAGACATCACGCAG 60.664 50.000 0.00 0.00 0.00 5.18
1845 1905 1.264020 GCAGTTTCAAGACATCACGCA 59.736 47.619 0.00 0.00 0.00 5.24
1846 1906 1.532868 AGCAGTTTCAAGACATCACGC 59.467 47.619 0.00 0.00 0.00 5.34
1847 1907 4.211164 TGTTAGCAGTTTCAAGACATCACG 59.789 41.667 0.00 0.00 0.00 4.35
1909 1969 2.162338 CTGCTGGTTCGGGTCCGTAA 62.162 60.000 9.36 0.34 40.74 3.18
1952 2016 7.712204 TTCCTCAACTGAAAACTAGGTTTTT 57.288 32.000 7.31 0.00 44.33 1.94
1994 2220 1.077265 CAGTTGCCAGGTGGGGATT 59.923 57.895 0.00 0.00 36.59 3.01
2001 2227 3.605749 ATACGCGCAGTTGCCAGGT 62.606 57.895 5.73 0.00 37.91 4.00
2006 2232 2.576847 GCCAATACGCGCAGTTGC 60.577 61.111 5.73 0.00 37.78 4.17
2055 2281 0.465824 GCATGGGCTGAGCTTCTCAT 60.466 55.000 3.72 1.02 39.92 2.90
2062 2288 1.176619 TATGCATGCATGGGCTGAGC 61.177 55.000 37.43 12.10 41.91 4.26
2089 2315 6.455647 CCCTGTCAACGATTGATATAAGCTA 58.544 40.000 0.00 0.00 42.47 3.32
2158 2384 1.132453 CACTTGTAGATGCCGACGAGA 59.868 52.381 0.00 0.00 34.62 4.04
2201 2427 2.012673 CTATGCTCAAGGCTTGTGGAC 58.987 52.381 25.39 14.07 42.39 4.02
2202 2428 1.065199 CCTATGCTCAAGGCTTGTGGA 60.065 52.381 25.39 23.89 42.39 4.02
2203 2429 1.340405 ACCTATGCTCAAGGCTTGTGG 60.340 52.381 25.39 19.41 42.39 4.17
2204 2430 2.012673 GACCTATGCTCAAGGCTTGTG 58.987 52.381 25.39 23.42 42.39 3.33
2205 2431 1.065126 GGACCTATGCTCAAGGCTTGT 60.065 52.381 25.39 10.01 42.39 3.16
2206 2432 1.065199 TGGACCTATGCTCAAGGCTTG 60.065 52.381 21.17 21.17 42.39 4.01
2240 2470 0.677842 AGCTGCTGCAAGAAAAAGGG 59.322 50.000 18.42 0.00 42.74 3.95
2257 2487 2.079925 ACGAGCATGGAGAAGAAAAGC 58.920 47.619 0.00 0.00 0.00 3.51
2295 2525 1.562783 GCCTGTAGTTCAGTCTCCCT 58.437 55.000 0.00 0.00 42.19 4.20
2300 2581 1.448013 GCCCGCCTGTAGTTCAGTC 60.448 63.158 0.00 0.00 42.19 3.51
2338 2621 0.108804 TTCGCCGCCTGAAGAACTAG 60.109 55.000 0.00 0.00 0.00 2.57
2351 2643 2.931386 GAGCATCCGATTTCGCCG 59.069 61.111 0.00 0.00 38.18 6.46
2572 2870 4.394712 GAGCTGTGTCACCCCCGG 62.395 72.222 0.00 0.00 0.00 5.73
2573 2871 3.625897 TGAGCTGTGTCACCCCCG 61.626 66.667 0.00 0.00 0.00 5.73
2574 2872 2.032681 GTGAGCTGTGTCACCCCC 59.967 66.667 0.00 0.00 40.96 5.40
2576 2874 0.814010 AAACGTGAGCTGTGTCACCC 60.814 55.000 0.00 0.00 43.45 4.61
2577 2875 1.860676 TAAACGTGAGCTGTGTCACC 58.139 50.000 0.00 0.00 43.45 4.02
2578 2876 3.057019 TCATAAACGTGAGCTGTGTCAC 58.943 45.455 0.00 0.00 43.01 3.67
2579 2877 3.057019 GTCATAAACGTGAGCTGTGTCA 58.943 45.455 0.00 0.00 0.00 3.58
2580 2878 2.090658 CGTCATAAACGTGAGCTGTGTC 59.909 50.000 0.00 0.00 46.42 3.67
2581 2879 2.058798 CGTCATAAACGTGAGCTGTGT 58.941 47.619 0.00 0.00 46.42 3.72
2601 2899 4.077188 GTGCGACCGCTTCTGCAC 62.077 66.667 15.61 12.60 42.94 4.57
2637 2935 6.405278 AATAACAAGAACCCCTGACAAAAG 57.595 37.500 0.00 0.00 0.00 2.27
2650 2948 6.239176 CCAGGCTGTAAACCAAATAACAAGAA 60.239 38.462 14.43 0.00 0.00 2.52
2651 2949 5.242838 CCAGGCTGTAAACCAAATAACAAGA 59.757 40.000 14.43 0.00 0.00 3.02
2662 2960 4.017177 ACTAAACTCCAGGCTGTAAACC 57.983 45.455 14.43 0.00 0.00 3.27
2664 2962 5.061179 GTCAACTAAACTCCAGGCTGTAAA 58.939 41.667 14.43 0.00 0.00 2.01
2684 3016 1.214175 TGCTTGGAGGGACAAAAGTCA 59.786 47.619 0.00 0.00 0.00 3.41
2686 3018 2.452600 TTGCTTGGAGGGACAAAAGT 57.547 45.000 0.00 0.00 0.00 2.66
2692 3024 1.979155 GGCCTTTGCTTGGAGGGAC 60.979 63.158 0.00 0.00 37.74 4.46
2703 3035 0.868406 GTTCTCAGACACGGCCTTTG 59.132 55.000 0.00 0.00 0.00 2.77
2705 3037 1.546476 CTAGTTCTCAGACACGGCCTT 59.454 52.381 0.00 0.00 0.00 4.35
2706 3038 1.178276 CTAGTTCTCAGACACGGCCT 58.822 55.000 0.00 0.00 0.00 5.19
2713 3045 2.763448 ACTGGGCATCTAGTTCTCAGAC 59.237 50.000 12.91 0.00 30.03 3.51
2714 3046 3.107402 ACTGGGCATCTAGTTCTCAGA 57.893 47.619 12.91 0.00 30.03 3.27
2730 3062 9.831737 CTAGAAAAGAACATTTGTCATAACTGG 57.168 33.333 0.00 0.00 0.00 4.00
2741 3073 8.627208 TGAAGATGCTCTAGAAAAGAACATTT 57.373 30.769 0.00 0.00 40.38 2.32
2742 3074 8.510505 GTTGAAGATGCTCTAGAAAAGAACATT 58.489 33.333 0.00 0.00 40.38 2.71
2743 3075 7.120432 GGTTGAAGATGCTCTAGAAAAGAACAT 59.880 37.037 0.00 0.00 42.47 2.71
2771 3103 5.880054 AATGGACCGAATTAGTCAAAGTG 57.120 39.130 9.61 0.00 35.89 3.16
2772 3104 9.273016 CATATAATGGACCGAATTAGTCAAAGT 57.727 33.333 9.61 1.22 35.89 2.66
2773 3105 9.273016 ACATATAATGGACCGAATTAGTCAAAG 57.727 33.333 9.61 0.00 35.89 2.77
2774 3106 9.268268 GACATATAATGGACCGAATTAGTCAAA 57.732 33.333 9.61 0.00 35.89 2.69
2775 3107 7.876068 GGACATATAATGGACCGAATTAGTCAA 59.124 37.037 9.61 0.00 35.89 3.18
2776 3108 7.015779 TGGACATATAATGGACCGAATTAGTCA 59.984 37.037 9.61 0.00 35.89 3.41
2777 3109 7.331193 GTGGACATATAATGGACCGAATTAGTC 59.669 40.741 0.38 0.38 34.94 2.59
2778 3110 7.159372 GTGGACATATAATGGACCGAATTAGT 58.841 38.462 0.00 0.00 34.94 2.24
2779 3111 6.310467 CGTGGACATATAATGGACCGAATTAG 59.690 42.308 0.00 0.00 34.94 1.73
2780 3112 6.160684 CGTGGACATATAATGGACCGAATTA 58.839 40.000 0.00 0.00 34.94 1.40
2781 3113 4.994852 CGTGGACATATAATGGACCGAATT 59.005 41.667 0.00 0.00 34.94 2.17
2782 3114 4.562757 CCGTGGACATATAATGGACCGAAT 60.563 45.833 0.00 0.00 34.94 3.34
2783 3115 3.243941 CCGTGGACATATAATGGACCGAA 60.244 47.826 0.00 0.00 34.94 4.30
2784 3116 2.297880 CCGTGGACATATAATGGACCGA 59.702 50.000 0.00 0.00 34.94 4.69
2785 3117 2.297880 TCCGTGGACATATAATGGACCG 59.702 50.000 0.00 0.00 34.94 4.79
2786 3118 3.660865 GTCCGTGGACATATAATGGACC 58.339 50.000 14.10 0.00 42.01 4.46
2798 3130 1.740296 CCCGAACATGTCCGTGGAC 60.740 63.158 12.17 12.17 44.77 4.02
2799 3131 1.909287 TCCCGAACATGTCCGTGGA 60.909 57.895 9.92 9.92 0.00 4.02
2800 3132 1.740296 GTCCCGAACATGTCCGTGG 60.740 63.158 3.13 4.68 0.00 4.94
2801 3133 1.005512 TGTCCCGAACATGTCCGTG 60.006 57.895 3.13 0.00 31.20 4.94
2802 3134 1.183030 TCTGTCCCGAACATGTCCGT 61.183 55.000 3.13 0.00 37.23 4.69
2803 3135 0.037697 TTCTGTCCCGAACATGTCCG 60.038 55.000 0.00 0.00 37.23 4.79
2804 3136 1.726853 CTTCTGTCCCGAACATGTCC 58.273 55.000 0.00 0.00 37.23 4.02
2820 3152 2.543067 AATGGGAGACAGGCGGCTTC 62.543 60.000 9.66 10.83 0.00 3.86
2827 3159 2.648059 GATGGACAAATGGGAGACAGG 58.352 52.381 0.00 0.00 0.00 4.00
2833 3165 0.107214 GCTCGGATGGACAAATGGGA 60.107 55.000 0.00 0.00 0.00 4.37
2837 3169 1.271871 TGGTTGCTCGGATGGACAAAT 60.272 47.619 0.00 0.00 0.00 2.32
2848 3180 2.358737 GAGGGGTGTGGTTGCTCG 60.359 66.667 0.00 0.00 0.00 5.03
2858 3190 3.077359 GAGAGTTTCATTGTGAGGGGTG 58.923 50.000 0.00 0.00 0.00 4.61
2859 3191 2.711009 TGAGAGTTTCATTGTGAGGGGT 59.289 45.455 0.00 0.00 0.00 4.95
2869 3201 8.641498 AGTTTGTATGGATTTGAGAGTTTCAT 57.359 30.769 0.00 0.00 35.27 2.57
2875 3207 6.094464 TGCATGAGTTTGTATGGATTTGAGAG 59.906 38.462 0.00 0.00 0.00 3.20
2876 3208 5.945191 TGCATGAGTTTGTATGGATTTGAGA 59.055 36.000 0.00 0.00 0.00 3.27
2893 3225 5.580691 TGAAGAAATAACCTACGTGCATGAG 59.419 40.000 14.17 5.70 0.00 2.90
2964 3296 1.588674 CGCCCCGCTTATGTATGAAA 58.411 50.000 0.00 0.00 0.00 2.69
3006 3338 3.399305 AGAAGGTCAAGGAGGAAACCAAT 59.601 43.478 0.00 0.00 34.09 3.16
3014 3346 5.810095 ACAAATAGAAGAAGGTCAAGGAGG 58.190 41.667 0.00 0.00 0.00 4.30
3099 3431 8.648698 TGGAGAAGATGGATAAATGACAAAAA 57.351 30.769 0.00 0.00 0.00 1.94
3100 3432 8.689061 CATGGAGAAGATGGATAAATGACAAAA 58.311 33.333 0.00 0.00 0.00 2.44
3101 3433 7.835682 ACATGGAGAAGATGGATAAATGACAAA 59.164 33.333 0.00 0.00 0.00 2.83
3102 3434 7.348815 ACATGGAGAAGATGGATAAATGACAA 58.651 34.615 0.00 0.00 0.00 3.18
3103 3435 6.903516 ACATGGAGAAGATGGATAAATGACA 58.096 36.000 0.00 0.00 0.00 3.58
3104 3436 7.222872 AGACATGGAGAAGATGGATAAATGAC 58.777 38.462 0.00 0.00 0.00 3.06
3105 3437 7.384524 AGACATGGAGAAGATGGATAAATGA 57.615 36.000 0.00 0.00 0.00 2.57
3106 3438 9.381033 GATAGACATGGAGAAGATGGATAAATG 57.619 37.037 0.00 0.00 0.00 2.32
3107 3439 9.109246 TGATAGACATGGAGAAGATGGATAAAT 57.891 33.333 0.00 0.00 0.00 1.40
3108 3440 8.496534 TGATAGACATGGAGAAGATGGATAAA 57.503 34.615 0.00 0.00 0.00 1.40
3109 3441 8.676397 ATGATAGACATGGAGAAGATGGATAA 57.324 34.615 0.00 0.00 37.87 1.75
3110 3442 7.344093 GGATGATAGACATGGAGAAGATGGATA 59.656 40.741 0.00 0.00 39.56 2.59
3111 3443 6.156602 GGATGATAGACATGGAGAAGATGGAT 59.843 42.308 0.00 0.00 39.56 3.41
3112 3444 5.483231 GGATGATAGACATGGAGAAGATGGA 59.517 44.000 0.00 0.00 39.56 3.41
3113 3445 5.338219 GGGATGATAGACATGGAGAAGATGG 60.338 48.000 0.00 0.00 39.56 3.51
3114 3446 5.338219 GGGGATGATAGACATGGAGAAGATG 60.338 48.000 0.00 0.00 39.56 2.90
3115 3447 4.782156 GGGGATGATAGACATGGAGAAGAT 59.218 45.833 0.00 0.00 39.56 2.40
3116 3448 4.163427 GGGGATGATAGACATGGAGAAGA 58.837 47.826 0.00 0.00 39.56 2.87
3117 3449 3.262915 GGGGGATGATAGACATGGAGAAG 59.737 52.174 0.00 0.00 39.56 2.85
3118 3450 3.116199 AGGGGGATGATAGACATGGAGAA 60.116 47.826 0.00 0.00 39.56 2.87
3119 3451 2.456340 AGGGGGATGATAGACATGGAGA 59.544 50.000 0.00 0.00 39.56 3.71
3120 3452 2.836981 GAGGGGGATGATAGACATGGAG 59.163 54.545 0.00 0.00 39.56 3.86
3121 3453 2.456340 AGAGGGGGATGATAGACATGGA 59.544 50.000 0.00 0.00 39.56 3.41
3122 3454 2.836981 GAGAGGGGGATGATAGACATGG 59.163 54.545 0.00 0.00 39.56 3.66
3123 3455 3.514539 TGAGAGGGGGATGATAGACATG 58.485 50.000 0.00 0.00 39.56 3.21
3124 3456 3.931241 TGAGAGGGGGATGATAGACAT 57.069 47.619 0.00 0.00 42.47 3.06
3125 3457 3.706389 TTGAGAGGGGGATGATAGACA 57.294 47.619 0.00 0.00 0.00 3.41
3126 3458 3.262915 CCATTGAGAGGGGGATGATAGAC 59.737 52.174 0.00 0.00 0.00 2.59
3127 3459 3.524826 CCATTGAGAGGGGGATGATAGA 58.475 50.000 0.00 0.00 0.00 1.98
3128 3460 2.026449 GCCATTGAGAGGGGGATGATAG 60.026 54.545 0.00 0.00 0.00 2.08
3129 3461 1.988107 GCCATTGAGAGGGGGATGATA 59.012 52.381 0.00 0.00 0.00 2.15
3130 3462 0.776176 GCCATTGAGAGGGGGATGAT 59.224 55.000 0.00 0.00 0.00 2.45
3131 3463 0.624206 TGCCATTGAGAGGGGGATGA 60.624 55.000 0.00 0.00 0.00 2.92
3132 3464 0.481567 ATGCCATTGAGAGGGGGATG 59.518 55.000 0.00 0.00 30.98 3.51
3133 3465 0.776176 GATGCCATTGAGAGGGGGAT 59.224 55.000 0.00 0.00 35.26 3.85
3134 3466 1.355718 GGATGCCATTGAGAGGGGGA 61.356 60.000 0.00 0.00 0.00 4.81
3135 3467 1.152368 GGATGCCATTGAGAGGGGG 59.848 63.158 0.00 0.00 0.00 5.40
3136 3468 0.110104 GAGGATGCCATTGAGAGGGG 59.890 60.000 0.00 0.00 0.00 4.79
3137 3469 0.110104 GGAGGATGCCATTGAGAGGG 59.890 60.000 0.00 0.00 0.00 4.30
3138 3470 3.721793 GGAGGATGCCATTGAGAGG 57.278 57.895 0.00 0.00 0.00 3.69
3148 3480 0.319125 GTTCGATCGAGGGAGGATGC 60.319 60.000 18.54 0.00 0.00 3.91
3149 3481 1.000827 CAGTTCGATCGAGGGAGGATG 60.001 57.143 18.54 6.84 0.00 3.51
3150 3482 1.323412 CAGTTCGATCGAGGGAGGAT 58.677 55.000 18.54 0.00 0.00 3.24
3151 3483 1.384989 GCAGTTCGATCGAGGGAGGA 61.385 60.000 18.54 0.00 0.00 3.71
3152 3484 1.066587 GCAGTTCGATCGAGGGAGG 59.933 63.158 18.54 8.67 0.00 4.30
3153 3485 0.387202 ATGCAGTTCGATCGAGGGAG 59.613 55.000 18.54 10.71 0.00 4.30
3154 3486 0.385751 GATGCAGTTCGATCGAGGGA 59.614 55.000 18.54 13.28 0.00 4.20
3155 3487 0.598680 GGATGCAGTTCGATCGAGGG 60.599 60.000 18.54 12.46 0.00 4.30
3156 3488 0.387202 AGGATGCAGTTCGATCGAGG 59.613 55.000 18.54 12.81 0.00 4.63
3157 3489 1.336440 AGAGGATGCAGTTCGATCGAG 59.664 52.381 18.54 8.21 0.00 4.04
3158 3490 1.335182 GAGAGGATGCAGTTCGATCGA 59.665 52.381 15.15 15.15 0.00 3.59
3159 3491 1.601663 GGAGAGGATGCAGTTCGATCG 60.602 57.143 9.36 9.36 0.00 3.69
3160 3492 2.147436 GGAGAGGATGCAGTTCGATC 57.853 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.