Multiple sequence alignment - TraesCS5A01G180100

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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 TraesCS5A01G180100 chr5A 100.000 2753 0 0 1 2753 378728921 378726169 0.000000e+00 5084.0
1 TraesCS5A01G180100 chr5A 82.278 158 16 2 1848 2005 378712184 378712039 2.880000e-25 126.0
2 TraesCS5A01G180100 chr5B 91.807 1013 51 10 866 1853 325551538 325550533 0.000000e+00 1382.0
3 TraesCS5A01G180100 chr5B 93.125 160 8 2 21 180 325555251 325555095 5.930000e-57 231.0
4 TraesCS5A01G180100 chr5B 90.698 172 10 3 692 863 325554503 325554338 9.920000e-55 224.0
5 TraesCS5A01G180100 chr5B 85.185 81 9 3 1867 1946 689312308 689312230 2.270000e-11 80.5
6 TraesCS5A01G180100 chr6A 83.987 893 78 28 1848 2710 50432270 50433127 0.000000e+00 797.0
7 TraesCS5A01G180100 chr6A 82.380 874 73 27 1847 2691 50471718 50472539 0.000000e+00 686.0
8 TraesCS5A01G180100 chr5D 89.885 524 22 5 1327 1822 286455817 286455297 0.000000e+00 645.0
9 TraesCS5A01G180100 chr5D 84.000 100 14 2 1848 1946 294406122 294406220 8.120000e-16 95.3
10 TraesCS5A01G180100 chr2A 90.172 407 15 2 2305 2710 39239431 39239049 8.800000e-140 507.0
11 TraesCS5A01G180100 chr2B 84.483 406 27 19 2305 2710 485301901 485302270 4.330000e-98 368.0
12 TraesCS5A01G180100 chr2B 90.722 97 7 2 2596 2691 485302246 485302341 8.000000e-26 128.0
13 TraesCS5A01G180100 chr2B 86.486 74 8 2 1874 1946 254364479 254364551 2.270000e-11 80.5
14 TraesCS5A01G180100 chr7A 81.188 303 33 16 2389 2691 451978658 451978936 3.570000e-54 222.0
15 TraesCS5A01G180100 chr3A 82.424 165 17 4 1848 2012 389136248 389136400 1.720000e-27 134.0
16 TraesCS5A01G180100 chr3A 80.723 166 19 5 1848 2012 651597002 651597155 1.730000e-22 117.0
17 TraesCS5A01G180100 chr3D 84.158 101 11 3 1848 1946 364727838 364727935 2.920000e-15 93.5


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 TraesCS5A01G180100 chr5A 378726169 378728921 2752 True 5084.000000 5084 100.000000 1 2753 1 chr5A.!!$R2 2752
1 TraesCS5A01G180100 chr5B 325550533 325555251 4718 True 612.333333 1382 91.876667 21 1853 3 chr5B.!!$R2 1832
2 TraesCS5A01G180100 chr6A 50432270 50433127 857 False 797.000000 797 83.987000 1848 2710 1 chr6A.!!$F1 862
3 TraesCS5A01G180100 chr6A 50471718 50472539 821 False 686.000000 686 82.380000 1847 2691 1 chr6A.!!$F2 844
4 TraesCS5A01G180100 chr5D 286455297 286455817 520 True 645.000000 645 89.885000 1327 1822 1 chr5D.!!$R1 495

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
707 896 0.392595 GGGTCAAGGATCCAACGGAC 60.393 60.0 15.82 14.41 32.11 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 5530 0.179029 ACAGGTCAGGGGAAACAACG 60.179 55.0 0.0 0.0 0.0 4.1 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
73 74 3.421844 ACCAGGCACAGATAAGGTTTTC 58.578 45.455 0.00 0.00 0.00 2.29
113 114 9.319060 AGTAGGATCTTGAGCAATGAATAGATA 57.681 33.333 0.00 0.00 0.00 1.98
208 209 9.974980 TTTTAGCTTCATAAAAACGAAAGGATT 57.025 25.926 0.00 0.00 32.97 3.01
212 213 8.122952 AGCTTCATAAAAACGAAAGGATTATCG 58.877 33.333 0.00 0.00 44.33 2.92
216 217 5.970317 AAAAACGAAAGGATTATCGGGTT 57.030 34.783 0.00 0.00 43.11 4.11
230 231 8.129211 GGATTATCGGGTTCTTAGAAAACAATG 58.871 37.037 0.00 0.00 0.00 2.82
238 239 6.374578 GTTCTTAGAAAACAATGTGAGAGGC 58.625 40.000 0.00 0.00 0.00 4.70
240 241 2.851195 AGAAAACAATGTGAGAGGCGT 58.149 42.857 0.00 0.00 0.00 5.68
260 261 2.877168 GTGATTTGATGCCTAGGCTCAG 59.123 50.000 33.07 0.00 42.51 3.35
299 300 7.860373 CAGTTGGTCGTCTATTTTTGAATTTGA 59.140 33.333 0.00 0.00 0.00 2.69
307 308 8.427012 CGTCTATTTTTGAATTTGAATGGTGTG 58.573 33.333 0.00 0.00 0.00 3.82
331 508 5.397142 AAAGTGGGCAAAAGATCTCATTC 57.603 39.130 0.00 0.00 0.00 2.67
369 546 2.743636 TAGTACAGTCTGTTGCTGGC 57.256 50.000 11.54 0.00 38.22 4.85
376 553 3.452264 ACAGTCTGTTGCTGGCTATATGA 59.548 43.478 0.00 0.00 38.22 2.15
386 563 6.806388 TGCTGGCTATATGATGTTGTTATG 57.194 37.500 0.00 0.00 0.00 1.90
387 564 6.532826 TGCTGGCTATATGATGTTGTTATGA 58.467 36.000 0.00 0.00 0.00 2.15
412 589 9.856488 GACATCTATTATCAAACTTATAGCCGA 57.144 33.333 0.00 0.00 0.00 5.54
418 595 7.534085 TTATCAAACTTATAGCCGACAAGTG 57.466 36.000 0.00 0.00 32.96 3.16
427 604 3.328382 AGCCGACAAGTGCAATAGTTA 57.672 42.857 0.00 0.00 0.00 2.24
428 605 3.670625 AGCCGACAAGTGCAATAGTTAA 58.329 40.909 0.00 0.00 0.00 2.01
466 643 8.718102 ACTACTTTATTGATACATGGTCACAC 57.282 34.615 0.00 0.00 0.00 3.82
467 644 8.540388 ACTACTTTATTGATACATGGTCACACT 58.460 33.333 0.00 0.00 0.00 3.55
469 646 8.268850 ACTTTATTGATACATGGTCACACTTC 57.731 34.615 0.00 0.00 0.00 3.01
485 662 4.393062 CACACTTCACTGTCTCACAAAGTT 59.607 41.667 0.00 0.00 27.62 2.66
491 668 5.601662 TCACTGTCTCACAAAGTTTCTAGG 58.398 41.667 0.00 0.00 0.00 3.02
492 669 4.212214 CACTGTCTCACAAAGTTTCTAGGC 59.788 45.833 0.00 0.00 0.00 3.93
494 671 3.181469 TGTCTCACAAAGTTTCTAGGCGT 60.181 43.478 0.00 0.00 0.00 5.68
514 691 4.087265 CGTTCGTGTTGTAGCTAGTAGTC 58.913 47.826 0.00 0.00 0.00 2.59
517 694 3.126514 TCGTGTTGTAGCTAGTAGTCTGC 59.873 47.826 0.00 1.49 0.00 4.26
529 706 6.831353 AGCTAGTAGTCTGCTTCTCTTCATTA 59.169 38.462 0.00 0.00 32.61 1.90
537 714 7.552330 AGTCTGCTTCTCTTCATTATCCTTTTC 59.448 37.037 0.00 0.00 0.00 2.29
539 716 7.768120 TCTGCTTCTCTTCATTATCCTTTTCTC 59.232 37.037 0.00 0.00 0.00 2.87
547 724 9.883142 TCTTCATTATCCTTTTCTCTCTCTTTC 57.117 33.333 0.00 0.00 0.00 2.62
556 733 6.765512 CCTTTTCTCTCTCTTTCAACTCAGTT 59.234 38.462 0.00 0.00 0.00 3.16
557 734 7.928706 CCTTTTCTCTCTCTTTCAACTCAGTTA 59.071 37.037 0.00 0.00 0.00 2.24
561 738 9.838339 TTCTCTCTCTTTCAACTCAGTTAAAAT 57.162 29.630 0.00 0.00 0.00 1.82
592 769 7.734924 TCTAAAGTCTTACGACACTTCTACA 57.265 36.000 1.85 0.00 42.73 2.74
593 770 8.332996 TCTAAAGTCTTACGACACTTCTACAT 57.667 34.615 1.85 0.00 42.73 2.29
595 772 6.821031 AAGTCTTACGACACTTCTACATCT 57.179 37.500 1.85 0.00 42.73 2.90
597 774 5.354792 AGTCTTACGACACTTCTACATCTCC 59.645 44.000 1.85 0.00 42.73 3.71
598 775 4.331992 TCTTACGACACTTCTACATCTCCG 59.668 45.833 0.00 0.00 0.00 4.63
599 776 2.434428 ACGACACTTCTACATCTCCGT 58.566 47.619 0.00 0.00 0.00 4.69
600 777 3.603532 ACGACACTTCTACATCTCCGTA 58.396 45.455 0.00 0.00 0.00 4.02
601 778 3.373439 ACGACACTTCTACATCTCCGTAC 59.627 47.826 0.00 0.00 0.00 3.67
602 779 3.622163 CGACACTTCTACATCTCCGTACT 59.378 47.826 0.00 0.00 0.00 2.73
603 780 4.094590 CGACACTTCTACATCTCCGTACTT 59.905 45.833 0.00 0.00 0.00 2.24
604 781 5.312120 ACACTTCTACATCTCCGTACTTG 57.688 43.478 0.00 0.00 0.00 3.16
605 782 4.106197 CACTTCTACATCTCCGTACTTGC 58.894 47.826 0.00 0.00 0.00 4.01
606 783 4.017808 ACTTCTACATCTCCGTACTTGCT 58.982 43.478 0.00 0.00 0.00 3.91
607 784 4.096682 ACTTCTACATCTCCGTACTTGCTC 59.903 45.833 0.00 0.00 0.00 4.26
608 785 3.887352 TCTACATCTCCGTACTTGCTCT 58.113 45.455 0.00 0.00 0.00 4.09
609 786 5.032327 TCTACATCTCCGTACTTGCTCTA 57.968 43.478 0.00 0.00 0.00 2.43
610 787 5.434408 TCTACATCTCCGTACTTGCTCTAA 58.566 41.667 0.00 0.00 0.00 2.10
611 788 4.373348 ACATCTCCGTACTTGCTCTAAC 57.627 45.455 0.00 0.00 0.00 2.34
612 789 4.017808 ACATCTCCGTACTTGCTCTAACT 58.982 43.478 0.00 0.00 0.00 2.24
613 790 4.142359 ACATCTCCGTACTTGCTCTAACTG 60.142 45.833 0.00 0.00 0.00 3.16
614 791 2.753452 TCTCCGTACTTGCTCTAACTGG 59.247 50.000 0.00 0.00 0.00 4.00
615 792 2.492484 CTCCGTACTTGCTCTAACTGGT 59.508 50.000 0.00 0.00 0.00 4.00
616 793 2.230508 TCCGTACTTGCTCTAACTGGTG 59.769 50.000 0.00 0.00 0.00 4.17
617 794 2.607187 CGTACTTGCTCTAACTGGTGG 58.393 52.381 0.00 0.00 0.00 4.61
618 795 2.674177 CGTACTTGCTCTAACTGGTGGG 60.674 54.545 0.00 0.00 0.00 4.61
619 796 1.729586 ACTTGCTCTAACTGGTGGGA 58.270 50.000 0.00 0.00 0.00 4.37
620 797 2.269940 ACTTGCTCTAACTGGTGGGAT 58.730 47.619 0.00 0.00 0.00 3.85
621 798 2.644798 ACTTGCTCTAACTGGTGGGATT 59.355 45.455 0.00 0.00 0.00 3.01
622 799 3.074538 ACTTGCTCTAACTGGTGGGATTT 59.925 43.478 0.00 0.00 0.00 2.17
623 800 4.288626 ACTTGCTCTAACTGGTGGGATTTA 59.711 41.667 0.00 0.00 0.00 1.40
624 801 4.919774 TGCTCTAACTGGTGGGATTTAA 57.080 40.909 0.00 0.00 0.00 1.52
625 802 5.249780 TGCTCTAACTGGTGGGATTTAAA 57.750 39.130 0.00 0.00 0.00 1.52
626 803 5.826643 TGCTCTAACTGGTGGGATTTAAAT 58.173 37.500 0.00 0.00 0.00 1.40
627 804 6.964464 TGCTCTAACTGGTGGGATTTAAATA 58.036 36.000 0.00 0.00 0.00 1.40
628 805 7.406916 TGCTCTAACTGGTGGGATTTAAATAA 58.593 34.615 0.00 0.00 0.00 1.40
629 806 8.058847 TGCTCTAACTGGTGGGATTTAAATAAT 58.941 33.333 0.00 0.00 0.00 1.28
630 807 8.914011 GCTCTAACTGGTGGGATTTAAATAATT 58.086 33.333 0.00 0.00 0.00 1.40
632 809 9.416284 TCTAACTGGTGGGATTTAAATAATTCC 57.584 33.333 0.00 0.00 35.84 3.01
633 810 6.709018 ACTGGTGGGATTTAAATAATTCCG 57.291 37.500 0.00 2.76 36.86 4.30
634 811 6.192044 ACTGGTGGGATTTAAATAATTCCGT 58.808 36.000 0.00 3.26 36.86 4.69
635 812 6.096282 ACTGGTGGGATTTAAATAATTCCGTG 59.904 38.462 0.00 3.09 36.86 4.94
636 813 5.361285 TGGTGGGATTTAAATAATTCCGTGG 59.639 40.000 0.00 0.00 36.86 4.94
637 814 5.221362 GGTGGGATTTAAATAATTCCGTGGG 60.221 44.000 0.00 0.00 36.86 4.61
638 815 5.595133 GTGGGATTTAAATAATTCCGTGGGA 59.405 40.000 0.00 0.00 36.86 4.37
639 816 6.097129 GTGGGATTTAAATAATTCCGTGGGAA 59.903 38.462 0.00 0.00 46.39 3.97
640 817 6.097129 TGGGATTTAAATAATTCCGTGGGAAC 59.903 38.462 0.00 0.00 45.07 3.62
641 818 6.097129 GGGATTTAAATAATTCCGTGGGAACA 59.903 38.462 0.00 0.00 45.07 3.18
642 819 7.363968 GGGATTTAAATAATTCCGTGGGAACAA 60.364 37.037 0.00 0.00 45.07 2.83
643 820 8.035984 GGATTTAAATAATTCCGTGGGAACAAA 58.964 33.333 0.00 0.00 45.07 2.83
644 821 9.594478 GATTTAAATAATTCCGTGGGAACAAAT 57.406 29.630 0.00 0.50 45.07 2.32
645 822 8.989653 TTTAAATAATTCCGTGGGAACAAATC 57.010 30.769 0.00 0.00 45.07 2.17
646 823 6.597832 AAATAATTCCGTGGGAACAAATCA 57.402 33.333 0.00 0.00 45.07 2.57
647 824 6.790232 AATAATTCCGTGGGAACAAATCAT 57.210 33.333 0.00 0.00 45.07 2.45
648 825 6.790232 ATAATTCCGTGGGAACAAATCATT 57.210 33.333 0.00 0.00 45.07 2.57
649 826 5.482163 AATTCCGTGGGAACAAATCATTT 57.518 34.783 0.00 0.00 45.07 2.32
650 827 4.946478 TTCCGTGGGAACAAATCATTTT 57.054 36.364 0.00 0.00 46.06 1.82
651 828 4.946478 TCCGTGGGAACAAATCATTTTT 57.054 36.364 0.00 0.00 46.06 1.94
652 829 4.626042 TCCGTGGGAACAAATCATTTTTG 58.374 39.130 0.00 0.00 46.06 2.44
653 830 4.342378 TCCGTGGGAACAAATCATTTTTGA 59.658 37.500 5.17 0.00 46.06 2.69
654 831 4.447389 CCGTGGGAACAAATCATTTTTGAC 59.553 41.667 5.17 0.01 46.06 3.18
655 832 4.447389 CGTGGGAACAAATCATTTTTGACC 59.553 41.667 5.17 7.48 46.06 4.02
656 833 5.363939 GTGGGAACAAATCATTTTTGACCA 58.636 37.500 5.17 7.23 46.06 4.02
657 834 5.466393 GTGGGAACAAATCATTTTTGACCAG 59.534 40.000 5.17 0.00 46.06 4.00
658 835 4.452114 GGGAACAAATCATTTTTGACCAGC 59.548 41.667 5.17 0.00 34.25 4.85
659 836 5.299949 GGAACAAATCATTTTTGACCAGCT 58.700 37.500 5.17 0.00 33.52 4.24
660 837 5.178067 GGAACAAATCATTTTTGACCAGCTG 59.822 40.000 6.78 6.78 33.52 4.24
661 838 4.060205 ACAAATCATTTTTGACCAGCTGC 58.940 39.130 8.66 0.00 33.83 5.25
662 839 4.202284 ACAAATCATTTTTGACCAGCTGCT 60.202 37.500 8.66 0.00 33.83 4.24
663 840 3.587797 ATCATTTTTGACCAGCTGCTG 57.412 42.857 22.44 22.44 0.00 4.41
664 841 2.309613 TCATTTTTGACCAGCTGCTGT 58.690 42.857 26.41 15.39 0.00 4.40
665 842 3.485394 TCATTTTTGACCAGCTGCTGTA 58.515 40.909 26.41 11.09 0.00 2.74
666 843 4.081406 TCATTTTTGACCAGCTGCTGTAT 58.919 39.130 26.41 15.31 0.00 2.29
670 847 1.866015 TGACCAGCTGCTGTATAGGT 58.134 50.000 26.41 17.53 0.00 3.08
674 851 2.695666 ACCAGCTGCTGTATAGGTGTAG 59.304 50.000 26.41 10.67 40.94 2.74
682 859 5.404946 TGCTGTATAGGTGTAGTTCGAAAC 58.595 41.667 0.00 0.00 0.00 2.78
686 863 7.088589 TGTATAGGTGTAGTTCGAAACCTAC 57.911 40.000 22.65 19.05 45.57 3.18
707 896 0.392595 GGGTCAAGGATCCAACGGAC 60.393 60.000 15.82 14.41 32.11 4.79
715 904 3.282021 AGGATCCAACGGACATGATTTG 58.718 45.455 15.82 0.00 32.98 2.32
764 953 4.277515 GATGGAATCGGATCCTTCATCA 57.722 45.455 10.75 3.41 41.18 3.07
791 980 5.124457 GTGACCGACCACTTACTCACTTATA 59.876 44.000 0.00 0.00 34.38 0.98
792 981 5.889853 TGACCGACCACTTACTCACTTATAT 59.110 40.000 0.00 0.00 0.00 0.86
793 982 6.379133 TGACCGACCACTTACTCACTTATATT 59.621 38.462 0.00 0.00 0.00 1.28
794 983 6.803642 ACCGACCACTTACTCACTTATATTC 58.196 40.000 0.00 0.00 0.00 1.75
856 1045 4.694339 ACGGAAGTAATGATCCTTAGCAC 58.306 43.478 0.00 0.00 46.88 4.40
863 1052 4.322057 AATGATCCTTAGCACCCAAGTT 57.678 40.909 0.00 0.00 0.00 2.66
922 3908 7.068702 TCCTTTCCTATATAAACCCAGACGTA 58.931 38.462 0.00 0.00 0.00 3.57
923 3909 7.014615 TCCTTTCCTATATAAACCCAGACGTAC 59.985 40.741 0.00 0.00 0.00 3.67
1005 3995 0.654683 GCAAGTGATCGAGCATGTCC 59.345 55.000 6.66 0.00 0.00 4.02
1100 4090 0.177141 CCTGAACCTTATCCGCCGAA 59.823 55.000 0.00 0.00 0.00 4.30
1168 4158 0.459585 TTATGAGCCGCCGTCAGAAC 60.460 55.000 0.00 0.00 0.00 3.01
1177 4167 1.071471 CCGTCAGAACTGGTGCCTT 59.929 57.895 1.93 0.00 0.00 4.35
1238 4228 2.222027 GCAACCGCCTTATTATCAGCT 58.778 47.619 0.00 0.00 0.00 4.24
1266 4256 2.019984 GAATTGGTGCCTCCTCATCAC 58.980 52.381 0.00 0.00 37.07 3.06
1275 4265 2.212900 CTCCTCATCACGTGTCGCCA 62.213 60.000 16.51 0.00 0.00 5.69
1320 4313 2.094659 GGTGACGACTCATGTGCCG 61.095 63.158 1.81 1.81 0.00 5.69
1323 4316 2.048222 ACGACTCATGTGCCGGTG 60.048 61.111 1.90 0.00 0.00 4.94
1325 4318 3.127533 GACTCATGTGCCGGTGCC 61.128 66.667 1.90 0.00 36.33 5.01
1400 4393 0.106708 GCCGTGCCATCCAAGAGATA 59.893 55.000 0.00 0.00 32.37 1.98
1454 4447 4.681978 GCCCAACGAGACGCCTGT 62.682 66.667 0.00 0.00 0.00 4.00
1458 4451 2.108157 AACGAGACGCCTGTGCAA 59.892 55.556 0.00 0.00 37.32 4.08
1530 4538 0.039437 CGCCTGTTACTGTCACGTCT 60.039 55.000 0.00 0.00 0.00 4.18
1539 4547 0.311165 CTGTCACGTCTCAACCGTCT 59.689 55.000 0.00 0.00 36.17 4.18
1583 4600 3.632189 GTGTAAAGTCCAAGACGTACGT 58.368 45.455 23.04 23.04 37.67 3.57
1692 4709 3.550431 CACCCTCATCCCGGCGAT 61.550 66.667 9.30 0.00 0.00 4.58
1788 4814 4.057428 GCGAGGGTGCGTCTGTCT 62.057 66.667 0.00 0.00 0.00 3.41
1789 4815 2.126307 CGAGGGTGCGTCTGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
1790 4816 2.920645 CGAGGGTGCGTCTGTCTGT 61.921 63.158 0.00 0.00 0.00 3.41
1822 4848 1.378531 TCTGTTATTCGCACCATGCC 58.621 50.000 0.00 0.00 41.12 4.40
1823 4849 1.093972 CTGTTATTCGCACCATGCCA 58.906 50.000 0.00 0.00 41.12 4.92
1824 4850 0.808125 TGTTATTCGCACCATGCCAC 59.192 50.000 0.00 0.00 41.12 5.01
1826 4852 1.987704 TTATTCGCACCATGCCACGC 61.988 55.000 0.00 0.00 41.12 5.34
1841 4867 2.889988 CGCCATCGTCGCATGGAA 60.890 61.111 20.86 0.00 45.79 3.53
1853 4879 4.651994 GTCGCATGGAACTTAATGTTGAG 58.348 43.478 0.00 0.00 39.30 3.02
1859 4885 9.203421 CGCATGGAACTTAATGTTGAGTATATA 57.797 33.333 0.00 0.00 39.30 0.86
1872 4898 8.880878 TGTTGAGTATATATGTTACGTGCATT 57.119 30.769 11.66 4.63 0.00 3.56
1876 4902 8.279800 TGAGTATATATGTTACGTGCATTTTGC 58.720 33.333 11.66 0.00 45.29 3.68
1899 4925 6.701841 TGCGTATTGAGTTCATCTCCTAATTC 59.298 38.462 0.00 0.00 42.12 2.17
1921 4947 8.873215 ATTCTTTGTATAGTTGAGATACGTGG 57.127 34.615 0.00 0.00 33.27 4.94
1938 4964 2.672760 CGTGGTCCATCGTTGTACATCA 60.673 50.000 0.00 0.00 0.00 3.07
1939 4965 3.531538 GTGGTCCATCGTTGTACATCAT 58.468 45.455 0.00 0.00 0.00 2.45
1940 4966 4.689071 GTGGTCCATCGTTGTACATCATA 58.311 43.478 0.00 0.00 0.00 2.15
1941 4967 5.297547 GTGGTCCATCGTTGTACATCATAT 58.702 41.667 0.00 0.00 0.00 1.78
1942 4968 6.452242 GTGGTCCATCGTTGTACATCATATA 58.548 40.000 0.00 0.00 0.00 0.86
1943 4969 7.097192 GTGGTCCATCGTTGTACATCATATAT 58.903 38.462 0.00 0.00 0.00 0.86
1944 4970 8.248253 GTGGTCCATCGTTGTACATCATATATA 58.752 37.037 0.00 0.00 0.00 0.86
1945 4971 8.248253 TGGTCCATCGTTGTACATCATATATAC 58.752 37.037 0.00 0.00 0.00 1.47
1946 4972 8.467598 GGTCCATCGTTGTACATCATATATACT 58.532 37.037 0.00 0.00 0.00 2.12
2037 5064 5.622770 TTTTAGATTTCTTCACTTCCGCC 57.377 39.130 0.00 0.00 0.00 6.13
2038 5065 2.859165 AGATTTCTTCACTTCCGCCA 57.141 45.000 0.00 0.00 0.00 5.69
2039 5066 2.427506 AGATTTCTTCACTTCCGCCAC 58.572 47.619 0.00 0.00 0.00 5.01
2040 5067 1.468914 GATTTCTTCACTTCCGCCACC 59.531 52.381 0.00 0.00 0.00 4.61
2041 5068 0.882927 TTTCTTCACTTCCGCCACCG 60.883 55.000 0.00 0.00 0.00 4.94
2209 5249 4.674904 CTCGCTCGATCTCGCCCG 62.675 72.222 0.00 0.58 39.60 6.13
2314 5361 4.271816 CCGCTAGCGCCTGATCGT 62.272 66.667 31.35 0.00 38.24 3.73
2322 5369 1.079819 CGCCTGATCGTCAACACCT 60.080 57.895 0.00 0.00 0.00 4.00
2325 5372 1.909376 CCTGATCGTCAACACCTACG 58.091 55.000 0.00 0.00 40.40 3.51
2336 5383 2.867368 CAACACCTACGTGCTTGTACAA 59.133 45.455 8.28 8.28 44.40 2.41
2359 5406 2.478134 CGAGCAATCGATCCAGGAAATC 59.522 50.000 0.00 0.00 34.64 2.17
2369 5429 4.503817 CGATCCAGGAAATCCATCAGCTTA 60.504 45.833 1.67 0.00 38.89 3.09
2395 5455 1.886861 CTTGTACGTGCACCAGCGTC 61.887 60.000 12.15 1.23 46.23 5.19
2396 5456 2.049433 GTACGTGCACCAGCGTCT 60.049 61.111 12.15 0.00 46.23 4.18
2410 5470 2.107953 GTCTGCTCTGCCCCGATC 59.892 66.667 0.00 0.00 0.00 3.69
2483 5549 2.114411 GGCCGTTGTTTCCCCTGA 59.886 61.111 0.00 0.00 0.00 3.86
2486 5552 1.454539 CCGTTGTTTCCCCTGACCT 59.545 57.895 0.00 0.00 0.00 3.85
2511 5577 0.807496 GATCCAACTGCTGCTGTTCC 59.193 55.000 20.04 7.99 0.00 3.62
2512 5578 0.957395 ATCCAACTGCTGCTGTTCCG 60.957 55.000 20.04 13.74 0.00 4.30
2513 5579 2.253452 CAACTGCTGCTGTTCCGC 59.747 61.111 20.04 0.00 0.00 5.54
2514 5580 2.980233 AACTGCTGCTGTTCCGCC 60.980 61.111 17.65 0.00 0.00 6.13
2522 5588 4.394078 CTGTTCCGCCGTCGTCGA 62.394 66.667 2.98 0.00 39.71 4.20
2523 5589 4.688419 TGTTCCGCCGTCGTCGAC 62.688 66.667 15.51 15.51 39.71 4.20
2524 5590 4.395583 GTTCCGCCGTCGTCGACT 62.396 66.667 22.18 0.00 39.71 4.18
2525 5591 4.394078 TTCCGCCGTCGTCGACTG 62.394 66.667 22.18 17.10 39.71 3.51
2530 5596 4.406173 CCGTCGTCGACTGCTGCT 62.406 66.667 22.18 0.00 39.71 4.24
2531 5597 3.168604 CGTCGTCGACTGCTGCTG 61.169 66.667 22.18 4.89 39.71 4.41
2532 5598 2.049985 GTCGTCGACTGCTGCTGT 60.050 61.111 18.09 12.15 0.00 4.40
2533 5599 1.661821 GTCGTCGACTGCTGCTGTT 60.662 57.895 18.09 0.00 0.00 3.16
2534 5600 1.371758 TCGTCGACTGCTGCTGTTC 60.372 57.895 14.70 6.38 0.00 3.18
2613 5679 2.516930 GGGCGTACATGCAGGCAT 60.517 61.111 12.40 0.00 37.08 4.40
2656 5722 1.899617 GTGGCCAAACCCATCCATG 59.100 57.895 7.24 0.00 37.20 3.66
2658 5724 1.306056 GGCCAAACCCATCCATGGT 60.306 57.895 12.58 0.00 46.65 3.55
2692 5785 4.522689 ATGCATGGCGCGGACGTA 62.523 61.111 8.83 0.00 46.97 3.57
2695 5788 2.811747 CATGGCGCGGACGTACAA 60.812 61.111 8.83 0.00 42.83 2.41
2696 5789 2.508439 ATGGCGCGGACGTACAAG 60.508 61.111 8.83 0.00 42.83 3.16
2699 5792 3.838795 GCGCGGACGTACAAGCAG 61.839 66.667 8.83 0.00 42.83 4.24
2700 5793 3.179265 CGCGGACGTACAAGCAGG 61.179 66.667 0.00 0.00 33.53 4.85
2701 5794 3.488090 GCGGACGTACAAGCAGGC 61.488 66.667 0.00 0.00 0.00 4.85
2702 5795 2.048597 CGGACGTACAAGCAGGCA 60.049 61.111 0.00 0.00 0.00 4.75
2703 5796 1.447838 CGGACGTACAAGCAGGCAT 60.448 57.895 0.00 0.00 0.00 4.40
2704 5797 1.695893 CGGACGTACAAGCAGGCATG 61.696 60.000 0.00 0.00 0.00 4.06
2714 5807 3.896133 CAGGCATGCATGGGCGTC 61.896 66.667 27.34 10.53 45.35 5.19
2715 5808 4.429522 AGGCATGCATGGGCGTCA 62.430 61.111 27.34 0.00 45.35 4.35
2716 5809 3.896133 GGCATGCATGGGCGTCAG 61.896 66.667 27.34 0.11 45.35 3.51
2717 5810 4.564116 GCATGCATGGGCGTCAGC 62.564 66.667 27.34 7.22 45.35 4.26
2728 5821 3.460648 GCGTCAGCCCTACTTTCAT 57.539 52.632 0.00 0.00 37.42 2.57
2729 5822 1.739067 GCGTCAGCCCTACTTTCATT 58.261 50.000 0.00 0.00 37.42 2.57
2730 5823 2.084546 GCGTCAGCCCTACTTTCATTT 58.915 47.619 0.00 0.00 37.42 2.32
2731 5824 2.096013 GCGTCAGCCCTACTTTCATTTC 59.904 50.000 0.00 0.00 37.42 2.17
2732 5825 3.600388 CGTCAGCCCTACTTTCATTTCT 58.400 45.455 0.00 0.00 0.00 2.52
2733 5826 4.003648 CGTCAGCCCTACTTTCATTTCTT 58.996 43.478 0.00 0.00 0.00 2.52
2734 5827 4.093556 CGTCAGCCCTACTTTCATTTCTTC 59.906 45.833 0.00 0.00 0.00 2.87
2735 5828 5.249420 GTCAGCCCTACTTTCATTTCTTCT 58.751 41.667 0.00 0.00 0.00 2.85
2736 5829 5.707764 GTCAGCCCTACTTTCATTTCTTCTT 59.292 40.000 0.00 0.00 0.00 2.52
2737 5830 5.940470 TCAGCCCTACTTTCATTTCTTCTTC 59.060 40.000 0.00 0.00 0.00 2.87
2738 5831 5.124617 CAGCCCTACTTTCATTTCTTCTTCC 59.875 44.000 0.00 0.00 0.00 3.46
2739 5832 4.399618 GCCCTACTTTCATTTCTTCTTCCC 59.600 45.833 0.00 0.00 0.00 3.97
2740 5833 5.570320 CCCTACTTTCATTTCTTCTTCCCA 58.430 41.667 0.00 0.00 0.00 4.37
2741 5834 6.010219 CCCTACTTTCATTTCTTCTTCCCAA 58.990 40.000 0.00 0.00 0.00 4.12
2742 5835 6.665248 CCCTACTTTCATTTCTTCTTCCCAAT 59.335 38.462 0.00 0.00 0.00 3.16
2743 5836 7.834181 CCCTACTTTCATTTCTTCTTCCCAATA 59.166 37.037 0.00 0.00 0.00 1.90
2744 5837 8.678199 CCTACTTTCATTTCTTCTTCCCAATAC 58.322 37.037 0.00 0.00 0.00 1.89
2745 5838 7.145932 ACTTTCATTTCTTCTTCCCAATACG 57.854 36.000 0.00 0.00 0.00 3.06
2746 5839 6.715264 ACTTTCATTTCTTCTTCCCAATACGT 59.285 34.615 0.00 0.00 0.00 3.57
2747 5840 7.881232 ACTTTCATTTCTTCTTCCCAATACGTA 59.119 33.333 0.00 0.00 0.00 3.57
2748 5841 7.605410 TTCATTTCTTCTTCCCAATACGTAC 57.395 36.000 0.00 0.00 0.00 3.67
2749 5842 6.110707 TCATTTCTTCTTCCCAATACGTACC 58.889 40.000 0.00 0.00 0.00 3.34
2750 5843 4.476628 TTCTTCTTCCCAATACGTACCC 57.523 45.455 0.00 0.00 0.00 3.69
2751 5844 3.716431 TCTTCTTCCCAATACGTACCCT 58.284 45.455 0.00 0.00 0.00 4.34
2752 5845 3.703052 TCTTCTTCCCAATACGTACCCTC 59.297 47.826 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.535030 CCTTAGCTTAATTATGGTTGGGGAC 59.465 44.000 8.19 0.00 0.00 4.46
1 2 5.433712 TCCTTAGCTTAATTATGGTTGGGGA 59.566 40.000 8.19 10.04 0.00 4.81
2 3 5.701224 TCCTTAGCTTAATTATGGTTGGGG 58.299 41.667 8.19 8.35 0.00 4.96
3 4 7.725844 AGATTCCTTAGCTTAATTATGGTTGGG 59.274 37.037 8.19 10.26 0.00 4.12
4 5 8.697507 AGATTCCTTAGCTTAATTATGGTTGG 57.302 34.615 8.19 10.57 0.00 3.77
50 51 2.789409 ACCTTATCTGTGCCTGGTTC 57.211 50.000 0.00 0.00 0.00 3.62
87 88 7.609097 TCTATTCATTGCTCAAGATCCTACT 57.391 36.000 0.00 0.00 0.00 2.57
182 183 9.974980 AATCCTTTCGTTTTTATGAAGCTAAAA 57.025 25.926 0.00 0.00 0.00 1.52
186 187 8.122952 CGATAATCCTTTCGTTTTTATGAAGCT 58.877 33.333 0.00 0.00 0.00 3.74
187 188 7.376072 CCGATAATCCTTTCGTTTTTATGAAGC 59.624 37.037 0.00 0.00 33.60 3.86
188 189 7.855904 CCCGATAATCCTTTCGTTTTTATGAAG 59.144 37.037 0.00 0.00 33.60 3.02
189 190 7.337436 ACCCGATAATCCTTTCGTTTTTATGAA 59.663 33.333 0.00 0.00 33.60 2.57
190 191 6.824704 ACCCGATAATCCTTTCGTTTTTATGA 59.175 34.615 0.00 0.00 33.60 2.15
191 192 7.023197 ACCCGATAATCCTTTCGTTTTTATG 57.977 36.000 0.00 0.00 33.60 1.90
192 193 7.555195 AGAACCCGATAATCCTTTCGTTTTTAT 59.445 33.333 0.00 0.00 33.60 1.40
193 194 6.880529 AGAACCCGATAATCCTTTCGTTTTTA 59.119 34.615 0.00 0.00 33.60 1.52
194 195 5.708697 AGAACCCGATAATCCTTTCGTTTTT 59.291 36.000 0.00 0.00 33.60 1.94
195 196 5.250982 AGAACCCGATAATCCTTTCGTTTT 58.749 37.500 0.00 0.00 33.60 2.43
196 197 4.840271 AGAACCCGATAATCCTTTCGTTT 58.160 39.130 0.00 0.00 33.60 3.60
197 198 4.482952 AGAACCCGATAATCCTTTCGTT 57.517 40.909 0.00 0.00 33.60 3.85
198 199 4.482952 AAGAACCCGATAATCCTTTCGT 57.517 40.909 0.00 0.00 33.60 3.85
199 200 5.839621 TCTAAGAACCCGATAATCCTTTCG 58.160 41.667 0.00 0.00 35.19 3.46
200 201 8.396390 GTTTTCTAAGAACCCGATAATCCTTTC 58.604 37.037 0.00 0.00 0.00 2.62
201 202 7.886446 TGTTTTCTAAGAACCCGATAATCCTTT 59.114 33.333 0.00 0.00 0.00 3.11
202 203 7.399634 TGTTTTCTAAGAACCCGATAATCCTT 58.600 34.615 0.00 0.00 0.00 3.36
203 204 6.954232 TGTTTTCTAAGAACCCGATAATCCT 58.046 36.000 0.00 0.00 0.00 3.24
204 205 7.619964 TTGTTTTCTAAGAACCCGATAATCC 57.380 36.000 0.00 0.00 0.00 3.01
205 206 8.674607 ACATTGTTTTCTAAGAACCCGATAATC 58.325 33.333 0.00 0.00 0.00 1.75
206 207 8.458843 CACATTGTTTTCTAAGAACCCGATAAT 58.541 33.333 0.00 0.00 0.00 1.28
207 208 7.662258 TCACATTGTTTTCTAAGAACCCGATAA 59.338 33.333 0.00 0.00 0.00 1.75
208 209 7.162761 TCACATTGTTTTCTAAGAACCCGATA 58.837 34.615 0.00 0.00 0.00 2.92
209 210 6.001460 TCACATTGTTTTCTAAGAACCCGAT 58.999 36.000 0.00 0.00 0.00 4.18
210 211 5.369833 TCACATTGTTTTCTAAGAACCCGA 58.630 37.500 0.00 0.00 0.00 5.14
211 212 5.468746 TCTCACATTGTTTTCTAAGAACCCG 59.531 40.000 0.00 0.00 0.00 5.28
212 213 6.072452 CCTCTCACATTGTTTTCTAAGAACCC 60.072 42.308 0.00 0.00 0.00 4.11
216 217 4.690748 CGCCTCTCACATTGTTTTCTAAGA 59.309 41.667 0.00 0.00 0.00 2.10
230 231 1.063174 GCATCAAATCACGCCTCTCAC 59.937 52.381 0.00 0.00 0.00 3.51
238 239 1.869767 GAGCCTAGGCATCAAATCACG 59.130 52.381 34.70 0.00 44.88 4.35
240 241 2.773661 TCTGAGCCTAGGCATCAAATCA 59.226 45.455 34.70 25.12 44.88 2.57
274 275 7.936584 TCAAATTCAAAAATAGACGACCAACT 58.063 30.769 0.00 0.00 0.00 3.16
281 282 8.427012 CACACCATTCAAATTCAAAAATAGACG 58.573 33.333 0.00 0.00 0.00 4.18
299 300 1.786937 TGCCCACTTTTCACACCATT 58.213 45.000 0.00 0.00 0.00 3.16
307 308 4.853924 TGAGATCTTTTGCCCACTTTTC 57.146 40.909 0.00 0.00 0.00 2.29
344 521 6.316390 GCCAGCAACAGACTGTACTATTAATT 59.684 38.462 8.91 0.00 33.09 1.40
348 525 3.261897 AGCCAGCAACAGACTGTACTATT 59.738 43.478 8.91 0.00 33.09 1.73
360 537 4.525996 ACAACATCATATAGCCAGCAACA 58.474 39.130 0.00 0.00 0.00 3.33
361 538 5.505173 AACAACATCATATAGCCAGCAAC 57.495 39.130 0.00 0.00 0.00 4.17
386 563 9.856488 TCGGCTATAAGTTTGATAATAGATGTC 57.144 33.333 0.00 0.00 0.00 3.06
387 564 9.640963 GTCGGCTATAAGTTTGATAATAGATGT 57.359 33.333 0.00 0.00 0.00 3.06
391 568 9.477484 ACTTGTCGGCTATAAGTTTGATAATAG 57.523 33.333 0.00 0.00 36.21 1.73
393 570 7.254795 GCACTTGTCGGCTATAAGTTTGATAAT 60.255 37.037 0.00 0.00 37.43 1.28
408 585 4.413495 TTTAACTATTGCACTTGTCGGC 57.587 40.909 0.00 0.00 0.00 5.54
445 622 8.177663 GTGAAGTGTGACCATGTATCAATAAAG 58.822 37.037 0.00 0.00 0.00 1.85
449 626 5.645067 CAGTGAAGTGTGACCATGTATCAAT 59.355 40.000 0.00 0.00 0.00 2.57
457 634 2.700371 TGAGACAGTGAAGTGTGACCAT 59.300 45.455 0.00 0.00 0.00 3.55
466 643 6.201806 CCTAGAAACTTTGTGAGACAGTGAAG 59.798 42.308 0.00 0.00 0.00 3.02
467 644 6.049149 CCTAGAAACTTTGTGAGACAGTGAA 58.951 40.000 0.00 0.00 0.00 3.18
469 646 4.212214 GCCTAGAAACTTTGTGAGACAGTG 59.788 45.833 0.00 0.00 0.00 3.66
485 662 2.923605 GCTACAACACGAACGCCTAGAA 60.924 50.000 0.00 0.00 0.00 2.10
491 668 1.694639 ACTAGCTACAACACGAACGC 58.305 50.000 0.00 0.00 0.00 4.84
492 669 4.075763 ACTACTAGCTACAACACGAACG 57.924 45.455 0.00 0.00 0.00 3.95
494 671 4.379186 GCAGACTACTAGCTACAACACGAA 60.379 45.833 0.00 0.00 0.00 3.85
514 691 7.769970 AGAGAAAAGGATAATGAAGAGAAGCAG 59.230 37.037 0.00 0.00 0.00 4.24
517 694 9.533253 GAGAGAGAAAAGGATAATGAAGAGAAG 57.467 37.037 0.00 0.00 0.00 2.85
529 706 7.072263 TGAGTTGAAAGAGAGAGAAAAGGAT 57.928 36.000 0.00 0.00 0.00 3.24
577 754 4.005650 ACGGAGATGTAGAAGTGTCGTAA 58.994 43.478 0.00 0.00 0.00 3.18
581 758 5.333513 CAAGTACGGAGATGTAGAAGTGTC 58.666 45.833 0.00 0.00 0.00 3.67
592 769 3.381908 CCAGTTAGAGCAAGTACGGAGAT 59.618 47.826 0.00 0.00 0.00 2.75
593 770 2.753452 CCAGTTAGAGCAAGTACGGAGA 59.247 50.000 0.00 0.00 0.00 3.71
595 772 2.230508 CACCAGTTAGAGCAAGTACGGA 59.769 50.000 0.00 0.00 0.00 4.69
597 774 2.607187 CCACCAGTTAGAGCAAGTACG 58.393 52.381 0.00 0.00 0.00 3.67
598 775 2.565834 TCCCACCAGTTAGAGCAAGTAC 59.434 50.000 0.00 0.00 0.00 2.73
599 776 2.897350 TCCCACCAGTTAGAGCAAGTA 58.103 47.619 0.00 0.00 0.00 2.24
600 777 1.729586 TCCCACCAGTTAGAGCAAGT 58.270 50.000 0.00 0.00 0.00 3.16
601 778 3.356529 AATCCCACCAGTTAGAGCAAG 57.643 47.619 0.00 0.00 0.00 4.01
602 779 3.806949 AAATCCCACCAGTTAGAGCAA 57.193 42.857 0.00 0.00 0.00 3.91
603 780 4.919774 TTAAATCCCACCAGTTAGAGCA 57.080 40.909 0.00 0.00 0.00 4.26
604 781 7.875327 TTATTTAAATCCCACCAGTTAGAGC 57.125 36.000 3.39 0.00 0.00 4.09
606 783 9.416284 GGAATTATTTAAATCCCACCAGTTAGA 57.584 33.333 3.39 0.00 30.66 2.10
607 784 8.349983 CGGAATTATTTAAATCCCACCAGTTAG 58.650 37.037 3.39 0.00 32.77 2.34
608 785 7.835181 ACGGAATTATTTAAATCCCACCAGTTA 59.165 33.333 3.39 0.00 32.77 2.24
609 786 6.666113 ACGGAATTATTTAAATCCCACCAGTT 59.334 34.615 3.39 0.00 32.77 3.16
610 787 6.096282 CACGGAATTATTTAAATCCCACCAGT 59.904 38.462 3.39 5.43 32.77 4.00
611 788 6.460953 CCACGGAATTATTTAAATCCCACCAG 60.461 42.308 3.39 4.92 32.77 4.00
612 789 5.361285 CCACGGAATTATTTAAATCCCACCA 59.639 40.000 3.39 0.00 32.77 4.17
613 790 5.221362 CCCACGGAATTATTTAAATCCCACC 60.221 44.000 3.39 4.48 32.77 4.61
614 791 5.595133 TCCCACGGAATTATTTAAATCCCAC 59.405 40.000 3.39 0.00 32.77 4.61
615 792 5.767670 TCCCACGGAATTATTTAAATCCCA 58.232 37.500 3.39 0.00 32.77 4.37
616 793 6.097129 TGTTCCCACGGAATTATTTAAATCCC 59.903 38.462 3.39 1.94 44.04 3.85
617 794 7.102847 TGTTCCCACGGAATTATTTAAATCC 57.897 36.000 3.39 0.00 44.04 3.01
618 795 8.989653 TTTGTTCCCACGGAATTATTTAAATC 57.010 30.769 3.39 0.00 44.04 2.17
619 796 9.594478 GATTTGTTCCCACGGAATTATTTAAAT 57.406 29.630 5.89 5.89 44.04 1.40
620 797 8.585881 TGATTTGTTCCCACGGAATTATTTAAA 58.414 29.630 0.00 0.00 44.04 1.52
621 798 8.123639 TGATTTGTTCCCACGGAATTATTTAA 57.876 30.769 0.00 0.00 44.04 1.52
622 799 7.704578 TGATTTGTTCCCACGGAATTATTTA 57.295 32.000 0.00 0.00 44.04 1.40
623 800 6.597832 TGATTTGTTCCCACGGAATTATTT 57.402 33.333 0.00 0.00 44.04 1.40
624 801 6.790232 ATGATTTGTTCCCACGGAATTATT 57.210 33.333 0.00 0.00 44.04 1.40
625 802 6.790232 AATGATTTGTTCCCACGGAATTAT 57.210 33.333 0.00 0.00 44.04 1.28
626 803 6.597832 AAATGATTTGTTCCCACGGAATTA 57.402 33.333 0.00 0.00 44.04 1.40
627 804 5.482163 AAATGATTTGTTCCCACGGAATT 57.518 34.783 0.00 0.00 44.04 2.17
628 805 5.482163 AAAATGATTTGTTCCCACGGAAT 57.518 34.783 0.00 0.00 44.04 3.01
629 806 4.946478 AAAATGATTTGTTCCCACGGAA 57.054 36.364 0.00 0.00 39.66 4.30
630 807 4.342378 TCAAAAATGATTTGTTCCCACGGA 59.658 37.500 0.00 0.00 0.00 4.69
631 808 4.447389 GTCAAAAATGATTTGTTCCCACGG 59.553 41.667 0.00 0.00 0.00 4.94
632 809 4.447389 GGTCAAAAATGATTTGTTCCCACG 59.553 41.667 0.00 0.00 0.00 4.94
633 810 5.363939 TGGTCAAAAATGATTTGTTCCCAC 58.636 37.500 0.00 0.00 0.00 4.61
634 811 5.609423 CTGGTCAAAAATGATTTGTTCCCA 58.391 37.500 0.00 0.00 0.00 4.37
635 812 4.452114 GCTGGTCAAAAATGATTTGTTCCC 59.548 41.667 0.00 0.00 0.00 3.97
636 813 5.178067 CAGCTGGTCAAAAATGATTTGTTCC 59.822 40.000 5.57 6.08 0.00 3.62
637 814 5.333568 GCAGCTGGTCAAAAATGATTTGTTC 60.334 40.000 17.12 0.00 0.00 3.18
638 815 4.512571 GCAGCTGGTCAAAAATGATTTGTT 59.487 37.500 17.12 0.00 0.00 2.83
639 816 4.060205 GCAGCTGGTCAAAAATGATTTGT 58.940 39.130 17.12 0.00 0.00 2.83
640 817 4.151689 CAGCAGCTGGTCAAAAATGATTTG 59.848 41.667 17.16 0.00 0.00 2.32
641 818 4.202284 ACAGCAGCTGGTCAAAAATGATTT 60.202 37.500 26.38 0.00 35.51 2.17
642 819 3.322828 ACAGCAGCTGGTCAAAAATGATT 59.677 39.130 26.38 0.00 35.51 2.57
643 820 2.895404 ACAGCAGCTGGTCAAAAATGAT 59.105 40.909 26.38 0.00 35.51 2.45
644 821 2.309613 ACAGCAGCTGGTCAAAAATGA 58.690 42.857 26.38 0.00 35.51 2.57
645 822 2.806608 ACAGCAGCTGGTCAAAAATG 57.193 45.000 26.38 5.48 35.51 2.32
646 823 4.641989 CCTATACAGCAGCTGGTCAAAAAT 59.358 41.667 26.38 7.70 35.51 1.82
647 824 4.009675 CCTATACAGCAGCTGGTCAAAAA 58.990 43.478 26.38 0.00 35.51 1.94
648 825 3.009033 ACCTATACAGCAGCTGGTCAAAA 59.991 43.478 26.38 1.80 35.51 2.44
649 826 2.571653 ACCTATACAGCAGCTGGTCAAA 59.428 45.455 26.38 4.55 35.51 2.69
650 827 2.093500 CACCTATACAGCAGCTGGTCAA 60.093 50.000 26.38 7.35 35.51 3.18
651 828 1.482182 CACCTATACAGCAGCTGGTCA 59.518 52.381 26.38 11.40 35.51 4.02
652 829 1.482593 ACACCTATACAGCAGCTGGTC 59.517 52.381 26.38 0.00 35.51 4.02
653 830 1.573108 ACACCTATACAGCAGCTGGT 58.427 50.000 26.38 13.85 35.51 4.00
654 831 2.695666 ACTACACCTATACAGCAGCTGG 59.304 50.000 26.38 10.73 35.51 4.85
655 832 4.363999 GAACTACACCTATACAGCAGCTG 58.636 47.826 21.54 21.54 37.52 4.24
656 833 3.066900 CGAACTACACCTATACAGCAGCT 59.933 47.826 0.00 0.00 0.00 4.24
657 834 3.066342 TCGAACTACACCTATACAGCAGC 59.934 47.826 0.00 0.00 0.00 5.25
658 835 4.895224 TCGAACTACACCTATACAGCAG 57.105 45.455 0.00 0.00 0.00 4.24
659 836 5.404946 GTTTCGAACTACACCTATACAGCA 58.595 41.667 0.00 0.00 0.00 4.41
660 837 4.802563 GGTTTCGAACTACACCTATACAGC 59.197 45.833 9.10 0.00 0.00 4.40
661 838 6.205101 AGGTTTCGAACTACACCTATACAG 57.795 41.667 15.97 0.00 37.91 2.74
662 839 6.183360 CGTAGGTTTCGAACTACACCTATACA 60.183 42.308 22.91 6.37 42.56 2.29
663 840 6.195165 CGTAGGTTTCGAACTACACCTATAC 58.805 44.000 22.91 15.63 42.56 1.47
664 841 6.363577 CGTAGGTTTCGAACTACACCTATA 57.636 41.667 22.91 7.26 42.56 1.31
665 842 5.240713 CGTAGGTTTCGAACTACACCTAT 57.759 43.478 22.91 6.71 42.56 2.57
666 843 4.685169 CGTAGGTTTCGAACTACACCTA 57.315 45.455 18.38 18.38 40.32 3.08
686 863 1.449601 CGTTGGATCCTTGACCCCG 60.450 63.158 14.23 0.97 0.00 5.73
707 896 3.313249 TGTAATGCTCTCGCCAAATCATG 59.687 43.478 0.00 0.00 34.43 3.07
715 904 1.398390 CCAACTTGTAATGCTCTCGCC 59.602 52.381 0.00 0.00 34.43 5.54
727 916 1.270839 CCATCGACCACTCCAACTTGT 60.271 52.381 0.00 0.00 0.00 3.16
791 980 8.731275 TGATATTTACATTGACTTGACCGAAT 57.269 30.769 0.00 0.00 0.00 3.34
792 981 8.554835 TTGATATTTACATTGACTTGACCGAA 57.445 30.769 0.00 0.00 0.00 4.30
793 982 7.201609 GCTTGATATTTACATTGACTTGACCGA 60.202 37.037 0.00 0.00 0.00 4.69
794 983 6.907212 GCTTGATATTTACATTGACTTGACCG 59.093 38.462 0.00 0.00 0.00 4.79
822 1011 4.465632 TTACTTCCGTCTGTATGCATGT 57.534 40.909 10.16 0.00 0.00 3.21
823 1012 5.049828 TCATTACTTCCGTCTGTATGCATG 58.950 41.667 10.16 0.00 0.00 4.06
824 1013 5.276461 TCATTACTTCCGTCTGTATGCAT 57.724 39.130 3.79 3.79 0.00 3.96
825 1014 4.729227 TCATTACTTCCGTCTGTATGCA 57.271 40.909 0.00 0.00 0.00 3.96
835 1024 4.058817 GGTGCTAAGGATCATTACTTCCG 58.941 47.826 0.00 0.00 37.10 4.30
839 1028 4.475016 ACTTGGGTGCTAAGGATCATTACT 59.525 41.667 0.00 0.00 0.00 2.24
855 1044 4.141688 GCTTAGTGAGCCTATAACTTGGGT 60.142 45.833 0.00 0.00 46.01 4.51
856 1045 4.381411 GCTTAGTGAGCCTATAACTTGGG 58.619 47.826 0.00 0.00 46.01 4.12
922 3908 0.109723 ACCTGGCCACATGTTTACGT 59.890 50.000 0.00 0.00 0.00 3.57
923 3909 1.735571 GTACCTGGCCACATGTTTACG 59.264 52.381 0.00 0.00 0.00 3.18
1005 3995 1.414181 AGGGTAAGAGATGGACATGCG 59.586 52.381 0.00 0.00 0.00 4.73
1168 4158 0.617413 ACCTGATGAGAAGGCACCAG 59.383 55.000 0.00 0.00 38.48 4.00
1177 4167 2.710902 CCGGCGACACCTGATGAGA 61.711 63.158 9.30 0.00 35.61 3.27
1215 4205 3.610114 GCTGATAATAAGGCGGTTGCATG 60.610 47.826 0.00 0.00 45.35 4.06
1220 4210 2.222027 GCAGCTGATAATAAGGCGGTT 58.778 47.619 20.43 0.00 0.00 4.44
1222 4212 1.160137 GGCAGCTGATAATAAGGCGG 58.840 55.000 20.43 0.00 0.00 6.13
1238 4228 1.971167 GGCACCAATTCTGACGGCA 60.971 57.895 0.00 0.00 0.00 5.69
1320 4313 3.297620 CTGTTGCAGGGTGGCACC 61.298 66.667 28.69 28.69 44.86 5.01
1451 4444 1.240641 TGGCATTACCCGTTGCACAG 61.241 55.000 0.00 0.00 40.66 3.66
1454 4447 0.529833 CAATGGCATTACCCGTTGCA 59.470 50.000 13.23 0.00 42.92 4.08
1458 4451 1.037030 CAGGCAATGGCATTACCCGT 61.037 55.000 22.98 5.71 43.71 5.28
1539 4547 0.605319 GAGGCCATGTTGTCCGTGAA 60.605 55.000 5.01 0.00 31.20 3.18
1670 4687 3.083349 CGGGATGAGGGTGAGGCA 61.083 66.667 0.00 0.00 0.00 4.75
1780 4806 1.607148 TGGTACACAGACAGACAGACG 59.393 52.381 0.00 0.00 0.00 4.18
1824 4850 2.889988 TTCCATGCGACGATGGCG 60.890 61.111 16.72 0.00 42.52 5.69
1826 4852 1.934589 TAAGTTCCATGCGACGATGG 58.065 50.000 15.86 15.86 43.96 3.51
1853 4879 7.067116 ACGCAAAATGCACGTAACATATATAC 58.933 34.615 3.87 0.00 45.36 1.47
1859 4885 2.697431 ACGCAAAATGCACGTAACAT 57.303 40.000 2.99 0.00 45.36 2.71
1865 4891 2.850321 ACTCAATACGCAAAATGCACG 58.150 42.857 2.99 0.00 45.36 5.34
1872 4898 4.832248 AGGAGATGAACTCAATACGCAAA 58.168 39.130 0.00 0.00 46.54 3.68
1876 4902 8.879342 AAGAATTAGGAGATGAACTCAATACG 57.121 34.615 0.00 0.00 46.54 3.06
1899 4925 6.696148 GGACCACGTATCTCAACTATACAAAG 59.304 42.308 0.00 0.00 31.43 2.77
1914 4940 2.492881 TGTACAACGATGGACCACGTAT 59.507 45.455 18.26 13.48 39.90 3.06
1916 4942 0.675083 TGTACAACGATGGACCACGT 59.325 50.000 13.98 13.98 39.90 4.49
1917 4943 1.924524 GATGTACAACGATGGACCACG 59.075 52.381 5.49 12.90 39.90 4.94
1962 4988 5.049886 CACAACGTATTGCTCTCATGCATAT 60.050 40.000 0.00 0.00 42.96 1.78
1981 5007 9.616634 CCATGTAGAATATATGAATTGCACAAC 57.383 33.333 0.00 0.00 42.05 3.32
2021 5048 1.534729 GGTGGCGGAAGTGAAGAAAT 58.465 50.000 0.00 0.00 0.00 2.17
2226 5266 3.288290 CGGGATCGGTAGCGAGCT 61.288 66.667 28.71 11.30 0.00 4.09
2314 5361 2.101082 TGTACAAGCACGTAGGTGTTGA 59.899 45.455 24.44 13.21 46.13 3.18
2322 5369 1.931709 GCTCGGTTGTACAAGCACGTA 60.932 52.381 30.88 15.66 38.62 3.57
2325 5372 0.941542 TTGCTCGGTTGTACAAGCAC 59.058 50.000 30.88 21.52 43.94 4.40
2336 5383 1.043116 TCCTGGATCGATTGCTCGGT 61.043 55.000 0.00 0.00 45.10 4.69
2359 5406 3.198068 ACAAGCACGTATAAGCTGATGG 58.802 45.455 0.00 0.00 41.70 3.51
2395 5455 3.781770 GACGATCGGGGCAGAGCAG 62.782 68.421 20.98 0.00 0.00 4.24
2396 5456 3.838271 GACGATCGGGGCAGAGCA 61.838 66.667 20.98 0.00 0.00 4.26
2469 5530 0.179029 ACAGGTCAGGGGAAACAACG 60.179 55.000 0.00 0.00 0.00 4.10
2483 5549 1.003355 CAGTTGGATCGGCACAGGT 60.003 57.895 0.00 0.00 0.00 4.00
2486 5552 1.672030 CAGCAGTTGGATCGGCACA 60.672 57.895 0.00 0.00 0.00 4.57
2513 5579 4.406173 AGCAGCAGTCGACGACGG 62.406 66.667 21.61 21.61 37.67 4.79
2514 5580 3.168604 CAGCAGCAGTCGACGACG 61.169 66.667 21.44 16.80 37.67 5.12
2515 5581 1.609840 GAACAGCAGCAGTCGACGAC 61.610 60.000 20.25 20.25 0.00 4.34
2516 5582 1.371758 GAACAGCAGCAGTCGACGA 60.372 57.895 10.46 0.00 0.00 4.20
2517 5583 2.375766 GGAACAGCAGCAGTCGACG 61.376 63.158 10.46 6.47 0.00 5.12
2518 5584 2.375766 CGGAACAGCAGCAGTCGAC 61.376 63.158 7.70 7.70 0.00 4.20
2519 5585 2.049156 CGGAACAGCAGCAGTCGA 60.049 61.111 0.00 0.00 0.00 4.20
2520 5586 3.782244 GCGGAACAGCAGCAGTCG 61.782 66.667 0.00 0.00 37.65 4.18
2521 5587 3.426568 GGCGGAACAGCAGCAGTC 61.427 66.667 0.00 0.00 39.65 3.51
2529 5595 4.394078 TCGACGACGGCGGAACAG 62.394 66.667 24.91 0.43 43.17 3.16
2530 5596 4.688419 GTCGACGACGGCGGAACA 62.688 66.667 24.91 0.00 43.17 3.18
2583 5649 4.854924 CGCCCGTGATGGATGGCA 62.855 66.667 0.00 0.00 44.22 4.92
2656 5722 2.464459 GCCTGCATGTACGCTGACC 61.464 63.158 0.00 0.00 33.02 4.02
2658 5724 1.091197 CATGCCTGCATGTACGCTGA 61.091 55.000 21.12 0.00 46.20 4.26
2687 5780 1.425428 GCATGCCTGCTTGTACGTC 59.575 57.895 6.36 0.00 45.32 4.34
2697 5790 3.896133 GACGCCCATGCATGCCTG 61.896 66.667 21.69 15.92 37.32 4.85
2698 5791 4.429522 TGACGCCCATGCATGCCT 62.430 61.111 21.69 1.31 37.32 4.75
2699 5792 3.896133 CTGACGCCCATGCATGCC 61.896 66.667 21.69 12.71 37.32 4.40
2700 5793 4.564116 GCTGACGCCCATGCATGC 62.564 66.667 21.69 11.82 37.32 4.06
2710 5803 1.739067 AATGAAAGTAGGGCTGACGC 58.261 50.000 0.00 0.00 0.00 5.19
2711 5804 3.600388 AGAAATGAAAGTAGGGCTGACG 58.400 45.455 0.00 0.00 0.00 4.35
2712 5805 5.249420 AGAAGAAATGAAAGTAGGGCTGAC 58.751 41.667 0.00 0.00 0.00 3.51
2713 5806 5.505181 AGAAGAAATGAAAGTAGGGCTGA 57.495 39.130 0.00 0.00 0.00 4.26
2714 5807 5.124617 GGAAGAAGAAATGAAAGTAGGGCTG 59.875 44.000 0.00 0.00 0.00 4.85
2715 5808 5.257262 GGAAGAAGAAATGAAAGTAGGGCT 58.743 41.667 0.00 0.00 0.00 5.19
2716 5809 4.399618 GGGAAGAAGAAATGAAAGTAGGGC 59.600 45.833 0.00 0.00 0.00 5.19
2717 5810 5.570320 TGGGAAGAAGAAATGAAAGTAGGG 58.430 41.667 0.00 0.00 0.00 3.53
2718 5811 7.709149 ATTGGGAAGAAGAAATGAAAGTAGG 57.291 36.000 0.00 0.00 0.00 3.18
2719 5812 8.391106 CGTATTGGGAAGAAGAAATGAAAGTAG 58.609 37.037 0.00 0.00 0.00 2.57
2720 5813 7.881232 ACGTATTGGGAAGAAGAAATGAAAGTA 59.119 33.333 0.00 0.00 0.00 2.24
2721 5814 6.715264 ACGTATTGGGAAGAAGAAATGAAAGT 59.285 34.615 0.00 0.00 0.00 2.66
2722 5815 7.145932 ACGTATTGGGAAGAAGAAATGAAAG 57.854 36.000 0.00 0.00 0.00 2.62
2723 5816 7.120138 GGTACGTATTGGGAAGAAGAAATGAAA 59.880 37.037 0.00 0.00 0.00 2.69
2724 5817 6.596497 GGTACGTATTGGGAAGAAGAAATGAA 59.404 38.462 0.00 0.00 0.00 2.57
2725 5818 6.110707 GGTACGTATTGGGAAGAAGAAATGA 58.889 40.000 0.00 0.00 0.00 2.57
2726 5819 5.296035 GGGTACGTATTGGGAAGAAGAAATG 59.704 44.000 0.00 0.00 0.00 2.32
2727 5820 5.191124 AGGGTACGTATTGGGAAGAAGAAAT 59.809 40.000 0.00 0.00 0.00 2.17
2728 5821 4.533311 AGGGTACGTATTGGGAAGAAGAAA 59.467 41.667 0.00 0.00 0.00 2.52
2729 5822 4.098894 AGGGTACGTATTGGGAAGAAGAA 58.901 43.478 0.00 0.00 0.00 2.52
2730 5823 3.703052 GAGGGTACGTATTGGGAAGAAGA 59.297 47.826 0.00 0.00 0.00 2.87
2731 5824 4.056092 GAGGGTACGTATTGGGAAGAAG 57.944 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.