Multiple sequence alignment - TraesCS4A01G290600

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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 TraesCS4A01G290600 chr4A 100.000 3251 0 0 1 3251 594285324 594282074 0.000000e+00 6004
1 TraesCS4A01G290600 chr4D 90.239 2551 131 42 123 2603 9183016 9185518 0.000000e+00 3223
2 TraesCS4A01G290600 chr4D 92.135 267 15 4 2955 3215 9197770 9198036 3.960000e-99 372
3 TraesCS4A01G290600 chr4D 97.761 134 2 1 1 133 9182861 9182994 2.520000e-56 230
4 TraesCS4A01G290600 chr4D 94.521 73 4 0 768 840 18693443 18693515 2.650000e-21 113
5 TraesCS4A01G290600 chr4B 92.297 1441 56 22 973 2374 17061217 17062641 0.000000e+00 1995
6 TraesCS4A01G290600 chr4B 84.080 804 54 29 1 740 17060331 17061124 0.000000e+00 708
7 TraesCS4A01G290600 chr4B 94.350 177 10 0 3039 3215 17064854 17065030 4.130000e-69 272
8 TraesCS4A01G290600 chr4B 84.112 214 26 7 2524 2736 17062776 17062982 1.980000e-47 200
9 TraesCS4A01G290600 chr2D 95.775 71 3 0 770 840 380407687 380407757 7.370000e-22 115
10 TraesCS4A01G290600 chr5B 95.714 70 3 0 771 840 70795563 70795632 2.650000e-21 113
11 TraesCS4A01G290600 chr2B 91.358 81 6 1 760 840 169856156 169856235 3.430000e-20 110
12 TraesCS4A01G290600 chr2B 93.243 74 5 0 770 843 758596339 758596266 3.430000e-20 110
13 TraesCS4A01G290600 chr2A 94.444 72 3 1 768 839 10382001 10382071 3.430000e-20 110
14 TraesCS4A01G290600 chr2A 94.366 71 4 0 770 840 515942526 515942596 3.430000e-20 110
15 TraesCS4A01G290600 chr7B 91.667 72 4 2 768 838 633676740 633676810 7.420000e-17 99


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 TraesCS4A01G290600 chr4A 594282074 594285324 3250 True 6004.00 6004 100.00000 1 3251 1 chr4A.!!$R1 3250
1 TraesCS4A01G290600 chr4D 9182861 9185518 2657 False 1726.50 3223 94.00000 1 2603 2 chr4D.!!$F3 2602
2 TraesCS4A01G290600 chr4B 17060331 17065030 4699 False 793.75 1995 88.70975 1 3215 4 chr4B.!!$F1 3214

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
592 661 0.108138 GCAGGCTGAACCGTGTAGAT 60.108 55.0 20.86 0.00 46.52 1.98 F
1334 1443 0.174389 TTTGCTTTGAGTTGCCGCAA 59.826 45.0 0.38 0.38 38.65 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1914 1.526575 CCATATGCCCGCCATGGAAC 61.527 60.0 18.4 0.91 41.53 3.62 R
3044 3224 0.110678 TCGGTGGTGCCCAAAATACA 59.889 50.0 0.0 0.00 34.18 2.29 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
170 209 2.041928 CTGCCCTCCCTCCCTCTT 59.958 66.667 0.00 0.00 0.00 2.85
188 231 0.239879 TTGCTCCGCGTGAAATTTCC 59.760 50.000 15.48 6.21 0.00 3.13
211 254 5.001237 TCGTGATTTAGGATTTACGAGCA 57.999 39.130 0.00 0.00 35.88 4.26
261 318 1.227383 GGGTCTGGGCCGATTCATT 59.773 57.895 0.00 0.00 0.00 2.57
262 319 0.819666 GGGTCTGGGCCGATTCATTC 60.820 60.000 0.00 0.00 0.00 2.67
371 433 1.254975 GCGGCTTGGTAATTTGGGGT 61.255 55.000 0.00 0.00 0.00 4.95
377 439 5.569832 CGGCTTGGTAATTTGGGGTAAATTT 60.570 40.000 0.00 0.00 44.49 1.82
381 443 7.575499 TTGGTAATTTGGGGTAAATTTGGAT 57.425 32.000 0.00 0.00 44.49 3.41
403 466 5.761165 TTTTTCCTCCCGTTTGTTAAGAG 57.239 39.130 0.00 0.00 0.00 2.85
406 469 4.903045 TCCTCCCGTTTGTTAAGAGATT 57.097 40.909 0.00 0.00 0.00 2.40
509 577 1.112113 ATCGATCTGGTGTAGCCGTT 58.888 50.000 0.00 0.00 41.21 4.44
514 582 0.320374 TCTGGTGTAGCCGTTTCTGG 59.680 55.000 0.00 0.00 41.21 3.86
543 611 6.095432 AGAGGGTCTGATGAATATTCTTCG 57.905 41.667 20.42 16.24 34.97 3.79
558 626 4.459390 TTCTTCGGTGGATAATCGACAA 57.541 40.909 0.00 0.00 32.39 3.18
559 627 4.665833 TCTTCGGTGGATAATCGACAAT 57.334 40.909 0.00 0.00 32.39 2.71
583 652 2.869233 TTTGTTTGAGCAGGCTGAAC 57.131 45.000 20.86 13.96 0.00 3.18
584 653 1.032014 TTGTTTGAGCAGGCTGAACC 58.968 50.000 20.86 6.48 39.61 3.62
586 655 1.148273 TTTGAGCAGGCTGAACCGT 59.852 52.632 20.86 0.00 46.52 4.83
589 658 1.292223 GAGCAGGCTGAACCGTGTA 59.708 57.895 20.86 0.00 46.52 2.90
590 659 0.737715 GAGCAGGCTGAACCGTGTAG 60.738 60.000 20.86 0.00 46.52 2.74
592 661 0.108138 GCAGGCTGAACCGTGTAGAT 60.108 55.000 20.86 0.00 46.52 1.98
606 679 8.701908 AACCGTGTAGATTATTAGTGATCCTA 57.298 34.615 0.00 0.00 0.00 2.94
637 710 8.308931 TGTCGGTACTCAGATTATTTTGTAAGT 58.691 33.333 0.00 0.00 0.00 2.24
722 812 5.308825 CCCTGTGGATTAGGCTAAATACTG 58.691 45.833 11.59 12.96 33.86 2.74
784 874 3.484649 CGTATGTCCGGAATTACTTGACG 59.515 47.826 5.23 4.11 0.00 4.35
785 875 1.717194 TGTCCGGAATTACTTGACGC 58.283 50.000 5.23 0.00 0.00 5.19
786 876 1.274167 TGTCCGGAATTACTTGACGCT 59.726 47.619 5.23 0.00 0.00 5.07
787 877 1.925185 GTCCGGAATTACTTGACGCTC 59.075 52.381 5.23 0.00 0.00 5.03
788 878 1.546923 TCCGGAATTACTTGACGCTCA 59.453 47.619 0.00 0.00 0.00 4.26
789 879 2.028839 TCCGGAATTACTTGACGCTCAA 60.029 45.455 0.00 1.48 34.79 3.02
790 880 2.739913 CCGGAATTACTTGACGCTCAAA 59.260 45.455 0.00 0.00 35.73 2.69
791 881 3.374058 CCGGAATTACTTGACGCTCAAAT 59.626 43.478 0.00 0.00 35.73 2.32
792 882 4.334443 CGGAATTACTTGACGCTCAAATG 58.666 43.478 2.82 0.00 35.73 2.32
793 883 4.662145 GGAATTACTTGACGCTCAAATGG 58.338 43.478 2.82 0.00 35.73 3.16
794 884 4.394920 GGAATTACTTGACGCTCAAATGGA 59.605 41.667 2.82 0.00 35.73 3.41
795 885 5.066505 GGAATTACTTGACGCTCAAATGGAT 59.933 40.000 2.82 0.00 35.73 3.41
796 886 4.944962 TTACTTGACGCTCAAATGGATG 57.055 40.909 2.82 0.00 35.73 3.51
797 887 2.783135 ACTTGACGCTCAAATGGATGT 58.217 42.857 2.82 0.00 35.73 3.06
798 888 3.937814 ACTTGACGCTCAAATGGATGTA 58.062 40.909 2.82 0.00 35.73 2.29
799 889 4.517285 ACTTGACGCTCAAATGGATGTAT 58.483 39.130 2.82 0.00 35.73 2.29
800 890 4.572389 ACTTGACGCTCAAATGGATGTATC 59.428 41.667 2.82 0.00 35.73 2.24
849 939 4.700692 TCTGTTTGAGCGTCTACATCTAGT 59.299 41.667 0.00 0.00 0.00 2.57
852 942 1.676529 TGAGCGTCTACATCTAGTGCC 59.323 52.381 0.00 0.00 0.00 5.01
962 1052 9.244799 GTGATCTTTTTGTTAGATTTCCGTTTT 57.755 29.630 0.00 0.00 32.64 2.43
1127 1219 3.194861 TCTGTGTGTTGTGTAACTCTGC 58.805 45.455 0.00 0.00 38.04 4.26
1137 1229 4.006989 TGTGTAACTCTGCACTGTTTGTT 58.993 39.130 5.11 0.00 38.82 2.83
1158 1251 8.597662 TTGTTATAACTTGTAGTGTTGAGGAC 57.402 34.615 16.33 0.00 0.00 3.85
1167 1260 6.268825 TGTAGTGTTGAGGACTACATTCTC 57.731 41.667 8.35 0.00 46.93 2.87
1331 1440 4.828291 CAATATTTGCTTTGAGTTGCCG 57.172 40.909 0.00 0.00 0.00 5.69
1334 1443 0.174389 TTTGCTTTGAGTTGCCGCAA 59.826 45.000 0.38 0.38 38.65 4.85
1519 1628 0.250295 TCAAAGAACACGCCTGGAGG 60.250 55.000 0.00 0.00 38.53 4.30
1589 1698 3.573967 AGGCTGATCCGAACAACAATTTT 59.426 39.130 0.00 0.00 40.77 1.82
1721 1830 1.615262 GGGCCTGTTCCCTATGCTT 59.385 57.895 0.84 0.00 43.13 3.91
1727 1836 3.891049 CCTGTTCCCTATGCTTAGCTTT 58.109 45.455 5.60 0.00 0.00 3.51
1742 1851 3.323751 AGCTTTCAAATGCATGGGTTC 57.676 42.857 0.00 0.00 0.00 3.62
1805 1914 2.282816 TTTGGTCACGGCCATGGG 60.283 61.111 15.13 0.00 38.48 4.00
1916 2025 1.416401 GCCCTTCTTATCATGGTCGGA 59.584 52.381 0.00 0.00 0.00 4.55
1951 2060 0.107945 AGCCTCCTCGCAGCTTAAAG 60.108 55.000 0.00 0.00 31.27 1.85
1953 2062 1.946283 GCCTCCTCGCAGCTTAAAGTT 60.946 52.381 0.00 0.00 0.00 2.66
2035 2144 4.649674 TGGTGTAGGCTTATCTCTACCAAG 59.350 45.833 0.00 0.00 36.07 3.61
2037 2146 5.452077 GGTGTAGGCTTATCTCTACCAAGTG 60.452 48.000 0.00 0.00 36.07 3.16
2049 2158 2.005370 ACCAAGTGGGAGACGAGTTA 57.995 50.000 1.69 0.00 41.15 2.24
2050 2159 2.322658 ACCAAGTGGGAGACGAGTTAA 58.677 47.619 1.69 0.00 41.15 2.01
2051 2160 2.904434 ACCAAGTGGGAGACGAGTTAAT 59.096 45.455 1.69 0.00 41.15 1.40
2052 2161 3.326880 ACCAAGTGGGAGACGAGTTAATT 59.673 43.478 1.69 0.00 41.15 1.40
2175 2306 5.614923 TGATAAACGTGGTGTACAATTGG 57.385 39.130 10.83 0.00 0.00 3.16
2325 2456 1.068333 CAAGGTGTTGCCATTCTTCGG 60.068 52.381 0.00 0.00 40.61 4.30
2326 2457 0.400213 AGGTGTTGCCATTCTTCGGA 59.600 50.000 0.00 0.00 40.61 4.55
2390 2552 0.770499 TGTGAAGGTTGCAGATGGGA 59.230 50.000 0.00 0.00 0.00 4.37
2458 2620 4.082625 TGAATCTTCTACTGTAACGGCGAA 60.083 41.667 16.62 0.00 0.00 4.70
2459 2621 3.207474 TCTTCTACTGTAACGGCGAAC 57.793 47.619 16.62 12.23 0.00 3.95
2482 2653 1.198637 GCTCCACACACAAGCAGAATC 59.801 52.381 0.00 0.00 36.06 2.52
2523 2694 2.880890 AGACCTGTGAATTTGTCTGCAC 59.119 45.455 0.00 0.00 36.74 4.57
2548 2719 2.877168 GGCTATTCTGCTGAATCACCAG 59.123 50.000 20.59 13.92 41.55 4.00
2607 2784 2.760092 AGACAAAGCAAAACAAGCCTGA 59.240 40.909 0.00 0.00 0.00 3.86
2613 2790 1.134551 GCAAAACAAGCCTGAAACCCA 60.135 47.619 0.00 0.00 0.00 4.51
2616 2793 2.683211 AACAAGCCTGAAACCCAGAT 57.317 45.000 0.00 0.00 45.78 2.90
2617 2794 2.683211 ACAAGCCTGAAACCCAGATT 57.317 45.000 0.00 0.00 45.78 2.40
2618 2795 2.519013 ACAAGCCTGAAACCCAGATTC 58.481 47.619 0.00 0.00 45.78 2.52
2619 2796 1.821136 CAAGCCTGAAACCCAGATTCC 59.179 52.381 0.00 0.00 45.78 3.01
2620 2797 0.332972 AGCCTGAAACCCAGATTCCC 59.667 55.000 0.00 0.00 45.78 3.97
2621 2798 0.332972 GCCTGAAACCCAGATTCCCT 59.667 55.000 0.00 0.00 45.78 4.20
2623 2800 1.635487 CCTGAAACCCAGATTCCCTGA 59.365 52.381 0.00 0.00 45.78 3.86
2624 2801 2.041620 CCTGAAACCCAGATTCCCTGAA 59.958 50.000 0.00 0.00 45.78 3.02
2625 2802 3.084786 CTGAAACCCAGATTCCCTGAAC 58.915 50.000 0.00 0.00 45.78 3.18
2626 2803 2.445145 TGAAACCCAGATTCCCTGAACA 59.555 45.455 0.00 0.00 45.78 3.18
2627 2804 2.887151 AACCCAGATTCCCTGAACAG 57.113 50.000 0.00 0.00 45.78 3.16
2628 2805 1.747444 ACCCAGATTCCCTGAACAGT 58.253 50.000 1.18 0.00 45.78 3.55
2629 2806 1.630878 ACCCAGATTCCCTGAACAGTC 59.369 52.381 1.18 0.00 45.78 3.51
2630 2807 1.630369 CCCAGATTCCCTGAACAGTCA 59.370 52.381 1.18 0.00 45.78 3.41
2666 2844 3.629398 GTGATTCCCCATGTTCACAGATC 59.371 47.826 0.00 0.00 38.63 2.75
2668 2846 0.107703 TCCCCATGTTCACAGATCGC 60.108 55.000 0.00 0.00 0.00 4.58
2678 2856 4.391830 TGTTCACAGATCGCACTATTTTCC 59.608 41.667 0.00 0.00 0.00 3.13
2679 2857 4.471904 TCACAGATCGCACTATTTTCCT 57.528 40.909 0.00 0.00 0.00 3.36
2680 2858 4.832248 TCACAGATCGCACTATTTTCCTT 58.168 39.130 0.00 0.00 0.00 3.36
2682 2860 6.403049 TCACAGATCGCACTATTTTCCTTAA 58.597 36.000 0.00 0.00 0.00 1.85
2683 2861 6.876789 TCACAGATCGCACTATTTTCCTTAAA 59.123 34.615 0.00 0.00 0.00 1.52
2687 2865 8.616076 CAGATCGCACTATTTTCCTTAAAGATT 58.384 33.333 0.00 0.00 0.00 2.40
2689 2867 6.551736 TCGCACTATTTTCCTTAAAGATTGC 58.448 36.000 0.00 0.00 39.10 3.56
2690 2868 6.150307 TCGCACTATTTTCCTTAAAGATTGCA 59.850 34.615 0.00 0.00 41.16 4.08
2699 2877 6.509418 TCCTTAAAGATTGCATGGTTACAC 57.491 37.500 0.00 0.00 0.00 2.90
2708 2886 4.717233 TGCATGGTTACACAAATCATCC 57.283 40.909 0.00 0.00 36.76 3.51
2710 2888 4.082300 TGCATGGTTACACAAATCATCCAC 60.082 41.667 0.00 0.00 36.76 4.02
2715 2893 2.925578 ACACAAATCATCCACATGCG 57.074 45.000 0.00 0.00 0.00 4.73
2718 2896 3.173599 CACAAATCATCCACATGCGAAC 58.826 45.455 0.00 0.00 0.00 3.95
2719 2897 3.084039 ACAAATCATCCACATGCGAACT 58.916 40.909 0.00 0.00 0.00 3.01
2727 2905 2.235155 TCCACATGCGAACTAAGCCTAA 59.765 45.455 0.00 0.00 0.00 2.69
2729 2907 3.262420 CACATGCGAACTAAGCCTAACT 58.738 45.455 0.00 0.00 0.00 2.24
2741 2919 3.567478 AGCCTAACTTAGATGGCCAAG 57.433 47.619 10.96 4.73 45.94 3.61
2742 2920 2.846827 AGCCTAACTTAGATGGCCAAGT 59.153 45.455 10.96 5.56 45.94 3.16
2745 2923 4.626529 GCCTAACTTAGATGGCCAAGTTCT 60.627 45.833 21.08 16.66 42.48 3.01
2747 2925 5.946377 CCTAACTTAGATGGCCAAGTTCTTT 59.054 40.000 21.08 9.07 42.48 2.52
2748 2926 6.434340 CCTAACTTAGATGGCCAAGTTCTTTT 59.566 38.462 21.08 10.99 42.48 2.27
2749 2927 6.731292 AACTTAGATGGCCAAGTTCTTTTT 57.269 33.333 10.96 0.00 40.12 1.94
2750 2928 6.089249 ACTTAGATGGCCAAGTTCTTTTTG 57.911 37.500 10.96 2.41 30.89 2.44
2752 2930 4.326504 AGATGGCCAAGTTCTTTTTGTG 57.673 40.909 10.96 0.00 0.00 3.33
2755 2933 2.834549 TGGCCAAGTTCTTTTTGTGGAA 59.165 40.909 0.61 0.00 0.00 3.53
2756 2934 3.194861 GGCCAAGTTCTTTTTGTGGAAC 58.805 45.455 0.00 0.00 41.24 3.62
2765 2943 6.990939 AGTTCTTTTTGTGGAACTAGACTACC 59.009 38.462 0.00 0.00 46.72 3.18
2766 2944 5.861727 TCTTTTTGTGGAACTAGACTACCC 58.138 41.667 0.00 0.00 38.04 3.69
2767 2945 5.367352 TCTTTTTGTGGAACTAGACTACCCA 59.633 40.000 0.00 0.00 38.04 4.51
2768 2946 4.884668 TTTGTGGAACTAGACTACCCAG 57.115 45.455 0.00 0.00 38.04 4.45
2769 2947 3.820195 TGTGGAACTAGACTACCCAGA 57.180 47.619 0.00 0.00 38.04 3.86
2770 2948 4.332683 TGTGGAACTAGACTACCCAGAT 57.667 45.455 0.00 0.00 38.04 2.90
2771 2949 4.684724 TGTGGAACTAGACTACCCAGATT 58.315 43.478 0.00 0.00 38.04 2.40
2772 2950 4.710375 TGTGGAACTAGACTACCCAGATTC 59.290 45.833 0.00 0.00 38.04 2.52
2773 2951 4.710375 GTGGAACTAGACTACCCAGATTCA 59.290 45.833 0.00 0.00 0.00 2.57
2774 2952 5.187186 GTGGAACTAGACTACCCAGATTCAA 59.813 44.000 0.00 0.00 0.00 2.69
2775 2953 5.783360 TGGAACTAGACTACCCAGATTCAAA 59.217 40.000 0.00 0.00 0.00 2.69
2776 2954 6.443849 TGGAACTAGACTACCCAGATTCAAAT 59.556 38.462 0.00 0.00 0.00 2.32
2777 2955 7.037586 TGGAACTAGACTACCCAGATTCAAATT 60.038 37.037 0.00 0.00 0.00 1.82
2778 2956 7.829706 GGAACTAGACTACCCAGATTCAAATTT 59.170 37.037 0.00 0.00 0.00 1.82
2779 2957 9.232473 GAACTAGACTACCCAGATTCAAATTTT 57.768 33.333 0.00 0.00 0.00 1.82
2781 2959 9.892130 ACTAGACTACCCAGATTCAAATTTTAG 57.108 33.333 0.00 0.00 0.00 1.85
2783 2961 8.794335 AGACTACCCAGATTCAAATTTTAGAC 57.206 34.615 0.00 0.00 0.00 2.59
2784 2962 7.829706 AGACTACCCAGATTCAAATTTTAGACC 59.170 37.037 0.00 0.00 0.00 3.85
2785 2963 7.699878 ACTACCCAGATTCAAATTTTAGACCT 58.300 34.615 0.00 0.00 0.00 3.85
2786 2964 8.832735 ACTACCCAGATTCAAATTTTAGACCTA 58.167 33.333 0.00 0.00 0.00 3.08
2787 2965 7.939784 ACCCAGATTCAAATTTTAGACCTAC 57.060 36.000 0.00 0.00 0.00 3.18
2788 2966 7.466804 ACCCAGATTCAAATTTTAGACCTACA 58.533 34.615 0.00 0.00 0.00 2.74
2789 2967 8.116026 ACCCAGATTCAAATTTTAGACCTACAT 58.884 33.333 0.00 0.00 0.00 2.29
2790 2968 8.971073 CCCAGATTCAAATTTTAGACCTACATT 58.029 33.333 0.00 0.00 0.00 2.71
2821 2999 1.134367 TGCCGGTACATTCTCTCGAAG 59.866 52.381 1.90 0.00 31.60 3.79
2822 3000 1.536284 GCCGGTACATTCTCTCGAAGG 60.536 57.143 1.90 0.00 37.00 3.46
2832 3010 3.283259 TCTCTCGAAGGTGCTCATAGA 57.717 47.619 0.00 0.00 0.00 1.98
2833 3011 3.621558 TCTCTCGAAGGTGCTCATAGAA 58.378 45.455 0.00 0.00 0.00 2.10
2834 3012 4.017126 TCTCTCGAAGGTGCTCATAGAAA 58.983 43.478 0.00 0.00 0.00 2.52
2836 3014 5.828328 TCTCTCGAAGGTGCTCATAGAAATA 59.172 40.000 0.00 0.00 0.00 1.40
2837 3015 6.016693 TCTCTCGAAGGTGCTCATAGAAATAG 60.017 42.308 0.00 0.00 0.00 1.73
2845 3023 5.277058 GGTGCTCATAGAAATAGAGTTTGCG 60.277 44.000 0.00 0.00 0.00 4.85
2847 3025 5.874810 TGCTCATAGAAATAGAGTTTGCGTT 59.125 36.000 0.00 0.00 0.00 4.84
2848 3026 6.371548 TGCTCATAGAAATAGAGTTTGCGTTT 59.628 34.615 0.00 0.00 0.00 3.60
2849 3027 6.902417 GCTCATAGAAATAGAGTTTGCGTTTC 59.098 38.462 0.00 0.00 0.00 2.78
2851 3029 7.963981 TCATAGAAATAGAGTTTGCGTTTCTG 58.036 34.615 8.46 0.00 38.95 3.02
2861 3039 6.313905 AGAGTTTGCGTTTCTGTATTCATAGG 59.686 38.462 0.00 0.00 0.00 2.57
2872 3050 4.960938 TGTATTCATAGGGATGAGTGTGC 58.039 43.478 0.00 0.00 43.03 4.57
2882 3060 3.399770 GAGTGTGCGCGCGTGTTA 61.400 61.111 32.35 12.81 0.00 2.41
2887 3065 2.431771 TGCGCGCGTGTTATGAGT 60.432 55.556 32.35 0.00 0.00 3.41
2888 3066 2.024868 TGCGCGCGTGTTATGAGTT 61.025 52.632 32.35 0.00 0.00 3.01
2891 3069 0.436913 CGCGCGTGTTATGAGTTTCA 59.563 50.000 24.19 0.00 0.00 2.69
2892 3070 1.060553 CGCGCGTGTTATGAGTTTCAT 59.939 47.619 24.19 0.00 40.72 2.57
2893 3071 2.473868 CGCGCGTGTTATGAGTTTCATT 60.474 45.455 24.19 0.00 38.26 2.57
2895 3073 4.643953 GCGCGTGTTATGAGTTTCATTAA 58.356 39.130 8.43 0.00 38.26 1.40
2896 3074 4.490890 GCGCGTGTTATGAGTTTCATTAAC 59.509 41.667 8.43 2.02 38.26 2.01
2915 3093 9.692749 TCATTAACTCTGTACTGTGTTTAGAAG 57.307 33.333 20.49 9.70 0.00 2.85
2916 3094 9.692749 CATTAACTCTGTACTGTGTTTAGAAGA 57.307 33.333 20.49 4.24 0.00 2.87
2919 3097 8.649973 AACTCTGTACTGTGTTTAGAAGAAAG 57.350 34.615 12.67 0.00 0.00 2.62
2920 3098 8.008513 ACTCTGTACTGTGTTTAGAAGAAAGA 57.991 34.615 2.04 0.00 0.00 2.52
2921 3099 8.475639 ACTCTGTACTGTGTTTAGAAGAAAGAA 58.524 33.333 2.04 0.00 0.00 2.52
2954 3132 8.916654 CATCAATATACTTGGCTAGTTTAGTCG 58.083 37.037 6.96 0.01 38.33 4.18
2955 3133 8.229253 TCAATATACTTGGCTAGTTTAGTCGA 57.771 34.615 6.96 2.10 38.33 4.20
2956 3134 8.133627 TCAATATACTTGGCTAGTTTAGTCGAC 58.866 37.037 7.70 7.70 38.33 4.20
2957 3135 3.213249 ACTTGGCTAGTTTAGTCGACG 57.787 47.619 10.46 0.00 31.29 5.12
2971 3149 1.198408 GTCGACGCGGGTATATCATCA 59.802 52.381 12.47 0.00 0.00 3.07
2978 3156 4.112634 CGCGGGTATATCATCATCGAAAT 58.887 43.478 0.00 0.00 0.00 2.17
2979 3157 4.026558 CGCGGGTATATCATCATCGAAATG 60.027 45.833 0.00 5.10 0.00 2.32
2982 3160 6.199154 GCGGGTATATCATCATCGAAATGTAG 59.801 42.308 10.03 0.00 34.32 2.74
2988 3166 5.500645 TCATCATCGAAATGTAGAGTCGT 57.499 39.130 10.03 0.00 36.21 4.34
2993 3171 1.466866 CGAAATGTAGAGTCGTCGCCA 60.467 52.381 0.00 0.00 0.00 5.69
3004 3182 1.070577 GTCGTCGCCATGTATGATTGC 60.071 52.381 0.00 0.00 0.00 3.56
3005 3183 0.936600 CGTCGCCATGTATGATTGCA 59.063 50.000 0.00 0.00 0.00 4.08
3013 3193 4.786292 GCCATGTATGATTGCACTGTTACG 60.786 45.833 0.00 0.00 0.00 3.18
3028 3208 4.035909 ACTGTTACGGCAACTTCGAATTTT 59.964 37.500 0.00 0.00 38.05 1.82
3030 3210 3.596562 GTTACGGCAACTTCGAATTTTCG 59.403 43.478 14.68 14.68 41.71 3.46
3031 3211 6.973888 TGTTACGGCAACTTCGAATTTTCGA 61.974 40.000 19.88 11.11 45.85 3.71
3081 4866 2.480419 CCGATTCGCATCTATCCAAACC 59.520 50.000 0.00 0.00 0.00 3.27
3086 4871 5.560966 TTCGCATCTATCCAAACCTTTTC 57.439 39.130 0.00 0.00 0.00 2.29
3155 4940 8.062448 CCGATTCGTATCTATCCAAACTTTTTC 58.938 37.037 5.20 0.00 0.00 2.29
3169 4954 5.941948 AACTTTTTCCTTCATGGACGTAG 57.058 39.130 0.00 0.00 46.14 3.51
3199 4984 1.029408 ACCGCCGATGCAATGCTTTA 61.029 50.000 6.82 0.00 37.32 1.85
3215 5000 5.964958 TGCTTTAGCTTGCTCACTTTTAT 57.035 34.783 0.00 0.00 42.66 1.40
3216 5001 6.331369 TGCTTTAGCTTGCTCACTTTTATT 57.669 33.333 0.00 0.00 42.66 1.40
3217 5002 6.748132 TGCTTTAGCTTGCTCACTTTTATTT 58.252 32.000 0.00 0.00 42.66 1.40
3218 5003 7.209475 TGCTTTAGCTTGCTCACTTTTATTTT 58.791 30.769 0.00 0.00 42.66 1.82
3219 5004 7.382218 TGCTTTAGCTTGCTCACTTTTATTTTC 59.618 33.333 0.00 0.00 42.66 2.29
3220 5005 7.409767 GCTTTAGCTTGCTCACTTTTATTTTCG 60.410 37.037 0.00 0.00 38.21 3.46
3221 5006 4.229876 AGCTTGCTCACTTTTATTTTCGC 58.770 39.130 0.00 0.00 0.00 4.70
3222 5007 3.980775 GCTTGCTCACTTTTATTTTCGCA 59.019 39.130 0.00 0.00 0.00 5.10
3223 5008 4.444056 GCTTGCTCACTTTTATTTTCGCAA 59.556 37.500 0.00 0.00 35.22 4.85
3224 5009 5.051106 GCTTGCTCACTTTTATTTTCGCAAA 60.051 36.000 0.00 0.00 35.95 3.68
3225 5010 6.509358 GCTTGCTCACTTTTATTTTCGCAAAA 60.509 34.615 0.00 0.00 35.95 2.44
3226 5011 6.893958 TGCTCACTTTTATTTTCGCAAAAA 57.106 29.167 0.00 0.00 38.66 1.94
3227 5012 6.932051 TGCTCACTTTTATTTTCGCAAAAAG 58.068 32.000 5.48 5.48 42.94 2.27
3228 5013 6.754209 TGCTCACTTTTATTTTCGCAAAAAGA 59.246 30.769 12.32 0.00 40.87 2.52
3229 5014 7.276658 TGCTCACTTTTATTTTCGCAAAAAGAA 59.723 29.630 12.32 0.00 40.87 2.52
3230 5015 8.113675 GCTCACTTTTATTTTCGCAAAAAGAAA 58.886 29.630 12.32 0.00 41.38 2.52
3231 5016 9.965748 CTCACTTTTATTTTCGCAAAAAGAAAA 57.034 25.926 13.13 13.13 45.81 2.29
3234 5019 9.272901 ACTTTTATTTTCGCAAAAAGAAAAAGC 57.727 25.926 21.48 0.00 46.54 3.51
3235 5020 9.489393 CTTTTATTTTCGCAAAAAGAAAAAGCT 57.511 25.926 14.31 0.00 46.54 3.74
3236 5021 9.833182 TTTTATTTTCGCAAAAAGAAAAAGCTT 57.167 22.222 11.79 0.00 45.40 3.74
3237 5022 8.819152 TTATTTTCGCAAAAAGAAAAAGCTTG 57.181 26.923 0.00 0.00 46.45 4.01
3238 5023 3.923827 TCGCAAAAAGAAAAAGCTTGC 57.076 38.095 0.00 0.00 39.16 4.01
3239 5024 3.520569 TCGCAAAAAGAAAAAGCTTGCT 58.479 36.364 0.00 0.00 40.13 3.91
3240 5025 3.551485 TCGCAAAAAGAAAAAGCTTGCTC 59.449 39.130 0.00 0.00 40.13 4.26
3241 5026 3.306703 CGCAAAAAGAAAAAGCTTGCTCA 59.693 39.130 0.00 0.00 40.13 4.26
3242 5027 4.581493 GCAAAAAGAAAAAGCTTGCTCAC 58.419 39.130 0.00 0.00 39.39 3.51
3243 5028 4.330894 GCAAAAAGAAAAAGCTTGCTCACT 59.669 37.500 0.00 0.00 39.39 3.41
3244 5029 5.163824 GCAAAAAGAAAAAGCTTGCTCACTT 60.164 36.000 0.00 0.00 39.39 3.16
3245 5030 6.621380 GCAAAAAGAAAAAGCTTGCTCACTTT 60.621 34.615 0.00 5.73 39.39 2.66
3246 5031 7.300320 CAAAAAGAAAAAGCTTGCTCACTTTT 58.700 30.769 0.00 11.09 45.53 2.27
3247 5032 8.442384 CAAAAAGAAAAAGCTTGCTCACTTTTA 58.558 29.630 19.80 0.00 43.45 1.52
3248 5033 7.525688 AAAGAAAAAGCTTGCTCACTTTTAC 57.474 32.000 0.00 0.00 43.45 2.01
3249 5034 5.273944 AGAAAAAGCTTGCTCACTTTTACG 58.726 37.500 0.00 0.00 43.45 3.18
3250 5035 4.632538 AAAAGCTTGCTCACTTTTACGT 57.367 36.364 0.00 0.00 42.67 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 178 4.551729 GCAGGCGCCATTTACCTA 57.448 55.556 31.54 0.00 30.84 3.08
211 254 3.492353 CATCCGCCCCCACAGGAT 61.492 66.667 0.00 0.00 44.91 3.24
261 318 1.430632 GACGCCGACAGAATACCGA 59.569 57.895 0.00 0.00 0.00 4.69
262 319 1.588139 GGACGCCGACAGAATACCG 60.588 63.158 0.00 0.00 0.00 4.02
371 433 6.673839 AACGGGAGGAAAAATCCAAATTTA 57.326 33.333 0.00 0.00 38.70 1.40
377 439 2.952116 ACAAACGGGAGGAAAAATCCA 58.048 42.857 0.00 0.00 38.70 3.41
381 443 5.438833 TCTCTTAACAAACGGGAGGAAAAA 58.561 37.500 0.00 0.00 0.00 1.94
449 517 8.538856 CACGCTCTAGAAGAAGATTAATTTCTG 58.461 37.037 9.44 2.46 35.20 3.02
509 577 4.127918 TCAGACCCTCTAGAAACCAGAA 57.872 45.455 0.00 0.00 0.00 3.02
514 582 8.646900 AGAATATTCATCAGACCCTCTAGAAAC 58.353 37.037 17.56 0.00 0.00 2.78
575 644 4.755266 AATAATCTACACGGTTCAGCCT 57.245 40.909 0.00 0.00 34.25 4.58
583 652 9.574458 CAATAGGATCACTAATAATCTACACGG 57.426 37.037 0.00 0.00 34.79 4.94
584 653 9.077674 GCAATAGGATCACTAATAATCTACACG 57.922 37.037 0.00 0.00 34.79 4.49
589 658 8.031864 CGACAGCAATAGGATCACTAATAATCT 58.968 37.037 0.00 0.00 34.79 2.40
590 659 7.276658 CCGACAGCAATAGGATCACTAATAATC 59.723 40.741 0.00 0.00 34.79 1.75
592 661 6.041637 ACCGACAGCAATAGGATCACTAATAA 59.958 38.462 0.00 0.00 34.79 1.40
606 679 3.895232 AATCTGAGTACCGACAGCAAT 57.105 42.857 7.24 0.00 34.57 3.56
637 710 6.293735 CCCAGAAACGTTGATTTTGCTACTTA 60.294 38.462 0.00 0.00 0.00 2.24
774 864 4.943705 ACATCCATTTGAGCGTCAAGTAAT 59.056 37.500 1.72 0.00 37.70 1.89
775 865 4.323417 ACATCCATTTGAGCGTCAAGTAA 58.677 39.130 1.72 0.00 37.70 2.24
778 868 4.813161 AGATACATCCATTTGAGCGTCAAG 59.187 41.667 1.72 0.00 37.70 3.02
779 869 4.769688 AGATACATCCATTTGAGCGTCAA 58.230 39.130 0.00 0.00 34.03 3.18
780 870 4.406648 AGATACATCCATTTGAGCGTCA 57.593 40.909 0.00 0.00 0.00 4.35
781 871 5.753438 TGTTAGATACATCCATTTGAGCGTC 59.247 40.000 0.00 0.00 0.00 5.19
782 872 5.523916 GTGTTAGATACATCCATTTGAGCGT 59.476 40.000 0.00 0.00 39.39 5.07
783 873 5.755375 AGTGTTAGATACATCCATTTGAGCG 59.245 40.000 0.00 0.00 39.39 5.03
784 874 8.662781 TTAGTGTTAGATACATCCATTTGAGC 57.337 34.615 0.00 0.00 39.39 4.26
791 881 9.740239 GACGTATTTTAGTGTTAGATACATCCA 57.260 33.333 0.00 0.00 39.39 3.41
792 882 9.962783 AGACGTATTTTAGTGTTAGATACATCC 57.037 33.333 0.00 0.00 39.39 3.51
832 922 1.676529 GGCACTAGATGTAGACGCTCA 59.323 52.381 3.49 0.00 32.26 4.26
849 939 2.421388 CCATCCGGAATTACTTGAGGCA 60.421 50.000 9.01 0.00 0.00 4.75
852 942 3.388024 TCCTCCATCCGGAATTACTTGAG 59.612 47.826 9.01 1.80 42.21 3.02
882 972 5.290158 GCTAAAATACAGCTGCGTTGTAGTA 59.710 40.000 15.27 0.00 33.21 1.82
883 973 4.092968 GCTAAAATACAGCTGCGTTGTAGT 59.907 41.667 15.27 0.00 33.21 2.73
884 974 4.092821 TGCTAAAATACAGCTGCGTTGTAG 59.907 41.667 15.27 17.15 39.83 2.74
1008 1099 8.410912 CAATGTGAAAATACATCATCCATGTCT 58.589 33.333 0.00 0.00 42.62 3.41
1009 1100 7.650504 CCAATGTGAAAATACATCATCCATGTC 59.349 37.037 0.00 0.00 42.62 3.06
1127 1219 9.433317 CAACACTACAAGTTATAACAAACAGTG 57.567 33.333 24.14 24.14 35.73 3.66
1158 1251 7.319646 ACACTGCTAGAAAGAAGAGAATGTAG 58.680 38.462 0.00 0.00 31.96 2.74
1167 1260 4.380531 TCACCAACACTGCTAGAAAGAAG 58.619 43.478 0.00 0.00 34.06 2.85
1221 1330 2.611292 CGGCCATCTTGAGCTTCTTAAG 59.389 50.000 2.24 0.00 0.00 1.85
1331 1440 4.808364 CAGAGAGTTACTATTGGCTCTTGC 59.192 45.833 0.00 0.00 38.31 4.01
1334 1443 4.404073 CCACAGAGAGTTACTATTGGCTCT 59.596 45.833 0.00 0.00 40.58 4.09
1519 1628 3.567797 GGCGCTGAGGAATGTCGC 61.568 66.667 7.64 0.00 44.39 5.19
1577 1686 2.967781 GCGTTGCCAAAATTGTTGTTC 58.032 42.857 0.00 0.00 0.00 3.18
1655 1764 2.047274 CACCGTCCATTCGCCAGT 60.047 61.111 0.00 0.00 0.00 4.00
1721 1830 3.195396 GGAACCCATGCATTTGAAAGCTA 59.805 43.478 0.00 0.00 0.00 3.32
1742 1851 1.822506 CATATGCAGCTGGATCTGGG 58.177 55.000 25.15 8.78 34.74 4.45
1805 1914 1.526575 CCATATGCCCGCCATGGAAC 61.527 60.000 18.40 0.91 41.53 3.62
1951 2060 8.853345 CACAATTTTGATGATAGCAGTAACAAC 58.147 33.333 0.00 0.00 0.00 3.32
1953 2062 7.176515 ACCACAATTTTGATGATAGCAGTAACA 59.823 33.333 0.00 0.00 0.00 2.41
2012 2121 4.259933 TGGTAGAGATAAGCCTACACCA 57.740 45.455 0.00 0.00 37.56 4.17
2035 2144 4.189639 ACAGAATTAACTCGTCTCCCAC 57.810 45.455 0.00 0.00 0.00 4.61
2037 2146 3.858238 CGAACAGAATTAACTCGTCTCCC 59.142 47.826 0.00 0.00 0.00 4.30
2044 2153 7.855904 ACAAACATGAACGAACAGAATTAACTC 59.144 33.333 0.00 0.00 0.00 3.01
2049 2158 7.870826 TCATACAAACATGAACGAACAGAATT 58.129 30.769 0.00 0.00 32.01 2.17
2050 2159 7.433708 TCATACAAACATGAACGAACAGAAT 57.566 32.000 0.00 0.00 32.01 2.40
2051 2160 6.852858 TCATACAAACATGAACGAACAGAA 57.147 33.333 0.00 0.00 32.01 3.02
2052 2161 6.481976 ACTTCATACAAACATGAACGAACAGA 59.518 34.615 0.00 0.00 39.43 3.41
2256 2387 3.181488 TGTCACTTTGTGCAAACATGAGG 60.181 43.478 0.00 0.00 32.98 3.86
2390 2552 8.985315 TGAGATAGCCAACAAAGATGAAATAT 57.015 30.769 0.00 0.00 0.00 1.28
2458 2620 1.526917 GCTTGTGTGTGGAGCAGGT 60.527 57.895 0.00 0.00 36.45 4.00
2459 2621 1.526686 TGCTTGTGTGTGGAGCAGG 60.527 57.895 0.00 0.00 41.15 4.85
2482 2653 2.601067 TTGCACATGCCACAGGGG 60.601 61.111 0.49 0.00 41.18 4.79
2523 2694 2.158711 TGATTCAGCAGAATAGCCTGGG 60.159 50.000 4.09 0.00 44.30 4.45
2548 2719 3.426568 GTCGGCACAAGAGGCTGC 61.427 66.667 0.00 0.00 37.56 5.25
2571 2748 4.212214 GCTTTGTCTTCGTTCAGTTCATCT 59.788 41.667 0.00 0.00 0.00 2.90
2607 2784 2.447047 ACTGTTCAGGGAATCTGGGTTT 59.553 45.455 4.82 0.00 43.53 3.27
2619 2796 1.830279 ATGTGCCATGACTGTTCAGG 58.170 50.000 0.00 0.00 34.35 3.86
2620 2797 3.079578 AGAATGTGCCATGACTGTTCAG 58.920 45.455 0.00 0.00 34.35 3.02
2621 2798 2.815503 CAGAATGTGCCATGACTGTTCA 59.184 45.455 0.00 0.00 35.73 3.18
2639 2816 2.374839 TGAACATGGGGAATCACACAGA 59.625 45.455 0.00 0.00 0.00 3.41
2666 2844 6.321717 TGCAATCTTTAAGGAAAATAGTGCG 58.678 36.000 0.00 0.00 43.88 5.34
2668 2846 8.253113 ACCATGCAATCTTTAAGGAAAATAGTG 58.747 33.333 0.00 0.00 0.00 2.74
2678 2856 8.761575 ATTTGTGTAACCATGCAATCTTTAAG 57.238 30.769 0.00 0.00 34.36 1.85
2679 2857 8.363390 TGATTTGTGTAACCATGCAATCTTTAA 58.637 29.630 0.00 0.00 34.36 1.52
2680 2858 7.890515 TGATTTGTGTAACCATGCAATCTTTA 58.109 30.769 0.00 0.00 34.36 1.85
2682 2860 6.343716 TGATTTGTGTAACCATGCAATCTT 57.656 33.333 0.00 0.00 34.36 2.40
2683 2861 5.981088 TGATTTGTGTAACCATGCAATCT 57.019 34.783 0.00 0.00 34.36 2.40
2687 2865 4.082300 GTGGATGATTTGTGTAACCATGCA 60.082 41.667 0.00 0.00 34.13 3.96
2689 2867 5.641783 TGTGGATGATTTGTGTAACCATG 57.358 39.130 0.00 0.00 34.36 3.66
2690 2868 5.394443 GCATGTGGATGATTTGTGTAACCAT 60.394 40.000 0.00 0.00 34.36 3.55
2699 2877 3.770263 AGTTCGCATGTGGATGATTTG 57.230 42.857 6.39 0.00 0.00 2.32
2708 2886 3.262420 AGTTAGGCTTAGTTCGCATGTG 58.738 45.455 0.00 0.00 0.00 3.21
2719 2897 4.473559 ACTTGGCCATCTAAGTTAGGCTTA 59.526 41.667 6.09 0.00 46.23 3.09
2727 2905 5.598417 ACAAAAAGAACTTGGCCATCTAAGT 59.402 36.000 6.09 3.52 38.70 2.24
2729 2907 5.221422 CCACAAAAAGAACTTGGCCATCTAA 60.221 40.000 6.09 0.00 0.00 2.10
2741 2919 6.204301 GGGTAGTCTAGTTCCACAAAAAGAAC 59.796 42.308 0.00 0.00 42.18 3.01
2742 2920 6.126710 TGGGTAGTCTAGTTCCACAAAAAGAA 60.127 38.462 0.00 0.00 0.00 2.52
2745 2923 5.367352 TCTGGGTAGTCTAGTTCCACAAAAA 59.633 40.000 0.00 0.00 0.00 1.94
2747 2925 4.485875 TCTGGGTAGTCTAGTTCCACAAA 58.514 43.478 0.00 0.00 0.00 2.83
2748 2926 4.122337 TCTGGGTAGTCTAGTTCCACAA 57.878 45.455 0.00 0.00 0.00 3.33
2749 2927 3.820195 TCTGGGTAGTCTAGTTCCACA 57.180 47.619 0.00 0.00 0.00 4.17
2750 2928 4.710375 TGAATCTGGGTAGTCTAGTTCCAC 59.290 45.833 0.00 0.00 0.00 4.02
2752 2930 5.934402 TTGAATCTGGGTAGTCTAGTTCC 57.066 43.478 0.00 0.00 0.00 3.62
2755 2933 9.892130 CTAAAATTTGAATCTGGGTAGTCTAGT 57.108 33.333 0.00 0.00 0.00 2.57
2757 2935 9.886132 GTCTAAAATTTGAATCTGGGTAGTCTA 57.114 33.333 0.00 0.00 0.00 2.59
2758 2936 7.829706 GGTCTAAAATTTGAATCTGGGTAGTCT 59.170 37.037 0.00 0.00 0.00 3.24
2760 2938 7.699878 AGGTCTAAAATTTGAATCTGGGTAGT 58.300 34.615 0.00 0.00 0.00 2.73
2761 2939 9.110502 GTAGGTCTAAAATTTGAATCTGGGTAG 57.889 37.037 0.00 0.00 0.00 3.18
2762 2940 8.607713 TGTAGGTCTAAAATTTGAATCTGGGTA 58.392 33.333 0.00 0.00 0.00 3.69
2763 2941 7.466804 TGTAGGTCTAAAATTTGAATCTGGGT 58.533 34.615 0.00 0.00 0.00 4.51
2764 2942 7.938140 TGTAGGTCTAAAATTTGAATCTGGG 57.062 36.000 0.00 0.00 0.00 4.45
2776 2954 9.330063 CAGATCTTGCATAATGTAGGTCTAAAA 57.670 33.333 0.00 0.00 0.00 1.52
2777 2955 8.893219 CAGATCTTGCATAATGTAGGTCTAAA 57.107 34.615 0.00 0.00 0.00 1.85
2797 2975 2.605823 CGAGAGAATGTACCGGCAGATC 60.606 54.545 0.00 0.00 0.00 2.75
2821 2999 5.277058 CGCAAACTCTATTTCTATGAGCACC 60.277 44.000 0.00 0.00 0.00 5.01
2822 3000 5.292101 ACGCAAACTCTATTTCTATGAGCAC 59.708 40.000 0.00 0.00 0.00 4.40
2832 3010 8.094798 TGAATACAGAAACGCAAACTCTATTT 57.905 30.769 0.00 0.00 0.00 1.40
2833 3011 7.667043 TGAATACAGAAACGCAAACTCTATT 57.333 32.000 0.00 0.00 0.00 1.73
2834 3012 7.849804 ATGAATACAGAAACGCAAACTCTAT 57.150 32.000 0.00 0.00 0.00 1.98
2836 3014 6.313905 CCTATGAATACAGAAACGCAAACTCT 59.686 38.462 0.00 0.00 0.00 3.24
2837 3015 6.456988 CCCTATGAATACAGAAACGCAAACTC 60.457 42.308 0.00 0.00 0.00 3.01
2845 3023 7.225538 CACACTCATCCCTATGAATACAGAAAC 59.774 40.741 0.00 0.00 41.57 2.78
2847 3025 6.686378 GCACACTCATCCCTATGAATACAGAA 60.686 42.308 0.00 0.00 41.57 3.02
2848 3026 5.221521 GCACACTCATCCCTATGAATACAGA 60.222 44.000 0.00 0.00 41.57 3.41
2849 3027 4.993584 GCACACTCATCCCTATGAATACAG 59.006 45.833 0.00 0.00 41.57 2.74
2851 3029 3.990469 CGCACACTCATCCCTATGAATAC 59.010 47.826 0.00 0.00 41.57 1.89
2872 3050 0.436913 TGAAACTCATAACACGCGCG 59.563 50.000 30.96 30.96 0.00 6.86
2893 3071 9.745880 CTTTCTTCTAAACACAGTACAGAGTTA 57.254 33.333 1.76 0.00 0.00 2.24
2895 3073 8.008513 TCTTTCTTCTAAACACAGTACAGAGT 57.991 34.615 0.00 0.00 0.00 3.24
2896 3074 8.873215 TTCTTTCTTCTAAACACAGTACAGAG 57.127 34.615 0.00 0.00 0.00 3.35
2927 3105 9.765795 GACTAAACTAGCCAAGTATATTGATGT 57.234 33.333 0.00 0.00 37.50 3.06
2931 3109 7.113124 CGTCGACTAAACTAGCCAAGTATATTG 59.887 40.741 14.70 0.00 37.50 1.90
2932 3110 7.137426 CGTCGACTAAACTAGCCAAGTATATT 58.863 38.462 14.70 0.00 37.50 1.28
2935 3113 4.732938 GCGTCGACTAAACTAGCCAAGTAT 60.733 45.833 14.70 0.00 37.50 2.12
2939 3117 1.730121 CGCGTCGACTAAACTAGCCAA 60.730 52.381 14.70 0.00 0.00 4.52
2942 3120 0.864797 CCCGCGTCGACTAAACTAGC 60.865 60.000 14.70 6.63 0.00 3.42
2952 3130 1.525941 TGATGATATACCCGCGTCGA 58.474 50.000 4.92 0.00 0.00 4.20
2954 3132 2.096980 TCGATGATGATATACCCGCGTC 59.903 50.000 4.92 0.00 0.00 5.19
2955 3133 2.089201 TCGATGATGATATACCCGCGT 58.911 47.619 4.92 0.00 0.00 6.01
2956 3134 2.844122 TCGATGATGATATACCCGCG 57.156 50.000 0.00 0.00 0.00 6.46
2957 3135 4.870426 ACATTTCGATGATGATATACCCGC 59.130 41.667 14.16 0.00 0.00 6.13
2971 3149 2.541178 GGCGACGACTCTACATTTCGAT 60.541 50.000 0.00 0.00 36.58 3.59
2978 3156 1.741528 TACATGGCGACGACTCTACA 58.258 50.000 0.65 0.00 0.00 2.74
2979 3157 2.289820 TCATACATGGCGACGACTCTAC 59.710 50.000 0.65 0.00 0.00 2.59
2982 3160 2.423926 ATCATACATGGCGACGACTC 57.576 50.000 0.65 0.00 0.00 3.36
2988 3166 1.941975 CAGTGCAATCATACATGGCGA 59.058 47.619 0.00 0.00 0.00 5.54
2993 3171 3.312421 GCCGTAACAGTGCAATCATACAT 59.688 43.478 0.00 0.00 0.00 2.29
3004 3182 1.493772 TCGAAGTTGCCGTAACAGTG 58.506 50.000 2.03 0.00 41.88 3.66
3005 3183 2.228138 TTCGAAGTTGCCGTAACAGT 57.772 45.000 0.00 0.00 41.88 3.55
3031 3211 9.869757 GTGCCCAAAATACAAGTAAAAGATAAT 57.130 29.630 0.00 0.00 0.00 1.28
3039 3219 3.574826 GGTGGTGCCCAAAATACAAGTAA 59.425 43.478 0.00 0.00 34.18 2.24
3042 3222 1.067915 CGGTGGTGCCCAAAATACAAG 60.068 52.381 0.00 0.00 34.18 3.16
3043 3223 0.962489 CGGTGGTGCCCAAAATACAA 59.038 50.000 0.00 0.00 34.18 2.41
3044 3224 0.110678 TCGGTGGTGCCCAAAATACA 59.889 50.000 0.00 0.00 34.18 2.29
3045 3225 1.470051 ATCGGTGGTGCCCAAAATAC 58.530 50.000 0.00 0.00 34.18 1.89
3065 4850 3.945285 GGAAAAGGTTTGGATAGATGCGA 59.055 43.478 0.00 0.00 0.00 5.10
3068 4853 7.417116 CCATGAAGGAAAAGGTTTGGATAGATG 60.417 40.741 0.00 0.00 41.22 2.90
3086 4871 1.139853 GGACAGCTACCTCCATGAAGG 59.860 57.143 0.00 0.00 42.55 3.46
3096 4881 1.019805 GCCAAGTTCGGACAGCTACC 61.020 60.000 0.00 0.00 0.00 3.18
3155 4940 2.165641 TGTACAGCTACGTCCATGAAGG 59.834 50.000 0.00 0.00 39.47 3.46
3169 4954 2.644555 ATCGGCGGTCCATGTACAGC 62.645 60.000 7.21 4.98 39.48 4.40
3199 4984 4.229876 GCGAAAATAAAAGTGAGCAAGCT 58.770 39.130 0.00 0.00 0.00 3.74
3215 5000 5.085390 GCAAGCTTTTTCTTTTTGCGAAAA 58.915 33.333 11.37 11.37 38.26 2.29
3216 5001 4.391523 AGCAAGCTTTTTCTTTTTGCGAAA 59.608 33.333 0.00 0.00 46.38 3.46
3217 5002 3.932089 AGCAAGCTTTTTCTTTTTGCGAA 59.068 34.783 0.00 0.00 46.38 4.70
3218 5003 3.520569 AGCAAGCTTTTTCTTTTTGCGA 58.479 36.364 0.00 0.00 46.38 5.10
3219 5004 3.306703 TGAGCAAGCTTTTTCTTTTTGCG 59.693 39.130 0.00 0.00 46.38 4.85
3220 5005 4.330894 AGTGAGCAAGCTTTTTCTTTTTGC 59.669 37.500 0.00 0.00 43.23 3.68
3221 5006 6.413018 AAGTGAGCAAGCTTTTTCTTTTTG 57.587 33.333 0.00 0.00 0.00 2.44
3222 5007 7.439157 AAAAGTGAGCAAGCTTTTTCTTTTT 57.561 28.000 0.00 6.59 40.68 1.94
3223 5008 7.201435 CGTAAAAGTGAGCAAGCTTTTTCTTTT 60.201 33.333 18.97 18.97 42.63 2.27
3224 5009 6.253512 CGTAAAAGTGAGCAAGCTTTTTCTTT 59.746 34.615 14.23 1.47 42.63 2.52
3225 5010 5.743872 CGTAAAAGTGAGCAAGCTTTTTCTT 59.256 36.000 14.23 0.00 42.63 2.52
3226 5011 5.163652 ACGTAAAAGTGAGCAAGCTTTTTCT 60.164 36.000 14.23 0.00 42.63 2.52
3227 5012 5.034797 ACGTAAAAGTGAGCAAGCTTTTTC 58.965 37.500 14.23 0.00 42.63 2.29
3228 5013 4.993905 ACGTAAAAGTGAGCAAGCTTTTT 58.006 34.783 14.23 2.36 42.63 1.94
3229 5014 4.632538 ACGTAAAAGTGAGCAAGCTTTT 57.367 36.364 0.00 13.73 44.21 2.27


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

AutoCloner maintained by Alex Coulton.