Multiple sequence alignment - TraesCS1D01G437600

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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 TraesCS1D01G437600 chr1D 100.000 4655 0 0 1 4655 485024740 485020086 0.000000e+00 8597.0
1 TraesCS1D01G437600 chr1D 84.729 203 21 4 4201 4393 484871407 484871205 1.320000e-45 195.0
2 TraesCS1D01G437600 chr1D 83.962 212 18 8 4198 4393 484796984 484796773 6.150000e-44 189.0
3 TraesCS1D01G437600 chr1D 97.872 47 1 0 4201 4247 484566414 484566368 1.070000e-11 82.4
4 TraesCS1D01G437600 chr1A 93.695 2823 98 24 7 2802 582222916 582220147 0.000000e+00 4154.0
5 TraesCS1D01G437600 chr1A 89.442 1667 71 31 2946 4585 582220053 582218465 0.000000e+00 2006.0
6 TraesCS1D01G437600 chr1A 85.294 204 20 5 4201 4394 581960400 581960197 7.900000e-48 202.0
7 TraesCS1D01G437600 chr1A 82.160 213 17 9 4198 4393 581916614 581916406 3.730000e-36 163.0
8 TraesCS1D01G437600 chr1A 97.872 47 1 0 4201 4247 581880499 581880453 1.070000e-11 82.4
9 TraesCS1D01G437600 chr1B 93.293 1491 61 16 1340 2802 675314505 675313026 0.000000e+00 2163.0
10 TraesCS1D01G437600 chr1B 96.623 1303 32 6 7 1303 675315790 675314494 0.000000e+00 2152.0
11 TraesCS1D01G437600 chr1B 93.696 1047 31 12 2946 3976 675312926 675311899 0.000000e+00 1535.0
12 TraesCS1D01G437600 chr1B 88.679 636 29 8 4056 4655 675311900 675311272 0.000000e+00 736.0
13 TraesCS1D01G437600 chr1B 83.981 206 23 4 4198 4393 674895157 674894952 6.150000e-44 189.0
14 TraesCS1D01G437600 chr1B 83.981 206 23 5 4198 4393 675220740 675220945 6.150000e-44 189.0
15 TraesCS1D01G437600 chr1B 82.609 207 16 8 4198 4386 646687345 646687141 1.040000e-36 165.0
16 TraesCS1D01G437600 chr1B 94.059 101 6 0 4293 4393 675227265 675227365 2.240000e-33 154.0
17 TraesCS1D01G437600 chr1B 97.872 47 1 0 4201 4247 674821357 674821311 1.070000e-11 82.4


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 TraesCS1D01G437600 chr1D 485020086 485024740 4654 True 8597.0 8597 100.00000 1 4655 1 chr1D.!!$R4 4654
1 TraesCS1D01G437600 chr1A 582218465 582222916 4451 True 3080.0 4154 91.56850 7 4585 2 chr1A.!!$R4 4578
2 TraesCS1D01G437600 chr1B 675311272 675315790 4518 True 1646.5 2163 93.07275 7 4655 4 chr1B.!!$R4 4648

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
183 184 0.758734 TCAGCCGATATGGTTCCCTG 59.241 55.000 0.00 0.00 41.21 4.45 F
626 628 0.890542 TCAACCTGTGTGCCAGATGC 60.891 55.000 0.00 0.00 44.49 3.91 F
2200 2262 1.410153 CCTTGCCCAATGTAAGCATCC 59.590 52.381 0.00 0.00 35.54 3.51 F
2707 2770 0.105039 CCGAGCCTTCTGATGGTACC 59.895 60.000 4.43 4.43 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1813 1.213296 GCCAAGACAGGGGATAGGAA 58.787 55.0 0.00 0.0 0.00 3.36 R
2451 2514 0.040067 GAAGCAGTGCCTCAAAACCG 60.040 55.0 12.58 0.0 0.00 4.44 R
3497 3580 0.693049 GGAAGAGCTTTGTCAGGGGA 59.307 55.0 0.00 0.0 0.00 4.81 R
4550 4711 0.818445 GATACCAGCAGCAGCAGCAT 60.818 55.0 12.92 0.0 45.49 3.79 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
108 109 5.780793 ACAGTGTACTTAGGTCTCAGGAATT 59.219 40.000 0.00 0.00 0.00 2.17
109 110 6.952358 ACAGTGTACTTAGGTCTCAGGAATTA 59.048 38.462 0.00 0.00 0.00 1.40
110 111 7.453752 ACAGTGTACTTAGGTCTCAGGAATTAA 59.546 37.037 0.00 0.00 0.00 1.40
111 112 8.478877 CAGTGTACTTAGGTCTCAGGAATTAAT 58.521 37.037 0.00 0.00 0.00 1.40
120 121 8.196378 AGGTCTCAGGAATTAATATGTACCTC 57.804 38.462 13.27 0.00 29.91 3.85
183 184 0.758734 TCAGCCGATATGGTTCCCTG 59.241 55.000 0.00 0.00 41.21 4.45
232 233 5.450818 TGATAGGTACTCCTGGCAAAATT 57.549 39.130 0.00 0.00 44.81 1.82
281 282 6.207417 CCTGATTGTATCCTGAAACAAGTTGT 59.793 38.462 1.64 1.64 38.87 3.32
345 346 6.956202 ATGATTTCTGAAAGTCCATGGATC 57.044 37.500 19.62 12.39 33.76 3.36
365 366 6.322456 TGGATCAGTGATACTTGAGGTAAGAG 59.678 42.308 16.43 0.00 39.76 2.85
405 406 8.831550 GCTTCATCTCTAGGAAATAAAATTCGT 58.168 33.333 0.00 0.00 0.00 3.85
546 548 5.716228 TGGTTGGCTGTAAAATGAGATCAAT 59.284 36.000 0.00 0.00 0.00 2.57
609 611 4.337274 CACTGCCAAAGATGCATCTTATCA 59.663 41.667 35.78 29.02 45.83 2.15
610 612 4.951715 ACTGCCAAAGATGCATCTTATCAA 59.048 37.500 35.78 22.55 45.83 2.57
611 613 5.163581 ACTGCCAAAGATGCATCTTATCAAC 60.164 40.000 35.78 24.24 45.83 3.18
612 614 4.098349 TGCCAAAGATGCATCTTATCAACC 59.902 41.667 35.78 22.11 45.83 3.77
613 615 4.340381 GCCAAAGATGCATCTTATCAACCT 59.660 41.667 35.78 19.54 45.83 3.50
614 616 5.735354 GCCAAAGATGCATCTTATCAACCTG 60.735 44.000 35.78 27.40 45.83 4.00
615 617 5.359009 CCAAAGATGCATCTTATCAACCTGT 59.641 40.000 35.78 18.20 45.83 4.00
616 618 6.263344 CAAAGATGCATCTTATCAACCTGTG 58.737 40.000 35.78 24.21 45.83 3.66
617 619 5.108187 AGATGCATCTTATCAACCTGTGT 57.892 39.130 23.75 0.00 31.97 3.72
618 620 4.880120 AGATGCATCTTATCAACCTGTGTG 59.120 41.667 23.75 0.00 31.97 3.82
619 621 2.749076 TGCATCTTATCAACCTGTGTGC 59.251 45.455 0.00 0.00 0.00 4.57
620 622 2.098117 GCATCTTATCAACCTGTGTGCC 59.902 50.000 0.00 0.00 0.00 5.01
621 623 3.346315 CATCTTATCAACCTGTGTGCCA 58.654 45.455 0.00 0.00 0.00 4.92
622 624 3.057969 TCTTATCAACCTGTGTGCCAG 57.942 47.619 0.00 0.00 41.15 4.85
623 625 2.637382 TCTTATCAACCTGTGTGCCAGA 59.363 45.455 0.00 0.00 44.49 3.86
624 626 3.264193 TCTTATCAACCTGTGTGCCAGAT 59.736 43.478 0.00 0.00 44.49 2.90
625 627 1.830279 ATCAACCTGTGTGCCAGATG 58.170 50.000 0.00 0.00 44.49 2.90
626 628 0.890542 TCAACCTGTGTGCCAGATGC 60.891 55.000 0.00 0.00 44.49 3.91
713 739 4.502105 TTGTGCCAGATGCTTCCTTATA 57.498 40.909 0.00 0.00 42.00 0.98
1301 1333 2.482494 CCCCTCCAGGACTTAACATCT 58.518 52.381 0.00 0.00 38.24 2.90
1304 1336 3.133721 CCCTCCAGGACTTAACATCTCAG 59.866 52.174 0.00 0.00 38.24 3.35
1306 1338 3.772025 CTCCAGGACTTAACATCTCAGGT 59.228 47.826 0.00 0.00 0.00 4.00
1321 1353 2.738846 CTCAGGTGTCTGGTTTTGATCG 59.261 50.000 0.00 0.00 41.23 3.69
1324 1356 2.104111 AGGTGTCTGGTTTTGATCGTCA 59.896 45.455 0.00 0.00 0.00 4.35
1481 1513 2.260844 ACCACACATGTCAACCAGAG 57.739 50.000 0.00 0.00 0.00 3.35
1801 1836 2.291540 CCTATCCCCTGTCTTGGCAAAA 60.292 50.000 0.00 0.00 0.00 2.44
1822 1857 9.912634 GCAAAACATGTAAATATGCCATATAGT 57.087 29.630 0.00 0.00 0.00 2.12
2080 2142 2.818714 CGCTGCAGGAAGCTGGAG 60.819 66.667 17.12 0.00 45.94 3.86
2200 2262 1.410153 CCTTGCCCAATGTAAGCATCC 59.590 52.381 0.00 0.00 35.54 3.51
2293 2356 2.510768 AACCTGTCGTGTTCAGAGAC 57.489 50.000 0.00 2.79 35.20 3.36
2298 2361 3.253677 CCTGTCGTGTTCAGAGACTAGTT 59.746 47.826 0.00 0.00 36.01 2.24
2312 2375 4.130118 AGACTAGTTCTGTTGCAACCAAG 58.870 43.478 26.14 17.62 31.12 3.61
2441 2504 4.704540 TGTGAGTTTCTTCTTGCTTGGAAA 59.295 37.500 0.00 0.00 0.00 3.13
2450 2513 1.458064 CTTGCTTGGAAATTTGCTGCG 59.542 47.619 11.22 0.87 0.00 5.18
2451 2514 0.945265 TGCTTGGAAATTTGCTGCGC 60.945 50.000 11.22 0.00 0.00 6.09
2463 2526 3.659092 CTGCGCGGTTTTGAGGCA 61.659 61.111 8.83 0.00 0.00 4.75
2566 2629 5.043248 AGAGCGGTGAATTTTGAAAACTTG 58.957 37.500 0.00 0.00 0.00 3.16
2577 2640 8.504812 AATTTTGAAAACTTGCTAAACACCAT 57.495 26.923 0.00 0.00 0.00 3.55
2629 2692 0.460284 ATGACACTTCGGTCGATGGC 60.460 55.000 10.25 2.68 40.72 4.40
2686 2749 2.159421 ACACATAGCGAACCTACTGTCG 60.159 50.000 0.00 0.00 0.00 4.35
2707 2770 0.105039 CCGAGCCTTCTGATGGTACC 59.895 60.000 4.43 4.43 0.00 3.34
2709 2772 1.414181 CGAGCCTTCTGATGGTACCAT 59.586 52.381 27.70 27.70 39.69 3.55
2728 2794 4.141756 ACCATCTGCTTACTTCAGGATCAG 60.142 45.833 0.00 0.00 32.63 2.90
2729 2795 4.378774 CATCTGCTTACTTCAGGATCAGG 58.621 47.826 0.00 0.00 32.63 3.86
2733 2799 6.080682 TCTGCTTACTTCAGGATCAGGATAT 58.919 40.000 0.00 0.00 32.63 1.63
2735 2801 6.763355 TGCTTACTTCAGGATCAGGATATTC 58.237 40.000 0.00 0.00 0.00 1.75
2736 2802 6.327365 TGCTTACTTCAGGATCAGGATATTCA 59.673 38.462 0.00 0.00 0.00 2.57
2737 2803 6.648725 GCTTACTTCAGGATCAGGATATTCAC 59.351 42.308 0.00 0.00 0.00 3.18
2739 2805 6.172136 ACTTCAGGATCAGGATATTCACTG 57.828 41.667 0.00 0.00 36.07 3.66
2742 2808 7.345653 ACTTCAGGATCAGGATATTCACTGTTA 59.654 37.037 0.00 0.00 36.17 2.41
2744 2810 7.730084 TCAGGATCAGGATATTCACTGTTAAG 58.270 38.462 0.00 0.00 36.17 1.85
2745 2811 7.565029 TCAGGATCAGGATATTCACTGTTAAGA 59.435 37.037 0.00 0.00 36.17 2.10
2747 2813 8.772250 AGGATCAGGATATTCACTGTTAAGAAA 58.228 33.333 0.00 0.00 36.17 2.52
2748 2814 9.566432 GGATCAGGATATTCACTGTTAAGAAAT 57.434 33.333 0.00 0.00 36.17 2.17
2779 2849 3.264450 AGTGTTATTTGAGTGCTAGGCCT 59.736 43.478 11.78 11.78 0.00 5.19
2788 2858 2.100087 GAGTGCTAGGCCTAGTGTTCTC 59.900 54.545 34.85 28.75 35.65 2.87
2790 2860 2.100087 GTGCTAGGCCTAGTGTTCTCTC 59.900 54.545 34.85 19.21 35.65 3.20
2794 2865 3.012934 AGGCCTAGTGTTCTCTCTCTC 57.987 52.381 1.29 0.00 0.00 3.20
2800 2871 5.360591 CCTAGTGTTCTCTCTCTCTCTCTC 58.639 50.000 0.00 0.00 0.00 3.20
2801 2872 5.129485 CCTAGTGTTCTCTCTCTCTCTCTCT 59.871 48.000 0.00 0.00 0.00 3.10
2802 2873 5.091261 AGTGTTCTCTCTCTCTCTCTCTC 57.909 47.826 0.00 0.00 0.00 3.20
2803 2874 4.780021 AGTGTTCTCTCTCTCTCTCTCTCT 59.220 45.833 0.00 0.00 0.00 3.10
2804 2875 5.105146 AGTGTTCTCTCTCTCTCTCTCTCTC 60.105 48.000 0.00 0.00 0.00 3.20
2805 2876 5.026121 TGTTCTCTCTCTCTCTCTCTCTCT 58.974 45.833 0.00 0.00 0.00 3.10
2806 2877 5.127845 TGTTCTCTCTCTCTCTCTCTCTCTC 59.872 48.000 0.00 0.00 0.00 3.20
2807 2878 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2808 2879 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2809 2880 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2810 2881 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2811 2882 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2812 2883 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2813 2884 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2814 2885 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2815 2886 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2816 2887 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2820 2891 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
2821 2892 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
2822 2893 4.646945 TCTCTCTCTCTCTCTCTCTCTGTC 59.353 50.000 0.00 0.00 0.00 3.51
2823 2894 4.614475 TCTCTCTCTCTCTCTCTCTGTCT 58.386 47.826 0.00 0.00 0.00 3.41
2824 2895 4.646945 TCTCTCTCTCTCTCTCTCTGTCTC 59.353 50.000 0.00 0.00 0.00 3.36
2825 2896 4.614475 TCTCTCTCTCTCTCTCTGTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2828 2899 4.646945 TCTCTCTCTCTCTCTGTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2829 2900 4.614475 TCTCTCTCTCTCTGTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2831 2902 4.614475 TCTCTCTCTCTGTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2832 2903 4.646945 TCTCTCTCTCTGTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2833 2904 3.706594 TCTCTCTCTGTCTCTCTCTCTCC 59.293 52.174 0.00 0.00 0.00 3.71
2834 2905 3.449918 TCTCTCTGTCTCTCTCTCTCCA 58.550 50.000 0.00 0.00 0.00 3.86
2835 2906 3.843619 TCTCTCTGTCTCTCTCTCTCCAA 59.156 47.826 0.00 0.00 0.00 3.53
2836 2907 4.080919 TCTCTCTGTCTCTCTCTCTCCAAG 60.081 50.000 0.00 0.00 0.00 3.61
2837 2908 3.843619 TCTCTGTCTCTCTCTCTCCAAGA 59.156 47.826 0.00 0.00 0.00 3.02
2844 2915 3.830679 CTCTCTCCAAGAGCACACC 57.169 57.895 0.00 0.00 44.95 4.16
2845 2916 0.972134 CTCTCTCCAAGAGCACACCA 59.028 55.000 0.00 0.00 44.95 4.17
2847 2918 1.552337 TCTCTCCAAGAGCACACCATC 59.448 52.381 0.00 0.00 42.04 3.51
2873 2944 2.673368 CCTGTCGTTTCATTAGACTGCC 59.327 50.000 0.00 0.00 36.01 4.85
2875 2946 3.935203 CTGTCGTTTCATTAGACTGCCAT 59.065 43.478 0.00 0.00 36.01 4.40
2877 2948 5.483811 TGTCGTTTCATTAGACTGCCATTA 58.516 37.500 0.00 0.00 36.01 1.90
2880 2951 7.120579 TGTCGTTTCATTAGACTGCCATTAAAT 59.879 33.333 0.00 0.00 36.01 1.40
2916 2990 8.256611 ACTATGAAATTATATGATGACGGTGC 57.743 34.615 0.00 0.00 0.00 5.01
2917 2991 8.097038 ACTATGAAATTATATGATGACGGTGCT 58.903 33.333 0.00 0.00 0.00 4.40
2918 2992 6.544038 TGAAATTATATGATGACGGTGCTG 57.456 37.500 0.00 0.00 0.00 4.41
2919 2993 6.054941 TGAAATTATATGATGACGGTGCTGT 58.945 36.000 0.00 0.00 0.00 4.40
2920 2994 6.542005 TGAAATTATATGATGACGGTGCTGTT 59.458 34.615 0.00 0.00 0.00 3.16
2921 2995 7.713073 TGAAATTATATGATGACGGTGCTGTTA 59.287 33.333 0.00 0.00 0.00 2.41
2922 2996 8.445275 AAATTATATGATGACGGTGCTGTTAA 57.555 30.769 0.00 0.00 0.00 2.01
2923 2997 8.445275 AATTATATGATGACGGTGCTGTTAAA 57.555 30.769 0.00 0.00 0.00 1.52
2924 2998 5.734855 ATATGATGACGGTGCTGTTAAAC 57.265 39.130 0.00 0.00 0.00 2.01
2925 2999 1.795872 TGATGACGGTGCTGTTAAACG 59.204 47.619 0.00 0.00 0.00 3.60
2926 3000 1.127951 GATGACGGTGCTGTTAAACGG 59.872 52.381 0.00 0.00 0.00 4.44
2927 3001 0.881159 TGACGGTGCTGTTAAACGGG 60.881 55.000 0.00 0.00 0.00 5.28
2928 3002 0.600782 GACGGTGCTGTTAAACGGGA 60.601 55.000 0.00 0.00 0.00 5.14
2929 3003 0.179051 ACGGTGCTGTTAAACGGGAA 60.179 50.000 0.00 0.00 0.00 3.97
2930 3004 1.161843 CGGTGCTGTTAAACGGGAAT 58.838 50.000 0.00 0.00 0.00 3.01
2931 3005 1.538075 CGGTGCTGTTAAACGGGAATT 59.462 47.619 0.00 0.00 0.00 2.17
2932 3006 2.413634 CGGTGCTGTTAAACGGGAATTC 60.414 50.000 0.00 0.00 0.00 2.17
2933 3007 2.413634 GGTGCTGTTAAACGGGAATTCG 60.414 50.000 0.00 0.00 0.00 3.34
2934 3008 1.807742 TGCTGTTAAACGGGAATTCGG 59.192 47.619 0.00 0.00 0.00 4.30
2935 3009 1.466866 GCTGTTAAACGGGAATTCGGC 60.467 52.381 0.00 0.00 0.00 5.54
2936 3010 1.807742 CTGTTAAACGGGAATTCGGCA 59.192 47.619 0.00 0.00 0.00 5.69
2937 3011 1.807742 TGTTAAACGGGAATTCGGCAG 59.192 47.619 0.00 0.00 0.00 4.85
2938 3012 1.808343 GTTAAACGGGAATTCGGCAGT 59.192 47.619 0.00 0.00 0.00 4.40
2939 3013 2.188062 TAAACGGGAATTCGGCAGTT 57.812 45.000 0.00 0.53 0.00 3.16
2940 3014 0.596082 AAACGGGAATTCGGCAGTTG 59.404 50.000 0.00 0.00 0.00 3.16
2941 3015 1.862602 AACGGGAATTCGGCAGTTGC 61.863 55.000 0.00 0.00 41.14 4.17
2942 3016 2.331893 CGGGAATTCGGCAGTTGCA 61.332 57.895 6.43 0.00 44.36 4.08
2943 3017 1.508088 GGGAATTCGGCAGTTGCAG 59.492 57.895 6.43 1.92 44.36 4.41
2944 3018 0.960364 GGGAATTCGGCAGTTGCAGA 60.960 55.000 6.43 4.58 43.16 4.26
3051 3125 1.375396 ATGCTACGCTCACGGCAAA 60.375 52.632 0.00 0.00 46.04 3.68
3081 3155 2.443390 ACCCCCTACCCGATCACG 60.443 66.667 0.00 0.00 39.43 4.35
3336 3419 2.026449 AGGCTAGCTGCTGATTCAAAGT 60.026 45.455 15.72 0.00 42.39 2.66
3485 3568 7.734287 ACTTTCAAGTCCTACAACGGGTACG 62.734 48.000 0.00 0.00 39.79 3.67
3497 3580 0.458669 CGGGTACGCATCTTACACCT 59.541 55.000 10.84 0.00 0.00 4.00
3723 3811 5.337571 GTGGCTTCCATAGTAGCATATAGCA 60.338 44.000 0.00 0.00 40.32 3.49
3724 3812 7.123418 GTGGCTTCCATAGTAGCATATAGCAG 61.123 46.154 0.00 0.00 40.32 4.24
3806 3896 1.007964 CTGATCTCTACAGGCGCCG 60.008 63.158 23.20 18.60 0.00 6.46
3807 3897 2.336809 GATCTCTACAGGCGCCGG 59.663 66.667 25.72 25.72 0.00 6.13
3809 3899 2.017559 GATCTCTACAGGCGCCGGTT 62.018 60.000 36.42 19.14 0.00 4.44
3810 3900 2.298158 ATCTCTACAGGCGCCGGTTG 62.298 60.000 36.42 32.36 0.00 3.77
3811 3901 4.752879 TCTACAGGCGCCGGTTGC 62.753 66.667 36.42 11.81 0.00 4.17
3812 3902 4.760047 CTACAGGCGCCGGTTGCT 62.760 66.667 36.42 15.09 38.05 3.91
3822 3912 3.376078 CGGTTGCTGGCTGCCATT 61.376 61.111 23.64 0.00 42.00 3.16
3823 3913 2.263540 GGTTGCTGGCTGCCATTG 59.736 61.111 23.64 12.89 42.00 2.82
3824 3914 2.433664 GTTGCTGGCTGCCATTGC 60.434 61.111 23.64 22.70 42.00 3.56
3825 3915 2.602267 TTGCTGGCTGCCATTGCT 60.602 55.556 26.77 0.00 42.00 3.91
3826 3916 2.938086 TTGCTGGCTGCCATTGCTG 61.938 57.895 26.77 15.54 42.00 4.41
3978 4071 8.432013 AGATTATACAATTCATGCTACCAGTGA 58.568 33.333 0.00 0.00 0.00 3.41
3982 4075 5.121811 ACAATTCATGCTACCAGTGATCTC 58.878 41.667 0.00 0.00 0.00 2.75
3983 4076 5.121105 CAATTCATGCTACCAGTGATCTCA 58.879 41.667 0.00 0.00 0.00 3.27
3985 4078 4.597404 TCATGCTACCAGTGATCTCATC 57.403 45.455 0.00 0.00 0.00 2.92
3986 4079 3.962718 TCATGCTACCAGTGATCTCATCA 59.037 43.478 0.00 0.00 36.84 3.07
3987 4080 4.406649 TCATGCTACCAGTGATCTCATCAA 59.593 41.667 0.00 0.00 41.69 2.57
3988 4081 5.071384 TCATGCTACCAGTGATCTCATCAAT 59.929 40.000 0.00 0.00 41.69 2.57
3989 4082 4.953667 TGCTACCAGTGATCTCATCAATC 58.046 43.478 0.00 0.00 41.69 2.67
3990 4083 4.202295 TGCTACCAGTGATCTCATCAATCC 60.202 45.833 0.00 0.00 41.69 3.01
3991 4084 4.040217 GCTACCAGTGATCTCATCAATCCT 59.960 45.833 0.00 0.00 41.69 3.24
3992 4085 5.244851 GCTACCAGTGATCTCATCAATCCTA 59.755 44.000 0.00 0.00 41.69 2.94
3993 4086 5.804944 ACCAGTGATCTCATCAATCCTAG 57.195 43.478 0.00 0.00 41.69 3.02
3994 4087 5.462240 ACCAGTGATCTCATCAATCCTAGA 58.538 41.667 0.00 0.00 41.69 2.43
3995 4088 5.304101 ACCAGTGATCTCATCAATCCTAGAC 59.696 44.000 0.00 0.00 41.69 2.59
3996 4089 5.539574 CCAGTGATCTCATCAATCCTAGACT 59.460 44.000 0.00 0.00 41.69 3.24
3997 4090 6.041865 CCAGTGATCTCATCAATCCTAGACTT 59.958 42.308 0.00 0.00 41.69 3.01
3998 4091 7.418827 CCAGTGATCTCATCAATCCTAGACTTT 60.419 40.741 0.00 0.00 41.69 2.66
3999 4092 7.986320 CAGTGATCTCATCAATCCTAGACTTTT 59.014 37.037 0.00 0.00 41.69 2.27
4000 4093 9.206690 AGTGATCTCATCAATCCTAGACTTTTA 57.793 33.333 0.00 0.00 41.69 1.52
4001 4094 9.823647 GTGATCTCATCAATCCTAGACTTTTAA 57.176 33.333 0.00 0.00 41.69 1.52
4024 4117 9.567848 TTAAGTTTCAAAGACTTTGTCACAATC 57.432 29.630 23.78 11.94 41.36 2.67
4182 4275 3.201290 CATCTGAGGCTAACTTTGCGAT 58.799 45.455 0.00 0.00 0.00 4.58
4399 4528 2.572104 AGATCACCAGGGTTACCAACTC 59.428 50.000 2.98 0.00 40.13 3.01
4400 4529 2.112279 TCACCAGGGTTACCAACTCT 57.888 50.000 2.98 0.00 44.95 3.24
4401 4530 1.975680 TCACCAGGGTTACCAACTCTC 59.024 52.381 2.98 0.00 41.23 3.20
4402 4531 1.697432 CACCAGGGTTACCAACTCTCA 59.303 52.381 2.98 0.00 41.23 3.27
4403 4532 1.697982 ACCAGGGTTACCAACTCTCAC 59.302 52.381 2.98 0.00 41.23 3.51
4404 4533 1.003233 CCAGGGTTACCAACTCTCACC 59.997 57.143 2.98 0.00 41.23 4.02
4405 4534 1.697432 CAGGGTTACCAACTCTCACCA 59.303 52.381 2.98 0.00 41.23 4.17
4406 4535 1.978580 AGGGTTACCAACTCTCACCAG 59.021 52.381 2.98 0.00 37.85 4.00
4407 4536 1.975680 GGGTTACCAACTCTCACCAGA 59.024 52.381 2.98 0.00 36.50 3.86
4408 4537 2.289506 GGGTTACCAACTCTCACCAGAC 60.290 54.545 2.98 0.00 36.50 3.51
4409 4538 2.367567 GGTTACCAACTCTCACCAGACA 59.632 50.000 0.00 0.00 0.00 3.41
4410 4539 3.008049 GGTTACCAACTCTCACCAGACAT 59.992 47.826 0.00 0.00 0.00 3.06
4411 4540 4.222145 GGTTACCAACTCTCACCAGACATA 59.778 45.833 0.00 0.00 0.00 2.29
4412 4541 3.963428 ACCAACTCTCACCAGACATAC 57.037 47.619 0.00 0.00 0.00 2.39
4413 4542 3.239449 ACCAACTCTCACCAGACATACA 58.761 45.455 0.00 0.00 0.00 2.29
4453 4597 1.078709 GCGAACTGCACAGATAAGCA 58.921 50.000 4.31 0.00 45.45 3.91
4486 4630 1.672881 CACCTCGAATCTTGGCCATTC 59.327 52.381 6.09 6.92 0.00 2.67
4489 4633 2.397751 CGAATCTTGGCCATTCGCT 58.602 52.632 22.90 1.08 44.36 4.93
4490 4634 0.305922 CGAATCTTGGCCATTCGCTC 59.694 55.000 22.90 9.11 44.36 5.03
4491 4635 0.305922 GAATCTTGGCCATTCGCTCG 59.694 55.000 6.09 0.00 37.74 5.03
4492 4636 1.097547 AATCTTGGCCATTCGCTCGG 61.098 55.000 6.09 0.00 37.74 4.63
4493 4637 2.947938 ATCTTGGCCATTCGCTCGGG 62.948 60.000 6.09 0.00 37.74 5.14
4494 4638 3.976701 CTTGGCCATTCGCTCGGGT 62.977 63.158 6.09 0.00 37.74 5.28
4495 4639 3.969250 TTGGCCATTCGCTCGGGTC 62.969 63.158 6.09 0.00 37.74 4.46
4496 4640 4.467084 GGCCATTCGCTCGGGTCA 62.467 66.667 0.00 0.00 37.74 4.02
4497 4641 2.892425 GCCATTCGCTCGGGTCAG 60.892 66.667 0.00 0.00 0.00 3.51
4518 4676 0.737715 GCACCAGTCGTCCACAGATC 60.738 60.000 0.00 0.00 0.00 2.75
4549 4710 2.167075 GCCCCAAATATGATATGCTGCC 59.833 50.000 0.00 0.00 0.00 4.85
4550 4711 3.433343 CCCCAAATATGATATGCTGCCA 58.567 45.455 0.00 0.00 0.00 4.92
4564 4725 4.498520 GCCATGCTGCTGCTGCTG 62.499 66.667 27.67 21.90 40.48 4.41
4648 4812 2.903357 CCTACGCCATCAGCACCT 59.097 61.111 0.00 0.00 44.04 4.00
4651 4815 1.680522 CTACGCCATCAGCACCTCCT 61.681 60.000 0.00 0.00 44.04 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.735917 TCTCTTCTAACTTTCACTGGATCAAA 58.264 34.615 0.00 0.00 0.00 2.69
1 2 7.303182 TCTCTTCTAACTTTCACTGGATCAA 57.697 36.000 0.00 0.00 0.00 2.57
2 3 6.918067 TCTCTTCTAACTTTCACTGGATCA 57.082 37.500 0.00 0.00 0.00 2.92
3 4 6.592220 GGTTCTCTTCTAACTTTCACTGGATC 59.408 42.308 0.00 0.00 0.00 3.36
4 5 6.043243 TGGTTCTCTTCTAACTTTCACTGGAT 59.957 38.462 0.00 0.00 0.00 3.41
5 6 5.365605 TGGTTCTCTTCTAACTTTCACTGGA 59.634 40.000 0.00 0.00 0.00 3.86
108 109 6.326323 TGCACTCTTCATGGAGGTACATATTA 59.674 38.462 0.00 0.00 37.63 0.98
109 110 5.130975 TGCACTCTTCATGGAGGTACATATT 59.869 40.000 0.00 0.00 37.63 1.28
110 111 4.655649 TGCACTCTTCATGGAGGTACATAT 59.344 41.667 0.00 0.00 37.63 1.78
111 112 4.030216 TGCACTCTTCATGGAGGTACATA 58.970 43.478 0.00 0.00 37.63 2.29
120 121 0.603707 ACGTGGTGCACTCTTCATGG 60.604 55.000 17.98 5.23 31.34 3.66
183 184 2.926200 CGATACCCAATCAGCATCGATC 59.074 50.000 0.00 0.00 40.62 3.69
232 233 1.722034 AGAGCCAAGGAAGAGTGACA 58.278 50.000 0.00 0.00 0.00 3.58
281 282 4.634004 CAGTGCGGAAAGAATTGTATACCA 59.366 41.667 0.00 0.00 0.00 3.25
345 346 5.590530 AGCTCTTACCTCAAGTATCACTG 57.409 43.478 0.00 0.00 35.58 3.66
365 366 1.151668 TGAAGCTTTCTCGCAGAAGC 58.848 50.000 0.00 7.97 35.37 3.86
405 406 2.357637 GGCAAGGAATATAAAGCGCACA 59.642 45.455 11.47 0.00 0.00 4.57
465 466 0.183492 ACTGCTTTCTTCTGCCCACA 59.817 50.000 0.00 0.00 0.00 4.17
546 548 4.177537 TCAAATGTTGTTTCCTCTCCCA 57.822 40.909 0.00 0.00 0.00 4.37
618 620 2.409948 AGGTTAAGAGTGCATCTGGC 57.590 50.000 0.00 0.00 38.67 4.85
619 621 3.119708 GCAAAGGTTAAGAGTGCATCTGG 60.120 47.826 0.00 0.00 38.67 3.86
620 622 3.503363 TGCAAAGGTTAAGAGTGCATCTG 59.497 43.478 0.00 0.00 40.14 2.90
621 623 3.754965 TGCAAAGGTTAAGAGTGCATCT 58.245 40.909 0.00 0.00 40.14 2.90
625 627 4.503741 TTCATGCAAAGGTTAAGAGTGC 57.496 40.909 0.00 0.00 35.75 4.40
626 628 5.865552 CCATTTCATGCAAAGGTTAAGAGTG 59.134 40.000 0.00 0.00 0.00 3.51
627 629 5.539955 ACCATTTCATGCAAAGGTTAAGAGT 59.460 36.000 0.00 0.00 0.00 3.24
628 630 6.029346 ACCATTTCATGCAAAGGTTAAGAG 57.971 37.500 0.00 0.00 0.00 2.85
629 631 6.152661 CCTACCATTTCATGCAAAGGTTAAGA 59.847 38.462 10.20 0.00 31.63 2.10
630 632 6.071391 ACCTACCATTTCATGCAAAGGTTAAG 60.071 38.462 10.20 3.30 33.87 1.85
631 633 5.777732 ACCTACCATTTCATGCAAAGGTTAA 59.222 36.000 10.20 0.00 33.87 2.01
632 634 5.329399 ACCTACCATTTCATGCAAAGGTTA 58.671 37.500 10.20 0.00 33.87 2.85
713 739 7.466746 TTGTTTTTGAAGGCTATATTGCTCT 57.533 32.000 9.02 2.27 0.00 4.09
1035 1063 6.765915 TGATCATATCTACGGAGAAGATGG 57.234 41.667 18.23 1.99 35.36 3.51
1269 1301 1.997874 GGAGGGGCATCACCTGAGT 60.998 63.158 0.00 0.00 38.79 3.41
1301 1333 2.104111 ACGATCAAAACCAGACACCTGA 59.896 45.455 0.00 0.00 43.02 3.86
1304 1336 2.480419 CTGACGATCAAAACCAGACACC 59.520 50.000 0.00 0.00 0.00 4.16
1306 1338 3.744238 TCTGACGATCAAAACCAGACA 57.256 42.857 0.00 0.00 0.00 3.41
1321 1353 3.341857 AGTGCGTTAGATCGATCTGAC 57.658 47.619 33.22 31.77 39.30 3.51
1324 1356 3.378742 AGTGAAGTGCGTTAGATCGATCT 59.621 43.478 29.58 29.58 40.86 2.75
1328 1360 3.502920 AGAAGTGAAGTGCGTTAGATCG 58.497 45.455 0.00 0.00 0.00 3.69
1337 1369 6.597614 CATTCAGTTAAGAGAAGTGAAGTGC 58.402 40.000 11.87 0.00 41.30 4.40
1481 1513 4.864633 TGCGATCATCTACTCATGTCTTC 58.135 43.478 0.00 0.00 0.00 2.87
1778 1813 1.213296 GCCAAGACAGGGGATAGGAA 58.787 55.000 0.00 0.00 0.00 3.36
1976 2020 5.399152 GGCTGGGGTCTTTTTATTCTCCTAT 60.399 44.000 0.00 0.00 0.00 2.57
2080 2142 6.691818 CAGAATTGCAGCAGAAGATATTTCAC 59.308 38.462 0.00 0.00 0.00 3.18
2200 2262 5.695851 AGAGTGCTCCAAGTACAAAAATG 57.304 39.130 0.00 0.00 32.98 2.32
2293 2356 4.900635 AACTTGGTTGCAACAGAACTAG 57.099 40.909 29.55 19.24 0.00 2.57
2346 2409 3.597182 TGGGGCATATCCACTTGATCTA 58.403 45.455 0.00 0.00 39.70 1.98
2450 2513 2.050077 GCAGTGCCTCAAAACCGC 60.050 61.111 2.85 0.00 0.00 5.68
2451 2514 0.040067 GAAGCAGTGCCTCAAAACCG 60.040 55.000 12.58 0.00 0.00 4.44
2463 2526 0.739813 GTTCCCGCATACGAAGCAGT 60.740 55.000 0.00 0.00 43.93 4.40
2584 2647 3.242739 CGTCAAACCCTGTTTCAGTTCAG 60.243 47.826 0.00 0.00 0.00 3.02
2686 2749 1.112113 TACCATCAGAAGGCTCGGAC 58.888 55.000 0.00 0.00 0.00 4.79
2707 2770 4.100653 TCCTGATCCTGAAGTAAGCAGATG 59.899 45.833 0.00 0.00 35.39 2.90
2709 2772 3.713003 TCCTGATCCTGAAGTAAGCAGA 58.287 45.455 0.00 0.00 35.39 4.26
2712 2778 6.648725 GTGAATATCCTGATCCTGAAGTAAGC 59.351 42.308 0.00 0.00 0.00 3.09
2715 2781 6.841229 ACAGTGAATATCCTGATCCTGAAGTA 59.159 38.462 0.00 0.00 32.93 2.24
2747 2813 8.960591 AGCACTCAAATAACACTTTTAGCATAT 58.039 29.630 0.00 0.00 0.00 1.78
2748 2814 8.335532 AGCACTCAAATAACACTTTTAGCATA 57.664 30.769 0.00 0.00 0.00 3.14
2751 2817 7.244192 CCTAGCACTCAAATAACACTTTTAGC 58.756 38.462 0.00 0.00 0.00 3.09
2752 2818 7.244192 GCCTAGCACTCAAATAACACTTTTAG 58.756 38.462 0.00 0.00 0.00 1.85
2757 2827 3.264450 AGGCCTAGCACTCAAATAACACT 59.736 43.478 1.29 0.00 0.00 3.55
2767 2837 2.100087 GAGAACACTAGGCCTAGCACTC 59.900 54.545 35.21 29.36 36.66 3.51
2779 2849 5.958380 AGAGAGAGAGAGAGAGAGAACACTA 59.042 44.000 0.00 0.00 0.00 2.74
2788 2858 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2790 2860 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2794 2865 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2800 2871 4.648762 AGACAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2801 2872 4.614475 AGACAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2802 2873 4.648762 AGAGACAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2803 2874 4.614475 AGAGACAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2804 2875 4.648762 AGAGAGACAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2805 2876 4.614475 AGAGAGACAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2806 2877 4.648762 AGAGAGAGACAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2807 2878 4.614475 AGAGAGAGACAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2808 2879 4.648762 AGAGAGAGAGACAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2809 2880 4.614475 AGAGAGAGAGACAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2810 2881 4.202202 GGAGAGAGAGAGACAGAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
2811 2882 3.706594 GGAGAGAGAGAGACAGAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
2812 2883 3.452264 TGGAGAGAGAGAGACAGAGAGAG 59.548 52.174 0.00 0.00 0.00 3.20
2813 2884 3.449918 TGGAGAGAGAGAGACAGAGAGA 58.550 50.000 0.00 0.00 0.00 3.10
2814 2885 3.912496 TGGAGAGAGAGAGACAGAGAG 57.088 52.381 0.00 0.00 0.00 3.20
2815 2886 3.843619 TCTTGGAGAGAGAGAGACAGAGA 59.156 47.826 0.00 0.00 0.00 3.10
2816 2887 4.220693 TCTTGGAGAGAGAGAGACAGAG 57.779 50.000 0.00 0.00 0.00 3.35
2828 2899 1.554160 AGATGGTGTGCTCTTGGAGAG 59.446 52.381 0.61 0.61 45.04 3.20
2829 2900 1.277273 CAGATGGTGTGCTCTTGGAGA 59.723 52.381 0.00 0.00 0.00 3.71
2831 2902 0.325933 CCAGATGGTGTGCTCTTGGA 59.674 55.000 0.00 0.00 0.00 3.53
2832 2903 2.864114 CCAGATGGTGTGCTCTTGG 58.136 57.895 0.00 0.00 0.00 3.61
2843 2914 1.001974 TGAAACGACAGGACCAGATGG 59.998 52.381 0.00 0.00 42.17 3.51
2844 2915 2.455674 TGAAACGACAGGACCAGATG 57.544 50.000 0.00 0.00 0.00 2.90
2845 2916 3.703001 AATGAAACGACAGGACCAGAT 57.297 42.857 0.00 0.00 0.00 2.90
2847 2918 3.927142 GTCTAATGAAACGACAGGACCAG 59.073 47.826 0.00 0.00 0.00 4.00
2857 2928 7.582679 CGTATTTAATGGCAGTCTAATGAAACG 59.417 37.037 0.00 0.00 0.00 3.60
2859 2930 8.394877 CACGTATTTAATGGCAGTCTAATGAAA 58.605 33.333 0.00 0.00 0.00 2.69
2900 2974 6.019398 CGTTTAACAGCACCGTCATCATATAA 60.019 38.462 0.00 0.00 0.00 0.98
2907 2981 1.153353 CCGTTTAACAGCACCGTCAT 58.847 50.000 0.00 0.00 0.00 3.06
2908 2982 0.881159 CCCGTTTAACAGCACCGTCA 60.881 55.000 0.00 0.00 0.00 4.35
2909 2983 0.600782 TCCCGTTTAACAGCACCGTC 60.601 55.000 0.00 0.00 0.00 4.79
2910 2984 0.179051 TTCCCGTTTAACAGCACCGT 60.179 50.000 0.00 0.00 0.00 4.83
2911 2985 1.161843 ATTCCCGTTTAACAGCACCG 58.838 50.000 0.00 0.00 0.00 4.94
2912 2986 2.413634 CGAATTCCCGTTTAACAGCACC 60.414 50.000 0.00 0.00 0.00 5.01
2913 2987 2.413634 CCGAATTCCCGTTTAACAGCAC 60.414 50.000 0.00 0.00 0.00 4.40
2914 2988 1.807742 CCGAATTCCCGTTTAACAGCA 59.192 47.619 0.00 0.00 0.00 4.41
2915 2989 1.466866 GCCGAATTCCCGTTTAACAGC 60.467 52.381 0.00 0.00 0.00 4.40
2916 2990 1.807742 TGCCGAATTCCCGTTTAACAG 59.192 47.619 0.00 0.00 0.00 3.16
2917 2991 1.807742 CTGCCGAATTCCCGTTTAACA 59.192 47.619 0.00 0.00 0.00 2.41
2918 2992 1.808343 ACTGCCGAATTCCCGTTTAAC 59.192 47.619 0.00 0.00 0.00 2.01
2919 2993 2.188062 ACTGCCGAATTCCCGTTTAA 57.812 45.000 0.00 0.00 0.00 1.52
2920 2994 1.807742 CAACTGCCGAATTCCCGTTTA 59.192 47.619 0.00 0.00 0.00 2.01
2921 2995 0.596082 CAACTGCCGAATTCCCGTTT 59.404 50.000 0.00 0.00 0.00 3.60
2922 2996 1.862602 GCAACTGCCGAATTCCCGTT 61.863 55.000 0.00 0.00 34.31 4.44
2923 2997 2.332654 GCAACTGCCGAATTCCCGT 61.333 57.895 0.00 0.00 34.31 5.28
2924 2998 2.257286 CTGCAACTGCCGAATTCCCG 62.257 60.000 0.00 0.00 41.18 5.14
2925 2999 0.960364 TCTGCAACTGCCGAATTCCC 60.960 55.000 0.00 0.00 41.18 3.97
2926 3000 1.098050 ATCTGCAACTGCCGAATTCC 58.902 50.000 0.00 0.00 37.79 3.01
2927 3001 3.375299 AGTTATCTGCAACTGCCGAATTC 59.625 43.478 0.00 0.00 37.79 2.17
2928 3002 3.127548 CAGTTATCTGCAACTGCCGAATT 59.872 43.478 3.44 0.00 46.37 2.17
2929 3003 2.679837 CAGTTATCTGCAACTGCCGAAT 59.320 45.455 3.44 0.00 46.37 3.34
2930 3004 2.076100 CAGTTATCTGCAACTGCCGAA 58.924 47.619 3.44 0.00 46.37 4.30
2931 3005 1.725641 CAGTTATCTGCAACTGCCGA 58.274 50.000 3.44 0.00 46.37 5.54
2936 3010 7.275888 TGTGAAAAATCAGTTATCTGCAACT 57.724 32.000 0.00 0.00 41.10 3.16
2937 3011 7.928908 TTGTGAAAAATCAGTTATCTGCAAC 57.071 32.000 0.00 0.00 41.10 4.17
2938 3012 9.545105 AAATTGTGAAAAATCAGTTATCTGCAA 57.455 25.926 0.00 0.00 41.10 4.08
2939 3013 8.980610 CAAATTGTGAAAAATCAGTTATCTGCA 58.019 29.630 0.00 0.00 41.10 4.41
2940 3014 8.981647 ACAAATTGTGAAAAATCAGTTATCTGC 58.018 29.630 0.00 0.00 41.10 4.26
2942 3016 9.398170 CGACAAATTGTGAAAAATCAGTTATCT 57.602 29.630 2.20 0.00 0.00 1.98
2943 3017 9.393249 TCGACAAATTGTGAAAAATCAGTTATC 57.607 29.630 2.20 0.00 0.00 1.75
2944 3018 9.912634 ATCGACAAATTGTGAAAAATCAGTTAT 57.087 25.926 2.20 0.00 0.00 1.89
2954 3028 4.036144 TCACTGCATCGACAAATTGTGAAA 59.964 37.500 2.20 0.00 31.49 2.69
2967 3041 0.674581 TCCCAAGCTTCACTGCATCG 60.675 55.000 0.00 0.00 34.99 3.84
3162 3240 7.598869 GGTTTGTTTAGGAATTAGGAGCAAAAG 59.401 37.037 0.00 0.00 0.00 2.27
3336 3419 7.448161 AGAATTCAGTGACACCATGAAATACAA 59.552 33.333 12.64 0.00 36.59 2.41
3485 3568 1.134371 GTCAGGGGAGGTGTAAGATGC 60.134 57.143 0.00 0.00 0.00 3.91
3497 3580 0.693049 GGAAGAGCTTTGTCAGGGGA 59.307 55.000 0.00 0.00 0.00 4.81
3564 3647 3.246112 TAGTGGCCCAACCTGCGT 61.246 61.111 0.00 0.00 40.22 5.24
3664 3748 1.741770 ACGCGGAATGACAGAAGCC 60.742 57.895 12.47 0.00 0.00 4.35
3708 3796 9.303116 AGTTTACACTCTGCTATATGCTACTAT 57.697 33.333 0.00 0.00 43.37 2.12
3723 3811 9.398538 CACCTCTCTATAGTAAGTTTACACTCT 57.601 37.037 0.00 0.00 36.12 3.24
3724 3812 9.393512 TCACCTCTCTATAGTAAGTTTACACTC 57.606 37.037 0.00 0.00 36.12 3.51
3810 3900 4.814294 GCAGCAATGGCAGCCAGC 62.814 66.667 21.51 18.67 45.79 4.85
3815 3905 1.736645 GCAACAGCAGCAATGGCAG 60.737 57.895 0.00 0.00 44.61 4.85
3816 3906 2.149803 GAGCAACAGCAGCAATGGCA 62.150 55.000 0.00 0.00 44.61 4.92
3817 3907 1.445582 GAGCAACAGCAGCAATGGC 60.446 57.895 0.00 0.00 41.61 4.40
3818 3908 1.456296 TAGAGCAACAGCAGCAATGG 58.544 50.000 0.00 0.00 0.00 3.16
3819 3909 2.731341 GCTTAGAGCAACAGCAGCAATG 60.731 50.000 0.00 0.00 41.89 2.82
3820 3910 1.471684 GCTTAGAGCAACAGCAGCAAT 59.528 47.619 0.00 0.00 41.89 3.56
3821 3911 0.877071 GCTTAGAGCAACAGCAGCAA 59.123 50.000 0.00 0.00 41.89 3.91
3822 3912 2.548178 GCTTAGAGCAACAGCAGCA 58.452 52.632 0.00 0.00 41.89 4.41
3961 4054 5.363562 TGAGATCACTGGTAGCATGAATT 57.636 39.130 0.00 3.76 0.00 2.17
3988 4081 9.901172 AAGTCTTTGAAACTTAAAAGTCTAGGA 57.099 29.630 0.00 0.00 38.57 2.94
3992 4085 9.841880 GACAAAGTCTTTGAAACTTAAAAGTCT 57.158 29.630 28.07 3.99 43.26 3.24
3993 4086 9.620660 TGACAAAGTCTTTGAAACTTAAAAGTC 57.379 29.630 28.07 12.89 43.26 3.01
3994 4087 9.406828 GTGACAAAGTCTTTGAAACTTAAAAGT 57.593 29.630 28.07 4.59 43.26 2.66
3995 4088 9.405587 TGTGACAAAGTCTTTGAAACTTAAAAG 57.594 29.630 28.07 1.43 43.26 2.27
3996 4089 9.751542 TTGTGACAAAGTCTTTGAAACTTAAAA 57.248 25.926 28.07 13.66 43.26 1.52
3997 4090 9.921637 ATTGTGACAAAGTCTTTGAAACTTAAA 57.078 25.926 28.07 15.96 43.26 1.52
3998 4091 9.567848 GATTGTGACAAAGTCTTTGAAACTTAA 57.432 29.630 28.07 16.49 43.26 1.85
3999 4092 8.956426 AGATTGTGACAAAGTCTTTGAAACTTA 58.044 29.630 28.07 17.02 43.26 2.24
4000 4093 7.830739 AGATTGTGACAAAGTCTTTGAAACTT 58.169 30.769 28.07 16.56 43.26 2.66
4001 4094 7.396540 AGATTGTGACAAAGTCTTTGAAACT 57.603 32.000 28.07 14.37 43.26 2.66
4024 4117 9.612066 AAGCTTTTTCTCTGATATTCTAGGAAG 57.388 33.333 0.00 0.00 0.00 3.46
4047 4140 4.212150 GCTTCAGTTCGTTCTTACAAAGC 58.788 43.478 0.00 0.00 32.25 3.51
4182 4275 3.147595 CTCCGGACATCCTCGGCA 61.148 66.667 0.00 0.00 45.31 5.69
4399 4528 4.527509 AGTTCAGTGTATGTCTGGTGAG 57.472 45.455 0.00 0.00 34.15 3.51
4400 4529 4.955811 AAGTTCAGTGTATGTCTGGTGA 57.044 40.909 0.00 0.00 34.15 4.02
4401 4530 5.056480 TCAAAGTTCAGTGTATGTCTGGTG 58.944 41.667 0.00 0.00 34.15 4.17
4402 4531 5.290493 TCAAAGTTCAGTGTATGTCTGGT 57.710 39.130 0.00 0.00 34.15 4.00
4403 4532 6.808008 AATCAAAGTTCAGTGTATGTCTGG 57.192 37.500 0.00 0.00 34.15 3.86
4404 4533 8.092521 AGAAATCAAAGTTCAGTGTATGTCTG 57.907 34.615 0.00 0.00 0.00 3.51
4405 4534 8.153550 AGAGAAATCAAAGTTCAGTGTATGTCT 58.846 33.333 0.00 0.00 0.00 3.41
4406 4535 8.316640 AGAGAAATCAAAGTTCAGTGTATGTC 57.683 34.615 0.00 0.00 0.00 3.06
4407 4536 7.116948 CGAGAGAAATCAAAGTTCAGTGTATGT 59.883 37.037 0.00 0.00 0.00 2.29
4408 4537 7.412346 CCGAGAGAAATCAAAGTTCAGTGTATG 60.412 40.741 0.00 0.00 0.00 2.39
4409 4538 6.591834 CCGAGAGAAATCAAAGTTCAGTGTAT 59.408 38.462 0.00 0.00 0.00 2.29
4410 4539 5.926542 CCGAGAGAAATCAAAGTTCAGTGTA 59.073 40.000 0.00 0.00 0.00 2.90
4411 4540 4.752101 CCGAGAGAAATCAAAGTTCAGTGT 59.248 41.667 0.00 0.00 0.00 3.55
4412 4541 4.377841 GCCGAGAGAAATCAAAGTTCAGTG 60.378 45.833 0.00 0.00 0.00 3.66
4413 4542 3.748568 GCCGAGAGAAATCAAAGTTCAGT 59.251 43.478 0.00 0.00 0.00 3.41
4453 4597 1.016130 CGAGGTGAGTTTGCGCATCT 61.016 55.000 12.75 13.53 38.58 2.90
4488 4632 2.219325 GACTGGTGCTCTGACCCGAG 62.219 65.000 0.00 0.00 34.79 4.63
4489 4633 2.203640 ACTGGTGCTCTGACCCGA 60.204 61.111 0.00 0.00 34.79 5.14
4490 4634 2.262915 GACTGGTGCTCTGACCCG 59.737 66.667 0.00 0.00 34.79 5.28
4491 4635 2.262915 CGACTGGTGCTCTGACCC 59.737 66.667 0.00 0.00 34.79 4.46
4492 4636 1.080434 GACGACTGGTGCTCTGACC 60.080 63.158 0.00 0.00 36.43 4.02
4493 4637 1.080434 GGACGACTGGTGCTCTGAC 60.080 63.158 0.00 0.00 33.58 3.51
4494 4638 1.530655 TGGACGACTGGTGCTCTGA 60.531 57.895 0.00 0.00 37.93 3.27
4495 4639 1.373497 GTGGACGACTGGTGCTCTG 60.373 63.158 0.00 0.00 37.93 3.35
4496 4640 1.810606 CTGTGGACGACTGGTGCTCT 61.811 60.000 0.00 0.00 37.93 4.09
4497 4641 1.373497 CTGTGGACGACTGGTGCTC 60.373 63.158 0.00 0.00 37.93 4.26
4530 4688 4.679639 GCATGGCAGCATATCATATTTGGG 60.680 45.833 0.00 0.00 0.00 4.12
4540 4701 1.806461 GCAGCAGCATGGCAGCATAT 61.806 55.000 8.29 0.00 43.44 1.78
4541 4702 2.486663 GCAGCAGCATGGCAGCATA 61.487 57.895 8.29 0.00 43.44 3.14
4549 4710 1.101635 ATACCAGCAGCAGCAGCATG 61.102 55.000 12.92 7.32 45.49 4.06
4550 4711 0.818445 GATACCAGCAGCAGCAGCAT 60.818 55.000 12.92 0.00 45.49 3.79
4564 4725 3.978876 ACCAAGGCAGGTTGATACC 57.021 52.632 0.00 0.00 45.39 2.73
4578 4739 4.522405 CCACACCATCAATTACTGAACCAA 59.478 41.667 0.00 0.00 37.67 3.67


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

AutoCloner maintained by Alex Coulton.