Multiple sequence alignment - TraesCS2D01G211800

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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 TraesCS2D01G211800 chr2D 100.000 3429 0 0 1 3429 169988885 169985457 0.000000e+00 6333.0
1 TraesCS2D01G211800 chr2D 79.512 205 39 3 3156 3359 626651687 626651485 3.570000e-30 143.0
2 TraesCS2D01G211800 chr2D 97.619 42 1 0 3117 3158 612198882 612198841 4.750000e-09 73.1
3 TraesCS2D01G211800 chr2B 94.976 2050 71 17 802 2842 227687393 227689419 0.000000e+00 3186.0
4 TraesCS2D01G211800 chr2B 83.374 818 42 45 30 811 227686454 227687213 0.000000e+00 671.0
5 TraesCS2D01G211800 chr2B 85.874 269 38 0 3156 3424 227689867 227690135 1.560000e-73 287.0
6 TraesCS2D01G211800 chr2B 80.000 220 30 11 3160 3375 368384337 368384128 2.130000e-32 150.0
7 TraesCS2D01G211800 chr2A 91.535 1205 67 16 577 1764 180112694 180113880 0.000000e+00 1628.0
8 TraesCS2D01G211800 chr2A 92.687 1094 53 15 1778 2860 180113866 180114943 0.000000e+00 1552.0
9 TraesCS2D01G211800 chr2A 89.755 449 15 8 133 569 180112197 180112626 2.330000e-151 545.0
10 TraesCS2D01G211800 chr2A 88.104 269 32 0 3156 3424 180115451 180115719 1.540000e-83 320.0
11 TraesCS2D01G211800 chr2A 89.928 139 10 3 1 136 180103112 180103249 3.520000e-40 176.0
12 TraesCS2D01G211800 chr2A 88.393 112 12 1 3048 3158 180115135 180115246 2.150000e-27 134.0
13 TraesCS2D01G211800 chr1D 81.159 207 36 1 3156 3362 204986356 204986559 2.740000e-36 163.0
14 TraesCS2D01G211800 chr3B 81.373 204 27 6 3160 3361 558190633 558190827 4.580000e-34 156.0
15 TraesCS2D01G211800 chr4D 80.829 193 31 4 3161 3351 294341455 294341267 2.760000e-31 147.0
16 TraesCS2D01G211800 chr7A 79.808 208 30 7 3156 3360 166480947 166481145 1.280000e-29 141.0
17 TraesCS2D01G211800 chr6D 79.592 196 32 5 3158 3350 51971023 51970833 2.150000e-27 134.0
18 TraesCS2D01G211800 chr6D 84.270 89 5 4 3074 3153 313886466 313886554 1.020000e-10 78.7
19 TraesCS2D01G211800 chr6A 95.122 41 2 0 3115 3155 451404373 451404413 7.940000e-07 65.8
20 TraesCS2D01G211800 chr5B 84.483 58 8 1 3356 3413 304818048 304817992 4.780000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G211800 chr2D 169985457 169988885 3428 True 6333.000000 6333 100.000000 1 3429 1 chr2D.!!$R1 3428
1 TraesCS2D01G211800 chr2B 227686454 227690135 3681 False 1381.333333 3186 88.074667 30 3424 3 chr2B.!!$F1 3394
2 TraesCS2D01G211800 chr2A 180112197 180115719 3522 False 835.800000 1628 90.094800 133 3424 5 chr2A.!!$F2 3291

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
244 289 0.108945 TAGACACGAGACGAGAGCGA 60.109 55.000 0.0 0.0 41.64 4.93 F
245 290 1.059681 GACACGAGACGAGAGCGAG 59.940 63.158 0.0 0.0 41.64 5.03 F
1088 1409 1.082954 TGGGGGAGAAGGAAGGAGG 59.917 63.158 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 2142 0.165944 AAAGCGTTCAAGATTCGGCG 59.834 50.0 0.00 0.0 0.00 6.46 R
1852 2175 7.664082 TCAACACAAAATTTCTTTTCTTGCA 57.336 28.0 0.00 0.0 32.21 4.08 R
2967 3426 0.033366 CGCGGATATGGACATGTGGA 59.967 55.0 1.15 0.0 0.00 4.02 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
23 24 5.972107 TGGCTTAACTAAACTCGAGTAGT 57.028 39.130 20.39 16.74 41.49 2.73
24 25 5.706916 TGGCTTAACTAAACTCGAGTAGTG 58.293 41.667 20.39 13.59 38.88 2.74
25 26 5.100943 GGCTTAACTAAACTCGAGTAGTGG 58.899 45.833 20.39 14.16 38.88 4.00
26 27 5.336293 GGCTTAACTAAACTCGAGTAGTGGT 60.336 44.000 20.39 14.82 38.88 4.16
27 28 6.127897 GGCTTAACTAAACTCGAGTAGTGGTA 60.128 42.308 20.39 11.45 38.88 3.25
28 29 7.416101 GGCTTAACTAAACTCGAGTAGTGGTAT 60.416 40.741 20.39 7.04 38.88 2.73
29 30 7.431668 GCTTAACTAAACTCGAGTAGTGGTATG 59.568 40.741 20.39 15.69 38.88 2.39
30 31 5.831702 ACTAAACTCGAGTAGTGGTATGG 57.168 43.478 20.39 4.27 38.88 2.74
31 32 4.643784 ACTAAACTCGAGTAGTGGTATGGG 59.356 45.833 20.39 0.81 38.88 4.00
32 33 2.068834 ACTCGAGTAGTGGTATGGGG 57.931 55.000 18.46 0.00 36.93 4.96
33 34 1.287146 ACTCGAGTAGTGGTATGGGGT 59.713 52.381 18.46 0.00 36.93 4.95
39 40 4.563993 CGAGTAGTGGTATGGGGTCAAAAA 60.564 45.833 0.00 0.00 0.00 1.94
62 69 5.707931 AGAAAACGGAGCAGTAGTAGTAAC 58.292 41.667 0.00 0.00 0.00 2.50
71 78 6.036191 GGAGCAGTAGTAGTAACAGAATTTGC 59.964 42.308 0.00 0.00 0.00 3.68
114 121 3.096852 ACTGTCAGAATCGTCATGGGTA 58.903 45.455 6.91 0.00 0.00 3.69
126 133 5.121811 TCGTCATGGGTAGAGTAGTAGTTC 58.878 45.833 0.00 0.00 0.00 3.01
129 136 5.007528 GTCATGGGTAGAGTAGTAGTTCGTC 59.992 48.000 0.00 0.00 0.00 4.20
133 140 4.940654 GGGTAGAGTAGTAGTTCGTCTTGT 59.059 45.833 0.00 0.00 0.00 3.16
136 143 6.591834 GGTAGAGTAGTAGTTCGTCTTGTACA 59.408 42.308 0.00 0.00 0.00 2.90
162 195 1.618343 TGAGTCGCTCAAAGACATGGA 59.382 47.619 7.02 0.00 37.57 3.41
163 196 2.266554 GAGTCGCTCAAAGACATGGAG 58.733 52.381 0.00 0.00 40.84 3.86
242 287 2.206750 AGATAGACACGAGACGAGAGC 58.793 52.381 0.00 0.00 0.00 4.09
243 288 0.931702 ATAGACACGAGACGAGAGCG 59.068 55.000 0.00 0.00 44.79 5.03
244 289 0.108945 TAGACACGAGACGAGAGCGA 60.109 55.000 0.00 0.00 41.64 4.93
245 290 1.059681 GACACGAGACGAGAGCGAG 59.940 63.158 0.00 0.00 41.64 5.03
246 291 2.276994 CACGAGACGAGAGCGAGC 60.277 66.667 0.00 0.00 41.64 5.03
335 386 2.445438 GCTGGACAGTTAGCGCGAC 61.445 63.158 12.10 5.15 0.00 5.19
354 405 2.361104 GGAAGCGGATGCCACCAA 60.361 61.111 0.00 0.00 44.31 3.67
484 539 1.186200 GTTTGAAGATGGAAGCCCCC 58.814 55.000 0.00 0.00 0.00 5.40
510 565 3.199289 TCTCTCAACAGCCATCATCATGT 59.801 43.478 0.00 0.00 0.00 3.21
511 566 4.406649 TCTCTCAACAGCCATCATCATGTA 59.593 41.667 0.00 0.00 0.00 2.29
512 567 5.071384 TCTCTCAACAGCCATCATCATGTAT 59.929 40.000 0.00 0.00 0.00 2.29
513 568 5.687780 TCTCAACAGCCATCATCATGTATT 58.312 37.500 0.00 0.00 0.00 1.89
514 569 6.829849 TCTCAACAGCCATCATCATGTATTA 58.170 36.000 0.00 0.00 0.00 0.98
515 570 7.281841 TCTCAACAGCCATCATCATGTATTAA 58.718 34.615 0.00 0.00 0.00 1.40
516 571 7.940688 TCTCAACAGCCATCATCATGTATTAAT 59.059 33.333 0.00 0.00 0.00 1.40
517 572 8.467963 TCAACAGCCATCATCATGTATTAATT 57.532 30.769 0.00 0.00 0.00 1.40
518 573 8.570488 TCAACAGCCATCATCATGTATTAATTC 58.430 33.333 0.00 0.00 0.00 2.17
519 574 8.354426 CAACAGCCATCATCATGTATTAATTCA 58.646 33.333 0.00 0.00 0.00 2.57
579 686 1.470098 CCAGCCTGTACAAAGACATGC 59.530 52.381 0.00 0.00 40.18 4.06
590 705 1.730501 AAGACATGCCACGACATCTG 58.269 50.000 0.00 0.00 0.00 2.90
636 757 8.768955 GCAGTAACAGAGTTGATTAAGATATGG 58.231 37.037 0.00 0.00 0.00 2.74
694 815 8.879759 GTTTGATTAAGCATAAGCACAGTAGTA 58.120 33.333 0.00 0.00 45.49 1.82
695 816 9.443323 TTTGATTAAGCATAAGCACAGTAGTAA 57.557 29.630 0.00 0.00 45.49 2.24
697 818 9.613428 TGATTAAGCATAAGCACAGTAGTAATT 57.387 29.630 0.00 0.00 45.49 1.40
704 825 7.530861 GCATAAGCACAGTAGTAATTTATTCGC 59.469 37.037 0.00 0.00 41.58 4.70
706 827 6.978343 AGCACAGTAGTAATTTATTCGCAA 57.022 33.333 0.00 0.00 0.00 4.85
707 828 7.372451 AGCACAGTAGTAATTTATTCGCAAA 57.628 32.000 0.00 0.00 0.00 3.68
708 829 7.464358 AGCACAGTAGTAATTTATTCGCAAAG 58.536 34.615 0.00 0.00 0.00 2.77
710 831 7.960738 GCACAGTAGTAATTTATTCGCAAAGAA 59.039 33.333 0.00 0.00 43.93 2.52
711 832 9.820229 CACAGTAGTAATTTATTCGCAAAGAAA 57.180 29.630 0.00 0.00 42.91 2.52
720 841 8.755696 ATTTATTCGCAAAGAAAATAAGCACA 57.244 26.923 0.00 0.00 42.91 4.57
721 842 7.795431 TTATTCGCAAAGAAAATAAGCACAG 57.205 32.000 0.00 0.00 42.91 3.66
722 843 4.829064 TCGCAAAGAAAATAAGCACAGT 57.171 36.364 0.00 0.00 0.00 3.55
723 844 5.933187 TCGCAAAGAAAATAAGCACAGTA 57.067 34.783 0.00 0.00 0.00 2.74
724 845 5.927030 TCGCAAAGAAAATAAGCACAGTAG 58.073 37.500 0.00 0.00 0.00 2.57
725 846 5.468746 TCGCAAAGAAAATAAGCACAGTAGT 59.531 36.000 0.00 0.00 0.00 2.73
726 847 6.647481 TCGCAAAGAAAATAAGCACAGTAGTA 59.353 34.615 0.00 0.00 0.00 1.82
727 848 7.171848 TCGCAAAGAAAATAAGCACAGTAGTAA 59.828 33.333 0.00 0.00 0.00 2.24
728 849 7.962918 CGCAAAGAAAATAAGCACAGTAGTAAT 59.037 33.333 0.00 0.00 0.00 1.89
729 850 9.626045 GCAAAGAAAATAAGCACAGTAGTAATT 57.374 29.630 0.00 0.00 0.00 1.40
737 858 9.811995 AATAAGCACAGTAGTAATTCGTAATCA 57.188 29.630 0.00 0.00 0.00 2.57
1088 1409 1.082954 TGGGGGAGAAGGAAGGAGG 59.917 63.158 0.00 0.00 0.00 4.30
1604 1925 3.382832 AGCGAAGGGTCACGGAGG 61.383 66.667 0.00 0.00 0.00 4.30
1759 2080 5.748152 GCAATTCGCCAAGCTATTTAATTCA 59.252 36.000 0.00 0.00 32.94 2.57
1760 2081 6.421801 GCAATTCGCCAAGCTATTTAATTCAT 59.578 34.615 0.00 0.00 32.94 2.57
1761 2082 7.358683 GCAATTCGCCAAGCTATTTAATTCATC 60.359 37.037 0.00 0.00 32.94 2.92
1762 2083 5.342806 TCGCCAAGCTATTTAATTCATCG 57.657 39.130 0.00 0.00 0.00 3.84
1763 2084 5.053811 TCGCCAAGCTATTTAATTCATCGA 58.946 37.500 0.00 0.00 0.00 3.59
1772 2094 9.807649 AGCTATTTAATTCATCGAATTTTGCTT 57.192 25.926 7.22 0.00 41.64 3.91
1804 2126 5.808366 AATTCATCGACTATTCTGGCCTA 57.192 39.130 3.32 0.00 0.00 3.93
1819 2142 2.038557 TGGCCTACAAAGACCAGACTTC 59.961 50.000 3.32 0.00 0.00 3.01
1849 2172 4.338118 TCTTGAACGCTTTTGTGGAATTCT 59.662 37.500 5.23 0.00 0.00 2.40
1850 2173 4.223320 TGAACGCTTTTGTGGAATTCTC 57.777 40.909 5.23 0.09 0.00 2.87
1852 2175 4.338118 TGAACGCTTTTGTGGAATTCTCTT 59.662 37.500 5.23 0.00 0.00 2.85
2115 2438 1.285023 CGAGACGTTCAACGACCCT 59.715 57.895 18.84 10.31 46.05 4.34
2119 2442 2.280524 CGTTCAACGACCCTGCCA 60.281 61.111 3.01 0.00 46.05 4.92
2120 2443 1.671054 CGTTCAACGACCCTGCCAT 60.671 57.895 3.01 0.00 46.05 4.40
2121 2444 1.635663 CGTTCAACGACCCTGCCATC 61.636 60.000 3.01 0.00 46.05 3.51
2301 2624 2.442188 CGGCGGTCGTTACTGAAGC 61.442 63.158 0.00 0.00 33.42 3.86
2332 2655 1.938585 AGGAACTGAACTCGGGATGA 58.061 50.000 0.00 0.00 37.18 2.92
2442 2770 8.623030 GGTTCTGTCAATAACTCCTAGTAGTAG 58.377 40.741 0.00 0.00 0.00 2.57
2443 2771 9.176460 GTTCTGTCAATAACTCCTAGTAGTAGT 57.824 37.037 3.91 0.00 0.00 2.73
2446 2774 9.835389 CTGTCAATAACTCCTAGTAGTAGTAGT 57.165 37.037 10.49 0.54 26.81 2.73
2483 2811 4.330074 CGATAGTAGTTTTGCACAAGGGAG 59.670 45.833 0.00 0.00 0.00 4.30
2495 2825 4.263462 TGCACAAGGGAGTCAAGTTGATAT 60.263 41.667 9.18 0.76 0.00 1.63
2622 2954 1.129437 GTTCCTTTGCTCGATCTGTGC 59.871 52.381 0.00 0.00 37.59 4.57
2623 2955 0.610174 TCCTTTGCTCGATCTGTGCT 59.390 50.000 11.06 0.00 37.94 4.40
2624 2956 0.725686 CCTTTGCTCGATCTGTGCTG 59.274 55.000 11.06 4.37 37.94 4.41
2625 2957 1.436600 CTTTGCTCGATCTGTGCTGT 58.563 50.000 11.06 0.00 37.94 4.40
2626 2958 1.128136 CTTTGCTCGATCTGTGCTGTG 59.872 52.381 11.06 1.42 37.94 3.66
2701 3033 3.438087 CCTGAAGCTGTCGATTTGTTCAT 59.562 43.478 0.00 0.00 0.00 2.57
2715 3047 6.201044 CGATTTGTTCATACAGTAGGGATCAC 59.799 42.308 0.00 0.00 35.28 3.06
2718 3050 4.142249 TGTTCATACAGTAGGGATCACACG 60.142 45.833 0.00 0.00 0.00 4.49
2724 3056 1.825474 AGTAGGGATCACACGACAAGG 59.175 52.381 0.00 0.00 0.00 3.61
2827 3162 1.298859 CTACAGCCGGACTTGCCAAC 61.299 60.000 5.05 0.00 35.94 3.77
2828 3163 2.046009 TACAGCCGGACTTGCCAACA 62.046 55.000 5.05 0.00 35.94 3.33
2829 3164 2.192861 CAGCCGGACTTGCCAACAA 61.193 57.895 5.05 0.00 35.94 2.83
2830 3165 1.454847 AGCCGGACTTGCCAACAAA 60.455 52.632 5.05 0.00 34.74 2.83
2831 3166 0.827507 AGCCGGACTTGCCAACAAAT 60.828 50.000 5.05 0.00 34.74 2.32
2832 3167 0.388520 GCCGGACTTGCCAACAAATC 60.389 55.000 5.05 0.00 34.74 2.17
2834 3169 3.792716 GGACTTGCCAACAAATCCG 57.207 52.632 0.00 0.00 41.90 4.18
2845 3184 3.753272 CCAACAAATCCGGCATCCTATAG 59.247 47.826 0.00 0.00 0.00 1.31
2847 3186 2.305927 ACAAATCCGGCATCCTATAGGG 59.694 50.000 18.97 4.82 35.41 3.53
2852 3191 1.078848 GGCATCCTATAGGGCTGCG 60.079 63.158 27.05 12.49 41.81 5.18
2888 3347 0.324275 GGGCAGCCCTTAAATCCACA 60.324 55.000 24.99 0.00 41.34 4.17
2904 3363 0.459411 CACATGTCCACATCCGCGTA 60.459 55.000 4.92 0.00 33.61 4.42
2905 3364 0.464036 ACATGTCCACATCCGCGTAT 59.536 50.000 4.92 0.00 33.61 3.06
2906 3365 1.139989 CATGTCCACATCCGCGTATC 58.860 55.000 4.92 0.00 33.61 2.24
2907 3366 1.040646 ATGTCCACATCCGCGTATCT 58.959 50.000 4.92 0.00 28.78 1.98
2908 3367 0.384309 TGTCCACATCCGCGTATCTC 59.616 55.000 4.92 0.00 0.00 2.75
2909 3368 0.384309 GTCCACATCCGCGTATCTCA 59.616 55.000 4.92 0.00 0.00 3.27
2910 3369 1.000163 GTCCACATCCGCGTATCTCAT 60.000 52.381 4.92 0.00 0.00 2.90
2911 3370 2.228103 GTCCACATCCGCGTATCTCATA 59.772 50.000 4.92 0.00 0.00 2.15
2912 3371 3.089284 TCCACATCCGCGTATCTCATAT 58.911 45.455 4.92 0.00 0.00 1.78
2913 3372 3.509967 TCCACATCCGCGTATCTCATATT 59.490 43.478 4.92 0.00 0.00 1.28
2914 3373 3.859961 CCACATCCGCGTATCTCATATTC 59.140 47.826 4.92 0.00 0.00 1.75
2915 3374 3.543889 CACATCCGCGTATCTCATATTCG 59.456 47.826 4.92 0.00 0.00 3.34
2916 3375 3.439129 ACATCCGCGTATCTCATATTCGA 59.561 43.478 4.92 0.00 0.00 3.71
2917 3376 3.466712 TCCGCGTATCTCATATTCGAC 57.533 47.619 4.92 0.00 0.00 4.20
2918 3377 2.809696 TCCGCGTATCTCATATTCGACA 59.190 45.455 4.92 0.00 0.00 4.35
2919 3378 3.439129 TCCGCGTATCTCATATTCGACAT 59.561 43.478 4.92 0.00 0.00 3.06
2920 3379 3.786576 CCGCGTATCTCATATTCGACATC 59.213 47.826 4.92 0.00 0.00 3.06
2921 3380 3.786576 CGCGTATCTCATATTCGACATCC 59.213 47.826 0.00 0.00 0.00 3.51
2922 3381 4.437524 CGCGTATCTCATATTCGACATCCT 60.438 45.833 0.00 0.00 0.00 3.24
2923 3382 5.220605 CGCGTATCTCATATTCGACATCCTA 60.221 44.000 0.00 0.00 0.00 2.94
2924 3383 6.511929 CGCGTATCTCATATTCGACATCCTAT 60.512 42.308 0.00 0.00 0.00 2.57
2925 3384 7.307219 CGCGTATCTCATATTCGACATCCTATA 60.307 40.741 0.00 0.00 0.00 1.31
2926 3385 8.508062 GCGTATCTCATATTCGACATCCTATAT 58.492 37.037 0.00 0.00 0.00 0.86
2930 3389 9.599056 ATCTCATATTCGACATCCTATATCCAT 57.401 33.333 0.00 0.00 0.00 3.41
2933 3392 9.640952 TCATATTCGACATCCTATATCCATACA 57.359 33.333 0.00 0.00 0.00 2.29
2939 3398 9.640952 TCGACATCCTATATCCATACAATATCA 57.359 33.333 0.00 0.00 0.00 2.15
2945 3404 9.836864 TCCTATATCCATACAATATCATGCAAC 57.163 33.333 0.00 0.00 0.00 4.17
2946 3405 8.768019 CCTATATCCATACAATATCATGCAACG 58.232 37.037 0.00 0.00 0.00 4.10
2947 3406 9.317936 CTATATCCATACAATATCATGCAACGT 57.682 33.333 0.00 0.00 0.00 3.99
2949 3408 7.601073 ATCCATACAATATCATGCAACGTAG 57.399 36.000 0.00 0.00 0.00 3.51
2951 3410 6.423604 TCCATACAATATCATGCAACGTAGTG 59.576 38.462 0.00 0.00 45.00 2.74
2952 3411 4.536364 ACAATATCATGCAACGTAGTGC 57.464 40.909 5.26 5.26 45.00 4.40
2953 3412 3.001228 ACAATATCATGCAACGTAGTGCG 59.999 43.478 7.66 0.00 45.00 5.34
2954 3413 1.566404 TATCATGCAACGTAGTGCGG 58.434 50.000 5.41 3.07 45.00 5.69
2955 3414 1.089481 ATCATGCAACGTAGTGCGGG 61.089 55.000 5.41 2.74 45.00 6.13
2956 3415 3.124921 ATGCAACGTAGTGCGGGC 61.125 61.111 5.41 8.98 45.00 6.13
2957 3416 4.610714 TGCAACGTAGTGCGGGCA 62.611 61.111 15.81 15.81 45.00 5.36
2958 3417 3.350612 GCAACGTAGTGCGGGCAA 61.351 61.111 13.04 0.00 45.00 4.52
2959 3418 2.899044 GCAACGTAGTGCGGGCAAA 61.899 57.895 13.04 0.00 45.00 3.68
2960 3419 1.649815 CAACGTAGTGCGGGCAAAA 59.350 52.632 5.41 0.00 45.00 2.44
2961 3420 0.239879 CAACGTAGTGCGGGCAAAAT 59.760 50.000 5.41 0.00 45.00 1.82
2962 3421 0.519961 AACGTAGTGCGGGCAAAATC 59.480 50.000 5.41 0.00 45.00 2.17
2963 3422 0.604243 ACGTAGTGCGGGCAAAATCA 60.604 50.000 5.41 0.00 46.52 2.57
2964 3423 0.519519 CGTAGTGCGGGCAAAATCAA 59.480 50.000 0.00 0.00 36.85 2.57
2965 3424 1.068885 CGTAGTGCGGGCAAAATCAAA 60.069 47.619 0.00 0.00 36.85 2.69
2966 3425 2.605823 CGTAGTGCGGGCAAAATCAAAA 60.606 45.455 0.00 0.00 36.85 2.44
2967 3426 2.837532 AGTGCGGGCAAAATCAAAAT 57.162 40.000 0.00 0.00 0.00 1.82
2968 3427 2.687370 AGTGCGGGCAAAATCAAAATC 58.313 42.857 0.00 0.00 0.00 2.17
2969 3428 1.731709 GTGCGGGCAAAATCAAAATCC 59.268 47.619 0.00 0.00 0.00 3.01
2970 3429 1.345741 TGCGGGCAAAATCAAAATCCA 59.654 42.857 0.00 0.00 0.00 3.41
2971 3430 1.731709 GCGGGCAAAATCAAAATCCAC 59.268 47.619 0.00 0.00 0.00 4.02
2972 3431 2.869636 GCGGGCAAAATCAAAATCCACA 60.870 45.455 0.00 0.00 0.00 4.17
2973 3432 3.598299 CGGGCAAAATCAAAATCCACAT 58.402 40.909 0.00 0.00 0.00 3.21
2974 3433 3.371591 CGGGCAAAATCAAAATCCACATG 59.628 43.478 0.00 0.00 0.00 3.21
2975 3434 4.325972 GGGCAAAATCAAAATCCACATGT 58.674 39.130 0.00 0.00 0.00 3.21
2976 3435 4.392754 GGGCAAAATCAAAATCCACATGTC 59.607 41.667 0.00 0.00 0.00 3.06
2977 3436 4.392754 GGCAAAATCAAAATCCACATGTCC 59.607 41.667 0.00 0.00 0.00 4.02
2978 3437 4.996122 GCAAAATCAAAATCCACATGTCCA 59.004 37.500 0.00 0.00 0.00 4.02
2979 3438 5.644636 GCAAAATCAAAATCCACATGTCCAT 59.355 36.000 0.00 0.00 0.00 3.41
2980 3439 6.817641 GCAAAATCAAAATCCACATGTCCATA 59.182 34.615 0.00 0.00 0.00 2.74
2981 3440 7.496591 GCAAAATCAAAATCCACATGTCCATAT 59.503 33.333 0.00 0.00 0.00 1.78
2982 3441 9.037737 CAAAATCAAAATCCACATGTCCATATC 57.962 33.333 0.00 0.00 0.00 1.63
2983 3442 6.906157 ATCAAAATCCACATGTCCATATCC 57.094 37.500 0.00 0.00 0.00 2.59
2984 3443 4.821260 TCAAAATCCACATGTCCATATCCG 59.179 41.667 0.00 0.00 0.00 4.18
2985 3444 2.479566 ATCCACATGTCCATATCCGC 57.520 50.000 0.00 0.00 0.00 5.54
2986 3445 0.033366 TCCACATGTCCATATCCGCG 59.967 55.000 0.00 0.00 0.00 6.46
2987 3446 0.249868 CCACATGTCCATATCCGCGT 60.250 55.000 4.92 0.00 0.00 6.01
2988 3447 1.000394 CCACATGTCCATATCCGCGTA 60.000 52.381 4.92 0.00 0.00 4.42
2989 3448 2.353704 CCACATGTCCATATCCGCGTAT 60.354 50.000 4.92 0.00 0.00 3.06
2990 3449 2.923655 CACATGTCCATATCCGCGTATC 59.076 50.000 4.92 0.00 0.00 2.24
2991 3450 2.826128 ACATGTCCATATCCGCGTATCT 59.174 45.455 4.92 0.00 0.00 1.98
2992 3451 3.119459 ACATGTCCATATCCGCGTATCTC 60.119 47.826 4.92 0.00 0.00 2.75
2993 3452 2.510613 TGTCCATATCCGCGTATCTCA 58.489 47.619 4.92 0.00 0.00 3.27
2994 3453 3.089284 TGTCCATATCCGCGTATCTCAT 58.911 45.455 4.92 0.00 0.00 2.90
2995 3454 4.266714 TGTCCATATCCGCGTATCTCATA 58.733 43.478 4.92 0.00 0.00 2.15
2996 3455 4.887655 TGTCCATATCCGCGTATCTCATAT 59.112 41.667 4.92 0.00 0.00 1.78
2997 3456 5.008712 TGTCCATATCCGCGTATCTCATATC 59.991 44.000 4.92 0.00 0.00 1.63
2998 3457 4.519350 TCCATATCCGCGTATCTCATATCC 59.481 45.833 4.92 0.00 0.00 2.59
2999 3458 4.467735 CATATCCGCGTATCTCATATCCG 58.532 47.826 4.92 0.00 0.00 4.18
3000 3459 2.103537 TCCGCGTATCTCATATCCGA 57.896 50.000 4.92 0.00 0.00 4.55
3001 3460 1.736126 TCCGCGTATCTCATATCCGAC 59.264 52.381 4.92 0.00 0.00 4.79
3002 3461 1.467342 CCGCGTATCTCATATCCGACA 59.533 52.381 4.92 0.00 0.00 4.35
3003 3462 2.097629 CCGCGTATCTCATATCCGACAT 59.902 50.000 4.92 0.00 0.00 3.06
3004 3463 3.355270 CGCGTATCTCATATCCGACATC 58.645 50.000 0.00 0.00 0.00 3.06
3005 3464 3.181510 CGCGTATCTCATATCCGACATCA 60.182 47.826 0.00 0.00 0.00 3.07
3006 3465 4.099120 GCGTATCTCATATCCGACATCAC 58.901 47.826 0.00 0.00 0.00 3.06
3007 3466 4.379499 GCGTATCTCATATCCGACATCACA 60.379 45.833 0.00 0.00 0.00 3.58
3008 3467 5.677344 GCGTATCTCATATCCGACATCACAT 60.677 44.000 0.00 0.00 0.00 3.21
3009 3468 6.458342 GCGTATCTCATATCCGACATCACATA 60.458 42.308 0.00 0.00 0.00 2.29
3010 3469 7.643579 CGTATCTCATATCCGACATCACATAT 58.356 38.462 0.00 0.00 0.00 1.78
3011 3470 7.800847 CGTATCTCATATCCGACATCACATATC 59.199 40.741 0.00 0.00 0.00 1.63
3012 3471 6.456795 TCTCATATCCGACATCACATATCC 57.543 41.667 0.00 0.00 0.00 2.59
3029 3488 9.169592 TCACATATCCATACAATATCATGCAAG 57.830 33.333 0.00 0.00 0.00 4.01
3037 3496 7.063426 CCATACAATATCATGCAAGGTAGTACG 59.937 40.741 0.00 0.00 0.00 3.67
3051 3510 1.435577 AGTACGGGCAAAATCGACAC 58.564 50.000 0.00 0.00 0.00 3.67
3052 3511 1.001633 AGTACGGGCAAAATCGACACT 59.998 47.619 0.00 0.00 0.00 3.55
3057 3516 2.482721 CGGGCAAAATCGACACTAAACT 59.517 45.455 0.00 0.00 0.00 2.66
3059 3518 3.365969 GGGCAAAATCGACACTAAACTGG 60.366 47.826 0.00 0.00 0.00 4.00
3060 3519 3.252458 GGCAAAATCGACACTAAACTGGT 59.748 43.478 0.00 0.00 0.00 4.00
3065 3544 7.095523 GCAAAATCGACACTAAACTGGTAACTA 60.096 37.037 0.00 0.00 37.61 2.24
3074 3553 8.996271 ACACTAAACTGGTAACTAATAGCAAAC 58.004 33.333 0.00 0.00 41.23 2.93
3133 3626 0.616111 AGCTAGATATGGGAGGGCGG 60.616 60.000 0.00 0.00 0.00 6.13
3153 3646 1.004440 GCTTCACCACTTCCTCGCT 60.004 57.895 0.00 0.00 0.00 4.93
3196 3896 0.323087 TTGATCCTCCGGAGTCGTCA 60.323 55.000 29.25 24.14 34.05 4.35
3208 3908 0.814457 AGTCGTCAGGCATCTGTCTC 59.186 55.000 0.00 0.00 41.59 3.36
3219 3919 1.437772 ATCTGTCTCCGCCGTCGTAG 61.438 60.000 0.00 0.00 0.00 3.51
3247 3947 2.038863 TGGTACACCCACTGGAAGAT 57.961 50.000 0.00 0.00 38.72 2.40
3249 3949 3.731431 TGGTACACCCACTGGAAGATAT 58.269 45.455 0.00 0.00 38.72 1.63
3250 3950 3.454447 TGGTACACCCACTGGAAGATATG 59.546 47.826 0.00 0.00 38.72 1.78
3256 3956 5.195940 CACCCACTGGAAGATATGTTCATT 58.804 41.667 14.01 0.00 37.43 2.57
3259 3959 6.125029 CCCACTGGAAGATATGTTCATTCTT 58.875 40.000 14.01 0.00 37.43 2.52
3382 4082 2.826128 CAGTAGAACCCACTGCTGTCTA 59.174 50.000 0.00 0.00 42.59 2.59
3383 4083 3.449018 CAGTAGAACCCACTGCTGTCTAT 59.551 47.826 0.00 0.00 42.59 1.98
3384 4084 3.449018 AGTAGAACCCACTGCTGTCTATG 59.551 47.826 0.00 0.00 32.11 2.23
3390 4090 0.457443 CACTGCTGTCTATGCGGAGA 59.543 55.000 1.34 0.00 39.85 3.71
3417 4117 1.305718 GAGGTGGAGGAGGCTGTCT 60.306 63.158 0.00 0.00 0.00 3.41
3424 4124 1.000993 AGGAGGCTGTCTGACGGAT 59.999 57.895 20.43 7.60 0.00 4.18
3425 4125 1.142748 GGAGGCTGTCTGACGGATG 59.857 63.158 20.43 3.50 0.00 3.51
3426 4126 1.142748 GAGGCTGTCTGACGGATGG 59.857 63.158 20.43 1.15 0.00 3.51
3427 4127 2.512515 GGCTGTCTGACGGATGGC 60.513 66.667 20.43 10.13 0.00 4.40
3428 4128 2.887568 GCTGTCTGACGGATGGCG 60.888 66.667 20.43 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.154445 CACTACTCGAGTTTAGTTAAGCCAA 58.846 40.000 25.44 0.00 35.64 4.52
1 2 5.336213 CCACTACTCGAGTTTAGTTAAGCCA 60.336 44.000 25.44 0.00 35.64 4.75
3 4 5.707931 ACCACTACTCGAGTTTAGTTAAGC 58.292 41.667 25.44 0.00 35.64 3.09
4 5 7.914346 CCATACCACTACTCGAGTTTAGTTAAG 59.086 40.741 25.44 15.22 35.64 1.85
6 7 6.319658 CCCATACCACTACTCGAGTTTAGTTA 59.680 42.308 25.44 12.14 35.64 2.24
7 8 5.126707 CCCATACCACTACTCGAGTTTAGTT 59.873 44.000 25.44 10.31 35.64 2.24
8 9 4.643784 CCCATACCACTACTCGAGTTTAGT 59.356 45.833 25.44 18.99 35.64 2.24
9 10 4.037684 CCCCATACCACTACTCGAGTTTAG 59.962 50.000 25.44 18.27 35.64 1.85
10 11 3.956199 CCCCATACCACTACTCGAGTTTA 59.044 47.826 25.44 5.50 35.64 2.01
11 12 2.764572 CCCCATACCACTACTCGAGTTT 59.235 50.000 25.44 8.58 35.64 2.66
12 13 2.292061 ACCCCATACCACTACTCGAGTT 60.292 50.000 25.44 7.75 35.64 3.01
13 14 1.287146 ACCCCATACCACTACTCGAGT 59.713 52.381 23.66 23.66 39.82 4.18
14 15 1.955080 GACCCCATACCACTACTCGAG 59.045 57.143 11.84 11.84 0.00 4.04
15 16 1.285667 TGACCCCATACCACTACTCGA 59.714 52.381 0.00 0.00 0.00 4.04
16 17 1.771565 TGACCCCATACCACTACTCG 58.228 55.000 0.00 0.00 0.00 4.18
17 18 4.563140 TTTTGACCCCATACCACTACTC 57.437 45.455 0.00 0.00 0.00 2.59
18 19 4.600111 TCTTTTTGACCCCATACCACTACT 59.400 41.667 0.00 0.00 0.00 2.57
19 20 4.913784 TCTTTTTGACCCCATACCACTAC 58.086 43.478 0.00 0.00 0.00 2.73
20 21 5.586155 TTCTTTTTGACCCCATACCACTA 57.414 39.130 0.00 0.00 0.00 2.74
21 22 4.463050 TTCTTTTTGACCCCATACCACT 57.537 40.909 0.00 0.00 0.00 4.00
22 23 5.294356 GTTTTCTTTTTGACCCCATACCAC 58.706 41.667 0.00 0.00 0.00 4.16
23 24 4.038162 CGTTTTCTTTTTGACCCCATACCA 59.962 41.667 0.00 0.00 0.00 3.25
24 25 4.552355 CGTTTTCTTTTTGACCCCATACC 58.448 43.478 0.00 0.00 0.00 2.73
25 26 4.278919 TCCGTTTTCTTTTTGACCCCATAC 59.721 41.667 0.00 0.00 0.00 2.39
26 27 4.471548 TCCGTTTTCTTTTTGACCCCATA 58.528 39.130 0.00 0.00 0.00 2.74
27 28 3.301274 TCCGTTTTCTTTTTGACCCCAT 58.699 40.909 0.00 0.00 0.00 4.00
28 29 2.691011 CTCCGTTTTCTTTTTGACCCCA 59.309 45.455 0.00 0.00 0.00 4.96
29 30 2.545113 GCTCCGTTTTCTTTTTGACCCC 60.545 50.000 0.00 0.00 0.00 4.95
30 31 2.100087 TGCTCCGTTTTCTTTTTGACCC 59.900 45.455 0.00 0.00 0.00 4.46
31 32 3.181490 ACTGCTCCGTTTTCTTTTTGACC 60.181 43.478 0.00 0.00 0.00 4.02
32 33 4.028852 ACTGCTCCGTTTTCTTTTTGAC 57.971 40.909 0.00 0.00 0.00 3.18
33 34 4.879545 ACTACTGCTCCGTTTTCTTTTTGA 59.120 37.500 0.00 0.00 0.00 2.69
39 40 5.242393 TGTTACTACTACTGCTCCGTTTTCT 59.758 40.000 0.00 0.00 0.00 2.52
105 112 4.880696 ACGAACTACTACTCTACCCATGAC 59.119 45.833 0.00 0.00 0.00 3.06
114 121 5.119898 CGTGTACAAGACGAACTACTACTCT 59.880 44.000 2.23 0.00 39.21 3.24
126 133 2.909244 GACTCATGACGTGTACAAGACG 59.091 50.000 16.00 9.23 42.62 4.18
129 136 1.649171 GCGACTCATGACGTGTACAAG 59.351 52.381 7.29 7.29 34.17 3.16
133 140 1.161843 TGAGCGACTCATGACGTGTA 58.838 50.000 0.00 0.00 35.39 2.90
136 143 1.269723 TCTTTGAGCGACTCATGACGT 59.730 47.619 9.78 0.00 40.39 4.34
162 195 0.389556 CACACACATCGAGCTGAGCT 60.390 55.000 6.69 6.69 43.88 4.09
163 196 0.389037 TCACACACATCGAGCTGAGC 60.389 55.000 0.00 0.00 0.00 4.26
164 197 1.626747 CTCACACACATCGAGCTGAG 58.373 55.000 0.00 0.00 0.00 3.35
165 198 0.244721 CCTCACACACATCGAGCTGA 59.755 55.000 0.00 0.00 0.00 4.26
166 199 0.244721 TCCTCACACACATCGAGCTG 59.755 55.000 0.00 0.00 0.00 4.24
260 305 4.592192 GCTCATCGGCGGCAGCTA 62.592 66.667 10.53 0.00 44.37 3.32
324 375 2.181021 CTTCCCGTCGCGCTAACT 59.819 61.111 5.56 0.00 0.00 2.24
484 539 1.829849 TGATGGCTGTTGAGAGAGAGG 59.170 52.381 0.00 0.00 0.00 3.69
489 544 3.542648 ACATGATGATGGCTGTTGAGAG 58.457 45.455 0.00 0.00 33.39 3.20
490 545 3.639672 ACATGATGATGGCTGTTGAGA 57.360 42.857 0.00 0.00 33.39 3.27
511 566 9.429359 GTGATCGGAGATTGTAGATGAATTAAT 57.571 33.333 0.00 0.00 45.12 1.40
512 567 8.642432 AGTGATCGGAGATTGTAGATGAATTAA 58.358 33.333 0.00 0.00 45.12 1.40
513 568 8.183104 AGTGATCGGAGATTGTAGATGAATTA 57.817 34.615 0.00 0.00 45.12 1.40
514 569 7.060383 AGTGATCGGAGATTGTAGATGAATT 57.940 36.000 0.00 0.00 45.12 2.17
515 570 6.662865 AGTGATCGGAGATTGTAGATGAAT 57.337 37.500 0.00 0.00 45.12 2.57
516 571 6.322456 AGAAGTGATCGGAGATTGTAGATGAA 59.678 38.462 0.00 0.00 45.12 2.57
517 572 5.830457 AGAAGTGATCGGAGATTGTAGATGA 59.170 40.000 0.00 0.00 45.12 2.92
518 573 5.919707 CAGAAGTGATCGGAGATTGTAGATG 59.080 44.000 0.00 0.00 45.12 2.90
519 574 5.508825 GCAGAAGTGATCGGAGATTGTAGAT 60.509 44.000 0.00 0.00 45.12 1.98
579 686 3.914312 AGTAACAGTTCAGATGTCGTGG 58.086 45.455 0.00 0.00 0.00 4.94
590 705 4.482386 TGCAGATGTACGAGTAACAGTTC 58.518 43.478 0.00 0.00 0.00 3.01
636 757 2.206576 ACCTGCTGGTGAAGAAATCC 57.793 50.000 15.36 0.00 46.51 3.01
694 815 9.202273 TGTGCTTATTTTCTTTGCGAATAAATT 57.798 25.926 10.50 5.25 0.00 1.82
695 816 8.755696 TGTGCTTATTTTCTTTGCGAATAAAT 57.244 26.923 10.22 10.22 0.00 1.40
697 818 7.367285 ACTGTGCTTATTTTCTTTGCGAATAA 58.633 30.769 0.00 0.00 0.00 1.40
698 819 6.908825 ACTGTGCTTATTTTCTTTGCGAATA 58.091 32.000 0.00 0.00 0.00 1.75
699 820 5.772521 ACTGTGCTTATTTTCTTTGCGAAT 58.227 33.333 0.00 0.00 0.00 3.34
700 821 5.181690 ACTGTGCTTATTTTCTTTGCGAA 57.818 34.783 0.00 0.00 0.00 4.70
702 823 5.689819 ACTACTGTGCTTATTTTCTTTGCG 58.310 37.500 0.00 0.00 0.00 4.85
706 827 9.216117 ACGAATTACTACTGTGCTTATTTTCTT 57.784 29.630 0.00 0.00 0.00 2.52
707 828 8.773404 ACGAATTACTACTGTGCTTATTTTCT 57.227 30.769 0.00 0.00 0.00 2.52
711 832 9.811995 TGATTACGAATTACTACTGTGCTTATT 57.188 29.630 0.00 0.00 0.00 1.40
713 834 7.919091 CCTGATTACGAATTACTACTGTGCTTA 59.081 37.037 0.00 0.00 0.00 3.09
714 835 6.757010 CCTGATTACGAATTACTACTGTGCTT 59.243 38.462 0.00 0.00 0.00 3.91
716 837 6.270815 TCCTGATTACGAATTACTACTGTGC 58.729 40.000 0.00 0.00 0.00 4.57
717 838 8.697846 TTTCCTGATTACGAATTACTACTGTG 57.302 34.615 0.00 0.00 0.00 3.66
718 839 7.980099 CCTTTCCTGATTACGAATTACTACTGT 59.020 37.037 0.00 0.00 0.00 3.55
719 840 7.980099 ACCTTTCCTGATTACGAATTACTACTG 59.020 37.037 0.00 0.00 0.00 2.74
720 841 8.075761 ACCTTTCCTGATTACGAATTACTACT 57.924 34.615 0.00 0.00 0.00 2.57
721 842 7.167136 CGACCTTTCCTGATTACGAATTACTAC 59.833 40.741 0.00 0.00 0.00 2.73
722 843 7.067372 TCGACCTTTCCTGATTACGAATTACTA 59.933 37.037 0.00 0.00 0.00 1.82
723 844 6.040878 CGACCTTTCCTGATTACGAATTACT 58.959 40.000 0.00 0.00 0.00 2.24
724 845 6.020041 GTCGACCTTTCCTGATTACGAATTAC 60.020 42.308 3.51 0.00 0.00 1.89
725 846 6.038356 GTCGACCTTTCCTGATTACGAATTA 58.962 40.000 3.51 0.00 0.00 1.40
726 847 4.868734 GTCGACCTTTCCTGATTACGAATT 59.131 41.667 3.51 0.00 0.00 2.17
727 848 4.430908 GTCGACCTTTCCTGATTACGAAT 58.569 43.478 3.51 0.00 0.00 3.34
728 849 3.671433 CGTCGACCTTTCCTGATTACGAA 60.671 47.826 10.58 0.00 0.00 3.85
729 850 2.159476 CGTCGACCTTTCCTGATTACGA 60.159 50.000 10.58 0.00 0.00 3.43
730 851 2.182825 CGTCGACCTTTCCTGATTACG 58.817 52.381 10.58 0.00 0.00 3.18
737 858 0.826672 AGTGGACGTCGACCTTTCCT 60.827 55.000 24.70 4.67 0.00 3.36
838 1153 4.700365 GGCCTGCCGCACGTTTTC 62.700 66.667 0.00 0.00 40.31 2.29
941 1257 1.475930 GGCTTTGAGCTCCCCTGATAC 60.476 57.143 12.15 0.00 41.99 2.24
946 1262 4.416738 GCGGCTTTGAGCTCCCCT 62.417 66.667 12.15 0.00 41.99 4.79
1088 1409 0.382515 CCAGAATCCTCTCGACCGTC 59.617 60.000 0.00 0.00 0.00 4.79
1477 1798 1.362717 CACGTCCTCAGGAACACGT 59.637 57.895 3.24 3.24 33.35 4.49
1542 1863 3.942601 GGAAGTCCTCCTCCTCCG 58.057 66.667 0.00 0.00 41.61 4.63
1777 2099 7.721399 AGGCCAGAATAGTCGATGAATTAATTT 59.279 33.333 5.01 0.00 0.00 1.82
1804 2126 0.600255 CGGCGAAGTCTGGTCTTTGT 60.600 55.000 0.00 0.00 32.94 2.83
1819 2142 0.165944 AAAGCGTTCAAGATTCGGCG 59.834 50.000 0.00 0.00 0.00 6.46
1849 2172 7.903995 ACACAAAATTTCTTTTCTTGCAAGA 57.096 28.000 25.16 25.16 32.21 3.02
1850 2173 8.229137 TCAACACAAAATTTCTTTTCTTGCAAG 58.771 29.630 20.81 20.81 32.21 4.01
1852 2175 7.664082 TCAACACAAAATTTCTTTTCTTGCA 57.336 28.000 0.00 0.00 32.21 4.08
2289 2612 1.884579 AGGAACTCGCTTCAGTAACGA 59.115 47.619 0.00 0.00 0.00 3.85
2332 2655 4.884164 AGAAGTAACTTGCTTTGCTGTTCT 59.116 37.500 0.00 0.00 31.56 3.01
2442 2770 7.437793 ACTATCGCTATCACCTTCTTACTAC 57.562 40.000 0.00 0.00 0.00 2.73
2443 2771 8.373981 ACTACTATCGCTATCACCTTCTTACTA 58.626 37.037 0.00 0.00 0.00 1.82
2444 2772 7.225725 ACTACTATCGCTATCACCTTCTTACT 58.774 38.462 0.00 0.00 0.00 2.24
2445 2773 7.437793 ACTACTATCGCTATCACCTTCTTAC 57.562 40.000 0.00 0.00 0.00 2.34
2446 2774 8.461249 AAACTACTATCGCTATCACCTTCTTA 57.539 34.615 0.00 0.00 0.00 2.10
2447 2775 6.963083 AACTACTATCGCTATCACCTTCTT 57.037 37.500 0.00 0.00 0.00 2.52
2483 2811 4.217118 GCATCATCCCCATATCAACTTGAC 59.783 45.833 0.00 0.00 0.00 3.18
2495 2825 3.047857 TCACTAATCTGCATCATCCCCA 58.952 45.455 0.00 0.00 0.00 4.96
2622 2954 2.094442 ACCCAAACAACGAAAACCACAG 60.094 45.455 0.00 0.00 0.00 3.66
2623 2955 1.893801 ACCCAAACAACGAAAACCACA 59.106 42.857 0.00 0.00 0.00 4.17
2624 2956 2.658373 ACCCAAACAACGAAAACCAC 57.342 45.000 0.00 0.00 0.00 4.16
2625 2957 2.561419 TGAACCCAAACAACGAAAACCA 59.439 40.909 0.00 0.00 0.00 3.67
2626 2958 2.924926 GTGAACCCAAACAACGAAAACC 59.075 45.455 0.00 0.00 0.00 3.27
2701 3033 3.076079 TGTCGTGTGATCCCTACTGTA 57.924 47.619 0.00 0.00 0.00 2.74
2715 3047 0.535102 AAACCTGGCTCCTTGTCGTG 60.535 55.000 0.00 0.00 0.00 4.35
2718 3050 1.072331 TCTCAAACCTGGCTCCTTGTC 59.928 52.381 0.00 0.00 0.00 3.18
2724 3056 2.155279 GTTTCCTCTCAAACCTGGCTC 58.845 52.381 0.00 0.00 31.10 4.70
2804 3137 1.432270 GCAAGTCCGGCTGTAGATGC 61.432 60.000 0.00 0.00 0.00 3.91
2827 3162 2.941415 GCCCTATAGGATGCCGGATTTG 60.941 54.545 21.07 0.00 38.24 2.32
2828 3163 1.282157 GCCCTATAGGATGCCGGATTT 59.718 52.381 21.07 0.00 38.24 2.17
2829 3164 0.912486 GCCCTATAGGATGCCGGATT 59.088 55.000 21.07 0.00 38.24 3.01
2830 3165 0.043334 AGCCCTATAGGATGCCGGAT 59.957 55.000 21.07 0.00 38.24 4.18
2831 3166 1.469708 AGCCCTATAGGATGCCGGA 59.530 57.895 21.07 0.00 38.24 5.14
2832 3167 4.136978 AGCCCTATAGGATGCCGG 57.863 61.111 21.07 0.00 38.24 6.13
2875 3334 3.696045 TGTGGACATGTGGATTTAAGGG 58.304 45.455 1.15 0.00 0.00 3.95
2878 3337 3.944650 CGGATGTGGACATGTGGATTTAA 59.055 43.478 1.15 0.00 36.57 1.52
2888 3347 1.000163 GAGATACGCGGATGTGGACAT 60.000 52.381 9.57 0.00 39.70 3.06
2904 3363 9.599056 ATGGATATAGGATGTCGAATATGAGAT 57.401 33.333 0.00 0.00 0.00 2.75
2907 3366 9.640952 TGTATGGATATAGGATGTCGAATATGA 57.359 33.333 0.00 0.00 0.00 2.15
2913 3372 9.640952 TGATATTGTATGGATATAGGATGTCGA 57.359 33.333 0.00 0.00 0.00 4.20
2919 3378 9.836864 GTTGCATGATATTGTATGGATATAGGA 57.163 33.333 0.00 0.00 0.00 2.94
2920 3379 8.768019 CGTTGCATGATATTGTATGGATATAGG 58.232 37.037 0.00 0.00 0.00 2.57
2921 3380 9.317936 ACGTTGCATGATATTGTATGGATATAG 57.682 33.333 0.00 0.00 0.00 1.31
2923 3382 9.317936 CTACGTTGCATGATATTGTATGGATAT 57.682 33.333 0.00 0.00 0.00 1.63
2924 3383 8.311109 ACTACGTTGCATGATATTGTATGGATA 58.689 33.333 0.00 0.00 0.00 2.59
2925 3384 7.118245 CACTACGTTGCATGATATTGTATGGAT 59.882 37.037 0.00 0.00 0.00 3.41
2926 3385 6.423604 CACTACGTTGCATGATATTGTATGGA 59.576 38.462 0.00 0.00 0.00 3.41
2927 3386 6.593072 CACTACGTTGCATGATATTGTATGG 58.407 40.000 0.00 0.00 0.00 2.74
2928 3387 6.073369 GCACTACGTTGCATGATATTGTATG 58.927 40.000 7.34 0.00 42.49 2.39
2929 3388 5.107491 CGCACTACGTTGCATGATATTGTAT 60.107 40.000 12.40 0.00 43.15 2.29
2930 3389 4.208253 CGCACTACGTTGCATGATATTGTA 59.792 41.667 12.40 0.00 43.15 2.41
2931 3390 3.001228 CGCACTACGTTGCATGATATTGT 59.999 43.478 12.40 0.00 43.15 2.71
2932 3391 3.534889 CGCACTACGTTGCATGATATTG 58.465 45.455 12.40 0.00 43.15 1.90
2933 3392 2.543848 CCGCACTACGTTGCATGATATT 59.456 45.455 12.40 0.00 43.15 1.28
2934 3393 2.135139 CCGCACTACGTTGCATGATAT 58.865 47.619 12.40 0.00 43.15 1.63
2935 3394 1.566404 CCGCACTACGTTGCATGATA 58.434 50.000 12.40 0.00 43.15 2.15
2936 3395 1.089481 CCCGCACTACGTTGCATGAT 61.089 55.000 12.40 0.00 43.15 2.45
2937 3396 1.739929 CCCGCACTACGTTGCATGA 60.740 57.895 12.40 0.00 43.15 3.07
2938 3397 2.784596 CCCGCACTACGTTGCATG 59.215 61.111 12.40 2.96 43.15 4.06
2939 3398 3.124921 GCCCGCACTACGTTGCAT 61.125 61.111 12.40 0.00 43.15 3.96
2940 3399 4.610714 TGCCCGCACTACGTTGCA 62.611 61.111 12.40 0.00 43.15 4.08
2941 3400 2.395367 TTTTGCCCGCACTACGTTGC 62.395 55.000 2.02 2.02 41.42 4.17
2942 3401 0.239879 ATTTTGCCCGCACTACGTTG 59.760 50.000 0.00 0.00 41.42 4.10
2943 3402 0.519961 GATTTTGCCCGCACTACGTT 59.480 50.000 0.00 0.00 41.42 3.99
2944 3403 0.604243 TGATTTTGCCCGCACTACGT 60.604 50.000 0.00 0.00 41.42 3.57
2945 3404 0.519519 TTGATTTTGCCCGCACTACG 59.480 50.000 0.00 0.00 43.15 3.51
2946 3405 2.715737 TTTGATTTTGCCCGCACTAC 57.284 45.000 0.00 0.00 0.00 2.73
2947 3406 3.367910 GGATTTTGATTTTGCCCGCACTA 60.368 43.478 0.00 0.00 0.00 2.74
2948 3407 2.612721 GGATTTTGATTTTGCCCGCACT 60.613 45.455 0.00 0.00 0.00 4.40
2949 3408 1.731709 GGATTTTGATTTTGCCCGCAC 59.268 47.619 0.00 0.00 0.00 5.34
2950 3409 1.345741 TGGATTTTGATTTTGCCCGCA 59.654 42.857 0.00 0.00 0.00 5.69
2951 3410 1.731709 GTGGATTTTGATTTTGCCCGC 59.268 47.619 0.00 0.00 0.00 6.13
2952 3411 3.037431 TGTGGATTTTGATTTTGCCCG 57.963 42.857 0.00 0.00 0.00 6.13
2953 3412 4.325972 ACATGTGGATTTTGATTTTGCCC 58.674 39.130 0.00 0.00 0.00 5.36
2954 3413 4.392754 GGACATGTGGATTTTGATTTTGCC 59.607 41.667 1.15 0.00 0.00 4.52
2955 3414 4.996122 TGGACATGTGGATTTTGATTTTGC 59.004 37.500 1.15 0.00 0.00 3.68
2956 3415 8.951787 ATATGGACATGTGGATTTTGATTTTG 57.048 30.769 1.15 0.00 0.00 2.44
2957 3416 8.206189 GGATATGGACATGTGGATTTTGATTTT 58.794 33.333 1.15 0.00 0.00 1.82
2958 3417 7.470424 CGGATATGGACATGTGGATTTTGATTT 60.470 37.037 1.15 0.00 0.00 2.17
2959 3418 6.016024 CGGATATGGACATGTGGATTTTGATT 60.016 38.462 1.15 0.00 0.00 2.57
2960 3419 5.474532 CGGATATGGACATGTGGATTTTGAT 59.525 40.000 1.15 0.00 0.00 2.57
2961 3420 4.821260 CGGATATGGACATGTGGATTTTGA 59.179 41.667 1.15 0.00 0.00 2.69
2962 3421 4.557296 GCGGATATGGACATGTGGATTTTG 60.557 45.833 1.15 0.00 0.00 2.44
2963 3422 3.569701 GCGGATATGGACATGTGGATTTT 59.430 43.478 1.15 0.00 0.00 1.82
2964 3423 3.149196 GCGGATATGGACATGTGGATTT 58.851 45.455 1.15 0.00 0.00 2.17
2965 3424 2.783135 GCGGATATGGACATGTGGATT 58.217 47.619 1.15 0.00 0.00 3.01
2966 3425 1.338105 CGCGGATATGGACATGTGGAT 60.338 52.381 1.15 0.00 0.00 3.41
2967 3426 0.033366 CGCGGATATGGACATGTGGA 59.967 55.000 1.15 0.00 0.00 4.02
2968 3427 0.249868 ACGCGGATATGGACATGTGG 60.250 55.000 12.47 0.00 0.00 4.17
2969 3428 2.432206 TACGCGGATATGGACATGTG 57.568 50.000 12.47 0.00 0.00 3.21
2970 3429 2.826128 AGATACGCGGATATGGACATGT 59.174 45.455 12.47 0.00 0.00 3.21
2971 3430 3.119495 TGAGATACGCGGATATGGACATG 60.119 47.826 12.47 0.00 0.00 3.21
2972 3431 3.089284 TGAGATACGCGGATATGGACAT 58.911 45.455 12.47 0.00 0.00 3.06
2973 3432 2.510613 TGAGATACGCGGATATGGACA 58.489 47.619 12.47 0.00 0.00 4.02
2974 3433 3.784701 ATGAGATACGCGGATATGGAC 57.215 47.619 12.47 0.00 0.00 4.02
2975 3434 4.519350 GGATATGAGATACGCGGATATGGA 59.481 45.833 12.47 0.00 0.00 3.41
2976 3435 4.613850 CGGATATGAGATACGCGGATATGG 60.614 50.000 12.47 0.00 0.00 2.74
2977 3436 4.213482 TCGGATATGAGATACGCGGATATG 59.787 45.833 12.47 0.00 0.00 1.78
2978 3437 4.213694 GTCGGATATGAGATACGCGGATAT 59.786 45.833 12.47 3.76 0.00 1.63
2979 3438 3.558829 GTCGGATATGAGATACGCGGATA 59.441 47.826 12.47 0.00 0.00 2.59
2980 3439 2.355132 GTCGGATATGAGATACGCGGAT 59.645 50.000 1.69 1.69 0.00 4.18
2981 3440 1.736126 GTCGGATATGAGATACGCGGA 59.264 52.381 12.47 0.00 0.00 5.54
2982 3441 1.467342 TGTCGGATATGAGATACGCGG 59.533 52.381 12.47 0.00 0.00 6.46
2983 3442 2.894307 TGTCGGATATGAGATACGCG 57.106 50.000 3.53 3.53 0.00 6.01
2984 3443 4.099120 GTGATGTCGGATATGAGATACGC 58.901 47.826 0.00 0.00 0.00 4.42
2985 3444 5.296813 TGTGATGTCGGATATGAGATACG 57.703 43.478 0.00 0.00 0.00 3.06
2986 3445 8.079203 GGATATGTGATGTCGGATATGAGATAC 58.921 40.741 0.00 0.00 0.00 2.24
2987 3446 7.779798 TGGATATGTGATGTCGGATATGAGATA 59.220 37.037 0.00 0.00 0.00 1.98
2988 3447 6.608808 TGGATATGTGATGTCGGATATGAGAT 59.391 38.462 0.00 0.00 0.00 2.75
2989 3448 5.951747 TGGATATGTGATGTCGGATATGAGA 59.048 40.000 0.00 0.00 0.00 3.27
2990 3449 6.212888 TGGATATGTGATGTCGGATATGAG 57.787 41.667 0.00 0.00 0.00 2.90
2991 3450 6.796785 ATGGATATGTGATGTCGGATATGA 57.203 37.500 0.00 0.00 0.00 2.15
2992 3451 7.491682 TGTATGGATATGTGATGTCGGATATG 58.508 38.462 0.00 0.00 0.00 1.78
2993 3452 7.660030 TGTATGGATATGTGATGTCGGATAT 57.340 36.000 0.00 0.00 0.00 1.63
2994 3453 7.475137 TTGTATGGATATGTGATGTCGGATA 57.525 36.000 0.00 0.00 0.00 2.59
2995 3454 6.358974 TTGTATGGATATGTGATGTCGGAT 57.641 37.500 0.00 0.00 0.00 4.18
2996 3455 5.799827 TTGTATGGATATGTGATGTCGGA 57.200 39.130 0.00 0.00 0.00 4.55
2997 3456 7.981225 TGATATTGTATGGATATGTGATGTCGG 59.019 37.037 0.00 0.00 0.00 4.79
2998 3457 8.931385 TGATATTGTATGGATATGTGATGTCG 57.069 34.615 0.00 0.00 0.00 4.35
3000 3459 9.117183 GCATGATATTGTATGGATATGTGATGT 57.883 33.333 0.00 0.00 0.00 3.06
3001 3460 9.116067 TGCATGATATTGTATGGATATGTGATG 57.884 33.333 0.00 0.00 0.00 3.07
3002 3461 9.689501 TTGCATGATATTGTATGGATATGTGAT 57.310 29.630 0.00 0.00 0.00 3.06
3003 3462 9.169592 CTTGCATGATATTGTATGGATATGTGA 57.830 33.333 0.00 0.00 0.00 3.58
3004 3463 8.403236 CCTTGCATGATATTGTATGGATATGTG 58.597 37.037 0.00 0.00 31.01 3.21
3005 3464 8.111545 ACCTTGCATGATATTGTATGGATATGT 58.888 33.333 0.00 0.00 32.91 2.29
3006 3465 8.515695 ACCTTGCATGATATTGTATGGATATG 57.484 34.615 0.00 0.00 32.91 1.78
3007 3466 9.842775 CTACCTTGCATGATATTGTATGGATAT 57.157 33.333 0.00 0.00 32.91 1.63
3008 3467 8.825774 ACTACCTTGCATGATATTGTATGGATA 58.174 33.333 0.00 0.00 32.91 2.59
3009 3468 7.693132 ACTACCTTGCATGATATTGTATGGAT 58.307 34.615 0.00 0.00 32.91 3.41
3010 3469 7.078249 ACTACCTTGCATGATATTGTATGGA 57.922 36.000 0.00 0.00 32.91 3.41
3011 3470 7.063426 CGTACTACCTTGCATGATATTGTATGG 59.937 40.741 0.00 0.00 34.20 2.74
3012 3471 7.063426 CCGTACTACCTTGCATGATATTGTATG 59.937 40.741 0.00 4.07 0.00 2.39
3029 3488 1.929169 GTCGATTTTGCCCGTACTACC 59.071 52.381 0.00 0.00 0.00 3.18
3037 3496 3.365969 CCAGTTTAGTGTCGATTTTGCCC 60.366 47.826 0.00 0.00 0.00 5.36
3051 3510 9.216117 ACTGTTTGCTATTAGTTACCAGTTTAG 57.784 33.333 0.00 0.00 0.00 1.85
3052 3511 9.211485 GACTGTTTGCTATTAGTTACCAGTTTA 57.789 33.333 0.00 0.00 31.31 2.01
3057 3516 8.537016 ACTATGACTGTTTGCTATTAGTTACCA 58.463 33.333 0.00 0.00 0.00 3.25
3065 3544 8.615878 TGTGTAAACTATGACTGTTTGCTATT 57.384 30.769 0.00 0.00 39.53 1.73
3074 3553 8.142994 AGTTTGAACTGTGTAAACTATGACTG 57.857 34.615 16.35 0.00 41.40 3.51
3103 3582 4.872691 CCCATATCTAGCTAGAATTTGCCG 59.127 45.833 26.62 12.49 35.69 5.69
3133 3626 1.016653 GCGAGGAAGTGGTGAAGCTC 61.017 60.000 0.00 0.00 0.00 4.09
3161 3861 2.753043 AATGCCAAGCAGCTCCGG 60.753 61.111 0.00 0.02 43.65 5.14
3196 3896 3.842923 CGGCGGAGACAGATGCCT 61.843 66.667 0.00 0.00 45.36 4.75
3208 3908 4.487412 GGTCACCTACGACGGCGG 62.487 72.222 18.49 0.00 43.17 6.13
3219 3919 1.219935 GGGTGTACCATCGGTCACC 59.780 63.158 18.70 18.70 44.90 4.02
3247 3947 4.096231 CGATGCCCAACAAGAATGAACATA 59.904 41.667 0.00 0.00 0.00 2.29
3249 3949 2.228582 CGATGCCCAACAAGAATGAACA 59.771 45.455 0.00 0.00 0.00 3.18
3250 3950 2.867429 CGATGCCCAACAAGAATGAAC 58.133 47.619 0.00 0.00 0.00 3.18
3318 4018 4.760220 AAGGGAGATGGGGGCCGT 62.760 66.667 0.00 0.00 0.00 5.68
3356 4056 2.214216 AGTGGGTTCTACTGCCGCA 61.214 57.895 0.00 0.00 0.00 5.69
3411 4111 2.887568 CGCCATCCGTCAGACAGC 60.888 66.667 0.41 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.