Multiple sequence alignment - TraesCS5A01G181000

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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 TraesCS5A01G181000 chr5A 100.000 3076 0 0 1 3076 379402488 379399413 0.000000e+00 5681.0
1 TraesCS5A01G181000 chr5D 94.140 2355 104 14 1 2333 287572736 287570394 0.000000e+00 3554.0
2 TraesCS5A01G181000 chr5D 94.118 187 9 2 2315 2499 287570381 287570195 1.810000e-72 283.0
3 TraesCS5A01G181000 chr5B 92.414 2452 91 35 280 2687 326613560 326611160 0.000000e+00 3410.0
4 TraesCS5A01G181000 chr6D 86.932 880 85 17 789 1645 465011752 465010880 0.000000e+00 961.0
5 TraesCS5A01G181000 chr6D 86.842 874 91 16 788 1644 464984285 464985151 0.000000e+00 955.0
6 TraesCS5A01G181000 chr6D 95.597 159 7 0 1724 1882 464985273 464985431 3.940000e-64 255.0
7 TraesCS5A01G181000 chr6D 92.810 153 11 0 1724 1876 465010805 465010653 3.990000e-54 222.0
8 TraesCS5A01G181000 chr6D 89.209 139 11 3 1977 2114 464985538 464985673 1.470000e-38 171.0
9 TraesCS5A01G181000 chr6D 92.105 114 6 2 1966 2076 465010535 465010422 1.140000e-34 158.0
10 TraesCS5A01G181000 chr6B 86.902 878 85 18 789 1642 708988591 708989462 0.000000e+00 957.0
11 TraesCS5A01G181000 chr6B 88.496 791 77 7 862 1645 709020832 709020049 0.000000e+00 944.0
12 TraesCS5A01G181000 chr6B 93.711 159 10 0 1724 1882 708989566 708989724 3.960000e-59 239.0
13 TraesCS5A01G181000 chr6B 93.082 159 11 0 1724 1882 709019970 709019812 1.840000e-57 233.0
14 TraesCS5A01G181000 chr6B 89.437 142 11 3 1976 2114 708989822 708989962 3.150000e-40 176.0
15 TraesCS5A01G181000 chr6B 95.000 100 5 0 1977 2076 709019738 709019639 1.140000e-34 158.0
16 TraesCS5A01G181000 chr6A 88.198 788 66 13 862 1642 611523316 611522549 0.000000e+00 915.0
17 TraesCS5A01G181000 chr6A 85.812 874 99 17 788 1642 611513094 611513961 0.000000e+00 904.0
18 TraesCS5A01G181000 chr6A 82.920 363 47 11 1724 2076 611522442 611522085 2.300000e-81 313.0
19 TraesCS5A01G181000 chr6A 80.132 453 60 22 1724 2153 611514080 611514525 8.280000e-81 311.0
20 TraesCS5A01G181000 chr6A 77.143 175 28 9 2452 2620 595005468 595005300 1.170000e-14 91.6
21 TraesCS5A01G181000 chr6A 83.562 73 12 0 2550 2622 9250388 9250316 5.500000e-08 69.4
22 TraesCS5A01G181000 chr2A 81.901 547 78 16 1340 1874 663329711 663329174 2.810000e-120 442.0
23 TraesCS5A01G181000 chr2D 78.993 576 96 14 1090 1642 480181624 480181051 1.350000e-98 370.0
24 TraesCS5A01G181000 chr2D 83.908 87 11 3 2525 2609 139025628 139025713 2.540000e-11 80.5
25 TraesCS5A01G181000 chr2B 75.983 229 35 15 2400 2609 508959385 508959612 1.950000e-17 100.0
26 TraesCS5A01G181000 chr3B 74.752 202 33 16 2423 2609 617418063 617417865 1.180000e-09 75.0
27 TraesCS5A01G181000 chr3A 100.000 39 0 0 2420 2458 63467120 63467082 4.250000e-09 73.1
28 TraesCS5A01G181000 chr1D 82.432 74 12 1 2425 2497 465098568 465098641 2.560000e-06 63.9
29 TraesCS5A01G181000 chr7A 89.362 47 5 0 2563 2609 727460900 727460854 3.310000e-05 60.2


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 TraesCS5A01G181000 chr5A 379399413 379402488 3075 True 5681.000000 5681 100.000000 1 3076 1 chr5A.!!$R1 3075
1 TraesCS5A01G181000 chr5D 287570195 287572736 2541 True 1918.500000 3554 94.129000 1 2499 2 chr5D.!!$R1 2498
2 TraesCS5A01G181000 chr5B 326611160 326613560 2400 True 3410.000000 3410 92.414000 280 2687 1 chr5B.!!$R1 2407
3 TraesCS5A01G181000 chr6D 464984285 464985673 1388 False 460.333333 955 90.549333 788 2114 3 chr6D.!!$F1 1326
4 TraesCS5A01G181000 chr6D 465010422 465011752 1330 True 447.000000 961 90.615667 789 2076 3 chr6D.!!$R1 1287
5 TraesCS5A01G181000 chr6B 708988591 708989962 1371 False 457.333333 957 90.016667 789 2114 3 chr6B.!!$F1 1325
6 TraesCS5A01G181000 chr6B 709019639 709020832 1193 True 445.000000 944 92.192667 862 2076 3 chr6B.!!$R1 1214
7 TraesCS5A01G181000 chr6A 611522085 611523316 1231 True 614.000000 915 85.559000 862 2076 2 chr6A.!!$R3 1214
8 TraesCS5A01G181000 chr6A 611513094 611514525 1431 False 607.500000 904 82.972000 788 2153 2 chr6A.!!$F1 1365
9 TraesCS5A01G181000 chr2A 663329174 663329711 537 True 442.000000 442 81.901000 1340 1874 1 chr2A.!!$R1 534
10 TraesCS5A01G181000 chr2D 480181051 480181624 573 True 370.000000 370 78.993000 1090 1642 1 chr2D.!!$R1 552

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
392 397 0.195096 TTATTATCCCTCCCCCGCCT 59.805 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2437 0.249489 GACTGAAGGACACACACGCT 60.249 55.0 0.0 0.0 0.0 5.07 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
24 25 2.473235 GTCGCTCGGCTTTCATCTAATC 59.527 50.000 0.00 0.00 0.00 1.75
31 32 2.234143 GCTTTCATCTAATCCAGGGGC 58.766 52.381 0.00 0.00 0.00 5.80
36 37 0.853530 ATCTAATCCAGGGGCCAACC 59.146 55.000 4.39 0.00 39.11 3.77
38 39 0.395724 CTAATCCAGGGGCCAACCAC 60.396 60.000 4.39 0.00 42.91 4.16
45 46 2.440599 GGGCCAACCACAGGACAT 59.559 61.111 4.39 0.00 39.85 3.06
50 51 1.238439 CCAACCACAGGACATCACAC 58.762 55.000 0.00 0.00 0.00 3.82
66 67 9.774742 GGACATCACACTTTCATAAAATAAGTC 57.225 33.333 0.00 0.00 30.08 3.01
81 82 2.131776 AAGTCGAGTGTCTAGAGGGG 57.868 55.000 0.00 0.00 0.00 4.79
90 91 1.077805 TCTAGAGGGGGCACACGAA 59.922 57.895 0.00 0.00 0.00 3.85
94 95 0.988832 AGAGGGGGCACACGAAATAA 59.011 50.000 0.00 0.00 0.00 1.40
111 112 0.892755 TAAGTGTAGGCCAGGTGTCG 59.107 55.000 5.01 0.00 0.00 4.35
114 115 1.532078 TGTAGGCCAGGTGTCGACA 60.532 57.895 15.76 15.76 0.00 4.35
127 128 1.203758 TGTCGACACGGCATCTTACAT 59.796 47.619 15.76 0.00 36.25 2.29
129 130 2.671396 GTCGACACGGCATCTTACATTT 59.329 45.455 11.55 0.00 0.00 2.32
131 132 2.285026 CGACACGGCATCTTACATTTCG 60.285 50.000 0.00 0.00 0.00 3.46
133 134 2.276201 CACGGCATCTTACATTTCGGA 58.724 47.619 0.00 0.00 0.00 4.55
184 185 8.633408 GTGTACGTCATATAAACCGAATATCAC 58.367 37.037 0.00 0.00 0.00 3.06
189 190 7.217636 CGTCATATAAACCGAATATCACGTAGG 59.782 40.741 0.00 0.00 0.00 3.18
190 191 8.239314 GTCATATAAACCGAATATCACGTAGGA 58.761 37.037 0.00 0.00 0.00 2.94
191 192 8.963725 TCATATAAACCGAATATCACGTAGGAT 58.036 33.333 0.00 0.00 0.00 3.24
215 216 3.576550 TGCACATCATAGGTATAAGCCGA 59.423 43.478 0.00 0.00 0.00 5.54
220 221 2.228103 TCATAGGTATAAGCCGAGCGTG 59.772 50.000 0.00 0.00 0.00 5.34
222 223 1.300697 GGTATAAGCCGAGCGTGGG 60.301 63.158 0.00 0.00 0.00 4.61
243 244 4.056092 GCCCTCGGCTTATATATACACC 57.944 50.000 0.00 0.00 46.69 4.16
252 253 4.031426 GCTTATATATACACCGTGCTTCGC 59.969 45.833 0.00 0.00 38.35 4.70
255 256 0.462375 TATACACCGTGCTTCGCCAT 59.538 50.000 0.00 0.00 38.35 4.40
273 274 1.860950 CATTAGGATTGGTGCTCGTCG 59.139 52.381 0.00 0.00 0.00 5.12
392 397 0.195096 TTATTATCCCTCCCCCGCCT 59.805 55.000 0.00 0.00 0.00 5.52
393 398 0.546747 TATTATCCCTCCCCCGCCTG 60.547 60.000 0.00 0.00 0.00 4.85
460 466 2.360801 GCAACCTTTTGGAAGCACTACA 59.639 45.455 0.00 0.00 44.07 2.74
493 499 5.818336 TCTGTCTAGCAACTAGTACTAGCTG 59.182 44.000 26.54 24.83 35.72 4.24
532 538 5.448768 CCACTTTCTGCTCTCATAATGCAAG 60.449 44.000 0.00 0.00 36.22 4.01
683 689 0.898320 ATGGAAGGTGAGGTGAGACG 59.102 55.000 0.00 0.00 0.00 4.18
686 692 2.508586 GAAGGTGAGGTGAGACGCCC 62.509 65.000 0.00 0.00 37.38 6.13
839 854 7.464977 GCAAAGGCAAAATAAGCACATTATCAG 60.465 37.037 0.00 0.00 40.72 2.90
840 855 6.780457 AGGCAAAATAAGCACATTATCAGT 57.220 33.333 0.00 0.00 32.71 3.41
841 856 7.174107 AGGCAAAATAAGCACATTATCAGTT 57.826 32.000 0.00 0.00 32.71 3.16
842 857 7.614494 AGGCAAAATAAGCACATTATCAGTTT 58.386 30.769 0.00 0.00 32.71 2.66
844 859 9.533253 GGCAAAATAAGCACATTATCAGTTTAT 57.467 29.630 0.00 0.00 32.71 1.40
953 980 3.409570 CACACCCATCCATCATCATCTC 58.590 50.000 0.00 0.00 0.00 2.75
954 981 3.050835 ACACCCATCCATCATCATCTCA 58.949 45.455 0.00 0.00 0.00 3.27
955 982 3.656264 ACACCCATCCATCATCATCTCAT 59.344 43.478 0.00 0.00 0.00 2.90
956 983 4.262617 CACCCATCCATCATCATCTCATC 58.737 47.826 0.00 0.00 0.00 2.92
957 984 4.019231 CACCCATCCATCATCATCTCATCT 60.019 45.833 0.00 0.00 0.00 2.90
1693 1782 7.041167 GGAACATATCATTTCGTGGATGATGAA 60.041 37.037 15.88 3.68 42.54 2.57
1720 1827 9.903682 CAAATTAACTGATGTATGGATGGATTC 57.096 33.333 0.00 0.00 0.00 2.52
2154 2389 1.446099 GATCGTTGCTCCTGCGTGA 60.446 57.895 0.00 0.00 43.34 4.35
2167 2402 2.415625 CCTGCGTGAGTACTCCTGTAAC 60.416 54.545 20.11 9.99 0.00 2.50
2200 2437 0.958876 TACTGTTCCTGAGCGAGCGA 60.959 55.000 0.00 0.00 0.00 4.93
2201 2438 1.515952 CTGTTCCTGAGCGAGCGAG 60.516 63.158 0.00 0.00 0.00 5.03
2202 2439 2.883253 GTTCCTGAGCGAGCGAGC 60.883 66.667 0.00 0.00 37.41 5.03
2220 2457 1.548973 GCGTGTGTGTCCTTCAGTCG 61.549 60.000 0.00 0.00 0.00 4.18
2260 2501 2.551270 GTGCACTTCTTCACCGCG 59.449 61.111 10.32 0.00 0.00 6.46
2370 2641 6.492286 TCGAATTAACGATCGATCTTCAAC 57.508 37.500 24.34 7.59 42.61 3.18
2409 2680 4.211794 TCGATACTTGTTCCGTTCCAAAAC 59.788 41.667 0.00 0.00 0.00 2.43
2445 2716 6.540914 TCTGGGTTTGTACTAAGTCAAACTTG 59.459 38.462 18.62 12.58 46.88 3.16
2545 2836 9.851686 AGCTAATTTGATGTTGTAGATATTGGA 57.148 29.630 0.00 0.00 0.00 3.53
2585 2876 6.861065 TGGTCAGATGTAAAGAAGTTTGAC 57.139 37.500 0.00 0.00 34.48 3.18
2610 2901 8.188799 ACTTAAGACAAACCTAAAACTTCAAGC 58.811 33.333 10.09 0.00 0.00 4.01
2621 2912 8.700973 ACCTAAAACTTCAAGCCTTTTGAAATA 58.299 29.630 4.18 0.00 37.89 1.40
2631 2922 8.987890 TCAAGCCTTTTGAAATAAATTAAGTGC 58.012 29.630 0.00 0.00 0.00 4.40
2632 2923 8.772705 CAAGCCTTTTGAAATAAATTAAGTGCA 58.227 29.630 0.00 0.00 0.00 4.57
2633 2924 9.506018 AAGCCTTTTGAAATAAATTAAGTGCAT 57.494 25.926 0.00 0.00 0.00 3.96
2679 2970 7.488187 AATGTTCTCTATATGTGTGTCATGC 57.512 36.000 0.00 0.00 37.91 4.06
2681 2972 6.276091 TGTTCTCTATATGTGTGTCATGCTC 58.724 40.000 0.00 0.00 37.91 4.26
2687 2978 1.232119 TGTGTGTCATGCTCTGCTTG 58.768 50.000 0.00 0.00 35.46 4.01
2688 2979 1.233019 GTGTGTCATGCTCTGCTTGT 58.767 50.000 5.57 0.00 35.60 3.16
2689 2980 1.196354 GTGTGTCATGCTCTGCTTGTC 59.804 52.381 5.57 1.78 35.60 3.18
2690 2981 1.071228 TGTGTCATGCTCTGCTTGTCT 59.929 47.619 5.57 0.00 35.60 3.41
2691 2982 1.731160 GTGTCATGCTCTGCTTGTCTC 59.269 52.381 5.57 0.00 35.60 3.36
2692 2983 1.622312 TGTCATGCTCTGCTTGTCTCT 59.378 47.619 5.57 0.00 35.60 3.10
2693 2984 2.827921 TGTCATGCTCTGCTTGTCTCTA 59.172 45.455 5.57 0.00 35.60 2.43
2694 2985 3.259123 TGTCATGCTCTGCTTGTCTCTAA 59.741 43.478 5.57 0.00 35.60 2.10
2695 2986 3.864583 GTCATGCTCTGCTTGTCTCTAAG 59.135 47.826 5.57 0.00 35.60 2.18
2704 2995 1.989165 CTTGTCTCTAAGCACTCACGC 59.011 52.381 0.00 0.00 0.00 5.34
2705 2996 0.109735 TGTCTCTAAGCACTCACGCG 60.110 55.000 3.53 3.53 36.85 6.01
2706 2997 0.168348 GTCTCTAAGCACTCACGCGA 59.832 55.000 15.93 0.00 36.85 5.87
2707 2998 0.448197 TCTCTAAGCACTCACGCGAG 59.552 55.000 15.93 4.59 45.49 5.03
2708 2999 0.448197 CTCTAAGCACTCACGCGAGA 59.552 55.000 15.93 10.37 42.34 4.04
2709 3000 1.064803 CTCTAAGCACTCACGCGAGAT 59.935 52.381 15.93 0.00 42.34 2.75
2710 3001 1.195347 CTAAGCACTCACGCGAGATG 58.805 55.000 15.93 11.99 42.34 2.90
2711 3002 0.179137 TAAGCACTCACGCGAGATGG 60.179 55.000 15.93 6.67 42.34 3.51
2712 3003 1.877576 AAGCACTCACGCGAGATGGA 61.878 55.000 15.93 0.75 42.34 3.41
2713 3004 1.875813 GCACTCACGCGAGATGGAG 60.876 63.158 15.93 13.45 42.34 3.86
2714 3005 1.875813 CACTCACGCGAGATGGAGC 60.876 63.158 15.93 0.00 42.34 4.70
2715 3006 2.049185 ACTCACGCGAGATGGAGCT 61.049 57.895 15.93 0.00 42.34 4.09
2716 3007 1.588403 CTCACGCGAGATGGAGCTG 60.588 63.158 15.93 0.00 42.34 4.24
2717 3008 2.584418 CACGCGAGATGGAGCTGG 60.584 66.667 15.93 0.00 0.00 4.85
2718 3009 3.842923 ACGCGAGATGGAGCTGGG 61.843 66.667 15.93 0.00 0.00 4.45
2720 3011 3.859414 GCGAGATGGAGCTGGGCT 61.859 66.667 0.00 0.00 43.88 5.19
2721 3012 2.108566 CGAGATGGAGCTGGGCTG 59.891 66.667 0.00 0.00 39.88 4.85
2722 3013 2.429767 CGAGATGGAGCTGGGCTGA 61.430 63.158 0.00 0.00 39.88 4.26
2723 3014 1.145819 GAGATGGAGCTGGGCTGAC 59.854 63.158 0.00 0.00 39.88 3.51
2724 3015 1.306825 AGATGGAGCTGGGCTGACT 60.307 57.895 0.00 0.00 39.88 3.41
2725 3016 1.153208 GATGGAGCTGGGCTGACTG 60.153 63.158 0.00 0.00 39.88 3.51
2726 3017 2.605854 GATGGAGCTGGGCTGACTGG 62.606 65.000 0.00 0.00 39.88 4.00
2727 3018 3.325753 GGAGCTGGGCTGACTGGT 61.326 66.667 0.00 0.00 39.88 4.00
2728 3019 2.046507 GAGCTGGGCTGACTGGTG 60.047 66.667 0.00 0.00 39.88 4.17
2729 3020 3.618780 GAGCTGGGCTGACTGGTGG 62.619 68.421 0.00 0.00 39.88 4.61
2730 3021 4.729918 GCTGGGCTGACTGGTGGG 62.730 72.222 0.00 0.00 0.00 4.61
2731 3022 4.729918 CTGGGCTGACTGGTGGGC 62.730 72.222 0.00 0.00 0.00 5.36
2733 3024 3.971702 GGGCTGACTGGTGGGCTT 61.972 66.667 0.00 0.00 0.00 4.35
2734 3025 2.602676 GGGCTGACTGGTGGGCTTA 61.603 63.158 0.00 0.00 0.00 3.09
2735 3026 1.378762 GGCTGACTGGTGGGCTTAA 59.621 57.895 0.00 0.00 0.00 1.85
2736 3027 0.960861 GGCTGACTGGTGGGCTTAAC 60.961 60.000 0.00 0.00 0.00 2.01
2737 3028 0.250727 GCTGACTGGTGGGCTTAACA 60.251 55.000 0.00 0.00 0.00 2.41
2738 3029 1.813513 CTGACTGGTGGGCTTAACAG 58.186 55.000 5.93 5.93 37.01 3.16
2739 3030 0.400213 TGACTGGTGGGCTTAACAGG 59.600 55.000 11.05 0.00 35.34 4.00
2740 3031 0.960861 GACTGGTGGGCTTAACAGGC 60.961 60.000 11.05 5.10 45.20 4.85
2751 3042 4.529109 GCTTAACAGGCCAAAATACCAA 57.471 40.909 5.01 0.00 0.00 3.67
2752 3043 5.084818 GCTTAACAGGCCAAAATACCAAT 57.915 39.130 5.01 0.00 0.00 3.16
2753 3044 6.215495 GCTTAACAGGCCAAAATACCAATA 57.785 37.500 5.01 0.00 0.00 1.90
2754 3045 6.040247 GCTTAACAGGCCAAAATACCAATAC 58.960 40.000 5.01 0.00 0.00 1.89
2755 3046 6.127451 GCTTAACAGGCCAAAATACCAATACT 60.127 38.462 5.01 0.00 0.00 2.12
2756 3047 5.659440 AACAGGCCAAAATACCAATACTG 57.341 39.130 5.01 0.00 0.00 2.74
2757 3048 4.929479 ACAGGCCAAAATACCAATACTGA 58.071 39.130 5.01 0.00 0.00 3.41
2758 3049 4.705023 ACAGGCCAAAATACCAATACTGAC 59.295 41.667 5.01 0.00 0.00 3.51
2759 3050 3.945285 AGGCCAAAATACCAATACTGACG 59.055 43.478 5.01 0.00 0.00 4.35
2760 3051 3.066203 GGCCAAAATACCAATACTGACGG 59.934 47.826 0.00 0.00 0.00 4.79
2761 3052 3.066203 GCCAAAATACCAATACTGACGGG 59.934 47.826 0.00 0.00 0.00 5.28
2762 3053 3.066203 CCAAAATACCAATACTGACGGGC 59.934 47.826 0.00 0.00 0.00 6.13
2763 3054 2.632987 AATACCAATACTGACGGGCC 57.367 50.000 0.00 0.00 0.00 5.80
2764 3055 0.391597 ATACCAATACTGACGGGCCG 59.608 55.000 27.06 27.06 0.00 6.13
2765 3056 0.683828 TACCAATACTGACGGGCCGA 60.684 55.000 35.78 10.47 0.00 5.54
2766 3057 1.219664 CCAATACTGACGGGCCGAA 59.780 57.895 35.78 19.30 0.00 4.30
2767 3058 0.391927 CCAATACTGACGGGCCGAAA 60.392 55.000 35.78 18.90 0.00 3.46
2768 3059 1.444836 CAATACTGACGGGCCGAAAA 58.555 50.000 35.78 16.17 0.00 2.29
2769 3060 2.014128 CAATACTGACGGGCCGAAAAT 58.986 47.619 35.78 17.32 0.00 1.82
2770 3061 3.199677 CAATACTGACGGGCCGAAAATA 58.800 45.455 35.78 18.96 0.00 1.40
2771 3062 2.298411 TACTGACGGGCCGAAAATAC 57.702 50.000 35.78 15.65 0.00 1.89
2772 3063 0.738412 ACTGACGGGCCGAAAATACG 60.738 55.000 35.78 14.83 0.00 3.06
2788 3079 8.758633 CGAAAATACGGACTGATATCCTATTT 57.241 34.615 0.00 0.00 35.65 1.40
2789 3080 8.648097 CGAAAATACGGACTGATATCCTATTTG 58.352 37.037 0.00 0.00 35.07 2.32
2790 3081 8.848474 AAAATACGGACTGATATCCTATTTGG 57.152 34.615 0.00 0.00 35.07 3.28
2791 3082 4.273148 ACGGACTGATATCCTATTTGGC 57.727 45.455 0.00 0.00 36.52 4.52
2792 3083 3.254060 CGGACTGATATCCTATTTGGCG 58.746 50.000 0.00 0.00 36.52 5.69
2793 3084 3.003480 GGACTGATATCCTATTTGGCGC 58.997 50.000 0.00 0.00 35.68 6.53
2794 3085 3.557054 GGACTGATATCCTATTTGGCGCA 60.557 47.826 10.83 0.00 35.68 6.09
2795 3086 4.256920 GACTGATATCCTATTTGGCGCAT 58.743 43.478 10.83 0.00 35.26 4.73
2796 3087 5.419542 GACTGATATCCTATTTGGCGCATA 58.580 41.667 10.83 0.00 35.26 3.14
2797 3088 5.804639 ACTGATATCCTATTTGGCGCATAA 58.195 37.500 10.83 2.16 35.26 1.90
2798 3089 5.877012 ACTGATATCCTATTTGGCGCATAAG 59.123 40.000 10.83 0.00 35.26 1.73
2799 3090 4.635765 TGATATCCTATTTGGCGCATAAGC 59.364 41.667 10.83 0.00 35.26 3.09
2809 3100 2.405892 GCGCATAAGCCACCAAATAG 57.594 50.000 0.30 0.00 37.52 1.73
2810 3101 1.676006 GCGCATAAGCCACCAAATAGT 59.324 47.619 0.30 0.00 37.52 2.12
2811 3102 2.875933 GCGCATAAGCCACCAAATAGTA 59.124 45.455 0.30 0.00 37.52 1.82
2812 3103 3.058914 GCGCATAAGCCACCAAATAGTAG 60.059 47.826 0.30 0.00 37.52 2.57
2813 3104 3.058914 CGCATAAGCCACCAAATAGTAGC 60.059 47.826 0.00 0.00 37.52 3.58
2814 3105 3.253432 GCATAAGCCACCAAATAGTAGCC 59.747 47.826 0.00 0.00 33.58 3.93
2815 3106 4.460263 CATAAGCCACCAAATAGTAGCCA 58.540 43.478 0.00 0.00 0.00 4.75
2816 3107 3.669939 AAGCCACCAAATAGTAGCCAT 57.330 42.857 0.00 0.00 0.00 4.40
2817 3108 3.669939 AGCCACCAAATAGTAGCCATT 57.330 42.857 0.00 0.00 0.00 3.16
2818 3109 3.981212 AGCCACCAAATAGTAGCCATTT 58.019 40.909 0.00 0.00 0.00 2.32
2819 3110 3.954258 AGCCACCAAATAGTAGCCATTTC 59.046 43.478 0.00 0.00 0.00 2.17
2820 3111 3.243068 GCCACCAAATAGTAGCCATTTCG 60.243 47.826 0.00 0.00 0.00 3.46
2821 3112 3.945285 CCACCAAATAGTAGCCATTTCGT 59.055 43.478 0.00 0.00 0.00 3.85
2822 3113 5.120399 CCACCAAATAGTAGCCATTTCGTA 58.880 41.667 0.00 0.00 0.00 3.43
2823 3114 5.236478 CCACCAAATAGTAGCCATTTCGTAG 59.764 44.000 0.00 0.00 0.00 3.51
2824 3115 6.046593 CACCAAATAGTAGCCATTTCGTAGA 58.953 40.000 0.00 0.00 0.00 2.59
2825 3116 6.537301 CACCAAATAGTAGCCATTTCGTAGAA 59.463 38.462 0.00 0.00 45.90 2.10
2826 3117 7.065324 CACCAAATAGTAGCCATTTCGTAGAAA 59.935 37.037 0.00 0.00 45.90 2.52
2827 3118 7.608761 ACCAAATAGTAGCCATTTCGTAGAAAA 59.391 33.333 0.00 0.00 45.90 2.29
2828 3119 7.908601 CCAAATAGTAGCCATTTCGTAGAAAAC 59.091 37.037 0.00 0.00 45.90 2.43
2829 3120 8.447833 CAAATAGTAGCCATTTCGTAGAAAACA 58.552 33.333 0.00 0.00 45.90 2.83
2830 3121 5.857822 AGTAGCCATTTCGTAGAAAACAC 57.142 39.130 0.00 0.00 45.90 3.32
2831 3122 3.806316 AGCCATTTCGTAGAAAACACG 57.194 42.857 0.00 0.00 45.90 4.49
2832 3123 2.095919 AGCCATTTCGTAGAAAACACGC 60.096 45.455 0.00 0.31 45.90 5.34
2833 3124 2.350007 GCCATTTCGTAGAAAACACGCA 60.350 45.455 0.00 0.00 45.90 5.24
2834 3125 3.223157 CCATTTCGTAGAAAACACGCAC 58.777 45.455 0.00 0.00 45.90 5.34
2835 3126 3.223157 CATTTCGTAGAAAACACGCACC 58.777 45.455 0.00 0.00 45.90 5.01
2836 3127 1.219646 TTCGTAGAAAACACGCACCC 58.780 50.000 0.00 0.00 45.90 4.61
2837 3128 0.600782 TCGTAGAAAACACGCACCCC 60.601 55.000 0.00 0.00 39.23 4.95
2838 3129 1.571215 CGTAGAAAACACGCACCCCC 61.571 60.000 0.00 0.00 31.94 5.40
2839 3130 0.250597 GTAGAAAACACGCACCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
2840 3131 0.035739 TAGAAAACACGCACCCCCTC 59.964 55.000 0.00 0.00 0.00 4.30
2841 3132 2.593436 AAAACACGCACCCCCTCG 60.593 61.111 0.00 0.00 0.00 4.63
2842 3133 2.999739 GAAAACACGCACCCCCTCGA 63.000 60.000 0.00 0.00 0.00 4.04
2843 3134 3.530910 AAACACGCACCCCCTCGAG 62.531 63.158 5.13 5.13 0.00 4.04
2848 3139 3.075005 GCACCCCCTCGAGCACTA 61.075 66.667 6.99 0.00 0.00 2.74
2849 3140 2.893398 CACCCCCTCGAGCACTAC 59.107 66.667 6.99 0.00 0.00 2.73
2850 3141 2.363925 ACCCCCTCGAGCACTACC 60.364 66.667 6.99 0.00 0.00 3.18
2851 3142 2.363795 CCCCCTCGAGCACTACCA 60.364 66.667 6.99 0.00 0.00 3.25
2852 3143 2.722201 CCCCCTCGAGCACTACCAC 61.722 68.421 6.99 0.00 0.00 4.16
2853 3144 2.490217 CCCTCGAGCACTACCACG 59.510 66.667 6.99 0.00 0.00 4.94
2854 3145 2.044555 CCCTCGAGCACTACCACGA 61.045 63.158 6.99 0.00 0.00 4.35
2855 3146 1.384989 CCCTCGAGCACTACCACGAT 61.385 60.000 6.99 0.00 34.41 3.73
2856 3147 1.306148 CCTCGAGCACTACCACGATA 58.694 55.000 6.99 0.00 34.41 2.92
2857 3148 1.674441 CCTCGAGCACTACCACGATAA 59.326 52.381 6.99 0.00 34.41 1.75
2858 3149 2.287069 CCTCGAGCACTACCACGATAAG 60.287 54.545 6.99 0.00 34.41 1.73
2859 3150 2.355132 CTCGAGCACTACCACGATAAGT 59.645 50.000 0.00 0.00 34.41 2.24
2860 3151 3.534554 TCGAGCACTACCACGATAAGTA 58.465 45.455 0.00 0.00 0.00 2.24
2861 3152 3.558829 TCGAGCACTACCACGATAAGTAG 59.441 47.826 0.00 0.00 41.44 2.57
2862 3153 3.303857 CGAGCACTACCACGATAAGTAGG 60.304 52.174 0.00 0.00 40.25 3.18
2863 3154 2.361438 AGCACTACCACGATAAGTAGGC 59.639 50.000 0.00 1.16 40.25 3.93
2864 3155 2.545322 GCACTACCACGATAAGTAGGCC 60.545 54.545 0.00 0.00 40.25 5.19
2865 3156 2.691526 CACTACCACGATAAGTAGGCCA 59.308 50.000 5.01 0.00 40.25 5.36
2866 3157 3.131577 CACTACCACGATAAGTAGGCCAA 59.868 47.826 5.01 0.00 40.25 4.52
2867 3158 2.685850 ACCACGATAAGTAGGCCAAC 57.314 50.000 5.01 0.00 0.00 3.77
2868 3159 1.208776 ACCACGATAAGTAGGCCAACC 59.791 52.381 5.01 0.00 0.00 3.77
2869 3160 1.474498 CCACGATAAGTAGGCCAACCC 60.474 57.143 5.01 0.00 36.11 4.11
2870 3161 1.208535 CACGATAAGTAGGCCAACCCA 59.791 52.381 5.01 0.00 36.11 4.51
2871 3162 2.124411 ACGATAAGTAGGCCAACCCAT 58.876 47.619 5.01 0.00 36.11 4.00
2872 3163 2.158813 ACGATAAGTAGGCCAACCCATG 60.159 50.000 5.01 0.00 36.11 3.66
2873 3164 2.230660 GATAAGTAGGCCAACCCATGC 58.769 52.381 5.01 0.00 36.11 4.06
2874 3165 0.995803 TAAGTAGGCCAACCCATGCA 59.004 50.000 5.01 0.00 36.11 3.96
2875 3166 0.323725 AAGTAGGCCAACCCATGCAG 60.324 55.000 5.01 0.00 36.11 4.41
2876 3167 2.044053 TAGGCCAACCCATGCAGC 60.044 61.111 5.01 0.00 36.11 5.25
2877 3168 2.615465 TAGGCCAACCCATGCAGCT 61.615 57.895 5.01 0.00 36.11 4.24
2878 3169 1.278302 TAGGCCAACCCATGCAGCTA 61.278 55.000 5.01 0.00 36.11 3.32
2879 3170 2.418083 GGCCAACCCATGCAGCTAC 61.418 63.158 0.00 0.00 0.00 3.58
2880 3171 2.418083 GCCAACCCATGCAGCTACC 61.418 63.158 0.00 0.00 0.00 3.18
2881 3172 1.304282 CCAACCCATGCAGCTACCT 59.696 57.895 0.00 0.00 0.00 3.08
2882 3173 0.323725 CCAACCCATGCAGCTACCTT 60.324 55.000 0.00 0.00 0.00 3.50
2883 3174 1.098050 CAACCCATGCAGCTACCTTC 58.902 55.000 0.00 0.00 0.00 3.46
2884 3175 0.698238 AACCCATGCAGCTACCTTCA 59.302 50.000 0.00 0.00 0.00 3.02
2885 3176 0.035056 ACCCATGCAGCTACCTTCAC 60.035 55.000 0.00 0.00 0.00 3.18
2886 3177 0.749454 CCCATGCAGCTACCTTCACC 60.749 60.000 0.00 0.00 0.00 4.02
2887 3178 1.091771 CCATGCAGCTACCTTCACCG 61.092 60.000 0.00 0.00 0.00 4.94
2888 3179 1.091771 CATGCAGCTACCTTCACCGG 61.092 60.000 0.00 0.00 0.00 5.28
2889 3180 2.820037 GCAGCTACCTTCACCGGC 60.820 66.667 0.00 0.00 0.00 6.13
2890 3181 2.982130 CAGCTACCTTCACCGGCT 59.018 61.111 0.00 0.00 0.00 5.52
2891 3182 1.296715 CAGCTACCTTCACCGGCTT 59.703 57.895 0.00 0.00 0.00 4.35
2892 3183 0.321653 CAGCTACCTTCACCGGCTTT 60.322 55.000 0.00 0.00 0.00 3.51
2893 3184 0.321653 AGCTACCTTCACCGGCTTTG 60.322 55.000 0.00 0.00 0.00 2.77
2894 3185 1.305930 GCTACCTTCACCGGCTTTGG 61.306 60.000 0.00 1.31 0.00 3.28
2895 3186 0.323629 CTACCTTCACCGGCTTTGGA 59.676 55.000 0.00 0.00 0.00 3.53
2896 3187 0.323629 TACCTTCACCGGCTTTGGAG 59.676 55.000 0.00 0.00 0.00 3.86
2897 3188 1.073199 CCTTCACCGGCTTTGGAGT 59.927 57.895 0.00 0.00 0.00 3.85
2898 3189 0.955919 CCTTCACCGGCTTTGGAGTC 60.956 60.000 0.00 0.00 0.00 3.36
2899 3190 0.250295 CTTCACCGGCTTTGGAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
2900 3191 0.534203 TTCACCGGCTTTGGAGTCAC 60.534 55.000 0.00 0.00 0.00 3.67
2901 3192 1.966451 CACCGGCTTTGGAGTCACC 60.966 63.158 0.00 0.00 39.54 4.02
2962 3253 7.945326 TTTTTCAAATTCGCATTTGTTTGTC 57.055 28.000 17.95 0.00 46.61 3.18
2963 3254 6.653273 TTTCAAATTCGCATTTGTTTGTCA 57.347 29.167 17.95 0.00 46.61 3.58
2964 3255 6.653273 TTCAAATTCGCATTTGTTTGTCAA 57.347 29.167 17.95 3.77 46.61 3.18
2965 3256 6.653273 TCAAATTCGCATTTGTTTGTCAAA 57.347 29.167 17.95 0.00 46.61 2.69
3063 3354 8.582433 AAAATACGACCATTTTCAAAATTCGT 57.418 26.923 20.70 20.70 40.93 3.85
3064 3355 9.680315 AAAATACGACCATTTTCAAAATTCGTA 57.320 25.926 22.78 22.78 42.65 3.43
3065 3356 8.889849 AATACGACCATTTTCAAAATTCGTAG 57.110 30.769 23.90 13.42 42.00 3.51
3066 3357 6.548441 ACGACCATTTTCAAAATTCGTAGA 57.452 33.333 17.18 0.00 36.52 2.59
3067 3358 6.368213 ACGACCATTTTCAAAATTCGTAGAC 58.632 36.000 17.18 0.00 36.52 2.59
3068 3359 6.204108 ACGACCATTTTCAAAATTCGTAGACT 59.796 34.615 17.18 0.00 36.52 3.24
3069 3360 7.075741 CGACCATTTTCAAAATTCGTAGACTT 58.924 34.615 8.27 0.00 34.32 3.01
3070 3361 7.589954 CGACCATTTTCAAAATTCGTAGACTTT 59.410 33.333 8.27 0.00 41.16 2.66
3072 3363 9.594478 ACCATTTTCAAAATTCGTAGACTTTTT 57.406 25.926 0.00 0.00 44.95 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.868899 CCCCTGGATTAGATGAAAGCC 58.131 52.381 0.00 0.00 35.42 4.35
12 13 2.175499 TGGCCCCTGGATTAGATGAAAG 59.825 50.000 0.00 0.00 0.00 2.62
24 25 4.684134 CCTGTGGTTGGCCCCTGG 62.684 72.222 0.00 0.00 0.00 4.45
31 32 1.202806 AGTGTGATGTCCTGTGGTTGG 60.203 52.381 0.00 0.00 0.00 3.77
36 37 6.558771 TTTATGAAAGTGTGATGTCCTGTG 57.441 37.500 0.00 0.00 0.00 3.66
38 39 9.778993 CTTATTTTATGAAAGTGTGATGTCCTG 57.221 33.333 0.00 0.00 0.00 3.86
45 46 8.708742 CACTCGACTTATTTTATGAAAGTGTGA 58.291 33.333 0.00 0.00 33.72 3.58
66 67 1.379977 TGCCCCCTCTAGACACTCG 60.380 63.158 0.00 0.00 0.00 4.18
81 82 2.095372 GCCTACACTTATTTCGTGTGCC 59.905 50.000 6.10 0.00 44.63 5.01
90 91 2.093658 CGACACCTGGCCTACACTTATT 60.094 50.000 3.32 0.00 0.00 1.40
94 95 1.228769 TCGACACCTGGCCTACACT 60.229 57.895 3.32 0.00 0.00 3.55
102 103 3.589654 ATGCCGTGTCGACACCTGG 62.590 63.158 36.01 31.88 43.66 4.45
105 106 0.108992 TAAGATGCCGTGTCGACACC 60.109 55.000 36.01 25.60 43.66 4.16
111 112 2.030457 CCGAAATGTAAGATGCCGTGTC 59.970 50.000 0.00 0.00 0.00 3.67
114 115 2.277084 GTCCGAAATGTAAGATGCCGT 58.723 47.619 0.00 0.00 0.00 5.68
116 117 3.063997 CACTGTCCGAAATGTAAGATGCC 59.936 47.826 0.00 0.00 0.00 4.40
117 118 3.063997 CCACTGTCCGAAATGTAAGATGC 59.936 47.826 0.00 0.00 0.00 3.91
119 120 4.020573 TGACCACTGTCCGAAATGTAAGAT 60.021 41.667 0.00 0.00 41.01 2.40
127 128 3.927555 GGATGACCACTGTCCGAAA 57.072 52.632 0.00 0.00 41.01 3.46
131 132 1.275291 TCTTTCGGATGACCACTGTCC 59.725 52.381 0.00 0.00 41.01 4.02
167 168 8.746530 ACATCCTACGTGATATTCGGTTTATAT 58.253 33.333 0.00 0.00 0.00 0.86
173 174 3.552273 GCACATCCTACGTGATATTCGGT 60.552 47.826 0.00 0.00 36.43 4.69
178 179 4.560128 GATGTGCACATCCTACGTGATAT 58.440 43.478 38.64 13.95 45.24 1.63
179 180 3.977427 GATGTGCACATCCTACGTGATA 58.023 45.455 38.64 7.81 45.24 2.15
190 191 5.248640 GGCTTATACCTATGATGTGCACAT 58.751 41.667 31.82 31.82 39.70 3.21
191 192 4.641396 GGCTTATACCTATGATGTGCACA 58.359 43.478 24.08 24.08 0.00 4.57
207 208 4.547367 GGCCCACGCTCGGCTTAT 62.547 66.667 7.80 0.00 46.24 1.73
226 227 3.760151 AGCACGGTGTATATATAAGCCGA 59.240 43.478 28.37 0.00 41.45 5.54
228 229 4.561606 CGAAGCACGGTGTATATATAAGCC 59.438 45.833 10.24 0.00 38.46 4.35
252 253 2.213499 GACGAGCACCAATCCTAATGG 58.787 52.381 0.00 0.00 43.84 3.16
255 256 0.892755 ACGACGAGCACCAATCCTAA 59.107 50.000 0.00 0.00 0.00 2.69
273 274 1.071605 CTCCGCTTACAGCAGTGAAC 58.928 55.000 0.00 0.00 42.58 3.18
304 305 3.853831 TTCGTCATAAGCCGAGTGTAA 57.146 42.857 0.00 0.00 34.16 2.41
330 331 7.587037 AATAAACATACATGCAACCATAGCT 57.413 32.000 0.00 0.00 0.00 3.32
331 332 8.647143 AAAATAAACATACATGCAACCATAGC 57.353 30.769 0.00 0.00 0.00 2.97
460 466 1.545841 TGCTAGACAGACACGGACAT 58.454 50.000 0.00 0.00 0.00 3.06
493 499 4.159693 AGAAAGTGGTGTCCTTTTTGTTCC 59.840 41.667 0.00 0.00 32.47 3.62
532 538 6.127647 TGGGCTGAATTCATTTGTACAGAATC 60.128 38.462 8.96 4.87 31.21 2.52
683 689 2.290071 TGGCTTGTTTACTACTCTGGGC 60.290 50.000 0.00 0.00 0.00 5.36
686 692 4.814234 TGTTGTGGCTTGTTTACTACTCTG 59.186 41.667 0.00 0.00 0.00 3.35
839 854 3.980775 GCATTGTGTGTGTGGTGATAAAC 59.019 43.478 0.00 0.00 0.00 2.01
840 855 3.633986 TGCATTGTGTGTGTGGTGATAAA 59.366 39.130 0.00 0.00 0.00 1.40
841 856 3.217626 TGCATTGTGTGTGTGGTGATAA 58.782 40.909 0.00 0.00 0.00 1.75
842 857 2.813172 CTGCATTGTGTGTGTGGTGATA 59.187 45.455 0.00 0.00 0.00 2.15
844 859 1.023502 CTGCATTGTGTGTGTGGTGA 58.976 50.000 0.00 0.00 0.00 4.02
845 860 1.002142 CTCTGCATTGTGTGTGTGGTG 60.002 52.381 0.00 0.00 0.00 4.17
1693 1782 9.425248 AATCCATCCATACATCAGTTAATTTGT 57.575 29.630 0.00 0.00 0.00 2.83
1939 2079 5.380043 TGATCATCAAGCTTAATTCCTCCC 58.620 41.667 0.00 0.00 0.00 4.30
2071 2290 1.270305 TGGCCGATTGAGTATGCTAGC 60.270 52.381 8.10 8.10 0.00 3.42
2076 2295 2.549064 TCCATGGCCGATTGAGTATG 57.451 50.000 6.96 0.00 0.00 2.39
2154 2389 5.124645 CAGACCGATAGTTACAGGAGTACT 58.875 45.833 0.00 0.00 0.00 2.73
2200 2437 0.249489 GACTGAAGGACACACACGCT 60.249 55.000 0.00 0.00 0.00 5.07
2201 2438 1.548973 CGACTGAAGGACACACACGC 61.549 60.000 0.00 0.00 0.00 5.34
2202 2439 0.939577 CCGACTGAAGGACACACACG 60.940 60.000 0.00 0.00 0.00 4.49
2220 2457 1.260561 CACTTGTAACGCTGACACACC 59.739 52.381 0.00 0.00 0.00 4.16
2260 2501 2.829741 TTTGCACATTTTGGGTAGGC 57.170 45.000 0.00 0.00 0.00 3.93
2370 2641 6.260870 AGTATCGATGTAATAGCACTCCAG 57.739 41.667 8.54 0.00 0.00 3.86
2409 2680 4.622260 ACAAACCCAGAAATCCCAAATG 57.378 40.909 0.00 0.00 0.00 2.32
2542 2833 8.754991 TGACCAAGTTAATAGAAAACTTTCCA 57.245 30.769 0.00 0.00 42.97 3.53
2556 2847 8.974060 AACTTCTTTACATCTGACCAAGTTAA 57.026 30.769 0.00 0.00 32.42 2.01
2557 2848 8.836413 CAAACTTCTTTACATCTGACCAAGTTA 58.164 33.333 0.00 0.00 32.90 2.24
2559 2850 7.012421 GTCAAACTTCTTTACATCTGACCAAGT 59.988 37.037 0.00 0.00 0.00 3.16
2585 2876 7.648112 GGCTTGAAGTTTTAGGTTTGTCTTAAG 59.352 37.037 0.00 0.00 0.00 1.85
2687 2978 0.168348 TCGCGTGAGTGCTTAGAGAC 59.832 55.000 5.77 0.00 42.50 3.36
2688 2979 0.448197 CTCGCGTGAGTGCTTAGAGA 59.552 55.000 17.90 0.00 42.50 3.10
2689 2980 0.448197 TCTCGCGTGAGTGCTTAGAG 59.552 55.000 24.36 0.00 43.09 2.43
2690 2981 1.095600 ATCTCGCGTGAGTGCTTAGA 58.904 50.000 24.36 5.11 43.09 2.10
2691 2982 1.195347 CATCTCGCGTGAGTGCTTAG 58.805 55.000 24.36 6.75 43.09 2.18
2692 2983 0.179137 CCATCTCGCGTGAGTGCTTA 60.179 55.000 24.36 6.33 43.09 3.09
2693 2984 1.446792 CCATCTCGCGTGAGTGCTT 60.447 57.895 24.36 6.75 43.09 3.91
2694 2985 2.182791 CCATCTCGCGTGAGTGCT 59.817 61.111 24.36 8.95 43.09 4.40
2695 2986 1.875813 CTCCATCTCGCGTGAGTGC 60.876 63.158 24.36 0.00 43.09 4.40
2696 2987 1.875813 GCTCCATCTCGCGTGAGTG 60.876 63.158 24.36 19.90 43.09 3.51
2697 2988 2.049185 AGCTCCATCTCGCGTGAGT 61.049 57.895 24.36 10.18 43.09 3.41
2698 2989 1.588403 CAGCTCCATCTCGCGTGAG 60.588 63.158 19.99 19.99 43.99 3.51
2699 2990 2.491621 CAGCTCCATCTCGCGTGA 59.508 61.111 13.84 13.84 0.00 4.35
2700 2991 2.584418 CCAGCTCCATCTCGCGTG 60.584 66.667 5.77 3.13 0.00 5.34
2701 2992 3.842923 CCCAGCTCCATCTCGCGT 61.843 66.667 5.77 0.00 0.00 6.01
2703 2994 3.859414 AGCCCAGCTCCATCTCGC 61.859 66.667 0.00 0.00 30.62 5.03
2704 2995 2.108566 CAGCCCAGCTCCATCTCG 59.891 66.667 0.00 0.00 36.40 4.04
2705 2996 1.145819 GTCAGCCCAGCTCCATCTC 59.854 63.158 0.00 0.00 36.40 2.75
2706 2997 1.306825 AGTCAGCCCAGCTCCATCT 60.307 57.895 0.00 0.00 36.40 2.90
2707 2998 1.153208 CAGTCAGCCCAGCTCCATC 60.153 63.158 0.00 0.00 36.40 3.51
2708 2999 2.677289 CCAGTCAGCCCAGCTCCAT 61.677 63.158 0.00 0.00 36.40 3.41
2709 3000 3.324930 CCAGTCAGCCCAGCTCCA 61.325 66.667 0.00 0.00 36.40 3.86
2710 3001 3.325753 ACCAGTCAGCCCAGCTCC 61.326 66.667 0.00 0.00 36.40 4.70
2711 3002 2.046507 CACCAGTCAGCCCAGCTC 60.047 66.667 0.00 0.00 36.40 4.09
2712 3003 3.644606 CCACCAGTCAGCCCAGCT 61.645 66.667 0.00 0.00 40.77 4.24
2713 3004 4.729918 CCCACCAGTCAGCCCAGC 62.730 72.222 0.00 0.00 0.00 4.85
2714 3005 4.729918 GCCCACCAGTCAGCCCAG 62.730 72.222 0.00 0.00 0.00 4.45
2716 3007 2.137177 TTAAGCCCACCAGTCAGCCC 62.137 60.000 0.00 0.00 0.00 5.19
2717 3008 0.960861 GTTAAGCCCACCAGTCAGCC 60.961 60.000 0.00 0.00 0.00 4.85
2718 3009 0.250727 TGTTAAGCCCACCAGTCAGC 60.251 55.000 0.00 0.00 0.00 4.26
2719 3010 1.611673 CCTGTTAAGCCCACCAGTCAG 60.612 57.143 0.00 0.00 0.00 3.51
2720 3011 0.400213 CCTGTTAAGCCCACCAGTCA 59.600 55.000 0.00 0.00 0.00 3.41
2721 3012 0.960861 GCCTGTTAAGCCCACCAGTC 60.961 60.000 0.00 0.00 0.00 3.51
2722 3013 1.074951 GCCTGTTAAGCCCACCAGT 59.925 57.895 0.00 0.00 0.00 4.00
2723 3014 1.678970 GGCCTGTTAAGCCCACCAG 60.679 63.158 0.00 0.00 45.16 4.00
2724 3015 2.438795 GGCCTGTTAAGCCCACCA 59.561 61.111 0.00 0.00 45.16 4.17
2730 3021 4.529109 TTGGTATTTTGGCCTGTTAAGC 57.471 40.909 3.32 0.00 0.00 3.09
2731 3022 7.122055 TCAGTATTGGTATTTTGGCCTGTTAAG 59.878 37.037 3.32 0.00 0.00 1.85
2732 3023 6.948886 TCAGTATTGGTATTTTGGCCTGTTAA 59.051 34.615 3.32 0.00 0.00 2.01
2733 3024 6.376018 GTCAGTATTGGTATTTTGGCCTGTTA 59.624 38.462 3.32 0.00 0.00 2.41
2734 3025 5.185056 GTCAGTATTGGTATTTTGGCCTGTT 59.815 40.000 3.32 0.00 0.00 3.16
2735 3026 4.705023 GTCAGTATTGGTATTTTGGCCTGT 59.295 41.667 3.32 0.00 0.00 4.00
2736 3027 4.201910 CGTCAGTATTGGTATTTTGGCCTG 60.202 45.833 3.32 0.00 0.00 4.85
2737 3028 3.945285 CGTCAGTATTGGTATTTTGGCCT 59.055 43.478 3.32 0.00 0.00 5.19
2738 3029 3.066203 CCGTCAGTATTGGTATTTTGGCC 59.934 47.826 0.00 0.00 0.00 5.36
2739 3030 3.066203 CCCGTCAGTATTGGTATTTTGGC 59.934 47.826 0.00 0.00 0.00 4.52
2740 3031 3.066203 GCCCGTCAGTATTGGTATTTTGG 59.934 47.826 0.00 0.00 0.00 3.28
2741 3032 3.066203 GGCCCGTCAGTATTGGTATTTTG 59.934 47.826 0.00 0.00 0.00 2.44
2742 3033 3.284617 GGCCCGTCAGTATTGGTATTTT 58.715 45.455 0.00 0.00 0.00 1.82
2743 3034 2.743838 CGGCCCGTCAGTATTGGTATTT 60.744 50.000 0.00 0.00 0.00 1.40
2744 3035 1.202604 CGGCCCGTCAGTATTGGTATT 60.203 52.381 0.00 0.00 0.00 1.89
2745 3036 0.391597 CGGCCCGTCAGTATTGGTAT 59.608 55.000 0.00 0.00 0.00 2.73
2746 3037 0.683828 TCGGCCCGTCAGTATTGGTA 60.684 55.000 1.63 0.00 0.00 3.25
2747 3038 1.546589 TTCGGCCCGTCAGTATTGGT 61.547 55.000 1.63 0.00 0.00 3.67
2748 3039 0.391927 TTTCGGCCCGTCAGTATTGG 60.392 55.000 1.63 0.00 0.00 3.16
2749 3040 1.444836 TTTTCGGCCCGTCAGTATTG 58.555 50.000 1.63 0.00 0.00 1.90
2750 3041 2.413310 ATTTTCGGCCCGTCAGTATT 57.587 45.000 1.63 0.00 0.00 1.89
2751 3042 2.800629 CGTATTTTCGGCCCGTCAGTAT 60.801 50.000 1.63 0.00 0.00 2.12
2752 3043 1.469595 CGTATTTTCGGCCCGTCAGTA 60.470 52.381 1.63 0.00 0.00 2.74
2753 3044 0.738412 CGTATTTTCGGCCCGTCAGT 60.738 55.000 1.63 0.00 0.00 3.41
2754 3045 1.426041 CCGTATTTTCGGCCCGTCAG 61.426 60.000 1.63 0.00 43.96 3.51
2755 3046 1.448189 CCGTATTTTCGGCCCGTCA 60.448 57.895 1.63 0.00 43.96 4.35
2756 3047 3.402185 CCGTATTTTCGGCCCGTC 58.598 61.111 1.63 0.00 43.96 4.79
2763 3054 8.648097 CAAATAGGATATCAGTCCGTATTTTCG 58.352 37.037 4.83 0.00 43.27 3.46
2764 3055 8.936864 CCAAATAGGATATCAGTCCGTATTTTC 58.063 37.037 4.83 0.00 43.27 2.29
2765 3056 7.390718 GCCAAATAGGATATCAGTCCGTATTTT 59.609 37.037 4.83 0.00 43.27 1.82
2766 3057 6.879458 GCCAAATAGGATATCAGTCCGTATTT 59.121 38.462 4.83 0.03 43.27 1.40
2767 3058 6.407202 GCCAAATAGGATATCAGTCCGTATT 58.593 40.000 4.83 0.00 43.27 1.89
2768 3059 5.394224 CGCCAAATAGGATATCAGTCCGTAT 60.394 44.000 4.83 0.00 43.27 3.06
2769 3060 4.082408 CGCCAAATAGGATATCAGTCCGTA 60.082 45.833 4.83 0.00 43.27 4.02
2770 3061 3.306088 CGCCAAATAGGATATCAGTCCGT 60.306 47.826 4.83 0.00 43.27 4.69
2771 3062 3.254060 CGCCAAATAGGATATCAGTCCG 58.746 50.000 4.83 0.00 43.27 4.79
2772 3063 3.003480 GCGCCAAATAGGATATCAGTCC 58.997 50.000 4.83 0.00 41.22 3.85
2773 3064 3.664107 TGCGCCAAATAGGATATCAGTC 58.336 45.455 4.18 0.00 41.22 3.51
2774 3065 3.769739 TGCGCCAAATAGGATATCAGT 57.230 42.857 4.18 0.00 41.22 3.41
2775 3066 5.220739 GCTTATGCGCCAAATAGGATATCAG 60.221 44.000 4.18 0.00 41.22 2.90
2776 3067 4.635765 GCTTATGCGCCAAATAGGATATCA 59.364 41.667 4.18 0.00 41.22 2.15
2777 3068 5.162000 GCTTATGCGCCAAATAGGATATC 57.838 43.478 4.18 0.00 41.22 1.63
2790 3081 1.676006 ACTATTTGGTGGCTTATGCGC 59.324 47.619 0.00 0.00 40.82 6.09
2791 3082 3.058914 GCTACTATTTGGTGGCTTATGCG 60.059 47.826 0.00 0.00 39.92 4.73
2792 3083 3.253432 GGCTACTATTTGGTGGCTTATGC 59.747 47.826 2.71 0.00 42.15 3.14
2793 3084 4.460263 TGGCTACTATTTGGTGGCTTATG 58.540 43.478 2.71 0.00 42.15 1.90
2794 3085 4.788925 TGGCTACTATTTGGTGGCTTAT 57.211 40.909 2.71 0.00 42.15 1.73
2795 3086 4.788925 ATGGCTACTATTTGGTGGCTTA 57.211 40.909 2.71 0.00 42.15 3.09
2796 3087 3.669939 ATGGCTACTATTTGGTGGCTT 57.330 42.857 2.71 0.00 42.15 4.35
2797 3088 3.669939 AATGGCTACTATTTGGTGGCT 57.330 42.857 2.71 0.00 42.15 4.75
2798 3089 3.243068 CGAAATGGCTACTATTTGGTGGC 60.243 47.826 0.00 0.00 41.84 5.01
2799 3090 3.945285 ACGAAATGGCTACTATTTGGTGG 59.055 43.478 3.88 0.00 35.87 4.61
2800 3091 6.046593 TCTACGAAATGGCTACTATTTGGTG 58.953 40.000 12.13 5.22 37.16 4.17
2801 3092 6.229936 TCTACGAAATGGCTACTATTTGGT 57.770 37.500 8.58 8.58 39.03 3.67
2802 3093 7.548196 TTTCTACGAAATGGCTACTATTTGG 57.452 36.000 0.00 0.00 31.94 3.28
2803 3094 8.447833 TGTTTTCTACGAAATGGCTACTATTTG 58.552 33.333 0.00 0.00 0.00 2.32
2804 3095 8.448615 GTGTTTTCTACGAAATGGCTACTATTT 58.551 33.333 0.00 0.00 0.00 1.40
2805 3096 7.201496 CGTGTTTTCTACGAAATGGCTACTATT 60.201 37.037 0.00 0.00 43.82 1.73
2806 3097 6.255020 CGTGTTTTCTACGAAATGGCTACTAT 59.745 38.462 0.00 0.00 43.82 2.12
2807 3098 5.574055 CGTGTTTTCTACGAAATGGCTACTA 59.426 40.000 0.00 0.00 43.82 1.82
2808 3099 4.387862 CGTGTTTTCTACGAAATGGCTACT 59.612 41.667 0.00 0.00 43.82 2.57
2809 3100 4.634991 CGTGTTTTCTACGAAATGGCTAC 58.365 43.478 0.00 0.00 43.82 3.58
2810 3101 3.123959 GCGTGTTTTCTACGAAATGGCTA 59.876 43.478 1.32 0.00 43.82 3.93
2811 3102 2.095919 GCGTGTTTTCTACGAAATGGCT 60.096 45.455 1.32 0.00 43.82 4.75
2812 3103 2.239201 GCGTGTTTTCTACGAAATGGC 58.761 47.619 1.32 0.00 43.82 4.40
2813 3104 3.223157 GTGCGTGTTTTCTACGAAATGG 58.777 45.455 1.32 0.00 43.82 3.16
2814 3105 3.223157 GGTGCGTGTTTTCTACGAAATG 58.777 45.455 1.32 0.00 43.82 2.32
2815 3106 2.224784 GGGTGCGTGTTTTCTACGAAAT 59.775 45.455 1.32 0.00 43.82 2.17
2816 3107 1.598601 GGGTGCGTGTTTTCTACGAAA 59.401 47.619 1.32 0.00 43.82 3.46
2817 3108 1.219646 GGGTGCGTGTTTTCTACGAA 58.780 50.000 1.32 0.00 43.82 3.85
2818 3109 0.600782 GGGGTGCGTGTTTTCTACGA 60.601 55.000 1.32 0.00 43.82 3.43
2819 3110 1.571215 GGGGGTGCGTGTTTTCTACG 61.571 60.000 0.00 0.00 43.93 3.51
2820 3111 0.250597 AGGGGGTGCGTGTTTTCTAC 60.251 55.000 0.00 0.00 0.00 2.59
2821 3112 0.035739 GAGGGGGTGCGTGTTTTCTA 59.964 55.000 0.00 0.00 0.00 2.10
2822 3113 1.228154 GAGGGGGTGCGTGTTTTCT 60.228 57.895 0.00 0.00 0.00 2.52
2823 3114 2.613506 CGAGGGGGTGCGTGTTTTC 61.614 63.158 0.00 0.00 0.00 2.29
2824 3115 2.593436 CGAGGGGGTGCGTGTTTT 60.593 61.111 0.00 0.00 0.00 2.43
2825 3116 3.530910 CTCGAGGGGGTGCGTGTTT 62.531 63.158 3.91 0.00 0.00 2.83
2826 3117 4.003788 CTCGAGGGGGTGCGTGTT 62.004 66.667 3.91 0.00 0.00 3.32
2831 3122 3.075005 TAGTGCTCGAGGGGGTGC 61.075 66.667 15.58 0.00 0.00 5.01
2832 3123 2.722201 GGTAGTGCTCGAGGGGGTG 61.722 68.421 15.58 0.00 0.00 4.61
2833 3124 2.363925 GGTAGTGCTCGAGGGGGT 60.364 66.667 15.58 0.00 0.00 4.95
2834 3125 2.363795 TGGTAGTGCTCGAGGGGG 60.364 66.667 15.58 0.00 0.00 5.40
2835 3126 2.893398 GTGGTAGTGCTCGAGGGG 59.107 66.667 15.58 0.00 0.00 4.79
2836 3127 1.384989 ATCGTGGTAGTGCTCGAGGG 61.385 60.000 15.58 0.00 35.85 4.30
2837 3128 1.306148 TATCGTGGTAGTGCTCGAGG 58.694 55.000 15.58 0.00 35.85 4.63
2838 3129 2.355132 ACTTATCGTGGTAGTGCTCGAG 59.645 50.000 8.45 8.45 35.85 4.04
2839 3130 2.362736 ACTTATCGTGGTAGTGCTCGA 58.637 47.619 0.00 0.00 36.77 4.04
2840 3131 2.846039 ACTTATCGTGGTAGTGCTCG 57.154 50.000 0.00 0.00 0.00 5.03
2841 3132 3.550436 GCCTACTTATCGTGGTAGTGCTC 60.550 52.174 0.00 0.00 35.10 4.26
2842 3133 2.361438 GCCTACTTATCGTGGTAGTGCT 59.639 50.000 0.00 0.00 35.10 4.40
2843 3134 2.545322 GGCCTACTTATCGTGGTAGTGC 60.545 54.545 0.00 0.00 35.10 4.40
2844 3135 2.691526 TGGCCTACTTATCGTGGTAGTG 59.308 50.000 3.32 0.00 35.10 2.74
2845 3136 3.022557 TGGCCTACTTATCGTGGTAGT 57.977 47.619 3.32 0.00 35.10 2.73
2846 3137 3.492137 GGTTGGCCTACTTATCGTGGTAG 60.492 52.174 17.03 0.00 36.23 3.18
2847 3138 2.431782 GGTTGGCCTACTTATCGTGGTA 59.568 50.000 17.03 0.00 0.00 3.25
2848 3139 1.208776 GGTTGGCCTACTTATCGTGGT 59.791 52.381 17.03 0.00 0.00 4.16
2849 3140 1.474498 GGGTTGGCCTACTTATCGTGG 60.474 57.143 17.03 0.00 34.45 4.94
2850 3141 1.208535 TGGGTTGGCCTACTTATCGTG 59.791 52.381 17.03 0.00 34.45 4.35
2851 3142 1.575419 TGGGTTGGCCTACTTATCGT 58.425 50.000 17.03 0.00 34.45 3.73
2852 3143 2.494059 CATGGGTTGGCCTACTTATCG 58.506 52.381 17.03 0.00 34.45 2.92
2853 3144 2.230660 GCATGGGTTGGCCTACTTATC 58.769 52.381 17.03 0.08 34.45 1.75
2854 3145 1.568597 TGCATGGGTTGGCCTACTTAT 59.431 47.619 17.03 8.83 34.45 1.73
2855 3146 0.995803 TGCATGGGTTGGCCTACTTA 59.004 50.000 17.03 6.88 34.45 2.24
2856 3147 0.323725 CTGCATGGGTTGGCCTACTT 60.324 55.000 17.03 0.07 34.45 2.24
2857 3148 1.304282 CTGCATGGGTTGGCCTACT 59.696 57.895 17.03 0.00 34.45 2.57
2858 3149 2.418083 GCTGCATGGGTTGGCCTAC 61.418 63.158 9.03 9.03 34.45 3.18
2859 3150 1.278302 TAGCTGCATGGGTTGGCCTA 61.278 55.000 3.32 0.00 34.45 3.93
2860 3151 2.615465 TAGCTGCATGGGTTGGCCT 61.615 57.895 3.32 0.00 34.45 5.19
2861 3152 2.044053 TAGCTGCATGGGTTGGCC 60.044 61.111 1.02 0.00 0.00 5.36
2862 3153 2.418083 GGTAGCTGCATGGGTTGGC 61.418 63.158 3.61 0.00 0.00 4.52
2863 3154 0.323725 AAGGTAGCTGCATGGGTTGG 60.324 55.000 3.61 0.00 0.00 3.77
2864 3155 1.098050 GAAGGTAGCTGCATGGGTTG 58.902 55.000 3.61 0.00 0.00 3.77
2865 3156 0.698238 TGAAGGTAGCTGCATGGGTT 59.302 50.000 3.61 0.00 0.00 4.11
2866 3157 0.035056 GTGAAGGTAGCTGCATGGGT 60.035 55.000 5.75 0.00 0.00 4.51
2867 3158 0.749454 GGTGAAGGTAGCTGCATGGG 60.749 60.000 5.75 0.00 0.00 4.00
2868 3159 1.091771 CGGTGAAGGTAGCTGCATGG 61.092 60.000 5.75 0.00 0.00 3.66
2869 3160 1.091771 CCGGTGAAGGTAGCTGCATG 61.092 60.000 5.75 2.08 0.00 4.06
2870 3161 1.221840 CCGGTGAAGGTAGCTGCAT 59.778 57.895 5.75 0.00 0.00 3.96
2871 3162 2.662596 CCGGTGAAGGTAGCTGCA 59.337 61.111 3.61 0.00 0.00 4.41
2872 3163 2.804828 AAGCCGGTGAAGGTAGCTGC 62.805 60.000 1.90 0.00 33.18 5.25
2873 3164 0.321653 AAAGCCGGTGAAGGTAGCTG 60.322 55.000 1.90 0.00 33.18 4.24
2874 3165 0.321653 CAAAGCCGGTGAAGGTAGCT 60.322 55.000 1.90 0.00 34.64 3.32
2875 3166 1.305930 CCAAAGCCGGTGAAGGTAGC 61.306 60.000 1.90 0.00 0.00 3.58
2876 3167 0.323629 TCCAAAGCCGGTGAAGGTAG 59.676 55.000 1.90 0.00 0.00 3.18
2877 3168 0.323629 CTCCAAAGCCGGTGAAGGTA 59.676 55.000 1.90 0.00 0.00 3.08
2878 3169 1.073199 CTCCAAAGCCGGTGAAGGT 59.927 57.895 1.90 0.00 0.00 3.50
2879 3170 0.955919 GACTCCAAAGCCGGTGAAGG 60.956 60.000 1.90 0.44 0.00 3.46
2880 3171 0.250295 TGACTCCAAAGCCGGTGAAG 60.250 55.000 1.90 0.00 0.00 3.02
2881 3172 0.534203 GTGACTCCAAAGCCGGTGAA 60.534 55.000 1.90 0.00 0.00 3.18
2882 3173 1.070786 GTGACTCCAAAGCCGGTGA 59.929 57.895 1.90 0.00 0.00 4.02
2883 3174 1.966451 GGTGACTCCAAAGCCGGTG 60.966 63.158 1.90 0.00 35.97 4.94
2884 3175 2.430367 GGTGACTCCAAAGCCGGT 59.570 61.111 1.90 0.00 35.97 5.28
2885 3176 2.429930 TGGTGACTCCAAAGCCGG 59.570 61.111 0.00 0.00 44.12 6.13
2936 3227 9.643652 GACAAACAAATGCGAATTTGAAAAATA 57.356 25.926 31.21 0.00 42.47 1.40
2937 3228 8.180267 TGACAAACAAATGCGAATTTGAAAAAT 58.820 25.926 31.21 14.43 42.47 1.82
2938 3229 7.521529 TGACAAACAAATGCGAATTTGAAAAA 58.478 26.923 31.21 11.44 42.47 1.94
2939 3230 7.065216 TGACAAACAAATGCGAATTTGAAAA 57.935 28.000 31.21 10.53 42.47 2.29
2940 3231 6.653273 TGACAAACAAATGCGAATTTGAAA 57.347 29.167 31.21 9.92 42.47 2.69
2941 3232 6.653273 TTGACAAACAAATGCGAATTTGAA 57.347 29.167 31.21 13.74 42.47 2.69
2942 3233 6.653273 TTTGACAAACAAATGCGAATTTGA 57.347 29.167 31.21 8.54 42.57 2.69
3037 3328 9.036671 ACGAATTTTGAAAATGGTCGTATTTTT 57.963 25.926 21.76 3.99 39.60 1.94
3038 3329 8.582433 ACGAATTTTGAAAATGGTCGTATTTT 57.418 26.923 21.76 4.54 41.55 1.82
3039 3330 9.337091 CTACGAATTTTGAAAATGGTCGTATTT 57.663 29.630 25.28 11.60 40.47 1.40
3040 3331 8.723311 TCTACGAATTTTGAAAATGGTCGTATT 58.277 29.630 25.28 11.84 40.47 1.89
3041 3332 8.173130 GTCTACGAATTTTGAAAATGGTCGTAT 58.827 33.333 25.28 12.34 40.47 3.06
3042 3333 7.385752 AGTCTACGAATTTTGAAAATGGTCGTA 59.614 33.333 24.31 24.31 40.40 3.43
3043 3334 6.204108 AGTCTACGAATTTTGAAAATGGTCGT 59.796 34.615 24.58 24.58 42.35 4.34
3044 3335 6.599437 AGTCTACGAATTTTGAAAATGGTCG 58.401 36.000 18.03 18.03 0.00 4.79
3045 3336 8.797266 AAAGTCTACGAATTTTGAAAATGGTC 57.203 30.769 3.62 0.00 0.00 4.02
3046 3337 9.594478 AAAAAGTCTACGAATTTTGAAAATGGT 57.406 25.926 3.62 8.12 38.56 3.55


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

AutoCloner maintained by Alex Coulton.