Multiple sequence alignment - TraesCS4B01G180300

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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 TraesCS4B01G180300 chr4B 100.000 5977 0 0 1 5977 394620298 394626274 0.000000e+00 11038.0
1 TraesCS4B01G180300 chr4B 86.186 970 110 12 48 1005 615825451 615826408 0.000000e+00 1027.0
2 TraesCS4B01G180300 chr4B 92.188 64 1 4 1 64 423382280 423382221 2.970000e-13 87.9
3 TraesCS4B01G180300 chr4D 90.536 2071 129 28 3406 5461 317598885 317600903 0.000000e+00 2676.0
4 TraesCS4B01G180300 chr4D 89.157 1328 64 38 974 2269 317541965 317543244 0.000000e+00 1581.0
5 TraesCS4B01G180300 chr4A 87.405 2374 196 48 3138 5461 157210699 157208379 0.000000e+00 2632.0
6 TraesCS4B01G180300 chr4A 90.350 1171 61 20 974 2113 157318278 157317129 0.000000e+00 1489.0
7 TraesCS4B01G180300 chr4A 90.063 473 43 3 2613 3083 157211189 157210719 1.420000e-170 610.0
8 TraesCS4B01G180300 chr4A 89.765 469 38 7 2107 2571 157211820 157211358 5.160000e-165 592.0
9 TraesCS4B01G180300 chr3A 94.409 930 52 0 48 977 671758923 671759852 0.000000e+00 1430.0
10 TraesCS4B01G180300 chr3A 93.117 494 29 4 5488 5977 596750299 596749807 0.000000e+00 719.0
11 TraesCS4B01G180300 chr3A 79.213 356 59 11 4307 4654 737302868 737302520 3.600000e-57 233.0
12 TraesCS4B01G180300 chr2B 94.498 927 51 0 47 973 29192458 29191532 0.000000e+00 1430.0
13 TraesCS4B01G180300 chr2B 91.189 942 80 3 44 983 137929054 137928114 0.000000e+00 1277.0
14 TraesCS4B01G180300 chr2B 80.420 286 47 8 4019 4301 659788866 659788587 6.070000e-50 209.0
15 TraesCS4B01G180300 chr2B 75.532 282 47 17 4024 4298 793334469 793334735 1.050000e-22 119.0
16 TraesCS4B01G180300 chr2B 86.747 83 6 4 1 83 678352673 678352750 2.970000e-13 87.9
17 TraesCS4B01G180300 chr7B 91.793 926 76 0 48 973 680121311 680122236 0.000000e+00 1290.0
18 TraesCS4B01G180300 chr7B 95.540 426 19 0 47 472 730126300 730125875 0.000000e+00 682.0
19 TraesCS4B01G180300 chr7B 94.159 428 15 2 547 973 730125555 730125137 1.400000e-180 643.0
20 TraesCS4B01G180300 chr7B 88.368 533 41 15 5461 5977 64285994 64285467 6.580000e-174 621.0
21 TraesCS4B01G180300 chr7B 75.364 1169 202 37 3172 4301 179916070 179917191 9.010000e-133 484.0
22 TraesCS4B01G180300 chr2A 89.860 927 92 2 48 973 762611862 762610937 0.000000e+00 1190.0
23 TraesCS4B01G180300 chr2A 94.012 501 26 4 5480 5977 9361931 9361432 0.000000e+00 756.0
24 TraesCS4B01G180300 chr2A 91.617 501 29 7 5480 5977 12259271 12258781 0.000000e+00 680.0
25 TraesCS4B01G180300 chr2A 76.709 468 81 22 3855 4301 677479672 677480132 1.000000e-57 235.0
26 TraesCS4B01G180300 chr2A 96.491 57 1 1 4 59 24587300 24587356 6.380000e-15 93.5
27 TraesCS4B01G180300 chr2A 96.491 57 1 1 4 59 24616684 24616740 6.380000e-15 93.5
28 TraesCS4B01G180300 chr7A 88.639 933 104 2 48 979 204182224 204181293 0.000000e+00 1134.0
29 TraesCS4B01G180300 chr7A 90.688 494 37 5 5488 5977 80495859 80495371 0.000000e+00 649.0
30 TraesCS4B01G180300 chr7A 93.750 64 3 1 1 63 637899403 637899466 1.770000e-15 95.3
31 TraesCS4B01G180300 chr6B 83.531 929 145 5 48 972 617164735 617165659 0.000000e+00 861.0
32 TraesCS4B01G180300 chr6B 83.969 892 137 4 48 939 457871695 457872580 0.000000e+00 850.0
33 TraesCS4B01G180300 chr6B 86.739 641 83 2 48 688 118977250 118977888 0.000000e+00 712.0
34 TraesCS4B01G180300 chr2D 96.000 500 14 4 5480 5977 534284613 534285108 0.000000e+00 808.0
35 TraesCS4B01G180300 chr2D 79.783 277 49 6 4019 4293 553932442 553932171 1.700000e-45 195.0
36 TraesCS4B01G180300 chr5A 92.617 447 25 4 5488 5930 638765051 638765493 2.350000e-178 636.0
37 TraesCS4B01G180300 chr5A 98.148 54 1 0 1 54 214038457 214038404 1.770000e-15 95.3
38 TraesCS4B01G180300 chr7D 91.886 456 23 12 5531 5977 18019040 18018590 5.090000e-175 625.0
39 TraesCS4B01G180300 chr7D 75.743 404 75 18 3893 4282 64680769 64680375 1.320000e-41 182.0
40 TraesCS4B01G180300 chr1B 87.643 526 40 22 5461 5977 1934401 1934910 6.670000e-164 588.0
41 TraesCS4B01G180300 chr6D 71.354 1337 265 69 3024 4296 439803431 439802149 7.740000e-59 239.0
42 TraesCS4B01G180300 chr3B 76.984 378 71 13 4293 4662 813985800 813985431 1.020000e-47 202.0
43 TraesCS4B01G180300 chr3B 75.792 442 79 13 3748 4166 813999717 813999281 1.310000e-46 198.0
44 TraesCS4B01G180300 chr3B 80.992 121 23 0 3435 3555 814000278 814000158 4.930000e-16 97.1
45 TraesCS4B01G180300 chr3B 100.000 50 0 0 1 50 464379971 464380020 6.380000e-15 93.5
46 TraesCS4B01G180300 chr6A 72.594 748 152 32 3570 4293 526955819 526956537 4.730000e-46 196.0
47 TraesCS4B01G180300 chr5D 85.567 97 13 1 3745 3841 244149448 244149543 3.810000e-17 100.0
48 TraesCS4B01G180300 chr5B 98.148 54 1 0 1 54 199031789 199031842 1.770000e-15 95.3
49 TraesCS4B01G180300 chr1A 98.182 55 0 1 1 54 24072831 24072885 1.770000e-15 95.3


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 TraesCS4B01G180300 chr4B 394620298 394626274 5976 False 11038.0 11038 100.000000 1 5977 1 chr4B.!!$F1 5976
1 TraesCS4B01G180300 chr4B 615825451 615826408 957 False 1027.0 1027 86.186000 48 1005 1 chr4B.!!$F2 957
2 TraesCS4B01G180300 chr4D 317598885 317600903 2018 False 2676.0 2676 90.536000 3406 5461 1 chr4D.!!$F2 2055
3 TraesCS4B01G180300 chr4D 317541965 317543244 1279 False 1581.0 1581 89.157000 974 2269 1 chr4D.!!$F1 1295
4 TraesCS4B01G180300 chr4A 157317129 157318278 1149 True 1489.0 1489 90.350000 974 2113 1 chr4A.!!$R1 1139
5 TraesCS4B01G180300 chr4A 157208379 157211820 3441 True 1278.0 2632 89.077667 2107 5461 3 chr4A.!!$R2 3354
6 TraesCS4B01G180300 chr3A 671758923 671759852 929 False 1430.0 1430 94.409000 48 977 1 chr3A.!!$F1 929
7 TraesCS4B01G180300 chr2B 29191532 29192458 926 True 1430.0 1430 94.498000 47 973 1 chr2B.!!$R1 926
8 TraesCS4B01G180300 chr2B 137928114 137929054 940 True 1277.0 1277 91.189000 44 983 1 chr2B.!!$R2 939
9 TraesCS4B01G180300 chr7B 680121311 680122236 925 False 1290.0 1290 91.793000 48 973 1 chr7B.!!$F2 925
10 TraesCS4B01G180300 chr7B 730125137 730126300 1163 True 662.5 682 94.849500 47 973 2 chr7B.!!$R2 926
11 TraesCS4B01G180300 chr7B 64285467 64285994 527 True 621.0 621 88.368000 5461 5977 1 chr7B.!!$R1 516
12 TraesCS4B01G180300 chr7B 179916070 179917191 1121 False 484.0 484 75.364000 3172 4301 1 chr7B.!!$F1 1129
13 TraesCS4B01G180300 chr2A 762610937 762611862 925 True 1190.0 1190 89.860000 48 973 1 chr2A.!!$R3 925
14 TraesCS4B01G180300 chr7A 204181293 204182224 931 True 1134.0 1134 88.639000 48 979 1 chr7A.!!$R2 931
15 TraesCS4B01G180300 chr6B 617164735 617165659 924 False 861.0 861 83.531000 48 972 1 chr6B.!!$F3 924
16 TraesCS4B01G180300 chr6B 457871695 457872580 885 False 850.0 850 83.969000 48 939 1 chr6B.!!$F2 891
17 TraesCS4B01G180300 chr6B 118977250 118977888 638 False 712.0 712 86.739000 48 688 1 chr6B.!!$F1 640
18 TraesCS4B01G180300 chr1B 1934401 1934910 509 False 588.0 588 87.643000 5461 5977 1 chr1B.!!$F1 516
19 TraesCS4B01G180300 chr6D 439802149 439803431 1282 True 239.0 239 71.354000 3024 4296 1 chr6D.!!$R1 1272

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
670 917 0.755698 CACTAGCTCTAGCCCGGGAA 60.756 60.0 29.31 10.78 43.38 3.97 F
2555 2862 0.529773 GTGCAAGTCAGTCGGTCACA 60.530 55.0 0.00 0.00 0.00 3.58 F
2949 3397 0.179029 CCCACCACAACCTTCGTCTT 60.179 55.0 0.00 0.00 0.00 3.01 F
4544 5084 0.409876 TGGACAGCCAGACTAGGACT 59.590 55.0 0.00 0.00 39.92 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 3039 0.307760 CACACGCTTCGCTCCTTTTT 59.692 50.0 0.00 0.0 0.00 1.94 R
4522 5062 0.179062 CCTAGTCTGGCTGTCCATGC 60.179 60.0 0.00 0.0 42.51 4.06 R
4765 5306 0.662970 CAACGCGGTTCACCAAATGG 60.663 55.0 12.47 0.0 42.17 3.16 R
5515 6070 0.108615 CTACTCCTCCGGCTGTGTTG 60.109 60.0 0.00 0.0 0.00 3.33 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
45 46 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
55 56 4.452455 GCATATTTCCAACACTCTATCCCG 59.548 45.833 0.00 0.00 0.00 5.14
88 89 3.708121 TGAGACATGACAGACATATGGCT 59.292 43.478 4.82 4.82 42.65 4.75
135 136 1.496001 AGCAATGGAGGATACATGGCA 59.504 47.619 4.21 0.00 45.61 4.92
191 192 2.439507 GTTTGGGCTCTGGAGGATGATA 59.560 50.000 0.00 0.00 0.00 2.15
358 359 1.561542 GAGGAGGAATTTCAGAGCCCA 59.438 52.381 0.00 0.00 0.00 5.36
542 544 2.979678 ACCTTAGGAGACAAAGGAGCAA 59.020 45.455 4.77 0.00 44.27 3.91
634 881 2.747855 CCGGCAAGTCTTGAGGCC 60.748 66.667 16.99 9.38 42.98 5.19
670 917 0.755698 CACTAGCTCTAGCCCGGGAA 60.756 60.000 29.31 10.78 43.38 3.97
780 1039 7.037514 TCCTATCCTTCGAGAGATCCATACTAA 60.038 40.741 2.82 0.00 41.60 2.24
820 1079 5.040635 TCTGTTGATTTCCGTTTTGAAAGC 58.959 37.500 0.00 0.00 40.21 3.51
955 1223 9.974980 GTTGTGAACTTTGAATAAAATCCCTAA 57.025 29.630 0.00 0.00 0.00 2.69
1563 1842 5.440234 CTAGTACTACTAGCCACCATGTG 57.560 47.826 9.82 0.00 41.36 3.21
1636 1922 5.819379 TGATTCTGCCAAGACATAAGACATC 59.181 40.000 0.00 0.00 29.98 3.06
1881 2184 2.247358 GGGCTGACTTCAATTTTGGGA 58.753 47.619 0.00 0.00 0.00 4.37
1882 2185 2.632512 GGGCTGACTTCAATTTTGGGAA 59.367 45.455 0.00 0.00 0.00 3.97
1993 2296 1.067295 TTCCATGTGGAGCTGGAGTT 58.933 50.000 0.00 0.00 46.36 3.01
1998 2301 1.032014 TGTGGAGCTGGAGTTTTTGC 58.968 50.000 0.00 0.00 0.00 3.68
2014 2317 7.224557 GGAGTTTTTGCATATTTGTGTTGTTCT 59.775 33.333 0.00 0.00 0.00 3.01
2038 2341 0.762418 TGGTAGGTGGTTGTGGAGTG 59.238 55.000 0.00 0.00 0.00 3.51
2043 2346 0.605589 GGTGGTTGTGGAGTGGTAGC 60.606 60.000 0.00 0.00 0.00 3.58
2059 2362 2.593257 GTAGCACAGTCGTACAAGTCC 58.407 52.381 0.00 0.00 0.00 3.85
2085 2388 4.803098 TGGAAGGTTAGAGCAACTCTAC 57.197 45.455 3.84 1.00 41.99 2.59
2088 2391 4.496360 GAAGGTTAGAGCAACTCTACCAC 58.504 47.826 17.70 10.12 41.99 4.16
2089 2392 2.492484 AGGTTAGAGCAACTCTACCACG 59.508 50.000 17.70 0.00 41.99 4.94
2104 2407 1.736645 CACGGTCGTTGTAGGGCTG 60.737 63.158 0.00 0.00 0.00 4.85
2122 2425 4.382901 GGGCTGCAATGGTCAAAATAATCA 60.383 41.667 0.50 0.00 0.00 2.57
2178 2481 1.560923 CAAAGTCCTCGTATGGCTCG 58.439 55.000 0.00 0.00 0.00 5.03
2204 2508 4.703093 TCTCGTCGCCATATATTATGGACA 59.297 41.667 16.01 0.39 41.64 4.02
2206 2510 5.972935 TCGTCGCCATATATTATGGACATT 58.027 37.500 16.01 0.00 41.64 2.71
2253 2557 4.297664 TCCATATATGAAGGCTAGGGAGGA 59.702 45.833 14.54 0.00 0.00 3.71
2262 2566 1.133136 GGCTAGGGAGGACCAGTATGA 60.133 57.143 0.00 0.00 43.89 2.15
2282 2586 2.520536 GCTCGCTCCATACCCCCAT 61.521 63.158 0.00 0.00 0.00 4.00
2283 2587 1.372683 CTCGCTCCATACCCCCATG 59.627 63.158 0.00 0.00 0.00 3.66
2284 2588 2.116983 CTCGCTCCATACCCCCATGG 62.117 65.000 4.14 4.14 45.93 3.66
2327 2631 1.406614 CCTTCTTTCTCCTCGCAGCAT 60.407 52.381 0.00 0.00 0.00 3.79
2334 2638 1.153107 TCCTCGCAGCATGAATGGG 60.153 57.895 0.00 2.76 39.69 4.00
2353 2659 1.199327 GGTTTTGAAGCTACGGCCTTC 59.801 52.381 0.00 0.00 39.73 3.46
2357 2663 1.295423 GAAGCTACGGCCTTCCACA 59.705 57.895 0.00 0.00 39.73 4.17
2382 2688 2.184579 GGCGACAGACACCTAGGC 59.815 66.667 9.30 0.00 0.00 3.93
2388 2694 2.223829 CGACAGACACCTAGGCCATTAG 60.224 54.545 9.30 0.00 0.00 1.73
2389 2695 3.031736 GACAGACACCTAGGCCATTAGA 58.968 50.000 9.30 0.00 0.00 2.10
2433 2739 1.228124 GTGCAACCCTAGCCACACA 60.228 57.895 0.00 0.00 0.00 3.72
2513 2819 1.586154 GGAACACTCACCAATGGCGG 61.586 60.000 0.00 0.00 0.00 6.13
2555 2862 0.529773 GTGCAAGTCAGTCGGTCACA 60.530 55.000 0.00 0.00 0.00 3.58
2577 2884 4.343581 CGACATATGGCGGTGAGG 57.656 61.111 23.66 0.00 44.21 3.86
2578 2885 1.956170 CGACATATGGCGGTGAGGC 60.956 63.158 23.66 0.00 44.21 4.70
2593 3039 5.350365 GCGGTGAGGCAATTAATATCGATTA 59.650 40.000 1.71 0.00 0.00 1.75
2602 3048 9.129209 GGCAATTAATATCGATTAAAAAGGAGC 57.871 33.333 1.71 0.00 40.17 4.70
2603 3049 8.840867 GCAATTAATATCGATTAAAAAGGAGCG 58.159 33.333 1.71 0.00 40.17 5.03
2607 3053 8.280497 TTAATATCGATTAAAAAGGAGCGAAGC 58.720 33.333 1.71 0.00 43.46 3.86
2656 3102 5.163519 ACTCCATTTCTTTGTTGTGGAACTG 60.164 40.000 0.00 0.00 38.41 3.16
2658 3104 5.888724 TCCATTTCTTTGTTGTGGAACTGTA 59.111 36.000 0.00 0.00 36.12 2.74
2666 3112 2.367567 GTTGTGGAACTGTACCTCCAGA 59.632 50.000 8.32 5.37 42.41 3.86
2667 3113 2.248248 TGTGGAACTGTACCTCCAGAG 58.752 52.381 8.32 0.00 42.41 3.35
2689 3135 5.363939 AGATGATAGCTCACTTAACAAGCC 58.636 41.667 0.00 0.00 36.69 4.35
2695 3141 2.162681 CTCACTTAACAAGCCAAGGGG 58.837 52.381 0.00 0.00 37.18 4.79
2706 3152 1.971695 CCAAGGGGAACTCCAACGC 60.972 63.158 0.00 0.00 37.91 4.84
2714 3160 1.608025 GGAACTCCAACGCAGATCACA 60.608 52.381 0.00 0.00 35.64 3.58
2739 3185 8.733458 CAAGATCAGTCCTAAATGTTTGAATCA 58.267 33.333 0.00 0.00 0.00 2.57
2742 3188 7.672983 TCAGTCCTAAATGTTTGAATCAGAC 57.327 36.000 0.00 0.00 0.00 3.51
2749 3195 3.469008 TGTTTGAATCAGACTGTCCGT 57.531 42.857 3.76 0.00 0.00 4.69
2767 3215 1.604947 CGTGCATTTTGCCATCCAACA 60.605 47.619 0.00 0.00 44.23 3.33
2786 3234 2.103941 ACACCGGGCATCAAATTTGTTT 59.896 40.909 17.47 4.52 0.00 2.83
2792 3240 4.321601 CGGGCATCAAATTTGTTTAGACCA 60.322 41.667 17.47 0.00 0.00 4.02
2795 3243 5.863935 GGCATCAAATTTGTTTAGACCACTC 59.136 40.000 17.47 0.00 0.00 3.51
2801 3249 9.219603 TCAAATTTGTTTAGACCACTCTAGATG 57.780 33.333 17.47 0.00 30.31 2.90
2818 3266 8.538701 ACTCTAGATGTCTGAAATCTCACAAAT 58.461 33.333 13.54 0.00 35.92 2.32
2820 3268 6.659361 AGATGTCTGAAATCTCACAAATCG 57.341 37.500 4.45 0.00 27.78 3.34
2825 3273 6.080406 GTCTGAAATCTCACAAATCGAAACC 58.920 40.000 0.00 0.00 0.00 3.27
2828 3276 6.437928 TGAAATCTCACAAATCGAAACCAAG 58.562 36.000 0.00 0.00 0.00 3.61
2856 3304 1.009335 GGTTTGCGGACGTCCAAAC 60.009 57.895 32.80 30.74 46.11 2.93
2859 3307 0.748729 TTTGCGGACGTCCAAACCTT 60.749 50.000 32.80 0.00 35.14 3.50
2866 3314 1.453148 GACGTCCAAACCTTCGTTACG 59.547 52.381 3.51 0.00 37.44 3.18
2868 3316 1.860326 CGTCCAAACCTTCGTTACGTT 59.140 47.619 4.24 0.00 30.43 3.99
2906 3354 1.198094 CCCATCCAAAAACCCCACCC 61.198 60.000 0.00 0.00 0.00 4.61
2907 3355 1.540435 CCATCCAAAAACCCCACCCG 61.540 60.000 0.00 0.00 0.00 5.28
2946 3394 0.476771 ATTCCCACCACAACCTTCGT 59.523 50.000 0.00 0.00 0.00 3.85
2949 3397 0.179029 CCCACCACAACCTTCGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
2953 3401 2.878406 CACCACAACCTTCGTCTTGATT 59.122 45.455 0.00 0.00 0.00 2.57
2960 3408 2.368875 ACCTTCGTCTTGATTGTCACCT 59.631 45.455 0.00 0.00 0.00 4.00
2977 3425 1.538666 CTTCCCCCACCCCATCATC 59.461 63.158 0.00 0.00 0.00 2.92
3105 3567 2.751166 CCAGAAGGCGAAGAAGAAGA 57.249 50.000 0.00 0.00 0.00 2.87
3106 3568 3.045601 CCAGAAGGCGAAGAAGAAGAA 57.954 47.619 0.00 0.00 0.00 2.52
3108 3570 3.556004 CCAGAAGGCGAAGAAGAAGAAGT 60.556 47.826 0.00 0.00 0.00 3.01
3109 3571 4.322049 CCAGAAGGCGAAGAAGAAGAAGTA 60.322 45.833 0.00 0.00 0.00 2.24
3110 3572 4.862018 CAGAAGGCGAAGAAGAAGAAGTAG 59.138 45.833 0.00 0.00 0.00 2.57
3111 3573 4.767928 AGAAGGCGAAGAAGAAGAAGTAGA 59.232 41.667 0.00 0.00 0.00 2.59
3112 3574 5.244178 AGAAGGCGAAGAAGAAGAAGTAGAA 59.756 40.000 0.00 0.00 0.00 2.10
3113 3575 5.066968 AGGCGAAGAAGAAGAAGTAGAAG 57.933 43.478 0.00 0.00 0.00 2.85
3114 3576 4.767928 AGGCGAAGAAGAAGAAGTAGAAGA 59.232 41.667 0.00 0.00 0.00 2.87
3115 3577 5.244178 AGGCGAAGAAGAAGAAGTAGAAGAA 59.756 40.000 0.00 0.00 0.00 2.52
3116 3578 5.575218 GGCGAAGAAGAAGAAGTAGAAGAAG 59.425 44.000 0.00 0.00 0.00 2.85
3117 3579 6.383415 GCGAAGAAGAAGAAGTAGAAGAAGA 58.617 40.000 0.00 0.00 0.00 2.87
3118 3580 6.864165 GCGAAGAAGAAGAAGTAGAAGAAGAA 59.136 38.462 0.00 0.00 0.00 2.52
3119 3581 7.061789 GCGAAGAAGAAGAAGTAGAAGAAGAAG 59.938 40.741 0.00 0.00 0.00 2.85
3120 3582 7.540745 CGAAGAAGAAGAAGTAGAAGAAGAAGG 59.459 40.741 0.00 0.00 0.00 3.46
3121 3583 6.697395 AGAAGAAGAAGTAGAAGAAGAAGGC 58.303 40.000 0.00 0.00 0.00 4.35
3122 3584 5.066968 AGAAGAAGTAGAAGAAGAAGGCG 57.933 43.478 0.00 0.00 0.00 5.52
3124 3586 2.498078 AGAAGTAGAAGAAGAAGGCGGG 59.502 50.000 0.00 0.00 0.00 6.13
3170 3632 1.134220 AGACCTCGTCCAACAAAGCAA 60.134 47.619 0.00 0.00 32.18 3.91
3221 3684 2.927856 ATGTGGTCGTCCCAGCCA 60.928 61.111 0.00 0.00 46.45 4.75
3234 3697 2.689034 AGCCACAGCCTCCCTACC 60.689 66.667 0.00 0.00 41.25 3.18
3308 3782 1.107114 CACTCACCTCTAGCCATCGT 58.893 55.000 0.00 0.00 0.00 3.73
3319 3793 4.832248 TCTAGCCATCGTGTCTCATTTTT 58.168 39.130 0.00 0.00 0.00 1.94
3333 3807 2.473609 TCATTTTTCGTCGACCTCAACG 59.526 45.455 10.58 0.00 40.17 4.10
3400 3876 2.033448 GGCCGATTGTGGACCACA 59.967 61.111 23.72 23.72 43.02 4.17
3498 3974 9.324269 ATGATGAACATTATCCATGACGGAGGT 62.324 40.741 0.00 0.00 41.26 3.85
3675 4171 0.537143 TGGTGTGTGAGGCATGGTTC 60.537 55.000 0.00 0.00 0.00 3.62
3716 4212 2.437895 GGGTACGGAGCAAAGGGC 60.438 66.667 0.00 0.00 45.30 5.19
3729 4225 1.033202 AAAGGGCCGTGACGTTTTGT 61.033 50.000 3.64 0.00 0.00 2.83
3730 4226 1.033202 AAGGGCCGTGACGTTTTGTT 61.033 50.000 3.64 0.00 0.00 2.83
3872 4391 4.676723 GCTGCTACAAACAAGTGAAAACCA 60.677 41.667 0.00 0.00 0.00 3.67
3905 4424 1.202417 GCGTCGGAATCCAAGATCTCA 60.202 52.381 0.00 0.00 0.00 3.27
3973 4495 5.590530 TTAAATGTTGCACCTTGTTGACT 57.409 34.783 0.00 0.00 0.00 3.41
3996 4518 3.295093 TCCATTGTGTTTCTTTGCCAGA 58.705 40.909 0.00 0.00 0.00 3.86
4016 4548 1.898938 TCGTACCTGCGTTCGTTATG 58.101 50.000 0.00 0.00 34.69 1.90
4105 4637 7.412346 GCAAGTGGATCGACATGATTGTATATC 60.412 40.741 15.99 0.00 37.47 1.63
4170 4703 1.675552 CCGTTCAACACAAGAAGGGT 58.324 50.000 0.00 0.00 42.88 4.34
4246 4784 1.590147 GAGAAACGAGAAGGGGCGA 59.410 57.895 0.00 0.00 0.00 5.54
4318 4857 2.982470 GCAAAGAGGTTTTGCATCTTCG 59.018 45.455 17.04 0.00 46.13 3.79
4386 4925 1.222936 CAAGGCCGCTTCAGAGGAT 59.777 57.895 0.00 0.00 37.14 3.24
4405 4944 5.841810 AGGATTTCAAAATGCTTCGTGAAA 58.158 33.333 3.91 10.94 43.34 2.69
4418 4957 3.153676 TCGTGAAAACGTCAGACTTGA 57.846 42.857 0.00 0.00 36.74 3.02
4421 4960 3.120991 CGTGAAAACGTCAGACTTGATCC 60.121 47.826 0.00 0.00 36.74 3.36
4423 4962 3.181459 TGAAAACGTCAGACTTGATCCCA 60.181 43.478 0.00 0.00 35.39 4.37
4454 4993 6.295292 GGAAAGATTGTTTGTCCAAGCCTATT 60.295 38.462 0.00 0.00 31.19 1.73
4460 5000 1.062525 GTCCAAGCCTATTTGCGCG 59.937 57.895 0.00 0.00 36.02 6.86
4489 5029 1.916697 GCGCTTCACAGAAAGGGAGC 61.917 60.000 0.00 0.00 40.58 4.70
4490 5030 1.630244 CGCTTCACAGAAAGGGAGCG 61.630 60.000 0.00 0.00 40.58 5.03
4515 5055 0.683504 GACTAGGCGAAGAGTGGGGA 60.684 60.000 0.00 0.00 0.00 4.81
4517 5057 1.123928 CTAGGCGAAGAGTGGGGATT 58.876 55.000 0.00 0.00 0.00 3.01
4522 5062 1.202348 GCGAAGAGTGGGGATTTTTGG 59.798 52.381 0.00 0.00 0.00 3.28
4544 5084 0.409876 TGGACAGCCAGACTAGGACT 59.590 55.000 0.00 0.00 39.92 3.85
4609 5149 7.614494 ACTTTGGGATTGATTGGATGTAAAAG 58.386 34.615 0.00 0.00 0.00 2.27
4612 5152 6.430864 TGGGATTGATTGGATGTAAAAGCTA 58.569 36.000 0.00 0.00 0.00 3.32
4623 5163 9.995003 TTGGATGTAAAAGCTAATTGAACATTT 57.005 25.926 0.00 0.00 30.89 2.32
4691 5232 7.265647 TGACAAATAGTAGAGAAGATCGGAG 57.734 40.000 0.00 0.00 0.00 4.63
4698 5239 1.064017 AGAGAAGATCGGAGCAGAGGT 60.064 52.381 0.00 0.00 0.00 3.85
4718 5259 2.875933 GTGGACATTTGACGACTTTGGA 59.124 45.455 0.00 0.00 0.00 3.53
4722 5263 2.878406 ACATTTGACGACTTTGGACAGG 59.122 45.455 0.00 0.00 0.00 4.00
4765 5306 1.062587 CCGCGAACATTTGAGGATGTC 59.937 52.381 8.23 0.00 39.25 3.06
4803 5344 1.711375 TGTATTTGCCCTAACCCCACA 59.289 47.619 0.00 0.00 0.00 4.17
4804 5345 2.110188 TGTATTTGCCCTAACCCCACAA 59.890 45.455 0.00 0.00 0.00 3.33
4811 5352 1.003839 CTAACCCCACAAGCAGCGA 60.004 57.895 0.00 0.00 0.00 4.93
4835 5386 1.098050 GCCAAACAGCTCCCACATAG 58.902 55.000 0.00 0.00 0.00 2.23
4895 5446 1.374190 CCCAGCAGTTGAGCACTCT 59.626 57.895 0.00 0.00 36.85 3.24
4898 5449 3.261933 GCAGTTGAGCACTCTGCC 58.738 61.111 16.03 4.29 46.52 4.85
4908 5459 1.001406 AGCACTCTGCCTGTCAACTAC 59.999 52.381 0.00 0.00 46.52 2.73
4984 5535 0.108615 ATCAGCGTGTCACTGTAGGC 60.109 55.000 0.65 0.00 36.50 3.93
4999 5550 1.923227 TAGGCGTCGTCTCAGCAGTG 61.923 60.000 0.73 0.00 0.00 3.66
5018 5569 3.598688 GTGGCTAGATGGAGACACGGAT 61.599 54.545 0.00 0.00 45.32 4.18
5058 5609 3.691342 CTGGAACCGGAGCGACCA 61.691 66.667 9.46 8.97 38.90 4.02
5109 5660 0.673644 CCGAGAAGAATGTTGCCGGT 60.674 55.000 1.90 0.00 0.00 5.28
5182 5737 0.393077 CCGCCGGATAAGGATGAACT 59.607 55.000 5.05 0.00 0.00 3.01
5192 5747 6.625081 CGGATAAGGATGAACTTGGTTTTTCC 60.625 42.308 0.00 0.00 31.45 3.13
5193 5748 6.437477 GGATAAGGATGAACTTGGTTTTTCCT 59.563 38.462 8.36 8.36 38.18 3.36
5194 5749 7.039011 GGATAAGGATGAACTTGGTTTTTCCTT 60.039 37.037 20.63 20.63 43.22 3.36
5195 5750 6.560003 AAGGATGAACTTGGTTTTTCCTTT 57.440 33.333 15.58 6.68 40.71 3.11
5196 5751 6.161855 AGGATGAACTTGGTTTTTCCTTTC 57.838 37.500 8.36 0.00 35.29 2.62
5197 5752 5.899547 AGGATGAACTTGGTTTTTCCTTTCT 59.100 36.000 8.36 0.00 35.29 2.52
5198 5753 6.040955 AGGATGAACTTGGTTTTTCCTTTCTC 59.959 38.462 8.36 0.00 35.29 2.87
5199 5754 6.040955 GGATGAACTTGGTTTTTCCTTTCTCT 59.959 38.462 0.00 0.00 37.07 3.10
5200 5755 7.230712 GGATGAACTTGGTTTTTCCTTTCTCTA 59.769 37.037 0.00 0.00 37.07 2.43
5201 5756 7.948034 TGAACTTGGTTTTTCCTTTCTCTAA 57.052 32.000 0.00 0.00 37.07 2.10
5202 5757 8.533569 TGAACTTGGTTTTTCCTTTCTCTAAT 57.466 30.769 0.00 0.00 37.07 1.73
5203 5758 8.630037 TGAACTTGGTTTTTCCTTTCTCTAATC 58.370 33.333 0.00 0.00 37.07 1.75
5204 5759 8.533569 AACTTGGTTTTTCCTTTCTCTAATCA 57.466 30.769 0.00 0.00 37.07 2.57
5205 5760 8.712228 ACTTGGTTTTTCCTTTCTCTAATCAT 57.288 30.769 0.00 0.00 37.07 2.45
5206 5761 8.579863 ACTTGGTTTTTCCTTTCTCTAATCATG 58.420 33.333 0.00 0.00 37.07 3.07
5207 5762 7.466746 TGGTTTTTCCTTTCTCTAATCATGG 57.533 36.000 0.00 0.00 37.07 3.66
5208 5763 7.010160 TGGTTTTTCCTTTCTCTAATCATGGT 58.990 34.615 0.00 0.00 37.07 3.55
5209 5764 7.508977 TGGTTTTTCCTTTCTCTAATCATGGTT 59.491 33.333 0.00 0.00 37.07 3.67
5251 5806 4.642437 AGAGATTCTTCTATGTCGCTGTCA 59.358 41.667 0.00 0.00 30.30 3.58
5252 5807 4.930963 AGATTCTTCTATGTCGCTGTCAG 58.069 43.478 0.00 0.00 0.00 3.51
5296 5851 2.749541 CGTAGCATTGGAGACGCAA 58.250 52.632 0.00 0.00 0.00 4.85
5297 5852 1.290203 CGTAGCATTGGAGACGCAAT 58.710 50.000 0.00 0.00 0.00 3.56
5304 5859 4.037690 GCATTGGAGACGCAATATCAAAC 58.962 43.478 0.00 0.00 0.00 2.93
5309 5864 3.485877 GGAGACGCAATATCAAACAGCAC 60.486 47.826 0.00 0.00 0.00 4.40
5324 5879 0.546122 AGCACCATATGAGGGCGAAA 59.454 50.000 3.65 0.00 32.32 3.46
5426 5981 4.641645 CTGTGGGGCGCTTGTGGA 62.642 66.667 7.64 0.00 0.00 4.02
5474 6029 6.040166 GGCTATCAATCCTGTCAAACATGATT 59.960 38.462 0.00 5.19 41.82 2.57
5475 6030 7.137426 GCTATCAATCCTGTCAAACATGATTC 58.863 38.462 0.00 0.00 40.05 2.52
5476 6031 7.201758 GCTATCAATCCTGTCAAACATGATTCA 60.202 37.037 0.00 0.00 40.05 2.57
5477 6032 6.505044 TCAATCCTGTCAAACATGATTCAG 57.495 37.500 0.00 0.00 40.05 3.02
5479 6034 6.491062 TCAATCCTGTCAAACATGATTCAGTT 59.509 34.615 0.00 0.00 40.05 3.16
5481 6036 4.022935 TCCTGTCAAACATGATTCAGTTGC 60.023 41.667 0.00 0.00 0.00 4.17
5482 6037 4.261698 CCTGTCAAACATGATTCAGTTGCA 60.262 41.667 0.00 0.00 0.00 4.08
5483 6038 4.862350 TGTCAAACATGATTCAGTTGCAG 58.138 39.130 0.00 0.00 0.00 4.41
5493 6048 0.179070 TCAGTTGCAGGCGTGTACAA 60.179 50.000 8.40 1.91 0.00 2.41
5504 6059 2.466846 GCGTGTACAAGGCGTATACAT 58.533 47.619 10.87 0.00 41.07 2.29
5506 6061 3.697982 CGTGTACAAGGCGTATACATGA 58.302 45.455 5.30 0.00 41.07 3.07
5509 6064 5.345702 GTGTACAAGGCGTATACATGAAGA 58.654 41.667 0.00 0.00 40.80 2.87
5512 6067 6.533723 TGTACAAGGCGTATACATGAAGAAAG 59.466 38.462 0.00 0.00 31.20 2.62
5514 6069 6.349300 ACAAGGCGTATACATGAAGAAAGAT 58.651 36.000 0.00 0.00 0.00 2.40
5515 6070 6.480320 ACAAGGCGTATACATGAAGAAAGATC 59.520 38.462 0.00 0.00 0.00 2.75
5516 6071 6.161855 AGGCGTATACATGAAGAAAGATCA 57.838 37.500 0.00 0.00 0.00 2.92
5521 6087 7.201522 GCGTATACATGAAGAAAGATCAACACA 60.202 37.037 0.00 0.00 0.00 3.72
5522 6088 8.323854 CGTATACATGAAGAAAGATCAACACAG 58.676 37.037 0.00 0.00 0.00 3.66
5548 6114 7.093322 CGGAGGAGTAGTTAGTTAGCTAAAA 57.907 40.000 7.99 0.00 38.74 1.52
5606 6173 6.748333 TTCTTCCTTTGCAAGATGTATCTG 57.252 37.500 0.00 0.00 37.19 2.90
5608 6175 6.240894 TCTTCCTTTGCAAGATGTATCTGTT 58.759 36.000 0.00 0.00 37.19 3.16
5624 6191 2.610374 TCTGTTTCAACAACCTGTACGC 59.390 45.455 0.00 0.00 38.66 4.42
5733 6306 4.077822 CAGAGCCTTCTTCTTCCACAAAT 58.922 43.478 0.00 0.00 0.00 2.32
5740 6313 5.495640 CTTCTTCTTCCACAAATCCTAGCT 58.504 41.667 0.00 0.00 0.00 3.32
5741 6314 6.352222 CCTTCTTCTTCCACAAATCCTAGCTA 60.352 42.308 0.00 0.00 0.00 3.32
5763 6336 1.442526 CCATCTCCATCAAGTGCGCC 61.443 60.000 4.18 0.00 0.00 6.53
5841 6414 1.448013 GCTCTCCCGCACCAACTAC 60.448 63.158 0.00 0.00 0.00 2.73
5844 6417 1.005394 CTCCCGCACCAACTACGTT 60.005 57.895 0.00 0.00 0.00 3.99
5845 6418 1.005867 TCCCGCACCAACTACGTTC 60.006 57.895 0.00 0.00 0.00 3.95
5872 6445 4.457496 CCCAGATCACGCCGCAGT 62.457 66.667 0.00 0.00 0.00 4.40
5967 6540 3.637273 ACCGGCAAGGAGACCACC 61.637 66.667 0.00 0.00 45.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
25 26 5.041191 AGTGTTGGAAATATGCCCTAGAG 57.959 43.478 0.00 0.00 0.00 2.43
26 27 4.721776 AGAGTGTTGGAAATATGCCCTAGA 59.278 41.667 0.00 0.00 0.00 2.43
27 28 5.041191 AGAGTGTTGGAAATATGCCCTAG 57.959 43.478 0.00 0.00 0.00 3.02
28 29 6.239887 GGATAGAGTGTTGGAAATATGCCCTA 60.240 42.308 0.00 0.00 0.00 3.53
29 30 5.456763 GGATAGAGTGTTGGAAATATGCCCT 60.457 44.000 0.00 0.00 0.00 5.19
30 31 4.762251 GGATAGAGTGTTGGAAATATGCCC 59.238 45.833 0.00 0.00 0.00 5.36
31 32 4.762251 GGGATAGAGTGTTGGAAATATGCC 59.238 45.833 0.00 0.00 0.00 4.40
32 33 4.452455 CGGGATAGAGTGTTGGAAATATGC 59.548 45.833 0.00 0.00 0.00 3.14
33 34 5.696724 GTCGGGATAGAGTGTTGGAAATATG 59.303 44.000 0.00 0.00 0.00 1.78
34 35 5.221661 GGTCGGGATAGAGTGTTGGAAATAT 60.222 44.000 0.00 0.00 0.00 1.28
35 36 4.100498 GGTCGGGATAGAGTGTTGGAAATA 59.900 45.833 0.00 0.00 0.00 1.40
36 37 3.118371 GGTCGGGATAGAGTGTTGGAAAT 60.118 47.826 0.00 0.00 0.00 2.17
37 38 2.235402 GGTCGGGATAGAGTGTTGGAAA 59.765 50.000 0.00 0.00 0.00 3.13
38 39 1.829222 GGTCGGGATAGAGTGTTGGAA 59.171 52.381 0.00 0.00 0.00 3.53
39 40 1.481871 GGTCGGGATAGAGTGTTGGA 58.518 55.000 0.00 0.00 0.00 3.53
40 41 0.102481 CGGTCGGGATAGAGTGTTGG 59.898 60.000 0.00 0.00 0.00 3.77
41 42 0.102481 CCGGTCGGGATAGAGTGTTG 59.898 60.000 0.74 0.00 38.47 3.33
42 43 1.673808 GCCGGTCGGGATAGAGTGTT 61.674 60.000 11.60 0.00 38.47 3.32
43 44 2.125961 GCCGGTCGGGATAGAGTGT 61.126 63.158 11.60 0.00 38.47 3.55
44 45 2.728817 GCCGGTCGGGATAGAGTG 59.271 66.667 11.60 0.00 38.47 3.51
45 46 2.521224 GGCCGGTCGGGATAGAGT 60.521 66.667 11.60 0.00 38.47 3.24
135 136 0.038159 GCAACTCAGTAGCGAGTGGT 60.038 55.000 1.54 0.00 45.56 4.16
191 192 8.408601 GTTTGATATCATATGCTCAACCAGTTT 58.591 33.333 6.17 0.00 0.00 2.66
358 359 6.987992 TGTTTACGAAAGACATAGTGGAAAGT 59.012 34.615 0.00 0.00 0.00 2.66
484 486 5.670485 TCACAGTTTAGCTTTGAAGTCTCA 58.330 37.500 0.00 0.00 31.58 3.27
520 522 2.567615 TGCTCCTTTGTCTCCTAAGGTC 59.432 50.000 0.00 0.00 42.23 3.85
542 544 4.948004 TCTATCACGACACACAACTCCTAT 59.052 41.667 0.00 0.00 0.00 2.57
634 881 2.278596 GCTTCGCTGCATGCATGG 60.279 61.111 27.34 15.96 43.06 3.66
670 917 5.705397 TGGTGAGATCCTGAAGATTCAAT 57.295 39.130 0.00 0.00 36.64 2.57
820 1079 6.015940 GGTGGGCCTCAAAATTATTATCTCTG 60.016 42.308 4.53 0.00 0.00 3.35
1040 1308 4.845060 CGTGTCTCTTGTTCGTACTTCTAC 59.155 45.833 0.00 0.00 0.00 2.59
1041 1309 4.612259 GCGTGTCTCTTGTTCGTACTTCTA 60.612 45.833 0.00 0.00 0.00 2.10
1042 1310 3.852572 GCGTGTCTCTTGTTCGTACTTCT 60.853 47.826 0.00 0.00 0.00 2.85
1558 1837 1.539388 TCAAAAGGCTAACCGCACATG 59.461 47.619 0.00 0.00 42.76 3.21
1563 1842 3.850122 AGAAATCAAAAGGCTAACCGC 57.150 42.857 0.00 0.00 42.76 5.68
1666 1952 9.903682 GATACGAGTGCTTACCAAATTAGTATA 57.096 33.333 0.00 0.00 0.00 1.47
1667 1953 8.639761 AGATACGAGTGCTTACCAAATTAGTAT 58.360 33.333 0.00 0.00 0.00 2.12
1683 1969 8.703604 TTTTCTCCAAGATAAAGATACGAGTG 57.296 34.615 0.00 0.00 0.00 3.51
1729 2015 0.804989 CAATTCCACTCACGCTTCCC 59.195 55.000 0.00 0.00 0.00 3.97
1955 2258 5.248640 TGGAACAAGATCCATTCTGAAGAC 58.751 41.667 0.00 0.00 44.52 3.01
2014 2317 4.105057 ACTCCACAACCACCTACCAATTAA 59.895 41.667 0.00 0.00 0.00 1.40
2038 2341 2.593257 GACTTGTACGACTGTGCTACC 58.407 52.381 0.00 0.00 0.00 3.18
2043 2346 0.313043 ACGGGACTTGTACGACTGTG 59.687 55.000 0.00 0.00 0.00 3.66
2059 2362 2.178912 TGCTCTAACCTTCCAAACGG 57.821 50.000 0.00 0.00 0.00 4.44
2085 2388 2.433664 GCCCTACAACGACCGTGG 60.434 66.667 0.00 0.00 0.00 4.94
2088 2391 2.813908 GCAGCCCTACAACGACCG 60.814 66.667 0.00 0.00 0.00 4.79
2089 2392 0.676782 ATTGCAGCCCTACAACGACC 60.677 55.000 0.00 0.00 0.00 4.79
2218 2522 4.673968 TCATATATGGAGGCTACGAGGTT 58.326 43.478 12.78 0.00 0.00 3.50
2253 2557 0.461961 GGAGCGAGCTTCATACTGGT 59.538 55.000 0.00 0.00 0.00 4.00
2262 2566 2.444256 GGGGGTATGGAGCGAGCTT 61.444 63.158 0.00 0.00 0.00 3.74
2284 2588 4.821589 CTTCCCCCTCGCGCTGAC 62.822 72.222 5.56 0.00 0.00 3.51
2286 2590 3.901797 AAACTTCCCCCTCGCGCTG 62.902 63.158 5.56 0.00 0.00 5.18
2287 2591 1.833787 TAAAACTTCCCCCTCGCGCT 61.834 55.000 5.56 0.00 0.00 5.92
2288 2592 1.376295 TAAAACTTCCCCCTCGCGC 60.376 57.895 0.00 0.00 0.00 6.86
2289 2593 1.022982 GGTAAAACTTCCCCCTCGCG 61.023 60.000 0.00 0.00 0.00 5.87
2290 2594 0.327259 AGGTAAAACTTCCCCCTCGC 59.673 55.000 0.00 0.00 0.00 5.03
2291 2595 2.305052 AGAAGGTAAAACTTCCCCCTCG 59.695 50.000 4.14 0.00 46.24 4.63
2295 2599 4.765856 GGAGAAAGAAGGTAAAACTTCCCC 59.234 45.833 4.14 0.00 46.24 4.81
2298 2602 5.107026 GCGAGGAGAAAGAAGGTAAAACTTC 60.107 44.000 0.00 0.00 45.59 3.01
2327 2631 2.817258 CCGTAGCTTCAAAACCCATTCA 59.183 45.455 0.00 0.00 0.00 2.57
2334 2638 1.199327 GGAAGGCCGTAGCTTCAAAAC 59.801 52.381 0.00 0.00 39.73 2.43
2353 2659 3.055719 GTCGCCCATGGTGTGTGG 61.056 66.667 11.73 0.00 34.40 4.17
2357 2663 2.347490 GTCTGTCGCCCATGGTGT 59.653 61.111 11.73 0.00 34.40 4.16
2382 2688 1.683011 CCAAGGGTGTGGCTCTAATGG 60.683 57.143 0.00 0.00 0.00 3.16
2388 2694 1.477558 CCATATCCAAGGGTGTGGCTC 60.478 57.143 1.96 0.00 38.68 4.70
2389 2695 0.552848 CCATATCCAAGGGTGTGGCT 59.447 55.000 1.96 0.00 38.68 4.75
2489 2795 1.423794 ATTGGTGAGTGTTCCCGGGT 61.424 55.000 22.86 0.00 0.00 5.28
2492 2798 1.586154 GCCATTGGTGAGTGTTCCCG 61.586 60.000 4.26 0.00 0.00 5.14
2497 2803 2.672996 GCCGCCATTGGTGAGTGT 60.673 61.111 17.90 0.00 34.74 3.55
2543 2850 2.626780 CGCTCCTGTGACCGACTGA 61.627 63.158 0.00 0.00 0.00 3.41
2555 2862 2.134287 ACCGCCATATGTCGCTCCT 61.134 57.895 0.00 0.00 0.00 3.69
2571 2878 9.959749 TTTTTAATCGATATTAATTGCCTCACC 57.040 29.630 0.00 0.00 37.40 4.02
2576 2883 9.129209 GCTCCTTTTTAATCGATATTAATTGCC 57.871 33.333 0.00 0.00 37.40 4.52
2577 2884 8.840867 CGCTCCTTTTTAATCGATATTAATTGC 58.159 33.333 0.00 0.00 37.40 3.56
2581 2888 8.280497 GCTTCGCTCCTTTTTAATCGATATTAA 58.720 33.333 0.00 0.00 36.09 1.40
2583 2890 6.564125 CGCTTCGCTCCTTTTTAATCGATATT 60.564 38.462 0.00 0.00 0.00 1.28
2584 2891 5.107453 CGCTTCGCTCCTTTTTAATCGATAT 60.107 40.000 0.00 0.00 0.00 1.63
2593 3039 0.307760 CACACGCTTCGCTCCTTTTT 59.692 50.000 0.00 0.00 0.00 1.94
2600 3046 1.927174 GTTGATATCACACGCTTCGCT 59.073 47.619 4.48 0.00 0.00 4.93
2601 3047 1.658596 TGTTGATATCACACGCTTCGC 59.341 47.619 4.48 0.00 0.00 4.70
2602 3048 3.989705 TTGTTGATATCACACGCTTCG 57.010 42.857 4.48 0.00 0.00 3.79
2603 3049 8.338259 AGATTAATTGTTGATATCACACGCTTC 58.662 33.333 4.48 0.00 0.00 3.86
2604 3050 8.213518 AGATTAATTGTTGATATCACACGCTT 57.786 30.769 4.48 7.29 0.00 4.68
2605 3051 7.712639 AGAGATTAATTGTTGATATCACACGCT 59.287 33.333 4.48 0.00 0.00 5.07
2606 3052 7.855545 AGAGATTAATTGTTGATATCACACGC 58.144 34.615 4.48 0.00 0.00 5.34
2642 3088 3.054287 TGGAGGTACAGTTCCACAACAAA 60.054 43.478 8.44 0.00 38.53 2.83
2647 3093 2.158370 TCTCTGGAGGTACAGTTCCACA 60.158 50.000 8.44 0.00 38.53 4.17
2656 3102 4.217550 GTGAGCTATCATCTCTGGAGGTAC 59.782 50.000 0.00 0.00 37.87 3.34
2658 3104 3.117169 AGTGAGCTATCATCTCTGGAGGT 60.117 47.826 0.00 0.00 37.87 3.85
2666 3112 5.104776 TGGCTTGTTAAGTGAGCTATCATCT 60.105 40.000 0.00 0.00 37.87 2.90
2667 3113 5.118990 TGGCTTGTTAAGTGAGCTATCATC 58.881 41.667 0.00 0.00 37.87 2.92
2689 3135 1.228124 TGCGTTGGAGTTCCCCTTG 60.228 57.895 0.00 0.00 34.29 3.61
2695 3141 1.795768 TGTGATCTGCGTTGGAGTTC 58.204 50.000 0.00 0.00 0.00 3.01
2706 3152 7.046652 ACATTTAGGACTGATCTTGTGATCTG 58.953 38.462 10.08 10.08 46.84 2.90
2714 3160 8.868522 TGATTCAAACATTTAGGACTGATCTT 57.131 30.769 0.00 0.00 0.00 2.40
2721 3167 7.361286 GGACAGTCTGATTCAAACATTTAGGAC 60.361 40.741 6.91 0.00 0.00 3.85
2722 3168 6.655003 GGACAGTCTGATTCAAACATTTAGGA 59.345 38.462 6.91 0.00 0.00 2.94
2739 3185 0.593128 GCAAAATGCACGGACAGTCT 59.407 50.000 0.00 0.00 44.26 3.24
2767 3215 3.829601 TCTAAACAAATTTGATGCCCGGT 59.170 39.130 24.64 0.00 0.00 5.28
2786 3234 7.350382 AGATTTCAGACATCTAGAGTGGTCTA 58.650 38.462 18.61 8.79 38.48 2.59
2792 3240 7.473735 TTGTGAGATTTCAGACATCTAGAGT 57.526 36.000 0.00 0.00 32.98 3.24
2795 3243 7.704047 TCGATTTGTGAGATTTCAGACATCTAG 59.296 37.037 0.00 0.00 33.76 2.43
2801 3249 6.080406 GGTTTCGATTTGTGAGATTTCAGAC 58.920 40.000 0.00 0.00 32.98 3.51
2818 3266 2.421388 CCTCCCATATGCTTGGTTTCGA 60.421 50.000 0.00 0.00 34.77 3.71
2820 3268 3.018423 ACCTCCCATATGCTTGGTTTC 57.982 47.619 0.00 0.00 34.77 2.78
2825 3273 1.066002 CGCAAACCTCCCATATGCTTG 59.934 52.381 0.00 0.00 34.93 4.01
2828 3276 0.465460 TCCGCAAACCTCCCATATGC 60.465 55.000 0.00 0.00 0.00 3.14
2856 3304 1.000060 TGGAGTCCAACGTAACGAAGG 60.000 52.381 10.20 0.00 0.00 3.46
2868 3316 2.220586 TCGGGCATGTTGGAGTCCA 61.221 57.895 8.12 8.12 0.00 4.02
2906 3354 0.821711 TTCAAAAGTGTGGGGCTCCG 60.822 55.000 0.00 0.00 35.24 4.63
2907 3355 0.673985 GTTCAAAAGTGTGGGGCTCC 59.326 55.000 0.00 0.00 0.00 4.70
2914 3362 3.131933 TGGTGGGAATGTTCAAAAGTGTG 59.868 43.478 0.00 0.00 0.00 3.82
2916 3364 3.131933 TGTGGTGGGAATGTTCAAAAGTG 59.868 43.478 0.00 0.00 0.00 3.16
2917 3365 3.370104 TGTGGTGGGAATGTTCAAAAGT 58.630 40.909 0.00 0.00 0.00 2.66
2918 3366 4.119136 GTTGTGGTGGGAATGTTCAAAAG 58.881 43.478 0.00 0.00 0.00 2.27
2919 3367 3.118592 GGTTGTGGTGGGAATGTTCAAAA 60.119 43.478 0.00 0.00 0.00 2.44
2946 3394 1.354368 GGGGGAAGGTGACAATCAAGA 59.646 52.381 0.00 0.00 0.00 3.02
2949 3397 0.404040 GTGGGGGAAGGTGACAATCA 59.596 55.000 0.00 0.00 0.00 2.57
2953 3401 2.856988 GGGTGGGGGAAGGTGACA 60.857 66.667 0.00 0.00 0.00 3.58
2960 3408 2.012210 GGATGATGGGGTGGGGGAA 61.012 63.158 0.00 0.00 0.00 3.97
3089 3551 5.061920 TCTACTTCTTCTTCTTCGCCTTC 57.938 43.478 0.00 0.00 0.00 3.46
3094 3556 7.540745 CCTTCTTCTTCTACTTCTTCTTCTTCG 59.459 40.741 0.00 0.00 0.00 3.79
3103 3565 2.498078 CCCGCCTTCTTCTTCTACTTCT 59.502 50.000 0.00 0.00 0.00 2.85
3104 3566 2.894902 CCCGCCTTCTTCTTCTACTTC 58.105 52.381 0.00 0.00 0.00 3.01
3105 3567 1.066071 GCCCGCCTTCTTCTTCTACTT 60.066 52.381 0.00 0.00 0.00 2.24
3106 3568 0.537653 GCCCGCCTTCTTCTTCTACT 59.462 55.000 0.00 0.00 0.00 2.57
3108 3570 1.515954 CGCCCGCCTTCTTCTTCTA 59.484 57.895 0.00 0.00 0.00 2.10
3109 3571 2.266055 CGCCCGCCTTCTTCTTCT 59.734 61.111 0.00 0.00 0.00 2.85
3110 3572 2.820037 CCGCCCGCCTTCTTCTTC 60.820 66.667 0.00 0.00 0.00 2.87
3111 3573 3.637273 ACCGCCCGCCTTCTTCTT 61.637 61.111 0.00 0.00 0.00 2.52
3112 3574 4.394712 CACCGCCCGCCTTCTTCT 62.395 66.667 0.00 0.00 0.00 2.85
3131 3593 4.115199 CCCTGGCAGGCCACCTAC 62.115 72.222 28.51 0.00 41.89 3.18
3143 3605 3.775654 GGACGAGGTCTGCCCTGG 61.776 72.222 0.00 0.00 46.51 4.45
3221 3684 1.794714 CATAGTGGTAGGGAGGCTGT 58.205 55.000 0.00 0.00 0.00 4.40
3234 3697 1.091771 CGGTGCTGGAAGGCATAGTG 61.092 60.000 0.00 0.00 44.34 2.74
3253 3716 2.526120 GGCGATTGCTACGGTCTGC 61.526 63.158 4.59 0.00 42.25 4.26
3287 3761 1.066303 CGATGGCTAGAGGTGAGTGAC 59.934 57.143 0.00 0.00 0.00 3.67
3308 3782 3.243602 TGAGGTCGACGAAAAATGAGACA 60.244 43.478 9.92 0.00 0.00 3.41
3498 3974 4.891168 TCCAGTTGTCCATATTCGTAGCTA 59.109 41.667 0.00 0.00 0.00 3.32
3535 4013 3.550656 CGACTGCGGTTGTTCCTC 58.449 61.111 0.00 0.00 0.00 3.71
3594 4089 3.491598 CTTTGGGTCGGCACCAGGT 62.492 63.158 8.11 0.00 45.94 4.00
3675 4171 5.109210 TGAAACAGATTGATACTACTGGCG 58.891 41.667 0.00 0.00 35.08 5.69
3716 4212 3.328237 AGCTTTAACAAAACGTCACGG 57.672 42.857 0.35 0.00 0.00 4.94
3729 4225 4.081972 TGAAACCAAGTGTGCAAGCTTTAA 60.082 37.500 0.00 0.00 0.00 1.52
3730 4226 3.445450 TGAAACCAAGTGTGCAAGCTTTA 59.555 39.130 0.00 0.00 0.00 1.85
3841 4360 3.516981 TGTTTGTAGCAGCTGCAAAAA 57.483 38.095 38.24 27.10 44.69 1.94
3905 4424 9.248291 CATAGAGCAACAAACAACAAAACTTAT 57.752 29.630 0.00 0.00 0.00 1.73
3935 4454 9.605305 GCAACATTTAAATCAATAAAACGATCG 57.395 29.630 14.88 14.88 0.00 3.69
3973 4495 5.076182 TCTGGCAAAGAAACACAATGGATA 58.924 37.500 0.00 0.00 29.54 2.59
3996 4518 2.456989 CATAACGAACGCAGGTACGAT 58.543 47.619 0.00 0.00 36.70 3.73
4016 4548 8.056638 GAAGTGATTCTTCTCCATCTTGTGGC 62.057 46.154 0.00 0.00 46.36 5.01
4044 4576 7.312154 TCAACTTCAACCAACAATGCATATAC 58.688 34.615 0.00 0.00 0.00 1.47
4105 4637 0.833287 ACCATGGAGATCTTGACGGG 59.167 55.000 21.47 0.00 0.00 5.28
4203 4736 1.081092 CTCCTCCCACTTCCTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
4246 4784 1.424302 CTCCTCCATCATCTTGGCCAT 59.576 52.381 6.09 0.00 36.66 4.40
4318 4857 6.336566 TGAGATTCTTGTCTTGCATCTCTAC 58.663 40.000 9.01 0.00 33.13 2.59
4405 4944 3.244561 ACATTGGGATCAAGTCTGACGTT 60.245 43.478 1.52 0.00 36.19 3.99
4421 4960 4.959723 ACAAACAATCTTTCCCACATTGG 58.040 39.130 0.00 0.00 37.25 3.16
4423 4962 4.653341 TGGACAAACAATCTTTCCCACATT 59.347 37.500 0.00 0.00 0.00 2.71
4437 4976 2.030363 CGCAAATAGGCTTGGACAAACA 60.030 45.455 0.00 0.00 0.00 2.83
4438 4977 2.595386 CGCAAATAGGCTTGGACAAAC 58.405 47.619 0.00 0.00 0.00 2.93
4439 4978 1.067915 GCGCAAATAGGCTTGGACAAA 60.068 47.619 0.30 0.00 0.00 2.83
4440 4979 0.525761 GCGCAAATAGGCTTGGACAA 59.474 50.000 0.30 0.00 0.00 3.18
4441 4980 1.643868 CGCGCAAATAGGCTTGGACA 61.644 55.000 8.75 0.00 0.00 4.02
4454 4993 1.297524 CGCTTCAATATGCGCGCAA 60.298 52.632 39.68 26.33 45.50 4.85
4479 5019 3.721706 CCAGCCCGCTCCCTTTCT 61.722 66.667 0.00 0.00 0.00 2.52
4489 5029 3.432051 CTTCGCCTAGTCCAGCCCG 62.432 68.421 0.00 0.00 0.00 6.13
4490 5030 2.022240 CTCTTCGCCTAGTCCAGCCC 62.022 65.000 0.00 0.00 0.00 5.19
4504 5044 2.247358 TGCCAAAAATCCCCACTCTTC 58.753 47.619 0.00 0.00 0.00 2.87
4522 5062 0.179062 CCTAGTCTGGCTGTCCATGC 60.179 60.000 0.00 0.00 42.51 4.06
4544 5084 1.338200 GCCAAAGAGCTCCTTCTTCGA 60.338 52.381 10.93 0.00 36.42 3.71
4609 5149 8.981647 ACAAAAGACATCAAATGTTCAATTAGC 58.018 29.630 0.00 0.00 45.03 3.09
4612 5152 9.165035 ACAACAAAAGACATCAAATGTTCAATT 57.835 25.926 0.00 0.00 45.03 2.32
4623 5163 5.259832 TGCAATCACAACAAAAGACATCA 57.740 34.783 0.00 0.00 0.00 3.07
4669 5210 5.594725 TGCTCCGATCTTCTCTACTATTTGT 59.405 40.000 0.00 0.00 0.00 2.83
4674 5215 4.504165 CCTCTGCTCCGATCTTCTCTACTA 60.504 50.000 0.00 0.00 0.00 1.82
4675 5216 3.476552 CTCTGCTCCGATCTTCTCTACT 58.523 50.000 0.00 0.00 0.00 2.57
4676 5217 2.552315 CCTCTGCTCCGATCTTCTCTAC 59.448 54.545 0.00 0.00 0.00 2.59
4691 5232 0.798776 CGTCAAATGTCCACCTCTGC 59.201 55.000 0.00 0.00 0.00 4.26
4698 5239 2.875933 GTCCAAAGTCGTCAAATGTCCA 59.124 45.455 0.00 0.00 0.00 4.02
4765 5306 0.662970 CAACGCGGTTCACCAAATGG 60.663 55.000 12.47 0.00 42.17 3.16
4803 5344 3.790416 TTTGGCCCTGTCGCTGCTT 62.790 57.895 0.00 0.00 0.00 3.91
4804 5345 4.269523 TTTGGCCCTGTCGCTGCT 62.270 61.111 0.00 0.00 0.00 4.24
4811 5352 2.116125 GGAGCTGTTTGGCCCTGT 59.884 61.111 0.00 0.00 0.00 4.00
4835 5386 1.202382 GCTGATGATTTTGGCAGCCTC 60.202 52.381 14.15 1.73 45.92 4.70
4895 5446 1.977854 ACCATGAGTAGTTGACAGGCA 59.022 47.619 0.00 0.00 0.00 4.75
4897 5448 2.881074 CGACCATGAGTAGTTGACAGG 58.119 52.381 0.00 0.00 0.00 4.00
4898 5449 2.263077 GCGACCATGAGTAGTTGACAG 58.737 52.381 0.00 0.00 0.00 3.51
4984 5535 2.807045 GCCACTGCTGAGACGACG 60.807 66.667 0.00 0.00 33.53 5.12
4999 5550 1.000283 CATCCGTGTCTCCATCTAGCC 60.000 57.143 0.00 0.00 0.00 3.93
5018 5569 1.819288 GACACGTGAGAAGGGAGATCA 59.181 52.381 25.01 0.00 0.00 2.92
5109 5660 7.601886 TCGATTCGTTGGGTAACATTTTACTTA 59.398 33.333 5.89 0.00 38.17 2.24
5146 5701 3.112709 GCGTGAGGAGACGTTGGC 61.113 66.667 0.00 0.00 41.54 4.52
5156 5711 4.215742 TTATCCGGCGGCGTGAGG 62.216 66.667 30.09 14.77 0.00 3.86
5182 5737 7.508977 ACCATGATTAGAGAAAGGAAAAACCAA 59.491 33.333 0.00 0.00 42.04 3.67
5251 5806 1.202879 TGGGATTCGTTTGCAAGACCT 60.203 47.619 0.00 0.00 0.00 3.85
5252 5807 1.243902 TGGGATTCGTTTGCAAGACC 58.756 50.000 0.00 0.00 0.00 3.85
5296 5851 5.319453 CCCTCATATGGTGCTGTTTGATAT 58.681 41.667 2.13 0.00 0.00 1.63
5297 5852 4.717877 CCCTCATATGGTGCTGTTTGATA 58.282 43.478 2.13 0.00 0.00 2.15
5304 5859 0.179048 TTCGCCCTCATATGGTGCTG 60.179 55.000 2.13 1.39 33.31 4.41
5324 5879 0.031178 CTCTTGCCAGTGCGCTTTTT 59.969 50.000 9.73 0.00 41.78 1.94
5338 5893 2.409975 CACCCTTTGCATTTGCTCTTG 58.590 47.619 3.94 0.00 42.66 3.02
5426 5981 4.448395 CGCACATGACCAAATTGTTTCATT 59.552 37.500 0.00 0.00 0.00 2.57
5474 6029 0.179070 TTGTACACGCCTGCAACTGA 60.179 50.000 0.00 0.00 0.00 3.41
5475 6030 0.235665 CTTGTACACGCCTGCAACTG 59.764 55.000 0.00 0.00 0.00 3.16
5476 6031 0.884704 CCTTGTACACGCCTGCAACT 60.885 55.000 0.00 0.00 0.00 3.16
5477 6032 1.574428 CCTTGTACACGCCTGCAAC 59.426 57.895 0.00 0.00 0.00 4.17
5479 6034 2.668212 GCCTTGTACACGCCTGCA 60.668 61.111 0.00 0.00 0.00 4.41
5481 6036 0.459585 ATACGCCTTGTACACGCCTG 60.460 55.000 0.00 0.00 35.44 4.85
5482 6037 1.105457 TATACGCCTTGTACACGCCT 58.895 50.000 0.00 0.00 35.44 5.52
5483 6038 1.203065 GTATACGCCTTGTACACGCC 58.797 55.000 0.00 0.00 35.44 5.68
5493 6048 6.161855 TGATCTTTCTTCATGTATACGCCT 57.838 37.500 0.00 0.00 0.00 5.52
5504 6059 2.807967 CGGCTGTGTTGATCTTTCTTCA 59.192 45.455 0.00 0.00 0.00 3.02
5506 6061 2.154462 CCGGCTGTGTTGATCTTTCTT 58.846 47.619 0.00 0.00 0.00 2.52
5509 6064 1.611673 CCTCCGGCTGTGTTGATCTTT 60.612 52.381 0.00 0.00 0.00 2.52
5512 6067 0.460987 CTCCTCCGGCTGTGTTGATC 60.461 60.000 0.00 0.00 0.00 2.92
5514 6069 0.541063 TACTCCTCCGGCTGTGTTGA 60.541 55.000 0.00 0.00 0.00 3.18
5515 6070 0.108615 CTACTCCTCCGGCTGTGTTG 60.109 60.000 0.00 0.00 0.00 3.33
5516 6071 0.542232 ACTACTCCTCCGGCTGTGTT 60.542 55.000 0.00 0.00 0.00 3.32
5521 6087 2.528673 AACTAACTACTCCTCCGGCT 57.471 50.000 0.00 0.00 0.00 5.52
5522 6088 2.034432 GCTAACTAACTACTCCTCCGGC 59.966 54.545 0.00 0.00 0.00 6.13
5606 6173 1.328374 ACGCGTACAGGTTGTTGAAAC 59.672 47.619 11.67 0.00 0.00 2.78
5608 6175 2.505628 TACGCGTACAGGTTGTTGAA 57.494 45.000 16.41 0.00 0.00 2.69
5624 6191 2.469516 GGGTTGCGAGCCCAATACG 61.470 63.158 11.45 0.00 45.40 3.06
5733 6306 5.015813 TGATGGAGATGGATTAGCTAGGA 57.984 43.478 0.00 0.00 0.00 2.94
5740 6313 3.732212 CGCACTTGATGGAGATGGATTA 58.268 45.455 0.00 0.00 0.00 1.75
5741 6314 2.569059 CGCACTTGATGGAGATGGATT 58.431 47.619 0.00 0.00 0.00 3.01
5763 6336 1.144936 GGAGGAGGAAGACATGGCG 59.855 63.158 0.00 0.00 0.00 5.69
5841 6414 4.308458 TGGGTCCGCCACAGAACG 62.308 66.667 0.00 0.00 36.17 3.95
5844 6417 2.284625 ATCTGGGTCCGCCACAGA 60.285 61.111 7.60 7.60 42.25 3.41
5845 6418 2.187946 GATCTGGGTCCGCCACAG 59.812 66.667 0.00 0.00 35.63 3.66


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

AutoCloner maintained by Alex Coulton.