Multiple sequence alignment - TraesCS6D01G155000

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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 TraesCS6D01G155000 chr6D 100.000 4613 0 0 1 4613 130215386 130210774 0.000000e+00 8519.0
1 TraesCS6D01G155000 chr6D 95.654 3037 75 16 1212 4215 146506101 146509113 0.000000e+00 4824.0
2 TraesCS6D01G155000 chr6D 98.082 2503 19 3 1742 4218 131032865 131030366 0.000000e+00 4329.0
3 TraesCS6D01G155000 chr6D 93.048 561 28 4 1152 1712 131033416 131032867 0.000000e+00 809.0
4 TraesCS6D01G155000 chr6D 94.602 352 18 1 804 1154 146390098 146390449 1.130000e-150 544.0
5 TraesCS6D01G155000 chr6D 83.886 422 24 18 4233 4613 131030379 131029961 3.390000e-96 363.0
6 TraesCS6D01G155000 chr6D 81.713 432 25 17 4233 4613 146509103 146509531 1.250000e-80 311.0
7 TraesCS6D01G155000 chr6D 94.949 198 9 1 804 1000 283735806 283735609 4.480000e-80 309.0
8 TraesCS6D01G155000 chr6D 94.359 195 10 1 804 997 117988446 117988640 9.700000e-77 298.0
9 TraesCS6D01G155000 chr6D 90.370 135 11 2 1482 1616 146387656 146387788 4.740000e-40 176.0
10 TraesCS6D01G155000 chr6D 86.885 122 12 3 1037 1154 131033645 131033524 2.900000e-27 134.0
11 TraesCS6D01G155000 chr6D 80.822 146 25 3 1338 1481 408898062 408897918 1.360000e-20 111.0
12 TraesCS6D01G155000 chr6B 92.947 3502 141 35 1152 4613 228758118 228754683 0.000000e+00 5001.0
13 TraesCS6D01G155000 chr6B 94.473 3094 100 17 1152 4218 257783595 257780546 0.000000e+00 4700.0
14 TraesCS6D01G155000 chr6B 92.788 2565 115 26 1681 4215 230602352 230604876 0.000000e+00 3648.0
15 TraesCS6D01G155000 chr6B 87.587 1289 103 27 1818 3073 213521279 213522543 0.000000e+00 1441.0
16 TraesCS6D01G155000 chr6B 92.925 523 37 0 3069 3591 213535002 213535524 0.000000e+00 761.0
17 TraesCS6D01G155000 chr6B 92.614 352 24 2 804 1154 257790389 257790039 5.330000e-139 505.0
18 TraesCS6D01G155000 chr6B 89.735 302 17 7 4325 4613 230604988 230605288 1.570000e-99 374.0
19 TraesCS6D01G155000 chr6B 82.394 426 26 17 4234 4613 257780558 257780136 4.450000e-85 326.0
20 TraesCS6D01G155000 chr6B 91.111 135 10 2 1482 1616 257792712 257792580 1.020000e-41 182.0
21 TraesCS6D01G155000 chr6B 83.444 151 23 2 1333 1481 613582458 613582308 6.220000e-29 139.0
22 TraesCS6D01G155000 chr6B 88.235 102 12 0 1053 1154 228758328 228758227 6.270000e-24 122.0
23 TraesCS6D01G155000 chr6A 93.380 2145 73 14 1680 3786 171738711 171740824 0.000000e+00 3110.0
24 TraesCS6D01G155000 chr6A 93.337 1906 72 19 1482 3353 169226964 169225080 0.000000e+00 2765.0
25 TraesCS6D01G155000 chr6A 96.782 870 23 4 3349 4214 169221052 169220184 0.000000e+00 1447.0
26 TraesCS6D01G155000 chr6A 87.741 1142 85 28 1818 2947 162911123 162912221 0.000000e+00 1282.0
27 TraesCS6D01G155000 chr6A 93.871 620 25 2 3178 3786 162913035 162913652 0.000000e+00 922.0
28 TraesCS6D01G155000 chr6A 87.500 656 65 5 1216 1868 169254955 169254314 0.000000e+00 741.0
29 TraesCS6D01G155000 chr6A 95.673 416 13 4 3805 4215 171740812 171741227 0.000000e+00 664.0
30 TraesCS6D01G155000 chr6A 86.486 407 46 4 3805 4211 162913640 162914037 5.480000e-119 438.0
31 TraesCS6D01G155000 chr6A 86.874 419 17 9 4233 4613 169220193 169219775 7.090000e-118 435.0
32 TraesCS6D01G155000 chr6A 92.929 297 13 3 4325 4613 171741339 171741635 4.270000e-115 425.0
33 TraesCS6D01G155000 chr6A 88.215 297 23 4 4325 4613 162914152 162914444 1.230000e-90 344.0
34 TraesCS6D01G155000 chr6A 94.359 195 10 1 804 997 109375689 109375495 9.700000e-77 298.0
35 TraesCS6D01G155000 chr6A 84.528 265 34 5 1212 1474 169227283 169227024 5.920000e-64 255.0
36 TraesCS6D01G155000 chr6A 91.667 156 13 0 3031 3186 162912224 162912379 2.790000e-52 217.0
37 TraesCS6D01G155000 chr6A 94.286 105 3 1 4233 4334 171741217 171741321 1.720000e-34 158.0
38 TraesCS6D01G155000 chr6A 76.357 258 40 13 1528 1777 162909448 162909692 8.110000e-23 119.0
39 TraesCS6D01G155000 chr5B 94.616 1133 51 4 2666 3789 84884569 84883438 0.000000e+00 1746.0
40 TraesCS6D01G155000 chr5B 89.189 629 30 16 1862 2462 84890698 84890080 0.000000e+00 750.0
41 TraesCS6D01G155000 chr5B 96.591 264 9 0 3952 4215 84883226 84882963 5.480000e-119 438.0
42 TraesCS6D01G155000 chr5B 86.874 419 17 15 4233 4613 84882973 84882555 7.090000e-118 435.0
43 TraesCS6D01G155000 chr5B 96.026 151 4 1 3805 3955 84883453 84883305 1.280000e-60 244.0
44 TraesCS6D01G155000 chr4D 98.755 803 10 0 1 803 483047152 483046350 0.000000e+00 1428.0
45 TraesCS6D01G155000 chr4D 98.630 803 11 0 1 803 481095585 481094783 0.000000e+00 1423.0
46 TraesCS6D01G155000 chr3D 98.755 803 10 0 1 803 411118057 411117255 0.000000e+00 1428.0
47 TraesCS6D01G155000 chr3D 98.755 803 10 0 1 803 532926936 532927738 0.000000e+00 1428.0
48 TraesCS6D01G155000 chr3D 80.399 301 48 8 1186 1481 20556400 20556694 7.770000e-53 219.0
49 TraesCS6D01G155000 chr2D 98.753 802 9 1 1 802 459860165 459860965 0.000000e+00 1424.0
50 TraesCS6D01G155000 chr2D 79.268 164 26 4 998 1154 20428431 20428269 1.760000e-19 108.0
51 TraesCS6D01G155000 chr1D 98.397 811 11 2 1 810 64072224 64073033 0.000000e+00 1424.0
52 TraesCS6D01G155000 chr1D 88.889 135 12 3 1482 1616 266787784 266787653 3.690000e-36 163.0
53 TraesCS6D01G155000 chr7D 98.630 803 11 0 1 803 95007311 95008113 0.000000e+00 1423.0
54 TraesCS6D01G155000 chr5D 98.630 803 11 0 1 803 246790924 246791726 0.000000e+00 1423.0
55 TraesCS6D01G155000 chr5D 93.596 203 10 3 804 1005 560041628 560041428 2.700000e-77 300.0
56 TraesCS6D01G155000 chr5D 93.939 198 11 1 804 1000 211324162 211323965 9.700000e-77 298.0
57 TraesCS6D01G155000 chr5D 80.328 122 23 1 998 1119 449127461 449127581 1.770000e-14 91.6
58 TraesCS6D01G155000 chr4B 91.200 1000 80 6 5 997 41305911 41306909 0.000000e+00 1352.0
59 TraesCS6D01G155000 chr5A 94.359 195 10 1 804 997 41168676 41168482 9.700000e-77 298.0
60 TraesCS6D01G155000 chr1B 81.068 206 29 7 1174 1377 629711973 629711776 6.180000e-34 156.0
61 TraesCS6D01G155000 chr1B 78.882 161 27 1 998 1151 672424441 672424601 8.170000e-18 102.0
62 TraesCS6D01G155000 chr1A 86.607 112 13 1 1363 1474 514543087 514543196 6.270000e-24 122.0
63 TraesCS6D01G155000 chr3B 82.258 124 21 1 998 1120 417737140 417737263 6.310000e-19 106.0
64 TraesCS6D01G155000 chr4A 78.528 163 29 1 998 1154 60031591 60031429 8.170000e-18 102.0


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 TraesCS6D01G155000 chr6D 130210774 130215386 4612 True 8519.000000 8519 100.00000 1 4613 1 chr6D.!!$R1 4612
1 TraesCS6D01G155000 chr6D 146506101 146509531 3430 False 2567.500000 4824 88.68350 1212 4613 2 chr6D.!!$F3 3401
2 TraesCS6D01G155000 chr6D 131029961 131033645 3684 True 1408.750000 4329 90.47525 1037 4613 4 chr6D.!!$R4 3576
3 TraesCS6D01G155000 chr6D 146387656 146390449 2793 False 360.000000 544 92.48600 804 1616 2 chr6D.!!$F2 812
4 TraesCS6D01G155000 chr6B 228754683 228758328 3645 True 2561.500000 5001 90.59100 1053 4613 2 chr6B.!!$R2 3560
5 TraesCS6D01G155000 chr6B 257780136 257783595 3459 True 2513.000000 4700 88.43350 1152 4613 2 chr6B.!!$R3 3461
6 TraesCS6D01G155000 chr6B 230602352 230605288 2936 False 2011.000000 3648 91.26150 1681 4613 2 chr6B.!!$F3 2932
7 TraesCS6D01G155000 chr6B 213521279 213522543 1264 False 1441.000000 1441 87.58700 1818 3073 1 chr6B.!!$F1 1255
8 TraesCS6D01G155000 chr6B 213535002 213535524 522 False 761.000000 761 92.92500 3069 3591 1 chr6B.!!$F2 522
9 TraesCS6D01G155000 chr6B 257790039 257792712 2673 True 343.500000 505 91.86250 804 1616 2 chr6B.!!$R4 812
10 TraesCS6D01G155000 chr6A 169225080 169227283 2203 True 1510.000000 2765 88.93250 1212 3353 2 chr6A.!!$R4 2141
11 TraesCS6D01G155000 chr6A 171738711 171741635 2924 False 1089.250000 3110 94.06700 1680 4613 4 chr6A.!!$F2 2933
12 TraesCS6D01G155000 chr6A 169219775 169221052 1277 True 941.000000 1447 91.82800 3349 4613 2 chr6A.!!$R3 1264
13 TraesCS6D01G155000 chr6A 169254314 169254955 641 True 741.000000 741 87.50000 1216 1868 1 chr6A.!!$R2 652
14 TraesCS6D01G155000 chr6A 162909448 162914444 4996 False 553.666667 1282 87.38950 1528 4613 6 chr6A.!!$F1 3085
15 TraesCS6D01G155000 chr5B 84890080 84890698 618 True 750.000000 750 89.18900 1862 2462 1 chr5B.!!$R1 600
16 TraesCS6D01G155000 chr5B 84882555 84884569 2014 True 715.750000 1746 93.52675 2666 4613 4 chr5B.!!$R2 1947
17 TraesCS6D01G155000 chr4D 483046350 483047152 802 True 1428.000000 1428 98.75500 1 803 1 chr4D.!!$R2 802
18 TraesCS6D01G155000 chr4D 481094783 481095585 802 True 1423.000000 1423 98.63000 1 803 1 chr4D.!!$R1 802
19 TraesCS6D01G155000 chr3D 411117255 411118057 802 True 1428.000000 1428 98.75500 1 803 1 chr3D.!!$R1 802
20 TraesCS6D01G155000 chr3D 532926936 532927738 802 False 1428.000000 1428 98.75500 1 803 1 chr3D.!!$F2 802
21 TraesCS6D01G155000 chr2D 459860165 459860965 800 False 1424.000000 1424 98.75300 1 802 1 chr2D.!!$F1 801
22 TraesCS6D01G155000 chr1D 64072224 64073033 809 False 1424.000000 1424 98.39700 1 810 1 chr1D.!!$F1 809
23 TraesCS6D01G155000 chr7D 95007311 95008113 802 False 1423.000000 1423 98.63000 1 803 1 chr7D.!!$F1 802
24 TraesCS6D01G155000 chr5D 246790924 246791726 802 False 1423.000000 1423 98.63000 1 803 1 chr5D.!!$F1 802
25 TraesCS6D01G155000 chr4B 41305911 41306909 998 False 1352.000000 1352 91.20000 5 997 1 chr4B.!!$F1 992

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
943 949 0.108804 TGCTCCTCGTTGGATTCGAC 60.109 55.0 0.0 0.0 45.16 4.20 F
1060 1066 0.031585 TGACGTGGTCACCTTCTTCG 59.968 55.0 0.0 0.0 37.67 3.79 F
1062 1068 0.249322 ACGTGGTCACCTTCTTCGTG 60.249 55.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 4388 2.683933 TCCTGGTCGGGAAGGAGC 60.684 66.667 0.0 0.0 37.68 4.70 R
3359 7404 1.002659 AGTGGTTAATACGTGCCAGCA 59.997 47.619 0.0 0.0 0.00 4.41 R
4004 8162 8.854614 ATATTGTCTTGAAGAGCTTTACAGTT 57.145 30.769 0.0 0.0 0.00 3.16 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
49 50 2.711009 GGATCTGGATACCCATGTTGGA 59.289 50.000 0.00 0.00 40.96 3.53
123 124 9.490379 GATTCAAGTAATCCCGTATACAATTCT 57.510 33.333 3.32 0.00 38.47 2.40
196 197 3.928727 ACCTCGTTCAATCTCGTTACA 57.071 42.857 0.00 0.00 0.00 2.41
807 813 1.416030 GGGCATTTTTCCAACACACCT 59.584 47.619 0.00 0.00 0.00 4.00
809 815 3.540617 GGCATTTTTCCAACACACCTTT 58.459 40.909 0.00 0.00 0.00 3.11
810 816 3.312146 GGCATTTTTCCAACACACCTTTG 59.688 43.478 0.00 0.00 0.00 2.77
816 822 7.463961 TTTTTCCAACACACCTTTGTTACTA 57.536 32.000 0.00 0.00 37.62 1.82
817 823 6.687081 TTTCCAACACACCTTTGTTACTAG 57.313 37.500 0.00 0.00 37.62 2.57
821 827 7.156673 TCCAACACACCTTTGTTACTAGTATC 58.843 38.462 2.79 3.65 37.62 2.24
822 828 6.090358 CCAACACACCTTTGTTACTAGTATCG 59.910 42.308 2.79 0.00 37.62 2.92
825 831 6.151648 ACACACCTTTGTTACTAGTATCGCTA 59.848 38.462 2.79 0.00 31.66 4.26
826 832 6.471519 CACACCTTTGTTACTAGTATCGCTAC 59.528 42.308 2.79 0.00 31.66 3.58
829 835 7.220300 CACCTTTGTTACTAGTATCGCTACTTG 59.780 40.741 3.98 5.34 39.04 3.16
831 837 6.446781 TTGTTACTAGTATCGCTACTTGCT 57.553 37.500 3.98 0.00 39.04 3.91
838 844 2.933495 ATCGCTACTTGCTCGTTACA 57.067 45.000 0.00 0.00 40.11 2.41
844 850 5.808540 TCGCTACTTGCTCGTTACAAATTAT 59.191 36.000 0.00 0.00 40.11 1.28
848 854 7.636359 GCTACTTGCTCGTTACAAATTATCTTG 59.364 37.037 0.00 0.00 38.95 3.02
850 856 7.871853 ACTTGCTCGTTACAAATTATCTTGTT 58.128 30.769 0.00 0.00 40.08 2.83
853 859 9.982291 TTGCTCGTTACAAATTATCTTGTTATC 57.018 29.630 0.00 0.00 40.08 1.75
886 892 8.964420 TTGTTACTTATAATTTCAGTGCTTGC 57.036 30.769 0.00 0.00 0.00 4.01
887 893 8.105097 TGTTACTTATAATTTCAGTGCTTGCA 57.895 30.769 0.00 0.00 0.00 4.08
888 894 8.236586 TGTTACTTATAATTTCAGTGCTTGCAG 58.763 33.333 0.00 0.00 0.00 4.41
889 895 8.450964 GTTACTTATAATTTCAGTGCTTGCAGA 58.549 33.333 0.00 0.00 0.00 4.26
890 896 7.081526 ACTTATAATTTCAGTGCTTGCAGAG 57.918 36.000 0.00 0.00 0.00 3.35
891 897 6.881065 ACTTATAATTTCAGTGCTTGCAGAGA 59.119 34.615 0.00 0.00 0.00 3.10
892 898 7.391554 ACTTATAATTTCAGTGCTTGCAGAGAA 59.608 33.333 0.00 0.75 0.00 2.87
893 899 6.770746 ATAATTTCAGTGCTTGCAGAGAAT 57.229 33.333 9.42 1.04 0.00 2.40
894 900 7.870509 ATAATTTCAGTGCTTGCAGAGAATA 57.129 32.000 9.42 3.19 0.00 1.75
895 901 5.557891 ATTTCAGTGCTTGCAGAGAATAC 57.442 39.130 9.42 0.00 0.00 1.89
896 902 2.977914 TCAGTGCTTGCAGAGAATACC 58.022 47.619 0.00 0.00 0.00 2.73
897 903 2.568956 TCAGTGCTTGCAGAGAATACCT 59.431 45.455 0.00 0.00 0.00 3.08
898 904 3.008375 TCAGTGCTTGCAGAGAATACCTT 59.992 43.478 0.00 0.00 0.00 3.50
899 905 3.126514 CAGTGCTTGCAGAGAATACCTTG 59.873 47.826 0.00 0.00 0.00 3.61
900 906 2.086869 TGCTTGCAGAGAATACCTTGC 58.913 47.619 0.00 0.00 0.00 4.01
901 907 2.290514 TGCTTGCAGAGAATACCTTGCT 60.291 45.455 0.00 0.00 0.00 3.91
902 908 3.055167 TGCTTGCAGAGAATACCTTGCTA 60.055 43.478 0.00 0.00 0.00 3.49
903 909 3.941483 GCTTGCAGAGAATACCTTGCTAA 59.059 43.478 0.00 0.00 0.00 3.09
904 910 4.396166 GCTTGCAGAGAATACCTTGCTAAA 59.604 41.667 0.00 0.00 0.00 1.85
905 911 5.106157 GCTTGCAGAGAATACCTTGCTAAAA 60.106 40.000 0.00 0.00 0.00 1.52
906 912 5.880054 TGCAGAGAATACCTTGCTAAAAC 57.120 39.130 0.00 0.00 0.00 2.43
907 913 4.700213 TGCAGAGAATACCTTGCTAAAACC 59.300 41.667 0.00 0.00 0.00 3.27
908 914 4.700213 GCAGAGAATACCTTGCTAAAACCA 59.300 41.667 0.00 0.00 0.00 3.67
909 915 5.392057 GCAGAGAATACCTTGCTAAAACCAC 60.392 44.000 0.00 0.00 0.00 4.16
910 916 5.940470 CAGAGAATACCTTGCTAAAACCACT 59.060 40.000 0.00 0.00 0.00 4.00
911 917 6.431234 CAGAGAATACCTTGCTAAAACCACTT 59.569 38.462 0.00 0.00 0.00 3.16
912 918 6.431234 AGAGAATACCTTGCTAAAACCACTTG 59.569 38.462 0.00 0.00 0.00 3.16
913 919 6.068670 AGAATACCTTGCTAAAACCACTTGT 58.931 36.000 0.00 0.00 0.00 3.16
914 920 5.959618 ATACCTTGCTAAAACCACTTGTC 57.040 39.130 0.00 0.00 0.00 3.18
915 921 3.626930 ACCTTGCTAAAACCACTTGTCA 58.373 40.909 0.00 0.00 0.00 3.58
916 922 4.215109 ACCTTGCTAAAACCACTTGTCAT 58.785 39.130 0.00 0.00 0.00 3.06
917 923 4.649218 ACCTTGCTAAAACCACTTGTCATT 59.351 37.500 0.00 0.00 0.00 2.57
918 924 5.128663 ACCTTGCTAAAACCACTTGTCATTT 59.871 36.000 0.00 0.00 0.00 2.32
919 925 5.691754 CCTTGCTAAAACCACTTGTCATTTC 59.308 40.000 0.00 0.00 0.00 2.17
920 926 5.195001 TGCTAAAACCACTTGTCATTTCC 57.805 39.130 0.00 0.00 0.00 3.13
921 927 4.892934 TGCTAAAACCACTTGTCATTTCCT 59.107 37.500 0.00 0.00 0.00 3.36
922 928 5.362430 TGCTAAAACCACTTGTCATTTCCTT 59.638 36.000 0.00 0.00 0.00 3.36
923 929 5.920840 GCTAAAACCACTTGTCATTTCCTTC 59.079 40.000 0.00 0.00 0.00 3.46
924 930 6.239036 GCTAAAACCACTTGTCATTTCCTTCT 60.239 38.462 0.00 0.00 0.00 2.85
925 931 5.520376 AAACCACTTGTCATTTCCTTCTG 57.480 39.130 0.00 0.00 0.00 3.02
926 932 2.887152 ACCACTTGTCATTTCCTTCTGC 59.113 45.455 0.00 0.00 0.00 4.26
927 933 3.152341 CCACTTGTCATTTCCTTCTGCT 58.848 45.455 0.00 0.00 0.00 4.24
928 934 3.190118 CCACTTGTCATTTCCTTCTGCTC 59.810 47.826 0.00 0.00 0.00 4.26
929 935 3.190118 CACTTGTCATTTCCTTCTGCTCC 59.810 47.826 0.00 0.00 0.00 4.70
930 936 3.073650 ACTTGTCATTTCCTTCTGCTCCT 59.926 43.478 0.00 0.00 0.00 3.69
931 937 3.340814 TGTCATTTCCTTCTGCTCCTC 57.659 47.619 0.00 0.00 0.00 3.71
932 938 2.275318 GTCATTTCCTTCTGCTCCTCG 58.725 52.381 0.00 0.00 0.00 4.63
933 939 1.902508 TCATTTCCTTCTGCTCCTCGT 59.097 47.619 0.00 0.00 0.00 4.18
934 940 2.303022 TCATTTCCTTCTGCTCCTCGTT 59.697 45.455 0.00 0.00 0.00 3.85
935 941 2.169832 TTTCCTTCTGCTCCTCGTTG 57.830 50.000 0.00 0.00 0.00 4.10
936 942 0.321671 TTCCTTCTGCTCCTCGTTGG 59.678 55.000 0.00 0.00 37.10 3.77
937 943 0.541998 TCCTTCTGCTCCTCGTTGGA 60.542 55.000 0.58 0.58 43.86 3.53
938 944 0.539051 CCTTCTGCTCCTCGTTGGAT 59.461 55.000 0.85 0.00 45.16 3.41
939 945 1.065854 CCTTCTGCTCCTCGTTGGATT 60.066 52.381 0.85 0.00 45.16 3.01
940 946 2.275318 CTTCTGCTCCTCGTTGGATTC 58.725 52.381 0.85 0.00 45.16 2.52
941 947 0.173481 TCTGCTCCTCGTTGGATTCG 59.827 55.000 0.85 0.00 45.16 3.34
942 948 0.173481 CTGCTCCTCGTTGGATTCGA 59.827 55.000 0.85 0.00 45.16 3.71
943 949 0.108804 TGCTCCTCGTTGGATTCGAC 60.109 55.000 0.00 0.00 45.16 4.20
944 950 0.108804 GCTCCTCGTTGGATTCGACA 60.109 55.000 0.00 0.00 45.16 4.35
945 951 1.630148 CTCCTCGTTGGATTCGACAC 58.370 55.000 0.00 0.00 45.16 3.67
946 952 1.202582 CTCCTCGTTGGATTCGACACT 59.797 52.381 0.00 0.00 45.16 3.55
947 953 1.201647 TCCTCGTTGGATTCGACACTC 59.798 52.381 0.00 0.00 40.56 3.51
948 954 1.202582 CCTCGTTGGATTCGACACTCT 59.797 52.381 0.00 0.00 38.35 3.24
949 955 2.352814 CCTCGTTGGATTCGACACTCTT 60.353 50.000 0.00 0.00 38.35 2.85
950 956 3.119602 CCTCGTTGGATTCGACACTCTTA 60.120 47.826 0.00 0.00 38.35 2.10
951 957 3.829948 TCGTTGGATTCGACACTCTTAC 58.170 45.455 0.00 0.00 32.30 2.34
952 958 3.504906 TCGTTGGATTCGACACTCTTACT 59.495 43.478 0.00 0.00 32.30 2.24
953 959 4.022589 TCGTTGGATTCGACACTCTTACTT 60.023 41.667 0.00 0.00 32.30 2.24
954 960 5.181811 TCGTTGGATTCGACACTCTTACTTA 59.818 40.000 0.00 0.00 32.30 2.24
955 961 6.034591 CGTTGGATTCGACACTCTTACTTAT 58.965 40.000 0.00 0.00 0.00 1.73
956 962 6.196724 CGTTGGATTCGACACTCTTACTTATC 59.803 42.308 0.00 0.00 0.00 1.75
957 963 5.817988 TGGATTCGACACTCTTACTTATCG 58.182 41.667 0.00 0.00 0.00 2.92
958 964 5.587443 TGGATTCGACACTCTTACTTATCGA 59.413 40.000 0.00 0.00 36.85 3.59
962 968 5.877031 TCGACACTCTTACTTATCGAAAGG 58.123 41.667 10.65 0.00 35.80 3.11
963 969 5.645067 TCGACACTCTTACTTATCGAAAGGA 59.355 40.000 10.65 1.49 35.80 3.36
964 970 5.738225 CGACACTCTTACTTATCGAAAGGAC 59.262 44.000 10.65 0.00 0.00 3.85
965 971 6.403418 CGACACTCTTACTTATCGAAAGGACT 60.403 42.308 10.65 0.00 0.00 3.85
966 972 7.201591 CGACACTCTTACTTATCGAAAGGACTA 60.202 40.741 10.65 0.00 0.00 2.59
967 973 7.760437 ACACTCTTACTTATCGAAAGGACTAC 58.240 38.462 10.65 0.00 0.00 2.73
968 974 7.392673 ACACTCTTACTTATCGAAAGGACTACA 59.607 37.037 10.65 0.00 0.00 2.74
969 975 8.242053 CACTCTTACTTATCGAAAGGACTACAA 58.758 37.037 10.65 0.00 0.00 2.41
970 976 8.968969 ACTCTTACTTATCGAAAGGACTACAAT 58.031 33.333 10.65 0.00 0.00 2.71
971 977 9.804758 CTCTTACTTATCGAAAGGACTACAATT 57.195 33.333 10.65 0.00 0.00 2.32
972 978 9.582431 TCTTACTTATCGAAAGGACTACAATTG 57.418 33.333 3.24 3.24 0.00 2.32
973 979 9.582431 CTTACTTATCGAAAGGACTACAATTGA 57.418 33.333 13.59 0.00 0.00 2.57
975 981 8.649973 ACTTATCGAAAGGACTACAATTGATC 57.350 34.615 13.59 6.52 0.00 2.92
976 982 7.435488 ACTTATCGAAAGGACTACAATTGATCG 59.565 37.037 13.59 8.45 0.00 3.69
977 983 3.863424 TCGAAAGGACTACAATTGATCGC 59.137 43.478 13.59 0.00 0.00 4.58
978 984 3.616821 CGAAAGGACTACAATTGATCGCA 59.383 43.478 13.59 0.00 0.00 5.10
979 985 4.271049 CGAAAGGACTACAATTGATCGCAT 59.729 41.667 13.59 0.00 0.00 4.73
980 986 5.462068 CGAAAGGACTACAATTGATCGCATA 59.538 40.000 13.59 0.00 0.00 3.14
981 987 6.146184 CGAAAGGACTACAATTGATCGCATAT 59.854 38.462 13.59 0.00 0.00 1.78
982 988 7.328493 CGAAAGGACTACAATTGATCGCATATA 59.672 37.037 13.59 0.00 0.00 0.86
983 989 7.891183 AAGGACTACAATTGATCGCATATAC 57.109 36.000 13.59 0.00 0.00 1.47
984 990 7.233389 AGGACTACAATTGATCGCATATACT 57.767 36.000 13.59 0.00 0.00 2.12
985 991 7.671302 AGGACTACAATTGATCGCATATACTT 58.329 34.615 13.59 0.00 0.00 2.24
986 992 7.600375 AGGACTACAATTGATCGCATATACTTG 59.400 37.037 13.59 0.00 0.00 3.16
987 993 7.385205 GGACTACAATTGATCGCATATACTTGT 59.615 37.037 13.59 0.00 0.00 3.16
988 994 8.076714 ACTACAATTGATCGCATATACTTGTG 57.923 34.615 13.59 0.00 0.00 3.33
989 995 6.304356 ACAATTGATCGCATATACTTGTGG 57.696 37.500 13.59 0.00 0.00 4.17
990 996 5.239306 ACAATTGATCGCATATACTTGTGGG 59.761 40.000 13.59 0.00 0.00 4.61
991 997 4.415881 TTGATCGCATATACTTGTGGGT 57.584 40.909 0.00 0.00 0.00 4.51
992 998 3.990092 TGATCGCATATACTTGTGGGTC 58.010 45.455 0.00 0.00 0.00 4.46
993 999 3.386402 TGATCGCATATACTTGTGGGTCA 59.614 43.478 0.00 0.00 0.00 4.02
994 1000 4.040339 TGATCGCATATACTTGTGGGTCAT 59.960 41.667 0.00 0.00 0.00 3.06
995 1001 3.990092 TCGCATATACTTGTGGGTCATC 58.010 45.455 0.00 0.00 0.00 2.92
996 1002 3.386402 TCGCATATACTTGTGGGTCATCA 59.614 43.478 0.00 0.00 0.00 3.07
997 1003 4.040339 TCGCATATACTTGTGGGTCATCAT 59.960 41.667 0.00 0.00 0.00 2.45
998 1004 4.152938 CGCATATACTTGTGGGTCATCATG 59.847 45.833 0.00 0.00 0.00 3.07
999 1005 4.456911 GCATATACTTGTGGGTCATCATGG 59.543 45.833 0.00 0.00 0.00 3.66
1000 1006 5.745770 GCATATACTTGTGGGTCATCATGGA 60.746 44.000 0.00 0.00 0.00 3.41
1001 1007 6.479006 CATATACTTGTGGGTCATCATGGAT 58.521 40.000 0.00 0.00 0.00 3.41
1002 1008 3.008835 ACTTGTGGGTCATCATGGATG 57.991 47.619 0.00 0.00 41.00 3.51
1003 1009 1.679680 CTTGTGGGTCATCATGGATGC 59.320 52.381 1.37 0.00 39.63 3.91
1004 1010 0.106569 TGTGGGTCATCATGGATGCC 60.107 55.000 1.37 6.31 39.63 4.40
1005 1011 1.148949 TGGGTCATCATGGATGCCG 59.851 57.895 1.37 0.00 39.63 5.69
1006 1012 1.601759 GGGTCATCATGGATGCCGG 60.602 63.158 0.00 0.00 39.63 6.13
1007 1013 1.601759 GGTCATCATGGATGCCGGG 60.602 63.158 2.18 0.00 39.63 5.73
1008 1014 1.601759 GTCATCATGGATGCCGGGG 60.602 63.158 2.18 0.00 39.63 5.73
1009 1015 2.282674 CATCATGGATGCCGGGGG 60.283 66.667 2.18 0.00 33.17 5.40
1023 1029 4.388499 GGGGCTGCGGAAGTCGAA 62.388 66.667 0.00 0.00 42.43 3.71
1025 1031 2.815647 GGCTGCGGAAGTCGAAGG 60.816 66.667 0.00 0.00 44.62 3.46
1026 1032 2.261671 GCTGCGGAAGTCGAAGGA 59.738 61.111 0.00 0.00 44.62 3.36
1027 1033 1.807573 GCTGCGGAAGTCGAAGGAG 60.808 63.158 0.00 0.00 44.62 3.69
1028 1034 1.153745 CTGCGGAAGTCGAAGGAGG 60.154 63.158 0.00 0.00 40.82 4.30
1029 1035 1.595993 CTGCGGAAGTCGAAGGAGGA 61.596 60.000 0.00 0.00 40.82 3.71
1030 1036 1.139947 GCGGAAGTCGAAGGAGGAG 59.860 63.158 0.00 0.00 42.43 3.69
1031 1037 1.139947 CGGAAGTCGAAGGAGGAGC 59.860 63.158 0.00 0.00 42.43 4.70
1032 1038 1.518302 GGAAGTCGAAGGAGGAGCC 59.482 63.158 0.00 0.00 0.00 4.70
1033 1039 1.518302 GAAGTCGAAGGAGGAGCCC 59.482 63.158 0.00 0.00 37.37 5.19
1034 1040 1.229209 AAGTCGAAGGAGGAGCCCA 60.229 57.895 0.00 0.00 37.37 5.36
1035 1041 0.836400 AAGTCGAAGGAGGAGCCCAA 60.836 55.000 0.00 0.00 37.37 4.12
1036 1042 1.079057 GTCGAAGGAGGAGCCCAAC 60.079 63.158 0.00 0.00 37.37 3.77
1037 1043 2.269241 CGAAGGAGGAGCCCAACC 59.731 66.667 0.00 0.00 37.37 3.77
1038 1044 2.677848 GAAGGAGGAGCCCAACCC 59.322 66.667 0.00 0.00 37.37 4.11
1039 1045 2.941583 AAGGAGGAGCCCAACCCC 60.942 66.667 0.00 0.00 37.37 4.95
1060 1066 0.031585 TGACGTGGTCACCTTCTTCG 59.968 55.000 0.00 0.00 37.67 3.79
1062 1068 0.249322 ACGTGGTCACCTTCTTCGTG 60.249 55.000 0.00 0.00 0.00 4.35
1063 1069 0.031585 CGTGGTCACCTTCTTCGTGA 59.968 55.000 0.00 0.00 37.91 4.35
1068 1074 1.006102 CACCTTCTTCGTGAGCGGT 60.006 57.895 0.00 0.00 38.89 5.68
1120 1126 1.021920 GGTCTTCTTCCTCTTGGCGC 61.022 60.000 0.00 0.00 0.00 6.53
1129 1138 4.243008 TCTTGGCGCGTGGAACCA 62.243 61.111 8.43 2.47 0.00 3.67
1137 1146 4.760047 CGTGGAACCAGAGCGGGG 62.760 72.222 0.00 0.00 40.22 5.73
1196 1316 2.828095 GCGGCACATGGTATGGCA 60.828 61.111 8.72 0.00 42.55 4.92
1272 1392 1.437986 CGAGGTTGGAGGACGGATC 59.562 63.158 0.00 0.00 0.00 3.36
1273 1393 1.823976 GAGGTTGGAGGACGGATCC 59.176 63.158 0.00 0.00 46.69 3.36
1368 1506 1.548269 GGCAAAATCGGGTGAAATCCA 59.452 47.619 0.00 0.00 0.00 3.41
1369 1507 2.028567 GGCAAAATCGGGTGAAATCCAA 60.029 45.455 0.00 0.00 0.00 3.53
1676 2251 2.048222 CGCCAGCCTGACTCGAAA 60.048 61.111 0.00 0.00 0.00 3.46
1804 2577 2.541762 CTCCCGCGAAATCTCAATCTTC 59.458 50.000 8.23 0.00 0.00 2.87
3359 7404 2.270352 TTCAAAAGCATCTGGACCGT 57.730 45.000 0.00 0.00 0.00 4.83
4215 8374 6.351711 CCTGAGAGCATTTTCCCTATCGATAT 60.352 42.308 5.40 0.00 0.00 1.63
4216 8375 7.009179 TGAGAGCATTTTCCCTATCGATATT 57.991 36.000 5.40 0.00 0.00 1.28
4217 8376 7.453393 TGAGAGCATTTTCCCTATCGATATTT 58.547 34.615 5.40 0.00 0.00 1.40
4218 8377 7.939039 TGAGAGCATTTTCCCTATCGATATTTT 59.061 33.333 5.40 0.00 0.00 1.82
4219 8378 8.697507 AGAGCATTTTCCCTATCGATATTTTT 57.302 30.769 5.40 0.00 0.00 1.94
4268 8427 5.376854 AGCAGTTTGTTTTCGCTATTCAT 57.623 34.783 0.00 0.00 0.00 2.57
4300 8462 6.147864 TGTTCTTTTTCCATCTTGAACTGG 57.852 37.500 0.00 0.00 35.99 4.00
4370 8559 6.813649 GCTAAAATTGGATGACTTCTTTTCCC 59.186 38.462 0.00 0.00 0.00 3.97
4447 8636 1.364626 GGAGCACGACATGAAGCCTG 61.365 60.000 0.00 0.00 0.00 4.85
4563 8777 8.818141 TTTCTTAAGTATCTATTGGCTGATCG 57.182 34.615 1.63 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.395686 CATCGAGGAGCATGTGGGAT 59.604 55.000 0.00 0.00 0.00 3.85
123 124 5.125100 AGTAACGTACCGATTGACAAAGA 57.875 39.130 0.00 0.00 0.00 2.52
196 197 3.391049 GAACGAGTAAAGTGACTTGCCT 58.609 45.455 0.00 0.00 34.59 4.75
793 795 5.986501 AGTAACAAAGGTGTGTTGGAAAA 57.013 34.783 0.92 0.00 41.75 2.29
822 828 7.235430 AGATAATTTGTAACGAGCAAGTAGC 57.765 36.000 0.00 0.00 46.19 3.58
825 831 7.435068 ACAAGATAATTTGTAACGAGCAAGT 57.565 32.000 0.00 0.00 39.40 3.16
826 832 9.988350 ATAACAAGATAATTTGTAACGAGCAAG 57.012 29.630 0.00 0.00 40.24 4.01
829 835 9.982291 TTGATAACAAGATAATTTGTAACGAGC 57.018 29.630 0.00 0.00 40.24 5.03
860 866 9.065871 GCAAGCACTGAAATTATAAGTAACAAG 57.934 33.333 0.00 0.00 0.00 3.16
868 874 7.686438 TTCTCTGCAAGCACTGAAATTATAA 57.314 32.000 0.00 0.00 0.00 0.98
869 875 7.870509 ATTCTCTGCAAGCACTGAAATTATA 57.129 32.000 8.38 0.00 0.00 0.98
870 876 6.770746 ATTCTCTGCAAGCACTGAAATTAT 57.229 33.333 8.38 0.00 0.00 1.28
871 877 6.094048 GGTATTCTCTGCAAGCACTGAAATTA 59.906 38.462 8.38 0.00 0.00 1.40
872 878 5.105997 GGTATTCTCTGCAAGCACTGAAATT 60.106 40.000 8.38 0.00 0.00 1.82
873 879 4.397417 GGTATTCTCTGCAAGCACTGAAAT 59.603 41.667 8.38 2.42 0.00 2.17
874 880 3.753272 GGTATTCTCTGCAAGCACTGAAA 59.247 43.478 8.38 0.00 0.00 2.69
875 881 3.008375 AGGTATTCTCTGCAAGCACTGAA 59.992 43.478 7.21 7.21 0.00 3.02
876 882 2.568956 AGGTATTCTCTGCAAGCACTGA 59.431 45.455 0.00 0.00 0.00 3.41
877 883 2.983229 AGGTATTCTCTGCAAGCACTG 58.017 47.619 0.00 0.00 0.00 3.66
878 884 3.341823 CAAGGTATTCTCTGCAAGCACT 58.658 45.455 0.00 0.00 0.00 4.40
879 885 2.159462 GCAAGGTATTCTCTGCAAGCAC 60.159 50.000 0.00 0.00 33.11 4.40
880 886 2.086869 GCAAGGTATTCTCTGCAAGCA 58.913 47.619 0.00 0.00 33.11 3.91
881 887 2.363683 AGCAAGGTATTCTCTGCAAGC 58.636 47.619 0.00 0.00 34.34 4.01
882 888 6.317857 GTTTTAGCAAGGTATTCTCTGCAAG 58.682 40.000 0.00 0.00 34.34 4.01
883 889 5.183140 GGTTTTAGCAAGGTATTCTCTGCAA 59.817 40.000 0.00 0.00 34.34 4.08
884 890 4.700213 GGTTTTAGCAAGGTATTCTCTGCA 59.300 41.667 0.00 0.00 34.34 4.41
885 891 4.700213 TGGTTTTAGCAAGGTATTCTCTGC 59.300 41.667 0.00 0.00 33.07 4.26
886 892 5.940470 AGTGGTTTTAGCAAGGTATTCTCTG 59.060 40.000 0.00 0.00 0.00 3.35
887 893 6.128138 AGTGGTTTTAGCAAGGTATTCTCT 57.872 37.500 0.00 0.00 0.00 3.10
888 894 6.206829 ACAAGTGGTTTTAGCAAGGTATTCTC 59.793 38.462 0.00 0.00 0.00 2.87
889 895 6.068670 ACAAGTGGTTTTAGCAAGGTATTCT 58.931 36.000 0.00 0.00 0.00 2.40
890 896 6.016610 TGACAAGTGGTTTTAGCAAGGTATTC 60.017 38.462 0.00 0.00 0.00 1.75
891 897 5.830991 TGACAAGTGGTTTTAGCAAGGTATT 59.169 36.000 0.00 0.00 0.00 1.89
892 898 5.381757 TGACAAGTGGTTTTAGCAAGGTAT 58.618 37.500 0.00 0.00 0.00 2.73
893 899 4.783055 TGACAAGTGGTTTTAGCAAGGTA 58.217 39.130 0.00 0.00 0.00 3.08
894 900 3.626930 TGACAAGTGGTTTTAGCAAGGT 58.373 40.909 0.00 0.00 0.00 3.50
895 901 4.853924 ATGACAAGTGGTTTTAGCAAGG 57.146 40.909 0.00 0.00 0.00 3.61
896 902 5.691754 GGAAATGACAAGTGGTTTTAGCAAG 59.308 40.000 0.00 0.00 0.00 4.01
897 903 5.362430 AGGAAATGACAAGTGGTTTTAGCAA 59.638 36.000 0.00 0.00 0.00 3.91
898 904 4.892934 AGGAAATGACAAGTGGTTTTAGCA 59.107 37.500 0.00 0.00 0.00 3.49
899 905 5.453567 AGGAAATGACAAGTGGTTTTAGC 57.546 39.130 0.00 0.00 0.00 3.09
900 906 7.141363 CAGAAGGAAATGACAAGTGGTTTTAG 58.859 38.462 0.00 0.00 0.00 1.85
901 907 6.460953 GCAGAAGGAAATGACAAGTGGTTTTA 60.461 38.462 0.00 0.00 0.00 1.52
902 908 5.682212 GCAGAAGGAAATGACAAGTGGTTTT 60.682 40.000 0.00 0.00 0.00 2.43
903 909 4.202151 GCAGAAGGAAATGACAAGTGGTTT 60.202 41.667 0.00 0.00 0.00 3.27
904 910 3.319122 GCAGAAGGAAATGACAAGTGGTT 59.681 43.478 0.00 0.00 0.00 3.67
905 911 2.887152 GCAGAAGGAAATGACAAGTGGT 59.113 45.455 0.00 0.00 0.00 4.16
906 912 3.152341 AGCAGAAGGAAATGACAAGTGG 58.848 45.455 0.00 0.00 0.00 4.00
907 913 3.190118 GGAGCAGAAGGAAATGACAAGTG 59.810 47.826 0.00 0.00 0.00 3.16
908 914 3.073650 AGGAGCAGAAGGAAATGACAAGT 59.926 43.478 0.00 0.00 0.00 3.16
909 915 3.683802 AGGAGCAGAAGGAAATGACAAG 58.316 45.455 0.00 0.00 0.00 3.16
910 916 3.679389 GAGGAGCAGAAGGAAATGACAA 58.321 45.455 0.00 0.00 0.00 3.18
911 917 2.354103 CGAGGAGCAGAAGGAAATGACA 60.354 50.000 0.00 0.00 0.00 3.58
912 918 2.275318 CGAGGAGCAGAAGGAAATGAC 58.725 52.381 0.00 0.00 0.00 3.06
913 919 1.902508 ACGAGGAGCAGAAGGAAATGA 59.097 47.619 0.00 0.00 0.00 2.57
914 920 2.393271 ACGAGGAGCAGAAGGAAATG 57.607 50.000 0.00 0.00 0.00 2.32
915 921 2.616510 CCAACGAGGAGCAGAAGGAAAT 60.617 50.000 0.00 0.00 41.22 2.17
916 922 1.270839 CCAACGAGGAGCAGAAGGAAA 60.271 52.381 0.00 0.00 41.22 3.13
917 923 0.321671 CCAACGAGGAGCAGAAGGAA 59.678 55.000 0.00 0.00 41.22 3.36
918 924 0.541998 TCCAACGAGGAGCAGAAGGA 60.542 55.000 0.00 0.00 43.07 3.36
919 925 1.975327 TCCAACGAGGAGCAGAAGG 59.025 57.895 0.00 0.00 43.07 3.46
928 934 1.202582 AGAGTGTCGAATCCAACGAGG 59.797 52.381 0.00 0.00 40.37 4.63
929 935 2.638556 AGAGTGTCGAATCCAACGAG 57.361 50.000 0.00 0.00 40.37 4.18
930 936 3.504906 AGTAAGAGTGTCGAATCCAACGA 59.495 43.478 0.00 0.00 37.43 3.85
931 937 3.834610 AGTAAGAGTGTCGAATCCAACG 58.165 45.455 0.00 0.00 0.00 4.10
932 938 6.196724 CGATAAGTAAGAGTGTCGAATCCAAC 59.803 42.308 0.00 0.00 0.00 3.77
933 939 6.094464 TCGATAAGTAAGAGTGTCGAATCCAA 59.906 38.462 0.00 0.00 35.48 3.53
934 940 5.587443 TCGATAAGTAAGAGTGTCGAATCCA 59.413 40.000 0.00 0.00 35.48 3.41
935 941 6.057627 TCGATAAGTAAGAGTGTCGAATCC 57.942 41.667 0.00 0.00 35.48 3.01
936 942 7.166142 CCTTTCGATAAGTAAGAGTGTCGAATC 59.834 40.741 8.54 0.00 44.33 2.52
937 943 6.973474 CCTTTCGATAAGTAAGAGTGTCGAAT 59.027 38.462 8.54 0.00 44.33 3.34
938 944 6.149973 TCCTTTCGATAAGTAAGAGTGTCGAA 59.850 38.462 4.17 4.17 43.60 3.71
939 945 5.645067 TCCTTTCGATAAGTAAGAGTGTCGA 59.355 40.000 0.00 0.00 36.46 4.20
940 946 5.738225 GTCCTTTCGATAAGTAAGAGTGTCG 59.262 44.000 0.00 0.00 29.89 4.35
941 947 6.854778 AGTCCTTTCGATAAGTAAGAGTGTC 58.145 40.000 0.00 0.00 29.89 3.67
942 948 6.837471 AGTCCTTTCGATAAGTAAGAGTGT 57.163 37.500 0.00 0.00 29.89 3.55
943 949 7.759465 TGTAGTCCTTTCGATAAGTAAGAGTG 58.241 38.462 0.00 0.00 29.89 3.51
944 950 7.934855 TGTAGTCCTTTCGATAAGTAAGAGT 57.065 36.000 0.00 0.00 29.89 3.24
945 951 9.804758 AATTGTAGTCCTTTCGATAAGTAAGAG 57.195 33.333 0.00 0.00 29.89 2.85
946 952 9.582431 CAATTGTAGTCCTTTCGATAAGTAAGA 57.418 33.333 0.00 0.00 29.89 2.10
947 953 9.582431 TCAATTGTAGTCCTTTCGATAAGTAAG 57.418 33.333 5.13 0.00 0.00 2.34
949 955 9.745880 GATCAATTGTAGTCCTTTCGATAAGTA 57.254 33.333 5.13 0.00 0.00 2.24
950 956 7.435488 CGATCAATTGTAGTCCTTTCGATAAGT 59.565 37.037 5.13 0.00 0.00 2.24
951 957 7.567771 GCGATCAATTGTAGTCCTTTCGATAAG 60.568 40.741 5.13 0.00 0.00 1.73
952 958 6.200286 GCGATCAATTGTAGTCCTTTCGATAA 59.800 38.462 5.13 0.00 0.00 1.75
953 959 5.690409 GCGATCAATTGTAGTCCTTTCGATA 59.310 40.000 5.13 0.00 0.00 2.92
954 960 4.508124 GCGATCAATTGTAGTCCTTTCGAT 59.492 41.667 5.13 0.00 0.00 3.59
955 961 3.863424 GCGATCAATTGTAGTCCTTTCGA 59.137 43.478 5.13 0.00 0.00 3.71
956 962 3.616821 TGCGATCAATTGTAGTCCTTTCG 59.383 43.478 5.13 4.43 0.00 3.46
957 963 5.741388 ATGCGATCAATTGTAGTCCTTTC 57.259 39.130 5.13 0.00 0.00 2.62
958 964 8.150945 AGTATATGCGATCAATTGTAGTCCTTT 58.849 33.333 5.13 0.00 0.00 3.11
959 965 7.671302 AGTATATGCGATCAATTGTAGTCCTT 58.329 34.615 5.13 0.16 0.00 3.36
960 966 7.233389 AGTATATGCGATCAATTGTAGTCCT 57.767 36.000 5.13 0.00 0.00 3.85
961 967 7.385205 ACAAGTATATGCGATCAATTGTAGTCC 59.615 37.037 5.13 0.00 0.00 3.85
962 968 8.217115 CACAAGTATATGCGATCAATTGTAGTC 58.783 37.037 5.13 2.19 0.00 2.59
963 969 7.171508 CCACAAGTATATGCGATCAATTGTAGT 59.828 37.037 5.13 0.00 0.00 2.73
964 970 7.360353 CCCACAAGTATATGCGATCAATTGTAG 60.360 40.741 5.13 0.00 0.00 2.74
965 971 6.426633 CCCACAAGTATATGCGATCAATTGTA 59.573 38.462 5.13 0.00 0.00 2.41
966 972 5.239306 CCCACAAGTATATGCGATCAATTGT 59.761 40.000 5.13 0.00 0.00 2.71
967 973 5.239306 ACCCACAAGTATATGCGATCAATTG 59.761 40.000 0.00 0.00 0.00 2.32
968 974 5.376625 ACCCACAAGTATATGCGATCAATT 58.623 37.500 0.00 0.00 0.00 2.32
969 975 4.973168 ACCCACAAGTATATGCGATCAAT 58.027 39.130 0.00 0.00 0.00 2.57
970 976 4.141824 TGACCCACAAGTATATGCGATCAA 60.142 41.667 0.00 0.00 0.00 2.57
971 977 3.386402 TGACCCACAAGTATATGCGATCA 59.614 43.478 0.00 0.00 0.00 2.92
972 978 3.990092 TGACCCACAAGTATATGCGATC 58.010 45.455 0.00 0.00 0.00 3.69
973 979 4.040339 TGATGACCCACAAGTATATGCGAT 59.960 41.667 0.00 0.00 0.00 4.58
974 980 3.386402 TGATGACCCACAAGTATATGCGA 59.614 43.478 0.00 0.00 0.00 5.10
975 981 3.727726 TGATGACCCACAAGTATATGCG 58.272 45.455 0.00 0.00 0.00 4.73
976 982 4.456911 CCATGATGACCCACAAGTATATGC 59.543 45.833 0.00 0.00 0.00 3.14
977 983 5.868454 TCCATGATGACCCACAAGTATATG 58.132 41.667 0.00 0.00 0.00 1.78
978 984 6.479006 CATCCATGATGACCCACAAGTATAT 58.521 40.000 0.00 0.00 42.09 0.86
979 985 5.745770 GCATCCATGATGACCCACAAGTATA 60.746 44.000 8.21 0.00 42.09 1.47
980 986 4.722220 CATCCATGATGACCCACAAGTAT 58.278 43.478 0.00 0.00 42.09 2.12
981 987 3.685265 GCATCCATGATGACCCACAAGTA 60.685 47.826 8.21 0.00 42.09 2.24
982 988 2.947243 GCATCCATGATGACCCACAAGT 60.947 50.000 8.21 0.00 42.09 3.16
983 989 1.679680 GCATCCATGATGACCCACAAG 59.320 52.381 8.21 0.00 42.09 3.16
984 990 1.685803 GGCATCCATGATGACCCACAA 60.686 52.381 8.21 0.00 41.86 3.33
985 991 0.106569 GGCATCCATGATGACCCACA 60.107 55.000 8.21 0.00 41.86 4.17
986 992 1.168407 CGGCATCCATGATGACCCAC 61.168 60.000 8.21 0.00 44.59 4.61
987 993 1.148949 CGGCATCCATGATGACCCA 59.851 57.895 8.21 0.00 44.59 4.51
988 994 1.601759 CCGGCATCCATGATGACCC 60.602 63.158 8.21 0.31 44.59 4.46
989 995 1.601759 CCCGGCATCCATGATGACC 60.602 63.158 8.21 7.61 44.59 4.02
990 996 1.601759 CCCCGGCATCCATGATGAC 60.602 63.158 8.21 4.05 44.03 3.06
991 997 2.832778 CCCCCGGCATCCATGATGA 61.833 63.158 8.21 0.00 42.09 2.92
992 998 2.282674 CCCCCGGCATCCATGATG 60.283 66.667 0.00 0.00 42.37 3.07
1006 1012 4.388499 TTCGACTTCCGCAGCCCC 62.388 66.667 0.00 0.00 38.37 5.80
1007 1013 2.815647 CTTCGACTTCCGCAGCCC 60.816 66.667 0.00 0.00 38.37 5.19
1008 1014 2.815647 CCTTCGACTTCCGCAGCC 60.816 66.667 0.00 0.00 38.37 4.85
1009 1015 1.807573 CTCCTTCGACTTCCGCAGC 60.808 63.158 0.00 0.00 38.37 5.25
1010 1016 1.153745 CCTCCTTCGACTTCCGCAG 60.154 63.158 0.00 0.00 38.37 5.18
1011 1017 1.595993 CTCCTCCTTCGACTTCCGCA 61.596 60.000 0.00 0.00 38.37 5.69
1012 1018 1.139947 CTCCTCCTTCGACTTCCGC 59.860 63.158 0.00 0.00 38.37 5.54
1013 1019 1.139947 GCTCCTCCTTCGACTTCCG 59.860 63.158 0.00 0.00 40.25 4.30
1014 1020 1.518302 GGCTCCTCCTTCGACTTCC 59.482 63.158 0.00 0.00 0.00 3.46
1015 1021 1.258445 TGGGCTCCTCCTTCGACTTC 61.258 60.000 0.00 0.00 34.39 3.01
1016 1022 0.836400 TTGGGCTCCTCCTTCGACTT 60.836 55.000 0.00 0.00 34.39 3.01
1017 1023 1.229209 TTGGGCTCCTCCTTCGACT 60.229 57.895 0.00 0.00 34.39 4.18
1018 1024 1.079057 GTTGGGCTCCTCCTTCGAC 60.079 63.158 0.00 0.00 34.39 4.20
1019 1025 2.291043 GGTTGGGCTCCTCCTTCGA 61.291 63.158 0.00 0.00 34.39 3.71
1020 1026 2.269241 GGTTGGGCTCCTCCTTCG 59.731 66.667 0.00 0.00 34.39 3.79
1021 1027 2.677848 GGGTTGGGCTCCTCCTTC 59.322 66.667 0.00 0.00 34.39 3.46
1022 1028 2.941583 GGGGTTGGGCTCCTCCTT 60.942 66.667 0.00 0.00 33.93 3.36
1025 1031 4.410400 CACGGGGTTGGGCTCCTC 62.410 72.222 0.00 0.00 34.84 3.71
1026 1032 4.974438 TCACGGGGTTGGGCTCCT 62.974 66.667 0.00 0.00 34.84 3.69
1027 1033 4.717313 GTCACGGGGTTGGGCTCC 62.717 72.222 0.00 0.00 0.00 4.70
1120 1126 4.760047 CCCCGCTCTGGTTCCACG 62.760 72.222 0.00 0.00 35.15 4.94
1184 1304 1.077787 CGGGTGTGCCATACCATGT 60.078 57.895 12.99 0.00 40.03 3.21
1237 1357 4.070552 GCAGTCCTTCCTCGCGGT 62.071 66.667 6.13 0.00 0.00 5.68
1368 1506 3.010584 AGCCCAACTCCTTCATATGTGTT 59.989 43.478 1.90 0.00 0.00 3.32
1369 1507 2.578021 AGCCCAACTCCTTCATATGTGT 59.422 45.455 1.90 0.00 0.00 3.72
1423 1561 1.568504 TACTCCAAATCAGGCCGTCT 58.431 50.000 0.00 0.00 0.00 4.18
2202 4388 2.683933 TCCTGGTCGGGAAGGAGC 60.684 66.667 0.00 0.00 37.68 4.70
3359 7404 1.002659 AGTGGTTAATACGTGCCAGCA 59.997 47.619 0.00 0.00 0.00 4.41
4004 8162 8.854614 ATATTGTCTTGAAGAGCTTTACAGTT 57.145 30.769 0.00 0.00 0.00 3.16
4046 8204 9.691362 GAAAACAATGTGTAGGTTTATGTCATT 57.309 29.630 0.00 0.00 33.91 2.57
4218 8377 8.765517 ACTATCGATAGGGTCCTTTTCTAAAAA 58.234 33.333 30.71 0.00 34.69 1.94
4219 8378 8.315220 ACTATCGATAGGGTCCTTTTCTAAAA 57.685 34.615 30.71 0.00 34.69 1.52
4220 8379 7.909485 ACTATCGATAGGGTCCTTTTCTAAA 57.091 36.000 30.71 0.00 34.69 1.85
4221 8380 7.909485 AACTATCGATAGGGTCCTTTTCTAA 57.091 36.000 30.71 0.00 34.69 2.10
4222 8381 7.176340 GCTAACTATCGATAGGGTCCTTTTCTA 59.824 40.741 30.71 5.41 34.69 2.10
4223 8382 6.015265 GCTAACTATCGATAGGGTCCTTTTCT 60.015 42.308 30.71 8.00 34.69 2.52
4224 8383 6.157904 GCTAACTATCGATAGGGTCCTTTTC 58.842 44.000 30.71 10.95 34.69 2.29
4225 8384 5.601313 TGCTAACTATCGATAGGGTCCTTTT 59.399 40.000 30.71 18.46 34.69 2.27
4226 8385 5.145564 TGCTAACTATCGATAGGGTCCTTT 58.854 41.667 30.71 19.05 34.69 3.11
4227 8386 4.737578 TGCTAACTATCGATAGGGTCCTT 58.262 43.478 30.71 19.65 34.69 3.36
4228 8387 4.202588 ACTGCTAACTATCGATAGGGTCCT 60.203 45.833 30.71 11.34 34.69 3.85
4229 8388 4.080687 ACTGCTAACTATCGATAGGGTCC 58.919 47.826 30.71 18.46 34.69 4.46
4230 8389 5.708877 AACTGCTAACTATCGATAGGGTC 57.291 43.478 30.71 18.64 34.69 4.46
4231 8390 5.363005 ACAAACTGCTAACTATCGATAGGGT 59.637 40.000 30.71 21.76 34.69 4.34
4232 8391 5.844004 ACAAACTGCTAACTATCGATAGGG 58.156 41.667 30.71 21.61 34.69 3.53
4233 8392 7.772332 AAACAAACTGCTAACTATCGATAGG 57.228 36.000 30.71 17.30 34.69 2.57
4234 8393 8.050750 CGAAAACAAACTGCTAACTATCGATAG 58.949 37.037 27.15 27.15 36.46 2.08
4235 8394 7.463648 GCGAAAACAAACTGCTAACTATCGATA 60.464 37.037 4.78 4.78 0.00 2.92
4236 8395 6.672357 GCGAAAACAAACTGCTAACTATCGAT 60.672 38.462 2.16 2.16 0.00 3.59
4237 8396 5.389098 GCGAAAACAAACTGCTAACTATCGA 60.389 40.000 0.00 0.00 0.00 3.59
4238 8397 4.781528 GCGAAAACAAACTGCTAACTATCG 59.218 41.667 0.00 0.00 0.00 2.92
4239 8398 5.928153 AGCGAAAACAAACTGCTAACTATC 58.072 37.500 0.00 0.00 33.37 2.08
4240 8399 5.941948 AGCGAAAACAAACTGCTAACTAT 57.058 34.783 0.00 0.00 33.37 2.12
4241 8400 7.171848 TGAATAGCGAAAACAAACTGCTAACTA 59.828 33.333 0.00 0.00 41.06 2.24
4242 8401 5.941948 ATAGCGAAAACAAACTGCTAACT 57.058 34.783 0.00 0.00 41.06 2.24
4268 8427 3.023119 TGGAAAAAGAACAGCAAGAGCA 58.977 40.909 0.00 0.00 45.49 4.26
4370 8559 6.366877 CCAACTGTTAAGCCAAAATCATTCAG 59.633 38.462 0.00 0.00 0.00 3.02
4458 8668 4.351054 CCAGCCCACACAGACCCC 62.351 72.222 0.00 0.00 0.00 4.95
4530 8740 9.853177 CCAATAGATACTTAAGAAATGGACCTT 57.147 33.333 10.09 0.00 0.00 3.50
4563 8777 7.029563 CAGAATAGAAGCCAAACAACCATAAC 58.970 38.462 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.