Multiple sequence alignment - TraesCS2A01G040200

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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 TraesCS2A01G040200 chr2A 100.000 4879 0 0 1 4879 16553223 16558101 0.000000e+00 9010.0
1 TraesCS2A01G040200 chr2A 85.000 480 40 20 1048 1524 366608687 366608237 4.450000e-125 459.0
2 TraesCS2A01G040200 chr2A 94.048 84 3 2 115 197 16553279 16553361 5.130000e-25 126.0
3 TraesCS2A01G040200 chr2A 94.048 84 3 2 57 139 16553337 16553419 5.130000e-25 126.0
4 TraesCS2A01G040200 chr2A 89.583 48 5 0 4175 4222 464164540 464164587 1.470000e-05 62.1
5 TraesCS2A01G040200 chr2A 100.000 29 0 0 4194 4222 163486480 163486508 2.000000e-03 54.7
6 TraesCS2A01G040200 chr2D 89.821 3291 176 60 286 3517 14257759 14260949 0.000000e+00 4074.0
7 TraesCS2A01G040200 chr2D 94.876 605 23 4 3556 4159 14260954 14261551 0.000000e+00 939.0
8 TraesCS2A01G040200 chr2D 88.139 548 37 12 4275 4816 14265870 14266395 1.150000e-175 627.0
9 TraesCS2A01G040200 chr2D 96.154 78 2 1 1 78 14256048 14256124 5.130000e-25 126.0
10 TraesCS2A01G040200 chr2D 92.308 65 2 3 4818 4879 14266435 14266499 6.730000e-14 89.8
11 TraesCS2A01G040200 chr2D 88.710 62 4 3 4818 4879 14261351 14261409 6.770000e-09 73.1
12 TraesCS2A01G040200 chr2B 92.210 2747 142 32 1352 4088 26104008 26106692 0.000000e+00 3821.0
13 TraesCS2A01G040200 chr2B 86.071 481 28 25 831 1286 26103506 26103972 9.500000e-132 481.0
14 TraesCS2A01G040200 chr2B 96.528 144 1 2 4736 4879 26106695 26106834 8.160000e-58 235.0
15 TraesCS2A01G040200 chr2B 89.706 136 10 3 690 821 356544811 356544676 2.340000e-38 171.0
16 TraesCS2A01G040200 chr2B 85.256 156 20 3 691 844 455464323 455464169 1.820000e-34 158.0
17 TraesCS2A01G040200 chr2B 97.143 35 1 0 441 475 790587341 790587375 5.270000e-05 60.2
18 TraesCS2A01G040200 chr2B 100.000 29 0 0 183 211 26102131 26102159 2.000000e-03 54.7
19 TraesCS2A01G040200 chr3A 90.795 1760 105 33 2289 4013 724634909 724636646 0.000000e+00 2300.0
20 TraesCS2A01G040200 chr3A 90.766 509 23 7 1660 2158 724634355 724634849 0.000000e+00 658.0
21 TraesCS2A01G040200 chr3A 93.766 385 20 2 1723 2107 714722066 714721686 4.240000e-160 575.0
22 TraesCS2A01G040200 chr3A 83.789 549 44 24 996 1532 724633839 724634354 3.420000e-131 479.0
23 TraesCS2A01G040200 chr3B 90.439 1778 114 39 2289 4029 796546838 796545080 0.000000e+00 2290.0
24 TraesCS2A01G040200 chr3B 88.333 540 28 7 1652 2176 796547413 796546894 2.500000e-172 616.0
25 TraesCS2A01G040200 chr3B 88.088 319 26 9 996 1307 796548005 796547692 7.720000e-98 368.0
26 TraesCS2A01G040200 chr3B 94.304 158 9 0 1385 1542 796547652 796547495 4.880000e-60 243.0
27 TraesCS2A01G040200 chr3B 90.566 106 7 3 591 695 796549555 796549452 2.370000e-28 137.0
28 TraesCS2A01G040200 chr3B 97.222 36 1 0 441 476 31101033 31100998 1.470000e-05 62.1
29 TraesCS2A01G040200 chr3B 100.000 30 0 0 4194 4223 629956346 629956375 6.820000e-04 56.5
30 TraesCS2A01G040200 chr3D 87.709 1432 85 41 934 2362 3504644 3505987 0.000000e+00 1585.0
31 TraesCS2A01G040200 chr3D 89.547 1148 79 27 2900 4029 593346600 593345476 0.000000e+00 1417.0
32 TraesCS2A01G040200 chr3D 89.453 768 48 5 3283 4049 3506044 3506779 0.000000e+00 939.0
33 TraesCS2A01G040200 chr3D 91.456 632 36 12 2289 2909 593347390 593346766 0.000000e+00 852.0
34 TraesCS2A01G040200 chr3D 88.087 596 35 13 1660 2232 593347986 593347404 0.000000e+00 675.0
35 TraesCS2A01G040200 chr3D 86.337 505 30 24 1035 1532 593348459 593347987 9.360000e-142 514.0
36 TraesCS2A01G040200 chr3D 79.888 537 49 27 4243 4756 593345262 593344762 6.050000e-89 339.0
37 TraesCS2A01G040200 chr3D 87.162 148 16 2 689 834 281391863 281391717 1.090000e-36 165.0
38 TraesCS2A01G040200 chr3D 87.850 107 9 4 591 696 593410745 593410642 6.630000e-24 122.0
39 TraesCS2A01G040200 chr3D 100.000 30 0 0 4194 4223 474442021 474441992 6.820000e-04 56.5
40 TraesCS2A01G040200 chr6D 86.950 1433 95 43 934 2362 76563447 76562103 0.000000e+00 1526.0
41 TraesCS2A01G040200 chr6D 93.987 765 38 6 3286 4049 76562043 76561286 0.000000e+00 1151.0
42 TraesCS2A01G040200 chr6D 93.490 768 42 6 3283 4049 425434012 425434772 0.000000e+00 1134.0
43 TraesCS2A01G040200 chr6D 85.403 1055 75 29 1310 2362 425432978 425433955 0.000000e+00 1022.0
44 TraesCS2A01G040200 chr5B 92.526 388 25 2 1720 2107 483302523 483302140 1.980000e-153 553.0
45 TraesCS2A01G040200 chr5B 89.655 145 11 2 692 836 578545749 578545889 1.080000e-41 182.0
46 TraesCS2A01G040200 chr5A 87.292 480 33 20 1048 1524 431301962 431301508 1.560000e-144 523.0
47 TraesCS2A01G040200 chr7A 86.221 479 38 19 1048 1523 704399952 704399499 1.220000e-135 494.0
48 TraesCS2A01G040200 chr7A 92.771 83 6 0 692 774 521903835 521903917 2.390000e-23 121.0
49 TraesCS2A01G040200 chr4D 93.939 132 6 1 690 821 28103737 28103866 1.070000e-46 198.0
50 TraesCS2A01G040200 chr4D 91.489 47 4 0 4176 4222 494147940 494147986 1.130000e-06 65.8
51 TraesCS2A01G040200 chr4B 90.909 132 11 1 691 821 54291554 54291423 5.020000e-40 176.0
52 TraesCS2A01G040200 chr4B 86.000 150 13 5 690 833 369280432 369280579 2.350000e-33 154.0
53 TraesCS2A01G040200 chr4B 97.143 35 0 1 439 472 436317237 436317203 1.900000e-04 58.4
54 TraesCS2A01G040200 chr7B 86.525 141 13 4 697 833 623571170 623571308 3.040000e-32 150.0
55 TraesCS2A01G040200 chr7B 100.000 30 0 0 4194 4223 464537868 464537897 6.820000e-04 56.5
56 TraesCS2A01G040200 chr6B 97.143 35 1 0 441 475 696500912 696500878 5.270000e-05 60.2
57 TraesCS2A01G040200 chr6B 83.582 67 5 6 4161 4223 135877068 135877132 1.900000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G040200 chr2A 16553223 16558101 4878 False 9010.000000 9010 100.00000 1 4879 1 chr2A.!!$F1 4878
1 TraesCS2A01G040200 chr2D 14256048 14261551 5503 False 1303.025000 4074 92.39025 1 4879 4 chr2D.!!$F1 4878
2 TraesCS2A01G040200 chr2D 14265870 14266499 629 False 358.400000 627 90.22350 4275 4879 2 chr2D.!!$F2 604
3 TraesCS2A01G040200 chr2B 26102131 26106834 4703 False 1147.925000 3821 93.70225 183 4879 4 chr2B.!!$F2 4696
4 TraesCS2A01G040200 chr3A 724633839 724636646 2807 False 1145.666667 2300 88.45000 996 4013 3 chr3A.!!$F1 3017
5 TraesCS2A01G040200 chr3B 796545080 796549555 4475 True 730.800000 2290 90.34600 591 4029 5 chr3B.!!$R2 3438
6 TraesCS2A01G040200 chr3D 3504644 3506779 2135 False 1262.000000 1585 88.58100 934 4049 2 chr3D.!!$F1 3115
7 TraesCS2A01G040200 chr3D 593344762 593348459 3697 True 759.400000 1417 87.06300 1035 4756 5 chr3D.!!$R4 3721
8 TraesCS2A01G040200 chr6D 76561286 76563447 2161 True 1338.500000 1526 90.46850 934 4049 2 chr6D.!!$R1 3115
9 TraesCS2A01G040200 chr6D 425432978 425434772 1794 False 1078.000000 1134 89.44650 1310 4049 2 chr6D.!!$F1 2739

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
906 3503 0.183252 GGCCTAGTCGAGTAGGGAGT 59.817 60.0 36.22 0.0 40.2 3.85 F
1299 4757 0.044397 AAAGGTACCTCTCCCCTCCC 59.956 60.0 16.64 0.0 0.0 4.30 F
1630 5109 0.716108 CCTGACGACGAATCTTGTGC 59.284 55.0 0.00 0.0 0.0 4.57 F
2477 6025 0.105039 GAAGATGTCCCCTACAGGCG 59.895 60.0 0.00 0.0 42.7 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 5688 0.248012 TAAAGGCGGAGATGCGAACA 59.752 50.0 0.00 0.0 35.06 3.18 R
2168 5693 0.466124 AGACCTAAAGGCGGAGATGC 59.534 55.0 0.00 0.0 39.32 3.91 R
2549 6102 1.821216 GCCCTACAAAGCAGTAGCAA 58.179 50.0 5.71 0.0 45.49 3.91 R
3935 7703 0.031616 ACCCCAAAGCCAAACCTTGA 60.032 50.0 0.00 0.0 0.00 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.591202 CCACAATTGTTATGCAGATCGAC 58.409 43.478 8.77 0.00 0.00 4.20
49 50 5.961843 CACAATTGTTATGCAGATCGACTTC 59.038 40.000 8.77 0.00 0.00 3.01
80 81 8.085296 ACTTATTGTGTATAGTCTGCTCATAGC 58.915 37.037 0.00 0.00 42.82 2.97
81 82 6.662865 ATTGTGTATAGTCTGCTCATAGCT 57.337 37.500 0.00 0.00 42.97 3.32
83 84 5.836347 TGTGTATAGTCTGCTCATAGCTTG 58.164 41.667 0.00 0.00 42.97 4.01
84 85 4.683781 GTGTATAGTCTGCTCATAGCTTGC 59.316 45.833 0.00 0.00 42.97 4.01
86 87 4.686191 ATAGTCTGCTCATAGCTTGCTT 57.314 40.909 0.00 0.00 42.97 3.91
89 90 5.033589 AGTCTGCTCATAGCTTGCTTTAT 57.966 39.130 0.00 0.00 42.97 1.40
92 93 7.222872 AGTCTGCTCATAGCTTGCTTTATAAT 58.777 34.615 0.00 0.00 42.97 1.28
93 94 7.387397 AGTCTGCTCATAGCTTGCTTTATAATC 59.613 37.037 0.00 0.00 42.97 1.75
94 95 7.387397 GTCTGCTCATAGCTTGCTTTATAATCT 59.613 37.037 0.00 0.00 42.97 2.40
95 96 7.387122 TCTGCTCATAGCTTGCTTTATAATCTG 59.613 37.037 0.00 0.00 42.97 2.90
96 97 7.219322 TGCTCATAGCTTGCTTTATAATCTGA 58.781 34.615 0.00 0.00 42.97 3.27
99 100 8.092521 TCATAGCTTGCTTTATAATCTGAAGC 57.907 34.615 0.00 0.00 44.54 3.86
100 101 5.415415 AGCTTGCTTTATAATCTGAAGCG 57.585 39.130 0.00 0.00 46.61 4.68
103 104 3.476552 TGCTTTATAATCTGAAGCGGGG 58.523 45.455 0.00 0.00 46.61 5.73
106 107 4.714632 CTTTATAATCTGAAGCGGGGGAA 58.285 43.478 0.00 0.00 0.00 3.97
107 108 4.781775 TTATAATCTGAAGCGGGGGAAA 57.218 40.909 0.00 0.00 0.00 3.13
108 109 2.413310 TAATCTGAAGCGGGGGAAAC 57.587 50.000 0.00 0.00 0.00 2.78
141 142 7.870509 TTTTGTCATATTCTGCTCATAGCTT 57.129 32.000 0.00 0.00 42.97 3.74
142 143 6.856135 TTGTCATATTCTGCTCATAGCTTG 57.144 37.500 0.00 0.00 42.97 4.01
143 144 4.753610 TGTCATATTCTGCTCATAGCTTGC 59.246 41.667 0.00 0.00 42.97 4.01
144 145 4.996122 GTCATATTCTGCTCATAGCTTGCT 59.004 41.667 0.00 0.00 42.97 3.91
146 147 6.017275 GTCATATTCTGCTCATAGCTTGCTTT 60.017 38.462 0.00 0.00 42.97 3.51
147 148 7.172190 GTCATATTCTGCTCATAGCTTGCTTTA 59.828 37.037 0.00 0.00 42.97 1.85
148 149 7.881751 TCATATTCTGCTCATAGCTTGCTTTAT 59.118 33.333 0.00 0.00 42.97 1.40
149 150 9.159364 CATATTCTGCTCATAGCTTGCTTTATA 57.841 33.333 0.00 0.00 42.97 0.98
154 155 7.387122 TCTGCTCATAGCTTGCTTTATAATCTG 59.613 37.037 0.00 0.00 42.97 2.90
156 157 7.716560 TGCTCATAGCTTGCTTTATAATCTGAA 59.283 33.333 0.00 0.00 42.97 3.02
158 159 8.092521 TCATAGCTTGCTTTATAATCTGAAGC 57.907 34.615 0.00 0.00 44.54 3.86
159 160 5.415415 AGCTTGCTTTATAATCTGAAGCG 57.585 39.130 0.00 0.00 46.61 4.68
160 161 4.274459 AGCTTGCTTTATAATCTGAAGCGG 59.726 41.667 0.00 4.89 46.61 5.52
161 162 4.555511 GCTTGCTTTATAATCTGAAGCGGG 60.556 45.833 0.00 0.00 46.61 6.13
164 165 3.496160 GCTTTATAATCTGAAGCGGGGGA 60.496 47.826 0.00 0.00 36.82 4.81
166 167 4.781775 TTATAATCTGAAGCGGGGGAAA 57.218 40.909 0.00 0.00 0.00 3.13
167 168 2.413310 TAATCTGAAGCGGGGGAAAC 57.587 50.000 0.00 0.00 0.00 2.78
220 1476 5.988310 ATCAAAAGCTGATGGTCAAATGA 57.012 34.783 0.00 0.00 43.49 2.57
263 1519 5.611374 CCCACGAATGAATATTAGTCCACT 58.389 41.667 0.00 0.00 30.96 4.00
277 1533 1.210931 CCACTGCAATGCCGAACAG 59.789 57.895 1.53 0.00 36.22 3.16
283 1539 0.527565 GCAATGCCGAACAGTTCCAT 59.472 50.000 7.76 3.70 0.00 3.41
304 1735 8.925161 TCCATTTAAAAATATTCTTTGCTCGG 57.075 30.769 0.00 0.00 0.00 4.63
320 1751 3.078837 GCTCGGGTGGAAATTTACAAGA 58.921 45.455 4.20 4.65 0.00 3.02
323 1754 4.462133 TCGGGTGGAAATTTACAAGAACA 58.538 39.130 4.20 0.00 0.00 3.18
328 1759 6.389906 GGTGGAAATTTACAAGAACATGGAG 58.610 40.000 4.20 0.00 0.00 3.86
363 1797 4.592485 ACGAGTGATCTTTCTGTGACTT 57.408 40.909 0.00 0.00 0.00 3.01
364 1798 4.950050 ACGAGTGATCTTTCTGTGACTTT 58.050 39.130 0.00 0.00 0.00 2.66
668 2793 9.974980 TTCCAAAACCTCAAACAATTAAGATAC 57.025 29.630 0.00 0.00 0.00 2.24
718 3268 4.820173 CCCTCCGTTCCTAAATATTTGTCC 59.180 45.833 11.05 0.00 0.00 4.02
720 3270 6.120220 CCTCCGTTCCTAAATATTTGTCCTT 58.880 40.000 11.05 0.00 0.00 3.36
798 3374 6.258727 ACTGTGTAGTCAGTTGTTGAAATCTG 59.741 38.462 0.00 0.00 44.92 2.90
823 3399 9.932207 TGTAGAAAGACAAATATTTAGGAACGA 57.068 29.630 0.00 0.00 0.00 3.85
905 3502 0.537828 GGGCCTAGTCGAGTAGGGAG 60.538 65.000 36.22 19.03 40.20 4.30
906 3503 0.183252 GGCCTAGTCGAGTAGGGAGT 59.817 60.000 36.22 0.00 40.20 3.85
907 3504 1.419387 GGCCTAGTCGAGTAGGGAGTA 59.581 57.143 36.22 2.67 40.20 2.59
909 3506 2.158842 GCCTAGTCGAGTAGGGAGTACA 60.159 54.545 36.22 1.25 40.20 2.90
910 3507 3.465871 CCTAGTCGAGTAGGGAGTACAC 58.534 54.545 31.18 0.00 36.63 2.90
911 3508 2.021355 AGTCGAGTAGGGAGTACACG 57.979 55.000 0.00 0.00 44.39 4.49
912 3509 1.012841 GTCGAGTAGGGAGTACACGG 58.987 60.000 0.00 0.00 43.54 4.94
920 3517 1.602327 GGGAGTACACGGACTGACCC 61.602 65.000 0.00 0.00 34.64 4.46
952 3555 2.648304 GGGTTTTAGGGTTTCCTCCTCT 59.352 50.000 0.00 0.00 43.66 3.69
975 4401 1.815613 CTCTCTTTGGCTCTCTGTCGA 59.184 52.381 0.00 0.00 0.00 4.20
1052 4510 1.819905 GGAAGAGAGAAGGAGCCGG 59.180 63.158 0.00 0.00 0.00 6.13
1298 4756 1.205055 CAAAGGTACCTCTCCCCTCC 58.795 60.000 16.64 0.00 0.00 4.30
1299 4757 0.044397 AAAGGTACCTCTCCCCTCCC 59.956 60.000 16.64 0.00 0.00 4.30
1300 4758 1.899345 AAGGTACCTCTCCCCTCCCC 61.899 65.000 16.64 0.00 0.00 4.81
1301 4759 2.286213 GTACCTCTCCCCTCCCCC 59.714 72.222 0.00 0.00 0.00 5.40
1302 4760 2.134652 TACCTCTCCCCTCCCCCT 59.865 66.667 0.00 0.00 0.00 4.79
1303 4761 2.019272 TACCTCTCCCCTCCCCCTC 61.019 68.421 0.00 0.00 0.00 4.30
1348 4806 7.148086 CCATCCCTATCGATTTCTTGTTGAAAA 60.148 37.037 1.71 0.00 46.32 2.29
1584 5055 2.338809 CCATCCCTGCCTCCTTGTATA 58.661 52.381 0.00 0.00 0.00 1.47
1630 5109 0.716108 CCTGACGACGAATCTTGTGC 59.284 55.000 0.00 0.00 0.00 4.57
1731 5220 3.832492 AGGAAGGCGCTCGAGCTC 61.832 66.667 32.88 26.34 39.32 4.09
2168 5693 7.429636 TCAGGTACTTTTATCCTTTTGTTCG 57.570 36.000 0.00 0.00 34.60 3.95
2181 5712 0.605319 TTGTTCGCATCTCCGCCTTT 60.605 50.000 0.00 0.00 0.00 3.11
2197 5728 2.288213 GCCTTTAGGTCTTGTGTTTGGC 60.288 50.000 0.00 0.00 37.57 4.52
2198 5729 2.955660 CCTTTAGGTCTTGTGTTTGGCA 59.044 45.455 0.00 0.00 0.00 4.92
2201 5733 1.680338 AGGTCTTGTGTTTGGCAGAC 58.320 50.000 0.39 0.39 0.00 3.51
2227 5759 6.445451 AATCTAGTGGGAGACATAATGCAT 57.555 37.500 0.00 0.00 0.00 3.96
2275 5808 4.002982 TGATGTATCGCTTTCTTTGTGCT 58.997 39.130 0.00 0.00 0.00 4.40
2311 5844 4.028131 ACATGCCATTCTCCAATCATGTT 58.972 39.130 0.00 0.00 35.43 2.71
2453 6000 0.110486 ACCAGACCGAGCCAACATTT 59.890 50.000 0.00 0.00 0.00 2.32
2458 6005 1.197721 GACCGAGCCAACATTTGTGAG 59.802 52.381 0.00 0.00 0.00 3.51
2469 6017 3.690460 ACATTTGTGAGAAGATGTCCCC 58.310 45.455 0.00 0.00 0.00 4.81
2474 6022 3.099905 TGTGAGAAGATGTCCCCTACAG 58.900 50.000 0.00 0.00 42.70 2.74
2477 6025 0.105039 GAAGATGTCCCCTACAGGCG 59.895 60.000 0.00 0.00 42.70 5.52
2549 6102 2.745281 GCATTGCATTGCACAATTCCTT 59.255 40.909 24.71 0.00 42.31 3.36
2565 6118 5.886960 ATTCCTTTGCTACTGCTTTGTAG 57.113 39.130 7.44 7.44 41.91 2.74
2647 6201 6.481976 GCAAGTTTTAACCTTGGCAAACTATT 59.518 34.615 0.00 0.00 38.28 1.73
2654 6208 4.406456 ACCTTGGCAAACTATTCATGTGA 58.594 39.130 0.00 0.00 0.00 3.58
2820 6383 7.174253 CGAGCTACTGAAGATATTCCTTACTCT 59.826 40.741 0.00 0.00 0.00 3.24
2926 6664 4.151798 GCAATTCTACGTTGCTTCAACTC 58.848 43.478 0.00 0.00 46.34 3.01
3078 6817 1.668419 CCCTTGAGGTAATCGGCTTG 58.332 55.000 0.00 0.00 0.00 4.01
3406 7146 2.257207 CTTGGAGTGTGGAGGGTAAGA 58.743 52.381 0.00 0.00 0.00 2.10
3409 7149 2.258109 GGAGTGTGGAGGGTAAGACTT 58.742 52.381 0.00 0.00 0.00 3.01
3531 7285 4.497291 ACTCCTACAGTGACCTAGAGAG 57.503 50.000 0.00 1.02 32.26 3.20
3550 7308 5.845065 AGAGAGGAACTTTTAGGTGGTTACT 59.155 40.000 0.00 0.00 41.55 2.24
3553 7311 6.100714 AGAGGAACTTTTAGGTGGTTACTGAA 59.899 38.462 0.00 0.00 41.55 3.02
3554 7312 6.849151 AGGAACTTTTAGGTGGTTACTGAAT 58.151 36.000 0.00 0.00 33.44 2.57
4095 7962 7.077605 CGATAATTGTCTTCAAAGCAAGTTGA 58.922 34.615 7.16 0.00 37.11 3.18
4120 7987 7.227156 AGTTCTGAGTTTGTTCATCCAGTATT 58.773 34.615 0.00 0.00 0.00 1.89
4121 7988 7.173907 AGTTCTGAGTTTGTTCATCCAGTATTG 59.826 37.037 0.00 0.00 0.00 1.90
4122 7989 6.768483 TCTGAGTTTGTTCATCCAGTATTGA 58.232 36.000 0.00 0.00 0.00 2.57
4123 7990 6.875726 TCTGAGTTTGTTCATCCAGTATTGAG 59.124 38.462 0.00 0.00 0.00 3.02
4124 7991 6.533730 TGAGTTTGTTCATCCAGTATTGAGT 58.466 36.000 0.00 0.00 0.00 3.41
4125 7992 6.427853 TGAGTTTGTTCATCCAGTATTGAGTG 59.572 38.462 0.00 0.00 0.00 3.51
4127 7994 4.284829 TGTTCATCCAGTATTGAGTGCA 57.715 40.909 0.00 0.00 0.00 4.57
4128 7995 4.847198 TGTTCATCCAGTATTGAGTGCAT 58.153 39.130 0.00 0.00 0.00 3.96
4129 7996 4.637091 TGTTCATCCAGTATTGAGTGCATG 59.363 41.667 0.00 0.00 0.00 4.06
4130 7997 3.208594 TCATCCAGTATTGAGTGCATGC 58.791 45.455 11.82 11.82 0.00 4.06
4131 7998 3.118149 TCATCCAGTATTGAGTGCATGCT 60.118 43.478 20.33 0.00 0.00 3.79
4132 7999 2.910199 TCCAGTATTGAGTGCATGCTC 58.090 47.619 20.33 15.94 36.12 4.26
4160 8027 5.056480 TCAAATGGATTGAGCGTAGTATGG 58.944 41.667 0.00 0.00 43.08 2.74
4161 8028 3.685139 ATGGATTGAGCGTAGTATGGG 57.315 47.619 0.00 0.00 0.00 4.00
4162 8029 1.691976 TGGATTGAGCGTAGTATGGGG 59.308 52.381 0.00 0.00 0.00 4.96
4163 8030 1.608283 GGATTGAGCGTAGTATGGGGC 60.608 57.143 0.00 0.00 0.00 5.80
4164 8031 1.344763 GATTGAGCGTAGTATGGGGCT 59.655 52.381 0.00 0.00 38.70 5.19
4165 8032 1.200519 TTGAGCGTAGTATGGGGCTT 58.799 50.000 0.00 0.00 35.54 4.35
4166 8033 1.200519 TGAGCGTAGTATGGGGCTTT 58.799 50.000 0.00 0.00 35.54 3.51
4167 8034 1.557832 TGAGCGTAGTATGGGGCTTTT 59.442 47.619 0.00 0.00 35.54 2.27
4168 8035 2.026636 TGAGCGTAGTATGGGGCTTTTT 60.027 45.455 0.00 0.00 35.54 1.94
4169 8036 2.612672 GAGCGTAGTATGGGGCTTTTTC 59.387 50.000 0.00 0.00 35.54 2.29
4170 8037 1.674441 GCGTAGTATGGGGCTTTTTCC 59.326 52.381 0.00 0.00 0.00 3.13
4171 8038 2.294979 CGTAGTATGGGGCTTTTTCCC 58.705 52.381 0.00 0.00 45.80 3.97
4177 8044 3.373226 GGGCTTTTTCCCCGTTCC 58.627 61.111 0.00 0.00 40.51 3.62
4178 8045 1.228769 GGGCTTTTTCCCCGTTCCT 60.229 57.895 0.00 0.00 40.51 3.36
4179 8046 0.830444 GGGCTTTTTCCCCGTTCCTT 60.830 55.000 0.00 0.00 40.51 3.36
4180 8047 0.601558 GGCTTTTTCCCCGTTCCTTC 59.398 55.000 0.00 0.00 0.00 3.46
4181 8048 1.617322 GCTTTTTCCCCGTTCCTTCT 58.383 50.000 0.00 0.00 0.00 2.85
4182 8049 1.540267 GCTTTTTCCCCGTTCCTTCTC 59.460 52.381 0.00 0.00 0.00 2.87
4183 8050 2.814469 GCTTTTTCCCCGTTCCTTCTCT 60.814 50.000 0.00 0.00 0.00 3.10
4184 8051 3.558533 GCTTTTTCCCCGTTCCTTCTCTA 60.559 47.826 0.00 0.00 0.00 2.43
4185 8052 4.648651 CTTTTTCCCCGTTCCTTCTCTAA 58.351 43.478 0.00 0.00 0.00 2.10
4186 8053 4.921644 TTTTCCCCGTTCCTTCTCTAAT 57.078 40.909 0.00 0.00 0.00 1.73
4187 8054 3.906720 TTCCCCGTTCCTTCTCTAATG 57.093 47.619 0.00 0.00 0.00 1.90
4188 8055 2.116238 TCCCCGTTCCTTCTCTAATGG 58.884 52.381 0.00 0.00 0.00 3.16
4189 8056 2.116238 CCCCGTTCCTTCTCTAATGGA 58.884 52.381 0.00 0.00 34.26 3.41
4190 8057 2.706190 CCCCGTTCCTTCTCTAATGGAT 59.294 50.000 0.00 0.00 34.26 3.41
4191 8058 3.495100 CCCCGTTCCTTCTCTAATGGATG 60.495 52.174 0.00 0.00 34.26 3.51
4192 8059 3.388024 CCCGTTCCTTCTCTAATGGATGA 59.612 47.826 0.00 0.00 34.26 2.92
4193 8060 4.040952 CCCGTTCCTTCTCTAATGGATGAT 59.959 45.833 0.00 0.00 34.26 2.45
4194 8061 5.246203 CCCGTTCCTTCTCTAATGGATGATA 59.754 44.000 0.00 0.00 34.26 2.15
4195 8062 6.159988 CCGTTCCTTCTCTAATGGATGATAC 58.840 44.000 0.00 0.00 34.26 2.24
4196 8063 5.859114 CGTTCCTTCTCTAATGGATGATACG 59.141 44.000 0.00 0.00 0.00 3.06
4197 8064 5.392767 TCCTTCTCTAATGGATGATACGC 57.607 43.478 0.00 0.00 0.00 4.42
4198 8065 4.832823 TCCTTCTCTAATGGATGATACGCA 59.167 41.667 0.00 0.00 0.00 5.24
4199 8066 4.926238 CCTTCTCTAATGGATGATACGCAC 59.074 45.833 0.00 0.00 0.00 5.34
4200 8067 5.509670 CCTTCTCTAATGGATGATACGCACA 60.510 44.000 0.00 0.00 0.00 4.57
4201 8068 4.871513 TCTCTAATGGATGATACGCACAC 58.128 43.478 0.00 0.00 0.00 3.82
4202 8069 4.584743 TCTCTAATGGATGATACGCACACT 59.415 41.667 0.00 0.00 0.00 3.55
4203 8070 4.871513 TCTAATGGATGATACGCACACTC 58.128 43.478 0.00 0.00 0.00 3.51
4204 8071 3.541996 AATGGATGATACGCACACTCA 57.458 42.857 0.00 0.00 0.00 3.41
4205 8072 3.758755 ATGGATGATACGCACACTCAT 57.241 42.857 0.00 0.00 32.46 2.90
4206 8073 2.825205 TGGATGATACGCACACTCATG 58.175 47.619 0.00 0.00 30.00 3.07
4207 8074 1.528586 GGATGATACGCACACTCATGC 59.471 52.381 0.00 0.00 42.48 4.06
4216 8083 3.043635 GCACACTCATGCGTATTCAAG 57.956 47.619 0.00 0.00 35.50 3.02
4217 8084 2.672874 GCACACTCATGCGTATTCAAGA 59.327 45.455 0.00 0.00 35.50 3.02
4218 8085 3.125146 GCACACTCATGCGTATTCAAGAA 59.875 43.478 0.00 0.00 35.50 2.52
4219 8086 4.378356 GCACACTCATGCGTATTCAAGAAA 60.378 41.667 0.00 0.00 35.50 2.52
4220 8087 5.688823 CACACTCATGCGTATTCAAGAAAA 58.311 37.500 0.00 0.00 0.00 2.29
4221 8088 6.142139 CACACTCATGCGTATTCAAGAAAAA 58.858 36.000 0.00 0.00 0.00 1.94
4256 8123 8.812972 TGTAGTATCACCAACTATTTGAGTCTT 58.187 33.333 0.00 0.00 37.44 3.01
4258 8125 8.779354 AGTATCACCAACTATTTGAGTCTTTC 57.221 34.615 0.00 0.00 37.44 2.62
4259 8126 8.598041 AGTATCACCAACTATTTGAGTCTTTCT 58.402 33.333 0.00 0.00 37.44 2.52
4267 8136 5.721960 ACTATTTGAGTCTTTCTGAGGGCTA 59.278 40.000 0.00 0.00 29.95 3.93
4273 8142 3.904339 AGTCTTTCTGAGGGCTACTTTGA 59.096 43.478 0.00 0.00 0.00 2.69
4275 8144 5.013599 AGTCTTTCTGAGGGCTACTTTGATT 59.986 40.000 0.00 0.00 0.00 2.57
4276 8145 5.352846 GTCTTTCTGAGGGCTACTTTGATTC 59.647 44.000 0.00 0.00 0.00 2.52
4278 8147 4.908601 TCTGAGGGCTACTTTGATTCAA 57.091 40.909 0.00 0.00 0.00 2.69
4279 8148 5.241403 TCTGAGGGCTACTTTGATTCAAA 57.759 39.130 11.19 11.19 0.00 2.69
4393 8271 5.240183 TGAAAAGATTGCTCTTGACTCCTTG 59.760 40.000 0.00 0.00 40.93 3.61
4394 8272 3.347077 AGATTGCTCTTGACTCCTTGG 57.653 47.619 0.00 0.00 0.00 3.61
4395 8273 2.909006 AGATTGCTCTTGACTCCTTGGA 59.091 45.455 0.00 0.00 0.00 3.53
4396 8274 2.847327 TTGCTCTTGACTCCTTGGAG 57.153 50.000 14.58 14.58 0.00 3.86
4398 8276 1.270907 GCTCTTGACTCCTTGGAGGA 58.729 55.000 19.51 5.68 43.43 3.71
4399 8277 1.625818 GCTCTTGACTCCTTGGAGGAA 59.374 52.381 19.51 11.16 45.28 3.36
4400 8278 2.039084 GCTCTTGACTCCTTGGAGGAAA 59.961 50.000 19.51 12.23 45.28 3.13
4401 8279 3.496870 GCTCTTGACTCCTTGGAGGAAAA 60.497 47.826 19.51 10.14 45.28 2.29
4402 8280 4.809007 GCTCTTGACTCCTTGGAGGAAAAT 60.809 45.833 19.51 0.00 45.28 1.82
4403 8281 5.320277 CTCTTGACTCCTTGGAGGAAAATT 58.680 41.667 19.51 0.00 45.28 1.82
4404 8282 5.705400 TCTTGACTCCTTGGAGGAAAATTT 58.295 37.500 19.51 0.00 45.28 1.82
4405 8283 5.770162 TCTTGACTCCTTGGAGGAAAATTTC 59.230 40.000 19.51 7.69 45.28 2.17
4406 8284 4.407365 TGACTCCTTGGAGGAAAATTTCC 58.593 43.478 16.59 16.59 45.28 3.13
4540 8418 9.436957 GACAGTCAACTTCAATTTCTCCTATTA 57.563 33.333 0.00 0.00 0.00 0.98
4557 8435 7.987458 TCTCCTATTACTGCATTTCGAAAATCT 59.013 33.333 15.66 0.00 0.00 2.40
4589 8468 3.072211 AGAGCGCCTTTAACCTTTGTAC 58.928 45.455 2.29 0.00 0.00 2.90
4685 8575 8.641499 TTCCAACTCAACAAATGAATACAAAC 57.359 30.769 0.00 0.00 37.67 2.93
4688 8578 5.219633 ACTCAACAAATGAATACAAACCGC 58.780 37.500 0.00 0.00 37.67 5.68
4694 8584 3.740044 ATGAATACAAACCGCGACAAG 57.260 42.857 8.23 0.00 0.00 3.16
4705 8595 4.078363 ACCGCGACAAGATTTACATTTG 57.922 40.909 8.23 0.00 0.00 2.32
4708 8598 3.297979 CGCGACAAGATTTACATTTGCAC 59.702 43.478 0.00 0.00 0.00 4.57
4711 8601 4.612712 CGACAAGATTTACATTTGCACGGT 60.613 41.667 0.00 0.00 0.00 4.83
4749 8639 1.486726 CCACCAGTTCTCCATCCTACC 59.513 57.143 0.00 0.00 0.00 3.18
4847 8778 9.295825 TGTTCAGAATTTGTATCAGGTATGTTT 57.704 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.672086 GAGCAGACTATACACAATAAGTAAGAG 57.328 37.037 0.00 0.00 0.00 2.85
68 69 6.851222 TTATAAAGCAAGCTATGAGCAGAC 57.149 37.500 0.64 0.00 45.56 3.51
78 79 4.274459 CCGCTTCAGATTATAAAGCAAGCT 59.726 41.667 14.72 0.00 44.39 3.74
79 80 4.531332 CCGCTTCAGATTATAAAGCAAGC 58.469 43.478 7.06 8.53 44.39 4.01
80 81 4.023707 CCCCGCTTCAGATTATAAAGCAAG 60.024 45.833 7.06 1.32 44.39 4.01
81 82 3.882888 CCCCGCTTCAGATTATAAAGCAA 59.117 43.478 7.06 0.00 44.39 3.91
83 84 2.814336 CCCCCGCTTCAGATTATAAAGC 59.186 50.000 0.00 0.00 41.51 3.51
84 85 4.351874 TCCCCCGCTTCAGATTATAAAG 57.648 45.455 0.00 0.00 0.00 1.85
86 87 4.457466 GTTTCCCCCGCTTCAGATTATAA 58.543 43.478 0.00 0.00 0.00 0.98
89 90 1.064979 GGTTTCCCCCGCTTCAGATTA 60.065 52.381 0.00 0.00 0.00 1.75
92 93 2.754375 GGTTTCCCCCGCTTCAGA 59.246 61.111 0.00 0.00 0.00 3.27
93 94 2.361230 GGGTTTCCCCCGCTTCAG 60.361 66.667 0.00 0.00 45.80 3.02
116 117 7.870509 AGCTATGAGCAGAATATGACAAAAA 57.129 32.000 0.64 0.00 45.56 1.94
117 118 7.680350 GCAAGCTATGAGCAGAATATGACAAAA 60.680 37.037 0.64 0.00 45.56 2.44
119 120 5.237996 GCAAGCTATGAGCAGAATATGACAA 59.762 40.000 0.64 0.00 45.56 3.18
121 122 4.996122 AGCAAGCTATGAGCAGAATATGAC 59.004 41.667 0.64 0.00 45.56 3.06
122 123 5.224821 AGCAAGCTATGAGCAGAATATGA 57.775 39.130 0.64 0.00 45.56 2.15
123 124 5.943706 AAGCAAGCTATGAGCAGAATATG 57.056 39.130 0.64 0.00 45.56 1.78
124 125 9.730705 TTATAAAGCAAGCTATGAGCAGAATAT 57.269 29.630 0.64 0.00 45.56 1.28
125 126 9.730705 ATTATAAAGCAAGCTATGAGCAGAATA 57.269 29.630 0.64 0.00 45.56 1.75
126 127 8.632906 ATTATAAAGCAAGCTATGAGCAGAAT 57.367 30.769 0.64 0.00 45.56 2.40
127 128 7.935755 AGATTATAAAGCAAGCTATGAGCAGAA 59.064 33.333 0.64 0.00 45.56 3.02
128 129 7.387122 CAGATTATAAAGCAAGCTATGAGCAGA 59.613 37.037 0.64 0.00 45.56 4.26
129 130 7.387122 TCAGATTATAAAGCAAGCTATGAGCAG 59.613 37.037 0.64 0.00 45.56 4.24
130 131 7.219322 TCAGATTATAAAGCAAGCTATGAGCA 58.781 34.615 0.64 0.00 45.56 4.26
131 132 7.664082 TCAGATTATAAAGCAAGCTATGAGC 57.336 36.000 0.00 0.00 42.84 4.26
132 133 8.229137 GCTTCAGATTATAAAGCAAGCTATGAG 58.771 37.037 11.64 0.00 43.77 2.90
134 135 7.014115 CGCTTCAGATTATAAAGCAAGCTATG 58.986 38.462 14.72 0.00 44.39 2.23
135 136 6.148480 CCGCTTCAGATTATAAAGCAAGCTAT 59.852 38.462 14.72 0.00 44.39 2.97
136 137 5.466728 CCGCTTCAGATTATAAAGCAAGCTA 59.533 40.000 14.72 0.00 44.39 3.32
137 138 4.274459 CCGCTTCAGATTATAAAGCAAGCT 59.726 41.667 14.72 0.00 44.39 3.74
138 139 4.531332 CCGCTTCAGATTATAAAGCAAGC 58.469 43.478 7.06 8.53 44.39 4.01
139 140 4.023707 CCCCGCTTCAGATTATAAAGCAAG 60.024 45.833 7.06 1.32 44.39 4.01
141 142 3.476552 CCCCGCTTCAGATTATAAAGCA 58.523 45.455 7.06 0.00 44.39 3.91
142 143 2.814336 CCCCCGCTTCAGATTATAAAGC 59.186 50.000 0.00 0.00 41.51 3.51
143 144 4.351874 TCCCCCGCTTCAGATTATAAAG 57.648 45.455 0.00 0.00 0.00 1.85
144 145 4.781775 TTCCCCCGCTTCAGATTATAAA 57.218 40.909 0.00 0.00 0.00 1.40
146 147 3.181448 GGTTTCCCCCGCTTCAGATTATA 60.181 47.826 0.00 0.00 0.00 0.98
147 148 2.422945 GGTTTCCCCCGCTTCAGATTAT 60.423 50.000 0.00 0.00 0.00 1.28
148 149 1.064979 GGTTTCCCCCGCTTCAGATTA 60.065 52.381 0.00 0.00 0.00 1.75
149 150 0.323451 GGTTTCCCCCGCTTCAGATT 60.323 55.000 0.00 0.00 0.00 2.40
181 182 9.217278 AGCTTTTGATACTATGAGCAGAATATG 57.783 33.333 0.00 0.00 32.78 1.78
182 183 9.217278 CAGCTTTTGATACTATGAGCAGAATAT 57.783 33.333 0.00 0.00 32.78 1.28
183 184 8.424133 TCAGCTTTTGATACTATGAGCAGAATA 58.576 33.333 0.00 0.00 32.78 1.75
184 185 7.278135 TCAGCTTTTGATACTATGAGCAGAAT 58.722 34.615 0.00 0.00 32.78 2.40
185 186 6.643388 TCAGCTTTTGATACTATGAGCAGAA 58.357 36.000 0.00 0.00 32.78 3.02
186 187 6.225981 TCAGCTTTTGATACTATGAGCAGA 57.774 37.500 0.00 0.00 32.78 4.26
187 188 6.073167 CCATCAGCTTTTGATACTATGAGCAG 60.073 42.308 0.00 0.00 44.76 4.24
192 1448 7.558161 TTGACCATCAGCTTTTGATACTATG 57.442 36.000 0.00 0.00 44.76 2.23
193 1449 8.627403 CATTTGACCATCAGCTTTTGATACTAT 58.373 33.333 0.00 0.00 44.76 2.12
263 1519 0.821301 TGGAACTGTTCGGCATTGCA 60.821 50.000 13.89 2.35 0.00 4.08
283 1539 7.039644 TCCACCCGAGCAAAGAATATTTTTAAA 60.040 33.333 0.00 0.00 0.00 1.52
304 1735 6.208599 TCTCCATGTTCTTGTAAATTTCCACC 59.791 38.462 0.00 0.00 0.00 4.61
320 1751 6.542005 TCGTATAAAATGTGCATCTCCATGTT 59.458 34.615 0.00 0.00 31.86 2.71
323 1754 6.203530 CACTCGTATAAAATGTGCATCTCCAT 59.796 38.462 0.00 0.00 0.00 3.41
328 1759 7.413475 AGATCACTCGTATAAAATGTGCATC 57.587 36.000 0.00 0.00 0.00 3.91
390 1824 9.474920 GGAATCAAAATGAACAACATAACTCAA 57.525 29.630 0.00 0.00 38.38 3.02
397 1831 6.351286 GCCCTAGGAATCAAAATGAACAACAT 60.351 38.462 11.48 0.00 41.45 2.71
685 3235 4.750021 AGGAACGGAGGGAGTATAAAAC 57.250 45.455 0.00 0.00 0.00 2.43
720 3270 9.137459 TGTGGTAGTCCATTTGAAATCTTTAAA 57.863 29.630 0.00 0.00 46.20 1.52
778 3330 8.589335 TTCTACAGATTTCAACAACTGACTAC 57.411 34.615 0.00 0.00 32.21 2.73
886 3483 0.537828 CTCCCTACTCGACTAGGCCC 60.538 65.000 11.53 0.00 33.02 5.80
920 3517 3.256824 TAAAACCCTCGGGCCCACG 62.257 63.158 24.92 11.84 39.32 4.94
952 3555 2.564947 GACAGAGAGCCAAAGAGAGGAA 59.435 50.000 0.00 0.00 0.00 3.36
975 4401 0.254299 AGGGGATTGGGATTGGGAGT 60.254 55.000 0.00 0.00 0.00 3.85
1028 4471 1.216710 CCTTCTCTCTTCCGCGCTT 59.783 57.895 5.56 0.00 0.00 4.68
1052 4510 3.330853 GACGATCGTCGCCATGGC 61.331 66.667 30.46 27.67 45.12 4.40
1227 4685 2.434884 CGTTGGCGAGCATGAGGT 60.435 61.111 0.00 0.00 41.33 3.85
1299 4757 4.179599 GAGAGGGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1300 4758 4.179599 GGAGAGGGGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1301 4759 2.613576 GAAGGAGAGGGGAGGGGGAG 62.614 70.000 0.00 0.00 0.00 4.30
1302 4760 2.543637 AAGGAGAGGGGAGGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
1303 4761 2.040359 GAAGGAGAGGGGAGGGGG 60.040 72.222 0.00 0.00 0.00 5.40
1347 4805 1.767759 AGGATAAGCAAGGCGCAATT 58.232 45.000 10.83 0.00 46.13 2.32
1348 4806 2.222027 GTAGGATAAGCAAGGCGCAAT 58.778 47.619 10.83 0.00 46.13 3.56
1563 5034 0.988145 TACAAGGAGGCAGGGATGGG 60.988 60.000 0.00 0.00 0.00 4.00
1599 5070 8.794553 AGATTCGTCGTCAGGAAACTTATATAT 58.205 33.333 0.00 0.00 40.21 0.86
1600 5071 8.162878 AGATTCGTCGTCAGGAAACTTATATA 57.837 34.615 0.00 0.00 40.21 0.86
1630 5109 1.210931 CACACATTGGCAGCGGAAG 59.789 57.895 0.00 0.00 0.00 3.46
1888 5386 4.021719 ACTTGGAAGCAAAGGACAATGATG 60.022 41.667 0.00 0.00 0.00 3.07
1890 5388 3.565307 ACTTGGAAGCAAAGGACAATGA 58.435 40.909 0.00 0.00 0.00 2.57
1939 5446 5.376854 ACAACAATCTTGCCATGTTACTC 57.623 39.130 0.00 0.00 35.63 2.59
2162 5687 0.605319 AAAGGCGGAGATGCGAACAA 60.605 50.000 0.00 0.00 35.06 2.83
2163 5688 0.248012 TAAAGGCGGAGATGCGAACA 59.752 50.000 0.00 0.00 35.06 3.18
2168 5693 0.466124 AGACCTAAAGGCGGAGATGC 59.534 55.000 0.00 0.00 39.32 3.91
2181 5712 2.171659 TGTCTGCCAAACACAAGACCTA 59.828 45.455 0.00 0.00 0.00 3.08
2197 5728 5.152623 TGTCTCCCACTAGATTTTGTCTG 57.847 43.478 0.00 0.00 37.83 3.51
2198 5729 7.496346 TTATGTCTCCCACTAGATTTTGTCT 57.504 36.000 0.00 0.00 41.11 3.41
2201 5733 6.543465 TGCATTATGTCTCCCACTAGATTTTG 59.457 38.462 0.00 0.00 0.00 2.44
2227 5759 6.466812 TCACAGAGAATCAAACTCATAAGCA 58.533 36.000 0.00 0.00 37.82 3.91
2275 5808 9.440773 GAGAATGGCATGTTATATCATGTTCTA 57.559 33.333 19.97 7.45 44.68 2.10
2453 6000 3.099905 CTGTAGGGGACATCTTCTCACA 58.900 50.000 0.00 0.00 37.45 3.58
2469 6017 3.139077 ACCAAAAGAAGAACGCCTGTAG 58.861 45.455 0.00 0.00 0.00 2.74
2474 6022 3.430333 TCAAACCAAAAGAAGAACGCC 57.570 42.857 0.00 0.00 0.00 5.68
2477 6025 9.710900 AATAATCCATCAAACCAAAAGAAGAAC 57.289 29.630 0.00 0.00 0.00 3.01
2549 6102 1.821216 GCCCTACAAAGCAGTAGCAA 58.179 50.000 5.71 0.00 45.49 3.91
2661 6215 4.007659 CCGGTGCTAGATTTTTAACTGGT 58.992 43.478 0.00 0.00 30.84 4.00
2681 6235 8.595533 CAATACAGTATATAAGTTATGCAGCCG 58.404 37.037 5.61 0.00 0.00 5.52
2764 6327 5.423290 TGGCTGATACTTCTCATCTTTCTCA 59.577 40.000 0.00 0.00 0.00 3.27
2820 6383 3.305403 CGCTAAATAGGAATCGAGCCTCA 60.305 47.826 12.44 1.92 36.96 3.86
2926 6664 5.940617 TGGTCCCACCATTAGATATCAAAG 58.059 41.667 5.32 0.00 44.79 2.77
3078 6817 2.171003 ACAACAATAGGAAGGCAAGGC 58.829 47.619 0.00 0.00 0.00 4.35
3406 7146 7.881775 ACTGAAATTCAAGACAAGGTAAAGT 57.118 32.000 0.00 0.00 0.00 2.66
3473 7225 6.567050 TCATCAAGAAATTGGAAAGCTATGC 58.433 36.000 0.00 0.00 0.00 3.14
3474 7226 9.031360 CATTCATCAAGAAATTGGAAAGCTATG 57.969 33.333 0.00 0.00 40.22 2.23
3475 7227 8.755977 ACATTCATCAAGAAATTGGAAAGCTAT 58.244 29.630 0.00 0.00 40.22 2.97
3476 7228 8.125978 ACATTCATCAAGAAATTGGAAAGCTA 57.874 30.769 0.00 0.00 40.22 3.32
3531 7285 8.509690 GTTATTCAGTAACCACCTAAAAGTTCC 58.490 37.037 0.00 0.00 37.33 3.62
3935 7703 0.031616 ACCCCAAAGCCAAACCTTGA 60.032 50.000 0.00 0.00 0.00 3.02
4003 7772 3.676291 TTCATCACACGACATCCAGAA 57.324 42.857 0.00 0.00 0.00 3.02
4095 7962 5.041191 ACTGGATGAACAAACTCAGAACT 57.959 39.130 0.00 0.00 0.00 3.01
4125 7992 7.684450 TCAATCCATTTGAGCATGAGCATGC 62.684 44.000 23.96 23.96 46.35 4.06
4127 7994 3.958147 TCAATCCATTTGAGCATGAGCAT 59.042 39.130 0.00 0.00 39.44 3.79
4128 7995 3.358118 TCAATCCATTTGAGCATGAGCA 58.642 40.909 0.00 0.00 39.44 4.26
4143 8010 1.608283 GCCCCATACTACGCTCAATCC 60.608 57.143 0.00 0.00 0.00 3.01
4161 8028 0.601558 GAAGGAACGGGGAAAAAGCC 59.398 55.000 0.00 0.00 0.00 4.35
4162 8029 1.540267 GAGAAGGAACGGGGAAAAAGC 59.460 52.381 0.00 0.00 0.00 3.51
4163 8030 3.141767 AGAGAAGGAACGGGGAAAAAG 57.858 47.619 0.00 0.00 0.00 2.27
4164 8031 4.710313 TTAGAGAAGGAACGGGGAAAAA 57.290 40.909 0.00 0.00 0.00 1.94
4165 8032 4.566907 CCATTAGAGAAGGAACGGGGAAAA 60.567 45.833 0.00 0.00 0.00 2.29
4166 8033 3.054655 CCATTAGAGAAGGAACGGGGAAA 60.055 47.826 0.00 0.00 0.00 3.13
4167 8034 2.504175 CCATTAGAGAAGGAACGGGGAA 59.496 50.000 0.00 0.00 0.00 3.97
4168 8035 2.116238 CCATTAGAGAAGGAACGGGGA 58.884 52.381 0.00 0.00 0.00 4.81
4169 8036 2.116238 TCCATTAGAGAAGGAACGGGG 58.884 52.381 0.00 0.00 0.00 5.73
4170 8037 3.388024 TCATCCATTAGAGAAGGAACGGG 59.612 47.826 0.00 0.00 34.62 5.28
4171 8038 4.672587 TCATCCATTAGAGAAGGAACGG 57.327 45.455 0.00 0.00 34.62 4.44
4172 8039 5.859114 CGTATCATCCATTAGAGAAGGAACG 59.141 44.000 0.00 0.00 34.62 3.95
4173 8040 5.635700 GCGTATCATCCATTAGAGAAGGAAC 59.364 44.000 0.00 0.00 34.62 3.62
4174 8041 5.304357 TGCGTATCATCCATTAGAGAAGGAA 59.696 40.000 0.00 0.00 34.62 3.36
4175 8042 4.832823 TGCGTATCATCCATTAGAGAAGGA 59.167 41.667 0.00 0.00 35.59 3.36
4176 8043 4.926238 GTGCGTATCATCCATTAGAGAAGG 59.074 45.833 0.00 0.00 0.00 3.46
4177 8044 5.403766 GTGTGCGTATCATCCATTAGAGAAG 59.596 44.000 0.00 0.00 0.00 2.85
4178 8045 5.069119 AGTGTGCGTATCATCCATTAGAGAA 59.931 40.000 0.00 0.00 0.00 2.87
4179 8046 4.584743 AGTGTGCGTATCATCCATTAGAGA 59.415 41.667 0.00 0.00 0.00 3.10
4180 8047 4.876125 AGTGTGCGTATCATCCATTAGAG 58.124 43.478 0.00 0.00 0.00 2.43
4181 8048 4.340950 TGAGTGTGCGTATCATCCATTAGA 59.659 41.667 0.00 0.00 0.00 2.10
4182 8049 4.620982 TGAGTGTGCGTATCATCCATTAG 58.379 43.478 0.00 0.00 0.00 1.73
4183 8050 4.664150 TGAGTGTGCGTATCATCCATTA 57.336 40.909 0.00 0.00 0.00 1.90
4184 8051 3.541996 TGAGTGTGCGTATCATCCATT 57.458 42.857 0.00 0.00 0.00 3.16
4185 8052 3.396560 CATGAGTGTGCGTATCATCCAT 58.603 45.455 0.00 0.00 31.38 3.41
4186 8053 2.825205 CATGAGTGTGCGTATCATCCA 58.175 47.619 0.00 0.00 31.38 3.41
4187 8054 1.528586 GCATGAGTGTGCGTATCATCC 59.471 52.381 0.00 0.00 35.10 3.51
4188 8055 2.937994 GCATGAGTGTGCGTATCATC 57.062 50.000 0.00 0.00 35.10 2.92
4196 8063 2.672874 TCTTGAATACGCATGAGTGTGC 59.327 45.455 12.80 4.74 39.47 4.57
4197 8064 4.926860 TTCTTGAATACGCATGAGTGTG 57.073 40.909 12.80 0.00 39.22 3.82
4198 8065 5.940192 TTTTCTTGAATACGCATGAGTGT 57.060 34.783 12.80 2.11 42.14 3.55
4218 8085 8.784043 GTTGGTGATACTACACTCAATCTTTTT 58.216 33.333 0.00 0.00 40.22 1.94
4219 8086 8.157476 AGTTGGTGATACTACACTCAATCTTTT 58.843 33.333 0.00 0.00 40.22 2.27
4220 8087 7.680730 AGTTGGTGATACTACACTCAATCTTT 58.319 34.615 0.00 0.00 40.22 2.52
4221 8088 7.246171 AGTTGGTGATACTACACTCAATCTT 57.754 36.000 0.00 0.00 40.22 2.40
4222 8089 6.859112 AGTTGGTGATACTACACTCAATCT 57.141 37.500 0.00 0.00 40.22 2.40
4223 8090 9.601217 AAATAGTTGGTGATACTACACTCAATC 57.399 33.333 0.00 0.00 40.22 2.67
4224 8091 9.383519 CAAATAGTTGGTGATACTACACTCAAT 57.616 33.333 0.00 0.00 40.22 2.57
4225 8092 8.590204 TCAAATAGTTGGTGATACTACACTCAA 58.410 33.333 2.65 0.00 40.22 3.02
4226 8093 8.129496 TCAAATAGTTGGTGATACTACACTCA 57.871 34.615 2.65 0.00 40.22 3.41
4227 8094 8.251721 ACTCAAATAGTTGGTGATACTACACTC 58.748 37.037 2.65 0.00 36.69 3.51
4228 8095 8.135382 ACTCAAATAGTTGGTGATACTACACT 57.865 34.615 2.65 0.00 36.69 3.55
4229 8096 8.251721 AGACTCAAATAGTTGGTGATACTACAC 58.748 37.037 2.65 0.00 39.07 2.90
4230 8097 8.362464 AGACTCAAATAGTTGGTGATACTACA 57.638 34.615 2.65 0.00 39.07 2.74
4231 8098 9.654663 AAAGACTCAAATAGTTGGTGATACTAC 57.345 33.333 2.65 0.00 39.07 2.73
4232 8099 9.871238 GAAAGACTCAAATAGTTGGTGATACTA 57.129 33.333 2.65 0.00 39.07 1.82
4233 8100 8.598041 AGAAAGACTCAAATAGTTGGTGATACT 58.402 33.333 2.65 0.00 39.07 2.12
4234 8101 8.660373 CAGAAAGACTCAAATAGTTGGTGATAC 58.340 37.037 2.65 0.00 39.07 2.24
4235 8102 8.593679 TCAGAAAGACTCAAATAGTTGGTGATA 58.406 33.333 2.65 0.00 39.07 2.15
4236 8103 7.453393 TCAGAAAGACTCAAATAGTTGGTGAT 58.547 34.615 2.65 0.00 39.07 3.06
4237 8104 6.826668 TCAGAAAGACTCAAATAGTTGGTGA 58.173 36.000 2.65 0.00 39.07 4.02
4238 8105 6.148480 CCTCAGAAAGACTCAAATAGTTGGTG 59.852 42.308 2.65 0.00 39.07 4.17
4239 8106 6.234177 CCTCAGAAAGACTCAAATAGTTGGT 58.766 40.000 2.65 0.02 39.07 3.67
4240 8107 5.645497 CCCTCAGAAAGACTCAAATAGTTGG 59.355 44.000 2.65 0.00 39.07 3.77
4241 8108 5.123027 GCCCTCAGAAAGACTCAAATAGTTG 59.877 44.000 0.00 0.00 39.07 3.16
4256 8123 4.908601 TGAATCAAAGTAGCCCTCAGAA 57.091 40.909 0.00 0.00 0.00 3.02
4258 8125 5.557891 CTTTGAATCAAAGTAGCCCTCAG 57.442 43.478 23.52 0.00 43.85 3.35
4370 8243 5.335504 CCAAGGAGTCAAGAGCAATCTTTTC 60.336 44.000 0.00 0.00 0.00 2.29
4371 8244 4.522022 CCAAGGAGTCAAGAGCAATCTTTT 59.478 41.667 0.00 0.00 0.00 2.27
4393 8271 6.655003 GGAATTTTCCTTGGAAATTTTCCTCC 59.345 38.462 28.06 16.91 45.83 4.30
4394 8272 7.672983 GGAATTTTCCTTGGAAATTTTCCTC 57.327 36.000 28.06 12.75 45.83 3.71
4398 8276 6.947733 GGATGGGAATTTTCCTTGGAAATTTT 59.052 34.615 14.66 11.58 46.72 1.82
4399 8277 6.045341 TGGATGGGAATTTTCCTTGGAAATTT 59.955 34.615 14.66 16.04 46.72 1.82
4400 8278 5.551189 TGGATGGGAATTTTCCTTGGAAATT 59.449 36.000 14.66 9.19 46.72 1.82
4401 8279 5.045651 GTGGATGGGAATTTTCCTTGGAAAT 60.046 40.000 14.66 2.20 46.72 2.17
4402 8280 4.285775 GTGGATGGGAATTTTCCTTGGAAA 59.714 41.667 10.47 10.47 46.72 3.13
4403 8281 3.837731 GTGGATGGGAATTTTCCTTGGAA 59.162 43.478 9.13 0.00 46.72 3.53
4404 8282 3.077391 AGTGGATGGGAATTTTCCTTGGA 59.923 43.478 9.13 0.00 46.72 3.53
4405 8283 3.444029 AGTGGATGGGAATTTTCCTTGG 58.556 45.455 9.13 0.00 46.72 3.61
4406 8284 4.088634 TGAGTGGATGGGAATTTTCCTTG 58.911 43.478 9.13 0.00 46.72 3.61
4407 8285 4.402616 TGAGTGGATGGGAATTTTCCTT 57.597 40.909 9.13 0.00 46.72 3.36
4417 8295 0.409484 AAGGGGTTTGAGTGGATGGG 59.591 55.000 0.00 0.00 0.00 4.00
4540 8418 3.058293 TCGCAAGATTTTCGAAATGCAGT 60.058 39.130 25.50 7.27 45.01 4.40
4589 8468 5.391310 GCACATTGTCTTGGTAGATGTTCAG 60.391 44.000 0.00 0.00 31.86 3.02
4660 8549 7.708752 GGTTTGTATTCATTTGTTGAGTTGGAA 59.291 33.333 0.00 0.00 35.27 3.53
4661 8550 7.206687 GGTTTGTATTCATTTGTTGAGTTGGA 58.793 34.615 0.00 0.00 35.27 3.53
4685 8575 2.845967 GCAAATGTAAATCTTGTCGCGG 59.154 45.455 6.13 0.00 0.00 6.46
4688 8578 3.845775 CCGTGCAAATGTAAATCTTGTCG 59.154 43.478 0.00 0.00 0.00 4.35
4694 8584 6.608610 ACTCTTTACCGTGCAAATGTAAATC 58.391 36.000 13.77 0.00 34.85 2.17
4705 8595 2.726832 ACTCTGACTCTTTACCGTGC 57.273 50.000 0.00 0.00 0.00 5.34
4708 8598 2.338500 GGCAACTCTGACTCTTTACCG 58.662 52.381 0.00 0.00 0.00 4.02
4711 8601 2.038557 GTGGGGCAACTCTGACTCTTTA 59.961 50.000 0.00 0.00 38.64 1.85
4749 8639 2.669364 GGCTGACTTCAAGCATTTGTG 58.331 47.619 0.00 0.00 35.73 3.33
4847 8778 6.588719 AAACACCAGCTGCTTGATAAATAA 57.411 33.333 17.80 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.