Multiple sequence alignment - TraesCS2B01G220000

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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 TraesCS2B01G220000 chr2B 100.000 6897 0 0 1 6897 210468780 210461884 0.000000e+00 12737.0
1 TraesCS2B01G220000 chr2B 89.892 277 26 1 5045 5319 532481656 532481380 8.510000e-94 355.0
2 TraesCS2B01G220000 chr2B 93.966 116 7 0 4879 4994 723434347 723434232 7.110000e-40 176.0
3 TraesCS2B01G220000 chr2B 96.552 58 1 1 4970 5026 210463759 210463702 2.050000e-15 95.3
4 TraesCS2B01G220000 chr2B 96.552 58 1 1 5022 5079 210463811 210463755 2.050000e-15 95.3
5 TraesCS2B01G220000 chr2D 96.043 4220 100 24 848 5010 152108731 152104522 0.000000e+00 6806.0
6 TraesCS2B01G220000 chr2D 94.211 1883 68 21 5022 6897 152104561 152102713 0.000000e+00 2835.0
7 TraesCS2B01G220000 chr2D 97.372 837 22 0 1 837 40789062 40789898 0.000000e+00 1424.0
8 TraesCS2B01G220000 chr2D 88.087 277 31 1 5045 5319 180525922 180525646 1.850000e-85 327.0
9 TraesCS2B01G220000 chr2D 89.922 129 13 0 4876 5004 441085766 441085894 4.280000e-37 167.0
10 TraesCS2B01G220000 chr2A 92.331 1669 69 14 848 2463 149064034 149065696 0.000000e+00 2318.0
11 TraesCS2B01G220000 chr2A 92.459 1578 86 20 2516 4078 149065703 149067262 0.000000e+00 2224.0
12 TraesCS2B01G220000 chr2A 92.806 987 46 13 5045 6020 149067956 149068928 0.000000e+00 1406.0
13 TraesCS2B01G220000 chr2A 88.559 708 49 13 4188 4877 149067263 149067956 0.000000e+00 830.0
14 TraesCS2B01G220000 chr2A 91.667 60 5 0 6835 6894 15934459 15934518 4.430000e-12 84.2
15 TraesCS2B01G220000 chr2A 94.872 39 2 0 3768 3806 79308141 79308179 2.080000e-05 62.1
16 TraesCS2B01G220000 chr2A 100.000 29 0 0 6746 6774 263527473 263527445 3.000000e-03 54.7
17 TraesCS2B01G220000 chr3A 95.865 798 31 2 42 837 745568073 745568870 0.000000e+00 1290.0
18 TraesCS2B01G220000 chr3A 92.982 57 2 2 3767 3822 518896363 518896308 1.590000e-11 82.4
19 TraesCS2B01G220000 chr5B 92.491 839 61 2 1 837 44456572 44455734 0.000000e+00 1199.0
20 TraesCS2B01G220000 chr5B 92.814 821 57 1 19 837 658228861 658228041 0.000000e+00 1188.0
21 TraesCS2B01G220000 chr5B 90.476 126 12 0 4869 4994 611922695 611922820 4.280000e-37 167.0
22 TraesCS2B01G220000 chr5B 88.406 138 13 2 4874 5011 571209385 571209251 5.540000e-36 163.0
23 TraesCS2B01G220000 chr5B 93.333 60 3 1 3164 3223 545002227 545002169 3.430000e-13 87.9
24 TraesCS2B01G220000 chr3B 92.143 840 58 3 1 837 383689133 383688299 0.000000e+00 1179.0
25 TraesCS2B01G220000 chr3B 83.036 112 8 4 6123 6223 526689435 526689546 2.650000e-14 91.6
26 TraesCS2B01G220000 chr3B 93.333 60 3 1 3164 3223 57331864 57331806 3.430000e-13 87.9
27 TraesCS2B01G220000 chr3B 93.333 60 3 1 3164 3223 752248280 752248222 3.430000e-13 87.9
28 TraesCS2B01G220000 chr3B 91.111 45 2 2 3764 3807 430523478 430523521 7.470000e-05 60.2
29 TraesCS2B01G220000 chr3B 100.000 30 0 0 6798 6827 513938773 513938802 1.000000e-03 56.5
30 TraesCS2B01G220000 chr7A 95.967 719 29 0 1 719 718237963 718237245 0.000000e+00 1168.0
31 TraesCS2B01G220000 chr7A 91.803 122 8 2 718 837 718224385 718224264 1.190000e-37 169.0
32 TraesCS2B01G220000 chr7A 92.188 64 4 1 6835 6897 6955761 6955698 9.530000e-14 89.8
33 TraesCS2B01G220000 chr7A 97.674 43 0 1 6125 6166 126929077 126929119 9.600000e-09 73.1
34 TraesCS2B01G220000 chr7A 83.871 62 9 1 3746 3806 623742078 623742139 2.690000e-04 58.4
35 TraesCS2B01G220000 chr4A 87.726 277 32 1 5045 5319 722429630 722429354 8.630000e-84 322.0
36 TraesCS2B01G220000 chr4A 93.913 115 7 0 4879 4993 702148907 702148793 2.560000e-39 174.0
37 TraesCS2B01G220000 chr4A 93.333 60 3 1 3164 3223 82438602 82438544 3.430000e-13 87.9
38 TraesCS2B01G220000 chr4A 90.476 63 5 1 6836 6897 720293549 720293487 1.590000e-11 82.4
39 TraesCS2B01G220000 chr4A 94.737 38 2 0 6799 6836 714842055 714842018 7.470000e-05 60.2
40 TraesCS2B01G220000 chr4A 100.000 29 0 0 6746 6774 77224819 77224847 3.000000e-03 54.7
41 TraesCS2B01G220000 chr4B 86.282 277 34 3 5045 5317 645801261 645800985 1.450000e-76 298.0
42 TraesCS2B01G220000 chr4B 85.921 277 35 3 5045 5317 645630128 645629852 6.770000e-75 292.0
43 TraesCS2B01G220000 chr4B 85.507 276 37 2 5045 5317 645709193 645708918 1.130000e-72 285.0
44 TraesCS2B01G220000 chr4B 91.870 123 9 1 4871 4993 628068098 628067977 3.310000e-38 171.0
45 TraesCS2B01G220000 chr1A 83.083 266 24 5 4150 4402 482775082 482774825 9.000000e-54 222.0
46 TraesCS2B01G220000 chr1A 93.182 44 2 1 6794 6836 572979905 572979862 5.780000e-06 63.9
47 TraesCS2B01G220000 chr1A 91.111 45 3 1 3763 3806 281892575 281892531 7.470000e-05 60.2
48 TraesCS2B01G220000 chr1A 92.857 42 2 1 3765 3806 550342518 550342558 7.470000e-05 60.2
49 TraesCS2B01G220000 chr1B 93.277 119 8 0 4875 4993 357422996 357422878 7.110000e-40 176.0
50 TraesCS2B01G220000 chr6B 89.922 129 12 1 4865 4993 618132671 618132544 1.540000e-36 165.0
51 TraesCS2B01G220000 chr6B 91.667 60 5 0 6838 6897 659672385 659672326 4.430000e-12 84.2
52 TraesCS2B01G220000 chr6B 79.630 108 14 8 6124 6227 441260910 441261013 3.450000e-08 71.3
53 TraesCS2B01G220000 chr6B 77.391 115 14 4 6124 6227 408246532 408246645 2.690000e-04 58.4
54 TraesCS2B01G220000 chr6A 74.671 304 60 14 6485 6775 28668934 28668635 1.220000e-22 119.0
55 TraesCS2B01G220000 chr5D 90.769 65 6 0 6833 6897 320377203 320377267 3.430000e-13 87.9
56 TraesCS2B01G220000 chr5D 94.595 37 2 0 6798 6834 420912845 420912809 2.690000e-04 58.4
57 TraesCS2B01G220000 chr5D 100.000 31 0 0 6795 6825 484671709 484671679 2.690000e-04 58.4
58 TraesCS2B01G220000 chr5D 97.059 34 0 1 6743 6775 504479524 504479557 1.000000e-03 56.5
59 TraesCS2B01G220000 chr5D 88.889 45 4 1 6786 6829 214712106 214712150 3.000000e-03 54.7
60 TraesCS2B01G220000 chr7B 91.803 61 4 1 6838 6897 666326560 666326500 4.430000e-12 84.2
61 TraesCS2B01G220000 chr7B 88.710 62 7 0 6162 6223 488368101 488368162 7.420000e-10 76.8
62 TraesCS2B01G220000 chr3D 91.667 60 3 2 6839 6897 595755283 595755341 1.590000e-11 82.4
63 TraesCS2B01G220000 chr3D 91.111 45 2 2 3764 3807 331192960 331193003 7.470000e-05 60.2
64 TraesCS2B01G220000 chr3D 82.609 69 9 3 6711 6777 121728582 121728649 2.690000e-04 58.4
65 TraesCS2B01G220000 chr3D 100.000 28 0 0 6798 6825 45035899 45035926 1.300000e-02 52.8
66 TraesCS2B01G220000 chr4D 90.323 62 5 1 6837 6897 78672990 78672929 5.730000e-11 80.5
67 TraesCS2B01G220000 chrUn 94.737 38 2 0 6799 6836 315202472 315202509 7.470000e-05 60.2
68 TraesCS2B01G220000 chr7D 75.000 132 31 2 6646 6775 521740030 521740161 7.470000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G220000 chr2B 210461884 210468780 6896 True 12737.0 12737 100.00000 1 6897 1 chr2B.!!$R1 6896
1 TraesCS2B01G220000 chr2D 152102713 152108731 6018 True 4820.5 6806 95.12700 848 6897 2 chr2D.!!$R2 6049
2 TraesCS2B01G220000 chr2D 40789062 40789898 836 False 1424.0 1424 97.37200 1 837 1 chr2D.!!$F1 836
3 TraesCS2B01G220000 chr2A 149064034 149068928 4894 False 1694.5 2318 91.53875 848 6020 4 chr2A.!!$F3 5172
4 TraesCS2B01G220000 chr3A 745568073 745568870 797 False 1290.0 1290 95.86500 42 837 1 chr3A.!!$F1 795
5 TraesCS2B01G220000 chr5B 44455734 44456572 838 True 1199.0 1199 92.49100 1 837 1 chr5B.!!$R1 836
6 TraesCS2B01G220000 chr5B 658228041 658228861 820 True 1188.0 1188 92.81400 19 837 1 chr5B.!!$R4 818
7 TraesCS2B01G220000 chr3B 383688299 383689133 834 True 1179.0 1179 92.14300 1 837 1 chr3B.!!$R2 836
8 TraesCS2B01G220000 chr7A 718237245 718237963 718 True 1168.0 1168 95.96700 1 719 1 chr7A.!!$R3 718

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
789 795 0.481128 ACCCCGGGTTTTTGATCAGT 59.519 50.000 21.85 2.31 27.29 3.41 F
1649 1660 0.106769 ATTACCATGATGCACGCCCA 60.107 50.000 0.00 0.00 0.00 5.36 F
2773 2856 3.983044 TCAGAAGGCTCCCTTTCTTAC 57.017 47.619 0.00 0.00 44.82 2.34 F
3424 3508 1.152881 CTGGGCCTTGCTGATACCC 60.153 63.158 4.53 0.00 41.24 3.69 F
4898 5001 1.000955 CTCCCTCCATCCGGAAATACG 59.999 57.143 9.01 0.00 42.21 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 2523 1.654954 CTCAGCTTGCATGGACAGCC 61.655 60.000 14.47 0.00 0.00 4.85 R
3399 3482 1.077985 AGCAAGGCCCAGAGCAAAT 59.922 52.632 0.00 0.00 46.50 2.32 R
3815 3900 2.822707 AGAAGCATGCAAATCCCTCT 57.177 45.000 21.98 6.63 0.00 3.69 R
5365 5471 1.330521 CAGTGTGGGTGAAACAGTTCG 59.669 52.381 0.00 0.00 39.98 3.95 R
6538 6659 0.321653 AGTCATCAACCACCGAAGCC 60.322 55.000 0.00 0.00 0.00 4.35 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
81 82 3.366476 GGATCATATAGAGCAAGCGACGT 60.366 47.826 0.00 0.00 33.23 4.34
386 387 4.425577 AAATGTCGATGCTTCCTTTCAC 57.574 40.909 0.00 0.00 0.00 3.18
483 484 2.316108 TCATTCAGGTAGCGGCAGATA 58.684 47.619 1.45 0.00 0.00 1.98
494 495 0.735978 CGGCAGATACAGCGACAACA 60.736 55.000 0.00 0.00 0.00 3.33
627 628 3.695606 GGTGGGACTCAGCAGCGA 61.696 66.667 0.00 0.00 42.97 4.93
716 717 3.126000 GTGAGGCAAATTCAGTAGCTCAC 59.874 47.826 0.00 0.00 32.48 3.51
789 795 0.481128 ACCCCGGGTTTTTGATCAGT 59.519 50.000 21.85 2.31 27.29 3.41
791 797 1.271926 CCCCGGGTTTTTGATCAGTCT 60.272 52.381 21.85 0.00 0.00 3.24
803 809 7.827819 TTTTGATCAGTCTATTAGTGAACGG 57.172 36.000 0.00 0.00 40.93 4.44
908 914 6.957631 TGGAAATAGTCATCCATGTGTTAGT 58.042 36.000 0.00 0.00 40.74 2.24
1031 1037 0.958382 CCGAGCCCCAAACGAAATCA 60.958 55.000 0.00 0.00 0.00 2.57
1046 1052 4.047822 CGAAATCAAATCGAGAGGAGAGG 58.952 47.826 0.00 0.00 42.76 3.69
1163 1169 2.202932 CCTCCTCCATTCGCGTGG 60.203 66.667 5.77 7.88 40.76 4.94
1346 1353 2.536365 TGTATTGCTCGATCCGTTCAC 58.464 47.619 0.00 0.00 0.00 3.18
1348 1355 1.927895 ATTGCTCGATCCGTTCACTC 58.072 50.000 0.00 0.00 0.00 3.51
1357 1366 0.959372 TCCGTTCACTCCGTCCTCTC 60.959 60.000 0.00 0.00 0.00 3.20
1358 1367 0.961358 CCGTTCACTCCGTCCTCTCT 60.961 60.000 0.00 0.00 0.00 3.10
1359 1368 0.882474 CGTTCACTCCGTCCTCTCTT 59.118 55.000 0.00 0.00 0.00 2.85
1493 1504 2.274542 TGCTCCAGGGGTATTCTTCAA 58.725 47.619 0.00 0.00 0.00 2.69
1505 1516 2.443887 TTCTTCAATTTGCAGCCAGC 57.556 45.000 0.00 0.00 45.96 4.85
1529 1540 9.035607 AGCACTTGAGTATTTTATTATGACTCG 57.964 33.333 0.00 0.00 39.52 4.18
1613 1624 3.556365 GGCCTGCTCGATCTAAACTTAAC 59.444 47.826 0.00 0.00 0.00 2.01
1619 1630 6.100004 TGCTCGATCTAAACTTAACAAGAGG 58.900 40.000 0.00 0.00 0.00 3.69
1623 1634 6.872020 TCGATCTAAACTTAACAAGAGGTTGG 59.128 38.462 0.00 0.00 40.73 3.77
1625 1636 6.503560 TCTAAACTTAACAAGAGGTTGGGA 57.496 37.500 0.00 0.00 40.73 4.37
1633 1644 7.562088 ACTTAACAAGAGGTTGGGAAACAATTA 59.438 33.333 0.00 0.00 41.95 1.40
1649 1660 0.106769 ATTACCATGATGCACGCCCA 60.107 50.000 0.00 0.00 0.00 5.36
1670 1681 5.300034 CCCATGTATTTTCAAGCTGCTATGA 59.700 40.000 0.90 6.51 0.00 2.15
1812 1854 5.801947 GCATAACAAAACTGTCATGTGGATC 59.198 40.000 0.00 0.00 0.00 3.36
1983 2046 5.589855 TGCAATGATACCTTTGTACCATCAG 59.410 40.000 0.00 0.00 29.34 2.90
1990 2053 5.762179 ACCTTTGTACCATCAGATCAAGA 57.238 39.130 0.00 0.00 0.00 3.02
2136 2199 7.910441 CATCAAATGATGCCCTTTTAACTTT 57.090 32.000 10.23 0.00 44.44 2.66
2459 2523 4.378774 TGTGATGCCATTTGTTTTCCTTG 58.621 39.130 0.00 0.00 0.00 3.61
2527 2598 5.518848 TTTTTGCTTGTGATCAGTGTCAT 57.481 34.783 0.00 0.00 0.00 3.06
2652 2734 9.734620 TCAATTTATTGATATTAAGTGCAGTGC 57.265 29.630 8.58 8.58 41.51 4.40
2773 2856 3.983044 TCAGAAGGCTCCCTTTCTTAC 57.017 47.619 0.00 0.00 44.82 2.34
2973 3056 5.408604 CGGTATGCCCATTATTGTAGACTTC 59.591 44.000 0.00 0.00 0.00 3.01
2974 3057 5.408604 GGTATGCCCATTATTGTAGACTTCG 59.591 44.000 0.00 0.00 0.00 3.79
3004 3087 4.339872 TTGAATGCATTTGCCTGAACTT 57.660 36.364 14.33 0.00 41.18 2.66
3006 3089 4.706035 TGAATGCATTTGCCTGAACTTTT 58.294 34.783 14.33 0.00 41.18 2.27
3399 3482 3.289836 CATGAGGGCATCACACCAATTA 58.710 45.455 3.00 0.00 41.91 1.40
3424 3508 1.152881 CTGGGCCTTGCTGATACCC 60.153 63.158 4.53 0.00 41.24 3.69
3525 3609 8.517878 AGTAATTAATGCATATGAATGTCCTGC 58.482 33.333 6.97 0.00 35.38 4.85
3716 3801 4.393371 GTGAGAGTTTTGTTGGGATAGCTC 59.607 45.833 0.00 0.00 0.00 4.09
3815 3900 3.071479 GTCGCTGACTTATTTTGGGACA 58.929 45.455 0.00 0.00 39.38 4.02
3822 3907 4.540099 TGACTTATTTTGGGACAGAGGGAT 59.460 41.667 0.00 0.00 42.39 3.85
3824 3909 5.903923 ACTTATTTTGGGACAGAGGGATTT 58.096 37.500 0.00 0.00 42.39 2.17
3990 4075 6.069381 AGCCCTTCTGACATAACCTTTAGATT 60.069 38.462 0.00 0.00 0.00 2.40
4089 4175 3.550437 TCTAAGCTTCAAGCCATCTCC 57.450 47.619 5.53 0.00 43.77 3.71
4090 4176 2.840038 TCTAAGCTTCAAGCCATCTCCA 59.160 45.455 5.53 0.00 43.77 3.86
4122 4208 5.046014 CAGGCCTAGCTTGAGATTATATGGT 60.046 44.000 3.98 0.00 37.87 3.55
4889 4992 4.379302 AAGATAAATGCTCCCTCCATCC 57.621 45.455 0.00 0.00 0.00 3.51
4898 5001 1.000955 CTCCCTCCATCCGGAAATACG 59.999 57.143 9.01 0.00 42.21 3.06
4972 5077 2.795329 ACATTCATTTCTCCGGCAAGT 58.205 42.857 0.00 0.00 0.00 3.16
4973 5078 3.950397 ACATTCATTTCTCCGGCAAGTA 58.050 40.909 0.00 0.00 0.00 2.24
4974 5079 4.526970 ACATTCATTTCTCCGGCAAGTAT 58.473 39.130 0.00 0.00 0.00 2.12
4975 5080 4.949856 ACATTCATTTCTCCGGCAAGTATT 59.050 37.500 0.00 0.00 0.00 1.89
4976 5081 5.418840 ACATTCATTTCTCCGGCAAGTATTT 59.581 36.000 0.00 0.00 0.00 1.40
4977 5082 5.560966 TTCATTTCTCCGGCAAGTATTTC 57.439 39.130 0.00 0.00 0.00 2.17
4978 5083 4.843728 TCATTTCTCCGGCAAGTATTTCT 58.156 39.130 0.00 0.00 0.00 2.52
4979 5084 4.635765 TCATTTCTCCGGCAAGTATTTCTG 59.364 41.667 0.00 0.00 0.00 3.02
4980 5085 2.691409 TCTCCGGCAAGTATTTCTGG 57.309 50.000 0.00 0.00 0.00 3.86
4981 5086 2.184533 TCTCCGGCAAGTATTTCTGGA 58.815 47.619 0.00 0.00 0.00 3.86
4982 5087 2.093658 TCTCCGGCAAGTATTTCTGGAC 60.094 50.000 0.00 0.00 0.00 4.02
4983 5088 1.626321 TCCGGCAAGTATTTCTGGACA 59.374 47.619 0.00 0.00 0.00 4.02
4984 5089 2.009774 CCGGCAAGTATTTCTGGACAG 58.990 52.381 0.00 0.00 0.00 3.51
4985 5090 2.354704 CCGGCAAGTATTTCTGGACAGA 60.355 50.000 0.00 0.00 35.27 3.41
4986 5091 2.932614 CGGCAAGTATTTCTGGACAGAG 59.067 50.000 1.92 0.00 38.88 3.35
4987 5092 3.274288 GGCAAGTATTTCTGGACAGAGG 58.726 50.000 1.92 0.00 38.88 3.69
4988 5093 3.274288 GCAAGTATTTCTGGACAGAGGG 58.726 50.000 1.92 0.00 38.88 4.30
4989 5094 3.055094 GCAAGTATTTCTGGACAGAGGGA 60.055 47.826 1.92 0.00 38.88 4.20
4990 5095 4.764172 CAAGTATTTCTGGACAGAGGGAG 58.236 47.826 1.92 0.00 38.88 4.30
4991 5096 4.067944 AGTATTTCTGGACAGAGGGAGT 57.932 45.455 1.92 0.00 38.88 3.85
4992 5097 5.208294 AGTATTTCTGGACAGAGGGAGTA 57.792 43.478 1.92 0.00 38.88 2.59
4993 5098 4.957327 AGTATTTCTGGACAGAGGGAGTAC 59.043 45.833 1.92 0.68 38.88 2.73
4994 5099 2.233305 TTCTGGACAGAGGGAGTACC 57.767 55.000 1.92 0.00 38.88 3.34
5009 5114 6.356186 GGGAGTACCTAAGAAGTTTTCAGA 57.644 41.667 0.00 0.00 35.85 3.27
5010 5115 6.948589 GGGAGTACCTAAGAAGTTTTCAGAT 58.051 40.000 0.00 0.00 35.85 2.90
5011 5116 7.395617 GGGAGTACCTAAGAAGTTTTCAGATT 58.604 38.462 0.00 0.00 35.85 2.40
5012 5117 7.883833 GGGAGTACCTAAGAAGTTTTCAGATTT 59.116 37.037 0.00 0.00 35.85 2.17
5013 5118 8.722394 GGAGTACCTAAGAAGTTTTCAGATTTG 58.278 37.037 0.00 0.00 0.00 2.32
5014 5119 9.490379 GAGTACCTAAGAAGTTTTCAGATTTGA 57.510 33.333 0.00 0.00 0.00 2.69
5015 5120 9.495572 AGTACCTAAGAAGTTTTCAGATTTGAG 57.504 33.333 0.00 0.00 34.15 3.02
5016 5121 9.274206 GTACCTAAGAAGTTTTCAGATTTGAGT 57.726 33.333 0.00 0.00 34.15 3.41
5040 5145 4.575885 TGAAAGTTATTTCTGGACGGAGG 58.424 43.478 2.75 0.00 44.35 4.30
6057 6173 0.250295 TACCAAGACAGCTGTGCACC 60.250 55.000 27.27 9.92 0.00 5.01
6061 6177 3.720193 GACAGCTGTGCACCGCAG 61.720 66.667 30.93 26.02 43.89 5.18
6072 6188 1.134936 TGCACCGCAGTACGTGATATT 60.135 47.619 0.00 0.00 41.42 1.28
6115 6231 7.485810 TGAAATTGCCACTAAGATCAATGATG 58.514 34.615 0.00 0.00 30.47 3.07
6117 6233 8.523915 AAATTGCCACTAAGATCAATGATGTA 57.476 30.769 0.00 0.00 30.47 2.29
6119 6235 7.936496 TTGCCACTAAGATCAATGATGTAAA 57.064 32.000 0.00 0.00 0.00 2.01
6121 6237 8.523915 TGCCACTAAGATCAATGATGTAAAAT 57.476 30.769 0.00 0.00 0.00 1.82
6122 6238 8.623903 TGCCACTAAGATCAATGATGTAAAATC 58.376 33.333 0.00 0.00 0.00 2.17
6123 6239 7.800380 GCCACTAAGATCAATGATGTAAAATCG 59.200 37.037 0.00 0.00 0.00 3.34
6129 6245 8.594881 AGATCAATGATGTAAAATCGTACTCC 57.405 34.615 0.00 0.00 0.00 3.85
6130 6246 7.657761 AGATCAATGATGTAAAATCGTACTCCC 59.342 37.037 0.00 0.00 0.00 4.30
6131 6247 6.884832 TCAATGATGTAAAATCGTACTCCCT 58.115 36.000 0.00 0.00 0.00 4.20
6132 6248 6.984474 TCAATGATGTAAAATCGTACTCCCTC 59.016 38.462 0.00 0.00 0.00 4.30
6133 6249 5.272283 TGATGTAAAATCGTACTCCCTCC 57.728 43.478 0.00 0.00 0.00 4.30
6134 6250 3.788333 TGTAAAATCGTACTCCCTCCG 57.212 47.619 0.00 0.00 0.00 4.63
6135 6251 3.091545 TGTAAAATCGTACTCCCTCCGT 58.908 45.455 0.00 0.00 0.00 4.69
6136 6252 2.955477 AAAATCGTACTCCCTCCGTC 57.045 50.000 0.00 0.00 0.00 4.79
6137 6253 1.109609 AAATCGTACTCCCTCCGTCC 58.890 55.000 0.00 0.00 0.00 4.79
6138 6254 1.099879 AATCGTACTCCCTCCGTCCG 61.100 60.000 0.00 0.00 0.00 4.79
6139 6255 3.885521 CGTACTCCCTCCGTCCGC 61.886 72.222 0.00 0.00 0.00 5.54
6144 6260 0.974010 ACTCCCTCCGTCCGCAAATA 60.974 55.000 0.00 0.00 0.00 1.40
6145 6261 0.393077 CTCCCTCCGTCCGCAAATAT 59.607 55.000 0.00 0.00 0.00 1.28
6146 6262 0.834612 TCCCTCCGTCCGCAAATATT 59.165 50.000 0.00 0.00 0.00 1.28
6150 6266 2.031683 CCTCCGTCCGCAAATATTTGTC 59.968 50.000 25.15 17.41 40.24 3.18
6151 6267 1.661617 TCCGTCCGCAAATATTTGTCG 59.338 47.619 25.15 25.13 40.24 4.35
6159 6275 5.854835 CGCAAATATTTGTCGGAGAAATG 57.145 39.130 25.15 8.50 39.69 2.32
6160 6276 4.734854 CGCAAATATTTGTCGGAGAAATGG 59.265 41.667 25.15 9.87 39.69 3.16
6215 6331 6.249035 TCCATTTTCGTGACAAGTAATTCC 57.751 37.500 0.00 0.00 0.00 3.01
6296 6412 4.214545 TGTTTCTCATTCGCACGGTAATTT 59.785 37.500 0.00 0.00 0.00 1.82
6381 6497 5.518848 TTGCTAATGGTGCAATCATAAGG 57.481 39.130 4.49 0.97 44.24 2.69
6440 6556 5.528600 TCCACCTTGGAAAATGAGGATTA 57.471 39.130 0.00 0.00 45.00 1.75
6441 6557 5.509498 TCCACCTTGGAAAATGAGGATTAG 58.491 41.667 0.00 0.00 45.00 1.73
6442 6558 5.015178 TCCACCTTGGAAAATGAGGATTAGT 59.985 40.000 0.00 0.00 45.00 2.24
6443 6559 6.216662 TCCACCTTGGAAAATGAGGATTAGTA 59.783 38.462 0.00 0.00 45.00 1.82
6444 6560 6.543831 CCACCTTGGAAAATGAGGATTAGTAG 59.456 42.308 0.00 0.00 40.96 2.57
6445 6561 6.038714 CACCTTGGAAAATGAGGATTAGTAGC 59.961 42.308 0.00 0.00 34.61 3.58
6446 6562 6.122277 CCTTGGAAAATGAGGATTAGTAGCA 58.878 40.000 0.00 0.00 32.11 3.49
6447 6563 6.603201 CCTTGGAAAATGAGGATTAGTAGCAA 59.397 38.462 0.00 0.00 32.11 3.91
6448 6564 7.286316 CCTTGGAAAATGAGGATTAGTAGCAAT 59.714 37.037 0.00 0.00 32.11 3.56
6449 6565 9.342308 CTTGGAAAATGAGGATTAGTAGCAATA 57.658 33.333 0.00 0.00 0.00 1.90
6450 6566 8.677148 TGGAAAATGAGGATTAGTAGCAATAC 57.323 34.615 0.00 0.00 0.00 1.89
6451 6567 7.719633 TGGAAAATGAGGATTAGTAGCAATACC 59.280 37.037 0.00 0.00 0.00 2.73
6452 6568 7.939588 GGAAAATGAGGATTAGTAGCAATACCT 59.060 37.037 0.00 0.00 0.00 3.08
6453 6569 9.998106 GAAAATGAGGATTAGTAGCAATACCTA 57.002 33.333 0.00 0.00 0.00 3.08
6454 6570 9.780186 AAAATGAGGATTAGTAGCAATACCTAC 57.220 33.333 0.00 0.00 38.34 3.18
6468 6584 5.243207 CAATACCTACCGTGTTTTCTCCTT 58.757 41.667 0.00 0.00 0.00 3.36
6470 6586 2.038164 ACCTACCGTGTTTTCTCCTTCC 59.962 50.000 0.00 0.00 0.00 3.46
6471 6587 2.614734 CCTACCGTGTTTTCTCCTTCCC 60.615 54.545 0.00 0.00 0.00 3.97
6472 6588 1.137697 ACCGTGTTTTCTCCTTCCCT 58.862 50.000 0.00 0.00 0.00 4.20
6473 6589 2.332117 ACCGTGTTTTCTCCTTCCCTA 58.668 47.619 0.00 0.00 0.00 3.53
6474 6590 2.910977 ACCGTGTTTTCTCCTTCCCTAT 59.089 45.455 0.00 0.00 0.00 2.57
6475 6591 3.055312 ACCGTGTTTTCTCCTTCCCTATC 60.055 47.826 0.00 0.00 0.00 2.08
6476 6592 3.055385 CCGTGTTTTCTCCTTCCCTATCA 60.055 47.826 0.00 0.00 0.00 2.15
6477 6593 4.384208 CCGTGTTTTCTCCTTCCCTATCAT 60.384 45.833 0.00 0.00 0.00 2.45
6478 6594 5.186198 CGTGTTTTCTCCTTCCCTATCATT 58.814 41.667 0.00 0.00 0.00 2.57
6479 6595 6.346096 CGTGTTTTCTCCTTCCCTATCATTA 58.654 40.000 0.00 0.00 0.00 1.90
6480 6596 6.480320 CGTGTTTTCTCCTTCCCTATCATTAG 59.520 42.308 0.00 0.00 0.00 1.73
6481 6597 7.339482 GTGTTTTCTCCTTCCCTATCATTAGT 58.661 38.462 0.00 0.00 0.00 2.24
6508 6629 1.892819 CTCTCCTCCAAGCTTCGCCA 61.893 60.000 0.00 0.00 0.00 5.69
6524 6645 0.743097 GCCAATGAGCCTGTGGATTC 59.257 55.000 0.00 0.00 34.05 2.52
6538 6659 3.486252 GATTCGTCTCCCCTCCGCG 62.486 68.421 0.00 0.00 0.00 6.46
6603 6725 5.245301 TGTCCAGCTAGTAGTTTTGCTAGAA 59.755 40.000 0.00 0.00 40.79 2.10
6630 6753 6.833342 TTTTTAGTTTCTCGTAGGTGTGAC 57.167 37.500 0.00 0.00 0.00 3.67
6633 6756 0.038892 TTTCTCGTAGGTGTGACGCC 60.039 55.000 7.17 7.17 40.14 5.68
6646 6769 2.047274 ACGCCTGGGTGAATGACG 60.047 61.111 7.22 0.00 0.00 4.35
6647 6770 2.264480 CGCCTGGGTGAATGACGA 59.736 61.111 0.00 0.00 0.00 4.20
6658 6781 2.917971 GTGAATGACGACTCTTCTTCGG 59.082 50.000 0.00 0.00 40.92 4.30
6695 6818 1.202348 CCGGCCCTTCTTGAATTTGTC 59.798 52.381 0.00 0.00 0.00 3.18
6698 6821 2.095212 GGCCCTTCTTGAATTTGTCGAC 60.095 50.000 9.11 9.11 0.00 4.20
6699 6822 2.814336 GCCCTTCTTGAATTTGTCGACT 59.186 45.455 17.92 0.00 0.00 4.18
6700 6823 4.000988 GCCCTTCTTGAATTTGTCGACTA 58.999 43.478 17.92 6.32 0.00 2.59
6759 6882 0.323629 TTCTTGGGTGGCGAGGTTAG 59.676 55.000 0.00 0.00 0.00 2.34
6775 6898 3.642848 AGGTTAGGGTTTCTTGTCGTGTA 59.357 43.478 0.00 0.00 0.00 2.90
6813 6936 1.697982 AGCAAGGTTAGGGTTTCTCGT 59.302 47.619 0.00 0.00 0.00 4.18
6884 7007 3.885724 TCATCTTCAATCACGGCAGTA 57.114 42.857 0.00 0.00 0.00 2.74
6890 7013 1.000052 TCAATCACGGCAGTACAACGA 60.000 47.619 10.19 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 2.560105 CTGATCCTGAGCGATCCACATA 59.440 50.000 0.00 0.00 38.32 2.29
129 130 2.119886 CCAGGGTTTTGGTTTGCGA 58.880 52.632 0.00 0.00 33.38 5.10
386 387 2.721274 CTCCTGAGCCTACATCATCG 57.279 55.000 0.00 0.00 0.00 3.84
411 412 1.471684 GTCGTCCCGAAGTACACATCT 59.528 52.381 0.00 0.00 37.72 2.90
483 484 1.265095 CATTGCTTCTGTTGTCGCTGT 59.735 47.619 0.00 0.00 0.00 4.40
494 495 0.108992 CACGCATTGCCATTGCTTCT 60.109 50.000 9.61 0.00 37.96 2.85
627 628 6.585695 ATCAAGACATTCAGCAAAGATTGT 57.414 33.333 0.00 0.00 35.49 2.71
789 795 6.432162 ACAGAGTTACACCGTTCACTAATAGA 59.568 38.462 0.00 0.00 0.00 1.98
791 797 6.579666 ACAGAGTTACACCGTTCACTAATA 57.420 37.500 0.00 0.00 0.00 0.98
840 846 6.660887 TCGGTCAGTACGTTTTAAGTTTTT 57.339 33.333 0.00 0.00 0.00 1.94
841 847 6.660887 TTCGGTCAGTACGTTTTAAGTTTT 57.339 33.333 0.00 0.00 0.00 2.43
842 848 5.277011 GCTTCGGTCAGTACGTTTTAAGTTT 60.277 40.000 0.00 0.00 0.00 2.66
843 849 4.209911 GCTTCGGTCAGTACGTTTTAAGTT 59.790 41.667 0.00 0.00 0.00 2.66
844 850 3.737774 GCTTCGGTCAGTACGTTTTAAGT 59.262 43.478 0.00 0.00 0.00 2.24
845 851 3.122445 GGCTTCGGTCAGTACGTTTTAAG 59.878 47.826 0.00 0.00 0.00 1.85
846 852 3.059166 GGCTTCGGTCAGTACGTTTTAA 58.941 45.455 0.00 0.00 0.00 1.52
856 862 2.391389 GGAAAGCGGCTTCGGTCAG 61.391 63.158 16.70 0.00 44.35 3.51
862 868 3.134127 ATGCGGGAAAGCGGCTTC 61.134 61.111 16.70 9.39 40.67 3.86
908 914 2.158058 CGTTTGTCGCTATTTCCGGAAA 59.842 45.455 30.71 30.71 34.46 3.13
1031 1037 4.605183 TCTTTCTCCTCTCCTCTCGATTT 58.395 43.478 0.00 0.00 0.00 2.17
1046 1052 1.469079 GCGTGCTCCTCTCTCTTTCTC 60.469 57.143 0.00 0.00 0.00 2.87
1346 1353 1.153939 CGCACAAGAGAGGACGGAG 60.154 63.158 0.00 0.00 0.00 4.63
1348 1355 2.125912 CCGCACAAGAGAGGACGG 60.126 66.667 0.00 0.00 0.00 4.79
1357 1366 1.535462 CAAACCCTAGAACCGCACAAG 59.465 52.381 0.00 0.00 0.00 3.16
1358 1367 1.141254 TCAAACCCTAGAACCGCACAA 59.859 47.619 0.00 0.00 0.00 3.33
1359 1368 0.759959 TCAAACCCTAGAACCGCACA 59.240 50.000 0.00 0.00 0.00 4.57
1412 1423 2.607750 ATCGACAGCCACCCACCT 60.608 61.111 0.00 0.00 0.00 4.00
1510 1521 9.731819 TGTCTGACGAGTCATAATAAAATACTC 57.268 33.333 6.37 0.00 39.13 2.59
1511 1522 9.737427 CTGTCTGACGAGTCATAATAAAATACT 57.263 33.333 6.37 0.00 39.13 2.12
1529 1540 3.141398 TCTCCATGTTTTGCTGTCTGAC 58.859 45.455 0.00 0.00 0.00 3.51
1613 1624 4.586841 TGGTAATTGTTTCCCAACCTCTTG 59.413 41.667 0.00 0.00 35.44 3.02
1619 1630 4.869861 GCATCATGGTAATTGTTTCCCAAC 59.130 41.667 0.00 0.00 35.44 3.77
1623 1634 4.104776 CGTGCATCATGGTAATTGTTTCC 58.895 43.478 0.00 0.00 0.00 3.13
1625 1636 3.510719 GCGTGCATCATGGTAATTGTTT 58.489 40.909 0.00 0.00 0.00 2.83
1633 1644 2.122797 CATGGGCGTGCATCATGGT 61.123 57.895 15.19 0.00 35.82 3.55
1649 1660 9.880157 ATTTTTCATAGCAGCTTGAAAATACAT 57.120 25.926 27.69 21.03 45.87 2.29
1670 1681 9.769093 CATAAGATTTAGTTCGGTTCGATTTTT 57.231 29.630 0.00 0.00 35.23 1.94
1812 1854 7.328493 TCTCGGAATGCATACATAATTCTTACG 59.672 37.037 0.00 0.00 34.62 3.18
1854 1917 2.503356 AGCTCCTGGTCAAGAATGTAGG 59.497 50.000 0.00 0.00 0.00 3.18
1983 2046 3.755378 AGAAACATGCCAGTGTCTTGATC 59.245 43.478 0.00 0.00 32.09 2.92
1990 2053 3.149196 CCTTACAGAAACATGCCAGTGT 58.851 45.455 0.00 0.00 0.00 3.55
2136 2199 4.530710 ACCTGTTCAATGCGAAGTACTA 57.469 40.909 0.00 0.00 33.09 1.82
2390 2453 3.365820 GCAAACAATGTGCTTAGTGATGC 59.634 43.478 0.00 0.00 39.00 3.91
2459 2523 1.654954 CTCAGCTTGCATGGACAGCC 61.655 60.000 14.47 0.00 0.00 4.85
2551 2631 3.431626 CCCGTTCAATGTGTGCCTATCTA 60.432 47.826 0.00 0.00 0.00 1.98
2773 2856 3.004106 CAGCTTTCACTTTCACCTGGAAG 59.996 47.826 0.00 0.00 36.72 3.46
2973 3056 5.315195 GCAAATGCATTCAATGGTTAAACG 58.685 37.500 13.38 0.00 41.59 3.60
2974 3057 5.412286 AGGCAAATGCATTCAATGGTTAAAC 59.588 36.000 13.38 0.00 44.36 2.01
3006 3089 9.496873 TGAAACACCTATCGATAAGAAAGAAAA 57.503 29.630 8.04 0.00 0.00 2.29
3390 3473 2.497273 GCCCAGAGCAAATAATTGGTGT 59.503 45.455 0.00 0.00 46.70 4.16
3399 3482 1.077985 AGCAAGGCCCAGAGCAAAT 59.922 52.632 0.00 0.00 46.50 2.32
3454 3538 2.777832 AGTCACAAATCAGGGAGCTC 57.222 50.000 4.71 4.71 0.00 4.09
3525 3609 9.208022 TGAAAGACACAGTATCAAAGAATGTAG 57.792 33.333 0.00 0.00 0.00 2.74
3716 3801 3.293311 CAGGACATGCAACAAGGAAAG 57.707 47.619 0.00 0.00 0.00 2.62
3761 3846 4.833938 GGGACAGAGGGACTACTATTTAGG 59.166 50.000 0.00 0.00 41.55 2.69
3815 3900 2.822707 AGAAGCATGCAAATCCCTCT 57.177 45.000 21.98 6.63 0.00 3.69
3822 3907 4.523943 ACAGGACATAAAGAAGCATGCAAA 59.476 37.500 21.98 0.00 0.00 3.68
3824 3909 3.689347 ACAGGACATAAAGAAGCATGCA 58.311 40.909 21.98 0.00 0.00 3.96
4122 4208 4.278669 ACTTCTAAAGCTTCAGACTCGTGA 59.721 41.667 0.00 0.00 0.00 4.35
4842 4945 9.926158 TTTGTTATCTGTCAATTATTGCACAAT 57.074 25.926 0.00 0.94 34.93 2.71
4855 4958 8.677300 GGAGCATTTATCTTTTGTTATCTGTCA 58.323 33.333 0.00 0.00 0.00 3.58
4889 4992 2.267188 TTCTCCGACACGTATTTCCG 57.733 50.000 0.00 0.00 0.00 4.30
4898 5001 7.083875 TCATTTTTATCCATTTCTCCGACAC 57.916 36.000 0.00 0.00 0.00 3.67
4972 5077 4.016479 AGGTACTCCCTCTGTCCAGAAATA 60.016 45.833 0.00 0.00 40.71 1.40
4973 5078 3.108376 GGTACTCCCTCTGTCCAGAAAT 58.892 50.000 0.00 0.00 36.94 2.17
4974 5079 2.111972 AGGTACTCCCTCTGTCCAGAAA 59.888 50.000 0.00 0.00 40.71 2.52
4975 5080 1.717077 AGGTACTCCCTCTGTCCAGAA 59.283 52.381 0.00 0.00 40.71 3.02
4976 5081 1.383963 AGGTACTCCCTCTGTCCAGA 58.616 55.000 0.00 0.00 40.71 3.86
4977 5082 3.053544 TCTTAGGTACTCCCTCTGTCCAG 60.054 52.174 0.00 0.00 44.81 3.86
4978 5083 2.924302 TCTTAGGTACTCCCTCTGTCCA 59.076 50.000 0.00 0.00 44.81 4.02
4979 5084 3.666345 TCTTAGGTACTCCCTCTGTCC 57.334 52.381 0.00 0.00 44.81 4.02
4980 5085 4.602107 ACTTCTTAGGTACTCCCTCTGTC 58.398 47.826 0.00 0.00 44.81 3.51
4981 5086 4.678538 ACTTCTTAGGTACTCCCTCTGT 57.321 45.455 0.00 0.00 44.81 3.41
4982 5087 6.014499 TGAAAACTTCTTAGGTACTCCCTCTG 60.014 42.308 0.00 0.00 44.81 3.35
4983 5088 6.082707 TGAAAACTTCTTAGGTACTCCCTCT 58.917 40.000 0.00 0.00 44.81 3.69
4984 5089 6.210984 TCTGAAAACTTCTTAGGTACTCCCTC 59.789 42.308 0.00 0.00 44.81 4.30
4986 5091 6.356186 TCTGAAAACTTCTTAGGTACTCCC 57.644 41.667 0.00 0.00 41.75 4.30
4987 5092 8.722394 CAAATCTGAAAACTTCTTAGGTACTCC 58.278 37.037 0.00 0.00 41.75 3.85
4988 5093 9.490379 TCAAATCTGAAAACTTCTTAGGTACTC 57.510 33.333 0.00 0.00 41.75 2.59
4989 5094 9.495572 CTCAAATCTGAAAACTTCTTAGGTACT 57.504 33.333 0.00 0.00 46.37 2.73
4990 5095 9.274206 ACTCAAATCTGAAAACTTCTTAGGTAC 57.726 33.333 0.00 0.00 0.00 3.34
5010 5115 8.717821 CGTCCAGAAATAACTTTCATACTCAAA 58.282 33.333 1.40 0.00 42.71 2.69
5011 5116 7.333423 CCGTCCAGAAATAACTTTCATACTCAA 59.667 37.037 1.40 0.00 42.71 3.02
5012 5117 6.816640 CCGTCCAGAAATAACTTTCATACTCA 59.183 38.462 1.40 0.00 42.71 3.41
5013 5118 7.039882 TCCGTCCAGAAATAACTTTCATACTC 58.960 38.462 1.40 0.00 42.71 2.59
5014 5119 6.942976 TCCGTCCAGAAATAACTTTCATACT 58.057 36.000 1.40 0.00 42.71 2.12
5015 5120 6.258068 CCTCCGTCCAGAAATAACTTTCATAC 59.742 42.308 1.40 0.00 42.71 2.39
5016 5121 6.346096 CCTCCGTCCAGAAATAACTTTCATA 58.654 40.000 1.40 0.00 42.71 2.15
5017 5122 5.186198 CCTCCGTCCAGAAATAACTTTCAT 58.814 41.667 1.40 0.00 42.71 2.57
5018 5123 4.564821 CCCTCCGTCCAGAAATAACTTTCA 60.565 45.833 1.40 0.00 42.71 2.69
5019 5124 3.939592 CCCTCCGTCCAGAAATAACTTTC 59.060 47.826 0.00 0.00 40.95 2.62
5020 5125 3.585732 TCCCTCCGTCCAGAAATAACTTT 59.414 43.478 0.00 0.00 0.00 2.66
5021 5126 3.178865 TCCCTCCGTCCAGAAATAACTT 58.821 45.455 0.00 0.00 0.00 2.66
5022 5127 2.766828 CTCCCTCCGTCCAGAAATAACT 59.233 50.000 0.00 0.00 0.00 2.24
5023 5128 2.500504 ACTCCCTCCGTCCAGAAATAAC 59.499 50.000 0.00 0.00 0.00 1.89
5024 5129 2.829023 ACTCCCTCCGTCCAGAAATAA 58.171 47.619 0.00 0.00 0.00 1.40
5040 5145 8.722394 CAAATCTGAAAACTTCTTAGGTACTCC 58.278 37.037 0.00 0.00 41.75 3.85
5177 5282 9.934190 GTCCAAAATACTGTTTCGTTACTTTAA 57.066 29.630 0.00 0.00 0.00 1.52
5187 5292 5.784578 AACCAGGTCCAAAATACTGTTTC 57.215 39.130 0.00 0.00 0.00 2.78
5313 5419 8.087750 TGCCAATCATTTTAGTAAAAGAACAGG 58.912 33.333 13.25 12.28 33.22 4.00
5365 5471 1.330521 CAGTGTGGGTGAAACAGTTCG 59.669 52.381 0.00 0.00 39.98 3.95
5578 5684 2.354259 CTGAGTGCCTTGATCTTGTCC 58.646 52.381 0.00 0.00 0.00 4.02
6034 6150 1.936547 GCACAGCTGTCTTGGTATAGC 59.063 52.381 18.64 10.43 36.45 2.97
6047 6163 2.357517 GTACTGCGGTGCACAGCT 60.358 61.111 35.67 22.74 38.79 4.24
6115 6231 3.489908 GGACGGAGGGAGTACGATTTTAC 60.490 52.174 0.00 0.00 0.00 2.01
6117 6233 1.479730 GGACGGAGGGAGTACGATTTT 59.520 52.381 0.00 0.00 0.00 1.82
6119 6235 2.804549 GGACGGAGGGAGTACGATT 58.195 57.895 0.00 0.00 0.00 3.34
6123 6239 1.880819 TTTGCGGACGGAGGGAGTAC 61.881 60.000 0.00 0.00 0.00 2.73
6128 6244 1.333619 CAAATATTTGCGGACGGAGGG 59.666 52.381 14.96 0.00 0.00 4.30
6129 6245 2.014128 ACAAATATTTGCGGACGGAGG 58.986 47.619 24.82 1.29 41.79 4.30
6130 6246 2.285602 CGACAAATATTTGCGGACGGAG 60.286 50.000 24.82 6.72 41.79 4.63
6131 6247 1.661617 CGACAAATATTTGCGGACGGA 59.338 47.619 24.82 0.00 41.79 4.69
6132 6248 2.085532 CGACAAATATTTGCGGACGG 57.914 50.000 24.82 7.09 41.79 4.79
6137 6253 4.734854 CCATTTCTCCGACAAATATTTGCG 59.265 41.667 24.82 24.99 41.79 4.85
6138 6254 5.516339 CACCATTTCTCCGACAAATATTTGC 59.484 40.000 24.82 17.01 41.79 3.68
6139 6255 5.516339 GCACCATTTCTCCGACAAATATTTG 59.484 40.000 23.60 23.60 43.62 2.32
6144 6260 2.513753 TGCACCATTTCTCCGACAAAT 58.486 42.857 0.00 0.00 0.00 2.32
6145 6261 1.974265 TGCACCATTTCTCCGACAAA 58.026 45.000 0.00 0.00 0.00 2.83
6146 6262 2.198827 ATGCACCATTTCTCCGACAA 57.801 45.000 0.00 0.00 0.00 3.18
6150 6266 4.701956 ACTAAAATGCACCATTTCTCCG 57.298 40.909 3.90 0.00 42.32 4.63
6151 6267 6.272822 AGAACTAAAATGCACCATTTCTCC 57.727 37.500 3.90 0.00 42.32 3.71
6152 6268 9.860898 ATTTAGAACTAAAATGCACCATTTCTC 57.139 29.630 10.38 0.81 42.32 2.87
6184 6300 7.383687 ACTTGTCACGAAAATGGATAGAAGTA 58.616 34.615 0.00 0.00 0.00 2.24
6189 6305 8.122952 GGAATTACTTGTCACGAAAATGGATAG 58.877 37.037 0.00 0.00 0.00 2.08
6200 6316 1.652124 CGTCCGGAATTACTTGTCACG 59.348 52.381 5.23 0.00 0.00 4.35
6202 6318 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
6276 6392 5.365403 AAAAATTACCGTGCGAATGAGAA 57.635 34.783 0.00 0.00 0.00 2.87
6381 6497 4.577693 TGCTGCAACTCCATTTCTCATATC 59.422 41.667 0.00 0.00 0.00 1.63
6440 6556 4.813750 AAACACGGTAGGTATTGCTACT 57.186 40.909 0.00 0.00 0.00 2.57
6441 6557 5.173664 AGAAAACACGGTAGGTATTGCTAC 58.826 41.667 0.00 0.00 0.00 3.58
6442 6558 5.410355 AGAAAACACGGTAGGTATTGCTA 57.590 39.130 0.00 0.00 0.00 3.49
6443 6559 4.251268 GAGAAAACACGGTAGGTATTGCT 58.749 43.478 0.00 0.00 0.00 3.91
6444 6560 3.373130 GGAGAAAACACGGTAGGTATTGC 59.627 47.826 0.00 0.00 0.00 3.56
6445 6561 4.828829 AGGAGAAAACACGGTAGGTATTG 58.171 43.478 0.00 0.00 0.00 1.90
6446 6562 5.485620 GAAGGAGAAAACACGGTAGGTATT 58.514 41.667 0.00 0.00 0.00 1.89
6447 6563 4.081254 GGAAGGAGAAAACACGGTAGGTAT 60.081 45.833 0.00 0.00 0.00 2.73
6448 6564 3.259123 GGAAGGAGAAAACACGGTAGGTA 59.741 47.826 0.00 0.00 0.00 3.08
6449 6565 2.038164 GGAAGGAGAAAACACGGTAGGT 59.962 50.000 0.00 0.00 0.00 3.08
6450 6566 2.614734 GGGAAGGAGAAAACACGGTAGG 60.615 54.545 0.00 0.00 0.00 3.18
6451 6567 2.302157 AGGGAAGGAGAAAACACGGTAG 59.698 50.000 0.00 0.00 0.00 3.18
6452 6568 2.332117 AGGGAAGGAGAAAACACGGTA 58.668 47.619 0.00 0.00 0.00 4.02
6453 6569 1.137697 AGGGAAGGAGAAAACACGGT 58.862 50.000 0.00 0.00 0.00 4.83
6454 6570 3.055385 TGATAGGGAAGGAGAAAACACGG 60.055 47.826 0.00 0.00 0.00 4.94
6468 6584 5.663106 AGAGAGTTTGCACTAATGATAGGGA 59.337 40.000 0.00 0.00 34.19 4.20
6470 6586 5.988561 GGAGAGAGTTTGCACTAATGATAGG 59.011 44.000 0.00 0.00 31.22 2.57
6471 6587 6.815089 AGGAGAGAGTTTGCACTAATGATAG 58.185 40.000 0.00 0.00 31.22 2.08
6472 6588 6.183360 GGAGGAGAGAGTTTGCACTAATGATA 60.183 42.308 0.00 0.00 31.22 2.15
6473 6589 5.396213 GGAGGAGAGAGTTTGCACTAATGAT 60.396 44.000 0.00 0.00 31.22 2.45
6474 6590 4.081420 GGAGGAGAGAGTTTGCACTAATGA 60.081 45.833 0.00 0.00 31.22 2.57
6475 6591 4.187694 GGAGGAGAGAGTTTGCACTAATG 58.812 47.826 0.00 0.00 31.22 1.90
6476 6592 3.840666 TGGAGGAGAGAGTTTGCACTAAT 59.159 43.478 0.00 0.00 31.22 1.73
6477 6593 3.239449 TGGAGGAGAGAGTTTGCACTAA 58.761 45.455 0.00 0.00 31.22 2.24
6478 6594 2.889512 TGGAGGAGAGAGTTTGCACTA 58.110 47.619 0.00 0.00 31.22 2.74
6479 6595 1.722034 TGGAGGAGAGAGTTTGCACT 58.278 50.000 0.00 0.00 35.17 4.40
6480 6596 2.421619 CTTGGAGGAGAGAGTTTGCAC 58.578 52.381 0.00 0.00 0.00 4.57
6481 6597 1.271054 GCTTGGAGGAGAGAGTTTGCA 60.271 52.381 0.00 0.00 0.00 4.08
6508 6629 1.556911 AGACGAATCCACAGGCTCATT 59.443 47.619 0.00 0.00 0.00 2.57
6538 6659 0.321653 AGTCATCAACCACCGAAGCC 60.322 55.000 0.00 0.00 0.00 4.35
6630 6753 2.100631 GTCGTCATTCACCCAGGCG 61.101 63.158 0.00 0.00 0.00 5.52
6633 6756 2.232452 AGAAGAGTCGTCATTCACCCAG 59.768 50.000 8.82 0.00 0.00 4.45
6646 6769 3.388345 AGACAAACCCGAAGAAGAGTC 57.612 47.619 0.00 0.00 0.00 3.36
6647 6770 3.840124 AAGACAAACCCGAAGAAGAGT 57.160 42.857 0.00 0.00 0.00 3.24
6658 6781 0.875059 CGGAGCCTGAAAGACAAACC 59.125 55.000 0.00 0.00 34.07 3.27
6698 6821 2.477375 GAGCTCCGTCGACTATGTCTAG 59.523 54.545 14.70 1.68 0.00 2.43
6699 6822 2.481854 GAGCTCCGTCGACTATGTCTA 58.518 52.381 14.70 0.00 0.00 2.59
6700 6823 1.301423 GAGCTCCGTCGACTATGTCT 58.699 55.000 14.70 4.07 0.00 3.41
6759 6882 2.095919 GCACATACACGACAAGAAACCC 60.096 50.000 0.00 0.00 0.00 4.11
6775 6898 2.094675 GCTATCCAAGGTGTTGCACAT 58.905 47.619 1.61 0.00 35.86 3.21
6857 6980 6.057533 TGCCGTGATTGAAGATGAATAGATT 58.942 36.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.