Multiple sequence alignment - TraesCS7D01G148300

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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 TraesCS7D01G148300 chr7D 100.000 5116 0 0 1 5116 95101049 95095934 0.000000e+00 9448.0
1 TraesCS7D01G148300 chr7D 97.262 4420 64 10 147 4540 590592671 590588283 0.000000e+00 7439.0
2 TraesCS7D01G148300 chr7D 97.513 4302 74 16 143 4436 362367308 362371584 0.000000e+00 7321.0
3 TraesCS7D01G148300 chr7D 94.599 1759 57 15 2696 4436 550666249 550667987 0.000000e+00 2687.0
4 TraesCS7D01G148300 chr7D 97.809 913 18 2 4205 5116 590588573 590587662 0.000000e+00 1574.0
5 TraesCS7D01G148300 chr7D 94.451 811 34 4 4307 5116 362371365 362372165 0.000000e+00 1238.0
6 TraesCS7D01G148300 chr7D 100.000 280 0 0 5454 5733 95095596 95095317 8.520000e-143 518.0
7 TraesCS7D01G148300 chr7D 96.429 280 9 1 5454 5733 362372442 362372720 1.460000e-125 460.0
8 TraesCS7D01G148300 chr7D 95.572 271 10 2 5454 5723 590587748 590587479 3.170000e-117 433.0
9 TraesCS7D01G148300 chr7D 97.409 193 4 1 4925 5116 550680222 550680414 1.540000e-85 327.0
10 TraesCS7D01G148300 chr7D 96.241 133 4 1 4985 5116 362372082 362372214 3.480000e-52 217.0
11 TraesCS7D01G148300 chr7D 95.489 133 4 2 4985 5116 362372131 362372262 1.620000e-50 211.0
12 TraesCS7D01G148300 chr7D 100.000 44 0 0 1 44 184578786 184578829 1.320000e-11 82.4
13 TraesCS7D01G148300 chr7D 100.000 43 0 0 1 43 93950469 93950511 4.760000e-11 80.5
14 TraesCS7D01G148300 chr2A 95.472 4991 151 19 147 5116 2356026 2360962 0.000000e+00 7895.0
15 TraesCS7D01G148300 chr2A 95.143 3397 105 14 1594 4989 712853326 712849989 0.000000e+00 5304.0
16 TraesCS7D01G148300 chr2A 94.075 1519 51 3 147 1650 712854797 712853303 0.000000e+00 2270.0
17 TraesCS7D01G148300 chr2A 93.929 280 16 1 5454 5733 2360877 2361155 6.870000e-114 422.0
18 TraesCS7D01G148300 chr2A 97.297 222 6 0 147 368 2362926 2362705 1.510000e-100 377.0
19 TraesCS7D01G148300 chr2A 96.861 223 7 0 146 368 712847304 712847526 1.950000e-99 374.0
20 TraesCS7D01G148300 chr6D 97.572 4324 73 13 147 4450 102252338 102248027 0.000000e+00 7374.0
21 TraesCS7D01G148300 chr6D 94.628 2718 119 5 147 2839 277340135 277337420 0.000000e+00 4185.0
22 TraesCS7D01G148300 chr6D 94.826 831 18 4 4307 5116 102248260 102247434 0.000000e+00 1273.0
23 TraesCS7D01G148300 chr6D 96.429 280 9 1 5454 5733 102247374 102247096 1.460000e-125 460.0
24 TraesCS7D01G148300 chr6D 96.296 270 9 1 5454 5723 102247471 102247203 5.270000e-120 442.0
25 TraesCS7D01G148300 chr6D 92.143 280 18 4 5456 5733 102247421 102247144 5.390000e-105 392.0
26 TraesCS7D01G148300 chr4D 96.951 4296 95 14 147 4436 122726627 122722362 0.000000e+00 7175.0
27 TraesCS7D01G148300 chr4D 94.205 811 36 4 4307 5116 122722581 122721781 0.000000e+00 1227.0
28 TraesCS7D01G148300 chr4D 96.071 280 10 1 5454 5733 122721769 122721491 6.770000e-124 455.0
29 TraesCS7D01G148300 chr4D 95.556 270 12 0 5454 5723 122721867 122721598 3.170000e-117 433.0
30 TraesCS7D01G148300 chr4D 91.844 282 19 4 5454 5733 122721818 122721539 1.940000e-104 390.0
31 TraesCS7D01G148300 chr4D 97.297 37 1 0 7 43 80461158 80461122 4.800000e-06 63.9
32 TraesCS7D01G148300 chr3D 98.384 3961 40 4 307 4247 53788544 53792500 0.000000e+00 6938.0
33 TraesCS7D01G148300 chr3D 98.512 2822 22 3 147 2959 5493961 5496771 0.000000e+00 4961.0
34 TraesCS7D01G148300 chr3D 98.260 862 10 3 4256 5116 5497427 5498284 0.000000e+00 1504.0
35 TraesCS7D01G148300 chr3D 97.691 823 16 1 4294 5116 53811380 53812199 0.000000e+00 1411.0
36 TraesCS7D01G148300 chr3D 98.655 223 3 0 146 368 53814859 53814637 4.160000e-106 396.0
37 TraesCS7D01G148300 chr3D 98.649 222 3 0 147 368 5500824 5500603 1.500000e-105 394.0
38 TraesCS7D01G148300 chr3D 100.000 43 0 0 1 43 144783344 144783386 4.760000e-11 80.5
39 TraesCS7D01G148300 chr3D 100.000 31 0 0 13 43 612306158 612306128 2.230000e-04 58.4
40 TraesCS7D01G148300 chr4A 92.490 3755 231 32 758 4495 706492715 706488995 0.000000e+00 5325.0
41 TraesCS7D01G148300 chr4A 96.431 2886 87 8 1594 4478 84937030 84939900 0.000000e+00 4745.0
42 TraesCS7D01G148300 chr4A 90.579 881 52 10 4256 5116 84939633 84940502 0.000000e+00 1138.0
43 TraesCS7D01G148300 chr5A 94.580 3395 118 14 1594 4987 273997184 273993855 0.000000e+00 5190.0
44 TraesCS7D01G148300 chr5A 95.158 2024 76 8 2462 4478 35060153 35062161 0.000000e+00 3175.0
45 TraesCS7D01G148300 chr1D 94.785 2953 110 18 147 3091 80650664 80647748 0.000000e+00 4560.0
46 TraesCS7D01G148300 chr1D 93.711 811 36 5 4307 5116 386771502 386770706 0.000000e+00 1201.0
47 TraesCS7D01G148300 chr1D 100.000 43 0 0 1 43 224140732 224140774 4.760000e-11 80.5
48 TraesCS7D01G148300 chrUn 98.183 2201 25 2 2093 4279 108019461 108021660 0.000000e+00 3829.0
49 TraesCS7D01G148300 chr1A 90.543 645 46 10 4256 4899 582352738 582353368 0.000000e+00 839.0
50 TraesCS7D01G148300 chr7A 97.561 41 1 0 106 146 98755631 98755591 2.870000e-08 71.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G148300 chr7D 95095317 95101049 5732 True 4983.000000 9448 100.0000 1 5733 2 chr7D.!!$R1 5732
1 TraesCS7D01G148300 chr7D 590587479 590592671 5192 True 3148.666667 7439 96.8810 147 5723 3 chr7D.!!$R2 5576
2 TraesCS7D01G148300 chr7D 550666249 550667987 1738 False 2687.000000 2687 94.5990 2696 4436 1 chr7D.!!$F3 1740
3 TraesCS7D01G148300 chr7D 362367308 362372720 5412 False 1889.400000 7321 96.0246 143 5733 5 chr7D.!!$F5 5590
4 TraesCS7D01G148300 chr2A 2356026 2361155 5129 False 4158.500000 7895 94.7005 147 5733 2 chr2A.!!$F2 5586
5 TraesCS7D01G148300 chr2A 712849989 712854797 4808 True 3787.000000 5304 94.6090 147 4989 2 chr2A.!!$R2 4842
6 TraesCS7D01G148300 chr6D 277337420 277340135 2715 True 4185.000000 4185 94.6280 147 2839 1 chr6D.!!$R1 2692
7 TraesCS7D01G148300 chr6D 102247096 102252338 5242 True 1988.200000 7374 95.4532 147 5733 5 chr6D.!!$R2 5586
8 TraesCS7D01G148300 chr4D 122721491 122726627 5136 True 1936.000000 7175 94.9254 147 5733 5 chr4D.!!$R2 5586
9 TraesCS7D01G148300 chr3D 53788544 53792500 3956 False 6938.000000 6938 98.3840 307 4247 1 chr3D.!!$F1 3940
10 TraesCS7D01G148300 chr3D 5493961 5498284 4323 False 3232.500000 4961 98.3860 147 5116 2 chr3D.!!$F4 4969
11 TraesCS7D01G148300 chr3D 53811380 53812199 819 False 1411.000000 1411 97.6910 4294 5116 1 chr3D.!!$F2 822
12 TraesCS7D01G148300 chr4A 706488995 706492715 3720 True 5325.000000 5325 92.4900 758 4495 1 chr4A.!!$R1 3737
13 TraesCS7D01G148300 chr4A 84937030 84940502 3472 False 2941.500000 4745 93.5050 1594 5116 2 chr4A.!!$F1 3522
14 TraesCS7D01G148300 chr5A 273993855 273997184 3329 True 5190.000000 5190 94.5800 1594 4987 1 chr5A.!!$R1 3393
15 TraesCS7D01G148300 chr5A 35060153 35062161 2008 False 3175.000000 3175 95.1580 2462 4478 1 chr5A.!!$F1 2016
16 TraesCS7D01G148300 chr1D 80647748 80650664 2916 True 4560.000000 4560 94.7850 147 3091 1 chr1D.!!$R1 2944
17 TraesCS7D01G148300 chr1D 386770706 386771502 796 True 1201.000000 1201 93.7110 4307 5116 1 chr1D.!!$R2 809
18 TraesCS7D01G148300 chrUn 108019461 108021660 2199 False 3829.000000 3829 98.1830 2093 4279 1 chrUn.!!$F1 2186
19 TraesCS7D01G148300 chr1A 582352738 582353368 630 False 839.000000 839 90.5430 4256 4899 1 chr1A.!!$F1 643

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
124 125 0.036164 TTAATGGATGGCCCGATCCG 59.964 55.000 15.52 0.0 44.52 4.18 F
143 144 0.591741 GTCGATCCGTTGCTCCGTAG 60.592 60.000 0.00 0.0 0.00 3.51 F
406 433 0.640495 TATCCCCCGTCTTCTTCCCT 59.360 55.000 0.00 0.0 0.00 4.20 F
1447 1511 1.066002 CCTTGCAGTTTGACACACAGG 59.934 52.381 0.00 0.0 0.00 4.00 F
1458 1522 2.289257 TGACACACAGGAGAGCAGAATG 60.289 50.000 0.00 0.0 40.87 2.67 F
3357 3512 1.185315 GCTGCTTGGGAATGGCTAAA 58.815 50.000 0.00 0.0 0.00 1.85 F
3971 4131 1.570501 AGGGCCAATATGAGAAGCCAA 59.429 47.619 6.18 0.0 45.72 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1522 1.457346 CAGGTTCCAGGCTCACATTC 58.543 55.000 0.00 0.00 0.00 2.67 R
1977 2077 3.647113 CAGATGATGGAATCCAGTCCTCT 59.353 47.826 8.40 10.08 44.73 3.69 R
2718 2818 1.821136 CAGCCATTGAGAAACCCTTCC 59.179 52.381 0.00 0.00 31.28 3.46 R
3357 3512 5.221362 GCCCAAGTGTGTTTAGGTATTTTGT 60.221 40.000 0.00 0.00 0.00 2.83 R
3971 4131 3.662759 TTTTGAGGTGTCTTTGGGAGT 57.337 42.857 0.00 0.00 0.00 3.85 R
4710 5312 0.038166 TTCCCATGGAGCACCTGAAC 59.962 55.000 15.22 0.00 37.04 3.18 R
5085 5729 1.291132 GGCTTTGTCGACATCTAGCC 58.709 55.000 32.73 32.73 37.78 3.93 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
22 23 3.181507 CCGTGCTTTCACTGAATGTATGG 60.182 47.826 15.23 15.23 40.99 2.74
24 25 4.083324 CGTGCTTTCACTGAATGTATGGTT 60.083 41.667 6.55 0.00 40.99 3.67
26 27 6.215845 GTGCTTTCACTGAATGTATGGTTTT 58.784 36.000 6.55 0.00 40.03 2.43
27 28 6.363357 GTGCTTTCACTGAATGTATGGTTTTC 59.637 38.462 6.55 0.00 40.03 2.29
28 29 6.040278 TGCTTTCACTGAATGTATGGTTTTCA 59.960 34.615 6.55 0.00 0.00 2.69
29 30 6.363357 GCTTTCACTGAATGTATGGTTTTCAC 59.637 38.462 6.55 0.00 0.00 3.18
30 31 7.581213 TTTCACTGAATGTATGGTTTTCACT 57.419 32.000 0.00 0.00 0.00 3.41
31 32 8.684386 TTTCACTGAATGTATGGTTTTCACTA 57.316 30.769 0.00 0.00 0.00 2.74
32 33 7.905604 TCACTGAATGTATGGTTTTCACTAG 57.094 36.000 0.00 0.00 0.00 2.57
33 34 7.676004 TCACTGAATGTATGGTTTTCACTAGA 58.324 34.615 0.00 0.00 0.00 2.43
34 35 8.321353 TCACTGAATGTATGGTTTTCACTAGAT 58.679 33.333 0.00 0.00 0.00 1.98
35 36 9.599866 CACTGAATGTATGGTTTTCACTAGATA 57.400 33.333 0.00 0.00 0.00 1.98
45 46 9.770097 ATGGTTTTCACTAGATATGTACTCATG 57.230 33.333 0.00 0.00 35.70 3.07
46 47 8.204160 TGGTTTTCACTAGATATGTACTCATGG 58.796 37.037 0.00 0.00 35.70 3.66
47 48 8.421784 GGTTTTCACTAGATATGTACTCATGGA 58.578 37.037 0.00 0.00 35.70 3.41
48 49 9.250624 GTTTTCACTAGATATGTACTCATGGAC 57.749 37.037 0.00 0.00 35.70 4.02
49 50 8.533569 TTTCACTAGATATGTACTCATGGACA 57.466 34.615 0.00 0.00 35.70 4.02
50 51 8.712228 TTCACTAGATATGTACTCATGGACAT 57.288 34.615 0.00 11.76 39.57 3.06
51 52 9.807921 TTCACTAGATATGTACTCATGGACATA 57.192 33.333 14.40 14.40 41.50 2.29
52 53 9.981460 TCACTAGATATGTACTCATGGACATAT 57.019 33.333 19.88 19.88 46.86 1.78
54 55 9.194972 ACTAGATATGTACTCATGGACATATGG 57.805 37.037 22.63 16.89 45.14 2.74
55 56 9.194972 CTAGATATGTACTCATGGACATATGGT 57.805 37.037 22.63 15.79 45.14 3.55
56 57 7.845037 AGATATGTACTCATGGACATATGGTG 58.155 38.462 22.63 0.89 45.14 4.17
57 58 5.894298 ATGTACTCATGGACATATGGTGT 57.106 39.130 7.80 0.00 36.98 4.16
58 59 5.022282 TGTACTCATGGACATATGGTGTG 57.978 43.478 7.80 4.37 42.36 3.82
59 60 4.469586 TGTACTCATGGACATATGGTGTGT 59.530 41.667 7.80 9.36 42.36 3.72
60 61 3.877559 ACTCATGGACATATGGTGTGTG 58.122 45.455 7.80 4.37 42.36 3.82
61 62 2.615447 CTCATGGACATATGGTGTGTGC 59.385 50.000 7.80 0.00 42.36 4.57
63 64 2.112380 TGGACATATGGTGTGTGCAG 57.888 50.000 7.80 0.00 41.94 4.41
64 65 1.339920 TGGACATATGGTGTGTGCAGG 60.340 52.381 7.80 0.00 41.94 4.85
65 66 0.734889 GACATATGGTGTGTGCAGGC 59.265 55.000 7.80 0.00 42.36 4.85
66 67 0.680921 ACATATGGTGTGTGCAGGCC 60.681 55.000 7.80 0.00 40.28 5.19
67 68 0.680601 CATATGGTGTGTGCAGGCCA 60.681 55.000 5.01 0.00 35.28 5.36
68 69 0.394762 ATATGGTGTGTGCAGGCCAG 60.395 55.000 5.01 0.00 34.18 4.85
69 70 2.482796 TATGGTGTGTGCAGGCCAGG 62.483 60.000 5.01 0.00 34.18 4.45
72 73 4.960866 TGTGTGCAGGCCAGGCAG 62.961 66.667 20.91 6.23 42.85 4.85
78 79 3.095163 CAGGCCAGGCAGGGAGAT 61.095 66.667 15.19 0.00 38.09 2.75
79 80 2.286732 AGGCCAGGCAGGGAGATT 60.287 61.111 15.19 0.00 38.09 2.40
80 81 2.194326 GGCCAGGCAGGGAGATTC 59.806 66.667 15.19 0.00 38.09 2.52
81 82 2.683465 GGCCAGGCAGGGAGATTCA 61.683 63.158 15.19 0.00 38.09 2.57
82 83 1.535685 GCCAGGCAGGGAGATTCAT 59.464 57.895 6.55 0.00 38.09 2.57
83 84 0.767375 GCCAGGCAGGGAGATTCATA 59.233 55.000 6.55 0.00 38.09 2.15
84 85 1.353694 GCCAGGCAGGGAGATTCATAT 59.646 52.381 6.55 0.00 38.09 1.78
85 86 2.617532 GCCAGGCAGGGAGATTCATATC 60.618 54.545 6.55 0.00 38.09 1.63
86 87 2.354503 CCAGGCAGGGAGATTCATATCG 60.355 54.545 0.00 0.00 35.85 2.92
87 88 1.277557 AGGCAGGGAGATTCATATCGC 59.722 52.381 0.00 0.00 35.85 4.58
88 89 1.354040 GCAGGGAGATTCATATCGCG 58.646 55.000 0.00 0.00 36.28 5.87
89 90 2.001812 CAGGGAGATTCATATCGCGG 57.998 55.000 6.13 0.00 36.28 6.46
90 91 0.898320 AGGGAGATTCATATCGCGGG 59.102 55.000 6.13 0.00 36.28 6.13
91 92 0.108138 GGGAGATTCATATCGCGGGG 60.108 60.000 6.13 0.00 35.85 5.73
92 93 0.108138 GGAGATTCATATCGCGGGGG 60.108 60.000 6.13 0.00 35.85 5.40
93 94 0.608640 GAGATTCATATCGCGGGGGT 59.391 55.000 6.13 0.00 35.85 4.95
94 95 1.002087 GAGATTCATATCGCGGGGGTT 59.998 52.381 6.13 0.00 35.85 4.11
95 96 1.420138 AGATTCATATCGCGGGGGTTT 59.580 47.619 6.13 0.00 35.85 3.27
96 97 2.635915 AGATTCATATCGCGGGGGTTTA 59.364 45.455 6.13 0.00 35.85 2.01
97 98 2.243602 TTCATATCGCGGGGGTTTAC 57.756 50.000 6.13 0.00 0.00 2.01
98 99 0.393820 TCATATCGCGGGGGTTTACC 59.606 55.000 6.13 0.00 39.11 2.85
99 100 0.395312 CATATCGCGGGGGTTTACCT 59.605 55.000 6.13 0.00 40.03 3.08
100 101 1.134228 ATATCGCGGGGGTTTACCTT 58.866 50.000 6.13 0.00 40.03 3.50
101 102 0.911053 TATCGCGGGGGTTTACCTTT 59.089 50.000 6.13 0.00 40.03 3.11
102 103 0.911053 ATCGCGGGGGTTTACCTTTA 59.089 50.000 6.13 0.00 40.03 1.85
103 104 0.036483 TCGCGGGGGTTTACCTTTAC 60.036 55.000 6.13 0.00 40.03 2.01
104 105 1.026182 CGCGGGGGTTTACCTTTACC 61.026 60.000 0.00 0.00 40.03 2.85
105 106 0.329261 GCGGGGGTTTACCTTTACCT 59.671 55.000 0.00 0.00 40.03 3.08
106 107 1.272092 GCGGGGGTTTACCTTTACCTT 60.272 52.381 0.00 0.00 40.03 3.50
107 108 2.026356 GCGGGGGTTTACCTTTACCTTA 60.026 50.000 0.00 0.00 40.03 2.69
108 109 3.561097 GCGGGGGTTTACCTTTACCTTAA 60.561 47.826 0.00 0.00 40.03 1.85
109 110 4.858850 CGGGGGTTTACCTTTACCTTAAT 58.141 43.478 0.00 0.00 40.03 1.40
110 111 4.641541 CGGGGGTTTACCTTTACCTTAATG 59.358 45.833 0.00 0.00 40.03 1.90
111 112 4.957954 GGGGGTTTACCTTTACCTTAATGG 59.042 45.833 0.00 0.00 40.03 3.16
112 113 5.281663 GGGGGTTTACCTTTACCTTAATGGA 60.282 44.000 0.00 0.00 40.03 3.41
113 114 6.437755 GGGGTTTACCTTTACCTTAATGGAT 58.562 40.000 0.00 0.00 40.03 3.41
114 115 6.322969 GGGGTTTACCTTTACCTTAATGGATG 59.677 42.308 0.00 0.00 40.03 3.51
115 116 6.322969 GGGTTTACCTTTACCTTAATGGATGG 59.677 42.308 0.00 0.00 36.69 3.51
116 117 6.183360 GGTTTACCTTTACCTTAATGGATGGC 60.183 42.308 5.18 0.00 39.71 4.40
117 118 3.910989 ACCTTTACCTTAATGGATGGCC 58.089 45.455 0.00 0.00 39.71 5.36
118 119 3.230976 CCTTTACCTTAATGGATGGCCC 58.769 50.000 0.00 0.00 39.71 5.80
119 120 2.649531 TTACCTTAATGGATGGCCCG 57.350 50.000 0.00 0.00 39.71 6.13
120 121 1.809133 TACCTTAATGGATGGCCCGA 58.191 50.000 0.00 0.00 39.71 5.14
121 122 1.149101 ACCTTAATGGATGGCCCGAT 58.851 50.000 0.00 0.00 39.71 4.18
122 123 1.073923 ACCTTAATGGATGGCCCGATC 59.926 52.381 0.00 0.00 39.71 3.69
123 124 1.614317 CCTTAATGGATGGCCCGATCC 60.614 57.143 14.06 14.06 42.23 3.36
124 125 0.036164 TTAATGGATGGCCCGATCCG 59.964 55.000 15.52 0.00 44.52 4.18
125 126 1.125093 TAATGGATGGCCCGATCCGT 61.125 55.000 15.52 13.07 44.52 4.69
126 127 2.397413 AATGGATGGCCCGATCCGTC 62.397 60.000 15.46 6.59 44.52 4.79
136 137 3.614143 GATCCGTCGATCCGTTGC 58.386 61.111 0.00 0.00 39.29 4.17
137 138 1.065928 GATCCGTCGATCCGTTGCT 59.934 57.895 0.00 0.00 39.29 3.91
138 139 0.935366 GATCCGTCGATCCGTTGCTC 60.935 60.000 0.00 0.00 39.29 4.26
139 140 2.351336 ATCCGTCGATCCGTTGCTCC 62.351 60.000 0.00 0.00 0.00 4.70
140 141 2.949678 CGTCGATCCGTTGCTCCG 60.950 66.667 0.00 0.00 0.00 4.63
141 142 2.181021 GTCGATCCGTTGCTCCGT 59.819 61.111 0.00 0.00 0.00 4.69
142 143 1.430632 GTCGATCCGTTGCTCCGTA 59.569 57.895 0.00 0.00 0.00 4.02
143 144 0.591741 GTCGATCCGTTGCTCCGTAG 60.592 60.000 0.00 0.00 0.00 3.51
355 368 2.508663 GGACAGCCGTTAGACGCC 60.509 66.667 0.00 0.00 40.91 5.68
406 433 0.640495 TATCCCCCGTCTTCTTCCCT 59.360 55.000 0.00 0.00 0.00 4.20
500 529 1.298413 GCGAAGTCGAGCGATGCTA 60.298 57.895 4.59 0.00 39.88 3.49
1250 1314 2.910319 TGACAATAGTTAGGGCCAGTGT 59.090 45.455 6.18 0.00 0.00 3.55
1447 1511 1.066002 CCTTGCAGTTTGACACACAGG 59.934 52.381 0.00 0.00 0.00 4.00
1458 1522 2.289257 TGACACACAGGAGAGCAGAATG 60.289 50.000 0.00 0.00 40.87 2.67
1516 1580 6.895756 AGTAGTGGAAGAATACCATGTGACTA 59.104 38.462 0.00 0.00 39.69 2.59
1977 2077 7.252612 TGGGAGTATAGAAGACATGTTTGAA 57.747 36.000 0.00 0.00 0.00 2.69
2718 2818 5.447624 TCATATGCTTGAATGGATGCAAG 57.552 39.130 3.24 3.24 43.26 4.01
3357 3512 1.185315 GCTGCTTGGGAATGGCTAAA 58.815 50.000 0.00 0.00 0.00 1.85
3971 4131 1.570501 AGGGCCAATATGAGAAGCCAA 59.429 47.619 6.18 0.00 45.72 4.52
4007 4167 4.383010 CCTCAAAAATGGCCTCAATTACCC 60.383 45.833 3.32 0.00 0.00 3.69
4148 4308 7.223260 TGATGTTGCTTTGAATTCATCTTCT 57.777 32.000 9.40 0.00 34.63 2.85
4546 5148 2.113986 GCTGCACCACCAAGGAGT 59.886 61.111 0.00 0.00 41.22 3.85
4710 5312 8.887717 CCAGAAAATTAGAGATTACTTGACTGG 58.112 37.037 0.00 0.00 33.24 4.00
5076 5720 4.382901 GCCATCAAAGATGCCAAAATACCA 60.383 41.667 1.52 0.00 0.00 3.25
5079 5723 7.149973 CCATCAAAGATGCCAAAATACCATAG 58.850 38.462 1.52 0.00 0.00 2.23
5080 5724 7.014518 CCATCAAAGATGCCAAAATACCATAGA 59.985 37.037 1.52 0.00 0.00 1.98
5081 5725 8.582437 CATCAAAGATGCCAAAATACCATAGAT 58.418 33.333 0.00 0.00 0.00 1.98
5082 5726 7.944061 TCAAAGATGCCAAAATACCATAGATG 58.056 34.615 0.00 0.00 0.00 2.90
5083 5727 7.779326 TCAAAGATGCCAAAATACCATAGATGA 59.221 33.333 0.00 0.00 0.00 2.92
5084 5728 8.582437 CAAAGATGCCAAAATACCATAGATGAT 58.418 33.333 0.00 0.00 0.00 2.45
5085 5729 7.698506 AGATGCCAAAATACCATAGATGATG 57.301 36.000 0.00 0.00 35.05 3.07
5097 5741 5.573337 CATAGATGATGGCTAGATGTCGA 57.427 43.478 0.00 0.00 31.20 4.20
5098 5742 3.932545 AGATGATGGCTAGATGTCGAC 57.067 47.619 9.11 9.11 0.00 4.20
5099 5743 3.225940 AGATGATGGCTAGATGTCGACA 58.774 45.455 22.48 22.48 0.00 4.35
5100 5744 3.638627 AGATGATGGCTAGATGTCGACAA 59.361 43.478 24.13 5.15 0.00 3.18
5101 5745 3.885724 TGATGGCTAGATGTCGACAAA 57.114 42.857 24.13 10.26 0.00 2.83
5102 5746 3.785486 TGATGGCTAGATGTCGACAAAG 58.215 45.455 24.13 19.82 0.00 2.77
5103 5747 2.010145 TGGCTAGATGTCGACAAAGC 57.990 50.000 28.81 28.81 32.71 3.51
5104 5748 1.291132 GGCTAGATGTCGACAAAGCC 58.709 55.000 34.72 34.72 40.56 4.35
5105 5749 1.405526 GGCTAGATGTCGACAAAGCCA 60.406 52.381 38.51 19.91 43.72 4.75
5106 5750 2.555199 GCTAGATGTCGACAAAGCCAT 58.445 47.619 27.51 12.11 0.00 4.40
5107 5751 2.541762 GCTAGATGTCGACAAAGCCATC 59.458 50.000 27.51 18.68 35.13 3.51
5108 5752 2.768253 AGATGTCGACAAAGCCATCA 57.232 45.000 24.13 0.00 36.91 3.07
5109 5753 3.057969 AGATGTCGACAAAGCCATCAA 57.942 42.857 24.13 0.00 36.91 2.57
5110 5754 3.411446 AGATGTCGACAAAGCCATCAAA 58.589 40.909 24.13 0.00 36.91 2.69
5111 5755 3.438087 AGATGTCGACAAAGCCATCAAAG 59.562 43.478 24.13 0.00 36.91 2.77
5112 5756 2.844946 TGTCGACAAAGCCATCAAAGA 58.155 42.857 17.62 0.00 0.00 2.52
5113 5757 3.411446 TGTCGACAAAGCCATCAAAGAT 58.589 40.909 17.62 0.00 0.00 2.40
5114 5758 3.189080 TGTCGACAAAGCCATCAAAGATG 59.811 43.478 17.62 0.07 0.00 2.90
5115 5759 2.162208 TCGACAAAGCCATCAAAGATGC 59.838 45.455 1.52 0.00 0.00 3.91
5472 6116 2.073252 AGGTGATGGCTAGATGTCGA 57.927 50.000 0.00 0.00 0.00 4.20
5473 6117 1.683917 AGGTGATGGCTAGATGTCGAC 59.316 52.381 9.11 9.11 0.00 4.20
5474 6118 1.409064 GGTGATGGCTAGATGTCGACA 59.591 52.381 22.48 22.48 0.00 4.35
5475 6119 2.159099 GGTGATGGCTAGATGTCGACAA 60.159 50.000 24.13 5.15 0.00 3.18
5476 6120 3.521560 GTGATGGCTAGATGTCGACAAA 58.478 45.455 24.13 10.26 0.00 2.83
5477 6121 3.932710 GTGATGGCTAGATGTCGACAAAA 59.067 43.478 24.13 9.89 0.00 2.44
5478 6122 3.932710 TGATGGCTAGATGTCGACAAAAC 59.067 43.478 24.13 16.32 0.00 2.43
5479 6123 2.695359 TGGCTAGATGTCGACAAAACC 58.305 47.619 24.13 18.79 0.00 3.27
5480 6124 2.037902 TGGCTAGATGTCGACAAAACCA 59.962 45.455 24.13 21.01 0.00 3.67
5481 6125 3.270877 GGCTAGATGTCGACAAAACCAT 58.729 45.455 24.13 4.23 0.00 3.55
5482 6126 3.309954 GGCTAGATGTCGACAAAACCATC 59.690 47.826 24.13 14.24 35.13 3.51
5483 6127 3.000322 GCTAGATGTCGACAAAACCATCG 60.000 47.826 24.13 6.97 38.91 3.84
5484 6128 3.313012 AGATGTCGACAAAACCATCGA 57.687 42.857 24.13 0.00 44.68 3.59
5489 6133 3.804518 TCGACAAAACCATCGAACATG 57.195 42.857 0.00 0.00 43.97 3.21
5490 6134 2.095969 TCGACAAAACCATCGAACATGC 60.096 45.455 0.00 0.00 43.97 4.06
5491 6135 2.595386 GACAAAACCATCGAACATGCC 58.405 47.619 0.00 0.00 0.00 4.40
5492 6136 2.228822 GACAAAACCATCGAACATGCCT 59.771 45.455 0.00 0.00 0.00 4.75
5493 6137 3.417101 ACAAAACCATCGAACATGCCTA 58.583 40.909 0.00 0.00 0.00 3.93
5494 6138 3.823873 ACAAAACCATCGAACATGCCTAA 59.176 39.130 0.00 0.00 0.00 2.69
5495 6139 4.279671 ACAAAACCATCGAACATGCCTAAA 59.720 37.500 0.00 0.00 0.00 1.85
5496 6140 5.221342 ACAAAACCATCGAACATGCCTAAAA 60.221 36.000 0.00 0.00 0.00 1.52
5497 6141 5.461032 AAACCATCGAACATGCCTAAAAA 57.539 34.783 0.00 0.00 0.00 1.94
5498 6142 4.434713 ACCATCGAACATGCCTAAAAAC 57.565 40.909 0.00 0.00 0.00 2.43
5541 6185 3.057315 CGACAAAACCATCAAAGATGCCT 60.057 43.478 1.52 0.00 0.00 4.75
5668 6868 2.388735 AGGTGATGGCTAGATGTCGAA 58.611 47.619 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.376854 AACCATACATTCAGTGAAAGCAC 57.623 39.130 10.14 0.00 45.49 4.40
3 4 6.040278 TGAAAACCATACATTCAGTGAAAGCA 59.960 34.615 10.14 0.00 0.00 3.91
5 6 7.651808 AGTGAAAACCATACATTCAGTGAAAG 58.348 34.615 10.14 8.20 35.86 2.62
9 10 7.905604 TCTAGTGAAAACCATACATTCAGTG 57.094 36.000 5.56 0.00 37.33 3.66
19 20 9.770097 CATGAGTACATATCTAGTGAAAACCAT 57.230 33.333 0.00 0.00 35.09 3.55
20 21 8.204160 CCATGAGTACATATCTAGTGAAAACCA 58.796 37.037 0.00 0.00 35.09 3.67
22 23 9.250624 GTCCATGAGTACATATCTAGTGAAAAC 57.749 37.037 0.00 0.00 35.09 2.43
24 25 8.533569 TGTCCATGAGTACATATCTAGTGAAA 57.466 34.615 0.00 0.00 35.09 2.69
26 27 9.981460 ATATGTCCATGAGTACATATCTAGTGA 57.019 33.333 16.33 0.65 42.77 3.41
28 29 9.194972 CCATATGTCCATGAGTACATATCTAGT 57.805 37.037 18.00 4.06 43.89 2.57
29 30 9.194972 ACCATATGTCCATGAGTACATATCTAG 57.805 37.037 18.00 14.14 43.89 2.43
30 31 8.971073 CACCATATGTCCATGAGTACATATCTA 58.029 37.037 18.00 3.42 43.89 1.98
31 32 7.455953 ACACCATATGTCCATGAGTACATATCT 59.544 37.037 18.00 9.21 43.89 1.98
32 33 7.547019 CACACCATATGTCCATGAGTACATATC 59.453 40.741 18.00 0.00 43.89 1.63
33 34 7.016563 ACACACCATATGTCCATGAGTACATAT 59.983 37.037 16.33 16.33 45.65 1.78
34 35 6.326323 ACACACCATATGTCCATGAGTACATA 59.674 38.462 14.09 14.09 40.64 2.29
35 36 5.130975 ACACACCATATGTCCATGAGTACAT 59.869 40.000 1.24 11.43 40.64 2.29
36 37 4.469586 ACACACCATATGTCCATGAGTACA 59.530 41.667 1.24 0.00 40.64 2.90
37 38 4.811024 CACACACCATATGTCCATGAGTAC 59.189 45.833 1.24 0.00 40.64 2.73
38 39 4.683129 GCACACACCATATGTCCATGAGTA 60.683 45.833 1.24 0.00 40.64 2.59
39 40 3.877559 CACACACCATATGTCCATGAGT 58.122 45.455 1.24 0.00 40.64 3.41
40 41 2.615447 GCACACACCATATGTCCATGAG 59.385 50.000 1.24 0.00 40.64 2.90
41 42 2.026449 TGCACACACCATATGTCCATGA 60.026 45.455 1.24 0.00 40.64 3.07
42 43 2.356695 CTGCACACACCATATGTCCATG 59.643 50.000 1.24 0.00 40.64 3.66
43 44 2.646930 CTGCACACACCATATGTCCAT 58.353 47.619 1.24 0.00 40.64 3.41
44 45 1.339920 CCTGCACACACCATATGTCCA 60.340 52.381 1.24 0.00 40.64 4.02
45 46 1.382522 CCTGCACACACCATATGTCC 58.617 55.000 1.24 0.00 40.64 4.02
46 47 0.734889 GCCTGCACACACCATATGTC 59.265 55.000 1.24 0.00 40.64 3.06
47 48 0.680921 GGCCTGCACACACCATATGT 60.681 55.000 0.00 0.00 44.81 2.29
48 49 0.680601 TGGCCTGCACACACCATATG 60.681 55.000 3.32 0.00 0.00 1.78
49 50 0.394762 CTGGCCTGCACACACCATAT 60.395 55.000 3.32 0.00 0.00 1.78
50 51 1.002257 CTGGCCTGCACACACCATA 60.002 57.895 3.32 0.00 0.00 2.74
51 52 2.282674 CTGGCCTGCACACACCAT 60.283 61.111 3.32 0.00 0.00 3.55
52 53 4.584518 CCTGGCCTGCACACACCA 62.585 66.667 3.32 0.00 0.00 4.17
55 56 4.960866 CTGCCTGGCCTGCACACA 62.961 66.667 17.53 4.90 34.46 3.72
61 62 2.621517 GAATCTCCCTGCCTGGCCTG 62.622 65.000 17.53 9.01 0.00 4.85
62 63 2.286732 AATCTCCCTGCCTGGCCT 60.287 61.111 17.53 0.00 0.00 5.19
63 64 2.004408 ATGAATCTCCCTGCCTGGCC 62.004 60.000 17.53 0.00 0.00 5.36
64 65 0.767375 TATGAATCTCCCTGCCTGGC 59.233 55.000 12.87 12.87 0.00 4.85
65 66 2.354503 CGATATGAATCTCCCTGCCTGG 60.355 54.545 0.00 0.00 0.00 4.45
66 67 2.934364 GCGATATGAATCTCCCTGCCTG 60.934 54.545 0.00 0.00 0.00 4.85
67 68 1.277557 GCGATATGAATCTCCCTGCCT 59.722 52.381 0.00 0.00 0.00 4.75
68 69 1.731720 GCGATATGAATCTCCCTGCC 58.268 55.000 0.00 0.00 0.00 4.85
69 70 1.354040 CGCGATATGAATCTCCCTGC 58.646 55.000 0.00 0.00 0.00 4.85
70 71 1.404717 CCCGCGATATGAATCTCCCTG 60.405 57.143 8.23 0.00 0.00 4.45
71 72 0.898320 CCCGCGATATGAATCTCCCT 59.102 55.000 8.23 0.00 0.00 4.20
72 73 0.108138 CCCCGCGATATGAATCTCCC 60.108 60.000 8.23 0.00 0.00 4.30
73 74 0.108138 CCCCCGCGATATGAATCTCC 60.108 60.000 8.23 0.00 0.00 3.71
74 75 0.608640 ACCCCCGCGATATGAATCTC 59.391 55.000 8.23 0.00 0.00 2.75
75 76 1.056660 AACCCCCGCGATATGAATCT 58.943 50.000 8.23 0.00 0.00 2.40
76 77 1.892209 AAACCCCCGCGATATGAATC 58.108 50.000 8.23 0.00 0.00 2.52
77 78 2.551504 GGTAAACCCCCGCGATATGAAT 60.552 50.000 8.23 0.00 0.00 2.57
78 79 1.202675 GGTAAACCCCCGCGATATGAA 60.203 52.381 8.23 0.00 0.00 2.57
79 80 0.393820 GGTAAACCCCCGCGATATGA 59.606 55.000 8.23 0.00 0.00 2.15
80 81 0.395312 AGGTAAACCCCCGCGATATG 59.605 55.000 8.23 0.00 36.42 1.78
81 82 1.134228 AAGGTAAACCCCCGCGATAT 58.866 50.000 8.23 0.00 36.42 1.63
82 83 0.911053 AAAGGTAAACCCCCGCGATA 59.089 50.000 8.23 0.00 36.42 2.92
83 84 0.911053 TAAAGGTAAACCCCCGCGAT 59.089 50.000 8.23 0.00 36.42 4.58
84 85 0.036483 GTAAAGGTAAACCCCCGCGA 60.036 55.000 8.23 0.00 36.42 5.87
85 86 1.026182 GGTAAAGGTAAACCCCCGCG 61.026 60.000 0.00 0.00 36.42 6.46
86 87 0.329261 AGGTAAAGGTAAACCCCCGC 59.671 55.000 0.00 0.00 36.34 6.13
87 88 2.885135 AAGGTAAAGGTAAACCCCCG 57.115 50.000 0.00 0.00 36.34 5.73
88 89 4.957954 CCATTAAGGTAAAGGTAAACCCCC 59.042 45.833 0.00 0.00 36.34 5.40
89 90 5.829986 TCCATTAAGGTAAAGGTAAACCCC 58.170 41.667 0.00 0.00 36.34 4.95
90 91 6.322969 CCATCCATTAAGGTAAAGGTAAACCC 59.677 42.308 0.00 0.00 36.34 4.11
91 92 6.183360 GCCATCCATTAAGGTAAAGGTAAACC 60.183 42.308 0.00 0.00 39.02 3.27
92 93 6.183360 GGCCATCCATTAAGGTAAAGGTAAAC 60.183 42.308 0.00 0.00 39.02 2.01
93 94 5.894964 GGCCATCCATTAAGGTAAAGGTAAA 59.105 40.000 0.00 0.00 39.02 2.01
94 95 5.451354 GGCCATCCATTAAGGTAAAGGTAA 58.549 41.667 0.00 0.00 39.02 2.85
95 96 4.141111 GGGCCATCCATTAAGGTAAAGGTA 60.141 45.833 4.39 0.00 39.02 3.08
96 97 3.373767 GGGCCATCCATTAAGGTAAAGGT 60.374 47.826 4.39 0.00 39.02 3.50
97 98 3.230976 GGGCCATCCATTAAGGTAAAGG 58.769 50.000 4.39 0.00 39.02 3.11
98 99 2.884639 CGGGCCATCCATTAAGGTAAAG 59.115 50.000 4.39 0.00 39.02 1.85
99 100 2.510382 TCGGGCCATCCATTAAGGTAAA 59.490 45.455 4.39 0.00 39.02 2.01
100 101 2.128535 TCGGGCCATCCATTAAGGTAA 58.871 47.619 4.39 0.00 39.02 2.85
101 102 1.809133 TCGGGCCATCCATTAAGGTA 58.191 50.000 4.39 0.00 39.02 3.08
102 103 1.073923 GATCGGGCCATCCATTAAGGT 59.926 52.381 4.39 0.00 39.02 3.50
103 104 1.614317 GGATCGGGCCATCCATTAAGG 60.614 57.143 22.48 0.00 42.02 2.69
104 105 1.826385 GGATCGGGCCATCCATTAAG 58.174 55.000 22.48 0.00 42.02 1.85
105 106 0.036164 CGGATCGGGCCATCCATTAA 59.964 55.000 25.06 0.00 42.50 1.40
106 107 1.125093 ACGGATCGGGCCATCCATTA 61.125 55.000 25.06 0.00 42.50 1.90
107 108 2.397413 GACGGATCGGGCCATCCATT 62.397 60.000 25.06 15.94 42.50 3.16
108 109 2.849162 ACGGATCGGGCCATCCAT 60.849 61.111 25.06 14.10 42.50 3.41
109 110 3.546543 GACGGATCGGGCCATCCA 61.547 66.667 25.06 0.69 42.50 3.41
110 111 4.664677 CGACGGATCGGGCCATCC 62.665 72.222 19.31 19.31 44.99 3.51
119 120 0.935366 GAGCAACGGATCGACGGATC 60.935 60.000 0.00 0.00 46.85 3.36
120 121 1.065928 GAGCAACGGATCGACGGAT 59.934 57.895 0.00 0.00 38.39 4.18
121 122 2.488355 GAGCAACGGATCGACGGA 59.512 61.111 0.00 0.00 38.39 4.69
122 123 2.582498 GGAGCAACGGATCGACGG 60.582 66.667 0.00 0.00 38.39 4.79
123 124 2.313717 TACGGAGCAACGGATCGACG 62.314 60.000 5.09 0.00 38.39 5.12
124 125 0.591741 CTACGGAGCAACGGATCGAC 60.592 60.000 5.09 0.00 38.39 4.20
125 126 1.725665 CTACGGAGCAACGGATCGA 59.274 57.895 5.09 0.00 38.39 3.59
126 127 4.303853 CTACGGAGCAACGGATCG 57.696 61.111 5.09 0.00 38.39 3.69
136 137 3.521560 TGCAATTTACTCTGCTACGGAG 58.478 45.455 1.86 1.86 42.15 4.63
137 138 3.194755 TCTGCAATTTACTCTGCTACGGA 59.805 43.478 0.00 0.00 39.38 4.69
138 139 3.521560 TCTGCAATTTACTCTGCTACGG 58.478 45.455 0.00 0.00 39.38 4.02
139 140 5.530519 TTTCTGCAATTTACTCTGCTACG 57.469 39.130 0.00 0.00 39.38 3.51
140 141 6.086871 GGTTTTCTGCAATTTACTCTGCTAC 58.913 40.000 0.00 0.00 39.38 3.58
141 142 5.767665 TGGTTTTCTGCAATTTACTCTGCTA 59.232 36.000 0.00 0.00 39.38 3.49
142 143 4.584325 TGGTTTTCTGCAATTTACTCTGCT 59.416 37.500 0.00 0.00 39.38 4.24
143 144 4.681483 GTGGTTTTCTGCAATTTACTCTGC 59.319 41.667 0.00 0.00 39.09 4.26
144 145 5.221224 TGGTGGTTTTCTGCAATTTACTCTG 60.221 40.000 0.00 0.00 0.00 3.35
406 433 1.841919 GGGAGAATAAGGGGGAAACGA 59.158 52.381 0.00 0.00 0.00 3.85
655 693 1.608590 CCGAAACCTGAAGCAATGTGT 59.391 47.619 0.00 0.00 0.00 3.72
1144 1208 9.878737 ATCATCATCTATTTCTTCCATTCCTTT 57.121 29.630 0.00 0.00 0.00 3.11
1447 1511 2.613133 GGCTCACATTCATTCTGCTCTC 59.387 50.000 0.00 0.00 0.00 3.20
1458 1522 1.457346 CAGGTTCCAGGCTCACATTC 58.543 55.000 0.00 0.00 0.00 2.67
1516 1580 3.825328 ACAGTTGCTCCTCTGAATTGTT 58.175 40.909 0.00 0.00 35.84 2.83
1977 2077 3.647113 CAGATGATGGAATCCAGTCCTCT 59.353 47.826 8.40 10.08 44.73 3.69
2718 2818 1.821136 CAGCCATTGAGAAACCCTTCC 59.179 52.381 0.00 0.00 31.28 3.46
3357 3512 5.221362 GCCCAAGTGTGTTTAGGTATTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
3971 4131 3.662759 TTTTGAGGTGTCTTTGGGAGT 57.337 42.857 0.00 0.00 0.00 3.85
4007 4167 3.674753 CCAACCTTTTTGCAATTAGAGCG 59.325 43.478 0.00 0.00 33.85 5.03
4546 5148 4.820897 CTGATGAACTACCAGCAGTTGTA 58.179 43.478 0.00 0.00 43.38 2.41
4710 5312 0.038166 TTCCCATGGAGCACCTGAAC 59.962 55.000 15.22 0.00 37.04 3.18
5076 5720 5.012893 TGTCGACATCTAGCCATCATCTAT 58.987 41.667 15.76 0.00 0.00 1.98
5079 5723 3.650070 TGTCGACATCTAGCCATCATC 57.350 47.619 15.76 0.00 0.00 2.92
5080 5724 4.375272 CTTTGTCGACATCTAGCCATCAT 58.625 43.478 20.80 0.00 0.00 2.45
5081 5725 3.785486 CTTTGTCGACATCTAGCCATCA 58.215 45.455 20.80 0.00 0.00 3.07
5082 5726 2.541762 GCTTTGTCGACATCTAGCCATC 59.458 50.000 25.43 8.54 0.00 3.51
5083 5727 2.555199 GCTTTGTCGACATCTAGCCAT 58.445 47.619 25.43 0.00 0.00 4.40
5084 5728 1.405526 GGCTTTGTCGACATCTAGCCA 60.406 52.381 36.65 17.34 41.21 4.75
5085 5729 1.291132 GGCTTTGTCGACATCTAGCC 58.709 55.000 32.73 32.73 37.78 3.93
5086 5730 2.010145 TGGCTTTGTCGACATCTAGC 57.990 50.000 26.76 26.76 0.00 3.42
5087 5731 3.785486 TGATGGCTTTGTCGACATCTAG 58.215 45.455 20.80 17.13 40.18 2.43
5088 5732 3.885724 TGATGGCTTTGTCGACATCTA 57.114 42.857 20.80 10.04 40.18 1.98
5089 5733 2.768253 TGATGGCTTTGTCGACATCT 57.232 45.000 20.80 0.40 40.18 2.90
5090 5734 3.436704 TCTTTGATGGCTTTGTCGACATC 59.563 43.478 20.80 13.17 39.99 3.06
5091 5735 3.411446 TCTTTGATGGCTTTGTCGACAT 58.589 40.909 20.80 2.29 0.00 3.06
5092 5736 2.844946 TCTTTGATGGCTTTGTCGACA 58.155 42.857 15.76 15.76 0.00 4.35
5093 5737 3.751621 CATCTTTGATGGCTTTGTCGAC 58.248 45.455 9.11 9.11 0.00 4.20
5094 5738 2.162208 GCATCTTTGATGGCTTTGTCGA 59.838 45.455 9.24 0.00 0.00 4.20
5095 5739 2.523015 GCATCTTTGATGGCTTTGTCG 58.477 47.619 9.24 0.00 0.00 4.35
5453 6097 1.683917 GTCGACATCTAGCCATCACCT 59.316 52.381 11.55 0.00 0.00 4.00
5454 6098 1.409064 TGTCGACATCTAGCCATCACC 59.591 52.381 15.76 0.00 0.00 4.02
5455 6099 2.871182 TGTCGACATCTAGCCATCAC 57.129 50.000 15.76 0.00 0.00 3.06
5456 6100 3.885724 TTTGTCGACATCTAGCCATCA 57.114 42.857 20.80 0.00 0.00 3.07
5457 6101 3.309954 GGTTTTGTCGACATCTAGCCATC 59.690 47.826 20.80 3.03 0.00 3.51
5458 6102 3.270877 GGTTTTGTCGACATCTAGCCAT 58.729 45.455 20.80 0.00 0.00 4.40
5459 6103 2.037902 TGGTTTTGTCGACATCTAGCCA 59.962 45.455 20.80 20.27 0.00 4.75
5460 6104 2.695359 TGGTTTTGTCGACATCTAGCC 58.305 47.619 20.80 18.10 0.00 3.93
5461 6105 3.000322 CGATGGTTTTGTCGACATCTAGC 60.000 47.826 20.80 16.46 40.11 3.42
5462 6106 4.421058 TCGATGGTTTTGTCGACATCTAG 58.579 43.478 20.80 6.12 41.44 2.43
5463 6107 4.443913 TCGATGGTTTTGTCGACATCTA 57.556 40.909 20.80 11.26 41.44 1.98
5464 6108 3.313012 TCGATGGTTTTGTCGACATCT 57.687 42.857 20.80 0.40 41.44 2.90
5465 6109 3.185594 TGTTCGATGGTTTTGTCGACATC 59.814 43.478 20.80 11.69 45.43 3.06
5466 6110 3.135225 TGTTCGATGGTTTTGTCGACAT 58.865 40.909 20.80 2.29 45.43 3.06
5467 6111 2.552031 TGTTCGATGGTTTTGTCGACA 58.448 42.857 15.76 15.76 45.43 4.35
5468 6112 3.479006 CATGTTCGATGGTTTTGTCGAC 58.521 45.455 9.11 9.11 45.43 4.20
5469 6113 2.095969 GCATGTTCGATGGTTTTGTCGA 60.096 45.455 0.00 0.00 44.25 4.20
5470 6114 2.241722 GCATGTTCGATGGTTTTGTCG 58.758 47.619 0.00 0.00 39.11 4.35
5471 6115 2.228822 AGGCATGTTCGATGGTTTTGTC 59.771 45.455 0.00 0.00 0.00 3.18
5472 6116 2.238521 AGGCATGTTCGATGGTTTTGT 58.761 42.857 0.00 0.00 0.00 2.83
5473 6117 4.433186 TTAGGCATGTTCGATGGTTTTG 57.567 40.909 0.00 0.00 0.00 2.44
5474 6118 5.461032 TTTTAGGCATGTTCGATGGTTTT 57.539 34.783 0.00 0.00 0.00 2.43
5475 6119 5.227152 GTTTTTAGGCATGTTCGATGGTTT 58.773 37.500 0.00 0.00 0.00 3.27
5476 6120 4.321675 GGTTTTTAGGCATGTTCGATGGTT 60.322 41.667 0.00 0.00 0.00 3.67
5477 6121 3.192633 GGTTTTTAGGCATGTTCGATGGT 59.807 43.478 0.00 0.00 0.00 3.55
5478 6122 3.428862 GGGTTTTTAGGCATGTTCGATGG 60.429 47.826 0.00 0.00 0.00 3.51
5479 6123 3.443681 AGGGTTTTTAGGCATGTTCGATG 59.556 43.478 0.00 0.00 0.00 3.84
5480 6124 3.697166 AGGGTTTTTAGGCATGTTCGAT 58.303 40.909 0.00 0.00 0.00 3.59
5481 6125 3.149005 AGGGTTTTTAGGCATGTTCGA 57.851 42.857 0.00 0.00 0.00 3.71
5482 6126 3.377172 CCTAGGGTTTTTAGGCATGTTCG 59.623 47.826 0.00 0.00 31.92 3.95
5483 6127 4.157840 CACCTAGGGTTTTTAGGCATGTTC 59.842 45.833 14.81 0.00 41.16 3.18
5484 6128 4.086457 CACCTAGGGTTTTTAGGCATGTT 58.914 43.478 14.81 0.00 41.16 2.71
5485 6129 3.332485 TCACCTAGGGTTTTTAGGCATGT 59.668 43.478 14.81 0.00 41.16 3.21
5486 6130 3.963129 TCACCTAGGGTTTTTAGGCATG 58.037 45.455 14.81 0.00 41.16 4.06
5487 6131 4.536765 CATCACCTAGGGTTTTTAGGCAT 58.463 43.478 14.81 0.00 41.16 4.40
5488 6132 3.308832 CCATCACCTAGGGTTTTTAGGCA 60.309 47.826 14.81 0.00 41.16 4.75
5489 6133 3.288092 CCATCACCTAGGGTTTTTAGGC 58.712 50.000 14.81 0.00 41.16 3.93
5490 6134 3.053619 AGCCATCACCTAGGGTTTTTAGG 60.054 47.826 14.81 6.60 42.78 2.69
5491 6135 4.236527 AGCCATCACCTAGGGTTTTTAG 57.763 45.455 14.81 0.00 31.02 1.85
5492 6136 5.034200 TCTAGCCATCACCTAGGGTTTTTA 58.966 41.667 14.81 0.00 36.86 1.52
5493 6137 3.850173 TCTAGCCATCACCTAGGGTTTTT 59.150 43.478 14.81 0.00 36.86 1.94
5494 6138 3.460825 TCTAGCCATCACCTAGGGTTTT 58.539 45.455 14.81 0.00 36.86 2.43
5495 6139 3.130734 TCTAGCCATCACCTAGGGTTT 57.869 47.619 14.81 0.00 36.86 3.27
5496 6140 2.868964 TCTAGCCATCACCTAGGGTT 57.131 50.000 14.81 0.00 36.86 4.11
5497 6141 2.090494 ACATCTAGCCATCACCTAGGGT 60.090 50.000 14.81 0.00 39.33 4.34
5498 6142 2.564947 GACATCTAGCCATCACCTAGGG 59.435 54.545 14.81 2.03 34.43 3.53
5541 6185 5.034200 TCTAGCCATCACCTAGGGTTTTTA 58.966 41.667 14.81 0.00 36.86 1.52
5668 6868 5.975693 TTTAGGCATCTTCGATGGTTTTT 57.024 34.783 6.04 0.00 0.00 1.94
5678 6878 5.497474 TCACTAGGGTTTTTAGGCATCTTC 58.503 41.667 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.