Multiple sequence alignment - TraesCS7A01G229000

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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 TraesCS7A01G229000 chr7A 100.000 4504 0 0 1 4504 199278726 199283229 0.000000e+00 8318.0
1 TraesCS7A01G229000 chr7A 95.149 907 42 2 3476 4381 381154395 381155300 0.000000e+00 1430.0
2 TraesCS7A01G229000 chr7A 95.455 880 40 0 3502 4381 94799124 94798245 0.000000e+00 1404.0
3 TraesCS7A01G229000 chr7A 98.374 123 2 0 4382 4504 199290936 199291058 2.730000e-52 217.0
4 TraesCS7A01G229000 chr7A 95.455 132 6 0 4373 4504 187500585 187500716 1.270000e-50 211.0
5 TraesCS7A01G229000 chr2A 95.249 1747 80 3 1757 3501 615123547 615121802 0.000000e+00 2763.0
6 TraesCS7A01G229000 chr2A 95.573 881 39 0 3501 4381 467373894 467374774 0.000000e+00 1411.0
7 TraesCS7A01G229000 chr2A 95.568 880 39 0 3502 4381 457485217 457486096 0.000000e+00 1410.0
8 TraesCS7A01G229000 chr2A 98.374 123 2 0 4382 4504 408385328 408385450 2.730000e-52 217.0
9 TraesCS7A01G229000 chr2A 98.374 123 2 0 4382 4504 555789897 555789775 2.730000e-52 217.0
10 TraesCS7A01G229000 chr2A 91.803 61 2 1 2 59 156758621 156758681 1.040000e-11 82.4
11 TraesCS7A01G229000 chr1D 94.524 1753 71 8 1757 3501 70102732 70104467 0.000000e+00 2682.0
12 TraesCS7A01G229000 chr1D 90.877 1414 116 8 353 1758 399938868 399940276 0.000000e+00 1884.0
13 TraesCS7A01G229000 chr1D 95.918 49 2 0 61 109 70102689 70102737 3.730000e-11 80.5
14 TraesCS7A01G229000 chr3B 90.462 1625 142 11 138 1757 703881970 703883586 0.000000e+00 2130.0
15 TraesCS7A01G229000 chr3B 89.340 1501 148 10 264 1759 809334540 809336033 0.000000e+00 1875.0
16 TraesCS7A01G229000 chr3B 91.803 61 2 1 2 59 32462999 32463059 1.040000e-11 82.4
17 TraesCS7A01G229000 chr3B 89.831 59 3 1 4 59 32540389 32540447 6.250000e-09 73.1
18 TraesCS7A01G229000 chr3D 88.820 1610 157 14 156 1757 120619174 120617580 0.000000e+00 1954.0
19 TraesCS7A01G229000 chr3D 91.803 61 4 1 2 62 19738310 19738251 2.890000e-12 84.2
20 TraesCS7A01G229000 chr1B 89.450 1526 139 17 244 1759 649677460 649678973 0.000000e+00 1906.0
21 TraesCS7A01G229000 chr1B 88.474 1527 153 18 244 1757 32035928 32037444 0.000000e+00 1823.0
22 TraesCS7A01G229000 chr1B 88.710 62 4 2 20 81 579964612 579964554 6.250000e-09 73.1
23 TraesCS7A01G229000 chr3A 89.311 1525 144 14 244 1758 702920877 702922392 0.000000e+00 1895.0
24 TraesCS7A01G229000 chr3A 95.460 881 40 0 3501 4381 646153286 646154166 0.000000e+00 1406.0
25 TraesCS7A01G229000 chr3A 90.801 337 31 0 1975 2311 405308777 405309113 6.870000e-123 451.0
26 TraesCS7A01G229000 chr3A 90.179 224 18 3 1757 1978 405299458 405299679 5.700000e-74 289.0
27 TraesCS7A01G229000 chr3A 98.374 123 2 0 4382 4504 612173848 612173726 2.730000e-52 217.0
28 TraesCS7A01G229000 chr3A 95.918 49 2 0 61 109 405299415 405299463 3.730000e-11 80.5
29 TraesCS7A01G229000 chr2B 91.051 1408 117 7 353 1757 413458940 413460341 0.000000e+00 1893.0
30 TraesCS7A01G229000 chr2B 87.143 70 7 2 2 69 773417261 773417330 1.340000e-10 78.7
31 TraesCS7A01G229000 chr4A 88.301 1530 157 15 244 1760 646572075 646570555 0.000000e+00 1814.0
32 TraesCS7A01G229000 chr4A 98.374 123 2 0 4382 4504 354981483 354981361 2.730000e-52 217.0
33 TraesCS7A01G229000 chr4A 96.183 131 4 1 4374 4504 257229867 257229738 3.530000e-51 213.0
34 TraesCS7A01G229000 chr4A 96.183 131 4 1 4375 4504 469073116 469073246 3.530000e-51 213.0
35 TraesCS7A01G229000 chr6A 95.573 881 39 0 3501 4381 506102417 506103297 0.000000e+00 1411.0
36 TraesCS7A01G229000 chr6A 95.568 880 39 0 3502 4381 467877207 467876328 0.000000e+00 1410.0
37 TraesCS7A01G229000 chr6A 95.372 886 39 2 3498 4381 264773258 264772373 0.000000e+00 1408.0
38 TraesCS7A01G229000 chr6A 95.460 881 40 0 3501 4381 162105334 162106214 0.000000e+00 1406.0
39 TraesCS7A01G229000 chr6A 89.394 66 2 1 2 62 438580348 438580283 1.340000e-10 78.7
40 TraesCS7A01G229000 chr5A 97.619 126 3 0 4379 4504 276558982 276558857 2.730000e-52 217.0
41 TraesCS7A01G229000 chr2D 93.443 61 1 1 2 59 627954990 627955050 2.230000e-13 87.9
42 TraesCS7A01G229000 chr1A 95.556 45 2 0 21 65 13490993 13491037 6.250000e-09 73.1


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 TraesCS7A01G229000 chr7A 199278726 199283229 4503 False 8318.00 8318 100.000 1 4504 1 chr7A.!!$F2 4503
1 TraesCS7A01G229000 chr7A 381154395 381155300 905 False 1430.00 1430 95.149 3476 4381 1 chr7A.!!$F4 905
2 TraesCS7A01G229000 chr7A 94798245 94799124 879 True 1404.00 1404 95.455 3502 4381 1 chr7A.!!$R1 879
3 TraesCS7A01G229000 chr2A 615121802 615123547 1745 True 2763.00 2763 95.249 1757 3501 1 chr2A.!!$R2 1744
4 TraesCS7A01G229000 chr2A 467373894 467374774 880 False 1411.00 1411 95.573 3501 4381 1 chr2A.!!$F4 880
5 TraesCS7A01G229000 chr2A 457485217 457486096 879 False 1410.00 1410 95.568 3502 4381 1 chr2A.!!$F3 879
6 TraesCS7A01G229000 chr1D 399938868 399940276 1408 False 1884.00 1884 90.877 353 1758 1 chr1D.!!$F1 1405
7 TraesCS7A01G229000 chr1D 70102689 70104467 1778 False 1381.25 2682 95.221 61 3501 2 chr1D.!!$F2 3440
8 TraesCS7A01G229000 chr3B 703881970 703883586 1616 False 2130.00 2130 90.462 138 1757 1 chr3B.!!$F3 1619
9 TraesCS7A01G229000 chr3B 809334540 809336033 1493 False 1875.00 1875 89.340 264 1759 1 chr3B.!!$F4 1495
10 TraesCS7A01G229000 chr3D 120617580 120619174 1594 True 1954.00 1954 88.820 156 1757 1 chr3D.!!$R2 1601
11 TraesCS7A01G229000 chr1B 649677460 649678973 1513 False 1906.00 1906 89.450 244 1759 1 chr1B.!!$F2 1515
12 TraesCS7A01G229000 chr1B 32035928 32037444 1516 False 1823.00 1823 88.474 244 1757 1 chr1B.!!$F1 1513
13 TraesCS7A01G229000 chr3A 702920877 702922392 1515 False 1895.00 1895 89.311 244 1758 1 chr3A.!!$F3 1514
14 TraesCS7A01G229000 chr3A 646153286 646154166 880 False 1406.00 1406 95.460 3501 4381 1 chr3A.!!$F2 880
15 TraesCS7A01G229000 chr2B 413458940 413460341 1401 False 1893.00 1893 91.051 353 1757 1 chr2B.!!$F1 1404
16 TraesCS7A01G229000 chr4A 646570555 646572075 1520 True 1814.00 1814 88.301 244 1760 1 chr4A.!!$R3 1516
17 TraesCS7A01G229000 chr6A 506102417 506103297 880 False 1411.00 1411 95.573 3501 4381 1 chr6A.!!$F2 880
18 TraesCS7A01G229000 chr6A 467876328 467877207 879 True 1410.00 1410 95.568 3502 4381 1 chr6A.!!$R3 879
19 TraesCS7A01G229000 chr6A 264772373 264773258 885 True 1408.00 1408 95.372 3498 4381 1 chr6A.!!$R1 883
20 TraesCS7A01G229000 chr6A 162105334 162106214 880 False 1406.00 1406 95.460 3501 4381 1 chr6A.!!$F1 880

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
388 399 0.317160 TGCACTCGGACAAGTTCGAT 59.683 50.0 3.78 0.0 34.77 3.59 F
826 851 0.382873 CGGTCGGTGATAATCGGTGA 59.617 55.0 0.00 0.0 0.00 4.02 F
1939 1982 0.535335 GGAGTGGTCGTGCCTAATCA 59.465 55.0 1.06 0.0 38.35 2.57 F
2891 2941 0.544595 ACCCCGTCCTAGCAAGAAGT 60.545 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2253 0.325296 ATCCAGAACCTCGGCCACTA 60.325 55.000 2.24 0.0 0.0 2.74 R
2380 2424 1.416030 ACAAATGCCCTTTTCCACACC 59.584 47.619 0.00 0.0 0.0 4.16 R
3276 3326 0.107703 CGTTCTCCATTAGCCTGCCA 60.108 55.000 0.00 0.0 0.0 4.92 R
4475 4526 0.038166 TGGGGCCTTGAGTTGCTTAG 59.962 55.000 0.84 0.0 0.0 2.18 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
26 27 9.712305 CTCATCTATTTTGGAACGGATTAGTAT 57.288 33.333 0.00 0.00 0.00 2.12
34 35 7.852971 TTGGAACGGATTAGTATAAAGTTGG 57.147 36.000 0.00 0.00 0.00 3.77
35 36 6.350906 TGGAACGGATTAGTATAAAGTTGGG 58.649 40.000 0.00 0.00 0.00 4.12
36 37 6.070078 TGGAACGGATTAGTATAAAGTTGGGT 60.070 38.462 0.00 0.00 0.00 4.51
37 38 6.481313 GGAACGGATTAGTATAAAGTTGGGTC 59.519 42.308 0.00 0.00 0.00 4.46
38 39 6.549433 ACGGATTAGTATAAAGTTGGGTCA 57.451 37.500 0.00 0.00 0.00 4.02
39 40 7.133133 ACGGATTAGTATAAAGTTGGGTCAT 57.867 36.000 0.00 0.00 0.00 3.06
40 41 7.215085 ACGGATTAGTATAAAGTTGGGTCATC 58.785 38.462 0.00 0.00 0.00 2.92
41 42 7.070821 ACGGATTAGTATAAAGTTGGGTCATCT 59.929 37.037 0.00 0.00 0.00 2.90
42 43 8.582437 CGGATTAGTATAAAGTTGGGTCATCTA 58.418 37.037 0.00 0.00 0.00 1.98
48 49 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
49 50 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
50 51 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
51 52 7.610580 AAAGTTGGGTCATCTATTTTGGAAA 57.389 32.000 0.00 0.00 0.00 3.13
52 53 6.840780 AGTTGGGTCATCTATTTTGGAAAG 57.159 37.500 0.00 0.00 0.00 2.62
53 54 5.716703 AGTTGGGTCATCTATTTTGGAAAGG 59.283 40.000 0.00 0.00 0.00 3.11
54 55 5.528600 TGGGTCATCTATTTTGGAAAGGA 57.471 39.130 0.00 0.00 0.00 3.36
55 56 5.509498 TGGGTCATCTATTTTGGAAAGGAG 58.491 41.667 0.00 0.00 0.00 3.69
56 57 4.889995 GGGTCATCTATTTTGGAAAGGAGG 59.110 45.833 0.00 0.00 0.00 4.30
57 58 4.889995 GGTCATCTATTTTGGAAAGGAGGG 59.110 45.833 0.00 0.00 0.00 4.30
58 59 5.340027 GGTCATCTATTTTGGAAAGGAGGGA 60.340 44.000 0.00 0.00 0.00 4.20
59 60 6.187682 GTCATCTATTTTGGAAAGGAGGGAA 58.812 40.000 0.00 0.00 0.00 3.97
60 61 6.836007 GTCATCTATTTTGGAAAGGAGGGAAT 59.164 38.462 0.00 0.00 0.00 3.01
61 62 7.998964 GTCATCTATTTTGGAAAGGAGGGAATA 59.001 37.037 0.00 0.00 0.00 1.75
62 63 7.998964 TCATCTATTTTGGAAAGGAGGGAATAC 59.001 37.037 0.00 0.00 0.00 1.89
63 64 7.278724 TCTATTTTGGAAAGGAGGGAATACA 57.721 36.000 0.00 0.00 0.00 2.29
64 65 7.882755 TCTATTTTGGAAAGGAGGGAATACAT 58.117 34.615 0.00 0.00 0.00 2.29
69 70 6.652205 TGGAAAGGAGGGAATACATTACTT 57.348 37.500 0.00 0.00 0.00 2.24
103 104 1.619827 CAAGTAGACCCACCGGTGTAA 59.380 52.381 31.80 10.36 44.88 2.41
104 105 1.553706 AGTAGACCCACCGGTGTAAG 58.446 55.000 31.80 21.91 44.88 2.34
105 106 1.076024 AGTAGACCCACCGGTGTAAGA 59.924 52.381 31.80 11.27 44.88 2.10
106 107 1.895131 GTAGACCCACCGGTGTAAGAA 59.105 52.381 31.80 12.53 44.88 2.52
107 108 1.426751 AGACCCACCGGTGTAAGAAA 58.573 50.000 31.80 0.00 44.88 2.52
108 109 1.982958 AGACCCACCGGTGTAAGAAAT 59.017 47.619 31.80 9.71 44.88 2.17
109 110 2.374170 AGACCCACCGGTGTAAGAAATT 59.626 45.455 31.80 7.45 44.88 1.82
110 111 3.151554 GACCCACCGGTGTAAGAAATTT 58.848 45.455 31.80 5.18 44.88 1.82
111 112 3.568443 ACCCACCGGTGTAAGAAATTTT 58.432 40.909 31.80 1.92 42.48 1.82
112 113 3.319689 ACCCACCGGTGTAAGAAATTTTG 59.680 43.478 31.80 12.44 42.48 2.44
113 114 3.305744 CCCACCGGTGTAAGAAATTTTGG 60.306 47.826 31.80 17.45 0.00 3.28
114 115 3.570550 CCACCGGTGTAAGAAATTTTGGA 59.429 43.478 31.80 0.00 0.00 3.53
115 116 4.320935 CCACCGGTGTAAGAAATTTTGGAG 60.321 45.833 31.80 7.84 0.00 3.86
116 117 4.277423 CACCGGTGTAAGAAATTTTGGAGT 59.723 41.667 26.95 0.00 0.00 3.85
117 118 4.891168 ACCGGTGTAAGAAATTTTGGAGTT 59.109 37.500 6.12 0.00 0.00 3.01
118 119 5.219633 CCGGTGTAAGAAATTTTGGAGTTG 58.780 41.667 0.00 0.00 0.00 3.16
119 120 5.221165 CCGGTGTAAGAAATTTTGGAGTTGT 60.221 40.000 0.00 0.00 0.00 3.32
120 121 5.685511 CGGTGTAAGAAATTTTGGAGTTGTG 59.314 40.000 0.00 0.00 0.00 3.33
121 122 6.569780 GGTGTAAGAAATTTTGGAGTTGTGT 58.430 36.000 0.00 0.00 0.00 3.72
122 123 6.695713 GGTGTAAGAAATTTTGGAGTTGTGTC 59.304 38.462 0.00 0.00 0.00 3.67
123 124 6.413818 GTGTAAGAAATTTTGGAGTTGTGTCG 59.586 38.462 0.00 0.00 0.00 4.35
124 125 5.828299 AAGAAATTTTGGAGTTGTGTCGA 57.172 34.783 0.00 0.00 0.00 4.20
125 126 5.828299 AGAAATTTTGGAGTTGTGTCGAA 57.172 34.783 0.00 0.00 0.00 3.71
126 127 6.391227 AGAAATTTTGGAGTTGTGTCGAAT 57.609 33.333 0.00 0.00 0.00 3.34
127 128 7.504924 AGAAATTTTGGAGTTGTGTCGAATA 57.495 32.000 0.00 0.00 0.00 1.75
128 129 8.110860 AGAAATTTTGGAGTTGTGTCGAATAT 57.889 30.769 0.00 0.00 0.00 1.28
129 130 8.576442 AGAAATTTTGGAGTTGTGTCGAATATT 58.424 29.630 0.00 0.00 0.00 1.28
130 131 8.519492 AAATTTTGGAGTTGTGTCGAATATTG 57.481 30.769 0.00 0.00 0.00 1.90
131 132 6.627395 TTTTGGAGTTGTGTCGAATATTGT 57.373 33.333 0.00 0.00 0.00 2.71
132 133 5.605564 TTGGAGTTGTGTCGAATATTGTG 57.394 39.130 0.00 0.00 0.00 3.33
133 134 3.435327 TGGAGTTGTGTCGAATATTGTGC 59.565 43.478 0.00 0.00 0.00 4.57
134 135 3.684788 GGAGTTGTGTCGAATATTGTGCT 59.315 43.478 0.00 0.00 0.00 4.40
135 136 4.436050 GGAGTTGTGTCGAATATTGTGCTG 60.436 45.833 0.00 0.00 0.00 4.41
136 137 4.314961 AGTTGTGTCGAATATTGTGCTGA 58.685 39.130 0.00 0.00 0.00 4.26
212 213 8.955388 GCTATCAAGAAAGAAAGGAAAAGATCT 58.045 33.333 0.00 0.00 0.00 2.75
234 235 0.670162 AAGCTACGTACGTGTGGTGT 59.330 50.000 30.25 14.75 0.00 4.16
278 283 0.672711 GGTTCACACGGGAAGGCTAC 60.673 60.000 0.00 0.00 0.00 3.58
286 292 2.042230 GGAAGGCTACGGGGGAGA 60.042 66.667 0.00 0.00 0.00 3.71
313 319 4.734398 TTGGTTTTCTTTGTCAGTGCAT 57.266 36.364 0.00 0.00 0.00 3.96
331 337 4.082300 GTGCATGTTTTGTGTATGGATGGA 60.082 41.667 0.00 0.00 0.00 3.41
387 398 0.596600 GTGCACTCGGACAAGTTCGA 60.597 55.000 10.32 3.29 32.83 3.71
388 399 0.317160 TGCACTCGGACAAGTTCGAT 59.683 50.000 3.78 0.00 34.77 3.59
391 402 2.404215 CACTCGGACAAGTTCGATTGT 58.596 47.619 11.69 4.10 45.89 2.71
456 467 1.001974 CAGAAGACGGTGGTGGAATCA 59.998 52.381 0.00 0.00 0.00 2.57
461 472 4.713946 GGTGGTGGAATCAGCGAA 57.286 55.556 0.00 0.00 43.77 4.70
525 540 1.822186 GGAAACACGTGGTGCAGGT 60.822 57.895 21.57 0.00 36.98 4.00
531 547 1.832608 ACGTGGTGCAGGTCTGAGA 60.833 57.895 1.65 0.00 0.00 3.27
548 564 2.046892 AGCTTGTGCGGCTTCGAT 60.047 55.556 0.00 0.00 45.42 3.59
552 568 0.652592 CTTGTGCGGCTTCGATAAGG 59.347 55.000 0.00 0.00 35.61 2.69
666 686 2.327325 AAAGGTGGAGCTGGAGTCTA 57.673 50.000 0.00 0.00 0.00 2.59
667 687 1.859302 AAGGTGGAGCTGGAGTCTAG 58.141 55.000 0.00 0.00 0.00 2.43
693 713 5.473931 GAAGACTTCACTCAGTGCTGATTA 58.526 41.667 10.42 0.00 39.13 1.75
765 790 1.284982 GCGAGTGACATGCAGTTCGT 61.285 55.000 17.08 0.00 37.22 3.85
766 791 0.710567 CGAGTGACATGCAGTTCGTC 59.289 55.000 0.00 0.00 32.90 4.20
806 831 0.507358 GGAAGCGTGAAACTCGTCAC 59.493 55.000 0.00 0.00 43.75 3.67
826 851 0.382873 CGGTCGGTGATAATCGGTGA 59.617 55.000 0.00 0.00 0.00 4.02
840 865 3.639672 TCGGTGATACTCTGTAGTGGA 57.360 47.619 0.00 0.00 36.36 4.02
898 924 1.903877 CGGGACAGTGGAGGCTCAAT 61.904 60.000 17.69 0.00 0.00 2.57
918 944 2.420043 GGTAATAGCGGCGAGGCA 59.580 61.111 12.98 0.00 34.64 4.75
943 972 1.070758 GTATGCACGGGACATGGAGAT 59.929 52.381 0.00 0.00 0.00 2.75
955 984 0.992431 ATGGAGATGGGCCAGAGCTT 60.992 55.000 13.78 0.00 39.11 3.74
981 1010 3.519107 TGGTCATACATGTGGTGAGACAT 59.481 43.478 9.11 0.00 36.75 3.06
989 1018 1.337167 TGTGGTGAGACATCTGCGAAG 60.337 52.381 0.00 0.00 0.00 3.79
1005 1034 1.067846 CGAAGTTGACTCGGGATGACA 60.068 52.381 0.00 0.00 0.00 3.58
1221 1250 8.126700 GGAACTTAATTTTTCTCGAGTGTTGAA 58.873 33.333 13.13 0.00 0.00 2.69
1283 1314 6.098409 GGAGTCATATGGAGTCTTTGGAGTAA 59.902 42.308 2.13 0.00 44.09 2.24
1360 1395 2.558359 GACAAATTCAAGGTGGTGGAGG 59.442 50.000 0.00 0.00 0.00 4.30
1367 1402 3.459828 TCAAGGTGGTGGAGGATATTCA 58.540 45.455 0.00 0.00 0.00 2.57
1403 1438 6.627395 TTGTTGGAGTTGTGTCGAATATTT 57.373 33.333 0.00 0.00 0.00 1.40
1433 1468 3.056035 GGTAGGTTACAGTTGGACTCTGG 60.056 52.174 0.00 0.00 37.25 3.86
1470 1505 8.569641 GTTTAGATAGGATATGAAGTCGTGTCT 58.430 37.037 0.00 0.00 36.42 3.41
1530 1565 4.279145 AGAGGGTAGACACACGATGTAAT 58.721 43.478 0.00 0.00 43.56 1.89
1573 1610 0.606401 AACGTAGGGGAAGTCGACGA 60.606 55.000 10.46 0.00 36.87 4.20
1824 1867 7.771927 ATTCATTGCCCCTTAGAATTCATAG 57.228 36.000 8.44 4.15 0.00 2.23
1883 1926 1.522668 CATTTCTCTTGTCCACCGCA 58.477 50.000 0.00 0.00 0.00 5.69
1903 1946 3.367910 GCAGAGGAGAAAACAGATCGAGT 60.368 47.826 0.00 0.00 0.00 4.18
1939 1982 0.535335 GGAGTGGTCGTGCCTAATCA 59.465 55.000 1.06 0.00 38.35 2.57
2060 2103 2.672996 GCCAAGCTGGAAAGGCGA 60.673 61.111 6.40 0.00 40.96 5.54
2175 2218 1.028330 CGCATGTGGCTGGATGAGTT 61.028 55.000 0.00 0.00 41.67 3.01
2176 2219 1.180029 GCATGTGGCTGGATGAGTTT 58.820 50.000 0.00 0.00 40.25 2.66
2205 2248 4.099881 TCAAACTTTCAATGCTTGAGGCTT 59.900 37.500 0.00 0.00 41.38 4.35
2210 2253 0.601558 CAATGCTTGAGGCTTGCTGT 59.398 50.000 8.94 0.00 42.39 4.40
2248 2291 3.555324 TTGGTGTCTGCTGGCCGA 61.555 61.111 0.00 0.00 0.00 5.54
2296 2339 2.232941 TGTTGTCGGACTCCTACCATTC 59.767 50.000 9.88 0.00 0.00 2.67
2380 2424 6.831769 AGCAATACTCACATTACAACTTTCG 58.168 36.000 0.00 0.00 0.00 3.46
2444 2488 5.003160 TGAACATATGGATCCGCCTAATTG 58.997 41.667 7.39 0.54 37.63 2.32
2452 2496 2.818751 TCCGCCTAATTGGGTTGATT 57.181 45.000 9.87 0.00 36.00 2.57
2570 2620 3.925379 TGAAGTGAGACATGCATAACGT 58.075 40.909 0.00 0.00 0.00 3.99
2648 2698 5.526846 CCCATGTTCTCTTATCTTGCTTCTC 59.473 44.000 0.00 0.00 0.00 2.87
2650 2700 5.392767 TGTTCTCTTATCTTGCTTCTCGT 57.607 39.130 0.00 0.00 0.00 4.18
2746 2796 5.334569 GCAGTACACCAATCGTTTTGTATGT 60.335 40.000 0.00 10.44 0.00 2.29
2891 2941 0.544595 ACCCCGTCCTAGCAAGAAGT 60.545 55.000 0.00 0.00 0.00 3.01
2939 2989 6.183360 TGGTTCATATGTCACATACAATTGGC 60.183 38.462 10.83 0.00 42.70 4.52
3157 3207 6.078456 TCAATTAGTGGTGAGGGATTTCAT 57.922 37.500 0.00 0.00 0.00 2.57
3172 3222 0.994247 TTCATGGAGCATGGACCACT 59.006 50.000 0.00 0.00 41.66 4.00
3365 3415 0.325860 AGAGGTATGGGGTAACGGCA 60.326 55.000 0.00 0.00 37.60 5.69
3366 3416 0.179065 GAGGTATGGGGTAACGGCAC 60.179 60.000 0.00 0.00 37.60 5.01
3388 3438 6.625300 GCACCATATTCGTATAAGGAGATCGT 60.625 42.308 9.90 0.00 31.12 3.73
3402 3452 3.751698 GGAGATCGTGGGGCAAATAATAC 59.248 47.826 0.00 0.00 0.00 1.89
3404 3454 4.787551 AGATCGTGGGGCAAATAATACAA 58.212 39.130 0.00 0.00 0.00 2.41
3420 3470 2.267174 ACAACAGCAAGATGAGCAGT 57.733 45.000 0.00 0.00 32.84 4.40
3467 3517 1.884579 CTCCTCATTGTTGTTGCTGCT 59.115 47.619 0.00 0.00 0.00 4.24
3558 3608 1.111715 ACTATACCTTCGGCCGGACC 61.112 60.000 27.83 4.99 0.00 4.46
3574 3624 1.763545 GGACCCCTGGACTATGAAGAC 59.236 57.143 0.00 0.00 0.00 3.01
3663 3713 6.651643 GCGATACGGATATGTAGATCTCCTAT 59.348 42.308 0.00 0.00 0.00 2.57
3680 3730 9.290988 GATCTCCTATCATTGTAACTGACTCTA 57.709 37.037 0.00 0.00 0.00 2.43
3847 3898 7.722363 TCAATATTAATCAAGCAGGACGTAGA 58.278 34.615 0.00 0.00 0.00 2.59
3859 3910 2.751806 AGGACGTAGAGTTTTACCTCCG 59.248 50.000 0.00 0.00 35.30 4.63
3969 4020 2.851263 TATCCGCCAGTTTTGACACT 57.149 45.000 0.00 0.00 0.00 3.55
3988 4039 4.099881 ACACTGACATTGGTGCTTTCATTT 59.900 37.500 0.00 0.00 36.99 2.32
4018 4069 2.364324 TCTGTGTCGTCACTTTTAGGCT 59.636 45.455 13.77 0.00 44.14 4.58
4076 4127 2.445200 GGGTGAGACTTTTCTCCCCGA 61.445 57.143 10.61 0.00 45.14 5.14
4182 4233 5.945784 CCATCAGGTCAGATTTGGAAGTTTA 59.054 40.000 0.00 0.00 0.00 2.01
4193 4244 6.769341 AGATTTGGAAGTTTAAACTACACGGT 59.231 34.615 20.83 4.49 38.57 4.83
4387 4438 3.697747 CCGCCTCGGGGTGTAACA 61.698 66.667 15.14 0.00 44.15 2.41
4388 4439 2.582436 CGCCTCGGGGTGTAACAT 59.418 61.111 6.75 0.00 39.98 2.71
4389 4440 1.520787 CGCCTCGGGGTGTAACATC 60.521 63.158 6.75 0.00 39.98 3.06
4390 4441 1.153229 GCCTCGGGGTGTAACATCC 60.153 63.158 1.62 0.00 39.98 3.51
4400 4451 5.476091 GGGTGTAACATCCCAAATTTTCA 57.524 39.130 0.00 0.00 42.95 2.69
4401 4452 5.859495 GGGTGTAACATCCCAAATTTTCAA 58.141 37.500 0.00 0.00 42.95 2.69
4402 4453 6.472016 GGGTGTAACATCCCAAATTTTCAAT 58.528 36.000 0.00 0.00 42.95 2.57
4403 4454 6.939730 GGGTGTAACATCCCAAATTTTCAATT 59.060 34.615 0.00 0.00 42.95 2.32
4404 4455 7.446931 GGGTGTAACATCCCAAATTTTCAATTT 59.553 33.333 0.00 0.00 42.95 1.82
4405 4456 8.288913 GGTGTAACATCCCAAATTTTCAATTTG 58.711 33.333 12.97 12.97 39.98 2.32
4406 4457 8.288913 GTGTAACATCCCAAATTTTCAATTTGG 58.711 33.333 25.00 25.00 45.86 3.28
4475 4526 9.574458 GCTTTTAGTTTTGATCCTAGAAAATCC 57.426 33.333 0.00 0.00 0.00 3.01
4480 4531 8.512966 AGTTTTGATCCTAGAAAATCCTAAGC 57.487 34.615 0.00 0.00 0.00 3.09
4481 4532 8.109634 AGTTTTGATCCTAGAAAATCCTAAGCA 58.890 33.333 0.00 0.00 0.00 3.91
4482 4533 8.739972 GTTTTGATCCTAGAAAATCCTAAGCAA 58.260 33.333 0.00 0.00 0.00 3.91
4483 4534 7.865706 TTGATCCTAGAAAATCCTAAGCAAC 57.134 36.000 0.00 0.00 0.00 4.17
4484 4535 7.200434 TGATCCTAGAAAATCCTAAGCAACT 57.800 36.000 0.00 0.00 0.00 3.16
4485 4536 7.275920 TGATCCTAGAAAATCCTAAGCAACTC 58.724 38.462 0.00 0.00 0.00 3.01
4486 4537 6.620877 TCCTAGAAAATCCTAAGCAACTCA 57.379 37.500 0.00 0.00 0.00 3.41
4487 4538 7.016153 TCCTAGAAAATCCTAAGCAACTCAA 57.984 36.000 0.00 0.00 0.00 3.02
4488 4539 7.106239 TCCTAGAAAATCCTAAGCAACTCAAG 58.894 38.462 0.00 0.00 0.00 3.02
4489 4540 6.317391 CCTAGAAAATCCTAAGCAACTCAAGG 59.683 42.308 0.00 0.00 0.00 3.61
4490 4541 4.460731 AGAAAATCCTAAGCAACTCAAGGC 59.539 41.667 0.00 0.00 0.00 4.35
4491 4542 2.426842 ATCCTAAGCAACTCAAGGCC 57.573 50.000 0.00 0.00 0.00 5.19
4492 4543 0.328258 TCCTAAGCAACTCAAGGCCC 59.672 55.000 0.00 0.00 0.00 5.80
4493 4544 0.681243 CCTAAGCAACTCAAGGCCCC 60.681 60.000 0.00 0.00 0.00 5.80
4494 4545 0.038166 CTAAGCAACTCAAGGCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
4495 4546 0.251165 TAAGCAACTCAAGGCCCCAC 60.251 55.000 0.00 0.00 0.00 4.61
4496 4547 3.365265 GCAACTCAAGGCCCCACG 61.365 66.667 0.00 0.00 0.00 4.94
4497 4548 2.672996 CAACTCAAGGCCCCACGG 60.673 66.667 0.00 0.00 0.00 4.94
4498 4549 2.852075 AACTCAAGGCCCCACGGA 60.852 61.111 0.00 0.00 0.00 4.69
4499 4550 2.895424 AACTCAAGGCCCCACGGAG 61.895 63.158 0.00 1.85 0.00 4.63
4500 4551 3.003173 CTCAAGGCCCCACGGAGA 61.003 66.667 0.00 0.00 0.00 3.71
4501 4552 3.003173 TCAAGGCCCCACGGAGAG 61.003 66.667 0.00 0.00 0.00 3.20
4502 4553 3.003173 CAAGGCCCCACGGAGAGA 61.003 66.667 0.00 0.00 0.00 3.10
4503 4554 2.685380 AAGGCCCCACGGAGAGAG 60.685 66.667 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.712305 ATACTAATCCGTTCCAAAATAGATGAG 57.288 33.333 0.00 0.00 0.00 2.90
8 9 8.732531 CCAACTTTATACTAATCCGTTCCAAAA 58.267 33.333 0.00 0.00 0.00 2.44
9 10 7.337436 CCCAACTTTATACTAATCCGTTCCAAA 59.663 37.037 0.00 0.00 0.00 3.28
10 11 6.824704 CCCAACTTTATACTAATCCGTTCCAA 59.175 38.462 0.00 0.00 0.00 3.53
11 12 6.070078 ACCCAACTTTATACTAATCCGTTCCA 60.070 38.462 0.00 0.00 0.00 3.53
12 13 6.351711 ACCCAACTTTATACTAATCCGTTCC 58.648 40.000 0.00 0.00 0.00 3.62
13 14 7.043565 TGACCCAACTTTATACTAATCCGTTC 58.956 38.462 0.00 0.00 0.00 3.95
14 15 6.949715 TGACCCAACTTTATACTAATCCGTT 58.050 36.000 0.00 0.00 0.00 4.44
15 16 6.549433 TGACCCAACTTTATACTAATCCGT 57.451 37.500 0.00 0.00 0.00 4.69
16 17 7.442656 AGATGACCCAACTTTATACTAATCCG 58.557 38.462 0.00 0.00 0.00 4.18
22 23 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
23 24 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
24 25 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
25 26 8.893563 TTCCAAAATAGATGACCCAACTTTAT 57.106 30.769 0.00 0.00 0.00 1.40
26 27 8.713708 TTTCCAAAATAGATGACCCAACTTTA 57.286 30.769 0.00 0.00 0.00 1.85
27 28 7.256296 CCTTTCCAAAATAGATGACCCAACTTT 60.256 37.037 0.00 0.00 0.00 2.66
28 29 6.211384 CCTTTCCAAAATAGATGACCCAACTT 59.789 38.462 0.00 0.00 0.00 2.66
29 30 5.716703 CCTTTCCAAAATAGATGACCCAACT 59.283 40.000 0.00 0.00 0.00 3.16
30 31 5.714806 TCCTTTCCAAAATAGATGACCCAAC 59.285 40.000 0.00 0.00 0.00 3.77
31 32 5.898120 TCCTTTCCAAAATAGATGACCCAA 58.102 37.500 0.00 0.00 0.00 4.12
32 33 5.509498 CTCCTTTCCAAAATAGATGACCCA 58.491 41.667 0.00 0.00 0.00 4.51
33 34 4.889995 CCTCCTTTCCAAAATAGATGACCC 59.110 45.833 0.00 0.00 0.00 4.46
34 35 4.889995 CCCTCCTTTCCAAAATAGATGACC 59.110 45.833 0.00 0.00 0.00 4.02
35 36 5.755849 TCCCTCCTTTCCAAAATAGATGAC 58.244 41.667 0.00 0.00 0.00 3.06
36 37 6.401537 TTCCCTCCTTTCCAAAATAGATGA 57.598 37.500 0.00 0.00 0.00 2.92
37 38 7.779798 TGTATTCCCTCCTTTCCAAAATAGATG 59.220 37.037 0.00 0.00 0.00 2.90
38 39 7.882755 TGTATTCCCTCCTTTCCAAAATAGAT 58.117 34.615 0.00 0.00 0.00 1.98
39 40 7.278724 TGTATTCCCTCCTTTCCAAAATAGA 57.721 36.000 0.00 0.00 0.00 1.98
40 41 8.539117 AATGTATTCCCTCCTTTCCAAAATAG 57.461 34.615 0.00 0.00 0.00 1.73
41 42 9.416284 GTAATGTATTCCCTCCTTTCCAAAATA 57.584 33.333 0.00 0.00 0.00 1.40
42 43 8.122481 AGTAATGTATTCCCTCCTTTCCAAAAT 58.878 33.333 0.00 0.00 0.00 1.82
43 44 7.475299 AGTAATGTATTCCCTCCTTTCCAAAA 58.525 34.615 0.00 0.00 0.00 2.44
44 45 7.039722 AGTAATGTATTCCCTCCTTTCCAAA 57.960 36.000 0.00 0.00 0.00 3.28
45 46 6.652205 AGTAATGTATTCCCTCCTTTCCAA 57.348 37.500 0.00 0.00 0.00 3.53
46 47 6.353602 GGAAGTAATGTATTCCCTCCTTTCCA 60.354 42.308 0.00 0.00 39.29 3.53
47 48 6.062749 GGAAGTAATGTATTCCCTCCTTTCC 58.937 44.000 0.00 0.00 39.29 3.13
48 49 6.659824 TGGAAGTAATGTATTCCCTCCTTTC 58.340 40.000 1.74 0.00 43.68 2.62
49 50 6.652205 TGGAAGTAATGTATTCCCTCCTTT 57.348 37.500 1.74 0.00 43.68 3.11
50 51 6.652205 TTGGAAGTAATGTATTCCCTCCTT 57.348 37.500 1.74 0.00 43.68 3.36
51 52 6.217693 ACTTTGGAAGTAATGTATTCCCTCCT 59.782 38.462 1.74 0.00 43.68 3.69
52 53 6.424032 ACTTTGGAAGTAATGTATTCCCTCC 58.576 40.000 1.74 0.00 43.68 4.30
53 54 7.281100 CAGACTTTGGAAGTAATGTATTCCCTC 59.719 40.741 1.74 0.00 43.68 4.30
54 55 7.112779 CAGACTTTGGAAGTAATGTATTCCCT 58.887 38.462 1.74 0.00 43.68 4.20
55 56 6.884836 ACAGACTTTGGAAGTAATGTATTCCC 59.115 38.462 8.54 0.00 43.68 3.97
56 57 7.923414 ACAGACTTTGGAAGTAATGTATTCC 57.077 36.000 8.54 0.00 43.03 3.01
57 58 8.604890 GCTACAGACTTTGGAAGTAATGTATTC 58.395 37.037 13.96 8.81 43.03 1.75
58 59 8.100791 TGCTACAGACTTTGGAAGTAATGTATT 58.899 33.333 13.96 0.00 43.03 1.89
59 60 7.620880 TGCTACAGACTTTGGAAGTAATGTAT 58.379 34.615 13.96 0.00 43.03 2.29
60 61 6.999950 TGCTACAGACTTTGGAAGTAATGTA 58.000 36.000 13.35 13.35 43.03 2.29
61 62 5.865085 TGCTACAGACTTTGGAAGTAATGT 58.135 37.500 12.75 12.75 43.03 2.71
62 63 6.428159 ACTTGCTACAGACTTTGGAAGTAATG 59.572 38.462 0.00 0.00 43.03 1.90
63 64 6.534634 ACTTGCTACAGACTTTGGAAGTAAT 58.465 36.000 0.00 0.00 43.03 1.89
64 65 5.925509 ACTTGCTACAGACTTTGGAAGTAA 58.074 37.500 0.00 0.00 43.03 2.24
69 70 4.021368 GGTCTACTTGCTACAGACTTTGGA 60.021 45.833 0.00 0.00 38.95 3.53
103 104 5.828299 TTCGACACAACTCCAAAATTTCT 57.172 34.783 0.00 0.00 0.00 2.52
104 105 8.638565 CAATATTCGACACAACTCCAAAATTTC 58.361 33.333 0.00 0.00 0.00 2.17
105 106 8.141268 ACAATATTCGACACAACTCCAAAATTT 58.859 29.630 0.00 0.00 0.00 1.82
106 107 7.594758 CACAATATTCGACACAACTCCAAAATT 59.405 33.333 0.00 0.00 0.00 1.82
107 108 7.083858 CACAATATTCGACACAACTCCAAAAT 58.916 34.615 0.00 0.00 0.00 1.82
108 109 6.434596 CACAATATTCGACACAACTCCAAAA 58.565 36.000 0.00 0.00 0.00 2.44
109 110 5.561919 GCACAATATTCGACACAACTCCAAA 60.562 40.000 0.00 0.00 0.00 3.28
110 111 4.083537 GCACAATATTCGACACAACTCCAA 60.084 41.667 0.00 0.00 0.00 3.53
111 112 3.435327 GCACAATATTCGACACAACTCCA 59.565 43.478 0.00 0.00 0.00 3.86
112 113 3.684788 AGCACAATATTCGACACAACTCC 59.315 43.478 0.00 0.00 0.00 3.85
113 114 4.388773 TCAGCACAATATTCGACACAACTC 59.611 41.667 0.00 0.00 0.00 3.01
114 115 4.314961 TCAGCACAATATTCGACACAACT 58.685 39.130 0.00 0.00 0.00 3.16
115 116 4.661993 TCAGCACAATATTCGACACAAC 57.338 40.909 0.00 0.00 0.00 3.32
116 117 5.878332 AATCAGCACAATATTCGACACAA 57.122 34.783 0.00 0.00 0.00 3.33
117 118 6.976636 TTAATCAGCACAATATTCGACACA 57.023 33.333 0.00 0.00 0.00 3.72
118 119 9.929722 TTATTTAATCAGCACAATATTCGACAC 57.070 29.630 0.00 0.00 0.00 3.67
129 130 9.638239 GTCATTTCCTTTTATTTAATCAGCACA 57.362 29.630 0.00 0.00 0.00 4.57
130 131 9.638239 TGTCATTTCCTTTTATTTAATCAGCAC 57.362 29.630 0.00 0.00 0.00 4.40
131 132 9.638239 GTGTCATTTCCTTTTATTTAATCAGCA 57.362 29.630 0.00 0.00 0.00 4.41
132 133 9.638239 TGTGTCATTTCCTTTTATTTAATCAGC 57.362 29.630 0.00 0.00 0.00 4.26
152 153 1.688735 CCAGACTCTGTCCTTGTGTCA 59.311 52.381 5.32 0.00 32.18 3.58
212 213 2.160219 CACCACACGTACGTAGCTTCTA 59.840 50.000 22.34 0.00 0.00 2.10
234 235 8.786898 CCAAAAGAGATCAACAAACTCTTCATA 58.213 33.333 0.00 0.00 46.03 2.15
278 283 0.611896 AACCAAAGCAATCTCCCCCG 60.612 55.000 0.00 0.00 0.00 5.73
286 292 5.581874 CACTGACAAAGAAAACCAAAGCAAT 59.418 36.000 0.00 0.00 0.00 3.56
313 319 5.600484 ACCTTTTCCATCCATACACAAAACA 59.400 36.000 0.00 0.00 0.00 2.83
331 337 1.890510 GCCGTCACCGTGACCTTTT 60.891 57.895 23.01 0.00 44.20 2.27
373 383 2.404215 ACACAATCGAACTTGTCCGAG 58.596 47.619 1.41 0.00 37.25 4.63
456 467 1.000827 CGCTCCTATGTCATCTTCGCT 60.001 52.381 0.00 0.00 0.00 4.93
461 472 2.288702 GCATCACGCTCCTATGTCATCT 60.289 50.000 0.00 0.00 37.77 2.90
525 540 2.047844 GCCGCACAAGCTCTCAGA 60.048 61.111 0.00 0.00 39.10 3.27
531 547 0.391130 TTATCGAAGCCGCACAAGCT 60.391 50.000 0.00 0.00 44.19 3.74
548 564 3.936203 CCCCGCGCCATAGCCTTA 61.936 66.667 0.00 0.00 34.57 2.69
552 568 4.849310 TCAACCCCGCGCCATAGC 62.849 66.667 0.00 0.00 0.00 2.97
599 616 0.602106 CATCCTTGCGCCTCATCGAT 60.602 55.000 4.18 0.00 0.00 3.59
647 664 2.183679 CTAGACTCCAGCTCCACCTTT 58.816 52.381 0.00 0.00 0.00 3.11
666 686 1.000283 CACTGAGTGAAGTCTTCCGCT 60.000 52.381 6.79 8.10 35.23 5.52
667 687 1.423395 CACTGAGTGAAGTCTTCCGC 58.577 55.000 6.79 3.47 35.23 5.54
806 831 0.596600 CACCGATTATCACCGACCGG 60.597 60.000 6.94 6.94 42.30 5.28
818 843 4.533815 TCCACTACAGAGTATCACCGATT 58.466 43.478 0.00 0.00 37.82 3.34
826 851 4.707448 CACTCAACCTCCACTACAGAGTAT 59.293 45.833 0.00 0.00 33.90 2.12
840 865 0.182775 GAACCCACACCACTCAACCT 59.817 55.000 0.00 0.00 0.00 3.50
898 924 2.027024 CTCGCCGCTATTACCGCA 59.973 61.111 0.00 0.00 0.00 5.69
943 972 2.115910 CACCAAAGCTCTGGCCCA 59.884 61.111 5.81 0.00 40.45 5.36
955 984 2.373502 TCACCACATGTATGACCACCAA 59.626 45.455 0.00 0.00 0.00 3.67
981 1010 1.176619 TCCCGAGTCAACTTCGCAGA 61.177 55.000 0.00 0.00 0.00 4.26
989 1018 2.163818 TGTTGTCATCCCGAGTCAAC 57.836 50.000 0.00 0.00 38.82 3.18
1005 1034 4.961438 AGGAATTTCACCATTGCTTGTT 57.039 36.364 0.00 0.00 31.16 2.83
1208 1237 2.364002 TGACCACATTCAACACTCGAGA 59.636 45.455 21.68 0.00 0.00 4.04
1221 1250 2.716424 TCCCTCCTTTTCTTGACCACAT 59.284 45.455 0.00 0.00 0.00 3.21
1283 1314 1.644509 TATCCCATGAGCACCGCTAT 58.355 50.000 0.00 0.00 39.88 2.97
1360 1395 5.010282 ACAAACTCCACCTTGGTGAATATC 58.990 41.667 20.27 0.00 39.03 1.63
1367 1402 1.286553 TCCAACAAACTCCACCTTGGT 59.713 47.619 0.00 0.00 39.03 3.67
1403 1438 5.366186 TCCAACTGTAACCTACCTTGTACAA 59.634 40.000 8.28 8.28 0.00 2.41
1508 1543 2.217510 ACATCGTGTGTCTACCCTCT 57.782 50.000 0.00 0.00 35.77 3.69
1530 1565 4.314961 CGGTGCTATTATGTTGGCATAGA 58.685 43.478 0.00 0.00 38.64 1.98
1567 1604 3.676605 ACCGGCACATGTCGTCGA 61.677 61.111 19.25 0.00 42.34 4.20
1573 1610 2.032528 CTGGACACCGGCACATGT 59.967 61.111 0.00 0.00 0.00 3.21
1807 1850 3.416156 CCTGCTATGAATTCTAAGGGGC 58.584 50.000 7.05 3.73 0.00 5.80
1822 1865 6.550108 CACTCTAGGATAAGTTTACCCTGCTA 59.450 42.308 0.00 0.00 0.00 3.49
1824 1867 5.128991 ACACTCTAGGATAAGTTTACCCTGC 59.871 44.000 0.00 0.00 0.00 4.85
1883 1926 4.340617 AGACTCGATCTGTTTTCTCCTCT 58.659 43.478 0.00 0.00 35.81 3.69
1927 1970 3.733236 CCGACTTGATTAGGCACGA 57.267 52.632 0.00 0.00 0.00 4.35
2046 2089 1.303643 CCCTTCGCCTTTCCAGCTT 60.304 57.895 0.00 0.00 0.00 3.74
2086 2129 1.855295 TCACCTATCTGTACGGGCAA 58.145 50.000 0.85 0.00 0.00 4.52
2091 2134 6.574350 AGGAAGAAAATCACCTATCTGTACG 58.426 40.000 0.00 0.00 0.00 3.67
2175 2218 5.534207 AGCATTGAAAGTTTGATCCACAA 57.466 34.783 0.00 0.00 36.65 3.33
2176 2219 5.534207 AAGCATTGAAAGTTTGATCCACA 57.466 34.783 0.00 0.00 0.00 4.17
2205 2248 2.167398 GAACCTCGGCCACTACAGCA 62.167 60.000 2.24 0.00 0.00 4.41
2210 2253 0.325296 ATCCAGAACCTCGGCCACTA 60.325 55.000 2.24 0.00 0.00 2.74
2248 2291 4.510167 AATGAGGGTAGCAACTAAGCAT 57.490 40.909 0.00 0.00 36.85 3.79
2296 2339 5.671493 AGATGGGAATTTGGAGTACTTACG 58.329 41.667 0.00 0.00 0.00 3.18
2359 2403 6.708949 ACACCGAAAGTTGTAATGTGAGTATT 59.291 34.615 0.00 0.00 0.00 1.89
2380 2424 1.416030 ACAAATGCCCTTTTCCACACC 59.584 47.619 0.00 0.00 0.00 4.16
2421 2465 4.908601 ATTAGGCGGATCCATATGTTCA 57.091 40.909 13.41 0.00 37.29 3.18
2570 2620 3.483808 TCACCAATATAGCATTGCCGA 57.516 42.857 4.70 0.00 0.00 5.54
2648 2698 9.900710 AACTCTAGCATTAGTCAATAAGATACG 57.099 33.333 0.00 0.00 0.00 3.06
2696 2746 5.590530 ACAAAATTTGTAGAAGTGGCACA 57.409 34.783 21.41 0.00 43.27 4.57
3008 3058 4.757149 AGGCTTCAGATGTTGTACTTGAAC 59.243 41.667 0.00 0.00 0.00 3.18
3157 3207 1.426251 AACCAGTGGTCCATGCTCCA 61.426 55.000 17.06 3.47 33.12 3.86
3172 3222 2.593026 GTCCCAGAAATTCACCAACCA 58.407 47.619 0.00 0.00 0.00 3.67
3276 3326 0.107703 CGTTCTCCATTAGCCTGCCA 60.108 55.000 0.00 0.00 0.00 4.92
3320 3370 3.081409 ATAGCCGCGGTTCCACCT 61.081 61.111 28.70 16.41 35.66 4.00
3365 3415 6.127703 CCACGATCTCCTTATACGAATATGGT 60.128 42.308 0.00 0.00 35.39 3.55
3366 3416 6.266323 CCACGATCTCCTTATACGAATATGG 58.734 44.000 0.00 0.00 35.25 2.74
3388 3438 3.435275 TGCTGTTGTATTATTTGCCCCA 58.565 40.909 0.00 0.00 0.00 4.96
3402 3452 1.401148 GCACTGCTCATCTTGCTGTTG 60.401 52.381 0.00 0.00 39.86 3.33
3404 3454 0.959372 GGCACTGCTCATCTTGCTGT 60.959 55.000 0.00 0.00 41.94 4.40
3467 3517 6.543465 CAGCACTTACATTTGATAGGATTCCA 59.457 38.462 5.29 0.00 0.00 3.53
3558 3608 3.515502 TCTTGTGTCTTCATAGTCCAGGG 59.484 47.826 0.00 0.00 0.00 4.45
3663 3713 7.399191 AGGGTTACATAGAGTCAGTTACAATGA 59.601 37.037 0.00 0.00 0.00 2.57
3680 3730 1.758123 CGGAGAGGGCTAGGGTTACAT 60.758 57.143 0.00 0.00 0.00 2.29
3847 3898 3.679824 CCTCTTGACGGAGGTAAAACT 57.320 47.619 2.65 0.00 45.65 2.66
3859 3910 2.046217 GGTTCGGGCCCTCTTGAC 60.046 66.667 22.43 10.55 0.00 3.18
3950 4001 2.037902 TCAGTGTCAAAACTGGCGGATA 59.962 45.455 0.00 0.00 46.27 2.59
3969 4020 5.769662 ACTCTAAATGAAAGCACCAATGTCA 59.230 36.000 0.00 0.00 0.00 3.58
4076 4127 2.350498 CCGCCGAATACGAAGATTTGTT 59.650 45.455 0.00 0.00 42.66 2.83
4182 4233 1.401931 CGGATGTCGACCGTGTAGTTT 60.402 52.381 14.12 0.00 44.57 2.66
4193 4244 2.437895 AGTCTCCGCGGATGTCGA 60.438 61.111 31.19 19.91 42.43 4.20
4449 4500 9.574458 GGATTTTCTAGGATCAAAACTAAAAGC 57.426 33.333 0.00 0.00 0.00 3.51
4454 4505 9.614792 GCTTAGGATTTTCTAGGATCAAAACTA 57.385 33.333 0.00 0.00 0.00 2.24
4455 4506 8.109634 TGCTTAGGATTTTCTAGGATCAAAACT 58.890 33.333 0.00 0.00 0.00 2.66
4456 4507 8.281212 TGCTTAGGATTTTCTAGGATCAAAAC 57.719 34.615 0.00 0.00 0.00 2.43
4457 4508 8.739972 GTTGCTTAGGATTTTCTAGGATCAAAA 58.260 33.333 0.00 0.00 0.00 2.44
4458 4509 8.109634 AGTTGCTTAGGATTTTCTAGGATCAAA 58.890 33.333 0.00 0.00 0.00 2.69
4459 4510 7.633789 AGTTGCTTAGGATTTTCTAGGATCAA 58.366 34.615 0.00 0.00 0.00 2.57
4460 4511 7.092891 TGAGTTGCTTAGGATTTTCTAGGATCA 60.093 37.037 0.00 0.00 0.00 2.92
4461 4512 7.275920 TGAGTTGCTTAGGATTTTCTAGGATC 58.724 38.462 0.00 0.00 0.00 3.36
4462 4513 7.200434 TGAGTTGCTTAGGATTTTCTAGGAT 57.800 36.000 0.00 0.00 0.00 3.24
4463 4514 6.620877 TGAGTTGCTTAGGATTTTCTAGGA 57.379 37.500 0.00 0.00 0.00 2.94
4464 4515 6.317391 CCTTGAGTTGCTTAGGATTTTCTAGG 59.683 42.308 0.00 0.00 0.00 3.02
4465 4516 6.183360 GCCTTGAGTTGCTTAGGATTTTCTAG 60.183 42.308 0.00 0.00 0.00 2.43
4466 4517 5.648092 GCCTTGAGTTGCTTAGGATTTTCTA 59.352 40.000 0.00 0.00 0.00 2.10
4467 4518 4.460731 GCCTTGAGTTGCTTAGGATTTTCT 59.539 41.667 0.00 0.00 0.00 2.52
4468 4519 4.380973 GGCCTTGAGTTGCTTAGGATTTTC 60.381 45.833 0.00 0.00 0.00 2.29
4469 4520 3.511540 GGCCTTGAGTTGCTTAGGATTTT 59.488 43.478 0.00 0.00 0.00 1.82
4470 4521 3.092301 GGCCTTGAGTTGCTTAGGATTT 58.908 45.455 0.00 0.00 0.00 2.17
4471 4522 2.621668 GGGCCTTGAGTTGCTTAGGATT 60.622 50.000 0.84 0.00 0.00 3.01
4472 4523 1.064389 GGGCCTTGAGTTGCTTAGGAT 60.064 52.381 0.84 0.00 0.00 3.24
4473 4524 0.328258 GGGCCTTGAGTTGCTTAGGA 59.672 55.000 0.84 0.00 0.00 2.94
4474 4525 0.681243 GGGGCCTTGAGTTGCTTAGG 60.681 60.000 0.84 0.00 0.00 2.69
4475 4526 0.038166 TGGGGCCTTGAGTTGCTTAG 59.962 55.000 0.84 0.00 0.00 2.18
4476 4527 0.251165 GTGGGGCCTTGAGTTGCTTA 60.251 55.000 0.84 0.00 0.00 3.09
4477 4528 1.531602 GTGGGGCCTTGAGTTGCTT 60.532 57.895 0.84 0.00 0.00 3.91
4478 4529 2.116125 GTGGGGCCTTGAGTTGCT 59.884 61.111 0.84 0.00 0.00 3.91
4479 4530 3.365265 CGTGGGGCCTTGAGTTGC 61.365 66.667 0.84 0.00 0.00 4.17
4480 4531 2.672996 CCGTGGGGCCTTGAGTTG 60.673 66.667 0.84 0.00 0.00 3.16
4481 4532 2.852075 TCCGTGGGGCCTTGAGTT 60.852 61.111 0.84 0.00 0.00 3.01
4482 4533 3.322466 CTCCGTGGGGCCTTGAGT 61.322 66.667 0.84 0.00 0.00 3.41
4483 4534 3.003173 TCTCCGTGGGGCCTTGAG 61.003 66.667 0.84 4.68 0.00 3.02
4484 4535 3.003173 CTCTCCGTGGGGCCTTGA 61.003 66.667 0.84 0.00 0.00 3.02
4485 4536 3.003173 TCTCTCCGTGGGGCCTTG 61.003 66.667 0.84 0.00 0.00 3.61
4486 4537 2.685380 CTCTCTCCGTGGGGCCTT 60.685 66.667 0.84 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.