Multiple sequence alignment - TraesCS3B01G164800

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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 TraesCS3B01G164800 chr3B 100.000 3641 0 0 1 3641 162638197 162641837 0.000000e+00 6724.0
1 TraesCS3B01G164800 chr3B 84.036 332 43 5 1057 1378 162688564 162688895 9.820000e-81 311.0
2 TraesCS3B01G164800 chr3D 89.849 1793 96 21 170 1907 111955239 111957000 0.000000e+00 2224.0
3 TraesCS3B01G164800 chr3D 95.368 367 17 0 1910 2276 111957042 111957408 5.240000e-163 584.0
4 TraesCS3B01G164800 chr3D 88.919 370 35 4 1910 2276 217124821 217124455 5.540000e-123 451.0
5 TraesCS3B01G164800 chr3D 88.503 374 35 6 1910 2279 611760827 611760458 2.580000e-121 446.0
6 TraesCS3B01G164800 chr3D 82.933 416 57 9 1057 1459 111963824 111964238 2.670000e-96 363.0
7 TraesCS3B01G164800 chr3D 93.893 131 8 0 2268 2398 111957441 111957571 7.970000e-47 198.0
8 TraesCS3B01G164800 chr3D 93.496 123 8 0 2520 2642 111957771 111957893 2.230000e-42 183.0
9 TraesCS3B01G164800 chr2B 94.231 936 54 0 2706 3641 772202260 772201325 0.000000e+00 1430.0
10 TraesCS3B01G164800 chr4B 92.415 936 71 0 2706 3641 29651606 29650671 0.000000e+00 1336.0
11 TraesCS3B01G164800 chr4B 88.649 370 36 4 1910 2276 389535369 389535735 2.580000e-121 446.0
12 TraesCS3B01G164800 chr4B 78.289 152 22 8 719 861 399194894 399194745 1.800000e-13 87.9
13 TraesCS3B01G164800 chr5B 91.132 936 83 0 2706 3641 230348517 230347582 0.000000e+00 1269.0
14 TraesCS3B01G164800 chr5B 89.617 366 32 4 1910 2272 185210110 185209748 9.210000e-126 460.0
15 TraesCS3B01G164800 chr5B 89.189 370 34 4 1910 2276 660237772 660237406 1.190000e-124 457.0
16 TraesCS3B01G164800 chr3A 89.278 970 68 14 862 1803 118546973 118546012 0.000000e+00 1182.0
17 TraesCS3B01G164800 chr3A 91.855 221 15 2 168 386 118547426 118547207 4.570000e-79 305.0
18 TraesCS3B01G164800 chr6A 76.862 886 198 6 2759 3641 436109603 436108722 9.080000e-136 494.0
19 TraesCS3B01G164800 chr7B 90.000 370 31 4 1910 2276 592397996 592398362 1.180000e-129 473.0
20 TraesCS3B01G164800 chr5D 89.544 373 32 5 1910 2279 330727488 330727120 1.980000e-127 466.0
21 TraesCS3B01G164800 chr7A 89.189 370 34 4 1910 2276 16741686 16741320 1.190000e-124 457.0
22 TraesCS3B01G164800 chr7A 95.294 170 8 0 7 176 115807687 115807518 1.670000e-68 270.0
23 TraesCS3B01G164800 chr5A 95.210 167 8 0 6 172 456897737 456897903 7.750000e-67 265.0
24 TraesCS3B01G164800 chr5A 94.675 169 9 0 7 175 290391861 290391693 2.790000e-66 263.0
25 TraesCS3B01G164800 chr5A 92.308 182 12 2 3 184 687682753 687682574 1.300000e-64 257.0
26 TraesCS3B01G164800 chr4D 94.675 169 9 0 6 174 75782052 75782220 2.790000e-66 263.0
27 TraesCS3B01G164800 chr4D 94.643 168 9 0 7 174 93338206 93338039 1.000000e-65 261.0
28 TraesCS3B01G164800 chr1D 94.643 168 9 0 7 174 178466306 178466473 1.000000e-65 261.0
29 TraesCS3B01G164800 chr1D 94.643 168 9 0 6 173 238940215 238940382 1.000000e-65 261.0
30 TraesCS3B01G164800 chr2A 93.678 174 10 1 7 180 31878241 31878413 3.610000e-65 259.0
31 TraesCS3B01G164800 chr1A 91.111 45 2 2 3526 3569 439335833 439335790 3.930000e-05 60.2
32 TraesCS3B01G164800 chr1B 100.000 29 0 0 3541 3569 296481957 296481929 2.000000e-03 54.7


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 TraesCS3B01G164800 chr3B 162638197 162641837 3640 False 6724.00 6724 100.0000 1 3641 1 chr3B.!!$F1 3640
1 TraesCS3B01G164800 chr3D 111955239 111957893 2654 False 797.25 2224 93.1515 170 2642 4 chr3D.!!$F2 2472
2 TraesCS3B01G164800 chr2B 772201325 772202260 935 True 1430.00 1430 94.2310 2706 3641 1 chr2B.!!$R1 935
3 TraesCS3B01G164800 chr4B 29650671 29651606 935 True 1336.00 1336 92.4150 2706 3641 1 chr4B.!!$R1 935
4 TraesCS3B01G164800 chr5B 230347582 230348517 935 True 1269.00 1269 91.1320 2706 3641 1 chr5B.!!$R2 935
5 TraesCS3B01G164800 chr3A 118546012 118547426 1414 True 743.50 1182 90.5665 168 1803 2 chr3A.!!$R1 1635
6 TraesCS3B01G164800 chr6A 436108722 436109603 881 True 494.00 494 76.8620 2759 3641 1 chr6A.!!$R1 882

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
749 814 0.246360 GTCGGGGCAAAGAAATTGGG 59.754 55.0 0.0 0.0 39.54 4.12 F
1814 1920 0.098728 AACTTGCACGCACACTTGTC 59.901 50.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2806 0.034756 ATATGATGCAGCGCGGGTAA 59.965 50.0 8.83 0.0 0.00 2.85 R
3454 3749 0.317436 CGCGCAAGTAAGCACCAAAA 60.317 50.0 8.75 0.0 41.68 2.44 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
31 32 9.901172 ATACTTCCTCCGTTTCTAAATATTTGT 57.099 29.630 11.05 0.00 0.00 2.83
32 33 8.265165 ACTTCCTCCGTTTCTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
33 34 8.101419 ACTTCCTCCGTTTCTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
34 35 8.857694 TTCCTCCGTTTCTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
35 36 8.857694 TCCTCCGTTTCTAAATATTTGTCTTT 57.142 30.769 11.05 0.00 0.00 2.52
36 37 9.292195 TCCTCCGTTTCTAAATATTTGTCTTTT 57.708 29.630 11.05 0.00 0.00 2.27
37 38 9.908152 CCTCCGTTTCTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
61 62 9.567776 TTTAGAGATTTCAAATTGACTACCACA 57.432 29.630 0.00 0.00 0.00 4.17
62 63 9.739276 TTAGAGATTTCAAATTGACTACCACAT 57.261 29.630 0.00 0.00 0.00 3.21
64 65 9.167311 AGAGATTTCAAATTGACTACCACATAC 57.833 33.333 0.00 0.00 0.00 2.39
65 66 7.974675 AGATTTCAAATTGACTACCACATACG 58.025 34.615 0.00 0.00 0.00 3.06
66 67 6.489127 TTTCAAATTGACTACCACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
67 68 5.408880 TCAAATTGACTACCACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
68 69 5.984725 TCAAATTGACTACCACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
69 70 5.815222 TCAAATTGACTACCACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
71 72 6.474140 AATTGACTACCACATACGGATGTA 57.526 37.500 14.23 0.00 44.82 2.29
72 73 6.665992 ATTGACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
73 74 7.770366 ATTGACTACCACATACGGATGTATA 57.230 36.000 14.23 8.27 44.82 1.47
74 75 7.770366 TTGACTACCACATACGGATGTATAT 57.230 36.000 14.23 4.37 44.82 0.86
75 76 8.866970 TTGACTACCACATACGGATGTATATA 57.133 34.615 14.23 5.36 44.82 0.86
76 77 8.502105 TGACTACCACATACGGATGTATATAG 57.498 38.462 14.23 16.35 44.82 1.31
77 78 8.323567 TGACTACCACATACGGATGTATATAGA 58.676 37.037 22.62 7.05 44.82 1.98
78 79 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
79 80 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
80 81 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
82 83 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
112 113 9.220767 AGAGTGTAGATTCACTTATTTTGTTCC 57.779 33.333 0.98 0.00 46.81 3.62
113 114 8.029642 AGTGTAGATTCACTTATTTTGTTCCG 57.970 34.615 0.00 0.00 44.92 4.30
114 115 7.660208 AGTGTAGATTCACTTATTTTGTTCCGT 59.340 33.333 0.00 0.00 44.92 4.69
115 116 8.928733 GTGTAGATTCACTTATTTTGTTCCGTA 58.071 33.333 0.00 0.00 35.68 4.02
116 117 9.661563 TGTAGATTCACTTATTTTGTTCCGTAT 57.338 29.630 0.00 0.00 0.00 3.06
130 131 9.577110 TTTTGTTCCGTATATAGTCACTAGTTG 57.423 33.333 0.00 0.00 0.00 3.16
131 132 8.510243 TTGTTCCGTATATAGTCACTAGTTGA 57.490 34.615 0.00 0.00 0.00 3.18
132 133 8.510243 TGTTCCGTATATAGTCACTAGTTGAA 57.490 34.615 0.00 0.00 35.39 2.69
133 134 8.959548 TGTTCCGTATATAGTCACTAGTTGAAA 58.040 33.333 0.00 0.00 35.39 2.69
134 135 9.962783 GTTCCGTATATAGTCACTAGTTGAAAT 57.037 33.333 0.00 0.00 35.39 2.17
136 137 9.570468 TCCGTATATAGTCACTAGTTGAAATCT 57.430 33.333 0.00 0.00 35.39 2.40
137 138 9.828852 CCGTATATAGTCACTAGTTGAAATCTC 57.171 37.037 0.00 0.00 35.39 2.75
145 146 9.303116 AGTCACTAGTTGAAATCTCTAGAAAGA 57.697 33.333 14.89 0.00 35.39 2.52
146 147 9.349145 GTCACTAGTTGAAATCTCTAGAAAGAC 57.651 37.037 14.89 14.16 35.39 3.01
147 148 9.078990 TCACTAGTTGAAATCTCTAGAAAGACA 57.921 33.333 14.89 0.00 36.17 3.41
148 149 9.698309 CACTAGTTGAAATCTCTAGAAAGACAA 57.302 33.333 14.89 0.00 36.17 3.18
152 153 9.566432 AGTTGAAATCTCTAGAAAGACAAATGT 57.434 29.630 0.00 0.00 0.00 2.71
160 161 9.490379 TCTCTAGAAAGACAAATGTTTAGGAAC 57.510 33.333 0.00 0.00 36.29 3.62
161 162 8.306680 TCTAGAAAGACAAATGTTTAGGAACG 57.693 34.615 0.00 0.00 38.65 3.95
162 163 6.313744 AGAAAGACAAATGTTTAGGAACGG 57.686 37.500 0.00 0.00 38.65 4.44
163 164 6.059484 AGAAAGACAAATGTTTAGGAACGGA 58.941 36.000 0.00 0.00 38.65 4.69
164 165 5.941948 AAGACAAATGTTTAGGAACGGAG 57.058 39.130 0.00 0.00 38.65 4.63
165 166 5.223449 AGACAAATGTTTAGGAACGGAGA 57.777 39.130 0.00 0.00 38.65 3.71
166 167 5.238583 AGACAAATGTTTAGGAACGGAGAG 58.761 41.667 0.00 0.00 38.65 3.20
222 223 7.282224 CCTCCAATGGAAAACACGAGAATATAA 59.718 37.037 2.61 0.00 0.00 0.98
467 506 4.022464 TCAAAACGTTGACATGTTGTCC 57.978 40.909 0.00 0.00 46.40 4.02
475 514 2.412870 TGACATGTTGTCCACGACATC 58.587 47.619 9.31 2.44 45.33 3.06
477 516 3.002791 GACATGTTGTCCACGACATCAT 58.997 45.455 9.31 10.96 46.98 2.45
519 569 1.066605 CCAGCAGCATAAATGAGCCAC 59.933 52.381 0.00 0.00 32.90 5.01
561 620 7.920151 TGCCTTATTTAAACATGCATGATGTAC 59.080 33.333 32.75 9.93 45.12 2.90
581 644 9.102757 GATGTACTTTTAATCTGATCAAGAGCA 57.897 33.333 0.00 8.38 38.67 4.26
586 649 5.682234 TTAATCTGATCAAGAGCACTCCA 57.318 39.130 0.00 0.00 38.67 3.86
595 658 2.393271 AGAGCACTCCAATCCGAAAG 57.607 50.000 0.00 0.00 0.00 2.62
619 682 0.255890 TGGCCTCCCTTACAATGCTC 59.744 55.000 3.32 0.00 0.00 4.26
621 684 1.383523 GCCTCCCTTACAATGCTCAC 58.616 55.000 0.00 0.00 0.00 3.51
624 687 2.237143 CCTCCCTTACAATGCTCACTGA 59.763 50.000 0.00 0.00 0.00 3.41
627 690 4.264253 TCCCTTACAATGCTCACTGAATG 58.736 43.478 0.00 0.00 0.00 2.67
629 692 3.379372 CCTTACAATGCTCACTGAATGGG 59.621 47.826 0.00 0.00 0.00 4.00
637 700 2.449464 CTCACTGAATGGGCCATTTGA 58.551 47.619 31.17 26.91 33.90 2.69
651 714 2.030946 CCATTTGAATCGAGAGGAACGC 59.969 50.000 0.00 0.00 0.00 4.84
652 715 2.743636 TTTGAATCGAGAGGAACGCT 57.256 45.000 0.00 0.00 44.68 5.07
662 727 0.673956 GAGGAACGCTGGGTCTTTCC 60.674 60.000 6.07 6.07 38.26 3.13
664 729 0.322546 GGAACGCTGGGTCTTTCCAT 60.323 55.000 8.66 0.00 37.94 3.41
685 750 6.122277 CCATAAAAGAGTATGGCTCCAAGAA 58.878 40.000 0.00 0.00 43.09 2.52
702 767 8.125448 GCTCCAAGAATATTACTCAACAACATC 58.875 37.037 0.00 0.00 0.00 3.06
711 776 6.993786 TTACTCAACAACATCAAGTGTGAA 57.006 33.333 0.00 0.00 41.14 3.18
721 786 3.228188 TCAAGTGTGAAGCCATCCTTT 57.772 42.857 0.00 0.00 32.78 3.11
749 814 0.246360 GTCGGGGCAAAGAAATTGGG 59.754 55.000 0.00 0.00 39.54 4.12
751 816 0.532115 CGGGGCAAAGAAATTGGGAG 59.468 55.000 0.00 0.00 39.54 4.30
752 817 0.250234 GGGGCAAAGAAATTGGGAGC 59.750 55.000 0.00 0.00 39.54 4.70
760 825 5.594926 CAAAGAAATTGGGAGCCATCATAC 58.405 41.667 0.00 0.00 35.27 2.39
761 826 4.803329 AGAAATTGGGAGCCATCATACT 57.197 40.909 0.00 0.00 31.53 2.12
762 827 4.467769 AGAAATTGGGAGCCATCATACTG 58.532 43.478 0.00 0.00 31.53 2.74
766 831 0.689623 GGGAGCCATCATACTGGGAG 59.310 60.000 0.00 0.00 36.75 4.30
767 832 0.689623 GGAGCCATCATACTGGGAGG 59.310 60.000 0.00 0.00 36.75 4.30
773 838 2.372172 CCATCATACTGGGAGGGTAACC 59.628 54.545 0.00 0.00 45.11 2.85
792 857 6.804783 GGTAACCGTTTTTCATTTAGGATGTG 59.195 38.462 0.00 0.00 0.00 3.21
793 858 6.399639 AACCGTTTTTCATTTAGGATGTGT 57.600 33.333 0.00 0.00 0.00 3.72
796 861 7.364970 ACCGTTTTTCATTTAGGATGTGTAAC 58.635 34.615 0.00 0.00 37.35 2.50
852 917 3.568538 CAAATCCTTTGCCTCAGTTTCG 58.431 45.455 0.00 0.00 33.36 3.46
926 999 5.568620 ACATACCTAAATGATCTGTCCCC 57.431 43.478 0.00 0.00 0.00 4.81
955 1028 6.654161 AGAGAACCAGTCTGAATTTTGAGATG 59.346 38.462 0.00 0.00 36.41 2.90
1004 1080 2.158726 TGTAGCTTCGGTTTCCCAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
1034 1110 3.389002 TCCACCATGTCCTCATACATCAG 59.611 47.826 0.00 0.00 38.01 2.90
1038 1114 1.878211 TGTCCTCATACATCAGGCCA 58.122 50.000 5.01 0.00 0.00 5.36
1386 1468 1.391157 GCAAGCACCTGTTCCACCAA 61.391 55.000 0.00 0.00 0.00 3.67
1410 1492 2.486042 GTCGACGTCTGGCTCCTC 59.514 66.667 14.70 0.00 0.00 3.71
1545 1627 0.732880 ACGATGAAACGCTGTCTCCG 60.733 55.000 0.00 0.00 36.70 4.63
1698 1786 1.998315 AGATATGATTGCGCGATCTGC 59.002 47.619 32.19 20.15 41.47 4.26
1703 1791 0.315706 GATTGCGCGATCTGCTGAAC 60.316 55.000 27.16 1.77 43.27 3.18
1717 1822 3.997021 CTGCTGAACTAGGTTCGTCATTT 59.003 43.478 0.00 0.00 44.55 2.32
1743 1848 0.099082 GCAGATTGCAGAGAGCTTGC 59.901 55.000 1.77 1.77 44.26 4.01
1803 1908 1.130561 GATTGCGACCCTAACTTGCAC 59.869 52.381 0.00 0.00 34.90 4.57
1804 1909 1.225376 TTGCGACCCTAACTTGCACG 61.225 55.000 0.00 0.00 34.90 5.34
1806 1911 1.666553 CGACCCTAACTTGCACGCA 60.667 57.895 0.00 0.00 0.00 5.24
1814 1920 0.098728 AACTTGCACGCACACTTGTC 59.901 50.000 0.00 0.00 0.00 3.18
1837 1943 7.865385 TGTCCATTTTATTTTGCTCTGTGTTAC 59.135 33.333 0.00 0.00 0.00 2.50
1840 1946 9.260002 CCATTTTATTTTGCTCTGTGTTACTTT 57.740 29.630 0.00 0.00 0.00 2.66
1860 1966 6.273071 ACTTTGCTTCACAAATGACTAAACC 58.727 36.000 0.00 0.00 46.90 3.27
1907 2015 1.889829 CGGGCCCAAACTGTATTTCAA 59.110 47.619 24.92 0.00 0.00 2.69
1908 2016 2.297597 CGGGCCCAAACTGTATTTCAAA 59.702 45.455 24.92 0.00 0.00 2.69
1937 2084 5.032846 TGAAGATTGGTGATAGTCCTTCCT 58.967 41.667 0.00 0.00 0.00 3.36
1938 2085 5.129485 TGAAGATTGGTGATAGTCCTTCCTC 59.871 44.000 0.00 0.00 0.00 3.71
1946 2093 3.207777 TGATAGTCCTTCCTCCTAGCCTT 59.792 47.826 0.00 0.00 0.00 4.35
1972 2119 3.677700 CGACCCCGAACTGTATTTCATCA 60.678 47.826 0.00 0.00 38.22 3.07
1999 2146 2.214376 TGGGCACTGGAATACCTTTG 57.786 50.000 0.00 0.00 37.04 2.77
2002 2149 2.369394 GGCACTGGAATACCTTTGGAG 58.631 52.381 0.00 0.00 37.04 3.86
2012 2159 5.163612 GGAATACCTTTGGAGTTGCAGAATC 60.164 44.000 0.00 0.00 0.00 2.52
2025 2172 2.092753 TGCAGAATCCTTGGACCTCATC 60.093 50.000 0.00 0.00 0.00 2.92
2032 2179 4.722526 TCCTTGGACCTCATCAAAAAGA 57.277 40.909 0.00 0.00 0.00 2.52
2125 2272 8.610896 CACAATATTTGTTTCCTTTCTTTGCAA 58.389 29.630 0.00 0.00 43.23 4.08
2148 2295 6.942532 AGAGTTGTGAAAGCTCATTTGTTA 57.057 33.333 0.00 0.00 33.05 2.41
2175 2322 7.320399 ACCAAACAACTTTAGCATAATAAGCC 58.680 34.615 0.00 0.00 0.00 4.35
2176 2323 6.756542 CCAAACAACTTTAGCATAATAAGCCC 59.243 38.462 0.00 0.00 0.00 5.19
2196 2343 3.950395 CCCCAAAACAAAAGCAAATTGGA 59.050 39.130 4.01 0.00 39.69 3.53
2217 2364 6.370433 GGAAGCACTCCATCTTTTCTATTC 57.630 41.667 0.10 0.00 44.67 1.75
2278 2466 7.615403 TCAACTGTGCTAAGAACTTCTATGAT 58.385 34.615 0.00 0.00 0.00 2.45
2284 2472 7.331934 TGTGCTAAGAACTTCTATGATGTGAAC 59.668 37.037 0.00 0.00 0.00 3.18
2298 2486 7.609097 ATGATGTGAACACCATCTAGTATCT 57.391 36.000 2.46 0.00 0.00 1.98
2329 2517 1.662629 CAAGGCTAGTCTGTTGATGCG 59.337 52.381 0.00 0.00 0.00 4.73
2366 2554 2.149973 ATTTCACCCATCTCAAGCCC 57.850 50.000 0.00 0.00 0.00 5.19
2380 2568 5.393866 TCTCAAGCCCTTCCAAAGTATTTT 58.606 37.500 0.00 0.00 35.03 1.82
2384 2572 5.468540 AGCCCTTCCAAAGTATTTTTGTC 57.531 39.130 0.00 0.00 35.03 3.18
2433 2728 0.396139 ATGGCCGTGGAAAGCATGAT 60.396 50.000 0.00 0.00 0.00 2.45
2464 2759 8.334263 TCATGTAGAATGTATCTTTGCAAACA 57.666 30.769 8.05 5.91 39.71 2.83
2505 2800 2.028420 TCAAGCTGCGTCATATGCTT 57.972 45.000 0.00 0.00 45.22 3.91
2506 2801 2.358957 TCAAGCTGCGTCATATGCTTT 58.641 42.857 0.00 0.00 42.89 3.51
2507 2802 2.749076 TCAAGCTGCGTCATATGCTTTT 59.251 40.909 0.00 0.00 42.89 2.27
2508 2803 3.191162 TCAAGCTGCGTCATATGCTTTTT 59.809 39.130 0.00 0.00 42.89 1.94
2525 2820 3.674906 TTTTTACCCGCGCTGCAT 58.325 50.000 5.56 0.00 0.00 3.96
2526 2821 1.504446 TTTTTACCCGCGCTGCATC 59.496 52.632 5.56 0.00 0.00 3.91
2527 2822 1.237954 TTTTTACCCGCGCTGCATCA 61.238 50.000 5.56 0.00 0.00 3.07
2528 2823 1.029408 TTTTACCCGCGCTGCATCAT 61.029 50.000 5.56 0.00 0.00 2.45
2529 2824 0.179070 TTTACCCGCGCTGCATCATA 60.179 50.000 5.56 0.00 0.00 2.15
2530 2825 0.034756 TTACCCGCGCTGCATCATAT 59.965 50.000 5.56 0.00 0.00 1.78
2531 2826 0.670239 TACCCGCGCTGCATCATATG 60.670 55.000 5.56 0.00 0.00 1.78
2545 2840 3.708403 TCATATGCTTGCCCTCATAGG 57.292 47.619 0.00 0.00 34.30 2.57
2562 2857 6.071728 CCTCATAGGCTTGAAATTGACAACTT 60.072 38.462 0.00 0.00 0.00 2.66
2602 2897 2.230660 ACAAGAGCTAACTTTGGTGCC 58.769 47.619 0.00 0.00 0.00 5.01
2619 2914 4.227300 TGGTGCCCAAGATGTAGTATCTTT 59.773 41.667 0.00 0.00 36.32 2.52
2625 2920 6.017605 GCCCAAGATGTAGTATCTTTGATGTG 60.018 42.308 0.00 0.00 36.32 3.21
2637 2932 8.103305 AGTATCTTTGATGTGGTGTAGACAAAT 58.897 33.333 0.00 0.00 0.00 2.32
2642 2937 9.559958 CTTTGATGTGGTGTAGACAAATAAATC 57.440 33.333 0.00 0.00 0.00 2.17
2643 2938 7.302350 TGATGTGGTGTAGACAAATAAATCG 57.698 36.000 0.00 0.00 0.00 3.34
2644 2939 6.876789 TGATGTGGTGTAGACAAATAAATCGT 59.123 34.615 0.00 0.00 0.00 3.73
2645 2940 7.389330 TGATGTGGTGTAGACAAATAAATCGTT 59.611 33.333 0.00 0.00 0.00 3.85
2646 2941 7.124347 TGTGGTGTAGACAAATAAATCGTTC 57.876 36.000 0.00 0.00 0.00 3.95
2647 2942 6.148150 TGTGGTGTAGACAAATAAATCGTTCC 59.852 38.462 0.00 0.00 0.00 3.62
2648 2943 6.148150 GTGGTGTAGACAAATAAATCGTTCCA 59.852 38.462 0.00 0.00 0.00 3.53
2649 2944 6.148150 TGGTGTAGACAAATAAATCGTTCCAC 59.852 38.462 0.00 0.00 0.00 4.02
2650 2945 6.148150 GGTGTAGACAAATAAATCGTTCCACA 59.852 38.462 0.00 0.00 0.00 4.17
2651 2946 7.308109 GGTGTAGACAAATAAATCGTTCCACAA 60.308 37.037 0.00 0.00 0.00 3.33
2652 2947 7.532884 GTGTAGACAAATAAATCGTTCCACAAC 59.467 37.037 0.00 0.00 0.00 3.32
2653 2948 6.009115 AGACAAATAAATCGTTCCACAACC 57.991 37.500 0.00 0.00 0.00 3.77
2654 2949 5.768164 AGACAAATAAATCGTTCCACAACCT 59.232 36.000 0.00 0.00 0.00 3.50
2655 2950 6.264518 AGACAAATAAATCGTTCCACAACCTT 59.735 34.615 0.00 0.00 0.00 3.50
2656 2951 6.443792 ACAAATAAATCGTTCCACAACCTTC 58.556 36.000 0.00 0.00 0.00 3.46
2657 2952 5.638596 AATAAATCGTTCCACAACCTTCC 57.361 39.130 0.00 0.00 0.00 3.46
2658 2953 2.649531 AATCGTTCCACAACCTTCCA 57.350 45.000 0.00 0.00 0.00 3.53
2659 2954 1.892209 ATCGTTCCACAACCTTCCAC 58.108 50.000 0.00 0.00 0.00 4.02
2660 2955 0.531090 TCGTTCCACAACCTTCCACG 60.531 55.000 0.00 0.00 0.00 4.94
2661 2956 0.812412 CGTTCCACAACCTTCCACGT 60.812 55.000 0.00 0.00 0.00 4.49
2662 2957 1.385528 GTTCCACAACCTTCCACGTT 58.614 50.000 0.00 0.00 0.00 3.99
2663 2958 1.064952 GTTCCACAACCTTCCACGTTG 59.935 52.381 0.00 0.00 44.95 4.10
2664 2959 1.098712 TCCACAACCTTCCACGTTGC 61.099 55.000 0.78 0.00 43.57 4.17
2665 2960 1.380403 CCACAACCTTCCACGTTGCA 61.380 55.000 0.78 0.00 43.57 4.08
2666 2961 0.667993 CACAACCTTCCACGTTGCAT 59.332 50.000 0.78 0.00 43.57 3.96
2667 2962 1.066908 CACAACCTTCCACGTTGCATT 59.933 47.619 0.78 0.00 43.57 3.56
2668 2963 2.292016 CACAACCTTCCACGTTGCATTA 59.708 45.455 0.78 0.00 43.57 1.90
2669 2964 2.292292 ACAACCTTCCACGTTGCATTAC 59.708 45.455 0.78 0.00 43.57 1.89
2670 2965 2.264005 ACCTTCCACGTTGCATTACA 57.736 45.000 0.00 0.00 0.00 2.41
2671 2966 2.151202 ACCTTCCACGTTGCATTACAG 58.849 47.619 0.00 0.00 0.00 2.74
2672 2967 2.151202 CCTTCCACGTTGCATTACAGT 58.849 47.619 0.00 0.00 0.00 3.55
2673 2968 3.244284 ACCTTCCACGTTGCATTACAGTA 60.244 43.478 0.00 0.00 0.00 2.74
2674 2969 3.938963 CCTTCCACGTTGCATTACAGTAT 59.061 43.478 0.00 0.00 0.00 2.12
2675 2970 4.394920 CCTTCCACGTTGCATTACAGTATT 59.605 41.667 0.00 0.00 0.00 1.89
2676 2971 5.106317 CCTTCCACGTTGCATTACAGTATTT 60.106 40.000 0.00 0.00 0.00 1.40
2677 2972 5.950758 TCCACGTTGCATTACAGTATTTT 57.049 34.783 0.00 0.00 0.00 1.82
2678 2973 6.320494 TCCACGTTGCATTACAGTATTTTT 57.680 33.333 0.00 0.00 0.00 1.94
2756 3051 1.599047 CGGAGCATTCCCTGTGTCT 59.401 57.895 0.00 0.00 40.67 3.41
2796 3091 2.434336 CCTCCGATTATGTCCTGGAACA 59.566 50.000 0.00 0.00 0.00 3.18
2805 3100 0.908198 GTCCTGGAACATCAGAGGCT 59.092 55.000 0.00 0.00 38.20 4.58
3104 3399 3.955771 TTCTGGCTCACAAACGTTTAC 57.044 42.857 14.20 1.22 0.00 2.01
3134 3429 4.024472 GTGGAAGACAGTGAAAAAGAGAGC 60.024 45.833 0.00 0.00 0.00 4.09
3158 3453 5.407407 TCTTTCAGGAGATGACTAACACC 57.593 43.478 0.00 0.00 37.77 4.16
3361 3656 0.179062 GCCCAACCAACAATGTGCAA 60.179 50.000 0.00 0.00 0.00 4.08
3454 3749 2.405618 TCCATCTCCGATCATTCCCT 57.594 50.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.901172 ACAAATATTTAGAAACGGAGGAAGTAT 57.099 29.630 0.00 0.00 0.00 2.12
6 7 9.374838 GACAAATATTTAGAAACGGAGGAAGTA 57.625 33.333 0.00 0.00 0.00 2.24
7 8 8.101419 AGACAAATATTTAGAAACGGAGGAAGT 58.899 33.333 0.00 0.00 0.00 3.01
8 9 8.494016 AGACAAATATTTAGAAACGGAGGAAG 57.506 34.615 0.00 0.00 0.00 3.46
9 10 8.857694 AAGACAAATATTTAGAAACGGAGGAA 57.142 30.769 0.00 0.00 0.00 3.36
10 11 8.857694 AAAGACAAATATTTAGAAACGGAGGA 57.142 30.769 0.00 0.00 0.00 3.71
11 12 9.908152 AAAAAGACAAATATTTAGAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
35 36 9.567776 TGTGGTAGTCAATTTGAAATCTCTAAA 57.432 29.630 0.00 0.00 0.00 1.85
36 37 9.739276 ATGTGGTAGTCAATTTGAAATCTCTAA 57.261 29.630 0.00 0.00 0.00 2.10
38 39 9.167311 GTATGTGGTAGTCAATTTGAAATCTCT 57.833 33.333 0.00 0.00 0.00 3.10
39 40 8.116753 CGTATGTGGTAGTCAATTTGAAATCTC 58.883 37.037 0.00 0.00 0.00 2.75
40 41 7.065803 CCGTATGTGGTAGTCAATTTGAAATCT 59.934 37.037 0.00 0.00 0.00 2.40
41 42 7.065324 TCCGTATGTGGTAGTCAATTTGAAATC 59.935 37.037 0.00 0.00 0.00 2.17
42 43 6.882140 TCCGTATGTGGTAGTCAATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
43 44 6.231951 TCCGTATGTGGTAGTCAATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
44 45 5.795972 TCCGTATGTGGTAGTCAATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
45 46 5.408880 TCCGTATGTGGTAGTCAATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
46 47 5.584649 ACATCCGTATGTGGTAGTCAATTTG 59.415 40.000 0.00 0.00 44.79 2.32
47 48 5.741011 ACATCCGTATGTGGTAGTCAATTT 58.259 37.500 0.00 0.00 44.79 1.82
48 49 5.353394 ACATCCGTATGTGGTAGTCAATT 57.647 39.130 0.00 0.00 44.79 2.32
49 50 6.665992 ATACATCCGTATGTGGTAGTCAAT 57.334 37.500 3.56 0.00 45.99 2.57
50 51 7.770366 ATATACATCCGTATGTGGTAGTCAA 57.230 36.000 3.56 0.00 45.99 3.18
51 52 8.323567 TCTATATACATCCGTATGTGGTAGTCA 58.676 37.037 3.56 0.00 45.99 3.41
52 53 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
53 54 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
54 55 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
56 57 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
89 90 7.803724 ACGGAACAAAATAAGTGAATCTACAC 58.196 34.615 0.00 0.00 40.60 2.90
90 91 7.972832 ACGGAACAAAATAAGTGAATCTACA 57.027 32.000 0.00 0.00 0.00 2.74
104 105 9.577110 CAACTAGTGACTATATACGGAACAAAA 57.423 33.333 0.00 0.00 0.00 2.44
105 106 8.959548 TCAACTAGTGACTATATACGGAACAAA 58.040 33.333 0.00 0.00 0.00 2.83
106 107 8.510243 TCAACTAGTGACTATATACGGAACAA 57.490 34.615 0.00 0.00 0.00 2.83
107 108 8.510243 TTCAACTAGTGACTATATACGGAACA 57.490 34.615 0.00 0.00 35.39 3.18
108 109 9.962783 ATTTCAACTAGTGACTATATACGGAAC 57.037 33.333 0.00 0.00 35.39 3.62
110 111 9.570468 AGATTTCAACTAGTGACTATATACGGA 57.430 33.333 0.00 0.00 35.39 4.69
111 112 9.828852 GAGATTTCAACTAGTGACTATATACGG 57.171 37.037 0.00 0.00 35.39 4.02
119 120 9.303116 TCTTTCTAGAGATTTCAACTAGTGACT 57.697 33.333 0.00 0.00 35.39 3.41
120 121 9.349145 GTCTTTCTAGAGATTTCAACTAGTGAC 57.651 37.037 0.00 0.00 35.39 3.67
121 122 9.078990 TGTCTTTCTAGAGATTTCAACTAGTGA 57.921 33.333 0.00 0.00 36.17 3.41
122 123 9.698309 TTGTCTTTCTAGAGATTTCAACTAGTG 57.302 33.333 0.00 0.00 36.17 2.74
126 127 9.566432 ACATTTGTCTTTCTAGAGATTTCAACT 57.434 29.630 0.00 0.00 0.00 3.16
134 135 9.490379 GTTCCTAAACATTTGTCTTTCTAGAGA 57.510 33.333 0.00 0.00 35.36 3.10
135 136 8.436200 CGTTCCTAAACATTTGTCTTTCTAGAG 58.564 37.037 0.00 0.00 34.93 2.43
136 137 7.386848 CCGTTCCTAAACATTTGTCTTTCTAGA 59.613 37.037 0.00 0.00 34.93 2.43
137 138 7.386848 TCCGTTCCTAAACATTTGTCTTTCTAG 59.613 37.037 0.00 0.00 34.93 2.43
138 139 7.218614 TCCGTTCCTAAACATTTGTCTTTCTA 58.781 34.615 0.00 0.00 34.93 2.10
139 140 6.059484 TCCGTTCCTAAACATTTGTCTTTCT 58.941 36.000 0.00 0.00 34.93 2.52
140 141 6.204108 TCTCCGTTCCTAAACATTTGTCTTTC 59.796 38.462 0.00 0.00 34.93 2.62
141 142 6.059484 TCTCCGTTCCTAAACATTTGTCTTT 58.941 36.000 0.00 0.00 34.93 2.52
142 143 5.617252 TCTCCGTTCCTAAACATTTGTCTT 58.383 37.500 0.00 0.00 34.93 3.01
143 144 5.011738 TCTCTCCGTTCCTAAACATTTGTCT 59.988 40.000 0.00 0.00 34.93 3.41
144 145 5.235516 TCTCTCCGTTCCTAAACATTTGTC 58.764 41.667 0.00 0.00 34.93 3.18
145 146 5.221661 ACTCTCTCCGTTCCTAAACATTTGT 60.222 40.000 0.00 0.00 34.93 2.83
146 147 5.238583 ACTCTCTCCGTTCCTAAACATTTG 58.761 41.667 0.00 0.00 34.93 2.32
147 148 5.485209 ACTCTCTCCGTTCCTAAACATTT 57.515 39.130 0.00 0.00 34.93 2.32
148 149 6.793505 ATACTCTCTCCGTTCCTAAACATT 57.206 37.500 0.00 0.00 34.93 2.71
149 150 7.945664 AGATATACTCTCTCCGTTCCTAAACAT 59.054 37.037 0.00 0.00 34.93 2.71
150 151 7.288560 AGATATACTCTCTCCGTTCCTAAACA 58.711 38.462 0.00 0.00 34.93 2.83
151 152 7.748691 AGATATACTCTCTCCGTTCCTAAAC 57.251 40.000 0.00 0.00 0.00 2.01
152 153 7.982761 GAGATATACTCTCTCCGTTCCTAAA 57.017 40.000 0.00 0.00 45.97 1.85
165 166 4.261825 GCCGCTTGACTTGAGATATACTCT 60.262 45.833 0.00 0.00 45.13 3.24
166 167 3.984633 GCCGCTTGACTTGAGATATACTC 59.015 47.826 0.00 0.00 45.11 2.59
185 186 1.270518 CCATTGGAGGTAGAGATGCCG 60.271 57.143 0.00 0.00 0.00 5.69
222 223 3.922375 TCAAAATGAAGGTTGAAGGGGT 58.078 40.909 0.00 0.00 30.93 4.95
319 322 7.785028 TGATAATAGAGTTGACCTACCAGACAT 59.215 37.037 0.00 0.00 0.00 3.06
477 516 9.605275 GCTGGCTTATCAATAGATTATATGTGA 57.395 33.333 0.00 0.00 35.67 3.58
548 598 9.608617 GATCAGATTAAAAGTACATCATGCATG 57.391 33.333 21.07 21.07 38.64 4.06
549 599 9.346005 TGATCAGATTAAAAGTACATCATGCAT 57.654 29.630 0.00 0.00 0.00 3.96
561 620 6.596888 TGGAGTGCTCTTGATCAGATTAAAAG 59.403 38.462 0.00 0.00 0.00 2.27
566 625 4.564782 TTGGAGTGCTCTTGATCAGATT 57.435 40.909 0.00 0.00 0.00 2.40
581 644 2.094675 CATTGCCTTTCGGATTGGAGT 58.905 47.619 1.63 0.00 0.00 3.85
598 661 1.288932 AGCATTGTAAGGGAGGCCATT 59.711 47.619 5.01 0.00 0.00 3.16
601 664 0.255890 TGAGCATTGTAAGGGAGGCC 59.744 55.000 0.00 0.00 0.00 5.19
608 671 3.181493 GCCCATTCAGTGAGCATTGTAAG 60.181 47.826 0.00 0.00 30.86 2.34
611 674 1.180029 GCCCATTCAGTGAGCATTGT 58.820 50.000 0.00 0.00 30.86 2.71
619 682 3.735820 CGATTCAAATGGCCCATTCAGTG 60.736 47.826 9.93 4.83 32.43 3.66
621 684 2.689471 TCGATTCAAATGGCCCATTCAG 59.311 45.455 9.93 5.99 32.43 3.02
624 687 2.954318 CTCTCGATTCAAATGGCCCATT 59.046 45.455 2.23 2.23 35.39 3.16
627 690 1.134098 TCCTCTCGATTCAAATGGCCC 60.134 52.381 0.00 0.00 0.00 5.80
629 692 2.030946 CGTTCCTCTCGATTCAAATGGC 59.969 50.000 0.00 0.00 0.00 4.40
630 693 2.030946 GCGTTCCTCTCGATTCAAATGG 59.969 50.000 0.00 0.00 0.00 3.16
637 700 1.258445 ACCCAGCGTTCCTCTCGATT 61.258 55.000 0.00 0.00 0.00 3.34
651 714 7.559590 CATACTCTTTTATGGAAAGACCCAG 57.440 40.000 2.91 0.00 46.69 4.45
662 727 7.814264 ATTCTTGGAGCCATACTCTTTTATG 57.186 36.000 0.00 0.00 45.48 1.90
679 744 9.778993 CTTGATGTTGTTGAGTAATATTCTTGG 57.221 33.333 0.00 0.00 0.00 3.61
683 748 9.546909 CACACTTGATGTTGTTGAGTAATATTC 57.453 33.333 0.00 0.00 40.64 1.75
685 750 8.846943 TCACACTTGATGTTGTTGAGTAATAT 57.153 30.769 0.00 0.00 40.64 1.28
702 767 2.029649 CCAAAGGATGGCTTCACACTTG 60.030 50.000 2.60 0.73 43.80 3.16
749 814 0.689623 CCCTCCCAGTATGATGGCTC 59.310 60.000 0.00 0.00 39.69 4.70
751 816 1.729586 TACCCTCCCAGTATGATGGC 58.270 55.000 0.00 0.00 39.69 4.40
752 817 2.372172 GGTTACCCTCCCAGTATGATGG 59.628 54.545 0.00 0.00 39.69 3.51
760 825 2.156917 GAAAAACGGTTACCCTCCCAG 58.843 52.381 0.00 0.00 0.00 4.45
761 826 1.493871 TGAAAAACGGTTACCCTCCCA 59.506 47.619 0.00 0.00 0.00 4.37
762 827 2.275134 TGAAAAACGGTTACCCTCCC 57.725 50.000 0.00 0.00 0.00 4.30
766 831 5.963176 TCCTAAATGAAAAACGGTTACCC 57.037 39.130 0.00 0.00 0.00 3.69
767 832 6.804783 CACATCCTAAATGAAAAACGGTTACC 59.195 38.462 0.00 0.00 0.00 2.85
874 939 7.201626 CCGACTATTTCAGATATACTACTCCCG 60.202 44.444 0.00 0.00 0.00 5.14
875 940 7.415429 GCCGACTATTTCAGATATACTACTCCC 60.415 44.444 0.00 0.00 0.00 4.30
879 944 9.719279 GTATGCCGACTATTTCAGATATACTAC 57.281 37.037 0.00 0.00 0.00 2.73
926 999 2.154854 TTCAGACTGGTTCTCTTGCG 57.845 50.000 1.81 0.00 28.96 4.85
955 1028 4.932200 GCTATATATGCAGACAGGTTGGTC 59.068 45.833 0.00 0.00 38.08 4.02
1004 1080 2.239654 GAGGACATGGTGGAGGAAATGA 59.760 50.000 0.00 0.00 0.00 2.57
1386 1468 2.556792 CAGACGTCGACGCACTCT 59.443 61.111 35.92 27.31 44.43 3.24
1468 1550 4.257510 TCTCTCGCGCTGATCGGC 62.258 66.667 17.01 17.01 38.94 5.54
1469 1551 2.051435 CTCTCTCGCGCTGATCGG 60.051 66.667 5.56 0.00 38.94 4.18
1470 1552 2.725450 GCTCTCTCGCGCTGATCG 60.725 66.667 5.56 0.00 42.12 3.69
1471 1553 2.354539 GGCTCTCTCGCGCTGATC 60.355 66.667 5.56 0.00 0.00 2.92
1698 1786 8.755941 CATATACAAATGACGAACCTAGTTCAG 58.244 37.037 8.11 3.72 42.05 3.02
1703 1791 6.923508 TCTGCATATACAAATGACGAACCTAG 59.076 38.462 0.00 0.00 0.00 3.02
1743 1848 1.003116 GAATAGAATGCGTGCTGCCAG 60.003 52.381 0.00 0.00 45.60 4.85
1758 1863 3.680642 TCGTTTACTCCGACCGAATAG 57.319 47.619 0.00 0.00 0.00 1.73
1803 1908 5.612276 GCAAAATAAAATGGACAAGTGTGCG 60.612 40.000 0.00 0.00 39.39 5.34
1804 1909 5.466393 AGCAAAATAAAATGGACAAGTGTGC 59.534 36.000 0.00 0.00 36.87 4.57
1806 1911 6.925165 CAGAGCAAAATAAAATGGACAAGTGT 59.075 34.615 0.00 0.00 0.00 3.55
1814 1920 8.816640 AAGTAACACAGAGCAAAATAAAATGG 57.183 30.769 0.00 0.00 0.00 3.16
1837 1943 7.894934 ACTGGTTTAGTCATTTGTGAAGCAAAG 60.895 37.037 0.00 0.00 42.10 2.77
1840 1946 4.887071 ACTGGTTTAGTCATTTGTGAAGCA 59.113 37.500 0.00 0.00 33.17 3.91
1884 1992 0.965363 AATACAGTTTGGGCCCGCAG 60.965 55.000 19.37 9.45 0.00 5.18
1886 1994 0.172578 GAAATACAGTTTGGGCCCGC 59.827 55.000 19.37 10.20 0.00 6.13
1907 2015 9.927081 AGGACTATCACCAATCTTCATTATTTT 57.073 29.630 0.00 0.00 0.00 1.82
1908 2016 9.927081 AAGGACTATCACCAATCTTCATTATTT 57.073 29.630 0.00 0.00 0.00 1.40
1937 2084 2.058595 GGGTCGCTCAAGGCTAGGA 61.059 63.158 0.00 0.00 39.13 2.94
1938 2085 2.501610 GGGTCGCTCAAGGCTAGG 59.498 66.667 0.00 0.00 39.13 3.02
1946 2093 0.968901 ATACAGTTCGGGGTCGCTCA 60.969 55.000 0.00 0.00 36.13 4.26
1972 2119 3.909427 ATTCCAGTGCCCAATATGGAT 57.091 42.857 0.00 0.00 40.96 3.41
1999 2146 2.087646 GTCCAAGGATTCTGCAACTCC 58.912 52.381 0.00 0.00 0.00 3.85
2002 2149 2.087646 GAGGTCCAAGGATTCTGCAAC 58.912 52.381 0.00 0.00 0.00 4.17
2012 2159 4.401925 AGTCTTTTTGATGAGGTCCAAGG 58.598 43.478 0.00 0.00 0.00 3.61
2025 2172 5.316987 AGATAGTGGTTGGGAGTCTTTTTG 58.683 41.667 0.00 0.00 0.00 2.44
2032 2179 3.474798 TGAGAGATAGTGGTTGGGAGT 57.525 47.619 0.00 0.00 0.00 3.85
2125 2272 5.841957 AACAAATGAGCTTTCACAACTCT 57.158 34.783 0.00 0.00 0.00 3.24
2148 2295 8.244113 GCTTATTATGCTAAAGTTGTTTGGTCT 58.756 33.333 0.00 0.00 0.00 3.85
2175 2322 5.573337 TTCCAATTTGCTTTTGTTTTGGG 57.427 34.783 0.00 0.00 35.44 4.12
2176 2323 5.036090 GCTTCCAATTTGCTTTTGTTTTGG 58.964 37.500 0.00 0.00 35.93 3.28
2196 2343 6.151817 GGTTGAATAGAAAAGATGGAGTGCTT 59.848 38.462 0.00 0.00 0.00 3.91
2235 2382 1.748493 TGATGCAAAAGGGCGTAATCC 59.252 47.619 0.00 0.00 36.28 3.01
2278 2466 5.519808 AGGAGATACTAGATGGTGTTCACA 58.480 41.667 0.00 0.00 0.00 3.58
2284 2472 6.072175 GCTAGACAAGGAGATACTAGATGGTG 60.072 46.154 0.00 0.00 34.36 4.17
2313 2501 0.926846 GCTCGCATCAACAGACTAGC 59.073 55.000 0.00 0.00 0.00 3.42
2329 2517 7.759886 GGGTGAAATATTTACAAAAAGAGGCTC 59.240 37.037 6.34 6.34 0.00 4.70
2366 2554 9.097257 ACACAATTGACAAAAATACTTTGGAAG 57.903 29.630 13.59 0.00 33.92 3.46
2380 2568 3.371285 TCGTCGAAACACACAATTGACAA 59.629 39.130 13.59 0.00 0.00 3.18
2384 2572 3.279950 CTGTCGTCGAAACACACAATTG 58.720 45.455 3.24 3.24 0.00 2.32
2408 2703 0.109132 CTTTCCACGGCCATTGCTTC 60.109 55.000 2.24 0.00 37.74 3.86
2418 2713 5.649557 TGAAAAATATCATGCTTTCCACGG 58.350 37.500 0.00 0.00 0.00 4.94
2477 2772 1.800586 GACGCAGCTTGAAACATGAGA 59.199 47.619 0.00 0.00 0.00 3.27
2487 2782 2.838386 AAAGCATATGACGCAGCTTG 57.162 45.000 6.97 0.00 45.73 4.01
2508 2803 1.237954 TGATGCAGCGCGGGTAAAAA 61.238 50.000 8.83 0.00 0.00 1.94
2509 2804 1.029408 ATGATGCAGCGCGGGTAAAA 61.029 50.000 8.83 0.00 0.00 1.52
2510 2805 0.179070 TATGATGCAGCGCGGGTAAA 60.179 50.000 8.83 0.00 0.00 2.01
2511 2806 0.034756 ATATGATGCAGCGCGGGTAA 59.965 50.000 8.83 0.00 0.00 2.85
2512 2807 0.670239 CATATGATGCAGCGCGGGTA 60.670 55.000 8.83 2.09 0.00 3.69
2513 2808 1.962822 CATATGATGCAGCGCGGGT 60.963 57.895 8.83 0.00 0.00 5.28
2514 2809 2.865308 CATATGATGCAGCGCGGG 59.135 61.111 8.83 3.39 0.00 6.13
2523 2818 3.945921 CCTATGAGGGCAAGCATATGATG 59.054 47.826 6.97 5.75 0.00 3.07
2524 2819 4.232188 CCTATGAGGGCAAGCATATGAT 57.768 45.455 6.97 0.00 0.00 2.45
2525 2820 3.708403 CCTATGAGGGCAAGCATATGA 57.292 47.619 6.97 0.00 0.00 2.15
2545 2840 7.985634 TCTTTACAAGTTGTCAATTTCAAGC 57.014 32.000 12.82 0.00 0.00 4.01
2571 2866 8.668353 CAAAGTTAGCTCTTGTAATGCATCTTA 58.332 33.333 0.00 0.00 0.00 2.10
2602 2897 7.011763 CACCACATCAAAGATACTACATCTTGG 59.988 40.741 0.49 0.00 38.29 3.61
2619 2914 6.876789 ACGATTTATTTGTCTACACCACATCA 59.123 34.615 0.00 0.00 0.00 3.07
2625 2920 6.148150 TGTGGAACGATTTATTTGTCTACACC 59.852 38.462 0.00 0.00 42.39 4.16
2637 2932 3.816523 GTGGAAGGTTGTGGAACGATTTA 59.183 43.478 0.00 0.00 42.39 1.40
2642 2937 0.812412 ACGTGGAAGGTTGTGGAACG 60.812 55.000 0.00 0.00 42.39 3.95
2643 2938 1.385528 AACGTGGAAGGTTGTGGAAC 58.614 50.000 0.00 0.00 44.19 3.62
2644 2939 3.886324 AACGTGGAAGGTTGTGGAA 57.114 47.368 0.00 0.00 44.19 3.53
2651 2946 2.151202 CTGTAATGCAACGTGGAAGGT 58.849 47.619 0.00 0.00 35.82 3.50
2652 2947 2.151202 ACTGTAATGCAACGTGGAAGG 58.849 47.619 0.00 0.00 0.00 3.46
2653 2948 5.545658 AATACTGTAATGCAACGTGGAAG 57.454 39.130 0.00 0.00 0.00 3.46
2654 2949 5.950758 AAATACTGTAATGCAACGTGGAA 57.049 34.783 0.00 0.00 0.00 3.53
2655 2950 5.950758 AAAATACTGTAATGCAACGTGGA 57.049 34.783 0.00 0.00 0.00 4.02
2756 3051 5.356751 CGGAGGGTTGTGATTATTCATCAAA 59.643 40.000 0.00 0.00 43.93 2.69
2796 3091 2.401967 GCGCATTGAAGCCTCTGAT 58.598 52.632 0.30 0.00 0.00 2.90
2805 3100 4.713735 TCTGGCCGGCGCATTGAA 62.714 61.111 22.54 0.00 36.38 2.69
3104 3399 2.261671 CTGTCTTCCACCGGTCCG 59.738 66.667 2.59 3.60 0.00 4.79
3134 3429 5.872070 GGTGTTAGTCATCTCCTGAAAGAAG 59.128 44.000 0.00 0.00 35.07 2.85
3158 3453 3.835790 TTGGTTTGTCGGGGGAGCG 62.836 63.158 0.00 0.00 0.00 5.03
3190 3485 7.447374 TCGTAAATGTTGTTGAAATCTCCAT 57.553 32.000 0.00 0.00 0.00 3.41
3212 3507 0.878523 TGTTCTTGTCCCGTGCTTCG 60.879 55.000 0.00 0.00 39.52 3.79
3299 3594 6.801377 TGTATCGTCTGTTTTTGCATTTGATC 59.199 34.615 0.00 0.00 0.00 2.92
3454 3749 0.317436 CGCGCAAGTAAGCACCAAAA 60.317 50.000 8.75 0.00 41.68 2.44


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

AutoCloner maintained by Alex Coulton.