Multiple sequence alignment - TraesCS3A01G365800

Loading Multiple Alignment...

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 TraesCS3A01G365800 chr3A 100.000 5962 0 0 1 5962 614764877 614758916 0.000000e+00 11010.0
1 TraesCS3A01G365800 chr3A 97.297 111 2 1 5472 5582 90878057 90877948 2.840000e-43 187.0
2 TraesCS3A01G365800 chr3D 96.891 2991 73 8 2501 5475 472404827 472401841 0.000000e+00 4990.0
3 TraesCS3A01G365800 chr3D 88.465 1231 63 33 645 1848 472406808 472405630 0.000000e+00 1413.0
4 TraesCS3A01G365800 chr3D 96.606 383 12 1 5580 5962 472401843 472401462 8.430000e-178 634.0
5 TraesCS3A01G365800 chr3D 85.137 619 48 17 1873 2460 472405425 472404820 1.430000e-165 593.0
6 TraesCS3A01G365800 chr3B 93.538 3064 161 20 2307 5355 627909599 627906558 0.000000e+00 4527.0
7 TraesCS3A01G365800 chr3B 85.915 1569 88 56 645 2161 627911414 627909927 0.000000e+00 1550.0
8 TraesCS3A01G365800 chr3B 93.590 312 20 0 5651 5962 627906457 627906146 3.250000e-127 466.0
9 TraesCS3A01G365800 chr3B 97.248 109 2 1 5473 5581 373883179 373883286 3.670000e-42 183.0
10 TraesCS3A01G365800 chr3B 94.737 114 4 2 5472 5584 561100853 561100965 6.140000e-40 176.0
11 TraesCS3A01G365800 chrUn 98.913 644 5 2 1 644 959211 959852 0.000000e+00 1149.0
12 TraesCS3A01G365800 chrUn 90.698 301 20 3 4 302 49293864 49293570 1.560000e-105 394.0
13 TraesCS3A01G365800 chrUn 90.365 301 21 3 4 302 49288424 49288130 7.250000e-104 388.0
14 TraesCS3A01G365800 chr1A 98.913 644 3 3 1 644 517864375 517865014 0.000000e+00 1147.0
15 TraesCS3A01G365800 chr1B 92.359 301 16 2 3 301 130548695 130548990 7.140000e-114 422.0
16 TraesCS3A01G365800 chr1B 91.447 304 19 2 1 302 211993308 211993010 1.550000e-110 411.0
17 TraesCS3A01G365800 chr7B 91.475 305 18 3 1 303 589684849 589685147 4.300000e-111 412.0
18 TraesCS3A01G365800 chr7B 79.909 219 26 7 439 648 649010833 649010624 1.730000e-30 145.0
19 TraesCS3A01G365800 chr4A 91.148 305 20 2 2 304 675158019 675158318 2.000000e-109 407.0
20 TraesCS3A01G365800 chr4A 91.148 305 20 2 2 304 675180819 675181118 2.000000e-109 407.0
21 TraesCS3A01G365800 chr5A 95.263 190 8 1 251 440 622116148 622116336 3.490000e-77 300.0
22 TraesCS3A01G365800 chr5A 95.082 183 2 3 257 439 268473697 268473872 1.270000e-71 281.0
23 TraesCS3A01G365800 chr5A 86.531 245 24 5 196 439 282871025 282871261 1.650000e-65 261.0
24 TraesCS3A01G365800 chr5A 80.952 105 18 2 438 542 473087505 473087403 1.380000e-11 82.4
25 TraesCS3A01G365800 chr5A 100.000 29 0 0 2221 2249 694968224 694968196 3.000000e-03 54.7
26 TraesCS3A01G365800 chr6A 94.054 185 8 3 257 440 595606512 595606694 1.640000e-70 278.0
27 TraesCS3A01G365800 chr6A 94.022 184 4 4 256 439 602185244 602185068 7.610000e-69 272.0
28 TraesCS3A01G365800 chr6A 91.795 195 9 4 256 450 602212266 602212453 1.270000e-66 265.0
29 TraesCS3A01G365800 chr6A 98.165 109 1 1 5473 5581 596198536 596198643 7.890000e-44 189.0
30 TraesCS3A01G365800 chr6A 95.614 114 4 1 5473 5586 116959498 116959610 1.320000e-41 182.0
31 TraesCS3A01G365800 chr7A 93.583 187 8 2 257 440 27668063 27667878 5.890000e-70 276.0
32 TraesCS3A01G365800 chr1D 84.804 204 23 7 442 644 470823292 470823488 1.310000e-46 198.0
33 TraesCS3A01G365800 chr2A 84.466 206 23 6 440 645 4990574 4990770 1.700000e-45 195.0
34 TraesCS3A01G365800 chr4B 97.345 113 1 2 5470 5581 621806 621917 2.190000e-44 191.0
35 TraesCS3A01G365800 chr2B 98.165 109 1 1 5473 5581 464021415 464021308 7.890000e-44 189.0
36 TraesCS3A01G365800 chr2B 95.726 117 4 1 5465 5581 146718127 146718012 2.840000e-43 187.0
37 TraesCS3A01G365800 chr6B 97.248 109 2 1 5473 5581 460906194 460906301 3.670000e-42 183.0
38 TraesCS3A01G365800 chr5B 81.019 216 23 8 438 644 382762806 382762600 8.000000e-34 156.0
39 TraesCS3A01G365800 chr4D 81.019 216 17 10 438 644 348129663 348129463 3.720000e-32 150.0
40 TraesCS3A01G365800 chr4D 87.179 117 8 2 529 645 425152035 425152144 6.270000e-25 126.0
41 TraesCS3A01G365800 chr4D 88.889 72 3 3 571 642 495988311 495988377 3.830000e-12 84.2
42 TraesCS3A01G365800 chr4D 100.000 29 0 0 2221 2249 508679413 508679385 3.000000e-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 TraesCS3A01G365800 chr3A 614758916 614764877 5961 True 11010.0 11010 100.000000 1 5962 1 chr3A.!!$R2 5961
1 TraesCS3A01G365800 chr3D 472401462 472406808 5346 True 1907.5 4990 91.774750 645 5962 4 chr3D.!!$R1 5317
2 TraesCS3A01G365800 chr3B 627906146 627911414 5268 True 2181.0 4527 91.014333 645 5962 3 chr3B.!!$R1 5317
3 TraesCS3A01G365800 chrUn 959211 959852 641 False 1149.0 1149 98.913000 1 644 1 chrUn.!!$F1 643
4 TraesCS3A01G365800 chr1A 517864375 517865014 639 False 1147.0 1147 98.913000 1 644 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
768 794 2.607038 GCGCAACTTTTAACTTCCCCTG 60.607 50.000 0.30 0.00 0.00 4.45 F
1513 1574 0.030638 GCCAAGTTCGCTGCAGAAAA 59.969 50.000 20.43 7.56 0.00 2.29 F
2291 2672 0.320374 CGAGAGGGTGGTGTAAAGCA 59.680 55.000 0.00 0.00 0.00 3.91 F
2600 3090 0.940126 CCGCTGATTGGACAGTATGC 59.060 55.000 0.00 0.00 42.53 3.14 F
3451 3950 0.770499 TGATTGTGGACTCCTTGCCA 59.230 50.000 0.00 0.00 0.00 4.92 F
4003 4502 1.272490 CTAACACGTCAGGAGGCAGAA 59.728 52.381 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 3203 0.035152 TCGCAGCTGGGAACATCATT 60.035 50.000 29.22 0.00 41.51 2.57 R
2716 3206 0.179062 AGATCGCAGCTGGGAACATC 60.179 55.000 33.68 26.07 41.51 3.06 R
3451 3950 1.629043 TCGACCTTCTGTAAGCTGGT 58.371 50.000 0.00 0.00 40.83 4.00 R
3576 4075 2.499289 AGAAGTCCATCATCGTTCAGCT 59.501 45.455 0.00 0.00 0.00 4.24 R
4618 5117 1.601171 CTCCTCTTGCCTGGGACTG 59.399 63.158 0.00 0.00 0.00 3.51 R
5518 6031 0.316204 GACAACATGCAAAGCAGCCT 59.684 50.000 0.00 0.00 43.65 4.58 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
42 43 2.786512 GATGTTTGGGAGGGCAGGCA 62.787 60.000 0.00 0.00 0.00 4.75
593 594 3.771798 TGTTGCCGTTGGTTAGTTTTTC 58.228 40.909 0.00 0.00 0.00 2.29
669 670 4.143179 GGAAAGGCGATCGATATAAAACGG 60.143 45.833 21.57 0.00 0.00 4.44
718 723 2.653702 CGAGCGAGGGATCCATCC 59.346 66.667 20.33 12.93 46.41 3.51
768 794 2.607038 GCGCAACTTTTAACTTCCCCTG 60.607 50.000 0.30 0.00 0.00 4.45
962 995 3.826754 CAGCTAGCGAGGCGTCCA 61.827 66.667 9.55 0.00 34.52 4.02
1024 1072 2.026169 ACCGATCGATCAGGCTCCTATA 60.026 50.000 25.99 0.00 0.00 1.31
1025 1073 3.218453 CCGATCGATCAGGCTCCTATAT 58.782 50.000 24.40 0.00 0.00 0.86
1028 1076 4.578516 CGATCGATCAGGCTCCTATATTCT 59.421 45.833 24.40 0.00 0.00 2.40
1029 1077 5.067153 CGATCGATCAGGCTCCTATATTCTT 59.933 44.000 24.40 0.00 0.00 2.52
1039 1088 1.641577 CTATATTCTTAGCCCGCGCC 58.358 55.000 0.00 0.00 34.57 6.53
1210 1271 2.741211 GGGCGTTGTTCTCCGTCC 60.741 66.667 0.00 0.00 42.17 4.79
1490 1551 3.505184 CCCGCGCGGCTTATTGTT 61.505 61.111 42.39 0.00 0.00 2.83
1491 1552 2.174969 CCCGCGCGGCTTATTGTTA 61.175 57.895 42.39 0.00 0.00 2.41
1504 1565 0.519961 ATTGTTACCGCCAAGTTCGC 59.480 50.000 0.00 0.00 0.00 4.70
1509 1570 4.093952 CCGCCAAGTTCGCTGCAG 62.094 66.667 10.11 10.11 0.00 4.41
1513 1574 0.030638 GCCAAGTTCGCTGCAGAAAA 59.969 50.000 20.43 7.56 0.00 2.29
1514 1575 1.535860 GCCAAGTTCGCTGCAGAAAAA 60.536 47.619 20.43 4.73 0.00 1.94
1567 1628 3.643159 CACCGCATGCACTAGTATAGA 57.357 47.619 19.57 0.00 42.77 1.98
1568 1629 3.309388 CACCGCATGCACTAGTATAGAC 58.691 50.000 19.57 0.00 42.77 2.59
1569 1630 3.004839 CACCGCATGCACTAGTATAGACT 59.995 47.826 19.57 0.00 42.77 3.24
1570 1631 4.215613 CACCGCATGCACTAGTATAGACTA 59.784 45.833 19.57 0.00 42.77 2.59
1571 1632 5.010933 ACCGCATGCACTAGTATAGACTAT 58.989 41.667 19.57 0.00 42.77 2.12
1572 1633 6.093633 CACCGCATGCACTAGTATAGACTATA 59.906 42.308 19.57 0.00 42.77 1.31
1573 1634 6.316640 ACCGCATGCACTAGTATAGACTATAG 59.683 42.308 19.57 0.00 42.77 1.31
1756 1824 1.135141 CACGCAAGAGAGGAGAAGAGG 60.135 57.143 0.00 0.00 43.62 3.69
1795 1873 2.551270 GCGTTCAGCCGTTCACAG 59.449 61.111 0.00 0.00 40.81 3.66
1796 1874 2.551270 CGTTCAGCCGTTCACAGC 59.449 61.111 0.00 0.00 0.00 4.40
1797 1875 2.946762 GTTCAGCCGTTCACAGCC 59.053 61.111 0.00 0.00 0.00 4.85
1798 1876 1.891919 GTTCAGCCGTTCACAGCCA 60.892 57.895 0.00 0.00 0.00 4.75
1822 1900 1.667154 CTCAGGCCGTAGCAGTAGCA 61.667 60.000 0.00 0.00 45.49 3.49
1824 1902 0.877649 CAGGCCGTAGCAGTAGCATG 60.878 60.000 0.00 0.00 45.49 4.06
1834 1912 3.545703 AGCAGTAGCATGGTTGTATTCC 58.454 45.455 1.12 0.00 45.49 3.01
1848 1926 4.746535 TGTATTCCTGCCGTAGAATCAA 57.253 40.909 0.00 0.00 34.60 2.57
1850 1928 5.492895 TGTATTCCTGCCGTAGAATCAAAA 58.507 37.500 0.00 0.00 34.60 2.44
1851 2115 4.965119 ATTCCTGCCGTAGAATCAAAAC 57.035 40.909 0.00 0.00 0.00 2.43
1852 2116 2.343101 TCCTGCCGTAGAATCAAAACG 58.657 47.619 0.00 0.00 36.42 3.60
1856 2120 1.266891 GCCGTAGAATCAAAACGAGCG 60.267 52.381 4.74 0.00 38.89 5.03
1863 2127 5.000012 AGAATCAAAACGAGCGAGTAGAT 58.000 39.130 0.00 0.00 0.00 1.98
1864 2128 6.132791 AGAATCAAAACGAGCGAGTAGATA 57.867 37.500 0.00 0.00 0.00 1.98
1867 2131 4.906423 TCAAAACGAGCGAGTAGATAGAC 58.094 43.478 0.00 0.00 0.00 2.59
1868 2132 3.589061 AAACGAGCGAGTAGATAGACG 57.411 47.619 0.00 0.00 0.00 4.18
1870 2134 2.396601 ACGAGCGAGTAGATAGACGAG 58.603 52.381 0.00 0.00 0.00 4.18
1871 2135 2.223782 ACGAGCGAGTAGATAGACGAGT 60.224 50.000 0.00 0.00 0.00 4.18
1872 2136 3.004210 ACGAGCGAGTAGATAGACGAGTA 59.996 47.826 0.00 0.00 0.00 2.59
1873 2137 3.605056 CGAGCGAGTAGATAGACGAGTAG 59.395 52.174 0.00 0.00 0.00 2.57
1874 2138 4.549458 GAGCGAGTAGATAGACGAGTAGT 58.451 47.826 0.00 0.00 0.00 2.73
1875 2139 5.616645 CGAGCGAGTAGATAGACGAGTAGTA 60.617 48.000 0.00 0.00 0.00 1.82
1876 2140 5.460646 AGCGAGTAGATAGACGAGTAGTAC 58.539 45.833 0.00 0.00 0.00 2.73
1893 2157 7.466746 AGTAGTACGTACAAAATACCCTTCA 57.533 36.000 26.55 0.00 33.55 3.02
1894 2158 7.542025 AGTAGTACGTACAAAATACCCTTCAG 58.458 38.462 26.55 0.00 33.55 3.02
1897 2161 4.828829 ACGTACAAAATACCCTTCAGAGG 58.171 43.478 0.00 0.00 43.15 3.69
1901 2165 4.663334 ACAAAATACCCTTCAGAGGTTCC 58.337 43.478 0.00 0.00 41.85 3.62
1907 2171 1.301293 CTTCAGAGGTTCCAGGGGC 59.699 63.158 0.00 0.00 0.00 5.80
2047 2312 8.055279 TCCTTTTTCCTGTGTATTCATGATTC 57.945 34.615 0.00 0.00 0.00 2.52
2048 2313 6.968904 CCTTTTTCCTGTGTATTCATGATTCG 59.031 38.462 0.00 0.00 0.00 3.34
2081 2346 2.351350 CCCCGTTGGAAAATTCAACTCG 60.351 50.000 6.86 0.00 41.47 4.18
2085 2350 4.403453 CGTTGGAAAATTCAACTCGATCC 58.597 43.478 6.86 0.00 41.47 3.36
2089 2354 2.038387 AAATTCAACTCGATCCGGGG 57.962 50.000 0.00 0.00 0.00 5.73
2120 2390 1.006162 GGTGGTTTAAGGCCATGGGTA 59.994 52.381 15.13 0.00 38.40 3.69
2189 2459 3.874543 TGCAACGACACTTGTAGAAACAT 59.125 39.130 0.00 0.00 34.97 2.71
2192 2462 5.176958 GCAACGACACTTGTAGAAACATACT 59.823 40.000 0.00 0.00 34.97 2.12
2211 2481 3.326747 ACTGTCAATTTCTACTGTCGCC 58.673 45.455 0.00 0.00 0.00 5.54
2213 2483 2.029739 TGTCAATTTCTACTGTCGCCGA 60.030 45.455 0.00 0.00 0.00 5.54
2218 2497 0.656259 TTCTACTGTCGCCGAGATCG 59.344 55.000 0.00 0.00 39.44 3.69
2235 2514 1.717194 TCGGAAATAAGTGTCGTGGC 58.283 50.000 0.00 0.00 0.00 5.01
2256 2637 5.158494 GGCTTTACTTCAAATTAACCACGG 58.842 41.667 0.00 0.00 0.00 4.94
2272 2653 1.597663 CACGGCACTTATTTCCGATCC 59.402 52.381 6.91 0.00 45.53 3.36
2276 2657 2.223971 GGCACTTATTTCCGATCCGAGA 60.224 50.000 0.00 0.00 0.00 4.04
2291 2672 0.320374 CGAGAGGGTGGTGTAAAGCA 59.680 55.000 0.00 0.00 0.00 3.91
2296 2677 3.393278 AGAGGGTGGTGTAAAGCAGTTTA 59.607 43.478 0.00 0.00 0.00 2.01
2356 2843 4.314440 AGGCGCCGAGTTCTGCAA 62.314 61.111 23.20 0.00 0.00 4.08
2364 2851 2.095059 GCCGAGTTCTGCAAATGAACAT 60.095 45.455 16.81 5.05 44.30 2.71
2383 2871 3.775316 ACATAACACTGGAGGTTCCTAGG 59.225 47.826 0.82 0.82 37.46 3.02
2384 2872 1.657804 AACACTGGAGGTTCCTAGGG 58.342 55.000 9.46 0.00 37.46 3.53
2392 2880 2.093075 GGAGGTTCCTAGGGTTGCTTAC 60.093 54.545 9.46 0.00 32.53 2.34
2403 2891 4.395625 AGGGTTGCTTACTCTACAAAACC 58.604 43.478 0.00 0.00 35.16 3.27
2432 2922 6.814146 ACATAAGCTTCTAGGAAAAGAGAACG 59.186 38.462 0.00 0.00 0.00 3.95
2454 2944 1.078848 GTGCTGCATTCTCTCCGGT 60.079 57.895 5.27 0.00 0.00 5.28
2470 2960 6.662234 TCTCTCCGGTCTACAAAGAGAAAATA 59.338 38.462 12.90 0.00 39.49 1.40
2600 3090 0.940126 CCGCTGATTGGACAGTATGC 59.060 55.000 0.00 0.00 42.53 3.14
2602 3092 1.596260 CGCTGATTGGACAGTATGCAG 59.404 52.381 0.00 0.00 42.53 4.41
2676 3166 3.719268 TGATGTAGCAGAATGGGTGTT 57.281 42.857 0.00 0.00 35.86 3.32
2766 3259 7.530861 CGTCTAGTTTTGTTTAGCTAGCTTTTG 59.469 37.037 24.88 0.00 33.06 2.44
2767 3260 8.343366 GTCTAGTTTTGTTTAGCTAGCTTTTGT 58.657 33.333 24.88 0.00 33.06 2.83
2768 3261 8.899771 TCTAGTTTTGTTTAGCTAGCTTTTGTT 58.100 29.630 24.88 0.00 33.06 2.83
2769 3262 7.755582 AGTTTTGTTTAGCTAGCTTTTGTTG 57.244 32.000 24.88 0.00 0.00 3.33
2789 3282 6.038382 TTGTTGTTCATGCATGAAAAGCAAAT 59.962 30.769 38.56 1.05 45.78 2.32
2819 3312 7.387122 TGTTCAAATGATATGATCAGCTAGCTC 59.613 37.037 16.15 4.71 43.53 4.09
2841 3334 6.561737 TCTGTAGTACTGAAGTTCACTGAG 57.438 41.667 5.39 0.00 0.00 3.35
2861 3354 5.139727 TGAGAACACAAACAGATTCCCAAT 58.860 37.500 0.00 0.00 0.00 3.16
2952 3445 1.480312 CCCCACTTCCACATCCAACAA 60.480 52.381 0.00 0.00 0.00 2.83
3023 3516 4.855531 AGCGTGTAAACTTGACCAAAATC 58.144 39.130 0.00 0.00 0.00 2.17
3026 3519 3.662186 GTGTAAACTTGACCAAAATCGCG 59.338 43.478 0.00 0.00 0.00 5.87
3033 3526 1.539388 TGACCAAAATCGCGATGCTTT 59.461 42.857 24.47 17.28 0.00 3.51
3064 3557 1.481772 ACAAACAATGCAACAGCTGGT 59.518 42.857 19.93 9.19 0.00 4.00
3070 3563 7.093988 ACAAACAATGCAACAGCTGGTTATATA 60.094 33.333 19.93 0.00 37.72 0.86
3139 3632 4.096382 AGTGCACGTTCATGTTTTTCTTCT 59.904 37.500 12.01 0.00 0.00 2.85
3172 3665 7.984617 ACTAAATTTAGAGTCTGAAGATGCCTC 59.015 37.037 27.92 0.00 34.84 4.70
3178 3676 3.172339 AGTCTGAAGATGCCTCAGTTCT 58.828 45.455 0.16 0.00 33.57 3.01
3180 3678 3.056250 GTCTGAAGATGCCTCAGTTCTCA 60.056 47.826 0.16 0.00 33.57 3.27
3187 3685 5.609423 AGATGCCTCAGTTCTCATACATTC 58.391 41.667 0.00 0.00 0.00 2.67
3204 3702 5.221891 ACATTCGTTTGAAATCATCCTCG 57.778 39.130 0.00 0.00 37.71 4.63
3451 3950 0.770499 TGATTGTGGACTCCTTGCCA 59.230 50.000 0.00 0.00 0.00 4.92
3538 4037 3.764972 ACTACTCCAGGAACTACTCAAGC 59.235 47.826 0.00 0.00 36.02 4.01
3593 4092 5.378292 TCTATAGCTGAACGATGATGGAC 57.622 43.478 0.00 0.00 0.00 4.02
3599 4098 4.160439 AGCTGAACGATGATGGACTTCTAA 59.840 41.667 0.00 0.00 0.00 2.10
3894 4393 6.712241 TCTAATATAATTTCGCTGCAGAGC 57.288 37.500 20.43 2.06 42.37 4.09
4003 4502 1.272490 CTAACACGTCAGGAGGCAGAA 59.728 52.381 0.00 0.00 0.00 3.02
4318 4817 2.158943 GGACTACAATGTAGCCCTCCAC 60.159 54.545 19.38 3.87 0.00 4.02
4487 4986 8.236084 TCTACGTGCTAATTCTTTAACTGTTC 57.764 34.615 0.00 0.00 0.00 3.18
4546 5045 6.969043 TGATGAGGGTACAATTACTTGGAAT 58.031 36.000 0.00 0.00 36.64 3.01
4618 5117 4.437239 CATATCAGAGGTTGTCTGGTCAC 58.563 47.826 2.30 0.00 43.91 3.67
4698 5197 3.806316 AACACAAAGGATTTAGCGACG 57.194 42.857 0.00 0.00 35.03 5.12
4900 5404 1.678101 GTTCTTGCATATGGAGGTGGC 59.322 52.381 4.56 0.00 0.00 5.01
4974 5478 5.527582 GGTTATTCAAGTGTAGCGATGGATT 59.472 40.000 0.00 0.00 0.00 3.01
5043 5547 5.663106 ACAGAGGATAGGATTAGCAAGACAA 59.337 40.000 0.00 0.00 0.00 3.18
5152 5656 8.707796 AGGAAGTATCGACTTTATTCAGGATA 57.292 34.615 0.00 0.00 46.23 2.59
5329 5841 7.606349 TCTGTCATCAGATATATTGCAGGTAC 58.394 38.462 0.00 0.00 44.58 3.34
5410 5922 6.184068 TGCTTAGTGGATAGGCATTAAACAA 58.816 36.000 0.00 0.00 41.19 2.83
5481 5994 9.256228 TCACTATGTATTTGATATACTCCCTCC 57.744 37.037 0.00 0.00 0.00 4.30
5482 5995 8.191446 CACTATGTATTTGATATACTCCCTCCG 58.809 40.741 0.00 0.00 0.00 4.63
5483 5996 7.894364 ACTATGTATTTGATATACTCCCTCCGT 59.106 37.037 0.00 0.00 0.00 4.69
5484 5997 6.989155 TGTATTTGATATACTCCCTCCGTT 57.011 37.500 0.00 0.00 0.00 4.44
5485 5998 6.989659 TGTATTTGATATACTCCCTCCGTTC 58.010 40.000 0.00 0.00 0.00 3.95
5486 5999 6.551975 TGTATTTGATATACTCCCTCCGTTCA 59.448 38.462 0.00 0.00 0.00 3.18
5487 6000 4.931661 TTGATATACTCCCTCCGTTCAC 57.068 45.455 0.00 0.00 0.00 3.18
5488 6001 4.180377 TGATATACTCCCTCCGTTCACT 57.820 45.455 0.00 0.00 0.00 3.41
5489 6002 4.543689 TGATATACTCCCTCCGTTCACTT 58.456 43.478 0.00 0.00 0.00 3.16
5490 6003 4.960469 TGATATACTCCCTCCGTTCACTTT 59.040 41.667 0.00 0.00 0.00 2.66
5491 6004 5.424252 TGATATACTCCCTCCGTTCACTTTT 59.576 40.000 0.00 0.00 0.00 2.27
5492 6005 6.608405 TGATATACTCCCTCCGTTCACTTTTA 59.392 38.462 0.00 0.00 0.00 1.52
5493 6006 5.952347 ATACTCCCTCCGTTCACTTTTAT 57.048 39.130 0.00 0.00 0.00 1.40
5494 6007 8.716674 ATATACTCCCTCCGTTCACTTTTATA 57.283 34.615 0.00 0.00 0.00 0.98
5495 6008 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
5496 6009 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
5497 6010 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
5498 6011 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
5499 6012 5.246656 TCCCTCCGTTCACTTTTATAAGTCA 59.753 40.000 0.00 0.00 42.67 3.41
5500 6013 6.070424 TCCCTCCGTTCACTTTTATAAGTCAT 60.070 38.462 0.00 0.00 42.67 3.06
5501 6014 6.598064 CCCTCCGTTCACTTTTATAAGTCATT 59.402 38.462 0.00 0.00 42.67 2.57
5502 6015 7.120726 CCCTCCGTTCACTTTTATAAGTCATTT 59.879 37.037 0.00 0.00 42.67 2.32
5503 6016 8.175716 CCTCCGTTCACTTTTATAAGTCATTTC 58.824 37.037 0.00 0.00 42.67 2.17
5504 6017 8.610248 TCCGTTCACTTTTATAAGTCATTTCA 57.390 30.769 0.00 0.00 42.67 2.69
5505 6018 8.717821 TCCGTTCACTTTTATAAGTCATTTCAG 58.282 33.333 0.00 0.00 42.67 3.02
5506 6019 8.717821 CCGTTCACTTTTATAAGTCATTTCAGA 58.282 33.333 0.00 0.00 42.67 3.27
5507 6020 9.530129 CGTTCACTTTTATAAGTCATTTCAGAC 57.470 33.333 0.00 0.00 42.67 3.51
5511 6024 9.612620 CACTTTTATAAGTCATTTCAGACAACC 57.387 33.333 0.00 0.00 42.67 3.77
5512 6025 8.504005 ACTTTTATAAGTCATTTCAGACAACCG 58.496 33.333 0.00 0.00 40.60 4.44
5513 6026 8.610248 TTTTATAAGTCATTTCAGACAACCGA 57.390 30.769 0.00 0.00 40.98 4.69
5514 6027 8.610248 TTTATAAGTCATTTCAGACAACCGAA 57.390 30.769 0.00 0.00 40.98 4.30
5515 6028 8.610248 TTATAAGTCATTTCAGACAACCGAAA 57.390 30.769 0.00 0.00 40.98 3.46
5516 6029 5.828299 AAGTCATTTCAGACAACCGAAAA 57.172 34.783 0.00 0.00 40.98 2.29
5517 6030 6.391227 AAGTCATTTCAGACAACCGAAAAT 57.609 33.333 0.00 0.00 40.98 1.82
5518 6031 7.504924 AAGTCATTTCAGACAACCGAAAATA 57.495 32.000 0.00 0.00 40.98 1.40
5519 6032 7.133891 AGTCATTTCAGACAACCGAAAATAG 57.866 36.000 0.00 0.00 40.98 1.73
5520 6033 6.149474 AGTCATTTCAGACAACCGAAAATAGG 59.851 38.462 0.00 0.00 40.98 2.57
5521 6034 4.759516 TTTCAGACAACCGAAAATAGGC 57.240 40.909 0.00 0.00 0.00 3.93
5522 6035 3.695830 TCAGACAACCGAAAATAGGCT 57.304 42.857 0.00 0.00 0.00 4.58
5523 6036 3.334691 TCAGACAACCGAAAATAGGCTG 58.665 45.455 0.00 0.00 0.00 4.85
5524 6037 2.084546 AGACAACCGAAAATAGGCTGC 58.915 47.619 0.00 0.00 0.00 5.25
5525 6038 2.084546 GACAACCGAAAATAGGCTGCT 58.915 47.619 0.00 0.00 0.00 4.24
5526 6039 2.488153 GACAACCGAAAATAGGCTGCTT 59.512 45.455 0.00 0.00 0.00 3.91
5527 6040 2.890945 ACAACCGAAAATAGGCTGCTTT 59.109 40.909 0.00 0.00 0.00 3.51
5528 6041 3.244976 CAACCGAAAATAGGCTGCTTTG 58.755 45.455 0.00 0.00 0.00 2.77
5529 6042 1.202348 ACCGAAAATAGGCTGCTTTGC 59.798 47.619 0.00 0.00 0.00 3.68
5530 6043 1.202114 CCGAAAATAGGCTGCTTTGCA 59.798 47.619 0.00 0.00 36.92 4.08
5531 6044 2.159198 CCGAAAATAGGCTGCTTTGCAT 60.159 45.455 0.00 0.00 38.13 3.96
5532 6045 2.855963 CGAAAATAGGCTGCTTTGCATG 59.144 45.455 0.00 0.00 38.13 4.06
5533 6046 3.674138 CGAAAATAGGCTGCTTTGCATGT 60.674 43.478 0.00 0.00 38.13 3.21
5534 6047 3.967332 AAATAGGCTGCTTTGCATGTT 57.033 38.095 0.00 0.00 38.13 2.71
5535 6048 2.953466 ATAGGCTGCTTTGCATGTTG 57.047 45.000 0.00 0.00 38.13 3.33
5536 6049 1.619654 TAGGCTGCTTTGCATGTTGT 58.380 45.000 0.00 0.00 38.13 3.32
5537 6050 0.316204 AGGCTGCTTTGCATGTTGTC 59.684 50.000 0.00 0.00 38.13 3.18
5538 6051 0.316204 GGCTGCTTTGCATGTTGTCT 59.684 50.000 0.00 0.00 38.13 3.41
5539 6052 1.415374 GCTGCTTTGCATGTTGTCTG 58.585 50.000 0.00 0.00 38.13 3.51
5540 6053 1.001048 GCTGCTTTGCATGTTGTCTGA 60.001 47.619 0.00 0.00 38.13 3.27
5541 6054 2.544277 GCTGCTTTGCATGTTGTCTGAA 60.544 45.455 0.00 0.00 38.13 3.02
5542 6055 3.708890 CTGCTTTGCATGTTGTCTGAAA 58.291 40.909 0.00 0.00 38.13 2.69
5543 6056 4.304110 CTGCTTTGCATGTTGTCTGAAAT 58.696 39.130 0.00 0.00 38.13 2.17
5544 6057 4.052608 TGCTTTGCATGTTGTCTGAAATG 58.947 39.130 0.00 0.00 31.71 2.32
5545 6058 4.053295 GCTTTGCATGTTGTCTGAAATGT 58.947 39.130 0.00 0.00 0.00 2.71
5546 6059 4.149396 GCTTTGCATGTTGTCTGAAATGTC 59.851 41.667 0.00 0.00 0.00 3.06
5547 6060 5.518848 TTTGCATGTTGTCTGAAATGTCT 57.481 34.783 0.00 0.00 0.00 3.41
5548 6061 5.518848 TTGCATGTTGTCTGAAATGTCTT 57.481 34.783 0.00 0.00 0.00 3.01
5549 6062 5.112220 TGCATGTTGTCTGAAATGTCTTC 57.888 39.130 0.00 0.00 0.00 2.87
5550 6063 4.022935 TGCATGTTGTCTGAAATGTCTTCC 60.023 41.667 0.00 0.00 0.00 3.46
5551 6064 4.022935 GCATGTTGTCTGAAATGTCTTCCA 60.023 41.667 0.00 0.00 0.00 3.53
5552 6065 5.507817 GCATGTTGTCTGAAATGTCTTCCAA 60.508 40.000 0.00 0.00 0.00 3.53
5553 6066 5.756195 TGTTGTCTGAAATGTCTTCCAAG 57.244 39.130 0.00 0.00 0.00 3.61
5554 6067 4.580167 TGTTGTCTGAAATGTCTTCCAAGG 59.420 41.667 0.00 0.00 0.00 3.61
5555 6068 4.705110 TGTCTGAAATGTCTTCCAAGGA 57.295 40.909 0.00 0.00 0.00 3.36
5556 6069 4.389374 TGTCTGAAATGTCTTCCAAGGAC 58.611 43.478 0.00 0.00 0.00 3.85
5557 6070 4.103153 TGTCTGAAATGTCTTCCAAGGACT 59.897 41.667 0.00 0.00 35.04 3.85
5558 6071 5.066593 GTCTGAAATGTCTTCCAAGGACTT 58.933 41.667 0.00 0.00 35.04 3.01
5559 6072 6.183361 TGTCTGAAATGTCTTCCAAGGACTTA 60.183 38.462 0.00 0.00 35.04 2.24
5560 6073 6.881602 GTCTGAAATGTCTTCCAAGGACTTAT 59.118 38.462 0.00 0.00 35.04 1.73
5561 6074 8.041323 GTCTGAAATGTCTTCCAAGGACTTATA 58.959 37.037 0.00 0.00 35.04 0.98
5562 6075 8.602424 TCTGAAATGTCTTCCAAGGACTTATAA 58.398 33.333 0.00 0.00 35.04 0.98
5563 6076 9.231297 CTGAAATGTCTTCCAAGGACTTATAAA 57.769 33.333 0.00 0.00 35.04 1.40
5564 6077 9.581289 TGAAATGTCTTCCAAGGACTTATAAAA 57.419 29.630 0.00 0.00 35.04 1.52
5567 6080 7.979444 TGTCTTCCAAGGACTTATAAAAGTG 57.021 36.000 0.00 0.00 46.09 3.16
5568 6081 7.741785 TGTCTTCCAAGGACTTATAAAAGTGA 58.258 34.615 0.00 0.00 46.09 3.41
5569 6082 8.215050 TGTCTTCCAAGGACTTATAAAAGTGAA 58.785 33.333 0.00 0.00 46.09 3.18
5570 6083 8.504815 GTCTTCCAAGGACTTATAAAAGTGAAC 58.495 37.037 0.00 0.00 46.09 3.18
5571 6084 8.215050 TCTTCCAAGGACTTATAAAAGTGAACA 58.785 33.333 0.00 0.00 46.09 3.18
5572 6085 7.979444 TCCAAGGACTTATAAAAGTGAACAG 57.021 36.000 0.00 0.00 46.09 3.16
5573 6086 7.741785 TCCAAGGACTTATAAAAGTGAACAGA 58.258 34.615 0.00 0.00 46.09 3.41
5574 6087 7.878127 TCCAAGGACTTATAAAAGTGAACAGAG 59.122 37.037 0.00 0.00 46.09 3.35
5575 6088 7.119846 CCAAGGACTTATAAAAGTGAACAGAGG 59.880 40.741 0.00 0.00 46.09 3.69
5576 6089 6.712276 AGGACTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 46.09 4.30
5577 6090 6.500751 AGGACTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 46.09 4.20
5578 6091 6.819146 GGACTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 46.09 4.30
5579 6092 7.317722 ACTTATAAAAGTGAACAGAGGGAGT 57.682 36.000 0.00 0.00 44.40 3.85
5580 6093 8.431910 ACTTATAAAAGTGAACAGAGGGAGTA 57.568 34.615 0.00 0.00 44.40 2.59
5581 6094 8.312564 ACTTATAAAAGTGAACAGAGGGAGTAC 58.687 37.037 0.00 0.00 44.40 2.73
5582 6095 6.681729 ATAAAAGTGAACAGAGGGAGTACA 57.318 37.500 0.00 0.00 0.00 2.90
5583 6096 5.367945 AAAAGTGAACAGAGGGAGTACAA 57.632 39.130 0.00 0.00 0.00 2.41
5584 6097 5.568620 AAAGTGAACAGAGGGAGTACAAT 57.431 39.130 0.00 0.00 0.00 2.71
5585 6098 6.681729 AAAGTGAACAGAGGGAGTACAATA 57.318 37.500 0.00 0.00 0.00 1.90
5617 6136 8.668510 TCATCAGGCAATATAAGTCTTTCTTC 57.331 34.615 0.00 0.00 37.56 2.87
5620 6139 6.535150 TCAGGCAATATAAGTCTTTCTTCACG 59.465 38.462 0.00 0.00 37.56 4.35
5645 6165 6.015772 GGGCACATTTTCCTACTGAAGTTTAA 60.016 38.462 0.00 0.00 33.63 1.52
5648 6168 9.129209 GCACATTTTCCTACTGAAGTTTAAATC 57.871 33.333 0.00 0.00 33.63 2.17
5816 6336 8.668510 TCCTTCATCAGAAATGATTTACTAGC 57.331 34.615 0.00 0.00 32.35 3.42
5914 6434 0.036388 CGGCACCAATAGTCCACTGT 60.036 55.000 0.00 0.00 0.00 3.55
5953 6473 3.728385 ACAGCAAATCTTAGCTCCCTT 57.272 42.857 0.00 0.00 39.50 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
490 491 9.884636 ACAAAGTACACATATGATTAGCAGTAA 57.115 29.630 10.38 0.00 0.00 2.24
612 613 3.782523 AGCTTGACAAGAATCTATGGGGA 59.217 43.478 19.51 0.00 0.00 4.81
739 744 2.123988 TAAAAGTTGCGCGCTGGGTG 62.124 55.000 33.29 0.35 0.00 4.61
943 976 4.200283 GACGCCTCGCTAGCTGCT 62.200 66.667 13.93 7.57 40.11 4.24
961 994 1.762222 GAATCAATCGGACGCGGGTG 61.762 60.000 10.96 0.00 0.00 4.61
962 995 1.520787 GAATCAATCGGACGCGGGT 60.521 57.895 12.47 4.12 0.00 5.28
1024 1072 2.109181 GAGGCGCGGGCTAAGAAT 59.891 61.111 24.48 3.64 38.98 2.40
1025 1073 4.508128 CGAGGCGCGGGCTAAGAA 62.508 66.667 24.48 0.00 38.98 2.52
1210 1271 2.105128 CTTGCCGTAGCTCCTCCG 59.895 66.667 0.00 0.00 40.80 4.63
1489 1550 2.322081 GCAGCGAACTTGGCGGTAA 61.322 57.895 0.00 0.00 37.75 2.85
1490 1551 2.740826 GCAGCGAACTTGGCGGTA 60.741 61.111 0.00 0.00 37.75 4.02
1491 1552 4.927782 TGCAGCGAACTTGGCGGT 62.928 61.111 0.00 0.00 40.43 5.68
1513 1574 4.159506 TGTGCTCTGGTTTTTAGCTTGTTT 59.840 37.500 0.00 0.00 37.16 2.83
1514 1575 3.699038 TGTGCTCTGGTTTTTAGCTTGTT 59.301 39.130 0.00 0.00 37.16 2.83
1515 1576 3.066760 GTGTGCTCTGGTTTTTAGCTTGT 59.933 43.478 0.00 0.00 37.16 3.16
1546 1607 6.575400 AGTCTATACTAGTGCATGCGGTGC 62.575 50.000 14.09 6.92 43.86 5.01
1567 1628 8.459911 AACAAAACCAAAAGTGCTACTATAGT 57.540 30.769 10.87 10.87 0.00 2.12
1571 1632 9.356433 GTTTTAACAAAACCAAAAGTGCTACTA 57.644 29.630 3.63 0.00 43.78 1.82
1572 1633 7.062488 CGTTTTAACAAAACCAAAAGTGCTACT 59.938 33.333 8.50 0.00 46.12 2.57
1573 1634 7.168138 CGTTTTAACAAAACCAAAAGTGCTAC 58.832 34.615 8.50 0.00 46.12 3.58
1732 1800 2.049156 TCCTCTCTTGCGTGCACG 60.049 61.111 34.01 34.01 43.27 5.34
1734 1802 0.037882 CTTCTCCTCTCTTGCGTGCA 60.038 55.000 0.00 0.00 0.00 4.57
1747 1815 6.472016 AGAAACTTCTCAAATCCTCTTCTCC 58.528 40.000 0.00 0.00 29.94 3.71
1756 1824 3.366374 CCCGCCAAGAAACTTCTCAAATC 60.366 47.826 0.00 0.00 36.28 2.17
1809 1887 1.290203 CAACCATGCTACTGCTACGG 58.710 55.000 0.00 0.00 40.48 4.02
1822 1900 2.769663 TCTACGGCAGGAATACAACCAT 59.230 45.455 0.00 0.00 0.00 3.55
1824 1902 2.973694 TCTACGGCAGGAATACAACC 57.026 50.000 0.00 0.00 0.00 3.77
1834 1912 2.222819 GCTCGTTTTGATTCTACGGCAG 60.223 50.000 0.00 0.00 36.06 4.85
1848 1926 3.193263 TCGTCTATCTACTCGCTCGTTT 58.807 45.455 0.00 0.00 0.00 3.60
1850 1928 2.223782 ACTCGTCTATCTACTCGCTCGT 60.224 50.000 0.00 0.00 0.00 4.18
1851 2115 2.396601 ACTCGTCTATCTACTCGCTCG 58.603 52.381 0.00 0.00 0.00 5.03
1852 2116 4.549458 ACTACTCGTCTATCTACTCGCTC 58.451 47.826 0.00 0.00 0.00 5.03
1856 2120 7.356540 TGTACGTACTACTCGTCTATCTACTC 58.643 42.308 25.12 0.00 41.72 2.59
1863 2127 7.011109 GGGTATTTTGTACGTACTACTCGTCTA 59.989 40.741 25.12 0.00 41.72 2.59
1864 2128 6.183360 GGGTATTTTGTACGTACTACTCGTCT 60.183 42.308 25.12 6.00 41.72 4.18
1867 2131 6.124088 AGGGTATTTTGTACGTACTACTCG 57.876 41.667 25.12 0.00 0.00 4.18
1868 2132 7.538575 TGAAGGGTATTTTGTACGTACTACTC 58.461 38.462 25.12 18.19 0.00 2.59
1870 2134 7.538575 TCTGAAGGGTATTTTGTACGTACTAC 58.461 38.462 25.12 17.97 0.00 2.73
1871 2135 7.148018 CCTCTGAAGGGTATTTTGTACGTACTA 60.148 40.741 25.12 16.12 39.21 1.82
1872 2136 6.350780 CCTCTGAAGGGTATTTTGTACGTACT 60.351 42.308 25.12 8.71 39.21 2.73
1873 2137 5.809051 CCTCTGAAGGGTATTTTGTACGTAC 59.191 44.000 18.90 18.90 39.21 3.67
1874 2138 5.969423 CCTCTGAAGGGTATTTTGTACGTA 58.031 41.667 0.00 0.00 39.21 3.57
1875 2139 4.828829 CCTCTGAAGGGTATTTTGTACGT 58.171 43.478 0.00 0.00 39.21 3.57
1876 2140 5.243207 AACCTCTGAAGGGTATTTTGTACG 58.757 41.667 0.00 0.00 42.48 3.67
1893 2157 3.334054 GCTGCCCCTGGAACCTCT 61.334 66.667 0.00 0.00 0.00 3.69
1894 2158 4.785453 CGCTGCCCCTGGAACCTC 62.785 72.222 0.00 0.00 0.00 3.85
1955 2219 0.110373 CGAAACGAAAAGAAGGGGCG 60.110 55.000 0.00 0.00 0.00 6.13
2081 2346 2.908796 GGAACCACTCCCCGGATC 59.091 66.667 0.73 0.00 38.44 3.36
2120 2390 3.005554 CCTCAACTTGAGCATCGACATT 58.994 45.455 12.69 0.00 42.98 2.71
2189 2459 4.491676 GGCGACAGTAGAAATTGACAGTA 58.508 43.478 0.00 0.00 0.00 2.74
2192 2462 2.029739 TCGGCGACAGTAGAAATTGACA 60.030 45.455 4.99 0.00 0.00 3.58
2211 2481 3.482472 CACGACACTTATTTCCGATCTCG 59.518 47.826 0.00 0.00 39.44 4.04
2213 2483 3.782046 CCACGACACTTATTTCCGATCT 58.218 45.455 0.00 0.00 0.00 2.75
2218 2497 4.694037 AGTAAAGCCACGACACTTATTTCC 59.306 41.667 0.00 0.00 0.00 3.13
2235 2514 5.627780 GTGCCGTGGTTAATTTGAAGTAAAG 59.372 40.000 0.00 0.00 0.00 1.85
2256 2637 3.053455 CTCTCGGATCGGAAATAAGTGC 58.947 50.000 4.39 0.00 0.00 4.40
2272 2653 0.320374 TGCTTTACACCACCCTCTCG 59.680 55.000 0.00 0.00 0.00 4.04
2276 2657 2.748209 AAACTGCTTTACACCACCCT 57.252 45.000 0.00 0.00 0.00 4.34
2318 2805 5.435291 CCTCTGCTGGTCATTTCTATCTTT 58.565 41.667 0.00 0.00 0.00 2.52
2356 2843 5.010282 GGAACCTCCAGTGTTATGTTCATT 58.990 41.667 11.64 0.00 36.28 2.57
2364 2851 2.113052 ACCCTAGGAACCTCCAGTGTTA 59.887 50.000 11.48 0.00 39.61 2.41
2383 2871 5.306394 AGAGGTTTTGTAGAGTAAGCAACC 58.694 41.667 0.00 0.00 33.70 3.77
2384 2872 6.927381 TGTAGAGGTTTTGTAGAGTAAGCAAC 59.073 38.462 0.00 0.00 0.00 4.17
2392 2880 8.254508 AGAAGCTTATGTAGAGGTTTTGTAGAG 58.745 37.037 0.00 0.00 35.20 2.43
2403 2891 8.908903 TCTCTTTTCCTAGAAGCTTATGTAGAG 58.091 37.037 3.25 6.71 0.00 2.43
2432 2922 0.463474 GGAGAGAATGCAGCACTCCC 60.463 60.000 18.87 10.26 40.58 4.30
2491 2981 3.685139 TTGATGTGAGACTCCCACTTC 57.315 47.619 0.00 2.13 38.44 3.01
2645 3135 6.985188 TTCTGCTACATCATTTTCAGGTAC 57.015 37.500 0.00 0.00 0.00 3.34
2676 3166 6.773200 AGAGAATGAACATCGGTATCTGACTA 59.227 38.462 0.00 0.00 0.00 2.59
2712 3202 1.209261 TCGCAGCTGGGAACATCATTA 59.791 47.619 29.22 4.97 41.51 1.90
2713 3203 0.035152 TCGCAGCTGGGAACATCATT 60.035 50.000 29.22 0.00 41.51 2.57
2716 3206 0.179062 AGATCGCAGCTGGGAACATC 60.179 55.000 33.68 26.07 41.51 3.06
2717 3207 0.463295 CAGATCGCAGCTGGGAACAT 60.463 55.000 33.68 19.98 41.51 2.71
2724 3214 2.584418 CGGTCCAGATCGCAGCTG 60.584 66.667 10.11 10.11 0.00 4.24
2766 3259 5.406767 TTTGCTTTTCATGCATGAACAAC 57.593 34.783 35.75 26.30 45.63 3.32
2767 3260 6.930164 AGTATTTGCTTTTCATGCATGAACAA 59.070 30.769 35.75 30.88 45.63 2.83
2768 3261 6.457355 AGTATTTGCTTTTCATGCATGAACA 58.543 32.000 35.75 29.24 45.63 3.18
2769 3262 6.956299 AGTATTTGCTTTTCATGCATGAAC 57.044 33.333 35.75 25.86 45.63 3.18
2789 3282 8.969260 AGCTGATCATATCATTTGAACAAGTA 57.031 30.769 0.00 0.00 38.85 2.24
2819 3312 6.561737 TCTCAGTGAACTTCAGTACTACAG 57.438 41.667 0.00 0.00 0.00 2.74
2841 3334 8.137437 CCATATATTGGGAATCTGTTTGTGTTC 58.863 37.037 0.00 0.00 42.33 3.18
2861 3354 1.749063 CTAGCCGGCATCGTCCATATA 59.251 52.381 31.54 6.89 33.95 0.86
2952 3445 5.374071 AGGTTGAAGGTCGTTAGTTCAAAT 58.626 37.500 0.00 0.00 40.82 2.32
3033 3526 4.836825 TGCATTGTTTGTTCCTGGAAAAA 58.163 34.783 11.40 9.58 0.00 1.94
3064 3557 7.039152 CCACCATTGGCATCAACCATTATATAA 60.039 37.037 1.54 0.00 40.13 0.98
3070 3563 1.555992 CCACCATTGGCATCAACCATT 59.444 47.619 1.54 0.00 40.13 3.16
3172 3665 8.229811 TGATTTCAAACGAATGTATGAGAACTG 58.770 33.333 0.00 0.00 0.00 3.16
3178 3676 7.254421 CGAGGATGATTTCAAACGAATGTATGA 60.254 37.037 0.00 0.00 0.00 2.15
3180 3678 6.511767 GCGAGGATGATTTCAAACGAATGTAT 60.512 38.462 0.00 0.00 0.00 2.29
3187 3685 2.672874 TCTGCGAGGATGATTTCAAACG 59.327 45.455 0.00 0.00 0.00 3.60
3204 3702 2.807967 TGCAACCATATCGCTTATCTGC 59.192 45.455 0.00 0.00 0.00 4.26
3299 3797 9.965902 ATCCTTGTTATTGTTATGAAGAGAAGT 57.034 29.630 0.00 0.00 0.00 3.01
3320 3818 6.996180 TCGGAATAGTTTGATAGGATCCTT 57.004 37.500 22.03 7.92 0.00 3.36
3451 3950 1.629043 TCGACCTTCTGTAAGCTGGT 58.371 50.000 0.00 0.00 40.83 4.00
3538 4037 9.979270 CTTATTTCTAAGCAACTACAATGTCAG 57.021 33.333 0.00 0.00 0.00 3.51
3576 4075 2.499289 AGAAGTCCATCATCGTTCAGCT 59.501 45.455 0.00 0.00 0.00 4.24
3593 4092 5.397142 AGCCTGCAAAAAGGAATTAGAAG 57.603 39.130 0.00 0.00 40.02 2.85
3599 4098 4.835056 AGTAAGAAGCCTGCAAAAAGGAAT 59.165 37.500 0.00 0.00 40.02 3.01
4003 4502 4.343231 TGAGTCTCATTTCTCTCAGCTCT 58.657 43.478 0.00 0.00 33.77 4.09
4466 4965 6.655062 TGTGAACAGTTAAAGAATTAGCACG 58.345 36.000 0.00 0.00 0.00 5.34
4546 5045 6.145371 GTGTTTTCACTTTGCTTTGAAAGTCA 59.855 34.615 6.81 2.64 42.96 3.41
4618 5117 1.601171 CTCCTCTTGCCTGGGACTG 59.399 63.158 0.00 0.00 0.00 3.51
4698 5197 4.081586 CCCACCTCTTTAGAGTAAGTCCAC 60.082 50.000 6.06 0.00 40.48 4.02
4900 5404 6.234177 AGGACAATTAGTGAACCTCTCTTTG 58.766 40.000 0.00 0.00 34.33 2.77
4974 5478 5.215252 ACTCGAAATCTCTTTGTCTTCCA 57.785 39.130 0.00 0.00 0.00 3.53
5043 5547 7.159372 AGTACAAACATGTATCGGAAGTCTTT 58.841 34.615 0.00 0.00 0.00 2.52
5307 5819 7.547370 GGAAGTACCTGCAATATATCTGATGAC 59.453 40.741 0.00 0.00 35.41 3.06
5329 5841 8.713271 GGAATATAGAAGTTTAATGCGAGGAAG 58.287 37.037 0.00 0.00 0.00 3.46
5475 5988 5.246656 TGACTTATAAAAGTGAACGGAGGGA 59.753 40.000 0.00 0.00 46.09 4.20
5476 5989 5.484715 TGACTTATAAAAGTGAACGGAGGG 58.515 41.667 0.00 0.00 46.09 4.30
5477 5990 7.611213 AATGACTTATAAAAGTGAACGGAGG 57.389 36.000 0.00 0.00 46.09 4.30
5478 5991 8.717821 TGAAATGACTTATAAAAGTGAACGGAG 58.282 33.333 0.00 0.00 46.09 4.63
5479 5992 8.610248 TGAAATGACTTATAAAAGTGAACGGA 57.390 30.769 0.00 0.00 46.09 4.69
5480 5993 8.717821 TCTGAAATGACTTATAAAAGTGAACGG 58.282 33.333 0.00 0.00 46.09 4.44
5481 5994 9.530129 GTCTGAAATGACTTATAAAAGTGAACG 57.470 33.333 0.00 0.00 46.09 3.95
5485 5998 9.612620 GGTTGTCTGAAATGACTTATAAAAGTG 57.387 33.333 0.00 0.00 46.09 3.16
5487 6000 8.717821 TCGGTTGTCTGAAATGACTTATAAAAG 58.282 33.333 0.00 0.00 37.79 2.27
5488 6001 8.610248 TCGGTTGTCTGAAATGACTTATAAAA 57.390 30.769 0.00 0.00 37.79 1.52
5489 6002 8.610248 TTCGGTTGTCTGAAATGACTTATAAA 57.390 30.769 0.00 0.00 36.19 1.40
5490 6003 8.610248 TTTCGGTTGTCTGAAATGACTTATAA 57.390 30.769 0.00 0.00 42.02 0.98
5491 6004 8.610248 TTTTCGGTTGTCTGAAATGACTTATA 57.390 30.769 3.58 0.00 44.92 0.98
5492 6005 7.504924 TTTTCGGTTGTCTGAAATGACTTAT 57.495 32.000 3.58 0.00 44.92 1.73
5493 6006 6.928979 TTTTCGGTTGTCTGAAATGACTTA 57.071 33.333 3.58 0.00 44.92 2.24
5494 6007 5.828299 TTTTCGGTTGTCTGAAATGACTT 57.172 34.783 3.58 0.00 44.92 3.01
5495 6008 6.149474 CCTATTTTCGGTTGTCTGAAATGACT 59.851 38.462 3.58 0.00 44.92 3.41
5496 6009 6.314784 CCTATTTTCGGTTGTCTGAAATGAC 58.685 40.000 3.58 0.00 44.92 3.06
5497 6010 5.106317 GCCTATTTTCGGTTGTCTGAAATGA 60.106 40.000 3.58 0.00 44.92 2.57
5498 6011 5.095490 GCCTATTTTCGGTTGTCTGAAATG 58.905 41.667 3.58 0.00 44.92 2.32
5499 6012 5.010282 AGCCTATTTTCGGTTGTCTGAAAT 58.990 37.500 3.58 0.00 44.92 2.17
5500 6013 4.215399 CAGCCTATTTTCGGTTGTCTGAAA 59.785 41.667 0.00 0.00 44.22 2.69
5501 6014 3.751175 CAGCCTATTTTCGGTTGTCTGAA 59.249 43.478 0.00 0.00 37.19 3.02
5502 6015 3.334691 CAGCCTATTTTCGGTTGTCTGA 58.665 45.455 0.00 0.00 0.00 3.27
5503 6016 2.159517 GCAGCCTATTTTCGGTTGTCTG 60.160 50.000 0.00 0.00 35.46 3.51
5504 6017 2.084546 GCAGCCTATTTTCGGTTGTCT 58.915 47.619 0.00 0.00 35.46 3.41
5505 6018 2.084546 AGCAGCCTATTTTCGGTTGTC 58.915 47.619 0.00 0.00 35.46 3.18
5506 6019 2.200373 AGCAGCCTATTTTCGGTTGT 57.800 45.000 0.00 0.00 35.46 3.32
5507 6020 3.244976 CAAAGCAGCCTATTTTCGGTTG 58.755 45.455 0.00 0.00 36.04 3.77
5508 6021 2.352715 GCAAAGCAGCCTATTTTCGGTT 60.353 45.455 0.00 0.00 0.00 4.44
5509 6022 1.202348 GCAAAGCAGCCTATTTTCGGT 59.798 47.619 0.00 0.00 0.00 4.69
5510 6023 1.202114 TGCAAAGCAGCCTATTTTCGG 59.798 47.619 0.00 0.00 33.32 4.30
5511 6024 2.634982 TGCAAAGCAGCCTATTTTCG 57.365 45.000 0.00 0.00 33.32 3.46
5512 6025 3.853475 ACATGCAAAGCAGCCTATTTTC 58.147 40.909 0.00 0.00 43.65 2.29
5513 6026 3.967332 ACATGCAAAGCAGCCTATTTT 57.033 38.095 0.00 0.00 43.65 1.82
5514 6027 3.007182 ACAACATGCAAAGCAGCCTATTT 59.993 39.130 0.00 0.00 43.65 1.40
5515 6028 2.564062 ACAACATGCAAAGCAGCCTATT 59.436 40.909 0.00 0.00 43.65 1.73
5516 6029 2.165030 GACAACATGCAAAGCAGCCTAT 59.835 45.455 0.00 0.00 43.65 2.57
5517 6030 1.541147 GACAACATGCAAAGCAGCCTA 59.459 47.619 0.00 0.00 43.65 3.93
5518 6031 0.316204 GACAACATGCAAAGCAGCCT 59.684 50.000 0.00 0.00 43.65 4.58
5519 6032 0.316204 AGACAACATGCAAAGCAGCC 59.684 50.000 0.00 0.00 43.65 4.85
5520 6033 1.001048 TCAGACAACATGCAAAGCAGC 60.001 47.619 0.00 0.00 43.65 5.25
5521 6034 3.358707 TTCAGACAACATGCAAAGCAG 57.641 42.857 0.00 0.00 43.65 4.24
5522 6035 3.797451 TTTCAGACAACATGCAAAGCA 57.203 38.095 0.00 0.00 44.86 3.91
5523 6036 4.053295 ACATTTCAGACAACATGCAAAGC 58.947 39.130 0.00 0.00 0.00 3.51
5524 6037 5.526115 AGACATTTCAGACAACATGCAAAG 58.474 37.500 0.00 0.00 0.00 2.77
5525 6038 5.518848 AGACATTTCAGACAACATGCAAA 57.481 34.783 0.00 0.00 0.00 3.68
5526 6039 5.507817 GGAAGACATTTCAGACAACATGCAA 60.508 40.000 0.00 0.00 0.00 4.08
5527 6040 4.022935 GGAAGACATTTCAGACAACATGCA 60.023 41.667 0.00 0.00 0.00 3.96
5528 6041 4.022935 TGGAAGACATTTCAGACAACATGC 60.023 41.667 0.00 0.00 0.00 4.06
5529 6042 5.694231 TGGAAGACATTTCAGACAACATG 57.306 39.130 0.00 0.00 0.00 3.21
5530 6043 5.242393 CCTTGGAAGACATTTCAGACAACAT 59.758 40.000 0.00 0.00 0.00 2.71
5531 6044 4.580167 CCTTGGAAGACATTTCAGACAACA 59.420 41.667 0.00 0.00 0.00 3.33
5532 6045 4.821805 TCCTTGGAAGACATTTCAGACAAC 59.178 41.667 0.00 0.00 0.00 3.32
5533 6046 4.821805 GTCCTTGGAAGACATTTCAGACAA 59.178 41.667 0.00 0.00 34.27 3.18
5534 6047 4.103153 AGTCCTTGGAAGACATTTCAGACA 59.897 41.667 0.00 0.00 36.68 3.41
5535 6048 4.646572 AGTCCTTGGAAGACATTTCAGAC 58.353 43.478 0.00 0.00 36.68 3.51
5536 6049 4.982241 AGTCCTTGGAAGACATTTCAGA 57.018 40.909 0.00 0.00 36.68 3.27
5537 6050 8.792830 TTATAAGTCCTTGGAAGACATTTCAG 57.207 34.615 0.00 0.00 36.68 3.02
5538 6051 9.581289 TTTTATAAGTCCTTGGAAGACATTTCA 57.419 29.630 0.00 0.00 36.68 2.69
5540 6053 9.588096 ACTTTTATAAGTCCTTGGAAGACATTT 57.412 29.630 0.00 0.00 40.60 2.32
5541 6054 9.014297 CACTTTTATAAGTCCTTGGAAGACATT 57.986 33.333 0.00 0.00 42.67 2.71
5542 6055 8.383175 TCACTTTTATAAGTCCTTGGAAGACAT 58.617 33.333 0.00 0.00 42.67 3.06
5543 6056 7.741785 TCACTTTTATAAGTCCTTGGAAGACA 58.258 34.615 0.00 0.00 42.67 3.41
5544 6057 8.504815 GTTCACTTTTATAAGTCCTTGGAAGAC 58.495 37.037 0.00 0.00 42.67 3.01
5545 6058 8.215050 TGTTCACTTTTATAAGTCCTTGGAAGA 58.785 33.333 0.00 0.00 42.67 2.87
5546 6059 8.391075 TGTTCACTTTTATAAGTCCTTGGAAG 57.609 34.615 0.00 0.00 42.67 3.46
5547 6060 8.215050 TCTGTTCACTTTTATAAGTCCTTGGAA 58.785 33.333 0.00 0.00 42.67 3.53
5548 6061 7.741785 TCTGTTCACTTTTATAAGTCCTTGGA 58.258 34.615 0.00 0.00 42.67 3.53
5549 6062 7.119846 CCTCTGTTCACTTTTATAAGTCCTTGG 59.880 40.741 0.00 0.00 42.67 3.61
5550 6063 7.119846 CCCTCTGTTCACTTTTATAAGTCCTTG 59.880 40.741 0.00 0.00 42.67 3.61
5551 6064 7.017254 TCCCTCTGTTCACTTTTATAAGTCCTT 59.983 37.037 0.00 0.00 42.67 3.36
5552 6065 6.500751 TCCCTCTGTTCACTTTTATAAGTCCT 59.499 38.462 0.00 0.00 42.67 3.85
5553 6066 6.708285 TCCCTCTGTTCACTTTTATAAGTCC 58.292 40.000 0.00 0.00 42.67 3.85
5554 6067 7.387643 ACTCCCTCTGTTCACTTTTATAAGTC 58.612 38.462 0.00 0.00 42.67 3.01
5555 6068 7.317722 ACTCCCTCTGTTCACTTTTATAAGT 57.682 36.000 0.00 0.00 45.40 2.24
5556 6069 8.311836 TGTACTCCCTCTGTTCACTTTTATAAG 58.688 37.037 0.00 0.00 37.40 1.73
5557 6070 8.197592 TGTACTCCCTCTGTTCACTTTTATAA 57.802 34.615 0.00 0.00 0.00 0.98
5558 6071 7.786046 TGTACTCCCTCTGTTCACTTTTATA 57.214 36.000 0.00 0.00 0.00 0.98
5559 6072 6.681729 TGTACTCCCTCTGTTCACTTTTAT 57.318 37.500 0.00 0.00 0.00 1.40
5560 6073 6.488769 TTGTACTCCCTCTGTTCACTTTTA 57.511 37.500 0.00 0.00 0.00 1.52
5561 6074 5.367945 TTGTACTCCCTCTGTTCACTTTT 57.632 39.130 0.00 0.00 0.00 2.27
5562 6075 5.568620 ATTGTACTCCCTCTGTTCACTTT 57.431 39.130 0.00 0.00 0.00 2.66
5563 6076 6.681729 TTATTGTACTCCCTCTGTTCACTT 57.318 37.500 0.00 0.00 0.00 3.16
5564 6077 6.681729 TTTATTGTACTCCCTCTGTTCACT 57.318 37.500 0.00 0.00 0.00 3.41
5565 6078 7.739498 TTTTTATTGTACTCCCTCTGTTCAC 57.261 36.000 0.00 0.00 0.00 3.18
5617 6136 1.468520 CAGTAGGAAAATGTGCCCGTG 59.531 52.381 0.00 0.00 0.00 4.94
5620 6139 3.421844 ACTTCAGTAGGAAAATGTGCCC 58.578 45.455 0.00 0.00 34.44 5.36
5687 6207 4.040095 ACAGGTACCTTTGTCTACCAGTTC 59.960 45.833 13.15 0.00 35.71 3.01
5816 6336 4.194640 CCTTCTATGTGGTGATTGGTGAG 58.805 47.826 0.00 0.00 0.00 3.51
5914 6434 3.419943 TGTTGCTGCTGGTATCATTTCA 58.580 40.909 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.