Multiple sequence alignment - TraesCS4A01G484900

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 TraesCS4A01G484900 chr4A 100.000 2779 0 0 1 2779 738932836 738935614 0.000000e+00 5132.0
1 TraesCS4A01G484900 chr4A 94.892 372 12 3 271 642 738972136 738971772 2.400000e-160 575.0
2 TraesCS4A01G484900 chr7D 87.518 1386 99 29 220 1571 4706663 4705318 0.000000e+00 1533.0
3 TraesCS4A01G484900 chr7D 88.410 673 46 12 926 1571 4718278 4717611 0.000000e+00 782.0
4 TraesCS4A01G484900 chr7D 81.126 604 55 24 322 910 4718895 4718336 1.980000e-116 429.0
5 TraesCS4A01G484900 chr7D 90.476 294 23 4 1565 1858 4705274 4704986 1.560000e-102 383.0
6 TraesCS4A01G484900 chr7D 89.925 268 23 2 1887 2150 4717307 4717040 2.650000e-90 342.0
7 TraesCS4A01G484900 chr7D 92.500 200 15 0 1 200 4706929 4706730 1.260000e-73 287.0
8 TraesCS4A01G484900 chr7D 89.503 181 8 4 2151 2321 4704313 4704134 4.660000e-53 219.0
9 TraesCS4A01G484900 chr7D 84.571 175 14 6 2479 2640 4716979 4716805 7.970000e-36 161.0
10 TraesCS4A01G484900 chr7D 83.648 159 15 6 2482 2640 4703983 4703836 3.730000e-29 139.0
11 TraesCS4A01G484900 chr7D 86.885 122 11 2 2360 2477 4704136 4704016 6.250000e-27 132.0
12 TraesCS4A01G484900 chr7D 100.000 30 0 0 2339 2368 42416335 42416306 3.870000e-04 56.5
13 TraesCS4A01G484900 chr7A 86.259 1259 120 27 348 1571 4531044 4529804 0.000000e+00 1317.0
14 TraesCS4A01G484900 chr7A 86.275 867 71 20 730 1571 4586669 4585826 0.000000e+00 898.0
15 TraesCS4A01G484900 chr7A 90.317 568 49 5 1565 2131 4529759 4529197 0.000000e+00 739.0
16 TraesCS4A01G484900 chr7A 90.421 261 22 1 1893 2150 4585521 4585261 9.530000e-90 340.0
17 TraesCS4A01G484900 chr7A 93.750 160 9 1 2482 2640 4486874 4486715 3.580000e-59 239.0
18 TraesCS4A01G484900 chr7A 93.082 159 11 0 2482 2640 4528675 4528517 1.660000e-57 233.0
19 TraesCS4A01G484900 chr7A 80.000 320 26 12 2167 2477 4528998 4528708 4.690000e-48 202.0
20 TraesCS4A01G484900 chr7A 98.214 112 1 1 2636 2747 671186449 671186559 7.850000e-46 195.0
21 TraesCS4A01G484900 chr7A 87.742 155 16 2 1591 1745 4585758 4585607 7.910000e-41 178.0
22 TraesCS4A01G484900 chr7A 85.799 169 11 6 2482 2637 4585194 4585026 1.710000e-37 167.0
23 TraesCS4A01G484900 chr5B 86.000 200 26 1 680 877 430263892 430263693 2.170000e-51 213.0
24 TraesCS4A01G484900 chr5B 88.652 141 16 0 680 820 430165843 430165703 3.680000e-39 172.0
25 TraesCS4A01G484900 chr3B 86.294 197 25 1 680 874 202592363 202592559 2.170000e-51 213.0
26 TraesCS4A01G484900 chr3B 100.000 109 0 0 2637 2745 251325893 251325785 4.690000e-48 202.0
27 TraesCS4A01G484900 chr3A 96.825 126 1 3 2637 2762 608386810 608386688 1.010000e-49 207.0
28 TraesCS4A01G484900 chr3A 100.000 110 0 0 2636 2745 683742424 683742533 1.300000e-48 204.0
29 TraesCS4A01G484900 chr3A 99.107 112 1 0 2637 2748 740109924 740110035 4.690000e-48 202.0
30 TraesCS4A01G484900 chr3A 98.214 112 1 1 2636 2747 700359824 700359934 7.850000e-46 195.0
31 TraesCS4A01G484900 chr3A 100.000 28 0 0 2339 2366 51753308 51753335 5.000000e-03 52.8
32 TraesCS4A01G484900 chr6A 98.246 114 1 1 2630 2743 8193077 8192965 6.070000e-47 198.0
33 TraesCS4A01G484900 chr6A 100.000 28 0 0 2339 2366 438580303 438580276 5.000000e-03 52.8
34 TraesCS4A01G484900 chr5A 99.091 110 1 0 2637 2746 653853561 653853670 6.070000e-47 198.0
35 TraesCS4A01G484900 chr2A 96.581 117 3 1 2629 2745 738986222 738986337 2.820000e-45 193.0
36 TraesCS4A01G484900 chrUn 88.652 141 16 0 680 820 342509007 342509147 3.680000e-39 172.0
37 TraesCS4A01G484900 chrUn 88.652 141 16 0 680 820 382684603 382684463 3.680000e-39 172.0
38 TraesCS4A01G484900 chrUn 88.652 141 16 0 680 820 399641170 399641030 3.680000e-39 172.0
39 TraesCS4A01G484900 chrUn 100.000 30 0 0 2339 2368 317648568 317648539 3.870000e-04 56.5
40 TraesCS4A01G484900 chr6D 83.582 67 10 1 4 70 12640766 12640831 8.310000e-06 62.1
41 TraesCS4A01G484900 chr4B 90.476 42 2 2 2327 2367 327517390 327517430 1.000000e-03 54.7
42 TraesCS4A01G484900 chr5D 100.000 28 0 0 2339 2366 7423686 7423659 5.000000e-03 52.8
43 TraesCS4A01G484900 chr4D 100.000 28 0 0 2339 2366 4803444 4803471 5.000000e-03 52.8
44 TraesCS4A01G484900 chr1B 90.244 41 2 2 2327 2366 82036134 82036173 5.000000e-03 52.8


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 TraesCS4A01G484900 chr4A 738932836 738935614 2778 False 5132.000000 5132 100.000000 1 2779 1 chr4A.!!$F1 2778
1 TraesCS4A01G484900 chr7D 4703836 4706929 3093 True 448.833333 1533 88.421667 1 2640 6 chr7D.!!$R2 2639
2 TraesCS4A01G484900 chr7D 4716805 4718895 2090 True 428.500000 782 86.008000 322 2640 4 chr7D.!!$R3 2318
3 TraesCS4A01G484900 chr7A 4528517 4531044 2527 True 622.750000 1317 87.414500 348 2640 4 chr7A.!!$R2 2292
4 TraesCS4A01G484900 chr7A 4585026 4586669 1643 True 395.750000 898 87.559250 730 2637 4 chr7A.!!$R3 1907

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
186 187 0.549950 CACCATCCCAGCCTCTGATT 59.450 55.0 0.0 0.0 32.44 2.57 F
1717 1920 0.168128 GGACATCGCCCAAAGAAACG 59.832 55.0 0.0 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1933 0.179111 CATCTTGGCTTGCATGCTGG 60.179 55.0 22.27 12.33 0.0 4.85 R
2659 3394 2.604046 AGCAAGTTGTCTGAACGTCT 57.396 45.0 4.48 0.00 0.0 4.18 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
22 23 1.621992 TCTCTTCGTCTTGCTCCTGT 58.378 50.000 0.00 0.00 0.00 4.00
25 26 1.143305 CTTCGTCTTGCTCCTGTGTG 58.857 55.000 0.00 0.00 0.00 3.82
31 32 3.493028 TTGCTCCTGTGTGCAAGAA 57.507 47.368 0.00 0.00 43.78 2.52
33 34 1.024271 TGCTCCTGTGTGCAAGAAAC 58.976 50.000 0.00 0.00 37.99 2.78
48 49 4.646572 CAAGAAACCTCCAAGCTCTAGTT 58.353 43.478 0.00 0.00 0.00 2.24
51 52 2.632763 ACCTCCAAGCTCTAGTTCCT 57.367 50.000 0.00 0.00 0.00 3.36
60 61 5.221224 CCAAGCTCTAGTTCCTCATCTAGTG 60.221 48.000 0.00 0.00 36.17 2.74
79 80 3.829601 AGTGTTCCTCTCTCTCGTGAATT 59.170 43.478 0.00 0.00 0.00 2.17
108 109 4.056050 TCGTGAAAGGTTAGCTTTCTCAC 58.944 43.478 29.01 22.01 40.39 3.51
109 110 3.186613 CGTGAAAGGTTAGCTTTCTCACC 59.813 47.826 29.01 16.98 40.39 4.02
115 116 1.727335 GTTAGCTTTCTCACCGTGCTC 59.273 52.381 0.00 0.00 35.47 4.26
186 187 0.549950 CACCATCCCAGCCTCTGATT 59.450 55.000 0.00 0.00 32.44 2.57
238 286 3.049344 AGAGGGTTGAAGGAACTGTTCT 58.951 45.455 19.05 1.23 40.86 3.01
312 360 6.164408 CTTTTCAAGGAAAAACAACCACAC 57.836 37.500 5.73 0.00 40.34 3.82
313 361 4.873746 TTCAAGGAAAAACAACCACACA 57.126 36.364 0.00 0.00 0.00 3.72
314 362 4.181309 TCAAGGAAAAACAACCACACAC 57.819 40.909 0.00 0.00 0.00 3.82
315 363 3.574396 TCAAGGAAAAACAACCACACACA 59.426 39.130 0.00 0.00 0.00 3.72
316 364 3.586100 AGGAAAAACAACCACACACAC 57.414 42.857 0.00 0.00 0.00 3.82
476 528 6.493802 AGACTCTGTTTCTAGGACACAACATA 59.506 38.462 0.00 0.00 0.00 2.29
494 547 2.526304 TATTAGCTTGTAGCCCTGCG 57.474 50.000 0.00 0.00 43.77 5.18
500 561 1.009829 CTTGTAGCCCTGCGATTGTC 58.990 55.000 0.00 0.00 0.00 3.18
511 572 1.154205 GCGATTGTCCGGATCAGTGG 61.154 60.000 7.81 7.26 0.00 4.00
532 593 3.181500 GGTAATGCCTTGGCTACTTTTCG 60.181 47.826 13.18 0.00 0.00 3.46
543 604 4.988540 TGGCTACTTTTCGGAATATCGATG 59.011 41.667 8.54 0.00 39.03 3.84
546 607 6.346678 GGCTACTTTTCGGAATATCGATGTTC 60.347 42.308 22.55 22.55 39.03 3.18
547 608 6.421202 GCTACTTTTCGGAATATCGATGTTCT 59.579 38.462 27.30 13.14 39.03 3.01
548 609 7.594015 GCTACTTTTCGGAATATCGATGTTCTA 59.406 37.037 27.30 16.74 39.03 2.10
549 610 7.695869 ACTTTTCGGAATATCGATGTTCTAC 57.304 36.000 27.30 15.03 39.03 2.59
585 646 4.276678 AGTTTGTGAACACCAGATGACATG 59.723 41.667 0.00 0.00 38.26 3.21
586 647 3.490439 TGTGAACACCAGATGACATGT 57.510 42.857 0.00 0.00 0.00 3.21
600 661 8.373981 CCAGATGACATGTATTCCTCTATTTCT 58.626 37.037 0.00 0.00 0.00 2.52
653 725 7.569111 AGATAAGAACACATAGTATGAACCCCT 59.431 37.037 17.13 4.50 0.00 4.79
654 726 5.359194 AGAACACATAGTATGAACCCCTG 57.641 43.478 17.13 5.96 0.00 4.45
675 751 8.043710 CCCCTGATTCTGTTATTAGGACATATC 58.956 40.741 0.00 0.00 34.14 1.63
676 752 7.761704 CCCTGATTCTGTTATTAGGACATATCG 59.238 40.741 0.00 0.00 34.14 2.92
687 763 9.562408 TTATTAGGACATATCGTTGCCATTTTA 57.438 29.630 0.00 0.00 0.00 1.52
688 764 7.867305 TTAGGACATATCGTTGCCATTTTAA 57.133 32.000 0.00 0.00 0.00 1.52
772 848 6.096141 TCCAAATGAACACTGTGTTGTTATGT 59.904 34.615 29.06 13.31 41.28 2.29
832 908 5.929697 TTTCATTCATCAGTGACACTGTC 57.070 39.130 29.87 1.86 46.03 3.51
833 909 4.605640 TCATTCATCAGTGACACTGTCA 57.394 40.909 29.87 16.00 46.03 3.58
939 1059 6.125029 ACTGCTTATGCTAATTGTCCATTCT 58.875 36.000 1.96 0.00 40.48 2.40
940 1060 7.282585 ACTGCTTATGCTAATTGTCCATTCTA 58.717 34.615 1.96 0.00 40.48 2.10
941 1061 7.443575 ACTGCTTATGCTAATTGTCCATTCTAG 59.556 37.037 1.96 0.00 40.48 2.43
949 1069 9.679661 TGCTAATTGTCCATTCTAGTAAATGAA 57.320 29.630 5.87 0.00 38.64 2.57
988 1108 8.022550 TGTGACATTATGTTAGCAATTGAACTG 58.977 33.333 10.34 3.01 0.00 3.16
999 1119 4.399303 AGCAATTGAACTGGCAGGTTATAC 59.601 41.667 20.34 0.01 0.00 1.47
1053 1173 6.917217 AAGCTTCAGTCAAAGATATGCTAC 57.083 37.500 0.00 0.00 0.00 3.58
1074 1194 1.043816 ATAGGGATGCCAGTGTCGAG 58.956 55.000 5.86 0.00 0.00 4.04
1090 1210 3.576982 TGTCGAGTACCTGGAAATCAAGT 59.423 43.478 0.00 0.00 0.00 3.16
1092 1212 4.082136 GTCGAGTACCTGGAAATCAAGTCT 60.082 45.833 0.00 0.00 0.00 3.24
1116 1236 5.142061 TGGTTGATAAACTCGTAGAAGCA 57.858 39.130 0.00 0.00 34.09 3.91
1229 1349 7.828717 TCAAGGTTTGTGATCTTTCATATAGCA 59.171 33.333 0.00 0.00 33.56 3.49
1288 1439 2.237143 CAGTAATCAAGGAGCAGGTGGA 59.763 50.000 0.00 0.00 0.00 4.02
1392 1543 4.671831 TGAGGAAGAAAAACATGGCCATA 58.328 39.130 20.30 0.00 0.00 2.74
1394 1545 5.721000 TGAGGAAGAAAAACATGGCCATATT 59.279 36.000 20.30 11.66 0.00 1.28
1446 1597 3.119137 ACAACAACTTGCTCAAAGGAACC 60.119 43.478 0.00 0.00 40.51 3.62
1473 1624 3.009143 GCTGGAGGGTTTAAGGAAGAAGA 59.991 47.826 0.00 0.00 0.00 2.87
1523 1674 6.405397 CCACAAGGGTAAAACCTAATGCATAC 60.405 42.308 0.00 0.00 40.87 2.39
1534 1685 4.248859 CCTAATGCATACATCCTTCTCCG 58.751 47.826 0.00 0.00 34.62 4.63
1617 1820 2.874086 GGGGTCGTATTTTGATTACCGG 59.126 50.000 0.00 0.00 0.00 5.28
1689 1892 1.071542 TCCAAGGATCGTTGAGCAACA 59.928 47.619 25.74 3.54 41.20 3.33
1717 1920 0.168128 GGACATCGCCCAAAGAAACG 59.832 55.000 0.00 0.00 0.00 3.60
1720 1923 2.073816 ACATCGCCCAAAGAAACGTAG 58.926 47.619 0.00 0.00 0.00 3.51
1721 1924 1.396996 CATCGCCCAAAGAAACGTAGG 59.603 52.381 0.00 0.00 0.00 3.18
1722 1925 0.680618 TCGCCCAAAGAAACGTAGGA 59.319 50.000 0.00 0.00 0.00 2.94
1750 1953 0.815095 CAGCATGCAAGCCAAGATGA 59.185 50.000 21.98 0.00 30.64 2.92
1751 1954 0.815734 AGCATGCAAGCCAAGATGAC 59.184 50.000 21.98 0.00 34.23 3.06
1752 1955 0.528924 GCATGCAAGCCAAGATGACA 59.471 50.000 14.21 0.00 0.00 3.58
1823 2026 7.125659 TCCCTGAATTTGTACTGATCATCTACA 59.874 37.037 0.00 2.56 0.00 2.74
1858 2093 4.184629 ACACTCTAAATCCATGAGTTCGC 58.815 43.478 0.00 0.00 38.80 4.70
1860 2095 4.505922 CACTCTAAATCCATGAGTTCGCTC 59.494 45.833 0.00 0.00 44.33 5.03
1862 2097 4.686972 TCTAAATCCATGAGTTCGCTCTG 58.313 43.478 0.00 0.00 44.38 3.35
1863 2098 3.616956 AAATCCATGAGTTCGCTCTGA 57.383 42.857 0.00 0.00 44.38 3.27
1864 2099 2.886862 ATCCATGAGTTCGCTCTGAG 57.113 50.000 0.00 0.00 44.38 3.35
1865 2100 0.174389 TCCATGAGTTCGCTCTGAGC 59.826 55.000 19.53 19.53 44.38 4.26
1866 2101 0.108472 CCATGAGTTCGCTCTGAGCA 60.108 55.000 27.46 13.12 42.58 4.26
1867 2102 1.472904 CCATGAGTTCGCTCTGAGCAT 60.473 52.381 27.46 10.83 42.58 3.79
1868 2103 2.223900 CCATGAGTTCGCTCTGAGCATA 60.224 50.000 27.46 13.38 42.58 3.14
1869 2104 3.554544 CCATGAGTTCGCTCTGAGCATAT 60.555 47.826 27.46 11.34 42.58 1.78
1870 2105 4.321527 CCATGAGTTCGCTCTGAGCATATA 60.322 45.833 27.46 10.03 42.58 0.86
1871 2106 4.495911 TGAGTTCGCTCTGAGCATATAG 57.504 45.455 27.46 12.16 42.58 1.31
1872 2107 4.137543 TGAGTTCGCTCTGAGCATATAGA 58.862 43.478 27.46 14.22 42.58 1.98
1873 2108 4.764308 TGAGTTCGCTCTGAGCATATAGAT 59.236 41.667 27.46 7.77 42.58 1.98
1874 2109 5.940470 TGAGTTCGCTCTGAGCATATAGATA 59.060 40.000 27.46 5.58 42.58 1.98
1875 2110 6.093357 TGAGTTCGCTCTGAGCATATAGATAG 59.907 42.308 27.46 9.40 42.58 2.08
1876 2111 5.356751 AGTTCGCTCTGAGCATATAGATAGG 59.643 44.000 27.46 8.72 42.58 2.57
1877 2112 4.849518 TCGCTCTGAGCATATAGATAGGT 58.150 43.478 27.46 0.00 42.58 3.08
1878 2113 4.637977 TCGCTCTGAGCATATAGATAGGTG 59.362 45.833 27.46 8.04 42.58 4.00
1879 2114 4.397730 CGCTCTGAGCATATAGATAGGTGT 59.602 45.833 27.46 0.00 42.58 4.16
1880 2115 5.105957 CGCTCTGAGCATATAGATAGGTGTT 60.106 44.000 27.46 0.00 42.58 3.32
1881 2116 6.098679 GCTCTGAGCATATAGATAGGTGTTG 58.901 44.000 24.02 0.00 41.89 3.33
1882 2117 6.030548 TCTGAGCATATAGATAGGTGTTGC 57.969 41.667 0.00 0.00 0.00 4.17
1883 2118 5.777223 TCTGAGCATATAGATAGGTGTTGCT 59.223 40.000 0.00 0.00 41.32 3.91
1884 2119 6.268617 TCTGAGCATATAGATAGGTGTTGCTT 59.731 38.462 0.00 0.00 38.93 3.91
1885 2120 7.451566 TCTGAGCATATAGATAGGTGTTGCTTA 59.548 37.037 0.00 0.00 38.93 3.09
1886 2121 8.138928 TGAGCATATAGATAGGTGTTGCTTAT 57.861 34.615 0.00 0.00 38.93 1.73
1887 2122 9.255029 TGAGCATATAGATAGGTGTTGCTTATA 57.745 33.333 0.00 0.00 38.93 0.98
1888 2123 9.522804 GAGCATATAGATAGGTGTTGCTTATAC 57.477 37.037 0.00 0.00 38.93 1.47
1889 2124 9.035890 AGCATATAGATAGGTGTTGCTTATACA 57.964 33.333 0.00 0.00 35.57 2.29
1890 2125 9.088512 GCATATAGATAGGTGTTGCTTATACAC 57.911 37.037 0.00 0.00 43.96 2.90
1896 2396 8.651389 AGATAGGTGTTGCTTATACACATACAT 58.349 33.333 8.22 0.00 43.04 2.29
1920 2420 2.770164 ACAGGTATGGCTTCAGTGAC 57.230 50.000 0.00 0.00 0.00 3.67
1984 2490 7.452813 ACTGGAGTATAAGATCATATGAGCACA 59.547 37.037 22.20 9.99 31.88 4.57
1995 2501 6.682423 TCATATGAGCACACCAACATTTAG 57.318 37.500 0.00 0.00 0.00 1.85
2163 2840 7.979786 AGACATCCTGTTATCTTAGAAAGGA 57.020 36.000 8.19 8.19 38.16 3.36
2193 2870 8.635765 AGGATCAAAGAAATAAGTAGCAAACA 57.364 30.769 0.00 0.00 0.00 2.83
2194 2871 8.515414 AGGATCAAAGAAATAAGTAGCAAACAC 58.485 33.333 0.00 0.00 0.00 3.32
2216 2893 5.878116 CACGGAATTGATAGGTTTCAGGTAA 59.122 40.000 0.00 0.00 0.00 2.85
2227 2913 9.561069 GATAGGTTTCAGGTAACATAATGTGAT 57.439 33.333 0.00 0.00 41.41 3.06
2228 2914 9.920946 ATAGGTTTCAGGTAACATAATGTGATT 57.079 29.630 0.00 0.00 41.41 2.57
2229 2915 8.650143 AGGTTTCAGGTAACATAATGTGATTT 57.350 30.769 0.00 0.00 41.41 2.17
2325 3013 4.242475 TGGTGAAGTTACATAGCTGAACG 58.758 43.478 0.00 0.00 0.00 3.95
2326 3014 4.021807 TGGTGAAGTTACATAGCTGAACGA 60.022 41.667 0.00 0.00 0.00 3.85
2327 3015 4.563184 GGTGAAGTTACATAGCTGAACGAG 59.437 45.833 0.00 0.00 0.00 4.18
2328 3016 5.162075 GTGAAGTTACATAGCTGAACGAGT 58.838 41.667 0.00 0.00 0.00 4.18
2329 3017 5.634020 GTGAAGTTACATAGCTGAACGAGTT 59.366 40.000 0.00 0.00 0.00 3.01
2330 3018 6.805271 GTGAAGTTACATAGCTGAACGAGTTA 59.195 38.462 0.00 0.00 0.00 2.24
2331 3019 6.805271 TGAAGTTACATAGCTGAACGAGTTAC 59.195 38.462 0.00 0.00 0.00 2.50
2332 3020 6.512342 AGTTACATAGCTGAACGAGTTACT 57.488 37.500 0.00 0.00 0.00 2.24
2333 3021 6.553524 AGTTACATAGCTGAACGAGTTACTC 58.446 40.000 1.64 1.64 0.00 2.59
2334 3022 6.150641 AGTTACATAGCTGAACGAGTTACTCA 59.849 38.462 13.14 0.00 0.00 3.41
2335 3023 5.386958 ACATAGCTGAACGAGTTACTCAA 57.613 39.130 13.14 0.00 0.00 3.02
2336 3024 5.162075 ACATAGCTGAACGAGTTACTCAAC 58.838 41.667 13.14 3.70 34.67 3.18
2337 3025 2.662700 AGCTGAACGAGTTACTCAACG 58.337 47.619 13.14 1.77 39.78 4.10
2338 3026 2.034305 AGCTGAACGAGTTACTCAACGT 59.966 45.455 13.14 2.44 39.78 3.99
2339 3027 3.251729 AGCTGAACGAGTTACTCAACGTA 59.748 43.478 13.14 0.00 39.78 3.57
2340 3028 4.082895 AGCTGAACGAGTTACTCAACGTAT 60.083 41.667 13.14 0.00 39.78 3.06
2341 3029 4.620184 GCTGAACGAGTTACTCAACGTATT 59.380 41.667 13.14 0.00 39.78 1.89
2342 3030 5.118203 GCTGAACGAGTTACTCAACGTATTT 59.882 40.000 13.14 0.00 39.78 1.40
2343 3031 6.346359 GCTGAACGAGTTACTCAACGTATTTT 60.346 38.462 13.14 0.00 39.78 1.82
2344 3032 6.869473 TGAACGAGTTACTCAACGTATTTTG 58.131 36.000 13.14 0.00 39.78 2.44
2345 3033 5.834239 ACGAGTTACTCAACGTATTTTGG 57.166 39.130 13.14 0.00 39.78 3.28
2346 3034 5.531634 ACGAGTTACTCAACGTATTTTGGA 58.468 37.500 13.14 0.00 39.78 3.53
2347 3035 5.984926 ACGAGTTACTCAACGTATTTTGGAA 59.015 36.000 13.14 0.00 39.78 3.53
2348 3036 6.074142 ACGAGTTACTCAACGTATTTTGGAAC 60.074 38.462 13.14 0.00 39.78 3.62
2349 3037 6.219302 AGTTACTCAACGTATTTTGGAACG 57.781 37.500 0.00 0.00 44.47 3.95
2350 3038 5.178067 AGTTACTCAACGTATTTTGGAACGG 59.822 40.000 0.00 0.00 43.25 4.44
2351 3039 3.731089 ACTCAACGTATTTTGGAACGGA 58.269 40.909 0.00 0.00 43.25 4.69
2352 3040 3.744426 ACTCAACGTATTTTGGAACGGAG 59.256 43.478 0.00 0.00 43.25 4.63
2353 3041 3.068560 TCAACGTATTTTGGAACGGAGG 58.931 45.455 0.00 0.00 43.25 4.30
2354 3042 2.103537 ACGTATTTTGGAACGGAGGG 57.896 50.000 0.00 0.00 43.25 4.30
2355 3043 1.624813 ACGTATTTTGGAACGGAGGGA 59.375 47.619 0.00 0.00 43.25 4.20
2356 3044 2.277084 CGTATTTTGGAACGGAGGGAG 58.723 52.381 0.00 0.00 35.51 4.30
2376 3064 3.428532 AGTAGCTTCTAAACCTCGACCA 58.571 45.455 0.00 0.00 0.00 4.02
2377 3065 2.745515 AGCTTCTAAACCTCGACCAC 57.254 50.000 0.00 0.00 0.00 4.16
2402 3090 2.878406 TCTTGTACCTTTTGCTCTGTGC 59.122 45.455 0.00 0.00 43.25 4.57
2427 3115 7.254522 GCATGCCACAATTACCTTTTGATATTG 60.255 37.037 6.36 0.00 33.55 1.90
2431 3119 9.034544 GCCACAATTACCTTTTGATATTGAATC 57.965 33.333 0.00 0.00 32.15 2.52
2446 3137 4.678509 TTGAATCACTTTATGTCGCCAC 57.321 40.909 0.00 0.00 0.00 5.01
2477 3168 3.523564 CCAGGAGGGTTTTCTCTTCCATA 59.476 47.826 0.00 0.00 34.39 2.74
2514 3233 1.879380 TGCTGCATAAGTTTCTGCGTT 59.121 42.857 0.00 0.00 41.32 4.84
2536 3255 5.330455 TGAGCTCATACTTACCTTCTGTG 57.670 43.478 13.74 0.00 0.00 3.66
2651 3386 3.851458 AAAGTTACTCCCTCCGTTTGT 57.149 42.857 0.00 0.00 0.00 2.83
2652 3387 3.851458 AAGTTACTCCCTCCGTTTGTT 57.149 42.857 0.00 0.00 0.00 2.83
2653 3388 3.851458 AGTTACTCCCTCCGTTTGTTT 57.149 42.857 0.00 0.00 0.00 2.83
2654 3389 4.160642 AGTTACTCCCTCCGTTTGTTTT 57.839 40.909 0.00 0.00 0.00 2.43
2655 3390 4.529897 AGTTACTCCCTCCGTTTGTTTTT 58.470 39.130 0.00 0.00 0.00 1.94
2656 3391 5.683681 AGTTACTCCCTCCGTTTGTTTTTA 58.316 37.500 0.00 0.00 0.00 1.52
2657 3392 6.301486 AGTTACTCCCTCCGTTTGTTTTTAT 58.699 36.000 0.00 0.00 0.00 1.40
2658 3393 7.452562 AGTTACTCCCTCCGTTTGTTTTTATA 58.547 34.615 0.00 0.00 0.00 0.98
2659 3394 7.938490 AGTTACTCCCTCCGTTTGTTTTTATAA 59.062 33.333 0.00 0.00 0.00 0.98
2660 3395 6.812879 ACTCCCTCCGTTTGTTTTTATAAG 57.187 37.500 0.00 0.00 0.00 1.73
2661 3396 6.536447 ACTCCCTCCGTTTGTTTTTATAAGA 58.464 36.000 0.00 0.00 0.00 2.10
2662 3397 6.429078 ACTCCCTCCGTTTGTTTTTATAAGAC 59.571 38.462 0.00 0.00 0.00 3.01
2663 3398 5.409214 TCCCTCCGTTTGTTTTTATAAGACG 59.591 40.000 0.00 0.00 0.00 4.18
2664 3399 5.179929 CCCTCCGTTTGTTTTTATAAGACGT 59.820 40.000 0.00 0.00 0.00 4.34
2665 3400 6.293571 CCCTCCGTTTGTTTTTATAAGACGTT 60.294 38.462 0.00 0.00 0.00 3.99
2666 3401 6.793680 CCTCCGTTTGTTTTTATAAGACGTTC 59.206 38.462 0.00 0.00 0.00 3.95
2667 3402 7.244166 TCCGTTTGTTTTTATAAGACGTTCA 57.756 32.000 0.00 0.00 0.00 3.18
2668 3403 7.346695 TCCGTTTGTTTTTATAAGACGTTCAG 58.653 34.615 0.00 0.00 0.00 3.02
2669 3404 7.224362 TCCGTTTGTTTTTATAAGACGTTCAGA 59.776 33.333 0.00 0.00 0.00 3.27
2670 3405 7.319615 CCGTTTGTTTTTATAAGACGTTCAGAC 59.680 37.037 0.00 0.00 0.00 3.51
2671 3406 7.847078 CGTTTGTTTTTATAAGACGTTCAGACA 59.153 33.333 0.00 0.00 0.00 3.41
2672 3407 9.493206 GTTTGTTTTTATAAGACGTTCAGACAA 57.507 29.630 0.00 0.00 0.00 3.18
2673 3408 9.493206 TTTGTTTTTATAAGACGTTCAGACAAC 57.507 29.630 0.00 0.00 0.00 3.32
2674 3409 8.428186 TGTTTTTATAAGACGTTCAGACAACT 57.572 30.769 0.00 0.00 0.00 3.16
2675 3410 8.885722 TGTTTTTATAAGACGTTCAGACAACTT 58.114 29.630 0.00 0.00 0.00 2.66
2676 3411 9.155053 GTTTTTATAAGACGTTCAGACAACTTG 57.845 33.333 0.00 0.00 0.00 3.16
2677 3412 4.992381 ATAAGACGTTCAGACAACTTGC 57.008 40.909 0.00 0.00 0.00 4.01
2678 3413 2.604046 AGACGTTCAGACAACTTGCT 57.396 45.000 0.00 0.00 0.00 3.91
2679 3414 2.906354 AGACGTTCAGACAACTTGCTT 58.094 42.857 0.00 0.00 0.00 3.91
2680 3415 3.270877 AGACGTTCAGACAACTTGCTTT 58.729 40.909 0.00 0.00 0.00 3.51
2681 3416 3.063997 AGACGTTCAGACAACTTGCTTTG 59.936 43.478 0.00 0.00 0.00 2.77
2682 3417 2.747446 ACGTTCAGACAACTTGCTTTGT 59.253 40.909 0.00 0.00 42.55 2.83
2683 3418 3.100817 CGTTCAGACAACTTGCTTTGTG 58.899 45.455 4.00 0.00 39.88 3.33
2684 3419 2.849880 TCAGACAACTTGCTTTGTGC 57.150 45.000 4.00 0.00 39.88 4.57
2685 3420 2.368439 TCAGACAACTTGCTTTGTGCT 58.632 42.857 4.00 0.34 39.88 4.40
2686 3421 2.097954 TCAGACAACTTGCTTTGTGCTG 59.902 45.455 4.00 9.87 39.88 4.41
2687 3422 2.094675 AGACAACTTGCTTTGTGCTGT 58.905 42.857 4.00 0.00 39.88 4.40
2688 3423 2.493278 AGACAACTTGCTTTGTGCTGTT 59.507 40.909 4.00 0.00 39.88 3.16
2689 3424 3.056607 AGACAACTTGCTTTGTGCTGTTT 60.057 39.130 4.00 0.00 39.88 2.83
2690 3425 3.663025 ACAACTTGCTTTGTGCTGTTTT 58.337 36.364 0.00 0.00 43.37 2.43
2691 3426 4.064388 ACAACTTGCTTTGTGCTGTTTTT 58.936 34.783 0.00 0.00 43.37 1.94
2692 3427 4.083908 ACAACTTGCTTTGTGCTGTTTTTG 60.084 37.500 0.00 0.00 43.37 2.44
2693 3428 3.924144 ACTTGCTTTGTGCTGTTTTTGA 58.076 36.364 0.00 0.00 43.37 2.69
2694 3429 4.314121 ACTTGCTTTGTGCTGTTTTTGAA 58.686 34.783 0.00 0.00 43.37 2.69
2695 3430 4.152223 ACTTGCTTTGTGCTGTTTTTGAAC 59.848 37.500 0.00 0.00 43.37 3.18
2696 3431 3.657634 TGCTTTGTGCTGTTTTTGAACA 58.342 36.364 0.00 0.00 43.37 3.18
2707 3442 6.859715 CTGTTTTTGAACAGTGTCTGAAAG 57.140 37.500 10.34 0.00 43.80 2.62
2708 3443 6.325919 TGTTTTTGAACAGTGTCTGAAAGT 57.674 33.333 0.00 0.00 35.18 2.66
2709 3444 6.378582 TGTTTTTGAACAGTGTCTGAAAGTC 58.621 36.000 0.00 0.00 35.18 3.01
2710 3445 6.206634 TGTTTTTGAACAGTGTCTGAAAGTCT 59.793 34.615 0.00 0.00 35.18 3.24
2711 3446 7.389330 TGTTTTTGAACAGTGTCTGAAAGTCTA 59.611 33.333 0.00 0.00 35.18 2.59
2712 3447 7.915293 TTTTGAACAGTGTCTGAAAGTCTAA 57.085 32.000 0.00 0.00 35.18 2.10
2713 3448 7.915293 TTTGAACAGTGTCTGAAAGTCTAAA 57.085 32.000 0.00 0.00 35.18 1.85
2714 3449 7.915293 TTGAACAGTGTCTGAAAGTCTAAAA 57.085 32.000 0.00 0.00 35.18 1.52
2715 3450 7.303634 TGAACAGTGTCTGAAAGTCTAAAAC 57.696 36.000 0.00 0.00 35.18 2.43
2716 3451 5.968387 ACAGTGTCTGAAAGTCTAAAACG 57.032 39.130 3.70 0.00 35.18 3.60
2717 3452 5.416947 ACAGTGTCTGAAAGTCTAAAACGT 58.583 37.500 3.70 0.00 35.18 3.99
2718 3453 5.519206 ACAGTGTCTGAAAGTCTAAAACGTC 59.481 40.000 3.70 0.00 35.18 4.34
2719 3454 5.749109 CAGTGTCTGAAAGTCTAAAACGTCT 59.251 40.000 0.00 0.00 32.44 4.18
2720 3455 6.255887 CAGTGTCTGAAAGTCTAAAACGTCTT 59.744 38.462 0.00 0.00 32.44 3.01
2721 3456 7.434307 CAGTGTCTGAAAGTCTAAAACGTCTTA 59.566 37.037 0.00 0.00 32.44 2.10
2722 3457 8.142551 AGTGTCTGAAAGTCTAAAACGTCTTAT 58.857 33.333 0.00 0.00 33.76 1.73
2723 3458 9.403110 GTGTCTGAAAGTCTAAAACGTCTTATA 57.597 33.333 0.00 0.00 33.76 0.98
2724 3459 9.970395 TGTCTGAAAGTCTAAAACGTCTTATAA 57.030 29.630 0.00 0.00 33.76 0.98
2737 3472 9.511144 AAAACGTCTTATAAAAACAAACAGAGG 57.489 29.630 0.00 0.00 0.00 3.69
2738 3473 7.797038 ACGTCTTATAAAAACAAACAGAGGT 57.203 32.000 0.00 0.00 0.00 3.85
2739 3474 8.891671 ACGTCTTATAAAAACAAACAGAGGTA 57.108 30.769 0.00 0.00 0.00 3.08
2740 3475 8.985805 ACGTCTTATAAAAACAAACAGAGGTAG 58.014 33.333 0.00 0.00 0.00 3.18
2741 3476 8.985805 CGTCTTATAAAAACAAACAGAGGTAGT 58.014 33.333 0.00 0.00 0.00 2.73
2762 3497 8.945057 GGTAGTACTATGTTAGCTACCTATGAC 58.055 40.741 5.75 0.00 44.84 3.06
2763 3498 9.499479 GTAGTACTATGTTAGCTACCTATGACA 57.501 37.037 5.75 0.00 0.00 3.58
2764 3499 8.393671 AGTACTATGTTAGCTACCTATGACAC 57.606 38.462 0.00 0.00 0.00 3.67
2765 3500 8.219178 AGTACTATGTTAGCTACCTATGACACT 58.781 37.037 0.00 0.00 0.00 3.55
2766 3501 7.278461 ACTATGTTAGCTACCTATGACACTG 57.722 40.000 0.00 0.00 0.00 3.66
2767 3502 7.061054 ACTATGTTAGCTACCTATGACACTGA 58.939 38.462 0.00 0.00 0.00 3.41
2768 3503 6.985653 ATGTTAGCTACCTATGACACTGAT 57.014 37.500 0.00 0.00 0.00 2.90
2769 3504 6.149129 TGTTAGCTACCTATGACACTGATG 57.851 41.667 0.00 0.00 0.00 3.07
2770 3505 5.656859 TGTTAGCTACCTATGACACTGATGT 59.343 40.000 0.00 0.00 43.71 3.06
2771 3506 6.154534 TGTTAGCTACCTATGACACTGATGTT 59.845 38.462 0.00 0.00 39.95 2.71
2772 3507 5.016051 AGCTACCTATGACACTGATGTTG 57.984 43.478 0.00 0.00 39.95 3.33
2773 3508 4.711846 AGCTACCTATGACACTGATGTTGA 59.288 41.667 0.00 0.00 39.95 3.18
2774 3509 5.187772 AGCTACCTATGACACTGATGTTGAA 59.812 40.000 0.00 0.00 39.95 2.69
2775 3510 6.051717 GCTACCTATGACACTGATGTTGAAT 58.948 40.000 0.00 0.00 39.95 2.57
2776 3511 7.069950 AGCTACCTATGACACTGATGTTGAATA 59.930 37.037 0.00 0.00 39.95 1.75
2777 3512 7.383572 GCTACCTATGACACTGATGTTGAATAG 59.616 40.741 0.00 0.00 39.95 1.73
2778 3513 7.187824 ACCTATGACACTGATGTTGAATAGT 57.812 36.000 0.00 0.00 39.95 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.706636 TTGCACACAGGAGCAAGAC 58.293 52.632 0.00 0.00 44.03 3.01
22 23 1.032014 GCTTGGAGGTTTCTTGCACA 58.968 50.000 0.00 0.00 0.00 4.57
25 26 1.902938 AGAGCTTGGAGGTTTCTTGC 58.097 50.000 0.00 0.00 0.00 4.01
31 32 2.835156 GAGGAACTAGAGCTTGGAGGTT 59.165 50.000 0.00 0.00 41.55 3.50
33 34 2.461695 TGAGGAACTAGAGCTTGGAGG 58.538 52.381 0.00 0.00 41.55 4.30
48 49 4.476846 AGAGAGAGGAACACTAGATGAGGA 59.523 45.833 0.00 0.00 0.00 3.71
51 52 4.080807 ACGAGAGAGAGGAACACTAGATGA 60.081 45.833 0.00 0.00 0.00 2.92
60 61 4.561105 ACAAATTCACGAGAGAGAGGAAC 58.439 43.478 0.00 0.00 30.88 3.62
79 80 4.890088 AGCTAACCTTTCACGATGTACAA 58.110 39.130 0.00 0.00 0.00 2.41
108 109 1.061131 CGCAGAATAACAAGAGCACGG 59.939 52.381 0.00 0.00 0.00 4.94
109 110 1.527793 GCGCAGAATAACAAGAGCACG 60.528 52.381 0.30 0.00 0.00 5.34
115 116 7.005062 ACATAAACTAGCGCAGAATAACAAG 57.995 36.000 11.47 0.00 0.00 3.16
170 171 1.270199 CGAGAATCAGAGGCTGGGATG 60.270 57.143 0.00 0.00 33.17 3.51
173 174 0.826715 TTCGAGAATCAGAGGCTGGG 59.173 55.000 0.00 0.00 33.17 4.45
186 187 5.185249 AGCTAACTGGTGAAAGTATTCGAGA 59.815 40.000 0.00 0.00 38.46 4.04
238 286 3.513515 AGGAAAGGCTCAAACACAAACAA 59.486 39.130 0.00 0.00 0.00 2.83
303 351 0.878416 GTGTGTGTGTGTGTGGTTGT 59.122 50.000 0.00 0.00 0.00 3.32
304 352 0.877743 TGTGTGTGTGTGTGTGGTTG 59.122 50.000 0.00 0.00 0.00 3.77
305 353 0.878416 GTGTGTGTGTGTGTGTGGTT 59.122 50.000 0.00 0.00 0.00 3.67
306 354 0.250510 TGTGTGTGTGTGTGTGTGGT 60.251 50.000 0.00 0.00 0.00 4.16
307 355 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
308 356 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
309 357 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
310 358 0.179192 GCTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
311 359 0.605050 TGCTGTGTGTGTGTGTGTGT 60.605 50.000 0.00 0.00 0.00 3.72
312 360 0.734309 ATGCTGTGTGTGTGTGTGTG 59.266 50.000 0.00 0.00 0.00 3.82
313 361 1.401552 GAATGCTGTGTGTGTGTGTGT 59.598 47.619 0.00 0.00 0.00 3.72
314 362 1.672363 AGAATGCTGTGTGTGTGTGTG 59.328 47.619 0.00 0.00 0.00 3.82
315 363 1.942657 GAGAATGCTGTGTGTGTGTGT 59.057 47.619 0.00 0.00 0.00 3.72
316 364 1.070376 CGAGAATGCTGTGTGTGTGTG 60.070 52.381 0.00 0.00 0.00 3.82
450 502 5.831525 TGTTGTGTCCTAGAAACAGAGTCTA 59.168 40.000 0.00 0.00 30.92 2.59
453 505 5.552870 ATGTTGTGTCCTAGAAACAGAGT 57.447 39.130 0.00 0.00 36.09 3.24
476 528 0.830648 TCGCAGGGCTACAAGCTAAT 59.169 50.000 0.00 0.00 41.99 1.73
494 547 3.536956 TTACCACTGATCCGGACAATC 57.463 47.619 6.12 0.09 0.00 2.67
500 561 0.469917 AGGCATTACCACTGATCCGG 59.530 55.000 0.00 0.00 43.14 5.14
511 572 3.181500 CCGAAAAGTAGCCAAGGCATTAC 60.181 47.826 14.40 8.03 44.88 1.89
563 624 4.036734 ACATGTCATCTGGTGTTCACAAAC 59.963 41.667 0.00 0.00 35.85 2.93
644 713 6.389869 TCCTAATAACAGAATCAGGGGTTCAT 59.610 38.462 0.00 0.00 0.00 2.57
648 717 5.036916 TGTCCTAATAACAGAATCAGGGGT 58.963 41.667 0.00 0.00 0.00 4.95
653 725 9.476202 CAACGATATGTCCTAATAACAGAATCA 57.524 33.333 0.00 0.00 0.00 2.57
654 726 8.436200 GCAACGATATGTCCTAATAACAGAATC 58.564 37.037 0.00 0.00 0.00 2.52
696 772 9.687210 GCTCATTATTGCTCATTTCATGAATTA 57.313 29.630 9.40 0.00 39.11 1.40
721 797 6.978659 CCATCCAGAATATTTCATATGCATGC 59.021 38.462 11.82 11.82 31.73 4.06
757 833 7.815641 TGGATATGAAACATAACAACACAGTG 58.184 34.615 0.00 0.00 0.00 3.66
874 952 0.034089 ATTTGTGACCCTAGCCCAGC 60.034 55.000 0.00 0.00 0.00 4.85
952 1072 9.922305 GCTAACATAATGTCACAAAGATAGAAC 57.078 33.333 0.00 0.00 0.00 3.01
967 1087 6.331845 TGCCAGTTCAATTGCTAACATAATG 58.668 36.000 11.37 2.77 0.00 1.90
971 1091 3.194116 CCTGCCAGTTCAATTGCTAACAT 59.806 43.478 11.37 0.00 0.00 2.71
981 1101 4.018870 TCCATGTATAACCTGCCAGTTCAA 60.019 41.667 0.00 0.00 0.00 2.69
988 1108 4.085357 TGTCATCCATGTATAACCTGCC 57.915 45.455 0.00 0.00 0.00 4.85
1011 1131 3.821841 CTTAAGAACCAATGCGTCAACC 58.178 45.455 0.00 0.00 0.00 3.77
1017 1137 3.189287 ACTGAAGCTTAAGAACCAATGCG 59.811 43.478 18.30 0.00 0.00 4.73
1053 1173 0.250038 CGACACTGGCATCCCTATGG 60.250 60.000 0.00 0.00 33.38 2.74
1074 1194 5.990668 ACCATAGACTTGATTTCCAGGTAC 58.009 41.667 0.00 0.00 35.02 3.34
1090 1210 7.147966 TGCTTCTACGAGTTTATCAACCATAGA 60.148 37.037 0.00 0.00 32.70 1.98
1092 1212 6.869695 TGCTTCTACGAGTTTATCAACCATA 58.130 36.000 0.00 0.00 32.70 2.74
1392 1543 3.801293 GCAAGCTCCTTCTTTGTTGCAAT 60.801 43.478 0.59 0.00 40.01 3.56
1394 1545 1.067516 GCAAGCTCCTTCTTTGTTGCA 59.932 47.619 0.00 0.00 40.01 4.08
1446 1597 2.305927 TCCTTAAACCCTCCAGCTCTTG 59.694 50.000 0.00 0.00 0.00 3.02
1473 1624 6.365970 AGGTACATGTTCACTCTCTTGAAT 57.634 37.500 2.30 0.00 37.80 2.57
1523 1674 0.462759 GGCTTCCACGGAGAAGGATG 60.463 60.000 15.79 5.59 42.94 3.51
1587 1790 4.517453 TCAAAATACGACCCCACAAGAAAG 59.483 41.667 0.00 0.00 0.00 2.62
1596 1799 2.874086 CCGGTAATCAAAATACGACCCC 59.126 50.000 0.00 0.00 0.00 4.95
1617 1820 4.022242 TGTTACCTGCTTACACAGAGACTC 60.022 45.833 0.00 0.00 40.25 3.36
1689 1892 1.893808 GGCGATGTCCATCCGCATT 60.894 57.895 18.59 0.00 38.30 3.56
1720 1923 1.147153 GCATGCTGGTAGGACCTCC 59.853 63.158 11.37 0.00 39.58 4.30
1721 1924 0.253044 TTGCATGCTGGTAGGACCTC 59.747 55.000 20.33 0.00 39.58 3.85
1722 1925 0.254178 CTTGCATGCTGGTAGGACCT 59.746 55.000 20.33 0.00 39.58 3.85
1730 1933 0.179111 CATCTTGGCTTGCATGCTGG 60.179 55.000 22.27 12.33 0.00 4.85
1750 1953 1.271597 GCCTGATCACCTCCAAGTTGT 60.272 52.381 1.45 0.00 0.00 3.32
1751 1954 1.271543 TGCCTGATCACCTCCAAGTTG 60.272 52.381 0.00 0.00 0.00 3.16
1752 1955 1.067295 TGCCTGATCACCTCCAAGTT 58.933 50.000 0.00 0.00 0.00 2.66
1858 2093 6.071447 AGCAACACCTATCTATATGCTCAGAG 60.071 42.308 0.00 0.00 38.16 3.35
1860 2095 6.035368 AGCAACACCTATCTATATGCTCAG 57.965 41.667 0.00 0.00 38.16 3.35
1862 2097 9.522804 GTATAAGCAACACCTATCTATATGCTC 57.477 37.037 0.00 0.00 41.42 4.26
1863 2098 9.035890 TGTATAAGCAACACCTATCTATATGCT 57.964 33.333 0.00 0.00 43.89 3.79
1864 2099 9.088512 GTGTATAAGCAACACCTATCTATATGC 57.911 37.037 0.00 0.00 41.10 3.14
1869 2104 9.138596 TGTATGTGTATAAGCAACACCTATCTA 57.861 33.333 4.09 0.00 45.33 1.98
1870 2105 8.018537 TGTATGTGTATAAGCAACACCTATCT 57.981 34.615 4.09 0.00 45.33 1.98
1871 2106 8.833231 ATGTATGTGTATAAGCAACACCTATC 57.167 34.615 4.09 0.00 45.33 2.08
1872 2107 9.706691 GTATGTATGTGTATAAGCAACACCTAT 57.293 33.333 4.09 0.00 45.33 2.57
1873 2108 8.697292 TGTATGTATGTGTATAAGCAACACCTA 58.303 33.333 4.09 0.00 45.33 3.08
1874 2109 7.561251 TGTATGTATGTGTATAAGCAACACCT 58.439 34.615 4.09 0.00 45.33 4.00
1875 2110 7.780008 TGTATGTATGTGTATAAGCAACACC 57.220 36.000 4.09 0.00 45.33 4.16
1879 2114 9.705290 CCTGTATGTATGTATGTGTATAAGCAA 57.295 33.333 0.00 0.00 0.00 3.91
1880 2115 8.866093 ACCTGTATGTATGTATGTGTATAAGCA 58.134 33.333 0.00 0.00 0.00 3.91
1885 2120 8.258007 GCCATACCTGTATGTATGTATGTGTAT 58.742 37.037 14.42 0.00 44.24 2.29
1886 2121 7.453439 AGCCATACCTGTATGTATGTATGTGTA 59.547 37.037 14.42 0.00 44.24 2.90
1887 2122 6.270000 AGCCATACCTGTATGTATGTATGTGT 59.730 38.462 14.42 0.00 44.24 3.72
1888 2123 6.701340 AGCCATACCTGTATGTATGTATGTG 58.299 40.000 14.42 0.12 44.24 3.21
1889 2124 6.935240 AGCCATACCTGTATGTATGTATGT 57.065 37.500 14.42 0.00 44.24 2.29
1890 2125 7.386059 TGAAGCCATACCTGTATGTATGTATG 58.614 38.462 14.42 0.00 44.24 2.39
1891 2126 7.235606 ACTGAAGCCATACCTGTATGTATGTAT 59.764 37.037 14.42 0.00 44.24 2.29
1896 2396 4.959839 TCACTGAAGCCATACCTGTATGTA 59.040 41.667 14.42 0.00 40.90 2.29
1920 2420 6.030849 CGAGATGGTTGTACTAAGTTCAGAG 58.969 44.000 0.00 0.00 0.00 3.35
1973 2479 6.441093 ACTAAATGTTGGTGTGCTCATATG 57.559 37.500 0.00 0.00 0.00 1.78
1984 2490 9.063615 CAAGGACTAACTTAACTAAATGTTGGT 57.936 33.333 0.00 0.00 39.55 3.67
1995 2501 5.148651 TCAGGAGCAAGGACTAACTTAAC 57.851 43.478 0.00 0.00 0.00 2.01
2028 2534 3.598019 AACCGGCGATAAAACTAGTCA 57.402 42.857 9.30 0.00 0.00 3.41
2070 2576 9.076596 GCATCTTGGTGTCTTAAATAATTGAAC 57.923 33.333 0.00 0.00 0.00 3.18
2073 2579 9.722056 GTAGCATCTTGGTGTCTTAAATAATTG 57.278 33.333 0.00 0.00 0.00 2.32
2193 2870 4.569719 ACCTGAAACCTATCAATTCCGT 57.430 40.909 0.00 0.00 0.00 4.69
2194 2871 5.878116 TGTTACCTGAAACCTATCAATTCCG 59.122 40.000 0.00 0.00 0.00 4.30
2227 2913 9.974980 GGTTTCTGTAATTCTTGACCATAAAAA 57.025 29.630 0.00 0.00 0.00 1.94
2228 2914 9.362151 AGGTTTCTGTAATTCTTGACCATAAAA 57.638 29.630 0.00 0.00 0.00 1.52
2229 2915 8.934023 AGGTTTCTGTAATTCTTGACCATAAA 57.066 30.769 0.00 0.00 0.00 1.40
2237 2925 6.587608 GCATCCAAAGGTTTCTGTAATTCTTG 59.412 38.462 0.00 0.00 0.00 3.02
2285 2973 4.020218 TCACCAGAACCTGAAACTAGGATG 60.020 45.833 0.00 0.00 40.42 3.51
2325 3013 6.294363 CGTTCCAAAATACGTTGAGTAACTC 58.706 40.000 0.00 0.00 39.04 3.01
2326 3014 5.178067 CCGTTCCAAAATACGTTGAGTAACT 59.822 40.000 0.00 0.00 39.04 2.24
2327 3015 5.177327 TCCGTTCCAAAATACGTTGAGTAAC 59.823 40.000 0.00 0.00 39.04 2.50
2328 3016 5.295950 TCCGTTCCAAAATACGTTGAGTAA 58.704 37.500 0.00 0.00 39.04 2.24
2329 3017 4.880759 TCCGTTCCAAAATACGTTGAGTA 58.119 39.130 0.00 0.00 40.03 2.59
2330 3018 3.731089 TCCGTTCCAAAATACGTTGAGT 58.269 40.909 0.00 0.00 36.09 3.41
2331 3019 3.124636 CCTCCGTTCCAAAATACGTTGAG 59.875 47.826 0.00 0.00 36.09 3.02
2332 3020 3.068560 CCTCCGTTCCAAAATACGTTGA 58.931 45.455 0.00 0.00 36.09 3.18
2333 3021 2.160813 CCCTCCGTTCCAAAATACGTTG 59.839 50.000 0.00 0.00 36.09 4.10
2334 3022 2.038820 TCCCTCCGTTCCAAAATACGTT 59.961 45.455 0.00 0.00 36.09 3.99
2335 3023 1.624813 TCCCTCCGTTCCAAAATACGT 59.375 47.619 0.00 0.00 36.09 3.57
2336 3024 2.277084 CTCCCTCCGTTCCAAAATACG 58.723 52.381 0.00 0.00 37.50 3.06
2337 3025 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
2338 3026 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
2339 3027 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2340 3028 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
2341 3029 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2342 3030 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2343 3031 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
2344 3032 0.460722 GAAGCTACTCCCTCCGTTCC 59.539 60.000 0.00 0.00 0.00 3.62
2345 3033 1.476477 AGAAGCTACTCCCTCCGTTC 58.524 55.000 0.00 0.00 0.00 3.95
2346 3034 2.822707 TAGAAGCTACTCCCTCCGTT 57.177 50.000 0.00 0.00 0.00 4.44
2347 3035 2.759535 GTTTAGAAGCTACTCCCTCCGT 59.240 50.000 0.00 0.00 0.00 4.69
2348 3036 2.101082 GGTTTAGAAGCTACTCCCTCCG 59.899 54.545 0.00 0.00 0.00 4.63
2349 3037 3.376636 AGGTTTAGAAGCTACTCCCTCC 58.623 50.000 0.00 0.00 37.49 4.30
2350 3038 3.067040 CGAGGTTTAGAAGCTACTCCCTC 59.933 52.174 0.00 0.00 39.77 4.30
2351 3039 3.025262 CGAGGTTTAGAAGCTACTCCCT 58.975 50.000 0.00 0.00 39.77 4.20
2352 3040 3.022406 TCGAGGTTTAGAAGCTACTCCC 58.978 50.000 0.00 0.00 39.77 4.30
2353 3041 3.181488 GGTCGAGGTTTAGAAGCTACTCC 60.181 52.174 0.00 0.00 39.77 3.85
2354 3042 3.442977 TGGTCGAGGTTTAGAAGCTACTC 59.557 47.826 0.00 0.00 39.77 2.59
2355 3043 3.193056 GTGGTCGAGGTTTAGAAGCTACT 59.807 47.826 0.00 0.00 39.77 2.57
2356 3044 3.057033 TGTGGTCGAGGTTTAGAAGCTAC 60.057 47.826 0.00 0.00 39.77 3.58
2376 3064 3.136626 AGAGCAAAAGGTACAAGAGGTGT 59.863 43.478 0.00 0.00 44.82 4.16
2377 3065 3.499918 CAGAGCAAAAGGTACAAGAGGTG 59.500 47.826 0.00 0.00 0.00 4.00
2402 3090 7.980662 TCAATATCAAAAGGTAATTGTGGCATG 59.019 33.333 0.00 0.00 0.00 4.06
2427 3115 4.882671 ATGTGGCGACATAAAGTGATTC 57.117 40.909 13.16 0.00 46.14 2.52
2431 3119 4.212004 CCTGATATGTGGCGACATAAAGTG 59.788 45.833 23.00 13.84 45.99 3.16
2432 3120 4.380531 CCTGATATGTGGCGACATAAAGT 58.619 43.478 23.00 9.11 45.99 2.66
2446 3137 1.143813 AACCCTCCTGGCCTGATATG 58.856 55.000 11.88 0.00 37.83 1.78
2477 3168 3.739519 GCAGCATAGGAACTCGATTGACT 60.740 47.826 0.00 0.00 41.75 3.41
2514 3233 4.160439 CCACAGAAGGTAAGTATGAGCTCA 59.840 45.833 20.79 20.79 0.00 4.26
2536 3255 4.012895 CACACAACCTGCGCGACC 62.013 66.667 12.10 0.00 0.00 4.79
2630 3365 4.160642 ACAAACGGAGGGAGTAACTTTT 57.839 40.909 0.00 0.00 0.00 2.27
2640 3375 5.179929 ACGTCTTATAAAAACAAACGGAGGG 59.820 40.000 0.00 0.00 33.26 4.30
2641 3376 6.232139 ACGTCTTATAAAAACAAACGGAGG 57.768 37.500 0.00 0.00 33.26 4.30
2642 3377 7.346695 TGAACGTCTTATAAAAACAAACGGAG 58.653 34.615 0.00 0.00 33.26 4.63
2643 3378 7.224362 TCTGAACGTCTTATAAAAACAAACGGA 59.776 33.333 0.00 0.00 33.26 4.69
2644 3379 7.319615 GTCTGAACGTCTTATAAAAACAAACGG 59.680 37.037 0.00 0.00 33.26 4.44
2645 3380 7.847078 TGTCTGAACGTCTTATAAAAACAAACG 59.153 33.333 0.00 0.00 35.00 3.60
2646 3381 9.493206 TTGTCTGAACGTCTTATAAAAACAAAC 57.507 29.630 0.00 0.00 0.00 2.93
2647 3382 9.493206 GTTGTCTGAACGTCTTATAAAAACAAA 57.507 29.630 0.00 0.00 0.00 2.83
2648 3383 8.885722 AGTTGTCTGAACGTCTTATAAAAACAA 58.114 29.630 0.00 0.00 0.00 2.83
2649 3384 8.428186 AGTTGTCTGAACGTCTTATAAAAACA 57.572 30.769 0.00 0.00 0.00 2.83
2650 3385 9.155053 CAAGTTGTCTGAACGTCTTATAAAAAC 57.845 33.333 0.00 0.00 0.00 2.43
2651 3386 7.853929 GCAAGTTGTCTGAACGTCTTATAAAAA 59.146 33.333 4.48 0.00 0.00 1.94
2652 3387 7.225931 AGCAAGTTGTCTGAACGTCTTATAAAA 59.774 33.333 4.48 0.00 0.00 1.52
2653 3388 6.704493 AGCAAGTTGTCTGAACGTCTTATAAA 59.296 34.615 4.48 0.00 0.00 1.40
2654 3389 6.220930 AGCAAGTTGTCTGAACGTCTTATAA 58.779 36.000 4.48 0.00 0.00 0.98
2655 3390 5.779922 AGCAAGTTGTCTGAACGTCTTATA 58.220 37.500 4.48 0.00 0.00 0.98
2656 3391 4.632153 AGCAAGTTGTCTGAACGTCTTAT 58.368 39.130 4.48 0.00 0.00 1.73
2657 3392 4.054780 AGCAAGTTGTCTGAACGTCTTA 57.945 40.909 4.48 0.00 0.00 2.10
2658 3393 2.906354 AGCAAGTTGTCTGAACGTCTT 58.094 42.857 4.48 0.00 0.00 3.01
2659 3394 2.604046 AGCAAGTTGTCTGAACGTCT 57.396 45.000 4.48 0.00 0.00 4.18
2660 3395 3.181510 ACAAAGCAAGTTGTCTGAACGTC 60.182 43.478 4.48 0.00 37.10 4.34
2661 3396 2.747446 ACAAAGCAAGTTGTCTGAACGT 59.253 40.909 4.48 0.00 37.10 3.99
2662 3397 3.100817 CACAAAGCAAGTTGTCTGAACG 58.899 45.455 4.48 0.00 39.73 3.95
2663 3398 2.854185 GCACAAAGCAAGTTGTCTGAAC 59.146 45.455 4.48 0.00 44.79 3.18
2664 3399 3.149436 GCACAAAGCAAGTTGTCTGAA 57.851 42.857 4.48 0.00 44.79 3.02
2665 3400 2.849880 GCACAAAGCAAGTTGTCTGA 57.150 45.000 4.48 0.00 44.79 3.27
2670 3405 9.565596 TGTTCAAAAACAGCACAAAGCAAGTTG 62.566 37.037 0.00 0.00 41.07 3.16
2671 3406 7.672933 TGTTCAAAAACAGCACAAAGCAAGTT 61.673 34.615 0.00 0.00 42.87 2.66
2672 3407 6.253117 TGTTCAAAAACAGCACAAAGCAAGT 61.253 36.000 0.00 0.00 40.45 3.16
2673 3408 4.152045 TGTTCAAAAACAGCACAAAGCAAG 59.848 37.500 0.00 0.00 40.45 4.01
2674 3409 4.060900 TGTTCAAAAACAGCACAAAGCAA 58.939 34.783 0.00 0.00 40.45 3.91
2675 3410 3.657634 TGTTCAAAAACAGCACAAAGCA 58.342 36.364 0.00 0.00 40.45 3.91
2685 3420 6.206634 AGACTTTCAGACACTGTTCAAAAACA 59.793 34.615 0.00 0.00 43.06 2.83
2686 3421 6.612306 AGACTTTCAGACACTGTTCAAAAAC 58.388 36.000 0.00 0.00 35.85 2.43
2687 3422 6.817765 AGACTTTCAGACACTGTTCAAAAA 57.182 33.333 0.00 0.00 32.61 1.94
2688 3423 7.915293 TTAGACTTTCAGACACTGTTCAAAA 57.085 32.000 0.00 0.00 32.61 2.44
2689 3424 7.915293 TTTAGACTTTCAGACACTGTTCAAA 57.085 32.000 0.00 0.00 32.61 2.69
2690 3425 7.412563 CGTTTTAGACTTTCAGACACTGTTCAA 60.413 37.037 0.00 0.00 32.61 2.69
2691 3426 6.035650 CGTTTTAGACTTTCAGACACTGTTCA 59.964 38.462 0.00 0.00 32.61 3.18
2692 3427 6.035758 ACGTTTTAGACTTTCAGACACTGTTC 59.964 38.462 0.00 0.00 32.61 3.18
2693 3428 5.873164 ACGTTTTAGACTTTCAGACACTGTT 59.127 36.000 0.00 0.00 32.61 3.16
2694 3429 5.416947 ACGTTTTAGACTTTCAGACACTGT 58.583 37.500 0.00 0.00 32.61 3.55
2695 3430 5.749109 AGACGTTTTAGACTTTCAGACACTG 59.251 40.000 0.00 0.00 0.00 3.66
2696 3431 5.903810 AGACGTTTTAGACTTTCAGACACT 58.096 37.500 0.00 0.00 0.00 3.55
2697 3432 6.585389 AAGACGTTTTAGACTTTCAGACAC 57.415 37.500 0.00 0.00 0.00 3.67
2698 3433 9.970395 TTATAAGACGTTTTAGACTTTCAGACA 57.030 29.630 4.75 0.00 0.00 3.41
2711 3446 9.511144 CCTCTGTTTGTTTTTATAAGACGTTTT 57.489 29.630 0.00 0.00 0.00 2.43
2712 3447 8.680001 ACCTCTGTTTGTTTTTATAAGACGTTT 58.320 29.630 0.00 0.00 0.00 3.60
2713 3448 8.217131 ACCTCTGTTTGTTTTTATAAGACGTT 57.783 30.769 0.00 0.00 0.00 3.99
2714 3449 7.797038 ACCTCTGTTTGTTTTTATAAGACGT 57.203 32.000 0.00 0.00 0.00 4.34
2715 3450 8.985805 ACTACCTCTGTTTGTTTTTATAAGACG 58.014 33.333 0.00 0.00 0.00 4.18
2723 3458 9.623000 AACATAGTACTACCTCTGTTTGTTTTT 57.377 29.630 4.31 0.00 30.28 1.94
2725 3460 9.924650 CTAACATAGTACTACCTCTGTTTGTTT 57.075 33.333 19.49 3.82 34.68 2.83
2726 3461 8.033626 GCTAACATAGTACTACCTCTGTTTGTT 58.966 37.037 19.49 17.18 34.68 2.83
2727 3462 7.396623 AGCTAACATAGTACTACCTCTGTTTGT 59.603 37.037 19.49 9.47 34.68 2.83
2728 3463 7.773149 AGCTAACATAGTACTACCTCTGTTTG 58.227 38.462 19.49 18.22 34.68 2.93
2729 3464 7.957992 AGCTAACATAGTACTACCTCTGTTT 57.042 36.000 19.49 5.02 34.68 2.83
2730 3465 7.501892 GGTAGCTAACATAGTACTACCTCTGTT 59.498 40.741 18.68 18.68 46.14 3.16
2731 3466 6.997476 GGTAGCTAACATAGTACTACCTCTGT 59.003 42.308 4.31 2.81 46.14 3.41
2732 3467 7.437793 GGTAGCTAACATAGTACTACCTCTG 57.562 44.000 4.31 2.13 46.14 3.35
2737 3472 9.499479 TGTCATAGGTAGCTAACATAGTACTAC 57.501 37.037 12.26 0.00 33.93 2.73
2738 3473 9.499479 GTGTCATAGGTAGCTAACATAGTACTA 57.501 37.037 12.26 4.77 0.00 1.82
2739 3474 8.219178 AGTGTCATAGGTAGCTAACATAGTACT 58.781 37.037 12.26 0.00 0.00 2.73
2740 3475 8.291032 CAGTGTCATAGGTAGCTAACATAGTAC 58.709 40.741 12.26 3.18 0.00 2.73
2741 3476 8.215736 TCAGTGTCATAGGTAGCTAACATAGTA 58.784 37.037 12.26 0.00 0.00 1.82
2742 3477 7.061054 TCAGTGTCATAGGTAGCTAACATAGT 58.939 38.462 12.26 0.00 0.00 2.12
2743 3478 7.511959 TCAGTGTCATAGGTAGCTAACATAG 57.488 40.000 12.26 0.00 0.00 2.23
2744 3479 7.505923 ACATCAGTGTCATAGGTAGCTAACATA 59.494 37.037 12.26 1.02 31.41 2.29
2745 3480 6.325028 ACATCAGTGTCATAGGTAGCTAACAT 59.675 38.462 12.26 0.00 31.41 2.71
2746 3481 5.656859 ACATCAGTGTCATAGGTAGCTAACA 59.343 40.000 12.26 4.11 31.41 2.41
2747 3482 6.150396 ACATCAGTGTCATAGGTAGCTAAC 57.850 41.667 5.62 0.00 31.41 2.34
2748 3483 6.379988 TCAACATCAGTGTCATAGGTAGCTAA 59.620 38.462 5.62 0.00 37.67 3.09
2749 3484 5.891551 TCAACATCAGTGTCATAGGTAGCTA 59.108 40.000 3.73 3.73 37.67 3.32
2750 3485 4.711846 TCAACATCAGTGTCATAGGTAGCT 59.288 41.667 0.00 0.00 37.67 3.32
2751 3486 5.011090 TCAACATCAGTGTCATAGGTAGC 57.989 43.478 0.00 0.00 37.67 3.58
2752 3487 8.417106 ACTATTCAACATCAGTGTCATAGGTAG 58.583 37.037 0.00 0.00 37.67 3.18
2753 3488 8.306313 ACTATTCAACATCAGTGTCATAGGTA 57.694 34.615 0.00 0.00 37.67 3.08
2754 3489 7.187824 ACTATTCAACATCAGTGTCATAGGT 57.812 36.000 0.00 0.00 37.67 3.08


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

AutoCloner maintained by Alex Coulton.