Multiple sequence alignment - TraesCS5B01G478900

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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 TraesCS5B01G478900 chr5B 100.000 2975 0 0 1 2975 650342676 650345650 0.000000e+00 5494.0
1 TraesCS5B01G478900 chr5B 93.827 81 3 1 2622 2702 644352469 644352391 1.450000e-23 121.0
2 TraesCS5B01G478900 chr5B 89.000 100 7 2 2626 2725 660271256 660271161 1.450000e-23 121.0
3 TraesCS5B01G478900 chr5B 92.308 78 6 0 2623 2700 194191117 194191040 8.720000e-21 111.0
4 TraesCS5B01G478900 chr5A 87.831 2646 168 80 77 2629 645130968 645133552 0.000000e+00 2961.0
5 TraesCS5B01G478900 chr5A 90.041 241 12 6 2743 2975 645133674 645133910 4.820000e-78 302.0
6 TraesCS5B01G478900 chr5D 90.264 1592 75 36 77 1637 517757443 517758985 0.000000e+00 2008.0
7 TraesCS5B01G478900 chr5D 81.573 966 78 33 1681 2603 517758992 517759900 0.000000e+00 706.0
8 TraesCS5B01G478900 chr5D 80.714 280 27 12 2704 2975 517759955 517760215 3.030000e-45 193.0
9 TraesCS5B01G478900 chr5D 94.805 77 4 0 2626 2702 169535244 169535168 1.450000e-23 121.0
10 TraesCS5B01G478900 chr5D 96.364 55 2 0 2549 2603 517759880 517759934 1.140000e-14 91.6
11 TraesCS5B01G478900 chr6B 97.290 701 18 1 1903 2602 7599094 7598394 0.000000e+00 1188.0
12 TraesCS5B01G478900 chr6B 91.986 287 9 7 2698 2975 7598381 7598100 1.000000e-104 390.0
13 TraesCS5B01G478900 chr2B 97.500 80 2 0 2627 2706 782533479 782533400 1.440000e-28 137.0
14 TraesCS5B01G478900 chr2B 94.937 79 3 1 2627 2705 772053322 772053245 4.030000e-24 122.0
15 TraesCS5B01G478900 chr2B 90.698 86 6 2 2627 2711 772053248 772053332 2.420000e-21 113.0
16 TraesCS5B01G478900 chr4B 96.104 77 1 1 2626 2702 668868292 668868218 1.120000e-24 124.0
17 TraesCS5B01G478900 chr4B 91.765 85 2 3 2626 2705 477150329 477150245 2.420000e-21 113.0
18 TraesCS5B01G478900 chr4A 82.883 111 7 4 2602 2702 607266485 607266593 4.080000e-14 89.8
19 TraesCS5B01G478900 chr7D 82.857 105 10 6 2604 2704 40483651 40483551 1.470000e-13 87.9


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 TraesCS5B01G478900 chr5B 650342676 650345650 2974 False 5494.00 5494 100.00000 1 2975 1 chr5B.!!$F1 2974
1 TraesCS5B01G478900 chr5A 645130968 645133910 2942 False 1631.50 2961 88.93600 77 2975 2 chr5A.!!$F1 2898
2 TraesCS5B01G478900 chr5D 517757443 517760215 2772 False 749.65 2008 87.22875 77 2975 4 chr5D.!!$F1 2898
3 TraesCS5B01G478900 chr6B 7598100 7599094 994 True 789.00 1188 94.63800 1903 2975 2 chr6B.!!$R1 1072

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
38 39 0.178990 AAACACCCTTCCACTGCCTC 60.179 55.0 0.00 0.00 0.0 4.70 F
43 44 0.178992 CCCTTCCACTGCCTCAACAA 60.179 55.0 0.00 0.00 0.0 2.83 F
385 402 0.687098 ATTTCCGGGCATGCATCCAA 60.687 50.0 21.36 5.54 0.0 3.53 F
796 823 0.716666 GCGGAAGAAGCTTCGAGTTC 59.283 55.0 20.43 17.46 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1798 0.966179 AATTTCAAGCGAACACCCCC 59.034 50.0 0.00 0.00 0.0 5.40 R
1800 1848 1.594331 AAATAGATTTCGGCCGCTCC 58.406 50.0 23.51 9.47 0.0 4.70 R
1801 1849 2.737252 CCTAAATAGATTTCGGCCGCTC 59.263 50.0 23.51 16.83 0.0 5.03 R
2684 2830 0.033796 TGTACTCCCTCCGTTCCGAT 60.034 55.0 0.00 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
24 25 7.470289 GACATCATACTACAGATCCAAACAC 57.530 40.000 0.00 0.00 0.00 3.32
25 26 6.349300 ACATCATACTACAGATCCAAACACC 58.651 40.000 0.00 0.00 0.00 4.16
26 27 5.353394 TCATACTACAGATCCAAACACCC 57.647 43.478 0.00 0.00 0.00 4.61
27 28 5.030147 TCATACTACAGATCCAAACACCCT 58.970 41.667 0.00 0.00 0.00 4.34
28 29 5.487488 TCATACTACAGATCCAAACACCCTT 59.513 40.000 0.00 0.00 0.00 3.95
29 30 4.287766 ACTACAGATCCAAACACCCTTC 57.712 45.455 0.00 0.00 0.00 3.46
30 31 2.586648 ACAGATCCAAACACCCTTCC 57.413 50.000 0.00 0.00 0.00 3.46
31 32 1.780309 ACAGATCCAAACACCCTTCCA 59.220 47.619 0.00 0.00 0.00 3.53
32 33 2.162681 CAGATCCAAACACCCTTCCAC 58.837 52.381 0.00 0.00 0.00 4.02
33 34 2.065799 AGATCCAAACACCCTTCCACT 58.934 47.619 0.00 0.00 0.00 4.00
34 35 2.162681 GATCCAAACACCCTTCCACTG 58.837 52.381 0.00 0.00 0.00 3.66
35 36 0.467290 TCCAAACACCCTTCCACTGC 60.467 55.000 0.00 0.00 0.00 4.40
36 37 1.463553 CCAAACACCCTTCCACTGCC 61.464 60.000 0.00 0.00 0.00 4.85
37 38 0.468029 CAAACACCCTTCCACTGCCT 60.468 55.000 0.00 0.00 0.00 4.75
38 39 0.178990 AAACACCCTTCCACTGCCTC 60.179 55.000 0.00 0.00 0.00 4.70
39 40 1.352622 AACACCCTTCCACTGCCTCA 61.353 55.000 0.00 0.00 0.00 3.86
40 41 1.352622 ACACCCTTCCACTGCCTCAA 61.353 55.000 0.00 0.00 0.00 3.02
41 42 0.890996 CACCCTTCCACTGCCTCAAC 60.891 60.000 0.00 0.00 0.00 3.18
42 43 1.352622 ACCCTTCCACTGCCTCAACA 61.353 55.000 0.00 0.00 0.00 3.33
43 44 0.178992 CCCTTCCACTGCCTCAACAA 60.179 55.000 0.00 0.00 0.00 2.83
44 45 1.548582 CCCTTCCACTGCCTCAACAAT 60.549 52.381 0.00 0.00 0.00 2.71
45 46 2.242043 CCTTCCACTGCCTCAACAATT 58.758 47.619 0.00 0.00 0.00 2.32
46 47 2.629617 CCTTCCACTGCCTCAACAATTT 59.370 45.455 0.00 0.00 0.00 1.82
47 48 3.826157 CCTTCCACTGCCTCAACAATTTA 59.174 43.478 0.00 0.00 0.00 1.40
48 49 4.463891 CCTTCCACTGCCTCAACAATTTAT 59.536 41.667 0.00 0.00 0.00 1.40
49 50 5.047092 CCTTCCACTGCCTCAACAATTTATT 60.047 40.000 0.00 0.00 0.00 1.40
50 51 6.418057 TTCCACTGCCTCAACAATTTATTT 57.582 33.333 0.00 0.00 0.00 1.40
51 52 5.782047 TCCACTGCCTCAACAATTTATTTG 58.218 37.500 0.00 0.00 41.36 2.32
52 53 4.389687 CCACTGCCTCAACAATTTATTTGC 59.610 41.667 0.00 0.00 39.03 3.68
53 54 4.989797 CACTGCCTCAACAATTTATTTGCA 59.010 37.500 0.00 0.00 39.03 4.08
54 55 5.119588 CACTGCCTCAACAATTTATTTGCAG 59.880 40.000 0.00 0.00 46.70 4.41
55 56 5.212532 TGCCTCAACAATTTATTTGCAGT 57.787 34.783 0.00 0.00 39.03 4.40
56 57 5.229423 TGCCTCAACAATTTATTTGCAGTC 58.771 37.500 0.00 0.00 39.03 3.51
57 58 5.010922 TGCCTCAACAATTTATTTGCAGTCT 59.989 36.000 0.00 0.00 39.03 3.24
58 59 6.208402 TGCCTCAACAATTTATTTGCAGTCTA 59.792 34.615 0.00 0.00 39.03 2.59
59 60 6.528072 GCCTCAACAATTTATTTGCAGTCTAC 59.472 38.462 0.00 0.00 39.03 2.59
60 61 7.592938 CCTCAACAATTTATTTGCAGTCTACA 58.407 34.615 0.00 0.00 39.03 2.74
61 62 7.752239 CCTCAACAATTTATTTGCAGTCTACAG 59.248 37.037 0.00 0.00 39.03 2.74
62 63 8.165239 TCAACAATTTATTTGCAGTCTACAGT 57.835 30.769 0.00 0.00 39.03 3.55
63 64 8.289618 TCAACAATTTATTTGCAGTCTACAGTC 58.710 33.333 0.00 0.00 39.03 3.51
64 65 7.986085 ACAATTTATTTGCAGTCTACAGTCT 57.014 32.000 0.00 0.00 39.03 3.24
65 66 9.502091 AACAATTTATTTGCAGTCTACAGTCTA 57.498 29.630 0.00 0.00 39.03 2.59
66 67 8.936864 ACAATTTATTTGCAGTCTACAGTCTAC 58.063 33.333 0.00 0.00 39.03 2.59
67 68 8.935844 CAATTTATTTGCAGTCTACAGTCTACA 58.064 33.333 0.00 0.00 0.00 2.74
68 69 7.884816 TTTATTTGCAGTCTACAGTCTACAC 57.115 36.000 0.00 0.00 0.00 2.90
69 70 4.929819 TTTGCAGTCTACAGTCTACACA 57.070 40.909 0.00 0.00 0.00 3.72
70 71 4.505313 TTGCAGTCTACAGTCTACACAG 57.495 45.455 0.00 0.00 0.00 3.66
71 72 3.487372 TGCAGTCTACAGTCTACACAGT 58.513 45.455 0.00 0.00 0.00 3.55
72 73 3.253432 TGCAGTCTACAGTCTACACAGTG 59.747 47.826 0.00 0.00 0.00 3.66
73 74 3.827625 CAGTCTACAGTCTACACAGTGC 58.172 50.000 0.00 0.00 0.00 4.40
74 75 3.253432 CAGTCTACAGTCTACACAGTGCA 59.747 47.826 0.00 0.00 0.00 4.57
75 76 4.082517 CAGTCTACAGTCTACACAGTGCAT 60.083 45.833 0.00 0.00 0.00 3.96
82 83 3.578716 AGTCTACACAGTGCATAAGTGGT 59.421 43.478 16.89 8.05 37.58 4.16
157 159 1.961793 ACAGCGGAAGTAAAGTGCAA 58.038 45.000 0.00 0.00 0.00 4.08
177 179 7.500559 AGTGCAAGTCAAACTAGAAATTCTTCT 59.499 33.333 0.00 0.00 44.37 2.85
183 189 9.579932 AGTCAAACTAGAAATTCTTCTTTCCAT 57.420 29.630 0.00 0.00 42.17 3.41
207 221 4.718961 ACTTTGCACACCAACTAATCTCT 58.281 39.130 0.00 0.00 31.97 3.10
209 223 3.334583 TGCACACCAACTAATCTCTCC 57.665 47.619 0.00 0.00 0.00 3.71
210 224 2.027192 TGCACACCAACTAATCTCTCCC 60.027 50.000 0.00 0.00 0.00 4.30
211 225 2.027192 GCACACCAACTAATCTCTCCCA 60.027 50.000 0.00 0.00 0.00 4.37
212 226 3.866651 CACACCAACTAATCTCTCCCAG 58.133 50.000 0.00 0.00 0.00 4.45
213 227 3.515502 CACACCAACTAATCTCTCCCAGA 59.484 47.826 0.00 0.00 34.78 3.86
214 228 4.163078 CACACCAACTAATCTCTCCCAGAT 59.837 45.833 0.00 0.00 44.56 2.90
215 229 5.363868 CACACCAACTAATCTCTCCCAGATA 59.636 44.000 0.00 0.00 41.47 1.98
216 230 5.964477 ACACCAACTAATCTCTCCCAGATAA 59.036 40.000 0.00 0.00 41.47 1.75
247 261 9.806448 TTAACAATATTACCCATGATATGCACT 57.194 29.630 0.00 0.00 0.00 4.40
248 262 7.928307 ACAATATTACCCATGATATGCACTC 57.072 36.000 0.00 0.00 0.00 3.51
249 263 6.886459 ACAATATTACCCATGATATGCACTCC 59.114 38.462 0.00 0.00 0.00 3.85
300 314 6.363357 CACACAAGGAAGCTAAATGTTTAAGC 59.637 38.462 0.00 0.00 0.00 3.09
332 346 1.635487 TCAGGGTTGCAGAATTAGCCT 59.365 47.619 0.13 0.13 40.24 4.58
353 370 4.391216 CCTCAGAAATAAGCATATCGGCAG 59.609 45.833 0.00 0.00 35.83 4.85
368 385 3.864243 TCGGCAGTTACGATAACCAATT 58.136 40.909 0.00 0.00 35.12 2.32
369 386 4.255301 TCGGCAGTTACGATAACCAATTT 58.745 39.130 0.00 0.00 35.12 1.82
385 402 0.687098 ATTTCCGGGCATGCATCCAA 60.687 50.000 21.36 5.54 0.00 3.53
404 421 1.384989 ATCCTCACCTGTACTCGCCG 61.385 60.000 0.00 0.00 0.00 6.46
474 497 5.198274 GCAGAAGCGATTAATTAAACGGAG 58.802 41.667 23.76 7.05 32.98 4.63
488 512 1.948391 ACGGAGCTAGGGTTTAAGGT 58.052 50.000 0.00 0.00 0.00 3.50
489 513 2.263545 ACGGAGCTAGGGTTTAAGGTT 58.736 47.619 0.00 0.00 0.00 3.50
498 522 2.283316 TTTAAGGTTGGGGCGGCC 60.283 61.111 22.00 22.00 0.00 6.13
796 823 0.716666 GCGGAAGAAGCTTCGAGTTC 59.283 55.000 20.43 17.46 0.00 3.01
797 824 0.985549 CGGAAGAAGCTTCGAGTTCG 59.014 55.000 20.43 15.78 41.45 3.95
865 892 1.436195 TATGCGCCAAGATTCGTGCC 61.436 55.000 4.18 0.00 34.58 5.01
866 893 3.430862 GCGCCAAGATTCGTGCCA 61.431 61.111 0.00 0.00 0.00 4.92
867 894 2.787249 CGCCAAGATTCGTGCCAG 59.213 61.111 0.00 0.00 0.00 4.85
899 927 2.125229 TCGAGAGTCGAGACCCCG 60.125 66.667 0.00 2.01 44.82 5.73
935 963 3.716195 CCGCCATGTGGGTCCAGA 61.716 66.667 0.54 0.00 39.65 3.86
937 965 2.439156 GCCATGTGGGTCCAGAGC 60.439 66.667 0.54 0.00 39.65 4.09
1023 1058 2.123033 GGAGGAGAGGAGGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1027 1062 2.371259 GGAGAGGAGGGAGGCAACC 61.371 68.421 0.00 0.00 37.17 3.77
1080 1115 2.824880 CCCCCAACCACAGACCGAA 61.825 63.158 0.00 0.00 0.00 4.30
1511 1552 1.811266 CCAACGACGCCTGATCCTG 60.811 63.158 0.00 0.00 0.00 3.86
1512 1553 2.125512 AACGACGCCTGATCCTGC 60.126 61.111 0.00 0.00 0.00 4.85
1520 1561 2.034879 CCTGATCCTGCGCGTGTTT 61.035 57.895 8.43 0.00 0.00 2.83
1521 1562 1.133253 CTGATCCTGCGCGTGTTTG 59.867 57.895 8.43 0.00 0.00 2.93
1525 1571 1.195900 GATCCTGCGCGTGTTTGTTTA 59.804 47.619 8.43 0.00 0.00 2.01
1546 1592 9.079833 TGTTTATTTAGTTAGAAATCGTCGAGG 57.920 33.333 0.00 0.00 31.51 4.63
1558 1604 1.000607 TCGTCGAGGGAAACTGTTGAG 60.001 52.381 5.12 0.00 0.00 3.02
1564 1610 1.978580 AGGGAAACTGTTGAGTCGGAT 59.021 47.619 0.00 0.00 0.00 4.18
1622 1668 2.088423 TGTTTGCGGTGGTTCCATATC 58.912 47.619 0.00 0.00 35.57 1.63
1643 1689 5.438761 TCGATATGATGAACATGACTCGT 57.561 39.130 0.00 0.00 39.77 4.18
1649 1695 5.784750 TGATGAACATGACTCGTTGATTC 57.215 39.130 0.00 0.00 0.00 2.52
1659 1705 5.045872 TGACTCGTTGATTCATAGCATCTG 58.954 41.667 0.00 0.00 0.00 2.90
1676 1722 1.799258 CTGCTTGGGTTGTCCTGTGC 61.799 60.000 0.00 0.00 36.20 4.57
1678 1724 1.109323 GCTTGGGTTGTCCTGTGCTT 61.109 55.000 0.00 0.00 36.20 3.91
1750 1798 6.128309 TGTGGATGTCAATGATCTGTTAAACG 60.128 38.462 0.00 0.00 0.00 3.60
1800 1848 6.126568 TGTGCATGATTGTTCAGATACATG 57.873 37.500 0.00 0.00 38.33 3.21
1801 1849 5.066764 TGTGCATGATTGTTCAGATACATGG 59.933 40.000 0.00 0.00 36.61 3.66
1805 1853 4.122046 TGATTGTTCAGATACATGGAGCG 58.878 43.478 0.00 0.00 0.00 5.03
1808 1856 0.106708 TTCAGATACATGGAGCGGCC 59.893 55.000 0.00 0.00 37.10 6.13
1810 1858 1.832608 AGATACATGGAGCGGCCGA 60.833 57.895 33.48 8.40 40.66 5.54
1819 1867 1.134220 TGGAGCGGCCGAAATCTATTT 60.134 47.619 33.48 0.92 40.66 1.40
1820 1868 2.103432 TGGAGCGGCCGAAATCTATTTA 59.897 45.455 33.48 6.14 40.66 1.40
1821 1869 2.737252 GGAGCGGCCGAAATCTATTTAG 59.263 50.000 33.48 0.00 0.00 1.85
1822 1870 2.737252 GAGCGGCCGAAATCTATTTAGG 59.263 50.000 33.48 9.49 42.97 2.69
1830 1878 6.645827 GGCCGAAATCTATTTAGGTAGAGAAC 59.354 42.308 13.82 0.00 42.35 3.01
1847 1895 5.819991 AGAGAACCAAATGTGTGATATGGT 58.180 37.500 0.00 0.00 45.97 3.55
1869 1928 5.064325 GGTGAGGATTCGTGTACAAATTACC 59.936 44.000 0.00 0.00 0.00 2.85
2005 2078 7.660112 TGATTATTGCTTGTTTGAACATCTGT 58.340 30.769 0.00 0.00 38.95 3.41
2151 2227 8.267894 AGTACTCATGCTATGTGATTTTACCTT 58.732 33.333 0.00 0.00 0.00 3.50
2178 2254 2.547913 TTGCTAATGCTGATTGTGCG 57.452 45.000 0.00 0.00 40.48 5.34
2358 2464 6.995511 TTGGTAGCAAATTAGCGTATCTTT 57.004 33.333 4.54 0.00 40.15 2.52
2362 2468 5.162000 AGCAAATTAGCGTATCTTTCTGC 57.838 39.130 0.00 0.00 40.15 4.26
2603 2749 2.237143 TGTCTTCCATTGACCAGCTAGG 59.763 50.000 0.00 0.00 45.67 3.02
2604 2750 1.210478 TCTTCCATTGACCAGCTAGGC 59.790 52.381 2.50 0.00 43.14 3.93
2605 2751 0.991146 TTCCATTGACCAGCTAGGCA 59.009 50.000 0.00 0.00 43.14 4.75
2606 2752 0.543277 TCCATTGACCAGCTAGGCAG 59.457 55.000 0.00 0.00 43.14 4.85
2626 2772 0.251354 CTAGTGGTGTGATGCCAGCT 59.749 55.000 0.00 0.00 36.57 4.24
2627 2773 1.482182 CTAGTGGTGTGATGCCAGCTA 59.518 52.381 0.00 0.00 36.57 3.32
2628 2774 0.036010 AGTGGTGTGATGCCAGCTAC 60.036 55.000 0.00 0.00 36.57 3.58
2629 2775 0.036010 GTGGTGTGATGCCAGCTACT 60.036 55.000 0.00 0.00 36.57 2.57
2630 2776 0.250234 TGGTGTGATGCCAGCTACTC 59.750 55.000 0.00 0.00 34.02 2.59
2631 2777 0.462759 GGTGTGATGCCAGCTACTCC 60.463 60.000 0.00 0.00 0.00 3.85
2632 2778 0.462759 GTGTGATGCCAGCTACTCCC 60.463 60.000 0.00 0.00 0.00 4.30
2633 2779 0.618680 TGTGATGCCAGCTACTCCCT 60.619 55.000 0.00 0.00 0.00 4.20
2634 2780 0.105778 GTGATGCCAGCTACTCCCTC 59.894 60.000 0.00 0.00 0.00 4.30
2635 2781 1.050988 TGATGCCAGCTACTCCCTCC 61.051 60.000 0.00 0.00 0.00 4.30
2636 2782 2.093537 GATGCCAGCTACTCCCTCCG 62.094 65.000 0.00 0.00 0.00 4.63
2637 2783 2.760385 GCCAGCTACTCCCTCCGT 60.760 66.667 0.00 0.00 0.00 4.69
2638 2784 2.359967 GCCAGCTACTCCCTCCGTT 61.360 63.158 0.00 0.00 0.00 4.44
2639 2785 1.817209 CCAGCTACTCCCTCCGTTC 59.183 63.158 0.00 0.00 0.00 3.95
2640 2786 1.677637 CCAGCTACTCCCTCCGTTCC 61.678 65.000 0.00 0.00 0.00 3.62
2641 2787 1.753463 AGCTACTCCCTCCGTTCCG 60.753 63.158 0.00 0.00 0.00 4.30
2642 2788 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
2643 2789 1.108132 GCTACTCCCTCCGTTCCGAT 61.108 60.000 0.00 0.00 0.00 4.18
2644 2790 1.400737 CTACTCCCTCCGTTCCGATT 58.599 55.000 0.00 0.00 0.00 3.34
2645 2791 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
2646 2792 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2647 2793 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2648 2794 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2649 2795 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2651 2797 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2652 2798 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2653 2799 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
2654 2800 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
2655 2801 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
2656 2802 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
2657 2803 0.452987 TCCGATTTACTCGTCGTGGG 59.547 55.000 0.00 0.00 46.18 4.61
2658 2804 0.452987 CCGATTTACTCGTCGTGGGA 59.547 55.000 0.00 0.00 46.18 4.37
2659 2805 1.066605 CCGATTTACTCGTCGTGGGAT 59.933 52.381 0.00 0.00 46.18 3.85
2660 2806 2.480759 CCGATTTACTCGTCGTGGGATT 60.481 50.000 0.00 0.00 46.18 3.01
2661 2807 3.184541 CGATTTACTCGTCGTGGGATTT 58.815 45.455 0.00 0.00 42.56 2.17
2662 2808 3.000078 CGATTTACTCGTCGTGGGATTTG 60.000 47.826 0.00 0.00 42.56 2.32
2663 2809 3.663995 TTTACTCGTCGTGGGATTTGA 57.336 42.857 0.00 0.00 0.00 2.69
2664 2810 3.663995 TTACTCGTCGTGGGATTTGAA 57.336 42.857 0.00 0.00 0.00 2.69
2665 2811 1.792006 ACTCGTCGTGGGATTTGAAC 58.208 50.000 0.00 0.00 0.00 3.18
2666 2812 1.343465 ACTCGTCGTGGGATTTGAACT 59.657 47.619 0.00 0.00 0.00 3.01
2667 2813 2.559668 ACTCGTCGTGGGATTTGAACTA 59.440 45.455 0.00 0.00 0.00 2.24
2668 2814 3.006110 ACTCGTCGTGGGATTTGAACTAA 59.994 43.478 0.00 0.00 0.00 2.24
2669 2815 3.991773 CTCGTCGTGGGATTTGAACTAAA 59.008 43.478 0.00 0.00 0.00 1.85
2670 2816 4.378774 TCGTCGTGGGATTTGAACTAAAA 58.621 39.130 0.00 0.00 0.00 1.52
2671 2817 4.211794 TCGTCGTGGGATTTGAACTAAAAC 59.788 41.667 0.00 0.00 0.00 2.43
2672 2818 4.612033 CGTCGTGGGATTTGAACTAAAACC 60.612 45.833 0.00 0.00 39.71 3.27
2673 2819 4.276431 GTCGTGGGATTTGAACTAAAACCA 59.724 41.667 0.00 0.00 41.59 3.67
2674 2820 5.048294 GTCGTGGGATTTGAACTAAAACCAT 60.048 40.000 0.00 0.00 41.59 3.55
2675 2821 5.048364 TCGTGGGATTTGAACTAAAACCATG 60.048 40.000 0.00 0.00 41.59 3.66
2676 2822 5.048364 CGTGGGATTTGAACTAAAACCATGA 60.048 40.000 0.00 0.00 42.74 3.07
2677 2823 6.156519 GTGGGATTTGAACTAAAACCATGAC 58.843 40.000 0.00 0.00 41.59 3.06
2678 2824 5.048364 TGGGATTTGAACTAAAACCATGACG 60.048 40.000 0.00 0.00 41.59 4.35
2679 2825 5.182380 GGGATTTGAACTAAAACCATGACGA 59.818 40.000 0.00 0.00 41.59 4.20
2680 2826 6.314784 GGATTTGAACTAAAACCATGACGAG 58.685 40.000 0.00 0.00 40.06 4.18
2681 2827 6.072673 GGATTTGAACTAAAACCATGACGAGT 60.073 38.462 0.00 0.00 40.06 4.18
2682 2828 7.118680 GGATTTGAACTAAAACCATGACGAGTA 59.881 37.037 0.00 0.00 40.06 2.59
2683 2829 7.789273 TTTGAACTAAAACCATGACGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
2684 2830 7.789273 TTGAACTAAAACCATGACGAGTAAA 57.211 32.000 0.00 0.00 0.00 2.01
2685 2831 7.972832 TGAACTAAAACCATGACGAGTAAAT 57.027 32.000 0.00 0.00 0.00 1.40
2686 2832 8.025243 TGAACTAAAACCATGACGAGTAAATC 57.975 34.615 0.00 0.00 0.00 2.17
2772 3002 6.002082 GGGAAACTGTACTGTCTATTTGGTT 58.998 40.000 5.81 0.00 0.00 3.67
2801 3031 3.985127 AGAGGCATGATTCCCAATTTGA 58.015 40.909 0.00 0.00 0.00 2.69
2867 3097 4.900635 AAATATAGCTTGTTTGCCTCGG 57.099 40.909 0.00 0.00 0.00 4.63
2880 3111 1.631388 TGCCTCGGAAAATCACCCTTA 59.369 47.619 0.00 0.00 0.00 2.69
2912 3151 0.107945 GTTTGTTTGCACCAAGGCCA 60.108 50.000 5.01 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.480320 GGTGTTTGGATCTGTAGTATGATGTC 59.520 42.308 0.00 0.00 0.00 3.06
1 2 6.349300 GGTGTTTGGATCTGTAGTATGATGT 58.651 40.000 0.00 0.00 0.00 3.06
2 3 5.760253 GGGTGTTTGGATCTGTAGTATGATG 59.240 44.000 0.00 0.00 0.00 3.07
3 4 5.667626 AGGGTGTTTGGATCTGTAGTATGAT 59.332 40.000 0.00 0.00 0.00 2.45
4 5 5.030147 AGGGTGTTTGGATCTGTAGTATGA 58.970 41.667 0.00 0.00 0.00 2.15
5 6 5.359194 AGGGTGTTTGGATCTGTAGTATG 57.641 43.478 0.00 0.00 0.00 2.39
6 7 5.104485 GGAAGGGTGTTTGGATCTGTAGTAT 60.104 44.000 0.00 0.00 0.00 2.12
7 8 4.224370 GGAAGGGTGTTTGGATCTGTAGTA 59.776 45.833 0.00 0.00 0.00 1.82
8 9 3.009143 GGAAGGGTGTTTGGATCTGTAGT 59.991 47.826 0.00 0.00 0.00 2.73
9 10 3.009033 TGGAAGGGTGTTTGGATCTGTAG 59.991 47.826 0.00 0.00 0.00 2.74
10 11 2.983192 TGGAAGGGTGTTTGGATCTGTA 59.017 45.455 0.00 0.00 0.00 2.74
11 12 1.780309 TGGAAGGGTGTTTGGATCTGT 59.220 47.619 0.00 0.00 0.00 3.41
12 13 2.162681 GTGGAAGGGTGTTTGGATCTG 58.837 52.381 0.00 0.00 0.00 2.90
13 14 2.065799 AGTGGAAGGGTGTTTGGATCT 58.934 47.619 0.00 0.00 0.00 2.75
14 15 2.162681 CAGTGGAAGGGTGTTTGGATC 58.837 52.381 0.00 0.00 0.00 3.36
15 16 1.823250 GCAGTGGAAGGGTGTTTGGAT 60.823 52.381 0.00 0.00 0.00 3.41
16 17 0.467290 GCAGTGGAAGGGTGTTTGGA 60.467 55.000 0.00 0.00 0.00 3.53
17 18 1.463553 GGCAGTGGAAGGGTGTTTGG 61.464 60.000 0.00 0.00 0.00 3.28
18 19 0.468029 AGGCAGTGGAAGGGTGTTTG 60.468 55.000 0.00 0.00 0.00 2.93
19 20 0.178990 GAGGCAGTGGAAGGGTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
20 21 1.352622 TGAGGCAGTGGAAGGGTGTT 61.353 55.000 0.00 0.00 0.00 3.32
21 22 1.352622 TTGAGGCAGTGGAAGGGTGT 61.353 55.000 0.00 0.00 0.00 4.16
22 23 0.890996 GTTGAGGCAGTGGAAGGGTG 60.891 60.000 0.00 0.00 0.00 4.61
23 24 1.352622 TGTTGAGGCAGTGGAAGGGT 61.353 55.000 0.00 0.00 0.00 4.34
24 25 0.178992 TTGTTGAGGCAGTGGAAGGG 60.179 55.000 0.00 0.00 0.00 3.95
25 26 1.915141 ATTGTTGAGGCAGTGGAAGG 58.085 50.000 0.00 0.00 0.00 3.46
26 27 5.649782 ATAAATTGTTGAGGCAGTGGAAG 57.350 39.130 0.00 0.00 0.00 3.46
27 28 6.222389 CAAATAAATTGTTGAGGCAGTGGAA 58.778 36.000 0.00 0.00 34.16 3.53
28 29 5.782047 CAAATAAATTGTTGAGGCAGTGGA 58.218 37.500 0.00 0.00 34.16 4.02
29 30 4.389687 GCAAATAAATTGTTGAGGCAGTGG 59.610 41.667 0.00 0.00 41.32 4.00
30 31 4.989797 TGCAAATAAATTGTTGAGGCAGTG 59.010 37.500 0.00 0.00 41.32 3.66
31 32 5.212532 TGCAAATAAATTGTTGAGGCAGT 57.787 34.783 0.00 0.00 41.32 4.40
32 33 5.773239 CTGCAAATAAATTGTTGAGGCAG 57.227 39.130 8.65 8.65 41.32 4.85
33 34 5.010922 AGACTGCAAATAAATTGTTGAGGCA 59.989 36.000 0.00 0.00 41.32 4.75
34 35 5.473039 AGACTGCAAATAAATTGTTGAGGC 58.527 37.500 0.00 0.00 41.32 4.70
35 36 7.592938 TGTAGACTGCAAATAAATTGTTGAGG 58.407 34.615 0.00 0.00 41.32 3.86
36 37 8.292448 ACTGTAGACTGCAAATAAATTGTTGAG 58.708 33.333 0.00 0.00 41.32 3.02
37 38 8.165239 ACTGTAGACTGCAAATAAATTGTTGA 57.835 30.769 0.00 0.00 41.32 3.18
38 39 8.292448 AGACTGTAGACTGCAAATAAATTGTTG 58.708 33.333 0.00 0.00 41.32 3.33
39 40 8.396272 AGACTGTAGACTGCAAATAAATTGTT 57.604 30.769 0.00 0.00 41.32 2.83
40 41 7.986085 AGACTGTAGACTGCAAATAAATTGT 57.014 32.000 0.00 0.00 41.32 2.71
41 42 8.935844 TGTAGACTGTAGACTGCAAATAAATTG 58.064 33.333 0.00 0.00 42.21 2.32
42 43 8.936864 GTGTAGACTGTAGACTGCAAATAAATT 58.063 33.333 4.12 0.00 34.93 1.82
43 44 8.094548 TGTGTAGACTGTAGACTGCAAATAAAT 58.905 33.333 4.12 0.00 34.93 1.40
44 45 7.438564 TGTGTAGACTGTAGACTGCAAATAAA 58.561 34.615 4.12 0.00 34.93 1.40
45 46 6.988522 TGTGTAGACTGTAGACTGCAAATAA 58.011 36.000 4.12 0.00 34.93 1.40
46 47 6.208797 ACTGTGTAGACTGTAGACTGCAAATA 59.791 38.462 0.37 0.00 34.93 1.40
47 48 5.011125 ACTGTGTAGACTGTAGACTGCAAAT 59.989 40.000 0.37 0.00 34.93 2.32
48 49 4.341235 ACTGTGTAGACTGTAGACTGCAAA 59.659 41.667 0.37 0.00 34.93 3.68
49 50 3.889538 ACTGTGTAGACTGTAGACTGCAA 59.110 43.478 0.37 0.00 34.93 4.08
50 51 3.253432 CACTGTGTAGACTGTAGACTGCA 59.747 47.826 2.14 0.00 33.27 4.41
51 52 3.827625 CACTGTGTAGACTGTAGACTGC 58.172 50.000 2.14 0.00 33.27 4.40
52 53 3.253432 TGCACTGTGTAGACTGTAGACTG 59.747 47.826 9.86 0.00 33.27 3.51
53 54 3.487372 TGCACTGTGTAGACTGTAGACT 58.513 45.455 9.86 0.00 33.27 3.24
54 55 3.917329 TGCACTGTGTAGACTGTAGAC 57.083 47.619 9.86 0.00 33.27 2.59
55 56 5.710567 ACTTATGCACTGTGTAGACTGTAGA 59.289 40.000 9.86 0.00 33.27 2.59
56 57 5.802451 CACTTATGCACTGTGTAGACTGTAG 59.198 44.000 9.86 0.00 33.27 2.74
57 58 5.336451 CCACTTATGCACTGTGTAGACTGTA 60.336 44.000 9.86 0.00 33.27 2.74
58 59 4.560128 CACTTATGCACTGTGTAGACTGT 58.440 43.478 9.86 0.00 34.78 3.55
59 60 3.928992 CCACTTATGCACTGTGTAGACTG 59.071 47.826 9.86 0.66 0.00 3.51
60 61 3.578716 ACCACTTATGCACTGTGTAGACT 59.421 43.478 9.86 0.00 0.00 3.24
61 62 3.926616 ACCACTTATGCACTGTGTAGAC 58.073 45.455 9.86 0.00 0.00 2.59
62 63 5.731957 TTACCACTTATGCACTGTGTAGA 57.268 39.130 9.86 0.00 0.00 2.59
63 64 5.220662 GCATTACCACTTATGCACTGTGTAG 60.221 44.000 9.86 5.00 44.99 2.74
64 65 4.634004 GCATTACCACTTATGCACTGTGTA 59.366 41.667 9.86 5.19 44.99 2.90
65 66 3.440173 GCATTACCACTTATGCACTGTGT 59.560 43.478 9.86 0.00 44.99 3.72
66 67 4.019919 GCATTACCACTTATGCACTGTG 57.980 45.455 2.76 2.76 44.99 3.66
72 73 4.399303 ACTTTGGAGCATTACCACTTATGC 59.601 41.667 0.00 0.00 45.77 3.14
73 74 5.415701 ACACTTTGGAGCATTACCACTTATG 59.584 40.000 0.00 0.00 37.13 1.90
74 75 5.570320 ACACTTTGGAGCATTACCACTTAT 58.430 37.500 0.00 0.00 37.13 1.73
75 76 4.980573 ACACTTTGGAGCATTACCACTTA 58.019 39.130 0.00 0.00 37.13 2.24
82 83 3.976169 GTGCAAACACTTTGGAGCATTA 58.024 40.909 0.00 0.00 41.75 1.90
157 159 8.980481 TGGAAAGAAGAATTTCTAGTTTGACT 57.020 30.769 0.00 0.00 42.80 3.41
177 179 2.382882 TGGTGTGCAAAGTCATGGAAA 58.617 42.857 0.00 0.00 0.00 3.13
183 189 4.460263 AGATTAGTTGGTGTGCAAAGTCA 58.540 39.130 0.00 0.00 0.00 3.41
228 242 6.959954 AGTAGGAGTGCATATCATGGGTAATA 59.040 38.462 0.00 0.00 0.00 0.98
229 243 5.787494 AGTAGGAGTGCATATCATGGGTAAT 59.213 40.000 0.00 0.00 0.00 1.89
243 257 3.320673 AGCTTGTGTTAGTAGGAGTGC 57.679 47.619 0.00 0.00 0.00 4.40
244 258 5.348997 GCTTAAGCTTGTGTTAGTAGGAGTG 59.651 44.000 20.38 0.00 38.21 3.51
245 259 5.011738 TGCTTAAGCTTGTGTTAGTAGGAGT 59.988 40.000 26.90 0.00 42.66 3.85
246 260 5.479306 TGCTTAAGCTTGTGTTAGTAGGAG 58.521 41.667 26.90 0.00 42.66 3.69
247 261 5.477607 TGCTTAAGCTTGTGTTAGTAGGA 57.522 39.130 26.90 0.00 42.66 2.94
248 262 5.468746 TGTTGCTTAAGCTTGTGTTAGTAGG 59.531 40.000 26.90 0.00 42.66 3.18
249 263 6.202954 AGTGTTGCTTAAGCTTGTGTTAGTAG 59.797 38.462 26.90 0.00 42.66 2.57
300 314 1.818674 CAACCCTGAATTCCTTTCCCG 59.181 52.381 2.27 0.00 33.04 5.14
332 346 4.960938 ACTGCCGATATGCTTATTTCTGA 58.039 39.130 0.00 0.00 0.00 3.27
353 370 3.242837 GCCCGGAAATTGGTTATCGTAAC 60.243 47.826 0.73 0.88 0.00 2.50
368 385 1.076118 ATTGGATGCATGCCCGGAA 60.076 52.632 16.68 3.37 0.00 4.30
369 386 1.529010 GATTGGATGCATGCCCGGA 60.529 57.895 16.68 3.38 0.00 5.14
385 402 1.384989 CGGCGAGTACAGGTGAGGAT 61.385 60.000 0.00 0.00 0.00 3.24
474 497 1.958549 GCCCCAACCTTAAACCCTAGC 60.959 57.143 0.00 0.00 0.00 3.42
498 522 0.460284 CAGGTAGTAACTGCGCCCTG 60.460 60.000 4.18 7.90 34.10 4.45
508 532 2.163010 CGCCGAGAACTTCAGGTAGTAA 59.837 50.000 5.53 0.00 0.00 2.24
509 533 1.741706 CGCCGAGAACTTCAGGTAGTA 59.258 52.381 5.53 0.00 0.00 1.82
510 534 0.526662 CGCCGAGAACTTCAGGTAGT 59.473 55.000 5.53 0.00 0.00 2.73
721 745 4.493747 GCTTCCGCGAGCGTACCT 62.494 66.667 8.23 0.00 37.81 3.08
727 751 3.191539 CCAGAAGCTTCCGCGAGC 61.192 66.667 22.81 10.26 42.32 5.03
728 752 1.079819 TTCCAGAAGCTTCCGCGAG 60.080 57.895 22.81 7.55 42.32 5.03
729 753 1.079819 CTTCCAGAAGCTTCCGCGA 60.080 57.895 22.81 12.61 42.32 5.87
773 800 2.391389 CGAAGCTTCTTCCGCACCC 61.391 63.158 23.50 0.00 0.00 4.61
774 801 1.355066 CTCGAAGCTTCTTCCGCACC 61.355 60.000 23.50 0.00 0.00 5.01
776 803 0.033504 AACTCGAAGCTTCTTCCGCA 59.966 50.000 23.50 1.93 0.00 5.69
865 892 1.535896 TCGAACGTTCAGGACTCTCTG 59.464 52.381 26.71 7.53 36.17 3.35
866 893 1.807742 CTCGAACGTTCAGGACTCTCT 59.192 52.381 26.71 0.00 0.00 3.10
867 894 1.805345 TCTCGAACGTTCAGGACTCTC 59.195 52.381 26.71 0.00 0.00 3.20
893 920 4.593864 GATCTCAGCCGCGGGGTC 62.594 72.222 29.38 12.31 34.97 4.46
996 1024 3.436761 CCTCCTCTCCTCCTTATTACGGT 60.437 52.174 0.00 0.00 0.00 4.83
1023 1058 1.555967 AATCGATTTGGGGGTGGTTG 58.444 50.000 4.39 0.00 0.00 3.77
1072 1107 2.423577 CTAGGGTTTGGTTTCGGTCTG 58.576 52.381 0.00 0.00 0.00 3.51
1073 1108 1.350019 CCTAGGGTTTGGTTTCGGTCT 59.650 52.381 0.00 0.00 0.00 3.85
1078 1113 1.592400 GCCGCCTAGGGTTTGGTTTC 61.592 60.000 11.72 0.00 41.48 2.78
1080 1115 2.035155 GCCGCCTAGGGTTTGGTT 59.965 61.111 11.72 0.00 41.48 3.67
1511 1552 6.072733 TCTAACTAAATAAACAAACACGCGC 58.927 36.000 5.73 0.00 0.00 6.86
1512 1553 8.478527 TTTCTAACTAAATAAACAAACACGCG 57.521 30.769 3.53 3.53 0.00 6.01
1520 1561 9.079833 CCTCGACGATTTCTAACTAAATAAACA 57.920 33.333 0.00 0.00 0.00 2.83
1521 1562 8.538039 CCCTCGACGATTTCTAACTAAATAAAC 58.462 37.037 0.00 0.00 0.00 2.01
1525 1571 6.461110 TCCCTCGACGATTTCTAACTAAAT 57.539 37.500 0.00 0.00 0.00 1.40
1546 1592 3.797256 CGATATCCGACTCAACAGTTTCC 59.203 47.826 0.00 0.00 41.76 3.13
1558 1604 3.757493 AGATTACAGGACCGATATCCGAC 59.243 47.826 0.00 0.00 44.22 4.79
1564 1610 3.296854 AGCACAGATTACAGGACCGATA 58.703 45.455 0.00 0.00 0.00 2.92
1622 1668 5.687285 TCAACGAGTCATGTTCATCATATCG 59.313 40.000 0.00 0.00 39.65 2.92
1649 1695 6.980716 AGGACAACCCAAGCAGATGCTATG 62.981 50.000 7.93 8.55 43.71 2.23
1659 1705 1.109323 AAGCACAGGACAACCCAAGC 61.109 55.000 0.00 0.00 37.41 4.01
1719 1765 5.529800 CAGATCATTGACATCCACAGCATAA 59.470 40.000 0.00 0.00 0.00 1.90
1750 1798 0.966179 AATTTCAAGCGAACACCCCC 59.034 50.000 0.00 0.00 0.00 5.40
1800 1848 1.594331 AAATAGATTTCGGCCGCTCC 58.406 50.000 23.51 9.47 0.00 4.70
1801 1849 2.737252 CCTAAATAGATTTCGGCCGCTC 59.263 50.000 23.51 16.83 0.00 5.03
1805 1853 6.342338 TCTCTACCTAAATAGATTTCGGCC 57.658 41.667 5.66 0.00 36.41 6.13
1822 1870 6.823689 ACCATATCACACATTTGGTTCTCTAC 59.176 38.462 0.00 0.00 37.40 2.59
1830 1878 4.525996 TCCTCACCATATCACACATTTGG 58.474 43.478 0.00 0.00 0.00 3.28
1836 1884 3.804325 CACGAATCCTCACCATATCACAC 59.196 47.826 0.00 0.00 0.00 3.82
1845 1893 5.064325 GGTAATTTGTACACGAATCCTCACC 59.936 44.000 0.00 0.00 0.00 4.02
1847 1895 5.795972 TGGTAATTTGTACACGAATCCTCA 58.204 37.500 0.00 0.00 0.00 3.86
1869 1928 4.553330 ACACCCACCTAAATCAGTACTG 57.447 45.455 17.17 17.17 0.00 2.74
2151 2227 6.812656 CACAATCAGCATTAGCAAACCATAAA 59.187 34.615 0.00 0.00 45.49 1.40
2195 2271 7.916914 ACCCATGAAAACACTAATACTACAC 57.083 36.000 0.00 0.00 0.00 2.90
2362 2468 7.304735 TGCACATAGCTGTTACAAATTTACAG 58.695 34.615 13.12 13.12 45.94 2.74
2603 2749 1.372087 GGCATCACACCACTAGCTGC 61.372 60.000 0.00 0.00 0.00 5.25
2604 2750 0.036105 TGGCATCACACCACTAGCTG 60.036 55.000 0.00 0.00 30.29 4.24
2605 2751 0.251354 CTGGCATCACACCACTAGCT 59.749 55.000 0.00 0.00 32.49 3.32
2606 2752 1.372087 GCTGGCATCACACCACTAGC 61.372 60.000 0.00 0.00 32.49 3.42
2607 2753 0.251354 AGCTGGCATCACACCACTAG 59.749 55.000 0.00 0.00 32.49 2.57
2608 2754 1.207089 GTAGCTGGCATCACACCACTA 59.793 52.381 0.00 0.00 32.49 2.74
2609 2755 0.036010 GTAGCTGGCATCACACCACT 60.036 55.000 0.00 0.00 32.49 4.00
2610 2756 0.036010 AGTAGCTGGCATCACACCAC 60.036 55.000 0.00 0.00 32.49 4.16
2641 2787 4.178540 TCAAATCCCACGACGAGTAAATC 58.821 43.478 0.00 0.00 0.00 2.17
2642 2788 4.196626 TCAAATCCCACGACGAGTAAAT 57.803 40.909 0.00 0.00 0.00 1.40
2643 2789 3.663995 TCAAATCCCACGACGAGTAAA 57.336 42.857 0.00 0.00 0.00 2.01
2644 2790 3.006110 AGTTCAAATCCCACGACGAGTAA 59.994 43.478 0.00 0.00 0.00 2.24
2645 2791 2.559668 AGTTCAAATCCCACGACGAGTA 59.440 45.455 0.00 0.00 0.00 2.59
2646 2792 1.343465 AGTTCAAATCCCACGACGAGT 59.657 47.619 0.00 0.00 0.00 4.18
2647 2793 2.080286 AGTTCAAATCCCACGACGAG 57.920 50.000 0.00 0.00 0.00 4.18
2648 2794 3.663995 TTAGTTCAAATCCCACGACGA 57.336 42.857 0.00 0.00 0.00 4.20
2649 2795 4.460505 GTTTTAGTTCAAATCCCACGACG 58.539 43.478 0.00 0.00 0.00 5.12
2650 2796 4.276431 TGGTTTTAGTTCAAATCCCACGAC 59.724 41.667 0.00 0.00 35.79 4.34
2651 2797 4.462133 TGGTTTTAGTTCAAATCCCACGA 58.538 39.130 0.00 0.00 35.79 4.35
2652 2798 4.839668 TGGTTTTAGTTCAAATCCCACG 57.160 40.909 0.00 0.00 35.79 4.94
2653 2799 6.156519 GTCATGGTTTTAGTTCAAATCCCAC 58.843 40.000 0.00 0.00 35.79 4.61
2654 2800 5.048364 CGTCATGGTTTTAGTTCAAATCCCA 60.048 40.000 0.00 0.00 35.79 4.37
2655 2801 5.182380 TCGTCATGGTTTTAGTTCAAATCCC 59.818 40.000 0.00 0.00 35.79 3.85
2656 2802 6.072673 ACTCGTCATGGTTTTAGTTCAAATCC 60.073 38.462 0.00 0.00 36.77 3.01
2657 2803 6.899114 ACTCGTCATGGTTTTAGTTCAAATC 58.101 36.000 0.00 0.00 0.00 2.17
2658 2804 6.877611 ACTCGTCATGGTTTTAGTTCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
2659 2805 7.789273 TTACTCGTCATGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
2660 2806 7.789273 TTTACTCGTCATGGTTTTAGTTCAA 57.211 32.000 0.00 0.00 0.00 2.69
2661 2807 7.148705 CGATTTACTCGTCATGGTTTTAGTTCA 60.149 37.037 0.00 0.00 42.56 3.18
2662 2808 7.171434 CGATTTACTCGTCATGGTTTTAGTTC 58.829 38.462 0.00 0.00 42.56 3.01
2663 2809 6.091713 CCGATTTACTCGTCATGGTTTTAGTT 59.908 38.462 0.00 0.00 46.18 2.24
2664 2810 5.579511 CCGATTTACTCGTCATGGTTTTAGT 59.420 40.000 0.00 0.00 46.18 2.24
2665 2811 5.808540 TCCGATTTACTCGTCATGGTTTTAG 59.191 40.000 0.00 0.00 46.18 1.85
2666 2812 5.722263 TCCGATTTACTCGTCATGGTTTTA 58.278 37.500 0.00 0.00 46.18 1.52
2667 2813 4.571919 TCCGATTTACTCGTCATGGTTTT 58.428 39.130 0.00 0.00 46.18 2.43
2668 2814 4.196626 TCCGATTTACTCGTCATGGTTT 57.803 40.909 0.00 0.00 46.18 3.27
2669 2815 3.880047 TCCGATTTACTCGTCATGGTT 57.120 42.857 0.00 0.00 46.18 3.67
2670 2816 3.518590 GTTCCGATTTACTCGTCATGGT 58.481 45.455 0.00 0.00 46.18 3.55
2671 2817 2.534349 CGTTCCGATTTACTCGTCATGG 59.466 50.000 0.00 0.00 46.18 3.66
2672 2818 2.534349 CCGTTCCGATTTACTCGTCATG 59.466 50.000 0.00 0.00 46.18 3.07
2673 2819 2.424601 TCCGTTCCGATTTACTCGTCAT 59.575 45.455 0.00 0.00 46.18 3.06
2674 2820 1.811965 TCCGTTCCGATTTACTCGTCA 59.188 47.619 0.00 0.00 46.18 4.35
2675 2821 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2676 2822 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2678 2824 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2679 2825 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2680 2826 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2681 2827 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2682 2828 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
2683 2829 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
2684 2830 0.033796 TGTACTCCCTCCGTTCCGAT 60.034 55.000 0.00 0.00 0.00 4.18
2685 2831 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2686 2832 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.000 0.00 0.00 0.00 4.30
2687 2833 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
2688 2834 4.667519 ATTACATGTACTCCCTCCGTTC 57.332 45.455 4.68 0.00 0.00 3.95
2689 2835 5.431179 AAATTACATGTACTCCCTCCGTT 57.569 39.130 4.68 0.00 0.00 4.44
2690 2836 5.659971 AGTAAATTACATGTACTCCCTCCGT 59.340 40.000 4.68 0.00 0.00 4.69
2691 2837 6.040616 AGAGTAAATTACATGTACTCCCTCCG 59.959 42.308 18.00 0.00 43.11 4.63
2692 2838 7.362802 AGAGTAAATTACATGTACTCCCTCC 57.637 40.000 18.00 2.99 43.11 4.30
2693 2839 9.134055 ACTAGAGTAAATTACATGTACTCCCTC 57.866 37.037 18.00 13.35 43.11 4.30
2726 2874 5.870978 CCCCAAATAGAAAAGTTCAAGCATG 59.129 40.000 0.00 0.00 0.00 4.06
2772 3002 6.012337 TGGGAATCATGCCTCTTTATACAA 57.988 37.500 0.00 0.00 38.04 2.41
2880 3111 7.230510 TGGTGCAAACAAACTATGAAATCTACT 59.769 33.333 0.00 0.00 0.00 2.57
2912 3151 9.802039 TGAAACTATAATGGTAACCAAAACTCT 57.198 29.630 0.00 0.00 36.95 3.24


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

AutoCloner maintained by Alex Coulton.