Multiple sequence alignment - TraesCS7D01G247100

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 TraesCS7D01G247100 chr7D 100.000 4588 0 0 1 4588 216835978 216840565 0.000000e+00 8473.0
1 TraesCS7D01G247100 chr7D 100.000 2331 0 0 4772 7102 216840749 216843079 0.000000e+00 4305.0
2 TraesCS7D01G247100 chr7D 90.196 51 3 2 481 530 214347912 214347863 1.650000e-06 65.8
3 TraesCS7D01G247100 chr7A 92.028 2810 104 51 250 3009 229604046 229606785 0.000000e+00 3838.0
4 TraesCS7D01G247100 chr7A 96.779 2235 53 11 4874 7102 229608578 229610799 0.000000e+00 3711.0
5 TraesCS7D01G247100 chr7A 93.565 1523 70 17 3065 4577 229606785 229608289 0.000000e+00 2244.0
6 TraesCS7D01G247100 chr7A 90.863 197 18 0 23 219 229603855 229604051 1.520000e-66 265.0
7 TraesCS7D01G247100 chr7A 87.143 70 6 3 4772 4840 149257423 149257490 7.640000e-10 76.8
8 TraesCS7D01G247100 chr7A 91.667 48 2 2 481 528 226752093 226752048 1.650000e-06 65.8
9 TraesCS7D01G247100 chr7B 91.421 2751 169 32 1 2737 183878309 183875612 0.000000e+00 3711.0
10 TraesCS7D01G247100 chr7B 91.457 1791 90 20 2792 4577 183875505 183873773 0.000000e+00 2401.0
11 TraesCS7D01G247100 chr7B 95.833 1224 35 8 4875 6091 183873230 183872016 0.000000e+00 1964.0
12 TraesCS7D01G247100 chr7B 96.016 979 20 8 6132 7102 183872017 183871050 0.000000e+00 1574.0
13 TraesCS7D01G247100 chr7B 89.831 59 4 2 481 538 186820928 186820985 2.750000e-09 75.0
14 TraesCS7D01G247100 chr5B 96.364 55 0 2 4772 4826 435154166 435154218 9.810000e-14 89.8
15 TraesCS7D01G247100 chr2B 98.039 51 0 1 4772 4822 615254299 615254250 3.530000e-13 87.9
16 TraesCS7D01G247100 chr2B 94.545 55 1 2 4772 4826 784705529 784705581 4.570000e-12 84.2
17 TraesCS7D01G247100 chr6B 96.154 52 2 0 4772 4823 20522041 20521990 1.270000e-12 86.1
18 TraesCS7D01G247100 chr6B 89.552 67 3 3 4772 4834 352368959 352368893 1.640000e-11 82.4
19 TraesCS7D01G247100 chr2A 96.154 52 2 0 4772 4823 39350218 39350167 1.270000e-12 86.1
20 TraesCS7D01G247100 chr2A 91.667 60 2 2 4772 4831 72366480 72366424 5.910000e-11 80.5
21 TraesCS7D01G247100 chr1D 94.444 54 3 0 4772 4825 21655244 21655191 4.570000e-12 84.2


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 TraesCS7D01G247100 chr7D 216835978 216843079 7101 False 6389.0 8473 100.00000 1 7102 2 chr7D.!!$F1 7101
1 TraesCS7D01G247100 chr7A 229603855 229610799 6944 False 2514.5 3838 93.30875 23 7102 4 chr7A.!!$F2 7079
2 TraesCS7D01G247100 chr7B 183871050 183878309 7259 True 2412.5 3711 93.68175 1 7102 4 chr7B.!!$R1 7101

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
112 113 0.317519 CAAAGTCCAAACGGCCGAAC 60.318 55.000 35.90 20.01 0.00 3.95 F
1684 1737 0.179051 CTGGCCATCCTTGCTCTCTC 60.179 60.000 5.51 0.00 0.00 3.20 F
1870 1925 0.028902 GTCTTGCACGGTCAAACACC 59.971 55.000 0.00 0.00 42.69 4.16 F
2211 2266 0.029567 CGGCGGCTGTGTTTTTACAA 59.970 50.000 7.61 0.00 0.00 2.41 F
2941 3097 0.108585 CACACCACTAGCCAACTGGT 59.891 55.000 0.00 0.00 38.30 4.00 F
2942 3098 0.396811 ACACCACTAGCCAACTGGTC 59.603 55.000 0.00 0.00 35.02 4.02 F
4535 4701 1.064906 CATCTCATTCCACAGCCACCT 60.065 52.381 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1812 0.677731 TTTCAGCAAGATGAGGCCGG 60.678 55.000 0.00 0.00 0.00 6.13 R
2619 2682 0.108041 TTTGGATTCTACCCGCGTCC 60.108 55.000 4.92 3.74 0.00 4.79 R
2927 3083 0.317160 TGTCGACCAGTTGGCTAGTG 59.683 55.000 14.12 0.00 39.32 2.74 R
4110 4275 0.741221 GCGCTTCCTACCACTTGGAG 60.741 60.000 0.00 0.00 38.94 3.86 R
4786 4952 2.124277 GGTTTCTCCCCGCTTTGTAT 57.876 50.000 0.00 0.00 0.00 2.29 R
4787 4953 3.637184 GGTTTCTCCCCGCTTTGTA 57.363 52.632 0.00 0.00 0.00 2.41 R
6156 6612 0.035176 GCAAAAAGCTGCCCCATCAA 59.965 50.000 0.00 0.00 41.15 2.57 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
112 113 0.317519 CAAAGTCCAAACGGCCGAAC 60.318 55.000 35.90 20.01 0.00 3.95
177 178 3.660865 AGATAAAAACGACAACCGAGCT 58.339 40.909 0.00 0.00 41.76 4.09
213 215 1.215382 CGACCTGAACCGAGCATGA 59.785 57.895 0.00 0.00 0.00 3.07
216 218 2.151202 GACCTGAACCGAGCATGAAAA 58.849 47.619 0.00 0.00 0.00 2.29
220 222 3.057315 CCTGAACCGAGCATGAAAACAAT 60.057 43.478 0.00 0.00 0.00 2.71
223 225 6.078202 TGAACCGAGCATGAAAACAATAAA 57.922 33.333 0.00 0.00 0.00 1.40
225 227 6.585702 TGAACCGAGCATGAAAACAATAAATG 59.414 34.615 0.00 0.00 0.00 2.32
229 231 5.220265 CGAGCATGAAAACAATAAATGCCAC 60.220 40.000 0.00 0.00 43.66 5.01
230 232 5.549347 AGCATGAAAACAATAAATGCCACA 58.451 33.333 0.00 0.00 43.66 4.17
243 245 4.518278 AATGCCACACCTAATACATCCA 57.482 40.909 0.00 0.00 0.00 3.41
244 246 3.558931 TGCCACACCTAATACATCCAG 57.441 47.619 0.00 0.00 0.00 3.86
377 379 2.095372 CGTTTCTACCCAGCCGAAAATC 59.905 50.000 0.00 0.00 0.00 2.17
453 457 1.938577 CACAGATACATGACAGGCAGC 59.061 52.381 0.00 0.00 0.00 5.25
454 458 1.556451 ACAGATACATGACAGGCAGCA 59.444 47.619 0.00 0.00 0.00 4.41
455 459 2.210961 CAGATACATGACAGGCAGCAG 58.789 52.381 0.00 0.00 0.00 4.24
464 468 4.057428 AGGCAGCAGACGGACGAC 62.057 66.667 0.00 0.00 0.00 4.34
478 482 2.815211 CGACCATGTGGAGCACCG 60.815 66.667 5.96 0.00 39.42 4.94
548 552 6.452494 TTTTCCGTTTCCATTTTGACTACA 57.548 33.333 0.00 0.00 0.00 2.74
558 573 5.705441 TCCATTTTGACTACACCACATTCTC 59.295 40.000 0.00 0.00 0.00 2.87
559 574 5.707298 CCATTTTGACTACACCACATTCTCT 59.293 40.000 0.00 0.00 0.00 3.10
670 689 2.824041 CATCGCCAGGGGTTTCGG 60.824 66.667 2.89 0.00 0.00 4.30
695 714 3.902063 CGCATCGCACCGAACGAG 61.902 66.667 7.37 0.00 43.74 4.18
851 887 9.434275 TTCCTTCCCTTTATTTTCTTTCTTTCT 57.566 29.630 0.00 0.00 0.00 2.52
852 888 9.434275 TCCTTCCCTTTATTTTCTTTCTTTCTT 57.566 29.630 0.00 0.00 0.00 2.52
1251 1304 2.806237 CGGGAGTACGCCTTCCTC 59.194 66.667 15.73 0.00 36.56 3.71
1494 1547 2.906354 CACCAGAATAGGAAACCCGAG 58.094 52.381 0.00 0.00 0.00 4.63
1650 1703 0.474614 TTCGGTTCCATTGACCCACA 59.525 50.000 0.00 0.00 33.49 4.17
1651 1704 0.250553 TCGGTTCCATTGACCCACAC 60.251 55.000 0.00 0.00 33.49 3.82
1652 1705 1.241315 CGGTTCCATTGACCCACACC 61.241 60.000 0.00 0.00 33.49 4.16
1656 1709 1.152599 CCATTGACCCACACCCACA 59.847 57.895 0.00 0.00 0.00 4.17
1657 1710 1.178534 CCATTGACCCACACCCACAC 61.179 60.000 0.00 0.00 0.00 3.82
1661 1714 3.785122 GACCCACACCCACACCCAC 62.785 68.421 0.00 0.00 0.00 4.61
1666 1719 3.889692 CACCCACACCCACTGCCT 61.890 66.667 0.00 0.00 0.00 4.75
1676 1729 2.357836 CACTGCCTGGCCATCCTT 59.642 61.111 17.53 0.00 0.00 3.36
1677 1730 2.050350 CACTGCCTGGCCATCCTTG 61.050 63.158 17.53 0.00 0.00 3.61
1684 1737 0.179051 CTGGCCATCCTTGCTCTCTC 60.179 60.000 5.51 0.00 0.00 3.20
1686 1739 0.254178 GGCCATCCTTGCTCTCTCAA 59.746 55.000 0.00 0.00 0.00 3.02
1687 1740 1.666054 GCCATCCTTGCTCTCTCAAG 58.334 55.000 0.00 0.00 42.23 3.02
1688 1741 1.666054 CCATCCTTGCTCTCTCAAGC 58.334 55.000 0.00 0.00 41.47 4.01
1689 1742 1.666054 CATCCTTGCTCTCTCAAGCC 58.334 55.000 0.00 0.00 41.47 4.35
1690 1743 1.209990 CATCCTTGCTCTCTCAAGCCT 59.790 52.381 0.00 0.00 41.47 4.58
1691 1744 0.612229 TCCTTGCTCTCTCAAGCCTG 59.388 55.000 0.00 0.00 41.47 4.85
1702 1755 6.053632 TCTCTCAAGCCTGAAATGATTACA 57.946 37.500 0.00 0.00 0.00 2.41
1715 1768 1.200716 TGATTACAGACACCGTCGTCC 59.799 52.381 0.00 0.00 37.67 4.79
1716 1769 0.529378 ATTACAGACACCGTCGTCCC 59.471 55.000 0.00 0.00 37.67 4.46
1718 1771 3.667282 CAGACACCGTCGTCCCGT 61.667 66.667 0.00 0.00 37.67 5.28
1719 1772 3.360340 AGACACCGTCGTCCCGTC 61.360 66.667 0.00 0.00 37.67 4.79
1721 1774 3.319926 GACACCGTCGTCCCGTCTC 62.320 68.421 0.00 0.00 0.00 3.36
1722 1775 4.456253 CACCGTCGTCCCGTCTCG 62.456 72.222 0.00 0.00 0.00 4.04
1741 1794 4.158764 TCTCGGCCTGAAAAACTTCAAAAA 59.841 37.500 0.00 0.00 0.00 1.94
1748 1801 3.060098 TGAAAAACTTCAAAAAGCGCACG 59.940 39.130 11.47 0.00 35.81 5.34
1823 1878 0.535797 ACCGGTGAGGCTAAGCTTAC 59.464 55.000 6.12 0.00 46.52 2.34
1870 1925 0.028902 GTCTTGCACGGTCAAACACC 59.971 55.000 0.00 0.00 42.69 4.16
1881 1936 2.610232 GGTCAAACACCACCGTATACGT 60.610 50.000 22.87 9.23 45.98 3.57
1918 1973 3.279434 ACAAGGTTCCAGATTAATCGCC 58.721 45.455 9.78 8.40 0.00 5.54
2017 2072 4.445452 CAAACTGCTTGGCATCACTAAT 57.555 40.909 0.00 0.00 38.13 1.73
2053 2108 1.208052 GGATTGCAGTGCTCTGACCTA 59.792 52.381 19.61 0.44 43.76 3.08
2104 2159 1.898574 CCAAGACCGTGCCAAAGCT 60.899 57.895 0.00 0.00 40.80 3.74
2105 2160 0.605319 CCAAGACCGTGCCAAAGCTA 60.605 55.000 0.00 0.00 40.80 3.32
2128 2183 1.378646 GCCCCTGCAAAGTCTACCC 60.379 63.158 0.00 0.00 37.47 3.69
2175 2230 4.107636 GGGGTTCCTAGAAGAGTCCCTATA 59.892 50.000 0.00 0.00 34.32 1.31
2176 2231 5.222589 GGGGTTCCTAGAAGAGTCCCTATAT 60.223 48.000 0.00 0.00 34.32 0.86
2179 2234 7.011382 GGTTCCTAGAAGAGTCCCTATATGAA 58.989 42.308 0.00 0.00 0.00 2.57
2182 2237 6.335850 TCCTAGAAGAGTCCCTATATGAAGGT 59.664 42.308 0.00 0.00 34.56 3.50
2208 2263 0.533308 AGACGGCGGCTGTGTTTTTA 60.533 50.000 17.94 0.00 0.00 1.52
2209 2264 0.385098 GACGGCGGCTGTGTTTTTAC 60.385 55.000 20.97 0.00 0.00 2.01
2211 2266 0.029567 CGGCGGCTGTGTTTTTACAA 59.970 50.000 7.61 0.00 0.00 2.41
2212 2267 1.766069 GGCGGCTGTGTTTTTACAAG 58.234 50.000 0.00 0.00 0.00 3.16
2213 2268 1.128513 GCGGCTGTGTTTTTACAAGC 58.871 50.000 0.00 0.00 0.00 4.01
2215 2270 2.650608 CGGCTGTGTTTTTACAAGCTC 58.349 47.619 0.00 0.00 0.00 4.09
2216 2271 2.650608 GGCTGTGTTTTTACAAGCTCG 58.349 47.619 0.00 0.00 0.00 5.03
2246 2301 4.557690 CGTAGTTACTGTTGATCCAGTTCG 59.442 45.833 9.52 5.12 42.99 3.95
2247 2302 4.866508 AGTTACTGTTGATCCAGTTCGA 57.133 40.909 9.52 0.00 42.99 3.71
2254 2309 4.514577 ATCCAGTTCGAGCCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
2265 2320 3.255379 GCCGCCGAAGATGACGTC 61.255 66.667 9.11 9.11 0.00 4.34
2308 2363 0.250510 TTGTGGCCAACTGCGTGATA 60.251 50.000 7.24 0.00 42.61 2.15
2391 2454 3.959535 TTGCCCTTGCTCCAAATAAAG 57.040 42.857 0.00 0.00 38.71 1.85
2394 2457 3.092301 GCCCTTGCTCCAAATAAAGAGT 58.908 45.455 0.00 0.00 32.47 3.24
2446 2509 4.922206 AGGCCAACTTTGATATCTCAACA 58.078 39.130 5.01 0.00 41.05 3.33
2535 2598 3.425772 GGGAACTAAGGGGCAGTTCTCT 61.426 54.545 13.20 0.00 45.93 3.10
2536 2599 3.704800 GAACTAAGGGGCAGTTCTCTT 57.295 47.619 7.88 0.00 45.50 2.85
2537 2600 3.601435 GAACTAAGGGGCAGTTCTCTTC 58.399 50.000 7.88 0.00 45.50 2.87
2538 2601 2.909217 ACTAAGGGGCAGTTCTCTTCT 58.091 47.619 0.00 0.00 0.00 2.85
2554 2617 1.298157 TTCTGATTTCACGCCCGCTG 61.298 55.000 0.00 0.00 0.00 5.18
2556 2619 1.078497 TGATTTCACGCCCGCTGAT 60.078 52.632 0.00 0.00 0.00 2.90
2601 2664 2.384382 CCTTGCCAAAATATTAGCGCG 58.616 47.619 0.00 0.00 0.00 6.86
2619 2682 1.510844 GCCCCATTTTGGTACAGCG 59.489 57.895 0.00 0.00 42.39 5.18
2724 2790 9.545105 GGCACCATCATATTTCATTATTTTGAA 57.455 29.630 0.00 0.00 33.89 2.69
2782 2931 5.679734 AAACTAACACACATGCTCTTCAG 57.320 39.130 0.00 0.00 0.00 3.02
2798 2947 9.638176 ATGCTCTTCAGATTTATGGAAACTAAT 57.362 29.630 0.00 0.00 0.00 1.73
2845 2994 7.284820 GGACTAGCCCCTACAACAATTTATTA 58.715 38.462 0.00 0.00 0.00 0.98
2846 2995 7.776500 GGACTAGCCCCTACAACAATTTATTAA 59.224 37.037 0.00 0.00 0.00 1.40
2847 2996 8.747538 ACTAGCCCCTACAACAATTTATTAAG 57.252 34.615 0.00 0.00 0.00 1.85
2867 3019 3.950397 AGAAGAAACAACCAGACACACA 58.050 40.909 0.00 0.00 0.00 3.72
2896 3048 3.141398 GAGCACAAGACTCAAATGTGGA 58.859 45.455 7.04 0.00 43.54 4.02
2935 3091 4.697756 GCCGCACACCACTAGCCA 62.698 66.667 0.00 0.00 0.00 4.75
2936 3092 2.031919 CCGCACACCACTAGCCAA 59.968 61.111 0.00 0.00 0.00 4.52
2937 3093 2.325082 CCGCACACCACTAGCCAAC 61.325 63.158 0.00 0.00 0.00 3.77
2938 3094 1.301716 CGCACACCACTAGCCAACT 60.302 57.895 0.00 0.00 0.00 3.16
2939 3095 1.568612 CGCACACCACTAGCCAACTG 61.569 60.000 0.00 0.00 0.00 3.16
2940 3096 1.237285 GCACACCACTAGCCAACTGG 61.237 60.000 0.00 0.00 38.53 4.00
2941 3097 0.108585 CACACCACTAGCCAACTGGT 59.891 55.000 0.00 0.00 38.30 4.00
2942 3098 0.396811 ACACCACTAGCCAACTGGTC 59.603 55.000 0.00 0.00 35.02 4.02
2957 3113 3.053831 CTGGTCGACACCCAGTTTTAT 57.946 47.619 18.91 0.00 43.73 1.40
2994 3150 7.887996 TGGCTTATTGAACAAATCACAATTC 57.112 32.000 0.00 0.00 37.92 2.17
3009 3165 4.036262 TCACAATTCAAACCTTTGTCGGAG 59.964 41.667 0.00 0.00 39.18 4.63
3015 3171 7.703058 ATTCAAACCTTTGTCGGAGATAATT 57.297 32.000 0.00 0.00 37.51 1.40
3045 3201 7.012327 CGAATAGCAGAAGATTTATGGGTCAAA 59.988 37.037 0.00 0.00 0.00 2.69
3072 3228 8.582437 TGGGTAGTATTCAGTAGTACAATATGC 58.418 37.037 2.52 0.00 39.83 3.14
3085 3241 3.831323 ACAATATGCGGGGAAATGATCA 58.169 40.909 0.00 0.00 0.00 2.92
3098 3256 5.973565 GGGAAATGATCAATGAAATGTCGAC 59.026 40.000 9.11 9.11 0.00 4.20
3259 3421 4.717877 TGATCAATGTATCAAAGCCGGAT 58.282 39.130 5.05 0.00 32.97 4.18
3264 3426 2.754472 TGTATCAAAGCCGGATGATCG 58.246 47.619 17.71 0.00 37.46 3.69
3266 3428 2.847327 ATCAAAGCCGGATGATCGAT 57.153 45.000 5.05 0.00 30.62 3.59
3285 3447 3.242091 CGATTACTGCTCCAACAATCACG 60.242 47.826 0.00 0.00 0.00 4.35
3320 3482 8.621532 TTATTTCAGTATTGAGTCCATATGGC 57.378 34.615 17.58 12.03 34.15 4.40
3397 3559 5.222007 CCCTATAATGCTCAACTCAAGGGAT 60.222 44.000 0.00 0.00 43.22 3.85
3398 3560 5.704515 CCTATAATGCTCAACTCAAGGGATG 59.295 44.000 0.00 0.00 0.00 3.51
3427 3589 9.003112 CGTCTTGTTAAATAATTCTGCTGATTG 57.997 33.333 0.00 0.00 0.00 2.67
3457 3619 7.656542 ACACTAGTAGCAAAAAGGAAACTACTC 59.343 37.037 4.39 0.00 41.87 2.59
3493 3655 7.719483 AGACAATGGGCAAATATTTAGACATG 58.281 34.615 0.00 0.00 0.00 3.21
3561 3724 9.301153 TGAGTAAATTTCTTTGAAGTTTCTTGC 57.699 29.630 0.00 0.00 0.00 4.01
3581 3744 7.073265 TCTTGCTTTTATGCTTTGTACGTTAC 58.927 34.615 0.00 0.00 0.00 2.50
3584 3747 7.073265 TGCTTTTATGCTTTGTACGTTACTTC 58.927 34.615 0.00 0.00 0.00 3.01
3724 3888 7.496529 TGTTTTCAAACTGATAAGGACTCTG 57.503 36.000 4.14 0.00 39.59 3.35
3958 4122 6.713450 GTCTCTTACCCAGTGTTTTTATTCCA 59.287 38.462 0.00 0.00 0.00 3.53
3972 4136 7.492669 TGTTTTTATTCCATTCTGCAAAAACGA 59.507 29.630 12.90 3.72 43.58 3.85
4110 4275 7.414540 CCAAGATAGTCATAACCAAAGCACTTC 60.415 40.741 0.00 0.00 0.00 3.01
4141 4306 4.262506 GGTAGGAAGCGCTACCTATCATTT 60.263 45.833 17.97 0.00 41.62 2.32
4148 4313 4.506654 AGCGCTACCTATCATTTTTACGTG 59.493 41.667 8.99 0.00 0.00 4.49
4181 4346 6.368516 CGATTACCCTTGTTTGCAATTTGAAT 59.631 34.615 0.00 0.00 33.65 2.57
4324 4489 8.934507 TCACGTTCTCAATTGGTTAAAAATTT 57.065 26.923 5.42 0.00 0.00 1.82
4369 4534 9.928236 GTTTTTGAATTGAAAATTTCGGATTGA 57.072 25.926 3.59 2.18 0.00 2.57
4506 4672 8.873830 ACGTATGATCTTCTAACTTTTCATGTG 58.126 33.333 0.00 0.00 0.00 3.21
4535 4701 1.064906 CATCTCATTCCACAGCCACCT 60.065 52.381 0.00 0.00 0.00 4.00
4539 4705 4.037222 TCTCATTCCACAGCCACCTATAA 58.963 43.478 0.00 0.00 0.00 0.98
4577 4743 9.758651 TTGATGGTGTCACTTATACATGTATAC 57.241 33.333 22.44 14.91 36.32 1.47
4578 4744 8.919145 TGATGGTGTCACTTATACATGTATACA 58.081 33.333 22.44 17.05 0.00 2.29
4579 4745 9.929180 GATGGTGTCACTTATACATGTATACAT 57.071 33.333 22.44 18.52 36.96 2.29
4581 4747 9.758651 TGGTGTCACTTATACATGTATACATTC 57.241 33.333 22.44 15.60 33.61 2.67
4582 4748 9.982651 GGTGTCACTTATACATGTATACATTCT 57.017 33.333 22.44 6.81 33.61 2.40
4586 4752 9.476202 TCACTTATACATGTATACATTCTGTGC 57.524 33.333 22.44 0.00 33.61 4.57
4587 4753 9.260002 CACTTATACATGTATACATTCTGTGCA 57.740 33.333 22.44 5.89 33.61 4.57
4801 4967 3.985019 TTTGTATACAAAGCGGGGAGA 57.015 42.857 23.91 2.19 40.55 3.71
4802 4968 3.985019 TTGTATACAAAGCGGGGAGAA 57.015 42.857 15.92 0.00 32.11 2.87
4803 4969 3.985019 TGTATACAAAGCGGGGAGAAA 57.015 42.857 2.20 0.00 0.00 2.52
4804 4970 3.602483 TGTATACAAAGCGGGGAGAAAC 58.398 45.455 2.20 0.00 0.00 2.78
4805 4971 2.124277 ATACAAAGCGGGGAGAAACC 57.876 50.000 0.00 0.00 38.08 3.27
4827 4993 6.687604 ACCCTTTTTCGGTAAAATGATGAAG 58.312 36.000 0.00 0.00 35.29 3.02
5028 5445 7.228840 GCATGTGCACTTGTATTGTTATTTTG 58.771 34.615 27.56 4.12 41.59 2.44
5184 5601 8.064336 TCACCTTCCTGTAAAGAAGACTATAC 57.936 38.462 2.16 0.00 42.80 1.47
5224 5641 6.085573 TGATTTTGAATTAGCATGACACACG 58.914 36.000 0.00 0.00 0.00 4.49
5284 5701 6.485393 CACAAACGTTGCATATATGTGATGA 58.515 36.000 17.82 0.00 39.10 2.92
5361 5779 5.957771 TCATGGAAGCTAACCTGAATAGT 57.042 39.130 10.52 0.00 0.00 2.12
5613 6031 2.098831 GTTCGGCTACCTTCGGCAC 61.099 63.158 0.00 0.00 0.00 5.01
5682 6100 1.003355 AGGCCACAAGGATGTCGTG 60.003 57.895 5.01 0.00 37.82 4.35
5700 6118 2.650116 GCGGCTCAAGGACCTCTCA 61.650 63.158 0.00 0.00 0.00 3.27
5754 6172 4.664150 GAGATTGGTCTCGAGGATTTCT 57.336 45.455 13.56 8.83 41.35 2.52
5806 6224 6.033341 CGTTCTGAAAAGTAGATGAGGAGAG 58.967 44.000 0.00 0.00 0.00 3.20
6094 6514 9.809096 TCTGTGTTTATCTCTGATCATTTAGAC 57.191 33.333 0.00 0.00 0.00 2.59
6095 6515 9.591792 CTGTGTTTATCTCTGATCATTTAGACA 57.408 33.333 0.00 0.00 0.00 3.41
6114 6534 8.812147 TTAGACATTTACAGTTATAGCATCGG 57.188 34.615 0.00 0.00 0.00 4.18
6115 6535 6.817184 AGACATTTACAGTTATAGCATCGGT 58.183 36.000 0.00 0.00 0.00 4.69
6116 6536 7.272978 AGACATTTACAGTTATAGCATCGGTT 58.727 34.615 0.00 0.00 0.00 4.44
6117 6537 7.438459 AGACATTTACAGTTATAGCATCGGTTC 59.562 37.037 0.00 0.00 0.00 3.62
6118 6538 7.045416 ACATTTACAGTTATAGCATCGGTTCA 58.955 34.615 0.00 0.00 0.00 3.18
6119 6539 7.551262 ACATTTACAGTTATAGCATCGGTTCAA 59.449 33.333 0.00 0.00 0.00 2.69
6120 6540 8.559536 CATTTACAGTTATAGCATCGGTTCAAT 58.440 33.333 0.00 0.00 0.00 2.57
6121 6541 9.772973 ATTTACAGTTATAGCATCGGTTCAATA 57.227 29.630 0.00 0.00 0.00 1.90
6122 6542 8.812147 TTACAGTTATAGCATCGGTTCAATAG 57.188 34.615 0.00 0.00 0.00 1.73
6123 6543 6.817184 ACAGTTATAGCATCGGTTCAATAGT 58.183 36.000 0.00 0.00 0.00 2.12
6124 6544 7.272978 ACAGTTATAGCATCGGTTCAATAGTT 58.727 34.615 0.00 0.00 0.00 2.24
6125 6545 7.438459 ACAGTTATAGCATCGGTTCAATAGTTC 59.562 37.037 0.00 0.00 0.00 3.01
6126 6546 7.438160 CAGTTATAGCATCGGTTCAATAGTTCA 59.562 37.037 0.00 0.00 0.00 3.18
6127 6547 7.985184 AGTTATAGCATCGGTTCAATAGTTCAA 59.015 33.333 0.00 0.00 0.00 2.69
6128 6548 4.946784 AGCATCGGTTCAATAGTTCAAC 57.053 40.909 0.00 0.00 0.00 3.18
6129 6549 4.323417 AGCATCGGTTCAATAGTTCAACA 58.677 39.130 0.00 0.00 0.00 3.33
6130 6550 4.393062 AGCATCGGTTCAATAGTTCAACAG 59.607 41.667 0.00 0.00 0.00 3.16
6131 6551 4.154195 GCATCGGTTCAATAGTTCAACAGT 59.846 41.667 0.00 0.00 0.00 3.55
6132 6552 5.334879 GCATCGGTTCAATAGTTCAACAGTT 60.335 40.000 0.00 0.00 0.00 3.16
6543 7007 3.555966 ACACCTCAAAAGCAAGCTTAGT 58.444 40.909 7.85 0.00 34.84 2.24
6544 7008 4.714632 ACACCTCAAAAGCAAGCTTAGTA 58.285 39.130 7.85 0.00 34.84 1.82
6545 7009 4.757149 ACACCTCAAAAGCAAGCTTAGTAG 59.243 41.667 7.85 5.64 34.84 2.57
6546 7010 4.997395 CACCTCAAAAGCAAGCTTAGTAGA 59.003 41.667 7.85 3.52 34.84 2.59
7077 7544 3.349927 TCTTCCCATCGTCTCGAAAGTA 58.650 45.455 0.00 0.00 39.99 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.878599 AAAGAAAGTCAATAAACTATGTCAACG 57.121 29.630 0.00 0.00 0.00 4.10
93 94 0.317519 GTTCGGCCGTTTGGACTTTG 60.318 55.000 27.15 0.00 43.41 2.77
213 215 8.589338 TGTATTAGGTGTGGCATTTATTGTTTT 58.411 29.630 0.00 0.00 0.00 2.43
216 218 7.014230 GGATGTATTAGGTGTGGCATTTATTGT 59.986 37.037 0.00 0.00 0.00 2.71
220 222 6.007485 TGGATGTATTAGGTGTGGCATTTA 57.993 37.500 0.00 0.00 0.00 1.40
223 225 3.181440 CCTGGATGTATTAGGTGTGGCAT 60.181 47.826 0.00 0.00 0.00 4.40
225 227 2.172717 ACCTGGATGTATTAGGTGTGGC 59.827 50.000 0.00 0.00 42.95 5.01
230 232 7.023171 TGTTTTACACCTGGATGTATTAGGT 57.977 36.000 0.00 0.00 45.36 3.08
243 245 9.555727 ACGCATAAATAGATATGTTTTACACCT 57.444 29.630 0.00 0.00 36.00 4.00
244 246 9.594038 CACGCATAAATAGATATGTTTTACACC 57.406 33.333 0.00 0.00 36.00 4.16
377 379 4.080638 AGGGAGTAGAAGAGAAATGGCAAG 60.081 45.833 0.00 0.00 0.00 4.01
453 457 1.446099 CCACATGGTCGTCCGTCTG 60.446 63.158 0.00 0.00 36.30 3.51
454 458 1.595993 CTCCACATGGTCGTCCGTCT 61.596 60.000 0.00 0.00 36.30 4.18
455 459 1.153823 CTCCACATGGTCGTCCGTC 60.154 63.158 0.00 0.00 36.30 4.79
464 468 2.436646 GGACGGTGCTCCACATGG 60.437 66.667 5.52 0.00 35.86 3.66
559 574 4.342951 TGAACTGTTTCCTCTTCGGTAGAA 59.657 41.667 0.00 0.00 30.91 2.10
575 590 0.464036 TGTGAAGGCTCGTGAACTGT 59.536 50.000 0.00 0.00 0.00 3.55
775 799 2.039624 GAGAGGGGTCTGAGGCCA 59.960 66.667 5.06 0.00 0.00 5.36
854 890 1.749334 CGGGGAGATTTCCGGAGAGG 61.749 65.000 3.34 0.00 45.04 3.69
1494 1547 1.547472 ATTTTGCAAGCCCTCCCTGC 61.547 55.000 0.00 0.00 0.00 4.85
1650 1703 3.889692 CAGGCAGTGGGTGTGGGT 61.890 66.667 0.00 0.00 0.00 4.51
1651 1704 4.666253 CCAGGCAGTGGGTGTGGG 62.666 72.222 0.00 0.00 43.63 4.61
1661 1714 3.145551 GCAAGGATGGCCAGGCAG 61.146 66.667 15.19 0.61 36.05 4.85
1666 1719 0.911045 TGAGAGAGCAAGGATGGCCA 60.911 55.000 8.56 8.56 33.19 5.36
1676 1729 2.303890 TCATTTCAGGCTTGAGAGAGCA 59.696 45.455 0.00 0.00 44.49 4.26
1677 1730 2.983229 TCATTTCAGGCTTGAGAGAGC 58.017 47.619 0.00 0.00 41.96 4.09
1684 1737 5.392380 GGTGTCTGTAATCATTTCAGGCTTG 60.392 44.000 9.71 0.00 35.24 4.01
1686 1739 4.265073 GGTGTCTGTAATCATTTCAGGCT 58.735 43.478 9.71 0.00 35.24 4.58
1687 1740 3.063997 CGGTGTCTGTAATCATTTCAGGC 59.936 47.826 1.78 1.78 34.84 4.85
1688 1741 4.253685 ACGGTGTCTGTAATCATTTCAGG 58.746 43.478 4.34 0.00 0.00 3.86
1689 1742 4.031765 CGACGGTGTCTGTAATCATTTCAG 59.968 45.833 0.00 0.00 0.00 3.02
1690 1743 3.924073 CGACGGTGTCTGTAATCATTTCA 59.076 43.478 0.00 0.00 0.00 2.69
1691 1744 3.924686 ACGACGGTGTCTGTAATCATTTC 59.075 43.478 0.00 0.00 0.00 2.17
1715 1768 4.002511 GAAGTTTTTCAGGCCGAGACGG 62.003 54.545 5.79 5.79 40.47 4.79
1716 1769 1.194772 GAAGTTTTTCAGGCCGAGACG 59.805 52.381 0.00 0.00 33.38 4.18
1718 1771 2.631160 TGAAGTTTTTCAGGCCGAGA 57.369 45.000 0.00 0.00 38.37 4.04
1719 1772 3.708563 TTTGAAGTTTTTCAGGCCGAG 57.291 42.857 0.00 0.00 43.76 4.63
1721 1774 3.001228 GCTTTTTGAAGTTTTTCAGGCCG 59.999 43.478 0.00 0.00 43.76 6.13
1722 1775 3.001228 CGCTTTTTGAAGTTTTTCAGGCC 59.999 43.478 0.00 0.00 43.76 5.19
1723 1776 3.544048 GCGCTTTTTGAAGTTTTTCAGGC 60.544 43.478 0.00 0.00 43.76 4.85
1724 1777 3.616379 TGCGCTTTTTGAAGTTTTTCAGG 59.384 39.130 9.73 0.00 43.76 3.86
1759 1812 0.677731 TTTCAGCAAGATGAGGCCGG 60.678 55.000 0.00 0.00 0.00 6.13
1881 1936 6.316890 GGAACCTTGTAAATAAATACAGCCGA 59.683 38.462 0.00 0.00 37.13 5.54
1918 1973 3.198635 TCAACCTCTAGATGAAAGCCCAG 59.801 47.826 1.64 0.00 0.00 4.45
2028 2083 1.375908 GAGCACTGCAATCCACGGA 60.376 57.895 3.30 0.00 0.00 4.69
2053 2108 6.728164 AGCATATAGGTCACTAATGGATGAGT 59.272 38.462 0.00 0.00 31.86 3.41
2104 2159 4.530946 GGTAGACTTTGCAGGGGCTATATA 59.469 45.833 6.81 0.00 41.91 0.86
2105 2160 3.328050 GGTAGACTTTGCAGGGGCTATAT 59.672 47.826 6.81 0.00 41.91 0.86
2128 2183 2.033194 GGCGACCGACAAAGGGAAG 61.033 63.158 0.00 0.00 35.02 3.46
2158 2213 6.557568 ACCTTCATATAGGGACTCTTCTAGG 58.442 44.000 0.00 0.00 41.75 3.02
2175 2230 0.460311 CCGTCTTCGCCTACCTTCAT 59.540 55.000 0.00 0.00 35.54 2.57
2176 2231 1.888018 CCGTCTTCGCCTACCTTCA 59.112 57.895 0.00 0.00 35.54 3.02
2179 2234 3.823330 CGCCGTCTTCGCCTACCT 61.823 66.667 0.00 0.00 35.54 3.08
2208 2263 2.797866 CTACGTCGTGCCGAGCTTGT 62.798 60.000 8.47 0.00 36.23 3.16
2209 2264 2.126618 TACGTCGTGCCGAGCTTG 60.127 61.111 8.47 0.00 36.23 4.01
2211 2266 1.300971 TAACTACGTCGTGCCGAGCT 61.301 55.000 8.47 0.00 36.23 4.09
2212 2267 1.130458 GTAACTACGTCGTGCCGAGC 61.130 60.000 8.47 0.00 36.23 5.03
2213 2268 0.445436 AGTAACTACGTCGTGCCGAG 59.555 55.000 8.47 0.00 36.23 4.63
2215 2270 0.110056 ACAGTAACTACGTCGTGCCG 60.110 55.000 8.47 0.00 0.00 5.69
2216 2271 1.717645 CAACAGTAACTACGTCGTGCC 59.282 52.381 8.47 0.00 0.00 5.01
2246 2301 2.956964 CGTCATCTTCGGCGGCTC 60.957 66.667 7.21 0.00 0.00 4.70
2247 2302 3.701604 GACGTCATCTTCGGCGGCT 62.702 63.158 11.55 0.00 0.00 5.52
2254 2309 1.630148 CAACCCTCGACGTCATCTTC 58.370 55.000 17.16 0.00 0.00 2.87
2265 2320 3.277133 CCAATGTGGCAACCCTCG 58.723 61.111 0.00 0.00 0.00 4.63
2303 2358 6.226787 AGCTAAGACATGGTATTGCTATCAC 58.773 40.000 0.00 0.00 0.00 3.06
2308 2363 4.080356 TCCAAGCTAAGACATGGTATTGCT 60.080 41.667 0.00 0.00 34.50 3.91
2470 2533 1.005924 CAGCCCCTTAGTTCCCACAAT 59.994 52.381 0.00 0.00 0.00 2.71
2534 2597 1.021390 AGCGGGCGTGAAATCAGAAG 61.021 55.000 0.00 0.00 0.00 2.85
2535 2598 1.003839 AGCGGGCGTGAAATCAGAA 60.004 52.632 0.00 0.00 0.00 3.02
2536 2599 1.741401 CAGCGGGCGTGAAATCAGA 60.741 57.895 0.00 0.00 0.00 3.27
2537 2600 1.091771 ATCAGCGGGCGTGAAATCAG 61.092 55.000 0.00 0.00 0.00 2.90
2538 2601 0.676466 AATCAGCGGGCGTGAAATCA 60.676 50.000 0.00 0.00 0.00 2.57
2554 2617 1.593469 GAGGCTTCCGTTTCGCTAATC 59.407 52.381 0.00 0.00 0.00 1.75
2556 2619 0.606604 AGAGGCTTCCGTTTCGCTAA 59.393 50.000 0.00 0.00 0.00 3.09
2563 2626 0.253327 GGGAATCAGAGGCTTCCGTT 59.747 55.000 0.00 0.00 41.57 4.44
2601 2664 1.510844 CGCTGTACCAAAATGGGGC 59.489 57.895 0.87 0.00 43.37 5.80
2619 2682 0.108041 TTTGGATTCTACCCGCGTCC 60.108 55.000 4.92 3.74 0.00 4.79
2628 2691 8.472007 TTGTTTTAGAGCCTTTTTGGATTCTA 57.528 30.769 0.00 0.00 38.35 2.10
2845 2994 4.156008 GTGTGTGTCTGGTTGTTTCTTCTT 59.844 41.667 0.00 0.00 0.00 2.52
2846 2995 3.689649 GTGTGTGTCTGGTTGTTTCTTCT 59.310 43.478 0.00 0.00 0.00 2.85
2847 2996 3.181500 GGTGTGTGTCTGGTTGTTTCTTC 60.181 47.826 0.00 0.00 0.00 2.87
2884 3036 1.076024 AGCCACCATCCACATTTGAGT 59.924 47.619 0.00 0.00 0.00 3.41
2927 3083 0.317160 TGTCGACCAGTTGGCTAGTG 59.683 55.000 14.12 0.00 39.32 2.74
2928 3084 0.317479 GTGTCGACCAGTTGGCTAGT 59.683 55.000 14.12 0.00 39.32 2.57
2929 3085 0.389948 GGTGTCGACCAGTTGGCTAG 60.390 60.000 14.12 0.00 42.59 3.42
2930 3086 1.669440 GGTGTCGACCAGTTGGCTA 59.331 57.895 14.12 0.00 42.59 3.93
2931 3087 2.426023 GGTGTCGACCAGTTGGCT 59.574 61.111 14.12 0.00 42.59 4.75
2932 3088 2.668550 GGGTGTCGACCAGTTGGC 60.669 66.667 14.12 0.00 45.25 4.52
2933 3089 2.825982 TGGGTGTCGACCAGTTGG 59.174 61.111 14.12 0.00 45.25 3.77
2938 3094 2.551287 CCATAAAACTGGGTGTCGACCA 60.551 50.000 14.12 2.71 45.25 4.02
2939 3095 2.081462 CCATAAAACTGGGTGTCGACC 58.919 52.381 14.12 4.20 42.27 4.79
2940 3096 3.048337 TCCATAAAACTGGGTGTCGAC 57.952 47.619 9.11 9.11 36.89 4.20
2941 3097 3.773418 TTCCATAAAACTGGGTGTCGA 57.227 42.857 0.00 0.00 36.89 4.20
2942 3098 4.155310 GTTTCCATAAAACTGGGTGTCG 57.845 45.455 0.00 0.00 43.30 4.35
2954 3110 3.627395 AGCCATGACGAGTTTCCATAA 57.373 42.857 0.00 0.00 0.00 1.90
2957 3113 3.627395 ATAAGCCATGACGAGTTTCCA 57.373 42.857 0.00 0.00 0.00 3.53
2994 3150 6.089417 GCAAAATTATCTCCGACAAAGGTTTG 59.911 38.462 0.77 0.77 43.62 2.93
3072 3228 5.266733 ACATTTCATTGATCATTTCCCCG 57.733 39.130 0.00 0.00 0.00 5.73
3085 3241 6.142818 TGTTTCCTTTGTCGACATTTCATT 57.857 33.333 20.80 0.00 0.00 2.57
3213 3375 9.581289 TCAAATTGGTACGATATTTATTCCCAT 57.419 29.630 0.00 0.00 0.00 4.00
3259 3421 3.885724 TGTTGGAGCAGTAATCGATCA 57.114 42.857 0.00 0.00 0.00 2.92
3264 3426 3.684788 ACGTGATTGTTGGAGCAGTAATC 59.315 43.478 0.00 0.00 0.00 1.75
3266 3428 3.064207 GACGTGATTGTTGGAGCAGTAA 58.936 45.455 0.00 0.00 0.00 2.24
3320 3482 1.966451 GCACGGACAAAGACCAGGG 60.966 63.158 0.00 0.00 0.00 4.45
3397 3559 6.072728 AGCAGAATTATTTAACAAGACGTGCA 60.073 34.615 0.00 0.00 0.00 4.57
3398 3560 6.249260 CAGCAGAATTATTTAACAAGACGTGC 59.751 38.462 0.00 0.00 0.00 5.34
3427 3589 7.226918 AGTTTCCTTTTTGCTACTAGTGTCTTC 59.773 37.037 5.39 0.00 0.00 2.87
3457 3619 5.389859 TGCCCATTGTCTTGAAATACTTG 57.610 39.130 0.00 0.00 0.00 3.16
3493 3655 9.955208 TCATCAGTCATTGTGCAAATAAATATC 57.045 29.630 0.00 0.00 0.00 1.63
3556 3719 5.682943 ACGTACAAAGCATAAAAGCAAGA 57.317 34.783 0.00 0.00 36.85 3.02
3561 3724 6.735063 CCGAAGTAACGTACAAAGCATAAAAG 59.265 38.462 0.00 0.00 0.00 2.27
3581 3744 4.211374 GGAATGATCAAATACGACCCGAAG 59.789 45.833 0.00 0.00 0.00 3.79
3584 3747 3.462982 TGGAATGATCAAATACGACCCG 58.537 45.455 0.00 0.00 0.00 5.28
3958 4122 3.555547 GCCAGTTTTCGTTTTTGCAGAAT 59.444 39.130 0.00 0.00 0.00 2.40
4066 4231 5.116180 TCTTGGTATACGAAGCCATTTGAG 58.884 41.667 19.58 0.00 32.65 3.02
4110 4275 0.741221 GCGCTTCCTACCACTTGGAG 60.741 60.000 0.00 0.00 38.94 3.86
4141 4306 4.236935 GGTAATCGAACCTGACACGTAAA 58.763 43.478 0.00 0.00 36.53 2.01
4148 4313 3.329929 ACAAGGGTAATCGAACCTGAC 57.670 47.619 6.26 0.00 39.65 3.51
4481 4647 8.331022 CCACATGAAAAGTTAGAAGATCATACG 58.669 37.037 0.00 0.00 0.00 3.06
4506 4672 2.948315 GTGGAATGAGATGGCTTTCTCC 59.052 50.000 13.18 2.68 41.24 3.71
4535 4701 7.353525 ACACCATCAATCATCCAACCTTTATA 58.646 34.615 0.00 0.00 0.00 0.98
4539 4705 4.019174 GACACCATCAATCATCCAACCTT 58.981 43.478 0.00 0.00 0.00 3.50
4781 4947 3.985019 TCTCCCCGCTTTGTATACAAA 57.015 42.857 25.48 25.48 42.90 2.83
4782 4948 3.985019 TTCTCCCCGCTTTGTATACAA 57.015 42.857 14.35 14.35 0.00 2.41
4783 4949 3.602483 GTTTCTCCCCGCTTTGTATACA 58.398 45.455 0.08 0.08 0.00 2.29
4784 4950 2.941064 GGTTTCTCCCCGCTTTGTATAC 59.059 50.000 0.00 0.00 0.00 1.47
4785 4951 3.271055 GGTTTCTCCCCGCTTTGTATA 57.729 47.619 0.00 0.00 0.00 1.47
4786 4952 2.124277 GGTTTCTCCCCGCTTTGTAT 57.876 50.000 0.00 0.00 0.00 2.29
4787 4953 3.637184 GGTTTCTCCCCGCTTTGTA 57.363 52.632 0.00 0.00 0.00 2.41
4788 4954 4.494515 GGTTTCTCCCCGCTTTGT 57.505 55.556 0.00 0.00 0.00 2.83
4795 4961 6.678672 TTTTACCGAAAAAGGGTTTCTCCCC 61.679 44.000 0.00 0.00 42.14 4.81
4796 4962 4.341806 TTTTACCGAAAAAGGGTTTCTCCC 59.658 41.667 0.00 0.00 41.82 4.30
4797 4963 5.518848 TTTTACCGAAAAAGGGTTTCTCC 57.481 39.130 0.00 0.00 38.99 3.71
4798 4964 6.741109 TCATTTTACCGAAAAAGGGTTTCTC 58.259 36.000 7.44 0.00 40.32 2.87
4799 4965 6.718522 TCATTTTACCGAAAAAGGGTTTCT 57.281 33.333 7.44 0.00 40.32 2.52
4800 4966 7.149307 TCATCATTTTACCGAAAAAGGGTTTC 58.851 34.615 7.44 0.00 40.32 2.78
4801 4967 7.056844 TCATCATTTTACCGAAAAAGGGTTT 57.943 32.000 7.44 0.00 40.32 3.27
4802 4968 6.658188 TCATCATTTTACCGAAAAAGGGTT 57.342 33.333 7.44 0.00 40.32 4.11
4803 4969 6.492087 TCTTCATCATTTTACCGAAAAAGGGT 59.508 34.615 7.44 0.00 40.32 4.34
4804 4970 6.919721 TCTTCATCATTTTACCGAAAAAGGG 58.080 36.000 7.44 1.56 40.32 3.95
5091 5508 2.808206 GCGGGCTGGTGGTAGCTAT 61.808 63.158 0.00 0.00 43.22 2.97
5224 5641 9.196552 CAGATTTGAAAGGAAAATAACAGGAAC 57.803 33.333 0.00 0.00 0.00 3.62
5284 5701 5.678583 CACCATAGATCAACTCAGGTGATT 58.321 41.667 6.67 0.00 46.92 2.57
5526 5944 0.679505 GGGTGTGCTCACTACAGACA 59.320 55.000 17.68 0.00 43.41 3.41
5613 6031 0.681887 TGCCACCATGGATCTTGCTG 60.682 55.000 21.47 3.74 40.96 4.41
5660 6078 2.142292 GACATCCTTGTGGCCTGGGT 62.142 60.000 3.32 0.00 35.79 4.51
5682 6100 2.185608 GAGAGGTCCTTGAGCCGC 59.814 66.667 0.00 0.00 0.00 6.53
5700 6118 1.067295 TGTTTCTGCAGGATCTGGGT 58.933 50.000 15.13 0.00 31.21 4.51
5754 6172 6.655078 TCTTCATCTCCATCGATCATAACA 57.345 37.500 0.00 0.00 0.00 2.41
5897 6317 2.358582 CAGCAGACCACACAAAACATGA 59.641 45.455 0.00 0.00 0.00 3.07
5980 6400 2.425143 TCCTGATCACAAATCCAGCC 57.575 50.000 0.00 0.00 0.00 4.85
6091 6511 6.817184 ACCGATGCTATAACTGTAAATGTCT 58.183 36.000 0.00 0.00 0.00 3.41
6092 6512 7.223971 TGAACCGATGCTATAACTGTAAATGTC 59.776 37.037 0.00 0.00 0.00 3.06
6093 6513 7.045416 TGAACCGATGCTATAACTGTAAATGT 58.955 34.615 0.00 0.00 0.00 2.71
6094 6514 7.477144 TGAACCGATGCTATAACTGTAAATG 57.523 36.000 0.00 0.00 0.00 2.32
6095 6515 8.677148 ATTGAACCGATGCTATAACTGTAAAT 57.323 30.769 0.00 0.00 0.00 1.40
6096 6516 9.256477 CTATTGAACCGATGCTATAACTGTAAA 57.744 33.333 0.00 0.00 0.00 2.01
6097 6517 8.418662 ACTATTGAACCGATGCTATAACTGTAA 58.581 33.333 0.00 0.00 0.00 2.41
6098 6518 7.948357 ACTATTGAACCGATGCTATAACTGTA 58.052 34.615 0.00 0.00 0.00 2.74
6099 6519 6.817184 ACTATTGAACCGATGCTATAACTGT 58.183 36.000 0.00 0.00 0.00 3.55
6100 6520 7.438160 TGAACTATTGAACCGATGCTATAACTG 59.562 37.037 0.00 0.00 0.00 3.16
6101 6521 7.497595 TGAACTATTGAACCGATGCTATAACT 58.502 34.615 0.00 0.00 0.00 2.24
6102 6522 7.709269 TGAACTATTGAACCGATGCTATAAC 57.291 36.000 0.00 0.00 0.00 1.89
6103 6523 7.766738 TGTTGAACTATTGAACCGATGCTATAA 59.233 33.333 0.00 0.00 0.00 0.98
6104 6524 7.269316 TGTTGAACTATTGAACCGATGCTATA 58.731 34.615 0.00 0.00 0.00 1.31
6105 6525 6.112734 TGTTGAACTATTGAACCGATGCTAT 58.887 36.000 0.00 0.00 0.00 2.97
6106 6526 5.483811 TGTTGAACTATTGAACCGATGCTA 58.516 37.500 0.00 0.00 0.00 3.49
6107 6527 4.323417 TGTTGAACTATTGAACCGATGCT 58.677 39.130 0.00 0.00 0.00 3.79
6108 6528 4.154195 ACTGTTGAACTATTGAACCGATGC 59.846 41.667 0.00 0.00 0.00 3.91
6109 6529 5.862924 ACTGTTGAACTATTGAACCGATG 57.137 39.130 0.00 0.00 0.00 3.84
6110 6530 6.262273 ACAAACTGTTGAACTATTGAACCGAT 59.738 34.615 12.65 0.00 38.20 4.18
6111 6531 5.587043 ACAAACTGTTGAACTATTGAACCGA 59.413 36.000 12.65 0.00 38.20 4.69
6112 6532 5.816919 ACAAACTGTTGAACTATTGAACCG 58.183 37.500 12.65 0.00 38.20 4.44
6113 6533 9.016623 GTTAACAAACTGTTGAACTATTGAACC 57.983 33.333 12.65 0.00 41.30 3.62
6114 6534 9.562583 TGTTAACAAACTGTTGAACTATTGAAC 57.437 29.630 5.64 9.09 41.30 3.18
6115 6535 9.781834 CTGTTAACAAACTGTTGAACTATTGAA 57.218 29.630 10.03 1.97 41.30 2.69
6116 6536 8.402472 CCTGTTAACAAACTGTTGAACTATTGA 58.598 33.333 10.03 0.00 41.30 2.57
6117 6537 8.188139 ACCTGTTAACAAACTGTTGAACTATTG 58.812 33.333 10.03 2.24 41.30 1.90
6118 6538 8.288689 ACCTGTTAACAAACTGTTGAACTATT 57.711 30.769 10.03 0.00 41.30 1.73
6119 6539 7.875327 ACCTGTTAACAAACTGTTGAACTAT 57.125 32.000 10.03 0.00 41.30 2.12
6120 6540 8.967664 ATACCTGTTAACAAACTGTTGAACTA 57.032 30.769 10.03 0.00 41.30 2.24
6121 6541 7.875327 ATACCTGTTAACAAACTGTTGAACT 57.125 32.000 10.03 0.00 41.30 3.01
6156 6612 0.035176 GCAAAAAGCTGCCCCATCAA 59.965 50.000 0.00 0.00 41.15 2.57
6543 7007 2.481276 CGCCATTGACGAGTCCAATCTA 60.481 50.000 0.34 0.00 32.40 1.98
6544 7008 1.740380 CGCCATTGACGAGTCCAATCT 60.740 52.381 0.34 0.00 32.40 2.40
6545 7009 0.652592 CGCCATTGACGAGTCCAATC 59.347 55.000 0.34 0.00 32.40 2.67
6546 7010 0.036388 ACGCCATTGACGAGTCCAAT 60.036 50.000 0.00 0.00 34.83 3.16
7077 7544 1.400846 ACGATCGATCTTGCGTACACT 59.599 47.619 24.34 0.00 34.93 3.55


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

AutoCloner maintained by Alex Coulton.