Multiple sequence alignment - TraesCS2D01G472500

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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 TraesCS2D01G472500 chr2D 100.000 5490 0 0 1 5490 576197534 576192045 0.000000e+00 10139.0
1 TraesCS2D01G472500 chr2A 92.015 3306 183 35 2235 5489 714211246 714207971 0.000000e+00 4567.0
2 TraesCS2D01G472500 chr2A 93.108 827 47 8 808 1630 714212768 714211948 0.000000e+00 1203.0
3 TraesCS2D01G472500 chr2A 91.532 555 26 7 229 776 714213439 714212899 0.000000e+00 745.0
4 TraesCS2D01G472500 chr2A 85.302 728 68 19 1613 2306 714211934 714211212 0.000000e+00 715.0
5 TraesCS2D01G472500 chr2A 89.500 200 14 3 1 197 714214038 714213843 4.250000e-61 246.0
6 TraesCS2D01G472500 chr2B 92.243 1676 78 19 2491 4146 692166111 692164468 0.000000e+00 2327.0
7 TraesCS2D01G472500 chr2B 94.075 1367 60 15 4144 5490 692164309 692162944 0.000000e+00 2056.0
8 TraesCS2D01G472500 chr2B 93.557 745 39 3 829 1572 692168111 692167375 0.000000e+00 1101.0
9 TraesCS2D01G472500 chr2B 92.747 455 26 2 1658 2105 692167353 692166899 0.000000e+00 651.0
10 TraesCS2D01G472500 chr2B 94.363 408 16 2 369 776 692168607 692168207 2.170000e-173 619.0
11 TraesCS2D01G472500 chr2B 97.468 79 2 0 229 307 692168715 692168637 9.590000e-28 135.0
12 TraesCS2D01G472500 chr7B 90.805 261 23 1 1844 2103 673310640 673310380 1.130000e-91 348.0
13 TraesCS2D01G472500 chr7B 76.836 531 65 30 4434 4950 171090649 171091135 4.250000e-61 246.0
14 TraesCS2D01G472500 chr6B 79.588 534 70 22 4437 4950 173817496 173816982 4.070000e-91 346.0
15 TraesCS2D01G472500 chr7A 90.421 261 24 1 1844 2103 688692087 688691827 5.270000e-90 342.0
16 TraesCS2D01G472500 chr7D 89.655 261 26 1 1844 2103 595729747 595729487 1.140000e-86 331.0
17 TraesCS2D01G472500 chr1B 80.132 302 43 11 4650 4950 87189375 87189660 5.570000e-50 209.0
18 TraesCS2D01G472500 chr5D 81.712 257 32 7 4694 4950 181607176 181607417 3.350000e-47 200.0
19 TraesCS2D01G472500 chr4A 92.683 82 5 1 4855 4935 20573330 20573249 3.470000e-22 117.0
20 TraesCS2D01G472500 chr3A 82.292 96 14 1 7 99 669177158 669177253 4.560000e-11 80.5


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 TraesCS2D01G472500 chr2D 576192045 576197534 5489 True 10139.000000 10139 100.0000 1 5490 1 chr2D.!!$R1 5489
1 TraesCS2D01G472500 chr2A 714207971 714214038 6067 True 1495.200000 4567 90.2914 1 5489 5 chr2A.!!$R1 5488
2 TraesCS2D01G472500 chr2B 692162944 692168715 5771 True 1148.166667 2327 94.0755 229 5490 6 chr2B.!!$R1 5261
3 TraesCS2D01G472500 chr6B 173816982 173817496 514 True 346.000000 346 79.5880 4437 4950 1 chr6B.!!$R1 513

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
350 722 0.107165 GCCATTAGACACCCCTCCAC 60.107 60.000 0.00 0.0 0.00 4.02 F
2037 2572 0.108019 AACCGGTCTTCACCAAGTCC 59.892 55.000 8.04 0.0 44.02 3.85 F
2264 2937 0.247460 CGGCATCCTTGTCACTCTCA 59.753 55.000 0.00 0.0 0.00 3.27 F
2333 3041 0.305313 TTGGTAGTGCGCGTGAAAAC 59.695 50.000 8.43 0.0 0.00 2.43 F
2340 3048 0.593518 TGCGCGTGAAAACCATTGTG 60.594 50.000 8.43 0.0 0.00 3.33 F
2796 3759 1.065199 CAGGAGTCCTTAGCATTGCCA 60.065 52.381 9.68 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2915 0.037326 GAGTGACAAGGATGCCGACA 60.037 55.000 0.00 0.0 0.00 4.35 R
3928 4919 0.323178 CTGGGCTTGCAGAATGAGGT 60.323 55.000 0.00 0.0 39.69 3.85 R
3936 4927 1.609208 AGTGTTAACTGGGCTTGCAG 58.391 50.000 7.22 0.0 34.48 4.41 R
4083 5075 2.930040 AGTGTCATAAACATCGAAGCCG 59.070 45.455 0.00 0.0 40.80 5.52 R
4084 5076 3.063997 CCAGTGTCATAAACATCGAAGCC 59.936 47.826 0.00 0.0 40.80 4.35 R
4660 5838 0.527565 CCCTGAAACATCTTTGCCCG 59.472 55.000 0.00 0.0 0.00 6.13 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
32 34 8.661352 ACATTTTGATTTACTTGAGGTTTTGG 57.339 30.769 0.00 0.00 0.00 3.28
43 45 7.654022 ACTTGAGGTTTTGGTAAGATTTGAA 57.346 32.000 0.00 0.00 0.00 2.69
75 77 1.573108 TGGCTAGAGAAGACAAGGGG 58.427 55.000 0.00 0.00 41.66 4.79
90 92 6.004574 AGACAAGGGGAGTTTTGATTTAGTC 58.995 40.000 0.00 0.00 0.00 2.59
157 161 2.548057 TGACATGTTTGGAAAGAGCGAC 59.452 45.455 0.00 0.00 0.00 5.19
171 175 0.388649 AGCGACGACCACAGATGAAC 60.389 55.000 0.00 0.00 0.00 3.18
173 177 0.109919 CGACGACCACAGATGAACGA 60.110 55.000 0.00 0.00 0.00 3.85
176 180 0.708370 CGACCACAGATGAACGAACG 59.292 55.000 0.00 0.00 0.00 3.95
177 181 1.779569 GACCACAGATGAACGAACGT 58.220 50.000 0.00 0.00 0.00 3.99
179 183 2.915463 GACCACAGATGAACGAACGTAG 59.085 50.000 0.00 0.00 0.00 3.51
194 513 6.360329 ACGAACGTAGAAACATCAAATCAAC 58.640 36.000 0.00 0.00 0.00 3.18
203 522 5.902613 AACATCAAATCAACCATCACGAT 57.097 34.783 0.00 0.00 0.00 3.73
207 526 6.767423 ACATCAAATCAACCATCACGATCATA 59.233 34.615 0.00 0.00 0.00 2.15
209 528 5.759763 TCAAATCAACCATCACGATCATAGG 59.240 40.000 0.00 0.00 0.00 2.57
221 540 3.508012 ACGATCATAGGCTCGCTTCTTAT 59.492 43.478 0.00 0.00 38.42 1.73
222 541 4.700692 ACGATCATAGGCTCGCTTCTTATA 59.299 41.667 0.00 0.00 38.42 0.98
223 542 5.183331 ACGATCATAGGCTCGCTTCTTATAA 59.817 40.000 0.00 0.00 38.42 0.98
224 543 6.093404 CGATCATAGGCTCGCTTCTTATAAA 58.907 40.000 0.00 0.00 0.00 1.40
226 545 7.116376 CGATCATAGGCTCGCTTCTTATAAAAA 59.884 37.037 0.00 0.00 0.00 1.94
327 699 2.282462 CCTTGCCTTGGTCCGCTT 60.282 61.111 0.00 0.00 0.00 4.68
350 722 0.107165 GCCATTAGACACCCCTCCAC 60.107 60.000 0.00 0.00 0.00 4.02
351 723 0.546598 CCATTAGACACCCCTCCACC 59.453 60.000 0.00 0.00 0.00 4.61
352 724 1.285280 CATTAGACACCCCTCCACCA 58.715 55.000 0.00 0.00 0.00 4.17
353 725 1.210478 CATTAGACACCCCTCCACCAG 59.790 57.143 0.00 0.00 0.00 4.00
354 726 0.192566 TTAGACACCCCTCCACCAGT 59.807 55.000 0.00 0.00 0.00 4.00
355 727 1.086565 TAGACACCCCTCCACCAGTA 58.913 55.000 0.00 0.00 0.00 2.74
395 773 2.800746 GTGCAACGCATTGACCGC 60.801 61.111 0.00 0.00 41.91 5.68
401 779 1.852067 AACGCATTGACCGCTTGACC 61.852 55.000 0.00 0.00 0.00 4.02
407 785 3.948719 GACCGCTTGACCCACCCA 61.949 66.667 0.00 0.00 0.00 4.51
410 788 2.589157 CCGCTTGACCCACCCACTA 61.589 63.158 0.00 0.00 0.00 2.74
411 789 1.602237 CGCTTGACCCACCCACTAT 59.398 57.895 0.00 0.00 0.00 2.12
435 813 2.888863 GCTCTCCGTCAGTCCCTG 59.111 66.667 0.00 0.00 0.00 4.45
436 814 1.979693 GCTCTCCGTCAGTCCCTGT 60.980 63.158 0.00 0.00 32.61 4.00
437 815 1.939769 GCTCTCCGTCAGTCCCTGTC 61.940 65.000 0.00 0.00 32.61 3.51
438 816 1.304217 TCTCCGTCAGTCCCTGTCC 60.304 63.158 0.00 0.00 32.61 4.02
439 817 2.283676 TCCGTCAGTCCCTGTCCC 60.284 66.667 0.00 0.00 32.61 4.46
440 818 2.283966 CCGTCAGTCCCTGTCCCT 60.284 66.667 0.00 0.00 32.61 4.20
550 929 2.820059 TCATGTGAGTGAGTGGTGAC 57.180 50.000 0.00 0.00 0.00 3.67
592 971 1.409064 TGTGCCGTGAGCTAGATTAGG 59.591 52.381 0.00 0.00 44.23 2.69
603 982 3.933332 AGCTAGATTAGGCGTTTTGTCAC 59.067 43.478 0.00 0.00 0.00 3.67
623 1002 2.280797 GCTTGGTGACGGCAGTGA 60.281 61.111 0.00 0.00 0.00 3.41
624 1003 2.320587 GCTTGGTGACGGCAGTGAG 61.321 63.158 0.00 0.00 0.00 3.51
679 1058 3.546543 TAGCGATTCCGGGGCTGG 61.547 66.667 16.80 0.00 37.62 4.85
880 1362 1.281867 TCAGTAGCCCAGGAACATTGG 59.718 52.381 0.00 0.00 35.41 3.16
1114 1596 2.057137 AGCAAACACTGAGAAAGGCA 57.943 45.000 0.00 0.00 0.00 4.75
1143 1625 1.761449 TGCAGTCCTTTGTGAAGCAA 58.239 45.000 0.00 0.00 34.87 3.91
1193 1675 2.222007 CTCCTGAATGAAGAGCTCGG 57.778 55.000 8.37 0.49 0.00 4.63
1203 1685 0.244178 AAGAGCTCGGTCGTCTTTCC 59.756 55.000 8.37 0.00 0.00 3.13
1204 1686 1.153804 GAGCTCGGTCGTCTTTCCC 60.154 63.158 0.00 0.00 0.00 3.97
1254 1736 2.712984 GCAAATGCTAGAGGAGGGC 58.287 57.895 0.00 0.00 38.21 5.19
1293 1778 1.333177 AGTGTTCGAGCCAAGAGAGT 58.667 50.000 0.00 0.00 0.00 3.24
1468 1953 3.790691 TTTCAGCCAGAAACACCGA 57.209 47.368 0.00 0.00 41.17 4.69
1470 1955 0.534203 TTCAGCCAGAAACACCGACC 60.534 55.000 0.00 0.00 32.05 4.79
1500 1985 0.519519 CTGCGATGTTAAAACGGGCA 59.480 50.000 0.00 5.54 32.64 5.36
1524 2009 7.012704 GCAGATTATTTCTTGCACCTGATTCTA 59.987 37.037 0.00 0.00 32.24 2.10
1561 2046 2.803030 AATTGCTCATCAGGTCTGCT 57.197 45.000 0.00 0.00 0.00 4.24
1562 2047 2.803030 ATTGCTCATCAGGTCTGCTT 57.197 45.000 0.00 0.00 0.00 3.91
1563 2048 2.574006 TTGCTCATCAGGTCTGCTTT 57.426 45.000 0.00 0.00 0.00 3.51
1564 2049 3.701205 TTGCTCATCAGGTCTGCTTTA 57.299 42.857 0.00 0.00 0.00 1.85
1565 2050 3.257469 TGCTCATCAGGTCTGCTTTAG 57.743 47.619 0.00 0.00 0.00 1.85
1566 2051 2.568956 TGCTCATCAGGTCTGCTTTAGT 59.431 45.455 0.00 0.00 0.00 2.24
1567 2052 2.935201 GCTCATCAGGTCTGCTTTAGTG 59.065 50.000 0.00 0.00 0.00 2.74
1568 2053 2.935201 CTCATCAGGTCTGCTTTAGTGC 59.065 50.000 0.00 0.00 0.00 4.40
1569 2054 2.568956 TCATCAGGTCTGCTTTAGTGCT 59.431 45.455 0.00 0.00 0.00 4.40
1570 2055 3.008375 TCATCAGGTCTGCTTTAGTGCTT 59.992 43.478 0.00 0.00 0.00 3.91
1572 2057 4.617253 TCAGGTCTGCTTTAGTGCTTTA 57.383 40.909 0.00 0.00 0.00 1.85
1582 2067 8.522830 TCTGCTTTAGTGCTTTATATGCTTTTT 58.477 29.630 0.00 0.00 0.00 1.94
1589 2074 5.286082 GTGCTTTATATGCTTTTTCACACCG 59.714 40.000 0.00 0.00 0.00 4.94
1595 2080 3.423996 TGCTTTTTCACACCGTTTACC 57.576 42.857 0.00 0.00 0.00 2.85
1596 2081 2.099427 TGCTTTTTCACACCGTTTACCC 59.901 45.455 0.00 0.00 0.00 3.69
1597 2082 2.359848 GCTTTTTCACACCGTTTACCCT 59.640 45.455 0.00 0.00 0.00 4.34
1598 2083 3.565063 GCTTTTTCACACCGTTTACCCTA 59.435 43.478 0.00 0.00 0.00 3.53
1600 2085 5.412286 GCTTTTTCACACCGTTTACCCTATA 59.588 40.000 0.00 0.00 0.00 1.31
1601 2086 6.094464 GCTTTTTCACACCGTTTACCCTATAT 59.906 38.462 0.00 0.00 0.00 0.86
1627 2122 4.922206 ACATTTAGGTTGCATTCCAGAGA 58.078 39.130 10.40 0.00 0.00 3.10
1630 2125 6.096001 ACATTTAGGTTGCATTCCAGAGAATC 59.904 38.462 10.40 0.00 40.89 2.52
1631 2126 3.726557 AGGTTGCATTCCAGAGAATCA 57.273 42.857 10.40 0.00 40.89 2.57
1634 2129 1.660167 TGCATTCCAGAGAATCAGCG 58.340 50.000 0.00 0.00 40.89 5.18
1654 2180 3.954837 GCCAAATAAGGGGGCTGG 58.045 61.111 0.00 0.00 44.32 4.85
1675 2201 8.362639 GGCTGGTACATGAAATTTGATGATATT 58.637 33.333 22.24 4.46 38.20 1.28
1713 2247 0.321346 TTCAGGATGCTGAGTTGCGA 59.679 50.000 16.95 0.00 34.56 5.10
1746 2280 8.561738 ACATATTTAATCACTTTCCGACACTT 57.438 30.769 0.00 0.00 0.00 3.16
1764 2298 2.290768 ACTTGCAGATGAGGTGAATGCT 60.291 45.455 0.00 0.00 37.76 3.79
1771 2305 1.702182 TGAGGTGAATGCTTTTGCCA 58.298 45.000 8.20 0.00 46.87 4.92
1788 2323 0.811281 CCACTGATTTTTCCGCTCCC 59.189 55.000 0.00 0.00 0.00 4.30
1796 2331 1.531739 TTTTCCGCTCCCCATTGTGC 61.532 55.000 0.00 0.00 0.00 4.57
1797 2332 2.705312 TTTCCGCTCCCCATTGTGCA 62.705 55.000 0.00 0.00 0.00 4.57
1805 2340 1.310933 CCCCATTGTGCACTGCTCTC 61.311 60.000 19.41 0.00 0.00 3.20
1813 2348 5.405935 TTGTGCACTGCTCTCTAATCTTA 57.594 39.130 19.41 0.00 0.00 2.10
1878 2413 8.877864 TTCAGGATGTTATTGGTAAAACAGAT 57.122 30.769 0.00 0.00 38.87 2.90
2037 2572 0.108019 AACCGGTCTTCACCAAGTCC 59.892 55.000 8.04 0.00 44.02 3.85
2082 2617 3.423749 TGTTGCAATGGACATCACAGAT 58.576 40.909 0.59 0.00 0.00 2.90
2128 2686 4.650754 TCTCGTACCTCCAAAATCTAGC 57.349 45.455 0.00 0.00 0.00 3.42
2133 2691 4.209288 CGTACCTCCAAAATCTAGCGAATG 59.791 45.833 0.00 0.00 0.00 2.67
2134 2692 4.487714 ACCTCCAAAATCTAGCGAATGA 57.512 40.909 0.00 0.00 0.00 2.57
2140 2813 7.095439 CCTCCAAAATCTAGCGAATGATAAGAC 60.095 40.741 0.00 0.00 0.00 3.01
2141 2814 7.272244 TCCAAAATCTAGCGAATGATAAGACA 58.728 34.615 0.00 0.00 0.00 3.41
2143 2816 8.562892 CCAAAATCTAGCGAATGATAAGACATT 58.437 33.333 0.00 0.00 42.19 2.71
2156 2829 7.311092 TGATAAGACATTATTACGGTCCCAT 57.689 36.000 0.00 0.00 31.57 4.00
2157 2830 7.741785 TGATAAGACATTATTACGGTCCCATT 58.258 34.615 0.00 0.00 31.57 3.16
2168 2841 6.995511 TTACGGTCCCATTTTTATTCTGAG 57.004 37.500 0.00 0.00 0.00 3.35
2170 2843 5.755849 ACGGTCCCATTTTTATTCTGAGAT 58.244 37.500 0.00 0.00 0.00 2.75
2190 2863 6.919662 TGAGATTGATTTTGTGCTTCTTTGTC 59.080 34.615 0.00 0.00 0.00 3.18
2193 2866 6.455360 TTGATTTTGTGCTTCTTTGTCTCT 57.545 33.333 0.00 0.00 0.00 3.10
2195 2868 4.900635 TTTTGTGCTTCTTTGTCTCTCC 57.099 40.909 0.00 0.00 0.00 3.71
2198 2871 2.224378 TGTGCTTCTTTGTCTCTCCTGG 60.224 50.000 0.00 0.00 0.00 4.45
2200 2873 2.037772 TGCTTCTTTGTCTCTCCTGGTC 59.962 50.000 0.00 0.00 0.00 4.02
2202 2875 2.704190 TCTTTGTCTCTCCTGGTCCT 57.296 50.000 0.00 0.00 0.00 3.85
2203 2876 2.251818 TCTTTGTCTCTCCTGGTCCTG 58.748 52.381 0.00 0.00 0.00 3.86
2204 2877 1.277557 CTTTGTCTCTCCTGGTCCTGG 59.722 57.143 8.53 8.53 0.00 4.45
2206 2879 0.542938 TGTCTCTCCTGGTCCTGGTG 60.543 60.000 14.11 11.93 0.00 4.17
2209 2882 1.229625 TCTCCTGGTCCTGGTGCAT 60.230 57.895 14.11 0.00 0.00 3.96
2214 2887 2.092429 TCCTGGTCCTGGTGCATAATTC 60.092 50.000 14.11 0.00 0.00 2.17
2219 2892 3.877508 GGTCCTGGTGCATAATTCTACAC 59.122 47.826 0.00 0.00 0.00 2.90
2257 2930 2.604046 ATAGTGTCGGCATCCTTGTC 57.396 50.000 0.00 0.00 0.00 3.18
2258 2931 1.262417 TAGTGTCGGCATCCTTGTCA 58.738 50.000 0.00 0.00 0.00 3.58
2259 2932 0.320771 AGTGTCGGCATCCTTGTCAC 60.321 55.000 0.00 0.00 0.00 3.67
2264 2937 0.247460 CGGCATCCTTGTCACTCTCA 59.753 55.000 0.00 0.00 0.00 3.27
2265 2938 1.134580 CGGCATCCTTGTCACTCTCAT 60.135 52.381 0.00 0.00 0.00 2.90
2266 2939 2.286872 GGCATCCTTGTCACTCTCATG 58.713 52.381 0.00 0.00 0.00 3.07
2267 2940 2.093288 GGCATCCTTGTCACTCTCATGA 60.093 50.000 0.00 0.00 0.00 3.07
2269 2942 4.197750 GCATCCTTGTCACTCTCATGAAT 58.802 43.478 0.00 0.00 0.00 2.57
2270 2943 5.363101 GCATCCTTGTCACTCTCATGAATA 58.637 41.667 0.00 0.00 0.00 1.75
2274 2947 8.733458 CATCCTTGTCACTCTCATGAATAAAAA 58.267 33.333 0.00 0.00 0.00 1.94
2299 2972 8.617290 AAAACATCGTTATCCTTGTTAGTTCT 57.383 30.769 0.00 0.00 32.31 3.01
2317 3025 4.461781 AGTTCTCCATGATTTCAGCTTTGG 59.538 41.667 0.00 0.00 0.00 3.28
2326 3034 1.565156 TTCAGCTTTGGTAGTGCGCG 61.565 55.000 0.00 0.00 0.00 6.86
2333 3041 0.305313 TTGGTAGTGCGCGTGAAAAC 59.695 50.000 8.43 0.00 0.00 2.43
2340 3048 0.593518 TGCGCGTGAAAACCATTGTG 60.594 50.000 8.43 0.00 0.00 3.33
2348 3056 4.320129 CGTGAAAACCATTGTGCAGTGATA 60.320 41.667 0.00 0.00 0.00 2.15
2393 3101 3.378512 AGAGTATTCTCCACATGAGCCA 58.621 45.455 0.00 0.00 41.18 4.75
2394 3102 3.972638 AGAGTATTCTCCACATGAGCCAT 59.027 43.478 0.00 0.00 41.18 4.40
2399 3107 4.987963 TTCTCCACATGAGCCATGATAT 57.012 40.909 18.41 0.00 43.81 1.63
2400 3108 4.548451 TCTCCACATGAGCCATGATATC 57.452 45.455 18.41 0.00 43.81 1.63
2411 3119 8.925700 CATGAGCCATGATATCATTTTCATTTG 58.074 33.333 22.06 15.23 43.81 2.32
2424 3133 8.278729 TCATTTTCATTTGAAATTAATGCCCC 57.721 30.769 6.57 0.00 42.83 5.80
2429 3138 6.777782 TCATTTGAAATTAATGCCCCAACTT 58.222 32.000 0.00 0.00 33.91 2.66
2434 3143 5.654650 TGAAATTAATGCCCCAACTTATCGT 59.345 36.000 0.00 0.00 0.00 3.73
2443 3152 6.539173 TGCCCCAACTTATCGTATTTCATAT 58.461 36.000 0.00 0.00 0.00 1.78
2495 3458 9.042008 TGAAATTACATCTTATTCTACGCTTCC 57.958 33.333 0.00 0.00 0.00 3.46
2496 3459 8.958119 AAATTACATCTTATTCTACGCTTCCA 57.042 30.769 0.00 0.00 0.00 3.53
2499 3462 6.663944 ACATCTTATTCTACGCTTCCAAAC 57.336 37.500 0.00 0.00 0.00 2.93
2502 3465 4.630069 TCTTATTCTACGCTTCCAAACTGC 59.370 41.667 0.00 0.00 0.00 4.40
2512 3475 3.181516 GCTTCCAAACTGCATCTACTTCG 60.182 47.826 0.00 0.00 0.00 3.79
2526 3489 1.641577 ACTTCGATGCGCTTTAGGTC 58.358 50.000 9.73 0.00 0.00 3.85
2550 3513 8.348507 GTCAAAACAAGAGAGAAAATGACAGAT 58.651 33.333 0.00 0.00 35.82 2.90
2562 3525 8.324191 AGAAAATGACAGATATAAGGGTGAGA 57.676 34.615 0.00 0.00 0.00 3.27
2600 3563 3.084039 CCAAGGAAACAGAGCATAGCAA 58.916 45.455 0.00 0.00 0.00 3.91
2627 3590 7.995289 TCACTTAATATTACAGGTTTGCATGG 58.005 34.615 0.00 0.00 0.00 3.66
2726 3689 6.651755 AAAAATGCAGAAGAAACAACACAG 57.348 33.333 0.00 0.00 0.00 3.66
2779 3742 3.316501 AGATCAGATCTCCCCTTTCAGG 58.683 50.000 7.15 0.00 33.42 3.86
2796 3759 1.065199 CAGGAGTCCTTAGCATTGCCA 60.065 52.381 9.68 0.00 0.00 4.92
2859 3822 4.164988 AGTTGCTTGAGGCTATGTTATCCT 59.835 41.667 0.00 0.00 42.39 3.24
2985 3948 7.960738 CGTCGATTAGTTACATTGTTGGATTTT 59.039 33.333 0.00 0.00 0.00 1.82
2998 3964 2.972625 TGGATTTTCTAGACACCTGCG 58.027 47.619 0.00 0.00 0.00 5.18
3009 3975 2.283966 ACCTGCGACTGGCCTAGT 60.284 61.111 3.32 5.85 44.02 2.57
3028 3994 6.183360 GCCTAGTGCATAACTAACTTGACAAG 60.183 42.308 13.77 13.77 40.92 3.16
3197 4180 8.311836 AGTGGAGATGAGTTTTAAGATTCGTTA 58.688 33.333 0.00 0.00 0.00 3.18
3232 4215 5.350365 TCAAAAGTCGGTCATGCATTAGTAC 59.650 40.000 0.00 0.00 0.00 2.73
3238 4221 5.121768 GTCGGTCATGCATTAGTACTTGTTT 59.878 40.000 0.00 0.00 0.00 2.83
3366 4351 5.300286 CCTGCAATATTTAGACCAAGGGAAG 59.700 44.000 0.00 0.00 0.00 3.46
3388 4373 9.059260 GGAAGTAGTTAAACATGTACTCCAAAA 57.941 33.333 0.00 0.00 0.00 2.44
3542 4529 8.851541 ATGTATTTGCAACTTGAATCCAATTT 57.148 26.923 0.00 0.00 0.00 1.82
3715 4706 2.554032 AGGTGAGCTTCCGTTTCATTTG 59.446 45.455 0.00 0.00 0.00 2.32
3782 4773 9.887629 AGATAATGAACAGATATGCTTGGATAG 57.112 33.333 0.00 0.00 0.00 2.08
3783 4774 9.881649 GATAATGAACAGATATGCTTGGATAGA 57.118 33.333 0.00 0.00 0.00 1.98
3799 4790 9.077674 GCTTGGATAGATATAGTACGAAACATG 57.922 37.037 0.00 0.00 0.00 3.21
3841 4832 6.538021 ACATTTAAAACAGTTTCAGCAATGCA 59.462 30.769 8.35 0.00 0.00 3.96
3878 4869 3.660669 TGAAGGGAAGGTTGGGATAAACT 59.339 43.478 0.00 0.00 0.00 2.66
3928 4919 8.347004 TGGAATGCAAAATAGAACATACAAGA 57.653 30.769 0.00 0.00 0.00 3.02
3936 4927 9.994432 CAAAATAGAACATACAAGACCTCATTC 57.006 33.333 0.00 0.00 0.00 2.67
4037 5029 2.159128 ACCGTGAAGATGCTCATCAGAG 60.159 50.000 11.90 0.00 44.96 3.35
4083 5075 0.875059 CGGAGGAAACTGTTTGGCTC 59.125 55.000 11.03 0.00 44.43 4.70
4084 5076 0.875059 GGAGGAAACTGTTTGGCTCG 59.125 55.000 11.03 0.00 44.43 5.03
4175 5328 6.700081 GCATGATCATAGTTTGCATGTTTCAT 59.300 34.615 8.15 0.00 38.76 2.57
4275 5429 3.371285 GCAGAGAAGTCATTACCGTTTCC 59.629 47.826 0.00 0.00 0.00 3.13
4292 5446 4.506654 CGTTTCCGTTCAAGAGGTATATGG 59.493 45.833 0.00 0.00 0.00 2.74
4374 5528 5.572896 GCAAGCAGTTGGTATGTATTTGTTC 59.427 40.000 0.00 0.00 33.87 3.18
4391 5545 3.230134 TGTTCCAGTTTGAATCCTTGGG 58.770 45.455 0.00 0.00 0.00 4.12
4578 5738 2.094854 CACAATTCCTGCAAGAGAAGCC 60.095 50.000 0.00 0.00 34.07 4.35
4630 5791 3.578716 CCTGTACCAGAACTTTCAGGAGA 59.421 47.826 7.37 0.00 43.28 3.71
4639 5800 6.370166 CCAGAACTTTCAGGAGAACTACATTC 59.630 42.308 0.00 0.00 36.05 2.67
4640 5801 6.931281 CAGAACTTTCAGGAGAACTACATTCA 59.069 38.462 0.00 0.00 40.09 2.57
4645 5806 7.451877 ACTTTCAGGAGAACTACATTCAGTCTA 59.548 37.037 0.00 0.00 40.09 2.59
4653 5826 7.093992 AGAACTACATTCAGTCTAACTGCTTC 58.906 38.462 2.18 0.00 45.54 3.86
4660 5838 6.604735 TTCAGTCTAACTGCTTCTGAAAAC 57.395 37.500 2.18 0.00 45.54 2.43
4691 5869 1.792757 TTTCAGGGCTGAGGCATGGT 61.793 55.000 20.33 0.00 40.21 3.55
4732 5914 5.956642 TGTGGTTTACAGTTTCCTTGTTTC 58.043 37.500 0.00 0.00 33.42 2.78
4769 5952 4.923281 GGGTGTTGATTTGTTGCTTCATAC 59.077 41.667 0.00 0.00 0.00 2.39
4773 5956 5.534278 TGTTGATTTGTTGCTTCATACCAGA 59.466 36.000 0.00 0.00 0.00 3.86
4774 5957 5.885230 TGATTTGTTGCTTCATACCAGAG 57.115 39.130 0.00 0.00 0.00 3.35
4826 6009 7.760794 TCAGGAAAGCATACAAATAAATTGCAG 59.239 33.333 0.00 0.00 43.13 4.41
4986 6169 6.422400 GGCTTACACAGAAGAGATATAACTGC 59.578 42.308 0.00 0.00 32.67 4.40
5174 6357 3.255725 GAATCCGTCGGTTAACATGACA 58.744 45.455 22.39 10.26 32.91 3.58
5267 6450 1.616994 GCTAAAGCCAGGGTGGTTGAT 60.617 52.381 0.00 0.00 40.46 2.57
5296 6479 2.159352 CCACATCAATTGCATCGCTCAA 60.159 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.108284 CCAAAACCTCAAGTAAATCAAAATGTT 57.892 29.630 0.00 0.00 0.00 2.71
8 9 8.661352 ACCAAAACCTCAAGTAAATCAAAATG 57.339 30.769 0.00 0.00 0.00 2.32
19 21 7.654022 TTCAAATCTTACCAAAACCTCAAGT 57.346 32.000 0.00 0.00 0.00 3.16
43 45 7.930865 GTCTTCTCTAGCCATAGTCAAATCAAT 59.069 37.037 0.00 0.00 0.00 2.57
116 120 7.517614 TGTCATGCATTAACTTAACCAAAGA 57.482 32.000 0.00 0.00 38.67 2.52
136 140 2.548057 GTCGCTCTTTCCAAACATGTCA 59.452 45.455 0.00 0.00 0.00 3.58
157 161 0.708370 CGTTCGTTCATCTGTGGTCG 59.292 55.000 0.00 0.00 0.00 4.79
171 175 5.788531 GGTTGATTTGATGTTTCTACGTTCG 59.211 40.000 0.00 0.00 0.00 3.95
173 177 6.627395 TGGTTGATTTGATGTTTCTACGTT 57.373 33.333 0.00 0.00 0.00 3.99
176 180 6.742718 CGTGATGGTTGATTTGATGTTTCTAC 59.257 38.462 0.00 0.00 0.00 2.59
177 181 6.652900 TCGTGATGGTTGATTTGATGTTTCTA 59.347 34.615 0.00 0.00 0.00 2.10
179 183 5.698832 TCGTGATGGTTGATTTGATGTTTC 58.301 37.500 0.00 0.00 0.00 2.78
194 513 1.988063 CGAGCCTATGATCGTGATGG 58.012 55.000 0.00 0.00 44.96 3.51
240 612 2.912025 AACGGGCCTGCAACTTGG 60.912 61.111 12.89 0.00 0.00 3.61
327 699 0.253160 AGGGGTGTCTAATGGCAGGA 60.253 55.000 0.00 0.00 0.00 3.86
350 722 1.757699 GGAGAGTGGTAGGCTTACTGG 59.242 57.143 5.91 0.00 0.00 4.00
351 723 1.757699 GGGAGAGTGGTAGGCTTACTG 59.242 57.143 5.91 0.00 0.00 2.74
352 724 1.361543 TGGGAGAGTGGTAGGCTTACT 59.638 52.381 5.91 0.00 0.00 2.24
353 725 1.757699 CTGGGAGAGTGGTAGGCTTAC 59.242 57.143 0.00 0.00 0.00 2.34
354 726 1.965318 GCTGGGAGAGTGGTAGGCTTA 60.965 57.143 0.00 0.00 0.00 3.09
355 727 1.268283 GCTGGGAGAGTGGTAGGCTT 61.268 60.000 0.00 0.00 0.00 4.35
395 773 1.064685 GGGAATAGTGGGTGGGTCAAG 60.065 57.143 0.00 0.00 0.00 3.02
401 779 2.915869 CGGGGGAATAGTGGGTGG 59.084 66.667 0.00 0.00 0.00 4.61
407 785 1.833049 CGGAGAGCGGGGGAATAGT 60.833 63.158 0.00 0.00 0.00 2.12
410 788 3.155167 GACGGAGAGCGGGGGAAT 61.155 66.667 0.00 0.00 0.00 3.01
411 789 4.689549 TGACGGAGAGCGGGGGAA 62.690 66.667 0.00 0.00 0.00 3.97
550 929 1.063912 TCAAATTAAGATGGCGCGCAG 59.936 47.619 34.42 6.94 0.00 5.18
558 937 4.154015 TCACGGCACAGTCAAATTAAGATG 59.846 41.667 0.00 0.00 0.00 2.90
592 971 1.130955 CCAAGCATGTGACAAAACGC 58.869 50.000 0.00 0.00 0.00 4.84
603 982 1.968017 ACTGCCGTCACCAAGCATG 60.968 57.895 0.00 0.00 35.64 4.06
679 1058 4.998788 ACTGAACTTTCCAAAAGAACAGC 58.001 39.130 19.32 0.00 32.95 4.40
680 1059 6.620678 TGAACTGAACTTTCCAAAAGAACAG 58.379 36.000 18.55 18.55 32.95 3.16
681 1060 6.432783 TCTGAACTGAACTTTCCAAAAGAACA 59.567 34.615 6.44 5.24 32.95 3.18
682 1061 6.852664 TCTGAACTGAACTTTCCAAAAGAAC 58.147 36.000 6.44 1.41 32.95 3.01
805 1254 9.402320 CACTACTGGATAGAGCATATACATACT 57.598 37.037 0.00 0.00 34.65 2.12
806 1255 9.179909 ACACTACTGGATAGAGCATATACATAC 57.820 37.037 0.00 0.00 34.65 2.39
810 1292 7.931578 AGACACTACTGGATAGAGCATATAC 57.068 40.000 0.00 0.00 34.65 1.47
821 1303 6.268847 ACTTTCTTCTCAAGACACTACTGGAT 59.731 38.462 0.00 0.00 37.23 3.41
880 1362 4.855388 CAGCTGATGAACACAATTTACTGC 59.145 41.667 8.42 0.00 0.00 4.40
1114 1596 5.105392 TCACAAAGGACTGCATTTGAAAAGT 60.105 36.000 15.53 0.00 45.80 2.66
1143 1625 1.607225 TGGCCCTCTTGTATTCCCAT 58.393 50.000 0.00 0.00 0.00 4.00
1193 1675 2.383527 CGCTGCTGGGAAAGACGAC 61.384 63.158 1.02 0.00 0.00 4.34
1203 1685 2.079158 TCAATCTCTTTTCGCTGCTGG 58.921 47.619 0.00 0.00 0.00 4.85
1204 1686 2.475852 GCTCAATCTCTTTTCGCTGCTG 60.476 50.000 0.00 0.00 0.00 4.41
1252 1734 2.175811 GGCATTGTGACGTTCGCC 59.824 61.111 0.00 0.00 0.00 5.54
1253 1735 2.175811 GGGCATTGTGACGTTCGC 59.824 61.111 0.00 0.00 0.00 4.70
1254 1736 0.948623 TCAGGGCATTGTGACGTTCG 60.949 55.000 0.00 0.00 0.00 3.95
1293 1778 3.515502 CCTGGTCATGAGAAAGGTCACTA 59.484 47.826 0.00 0.00 0.00 2.74
1468 1953 1.115467 ATCGCAGAGAATTCCTCGGT 58.885 50.000 0.65 0.00 46.49 4.69
1470 1955 2.215907 ACATCGCAGAGAATTCCTCG 57.784 50.000 0.65 1.12 46.49 4.63
1500 1985 8.049117 TGTAGAATCAGGTGCAAGAAATAATCT 58.951 33.333 0.00 0.00 41.32 2.40
1524 2009 4.561326 GCAATTACAATGGGAGCACTTTGT 60.561 41.667 8.71 8.71 40.46 2.83
1561 2046 9.405587 GTGTGAAAAAGCATATAAAGCACTAAA 57.594 29.630 0.00 0.00 0.00 1.85
1562 2047 8.026607 GGTGTGAAAAAGCATATAAAGCACTAA 58.973 33.333 0.00 0.00 0.00 2.24
1563 2048 7.535139 GGTGTGAAAAAGCATATAAAGCACTA 58.465 34.615 0.00 0.00 0.00 2.74
1564 2049 6.389906 GGTGTGAAAAAGCATATAAAGCACT 58.610 36.000 0.00 0.00 0.00 4.40
1565 2050 5.286082 CGGTGTGAAAAAGCATATAAAGCAC 59.714 40.000 3.73 0.00 0.00 4.40
1566 2051 5.048364 ACGGTGTGAAAAAGCATATAAAGCA 60.048 36.000 3.73 0.00 0.00 3.91
1567 2052 5.399013 ACGGTGTGAAAAAGCATATAAAGC 58.601 37.500 0.00 0.00 0.00 3.51
1568 2053 7.867445 AAACGGTGTGAAAAAGCATATAAAG 57.133 32.000 0.00 0.00 0.00 1.85
1569 2054 7.808856 GGTAAACGGTGTGAAAAAGCATATAAA 59.191 33.333 0.00 0.00 0.00 1.40
1570 2055 7.306953 GGTAAACGGTGTGAAAAAGCATATAA 58.693 34.615 0.00 0.00 0.00 0.98
1572 2057 5.336134 GGGTAAACGGTGTGAAAAAGCATAT 60.336 40.000 0.00 0.00 0.00 1.78
1582 2067 5.680594 ACAATATAGGGTAAACGGTGTGA 57.319 39.130 0.00 0.00 0.00 3.58
1597 2082 9.634021 TGGAATGCAACCTAAATGTACAATATA 57.366 29.630 0.00 0.00 0.00 0.86
1598 2083 8.532186 TGGAATGCAACCTAAATGTACAATAT 57.468 30.769 0.00 0.00 0.00 1.28
1600 2085 6.663093 TCTGGAATGCAACCTAAATGTACAAT 59.337 34.615 0.00 0.00 0.00 2.71
1601 2086 6.007076 TCTGGAATGCAACCTAAATGTACAA 58.993 36.000 0.00 0.00 0.00 2.41
1615 2110 1.207811 TCGCTGATTCTCTGGAATGCA 59.792 47.619 0.00 0.00 41.68 3.96
1622 2117 1.730501 TTGGCTTCGCTGATTCTCTG 58.269 50.000 0.00 0.00 0.00 3.35
1627 2122 2.689983 CCCTTATTTGGCTTCGCTGATT 59.310 45.455 0.00 0.00 0.00 2.57
1630 2125 0.740737 CCCCTTATTTGGCTTCGCTG 59.259 55.000 0.00 0.00 0.00 5.18
1631 2126 0.395724 CCCCCTTATTTGGCTTCGCT 60.396 55.000 0.00 0.00 0.00 4.93
1644 2170 1.080638 TTTCATGTACCAGCCCCCTT 58.919 50.000 0.00 0.00 0.00 3.95
1649 2175 5.581126 TCATCAAATTTCATGTACCAGCC 57.419 39.130 1.76 0.00 0.00 4.85
1675 2201 8.760980 TCCTGAAAAGGAGAAGAAATTGTTAA 57.239 30.769 0.00 0.00 33.38 2.01
1690 2224 2.094854 GCAACTCAGCATCCTGAAAAGG 60.095 50.000 0.00 0.00 46.84 3.11
1713 2247 9.216117 GGAAAGTGATTAAATATGTAGCGGTAT 57.784 33.333 0.00 0.00 0.00 2.73
1746 2280 2.502142 AAGCATTCACCTCATCTGCA 57.498 45.000 0.00 0.00 35.32 4.41
1764 2298 2.102252 AGCGGAAAAATCAGTGGCAAAA 59.898 40.909 0.00 0.00 0.00 2.44
1771 2305 0.404040 TGGGGAGCGGAAAAATCAGT 59.596 50.000 0.00 0.00 0.00 3.41
1788 2323 2.391616 TAGAGAGCAGTGCACAATGG 57.608 50.000 21.04 6.54 0.00 3.16
1796 2331 8.539770 TTGAAGTTTAAGATTAGAGAGCAGTG 57.460 34.615 0.00 0.00 0.00 3.66
1797 2332 8.371699 ACTTGAAGTTTAAGATTAGAGAGCAGT 58.628 33.333 13.86 0.00 0.00 4.40
1813 2348 6.092533 CAGCCAAAAATCACAACTTGAAGTTT 59.907 34.615 8.03 0.00 36.03 2.66
1827 2362 5.702209 ACAAATTGTGATCCAGCCAAAAATC 59.298 36.000 0.00 0.00 0.00 2.17
1878 2413 5.901853 ACCCTCTTCTGACAATATCTCATGA 59.098 40.000 0.00 0.00 0.00 3.07
1895 2430 7.394923 CCTTATTCATCTCGTCTATACCCTCTT 59.605 40.741 0.00 0.00 0.00 2.85
2001 2536 3.933955 CCGGTTCAATGTATACCACGAAA 59.066 43.478 0.00 0.00 32.12 3.46
2004 2539 2.861935 GACCGGTTCAATGTATACCACG 59.138 50.000 9.42 0.00 32.12 4.94
2037 2572 1.323412 TCACACCAATTGTTTCCCCG 58.677 50.000 4.43 0.00 35.67 5.73
2105 2640 5.602628 GCTAGATTTTGGAGGTACGAGATT 58.397 41.667 0.00 0.00 0.00 2.40
2106 2641 4.261656 CGCTAGATTTTGGAGGTACGAGAT 60.262 45.833 0.00 0.00 0.00 2.75
2111 2646 5.357257 TCATTCGCTAGATTTTGGAGGTAC 58.643 41.667 0.00 0.00 0.00 3.34
2114 2649 6.931281 TCTTATCATTCGCTAGATTTTGGAGG 59.069 38.462 0.00 0.00 0.00 4.30
2117 2675 7.482654 TGTCTTATCATTCGCTAGATTTTGG 57.517 36.000 0.00 0.00 0.00 3.28
2128 2686 7.063074 GGGACCGTAATAATGTCTTATCATTCG 59.937 40.741 0.00 0.00 38.68 3.34
2133 2691 8.617290 AAATGGGACCGTAATAATGTCTTATC 57.383 34.615 0.00 0.00 0.00 1.75
2134 2692 8.990163 AAAATGGGACCGTAATAATGTCTTAT 57.010 30.769 0.00 0.00 0.00 1.73
2140 2813 9.677567 CAGAATAAAAATGGGACCGTAATAATG 57.322 33.333 0.00 0.00 0.00 1.90
2141 2814 9.635404 TCAGAATAAAAATGGGACCGTAATAAT 57.365 29.630 0.00 0.00 0.00 1.28
2143 2816 8.487848 TCTCAGAATAAAAATGGGACCGTAATA 58.512 33.333 0.00 0.00 0.00 0.98
2144 2817 7.343357 TCTCAGAATAAAAATGGGACCGTAAT 58.657 34.615 0.00 0.00 0.00 1.89
2146 2819 6.302535 TCTCAGAATAAAAATGGGACCGTA 57.697 37.500 0.00 0.00 0.00 4.02
2147 2820 5.174037 TCTCAGAATAAAAATGGGACCGT 57.826 39.130 0.00 0.00 0.00 4.83
2148 2821 6.318648 TCAATCTCAGAATAAAAATGGGACCG 59.681 38.462 0.00 0.00 0.00 4.79
2156 2829 9.985730 AGCACAAAATCAATCTCAGAATAAAAA 57.014 25.926 0.00 0.00 0.00 1.94
2157 2830 9.985730 AAGCACAAAATCAATCTCAGAATAAAA 57.014 25.926 0.00 0.00 0.00 1.52
2168 2841 7.144000 AGAGACAAAGAAGCACAAAATCAATC 58.856 34.615 0.00 0.00 0.00 2.67
2170 2843 6.455360 AGAGACAAAGAAGCACAAAATCAA 57.545 33.333 0.00 0.00 0.00 2.57
2176 2849 3.470709 CAGGAGAGACAAAGAAGCACAA 58.529 45.455 0.00 0.00 0.00 3.33
2190 2863 1.270414 ATGCACCAGGACCAGGAGAG 61.270 60.000 10.44 0.41 0.00 3.20
2193 2866 1.595311 ATTATGCACCAGGACCAGGA 58.405 50.000 10.44 0.00 0.00 3.86
2195 2868 3.287867 AGAATTATGCACCAGGACCAG 57.712 47.619 0.00 0.00 0.00 4.00
2229 2902 6.646267 AGGATGCCGACACTATTTTAACTAA 58.354 36.000 0.00 0.00 0.00 2.24
2234 2907 4.839121 ACAAGGATGCCGACACTATTTTA 58.161 39.130 0.00 0.00 0.00 1.52
2242 2915 0.037326 GAGTGACAAGGATGCCGACA 60.037 55.000 0.00 0.00 0.00 4.35
2247 2920 3.257469 TCATGAGAGTGACAAGGATGC 57.743 47.619 0.00 0.00 0.00 3.91
2274 2947 8.617290 AGAACTAACAAGGATAACGATGTTTT 57.383 30.769 0.00 0.00 36.13 2.43
2275 2948 7.333672 GGAGAACTAACAAGGATAACGATGTTT 59.666 37.037 0.00 0.00 36.13 2.83
2277 2950 6.070995 TGGAGAACTAACAAGGATAACGATGT 60.071 38.462 0.00 0.00 0.00 3.06
2284 2957 8.548025 TGAAATCATGGAGAACTAACAAGGATA 58.452 33.333 0.00 0.00 0.00 2.59
2294 2967 4.461781 CCAAAGCTGAAATCATGGAGAACT 59.538 41.667 0.00 0.00 0.00 3.01
2297 2970 4.038271 ACCAAAGCTGAAATCATGGAGA 57.962 40.909 7.57 0.00 0.00 3.71
2298 2971 4.946157 ACTACCAAAGCTGAAATCATGGAG 59.054 41.667 7.57 4.26 0.00 3.86
2299 2972 4.701651 CACTACCAAAGCTGAAATCATGGA 59.298 41.667 7.57 0.00 0.00 3.41
2317 3025 0.515564 ATGGTTTTCACGCGCACTAC 59.484 50.000 5.73 0.00 0.00 2.73
2326 3034 3.435105 TCACTGCACAATGGTTTTCAC 57.565 42.857 0.00 0.00 0.00 3.18
2380 3088 4.281898 TGATATCATGGCTCATGTGGAG 57.718 45.455 0.00 0.00 46.93 3.86
2387 3095 8.240267 TCAAATGAAAATGATATCATGGCTCA 57.760 30.769 18.85 19.09 36.44 4.26
2399 3107 7.886970 TGGGGCATTAATTTCAAATGAAAATGA 59.113 29.630 17.15 6.94 45.81 2.57
2400 3108 8.053026 TGGGGCATTAATTTCAAATGAAAATG 57.947 30.769 12.17 11.98 45.81 2.32
2411 3119 6.144078 ACGATAAGTTGGGGCATTAATTTC 57.856 37.500 0.00 0.00 0.00 2.17
2415 3123 6.829298 TGAAATACGATAAGTTGGGGCATTAA 59.171 34.615 0.00 0.00 0.00 1.40
2420 3128 7.822822 AGTATATGAAATACGATAAGTTGGGGC 59.177 37.037 0.00 0.00 0.00 5.80
2429 3138 8.634475 GCAGATGCAGTATATGAAATACGATA 57.366 34.615 0.00 0.00 41.59 2.92
2465 3174 9.107367 GCGTAGAATAAGATGTAATTTCAATGC 57.893 33.333 0.00 0.00 0.00 3.56
2512 3475 3.552604 TGTTTTGACCTAAAGCGCATC 57.447 42.857 11.47 0.00 32.75 3.91
2550 3513 5.023452 TGAACAGCTTCTCTCACCCTTATA 58.977 41.667 0.00 0.00 0.00 0.98
2562 3525 3.181472 CCTTGGCTTTTTGAACAGCTTCT 60.181 43.478 2.34 0.00 36.20 2.85
2726 3689 0.602562 TGGCTAGCATTTGTTGTGCC 59.397 50.000 18.24 0.00 43.50 5.01
2779 3742 4.725790 ATTTTGGCAATGCTAAGGACTC 57.274 40.909 4.82 0.00 29.47 3.36
2796 3759 5.507315 CCAGTTTGGTAGTTGCGAGAATTTT 60.507 40.000 0.00 0.00 31.35 1.82
2848 3811 6.204301 CACAGCATTTCCAGAGGATAACATAG 59.796 42.308 0.00 0.00 0.00 2.23
2985 3948 1.595993 GCCAGTCGCAGGTGTCTAGA 61.596 60.000 0.00 0.00 37.47 2.43
2991 3957 2.185350 CTAGGCCAGTCGCAGGTG 59.815 66.667 5.01 0.00 40.31 4.00
2998 3964 2.990066 AGTTATGCACTAGGCCAGTC 57.010 50.000 5.01 2.22 43.89 3.51
3009 3975 5.373222 ACCACTTGTCAAGTTAGTTATGCA 58.627 37.500 15.73 0.00 40.46 3.96
3028 3994 9.601217 ACTGAATCAGTACTAATTATCAACCAC 57.399 33.333 15.09 0.00 43.46 4.16
3136 4119 7.806690 TCATTCTTGACTTATTTGCTACACAC 58.193 34.615 0.00 0.00 0.00 3.82
3207 4190 3.559238 AATGCATGACCGACTTTTGAC 57.441 42.857 0.00 0.00 0.00 3.18
3322 4307 6.055588 GCAGGCTGTAGTTTCATAATTCCTA 58.944 40.000 17.16 0.00 0.00 2.94
3327 4312 8.469309 AATATTGCAGGCTGTAGTTTCATAAT 57.531 30.769 17.16 1.94 0.00 1.28
3366 4351 8.293867 TGCATTTTGGAGTACATGTTTAACTAC 58.706 33.333 2.30 2.67 0.00 2.73
3388 4373 6.057533 TCCTTCTTCATAAATGACGATGCAT 58.942 36.000 0.00 0.00 35.41 3.96
3477 4462 4.339439 ACAAACAAAAAGCATGCAACAC 57.661 36.364 21.98 0.00 0.00 3.32
3577 4567 0.776810 TGAATCCCTGGACTGCCAAA 59.223 50.000 0.00 0.00 45.41 3.28
3782 4773 9.849607 CATCAAACACATGTTTCGTACTATATC 57.150 33.333 7.03 0.00 45.54 1.63
3783 4774 9.594478 TCATCAAACACATGTTTCGTACTATAT 57.406 29.630 7.03 0.00 45.54 0.86
3784 4775 8.989653 TCATCAAACACATGTTTCGTACTATA 57.010 30.769 7.03 0.00 45.54 1.31
3785 4776 7.899178 TCATCAAACACATGTTTCGTACTAT 57.101 32.000 7.03 0.00 45.54 2.12
3822 4813 3.866910 CACTGCATTGCTGAAACTGTTTT 59.133 39.130 20.66 0.00 0.00 2.43
3841 4832 5.304686 TCCCTTCATGTGTAAACTTCACT 57.695 39.130 0.00 0.00 36.83 3.41
3928 4919 0.323178 CTGGGCTTGCAGAATGAGGT 60.323 55.000 0.00 0.00 39.69 3.85
3936 4927 1.609208 AGTGTTAACTGGGCTTGCAG 58.391 50.000 7.22 0.00 34.48 4.41
4083 5075 2.930040 AGTGTCATAAACATCGAAGCCG 59.070 45.455 0.00 0.00 40.80 5.52
4084 5076 3.063997 CCAGTGTCATAAACATCGAAGCC 59.936 47.826 0.00 0.00 40.80 4.35
4275 5429 3.997021 GGCATCCATATACCTCTTGAACG 59.003 47.826 0.00 0.00 0.00 3.95
4292 5446 4.338964 TGTTGTATGGTCATCATTGGCATC 59.661 41.667 0.00 0.00 37.30 3.91
4374 5528 0.897621 GGCCCAAGGATTCAAACTGG 59.102 55.000 0.00 0.00 0.00 4.00
4578 5738 2.014857 CATTGTCAGGAGCATCACTGG 58.985 52.381 0.00 0.00 35.16 4.00
4640 5801 4.058817 CCGTTTTCAGAAGCAGTTAGACT 58.941 43.478 0.00 0.00 0.00 3.24
4645 5806 0.668535 GCCCGTTTTCAGAAGCAGTT 59.331 50.000 0.00 0.00 0.00 3.16
4653 5826 3.369546 AACATCTTTGCCCGTTTTCAG 57.630 42.857 0.00 0.00 0.00 3.02
4660 5838 0.527565 CCCTGAAACATCTTTGCCCG 59.472 55.000 0.00 0.00 0.00 6.13
4732 5914 0.537188 ACACCCTGGCTGATCTAACG 59.463 55.000 0.00 0.00 0.00 3.18
4788 5971 5.801350 TGCTTTCCTGAATCTTGATTACG 57.199 39.130 0.00 0.00 0.00 3.18
4799 5982 8.093307 TGCAATTTATTTGTATGCTTTCCTGAA 58.907 29.630 0.00 0.00 37.65 3.02
4986 6169 8.535592 GTTCAGAAATCTTACATCTGTATGTCG 58.464 37.037 0.00 0.00 42.92 4.35
5144 6327 0.933097 CCGACGGATTCAAGCATCTG 59.067 55.000 8.64 0.00 35.85 2.90
5267 6450 5.391843 CGATGCAATTGATGTGGAAACAGTA 60.392 40.000 10.34 0.00 44.46 2.74
5296 6479 1.312815 GCTGCTGTGTGAAAGGAAGT 58.687 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.