Multiple sequence alignment - TraesCS6A01G055200

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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 TraesCS6A01G055200 chr6A 100.000 2589 0 0 1 2589 28667584 28664996 0.000000e+00 4782
1 TraesCS6A01G055200 chr6A 89.371 875 52 20 847 1689 28640811 28641676 0.000000e+00 1062
2 TraesCS6A01G055200 chr6A 88.992 754 66 10 1 749 28640013 28640754 0.000000e+00 917
3 TraesCS6A01G055200 chr6A 89.466 712 47 18 815 1505 31264721 31264017 0.000000e+00 874
4 TraesCS6A01G055200 chr6A 85.358 601 47 23 738 1312 28773875 28773290 3.710000e-163 584
5 TraesCS6A01G055200 chrUn 84.524 1512 133 43 801 2250 103670323 103671795 0.000000e+00 1402
6 TraesCS6A01G055200 chrUn 88.148 810 60 23 816 1599 103772377 103771578 0.000000e+00 931
7 TraesCS6A01G055200 chrUn 90.123 81 5 3 1 80 103517245 103517167 4.560000e-18 102
8 TraesCS6A01G055200 chr6B 84.014 1470 120 53 798 2206 55436274 55437689 0.000000e+00 1306
9 TraesCS6A01G055200 chr6B 83.882 1185 109 41 723 1844 55651588 55650423 0.000000e+00 1055
10 TraesCS6A01G055200 chr6B 91.566 581 32 13 815 1387 54663200 54662629 0.000000e+00 785
11 TraesCS6A01G055200 chr6B 84.788 756 58 29 3 722 55652359 55651625 0.000000e+00 706
12 TraesCS6A01G055200 chr6B 89.617 183 11 4 2407 2588 55437727 55437902 2.590000e-55 226
13 TraesCS6A01G055200 chr6B 91.358 81 4 3 1 80 54856514 54856436 9.800000e-20 108
14 TraesCS6A01G055200 chr7A 83.165 790 75 38 817 1560 628524954 628524177 0.000000e+00 669
15 TraesCS6A01G055200 chr7A 86.432 199 24 2 2390 2588 89339118 89338923 5.610000e-52 215
16 TraesCS6A01G055200 chr7A 84.138 145 22 1 2250 2394 727721447 727721304 3.470000e-29 139
17 TraesCS6A01G055200 chr5A 88.519 540 43 15 855 1384 556534528 556533998 1.010000e-178 636
18 TraesCS6A01G055200 chr5A 89.447 199 18 2 2390 2588 559870153 559870348 5.530000e-62 248
19 TraesCS6A01G055200 chr5A 89.313 131 14 0 2262 2392 359737170 359737040 5.730000e-37 165
20 TraesCS6A01G055200 chr5D 87.266 534 55 11 855 1382 436349329 436349855 4.770000e-167 597
21 TraesCS6A01G055200 chr2D 87.699 439 26 12 1823 2250 133477610 133477189 1.080000e-133 486
22 TraesCS6A01G055200 chr2D 84.138 145 20 3 2250 2393 636425020 636425162 1.250000e-28 137
23 TraesCS6A01G055200 chr4D 90.278 144 13 1 2250 2393 98932842 98932984 1.220000e-43 187
24 TraesCS6A01G055200 chr2B 86.207 145 18 2 2250 2394 154722501 154722643 3.450000e-34 156


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 TraesCS6A01G055200 chr6A 28664996 28667584 2588 True 4782.0 4782 100.0000 1 2589 1 chr6A.!!$R1 2588
1 TraesCS6A01G055200 chr6A 28640013 28641676 1663 False 989.5 1062 89.1815 1 1689 2 chr6A.!!$F1 1688
2 TraesCS6A01G055200 chr6A 31264017 31264721 704 True 874.0 874 89.4660 815 1505 1 chr6A.!!$R3 690
3 TraesCS6A01G055200 chr6A 28773290 28773875 585 True 584.0 584 85.3580 738 1312 1 chr6A.!!$R2 574
4 TraesCS6A01G055200 chrUn 103670323 103671795 1472 False 1402.0 1402 84.5240 801 2250 1 chrUn.!!$F1 1449
5 TraesCS6A01G055200 chrUn 103771578 103772377 799 True 931.0 931 88.1480 816 1599 1 chrUn.!!$R2 783
6 TraesCS6A01G055200 chr6B 55650423 55652359 1936 True 880.5 1055 84.3350 3 1844 2 chr6B.!!$R3 1841
7 TraesCS6A01G055200 chr6B 54662629 54663200 571 True 785.0 785 91.5660 815 1387 1 chr6B.!!$R1 572
8 TraesCS6A01G055200 chr6B 55436274 55437902 1628 False 766.0 1306 86.8155 798 2588 2 chr6B.!!$F1 1790
9 TraesCS6A01G055200 chr7A 628524177 628524954 777 True 669.0 669 83.1650 817 1560 1 chr7A.!!$R2 743
10 TraesCS6A01G055200 chr5A 556533998 556534528 530 True 636.0 636 88.5190 855 1384 1 chr5A.!!$R2 529
11 TraesCS6A01G055200 chr5D 436349329 436349855 526 False 597.0 597 87.2660 855 1382 1 chr5D.!!$F1 527

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
787 859 0.321671 GGCTAGAGCTGTCAACACCA 59.678 55.0 0.0 0.0 41.7 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2558 0.172578 GCCGCTCCCCAAATTTGTAC 59.827 55.0 16.73 1.1 0.0 2.9 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
40 41 4.101741 ACGCCTTTCTAATGCTAATCCTCT 59.898 41.667 0.00 0.00 0.00 3.69
76 77 6.509317 AAATTGTTTTAGTGTTGATGTGCG 57.491 33.333 0.00 0.00 0.00 5.34
142 143 7.989416 AACGAACATATTTGGAGAACCTTTA 57.011 32.000 0.00 0.00 37.04 1.85
176 177 1.629043 TCTAACAGAGCAACCGGAGT 58.371 50.000 9.46 0.00 0.00 3.85
205 206 0.464036 TGCATGGTACGAGTGATCCC 59.536 55.000 0.00 0.00 0.00 3.85
207 208 0.744874 CATGGTACGAGTGATCCCGT 59.255 55.000 9.30 9.30 42.15 5.28
215 216 0.813184 GAGTGATCCCGTTCGTACCA 59.187 55.000 0.00 0.00 0.00 3.25
227 228 2.435234 GTACCATGCGGCGTCCAA 60.435 61.111 9.37 0.00 34.57 3.53
309 310 6.091437 CACCTCTACTTACTGACCTAAAACG 58.909 44.000 0.00 0.00 0.00 3.60
356 357 8.903820 GGGAGCAGATATTAGTTTTTGTGTTAT 58.096 33.333 0.00 0.00 0.00 1.89
465 467 7.730084 TGGTCCATATGTTTTGAAATGTTTGA 58.270 30.769 1.24 0.00 0.00 2.69
622 655 2.748461 TCCGAAAGCTTCACAAAACG 57.252 45.000 0.00 0.00 0.00 3.60
623 656 2.281517 TCCGAAAGCTTCACAAAACGA 58.718 42.857 0.00 0.00 0.00 3.85
636 669 8.539674 GCTTCACAAAACGAGTTGAAATAAAAT 58.460 29.630 9.31 0.00 32.59 1.82
638 671 9.796120 TTCACAAAACGAGTTGAAATAAAATCT 57.204 25.926 9.31 0.00 32.59 2.40
687 720 2.286294 GCATCTTTACATGAGCCAGTCG 59.714 50.000 0.00 0.00 0.00 4.18
690 723 3.585862 TCTTTACATGAGCCAGTCGTTC 58.414 45.455 0.00 0.00 0.00 3.95
749 819 1.228657 AACGGGTTCGAAGCTGCTTC 61.229 55.000 30.75 28.07 40.11 3.86
787 859 0.321671 GGCTAGAGCTGTCAACACCA 59.678 55.000 0.00 0.00 41.70 4.17
788 860 1.270839 GGCTAGAGCTGTCAACACCAA 60.271 52.381 0.00 0.00 41.70 3.67
789 861 1.801178 GCTAGAGCTGTCAACACCAAC 59.199 52.381 0.00 0.00 38.21 3.77
790 862 2.417719 CTAGAGCTGTCAACACCAACC 58.582 52.381 0.00 0.00 0.00 3.77
791 863 0.546122 AGAGCTGTCAACACCAACCA 59.454 50.000 0.00 0.00 0.00 3.67
832 904 3.041946 AGTGAGAAAACACACCTCCTCT 58.958 45.455 0.00 0.00 42.45 3.69
1408 1555 2.224159 TCCAGCAGAACCCACCTCC 61.224 63.158 0.00 0.00 0.00 4.30
1435 1598 3.864160 GCCAGATTCACTAGCTAGCCATC 60.864 52.174 20.91 17.44 30.92 3.51
1437 1600 2.560542 AGATTCACTAGCTAGCCATCGG 59.439 50.000 20.91 4.02 0.00 4.18
1439 1602 1.319541 TCACTAGCTAGCCATCGGTC 58.680 55.000 20.91 0.00 0.00 4.79
1440 1603 0.039978 CACTAGCTAGCCATCGGTCG 60.040 60.000 20.91 0.00 0.00 4.79
1443 1606 1.170919 TAGCTAGCCATCGGTCGTCC 61.171 60.000 12.13 0.00 0.00 4.79
1458 1621 1.069513 TCGTCCGTGTTCATGGTCTTT 59.930 47.619 10.35 0.00 0.00 2.52
1507 1680 3.740832 TGCTGTCTGTTGTTTCGATGTAG 59.259 43.478 0.00 0.00 0.00 2.74
1508 1681 3.741344 GCTGTCTGTTGTTTCGATGTAGT 59.259 43.478 0.00 0.00 0.00 2.73
1538 1719 2.787473 TGGAATGGAAATCTCAGCGT 57.213 45.000 0.00 0.00 0.00 5.07
1569 1750 4.380973 CCTGAATTCGTCTGCAGTCTCTTA 60.381 45.833 14.67 0.00 0.00 2.10
1570 1751 4.738124 TGAATTCGTCTGCAGTCTCTTAG 58.262 43.478 14.67 0.00 0.00 2.18
1572 1753 4.792521 ATTCGTCTGCAGTCTCTTAGTT 57.207 40.909 14.67 0.00 0.00 2.24
1576 1775 3.304726 CGTCTGCAGTCTCTTAGTTGTGA 60.305 47.826 14.67 0.00 0.00 3.58
1585 1784 5.525378 AGTCTCTTAGTTGTGAGCTTTGTTG 59.475 40.000 0.00 0.00 0.00 3.33
1604 1811 8.948853 TTTGTTGAATCTTAGCAGTTATTTCG 57.051 30.769 0.00 0.00 0.00 3.46
1610 1817 8.335356 TGAATCTTAGCAGTTATTTCGTATTGC 58.665 33.333 0.00 0.00 0.00 3.56
1616 1823 4.094294 GCAGTTATTTCGTATTGCCTGTCA 59.906 41.667 0.00 0.00 0.00 3.58
1642 1853 4.932911 AATTTTCTGCCCCAAATCCATT 57.067 36.364 0.00 0.00 0.00 3.16
1670 1881 1.225855 GTCGGTGTGCTGTTGATTCA 58.774 50.000 0.00 0.00 0.00 2.57
1689 1900 6.889177 TGATTCAAACCATACCTGCATTTCTA 59.111 34.615 0.00 0.00 0.00 2.10
1691 1902 6.942532 TCAAACCATACCTGCATTTCTATC 57.057 37.500 0.00 0.00 0.00 2.08
1697 1908 3.205784 ACCTGCATTTCTATCTCAGCC 57.794 47.619 0.00 0.00 0.00 4.85
1733 1953 2.766313 TGAACCGATTCACAACTCAGG 58.234 47.619 0.00 0.00 40.01 3.86
1739 1959 3.338249 CGATTCACAACTCAGGTGGAAT 58.662 45.455 6.22 6.22 36.90 3.01
1742 1962 5.617751 CGATTCACAACTCAGGTGGAATTTC 60.618 44.000 7.58 0.00 36.90 2.17
1767 1995 2.260844 ATCCCATGGCTGTTATCACG 57.739 50.000 6.09 0.00 0.00 4.35
1768 1996 0.908910 TCCCATGGCTGTTATCACGT 59.091 50.000 6.09 0.00 0.00 4.49
1769 1997 1.280710 TCCCATGGCTGTTATCACGTT 59.719 47.619 6.09 0.00 0.00 3.99
1787 2015 2.225019 CGTTTTCATCTTGTGCTCTGCT 59.775 45.455 0.00 0.00 0.00 4.24
1794 2022 4.633126 TCATCTTGTGCTCTGCTAATTGAC 59.367 41.667 0.00 0.00 0.00 3.18
1795 2023 4.277515 TCTTGTGCTCTGCTAATTGACT 57.722 40.909 0.00 0.00 0.00 3.41
1809 2037 9.334693 CTGCTAATTGACTCAAGTTTGAAATAC 57.665 33.333 0.00 0.00 36.64 1.89
1813 2041 5.591643 TGACTCAAGTTTGAAATACGAGC 57.408 39.130 0.00 0.00 36.64 5.03
1821 2049 4.083324 AGTTTGAAATACGAGCATGTGGTG 60.083 41.667 0.00 0.00 0.00 4.17
1844 2072 3.769844 CCCTTTTGAGACCTAGCTGTCTA 59.230 47.826 6.69 0.00 45.41 2.59
1845 2073 4.382147 CCCTTTTGAGACCTAGCTGTCTAC 60.382 50.000 6.69 2.73 45.41 2.59
1846 2074 4.464597 CCTTTTGAGACCTAGCTGTCTACT 59.535 45.833 6.69 0.00 45.41 2.57
1847 2075 5.393678 CCTTTTGAGACCTAGCTGTCTACTC 60.394 48.000 6.69 5.09 45.41 2.59
1848 2076 4.577988 TTGAGACCTAGCTGTCTACTCT 57.422 45.455 6.69 0.00 45.41 3.24
1901 2129 4.571919 CAATTGAACAAGTGCATGGGAAT 58.428 39.130 0.00 0.00 29.47 3.01
1904 2132 2.557924 TGAACAAGTGCATGGGAATCAC 59.442 45.455 0.00 0.00 0.00 3.06
1909 2137 1.567649 AGTGCATGGGAATCACCTGAT 59.432 47.619 0.00 0.00 38.98 2.90
1910 2138 2.024655 AGTGCATGGGAATCACCTGATT 60.025 45.455 0.00 0.00 46.54 2.57
1946 2181 5.741040 GCTAGTTTTTGAACATAGATGCTGC 59.259 40.000 0.00 0.00 0.00 5.25
1964 2199 3.454375 CTGCCCATCTGATGCATTTTTC 58.546 45.455 12.17 0.00 33.97 2.29
1965 2200 2.832733 TGCCCATCTGATGCATTTTTCA 59.167 40.909 12.17 0.00 0.00 2.69
1966 2201 3.261137 TGCCCATCTGATGCATTTTTCAA 59.739 39.130 12.17 0.00 0.00 2.69
1967 2202 4.080807 TGCCCATCTGATGCATTTTTCAAT 60.081 37.500 12.17 0.00 0.00 2.57
1968 2203 4.879545 GCCCATCTGATGCATTTTTCAATT 59.120 37.500 12.17 0.00 0.00 2.32
1969 2204 5.220777 GCCCATCTGATGCATTTTTCAATTG 60.221 40.000 12.17 0.00 0.00 2.32
1970 2205 5.878116 CCCATCTGATGCATTTTTCAATTGT 59.122 36.000 12.17 0.00 0.00 2.71
1971 2206 6.183360 CCCATCTGATGCATTTTTCAATTGTG 60.183 38.462 12.17 0.00 0.00 3.33
1972 2207 6.592220 CCATCTGATGCATTTTTCAATTGTGA 59.408 34.615 12.17 0.00 0.00 3.58
1974 2209 8.664798 CATCTGATGCATTTTTCAATTGTGAAT 58.335 29.630 0.00 0.00 43.29 2.57
2029 2269 3.118112 AGCATGGATTTCTGACTACCTGG 60.118 47.826 0.00 0.00 0.00 4.45
2034 2274 1.550130 TTTCTGACTACCTGGCCCGG 61.550 60.000 12.40 12.40 0.00 5.73
2035 2275 2.683933 CTGACTACCTGGCCCGGT 60.684 66.667 23.51 23.51 41.10 5.28
2042 2283 0.537828 TACCTGGCCCGGTTTTTGAC 60.538 55.000 25.17 0.00 38.49 3.18
2111 2353 1.821216 TGGAAAAGATGAACCGGAGC 58.179 50.000 9.46 0.00 0.00 4.70
2131 2373 0.673022 GGAGCTCAAGGTGCAGACAG 60.673 60.000 17.19 0.00 33.94 3.51
2167 2409 3.064820 AGTGTGCTTGGTTTACAGTTTCG 59.935 43.478 0.00 0.00 0.00 3.46
2245 2496 4.670896 TGATCAAAGGAGCACGATGATA 57.329 40.909 0.00 0.00 33.81 2.15
2250 2501 8.193438 TGATCAAAGGAGCACGATGATATATAG 58.807 37.037 0.00 0.00 33.81 1.31
2251 2502 6.867550 TCAAAGGAGCACGATGATATATAGG 58.132 40.000 0.00 0.00 0.00 2.57
2253 2504 4.541705 AGGAGCACGATGATATATAGGCT 58.458 43.478 0.00 0.00 0.00 4.58
2254 2505 4.582656 AGGAGCACGATGATATATAGGCTC 59.417 45.833 0.00 0.00 44.22 4.70
2256 2507 3.316588 AGCACGATGATATATAGGCTCCG 59.683 47.826 0.00 0.00 0.00 4.63
2257 2508 3.066900 GCACGATGATATATAGGCTCCGT 59.933 47.826 0.00 0.00 0.00 4.69
2258 2509 4.440250 GCACGATGATATATAGGCTCCGTT 60.440 45.833 0.00 0.00 0.00 4.44
2259 2510 5.274718 CACGATGATATATAGGCTCCGTTC 58.725 45.833 0.00 0.00 0.00 3.95
2261 2512 4.554919 CGATGATATATAGGCTCCGTTCGG 60.555 50.000 4.74 4.74 0.00 4.30
2262 2513 3.959293 TGATATATAGGCTCCGTTCGGA 58.041 45.455 13.34 13.34 0.00 4.55
2263 2514 4.338012 TGATATATAGGCTCCGTTCGGAA 58.662 43.478 14.79 0.81 33.41 4.30
2264 2515 4.954202 TGATATATAGGCTCCGTTCGGAAT 59.046 41.667 14.79 8.13 33.41 3.01
2265 2516 3.870633 ATATAGGCTCCGTTCGGAATC 57.129 47.619 14.79 9.70 33.41 2.52
2266 2517 0.680061 ATAGGCTCCGTTCGGAATCC 59.320 55.000 14.79 16.73 33.41 3.01
2267 2518 1.397390 TAGGCTCCGTTCGGAATCCC 61.397 60.000 20.48 17.10 33.41 3.85
2268 2519 2.732619 GGCTCCGTTCGGAATCCCT 61.733 63.158 14.79 0.00 33.41 4.20
2269 2520 1.227292 GCTCCGTTCGGAATCCCTC 60.227 63.158 14.79 0.00 33.41 4.30
2270 2521 1.442148 CTCCGTTCGGAATCCCTCC 59.558 63.158 14.79 0.00 41.40 4.30
2277 2528 3.155167 GGAATCCCTCCGCTCCGT 61.155 66.667 0.00 0.00 33.37 4.69
2278 2529 2.107141 GAATCCCTCCGCTCCGTG 59.893 66.667 0.00 0.00 0.00 4.94
2279 2530 2.363795 AATCCCTCCGCTCCGTGA 60.364 61.111 0.00 0.00 0.00 4.35
2280 2531 2.630592 GAATCCCTCCGCTCCGTGAC 62.631 65.000 0.00 0.00 0.00 3.67
2281 2532 3.663815 ATCCCTCCGCTCCGTGACT 62.664 63.158 0.00 0.00 0.00 3.41
2282 2533 3.827898 CCCTCCGCTCCGTGACTC 61.828 72.222 0.00 0.00 0.00 3.36
2283 2534 3.827898 CCTCCGCTCCGTGACTCC 61.828 72.222 0.00 0.00 0.00 3.85
2284 2535 2.752238 CTCCGCTCCGTGACTCCT 60.752 66.667 0.00 0.00 0.00 3.69
2285 2536 2.750637 TCCGCTCCGTGACTCCTC 60.751 66.667 0.00 0.00 0.00 3.71
2286 2537 2.752238 CCGCTCCGTGACTCCTCT 60.752 66.667 0.00 0.00 0.00 3.69
2287 2538 2.487428 CGCTCCGTGACTCCTCTG 59.513 66.667 0.00 0.00 0.00 3.35
2288 2539 2.183046 GCTCCGTGACTCCTCTGC 59.817 66.667 0.00 0.00 0.00 4.26
2289 2540 2.487428 CTCCGTGACTCCTCTGCG 59.513 66.667 0.00 0.00 0.00 5.18
2290 2541 3.057547 CTCCGTGACTCCTCTGCGG 62.058 68.421 0.00 0.00 43.32 5.69
2291 2542 3.062466 CCGTGACTCCTCTGCGGA 61.062 66.667 0.00 0.00 44.57 5.54
2305 2556 4.427394 CGGAGCTGAGTGGCATAC 57.573 61.111 0.00 0.00 34.17 2.39
2306 2557 1.517361 CGGAGCTGAGTGGCATACA 59.483 57.895 0.00 0.00 34.17 2.29
2307 2558 0.529337 CGGAGCTGAGTGGCATACAG 60.529 60.000 15.92 15.92 35.14 2.74
2308 2559 0.539051 GGAGCTGAGTGGCATACAGT 59.461 55.000 19.39 10.32 34.60 3.55
2309 2560 1.757118 GGAGCTGAGTGGCATACAGTA 59.243 52.381 19.39 0.00 34.60 2.74
2310 2561 2.482142 GGAGCTGAGTGGCATACAGTAC 60.482 54.545 19.39 14.65 34.60 2.73
2311 2562 2.166459 GAGCTGAGTGGCATACAGTACA 59.834 50.000 19.39 2.01 34.60 2.90
2312 2563 2.567169 AGCTGAGTGGCATACAGTACAA 59.433 45.455 19.39 0.00 34.60 2.41
2313 2564 3.007940 AGCTGAGTGGCATACAGTACAAA 59.992 43.478 19.39 0.00 34.60 2.83
2314 2565 3.941483 GCTGAGTGGCATACAGTACAAAT 59.059 43.478 19.39 0.00 34.60 2.32
2315 2566 4.396166 GCTGAGTGGCATACAGTACAAATT 59.604 41.667 19.39 0.00 34.60 1.82
2316 2567 5.106157 GCTGAGTGGCATACAGTACAAATTT 60.106 40.000 19.39 0.00 34.60 1.82
2317 2568 6.252967 TGAGTGGCATACAGTACAAATTTG 57.747 37.500 16.67 16.67 31.34 2.32
2318 2569 5.182950 TGAGTGGCATACAGTACAAATTTGG 59.817 40.000 21.74 6.85 31.34 3.28
2319 2570 4.462483 AGTGGCATACAGTACAAATTTGGG 59.538 41.667 21.74 10.67 0.00 4.12
2320 2571 3.766591 TGGCATACAGTACAAATTTGGGG 59.233 43.478 21.74 10.35 0.00 4.96
2321 2572 4.020543 GGCATACAGTACAAATTTGGGGA 58.979 43.478 21.74 6.03 0.00 4.81
2322 2573 4.097892 GGCATACAGTACAAATTTGGGGAG 59.902 45.833 21.74 11.30 0.00 4.30
2323 2574 4.440112 GCATACAGTACAAATTTGGGGAGC 60.440 45.833 21.74 10.52 0.00 4.70
2324 2575 2.159382 ACAGTACAAATTTGGGGAGCG 58.841 47.619 21.74 7.84 0.00 5.03
2325 2576 1.472480 CAGTACAAATTTGGGGAGCGG 59.528 52.381 21.74 4.74 0.00 5.52
2326 2577 0.172578 GTACAAATTTGGGGAGCGGC 59.827 55.000 21.74 0.00 0.00 6.53
2327 2578 0.968393 TACAAATTTGGGGAGCGGCC 60.968 55.000 21.74 0.00 0.00 6.13
2328 2579 2.119391 AAATTTGGGGAGCGGCCA 59.881 55.556 2.24 0.00 38.95 5.36
2329 2580 1.535202 AAATTTGGGGAGCGGCCAA 60.535 52.632 2.24 0.00 38.95 4.52
2330 2581 1.826340 AAATTTGGGGAGCGGCCAAC 61.826 55.000 2.24 0.00 38.95 3.77
2331 2582 3.521765 ATTTGGGGAGCGGCCAACA 62.522 57.895 2.24 0.00 38.95 3.33
2332 2583 4.659172 TTGGGGAGCGGCCAACAG 62.659 66.667 2.24 0.00 38.95 3.16
2335 2586 3.712907 GGGAGCGGCCAACAGGTA 61.713 66.667 2.24 0.00 38.95 3.08
2336 2587 2.125106 GGAGCGGCCAACAGGTAG 60.125 66.667 2.24 0.00 36.34 3.18
2337 2588 2.820037 GAGCGGCCAACAGGTAGC 60.820 66.667 2.24 0.00 0.00 3.58
2338 2589 3.316573 GAGCGGCCAACAGGTAGCT 62.317 63.158 2.24 0.00 39.01 3.32
2339 2590 2.820037 GCGGCCAACAGGTAGCTC 60.820 66.667 2.24 0.00 0.00 4.09
2340 2591 2.125106 CGGCCAACAGGTAGCTCC 60.125 66.667 2.24 0.00 0.00 4.70
2341 2592 2.125106 GGCCAACAGGTAGCTCCG 60.125 66.667 0.00 0.00 41.99 4.63
2342 2593 2.820037 GCCAACAGGTAGCTCCGC 60.820 66.667 0.00 0.00 41.99 5.54
2343 2594 2.662596 CCAACAGGTAGCTCCGCA 59.337 61.111 0.00 0.00 41.99 5.69
2344 2595 1.221840 CCAACAGGTAGCTCCGCAT 59.778 57.895 0.00 0.00 41.99 4.73
2345 2596 1.091771 CCAACAGGTAGCTCCGCATG 61.092 60.000 0.00 0.00 41.99 4.06
2346 2597 1.450312 AACAGGTAGCTCCGCATGC 60.450 57.895 7.91 7.91 41.99 4.06
2347 2598 1.903877 AACAGGTAGCTCCGCATGCT 61.904 55.000 17.13 0.00 43.79 3.79
2348 2599 1.593750 CAGGTAGCTCCGCATGCTC 60.594 63.158 17.13 2.09 41.46 4.26
2349 2600 2.280457 GGTAGCTCCGCATGCTCC 60.280 66.667 17.13 0.85 41.46 4.70
2350 2601 2.501128 GTAGCTCCGCATGCTCCA 59.499 61.111 17.13 0.00 41.46 3.86
2351 2602 1.884926 GTAGCTCCGCATGCTCCAC 60.885 63.158 17.13 2.74 41.46 4.02
2352 2603 2.060383 TAGCTCCGCATGCTCCACT 61.060 57.895 17.13 10.45 41.46 4.00
2353 2604 2.021068 TAGCTCCGCATGCTCCACTC 62.021 60.000 17.13 0.00 41.46 3.51
2354 2605 2.202987 CTCCGCATGCTCCACTCC 60.203 66.667 17.13 0.00 0.00 3.85
2355 2606 3.746949 CTCCGCATGCTCCACTCCC 62.747 68.421 17.13 0.00 0.00 4.30
2356 2607 3.790437 CCGCATGCTCCACTCCCT 61.790 66.667 17.13 0.00 0.00 4.20
2357 2608 2.513204 CGCATGCTCCACTCCCTG 60.513 66.667 17.13 0.00 0.00 4.45
2358 2609 2.124403 GCATGCTCCACTCCCTGG 60.124 66.667 11.37 0.00 42.29 4.45
2359 2610 2.976490 GCATGCTCCACTCCCTGGT 61.976 63.158 11.37 0.00 41.52 4.00
2360 2611 1.077930 CATGCTCCACTCCCTGGTG 60.078 63.158 0.00 0.00 41.52 4.17
2361 2612 1.229625 ATGCTCCACTCCCTGGTGA 60.230 57.895 0.00 0.00 41.52 4.02
2362 2613 0.842030 ATGCTCCACTCCCTGGTGAA 60.842 55.000 0.00 0.00 41.52 3.18
2363 2614 1.298014 GCTCCACTCCCTGGTGAAG 59.702 63.158 0.00 0.00 41.52 3.02
2364 2615 1.986413 CTCCACTCCCTGGTGAAGG 59.014 63.158 0.00 0.00 46.94 3.46
2374 2625 4.162690 GGTGAAGGAGCGGGCGAT 62.163 66.667 0.00 0.00 0.00 4.58
2375 2626 2.125106 GTGAAGGAGCGGGCGATT 60.125 61.111 0.00 0.00 0.00 3.34
2376 2627 2.125147 TGAAGGAGCGGGCGATTG 60.125 61.111 0.00 0.00 0.00 2.67
2377 2628 3.577313 GAAGGAGCGGGCGATTGC 61.577 66.667 0.00 0.00 41.71 3.56
2387 2638 2.202349 GCGATTGCCGAACACAGC 60.202 61.111 0.00 0.00 41.76 4.40
2388 2639 2.480555 CGATTGCCGAACACAGCC 59.519 61.111 0.00 0.00 41.76 4.85
2389 2640 2.324330 CGATTGCCGAACACAGCCA 61.324 57.895 0.00 0.00 41.76 4.75
2390 2641 1.647545 CGATTGCCGAACACAGCCAT 61.648 55.000 0.00 0.00 41.76 4.40
2391 2642 1.378531 GATTGCCGAACACAGCCATA 58.621 50.000 0.00 0.00 0.00 2.74
2392 2643 1.742831 GATTGCCGAACACAGCCATAA 59.257 47.619 0.00 0.00 0.00 1.90
2393 2644 1.610363 TTGCCGAACACAGCCATAAA 58.390 45.000 0.00 0.00 0.00 1.40
2394 2645 0.878416 TGCCGAACACAGCCATAAAC 59.122 50.000 0.00 0.00 0.00 2.01
2395 2646 0.878416 GCCGAACACAGCCATAAACA 59.122 50.000 0.00 0.00 0.00 2.83
2396 2647 1.135689 GCCGAACACAGCCATAAACAG 60.136 52.381 0.00 0.00 0.00 3.16
2397 2648 1.135689 CCGAACACAGCCATAAACAGC 60.136 52.381 0.00 0.00 0.00 4.40
2398 2649 1.806542 CGAACACAGCCATAAACAGCT 59.193 47.619 0.00 0.00 0.00 4.24
2399 2650 3.000041 CGAACACAGCCATAAACAGCTA 59.000 45.455 0.00 0.00 0.00 3.32
2400 2651 3.062639 CGAACACAGCCATAAACAGCTAG 59.937 47.826 0.00 0.00 0.00 3.42
2401 2652 3.703001 ACACAGCCATAAACAGCTAGT 57.297 42.857 0.00 0.00 0.00 2.57
2402 2653 4.021102 ACACAGCCATAAACAGCTAGTT 57.979 40.909 0.00 0.00 43.89 2.24
2403 2654 3.753272 ACACAGCCATAAACAGCTAGTTG 59.247 43.478 4.86 4.86 41.19 3.16
2404 2655 3.127548 CACAGCCATAAACAGCTAGTTGG 59.872 47.826 11.56 2.83 41.19 3.77
2405 2656 3.009033 ACAGCCATAAACAGCTAGTTGGA 59.991 43.478 11.56 0.00 41.19 3.53
2406 2657 4.009675 CAGCCATAAACAGCTAGTTGGAA 58.990 43.478 11.56 0.00 41.19 3.53
2407 2658 4.010349 AGCCATAAACAGCTAGTTGGAAC 58.990 43.478 11.56 0.00 41.19 3.62
2408 2659 4.010349 GCCATAAACAGCTAGTTGGAACT 58.990 43.478 11.56 0.00 41.19 3.01
2421 2672 4.070716 AGTTGGAACTTGCATCTGAAGAG 58.929 43.478 0.00 0.00 35.21 2.85
2423 2674 1.396301 GGAACTTGCATCTGAAGAGCG 59.604 52.381 0.00 0.00 0.00 5.03
2439 2690 2.567615 AGAGCGGTCTGGAAACTGTATT 59.432 45.455 17.85 0.00 0.00 1.89
2450 2701 6.061022 TGGAAACTGTATTGAGATTAGGCA 57.939 37.500 0.00 0.00 0.00 4.75
2452 2703 7.118723 TGGAAACTGTATTGAGATTAGGCAAT 58.881 34.615 0.00 0.00 38.24 3.56
2455 2706 9.294030 GAAACTGTATTGAGATTAGGCAATTTG 57.706 33.333 0.00 0.00 36.27 2.32
2456 2707 7.944729 ACTGTATTGAGATTAGGCAATTTGT 57.055 32.000 0.00 0.00 36.27 2.83
2513 2764 5.697633 ACATTTTGCAACTCATGGACATTTC 59.302 36.000 0.00 0.00 0.00 2.17
2561 2812 4.769345 TGAGTATCATATTGGCACCACA 57.231 40.909 0.00 0.00 42.56 4.17
2562 2813 4.707105 TGAGTATCATATTGGCACCACAG 58.293 43.478 0.00 0.00 42.56 3.66
2563 2814 4.408596 TGAGTATCATATTGGCACCACAGA 59.591 41.667 0.00 0.00 42.56 3.41
2564 2815 4.965814 AGTATCATATTGGCACCACAGAG 58.034 43.478 0.00 0.00 0.00 3.35
2565 2816 3.939740 ATCATATTGGCACCACAGAGT 57.060 42.857 0.00 0.00 0.00 3.24
2566 2817 3.719268 TCATATTGGCACCACAGAGTT 57.281 42.857 0.00 0.00 0.00 3.01
2569 2820 2.363306 ATTGGCACCACAGAGTTTCA 57.637 45.000 0.00 0.00 0.00 2.69
2570 2821 1.679139 TTGGCACCACAGAGTTTCAG 58.321 50.000 0.00 0.00 0.00 3.02
2571 2822 0.836606 TGGCACCACAGAGTTTCAGA 59.163 50.000 0.00 0.00 0.00 3.27
2572 2823 1.421268 TGGCACCACAGAGTTTCAGAT 59.579 47.619 0.00 0.00 0.00 2.90
2573 2824 2.637382 TGGCACCACAGAGTTTCAGATA 59.363 45.455 0.00 0.00 0.00 1.98
2574 2825 3.072330 TGGCACCACAGAGTTTCAGATAA 59.928 43.478 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 6.689178 ATATTTGTTTTCGCACATCAACAC 57.311 33.333 0.00 0.00 0.00 3.32
205 206 3.908951 CGCCGCATGGTACGAACG 61.909 66.667 0.00 0.00 37.67 3.95
207 208 2.507547 GACGCCGCATGGTACGAA 60.508 61.111 0.00 0.00 37.67 3.85
215 216 3.732892 CGGTTTTGGACGCCGCAT 61.733 61.111 0.00 0.00 38.99 4.73
297 298 9.563898 AACTTTTAGAAAAACGTTTTAGGTCAG 57.436 29.630 25.44 18.06 34.44 3.51
309 310 9.245962 GCTCCCTCTTTAAACTTTTAGAAAAAC 57.754 33.333 0.00 0.00 0.00 2.43
326 327 7.337942 CACAAAAACTAATATCTGCTCCCTCTT 59.662 37.037 0.00 0.00 0.00 2.85
328 329 6.599638 ACACAAAAACTAATATCTGCTCCCTC 59.400 38.462 0.00 0.00 0.00 4.30
439 441 7.871973 TCAAACATTTCAAAACATATGGACCAG 59.128 33.333 7.80 0.00 0.00 4.00
588 621 7.696992 AGCTTTCGGATTTATTTTTCCTGTA 57.303 32.000 0.00 0.00 0.00 2.74
657 690 6.433766 GCTCATGTAAAGATGCTATTCCAAC 58.566 40.000 0.00 0.00 0.00 3.77
661 694 5.762218 ACTGGCTCATGTAAAGATGCTATTC 59.238 40.000 0.00 0.00 0.00 1.75
667 700 3.525537 ACGACTGGCTCATGTAAAGATG 58.474 45.455 0.00 0.00 0.00 2.90
690 723 3.108144 CAGCTTCAAAACAGTTCCGTTG 58.892 45.455 0.00 0.00 0.00 4.10
749 819 1.068921 CGTTGTTTTGGGCCTTGGG 59.931 57.895 4.53 0.00 0.00 4.12
787 859 4.988598 CCCGCAGACGCACTGGTT 62.989 66.667 11.22 0.00 45.82 3.67
1408 1555 1.592669 CTAGTGAATCTGGCGGCGG 60.593 63.158 12.43 12.43 0.00 6.13
1437 1600 0.038526 AGACCATGAACACGGACGAC 60.039 55.000 0.00 0.00 0.00 4.34
1439 1602 1.194547 CAAAGACCATGAACACGGACG 59.805 52.381 0.00 0.00 0.00 4.79
1440 1603 2.218603 ACAAAGACCATGAACACGGAC 58.781 47.619 0.00 0.00 0.00 4.79
1443 1606 3.691049 ACAACAAAGACCATGAACACG 57.309 42.857 0.00 0.00 0.00 4.49
1458 1621 1.579084 GCGGCCGTTCCATTACAACA 61.579 55.000 28.70 0.00 34.01 3.33
1507 1680 7.445945 AGATTTCCATTCCATGCTAGTAGTAC 58.554 38.462 0.00 0.00 0.00 2.73
1508 1681 7.290014 TGAGATTTCCATTCCATGCTAGTAGTA 59.710 37.037 0.00 0.00 0.00 1.82
1538 1719 3.504520 GCAGACGAATTCAGGGGTAAAAA 59.495 43.478 6.22 0.00 0.00 1.94
1569 1750 5.841957 AAGATTCAACAAAGCTCACAACT 57.158 34.783 0.00 0.00 30.69 3.16
1570 1751 5.626955 GCTAAGATTCAACAAAGCTCACAAC 59.373 40.000 0.00 0.00 30.69 3.32
1572 1753 4.821260 TGCTAAGATTCAACAAAGCTCACA 59.179 37.500 0.00 0.00 30.69 3.58
1576 1775 7.693969 ATAACTGCTAAGATTCAACAAAGCT 57.306 32.000 0.00 0.00 34.29 3.74
1585 1784 7.798982 GGCAATACGAAATAACTGCTAAGATTC 59.201 37.037 0.00 0.00 0.00 2.52
1604 1811 7.023575 CAGAAAATTACAGTGACAGGCAATAC 58.976 38.462 0.00 0.00 0.00 1.89
1610 1817 3.191371 GGGCAGAAAATTACAGTGACAGG 59.809 47.826 0.00 0.00 0.00 4.00
1616 1823 4.222810 GGATTTGGGGCAGAAAATTACAGT 59.777 41.667 0.00 0.00 0.00 3.55
1642 1853 2.109739 GCACACCGACACCAACACA 61.110 57.895 0.00 0.00 0.00 3.72
1670 1881 6.662755 TGAGATAGAAATGCAGGTATGGTTT 58.337 36.000 0.00 0.00 0.00 3.27
1689 1900 3.786635 GTGAGTATTTCACGGCTGAGAT 58.213 45.455 0.00 0.00 46.13 2.75
1697 1908 9.503914 GAATCGGTTCATGGTGAGTATTTCACG 62.504 44.444 2.82 0.00 43.83 4.35
1716 1936 1.270839 CCACCTGAGTTGTGAATCGGT 60.271 52.381 0.00 0.00 35.74 4.69
1725 1945 2.171003 GGGGAAATTCCACCTGAGTTG 58.829 52.381 14.68 0.00 38.64 3.16
1733 1953 1.273552 TGGGATTGGGGGAAATTCCAC 60.274 52.381 14.68 10.47 39.82 4.02
1739 1959 1.002792 GCCATGGGATTGGGGGAAA 59.997 57.895 15.13 0.00 37.24 3.13
1742 1962 2.123164 CAGCCATGGGATTGGGGG 60.123 66.667 15.13 0.00 37.24 5.40
1767 1995 3.911661 AGCAGAGCACAAGATGAAAAC 57.088 42.857 0.00 0.00 0.00 2.43
1768 1996 6.207221 TCAATTAGCAGAGCACAAGATGAAAA 59.793 34.615 0.00 0.00 0.00 2.29
1769 1997 5.706833 TCAATTAGCAGAGCACAAGATGAAA 59.293 36.000 0.00 0.00 0.00 2.69
1787 2015 8.227791 GCTCGTATTTCAAACTTGAGTCAATTA 58.772 33.333 5.91 0.00 38.61 1.40
1794 2022 5.791974 CACATGCTCGTATTTCAAACTTGAG 59.208 40.000 0.00 0.00 38.61 3.02
1795 2023 5.334802 CCACATGCTCGTATTTCAAACTTGA 60.335 40.000 0.00 0.00 34.92 3.02
1821 2049 1.003696 ACAGCTAGGTCTCAAAAGGGC 59.996 52.381 0.00 0.00 0.00 5.19
1868 2096 1.532437 TGTTCAATTGCAGAGCACTCG 59.468 47.619 0.00 0.00 38.71 4.18
1946 2181 5.878116 ACAATTGAAAAATGCATCAGATGGG 59.122 36.000 13.59 0.00 0.00 4.00
1964 2199 7.092079 TGCCTCTTATCACAAATTCACAATTG 58.908 34.615 3.24 3.24 0.00 2.32
1965 2200 7.230849 TGCCTCTTATCACAAATTCACAATT 57.769 32.000 0.00 0.00 0.00 2.32
1966 2201 6.839124 TGCCTCTTATCACAAATTCACAAT 57.161 33.333 0.00 0.00 0.00 2.71
1967 2202 6.660521 AGATGCCTCTTATCACAAATTCACAA 59.339 34.615 0.00 0.00 0.00 3.33
1968 2203 6.094464 CAGATGCCTCTTATCACAAATTCACA 59.906 38.462 0.00 0.00 0.00 3.58
1969 2204 6.317140 TCAGATGCCTCTTATCACAAATTCAC 59.683 38.462 0.00 0.00 0.00 3.18
1970 2205 6.417258 TCAGATGCCTCTTATCACAAATTCA 58.583 36.000 0.00 0.00 0.00 2.57
1971 2206 6.932356 TCAGATGCCTCTTATCACAAATTC 57.068 37.500 0.00 0.00 0.00 2.17
1972 2207 7.893124 AATCAGATGCCTCTTATCACAAATT 57.107 32.000 0.00 0.00 0.00 1.82
1974 2209 7.114754 AGAAATCAGATGCCTCTTATCACAAA 58.885 34.615 0.00 0.00 0.00 2.83
2034 2274 4.584327 ACTGCTAACCATGGTCAAAAAC 57.416 40.909 20.07 5.63 0.00 2.43
2035 2275 4.646945 TCAACTGCTAACCATGGTCAAAAA 59.353 37.500 20.07 2.41 0.00 1.94
2042 2283 5.649782 AAGAAATCAACTGCTAACCATGG 57.350 39.130 11.19 11.19 0.00 3.66
2047 2289 4.919754 CAGCCAAAGAAATCAACTGCTAAC 59.080 41.667 0.00 0.00 0.00 2.34
2111 2353 1.739562 GTCTGCACCTTGAGCTCCG 60.740 63.158 12.15 1.89 0.00 4.63
2131 2373 2.093447 AGCACACTAACCATGAGCCTAC 60.093 50.000 0.00 0.00 34.59 3.18
2245 2496 2.496470 GGATTCCGAACGGAGCCTATAT 59.504 50.000 21.27 11.11 46.06 0.86
2250 2501 2.203029 GGGATTCCGAACGGAGCC 60.203 66.667 20.76 20.76 46.06 4.70
2251 2502 1.227292 GAGGGATTCCGAACGGAGC 60.227 63.158 15.34 11.67 46.06 4.70
2253 2504 3.625099 GGAGGGATTCCGAACGGA 58.375 61.111 12.04 12.04 43.52 4.69
2261 2512 2.107141 CACGGAGCGGAGGGATTC 59.893 66.667 0.00 0.00 0.00 2.52
2262 2513 2.363795 TCACGGAGCGGAGGGATT 60.364 61.111 0.00 0.00 0.00 3.01
2263 2514 3.148279 GTCACGGAGCGGAGGGAT 61.148 66.667 0.00 0.00 0.00 3.85
2264 2515 4.361971 AGTCACGGAGCGGAGGGA 62.362 66.667 0.00 0.00 0.00 4.20
2265 2516 3.827898 GAGTCACGGAGCGGAGGG 61.828 72.222 0.00 0.00 0.00 4.30
2266 2517 3.827898 GGAGTCACGGAGCGGAGG 61.828 72.222 0.00 0.00 0.00 4.30
2267 2518 2.752238 AGGAGTCACGGAGCGGAG 60.752 66.667 0.00 0.00 0.00 4.63
2268 2519 2.750637 GAGGAGTCACGGAGCGGA 60.751 66.667 0.00 0.00 0.00 5.54
2269 2520 2.752238 AGAGGAGTCACGGAGCGG 60.752 66.667 0.00 0.00 0.00 5.52
2270 2521 2.487428 CAGAGGAGTCACGGAGCG 59.513 66.667 0.00 0.00 0.00 5.03
2271 2522 2.183046 GCAGAGGAGTCACGGAGC 59.817 66.667 0.00 0.00 0.00 4.70
2272 2523 2.487428 CGCAGAGGAGTCACGGAG 59.513 66.667 0.00 0.00 0.00 4.63
2273 2524 3.062466 CCGCAGAGGAGTCACGGA 61.062 66.667 0.00 0.00 43.79 4.69
2274 2525 3.062466 TCCGCAGAGGAGTCACGG 61.062 66.667 0.00 0.00 45.98 4.94
2281 2532 2.036414 ACTCAGCTCCGCAGAGGA 59.964 61.111 11.94 0.00 44.58 3.71
2282 2533 2.183811 CACTCAGCTCCGCAGAGG 59.816 66.667 11.94 0.00 44.58 3.69
2283 2534 2.183811 CCACTCAGCTCCGCAGAG 59.816 66.667 6.70 6.70 45.53 3.35
2284 2535 4.074526 GCCACTCAGCTCCGCAGA 62.075 66.667 0.00 0.00 0.00 4.26
2285 2536 2.302199 TATGCCACTCAGCTCCGCAG 62.302 60.000 0.00 0.00 32.06 5.18
2286 2537 2.358372 TATGCCACTCAGCTCCGCA 61.358 57.895 0.00 0.00 0.00 5.69
2287 2538 1.884926 GTATGCCACTCAGCTCCGC 60.885 63.158 0.00 0.00 0.00 5.54
2288 2539 0.529337 CTGTATGCCACTCAGCTCCG 60.529 60.000 0.00 0.00 0.00 4.63
2289 2540 0.539051 ACTGTATGCCACTCAGCTCC 59.461 55.000 0.00 0.00 33.12 4.70
2290 2541 2.166459 TGTACTGTATGCCACTCAGCTC 59.834 50.000 0.00 0.00 33.12 4.09
2291 2542 2.179427 TGTACTGTATGCCACTCAGCT 58.821 47.619 0.00 0.00 33.12 4.24
2292 2543 2.672961 TGTACTGTATGCCACTCAGC 57.327 50.000 0.00 0.00 33.12 4.26
2293 2544 6.317088 CAAATTTGTACTGTATGCCACTCAG 58.683 40.000 10.15 0.00 35.60 3.35
2294 2545 5.182950 CCAAATTTGTACTGTATGCCACTCA 59.817 40.000 16.73 0.00 0.00 3.41
2295 2546 5.393027 CCCAAATTTGTACTGTATGCCACTC 60.393 44.000 16.73 0.00 0.00 3.51
2296 2547 4.462483 CCCAAATTTGTACTGTATGCCACT 59.538 41.667 16.73 0.00 0.00 4.00
2297 2548 4.381505 CCCCAAATTTGTACTGTATGCCAC 60.382 45.833 16.73 0.00 0.00 5.01
2298 2549 3.766591 CCCCAAATTTGTACTGTATGCCA 59.233 43.478 16.73 0.00 0.00 4.92
2299 2550 4.020543 TCCCCAAATTTGTACTGTATGCC 58.979 43.478 16.73 0.00 0.00 4.40
2300 2551 4.440112 GCTCCCCAAATTTGTACTGTATGC 60.440 45.833 16.73 6.49 0.00 3.14
2301 2552 4.201910 CGCTCCCCAAATTTGTACTGTATG 60.202 45.833 16.73 0.00 0.00 2.39
2302 2553 3.945285 CGCTCCCCAAATTTGTACTGTAT 59.055 43.478 16.73 0.00 0.00 2.29
2303 2554 3.340034 CGCTCCCCAAATTTGTACTGTA 58.660 45.455 16.73 0.00 0.00 2.74
2304 2555 2.159382 CGCTCCCCAAATTTGTACTGT 58.841 47.619 16.73 0.00 0.00 3.55
2305 2556 1.472480 CCGCTCCCCAAATTTGTACTG 59.528 52.381 16.73 5.91 0.00 2.74
2306 2557 1.834188 CCGCTCCCCAAATTTGTACT 58.166 50.000 16.73 0.00 0.00 2.73
2307 2558 0.172578 GCCGCTCCCCAAATTTGTAC 59.827 55.000 16.73 1.10 0.00 2.90
2308 2559 0.968393 GGCCGCTCCCCAAATTTGTA 60.968 55.000 16.73 1.71 0.00 2.41
2309 2560 2.282783 GGCCGCTCCCCAAATTTGT 61.283 57.895 16.73 0.00 0.00 2.83
2310 2561 1.825281 TTGGCCGCTCCCCAAATTTG 61.825 55.000 11.40 11.40 39.29 2.32
2311 2562 1.535202 TTGGCCGCTCCCCAAATTT 60.535 52.632 0.00 0.00 39.29 1.82
2312 2563 2.119391 TTGGCCGCTCCCCAAATT 59.881 55.556 0.00 0.00 39.29 1.82
2313 2564 2.679996 GTTGGCCGCTCCCCAAAT 60.680 61.111 0.00 0.00 43.46 2.32
2314 2565 4.211330 TGTTGGCCGCTCCCCAAA 62.211 61.111 0.00 0.00 43.46 3.28
2315 2566 4.659172 CTGTTGGCCGCTCCCCAA 62.659 66.667 0.00 0.00 39.91 4.12
2318 2569 3.682292 CTACCTGTTGGCCGCTCCC 62.682 68.421 0.00 0.00 36.63 4.30
2319 2570 2.125106 CTACCTGTTGGCCGCTCC 60.125 66.667 0.00 0.00 36.63 4.70
2320 2571 2.820037 GCTACCTGTTGGCCGCTC 60.820 66.667 0.00 0.00 36.63 5.03
2321 2572 3.316573 GAGCTACCTGTTGGCCGCT 62.317 63.158 0.00 0.00 42.39 5.52
2322 2573 2.820037 GAGCTACCTGTTGGCCGC 60.820 66.667 0.00 0.00 36.63 6.53
2323 2574 2.125106 GGAGCTACCTGTTGGCCG 60.125 66.667 0.00 0.00 36.63 6.13
2324 2575 2.125106 CGGAGCTACCTGTTGGCC 60.125 66.667 0.00 0.00 36.63 5.36
2337 2588 2.202987 GGAGTGGAGCATGCGGAG 60.203 66.667 13.01 0.00 0.00 4.63
2338 2589 3.785859 GGGAGTGGAGCATGCGGA 61.786 66.667 13.01 0.00 0.00 5.54
2339 2590 3.790437 AGGGAGTGGAGCATGCGG 61.790 66.667 13.01 0.00 0.00 5.69
2340 2591 2.513204 CAGGGAGTGGAGCATGCG 60.513 66.667 13.01 0.00 0.00 4.73
2352 2603 3.003173 CCGCTCCTTCACCAGGGA 61.003 66.667 0.00 0.00 44.12 4.20
2353 2604 4.101448 CCCGCTCCTTCACCAGGG 62.101 72.222 0.00 0.00 44.12 4.45
2354 2605 4.785453 GCCCGCTCCTTCACCAGG 62.785 72.222 0.00 0.00 45.64 4.45
2357 2608 3.682292 AATCGCCCGCTCCTTCACC 62.682 63.158 0.00 0.00 0.00 4.02
2358 2609 2.125106 AATCGCCCGCTCCTTCAC 60.125 61.111 0.00 0.00 0.00 3.18
2359 2610 2.125147 CAATCGCCCGCTCCTTCA 60.125 61.111 0.00 0.00 0.00 3.02
2360 2611 3.577313 GCAATCGCCCGCTCCTTC 61.577 66.667 0.00 0.00 0.00 3.46
2370 2621 2.202349 GCTGTGTTCGGCAATCGC 60.202 61.111 0.00 0.00 44.61 4.58
2371 2622 1.647545 ATGGCTGTGTTCGGCAATCG 61.648 55.000 1.58 0.00 46.81 3.34
2372 2623 1.378531 TATGGCTGTGTTCGGCAATC 58.621 50.000 1.58 0.00 46.81 2.67
2373 2624 1.832883 TTATGGCTGTGTTCGGCAAT 58.167 45.000 1.58 0.00 46.81 3.56
2374 2625 1.268352 GTTTATGGCTGTGTTCGGCAA 59.732 47.619 1.58 0.00 46.81 4.52
2375 2626 0.878416 GTTTATGGCTGTGTTCGGCA 59.122 50.000 1.58 0.00 46.81 5.69
2376 2627 0.878416 TGTTTATGGCTGTGTTCGGC 59.122 50.000 0.00 0.00 44.51 5.54
2377 2628 1.135689 GCTGTTTATGGCTGTGTTCGG 60.136 52.381 0.00 0.00 0.00 4.30
2378 2629 1.806542 AGCTGTTTATGGCTGTGTTCG 59.193 47.619 0.00 0.00 37.41 3.95
2379 2630 4.003648 ACTAGCTGTTTATGGCTGTGTTC 58.996 43.478 0.00 0.00 39.31 3.18
2380 2631 4.021102 ACTAGCTGTTTATGGCTGTGTT 57.979 40.909 0.00 0.00 39.31 3.32
2381 2632 3.703001 ACTAGCTGTTTATGGCTGTGT 57.297 42.857 0.00 0.00 39.31 3.72
2382 2633 3.127548 CCAACTAGCTGTTTATGGCTGTG 59.872 47.826 0.00 0.00 39.31 3.66
2383 2634 3.009033 TCCAACTAGCTGTTTATGGCTGT 59.991 43.478 0.00 0.00 39.31 4.40
2384 2635 3.609853 TCCAACTAGCTGTTTATGGCTG 58.390 45.455 0.00 0.00 39.31 4.85
2385 2636 4.010349 GTTCCAACTAGCTGTTTATGGCT 58.990 43.478 0.00 0.00 41.92 4.75
2386 2637 4.010349 AGTTCCAACTAGCTGTTTATGGC 58.990 43.478 0.00 0.00 37.52 4.40
2387 2638 5.619981 GCAAGTTCCAACTAGCTGTTTATGG 60.620 44.000 0.00 0.00 38.57 2.74
2388 2639 5.048782 TGCAAGTTCCAACTAGCTGTTTATG 60.049 40.000 0.00 0.00 38.57 1.90
2389 2640 5.070001 TGCAAGTTCCAACTAGCTGTTTAT 58.930 37.500 0.00 0.00 38.57 1.40
2390 2641 4.456535 TGCAAGTTCCAACTAGCTGTTTA 58.543 39.130 0.00 0.00 38.57 2.01
2391 2642 3.287222 TGCAAGTTCCAACTAGCTGTTT 58.713 40.909 0.00 0.00 38.57 2.83
2392 2643 2.930950 TGCAAGTTCCAACTAGCTGTT 58.069 42.857 0.00 0.00 38.57 3.16
2393 2644 2.638480 TGCAAGTTCCAACTAGCTGT 57.362 45.000 0.00 0.00 38.57 4.40
2394 2645 3.126514 CAGATGCAAGTTCCAACTAGCTG 59.873 47.826 0.00 0.00 38.57 4.24
2395 2646 3.008375 TCAGATGCAAGTTCCAACTAGCT 59.992 43.478 0.00 0.00 38.57 3.32
2396 2647 3.338249 TCAGATGCAAGTTCCAACTAGC 58.662 45.455 0.00 0.00 38.57 3.42
2397 2648 5.240891 TCTTCAGATGCAAGTTCCAACTAG 58.759 41.667 0.00 0.00 38.57 2.57
2398 2649 5.227569 TCTTCAGATGCAAGTTCCAACTA 57.772 39.130 0.00 0.00 38.57 2.24
2399 2650 4.070716 CTCTTCAGATGCAAGTTCCAACT 58.929 43.478 0.00 0.00 42.04 3.16
2400 2651 3.365767 GCTCTTCAGATGCAAGTTCCAAC 60.366 47.826 0.00 0.00 0.00 3.77
2401 2652 2.816087 GCTCTTCAGATGCAAGTTCCAA 59.184 45.455 0.00 0.00 0.00 3.53
2402 2653 2.430465 GCTCTTCAGATGCAAGTTCCA 58.570 47.619 0.00 0.00 0.00 3.53
2403 2654 1.396301 CGCTCTTCAGATGCAAGTTCC 59.604 52.381 0.00 0.00 0.00 3.62
2404 2655 1.396301 CCGCTCTTCAGATGCAAGTTC 59.604 52.381 0.00 0.00 0.00 3.01
2405 2656 1.271054 ACCGCTCTTCAGATGCAAGTT 60.271 47.619 0.00 0.00 0.00 2.66
2406 2657 0.322975 ACCGCTCTTCAGATGCAAGT 59.677 50.000 0.00 0.00 0.00 3.16
2407 2658 1.005340 GACCGCTCTTCAGATGCAAG 58.995 55.000 0.00 0.00 0.00 4.01
2408 2659 0.610174 AGACCGCTCTTCAGATGCAA 59.390 50.000 0.00 0.00 0.00 4.08
2421 2672 2.673368 CTCAATACAGTTTCCAGACCGC 59.327 50.000 0.00 0.00 0.00 5.68
2423 2674 6.763610 CCTAATCTCAATACAGTTTCCAGACC 59.236 42.308 0.00 0.00 0.00 3.85
2439 2690 7.275341 CGCAAAATAACAAATTGCCTAATCTCA 59.725 33.333 4.35 0.00 45.00 3.27
2450 2701 5.695816 ACTGTGCATCGCAAAATAACAAATT 59.304 32.000 0.00 0.00 41.47 1.82
2452 2703 4.615949 ACTGTGCATCGCAAAATAACAAA 58.384 34.783 0.00 0.00 41.47 2.83
2455 2706 3.786048 GCTACTGTGCATCGCAAAATAAC 59.214 43.478 0.00 0.00 41.47 1.89
2456 2707 3.438434 TGCTACTGTGCATCGCAAAATAA 59.562 39.130 0.00 0.00 41.47 1.40
2484 2735 4.582240 TCCATGAGTTGCAAAATGTACACA 59.418 37.500 0.00 0.00 0.00 3.72
2542 2793 4.410228 ACTCTGTGGTGCCAATATGATACT 59.590 41.667 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.