Multiple sequence alignment - TraesCS4A01G101700

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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 TraesCS4A01G101700 chr4A 100.000 2699 0 0 1 2699 114141037 114143735 0.000000e+00 4985.0
1 TraesCS4A01G101700 chr4A 87.000 200 19 7 2501 2697 114152543 114152738 4.520000e-53 219.0
2 TraesCS4A01G101700 chr4D 91.389 1800 72 28 73 1829 350832800 350831041 0.000000e+00 2388.0
3 TraesCS4A01G101700 chr4D 85.957 705 42 27 2013 2682 350830853 350830171 0.000000e+00 701.0
4 TraesCS4A01G101700 chr4B 89.241 1450 81 31 429 1828 434195017 434193593 0.000000e+00 1744.0
5 TraesCS4A01G101700 chr4B 82.466 730 55 32 1985 2682 434193435 434192747 3.010000e-159 571.0
6 TraesCS4A01G101700 chr4B 92.459 305 16 3 70 373 434195321 434195023 1.920000e-116 429.0
7 TraesCS4A01G101700 chr1D 97.727 44 1 0 1580 1623 384147318 384147275 2.880000e-10 76.8
8 TraesCS4A01G101700 chr1B 97.727 44 1 0 1580 1623 515455137 515455094 2.880000e-10 76.8
9 TraesCS4A01G101700 chr1B 100.000 30 0 0 1090 1119 227927792 227927763 3.750000e-04 56.5
10 TraesCS4A01G101700 chr1A 97.727 44 1 0 1580 1623 483928222 483928179 2.880000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G101700 chr4A 114141037 114143735 2698 False 4985.000000 4985 100.000000 1 2699 1 chr4A.!!$F1 2698
1 TraesCS4A01G101700 chr4D 350830171 350832800 2629 True 1544.500000 2388 88.673000 73 2682 2 chr4D.!!$R1 2609
2 TraesCS4A01G101700 chr4B 434192747 434195321 2574 True 914.666667 1744 88.055333 70 2682 3 chr4B.!!$R1 2612

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
386 402 0.110328 CAGCAACTCAGCAAGCTTCG 60.110 55.0 0.0 0.0 34.61 3.79 F
1282 1330 0.037447 GCTGCTCCCTTGGTTCTTCT 59.963 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1763 0.179089 CATTAGGAGCTGCTGTCGCT 60.179 55.0 19.25 0.00 41.15 4.93 R
2135 2302 0.595567 GAGCACGTTCGTGTACACCA 60.596 55.0 20.11 4.56 38.31 4.17 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
20 21 3.766676 ATAGGAGTATATGCGTGCTCG 57.233 47.619 3.31 3.31 40.37 5.03
31 32 3.036026 CGTGCTCGCATAGTTGTCT 57.964 52.632 0.00 0.00 0.00 3.41
32 33 0.642291 CGTGCTCGCATAGTTGTCTG 59.358 55.000 0.00 0.00 0.00 3.51
33 34 1.002366 GTGCTCGCATAGTTGTCTGG 58.998 55.000 0.00 0.00 0.00 3.86
34 35 0.608130 TGCTCGCATAGTTGTCTGGT 59.392 50.000 0.00 0.00 0.00 4.00
35 36 1.002366 GCTCGCATAGTTGTCTGGTG 58.998 55.000 0.00 0.00 0.00 4.17
36 37 1.002366 CTCGCATAGTTGTCTGGTGC 58.998 55.000 0.00 0.00 35.11 5.01
37 38 0.320050 TCGCATAGTTGTCTGGTGCA 59.680 50.000 0.00 0.00 36.86 4.57
38 39 1.155889 CGCATAGTTGTCTGGTGCAA 58.844 50.000 0.00 0.00 36.86 4.08
39 40 1.129251 CGCATAGTTGTCTGGTGCAAG 59.871 52.381 0.00 0.00 36.86 4.01
40 41 2.426522 GCATAGTTGTCTGGTGCAAGA 58.573 47.619 0.00 0.00 36.95 3.02
41 42 2.813754 GCATAGTTGTCTGGTGCAAGAA 59.186 45.455 0.00 0.00 36.95 2.52
42 43 3.253188 GCATAGTTGTCTGGTGCAAGAAA 59.747 43.478 0.00 0.00 36.95 2.52
43 44 4.261572 GCATAGTTGTCTGGTGCAAGAAAA 60.262 41.667 0.00 0.00 36.95 2.29
44 45 5.735922 GCATAGTTGTCTGGTGCAAGAAAAA 60.736 40.000 0.00 0.00 36.95 1.94
63 64 3.686916 AAAGACTTGGAGCAGTAGACC 57.313 47.619 0.00 0.00 0.00 3.85
64 65 1.178276 AGACTTGGAGCAGTAGACCG 58.822 55.000 0.00 0.00 0.00 4.79
65 66 0.458716 GACTTGGAGCAGTAGACCGC 60.459 60.000 0.00 0.00 0.00 5.68
66 67 1.185618 ACTTGGAGCAGTAGACCGCA 61.186 55.000 0.00 0.00 0.00 5.69
67 68 0.459237 CTTGGAGCAGTAGACCGCAG 60.459 60.000 0.00 0.00 0.00 5.18
68 69 0.898326 TTGGAGCAGTAGACCGCAGA 60.898 55.000 0.00 0.00 0.00 4.26
82 83 2.050077 CAGACGAGCGTGACTGCA 60.050 61.111 0.00 0.00 37.31 4.41
118 119 0.737715 CACTAGCAGCCACTCCGAAC 60.738 60.000 0.00 0.00 0.00 3.95
217 220 2.426406 GCCATGTAAGCCCCAAGCC 61.426 63.158 0.00 0.00 45.47 4.35
254 257 1.266718 GCAAGCATTTTGTCTGTCCGA 59.733 47.619 0.00 0.00 0.00 4.55
301 317 0.462375 GCTCCATCCATGCAATGCAA 59.538 50.000 13.45 0.00 44.97 4.08
302 318 1.070134 GCTCCATCCATGCAATGCAAT 59.930 47.619 13.45 0.00 44.97 3.56
303 319 2.754472 CTCCATCCATGCAATGCAATG 58.246 47.619 13.45 11.66 44.97 2.82
304 320 1.202592 TCCATCCATGCAATGCAATGC 60.203 47.619 19.99 19.99 44.97 3.56
365 381 1.080161 GCCTCTAGCGCTAGCCATC 60.080 63.158 34.65 20.59 46.67 3.51
373 389 1.717937 CGCTAGCCATCACAGCAAC 59.282 57.895 9.66 0.00 34.94 4.17
374 390 0.742281 CGCTAGCCATCACAGCAACT 60.742 55.000 9.66 0.00 34.94 3.16
375 391 1.012841 GCTAGCCATCACAGCAACTC 58.987 55.000 2.29 0.00 35.35 3.01
377 393 2.277969 CTAGCCATCACAGCAACTCAG 58.722 52.381 0.00 0.00 0.00 3.35
378 394 0.959372 AGCCATCACAGCAACTCAGC 60.959 55.000 0.00 0.00 0.00 4.26
379 395 1.239296 GCCATCACAGCAACTCAGCA 61.239 55.000 0.00 0.00 36.85 4.41
380 396 1.241165 CCATCACAGCAACTCAGCAA 58.759 50.000 0.00 0.00 36.85 3.91
381 397 1.199327 CCATCACAGCAACTCAGCAAG 59.801 52.381 0.00 0.00 36.85 4.01
382 398 0.879765 ATCACAGCAACTCAGCAAGC 59.120 50.000 0.00 0.00 36.85 4.01
383 399 0.179037 TCACAGCAACTCAGCAAGCT 60.179 50.000 0.00 0.00 37.95 3.74
384 400 0.666913 CACAGCAACTCAGCAAGCTT 59.333 50.000 0.00 0.00 34.61 3.74
385 401 0.950116 ACAGCAACTCAGCAAGCTTC 59.050 50.000 0.00 0.00 34.61 3.86
386 402 0.110328 CAGCAACTCAGCAAGCTTCG 60.110 55.000 0.00 0.00 34.61 3.79
387 403 0.533755 AGCAACTCAGCAAGCTTCGT 60.534 50.000 0.00 0.00 36.85 3.85
388 404 0.385223 GCAACTCAGCAAGCTTCGTG 60.385 55.000 0.00 0.00 0.00 4.35
389 405 1.220529 CAACTCAGCAAGCTTCGTGA 58.779 50.000 0.00 1.13 0.00 4.35
405 421 5.457148 GCTTCGTGAGTGAGTAGTATGATTG 59.543 44.000 0.00 0.00 0.00 2.67
413 429 7.493645 TGAGTGAGTAGTATGATTGCTTGATTG 59.506 37.037 0.00 0.00 0.00 2.67
432 448 1.423056 GTTGCGATGCTCACTGCTC 59.577 57.895 0.00 0.00 43.37 4.26
433 449 1.018226 GTTGCGATGCTCACTGCTCT 61.018 55.000 0.00 0.00 43.37 4.09
434 450 0.738762 TTGCGATGCTCACTGCTCTC 60.739 55.000 0.00 0.00 43.37 3.20
435 451 1.141449 GCGATGCTCACTGCTCTCT 59.859 57.895 0.00 0.00 43.37 3.10
436 452 1.146957 GCGATGCTCACTGCTCTCTG 61.147 60.000 0.00 0.00 43.37 3.35
549 570 2.226437 CACCACACTATTTGCCAGTGAC 59.774 50.000 9.33 0.00 45.10 3.67
579 600 4.266962 TGAGGATCCTCAGGCGAG 57.733 61.111 35.92 0.28 46.80 5.03
580 601 2.130426 TGAGGATCCTCAGGCGAGC 61.130 63.158 35.92 12.69 46.80 5.03
612 636 2.674380 GAACAGCACAGGGGCCAG 60.674 66.667 4.39 0.00 0.00 4.85
613 637 3.177884 AACAGCACAGGGGCCAGA 61.178 61.111 4.39 0.00 0.00 3.86
614 638 2.697147 GAACAGCACAGGGGCCAGAA 62.697 60.000 4.39 0.00 0.00 3.02
778 802 1.811266 CATGGACGACCTGGAAGCG 60.811 63.158 0.00 3.68 37.04 4.68
779 803 3.019003 ATGGACGACCTGGAAGCGG 62.019 63.158 0.00 0.00 37.04 5.52
780 804 3.379445 GGACGACCTGGAAGCGGA 61.379 66.667 0.00 0.00 0.00 5.54
781 805 2.126031 GACGACCTGGAAGCGGAC 60.126 66.667 0.00 0.00 0.00 4.79
808 832 1.174783 CCTACGACGGGATAGGGATG 58.825 60.000 0.00 0.00 35.26 3.51
823 847 3.825328 AGGGATGAGATATTTGCCACAC 58.175 45.455 0.00 0.00 0.00 3.82
885 909 3.089874 TCCTCCAATCCCCTGCCG 61.090 66.667 0.00 0.00 0.00 5.69
1120 1144 0.871722 CACAACCCCATACACACACG 59.128 55.000 0.00 0.00 0.00 4.49
1137 1161 2.094854 ACACGGTTCCTCAGATTACGAC 60.095 50.000 0.00 0.00 0.00 4.34
1259 1307 3.496160 CCATCCCCTAATTCGTACCTTGG 60.496 52.174 0.00 0.00 0.00 3.61
1279 1327 1.130054 TCTGCTGCTCCCTTGGTTCT 61.130 55.000 0.00 0.00 0.00 3.01
1280 1328 0.251077 CTGCTGCTCCCTTGGTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
1281 1329 0.250901 TGCTGCTCCCTTGGTTCTTC 60.251 55.000 0.00 0.00 0.00 2.87
1282 1330 0.037447 GCTGCTCCCTTGGTTCTTCT 59.963 55.000 0.00 0.00 0.00 2.85
1283 1331 1.279271 GCTGCTCCCTTGGTTCTTCTA 59.721 52.381 0.00 0.00 0.00 2.10
1284 1332 2.679349 GCTGCTCCCTTGGTTCTTCTAG 60.679 54.545 0.00 0.00 0.00 2.43
1362 1439 2.345641 CACGTCGACATCAGAATTGGTC 59.654 50.000 17.16 0.00 0.00 4.02
1379 1456 5.586155 TTGGTCAACTAATTAAGGTGGGA 57.414 39.130 0.00 0.00 43.71 4.37
1384 1461 7.511028 TGGTCAACTAATTAAGGTGGGATTTTT 59.489 33.333 0.00 0.00 43.71 1.94
1396 1473 5.073008 AGGTGGGATTTTTAATTTGCAGGTT 59.927 36.000 0.00 0.00 0.00 3.50
1519 1598 1.630148 GTCGGTCCGTCTCAAATCAG 58.370 55.000 11.88 0.00 0.00 2.90
1545 1627 4.100808 ACTTCCTCTGATCAGCAGGAATAC 59.899 45.833 33.40 0.00 44.98 1.89
1547 1629 3.386078 TCCTCTGATCAGCAGGAATACAC 59.614 47.826 27.76 0.00 44.98 2.90
1584 1666 1.227823 AGTTGGCGTGCTTGCAGTA 60.228 52.632 0.00 0.00 36.28 2.74
1702 1784 1.539929 GCGACAGCAGCTCCTAATGAT 60.540 52.381 0.00 0.00 44.35 2.45
1732 1819 2.378445 TGCGTGCTGCTTAGATGTTA 57.622 45.000 0.00 0.00 46.63 2.41
1776 1863 7.815068 AGAACGAATAATTAGAAGATCGATGGG 59.185 37.037 0.54 0.00 34.62 4.00
1783 1870 2.040009 GAAGATCGATGGGGCGGGAA 62.040 60.000 0.54 0.00 0.00 3.97
1799 1886 0.388134 GGAAGTCAGCTAACGCGACA 60.388 55.000 15.93 0.00 40.02 4.35
1834 1957 2.679837 CTGGTGCATGTACAGGAATCAC 59.320 50.000 12.53 9.73 0.00 3.06
1841 1964 3.719268 TGTACAGGAATCACAAGCCAT 57.281 42.857 0.00 0.00 0.00 4.40
1855 1978 0.108138 AGCCATCTCGTACTGTTGCC 60.108 55.000 0.00 0.00 0.00 4.52
1892 2025 9.710900 GATGTAATTGTACTCATCATGTATCCA 57.289 33.333 0.00 0.00 37.30 3.41
1894 2027 9.710900 TGTAATTGTACTCATCATGTATCCATC 57.289 33.333 0.00 0.00 0.00 3.51
1895 2028 9.935241 GTAATTGTACTCATCATGTATCCATCT 57.065 33.333 0.00 0.00 0.00 2.90
1897 2030 6.596309 TGTACTCATCATGTATCCATCTCC 57.404 41.667 0.00 0.00 0.00 3.71
1899 2032 4.496540 ACTCATCATGTATCCATCTCCCA 58.503 43.478 0.00 0.00 0.00 4.37
1901 2034 4.233729 TCATCATGTATCCATCTCCCACA 58.766 43.478 0.00 0.00 0.00 4.17
1902 2035 4.285260 TCATCATGTATCCATCTCCCACAG 59.715 45.833 0.00 0.00 0.00 3.66
1903 2036 2.369860 TCATGTATCCATCTCCCACAGC 59.630 50.000 0.00 0.00 0.00 4.40
1904 2037 2.180946 TGTATCCATCTCCCACAGCT 57.819 50.000 0.00 0.00 0.00 4.24
1905 2038 2.042464 TGTATCCATCTCCCACAGCTC 58.958 52.381 0.00 0.00 0.00 4.09
1906 2039 2.324541 GTATCCATCTCCCACAGCTCT 58.675 52.381 0.00 0.00 0.00 4.09
1907 2040 1.422531 ATCCATCTCCCACAGCTCTC 58.577 55.000 0.00 0.00 0.00 3.20
1908 2041 1.039785 TCCATCTCCCACAGCTCTCG 61.040 60.000 0.00 0.00 0.00 4.04
1909 2042 1.440893 CATCTCCCACAGCTCTCGG 59.559 63.158 0.00 0.00 0.00 4.63
1910 2043 1.000993 ATCTCCCACAGCTCTCGGT 59.999 57.895 0.00 0.00 0.00 4.69
1911 2044 0.616111 ATCTCCCACAGCTCTCGGTT 60.616 55.000 0.00 0.00 0.00 4.44
1912 2045 1.216710 CTCCCACAGCTCTCGGTTC 59.783 63.158 0.00 0.00 0.00 3.62
1913 2046 1.533033 TCCCACAGCTCTCGGTTCA 60.533 57.895 0.00 0.00 0.00 3.18
1914 2047 1.079543 CCCACAGCTCTCGGTTCAG 60.080 63.158 0.00 0.00 0.00 3.02
1915 2048 1.536073 CCCACAGCTCTCGGTTCAGA 61.536 60.000 0.00 0.00 0.00 3.27
1916 2049 0.389166 CCACAGCTCTCGGTTCAGAC 60.389 60.000 0.00 0.00 0.00 3.51
1917 2050 0.600557 CACAGCTCTCGGTTCAGACT 59.399 55.000 0.00 0.00 0.00 3.24
1918 2051 1.000283 CACAGCTCTCGGTTCAGACTT 60.000 52.381 0.00 0.00 0.00 3.01
1919 2052 1.689273 ACAGCTCTCGGTTCAGACTTT 59.311 47.619 0.00 0.00 0.00 2.66
1920 2053 2.103263 ACAGCTCTCGGTTCAGACTTTT 59.897 45.455 0.00 0.00 0.00 2.27
1921 2054 2.734079 CAGCTCTCGGTTCAGACTTTTC 59.266 50.000 0.00 0.00 0.00 2.29
1922 2055 2.365617 AGCTCTCGGTTCAGACTTTTCA 59.634 45.455 0.00 0.00 0.00 2.69
1923 2056 3.007398 AGCTCTCGGTTCAGACTTTTCAT 59.993 43.478 0.00 0.00 0.00 2.57
1924 2057 4.220821 AGCTCTCGGTTCAGACTTTTCATA 59.779 41.667 0.00 0.00 0.00 2.15
1925 2058 4.327627 GCTCTCGGTTCAGACTTTTCATAC 59.672 45.833 0.00 0.00 0.00 2.39
1926 2059 4.817517 TCTCGGTTCAGACTTTTCATACC 58.182 43.478 0.00 0.00 0.00 2.73
1927 2060 4.527038 TCTCGGTTCAGACTTTTCATACCT 59.473 41.667 0.00 0.00 0.00 3.08
1928 2061 4.817517 TCGGTTCAGACTTTTCATACCTC 58.182 43.478 0.00 0.00 0.00 3.85
1929 2062 4.527038 TCGGTTCAGACTTTTCATACCTCT 59.473 41.667 0.00 0.00 0.00 3.69
1930 2063 4.627467 CGGTTCAGACTTTTCATACCTCTG 59.373 45.833 0.00 0.00 0.00 3.35
1931 2064 5.552178 GGTTCAGACTTTTCATACCTCTGT 58.448 41.667 0.00 0.00 31.94 3.41
1932 2065 5.409826 GGTTCAGACTTTTCATACCTCTGTG 59.590 44.000 0.00 0.00 31.94 3.66
1933 2066 5.152623 TCAGACTTTTCATACCTCTGTGG 57.847 43.478 0.00 0.00 42.93 4.17
1934 2067 4.838423 TCAGACTTTTCATACCTCTGTGGA 59.162 41.667 2.23 0.00 39.71 4.02
1935 2068 5.047021 TCAGACTTTTCATACCTCTGTGGAG 60.047 44.000 2.23 0.00 39.71 3.86
1936 2069 5.047021 CAGACTTTTCATACCTCTGTGGAGA 60.047 44.000 2.23 0.00 41.86 3.71
1937 2070 5.723887 AGACTTTTCATACCTCTGTGGAGAT 59.276 40.000 2.23 0.00 41.86 2.75
1938 2071 6.214412 AGACTTTTCATACCTCTGTGGAGATT 59.786 38.462 2.23 0.00 41.86 2.40
1939 2072 7.400339 AGACTTTTCATACCTCTGTGGAGATTA 59.600 37.037 2.23 0.00 41.86 1.75
1940 2073 7.331791 ACTTTTCATACCTCTGTGGAGATTAC 58.668 38.462 2.23 0.00 41.86 1.89
1941 2074 5.871396 TTCATACCTCTGTGGAGATTACC 57.129 43.478 2.23 0.00 41.86 2.85
1942 2075 5.144159 TCATACCTCTGTGGAGATTACCT 57.856 43.478 2.23 0.00 41.86 3.08
1943 2076 6.275692 TCATACCTCTGTGGAGATTACCTA 57.724 41.667 2.23 0.00 41.86 3.08
1944 2077 6.069331 TCATACCTCTGTGGAGATTACCTAC 58.931 44.000 2.23 0.00 41.86 3.18
1945 2078 3.288964 ACCTCTGTGGAGATTACCTACG 58.711 50.000 2.23 0.00 41.86 3.51
1946 2079 2.623889 CCTCTGTGGAGATTACCTACGG 59.376 54.545 0.00 0.00 41.86 4.02
1947 2080 2.029623 TCTGTGGAGATTACCTACGGC 58.970 52.381 0.00 0.00 0.00 5.68
1948 2081 1.754803 CTGTGGAGATTACCTACGGCA 59.245 52.381 0.00 0.00 0.00 5.69
1975 2108 2.225491 GTGTGCTAATCGTCCAAGCAAA 59.775 45.455 0.00 0.00 47.00 3.68
1978 2111 1.740025 GCTAATCGTCCAAGCAAAGCT 59.260 47.619 0.00 0.00 42.56 3.74
1995 2128 8.071177 AGCAAAGCTTTATTCTGTAATTGGAT 57.929 30.769 12.25 0.00 33.89 3.41
1996 2129 8.193438 AGCAAAGCTTTATTCTGTAATTGGATC 58.807 33.333 12.25 0.00 33.89 3.36
1997 2130 8.193438 GCAAAGCTTTATTCTGTAATTGGATCT 58.807 33.333 12.25 0.00 0.00 2.75
1999 2132 8.457238 AAGCTTTATTCTGTAATTGGATCTCC 57.543 34.615 0.00 0.00 0.00 3.71
2000 2133 6.708054 AGCTTTATTCTGTAATTGGATCTCCG 59.292 38.462 0.00 0.00 39.43 4.63
2002 2135 7.307455 GCTTTATTCTGTAATTGGATCTCCGTC 60.307 40.741 0.00 0.00 39.43 4.79
2008 2167 4.956700 TGTAATTGGATCTCCGTCTTCTCT 59.043 41.667 0.00 0.00 39.43 3.10
2010 2169 5.428184 AATTGGATCTCCGTCTTCTCTTT 57.572 39.130 0.00 0.00 39.43 2.52
2011 2170 4.457834 TTGGATCTCCGTCTTCTCTTTC 57.542 45.455 0.00 0.00 39.43 2.62
2018 2177 4.392445 TCTCCGTCTTCTCTTTCTAACGAG 59.608 45.833 0.00 0.00 32.17 4.18
2048 2210 0.107410 AACGGTTGTCCTGCACAGAA 60.107 50.000 0.00 0.00 35.97 3.02
2049 2211 0.107410 ACGGTTGTCCTGCACAGAAA 60.107 50.000 0.00 0.00 35.97 2.52
2090 2252 7.502895 CCTAACCAGAGATACTAGTACACATGT 59.497 40.741 4.31 0.00 0.00 3.21
2102 2264 3.562557 AGTACACATGTTCACGGGAAAAC 59.437 43.478 0.00 0.00 34.13 2.43
2104 2266 1.600013 CACATGTTCACGGGAAAACGA 59.400 47.619 0.00 0.00 34.13 3.85
2114 2276 2.292292 ACGGGAAAACGAAGGAAACATG 59.708 45.455 0.00 0.00 37.61 3.21
2135 2302 3.068732 TGCTATATGCTCAGCGAGAAGTT 59.931 43.478 9.32 0.00 43.37 2.66
2190 2357 0.670546 ATCTTGTCGTTGGGTCGCTG 60.671 55.000 0.00 0.00 0.00 5.18
2279 2446 1.135094 ATCGGTGATGGGATTCTGCT 58.865 50.000 0.00 0.00 0.00 4.24
2280 2447 0.178767 TCGGTGATGGGATTCTGCTG 59.821 55.000 0.00 0.00 0.00 4.41
2281 2448 1.442526 CGGTGATGGGATTCTGCTGC 61.443 60.000 0.00 0.00 0.00 5.25
2300 2472 3.771160 CGGGACAAGGACCCCTCG 61.771 72.222 0.00 0.00 44.09 4.63
2391 2563 3.560481 TCGAAACGCCACTAATTCACAAA 59.440 39.130 0.00 0.00 0.00 2.83
2436 2642 6.800072 TTTTCACCCAACTAATCCTTTTGT 57.200 33.333 0.00 0.00 0.00 2.83
2441 2647 5.768164 CACCCAACTAATCCTTTTGTGTAGT 59.232 40.000 0.00 0.00 0.00 2.73
2459 2665 4.408921 TGTAGTGGCTGATTAATAGGTGCT 59.591 41.667 0.00 0.00 0.00 4.40
2465 2671 3.184581 GCTGATTAATAGGTGCTACACGC 59.815 47.826 0.00 0.00 34.83 5.34
2489 2696 3.640407 TGTGGCACCCTGAGGCTC 61.640 66.667 16.26 7.79 36.11 4.70
2517 2725 2.176889 GCCCACCTCACTCTAGTTGTA 58.823 52.381 0.00 0.00 0.00 2.41
2520 2728 3.576982 CCCACCTCACTCTAGTTGTACAA 59.423 47.826 3.59 3.59 0.00 2.41
2545 2753 2.802667 GCCGACATGCGCTACACTG 61.803 63.158 9.73 0.83 39.11 3.66
2547 2755 1.807165 CGACATGCGCTACACTGCT 60.807 57.895 9.73 0.00 0.00 4.24
2550 2758 0.518636 ACATGCGCTACACTGCTTTG 59.481 50.000 9.73 0.00 0.00 2.77
2565 2773 1.671850 GCTTTGTGTAGCGCCTAGACA 60.672 52.381 2.29 8.24 38.23 3.41
2596 2804 0.668401 ACGTGCACTTACTAACCGCC 60.668 55.000 16.19 0.00 0.00 6.13
2597 2805 0.668096 CGTGCACTTACTAACCGCCA 60.668 55.000 16.19 0.00 0.00 5.69
2598 2806 0.794473 GTGCACTTACTAACCGCCAC 59.206 55.000 10.32 0.00 0.00 5.01
2620 2834 1.537669 CGGTCCTCCCTAGCCTAGT 59.462 63.158 0.00 0.00 0.00 2.57
2633 2847 0.400594 GCCTAGTCCCCACACAAACT 59.599 55.000 0.00 0.00 0.00 2.66
2634 2848 1.202891 GCCTAGTCCCCACACAAACTT 60.203 52.381 0.00 0.00 0.00 2.66
2656 2870 4.067896 TCAAGAGCATTTGAACAGAGGAC 58.932 43.478 0.94 0.00 34.32 3.85
2657 2871 2.693069 AGAGCATTTGAACAGAGGACG 58.307 47.619 0.00 0.00 0.00 4.79
2658 2872 2.037772 AGAGCATTTGAACAGAGGACGT 59.962 45.455 0.00 0.00 0.00 4.34
2659 2873 2.413453 GAGCATTTGAACAGAGGACGTC 59.587 50.000 7.13 7.13 0.00 4.34
2660 2874 2.037772 AGCATTTGAACAGAGGACGTCT 59.962 45.455 16.46 0.90 35.00 4.18
2682 2896 2.210116 GACGCGATTCTCTCTCTCTCT 58.790 52.381 15.93 0.00 0.00 3.10
2683 2897 2.210116 ACGCGATTCTCTCTCTCTCTC 58.790 52.381 15.93 0.00 0.00 3.20
2684 2898 2.158957 ACGCGATTCTCTCTCTCTCTCT 60.159 50.000 15.93 0.00 0.00 3.10
2685 2899 2.476619 CGCGATTCTCTCTCTCTCTCTC 59.523 54.545 0.00 0.00 0.00 3.20
2686 2900 3.466836 GCGATTCTCTCTCTCTCTCTCA 58.533 50.000 0.00 0.00 0.00 3.27
2687 2901 3.248602 GCGATTCTCTCTCTCTCTCTCAC 59.751 52.174 0.00 0.00 0.00 3.51
2688 2902 4.697514 CGATTCTCTCTCTCTCTCTCACT 58.302 47.826 0.00 0.00 0.00 3.41
2689 2903 5.118990 CGATTCTCTCTCTCTCTCTCACTT 58.881 45.833 0.00 0.00 0.00 3.16
2690 2904 5.235186 CGATTCTCTCTCTCTCTCTCACTTC 59.765 48.000 0.00 0.00 0.00 3.01
2691 2905 5.762179 TTCTCTCTCTCTCTCTCACTTCT 57.238 43.478 0.00 0.00 0.00 2.85
2692 2906 5.762179 TCTCTCTCTCTCTCTCACTTCTT 57.238 43.478 0.00 0.00 0.00 2.52
2693 2907 6.867519 TCTCTCTCTCTCTCTCACTTCTTA 57.132 41.667 0.00 0.00 0.00 2.10
2694 2908 7.252612 TCTCTCTCTCTCTCTCACTTCTTAA 57.747 40.000 0.00 0.00 0.00 1.85
2695 2909 7.685481 TCTCTCTCTCTCTCTCACTTCTTAAA 58.315 38.462 0.00 0.00 0.00 1.52
2696 2910 8.328758 TCTCTCTCTCTCTCTCACTTCTTAAAT 58.671 37.037 0.00 0.00 0.00 1.40
2697 2911 8.877864 TCTCTCTCTCTCTCACTTCTTAAATT 57.122 34.615 0.00 0.00 0.00 1.82
2698 2912 8.956426 TCTCTCTCTCTCTCACTTCTTAAATTC 58.044 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.766676 CGAGCACGCATATACTCCTAT 57.233 47.619 0.00 0.00 0.00 2.57
13 14 0.642291 CAGACAACTATGCGAGCACG 59.358 55.000 0.00 0.00 42.93 5.34
14 15 1.002366 CCAGACAACTATGCGAGCAC 58.998 55.000 0.00 0.00 0.00 4.40
15 16 0.608130 ACCAGACAACTATGCGAGCA 59.392 50.000 0.00 0.00 0.00 4.26
16 17 1.002366 CACCAGACAACTATGCGAGC 58.998 55.000 0.00 0.00 0.00 5.03
17 18 1.002366 GCACCAGACAACTATGCGAG 58.998 55.000 0.00 0.00 31.18 5.03
18 19 0.320050 TGCACCAGACAACTATGCGA 59.680 50.000 0.00 0.00 39.07 5.10
19 20 1.129251 CTTGCACCAGACAACTATGCG 59.871 52.381 0.00 0.00 39.07 4.73
20 21 2.426522 TCTTGCACCAGACAACTATGC 58.573 47.619 0.00 0.00 37.70 3.14
21 22 5.437289 TTTTCTTGCACCAGACAACTATG 57.563 39.130 0.00 0.00 0.00 2.23
41 42 4.390264 GGTCTACTGCTCCAAGTCTTTTT 58.610 43.478 0.00 0.00 0.00 1.94
42 43 3.555168 CGGTCTACTGCTCCAAGTCTTTT 60.555 47.826 0.00 0.00 0.00 2.27
43 44 2.028930 CGGTCTACTGCTCCAAGTCTTT 60.029 50.000 0.00 0.00 0.00 2.52
44 45 1.546476 CGGTCTACTGCTCCAAGTCTT 59.454 52.381 0.00 0.00 0.00 3.01
45 46 1.178276 CGGTCTACTGCTCCAAGTCT 58.822 55.000 0.00 0.00 0.00 3.24
46 47 0.458716 GCGGTCTACTGCTCCAAGTC 60.459 60.000 6.67 0.00 44.58 3.01
47 48 1.592223 GCGGTCTACTGCTCCAAGT 59.408 57.895 6.67 0.00 44.58 3.16
48 49 4.504132 GCGGTCTACTGCTCCAAG 57.496 61.111 6.67 0.00 44.58 3.61
55 56 1.226435 GCTCGTCTGCGGTCTACTG 60.226 63.158 0.00 0.00 38.89 2.74
56 57 3.188965 GCTCGTCTGCGGTCTACT 58.811 61.111 0.00 0.00 38.89 2.57
64 65 3.474034 GCAGTCACGCTCGTCTGC 61.474 66.667 16.45 16.45 44.50 4.26
65 66 1.612469 CTTGCAGTCACGCTCGTCTG 61.612 60.000 6.72 6.72 0.00 3.51
66 67 1.372251 CTTGCAGTCACGCTCGTCT 60.372 57.895 0.00 0.00 0.00 4.18
67 68 1.609840 GACTTGCAGTCACGCTCGTC 61.610 60.000 10.30 0.00 44.45 4.20
68 69 1.661821 GACTTGCAGTCACGCTCGT 60.662 57.895 10.30 0.00 44.45 4.18
118 119 3.446873 TCATTCAAATCAATTGGTCCCGG 59.553 43.478 5.42 0.00 39.62 5.73
304 320 1.302431 TCTCCCGGTGCACAACATG 60.302 57.895 20.43 5.63 0.00 3.21
305 321 1.302511 GTCTCCCGGTGCACAACAT 60.303 57.895 20.43 0.00 0.00 2.71
365 381 0.666913 AAGCTTGCTGAGTTGCTGTG 59.333 50.000 0.00 0.00 35.79 3.66
373 389 0.788995 CACTCACGAAGCTTGCTGAG 59.211 55.000 21.04 21.04 36.90 3.35
374 390 0.389025 TCACTCACGAAGCTTGCTGA 59.611 50.000 2.10 2.87 0.00 4.26
375 391 0.788995 CTCACTCACGAAGCTTGCTG 59.211 55.000 2.10 0.00 0.00 4.41
377 393 1.989165 CTACTCACTCACGAAGCTTGC 59.011 52.381 2.10 0.00 0.00 4.01
378 394 3.290308 ACTACTCACTCACGAAGCTTG 57.710 47.619 2.10 0.00 0.00 4.01
379 395 4.700692 TCATACTACTCACTCACGAAGCTT 59.299 41.667 0.00 0.00 0.00 3.74
380 396 4.262617 TCATACTACTCACTCACGAAGCT 58.737 43.478 0.00 0.00 0.00 3.74
381 397 4.617808 TCATACTACTCACTCACGAAGC 57.382 45.455 0.00 0.00 0.00 3.86
382 398 5.457148 GCAATCATACTACTCACTCACGAAG 59.543 44.000 0.00 0.00 0.00 3.79
383 399 5.125578 AGCAATCATACTACTCACTCACGAA 59.874 40.000 0.00 0.00 0.00 3.85
384 400 4.640647 AGCAATCATACTACTCACTCACGA 59.359 41.667 0.00 0.00 0.00 4.35
385 401 4.926244 AGCAATCATACTACTCACTCACG 58.074 43.478 0.00 0.00 0.00 4.35
386 402 6.333416 TCAAGCAATCATACTACTCACTCAC 58.667 40.000 0.00 0.00 0.00 3.51
387 403 6.530019 TCAAGCAATCATACTACTCACTCA 57.470 37.500 0.00 0.00 0.00 3.41
388 404 7.042187 CCAATCAAGCAATCATACTACTCACTC 60.042 40.741 0.00 0.00 0.00 3.51
389 405 6.765036 CCAATCAAGCAATCATACTACTCACT 59.235 38.462 0.00 0.00 0.00 3.41
405 421 0.171903 AGCATCGCAACCAATCAAGC 59.828 50.000 0.00 0.00 0.00 4.01
432 448 0.317160 TGTGTACTTCCACCGCAGAG 59.683 55.000 0.00 0.00 34.35 3.35
433 449 0.317160 CTGTGTACTTCCACCGCAGA 59.683 55.000 0.00 0.00 34.35 4.26
434 450 0.033504 ACTGTGTACTTCCACCGCAG 59.966 55.000 0.00 0.00 34.35 5.18
435 451 0.249699 CACTGTGTACTTCCACCGCA 60.250 55.000 0.00 0.00 34.35 5.69
436 452 0.032952 TCACTGTGTACTTCCACCGC 59.967 55.000 7.79 0.00 34.35 5.68
440 461 1.758280 ACGGTTCACTGTGTACTTCCA 59.242 47.619 15.61 0.00 33.47 3.53
520 541 4.320202 GGCAAATAGTGTGGTGTTGTAGTG 60.320 45.833 0.00 0.00 0.00 2.74
549 570 3.118334 AGGATCCTCAAGTGCAGATTCAG 60.118 47.826 9.02 0.00 0.00 3.02
612 636 5.117745 GCCGCTCTTTTTCTTTCATTCTTTC 59.882 40.000 0.00 0.00 0.00 2.62
613 637 4.984785 GCCGCTCTTTTTCTTTCATTCTTT 59.015 37.500 0.00 0.00 0.00 2.52
614 638 4.550422 GCCGCTCTTTTTCTTTCATTCTT 58.450 39.130 0.00 0.00 0.00 2.52
646 670 2.754254 GGCCAACGTGGGGATTCC 60.754 66.667 11.96 0.00 38.19 3.01
778 802 3.138798 TCGTAGGCTCGGCTGTCC 61.139 66.667 2.95 0.00 0.00 4.02
779 803 2.102553 GTCGTAGGCTCGGCTGTC 59.897 66.667 2.95 0.00 32.43 3.51
780 804 3.812019 CGTCGTAGGCTCGGCTGT 61.812 66.667 2.95 0.00 33.02 4.40
781 805 4.554363 CCGTCGTAGGCTCGGCTG 62.554 72.222 2.95 0.00 37.90 4.85
808 832 3.817647 GGAGATGGTGTGGCAAATATCTC 59.182 47.826 19.05 19.05 39.66 2.75
823 847 1.475751 CGGAAAGGGATGTGGAGATGG 60.476 57.143 0.00 0.00 0.00 3.51
976 1000 4.736631 GCGTGCGGCGTTTCTTCC 62.737 66.667 9.37 0.00 43.66 3.46
1120 1144 3.624861 TCGTAGTCGTAATCTGAGGAACC 59.375 47.826 0.00 0.00 38.33 3.62
1137 1161 3.468770 TCTTCCTCTTCCTCGATCGTAG 58.531 50.000 15.94 10.89 0.00 3.51
1259 1307 0.957888 GAACCAAGGGAGCAGCAGAC 60.958 60.000 0.00 0.00 0.00 3.51
1279 1327 8.379331 TCATCTATCTGCTAGCTAGAACTAGAA 58.621 37.037 25.15 4.78 41.92 2.10
1280 1328 7.912719 TCATCTATCTGCTAGCTAGAACTAGA 58.087 38.462 25.15 18.77 41.92 2.43
1281 1329 8.737168 ATCATCTATCTGCTAGCTAGAACTAG 57.263 38.462 25.15 14.52 42.20 2.57
1282 1330 8.325046 TGATCATCTATCTGCTAGCTAGAACTA 58.675 37.037 25.15 3.11 35.45 2.24
1283 1331 7.121168 GTGATCATCTATCTGCTAGCTAGAACT 59.879 40.741 25.15 4.66 35.45 3.01
1284 1332 7.250569 GTGATCATCTATCTGCTAGCTAGAAC 58.749 42.308 25.15 8.16 35.45 3.01
1379 1456 7.388500 CAGATGGTGAACCTGCAAATTAAAAAT 59.612 33.333 0.37 0.00 36.82 1.82
1384 1461 4.661222 TCAGATGGTGAACCTGCAAATTA 58.339 39.130 0.37 0.00 36.82 1.40
1396 1473 4.026052 TGCACTTCTCTATCAGATGGTGA 58.974 43.478 0.00 0.00 37.38 4.02
1505 1582 4.527038 AGGAAGTAACTGATTTGAGACGGA 59.473 41.667 0.00 0.00 0.00 4.69
1519 1598 3.449018 TCCTGCTGATCAGAGGAAGTAAC 59.551 47.826 27.76 11.19 45.72 2.50
1545 1627 4.142578 ACTCAGCGTCAGTACAGATAAGTG 60.143 45.833 0.00 0.00 0.00 3.16
1547 1629 4.624336 ACTCAGCGTCAGTACAGATAAG 57.376 45.455 0.00 0.00 0.00 1.73
1584 1666 2.504996 CTCCTTCTCCAGCTCTTTCCAT 59.495 50.000 0.00 0.00 0.00 3.41
1681 1763 0.179089 CATTAGGAGCTGCTGTCGCT 60.179 55.000 19.25 0.00 41.15 4.93
1682 1764 0.179100 TCATTAGGAGCTGCTGTCGC 60.179 55.000 19.25 0.00 0.00 5.19
1683 1765 2.223900 TGATCATTAGGAGCTGCTGTCG 60.224 50.000 19.25 5.65 31.67 4.35
1702 1784 0.671472 CAGCACGCATCTCCTGTTGA 60.671 55.000 0.00 0.00 0.00 3.18
1732 1819 4.508662 GTTCTACTAAGTGCAGAATGGCT 58.491 43.478 0.00 0.00 35.86 4.75
1776 1863 1.810030 CGTTAGCTGACTTCCCGCC 60.810 63.158 7.09 0.00 0.00 6.13
1783 1870 1.442184 CGTGTCGCGTTAGCTGACT 60.442 57.895 5.77 0.00 42.74 3.41
1799 1886 1.740380 GCACCAGCACACATAGATCGT 60.740 52.381 0.00 0.00 41.58 3.73
1813 1900 2.679837 GTGATTCCTGTACATGCACCAG 59.320 50.000 0.00 0.00 0.00 4.00
1834 1957 1.394917 GCAACAGTACGAGATGGCTTG 59.605 52.381 0.00 0.00 0.00 4.01
1888 2021 1.422531 GAGAGCTGTGGGAGATGGAT 58.577 55.000 0.00 0.00 0.00 3.41
1892 2025 0.616111 AACCGAGAGCTGTGGGAGAT 60.616 55.000 19.17 1.61 0.00 2.75
1893 2026 1.228894 AACCGAGAGCTGTGGGAGA 60.229 57.895 19.17 0.00 0.00 3.71
1894 2027 1.216710 GAACCGAGAGCTGTGGGAG 59.783 63.158 19.17 0.00 0.00 4.30
1895 2028 1.533033 TGAACCGAGAGCTGTGGGA 60.533 57.895 19.17 0.00 0.00 4.37
1896 2029 1.079543 CTGAACCGAGAGCTGTGGG 60.080 63.158 10.58 10.58 0.00 4.61
1897 2030 0.389166 GTCTGAACCGAGAGCTGTGG 60.389 60.000 0.00 0.00 0.00 4.17
1899 2032 1.333177 AAGTCTGAACCGAGAGCTGT 58.667 50.000 0.00 0.00 0.00 4.40
1901 2034 2.365617 TGAAAAGTCTGAACCGAGAGCT 59.634 45.455 0.00 0.00 0.00 4.09
1902 2035 2.755650 TGAAAAGTCTGAACCGAGAGC 58.244 47.619 0.00 0.00 0.00 4.09
1903 2036 4.865365 GGTATGAAAAGTCTGAACCGAGAG 59.135 45.833 0.00 0.00 0.00 3.20
1904 2037 4.527038 AGGTATGAAAAGTCTGAACCGAGA 59.473 41.667 0.00 0.00 0.00 4.04
1905 2038 4.822026 AGGTATGAAAAGTCTGAACCGAG 58.178 43.478 0.00 0.00 0.00 4.63
1906 2039 4.527038 AGAGGTATGAAAAGTCTGAACCGA 59.473 41.667 0.00 0.00 0.00 4.69
1907 2040 4.627467 CAGAGGTATGAAAAGTCTGAACCG 59.373 45.833 0.00 0.00 37.43 4.44
1908 2041 5.409826 CACAGAGGTATGAAAAGTCTGAACC 59.590 44.000 4.72 0.00 38.41 3.62
1909 2042 5.409826 CCACAGAGGTATGAAAAGTCTGAAC 59.590 44.000 4.72 0.00 38.41 3.18
1910 2043 5.306937 TCCACAGAGGTATGAAAAGTCTGAA 59.693 40.000 4.72 0.00 38.41 3.02
1911 2044 4.838423 TCCACAGAGGTATGAAAAGTCTGA 59.162 41.667 4.72 0.00 38.41 3.27
1912 2045 5.047021 TCTCCACAGAGGTATGAAAAGTCTG 60.047 44.000 0.00 0.00 40.83 3.51
1913 2046 5.087323 TCTCCACAGAGGTATGAAAAGTCT 58.913 41.667 0.00 0.00 40.83 3.24
1914 2047 5.407407 TCTCCACAGAGGTATGAAAAGTC 57.593 43.478 0.00 0.00 40.83 3.01
1915 2048 6.380079 AATCTCCACAGAGGTATGAAAAGT 57.620 37.500 0.00 0.00 40.83 2.66
1916 2049 6.763610 GGTAATCTCCACAGAGGTATGAAAAG 59.236 42.308 0.00 0.00 40.83 2.27
1917 2050 6.443849 AGGTAATCTCCACAGAGGTATGAAAA 59.556 38.462 0.00 0.00 40.83 2.29
1918 2051 5.964477 AGGTAATCTCCACAGAGGTATGAAA 59.036 40.000 0.00 0.00 40.83 2.69
1919 2052 5.529289 AGGTAATCTCCACAGAGGTATGAA 58.471 41.667 0.00 0.00 40.83 2.57
1920 2053 5.144159 AGGTAATCTCCACAGAGGTATGA 57.856 43.478 0.00 0.00 40.83 2.15
1921 2054 5.048643 CGTAGGTAATCTCCACAGAGGTATG 60.049 48.000 0.00 0.00 40.83 2.39
1922 2055 5.071370 CGTAGGTAATCTCCACAGAGGTAT 58.929 45.833 0.00 0.00 40.83 2.73
1923 2056 4.458397 CGTAGGTAATCTCCACAGAGGTA 58.542 47.826 0.00 0.00 40.83 3.08
1924 2057 3.288964 CGTAGGTAATCTCCACAGAGGT 58.711 50.000 0.00 0.00 40.83 3.85
1925 2058 3.992260 CGTAGGTAATCTCCACAGAGG 57.008 52.381 0.00 0.00 40.83 3.69
1948 2081 1.337823 GGACGATTAGCACACAGTGGT 60.338 52.381 5.31 7.06 46.27 4.16
1975 2108 6.708054 CGGAGATCCAATTACAGAATAAAGCT 59.292 38.462 0.00 0.00 35.14 3.74
1978 2111 7.792032 AGACGGAGATCCAATTACAGAATAAA 58.208 34.615 0.00 0.00 35.14 1.40
1983 2116 4.956700 AGAAGACGGAGATCCAATTACAGA 59.043 41.667 0.00 0.00 35.14 3.41
1985 2118 4.956700 AGAGAAGACGGAGATCCAATTACA 59.043 41.667 0.00 0.00 35.14 2.41
1986 2119 5.523438 AGAGAAGACGGAGATCCAATTAC 57.477 43.478 0.00 0.00 35.14 1.89
1987 2120 6.381420 AGAAAGAGAAGACGGAGATCCAATTA 59.619 38.462 0.00 0.00 35.14 1.40
1988 2121 5.188751 AGAAAGAGAAGACGGAGATCCAATT 59.811 40.000 0.00 0.00 35.14 2.32
1989 2122 4.714308 AGAAAGAGAAGACGGAGATCCAAT 59.286 41.667 0.00 0.00 35.14 3.16
1990 2123 4.090090 AGAAAGAGAAGACGGAGATCCAA 58.910 43.478 0.00 0.00 35.14 3.53
1991 2124 3.702792 AGAAAGAGAAGACGGAGATCCA 58.297 45.455 0.00 0.00 35.14 3.41
1992 2125 5.584442 GTTAGAAAGAGAAGACGGAGATCC 58.416 45.833 0.00 0.00 0.00 3.36
1993 2126 5.064962 TCGTTAGAAAGAGAAGACGGAGATC 59.935 44.000 0.00 0.00 0.00 2.75
1995 2128 4.321718 TCGTTAGAAAGAGAAGACGGAGA 58.678 43.478 0.00 0.00 0.00 3.71
1996 2129 4.654015 CTCGTTAGAAAGAGAAGACGGAG 58.346 47.826 0.00 0.00 36.77 4.63
1997 2130 3.119919 GCTCGTTAGAAAGAGAAGACGGA 60.120 47.826 9.08 0.00 36.77 4.69
1999 2132 3.822996 TGCTCGTTAGAAAGAGAAGACG 58.177 45.455 9.08 0.00 36.77 4.18
2000 2133 6.526566 TTTTGCTCGTTAGAAAGAGAAGAC 57.473 37.500 9.08 0.00 36.77 3.01
2048 2210 4.212716 GGTTAGGGGAGAACAGTGTTTTT 58.787 43.478 10.45 1.65 0.00 1.94
2049 2211 3.203487 TGGTTAGGGGAGAACAGTGTTTT 59.797 43.478 10.45 3.99 0.00 2.43
2090 2252 2.328819 TTCCTTCGTTTTCCCGTGAA 57.671 45.000 0.00 0.00 0.00 3.18
2114 2276 3.296322 ACTTCTCGCTGAGCATATAGC 57.704 47.619 4.88 0.00 46.19 2.97
2135 2302 0.595567 GAGCACGTTCGTGTACACCA 60.596 55.000 20.11 4.56 38.31 4.17
2179 2346 2.281484 TGGCTTCAGCGACCCAAC 60.281 61.111 0.00 0.00 43.26 3.77
2190 2357 3.423154 CCGTTCCACGCTGGCTTC 61.423 66.667 0.00 0.00 40.91 3.86
2279 2446 3.948719 GGGTCCTTGTCCCGTGCA 61.949 66.667 0.00 0.00 35.27 4.57
2280 2447 4.717313 GGGGTCCTTGTCCCGTGC 62.717 72.222 0.00 0.00 45.46 5.34
2300 2472 5.006386 TCAAAATCAGAGGAAAGAAGAGGC 58.994 41.667 0.00 0.00 0.00 4.70
2421 2593 5.473504 AGCCACTACACAAAAGGATTAGTTG 59.526 40.000 0.00 0.00 0.00 3.16
2422 2594 5.473504 CAGCCACTACACAAAAGGATTAGTT 59.526 40.000 0.00 0.00 0.00 2.24
2423 2595 5.003804 CAGCCACTACACAAAAGGATTAGT 58.996 41.667 0.00 0.00 0.00 2.24
2424 2596 5.245531 TCAGCCACTACACAAAAGGATTAG 58.754 41.667 0.00 0.00 0.00 1.73
2425 2597 5.235850 TCAGCCACTACACAAAAGGATTA 57.764 39.130 0.00 0.00 0.00 1.75
2427 2599 3.788227 TCAGCCACTACACAAAAGGAT 57.212 42.857 0.00 0.00 0.00 3.24
2428 2600 3.788227 ATCAGCCACTACACAAAAGGA 57.212 42.857 0.00 0.00 0.00 3.36
2430 2602 7.336931 ACCTATTAATCAGCCACTACACAAAAG 59.663 37.037 0.00 0.00 0.00 2.27
2436 2642 4.408921 AGCACCTATTAATCAGCCACTACA 59.591 41.667 0.00 0.00 0.00 2.74
2441 2647 4.703897 GTGTAGCACCTATTAATCAGCCA 58.296 43.478 0.00 0.00 0.00 4.75
2545 2753 1.000145 GTCTAGGCGCTACACAAAGC 59.000 55.000 7.64 0.00 39.21 3.51
2547 2755 2.823924 TTGTCTAGGCGCTACACAAA 57.176 45.000 7.64 0.00 25.80 2.83
2550 2758 2.666994 GTCTTTTGTCTAGGCGCTACAC 59.333 50.000 7.64 0.00 0.00 2.90
2597 2805 4.835891 CTAGGGAGGACCGGCCGT 62.836 72.222 26.12 12.57 46.96 5.68
2605 2819 1.369855 GGGGACTAGGCTAGGGAGGA 61.370 65.000 24.57 0.00 0.00 3.71
2620 2834 2.930950 CTCTTGAAGTTTGTGTGGGGA 58.069 47.619 0.00 0.00 0.00 4.81
2633 2847 4.516698 GTCCTCTGTTCAAATGCTCTTGAA 59.483 41.667 9.00 9.00 41.80 2.69
2634 2848 4.067896 GTCCTCTGTTCAAATGCTCTTGA 58.932 43.478 0.00 0.00 33.48 3.02
2657 2871 0.736053 AGAGAGAATCGCGTCCAGAC 59.264 55.000 5.77 0.00 41.02 3.51
2658 2872 1.018148 GAGAGAGAATCGCGTCCAGA 58.982 55.000 5.77 0.00 41.02 3.86
2659 2873 1.002900 GAGAGAGAGAATCGCGTCCAG 60.003 57.143 5.77 0.00 41.02 3.86
2660 2874 1.018148 GAGAGAGAGAATCGCGTCCA 58.982 55.000 5.77 0.00 41.02 4.02
2661 2875 1.263217 GAGAGAGAGAGAATCGCGTCC 59.737 57.143 5.77 0.00 41.02 4.79
2662 2876 2.210116 AGAGAGAGAGAGAATCGCGTC 58.790 52.381 5.77 0.00 41.02 5.19
2663 2877 2.158957 AGAGAGAGAGAGAGAATCGCGT 60.159 50.000 5.77 0.00 41.02 6.01
2672 2886 8.877864 AATTTAAGAAGTGAGAGAGAGAGAGA 57.122 34.615 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.