Multiple sequence alignment - TraesCS4B01G216200

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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 TraesCS4B01G216200 chr4B 100.000 2439 0 0 1 2439 455978617 455981055 0.000000e+00 4505.0
1 TraesCS4B01G216200 chr4B 93.778 1977 92 15 1 1964 547410163 547408205 0.000000e+00 2940.0
2 TraesCS4B01G216200 chr4B 81.847 314 33 13 1654 1963 651058330 651058623 2.420000e-60 243.0
3 TraesCS4B01G216200 chr6B 93.273 1977 104 14 1 1964 22171382 22173342 0.000000e+00 2887.0
4 TraesCS4B01G216200 chr6B 90.628 1942 125 32 1 1929 114733763 114731866 0.000000e+00 2525.0
5 TraesCS4B01G216200 chr6B 91.824 477 33 6 1964 2439 337904816 337904345 0.000000e+00 660.0
6 TraesCS4B01G216200 chr6B 94.839 155 8 0 380 534 148307191 148307037 2.420000e-60 243.0
7 TraesCS4B01G216200 chr6B 84.211 95 7 4 1806 1899 247715819 247715732 4.320000e-13 86.1
8 TraesCS4B01G216200 chr2B 93.390 1528 72 13 449 1963 50247314 50248825 0.000000e+00 2235.0
9 TraesCS4B01G216200 chr2B 91.146 1073 73 10 525 1587 719584679 719583619 0.000000e+00 1435.0
10 TraesCS4B01G216200 chr2B 94.934 454 17 2 1 454 50224967 50225414 0.000000e+00 706.0
11 TraesCS4B01G216200 chr2B 91.807 476 35 4 1964 2439 186007585 186008056 0.000000e+00 660.0
12 TraesCS4B01G216200 chr2B 88.605 430 33 3 1152 1566 49187333 49187761 2.160000e-140 508.0
13 TraesCS4B01G216200 chr4D 90.331 1448 71 23 555 1963 46138719 46137302 0.000000e+00 1834.0
14 TraesCS4B01G216200 chr1A 88.904 1442 91 26 555 1963 570974071 570972666 0.000000e+00 1712.0
15 TraesCS4B01G216200 chr1A 88.853 1238 92 21 680 1876 145814545 145813313 0.000000e+00 1480.0
16 TraesCS4B01G216200 chr2D 90.340 1325 62 23 525 1810 582871454 582872751 0.000000e+00 1677.0
17 TraesCS4B01G216200 chr2D 85.736 666 45 19 1334 1963 29108227 29107576 0.000000e+00 658.0
18 TraesCS4B01G216200 chr2D 84.722 432 43 7 1063 1474 87980653 87980225 6.280000e-111 411.0
19 TraesCS4B01G216200 chr5D 91.096 1213 67 10 540 1715 13172561 13171353 0.000000e+00 1604.0
20 TraesCS4B01G216200 chr5D 89.095 486 25 1 7 492 13173019 13172562 1.630000e-161 579.0
21 TraesCS4B01G216200 chr5A 88.671 1324 96 15 680 1963 288890505 288891814 0.000000e+00 1565.0
22 TraesCS4B01G216200 chr3A 89.350 1277 83 19 718 1963 678042624 678041370 0.000000e+00 1555.0
23 TraesCS4B01G216200 chr3A 89.333 375 24 11 1592 1963 298800461 298800822 7.950000e-125 457.0
24 TraesCS4B01G216200 chr3A 93.431 137 7 2 380 515 678042762 678042627 4.110000e-48 202.0
25 TraesCS4B01G216200 chr3A 90.476 147 12 2 1836 1982 145003335 145003191 2.470000e-45 193.0
26 TraesCS4B01G216200 chr2A 88.620 1283 83 17 680 1923 188605911 188607169 0.000000e+00 1502.0
27 TraesCS4B01G216200 chr2A 85.370 581 71 5 906 1474 303672271 303672849 7.510000e-165 590.0
28 TraesCS4B01G216200 chr7A 91.532 1051 69 8 494 1527 56661014 56662061 0.000000e+00 1430.0
29 TraesCS4B01G216200 chr7A 90.762 1050 78 7 495 1527 56714778 56715825 0.000000e+00 1384.0
30 TraesCS4B01G216200 chr7A 86.562 320 26 11 1651 1965 708801197 708801504 1.080000e-88 337.0
31 TraesCS4B01G216200 chr7A 97.727 44 1 0 1 44 17844741 17844698 2.600000e-10 76.8
32 TraesCS4B01G216200 chr5B 89.957 926 60 13 1050 1963 571952646 571953550 0.000000e+00 1164.0
33 TraesCS4B01G216200 chr5B 91.232 479 33 8 1964 2439 158066510 158066038 0.000000e+00 643.0
34 TraesCS4B01G216200 chr5B 91.004 478 39 4 1964 2439 245769908 245769433 2.040000e-180 641.0
35 TraesCS4B01G216200 chr3D 86.441 1062 67 21 909 1933 596824864 596823843 0.000000e+00 1092.0
36 TraesCS4B01G216200 chr3D 86.095 338 28 12 1635 1968 453234640 453234318 1.800000e-91 346.0
37 TraesCS4B01G216200 chr3D 85.266 319 28 12 1650 1962 45265801 45266106 6.550000e-81 311.0
38 TraesCS4B01G216200 chr1B 82.969 869 66 31 1152 1963 663285815 663284972 0.000000e+00 710.0
39 TraesCS4B01G216200 chr1B 92.421 475 31 3 1964 2438 259617090 259616621 0.000000e+00 673.0
40 TraesCS4B01G216200 chr1B 91.304 138 12 0 1827 1964 335427628 335427765 3.200000e-44 189.0
41 TraesCS4B01G216200 chr1B 84.706 170 18 6 1803 1964 686258978 686258809 1.940000e-36 163.0
42 TraesCS4B01G216200 chr3B 91.423 478 38 2 1964 2439 98789559 98789083 0.000000e+00 652.0
43 TraesCS4B01G216200 chr3B 92.391 460 30 5 1964 2420 391308525 391308068 0.000000e+00 651.0
44 TraesCS4B01G216200 chr3B 91.314 472 35 6 1964 2432 512436783 512436315 7.350000e-180 640.0
45 TraesCS4B01G216200 chr7B 91.405 477 37 4 1964 2439 138802451 138801978 0.000000e+00 651.0
46 TraesCS4B01G216200 chr7B 85.075 335 39 9 1635 1964 591012245 591011917 5.030000e-87 331.0
47 TraesCS4B01G216200 chr6A 82.963 405 36 13 1592 1964 164498158 164498561 3.890000e-88 335.0
48 TraesCS4B01G216200 chr7D 95.041 121 6 0 375 495 11435373 11435253 8.900000e-45 191.0
49 TraesCS4B01G216200 chr4A 89.062 128 12 1 1 126 714434228 714434355 9.030000e-35 158.0
50 TraesCS4B01G216200 chr4A 84.375 96 9 3 1784 1876 669984387 669984479 3.340000e-14 89.8
51 TraesCS4B01G216200 chr6D 88.793 116 10 2 380 495 372614652 372614540 3.270000e-29 139.0


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 TraesCS4B01G216200 chr4B 455978617 455981055 2438 False 4505.0 4505 100.0000 1 2439 1 chr4B.!!$F1 2438
1 TraesCS4B01G216200 chr4B 547408205 547410163 1958 True 2940.0 2940 93.7780 1 1964 1 chr4B.!!$R1 1963
2 TraesCS4B01G216200 chr6B 22171382 22173342 1960 False 2887.0 2887 93.2730 1 1964 1 chr6B.!!$F1 1963
3 TraesCS4B01G216200 chr6B 114731866 114733763 1897 True 2525.0 2525 90.6280 1 1929 1 chr6B.!!$R1 1928
4 TraesCS4B01G216200 chr2B 50247314 50248825 1511 False 2235.0 2235 93.3900 449 1963 1 chr2B.!!$F3 1514
5 TraesCS4B01G216200 chr2B 719583619 719584679 1060 True 1435.0 1435 91.1460 525 1587 1 chr2B.!!$R1 1062
6 TraesCS4B01G216200 chr4D 46137302 46138719 1417 True 1834.0 1834 90.3310 555 1963 1 chr4D.!!$R1 1408
7 TraesCS4B01G216200 chr1A 570972666 570974071 1405 True 1712.0 1712 88.9040 555 1963 1 chr1A.!!$R2 1408
8 TraesCS4B01G216200 chr1A 145813313 145814545 1232 True 1480.0 1480 88.8530 680 1876 1 chr1A.!!$R1 1196
9 TraesCS4B01G216200 chr2D 582871454 582872751 1297 False 1677.0 1677 90.3400 525 1810 1 chr2D.!!$F1 1285
10 TraesCS4B01G216200 chr2D 29107576 29108227 651 True 658.0 658 85.7360 1334 1963 1 chr2D.!!$R1 629
11 TraesCS4B01G216200 chr5D 13171353 13173019 1666 True 1091.5 1604 90.0955 7 1715 2 chr5D.!!$R1 1708
12 TraesCS4B01G216200 chr5A 288890505 288891814 1309 False 1565.0 1565 88.6710 680 1963 1 chr5A.!!$F1 1283
13 TraesCS4B01G216200 chr3A 678041370 678042762 1392 True 878.5 1555 91.3905 380 1963 2 chr3A.!!$R2 1583
14 TraesCS4B01G216200 chr2A 188605911 188607169 1258 False 1502.0 1502 88.6200 680 1923 1 chr2A.!!$F1 1243
15 TraesCS4B01G216200 chr2A 303672271 303672849 578 False 590.0 590 85.3700 906 1474 1 chr2A.!!$F2 568
16 TraesCS4B01G216200 chr7A 56661014 56662061 1047 False 1430.0 1430 91.5320 494 1527 1 chr7A.!!$F1 1033
17 TraesCS4B01G216200 chr7A 56714778 56715825 1047 False 1384.0 1384 90.7620 495 1527 1 chr7A.!!$F2 1032
18 TraesCS4B01G216200 chr5B 571952646 571953550 904 False 1164.0 1164 89.9570 1050 1963 1 chr5B.!!$F1 913
19 TraesCS4B01G216200 chr3D 596823843 596824864 1021 True 1092.0 1092 86.4410 909 1933 1 chr3D.!!$R2 1024
20 TraesCS4B01G216200 chr1B 663284972 663285815 843 True 710.0 710 82.9690 1152 1963 1 chr1B.!!$R2 811

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
544 545 1.075374 TGCATCAAGGGGTTAAGCACT 59.925 47.619 2.89 2.89 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2436 0.036388 TCGCCGGCTTTCTTGATTCT 60.036 50.0 26.68 0.0 0.0 2.4 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
28 29 4.871933 TGCTGACAGAGTTTCACATCTA 57.128 40.909 6.65 0.00 0.00 1.98
98 99 2.798760 TACCCAGGAGCCCCACCAAT 62.799 60.000 0.00 0.00 33.88 3.16
126 127 6.568462 GCAGTAATTATTCATCCCATTGTCGG 60.568 42.308 0.00 0.00 0.00 4.79
271 272 8.259049 TCTAAAAATTTAGTGATGGTGGTACG 57.741 34.615 11.55 0.00 40.69 3.67
293 294 7.065120 ACGGAGTACAGAGTACAGAGTATAT 57.935 40.000 9.68 0.00 41.94 0.86
322 323 1.132643 GCAAAGCTCAGGCAGAATCAG 59.867 52.381 0.00 0.00 41.70 2.90
544 545 1.075374 TGCATCAAGGGGTTAAGCACT 59.925 47.619 2.89 2.89 0.00 4.40
616 617 9.661954 TCTGAGTATTTGGATCTTATCTAACCT 57.338 33.333 0.00 0.00 28.96 3.50
998 1011 2.839098 CTGCAGGGTTCTGGTGGT 59.161 61.111 5.57 0.00 41.19 4.16
1015 1028 0.946221 GGTGATGCCGATGATCGTCC 60.946 60.000 14.27 5.02 38.40 4.79
1420 1470 4.148825 GCCACGAGATCAGGCCGT 62.149 66.667 0.00 2.74 42.58 5.68
1444 1494 2.667318 CGCCACGCATTGACGAGTT 61.667 57.895 7.34 0.00 36.70 3.01
1485 1535 1.707117 CGTAACAACGTGTCTCAGTCG 59.293 52.381 0.00 0.00 0.00 4.18
1629 1732 7.167635 GTGATAGTAGATACGACAATTGTGTGG 59.832 40.741 17.58 7.55 38.41 4.17
1717 1822 8.745464 AAAAATAGCTCGCTACTAGTATTAGC 57.255 34.615 17.32 17.32 38.92 3.09
1738 1843 6.158023 AGCATACTAGTAGCGTTGGTATTT 57.842 37.500 8.85 0.00 0.00 1.40
1741 1846 6.645415 GCATACTAGTAGCGTTGGTATTTCAT 59.355 38.462 8.85 0.00 0.00 2.57
1792 1898 2.802816 CGCGGGTACGAATAGTAGTAGT 59.197 50.000 0.00 0.00 44.60 2.73
1818 1944 3.572584 GTTGCACACGCTACTACTAACT 58.427 45.455 0.00 0.00 40.25 2.24
1821 1947 5.571784 TGCACACGCTACTACTAACTATT 57.428 39.130 0.00 0.00 39.64 1.73
1822 1948 6.682423 TGCACACGCTACTACTAACTATTA 57.318 37.500 0.00 0.00 39.64 0.98
1823 1949 6.722301 TGCACACGCTACTACTAACTATTAG 58.278 40.000 0.00 0.00 39.64 1.73
1824 1950 5.624491 GCACACGCTACTACTAACTATTAGC 59.376 44.000 0.00 0.00 34.12 3.09
1825 1951 6.513066 GCACACGCTACTACTAACTATTAGCT 60.513 42.308 0.00 0.00 33.40 3.32
1826 1952 6.851837 CACACGCTACTACTAACTATTAGCTG 59.148 42.308 0.00 0.00 36.71 4.24
1827 1953 6.541641 ACACGCTACTACTAACTATTAGCTGT 59.458 38.462 0.00 0.00 36.71 4.40
1828 1954 7.712639 ACACGCTACTACTAACTATTAGCTGTA 59.287 37.037 0.00 0.00 36.71 2.74
1829 1955 8.222433 CACGCTACTACTAACTATTAGCTGTAG 58.778 40.741 16.26 16.26 40.86 2.74
1831 1957 7.235777 GCTACTACTAACTATTAGCTGTAGCG 58.764 42.308 22.86 10.15 46.05 4.26
1832 1958 8.092678 GCTACTACTAACTATTAGCTGTAGCGC 61.093 44.444 22.86 0.00 46.05 5.92
1964 2135 6.283544 AGTAGCCTTTTTCCTAGTAGTGTC 57.716 41.667 0.00 0.00 0.00 3.67
1965 2136 4.554960 AGCCTTTTTCCTAGTAGTGTCC 57.445 45.455 0.00 0.00 0.00 4.02
1966 2137 3.056035 AGCCTTTTTCCTAGTAGTGTCCG 60.056 47.826 0.00 0.00 0.00 4.79
1967 2138 3.306571 GCCTTTTTCCTAGTAGTGTCCGT 60.307 47.826 0.00 0.00 0.00 4.69
1968 2139 4.801914 GCCTTTTTCCTAGTAGTGTCCGTT 60.802 45.833 0.00 0.00 0.00 4.44
1969 2140 5.303165 CCTTTTTCCTAGTAGTGTCCGTTT 58.697 41.667 0.00 0.00 0.00 3.60
1970 2141 6.458210 CCTTTTTCCTAGTAGTGTCCGTTTA 58.542 40.000 0.00 0.00 0.00 2.01
1971 2142 6.367149 CCTTTTTCCTAGTAGTGTCCGTTTAC 59.633 42.308 0.00 0.00 0.00 2.01
1972 2143 6.655078 TTTTCCTAGTAGTGTCCGTTTACT 57.345 37.500 0.00 0.00 0.00 2.24
1973 2144 7.759489 TTTTCCTAGTAGTGTCCGTTTACTA 57.241 36.000 0.00 0.00 0.00 1.82
1974 2145 7.759489 TTTCCTAGTAGTGTCCGTTTACTAA 57.241 36.000 0.00 0.00 31.54 2.24
1975 2146 7.944729 TTCCTAGTAGTGTCCGTTTACTAAT 57.055 36.000 0.00 0.00 31.54 1.73
1976 2147 7.559590 TCCTAGTAGTGTCCGTTTACTAATC 57.440 40.000 0.00 0.00 31.54 1.75
1977 2148 7.341805 TCCTAGTAGTGTCCGTTTACTAATCT 58.658 38.462 0.00 0.00 31.54 2.40
1978 2149 7.281774 TCCTAGTAGTGTCCGTTTACTAATCTG 59.718 40.741 0.00 0.00 31.54 2.90
1979 2150 7.281774 CCTAGTAGTGTCCGTTTACTAATCTGA 59.718 40.741 0.00 0.00 31.54 3.27
1980 2151 7.458409 AGTAGTGTCCGTTTACTAATCTGAA 57.542 36.000 0.00 0.00 31.74 3.02
1981 2152 7.311408 AGTAGTGTCCGTTTACTAATCTGAAC 58.689 38.462 0.00 0.00 31.74 3.18
1982 2153 6.342338 AGTGTCCGTTTACTAATCTGAACT 57.658 37.500 0.00 0.00 0.00 3.01
1983 2154 7.458409 AGTGTCCGTTTACTAATCTGAACTA 57.542 36.000 0.00 0.00 0.00 2.24
1984 2155 7.889469 AGTGTCCGTTTACTAATCTGAACTAA 58.111 34.615 0.00 0.00 0.00 2.24
1985 2156 8.027771 AGTGTCCGTTTACTAATCTGAACTAAG 58.972 37.037 0.00 0.00 0.00 2.18
1986 2157 7.275123 GTGTCCGTTTACTAATCTGAACTAAGG 59.725 40.741 0.00 0.00 0.00 2.69
1987 2158 7.039504 TGTCCGTTTACTAATCTGAACTAAGGT 60.040 37.037 0.00 0.00 0.00 3.50
1988 2159 7.487509 GTCCGTTTACTAATCTGAACTAAGGTC 59.512 40.741 0.00 0.00 0.00 3.85
1989 2160 7.177216 TCCGTTTACTAATCTGAACTAAGGTCA 59.823 37.037 0.00 0.00 0.00 4.02
1990 2161 7.816031 CCGTTTACTAATCTGAACTAAGGTCAA 59.184 37.037 0.00 0.00 0.00 3.18
1991 2162 9.199982 CGTTTACTAATCTGAACTAAGGTCAAA 57.800 33.333 0.00 0.00 0.00 2.69
2000 2171 8.974060 TCTGAACTAAGGTCAAATTTTACAGT 57.026 30.769 4.96 0.00 0.00 3.55
2039 2210 8.990163 TTAAGTTGATTAAACAGAAAGAGGGT 57.010 30.769 0.00 0.00 41.61 4.34
2040 2211 7.511959 AAGTTGATTAAACAGAAAGAGGGTC 57.488 36.000 0.00 0.00 41.61 4.46
2041 2212 6.842676 AGTTGATTAAACAGAAAGAGGGTCT 58.157 36.000 0.00 0.00 41.61 3.85
2042 2213 7.290813 AGTTGATTAAACAGAAAGAGGGTCTT 58.709 34.615 0.00 0.00 41.61 3.01
2043 2214 7.229506 AGTTGATTAAACAGAAAGAGGGTCTTG 59.770 37.037 0.00 0.00 41.61 3.02
2044 2215 6.837312 TGATTAAACAGAAAGAGGGTCTTGA 58.163 36.000 0.00 0.00 36.71 3.02
2045 2216 6.936900 TGATTAAACAGAAAGAGGGTCTTGAG 59.063 38.462 0.00 0.00 36.71 3.02
2046 2217 6.494666 TTAAACAGAAAGAGGGTCTTGAGA 57.505 37.500 0.00 0.00 36.71 3.27
2047 2218 4.344359 AACAGAAAGAGGGTCTTGAGAC 57.656 45.455 2.51 2.51 44.04 3.36
2048 2219 2.297597 ACAGAAAGAGGGTCTTGAGACG 59.702 50.000 5.16 0.00 45.65 4.18
2049 2220 2.558795 CAGAAAGAGGGTCTTGAGACGA 59.441 50.000 5.16 0.00 45.65 4.20
2050 2221 3.005897 CAGAAAGAGGGTCTTGAGACGAA 59.994 47.826 5.16 0.00 45.65 3.85
2051 2222 3.641906 AGAAAGAGGGTCTTGAGACGAAA 59.358 43.478 5.16 0.00 45.65 3.46
2052 2223 3.388345 AAGAGGGTCTTGAGACGAAAC 57.612 47.619 5.16 0.00 45.65 2.78
2053 2224 2.599677 AGAGGGTCTTGAGACGAAACT 58.400 47.619 5.16 1.55 45.65 2.66
2054 2225 2.559231 AGAGGGTCTTGAGACGAAACTC 59.441 50.000 5.16 9.36 45.65 3.01
2055 2226 2.559231 GAGGGTCTTGAGACGAAACTCT 59.441 50.000 5.16 0.00 45.65 3.24
2056 2227 3.757493 GAGGGTCTTGAGACGAAACTCTA 59.243 47.826 5.16 0.00 45.65 2.43
2057 2228 3.759618 AGGGTCTTGAGACGAAACTCTAG 59.240 47.826 5.16 1.96 45.65 2.43
2058 2229 3.757493 GGGTCTTGAGACGAAACTCTAGA 59.243 47.826 14.19 14.19 45.65 2.43
2060 2231 4.665281 TCTTGAGACGAAACTCTAGACG 57.335 45.455 14.19 0.00 41.20 4.18
2061 2232 4.063689 TCTTGAGACGAAACTCTAGACGT 58.936 43.478 5.88 5.88 41.20 4.34
2062 2233 4.514441 TCTTGAGACGAAACTCTAGACGTT 59.486 41.667 7.46 4.99 41.20 3.99
2063 2234 4.825546 TGAGACGAAACTCTAGACGTTT 57.174 40.909 15.68 15.68 39.04 3.60
2064 2235 4.534168 TGAGACGAAACTCTAGACGTTTG 58.466 43.478 18.82 14.51 39.04 2.93
2065 2236 4.274214 TGAGACGAAACTCTAGACGTTTGA 59.726 41.667 18.82 3.10 39.04 2.69
2066 2237 5.179045 AGACGAAACTCTAGACGTTTGAA 57.821 39.130 18.82 0.00 39.04 2.69
2067 2238 5.770417 AGACGAAACTCTAGACGTTTGAAT 58.230 37.500 18.82 8.69 39.04 2.57
2068 2239 5.857517 AGACGAAACTCTAGACGTTTGAATC 59.142 40.000 18.82 14.14 39.04 2.52
2069 2240 5.526115 ACGAAACTCTAGACGTTTGAATCA 58.474 37.500 18.82 0.00 34.94 2.57
2070 2241 5.401674 ACGAAACTCTAGACGTTTGAATCAC 59.598 40.000 18.82 7.77 34.94 3.06
2071 2242 5.164080 CGAAACTCTAGACGTTTGAATCACC 60.164 44.000 18.82 7.29 34.94 4.02
2072 2243 5.470047 AACTCTAGACGTTTGAATCACCT 57.530 39.130 0.00 0.00 0.00 4.00
2073 2244 4.810790 ACTCTAGACGTTTGAATCACCTG 58.189 43.478 0.00 0.00 0.00 4.00
2074 2245 4.523173 ACTCTAGACGTTTGAATCACCTGA 59.477 41.667 0.00 0.00 0.00 3.86
2075 2246 5.186021 ACTCTAGACGTTTGAATCACCTGAT 59.814 40.000 0.00 0.00 36.07 2.90
2076 2247 6.037786 TCTAGACGTTTGAATCACCTGATT 57.962 37.500 0.00 0.00 46.54 2.57
2086 2257 2.933495 TCACCTGATTCCGACTAACG 57.067 50.000 0.00 0.00 42.18 3.18
2087 2258 2.439409 TCACCTGATTCCGACTAACGA 58.561 47.619 0.00 0.00 45.77 3.85
2088 2259 2.422479 TCACCTGATTCCGACTAACGAG 59.578 50.000 0.00 0.00 45.77 4.18
2089 2260 1.134560 ACCTGATTCCGACTAACGAGC 59.865 52.381 0.00 0.00 45.77 5.03
2090 2261 1.467875 CTGATTCCGACTAACGAGCG 58.532 55.000 0.00 0.00 45.77 5.03
2091 2262 1.063616 CTGATTCCGACTAACGAGCGA 59.936 52.381 0.00 0.00 45.77 4.93
2092 2263 1.469703 TGATTCCGACTAACGAGCGAA 59.530 47.619 0.00 0.00 45.77 4.70
2093 2264 2.095110 TGATTCCGACTAACGAGCGAAA 60.095 45.455 0.00 0.00 45.77 3.46
2094 2265 2.420628 TTCCGACTAACGAGCGAAAA 57.579 45.000 0.00 0.00 45.77 2.29
2095 2266 1.973138 TCCGACTAACGAGCGAAAAG 58.027 50.000 0.00 0.00 45.77 2.27
2096 2267 1.536766 TCCGACTAACGAGCGAAAAGA 59.463 47.619 0.00 0.00 45.77 2.52
2097 2268 2.163010 TCCGACTAACGAGCGAAAAGAT 59.837 45.455 0.00 0.00 45.77 2.40
2098 2269 3.374988 TCCGACTAACGAGCGAAAAGATA 59.625 43.478 0.00 0.00 45.77 1.98
2099 2270 4.100529 CCGACTAACGAGCGAAAAGATAA 58.899 43.478 0.00 0.00 45.77 1.75
2100 2271 4.560035 CCGACTAACGAGCGAAAAGATAAA 59.440 41.667 0.00 0.00 45.77 1.40
2101 2272 5.470244 CGACTAACGAGCGAAAAGATAAAC 58.530 41.667 0.00 0.00 45.77 2.01
2102 2273 5.060077 CGACTAACGAGCGAAAAGATAAACA 59.940 40.000 0.00 0.00 45.77 2.83
2103 2274 6.399249 CGACTAACGAGCGAAAAGATAAACAA 60.399 38.462 0.00 0.00 45.77 2.83
2104 2275 7.181143 ACTAACGAGCGAAAAGATAAACAAA 57.819 32.000 0.00 0.00 0.00 2.83
2105 2276 7.632721 ACTAACGAGCGAAAAGATAAACAAAA 58.367 30.769 0.00 0.00 0.00 2.44
2106 2277 8.124199 ACTAACGAGCGAAAAGATAAACAAAAA 58.876 29.630 0.00 0.00 0.00 1.94
2107 2278 6.727569 ACGAGCGAAAAGATAAACAAAAAC 57.272 33.333 0.00 0.00 0.00 2.43
2108 2279 6.492254 ACGAGCGAAAAGATAAACAAAAACT 58.508 32.000 0.00 0.00 0.00 2.66
2109 2280 7.632721 ACGAGCGAAAAGATAAACAAAAACTA 58.367 30.769 0.00 0.00 0.00 2.24
2110 2281 8.124199 ACGAGCGAAAAGATAAACAAAAACTAA 58.876 29.630 0.00 0.00 0.00 2.24
2111 2282 8.618952 CGAGCGAAAAGATAAACAAAAACTAAG 58.381 33.333 0.00 0.00 0.00 2.18
2112 2283 9.659830 GAGCGAAAAGATAAACAAAAACTAAGA 57.340 29.630 0.00 0.00 0.00 2.10
2120 2291 9.667107 AGATAAACAAAAACTAAGATCGGATCA 57.333 29.630 19.47 0.00 0.00 2.92
2121 2292 9.922305 GATAAACAAAAACTAAGATCGGATCAG 57.078 33.333 19.47 11.47 0.00 2.90
2122 2293 7.979444 AAACAAAAACTAAGATCGGATCAGA 57.021 32.000 19.47 0.00 0.00 3.27
2123 2294 7.979444 AACAAAAACTAAGATCGGATCAGAA 57.021 32.000 19.47 4.13 0.00 3.02
2124 2295 7.979444 ACAAAAACTAAGATCGGATCAGAAA 57.021 32.000 19.47 1.84 0.00 2.52
2125 2296 8.567285 ACAAAAACTAAGATCGGATCAGAAAT 57.433 30.769 19.47 0.89 0.00 2.17
2126 2297 8.669243 ACAAAAACTAAGATCGGATCAGAAATC 58.331 33.333 19.47 0.00 0.00 2.17
2127 2298 7.470289 AAAACTAAGATCGGATCAGAAATCG 57.530 36.000 19.47 3.96 0.00 3.34
2128 2299 4.551388 ACTAAGATCGGATCAGAAATCGC 58.449 43.478 19.47 0.00 0.00 4.58
2129 2300 2.057503 AGATCGGATCAGAAATCGCG 57.942 50.000 19.47 0.00 0.00 5.87
2130 2301 1.609072 AGATCGGATCAGAAATCGCGA 59.391 47.619 13.09 13.09 0.00 5.87
2131 2302 1.716581 GATCGGATCAGAAATCGCGAC 59.283 52.381 12.93 0.00 0.00 5.19
2132 2303 0.738975 TCGGATCAGAAATCGCGACT 59.261 50.000 12.93 0.00 0.00 4.18
2133 2304 0.848942 CGGATCAGAAATCGCGACTG 59.151 55.000 12.93 15.32 0.00 3.51
2134 2305 1.533965 CGGATCAGAAATCGCGACTGA 60.534 52.381 24.52 24.52 43.25 3.41
2135 2306 2.540515 GGATCAGAAATCGCGACTGAA 58.459 47.619 25.62 13.32 42.55 3.02
2136 2307 2.930040 GGATCAGAAATCGCGACTGAAA 59.070 45.455 25.62 9.75 42.55 2.69
2137 2308 3.370978 GGATCAGAAATCGCGACTGAAAA 59.629 43.478 25.62 9.14 42.55 2.29
2138 2309 4.034510 GGATCAGAAATCGCGACTGAAAAT 59.965 41.667 25.62 13.69 42.55 1.82
2139 2310 5.234329 GGATCAGAAATCGCGACTGAAAATA 59.766 40.000 25.62 8.52 42.55 1.40
2140 2311 6.238103 GGATCAGAAATCGCGACTGAAAATAA 60.238 38.462 25.62 7.91 42.55 1.40
2141 2312 6.662414 TCAGAAATCGCGACTGAAAATAAT 57.338 33.333 21.42 0.00 37.66 1.28
2142 2313 6.705782 TCAGAAATCGCGACTGAAAATAATC 58.294 36.000 21.42 0.00 37.66 1.75
2143 2314 5.613186 CAGAAATCGCGACTGAAAATAATCG 59.387 40.000 12.93 0.00 37.63 3.34
2153 2324 8.993852 CGACTGAAAATAATCGCAGATAAATT 57.006 30.769 0.00 0.00 45.12 1.82
2154 2325 9.096600 CGACTGAAAATAATCGCAGATAAATTC 57.903 33.333 0.00 0.00 45.12 2.17
2155 2326 8.993852 ACTGAAAATAATCGCAGATAAATTCG 57.006 30.769 0.00 0.00 45.12 3.34
2156 2327 8.826710 ACTGAAAATAATCGCAGATAAATTCGA 58.173 29.630 0.00 0.00 45.12 3.71
2157 2328 9.817365 CTGAAAATAATCGCAGATAAATTCGAT 57.183 29.630 0.00 0.00 45.12 3.59
2167 2338 9.485591 TCGCAGATAAATTCGATAAAAGAAAAC 57.514 29.630 0.00 0.00 0.00 2.43
2168 2339 9.490663 CGCAGATAAATTCGATAAAAGAAAACT 57.509 29.630 0.00 0.00 0.00 2.66
2175 2346 8.709496 AATTCGATAAAAGAAAACTGACGAAC 57.291 30.769 0.00 0.00 39.33 3.95
2176 2347 6.831727 TCGATAAAAGAAAACTGACGAACA 57.168 33.333 0.00 0.00 0.00 3.18
2188 2359 2.642995 TGACGAACAGACTAACGAACG 58.357 47.619 0.00 0.00 0.00 3.95
2189 2360 2.287644 TGACGAACAGACTAACGAACGA 59.712 45.455 0.14 0.00 0.00 3.85
2190 2361 2.901264 GACGAACAGACTAACGAACGAG 59.099 50.000 0.14 0.00 0.00 4.18
2191 2362 1.642843 CGAACAGACTAACGAACGAGC 59.357 52.381 0.14 0.00 0.00 5.03
2192 2363 1.642843 GAACAGACTAACGAACGAGCG 59.357 52.381 0.14 0.00 37.29 5.03
2208 2379 4.557276 CGAGCGTTCGTTATTTGTAACT 57.443 40.909 13.95 0.00 41.84 2.24
2209 2380 5.669535 CGAGCGTTCGTTATTTGTAACTA 57.330 39.130 13.95 0.00 41.84 2.24
2210 2381 6.069665 CGAGCGTTCGTTATTTGTAACTAA 57.930 37.500 13.95 0.00 41.84 2.24
2211 2382 5.942450 CGAGCGTTCGTTATTTGTAACTAAC 59.058 40.000 13.95 5.95 41.84 2.34
2214 2385 6.374707 CGTTCGTTATTTGTAACTAACGGA 57.625 37.500 20.73 13.05 46.20 4.69
2215 2386 6.806246 CGTTCGTTATTTGTAACTAACGGAA 58.194 36.000 20.73 13.18 46.20 4.30
2216 2387 6.944400 CGTTCGTTATTTGTAACTAACGGAAG 59.056 38.462 20.73 13.60 46.20 3.46
2217 2388 7.148983 CGTTCGTTATTTGTAACTAACGGAAGA 60.149 37.037 20.73 5.41 46.20 2.87
2218 2389 8.487176 GTTCGTTATTTGTAACTAACGGAAGAA 58.513 33.333 19.89 9.57 46.22 2.52
2219 2390 8.586570 TCGTTATTTGTAACTAACGGAAGAAA 57.413 30.769 19.89 4.63 46.22 2.52
2220 2391 9.039870 TCGTTATTTGTAACTAACGGAAGAAAA 57.960 29.630 19.89 4.11 46.22 2.29
2221 2392 9.095529 CGTTATTTGTAACTAACGGAAGAAAAC 57.904 33.333 15.26 0.00 43.87 2.43
2222 2393 9.385902 GTTATTTGTAACTAACGGAAGAAAACC 57.614 33.333 0.00 0.00 0.00 3.27
2230 2401 2.742954 CGGAAGAAAACCGTTCGTTT 57.257 45.000 0.00 0.00 46.92 3.60
2231 2402 3.857923 CGGAAGAAAACCGTTCGTTTA 57.142 42.857 0.00 0.00 44.09 2.01
2232 2403 4.194381 CGGAAGAAAACCGTTCGTTTAA 57.806 40.909 0.00 0.00 44.09 1.52
2233 2404 4.586334 CGGAAGAAAACCGTTCGTTTAAA 58.414 39.130 0.00 0.00 44.09 1.52
2234 2405 4.434266 CGGAAGAAAACCGTTCGTTTAAAC 59.566 41.667 8.35 8.35 44.09 2.01
2248 2419 4.027475 GTTTAAACGAACGTACGGACAG 57.973 45.455 21.06 10.20 37.61 3.51
2249 2420 3.617540 TTAAACGAACGTACGGACAGA 57.382 42.857 21.06 0.00 37.61 3.41
2250 2421 1.758783 AAACGAACGTACGGACAGAC 58.241 50.000 21.06 3.22 37.61 3.51
2251 2422 0.384725 AACGAACGTACGGACAGACG 60.385 55.000 21.06 16.07 44.57 4.18
2264 2435 3.687572 GACAGACGTCCGCTAATTAGA 57.312 47.619 16.85 0.00 36.02 2.10
2265 2436 4.025015 GACAGACGTCCGCTAATTAGAA 57.975 45.455 16.85 0.00 36.02 2.10
2266 2437 4.030134 ACAGACGTCCGCTAATTAGAAG 57.970 45.455 16.85 8.77 0.00 2.85
2267 2438 3.693085 ACAGACGTCCGCTAATTAGAAGA 59.307 43.478 16.85 8.54 0.00 2.87
2268 2439 4.157289 ACAGACGTCCGCTAATTAGAAGAA 59.843 41.667 16.85 0.00 0.00 2.52
2269 2440 5.163540 ACAGACGTCCGCTAATTAGAAGAAT 60.164 40.000 16.85 3.82 0.00 2.40
2270 2441 5.399892 CAGACGTCCGCTAATTAGAAGAATC 59.600 44.000 16.85 11.43 0.00 2.52
2271 2442 5.067413 AGACGTCCGCTAATTAGAAGAATCA 59.933 40.000 16.85 0.00 0.00 2.57
2272 2443 5.657474 ACGTCCGCTAATTAGAAGAATCAA 58.343 37.500 16.85 0.00 0.00 2.57
2273 2444 5.749109 ACGTCCGCTAATTAGAAGAATCAAG 59.251 40.000 16.85 4.69 0.00 3.02
2274 2445 5.977725 CGTCCGCTAATTAGAAGAATCAAGA 59.022 40.000 16.85 0.00 0.00 3.02
2275 2446 6.475727 CGTCCGCTAATTAGAAGAATCAAGAA 59.524 38.462 16.85 0.00 0.00 2.52
2276 2447 7.010183 CGTCCGCTAATTAGAAGAATCAAGAAA 59.990 37.037 16.85 0.00 0.00 2.52
2277 2448 8.331742 GTCCGCTAATTAGAAGAATCAAGAAAG 58.668 37.037 16.85 0.00 0.00 2.62
2278 2449 7.011482 TCCGCTAATTAGAAGAATCAAGAAAGC 59.989 37.037 16.85 0.00 0.00 3.51
2279 2450 7.128976 CGCTAATTAGAAGAATCAAGAAAGCC 58.871 38.462 16.85 0.00 0.00 4.35
2280 2451 7.128976 GCTAATTAGAAGAATCAAGAAAGCCG 58.871 38.462 16.85 0.00 0.00 5.52
2281 2452 6.442513 AATTAGAAGAATCAAGAAAGCCGG 57.557 37.500 0.00 0.00 0.00 6.13
2282 2453 2.087646 AGAAGAATCAAGAAAGCCGGC 58.912 47.619 21.89 21.89 0.00 6.13
2283 2454 0.804989 AAGAATCAAGAAAGCCGGCG 59.195 50.000 23.20 5.45 0.00 6.46
2284 2455 0.036388 AGAATCAAGAAAGCCGGCGA 60.036 50.000 23.20 11.77 0.00 5.54
2285 2456 0.802494 GAATCAAGAAAGCCGGCGAA 59.198 50.000 23.20 2.66 0.00 4.70
2286 2457 1.199097 GAATCAAGAAAGCCGGCGAAA 59.801 47.619 23.20 3.84 0.00 3.46
2287 2458 0.521735 ATCAAGAAAGCCGGCGAAAC 59.478 50.000 23.20 14.01 0.00 2.78
2288 2459 1.440353 CAAGAAAGCCGGCGAAACG 60.440 57.895 23.20 5.53 0.00 3.60
2289 2460 1.595929 AAGAAAGCCGGCGAAACGA 60.596 52.632 23.20 0.00 35.47 3.85
2290 2461 0.953960 AAGAAAGCCGGCGAAACGAT 60.954 50.000 23.20 0.00 35.47 3.73
2291 2462 1.060465 GAAAGCCGGCGAAACGATC 59.940 57.895 23.20 8.95 35.47 3.69
2292 2463 1.359459 GAAAGCCGGCGAAACGATCT 61.359 55.000 23.20 0.00 35.47 2.75
2293 2464 0.108520 AAAGCCGGCGAAACGATCTA 60.109 50.000 23.20 0.00 35.47 1.98
2294 2465 0.108520 AAGCCGGCGAAACGATCTAA 60.109 50.000 23.20 0.00 35.47 2.10
2295 2466 0.108520 AGCCGGCGAAACGATCTAAA 60.109 50.000 23.20 0.00 35.47 1.85
2296 2467 0.722848 GCCGGCGAAACGATCTAAAA 59.277 50.000 12.58 0.00 35.47 1.52
2297 2468 1.129064 GCCGGCGAAACGATCTAAAAA 59.871 47.619 12.58 0.00 35.47 1.94
2387 2558 3.775654 CTCCGGTGAGGTGGCTCC 61.776 72.222 0.00 0.00 41.99 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.407202 AGCACTATCTTATTTCGACAACCTT 58.593 36.000 0.00 0.00 0.00 3.50
98 99 7.062322 ACAATGGGATGAATAATTACTGCAGA 58.938 34.615 23.35 0.00 0.00 4.26
126 127 2.733956 TGGGTCCCATCTTGTAATTGC 58.266 47.619 6.47 0.00 0.00 3.56
271 272 9.206870 GTGTATATACTCTGTACTCTGTACTCC 57.793 40.741 13.89 0.00 0.00 3.85
293 294 2.153645 CCTGAGCTTTGCACATGTGTA 58.846 47.619 26.01 20.04 0.00 2.90
322 323 1.997874 ATCTCCCAGTCCCAGCCAC 60.998 63.158 0.00 0.00 0.00 5.01
421 422 1.257750 ACGGGCTACATCACTGCTCA 61.258 55.000 0.00 0.00 0.00 4.26
544 545 5.824097 GGAACTGTAGAAACCCAAAACTACA 59.176 40.000 0.00 0.00 41.47 2.74
616 617 5.645067 CCAACACATCTAAATCTCAGAGCAA 59.355 40.000 0.00 0.00 0.00 3.91
1015 1028 0.038159 GTCCAGTCCACGAACCTCTG 60.038 60.000 0.00 0.00 0.00 3.35
1466 1516 2.971915 CTCGACTGAGACACGTTGTTAC 59.028 50.000 0.00 0.00 45.57 2.50
1535 1594 1.872952 GTGTTGTGCATGTCAGCTACA 59.127 47.619 0.00 0.00 43.86 2.74
1590 1692 7.904558 ATCTACTATCACAGTTCCTCATTGA 57.095 36.000 0.00 0.00 38.80 2.57
1665 1769 7.941238 TCCCACGCTACTACTAACTTATTAGAT 59.059 37.037 1.17 0.00 40.38 1.98
1717 1822 9.125906 GTATGAAATACCAACGCTACTAGTATG 57.874 37.037 2.33 1.99 44.02 2.39
1738 1843 6.609237 ACGAAATAGTAGTAGCGTGTATGA 57.391 37.500 0.00 0.00 0.00 2.15
1741 1846 7.539712 ACTAACGAAATAGTAGTAGCGTGTA 57.460 36.000 0.00 0.00 34.40 2.90
1818 1944 4.934001 ACTAGTATCGCGCTACAGCTAATA 59.066 41.667 20.91 4.04 39.32 0.98
1821 1947 2.763933 ACTAGTATCGCGCTACAGCTA 58.236 47.619 20.91 5.34 39.32 3.32
1822 1948 1.595466 ACTAGTATCGCGCTACAGCT 58.405 50.000 20.91 4.45 39.32 4.24
1823 1949 2.725452 GCTACTAGTATCGCGCTACAGC 60.725 54.545 20.91 16.31 37.78 4.40
1824 1950 2.472560 CGCTACTAGTATCGCGCTACAG 60.473 54.545 20.91 16.91 39.11 2.74
1825 1951 1.458445 CGCTACTAGTATCGCGCTACA 59.542 52.381 20.91 7.33 39.11 2.74
1826 1952 2.142191 CGCTACTAGTATCGCGCTAC 57.858 55.000 19.57 12.01 39.11 3.58
1831 1957 1.154263 CCCGCGCTACTAGTATCGC 60.154 63.158 31.26 31.26 44.30 4.58
1832 1958 0.590195 AACCCGCGCTACTAGTATCG 59.410 55.000 19.22 19.22 0.00 2.92
1833 1959 2.789491 AAACCCGCGCTACTAGTATC 57.211 50.000 5.56 0.00 0.00 2.24
1834 1960 3.243535 GGTTAAACCCGCGCTACTAGTAT 60.244 47.826 5.56 0.00 30.04 2.12
1837 1963 1.564207 GGTTAAACCCGCGCTACTAG 58.436 55.000 5.56 0.00 30.04 2.57
1964 2135 7.318141 TGACCTTAGTTCAGATTAGTAAACGG 58.682 38.462 0.00 0.00 0.00 4.44
1965 2136 8.752766 TTGACCTTAGTTCAGATTAGTAAACG 57.247 34.615 0.00 0.00 0.00 3.60
1974 2145 9.574516 ACTGTAAAATTTGACCTTAGTTCAGAT 57.425 29.630 3.10 0.00 0.00 2.90
1975 2146 8.974060 ACTGTAAAATTTGACCTTAGTTCAGA 57.026 30.769 3.10 0.00 0.00 3.27
2013 2184 9.416284 ACCCTCTTTCTGTTTAATCAACTTAAA 57.584 29.630 0.00 0.00 37.05 1.52
2014 2185 8.990163 ACCCTCTTTCTGTTTAATCAACTTAA 57.010 30.769 0.00 0.00 36.21 1.85
2015 2186 8.437575 AGACCCTCTTTCTGTTTAATCAACTTA 58.562 33.333 0.00 0.00 36.21 2.24
2016 2187 7.290813 AGACCCTCTTTCTGTTTAATCAACTT 58.709 34.615 0.00 0.00 36.21 2.66
2017 2188 6.842676 AGACCCTCTTTCTGTTTAATCAACT 58.157 36.000 0.00 0.00 36.21 3.16
2018 2189 7.228706 TCAAGACCCTCTTTCTGTTTAATCAAC 59.771 37.037 0.00 0.00 33.78 3.18
2019 2190 7.287061 TCAAGACCCTCTTTCTGTTTAATCAA 58.713 34.615 0.00 0.00 33.78 2.57
2020 2191 6.837312 TCAAGACCCTCTTTCTGTTTAATCA 58.163 36.000 0.00 0.00 33.78 2.57
2021 2192 7.118535 GTCTCAAGACCCTCTTTCTGTTTAATC 59.881 40.741 0.00 0.00 39.07 1.75
2022 2193 6.937465 GTCTCAAGACCCTCTTTCTGTTTAAT 59.063 38.462 0.00 0.00 39.07 1.40
2023 2194 6.289064 GTCTCAAGACCCTCTTTCTGTTTAA 58.711 40.000 0.00 0.00 39.07 1.52
2024 2195 5.509163 CGTCTCAAGACCCTCTTTCTGTTTA 60.509 44.000 4.63 0.00 41.86 2.01
2025 2196 4.709250 GTCTCAAGACCCTCTTTCTGTTT 58.291 43.478 0.00 0.00 39.07 2.83
2026 2197 3.243907 CGTCTCAAGACCCTCTTTCTGTT 60.244 47.826 4.63 0.00 41.86 3.16
2027 2198 2.297597 CGTCTCAAGACCCTCTTTCTGT 59.702 50.000 4.63 0.00 41.86 3.41
2028 2199 2.558795 TCGTCTCAAGACCCTCTTTCTG 59.441 50.000 4.63 0.00 41.86 3.02
2029 2200 2.877866 TCGTCTCAAGACCCTCTTTCT 58.122 47.619 4.63 0.00 41.86 2.52
2030 2201 3.662247 TTCGTCTCAAGACCCTCTTTC 57.338 47.619 4.63 0.00 41.86 2.62
2031 2202 3.388350 AGTTTCGTCTCAAGACCCTCTTT 59.612 43.478 4.63 0.00 41.86 2.52
2032 2203 2.966516 AGTTTCGTCTCAAGACCCTCTT 59.033 45.455 4.63 0.00 41.86 2.85
2033 2204 2.559231 GAGTTTCGTCTCAAGACCCTCT 59.441 50.000 4.63 0.00 41.86 3.69
2034 2205 2.559231 AGAGTTTCGTCTCAAGACCCTC 59.441 50.000 4.63 5.47 41.86 4.30
2035 2206 2.599677 AGAGTTTCGTCTCAAGACCCT 58.400 47.619 4.63 0.00 41.86 4.34
2036 2207 3.757493 TCTAGAGTTTCGTCTCAAGACCC 59.243 47.826 4.63 0.00 41.86 4.46
2037 2208 4.669708 CGTCTAGAGTTTCGTCTCAAGACC 60.670 50.000 4.63 0.00 41.86 3.85
2038 2209 4.083908 ACGTCTAGAGTTTCGTCTCAAGAC 60.084 45.833 0.00 0.00 41.47 3.01
2039 2210 4.063689 ACGTCTAGAGTTTCGTCTCAAGA 58.936 43.478 0.00 0.00 36.97 3.02
2040 2211 4.407496 ACGTCTAGAGTTTCGTCTCAAG 57.593 45.455 0.00 0.00 36.97 3.02
2041 2212 4.825546 AACGTCTAGAGTTTCGTCTCAA 57.174 40.909 6.59 0.00 36.97 3.02
2042 2213 4.274214 TCAAACGTCTAGAGTTTCGTCTCA 59.726 41.667 13.88 0.00 39.50 3.27
2043 2214 4.781071 TCAAACGTCTAGAGTTTCGTCTC 58.219 43.478 13.88 0.00 39.50 3.36
2044 2215 4.825546 TCAAACGTCTAGAGTTTCGTCT 57.174 40.909 13.88 0.00 39.50 4.18
2045 2216 5.628193 TGATTCAAACGTCTAGAGTTTCGTC 59.372 40.000 13.88 12.51 39.50 4.20
2046 2217 5.401674 GTGATTCAAACGTCTAGAGTTTCGT 59.598 40.000 13.88 8.36 39.50 3.85
2047 2218 5.164080 GGTGATTCAAACGTCTAGAGTTTCG 60.164 44.000 13.88 7.81 39.50 3.46
2048 2219 5.927115 AGGTGATTCAAACGTCTAGAGTTTC 59.073 40.000 13.88 7.15 39.50 2.78
2049 2220 5.696724 CAGGTGATTCAAACGTCTAGAGTTT 59.303 40.000 11.99 11.99 41.90 2.66
2050 2221 5.010719 TCAGGTGATTCAAACGTCTAGAGTT 59.989 40.000 0.00 0.00 0.00 3.01
2051 2222 4.523173 TCAGGTGATTCAAACGTCTAGAGT 59.477 41.667 0.00 0.00 0.00 3.24
2052 2223 5.060662 TCAGGTGATTCAAACGTCTAGAG 57.939 43.478 0.00 0.00 0.00 2.43
2053 2224 5.661056 ATCAGGTGATTCAAACGTCTAGA 57.339 39.130 0.00 0.00 0.00 2.43
2065 2236 3.446161 TCGTTAGTCGGAATCAGGTGATT 59.554 43.478 4.86 4.86 41.62 2.57
2066 2237 3.021695 TCGTTAGTCGGAATCAGGTGAT 58.978 45.455 0.00 0.00 40.32 3.06
2067 2238 2.422479 CTCGTTAGTCGGAATCAGGTGA 59.578 50.000 0.00 0.00 40.32 4.02
2068 2239 2.798680 CTCGTTAGTCGGAATCAGGTG 58.201 52.381 0.00 0.00 40.32 4.00
2069 2240 1.134560 GCTCGTTAGTCGGAATCAGGT 59.865 52.381 0.00 0.00 40.32 4.00
2070 2241 1.841450 GCTCGTTAGTCGGAATCAGG 58.159 55.000 0.00 0.00 40.32 3.86
2071 2242 1.063616 TCGCTCGTTAGTCGGAATCAG 59.936 52.381 0.00 0.00 40.32 2.90
2072 2243 1.089112 TCGCTCGTTAGTCGGAATCA 58.911 50.000 0.00 0.00 40.32 2.57
2073 2244 2.184385 TTCGCTCGTTAGTCGGAATC 57.816 50.000 0.00 0.00 40.32 2.52
2074 2245 2.642139 TTTCGCTCGTTAGTCGGAAT 57.358 45.000 0.00 0.00 40.32 3.01
2075 2246 2.030893 TCTTTTCGCTCGTTAGTCGGAA 60.031 45.455 0.00 0.00 40.32 4.30
2076 2247 1.536766 TCTTTTCGCTCGTTAGTCGGA 59.463 47.619 0.00 0.00 40.32 4.55
2077 2248 1.973138 TCTTTTCGCTCGTTAGTCGG 58.027 50.000 0.00 0.00 40.32 4.79
2078 2249 5.060077 TGTTTATCTTTTCGCTCGTTAGTCG 59.940 40.000 0.00 0.00 41.41 4.18
2079 2250 6.385537 TGTTTATCTTTTCGCTCGTTAGTC 57.614 37.500 0.00 0.00 0.00 2.59
2080 2251 6.774354 TTGTTTATCTTTTCGCTCGTTAGT 57.226 33.333 0.00 0.00 0.00 2.24
2081 2252 8.407458 GTTTTTGTTTATCTTTTCGCTCGTTAG 58.593 33.333 0.00 0.00 0.00 2.34
2082 2253 8.124199 AGTTTTTGTTTATCTTTTCGCTCGTTA 58.876 29.630 0.00 0.00 0.00 3.18
2083 2254 6.970613 AGTTTTTGTTTATCTTTTCGCTCGTT 59.029 30.769 0.00 0.00 0.00 3.85
2084 2255 6.492254 AGTTTTTGTTTATCTTTTCGCTCGT 58.508 32.000 0.00 0.00 0.00 4.18
2085 2256 6.969669 AGTTTTTGTTTATCTTTTCGCTCG 57.030 33.333 0.00 0.00 0.00 5.03
2086 2257 9.659830 TCTTAGTTTTTGTTTATCTTTTCGCTC 57.340 29.630 0.00 0.00 0.00 5.03
2094 2265 9.667107 TGATCCGATCTTAGTTTTTGTTTATCT 57.333 29.630 9.78 0.00 0.00 1.98
2095 2266 9.922305 CTGATCCGATCTTAGTTTTTGTTTATC 57.078 33.333 9.78 0.00 0.00 1.75
2096 2267 9.667107 TCTGATCCGATCTTAGTTTTTGTTTAT 57.333 29.630 9.78 0.00 0.00 1.40
2097 2268 9.496873 TTCTGATCCGATCTTAGTTTTTGTTTA 57.503 29.630 9.78 0.00 0.00 2.01
2098 2269 7.979444 TCTGATCCGATCTTAGTTTTTGTTT 57.021 32.000 9.78 0.00 0.00 2.83
2099 2270 7.979444 TTCTGATCCGATCTTAGTTTTTGTT 57.021 32.000 9.78 0.00 0.00 2.83
2100 2271 7.979444 TTTCTGATCCGATCTTAGTTTTTGT 57.021 32.000 9.78 0.00 0.00 2.83
2101 2272 7.848051 CGATTTCTGATCCGATCTTAGTTTTTG 59.152 37.037 9.78 0.00 0.00 2.44
2102 2273 7.466050 GCGATTTCTGATCCGATCTTAGTTTTT 60.466 37.037 9.78 0.00 0.00 1.94
2103 2274 6.018669 GCGATTTCTGATCCGATCTTAGTTTT 60.019 38.462 9.78 0.00 0.00 2.43
2104 2275 5.463724 GCGATTTCTGATCCGATCTTAGTTT 59.536 40.000 9.78 0.00 0.00 2.66
2105 2276 4.985409 GCGATTTCTGATCCGATCTTAGTT 59.015 41.667 9.78 0.00 0.00 2.24
2106 2277 4.551388 GCGATTTCTGATCCGATCTTAGT 58.449 43.478 9.78 0.00 0.00 2.24
2107 2278 3.605916 CGCGATTTCTGATCCGATCTTAG 59.394 47.826 0.00 0.18 0.00 2.18
2108 2279 3.252458 TCGCGATTTCTGATCCGATCTTA 59.748 43.478 3.71 0.00 0.00 2.10
2109 2280 2.034685 TCGCGATTTCTGATCCGATCTT 59.965 45.455 3.71 0.00 0.00 2.40
2110 2281 1.609072 TCGCGATTTCTGATCCGATCT 59.391 47.619 3.71 0.00 0.00 2.75
2111 2282 1.716581 GTCGCGATTTCTGATCCGATC 59.283 52.381 14.06 1.01 0.00 3.69
2112 2283 1.338337 AGTCGCGATTTCTGATCCGAT 59.662 47.619 14.06 0.00 0.00 4.18
2113 2284 0.738975 AGTCGCGATTTCTGATCCGA 59.261 50.000 14.06 0.00 0.00 4.55
2114 2285 0.848942 CAGTCGCGATTTCTGATCCG 59.151 55.000 14.06 0.00 0.00 4.18
2115 2286 2.209838 TCAGTCGCGATTTCTGATCC 57.790 50.000 20.24 1.92 34.00 3.36
2116 2287 4.584029 TTTTCAGTCGCGATTTCTGATC 57.416 40.909 23.41 5.00 37.91 2.92
2117 2288 6.662414 TTATTTTCAGTCGCGATTTCTGAT 57.338 33.333 23.41 14.16 37.91 2.90
2118 2289 6.507929 CGATTATTTTCAGTCGCGATTTCTGA 60.508 38.462 20.24 20.24 36.59 3.27
2119 2290 5.613186 CGATTATTTTCAGTCGCGATTTCTG 59.387 40.000 14.06 15.69 0.00 3.02
2120 2291 5.728255 CGATTATTTTCAGTCGCGATTTCT 58.272 37.500 14.06 0.86 0.00 2.52
2128 2299 8.993852 AATTTATCTGCGATTATTTTCAGTCG 57.006 30.769 0.00 0.00 37.17 4.18
2129 2300 9.096600 CGAATTTATCTGCGATTATTTTCAGTC 57.903 33.333 0.00 0.00 0.00 3.51
2130 2301 8.826710 TCGAATTTATCTGCGATTATTTTCAGT 58.173 29.630 0.00 0.00 0.00 3.41
2131 2302 9.817365 ATCGAATTTATCTGCGATTATTTTCAG 57.183 29.630 0.00 0.00 40.18 3.02
2141 2312 9.485591 GTTTTCTTTTATCGAATTTATCTGCGA 57.514 29.630 0.00 0.00 37.17 5.10
2142 2313 9.490663 AGTTTTCTTTTATCGAATTTATCTGCG 57.509 29.630 0.00 0.00 0.00 5.18
2149 2320 9.166126 GTTCGTCAGTTTTCTTTTATCGAATTT 57.834 29.630 0.00 0.00 37.19 1.82
2150 2321 8.339714 TGTTCGTCAGTTTTCTTTTATCGAATT 58.660 29.630 0.00 0.00 37.19 2.17
2151 2322 7.857569 TGTTCGTCAGTTTTCTTTTATCGAAT 58.142 30.769 0.00 0.00 37.19 3.34
2152 2323 7.223193 TCTGTTCGTCAGTTTTCTTTTATCGAA 59.777 33.333 0.00 0.00 43.97 3.71
2153 2324 6.698329 TCTGTTCGTCAGTTTTCTTTTATCGA 59.302 34.615 9.34 0.00 43.97 3.59
2154 2325 6.786103 GTCTGTTCGTCAGTTTTCTTTTATCG 59.214 38.462 9.34 0.00 43.97 2.92
2155 2326 7.852516 AGTCTGTTCGTCAGTTTTCTTTTATC 58.147 34.615 9.34 0.00 43.97 1.75
2156 2327 7.787725 AGTCTGTTCGTCAGTTTTCTTTTAT 57.212 32.000 9.34 0.00 43.97 1.40
2157 2328 8.598075 GTTAGTCTGTTCGTCAGTTTTCTTTTA 58.402 33.333 9.34 0.00 43.97 1.52
2158 2329 7.461918 GTTAGTCTGTTCGTCAGTTTTCTTTT 58.538 34.615 9.34 0.00 43.97 2.27
2159 2330 6.237755 CGTTAGTCTGTTCGTCAGTTTTCTTT 60.238 38.462 9.34 0.00 43.97 2.52
2160 2331 5.231568 CGTTAGTCTGTTCGTCAGTTTTCTT 59.768 40.000 9.34 0.00 43.97 2.52
2161 2332 4.738740 CGTTAGTCTGTTCGTCAGTTTTCT 59.261 41.667 9.34 7.35 43.97 2.52
2162 2333 4.736793 TCGTTAGTCTGTTCGTCAGTTTTC 59.263 41.667 9.34 2.22 43.97 2.29
2163 2334 4.675510 TCGTTAGTCTGTTCGTCAGTTTT 58.324 39.130 9.34 1.99 43.97 2.43
2164 2335 4.297299 TCGTTAGTCTGTTCGTCAGTTT 57.703 40.909 9.34 3.78 43.97 2.66
2165 2336 3.976793 TCGTTAGTCTGTTCGTCAGTT 57.023 42.857 9.34 4.04 43.97 3.16
2166 2337 3.625938 GTTCGTTAGTCTGTTCGTCAGT 58.374 45.455 9.34 0.00 43.97 3.41
2167 2338 2.650765 CGTTCGTTAGTCTGTTCGTCAG 59.349 50.000 4.52 4.52 44.85 3.51
2168 2339 2.287644 TCGTTCGTTAGTCTGTTCGTCA 59.712 45.455 0.00 0.00 0.00 4.35
2169 2340 2.901264 CTCGTTCGTTAGTCTGTTCGTC 59.099 50.000 0.00 0.00 0.00 4.20
2170 2341 2.913613 CTCGTTCGTTAGTCTGTTCGT 58.086 47.619 0.00 0.00 0.00 3.85
2171 2342 1.642843 GCTCGTTCGTTAGTCTGTTCG 59.357 52.381 0.00 0.00 0.00 3.95
2172 2343 1.642843 CGCTCGTTCGTTAGTCTGTTC 59.357 52.381 0.00 0.00 0.00 3.18
2173 2344 1.002033 ACGCTCGTTCGTTAGTCTGTT 60.002 47.619 0.00 0.00 40.07 3.16
2174 2345 0.590195 ACGCTCGTTCGTTAGTCTGT 59.410 50.000 0.00 0.00 40.07 3.41
2175 2346 3.379682 ACGCTCGTTCGTTAGTCTG 57.620 52.632 0.00 0.00 40.07 3.51
2196 2367 9.385902 GGTTTTCTTCCGTTAGTTACAAATAAC 57.614 33.333 2.95 2.95 41.00 1.89
2197 2368 8.281893 CGGTTTTCTTCCGTTAGTTACAAATAA 58.718 33.333 0.00 0.00 42.62 1.40
2198 2369 7.795859 CGGTTTTCTTCCGTTAGTTACAAATA 58.204 34.615 0.00 0.00 42.62 1.40
2199 2370 6.661669 CGGTTTTCTTCCGTTAGTTACAAAT 58.338 36.000 0.00 0.00 42.62 2.32
2200 2371 6.046885 CGGTTTTCTTCCGTTAGTTACAAA 57.953 37.500 0.00 0.00 42.62 2.83
2201 2372 5.655893 CGGTTTTCTTCCGTTAGTTACAA 57.344 39.130 0.00 0.00 42.62 2.41
2211 2382 2.742954 AAACGAACGGTTTTCTTCCG 57.257 45.000 0.00 2.77 46.52 4.30
2212 2383 5.854835 GTTTAAACGAACGGTTTTCTTCC 57.145 39.130 1.89 0.00 46.52 3.46
2227 2398 3.728718 TCTGTCCGTACGTTCGTTTAAAC 59.271 43.478 15.21 8.35 0.00 2.01
2228 2399 3.728718 GTCTGTCCGTACGTTCGTTTAAA 59.271 43.478 15.21 0.00 0.00 1.52
2229 2400 3.296628 GTCTGTCCGTACGTTCGTTTAA 58.703 45.455 15.21 0.00 0.00 1.52
2230 2401 2.661709 CGTCTGTCCGTACGTTCGTTTA 60.662 50.000 15.21 0.00 34.48 2.01
2231 2402 1.758783 GTCTGTCCGTACGTTCGTTT 58.241 50.000 15.21 0.00 0.00 3.60
2232 2403 0.384725 CGTCTGTCCGTACGTTCGTT 60.385 55.000 15.21 0.00 34.48 3.85
2233 2404 1.205064 CGTCTGTCCGTACGTTCGT 59.795 57.895 15.21 2.91 34.48 3.85
2234 2405 4.032080 CGTCTGTCCGTACGTTCG 57.968 61.111 15.21 7.68 34.48 3.95
2244 2415 3.687572 TCTAATTAGCGGACGTCTGTC 57.312 47.619 24.68 16.71 44.72 3.51
2245 2416 3.693085 TCTTCTAATTAGCGGACGTCTGT 59.307 43.478 24.68 14.13 0.00 3.41
2246 2417 4.288670 TCTTCTAATTAGCGGACGTCTG 57.711 45.455 20.35 20.35 0.00 3.51
2247 2418 4.978083 TTCTTCTAATTAGCGGACGTCT 57.022 40.909 16.46 0.00 0.00 4.18
2248 2419 5.279384 TGATTCTTCTAATTAGCGGACGTC 58.721 41.667 7.13 7.13 0.00 4.34
2249 2420 5.258456 TGATTCTTCTAATTAGCGGACGT 57.742 39.130 7.67 0.00 0.00 4.34
2250 2421 5.977725 TCTTGATTCTTCTAATTAGCGGACG 59.022 40.000 7.67 0.00 0.00 4.79
2251 2422 7.772332 TTCTTGATTCTTCTAATTAGCGGAC 57.228 36.000 7.67 0.00 0.00 4.79
2252 2423 7.011482 GCTTTCTTGATTCTTCTAATTAGCGGA 59.989 37.037 7.67 5.52 0.00 5.54
2253 2424 7.128976 GCTTTCTTGATTCTTCTAATTAGCGG 58.871 38.462 7.67 3.30 0.00 5.52
2254 2425 7.128976 GGCTTTCTTGATTCTTCTAATTAGCG 58.871 38.462 7.67 1.85 0.00 4.26
2255 2426 7.128976 CGGCTTTCTTGATTCTTCTAATTAGC 58.871 38.462 7.67 0.00 0.00 3.09
2256 2427 7.634522 CCGGCTTTCTTGATTCTTCTAATTAG 58.365 38.462 6.11 6.11 0.00 1.73
2257 2428 6.038271 GCCGGCTTTCTTGATTCTTCTAATTA 59.962 38.462 22.15 0.00 0.00 1.40
2258 2429 5.163612 GCCGGCTTTCTTGATTCTTCTAATT 60.164 40.000 22.15 0.00 0.00 1.40
2259 2430 4.336713 GCCGGCTTTCTTGATTCTTCTAAT 59.663 41.667 22.15 0.00 0.00 1.73
2260 2431 3.689649 GCCGGCTTTCTTGATTCTTCTAA 59.310 43.478 22.15 0.00 0.00 2.10
2261 2432 3.270877 GCCGGCTTTCTTGATTCTTCTA 58.729 45.455 22.15 0.00 0.00 2.10
2262 2433 2.087646 GCCGGCTTTCTTGATTCTTCT 58.912 47.619 22.15 0.00 0.00 2.85
2263 2434 1.202076 CGCCGGCTTTCTTGATTCTTC 60.202 52.381 26.68 0.00 0.00 2.87
2264 2435 0.804989 CGCCGGCTTTCTTGATTCTT 59.195 50.000 26.68 0.00 0.00 2.52
2265 2436 0.036388 TCGCCGGCTTTCTTGATTCT 60.036 50.000 26.68 0.00 0.00 2.40
2266 2437 0.802494 TTCGCCGGCTTTCTTGATTC 59.198 50.000 26.68 0.00 0.00 2.52
2267 2438 1.068541 GTTTCGCCGGCTTTCTTGATT 60.069 47.619 26.68 0.00 0.00 2.57
2268 2439 0.521735 GTTTCGCCGGCTTTCTTGAT 59.478 50.000 26.68 0.00 0.00 2.57
2269 2440 1.837538 CGTTTCGCCGGCTTTCTTGA 61.838 55.000 26.68 10.44 0.00 3.02
2270 2441 1.440353 CGTTTCGCCGGCTTTCTTG 60.440 57.895 26.68 7.77 0.00 3.02
2271 2442 0.953960 ATCGTTTCGCCGGCTTTCTT 60.954 50.000 26.68 0.00 0.00 2.52
2272 2443 1.359459 GATCGTTTCGCCGGCTTTCT 61.359 55.000 26.68 1.79 0.00 2.52
2273 2444 1.060465 GATCGTTTCGCCGGCTTTC 59.940 57.895 26.68 11.06 0.00 2.62
2274 2445 0.108520 TAGATCGTTTCGCCGGCTTT 60.109 50.000 26.68 0.77 0.00 3.51
2275 2446 0.108520 TTAGATCGTTTCGCCGGCTT 60.109 50.000 26.68 0.00 0.00 4.35
2276 2447 0.108520 TTTAGATCGTTTCGCCGGCT 60.109 50.000 26.68 2.51 0.00 5.52
2277 2448 0.722848 TTTTAGATCGTTTCGCCGGC 59.277 50.000 19.07 19.07 0.00 6.13
2370 2541 3.775654 GGAGCCACCTCACCGGAG 61.776 72.222 9.46 0.00 39.96 4.63


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

AutoCloner maintained by Alex Coulton.