Multiple sequence alignment - TraesCS4D01G169900

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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 TraesCS4D01G169900 chr4D 100.000 2480 0 0 1 2480 295110655 295108176 0.000000e+00 4580.0
1 TraesCS4D01G169900 chr4A 92.803 1584 101 3 1 1580 198182968 198184542 0.000000e+00 2281.0
2 TraesCS4D01G169900 chr4A 83.458 671 68 22 1653 2317 198189311 198189944 3.550000e-163 584.0
3 TraesCS4D01G169900 chr4A 86.087 115 16 0 2308 2422 313632306 313632420 9.310000e-25 124.0
4 TraesCS4D01G169900 chr4A 100.000 36 0 0 1581 1616 198189280 198189315 1.590000e-07 67.6
5 TraesCS4D01G169900 chr4B 94.697 792 33 3 844 1630 364487728 364488515 0.000000e+00 1221.0
6 TraesCS4D01G169900 chr4B 88.620 413 29 4 2072 2478 364610702 364611102 1.030000e-133 486.0
7 TraesCS4D01G169900 chr4B 87.562 402 40 6 1681 2079 364599464 364599858 8.080000e-125 457.0
8 TraesCS4D01G169900 chr4B 80.175 686 69 16 170 825 364487095 364487743 3.760000e-123 451.0
9 TraesCS4D01G169900 chr4B 94.286 105 6 0 1 105 364486987 364487091 7.100000e-36 161.0
10 TraesCS4D01G169900 chr3B 75.987 304 56 13 185 478 20301681 20301385 9.250000e-30 141.0
11 TraesCS4D01G169900 chr3B 86.957 115 15 0 2315 2429 43186510 43186396 2.000000e-26 130.0
12 TraesCS4D01G169900 chrUn 89.189 111 10 2 2313 2422 321894215 321894324 1.200000e-28 137.0
13 TraesCS4D01G169900 chrUn 87.500 112 14 0 2311 2422 19227929 19227818 2.000000e-26 130.0
14 TraesCS4D01G169900 chr6A 89.189 111 10 2 2313 2422 295818405 295818514 1.200000e-28 137.0
15 TraesCS4D01G169900 chr2D 88.073 109 13 0 2316 2424 164392592 164392484 2.000000e-26 130.0
16 TraesCS4D01G169900 chr2A 87.963 108 12 1 2316 2423 469789786 469789680 2.590000e-25 126.0
17 TraesCS4D01G169900 chr2A 95.000 40 2 0 355 394 543988418 543988379 2.060000e-06 63.9
18 TraesCS4D01G169900 chr6D 86.087 115 16 0 2312 2426 302113754 302113640 9.310000e-25 124.0
19 TraesCS4D01G169900 chr6B 80.556 144 22 4 345 483 684019228 684019370 3.370000e-19 106.0
20 TraesCS4D01G169900 chr5D 78.443 167 32 4 412 578 2845968 2845806 3.370000e-19 106.0
21 TraesCS4D01G169900 chr7A 77.241 145 27 5 412 555 46294728 46294589 2.040000e-11 80.5
22 TraesCS4D01G169900 chr7D 89.831 59 5 1 403 461 561653073 561653130 9.510000e-10 75.0
23 TraesCS4D01G169900 chr5B 86.364 66 8 1 422 487 425176983 425177047 1.230000e-08 71.3


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 TraesCS4D01G169900 chr4D 295108176 295110655 2479 True 4580.0 4580 100.000000 1 2480 1 chr4D.!!$R1 2479
1 TraesCS4D01G169900 chr4A 198182968 198184542 1574 False 2281.0 2281 92.803000 1 1580 1 chr4A.!!$F1 1579
2 TraesCS4D01G169900 chr4A 198189280 198189944 664 False 325.8 584 91.729000 1581 2317 2 chr4A.!!$F3 736
3 TraesCS4D01G169900 chr4B 364486987 364488515 1528 False 611.0 1221 89.719333 1 1630 3 chr4B.!!$F3 1629

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
183 184 1.075970 AGCTCTACCCGGCTGATCA 60.076 57.895 0.00 0.0 37.41 2.92 F
193 194 1.091771 CGGCTGATCAATTGCCTCGT 61.092 55.000 19.09 0.0 44.09 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1464 0.111253 CAGACAAGGAGGCACCCTTT 59.889 55.0 8.26 2.05 43.68 3.11 R
1744 1782 0.532573 TTCACTCTCGAGCCCATGAC 59.467 55.0 7.81 0.00 0.00 3.06 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
74 75 3.198853 CCAAGGGGAAAAACTTCACCAAA 59.801 43.478 8.78 0.00 46.95 3.28
126 127 9.722056 GCATAATAAATGAGAAGTTCACGAAAT 57.278 29.630 5.50 0.00 38.99 2.17
162 163 2.048597 TTCGGTAGCACGCACCTG 60.049 61.111 8.38 3.95 33.62 4.00
183 184 1.075970 AGCTCTACCCGGCTGATCA 60.076 57.895 0.00 0.00 37.41 2.92
191 192 1.450531 CCCGGCTGATCAATTGCCTC 61.451 60.000 19.09 0.77 44.09 4.70
193 194 1.091771 CGGCTGATCAATTGCCTCGT 61.092 55.000 19.09 0.00 44.09 4.18
338 340 8.932945 TTAAGCATACATTTTTGTTGTTCACA 57.067 26.923 0.00 0.00 0.00 3.58
339 341 9.539825 TTAAGCATACATTTTTGTTGTTCACAT 57.460 25.926 0.00 0.00 34.43 3.21
370 372 1.588674 TGTGATTTTGTCGGTCGCTT 58.411 45.000 0.00 0.00 0.00 4.68
382 384 3.363128 GTCGGTCGCTTGTACTAAGTTTC 59.637 47.826 0.00 0.00 0.00 2.78
387 389 5.905733 GGTCGCTTGTACTAAGTTTCAAAAC 59.094 40.000 0.00 0.00 39.17 2.43
463 471 5.766670 TGAAAGCTCTCATCACAAGAAACAT 59.233 36.000 0.00 0.00 0.00 2.71
569 582 4.748144 GAGGGGCTGGGTGCAAGG 62.748 72.222 0.00 0.00 45.15 3.61
842 872 9.455847 CTAGGACAAATTCTCAAAGAACAAAAG 57.544 33.333 0.00 0.00 37.00 2.27
874 904 2.437359 AATGAGAGCACGGGCAGC 60.437 61.111 14.57 2.65 44.61 5.25
941 971 3.317150 TCGAGCAGACACAAACACATAG 58.683 45.455 0.00 0.00 0.00 2.23
942 972 2.159787 CGAGCAGACACAAACACATAGC 60.160 50.000 0.00 0.00 0.00 2.97
984 1014 2.809119 CCAAATAACCACGCACTGTACA 59.191 45.455 0.00 0.00 0.00 2.90
991 1021 4.303086 ACCACGCACTGTACATATAGAC 57.697 45.455 0.00 0.00 0.00 2.59
993 1023 4.042398 CCACGCACTGTACATATAGACAC 58.958 47.826 0.00 0.00 0.00 3.67
1053 1083 1.759445 AGCAGCGACATCAGGTTCTAT 59.241 47.619 0.00 0.00 0.00 1.98
1054 1084 2.169352 AGCAGCGACATCAGGTTCTATT 59.831 45.455 0.00 0.00 0.00 1.73
1176 1206 2.776913 CGTCTCTTCCTCCTCCGGC 61.777 68.421 0.00 0.00 0.00 6.13
1181 1211 1.821332 CTTCCTCCTCCGGCAATGC 60.821 63.158 0.00 0.00 0.00 3.56
1434 1464 3.630013 AGCACGCTGGAGGCTCAA 61.630 61.111 17.69 3.56 39.13 3.02
1503 1533 2.146342 CGTGCTTGTGTTCTCAATCCT 58.854 47.619 0.00 0.00 0.00 3.24
1568 1598 8.696410 AACTGTTCGTTTTGTTCAATTTGTAT 57.304 26.923 0.00 0.00 29.63 2.29
1630 1665 6.128526 GCTCACGCTCTTTTACACTCTTTTAT 60.129 38.462 0.00 0.00 0.00 1.40
1631 1666 7.117241 TCACGCTCTTTTACACTCTTTTATG 57.883 36.000 0.00 0.00 0.00 1.90
1632 1667 6.704493 TCACGCTCTTTTACACTCTTTTATGT 59.296 34.615 0.00 0.00 0.00 2.29
1633 1668 7.225931 TCACGCTCTTTTACACTCTTTTATGTT 59.774 33.333 0.00 0.00 0.00 2.71
1634 1669 7.321271 CACGCTCTTTTACACTCTTTTATGTTG 59.679 37.037 0.00 0.00 0.00 3.33
1635 1670 6.797033 CGCTCTTTTACACTCTTTTATGTTGG 59.203 38.462 0.00 0.00 0.00 3.77
1636 1671 7.084486 GCTCTTTTACACTCTTTTATGTTGGG 58.916 38.462 0.00 0.00 0.00 4.12
1637 1672 7.040686 GCTCTTTTACACTCTTTTATGTTGGGA 60.041 37.037 0.00 0.00 0.00 4.37
1638 1673 8.161699 TCTTTTACACTCTTTTATGTTGGGAC 57.838 34.615 0.00 0.00 0.00 4.46
1639 1674 6.548441 TTTACACTCTTTTATGTTGGGACG 57.452 37.500 0.00 0.00 0.00 4.79
1640 1675 4.081322 ACACTCTTTTATGTTGGGACGT 57.919 40.909 0.00 0.00 0.00 4.34
1641 1676 5.217978 ACACTCTTTTATGTTGGGACGTA 57.782 39.130 0.00 0.00 0.00 3.57
1642 1677 5.613329 ACACTCTTTTATGTTGGGACGTAA 58.387 37.500 0.00 0.00 35.89 3.18
1643 1678 6.056884 ACACTCTTTTATGTTGGGACGTAAA 58.943 36.000 0.00 1.05 42.53 2.01
1644 1679 6.543100 ACACTCTTTTATGTTGGGACGTAAAA 59.457 34.615 13.13 13.13 46.86 1.52
1649 1684 7.747155 TTTTATGTTGGGACGTAAAAGATCA 57.253 32.000 10.86 0.00 45.42 2.92
1650 1685 6.978343 TTATGTTGGGACGTAAAAGATCAG 57.022 37.500 0.00 0.00 35.01 2.90
1651 1686 3.670625 TGTTGGGACGTAAAAGATCAGG 58.329 45.455 0.00 0.00 0.00 3.86
1652 1687 3.007635 GTTGGGACGTAAAAGATCAGGG 58.992 50.000 0.00 0.00 0.00 4.45
1653 1688 1.065709 TGGGACGTAAAAGATCAGGGC 60.066 52.381 0.00 0.00 0.00 5.19
1654 1689 1.209747 GGGACGTAAAAGATCAGGGCT 59.790 52.381 0.00 0.00 0.00 5.19
1655 1690 2.433239 GGGACGTAAAAGATCAGGGCTA 59.567 50.000 0.00 0.00 0.00 3.93
1656 1691 3.071167 GGGACGTAAAAGATCAGGGCTAT 59.929 47.826 0.00 0.00 0.00 2.97
1674 1709 4.630505 GGCTATGCATGTAGTCTCATCATG 59.369 45.833 10.16 0.00 40.98 3.07
1680 1718 5.360714 TGCATGTAGTCTCATCATGTACTCA 59.639 40.000 0.00 0.42 40.40 3.41
1684 1722 7.468141 TGTAGTCTCATCATGTACTCAAGTT 57.532 36.000 0.00 0.00 0.00 2.66
1690 1728 5.430886 TCATCATGTACTCAAGTTCCCATG 58.569 41.667 0.00 9.24 33.04 3.66
1744 1782 3.373565 GGCGTTTTGGCTCCTGGG 61.374 66.667 0.00 0.00 40.72 4.45
1745 1783 2.597510 GCGTTTTGGCTCCTGGGT 60.598 61.111 0.00 0.00 0.00 4.51
1746 1784 2.626780 GCGTTTTGGCTCCTGGGTC 61.627 63.158 0.00 0.00 0.00 4.46
1747 1785 1.228124 CGTTTTGGCTCCTGGGTCA 60.228 57.895 0.00 0.00 0.00 4.02
1751 1789 2.153898 TTTGGCTCCTGGGTCATGGG 62.154 60.000 0.00 0.00 0.00 4.00
1752 1790 4.512914 GGCTCCTGGGTCATGGGC 62.513 72.222 0.00 0.00 0.00 5.36
1753 1791 3.415087 GCTCCTGGGTCATGGGCT 61.415 66.667 0.00 0.00 0.00 5.19
1754 1792 2.914289 CTCCTGGGTCATGGGCTC 59.086 66.667 0.00 0.00 0.00 4.70
1755 1793 3.083349 TCCTGGGTCATGGGCTCG 61.083 66.667 0.00 0.00 0.00 5.03
1756 1794 3.083349 CCTGGGTCATGGGCTCGA 61.083 66.667 0.00 0.00 0.00 4.04
1765 1803 0.534412 CATGGGCTCGAGAGTGAACT 59.466 55.000 18.75 0.00 0.00 3.01
1766 1804 0.534412 ATGGGCTCGAGAGTGAACTG 59.466 55.000 18.75 0.00 0.00 3.16
1776 1814 6.245115 TCGAGAGTGAACTGTAAATTCGTA 57.755 37.500 0.00 0.00 0.00 3.43
1777 1815 6.312487 TCGAGAGTGAACTGTAAATTCGTAG 58.688 40.000 0.00 0.00 0.00 3.51
1844 1883 4.193826 AGATGCTTGAGTACGTGATGTT 57.806 40.909 0.00 0.00 0.00 2.71
1849 1888 3.305964 CTTGAGTACGTGATGTTCGTGT 58.694 45.455 0.00 0.00 41.62 4.49
1853 1892 5.463286 TGAGTACGTGATGTTCGTGTAAAT 58.537 37.500 0.00 0.00 41.62 1.40
1861 1900 5.896432 GTGATGTTCGTGTAAATATTCAGCG 59.104 40.000 0.00 0.00 0.00 5.18
1868 1907 6.939627 TCGTGTAAATATTCAGCGTATTTGG 58.060 36.000 0.00 0.00 34.54 3.28
1873 1912 8.898761 TGTAAATATTCAGCGTATTTGGACATT 58.101 29.630 0.00 0.00 34.54 2.71
1878 1917 5.295431 TCAGCGTATTTGGACATTTGAAG 57.705 39.130 0.00 0.00 0.00 3.02
1879 1918 5.000591 TCAGCGTATTTGGACATTTGAAGA 58.999 37.500 0.00 0.00 0.00 2.87
1880 1919 5.122239 TCAGCGTATTTGGACATTTGAAGAG 59.878 40.000 0.00 0.00 0.00 2.85
1881 1920 5.003804 AGCGTATTTGGACATTTGAAGAGT 58.996 37.500 0.00 0.00 0.00 3.24
1882 1921 5.473504 AGCGTATTTGGACATTTGAAGAGTT 59.526 36.000 0.00 0.00 0.00 3.01
1883 1922 5.795441 GCGTATTTGGACATTTGAAGAGTTC 59.205 40.000 0.00 0.00 0.00 3.01
1884 1923 6.348540 GCGTATTTGGACATTTGAAGAGTTCT 60.349 38.462 0.00 0.00 0.00 3.01
1885 1924 7.237173 CGTATTTGGACATTTGAAGAGTTCTC 58.763 38.462 0.00 0.00 0.00 2.87
1886 1925 7.095229 CGTATTTGGACATTTGAAGAGTTCTCA 60.095 37.037 2.64 0.00 0.00 3.27
1887 1926 6.624352 TTTGGACATTTGAAGAGTTCTCAG 57.376 37.500 2.64 0.00 0.00 3.35
1888 1927 4.067896 TGGACATTTGAAGAGTTCTCAGC 58.932 43.478 2.64 0.00 0.00 4.26
1936 1975 9.781834 TGTGAAAAGATTTACTGTTTTACACTG 57.218 29.630 0.00 0.00 33.88 3.66
1946 1985 3.199677 TGTTTTACACTGTTCGGACCTG 58.800 45.455 0.00 0.00 0.00 4.00
1947 1986 3.118702 TGTTTTACACTGTTCGGACCTGA 60.119 43.478 0.00 0.00 0.00 3.86
1948 1987 4.062991 GTTTTACACTGTTCGGACCTGAT 58.937 43.478 0.00 0.00 0.00 2.90
1949 1988 4.345859 TTTACACTGTTCGGACCTGATT 57.654 40.909 0.00 0.00 0.00 2.57
1950 1989 2.930826 ACACTGTTCGGACCTGATTT 57.069 45.000 0.00 0.00 0.00 2.17
1979 2018 2.293170 CCGAGAGCTACTCAGATGTCA 58.707 52.381 11.93 0.00 45.14 3.58
1984 2023 5.518848 AGAGCTACTCAGATGTCAGAATG 57.481 43.478 0.00 0.00 32.06 2.67
1985 2024 4.341806 AGAGCTACTCAGATGTCAGAATGG 59.658 45.833 0.00 0.00 31.84 3.16
1996 2035 5.835280 AGATGTCAGAATGGGTTGAAACTTT 59.165 36.000 0.00 0.00 36.16 2.66
2009 2048 5.336744 GTTGAAACTTTTCACGGACATCAA 58.663 37.500 3.84 0.00 45.99 2.57
2024 2063 3.418995 ACATCAAGCACTCAAGCATCTT 58.581 40.909 0.00 0.00 36.85 2.40
2027 2066 2.481568 TCAAGCACTCAAGCATCTTTCG 59.518 45.455 0.00 0.00 36.85 3.46
2028 2067 0.801251 AGCACTCAAGCATCTTTCGC 59.199 50.000 0.00 0.00 36.85 4.70
2029 2068 0.179179 GCACTCAAGCATCTTTCGCC 60.179 55.000 0.00 0.00 0.00 5.54
2030 2069 1.159285 CACTCAAGCATCTTTCGCCA 58.841 50.000 0.00 0.00 0.00 5.69
2031 2070 1.741706 CACTCAAGCATCTTTCGCCAT 59.258 47.619 0.00 0.00 0.00 4.40
2032 2071 2.163010 CACTCAAGCATCTTTCGCCATT 59.837 45.455 0.00 0.00 0.00 3.16
2035 2074 4.641989 ACTCAAGCATCTTTCGCCATTATT 59.358 37.500 0.00 0.00 0.00 1.40
2038 2077 7.013655 ACTCAAGCATCTTTCGCCATTATTATT 59.986 33.333 0.00 0.00 0.00 1.40
2091 2131 5.782047 ACTATTCATAGAGTGCAGATGAGC 58.218 41.667 0.63 0.00 34.50 4.26
2094 2134 3.294214 TCATAGAGTGCAGATGAGCTCA 58.706 45.455 20.79 20.79 34.99 4.26
2095 2135 3.703052 TCATAGAGTGCAGATGAGCTCAA 59.297 43.478 22.50 0.00 34.99 3.02
2096 2136 4.344390 TCATAGAGTGCAGATGAGCTCAAT 59.656 41.667 22.50 9.92 34.99 2.57
2116 2156 9.617975 GCTCAATAGCTGAATTGAATATTTACC 57.382 33.333 11.97 0.00 43.42 2.85
2121 2161 7.573968 AGCTGAATTGAATATTTACCAGGTC 57.426 36.000 0.00 0.00 0.00 3.85
2122 2162 7.118723 AGCTGAATTGAATATTTACCAGGTCA 58.881 34.615 0.00 0.00 0.00 4.02
2123 2163 7.615365 AGCTGAATTGAATATTTACCAGGTCAA 59.385 33.333 0.00 0.00 0.00 3.18
2156 2196 5.529581 TTTTCTTCTTTTGCCTTACCCAG 57.470 39.130 0.00 0.00 0.00 4.45
2193 2234 1.815421 ATTGGTGCATCGGCTCGAC 60.815 57.895 0.00 0.00 39.18 4.20
2201 2242 1.805945 ATCGGCTCGACGCAAAGAC 60.806 57.895 8.71 0.00 39.18 3.01
2262 2303 4.037222 ACAACCATGTTTTTCTCCCCTTT 58.963 39.130 0.00 0.00 35.91 3.11
2290 2331 5.279156 GCCATCCAATGAAAGTTTTCTCACT 60.279 40.000 6.21 0.00 38.02 3.41
2295 2336 6.017934 TCCAATGAAAGTTTTCTCACTTCTCG 60.018 38.462 6.21 0.00 35.87 4.04
2296 2337 5.931441 ATGAAAGTTTTCTCACTTCTCGG 57.069 39.130 6.21 0.00 35.87 4.63
2298 2339 5.909477 TGAAAGTTTTCTCACTTCTCGGTA 58.091 37.500 6.21 0.00 35.87 4.02
2300 2341 4.931661 AGTTTTCTCACTTCTCGGTACA 57.068 40.909 0.00 0.00 0.00 2.90
2305 2346 2.760650 TCTCACTTCTCGGTACATGCAT 59.239 45.455 0.00 0.00 0.00 3.96
2317 2358 5.808540 TCGGTACATGCATGAACTTTAGTAC 59.191 40.000 32.75 19.72 0.00 2.73
2318 2359 5.810587 CGGTACATGCATGAACTTTAGTACT 59.189 40.000 32.75 8.41 33.16 2.73
2319 2360 6.019801 CGGTACATGCATGAACTTTAGTACTC 60.020 42.308 32.75 13.51 33.16 2.59
2320 2361 6.816640 GGTACATGCATGAACTTTAGTACTCA 59.183 38.462 32.75 0.00 33.16 3.41
2321 2362 7.495934 GGTACATGCATGAACTTTAGTACTCAT 59.504 37.037 32.75 7.09 33.16 2.90
2322 2363 7.928307 ACATGCATGAACTTTAGTACTCATT 57.072 32.000 32.75 0.95 0.00 2.57
2323 2364 7.978982 ACATGCATGAACTTTAGTACTCATTC 58.021 34.615 32.75 0.07 0.00 2.67
2324 2365 6.985188 TGCATGAACTTTAGTACTCATTCC 57.015 37.500 0.00 0.00 0.00 3.01
2325 2366 5.580691 TGCATGAACTTTAGTACTCATTCCG 59.419 40.000 0.00 0.00 0.00 4.30
2326 2367 5.810587 GCATGAACTTTAGTACTCATTCCGA 59.189 40.000 0.00 0.00 0.00 4.55
2327 2368 6.480320 GCATGAACTTTAGTACTCATTCCGAT 59.520 38.462 0.00 0.00 0.00 4.18
2328 2369 7.306866 GCATGAACTTTAGTACTCATTCCGATC 60.307 40.741 0.00 0.00 0.00 3.69
2329 2370 6.570692 TGAACTTTAGTACTCATTCCGATCC 58.429 40.000 0.00 0.00 0.00 3.36
2330 2371 6.153851 TGAACTTTAGTACTCATTCCGATCCA 59.846 38.462 0.00 0.00 0.00 3.41
2331 2372 6.732896 ACTTTAGTACTCATTCCGATCCAT 57.267 37.500 0.00 0.00 0.00 3.41
2332 2373 7.834881 ACTTTAGTACTCATTCCGATCCATA 57.165 36.000 0.00 0.00 0.00 2.74
2333 2374 8.423906 ACTTTAGTACTCATTCCGATCCATAT 57.576 34.615 0.00 0.00 0.00 1.78
2334 2375 8.871125 ACTTTAGTACTCATTCCGATCCATATT 58.129 33.333 0.00 0.00 0.00 1.28
2337 2378 9.529823 TTAGTACTCATTCCGATCCATATTACT 57.470 33.333 0.00 0.00 0.00 2.24
2338 2379 8.423906 AGTACTCATTCCGATCCATATTACTT 57.576 34.615 0.00 0.00 0.00 2.24
2339 2380 8.307483 AGTACTCATTCCGATCCATATTACTTG 58.693 37.037 0.00 0.00 0.00 3.16
2340 2381 7.067496 ACTCATTCCGATCCATATTACTTGT 57.933 36.000 0.00 0.00 0.00 3.16
2341 2382 7.155328 ACTCATTCCGATCCATATTACTTGTC 58.845 38.462 0.00 0.00 0.00 3.18
2342 2383 6.156519 TCATTCCGATCCATATTACTTGTCG 58.843 40.000 0.00 0.00 0.00 4.35
2343 2384 3.909430 TCCGATCCATATTACTTGTCGC 58.091 45.455 0.00 0.00 0.00 5.19
2344 2385 3.572682 TCCGATCCATATTACTTGTCGCT 59.427 43.478 0.00 0.00 0.00 4.93
2345 2386 3.921021 CCGATCCATATTACTTGTCGCTC 59.079 47.826 0.00 0.00 0.00 5.03
2346 2387 4.546570 CGATCCATATTACTTGTCGCTCA 58.453 43.478 0.00 0.00 0.00 4.26
2347 2388 4.982295 CGATCCATATTACTTGTCGCTCAA 59.018 41.667 0.00 0.00 34.61 3.02
2348 2389 5.462068 CGATCCATATTACTTGTCGCTCAAA 59.538 40.000 0.00 0.00 35.48 2.69
2349 2390 6.562270 CGATCCATATTACTTGTCGCTCAAAC 60.562 42.308 0.00 0.00 35.48 2.93
2350 2391 4.565166 TCCATATTACTTGTCGCTCAAACG 59.435 41.667 0.00 0.00 35.48 3.60
2351 2392 4.260212 CCATATTACTTGTCGCTCAAACGG 60.260 45.833 0.00 0.00 35.48 4.44
2352 2393 2.512485 TTACTTGTCGCTCAAACGGA 57.488 45.000 0.00 0.00 35.48 4.69
2353 2394 2.736144 TACTTGTCGCTCAAACGGAT 57.264 45.000 0.00 0.00 35.48 4.18
2354 2395 1.148310 ACTTGTCGCTCAAACGGATG 58.852 50.000 0.00 0.00 35.48 3.51
2355 2396 1.148310 CTTGTCGCTCAAACGGATGT 58.852 50.000 0.00 0.00 35.48 3.06
2356 2397 2.288579 ACTTGTCGCTCAAACGGATGTA 60.289 45.455 0.00 0.00 35.48 2.29
2357 2398 2.665649 TGTCGCTCAAACGGATGTAT 57.334 45.000 0.00 0.00 0.00 2.29
2358 2399 2.967362 TGTCGCTCAAACGGATGTATT 58.033 42.857 0.00 0.00 0.00 1.89
2359 2400 3.331150 TGTCGCTCAAACGGATGTATTT 58.669 40.909 0.00 0.00 0.00 1.40
2360 2401 4.496360 TGTCGCTCAAACGGATGTATTTA 58.504 39.130 0.00 0.00 0.00 1.40
2361 2402 4.565166 TGTCGCTCAAACGGATGTATTTAG 59.435 41.667 0.00 0.00 0.00 1.85
2362 2403 4.802039 GTCGCTCAAACGGATGTATTTAGA 59.198 41.667 0.00 0.00 0.00 2.10
2363 2404 4.802039 TCGCTCAAACGGATGTATTTAGAC 59.198 41.667 0.00 0.00 0.00 2.59
2364 2405 4.317139 CGCTCAAACGGATGTATTTAGACG 60.317 45.833 0.00 0.00 0.00 4.18
2365 2406 4.565564 GCTCAAACGGATGTATTTAGACGT 59.434 41.667 0.00 0.00 35.95 4.34
2366 2407 5.745294 GCTCAAACGGATGTATTTAGACGTA 59.255 40.000 0.00 0.00 33.85 3.57
2367 2408 6.420008 GCTCAAACGGATGTATTTAGACGTAT 59.580 38.462 0.00 0.00 33.85 3.06
2368 2409 7.042925 GCTCAAACGGATGTATTTAGACGTATT 60.043 37.037 0.00 0.00 33.85 1.89
2369 2410 8.706492 TCAAACGGATGTATTTAGACGTATTT 57.294 30.769 0.00 0.00 33.85 1.40
2370 2411 8.810427 TCAAACGGATGTATTTAGACGTATTTC 58.190 33.333 0.00 0.00 33.85 2.17
2371 2412 8.597227 CAAACGGATGTATTTAGACGTATTTCA 58.403 33.333 0.00 0.00 33.85 2.69
2372 2413 8.706492 AACGGATGTATTTAGACGTATTTCAA 57.294 30.769 0.00 0.00 33.85 2.69
2373 2414 8.882415 ACGGATGTATTTAGACGTATTTCAAT 57.118 30.769 0.00 0.00 32.30 2.57
2374 2415 8.761497 ACGGATGTATTTAGACGTATTTCAATG 58.239 33.333 0.00 0.00 32.30 2.82
2375 2416 8.221100 CGGATGTATTTAGACGTATTTCAATGG 58.779 37.037 0.00 0.00 0.00 3.16
2376 2417 9.052759 GGATGTATTTAGACGTATTTCAATGGT 57.947 33.333 0.00 0.00 0.00 3.55
2395 2436 9.208022 TCAATGGTAGATATATTCTTTTGAGCG 57.792 33.333 0.00 0.00 35.79 5.03
2396 2437 9.208022 CAATGGTAGATATATTCTTTTGAGCGA 57.792 33.333 0.00 0.00 35.79 4.93
2397 2438 9.950496 AATGGTAGATATATTCTTTTGAGCGAT 57.050 29.630 0.00 0.00 35.79 4.58
2409 2450 9.778741 ATTCTTTTGAGCGATAACTAATATGGA 57.221 29.630 0.00 0.00 0.00 3.41
2410 2451 9.778741 TTCTTTTGAGCGATAACTAATATGGAT 57.221 29.630 0.00 0.00 0.00 3.41
2411 2452 9.424319 TCTTTTGAGCGATAACTAATATGGATC 57.576 33.333 0.00 0.00 36.16 3.36
2412 2453 9.208022 CTTTTGAGCGATAACTAATATGGATCA 57.792 33.333 0.00 0.00 41.47 2.92
2413 2454 8.763049 TTTGAGCGATAACTAATATGGATCAG 57.237 34.615 0.00 0.00 43.14 2.90
2414 2455 7.703058 TGAGCGATAACTAATATGGATCAGA 57.297 36.000 0.00 0.00 39.31 3.27
2415 2456 7.766283 TGAGCGATAACTAATATGGATCAGAG 58.234 38.462 0.00 0.00 39.31 3.35
2416 2457 7.106439 AGCGATAACTAATATGGATCAGAGG 57.894 40.000 0.00 0.00 0.00 3.69
2417 2458 6.097554 AGCGATAACTAATATGGATCAGAGGG 59.902 42.308 0.00 0.00 0.00 4.30
2418 2459 6.096987 GCGATAACTAATATGGATCAGAGGGA 59.903 42.308 0.00 0.00 0.00 4.20
2419 2460 7.683222 GCGATAACTAATATGGATCAGAGGGAG 60.683 44.444 0.00 0.00 0.00 4.30
2420 2461 7.340743 CGATAACTAATATGGATCAGAGGGAGT 59.659 40.741 0.00 0.00 0.00 3.85
2421 2462 9.702253 GATAACTAATATGGATCAGAGGGAGTA 57.298 37.037 0.00 0.00 0.00 2.59
2423 2464 8.980832 AACTAATATGGATCAGAGGGAGTATT 57.019 34.615 0.00 0.00 0.00 1.89
2424 2465 8.980832 ACTAATATGGATCAGAGGGAGTATTT 57.019 34.615 0.00 0.00 0.00 1.40
2425 2466 9.041354 ACTAATATGGATCAGAGGGAGTATTTC 57.959 37.037 0.00 0.00 0.00 2.17
2426 2467 7.878621 AATATGGATCAGAGGGAGTATTTCA 57.121 36.000 0.00 0.00 0.00 2.69
2427 2468 7.878621 ATATGGATCAGAGGGAGTATTTCAA 57.121 36.000 0.00 0.00 0.00 2.69
2428 2469 6.581388 ATGGATCAGAGGGAGTATTTCAAA 57.419 37.500 0.00 0.00 0.00 2.69
2429 2470 6.581388 TGGATCAGAGGGAGTATTTCAAAT 57.419 37.500 0.00 0.00 0.00 2.32
2430 2471 6.595682 TGGATCAGAGGGAGTATTTCAAATC 58.404 40.000 0.00 0.00 0.00 2.17
2431 2472 5.698545 GGATCAGAGGGAGTATTTCAAATCG 59.301 44.000 0.00 0.00 0.00 3.34
2432 2473 4.442706 TCAGAGGGAGTATTTCAAATCGC 58.557 43.478 0.00 0.00 0.00 4.58
2433 2474 4.081142 TCAGAGGGAGTATTTCAAATCGCA 60.081 41.667 0.00 0.00 0.00 5.10
2434 2475 4.818546 CAGAGGGAGTATTTCAAATCGCAT 59.181 41.667 0.00 0.00 0.00 4.73
2435 2476 4.818546 AGAGGGAGTATTTCAAATCGCATG 59.181 41.667 0.00 0.00 0.00 4.06
2436 2477 4.526970 AGGGAGTATTTCAAATCGCATGT 58.473 39.130 0.00 0.00 0.00 3.21
2437 2478 4.949856 AGGGAGTATTTCAAATCGCATGTT 59.050 37.500 0.00 0.00 0.00 2.71
2438 2479 5.066505 AGGGAGTATTTCAAATCGCATGTTC 59.933 40.000 0.00 0.00 0.00 3.18
2439 2480 5.273944 GGAGTATTTCAAATCGCATGTTCC 58.726 41.667 0.00 0.00 0.00 3.62
2440 2481 5.066505 GGAGTATTTCAAATCGCATGTTCCT 59.933 40.000 0.00 0.00 0.00 3.36
2441 2482 6.404734 GGAGTATTTCAAATCGCATGTTCCTT 60.405 38.462 0.00 0.00 0.00 3.36
2442 2483 6.924111 AGTATTTCAAATCGCATGTTCCTTT 58.076 32.000 0.00 0.00 0.00 3.11
2443 2484 8.050778 AGTATTTCAAATCGCATGTTCCTTTA 57.949 30.769 0.00 0.00 0.00 1.85
2444 2485 8.184192 AGTATTTCAAATCGCATGTTCCTTTAG 58.816 33.333 0.00 0.00 0.00 1.85
2445 2486 4.963276 TCAAATCGCATGTTCCTTTAGG 57.037 40.909 0.00 0.00 0.00 2.69
2446 2487 4.331968 TCAAATCGCATGTTCCTTTAGGT 58.668 39.130 0.00 0.00 36.34 3.08
2447 2488 4.394920 TCAAATCGCATGTTCCTTTAGGTC 59.605 41.667 0.00 0.00 36.34 3.85
2448 2489 3.627395 ATCGCATGTTCCTTTAGGTCA 57.373 42.857 0.00 0.00 36.34 4.02
2449 2490 3.627395 TCGCATGTTCCTTTAGGTCAT 57.373 42.857 0.00 0.48 36.34 3.06
2450 2491 3.950397 TCGCATGTTCCTTTAGGTCATT 58.050 40.909 0.00 0.00 36.34 2.57
2451 2492 5.092554 TCGCATGTTCCTTTAGGTCATTA 57.907 39.130 0.00 0.00 36.34 1.90
2452 2493 5.492895 TCGCATGTTCCTTTAGGTCATTAA 58.507 37.500 0.00 0.00 36.34 1.40
2453 2494 5.353123 TCGCATGTTCCTTTAGGTCATTAAC 59.647 40.000 0.00 0.00 36.34 2.01
2454 2495 5.354234 CGCATGTTCCTTTAGGTCATTAACT 59.646 40.000 0.00 0.00 36.34 2.24
2455 2496 6.128007 CGCATGTTCCTTTAGGTCATTAACTT 60.128 38.462 0.00 0.00 36.34 2.66
2456 2497 7.065324 CGCATGTTCCTTTAGGTCATTAACTTA 59.935 37.037 0.00 0.00 36.34 2.24
2457 2498 8.398665 GCATGTTCCTTTAGGTCATTAACTTAG 58.601 37.037 0.00 0.00 36.34 2.18
2458 2499 9.667107 CATGTTCCTTTAGGTCATTAACTTAGA 57.333 33.333 0.00 0.00 36.34 2.10
2467 2508 9.609346 TTAGGTCATTAACTTAGAAATAGTGGC 57.391 33.333 0.00 0.00 0.00 5.01
2468 2509 7.054751 AGGTCATTAACTTAGAAATAGTGGCC 58.945 38.462 0.00 0.00 32.87 5.36
2469 2510 6.826741 GGTCATTAACTTAGAAATAGTGGCCA 59.173 38.462 0.00 0.00 32.93 5.36
2470 2511 7.201705 GGTCATTAACTTAGAAATAGTGGCCAC 60.202 40.741 29.22 29.22 32.93 5.01
2471 2512 7.335924 GTCATTAACTTAGAAATAGTGGCCACA 59.664 37.037 36.39 22.64 0.00 4.17
2472 2513 8.052748 TCATTAACTTAGAAATAGTGGCCACAT 58.947 33.333 36.39 23.78 0.00 3.21
2473 2514 9.337396 CATTAACTTAGAAATAGTGGCCACATA 57.663 33.333 36.39 24.42 0.00 2.29
2474 2515 9.914834 ATTAACTTAGAAATAGTGGCCACATAA 57.085 29.630 36.39 21.85 0.00 1.90
2475 2516 9.914834 TTAACTTAGAAATAGTGGCCACATAAT 57.085 29.630 36.39 23.05 0.00 1.28
2476 2517 8.823220 AACTTAGAAATAGTGGCCACATAATT 57.177 30.769 36.39 26.86 0.00 1.40
2477 2518 9.914834 AACTTAGAAATAGTGGCCACATAATTA 57.085 29.630 36.39 20.37 0.00 1.40
2478 2519 9.914834 ACTTAGAAATAGTGGCCACATAATTAA 57.085 29.630 36.39 23.07 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.182572 GCGGTCTAGATTAACTGATTGCG 59.817 47.826 0.00 0.00 0.00 4.85
74 75 4.770795 CCGGGTACTTGATCATTCTTCTT 58.229 43.478 0.00 0.00 0.00 2.52
168 169 1.475034 GCAATTGATCAGCCGGGTAGA 60.475 52.381 5.47 7.07 0.00 2.59
193 194 0.109532 TCCAACCACTTTGCGGATCA 59.890 50.000 0.00 0.00 33.34 2.92
269 270 3.342377 TGAACGGCCAACATTCAGATA 57.658 42.857 2.24 0.00 0.00 1.98
280 281 3.680490 TGAAACTTGATATGAACGGCCA 58.320 40.909 2.24 0.00 0.00 5.36
317 319 7.176285 ACATGTGAACAACAAAAATGTATGC 57.824 32.000 0.00 0.00 43.61 3.14
338 340 7.132213 CGACAAAATCACAAGTTTCAGTACAT 58.868 34.615 0.00 0.00 0.00 2.29
339 341 6.457663 CCGACAAAATCACAAGTTTCAGTACA 60.458 38.462 0.00 0.00 0.00 2.90
395 397 7.883229 ACGTTCTGACAAGTTTTTGATTTTT 57.117 28.000 0.00 0.00 37.73 1.94
396 398 9.581099 AATACGTTCTGACAAGTTTTTGATTTT 57.419 25.926 0.00 0.00 37.73 1.82
399 401 8.832521 TGTAATACGTTCTGACAAGTTTTTGAT 58.167 29.630 0.00 0.00 37.73 2.57
401 403 8.829514 TTGTAATACGTTCTGACAAGTTTTTG 57.170 30.769 0.00 0.00 40.24 2.44
403 405 9.445786 CATTTGTAATACGTTCTGACAAGTTTT 57.554 29.630 0.00 0.00 32.05 2.43
409 417 7.327975 AGATCCATTTGTAATACGTTCTGACA 58.672 34.615 0.00 0.00 0.00 3.58
410 418 7.772332 AGATCCATTTGTAATACGTTCTGAC 57.228 36.000 0.00 0.00 0.00 3.51
512 525 7.608308 TTTGACTTTTGGTTTCCAATCTTTG 57.392 32.000 1.97 0.00 43.55 2.77
842 872 6.644592 GTGCTCTCATTGTCCTAGAATATGTC 59.355 42.308 0.00 0.00 0.00 3.06
941 971 0.529378 CAAGGAGCAATGGGAAGTGC 59.471 55.000 0.00 0.00 41.22 4.40
942 972 0.529378 GCAAGGAGCAATGGGAAGTG 59.471 55.000 0.00 0.00 44.79 3.16
1431 1461 0.555769 ACAAGGAGGCACCCTTTTGA 59.444 50.000 8.26 0.00 43.68 2.69
1434 1464 0.111253 CAGACAAGGAGGCACCCTTT 59.889 55.000 8.26 2.05 43.68 3.11
1568 1598 7.206789 TGGGACAGAATATGACATTTCCTTA 57.793 36.000 0.00 0.00 0.00 2.69
1630 1665 3.558321 CCCTGATCTTTTACGTCCCAACA 60.558 47.826 0.00 0.00 0.00 3.33
1631 1666 3.007635 CCCTGATCTTTTACGTCCCAAC 58.992 50.000 0.00 0.00 0.00 3.77
1632 1667 2.617021 GCCCTGATCTTTTACGTCCCAA 60.617 50.000 0.00 0.00 0.00 4.12
1633 1668 1.065709 GCCCTGATCTTTTACGTCCCA 60.066 52.381 0.00 0.00 0.00 4.37
1634 1669 1.209747 AGCCCTGATCTTTTACGTCCC 59.790 52.381 0.00 0.00 0.00 4.46
1635 1670 2.693267 AGCCCTGATCTTTTACGTCC 57.307 50.000 0.00 0.00 0.00 4.79
1636 1671 3.495001 GCATAGCCCTGATCTTTTACGTC 59.505 47.826 0.00 0.00 0.00 4.34
1637 1672 3.118408 TGCATAGCCCTGATCTTTTACGT 60.118 43.478 0.00 0.00 0.00 3.57
1638 1673 3.466836 TGCATAGCCCTGATCTTTTACG 58.533 45.455 0.00 0.00 0.00 3.18
1639 1674 4.823989 ACATGCATAGCCCTGATCTTTTAC 59.176 41.667 0.00 0.00 0.00 2.01
1640 1675 5.052693 ACATGCATAGCCCTGATCTTTTA 57.947 39.130 0.00 0.00 0.00 1.52
1641 1676 3.907221 ACATGCATAGCCCTGATCTTTT 58.093 40.909 0.00 0.00 0.00 2.27
1642 1677 3.589951 ACATGCATAGCCCTGATCTTT 57.410 42.857 0.00 0.00 0.00 2.52
1643 1678 3.649981 ACTACATGCATAGCCCTGATCTT 59.350 43.478 0.00 0.00 0.00 2.40
1644 1679 3.246301 ACTACATGCATAGCCCTGATCT 58.754 45.455 0.00 0.00 0.00 2.75
1645 1680 3.260380 AGACTACATGCATAGCCCTGATC 59.740 47.826 0.00 0.00 0.00 2.92
1646 1681 3.246301 AGACTACATGCATAGCCCTGAT 58.754 45.455 0.00 0.00 0.00 2.90
1647 1682 2.630098 GAGACTACATGCATAGCCCTGA 59.370 50.000 0.00 0.00 0.00 3.86
1648 1683 2.366590 TGAGACTACATGCATAGCCCTG 59.633 50.000 0.00 0.00 0.00 4.45
1649 1684 2.682594 TGAGACTACATGCATAGCCCT 58.317 47.619 0.00 0.00 0.00 5.19
1650 1685 3.007290 TGATGAGACTACATGCATAGCCC 59.993 47.826 0.00 0.00 0.00 5.19
1651 1686 4.263018 TGATGAGACTACATGCATAGCC 57.737 45.455 0.00 0.00 0.00 3.93
1652 1687 5.236282 ACATGATGAGACTACATGCATAGC 58.764 41.667 0.00 0.00 43.21 2.97
1653 1688 7.600960 AGTACATGATGAGACTACATGCATAG 58.399 38.462 0.00 0.00 43.21 2.23
1654 1689 7.231317 TGAGTACATGATGAGACTACATGCATA 59.769 37.037 0.00 0.00 43.21 3.14
1655 1690 6.041296 TGAGTACATGATGAGACTACATGCAT 59.959 38.462 0.00 0.00 43.21 3.96
1656 1691 5.360714 TGAGTACATGATGAGACTACATGCA 59.639 40.000 0.00 0.00 43.21 3.96
1674 1709 6.407202 AGTAATGACATGGGAACTTGAGTAC 58.593 40.000 0.00 0.00 38.76 2.73
1741 1779 2.038813 TCTCGAGCCCATGACCCA 59.961 61.111 7.81 0.00 0.00 4.51
1744 1782 0.532573 TTCACTCTCGAGCCCATGAC 59.467 55.000 7.81 0.00 0.00 3.06
1745 1783 0.532573 GTTCACTCTCGAGCCCATGA 59.467 55.000 7.81 5.64 0.00 3.07
1746 1784 0.534412 AGTTCACTCTCGAGCCCATG 59.466 55.000 7.81 3.20 0.00 3.66
1747 1785 0.534412 CAGTTCACTCTCGAGCCCAT 59.466 55.000 7.81 0.00 0.00 4.00
1751 1789 4.030753 CGAATTTACAGTTCACTCTCGAGC 59.969 45.833 7.81 0.00 0.00 5.03
1752 1790 5.154932 ACGAATTTACAGTTCACTCTCGAG 58.845 41.667 5.93 5.93 0.00 4.04
1753 1791 5.117355 ACGAATTTACAGTTCACTCTCGA 57.883 39.130 0.00 0.00 0.00 4.04
1754 1792 6.312487 TCTACGAATTTACAGTTCACTCTCG 58.688 40.000 0.00 0.00 0.00 4.04
1755 1793 8.516811 TTTCTACGAATTTACAGTTCACTCTC 57.483 34.615 0.00 0.00 0.00 3.20
1808 1847 6.819284 TCAAGCATCTTTCACCAGAATTTTT 58.181 32.000 0.00 0.00 32.89 1.94
1809 1848 6.041296 ACTCAAGCATCTTTCACCAGAATTTT 59.959 34.615 0.00 0.00 32.89 1.82
1810 1849 5.537674 ACTCAAGCATCTTTCACCAGAATTT 59.462 36.000 0.00 0.00 32.89 1.82
1811 1850 5.075493 ACTCAAGCATCTTTCACCAGAATT 58.925 37.500 0.00 0.00 32.89 2.17
1812 1851 4.660168 ACTCAAGCATCTTTCACCAGAAT 58.340 39.130 0.00 0.00 32.89 2.40
1815 1854 3.369147 CGTACTCAAGCATCTTTCACCAG 59.631 47.826 0.00 0.00 0.00 4.00
1820 1859 4.627467 ACATCACGTACTCAAGCATCTTTC 59.373 41.667 0.00 0.00 0.00 2.62
1824 1863 3.000674 CGAACATCACGTACTCAAGCATC 60.001 47.826 0.00 0.00 0.00 3.91
1844 1883 6.757478 TCCAAATACGCTGAATATTTACACGA 59.243 34.615 0.00 0.00 32.27 4.35
1849 1888 9.729023 CAAATGTCCAAATACGCTGAATATTTA 57.271 29.630 0.00 0.00 32.27 1.40
1853 1892 6.993786 TCAAATGTCCAAATACGCTGAATA 57.006 33.333 0.00 0.00 0.00 1.75
1861 1900 8.099364 TGAGAACTCTTCAAATGTCCAAATAC 57.901 34.615 3.51 0.00 0.00 1.89
1868 1907 5.679734 TTGCTGAGAACTCTTCAAATGTC 57.320 39.130 3.51 0.00 0.00 3.06
1904 1943 8.706322 AAACAGTAAATCTTTTCACATACCCT 57.294 30.769 0.00 0.00 0.00 4.34
1919 1958 6.017687 GGTCCGAACAGTGTAAAACAGTAAAT 60.018 38.462 0.00 0.00 29.11 1.40
1926 1965 3.460103 TCAGGTCCGAACAGTGTAAAAC 58.540 45.455 0.00 0.00 0.00 2.43
1931 1970 2.930826 AAATCAGGTCCGAACAGTGT 57.069 45.000 0.00 0.00 0.00 3.55
1996 2035 1.069978 TGAGTGCTTGATGTCCGTGAA 59.930 47.619 0.00 0.00 0.00 3.18
2009 2048 0.801251 GCGAAAGATGCTTGAGTGCT 59.199 50.000 0.00 0.00 0.00 4.40
2071 2111 4.344390 TGAGCTCATCTGCACTCTATGAAT 59.656 41.667 13.74 0.00 34.99 2.57
2094 2134 9.646522 ACCTGGTAAATATTCAATTCAGCTATT 57.353 29.630 0.00 0.00 0.00 1.73
2095 2135 9.289782 GACCTGGTAAATATTCAATTCAGCTAT 57.710 33.333 0.00 0.00 0.00 2.97
2096 2136 8.271458 TGACCTGGTAAATATTCAATTCAGCTA 58.729 33.333 0.00 0.00 0.00 3.32
2100 2140 9.921637 GTTTTGACCTGGTAAATATTCAATTCA 57.078 29.630 0.00 0.00 0.00 2.57
2135 2175 4.542697 ACTGGGTAAGGCAAAAGAAGAAA 58.457 39.130 0.00 0.00 0.00 2.52
2156 2196 4.730657 CAATGCTTCTGAAGACATTGGAC 58.269 43.478 32.24 15.05 42.54 4.02
2201 2242 4.933064 GCGGCGATGACCTCTCGG 62.933 72.222 12.98 0.00 36.65 4.63
2215 2256 2.363711 TTTCGATCTCCCCATCGCGG 62.364 60.000 6.13 0.00 44.48 6.46
2229 2270 5.766150 AAACATGGTTGTTGATCTTTCGA 57.234 34.783 0.00 0.00 45.30 3.71
2230 2271 6.697019 AGAAAAACATGGTTGTTGATCTTTCG 59.303 34.615 0.00 0.00 45.30 3.46
2242 2283 6.154534 GCTATAAAGGGGAGAAAAACATGGTT 59.845 38.462 0.00 0.00 0.00 3.67
2257 2298 5.835280 ACTTTCATTGGATGGCTATAAAGGG 59.165 40.000 5.93 0.00 0.00 3.95
2262 2303 7.833682 TGAGAAAACTTTCATTGGATGGCTATA 59.166 33.333 5.07 0.00 39.61 1.31
2290 2331 3.610040 AGTTCATGCATGTACCGAGAA 57.390 42.857 26.93 11.00 0.00 2.87
2295 2336 6.816640 TGAGTACTAAAGTTCATGCATGTACC 59.183 38.462 26.93 16.03 32.15 3.34
2296 2337 7.827819 TGAGTACTAAAGTTCATGCATGTAC 57.172 36.000 24.31 24.31 0.00 2.90
2298 2339 7.066284 GGAATGAGTACTAAAGTTCATGCATGT 59.934 37.037 25.43 9.20 29.00 3.21
2300 2341 6.258727 CGGAATGAGTACTAAAGTTCATGCAT 59.741 38.462 0.00 0.00 29.00 3.96
2305 2346 6.153851 TGGATCGGAATGAGTACTAAAGTTCA 59.846 38.462 0.00 0.00 0.00 3.18
2317 2358 6.309009 CGACAAGTAATATGGATCGGAATGAG 59.691 42.308 0.00 0.00 0.00 2.90
2318 2359 6.156519 CGACAAGTAATATGGATCGGAATGA 58.843 40.000 0.00 0.00 0.00 2.57
2319 2360 5.163953 GCGACAAGTAATATGGATCGGAATG 60.164 44.000 0.00 0.00 0.00 2.67
2320 2361 4.929808 GCGACAAGTAATATGGATCGGAAT 59.070 41.667 0.00 0.00 0.00 3.01
2321 2362 4.038763 AGCGACAAGTAATATGGATCGGAA 59.961 41.667 0.00 0.00 0.00 4.30
2322 2363 3.572682 AGCGACAAGTAATATGGATCGGA 59.427 43.478 0.00 0.00 0.00 4.55
2323 2364 3.914312 AGCGACAAGTAATATGGATCGG 58.086 45.455 0.00 0.00 0.00 4.18
2324 2365 4.546570 TGAGCGACAAGTAATATGGATCG 58.453 43.478 0.00 0.00 0.00 3.69
2325 2366 6.562270 CGTTTGAGCGACAAGTAATATGGATC 60.562 42.308 0.00 0.00 39.77 3.36
2326 2367 5.234329 CGTTTGAGCGACAAGTAATATGGAT 59.766 40.000 0.00 0.00 39.77 3.41
2327 2368 4.565166 CGTTTGAGCGACAAGTAATATGGA 59.435 41.667 0.00 0.00 39.77 3.41
2328 2369 4.260212 CCGTTTGAGCGACAAGTAATATGG 60.260 45.833 0.00 0.00 39.77 2.74
2329 2370 4.565166 TCCGTTTGAGCGACAAGTAATATG 59.435 41.667 0.00 0.00 39.77 1.78
2330 2371 4.751060 TCCGTTTGAGCGACAAGTAATAT 58.249 39.130 0.00 0.00 39.77 1.28
2331 2372 4.177165 TCCGTTTGAGCGACAAGTAATA 57.823 40.909 0.00 0.00 39.77 0.98
2332 2373 3.034721 TCCGTTTGAGCGACAAGTAAT 57.965 42.857 0.00 0.00 39.77 1.89
2333 2374 2.512485 TCCGTTTGAGCGACAAGTAA 57.488 45.000 0.00 0.00 39.77 2.24
2334 2375 2.288579 ACATCCGTTTGAGCGACAAGTA 60.289 45.455 0.00 0.00 39.77 2.24
2335 2376 1.148310 CATCCGTTTGAGCGACAAGT 58.852 50.000 0.00 0.00 39.77 3.16
2336 2377 1.148310 ACATCCGTTTGAGCGACAAG 58.852 50.000 0.00 0.00 39.77 3.16
2337 2378 2.442212 TACATCCGTTTGAGCGACAA 57.558 45.000 0.00 0.00 36.65 3.18
2338 2379 2.665649 ATACATCCGTTTGAGCGACA 57.334 45.000 0.00 0.00 0.00 4.35
2339 2380 4.802039 TCTAAATACATCCGTTTGAGCGAC 59.198 41.667 0.00 0.00 0.00 5.19
2340 2381 4.802039 GTCTAAATACATCCGTTTGAGCGA 59.198 41.667 0.00 0.00 0.00 4.93
2341 2382 4.317139 CGTCTAAATACATCCGTTTGAGCG 60.317 45.833 0.00 0.00 0.00 5.03
2342 2383 4.565564 ACGTCTAAATACATCCGTTTGAGC 59.434 41.667 0.00 0.00 0.00 4.26
2343 2384 7.925703 ATACGTCTAAATACATCCGTTTGAG 57.074 36.000 0.00 0.00 0.00 3.02
2344 2385 8.706492 AAATACGTCTAAATACATCCGTTTGA 57.294 30.769 0.00 0.00 0.00 2.69
2345 2386 8.597227 TGAAATACGTCTAAATACATCCGTTTG 58.403 33.333 0.00 0.00 0.00 2.93
2346 2387 8.706492 TGAAATACGTCTAAATACATCCGTTT 57.294 30.769 0.00 0.00 0.00 3.60
2347 2388 8.706492 TTGAAATACGTCTAAATACATCCGTT 57.294 30.769 0.00 0.00 0.00 4.44
2348 2389 8.761497 CATTGAAATACGTCTAAATACATCCGT 58.239 33.333 0.00 0.00 0.00 4.69
2349 2390 8.221100 CCATTGAAATACGTCTAAATACATCCG 58.779 37.037 0.00 0.00 0.00 4.18
2350 2391 9.052759 ACCATTGAAATACGTCTAAATACATCC 57.947 33.333 0.00 0.00 0.00 3.51
2369 2410 9.208022 CGCTCAAAAGAATATATCTACCATTGA 57.792 33.333 0.00 0.00 37.42 2.57
2370 2411 9.208022 TCGCTCAAAAGAATATATCTACCATTG 57.792 33.333 0.00 0.00 37.42 2.82
2371 2412 9.950496 ATCGCTCAAAAGAATATATCTACCATT 57.050 29.630 0.00 0.00 37.42 3.16
2383 2424 9.778741 TCCATATTAGTTATCGCTCAAAAGAAT 57.221 29.630 0.00 0.00 0.00 2.40
2384 2425 9.778741 ATCCATATTAGTTATCGCTCAAAAGAA 57.221 29.630 0.00 0.00 0.00 2.52
2385 2426 9.424319 GATCCATATTAGTTATCGCTCAAAAGA 57.576 33.333 0.00 0.00 0.00 2.52
2386 2427 9.208022 TGATCCATATTAGTTATCGCTCAAAAG 57.792 33.333 0.00 0.00 0.00 2.27
2387 2428 9.208022 CTGATCCATATTAGTTATCGCTCAAAA 57.792 33.333 0.00 0.00 0.00 2.44
2388 2429 8.585018 TCTGATCCATATTAGTTATCGCTCAAA 58.415 33.333 0.00 0.00 0.00 2.69
2389 2430 8.122472 TCTGATCCATATTAGTTATCGCTCAA 57.878 34.615 0.00 0.00 0.00 3.02
2390 2431 7.148000 CCTCTGATCCATATTAGTTATCGCTCA 60.148 40.741 0.00 0.00 0.00 4.26
2391 2432 7.199766 CCTCTGATCCATATTAGTTATCGCTC 58.800 42.308 0.00 0.00 0.00 5.03
2392 2433 6.097554 CCCTCTGATCCATATTAGTTATCGCT 59.902 42.308 0.00 0.00 0.00 4.93
2393 2434 6.096987 TCCCTCTGATCCATATTAGTTATCGC 59.903 42.308 0.00 0.00 0.00 4.58
2394 2435 7.340743 ACTCCCTCTGATCCATATTAGTTATCG 59.659 40.741 0.00 0.00 0.00 2.92
2395 2436 8.602472 ACTCCCTCTGATCCATATTAGTTATC 57.398 38.462 0.00 0.00 0.00 1.75
2398 2439 8.980832 AATACTCCCTCTGATCCATATTAGTT 57.019 34.615 0.00 0.00 0.00 2.24
2399 2440 8.980832 AAATACTCCCTCTGATCCATATTAGT 57.019 34.615 0.00 0.00 0.00 2.24
2400 2441 9.040259 TGAAATACTCCCTCTGATCCATATTAG 57.960 37.037 0.00 0.00 0.00 1.73
2401 2442 8.972662 TGAAATACTCCCTCTGATCCATATTA 57.027 34.615 0.00 0.00 0.00 0.98
2402 2443 7.878621 TGAAATACTCCCTCTGATCCATATT 57.121 36.000 0.00 0.00 0.00 1.28
2403 2444 7.878621 TTGAAATACTCCCTCTGATCCATAT 57.121 36.000 0.00 0.00 0.00 1.78
2404 2445 7.690454 TTTGAAATACTCCCTCTGATCCATA 57.310 36.000 0.00 0.00 0.00 2.74
2405 2446 6.581388 TTTGAAATACTCCCTCTGATCCAT 57.419 37.500 0.00 0.00 0.00 3.41
2406 2447 6.581388 ATTTGAAATACTCCCTCTGATCCA 57.419 37.500 0.00 0.00 0.00 3.41
2407 2448 5.698545 CGATTTGAAATACTCCCTCTGATCC 59.301 44.000 0.00 0.00 0.00 3.36
2408 2449 5.178438 GCGATTTGAAATACTCCCTCTGATC 59.822 44.000 0.00 0.00 0.00 2.92
2409 2450 5.059833 GCGATTTGAAATACTCCCTCTGAT 58.940 41.667 0.00 0.00 0.00 2.90
2410 2451 4.081142 TGCGATTTGAAATACTCCCTCTGA 60.081 41.667 0.00 0.00 0.00 3.27
2411 2452 4.191544 TGCGATTTGAAATACTCCCTCTG 58.808 43.478 0.00 0.00 0.00 3.35
2412 2453 4.487714 TGCGATTTGAAATACTCCCTCT 57.512 40.909 0.00 0.00 0.00 3.69
2413 2454 4.576463 ACATGCGATTTGAAATACTCCCTC 59.424 41.667 0.00 0.00 0.00 4.30
2414 2455 4.526970 ACATGCGATTTGAAATACTCCCT 58.473 39.130 0.00 0.00 0.00 4.20
2415 2456 4.900635 ACATGCGATTTGAAATACTCCC 57.099 40.909 0.00 0.00 0.00 4.30
2416 2457 5.066505 AGGAACATGCGATTTGAAATACTCC 59.933 40.000 0.00 0.00 0.00 3.85
2417 2458 6.124088 AGGAACATGCGATTTGAAATACTC 57.876 37.500 0.00 0.00 0.00 2.59
2418 2459 6.515272 AAGGAACATGCGATTTGAAATACT 57.485 33.333 0.00 0.00 0.00 2.12
2419 2460 7.432252 CCTAAAGGAACATGCGATTTGAAATAC 59.568 37.037 0.00 0.00 37.39 1.89
2420 2461 7.122055 ACCTAAAGGAACATGCGATTTGAAATA 59.878 33.333 2.23 0.00 38.94 1.40
2421 2462 6.071391 ACCTAAAGGAACATGCGATTTGAAAT 60.071 34.615 2.23 0.00 38.94 2.17
2422 2463 5.242838 ACCTAAAGGAACATGCGATTTGAAA 59.757 36.000 2.23 0.00 38.94 2.69
2423 2464 4.764823 ACCTAAAGGAACATGCGATTTGAA 59.235 37.500 2.23 0.00 38.94 2.69
2424 2465 4.331968 ACCTAAAGGAACATGCGATTTGA 58.668 39.130 2.23 0.00 38.94 2.69
2425 2466 4.155826 TGACCTAAAGGAACATGCGATTTG 59.844 41.667 2.23 0.00 38.94 2.32
2426 2467 4.331968 TGACCTAAAGGAACATGCGATTT 58.668 39.130 2.23 0.00 38.94 2.17
2427 2468 3.950397 TGACCTAAAGGAACATGCGATT 58.050 40.909 2.23 0.00 38.94 3.34
2428 2469 3.627395 TGACCTAAAGGAACATGCGAT 57.373 42.857 2.23 0.00 38.94 4.58
2429 2470 3.627395 ATGACCTAAAGGAACATGCGA 57.373 42.857 2.23 0.00 38.94 5.10
2430 2471 5.354234 AGTTAATGACCTAAAGGAACATGCG 59.646 40.000 2.23 0.00 36.53 4.73
2431 2472 6.759497 AGTTAATGACCTAAAGGAACATGC 57.241 37.500 2.23 3.70 36.53 4.06
2432 2473 9.667107 TCTAAGTTAATGACCTAAAGGAACATG 57.333 33.333 2.23 0.00 36.53 3.21
2441 2482 9.609346 GCCACTATTTCTAAGTTAATGACCTAA 57.391 33.333 0.00 0.00 0.00 2.69
2442 2483 8.208903 GGCCACTATTTCTAAGTTAATGACCTA 58.791 37.037 0.00 0.00 0.00 3.08
2443 2484 7.054751 GGCCACTATTTCTAAGTTAATGACCT 58.945 38.462 0.00 0.00 0.00 3.85
2444 2485 6.826741 TGGCCACTATTTCTAAGTTAATGACC 59.173 38.462 0.00 0.00 0.00 4.02
2445 2486 7.335924 TGTGGCCACTATTTCTAAGTTAATGAC 59.664 37.037 34.75 3.06 0.00 3.06
2446 2487 7.398829 TGTGGCCACTATTTCTAAGTTAATGA 58.601 34.615 34.75 6.60 0.00 2.57
2447 2488 7.624360 TGTGGCCACTATTTCTAAGTTAATG 57.376 36.000 34.75 0.00 0.00 1.90
2448 2489 9.914834 TTATGTGGCCACTATTTCTAAGTTAAT 57.085 29.630 34.75 17.45 0.00 1.40
2449 2490 9.914834 ATTATGTGGCCACTATTTCTAAGTTAA 57.085 29.630 34.75 11.28 0.00 2.01
2450 2491 9.914834 AATTATGTGGCCACTATTTCTAAGTTA 57.085 29.630 34.75 11.74 0.00 2.24
2451 2492 8.823220 AATTATGTGGCCACTATTTCTAAGTT 57.177 30.769 34.75 13.47 0.00 2.66
2452 2493 9.914834 TTAATTATGTGGCCACTATTTCTAAGT 57.085 29.630 34.75 21.10 0.00 2.24


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

AutoCloner maintained by Alex Coulton.