Multiple sequence alignment - TraesCS7B01G107400

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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 TraesCS7B01G107400 chr7B 100.000 5665 0 0 1 5665 123857056 123862720 0.000000e+00 10462
1 TraesCS7B01G107400 chr7D 91.360 3889 221 69 1809 5635 161840556 161844391 0.000000e+00 5214
2 TraesCS7B01G107400 chr7D 89.748 1707 107 34 1 1679 161838883 161840549 0.000000e+00 2121
3 TraesCS7B01G107400 chr7A 93.425 1673 79 17 3986 5641 162925151 162926809 0.000000e+00 2451
4 TraesCS7B01G107400 chr7A 89.290 1606 112 24 98 1669 162920408 162921987 0.000000e+00 1958
5 TraesCS7B01G107400 chr7A 90.315 888 43 16 1806 2683 162921987 162922841 0.000000e+00 1123
6 TraesCS7B01G107400 chr7A 92.612 758 37 9 2708 3458 162923934 162924679 0.000000e+00 1072
7 TraesCS7B01G107400 chr7A 89.549 421 28 10 3585 4001 162924723 162925131 2.340000e-143 520
8 TraesCS7B01G107400 chr7A 90.511 137 10 1 1674 1810 2582136 2582003 1.620000e-40 178
9 TraesCS7B01G107400 chr7A 90.385 104 6 2 1 100 162920230 162920333 3.560000e-27 134
10 TraesCS7B01G107400 chr4D 91.367 139 8 2 1672 1810 492804414 492804280 2.690000e-43 187
11 TraesCS7B01G107400 chr4D 90.580 138 10 1 1670 1807 394190833 394190967 4.510000e-41 180
12 TraesCS7B01G107400 chrUn 91.729 133 8 1 1675 1807 11031657 11031786 1.250000e-41 182
13 TraesCS7B01G107400 chr5B 91.729 133 8 2 1675 1807 31287927 31288056 1.250000e-41 182
14 TraesCS7B01G107400 chr6D 91.603 131 8 1 1678 1808 193682581 193682454 1.620000e-40 178
15 TraesCS7B01G107400 chr1D 89.437 142 11 2 1666 1807 406733781 406733918 5.830000e-40 176
16 TraesCS7B01G107400 chr1B 87.421 159 13 4 1652 1809 5000891 5000739 5.830000e-40 176
17 TraesCS7B01G107400 chr4A 88.514 148 11 4 1668 1815 346062546 346062687 2.100000e-39 174


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 TraesCS7B01G107400 chr7B 123857056 123862720 5664 False 10462.000000 10462 100.000000 1 5665 1 chr7B.!!$F1 5664
1 TraesCS7B01G107400 chr7D 161838883 161844391 5508 False 3667.500000 5214 90.554000 1 5635 2 chr7D.!!$F1 5634
2 TraesCS7B01G107400 chr7A 162920230 162926809 6579 False 1209.666667 2451 90.929333 1 5641 6 chr7A.!!$F1 5640

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
641 745 0.382158 GCCCCAAGAAATAAGCGAGC 59.618 55.0 0.00 0.0 0.00 5.03 F
1331 1445 0.178891 TGCACCTTCCTCTCCTCCTT 60.179 55.0 0.00 0.0 0.00 3.36 F
2422 2607 0.176680 GATGATCAGCTGTGGACGGT 59.823 55.0 14.67 0.0 0.00 4.83 F
3781 5081 0.529378 GCCTTGTGGGATCAAAGCTG 59.471 55.0 0.00 0.0 37.23 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 2607 0.038892 GGCAAAGTACGACGAGGTCA 60.039 55.0 0.00 0.00 32.09 4.02 R
2671 2856 0.041238 ATCTTGGGTCCTGAGTCCGA 59.959 55.0 0.00 0.00 0.00 4.55 R
3851 5152 0.104487 CCGAGTGAGCATGCATCTCT 59.896 55.0 21.98 18.49 0.00 3.10 R
5603 6957 0.035176 AGGGCGCACATGCAATTTTT 59.965 45.0 14.57 0.00 42.21 1.94 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
53 54 9.801873 CTAAATATTCTACAAAAACACATGGGG 57.198 33.333 0.00 0.00 0.00 4.96
206 291 8.293699 ACTTCCAACTAAAATGAACACTTTCT 57.706 30.769 0.00 0.00 32.36 2.52
208 293 9.884465 CTTCCAACTAAAATGAACACTTTCTAG 57.116 33.333 0.00 0.00 32.36 2.43
235 320 7.893124 ATCTAGCCACAAAAGAATCATGAAT 57.107 32.000 0.00 0.00 0.00 2.57
238 323 4.460382 AGCCACAAAAGAATCATGAATCGT 59.540 37.500 0.00 0.00 0.00 3.73
249 334 5.929697 ATCATGAATCGTGCGATACAAAT 57.070 34.783 7.54 0.00 33.97 2.32
278 363 0.391263 AAACGATGAGGGAGCGGAAC 60.391 55.000 0.00 0.00 37.96 3.62
295 380 3.254657 CGGAACCAATAGAGGTGCAAAAA 59.745 43.478 0.00 0.00 42.25 1.94
352 438 1.915078 ATTTCAGAGACTGCCCGGGG 61.915 60.000 25.28 9.31 0.00 5.73
457 543 2.613133 ACTATGAGGCGACGAGTACTTC 59.387 50.000 0.00 0.00 0.00 3.01
462 548 0.524862 GGCGACGAGTACTTCTCCAA 59.475 55.000 0.00 0.00 39.84 3.53
513 599 6.769341 CAGTCATCATAGGGAATTTCATGTGA 59.231 38.462 0.00 0.00 0.00 3.58
517 603 7.500227 TCATCATAGGGAATTTCATGTGAGAAC 59.500 37.037 4.15 0.00 0.00 3.01
547 633 4.101448 CACCAGGAAGGCCCGGAG 62.101 72.222 0.73 0.00 43.14 4.63
641 745 0.382158 GCCCCAAGAAATAAGCGAGC 59.618 55.000 0.00 0.00 0.00 5.03
671 782 5.005682 GTGTTCAATTCAACAAGAAGCCAAC 59.994 40.000 0.00 0.00 40.15 3.77
680 791 3.020984 ACAAGAAGCCAACGAAAAAGGA 58.979 40.909 0.00 0.00 0.00 3.36
681 792 3.066760 ACAAGAAGCCAACGAAAAAGGAG 59.933 43.478 0.00 0.00 0.00 3.69
749 860 3.551496 CTTGCTCCCGCCACTTCCA 62.551 63.158 0.00 0.00 34.43 3.53
840 951 1.375853 CTCCAAATCGGCCATCGCAA 61.376 55.000 2.24 0.00 39.05 4.85
848 959 1.153086 GGCCATCGCAATCTCTGGT 60.153 57.895 0.00 0.00 36.38 4.00
879 990 2.664851 CACGAGCCAAGCCACGAA 60.665 61.111 9.92 0.00 34.35 3.85
926 1037 4.385825 TGCCTTTGACGTATTGAGAAACT 58.614 39.130 0.00 0.00 0.00 2.66
928 1039 5.147162 GCCTTTGACGTATTGAGAAACTTG 58.853 41.667 0.00 0.00 0.00 3.16
947 1058 1.657487 CGTCGATTGATCCGGTCCG 60.657 63.158 3.60 3.60 0.00 4.79
976 1087 1.643832 GCACCTAGCAAGCATACGC 59.356 57.895 0.00 0.00 44.79 4.42
1058 1169 3.842923 CGGCAGCGAGGAGATGGT 61.843 66.667 0.00 0.00 36.61 3.55
1331 1445 0.178891 TGCACCTTCCTCTCCTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
1357 1477 7.986085 TTTCTTGAGAGGTCCTCTAATTTTG 57.014 36.000 21.88 8.96 41.35 2.44
1405 1525 7.708322 GGAGAAGGATTTTGGCTAAAATGATTC 59.292 37.037 23.53 22.57 44.35 2.52
1407 1527 8.596293 AGAAGGATTTTGGCTAAAATGATTCAA 58.404 29.630 26.51 4.13 44.35 2.69
1414 1534 9.616156 TTTTGGCTAAAATGATTCAATATGCAT 57.384 25.926 3.79 3.79 31.13 3.96
1418 1538 7.171848 GGCTAAAATGATTCAATATGCATGCAA 59.828 33.333 26.68 14.46 0.00 4.08
1535 1675 7.502226 AGTCAAGTCATGAAACTATTGACCAAA 59.498 33.333 22.31 0.90 40.50 3.28
1536 1676 7.805071 GTCAAGTCATGAAACTATTGACCAAAG 59.195 37.037 18.70 0.00 40.50 2.77
1580 1720 1.201429 AGTTCCCTCGCAATCCCACT 61.201 55.000 0.00 0.00 0.00 4.00
1612 1754 1.539827 CTCCTCGCCGGTCAAATTTTT 59.460 47.619 1.90 0.00 0.00 1.94
1685 1827 9.886132 TTGACTTTCTTTACATAATACTCCCTC 57.114 33.333 0.00 0.00 0.00 4.30
1686 1828 8.483758 TGACTTTCTTTACATAATACTCCCTCC 58.516 37.037 0.00 0.00 0.00 4.30
1687 1829 7.498443 ACTTTCTTTACATAATACTCCCTCCG 58.502 38.462 0.00 0.00 0.00 4.63
1688 1830 7.125356 ACTTTCTTTACATAATACTCCCTCCGT 59.875 37.037 0.00 0.00 0.00 4.69
1689 1831 6.645790 TCTTTACATAATACTCCCTCCGTC 57.354 41.667 0.00 0.00 0.00 4.79
1690 1832 5.537674 TCTTTACATAATACTCCCTCCGTCC 59.462 44.000 0.00 0.00 0.00 4.79
1691 1833 2.606378 ACATAATACTCCCTCCGTCCC 58.394 52.381 0.00 0.00 0.00 4.46
1692 1834 2.090943 ACATAATACTCCCTCCGTCCCA 60.091 50.000 0.00 0.00 0.00 4.37
1693 1835 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
1694 1836 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
1695 1837 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1696 1838 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1697 1839 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1698 1840 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1699 1841 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1700 1842 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1701 1843 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1702 1844 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1703 1845 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1704 1846 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1705 1847 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1706 1848 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1707 1849 5.566469 TCCGTCCCAAAATTCTTGTCTTAT 58.434 37.500 0.00 0.00 0.00 1.73
1708 1850 6.007703 TCCGTCCCAAAATTCTTGTCTTATT 58.992 36.000 0.00 0.00 0.00 1.40
1709 1851 7.169591 TCCGTCCCAAAATTCTTGTCTTATTA 58.830 34.615 0.00 0.00 0.00 0.98
1710 1852 7.335924 TCCGTCCCAAAATTCTTGTCTTATTAG 59.664 37.037 0.00 0.00 0.00 1.73
1711 1853 7.335924 CCGTCCCAAAATTCTTGTCTTATTAGA 59.664 37.037 0.00 0.00 0.00 2.10
1712 1854 8.893727 CGTCCCAAAATTCTTGTCTTATTAGAT 58.106 33.333 0.00 0.00 31.86 1.98
1763 1905 9.725019 TCTTAAAACATGACTTGATACATCTGT 57.275 29.630 0.00 0.00 0.00 3.41
1803 1945 1.639722 AAAAATTTGGGACGGAGGGG 58.360 50.000 0.00 0.00 0.00 4.79
1804 1946 0.252057 AAAATTTGGGACGGAGGGGG 60.252 55.000 0.00 0.00 0.00 5.40
1822 1964 3.010250 GGGGGTAGTTGTCTTGAATCCTT 59.990 47.826 0.00 0.00 0.00 3.36
1847 1991 4.222145 AGTTCTTGACTAAGCCAACCGATA 59.778 41.667 0.00 0.00 36.65 2.92
1870 2014 9.899226 GATAGAACAGTTGCTACAAAAGAAAAT 57.101 29.630 0.13 0.00 0.00 1.82
1941 2106 0.248094 GCGACGGCCTCAAAATAAGC 60.248 55.000 0.00 0.00 0.00 3.09
1942 2107 1.369625 CGACGGCCTCAAAATAAGCT 58.630 50.000 0.00 0.00 0.00 3.74
1943 2108 2.546778 CGACGGCCTCAAAATAAGCTA 58.453 47.619 0.00 0.00 0.00 3.32
1944 2109 2.933906 CGACGGCCTCAAAATAAGCTAA 59.066 45.455 0.00 0.00 0.00 3.09
1945 2110 3.372822 CGACGGCCTCAAAATAAGCTAAA 59.627 43.478 0.00 0.00 0.00 1.85
1946 2111 4.142773 CGACGGCCTCAAAATAAGCTAAAA 60.143 41.667 0.00 0.00 0.00 1.52
1947 2112 5.055642 ACGGCCTCAAAATAAGCTAAAAC 57.944 39.130 0.00 0.00 0.00 2.43
1948 2113 4.521256 ACGGCCTCAAAATAAGCTAAAACA 59.479 37.500 0.00 0.00 0.00 2.83
1949 2114 4.857037 CGGCCTCAAAATAAGCTAAAACAC 59.143 41.667 0.00 0.00 0.00 3.32
1950 2115 5.168569 GGCCTCAAAATAAGCTAAAACACC 58.831 41.667 0.00 0.00 0.00 4.16
1951 2116 4.857037 GCCTCAAAATAAGCTAAAACACCG 59.143 41.667 0.00 0.00 0.00 4.94
1952 2117 4.857037 CCTCAAAATAAGCTAAAACACCGC 59.143 41.667 0.00 0.00 0.00 5.68
1953 2118 5.335661 CCTCAAAATAAGCTAAAACACCGCT 60.336 40.000 0.00 0.00 35.09 5.52
1954 2119 5.457140 TCAAAATAAGCTAAAACACCGCTG 58.543 37.500 0.00 0.00 33.64 5.18
1955 2120 3.487563 AATAAGCTAAAACACCGCTGC 57.512 42.857 0.00 0.00 33.64 5.25
1956 2121 2.178912 TAAGCTAAAACACCGCTGCT 57.821 45.000 0.00 0.00 33.64 4.24
1957 2122 0.593128 AAGCTAAAACACCGCTGCTG 59.407 50.000 0.00 0.00 33.64 4.41
1958 2123 0.250295 AGCTAAAACACCGCTGCTGA 60.250 50.000 0.00 0.00 31.82 4.26
1959 2124 0.591170 GCTAAAACACCGCTGCTGAA 59.409 50.000 0.00 0.00 0.00 3.02
1960 2125 1.200020 GCTAAAACACCGCTGCTGAAT 59.800 47.619 0.00 0.00 0.00 2.57
1961 2126 2.855180 CTAAAACACCGCTGCTGAATG 58.145 47.619 0.00 0.00 0.00 2.67
2048 2215 3.862267 GTGACTGTGGATCGAATCTTGAG 59.138 47.826 0.00 0.00 0.00 3.02
2049 2216 3.511540 TGACTGTGGATCGAATCTTGAGT 59.488 43.478 0.00 0.00 0.00 3.41
2061 2228 0.387929 TCTTGAGTTCTTGACCGCGT 59.612 50.000 4.92 0.00 0.00 6.01
2065 2232 3.335534 GTTCTTGACCGCGTGCGT 61.336 61.111 13.70 0.00 37.81 5.24
2324 2500 1.806623 CGTCAGCCATAGCAAGGTACC 60.807 57.143 2.73 2.73 43.56 3.34
2326 2502 0.179018 CAGCCATAGCAAGGTACCCC 60.179 60.000 8.74 0.00 43.56 4.95
2337 2522 0.547712 AGGTACCCCACAGTCTGCAT 60.548 55.000 8.74 0.00 0.00 3.96
2347 2532 3.878699 CCACAGTCTGCATTGCATACATA 59.121 43.478 23.86 2.67 37.96 2.29
2348 2533 4.260907 CCACAGTCTGCATTGCATACATAC 60.261 45.833 23.86 12.67 37.96 2.39
2349 2534 4.333372 CACAGTCTGCATTGCATACATACA 59.667 41.667 23.86 0.00 37.96 2.29
2350 2535 4.333649 ACAGTCTGCATTGCATACATACAC 59.666 41.667 23.86 8.70 37.96 2.90
2351 2536 4.333372 CAGTCTGCATTGCATACATACACA 59.667 41.667 23.86 0.00 37.96 3.72
2404 2589 2.667969 CGAATCATGCAAGTTGACGAGA 59.332 45.455 7.16 0.00 0.00 4.04
2422 2607 0.176680 GATGATCAGCTGTGGACGGT 59.823 55.000 14.67 0.00 0.00 4.83
2429 2614 2.258591 CTGTGGACGGTGACCTCG 59.741 66.667 0.00 0.00 0.00 4.63
2434 2619 3.566261 GACGGTGACCTCGTCGTA 58.434 61.111 0.00 0.00 45.53 3.43
2500 2685 3.000041 GTGGTGTGAAAGATCGTATGCA 59.000 45.455 0.00 0.00 0.00 3.96
2567 2752 5.238583 AGGTCTCGAATTACCTTTCACAAG 58.761 41.667 7.74 0.00 43.77 3.16
2582 2767 2.694616 ACAAGTTTGTGGGGCCTAAT 57.305 45.000 0.84 0.00 40.49 1.73
2583 2768 3.818295 ACAAGTTTGTGGGGCCTAATA 57.182 42.857 0.84 0.00 40.49 0.98
2617 2802 3.019564 CCCTGATCATTTCACCCTCAAC 58.980 50.000 0.00 0.00 0.00 3.18
2664 2849 2.158885 TGATGTTTTGTCGGTCAGGACA 60.159 45.455 1.41 0.00 44.74 4.02
2667 2852 3.659786 TGTTTTGTCGGTCAGGACATAG 58.340 45.455 1.41 0.00 45.62 2.23
2668 2853 3.000727 GTTTTGTCGGTCAGGACATAGG 58.999 50.000 1.41 0.00 45.62 2.57
2669 2854 2.225382 TTGTCGGTCAGGACATAGGA 57.775 50.000 1.41 0.00 45.62 2.94
2670 2855 1.471119 TGTCGGTCAGGACATAGGAC 58.529 55.000 1.41 4.05 41.76 3.85
2671 2856 1.005569 TGTCGGTCAGGACATAGGACT 59.994 52.381 1.41 0.00 41.76 3.85
2672 2857 1.677052 GTCGGTCAGGACATAGGACTC 59.323 57.143 1.41 0.00 36.91 3.36
2747 4016 2.231235 CTGCATGAAAACTAACCCCACC 59.769 50.000 0.00 0.00 0.00 4.61
2750 4023 2.668144 TGAAAACTAACCCCACCCTG 57.332 50.000 0.00 0.00 0.00 4.45
2775 4048 3.640498 TGAATTTGTGGGCAGTTTCATCA 59.360 39.130 0.00 0.00 0.00 3.07
2972 4245 4.597507 TCCAGAGATAACAAGACCAAGGTT 59.402 41.667 0.00 0.00 0.00 3.50
2973 4246 4.697352 CCAGAGATAACAAGACCAAGGTTG 59.303 45.833 0.00 0.00 0.00 3.77
2989 4262 9.974980 GACCAAGGTTGAGAAATTTTGTTAATA 57.025 29.630 0.00 0.00 0.00 0.98
3018 4291 7.103641 TGACCATCCTAAACTGAAACTATGAC 58.896 38.462 0.00 0.00 0.00 3.06
3102 4375 4.285807 CTTCAACGTGTTTGATGGTCAA 57.714 40.909 0.00 0.00 43.99 3.18
3198 4472 5.215160 CAAGTTGCAACTTATCAACAGTCC 58.785 41.667 37.19 5.21 46.89 3.85
3226 4500 4.409570 CAGGTCATCTTTGCTGATTTTCG 58.590 43.478 0.00 0.00 0.00 3.46
3353 4627 1.871126 GCTTCAAGCTTGTGCCCCTC 61.871 60.000 25.19 6.18 38.45 4.30
3386 4660 2.224159 GGGAGTGTCAGGCTTGGGA 61.224 63.158 0.00 0.00 0.00 4.37
3432 4706 5.686753 TCTACCTGAGATGTAAGACCTCTC 58.313 45.833 5.30 5.30 39.40 3.20
3434 4708 5.718801 ACCTGAGATGTAAGACCTCTCTA 57.281 43.478 11.55 1.11 39.58 2.43
3435 4709 6.274322 ACCTGAGATGTAAGACCTCTCTAT 57.726 41.667 11.55 0.00 39.58 1.98
3436 4710 6.303839 ACCTGAGATGTAAGACCTCTCTATC 58.696 44.000 11.55 0.00 39.58 2.08
3437 4711 6.102615 ACCTGAGATGTAAGACCTCTCTATCT 59.897 42.308 11.55 0.00 39.58 1.98
3438 4712 7.293771 ACCTGAGATGTAAGACCTCTCTATCTA 59.706 40.741 11.55 0.00 39.58 1.98
3472 4746 9.801873 AACAACATATTTATTGGTTAGTCATGC 57.198 29.630 0.00 0.00 0.00 4.06
3480 4754 3.558931 TGGTTAGTCATGCCATAGGTG 57.441 47.619 0.00 0.00 0.00 4.00
3483 4757 4.141801 TGGTTAGTCATGCCATAGGTGTAC 60.142 45.833 0.00 0.00 0.00 2.90
3484 4758 4.141801 GGTTAGTCATGCCATAGGTGTACA 60.142 45.833 0.00 0.00 0.00 2.90
3485 4759 5.424757 GTTAGTCATGCCATAGGTGTACAA 58.575 41.667 0.00 0.00 0.00 2.41
3487 4761 4.917385 AGTCATGCCATAGGTGTACAAAA 58.083 39.130 0.00 0.00 0.00 2.44
3511 4785 7.967890 ATTTCATGAAAATCCAACAAAGGAC 57.032 32.000 23.91 0.00 34.66 3.85
3512 4786 5.119931 TCATGAAAATCCAACAAAGGACG 57.880 39.130 0.00 0.00 41.30 4.79
3517 4791 0.768622 ATCCAACAAAGGACGGACCA 59.231 50.000 0.00 0.00 41.30 4.02
3522 4796 3.000727 CAACAAAGGACGGACCATCTAC 58.999 50.000 0.00 0.00 42.04 2.59
3523 4797 2.537143 ACAAAGGACGGACCATCTACT 58.463 47.619 0.00 0.00 42.04 2.57
3525 4799 3.056035 ACAAAGGACGGACCATCTACTTC 60.056 47.826 0.00 0.00 42.04 3.01
3526 4800 2.526888 AGGACGGACCATCTACTTCA 57.473 50.000 0.00 0.00 42.04 3.02
3527 4801 2.100989 AGGACGGACCATCTACTTCAC 58.899 52.381 0.00 0.00 42.04 3.18
3528 4802 1.822990 GGACGGACCATCTACTTCACA 59.177 52.381 0.00 0.00 38.79 3.58
3529 4803 2.232941 GGACGGACCATCTACTTCACAA 59.767 50.000 0.00 0.00 38.79 3.33
3530 4804 3.251571 GACGGACCATCTACTTCACAAC 58.748 50.000 0.00 0.00 0.00 3.32
3531 4805 2.028385 ACGGACCATCTACTTCACAACC 60.028 50.000 0.00 0.00 0.00 3.77
3532 4806 2.233922 CGGACCATCTACTTCACAACCT 59.766 50.000 0.00 0.00 0.00 3.50
3533 4807 3.676324 CGGACCATCTACTTCACAACCTC 60.676 52.174 0.00 0.00 0.00 3.85
3534 4808 3.369576 GGACCATCTACTTCACAACCTCC 60.370 52.174 0.00 0.00 0.00 4.30
3535 4809 3.248024 ACCATCTACTTCACAACCTCCA 58.752 45.455 0.00 0.00 0.00 3.86
3536 4810 3.650942 ACCATCTACTTCACAACCTCCAA 59.349 43.478 0.00 0.00 0.00 3.53
3537 4811 4.104102 ACCATCTACTTCACAACCTCCAAA 59.896 41.667 0.00 0.00 0.00 3.28
3538 4812 5.222130 ACCATCTACTTCACAACCTCCAAAT 60.222 40.000 0.00 0.00 0.00 2.32
3556 4830 6.047870 TCCAAATTTCCACAAACTTCATGTG 58.952 36.000 0.00 0.00 46.05 3.21
3558 4832 4.669206 ATTTCCACAAACTTCATGTGCA 57.331 36.364 1.24 0.00 45.32 4.57
3560 4834 4.669206 TTCCACAAACTTCATGTGCAAT 57.331 36.364 0.00 0.00 45.32 3.56
3561 4835 4.241590 TCCACAAACTTCATGTGCAATC 57.758 40.909 0.00 0.00 45.32 2.67
3562 4836 3.005684 TCCACAAACTTCATGTGCAATCC 59.994 43.478 0.00 0.00 45.32 3.01
3563 4837 3.243805 CCACAAACTTCATGTGCAATCCA 60.244 43.478 0.00 0.00 45.32 3.41
3567 4867 1.547372 ACTTCATGTGCAATCCAAGCC 59.453 47.619 0.00 0.00 0.00 4.35
3568 4868 1.822990 CTTCATGTGCAATCCAAGCCT 59.177 47.619 0.00 0.00 0.00 4.58
3624 4924 5.997746 TGCTTAACTATGTCACTGCTCTTTT 59.002 36.000 0.00 0.00 0.00 2.27
3627 4927 8.669243 GCTTAACTATGTCACTGCTCTTTTAAT 58.331 33.333 0.00 0.00 0.00 1.40
3643 4943 7.361286 GCTCTTTTAATAGACAAACCTCCAGTG 60.361 40.741 0.00 0.00 0.00 3.66
3781 5081 0.529378 GCCTTGTGGGATCAAAGCTG 59.471 55.000 0.00 0.00 37.23 4.24
3820 5120 3.169908 GGCAAGAAACCATTCCCCTTTA 58.830 45.455 0.00 0.00 36.12 1.85
3821 5121 3.195610 GGCAAGAAACCATTCCCCTTTAG 59.804 47.826 0.00 0.00 36.12 1.85
3823 5123 4.283467 GCAAGAAACCATTCCCCTTTAGTT 59.717 41.667 0.00 0.00 36.12 2.24
3824 5124 5.479027 GCAAGAAACCATTCCCCTTTAGTTA 59.521 40.000 0.00 0.00 36.12 2.24
3825 5125 6.014925 GCAAGAAACCATTCCCCTTTAGTTAA 60.015 38.462 0.00 0.00 36.12 2.01
3826 5126 7.472240 GCAAGAAACCATTCCCCTTTAGTTAAA 60.472 37.037 0.00 0.00 36.12 1.52
3827 5127 8.425703 CAAGAAACCATTCCCCTTTAGTTAAAA 58.574 33.333 0.00 0.00 36.12 1.52
3828 5128 8.190326 AGAAACCATTCCCCTTTAGTTAAAAG 57.810 34.615 0.00 0.00 39.22 2.27
3829 5129 8.008332 AGAAACCATTCCCCTTTAGTTAAAAGA 58.992 33.333 0.00 0.00 40.54 2.52
3851 5152 6.662755 AGATAAAACCATCTGCAGTCCAATA 58.337 36.000 14.67 0.00 33.93 1.90
3869 5170 2.789491 TAGAGATGCATGCTCACTCG 57.211 50.000 20.33 0.00 34.85 4.18
3870 5171 0.104487 AGAGATGCATGCTCACTCGG 59.896 55.000 20.33 0.00 34.85 4.63
3931 5232 2.079170 TGAGACTGCATCTAGAGGGG 57.921 55.000 6.52 0.00 38.00 4.79
3937 5238 3.452627 GACTGCATCTAGAGGGGAAGAAA 59.547 47.826 6.52 0.00 0.00 2.52
3949 5250 4.874199 AGGGGAAGAAAAACAACAGGTTA 58.126 39.130 0.00 0.00 39.29 2.85
3952 5253 4.341235 GGGAAGAAAAACAACAGGTTAGCT 59.659 41.667 0.00 0.00 39.29 3.32
3960 5261 3.670625 ACAACAGGTTAGCTGCGATTAA 58.329 40.909 11.64 0.00 0.00 1.40
3962 5263 3.328382 ACAGGTTAGCTGCGATTAACA 57.672 42.857 11.64 0.00 32.68 2.41
3965 5266 3.435327 CAGGTTAGCTGCGATTAACAACA 59.565 43.478 11.00 0.00 32.68 3.33
3969 5270 5.163754 GGTTAGCTGCGATTAACAACATTCT 60.164 40.000 11.00 0.00 32.68 2.40
3970 5271 4.346734 AGCTGCGATTAACAACATTCTG 57.653 40.909 0.00 0.00 0.00 3.02
3988 5290 6.998338 CATTCTGTTAGCAGTATGTTCAGTC 58.002 40.000 15.19 0.00 42.13 3.51
3996 5298 4.081752 AGCAGTATGTTCAGTCTCCTTCTG 60.082 45.833 0.00 0.00 39.31 3.02
4008 5345 3.503748 GTCTCCTTCTGTTGGAATGTTGG 59.496 47.826 0.00 0.00 33.01 3.77
4080 5417 1.303317 AGCACCCCAACGTTCATCC 60.303 57.895 0.00 0.00 0.00 3.51
4373 5710 3.303135 AACACGGCGAGGCTCTCA 61.303 61.111 16.62 0.00 0.00 3.27
4607 5944 2.034124 ACAGGTGCAAAGCTTGATGTT 58.966 42.857 0.00 0.00 0.00 2.71
4610 5947 2.035066 AGGTGCAAAGCTTGATGTTGAC 59.965 45.455 0.00 0.00 0.00 3.18
4628 5965 2.568956 TGACAAGGGGAAGATCTCACTG 59.431 50.000 0.00 0.00 0.00 3.66
4720 6057 7.423199 ACTTGCTATATCTTTGTCATGCATTG 58.577 34.615 0.00 0.00 0.00 2.82
4730 6067 7.040494 TCTTTGTCATGCATTGTTTCAGAAAA 58.960 30.769 0.00 0.00 0.00 2.29
4755 6092 3.335711 GGGAATCAGACCCAGGGG 58.664 66.667 11.37 6.87 46.05 4.79
4756 6093 1.307866 GGGAATCAGACCCAGGGGA 60.308 63.158 11.37 0.00 46.05 4.81
4757 6094 0.919289 GGGAATCAGACCCAGGGGAA 60.919 60.000 11.37 0.00 46.05 3.97
4758 6095 0.999712 GGAATCAGACCCAGGGGAAA 59.000 55.000 11.37 0.00 38.96 3.13
4759 6096 1.570979 GGAATCAGACCCAGGGGAAAT 59.429 52.381 11.37 0.00 38.96 2.17
4760 6097 2.423517 GGAATCAGACCCAGGGGAAATC 60.424 54.545 11.37 0.00 38.96 2.17
4761 6098 1.226311 ATCAGACCCAGGGGAAATCC 58.774 55.000 11.37 0.00 38.96 3.01
4773 6110 2.360209 GGGGAAATCCAATCCAATGGGA 60.360 50.000 0.00 0.00 42.62 4.37
4777 6114 4.680440 GGAAATCCAATCCAATGGGAAACG 60.680 45.833 0.00 0.00 40.69 3.60
4798 6135 4.214437 CGTTTCTGTTTCTGATTGTCAGC 58.786 43.478 2.13 0.00 43.95 4.26
4811 6148 6.012658 TGATTGTCAGCCTGAAATGTAAAC 57.987 37.500 0.00 0.00 0.00 2.01
4812 6149 5.769662 TGATTGTCAGCCTGAAATGTAAACT 59.230 36.000 0.00 0.00 0.00 2.66
4813 6150 6.265196 TGATTGTCAGCCTGAAATGTAAACTT 59.735 34.615 0.00 0.00 0.00 2.66
4815 6152 7.575414 TTGTCAGCCTGAAATGTAAACTTAA 57.425 32.000 0.00 0.00 0.00 1.85
4839 6176 6.884832 AGACGAGTATTGTAATGGAATTCCA 58.115 36.000 28.92 28.92 41.63 3.53
4841 6178 7.280205 AGACGAGTATTGTAATGGAATTCCAAC 59.720 37.037 30.28 23.82 40.99 3.77
4849 6186 2.584835 TGGAATTCCAACCCAGACAG 57.415 50.000 25.13 0.00 44.35 3.51
4851 6188 0.804989 GAATTCCAACCCAGACAGCG 59.195 55.000 0.00 0.00 0.00 5.18
4852 6189 0.609131 AATTCCAACCCAGACAGCGG 60.609 55.000 0.00 0.00 0.00 5.52
4911 6249 3.882888 ACAATATATTCACAACCTGGGCG 59.117 43.478 0.00 0.00 0.00 6.13
4972 6311 3.007398 GCTACATTACAGATGGGAGAGGG 59.993 52.174 0.00 0.00 0.00 4.30
4997 6337 1.115930 AGACCGCCCAGCCTATACAG 61.116 60.000 0.00 0.00 0.00 2.74
5156 6497 2.996249 ACAGGGTCATCTGTGCTATG 57.004 50.000 0.00 0.00 45.27 2.23
5285 6626 4.025401 CGTGCCAACCCACTTCGC 62.025 66.667 0.00 0.00 33.60 4.70
5331 6672 4.069304 CAAAATTCACGGTGGGTTAGAGA 58.931 43.478 8.50 0.00 0.00 3.10
5349 6690 9.660180 GGTTAGAGAAAGAAACTGTATGAAGAT 57.340 33.333 0.00 0.00 0.00 2.40
5362 6703 9.725019 AACTGTATGAAGATGTGTAATTTCAGA 57.275 29.630 0.00 0.00 33.53 3.27
5378 6719 7.855784 AATTTCAGAAAGAGGGTGGTAAAAT 57.144 32.000 1.28 0.00 0.00 1.82
5380 6721 7.996098 TTTCAGAAAGAGGGTGGTAAAATAG 57.004 36.000 0.00 0.00 0.00 1.73
5384 6725 9.053472 TCAGAAAGAGGGTGGTAAAATAGAATA 57.947 33.333 0.00 0.00 0.00 1.75
5417 6758 5.831997 ACTTTTTCAGTTTCACCACATAGC 58.168 37.500 0.00 0.00 27.32 2.97
5425 6766 2.768253 TCACCACATAGCAGTTGAGG 57.232 50.000 0.00 0.00 0.00 3.86
5427 6768 2.028112 TCACCACATAGCAGTTGAGGTC 60.028 50.000 0.83 0.00 36.13 3.85
5431 6772 4.225042 ACCACATAGCAGTTGAGGTCATAA 59.775 41.667 0.00 0.00 33.47 1.90
5433 6774 4.813161 CACATAGCAGTTGAGGTCATAAGG 59.187 45.833 0.00 0.00 0.00 2.69
5434 6775 4.471386 ACATAGCAGTTGAGGTCATAAGGT 59.529 41.667 0.00 0.00 0.00 3.50
5435 6776 5.045578 ACATAGCAGTTGAGGTCATAAGGTT 60.046 40.000 0.00 0.00 0.00 3.50
5436 6777 4.373156 AGCAGTTGAGGTCATAAGGTTT 57.627 40.909 0.00 0.00 0.00 3.27
5439 6782 5.013183 AGCAGTTGAGGTCATAAGGTTTAGT 59.987 40.000 0.00 0.00 0.00 2.24
5446 6789 6.070767 TGAGGTCATAAGGTTTAGTCTTGAGG 60.071 42.308 0.00 0.00 0.00 3.86
5482 6825 6.944557 ATCAAAATTACTAAGCGGCAAAAC 57.055 33.333 1.45 0.00 0.00 2.43
5520 6864 5.761234 TGTTGTAAATGTAGTTCTGTCACCC 59.239 40.000 0.00 0.00 0.00 4.61
5533 6877 5.097742 TCTGTCACCCGAATAATTCACAT 57.902 39.130 0.00 0.00 0.00 3.21
5534 6878 4.875536 TCTGTCACCCGAATAATTCACATG 59.124 41.667 0.00 0.00 0.00 3.21
5535 6879 3.376859 TGTCACCCGAATAATTCACATGC 59.623 43.478 0.00 0.00 0.00 4.06
5543 6896 4.531332 GAATAATTCACATGCTTCCTCGC 58.469 43.478 0.00 0.00 0.00 5.03
5603 6957 9.330063 CTAATCACTAAGAGCAAATATGGACAA 57.670 33.333 0.00 0.00 0.00 3.18
5621 6975 2.542432 AAAAATTGCATGTGCGCCC 58.458 47.368 4.18 0.00 45.83 6.13
5641 6995 5.163854 CGCCCTAACAAAACTAAGATCACTG 60.164 44.000 0.00 0.00 0.00 3.66
5642 6996 5.938125 GCCCTAACAAAACTAAGATCACTGA 59.062 40.000 0.00 0.00 0.00 3.41
5643 6997 6.599638 GCCCTAACAAAACTAAGATCACTGAT 59.400 38.462 0.00 0.00 0.00 2.90
5644 6998 7.769044 GCCCTAACAAAACTAAGATCACTGATA 59.231 37.037 0.00 0.00 0.00 2.15
5645 6999 9.838339 CCCTAACAAAACTAAGATCACTGATAT 57.162 33.333 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 9.772973 AACAACCTTTAGAAATTAATTGAACCC 57.227 29.630 0.39 0.00 0.00 4.11
117 199 8.141298 TGAAAGTGGATACTGTATCACCTAAA 57.859 34.615 24.71 9.30 37.19 1.85
129 211 5.649831 GCTTCCTCATTTGAAAGTGGATACT 59.350 40.000 0.00 0.00 39.32 2.12
130 212 5.163612 GGCTTCCTCATTTGAAAGTGGATAC 60.164 44.000 0.00 0.00 0.00 2.24
206 291 6.179756 TGATTCTTTTGTGGCTAGATTGCTA 58.820 36.000 0.00 0.00 0.00 3.49
208 293 5.314923 TGATTCTTTTGTGGCTAGATTGC 57.685 39.130 0.00 0.00 0.00 3.56
235 320 4.055360 CCCTGAATATTTGTATCGCACGA 58.945 43.478 0.00 0.00 0.00 4.35
238 323 4.698201 TCCCCTGAATATTTGTATCGCA 57.302 40.909 0.00 0.00 0.00 5.10
249 334 2.438021 CCCTCATCGTTTCCCCTGAATA 59.562 50.000 0.00 0.00 0.00 1.75
457 543 3.697045 CCCTAGAGTGACTAGTGTTGGAG 59.303 52.174 0.00 0.00 45.01 3.86
462 548 5.580998 TCAATTCCCTAGAGTGACTAGTGT 58.419 41.667 0.00 0.00 45.01 3.55
513 599 1.155390 TGACAGAGACCCGGGTTCT 59.845 57.895 30.89 26.77 0.00 3.01
517 603 2.603473 TGGTGACAGAGACCCGGG 60.603 66.667 22.25 22.25 35.01 5.73
547 633 3.694072 TGGACACCGGATTTGAATTGATC 59.306 43.478 9.46 0.00 0.00 2.92
641 745 7.593875 TTCTTGTTGAATTGAACACCTTTTG 57.406 32.000 10.16 0.00 35.56 2.44
671 782 5.685841 TGCTATTTTTCGTCTCCTTTTTCG 58.314 37.500 0.00 0.00 0.00 3.46
680 791 3.375299 GTCATGGCTGCTATTTTTCGTCT 59.625 43.478 0.00 0.00 0.00 4.18
681 792 3.487544 GGTCATGGCTGCTATTTTTCGTC 60.488 47.826 0.00 0.00 0.00 4.20
721 832 4.760220 GGAGCAAGGGGAGGGGGA 62.760 72.222 0.00 0.00 0.00 4.81
777 888 7.923344 GCACTTGTTGTCTCAGAGTATATACAT 59.077 37.037 15.18 0.44 0.00 2.29
778 889 7.258441 GCACTTGTTGTCTCAGAGTATATACA 58.742 38.462 15.18 0.00 0.00 2.29
779 890 6.697892 GGCACTTGTTGTCTCAGAGTATATAC 59.302 42.308 4.60 4.60 0.00 1.47
780 891 6.379988 TGGCACTTGTTGTCTCAGAGTATATA 59.620 38.462 0.00 0.00 0.00 0.86
781 892 5.187772 TGGCACTTGTTGTCTCAGAGTATAT 59.812 40.000 0.00 0.00 0.00 0.86
782 893 4.526650 TGGCACTTGTTGTCTCAGAGTATA 59.473 41.667 0.00 0.00 0.00 1.47
783 894 3.324846 TGGCACTTGTTGTCTCAGAGTAT 59.675 43.478 0.00 0.00 0.00 2.12
784 895 2.698274 TGGCACTTGTTGTCTCAGAGTA 59.302 45.455 0.00 0.00 0.00 2.59
785 896 1.486310 TGGCACTTGTTGTCTCAGAGT 59.514 47.619 0.00 0.00 0.00 3.24
848 959 2.664851 CGTGCTGCCTGGAAACGA 60.665 61.111 0.00 0.00 36.38 3.85
879 990 2.198827 TGCATCCAATTGTCCGTCTT 57.801 45.000 4.43 0.00 0.00 3.01
907 1018 4.840772 CGCAAGTTTCTCAATACGTCAAAG 59.159 41.667 0.00 0.00 0.00 2.77
908 1019 4.768145 CGCAAGTTTCTCAATACGTCAAA 58.232 39.130 0.00 0.00 0.00 2.69
926 1037 0.804544 GACCGGATCAATCGACGCAA 60.805 55.000 9.46 0.00 0.00 4.85
928 1039 1.949631 GGACCGGATCAATCGACGC 60.950 63.158 9.46 0.00 0.00 5.19
976 1087 0.914551 CGATCAACGAACCAGCGTAG 59.085 55.000 0.00 0.00 44.86 3.51
979 1090 1.289109 AACCGATCAACGAACCAGCG 61.289 55.000 0.00 0.00 45.77 5.18
1331 1445 8.850156 CAAAATTAGAGGACCTCTCAAGAAAAA 58.150 33.333 27.64 14.51 44.81 1.94
1345 1465 6.313519 AGGCATCAGTACAAAATTAGAGGA 57.686 37.500 0.00 0.00 0.00 3.71
1357 1477 3.432326 CCCCAACTCTAAGGCATCAGTAC 60.432 52.174 0.00 0.00 0.00 2.73
1405 1525 5.583061 ACAAATTCCACTTGCATGCATATTG 59.417 36.000 23.37 17.62 0.00 1.90
1407 1527 5.347620 ACAAATTCCACTTGCATGCATAT 57.652 34.783 23.37 10.00 0.00 1.78
1414 1534 2.694628 AGCTCAACAAATTCCACTTGCA 59.305 40.909 0.00 0.00 0.00 4.08
1418 1538 5.769662 TGAACATAGCTCAACAAATTCCACT 59.230 36.000 0.00 0.00 0.00 4.00
1549 1689 4.200092 GCGAGGGAACTGGATTAGAATTT 58.800 43.478 0.00 0.00 44.43 1.82
1550 1690 3.199946 TGCGAGGGAACTGGATTAGAATT 59.800 43.478 0.00 0.00 44.43 2.17
1580 1720 1.544691 GGCGAGGAGTTGAGTACTTGA 59.455 52.381 0.00 0.00 37.17 3.02
1612 1754 4.568359 GCTGCTCTGATTAGTTTGATCGAA 59.432 41.667 0.00 0.00 0.00 3.71
1613 1755 4.115516 GCTGCTCTGATTAGTTTGATCGA 58.884 43.478 0.00 0.00 0.00 3.59
1679 1821 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1681 1823 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1682 1824 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1684 1826 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1685 1827 5.897377 ATAAGACAAGAATTTTGGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
1686 1828 8.263940 TCTAATAAGACAAGAATTTTGGGACG 57.736 34.615 5.68 0.00 0.00 4.79
1737 1879 9.725019 ACAGATGTATCAAGTCATGTTTTAAGA 57.275 29.630 0.00 0.00 0.00 2.10
1784 1926 1.639722 CCCCTCCGTCCCAAATTTTT 58.360 50.000 0.00 0.00 0.00 1.94
1785 1927 0.252057 CCCCCTCCGTCCCAAATTTT 60.252 55.000 0.00 0.00 0.00 1.82
1786 1928 1.386550 CCCCCTCCGTCCCAAATTT 59.613 57.895 0.00 0.00 0.00 1.82
1787 1929 0.550638 TACCCCCTCCGTCCCAAATT 60.551 55.000 0.00 0.00 0.00 1.82
1788 1930 0.986550 CTACCCCCTCCGTCCCAAAT 60.987 60.000 0.00 0.00 0.00 2.32
1789 1931 1.614226 CTACCCCCTCCGTCCCAAA 60.614 63.158 0.00 0.00 0.00 3.28
1790 1932 2.039951 CTACCCCCTCCGTCCCAA 59.960 66.667 0.00 0.00 0.00 4.12
1791 1933 2.872250 AACTACCCCCTCCGTCCCA 61.872 63.158 0.00 0.00 0.00 4.37
1792 1934 2.040114 AACTACCCCCTCCGTCCC 59.960 66.667 0.00 0.00 0.00 4.46
1793 1935 1.611474 GACAACTACCCCCTCCGTCC 61.611 65.000 0.00 0.00 0.00 4.79
1794 1936 0.614134 AGACAACTACCCCCTCCGTC 60.614 60.000 0.00 0.00 0.00 4.79
1795 1937 0.178912 AAGACAACTACCCCCTCCGT 60.179 55.000 0.00 0.00 0.00 4.69
1796 1938 0.249398 CAAGACAACTACCCCCTCCG 59.751 60.000 0.00 0.00 0.00 4.63
1797 1939 1.652947 TCAAGACAACTACCCCCTCC 58.347 55.000 0.00 0.00 0.00 4.30
1798 1940 3.370633 GGATTCAAGACAACTACCCCCTC 60.371 52.174 0.00 0.00 0.00 4.30
1799 1941 2.576648 GGATTCAAGACAACTACCCCCT 59.423 50.000 0.00 0.00 0.00 4.79
1800 1942 2.576648 AGGATTCAAGACAACTACCCCC 59.423 50.000 0.00 0.00 0.00 5.40
1801 1943 4.010349 CAAGGATTCAAGACAACTACCCC 58.990 47.826 0.00 0.00 0.00 4.95
1802 1944 4.906618 TCAAGGATTCAAGACAACTACCC 58.093 43.478 0.00 0.00 0.00 3.69
1803 1945 5.552178 ACTCAAGGATTCAAGACAACTACC 58.448 41.667 0.00 0.00 0.00 3.18
1804 1946 6.931840 AGAACTCAAGGATTCAAGACAACTAC 59.068 38.462 0.00 0.00 0.00 2.73
1822 1964 3.740115 GGTTGGCTTAGTCAAGAACTCA 58.260 45.455 0.00 0.00 39.55 3.41
1847 1991 8.903820 AGTATTTTCTTTTGTAGCAACTGTTCT 58.096 29.630 0.00 0.00 0.00 3.01
1870 2014 9.905713 AACTTTGATAAATTCTCTGCCATAGTA 57.094 29.630 0.00 0.00 0.00 1.82
1905 2049 0.664166 CGCTGTTTGCCATTGTCCAC 60.664 55.000 0.00 0.00 38.78 4.02
1941 2106 2.483877 TCATTCAGCAGCGGTGTTTTAG 59.516 45.455 17.07 0.00 32.43 1.85
1942 2107 2.225491 GTCATTCAGCAGCGGTGTTTTA 59.775 45.455 17.07 0.46 32.43 1.52
1943 2108 1.001378 GTCATTCAGCAGCGGTGTTTT 60.001 47.619 17.07 0.00 32.43 2.43
1944 2109 0.593128 GTCATTCAGCAGCGGTGTTT 59.407 50.000 17.07 2.00 32.43 2.83
1945 2110 0.250467 AGTCATTCAGCAGCGGTGTT 60.250 50.000 17.07 7.43 32.43 3.32
1946 2111 0.608130 TAGTCATTCAGCAGCGGTGT 59.392 50.000 17.07 0.00 32.43 4.16
1947 2112 1.725641 TTAGTCATTCAGCAGCGGTG 58.274 50.000 10.98 10.98 0.00 4.94
1948 2113 2.472695 TTTAGTCATTCAGCAGCGGT 57.527 45.000 0.00 0.00 0.00 5.68
1949 2114 2.159517 GGTTTTAGTCATTCAGCAGCGG 60.160 50.000 0.00 0.00 0.00 5.52
1950 2115 2.474526 CGGTTTTAGTCATTCAGCAGCG 60.475 50.000 0.00 0.00 0.00 5.18
1951 2116 2.484264 ACGGTTTTAGTCATTCAGCAGC 59.516 45.455 0.00 0.00 0.00 5.25
1952 2117 4.749245 AACGGTTTTAGTCATTCAGCAG 57.251 40.909 0.00 0.00 0.00 4.24
1953 2118 7.225931 GGATATAACGGTTTTAGTCATTCAGCA 59.774 37.037 0.00 0.00 0.00 4.41
1954 2119 7.307811 GGGATATAACGGTTTTAGTCATTCAGC 60.308 40.741 0.00 0.00 0.00 4.26
1955 2120 7.095774 CGGGATATAACGGTTTTAGTCATTCAG 60.096 40.741 0.00 0.00 0.00 3.02
1956 2121 6.702723 CGGGATATAACGGTTTTAGTCATTCA 59.297 38.462 0.00 0.00 0.00 2.57
1957 2122 6.347160 GCGGGATATAACGGTTTTAGTCATTC 60.347 42.308 0.00 0.00 0.00 2.67
1958 2123 5.467735 GCGGGATATAACGGTTTTAGTCATT 59.532 40.000 0.00 0.00 0.00 2.57
1959 2124 4.992951 GCGGGATATAACGGTTTTAGTCAT 59.007 41.667 0.00 0.00 0.00 3.06
1960 2125 4.099881 AGCGGGATATAACGGTTTTAGTCA 59.900 41.667 0.00 0.00 37.57 3.41
1961 2126 4.625028 AGCGGGATATAACGGTTTTAGTC 58.375 43.478 0.00 0.00 37.57 2.59
2031 2198 4.808414 AGAACTCAAGATTCGATCCACA 57.192 40.909 0.00 0.00 0.00 4.17
2048 2215 3.335534 ACGCACGCGGTCAAGAAC 61.336 61.111 16.70 0.00 44.69 3.01
2049 2216 3.334751 CACGCACGCGGTCAAGAA 61.335 61.111 16.70 0.00 44.69 2.52
2065 2232 2.169146 CGTCATCTGCATGCTCGCA 61.169 57.895 20.33 0.00 40.32 5.10
2069 2236 1.523258 GCTCCGTCATCTGCATGCT 60.523 57.895 20.33 0.00 0.00 3.79
2324 2500 1.402968 GTATGCAATGCAGACTGTGGG 59.597 52.381 23.75 0.00 45.71 4.61
2337 2522 3.313249 GCTGCTCATGTGTATGTATGCAA 59.687 43.478 0.00 0.00 36.53 4.08
2367 2552 1.769733 TTCGTTTCCAAGTACGGTCG 58.230 50.000 0.00 0.00 38.26 4.79
2404 2589 0.107993 CACCGTCCACAGCTGATCAT 60.108 55.000 23.35 0.00 0.00 2.45
2422 2607 0.038892 GGCAAAGTACGACGAGGTCA 60.039 55.000 0.00 0.00 32.09 4.02
2429 2614 3.187700 CACTATCCTGGCAAAGTACGAC 58.812 50.000 0.00 0.00 0.00 4.34
2434 2619 2.440409 CTTGCACTATCCTGGCAAAGT 58.560 47.619 0.00 0.00 45.78 2.66
2500 2685 0.109319 GTCAATTTTCCACCGCGCAT 60.109 50.000 8.75 0.00 0.00 4.73
2567 2752 7.002276 ACATACTATTATTAGGCCCCACAAAC 58.998 38.462 0.00 0.00 0.00 2.93
2582 2767 9.778741 GAAATGATCAGGGTTCACATACTATTA 57.221 33.333 0.09 0.00 0.00 0.98
2583 2768 8.274322 TGAAATGATCAGGGTTCACATACTATT 58.726 33.333 12.75 0.00 33.04 1.73
2655 2840 1.033574 CCGAGTCCTATGTCCTGACC 58.966 60.000 0.00 0.00 0.00 4.02
2664 2849 1.133730 GGTCCTGAGTCCGAGTCCTAT 60.134 57.143 0.62 0.00 0.00 2.57
2667 2852 2.053277 GGGTCCTGAGTCCGAGTCC 61.053 68.421 0.62 0.00 0.00 3.85
2668 2853 0.898789 TTGGGTCCTGAGTCCGAGTC 60.899 60.000 0.00 0.00 0.00 3.36
2669 2854 0.900647 CTTGGGTCCTGAGTCCGAGT 60.901 60.000 0.00 0.00 0.00 4.18
2670 2855 0.612174 TCTTGGGTCCTGAGTCCGAG 60.612 60.000 0.00 0.00 34.22 4.63
2671 2856 0.041238 ATCTTGGGTCCTGAGTCCGA 59.959 55.000 0.00 0.00 0.00 4.55
2672 2857 0.176680 CATCTTGGGTCCTGAGTCCG 59.823 60.000 0.00 0.00 0.00 4.79
2747 4016 1.000060 CTGCCCACAAATTCACACAGG 60.000 52.381 0.00 0.00 0.00 4.00
2750 4023 2.888834 AACTGCCCACAAATTCACAC 57.111 45.000 0.00 0.00 0.00 3.82
2758 4031 2.942804 TCTTGATGAAACTGCCCACAA 58.057 42.857 0.00 0.00 0.00 3.33
2763 4036 3.125316 CCGTACTTCTTGATGAAACTGCC 59.875 47.826 0.00 0.00 33.79 4.85
2775 4048 0.606604 ATGTGCGTCCCGTACTTCTT 59.393 50.000 6.43 0.00 42.49 2.52
2873 4146 3.740764 GCTTCTCTAGGTGCTCCTTGATG 60.741 52.174 17.35 12.22 42.66 3.07
2989 4262 6.784031 AGTTTCAGTTTAGGATGGTCAGAAT 58.216 36.000 0.00 0.00 0.00 2.40
3002 4275 6.335471 TGAGGTCGTCATAGTTTCAGTTTA 57.665 37.500 0.00 0.00 0.00 2.01
3018 4291 2.146342 AGCACATTTCACTTGAGGTCG 58.854 47.619 0.00 0.00 0.00 4.79
3098 4371 1.737793 CCCTCGGCTGTGTTAATTGAC 59.262 52.381 0.00 0.00 0.00 3.18
3099 4372 1.349688 ACCCTCGGCTGTGTTAATTGA 59.650 47.619 0.00 0.00 0.00 2.57
3102 4375 1.349688 TCAACCCTCGGCTGTGTTAAT 59.650 47.619 0.00 0.00 0.00 1.40
3198 4472 2.161808 CAGCAAAGATGACCTGCTTCAG 59.838 50.000 0.00 0.00 43.83 3.02
3226 4500 2.042831 GTCACACCCTGCATCAGCC 61.043 63.158 0.00 0.00 41.13 4.85
3386 4660 4.414846 AGGTTTATGGCATGAGAGAGGAAT 59.585 41.667 10.98 0.00 0.00 3.01
3454 4728 7.231317 CACCTATGGCATGACTAACCAATAAAT 59.769 37.037 10.98 0.00 36.94 1.40
3458 4732 4.079787 ACACCTATGGCATGACTAACCAAT 60.080 41.667 10.98 0.00 36.94 3.16
3459 4733 3.265737 ACACCTATGGCATGACTAACCAA 59.734 43.478 10.98 0.00 36.94 3.67
3460 4734 2.843730 ACACCTATGGCATGACTAACCA 59.156 45.455 10.98 0.00 37.99 3.67
3461 4735 3.560636 ACACCTATGGCATGACTAACC 57.439 47.619 10.98 0.00 0.00 2.85
3471 4745 6.862209 TCATGAAATTTTGTACACCTATGGC 58.138 36.000 0.00 0.00 0.00 4.40
3472 4746 9.703892 TTTTCATGAAATTTTGTACACCTATGG 57.296 29.630 21.10 0.00 0.00 2.74
3483 4757 9.453325 CCTTTGTTGGATTTTCATGAAATTTTG 57.547 29.630 21.10 4.65 38.06 2.44
3484 4758 9.406113 TCCTTTGTTGGATTTTCATGAAATTTT 57.594 25.926 21.10 9.69 38.06 1.82
3485 4759 8.839343 GTCCTTTGTTGGATTTTCATGAAATTT 58.161 29.630 21.10 12.09 38.06 1.82
3487 4761 6.646240 CGTCCTTTGTTGGATTTTCATGAAAT 59.354 34.615 21.10 11.46 40.61 2.17
3499 4773 0.768622 ATGGTCCGTCCTTTGTTGGA 59.231 50.000 0.00 0.00 37.07 3.53
3500 4774 1.165270 GATGGTCCGTCCTTTGTTGG 58.835 55.000 0.00 0.00 37.07 3.77
3511 4785 2.233922 AGGTTGTGAAGTAGATGGTCCG 59.766 50.000 0.00 0.00 0.00 4.79
3512 4786 3.369576 GGAGGTTGTGAAGTAGATGGTCC 60.370 52.174 0.00 0.00 0.00 4.46
3517 4791 6.434340 GGAAATTTGGAGGTTGTGAAGTAGAT 59.566 38.462 0.00 0.00 0.00 1.98
3522 4796 4.099266 TGTGGAAATTTGGAGGTTGTGAAG 59.901 41.667 0.00 0.00 0.00 3.02
3523 4797 4.026744 TGTGGAAATTTGGAGGTTGTGAA 58.973 39.130 0.00 0.00 0.00 3.18
3525 4799 4.399004 TTGTGGAAATTTGGAGGTTGTG 57.601 40.909 0.00 0.00 0.00 3.33
3526 4800 4.469586 AGTTTGTGGAAATTTGGAGGTTGT 59.530 37.500 0.00 0.00 0.00 3.32
3527 4801 5.022282 AGTTTGTGGAAATTTGGAGGTTG 57.978 39.130 0.00 0.00 0.00 3.77
3528 4802 5.188751 TGAAGTTTGTGGAAATTTGGAGGTT 59.811 36.000 0.00 0.00 0.00 3.50
3529 4803 4.714308 TGAAGTTTGTGGAAATTTGGAGGT 59.286 37.500 0.00 0.00 0.00 3.85
3530 4804 5.275067 TGAAGTTTGTGGAAATTTGGAGG 57.725 39.130 0.00 0.00 0.00 4.30
3531 4805 6.201425 CACATGAAGTTTGTGGAAATTTGGAG 59.799 38.462 0.00 0.00 40.60 3.86
3532 4806 6.047870 CACATGAAGTTTGTGGAAATTTGGA 58.952 36.000 0.00 0.00 40.60 3.53
3533 4807 5.277442 GCACATGAAGTTTGTGGAAATTTGG 60.277 40.000 0.00 0.00 43.69 3.28
3534 4808 5.293814 TGCACATGAAGTTTGTGGAAATTTG 59.706 36.000 0.00 0.00 41.60 2.32
3535 4809 5.426504 TGCACATGAAGTTTGTGGAAATTT 58.573 33.333 0.00 0.00 41.60 1.82
3536 4810 5.021033 TGCACATGAAGTTTGTGGAAATT 57.979 34.783 0.00 0.00 41.60 1.82
3537 4811 4.669206 TGCACATGAAGTTTGTGGAAAT 57.331 36.364 0.00 0.00 41.60 2.17
3624 4924 5.783360 TCTTCCACTGGAGGTTTGTCTATTA 59.217 40.000 7.06 0.00 31.21 0.98
3627 4927 3.583228 TCTTCCACTGGAGGTTTGTCTA 58.417 45.455 7.06 0.00 31.21 2.59
3781 5081 1.336240 GCCTGGTTTGAGTTGACATGC 60.336 52.381 0.00 0.00 0.00 4.06
3820 5120 8.409358 ACTGCAGATGGTTTTATCTTTTAACT 57.591 30.769 23.35 0.00 35.28 2.24
3821 5121 7.755373 GGACTGCAGATGGTTTTATCTTTTAAC 59.245 37.037 23.35 0.00 35.28 2.01
3823 5123 6.945435 TGGACTGCAGATGGTTTTATCTTTTA 59.055 34.615 23.35 0.00 35.28 1.52
3824 5124 5.774690 TGGACTGCAGATGGTTTTATCTTTT 59.225 36.000 23.35 0.00 35.28 2.27
3825 5125 5.324409 TGGACTGCAGATGGTTTTATCTTT 58.676 37.500 23.35 0.00 35.28 2.52
3826 5126 4.922206 TGGACTGCAGATGGTTTTATCTT 58.078 39.130 23.35 0.00 35.28 2.40
3827 5127 4.574674 TGGACTGCAGATGGTTTTATCT 57.425 40.909 23.35 0.00 37.90 1.98
3828 5128 5.841957 ATTGGACTGCAGATGGTTTTATC 57.158 39.130 23.35 3.44 0.00 1.75
3829 5129 6.662755 TCTATTGGACTGCAGATGGTTTTAT 58.337 36.000 23.35 5.12 0.00 1.40
3844 5145 3.497640 GTGAGCATGCATCTCTATTGGAC 59.502 47.826 21.98 10.02 0.00 4.02
3851 5152 0.104487 CCGAGTGAGCATGCATCTCT 59.896 55.000 21.98 18.49 0.00 3.10
3869 5170 4.584325 TGGAATGATAACCTGCATTTAGCC 59.416 41.667 0.00 0.00 44.83 3.93
3870 5171 5.772825 TGGAATGATAACCTGCATTTAGC 57.227 39.130 0.00 0.00 45.96 3.09
3931 5232 4.740205 GCAGCTAACCTGTTGTTTTTCTTC 59.260 41.667 0.00 0.00 43.71 2.87
3937 5238 1.961793 TCGCAGCTAACCTGTTGTTT 58.038 45.000 0.00 0.00 43.71 2.83
3949 5250 4.346734 CAGAATGTTGTTAATCGCAGCT 57.653 40.909 0.00 0.00 0.00 4.24
3969 5270 4.772624 AGGAGACTGAACATACTGCTAACA 59.227 41.667 0.00 0.00 41.13 2.41
3970 5271 5.331876 AGGAGACTGAACATACTGCTAAC 57.668 43.478 0.00 0.00 41.13 2.34
3988 5290 2.229784 GCCAACATTCCAACAGAAGGAG 59.770 50.000 0.00 0.00 38.58 3.69
4008 5345 3.488721 GCCATGACATGAAGATGTTCAGC 60.489 47.826 17.24 3.51 45.96 4.26
4080 5417 4.760047 CTTGTCCCGCCGTCCCTG 62.760 72.222 0.00 0.00 0.00 4.45
4228 5565 1.136147 GACACGATGTACGCGGTCT 59.864 57.895 12.47 0.00 46.94 3.85
4274 5611 2.910479 AGCACGGTGGTCGAGTCA 60.910 61.111 7.07 0.00 42.43 3.41
4373 5710 1.909986 GACAGGAAGCTCCCTTTACCT 59.090 52.381 0.00 0.00 37.19 3.08
4418 5755 1.379176 TCTCTCAGTGGAGCCCGAG 60.379 63.158 4.29 0.00 41.13 4.63
4425 5762 1.679305 GCCGGTCTCTCTCAGTGGA 60.679 63.158 1.90 0.00 0.00 4.02
4428 5765 1.680651 CCTGCCGGTCTCTCTCAGT 60.681 63.158 1.90 0.00 0.00 3.41
4607 5944 2.568956 CAGTGAGATCTTCCCCTTGTCA 59.431 50.000 0.00 0.00 0.00 3.58
4610 5947 1.280133 TGCAGTGAGATCTTCCCCTTG 59.720 52.381 0.00 0.00 0.00 3.61
4628 5965 2.095869 CAGCAGTGAGAACTTGACATGC 60.096 50.000 0.00 0.00 0.00 4.06
4657 5994 1.888215 TGGAGCAGCTTGTCAAGAAG 58.112 50.000 16.99 8.36 0.00 2.85
4720 6057 7.657336 TGATTCCCTGTACAATTTTCTGAAAC 58.343 34.615 1.58 0.00 0.00 2.78
4730 6067 3.189606 TGGGTCTGATTCCCTGTACAAT 58.810 45.455 0.00 0.00 44.84 2.71
4755 6092 4.081697 ACGTTTCCCATTGGATTGGATTTC 60.082 41.667 3.62 0.00 41.40 2.17
4756 6093 3.837731 ACGTTTCCCATTGGATTGGATTT 59.162 39.130 3.62 0.00 41.40 2.17
4757 6094 3.440127 ACGTTTCCCATTGGATTGGATT 58.560 40.909 3.62 0.00 41.40 3.01
4758 6095 3.100207 ACGTTTCCCATTGGATTGGAT 57.900 42.857 3.62 0.00 41.40 3.41
4759 6096 2.595750 ACGTTTCCCATTGGATTGGA 57.404 45.000 3.62 0.00 41.40 3.53
4760 6097 3.258123 AGAAACGTTTCCCATTGGATTGG 59.742 43.478 31.87 0.00 41.40 3.16
4761 6098 4.236935 CAGAAACGTTTCCCATTGGATTG 58.763 43.478 31.87 18.74 41.40 2.67
4773 6110 6.189677 TGACAATCAGAAACAGAAACGTTT 57.810 33.333 14.57 14.57 41.72 3.60
4798 6135 7.653767 ACTCGTCTTAAGTTTACATTTCAGG 57.346 36.000 1.63 0.00 0.00 3.86
4812 6149 9.321562 GGAATTCCATTACAATACTCGTCTTAA 57.678 33.333 20.04 0.00 35.64 1.85
4813 6150 8.479689 TGGAATTCCATTACAATACTCGTCTTA 58.520 33.333 23.63 0.00 42.01 2.10
4815 6152 6.884832 TGGAATTCCATTACAATACTCGTCT 58.115 36.000 23.63 0.00 42.01 4.18
4837 6174 4.722700 CCCCGCTGTCTGGGTTGG 62.723 72.222 0.00 0.00 45.86 3.77
4845 6182 2.036089 CTCCTCTATTTACCCCGCTGTC 59.964 54.545 0.00 0.00 0.00 3.51
4847 6184 2.297597 CTCTCCTCTATTTACCCCGCTG 59.702 54.545 0.00 0.00 0.00 5.18
4848 6185 2.599677 CTCTCCTCTATTTACCCCGCT 58.400 52.381 0.00 0.00 0.00 5.52
4849 6186 1.001068 GCTCTCCTCTATTTACCCCGC 59.999 57.143 0.00 0.00 0.00 6.13
4851 6188 2.690840 TGGCTCTCCTCTATTTACCCC 58.309 52.381 0.00 0.00 0.00 4.95
4852 6189 4.984146 ATTGGCTCTCCTCTATTTACCC 57.016 45.455 0.00 0.00 0.00 3.69
4911 6249 3.242291 CTCCTCCATACCCCCGCC 61.242 72.222 0.00 0.00 0.00 6.13
4984 6324 2.369860 TGATGCTTCTGTATAGGCTGGG 59.630 50.000 0.00 0.00 0.00 4.45
5156 6497 7.923414 ACCTATTAGTTTTGTGGTTGAGATC 57.077 36.000 0.00 0.00 0.00 2.75
5349 6690 5.070001 CCACCCTCTTTCTGAAATTACACA 58.930 41.667 2.88 0.00 0.00 3.72
5350 6691 5.070685 ACCACCCTCTTTCTGAAATTACAC 58.929 41.667 2.88 0.00 0.00 2.90
5417 6758 6.702329 AGACTAAACCTTATGACCTCAACTG 58.298 40.000 0.00 0.00 0.00 3.16
5425 6766 4.876679 GCCCTCAAGACTAAACCTTATGAC 59.123 45.833 0.00 0.00 0.00 3.06
5427 6768 5.104259 AGCCCTCAAGACTAAACCTTATG 57.896 43.478 0.00 0.00 0.00 1.90
5431 6772 3.653352 AGAAAGCCCTCAAGACTAAACCT 59.347 43.478 0.00 0.00 0.00 3.50
5433 6774 4.004314 GGAGAAAGCCCTCAAGACTAAAC 58.996 47.826 0.00 0.00 34.94 2.01
5434 6775 3.650942 TGGAGAAAGCCCTCAAGACTAAA 59.349 43.478 0.00 0.00 34.94 1.85
5435 6776 3.248024 TGGAGAAAGCCCTCAAGACTAA 58.752 45.455 0.00 0.00 34.94 2.24
5436 6777 2.834549 CTGGAGAAAGCCCTCAAGACTA 59.165 50.000 0.00 0.00 36.53 2.59
5439 6782 1.734655 ACTGGAGAAAGCCCTCAAGA 58.265 50.000 9.09 0.00 36.53 3.02
5446 6789 7.631717 AGTAATTTTGATACTGGAGAAAGCC 57.368 36.000 0.00 0.00 32.50 4.35
5474 6817 5.234116 ACAAAAGCTTAGAATTGTTTTGCCG 59.766 36.000 8.17 0.00 40.28 5.69
5520 6864 4.766007 CGAGGAAGCATGTGAATTATTCG 58.234 43.478 0.23 0.00 0.00 3.34
5566 6919 8.417106 TGCTCTTAGTGATTAGTTCTCTTATGG 58.583 37.037 0.00 0.00 30.95 2.74
5603 6957 0.035176 AGGGCGCACATGCAATTTTT 59.965 45.000 14.57 0.00 42.21 1.94
5613 6967 2.257691 TAGTTTTGTTAGGGCGCACA 57.742 45.000 14.57 2.50 0.00 4.57
5618 6972 5.938125 TCAGTGATCTTAGTTTTGTTAGGGC 59.062 40.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.