Multiple sequence alignment - TraesCS5B01G234400

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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 TraesCS5B01G234400 chr5B 100.000 5910 0 0 1 5910 412451266 412457175 0.000000e+00 10914
1 TraesCS5B01G234400 chr5B 89.873 79 8 0 3187 3265 393755556 393755634 1.050000e-17 102
2 TraesCS5B01G234400 chr5D 93.061 2767 104 28 3161 5907 351396006 351398704 0.000000e+00 3965
3 TraesCS5B01G234400 chr5D 91.855 884 54 11 2210 3090 351394808 351395676 0.000000e+00 1218
4 TraesCS5B01G234400 chr5D 96.624 711 17 4 1 704 351336602 351337312 0.000000e+00 1173
5 TraesCS5B01G234400 chr5D 89.524 630 25 11 854 1453 351393063 351393681 0.000000e+00 760
6 TraesCS5B01G234400 chr5D 84.144 637 51 22 1511 2118 351393694 351394309 6.640000e-159 571
7 TraesCS5B01G234400 chr5D 89.439 303 27 4 1914 2212 351394317 351394618 1.550000e-100 377
8 TraesCS5B01G234400 chr5D 85.443 158 14 8 5106 5262 51902929 51903078 7.930000e-34 156
9 TraesCS5B01G234400 chr5D 91.250 80 6 1 3075 3154 351395702 351395780 2.250000e-19 108
10 TraesCS5B01G234400 chr5D 90.123 81 7 1 3074 3154 325462711 325462790 2.910000e-18 104
11 TraesCS5B01G234400 chr5A 92.517 2392 143 26 3161 5528 451734009 451736388 0.000000e+00 3393
12 TraesCS5B01G234400 chr5A 95.533 806 32 2 35 837 451730012 451730816 0.000000e+00 1286
13 TraesCS5B01G234400 chr5A 82.991 1070 82 45 854 1888 451730802 451731806 0.000000e+00 876
14 TraesCS5B01G234400 chr5A 91.444 374 28 3 2582 2955 451733443 451733812 1.470000e-140 510
15 TraesCS5B01G234400 chr5A 89.916 357 30 3 2208 2560 451732508 451732862 6.980000e-124 455
16 TraesCS5B01G234400 chr5A 83.832 334 16 13 5581 5909 451736403 451736703 3.490000e-72 283
17 TraesCS5B01G234400 chr5A 90.123 81 7 1 3074 3154 132781866 132781787 2.910000e-18 104
18 TraesCS5B01G234400 chr5A 90.123 81 7 1 3074 3154 132812423 132812344 2.910000e-18 104
19 TraesCS5B01G234400 chr7A 84.974 193 25 3 2964 3154 687313427 687313617 6.040000e-45 193
20 TraesCS5B01G234400 chr7A 89.764 127 10 3 2964 3090 339687789 339687666 6.130000e-35 159
21 TraesCS5B01G234400 chr1A 90.476 126 9 3 2965 3090 333918134 333918012 4.740000e-36 163
22 TraesCS5B01G234400 chr4D 89.683 126 11 2 2965 3090 303455618 303455495 6.130000e-35 159
23 TraesCS5B01G234400 chr4D 85.211 142 14 6 2954 3094 277233121 277233256 7.990000e-29 139
24 TraesCS5B01G234400 chr4D 94.521 73 2 2 3194 3265 134126450 134126521 1.740000e-20 111
25 TraesCS5B01G234400 chr3A 89.764 127 10 3 2964 3090 603606814 603606691 6.130000e-35 159
26 TraesCS5B01G234400 chr3A 91.139 79 4 3 3075 3152 53225299 53225223 2.910000e-18 104
27 TraesCS5B01G234400 chr6D 89.683 126 10 3 2965 3090 301892910 301893032 2.200000e-34 158
28 TraesCS5B01G234400 chr6D 88.148 135 13 3 2956 3090 446549559 446549428 2.200000e-34 158
29 TraesCS5B01G234400 chr6D 86.957 138 12 5 2954 3090 172089811 172089943 3.690000e-32 150
30 TraesCS5B01G234400 chr6D 94.521 73 3 1 3193 3265 16750790 16750861 1.740000e-20 111
31 TraesCS5B01G234400 chr6A 89.683 126 10 3 2965 3090 523245763 523245885 2.200000e-34 158
32 TraesCS5B01G234400 chr7D 88.095 126 13 2 2956 3081 634884021 634884144 1.330000e-31 148
33 TraesCS5B01G234400 chr7D 87.500 128 11 2 2956 3082 162791842 162791719 6.170000e-30 143
34 TraesCS5B01G234400 chr2B 94.521 73 4 0 3193 3265 760258415 760258343 4.840000e-21 113
35 TraesCS5B01G234400 chr2B 89.744 78 8 0 3187 3264 673092426 673092503 3.770000e-17 100
36 TraesCS5B01G234400 chr2A 91.358 81 6 1 3074 3154 709046080 709046159 6.260000e-20 110
37 TraesCS5B01G234400 chr2A 88.889 81 8 1 3074 3154 566591889 566591810 1.360000e-16 99
38 TraesCS5B01G234400 chr4B 93.243 74 3 2 3193 3265 159632282 159632210 2.250000e-19 108
39 TraesCS5B01G234400 chr3B 92.958 71 5 0 3195 3265 811444107 811444037 2.910000e-18 104
40 TraesCS5B01G234400 chr1D 92.000 75 5 1 3075 3149 318556667 318556594 2.910000e-18 104


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 TraesCS5B01G234400 chr5B 412451266 412457175 5909 False 10914.000000 10914 100.000000 1 5910 1 chr5B.!!$F2 5909
1 TraesCS5B01G234400 chr5D 351336602 351337312 710 False 1173.000000 1173 96.624000 1 704 1 chr5D.!!$F3 703
2 TraesCS5B01G234400 chr5D 351393063 351398704 5641 False 1166.500000 3965 89.878833 854 5907 6 chr5D.!!$F4 5053
3 TraesCS5B01G234400 chr5A 451730012 451736703 6691 False 1133.833333 3393 89.372167 35 5909 6 chr5A.!!$F1 5874

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
962 973 0.036765 CATCTCCGGTCCCAAAACGA 60.037 55.000 0.00 0.0 0.00 3.85 F
1621 1685 0.103937 TGGCCTTTTGCTTCGGTTTG 59.896 50.000 3.32 0.0 40.92 2.93 F
2129 2499 0.390860 TTGGCCATGTTTTTCACGGG 59.609 50.000 6.09 0.0 29.05 5.28 F
2133 2503 1.543802 GCCATGTTTTTCACGGGATGA 59.456 47.619 0.00 0.0 34.65 2.92 F
3207 4959 3.383505 AGTTTGTGGCCAGTTTTCCTTAC 59.616 43.478 5.11 0.0 0.00 2.34 F
4177 5934 0.828022 CCATTACACTACGCCCTCCA 59.172 55.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2403 0.974383 TCCCCCTTCTGACGTTCTTC 59.026 55.000 0.00 0.0 0.00 2.87 R
3332 5084 1.228769 AGTACCCTGACTCCGCACA 60.229 57.895 0.00 0.0 0.00 4.57 R
3391 5143 3.307480 GGCTCTAAGGAACAGTTTGGCTA 60.307 47.826 0.00 0.0 0.00 3.93 R
3817 5574 3.429085 GTTTATTGCTCCATGCTTCACG 58.571 45.455 0.00 0.0 43.37 4.35 R
4358 6115 0.250684 TGATCTGCCTCAAACGCCAA 60.251 50.000 0.00 0.0 0.00 4.52 R
5595 7381 0.034756 GAAACAACAACCCATGGCCC 59.965 55.000 6.09 0.0 0.00 5.80 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
605 616 3.000819 CGGTGGTGGTGGAGGCTA 61.001 66.667 0.00 0.00 0.00 3.93
714 725 0.463654 TCTGCTGTTCGGTGCTTTGT 60.464 50.000 0.00 0.00 0.00 2.83
715 726 0.040958 CTGCTGTTCGGTGCTTTGTC 60.041 55.000 0.00 0.00 0.00 3.18
731 742 3.078836 TCGGGCCGGTAAAGGAGG 61.079 66.667 27.98 0.00 0.00 4.30
737 748 0.544697 GCCGGTAAAGGAGGATGGAA 59.455 55.000 1.90 0.00 0.00 3.53
739 750 1.472728 CCGGTAAAGGAGGATGGAACG 60.473 57.143 0.00 0.00 0.00 3.95
745 756 2.190578 GAGGATGGAACGGCCCAG 59.809 66.667 0.00 0.00 39.97 4.45
775 786 0.790814 GGCTCTTCACAGTAACGCAC 59.209 55.000 0.00 0.00 0.00 5.34
793 804 1.069765 CTGTCGAGTGCCTGGTTGT 59.930 57.895 0.00 0.00 0.00 3.32
820 831 2.029073 ACAACGGACGGTCAGCAG 59.971 61.111 10.76 4.89 0.00 4.24
822 833 1.300620 CAACGGACGGTCAGCAGAA 60.301 57.895 10.76 0.00 0.00 3.02
823 834 0.878523 CAACGGACGGTCAGCAGAAA 60.879 55.000 10.76 0.00 0.00 2.52
824 835 0.878961 AACGGACGGTCAGCAGAAAC 60.879 55.000 10.76 0.00 0.00 2.78
825 836 2.027625 CGGACGGTCAGCAGAAACC 61.028 63.158 10.76 0.00 0.00 3.27
826 837 1.070786 GGACGGTCAGCAGAAACCA 59.929 57.895 10.76 0.00 35.13 3.67
827 838 0.951040 GGACGGTCAGCAGAAACCAG 60.951 60.000 10.76 0.00 35.13 4.00
828 839 0.249911 GACGGTCAGCAGAAACCAGT 60.250 55.000 2.62 0.00 35.13 4.00
829 840 0.249911 ACGGTCAGCAGAAACCAGTC 60.250 55.000 0.00 0.00 35.13 3.51
830 841 0.951040 CGGTCAGCAGAAACCAGTCC 60.951 60.000 0.00 0.00 35.13 3.85
831 842 0.108585 GGTCAGCAGAAACCAGTCCA 59.891 55.000 0.00 0.00 35.53 4.02
832 843 1.517242 GTCAGCAGAAACCAGTCCAG 58.483 55.000 0.00 0.00 0.00 3.86
833 844 1.070758 GTCAGCAGAAACCAGTCCAGA 59.929 52.381 0.00 0.00 0.00 3.86
834 845 1.980765 TCAGCAGAAACCAGTCCAGAT 59.019 47.619 0.00 0.00 0.00 2.90
835 846 2.373169 TCAGCAGAAACCAGTCCAGATT 59.627 45.455 0.00 0.00 0.00 2.40
836 847 2.746362 CAGCAGAAACCAGTCCAGATTC 59.254 50.000 0.00 0.00 0.00 2.52
837 848 2.641815 AGCAGAAACCAGTCCAGATTCT 59.358 45.455 0.00 0.00 0.00 2.40
838 849 3.073650 AGCAGAAACCAGTCCAGATTCTT 59.926 43.478 0.00 0.00 0.00 2.52
839 850 3.823304 GCAGAAACCAGTCCAGATTCTTT 59.177 43.478 0.00 0.00 0.00 2.52
840 851 4.279420 GCAGAAACCAGTCCAGATTCTTTT 59.721 41.667 0.00 0.00 0.00 2.27
841 852 5.221322 GCAGAAACCAGTCCAGATTCTTTTT 60.221 40.000 0.00 0.00 0.00 1.94
896 907 1.891919 GACAACGCTGGAGCCACAA 60.892 57.895 0.00 0.00 37.91 3.33
959 970 1.001393 GGCATCTCCGGTCCCAAAA 60.001 57.895 0.00 0.00 0.00 2.44
960 971 1.313091 GGCATCTCCGGTCCCAAAAC 61.313 60.000 0.00 0.00 0.00 2.43
961 972 1.644786 GCATCTCCGGTCCCAAAACG 61.645 60.000 0.00 0.00 0.00 3.60
962 973 0.036765 CATCTCCGGTCCCAAAACGA 60.037 55.000 0.00 0.00 0.00 3.85
963 974 0.249398 ATCTCCGGTCCCAAAACGAG 59.751 55.000 0.00 0.00 0.00 4.18
964 975 1.117142 TCTCCGGTCCCAAAACGAGT 61.117 55.000 0.00 0.00 0.00 4.18
965 976 0.604578 CTCCGGTCCCAAAACGAGTA 59.395 55.000 0.00 0.00 0.00 2.59
966 977 0.604578 TCCGGTCCCAAAACGAGTAG 59.395 55.000 0.00 0.00 0.00 2.57
967 978 0.390735 CCGGTCCCAAAACGAGTAGG 60.391 60.000 0.00 0.00 0.00 3.18
968 979 0.604578 CGGTCCCAAAACGAGTAGGA 59.395 55.000 0.00 0.00 0.00 2.94
969 980 1.403780 CGGTCCCAAAACGAGTAGGAG 60.404 57.143 0.00 0.00 0.00 3.69
970 981 1.622312 GGTCCCAAAACGAGTAGGAGT 59.378 52.381 0.00 0.00 0.00 3.85
971 982 2.827921 GGTCCCAAAACGAGTAGGAGTA 59.172 50.000 0.00 0.00 0.00 2.59
972 983 3.259123 GGTCCCAAAACGAGTAGGAGTAA 59.741 47.826 0.00 0.00 0.00 2.24
973 984 4.081254 GGTCCCAAAACGAGTAGGAGTAAT 60.081 45.833 0.00 0.00 0.00 1.89
1055 1066 2.203015 CATCCACCCTAACCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
1187 1202 2.194056 CATGAATCTGGCCGCCCT 59.806 61.111 7.03 0.00 0.00 5.19
1453 1492 2.103143 CGCCTCGCTAGGTGTCAG 59.897 66.667 9.63 0.00 46.60 3.51
1454 1493 2.202810 GCCTCGCTAGGTGTCAGC 60.203 66.667 6.11 0.00 45.64 4.26
1456 1495 2.496817 CTCGCTAGGTGTCAGCCC 59.503 66.667 0.00 0.00 35.53 5.19
1479 1543 0.734253 GCTCTGTGTGGCTACTCACG 60.734 60.000 0.64 0.00 42.45 4.35
1481 1545 1.738099 CTGTGTGGCTACTCACGGC 60.738 63.158 0.64 0.00 42.45 5.68
1499 1563 2.031870 GGCCGGGAATCAAAATTAGCT 58.968 47.619 2.18 0.00 0.00 3.32
1512 1576 7.907214 TCAAAATTAGCTTACCTCTGAACTC 57.093 36.000 0.00 0.00 0.00 3.01
1514 1578 7.604164 TCAAAATTAGCTTACCTCTGAACTCTG 59.396 37.037 0.00 0.00 0.00 3.35
1515 1579 6.859112 AATTAGCTTACCTCTGAACTCTGA 57.141 37.500 0.00 0.00 0.00 3.27
1516 1580 6.859112 ATTAGCTTACCTCTGAACTCTGAA 57.141 37.500 0.00 0.00 0.00 3.02
1519 1583 3.506810 CTTACCTCTGAACTCTGAAGCG 58.493 50.000 0.00 0.00 0.00 4.68
1520 1584 1.333177 ACCTCTGAACTCTGAAGCGT 58.667 50.000 0.00 0.00 0.00 5.07
1521 1585 2.515854 ACCTCTGAACTCTGAAGCGTA 58.484 47.619 0.00 0.00 0.00 4.42
1522 1586 3.093057 ACCTCTGAACTCTGAAGCGTAT 58.907 45.455 0.00 0.00 0.00 3.06
1523 1587 3.511934 ACCTCTGAACTCTGAAGCGTATT 59.488 43.478 0.00 0.00 0.00 1.89
1524 1588 3.862267 CCTCTGAACTCTGAAGCGTATTG 59.138 47.826 0.00 0.00 0.00 1.90
1559 1623 1.783284 TCGAACTACTGTTGCTGCAG 58.217 50.000 10.11 10.11 41.92 4.41
1621 1685 0.103937 TGGCCTTTTGCTTCGGTTTG 59.896 50.000 3.32 0.00 40.92 2.93
1628 1692 1.795170 TTGCTTCGGTTTGGCAGCTC 61.795 55.000 0.00 0.00 37.28 4.09
1681 1771 3.007473 GAGTAGCTCCAGTGTAGGACT 57.993 52.381 0.00 0.00 33.19 3.85
1682 1772 3.358118 GAGTAGCTCCAGTGTAGGACTT 58.642 50.000 0.00 0.00 33.19 3.01
1683 1773 4.525024 GAGTAGCTCCAGTGTAGGACTTA 58.475 47.826 0.00 0.00 33.19 2.24
1684 1774 5.132043 AGTAGCTCCAGTGTAGGACTTAT 57.868 43.478 0.00 0.00 33.19 1.73
1685 1775 5.520751 AGTAGCTCCAGTGTAGGACTTATT 58.479 41.667 0.00 0.00 33.19 1.40
1686 1776 5.958987 AGTAGCTCCAGTGTAGGACTTATTT 59.041 40.000 0.00 0.00 33.19 1.40
1687 1777 5.763876 AGCTCCAGTGTAGGACTTATTTT 57.236 39.130 0.00 0.00 33.19 1.82
1688 1778 5.491982 AGCTCCAGTGTAGGACTTATTTTG 58.508 41.667 0.00 0.00 33.19 2.44
1689 1779 5.013183 AGCTCCAGTGTAGGACTTATTTTGT 59.987 40.000 0.00 0.00 33.19 2.83
1690 1780 5.351740 GCTCCAGTGTAGGACTTATTTTGTC 59.648 44.000 0.00 0.00 33.19 3.18
1691 1781 6.428083 TCCAGTGTAGGACTTATTTTGTCA 57.572 37.500 0.00 0.00 36.26 3.58
1692 1782 6.228258 TCCAGTGTAGGACTTATTTTGTCAC 58.772 40.000 0.00 0.00 36.26 3.67
1693 1783 5.995282 CCAGTGTAGGACTTATTTTGTCACA 59.005 40.000 0.00 0.00 36.26 3.58
1694 1784 6.655003 CCAGTGTAGGACTTATTTTGTCACAT 59.345 38.462 0.00 0.00 36.26 3.21
1749 1840 2.290071 TGGGGCTAGTTACAACTTCAGC 60.290 50.000 7.92 7.92 39.01 4.26
1753 1844 3.437049 GGCTAGTTACAACTTCAGCTTGG 59.563 47.826 13.73 0.00 39.45 3.61
1754 1845 4.065789 GCTAGTTACAACTTCAGCTTGGT 58.934 43.478 8.85 0.00 37.54 3.67
1755 1846 4.083802 GCTAGTTACAACTTCAGCTTGGTG 60.084 45.833 8.85 0.00 37.54 4.17
1761 1852 1.103398 ACTTCAGCTTGGTGTGCCAC 61.103 55.000 0.00 0.00 46.01 5.01
1772 1863 2.026014 GTGCCACCACGTTTGCTG 59.974 61.111 0.00 0.00 31.34 4.41
1773 1864 2.439338 TGCCACCACGTTTGCTGT 60.439 55.556 0.00 0.00 0.00 4.40
1784 1875 2.118683 CGTTTGCTGTTGTGAATGGTG 58.881 47.619 0.00 0.00 0.00 4.17
1789 1880 1.067516 GCTGTTGTGAATGGTGTGCTT 59.932 47.619 0.00 0.00 0.00 3.91
1791 1882 3.853307 GCTGTTGTGAATGGTGTGCTTAC 60.853 47.826 0.00 0.00 0.00 2.34
1803 1894 3.334691 GTGTGCTTACCTGTATGCAGAA 58.665 45.455 12.93 0.00 45.28 3.02
1805 1896 2.939103 GTGCTTACCTGTATGCAGAAGG 59.061 50.000 12.93 9.89 45.28 3.46
1821 1912 4.507756 GCAGAAGGGAAACATTTGTTGAAC 59.492 41.667 0.00 0.00 38.44 3.18
1858 1949 2.850439 GGAAACCTAACTGCCGGAC 58.150 57.895 5.05 0.00 0.00 4.79
1869 1961 1.645034 CTGCCGGACAGTATTCAGTG 58.355 55.000 5.05 0.00 41.86 3.66
1889 1983 9.840427 TTCAGTGCAATTTTAGCTTCTTTATAC 57.160 29.630 0.00 0.00 0.00 1.47
1911 2043 1.014564 GTGCGGTTGTAGACCTGAGC 61.015 60.000 0.00 0.00 46.92 4.26
1912 2044 1.448013 GCGGTTGTAGACCTGAGCC 60.448 63.158 0.00 0.00 46.92 4.70
2016 2383 3.838244 AGTGCAGAAAGTAACCACTGA 57.162 42.857 0.00 0.00 35.60 3.41
2034 2403 5.278660 CCACTGAGGTTTTCTTCCAGAATTG 60.279 44.000 0.00 0.00 33.67 2.32
2127 2497 4.082787 ACTCTATTGGCCATGTTTTTCACG 60.083 41.667 6.09 0.00 0.00 4.35
2129 2499 0.390860 TTGGCCATGTTTTTCACGGG 59.609 50.000 6.09 0.00 29.05 5.28
2133 2503 1.543802 GCCATGTTTTTCACGGGATGA 59.456 47.619 0.00 0.00 34.65 2.92
2160 2530 6.590234 AAACTTGTAATGGAATCCCTTGTC 57.410 37.500 0.00 0.00 0.00 3.18
2161 2531 4.261801 ACTTGTAATGGAATCCCTTGTCG 58.738 43.478 0.00 0.00 0.00 4.35
2162 2532 3.992943 TGTAATGGAATCCCTTGTCGT 57.007 42.857 0.00 0.00 0.00 4.34
2176 2548 4.082787 CCCTTGTCGTGCAATTATTCAAGT 60.083 41.667 0.00 0.00 36.36 3.16
2194 2566 6.782082 TCAAGTAGAGAAGTGACAGCATAT 57.218 37.500 0.00 0.00 0.00 1.78
2255 3182 3.427503 GCCAATGACCCATGTAAAGAACG 60.428 47.826 0.00 0.00 0.00 3.95
2374 3301 7.413657 CGTCCATTTTGTCCTTACATAAATCGT 60.414 37.037 0.00 0.00 34.97 3.73
2375 3302 8.885722 GTCCATTTTGTCCTTACATAAATCGTA 58.114 33.333 0.00 0.00 34.97 3.43
2382 3309 5.178809 GTCCTTACATAAATCGTACATGGCC 59.821 44.000 0.00 0.00 0.00 5.36
2458 3385 5.418840 GGGAAATCAGACTTCTATTTTGGCA 59.581 40.000 0.00 0.00 0.00 4.92
2461 3388 7.148018 GGAAATCAGACTTCTATTTTGGCATGA 60.148 37.037 0.00 0.00 0.00 3.07
2571 3809 8.986477 ATTTTTACAACTTATGATGCAGAACC 57.014 30.769 0.00 0.00 0.00 3.62
2665 4155 8.345565 GGAACAAAATCTTAGCATACATGTAGG 58.654 37.037 13.10 13.10 0.00 3.18
2666 4156 8.807948 AACAAAATCTTAGCATACATGTAGGT 57.192 30.769 18.02 13.72 0.00 3.08
2667 4157 8.807948 ACAAAATCTTAGCATACATGTAGGTT 57.192 30.769 18.02 14.83 0.00 3.50
2805 4295 4.508551 TCCATGCTTGTTCTGACCATAT 57.491 40.909 0.00 0.00 0.00 1.78
2993 4484 6.238842 CCCTCTTTTCCATAATGTAGTGCATG 60.239 42.308 0.00 0.00 37.96 4.06
3030 4522 5.475220 TGAAGTCAAACCTCACAAACTTTGA 59.525 36.000 8.55 0.00 31.68 2.69
3053 4545 6.072728 TGACCAAGTTCGTGGAGAAAAATATG 60.073 38.462 11.33 0.00 41.65 1.78
3059 4551 8.197988 AGTTCGTGGAGAAAAATATGTACATC 57.802 34.615 12.68 0.00 41.10 3.06
3138 4668 7.223387 ATCAACTTGATCAAACTTTGCAAAGTC 59.777 33.333 37.59 26.64 39.44 3.01
3185 4937 5.008619 ACACACAATTGCAGATTTTGACA 57.991 34.783 5.05 0.00 0.00 3.58
3207 4959 3.383505 AGTTTGTGGCCAGTTTTCCTTAC 59.616 43.478 5.11 0.00 0.00 2.34
3220 4972 7.807680 CAGTTTTCCTTACTAACTGGTCAATC 58.192 38.462 0.00 0.00 43.03 2.67
3376 5128 6.314896 CCAAAATAGATGACAGAAGACAGGTC 59.685 42.308 0.00 0.00 0.00 3.85
3391 5143 3.551846 ACAGGTCGGACAGAAAAATGTT 58.448 40.909 10.76 0.00 32.25 2.71
3464 5216 3.806316 ATGTCGAATCAACGGTCAAAC 57.194 42.857 0.00 0.00 0.00 2.93
3579 5331 3.459828 TGAACCAGATGTCCAGGGATTA 58.540 45.455 0.00 0.00 0.00 1.75
3817 5574 1.523258 ACAGATGAGCATGCTCGCC 60.523 57.895 35.68 29.25 45.48 5.54
3950 5707 3.051581 AGAGGATATGGTGTGCCTGAAT 58.948 45.455 0.00 0.00 35.27 2.57
4153 5910 1.597797 CCATGGCTGGTGCGAATGTT 61.598 55.000 0.00 0.00 40.82 2.71
4168 5925 5.644206 TGCGAATGTTAAAGCCATTACACTA 59.356 36.000 0.00 0.00 32.84 2.74
4177 5934 0.828022 CCATTACACTACGCCCTCCA 59.172 55.000 0.00 0.00 0.00 3.86
4225 5982 1.153549 GGCCGCAGTCTCGAAGAAT 60.154 57.895 0.00 0.00 34.09 2.40
4258 6015 8.355169 GCAATAATGATCAATACACCTCACAAT 58.645 33.333 0.00 0.00 0.00 2.71
4324 6081 4.338682 GCTGATCTCTGCAAGGAAAATGAT 59.661 41.667 4.41 0.00 40.06 2.45
4339 6096 3.308438 AATGATGTGTTGCTCTTTGCC 57.692 42.857 0.00 0.00 42.00 4.52
4358 6115 2.101582 GCCGATGAGGTCTATGACAAGT 59.898 50.000 0.07 0.00 43.70 3.16
4372 6129 1.034838 ACAAGTTGGCGTTTGAGGCA 61.035 50.000 7.96 0.00 45.22 4.75
4393 6150 5.884232 GGCAGATCATATATCAATGGCTTCA 59.116 40.000 0.00 0.00 0.00 3.02
4546 6303 1.302431 CACATTCGCCACCTCCACA 60.302 57.895 0.00 0.00 0.00 4.17
4549 6306 2.525124 ATTCGCCACCTCCACACCA 61.525 57.895 0.00 0.00 0.00 4.17
4610 6367 1.746220 GCTACTTCGAGGAGCTGAAGA 59.254 52.381 16.14 0.00 43.34 2.87
4651 6408 4.379243 CTGCTGGTCGACGGGCTT 62.379 66.667 24.35 0.00 0.00 4.35
4699 6456 1.068055 TCAAGCGGAACCTACTTCGTC 60.068 52.381 0.00 0.00 0.00 4.20
4947 6712 4.641954 GTGTAGCTGTTGATTGATCGTTG 58.358 43.478 0.00 0.00 0.00 4.10
4948 6713 4.388773 GTGTAGCTGTTGATTGATCGTTGA 59.611 41.667 0.00 0.00 0.00 3.18
4949 6714 4.627035 TGTAGCTGTTGATTGATCGTTGAG 59.373 41.667 0.00 0.00 0.00 3.02
4950 6715 3.668447 AGCTGTTGATTGATCGTTGAGT 58.332 40.909 0.00 0.00 0.00 3.41
4952 6717 4.083643 AGCTGTTGATTGATCGTTGAGTTG 60.084 41.667 0.00 0.00 0.00 3.16
4953 6718 4.083855 GCTGTTGATTGATCGTTGAGTTGA 60.084 41.667 0.00 0.00 0.00 3.18
4954 6719 5.560760 GCTGTTGATTGATCGTTGAGTTGAA 60.561 40.000 0.00 0.00 0.00 2.69
4955 6720 6.558771 TGTTGATTGATCGTTGAGTTGAAT 57.441 33.333 0.00 0.00 0.00 2.57
4956 6721 7.624134 GCTGTTGATTGATCGTTGAGTTGAATA 60.624 37.037 0.00 0.00 0.00 1.75
4961 6726 8.998377 TGATTGATCGTTGAGTTGAATAAAAGA 58.002 29.630 0.00 0.00 0.00 2.52
5017 6785 4.215399 GCATGTAGTAACACTTTTCTGGCA 59.785 41.667 0.00 0.00 38.78 4.92
5020 6788 2.930950 AGTAACACTTTTCTGGCAGCA 58.069 42.857 10.34 0.00 0.00 4.41
5028 6796 4.937620 CACTTTTCTGGCAGCAGTTATCTA 59.062 41.667 10.34 0.00 0.00 1.98
5090 6860 0.391130 TGTCTGTGTAAGGCGATGGC 60.391 55.000 0.00 0.00 30.85 4.40
5133 6903 4.491602 CGGTCGTACGAGTACTAGAACTTG 60.492 50.000 20.18 0.00 36.99 3.16
5137 6907 4.377738 CGTACGAGTACTAGAACTTGTGCA 60.378 45.833 10.44 0.00 43.10 4.57
5165 6941 3.313750 GCGGCTCGTCTGCTATTG 58.686 61.111 0.00 0.00 43.74 1.90
5207 6983 2.612721 CGTGTCACCACTCCATCAATCA 60.613 50.000 0.00 0.00 39.55 2.57
5278 7060 6.303839 TGCACTTGTAAAATTCTACCTCCTT 58.696 36.000 0.00 0.00 0.00 3.36
5282 7064 9.372369 CACTTGTAAAATTCTACCTCCTTCTAG 57.628 37.037 0.00 0.00 0.00 2.43
5284 7066 9.372369 CTTGTAAAATTCTACCTCCTTCTAGTG 57.628 37.037 0.00 0.00 0.00 2.74
5334 7116 4.524316 TCATTGACATTTGAAAGCCCTG 57.476 40.909 0.00 0.00 0.00 4.45
5339 7121 3.896888 TGACATTTGAAAGCCCTGTCATT 59.103 39.130 7.72 0.00 40.77 2.57
5340 7122 4.344679 TGACATTTGAAAGCCCTGTCATTT 59.655 37.500 7.72 0.00 40.77 2.32
5341 7123 4.634199 ACATTTGAAAGCCCTGTCATTTG 58.366 39.130 0.00 0.00 0.00 2.32
5342 7124 4.344679 ACATTTGAAAGCCCTGTCATTTGA 59.655 37.500 5.61 0.00 0.00 2.69
5380 7163 1.200020 CAAGCCGCCTCCTTTTACTTG 59.800 52.381 0.00 0.00 0.00 3.16
5382 7165 1.241315 GCCGCCTCCTTTTACTTGCA 61.241 55.000 0.00 0.00 0.00 4.08
5407 7190 1.378762 CGGTTCCCCTGGTGTCATT 59.621 57.895 0.00 0.00 0.00 2.57
5455 7238 0.459934 TGTCCGGACAAAAACGTCGT 60.460 50.000 34.60 0.00 38.56 4.34
5464 7247 1.360194 AAAAACGTCGTCCGCACACA 61.360 50.000 0.00 0.00 41.42 3.72
5570 7353 2.747460 CCTCCACGGCCACATGTG 60.747 66.667 19.31 19.31 35.87 3.21
5590 7376 1.667467 GCTCCGGTGAAGATAGATCGC 60.667 57.143 7.92 0.00 0.00 4.58
5594 7380 1.273606 CGGTGAAGATAGATCGCCCAT 59.726 52.381 0.89 0.00 43.13 4.00
5595 7381 2.693069 GGTGAAGATAGATCGCCCATG 58.307 52.381 0.00 0.00 40.78 3.66
5596 7382 2.613977 GGTGAAGATAGATCGCCCATGG 60.614 54.545 4.14 4.14 40.78 3.66
5597 7383 1.625315 TGAAGATAGATCGCCCATGGG 59.375 52.381 27.87 27.87 38.57 4.00
5635 7423 0.030504 TGTGTGCGCCATGAAAACTG 59.969 50.000 4.18 0.00 0.00 3.16
5638 7426 0.310543 GTGCGCCATGAAAACTGTGA 59.689 50.000 4.18 0.00 0.00 3.58
5639 7427 0.310543 TGCGCCATGAAAACTGTGAC 59.689 50.000 4.18 0.00 0.00 3.67
5640 7428 0.725784 GCGCCATGAAAACTGTGACG 60.726 55.000 0.00 0.00 0.00 4.35
5641 7429 0.725784 CGCCATGAAAACTGTGACGC 60.726 55.000 0.00 0.00 0.00 5.19
5642 7430 0.387239 GCCATGAAAACTGTGACGCC 60.387 55.000 0.00 0.00 0.00 5.68
5643 7431 0.240945 CCATGAAAACTGTGACGCCC 59.759 55.000 0.00 0.00 0.00 6.13
5644 7432 0.110238 CATGAAAACTGTGACGCCCG 60.110 55.000 0.00 0.00 0.00 6.13
5645 7433 1.852067 ATGAAAACTGTGACGCCCGC 61.852 55.000 0.00 0.00 0.00 6.13
5646 7434 3.249973 GAAAACTGTGACGCCCGCC 62.250 63.158 0.00 0.00 0.00 6.13
5812 7605 2.277756 AGACGCGCGACCGTATTC 60.278 61.111 39.36 21.57 42.24 1.75
5855 7649 1.641677 GTTCACACACACCTCACGC 59.358 57.895 0.00 0.00 0.00 5.34
5856 7650 1.522806 TTCACACACACCTCACGCC 60.523 57.895 0.00 0.00 0.00 5.68
5909 7707 1.216178 GCCATGCTGATTGCCGTTT 59.784 52.632 0.00 0.00 42.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.862209 AGATTAATTTTGGCATTGCTACGAA 58.138 32.000 8.82 0.73 0.00 3.85
6 7 5.396362 CGAGATTAATTTTGGCATTGCTACG 59.604 40.000 8.82 0.00 0.00 3.51
201 203 1.822613 CTGGCTCTACTACCGCCGA 60.823 63.158 0.00 0.00 46.67 5.54
597 608 1.480954 CTAAAACCTCGCTAGCCTCCA 59.519 52.381 9.66 0.00 0.00 3.86
600 611 1.207329 CACCTAAAACCTCGCTAGCCT 59.793 52.381 9.66 0.00 0.00 4.58
605 616 1.131928 ACCCCACCTAAAACCTCGCT 61.132 55.000 0.00 0.00 0.00 4.93
714 725 2.884179 ATCCTCCTTTACCGGCCCGA 62.884 60.000 3.71 0.00 0.00 5.14
715 726 2.440817 ATCCTCCTTTACCGGCCCG 61.441 63.158 0.00 0.00 0.00 6.13
720 731 1.472728 CCGTTCCATCCTCCTTTACCG 60.473 57.143 0.00 0.00 0.00 4.02
731 742 2.825836 CTGCTGGGCCGTTCCATC 60.826 66.667 0.00 0.00 36.05 3.51
753 764 2.232696 TGCGTTACTGTGAAGAGCCATA 59.767 45.455 0.00 0.00 0.00 2.74
775 786 0.532862 AACAACCAGGCACTCGACAG 60.533 55.000 0.00 0.00 34.60 3.51
778 789 1.227823 CCAACAACCAGGCACTCGA 60.228 57.895 0.00 0.00 34.60 4.04
805 816 0.878961 GTTTCTGCTGACCGTCCGTT 60.879 55.000 0.00 0.00 0.00 4.44
841 852 5.927819 TCTGGACGGGTTAGTTTCTAAAAA 58.072 37.500 0.00 0.00 0.00 1.94
842 853 5.549742 TCTGGACGGGTTAGTTTCTAAAA 57.450 39.130 0.00 0.00 0.00 1.52
843 854 5.750352 ATCTGGACGGGTTAGTTTCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
844 855 5.246656 TGAATCTGGACGGGTTAGTTTCTAA 59.753 40.000 0.00 0.00 0.00 2.10
845 856 4.773674 TGAATCTGGACGGGTTAGTTTCTA 59.226 41.667 0.00 0.00 0.00 2.10
846 857 3.581332 TGAATCTGGACGGGTTAGTTTCT 59.419 43.478 0.00 0.00 0.00 2.52
847 858 3.934068 TGAATCTGGACGGGTTAGTTTC 58.066 45.455 0.00 0.00 0.00 2.78
848 859 4.360951 TTGAATCTGGACGGGTTAGTTT 57.639 40.909 0.00 0.00 0.00 2.66
849 860 4.261801 CATTGAATCTGGACGGGTTAGTT 58.738 43.478 0.00 0.00 0.00 2.24
850 861 3.370527 CCATTGAATCTGGACGGGTTAGT 60.371 47.826 0.00 0.00 35.70 2.24
851 862 3.206150 CCATTGAATCTGGACGGGTTAG 58.794 50.000 0.00 0.00 35.70 2.34
852 863 2.682563 GCCATTGAATCTGGACGGGTTA 60.683 50.000 0.00 0.00 35.70 2.85
896 907 3.362797 TCGTCGGCGAGTGAGCTT 61.363 61.111 8.66 0.00 42.81 3.74
922 933 1.548973 CGCCGTATGTGATTCGAGGC 61.549 60.000 0.00 0.00 39.68 4.70
959 970 4.081807 GGTTTGGTCATTACTCCTACTCGT 60.082 45.833 0.00 0.00 0.00 4.18
960 971 4.430908 GGTTTGGTCATTACTCCTACTCG 58.569 47.826 0.00 0.00 0.00 4.18
961 972 4.159135 TCGGTTTGGTCATTACTCCTACTC 59.841 45.833 0.00 0.00 0.00 2.59
962 973 4.091549 TCGGTTTGGTCATTACTCCTACT 58.908 43.478 0.00 0.00 0.00 2.57
963 974 4.460948 TCGGTTTGGTCATTACTCCTAC 57.539 45.455 0.00 0.00 0.00 3.18
964 975 5.484715 CTTTCGGTTTGGTCATTACTCCTA 58.515 41.667 0.00 0.00 0.00 2.94
965 976 4.324267 CTTTCGGTTTGGTCATTACTCCT 58.676 43.478 0.00 0.00 0.00 3.69
966 977 3.119955 GCTTTCGGTTTGGTCATTACTCC 60.120 47.826 0.00 0.00 0.00 3.85
967 978 3.500680 TGCTTTCGGTTTGGTCATTACTC 59.499 43.478 0.00 0.00 0.00 2.59
968 979 3.482436 TGCTTTCGGTTTGGTCATTACT 58.518 40.909 0.00 0.00 0.00 2.24
969 980 3.252458 ACTGCTTTCGGTTTGGTCATTAC 59.748 43.478 0.00 0.00 0.00 1.89
970 981 3.482436 ACTGCTTTCGGTTTGGTCATTA 58.518 40.909 0.00 0.00 0.00 1.90
971 982 2.306847 ACTGCTTTCGGTTTGGTCATT 58.693 42.857 0.00 0.00 0.00 2.57
972 983 1.981256 ACTGCTTTCGGTTTGGTCAT 58.019 45.000 0.00 0.00 0.00 3.06
973 984 1.757682 AACTGCTTTCGGTTTGGTCA 58.242 45.000 0.00 0.00 38.60 4.02
1060 1071 3.721706 GAGACTGCCAGGTGGGGG 61.722 72.222 0.00 0.00 37.04 5.40
1165 1180 1.147824 CGGCCAGATTCATGAGGCT 59.852 57.895 19.74 8.32 46.23 4.58
1417 1456 1.550327 GGCAGGAAGAAAAAGGGAGG 58.450 55.000 0.00 0.00 0.00 4.30
1456 1495 4.435436 TAGCCACACAGAGCCGCG 62.435 66.667 0.00 0.00 0.00 6.46
1479 1543 2.031870 AGCTAATTTTGATTCCCGGCC 58.968 47.619 0.00 0.00 0.00 6.13
1481 1545 4.887655 AGGTAAGCTAATTTTGATTCCCGG 59.112 41.667 0.00 0.00 0.00 5.73
1499 1563 2.891580 ACGCTTCAGAGTTCAGAGGTAA 59.108 45.455 0.00 0.00 0.00 2.85
1512 1576 1.394917 GACACTGGCAATACGCTTCAG 59.605 52.381 0.00 0.00 41.91 3.02
1514 1578 0.727398 GGACACTGGCAATACGCTTC 59.273 55.000 0.00 0.00 41.91 3.86
1515 1579 0.324943 AGGACACTGGCAATACGCTT 59.675 50.000 0.00 0.00 41.91 4.68
1516 1580 1.191535 TAGGACACTGGCAATACGCT 58.808 50.000 0.00 0.00 41.91 5.07
1519 1583 5.183331 TCGATAGATAGGACACTGGCAATAC 59.817 44.000 0.00 0.00 42.67 1.89
1520 1584 5.321927 TCGATAGATAGGACACTGGCAATA 58.678 41.667 0.00 0.00 42.67 1.90
1521 1585 4.152647 TCGATAGATAGGACACTGGCAAT 58.847 43.478 0.00 0.00 42.67 3.56
1522 1586 3.562182 TCGATAGATAGGACACTGGCAA 58.438 45.455 0.00 0.00 42.67 4.52
1523 1587 3.223674 TCGATAGATAGGACACTGGCA 57.776 47.619 0.00 0.00 42.67 4.92
1559 1623 3.295093 TCATCTGATCTCCAGTCCACTC 58.705 50.000 0.00 0.00 43.38 3.51
1628 1692 1.401552 CACATGGTTATTCACGGCAGG 59.598 52.381 0.00 0.00 0.00 4.85
1633 1697 4.690748 ACTCAGTTCACATGGTTATTCACG 59.309 41.667 0.00 0.00 0.00 4.35
1637 1701 7.458397 TCCTAAACTCAGTTCACATGGTTATT 58.542 34.615 0.00 0.00 0.00 1.40
1672 1742 6.072728 TGCATGTGACAAAATAAGTCCTACAC 60.073 38.462 0.00 0.00 35.15 2.90
1674 1744 6.494893 TGCATGTGACAAAATAAGTCCTAC 57.505 37.500 0.00 0.00 35.15 3.18
1678 1768 5.344128 CAGCTTGCATGTGACAAAATAAGTC 59.656 40.000 1.14 0.00 36.55 3.01
1679 1769 5.224888 CAGCTTGCATGTGACAAAATAAGT 58.775 37.500 1.14 0.00 0.00 2.24
1680 1770 4.090930 GCAGCTTGCATGTGACAAAATAAG 59.909 41.667 1.14 0.00 44.26 1.73
1681 1771 3.989167 GCAGCTTGCATGTGACAAAATAA 59.011 39.130 1.14 0.00 44.26 1.40
1682 1772 3.577667 GCAGCTTGCATGTGACAAAATA 58.422 40.909 1.14 0.00 44.26 1.40
1683 1773 2.409975 GCAGCTTGCATGTGACAAAAT 58.590 42.857 1.14 0.00 44.26 1.82
1684 1774 1.855513 GCAGCTTGCATGTGACAAAA 58.144 45.000 1.14 0.00 44.26 2.44
1685 1775 3.573569 GCAGCTTGCATGTGACAAA 57.426 47.368 1.14 0.00 44.26 2.83
1710 1800 4.820897 CCCCAAGATTACTTTGCTTTTCC 58.179 43.478 0.00 0.00 33.70 3.13
1729 1819 2.027100 AGCTGAAGTTGTAACTAGCCCC 60.027 50.000 13.24 0.00 40.04 5.80
1730 1820 3.336138 AGCTGAAGTTGTAACTAGCCC 57.664 47.619 13.24 0.04 40.04 5.19
1754 1845 2.439338 AGCAAACGTGGTGGCACA 60.439 55.556 20.82 2.61 33.11 4.57
1761 1852 2.118683 CATTCACAACAGCAAACGTGG 58.881 47.619 0.00 0.00 0.00 4.94
1762 1853 2.118683 CCATTCACAACAGCAAACGTG 58.881 47.619 0.00 0.00 0.00 4.49
1772 1863 2.884639 AGGTAAGCACACCATTCACAAC 59.115 45.455 9.20 0.00 41.40 3.32
1773 1864 2.884012 CAGGTAAGCACACCATTCACAA 59.116 45.455 9.20 0.00 41.40 3.33
1784 1875 2.939103 CCTTCTGCATACAGGTAAGCAC 59.061 50.000 5.35 0.00 44.59 4.40
1789 1880 3.585289 TGTTTCCCTTCTGCATACAGGTA 59.415 43.478 5.49 0.00 44.59 3.08
1791 1882 3.071874 TGTTTCCCTTCTGCATACAGG 57.928 47.619 0.00 0.00 44.59 4.00
1803 1894 3.379452 TGGGTTCAACAAATGTTTCCCT 58.621 40.909 21.12 0.00 39.46 4.20
1805 1896 7.497579 AGTTAAATGGGTTCAACAAATGTTTCC 59.502 33.333 0.00 0.60 35.83 3.13
1821 1912 4.873724 TCCCCTTTCCTAGTTAAATGGG 57.126 45.455 16.12 16.12 40.95 4.00
1841 1932 1.439679 CTGTCCGGCAGTTAGGTTTC 58.560 55.000 15.27 0.00 40.27 2.78
1856 1947 6.846350 AGCTAAAATTGCACTGAATACTGTC 58.154 36.000 0.00 0.00 0.00 3.51
1858 1949 7.533426 AGAAGCTAAAATTGCACTGAATACTG 58.467 34.615 0.00 0.00 0.00 2.74
1860 1951 8.748380 AAAGAAGCTAAAATTGCACTGAATAC 57.252 30.769 0.00 0.00 0.00 1.89
1866 1958 8.462016 CCAGTATAAAGAAGCTAAAATTGCACT 58.538 33.333 0.00 0.00 0.00 4.40
1869 1961 7.220875 GCACCAGTATAAAGAAGCTAAAATTGC 59.779 37.037 0.00 0.00 0.00 3.56
1889 1983 4.278956 GGTCTACAACCGCACCAG 57.721 61.111 0.00 0.00 38.58 4.00
2034 2403 0.974383 TCCCCCTTCTGACGTTCTTC 59.026 55.000 0.00 0.00 0.00 2.87
2097 2467 2.787473 TGGCCAATAGAGTCAACAGG 57.213 50.000 0.61 0.00 0.00 4.00
2133 2503 9.936329 ACAAGGGATTCCATTACAAGTTTATAT 57.064 29.630 1.63 0.00 34.83 0.86
2158 2528 6.887376 TCTCTACTTGAATAATTGCACGAC 57.113 37.500 0.00 0.00 0.00 4.34
2160 2530 7.063426 TCACTTCTCTACTTGAATAATTGCACG 59.937 37.037 0.00 0.00 0.00 5.34
2161 2531 8.171840 GTCACTTCTCTACTTGAATAATTGCAC 58.828 37.037 0.00 0.00 0.00 4.57
2162 2532 7.877612 TGTCACTTCTCTACTTGAATAATTGCA 59.122 33.333 0.00 0.00 0.00 4.08
2176 2548 6.209589 GGATGGTATATGCTGTCACTTCTCTA 59.790 42.308 0.00 0.00 0.00 2.43
2213 3140 3.338249 GCTCATAGCTGTGGAAAACTGA 58.662 45.455 10.87 0.00 38.45 3.41
2364 3291 7.648142 CATTTTAGGCCATGTACGATTTATGT 58.352 34.615 5.01 0.00 0.00 2.29
2374 3301 3.201930 TCTGGAGCATTTTAGGCCATGTA 59.798 43.478 5.01 0.00 0.00 2.29
2375 3302 2.025037 TCTGGAGCATTTTAGGCCATGT 60.025 45.455 5.01 0.00 0.00 3.21
2382 3309 4.090761 TGGGCTATCTGGAGCATTTTAG 57.909 45.455 0.00 0.00 44.76 1.85
2458 3385 1.483415 GGCATGGGAAACTGCAATCAT 59.517 47.619 0.00 0.00 40.18 2.45
2461 3388 1.575419 ATGGCATGGGAAACTGCAAT 58.425 45.000 0.00 0.00 40.18 3.56
2571 3809 2.437413 GAAGAAACCCCAAGTGGCTAG 58.563 52.381 0.00 0.00 0.00 3.42
2860 4350 7.093814 TGTGTATTTTCAATTTCCTCATGGGAG 60.094 37.037 0.00 0.00 46.01 4.30
2866 4356 9.258826 CACAAATGTGTATTTTCAATTTCCTCA 57.741 29.630 5.38 0.00 40.96 3.86
2906 4396 6.936279 TCGGAACTCAACATTTCTATCTTCT 58.064 36.000 0.00 0.00 0.00 2.85
2915 4405 6.086222 CGAATTTGATCGGAACTCAACATTT 58.914 36.000 0.00 0.00 39.12 2.32
2973 4464 8.978874 ATCTACATGCACTACATTATGGAAAA 57.021 30.769 0.00 0.00 36.64 2.29
2974 4465 8.978874 AATCTACATGCACTACATTATGGAAA 57.021 30.769 0.00 0.00 36.64 3.13
3006 4497 5.475220 TCAAAGTTTGTGAGGTTTGACTTCA 59.525 36.000 15.08 0.00 34.72 3.02
3007 4498 5.949735 TCAAAGTTTGTGAGGTTTGACTTC 58.050 37.500 15.08 0.00 34.72 3.01
3011 4502 4.082845 TGGTCAAAGTTTGTGAGGTTTGA 58.917 39.130 15.08 0.00 36.74 2.69
3012 4503 4.448537 TGGTCAAAGTTTGTGAGGTTTG 57.551 40.909 15.08 0.00 0.00 2.93
3030 4522 5.768164 ACATATTTTTCTCCACGAACTTGGT 59.232 36.000 0.00 0.00 37.93 3.67
3114 4644 6.651755 ACTTTGCAAAGTTTGATCAAGTTG 57.348 33.333 33.85 17.66 46.52 3.16
3156 4686 9.719279 CAAAATCTGCAATTGTGTGTAAATTTT 57.281 25.926 7.40 7.40 0.00 1.82
3157 4687 9.107177 TCAAAATCTGCAATTGTGTGTAAATTT 57.893 25.926 7.40 0.00 0.00 1.82
3158 4688 8.550376 GTCAAAATCTGCAATTGTGTGTAAATT 58.450 29.630 7.40 0.00 0.00 1.82
3167 4919 6.036300 CACAAACTGTCAAAATCTGCAATTGT 59.964 34.615 7.40 0.00 30.43 2.71
3185 4937 2.159179 AGGAAAACTGGCCACAAACT 57.841 45.000 0.00 0.00 0.00 2.66
3207 4959 6.293004 AGAAGAAGAGGATTGACCAGTTAG 57.707 41.667 0.00 0.00 42.04 2.34
3220 4972 7.504403 TCTGCCTTTTCATATAGAAGAAGAGG 58.496 38.462 7.37 7.37 44.59 3.69
3332 5084 1.228769 AGTACCCTGACTCCGCACA 60.229 57.895 0.00 0.00 0.00 4.57
3376 5128 4.497473 TTGGCTAACATTTTTCTGTCCG 57.503 40.909 0.00 0.00 0.00 4.79
3391 5143 3.307480 GGCTCTAAGGAACAGTTTGGCTA 60.307 47.826 0.00 0.00 0.00 3.93
3464 5216 9.191995 GTTTGTAAATTGGACAGATTTTACAGG 57.808 33.333 7.05 0.00 0.00 4.00
3660 5414 6.783708 AGAATGGGTACAAACACAAGAAAA 57.216 33.333 0.00 0.00 43.81 2.29
3676 5430 6.649557 ACAACTCTAACTCGTTTAAGAATGGG 59.350 38.462 0.00 0.00 0.00 4.00
3817 5574 3.429085 GTTTATTGCTCCATGCTTCACG 58.571 45.455 0.00 0.00 43.37 4.35
3909 5666 5.826737 CCTCTTGCATACTGATTCTTTCCAT 59.173 40.000 0.00 0.00 0.00 3.41
4153 5910 2.502538 AGGGCGTAGTGTAATGGCTTTA 59.497 45.455 0.00 0.00 0.00 1.85
4168 5925 2.032681 GCAAAGTCTGGAGGGCGT 59.967 61.111 0.00 0.00 0.00 5.68
4177 5934 2.050144 TCAAGAGGGACTGCAAAGTCT 58.950 47.619 6.11 0.00 41.55 3.24
4225 5982 7.661437 GGTGTATTGATCATTATTGCTCTGGTA 59.339 37.037 0.00 0.00 0.00 3.25
4258 6015 6.007703 CCTTGTAAACATTTTCCCAGTAGGA 58.992 40.000 0.00 0.00 45.68 2.94
4339 6096 4.115516 CCAACTTGTCATAGACCTCATCG 58.884 47.826 0.00 0.00 0.00 3.84
4358 6115 0.250684 TGATCTGCCTCAAACGCCAA 60.251 50.000 0.00 0.00 0.00 4.52
4372 6129 9.186837 GGAATTGAAGCCATTGATATATGATCT 57.813 33.333 0.00 0.00 0.00 2.75
4393 6150 3.718434 TCCTCTCATACATGCCAGGAATT 59.282 43.478 0.00 0.00 34.41 2.17
4453 6210 1.146263 GCCGATCTTCCATCCGGTT 59.854 57.895 0.00 0.00 43.51 4.44
4486 6243 4.033776 CCCCATGTCAGGTGCGGT 62.034 66.667 0.00 0.00 0.00 5.68
4610 6367 1.823169 TTCTTTGCGCCGTAGTCCCT 61.823 55.000 4.18 0.00 0.00 4.20
4947 6712 5.003804 TCAGGCAGGTCTTTTATTCAACTC 58.996 41.667 0.00 0.00 0.00 3.01
4948 6713 4.985538 TCAGGCAGGTCTTTTATTCAACT 58.014 39.130 0.00 0.00 0.00 3.16
4949 6714 5.649831 AGATCAGGCAGGTCTTTTATTCAAC 59.350 40.000 0.00 0.00 0.00 3.18
4950 6715 5.649395 CAGATCAGGCAGGTCTTTTATTCAA 59.351 40.000 0.00 0.00 0.00 2.69
4952 6717 5.431765 TCAGATCAGGCAGGTCTTTTATTC 58.568 41.667 0.00 0.00 0.00 1.75
4953 6718 5.441718 TCAGATCAGGCAGGTCTTTTATT 57.558 39.130 0.00 0.00 0.00 1.40
4954 6719 5.455899 GGATCAGATCAGGCAGGTCTTTTAT 60.456 44.000 12.66 0.00 0.00 1.40
4955 6720 4.141620 GGATCAGATCAGGCAGGTCTTTTA 60.142 45.833 12.66 0.00 0.00 1.52
4956 6721 3.371380 GGATCAGATCAGGCAGGTCTTTT 60.371 47.826 12.66 0.00 0.00 2.27
4961 6726 2.037620 GCGGATCAGATCAGGCAGGT 62.038 60.000 12.66 0.00 32.58 4.00
5017 6785 6.780031 ACAGACAGGACATATAGATAACTGCT 59.220 38.462 0.00 0.00 0.00 4.24
5020 6788 8.001875 AGTCACAGACAGGACATATAGATAACT 58.998 37.037 0.00 0.00 36.50 2.24
5028 6796 5.660417 AGATGAAGTCACAGACAGGACATAT 59.340 40.000 0.00 0.00 36.50 1.78
5207 6983 2.149578 GCACTCTGCTGTGATCACTTT 58.850 47.619 25.55 0.67 40.96 2.66
5243 7025 8.491331 AATTTTACAAGTGCATGTTTTTCACT 57.509 26.923 0.00 0.00 42.28 3.41
5278 7060 8.079211 AGCTTTGGTAGATCAATTACACTAGA 57.921 34.615 0.00 0.00 0.00 2.43
5282 7064 7.377766 TGAAGCTTTGGTAGATCAATTACAC 57.622 36.000 0.00 0.00 0.00 2.90
5284 7066 6.490534 GCTGAAGCTTTGGTAGATCAATTAC 58.509 40.000 0.00 0.00 38.21 1.89
5339 7121 6.647334 TTGACACATTTATTTGGCTCTCAA 57.353 33.333 0.00 0.00 0.00 3.02
5340 7122 5.335897 GCTTGACACATTTATTTGGCTCTCA 60.336 40.000 0.00 0.00 0.00 3.27
5341 7123 5.098211 GCTTGACACATTTATTTGGCTCTC 58.902 41.667 0.00 0.00 0.00 3.20
5342 7124 4.082026 GGCTTGACACATTTATTTGGCTCT 60.082 41.667 0.00 0.00 0.00 4.09
5407 7190 6.020201 CGTGCGTGTAATGTAACAATCTGATA 60.020 38.462 0.00 0.00 0.00 2.15
5455 7238 1.594833 GGATGGTACTGTGTGCGGA 59.405 57.895 0.00 0.00 0.00 5.54
5464 7247 0.248907 CGAATCGCACGGATGGTACT 60.249 55.000 0.00 0.00 34.93 2.73
5570 7353 1.667467 GCGATCTATCTTCACCGGAGC 60.667 57.143 9.46 0.00 0.00 4.70
5594 7380 0.692419 AAACAACAACCCATGGCCCA 60.692 50.000 6.09 0.00 0.00 5.36
5595 7381 0.034756 GAAACAACAACCCATGGCCC 59.965 55.000 6.09 0.00 0.00 5.80
5596 7382 1.047801 AGAAACAACAACCCATGGCC 58.952 50.000 6.09 0.00 0.00 5.36
5597 7383 2.158971 ACAAGAAACAACAACCCATGGC 60.159 45.455 6.09 0.00 0.00 4.40
5598 7384 3.118811 ACACAAGAAACAACAACCCATGG 60.119 43.478 4.14 4.14 0.00 3.66
5599 7385 3.864583 CACACAAGAAACAACAACCCATG 59.135 43.478 0.00 0.00 0.00 3.66
5600 7386 3.678529 GCACACAAGAAACAACAACCCAT 60.679 43.478 0.00 0.00 0.00 4.00
5645 7433 4.028490 TGGTAACAGCAGGGCGGG 62.028 66.667 0.00 0.00 46.17 6.13
5809 7602 1.153756 GGATTGGCATCGGGGGAAT 59.846 57.895 0.00 0.00 0.00 3.01
5812 7605 3.714487 AACGGATTGGCATCGGGGG 62.714 63.158 9.50 0.00 34.69 5.40


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

AutoCloner maintained by Alex Coulton.