Multiple sequence alignment - TraesCS2A01G430400

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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 TraesCS2A01G430400 chr2A 100.000 2549 0 0 1 2549 683537881 683535333 0.000000e+00 4708
1 TraesCS2A01G430400 chr2D 87.728 1646 103 51 447 2073 539896697 539895132 0.000000e+00 1829
2 TraesCS2A01G430400 chr2D 84.029 407 54 11 22 424 539897089 539896690 5.150000e-102 381
3 TraesCS2A01G430400 chr2D 96.396 111 4 0 2343 2453 539894828 539894718 1.560000e-42 183
4 TraesCS2A01G430400 chr2B 88.168 1496 92 52 447 1914 644169587 644168149 0.000000e+00 1703
5 TraesCS2A01G430400 chr2B 93.627 204 9 3 2346 2549 644167756 644167557 4.120000e-78 302


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 TraesCS2A01G430400 chr2A 683535333 683537881 2548 True 4708.000000 4708 100.000000 1 2549 1 chr2A.!!$R1 2548
1 TraesCS2A01G430400 chr2D 539894718 539897089 2371 True 797.666667 1829 89.384333 22 2453 3 chr2D.!!$R1 2431
2 TraesCS2A01G430400 chr2B 644167557 644169587 2030 True 1002.500000 1703 90.897500 447 2549 2 chr2B.!!$R1 2102

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
917 932 0.030504 CAACAGCAACATCAACGCCA 59.969 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1819 0.034574 AATGCGGGCAGTGGTAATGA 60.035 50.0 0.0 0.0 0.0 2.57 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
34 35 4.690184 TCTCTTTTATGTACGTGCGAGA 57.310 40.909 0.00 0.00 0.00 4.04
55 56 6.334102 AGACGACTAGATTTGGTATGATCC 57.666 41.667 0.00 0.00 0.00 3.36
59 60 6.931281 ACGACTAGATTTGGTATGATCCATTG 59.069 38.462 0.00 0.00 37.33 2.82
62 63 8.915057 ACTAGATTTGGTATGATCCATTGAAG 57.085 34.615 0.00 0.00 37.33 3.02
65 66 4.879295 TTGGTATGATCCATTGAAGGGT 57.121 40.909 0.00 0.00 37.33 4.34
94 95 2.871633 CAACAATTGCAACTTTGGGACC 59.128 45.455 15.33 0.00 0.00 4.46
95 96 2.397597 ACAATTGCAACTTTGGGACCT 58.602 42.857 15.33 0.00 0.00 3.85
96 97 2.365293 ACAATTGCAACTTTGGGACCTC 59.635 45.455 15.33 0.00 0.00 3.85
100 101 1.087501 GCAACTTTGGGACCTCGATC 58.912 55.000 0.00 0.00 0.00 3.69
106 107 3.780850 ACTTTGGGACCTCGATCCTTATT 59.219 43.478 5.09 0.00 38.95 1.40
108 109 2.047061 TGGGACCTCGATCCTTATTGG 58.953 52.381 5.09 0.00 38.95 3.16
115 116 3.470709 CTCGATCCTTATTGGCATGTGT 58.529 45.455 0.00 0.00 35.26 3.72
126 127 7.148018 CCTTATTGGCATGTGTATGAAGACTTT 60.148 37.037 0.00 0.00 36.36 2.66
133 134 5.970317 TGTGTATGAAGACTTTCCGACTA 57.030 39.130 0.00 0.00 32.09 2.59
137 138 7.033791 GTGTATGAAGACTTTCCGACTATCAA 58.966 38.462 0.00 0.00 32.09 2.57
159 160 1.377725 CATGGTCAAGCCGGCTCTT 60.378 57.895 32.93 13.32 41.21 2.85
176 177 3.370527 GCTCTTGTAAGGGAGTGGCAATA 60.371 47.826 0.00 0.00 32.67 1.90
178 179 5.440610 CTCTTGTAAGGGAGTGGCAATAAT 58.559 41.667 0.00 0.00 0.00 1.28
182 183 2.332063 AGGGAGTGGCAATAATGACG 57.668 50.000 0.00 0.00 37.40 4.35
186 187 3.218721 GTGGCAATAATGACGCGTG 57.781 52.632 20.70 0.00 37.40 5.34
208 209 1.777101 CAGCTCAATCTACTAGCGGC 58.223 55.000 0.00 0.00 41.19 6.53
209 210 0.676736 AGCTCAATCTACTAGCGGCC 59.323 55.000 0.00 0.00 41.19 6.13
217 218 1.735376 CTACTAGCGGCCGTGGTCAT 61.735 60.000 28.70 10.41 0.00 3.06
218 219 1.731433 TACTAGCGGCCGTGGTCATC 61.731 60.000 28.70 7.91 0.00 2.92
225 226 2.588877 CCGTGGTCATCCGATGGC 60.589 66.667 8.54 6.48 36.30 4.40
237 238 0.109153 CCGATGGCCCATGAATCTCA 59.891 55.000 0.00 0.00 0.00 3.27
250 251 8.800332 GCCCATGAATCTCAATGTAATTCTTAT 58.200 33.333 0.00 0.00 31.22 1.73
262 263 9.859427 CAATGTAATTCTTATCATGTTTGTGGT 57.141 29.630 0.00 0.00 31.22 4.16
263 264 9.859427 AATGTAATTCTTATCATGTTTGTGGTG 57.141 29.630 0.00 0.00 0.00 4.17
264 265 7.312154 TGTAATTCTTATCATGTTTGTGGTGC 58.688 34.615 0.00 0.00 0.00 5.01
282 283 3.558505 GTGCTGCTTTGTACATTCAGTG 58.441 45.455 16.04 0.00 0.00 3.66
284 285 3.882288 TGCTGCTTTGTACATTCAGTGAA 59.118 39.130 8.27 8.27 0.00 3.18
287 288 4.460263 TGCTTTGTACATTCAGTGAACCT 58.540 39.130 7.96 0.00 0.00 3.50
318 320 7.834681 AGTAGATTTAGATCCCTTTTCCCAAAC 59.165 37.037 0.00 0.00 32.44 2.93
327 329 8.272889 AGATCCCTTTTCCCAAACTATAGTTAC 58.727 37.037 18.31 0.00 37.25 2.50
356 358 7.707774 AAAACATTTTTATCCACTTTCACCG 57.292 32.000 0.00 0.00 0.00 4.94
390 392 9.389570 CTAACAAACTTTCGGTTAATAACAAGG 57.610 33.333 5.45 0.00 37.12 3.61
391 393 6.741109 ACAAACTTTCGGTTAATAACAAGGG 58.259 36.000 5.45 0.00 37.12 3.95
406 408 2.317040 CAAGGGGCTACTATCCTTCGA 58.683 52.381 0.00 0.00 38.70 3.71
442 444 7.545362 AAAACATCATCTCGATCTACCTTTG 57.455 36.000 0.00 0.00 29.21 2.77
443 445 6.471233 AACATCATCTCGATCTACCTTTGA 57.529 37.500 0.00 0.00 29.21 2.69
444 446 6.662865 ACATCATCTCGATCTACCTTTGAT 57.337 37.500 0.00 0.00 29.21 2.57
445 447 7.767250 ACATCATCTCGATCTACCTTTGATA 57.233 36.000 0.00 0.00 29.21 2.15
486 488 6.402456 AATCCAAGAGGGTTACGACTATAC 57.598 41.667 0.00 0.00 36.13 1.47
493 495 6.127793 AGAGGGTTACGACTATACACTTCAT 58.872 40.000 0.00 0.00 0.00 2.57
575 579 1.220529 ACACATGACACTGCGTGAAG 58.779 50.000 14.18 4.95 36.96 3.02
584 588 2.358898 ACACTGCGTGAAGAGCAAAAAT 59.641 40.909 14.18 0.00 44.67 1.82
590 594 5.631026 TGCGTGAAGAGCAAAAATAATCTC 58.369 37.500 0.00 0.00 42.18 2.75
606 610 3.668596 ATCTCGGTTAAATTTTCGCCG 57.331 42.857 16.54 16.54 43.32 6.46
608 612 1.465777 CTCGGTTAAATTTTCGCCGGT 59.534 47.619 20.04 0.00 42.35 5.28
638 642 0.318120 CCAGCACACATTTCCCCAAC 59.682 55.000 0.00 0.00 0.00 3.77
639 643 0.318120 CAGCACACATTTCCCCAACC 59.682 55.000 0.00 0.00 0.00 3.77
640 644 0.105760 AGCACACATTTCCCCAACCA 60.106 50.000 0.00 0.00 0.00 3.67
641 645 0.755686 GCACACATTTCCCCAACCAA 59.244 50.000 0.00 0.00 0.00 3.67
646 650 0.321346 CATTTCCCCAACCAAGGTGC 59.679 55.000 0.00 0.00 0.00 5.01
665 669 1.402325 GCCAATAACAAACGCAGGTCC 60.402 52.381 0.00 0.00 0.00 4.46
673 677 1.197721 CAAACGCAGGTCCATTCAGAC 59.802 52.381 0.00 0.00 35.95 3.51
709 713 5.507817 GCATTCACAAAACCTCATCTCAACA 60.508 40.000 0.00 0.00 0.00 3.33
808 822 0.616679 TAGAAACTGCCGCTACCCCT 60.617 55.000 0.00 0.00 0.00 4.79
824 838 0.036671 CCCTCACGGAAACCCTACAC 60.037 60.000 0.00 0.00 0.00 2.90
825 839 0.036671 CCTCACGGAAACCCTACACC 60.037 60.000 0.00 0.00 0.00 4.16
828 842 2.435410 CGGAAACCCTACACCGCC 60.435 66.667 0.00 0.00 38.98 6.13
902 917 2.773745 AAGCAGCGCAACAGCAACA 61.774 52.632 11.47 0.00 40.15 3.33
903 918 2.672908 AAGCAGCGCAACAGCAACAG 62.673 55.000 11.47 0.00 40.15 3.16
906 921 2.278726 GCGCAACAGCAACAGCAA 60.279 55.556 0.30 0.00 37.05 3.91
907 922 2.579574 GCGCAACAGCAACAGCAAC 61.580 57.895 0.30 0.00 37.05 4.17
908 923 1.226632 CGCAACAGCAACAGCAACA 60.227 52.632 0.00 0.00 0.00 3.33
909 924 0.595567 CGCAACAGCAACAGCAACAT 60.596 50.000 0.00 0.00 0.00 2.71
910 925 1.134226 GCAACAGCAACAGCAACATC 58.866 50.000 0.00 0.00 0.00 3.06
911 926 1.536496 GCAACAGCAACAGCAACATCA 60.536 47.619 0.00 0.00 0.00 3.07
912 927 2.811855 CAACAGCAACAGCAACATCAA 58.188 42.857 0.00 0.00 0.00 2.57
913 928 2.497107 ACAGCAACAGCAACATCAAC 57.503 45.000 0.00 0.00 0.00 3.18
914 929 1.268692 ACAGCAACAGCAACATCAACG 60.269 47.619 0.00 0.00 0.00 4.10
915 930 0.318107 AGCAACAGCAACATCAACGC 60.318 50.000 0.00 0.00 0.00 4.84
916 931 1.277495 GCAACAGCAACATCAACGCC 61.277 55.000 0.00 0.00 0.00 5.68
917 932 0.030504 CAACAGCAACATCAACGCCA 59.969 50.000 0.00 0.00 0.00 5.69
918 933 0.030638 AACAGCAACATCAACGCCAC 59.969 50.000 0.00 0.00 0.00 5.01
919 934 1.100463 ACAGCAACATCAACGCCACA 61.100 50.000 0.00 0.00 0.00 4.17
920 935 0.661187 CAGCAACATCAACGCCACAC 60.661 55.000 0.00 0.00 0.00 3.82
921 936 1.371635 GCAACATCAACGCCACACC 60.372 57.895 0.00 0.00 0.00 4.16
922 937 1.285641 CAACATCAACGCCACACCC 59.714 57.895 0.00 0.00 0.00 4.61
923 938 1.152860 AACATCAACGCCACACCCA 60.153 52.632 0.00 0.00 0.00 4.51
929 944 2.124693 AACGCCACACCCAAACCAG 61.125 57.895 0.00 0.00 0.00 4.00
935 950 2.672996 CACCCAAACCAGAGCCCG 60.673 66.667 0.00 0.00 0.00 6.13
956 971 3.491104 CGAAATCCCGTAGAAGAAGGAGG 60.491 52.174 0.00 0.00 0.00 4.30
959 974 3.179902 TCCCGTAGAAGAAGGAGGAAA 57.820 47.619 0.00 0.00 0.00 3.13
961 976 2.168728 CCCGTAGAAGAAGGAGGAAAGG 59.831 54.545 0.00 0.00 0.00 3.11
963 978 3.131400 CCGTAGAAGAAGGAGGAAAGGAG 59.869 52.174 0.00 0.00 0.00 3.69
1536 1578 2.600470 GGCACCCCCAACAACTCC 60.600 66.667 0.00 0.00 0.00 3.85
1551 1601 1.127343 ACTCCCTCTGCAGATAAGCC 58.873 55.000 18.63 0.00 0.00 4.35
1552 1602 0.396060 CTCCCTCTGCAGATAAGCCC 59.604 60.000 18.63 0.00 0.00 5.19
1553 1603 1.070445 CCCTCTGCAGATAAGCCCG 59.930 63.158 18.63 3.16 0.00 6.13
1554 1604 1.070445 CCTCTGCAGATAAGCCCGG 59.930 63.158 18.63 9.28 0.00 5.73
1555 1605 1.596477 CTCTGCAGATAAGCCCGGC 60.596 63.158 18.63 0.00 0.00 6.13
1613 1666 2.824341 CCACCGTTAGAAGTACCTGACT 59.176 50.000 0.00 0.00 41.56 3.41
1665 1722 7.777440 AGTTCTGTTCTCCATTTTTCTTCTTCT 59.223 33.333 0.00 0.00 0.00 2.85
1671 1728 7.426929 TCTCCATTTTTCTTCTTCTTCTTCG 57.573 36.000 0.00 0.00 0.00 3.79
1685 1742 1.925229 TCTTCGTCGGTCGTGTTTTT 58.075 45.000 0.00 0.00 40.80 1.94
1686 1743 1.854126 TCTTCGTCGGTCGTGTTTTTC 59.146 47.619 0.00 0.00 40.80 2.29
1786 1846 0.678048 ACTGCCCGCATTCTTTCTCC 60.678 55.000 0.00 0.00 0.00 3.71
1813 1873 1.416401 GATCTGGATTAGCCGGGTGAA 59.584 52.381 18.40 7.21 43.76 3.18
1814 1874 1.507140 TCTGGATTAGCCGGGTGAAT 58.493 50.000 18.40 11.86 43.76 2.57
1815 1875 1.140852 TCTGGATTAGCCGGGTGAATG 59.859 52.381 18.40 1.64 43.76 2.67
1816 1876 0.182537 TGGATTAGCCGGGTGAATGG 59.817 55.000 18.40 0.00 40.66 3.16
1885 1950 7.332678 GGAAAGATTGATGTGAAAAATGAAGGG 59.667 37.037 0.00 0.00 0.00 3.95
1888 1953 3.153130 TGATGTGAAAAATGAAGGGCGA 58.847 40.909 0.00 0.00 0.00 5.54
1889 1954 3.763360 TGATGTGAAAAATGAAGGGCGAT 59.237 39.130 0.00 0.00 0.00 4.58
1890 1955 3.574284 TGTGAAAAATGAAGGGCGATG 57.426 42.857 0.00 0.00 0.00 3.84
1891 1956 3.153130 TGTGAAAAATGAAGGGCGATGA 58.847 40.909 0.00 0.00 0.00 2.92
1892 1957 3.763360 TGTGAAAAATGAAGGGCGATGAT 59.237 39.130 0.00 0.00 0.00 2.45
1893 1958 4.142403 TGTGAAAAATGAAGGGCGATGATC 60.142 41.667 0.00 0.00 0.00 2.92
1923 1988 9.687210 TTTCTCTCTTGATTGATTGATTTGTTG 57.313 29.630 0.00 0.00 0.00 3.33
1934 1999 5.826737 TGATTGATTTGTTGTTGCCCATTTT 59.173 32.000 0.00 0.00 0.00 1.82
1935 2000 6.994496 TGATTGATTTGTTGTTGCCCATTTTA 59.006 30.769 0.00 0.00 0.00 1.52
1936 2001 7.664731 TGATTGATTTGTTGTTGCCCATTTTAT 59.335 29.630 0.00 0.00 0.00 1.40
1942 2007 2.465813 TGTTGCCCATTTTATCAGGGG 58.534 47.619 0.00 0.00 43.04 4.79
1983 2048 6.690704 GGAAAGATTTTGAATGTTCCGTTC 57.309 37.500 0.00 0.00 0.00 3.95
2001 2066 2.134201 TCGATACGCTGCAGTTATGG 57.866 50.000 16.64 13.15 0.00 2.74
2002 2067 1.139989 CGATACGCTGCAGTTATGGG 58.860 55.000 16.64 0.00 0.00 4.00
2003 2068 1.538204 CGATACGCTGCAGTTATGGGT 60.538 52.381 16.64 6.71 0.00 4.51
2004 2069 2.561569 GATACGCTGCAGTTATGGGTT 58.438 47.619 16.64 0.00 0.00 4.11
2034 2099 1.355971 ATTTCGCGTGCGTACATCTT 58.644 45.000 14.47 0.00 40.74 2.40
2035 2100 0.711670 TTTCGCGTGCGTACATCTTC 59.288 50.000 14.47 0.00 40.74 2.87
2036 2101 0.109458 TTCGCGTGCGTACATCTTCT 60.109 50.000 14.47 0.00 40.74 2.85
2037 2102 0.728542 TCGCGTGCGTACATCTTCTA 59.271 50.000 14.47 0.00 40.74 2.10
2038 2103 1.332686 TCGCGTGCGTACATCTTCTAT 59.667 47.619 14.47 0.00 40.74 1.98
2039 2104 1.448308 CGCGTGCGTACATCTTCTATG 59.552 52.381 6.00 0.00 34.35 2.23
2040 2105 1.787155 GCGTGCGTACATCTTCTATGG 59.213 52.381 4.09 0.00 0.00 2.74
2041 2106 1.787155 CGTGCGTACATCTTCTATGGC 59.213 52.381 4.09 0.00 0.00 4.40
2042 2107 2.798145 CGTGCGTACATCTTCTATGGCA 60.798 50.000 4.09 0.00 0.00 4.92
2062 2129 0.038983 GCCGGCCGTTGTTGTAAAAT 60.039 50.000 26.12 0.00 0.00 1.82
2069 2136 5.510323 CGGCCGTTGTTGTAAAATAATCTTC 59.490 40.000 19.50 0.00 0.00 2.87
2096 2190 1.581727 TATTGGCGCGCATGTGTTGT 61.582 50.000 34.42 11.44 0.00 3.32
2102 2196 1.346365 CGCGCATGTGTTGTAGTACT 58.654 50.000 8.75 0.00 0.00 2.73
2103 2197 2.521996 CGCGCATGTGTTGTAGTACTA 58.478 47.619 8.75 0.00 0.00 1.82
2105 2199 2.601763 GCGCATGTGTTGTAGTACTACC 59.398 50.000 26.41 14.68 35.26 3.18
2106 2200 3.840468 CGCATGTGTTGTAGTACTACCA 58.160 45.455 26.41 18.24 35.26 3.25
2107 2201 3.611113 CGCATGTGTTGTAGTACTACCAC 59.389 47.826 26.41 25.00 35.26 4.16
2108 2202 3.611113 GCATGTGTTGTAGTACTACCACG 59.389 47.826 26.41 16.98 35.27 4.94
2109 2203 4.801891 CATGTGTTGTAGTACTACCACGT 58.198 43.478 26.41 23.77 35.27 4.49
2110 2204 5.619757 GCATGTGTTGTAGTACTACCACGTA 60.620 44.000 26.41 18.64 35.27 3.57
2111 2205 5.356882 TGTGTTGTAGTACTACCACGTAC 57.643 43.478 26.41 20.17 39.97 3.67
2112 2206 4.215399 TGTGTTGTAGTACTACCACGTACC 59.785 45.833 26.41 15.81 40.42 3.34
2113 2207 4.455877 GTGTTGTAGTACTACCACGTACCT 59.544 45.833 26.41 0.00 40.42 3.08
2114 2208 4.455533 TGTTGTAGTACTACCACGTACCTG 59.544 45.833 26.41 0.00 40.42 4.00
2123 2217 1.255667 CCACGTACCTGCTGTACCCT 61.256 60.000 10.29 0.00 45.89 4.34
2140 2234 1.753073 CCCTCTGGTGAAATGAATGCC 59.247 52.381 0.00 0.00 0.00 4.40
2143 2237 2.165030 CTCTGGTGAAATGAATGCCACC 59.835 50.000 0.00 0.00 46.82 4.61
2146 2240 2.971330 TGGTGAAATGAATGCCACCTTT 59.029 40.909 11.10 0.00 46.77 3.11
2148 2242 6.314376 TGGTGAAATGAATGCCACCTTTGG 62.314 45.833 11.10 0.00 46.77 3.28
2160 2254 2.991250 CACCTTTGGATCAATCGGAGT 58.009 47.619 0.00 0.00 0.00 3.85
2161 2255 4.137116 CACCTTTGGATCAATCGGAGTA 57.863 45.455 0.00 0.00 0.00 2.59
2166 2260 4.987408 TTGGATCAATCGGAGTAACGTA 57.013 40.909 0.00 0.00 34.94 3.57
2167 2261 4.297299 TGGATCAATCGGAGTAACGTAC 57.703 45.455 0.00 0.00 34.94 3.67
2183 2277 3.531538 ACGTACTGCAATTCGATCCAAT 58.468 40.909 0.06 0.00 0.00 3.16
2184 2278 3.309682 ACGTACTGCAATTCGATCCAATG 59.690 43.478 0.06 0.00 0.00 2.82
2185 2279 2.857592 ACTGCAATTCGATCCAATGC 57.142 45.000 0.00 0.00 0.00 3.56
2186 2280 2.372264 ACTGCAATTCGATCCAATGCT 58.628 42.857 8.35 0.00 0.00 3.79
2187 2281 2.098607 ACTGCAATTCGATCCAATGCTG 59.901 45.455 10.61 10.61 0.00 4.41
2188 2282 1.406180 TGCAATTCGATCCAATGCTGG 59.594 47.619 8.35 0.00 45.08 4.85
2204 2298 6.201615 CCAATGCTGGAAAGAAGAAGAAAAAC 59.798 38.462 0.00 0.00 46.92 2.43
2209 2303 6.119144 TGGAAAGAAGAAGAAAAACAGTCG 57.881 37.500 0.00 0.00 0.00 4.18
2220 2314 1.100463 AAACAGTCGCCACATGCACA 61.100 50.000 0.00 0.00 41.33 4.57
2225 2319 1.525765 TCGCCACATGCACACAACT 60.526 52.632 0.00 0.00 41.33 3.16
2264 2363 2.014128 AGTCCACAGTGACGTTTTTGG 58.986 47.619 0.62 0.00 40.26 3.28
2265 2364 0.736053 TCCACAGTGACGTTTTTGGC 59.264 50.000 0.62 0.00 0.00 4.52
2268 2367 1.657181 CAGTGACGTTTTTGGCGCC 60.657 57.895 22.73 22.73 0.00 6.53
2273 2372 1.404391 TGACGTTTTTGGCGCCTTTTA 59.596 42.857 29.70 3.37 0.00 1.52
2274 2373 1.782569 GACGTTTTTGGCGCCTTTTAC 59.217 47.619 29.70 18.57 0.00 2.01
2275 2374 1.406180 ACGTTTTTGGCGCCTTTTACT 59.594 42.857 29.70 7.96 0.00 2.24
2277 2376 1.525197 GTTTTTGGCGCCTTTTACTGC 59.475 47.619 29.70 6.51 0.00 4.40
2280 2379 2.877691 GGCGCCTTTTACTGCCTG 59.122 61.111 22.15 0.00 44.16 4.85
2281 2380 1.971695 GGCGCCTTTTACTGCCTGT 60.972 57.895 22.15 0.00 44.16 4.00
2288 2405 1.537202 CTTTTACTGCCTGTCCACTGC 59.463 52.381 0.00 0.00 0.00 4.40
2310 2427 0.110056 GTCACATGAGGCAAAGCGTG 60.110 55.000 0.00 0.00 0.00 5.34
2320 2437 1.864862 CAAAGCGTGCACTCTGGAG 59.135 57.895 16.19 2.25 0.00 3.86
2321 2438 1.963338 AAAGCGTGCACTCTGGAGC 60.963 57.895 16.19 9.69 0.00 4.70
2322 2439 3.890936 AAGCGTGCACTCTGGAGCC 62.891 63.158 16.19 0.00 0.00 4.70
2324 2441 4.363990 CGTGCACTCTGGAGCCGT 62.364 66.667 16.19 0.00 0.00 5.68
2325 2442 2.031163 GTGCACTCTGGAGCCGTT 59.969 61.111 10.32 0.00 0.00 4.44
2326 2443 1.292223 GTGCACTCTGGAGCCGTTA 59.708 57.895 10.32 0.00 0.00 3.18
2327 2444 0.108138 GTGCACTCTGGAGCCGTTAT 60.108 55.000 10.32 0.00 0.00 1.89
2329 2446 0.461961 GCACTCTGGAGCCGTTATCT 59.538 55.000 0.00 0.00 0.00 1.98
2330 2447 1.804372 GCACTCTGGAGCCGTTATCTG 60.804 57.143 0.00 0.00 0.00 2.90
2331 2448 1.751351 CACTCTGGAGCCGTTATCTGA 59.249 52.381 0.00 0.00 0.00 3.27
2334 2451 0.461548 CTGGAGCCGTTATCTGAGCA 59.538 55.000 0.00 0.00 0.00 4.26
2336 2453 1.069204 TGGAGCCGTTATCTGAGCATC 59.931 52.381 0.00 0.00 0.00 3.91
2337 2454 1.413382 GAGCCGTTATCTGAGCATCG 58.587 55.000 0.00 0.00 38.61 3.84
2338 2455 0.032678 AGCCGTTATCTGAGCATCGG 59.967 55.000 0.00 0.00 44.94 4.18
2339 2456 2.522060 CCGTTATCTGAGCATCGGC 58.478 57.895 0.00 0.00 42.67 5.54
2378 2525 0.751643 AGCAAAACTGGCGACCAACT 60.752 50.000 0.00 0.00 36.08 3.16
2454 2601 0.038166 TCATGAAGGCCACTGTTCCC 59.962 55.000 5.01 0.00 0.00 3.97
2531 2678 1.735920 GGCTGCTGTCTGTCGTCAG 60.736 63.158 3.03 3.03 42.54 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.897349 GCACGTACATAAAAGAGAAAAGTATAC 57.103 33.333 0.00 0.00 0.00 1.47
5 6 8.800972 CGCACGTACATAAAAGAGAAAAGTATA 58.199 33.333 0.00 0.00 0.00 1.47
6 7 7.543172 TCGCACGTACATAAAAGAGAAAAGTAT 59.457 33.333 0.00 0.00 0.00 2.12
7 8 6.862608 TCGCACGTACATAAAAGAGAAAAGTA 59.137 34.615 0.00 0.00 0.00 2.24
8 9 5.693104 TCGCACGTACATAAAAGAGAAAAGT 59.307 36.000 0.00 0.00 0.00 2.66
9 10 6.089016 TCTCGCACGTACATAAAAGAGAAAAG 59.911 38.462 0.00 0.00 31.54 2.27
10 11 5.921976 TCTCGCACGTACATAAAAGAGAAAA 59.078 36.000 0.00 0.00 31.54 2.29
11 12 5.344128 GTCTCGCACGTACATAAAAGAGAAA 59.656 40.000 0.00 0.00 35.62 2.52
12 13 4.855388 GTCTCGCACGTACATAAAAGAGAA 59.145 41.667 0.00 0.00 35.62 2.87
13 14 4.409570 GTCTCGCACGTACATAAAAGAGA 58.590 43.478 0.00 0.00 0.00 3.10
14 15 3.237660 CGTCTCGCACGTACATAAAAGAG 59.762 47.826 0.00 0.00 44.07 2.85
15 16 3.165890 CGTCTCGCACGTACATAAAAGA 58.834 45.455 0.00 0.00 44.07 2.52
16 17 3.532213 CGTCTCGCACGTACATAAAAG 57.468 47.619 0.00 0.00 44.07 2.27
34 35 6.672266 ATGGATCATACCAAATCTAGTCGT 57.328 37.500 0.00 0.00 43.47 4.34
39 40 7.147141 ACCCTTCAATGGATCATACCAAATCTA 60.147 37.037 0.00 0.00 43.47 1.98
55 56 4.892433 TGTTGCCATTAAACCCTTCAATG 58.108 39.130 0.00 0.00 0.00 2.82
59 60 5.861222 CAATTGTTGCCATTAAACCCTTC 57.139 39.130 0.00 0.00 0.00 3.46
77 78 1.613437 CGAGGTCCCAAAGTTGCAATT 59.387 47.619 0.59 0.00 0.00 2.32
80 81 0.400213 ATCGAGGTCCCAAAGTTGCA 59.600 50.000 0.00 0.00 0.00 4.08
84 85 1.657804 AAGGATCGAGGTCCCAAAGT 58.342 50.000 1.30 0.00 39.17 2.66
94 95 3.470709 ACACATGCCAATAAGGATCGAG 58.529 45.455 0.00 0.00 41.22 4.04
95 96 3.558931 ACACATGCCAATAAGGATCGA 57.441 42.857 0.00 0.00 41.22 3.59
96 97 4.996758 TCATACACATGCCAATAAGGATCG 59.003 41.667 0.00 0.00 41.22 3.69
100 101 5.824624 AGTCTTCATACACATGCCAATAAGG 59.175 40.000 0.00 0.00 41.84 2.69
106 107 4.009675 GGAAAGTCTTCATACACATGCCA 58.990 43.478 0.00 0.00 32.75 4.92
108 109 3.932710 TCGGAAAGTCTTCATACACATGC 59.067 43.478 0.00 0.00 32.75 4.06
115 116 7.921214 GTCATTGATAGTCGGAAAGTCTTCATA 59.079 37.037 0.00 0.00 32.75 2.15
126 127 3.704061 TGACCATGTCATTGATAGTCGGA 59.296 43.478 0.00 0.00 37.67 4.55
133 134 2.019249 CGGCTTGACCATGTCATTGAT 58.981 47.619 0.00 0.00 42.40 2.57
137 138 1.750399 GCCGGCTTGACCATGTCAT 60.750 57.895 22.15 0.00 42.40 3.06
159 160 4.523083 GTCATTATTGCCACTCCCTTACA 58.477 43.478 0.00 0.00 0.00 2.41
176 177 2.047844 AGCTGCTCACGCGTCATT 60.048 55.556 9.86 0.00 39.65 2.57
178 179 2.770132 ATTGAGCTGCTCACGCGTCA 62.770 55.000 30.47 16.17 40.46 4.35
182 183 0.926846 GTAGATTGAGCTGCTCACGC 59.073 55.000 30.47 23.48 40.46 5.34
186 187 2.606795 CCGCTAGTAGATTGAGCTGCTC 60.607 54.545 22.38 22.38 32.89 4.26
190 191 0.676736 GGCCGCTAGTAGATTGAGCT 59.323 55.000 0.00 0.00 33.91 4.09
195 196 1.041447 ACCACGGCCGCTAGTAGATT 61.041 55.000 28.58 0.00 0.00 2.40
196 197 1.453762 GACCACGGCCGCTAGTAGAT 61.454 60.000 28.58 0.00 0.00 1.98
200 201 3.075005 ATGACCACGGCCGCTAGT 61.075 61.111 28.58 20.61 0.00 2.57
201 202 2.279517 GATGACCACGGCCGCTAG 60.280 66.667 28.58 17.04 0.00 3.42
208 209 2.588877 GCCATCGGATGACCACGG 60.589 66.667 19.30 2.56 35.59 4.94
209 210 2.588877 GGCCATCGGATGACCACG 60.589 66.667 19.30 3.37 32.44 4.94
217 218 0.397941 GAGATTCATGGGCCATCGGA 59.602 55.000 18.16 9.47 0.00 4.55
218 219 0.109153 TGAGATTCATGGGCCATCGG 59.891 55.000 18.16 6.80 0.00 4.18
220 221 3.228453 ACATTGAGATTCATGGGCCATC 58.772 45.455 18.16 6.37 0.00 3.51
221 222 3.323774 ACATTGAGATTCATGGGCCAT 57.676 42.857 14.78 14.78 0.00 4.40
237 238 9.859427 CACCACAAACATGATAAGAATTACATT 57.141 29.630 0.00 0.00 30.46 2.71
250 251 1.401761 AAGCAGCACCACAAACATGA 58.598 45.000 0.00 0.00 0.00 3.07
251 252 1.862201 CAAAGCAGCACCACAAACATG 59.138 47.619 0.00 0.00 0.00 3.21
259 260 2.553602 CTGAATGTACAAAGCAGCACCA 59.446 45.455 0.00 0.00 0.00 4.17
262 263 3.475575 TCACTGAATGTACAAAGCAGCA 58.524 40.909 17.66 6.89 0.00 4.41
263 264 4.222114 GTTCACTGAATGTACAAAGCAGC 58.778 43.478 17.66 0.00 0.00 5.25
264 265 4.516698 AGGTTCACTGAATGTACAAAGCAG 59.483 41.667 16.67 16.67 30.42 4.24
293 294 7.834681 AGTTTGGGAAAAGGGATCTAAATCTAC 59.165 37.037 0.00 0.00 32.12 2.59
299 300 8.401955 ACTATAGTTTGGGAAAAGGGATCTAA 57.598 34.615 0.00 0.00 0.00 2.10
300 301 8.401955 AACTATAGTTTGGGAAAAGGGATCTA 57.598 34.615 12.50 0.00 33.93 1.98
302 303 8.050930 TGTAACTATAGTTTGGGAAAAGGGATC 58.949 37.037 22.66 0.00 39.31 3.36
304 305 7.332433 TGTAACTATAGTTTGGGAAAAGGGA 57.668 36.000 22.66 0.00 39.31 4.20
332 334 7.269316 ACGGTGAAAGTGGATAAAAATGTTTT 58.731 30.769 0.00 0.00 0.00 2.43
336 338 6.019152 CGTACGGTGAAAGTGGATAAAAATG 58.981 40.000 7.57 0.00 0.00 2.32
337 339 5.933463 TCGTACGGTGAAAGTGGATAAAAAT 59.067 36.000 16.52 0.00 0.00 1.82
342 344 2.164219 GGTCGTACGGTGAAAGTGGATA 59.836 50.000 16.52 0.00 0.00 2.59
343 345 1.067354 GGTCGTACGGTGAAAGTGGAT 60.067 52.381 16.52 0.00 0.00 3.41
344 346 0.314935 GGTCGTACGGTGAAAGTGGA 59.685 55.000 16.52 0.00 0.00 4.02
345 347 0.668401 GGGTCGTACGGTGAAAGTGG 60.668 60.000 16.52 0.00 0.00 4.00
352 354 2.061028 GTTTGTTAGGGTCGTACGGTG 58.939 52.381 16.52 0.00 0.00 4.94
356 358 3.429881 CCGAAAGTTTGTTAGGGTCGTAC 59.570 47.826 0.00 0.00 0.00 3.67
390 392 2.289592 TCCTCGAAGGATAGTAGCCC 57.710 55.000 0.00 0.00 40.06 5.19
417 419 7.824289 TCAAAGGTAGATCGAGATGATGTTTTT 59.176 33.333 0.00 0.00 37.47 1.94
418 420 7.331026 TCAAAGGTAGATCGAGATGATGTTTT 58.669 34.615 0.00 0.00 37.47 2.43
419 421 6.878317 TCAAAGGTAGATCGAGATGATGTTT 58.122 36.000 0.00 0.00 37.47 2.83
420 422 6.471233 TCAAAGGTAGATCGAGATGATGTT 57.529 37.500 0.00 0.00 37.47 2.71
421 423 6.662865 ATCAAAGGTAGATCGAGATGATGT 57.337 37.500 0.00 0.00 37.47 3.06
422 424 9.481340 TTTTATCAAAGGTAGATCGAGATGATG 57.519 33.333 0.00 0.00 37.47 3.07
454 456 6.408891 CGTAACCCTCTTGGATTTTACCCTAT 60.409 42.308 0.00 0.00 38.00 2.57
458 460 4.633126 GTCGTAACCCTCTTGGATTTTACC 59.367 45.833 0.00 0.00 38.00 2.85
486 488 4.408182 AGGGTAGATCGGAAATGAAGTG 57.592 45.455 0.00 0.00 0.00 3.16
493 495 5.961398 TTTATCCAAGGGTAGATCGGAAA 57.039 39.130 0.00 0.00 0.00 3.13
584 588 4.034279 CCGGCGAAAATTTAACCGAGATTA 59.966 41.667 21.47 0.00 46.71 1.75
590 594 1.197264 TGACCGGCGAAAATTTAACCG 59.803 47.619 9.30 15.75 43.44 4.44
638 642 2.671596 CGTTTGTTATTGGCACCTTGG 58.328 47.619 0.00 0.00 0.00 3.61
639 643 2.058057 GCGTTTGTTATTGGCACCTTG 58.942 47.619 0.00 0.00 0.00 3.61
640 644 1.683917 TGCGTTTGTTATTGGCACCTT 59.316 42.857 0.00 0.00 0.00 3.50
641 645 1.269448 CTGCGTTTGTTATTGGCACCT 59.731 47.619 0.00 0.00 0.00 4.00
646 650 1.883275 TGGACCTGCGTTTGTTATTGG 59.117 47.619 0.00 0.00 0.00 3.16
665 669 1.391485 CCAGTTCGAAGCGTCTGAATG 59.609 52.381 13.44 2.61 34.39 2.67
673 677 0.179215 GTGAATGCCAGTTCGAAGCG 60.179 55.000 0.00 0.00 0.00 4.68
808 822 1.667151 CGGTGTAGGGTTTCCGTGA 59.333 57.895 0.00 0.00 38.45 4.35
851 865 0.398522 GAGGGGGCATTTAAAGGGGG 60.399 60.000 1.57 0.00 0.00 5.40
855 869 1.014352 CGTCGAGGGGGCATTTAAAG 58.986 55.000 0.00 0.00 0.00 1.85
858 872 0.108041 GTTCGTCGAGGGGGCATTTA 60.108 55.000 5.12 0.00 0.00 1.40
861 875 4.143333 CGTTCGTCGAGGGGGCAT 62.143 66.667 5.12 0.00 42.86 4.40
902 917 1.654220 GTGTGGCGTTGATGTTGCT 59.346 52.632 0.00 0.00 0.00 3.91
903 918 1.371635 GGTGTGGCGTTGATGTTGC 60.372 57.895 0.00 0.00 0.00 4.17
906 921 0.753479 TTTGGGTGTGGCGTTGATGT 60.753 50.000 0.00 0.00 0.00 3.06
907 922 0.318614 GTTTGGGTGTGGCGTTGATG 60.319 55.000 0.00 0.00 0.00 3.07
908 923 1.460273 GGTTTGGGTGTGGCGTTGAT 61.460 55.000 0.00 0.00 0.00 2.57
909 924 2.122167 GGTTTGGGTGTGGCGTTGA 61.122 57.895 0.00 0.00 0.00 3.18
910 925 2.348605 CTGGTTTGGGTGTGGCGTTG 62.349 60.000 0.00 0.00 0.00 4.10
911 926 2.043852 TGGTTTGGGTGTGGCGTT 60.044 55.556 0.00 0.00 0.00 4.84
912 927 2.518349 CTGGTTTGGGTGTGGCGT 60.518 61.111 0.00 0.00 0.00 5.68
913 928 2.203280 TCTGGTTTGGGTGTGGCG 60.203 61.111 0.00 0.00 0.00 5.69
914 929 2.564721 GCTCTGGTTTGGGTGTGGC 61.565 63.158 0.00 0.00 0.00 5.01
915 930 1.903404 GGCTCTGGTTTGGGTGTGG 60.903 63.158 0.00 0.00 0.00 4.17
916 931 1.903404 GGGCTCTGGTTTGGGTGTG 60.903 63.158 0.00 0.00 0.00 3.82
917 932 2.520968 GGGCTCTGGTTTGGGTGT 59.479 61.111 0.00 0.00 0.00 4.16
918 933 2.672996 CGGGCTCTGGTTTGGGTG 60.673 66.667 0.00 0.00 0.00 4.61
919 934 2.002018 TTTCGGGCTCTGGTTTGGGT 62.002 55.000 0.00 0.00 0.00 4.51
920 935 0.611896 ATTTCGGGCTCTGGTTTGGG 60.612 55.000 0.00 0.00 0.00 4.12
921 936 0.811281 GATTTCGGGCTCTGGTTTGG 59.189 55.000 0.00 0.00 0.00 3.28
922 937 0.811281 GGATTTCGGGCTCTGGTTTG 59.189 55.000 0.00 0.00 0.00 2.93
923 938 0.323451 GGGATTTCGGGCTCTGGTTT 60.323 55.000 0.00 0.00 0.00 3.27
929 944 0.462789 TTCTACGGGATTTCGGGCTC 59.537 55.000 0.00 0.00 0.00 4.70
935 950 3.705072 TCCTCCTTCTTCTACGGGATTTC 59.295 47.826 0.00 0.00 0.00 2.17
956 971 2.046217 GGGCGGTGGTCTCCTTTC 60.046 66.667 0.00 0.00 0.00 2.62
963 978 4.222847 GATCTCCGGGCGGTGGTC 62.223 72.222 0.00 0.00 36.47 4.02
975 1017 1.009449 CGCTCCGACGGAAGATCTC 60.009 63.158 18.93 2.40 0.00 2.75
1149 1191 4.314440 TTGCTCTCGCCGTTGCCT 62.314 61.111 0.00 0.00 34.43 4.75
1456 1498 3.284449 GGCGGCGTTGTCCTTGTT 61.284 61.111 9.37 0.00 0.00 2.83
1536 1578 1.070445 CCGGGCTTATCTGCAGAGG 59.930 63.158 22.96 11.89 34.04 3.69
1602 1655 4.538738 GAGAGGATGGTAGTCAGGTACTT 58.461 47.826 0.00 0.00 39.80 2.24
1613 1666 2.241281 TTTCGTGGGAGAGGATGGTA 57.759 50.000 0.00 0.00 0.00 3.25
1638 1695 7.888250 AGAAGAAAAATGGAGAACAGAACTT 57.112 32.000 0.00 0.00 0.00 2.66
1639 1696 7.777440 AGAAGAAGAAAAATGGAGAACAGAACT 59.223 33.333 0.00 0.00 0.00 3.01
1645 1702 7.800847 CGAAGAAGAAGAAGAAAAATGGAGAAC 59.199 37.037 0.00 0.00 0.00 3.01
1653 1710 5.114081 ACCGACGAAGAAGAAGAAGAAAAA 58.886 37.500 0.00 0.00 0.00 1.94
1654 1711 4.690122 ACCGACGAAGAAGAAGAAGAAAA 58.310 39.130 0.00 0.00 0.00 2.29
1655 1712 4.296690 GACCGACGAAGAAGAAGAAGAAA 58.703 43.478 0.00 0.00 0.00 2.52
1665 1722 1.925229 AAAACACGACCGACGAAGAA 58.075 45.000 0.00 0.00 45.77 2.52
1671 1728 0.041576 GCTGGAAAAACACGACCGAC 60.042 55.000 0.00 0.00 0.00 4.79
1685 1742 2.212900 CTCACCATCACGACGCTGGA 62.213 60.000 16.03 3.23 34.08 3.86
1686 1743 1.807165 CTCACCATCACGACGCTGG 60.807 63.158 9.44 9.44 36.09 4.85
1749 1809 5.940470 GGGCAGTGGTAATGATAATTCCTAG 59.060 44.000 0.00 0.00 0.00 3.02
1758 1818 0.183492 ATGCGGGCAGTGGTAATGAT 59.817 50.000 0.00 0.00 0.00 2.45
1759 1819 0.034574 AATGCGGGCAGTGGTAATGA 60.035 50.000 0.00 0.00 0.00 2.57
1760 1820 0.381801 GAATGCGGGCAGTGGTAATG 59.618 55.000 0.00 0.00 0.00 1.90
1786 1846 3.185330 CGGCTAATCCAGATCATCATCG 58.815 50.000 0.00 0.00 33.75 3.84
1905 1970 5.469421 GGGCAACAACAAATCAATCAATCAA 59.531 36.000 0.00 0.00 39.74 2.57
1906 1971 4.996122 GGGCAACAACAAATCAATCAATCA 59.004 37.500 0.00 0.00 39.74 2.57
1907 1972 4.996122 TGGGCAACAACAAATCAATCAATC 59.004 37.500 0.00 0.00 39.74 2.67
1908 1973 4.970711 TGGGCAACAACAAATCAATCAAT 58.029 34.783 0.00 0.00 39.74 2.57
1923 1988 2.430694 GACCCCTGATAAAATGGGCAAC 59.569 50.000 0.00 0.00 42.07 4.17
1934 1999 1.138859 CATCGCAACAGACCCCTGATA 59.861 52.381 0.00 0.00 43.02 2.15
1935 2000 0.107508 CATCGCAACAGACCCCTGAT 60.108 55.000 0.00 0.00 43.02 2.90
1936 2001 1.296392 CATCGCAACAGACCCCTGA 59.704 57.895 0.00 0.00 43.02 3.86
1942 2007 1.626654 CCGGTGACATCGCAACAGAC 61.627 60.000 1.54 0.00 0.00 3.51
1983 2048 1.139989 CCCATAACTGCAGCGTATCG 58.860 55.000 15.27 4.71 0.00 2.92
2001 2066 3.181504 ACGCGAAATATGTAAAGGCAACC 60.182 43.478 15.93 0.00 37.17 3.77
2002 2067 3.783943 CACGCGAAATATGTAAAGGCAAC 59.216 43.478 15.93 0.00 0.00 4.17
2003 2068 3.729462 GCACGCGAAATATGTAAAGGCAA 60.729 43.478 15.93 0.00 0.00 4.52
2004 2069 2.223157 GCACGCGAAATATGTAAAGGCA 60.223 45.455 15.93 0.00 0.00 4.75
2041 2106 1.787057 TTTACAACAACGGCCGGCTG 61.787 55.000 33.73 33.73 0.00 4.85
2042 2107 1.102222 TTTTACAACAACGGCCGGCT 61.102 50.000 31.76 13.86 0.00 5.52
2062 2129 4.570772 GCGCCAATAGTCAAGTGAAGATTA 59.429 41.667 0.00 0.00 0.00 1.75
2069 2136 1.060937 GCGCGCCAATAGTCAAGTG 59.939 57.895 23.24 0.00 0.00 3.16
2096 2190 3.273434 CAGCAGGTACGTGGTAGTACTA 58.727 50.000 18.83 0.00 44.59 1.82
2109 2203 3.300032 CCAGAGGGTACAGCAGGTA 57.700 57.895 0.00 0.00 0.00 3.08
2110 2204 4.136978 CCAGAGGGTACAGCAGGT 57.863 61.111 0.00 0.00 0.00 4.00
2123 2217 2.170166 GGTGGCATTCATTTCACCAGA 58.830 47.619 6.48 0.00 46.39 3.86
2129 2223 3.959535 TCCAAAGGTGGCATTCATTTC 57.040 42.857 0.00 0.00 45.54 2.17
2138 2232 0.740737 CCGATTGATCCAAAGGTGGC 59.259 55.000 0.00 0.00 45.54 5.01
2140 2234 2.991250 ACTCCGATTGATCCAAAGGTG 58.009 47.619 0.00 0.00 30.89 4.00
2143 2237 4.181578 ACGTTACTCCGATTGATCCAAAG 58.818 43.478 0.00 0.00 0.00 2.77
2146 2240 3.949754 AGTACGTTACTCCGATTGATCCA 59.050 43.478 0.00 0.00 32.47 3.41
2148 2242 3.729716 GCAGTACGTTACTCCGATTGATC 59.270 47.826 0.00 0.00 36.76 2.92
2149 2243 3.129813 TGCAGTACGTTACTCCGATTGAT 59.870 43.478 0.00 0.00 36.76 2.57
2150 2244 2.488937 TGCAGTACGTTACTCCGATTGA 59.511 45.455 0.00 0.00 36.76 2.57
2151 2245 2.871133 TGCAGTACGTTACTCCGATTG 58.129 47.619 0.00 0.00 36.76 2.67
2152 2246 3.581024 TTGCAGTACGTTACTCCGATT 57.419 42.857 0.00 0.00 36.76 3.34
2154 2248 3.504863 GAATTGCAGTACGTTACTCCGA 58.495 45.455 0.00 0.00 36.76 4.55
2155 2249 2.278094 CGAATTGCAGTACGTTACTCCG 59.722 50.000 0.00 0.00 36.76 4.63
2156 2250 3.504863 TCGAATTGCAGTACGTTACTCC 58.495 45.455 0.00 0.00 36.76 3.85
2157 2251 4.206609 GGATCGAATTGCAGTACGTTACTC 59.793 45.833 0.00 0.00 36.76 2.59
2158 2252 4.110482 GGATCGAATTGCAGTACGTTACT 58.890 43.478 0.00 0.00 40.28 2.24
2160 2254 4.112716 TGGATCGAATTGCAGTACGTTA 57.887 40.909 0.00 0.00 0.00 3.18
2161 2255 2.967362 TGGATCGAATTGCAGTACGTT 58.033 42.857 0.00 1.47 0.00 3.99
2166 2260 2.098607 CAGCATTGGATCGAATTGCAGT 59.901 45.455 19.12 5.07 0.00 4.40
2167 2261 2.727777 CAGCATTGGATCGAATTGCAG 58.272 47.619 19.12 11.99 0.00 4.41
2183 2277 5.418840 ACTGTTTTTCTTCTTCTTTCCAGCA 59.581 36.000 0.00 0.00 0.00 4.41
2184 2278 5.895928 ACTGTTTTTCTTCTTCTTTCCAGC 58.104 37.500 0.00 0.00 0.00 4.85
2185 2279 6.195165 CGACTGTTTTTCTTCTTCTTTCCAG 58.805 40.000 0.00 0.00 0.00 3.86
2186 2280 5.448632 GCGACTGTTTTTCTTCTTCTTTCCA 60.449 40.000 0.00 0.00 0.00 3.53
2187 2281 4.970611 GCGACTGTTTTTCTTCTTCTTTCC 59.029 41.667 0.00 0.00 0.00 3.13
2188 2282 4.970611 GGCGACTGTTTTTCTTCTTCTTTC 59.029 41.667 0.00 0.00 0.00 2.62
2189 2283 4.398044 TGGCGACTGTTTTTCTTCTTCTTT 59.602 37.500 0.00 0.00 0.00 2.52
2190 2284 3.945285 TGGCGACTGTTTTTCTTCTTCTT 59.055 39.130 0.00 0.00 0.00 2.52
2191 2285 3.312697 GTGGCGACTGTTTTTCTTCTTCT 59.687 43.478 0.00 0.00 0.00 2.85
2192 2286 3.064820 TGTGGCGACTGTTTTTCTTCTTC 59.935 43.478 0.00 0.00 0.00 2.87
2193 2287 3.013921 TGTGGCGACTGTTTTTCTTCTT 58.986 40.909 0.00 0.00 0.00 2.52
2194 2288 2.639065 TGTGGCGACTGTTTTTCTTCT 58.361 42.857 0.00 0.00 0.00 2.85
2195 2289 3.300009 CATGTGGCGACTGTTTTTCTTC 58.700 45.455 0.00 0.00 0.00 2.87
2196 2290 2.543653 GCATGTGGCGACTGTTTTTCTT 60.544 45.455 0.00 0.00 0.00 2.52
2197 2291 1.001378 GCATGTGGCGACTGTTTTTCT 60.001 47.619 0.00 0.00 0.00 2.52
2198 2292 1.408422 GCATGTGGCGACTGTTTTTC 58.592 50.000 0.00 0.00 0.00 2.29
2199 2293 3.568093 GCATGTGGCGACTGTTTTT 57.432 47.368 0.00 0.00 0.00 1.94
2209 2303 3.302365 AAATAGTTGTGTGCATGTGGC 57.698 42.857 0.00 0.00 45.13 5.01
2246 2340 0.736053 GCCAAAAACGTCACTGTGGA 59.264 50.000 8.11 0.00 0.00 4.02
2255 2354 1.406180 AGTAAAAGGCGCCAAAAACGT 59.594 42.857 31.54 1.71 0.00 3.99
2264 2363 1.502190 GACAGGCAGTAAAAGGCGC 59.498 57.895 0.00 0.00 36.55 6.53
2265 2364 0.605319 TGGACAGGCAGTAAAAGGCG 60.605 55.000 0.00 0.00 36.55 5.52
2268 2367 1.537202 GCAGTGGACAGGCAGTAAAAG 59.463 52.381 0.00 0.00 0.00 2.27
2273 2372 2.746359 GAGCAGTGGACAGGCAGT 59.254 61.111 0.00 0.00 0.00 4.40
2274 2373 2.433838 CGAGCAGTGGACAGGCAG 60.434 66.667 0.00 0.00 0.00 4.85
2275 2374 3.226429 GACGAGCAGTGGACAGGCA 62.226 63.158 0.00 0.00 0.00 4.75
2277 2376 1.373497 GTGACGAGCAGTGGACAGG 60.373 63.158 0.00 0.00 0.00 4.00
2278 2377 0.037882 ATGTGACGAGCAGTGGACAG 60.038 55.000 0.00 0.00 0.00 3.51
2279 2378 0.319813 CATGTGACGAGCAGTGGACA 60.320 55.000 0.00 0.00 0.00 4.02
2280 2379 0.038251 TCATGTGACGAGCAGTGGAC 60.038 55.000 0.00 0.00 0.00 4.02
2281 2380 0.244721 CTCATGTGACGAGCAGTGGA 59.755 55.000 0.00 0.00 0.00 4.02
2288 2405 0.445436 GCTTTGCCTCATGTGACGAG 59.555 55.000 0.00 0.00 0.00 4.18
2310 2427 0.461961 AGATAACGGCTCCAGAGTGC 59.538 55.000 0.00 0.00 0.00 4.40
2312 2429 2.028130 CTCAGATAACGGCTCCAGAGT 58.972 52.381 0.00 0.00 0.00 3.24
2313 2430 1.269517 GCTCAGATAACGGCTCCAGAG 60.270 57.143 0.00 0.00 0.00 3.35
2315 2432 0.461548 TGCTCAGATAACGGCTCCAG 59.538 55.000 0.00 0.00 0.00 3.86
2316 2433 1.069204 GATGCTCAGATAACGGCTCCA 59.931 52.381 0.00 0.00 0.00 3.86
2318 2435 1.413382 CGATGCTCAGATAACGGCTC 58.587 55.000 0.00 0.00 0.00 4.70
2320 2437 2.522060 CCGATGCTCAGATAACGGC 58.478 57.895 0.00 0.00 34.36 5.68
2321 2438 2.522060 GCCGATGCTCAGATAACGG 58.478 57.895 0.00 0.00 42.63 4.44
2334 2451 1.547372 ACCGTACAAGTGTTAGCCGAT 59.453 47.619 0.00 0.00 0.00 4.18
2336 2453 1.065358 CACCGTACAAGTGTTAGCCG 58.935 55.000 5.12 0.00 0.00 5.52
2337 2454 0.794473 GCACCGTACAAGTGTTAGCC 59.206 55.000 13.03 0.00 37.56 3.93
2338 2455 1.504359 TGCACCGTACAAGTGTTAGC 58.496 50.000 13.03 1.76 37.56 3.09
2339 2456 3.606153 GCTTTGCACCGTACAAGTGTTAG 60.606 47.826 13.03 9.45 37.56 2.34
2340 2457 2.288458 GCTTTGCACCGTACAAGTGTTA 59.712 45.455 13.03 2.68 37.56 2.41
2341 2458 1.064952 GCTTTGCACCGTACAAGTGTT 59.935 47.619 13.03 0.00 37.56 3.32
2378 2525 1.466167 GTCACCTAGCTTCGTCGTACA 59.534 52.381 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.