Multiple sequence alignment - TraesCS3B01G498700

Loading Multiple Alignment...

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 TraesCS3B01G498700 chr3B 100.000 2564 0 0 1 2564 742156204 742158767 0.000000e+00 4735.0
1 TraesCS3B01G498700 chr3B 80.068 592 74 18 1837 2397 742148228 742148806 1.430000e-107 399.0
2 TraesCS3B01G498700 chr3B 86.957 138 14 2 1687 1822 742148050 742148185 4.420000e-33 152.0
3 TraesCS3B01G498700 chr3B 90.000 70 4 1 1678 1747 742100936 742100870 1.260000e-13 87.9
4 TraesCS3B01G498700 chr3A 85.739 1746 139 64 904 2564 695657465 695659185 0.000000e+00 1744.0
5 TraesCS3B01G498700 chr3A 83.142 522 58 17 1694 2205 695609649 695610150 1.400000e-122 449.0
6 TraesCS3B01G498700 chr3A 88.571 70 5 2 1678 1747 695532854 695532920 5.880000e-12 82.4
7 TraesCS3B01G498700 chr3D 87.509 1385 99 39 885 2233 559158195 559159541 0.000000e+00 1531.0
8 TraesCS3B01G498700 chr3D 83.922 821 80 21 1 801 559157216 559158004 0.000000e+00 737.0
9 TraesCS3B01G498700 chr3D 82.749 742 87 16 1687 2397 559140288 559141019 7.790000e-175 623.0
10 TraesCS3B01G498700 chr3D 93.043 230 14 2 2335 2564 559159578 559159805 4.090000e-88 335.0
11 TraesCS3B01G498700 chr3D 76.650 197 44 2 120 315 26568306 26568501 9.700000e-20 108.0
12 TraesCS3B01G498700 chr3D 91.429 70 3 1 1678 1747 559125714 559125780 2.720000e-15 93.5
13 TraesCS3B01G498700 chr5A 80.405 296 49 9 17 309 258037147 258037436 1.540000e-52 217.0
14 TraesCS3B01G498700 chr5B 80.000 305 47 12 40 341 216860867 216860574 2.000000e-51 213.0
15 TraesCS3B01G498700 chrUn 81.022 274 41 11 40 309 115098436 115098702 9.300000e-50 207.0
16 TraesCS3B01G498700 chrUn 81.356 177 25 6 124 299 403575145 403575314 1.240000e-28 137.0
17 TraesCS3B01G498700 chr7B 82.065 184 32 1 122 305 562378622 562378440 3.420000e-34 156.0
18 TraesCS3B01G498700 chr1D 76.238 303 64 8 17 317 458476444 458476740 1.230000e-33 154.0
19 TraesCS3B01G498700 chr7A 78.771 179 34 4 126 303 727127798 727127623 1.610000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G498700 chr3B 742156204 742158767 2563 False 4735.000000 4735 100.0000 1 2564 1 chr3B.!!$F1 2563
1 TraesCS3B01G498700 chr3B 742148050 742148806 756 False 275.500000 399 83.5125 1687 2397 2 chr3B.!!$F2 710
2 TraesCS3B01G498700 chr3A 695657465 695659185 1720 False 1744.000000 1744 85.7390 904 2564 1 chr3A.!!$F3 1660
3 TraesCS3B01G498700 chr3A 695609649 695610150 501 False 449.000000 449 83.1420 1694 2205 1 chr3A.!!$F2 511
4 TraesCS3B01G498700 chr3D 559157216 559159805 2589 False 867.666667 1531 88.1580 1 2564 3 chr3D.!!$F4 2563
5 TraesCS3B01G498700 chr3D 559140288 559141019 731 False 623.000000 623 82.7490 1687 2397 1 chr3D.!!$F3 710

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
588 596 0.098376 ACGGTAGACTCGTCGAATGC 59.902 55.0 0.00 0.0 35.87 3.56 F
880 951 0.106894 CTTAAGGGCGATCCACCTCC 59.893 60.0 3.51 0.0 35.64 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1571 0.041982 GTTCTCCTGTCCCTCCTCCT 59.958 60.000 0.0 0.0 0.0 3.69 R
1705 1888 1.873591 CCCTTGAACCACTTCTTCACG 59.126 52.381 0.0 0.0 0.0 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.876550 GCCTCCGTTGTTTCTACAAGTT 59.123 45.455 0.00 0.00 44.53 2.66
31 32 4.448060 CCTCCGTTGTTTCTACAAGTTCTC 59.552 45.833 0.00 0.00 44.53 2.87
35 36 5.388475 CCGTTGTTTCTACAAGTTCTCATCG 60.388 44.000 0.00 0.00 44.53 3.84
43 44 7.173863 TCTACAAGTTCTCATCGTTGTTTTC 57.826 36.000 0.00 0.00 34.92 2.29
53 54 0.872388 CGTTGTTTTCTTCTCCGGGG 59.128 55.000 0.00 0.00 0.00 5.73
68 69 3.573491 GGGCGGCGATTTCCTTCG 61.573 66.667 12.98 0.00 41.99 3.79
75 76 1.999051 CGATTTCCTTCGCCAGTCG 59.001 57.895 0.00 0.00 40.15 4.18
79 80 2.377628 TTTCCTTCGCCAGTCGCAGT 62.378 55.000 0.00 0.00 37.30 4.40
80 81 2.765250 TTCCTTCGCCAGTCGCAGTC 62.765 60.000 0.00 0.00 37.30 3.51
97 98 4.052229 CGCGGACGTCTCCTGGTT 62.052 66.667 16.46 0.00 33.79 3.67
98 99 2.432628 GCGGACGTCTCCTGGTTG 60.433 66.667 16.46 0.00 33.79 3.77
99 100 2.261671 CGGACGTCTCCTGGTTGG 59.738 66.667 16.46 0.00 33.79 3.77
103 104 1.829222 GGACGTCTCCTGGTTGGAATA 59.171 52.381 16.46 0.00 45.63 1.75
104 105 2.434702 GGACGTCTCCTGGTTGGAATAT 59.565 50.000 16.46 0.00 45.63 1.28
105 106 3.492829 GGACGTCTCCTGGTTGGAATATC 60.493 52.174 16.46 0.00 45.63 1.63
106 107 2.100916 ACGTCTCCTGGTTGGAATATCG 59.899 50.000 0.00 0.00 45.63 2.92
107 108 2.545952 CGTCTCCTGGTTGGAATATCGG 60.546 54.545 0.00 0.00 45.63 4.18
108 109 1.416401 TCTCCTGGTTGGAATATCGGC 59.584 52.381 0.00 0.00 45.63 5.54
109 110 1.140852 CTCCTGGTTGGAATATCGGCA 59.859 52.381 0.00 0.00 45.63 5.69
110 111 1.134220 TCCTGGTTGGAATATCGGCAC 60.134 52.381 0.00 0.00 42.94 5.01
115 116 2.639065 GTTGGAATATCGGCACCTTCA 58.361 47.619 0.00 0.00 0.00 3.02
120 121 3.307059 GGAATATCGGCACCTTCATAGCT 60.307 47.826 0.00 0.00 0.00 3.32
122 123 0.833287 ATCGGCACCTTCATAGCTGT 59.167 50.000 0.00 0.00 36.11 4.40
151 152 4.665833 ACAAGCTCCTGGGTTTAAAAAC 57.334 40.909 0.00 0.00 38.17 2.43
182 183 1.755008 GAGCCAGACGCCTAGAGGT 60.755 63.158 0.00 0.00 38.78 3.85
193 194 1.115467 CCTAGAGGTGGCATCGAACT 58.885 55.000 0.00 0.00 0.00 3.01
207 208 1.566563 GAACTATGCTCATGGCGCG 59.433 57.895 0.00 0.00 45.43 6.86
291 292 9.881529 TTTTACGTTTCTATATGGTTGTGTTTC 57.118 29.630 0.00 0.00 0.00 2.78
309 310 4.696877 TGTTTCTAAGGACATGTGATGCTG 59.303 41.667 1.15 0.00 0.00 4.41
311 312 3.106827 TCTAAGGACATGTGATGCTGGA 58.893 45.455 1.15 0.00 0.00 3.86
312 313 3.713248 TCTAAGGACATGTGATGCTGGAT 59.287 43.478 1.15 0.00 0.00 3.41
324 325 7.936026 TGTGATGCTGGATATATATATGGGT 57.064 36.000 10.03 0.00 0.00 4.51
337 338 1.988539 TATGGGTCTTGGGCCCTTTA 58.011 50.000 25.70 7.54 46.22 1.85
344 345 1.497286 TCTTGGGCCCTTTAACACACT 59.503 47.619 25.70 0.00 0.00 3.55
345 346 1.886542 CTTGGGCCCTTTAACACACTC 59.113 52.381 25.70 0.00 0.00 3.51
348 349 2.312390 GGGCCCTTTAACACACTCAAA 58.688 47.619 17.04 0.00 0.00 2.69
349 350 2.696187 GGGCCCTTTAACACACTCAAAA 59.304 45.455 17.04 0.00 0.00 2.44
350 351 3.133183 GGGCCCTTTAACACACTCAAAAA 59.867 43.478 17.04 0.00 0.00 1.94
377 378 2.101249 ACACAACACATGCCTTCCAAAG 59.899 45.455 0.00 0.00 0.00 2.77
435 436 4.917906 AAGTAAGGGATTTCAGTCTGCT 57.082 40.909 0.00 0.00 0.00 4.24
436 437 4.213564 AGTAAGGGATTTCAGTCTGCTG 57.786 45.455 0.00 0.00 43.87 4.41
469 470 2.370349 TCTCTCCCACGTCTGATCTTC 58.630 52.381 0.00 0.00 0.00 2.87
470 471 1.407258 CTCTCCCACGTCTGATCTTCC 59.593 57.143 0.00 0.00 0.00 3.46
471 472 1.006043 TCTCCCACGTCTGATCTTCCT 59.994 52.381 0.00 0.00 0.00 3.36
473 474 3.117474 TCTCCCACGTCTGATCTTCCTAT 60.117 47.826 0.00 0.00 0.00 2.57
474 475 3.223435 TCCCACGTCTGATCTTCCTATC 58.777 50.000 0.00 0.00 0.00 2.08
475 476 2.959030 CCCACGTCTGATCTTCCTATCA 59.041 50.000 0.00 0.00 34.72 2.15
476 477 3.576118 CCCACGTCTGATCTTCCTATCAT 59.424 47.826 0.00 0.00 35.40 2.45
477 478 4.554292 CCACGTCTGATCTTCCTATCATG 58.446 47.826 0.00 0.00 35.40 3.07
481 482 5.478332 ACGTCTGATCTTCCTATCATGCATA 59.522 40.000 0.00 0.00 35.40 3.14
505 506 5.163302 TGTTATTTGAAACCGTGACACAG 57.837 39.130 6.37 0.00 0.00 3.66
511 512 2.004017 GAAACCGTGACACAGTTGACA 58.996 47.619 7.94 0.00 0.00 3.58
512 513 2.325583 AACCGTGACACAGTTGACAT 57.674 45.000 6.39 0.00 29.96 3.06
517 518 2.091122 CGTGACACAGTTGACATCATCG 59.909 50.000 6.37 0.00 29.96 3.84
534 535 2.384309 CGCGTACGCAATTGGACCA 61.384 57.895 36.44 0.00 42.06 4.02
535 536 1.133869 GCGTACGCAATTGGACCAC 59.866 57.895 33.90 0.00 41.49 4.16
536 537 1.418367 CGTACGCAATTGGACCACG 59.582 57.895 7.72 4.23 0.00 4.94
537 538 1.286354 CGTACGCAATTGGACCACGT 61.286 55.000 11.96 11.96 40.53 4.49
538 539 0.441145 GTACGCAATTGGACCACGTC 59.559 55.000 10.78 1.38 38.12 4.34
539 540 1.009903 TACGCAATTGGACCACGTCG 61.010 55.000 10.78 7.02 38.12 5.12
540 541 2.024868 CGCAATTGGACCACGTCGA 61.025 57.895 7.72 0.00 32.65 4.20
541 542 1.787847 GCAATTGGACCACGTCGAG 59.212 57.895 7.72 0.00 32.65 4.04
588 596 0.098376 ACGGTAGACTCGTCGAATGC 59.902 55.000 0.00 0.00 35.87 3.56
618 626 5.375417 CAATCATGCAGTACACCAGAAAA 57.625 39.130 0.00 0.00 0.00 2.29
619 627 5.957798 CAATCATGCAGTACACCAGAAAAT 58.042 37.500 0.00 0.00 0.00 1.82
728 737 9.444600 AACGAATAAATGTTAATGTGGTCTAGT 57.555 29.630 0.00 0.00 0.00 2.57
740 749 2.029020 GTGGTCTAGTCAGTCATGTGCA 60.029 50.000 0.00 0.00 0.00 4.57
743 752 3.368843 GGTCTAGTCAGTCATGTGCATGT 60.369 47.826 11.38 0.00 39.72 3.21
744 753 4.142160 GGTCTAGTCAGTCATGTGCATGTA 60.142 45.833 11.38 0.00 39.72 2.29
756 776 1.927210 GCATGTAGCGTCACCGATG 59.073 57.895 0.00 0.00 35.63 3.84
767 787 2.385013 TCACCGATGTGATGGAACAG 57.615 50.000 0.00 0.00 46.40 3.16
784 804 5.120519 TGGAACAGGTAAGTTAATTAACGCG 59.879 40.000 19.92 3.53 40.96 6.01
785 805 5.120674 GGAACAGGTAAGTTAATTAACGCGT 59.879 40.000 19.92 5.58 40.96 6.01
818 889 6.423302 GCCAAGAGGATGCATATATATCGAAG 59.577 42.308 0.00 0.00 36.89 3.79
847 918 6.779115 ATTTTAATTTCAAGCCAACGAACC 57.221 33.333 0.00 0.00 0.00 3.62
856 927 0.671251 GCCAACGAACCATTTGACCA 59.329 50.000 0.00 0.00 0.00 4.02
863 934 6.212955 CAACGAACCATTTGACCAAATACTT 58.787 36.000 7.56 3.02 38.84 2.24
865 936 7.513371 ACGAACCATTTGACCAAATACTTAA 57.487 32.000 7.56 0.00 38.84 1.85
868 939 6.850752 ACCATTTGACCAAATACTTAAGGG 57.149 37.500 7.53 0.14 38.84 3.95
869 940 5.186992 ACCATTTGACCAAATACTTAAGGGC 59.813 40.000 7.53 0.00 38.84 5.19
870 941 5.339990 CATTTGACCAAATACTTAAGGGCG 58.660 41.667 7.53 0.00 38.84 6.13
872 943 4.497291 TGACCAAATACTTAAGGGCGAT 57.503 40.909 7.53 0.00 29.31 4.58
873 944 4.448210 TGACCAAATACTTAAGGGCGATC 58.552 43.478 7.53 0.00 29.31 3.69
874 945 3.813724 GACCAAATACTTAAGGGCGATCC 59.186 47.826 7.53 0.00 0.00 3.36
875 946 3.201266 ACCAAATACTTAAGGGCGATCCA 59.799 43.478 7.53 0.00 38.24 3.41
876 947 3.564225 CCAAATACTTAAGGGCGATCCAC 59.436 47.826 7.53 0.00 38.24 4.02
877 948 3.487120 AATACTTAAGGGCGATCCACC 57.513 47.619 7.53 0.00 38.24 4.61
878 949 2.170012 TACTTAAGGGCGATCCACCT 57.830 50.000 7.53 0.00 39.21 4.00
879 950 0.831307 ACTTAAGGGCGATCCACCTC 59.169 55.000 7.53 0.00 35.64 3.85
880 951 0.106894 CTTAAGGGCGATCCACCTCC 59.893 60.000 3.51 0.00 35.64 4.30
882 953 0.399949 TAAGGGCGATCCACCTCCAT 60.400 55.000 3.51 0.00 35.64 3.41
883 954 1.700042 AAGGGCGATCCACCTCCATC 61.700 60.000 3.51 0.00 35.64 3.51
889 1016 2.869636 GCGATCCACCTCCATCAGAATC 60.870 54.545 0.00 0.00 0.00 2.52
898 1025 5.597182 CACCTCCATCAGAATCCATTCATTT 59.403 40.000 2.21 0.00 39.23 2.32
902 1029 5.831525 TCCATCAGAATCCATTCATTTCCAG 59.168 40.000 2.21 0.00 39.23 3.86
903 1030 5.831525 CCATCAGAATCCATTCATTTCCAGA 59.168 40.000 2.21 0.00 39.23 3.86
904 1031 6.322969 CCATCAGAATCCATTCATTTCCAGAA 59.677 38.462 2.21 0.00 39.23 3.02
907 1034 8.370266 TCAGAATCCATTCATTTCCAGAAAAT 57.630 30.769 2.21 0.00 39.23 1.82
908 1035 9.478238 TCAGAATCCATTCATTTCCAGAAAATA 57.522 29.630 2.21 0.00 39.23 1.40
917 1044 7.938563 TCATTTCCAGAAAATAAAAACACCG 57.061 32.000 0.00 0.00 35.77 4.94
922 1049 6.683715 TCCAGAAAATAAAAACACCGATTCC 58.316 36.000 0.00 0.00 0.00 3.01
950 1077 1.208776 ACTACAAATACCCCGTCCAGC 59.791 52.381 0.00 0.00 0.00 4.85
952 1079 1.817941 CAAATACCCCGTCCAGCCG 60.818 63.158 0.00 0.00 0.00 5.52
953 1080 3.692370 AAATACCCCGTCCAGCCGC 62.692 63.158 0.00 0.00 0.00 6.53
975 1107 0.609406 CCGTCTCCTCAGTCCACAGA 60.609 60.000 0.00 0.00 0.00 3.41
982 1114 1.068194 CCTCAGTCCACAGAAGACGTC 60.068 57.143 7.70 7.70 39.31 4.34
983 1115 1.883275 CTCAGTCCACAGAAGACGTCT 59.117 52.381 13.58 13.58 39.31 4.18
1042 1174 1.827789 CTGCTCCTCCTCTCCCTCG 60.828 68.421 0.00 0.00 0.00 4.63
1121 1253 1.078356 CCGTCCTCCTCACTCGAGA 60.078 63.158 21.68 0.00 42.34 4.04
1128 1260 2.553602 CCTCCTCACTCGAGATGATCAG 59.446 54.545 21.68 15.04 42.34 2.90
1172 1304 4.162690 CCTTCCGAGCTTCCCGGG 62.163 72.222 16.85 16.85 46.47 5.73
1206 1338 3.519930 GACGAGGACGAGCTCCCC 61.520 72.222 8.47 9.91 40.53 4.81
1317 1455 2.046217 GCGGTCTTCTTCCCCACC 60.046 66.667 0.00 0.00 0.00 4.61
1323 1461 0.836400 TCTTCTTCCCCACCGAGCTT 60.836 55.000 0.00 0.00 0.00 3.74
1351 1489 1.376466 GAAGAGCAAGCACCCTGGA 59.624 57.895 0.00 0.00 0.00 3.86
1390 1528 3.285371 CGGAGCCTTACCACGACT 58.715 61.111 0.00 0.00 0.00 4.18
1392 1530 1.592400 CGGAGCCTTACCACGACTCA 61.592 60.000 0.00 0.00 0.00 3.41
1395 1533 2.092882 GCCTTACCACGACTCACGC 61.093 63.158 0.00 0.00 46.94 5.34
1396 1534 1.800315 CCTTACCACGACTCACGCG 60.800 63.158 3.53 3.53 46.94 6.01
1397 1535 2.429571 TTACCACGACTCACGCGC 60.430 61.111 5.73 0.00 46.94 6.86
1398 1536 3.196913 TTACCACGACTCACGCGCA 62.197 57.895 5.73 0.00 46.94 6.09
1399 1537 3.604494 TACCACGACTCACGCGCAG 62.604 63.158 5.73 4.78 46.94 5.18
1425 1563 2.335011 GGCGAGCAAAAGCCGTTT 59.665 55.556 0.00 0.00 44.22 3.60
1432 1570 0.599728 GCAAAAGCCGTTTCATGCCA 60.600 50.000 0.00 0.00 0.00 4.92
1433 1571 1.863267 CAAAAGCCGTTTCATGCCAA 58.137 45.000 0.00 0.00 0.00 4.52
1434 1572 1.794116 CAAAAGCCGTTTCATGCCAAG 59.206 47.619 0.00 0.00 0.00 3.61
1443 1581 0.549902 TTCATGCCAAGGAGGAGGGA 60.550 55.000 0.00 0.00 41.22 4.20
1444 1582 1.225704 CATGCCAAGGAGGAGGGAC 59.774 63.158 0.00 0.00 41.22 4.46
1448 1586 1.081092 CCAAGGAGGAGGGACAGGA 59.919 63.158 0.00 0.00 41.22 3.86
1473 1629 1.817099 GGCAGTGAAGATGGCGAGG 60.817 63.158 0.00 0.00 33.23 4.63
1475 1631 0.809241 GCAGTGAAGATGGCGAGGAG 60.809 60.000 0.00 0.00 0.00 3.69
1481 1637 1.961180 AAGATGGCGAGGAGGTTCGG 61.961 60.000 0.00 0.00 40.79 4.30
1482 1638 2.683933 ATGGCGAGGAGGTTCGGT 60.684 61.111 0.00 0.00 40.79 4.69
1486 1642 2.637383 GCGAGGAGGTTCGGTCACT 61.637 63.158 0.00 0.00 40.79 3.41
1524 1680 2.813726 CCACCACCACGACCAGGAA 61.814 63.158 0.00 0.00 0.00 3.36
1528 1684 1.185618 CCACCACGACCAGGAAGAGA 61.186 60.000 0.00 0.00 0.00 3.10
1534 1690 1.257743 CGACCAGGAAGAGAAGGACA 58.742 55.000 0.00 0.00 0.00 4.02
1535 1691 1.618837 CGACCAGGAAGAGAAGGACAA 59.381 52.381 0.00 0.00 0.00 3.18
1536 1692 2.037251 CGACCAGGAAGAGAAGGACAAA 59.963 50.000 0.00 0.00 0.00 2.83
1537 1693 3.403968 GACCAGGAAGAGAAGGACAAAC 58.596 50.000 0.00 0.00 0.00 2.93
1541 1700 2.698797 AGGAAGAGAAGGACAAACGACA 59.301 45.455 0.00 0.00 0.00 4.35
1547 1706 1.004292 GAAGGACAAACGACAACCACG 60.004 52.381 0.00 0.00 0.00 4.94
1567 1726 1.680249 GGGCAGGACAAGGATGAAGAC 60.680 57.143 0.00 0.00 0.00 3.01
1592 1751 4.785512 CGAAGCTGCTCGGACGCT 62.786 66.667 1.00 0.00 35.14 5.07
1606 1765 4.680237 CGCTTCCACCTCCACGCA 62.680 66.667 0.00 0.00 0.00 5.24
1636 1795 2.571757 CACGAGGCTGGCGAACTA 59.428 61.111 2.34 0.00 0.00 2.24
1638 1797 1.677966 ACGAGGCTGGCGAACTAGA 60.678 57.895 2.34 0.00 0.00 2.43
1641 1800 0.533032 GAGGCTGGCGAACTAGAAGT 59.467 55.000 0.00 0.00 0.00 3.01
1648 1807 1.546834 GCGAACTAGAAGTACTGGCG 58.453 55.000 0.00 0.00 0.00 5.69
1651 1810 2.791849 CGAACTAGAAGTACTGGCGAGC 60.792 54.545 0.00 0.00 0.00 5.03
1653 1812 1.473278 ACTAGAAGTACTGGCGAGCAC 59.527 52.381 0.00 0.00 0.00 4.40
1655 1814 1.211969 GAAGTACTGGCGAGCACGA 59.788 57.895 8.01 0.00 42.66 4.35
1656 1815 0.798771 GAAGTACTGGCGAGCACGAG 60.799 60.000 8.01 0.00 42.66 4.18
1854 2083 3.666902 CGGCTGTTCTACCATTTCGTTTG 60.667 47.826 0.00 0.00 0.00 2.93
1858 2091 3.886505 TGTTCTACCATTTCGTTTGCCTT 59.113 39.130 0.00 0.00 0.00 4.35
1859 2092 4.023536 TGTTCTACCATTTCGTTTGCCTTC 60.024 41.667 0.00 0.00 0.00 3.46
1860 2093 2.739913 TCTACCATTTCGTTTGCCTTCG 59.260 45.455 0.00 0.00 0.00 3.79
1861 2094 0.596082 ACCATTTCGTTTGCCTTCGG 59.404 50.000 0.00 0.00 0.00 4.30
1862 2095 0.109319 CCATTTCGTTTGCCTTCGGG 60.109 55.000 0.00 0.00 38.37 5.14
1865 2098 1.964552 TTTCGTTTGCCTTCGGGTTA 58.035 45.000 0.00 0.00 37.45 2.85
1867 2100 2.188062 TCGTTTGCCTTCGGGTTATT 57.812 45.000 0.00 0.00 37.45 1.40
1869 2102 2.485038 TCGTTTGCCTTCGGGTTATTTC 59.515 45.455 0.00 0.00 37.45 2.17
1871 2104 3.571571 GTTTGCCTTCGGGTTATTTCAC 58.428 45.455 0.00 0.00 37.45 3.18
1872 2105 2.570415 TGCCTTCGGGTTATTTCACA 57.430 45.000 0.00 0.00 37.45 3.58
1874 2107 2.224670 TGCCTTCGGGTTATTTCACACT 60.225 45.455 0.00 0.00 37.45 3.55
1876 2109 4.196971 GCCTTCGGGTTATTTCACACTAT 58.803 43.478 0.00 0.00 37.45 2.12
1882 2115 8.578308 TTCGGGTTATTTCACACTATATTACG 57.422 34.615 0.00 0.00 0.00 3.18
1975 2230 7.061441 ACGTTACGTGTTTCTCATAACTACATG 59.939 37.037 10.39 0.00 39.18 3.21
1976 2231 7.061441 CGTTACGTGTTTCTCATAACTACATGT 59.939 37.037 2.69 2.69 40.76 3.21
1980 2235 9.084164 ACGTGTTTCTCATAACTACATGTAATC 57.916 33.333 7.06 0.00 37.24 1.75
1987 2242 9.098355 TCTCATAACTACATGTAATCACTTTGC 57.902 33.333 7.06 0.00 0.00 3.68
2005 2260 3.887621 TGCCTTCTTATGTACTCGCTT 57.112 42.857 0.00 0.00 0.00 4.68
2056 2311 6.744112 AGTTCAAATTTGATCTAAAACCGCA 58.256 32.000 23.97 3.81 35.94 5.69
2075 2330 3.731867 CGCAGCAAGAATTATGGAACCAC 60.732 47.826 0.00 0.00 0.00 4.16
2140 2395 4.096681 TCCCTGATGTGAACATAGTCTGT 58.903 43.478 0.00 0.00 40.84 3.41
2233 2488 8.868103 AGTTAATTAACTCTAGCACCCCTATAC 58.132 37.037 22.49 0.00 42.52 1.47
2251 2506 5.640357 CCTATACAAAACTTGCAACTCGGTA 59.360 40.000 0.00 0.00 0.00 4.02
2253 2508 7.493320 CCTATACAAAACTTGCAACTCGGTATA 59.507 37.037 0.00 4.41 0.00 1.47
2280 2541 0.239347 CTTTTGCAAGGGAGACGCTG 59.761 55.000 0.00 0.00 0.00 5.18
2328 2605 3.897505 TCTTGTCTCACACCTCTTCATCA 59.102 43.478 0.00 0.00 0.00 3.07
2342 2625 7.223582 CACCTCTTCATCAACCGATATATATGC 59.776 40.741 0.00 0.00 0.00 3.14
2352 2635 3.062099 CCGATATATATGCGCACAACCAC 59.938 47.826 14.90 0.81 0.00 4.16
2443 2726 8.630037 TCCTTTCTGTATTTTGTTTTTCTCCTC 58.370 33.333 0.00 0.00 0.00 3.71
2502 2786 6.436843 AATTGGTCTGGAAATCGAACATAC 57.563 37.500 0.00 0.00 0.00 2.39
2538 2822 7.904558 TGACTATAAGAATGGTGAGATCACT 57.095 36.000 12.43 0.00 45.73 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.377897 AGAACTTGTAGAAACAACGGAGG 58.622 43.478 0.00 0.00 40.69 4.30
11 12 5.388475 CGATGAGAACTTGTAGAAACAACGG 60.388 44.000 0.00 0.00 40.69 4.44
12 13 5.175126 ACGATGAGAACTTGTAGAAACAACG 59.825 40.000 0.00 0.00 40.69 4.10
16 17 6.526566 ACAACGATGAGAACTTGTAGAAAC 57.473 37.500 0.00 0.00 0.00 2.78
28 29 3.987868 CGGAGAAGAAAACAACGATGAGA 59.012 43.478 0.00 0.00 0.00 3.27
31 32 2.159627 CCCGGAGAAGAAAACAACGATG 59.840 50.000 0.73 0.00 0.00 3.84
35 36 0.596577 GCCCCGGAGAAGAAAACAAC 59.403 55.000 0.73 0.00 0.00 3.32
83 84 3.787394 TCCAACCAGGAGACGTCC 58.213 61.111 13.01 3.55 43.07 4.79
97 98 3.557054 GCTATGAAGGTGCCGATATTCCA 60.557 47.826 0.00 0.00 0.00 3.53
98 99 3.003480 GCTATGAAGGTGCCGATATTCC 58.997 50.000 0.00 0.00 0.00 3.01
99 100 3.681897 CAGCTATGAAGGTGCCGATATTC 59.318 47.826 0.00 0.00 43.73 1.75
103 104 3.694364 CAGCTATGAAGGTGCCGAT 57.306 52.632 0.00 0.00 43.73 4.18
109 110 3.710209 AGAAGCAACAGCTATGAAGGT 57.290 42.857 2.99 0.00 37.72 3.50
110 111 4.507710 TGTAGAAGCAACAGCTATGAAGG 58.492 43.478 2.99 0.00 37.72 3.46
176 177 2.035961 GCATAGTTCGATGCCACCTCTA 59.964 50.000 6.62 0.00 45.41 2.43
191 192 2.969238 GCGCGCCATGAGCATAGT 60.969 61.111 23.24 0.00 43.66 2.12
270 271 8.388103 CCTTAGAAACACAACCATATAGAAACG 58.612 37.037 0.00 0.00 0.00 3.60
275 276 8.830580 CATGTCCTTAGAAACACAACCATATAG 58.169 37.037 0.00 0.00 0.00 1.31
276 277 8.325787 ACATGTCCTTAGAAACACAACCATATA 58.674 33.333 0.00 0.00 0.00 0.86
283 284 5.048782 GCATCACATGTCCTTAGAAACACAA 60.049 40.000 0.00 0.00 0.00 3.33
291 292 3.548745 TCCAGCATCACATGTCCTTAG 57.451 47.619 0.00 0.00 0.00 2.18
309 310 6.128138 GGCCCAAGACCCATATATATATCC 57.872 45.833 2.03 0.00 0.00 2.59
324 325 1.497286 AGTGTGTTAAAGGGCCCAAGA 59.503 47.619 27.56 5.10 0.00 3.02
349 350 4.470334 AGGCATGTGTTGTGTTCTTTTT 57.530 36.364 0.00 0.00 0.00 1.94
350 351 4.432712 GAAGGCATGTGTTGTGTTCTTTT 58.567 39.130 0.00 0.00 0.00 2.27
351 352 3.181476 GGAAGGCATGTGTTGTGTTCTTT 60.181 43.478 0.00 0.00 0.00 2.52
352 353 2.362077 GGAAGGCATGTGTTGTGTTCTT 59.638 45.455 0.00 0.00 0.00 2.52
353 354 1.956477 GGAAGGCATGTGTTGTGTTCT 59.044 47.619 0.00 0.00 0.00 3.01
354 355 1.680735 TGGAAGGCATGTGTTGTGTTC 59.319 47.619 0.00 0.00 0.00 3.18
412 413 5.006386 AGCAGACTGAAATCCCTTACTTTG 58.994 41.667 6.65 0.00 0.00 2.77
441 442 3.634448 CAGACGTGGGAGAGATATTCAGT 59.366 47.826 0.00 0.00 0.00 3.41
442 443 3.885901 TCAGACGTGGGAGAGATATTCAG 59.114 47.826 0.00 0.00 0.00 3.02
457 458 3.638627 TGCATGATAGGAAGATCAGACGT 59.361 43.478 0.00 0.00 39.18 4.34
471 472 9.676195 CGGTTTCAAATAACAATATGCATGATA 57.324 29.630 10.16 0.00 0.00 2.15
473 474 7.487509 CACGGTTTCAAATAACAATATGCATGA 59.512 33.333 10.16 0.00 0.00 3.07
474 475 7.487509 TCACGGTTTCAAATAACAATATGCATG 59.512 33.333 10.16 0.00 0.00 4.06
475 476 7.487829 GTCACGGTTTCAAATAACAATATGCAT 59.512 33.333 3.79 3.79 0.00 3.96
476 477 6.804295 GTCACGGTTTCAAATAACAATATGCA 59.196 34.615 0.00 0.00 0.00 3.96
477 478 6.804295 TGTCACGGTTTCAAATAACAATATGC 59.196 34.615 0.00 0.00 0.00 3.14
481 482 6.137794 TGTGTCACGGTTTCAAATAACAAT 57.862 33.333 0.00 0.00 0.00 2.71
490 491 2.004017 GTCAACTGTGTCACGGTTTCA 58.996 47.619 24.60 13.28 44.74 2.69
491 492 2.004017 TGTCAACTGTGTCACGGTTTC 58.996 47.619 24.60 19.92 44.74 2.78
505 506 0.044161 GCGTACGCGATGATGTCAAC 60.044 55.000 26.17 0.00 41.33 3.18
511 512 0.581529 CCAATTGCGTACGCGATGAT 59.418 50.000 36.73 23.12 43.84 2.45
512 513 0.458716 TCCAATTGCGTACGCGATGA 60.459 50.000 36.73 28.20 43.84 2.92
517 518 1.133869 GTGGTCCAATTGCGTACGC 59.866 57.895 32.49 32.49 42.35 4.42
538 539 3.610786 ACTAGTATGTGTCGATGCTCG 57.389 47.619 0.00 0.00 42.10 5.03
539 540 3.969352 CGAACTAGTATGTGTCGATGCTC 59.031 47.826 7.94 0.00 0.00 4.26
540 541 3.792459 GCGAACTAGTATGTGTCGATGCT 60.792 47.826 16.10 0.00 0.00 3.79
541 542 2.468040 GCGAACTAGTATGTGTCGATGC 59.532 50.000 16.10 0.00 0.00 3.91
574 575 0.108615 CCCTTGCATTCGACGAGTCT 60.109 55.000 0.00 0.00 0.00 3.24
596 604 5.375417 TTTTCTGGTGTACTGCATGATTG 57.625 39.130 0.00 0.00 0.00 2.67
597 605 6.594788 AATTTTCTGGTGTACTGCATGATT 57.405 33.333 0.00 0.00 0.00 2.57
598 606 6.209192 TGAAATTTTCTGGTGTACTGCATGAT 59.791 34.615 10.33 0.00 0.00 2.45
599 607 5.534278 TGAAATTTTCTGGTGTACTGCATGA 59.466 36.000 10.33 0.00 0.00 3.07
600 608 5.771469 TGAAATTTTCTGGTGTACTGCATG 58.229 37.500 10.33 0.00 0.00 4.06
644 653 9.428097 TGAGTTGCACTGCATATATATAAAGAG 57.572 33.333 4.10 4.67 38.76 2.85
645 654 9.428097 CTGAGTTGCACTGCATATATATAAAGA 57.572 33.333 4.10 0.00 38.76 2.52
656 665 3.633525 TCTTTTTCTGAGTTGCACTGCAT 59.366 39.130 4.10 0.00 38.76 3.96
657 666 3.016031 TCTTTTTCTGAGTTGCACTGCA 58.984 40.909 0.00 0.00 36.47 4.41
658 667 3.698029 TCTTTTTCTGAGTTGCACTGC 57.302 42.857 0.00 0.00 0.00 4.40
659 668 5.180868 AGCTATCTTTTTCTGAGTTGCACTG 59.819 40.000 0.00 0.00 0.00 3.66
666 675 5.312079 ACTGCAAGCTATCTTTTTCTGAGT 58.688 37.500 0.00 0.00 37.60 3.41
669 678 5.048504 TGGAACTGCAAGCTATCTTTTTCTG 60.049 40.000 0.00 0.00 37.60 3.02
677 686 1.009829 CGGTGGAACTGCAAGCTATC 58.990 55.000 0.00 0.00 35.75 2.08
708 717 8.590204 TGACTGACTAGACCACATTAACATTTA 58.410 33.333 0.00 0.00 0.00 1.40
721 730 3.193263 CATGCACATGACTGACTAGACC 58.807 50.000 4.57 0.00 41.20 3.85
728 737 1.066929 ACGCTACATGCACATGACTGA 60.067 47.619 17.19 0.00 41.20 3.41
731 740 1.061131 GTGACGCTACATGCACATGAC 59.939 52.381 17.19 5.52 41.20 3.06
756 776 8.173130 CGTTAATTAACTTACCTGTTCCATCAC 58.827 37.037 22.57 0.00 34.12 3.06
765 785 5.005107 GGAGACGCGTTAATTAACTTACCTG 59.995 44.000 22.57 9.73 34.12 4.00
767 787 5.005107 CAGGAGACGCGTTAATTAACTTACC 59.995 44.000 22.57 16.37 34.12 2.85
784 804 1.965754 ATCCTCTTGGCGCAGGAGAC 61.966 60.000 17.96 0.00 42.28 3.36
785 805 1.687146 ATCCTCTTGGCGCAGGAGA 60.687 57.895 17.96 12.18 42.28 3.71
795 815 7.169476 CAGCTTCGATATATATGCATCCTCTTG 59.831 40.741 0.19 0.00 0.00 3.02
834 905 2.393764 GTCAAATGGTTCGTTGGCTTG 58.606 47.619 0.00 0.00 0.00 4.01
847 918 5.124776 TCGCCCTTAAGTATTTGGTCAAATG 59.875 40.000 16.52 1.97 40.83 2.32
856 927 3.458487 AGGTGGATCGCCCTTAAGTATTT 59.542 43.478 0.97 0.00 33.99 1.40
863 934 0.399949 ATGGAGGTGGATCGCCCTTA 60.400 55.000 3.54 0.00 33.99 2.69
865 936 2.040464 ATGGAGGTGGATCGCCCT 60.040 61.111 1.62 1.62 33.99 5.19
868 939 0.465705 TTCTGATGGAGGTGGATCGC 59.534 55.000 0.00 0.00 0.00 4.58
869 940 2.289320 GGATTCTGATGGAGGTGGATCG 60.289 54.545 0.00 0.00 0.00 3.69
870 941 2.707791 TGGATTCTGATGGAGGTGGATC 59.292 50.000 0.00 0.00 0.00 3.36
872 943 2.268796 TGGATTCTGATGGAGGTGGA 57.731 50.000 0.00 0.00 0.00 4.02
873 944 3.117776 TGAATGGATTCTGATGGAGGTGG 60.118 47.826 1.26 0.00 37.67 4.61
874 945 4.160642 TGAATGGATTCTGATGGAGGTG 57.839 45.455 1.26 0.00 37.67 4.00
875 946 5.399052 AATGAATGGATTCTGATGGAGGT 57.601 39.130 1.26 0.00 37.67 3.85
876 947 5.243283 GGAAATGAATGGATTCTGATGGAGG 59.757 44.000 1.26 0.00 37.67 4.30
877 948 5.831525 TGGAAATGAATGGATTCTGATGGAG 59.168 40.000 1.26 0.00 37.67 3.86
878 949 5.768752 TGGAAATGAATGGATTCTGATGGA 58.231 37.500 1.26 0.00 37.67 3.41
879 950 5.831525 TCTGGAAATGAATGGATTCTGATGG 59.168 40.000 1.26 0.00 37.67 3.51
880 951 6.954487 TCTGGAAATGAATGGATTCTGATG 57.046 37.500 1.26 0.00 37.67 3.07
882 953 7.779754 TTTTCTGGAAATGAATGGATTCTGA 57.220 32.000 1.26 0.00 37.67 3.27
898 1025 6.492087 AGGAATCGGTGTTTTTATTTTCTGGA 59.508 34.615 0.00 0.00 0.00 3.86
902 1029 8.812147 AGAAAGGAATCGGTGTTTTTATTTTC 57.188 30.769 0.00 0.00 0.00 2.29
903 1030 7.870954 GGAGAAAGGAATCGGTGTTTTTATTTT 59.129 33.333 0.00 0.00 0.00 1.82
904 1031 7.014808 TGGAGAAAGGAATCGGTGTTTTTATTT 59.985 33.333 0.00 0.00 0.00 1.40
907 1034 5.239963 GTGGAGAAAGGAATCGGTGTTTTTA 59.760 40.000 0.00 0.00 0.00 1.52
908 1035 4.037565 GTGGAGAAAGGAATCGGTGTTTTT 59.962 41.667 0.00 0.00 0.00 1.94
909 1036 3.568430 GTGGAGAAAGGAATCGGTGTTTT 59.432 43.478 0.00 0.00 0.00 2.43
913 1040 2.770164 AGTGGAGAAAGGAATCGGTG 57.230 50.000 0.00 0.00 0.00 4.94
915 1042 3.887621 TGTAGTGGAGAAAGGAATCGG 57.112 47.619 0.00 0.00 0.00 4.18
917 1044 6.542735 GGGTATTTGTAGTGGAGAAAGGAATC 59.457 42.308 0.00 0.00 0.00 2.52
922 1049 4.189231 CGGGGTATTTGTAGTGGAGAAAG 58.811 47.826 0.00 0.00 0.00 2.62
950 1077 3.522731 CTGAGGAGACGGGAGCGG 61.523 72.222 0.00 0.00 0.00 5.52
952 1079 2.419739 GGACTGAGGAGACGGGAGC 61.420 68.421 0.00 0.00 0.00 4.70
953 1080 1.000771 TGGACTGAGGAGACGGGAG 60.001 63.158 0.00 0.00 0.00 4.30
954 1081 1.304217 GTGGACTGAGGAGACGGGA 60.304 63.158 0.00 0.00 0.00 5.14
955 1082 1.599606 CTGTGGACTGAGGAGACGGG 61.600 65.000 0.00 0.00 0.00 5.28
956 1083 0.609406 TCTGTGGACTGAGGAGACGG 60.609 60.000 0.00 0.00 0.00 4.79
958 1085 2.230266 GTCTTCTGTGGACTGAGGAGAC 59.770 54.545 0.00 0.00 32.36 3.36
959 1086 2.520069 GTCTTCTGTGGACTGAGGAGA 58.480 52.381 0.00 0.00 32.36 3.71
960 1087 1.201181 CGTCTTCTGTGGACTGAGGAG 59.799 57.143 0.00 0.00 32.36 3.69
961 1088 1.248486 CGTCTTCTGTGGACTGAGGA 58.752 55.000 0.00 0.00 0.00 3.71
962 1089 0.962489 ACGTCTTCTGTGGACTGAGG 59.038 55.000 0.00 0.00 0.00 3.86
975 1107 0.969894 CTGGACCTGGAAGACGTCTT 59.030 55.000 30.12 30.12 39.23 3.01
982 1114 1.856539 ATGGTGGCTGGACCTGGAAG 61.857 60.000 0.00 0.00 40.22 3.46
983 1115 1.852157 ATGGTGGCTGGACCTGGAA 60.852 57.895 0.00 0.00 40.22 3.53
985 1117 2.044650 CATGGTGGCTGGACCTGG 60.045 66.667 0.01 0.00 40.22 4.45
1024 1156 1.827789 CGAGGGAGAGGAGGAGCAG 60.828 68.421 0.00 0.00 0.00 4.24
1042 1174 4.077188 GCAGCTTGCGACGGACAC 62.077 66.667 0.00 0.00 31.71 3.67
1121 1253 1.600076 GCAGCATCCGCCTGATCAT 60.600 57.895 0.00 0.00 39.83 2.45
1238 1370 2.027625 CGGTGGAAGAAGCCGTGAC 61.028 63.158 0.00 0.00 40.53 3.67
1304 1442 0.836400 AAGCTCGGTGGGGAAGAAGA 60.836 55.000 0.00 0.00 0.00 2.87
1323 1461 3.641159 TTGCTCTTCGCCGCGATCA 62.641 57.895 17.62 9.56 35.23 2.92
1332 1470 2.037136 CCAGGGTGCTTGCTCTTCG 61.037 63.158 0.00 0.00 0.00 3.79
1367 1505 2.818274 GGTAAGGCTCCGCAACCG 60.818 66.667 0.00 0.00 0.00 4.44
1371 1509 2.992689 TCGTGGTAAGGCTCCGCA 60.993 61.111 6.60 0.00 35.45 5.69
1416 1554 0.318120 CCTTGGCATGAAACGGCTTT 59.682 50.000 0.00 0.00 0.00 3.51
1425 1563 1.082766 TCCCTCCTCCTTGGCATGA 59.917 57.895 0.00 0.00 35.26 3.07
1432 1570 0.793617 TTCTCCTGTCCCTCCTCCTT 59.206 55.000 0.00 0.00 0.00 3.36
1433 1571 0.041982 GTTCTCCTGTCCCTCCTCCT 59.958 60.000 0.00 0.00 0.00 3.69
1434 1572 1.324005 CGTTCTCCTGTCCCTCCTCC 61.324 65.000 0.00 0.00 0.00 4.30
1443 1581 0.827925 TCACTGCCTCGTTCTCCTGT 60.828 55.000 0.00 0.00 0.00 4.00
1444 1582 0.318441 TTCACTGCCTCGTTCTCCTG 59.682 55.000 0.00 0.00 0.00 3.86
1448 1586 1.066573 CCATCTTCACTGCCTCGTTCT 60.067 52.381 0.00 0.00 0.00 3.01
1473 1629 2.338984 ACGCAGTGACCGAACCTC 59.661 61.111 0.00 0.00 42.51 3.85
1524 1680 2.169769 TGGTTGTCGTTTGTCCTTCTCT 59.830 45.455 0.00 0.00 0.00 3.10
1528 1684 1.011333 CGTGGTTGTCGTTTGTCCTT 58.989 50.000 0.00 0.00 0.00 3.36
1534 1690 2.124653 TGCCCGTGGTTGTCGTTT 60.125 55.556 0.00 0.00 0.00 3.60
1535 1691 2.590575 CTGCCCGTGGTTGTCGTT 60.591 61.111 0.00 0.00 0.00 3.85
1536 1692 4.619227 CCTGCCCGTGGTTGTCGT 62.619 66.667 0.00 0.00 0.00 4.34
1537 1693 4.308458 TCCTGCCCGTGGTTGTCG 62.308 66.667 0.00 0.00 0.00 4.35
1541 1700 2.113139 CTTGTCCTGCCCGTGGTT 59.887 61.111 0.00 0.00 0.00 3.67
1547 1706 0.620556 TCTTCATCCTTGTCCTGCCC 59.379 55.000 0.00 0.00 0.00 5.36
1567 1726 0.094216 CGAGCAGCTTCGTGTTCATG 59.906 55.000 0.00 0.00 35.91 3.07
1592 1751 2.110213 GTGTGCGTGGAGGTGGAA 59.890 61.111 0.00 0.00 0.00 3.53
1629 1788 1.131883 TCGCCAGTACTTCTAGTTCGC 59.868 52.381 0.00 0.00 0.00 4.70
1636 1795 1.213013 CGTGCTCGCCAGTACTTCT 59.787 57.895 0.00 0.00 33.23 2.85
1638 1797 1.213013 CTCGTGCTCGCCAGTACTT 59.787 57.895 2.69 0.00 33.23 2.24
1641 1800 2.360726 TCCTCGTGCTCGCCAGTA 60.361 61.111 2.69 0.00 36.96 2.74
1648 1807 1.140804 GAAGCTCCTCCTCGTGCTC 59.859 63.158 0.00 0.00 34.38 4.26
1651 1810 0.390472 GGTTGAAGCTCCTCCTCGTG 60.390 60.000 0.00 0.00 0.00 4.35
1653 1812 0.390472 GTGGTTGAAGCTCCTCCTCG 60.390 60.000 0.00 0.00 0.00 4.63
1655 1814 1.674057 CGTGGTTGAAGCTCCTCCT 59.326 57.895 0.00 0.00 0.00 3.69
1656 1815 1.376037 CCGTGGTTGAAGCTCCTCC 60.376 63.158 0.00 0.00 0.00 4.30
1705 1888 1.873591 CCCTTGAACCACTTCTTCACG 59.126 52.381 0.00 0.00 0.00 4.35
1835 2030 3.502211 AGGCAAACGAAATGGTAGAACAG 59.498 43.478 0.00 0.00 0.00 3.16
1858 2091 7.147312 CCGTAATATAGTGTGAAATAACCCGA 58.853 38.462 0.00 0.00 0.00 5.14
1859 2092 6.128742 GCCGTAATATAGTGTGAAATAACCCG 60.129 42.308 0.00 0.00 0.00 5.28
1860 2093 6.932960 AGCCGTAATATAGTGTGAAATAACCC 59.067 38.462 0.00 0.00 0.00 4.11
1861 2094 7.958053 AGCCGTAATATAGTGTGAAATAACC 57.042 36.000 0.00 0.00 0.00 2.85
1862 2095 8.212495 CGAAGCCGTAATATAGTGTGAAATAAC 58.788 37.037 0.00 0.00 0.00 1.89
1865 2098 5.694910 CCGAAGCCGTAATATAGTGTGAAAT 59.305 40.000 0.00 0.00 0.00 2.17
1867 2100 4.098349 ACCGAAGCCGTAATATAGTGTGAA 59.902 41.667 0.00 0.00 0.00 3.18
1869 2102 3.973657 ACCGAAGCCGTAATATAGTGTG 58.026 45.455 0.00 0.00 0.00 3.82
1871 2104 6.643770 ACATAAACCGAAGCCGTAATATAGTG 59.356 38.462 0.00 0.00 0.00 2.74
1872 2105 6.752168 ACATAAACCGAAGCCGTAATATAGT 58.248 36.000 0.00 0.00 0.00 2.12
1874 2107 7.809331 CAGTACATAAACCGAAGCCGTAATATA 59.191 37.037 0.00 0.00 0.00 0.86
1876 2109 5.978919 CAGTACATAAACCGAAGCCGTAATA 59.021 40.000 0.00 0.00 0.00 0.98
1882 2115 2.676342 CACCAGTACATAAACCGAAGCC 59.324 50.000 0.00 0.00 0.00 4.35
1975 2230 8.494016 AGTACATAAGAAGGCAAAGTGATTAC 57.506 34.615 0.00 0.00 0.00 1.89
1976 2231 7.491372 CGAGTACATAAGAAGGCAAAGTGATTA 59.509 37.037 0.00 0.00 0.00 1.75
1980 2235 4.201724 GCGAGTACATAAGAAGGCAAAGTG 60.202 45.833 0.00 0.00 0.00 3.16
1987 2242 6.147164 TGAAACAAAGCGAGTACATAAGAAGG 59.853 38.462 0.00 0.00 0.00 3.46
2056 2311 2.423538 GCGTGGTTCCATAATTCTTGCT 59.576 45.455 0.00 0.00 0.00 3.91
2185 2440 8.438676 AACTTGCTACATATAAGGAACATGAC 57.561 34.615 0.00 0.00 0.00 3.06
2233 2488 5.607119 AGTATACCGAGTTGCAAGTTTTG 57.393 39.130 8.48 2.90 0.00 2.44
2251 2506 6.207614 GTCTCCCTTGCAAAAGAGAAAAGTAT 59.792 38.462 22.91 0.00 37.14 2.12
2253 2508 4.339530 GTCTCCCTTGCAAAAGAGAAAAGT 59.660 41.667 22.91 0.00 37.14 2.66
2295 2556 2.026262 GTGAGACAAGAAATAGCCCCCA 60.026 50.000 0.00 0.00 0.00 4.96
2328 2605 3.682858 GGTTGTGCGCATATATATCGGTT 59.317 43.478 15.91 0.00 0.00 4.44
2342 2625 5.049680 ACTTTGTAAATAGAGTGGTTGTGCG 60.050 40.000 0.00 0.00 0.00 5.34
2384 2667 9.178758 CAACCCTAGCTTATCTCTTAATTTTGT 57.821 33.333 0.00 0.00 0.00 2.83
2436 2719 8.421249 AAAATTGTGAATATTGGTGAGGAGAA 57.579 30.769 0.00 0.00 0.00 2.87
2437 2720 8.421249 AAAAATTGTGAATATTGGTGAGGAGA 57.579 30.769 0.00 0.00 0.00 3.71
2482 2766 3.193903 TCGTATGTTCGATTTCCAGACCA 59.806 43.478 0.00 0.00 34.85 4.02


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

AutoCloner maintained by Alex Coulton.