Multiple sequence alignment - TraesCS7A01G208600

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 TraesCS7A01G208600 chr7A 100.000 5622 0 0 1 5622 171379877 171385498 0.000000e+00 10382
1 TraesCS7A01G208600 chr7B 94.894 1704 61 9 3941 5622 134557451 134559150 0.000000e+00 2641
2 TraesCS7A01G208600 chr7B 91.249 1497 114 9 2446 3937 134555918 134557402 0.000000e+00 2023
3 TraesCS7A01G208600 chr7B 87.544 1694 108 54 798 2452 134554237 134555866 0.000000e+00 1864
4 TraesCS7A01G208600 chr7B 86.364 220 24 4 2068 2285 43246656 43246441 9.420000e-58 235
5 TraesCS7A01G208600 chr7D 93.337 1696 71 16 3941 5622 169385510 169387177 0.000000e+00 2468
6 TraesCS7A01G208600 chr7D 84.208 2590 173 113 1 2452 169381413 169383904 0.000000e+00 2300
7 TraesCS7A01G208600 chr7D 91.739 1501 109 11 2446 3937 169383967 169385461 0.000000e+00 2071
8 TraesCS7A01G208600 chr7D 87.545 1389 133 17 2446 3828 638149854 638151208 0.000000e+00 1570
9 TraesCS7A01G208600 chr7D 89.057 530 48 6 1927 2452 638149271 638149794 0.000000e+00 649
10 TraesCS7A01G208600 chr7D 86.099 223 25 4 2065 2285 91688677 91688895 9.420000e-58 235
11 TraesCS7A01G208600 chr7D 80.984 305 28 11 1294 1593 638148827 638149106 1.230000e-51 215
12 TraesCS7A01G208600 chr3D 87.145 1338 136 11 2446 3777 570093859 570092552 0.000000e+00 1485
13 TraesCS7A01G208600 chr3D 86.924 543 56 7 1914 2452 570094450 570093919 3.750000e-166 595
14 TraesCS7A01G208600 chr3B 86.082 194 21 5 9 201 496681168 496681356 2.660000e-48 204
15 TraesCS7A01G208600 chr6D 84.456 193 24 5 11 201 424712399 424712211 9.620000e-43 185


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 TraesCS7A01G208600 chr7A 171379877 171385498 5621 False 10382.000000 10382 100.000000 1 5622 1 chr7A.!!$F1 5621
1 TraesCS7A01G208600 chr7B 134554237 134559150 4913 False 2176.000000 2641 91.229000 798 5622 3 chr7B.!!$F1 4824
2 TraesCS7A01G208600 chr7D 169381413 169387177 5764 False 2279.666667 2468 89.761333 1 5622 3 chr7D.!!$F2 5621
3 TraesCS7A01G208600 chr7D 638148827 638151208 2381 False 811.333333 1570 85.862000 1294 3828 3 chr7D.!!$F3 2534
4 TraesCS7A01G208600 chr3D 570092552 570094450 1898 True 1040.000000 1485 87.034500 1914 3777 2 chr3D.!!$R1 1863

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
769 824 0.110238 CGCCAACGACAATGACCTTG 60.110 55.0 0.00 0.0 43.93 3.61 F
1079 1211 0.032615 TCCTCCTCCTCCTCTCAAGC 60.033 60.0 0.00 0.0 0.00 4.01 F
1090 1222 0.240411 CTCTCAAGCTTGCAACAGCC 59.760 55.0 21.99 0.0 41.12 4.85 F
2491 2774 0.389817 TGTGTTCCTGATCGGCTTCG 60.390 55.0 0.00 0.0 0.00 3.79 F
3697 3984 0.110644 GCTTCGGTGAGTTTTCGCAG 60.111 55.0 0.00 0.0 35.49 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2203 0.107800 CCCAGCATGACAGGACAGAG 60.108 60.0 0.00 0.00 39.69 3.35 R
2473 2752 0.389948 ACGAAGCCGATCAGGAACAC 60.390 55.0 7.64 0.00 45.00 3.32 R
2696 2979 0.395312 TGTTTTCCCTCTCACCGTCC 59.605 55.0 0.00 0.00 0.00 4.79 R
4432 4767 0.670162 AAGTTGACTGCGCAATGCTT 59.330 45.0 13.05 8.91 46.63 3.91 R
5307 5664 0.251341 CCTCCACCTGGAAACCTTGG 60.251 60.0 0.00 0.00 44.91 3.61 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
30 31 2.445845 TGGCGGATCTAGGGGTGG 60.446 66.667 0.00 0.00 0.00 4.61
31 32 2.446036 GGCGGATCTAGGGGTGGT 60.446 66.667 0.00 0.00 0.00 4.16
33 34 2.808206 GCGGATCTAGGGGTGGTGG 61.808 68.421 0.00 0.00 0.00 4.61
58 59 4.764143 GCCATGGCCCCCATATAC 57.236 61.111 27.24 0.00 43.15 1.47
59 60 1.773635 GCCATGGCCCCCATATACA 59.226 57.895 27.24 0.00 43.15 2.29
60 61 0.114168 GCCATGGCCCCCATATACAA 59.886 55.000 27.24 0.00 43.15 2.41
61 62 1.273211 GCCATGGCCCCCATATACAAT 60.273 52.381 27.24 0.00 43.15 2.71
62 63 2.826616 GCCATGGCCCCCATATACAATT 60.827 50.000 27.24 0.00 43.15 2.32
63 64 2.833338 CCATGGCCCCCATATACAATTG 59.167 50.000 3.24 3.24 43.15 2.32
64 65 2.692709 TGGCCCCCATATACAATTGG 57.307 50.000 10.83 0.00 0.00 3.16
65 66 1.862911 TGGCCCCCATATACAATTGGT 59.137 47.619 10.83 0.45 0.00 3.67
66 67 3.064412 TGGCCCCCATATACAATTGGTA 58.936 45.455 10.83 2.89 36.16 3.25
67 68 3.075283 TGGCCCCCATATACAATTGGTAG 59.925 47.826 10.83 0.00 34.92 3.18
68 69 3.563479 GGCCCCCATATACAATTGGTAGG 60.563 52.174 10.83 4.30 34.92 3.18
69 70 3.075432 GCCCCCATATACAATTGGTAGGT 59.925 47.826 10.83 0.00 34.92 3.08
70 71 4.809691 GCCCCCATATACAATTGGTAGGTC 60.810 50.000 10.83 0.00 34.92 3.85
71 72 4.601857 CCCCCATATACAATTGGTAGGTCT 59.398 45.833 10.83 0.00 34.92 3.85
72 73 5.074515 CCCCCATATACAATTGGTAGGTCTT 59.925 44.000 10.83 0.00 34.92 3.01
105 106 8.278408 CAGTGCATTCATATGTGTATTCAGTAC 58.722 37.037 1.90 0.00 34.12 2.73
134 136 9.705471 TGTTAACTATTTGTAACGTGTTTTGAG 57.295 29.630 7.22 0.00 0.00 3.02
135 137 9.919348 GTTAACTATTTGTAACGTGTTTTGAGA 57.081 29.630 0.00 0.00 0.00 3.27
140 142 9.370126 CTATTTGTAACGTGTTTTGAGAAGAAG 57.630 33.333 0.00 0.00 0.00 2.85
171 173 4.765339 GCTACCCATTATAATGTTGTCCCC 59.235 45.833 21.20 8.49 34.60 4.81
172 174 4.890499 ACCCATTATAATGTTGTCCCCA 57.110 40.909 21.20 0.00 34.60 4.96
173 175 4.542697 ACCCATTATAATGTTGTCCCCAC 58.457 43.478 21.20 0.00 34.60 4.61
174 176 3.568007 CCCATTATAATGTTGTCCCCACG 59.432 47.826 21.20 4.82 34.60 4.94
175 177 4.456535 CCATTATAATGTTGTCCCCACGA 58.543 43.478 21.20 0.00 34.60 4.35
193 196 4.806247 CCACGATTGTCAAGTTCTAGATCC 59.194 45.833 0.00 0.00 0.00 3.36
235 239 2.496817 GCCTACGGCTGAGTCTGG 59.503 66.667 0.00 0.00 46.69 3.86
249 253 1.160137 GTCTGGAGGACAACATGTGC 58.840 55.000 0.00 0.00 43.94 4.57
266 270 2.245096 GTGCAGTGTTCGATGAAATGC 58.755 47.619 7.68 7.68 32.28 3.56
269 273 1.811965 CAGTGTTCGATGAAATGCCCA 59.188 47.619 0.00 0.00 0.00 5.36
291 295 3.515104 AGGAGAGAAAAGGCTTGAGAGAG 59.485 47.826 0.00 0.00 0.00 3.20
309 313 4.081752 AGAGAGGAGTGTTGATGATGACAC 60.082 45.833 0.00 0.00 44.93 3.67
318 322 3.680620 ATGATGACACGTGGGCCCG 62.681 63.158 21.57 8.84 0.00 6.13
379 389 4.778143 GGGCCGCGGATGTCAACT 62.778 66.667 33.48 0.00 0.00 3.16
383 393 1.573829 GCCGCGGATGTCAACTTCAA 61.574 55.000 33.48 0.00 0.00 2.69
398 408 0.953471 TTCAATGTGAGCCGAACGGG 60.953 55.000 15.01 0.00 39.58 5.28
421 431 0.248990 CCAGCGTTTCTTTGCAGCAA 60.249 50.000 2.83 2.83 0.00 3.91
447 457 3.059352 ACTCAAGTTGGTAGGCATCAC 57.941 47.619 2.34 0.00 0.00 3.06
448 458 2.290323 ACTCAAGTTGGTAGGCATCACC 60.290 50.000 2.34 0.00 39.61 4.02
456 490 0.179073 GTAGGCATCACCGCATCAGT 60.179 55.000 0.00 0.00 46.52 3.41
466 500 1.680735 ACCGCATCAGTCAAGCAAAAA 59.319 42.857 0.00 0.00 0.00 1.94
473 507 5.402270 GCATCAGTCAAGCAAAAATAACGTT 59.598 36.000 5.88 5.88 0.00 3.99
573 628 4.717233 ACAAGAAAGTGTCACAAATGCA 57.283 36.364 5.62 0.00 0.00 3.96
575 630 4.082300 ACAAGAAAGTGTCACAAATGCACA 60.082 37.500 5.62 0.00 36.14 4.57
576 631 4.717233 AGAAAGTGTCACAAATGCACAA 57.283 36.364 5.62 0.00 36.14 3.33
580 635 5.574891 AAGTGTCACAAATGCACAAGTAA 57.425 34.783 5.62 0.00 36.14 2.24
581 636 5.173774 AGTGTCACAAATGCACAAGTAAG 57.826 39.130 5.62 0.00 36.14 2.34
585 640 4.515191 GTCACAAATGCACAAGTAAGAGGA 59.485 41.667 0.00 0.00 0.00 3.71
619 674 4.657824 CCGCCGGTCGACACTTGT 62.658 66.667 18.91 0.00 41.67 3.16
628 683 0.595567 TCGACACTTGTACCGCACAC 60.596 55.000 0.00 0.00 36.69 3.82
629 684 1.554042 CGACACTTGTACCGCACACC 61.554 60.000 0.00 0.00 36.69 4.16
634 689 2.107041 CTTGTACCGCACACCCCAGA 62.107 60.000 0.00 0.00 36.69 3.86
652 707 3.166434 GGTCATCCACCACCACCA 58.834 61.111 0.00 0.00 45.98 4.17
659 714 2.520458 CACCACCACCACCACCAT 59.480 61.111 0.00 0.00 0.00 3.55
728 783 3.693578 TCAACAACATCAGCAACACAGAA 59.306 39.130 0.00 0.00 0.00 3.02
732 787 0.167470 CATCAGCAACACAGAAGCGG 59.833 55.000 0.00 0.00 0.00 5.52
733 788 1.580845 ATCAGCAACACAGAAGCGGC 61.581 55.000 0.00 0.00 0.00 6.53
734 789 2.980233 AGCAACACAGAAGCGGCC 60.980 61.111 0.00 0.00 0.00 6.13
735 790 3.286751 GCAACACAGAAGCGGCCA 61.287 61.111 2.24 0.00 0.00 5.36
736 791 2.639286 CAACACAGAAGCGGCCAC 59.361 61.111 2.24 0.00 0.00 5.01
737 792 2.972505 AACACAGAAGCGGCCACG 60.973 61.111 2.24 0.00 44.63 4.94
767 822 2.325082 GCGCCAACGACAATGACCT 61.325 57.895 0.00 0.00 43.93 3.85
768 823 1.852067 GCGCCAACGACAATGACCTT 61.852 55.000 0.00 0.00 43.93 3.50
769 824 0.110238 CGCCAACGACAATGACCTTG 60.110 55.000 0.00 0.00 43.93 3.61
770 825 0.387239 GCCAACGACAATGACCTTGC 60.387 55.000 0.00 0.00 38.50 4.01
771 826 1.238439 CCAACGACAATGACCTTGCT 58.762 50.000 0.00 0.00 38.50 3.91
772 827 1.069022 CCAACGACAATGACCTTGCTG 60.069 52.381 0.00 0.00 38.50 4.41
774 829 1.237285 ACGACAATGACCTTGCTGCC 61.237 55.000 0.00 0.00 38.50 4.85
795 900 1.856597 GCTGCTGCAAACTTCACTTTG 59.143 47.619 11.11 0.00 39.41 2.77
817 922 1.453928 CCTTCCAATTCCGCCCTCC 60.454 63.158 0.00 0.00 0.00 4.30
818 923 1.609783 CTTCCAATTCCGCCCTCCT 59.390 57.895 0.00 0.00 0.00 3.69
862 967 3.515286 CAAGCGGGCATGGCTCAG 61.515 66.667 19.78 11.81 40.53 3.35
878 986 4.320456 AGGCCCAGTCGCACACAG 62.320 66.667 0.00 0.00 0.00 3.66
903 1011 2.482374 GCACAGTCGCAAGCATCC 59.518 61.111 0.00 0.00 37.18 3.51
904 1012 2.327343 GCACAGTCGCAAGCATCCA 61.327 57.895 0.00 0.00 37.18 3.41
975 1083 0.248458 CCAAACCAAGCACACGACAC 60.248 55.000 0.00 0.00 0.00 3.67
976 1084 0.588730 CAAACCAAGCACACGACACG 60.589 55.000 0.00 0.00 0.00 4.49
982 1092 2.971428 AAGCACACGACACGACCCAG 62.971 60.000 0.00 0.00 0.00 4.45
1001 1111 0.886043 GCCAGCATCGCATCACCATA 60.886 55.000 0.00 0.00 0.00 2.74
1034 1166 1.450491 GCTCCTTCCCTTCCTTCGC 60.450 63.158 0.00 0.00 0.00 4.70
1060 1192 1.928714 GACCGTCTCCTCCTCCTCCT 61.929 65.000 0.00 0.00 0.00 3.69
1065 1197 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
1066 1198 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1067 1199 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1068 1200 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1069 1201 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1071 1203 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1073 1205 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1074 1206 0.998945 CCTCCTCCTCCTCCTCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1075 1207 0.478507 CTCCTCCTCCTCCTCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1076 1208 0.253868 TCCTCCTCCTCCTCCTCTCA 60.254 60.000 0.00 0.00 0.00 3.27
1077 1209 0.633921 CCTCCTCCTCCTCCTCTCAA 59.366 60.000 0.00 0.00 0.00 3.02
1078 1210 1.411501 CCTCCTCCTCCTCCTCTCAAG 60.412 61.905 0.00 0.00 0.00 3.02
1079 1211 0.032615 TCCTCCTCCTCCTCTCAAGC 60.033 60.000 0.00 0.00 0.00 4.01
1090 1222 0.240411 CTCTCAAGCTTGCAACAGCC 59.760 55.000 21.99 0.00 41.12 4.85
1091 1223 1.081641 CTCAAGCTTGCAACAGCCG 60.082 57.895 21.99 0.00 41.12 5.52
1094 1226 2.263741 AAGCTTGCAACAGCCGGAG 61.264 57.895 5.05 0.00 41.12 4.63
1414 1571 4.214327 CGCGCCTCCTCCTTCCTC 62.214 72.222 0.00 0.00 0.00 3.71
1515 1684 4.373116 GCCGGAGAGGTGCGTGAA 62.373 66.667 5.05 0.00 43.70 3.18
1516 1685 2.342279 CCGGAGAGGTGCGTGAAA 59.658 61.111 0.00 0.00 35.36 2.69
1517 1686 2.027625 CCGGAGAGGTGCGTGAAAC 61.028 63.158 0.00 0.00 35.36 2.78
1518 1687 1.300620 CGGAGAGGTGCGTGAAACA 60.301 57.895 0.00 0.00 35.74 2.83
1538 1716 3.264897 CCGGCGCAGGAATTCGAG 61.265 66.667 23.19 0.00 0.00 4.04
1593 1771 0.737367 GCCGCCTGGATTCTTTTTGC 60.737 55.000 0.00 0.00 37.49 3.68
1605 1783 2.343101 TCTTTTTGCATCCTACGACGG 58.657 47.619 0.00 0.00 0.00 4.79
1632 1810 1.127343 TTTGTTTCTTGGCCTTGGGG 58.873 50.000 3.32 0.00 0.00 4.96
1638 1816 1.459348 CTTGGCCTTGGGGTGGTTT 60.459 57.895 3.32 0.00 34.45 3.27
1673 1851 3.814945 CGCATTTGGTTCTTGTCTTCTC 58.185 45.455 0.00 0.00 0.00 2.87
1682 1860 3.662247 TCTTGTCTTCTCGGAGTTTCC 57.338 47.619 4.69 0.00 0.00 3.13
1734 1912 7.961351 TGGATCACCATTTTTGTCACTTTAAT 58.039 30.769 0.00 0.00 41.77 1.40
1737 1915 9.346725 GATCACCATTTTTGTCACTTTAATCTC 57.653 33.333 0.00 0.00 0.00 2.75
1765 1944 8.186178 TCTGTTTAATAACTTCTCATCTTCGC 57.814 34.615 0.00 0.00 35.24 4.70
1789 1968 6.677781 TCTCGATTCCTTTATTTTTCGCAT 57.322 33.333 0.00 0.00 0.00 4.73
1808 1987 7.290857 TCGCATATTAGTGTGTCTTTTTCTC 57.709 36.000 0.00 0.00 0.00 2.87
1810 1989 6.183360 CGCATATTAGTGTGTCTTTTTCTCGT 60.183 38.462 0.00 0.00 0.00 4.18
1811 1990 7.008901 CGCATATTAGTGTGTCTTTTTCTCGTA 59.991 37.037 0.00 0.00 0.00 3.43
1812 1991 8.108782 GCATATTAGTGTGTCTTTTTCTCGTAC 58.891 37.037 0.00 0.00 0.00 3.67
1813 1992 9.135843 CATATTAGTGTGTCTTTTTCTCGTACA 57.864 33.333 0.00 0.00 0.00 2.90
1826 2012 4.742438 TCTCGTACACTTTGCAAATTCC 57.258 40.909 13.23 0.00 0.00 3.01
1832 2018 1.788308 CACTTTGCAAATTCCACAGCG 59.212 47.619 13.23 0.00 0.00 5.18
1902 2089 9.527157 TTTCACATGAATAACCTATCAAAAGGA 57.473 29.630 0.00 0.00 35.61 3.36
1903 2090 9.527157 TTCACATGAATAACCTATCAAAAGGAA 57.473 29.630 0.00 0.00 39.15 3.36
1904 2091 9.527157 TCACATGAATAACCTATCAAAAGGAAA 57.473 29.630 0.00 0.00 39.15 3.13
1910 2097 9.803315 GAATAACCTATCAAAAGGAAATGAACC 57.197 33.333 0.00 0.00 39.15 3.62
1958 2158 5.888161 CCTTGCAGGAATTAGTCAAGGTAAT 59.112 40.000 14.96 0.00 45.22 1.89
1959 2159 6.378280 CCTTGCAGGAATTAGTCAAGGTAATT 59.622 38.462 14.96 0.00 45.22 1.40
1960 2160 7.556275 CCTTGCAGGAATTAGTCAAGGTAATTA 59.444 37.037 14.96 0.00 45.22 1.40
1961 2161 8.871629 TTGCAGGAATTAGTCAAGGTAATTAA 57.128 30.769 0.00 0.00 31.58 1.40
1962 2162 8.276252 TGCAGGAATTAGTCAAGGTAATTAAC 57.724 34.615 0.00 0.00 31.58 2.01
1963 2163 8.107095 TGCAGGAATTAGTCAAGGTAATTAACT 58.893 33.333 0.00 0.00 31.58 2.24
1974 2174 5.112129 AGGTAATTAACTAACTGGCCCAG 57.888 43.478 9.83 9.83 37.52 4.45
2003 2203 6.128472 GGATTTGTTCTTTGGAATGTTGCATC 60.128 38.462 0.00 0.00 33.71 3.91
2023 2229 0.837691 TCTGTCCTGTCATGCTGGGT 60.838 55.000 11.26 0.00 36.89 4.51
2062 2268 8.786937 TGACCGTCGACATATTAAAATAGTAC 57.213 34.615 17.16 0.00 0.00 2.73
2063 2269 8.623903 TGACCGTCGACATATTAAAATAGTACT 58.376 33.333 17.16 0.00 0.00 2.73
2100 2306 4.710423 AGATATAGGCATGTCGCTACTG 57.290 45.455 0.00 0.00 41.91 2.74
2101 2307 3.445450 AGATATAGGCATGTCGCTACTGG 59.555 47.826 0.00 0.00 41.91 4.00
2102 2308 1.414158 ATAGGCATGTCGCTACTGGT 58.586 50.000 0.00 0.00 41.91 4.00
2180 2386 6.500684 TGGTGTTCAGATTAATCTTTCTGC 57.499 37.500 15.49 6.43 39.36 4.26
2240 2446 7.381408 TCGATTCTGTTGCCTATTAAGAATACG 59.619 37.037 0.00 0.00 37.63 3.06
2252 2462 7.586300 CCTATTAAGAATACGGTGCAATTTTCG 59.414 37.037 0.00 0.00 0.00 3.46
2371 2581 8.605947 CCCTATTTCCTTGATATTGATACAGGA 58.394 37.037 0.00 0.00 0.00 3.86
2456 2735 7.417456 CCATTTTCAGTCACATTCCATCATGAT 60.417 37.037 1.18 1.18 0.00 2.45
2473 2752 6.519679 TCATGATCCTGATTTCCAAAGTTG 57.480 37.500 0.00 0.00 0.00 3.16
2474 2753 6.012113 TCATGATCCTGATTTCCAAAGTTGT 58.988 36.000 0.00 0.00 0.00 3.32
2491 2774 0.389817 TGTGTTCCTGATCGGCTTCG 60.390 55.000 0.00 0.00 0.00 3.79
2498 2781 2.293677 TCCTGATCGGCTTCGTATCTTC 59.706 50.000 0.00 0.00 35.06 2.87
2499 2782 2.294791 CCTGATCGGCTTCGTATCTTCT 59.705 50.000 0.00 0.00 35.06 2.85
2500 2783 3.243569 CCTGATCGGCTTCGTATCTTCTT 60.244 47.826 0.00 0.00 35.06 2.52
2501 2784 4.023107 CCTGATCGGCTTCGTATCTTCTTA 60.023 45.833 0.00 0.00 35.06 2.10
2510 2793 5.927115 GCTTCGTATCTTCTTATTACAGGGG 59.073 44.000 0.00 0.00 0.00 4.79
2522 2805 0.918983 TACAGGGGCCTCATCCTTTG 59.081 55.000 4.79 0.00 0.00 2.77
2684 2967 2.434185 GCGAGGGACAACATGCGA 60.434 61.111 0.00 0.00 0.00 5.10
2688 2971 1.003355 AGGGACAACATGCGACTGG 60.003 57.895 0.00 0.00 0.00 4.00
2723 3006 3.753797 GTGAGAGGGAAAACATGGACTTC 59.246 47.826 0.00 0.00 0.00 3.01
2771 3055 4.698304 TCCGATAACCAAACCTGTTCAATC 59.302 41.667 0.00 0.00 0.00 2.67
2865 3149 6.149973 CACATGATCAACAAGGAAAGCTTCTA 59.850 38.462 0.00 0.00 0.00 2.10
2907 3191 1.034292 GGATCCTTGGCCTCAGCAAC 61.034 60.000 3.84 0.00 42.56 4.17
3055 3339 3.998560 GGAATGACATGGGTTCCCA 57.001 52.632 13.29 13.29 40.75 4.37
3109 3393 5.907207 TCCCTTGTCTGAAGATTATTCTCG 58.093 41.667 0.00 0.00 0.00 4.04
3128 3412 1.535226 CGCATGTGGCCATCATTTCTG 60.535 52.381 9.72 5.56 40.31 3.02
3138 3422 4.321750 GGCCATCATTTCTGCCATGAATAG 60.322 45.833 0.00 0.00 43.46 1.73
3152 3436 0.949105 GAATAGCATGGTACCCCGCG 60.949 60.000 10.07 0.00 0.00 6.46
3322 3606 1.013596 TTGTGTCGCTTCCACAACTG 58.986 50.000 8.15 0.00 45.24 3.16
3361 3647 7.734924 TTTCAGTAGCCATAGCAATTGATAG 57.265 36.000 10.34 0.00 43.56 2.08
3362 3648 6.670695 TCAGTAGCCATAGCAATTGATAGA 57.329 37.500 10.34 0.00 43.56 1.98
3363 3649 6.695429 TCAGTAGCCATAGCAATTGATAGAG 58.305 40.000 10.34 4.03 43.56 2.43
3379 3665 0.532573 AGAGCATCACACCGTCGAAT 59.467 50.000 0.00 0.00 37.82 3.34
3382 3668 3.123804 GAGCATCACACCGTCGAATTAT 58.876 45.455 0.00 0.00 33.17 1.28
3390 3676 9.569167 CATCACACCGTCGAATTATAGTATATT 57.431 33.333 0.00 0.00 0.00 1.28
3408 3694 8.625786 AGTATATTCATGCATTATGCTGTGAA 57.374 30.769 26.90 26.90 45.23 3.18
3410 3696 9.681692 GTATATTCATGCATTATGCTGTGAAAA 57.318 29.630 27.74 18.99 44.76 2.29
3415 3701 6.976349 TCATGCATTATGCTGTGAAAAAGATC 59.024 34.615 18.44 0.00 45.31 2.75
3417 3703 6.558009 TGCATTATGCTGTGAAAAAGATCTC 58.442 36.000 18.44 0.00 45.31 2.75
3422 3708 3.822735 TGCTGTGAAAAAGATCTCCCTTG 59.177 43.478 0.00 0.00 0.00 3.61
3457 3744 1.469703 CATTGCGCTTCTTGTGATCCA 59.530 47.619 9.73 0.00 0.00 3.41
3509 3796 1.336887 ACGCGTATCTGACTGCAGTTT 60.337 47.619 22.65 9.13 42.84 2.66
3653 3940 4.511826 GGGAGCTCATACACTTATTTTCCG 59.488 45.833 17.19 0.00 0.00 4.30
3693 3980 3.365364 CCTGATTGCTTCGGTGAGTTTTC 60.365 47.826 0.00 0.00 0.00 2.29
3697 3984 0.110644 GCTTCGGTGAGTTTTCGCAG 60.111 55.000 0.00 0.00 35.49 5.18
3708 3997 4.056050 GAGTTTTCGCAGTAACTCTCCAA 58.944 43.478 12.19 0.00 42.37 3.53
3719 4008 5.991606 CAGTAACTCTCCAACAGATGAAACA 59.008 40.000 0.00 0.00 0.00 2.83
3807 4096 3.093814 TCTCCAGGCTTTGTACACGATA 58.906 45.455 0.00 0.00 0.00 2.92
3830 4119 2.229792 TCAGATCAAACGCTGCCTTTT 58.770 42.857 0.00 0.00 32.27 2.27
3865 4154 5.391312 AATTTTCCAGTGAGGTAATGTGC 57.609 39.130 0.00 0.00 39.02 4.57
3878 4167 5.815581 AGGTAATGTGCTGGAAATCTGTTA 58.184 37.500 0.00 0.00 0.00 2.41
3881 4170 6.151144 GGTAATGTGCTGGAAATCTGTTAGTT 59.849 38.462 0.00 0.00 0.00 2.24
3882 4171 5.886960 ATGTGCTGGAAATCTGTTAGTTC 57.113 39.130 0.00 0.00 0.00 3.01
3884 4173 4.997395 TGTGCTGGAAATCTGTTAGTTCTC 59.003 41.667 0.00 0.00 32.72 2.87
3891 4180 8.463930 TGGAAATCTGTTAGTTCTCAAAACAT 57.536 30.769 0.00 0.00 33.01 2.71
3892 4181 8.567948 TGGAAATCTGTTAGTTCTCAAAACATC 58.432 33.333 0.00 0.00 33.01 3.06
3898 4187 6.491394 TGTTAGTTCTCAAAACATCGTTTGG 58.509 36.000 0.00 0.00 38.72 3.28
3901 4190 5.961272 AGTTCTCAAAACATCGTTTGGTTT 58.039 33.333 0.00 0.00 46.27 3.27
3930 4219 7.800155 TCATCGCAATGGATGTAGAATTAAA 57.200 32.000 10.12 0.00 43.39 1.52
3932 4221 8.128582 TCATCGCAATGGATGTAGAATTAAAAC 58.871 33.333 10.12 0.00 43.39 2.43
3933 4222 7.624360 TCGCAATGGATGTAGAATTAAAACT 57.376 32.000 0.00 0.00 0.00 2.66
3935 4224 8.181573 TCGCAATGGATGTAGAATTAAAACTTC 58.818 33.333 0.00 0.00 0.00 3.01
3936 4225 7.967854 CGCAATGGATGTAGAATTAAAACTTCA 59.032 33.333 0.00 0.00 0.00 3.02
3937 4226 9.807649 GCAATGGATGTAGAATTAAAACTTCAT 57.192 29.630 4.85 4.85 0.00 2.57
4075 4410 2.560981 TCATCAGCGTAAGTTCACAGGA 59.439 45.455 0.00 0.00 41.68 3.86
4077 4412 3.462483 TCAGCGTAAGTTCACAGGAAA 57.538 42.857 0.00 0.00 41.68 3.13
4084 4419 1.222567 AGTTCACAGGAAACCCCAGT 58.777 50.000 0.00 0.00 37.41 4.00
4121 4456 3.777465 TTTCCTCTACGGAGTTCATCG 57.223 47.619 0.00 0.00 44.28 3.84
4411 4746 0.541296 AGGCCACAGAAAGCAAGCAT 60.541 50.000 5.01 0.00 0.00 3.79
4432 4767 2.158928 TGGTTCCGTTCTTCCTTTCGAA 60.159 45.455 0.00 0.00 0.00 3.71
4477 4812 1.153309 TGGCACAGGCAGATGATCG 60.153 57.895 0.00 0.00 43.71 3.69
4544 4879 2.006772 CGACCGAAGCTGCCATAAC 58.993 57.895 0.00 0.00 0.00 1.89
4545 4880 0.460284 CGACCGAAGCTGCCATAACT 60.460 55.000 0.00 0.00 0.00 2.24
4572 4907 9.807921 ATATAATGGATGTAGTTAAACAAGGGG 57.192 33.333 0.00 0.00 32.02 4.79
4677 5012 4.000331 CAGAACTCTGCATACCTATGGG 58.000 50.000 0.00 0.00 37.15 4.00
4750 5085 7.114529 GCATATCAATTTCAAATGAGTAGCAGC 59.885 37.037 0.00 0.00 0.00 5.25
5030 5387 2.632028 CCATCATCAGGTAGGTCAGGAG 59.368 54.545 0.00 0.00 0.00 3.69
5062 5419 7.553760 TCTCTTGCACACATTATACATGACATT 59.446 33.333 0.00 0.00 0.00 2.71
5090 5447 1.323534 GCGTGCAACTACCAACTATCG 59.676 52.381 0.00 0.00 31.75 2.92
5093 5450 3.060363 CGTGCAACTACCAACTATCGAAC 59.940 47.826 0.00 0.00 31.75 3.95
5095 5452 4.449743 GTGCAACTACCAACTATCGAACAA 59.550 41.667 0.00 0.00 0.00 2.83
5307 5664 4.558538 ACTGAATCACAAAAGTGAGTGC 57.441 40.909 3.14 0.00 36.73 4.40
5337 5694 2.224159 GGTGGAGGGACCTTGCAGA 61.224 63.158 0.00 0.00 39.86 4.26
5372 5729 1.876156 CAACTCTTCAGCCCAACAGAC 59.124 52.381 0.00 0.00 0.00 3.51
5373 5730 1.428869 ACTCTTCAGCCCAACAGACT 58.571 50.000 0.00 0.00 0.00 3.24
5392 5749 6.036517 ACAGACTTGCATATTTTAGCGAGAAG 59.963 38.462 8.53 0.00 43.47 2.85
5405 5762 0.034059 CGAGAAGCCCGCCATTATCT 59.966 55.000 0.00 0.00 0.00 1.98
5491 5848 7.418408 TCAAATGCGTTAACAACATTCTGTAA 58.582 30.769 18.88 5.99 33.01 2.41
5579 5936 3.120792 TGTTTTTGACTCCTCGTCTTCG 58.879 45.455 0.00 0.00 43.25 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.762460 CACCCCTAGATCCGCCACT 60.762 63.158 0.00 0.00 0.00 4.00
49 50 5.843019 AGACCTACCAATTGTATATGGGG 57.157 43.478 4.43 0.00 41.17 4.96
50 51 8.533569 AAAAAGACCTACCAATTGTATATGGG 57.466 34.615 4.43 1.37 41.17 4.00
72 73 7.225784 ACACATATGAATGCACTGGTAAAAA 57.774 32.000 10.38 0.00 36.50 1.94
78 79 6.261603 ACTGAATACACATATGAATGCACTGG 59.738 38.462 10.38 0.00 36.50 4.00
79 80 7.255491 ACTGAATACACATATGAATGCACTG 57.745 36.000 10.38 0.00 36.50 3.66
153 155 4.456535 TCGTGGGGACAACATTATAATGG 58.543 43.478 25.45 13.51 46.06 3.16
155 157 6.126409 ACAATCGTGGGGACAACATTATAAT 58.874 36.000 0.00 0.00 46.06 1.28
166 168 1.804748 GAACTTGACAATCGTGGGGAC 59.195 52.381 0.00 0.00 0.00 4.46
167 169 1.697432 AGAACTTGACAATCGTGGGGA 59.303 47.619 0.00 0.00 0.00 4.81
171 173 4.500837 CGGATCTAGAACTTGACAATCGTG 59.499 45.833 0.00 0.00 0.00 4.35
172 174 4.673441 CGGATCTAGAACTTGACAATCGT 58.327 43.478 0.00 0.00 0.00 3.73
173 175 3.487574 GCGGATCTAGAACTTGACAATCG 59.512 47.826 0.00 0.00 0.00 3.34
174 176 3.804873 GGCGGATCTAGAACTTGACAATC 59.195 47.826 0.00 0.00 0.00 2.67
175 177 3.197766 TGGCGGATCTAGAACTTGACAAT 59.802 43.478 0.00 0.00 0.00 2.71
233 237 0.473755 ACTGCACATGTTGTCCTCCA 59.526 50.000 0.00 0.00 0.00 3.86
235 239 1.597742 ACACTGCACATGTTGTCCTC 58.402 50.000 0.00 0.00 0.00 3.71
249 253 1.811965 TGGGCATTTCATCGAACACTG 59.188 47.619 0.00 0.00 0.00 3.66
266 270 1.352352 TCAAGCCTTTTCTCTCCTGGG 59.648 52.381 0.00 0.00 0.00 4.45
269 273 3.515104 CTCTCTCAAGCCTTTTCTCTCCT 59.485 47.826 0.00 0.00 0.00 3.69
291 295 2.413112 CACGTGTCATCATCAACACTCC 59.587 50.000 7.58 0.00 42.83 3.85
318 322 3.810941 TGATTGACCGTTAAGTTGGACAC 59.189 43.478 0.00 0.00 29.82 3.67
367 371 2.483877 TCACATTGAAGTTGACATCCGC 59.516 45.455 0.00 0.00 0.00 5.54
376 386 1.531149 CGTTCGGCTCACATTGAAGTT 59.469 47.619 0.00 0.00 0.00 2.66
379 389 0.953471 CCCGTTCGGCTCACATTGAA 60.953 55.000 5.66 0.00 0.00 2.69
383 393 0.390735 GTTACCCGTTCGGCTCACAT 60.391 55.000 5.66 0.00 33.26 3.21
398 408 2.650608 CTGCAAAGAAACGCTGGTTAC 58.349 47.619 0.00 0.00 34.62 2.50
399 409 1.001815 GCTGCAAAGAAACGCTGGTTA 60.002 47.619 0.00 0.00 34.62 2.85
401 411 1.360192 GCTGCAAAGAAACGCTGGT 59.640 52.632 0.00 0.00 0.00 4.00
402 412 0.248990 TTGCTGCAAAGAAACGCTGG 60.249 50.000 13.51 0.00 0.00 4.85
403 413 1.558741 TTTGCTGCAAAGAAACGCTG 58.441 45.000 22.84 0.00 0.00 5.18
404 414 2.514205 ATTTGCTGCAAAGAAACGCT 57.486 40.000 28.86 11.03 36.76 5.07
405 415 4.908966 ATAATTTGCTGCAAAGAAACGC 57.091 36.364 28.86 0.00 36.76 4.84
406 416 6.801377 TGAGTATAATTTGCTGCAAAGAAACG 59.199 34.615 28.86 0.00 36.76 3.60
421 431 7.499232 GTGATGCCTACCAACTTGAGTATAATT 59.501 37.037 0.00 0.00 0.00 1.40
447 457 2.420628 TTTTTGCTTGACTGATGCGG 57.579 45.000 0.00 0.00 0.00 5.69
448 458 4.029418 CGTTATTTTTGCTTGACTGATGCG 59.971 41.667 0.00 0.00 0.00 4.73
456 490 8.690680 AAAACTACAACGTTATTTTTGCTTGA 57.309 26.923 0.00 0.00 0.00 3.02
466 500 9.026074 CATGGTTTTCAAAAACTACAACGTTAT 57.974 29.630 15.72 0.00 45.70 1.89
473 507 5.422331 TGGGTCATGGTTTTCAAAAACTACA 59.578 36.000 15.72 8.45 45.70 2.74
548 584 7.860373 GTGCATTTGTGACACTTTCTTGTAATA 59.140 33.333 7.20 0.00 0.00 0.98
561 616 4.275689 CCTCTTACTTGTGCATTTGTGACA 59.724 41.667 0.00 0.00 0.00 3.58
573 628 4.597507 TCCACCTTTCATCCTCTTACTTGT 59.402 41.667 0.00 0.00 0.00 3.16
575 630 5.843019 TTCCACCTTTCATCCTCTTACTT 57.157 39.130 0.00 0.00 0.00 2.24
576 631 6.012508 TGAATTCCACCTTTCATCCTCTTACT 60.013 38.462 2.27 0.00 0.00 2.24
580 635 4.593956 GTGAATTCCACCTTTCATCCTCT 58.406 43.478 2.27 0.00 39.86 3.69
581 636 4.972514 GTGAATTCCACCTTTCATCCTC 57.027 45.455 2.27 0.00 39.86 3.71
619 674 3.000819 CCTCTGGGGTGTGCGGTA 61.001 66.667 0.00 0.00 0.00 4.02
628 683 1.616327 TGGTGGATGACCTCTGGGG 60.616 63.158 0.00 0.00 46.32 4.96
629 684 1.604378 GTGGTGGATGACCTCTGGG 59.396 63.158 0.00 0.00 46.32 4.45
634 689 1.463214 TGGTGGTGGTGGATGACCT 60.463 57.895 0.00 0.00 46.32 3.85
743 798 4.717629 TGTCGTTGGCGCTCTCCG 62.718 66.667 7.64 5.11 38.14 4.63
744 799 1.741770 ATTGTCGTTGGCGCTCTCC 60.742 57.895 7.64 0.00 38.14 3.71
745 800 1.014044 TCATTGTCGTTGGCGCTCTC 61.014 55.000 7.64 0.00 38.14 3.20
746 801 1.005037 TCATTGTCGTTGGCGCTCT 60.005 52.632 7.64 0.00 38.14 4.09
747 802 1.132640 GTCATTGTCGTTGGCGCTC 59.867 57.895 7.64 0.00 38.14 5.03
748 803 2.325082 GGTCATTGTCGTTGGCGCT 61.325 57.895 7.64 0.00 38.14 5.92
749 804 1.852067 AAGGTCATTGTCGTTGGCGC 61.852 55.000 0.00 0.00 38.14 6.53
750 805 0.110238 CAAGGTCATTGTCGTTGGCG 60.110 55.000 7.99 0.00 39.92 5.69
770 825 3.203546 AAGTTTGCAGCAGCGGCAG 62.204 57.895 19.89 3.80 46.23 4.85
771 826 3.198236 GAAGTTTGCAGCAGCGGCA 62.198 57.895 16.98 16.98 46.23 5.69
772 827 2.429739 GAAGTTTGCAGCAGCGGC 60.430 61.111 11.05 11.05 46.23 6.53
774 829 0.029834 AAGTGAAGTTTGCAGCAGCG 59.970 50.000 0.00 0.00 46.23 5.18
795 900 1.101635 GGGCGGAATTGGAAGGTAGC 61.102 60.000 0.00 0.00 0.00 3.58
891 999 0.388520 GGGTTTTGGATGCTTGCGAC 60.389 55.000 0.00 0.00 0.00 5.19
893 1001 1.444212 CGGGTTTTGGATGCTTGCG 60.444 57.895 0.00 0.00 0.00 4.85
933 1041 2.665649 TGGTATATTATGGCTCGCCG 57.334 50.000 3.14 0.00 39.42 6.46
934 1042 3.439129 GGTTTGGTATATTATGGCTCGCC 59.561 47.826 0.00 0.00 0.00 5.54
976 1084 4.783621 TGCGATGCTGGCTGGGTC 62.784 66.667 0.00 0.00 0.00 4.46
982 1092 0.886043 TATGGTGATGCGATGCTGGC 60.886 55.000 0.00 0.00 0.00 4.85
1023 1134 2.434359 GTGGACGCGAAGGAAGGG 60.434 66.667 15.93 0.00 0.00 3.95
1034 1166 3.036783 GAGGAGACGGTCGTGGACG 62.037 68.421 0.00 0.00 41.45 4.79
1045 1177 0.185175 GAGGAGGAGGAGGAGGAGAC 59.815 65.000 0.00 0.00 0.00 3.36
1060 1192 0.032615 GCTTGAGAGGAGGAGGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
1065 1197 0.612229 TGCAAGCTTGAGAGGAGGAG 59.388 55.000 30.39 0.00 0.00 3.69
1066 1198 1.059098 TTGCAAGCTTGAGAGGAGGA 58.941 50.000 30.39 0.00 0.00 3.71
1067 1199 1.163554 GTTGCAAGCTTGAGAGGAGG 58.836 55.000 30.39 0.76 0.00 4.30
1068 1200 1.805345 CTGTTGCAAGCTTGAGAGGAG 59.195 52.381 30.39 13.49 0.00 3.69
1069 1201 1.888215 CTGTTGCAAGCTTGAGAGGA 58.112 50.000 30.39 7.92 0.00 3.71
1071 1203 0.240411 GGCTGTTGCAAGCTTGAGAG 59.760 55.000 30.39 17.86 43.06 3.20
1073 1205 1.081641 CGGCTGTTGCAAGCTTGAG 60.082 57.895 30.39 18.37 43.06 3.02
1074 1206 2.554636 CCGGCTGTTGCAAGCTTGA 61.555 57.895 30.39 12.25 43.06 3.02
1075 1207 2.049802 CCGGCTGTTGCAAGCTTG 60.050 61.111 22.44 22.44 43.06 4.01
1076 1208 2.203337 TCCGGCTGTTGCAAGCTT 60.203 55.556 10.12 0.00 43.06 3.74
1077 1209 2.670934 CTCCGGCTGTTGCAAGCT 60.671 61.111 10.12 0.00 43.06 3.74
1078 1210 4.410743 GCTCCGGCTGTTGCAAGC 62.411 66.667 0.00 0.00 42.75 4.01
1090 1222 1.268352 GCCTGTAGAGATGTAGCTCCG 59.732 57.143 0.00 0.00 35.49 4.63
1091 1223 1.616374 GGCCTGTAGAGATGTAGCTCC 59.384 57.143 0.00 0.00 35.49 4.70
1094 1226 1.268352 CGAGGCCTGTAGAGATGTAGC 59.732 57.143 12.00 0.00 0.00 3.58
1098 1243 1.365633 GGCGAGGCCTGTAGAGATG 59.634 63.158 12.00 0.00 46.69 2.90
1099 1244 3.863606 GGCGAGGCCTGTAGAGAT 58.136 61.111 12.00 0.00 46.69 2.75
1405 1562 3.080121 AGCGGCAGGAGGAAGGAG 61.080 66.667 1.45 0.00 0.00 3.69
1465 1634 4.610714 GAATCCCTCTCCGCCGCC 62.611 72.222 0.00 0.00 0.00 6.13
1466 1635 4.951963 CGAATCCCTCTCCGCCGC 62.952 72.222 0.00 0.00 0.00 6.53
1467 1636 3.217017 TCGAATCCCTCTCCGCCG 61.217 66.667 0.00 0.00 0.00 6.46
1468 1637 2.417936 GTCGAATCCCTCTCCGCC 59.582 66.667 0.00 0.00 0.00 6.13
1469 1638 2.417936 GGTCGAATCCCTCTCCGC 59.582 66.667 0.00 0.00 0.00 5.54
1470 1639 1.437986 GTGGTCGAATCCCTCTCCG 59.562 63.158 0.00 0.00 0.00 4.63
1471 1640 1.437986 CGTGGTCGAATCCCTCTCC 59.562 63.158 0.00 0.00 39.71 3.71
1472 1641 1.437986 CCGTGGTCGAATCCCTCTC 59.562 63.158 0.00 0.00 39.71 3.20
1473 1642 2.722201 GCCGTGGTCGAATCCCTCT 61.722 63.158 0.00 0.00 39.71 3.69
1474 1643 2.202892 GCCGTGGTCGAATCCCTC 60.203 66.667 0.00 0.00 39.71 4.30
1475 1644 3.782443 GGCCGTGGTCGAATCCCT 61.782 66.667 0.00 0.00 39.71 4.20
1593 1771 1.749634 ACTTCCTTCCGTCGTAGGATG 59.250 52.381 17.70 17.70 40.15 3.51
1605 1783 3.384789 AGGCCAAGAAACAAACTTCCTTC 59.615 43.478 5.01 0.00 0.00 3.46
1632 1810 1.601914 GCACGGAATCAACCAAACCAC 60.602 52.381 0.00 0.00 0.00 4.16
1638 1816 1.240641 AATGCGCACGGAATCAACCA 61.241 50.000 14.90 0.00 0.00 3.67
1673 1851 0.673644 AATGCGACTGGGAAACTCCG 60.674 55.000 0.00 0.00 37.43 4.63
1682 1860 0.322456 TCCCTGGAAAATGCGACTGG 60.322 55.000 0.00 0.00 0.00 4.00
1765 1944 6.106877 TGCGAAAAATAAAGGAATCGAGAG 57.893 37.500 0.00 0.00 32.38 3.20
1789 1968 8.355169 AGTGTACGAGAAAAAGACACACTAATA 58.645 33.333 2.82 0.00 42.31 0.98
1808 1987 3.958704 TGTGGAATTTGCAAAGTGTACG 58.041 40.909 18.01 0.00 0.00 3.67
1810 1989 3.549827 CGCTGTGGAATTTGCAAAGTGTA 60.550 43.478 18.01 2.53 30.17 2.90
1811 1990 2.799207 CGCTGTGGAATTTGCAAAGTGT 60.799 45.455 18.01 4.62 30.17 3.55
1812 1991 1.788308 CGCTGTGGAATTTGCAAAGTG 59.212 47.619 18.01 8.36 27.43 3.16
1813 1992 1.869342 GCGCTGTGGAATTTGCAAAGT 60.869 47.619 18.19 15.58 0.00 2.66
1888 2075 6.553100 TGTGGTTCATTTCCTTTTGATAGGTT 59.447 34.615 0.00 0.00 36.63 3.50
1893 2080 5.867903 TGTGTGGTTCATTTCCTTTTGAT 57.132 34.783 0.00 0.00 0.00 2.57
1900 2087 3.820467 TCACTCATGTGTGGTTCATTTCC 59.180 43.478 23.69 0.00 44.14 3.13
1901 2088 4.516698 ACTCACTCATGTGTGGTTCATTTC 59.483 41.667 23.69 0.00 44.14 2.17
1902 2089 4.464008 ACTCACTCATGTGTGGTTCATTT 58.536 39.130 23.69 2.68 44.14 2.32
1903 2090 4.090761 ACTCACTCATGTGTGGTTCATT 57.909 40.909 23.69 0.76 44.14 2.57
1904 2091 3.777106 ACTCACTCATGTGTGGTTCAT 57.223 42.857 23.69 6.35 44.14 2.57
1905 2092 3.118445 TCAACTCACTCATGTGTGGTTCA 60.118 43.478 23.69 12.83 44.14 3.18
1910 2097 4.321718 AGGATTCAACTCACTCATGTGTG 58.678 43.478 19.49 19.49 44.14 3.82
1958 2158 1.004277 CCTGCTGGGCCAGTTAGTTAA 59.996 52.381 32.80 10.53 33.43 2.01
1959 2159 0.618458 CCTGCTGGGCCAGTTAGTTA 59.382 55.000 32.80 12.71 33.43 2.24
1960 2160 1.380302 CCTGCTGGGCCAGTTAGTT 59.620 57.895 32.80 0.00 33.43 2.24
1961 2161 3.081554 CCTGCTGGGCCAGTTAGT 58.918 61.111 32.80 0.00 33.43 2.24
1974 2174 4.248058 CATTCCAAAGAACAAATCCCTGC 58.752 43.478 0.00 0.00 33.97 4.85
2003 2203 0.107800 CCCAGCATGACAGGACAGAG 60.108 60.000 0.00 0.00 39.69 3.35
2023 2229 6.757478 TGTCGACGGTCAAATATGCTTATAAA 59.243 34.615 11.62 0.00 0.00 1.40
2100 2306 5.646360 TCTTTGCTTGCTGGTTTATACTACC 59.354 40.000 0.00 0.00 36.17 3.18
2101 2307 6.371825 AGTCTTTGCTTGCTGGTTTATACTAC 59.628 38.462 0.00 0.00 0.00 2.73
2102 2308 6.472887 AGTCTTTGCTTGCTGGTTTATACTA 58.527 36.000 0.00 0.00 0.00 1.82
2114 2320 1.602377 ACGGTGTAAGTCTTTGCTTGC 59.398 47.619 0.00 0.00 0.00 4.01
2180 2386 7.246311 ACTTTGTCAAAGATTAATCATGCGAG 58.754 34.615 28.07 13.46 41.02 5.03
2240 2446 4.752661 TGTTAGTACCGAAAATTGCACC 57.247 40.909 0.00 0.00 0.00 5.01
2252 2462 5.648092 AGAAGAACAATGCCATGTTAGTACC 59.352 40.000 4.40 0.00 43.31 3.34
2353 2563 6.017605 GTGCACTTCCTGTATCAATATCAAGG 60.018 42.308 10.32 0.00 0.00 3.61
2371 2581 1.352017 TGGATCCATGTGAGTGCACTT 59.648 47.619 22.65 0.92 45.36 3.16
2429 2639 3.940209 TGGAATGTGACTGAAAATGGC 57.060 42.857 0.00 0.00 0.00 4.40
2456 2735 4.340950 GGAACACAACTTTGGAAATCAGGA 59.659 41.667 0.00 0.00 0.00 3.86
2473 2752 0.389948 ACGAAGCCGATCAGGAACAC 60.390 55.000 7.64 0.00 45.00 3.32
2474 2753 1.179152 TACGAAGCCGATCAGGAACA 58.821 50.000 7.64 0.00 45.00 3.18
2491 2774 5.307196 TGAGGCCCCTGTAATAAGAAGATAC 59.693 44.000 0.00 0.00 0.00 2.24
2498 2781 2.982488 AGGATGAGGCCCCTGTAATAAG 59.018 50.000 0.00 0.00 0.00 1.73
2499 2782 3.074857 AGGATGAGGCCCCTGTAATAA 57.925 47.619 0.00 0.00 0.00 1.40
2500 2783 2.815357 AGGATGAGGCCCCTGTAATA 57.185 50.000 0.00 0.00 0.00 0.98
2501 2784 1.912862 AAGGATGAGGCCCCTGTAAT 58.087 50.000 0.00 0.00 32.12 1.89
2510 2793 3.149981 GGGCTTATACAAAGGATGAGGC 58.850 50.000 0.00 0.00 35.48 4.70
2522 2805 4.800784 TGTTTTCTTTTGCGGGCTTATAC 58.199 39.130 0.00 0.00 0.00 1.47
2660 2943 2.664851 TTGTCCCTCGCAAGCACG 60.665 61.111 0.00 0.00 37.18 5.34
2696 2979 0.395312 TGTTTTCCCTCTCACCGTCC 59.605 55.000 0.00 0.00 0.00 4.79
2723 3006 2.505557 GTGCCGTACCCGAAGACG 60.506 66.667 0.00 0.00 38.79 4.18
2742 3025 4.279922 ACAGGTTTGGTTATCGGAAAAAGG 59.720 41.667 0.00 0.00 0.00 3.11
2744 3027 5.360144 TGAACAGGTTTGGTTATCGGAAAAA 59.640 36.000 0.00 0.00 0.00 1.94
2771 3055 2.238144 ACATCACCACCCATCTCTGAAG 59.762 50.000 0.00 0.00 0.00 3.02
2865 3149 2.598565 TCAGTACTTGCTGGTGAGTCT 58.401 47.619 0.00 0.00 37.12 3.24
3089 3373 6.257411 ACATGCGAGAATAATCTTCAGACAAG 59.743 38.462 0.00 0.00 35.54 3.16
3093 3377 5.052481 CCACATGCGAGAATAATCTTCAGA 58.948 41.667 0.00 0.00 35.54 3.27
3109 3393 1.805120 GCAGAAATGATGGCCACATGC 60.805 52.381 8.16 11.32 37.47 4.06
3152 3436 1.298938 GTATCCCGCCGAAGACGAC 60.299 63.158 0.00 0.00 42.66 4.34
3348 3634 5.704515 GGTGTGATGCTCTATCAATTGCTAT 59.295 40.000 0.00 0.00 46.85 2.97
3361 3647 1.359848 AATTCGACGGTGTGATGCTC 58.640 50.000 0.00 0.00 0.00 4.26
3362 3648 2.665649 TAATTCGACGGTGTGATGCT 57.334 45.000 0.00 0.00 0.00 3.79
3363 3649 4.049186 ACTATAATTCGACGGTGTGATGC 58.951 43.478 0.00 0.00 0.00 3.91
3408 3694 5.779241 TGTATGGTCAAGGGAGATCTTTT 57.221 39.130 0.00 0.00 0.00 2.27
3410 3696 7.451731 TTTATGTATGGTCAAGGGAGATCTT 57.548 36.000 0.00 0.00 0.00 2.40
3415 3701 7.645058 ATGTTTTTATGTATGGTCAAGGGAG 57.355 36.000 0.00 0.00 0.00 4.30
3417 3703 6.534793 GCAATGTTTTTATGTATGGTCAAGGG 59.465 38.462 0.00 0.00 0.00 3.95
3422 3708 5.339990 AGCGCAATGTTTTTATGTATGGTC 58.660 37.500 11.47 0.00 0.00 4.02
3509 3796 3.317711 CCCTGACAGTACACAAAATGCAA 59.682 43.478 0.93 0.00 0.00 4.08
3546 3833 7.620094 ACCTCCATAGTTCACTTTCTGTACTAT 59.380 37.037 0.00 0.00 41.69 2.12
3653 3940 5.756195 TCAGGCTTGTGTATATTTCATGC 57.244 39.130 0.00 0.00 0.00 4.06
3693 3980 2.724977 TCTGTTGGAGAGTTACTGCG 57.275 50.000 0.00 0.00 39.87 5.18
3697 3984 6.483640 ACTTGTTTCATCTGTTGGAGAGTTAC 59.516 38.462 0.00 0.00 32.80 2.50
3708 3997 8.352942 GGAATTAACTGAACTTGTTTCATCTGT 58.647 33.333 0.00 0.00 43.54 3.41
3719 4008 4.523943 TGCAGCATGGAATTAACTGAACTT 59.476 37.500 0.00 0.00 35.86 2.66
3807 4096 2.440409 AGGCAGCGTTTGATCTGATTT 58.560 42.857 0.00 0.00 32.26 2.17
3830 4119 4.527816 ACTGGAAAATTAGGCTTCATGCAA 59.472 37.500 0.00 0.00 45.15 4.08
3865 4154 7.930217 TGTTTTGAGAACTAACAGATTTCCAG 58.070 34.615 0.00 0.00 0.00 3.86
3878 4167 5.576447 AACCAAACGATGTTTTGAGAACT 57.424 34.783 0.00 0.00 38.54 3.01
3901 4190 7.800155 TTCTACATCCATTGCGATGATAAAA 57.200 32.000 15.98 0.00 41.92 1.52
3904 4193 9.500785 TTTAATTCTACATCCATTGCGATGATA 57.499 29.630 15.98 3.51 41.92 2.15
3930 4219 5.765182 CCACAGACCTGAAAAGTATGAAGTT 59.235 40.000 3.76 0.00 31.03 2.66
3932 4221 5.551233 TCCACAGACCTGAAAAGTATGAAG 58.449 41.667 3.76 0.00 31.03 3.02
3933 4222 5.560722 TCCACAGACCTGAAAAGTATGAA 57.439 39.130 3.76 0.00 31.03 2.57
3935 4224 5.491070 TCATCCACAGACCTGAAAAGTATG 58.509 41.667 3.76 0.00 32.74 2.39
3936 4225 5.762179 TCATCCACAGACCTGAAAAGTAT 57.238 39.130 3.76 0.00 0.00 2.12
3937 4226 5.013079 ACATCATCCACAGACCTGAAAAGTA 59.987 40.000 3.76 0.00 0.00 2.24
3938 4227 4.202503 ACATCATCCACAGACCTGAAAAGT 60.203 41.667 3.76 0.00 0.00 2.66
3939 4228 4.155462 CACATCATCCACAGACCTGAAAAG 59.845 45.833 3.76 0.00 0.00 2.27
4075 4410 4.141018 AGGTTGAAGTGATTACTGGGGTTT 60.141 41.667 0.00 0.00 37.19 3.27
4077 4412 2.986728 AGGTTGAAGTGATTACTGGGGT 59.013 45.455 0.00 0.00 37.19 4.95
4084 4419 7.020827 AGAGGAAATGAGGTTGAAGTGATTA 57.979 36.000 0.00 0.00 0.00 1.75
4121 4456 4.781934 AGGTACAGGAAAAGTATGATGGC 58.218 43.478 0.00 0.00 0.00 4.40
4191 4526 0.694771 TTGAGCTGTGGCCAATCTCT 59.305 50.000 22.78 12.77 39.73 3.10
4337 4672 1.057636 CGTCGTTGTCATACGCAACT 58.942 50.000 6.61 0.00 42.73 3.16
4411 4746 1.413445 TCGAAAGGAAGAACGGAACCA 59.587 47.619 0.00 0.00 0.00 3.67
4432 4767 0.670162 AAGTTGACTGCGCAATGCTT 59.330 45.000 13.05 8.91 46.63 3.91
4467 4802 2.969238 CACGGGGCGATCATCTGC 60.969 66.667 0.00 0.00 0.00 4.26
4572 4907 9.639601 CTTTCTTCCAATTTGGTTTTCCTATAC 57.360 33.333 14.98 0.00 39.03 1.47
4670 5005 8.001875 AGATATACTCTACAGCATACCCATAGG 58.998 40.741 0.00 0.00 33.24 2.57
4677 5012 8.402472 GTGGATGAGATATACTCTACAGCATAC 58.598 40.741 0.00 0.00 45.13 2.39
4776 5111 9.265901 CTCCTGTATATTGGACAGAAAATACAG 57.734 37.037 11.51 11.51 46.01 2.74
5030 5387 6.758416 TGTATAATGTGTGCAAGAGAGATGTC 59.242 38.462 0.00 0.00 0.00 3.06
5095 5452 9.448438 TGAAGCACTCTGTAAATAACATGTTAT 57.552 29.630 22.70 22.70 37.50 1.89
5155 5512 7.499232 GCCACTAAGTTGATCAATATGGTAACT 59.501 37.037 12.12 0.00 37.61 2.24
5215 5572 4.565962 GTGTGTGTGCAATGAAAACATTGA 59.434 37.500 21.74 8.35 43.26 2.57
5230 5587 2.892373 ACAAAACTCGTGTGTGTGTG 57.108 45.000 6.45 0.00 0.00 3.82
5231 5588 6.854496 ATAATACAAAACTCGTGTGTGTGT 57.146 33.333 14.23 10.33 30.79 3.72
5307 5664 0.251341 CCTCCACCTGGAAACCTTGG 60.251 60.000 0.00 0.00 44.91 3.61
5337 5694 2.750166 AGAGTTGACATCGACGATGACT 59.250 45.455 37.26 29.72 42.09 3.41
5372 5729 4.531332 GGCTTCTCGCTAAAATATGCAAG 58.469 43.478 0.00 0.00 39.13 4.01
5373 5730 3.315191 GGGCTTCTCGCTAAAATATGCAA 59.685 43.478 0.00 0.00 39.13 4.08
5392 5749 2.678336 GTTAGCATAGATAATGGCGGGC 59.322 50.000 0.00 0.00 35.99 6.13
5418 5775 2.608988 CCCTGTGGAGGAGCCTGT 60.609 66.667 0.00 0.00 42.93 4.00
5491 5848 0.536460 AATCGAGTTTGTTGCCCGGT 60.536 50.000 0.00 0.00 0.00 5.28
5579 5936 0.960364 TCCATCCAAACTTGCCGCTC 60.960 55.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.