Multiple sequence alignment - TraesCS3A01G367500

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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 TraesCS3A01G367500 chr3A 100.000 5170 0 0 1 5170 616467781 616472950 0.000000e+00 9548.0
1 TraesCS3A01G367500 chr3D 92.788 4839 193 66 106 4842 474117214 474121998 0.000000e+00 6859.0
2 TraesCS3A01G367500 chr3D 85.185 486 38 16 4670 5138 474122330 474122798 7.840000e-128 468.0
3 TraesCS3A01G367500 chr3B 92.088 4512 201 79 103 4539 630363124 630367554 0.000000e+00 6211.0
4 TraesCS3A01G367500 chr3B 89.720 214 17 4 4960 5170 630368091 630368302 8.530000e-68 268.0
5 TraesCS3A01G367500 chr1A 90.310 516 48 2 998 1512 474702951 474702437 0.000000e+00 675.0
6 TraesCS3A01G367500 chr1A 80.508 118 21 2 4835 4951 564097384 564097500 7.130000e-14 89.8
7 TraesCS3A01G367500 chr1D 89.864 513 52 0 1000 1512 375957222 375956710 0.000000e+00 660.0
8 TraesCS3A01G367500 chr1B 89.729 516 51 2 998 1512 501368452 501367938 0.000000e+00 658.0
9 TraesCS3A01G367500 chr5B 82.963 135 22 1 4820 4953 615142273 615142139 2.530000e-23 121.0
10 TraesCS3A01G367500 chr5A 83.168 101 10 4 4821 4916 399297597 399297499 9.220000e-13 86.1
11 TraesCS3A01G367500 chr6A 91.111 45 3 1 4814 4858 611660963 611661006 5.590000e-05 60.2


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 TraesCS3A01G367500 chr3A 616467781 616472950 5169 False 9548.0 9548 100.0000 1 5170 1 chr3A.!!$F1 5169
1 TraesCS3A01G367500 chr3D 474117214 474122798 5584 False 3663.5 6859 88.9865 106 5138 2 chr3D.!!$F1 5032
2 TraesCS3A01G367500 chr3B 630363124 630368302 5178 False 3239.5 6211 90.9040 103 5170 2 chr3B.!!$F1 5067
3 TraesCS3A01G367500 chr1A 474702437 474702951 514 True 675.0 675 90.3100 998 1512 1 chr1A.!!$R1 514
4 TraesCS3A01G367500 chr1D 375956710 375957222 512 True 660.0 660 89.8640 1000 1512 1 chr1D.!!$R1 512
5 TraesCS3A01G367500 chr1B 501367938 501368452 514 True 658.0 658 89.7290 998 1512 1 chr1B.!!$R1 514

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
52 53 0.036010 ATGGCAAGGACGAGGACAAG 60.036 55.0 0.00 0.00 0.00 3.16 F
506 548 0.231279 CAGACAAAAACGTCGACGGG 59.769 55.0 37.89 23.77 44.95 5.28 F
1540 1620 0.249238 CTCTACTCACCTGCATCCGC 60.249 60.0 0.00 0.00 39.24 5.54 F
2114 2209 0.040646 ACTACATCCGTCCCTGTGGA 59.959 55.0 0.00 0.00 38.75 4.02 F
2772 2872 0.320683 TTGCGTGCTATCACTGCAGT 60.321 50.0 15.25 15.25 45.60 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1647 0.106268 TCAACAGGCAAGAGGGCAAA 60.106 50.000 0.00 0.0 46.44 3.68 R
1559 1648 0.112995 ATCAACAGGCAAGAGGGCAA 59.887 50.000 0.00 0.0 46.44 4.52 R
2512 2611 1.610038 CAGCCATTGCAGTCAAGTCAA 59.390 47.619 0.00 0.0 41.13 3.18 R
3836 3938 0.381801 GGTTGGTGCATCCTATTGCG 59.618 55.000 0.00 0.0 45.77 4.85 R
4214 4326 0.040499 GGGACCCAAGGGCAACATAA 59.960 55.000 5.33 0.0 39.32 1.90 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
38 39 4.478206 TTTCAACCAGAAAAACATGGCA 57.522 36.364 0.00 0.00 43.00 4.92
39 40 4.478206 TTCAACCAGAAAAACATGGCAA 57.522 36.364 0.00 0.00 40.45 4.52
40 41 4.057406 TCAACCAGAAAAACATGGCAAG 57.943 40.909 0.00 0.00 40.45 4.01
41 42 3.132925 CAACCAGAAAAACATGGCAAGG 58.867 45.455 0.00 0.00 40.45 3.61
42 43 2.676748 ACCAGAAAAACATGGCAAGGA 58.323 42.857 0.00 0.00 40.45 3.36
43 44 2.365293 ACCAGAAAAACATGGCAAGGAC 59.635 45.455 0.00 0.00 40.45 3.85
44 45 2.607771 CCAGAAAAACATGGCAAGGACG 60.608 50.000 0.00 0.00 0.00 4.79
45 46 2.293122 CAGAAAAACATGGCAAGGACGA 59.707 45.455 0.00 0.00 0.00 4.20
46 47 2.554032 AGAAAAACATGGCAAGGACGAG 59.446 45.455 0.00 0.00 0.00 4.18
47 48 1.247567 AAAACATGGCAAGGACGAGG 58.752 50.000 0.00 0.00 0.00 4.63
48 49 0.400213 AAACATGGCAAGGACGAGGA 59.600 50.000 0.00 0.00 0.00 3.71
49 50 0.321653 AACATGGCAAGGACGAGGAC 60.322 55.000 0.00 0.00 0.00 3.85
50 51 1.296392 CATGGCAAGGACGAGGACA 59.704 57.895 0.00 0.00 0.00 4.02
51 52 0.321564 CATGGCAAGGACGAGGACAA 60.322 55.000 0.00 0.00 0.00 3.18
52 53 0.036010 ATGGCAAGGACGAGGACAAG 60.036 55.000 0.00 0.00 0.00 3.16
53 54 1.376037 GGCAAGGACGAGGACAAGG 60.376 63.158 0.00 0.00 0.00 3.61
54 55 1.376037 GCAAGGACGAGGACAAGGG 60.376 63.158 0.00 0.00 0.00 3.95
55 56 1.296715 CAAGGACGAGGACAAGGGG 59.703 63.158 0.00 0.00 0.00 4.79
56 57 1.157751 AAGGACGAGGACAAGGGGA 59.842 57.895 0.00 0.00 0.00 4.81
57 58 1.192803 AAGGACGAGGACAAGGGGAC 61.193 60.000 0.00 0.00 0.00 4.46
70 71 2.047655 GGGACCATGCGAACACGA 60.048 61.111 0.00 0.00 0.00 4.35
71 72 1.449601 GGGACCATGCGAACACGAT 60.450 57.895 0.00 0.00 0.00 3.73
72 73 1.429148 GGGACCATGCGAACACGATC 61.429 60.000 0.00 0.00 0.00 3.69
73 74 0.460284 GGACCATGCGAACACGATCT 60.460 55.000 0.00 0.00 0.00 2.75
74 75 0.647410 GACCATGCGAACACGATCTG 59.353 55.000 0.00 0.00 0.00 2.90
75 76 1.349627 CCATGCGAACACGATCTGC 59.650 57.895 0.00 0.00 0.00 4.26
76 77 1.360931 CCATGCGAACACGATCTGCA 61.361 55.000 0.00 0.00 40.23 4.41
77 78 0.443478 CATGCGAACACGATCTGCAA 59.557 50.000 0.00 0.00 39.26 4.08
78 79 0.443869 ATGCGAACACGATCTGCAAC 59.556 50.000 0.00 0.00 39.26 4.17
79 80 1.225475 GCGAACACGATCTGCAACG 60.225 57.895 0.00 6.16 0.00 4.10
80 81 1.614227 GCGAACACGATCTGCAACGA 61.614 55.000 13.06 0.00 0.00 3.85
81 82 0.781787 CGAACACGATCTGCAACGAA 59.218 50.000 13.06 0.00 0.00 3.85
82 83 1.201704 CGAACACGATCTGCAACGAAG 60.202 52.381 13.06 8.26 0.00 3.79
83 84 0.512952 AACACGATCTGCAACGAAGC 59.487 50.000 13.06 0.00 0.00 3.86
84 85 0.599991 ACACGATCTGCAACGAAGCA 60.600 50.000 13.06 6.40 43.35 3.91
85 86 0.512518 CACGATCTGCAACGAAGCAA 59.487 50.000 13.06 1.11 45.13 3.91
86 87 1.069973 CACGATCTGCAACGAAGCAAA 60.070 47.619 13.06 0.00 45.13 3.68
87 88 1.806542 ACGATCTGCAACGAAGCAAAT 59.193 42.857 13.06 0.69 45.13 2.32
88 89 2.171567 CGATCTGCAACGAAGCAAATG 58.828 47.619 7.81 0.00 45.13 2.32
89 90 2.159667 CGATCTGCAACGAAGCAAATGA 60.160 45.455 7.81 3.18 45.13 2.57
90 91 2.686558 TCTGCAACGAAGCAAATGAC 57.313 45.000 7.81 0.00 45.13 3.06
91 92 1.946081 TCTGCAACGAAGCAAATGACA 59.054 42.857 7.81 0.00 45.13 3.58
92 93 2.553602 TCTGCAACGAAGCAAATGACAT 59.446 40.909 7.81 0.00 45.13 3.06
93 94 3.004629 TCTGCAACGAAGCAAATGACATT 59.995 39.130 7.81 0.00 45.13 2.71
94 95 3.307674 TGCAACGAAGCAAATGACATTC 58.692 40.909 0.05 0.00 42.46 2.67
95 96 3.004629 TGCAACGAAGCAAATGACATTCT 59.995 39.130 0.05 0.00 42.46 2.40
96 97 3.362831 GCAACGAAGCAAATGACATTCTG 59.637 43.478 0.05 3.95 0.00 3.02
97 98 3.207474 ACGAAGCAAATGACATTCTGC 57.793 42.857 19.24 19.24 34.96 4.26
98 99 2.816087 ACGAAGCAAATGACATTCTGCT 59.184 40.909 21.81 21.81 46.85 4.24
99 100 3.168963 CGAAGCAAATGACATTCTGCTG 58.831 45.455 25.21 16.29 44.18 4.41
100 101 2.649331 AGCAAATGACATTCTGCTGC 57.351 45.000 24.49 19.34 43.34 5.25
101 102 1.890489 AGCAAATGACATTCTGCTGCA 59.110 42.857 24.49 0.88 43.34 4.41
162 163 1.667724 GTCGCTGCTTTATCTGTGCAT 59.332 47.619 0.00 0.00 36.07 3.96
163 164 1.935873 TCGCTGCTTTATCTGTGCATC 59.064 47.619 0.00 0.00 36.07 3.91
189 196 5.512298 TGCATGCCCAGCTAATAATATCAT 58.488 37.500 16.68 0.00 0.00 2.45
196 203 7.394359 TGCCCAGCTAATAATATCATCTTTTCC 59.606 37.037 0.00 0.00 0.00 3.13
197 204 7.394359 GCCCAGCTAATAATATCATCTTTTCCA 59.606 37.037 0.00 0.00 0.00 3.53
211 218 5.112129 TCTTTTCCATTAGGGGAGCTAAC 57.888 43.478 0.00 0.00 38.42 2.34
224 231 3.360886 GCTAACCTCAGCTCTGCTC 57.639 57.895 0.00 0.00 36.40 4.26
229 236 1.079266 CCTCAGCTCTGCTCACACC 60.079 63.158 0.00 0.00 36.40 4.16
234 241 3.699894 CTCTGCTCACACCGGCCT 61.700 66.667 0.00 0.00 0.00 5.19
268 275 5.690409 TCCGTGTAGATATTTCGAGCAATTC 59.310 40.000 0.00 0.00 0.00 2.17
306 313 6.424032 AGAAGATACCCCCATACAGAAAAAC 58.576 40.000 0.00 0.00 0.00 2.43
313 320 3.199677 CCCATACAGAAAAACGCCGATA 58.800 45.455 0.00 0.00 0.00 2.92
369 376 3.673484 CCCGCAACCACAAGCCTG 61.673 66.667 0.00 0.00 0.00 4.85
419 443 1.539388 TGTTTTATCCACTTGCCGCTG 59.461 47.619 0.00 0.00 0.00 5.18
466 495 0.514691 CTGTCTTTTCAGCTCCGCAC 59.485 55.000 0.00 0.00 0.00 5.34
470 499 1.630244 CTTTTCAGCTCCGCACTCCG 61.630 60.000 0.00 0.00 0.00 4.63
471 500 4.742201 TTCAGCTCCGCACTCCGC 62.742 66.667 0.00 0.00 35.03 5.54
475 504 4.129737 GCTCCGCACTCCGCACTA 62.130 66.667 0.00 0.00 42.60 2.74
477 506 2.360726 TCCGCACTCCGCACTAGA 60.361 61.111 0.00 0.00 42.60 2.43
478 507 1.934220 CTCCGCACTCCGCACTAGAA 61.934 60.000 0.00 0.00 42.60 2.10
479 508 1.141881 CCGCACTCCGCACTAGAAT 59.858 57.895 0.00 0.00 42.60 2.40
480 509 0.384309 CCGCACTCCGCACTAGAATA 59.616 55.000 0.00 0.00 42.60 1.75
482 511 1.202256 CGCACTCCGCACTAGAATACA 60.202 52.381 0.00 0.00 42.60 2.29
489 531 3.130516 TCCGCACTAGAATACACCTTCAG 59.869 47.826 0.00 0.00 0.00 3.02
496 538 7.041372 GCACTAGAATACACCTTCAGACAAAAA 60.041 37.037 0.00 0.00 0.00 1.94
497 539 8.283291 CACTAGAATACACCTTCAGACAAAAAC 58.717 37.037 0.00 0.00 0.00 2.43
506 548 0.231279 CAGACAAAAACGTCGACGGG 59.769 55.000 37.89 23.77 44.95 5.28
509 551 3.340253 AAAAACGTCGACGGGGCG 61.340 61.111 37.89 16.53 44.95 6.13
527 576 2.223203 GGCGCAAGTGAGATCAAATCAG 60.223 50.000 10.83 0.00 41.68 2.90
539 588 7.224362 GTGAGATCAAATCAGTAATCCTGTGAG 59.776 40.741 0.00 0.00 42.19 3.51
551 600 0.438830 CCTGTGAGAAAAGCGTACGC 59.561 55.000 32.17 32.17 42.33 4.42
611 668 1.703438 CGCGTACGGTGCTAGAGAGT 61.703 60.000 18.39 0.00 34.97 3.24
616 673 3.490590 CGTACGGTGCTAGAGAGTAGAGA 60.491 52.174 7.57 0.00 0.00 3.10
617 674 3.849563 ACGGTGCTAGAGAGTAGAGAT 57.150 47.619 0.00 0.00 0.00 2.75
619 676 3.118186 ACGGTGCTAGAGAGTAGAGATGT 60.118 47.826 0.00 0.00 0.00 3.06
621 678 3.568007 GGTGCTAGAGAGTAGAGATGTGG 59.432 52.174 0.00 0.00 0.00 4.17
628 694 3.886505 GAGAGTAGAGATGTGGTGGTAGG 59.113 52.174 0.00 0.00 0.00 3.18
654 722 4.778143 GTGCTGGCTGTACCCGGG 62.778 72.222 22.25 22.25 37.83 5.73
677 745 2.145225 CGAGGCCATTTATCGCTCG 58.855 57.895 5.01 0.00 0.00 5.03
792 865 4.044484 CCCGGCTCGCTCCTATCG 62.044 72.222 0.00 0.00 0.00 2.92
817 890 4.137543 CCCTTCTCCCTCCAATAATTTCG 58.862 47.826 0.00 0.00 0.00 3.46
818 891 3.565902 CCTTCTCCCTCCAATAATTTCGC 59.434 47.826 0.00 0.00 0.00 4.70
820 893 4.503714 TCTCCCTCCAATAATTTCGCTT 57.496 40.909 0.00 0.00 0.00 4.68
823 896 3.202151 TCCCTCCAATAATTTCGCTTCCT 59.798 43.478 0.00 0.00 0.00 3.36
824 897 3.954258 CCCTCCAATAATTTCGCTTCCTT 59.046 43.478 0.00 0.00 0.00 3.36
825 898 4.036852 CCCTCCAATAATTTCGCTTCCTTC 59.963 45.833 0.00 0.00 0.00 3.46
826 899 4.640201 CCTCCAATAATTTCGCTTCCTTCA 59.360 41.667 0.00 0.00 0.00 3.02
880 954 1.077858 CAGCAGAAAGGGAGGGAGC 60.078 63.158 0.00 0.00 0.00 4.70
902 976 1.360911 GAGGAATCTCCGTCTCCGC 59.639 63.158 0.00 0.00 42.75 5.54
903 977 2.077821 GAGGAATCTCCGTCTCCGCC 62.078 65.000 0.00 0.00 42.75 6.13
904 978 2.128507 GGAATCTCCGTCTCCGCCT 61.129 63.158 0.00 0.00 0.00 5.52
905 979 1.360911 GAATCTCCGTCTCCGCCTC 59.639 63.158 0.00 0.00 0.00 4.70
906 980 2.077821 GAATCTCCGTCTCCGCCTCC 62.078 65.000 0.00 0.00 0.00 4.30
1517 1597 1.219393 GCTCCTGCAGGTAGTCCAC 59.781 63.158 31.58 10.97 39.41 4.02
1540 1620 0.249238 CTCTACTCACCTGCATCCGC 60.249 60.000 0.00 0.00 39.24 5.54
1608 1697 4.141597 TGGTGAGTTCCAGTAATTGTGACA 60.142 41.667 0.00 0.00 33.19 3.58
1691 1782 7.162082 CCAAATGGAGTATACTGGATAAGGAC 58.838 42.308 10.90 0.00 37.39 3.85
1700 1791 8.216423 AGTATACTGGATAAGGACGAGTTAAGA 58.784 37.037 4.10 0.00 0.00 2.10
1816 1907 0.100503 GTTTGGGCGCCATGATACAC 59.899 55.000 30.85 8.62 31.53 2.90
1933 2024 1.609061 CCTGTCGTTTCTGTCCAGCAT 60.609 52.381 0.00 0.00 0.00 3.79
1961 2052 3.429822 CGATCCGGCCTCTAGTTTGTAAA 60.430 47.826 0.00 0.00 0.00 2.01
1971 2066 7.040686 GGCCTCTAGTTTGTAAAATTGACTCAA 60.041 37.037 0.00 0.00 0.00 3.02
1973 2068 9.665264 CCTCTAGTTTGTAAAATTGACTCAAAC 57.335 33.333 14.91 14.91 44.27 2.93
1979 2074 5.830912 TGTAAAATTGACTCAAACCAGCTG 58.169 37.500 6.78 6.78 0.00 4.24
1998 2093 1.226746 GACAAGTCCCAACCAAGTCG 58.773 55.000 0.00 0.00 0.00 4.18
2018 2113 5.527582 AGTCGGGCTTAAGCAAACTATAATG 59.472 40.000 27.83 5.71 44.36 1.90
2019 2114 4.274950 TCGGGCTTAAGCAAACTATAATGC 59.725 41.667 27.83 6.59 44.36 3.56
2058 2153 1.127343 GATCTGTCTTCCCCAGGAGG 58.873 60.000 0.00 0.00 31.21 4.30
2093 2188 6.867662 ACTACTTTGATTGGACTTGAACAG 57.132 37.500 0.00 0.00 0.00 3.16
2114 2209 0.040646 ACTACATCCGTCCCTGTGGA 59.959 55.000 0.00 0.00 38.75 4.02
2134 2231 7.786030 TGTGGAACATCTTGAACCAAAATAAA 58.214 30.769 0.00 0.00 45.67 1.40
2149 2246 5.584251 CCAAAATAAAGTTGCAAGTTGGTGT 59.416 36.000 19.93 7.18 31.60 4.16
2202 2300 5.235831 CAGATTAGTGTGGCACTATGTCATG 59.764 44.000 19.83 6.82 44.85 3.07
2215 2313 2.134201 TGTCATGCCGTCATATCGAC 57.866 50.000 0.00 0.00 41.62 4.20
2220 2318 2.951457 TGCCGTCATATCGACTTTCA 57.049 45.000 0.00 0.00 42.98 2.69
2232 2330 4.934075 TCGACTTTCAAGCATCATCTTG 57.066 40.909 0.00 0.00 43.53 3.02
2417 2515 5.665459 AGACTAAAGGTTAGCATGCTACAG 58.335 41.667 26.87 17.24 0.00 2.74
2490 2589 3.385433 CCTGGAAATGCCTCATATGCAAA 59.615 43.478 0.00 0.00 42.92 3.68
2491 2590 4.039973 CCTGGAAATGCCTCATATGCAAAT 59.960 41.667 0.00 0.00 42.92 2.32
2683 2782 8.616076 CCATTCTTCCTTAGCTTACAACTATTG 58.384 37.037 0.00 0.00 0.00 1.90
2684 2783 7.611213 TTCTTCCTTAGCTTACAACTATTGC 57.389 36.000 0.00 0.00 0.00 3.56
2772 2872 0.320683 TTGCGTGCTATCACTGCAGT 60.321 50.000 15.25 15.25 45.60 4.40
2934 3034 0.535780 CTGAGCTCAAAGTGGTGCCA 60.536 55.000 18.85 0.00 0.00 4.92
3174 3274 3.387962 TGAGATGCCTGTTATCTTCCCT 58.612 45.455 0.00 0.00 35.14 4.20
3280 3380 5.035443 CGAACCTATTTGTTCTCGAGGTAG 58.965 45.833 13.56 5.89 41.95 3.18
3321 3423 8.043710 TCTTGTATTTTGGGTGTGAAATTTGTT 58.956 29.630 0.00 0.00 0.00 2.83
3398 3500 1.903183 GACAGAGGGCTAGAGGTTGTT 59.097 52.381 0.00 0.00 0.00 2.83
3401 3503 0.984995 GAGGGCTAGAGGTTGTTGGT 59.015 55.000 0.00 0.00 0.00 3.67
3566 3668 3.990092 TGTATCTGATATCACCAACGGC 58.010 45.455 0.00 0.00 0.00 5.68
3674 3776 1.659335 GCTCGACAACGGTGTTCGA 60.659 57.895 21.12 21.12 42.43 3.71
3809 3911 2.813908 CTACTGGGCAACGTCGGC 60.814 66.667 3.72 3.72 37.60 5.54
3815 3917 4.204891 GGCAACGTCGGCGAATCG 62.205 66.667 20.03 15.31 42.00 3.34
3959 4061 2.418368 TATGGGTGCAAGGCTACAAG 57.582 50.000 0.00 0.00 0.00 3.16
4115 4217 0.909623 TTGCCTACTACTCCCTTGCC 59.090 55.000 0.00 0.00 0.00 4.52
4163 4265 4.740822 ACCCCGTTGCATCCAGCC 62.741 66.667 0.00 0.00 44.83 4.85
4170 4272 1.678300 TTGCATCCAGCCGCATGAA 60.678 52.632 0.00 0.00 44.83 2.57
4204 4316 5.051891 ACATCTAGTTGTGTGTACGTACC 57.948 43.478 22.43 14.05 0.00 3.34
4209 4321 4.494350 AGTTGTGTGTACGTACCTACTG 57.506 45.455 22.43 0.00 0.00 2.74
4214 4326 4.003648 GTGTGTACGTACCTACTGTACCT 58.996 47.826 22.43 0.00 45.89 3.08
4218 4330 6.316140 TGTGTACGTACCTACTGTACCTTATG 59.684 42.308 22.43 0.00 45.89 1.90
4220 4332 6.884295 TGTACGTACCTACTGTACCTTATGTT 59.116 38.462 22.43 0.00 45.89 2.71
4221 4333 6.199937 ACGTACCTACTGTACCTTATGTTG 57.800 41.667 0.00 0.00 45.89 3.33
4226 4338 4.080526 CCTACTGTACCTTATGTTGCCCTT 60.081 45.833 0.00 0.00 0.00 3.95
4245 4357 0.469144 TGGGTCCCTTTGGCAAGAAC 60.469 55.000 10.00 0.00 30.57 3.01
4261 4373 4.083802 GCAAGAACCGTATCTGAATATGGC 60.084 45.833 4.02 0.00 45.16 4.40
4340 4463 2.753452 GTGCTGTAGCTGAGGTGTAGTA 59.247 50.000 5.38 0.00 42.66 1.82
4456 4591 1.686355 TGATCGGTTGCTGGTTTTGT 58.314 45.000 0.00 0.00 0.00 2.83
4474 4609 6.273071 GTTTTGTCTCTGCTTAAAACCACAT 58.727 36.000 0.00 0.00 37.16 3.21
4592 5105 3.611970 TCAACTTTTTCCTTCACGTCCA 58.388 40.909 0.00 0.00 0.00 4.02
4623 5160 8.703604 TTTTAGTCTTCGACTTAGGATTGATG 57.296 34.615 1.45 0.00 40.28 3.07
4704 5524 0.880278 CCGCGTTGGTATGATCCTGG 60.880 60.000 4.92 0.00 0.00 4.45
4705 5525 0.880278 CGCGTTGGTATGATCCTGGG 60.880 60.000 0.00 0.00 0.00 4.45
4714 5534 4.229582 TGGTATGATCCTGGGCTTAAACTT 59.770 41.667 0.00 0.00 0.00 2.66
4780 5601 9.656040 CAACCAATTCATCTGAAAATTCCATTA 57.344 29.630 0.00 0.00 37.61 1.90
4816 5864 2.223852 GGAGCTCTCCTTCGTGGATTAC 60.224 54.545 14.64 0.00 45.16 1.89
4884 5945 1.442526 CCCGCAGCCTATTTGCTCAG 61.443 60.000 0.00 0.00 40.32 3.35
4890 5951 1.827969 AGCCTATTTGCTCAGAGTCGT 59.172 47.619 0.00 0.00 36.75 4.34
4900 5961 2.311462 CTCAGAGTCGTCAAAGTGTCG 58.689 52.381 0.00 0.00 0.00 4.35
4903 5964 1.053811 GAGTCGTCAAAGTGTCGCTC 58.946 55.000 0.00 0.00 30.92 5.03
4904 5965 0.318784 AGTCGTCAAAGTGTCGCTCC 60.319 55.000 0.00 0.00 0.00 4.70
4907 5968 2.027625 GTCAAAGTGTCGCTCCCCG 61.028 63.158 0.00 0.00 38.61 5.73
4908 5969 3.423154 CAAAGTGTCGCTCCCCGC 61.423 66.667 0.00 0.00 36.73 6.13
4963 6025 6.910995 CCGAATAGGCTCTATATTATACGGG 58.089 44.000 0.00 0.00 30.10 5.28
4980 6042 1.465200 GGGCCTCTCCTACGTGGATC 61.465 65.000 0.84 0.00 45.16 3.36
5046 6108 1.881252 CTACCCCGGAATTCGTGCG 60.881 63.158 0.73 0.00 41.45 5.34
5095 6157 4.822107 CGTAATACGCAGACAAGAAATGG 58.178 43.478 0.00 0.00 33.65 3.16
5114 6176 4.067972 TGGAGTATAAAATCCACCTCGC 57.932 45.455 0.00 0.00 40.70 5.03
5130 6193 2.335011 GCTGGTGGCGGTTTGTTC 59.665 61.111 0.00 0.00 0.00 3.18
5132 6195 2.902846 TGGTGGCGGTTTGTTCGG 60.903 61.111 0.00 0.00 0.00 4.30
5145 6208 1.234821 TGTTCGGCTAGCAAACAAGG 58.765 50.000 24.47 4.34 30.39 3.61
5146 6209 0.109735 GTTCGGCTAGCAAACAAGGC 60.110 55.000 18.24 0.00 35.08 4.35
5159 6225 2.205307 ACAAGGCGCGTACTAGATTC 57.795 50.000 8.43 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.478206 TGCCATGTTTTTCTGGTTGAAA 57.522 36.364 0.00 0.00 42.33 2.69
18 19 4.440880 CTTGCCATGTTTTTCTGGTTGAA 58.559 39.130 0.00 0.00 34.86 2.69
19 20 3.181467 CCTTGCCATGTTTTTCTGGTTGA 60.181 43.478 0.00 0.00 34.86 3.18
20 21 3.132925 CCTTGCCATGTTTTTCTGGTTG 58.867 45.455 0.00 0.00 34.86 3.77
21 22 3.037549 TCCTTGCCATGTTTTTCTGGTT 58.962 40.909 0.00 0.00 34.86 3.67
22 23 2.365293 GTCCTTGCCATGTTTTTCTGGT 59.635 45.455 0.00 0.00 34.86 4.00
23 24 2.607771 CGTCCTTGCCATGTTTTTCTGG 60.608 50.000 0.00 0.00 35.53 3.86
24 25 2.293122 TCGTCCTTGCCATGTTTTTCTG 59.707 45.455 0.00 0.00 0.00 3.02
25 26 2.554032 CTCGTCCTTGCCATGTTTTTCT 59.446 45.455 0.00 0.00 0.00 2.52
26 27 2.351738 CCTCGTCCTTGCCATGTTTTTC 60.352 50.000 0.00 0.00 0.00 2.29
27 28 1.613437 CCTCGTCCTTGCCATGTTTTT 59.387 47.619 0.00 0.00 0.00 1.94
28 29 1.202879 TCCTCGTCCTTGCCATGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
29 30 0.400213 TCCTCGTCCTTGCCATGTTT 59.600 50.000 0.00 0.00 0.00 2.83
30 31 0.321653 GTCCTCGTCCTTGCCATGTT 60.322 55.000 0.00 0.00 0.00 2.71
31 32 1.296715 GTCCTCGTCCTTGCCATGT 59.703 57.895 0.00 0.00 0.00 3.21
32 33 0.321564 TTGTCCTCGTCCTTGCCATG 60.322 55.000 0.00 0.00 0.00 3.66
33 34 0.036010 CTTGTCCTCGTCCTTGCCAT 60.036 55.000 0.00 0.00 0.00 4.40
34 35 1.371183 CTTGTCCTCGTCCTTGCCA 59.629 57.895 0.00 0.00 0.00 4.92
35 36 1.376037 CCTTGTCCTCGTCCTTGCC 60.376 63.158 0.00 0.00 0.00 4.52
36 37 1.376037 CCCTTGTCCTCGTCCTTGC 60.376 63.158 0.00 0.00 0.00 4.01
37 38 1.192146 TCCCCTTGTCCTCGTCCTTG 61.192 60.000 0.00 0.00 0.00 3.61
38 39 1.157751 TCCCCTTGTCCTCGTCCTT 59.842 57.895 0.00 0.00 0.00 3.36
39 40 1.609794 GTCCCCTTGTCCTCGTCCT 60.610 63.158 0.00 0.00 0.00 3.85
40 41 2.657066 GGTCCCCTTGTCCTCGTCC 61.657 68.421 0.00 0.00 0.00 4.79
41 42 1.265454 ATGGTCCCCTTGTCCTCGTC 61.265 60.000 0.00 0.00 0.00 4.20
42 43 1.229529 ATGGTCCCCTTGTCCTCGT 60.230 57.895 0.00 0.00 0.00 4.18
43 44 1.221840 CATGGTCCCCTTGTCCTCG 59.778 63.158 0.00 0.00 0.00 4.63
44 45 1.077429 GCATGGTCCCCTTGTCCTC 60.077 63.158 0.00 0.00 32.20 3.71
45 46 2.971598 CGCATGGTCCCCTTGTCCT 61.972 63.158 0.00 0.00 32.20 3.85
46 47 2.438434 CGCATGGTCCCCTTGTCC 60.438 66.667 0.00 0.00 32.20 4.02
47 48 1.002624 TTCGCATGGTCCCCTTGTC 60.003 57.895 0.00 0.00 32.20 3.18
48 49 1.303317 GTTCGCATGGTCCCCTTGT 60.303 57.895 0.00 0.00 32.20 3.16
49 50 1.303236 TGTTCGCATGGTCCCCTTG 60.303 57.895 0.00 0.00 0.00 3.61
50 51 1.303317 GTGTTCGCATGGTCCCCTT 60.303 57.895 0.00 0.00 0.00 3.95
51 52 2.351276 GTGTTCGCATGGTCCCCT 59.649 61.111 0.00 0.00 0.00 4.79
52 53 2.869503 ATCGTGTTCGCATGGTCCCC 62.870 60.000 0.00 0.00 36.96 4.81
53 54 1.429148 GATCGTGTTCGCATGGTCCC 61.429 60.000 0.00 0.00 38.09 4.46
54 55 0.460284 AGATCGTGTTCGCATGGTCC 60.460 55.000 0.00 0.00 43.51 4.46
55 56 0.647410 CAGATCGTGTTCGCATGGTC 59.353 55.000 0.00 0.00 42.97 4.02
56 57 1.361668 GCAGATCGTGTTCGCATGGT 61.362 55.000 0.00 0.00 36.96 3.55
57 58 1.349627 GCAGATCGTGTTCGCATGG 59.650 57.895 0.00 0.00 36.96 3.66
58 59 0.443478 TTGCAGATCGTGTTCGCATG 59.557 50.000 0.00 0.00 36.96 4.06
59 60 0.443869 GTTGCAGATCGTGTTCGCAT 59.556 50.000 0.00 0.00 36.96 4.73
60 61 1.859398 GTTGCAGATCGTGTTCGCA 59.141 52.632 0.00 0.00 36.96 5.10
61 62 1.225475 CGTTGCAGATCGTGTTCGC 60.225 57.895 0.00 0.00 36.96 4.70
62 63 0.781787 TTCGTTGCAGATCGTGTTCG 59.218 50.000 7.62 0.00 38.55 3.95
63 64 1.462541 GCTTCGTTGCAGATCGTGTTC 60.463 52.381 7.62 0.00 0.00 3.18
64 65 0.512952 GCTTCGTTGCAGATCGTGTT 59.487 50.000 7.62 0.00 0.00 3.32
65 66 0.599991 TGCTTCGTTGCAGATCGTGT 60.600 50.000 7.62 0.00 38.12 4.49
66 67 0.512518 TTGCTTCGTTGCAGATCGTG 59.487 50.000 5.42 4.60 44.27 4.35
67 68 1.225855 TTTGCTTCGTTGCAGATCGT 58.774 45.000 5.42 0.00 44.27 3.73
68 69 2.159667 TCATTTGCTTCGTTGCAGATCG 60.160 45.455 5.72 0.00 44.27 3.69
69 70 3.166657 GTCATTTGCTTCGTTGCAGATC 58.833 45.455 5.72 0.00 44.27 2.75
70 71 2.553602 TGTCATTTGCTTCGTTGCAGAT 59.446 40.909 5.42 4.43 44.27 2.90
71 72 1.946081 TGTCATTTGCTTCGTTGCAGA 59.054 42.857 5.42 2.42 44.27 4.26
72 73 2.404265 TGTCATTTGCTTCGTTGCAG 57.596 45.000 5.42 0.00 44.27 4.41
73 74 3.004629 AGAATGTCATTTGCTTCGTTGCA 59.995 39.130 0.00 1.38 41.65 4.08
74 75 3.362831 CAGAATGTCATTTGCTTCGTTGC 59.637 43.478 0.00 0.00 0.00 4.17
75 76 3.362831 GCAGAATGTCATTTGCTTCGTTG 59.637 43.478 17.96 4.12 39.31 4.10
76 77 3.254166 AGCAGAATGTCATTTGCTTCGTT 59.746 39.130 20.35 7.17 43.91 3.85
77 78 2.816087 AGCAGAATGTCATTTGCTTCGT 59.184 40.909 20.35 7.42 43.91 3.85
78 79 3.168963 CAGCAGAATGTCATTTGCTTCG 58.831 45.455 22.11 13.92 43.91 3.79
79 80 2.921754 GCAGCAGAATGTCATTTGCTTC 59.078 45.455 22.11 17.35 43.91 3.86
80 81 2.297880 TGCAGCAGAATGTCATTTGCTT 59.702 40.909 22.11 11.88 43.91 3.91
82 83 2.357327 TGCAGCAGAATGTCATTTGC 57.643 45.000 17.72 17.72 39.31 3.68
83 84 3.616821 CCAATGCAGCAGAATGTCATTTG 59.383 43.478 0.00 0.00 39.31 2.32
84 85 3.857052 CCAATGCAGCAGAATGTCATTT 58.143 40.909 0.00 0.00 39.31 2.32
85 86 2.418197 GCCAATGCAGCAGAATGTCATT 60.418 45.455 0.00 0.00 36.27 2.57
86 87 1.136305 GCCAATGCAGCAGAATGTCAT 59.864 47.619 0.00 0.00 36.27 3.06
87 88 0.528924 GCCAATGCAGCAGAATGTCA 59.471 50.000 0.00 0.00 36.27 3.58
88 89 0.528924 TGCCAATGCAGCAGAATGTC 59.471 50.000 0.00 0.00 44.23 3.06
89 90 2.661054 TGCCAATGCAGCAGAATGT 58.339 47.368 0.00 0.00 44.23 2.71
99 100 0.033781 AACATGGTGTGTGCCAATGC 59.966 50.000 0.00 0.00 41.14 3.56
100 101 3.243670 TGTTAACATGGTGTGTGCCAATG 60.244 43.478 3.59 0.00 41.14 2.82
101 102 2.961741 TGTTAACATGGTGTGTGCCAAT 59.038 40.909 3.59 0.00 41.14 3.16
181 188 8.109634 GCTCCCCTAATGGAAAAGATGATATTA 58.890 37.037 0.00 0.00 35.39 0.98
182 189 6.950619 GCTCCCCTAATGGAAAAGATGATATT 59.049 38.462 0.00 0.00 35.39 1.28
183 190 6.276568 AGCTCCCCTAATGGAAAAGATGATAT 59.723 38.462 0.00 0.00 35.39 1.63
184 191 5.612688 AGCTCCCCTAATGGAAAAGATGATA 59.387 40.000 0.00 0.00 35.39 2.15
185 192 4.418190 AGCTCCCCTAATGGAAAAGATGAT 59.582 41.667 0.00 0.00 35.39 2.45
189 196 4.079958 GGTTAGCTCCCCTAATGGAAAAGA 60.080 45.833 0.00 0.00 38.25 2.52
196 203 2.224402 GCTGAGGTTAGCTCCCCTAATG 60.224 54.545 9.04 0.40 40.52 1.90
197 204 2.050918 GCTGAGGTTAGCTCCCCTAAT 58.949 52.381 9.04 0.00 40.52 1.73
211 218 1.079266 GGTGTGAGCAGAGCTGAGG 60.079 63.158 0.85 0.00 39.88 3.86
223 230 1.561769 ATTGGATGAGGCCGGTGTGA 61.562 55.000 1.90 0.00 0.00 3.58
224 231 0.680921 AATTGGATGAGGCCGGTGTG 60.681 55.000 1.90 0.00 0.00 3.82
229 236 0.748005 ACGGAAATTGGATGAGGCCG 60.748 55.000 0.00 0.00 42.64 6.13
234 241 7.170828 CGAAATATCTACACGGAAATTGGATGA 59.829 37.037 0.00 0.00 0.00 2.92
369 376 3.792047 TGCAAGATCGCGCTGCAC 61.792 61.111 16.25 0.24 33.35 4.57
374 381 3.168271 TCTTGTGCAAGATCGCGC 58.832 55.556 10.26 0.00 42.06 6.86
419 443 4.693095 GGCCTAGCAGCTATAGTCATTTTC 59.307 45.833 1.54 0.00 0.00 2.29
463 492 2.194271 GTGTATTCTAGTGCGGAGTGC 58.806 52.381 0.00 0.00 46.70 4.40
466 495 3.130516 TGAAGGTGTATTCTAGTGCGGAG 59.869 47.826 0.00 0.00 0.00 4.63
470 499 5.073311 TGTCTGAAGGTGTATTCTAGTGC 57.927 43.478 0.00 0.00 0.00 4.40
471 500 7.962964 TTTTGTCTGAAGGTGTATTCTAGTG 57.037 36.000 0.00 0.00 0.00 2.74
472 501 7.170998 CGTTTTTGTCTGAAGGTGTATTCTAGT 59.829 37.037 0.00 0.00 0.00 2.57
474 503 6.987992 ACGTTTTTGTCTGAAGGTGTATTCTA 59.012 34.615 0.00 0.00 0.00 2.10
475 504 5.820947 ACGTTTTTGTCTGAAGGTGTATTCT 59.179 36.000 0.00 0.00 0.00 2.40
477 506 5.277154 CGACGTTTTTGTCTGAAGGTGTATT 60.277 40.000 0.00 0.00 36.71 1.89
478 507 4.210537 CGACGTTTTTGTCTGAAGGTGTAT 59.789 41.667 0.00 0.00 36.71 2.29
479 508 3.552699 CGACGTTTTTGTCTGAAGGTGTA 59.447 43.478 0.00 0.00 36.71 2.90
480 509 2.350498 CGACGTTTTTGTCTGAAGGTGT 59.650 45.455 0.00 0.00 36.71 4.16
482 511 2.606272 GTCGACGTTTTTGTCTGAAGGT 59.394 45.455 0.00 0.00 36.71 3.50
489 531 1.566077 CCCCGTCGACGTTTTTGTC 59.434 57.895 33.49 0.00 37.74 3.18
506 548 1.739466 TGATTTGATCTCACTTGCGCC 59.261 47.619 4.18 0.00 0.00 6.53
509 551 6.541641 AGGATTACTGATTTGATCTCACTTGC 59.458 38.462 0.00 0.00 0.00 4.01
527 576 4.031426 CGTACGCTTTTCTCACAGGATTAC 59.969 45.833 0.52 0.00 0.00 1.89
539 588 0.024619 GGTGATCGCGTACGCTTTTC 59.975 55.000 34.69 26.52 39.84 2.29
593 650 1.261089 CTACTCTCTAGCACCGTACGC 59.739 57.143 10.49 0.00 0.00 4.42
599 656 3.568007 CCACATCTCTACTCTCTAGCACC 59.432 52.174 0.00 0.00 0.00 5.01
607 664 3.904717 CCTACCACCACATCTCTACTCT 58.095 50.000 0.00 0.00 0.00 3.24
611 668 2.388735 CAGCCTACCACCACATCTCTA 58.611 52.381 0.00 0.00 0.00 2.43
616 673 0.909623 GTACCAGCCTACCACCACAT 59.090 55.000 0.00 0.00 0.00 3.21
617 674 1.196104 GGTACCAGCCTACCACCACA 61.196 60.000 7.15 0.00 36.84 4.17
619 676 1.985662 CGGTACCAGCCTACCACCA 60.986 63.158 13.54 0.00 36.67 4.17
621 678 1.217244 CACGGTACCAGCCTACCAC 59.783 63.158 13.54 0.00 36.67 4.16
628 694 4.394712 AGCCAGCACGGTACCAGC 62.395 66.667 13.54 15.21 36.97 4.85
753 821 3.934391 GACGTGACTTGGGGAGGCG 62.934 68.421 0.00 0.00 35.50 5.52
778 851 2.257067 GAGCGATAGGAGCGAGCC 59.743 66.667 0.00 0.00 40.04 4.70
779 852 2.257067 GGAGCGATAGGAGCGAGC 59.743 66.667 0.00 0.00 40.04 5.03
780 853 1.175983 AAGGGAGCGATAGGAGCGAG 61.176 60.000 0.00 0.00 40.04 5.03
781 854 1.152735 AAGGGAGCGATAGGAGCGA 60.153 57.895 0.00 0.00 40.04 4.93
782 855 1.175983 AGAAGGGAGCGATAGGAGCG 61.176 60.000 0.00 0.00 40.04 5.03
792 865 1.807814 TATTGGAGGGAGAAGGGAGC 58.192 55.000 0.00 0.00 0.00 4.70
817 890 3.013219 GGGAGAAGTGAATGAAGGAAGC 58.987 50.000 0.00 0.00 0.00 3.86
818 891 3.265791 CGGGAGAAGTGAATGAAGGAAG 58.734 50.000 0.00 0.00 0.00 3.46
820 893 2.233922 GACGGGAGAAGTGAATGAAGGA 59.766 50.000 0.00 0.00 0.00 3.36
823 896 2.233922 GAGGACGGGAGAAGTGAATGAA 59.766 50.000 0.00 0.00 0.00 2.57
824 897 1.825474 GAGGACGGGAGAAGTGAATGA 59.175 52.381 0.00 0.00 0.00 2.57
825 898 1.134670 GGAGGACGGGAGAAGTGAATG 60.135 57.143 0.00 0.00 0.00 2.67
826 899 1.196012 GGAGGACGGGAGAAGTGAAT 58.804 55.000 0.00 0.00 0.00 2.57
903 977 4.888325 ATGGAGGGGGAGGCGGAG 62.888 72.222 0.00 0.00 0.00 4.63
1517 1597 0.829333 ATGCAGGTGAGTAGAGCTGG 59.171 55.000 0.00 0.00 41.01 4.85
1558 1647 0.106268 TCAACAGGCAAGAGGGCAAA 60.106 50.000 0.00 0.00 46.44 3.68
1559 1648 0.112995 ATCAACAGGCAAGAGGGCAA 59.887 50.000 0.00 0.00 46.44 4.52
1608 1697 6.120220 TCATTCATCAATGAGCAGATCAACT 58.880 36.000 0.00 0.00 42.99 3.16
1691 1782 8.649973 AATTATAGAAACTGGCTCTTAACTCG 57.350 34.615 0.00 0.00 0.00 4.18
1738 1829 3.247442 TGACCGTATTTGTTACAGCTCG 58.753 45.455 0.00 0.00 0.00 5.03
1816 1907 3.617263 GTCGTAGAAAACTAGTGCCATGG 59.383 47.826 7.63 7.63 39.69 3.66
1947 2038 9.665264 GTTTGAGTCAATTTTACAAACTAGAGG 57.335 33.333 6.36 0.00 43.51 3.69
1961 2052 3.554934 TGTCAGCTGGTTTGAGTCAATT 58.445 40.909 15.13 0.00 0.00 2.32
1971 2066 0.550914 TTGGGACTTGTCAGCTGGTT 59.449 50.000 15.13 0.00 0.00 3.67
1973 2068 0.890996 GGTTGGGACTTGTCAGCTGG 60.891 60.000 15.13 0.00 0.00 4.85
1979 2074 1.226746 CGACTTGGTTGGGACTTGTC 58.773 55.000 0.00 0.00 0.00 3.18
1998 2093 4.274950 TCGCATTATAGTTTGCTTAAGCCC 59.725 41.667 24.30 12.22 41.18 5.19
2058 2153 6.862090 CCAATCAAAGTAGTAGTACGATAGCC 59.138 42.308 2.04 0.00 42.67 3.93
2066 2161 8.644216 TGTTCAAGTCCAATCAAAGTAGTAGTA 58.356 33.333 0.00 0.00 0.00 1.82
2067 2162 7.506114 TGTTCAAGTCCAATCAAAGTAGTAGT 58.494 34.615 0.00 0.00 0.00 2.73
2068 2163 7.118390 CCTGTTCAAGTCCAATCAAAGTAGTAG 59.882 40.741 0.00 0.00 0.00 2.57
2105 2200 2.224769 GGTTCAAGATGTTCCACAGGGA 60.225 50.000 0.00 0.00 43.03 4.20
2110 2205 7.926018 ACTTTATTTTGGTTCAAGATGTTCCAC 59.074 33.333 0.00 0.00 0.00 4.02
2114 2209 7.768120 TGCAACTTTATTTTGGTTCAAGATGTT 59.232 29.630 0.00 0.00 0.00 2.71
2119 2216 7.538303 ACTTGCAACTTTATTTTGGTTCAAG 57.462 32.000 0.00 0.00 36.06 3.02
2134 2231 2.825532 ACAGAAACACCAACTTGCAACT 59.174 40.909 0.00 0.00 0.00 3.16
2215 2313 4.015084 AGGACCAAGATGATGCTTGAAAG 58.985 43.478 5.74 0.00 46.31 2.62
2220 2318 2.579860 AGGAAGGACCAAGATGATGCTT 59.420 45.455 0.00 0.00 42.04 3.91
2232 2330 5.509163 GCCAAAAGAGTAAAAAGGAAGGACC 60.509 44.000 0.00 0.00 39.35 4.46
2417 2515 8.773404 TTTTAACTAAAGCACTACAGATCCTC 57.227 34.615 0.00 0.00 0.00 3.71
2437 2535 5.335583 GGAGCACACTGTACATGCATTTTAA 60.336 40.000 19.26 0.00 41.97 1.52
2505 2604 6.369615 GCCATTGCAGTCAAGTCAATTTTATT 59.630 34.615 0.00 0.00 35.37 1.40
2506 2605 5.870978 GCCATTGCAGTCAAGTCAATTTTAT 59.129 36.000 0.00 0.00 35.37 1.40
2507 2606 5.010922 AGCCATTGCAGTCAAGTCAATTTTA 59.989 36.000 0.00 0.00 41.13 1.52
2512 2611 1.610038 CAGCCATTGCAGTCAAGTCAA 59.390 47.619 0.00 0.00 41.13 3.18
2523 2622 2.180017 CAGCGGAACAGCCATTGC 59.820 61.111 0.00 0.00 38.01 3.56
2832 2932 2.224843 ACCACCTTCATCAGCAATCACA 60.225 45.455 0.00 0.00 0.00 3.58
2839 2939 1.747355 CCATTCACCACCTTCATCAGC 59.253 52.381 0.00 0.00 0.00 4.26
3174 3274 8.474025 TCCAGTTTCTTTAATGAAGCAGAAAAA 58.526 29.630 16.61 0.00 37.08 1.94
3321 3423 9.074576 TCTACTGTCAGTAAAAATGAGAGTACA 57.925 33.333 13.63 0.00 46.15 2.90
3398 3500 3.354948 AGCTTCTTGCATGTATCACCA 57.645 42.857 0.00 0.00 45.94 4.17
3401 3503 4.385358 TCGTAGCTTCTTGCATGTATCA 57.615 40.909 0.00 0.00 45.94 2.15
3461 3563 1.627834 ACTCCTCCTTGCTCTTCTTGG 59.372 52.381 0.00 0.00 0.00 3.61
3809 3911 2.098233 CAACCCGTGGTCCGATTCG 61.098 63.158 0.00 0.00 39.56 3.34
3836 3938 0.381801 GGTTGGTGCATCCTATTGCG 59.618 55.000 0.00 0.00 45.77 4.85
4115 4217 4.463879 CAGTCCTGCCTCTGCCCG 62.464 72.222 0.00 0.00 36.33 6.13
4163 4265 9.750882 CTAGATGTATTTACAATCATTCATGCG 57.249 33.333 0.00 0.00 39.99 4.73
4204 4316 4.755266 AGGGCAACATAAGGTACAGTAG 57.245 45.455 0.00 0.00 39.74 2.57
4209 4321 2.291346 ACCCAAGGGCAACATAAGGTAC 60.291 50.000 4.70 0.00 34.48 3.34
4214 4326 0.040499 GGGACCCAAGGGCAACATAA 59.960 55.000 5.33 0.00 39.32 1.90
4218 4330 1.152333 AAAGGGACCCAAGGGCAAC 60.152 57.895 14.60 0.00 39.32 4.17
4220 4332 2.525592 CAAAGGGACCCAAGGGCA 59.474 61.111 14.60 0.00 39.32 5.36
4221 4333 2.283894 CCAAAGGGACCCAAGGGC 60.284 66.667 14.60 0.00 39.32 5.19
4226 4338 0.469144 GTTCTTGCCAAAGGGACCCA 60.469 55.000 14.60 0.00 35.59 4.51
4245 4357 6.317789 ACAAATTGCCATATTCAGATACGG 57.682 37.500 0.00 0.00 0.00 4.02
4340 4463 1.069500 GCGACAACGGCAACTTATTGT 60.069 47.619 0.00 0.00 37.80 2.71
4456 4591 6.296026 AGTACAATGTGGTTTTAAGCAGAGA 58.704 36.000 0.00 0.00 37.04 3.10
4474 4609 8.610896 CATTGCAAAAGGAAAATTTGAGTACAA 58.389 29.630 1.71 0.00 39.56 2.41
4576 5089 5.394224 AAAAGTTGGACGTGAAGGAAAAA 57.606 34.783 0.00 0.00 0.00 1.94
4608 5145 9.817365 CTTTAAATATGCATCAATCCTAAGTCG 57.183 33.333 0.19 0.00 0.00 4.18
4689 5509 2.736670 AAGCCCAGGATCATACCAAC 57.263 50.000 0.00 0.00 0.00 3.77
4701 5521 2.519013 AGCCTTCAAGTTTAAGCCCAG 58.481 47.619 0.00 0.00 0.00 4.45
4704 5524 4.058124 CCAAAAGCCTTCAAGTTTAAGCC 58.942 43.478 0.00 0.00 0.00 4.35
4705 5525 3.494626 GCCAAAAGCCTTCAAGTTTAAGC 59.505 43.478 0.00 0.00 34.35 3.09
4714 5534 2.014010 ATCCAAGCCAAAAGCCTTCA 57.986 45.000 0.00 0.00 45.47 3.02
4728 5549 9.585099 GAAGCATGAATTTAACATTGTATCCAA 57.415 29.630 0.00 0.00 34.45 3.53
4730 5551 9.585099 TTGAAGCATGAATTTAACATTGTATCC 57.415 29.630 0.00 0.00 0.00 2.59
4780 5601 1.893919 GCTCCTGGCCGACTCTCTTT 61.894 60.000 0.00 0.00 34.27 2.52
4879 5940 2.055100 GACACTTTGACGACTCTGAGC 58.945 52.381 4.19 0.00 0.00 4.26
4884 5945 1.053811 GAGCGACACTTTGACGACTC 58.946 55.000 2.28 4.95 37.72 3.36
4890 5951 2.342279 CGGGGAGCGACACTTTGA 59.658 61.111 0.00 0.00 0.00 2.69
4903 5964 2.110352 AAAATACGGAAGCGCGGGG 61.110 57.895 8.83 0.00 0.00 5.73
4904 5965 1.061887 CAAAATACGGAAGCGCGGG 59.938 57.895 8.83 0.00 0.00 6.13
4907 5968 3.962399 CGCAAAATACGGAAGCGC 58.038 55.556 0.00 0.00 41.95 5.92
4914 5975 1.003545 CATCCAGCTCCGCAAAATACG 60.004 52.381 0.00 0.00 0.00 3.06
4925 5986 1.602311 ATTCGGCAATCATCCAGCTC 58.398 50.000 0.00 0.00 0.00 4.09
4948 6009 5.697067 AGGAGAGGCCCGTATAATATAGAG 58.303 45.833 0.00 0.00 37.37 2.43
4980 6042 2.711924 GCCGGGACTACGTACTCG 59.288 66.667 2.18 0.00 43.34 4.18
5030 6092 4.770874 CCGCACGAATTCCGGGGT 62.771 66.667 12.31 0.00 43.17 4.95
5089 6151 6.293462 GCGAGGTGGATTTTATACTCCATTTC 60.293 42.308 0.00 0.00 43.20 2.17
5095 6157 4.058817 CCAGCGAGGTGGATTTTATACTC 58.941 47.826 15.61 0.00 40.44 2.59
5114 6176 2.637025 CGAACAAACCGCCACCAG 59.363 61.111 0.00 0.00 0.00 4.00
5120 6183 1.847890 TTGCTAGCCGAACAAACCGC 61.848 55.000 13.29 0.00 0.00 5.68
5121 6184 0.589223 TTTGCTAGCCGAACAAACCG 59.411 50.000 13.29 0.00 0.00 4.44
5130 6193 2.480555 CGCCTTGTTTGCTAGCCG 59.519 61.111 13.29 1.45 0.00 5.52
5132 6195 1.632046 TACGCGCCTTGTTTGCTAGC 61.632 55.000 5.73 8.10 0.00 3.42
5145 6208 0.997726 GCCTCGAATCTAGTACGCGC 60.998 60.000 5.73 0.00 0.00 6.86
5146 6209 0.385723 GGCCTCGAATCTAGTACGCG 60.386 60.000 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.