Multiple sequence alignment - TraesCS7A01G009200

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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 TraesCS7A01G009200 chr7A 100.000 4654 0 0 1 4654 4018160 4013507 0.000000e+00 8595.0
1 TraesCS7A01G009200 chr7A 89.085 1191 96 16 1678 2841 29784804 29785987 0.000000e+00 1448.0
2 TraesCS7A01G009200 chr7A 89.952 1045 86 12 2935 3970 29786037 29787071 0.000000e+00 1330.0
3 TraesCS7A01G009200 chr7A 85.586 888 115 9 2934 3817 3983867 3982989 0.000000e+00 918.0
4 TraesCS7A01G009200 chr7A 85.327 886 126 3 1909 2790 3985840 3984955 0.000000e+00 913.0
5 TraesCS7A01G009200 chr7A 81.851 821 71 34 818 1601 29783970 29784749 1.840000e-173 619.0
6 TraesCS7A01G009200 chr7A 75.862 667 151 9 2944 3605 4430764 4430103 9.650000e-87 331.0
7 TraesCS7A01G009200 chr7A 77.291 502 112 2 1907 2407 4254334 4253834 1.270000e-75 294.0
8 TraesCS7A01G009200 chr7A 83.758 314 28 10 1240 1538 3986285 3985980 4.590000e-70 276.0
9 TraesCS7A01G009200 chr7A 81.461 356 48 10 891 1236 3986666 3986319 4.590000e-70 276.0
10 TraesCS7A01G009200 chr7A 96.341 82 3 0 1289 1370 29665083 29665002 8.120000e-28 135.0
11 TraesCS7A01G009200 chr7A 88.073 109 12 1 4194 4301 29787776 29787884 1.360000e-25 128.0
12 TraesCS7A01G009200 chr7A 80.357 168 26 4 3808 3972 3982960 3982797 2.270000e-23 121.0
13 TraesCS7A01G009200 chr7D 90.872 3637 216 52 731 4323 4270913 4267349 0.000000e+00 4771.0
14 TraesCS7A01G009200 chr7D 89.848 1182 87 15 1687 2841 29550728 29551903 0.000000e+00 1487.0
15 TraesCS7A01G009200 chr7D 91.390 964 73 6 2935 3898 29551939 29552892 0.000000e+00 1312.0
16 TraesCS7A01G009200 chr7D 86.020 887 121 2 1907 2790 4201392 4200506 0.000000e+00 948.0
17 TraesCS7A01G009200 chr7D 85.795 887 115 7 2934 3817 4199504 4198626 0.000000e+00 929.0
18 TraesCS7A01G009200 chr7D 82.095 821 69 35 818 1601 29549888 29550667 8.500000e-177 630.0
19 TraesCS7A01G009200 chr7D 89.504 343 30 4 271 612 4271303 4270966 3.330000e-116 429.0
20 TraesCS7A01G009200 chr7D 78.775 702 78 38 891 1538 4202212 4201528 5.610000e-109 405.0
21 TraesCS7A01G009200 chr7D 76.248 661 147 8 2947 3605 29403471 29402819 4.460000e-90 342.0
22 TraesCS7A01G009200 chr7D 84.776 335 48 3 177 510 29537522 29537854 2.680000e-87 333.0
23 TraesCS7A01G009200 chr7D 88.571 245 18 4 4396 4640 4267328 4267094 5.890000e-74 289.0
24 TraesCS7A01G009200 chr7D 78.541 233 36 7 387 618 4202813 4202594 1.750000e-29 141.0
25 TraesCS7A01G009200 chr7D 89.908 109 10 1 4194 4301 29554168 29554276 6.280000e-29 139.0
26 TraesCS7A01G009200 chr7D 79.762 168 27 4 3808 3972 4198597 4198434 1.060000e-21 115.0
27 TraesCS7A01G009200 chr4A 92.300 1052 70 8 2936 3986 739312943 739313984 0.000000e+00 1483.0
28 TraesCS7A01G009200 chr4A 93.028 1004 64 6 1837 2838 739311248 739312247 0.000000e+00 1461.0
29 TraesCS7A01G009200 chr4A 87.117 947 71 25 813 1725 739310135 739311064 0.000000e+00 1026.0
30 TraesCS7A01G009200 chr4A 86.133 887 119 3 1908 2790 739416105 739416991 0.000000e+00 953.0
31 TraesCS7A01G009200 chr4A 85.698 888 114 8 2934 3817 739418007 739418885 0.000000e+00 924.0
32 TraesCS7A01G009200 chr4A 79.886 701 77 37 891 1534 739415303 739415996 5.490000e-124 455.0
33 TraesCS7A01G009200 chr4A 86.520 408 51 3 167 573 739309298 739309702 3.300000e-121 446.0
34 TraesCS7A01G009200 chr4A 76.818 660 145 6 2947 3605 739131522 739132174 9.520000e-97 364.0
35 TraesCS7A01G009200 chr4A 76.289 679 149 11 2944 3616 739067388 739068060 7.410000e-93 351.0
36 TraesCS7A01G009200 chr4A 78.770 504 103 4 1907 2408 739130019 739130520 7.460000e-88 335.0
37 TraesCS7A01G009200 chr4A 90.991 111 10 0 567 677 739309940 739310050 2.900000e-32 150.0
38 TraesCS7A01G009200 chr4A 96.341 82 3 0 1289 1370 739129611 739129692 8.120000e-28 135.0
39 TraesCS7A01G009200 chr4A 80.337 178 26 6 3799 3972 739418905 739419077 4.890000e-25 126.0
40 TraesCS7A01G009200 chr4A 86.607 112 11 3 4194 4302 739314173 739314283 2.270000e-23 121.0
41 TraesCS7A01G009200 chr4A 81.667 120 15 3 4210 4326 739445929 739445814 4.960000e-15 93.5
42 TraesCS7A01G009200 chr1D 90.000 70 7 0 6 75 318585853 318585922 1.780000e-14 91.6
43 TraesCS7A01G009200 chr1D 88.000 75 9 0 5 79 47945225 47945299 6.410000e-14 89.8
44 TraesCS7A01G009200 chr2D 83.544 79 10 2 4 79 603991720 603991798 2.320000e-08 71.3
45 TraesCS7A01G009200 chr5D 96.970 33 0 1 5 37 59911222 59911191 2.000000e-03 54.7


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 TraesCS7A01G009200 chr7A 4013507 4018160 4653 True 8595.000000 8595 100.000000 1 4654 1 chr7A.!!$R1 4653
1 TraesCS7A01G009200 chr7A 29783970 29787884 3914 False 881.250000 1448 87.240250 818 4301 4 chr7A.!!$F1 3483
2 TraesCS7A01G009200 chr7A 3982797 3986666 3869 True 500.800000 918 83.297800 891 3972 5 chr7A.!!$R5 3081
3 TraesCS7A01G009200 chr7A 4430103 4430764 661 True 331.000000 331 75.862000 2944 3605 1 chr7A.!!$R3 661
4 TraesCS7A01G009200 chr7A 4253834 4254334 500 True 294.000000 294 77.291000 1907 2407 1 chr7A.!!$R2 500
5 TraesCS7A01G009200 chr7D 4267094 4271303 4209 True 1829.666667 4771 89.649000 271 4640 3 chr7D.!!$R3 4369
6 TraesCS7A01G009200 chr7D 29549888 29554276 4388 False 892.000000 1487 88.310250 818 4301 4 chr7D.!!$F2 3483
7 TraesCS7A01G009200 chr7D 4198434 4202813 4379 True 507.600000 948 81.778600 387 3972 5 chr7D.!!$R2 3585
8 TraesCS7A01G009200 chr7D 29402819 29403471 652 True 342.000000 342 76.248000 2947 3605 1 chr7D.!!$R1 658
9 TraesCS7A01G009200 chr4A 739309298 739314283 4985 False 781.166667 1483 89.427167 167 4302 6 chr4A.!!$F3 4135
10 TraesCS7A01G009200 chr4A 739415303 739419077 3774 False 614.500000 953 83.013500 891 3972 4 chr4A.!!$F4 3081
11 TraesCS7A01G009200 chr4A 739067388 739068060 672 False 351.000000 351 76.289000 2944 3616 1 chr4A.!!$F1 672
12 TraesCS7A01G009200 chr4A 739129611 739132174 2563 False 278.000000 364 83.976333 1289 3605 3 chr4A.!!$F2 2316

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
49 50 0.035630 GCTGAGGATGCCAGTGTTCT 60.036 55.000 5.00 0.0 34.29 3.01 F
290 291 1.270358 GCTATCGTCCACCCATTCTCC 60.270 57.143 0.00 0.0 0.00 3.71 F
1449 1980 1.161843 CCGGCGTGGTTACTTTGATT 58.838 50.000 6.01 0.0 0.00 2.57 F
2925 3744 0.248949 GCACTATTCCGACTCCCGAC 60.249 60.000 0.00 0.0 41.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1980 1.540363 GGCAACGAGGTCAGTTTCTGA 60.540 52.381 0.00 0.0 38.25 3.27 R
1881 2601 3.059733 GCACAATGCATTTCAGCGAAAAA 60.060 39.130 9.83 0.0 44.26 1.94 R
2930 3749 0.101040 GCATGCACAACACACACACT 59.899 50.000 14.21 0.0 0.00 3.55 R
4612 7773 0.177836 TATGGCATCCAGTGACCACG 59.822 55.000 1.65 0.0 36.75 4.94 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
22 23 4.327680 AGATGAGCACCAGAACTTAAACC 58.672 43.478 0.00 0.00 0.00 3.27
23 24 2.858745 TGAGCACCAGAACTTAAACCC 58.141 47.619 0.00 0.00 0.00 4.11
24 25 2.441750 TGAGCACCAGAACTTAAACCCT 59.558 45.455 0.00 0.00 0.00 4.34
25 26 2.814336 GAGCACCAGAACTTAAACCCTG 59.186 50.000 0.00 0.00 0.00 4.45
29 30 2.514803 CCAGAACTTAAACCCTGGTGG 58.485 52.381 0.00 0.00 40.84 4.61
39 40 2.593978 CCTGGTGGGCTGAGGATG 59.406 66.667 0.00 0.00 0.00 3.51
40 41 2.124403 CTGGTGGGCTGAGGATGC 60.124 66.667 0.00 0.00 0.00 3.91
47 48 4.730487 GCTGAGGATGCCAGTGTT 57.270 55.556 5.00 0.00 34.29 3.32
48 49 2.475666 GCTGAGGATGCCAGTGTTC 58.524 57.895 5.00 0.00 34.29 3.18
49 50 0.035630 GCTGAGGATGCCAGTGTTCT 60.036 55.000 5.00 0.00 34.29 3.01
50 51 1.612726 GCTGAGGATGCCAGTGTTCTT 60.613 52.381 5.00 0.00 34.29 2.52
51 52 2.787994 CTGAGGATGCCAGTGTTCTTT 58.212 47.619 0.00 0.00 0.00 2.52
52 53 3.152341 CTGAGGATGCCAGTGTTCTTTT 58.848 45.455 0.00 0.00 0.00 2.27
53 54 4.326826 CTGAGGATGCCAGTGTTCTTTTA 58.673 43.478 0.00 0.00 0.00 1.52
54 55 4.724399 TGAGGATGCCAGTGTTCTTTTAA 58.276 39.130 0.00 0.00 0.00 1.52
55 56 4.518970 TGAGGATGCCAGTGTTCTTTTAAC 59.481 41.667 0.00 0.00 0.00 2.01
56 57 3.826729 AGGATGCCAGTGTTCTTTTAACC 59.173 43.478 0.00 0.00 0.00 2.85
57 58 3.572255 GGATGCCAGTGTTCTTTTAACCA 59.428 43.478 0.00 0.00 0.00 3.67
58 59 4.220602 GGATGCCAGTGTTCTTTTAACCAT 59.779 41.667 0.00 0.00 0.00 3.55
59 60 4.846779 TGCCAGTGTTCTTTTAACCATC 57.153 40.909 0.00 0.00 0.00 3.51
60 61 3.572255 TGCCAGTGTTCTTTTAACCATCC 59.428 43.478 0.00 0.00 0.00 3.51
61 62 3.572255 GCCAGTGTTCTTTTAACCATCCA 59.428 43.478 0.00 0.00 0.00 3.41
62 63 4.038642 GCCAGTGTTCTTTTAACCATCCAA 59.961 41.667 0.00 0.00 0.00 3.53
63 64 5.528870 CCAGTGTTCTTTTAACCATCCAAC 58.471 41.667 0.00 0.00 0.00 3.77
64 65 5.508994 CCAGTGTTCTTTTAACCATCCAACC 60.509 44.000 0.00 0.00 0.00 3.77
65 66 5.068460 CAGTGTTCTTTTAACCATCCAACCA 59.932 40.000 0.00 0.00 0.00 3.67
66 67 5.068591 AGTGTTCTTTTAACCATCCAACCAC 59.931 40.000 0.00 0.00 0.00 4.16
67 68 4.956700 TGTTCTTTTAACCATCCAACCACA 59.043 37.500 0.00 0.00 0.00 4.17
68 69 5.600484 TGTTCTTTTAACCATCCAACCACAT 59.400 36.000 0.00 0.00 0.00 3.21
69 70 5.720371 TCTTTTAACCATCCAACCACATG 57.280 39.130 0.00 0.00 0.00 3.21
70 71 5.144100 TCTTTTAACCATCCAACCACATGT 58.856 37.500 0.00 0.00 0.00 3.21
71 72 5.600484 TCTTTTAACCATCCAACCACATGTT 59.400 36.000 0.00 0.00 37.80 2.71
80 81 4.079446 CCACATGTTGGTCCGCTT 57.921 55.556 0.00 0.00 41.10 4.68
81 82 3.241493 CCACATGTTGGTCCGCTTA 57.759 52.632 0.00 0.00 41.10 3.09
82 83 1.750193 CCACATGTTGGTCCGCTTAT 58.250 50.000 0.00 0.00 41.10 1.73
83 84 2.912771 CCACATGTTGGTCCGCTTATA 58.087 47.619 0.00 0.00 41.10 0.98
84 85 3.476552 CCACATGTTGGTCCGCTTATAT 58.523 45.455 0.00 0.00 41.10 0.86
85 86 3.250762 CCACATGTTGGTCCGCTTATATG 59.749 47.826 0.00 0.00 41.10 1.78
86 87 3.250762 CACATGTTGGTCCGCTTATATGG 59.749 47.826 0.00 0.00 0.00 2.74
87 88 3.118038 ACATGTTGGTCCGCTTATATGGT 60.118 43.478 0.00 0.00 0.00 3.55
88 89 2.912771 TGTTGGTCCGCTTATATGGTG 58.087 47.619 0.00 0.00 0.00 4.17
89 90 2.237643 TGTTGGTCCGCTTATATGGTGT 59.762 45.455 0.00 0.00 0.00 4.16
90 91 3.275999 GTTGGTCCGCTTATATGGTGTT 58.724 45.455 0.00 0.00 0.00 3.32
91 92 3.637911 TGGTCCGCTTATATGGTGTTT 57.362 42.857 0.00 0.00 0.00 2.83
92 93 3.958018 TGGTCCGCTTATATGGTGTTTT 58.042 40.909 0.00 0.00 0.00 2.43
93 94 4.337145 TGGTCCGCTTATATGGTGTTTTT 58.663 39.130 0.00 0.00 0.00 1.94
189 190 7.014326 GGGATGAAACTAAAACTGGAAGACTTT 59.986 37.037 0.00 0.00 37.43 2.66
198 199 9.937175 CTAAAACTGGAAGACTTTGTAGAAAAG 57.063 33.333 0.00 0.00 37.43 2.27
200 201 8.575649 AAACTGGAAGACTTTGTAGAAAAGAA 57.424 30.769 4.91 0.00 37.43 2.52
201 202 8.575649 AACTGGAAGACTTTGTAGAAAAGAAA 57.424 30.769 4.91 0.00 37.43 2.52
228 229 7.706607 TCAATGTACTTGATCATAACCTCTTCG 59.293 37.037 0.00 0.00 38.97 3.79
235 236 7.607991 ACTTGATCATAACCTCTTCGACAAAAT 59.392 33.333 0.00 0.00 0.00 1.82
236 237 7.539712 TGATCATAACCTCTTCGACAAAATC 57.460 36.000 0.00 0.00 0.00 2.17
242 243 8.883731 CATAACCTCTTCGACAAAATCTTATGT 58.116 33.333 0.00 0.00 0.00 2.29
290 291 1.270358 GCTATCGTCCACCCATTCTCC 60.270 57.143 0.00 0.00 0.00 3.71
337 338 1.732259 GGATTGTCCAGCACTACAACG 59.268 52.381 0.60 0.00 38.35 4.10
366 367 2.435059 GACGGGCCAACAGAGAGC 60.435 66.667 4.39 0.00 0.00 4.09
369 370 2.743928 GGGCCAACAGAGAGCACG 60.744 66.667 4.39 0.00 0.00 5.34
372 373 1.364626 GGCCAACAGAGAGCACGATG 61.365 60.000 0.00 0.00 0.00 3.84
457 458 6.103997 TCTTAACAAACTCGGCGATAATCTT 58.896 36.000 11.27 2.24 0.00 2.40
466 467 2.639065 GGCGATAATCTTTGGGACACA 58.361 47.619 0.00 0.00 39.29 3.72
473 474 6.457392 CGATAATCTTTGGGACACACAATCTG 60.457 42.308 0.00 0.00 39.29 2.90
507 508 6.378280 AGGTGAGTTGGCAAATCCTATAAAAG 59.622 38.462 23.17 0.00 35.26 2.27
565 566 6.713792 AAAGAAATGCTCTAGAAAGTCGTC 57.286 37.500 0.00 0.00 32.46 4.20
572 818 6.228273 TGCTCTAGAAAGTCGTCATTTTTG 57.772 37.500 0.00 0.00 0.00 2.44
605 851 4.959723 ACTTGCTTTTTAACACATGGCAT 58.040 34.783 0.00 0.00 0.00 4.40
618 864 5.296748 ACACATGGCATAAAAGTTGGTTTC 58.703 37.500 0.00 0.00 0.00 2.78
629 875 5.755409 AAAGTTGGTTTCTTTCCTTGGTT 57.245 34.783 0.00 0.00 30.57 3.67
632 878 4.161565 AGTTGGTTTCTTTCCTTGGTTTCC 59.838 41.667 0.00 0.00 0.00 3.13
659 997 5.416952 CCTTGACTAAAAGCCAATGTGATCT 59.583 40.000 0.00 0.00 0.00 2.75
685 1023 5.787062 GCCGTCGTCTTGTTTCTAAATTTAC 59.213 40.000 0.00 0.00 0.00 2.01
708 1046 7.044589 ACTTTTTCAGTTTTGTTAAAGCACG 57.955 32.000 0.00 0.00 33.33 5.34
709 1047 6.643360 ACTTTTTCAGTTTTGTTAAAGCACGT 59.357 30.769 0.00 0.00 33.33 4.49
710 1048 6.620253 TTTTCAGTTTTGTTAAAGCACGTC 57.380 33.333 0.00 0.00 0.00 4.34
711 1049 5.554822 TTCAGTTTTGTTAAAGCACGTCT 57.445 34.783 0.00 0.00 0.00 4.18
712 1050 6.665474 TTCAGTTTTGTTAAAGCACGTCTA 57.335 33.333 0.00 0.00 0.00 2.59
713 1051 6.281848 TCAGTTTTGTTAAAGCACGTCTAG 57.718 37.500 0.00 0.00 0.00 2.43
714 1052 6.044046 TCAGTTTTGTTAAAGCACGTCTAGA 58.956 36.000 0.00 0.00 0.00 2.43
715 1053 6.704493 TCAGTTTTGTTAAAGCACGTCTAGAT 59.296 34.615 0.00 0.00 0.00 1.98
716 1054 7.868922 TCAGTTTTGTTAAAGCACGTCTAGATA 59.131 33.333 0.00 0.00 0.00 1.98
717 1055 8.656849 CAGTTTTGTTAAAGCACGTCTAGATAT 58.343 33.333 0.00 0.00 0.00 1.63
718 1056 8.656849 AGTTTTGTTAAAGCACGTCTAGATATG 58.343 33.333 0.00 0.00 0.00 1.78
719 1057 6.583912 TTGTTAAAGCACGTCTAGATATGC 57.416 37.500 18.73 18.73 38.39 3.14
724 1062 4.655762 AGCACGTCTAGATATGCTCAAA 57.344 40.909 21.81 0.00 45.11 2.69
725 1063 4.615949 AGCACGTCTAGATATGCTCAAAG 58.384 43.478 21.81 0.00 45.11 2.77
726 1064 4.098654 AGCACGTCTAGATATGCTCAAAGT 59.901 41.667 21.81 5.55 45.11 2.66
727 1065 5.299531 AGCACGTCTAGATATGCTCAAAGTA 59.700 40.000 21.81 0.00 45.11 2.24
728 1066 6.015856 AGCACGTCTAGATATGCTCAAAGTAT 60.016 38.462 21.81 4.41 45.11 2.12
729 1067 6.642950 GCACGTCTAGATATGCTCAAAGTATT 59.357 38.462 18.97 0.00 35.16 1.89
809 1179 5.169295 ACTAATCTAAGCGTGAGGTGTTTC 58.831 41.667 0.00 0.00 43.76 2.78
810 1180 2.450609 TCTAAGCGTGAGGTGTTTCC 57.549 50.000 0.00 0.00 43.76 3.13
811 1181 1.689813 TCTAAGCGTGAGGTGTTTCCA 59.310 47.619 0.00 0.00 43.76 3.53
867 1293 4.162320 CAGCTATAAACCTCCCTCTTGTCA 59.838 45.833 0.00 0.00 0.00 3.58
870 1296 6.615726 AGCTATAAACCTCCCTCTTGTCATAA 59.384 38.462 0.00 0.00 0.00 1.90
923 1353 2.757077 CTCCCCCACTGAACCCAC 59.243 66.667 0.00 0.00 0.00 4.61
924 1354 2.856988 TCCCCCACTGAACCCACC 60.857 66.667 0.00 0.00 0.00 4.61
925 1355 3.182263 CCCCCACTGAACCCACCA 61.182 66.667 0.00 0.00 0.00 4.17
926 1356 2.547595 CCCCCACTGAACCCACCAT 61.548 63.158 0.00 0.00 0.00 3.55
948 1378 2.052690 CCCATCCGTCGGTGAGAGT 61.053 63.158 11.88 0.00 0.00 3.24
1112 1567 4.222847 GGAGGACCGGCGGATCAC 62.223 72.222 35.78 20.64 0.00 3.06
1245 1742 1.324740 TACCGGCTACAGCGGAACAT 61.325 55.000 0.00 1.42 43.02 2.71
1252 1749 4.465512 CAGCGGAACATGGCGTGC 62.466 66.667 6.62 0.00 0.00 5.34
1261 1758 2.110967 CATGGCGTGCTGGAGAAGG 61.111 63.158 0.00 0.00 0.00 3.46
1449 1980 1.161843 CCGGCGTGGTTACTTTGATT 58.838 50.000 6.01 0.00 0.00 2.57
1480 2033 1.610624 CCTCGTTGCCTTTGCTTCCTA 60.611 52.381 0.00 0.00 38.71 2.94
1725 2343 9.990360 AAATGTTTTACCTCCATACGAAATTTT 57.010 25.926 0.00 0.00 0.00 1.82
1766 2464 2.029918 GCCTCCACAAATGTCCTTTCAC 60.030 50.000 0.00 0.00 0.00 3.18
1769 2467 3.636300 CTCCACAAATGTCCTTTCACCAA 59.364 43.478 0.00 0.00 0.00 3.67
1782 2500 6.019881 GTCCTTTCACCAAGAAATTTTTCACG 60.020 38.462 5.88 0.00 44.75 4.35
1879 2599 7.966812 TGCATATAAGCTCAGGATTAGAAGAA 58.033 34.615 1.16 0.00 34.99 2.52
1881 2601 8.093927 GCATATAAGCTCAGGATTAGAAGAACT 58.906 37.037 0.00 0.00 0.00 3.01
2074 2803 0.323178 ACTGGTACGACATCGAGGGT 60.323 55.000 8.54 0.00 43.02 4.34
2302 3031 0.670546 CGGCATGGTTCGACAACTCT 60.671 55.000 0.00 0.00 32.50 3.24
2422 3151 2.435372 TACCGGGATACTTGTACCGT 57.565 50.000 6.32 0.00 44.57 4.83
2470 3199 1.866601 TGCATCGATCTATTTGCCGTG 59.133 47.619 0.00 0.00 34.20 4.94
2831 3601 6.990349 ACCTTACAATTATCACTATTGGTCGG 59.010 38.462 0.00 0.00 37.32 4.79
2922 3741 0.530870 GCAGCACTATTCCGACTCCC 60.531 60.000 0.00 0.00 0.00 4.30
2925 3744 0.248949 GCACTATTCCGACTCCCGAC 60.249 60.000 0.00 0.00 41.76 4.79
2929 3748 2.100916 ACTATTCCGACTCCCGACATTG 59.899 50.000 0.00 0.00 41.76 2.82
2930 3749 1.191535 ATTCCGACTCCCGACATTGA 58.808 50.000 0.00 0.00 41.76 2.57
3064 5153 2.819667 CCGATCTTAGCGGCATCAG 58.180 57.895 1.45 0.00 42.55 2.90
3150 5239 3.247056 TTCCGCATCAACGCCTCCA 62.247 57.895 0.00 0.00 0.00 3.86
3248 5337 2.961424 CCCCTTTGGCATTCTCGTT 58.039 52.632 0.00 0.00 0.00 3.85
3383 5475 1.672854 CCGATGTGGCGAAGGAGGTA 61.673 60.000 0.00 0.00 0.00 3.08
3398 5490 2.094675 GAGGTAGTTGGTAGCACGGTA 58.905 52.381 0.00 0.00 0.00 4.02
3632 5727 3.056393 ACAACCGGATATTCACAGACGAA 60.056 43.478 9.46 0.00 0.00 3.85
3639 5734 5.411781 GGATATTCACAGACGAAGACTTGT 58.588 41.667 0.00 0.00 0.00 3.16
3657 5752 7.551035 GACTTGTTAGTCCTCGATTAGACTA 57.449 40.000 13.26 13.26 44.15 2.59
3671 5766 9.605955 CTCGATTAGACTAATCATCACTTACAG 57.394 37.037 27.04 12.17 43.65 2.74
3672 5767 9.121658 TCGATTAGACTAATCATCACTTACAGT 57.878 33.333 27.04 0.00 43.65 3.55
3683 5778 9.601217 AATCATCACTTACAGTAAGTTATGGAC 57.399 33.333 30.45 0.00 46.27 4.02
3698 5795 2.668280 GGACTGTTTGCTCGGTCGC 61.668 63.158 8.92 0.00 42.63 5.19
3723 5822 3.500299 GCTTCCTTTTCTCTTGGACAGAC 59.500 47.826 0.00 0.00 0.00 3.51
3724 5823 3.386768 TCCTTTTCTCTTGGACAGACG 57.613 47.619 0.00 0.00 0.00 4.18
3725 5824 2.963101 TCCTTTTCTCTTGGACAGACGA 59.037 45.455 0.00 0.00 0.00 4.20
3726 5825 3.060602 CCTTTTCTCTTGGACAGACGAC 58.939 50.000 0.00 0.00 0.00 4.34
3727 5826 3.492656 CCTTTTCTCTTGGACAGACGACA 60.493 47.826 0.00 0.00 0.00 4.35
3733 5833 0.387929 TTGGACAGACGACAGTGGTC 59.612 55.000 7.61 7.61 40.77 4.02
3832 5971 6.558771 TGATGTTGGTCACTTGTAAATCAG 57.441 37.500 0.00 0.00 0.00 2.90
3835 5974 6.130298 TGTTGGTCACTTGTAAATCAGTTG 57.870 37.500 0.00 0.00 0.00 3.16
3956 6482 9.626045 CCTTGTATTCTGTATTTTTGGAGAAAC 57.374 33.333 0.00 0.00 0.00 2.78
4012 7027 7.546316 GTCAAAGAATAGAAAGTAGACTCCCAC 59.454 40.741 0.00 0.00 0.00 4.61
4025 7040 1.143684 ACTCCCACCATACATGCATCC 59.856 52.381 0.00 0.00 0.00 3.51
4067 7082 4.944962 TTCAACTTTATGCATCTGACCG 57.055 40.909 0.19 0.00 0.00 4.79
4070 7085 2.009774 ACTTTATGCATCTGACCGCAC 58.990 47.619 0.19 0.00 41.79 5.34
4087 7102 3.365364 CCGCACTTTTTCTTCCTAAGCAG 60.365 47.826 0.00 0.00 0.00 4.24
4110 7125 2.123468 TCATGCCGAGGATCCCGA 60.123 61.111 20.20 5.59 0.00 5.14
4115 7130 1.289380 GCCGAGGATCCCGATACAC 59.711 63.158 20.20 4.74 0.00 2.90
4121 7136 1.132849 AGGATCCCGATACACCATCCA 60.133 52.381 8.55 0.00 36.26 3.41
4125 7140 1.909986 TCCCGATACACCATCCAAACA 59.090 47.619 0.00 0.00 0.00 2.83
4128 7143 4.349636 TCCCGATACACCATCCAAACATAT 59.650 41.667 0.00 0.00 0.00 1.78
4134 7149 7.647715 CGATACACCATCCAAACATATTTTTCC 59.352 37.037 0.00 0.00 0.00 3.13
4156 7171 7.540474 TCCTAATAACTGATCCTACATGACC 57.460 40.000 0.00 0.00 0.00 4.02
4160 7175 7.914427 AATAACTGATCCTACATGACCTACA 57.086 36.000 0.00 0.00 0.00 2.74
4161 7176 5.599999 AACTGATCCTACATGACCTACAC 57.400 43.478 0.00 0.00 0.00 2.90
4169 7184 1.290203 CATGACCTACACGGCATCAC 58.710 55.000 0.00 0.00 35.61 3.06
4175 7190 1.112113 CTACACGGCATCACCCTAGT 58.888 55.000 0.00 0.00 33.26 2.57
4177 7192 1.815421 CACGGCATCACCCTAGTGC 60.815 63.158 0.00 0.00 44.16 4.40
4180 7338 0.681733 CGGCATCACCCTAGTGCTAT 59.318 55.000 2.70 0.00 44.16 2.97
4182 7340 1.517242 GCATCACCCTAGTGCTATGC 58.483 55.000 4.69 4.69 43.09 3.14
4184 7342 2.551721 GCATCACCCTAGTGCTATGCAT 60.552 50.000 3.79 3.79 46.17 3.96
4203 7361 1.961793 TTGACCATGCCCTTATACGC 58.038 50.000 0.00 0.00 0.00 4.42
4206 7364 0.531974 ACCATGCCCTTATACGCACG 60.532 55.000 0.00 0.00 37.93 5.34
4258 7416 5.189928 TCCCGTAACTAAATGTCGTACCTA 58.810 41.667 0.00 0.00 0.00 3.08
4278 7436 6.967135 ACCTAGTGAATTCCGAAAAGAAAAC 58.033 36.000 2.27 0.00 0.00 2.43
4335 7496 3.862124 CGGGCTTCGTCTTCACAG 58.138 61.111 0.00 0.00 0.00 3.66
4336 7497 1.738099 CGGGCTTCGTCTTCACAGG 60.738 63.158 0.00 0.00 0.00 4.00
4337 7498 1.371558 GGGCTTCGTCTTCACAGGT 59.628 57.895 0.00 0.00 0.00 4.00
4338 7499 0.670854 GGGCTTCGTCTTCACAGGTC 60.671 60.000 0.00 0.00 0.00 3.85
4341 7502 2.417719 GCTTCGTCTTCACAGGTCAAT 58.582 47.619 0.00 0.00 0.00 2.57
4342 7503 2.808543 GCTTCGTCTTCACAGGTCAATT 59.191 45.455 0.00 0.00 0.00 2.32
4343 7504 3.251004 GCTTCGTCTTCACAGGTCAATTT 59.749 43.478 0.00 0.00 0.00 1.82
4344 7505 4.776743 CTTCGTCTTCACAGGTCAATTTG 58.223 43.478 0.00 0.00 0.00 2.32
4345 7506 3.804036 TCGTCTTCACAGGTCAATTTGT 58.196 40.909 0.00 0.00 0.00 2.83
4346 7507 3.559655 TCGTCTTCACAGGTCAATTTGTG 59.440 43.478 2.19 2.19 44.62 3.33
4347 7508 3.303990 CGTCTTCACAGGTCAATTTGTGG 60.304 47.826 7.88 0.00 43.69 4.17
4348 7509 3.632145 GTCTTCACAGGTCAATTTGTGGT 59.368 43.478 7.88 0.00 43.69 4.16
4349 7510 3.882888 TCTTCACAGGTCAATTTGTGGTC 59.117 43.478 7.88 0.00 43.69 4.02
4350 7511 3.576078 TCACAGGTCAATTTGTGGTCT 57.424 42.857 7.88 0.00 43.69 3.85
4351 7512 3.213506 TCACAGGTCAATTTGTGGTCTG 58.786 45.455 7.88 3.65 43.69 3.51
4352 7513 2.951642 CACAGGTCAATTTGTGGTCTGT 59.048 45.455 0.81 4.19 40.69 3.41
4353 7514 3.381272 CACAGGTCAATTTGTGGTCTGTT 59.619 43.478 0.81 0.00 40.69 3.16
4354 7515 4.023291 ACAGGTCAATTTGTGGTCTGTTT 58.977 39.130 0.00 0.00 37.50 2.83
4355 7516 4.142182 ACAGGTCAATTTGTGGTCTGTTTG 60.142 41.667 0.00 0.00 37.50 2.93
4356 7517 3.384467 AGGTCAATTTGTGGTCTGTTTGG 59.616 43.478 0.00 0.00 0.00 3.28
4357 7518 3.132111 GGTCAATTTGTGGTCTGTTTGGT 59.868 43.478 0.00 0.00 0.00 3.67
4358 7519 4.382577 GGTCAATTTGTGGTCTGTTTGGTT 60.383 41.667 0.00 0.00 0.00 3.67
4359 7520 4.803613 GTCAATTTGTGGTCTGTTTGGTTC 59.196 41.667 0.00 0.00 0.00 3.62
4360 7521 4.709397 TCAATTTGTGGTCTGTTTGGTTCT 59.291 37.500 0.00 0.00 0.00 3.01
4361 7522 5.186797 TCAATTTGTGGTCTGTTTGGTTCTT 59.813 36.000 0.00 0.00 0.00 2.52
4362 7523 5.675684 ATTTGTGGTCTGTTTGGTTCTTT 57.324 34.783 0.00 0.00 0.00 2.52
4363 7524 5.476091 TTTGTGGTCTGTTTGGTTCTTTT 57.524 34.783 0.00 0.00 0.00 2.27
4364 7525 5.476091 TTGTGGTCTGTTTGGTTCTTTTT 57.524 34.783 0.00 0.00 0.00 1.94
4365 7526 6.591750 TTGTGGTCTGTTTGGTTCTTTTTA 57.408 33.333 0.00 0.00 0.00 1.52
4366 7527 6.783708 TGTGGTCTGTTTGGTTCTTTTTAT 57.216 33.333 0.00 0.00 0.00 1.40
4367 7528 6.801575 TGTGGTCTGTTTGGTTCTTTTTATC 58.198 36.000 0.00 0.00 0.00 1.75
4368 7529 6.605594 TGTGGTCTGTTTGGTTCTTTTTATCT 59.394 34.615 0.00 0.00 0.00 1.98
4369 7530 7.123547 TGTGGTCTGTTTGGTTCTTTTTATCTT 59.876 33.333 0.00 0.00 0.00 2.40
4370 7531 7.979537 GTGGTCTGTTTGGTTCTTTTTATCTTT 59.020 33.333 0.00 0.00 0.00 2.52
4371 7532 8.194769 TGGTCTGTTTGGTTCTTTTTATCTTTC 58.805 33.333 0.00 0.00 0.00 2.62
4372 7533 8.414003 GGTCTGTTTGGTTCTTTTTATCTTTCT 58.586 33.333 0.00 0.00 0.00 2.52
4373 7534 9.803315 GTCTGTTTGGTTCTTTTTATCTTTCTT 57.197 29.630 0.00 0.00 0.00 2.52
4394 7555 3.945981 TTTTTGATAAAAGGGGTCGCC 57.054 42.857 0.00 0.00 0.00 5.54
4419 7580 1.273606 GCAGTCTGACTGGCTAGAACA 59.726 52.381 32.28 2.86 46.01 3.18
4433 7594 3.614390 GCTAGAACAGACTACACACCACC 60.614 52.174 0.00 0.00 0.00 4.61
4448 7609 1.481056 CCACCTGAACCTCCCGAAGT 61.481 60.000 0.00 0.00 0.00 3.01
4455 7616 2.291996 TGAACCTCCCGAAGTATCAGGA 60.292 50.000 0.00 0.00 31.23 3.86
4460 7621 3.570550 CCTCCCGAAGTATCAGGAACTAG 59.429 52.174 0.00 0.00 36.02 2.57
4461 7622 4.208746 CTCCCGAAGTATCAGGAACTAGT 58.791 47.826 0.00 0.00 36.02 2.57
4462 7623 5.374921 CTCCCGAAGTATCAGGAACTAGTA 58.625 45.833 0.00 0.00 36.02 1.82
4483 7644 3.307506 AGATCTAGCAGCACAGAGGAAT 58.692 45.455 0.00 0.00 0.00 3.01
4488 7649 1.484240 AGCAGCACAGAGGAATAGGAC 59.516 52.381 0.00 0.00 0.00 3.85
4492 7653 2.703007 AGCACAGAGGAATAGGACATCC 59.297 50.000 0.00 0.00 35.88 3.51
4493 7654 2.224402 GCACAGAGGAATAGGACATCCC 60.224 54.545 0.00 0.00 36.31 3.85
4516 7677 1.572085 CTGCCTTTGCACCAGAGACG 61.572 60.000 0.00 0.00 44.23 4.18
4517 7678 1.301716 GCCTTTGCACCAGAGACGA 60.302 57.895 0.00 0.00 37.47 4.20
4518 7679 1.569479 GCCTTTGCACCAGAGACGAC 61.569 60.000 0.00 0.00 37.47 4.34
4530 7691 0.653636 GAGACGACCACAAAACGCAA 59.346 50.000 0.00 0.00 0.00 4.85
4551 7712 1.144565 CGCGGAATCTCACAGCTCTG 61.145 60.000 0.00 0.00 0.00 3.35
4567 7728 1.989165 CTCTGTAGCTGCAAAGACGAC 59.011 52.381 5.84 0.00 0.00 4.34
4573 7734 1.618640 GCTGCAAAGACGACGGAGAC 61.619 60.000 0.00 0.00 0.00 3.36
4610 7771 4.633126 GCAGCAGATCTGTTTGTATGAAGA 59.367 41.667 23.38 0.00 44.66 2.87
4612 7773 4.874966 AGCAGATCTGTTTGTATGAAGAGC 59.125 41.667 23.38 4.29 0.00 4.09
4622 7783 2.263077 GTATGAAGAGCGTGGTCACTG 58.737 52.381 1.55 0.00 0.00 3.66
4640 7801 6.233434 GTCACTGGATGCCATAATATCAAGA 58.767 40.000 0.00 0.00 30.82 3.02
4641 7802 6.883217 GTCACTGGATGCCATAATATCAAGAT 59.117 38.462 0.00 0.00 30.82 2.40
4642 7803 6.882678 TCACTGGATGCCATAATATCAAGATG 59.117 38.462 0.00 0.00 30.82 2.90
4643 7804 6.882678 CACTGGATGCCATAATATCAAGATGA 59.117 38.462 0.00 0.00 30.82 2.92
4644 7805 7.392393 CACTGGATGCCATAATATCAAGATGAA 59.608 37.037 0.00 0.00 30.82 2.57
4645 7806 8.114102 ACTGGATGCCATAATATCAAGATGAAT 58.886 33.333 0.00 0.00 30.82 2.57
4646 7807 8.888836 TGGATGCCATAATATCAAGATGAATT 57.111 30.769 0.00 0.00 0.00 2.17
4647 7808 9.978336 TGGATGCCATAATATCAAGATGAATTA 57.022 29.630 0.00 0.00 0.00 1.40
4649 7810 9.947669 GATGCCATAATATCAAGATGAATTAGC 57.052 33.333 0.00 0.00 0.00 3.09
4650 7811 8.284945 TGCCATAATATCAAGATGAATTAGCC 57.715 34.615 0.00 0.00 0.00 3.93
4651 7812 8.111545 TGCCATAATATCAAGATGAATTAGCCT 58.888 33.333 0.00 0.00 0.00 4.58
4652 7813 8.619546 GCCATAATATCAAGATGAATTAGCCTC 58.380 37.037 0.00 0.00 0.00 4.70
4653 7814 9.902684 CCATAATATCAAGATGAATTAGCCTCT 57.097 33.333 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.327680 GGTTTAAGTTCTGGTGCTCATCT 58.672 43.478 0.00 0.00 0.00 2.90
1 2 3.440522 GGGTTTAAGTTCTGGTGCTCATC 59.559 47.826 0.00 0.00 0.00 2.92
2 3 3.074538 AGGGTTTAAGTTCTGGTGCTCAT 59.925 43.478 0.00 0.00 0.00 2.90
3 4 2.441750 AGGGTTTAAGTTCTGGTGCTCA 59.558 45.455 0.00 0.00 0.00 4.26
4 5 2.814336 CAGGGTTTAAGTTCTGGTGCTC 59.186 50.000 0.00 0.00 0.00 4.26
5 6 2.489073 CCAGGGTTTAAGTTCTGGTGCT 60.489 50.000 10.21 0.00 41.21 4.40
6 7 1.886542 CCAGGGTTTAAGTTCTGGTGC 59.113 52.381 10.21 0.00 41.21 5.01
22 23 2.593978 CATCCTCAGCCCACCAGG 59.406 66.667 0.00 0.00 39.47 4.45
23 24 2.124403 GCATCCTCAGCCCACCAG 60.124 66.667 0.00 0.00 0.00 4.00
24 25 3.731728 GGCATCCTCAGCCCACCA 61.732 66.667 0.00 0.00 46.50 4.17
30 31 0.035630 AGAACACTGGCATCCTCAGC 60.036 55.000 0.00 0.00 35.78 4.26
31 32 2.486472 AAGAACACTGGCATCCTCAG 57.514 50.000 0.00 0.00 38.16 3.35
32 33 2.957402 AAAGAACACTGGCATCCTCA 57.043 45.000 0.00 0.00 0.00 3.86
33 34 4.082733 GGTTAAAAGAACACTGGCATCCTC 60.083 45.833 0.00 0.00 0.00 3.71
34 35 3.826729 GGTTAAAAGAACACTGGCATCCT 59.173 43.478 0.00 0.00 0.00 3.24
35 36 3.572255 TGGTTAAAAGAACACTGGCATCC 59.428 43.478 0.00 0.00 0.00 3.51
36 37 4.846779 TGGTTAAAAGAACACTGGCATC 57.153 40.909 0.00 0.00 0.00 3.91
37 38 4.220602 GGATGGTTAAAAGAACACTGGCAT 59.779 41.667 0.00 0.00 0.00 4.40
38 39 3.572255 GGATGGTTAAAAGAACACTGGCA 59.428 43.478 0.00 0.00 0.00 4.92
39 40 3.572255 TGGATGGTTAAAAGAACACTGGC 59.428 43.478 0.00 0.00 0.00 4.85
40 41 5.508994 GGTTGGATGGTTAAAAGAACACTGG 60.509 44.000 0.00 0.00 0.00 4.00
41 42 5.068460 TGGTTGGATGGTTAAAAGAACACTG 59.932 40.000 0.00 0.00 0.00 3.66
42 43 5.068591 GTGGTTGGATGGTTAAAAGAACACT 59.931 40.000 0.00 0.00 0.00 3.55
43 44 5.163499 TGTGGTTGGATGGTTAAAAGAACAC 60.163 40.000 0.00 0.00 0.00 3.32
44 45 4.956700 TGTGGTTGGATGGTTAAAAGAACA 59.043 37.500 0.00 0.00 0.00 3.18
45 46 5.523438 TGTGGTTGGATGGTTAAAAGAAC 57.477 39.130 0.00 0.00 0.00 3.01
46 47 5.600484 ACATGTGGTTGGATGGTTAAAAGAA 59.400 36.000 0.00 0.00 0.00 2.52
47 48 5.144100 ACATGTGGTTGGATGGTTAAAAGA 58.856 37.500 0.00 0.00 0.00 2.52
48 49 5.467035 ACATGTGGTTGGATGGTTAAAAG 57.533 39.130 0.00 0.00 0.00 2.27
49 50 5.878406 AACATGTGGTTGGATGGTTAAAA 57.122 34.783 0.00 0.00 38.60 1.52
64 65 3.250762 CCATATAAGCGGACCAACATGTG 59.749 47.826 0.00 0.00 0.00 3.21
65 66 3.118038 ACCATATAAGCGGACCAACATGT 60.118 43.478 0.00 0.00 0.00 3.21
66 67 3.250762 CACCATATAAGCGGACCAACATG 59.749 47.826 0.00 0.00 0.00 3.21
67 68 3.118038 ACACCATATAAGCGGACCAACAT 60.118 43.478 0.00 0.00 0.00 2.71
68 69 2.237643 ACACCATATAAGCGGACCAACA 59.762 45.455 0.00 0.00 0.00 3.33
69 70 2.914059 ACACCATATAAGCGGACCAAC 58.086 47.619 0.00 0.00 0.00 3.77
70 71 3.637911 AACACCATATAAGCGGACCAA 57.362 42.857 0.00 0.00 0.00 3.67
71 72 3.637911 AAACACCATATAAGCGGACCA 57.362 42.857 0.00 0.00 0.00 4.02
72 73 4.976224 AAAAACACCATATAAGCGGACC 57.024 40.909 0.00 0.00 0.00 4.46
158 159 9.681062 CTTCCAGTTTTAGTTTCATCCCTTATA 57.319 33.333 0.00 0.00 0.00 0.98
159 160 8.390921 TCTTCCAGTTTTAGTTTCATCCCTTAT 58.609 33.333 0.00 0.00 0.00 1.73
160 161 7.664318 GTCTTCCAGTTTTAGTTTCATCCCTTA 59.336 37.037 0.00 0.00 0.00 2.69
161 162 6.490381 GTCTTCCAGTTTTAGTTTCATCCCTT 59.510 38.462 0.00 0.00 0.00 3.95
162 163 6.004574 GTCTTCCAGTTTTAGTTTCATCCCT 58.995 40.000 0.00 0.00 0.00 4.20
163 164 6.004574 AGTCTTCCAGTTTTAGTTTCATCCC 58.995 40.000 0.00 0.00 0.00 3.85
164 165 7.511959 AAGTCTTCCAGTTTTAGTTTCATCC 57.488 36.000 0.00 0.00 0.00 3.51
165 166 8.406297 ACAAAGTCTTCCAGTTTTAGTTTCATC 58.594 33.333 0.00 0.00 0.00 2.92
172 173 9.937175 CTTTTCTACAAAGTCTTCCAGTTTTAG 57.063 33.333 0.00 0.00 0.00 1.85
175 176 8.575649 TTCTTTTCTACAAAGTCTTCCAGTTT 57.424 30.769 0.00 0.00 0.00 2.66
209 210 5.661056 TGTCGAAGAGGTTATGATCAAGT 57.339 39.130 0.00 0.00 36.95 3.16
210 211 6.968131 TTTGTCGAAGAGGTTATGATCAAG 57.032 37.500 0.00 0.00 36.95 3.02
215 216 9.098355 CATAAGATTTTGTCGAAGAGGTTATGA 57.902 33.333 0.00 0.00 36.95 2.15
228 229 8.728088 ATTTTGTCGTCACATAAGATTTTGTC 57.272 30.769 0.00 0.00 30.55 3.18
255 256 2.609737 CGATAGCGTGGGTCTATTTCCC 60.610 54.545 0.00 0.00 44.81 3.97
337 338 2.806237 CCCGTCCGAAGAGCTACC 59.194 66.667 0.00 0.00 0.00 3.18
366 367 3.118454 GACCGCCACCACATCGTG 61.118 66.667 0.00 0.00 0.00 4.35
385 386 1.197721 AGTGCGTGTAGATGCAAAAGC 59.802 47.619 8.55 0.00 45.80 3.51
400 401 2.163818 TGTTTGTAGAAGGGAGTGCG 57.836 50.000 0.00 0.00 0.00 5.34
457 458 2.064434 TTGCAGATTGTGTGTCCCAA 57.936 45.000 0.00 0.00 0.00 4.12
473 474 0.032540 CCAACTCACCTGCCTTTTGC 59.967 55.000 0.00 0.00 41.77 3.68
484 485 7.391148 TCTTTTATAGGATTTGCCAACTCAC 57.609 36.000 0.00 0.00 40.02 3.51
545 546 6.654793 AATGACGACTTTCTAGAGCATTTC 57.345 37.500 0.00 0.00 0.00 2.17
546 547 7.440523 AAAATGACGACTTTCTAGAGCATTT 57.559 32.000 0.00 0.00 36.58 2.32
563 564 6.652245 CAAGTTCCATGCTTTCAAAAATGAC 58.348 36.000 0.00 0.00 0.00 3.06
565 566 5.445845 GCAAGTTCCATGCTTTCAAAAATG 58.554 37.500 0.00 0.00 40.64 2.32
605 851 6.860790 ACCAAGGAAAGAAACCAACTTTTA 57.139 33.333 0.00 0.00 37.64 1.52
618 864 4.038042 GTCAAGGAAGGAAACCAAGGAAAG 59.962 45.833 0.00 0.00 0.00 2.62
629 875 4.447138 TGGCTTTTAGTCAAGGAAGGAA 57.553 40.909 0.00 0.00 0.00 3.36
632 878 5.241506 TCACATTGGCTTTTAGTCAAGGAAG 59.758 40.000 11.96 5.06 43.49 3.46
659 997 2.512485 TAGAAACAAGACGACGGCAA 57.488 45.000 2.19 0.00 0.00 4.52
685 1023 7.044589 ACGTGCTTTAACAAAACTGAAAAAG 57.955 32.000 0.00 0.00 0.00 2.27
692 1030 8.656849 CATATCTAGACGTGCTTTAACAAAACT 58.343 33.333 0.00 0.00 0.00 2.66
694 1032 7.333423 AGCATATCTAGACGTGCTTTAACAAAA 59.667 33.333 21.81 0.00 44.92 2.44
695 1033 6.816640 AGCATATCTAGACGTGCTTTAACAAA 59.183 34.615 21.81 0.00 44.92 2.83
696 1034 6.338146 AGCATATCTAGACGTGCTTTAACAA 58.662 36.000 21.81 0.00 44.92 2.83
697 1035 5.902681 AGCATATCTAGACGTGCTTTAACA 58.097 37.500 21.81 0.00 44.92 2.41
698 1036 5.977725 TGAGCATATCTAGACGTGCTTTAAC 59.022 40.000 25.86 17.15 46.98 2.01
699 1037 6.144078 TGAGCATATCTAGACGTGCTTTAA 57.856 37.500 25.86 16.18 46.98 1.52
700 1038 5.767816 TGAGCATATCTAGACGTGCTTTA 57.232 39.130 25.86 18.31 46.98 1.85
702 1040 4.655762 TTGAGCATATCTAGACGTGCTT 57.344 40.909 25.86 14.86 46.98 3.91
704 1042 4.363999 ACTTTGAGCATATCTAGACGTGC 58.636 43.478 18.73 18.73 37.84 5.34
705 1043 7.327275 GGAATACTTTGAGCATATCTAGACGTG 59.673 40.741 0.00 0.00 0.00 4.49
706 1044 7.371936 GGAATACTTTGAGCATATCTAGACGT 58.628 38.462 0.00 0.00 0.00 4.34
707 1045 6.809196 GGGAATACTTTGAGCATATCTAGACG 59.191 42.308 0.00 0.00 0.00 4.18
708 1046 7.671302 TGGGAATACTTTGAGCATATCTAGAC 58.329 38.462 0.00 0.00 0.00 2.59
709 1047 7.855784 TGGGAATACTTTGAGCATATCTAGA 57.144 36.000 0.00 0.00 0.00 2.43
710 1048 8.370940 TCTTGGGAATACTTTGAGCATATCTAG 58.629 37.037 0.00 0.00 0.00 2.43
711 1049 8.262601 TCTTGGGAATACTTTGAGCATATCTA 57.737 34.615 0.00 0.00 0.00 1.98
712 1050 7.141758 TCTTGGGAATACTTTGAGCATATCT 57.858 36.000 0.00 0.00 0.00 1.98
713 1051 6.072783 GCTCTTGGGAATACTTTGAGCATATC 60.073 42.308 0.00 0.00 43.18 1.63
714 1052 5.767168 GCTCTTGGGAATACTTTGAGCATAT 59.233 40.000 0.00 0.00 43.18 1.78
715 1053 5.126067 GCTCTTGGGAATACTTTGAGCATA 58.874 41.667 0.00 0.00 43.18 3.14
716 1054 3.950395 GCTCTTGGGAATACTTTGAGCAT 59.050 43.478 0.00 0.00 43.18 3.79
717 1055 3.347216 GCTCTTGGGAATACTTTGAGCA 58.653 45.455 0.00 0.00 43.18 4.26
718 1056 3.347216 TGCTCTTGGGAATACTTTGAGC 58.653 45.455 0.00 0.00 43.73 4.26
719 1057 5.067023 GGATTGCTCTTGGGAATACTTTGAG 59.933 44.000 0.00 0.00 36.11 3.02
720 1058 4.949856 GGATTGCTCTTGGGAATACTTTGA 59.050 41.667 0.00 0.00 36.11 2.69
721 1059 4.098501 GGGATTGCTCTTGGGAATACTTTG 59.901 45.833 0.00 0.00 36.88 2.77
722 1060 4.017130 AGGGATTGCTCTTGGGAATACTTT 60.017 41.667 0.00 0.00 36.88 2.66
723 1061 3.529319 AGGGATTGCTCTTGGGAATACTT 59.471 43.478 0.00 0.00 36.88 2.24
724 1062 3.126453 AGGGATTGCTCTTGGGAATACT 58.874 45.455 0.00 0.00 36.88 2.12
725 1063 3.584733 AGGGATTGCTCTTGGGAATAC 57.415 47.619 0.00 0.00 36.11 1.89
726 1064 3.788142 AGAAGGGATTGCTCTTGGGAATA 59.212 43.478 0.00 0.00 34.15 1.75
727 1065 2.584498 AGAAGGGATTGCTCTTGGGAAT 59.416 45.455 0.00 0.00 34.15 3.01
728 1066 1.995542 AGAAGGGATTGCTCTTGGGAA 59.004 47.619 0.00 0.00 34.15 3.97
729 1067 1.561542 GAGAAGGGATTGCTCTTGGGA 59.438 52.381 0.00 0.00 34.15 4.37
809 1179 9.573133 GTGTAAAGATGAGAATTTTAATGGTGG 57.427 33.333 0.00 0.00 0.00 4.61
810 1180 9.573133 GGTGTAAAGATGAGAATTTTAATGGTG 57.427 33.333 0.00 0.00 0.00 4.17
811 1181 8.749354 GGGTGTAAAGATGAGAATTTTAATGGT 58.251 33.333 0.00 0.00 0.00 3.55
923 1353 2.108976 CGACGGATGGGTGGATGG 59.891 66.667 0.00 0.00 0.00 3.51
924 1354 2.108976 CCGACGGATGGGTGGATG 59.891 66.667 8.64 0.00 0.00 3.51
925 1355 2.365105 ACCGACGGATGGGTGGAT 60.365 61.111 23.38 0.00 35.21 3.41
948 1378 1.710816 GTGGGAATTTGGTGGGTTCA 58.289 50.000 0.00 0.00 0.00 3.18
1236 1703 4.704833 AGCACGCCATGTTCCGCT 62.705 61.111 0.00 0.00 0.00 5.52
1245 1742 4.704833 GCCTTCTCCAGCACGCCA 62.705 66.667 0.00 0.00 0.00 5.69
1252 1749 4.148825 CCCGGACGCCTTCTCCAG 62.149 72.222 0.73 0.00 0.00 3.86
1261 1758 4.603946 GGAGTATGGCCCGGACGC 62.604 72.222 0.73 0.00 0.00 5.19
1449 1980 1.540363 GGCAACGAGGTCAGTTTCTGA 60.540 52.381 0.00 0.00 38.25 3.27
1766 2464 5.212194 ACATCGACGTGAAAAATTTCTTGG 58.788 37.500 0.00 0.22 38.02 3.61
1769 2467 8.286800 TGATAAACATCGACGTGAAAAATTTCT 58.713 29.630 0.00 0.00 38.02 2.52
1879 2599 4.209703 CACAATGCATTTCAGCGAAAAAGT 59.790 37.500 9.83 0.00 35.11 2.66
1881 2601 3.059733 GCACAATGCATTTCAGCGAAAAA 60.060 39.130 9.83 0.00 44.26 1.94
2182 2911 4.658786 AGGAGGGGGTCGCTTGGT 62.659 66.667 0.00 0.00 0.00 3.67
2302 3031 2.590291 ATGCGCCACGTGTTGTCA 60.590 55.556 15.65 7.12 0.00 3.58
2483 3212 0.953471 TTGTACATGTCACTGGCGGC 60.953 55.000 0.00 0.00 0.00 6.53
2484 3213 1.737838 ATTGTACATGTCACTGGCGG 58.262 50.000 0.00 0.00 0.00 6.13
2491 3220 1.996898 GCCGTCGAATTGTACATGTCA 59.003 47.619 0.00 0.00 0.00 3.58
2831 3601 0.310543 TCAACGGTGCAGCAAATGAC 59.689 50.000 17.33 0.00 0.00 3.06
2922 3741 2.351418 ACAACACACACACTCAATGTCG 59.649 45.455 0.00 0.00 40.64 4.35
2925 3744 2.159407 TGCACAACACACACACTCAATG 60.159 45.455 0.00 0.00 0.00 2.82
2929 3748 1.861202 GCATGCACAACACACACACTC 60.861 52.381 14.21 0.00 0.00 3.51
2930 3749 0.101040 GCATGCACAACACACACACT 59.899 50.000 14.21 0.00 0.00 3.55
3161 5250 1.573436 GACGTCGACCTCGTTGAGT 59.427 57.895 10.58 0.00 41.64 3.41
3248 5337 3.936203 AGGGCGACGTTGGCAAGA 61.936 61.111 28.49 0.00 35.84 3.02
3383 5475 1.588082 CGGTACCGTGCTACCAACT 59.412 57.895 26.39 0.00 36.67 3.16
3632 5727 6.181908 AGTCTAATCGAGGACTAACAAGTCT 58.818 40.000 14.14 0.00 40.49 3.24
3671 5766 4.092968 CCGAGCAAACAGTCCATAACTTAC 59.907 45.833 0.00 0.00 35.45 2.34
3672 5767 4.250464 CCGAGCAAACAGTCCATAACTTA 58.750 43.478 0.00 0.00 35.45 2.24
3683 5778 2.671177 CCAGCGACCGAGCAAACAG 61.671 63.158 0.00 0.00 40.15 3.16
3698 5795 2.816672 GTCCAAGAGAAAAGGAAGCCAG 59.183 50.000 0.00 0.00 32.30 4.85
3756 5856 7.282585 CAGGACCAGGAACATAAATCAAGATA 58.717 38.462 0.00 0.00 0.00 1.98
3778 5878 7.519032 TCATCTTACTAAAACCAAAACCAGG 57.481 36.000 0.00 0.00 0.00 4.45
3832 5971 2.929161 GCCCTTTTAATTCACCCGCAAC 60.929 50.000 0.00 0.00 0.00 4.17
3835 5974 0.892063 TGCCCTTTTAATTCACCCGC 59.108 50.000 0.00 0.00 0.00 6.13
3939 6465 8.090214 ACCATGATTGTTTCTCCAAAAATACAG 58.910 33.333 0.00 0.00 0.00 2.74
3956 6482 5.887598 TCCCTTCTGAAATACACCATGATTG 59.112 40.000 0.00 0.00 0.00 2.67
4012 7027 4.040829 TGAAGAGTAGGGATGCATGTATGG 59.959 45.833 2.46 0.00 0.00 2.74
4025 7040 8.343366 GTTGAAAAGGTTAAAGTGAAGAGTAGG 58.657 37.037 0.00 0.00 0.00 3.18
4067 7082 3.569548 GCTGCTTAGGAAGAAAAAGTGC 58.430 45.455 0.00 0.00 0.00 4.40
4070 7085 2.414691 GCGGCTGCTTAGGAAGAAAAAG 60.415 50.000 11.21 0.00 38.39 2.27
4110 7125 8.608185 AGGAAAAATATGTTTGGATGGTGTAT 57.392 30.769 0.00 0.00 0.00 2.29
4134 7149 9.078990 TGTAGGTCATGTAGGATCAGTTATTAG 57.921 37.037 0.00 0.00 0.00 1.73
4140 7155 3.632604 CGTGTAGGTCATGTAGGATCAGT 59.367 47.826 0.00 0.00 0.00 3.41
4142 7157 2.956333 CCGTGTAGGTCATGTAGGATCA 59.044 50.000 0.00 0.00 34.51 2.92
4154 7169 0.324923 TAGGGTGATGCCGTGTAGGT 60.325 55.000 0.00 0.00 43.70 3.08
4156 7171 1.112113 ACTAGGGTGATGCCGTGTAG 58.888 55.000 0.00 0.00 38.44 2.74
4160 7175 0.686441 TAGCACTAGGGTGATGCCGT 60.686 55.000 0.00 0.00 45.61 5.68
4161 7176 0.681733 ATAGCACTAGGGTGATGCCG 59.318 55.000 0.00 0.00 45.61 5.69
4169 7184 2.158769 TGGTCAATGCATAGCACTAGGG 60.159 50.000 0.00 0.00 43.04 3.53
4182 7340 2.226437 GCGTATAAGGGCATGGTCAATG 59.774 50.000 0.00 0.00 39.49 2.82
4184 7342 1.210722 TGCGTATAAGGGCATGGTCAA 59.789 47.619 0.00 0.00 33.52 3.18
4203 7361 4.678287 ACTGTACTTTGATTACGTCACGTG 59.322 41.667 14.62 9.94 41.39 4.49
4206 7364 5.107220 CCCAACTGTACTTTGATTACGTCAC 60.107 44.000 0.00 0.00 36.32 3.67
4239 7397 9.578439 AATTCACTAGGTACGACATTTAGTTAC 57.422 33.333 0.00 0.00 0.00 2.50
4258 7416 6.451064 AGTGTTTTCTTTTCGGAATTCACT 57.549 33.333 7.93 0.00 36.15 3.41
4323 7484 4.035091 CACAAATTGACCTGTGAAGACGAA 59.965 41.667 0.00 0.00 44.68 3.85
4324 7485 3.559655 CACAAATTGACCTGTGAAGACGA 59.440 43.478 0.00 0.00 44.68 4.20
4325 7486 3.303990 CCACAAATTGACCTGTGAAGACG 60.304 47.826 9.14 0.00 44.68 4.18
4327 7488 3.882888 GACCACAAATTGACCTGTGAAGA 59.117 43.478 9.14 0.00 44.68 2.87
4328 7489 3.885297 AGACCACAAATTGACCTGTGAAG 59.115 43.478 9.14 0.00 44.68 3.02
4331 7492 2.951642 ACAGACCACAAATTGACCTGTG 59.048 45.455 0.00 1.68 42.14 3.66
4332 7493 3.297134 ACAGACCACAAATTGACCTGT 57.703 42.857 0.00 4.52 34.71 4.00
4333 7494 4.362279 CAAACAGACCACAAATTGACCTG 58.638 43.478 0.00 3.92 33.34 4.00
4334 7495 3.384467 CCAAACAGACCACAAATTGACCT 59.616 43.478 0.00 0.00 0.00 3.85
4335 7496 3.132111 ACCAAACAGACCACAAATTGACC 59.868 43.478 0.00 0.00 0.00 4.02
4336 7497 4.385358 ACCAAACAGACCACAAATTGAC 57.615 40.909 0.00 0.00 0.00 3.18
4337 7498 4.709397 AGAACCAAACAGACCACAAATTGA 59.291 37.500 0.00 0.00 0.00 2.57
4338 7499 5.009854 AGAACCAAACAGACCACAAATTG 57.990 39.130 0.00 0.00 0.00 2.32
4341 7502 5.476091 AAAAGAACCAAACAGACCACAAA 57.524 34.783 0.00 0.00 0.00 2.83
4342 7503 5.476091 AAAAAGAACCAAACAGACCACAA 57.524 34.783 0.00 0.00 0.00 3.33
4343 7504 6.605594 AGATAAAAAGAACCAAACAGACCACA 59.394 34.615 0.00 0.00 0.00 4.17
4344 7505 7.039313 AGATAAAAAGAACCAAACAGACCAC 57.961 36.000 0.00 0.00 0.00 4.16
4345 7506 7.654022 AAGATAAAAAGAACCAAACAGACCA 57.346 32.000 0.00 0.00 0.00 4.02
4346 7507 8.414003 AGAAAGATAAAAAGAACCAAACAGACC 58.586 33.333 0.00 0.00 0.00 3.85
4347 7508 9.803315 AAGAAAGATAAAAAGAACCAAACAGAC 57.197 29.630 0.00 0.00 0.00 3.51
4374 7535 3.945981 GGCGACCCCTTTTATCAAAAA 57.054 42.857 0.00 0.00 33.58 1.94
4389 7550 2.743928 CAGACTGCTTGGGGCGAC 60.744 66.667 0.00 0.00 45.43 5.19
4390 7551 2.922503 TCAGACTGCTTGGGGCGA 60.923 61.111 0.00 0.00 45.43 5.54
4391 7552 2.743928 GTCAGACTGCTTGGGGCG 60.744 66.667 0.00 0.00 45.43 6.13
4392 7553 1.673665 CAGTCAGACTGCTTGGGGC 60.674 63.158 17.77 0.00 39.62 5.80
4393 7554 1.002868 CCAGTCAGACTGCTTGGGG 60.003 63.158 23.46 6.51 44.63 4.96
4394 7555 1.673665 GCCAGTCAGACTGCTTGGG 60.674 63.158 23.46 11.73 44.63 4.12
4419 7580 1.692519 GGTTCAGGTGGTGTGTAGTCT 59.307 52.381 0.00 0.00 0.00 3.24
4433 7594 3.444703 CTGATACTTCGGGAGGTTCAG 57.555 52.381 4.08 4.08 0.00 3.02
4460 7621 3.218453 TCCTCTGTGCTGCTAGATCTAC 58.782 50.000 0.00 0.00 0.00 2.59
4461 7622 3.584733 TCCTCTGTGCTGCTAGATCTA 57.415 47.619 1.69 1.69 0.00 1.98
4462 7623 2.450867 TCCTCTGTGCTGCTAGATCT 57.549 50.000 0.00 0.00 0.00 2.75
4469 7630 1.208052 TGTCCTATTCCTCTGTGCTGC 59.792 52.381 0.00 0.00 0.00 5.25
4477 7638 1.349357 GGCAGGGATGTCCTATTCCTC 59.651 57.143 0.00 0.00 46.12 3.71
4483 7644 2.072487 GGCAGGCAGGGATGTCCTA 61.072 63.158 0.00 0.00 46.12 2.94
4488 7649 2.718073 GCAAAGGCAGGCAGGGATG 61.718 63.158 0.00 0.00 40.72 3.51
4516 7677 1.942223 GCGGTTGCGTTTTGTGGTC 60.942 57.895 0.00 0.00 0.00 4.02
4517 7678 2.103340 GCGGTTGCGTTTTGTGGT 59.897 55.556 0.00 0.00 0.00 4.16
4530 7691 2.125512 GCTGTGAGATTCCGCGGT 60.126 61.111 27.15 6.47 0.00 5.68
4535 7696 2.820330 GCTACAGAGCTGTGAGATTCC 58.180 52.381 19.13 0.00 45.98 3.01
4551 7712 0.388134 TCCGTCGTCTTTGCAGCTAC 60.388 55.000 0.00 0.00 0.00 3.58
4567 7728 1.971695 GTTTTGCTGGGGGTCTCCG 60.972 63.158 0.00 0.00 36.01 4.63
4573 7734 3.053828 CTGCTGTTTTGCTGGGGG 58.946 61.111 0.00 0.00 0.00 5.40
4610 7771 2.046892 GCATCCAGTGACCACGCT 60.047 61.111 0.00 0.00 37.34 5.07
4612 7773 0.177836 TATGGCATCCAGTGACCACG 59.822 55.000 1.65 0.00 36.75 4.94


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

AutoCloner maintained by Alex Coulton.