Multiple sequence alignment - TraesCS1B01G397100

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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 TraesCS1B01G397100 chr1B 100.000 2867 0 0 1 2867 628627186 628624320 0.000000e+00 5295.0
1 TraesCS1B01G397100 chr1B 98.310 1006 11 5 1847 2849 272383106 272384108 0.000000e+00 1759.0
2 TraesCS1B01G397100 chr1B 95.385 130 6 0 1902 2031 272383222 272383351 1.040000e-49 207.0
3 TraesCS1B01G397100 chr1B 89.535 86 6 1 48 130 532540742 532540657 3.910000e-19 106.0
4 TraesCS1B01G397100 chr1A 97.136 1257 36 0 600 1856 550638301 550637045 0.000000e+00 2122.0
5 TraesCS1B01G397100 chr1A 96.512 172 6 0 429 600 550638523 550638352 4.680000e-73 285.0
6 TraesCS1B01G397100 chr1A 93.333 90 4 1 348 437 550638633 550638546 6.450000e-27 132.0
7 TraesCS1B01G397100 chr1D 97.059 1258 33 2 600 1856 458147418 458146164 0.000000e+00 2115.0
8 TraesCS1B01G397100 chr1D 95.930 172 7 0 429 600 458147640 458147469 2.180000e-71 279.0
9 TraesCS1B01G397100 chr1D 95.556 90 2 1 348 437 458147750 458147663 2.980000e-30 143.0
10 TraesCS1B01G397100 chr2A 99.012 1012 6 2 1856 2867 67971962 67972969 0.000000e+00 1810.0
11 TraesCS1B01G397100 chr2A 98.066 879 13 4 1856 2732 154816187 154815311 0.000000e+00 1526.0
12 TraesCS1B01G397100 chr2A 88.545 873 47 22 2028 2867 81479437 81480289 0.000000e+00 1009.0
13 TraesCS1B01G397100 chr2A 92.424 132 7 2 1901 2031 67972065 67972194 4.880000e-43 185.0
14 TraesCS1B01G397100 chr2A 85.000 120 16 2 1835 1954 733138672 733138789 1.400000e-23 121.0
15 TraesCS1B01G397100 chr6B 98.428 1018 9 4 1856 2867 448369444 448368428 0.000000e+00 1784.0
16 TraesCS1B01G397100 chr6B 90.816 98 6 1 48 142 37930328 37930231 8.340000e-26 128.0
17 TraesCS1B01G397100 chr3A 98.633 878 7 3 1856 2732 671737733 671736860 0.000000e+00 1550.0
18 TraesCS1B01G397100 chr4A 92.857 924 35 17 1973 2867 730952948 730952027 0.000000e+00 1312.0
19 TraesCS1B01G397100 chr4A 91.006 934 34 19 1966 2867 699725186 699724271 0.000000e+00 1214.0
20 TraesCS1B01G397100 chr4A 90.341 176 8 5 1856 2031 730952995 730952829 3.720000e-54 222.0
21 TraesCS1B01G397100 chr7B 89.888 890 30 16 2028 2867 656245102 656244223 0.000000e+00 1090.0
22 TraesCS1B01G397100 chr7B 87.037 216 27 1 7 221 682274443 682274228 2.850000e-60 243.0
23 TraesCS1B01G397100 chr7B 88.525 61 7 0 85 145 707851861 707851921 1.100000e-09 75.0
24 TraesCS1B01G397100 chr2B 89.908 872 52 13 2026 2867 13679301 13678436 0.000000e+00 1090.0
25 TraesCS1B01G397100 chr2B 91.594 345 28 1 1 344 51190888 51190544 2.580000e-130 475.0
26 TraesCS1B01G397100 chr2B 87.640 89 7 2 1856 1944 446126952 446126868 1.820000e-17 100.0
27 TraesCS1B01G397100 chr2B 83.544 79 11 2 1856 1934 3600376 3600452 3.960000e-09 73.1
28 TraesCS1B01G397100 chr4B 84.866 859 122 7 1001 1855 3732446 3733300 0.000000e+00 859.0
29 TraesCS1B01G397100 chr4B 82.907 860 138 8 1001 1856 3484221 3483367 0.000000e+00 765.0
30 TraesCS1B01G397100 chr4B 82.674 860 141 7 1001 1856 3454107 3453252 0.000000e+00 756.0
31 TraesCS1B01G397100 chr4B 90.816 98 6 1 48 142 50403190 50403093 8.340000e-26 128.0
32 TraesCS1B01G397100 chr4D 84.364 857 130 4 1001 1855 1821950 1822804 0.000000e+00 837.0
33 TraesCS1B01G397100 chrUn 83.753 874 134 6 987 1856 47630216 47631085 0.000000e+00 821.0
34 TraesCS1B01G397100 chrUn 82.589 873 142 8 990 1856 48044872 48045740 0.000000e+00 761.0
35 TraesCS1B01G397100 chrUn 82.474 873 143 8 990 1856 48075143 48076011 0.000000e+00 756.0
36 TraesCS1B01G397100 chr3B 88.986 345 36 2 1 344 187557138 187556795 2.640000e-115 425.0
37 TraesCS1B01G397100 chr3D 87.879 264 24 8 104 364 204745503 204745245 1.290000e-78 303.0
38 TraesCS1B01G397100 chr5B 87.273 110 11 1 36 142 399784870 399784979 3.880000e-24 122.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G397100 chr1B 628624320 628627186 2866 True 5295.000000 5295 100.000000 1 2867 1 chr1B.!!$R2 2866
1 TraesCS1B01G397100 chr1B 272383106 272384108 1002 False 983.000000 1759 96.847500 1847 2849 2 chr1B.!!$F1 1002
2 TraesCS1B01G397100 chr1A 550637045 550638633 1588 True 846.333333 2122 95.660333 348 1856 3 chr1A.!!$R1 1508
3 TraesCS1B01G397100 chr1D 458146164 458147750 1586 True 845.666667 2115 96.181667 348 1856 3 chr1D.!!$R1 1508
4 TraesCS1B01G397100 chr2A 154815311 154816187 876 True 1526.000000 1526 98.066000 1856 2732 1 chr2A.!!$R1 876
5 TraesCS1B01G397100 chr2A 81479437 81480289 852 False 1009.000000 1009 88.545000 2028 2867 1 chr2A.!!$F1 839
6 TraesCS1B01G397100 chr2A 67971962 67972969 1007 False 997.500000 1810 95.718000 1856 2867 2 chr2A.!!$F3 1011
7 TraesCS1B01G397100 chr6B 448368428 448369444 1016 True 1784.000000 1784 98.428000 1856 2867 1 chr6B.!!$R2 1011
8 TraesCS1B01G397100 chr3A 671736860 671737733 873 True 1550.000000 1550 98.633000 1856 2732 1 chr3A.!!$R1 876
9 TraesCS1B01G397100 chr4A 699724271 699725186 915 True 1214.000000 1214 91.006000 1966 2867 1 chr4A.!!$R1 901
10 TraesCS1B01G397100 chr4A 730952027 730952995 968 True 767.000000 1312 91.599000 1856 2867 2 chr4A.!!$R2 1011
11 TraesCS1B01G397100 chr7B 656244223 656245102 879 True 1090.000000 1090 89.888000 2028 2867 1 chr7B.!!$R1 839
12 TraesCS1B01G397100 chr2B 13678436 13679301 865 True 1090.000000 1090 89.908000 2026 2867 1 chr2B.!!$R1 841
13 TraesCS1B01G397100 chr4B 3732446 3733300 854 False 859.000000 859 84.866000 1001 1855 1 chr4B.!!$F1 854
14 TraesCS1B01G397100 chr4B 3483367 3484221 854 True 765.000000 765 82.907000 1001 1856 1 chr4B.!!$R2 855
15 TraesCS1B01G397100 chr4B 3453252 3454107 855 True 756.000000 756 82.674000 1001 1856 1 chr4B.!!$R1 855
16 TraesCS1B01G397100 chr4D 1821950 1822804 854 False 837.000000 837 84.364000 1001 1855 1 chr4D.!!$F1 854
17 TraesCS1B01G397100 chrUn 47630216 47631085 869 False 821.000000 821 83.753000 987 1856 1 chrUn.!!$F1 869
18 TraesCS1B01G397100 chrUn 48044872 48045740 868 False 761.000000 761 82.589000 990 1856 1 chrUn.!!$F2 866
19 TraesCS1B01G397100 chrUn 48075143 48076011 868 False 756.000000 756 82.474000 990 1856 1 chrUn.!!$F3 866

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
41 42 0.034477 AATCTGGGTTGGGCTTACGG 60.034 55.0 0.00 0.0 0.00 4.02 F
144 145 0.036388 AAGGCAACGTGTCCATCGAT 60.036 50.0 8.78 0.0 46.39 3.59 F
145 146 0.036388 AGGCAACGTGTCCATCGATT 60.036 50.0 0.00 0.0 46.39 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1115 1.640428 CGAGCATGTTGGTCACGTAT 58.360 50.00 7.39 0.0 44.51 3.06 R
1112 1198 1.965754 GAGATCCCTGAGCTTGGCGT 61.966 60.00 0.00 0.0 0.00 5.68 R
1920 2011 5.103290 TGAGACGACTTACCAAAAATTGC 57.897 39.13 0.00 0.0 0.00 3.56 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
17 18 2.125753 GGACAGGAGACAGCAGCG 60.126 66.667 0.00 0.00 0.00 5.18
18 19 2.640302 GGACAGGAGACAGCAGCGA 61.640 63.158 0.00 0.00 0.00 4.93
19 20 1.290324 GACAGGAGACAGCAGCGAA 59.710 57.895 0.00 0.00 0.00 4.70
20 21 0.735632 GACAGGAGACAGCAGCGAAG 60.736 60.000 0.00 0.00 0.00 3.79
21 22 1.291588 CAGGAGACAGCAGCGAAGT 59.708 57.895 0.00 0.00 0.00 3.01
22 23 0.528017 CAGGAGACAGCAGCGAAGTA 59.472 55.000 0.00 0.00 0.00 2.24
23 24 1.067565 CAGGAGACAGCAGCGAAGTAA 60.068 52.381 0.00 0.00 0.00 2.24
24 25 1.827969 AGGAGACAGCAGCGAAGTAAT 59.172 47.619 0.00 0.00 0.00 1.89
25 26 2.159170 AGGAGACAGCAGCGAAGTAATC 60.159 50.000 0.00 0.00 0.00 1.75
26 27 2.159170 GGAGACAGCAGCGAAGTAATCT 60.159 50.000 0.00 0.00 0.00 2.40
27 28 2.857152 GAGACAGCAGCGAAGTAATCTG 59.143 50.000 0.00 0.00 0.00 2.90
28 29 1.929836 GACAGCAGCGAAGTAATCTGG 59.070 52.381 0.00 0.00 0.00 3.86
29 30 1.293924 CAGCAGCGAAGTAATCTGGG 58.706 55.000 0.00 0.00 0.00 4.45
30 31 0.905357 AGCAGCGAAGTAATCTGGGT 59.095 50.000 0.00 0.00 0.00 4.51
31 32 1.279271 AGCAGCGAAGTAATCTGGGTT 59.721 47.619 0.00 0.00 0.00 4.11
32 33 1.398390 GCAGCGAAGTAATCTGGGTTG 59.602 52.381 0.00 0.00 0.00 3.77
33 34 2.009774 CAGCGAAGTAATCTGGGTTGG 58.990 52.381 0.00 0.00 0.00 3.77
34 35 1.065418 AGCGAAGTAATCTGGGTTGGG 60.065 52.381 0.00 0.00 0.00 4.12
35 36 1.379527 CGAAGTAATCTGGGTTGGGC 58.620 55.000 0.00 0.00 0.00 5.36
36 37 1.065418 CGAAGTAATCTGGGTTGGGCT 60.065 52.381 0.00 0.00 0.00 5.19
37 38 2.618045 CGAAGTAATCTGGGTTGGGCTT 60.618 50.000 0.00 0.00 0.00 4.35
38 39 3.370103 CGAAGTAATCTGGGTTGGGCTTA 60.370 47.826 0.00 0.00 0.00 3.09
39 40 3.646736 AGTAATCTGGGTTGGGCTTAC 57.353 47.619 0.00 0.00 0.00 2.34
40 41 2.093128 AGTAATCTGGGTTGGGCTTACG 60.093 50.000 0.00 0.00 0.00 3.18
41 42 0.034477 AATCTGGGTTGGGCTTACGG 60.034 55.000 0.00 0.00 0.00 4.02
42 43 0.912487 ATCTGGGTTGGGCTTACGGA 60.912 55.000 0.00 0.00 0.00 4.69
43 44 1.078426 CTGGGTTGGGCTTACGGAG 60.078 63.158 0.00 0.00 0.00 4.63
44 45 1.536907 TGGGTTGGGCTTACGGAGA 60.537 57.895 0.00 0.00 0.00 3.71
45 46 1.128809 TGGGTTGGGCTTACGGAGAA 61.129 55.000 0.00 0.00 0.00 2.87
46 47 0.675837 GGGTTGGGCTTACGGAGAAC 60.676 60.000 0.00 0.00 0.00 3.01
57 58 2.980562 CGGAGAACGTGAACCAACA 58.019 52.632 0.00 0.00 37.93 3.33
58 59 0.859232 CGGAGAACGTGAACCAACAG 59.141 55.000 0.00 0.00 37.93 3.16
59 60 0.586802 GGAGAACGTGAACCAACAGC 59.413 55.000 0.00 0.00 0.00 4.40
60 61 1.295792 GAGAACGTGAACCAACAGCA 58.704 50.000 0.00 0.00 0.00 4.41
61 62 1.261619 GAGAACGTGAACCAACAGCAG 59.738 52.381 0.00 0.00 0.00 4.24
62 63 0.307760 GAACGTGAACCAACAGCAGG 59.692 55.000 0.00 0.00 0.00 4.85
63 64 1.724582 AACGTGAACCAACAGCAGGC 61.725 55.000 0.00 0.00 0.00 4.85
64 65 2.908073 CGTGAACCAACAGCAGGCC 61.908 63.158 0.00 0.00 0.00 5.19
65 66 1.827789 GTGAACCAACAGCAGGCCA 60.828 57.895 5.01 0.00 0.00 5.36
66 67 1.076412 TGAACCAACAGCAGGCCAA 60.076 52.632 5.01 0.00 0.00 4.52
67 68 1.363807 GAACCAACAGCAGGCCAAC 59.636 57.895 5.01 0.00 0.00 3.77
68 69 1.076044 AACCAACAGCAGGCCAACT 60.076 52.632 5.01 0.00 0.00 3.16
69 70 0.184933 AACCAACAGCAGGCCAACTA 59.815 50.000 5.01 0.00 0.00 2.24
70 71 0.537371 ACCAACAGCAGGCCAACTAC 60.537 55.000 5.01 0.00 0.00 2.73
71 72 0.250901 CCAACAGCAGGCCAACTACT 60.251 55.000 5.01 0.00 0.00 2.57
72 73 1.609208 CAACAGCAGGCCAACTACTT 58.391 50.000 5.01 0.00 0.00 2.24
73 74 2.552155 CCAACAGCAGGCCAACTACTTA 60.552 50.000 5.01 0.00 0.00 2.24
74 75 3.347216 CAACAGCAGGCCAACTACTTAT 58.653 45.455 5.01 0.00 0.00 1.73
75 76 4.513442 CAACAGCAGGCCAACTACTTATA 58.487 43.478 5.01 0.00 0.00 0.98
76 77 4.408182 ACAGCAGGCCAACTACTTATAG 57.592 45.455 5.01 0.00 34.25 1.31
77 78 4.030913 ACAGCAGGCCAACTACTTATAGA 58.969 43.478 5.01 0.00 32.23 1.98
78 79 4.141914 ACAGCAGGCCAACTACTTATAGAC 60.142 45.833 5.01 0.00 32.23 2.59
79 80 4.030913 AGCAGGCCAACTACTTATAGACA 58.969 43.478 5.01 0.00 32.23 3.41
80 81 4.100189 AGCAGGCCAACTACTTATAGACAG 59.900 45.833 5.01 0.00 32.23 3.51
81 82 4.141914 GCAGGCCAACTACTTATAGACAGT 60.142 45.833 5.01 0.00 32.23 3.55
82 83 5.593010 CAGGCCAACTACTTATAGACAGTC 58.407 45.833 5.01 0.00 32.23 3.51
83 84 4.338682 AGGCCAACTACTTATAGACAGTCG 59.661 45.833 5.01 0.00 32.23 4.18
84 85 4.337555 GGCCAACTACTTATAGACAGTCGA 59.662 45.833 0.00 0.00 32.23 4.20
85 86 5.163581 GGCCAACTACTTATAGACAGTCGAA 60.164 44.000 0.00 0.00 32.23 3.71
86 87 6.327934 GCCAACTACTTATAGACAGTCGAAA 58.672 40.000 0.00 0.00 32.23 3.46
87 88 6.472808 GCCAACTACTTATAGACAGTCGAAAG 59.527 42.308 9.70 9.70 32.23 2.62
88 89 7.627939 GCCAACTACTTATAGACAGTCGAAAGA 60.628 40.741 15.45 3.69 32.60 2.52
89 90 7.911205 CCAACTACTTATAGACAGTCGAAAGAG 59.089 40.741 15.45 11.59 34.61 2.85
90 91 8.666573 CAACTACTTATAGACAGTCGAAAGAGA 58.333 37.037 15.45 6.02 34.61 3.10
91 92 8.789825 ACTACTTATAGACAGTCGAAAGAGAA 57.210 34.615 15.45 4.48 34.61 2.87
92 93 9.228949 ACTACTTATAGACAGTCGAAAGAGAAA 57.771 33.333 15.45 2.82 34.61 2.52
112 113 3.751479 AAAACAAAGATGAAGCCCACC 57.249 42.857 0.00 0.00 0.00 4.61
113 114 2.380064 AACAAAGATGAAGCCCACCA 57.620 45.000 0.00 0.00 0.00 4.17
114 115 1.915141 ACAAAGATGAAGCCCACCAG 58.085 50.000 0.00 0.00 0.00 4.00
115 116 1.425066 ACAAAGATGAAGCCCACCAGA 59.575 47.619 0.00 0.00 0.00 3.86
116 117 2.158475 ACAAAGATGAAGCCCACCAGAA 60.158 45.455 0.00 0.00 0.00 3.02
117 118 2.892852 CAAAGATGAAGCCCACCAGAAA 59.107 45.455 0.00 0.00 0.00 2.52
118 119 2.978156 AGATGAAGCCCACCAGAAAA 57.022 45.000 0.00 0.00 0.00 2.29
119 120 2.800250 AGATGAAGCCCACCAGAAAAG 58.200 47.619 0.00 0.00 0.00 2.27
120 121 1.203287 GATGAAGCCCACCAGAAAAGC 59.797 52.381 0.00 0.00 0.00 3.51
121 122 0.827507 TGAAGCCCACCAGAAAAGCC 60.828 55.000 0.00 0.00 0.00 4.35
122 123 0.540597 GAAGCCCACCAGAAAAGCCT 60.541 55.000 0.00 0.00 0.00 4.58
123 124 0.777446 AAGCCCACCAGAAAAGCCTA 59.223 50.000 0.00 0.00 0.00 3.93
124 125 0.329596 AGCCCACCAGAAAAGCCTAG 59.670 55.000 0.00 0.00 0.00 3.02
125 126 0.328258 GCCCACCAGAAAAGCCTAGA 59.672 55.000 0.00 0.00 0.00 2.43
126 127 1.271926 GCCCACCAGAAAAGCCTAGAA 60.272 52.381 0.00 0.00 0.00 2.10
127 128 2.716217 CCCACCAGAAAAGCCTAGAAG 58.284 52.381 0.00 0.00 0.00 2.85
128 129 2.619074 CCCACCAGAAAAGCCTAGAAGG 60.619 54.545 0.00 0.00 38.80 3.46
138 139 3.139029 CCTAGAAGGCAACGTGTCC 57.861 57.895 0.00 0.00 46.39 4.02
139 140 0.320374 CCTAGAAGGCAACGTGTCCA 59.680 55.000 8.78 0.00 46.39 4.02
140 141 1.066143 CCTAGAAGGCAACGTGTCCAT 60.066 52.381 8.78 0.00 46.39 3.41
141 142 2.271800 CTAGAAGGCAACGTGTCCATC 58.728 52.381 8.78 6.34 46.39 3.51
142 143 0.670546 AGAAGGCAACGTGTCCATCG 60.671 55.000 8.78 0.00 46.39 3.84
143 144 0.669318 GAAGGCAACGTGTCCATCGA 60.669 55.000 8.78 0.00 46.39 3.59
144 145 0.036388 AAGGCAACGTGTCCATCGAT 60.036 50.000 8.78 0.00 46.39 3.59
145 146 0.036388 AGGCAACGTGTCCATCGATT 60.036 50.000 0.00 0.00 46.39 3.34
146 147 0.096976 GGCAACGTGTCCATCGATTG 59.903 55.000 0.00 0.00 0.00 2.67
147 148 1.075542 GCAACGTGTCCATCGATTGA 58.924 50.000 0.00 0.00 0.00 2.57
148 149 1.061131 GCAACGTGTCCATCGATTGAG 59.939 52.381 0.00 0.00 0.00 3.02
149 150 2.337583 CAACGTGTCCATCGATTGAGT 58.662 47.619 0.00 0.00 0.00 3.41
150 151 1.996292 ACGTGTCCATCGATTGAGTG 58.004 50.000 0.00 0.00 0.00 3.51
151 152 1.280982 CGTGTCCATCGATTGAGTGG 58.719 55.000 0.00 0.00 0.00 4.00
152 153 1.009829 GTGTCCATCGATTGAGTGGC 58.990 55.000 0.00 0.00 33.01 5.01
153 154 0.612744 TGTCCATCGATTGAGTGGCA 59.387 50.000 0.00 0.00 33.01 4.92
154 155 1.293924 GTCCATCGATTGAGTGGCAG 58.706 55.000 0.00 0.00 33.01 4.85
155 156 0.904649 TCCATCGATTGAGTGGCAGT 59.095 50.000 0.00 0.00 33.01 4.40
156 157 1.134699 TCCATCGATTGAGTGGCAGTC 60.135 52.381 15.47 15.47 33.01 3.51
157 158 1.405933 CCATCGATTGAGTGGCAGTCA 60.406 52.381 20.75 20.75 33.18 3.41
158 159 2.349590 CATCGATTGAGTGGCAGTCAA 58.650 47.619 33.07 33.07 41.31 3.18
159 160 1.795768 TCGATTGAGTGGCAGTCAAC 58.204 50.000 33.51 25.27 40.03 3.18
160 161 0.439985 CGATTGAGTGGCAGTCAACG 59.560 55.000 33.51 30.38 40.03 4.10
161 162 1.795768 GATTGAGTGGCAGTCAACGA 58.204 50.000 33.51 17.25 40.03 3.85
162 163 1.461127 GATTGAGTGGCAGTCAACGAC 59.539 52.381 33.51 24.06 40.03 4.34
163 164 0.176910 TTGAGTGGCAGTCAACGACA 59.823 50.000 29.05 11.16 32.96 4.35
164 165 0.529773 TGAGTGGCAGTCAACGACAC 60.530 55.000 22.22 0.00 34.60 3.67
165 166 0.529773 GAGTGGCAGTCAACGACACA 60.530 55.000 17.32 0.00 34.60 3.72
166 167 0.107897 AGTGGCAGTCAACGACACAA 60.108 50.000 11.58 0.00 34.60 3.33
167 168 0.304705 GTGGCAGTCAACGACACAAG 59.695 55.000 0.00 0.00 34.60 3.16
168 169 0.813610 TGGCAGTCAACGACACAAGG 60.814 55.000 0.00 0.00 34.60 3.61
169 170 0.531974 GGCAGTCAACGACACAAGGA 60.532 55.000 0.00 0.00 34.60 3.36
170 171 0.582005 GCAGTCAACGACACAAGGAC 59.418 55.000 0.00 0.00 34.60 3.85
171 172 1.934589 CAGTCAACGACACAAGGACA 58.065 50.000 0.00 0.00 34.60 4.02
172 173 1.593006 CAGTCAACGACACAAGGACAC 59.407 52.381 0.00 0.00 34.60 3.67
173 174 1.480954 AGTCAACGACACAAGGACACT 59.519 47.619 0.00 0.00 34.60 3.55
174 175 1.593006 GTCAACGACACAAGGACACTG 59.407 52.381 0.00 0.00 32.09 3.66
175 176 0.937304 CAACGACACAAGGACACTGG 59.063 55.000 0.00 0.00 0.00 4.00
176 177 0.828022 AACGACACAAGGACACTGGA 59.172 50.000 0.00 0.00 0.00 3.86
177 178 0.104304 ACGACACAAGGACACTGGAC 59.896 55.000 0.00 0.00 0.00 4.02
178 179 0.939577 CGACACAAGGACACTGGACG 60.940 60.000 0.00 0.00 0.00 4.79
179 180 0.104304 GACACAAGGACACTGGACGT 59.896 55.000 0.00 0.00 0.00 4.34
187 188 2.591429 CACTGGACGTGGCAAGCA 60.591 61.111 0.00 0.00 40.02 3.91
188 189 1.968017 CACTGGACGTGGCAAGCAT 60.968 57.895 0.00 0.00 40.02 3.79
189 190 1.968017 ACTGGACGTGGCAAGCATG 60.968 57.895 0.00 0.00 0.00 4.06
202 203 3.132629 CAAGCATGCACAGAATCAGAC 57.867 47.619 21.98 0.00 0.00 3.51
203 204 1.366679 AGCATGCACAGAATCAGACG 58.633 50.000 21.98 0.00 0.00 4.18
204 205 1.081892 GCATGCACAGAATCAGACGT 58.918 50.000 14.21 0.00 0.00 4.34
205 206 1.201998 GCATGCACAGAATCAGACGTG 60.202 52.381 14.21 0.00 0.00 4.49
210 211 3.494045 CACAGAATCAGACGTGCTAGA 57.506 47.619 0.00 0.00 0.00 2.43
211 212 3.838120 CACAGAATCAGACGTGCTAGAA 58.162 45.455 0.00 0.00 0.00 2.10
212 213 3.610242 CACAGAATCAGACGTGCTAGAAC 59.390 47.826 0.00 0.00 0.00 3.01
213 214 3.255888 ACAGAATCAGACGTGCTAGAACA 59.744 43.478 0.74 0.00 0.00 3.18
214 215 4.237724 CAGAATCAGACGTGCTAGAACAA 58.762 43.478 0.74 0.00 0.00 2.83
215 216 4.867047 CAGAATCAGACGTGCTAGAACAAT 59.133 41.667 0.74 0.00 0.00 2.71
216 217 5.005203 CAGAATCAGACGTGCTAGAACAATC 59.995 44.000 0.74 0.00 0.00 2.67
217 218 3.232213 TCAGACGTGCTAGAACAATCC 57.768 47.619 0.74 0.00 0.00 3.01
218 219 2.094182 TCAGACGTGCTAGAACAATCCC 60.094 50.000 0.74 0.00 0.00 3.85
219 220 1.899814 AGACGTGCTAGAACAATCCCA 59.100 47.619 0.74 0.00 0.00 4.37
220 221 2.000447 GACGTGCTAGAACAATCCCAC 59.000 52.381 0.74 0.00 0.00 4.61
221 222 1.338769 ACGTGCTAGAACAATCCCACC 60.339 52.381 0.74 0.00 0.00 4.61
222 223 1.338674 CGTGCTAGAACAATCCCACCA 60.339 52.381 0.74 0.00 0.00 4.17
223 224 2.790433 GTGCTAGAACAATCCCACCAA 58.210 47.619 0.00 0.00 0.00 3.67
224 225 2.749621 GTGCTAGAACAATCCCACCAAG 59.250 50.000 0.00 0.00 0.00 3.61
225 226 1.745653 GCTAGAACAATCCCACCAAGC 59.254 52.381 0.00 0.00 0.00 4.01
226 227 2.879756 GCTAGAACAATCCCACCAAGCA 60.880 50.000 0.00 0.00 0.00 3.91
227 228 2.380064 AGAACAATCCCACCAAGCAA 57.620 45.000 0.00 0.00 0.00 3.91
228 229 2.676748 AGAACAATCCCACCAAGCAAA 58.323 42.857 0.00 0.00 0.00 3.68
229 230 3.037549 AGAACAATCCCACCAAGCAAAA 58.962 40.909 0.00 0.00 0.00 2.44
230 231 3.454082 AGAACAATCCCACCAAGCAAAAA 59.546 39.130 0.00 0.00 0.00 1.94
252 253 8.990163 AAAAATAAAACCAGTCCACTCTAGAA 57.010 30.769 0.00 0.00 0.00 2.10
253 254 8.990163 AAAATAAAACCAGTCCACTCTAGAAA 57.010 30.769 0.00 0.00 0.00 2.52
254 255 8.990163 AAATAAAACCAGTCCACTCTAGAAAA 57.010 30.769 0.00 0.00 0.00 2.29
255 256 7.981102 ATAAAACCAGTCCACTCTAGAAAAC 57.019 36.000 0.00 0.00 0.00 2.43
256 257 4.353383 AACCAGTCCACTCTAGAAAACC 57.647 45.455 0.00 0.00 0.00 3.27
257 258 3.314693 ACCAGTCCACTCTAGAAAACCA 58.685 45.455 0.00 0.00 0.00 3.67
258 259 3.714798 ACCAGTCCACTCTAGAAAACCAA 59.285 43.478 0.00 0.00 0.00 3.67
259 260 4.065789 CCAGTCCACTCTAGAAAACCAAC 58.934 47.826 0.00 0.00 0.00 3.77
260 261 4.065789 CAGTCCACTCTAGAAAACCAACC 58.934 47.826 0.00 0.00 0.00 3.77
261 262 3.974642 AGTCCACTCTAGAAAACCAACCT 59.025 43.478 0.00 0.00 0.00 3.50
262 263 4.065789 GTCCACTCTAGAAAACCAACCTG 58.934 47.826 0.00 0.00 0.00 4.00
263 264 2.814336 CCACTCTAGAAAACCAACCTGC 59.186 50.000 0.00 0.00 0.00 4.85
264 265 3.476552 CACTCTAGAAAACCAACCTGCA 58.523 45.455 0.00 0.00 0.00 4.41
265 266 3.251004 CACTCTAGAAAACCAACCTGCAC 59.749 47.826 0.00 0.00 0.00 4.57
266 267 3.118038 ACTCTAGAAAACCAACCTGCACA 60.118 43.478 0.00 0.00 0.00 4.57
267 268 3.211045 TCTAGAAAACCAACCTGCACAC 58.789 45.455 0.00 0.00 0.00 3.82
268 269 0.738389 AGAAAACCAACCTGCACACG 59.262 50.000 0.00 0.00 0.00 4.49
269 270 0.454196 GAAAACCAACCTGCACACGT 59.546 50.000 0.00 0.00 0.00 4.49
270 271 0.172352 AAAACCAACCTGCACACGTG 59.828 50.000 15.48 15.48 0.00 4.49
271 272 0.963355 AAACCAACCTGCACACGTGT 60.963 50.000 17.22 17.22 0.00 4.49
272 273 1.373590 AACCAACCTGCACACGTGTC 61.374 55.000 20.49 14.17 0.00 3.67
273 274 2.542907 CCAACCTGCACACGTGTCC 61.543 63.158 20.49 11.32 0.00 4.02
274 275 2.203153 AACCTGCACACGTGTCCC 60.203 61.111 20.49 13.44 0.00 4.46
275 276 2.742116 AACCTGCACACGTGTCCCT 61.742 57.895 20.49 0.00 0.00 4.20
276 277 2.357517 CCTGCACACGTGTCCCTC 60.358 66.667 20.49 8.90 0.00 4.30
277 278 2.421314 CTGCACACGTGTCCCTCA 59.579 61.111 20.49 13.00 0.00 3.86
278 279 1.227527 CTGCACACGTGTCCCTCAA 60.228 57.895 20.49 0.00 0.00 3.02
279 280 0.813610 CTGCACACGTGTCCCTCAAA 60.814 55.000 20.49 0.00 0.00 2.69
280 281 1.092921 TGCACACGTGTCCCTCAAAC 61.093 55.000 20.49 1.65 0.00 2.93
281 282 1.092921 GCACACGTGTCCCTCAAACA 61.093 55.000 20.49 0.00 0.00 2.83
282 283 1.374560 CACACGTGTCCCTCAAACAA 58.625 50.000 20.49 0.00 0.00 2.83
283 284 1.330521 CACACGTGTCCCTCAAACAAG 59.669 52.381 20.49 0.00 33.16 3.16
284 285 0.944386 CACGTGTCCCTCAAACAAGG 59.056 55.000 7.58 0.00 36.08 3.61
294 295 4.664150 CCTCAAACAAGGGCAGTAAAAA 57.336 40.909 0.00 0.00 32.35 1.94
326 327 5.607939 AAAAACCAGAAAATTCGAACCCT 57.392 34.783 0.00 0.00 0.00 4.34
327 328 5.607939 AAAACCAGAAAATTCGAACCCTT 57.392 34.783 0.00 0.00 0.00 3.95
328 329 6.718522 AAAACCAGAAAATTCGAACCCTTA 57.281 33.333 0.00 0.00 0.00 2.69
329 330 5.700722 AACCAGAAAATTCGAACCCTTAC 57.299 39.130 0.00 0.00 0.00 2.34
330 331 3.749609 ACCAGAAAATTCGAACCCTTACG 59.250 43.478 0.00 0.00 0.00 3.18
331 332 3.126343 CCAGAAAATTCGAACCCTTACGG 59.874 47.826 0.00 0.00 37.81 4.02
346 347 5.629125 CCCTTACGGGTCTAGTATTCTAGT 58.371 45.833 6.31 0.00 46.12 2.57
347 348 6.773638 CCCTTACGGGTCTAGTATTCTAGTA 58.226 44.000 6.31 0.00 46.12 1.82
348 349 7.227156 CCCTTACGGGTCTAGTATTCTAGTAA 58.773 42.308 6.31 0.00 46.12 2.24
349 350 7.887495 CCCTTACGGGTCTAGTATTCTAGTAAT 59.113 40.741 6.31 0.00 46.12 1.89
350 351 9.950496 CCTTACGGGTCTAGTATTCTAGTAATA 57.050 37.037 6.31 0.00 42.88 0.98
353 354 8.804912 ACGGGTCTAGTATTCTAGTAATATGG 57.195 38.462 6.31 0.00 42.88 2.74
454 486 3.149981 CACAAGAAGGAAGGAAGGAACC 58.850 50.000 0.00 0.00 0.00 3.62
717 800 9.983804 GCTTCGTAGCTATTTTTAGTGTAAAAT 57.016 29.630 6.80 0.00 44.27 1.82
731 814 3.883489 GTGTAAAATAGATGGTGCCCTCC 59.117 47.826 0.00 0.00 0.00 4.30
732 815 3.525609 TGTAAAATAGATGGTGCCCTCCA 59.474 43.478 0.00 0.00 42.01 3.86
777 861 6.092122 TGTGATATTCATTCGTGGTTCAGTTC 59.908 38.462 0.00 0.00 0.00 3.01
798 882 5.794687 TCTGTTTTCACGTATAGCAATGG 57.205 39.130 0.00 0.00 0.00 3.16
811 895 5.927281 ATAGCAATGGCATTCTTCTTTGT 57.073 34.783 10.36 0.00 44.61 2.83
950 1034 9.965902 AGTTGTTATCAAGAGGAGTAATTTGAT 57.034 29.630 4.28 4.28 41.61 2.57
1102 1188 1.173444 CGGGGTCTCTAGTGGGATCG 61.173 65.000 0.00 0.00 0.00 3.69
1112 1198 5.071923 TCTCTAGTGGGATCGATGAACTAGA 59.928 44.000 25.28 25.28 44.28 2.43
1337 1423 0.105862 AATCCCCTGCATGTCCATGG 60.106 55.000 4.97 4.97 39.16 3.66
2573 2779 4.263677 CACGATGTATGCAAACATTTGAGC 59.736 41.667 8.54 0.00 40.17 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.125753 CGCTGCTGTCTCCTGTCC 60.126 66.667 0.00 0.00 0.00 4.02
3 4 0.528017 TACTTCGCTGCTGTCTCCTG 59.472 55.000 0.00 0.00 0.00 3.86
6 7 2.857152 CAGATTACTTCGCTGCTGTCTC 59.143 50.000 0.00 0.00 0.00 3.36
9 10 1.406069 CCCAGATTACTTCGCTGCTGT 60.406 52.381 0.00 0.00 0.00 4.40
10 11 1.293924 CCCAGATTACTTCGCTGCTG 58.706 55.000 0.00 0.00 0.00 4.41
11 12 0.905357 ACCCAGATTACTTCGCTGCT 59.095 50.000 0.00 0.00 0.00 4.24
12 13 1.398390 CAACCCAGATTACTTCGCTGC 59.602 52.381 0.00 0.00 0.00 5.25
13 14 2.009774 CCAACCCAGATTACTTCGCTG 58.990 52.381 0.00 0.00 0.00 5.18
14 15 1.065418 CCCAACCCAGATTACTTCGCT 60.065 52.381 0.00 0.00 0.00 4.93
15 16 1.379527 CCCAACCCAGATTACTTCGC 58.620 55.000 0.00 0.00 0.00 4.70
16 17 1.065418 AGCCCAACCCAGATTACTTCG 60.065 52.381 0.00 0.00 0.00 3.79
17 18 2.808906 AGCCCAACCCAGATTACTTC 57.191 50.000 0.00 0.00 0.00 3.01
18 19 3.621461 CGTAAGCCCAACCCAGATTACTT 60.621 47.826 0.00 0.00 0.00 2.24
19 20 2.093128 CGTAAGCCCAACCCAGATTACT 60.093 50.000 0.00 0.00 0.00 2.24
20 21 2.285977 CGTAAGCCCAACCCAGATTAC 58.714 52.381 0.00 0.00 0.00 1.89
21 22 1.210967 CCGTAAGCCCAACCCAGATTA 59.789 52.381 0.00 0.00 0.00 1.75
22 23 0.034477 CCGTAAGCCCAACCCAGATT 60.034 55.000 0.00 0.00 0.00 2.40
23 24 0.912487 TCCGTAAGCCCAACCCAGAT 60.912 55.000 0.00 0.00 0.00 2.90
24 25 1.536907 TCCGTAAGCCCAACCCAGA 60.537 57.895 0.00 0.00 0.00 3.86
25 26 1.078426 CTCCGTAAGCCCAACCCAG 60.078 63.158 0.00 0.00 0.00 4.45
26 27 1.128809 TTCTCCGTAAGCCCAACCCA 61.129 55.000 0.00 0.00 0.00 4.51
27 28 0.675837 GTTCTCCGTAAGCCCAACCC 60.676 60.000 0.00 0.00 0.00 4.11
28 29 1.017701 CGTTCTCCGTAAGCCCAACC 61.018 60.000 0.00 0.00 0.00 3.77
29 30 2.452767 CGTTCTCCGTAAGCCCAAC 58.547 57.895 0.00 0.00 0.00 3.77
39 40 0.859232 CTGTTGGTTCACGTTCTCCG 59.141 55.000 0.00 0.00 44.03 4.63
40 41 0.586802 GCTGTTGGTTCACGTTCTCC 59.413 55.000 0.00 0.00 0.00 3.71
41 42 1.261619 CTGCTGTTGGTTCACGTTCTC 59.738 52.381 0.00 0.00 0.00 2.87
42 43 1.299541 CTGCTGTTGGTTCACGTTCT 58.700 50.000 0.00 0.00 0.00 3.01
43 44 0.307760 CCTGCTGTTGGTTCACGTTC 59.692 55.000 0.00 0.00 0.00 3.95
44 45 1.724582 GCCTGCTGTTGGTTCACGTT 61.725 55.000 0.00 0.00 0.00 3.99
45 46 2.186826 GCCTGCTGTTGGTTCACGT 61.187 57.895 0.00 0.00 0.00 4.49
46 47 2.639286 GCCTGCTGTTGGTTCACG 59.361 61.111 0.00 0.00 0.00 4.35
47 48 1.391157 TTGGCCTGCTGTTGGTTCAC 61.391 55.000 3.32 0.00 0.00 3.18
48 49 1.076412 TTGGCCTGCTGTTGGTTCA 60.076 52.632 3.32 0.00 0.00 3.18
49 50 1.109323 AGTTGGCCTGCTGTTGGTTC 61.109 55.000 3.32 0.00 0.00 3.62
50 51 0.184933 TAGTTGGCCTGCTGTTGGTT 59.815 50.000 3.32 0.00 0.00 3.67
51 52 0.537371 GTAGTTGGCCTGCTGTTGGT 60.537 55.000 3.32 0.00 0.00 3.67
52 53 0.250901 AGTAGTTGGCCTGCTGTTGG 60.251 55.000 3.32 0.00 34.49 3.77
53 54 1.609208 AAGTAGTTGGCCTGCTGTTG 58.391 50.000 3.32 0.00 36.13 3.33
54 55 3.721087 ATAAGTAGTTGGCCTGCTGTT 57.279 42.857 3.32 3.43 36.13 3.16
55 56 4.030913 TCTATAAGTAGTTGGCCTGCTGT 58.969 43.478 3.32 0.00 36.13 4.40
56 57 4.141937 TGTCTATAAGTAGTTGGCCTGCTG 60.142 45.833 3.32 0.00 36.13 4.41
57 58 4.030913 TGTCTATAAGTAGTTGGCCTGCT 58.969 43.478 3.32 4.41 37.79 4.24
58 59 4.141914 ACTGTCTATAAGTAGTTGGCCTGC 60.142 45.833 3.32 0.00 0.00 4.85
59 60 5.593010 GACTGTCTATAAGTAGTTGGCCTG 58.407 45.833 3.32 0.00 0.00 4.85
60 61 4.338682 CGACTGTCTATAAGTAGTTGGCCT 59.661 45.833 3.32 0.00 0.00 5.19
61 62 4.337555 TCGACTGTCTATAAGTAGTTGGCC 59.662 45.833 6.21 0.00 0.00 5.36
62 63 5.496133 TCGACTGTCTATAAGTAGTTGGC 57.504 43.478 6.21 0.00 0.00 4.52
63 64 7.759465 TCTTTCGACTGTCTATAAGTAGTTGG 58.241 38.462 6.21 0.00 0.00 3.77
64 65 8.666573 TCTCTTTCGACTGTCTATAAGTAGTTG 58.333 37.037 6.21 0.00 0.00 3.16
65 66 8.789825 TCTCTTTCGACTGTCTATAAGTAGTT 57.210 34.615 6.21 0.00 0.00 2.24
66 67 8.789825 TTCTCTTTCGACTGTCTATAAGTAGT 57.210 34.615 6.21 0.00 0.00 2.73
91 92 3.454082 TGGTGGGCTTCATCTTTGTTTTT 59.546 39.130 0.00 0.00 0.00 1.94
92 93 3.037549 TGGTGGGCTTCATCTTTGTTTT 58.962 40.909 0.00 0.00 0.00 2.43
93 94 2.629617 CTGGTGGGCTTCATCTTTGTTT 59.370 45.455 0.00 0.00 0.00 2.83
94 95 2.158475 TCTGGTGGGCTTCATCTTTGTT 60.158 45.455 0.00 0.00 0.00 2.83
95 96 1.425066 TCTGGTGGGCTTCATCTTTGT 59.575 47.619 0.00 0.00 0.00 2.83
96 97 2.205022 TCTGGTGGGCTTCATCTTTG 57.795 50.000 0.00 0.00 0.00 2.77
97 98 2.978156 TTCTGGTGGGCTTCATCTTT 57.022 45.000 0.00 0.00 0.00 2.52
98 99 2.978156 TTTCTGGTGGGCTTCATCTT 57.022 45.000 0.00 0.00 0.00 2.40
99 100 2.800250 CTTTTCTGGTGGGCTTCATCT 58.200 47.619 0.00 0.00 0.00 2.90
100 101 1.203287 GCTTTTCTGGTGGGCTTCATC 59.797 52.381 0.00 0.00 0.00 2.92
101 102 1.260544 GCTTTTCTGGTGGGCTTCAT 58.739 50.000 0.00 0.00 0.00 2.57
102 103 0.827507 GGCTTTTCTGGTGGGCTTCA 60.828 55.000 0.00 0.00 0.00 3.02
103 104 0.540597 AGGCTTTTCTGGTGGGCTTC 60.541 55.000 0.00 0.00 0.00 3.86
104 105 0.777446 TAGGCTTTTCTGGTGGGCTT 59.223 50.000 0.00 0.00 36.11 4.35
105 106 0.329596 CTAGGCTTTTCTGGTGGGCT 59.670 55.000 0.00 0.00 38.17 5.19
106 107 0.328258 TCTAGGCTTTTCTGGTGGGC 59.672 55.000 0.00 0.00 0.00 5.36
107 108 2.619074 CCTTCTAGGCTTTTCTGGTGGG 60.619 54.545 0.00 0.00 0.00 4.61
108 109 2.716217 CCTTCTAGGCTTTTCTGGTGG 58.284 52.381 0.00 0.00 0.00 4.61
120 121 0.320374 TGGACACGTTGCCTTCTAGG 59.680 55.000 5.17 0.00 38.80 3.02
121 122 2.271800 GATGGACACGTTGCCTTCTAG 58.728 52.381 10.45 0.00 0.00 2.43
122 123 1.403647 CGATGGACACGTTGCCTTCTA 60.404 52.381 13.93 0.00 0.00 2.10
123 124 0.670546 CGATGGACACGTTGCCTTCT 60.671 55.000 13.93 0.00 0.00 2.85
124 125 0.669318 TCGATGGACACGTTGCCTTC 60.669 55.000 5.17 7.03 0.00 3.46
125 126 0.036388 ATCGATGGACACGTTGCCTT 60.036 50.000 0.00 0.00 0.00 4.35
126 127 0.036388 AATCGATGGACACGTTGCCT 60.036 50.000 0.00 0.00 0.00 4.75
127 128 0.096976 CAATCGATGGACACGTTGCC 59.903 55.000 0.00 0.00 0.00 4.52
128 129 1.061131 CTCAATCGATGGACACGTTGC 59.939 52.381 0.00 0.00 0.00 4.17
129 130 2.092681 CACTCAATCGATGGACACGTTG 59.907 50.000 0.00 0.00 0.00 4.10
130 131 2.337583 CACTCAATCGATGGACACGTT 58.662 47.619 0.00 0.00 0.00 3.99
131 132 1.404181 CCACTCAATCGATGGACACGT 60.404 52.381 0.00 0.00 35.33 4.49
132 133 1.280982 CCACTCAATCGATGGACACG 58.719 55.000 0.00 0.00 35.33 4.49
133 134 1.009829 GCCACTCAATCGATGGACAC 58.990 55.000 6.18 0.00 35.33 3.67
134 135 0.612744 TGCCACTCAATCGATGGACA 59.387 50.000 6.18 0.00 35.33 4.02
135 136 1.293924 CTGCCACTCAATCGATGGAC 58.706 55.000 6.18 0.00 35.33 4.02
136 137 0.904649 ACTGCCACTCAATCGATGGA 59.095 50.000 6.18 4.08 35.33 3.41
137 138 1.293924 GACTGCCACTCAATCGATGG 58.706 55.000 0.00 0.00 36.51 3.51
138 139 2.014335 TGACTGCCACTCAATCGATG 57.986 50.000 0.00 0.00 0.00 3.84
139 140 2.350522 GTTGACTGCCACTCAATCGAT 58.649 47.619 0.00 0.00 30.46 3.59
140 141 1.795768 GTTGACTGCCACTCAATCGA 58.204 50.000 0.00 0.00 30.46 3.59
141 142 0.439985 CGTTGACTGCCACTCAATCG 59.560 55.000 0.00 0.00 30.46 3.34
142 143 1.461127 GTCGTTGACTGCCACTCAATC 59.539 52.381 0.00 0.00 30.46 2.67
143 144 1.202639 TGTCGTTGACTGCCACTCAAT 60.203 47.619 0.00 0.00 33.15 2.57
144 145 0.176910 TGTCGTTGACTGCCACTCAA 59.823 50.000 0.00 0.00 33.15 3.02
145 146 0.529773 GTGTCGTTGACTGCCACTCA 60.530 55.000 0.00 0.00 33.15 3.41
146 147 0.529773 TGTGTCGTTGACTGCCACTC 60.530 55.000 0.00 0.00 33.15 3.51
147 148 0.107897 TTGTGTCGTTGACTGCCACT 60.108 50.000 0.00 0.00 33.15 4.00
148 149 0.304705 CTTGTGTCGTTGACTGCCAC 59.695 55.000 0.00 0.00 33.15 5.01
149 150 0.813610 CCTTGTGTCGTTGACTGCCA 60.814 55.000 0.00 0.00 33.15 4.92
150 151 0.531974 TCCTTGTGTCGTTGACTGCC 60.532 55.000 0.00 0.00 33.15 4.85
151 152 0.582005 GTCCTTGTGTCGTTGACTGC 59.418 55.000 0.00 0.00 33.15 4.40
152 153 1.593006 GTGTCCTTGTGTCGTTGACTG 59.407 52.381 0.00 0.00 33.15 3.51
153 154 1.480954 AGTGTCCTTGTGTCGTTGACT 59.519 47.619 0.00 0.00 33.15 3.41
154 155 1.593006 CAGTGTCCTTGTGTCGTTGAC 59.407 52.381 0.00 0.00 0.00 3.18
155 156 1.472552 CCAGTGTCCTTGTGTCGTTGA 60.473 52.381 0.00 0.00 0.00 3.18
156 157 0.937304 CCAGTGTCCTTGTGTCGTTG 59.063 55.000 0.00 0.00 0.00 4.10
157 158 0.828022 TCCAGTGTCCTTGTGTCGTT 59.172 50.000 0.00 0.00 0.00 3.85
158 159 0.104304 GTCCAGTGTCCTTGTGTCGT 59.896 55.000 0.00 0.00 0.00 4.34
159 160 0.939577 CGTCCAGTGTCCTTGTGTCG 60.940 60.000 0.00 0.00 0.00 4.35
160 161 0.104304 ACGTCCAGTGTCCTTGTGTC 59.896 55.000 0.00 0.00 0.00 3.67
161 162 0.179084 CACGTCCAGTGTCCTTGTGT 60.179 55.000 0.00 0.00 45.51 3.72
162 163 2.605094 CACGTCCAGTGTCCTTGTG 58.395 57.895 0.00 0.00 45.51 3.33
171 172 1.968017 CATGCTTGCCACGTCCAGT 60.968 57.895 0.00 0.00 0.00 4.00
172 173 2.872557 CATGCTTGCCACGTCCAG 59.127 61.111 0.00 0.00 0.00 3.86
173 174 3.364441 GCATGCTTGCCACGTCCA 61.364 61.111 11.37 0.00 43.38 4.02
182 183 2.475685 CGTCTGATTCTGTGCATGCTTG 60.476 50.000 20.33 8.92 0.00 4.01
183 184 1.736126 CGTCTGATTCTGTGCATGCTT 59.264 47.619 20.33 0.00 0.00 3.91
184 185 1.338484 ACGTCTGATTCTGTGCATGCT 60.338 47.619 20.33 0.00 0.00 3.79
185 186 1.081892 ACGTCTGATTCTGTGCATGC 58.918 50.000 11.82 11.82 0.00 4.06
186 187 2.800694 CACGTCTGATTCTGTGCATG 57.199 50.000 0.00 0.00 0.00 4.06
190 191 3.494045 TCTAGCACGTCTGATTCTGTG 57.506 47.619 0.00 0.00 35.48 3.66
191 192 3.255888 TGTTCTAGCACGTCTGATTCTGT 59.744 43.478 0.00 0.00 0.00 3.41
192 193 3.838120 TGTTCTAGCACGTCTGATTCTG 58.162 45.455 0.00 0.00 0.00 3.02
193 194 4.521130 TTGTTCTAGCACGTCTGATTCT 57.479 40.909 0.00 0.00 0.00 2.40
194 195 4.268884 GGATTGTTCTAGCACGTCTGATTC 59.731 45.833 0.00 0.00 0.00 2.52
195 196 4.184629 GGATTGTTCTAGCACGTCTGATT 58.815 43.478 0.00 0.00 0.00 2.57
196 197 3.430929 GGGATTGTTCTAGCACGTCTGAT 60.431 47.826 0.00 0.00 0.00 2.90
197 198 2.094182 GGGATTGTTCTAGCACGTCTGA 60.094 50.000 0.00 0.00 0.00 3.27
198 199 2.271800 GGGATTGTTCTAGCACGTCTG 58.728 52.381 0.00 0.00 0.00 3.51
199 200 1.899814 TGGGATTGTTCTAGCACGTCT 59.100 47.619 0.00 0.00 0.00 4.18
200 201 2.000447 GTGGGATTGTTCTAGCACGTC 59.000 52.381 0.00 0.00 0.00 4.34
201 202 1.338769 GGTGGGATTGTTCTAGCACGT 60.339 52.381 0.00 0.00 0.00 4.49
202 203 1.338674 TGGTGGGATTGTTCTAGCACG 60.339 52.381 0.00 0.00 0.00 5.34
203 204 2.489938 TGGTGGGATTGTTCTAGCAC 57.510 50.000 0.00 0.00 0.00 4.40
204 205 2.879756 GCTTGGTGGGATTGTTCTAGCA 60.880 50.000 0.00 0.00 0.00 3.49
205 206 1.745653 GCTTGGTGGGATTGTTCTAGC 59.254 52.381 0.00 0.00 0.00 3.42
206 207 3.071874 TGCTTGGTGGGATTGTTCTAG 57.928 47.619 0.00 0.00 0.00 2.43
207 208 3.517296 TTGCTTGGTGGGATTGTTCTA 57.483 42.857 0.00 0.00 0.00 2.10
208 209 2.380064 TTGCTTGGTGGGATTGTTCT 57.620 45.000 0.00 0.00 0.00 3.01
209 210 3.467374 TTTTGCTTGGTGGGATTGTTC 57.533 42.857 0.00 0.00 0.00 3.18
210 211 3.922171 TTTTTGCTTGGTGGGATTGTT 57.078 38.095 0.00 0.00 0.00 2.83
227 228 8.990163 TTCTAGAGTGGACTGGTTTTATTTTT 57.010 30.769 0.00 0.00 0.00 1.94
228 229 8.990163 TTTCTAGAGTGGACTGGTTTTATTTT 57.010 30.769 0.00 0.00 0.00 1.82
229 230 8.847196 GTTTTCTAGAGTGGACTGGTTTTATTT 58.153 33.333 0.00 0.00 0.00 1.40
230 231 7.447545 GGTTTTCTAGAGTGGACTGGTTTTATT 59.552 37.037 0.00 0.00 0.00 1.40
231 232 6.940867 GGTTTTCTAGAGTGGACTGGTTTTAT 59.059 38.462 0.00 0.00 0.00 1.40
232 233 6.126710 TGGTTTTCTAGAGTGGACTGGTTTTA 60.127 38.462 0.00 0.00 0.00 1.52
233 234 5.131067 GGTTTTCTAGAGTGGACTGGTTTT 58.869 41.667 0.00 0.00 0.00 2.43
234 235 4.165372 TGGTTTTCTAGAGTGGACTGGTTT 59.835 41.667 0.00 0.00 0.00 3.27
235 236 3.714798 TGGTTTTCTAGAGTGGACTGGTT 59.285 43.478 0.00 0.00 0.00 3.67
236 237 3.314693 TGGTTTTCTAGAGTGGACTGGT 58.685 45.455 0.00 0.00 0.00 4.00
237 238 4.065789 GTTGGTTTTCTAGAGTGGACTGG 58.934 47.826 0.00 0.00 0.00 4.00
238 239 4.065789 GGTTGGTTTTCTAGAGTGGACTG 58.934 47.826 0.00 0.00 0.00 3.51
239 240 3.974642 AGGTTGGTTTTCTAGAGTGGACT 59.025 43.478 0.00 0.00 0.00 3.85
240 241 4.065789 CAGGTTGGTTTTCTAGAGTGGAC 58.934 47.826 0.00 0.00 0.00 4.02
241 242 3.496160 GCAGGTTGGTTTTCTAGAGTGGA 60.496 47.826 0.00 0.00 0.00 4.02
242 243 2.814336 GCAGGTTGGTTTTCTAGAGTGG 59.186 50.000 0.00 0.00 0.00 4.00
243 244 3.251004 GTGCAGGTTGGTTTTCTAGAGTG 59.749 47.826 0.00 0.00 0.00 3.51
244 245 3.118038 TGTGCAGGTTGGTTTTCTAGAGT 60.118 43.478 0.00 0.00 0.00 3.24
245 246 3.251004 GTGTGCAGGTTGGTTTTCTAGAG 59.749 47.826 0.00 0.00 0.00 2.43
246 247 3.211045 GTGTGCAGGTTGGTTTTCTAGA 58.789 45.455 0.00 0.00 0.00 2.43
247 248 2.032030 CGTGTGCAGGTTGGTTTTCTAG 60.032 50.000 0.00 0.00 0.00 2.43
248 249 1.944024 CGTGTGCAGGTTGGTTTTCTA 59.056 47.619 0.00 0.00 0.00 2.10
249 250 0.738389 CGTGTGCAGGTTGGTTTTCT 59.262 50.000 0.00 0.00 0.00 2.52
250 251 0.454196 ACGTGTGCAGGTTGGTTTTC 59.546 50.000 0.00 0.00 0.00 2.29
251 252 0.172352 CACGTGTGCAGGTTGGTTTT 59.828 50.000 7.58 0.00 0.00 2.43
252 253 0.963355 ACACGTGTGCAGGTTGGTTT 60.963 50.000 22.71 0.00 0.00 3.27
253 254 1.373590 GACACGTGTGCAGGTTGGTT 61.374 55.000 28.82 0.00 0.00 3.67
254 255 1.817941 GACACGTGTGCAGGTTGGT 60.818 57.895 28.82 0.00 0.00 3.67
255 256 2.542907 GGACACGTGTGCAGGTTGG 61.543 63.158 31.95 0.00 36.33 3.77
256 257 2.542907 GGGACACGTGTGCAGGTTG 61.543 63.158 35.92 2.26 38.19 3.77
257 258 2.203153 GGGACACGTGTGCAGGTT 60.203 61.111 35.92 7.44 38.19 3.50
258 259 3.161450 AGGGACACGTGTGCAGGT 61.161 61.111 35.92 20.24 38.19 4.00
259 260 2.357517 GAGGGACACGTGTGCAGG 60.358 66.667 35.92 4.55 38.19 4.85
260 261 0.813610 TTTGAGGGACACGTGTGCAG 60.814 55.000 35.92 5.34 38.19 4.41
261 262 1.092921 GTTTGAGGGACACGTGTGCA 61.093 55.000 35.92 20.72 38.19 4.57
262 263 1.092921 TGTTTGAGGGACACGTGTGC 61.093 55.000 29.68 29.68 35.50 4.57
263 264 1.330521 CTTGTTTGAGGGACACGTGTG 59.669 52.381 28.82 2.53 0.00 3.82
264 265 1.663695 CTTGTTTGAGGGACACGTGT 58.336 50.000 23.64 23.64 0.00 4.49
265 266 0.944386 CCTTGTTTGAGGGACACGTG 59.056 55.000 15.48 15.48 32.94 4.49
266 267 3.396951 CCTTGTTTGAGGGACACGT 57.603 52.632 0.00 0.00 32.94 4.49
273 274 4.664150 TTTTTACTGCCCTTGTTTGAGG 57.336 40.909 0.00 0.00 36.52 3.86
304 305 5.607939 AGGGTTCGAATTTTCTGGTTTTT 57.392 34.783 0.00 0.00 0.00 1.94
305 306 5.607939 AAGGGTTCGAATTTTCTGGTTTT 57.392 34.783 0.00 0.00 0.00 2.43
306 307 5.278120 CGTAAGGGTTCGAATTTTCTGGTTT 60.278 40.000 0.00 0.00 0.00 3.27
307 308 4.214758 CGTAAGGGTTCGAATTTTCTGGTT 59.785 41.667 0.00 0.00 0.00 3.67
308 309 3.749609 CGTAAGGGTTCGAATTTTCTGGT 59.250 43.478 0.00 0.00 0.00 4.00
309 310 4.336532 CGTAAGGGTTCGAATTTTCTGG 57.663 45.455 0.00 0.00 0.00 3.86
327 328 9.896645 CCATATTACTAGAATACTAGACCCGTA 57.103 37.037 10.60 0.00 46.34 4.02
328 329 8.609483 TCCATATTACTAGAATACTAGACCCGT 58.391 37.037 10.60 0.00 46.34 5.28
329 330 8.891720 GTCCATATTACTAGAATACTAGACCCG 58.108 40.741 10.60 0.00 46.34 5.28
330 331 9.187996 GGTCCATATTACTAGAATACTAGACCC 57.812 40.741 10.60 0.00 46.34 4.46
331 332 9.750783 TGGTCCATATTACTAGAATACTAGACC 57.249 37.037 18.55 18.55 46.34 3.85
341 342 9.877222 TCAGATTAACTGGTCCATATTACTAGA 57.123 33.333 0.00 0.00 45.76 2.43
344 345 7.880195 GCATCAGATTAACTGGTCCATATTACT 59.120 37.037 0.00 0.00 45.76 2.24
345 346 7.880195 AGCATCAGATTAACTGGTCCATATTAC 59.120 37.037 0.00 0.00 45.76 1.89
346 347 7.977818 AGCATCAGATTAACTGGTCCATATTA 58.022 34.615 0.00 0.00 45.76 0.98
347 348 6.845908 AGCATCAGATTAACTGGTCCATATT 58.154 36.000 0.00 0.00 45.76 1.28
348 349 6.445451 AGCATCAGATTAACTGGTCCATAT 57.555 37.500 0.00 0.00 45.76 1.78
349 350 5.894298 AGCATCAGATTAACTGGTCCATA 57.106 39.130 0.00 0.00 45.76 2.74
350 351 4.785346 AGCATCAGATTAACTGGTCCAT 57.215 40.909 0.00 0.00 45.76 3.41
351 352 4.264253 CAAGCATCAGATTAACTGGTCCA 58.736 43.478 0.00 0.00 45.76 4.02
352 353 3.629398 CCAAGCATCAGATTAACTGGTCC 59.371 47.826 0.00 0.00 45.76 4.46
353 354 4.333926 GTCCAAGCATCAGATTAACTGGTC 59.666 45.833 0.00 0.00 45.76 4.02
415 416 4.022464 TGTGTTTGTTTGGTTCGACATC 57.978 40.909 0.00 0.00 0.00 3.06
454 486 1.066645 GGCAGGGCAAGAAAGGAATTG 60.067 52.381 0.00 0.00 0.00 2.32
609 692 1.261480 TCAGAGCTCCAGACCAACTC 58.739 55.000 10.93 0.00 0.00 3.01
731 814 9.787532 ATCACAATGGTTACTCGAAATAAAATG 57.212 29.630 0.00 0.00 0.00 2.32
777 861 4.142708 TGCCATTGCTATACGTGAAAACAG 60.143 41.667 0.00 0.00 38.71 3.16
798 882 8.707938 AAAATATGGCTTACAAAGAAGAATGC 57.292 30.769 0.00 0.00 0.00 3.56
811 895 7.104939 AGCTTGCAAATGAAAAATATGGCTTA 58.895 30.769 0.00 0.00 0.00 3.09
933 1017 6.255020 GCATGCAAATCAAATTACTCCTCTTG 59.745 38.462 14.21 0.00 0.00 3.02
948 1032 9.390795 CTATACTGAAAATAGTGCATGCAAATC 57.609 33.333 24.58 10.63 32.19 2.17
950 1034 7.148103 TGCTATACTGAAAATAGTGCATGCAAA 60.148 33.333 24.58 14.49 32.19 3.68
1029 1115 1.640428 CGAGCATGTTGGTCACGTAT 58.360 50.000 7.39 0.00 44.51 3.06
1102 1188 2.197577 GAGCTTGGCGTCTAGTTCATC 58.802 52.381 10.14 0.00 0.00 2.92
1112 1198 1.965754 GAGATCCCTGAGCTTGGCGT 61.966 60.000 0.00 0.00 0.00 5.68
1920 2011 5.103290 TGAGACGACTTACCAAAAATTGC 57.897 39.130 0.00 0.00 0.00 3.56
1921 2012 6.142817 CCTTGAGACGACTTACCAAAAATTG 58.857 40.000 0.00 0.00 0.00 2.32
2573 2779 9.894783 CAGATTTCAATCCTGATATTAAAGCAG 57.105 33.333 0.00 0.00 36.04 4.24


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

AutoCloner maintained by Alex Coulton.