Multiple sequence alignment - TraesCS3A01G466600

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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 TraesCS3A01G466600 chr3A 100.000 3155 0 0 1 3155 700424417 700421263 0.000000e+00 5827.0
1 TraesCS3A01G466600 chr3A 77.974 1135 183 36 1027 2118 700352268 700351158 0.000000e+00 649.0
2 TraesCS3A01G466600 chr3A 84.000 250 24 5 2430 2677 701453358 701453593 3.170000e-55 226.0
3 TraesCS3A01G466600 chr3A 84.404 109 15 2 75 182 725153015 725153122 4.300000e-19 106.0
4 TraesCS3A01G466600 chr3A 83.486 109 15 3 75 182 17572418 17572312 7.200000e-17 99.0
5 TraesCS3A01G466600 chr3A 94.737 38 2 0 3092 3129 700741800 700741837 3.400000e-05 60.2
6 TraesCS3A01G466600 chr3D 93.785 2896 132 19 265 3155 568180425 568183277 0.000000e+00 4307.0
7 TraesCS3A01G466600 chr3D 84.511 1982 252 27 922 2870 569888749 569886790 0.000000e+00 1908.0
8 TraesCS3A01G466600 chr3D 90.466 451 39 3 178 628 12382113 12382559 2.710000e-165 592.0
9 TraesCS3A01G466600 chr3D 82.812 384 47 5 2652 3032 569126850 569126483 3.030000e-85 326.0
10 TraesCS3A01G466600 chr3D 82.789 337 49 4 977 1307 569132378 569132711 3.080000e-75 292.0
11 TraesCS3A01G466600 chr3D 80.645 403 49 11 917 1307 569467351 569466966 5.150000e-73 285.0
12 TraesCS3A01G466600 chr3D 77.155 464 99 6 1657 2118 566609555 566610013 2.410000e-66 263.0
13 TraesCS3A01G466600 chr3D 77.598 433 90 6 1688 2118 568018113 568018540 4.040000e-64 255.0
14 TraesCS3A01G466600 chr3D 76.382 398 80 11 1729 2119 566629274 566629664 5.340000e-48 202.0
15 TraesCS3A01G466600 chr3D 82.069 145 22 3 2558 2699 567688665 567688522 1.540000e-23 121.0
16 TraesCS3A01G466600 chr3D 76.293 232 33 12 2468 2695 568113155 568113368 1.550000e-18 104.0
17 TraesCS3A01G466600 chr1D 89.633 627 50 10 183 802 485491786 485492404 0.000000e+00 784.0
18 TraesCS3A01G466600 chr4A 86.907 611 52 11 199 802 733923183 733923772 0.000000e+00 660.0
19 TraesCS3A01G466600 chr4A 93.514 185 10 1 1 183 181816250 181816434 1.110000e-69 274.0
20 TraesCS3A01G466600 chrUn 87.316 339 26 10 470 802 88913436 88913763 3.840000e-99 372.0
21 TraesCS3A01G466600 chrUn 82.143 392 49 10 922 1307 329510149 329510525 1.830000e-82 316.0
22 TraesCS3A01G466600 chrUn 81.633 392 51 10 922 1307 250747455 250747831 3.950000e-79 305.0
23 TraesCS3A01G466600 chrUn 81.633 392 51 10 922 1307 258534255 258533879 3.950000e-79 305.0
24 TraesCS3A01G466600 chrUn 80.867 392 54 10 922 1307 319041040 319040664 3.980000e-74 289.0
25 TraesCS3A01G466600 chrUn 76.336 393 84 8 1729 2118 41057776 41058162 5.340000e-48 202.0
26 TraesCS3A01G466600 chrUn 80.000 140 25 2 2558 2695 40895159 40895297 2.000000e-17 100.0
27 TraesCS3A01G466600 chrUn 91.781 73 5 1 922 994 217837239 217837310 2.000000e-17 100.0
28 TraesCS3A01G466600 chr3B 82.412 398 47 11 917 1307 756379550 756379169 3.030000e-85 326.0
29 TraesCS3A01G466600 chr3B 81.633 294 44 6 966 1259 202001185 202000902 5.260000e-58 235.0
30 TraesCS3A01G466600 chr3B 80.000 190 33 4 1670 1855 754303008 754303196 5.490000e-28 135.0
31 TraesCS3A01G466600 chr1A 95.556 180 7 1 1 179 550726852 550727031 1.430000e-73 287.0
32 TraesCS3A01G466600 chr5B 93.617 188 11 1 1 187 128354745 128354558 2.400000e-71 279.0
33 TraesCS3A01G466600 chr6B 87.429 175 20 2 9 182 114364545 114364718 1.920000e-47 200.0
34 TraesCS3A01G466600 chr7B 92.920 113 8 0 70 182 733271927 733271815 7.000000e-37 165.0
35 TraesCS3A01G466600 chr5A 81.208 149 22 5 38 182 605253425 605253571 7.150000e-22 115.0
36 TraesCS3A01G466600 chr2D 82.400 125 19 2 61 184 648419435 648419313 4.300000e-19 106.0


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 TraesCS3A01G466600 chr3A 700421263 700424417 3154 True 5827 5827 100.000 1 3155 1 chr3A.!!$R3 3154
1 TraesCS3A01G466600 chr3A 700351158 700352268 1110 True 649 649 77.974 1027 2118 1 chr3A.!!$R2 1091
2 TraesCS3A01G466600 chr3D 568180425 568183277 2852 False 4307 4307 93.785 265 3155 1 chr3D.!!$F6 2890
3 TraesCS3A01G466600 chr3D 569886790 569888749 1959 True 1908 1908 84.511 922 2870 1 chr3D.!!$R4 1948
4 TraesCS3A01G466600 chr1D 485491786 485492404 618 False 784 784 89.633 183 802 1 chr1D.!!$F1 619
5 TraesCS3A01G466600 chr4A 733923183 733923772 589 False 660 660 86.907 199 802 1 chr4A.!!$F2 603

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
81 82 0.178861 ACCTCATCAGAACCCCCAGT 60.179 55.0 0.00 0.00 0.00 4.00 F
106 107 0.179084 ACGTGTCGCATCCCTATTGG 60.179 55.0 0.00 0.00 0.00 3.16 F
107 108 0.179084 CGTGTCGCATCCCTATTGGT 60.179 55.0 0.00 0.00 34.77 3.67 F
1330 1347 0.478942 CTCCTATCCCGGTCTGGAGA 59.521 60.0 19.14 1.67 45.07 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1347 0.105760 AGGAGACCATCGCAGGAGAT 60.106 55.000 0.0 0.0 0.00 2.75 R
1443 1466 0.840288 TGTGCAGGTACATCCCCAGT 60.840 55.000 0.0 0.0 36.75 4.00 R
1766 1816 1.202915 TGGTTGCCTCATCAAAGCTGA 60.203 47.619 0.0 0.0 35.56 4.26 R
2950 3026 0.381801 AACGCAACAGCAAAGACAGG 59.618 50.000 0.0 0.0 0.00 4.00 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
21 22 4.966787 GCCCCGGTTGACTTGGCA 62.967 66.667 10.38 0.00 41.76 4.92
22 23 2.035626 CCCCGGTTGACTTGGCAT 59.964 61.111 0.00 0.00 0.00 4.40
23 24 1.301623 CCCCGGTTGACTTGGCATA 59.698 57.895 0.00 0.00 0.00 3.14
24 25 0.322997 CCCCGGTTGACTTGGCATAA 60.323 55.000 0.00 0.00 0.00 1.90
25 26 1.540267 CCCGGTTGACTTGGCATAAA 58.460 50.000 0.00 0.00 0.00 1.40
26 27 1.889829 CCCGGTTGACTTGGCATAAAA 59.110 47.619 0.00 0.00 0.00 1.52
27 28 2.495669 CCCGGTTGACTTGGCATAAAAT 59.504 45.455 0.00 0.00 0.00 1.82
28 29 3.428862 CCCGGTTGACTTGGCATAAAATC 60.429 47.826 0.00 0.00 0.00 2.17
29 30 3.428862 CCGGTTGACTTGGCATAAAATCC 60.429 47.826 0.00 0.00 0.00 3.01
30 31 3.443681 CGGTTGACTTGGCATAAAATCCT 59.556 43.478 0.00 0.00 0.00 3.24
31 32 4.675146 CGGTTGACTTGGCATAAAATCCTG 60.675 45.833 0.00 0.00 0.00 3.86
32 33 4.462483 GGTTGACTTGGCATAAAATCCTGA 59.538 41.667 0.00 0.00 0.00 3.86
33 34 5.047377 GGTTGACTTGGCATAAAATCCTGAA 60.047 40.000 0.00 0.00 0.00 3.02
34 35 5.902613 TGACTTGGCATAAAATCCTGAAG 57.097 39.130 0.00 0.00 0.00 3.02
35 36 5.569355 TGACTTGGCATAAAATCCTGAAGA 58.431 37.500 0.00 0.00 0.00 2.87
36 37 6.009589 TGACTTGGCATAAAATCCTGAAGAA 58.990 36.000 0.00 0.00 0.00 2.52
37 38 6.493115 TGACTTGGCATAAAATCCTGAAGAAA 59.507 34.615 0.00 0.00 0.00 2.52
38 39 7.015098 TGACTTGGCATAAAATCCTGAAGAAAA 59.985 33.333 0.00 0.00 0.00 2.29
39 40 7.910584 ACTTGGCATAAAATCCTGAAGAAAAT 58.089 30.769 0.00 0.00 0.00 1.82
40 41 8.037166 ACTTGGCATAAAATCCTGAAGAAAATC 58.963 33.333 0.00 0.00 0.00 2.17
41 42 7.722949 TGGCATAAAATCCTGAAGAAAATCT 57.277 32.000 0.00 0.00 0.00 2.40
42 43 7.775120 TGGCATAAAATCCTGAAGAAAATCTC 58.225 34.615 0.00 0.00 0.00 2.75
43 44 7.616935 TGGCATAAAATCCTGAAGAAAATCTCT 59.383 33.333 0.00 0.00 35.13 3.10
44 45 9.125026 GGCATAAAATCCTGAAGAAAATCTCTA 57.875 33.333 0.00 0.00 32.46 2.43
48 49 8.572855 AAAATCCTGAAGAAAATCTCTAGGTG 57.427 34.615 8.71 0.00 33.66 4.00
49 50 5.091261 TCCTGAAGAAAATCTCTAGGTGC 57.909 43.478 8.71 0.00 33.66 5.01
50 51 4.532126 TCCTGAAGAAAATCTCTAGGTGCA 59.468 41.667 8.71 0.00 33.66 4.57
51 52 4.633565 CCTGAAGAAAATCTCTAGGTGCAC 59.366 45.833 8.80 8.80 32.46 4.57
52 53 4.579869 TGAAGAAAATCTCTAGGTGCACC 58.420 43.478 29.22 29.22 32.46 5.01
53 54 4.041567 TGAAGAAAATCTCTAGGTGCACCA 59.958 41.667 36.39 21.17 33.39 4.17
54 55 3.944087 AGAAAATCTCTAGGTGCACCAC 58.056 45.455 36.39 12.03 38.89 4.16
55 56 3.327757 AGAAAATCTCTAGGTGCACCACA 59.672 43.478 36.39 22.58 38.89 4.17
56 57 3.788227 AAATCTCTAGGTGCACCACAA 57.212 42.857 36.39 20.37 38.89 3.33
57 58 4.307032 AAATCTCTAGGTGCACCACAAT 57.693 40.909 36.39 19.17 38.89 2.71
58 59 2.768253 TCTCTAGGTGCACCACAATG 57.232 50.000 36.39 21.19 38.89 2.82
59 60 1.977854 TCTCTAGGTGCACCACAATGT 59.022 47.619 36.39 18.01 38.89 2.71
60 61 2.079158 CTCTAGGTGCACCACAATGTG 58.921 52.381 36.39 17.23 38.89 3.21
61 62 1.419762 TCTAGGTGCACCACAATGTGT 59.580 47.619 36.39 16.49 38.52 3.72
62 63 2.635427 TCTAGGTGCACCACAATGTGTA 59.365 45.455 36.39 16.74 38.52 2.90
63 64 1.604604 AGGTGCACCACAATGTGTAC 58.395 50.000 36.39 5.92 46.92 2.90
65 66 1.604604 GTGCACCACAATGTGTACCT 58.395 50.000 12.79 0.00 43.43 3.08
66 67 1.535462 GTGCACCACAATGTGTACCTC 59.465 52.381 12.79 0.00 43.43 3.85
67 68 1.141858 TGCACCACAATGTGTACCTCA 59.858 47.619 12.79 0.43 38.52 3.86
68 69 2.224744 TGCACCACAATGTGTACCTCAT 60.225 45.455 12.79 0.00 38.52 2.90
69 70 2.420022 GCACCACAATGTGTACCTCATC 59.580 50.000 12.79 0.00 38.52 2.92
70 71 3.673902 CACCACAATGTGTACCTCATCA 58.326 45.455 12.79 0.00 0.00 3.07
71 72 3.686241 CACCACAATGTGTACCTCATCAG 59.314 47.826 12.79 0.00 0.00 2.90
72 73 3.582647 ACCACAATGTGTACCTCATCAGA 59.417 43.478 12.79 0.00 0.00 3.27
73 74 4.041567 ACCACAATGTGTACCTCATCAGAA 59.958 41.667 12.79 0.00 0.00 3.02
74 75 4.393062 CCACAATGTGTACCTCATCAGAAC 59.607 45.833 12.79 0.00 0.00 3.01
75 76 4.393062 CACAATGTGTACCTCATCAGAACC 59.607 45.833 5.00 0.00 0.00 3.62
76 77 3.914426 ATGTGTACCTCATCAGAACCC 57.086 47.619 0.00 0.00 0.00 4.11
77 78 1.906574 TGTGTACCTCATCAGAACCCC 59.093 52.381 0.00 0.00 0.00 4.95
78 79 1.209747 GTGTACCTCATCAGAACCCCC 59.790 57.143 0.00 0.00 0.00 5.40
79 80 1.203376 TGTACCTCATCAGAACCCCCA 60.203 52.381 0.00 0.00 0.00 4.96
80 81 1.486726 GTACCTCATCAGAACCCCCAG 59.513 57.143 0.00 0.00 0.00 4.45
81 82 0.178861 ACCTCATCAGAACCCCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
82 83 1.080498 ACCTCATCAGAACCCCCAGTA 59.920 52.381 0.00 0.00 0.00 2.74
83 84 2.196595 CCTCATCAGAACCCCCAGTAA 58.803 52.381 0.00 0.00 0.00 2.24
84 85 2.576191 CCTCATCAGAACCCCCAGTAAA 59.424 50.000 0.00 0.00 0.00 2.01
85 86 3.203040 CCTCATCAGAACCCCCAGTAAAT 59.797 47.826 0.00 0.00 0.00 1.40
86 87 4.412199 CCTCATCAGAACCCCCAGTAAATA 59.588 45.833 0.00 0.00 0.00 1.40
87 88 5.104109 CCTCATCAGAACCCCCAGTAAATAA 60.104 44.000 0.00 0.00 0.00 1.40
88 89 5.751586 TCATCAGAACCCCCAGTAAATAAC 58.248 41.667 0.00 0.00 0.00 1.89
89 90 4.210724 TCAGAACCCCCAGTAAATAACG 57.789 45.455 0.00 0.00 0.00 3.18
90 91 3.583966 TCAGAACCCCCAGTAAATAACGT 59.416 43.478 0.00 0.00 0.00 3.99
91 92 3.687698 CAGAACCCCCAGTAAATAACGTG 59.312 47.826 0.00 0.00 0.00 4.49
92 93 3.328637 AGAACCCCCAGTAAATAACGTGT 59.671 43.478 0.00 0.00 0.00 4.49
93 94 3.339253 ACCCCCAGTAAATAACGTGTC 57.661 47.619 0.00 0.00 0.00 3.67
94 95 2.273557 CCCCCAGTAAATAACGTGTCG 58.726 52.381 0.00 0.00 0.00 4.35
95 96 1.662122 CCCCAGTAAATAACGTGTCGC 59.338 52.381 0.00 0.00 0.00 5.19
96 97 2.339418 CCCAGTAAATAACGTGTCGCA 58.661 47.619 0.00 0.00 0.00 5.10
97 98 2.933906 CCCAGTAAATAACGTGTCGCAT 59.066 45.455 0.00 0.00 0.00 4.73
98 99 3.000925 CCCAGTAAATAACGTGTCGCATC 59.999 47.826 0.00 0.00 0.00 3.91
99 100 3.000925 CCAGTAAATAACGTGTCGCATCC 59.999 47.826 0.00 0.00 0.00 3.51
100 101 3.000925 CAGTAAATAACGTGTCGCATCCC 59.999 47.826 0.00 0.00 0.00 3.85
101 102 2.396590 AAATAACGTGTCGCATCCCT 57.603 45.000 0.00 0.00 0.00 4.20
102 103 3.530265 AAATAACGTGTCGCATCCCTA 57.470 42.857 0.00 0.00 0.00 3.53
103 104 3.746045 AATAACGTGTCGCATCCCTAT 57.254 42.857 0.00 0.00 0.00 2.57
104 105 3.746045 ATAACGTGTCGCATCCCTATT 57.254 42.857 0.00 0.00 0.00 1.73
105 106 1.651987 AACGTGTCGCATCCCTATTG 58.348 50.000 0.00 0.00 0.00 1.90
106 107 0.179084 ACGTGTCGCATCCCTATTGG 60.179 55.000 0.00 0.00 0.00 3.16
107 108 0.179084 CGTGTCGCATCCCTATTGGT 60.179 55.000 0.00 0.00 34.77 3.67
108 109 1.742411 CGTGTCGCATCCCTATTGGTT 60.742 52.381 0.00 0.00 34.77 3.67
109 110 1.670811 GTGTCGCATCCCTATTGGTTG 59.329 52.381 0.00 0.00 36.96 3.77
110 111 1.308998 GTCGCATCCCTATTGGTTGG 58.691 55.000 0.00 0.00 34.82 3.77
111 112 0.916086 TCGCATCCCTATTGGTTGGT 59.084 50.000 0.00 0.00 34.82 3.67
112 113 1.283613 TCGCATCCCTATTGGTTGGTT 59.716 47.619 0.00 0.00 34.82 3.67
113 114 2.099405 CGCATCCCTATTGGTTGGTTT 58.901 47.619 0.00 0.00 34.82 3.27
114 115 2.495669 CGCATCCCTATTGGTTGGTTTT 59.504 45.455 0.00 0.00 34.82 2.43
115 116 3.056179 CGCATCCCTATTGGTTGGTTTTT 60.056 43.478 0.00 0.00 34.82 1.94
116 117 4.503910 GCATCCCTATTGGTTGGTTTTTC 58.496 43.478 0.00 0.00 34.82 2.29
117 118 4.020662 GCATCCCTATTGGTTGGTTTTTCA 60.021 41.667 0.00 0.00 34.82 2.69
118 119 5.478407 CATCCCTATTGGTTGGTTTTTCAC 58.522 41.667 0.00 0.00 34.77 3.18
119 120 4.810345 TCCCTATTGGTTGGTTTTTCACT 58.190 39.130 0.00 0.00 34.77 3.41
120 121 4.586841 TCCCTATTGGTTGGTTTTTCACTG 59.413 41.667 0.00 0.00 34.77 3.66
121 122 4.586841 CCCTATTGGTTGGTTTTTCACTGA 59.413 41.667 0.00 0.00 0.00 3.41
122 123 5.245977 CCCTATTGGTTGGTTTTTCACTGAT 59.754 40.000 0.00 0.00 0.00 2.90
123 124 6.239572 CCCTATTGGTTGGTTTTTCACTGATT 60.240 38.462 0.00 0.00 0.00 2.57
124 125 6.646240 CCTATTGGTTGGTTTTTCACTGATTG 59.354 38.462 0.00 0.00 0.00 2.67
125 126 5.667539 TTGGTTGGTTTTTCACTGATTGA 57.332 34.783 0.00 0.00 0.00 2.57
126 127 5.667539 TGGTTGGTTTTTCACTGATTGAA 57.332 34.783 0.00 0.00 42.83 2.69
162 163 3.827722 CAGGGTAAAAGAAACCTGGTCA 58.172 45.455 0.00 0.00 45.21 4.02
163 164 3.821033 CAGGGTAAAAGAAACCTGGTCAG 59.179 47.826 0.00 0.00 45.21 3.51
164 165 3.720002 AGGGTAAAAGAAACCTGGTCAGA 59.280 43.478 0.00 0.00 37.18 3.27
165 166 4.354087 AGGGTAAAAGAAACCTGGTCAGAT 59.646 41.667 0.00 0.00 37.18 2.90
166 167 5.077564 GGGTAAAAGAAACCTGGTCAGATT 58.922 41.667 0.00 0.00 37.18 2.40
167 168 5.538813 GGGTAAAAGAAACCTGGTCAGATTT 59.461 40.000 0.00 3.06 37.18 2.17
168 169 6.717997 GGGTAAAAGAAACCTGGTCAGATTTA 59.282 38.462 0.00 2.10 37.18 1.40
169 170 7.094334 GGGTAAAAGAAACCTGGTCAGATTTAG 60.094 40.741 0.00 0.00 37.18 1.85
170 171 7.447545 GGTAAAAGAAACCTGGTCAGATTTAGT 59.552 37.037 0.00 0.00 33.97 2.24
171 172 9.498176 GTAAAAGAAACCTGGTCAGATTTAGTA 57.502 33.333 0.00 0.00 0.00 1.82
175 176 9.838339 AAGAAACCTGGTCAGATTTAGTATATG 57.162 33.333 0.00 0.00 0.00 1.78
176 177 8.993424 AGAAACCTGGTCAGATTTAGTATATGT 58.007 33.333 0.00 0.00 0.00 2.29
280 281 6.074516 CCAAAAGTATACATGTACATCGGACG 60.075 42.308 7.96 0.00 0.00 4.79
433 436 9.559958 CCTAATTTGTTACAATAGCACTTCAAG 57.440 33.333 0.00 0.00 0.00 3.02
504 507 7.820872 AGTGGAATAGATGGAAATTGCTTTTTG 59.179 33.333 0.00 0.00 0.00 2.44
507 510 9.822185 GGAATAGATGGAAATTGCTTTTTGTAT 57.178 29.630 0.00 0.00 0.00 2.29
517 520 9.374960 GAAATTGCTTTTTGTATAGAGATAGCG 57.625 33.333 0.00 0.00 0.00 4.26
519 522 4.444388 TGCTTTTTGTATAGAGATAGCGCG 59.556 41.667 0.00 0.00 0.00 6.86
606 610 2.674796 AGATTGCTCGGTCCAACTAC 57.325 50.000 0.00 0.00 0.00 2.73
802 813 1.339631 CCAAATTCTCAGTACGGCCCA 60.340 52.381 0.00 0.00 0.00 5.36
816 827 4.972875 CCCAGTGGCCATTCTCTC 57.027 61.111 9.72 0.00 0.00 3.20
854 865 1.566231 GGATCAGATCCCTGGTGGTTT 59.434 52.381 17.97 0.00 43.88 3.27
855 866 2.648059 GATCAGATCCCTGGTGGTTTG 58.352 52.381 0.00 0.00 40.76 2.93
856 867 1.444933 TCAGATCCCTGGTGGTTTGT 58.555 50.000 0.00 0.00 40.76 2.83
857 868 1.351017 TCAGATCCCTGGTGGTTTGTC 59.649 52.381 0.00 0.00 40.76 3.18
859 870 1.630878 AGATCCCTGGTGGTTTGTCTC 59.369 52.381 0.00 0.00 34.77 3.36
860 871 1.351017 GATCCCTGGTGGTTTGTCTCA 59.649 52.381 0.00 0.00 34.77 3.27
862 873 1.566703 TCCCTGGTGGTTTGTCTCAAA 59.433 47.619 0.00 0.00 34.77 2.69
864 875 2.763448 CCCTGGTGGTTTGTCTCAAAAA 59.237 45.455 0.00 0.00 0.00 1.94
884 895 2.604912 AAAAGATCCCTGGTGGTTCC 57.395 50.000 0.00 0.00 33.89 3.62
885 896 0.704664 AAAGATCCCTGGTGGTTCCC 59.295 55.000 0.00 0.00 33.89 3.97
894 905 5.429518 TCCCTGGTGGTTCCCATATATATT 58.570 41.667 0.00 0.00 35.28 1.28
903 914 7.934120 GTGGTTCCCATATATATTCTATCTGCC 59.066 40.741 0.00 0.00 35.28 4.85
981 992 3.193267 GCTATCGAGATCCAGATTGAGCT 59.807 47.826 11.56 0.00 32.74 4.09
984 995 1.000731 CGAGATCCAGATTGAGCTCCC 59.999 57.143 12.15 0.16 43.23 4.30
1098 1109 3.330720 CCCAAAGCCCTCCTCCGT 61.331 66.667 0.00 0.00 0.00 4.69
1117 1128 3.632107 GTCGTGCCGTTTGTCGCA 61.632 61.111 0.00 0.00 38.35 5.10
1164 1175 1.280421 GACTTCCTCCTTGCTCACCAT 59.720 52.381 0.00 0.00 0.00 3.55
1199 1210 1.076192 TCCCCCTCTTCTACGCCTC 60.076 63.158 0.00 0.00 0.00 4.70
1267 1278 3.080641 TCGACCACCGAGTAGGGA 58.919 61.111 0.00 0.00 46.96 4.20
1330 1347 0.478942 CTCCTATCCCGGTCTGGAGA 59.521 60.000 19.14 1.67 45.07 3.71
1383 1406 4.918810 AGGCGAAAACAGAAATTTGTCT 57.081 36.364 0.00 0.00 0.00 3.41
1395 1418 6.846350 CAGAAATTTGTCTGTCTACAATCCC 58.154 40.000 0.00 0.00 40.22 3.85
1443 1466 3.441222 CACAGATTGCTGGCTTCATGTTA 59.559 43.478 0.00 0.00 46.60 2.41
1457 1480 3.731431 TCATGTTACTGGGGATGTACCT 58.269 45.455 0.00 0.00 38.98 3.08
1517 1552 2.040145 TGAGTGATGCAAATCTGGGACA 59.960 45.455 0.00 0.00 0.00 4.02
1518 1553 2.421424 GAGTGATGCAAATCTGGGACAC 59.579 50.000 0.00 0.00 0.00 3.67
1519 1554 2.161855 GTGATGCAAATCTGGGACACA 58.838 47.619 0.00 0.00 0.00 3.72
1540 1584 4.946157 ACAATGGCTCCTATGTCTTTTCAG 59.054 41.667 0.00 0.00 0.00 3.02
1675 1725 4.156922 CGGGCAACATGTTAAAGGTATTCA 59.843 41.667 11.53 0.00 39.74 2.57
1680 1730 6.087555 GCAACATGTTAAAGGTATTCAACACG 59.912 38.462 11.53 0.00 34.00 4.49
1685 1735 2.825861 AAGGTATTCAACACGACCGT 57.174 45.000 0.00 0.00 37.04 4.83
1878 1928 4.558226 ATTACCAGTTGCAGATCTCACA 57.442 40.909 0.00 0.00 0.00 3.58
1883 1933 0.441533 GTTGCAGATCTCACAGTGCG 59.558 55.000 0.00 0.00 38.84 5.34
2025 2075 4.089361 CCAGTTTCCATTTTAGAGGCCTT 58.911 43.478 6.77 0.00 0.00 4.35
2026 2076 4.528206 CCAGTTTCCATTTTAGAGGCCTTT 59.472 41.667 6.77 2.86 0.00 3.11
2070 2120 4.136796 AGCAAACTCTTGTTCAGCATACA 58.863 39.130 0.00 0.00 38.63 2.29
2103 2153 4.720046 TGCTACAGGGTTATGTTGTGAAA 58.280 39.130 0.00 0.00 34.56 2.69
2123 2173 3.698029 AAATTCGCCTTTCATCGGATG 57.302 42.857 11.79 11.79 0.00 3.51
2124 2174 2.332063 ATTCGCCTTTCATCGGATGT 57.668 45.000 17.01 0.00 0.00 3.06
2145 2195 1.208052 GATAGCTGTCCAGTGAGGCAA 59.792 52.381 0.00 0.00 37.29 4.52
2236 2290 4.957759 TGATGCATGAAGTTGTGATCAG 57.042 40.909 2.46 0.00 0.00 2.90
2315 2369 3.705604 CCAAGTCATTTTGGTGTGTGTC 58.294 45.455 0.00 0.00 42.16 3.67
2348 2402 1.226802 CGGTCTGCCTCATGTCTCG 60.227 63.158 0.00 0.00 0.00 4.04
2350 2404 1.520342 GTCTGCCTCATGTCTCGGC 60.520 63.158 9.89 9.89 44.02 5.54
2352 2406 0.395724 TCTGCCTCATGTCTCGGCTA 60.396 55.000 15.27 5.29 44.09 3.93
2388 2460 2.036475 AGGTAGCAATCTACATGCCTCG 59.964 50.000 0.00 0.00 45.42 4.63
2429 2501 6.373759 ACTGGAGGATTGACTTTACCTTTTT 58.626 36.000 0.00 0.00 32.53 1.94
2544 2618 4.899352 AAGTTCTGTTCTAGCTGACCAT 57.101 40.909 0.00 0.00 0.00 3.55
2556 2630 4.510038 AGCTGACCATTGAATGTGAAAC 57.490 40.909 4.27 0.00 37.35 2.78
2629 2705 7.066307 TCCTCATGAGCTGCTATGTATAAAA 57.934 36.000 17.76 0.00 0.00 1.52
2717 2793 4.973051 TGCATAAATTTCGTGTGTGTGAAC 59.027 37.500 0.00 0.00 0.00 3.18
2756 2832 1.543429 GCTACCAGTTCTGTTGTGGCT 60.543 52.381 9.08 0.00 34.40 4.75
2830 2906 6.379988 ACTTGGGTTTTTAAAGAGCTTGAAGA 59.620 34.615 7.73 0.00 0.00 2.87
2899 2975 4.641396 TGTTCGTTCATTCCTCTTCATGT 58.359 39.130 0.00 0.00 0.00 3.21
2902 2978 6.878923 TGTTCGTTCATTCCTCTTCATGTATT 59.121 34.615 0.00 0.00 0.00 1.89
2903 2979 7.064609 TGTTCGTTCATTCCTCTTCATGTATTC 59.935 37.037 0.00 0.00 0.00 1.75
2904 2980 6.639563 TCGTTCATTCCTCTTCATGTATTCA 58.360 36.000 0.00 0.00 0.00 2.57
2905 2981 7.275183 TCGTTCATTCCTCTTCATGTATTCAT 58.725 34.615 0.00 0.00 34.21 2.57
2906 2982 7.770433 TCGTTCATTCCTCTTCATGTATTCATT 59.230 33.333 0.00 0.00 31.15 2.57
2907 2983 7.854422 CGTTCATTCCTCTTCATGTATTCATTG 59.146 37.037 0.00 0.00 31.15 2.82
2908 2984 7.268199 TCATTCCTCTTCATGTATTCATTGC 57.732 36.000 0.00 0.00 31.15 3.56
2909 2985 7.058525 TCATTCCTCTTCATGTATTCATTGCT 58.941 34.615 0.00 0.00 31.15 3.91
2910 2986 7.558807 TCATTCCTCTTCATGTATTCATTGCTT 59.441 33.333 0.00 0.00 31.15 3.91
2911 2987 6.932356 TCCTCTTCATGTATTCATTGCTTC 57.068 37.500 0.00 0.00 31.15 3.86
2912 2988 6.656902 TCCTCTTCATGTATTCATTGCTTCT 58.343 36.000 0.00 0.00 31.15 2.85
2913 2989 6.541278 TCCTCTTCATGTATTCATTGCTTCTG 59.459 38.462 0.00 0.00 31.15 3.02
2914 2990 6.238676 CCTCTTCATGTATTCATTGCTTCTGG 60.239 42.308 0.00 0.00 31.15 3.86
2915 2991 6.182627 TCTTCATGTATTCATTGCTTCTGGT 58.817 36.000 0.00 0.00 31.15 4.00
2916 2992 6.660521 TCTTCATGTATTCATTGCTTCTGGTT 59.339 34.615 0.00 0.00 31.15 3.67
2917 2993 7.828717 TCTTCATGTATTCATTGCTTCTGGTTA 59.171 33.333 0.00 0.00 31.15 2.85
2918 2994 7.558161 TCATGTATTCATTGCTTCTGGTTAG 57.442 36.000 0.00 0.00 31.15 2.34
2919 2995 7.337938 TCATGTATTCATTGCTTCTGGTTAGA 58.662 34.615 0.00 0.00 31.15 2.10
2920 2996 7.994911 TCATGTATTCATTGCTTCTGGTTAGAT 59.005 33.333 0.00 0.00 29.95 1.98
2921 2997 9.276590 CATGTATTCATTGCTTCTGGTTAGATA 57.723 33.333 0.00 0.00 29.95 1.98
2922 2998 8.662781 TGTATTCATTGCTTCTGGTTAGATAC 57.337 34.615 0.00 0.00 31.81 2.24
3099 3175 2.094182 TCGAGTACCATTGGTCTCAAGC 60.094 50.000 23.36 8.32 37.09 4.01
3134 3210 8.939929 TCAAGTTCACTCTGATCATTTGTTATC 58.060 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.830186 TATGCCAAGTCAACCGGGGC 62.830 60.000 6.32 7.66 44.82 5.80
5 6 0.322997 TTATGCCAAGTCAACCGGGG 60.323 55.000 6.32 0.00 0.00 5.73
6 7 1.540267 TTTATGCCAAGTCAACCGGG 58.460 50.000 6.32 0.00 0.00 5.73
7 8 3.428862 GGATTTTATGCCAAGTCAACCGG 60.429 47.826 0.00 0.00 0.00 5.28
8 9 3.443681 AGGATTTTATGCCAAGTCAACCG 59.556 43.478 0.00 0.00 0.00 4.44
9 10 4.462483 TCAGGATTTTATGCCAAGTCAACC 59.538 41.667 0.00 0.00 0.00 3.77
10 11 5.643379 TCAGGATTTTATGCCAAGTCAAC 57.357 39.130 0.00 0.00 0.00 3.18
11 12 6.009589 TCTTCAGGATTTTATGCCAAGTCAA 58.990 36.000 0.00 0.00 0.00 3.18
12 13 5.569355 TCTTCAGGATTTTATGCCAAGTCA 58.431 37.500 0.00 0.00 0.00 3.41
13 14 6.515272 TTCTTCAGGATTTTATGCCAAGTC 57.485 37.500 0.00 0.00 0.00 3.01
14 15 6.916360 TTTCTTCAGGATTTTATGCCAAGT 57.084 33.333 0.00 0.00 0.00 3.16
15 16 8.255905 AGATTTTCTTCAGGATTTTATGCCAAG 58.744 33.333 0.00 0.00 0.00 3.61
16 17 8.137745 AGATTTTCTTCAGGATTTTATGCCAA 57.862 30.769 0.00 0.00 0.00 4.52
17 18 7.616935 AGAGATTTTCTTCAGGATTTTATGCCA 59.383 33.333 0.00 0.00 29.61 4.92
18 19 8.005192 AGAGATTTTCTTCAGGATTTTATGCC 57.995 34.615 0.00 0.00 29.61 4.40
22 23 9.672673 CACCTAGAGATTTTCTTCAGGATTTTA 57.327 33.333 10.58 0.00 37.36 1.52
23 24 7.121907 GCACCTAGAGATTTTCTTCAGGATTTT 59.878 37.037 10.58 0.00 37.36 1.82
24 25 6.601217 GCACCTAGAGATTTTCTTCAGGATTT 59.399 38.462 10.58 0.00 37.36 2.17
25 26 6.118852 GCACCTAGAGATTTTCTTCAGGATT 58.881 40.000 10.58 0.00 37.36 3.01
26 27 5.190528 TGCACCTAGAGATTTTCTTCAGGAT 59.809 40.000 10.58 0.00 37.36 3.24
27 28 4.532126 TGCACCTAGAGATTTTCTTCAGGA 59.468 41.667 10.58 0.00 37.36 3.86
28 29 4.633565 GTGCACCTAGAGATTTTCTTCAGG 59.366 45.833 5.22 4.62 37.36 3.86
29 30 4.633565 GGTGCACCTAGAGATTTTCTTCAG 59.366 45.833 29.12 0.00 37.36 3.02
30 31 4.041567 TGGTGCACCTAGAGATTTTCTTCA 59.958 41.667 34.75 7.38 37.36 3.02
31 32 4.393371 GTGGTGCACCTAGAGATTTTCTTC 59.607 45.833 34.75 4.57 37.36 2.87
32 33 4.202461 TGTGGTGCACCTAGAGATTTTCTT 60.202 41.667 34.75 0.00 33.79 2.52
33 34 3.327757 TGTGGTGCACCTAGAGATTTTCT 59.672 43.478 34.75 0.00 35.23 2.52
34 35 3.674997 TGTGGTGCACCTAGAGATTTTC 58.325 45.455 34.75 12.93 36.82 2.29
35 36 3.788227 TGTGGTGCACCTAGAGATTTT 57.212 42.857 34.75 0.00 36.82 1.82
36 37 3.788227 TTGTGGTGCACCTAGAGATTT 57.212 42.857 34.75 0.00 36.82 2.17
37 38 3.009473 ACATTGTGGTGCACCTAGAGATT 59.991 43.478 34.75 12.39 36.82 2.40
38 39 2.573462 ACATTGTGGTGCACCTAGAGAT 59.427 45.455 34.75 18.55 36.82 2.75
39 40 1.977854 ACATTGTGGTGCACCTAGAGA 59.022 47.619 34.75 13.35 36.82 3.10
40 41 2.079158 CACATTGTGGTGCACCTAGAG 58.921 52.381 34.75 22.21 36.82 2.43
41 42 1.419762 ACACATTGTGGTGCACCTAGA 59.580 47.619 34.75 20.64 42.55 2.43
42 43 1.896220 ACACATTGTGGTGCACCTAG 58.104 50.000 34.75 21.23 42.55 3.02
43 44 2.551287 GGTACACATTGTGGTGCACCTA 60.551 50.000 34.75 21.70 46.96 3.08
44 45 1.604604 GTACACATTGTGGTGCACCT 58.395 50.000 34.75 13.76 42.55 4.00
45 46 0.596082 GGTACACATTGTGGTGCACC 59.404 55.000 29.67 29.67 45.25 5.01
46 47 1.535462 GAGGTACACATTGTGGTGCAC 59.465 52.381 20.33 8.80 42.55 4.57
47 48 1.141858 TGAGGTACACATTGTGGTGCA 59.858 47.619 20.33 8.45 42.55 4.57
48 49 1.890876 TGAGGTACACATTGTGGTGC 58.109 50.000 20.33 9.71 42.55 5.01
49 50 3.673902 TGATGAGGTACACATTGTGGTG 58.326 45.455 20.33 0.00 40.32 4.17
50 51 3.582647 TCTGATGAGGTACACATTGTGGT 59.417 43.478 20.33 8.98 40.32 4.16
51 52 4.206477 TCTGATGAGGTACACATTGTGG 57.794 45.455 20.33 3.56 40.32 4.17
52 53 4.393062 GGTTCTGATGAGGTACACATTGTG 59.607 45.833 15.18 15.18 40.32 3.33
53 54 4.565652 GGGTTCTGATGAGGTACACATTGT 60.566 45.833 0.00 0.00 40.32 2.71
54 55 3.941483 GGGTTCTGATGAGGTACACATTG 59.059 47.826 0.00 0.00 40.32 2.82
55 56 3.054361 GGGGTTCTGATGAGGTACACATT 60.054 47.826 0.00 0.00 40.32 2.71
56 57 2.505819 GGGGTTCTGATGAGGTACACAT 59.494 50.000 4.80 4.80 43.56 3.21
57 58 1.906574 GGGGTTCTGATGAGGTACACA 59.093 52.381 0.00 0.00 0.00 3.72
58 59 1.209747 GGGGGTTCTGATGAGGTACAC 59.790 57.143 0.00 0.00 0.00 2.90
59 60 1.203376 TGGGGGTTCTGATGAGGTACA 60.203 52.381 0.00 0.00 0.00 2.90
60 61 1.486726 CTGGGGGTTCTGATGAGGTAC 59.513 57.143 0.00 0.00 0.00 3.34
61 62 1.080498 ACTGGGGGTTCTGATGAGGTA 59.920 52.381 0.00 0.00 0.00 3.08
62 63 0.178861 ACTGGGGGTTCTGATGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
63 64 1.879575 TACTGGGGGTTCTGATGAGG 58.120 55.000 0.00 0.00 0.00 3.86
64 65 4.510167 ATTTACTGGGGGTTCTGATGAG 57.490 45.455 0.00 0.00 0.00 2.90
65 66 5.628200 CGTTATTTACTGGGGGTTCTGATGA 60.628 44.000 0.00 0.00 0.00 2.92
66 67 4.574828 CGTTATTTACTGGGGGTTCTGATG 59.425 45.833 0.00 0.00 0.00 3.07
67 68 4.226620 ACGTTATTTACTGGGGGTTCTGAT 59.773 41.667 0.00 0.00 0.00 2.90
68 69 3.583966 ACGTTATTTACTGGGGGTTCTGA 59.416 43.478 0.00 0.00 0.00 3.27
69 70 3.687698 CACGTTATTTACTGGGGGTTCTG 59.312 47.826 0.00 0.00 0.00 3.02
70 71 3.328637 ACACGTTATTTACTGGGGGTTCT 59.671 43.478 0.00 0.00 0.00 3.01
71 72 3.678289 ACACGTTATTTACTGGGGGTTC 58.322 45.455 0.00 0.00 0.00 3.62
72 73 3.678289 GACACGTTATTTACTGGGGGTT 58.322 45.455 0.00 0.00 0.00 4.11
73 74 2.354003 CGACACGTTATTTACTGGGGGT 60.354 50.000 0.00 0.00 0.00 4.95
74 75 2.273557 CGACACGTTATTTACTGGGGG 58.726 52.381 0.00 0.00 0.00 5.40
75 76 1.662122 GCGACACGTTATTTACTGGGG 59.338 52.381 0.00 0.00 0.00 4.96
76 77 2.339418 TGCGACACGTTATTTACTGGG 58.661 47.619 0.00 0.00 0.00 4.45
77 78 3.000925 GGATGCGACACGTTATTTACTGG 59.999 47.826 0.00 0.00 0.00 4.00
78 79 3.000925 GGGATGCGACACGTTATTTACTG 59.999 47.826 0.00 0.00 0.00 2.74
79 80 3.118884 AGGGATGCGACACGTTATTTACT 60.119 43.478 0.00 0.00 0.00 2.24
80 81 3.192466 AGGGATGCGACACGTTATTTAC 58.808 45.455 0.00 0.00 0.00 2.01
81 82 3.530265 AGGGATGCGACACGTTATTTA 57.470 42.857 0.00 0.00 0.00 1.40
82 83 2.396590 AGGGATGCGACACGTTATTT 57.603 45.000 0.00 0.00 0.00 1.40
83 84 3.746045 ATAGGGATGCGACACGTTATT 57.254 42.857 0.00 0.00 0.00 1.40
84 85 3.390135 CAATAGGGATGCGACACGTTAT 58.610 45.455 0.00 0.00 0.00 1.89
85 86 2.482316 CCAATAGGGATGCGACACGTTA 60.482 50.000 0.00 0.00 40.01 3.18
86 87 1.651987 CAATAGGGATGCGACACGTT 58.348 50.000 0.00 0.00 0.00 3.99
87 88 0.179084 CCAATAGGGATGCGACACGT 60.179 55.000 0.00 0.00 40.01 4.49
88 89 0.179084 ACCAATAGGGATGCGACACG 60.179 55.000 0.00 0.00 41.15 4.49
89 90 1.670811 CAACCAATAGGGATGCGACAC 59.329 52.381 0.00 0.00 41.15 3.67
90 91 1.408127 CCAACCAATAGGGATGCGACA 60.408 52.381 0.00 0.00 38.09 4.35
91 92 1.308998 CCAACCAATAGGGATGCGAC 58.691 55.000 0.00 0.00 38.09 5.19
92 93 0.916086 ACCAACCAATAGGGATGCGA 59.084 50.000 0.00 0.00 38.09 5.10
93 94 1.762708 AACCAACCAATAGGGATGCG 58.237 50.000 0.00 0.00 38.09 4.73
94 95 4.020662 TGAAAAACCAACCAATAGGGATGC 60.021 41.667 0.00 0.00 38.09 3.91
95 96 5.245977 AGTGAAAAACCAACCAATAGGGATG 59.754 40.000 0.00 0.00 41.15 3.51
96 97 5.245977 CAGTGAAAAACCAACCAATAGGGAT 59.754 40.000 0.00 0.00 41.15 3.85
97 98 4.586841 CAGTGAAAAACCAACCAATAGGGA 59.413 41.667 0.00 0.00 41.15 4.20
98 99 4.586841 TCAGTGAAAAACCAACCAATAGGG 59.413 41.667 0.00 0.00 44.81 3.53
99 100 5.782893 TCAGTGAAAAACCAACCAATAGG 57.217 39.130 0.00 0.00 42.21 2.57
100 101 7.432869 TCAATCAGTGAAAAACCAACCAATAG 58.567 34.615 0.00 0.00 31.51 1.73
101 102 7.353414 TCAATCAGTGAAAAACCAACCAATA 57.647 32.000 0.00 0.00 31.51 1.90
102 103 6.232581 TCAATCAGTGAAAAACCAACCAAT 57.767 33.333 0.00 0.00 31.51 3.16
103 104 5.667539 TCAATCAGTGAAAAACCAACCAA 57.332 34.783 0.00 0.00 31.51 3.67
104 105 5.667539 TTCAATCAGTGAAAAACCAACCA 57.332 34.783 0.00 0.00 43.43 3.67
136 137 5.486063 ACCAGGTTTCTTTTACCCTGTTTTT 59.514 36.000 0.00 0.00 42.39 1.94
137 138 5.027460 ACCAGGTTTCTTTTACCCTGTTTT 58.973 37.500 0.00 0.00 42.39 2.43
138 139 4.616553 ACCAGGTTTCTTTTACCCTGTTT 58.383 39.130 0.00 0.00 42.39 2.83
139 140 4.212716 GACCAGGTTTCTTTTACCCTGTT 58.787 43.478 0.00 0.00 42.39 3.16
140 141 3.203487 TGACCAGGTTTCTTTTACCCTGT 59.797 43.478 0.00 0.00 42.39 4.00
141 142 3.821033 CTGACCAGGTTTCTTTTACCCTG 59.179 47.826 0.00 0.00 43.34 4.45
142 143 3.720002 TCTGACCAGGTTTCTTTTACCCT 59.280 43.478 0.00 0.00 36.27 4.34
143 144 4.094830 TCTGACCAGGTTTCTTTTACCC 57.905 45.455 0.00 0.00 36.27 3.69
144 145 6.650427 AAATCTGACCAGGTTTCTTTTACC 57.350 37.500 2.62 0.00 37.15 2.85
145 146 8.392372 ACTAAATCTGACCAGGTTTCTTTTAC 57.608 34.615 11.14 0.00 40.62 2.01
149 150 9.838339 CATATACTAAATCTGACCAGGTTTCTT 57.162 33.333 11.14 3.61 40.62 2.52
150 151 8.993424 ACATATACTAAATCTGACCAGGTTTCT 58.007 33.333 11.14 2.31 40.62 2.52
252 253 7.825270 TCCGATGTACATGTATACTTTTGGTTT 59.175 33.333 14.43 0.00 0.00 3.27
280 281 7.792508 CCTTATTTAATTGTTGCGACGACTATC 59.207 37.037 0.00 0.00 0.00 2.08
289 290 7.116233 GGAATATGCCCTTATTTAATTGTTGCG 59.884 37.037 0.00 0.00 0.00 4.85
410 411 9.893305 GTACTTGAAGTGCTATTGTAACAAATT 57.107 29.630 8.33 0.00 0.00 1.82
433 436 1.004595 GGAACGCGATCCTTTGGTAC 58.995 55.000 26.40 0.00 36.50 3.34
504 507 6.144080 ACAATTTTGACGCGCTATCTCTATAC 59.856 38.462 5.73 0.00 0.00 1.47
507 510 4.267690 CACAATTTTGACGCGCTATCTCTA 59.732 41.667 5.73 0.00 0.00 2.43
517 520 4.513000 TTTTCAAGCACAATTTTGACGC 57.487 36.364 0.00 0.00 33.36 5.19
569 572 8.554835 AGCAATCTTTCTAGAACTTACTTTCC 57.445 34.615 4.18 0.00 33.20 3.13
575 578 6.282199 ACCGAGCAATCTTTCTAGAACTTA 57.718 37.500 4.18 0.00 33.20 2.24
576 579 5.153950 ACCGAGCAATCTTTCTAGAACTT 57.846 39.130 4.18 0.00 33.20 2.66
765 775 2.366393 GGGGGCCCGATGCAAAATT 61.366 57.895 17.79 0.00 43.89 1.82
802 813 0.534412 CAGACGAGAGAATGGCCACT 59.466 55.000 8.16 0.00 0.00 4.00
811 822 1.006043 AGGGTTCCATCAGACGAGAGA 59.994 52.381 0.00 0.00 0.00 3.10
816 827 0.753262 CCCTAGGGTTCCATCAGACG 59.247 60.000 20.88 0.00 0.00 4.18
864 875 2.889512 GGAACCACCAGGGATCTTTTT 58.110 47.619 0.00 0.00 38.47 1.94
880 891 8.268878 AGGGCAGATAGAATATATATGGGAAC 57.731 38.462 0.00 0.00 0.00 3.62
881 892 9.607333 CTAGGGCAGATAGAATATATATGGGAA 57.393 37.037 0.00 0.00 0.00 3.97
882 893 8.970813 TCTAGGGCAGATAGAATATATATGGGA 58.029 37.037 0.00 0.00 0.00 4.37
883 894 9.253832 CTCTAGGGCAGATAGAATATATATGGG 57.746 40.741 0.00 0.00 31.13 4.00
884 895 8.748412 GCTCTAGGGCAGATAGAATATATATGG 58.252 40.741 10.54 0.00 31.13 2.74
885 896 9.532494 AGCTCTAGGGCAGATAGAATATATATG 57.468 37.037 18.89 0.00 31.13 1.78
894 905 1.783365 TGGAGCTCTAGGGCAGATAGA 59.217 52.381 18.89 0.00 31.13 1.98
903 914 2.578714 GGGGCGATGGAGCTCTAGG 61.579 68.421 14.64 5.10 37.84 3.02
1199 1210 0.729140 GCCGTCGCACTTGAAATTGG 60.729 55.000 0.00 0.00 34.03 3.16
1299 1310 2.966516 GGGATAGGAGAGGTCAATTCGT 59.033 50.000 0.00 0.00 0.00 3.85
1330 1347 0.105760 AGGAGACCATCGCAGGAGAT 60.106 55.000 0.00 0.00 0.00 2.75
1383 1406 1.403647 CGAGTTGCGGGATTGTAGACA 60.404 52.381 0.00 0.00 36.03 3.41
1443 1466 0.840288 TGTGCAGGTACATCCCCAGT 60.840 55.000 0.00 0.00 36.75 4.00
1517 1552 4.922206 TGAAAAGACATAGGAGCCATTGT 58.078 39.130 0.00 0.00 0.00 2.71
1518 1553 4.946157 ACTGAAAAGACATAGGAGCCATTG 59.054 41.667 0.00 0.00 0.00 2.82
1519 1554 5.184892 ACTGAAAAGACATAGGAGCCATT 57.815 39.130 0.00 0.00 0.00 3.16
1675 1725 2.132762 GAATGACTCAACGGTCGTGTT 58.867 47.619 0.00 0.00 38.91 3.32
1680 1730 1.359459 GCCGGAATGACTCAACGGTC 61.359 60.000 5.05 9.04 45.85 4.79
1685 1735 2.013563 GCATCTGCCGGAATGACTCAA 61.014 52.381 5.05 0.00 34.31 3.02
1766 1816 1.202915 TGGTTGCCTCATCAAAGCTGA 60.203 47.619 0.00 0.00 35.56 4.26
1827 1877 3.117663 GGTATTTCAAGGCCCATACCTCA 60.118 47.826 0.00 0.00 39.93 3.86
1878 1928 1.822371 ACAAACTTTCCAAACCGCACT 59.178 42.857 0.00 0.00 0.00 4.40
1883 1933 6.478673 CCAATACTCAACAAACTTTCCAAACC 59.521 38.462 0.00 0.00 0.00 3.27
1998 2048 5.253330 CCTCTAAAATGGAAACTGGCACTA 58.747 41.667 0.00 0.00 0.00 2.74
2000 2050 3.367395 GCCTCTAAAATGGAAACTGGCAC 60.367 47.826 0.00 0.00 37.91 5.01
2025 2075 4.206375 TGAGACAATGTTCAGCAGGAAAA 58.794 39.130 0.00 0.00 37.23 2.29
2026 2076 3.819368 TGAGACAATGTTCAGCAGGAAA 58.181 40.909 0.00 0.00 37.23 3.13
2070 2120 4.322057 ACCCTGTAGCATTGGAAAGAAT 57.678 40.909 0.00 0.00 0.00 2.40
2103 2153 3.016736 ACATCCGATGAAAGGCGAATTT 58.983 40.909 15.47 0.00 0.00 1.82
2123 2173 1.472376 GCCTCACTGGACAGCTATCAC 60.472 57.143 0.00 0.00 38.35 3.06
2124 2174 0.826715 GCCTCACTGGACAGCTATCA 59.173 55.000 0.00 0.00 38.35 2.15
2145 2195 0.459759 GCTAGGCCGTTTAGAAGCGT 60.460 55.000 0.00 0.00 0.00 5.07
2236 2290 3.265791 CCACATAACAGTGAGAGCTTCC 58.734 50.000 0.00 0.00 42.05 3.46
2315 2369 1.066573 AGACCGGAGCACATCTTTCAG 60.067 52.381 9.46 0.00 0.00 3.02
2369 2441 2.797156 CACGAGGCATGTAGATTGCTAC 59.203 50.000 0.00 0.00 45.80 3.58
2388 2460 5.449177 CCTCCAGTTCAAGAAACAGAAACAC 60.449 44.000 0.00 0.00 40.56 3.32
2429 2501 6.712998 TCATGGAATAAAACGAAGACCAAGAA 59.287 34.615 0.00 0.00 0.00 2.52
2494 2568 5.816258 ACATGAGACACATCAAGATTGCTAG 59.184 40.000 0.00 0.00 37.07 3.42
2544 2618 5.049167 GCCACATTCAAGTTTCACATTCAA 58.951 37.500 0.00 0.00 0.00 2.69
2556 2630 6.264744 AGGATAATCAATCTGCCACATTCAAG 59.735 38.462 0.00 0.00 34.75 3.02
2717 2793 1.538047 CCATTCGGCCCAATAGGATG 58.462 55.000 0.00 0.00 38.24 3.51
2830 2906 1.265095 CATGCACTTCAACGAGCAGTT 59.735 47.619 0.00 0.00 45.45 3.16
2902 2978 8.306313 TCTAAGTATCTAACCAGAAGCAATGA 57.694 34.615 0.00 0.00 33.50 2.57
2903 2979 8.986847 CATCTAAGTATCTAACCAGAAGCAATG 58.013 37.037 0.00 0.00 33.50 2.82
2904 2980 8.709308 ACATCTAAGTATCTAACCAGAAGCAAT 58.291 33.333 0.00 0.00 33.50 3.56
2905 2981 8.079211 ACATCTAAGTATCTAACCAGAAGCAA 57.921 34.615 0.00 0.00 33.50 3.91
2906 2982 7.661536 ACATCTAAGTATCTAACCAGAAGCA 57.338 36.000 0.00 0.00 33.50 3.91
2939 3015 5.711976 ACAGCAAAGACAGGTTTATAGCATT 59.288 36.000 0.00 0.00 0.00 3.56
2950 3026 0.381801 AACGCAACAGCAAAGACAGG 59.618 50.000 0.00 0.00 0.00 4.00
3099 3175 5.842619 CAGAGTGAACTTGAGACAATCTG 57.157 43.478 17.41 17.41 45.22 2.90


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

AutoCloner maintained by Alex Coulton.