Multiple sequence alignment - TraesCS3A01G370800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G370800 chr3A 100.000 3671 0 0 1 3671 621225876 621229546 0.000000e+00 6780.0
1 TraesCS3A01G370800 chr3B 95.753 2755 93 15 927 3671 637072806 637075546 0.000000e+00 4418.0
2 TraesCS3A01G370800 chr3B 82.353 544 65 16 150 669 637072178 637072714 9.350000e-121 444.0
3 TraesCS3A01G370800 chr3B 84.706 170 17 6 752 915 681095013 681095179 1.050000e-35 161.0
4 TraesCS3A01G370800 chr3B 83.333 180 17 9 751 921 423468487 423468312 1.770000e-33 154.0
5 TraesCS3A01G370800 chr3D 95.711 2751 91 9 927 3671 477892213 477894942 0.000000e+00 4401.0
6 TraesCS3A01G370800 chr3D 90.234 1884 155 13 1048 2924 253394923 253393062 0.000000e+00 2433.0
7 TraesCS3A01G370800 chr3D 85.390 308 29 9 409 706 477890724 477891025 4.610000e-79 305.0
8 TraesCS3A01G370800 chr3D 85.030 167 17 5 752 912 79558705 79558541 2.930000e-36 163.0
9 TraesCS3A01G370800 chr2D 85.882 170 14 8 751 913 75564517 75564683 4.870000e-39 172.0
10 TraesCS3A01G370800 chr2D 83.333 180 21 8 743 916 70500117 70500293 1.360000e-34 158.0
11 TraesCS3A01G370800 chr6B 85.119 168 17 5 752 913 276259261 276259096 8.160000e-37 165.0
12 TraesCS3A01G370800 chr6B 100.000 30 0 0 633 662 268718283 268718254 5.120000e-04 56.5
13 TraesCS3A01G370800 chr1A 84.302 172 19 5 751 916 443211613 443211782 1.050000e-35 161.0
14 TraesCS3A01G370800 chr7D 84.431 167 18 5 752 912 616209253 616209417 1.360000e-34 158.0
15 TraesCS3A01G370800 chr7D 100.000 29 0 0 634 662 89759343 89759315 2.000000e-03 54.7
16 TraesCS3A01G370800 chr5A 84.431 167 18 5 752 912 115664844 115664680 1.360000e-34 158.0
17 TraesCS3A01G370800 chr5A 100.000 30 0 0 633 662 535146364 535146393 5.120000e-04 56.5
18 TraesCS3A01G370800 chr7A 100.000 30 0 0 633 662 92085043 92085072 5.120000e-04 56.5
19 TraesCS3A01G370800 chr7A 100.000 29 0 0 634 662 486928473 486928501 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 TraesCS3A01G370800 chr3A 621225876 621229546 3670 False 6780 6780 100.0000 1 3671 1 chr3A.!!$F1 3670
1 TraesCS3A01G370800 chr3B 637072178 637075546 3368 False 2431 4418 89.0530 150 3671 2 chr3B.!!$F2 3521
2 TraesCS3A01G370800 chr3D 253393062 253394923 1861 True 2433 2433 90.2340 1048 2924 1 chr3D.!!$R2 1876
3 TraesCS3A01G370800 chr3D 477890724 477894942 4218 False 2353 4401 90.5505 409 3671 2 chr3D.!!$F1 3262

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
109 110 0.107508 ATGCCCTGATGTCGTTGGAG 60.108 55.000 0.00 0.00 0.0 3.86 F
112 113 0.321671 CCCTGATGTCGTTGGAGTGT 59.678 55.000 0.00 0.00 0.0 3.55 F
290 296 0.323451 TCGGTGCTCTTCTCTAGGCA 60.323 55.000 0.00 0.00 0.0 4.75 F
374 380 1.216710 GGAAGTCACCGAGCTCCTG 59.783 63.158 8.47 3.82 0.0 3.86 F
377 383 1.544691 GAAGTCACCGAGCTCCTGTTA 59.455 52.381 8.47 0.00 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2840 0.249120 CCGCACCTGAAGTACATGGA 59.751 55.0 0.00 0.00 0.00 3.41 R
1748 2841 1.369091 GCCGCACCTGAAGTACATGG 61.369 60.0 0.00 0.00 0.00 3.66 R
2160 3253 0.323269 TGGCCTTCATCGCAAATCCA 60.323 50.0 3.32 0.00 0.00 3.41 R
2372 3465 0.548510 GGCCTCCTTCAGCTGGTTAT 59.451 55.0 15.13 0.00 0.00 1.89 R
2678 3778 5.924254 CGGCATATTTCTCAATGATGCAAAT 59.076 36.0 6.59 4.14 43.74 2.32 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
23 24 6.681571 GAAGAAAGTGCAACAAATTAGCTC 57.318 37.500 0.00 0.00 41.43 4.09
24 25 5.772825 AGAAAGTGCAACAAATTAGCTCA 57.227 34.783 0.00 0.00 41.43 4.26
25 26 6.336842 AGAAAGTGCAACAAATTAGCTCAT 57.663 33.333 0.00 0.00 41.43 2.90
26 27 6.154445 AGAAAGTGCAACAAATTAGCTCATG 58.846 36.000 0.00 0.00 41.43 3.07
27 28 5.710513 AAGTGCAACAAATTAGCTCATGA 57.289 34.783 0.00 0.00 41.43 3.07
28 29 5.306532 AGTGCAACAAATTAGCTCATGAG 57.693 39.130 18.84 18.84 41.43 2.90
29 30 5.005740 AGTGCAACAAATTAGCTCATGAGA 58.994 37.500 27.04 5.94 41.43 3.27
30 31 5.651139 AGTGCAACAAATTAGCTCATGAGAT 59.349 36.000 27.04 22.97 41.43 2.75
31 32 6.152323 AGTGCAACAAATTAGCTCATGAGATT 59.848 34.615 27.04 13.94 41.43 2.40
32 33 6.252869 GTGCAACAAATTAGCTCATGAGATTG 59.747 38.462 27.04 16.90 36.32 2.67
33 34 5.231568 GCAACAAATTAGCTCATGAGATTGC 59.768 40.000 27.04 19.60 0.00 3.56
34 35 5.165911 ACAAATTAGCTCATGAGATTGCG 57.834 39.130 27.04 13.36 0.00 4.85
35 36 4.036027 ACAAATTAGCTCATGAGATTGCGG 59.964 41.667 27.04 11.56 0.00 5.69
36 37 1.586422 TTAGCTCATGAGATTGCGGC 58.414 50.000 27.04 9.83 0.00 6.53
37 38 0.755079 TAGCTCATGAGATTGCGGCT 59.245 50.000 27.04 16.71 32.88 5.52
38 39 0.755079 AGCTCATGAGATTGCGGCTA 59.245 50.000 27.04 0.00 0.00 3.93
39 40 0.864455 GCTCATGAGATTGCGGCTAC 59.136 55.000 27.04 0.27 0.00 3.58
40 41 1.539929 GCTCATGAGATTGCGGCTACT 60.540 52.381 27.04 0.00 0.00 2.57
41 42 2.133553 CTCATGAGATTGCGGCTACTG 58.866 52.381 18.34 0.00 0.00 2.74
42 43 1.756538 TCATGAGATTGCGGCTACTGA 59.243 47.619 0.00 0.00 0.00 3.41
43 44 1.863454 CATGAGATTGCGGCTACTGAC 59.137 52.381 0.00 0.00 0.00 3.51
44 45 0.894835 TGAGATTGCGGCTACTGACA 59.105 50.000 0.00 0.00 0.00 3.58
45 46 1.134995 TGAGATTGCGGCTACTGACAG 60.135 52.381 0.00 0.00 0.00 3.51
46 47 0.176680 AGATTGCGGCTACTGACAGG 59.823 55.000 7.51 0.00 0.00 4.00
47 48 1.432270 GATTGCGGCTACTGACAGGC 61.432 60.000 7.51 1.06 37.73 4.85
51 52 2.184579 GGCTACTGACAGGCGGAC 59.815 66.667 7.51 0.00 0.00 4.79
52 53 2.646175 GGCTACTGACAGGCGGACA 61.646 63.158 7.51 0.00 0.00 4.02
53 54 1.517832 GCTACTGACAGGCGGACAT 59.482 57.895 7.51 0.00 0.00 3.06
54 55 0.807667 GCTACTGACAGGCGGACATG 60.808 60.000 7.51 0.00 0.00 3.21
55 56 0.532573 CTACTGACAGGCGGACATGT 59.467 55.000 7.51 0.00 0.00 3.21
56 57 0.246360 TACTGACAGGCGGACATGTG 59.754 55.000 1.15 0.00 0.00 3.21
57 58 1.293179 CTGACAGGCGGACATGTGA 59.707 57.895 1.15 0.00 0.00 3.58
58 59 1.005037 TGACAGGCGGACATGTGAC 60.005 57.895 1.15 0.00 0.00 3.67
59 60 1.005037 GACAGGCGGACATGTGACA 60.005 57.895 1.15 0.00 0.00 3.58
60 61 0.391661 GACAGGCGGACATGTGACAT 60.392 55.000 1.15 0.00 0.00 3.06
61 62 0.391661 ACAGGCGGACATGTGACATC 60.392 55.000 1.15 0.00 0.00 3.06
62 63 0.107993 CAGGCGGACATGTGACATCT 60.108 55.000 1.15 0.00 0.00 2.90
63 64 0.615331 AGGCGGACATGTGACATCTT 59.385 50.000 1.15 0.00 0.00 2.40
64 65 1.009829 GGCGGACATGTGACATCTTC 58.990 55.000 1.15 0.00 0.00 2.87
65 66 1.675714 GGCGGACATGTGACATCTTCA 60.676 52.381 1.15 0.00 0.00 3.02
66 67 2.283298 GCGGACATGTGACATCTTCAT 58.717 47.619 1.15 0.00 36.32 2.57
67 68 2.679837 GCGGACATGTGACATCTTCATT 59.320 45.455 1.15 0.00 36.32 2.57
68 69 3.871006 GCGGACATGTGACATCTTCATTA 59.129 43.478 1.15 0.00 36.32 1.90
69 70 4.260375 GCGGACATGTGACATCTTCATTAC 60.260 45.833 1.15 0.00 36.32 1.89
70 71 5.111989 CGGACATGTGACATCTTCATTACT 58.888 41.667 1.15 0.00 36.32 2.24
71 72 5.006068 CGGACATGTGACATCTTCATTACTG 59.994 44.000 1.15 0.00 36.32 2.74
72 73 6.108687 GGACATGTGACATCTTCATTACTGA 58.891 40.000 1.15 0.00 36.32 3.41
73 74 6.036517 GGACATGTGACATCTTCATTACTGAC 59.963 42.308 1.15 0.00 36.32 3.51
74 75 5.578336 ACATGTGACATCTTCATTACTGACG 59.422 40.000 0.00 0.00 36.32 4.35
75 76 5.134202 TGTGACATCTTCATTACTGACGT 57.866 39.130 0.00 0.00 36.32 4.34
76 77 4.923281 TGTGACATCTTCATTACTGACGTG 59.077 41.667 0.00 0.00 36.32 4.49
77 78 3.926527 TGACATCTTCATTACTGACGTGC 59.073 43.478 0.00 0.00 0.00 5.34
78 79 4.177026 GACATCTTCATTACTGACGTGCT 58.823 43.478 0.00 0.00 0.00 4.40
79 80 4.569943 ACATCTTCATTACTGACGTGCTT 58.430 39.130 0.00 0.00 0.00 3.91
80 81 4.389992 ACATCTTCATTACTGACGTGCTTG 59.610 41.667 0.00 0.00 0.00 4.01
81 82 4.251543 TCTTCATTACTGACGTGCTTGA 57.748 40.909 0.00 0.00 0.00 3.02
82 83 4.627058 TCTTCATTACTGACGTGCTTGAA 58.373 39.130 0.00 0.00 0.00 2.69
83 84 5.053811 TCTTCATTACTGACGTGCTTGAAA 58.946 37.500 0.00 0.00 0.00 2.69
84 85 4.990543 TCATTACTGACGTGCTTGAAAG 57.009 40.909 0.00 0.00 0.00 2.62
85 86 4.377021 TCATTACTGACGTGCTTGAAAGT 58.623 39.130 0.00 0.00 0.00 2.66
86 87 4.447724 TCATTACTGACGTGCTTGAAAGTC 59.552 41.667 0.00 0.00 0.00 3.01
87 88 2.604046 ACTGACGTGCTTGAAAGTCT 57.396 45.000 0.00 0.00 34.92 3.24
88 89 2.474816 ACTGACGTGCTTGAAAGTCTC 58.525 47.619 0.00 0.00 34.92 3.36
89 90 2.159099 ACTGACGTGCTTGAAAGTCTCA 60.159 45.455 0.00 0.00 34.92 3.27
90 91 2.866156 CTGACGTGCTTGAAAGTCTCAA 59.134 45.455 0.00 0.00 41.93 3.02
91 92 3.466836 TGACGTGCTTGAAAGTCTCAAT 58.533 40.909 0.00 0.00 43.20 2.57
92 93 3.248363 TGACGTGCTTGAAAGTCTCAATG 59.752 43.478 0.00 0.00 43.20 2.82
93 94 2.031682 ACGTGCTTGAAAGTCTCAATGC 60.032 45.455 0.00 0.00 43.20 3.56
94 95 2.666619 CGTGCTTGAAAGTCTCAATGCC 60.667 50.000 0.00 0.00 43.20 4.40
95 96 1.888512 TGCTTGAAAGTCTCAATGCCC 59.111 47.619 0.00 0.00 43.20 5.36
96 97 2.165998 GCTTGAAAGTCTCAATGCCCT 58.834 47.619 0.00 0.00 43.20 5.19
97 98 2.094854 GCTTGAAAGTCTCAATGCCCTG 60.095 50.000 0.00 0.00 43.20 4.45
98 99 3.415212 CTTGAAAGTCTCAATGCCCTGA 58.585 45.455 0.00 0.00 43.20 3.86
99 100 3.726557 TGAAAGTCTCAATGCCCTGAT 57.273 42.857 0.00 0.00 0.00 2.90
100 101 3.349927 TGAAAGTCTCAATGCCCTGATG 58.650 45.455 0.00 0.00 0.00 3.07
101 102 3.245016 TGAAAGTCTCAATGCCCTGATGT 60.245 43.478 0.00 0.00 0.00 3.06
102 103 2.706339 AGTCTCAATGCCCTGATGTC 57.294 50.000 0.00 0.00 0.00 3.06
103 104 1.134580 AGTCTCAATGCCCTGATGTCG 60.135 52.381 0.00 0.00 0.00 4.35
104 105 0.904649 TCTCAATGCCCTGATGTCGT 59.095 50.000 0.00 0.00 0.00 4.34
105 106 1.278985 TCTCAATGCCCTGATGTCGTT 59.721 47.619 0.00 0.00 0.00 3.85
106 107 1.399440 CTCAATGCCCTGATGTCGTTG 59.601 52.381 0.00 0.00 0.00 4.10
107 108 0.452987 CAATGCCCTGATGTCGTTGG 59.547 55.000 0.00 0.00 0.00 3.77
108 109 0.327924 AATGCCCTGATGTCGTTGGA 59.672 50.000 0.00 0.00 0.00 3.53
109 110 0.107508 ATGCCCTGATGTCGTTGGAG 60.108 55.000 0.00 0.00 0.00 3.86
110 111 1.296715 GCCCTGATGTCGTTGGAGT 59.703 57.895 0.00 0.00 0.00 3.85
111 112 1.021390 GCCCTGATGTCGTTGGAGTG 61.021 60.000 0.00 0.00 0.00 3.51
112 113 0.321671 CCCTGATGTCGTTGGAGTGT 59.678 55.000 0.00 0.00 0.00 3.55
113 114 1.548719 CCCTGATGTCGTTGGAGTGTA 59.451 52.381 0.00 0.00 0.00 2.90
114 115 2.028476 CCCTGATGTCGTTGGAGTGTAA 60.028 50.000 0.00 0.00 0.00 2.41
115 116 3.556213 CCCTGATGTCGTTGGAGTGTAAA 60.556 47.826 0.00 0.00 0.00 2.01
116 117 3.432252 CCTGATGTCGTTGGAGTGTAAAC 59.568 47.826 0.00 0.00 0.00 2.01
117 118 4.055360 CTGATGTCGTTGGAGTGTAAACA 58.945 43.478 0.00 0.00 0.00 2.83
118 119 4.637276 TGATGTCGTTGGAGTGTAAACAT 58.363 39.130 0.00 0.00 0.00 2.71
119 120 4.688879 TGATGTCGTTGGAGTGTAAACATC 59.311 41.667 0.00 0.00 41.03 3.06
120 121 3.395639 TGTCGTTGGAGTGTAAACATCC 58.604 45.455 0.00 5.24 0.00 3.51
121 122 2.740447 GTCGTTGGAGTGTAAACATCCC 59.260 50.000 8.27 3.98 31.73 3.85
122 123 2.369203 TCGTTGGAGTGTAAACATCCCA 59.631 45.455 8.27 5.98 31.73 4.37
123 124 3.008594 TCGTTGGAGTGTAAACATCCCAT 59.991 43.478 7.09 0.00 32.84 4.00
124 125 3.756434 CGTTGGAGTGTAAACATCCCATT 59.244 43.478 7.09 0.00 32.84 3.16
125 126 4.379394 CGTTGGAGTGTAAACATCCCATTG 60.379 45.833 7.09 1.61 32.84 2.82
126 127 4.649267 TGGAGTGTAAACATCCCATTGA 57.351 40.909 8.27 0.00 31.73 2.57
127 128 4.588899 TGGAGTGTAAACATCCCATTGAG 58.411 43.478 8.27 0.00 31.73 3.02
128 129 4.042809 TGGAGTGTAAACATCCCATTGAGT 59.957 41.667 8.27 0.00 31.73 3.41
129 130 5.249622 TGGAGTGTAAACATCCCATTGAGTA 59.750 40.000 8.27 0.00 31.73 2.59
130 131 6.177610 GGAGTGTAAACATCCCATTGAGTAA 58.822 40.000 0.00 0.00 0.00 2.24
131 132 6.657541 GGAGTGTAAACATCCCATTGAGTAAA 59.342 38.462 0.00 0.00 0.00 2.01
132 133 7.339466 GGAGTGTAAACATCCCATTGAGTAAAT 59.661 37.037 0.00 0.00 0.00 1.40
133 134 8.650143 AGTGTAAACATCCCATTGAGTAAATT 57.350 30.769 0.00 0.00 0.00 1.82
134 135 9.088987 AGTGTAAACATCCCATTGAGTAAATTT 57.911 29.630 0.00 0.00 0.00 1.82
173 174 2.955660 GACAAAATGGAGGGTGACAACA 59.044 45.455 0.00 0.00 0.00 3.33
176 177 2.746279 AATGGAGGGTGACAACAACA 57.254 45.000 0.00 0.00 35.07 3.33
225 229 4.884668 AACCCTCGACATGTAAAGAGAA 57.115 40.909 20.52 0.00 32.84 2.87
231 235 6.033341 CCTCGACATGTAAAGAGAAAGAGAG 58.967 44.000 20.52 7.18 32.84 3.20
232 236 6.127869 CCTCGACATGTAAAGAGAAAGAGAGA 60.128 42.308 20.52 0.00 32.84 3.10
233 237 6.847400 TCGACATGTAAAGAGAAAGAGAGAG 58.153 40.000 0.00 0.00 0.00 3.20
234 238 6.655425 TCGACATGTAAAGAGAAAGAGAGAGA 59.345 38.462 0.00 0.00 0.00 3.10
242 246 6.780457 AAGAGAAAGAGAGAGATGAGAAGG 57.220 41.667 0.00 0.00 0.00 3.46
246 250 3.600448 AGAGAGAGATGAGAAGGAGGG 57.400 52.381 0.00 0.00 0.00 4.30
268 272 4.383010 GGGGGTGATGGTTCATTTTGATTC 60.383 45.833 0.00 0.00 33.56 2.52
276 280 5.468592 TGGTTCATTTTGATTCATTCGGTG 58.531 37.500 0.00 0.00 0.00 4.94
283 289 3.616956 TGATTCATTCGGTGCTCTTCT 57.383 42.857 0.00 0.00 0.00 2.85
287 293 4.377839 TTCATTCGGTGCTCTTCTCTAG 57.622 45.455 0.00 0.00 0.00 2.43
288 294 2.690497 TCATTCGGTGCTCTTCTCTAGG 59.310 50.000 0.00 0.00 0.00 3.02
290 296 0.323451 TCGGTGCTCTTCTCTAGGCA 60.323 55.000 0.00 0.00 0.00 4.75
293 299 2.419297 CGGTGCTCTTCTCTAGGCAAAT 60.419 50.000 0.00 0.00 33.67 2.32
313 319 7.202001 GGCAAATCCCTAGTATAAAATTGGCTT 60.202 37.037 0.00 0.00 37.69 4.35
316 322 8.838649 AATCCCTAGTATAAAATTGGCTTTGT 57.161 30.769 0.00 0.00 0.00 2.83
329 335 7.832503 AATTGGCTTTGTGTATTATCTTTGC 57.167 32.000 0.00 0.00 0.00 3.68
347 353 6.773638 TCTTTGCTGAATTATATCCCCTCTC 58.226 40.000 0.00 0.00 0.00 3.20
350 356 5.915628 TGCTGAATTATATCCCCTCTCCTA 58.084 41.667 0.00 0.00 0.00 2.94
354 360 8.993424 GCTGAATTATATCCCCTCTCCTATTAA 58.007 37.037 0.00 0.00 0.00 1.40
360 366 9.507381 TTATATCCCCTCTCCTATTAATGGAAG 57.493 37.037 0.00 0.00 32.61 3.46
365 371 5.221742 CCCTCTCCTATTAATGGAAGTCACC 60.222 48.000 0.00 0.00 32.61 4.02
374 380 1.216710 GGAAGTCACCGAGCTCCTG 59.783 63.158 8.47 3.82 0.00 3.86
377 383 1.544691 GAAGTCACCGAGCTCCTGTTA 59.455 52.381 8.47 0.00 0.00 2.41
378 384 1.629043 AGTCACCGAGCTCCTGTTAA 58.371 50.000 8.47 0.00 0.00 2.01
382 388 3.751698 GTCACCGAGCTCCTGTTAATTTT 59.248 43.478 8.47 0.00 0.00 1.82
438 446 8.788806 AGTAATTGTTGGTTCATTTTGATACGA 58.211 29.630 0.00 0.00 0.00 3.43
555 578 2.765122 AGTTGCACTTGAAGCTCTCTC 58.235 47.619 0.00 0.00 0.00 3.20
560 583 2.594321 CACTTGAAGCTCTCTCGTCAG 58.406 52.381 0.00 0.00 0.00 3.51
579 602 8.956533 TCGTCAGATCCAATTATATGAAACAA 57.043 30.769 0.00 0.00 29.45 2.83
600 623 7.289587 ACAAGTGAAAGAAATTTTGTTTCGG 57.710 32.000 20.37 14.34 43.56 4.30
605 628 6.309251 GTGAAAGAAATTTTGTTTCGGACACA 59.691 34.615 20.37 6.08 43.56 3.72
606 629 6.868864 TGAAAGAAATTTTGTTTCGGACACAA 59.131 30.769 20.37 5.65 43.56 3.33
615 638 5.506686 TGTTTCGGACACAAATTCAATGA 57.493 34.783 0.00 0.00 32.00 2.57
619 642 5.463499 TCGGACACAAATTCAATGATACG 57.537 39.130 0.00 0.00 0.00 3.06
696 734 6.850752 TTCTAGGACACATCACTCATACAA 57.149 37.500 0.00 0.00 0.00 2.41
702 740 7.212976 AGGACACATCACTCATACAATCATAC 58.787 38.462 0.00 0.00 0.00 2.39
708 746 8.699130 ACATCACTCATACAATCATACTCTTGA 58.301 33.333 0.00 0.00 0.00 3.02
746 1837 6.559810 TGATTAAAAACAATGCGGTGATAGG 58.440 36.000 0.00 0.00 0.00 2.57
748 1839 7.337184 TGATTAAAAACAATGCGGTGATAGGTA 59.663 33.333 0.00 0.00 0.00 3.08
750 1841 5.968528 AAAACAATGCGGTGATAGGTAAA 57.031 34.783 0.00 0.00 0.00 2.01
755 1846 5.989777 ACAATGCGGTGATAGGTAAATACTC 59.010 40.000 0.00 0.00 0.00 2.59
757 1848 3.322828 TGCGGTGATAGGTAAATACTCCC 59.677 47.826 0.00 0.00 0.00 4.30
759 1850 4.321824 GCGGTGATAGGTAAATACTCCCTC 60.322 50.000 0.00 0.00 0.00 4.30
763 1854 6.326843 GGTGATAGGTAAATACTCCCTCTGTT 59.673 42.308 0.00 0.00 0.00 3.16
764 1855 7.147532 GGTGATAGGTAAATACTCCCTCTGTTT 60.148 40.741 0.00 0.00 0.00 2.83
765 1856 7.927092 GTGATAGGTAAATACTCCCTCTGTTTC 59.073 40.741 0.00 0.00 0.00 2.78
766 1857 7.844779 TGATAGGTAAATACTCCCTCTGTTTCT 59.155 37.037 0.00 0.00 0.00 2.52
770 1861 8.887393 AGGTAAATACTCCCTCTGTTTCTTAAA 58.113 33.333 0.00 0.00 0.00 1.52
771 1862 9.682465 GGTAAATACTCCCTCTGTTTCTTAAAT 57.318 33.333 0.00 0.00 0.00 1.40
778 1869 9.588096 ACTCCCTCTGTTTCTTAAATATTTGTT 57.412 29.630 11.05 0.00 0.00 2.83
880 1971 9.676861 ATGTGATAGTTCATTTGAAATCTCTGA 57.323 29.630 0.00 0.00 35.58 3.27
881 1972 9.506018 TGTGATAGTTCATTTGAAATCTCTGAA 57.494 29.630 0.00 0.00 35.58 3.02
887 1978 9.741647 AGTTCATTTGAAATCTCTGAAAAAGAC 57.258 29.630 0.00 0.00 35.58 3.01
888 1979 9.520204 GTTCATTTGAAATCTCTGAAAAAGACA 57.480 29.630 0.00 0.00 35.58 3.41
889 1980 9.740239 TTCATTTGAAATCTCTGAAAAAGACAG 57.260 29.630 0.00 0.00 36.80 3.51
890 1981 9.123902 TCATTTGAAATCTCTGAAAAAGACAGA 57.876 29.630 0.00 0.00 41.26 3.41
891 1982 9.909644 CATTTGAAATCTCTGAAAAAGACAGAT 57.090 29.630 0.00 0.00 42.32 2.90
902 1993 9.663904 TCTGAAAAAGACAGATATTTTGAAACG 57.336 29.630 0.00 0.00 39.10 3.60
903 1994 8.795786 TGAAAAAGACAGATATTTTGAAACGG 57.204 30.769 0.00 0.00 29.76 4.44
904 1995 8.625651 TGAAAAAGACAGATATTTTGAAACGGA 58.374 29.630 0.00 0.00 29.76 4.69
905 1996 9.626045 GAAAAAGACAGATATTTTGAAACGGAT 57.374 29.630 0.00 0.00 29.76 4.18
906 1997 8.970691 AAAAGACAGATATTTTGAAACGGATG 57.029 30.769 0.00 0.00 28.15 3.51
907 1998 7.921786 AAGACAGATATTTTGAAACGGATGA 57.078 32.000 0.00 0.00 0.00 2.92
908 1999 7.921786 AGACAGATATTTTGAAACGGATGAA 57.078 32.000 0.00 0.00 0.00 2.57
909 2000 7.978982 AGACAGATATTTTGAAACGGATGAAG 58.021 34.615 0.00 0.00 0.00 3.02
910 2001 7.607991 AGACAGATATTTTGAAACGGATGAAGT 59.392 33.333 0.00 0.00 0.00 3.01
911 2002 8.786826 ACAGATATTTTGAAACGGATGAAGTA 57.213 30.769 0.00 0.00 0.00 2.24
912 2003 8.665685 ACAGATATTTTGAAACGGATGAAGTAC 58.334 33.333 0.00 0.00 0.00 2.73
913 2004 8.883731 CAGATATTTTGAAACGGATGAAGTACT 58.116 33.333 0.00 0.00 0.00 2.73
914 2005 9.449719 AGATATTTTGAAACGGATGAAGTACTT 57.550 29.630 8.13 8.13 0.00 2.24
918 2009 8.441312 TTTTGAAACGGATGAAGTACTTTACT 57.559 30.769 10.02 0.00 41.73 2.24
919 2010 9.545105 TTTTGAAACGGATGAAGTACTTTACTA 57.455 29.630 10.02 0.00 38.26 1.82
920 2011 9.545105 TTTGAAACGGATGAAGTACTTTACTAA 57.455 29.630 10.02 0.00 38.26 2.24
921 2012 9.715121 TTGAAACGGATGAAGTACTTTACTAAT 57.285 29.630 10.02 0.00 38.26 1.73
937 2028 9.374838 ACTTTACTAATAAGTATCCAACGGTTG 57.625 33.333 13.86 13.86 38.02 3.77
1011 2104 1.600636 CCATGGTATGCGCCGGAAT 60.601 57.895 5.05 0.00 0.00 3.01
1077 2170 2.651361 CCGTGGACGAAGCAGTCT 59.349 61.111 0.00 0.00 43.02 3.24
1116 2209 4.557149 TCCCCTCGCATCCCCGAT 62.557 66.667 0.00 0.00 36.54 4.18
1125 2218 2.134287 CATCCCCGATGACCTCCGT 61.134 63.158 0.00 0.00 42.09 4.69
1134 2227 3.069318 GACCTCCGTCTCCGCCTT 61.069 66.667 0.00 0.00 35.99 4.35
1434 2527 2.537560 CCATCCAATCGTCGGCAGC 61.538 63.158 0.00 0.00 0.00 5.25
1551 2644 2.409064 TGATGTCCGGGTATGGGTAT 57.591 50.000 0.00 0.00 0.00 2.73
1811 2904 3.561143 TGTTTGGTAGTTTGCTGGATGT 58.439 40.909 0.00 0.00 0.00 3.06
1904 2997 6.545504 TTTGTTCAGAGAAATGTGCTACTC 57.454 37.500 0.00 0.00 0.00 2.59
2046 3139 3.931468 ACATCAAAGTCTCATCTTCGCTG 59.069 43.478 0.00 0.00 0.00 5.18
2112 3205 4.008330 TGGTATTCCGCCAAATTCGTAAA 58.992 39.130 0.00 0.00 36.30 2.01
2160 3253 5.888161 GGTCATATCAAACCTTGGTTCTCAT 59.112 40.000 5.43 1.66 32.54 2.90
2272 3365 2.775890 CTTGTTGTCATGCAGGACTCT 58.224 47.619 29.42 0.00 38.61 3.24
2280 3373 3.089284 TCATGCAGGACTCTTAGACGAA 58.911 45.455 0.00 0.00 0.00 3.85
2372 3465 1.508632 GTGAGGCTTCTTGCAACGTA 58.491 50.000 0.00 0.00 45.15 3.57
2678 3778 5.200483 GGATACAAGGAAATGATGGTTGGA 58.800 41.667 0.00 0.00 0.00 3.53
2716 3816 2.157834 ATGCCGAACGTCAAGTACAA 57.842 45.000 0.00 0.00 0.00 2.41
2734 3834 9.599322 CAAGTACAATTGAACTCTGTATTGTTC 57.401 33.333 13.59 0.00 40.55 3.18
2947 4049 5.771666 TCGTGGAGTAATATAAGGTCGGAAT 59.228 40.000 0.00 0.00 0.00 3.01
2993 4095 4.985538 AGTGGAGTCCTGCATTTTTCTTA 58.014 39.130 11.33 0.00 32.40 2.10
2995 4097 4.762251 GTGGAGTCCTGCATTTTTCTTACT 59.238 41.667 11.33 0.00 32.40 2.24
3015 4117 3.073062 ACTTGGTTCACTTGCCTGTATCT 59.927 43.478 0.00 0.00 0.00 1.98
3018 4120 2.633488 GTTCACTTGCCTGTATCTCCC 58.367 52.381 0.00 0.00 0.00 4.30
3166 4268 7.832187 CCCTGTGAAAGACATATTAACCCTTTA 59.168 37.037 0.00 0.00 32.74 1.85
3275 4377 0.253044 GGCTGCCCTCACACAGAATA 59.747 55.000 7.66 0.00 35.90 1.75
3378 4482 2.159014 TGGCTCTGGCGATATTTAACGT 60.159 45.455 0.00 0.00 39.81 3.99
3379 4483 3.068448 TGGCTCTGGCGATATTTAACGTA 59.932 43.478 0.00 0.00 39.81 3.57
3440 4545 6.008331 TGAGGCTTAGTCAAGTAGTCAACTA 58.992 40.000 0.00 0.00 37.50 2.24
3488 4597 8.159344 TCTTTTAAAGAAAGCCAAAGAGAGAG 57.841 34.615 4.77 0.00 33.83 3.20
3501 4610 7.015974 AGCCAAAGAGAGAGAAAATGGATTTTT 59.984 33.333 0.00 0.00 39.86 1.94
3553 4662 0.798776 CAAGCGGTGGTAGAAGCAAG 59.201 55.000 0.00 0.00 0.00 4.01
3664 4773 4.024670 ACTCTTAGCTAGGTCGGTTTGAT 58.975 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.208644 TGAGCTAATTTGTTGCACTTTCTTC 58.791 36.000 0.00 0.00 0.00 2.87
6 7 5.005740 TCTCATGAGCTAATTTGTTGCACT 58.994 37.500 18.36 0.00 0.00 4.40
7 8 5.300969 TCTCATGAGCTAATTTGTTGCAC 57.699 39.130 18.36 0.00 0.00 4.57
8 9 6.327154 CAATCTCATGAGCTAATTTGTTGCA 58.673 36.000 18.36 0.00 0.00 4.08
9 10 5.231568 GCAATCTCATGAGCTAATTTGTTGC 59.768 40.000 18.36 16.56 0.00 4.17
10 11 5.454554 CGCAATCTCATGAGCTAATTTGTTG 59.545 40.000 18.36 11.87 0.00 3.33
11 12 5.449588 CCGCAATCTCATGAGCTAATTTGTT 60.450 40.000 18.36 0.26 0.00 2.83
12 13 4.036027 CCGCAATCTCATGAGCTAATTTGT 59.964 41.667 18.36 0.00 0.00 2.83
13 14 4.534168 CCGCAATCTCATGAGCTAATTTG 58.466 43.478 18.36 15.12 0.00 2.32
14 15 3.004106 GCCGCAATCTCATGAGCTAATTT 59.996 43.478 18.36 3.73 0.00 1.82
15 16 2.551459 GCCGCAATCTCATGAGCTAATT 59.449 45.455 18.36 9.84 0.00 1.40
16 17 2.149578 GCCGCAATCTCATGAGCTAAT 58.850 47.619 18.36 3.63 0.00 1.73
17 18 1.139654 AGCCGCAATCTCATGAGCTAA 59.860 47.619 18.36 0.99 31.96 3.09
18 19 0.755079 AGCCGCAATCTCATGAGCTA 59.245 50.000 18.36 1.80 31.96 3.32
19 20 0.755079 TAGCCGCAATCTCATGAGCT 59.245 50.000 18.36 12.71 36.08 4.09
20 21 0.864455 GTAGCCGCAATCTCATGAGC 59.136 55.000 18.36 6.21 0.00 4.26
21 22 2.133553 CAGTAGCCGCAATCTCATGAG 58.866 52.381 17.07 17.07 0.00 2.90
22 23 1.756538 TCAGTAGCCGCAATCTCATGA 59.243 47.619 0.00 0.00 0.00 3.07
23 24 1.863454 GTCAGTAGCCGCAATCTCATG 59.137 52.381 0.00 0.00 0.00 3.07
24 25 1.482182 TGTCAGTAGCCGCAATCTCAT 59.518 47.619 0.00 0.00 0.00 2.90
25 26 0.894835 TGTCAGTAGCCGCAATCTCA 59.105 50.000 0.00 0.00 0.00 3.27
26 27 1.565305 CTGTCAGTAGCCGCAATCTC 58.435 55.000 0.00 0.00 0.00 2.75
27 28 0.176680 CCTGTCAGTAGCCGCAATCT 59.823 55.000 0.00 0.00 0.00 2.40
28 29 1.432270 GCCTGTCAGTAGCCGCAATC 61.432 60.000 0.00 0.00 0.00 2.67
29 30 1.450312 GCCTGTCAGTAGCCGCAAT 60.450 57.895 0.00 0.00 0.00 3.56
30 31 2.047274 GCCTGTCAGTAGCCGCAA 60.047 61.111 0.00 0.00 0.00 4.85
31 32 4.435436 CGCCTGTCAGTAGCCGCA 62.435 66.667 0.00 0.00 0.00 5.69
33 34 3.449227 TCCGCCTGTCAGTAGCCG 61.449 66.667 0.00 0.00 0.00 5.52
34 35 1.961180 ATGTCCGCCTGTCAGTAGCC 61.961 60.000 0.00 0.00 0.00 3.93
35 36 0.807667 CATGTCCGCCTGTCAGTAGC 60.808 60.000 0.00 0.00 0.00 3.58
36 37 0.532573 ACATGTCCGCCTGTCAGTAG 59.467 55.000 0.00 0.00 0.00 2.57
37 38 0.246360 CACATGTCCGCCTGTCAGTA 59.754 55.000 0.00 0.00 0.00 2.74
38 39 1.004560 CACATGTCCGCCTGTCAGT 60.005 57.895 0.00 0.00 0.00 3.41
39 40 1.016130 GTCACATGTCCGCCTGTCAG 61.016 60.000 0.00 0.00 0.00 3.51
40 41 1.005037 GTCACATGTCCGCCTGTCA 60.005 57.895 0.00 0.00 0.00 3.58
41 42 0.391661 ATGTCACATGTCCGCCTGTC 60.392 55.000 0.00 0.00 0.00 3.51
42 43 0.391661 GATGTCACATGTCCGCCTGT 60.392 55.000 0.00 0.00 0.00 4.00
43 44 0.107993 AGATGTCACATGTCCGCCTG 60.108 55.000 0.00 0.00 0.00 4.85
44 45 0.615331 AAGATGTCACATGTCCGCCT 59.385 50.000 0.00 0.00 0.00 5.52
45 46 1.009829 GAAGATGTCACATGTCCGCC 58.990 55.000 0.00 0.00 0.00 6.13
46 47 1.725641 TGAAGATGTCACATGTCCGC 58.274 50.000 0.00 0.00 0.00 5.54
47 48 5.006068 CAGTAATGAAGATGTCACATGTCCG 59.994 44.000 0.00 0.00 39.72 4.79
48 49 6.036517 GTCAGTAATGAAGATGTCACATGTCC 59.963 42.308 0.00 0.00 39.72 4.02
49 50 6.237675 CGTCAGTAATGAAGATGTCACATGTC 60.238 42.308 0.00 0.00 39.72 3.06
50 51 5.578336 CGTCAGTAATGAAGATGTCACATGT 59.422 40.000 0.00 0.00 39.72 3.21
51 52 5.578336 ACGTCAGTAATGAAGATGTCACATG 59.422 40.000 12.98 0.00 39.72 3.21
52 53 5.578336 CACGTCAGTAATGAAGATGTCACAT 59.422 40.000 12.98 0.00 39.72 3.21
53 54 4.923281 CACGTCAGTAATGAAGATGTCACA 59.077 41.667 12.98 0.00 39.72 3.58
54 55 4.201628 GCACGTCAGTAATGAAGATGTCAC 60.202 45.833 12.98 0.00 39.72 3.67
55 56 3.926527 GCACGTCAGTAATGAAGATGTCA 59.073 43.478 12.98 0.00 41.67 3.58
56 57 4.177026 AGCACGTCAGTAATGAAGATGTC 58.823 43.478 12.98 4.77 29.56 3.06
57 58 4.193826 AGCACGTCAGTAATGAAGATGT 57.806 40.909 12.98 0.00 32.05 3.06
58 59 4.627035 TCAAGCACGTCAGTAATGAAGATG 59.373 41.667 12.98 8.31 0.00 2.90
59 60 4.820897 TCAAGCACGTCAGTAATGAAGAT 58.179 39.130 12.98 0.00 0.00 2.40
60 61 4.251543 TCAAGCACGTCAGTAATGAAGA 57.748 40.909 12.98 0.00 0.00 2.87
61 62 4.990543 TTCAAGCACGTCAGTAATGAAG 57.009 40.909 4.54 4.54 0.00 3.02
62 63 4.814234 ACTTTCAAGCACGTCAGTAATGAA 59.186 37.500 0.00 0.00 0.00 2.57
63 64 4.377021 ACTTTCAAGCACGTCAGTAATGA 58.623 39.130 0.00 0.00 0.00 2.57
64 65 4.449068 AGACTTTCAAGCACGTCAGTAATG 59.551 41.667 0.00 0.00 0.00 1.90
65 66 4.632153 AGACTTTCAAGCACGTCAGTAAT 58.368 39.130 0.00 0.00 0.00 1.89
66 67 4.049186 GAGACTTTCAAGCACGTCAGTAA 58.951 43.478 0.00 0.00 0.00 2.24
67 68 3.067601 TGAGACTTTCAAGCACGTCAGTA 59.932 43.478 0.00 0.00 31.34 2.74
68 69 2.159099 TGAGACTTTCAAGCACGTCAGT 60.159 45.455 0.00 0.00 31.34 3.41
69 70 2.473816 TGAGACTTTCAAGCACGTCAG 58.526 47.619 0.00 0.00 31.34 3.51
70 71 2.595124 TGAGACTTTCAAGCACGTCA 57.405 45.000 0.00 0.00 31.34 4.35
79 80 3.245016 ACATCAGGGCATTGAGACTTTCA 60.245 43.478 0.00 0.00 0.00 2.69
80 81 3.350833 ACATCAGGGCATTGAGACTTTC 58.649 45.455 0.00 0.00 0.00 2.62
81 82 3.350833 GACATCAGGGCATTGAGACTTT 58.649 45.455 0.00 0.00 0.00 2.66
82 83 2.679059 CGACATCAGGGCATTGAGACTT 60.679 50.000 0.00 0.00 0.00 3.01
83 84 1.134580 CGACATCAGGGCATTGAGACT 60.135 52.381 0.00 0.00 0.00 3.24
84 85 1.293924 CGACATCAGGGCATTGAGAC 58.706 55.000 0.00 0.00 0.00 3.36
85 86 0.904649 ACGACATCAGGGCATTGAGA 59.095 50.000 0.00 0.00 0.00 3.27
86 87 1.399440 CAACGACATCAGGGCATTGAG 59.601 52.381 0.00 0.00 0.00 3.02
87 88 1.452110 CAACGACATCAGGGCATTGA 58.548 50.000 0.00 0.00 0.00 2.57
88 89 0.452987 CCAACGACATCAGGGCATTG 59.547 55.000 0.00 0.00 0.00 2.82
89 90 0.327924 TCCAACGACATCAGGGCATT 59.672 50.000 0.00 0.00 0.00 3.56
90 91 0.107508 CTCCAACGACATCAGGGCAT 60.108 55.000 0.00 0.00 0.00 4.40
91 92 1.296392 CTCCAACGACATCAGGGCA 59.704 57.895 0.00 0.00 0.00 5.36
92 93 1.021390 CACTCCAACGACATCAGGGC 61.021 60.000 0.00 0.00 0.00 5.19
93 94 0.321671 ACACTCCAACGACATCAGGG 59.678 55.000 0.00 0.00 0.00 4.45
94 95 3.313012 TTACACTCCAACGACATCAGG 57.687 47.619 0.00 0.00 0.00 3.86
95 96 4.055360 TGTTTACACTCCAACGACATCAG 58.945 43.478 0.00 0.00 0.00 2.90
96 97 4.061357 TGTTTACACTCCAACGACATCA 57.939 40.909 0.00 0.00 0.00 3.07
97 98 4.092968 GGATGTTTACACTCCAACGACATC 59.907 45.833 0.00 0.00 40.49 3.06
98 99 4.000988 GGATGTTTACACTCCAACGACAT 58.999 43.478 0.00 0.00 0.00 3.06
99 100 3.395639 GGATGTTTACACTCCAACGACA 58.604 45.455 0.00 0.00 0.00 4.35
100 101 2.740447 GGGATGTTTACACTCCAACGAC 59.260 50.000 0.00 0.00 0.00 4.34
101 102 2.369203 TGGGATGTTTACACTCCAACGA 59.631 45.455 0.00 0.00 31.38 3.85
102 103 2.773487 TGGGATGTTTACACTCCAACG 58.227 47.619 11.07 0.00 31.38 4.10
103 104 4.764823 TCAATGGGATGTTTACACTCCAAC 59.235 41.667 9.19 0.00 35.77 3.77
104 105 4.991776 TCAATGGGATGTTTACACTCCAA 58.008 39.130 9.19 2.04 35.77 3.53
105 106 4.042809 ACTCAATGGGATGTTTACACTCCA 59.957 41.667 8.00 8.00 36.30 3.86
106 107 4.589908 ACTCAATGGGATGTTTACACTCC 58.410 43.478 0.00 0.00 0.00 3.85
107 108 7.681939 TTTACTCAATGGGATGTTTACACTC 57.318 36.000 0.00 0.00 0.00 3.51
108 109 8.650143 AATTTACTCAATGGGATGTTTACACT 57.350 30.769 0.00 0.00 0.00 3.55
144 145 7.093289 TGTCACCCTCCATTTTGTCTTTAAAAA 60.093 33.333 0.00 0.00 33.67 1.94
145 146 6.381420 TGTCACCCTCCATTTTGTCTTTAAAA 59.619 34.615 0.00 0.00 34.39 1.52
146 147 5.894393 TGTCACCCTCCATTTTGTCTTTAAA 59.106 36.000 0.00 0.00 0.00 1.52
147 148 5.450453 TGTCACCCTCCATTTTGTCTTTAA 58.550 37.500 0.00 0.00 0.00 1.52
148 149 5.055265 TGTCACCCTCCATTTTGTCTTTA 57.945 39.130 0.00 0.00 0.00 1.85
149 150 3.909732 TGTCACCCTCCATTTTGTCTTT 58.090 40.909 0.00 0.00 0.00 2.52
150 151 3.593442 TGTCACCCTCCATTTTGTCTT 57.407 42.857 0.00 0.00 0.00 3.01
151 152 3.222603 GTTGTCACCCTCCATTTTGTCT 58.777 45.455 0.00 0.00 0.00 3.41
152 153 2.955660 TGTTGTCACCCTCCATTTTGTC 59.044 45.455 0.00 0.00 0.00 3.18
153 154 3.025322 TGTTGTCACCCTCCATTTTGT 57.975 42.857 0.00 0.00 0.00 2.83
154 155 3.131933 TGTTGTTGTCACCCTCCATTTTG 59.868 43.478 0.00 0.00 0.00 2.44
155 156 3.370104 TGTTGTTGTCACCCTCCATTTT 58.630 40.909 0.00 0.00 0.00 1.82
190 191 2.223923 CGAGGGTTATGAGCTTCTGGAG 60.224 54.545 0.00 0.00 0.00 3.86
191 192 1.757118 CGAGGGTTATGAGCTTCTGGA 59.243 52.381 0.00 0.00 0.00 3.86
195 199 2.961526 TGTCGAGGGTTATGAGCTTC 57.038 50.000 0.00 0.00 0.00 3.86
209 213 6.655425 TCTCTCTCTTTCTCTTTACATGTCGA 59.345 38.462 0.00 0.00 0.00 4.20
225 229 3.374098 CCCCTCCTTCTCATCTCTCTCTT 60.374 52.174 0.00 0.00 0.00 2.85
246 250 4.222588 TGAATCAAAATGAACCATCACCCC 59.777 41.667 0.00 0.00 38.69 4.95
249 253 6.254157 CCGAATGAATCAAAATGAACCATCAC 59.746 38.462 0.00 0.00 38.69 3.06
252 256 6.101332 CACCGAATGAATCAAAATGAACCAT 58.899 36.000 0.00 0.00 0.00 3.55
253 257 5.468592 CACCGAATGAATCAAAATGAACCA 58.531 37.500 0.00 0.00 0.00 3.67
259 263 5.416952 AGAAGAGCACCGAATGAATCAAAAT 59.583 36.000 0.00 0.00 0.00 1.82
268 272 2.801342 GCCTAGAGAAGAGCACCGAATG 60.801 54.545 0.00 0.00 0.00 2.67
276 280 2.437651 AGGGATTTGCCTAGAGAAGAGC 59.562 50.000 0.00 0.00 36.66 4.09
283 289 9.793259 CAATTTTATACTAGGGATTTGCCTAGA 57.207 33.333 26.28 13.46 39.25 2.43
287 293 6.267699 AGCCAATTTTATACTAGGGATTTGCC 59.732 38.462 0.00 0.00 0.00 4.52
288 294 7.290110 AGCCAATTTTATACTAGGGATTTGC 57.710 36.000 0.00 0.00 0.00 3.68
290 296 9.267071 ACAAAGCCAATTTTATACTAGGGATTT 57.733 29.630 0.00 0.00 33.29 2.17
293 299 7.179269 ACACAAAGCCAATTTTATACTAGGGA 58.821 34.615 0.00 0.00 0.00 4.20
305 311 7.546667 CAGCAAAGATAATACACAAAGCCAATT 59.453 33.333 0.00 0.00 0.00 2.32
338 344 5.742743 ACTTCCATTAATAGGAGAGGGGAT 58.257 41.667 0.00 0.00 36.33 3.85
347 353 4.058817 GCTCGGTGACTTCCATTAATAGG 58.941 47.826 0.00 0.00 0.00 2.57
350 356 3.432326 GGAGCTCGGTGACTTCCATTAAT 60.432 47.826 7.83 0.00 0.00 1.40
354 360 0.616111 AGGAGCTCGGTGACTTCCAT 60.616 55.000 7.83 0.00 0.00 3.41
357 363 0.318762 AACAGGAGCTCGGTGACTTC 59.681 55.000 18.82 0.00 0.00 3.01
360 366 2.674796 ATTAACAGGAGCTCGGTGAC 57.325 50.000 18.82 0.50 0.00 3.67
400 406 7.176589 ACCAACAATTACTCCTTTCAAAACA 57.823 32.000 0.00 0.00 0.00 2.83
405 411 7.595819 AATGAACCAACAATTACTCCTTTCA 57.404 32.000 0.00 0.00 0.00 2.69
514 534 9.846248 GCAACTTTTGTAGTAATGAAGAATCAT 57.154 29.630 0.00 0.00 41.41 2.45
555 578 8.830580 ACTTGTTTCATATAATTGGATCTGACG 58.169 33.333 0.00 0.00 0.00 4.35
579 602 6.530181 GTGTCCGAAACAAAATTTCTTTCACT 59.470 34.615 16.05 0.00 40.31 3.41
598 621 5.216566 ACGTATCATTGAATTTGTGTCCG 57.783 39.130 0.00 0.00 0.00 4.79
600 623 8.629986 CAAAGAACGTATCATTGAATTTGTGTC 58.370 33.333 8.87 0.00 38.68 3.67
605 628 7.021196 CGGACAAAGAACGTATCATTGAATTT 58.979 34.615 16.77 1.82 38.68 1.82
606 629 6.403200 CCGGACAAAGAACGTATCATTGAATT 60.403 38.462 16.77 0.00 38.68 2.17
615 638 7.120138 ACAAATAATTCCGGACAAAGAACGTAT 59.880 33.333 1.83 0.00 0.00 3.06
619 642 5.793457 CGACAAATAATTCCGGACAAAGAAC 59.207 40.000 1.83 0.00 0.00 3.01
669 692 6.805016 ATGAGTGATGTGTCCTAGAAATCT 57.195 37.500 0.00 0.00 0.00 2.40
675 699 6.809869 TGATTGTATGAGTGATGTGTCCTAG 58.190 40.000 0.00 0.00 0.00 3.02
717 756 8.147642 TCACCGCATTGTTTTTAATCAAAAAT 57.852 26.923 0.00 0.00 43.56 1.82
727 766 5.968528 TTACCTATCACCGCATTGTTTTT 57.031 34.783 0.00 0.00 0.00 1.94
733 1824 5.512576 GGGAGTATTTACCTATCACCGCATT 60.513 44.000 0.00 0.00 0.00 3.56
734 1825 4.020485 GGGAGTATTTACCTATCACCGCAT 60.020 45.833 0.00 0.00 0.00 4.73
737 1828 5.047943 CAGAGGGAGTATTTACCTATCACCG 60.048 48.000 0.00 0.00 34.02 4.94
739 1830 6.980416 ACAGAGGGAGTATTTACCTATCAC 57.020 41.667 0.00 0.00 34.02 3.06
854 1945 9.676861 TCAGAGATTTCAAATGAACTATCACAT 57.323 29.630 9.73 0.00 38.69 3.21
855 1946 9.506018 TTCAGAGATTTCAAATGAACTATCACA 57.494 29.630 9.73 0.00 38.69 3.58
861 1952 9.741647 GTCTTTTTCAGAGATTTCAAATGAACT 57.258 29.630 0.00 0.00 29.81 3.01
862 1953 9.520204 TGTCTTTTTCAGAGATTTCAAATGAAC 57.480 29.630 0.00 0.00 29.81 3.18
863 1954 9.740239 CTGTCTTTTTCAGAGATTTCAAATGAA 57.260 29.630 0.00 0.00 35.20 2.57
864 1955 9.123902 TCTGTCTTTTTCAGAGATTTCAAATGA 57.876 29.630 0.00 0.00 37.07 2.57
865 1956 9.909644 ATCTGTCTTTTTCAGAGATTTCAAATG 57.090 29.630 0.00 0.00 43.66 2.32
876 1967 9.663904 CGTTTCAAAATATCTGTCTTTTTCAGA 57.336 29.630 0.00 0.00 44.37 3.27
877 1968 8.905702 CCGTTTCAAAATATCTGTCTTTTTCAG 58.094 33.333 0.00 0.00 0.00 3.02
878 1969 8.625651 TCCGTTTCAAAATATCTGTCTTTTTCA 58.374 29.630 0.00 0.00 0.00 2.69
879 1970 9.626045 ATCCGTTTCAAAATATCTGTCTTTTTC 57.374 29.630 0.00 0.00 0.00 2.29
880 1971 9.410556 CATCCGTTTCAAAATATCTGTCTTTTT 57.589 29.630 0.00 0.00 0.00 1.94
881 1972 8.792633 TCATCCGTTTCAAAATATCTGTCTTTT 58.207 29.630 0.00 0.00 0.00 2.27
882 1973 8.335532 TCATCCGTTTCAAAATATCTGTCTTT 57.664 30.769 0.00 0.00 0.00 2.52
883 1974 7.921786 TCATCCGTTTCAAAATATCTGTCTT 57.078 32.000 0.00 0.00 0.00 3.01
884 1975 7.607991 ACTTCATCCGTTTCAAAATATCTGTCT 59.392 33.333 0.00 0.00 0.00 3.41
885 1976 7.752695 ACTTCATCCGTTTCAAAATATCTGTC 58.247 34.615 0.00 0.00 0.00 3.51
886 1977 7.687941 ACTTCATCCGTTTCAAAATATCTGT 57.312 32.000 0.00 0.00 0.00 3.41
887 1978 8.883731 AGTACTTCATCCGTTTCAAAATATCTG 58.116 33.333 0.00 0.00 0.00 2.90
888 1979 9.449719 AAGTACTTCATCCGTTTCAAAATATCT 57.550 29.630 1.12 0.00 0.00 1.98
892 1983 9.063615 AGTAAAGTACTTCATCCGTTTCAAAAT 57.936 29.630 8.95 0.00 34.86 1.82
893 1984 8.441312 AGTAAAGTACTTCATCCGTTTCAAAA 57.559 30.769 8.95 0.00 34.86 2.44
894 1985 9.545105 TTAGTAAAGTACTTCATCCGTTTCAAA 57.455 29.630 8.95 0.00 40.14 2.69
895 1986 9.715121 ATTAGTAAAGTACTTCATCCGTTTCAA 57.285 29.630 8.95 0.00 40.14 2.69
911 2002 9.374838 CAACCGTTGGATACTTATTAGTAAAGT 57.625 33.333 3.10 0.00 40.14 2.66
912 2003 9.590451 TCAACCGTTGGATACTTATTAGTAAAG 57.410 33.333 11.35 0.00 40.14 1.85
913 2004 9.941325 TTCAACCGTTGGATACTTATTAGTAAA 57.059 29.630 11.35 0.00 40.14 2.01
914 2005 9.369904 GTTCAACCGTTGGATACTTATTAGTAA 57.630 33.333 11.35 0.00 40.14 2.24
915 2006 8.752187 AGTTCAACCGTTGGATACTTATTAGTA 58.248 33.333 11.35 0.00 40.96 1.82
916 2007 7.548075 CAGTTCAACCGTTGGATACTTATTAGT 59.452 37.037 11.35 0.00 38.44 2.24
917 2008 7.465513 GCAGTTCAACCGTTGGATACTTATTAG 60.466 40.741 11.35 3.00 37.61 1.73
918 2009 6.314400 GCAGTTCAACCGTTGGATACTTATTA 59.686 38.462 11.35 0.00 37.61 0.98
919 2010 5.123344 GCAGTTCAACCGTTGGATACTTATT 59.877 40.000 11.35 0.00 37.61 1.40
920 2011 4.634443 GCAGTTCAACCGTTGGATACTTAT 59.366 41.667 11.35 0.00 37.61 1.73
921 2012 3.998341 GCAGTTCAACCGTTGGATACTTA 59.002 43.478 11.35 0.00 37.61 2.24
922 2013 2.812011 GCAGTTCAACCGTTGGATACTT 59.188 45.455 11.35 0.00 37.61 2.24
923 2014 2.038557 AGCAGTTCAACCGTTGGATACT 59.961 45.455 11.35 9.41 37.61 2.12
924 2015 2.423577 AGCAGTTCAACCGTTGGATAC 58.576 47.619 11.35 7.50 0.00 2.24
925 2016 2.851263 AGCAGTTCAACCGTTGGATA 57.149 45.000 11.35 0.00 0.00 2.59
926 2017 1.880027 GAAGCAGTTCAACCGTTGGAT 59.120 47.619 11.35 0.00 32.36 3.41
927 2018 1.305201 GAAGCAGTTCAACCGTTGGA 58.695 50.000 11.35 0.00 32.36 3.53
928 2019 1.002468 CTGAAGCAGTTCAACCGTTGG 60.002 52.381 11.35 0.00 42.27 3.77
929 2020 1.002468 CCTGAAGCAGTTCAACCGTTG 60.002 52.381 4.78 4.78 42.27 4.10
930 2021 1.134220 TCCTGAAGCAGTTCAACCGTT 60.134 47.619 0.00 0.00 42.27 4.44
931 2022 0.468226 TCCTGAAGCAGTTCAACCGT 59.532 50.000 0.00 0.00 42.27 4.83
932 2023 1.151668 CTCCTGAAGCAGTTCAACCG 58.848 55.000 0.00 0.00 42.27 4.44
933 2024 2.550830 TCTCCTGAAGCAGTTCAACC 57.449 50.000 0.00 0.00 42.27 3.77
1060 2153 1.444553 GAGACTGCTTCGTCCACGG 60.445 63.158 0.00 0.00 40.29 4.94
1077 2170 4.485834 ACGATAAGGCGCGCGTGA 62.486 61.111 32.35 21.45 35.44 4.35
1125 2218 0.395862 AGGATCGAAGAAGGCGGAGA 60.396 55.000 0.00 0.00 43.58 3.71
1134 2227 1.355563 CGCAGCGTAGGATCGAAGA 59.644 57.895 6.65 0.00 45.75 2.87
1378 2471 2.969238 CGCGATGCCATGGAGGAC 60.969 66.667 18.40 0.00 41.22 3.85
1389 2482 2.589492 GCCGGAAGATGACGCGATG 61.589 63.158 15.93 0.00 0.00 3.84
1443 2536 3.155998 CAAGAACTTTGAATACGCGCTG 58.844 45.455 5.73 1.02 0.00 5.18
1551 2644 1.284785 CCCTCAAGCCACATTTCCCTA 59.715 52.381 0.00 0.00 0.00 3.53
1747 2840 0.249120 CCGCACCTGAAGTACATGGA 59.751 55.000 0.00 0.00 0.00 3.41
1748 2841 1.369091 GCCGCACCTGAAGTACATGG 61.369 60.000 0.00 0.00 0.00 3.66
1811 2904 4.819630 GTGAAGAACATGTAACCAAGTCCA 59.180 41.667 0.00 0.00 0.00 4.02
1921 3014 4.450053 AGAAGACTAGCAATCAAGATGCC 58.550 43.478 0.00 0.00 44.91 4.40
2076 3169 4.003648 GGAATACCAAATATCCCAGCTCG 58.996 47.826 0.00 0.00 35.97 5.03
2112 3205 8.103305 ACCATATTGTACATGACTGAGTTCTTT 58.897 33.333 0.00 0.00 0.00 2.52
2160 3253 0.323269 TGGCCTTCATCGCAAATCCA 60.323 50.000 3.32 0.00 0.00 3.41
2272 3365 4.884668 ACAACTTCCATCCTTCGTCTAA 57.115 40.909 0.00 0.00 0.00 2.10
2280 3373 5.843019 TTCTCCTAAACAACTTCCATCCT 57.157 39.130 0.00 0.00 0.00 3.24
2372 3465 0.548510 GGCCTCCTTCAGCTGGTTAT 59.451 55.000 15.13 0.00 0.00 1.89
2678 3778 5.924254 CGGCATATTTCTCAATGATGCAAAT 59.076 36.000 6.59 4.14 43.74 2.32
2716 3816 7.823745 AAACCAGAACAATACAGAGTTCAAT 57.176 32.000 7.88 0.00 44.94 2.57
2947 4049 8.972127 ACTAGAAAGAGTGCTTCAGATATTACA 58.028 33.333 0.00 0.00 31.82 2.41
2993 4095 3.073062 AGATACAGGCAAGTGAACCAAGT 59.927 43.478 0.00 0.00 0.00 3.16
2995 4097 3.559171 GGAGATACAGGCAAGTGAACCAA 60.559 47.826 0.00 0.00 0.00 3.67
3015 4117 7.705700 TGACACCTATATATAGCTAACAGGGA 58.294 38.462 13.49 0.00 0.00 4.20
3461 4566 9.136323 TCTCTCTTTGGCTTTCTTTAAAAGATT 57.864 29.630 1.85 0.00 36.55 2.40
3516 4625 3.484407 CTTGCTGCAGCCTTTAGGATAT 58.516 45.455 34.64 0.00 41.18 1.63
3539 4648 1.073284 TCCAACCTTGCTTCTACCACC 59.927 52.381 0.00 0.00 0.00 4.61
3553 4662 5.318630 TGACACCTAAGGTAAATTCCAACC 58.681 41.667 0.00 0.00 32.11 3.77


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

AutoCloner maintained by Alex Coulton.