Multiple sequence alignment - TraesCS1B01G092100

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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 TraesCS1B01G092100 chr1B 100.000 3578 0 0 1 3578 94185399 94181822 0.000000e+00 6608.0
1 TraesCS1B01G092100 chr1B 84.872 1560 150 40 841 2366 94200146 94198639 0.000000e+00 1495.0
2 TraesCS1B01G092100 chr1B 91.256 629 49 2 2956 3578 399323130 399322502 0.000000e+00 852.0
3 TraesCS1B01G092100 chr1B 91.200 625 47 4 2962 3578 306046667 306046043 0.000000e+00 843.0
4 TraesCS1B01G092100 chr1B 84.450 373 35 16 143 494 94201254 94200884 2.640000e-91 346.0
5 TraesCS1B01G092100 chr1B 94.444 36 2 0 606 641 94200522 94200487 4.990000e-04 56.5
6 TraesCS1B01G092100 chr1D 90.978 2782 128 57 147 2871 58450699 58453414 0.000000e+00 3633.0
7 TraesCS1B01G092100 chr1D 91.200 625 48 6 2960 3578 446669803 446669180 0.000000e+00 843.0
8 TraesCS1B01G092100 chr1A 91.873 2387 98 43 544 2871 57192038 57194387 0.000000e+00 3245.0
9 TraesCS1B01G092100 chr1A 81.740 1402 221 29 1042 2436 57392133 57390760 0.000000e+00 1138.0
10 TraesCS1B01G092100 chr1A 85.476 420 30 17 147 537 57191557 57191974 3.330000e-110 409.0
11 TraesCS1B01G092100 chr1A 85.326 368 31 17 147 494 57393053 57392689 3.400000e-95 359.0
12 TraesCS1B01G092100 chr5D 92.013 626 41 5 2960 3578 297553923 297553300 0.000000e+00 870.0
13 TraesCS1B01G092100 chr3D 91.892 629 40 7 2960 3578 359580763 359580136 0.000000e+00 869.0
14 TraesCS1B01G092100 chr3D 91.125 631 45 6 2956 3578 344832619 344833246 0.000000e+00 845.0
15 TraesCS1B01G092100 chr5B 91.346 624 47 6 2960 3578 480144065 480143444 0.000000e+00 846.0
16 TraesCS1B01G092100 chr7D 90.952 630 48 5 2956 3578 192102449 192101822 0.000000e+00 839.0
17 TraesCS1B01G092100 chr2D 90.938 629 49 4 2956 3578 338969800 338969174 0.000000e+00 839.0
18 TraesCS1B01G092100 chr6D 100.000 28 0 0 2932 2959 460310835 460310862 6.000000e-03 52.8


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 TraesCS1B01G092100 chr1B 94181822 94185399 3577 True 6608.0 6608 100.0000 1 3578 1 chr1B.!!$R1 3577
1 TraesCS1B01G092100 chr1B 399322502 399323130 628 True 852.0 852 91.2560 2956 3578 1 chr1B.!!$R3 622
2 TraesCS1B01G092100 chr1B 306046043 306046667 624 True 843.0 843 91.2000 2962 3578 1 chr1B.!!$R2 616
3 TraesCS1B01G092100 chr1B 94198639 94201254 2615 True 632.5 1495 87.9220 143 2366 3 chr1B.!!$R4 2223
4 TraesCS1B01G092100 chr1D 58450699 58453414 2715 False 3633.0 3633 90.9780 147 2871 1 chr1D.!!$F1 2724
5 TraesCS1B01G092100 chr1D 446669180 446669803 623 True 843.0 843 91.2000 2960 3578 1 chr1D.!!$R1 618
6 TraesCS1B01G092100 chr1A 57191557 57194387 2830 False 1827.0 3245 88.6745 147 2871 2 chr1A.!!$F1 2724
7 TraesCS1B01G092100 chr1A 57390760 57393053 2293 True 748.5 1138 83.5330 147 2436 2 chr1A.!!$R1 2289
8 TraesCS1B01G092100 chr5D 297553300 297553923 623 True 870.0 870 92.0130 2960 3578 1 chr5D.!!$R1 618
9 TraesCS1B01G092100 chr3D 359580136 359580763 627 True 869.0 869 91.8920 2960 3578 1 chr3D.!!$R1 618
10 TraesCS1B01G092100 chr3D 344832619 344833246 627 False 845.0 845 91.1250 2956 3578 1 chr3D.!!$F1 622
11 TraesCS1B01G092100 chr5B 480143444 480144065 621 True 846.0 846 91.3460 2960 3578 1 chr5B.!!$R1 618
12 TraesCS1B01G092100 chr7D 192101822 192102449 627 True 839.0 839 90.9520 2956 3578 1 chr7D.!!$R1 622
13 TraesCS1B01G092100 chr2D 338969174 338969800 626 True 839.0 839 90.9380 2956 3578 1 chr2D.!!$R1 622

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
101 102 0.036732 TTGAATCCTGCGTTGGAGCT 59.963 50.0 0.00 0.00 39.78 4.09 F
102 103 0.036732 TGAATCCTGCGTTGGAGCTT 59.963 50.0 4.95 0.00 39.78 3.74 F
111 112 0.237498 CGTTGGAGCTTCCGGAAAAC 59.763 55.0 19.39 17.19 40.17 2.43 F
182 183 0.327924 TCAAGGATCACATGGGCGTT 59.672 50.0 0.00 0.00 0.00 4.84 F
280 292 0.521735 AAAACAGAAATCTCGCGGGC 59.478 50.0 6.13 0.00 0.00 6.13 F
913 1477 0.694771 TCCAAGCTGGCATTCTGAGT 59.305 50.0 0.00 0.00 37.47 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 2192 0.389948 CGAACTCCGGCAGCTTAGTT 60.390 55.000 3.79 3.79 34.96 2.24 R
1826 2407 0.817654 CTGTGCCGTCTCTATCACCA 59.182 55.000 0.00 0.00 0.00 4.17 R
1986 2567 1.205064 CGCCTTCTTGAACTGCACG 59.795 57.895 0.00 0.00 0.00 5.34 R
2178 2759 2.496817 GGCGTCTTCATCGAGGCT 59.503 61.111 0.00 0.00 42.63 4.58 R
2517 3098 1.241990 TGGAGACGAAGGTGACGAGG 61.242 60.000 0.00 0.00 34.70 4.63 R
2932 3534 0.108615 GCGCCTATCACTCGCCATAT 60.109 55.000 0.00 0.00 42.71 1.78 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
45 46 4.385358 TTTTTCCTCAGCCAAACTTGAC 57.615 40.909 0.00 0.00 0.00 3.18
46 47 1.981256 TTCCTCAGCCAAACTTGACC 58.019 50.000 0.00 0.00 0.00 4.02
47 48 0.843309 TCCTCAGCCAAACTTGACCA 59.157 50.000 0.00 0.00 0.00 4.02
48 49 1.202806 TCCTCAGCCAAACTTGACCAG 60.203 52.381 0.00 0.00 0.00 4.00
49 50 1.202806 CCTCAGCCAAACTTGACCAGA 60.203 52.381 0.00 0.00 0.00 3.86
50 51 2.553904 CCTCAGCCAAACTTGACCAGAT 60.554 50.000 0.00 0.00 0.00 2.90
51 52 2.746362 CTCAGCCAAACTTGACCAGATC 59.254 50.000 0.00 0.00 0.00 2.75
52 53 2.373169 TCAGCCAAACTTGACCAGATCT 59.627 45.455 0.00 0.00 0.00 2.75
53 54 2.486982 CAGCCAAACTTGACCAGATCTG 59.513 50.000 16.24 16.24 0.00 2.90
75 76 3.777465 CATGAAGTGCTCCTTGAATGG 57.223 47.619 0.00 0.00 32.03 3.16
76 77 2.957402 TGAAGTGCTCCTTGAATGGT 57.043 45.000 0.00 0.00 32.03 3.55
77 78 3.228188 TGAAGTGCTCCTTGAATGGTT 57.772 42.857 0.00 0.00 32.03 3.67
78 79 4.365514 TGAAGTGCTCCTTGAATGGTTA 57.634 40.909 0.00 0.00 32.03 2.85
79 80 4.326826 TGAAGTGCTCCTTGAATGGTTAG 58.673 43.478 0.00 0.00 32.03 2.34
80 81 3.356529 AGTGCTCCTTGAATGGTTAGG 57.643 47.619 0.00 0.00 0.00 2.69
81 82 2.644798 AGTGCTCCTTGAATGGTTAGGT 59.355 45.455 0.00 0.00 0.00 3.08
82 83 3.074538 AGTGCTCCTTGAATGGTTAGGTT 59.925 43.478 0.00 0.00 0.00 3.50
83 84 3.826729 GTGCTCCTTGAATGGTTAGGTTT 59.173 43.478 0.00 0.00 0.00 3.27
84 85 3.826157 TGCTCCTTGAATGGTTAGGTTTG 59.174 43.478 0.00 0.00 0.00 2.93
85 86 4.079253 GCTCCTTGAATGGTTAGGTTTGA 58.921 43.478 0.00 0.00 0.00 2.69
86 87 4.522789 GCTCCTTGAATGGTTAGGTTTGAA 59.477 41.667 0.00 0.00 0.00 2.69
87 88 5.185828 GCTCCTTGAATGGTTAGGTTTGAAT 59.814 40.000 0.00 0.00 0.00 2.57
88 89 6.625960 GCTCCTTGAATGGTTAGGTTTGAATC 60.626 42.308 0.00 0.00 0.00 2.52
89 90 5.714806 TCCTTGAATGGTTAGGTTTGAATCC 59.285 40.000 0.00 0.00 0.00 3.01
90 91 5.716703 CCTTGAATGGTTAGGTTTGAATCCT 59.283 40.000 0.00 0.00 38.91 3.24
91 92 6.350445 CCTTGAATGGTTAGGTTTGAATCCTG 60.350 42.308 5.08 0.00 36.60 3.86
92 93 4.462483 TGAATGGTTAGGTTTGAATCCTGC 59.538 41.667 5.08 0.00 36.60 4.85
93 94 2.432444 TGGTTAGGTTTGAATCCTGCG 58.568 47.619 5.08 0.00 36.60 5.18
94 95 2.224670 TGGTTAGGTTTGAATCCTGCGT 60.225 45.455 5.08 0.00 36.60 5.24
95 96 2.817844 GGTTAGGTTTGAATCCTGCGTT 59.182 45.455 5.08 0.00 36.60 4.84
96 97 3.365969 GGTTAGGTTTGAATCCTGCGTTG 60.366 47.826 5.08 0.00 36.60 4.10
97 98 1.247567 AGGTTTGAATCCTGCGTTGG 58.752 50.000 0.00 0.00 33.62 3.77
98 99 1.202879 AGGTTTGAATCCTGCGTTGGA 60.203 47.619 0.00 1.27 40.82 3.53
99 100 1.200020 GGTTTGAATCCTGCGTTGGAG 59.800 52.381 4.95 0.00 39.78 3.86
100 101 0.881118 TTTGAATCCTGCGTTGGAGC 59.119 50.000 4.95 1.17 39.78 4.70
101 102 0.036732 TTGAATCCTGCGTTGGAGCT 59.963 50.000 0.00 0.00 39.78 4.09
102 103 0.036732 TGAATCCTGCGTTGGAGCTT 59.963 50.000 4.95 0.00 39.78 3.74
103 104 0.729690 GAATCCTGCGTTGGAGCTTC 59.270 55.000 4.95 0.00 39.78 3.86
104 105 0.678048 AATCCTGCGTTGGAGCTTCC 60.678 55.000 4.95 0.00 39.78 3.46
105 106 2.859273 ATCCTGCGTTGGAGCTTCCG 62.859 60.000 4.95 0.00 40.17 4.30
106 107 3.121030 CTGCGTTGGAGCTTCCGG 61.121 66.667 0.00 0.00 40.17 5.14
107 108 3.589654 CTGCGTTGGAGCTTCCGGA 62.590 63.158 0.00 0.00 40.17 5.14
108 109 2.358247 GCGTTGGAGCTTCCGGAA 60.358 61.111 17.73 17.73 40.17 4.30
109 110 1.964373 GCGTTGGAGCTTCCGGAAA 60.964 57.895 19.39 0.00 40.17 3.13
110 111 1.512156 GCGTTGGAGCTTCCGGAAAA 61.512 55.000 19.39 6.23 40.17 2.29
111 112 0.237498 CGTTGGAGCTTCCGGAAAAC 59.763 55.000 19.39 17.19 40.17 2.43
112 113 0.596577 GTTGGAGCTTCCGGAAAACC 59.403 55.000 19.39 19.92 40.17 3.27
113 114 0.476771 TTGGAGCTTCCGGAAAACCT 59.523 50.000 19.39 14.26 40.17 3.50
114 115 0.476771 TGGAGCTTCCGGAAAACCTT 59.523 50.000 19.39 1.80 40.17 3.50
115 116 1.700739 TGGAGCTTCCGGAAAACCTTA 59.299 47.619 19.39 4.41 40.17 2.69
116 117 2.307686 TGGAGCTTCCGGAAAACCTTAT 59.692 45.455 19.39 0.00 40.17 1.73
117 118 2.943690 GGAGCTTCCGGAAAACCTTATC 59.056 50.000 19.39 8.11 0.00 1.75
118 119 3.370633 GGAGCTTCCGGAAAACCTTATCT 60.371 47.826 19.39 5.15 0.00 1.98
119 120 3.872182 GAGCTTCCGGAAAACCTTATCTC 59.128 47.826 19.39 10.11 0.00 2.75
120 121 2.943690 GCTTCCGGAAAACCTTATCTCC 59.056 50.000 19.39 0.00 0.00 3.71
121 122 3.370633 GCTTCCGGAAAACCTTATCTCCT 60.371 47.826 19.39 0.00 0.00 3.69
122 123 4.844884 CTTCCGGAAAACCTTATCTCCTT 58.155 43.478 19.39 0.00 0.00 3.36
123 124 4.921644 TCCGGAAAACCTTATCTCCTTT 57.078 40.909 0.00 0.00 0.00 3.11
124 125 4.840271 TCCGGAAAACCTTATCTCCTTTC 58.160 43.478 0.00 0.00 0.00 2.62
125 126 3.945921 CCGGAAAACCTTATCTCCTTTCC 59.054 47.826 0.00 0.00 41.00 3.13
126 127 4.324331 CCGGAAAACCTTATCTCCTTTCCT 60.324 45.833 0.00 0.00 41.84 3.36
127 128 5.254115 CGGAAAACCTTATCTCCTTTCCTT 58.746 41.667 9.51 0.00 41.84 3.36
128 129 6.412214 CGGAAAACCTTATCTCCTTTCCTTA 58.588 40.000 9.51 0.00 41.84 2.69
129 130 6.539103 CGGAAAACCTTATCTCCTTTCCTTAG 59.461 42.308 9.51 0.00 41.84 2.18
130 131 6.319152 GGAAAACCTTATCTCCTTTCCTTAGC 59.681 42.308 4.93 0.00 41.14 3.09
131 132 5.375283 AACCTTATCTCCTTTCCTTAGCC 57.625 43.478 0.00 0.00 0.00 3.93
132 133 4.636536 ACCTTATCTCCTTTCCTTAGCCT 58.363 43.478 0.00 0.00 0.00 4.58
133 134 5.789535 ACCTTATCTCCTTTCCTTAGCCTA 58.210 41.667 0.00 0.00 0.00 3.93
134 135 6.210522 ACCTTATCTCCTTTCCTTAGCCTAA 58.789 40.000 0.00 0.00 0.00 2.69
135 136 6.677076 ACCTTATCTCCTTTCCTTAGCCTAAA 59.323 38.462 0.00 0.00 0.00 1.85
136 137 7.184022 ACCTTATCTCCTTTCCTTAGCCTAAAA 59.816 37.037 0.00 0.00 0.00 1.52
137 138 7.717436 CCTTATCTCCTTTCCTTAGCCTAAAAG 59.283 40.741 0.00 0.00 0.00 2.27
138 139 6.893020 ATCTCCTTTCCTTAGCCTAAAAGA 57.107 37.500 0.00 0.00 31.81 2.52
139 140 6.301169 TCTCCTTTCCTTAGCCTAAAAGAG 57.699 41.667 0.00 0.00 31.81 2.85
140 141 6.023603 TCTCCTTTCCTTAGCCTAAAAGAGA 58.976 40.000 0.00 0.00 31.81 3.10
141 142 6.500751 TCTCCTTTCCTTAGCCTAAAAGAGAA 59.499 38.462 0.00 0.00 31.81 2.87
142 143 7.017254 TCTCCTTTCCTTAGCCTAAAAGAGAAA 59.983 37.037 0.00 0.00 31.81 2.52
143 144 7.699878 TCCTTTCCTTAGCCTAAAAGAGAAAT 58.300 34.615 0.00 0.00 31.81 2.17
144 145 8.170730 TCCTTTCCTTAGCCTAAAAGAGAAATT 58.829 33.333 0.00 0.00 31.81 1.82
145 146 8.807118 CCTTTCCTTAGCCTAAAAGAGAAATTT 58.193 33.333 0.00 0.00 31.81 1.82
182 183 0.327924 TCAAGGATCACATGGGCGTT 59.672 50.000 0.00 0.00 0.00 4.84
191 192 1.665679 CACATGGGCGTTGATCTGTAC 59.334 52.381 0.00 0.00 0.00 2.90
200 201 2.205074 GTTGATCTGTACATGGAGCCG 58.795 52.381 0.00 0.00 0.00 5.52
215 216 4.000988 TGGAGCCGAATTTTGAAGACTAC 58.999 43.478 0.00 0.00 0.00 2.73
228 229 1.479709 AGACTACAGCTGCCAGGTAG 58.520 55.000 15.27 17.07 40.19 3.18
231 232 2.432510 GACTACAGCTGCCAGGTAGAAT 59.567 50.000 22.46 8.04 38.26 2.40
245 256 6.515696 GCCAGGTAGAATAAATTCAGGAATGC 60.516 42.308 5.55 0.00 39.23 3.56
247 258 7.232127 CCAGGTAGAATAAATTCAGGAATGCAT 59.768 37.037 0.00 0.00 39.23 3.96
248 259 8.080417 CAGGTAGAATAAATTCAGGAATGCATG 58.920 37.037 0.00 0.00 39.23 4.06
250 261 9.066892 GGTAGAATAAATTCAGGAATGCATGTA 57.933 33.333 0.00 0.00 39.23 2.29
271 283 9.740239 CATGTATTGCTATGCTAAAACAGAAAT 57.260 29.630 0.00 0.00 0.00 2.17
272 284 9.956720 ATGTATTGCTATGCTAAAACAGAAATC 57.043 29.630 0.00 0.00 0.00 2.17
273 285 9.177608 TGTATTGCTATGCTAAAACAGAAATCT 57.822 29.630 0.00 0.00 0.00 2.40
274 286 9.657121 GTATTGCTATGCTAAAACAGAAATCTC 57.343 33.333 0.00 0.00 0.00 2.75
275 287 6.349973 TGCTATGCTAAAACAGAAATCTCG 57.650 37.500 0.00 0.00 0.00 4.04
276 288 5.201181 GCTATGCTAAAACAGAAATCTCGC 58.799 41.667 0.00 0.00 0.00 5.03
278 290 2.415168 TGCTAAAACAGAAATCTCGCGG 59.585 45.455 6.13 0.00 0.00 6.46
279 291 2.223044 GCTAAAACAGAAATCTCGCGGG 60.223 50.000 6.13 1.01 0.00 6.13
280 292 0.521735 AAAACAGAAATCTCGCGGGC 59.478 50.000 6.13 0.00 0.00 6.13
302 317 4.662145 CATGCTCGTGTTTATCCCTTTTC 58.338 43.478 0.00 0.00 0.00 2.29
303 318 3.745799 TGCTCGTGTTTATCCCTTTTCA 58.254 40.909 0.00 0.00 0.00 2.69
325 355 2.992543 CAACCAAATGCCACCAATAACG 59.007 45.455 0.00 0.00 0.00 3.18
329 360 2.859538 CAAATGCCACCAATAACGATGC 59.140 45.455 0.00 0.00 0.00 3.91
335 366 2.009051 CACCAATAACGATGCTGCTCA 58.991 47.619 0.00 0.00 0.00 4.26
390 421 4.643387 ACACCGACAAGGCCCTGC 62.643 66.667 0.00 0.00 46.52 4.85
392 423 3.884774 ACCGACAAGGCCCTGCAA 61.885 61.111 0.00 0.00 46.52 4.08
410 441 2.242043 CAAGAACCCTGCTTGGACATT 58.758 47.619 0.00 0.00 39.18 2.71
514 545 3.932710 TCTGAAAGGACGCACATGATAAC 59.067 43.478 0.00 0.00 0.00 1.89
525 560 7.011828 ACGCACATGATAACTAAAATGGTAC 57.988 36.000 0.00 0.00 0.00 3.34
578 876 1.078143 CTGCTTCACCTGGGGCTAC 60.078 63.158 0.00 0.00 0.00 3.58
745 1110 5.078411 AGTTGAATCTCGTATTGTCTGCT 57.922 39.130 0.00 0.00 0.00 4.24
773 1138 2.103601 AGCAAAGCAAAGAATTGGCACT 59.896 40.909 0.00 0.00 37.02 4.40
774 1139 2.874086 GCAAAGCAAAGAATTGGCACTT 59.126 40.909 0.00 0.00 37.02 3.16
775 1140 3.059393 GCAAAGCAAAGAATTGGCACTTC 60.059 43.478 9.36 9.36 37.02 3.01
790 1269 2.341257 CACTTCCCTGATGTTCTGTCG 58.659 52.381 0.00 0.00 0.00 4.35
868 1420 4.080638 AGGGATCCTGTTCTCAGATTTGTC 60.081 45.833 12.58 0.00 43.76 3.18
888 1440 0.926155 CTTGCGTGTCCATCTCATCG 59.074 55.000 0.00 0.00 0.00 3.84
911 1475 0.986527 TCTCCAAGCTGGCATTCTGA 59.013 50.000 0.00 0.00 37.47 3.27
913 1477 0.694771 TCCAAGCTGGCATTCTGAGT 59.305 50.000 0.00 0.00 37.47 3.41
1611 2192 1.066152 CTCGTTGATCTCATCGCCAGA 59.934 52.381 5.92 0.00 38.52 3.86
1614 2195 2.736719 CGTTGATCTCATCGCCAGAACT 60.737 50.000 0.00 0.00 33.21 3.01
1686 2267 3.330766 GCTCGTGCTGTACTACCTG 57.669 57.895 1.41 0.00 36.03 4.00
1826 2407 4.082523 CACCATCCAGGACGGCGT 62.083 66.667 14.65 14.65 41.22 5.68
1986 2567 2.514824 GACCTGAAGCGGATGGGC 60.515 66.667 0.00 0.00 0.00 5.36
2586 3167 0.467844 ACCACAGCTGAAATGCACCA 60.468 50.000 23.35 0.00 34.99 4.17
2588 3169 0.038892 CACAGCTGAAATGCACCACC 60.039 55.000 23.35 0.00 34.99 4.61
2589 3170 0.467844 ACAGCTGAAATGCACCACCA 60.468 50.000 23.35 0.00 34.99 4.17
2591 3172 0.178981 AGCTGAAATGCACCACCAGT 60.179 50.000 0.00 0.00 34.99 4.00
2592 3173 0.242017 GCTGAAATGCACCACCAGTC 59.758 55.000 0.00 0.00 0.00 3.51
2594 3175 0.184692 TGAAATGCACCACCAGTCCA 59.815 50.000 0.00 0.00 0.00 4.02
2595 3176 0.598065 GAAATGCACCACCAGTCCAC 59.402 55.000 0.00 0.00 0.00 4.02
2596 3177 0.106268 AAATGCACCACCAGTCCACA 60.106 50.000 0.00 0.00 0.00 4.17
2597 3178 0.538057 AATGCACCACCAGTCCACAG 60.538 55.000 0.00 0.00 0.00 3.66
2598 3179 2.980233 GCACCACCAGTCCACAGC 60.980 66.667 0.00 0.00 0.00 4.40
2599 3180 2.666190 CACCACCAGTCCACAGCG 60.666 66.667 0.00 0.00 0.00 5.18
2600 3181 3.161450 ACCACCAGTCCACAGCGT 61.161 61.111 0.00 0.00 0.00 5.07
2606 3201 1.004560 CAGTCCACAGCGTGTCCAT 60.005 57.895 7.68 0.00 0.00 3.41
2615 3210 2.420022 ACAGCGTGTCCATAATCTTTGC 59.580 45.455 0.00 0.00 0.00 3.68
2618 3213 2.223340 GCGTGTCCATAATCTTTGCCAG 60.223 50.000 0.00 0.00 0.00 4.85
2628 3223 3.498774 ATCTTTGCCAGACTGACTGTT 57.501 42.857 3.32 0.00 44.40 3.16
2634 3229 0.109342 CCAGACTGACTGTTTGGGCT 59.891 55.000 12.68 0.00 44.53 5.19
2635 3230 1.517242 CAGACTGACTGTTTGGGCTC 58.483 55.000 0.00 0.00 41.30 4.70
2644 3240 0.534203 TGTTTGGGCTCGTGTTCTCC 60.534 55.000 0.00 0.00 0.00 3.71
2651 3247 1.079503 GCTCGTGTTCTCCCACATTC 58.920 55.000 0.00 0.00 34.98 2.67
2695 3295 2.821546 GCGTGTGCATATACAAGAGGA 58.178 47.619 0.00 0.00 42.15 3.71
2696 3296 2.797156 GCGTGTGCATATACAAGAGGAG 59.203 50.000 0.00 0.00 42.15 3.69
2705 3305 6.763135 TGCATATACAAGAGGAGTGATTTGAC 59.237 38.462 0.00 0.00 0.00 3.18
2719 3319 9.860898 GGAGTGATTTGACTTTTTATTTAGCAT 57.139 29.630 0.00 0.00 0.00 3.79
2793 3393 2.966050 AGGAACTTGAGCTCGATGAAC 58.034 47.619 9.64 0.00 27.25 3.18
2801 3401 5.408604 ACTTGAGCTCGATGAACGTTTAAAT 59.591 36.000 9.64 0.00 43.13 1.40
2803 3403 5.854157 TGAGCTCGATGAACGTTTAAATTC 58.146 37.500 9.64 0.00 43.13 2.17
2804 3404 5.637810 TGAGCTCGATGAACGTTTAAATTCT 59.362 36.000 9.64 0.00 43.13 2.40
2806 3406 6.899114 AGCTCGATGAACGTTTAAATTCTTT 58.101 32.000 0.46 0.00 43.13 2.52
2808 3408 7.534239 AGCTCGATGAACGTTTAAATTCTTTTC 59.466 33.333 0.46 0.00 43.13 2.29
2812 3412 9.382244 CGATGAACGTTTAAATTCTTTTCTTCT 57.618 29.630 0.46 0.00 37.22 2.85
2854 3456 7.970061 AGATGCAATGTCATGTAAAATGTGTAC 59.030 33.333 0.00 0.00 0.00 2.90
2860 3462 6.826612 TGTCATGTAAAATGTGTACGTCATG 58.173 36.000 0.00 0.00 34.62 3.07
2864 3466 8.989980 TCATGTAAAATGTGTACGTCATGTTTA 58.010 29.630 10.22 10.29 34.82 2.01
2899 3501 9.691362 ACAAATGGTTATACTTTGTCATGAAAC 57.309 29.630 0.00 0.00 38.38 2.78
2900 3502 9.912634 CAAATGGTTATACTTTGTCATGAAACT 57.087 29.630 0.00 0.00 0.00 2.66
2901 3503 9.912634 AAATGGTTATACTTTGTCATGAAACTG 57.087 29.630 0.00 0.00 0.00 3.16
2902 3504 8.635765 ATGGTTATACTTTGTCATGAAACTGT 57.364 30.769 0.00 0.00 0.00 3.55
2903 3505 7.870826 TGGTTATACTTTGTCATGAAACTGTG 58.129 34.615 0.00 0.00 0.00 3.66
2904 3506 6.801862 GGTTATACTTTGTCATGAAACTGTGC 59.198 38.462 0.00 0.00 0.00 4.57
2905 3507 7.359595 GTTATACTTTGTCATGAAACTGTGCA 58.640 34.615 0.00 0.00 0.00 4.57
2906 3508 4.297299 ACTTTGTCATGAAACTGTGCAG 57.703 40.909 0.00 0.00 0.00 4.41
2907 3509 3.947196 ACTTTGTCATGAAACTGTGCAGA 59.053 39.130 6.17 0.00 0.00 4.26
2908 3510 3.969117 TTGTCATGAAACTGTGCAGAC 57.031 42.857 6.17 0.00 0.00 3.51
2909 3511 2.916640 TGTCATGAAACTGTGCAGACA 58.083 42.857 6.17 0.00 32.70 3.41
2924 3526 4.736793 GTGCAGACACATGCTTTAATATGC 59.263 41.667 0.00 0.00 46.61 3.14
2925 3527 4.202040 TGCAGACACATGCTTTAATATGCC 60.202 41.667 0.00 0.00 46.63 4.40
2926 3528 4.202040 GCAGACACATGCTTTAATATGCCA 60.202 41.667 0.00 0.00 43.07 4.92
2927 3529 5.508489 GCAGACACATGCTTTAATATGCCAT 60.508 40.000 0.00 0.00 43.07 4.40
2928 3530 6.294120 GCAGACACATGCTTTAATATGCCATA 60.294 38.462 0.00 0.00 43.07 2.74
2929 3531 7.080099 CAGACACATGCTTTAATATGCCATAC 58.920 38.462 0.00 0.00 0.00 2.39
2930 3532 6.772233 AGACACATGCTTTAATATGCCATACA 59.228 34.615 0.00 0.00 0.00 2.29
2931 3533 7.285172 AGACACATGCTTTAATATGCCATACAA 59.715 33.333 0.00 0.00 0.00 2.41
2932 3534 7.780064 ACACATGCTTTAATATGCCATACAAA 58.220 30.769 0.00 0.00 0.00 2.83
2933 3535 8.423349 ACACATGCTTTAATATGCCATACAAAT 58.577 29.630 0.00 0.00 0.00 2.32
2934 3536 9.911138 CACATGCTTTAATATGCCATACAAATA 57.089 29.630 0.00 0.00 0.00 1.40
2948 3550 6.653273 CATACAAATATGGCGAGTGATAGG 57.347 41.667 0.00 0.00 35.45 2.57
2949 3551 3.403038 ACAAATATGGCGAGTGATAGGC 58.597 45.455 0.00 0.00 0.00 3.93
2950 3552 2.370281 AATATGGCGAGTGATAGGCG 57.630 50.000 0.00 0.00 35.52 5.52
2969 3571 1.153901 CCGGTGCGTGATACGTCTT 60.154 57.895 0.00 0.00 44.73 3.01
3087 3689 6.352823 GGAACTAACCTATTAACTGAAGGCCT 60.353 42.308 0.00 0.00 33.42 5.19
3168 3772 3.807622 GGAATGAAACCTTCGCGATGATA 59.192 43.478 22.25 0.25 0.00 2.15
3200 3805 3.813166 CCGAAAGCAAACCAGAAGACTTA 59.187 43.478 0.00 0.00 0.00 2.24
3310 3918 8.874744 ACCTAGTTCTTTCGCCTATATATACA 57.125 34.615 0.00 0.00 0.00 2.29
3311 3919 9.476928 ACCTAGTTCTTTCGCCTATATATACAT 57.523 33.333 0.00 0.00 0.00 2.29
3394 4004 1.123077 CCGTGAGATCCCATCTTGGA 58.877 55.000 0.00 0.00 40.96 3.53
3440 4056 1.343069 GGATCACGGAGGGCTTCTAT 58.657 55.000 0.00 0.00 0.00 1.98
3455 4071 5.408604 GGGCTTCTATATCAACACCATTACG 59.591 44.000 0.00 0.00 0.00 3.18
3461 4077 3.973206 ATCAACACCATTACGTCTCCA 57.027 42.857 0.00 0.00 0.00 3.86
3467 4083 4.843728 ACACCATTACGTCTCCAATGAAT 58.156 39.130 9.78 0.00 34.69 2.57
3485 4101 7.065803 CCAATGAATCGTGAGTAGTTTACCATT 59.934 37.037 0.00 0.00 0.00 3.16
3540 4156 6.172630 GGCTTCTTCTCTCTCTTTGATTCTT 58.827 40.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.132111 GGTCAAGTTTGGCTGAGGAAAAA 59.868 43.478 0.00 0.00 32.28 1.94
25 26 2.693074 GGTCAAGTTTGGCTGAGGAAAA 59.307 45.455 0.00 0.00 32.28 2.29
26 27 2.306847 GGTCAAGTTTGGCTGAGGAAA 58.693 47.619 0.00 0.00 32.28 3.13
27 28 1.214175 TGGTCAAGTTTGGCTGAGGAA 59.786 47.619 0.00 0.00 32.28 3.36
28 29 0.843309 TGGTCAAGTTTGGCTGAGGA 59.157 50.000 0.00 0.00 32.28 3.71
29 30 1.202806 TCTGGTCAAGTTTGGCTGAGG 60.203 52.381 0.00 0.00 32.28 3.86
30 31 2.260844 TCTGGTCAAGTTTGGCTGAG 57.739 50.000 0.00 0.00 32.28 3.35
31 32 2.373169 AGATCTGGTCAAGTTTGGCTGA 59.627 45.455 0.00 0.00 32.28 4.26
32 33 2.486982 CAGATCTGGTCAAGTTTGGCTG 59.513 50.000 15.38 0.00 32.28 4.85
33 34 2.553904 CCAGATCTGGTCAAGTTTGGCT 60.554 50.000 30.55 0.00 45.53 4.75
34 35 1.815003 CCAGATCTGGTCAAGTTTGGC 59.185 52.381 30.55 0.00 45.53 4.52
55 56 3.087031 ACCATTCAAGGAGCACTTCATG 58.913 45.455 0.00 0.00 37.29 3.07
56 57 3.446442 ACCATTCAAGGAGCACTTCAT 57.554 42.857 0.00 0.00 37.29 2.57
57 58 2.957402 ACCATTCAAGGAGCACTTCA 57.043 45.000 0.00 0.00 37.29 3.02
58 59 3.691609 CCTAACCATTCAAGGAGCACTTC 59.308 47.826 0.00 0.00 37.29 3.01
59 60 3.074538 ACCTAACCATTCAAGGAGCACTT 59.925 43.478 0.00 0.00 41.00 3.16
60 61 2.644798 ACCTAACCATTCAAGGAGCACT 59.355 45.455 0.00 0.00 34.34 4.40
61 62 3.073274 ACCTAACCATTCAAGGAGCAC 57.927 47.619 0.00 0.00 34.34 4.40
62 63 3.806949 AACCTAACCATTCAAGGAGCA 57.193 42.857 0.00 0.00 34.34 4.26
63 64 4.079253 TCAAACCTAACCATTCAAGGAGC 58.921 43.478 0.00 0.00 34.34 4.70
64 65 6.127619 GGATTCAAACCTAACCATTCAAGGAG 60.128 42.308 0.00 0.00 34.34 3.69
65 66 5.714806 GGATTCAAACCTAACCATTCAAGGA 59.285 40.000 0.00 0.00 34.34 3.36
66 67 5.716703 AGGATTCAAACCTAACCATTCAAGG 59.283 40.000 0.00 0.00 35.84 3.61
67 68 6.624423 CAGGATTCAAACCTAACCATTCAAG 58.376 40.000 0.00 0.00 35.84 3.02
68 69 5.047377 GCAGGATTCAAACCTAACCATTCAA 60.047 40.000 0.00 0.00 35.84 2.69
69 70 4.462483 GCAGGATTCAAACCTAACCATTCA 59.538 41.667 0.00 0.00 35.84 2.57
70 71 4.438744 CGCAGGATTCAAACCTAACCATTC 60.439 45.833 0.00 0.00 35.84 2.67
71 72 3.443681 CGCAGGATTCAAACCTAACCATT 59.556 43.478 0.00 0.00 35.84 3.16
72 73 3.016736 CGCAGGATTCAAACCTAACCAT 58.983 45.455 0.00 0.00 35.84 3.55
73 74 2.224670 ACGCAGGATTCAAACCTAACCA 60.225 45.455 0.00 0.00 35.84 3.67
74 75 2.433436 ACGCAGGATTCAAACCTAACC 58.567 47.619 0.00 0.00 35.84 2.85
75 76 3.365969 CCAACGCAGGATTCAAACCTAAC 60.366 47.826 0.00 0.00 35.84 2.34
76 77 2.817258 CCAACGCAGGATTCAAACCTAA 59.183 45.455 0.00 0.00 35.84 2.69
77 78 2.039216 TCCAACGCAGGATTCAAACCTA 59.961 45.455 0.00 0.00 35.84 3.08
78 79 1.202879 TCCAACGCAGGATTCAAACCT 60.203 47.619 0.00 0.00 38.40 3.50
79 80 1.200020 CTCCAACGCAGGATTCAAACC 59.800 52.381 0.00 0.00 36.99 3.27
80 81 1.401539 GCTCCAACGCAGGATTCAAAC 60.402 52.381 0.00 0.00 36.99 2.93
81 82 0.881118 GCTCCAACGCAGGATTCAAA 59.119 50.000 0.00 0.00 36.99 2.69
82 83 0.036732 AGCTCCAACGCAGGATTCAA 59.963 50.000 0.00 0.00 36.99 2.69
83 84 0.036732 AAGCTCCAACGCAGGATTCA 59.963 50.000 0.00 0.00 36.99 2.57
84 85 0.729690 GAAGCTCCAACGCAGGATTC 59.270 55.000 0.00 0.00 36.99 2.52
85 86 0.678048 GGAAGCTCCAACGCAGGATT 60.678 55.000 0.00 0.00 36.99 3.01
86 87 1.078143 GGAAGCTCCAACGCAGGAT 60.078 57.895 0.00 0.00 36.99 3.24
87 88 2.347490 GGAAGCTCCAACGCAGGA 59.653 61.111 0.00 0.00 36.28 3.86
88 89 3.121030 CGGAAGCTCCAACGCAGG 61.121 66.667 0.00 0.00 35.91 4.85
89 90 3.121030 CCGGAAGCTCCAACGCAG 61.121 66.667 0.00 0.00 35.91 5.18
90 91 2.668185 TTTCCGGAAGCTCCAACGCA 62.668 55.000 17.97 0.00 35.91 5.24
91 92 1.512156 TTTTCCGGAAGCTCCAACGC 61.512 55.000 17.97 0.00 35.91 4.84
92 93 0.237498 GTTTTCCGGAAGCTCCAACG 59.763 55.000 17.97 0.00 35.91 4.10
93 94 0.596577 GGTTTTCCGGAAGCTCCAAC 59.403 55.000 17.97 17.33 35.91 3.77
94 95 0.476771 AGGTTTTCCGGAAGCTCCAA 59.523 50.000 25.32 13.56 46.35 3.53
95 96 0.476771 AAGGTTTTCCGGAAGCTCCA 59.523 50.000 25.32 8.83 46.35 3.86
96 97 2.484742 TAAGGTTTTCCGGAAGCTCC 57.515 50.000 17.97 19.09 46.35 4.70
97 98 3.872182 GAGATAAGGTTTTCCGGAAGCTC 59.128 47.826 17.97 8.29 46.35 4.09
98 99 3.370633 GGAGATAAGGTTTTCCGGAAGCT 60.371 47.826 17.97 9.68 46.35 3.74
99 100 2.943690 GGAGATAAGGTTTTCCGGAAGC 59.056 50.000 17.97 14.00 46.35 3.86
100 101 4.489306 AGGAGATAAGGTTTTCCGGAAG 57.511 45.455 17.97 0.00 46.35 3.46
101 102 4.921644 AAGGAGATAAGGTTTTCCGGAA 57.078 40.909 14.35 14.35 46.35 4.30
102 103 4.324022 GGAAAGGAGATAAGGTTTTCCGGA 60.324 45.833 0.00 0.00 46.35 5.14
103 104 3.945921 GGAAAGGAGATAAGGTTTTCCGG 59.054 47.826 0.00 0.00 46.35 5.14
105 106 6.319152 GCTAAGGAAAGGAGATAAGGTTTTCC 59.681 42.308 6.25 6.25 44.43 3.13
106 107 6.319152 GGCTAAGGAAAGGAGATAAGGTTTTC 59.681 42.308 0.00 0.00 0.00 2.29
107 108 6.011540 AGGCTAAGGAAAGGAGATAAGGTTTT 60.012 38.462 0.00 0.00 0.00 2.43
108 109 5.492887 AGGCTAAGGAAAGGAGATAAGGTTT 59.507 40.000 0.00 0.00 0.00 3.27
109 110 5.040330 AGGCTAAGGAAAGGAGATAAGGTT 58.960 41.667 0.00 0.00 0.00 3.50
110 111 4.636536 AGGCTAAGGAAAGGAGATAAGGT 58.363 43.478 0.00 0.00 0.00 3.50
111 112 6.749036 TTAGGCTAAGGAAAGGAGATAAGG 57.251 41.667 2.04 0.00 0.00 2.69
112 113 8.487028 TCTTTTAGGCTAAGGAAAGGAGATAAG 58.513 37.037 14.19 8.31 31.69 1.73
113 114 8.388656 TCTTTTAGGCTAAGGAAAGGAGATAA 57.611 34.615 14.19 0.16 31.69 1.75
114 115 7.844779 TCTCTTTTAGGCTAAGGAAAGGAGATA 59.155 37.037 14.67 0.00 39.18 1.98
115 116 6.674419 TCTCTTTTAGGCTAAGGAAAGGAGAT 59.326 38.462 14.67 0.00 39.18 2.75
116 117 6.023603 TCTCTTTTAGGCTAAGGAAAGGAGA 58.976 40.000 14.67 14.67 40.75 3.71
117 118 6.301169 TCTCTTTTAGGCTAAGGAAAGGAG 57.699 41.667 14.19 12.80 37.53 3.69
118 119 6.697641 TTCTCTTTTAGGCTAAGGAAAGGA 57.302 37.500 14.19 9.35 31.69 3.36
119 120 7.946381 ATTTCTCTTTTAGGCTAAGGAAAGG 57.054 36.000 20.13 11.97 31.57 3.11
158 159 2.424956 GCCCATGTGATCCTTGAAGAAC 59.575 50.000 0.00 0.00 0.00 3.01
182 183 1.775385 TCGGCTCCATGTACAGATCA 58.225 50.000 0.33 0.00 0.00 2.92
191 192 3.441572 AGTCTTCAAAATTCGGCTCCATG 59.558 43.478 0.00 0.00 0.00 3.66
200 201 4.216257 TGGCAGCTGTAGTCTTCAAAATTC 59.784 41.667 16.64 0.00 0.00 2.17
215 216 4.883585 TGAATTTATTCTACCTGGCAGCTG 59.116 41.667 10.11 10.11 37.67 4.24
245 256 9.740239 ATTTCTGTTTTAGCATAGCAATACATG 57.260 29.630 0.00 0.00 0.00 3.21
247 258 9.177608 AGATTTCTGTTTTAGCATAGCAATACA 57.822 29.630 0.00 0.00 0.00 2.29
248 259 9.657121 GAGATTTCTGTTTTAGCATAGCAATAC 57.343 33.333 0.00 0.00 0.00 1.89
250 261 7.412853 CGAGATTTCTGTTTTAGCATAGCAAT 58.587 34.615 0.00 0.00 0.00 3.56
264 276 1.091771 CATGCCCGCGAGATTTCTGT 61.092 55.000 8.23 0.00 0.00 3.41
267 279 2.110734 GAGCATGCCCGCGAGATTTC 62.111 60.000 15.66 0.00 36.85 2.17
270 282 4.957684 CGAGCATGCCCGCGAGAT 62.958 66.667 15.66 0.00 36.85 2.75
275 287 1.714899 ATAAACACGAGCATGCCCGC 61.715 55.000 22.32 7.13 0.00 6.13
276 288 0.304705 GATAAACACGAGCATGCCCG 59.695 55.000 20.79 20.79 0.00 6.13
278 290 0.663153 GGGATAAACACGAGCATGCC 59.337 55.000 15.66 4.99 0.00 4.40
279 291 1.668419 AGGGATAAACACGAGCATGC 58.332 50.000 10.51 10.51 0.00 4.06
280 292 4.155826 TGAAAAGGGATAAACACGAGCATG 59.844 41.667 0.00 0.00 0.00 4.06
289 301 6.073276 GCATTTGGTTGTGAAAAGGGATAAAC 60.073 38.462 0.00 0.00 0.00 2.01
302 317 2.547299 ATTGGTGGCATTTGGTTGTG 57.453 45.000 0.00 0.00 0.00 3.33
303 318 3.553922 CGTTATTGGTGGCATTTGGTTGT 60.554 43.478 0.00 0.00 0.00 3.32
335 366 3.491447 GCACTCCAAAGTTGAACTGCAAT 60.491 43.478 0.00 0.00 39.03 3.56
390 421 1.915141 ATGTCCAAGCAGGGTTCTTG 58.085 50.000 0.00 0.00 40.31 3.02
392 423 2.242043 CAAATGTCCAAGCAGGGTTCT 58.758 47.619 0.00 0.00 38.24 3.01
410 441 2.623718 CGTCTCGCGTTTGTGCAA 59.376 55.556 5.77 0.00 35.54 4.08
525 560 8.068380 CCATTGCTGCATCATATCTAATATTCG 58.932 37.037 1.84 0.00 0.00 3.34
532 569 3.754850 GCACCATTGCTGCATCATATCTA 59.245 43.478 1.84 0.00 46.17 1.98
533 570 2.557056 GCACCATTGCTGCATCATATCT 59.443 45.455 1.84 0.00 46.17 1.98
534 571 2.942710 GCACCATTGCTGCATCATATC 58.057 47.619 1.84 0.00 46.17 1.63
578 876 7.042187 GCATACAAATCCATCTTCAGTCTAGTG 60.042 40.741 0.00 0.00 0.00 2.74
745 1110 5.523188 CCAATTCTTTGCTTTGCTTGTACAA 59.477 36.000 8.28 8.28 0.00 2.41
773 1138 2.248248 AGACGACAGAACATCAGGGAA 58.752 47.619 0.00 0.00 0.00 3.97
774 1139 1.924731 AGACGACAGAACATCAGGGA 58.075 50.000 0.00 0.00 0.00 4.20
775 1140 2.751166 AAGACGACAGAACATCAGGG 57.249 50.000 0.00 0.00 0.00 4.45
790 1269 1.588861 GCTTCCGTCAGCGATAAAGAC 59.411 52.381 0.00 0.00 41.33 3.01
868 1420 1.293924 GATGAGATGGACACGCAAGG 58.706 55.000 0.00 0.00 46.39 3.61
888 1440 0.674895 AATGCCAGCTTGGAGACGAC 60.675 55.000 6.40 0.00 40.96 4.34
911 1475 5.184892 AGTGGCAGAATGGAATCTAAACT 57.815 39.130 0.00 0.00 35.86 2.66
913 1477 8.439971 ACATATAGTGGCAGAATGGAATCTAAA 58.560 33.333 0.00 0.00 35.86 1.85
1386 1967 1.515954 CTCCCCGACGTACATTGCT 59.484 57.895 0.00 0.00 0.00 3.91
1611 2192 0.389948 CGAACTCCGGCAGCTTAGTT 60.390 55.000 3.79 3.79 34.96 2.24
1614 2195 1.511305 CTCGAACTCCGGCAGCTTA 59.489 57.895 0.00 0.00 39.14 3.09
1826 2407 0.817654 CTGTGCCGTCTCTATCACCA 59.182 55.000 0.00 0.00 0.00 4.17
1986 2567 1.205064 CGCCTTCTTGAACTGCACG 59.795 57.895 0.00 0.00 0.00 5.34
2178 2759 2.496817 GGCGTCTTCATCGAGGCT 59.503 61.111 0.00 0.00 42.63 4.58
2517 3098 1.241990 TGGAGACGAAGGTGACGAGG 61.242 60.000 0.00 0.00 34.70 4.63
2586 3167 2.421739 GACACGCTGTGGACTGGT 59.578 61.111 12.18 0.00 37.94 4.00
2588 3169 0.246360 TATGGACACGCTGTGGACTG 59.754 55.000 12.18 0.00 37.94 3.51
2589 3170 0.973632 TTATGGACACGCTGTGGACT 59.026 50.000 12.18 0.00 37.94 3.85
2591 3172 1.831106 AGATTATGGACACGCTGTGGA 59.169 47.619 12.18 0.00 37.94 4.02
2592 3173 2.315925 AGATTATGGACACGCTGTGG 57.684 50.000 12.18 0.00 37.94 4.17
2594 3175 2.420022 GCAAAGATTATGGACACGCTGT 59.580 45.455 0.00 0.00 0.00 4.40
2595 3176 2.223340 GGCAAAGATTATGGACACGCTG 60.223 50.000 0.00 0.00 0.00 5.18
2596 3177 2.017049 GGCAAAGATTATGGACACGCT 58.983 47.619 0.00 0.00 0.00 5.07
2597 3178 1.742831 TGGCAAAGATTATGGACACGC 59.257 47.619 0.00 0.00 0.00 5.34
2598 3179 3.063997 GTCTGGCAAAGATTATGGACACG 59.936 47.826 0.00 0.00 37.23 4.49
2599 3180 4.095483 CAGTCTGGCAAAGATTATGGACAC 59.905 45.833 0.00 0.00 37.23 3.67
2600 3181 4.019411 TCAGTCTGGCAAAGATTATGGACA 60.019 41.667 0.00 0.00 37.23 4.02
2618 3213 0.249911 ACGAGCCCAAACAGTCAGTC 60.250 55.000 0.00 0.00 0.00 3.51
2628 3223 2.747686 GGGAGAACACGAGCCCAA 59.252 61.111 0.00 0.00 40.39 4.12
2634 3229 2.094182 GCTAGAATGTGGGAGAACACGA 60.094 50.000 0.00 0.00 44.21 4.35
2635 3230 2.271800 GCTAGAATGTGGGAGAACACG 58.728 52.381 0.00 0.00 44.21 4.49
2644 3240 1.153168 CCCGTGGGCTAGAATGTGG 60.153 63.158 0.00 0.00 0.00 4.17
2692 3292 9.077885 TGCTAAATAAAAAGTCAAATCACTCCT 57.922 29.630 0.00 0.00 0.00 3.69
2693 3293 9.860898 ATGCTAAATAAAAAGTCAAATCACTCC 57.139 29.630 0.00 0.00 0.00 3.85
2771 3371 4.495422 GTTCATCGAGCTCAAGTTCCTTA 58.505 43.478 15.40 0.00 0.00 2.69
2775 3375 2.329379 ACGTTCATCGAGCTCAAGTTC 58.671 47.619 15.40 0.00 42.86 3.01
2786 3386 9.382244 AGAAGAAAAGAATTTAAACGTTCATCG 57.618 29.630 0.00 0.00 37.28 3.84
2839 3441 9.046821 GTAAACATGACGTACACATTTTACATG 57.953 33.333 21.79 0.00 39.42 3.21
2873 3475 9.691362 GTTTCATGACAAAGTATAACCATTTGT 57.309 29.630 0.00 2.43 46.75 2.83
2874 3476 9.912634 AGTTTCATGACAAAGTATAACCATTTG 57.087 29.630 0.00 0.00 39.32 2.32
2875 3477 9.912634 CAGTTTCATGACAAAGTATAACCATTT 57.087 29.630 0.00 0.00 0.00 2.32
2876 3478 9.077885 ACAGTTTCATGACAAAGTATAACCATT 57.922 29.630 0.00 0.00 0.00 3.16
2877 3479 8.514594 CACAGTTTCATGACAAAGTATAACCAT 58.485 33.333 0.00 0.00 0.00 3.55
2878 3480 7.521423 GCACAGTTTCATGACAAAGTATAACCA 60.521 37.037 0.00 0.00 0.00 3.67
2879 3481 6.801862 GCACAGTTTCATGACAAAGTATAACC 59.198 38.462 0.00 0.00 0.00 2.85
2880 3482 7.359595 TGCACAGTTTCATGACAAAGTATAAC 58.640 34.615 0.00 0.00 0.00 1.89
2881 3483 7.443879 TCTGCACAGTTTCATGACAAAGTATAA 59.556 33.333 0.00 0.00 0.00 0.98
2882 3484 6.934083 TCTGCACAGTTTCATGACAAAGTATA 59.066 34.615 0.00 0.00 0.00 1.47
2883 3485 5.764686 TCTGCACAGTTTCATGACAAAGTAT 59.235 36.000 0.00 0.00 0.00 2.12
2884 3486 5.007626 GTCTGCACAGTTTCATGACAAAGTA 59.992 40.000 0.00 0.00 0.00 2.24
2885 3487 3.947196 TCTGCACAGTTTCATGACAAAGT 59.053 39.130 0.00 0.00 0.00 2.66
2886 3488 4.201940 TGTCTGCACAGTTTCATGACAAAG 60.202 41.667 0.00 0.00 31.30 2.77
2887 3489 3.693578 TGTCTGCACAGTTTCATGACAAA 59.306 39.130 0.00 0.00 31.30 2.83
2888 3490 3.065233 GTGTCTGCACAGTTTCATGACAA 59.935 43.478 0.00 0.00 44.64 3.18
2889 3491 2.613595 GTGTCTGCACAGTTTCATGACA 59.386 45.455 0.00 0.00 44.64 3.58
2890 3492 3.259207 GTGTCTGCACAGTTTCATGAC 57.741 47.619 0.00 0.00 44.64 3.06
2901 3503 4.736793 GCATATTAAAGCATGTGTCTGCAC 59.263 41.667 0.00 0.00 44.77 4.57
2902 3504 4.202040 GGCATATTAAAGCATGTGTCTGCA 60.202 41.667 0.00 0.00 44.77 4.41
2903 3505 4.202040 TGGCATATTAAAGCATGTGTCTGC 60.202 41.667 0.00 0.00 42.62 4.26
2904 3506 5.503662 TGGCATATTAAAGCATGTGTCTG 57.496 39.130 0.00 0.00 0.00 3.51
2905 3507 6.772233 TGTATGGCATATTAAAGCATGTGTCT 59.228 34.615 10.92 0.00 0.00 3.41
2906 3508 6.969366 TGTATGGCATATTAAAGCATGTGTC 58.031 36.000 10.92 0.00 0.00 3.67
2907 3509 6.957920 TGTATGGCATATTAAAGCATGTGT 57.042 33.333 10.92 0.00 0.00 3.72
2908 3510 8.821147 ATTTGTATGGCATATTAAAGCATGTG 57.179 30.769 10.92 0.00 0.00 3.21
2925 3527 5.063944 GCCTATCACTCGCCATATTTGTATG 59.936 44.000 0.00 0.00 0.00 2.39
2926 3528 5.178797 GCCTATCACTCGCCATATTTGTAT 58.821 41.667 0.00 0.00 0.00 2.29
2927 3529 4.566004 GCCTATCACTCGCCATATTTGTA 58.434 43.478 0.00 0.00 0.00 2.41
2928 3530 3.403038 GCCTATCACTCGCCATATTTGT 58.597 45.455 0.00 0.00 0.00 2.83
2929 3531 2.413112 CGCCTATCACTCGCCATATTTG 59.587 50.000 0.00 0.00 0.00 2.32
2930 3532 2.688507 CGCCTATCACTCGCCATATTT 58.311 47.619 0.00 0.00 0.00 1.40
2931 3533 1.673033 GCGCCTATCACTCGCCATATT 60.673 52.381 0.00 0.00 42.71 1.28
2932 3534 0.108615 GCGCCTATCACTCGCCATAT 60.109 55.000 0.00 0.00 42.71 1.78
2933 3535 1.289066 GCGCCTATCACTCGCCATA 59.711 57.895 0.00 0.00 42.71 2.74
2934 3536 2.029666 GCGCCTATCACTCGCCAT 59.970 61.111 0.00 0.00 42.71 4.40
2938 3540 3.900892 ACCGGCGCCTATCACTCG 61.901 66.667 26.68 8.26 0.00 4.18
2939 3541 2.279517 CACCGGCGCCTATCACTC 60.280 66.667 26.68 0.00 0.00 3.51
2940 3542 4.530857 GCACCGGCGCCTATCACT 62.531 66.667 26.68 0.00 0.00 3.41
3064 3666 6.638021 AGGCCTTCAGTTAATAGGTTAGTT 57.362 37.500 0.00 0.00 0.00 2.24
3168 3772 3.243737 GGTTTGCTTTCGGTCCAAGAAAT 60.244 43.478 0.00 0.00 37.04 2.17
3200 3805 2.116827 ACGTCTCCGACTTCATCTCT 57.883 50.000 0.00 0.00 37.88 3.10
3328 3936 1.380380 GGTTTCATGGCTCCCCTGG 60.380 63.158 0.00 0.00 0.00 4.45
3440 4056 5.408880 TTGGAGACGTAATGGTGTTGATA 57.591 39.130 0.00 0.00 0.00 2.15
3455 4071 5.000012 ACTACTCACGATTCATTGGAGAC 58.000 43.478 0.00 0.00 0.00 3.36
3461 4077 7.822334 TCAATGGTAAACTACTCACGATTCATT 59.178 33.333 0.00 0.00 0.00 2.57
3467 4083 4.525487 AGGTCAATGGTAAACTACTCACGA 59.475 41.667 0.00 0.00 0.00 4.35
3540 4156 7.837863 AGAACATCGAGGAGAACTTTGTATTA 58.162 34.615 3.06 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.