Multiple sequence alignment - TraesCS5A01G357000

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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 TraesCS5A01G357000 chr5A 100.000 4632 0 0 1 4632 559068967 559073598 0.000000e+00 8554.0
1 TraesCS5A01G357000 chr5B 93.728 3922 154 41 764 4632 539292006 539295888 0.000000e+00 5795.0
2 TraesCS5A01G357000 chr5B 81.081 259 18 10 451 692 539291719 539291963 1.320000e-40 178.0
3 TraesCS5A01G357000 chr5B 84.733 131 11 5 4438 4567 539301624 539301746 6.290000e-24 122.0
4 TraesCS5A01G357000 chr5B 85.156 128 6 3 4434 4560 539306764 539306879 8.140000e-23 119.0
5 TraesCS5A01G357000 chr5B 84.034 119 12 5 215 332 539291404 539291516 1.760000e-19 108.0
6 TraesCS5A01G357000 chr5B 96.078 51 2 0 331 381 539291543 539291593 2.970000e-12 84.2
7 TraesCS5A01G357000 chr5D 93.639 3710 188 20 958 4632 443011618 443015314 0.000000e+00 5500.0
8 TraesCS5A01G357000 chr5D 84.354 294 18 9 448 727 443011025 443011304 3.550000e-66 263.0
9 TraesCS5A01G357000 chr5D 89.474 171 12 4 4398 4566 443018946 443019112 1.310000e-50 211.0
10 TraesCS5A01G357000 chr5D 98.039 51 0 1 331 381 443010923 443010972 2.300000e-13 87.9
11 TraesCS5A01G357000 chrUn 92.010 413 33 0 1349 1761 34768664 34768252 8.640000e-162 580.0
12 TraesCS5A01G357000 chrUn 92.473 93 7 0 1963 2055 34768254 34768162 2.910000e-27 134.0
13 TraesCS5A01G357000 chr2A 97.500 40 1 0 4354 4393 758523810 758523849 8.320000e-08 69.4


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 TraesCS5A01G357000 chr5A 559068967 559073598 4631 False 8554.000 8554 100.00000 1 4632 1 chr5A.!!$F1 4631
1 TraesCS5A01G357000 chr5B 539291404 539295888 4484 False 1541.300 5795 88.73025 215 4632 4 chr5B.!!$F3 4417
2 TraesCS5A01G357000 chr5D 443010923 443019112 8189 False 1515.475 5500 91.37650 331 4632 4 chr5D.!!$F1 4301
3 TraesCS5A01G357000 chrUn 34768162 34768664 502 True 357.000 580 92.24150 1349 2055 2 chrUn.!!$R1 706

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
672 782 0.035881 TTGAGCAGCTGGAAGGACTG 59.964 55.0 17.12 0.00 34.48 3.51 F
2328 2583 0.179234 GGAAGAGGCTGCTCTTACCC 59.821 60.0 12.24 8.28 43.03 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2657 2912 0.037590 TAGCACGGCATTTTCCAGGT 59.962 50.0 0.0 0.0 0.00 4.00 R
3764 4033 2.351726 CACATCTAACACGCTAAAGCCC 59.648 50.0 0.0 0.0 37.91 5.19 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
18 19 3.867723 ACTCTTGTCCTCGAACACG 57.132 52.632 0.00 0.00 0.00 4.49
19 20 0.318784 ACTCTTGTCCTCGAACACGC 60.319 55.000 0.00 0.00 0.00 5.34
20 21 1.006571 TCTTGTCCTCGAACACGCC 60.007 57.895 0.00 0.00 0.00 5.68
21 22 2.355363 TTGTCCTCGAACACGCCG 60.355 61.111 0.00 0.00 0.00 6.46
22 23 3.851845 TTGTCCTCGAACACGCCGG 62.852 63.158 0.00 0.00 0.00 6.13
48 49 4.695231 CGACGTCAACGCCTCGGT 62.695 66.667 17.16 0.00 44.43 4.69
49 50 3.103911 GACGTCAACGCCTCGGTG 61.104 66.667 11.55 0.00 46.80 4.94
68 69 4.910956 GCCTCTGCGATGTACACA 57.089 55.556 0.00 0.00 0.00 3.72
69 70 3.369381 GCCTCTGCGATGTACACAT 57.631 52.632 0.00 0.00 39.70 3.21
70 71 1.656652 GCCTCTGCGATGTACACATT 58.343 50.000 0.00 0.00 36.57 2.71
71 72 2.009774 GCCTCTGCGATGTACACATTT 58.990 47.619 0.00 0.00 36.57 2.32
72 73 2.420022 GCCTCTGCGATGTACACATTTT 59.580 45.455 0.00 0.00 36.57 1.82
73 74 3.621268 GCCTCTGCGATGTACACATTTTA 59.379 43.478 0.00 0.00 36.57 1.52
74 75 4.273480 GCCTCTGCGATGTACACATTTTAT 59.727 41.667 0.00 0.00 36.57 1.40
75 76 5.741425 CCTCTGCGATGTACACATTTTATG 58.259 41.667 0.00 0.00 36.57 1.90
76 77 5.294306 CCTCTGCGATGTACACATTTTATGT 59.706 40.000 0.00 0.00 46.22 2.29
98 99 7.606858 TGTGAAAAATCAATTTTGCTCACAA 57.393 28.000 21.81 12.46 45.16 3.33
99 100 8.037382 TGTGAAAAATCAATTTTGCTCACAAA 57.963 26.923 21.81 9.32 45.16 2.83
100 101 7.961827 TGTGAAAAATCAATTTTGCTCACAAAC 59.038 29.630 21.81 8.27 45.16 2.93
101 102 7.162385 GTGAAAAATCAATTTTGCTCACAAACG 59.838 33.333 18.97 0.00 45.29 3.60
102 103 6.660887 AAAATCAATTTTGCTCACAAACGT 57.339 29.167 0.05 0.00 45.29 3.99
103 104 5.888412 AATCAATTTTGCTCACAAACGTC 57.112 34.783 0.00 0.00 45.29 4.34
104 105 3.358775 TCAATTTTGCTCACAAACGTCG 58.641 40.909 0.00 0.00 45.29 5.12
105 106 3.064134 TCAATTTTGCTCACAAACGTCGA 59.936 39.130 0.00 0.00 45.29 4.20
106 107 2.730183 TTTTGCTCACAAACGTCGAG 57.270 45.000 0.00 0.00 45.29 4.04
107 108 0.934496 TTTGCTCACAAACGTCGAGG 59.066 50.000 3.03 3.03 40.84 4.63
108 109 0.878523 TTGCTCACAAACGTCGAGGG 60.879 55.000 10.27 0.00 31.21 4.30
109 110 1.006571 GCTCACAAACGTCGAGGGA 60.007 57.895 10.27 0.00 0.00 4.20
110 111 0.389948 GCTCACAAACGTCGAGGGAT 60.390 55.000 10.27 0.00 0.00 3.85
111 112 1.350193 CTCACAAACGTCGAGGGATG 58.650 55.000 10.27 10.02 35.23 3.51
112 113 0.037697 TCACAAACGTCGAGGGATGG 60.038 55.000 10.27 0.00 33.28 3.51
113 114 0.037697 CACAAACGTCGAGGGATGGA 60.038 55.000 10.27 0.00 33.28 3.41
114 115 0.682852 ACAAACGTCGAGGGATGGAA 59.317 50.000 10.27 0.00 33.28 3.53
115 116 1.278127 ACAAACGTCGAGGGATGGAAT 59.722 47.619 10.27 0.00 33.28 3.01
116 117 2.290071 ACAAACGTCGAGGGATGGAATT 60.290 45.455 10.27 0.00 33.28 2.17
117 118 2.747446 CAAACGTCGAGGGATGGAATTT 59.253 45.455 10.27 0.00 33.28 1.82
118 119 2.024176 ACGTCGAGGGATGGAATTTG 57.976 50.000 10.27 0.00 33.28 2.32
119 120 1.278127 ACGTCGAGGGATGGAATTTGT 59.722 47.619 10.27 0.00 33.28 2.83
120 121 1.665679 CGTCGAGGGATGGAATTTGTG 59.334 52.381 0.00 0.00 0.00 3.33
121 122 2.676750 CGTCGAGGGATGGAATTTGTGA 60.677 50.000 0.00 0.00 0.00 3.58
122 123 3.343617 GTCGAGGGATGGAATTTGTGAA 58.656 45.455 0.00 0.00 0.00 3.18
123 124 3.756434 GTCGAGGGATGGAATTTGTGAAA 59.244 43.478 0.00 0.00 0.00 2.69
124 125 4.009675 TCGAGGGATGGAATTTGTGAAAG 58.990 43.478 0.00 0.00 0.00 2.62
125 126 4.009675 CGAGGGATGGAATTTGTGAAAGA 58.990 43.478 0.00 0.00 0.00 2.52
126 127 4.095483 CGAGGGATGGAATTTGTGAAAGAG 59.905 45.833 0.00 0.00 0.00 2.85
127 128 5.256474 GAGGGATGGAATTTGTGAAAGAGA 58.744 41.667 0.00 0.00 0.00 3.10
128 129 5.644188 AGGGATGGAATTTGTGAAAGAGAA 58.356 37.500 0.00 0.00 0.00 2.87
129 130 5.713861 AGGGATGGAATTTGTGAAAGAGAAG 59.286 40.000 0.00 0.00 0.00 2.85
130 131 5.711976 GGGATGGAATTTGTGAAAGAGAAGA 59.288 40.000 0.00 0.00 0.00 2.87
131 132 6.209391 GGGATGGAATTTGTGAAAGAGAAGAA 59.791 38.462 0.00 0.00 0.00 2.52
132 133 7.093596 GGGATGGAATTTGTGAAAGAGAAGAAT 60.094 37.037 0.00 0.00 0.00 2.40
133 134 7.758528 GGATGGAATTTGTGAAAGAGAAGAATG 59.241 37.037 0.00 0.00 0.00 2.67
134 135 7.587037 TGGAATTTGTGAAAGAGAAGAATGT 57.413 32.000 0.00 0.00 0.00 2.71
135 136 8.010733 TGGAATTTGTGAAAGAGAAGAATGTT 57.989 30.769 0.00 0.00 0.00 2.71
136 137 8.477256 TGGAATTTGTGAAAGAGAAGAATGTTT 58.523 29.630 0.00 0.00 0.00 2.83
137 138 9.317936 GGAATTTGTGAAAGAGAAGAATGTTTT 57.682 29.630 0.00 0.00 0.00 2.43
143 144 8.345565 TGTGAAAGAGAAGAATGTTTTTAGAGC 58.654 33.333 0.00 0.00 0.00 4.09
144 145 8.563732 GTGAAAGAGAAGAATGTTTTTAGAGCT 58.436 33.333 0.00 0.00 0.00 4.09
145 146 9.125026 TGAAAGAGAAGAATGTTTTTAGAGCTT 57.875 29.630 0.00 0.00 0.00 3.74
146 147 9.958234 GAAAGAGAAGAATGTTTTTAGAGCTTT 57.042 29.630 0.00 0.00 0.00 3.51
147 148 9.958234 AAAGAGAAGAATGTTTTTAGAGCTTTC 57.042 29.630 0.00 0.00 0.00 2.62
148 149 8.916628 AGAGAAGAATGTTTTTAGAGCTTTCT 57.083 30.769 0.00 0.00 0.00 2.52
149 150 9.348476 AGAGAAGAATGTTTTTAGAGCTTTCTT 57.652 29.630 4.37 4.37 38.46 2.52
150 151 9.958234 GAGAAGAATGTTTTTAGAGCTTTCTTT 57.042 29.630 5.89 0.00 37.01 2.52
151 152 9.958234 AGAAGAATGTTTTTAGAGCTTTCTTTC 57.042 29.630 5.89 1.59 37.01 2.62
152 153 9.186323 GAAGAATGTTTTTAGAGCTTTCTTTCC 57.814 33.333 5.89 0.00 37.01 3.13
153 154 8.237811 AGAATGTTTTTAGAGCTTTCTTTCCA 57.762 30.769 0.00 0.00 0.00 3.53
154 155 8.138074 AGAATGTTTTTAGAGCTTTCTTTCCAC 58.862 33.333 0.00 0.00 0.00 4.02
155 156 5.816919 TGTTTTTAGAGCTTTCTTTCCACG 58.183 37.500 0.00 0.00 0.00 4.94
156 157 5.587043 TGTTTTTAGAGCTTTCTTTCCACGA 59.413 36.000 0.00 0.00 0.00 4.35
157 158 6.262273 TGTTTTTAGAGCTTTCTTTCCACGAT 59.738 34.615 0.00 0.00 0.00 3.73
158 159 6.877611 TTTTAGAGCTTTCTTTCCACGATT 57.122 33.333 0.00 0.00 0.00 3.34
159 160 6.877611 TTTAGAGCTTTCTTTCCACGATTT 57.122 33.333 0.00 0.00 0.00 2.17
160 161 6.877611 TTAGAGCTTTCTTTCCACGATTTT 57.122 33.333 0.00 0.00 0.00 1.82
161 162 5.774498 AGAGCTTTCTTTCCACGATTTTT 57.226 34.783 0.00 0.00 0.00 1.94
162 163 5.763088 AGAGCTTTCTTTCCACGATTTTTC 58.237 37.500 0.00 0.00 0.00 2.29
163 164 5.532779 AGAGCTTTCTTTCCACGATTTTTCT 59.467 36.000 0.00 0.00 0.00 2.52
164 165 6.710744 AGAGCTTTCTTTCCACGATTTTTCTA 59.289 34.615 0.00 0.00 0.00 2.10
165 166 7.391833 AGAGCTTTCTTTCCACGATTTTTCTAT 59.608 33.333 0.00 0.00 0.00 1.98
166 167 8.561738 AGCTTTCTTTCCACGATTTTTCTATA 57.438 30.769 0.00 0.00 0.00 1.31
167 168 9.178758 AGCTTTCTTTCCACGATTTTTCTATAT 57.821 29.630 0.00 0.00 0.00 0.86
168 169 9.788960 GCTTTCTTTCCACGATTTTTCTATATT 57.211 29.630 0.00 0.00 0.00 1.28
175 176 9.778741 TTCCACGATTTTTCTATATTATGAGCT 57.221 29.630 0.00 0.00 0.00 4.09
176 177 9.208022 TCCACGATTTTTCTATATTATGAGCTG 57.792 33.333 0.00 0.00 0.00 4.24
177 178 9.208022 CCACGATTTTTCTATATTATGAGCTGA 57.792 33.333 0.00 0.00 0.00 4.26
184 185 7.403312 TTCTATATTATGAGCTGAGAGGAGC 57.597 40.000 0.00 0.00 39.46 4.70
185 186 4.717233 ATATTATGAGCTGAGAGGAGCG 57.283 45.455 0.00 0.00 44.24 5.03
186 187 0.387202 TTATGAGCTGAGAGGAGCGC 59.613 55.000 0.00 0.00 44.24 5.92
187 188 2.677875 TGAGCTGAGAGGAGCGCA 60.678 61.111 11.47 0.00 45.17 6.09
188 189 2.056815 TGAGCTGAGAGGAGCGCAT 61.057 57.895 11.47 0.00 42.91 4.73
189 190 0.753111 TGAGCTGAGAGGAGCGCATA 60.753 55.000 11.47 0.00 42.91 3.14
190 191 0.318614 GAGCTGAGAGGAGCGCATAC 60.319 60.000 11.47 0.00 44.24 2.39
191 192 1.659954 GCTGAGAGGAGCGCATACG 60.660 63.158 11.47 0.00 44.07 3.06
192 193 1.007964 CTGAGAGGAGCGCATACGG 60.008 63.158 11.47 0.00 40.57 4.02
193 194 2.355244 GAGAGGAGCGCATACGGC 60.355 66.667 11.47 0.00 40.57 5.68
194 195 2.835431 AGAGGAGCGCATACGGCT 60.835 61.111 11.47 0.00 45.00 5.52
195 196 2.107141 GAGGAGCGCATACGGCTT 59.893 61.111 11.47 0.00 41.72 4.35
196 197 1.521681 GAGGAGCGCATACGGCTTT 60.522 57.895 11.47 0.00 41.72 3.51
197 198 1.078426 AGGAGCGCATACGGCTTTT 60.078 52.632 11.47 0.00 41.72 2.27
198 199 0.676782 AGGAGCGCATACGGCTTTTT 60.677 50.000 11.47 0.00 41.72 1.94
220 221 3.209091 TTTTTGAGGGAACGGCCAA 57.791 47.368 2.24 0.00 38.95 4.52
238 239 1.391485 CAATCGGCGAGTTGAGACAAG 59.609 52.381 17.22 0.00 0.00 3.16
241 242 0.784778 CGGCGAGTTGAGACAAGTTC 59.215 55.000 0.00 0.00 0.00 3.01
329 330 3.449227 CGCCTACGCTGTCCAGGA 61.449 66.667 0.00 0.00 0.00 3.86
399 460 3.181458 GCGAACCCTAATCTAATCCACCA 60.181 47.826 0.00 0.00 0.00 4.17
405 466 2.303660 AATCTAATCCACCACCCCCT 57.696 50.000 0.00 0.00 0.00 4.79
409 470 2.868790 TAATCCACCACCCCCTCCCC 62.869 65.000 0.00 0.00 0.00 4.81
463 553 1.829096 CCGACCCCAAAACCCGTTT 60.829 57.895 0.00 0.00 0.00 3.60
535 638 3.181967 CTTTCTCGCCAGTCGCCG 61.182 66.667 0.00 0.00 38.27 6.46
536 639 3.916392 CTTTCTCGCCAGTCGCCGT 62.916 63.158 0.00 0.00 38.27 5.68
581 686 4.947147 GCACGCAACCCCACCAGA 62.947 66.667 0.00 0.00 0.00 3.86
582 687 2.669569 CACGCAACCCCACCAGAG 60.670 66.667 0.00 0.00 0.00 3.35
583 688 2.847234 ACGCAACCCCACCAGAGA 60.847 61.111 0.00 0.00 0.00 3.10
584 689 2.358737 CGCAACCCCACCAGAGAC 60.359 66.667 0.00 0.00 0.00 3.36
585 690 2.034221 GCAACCCCACCAGAGACC 59.966 66.667 0.00 0.00 0.00 3.85
586 691 2.829384 GCAACCCCACCAGAGACCA 61.829 63.158 0.00 0.00 0.00 4.02
587 692 1.376466 CAACCCCACCAGAGACCAG 59.624 63.158 0.00 0.00 0.00 4.00
620 730 2.366153 GACCAAGGAAGCCAACCCCA 62.366 60.000 0.00 0.00 0.00 4.96
621 731 1.079073 CCAAGGAAGCCAACCCCAT 59.921 57.895 0.00 0.00 0.00 4.00
622 732 0.972471 CCAAGGAAGCCAACCCCATC 60.972 60.000 0.00 0.00 0.00 3.51
623 733 0.972471 CAAGGAAGCCAACCCCATCC 60.972 60.000 0.00 0.00 0.00 3.51
624 734 2.042944 GGAAGCCAACCCCATCCC 60.043 66.667 0.00 0.00 0.00 3.85
625 735 2.042944 GAAGCCAACCCCATCCCC 60.043 66.667 0.00 0.00 0.00 4.81
635 745 3.061848 CCATCCCCCACAACACGC 61.062 66.667 0.00 0.00 0.00 5.34
636 746 3.061848 CATCCCCCACAACACGCC 61.062 66.667 0.00 0.00 0.00 5.68
668 778 2.030451 GTCTTTTTGAGCAGCTGGAAGG 60.030 50.000 17.12 0.00 0.00 3.46
671 781 0.767375 TTTGAGCAGCTGGAAGGACT 59.233 50.000 17.12 1.91 0.00 3.85
672 782 0.035881 TTGAGCAGCTGGAAGGACTG 59.964 55.000 17.12 0.00 34.48 3.51
673 783 1.078567 GAGCAGCTGGAAGGACTGG 60.079 63.158 17.12 0.00 31.94 4.00
674 784 1.537397 AGCAGCTGGAAGGACTGGA 60.537 57.895 17.12 0.00 31.94 3.86
675 785 1.130054 AGCAGCTGGAAGGACTGGAA 61.130 55.000 17.12 0.00 31.94 3.53
718 828 1.834822 CCTTTGCCCCGTTCCCAAA 60.835 57.895 0.00 0.00 0.00 3.28
727 837 0.608308 CCGTTCCCAAACCTTCCTCC 60.608 60.000 0.00 0.00 31.27 4.30
728 838 0.953960 CGTTCCCAAACCTTCCTCCG 60.954 60.000 0.00 0.00 31.27 4.63
729 839 0.608308 GTTCCCAAACCTTCCTCCGG 60.608 60.000 0.00 0.00 0.00 5.14
730 840 2.361230 CCCAAACCTTCCTCCGGC 60.361 66.667 0.00 0.00 0.00 6.13
731 841 2.434331 CCAAACCTTCCTCCGGCA 59.566 61.111 0.00 0.00 0.00 5.69
732 842 1.000896 CCAAACCTTCCTCCGGCAT 60.001 57.895 0.00 0.00 0.00 4.40
733 843 0.611896 CCAAACCTTCCTCCGGCATT 60.612 55.000 0.00 0.00 0.00 3.56
735 845 0.323451 AAACCTTCCTCCGGCATTCC 60.323 55.000 0.00 0.00 0.00 3.01
737 847 2.679342 CCTTCCTCCGGCATTCCCA 61.679 63.158 0.00 0.00 0.00 4.37
738 848 1.302949 CTTCCTCCGGCATTCCCAA 59.697 57.895 0.00 0.00 0.00 4.12
739 849 0.323360 CTTCCTCCGGCATTCCCAAA 60.323 55.000 0.00 0.00 0.00 3.28
740 850 0.610785 TTCCTCCGGCATTCCCAAAC 60.611 55.000 0.00 0.00 0.00 2.93
742 852 1.000896 CTCCGGCATTCCCAAACCT 60.001 57.895 0.00 0.00 0.00 3.50
743 853 0.611896 CTCCGGCATTCCCAAACCTT 60.612 55.000 0.00 0.00 0.00 3.50
745 855 0.897863 CCGGCATTCCCAAACCTTCA 60.898 55.000 0.00 0.00 0.00 3.02
748 908 0.243636 GCATTCCCAAACCTTCACCG 59.756 55.000 0.00 0.00 0.00 4.94
785 972 1.014564 GTTCCTTTCCTCTGCCGTCG 61.015 60.000 0.00 0.00 0.00 5.12
786 973 1.183030 TTCCTTTCCTCTGCCGTCGA 61.183 55.000 0.00 0.00 0.00 4.20
787 974 1.446272 CCTTTCCTCTGCCGTCGAC 60.446 63.158 5.18 5.18 0.00 4.20
841 1059 1.553690 CGCCTTCCTTCCTTCCTGGA 61.554 60.000 0.00 0.00 44.51 3.86
864 1085 2.073101 GGGAATTCCTCCGCCTCCT 61.073 63.158 23.63 0.00 46.51 3.69
876 1097 3.532155 CCTCCTCGCCTTCTCCCG 61.532 72.222 0.00 0.00 0.00 5.14
881 1102 3.358076 CTCGCCTTCTCCCGTCCAC 62.358 68.421 0.00 0.00 0.00 4.02
882 1103 4.452733 CGCCTTCTCCCGTCCACC 62.453 72.222 0.00 0.00 0.00 4.61
883 1104 4.097361 GCCTTCTCCCGTCCACCC 62.097 72.222 0.00 0.00 0.00 4.61
884 1105 2.606519 CCTTCTCCCGTCCACCCA 60.607 66.667 0.00 0.00 0.00 4.51
892 1113 2.125269 CGTCCACCCACCGGATTC 60.125 66.667 9.46 0.00 34.32 2.52
898 1119 4.258206 CCCACCGGATTCATTGGG 57.742 61.111 9.46 10.36 42.92 4.12
906 1127 1.001378 CGGATTCATTGGGGAATTCGC 60.001 52.381 13.85 13.85 45.95 4.70
908 1129 2.035066 GGATTCATTGGGGAATTCGCTG 59.965 50.000 20.49 12.12 37.61 5.18
910 1131 1.037030 TCATTGGGGAATTCGCTGCC 61.037 55.000 20.49 6.22 0.00 4.85
911 1132 1.039233 CATTGGGGAATTCGCTGCCT 61.039 55.000 20.49 2.73 0.00 4.75
912 1133 0.753111 ATTGGGGAATTCGCTGCCTC 60.753 55.000 20.49 5.74 0.00 4.70
913 1134 2.517166 GGGGAATTCGCTGCCTCC 60.517 66.667 20.49 4.47 0.00 4.30
914 1135 2.592308 GGGAATTCGCTGCCTCCT 59.408 61.111 14.84 0.00 0.00 3.69
915 1136 1.821332 GGGAATTCGCTGCCTCCTG 60.821 63.158 14.84 0.00 0.00 3.86
916 1137 2.476320 GGAATTCGCTGCCTCCTGC 61.476 63.158 0.00 0.00 41.77 4.85
917 1138 1.451028 GAATTCGCTGCCTCCTGCT 60.451 57.895 0.00 0.00 42.00 4.24
918 1139 1.435408 GAATTCGCTGCCTCCTGCTC 61.435 60.000 0.00 0.00 42.00 4.26
919 1140 2.883267 AATTCGCTGCCTCCTGCTCC 62.883 60.000 0.00 0.00 42.00 4.70
967 1201 3.112709 GCGGCCGTCTGTCTGTTC 61.113 66.667 28.70 0.93 0.00 3.18
993 1227 1.437160 CGGATTTGGATTTGCGGGG 59.563 57.895 0.00 0.00 0.00 5.73
1533 1788 0.771755 AGGAGAAGGGGTTTGTGGTC 59.228 55.000 0.00 0.00 0.00 4.02
1953 2208 1.356124 ATGTCACTGAAGCTGACCCT 58.644 50.000 0.00 0.00 37.79 4.34
1965 2220 2.191641 GACCCTGAGCATGAGCCC 59.808 66.667 0.00 0.00 43.56 5.19
1978 2233 3.008375 GCATGAGCCCTATGTTGAGGATA 59.992 47.826 0.00 0.00 39.15 2.59
2115 2370 1.002900 CAGTTCGCTCGCCTTTTCAAA 60.003 47.619 0.00 0.00 0.00 2.69
2148 2403 2.881513 TGTCAGCTCCGATGAGTATCTC 59.118 50.000 0.00 0.00 40.95 2.75
2199 2454 0.734889 CCGATGCCATTGAAGACACC 59.265 55.000 0.00 0.00 0.00 4.16
2241 2496 1.949525 GAGGTGTTTCAGCTTGCTGAA 59.050 47.619 27.72 27.72 42.53 3.02
2328 2583 0.179234 GGAAGAGGCTGCTCTTACCC 59.821 60.000 12.24 8.28 43.03 3.69
2511 2766 5.335127 CAAGCAAAGCTGTCATGGTATTAC 58.665 41.667 0.00 0.00 39.62 1.89
2517 2772 5.215252 AGCTGTCATGGTATTACGCTATT 57.785 39.130 0.00 0.00 0.00 1.73
2574 2829 3.733337 TGAAGTCTTGGAGCTCTTCAAC 58.267 45.455 14.64 7.62 41.75 3.18
2586 2841 2.958213 CTCTTCAACAGAGCTGAGGAC 58.042 52.381 4.21 0.00 42.96 3.85
2595 2850 1.980765 AGAGCTGAGGACAACATGGAA 59.019 47.619 0.00 0.00 0.00 3.53
2620 2875 2.838202 GGTACAGAGATGTGGGAGGAAA 59.162 50.000 0.00 0.00 0.00 3.13
2629 2884 3.893753 TGTGGGAGGAAATGGAAGAAA 57.106 42.857 0.00 0.00 0.00 2.52
2657 2912 5.428253 CCTGAAGAATCGATCCAAACCTAA 58.572 41.667 0.00 0.00 0.00 2.69
2660 2915 5.045869 TGAAGAATCGATCCAAACCTAACCT 60.046 40.000 0.00 0.00 0.00 3.50
2670 2925 3.306710 CCAAACCTAACCTGGAAAATGCC 60.307 47.826 0.00 0.00 31.38 4.40
2994 3258 6.280855 TGTTCTTATCTCCTGATTCGTGAA 57.719 37.500 0.00 0.00 34.32 3.18
2999 3263 1.895798 TCTCCTGATTCGTGAAGCTGT 59.104 47.619 0.00 0.00 0.00 4.40
3064 3328 9.880064 TTGCACACAAAATCATCATTAAAATTG 57.120 25.926 0.00 0.00 31.21 2.32
3109 3373 3.450457 CCCTTCTCTAGAGATGCTGTGTT 59.550 47.826 22.93 0.00 37.29 3.32
3155 3419 3.290948 TCACTTTAAACTGGCCACTGT 57.709 42.857 0.00 0.00 0.00 3.55
3359 3628 8.797438 TGGTGCTGTTAATATTGTGAAAATACA 58.203 29.630 0.00 0.00 0.00 2.29
3424 3693 7.505258 TCGTCCCAATCATATGTTTCAATCTA 58.495 34.615 1.90 0.00 0.00 1.98
3496 3765 3.701664 CTTCCTAGGTTTGGGCTTCAAT 58.298 45.455 9.08 0.00 34.98 2.57
3669 3938 5.507985 GCTCCACACATATTAAATTCTGGGC 60.508 44.000 0.00 0.00 0.00 5.36
3673 3942 4.338118 ACACATATTAAATTCTGGGCCACG 59.662 41.667 0.00 0.00 0.00 4.94
3764 4033 8.865590 TCATATGCACATGAGAAATTTGAATG 57.134 30.769 2.84 0.00 31.34 2.67
3960 4230 7.095523 GCATGCATTTCATTTGTTTAGTTGTCT 60.096 33.333 14.21 0.00 31.79 3.41
4101 4371 3.057526 ACTTTAGTCCAATTTCTTGCGCC 60.058 43.478 4.18 0.00 0.00 6.53
4109 4379 0.887933 ATTTCTTGCGCCGATTGGTT 59.112 45.000 4.18 0.00 37.67 3.67
4137 4407 8.242053 AGATGATTCTGTAAACAAAATGCTGAG 58.758 33.333 0.00 0.00 0.00 3.35
4174 4444 5.489792 AGAAGTTCAGAAAGCATGGTAGA 57.510 39.130 5.50 0.00 0.00 2.59
4297 4567 3.641434 AGACTGCTTTCTGCCATACAT 57.359 42.857 0.00 0.00 42.00 2.29
4349 4623 8.585881 GCTAATACTCTGTCCCACAATATAAGA 58.414 37.037 0.00 0.00 0.00 2.10
4395 4669 1.304713 TGGGACGGAGGGAGTACAC 60.305 63.158 0.00 0.00 0.00 2.90
4444 4718 7.415989 GCTTAAGGGTTTAATTTACTGTAGGCC 60.416 40.741 4.29 0.00 0.00 5.19
4474 4748 8.239998 GGACTTTGAAATAAACTCTTCCTGATG 58.760 37.037 0.00 0.00 0.00 3.07
4568 4848 2.568623 ACTTAGTTCCTTGGGCAGTG 57.431 50.000 0.00 0.00 0.00 3.66
4578 4858 2.167693 CCTTGGGCAGTGTAGTCGAATA 59.832 50.000 0.00 0.00 0.00 1.75
4579 4859 3.369052 CCTTGGGCAGTGTAGTCGAATAA 60.369 47.826 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.318784 GCGTGTTCGAGGACAAGAGT 60.319 55.000 7.27 0.00 39.71 3.24
1 2 1.009389 GGCGTGTTCGAGGACAAGAG 61.009 60.000 7.27 0.00 39.71 2.85
2 3 1.006571 GGCGTGTTCGAGGACAAGA 60.007 57.895 7.27 0.00 39.71 3.02
4 5 2.355363 CGGCGTGTTCGAGGACAA 60.355 61.111 0.00 0.00 39.71 3.18
5 6 4.351938 CCGGCGTGTTCGAGGACA 62.352 66.667 6.01 0.00 38.15 4.02
32 33 3.103911 CACCGAGGCGTTGACGTC 61.104 66.667 9.11 9.11 45.56 4.34
51 52 1.656652 AATGTGTACATCGCAGAGGC 58.343 50.000 0.00 0.00 45.05 4.70
52 53 5.294306 ACATAAAATGTGTACATCGCAGAGG 59.706 40.000 0.00 0.00 43.28 3.69
53 54 6.349973 ACATAAAATGTGTACATCGCAGAG 57.650 37.500 0.00 0.00 41.13 3.35
71 72 9.322773 TGTGAGCAAAATTGATTTTTCACATAA 57.677 25.926 21.33 8.93 44.31 1.90
72 73 8.883954 TGTGAGCAAAATTGATTTTTCACATA 57.116 26.923 21.33 10.11 44.31 2.29
73 74 7.789273 TGTGAGCAAAATTGATTTTTCACAT 57.211 28.000 21.33 2.45 44.31 3.21
74 75 7.606858 TTGTGAGCAAAATTGATTTTTCACA 57.393 28.000 21.33 21.33 45.75 3.58
75 76 7.162385 CGTTTGTGAGCAAAATTGATTTTTCAC 59.838 33.333 18.34 18.34 45.01 3.18
76 77 7.148507 ACGTTTGTGAGCAAAATTGATTTTTCA 60.149 29.630 0.00 0.44 45.01 2.69
77 78 7.179410 ACGTTTGTGAGCAAAATTGATTTTTC 58.821 30.769 0.00 0.00 45.01 2.29
78 79 7.071014 ACGTTTGTGAGCAAAATTGATTTTT 57.929 28.000 0.00 0.00 45.01 1.94
79 80 6.507771 CGACGTTTGTGAGCAAAATTGATTTT 60.508 34.615 0.00 0.00 45.01 1.82
80 81 5.051774 CGACGTTTGTGAGCAAAATTGATTT 60.052 36.000 0.00 0.00 45.01 2.17
81 82 4.440758 CGACGTTTGTGAGCAAAATTGATT 59.559 37.500 0.00 0.00 45.01 2.57
82 83 3.974401 CGACGTTTGTGAGCAAAATTGAT 59.026 39.130 0.00 0.00 45.01 2.57
83 84 3.064134 TCGACGTTTGTGAGCAAAATTGA 59.936 39.130 0.00 0.00 45.01 2.57
84 85 3.358775 TCGACGTTTGTGAGCAAAATTG 58.641 40.909 0.00 0.00 45.01 2.32
85 86 3.548014 CCTCGACGTTTGTGAGCAAAATT 60.548 43.478 0.00 0.00 45.01 1.82
86 87 2.032030 CCTCGACGTTTGTGAGCAAAAT 60.032 45.455 0.00 0.00 45.01 1.82
87 88 1.329292 CCTCGACGTTTGTGAGCAAAA 59.671 47.619 0.00 0.00 45.01 2.44
88 89 0.934496 CCTCGACGTTTGTGAGCAAA 59.066 50.000 0.00 0.00 41.77 3.68
89 90 0.878523 CCCTCGACGTTTGTGAGCAA 60.879 55.000 0.00 0.00 0.00 3.91
90 91 1.300620 CCCTCGACGTTTGTGAGCA 60.301 57.895 0.00 0.00 0.00 4.26
91 92 0.389948 ATCCCTCGACGTTTGTGAGC 60.390 55.000 0.00 0.00 0.00 4.26
92 93 1.350193 CATCCCTCGACGTTTGTGAG 58.650 55.000 0.00 0.00 0.00 3.51
93 94 0.037697 CCATCCCTCGACGTTTGTGA 60.038 55.000 0.00 0.00 0.00 3.58
94 95 0.037697 TCCATCCCTCGACGTTTGTG 60.038 55.000 0.00 0.00 0.00 3.33
95 96 0.682852 TTCCATCCCTCGACGTTTGT 59.317 50.000 0.00 0.00 0.00 2.83
96 97 2.024176 ATTCCATCCCTCGACGTTTG 57.976 50.000 0.00 0.00 0.00 2.93
97 98 2.747446 CAAATTCCATCCCTCGACGTTT 59.253 45.455 0.00 0.00 0.00 3.60
98 99 2.290071 ACAAATTCCATCCCTCGACGTT 60.290 45.455 0.00 0.00 0.00 3.99
99 100 1.278127 ACAAATTCCATCCCTCGACGT 59.722 47.619 0.00 0.00 0.00 4.34
100 101 1.665679 CACAAATTCCATCCCTCGACG 59.334 52.381 0.00 0.00 0.00 5.12
101 102 2.985896 TCACAAATTCCATCCCTCGAC 58.014 47.619 0.00 0.00 0.00 4.20
102 103 3.712016 TTCACAAATTCCATCCCTCGA 57.288 42.857 0.00 0.00 0.00 4.04
103 104 4.009675 TCTTTCACAAATTCCATCCCTCG 58.990 43.478 0.00 0.00 0.00 4.63
104 105 5.256474 TCTCTTTCACAAATTCCATCCCTC 58.744 41.667 0.00 0.00 0.00 4.30
105 106 5.261040 TCTCTTTCACAAATTCCATCCCT 57.739 39.130 0.00 0.00 0.00 4.20
106 107 5.711976 TCTTCTCTTTCACAAATTCCATCCC 59.288 40.000 0.00 0.00 0.00 3.85
107 108 6.824305 TCTTCTCTTTCACAAATTCCATCC 57.176 37.500 0.00 0.00 0.00 3.51
108 109 8.302438 ACATTCTTCTCTTTCACAAATTCCATC 58.698 33.333 0.00 0.00 0.00 3.51
109 110 8.186709 ACATTCTTCTCTTTCACAAATTCCAT 57.813 30.769 0.00 0.00 0.00 3.41
110 111 7.587037 ACATTCTTCTCTTTCACAAATTCCA 57.413 32.000 0.00 0.00 0.00 3.53
111 112 8.877808 AAACATTCTTCTCTTTCACAAATTCC 57.122 30.769 0.00 0.00 0.00 3.01
117 118 8.345565 GCTCTAAAAACATTCTTCTCTTTCACA 58.654 33.333 0.00 0.00 0.00 3.58
118 119 8.563732 AGCTCTAAAAACATTCTTCTCTTTCAC 58.436 33.333 0.00 0.00 0.00 3.18
119 120 8.682936 AGCTCTAAAAACATTCTTCTCTTTCA 57.317 30.769 0.00 0.00 0.00 2.69
120 121 9.958234 AAAGCTCTAAAAACATTCTTCTCTTTC 57.042 29.630 0.00 0.00 0.00 2.62
121 122 9.958234 GAAAGCTCTAAAAACATTCTTCTCTTT 57.042 29.630 0.00 0.00 0.00 2.52
122 123 9.348476 AGAAAGCTCTAAAAACATTCTTCTCTT 57.652 29.630 0.00 0.00 0.00 2.85
123 124 8.916628 AGAAAGCTCTAAAAACATTCTTCTCT 57.083 30.769 0.00 0.00 0.00 3.10
124 125 9.958234 AAAGAAAGCTCTAAAAACATTCTTCTC 57.042 29.630 5.07 0.00 35.31 2.87
125 126 9.958234 GAAAGAAAGCTCTAAAAACATTCTTCT 57.042 29.630 5.07 0.00 35.31 2.85
126 127 9.186323 GGAAAGAAAGCTCTAAAAACATTCTTC 57.814 33.333 5.07 0.00 35.31 2.87
127 128 8.695456 TGGAAAGAAAGCTCTAAAAACATTCTT 58.305 29.630 0.00 0.00 37.27 2.52
128 129 8.138074 GTGGAAAGAAAGCTCTAAAAACATTCT 58.862 33.333 0.00 0.00 0.00 2.40
129 130 7.113544 CGTGGAAAGAAAGCTCTAAAAACATTC 59.886 37.037 0.00 0.00 0.00 2.67
130 131 6.918022 CGTGGAAAGAAAGCTCTAAAAACATT 59.082 34.615 0.00 0.00 0.00 2.71
131 132 6.262273 TCGTGGAAAGAAAGCTCTAAAAACAT 59.738 34.615 0.00 0.00 0.00 2.71
132 133 5.587043 TCGTGGAAAGAAAGCTCTAAAAACA 59.413 36.000 0.00 0.00 0.00 2.83
133 134 6.056428 TCGTGGAAAGAAAGCTCTAAAAAC 57.944 37.500 0.00 0.00 0.00 2.43
134 135 6.877611 ATCGTGGAAAGAAAGCTCTAAAAA 57.122 33.333 0.00 0.00 0.00 1.94
135 136 6.877611 AATCGTGGAAAGAAAGCTCTAAAA 57.122 33.333 0.00 0.00 0.00 1.52
136 137 6.877611 AAATCGTGGAAAGAAAGCTCTAAA 57.122 33.333 0.00 0.00 0.00 1.85
137 138 6.877611 AAAATCGTGGAAAGAAAGCTCTAA 57.122 33.333 0.00 0.00 0.00 2.10
138 139 6.710744 AGAAAAATCGTGGAAAGAAAGCTCTA 59.289 34.615 0.00 0.00 0.00 2.43
139 140 5.532779 AGAAAAATCGTGGAAAGAAAGCTCT 59.467 36.000 0.00 0.00 0.00 4.09
140 141 5.763088 AGAAAAATCGTGGAAAGAAAGCTC 58.237 37.500 0.00 0.00 0.00 4.09
141 142 5.774498 AGAAAAATCGTGGAAAGAAAGCT 57.226 34.783 0.00 0.00 0.00 3.74
142 143 9.788960 AATATAGAAAAATCGTGGAAAGAAAGC 57.211 29.630 0.00 0.00 0.00 3.51
149 150 9.778741 AGCTCATAATATAGAAAAATCGTGGAA 57.221 29.630 0.00 0.00 0.00 3.53
150 151 9.208022 CAGCTCATAATATAGAAAAATCGTGGA 57.792 33.333 0.00 0.00 0.00 4.02
151 152 9.208022 TCAGCTCATAATATAGAAAAATCGTGG 57.792 33.333 0.00 0.00 0.00 4.94
158 159 8.310382 GCTCCTCTCAGCTCATAATATAGAAAA 58.690 37.037 0.00 0.00 36.38 2.29
159 160 7.362487 CGCTCCTCTCAGCTCATAATATAGAAA 60.362 40.741 0.00 0.00 37.25 2.52
160 161 6.094742 CGCTCCTCTCAGCTCATAATATAGAA 59.905 42.308 0.00 0.00 37.25 2.10
161 162 5.588246 CGCTCCTCTCAGCTCATAATATAGA 59.412 44.000 0.00 0.00 37.25 1.98
162 163 5.733091 GCGCTCCTCTCAGCTCATAATATAG 60.733 48.000 0.00 0.00 37.25 1.31
163 164 4.097135 GCGCTCCTCTCAGCTCATAATATA 59.903 45.833 0.00 0.00 37.25 0.86
164 165 3.119173 GCGCTCCTCTCAGCTCATAATAT 60.119 47.826 0.00 0.00 37.25 1.28
165 166 2.230025 GCGCTCCTCTCAGCTCATAATA 59.770 50.000 0.00 0.00 37.25 0.98
166 167 1.000731 GCGCTCCTCTCAGCTCATAAT 59.999 52.381 0.00 0.00 37.25 1.28
167 168 0.387202 GCGCTCCTCTCAGCTCATAA 59.613 55.000 0.00 0.00 37.25 1.90
168 169 0.753111 TGCGCTCCTCTCAGCTCATA 60.753 55.000 9.73 0.00 37.25 2.15
169 170 1.401318 ATGCGCTCCTCTCAGCTCAT 61.401 55.000 9.73 0.00 39.50 2.90
170 171 0.753111 TATGCGCTCCTCTCAGCTCA 60.753 55.000 9.73 0.00 38.45 4.26
171 172 0.318614 GTATGCGCTCCTCTCAGCTC 60.319 60.000 9.73 0.00 37.25 4.09
172 173 1.739049 GTATGCGCTCCTCTCAGCT 59.261 57.895 9.73 0.00 37.25 4.24
173 174 1.659954 CGTATGCGCTCCTCTCAGC 60.660 63.158 9.73 0.00 35.90 4.26
174 175 1.007964 CCGTATGCGCTCCTCTCAG 60.008 63.158 9.73 0.00 36.67 3.35
175 176 3.120105 CCGTATGCGCTCCTCTCA 58.880 61.111 9.73 0.00 36.67 3.27
176 177 2.355244 GCCGTATGCGCTCCTCTC 60.355 66.667 9.73 0.00 36.67 3.20
202 203 1.616374 GATTGGCCGTTCCCTCAAAAA 59.384 47.619 0.00 0.00 0.00 1.94
203 204 1.253100 GATTGGCCGTTCCCTCAAAA 58.747 50.000 0.00 0.00 0.00 2.44
204 205 0.958382 CGATTGGCCGTTCCCTCAAA 60.958 55.000 0.00 0.00 0.00 2.69
205 206 1.376683 CGATTGGCCGTTCCCTCAA 60.377 57.895 0.00 0.00 0.00 3.02
206 207 2.267642 CGATTGGCCGTTCCCTCA 59.732 61.111 0.00 0.00 0.00 3.86
207 208 2.513897 CCGATTGGCCGTTCCCTC 60.514 66.667 0.00 0.00 0.00 4.30
217 218 0.389817 TGTCTCAACTCGCCGATTGG 60.390 55.000 0.00 0.00 38.77 3.16
218 219 1.391485 CTTGTCTCAACTCGCCGATTG 59.609 52.381 0.00 0.00 0.00 2.67
219 220 1.000955 ACTTGTCTCAACTCGCCGATT 59.999 47.619 0.00 0.00 0.00 3.34
220 221 0.603569 ACTTGTCTCAACTCGCCGAT 59.396 50.000 0.00 0.00 0.00 4.18
226 227 1.149148 GCCCGAACTTGTCTCAACTC 58.851 55.000 0.00 0.00 0.00 3.01
230 231 0.878523 CGTTGCCCGAACTTGTCTCA 60.879 55.000 0.00 0.00 39.56 3.27
262 263 2.749621 CCCATTTCGGCCTCATATAAGC 59.250 50.000 0.00 0.00 0.00 3.09
263 264 4.003648 GTCCCATTTCGGCCTCATATAAG 58.996 47.826 0.00 0.00 0.00 1.73
264 265 3.392947 TGTCCCATTTCGGCCTCATATAA 59.607 43.478 0.00 0.00 0.00 0.98
266 267 1.774254 TGTCCCATTTCGGCCTCATAT 59.226 47.619 0.00 0.00 0.00 1.78
267 268 1.208706 TGTCCCATTTCGGCCTCATA 58.791 50.000 0.00 0.00 0.00 2.15
268 269 0.331278 TTGTCCCATTTCGGCCTCAT 59.669 50.000 0.00 0.00 0.00 2.90
269 270 0.322456 CTTGTCCCATTTCGGCCTCA 60.322 55.000 0.00 0.00 0.00 3.86
270 271 1.032114 CCTTGTCCCATTTCGGCCTC 61.032 60.000 0.00 0.00 0.00 4.70
314 315 2.893398 GGTCCTGGACAGCGTAGG 59.107 66.667 26.94 0.00 33.68 3.18
409 470 2.358247 CAACCAAGGTCGGGTCGG 60.358 66.667 0.00 0.00 37.77 4.79
411 472 2.033602 CCCAACCAAGGTCGGGTC 59.966 66.667 7.12 0.00 37.57 4.46
412 473 3.576259 CCCCAACCAAGGTCGGGT 61.576 66.667 14.07 0.00 40.68 5.28
439 502 0.815095 GGTTTTGGGGTCGGCATTAG 59.185 55.000 0.00 0.00 0.00 1.73
440 503 0.612453 GGGTTTTGGGGTCGGCATTA 60.612 55.000 0.00 0.00 0.00 1.90
441 504 1.911269 GGGTTTTGGGGTCGGCATT 60.911 57.895 0.00 0.00 0.00 3.56
442 505 2.283604 GGGTTTTGGGGTCGGCAT 60.284 61.111 0.00 0.00 0.00 4.40
443 506 4.958897 CGGGTTTTGGGGTCGGCA 62.959 66.667 0.00 0.00 0.00 5.69
444 507 4.960866 ACGGGTTTTGGGGTCGGC 62.961 66.667 0.00 0.00 0.00 5.54
463 553 1.694856 GGGGGTGATTACTTGCCCA 59.305 57.895 0.00 0.00 42.79 5.36
576 681 0.765510 GGTTTGGTCTGGTCTCTGGT 59.234 55.000 0.00 0.00 0.00 4.00
577 682 0.036875 GGGTTTGGTCTGGTCTCTGG 59.963 60.000 0.00 0.00 0.00 3.86
578 683 0.764890 TGGGTTTGGTCTGGTCTCTG 59.235 55.000 0.00 0.00 0.00 3.35
579 684 0.765510 GTGGGTTTGGTCTGGTCTCT 59.234 55.000 0.00 0.00 0.00 3.10
580 685 0.250770 GGTGGGTTTGGTCTGGTCTC 60.251 60.000 0.00 0.00 0.00 3.36
581 686 1.844130 GGTGGGTTTGGTCTGGTCT 59.156 57.895 0.00 0.00 0.00 3.85
582 687 1.599797 CGGTGGGTTTGGTCTGGTC 60.600 63.158 0.00 0.00 0.00 4.02
583 688 2.513895 CGGTGGGTTTGGTCTGGT 59.486 61.111 0.00 0.00 0.00 4.00
584 689 2.282180 CCGGTGGGTTTGGTCTGG 60.282 66.667 0.00 0.00 0.00 3.86
585 690 1.599797 GTCCGGTGGGTTTGGTCTG 60.600 63.158 0.00 0.00 33.83 3.51
586 691 2.826003 GGTCCGGTGGGTTTGGTCT 61.826 63.158 0.00 0.00 33.83 3.85
587 692 2.281970 GGTCCGGTGGGTTTGGTC 60.282 66.667 0.00 0.00 33.83 4.02
620 730 4.360405 GGGCGTGTTGTGGGGGAT 62.360 66.667 0.00 0.00 0.00 3.85
622 732 4.904590 TTGGGCGTGTTGTGGGGG 62.905 66.667 0.00 0.00 0.00 5.40
623 733 1.961180 TTTTTGGGCGTGTTGTGGGG 61.961 55.000 0.00 0.00 0.00 4.96
624 734 0.105778 ATTTTTGGGCGTGTTGTGGG 59.894 50.000 0.00 0.00 0.00 4.61
625 735 1.068434 AGATTTTTGGGCGTGTTGTGG 59.932 47.619 0.00 0.00 0.00 4.17
627 737 1.001815 CGAGATTTTTGGGCGTGTTGT 60.002 47.619 0.00 0.00 0.00 3.32
658 768 0.979665 TCTTCCAGTCCTTCCAGCTG 59.020 55.000 6.78 6.78 0.00 4.24
668 778 6.754193 TCTTCTTCTTCTTCTTCTTCCAGTC 58.246 40.000 0.00 0.00 0.00 3.51
673 783 9.986833 GCAATATTCTTCTTCTTCTTCTTCTTC 57.013 33.333 0.00 0.00 0.00 2.87
674 784 8.955388 GGCAATATTCTTCTTCTTCTTCTTCTT 58.045 33.333 0.00 0.00 0.00 2.52
675 785 7.555914 GGGCAATATTCTTCTTCTTCTTCTTCT 59.444 37.037 0.00 0.00 0.00 2.85
727 837 0.243636 GTGAAGGTTTGGGAATGCCG 59.756 55.000 0.00 0.00 33.83 5.69
728 838 0.608130 GGTGAAGGTTTGGGAATGCC 59.392 55.000 0.00 0.00 0.00 4.40
729 839 0.243636 CGGTGAAGGTTTGGGAATGC 59.756 55.000 0.00 0.00 0.00 3.56
730 840 0.243636 GCGGTGAAGGTTTGGGAATG 59.756 55.000 0.00 0.00 0.00 2.67
731 841 0.898326 GGCGGTGAAGGTTTGGGAAT 60.898 55.000 0.00 0.00 0.00 3.01
732 842 1.529713 GGCGGTGAAGGTTTGGGAA 60.530 57.895 0.00 0.00 0.00 3.97
733 843 2.114411 GGCGGTGAAGGTTTGGGA 59.886 61.111 0.00 0.00 0.00 4.37
735 845 1.388065 TTGTGGCGGTGAAGGTTTGG 61.388 55.000 0.00 0.00 0.00 3.28
737 847 1.408969 ATTTGTGGCGGTGAAGGTTT 58.591 45.000 0.00 0.00 0.00 3.27
738 848 2.279935 TATTTGTGGCGGTGAAGGTT 57.720 45.000 0.00 0.00 0.00 3.50
739 849 2.507407 ATATTTGTGGCGGTGAAGGT 57.493 45.000 0.00 0.00 0.00 3.50
740 850 2.099098 GGAATATTTGTGGCGGTGAAGG 59.901 50.000 0.00 0.00 0.00 3.46
742 852 1.740585 CGGAATATTTGTGGCGGTGAA 59.259 47.619 0.00 0.00 0.00 3.18
743 853 1.339247 ACGGAATATTTGTGGCGGTGA 60.339 47.619 0.00 0.00 0.00 4.02
745 855 1.091537 CACGGAATATTTGTGGCGGT 58.908 50.000 11.83 0.00 0.00 5.68
748 908 0.450184 ACGCACGGAATATTTGTGGC 59.550 50.000 18.06 11.82 34.24 5.01
785 972 0.250338 AAGTCAAAGCAGGGTCGGTC 60.250 55.000 0.00 0.00 0.00 4.79
786 973 0.250338 GAAGTCAAAGCAGGGTCGGT 60.250 55.000 0.00 0.00 0.00 4.69
787 974 1.291877 CGAAGTCAAAGCAGGGTCGG 61.292 60.000 0.00 0.00 0.00 4.79
822 1009 1.078143 CCAGGAAGGAAGGAAGGCG 60.078 63.158 0.00 0.00 41.22 5.52
841 1059 1.148498 GCGGAGGAATTCCCCGATT 59.852 57.895 37.66 17.94 46.14 3.34
844 1062 3.462199 GAGGCGGAGGAATTCCCCG 62.462 68.421 33.08 33.08 46.06 5.73
864 1085 3.379445 GTGGACGGGAGAAGGCGA 61.379 66.667 0.00 0.00 0.00 5.54
876 1097 0.034477 AATGAATCCGGTGGGTGGAC 60.034 55.000 0.00 0.00 38.60 4.02
881 1102 4.258206 CCCAATGAATCCGGTGGG 57.742 61.111 10.91 10.91 44.69 4.61
882 1103 0.033601 TTCCCCAATGAATCCGGTGG 60.034 55.000 0.00 0.00 0.00 4.61
883 1104 2.071778 ATTCCCCAATGAATCCGGTG 57.928 50.000 0.00 0.00 28.88 4.94
884 1105 2.666317 GAATTCCCCAATGAATCCGGT 58.334 47.619 0.00 0.00 33.91 5.28
892 1113 1.039233 AGGCAGCGAATTCCCCAATG 61.039 55.000 0.00 0.00 0.00 2.82
898 1119 2.476320 GCAGGAGGCAGCGAATTCC 61.476 63.158 0.00 0.00 43.97 3.01
930 1151 2.182030 CGCCTCGAACCCTCAGAC 59.818 66.667 0.00 0.00 0.00 3.51
951 1172 2.432628 GGAACAGACAGACGGCCG 60.433 66.667 26.86 26.86 0.00 6.13
952 1173 2.047179 GGGAACAGACAGACGGCC 60.047 66.667 0.00 0.00 0.00 6.13
954 1175 2.261671 CCGGGAACAGACAGACGG 59.738 66.667 0.00 0.00 35.01 4.79
955 1176 2.432628 GCCGGGAACAGACAGACG 60.433 66.667 2.18 0.00 0.00 4.18
956 1177 2.432628 CGCCGGGAACAGACAGAC 60.433 66.667 2.18 0.00 0.00 3.51
993 1227 2.124278 GGCTTCCCCATCCGGAAC 60.124 66.667 9.01 0.00 36.98 3.62
1016 1250 1.203364 AGGAGGCCCTCTTCTTCTTGA 60.203 52.381 11.29 0.00 38.86 3.02
1017 1251 1.284313 AGGAGGCCCTCTTCTTCTTG 58.716 55.000 11.29 0.00 38.86 3.02
1158 1407 1.219393 GAGCTTGTTCCCCTCCTCG 59.781 63.158 0.00 0.00 0.00 4.63
1464 1719 4.514577 AGCGCCGTCAGATTCCCG 62.515 66.667 2.29 0.00 0.00 5.14
1596 1851 1.615384 CCCTTCTTCTTCCTGGGCTTG 60.615 57.143 0.00 0.00 0.00 4.01
1932 2187 2.234908 AGGGTCAGCTTCAGTGACATAC 59.765 50.000 5.52 0.00 45.24 2.39
1953 2208 1.839354 TCAACATAGGGCTCATGCTCA 59.161 47.619 0.00 0.00 43.51 4.26
1965 2220 5.791336 TGCTACTGGTATCCTCAACATAG 57.209 43.478 0.00 0.00 0.00 2.23
2016 2271 4.386867 TCTGATACTTCCATTGTCCGAC 57.613 45.455 0.00 0.00 0.00 4.79
2127 2382 2.881513 GAGATACTCATCGGAGCTGACA 59.118 50.000 0.00 0.00 45.42 3.58
2199 2454 1.135527 TGGGCTTCGTCGGTAGTAATG 59.864 52.381 0.00 0.00 0.00 1.90
2328 2583 4.935885 CAATTCCTTTGGAGAGTCTTCG 57.064 45.455 0.00 0.00 31.21 3.79
2517 2772 0.180171 CCAGATCCGCATTGGTACCA 59.820 55.000 11.60 11.60 39.52 3.25
2574 2829 1.277273 TCCATGTTGTCCTCAGCTCTG 59.723 52.381 0.00 0.00 0.00 3.35
2586 2841 4.651778 TCTCTGTACCCTTTTCCATGTTG 58.348 43.478 0.00 0.00 0.00 3.33
2595 2850 2.840651 CTCCCACATCTCTGTACCCTTT 59.159 50.000 0.00 0.00 33.14 3.11
2620 2875 1.815003 CTTCAGGCGCTTTTCTTCCAT 59.185 47.619 7.64 0.00 0.00 3.41
2629 2884 1.576356 GATCGATTCTTCAGGCGCTT 58.424 50.000 7.64 0.00 0.00 4.68
2657 2912 0.037590 TAGCACGGCATTTTCCAGGT 59.962 50.000 0.00 0.00 0.00 4.00
2660 2915 1.277842 TCTCTAGCACGGCATTTTCCA 59.722 47.619 0.00 0.00 0.00 3.53
2670 2925 0.461548 TGCCCATCTTCTCTAGCACG 59.538 55.000 0.00 0.00 0.00 5.34
2994 3258 5.435686 TCAACATTATAGTTCCCACAGCT 57.564 39.130 0.00 0.00 0.00 4.24
2999 3263 8.310382 CCAACAAAATCAACATTATAGTTCCCA 58.690 33.333 0.00 0.00 0.00 4.37
3064 3328 0.737219 GCAGGTCAATCAGCATCACC 59.263 55.000 0.00 0.00 0.00 4.02
3119 3383 0.108138 GTGATCAAGAGGACCACGGG 60.108 60.000 0.00 0.00 0.00 5.28
3121 3385 2.751166 AAGTGATCAAGAGGACCACG 57.249 50.000 0.00 0.00 33.37 4.94
3238 3503 7.305763 CCGGTTTTCTGTAAACAAATTTTCTCG 60.306 37.037 11.22 3.40 46.44 4.04
3305 3571 6.262944 GGCACACCATTATGATGAACTCAATA 59.737 38.462 0.00 0.00 34.71 1.90
3424 3693 7.910162 GTGATGCAATGAAAGTTACACGATTAT 59.090 33.333 0.00 0.00 0.00 1.28
3496 3765 3.069872 AGGCTTGCACAATTTCATCAACA 59.930 39.130 0.00 0.00 0.00 3.33
3673 3942 3.329929 AGAAGATTGGTGTCGGTAACC 57.670 47.619 0.00 0.00 38.26 2.85
3764 4033 2.351726 CACATCTAACACGCTAAAGCCC 59.648 50.000 0.00 0.00 37.91 5.19
3960 4230 5.765510 AGGCATCTATGGACCAATAACAAA 58.234 37.500 0.00 0.00 0.00 2.83
4308 4578 6.042552 AGAGTATTAGCTTACCATGTGCAGAT 59.957 38.462 0.00 0.00 0.00 2.90
4319 4589 5.593679 TGTGGGACAGAGTATTAGCTTAC 57.406 43.478 0.00 0.00 41.80 2.34
4349 4623 3.520569 ACGATGTTTTTGCAAGCTGTTT 58.479 36.364 0.00 0.00 0.00 2.83
4395 4669 4.697352 CACAGACCATCAGGAACTAAAAGG 59.303 45.833 0.00 0.00 36.02 3.11
4444 4718 7.173390 AGGAAGAGTTTATTTCAAAGTCCTTCG 59.827 37.037 0.00 0.00 31.61 3.79
4568 4848 8.705048 AGAAAACAGAGGATTTATTCGACTAC 57.295 34.615 0.00 0.00 0.00 2.73
4578 4858 4.501400 CGCCCAAAAGAAAACAGAGGATTT 60.501 41.667 0.00 0.00 0.00 2.17
4579 4859 3.005791 CGCCCAAAAGAAAACAGAGGATT 59.994 43.478 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.