Multiple sequence alignment - TraesCS5A01G158700

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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 TraesCS5A01G158700 chr5A 100.000 2644 0 0 1 2644 338557328 338559971 0.000000e+00 4883.0
1 TraesCS5A01G158700 chr5B 93.907 2183 104 13 473 2644 289145823 289143659 0.000000e+00 3267.0
2 TraesCS5A01G158700 chr5B 95.960 297 12 0 184 480 289146194 289145898 1.420000e-132 483.0
3 TraesCS5A01G158700 chr5D 94.727 512 17 6 754 1260 255474698 255475204 0.000000e+00 787.0
4 TraesCS5A01G158700 chr5D 95.408 392 16 2 1284 1675 255475200 255475589 8.040000e-175 623.0
5 TraesCS5A01G158700 chr5D 87.826 345 39 3 1772 2116 489685414 489685073 4.100000e-108 401.0
6 TraesCS5A01G158700 chr5D 87.135 342 38 5 1779 2117 553466450 553466112 1.480000e-102 383.0
7 TraesCS5A01G158700 chr5D 82.877 438 40 18 2231 2644 255475631 255476057 6.960000e-96 361.0
8 TraesCS5A01G158700 chr1A 88.218 331 37 2 1772 2102 49349780 49350108 6.860000e-106 394.0
9 TraesCS5A01G158700 chr1A 86.528 193 17 3 1 191 505557253 505557068 1.240000e-48 204.0
10 TraesCS5A01G158700 chr3D 86.555 357 42 5 1772 2128 590228687 590228337 3.190000e-104 388.0
11 TraesCS5A01G158700 chr3D 91.489 188 11 3 2 184 507776156 507776343 1.210000e-63 254.0
12 TraesCS5A01G158700 chr7D 85.753 372 45 6 1746 2112 228974761 228974393 1.150000e-103 387.0
13 TraesCS5A01G158700 chr7D 88.947 190 14 5 2 185 575528917 575528729 7.360000e-56 228.0
14 TraesCS5A01G158700 chr4A 86.782 348 41 3 1772 2117 597743187 597742843 1.480000e-102 383.0
15 TraesCS5A01G158700 chr4A 100.000 31 0 0 2498 2528 595293635 595293605 1.020000e-04 58.4
16 TraesCS5A01G158700 chr1D 86.455 347 46 1 1772 2117 488109448 488109102 1.920000e-101 379.0
17 TraesCS5A01G158700 chr1D 88.542 192 12 7 2 186 456131389 456131577 9.520000e-55 224.0
18 TraesCS5A01G158700 chr7A 86.455 347 42 5 1772 2117 730843627 730843285 2.480000e-100 375.0
19 TraesCS5A01G158700 chr7A 87.234 188 17 4 2 185 517575111 517574927 9.590000e-50 207.0
20 TraesCS5A01G158700 chr2B 90.000 190 11 8 2 185 616929377 616929190 3.400000e-59 239.0
21 TraesCS5A01G158700 chr2B 88.172 186 14 7 2 182 635201253 635201435 5.730000e-52 215.0
22 TraesCS5A01G158700 chr6B 88.421 190 11 7 4 185 659813295 659813481 4.430000e-53 219.0
23 TraesCS5A01G158700 chr2D 87.368 190 17 4 2 185 82905444 82905256 7.410000e-51 211.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G158700 chr5A 338557328 338559971 2643 False 4883.000000 4883 100.0000 1 2644 1 chr5A.!!$F1 2643
1 TraesCS5A01G158700 chr5B 289143659 289146194 2535 True 1875.000000 3267 94.9335 184 2644 2 chr5B.!!$R1 2460
2 TraesCS5A01G158700 chr5D 255474698 255476057 1359 False 590.333333 787 91.0040 754 2644 3 chr5D.!!$F1 1890

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
140 141 0.037232 GACCTCCACAACCCTCGAAG 60.037 60.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2063 0.453782 GTCATTTCGCGGAAAACCGG 60.454 55.0 2.72 0.0 35.11 5.28 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
40 41 8.661352 AAAGTGCACAAATTTTAATAAGTGCT 57.339 26.923 21.04 7.46 43.65 4.40
41 42 9.757227 AAAGTGCACAAATTTTAATAAGTGCTA 57.243 25.926 21.04 11.29 43.65 3.49
42 43 9.757227 AAGTGCACAAATTTTAATAAGTGCTAA 57.243 25.926 21.04 7.46 43.65 3.09
43 44 9.927668 AGTGCACAAATTTTAATAAGTGCTAAT 57.072 25.926 21.04 10.76 43.65 1.73
44 45 9.956797 GTGCACAAATTTTAATAAGTGCTAATG 57.043 29.630 22.13 0.00 43.65 1.90
45 46 9.920133 TGCACAAATTTTAATAAGTGCTAATGA 57.080 25.926 22.13 6.37 43.65 2.57
114 115 3.650369 CACTTACGTGTGTGGGGC 58.350 61.111 12.88 0.00 36.39 5.80
115 116 1.964373 CACTTACGTGTGTGGGGCC 60.964 63.158 12.88 0.00 36.39 5.80
116 117 2.359478 CTTACGTGTGTGGGGCCC 60.359 66.667 18.17 18.17 0.00 5.80
117 118 2.850130 TTACGTGTGTGGGGCCCT 60.850 61.111 25.93 3.35 0.00 5.19
118 119 1.535930 TTACGTGTGTGGGGCCCTA 60.536 57.895 25.93 14.71 0.00 3.53
119 120 1.546589 TTACGTGTGTGGGGCCCTAG 61.547 60.000 25.93 5.65 0.00 3.02
120 121 2.735151 TACGTGTGTGGGGCCCTAGT 62.735 60.000 25.93 12.21 0.00 2.57
121 122 2.351276 GTGTGTGGGGCCCTAGTG 59.649 66.667 25.93 0.00 0.00 2.74
122 123 2.205749 TGTGTGGGGCCCTAGTGA 59.794 61.111 25.93 0.00 0.00 3.41
123 124 2.221299 TGTGTGGGGCCCTAGTGAC 61.221 63.158 25.93 13.87 0.00 3.67
124 125 2.609610 TGTGGGGCCCTAGTGACC 60.610 66.667 25.93 3.29 0.00 4.02
125 126 2.285442 GTGGGGCCCTAGTGACCT 60.285 66.667 25.93 0.00 0.00 3.85
126 127 2.040606 TGGGGCCCTAGTGACCTC 59.959 66.667 25.93 1.06 0.00 3.85
127 128 2.768769 GGGGCCCTAGTGACCTCC 60.769 72.222 24.38 0.00 0.00 4.30
128 129 2.040606 GGGCCCTAGTGACCTCCA 59.959 66.667 17.04 0.00 0.00 3.86
129 130 2.368011 GGGCCCTAGTGACCTCCAC 61.368 68.421 17.04 0.00 46.03 4.02
137 138 1.004918 GTGACCTCCACAACCCTCG 60.005 63.158 0.00 0.00 45.03 4.63
138 139 1.152419 TGACCTCCACAACCCTCGA 60.152 57.895 0.00 0.00 0.00 4.04
139 140 0.761323 TGACCTCCACAACCCTCGAA 60.761 55.000 0.00 0.00 0.00 3.71
140 141 0.037232 GACCTCCACAACCCTCGAAG 60.037 60.000 0.00 0.00 0.00 3.79
141 142 1.376037 CCTCCACAACCCTCGAAGC 60.376 63.158 0.00 0.00 0.00 3.86
142 143 1.371183 CTCCACAACCCTCGAAGCA 59.629 57.895 0.00 0.00 0.00 3.91
143 144 0.951040 CTCCACAACCCTCGAAGCAC 60.951 60.000 0.00 0.00 0.00 4.40
144 145 1.966451 CCACAACCCTCGAAGCACC 60.966 63.158 0.00 0.00 0.00 5.01
145 146 1.227823 CACAACCCTCGAAGCACCA 60.228 57.895 0.00 0.00 0.00 4.17
146 147 1.227853 ACAACCCTCGAAGCACCAC 60.228 57.895 0.00 0.00 0.00 4.16
147 148 1.227823 CAACCCTCGAAGCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
148 149 0.817634 CAACCCTCGAAGCACCACAA 60.818 55.000 0.00 0.00 0.00 3.33
149 150 0.818040 AACCCTCGAAGCACCACAAC 60.818 55.000 0.00 0.00 0.00 3.32
150 151 2.317609 CCCTCGAAGCACCACAACG 61.318 63.158 0.00 0.00 0.00 4.10
151 152 2.551270 CTCGAAGCACCACAACGC 59.449 61.111 0.00 0.00 0.00 4.84
152 153 1.956170 CTCGAAGCACCACAACGCT 60.956 57.895 0.00 0.00 41.20 5.07
155 156 4.234019 AAGCACCACAACGCTTCA 57.766 50.000 0.00 0.00 45.10 3.02
156 157 2.487918 AAGCACCACAACGCTTCAA 58.512 47.368 0.00 0.00 45.10 2.69
157 158 1.032014 AAGCACCACAACGCTTCAAT 58.968 45.000 0.00 0.00 45.10 2.57
158 159 1.032014 AGCACCACAACGCTTCAATT 58.968 45.000 0.00 0.00 33.81 2.32
159 160 1.001378 AGCACCACAACGCTTCAATTC 60.001 47.619 0.00 0.00 33.81 2.17
160 161 1.673760 CACCACAACGCTTCAATTCG 58.326 50.000 0.00 0.00 0.00 3.34
161 162 1.262950 CACCACAACGCTTCAATTCGA 59.737 47.619 0.00 0.00 0.00 3.71
162 163 1.531149 ACCACAACGCTTCAATTCGAG 59.469 47.619 0.00 0.00 0.00 4.04
163 164 1.135972 CCACAACGCTTCAATTCGAGG 60.136 52.381 0.00 0.00 0.00 4.63
164 165 1.135972 CACAACGCTTCAATTCGAGGG 60.136 52.381 0.00 1.43 0.00 4.30
165 166 1.270625 ACAACGCTTCAATTCGAGGGA 60.271 47.619 8.19 0.00 0.00 4.20
166 167 1.394917 CAACGCTTCAATTCGAGGGAG 59.605 52.381 8.19 0.00 0.00 4.30
167 168 0.741221 ACGCTTCAATTCGAGGGAGC 60.741 55.000 8.19 4.50 0.00 4.70
168 169 0.460987 CGCTTCAATTCGAGGGAGCT 60.461 55.000 10.99 0.00 0.00 4.09
169 170 1.743996 GCTTCAATTCGAGGGAGCTT 58.256 50.000 6.80 0.00 0.00 3.74
170 171 2.738643 CGCTTCAATTCGAGGGAGCTTA 60.739 50.000 10.99 0.00 0.00 3.09
171 172 2.869192 GCTTCAATTCGAGGGAGCTTAG 59.131 50.000 6.80 0.00 0.00 2.18
172 173 3.680196 GCTTCAATTCGAGGGAGCTTAGT 60.680 47.826 6.80 0.00 0.00 2.24
173 174 4.441634 GCTTCAATTCGAGGGAGCTTAGTA 60.442 45.833 6.80 0.00 0.00 1.82
174 175 5.740513 GCTTCAATTCGAGGGAGCTTAGTAT 60.741 44.000 6.80 0.00 0.00 2.12
175 176 5.455056 TCAATTCGAGGGAGCTTAGTATC 57.545 43.478 0.00 0.00 0.00 2.24
176 177 5.141182 TCAATTCGAGGGAGCTTAGTATCT 58.859 41.667 0.00 0.00 0.00 1.98
177 178 5.241949 TCAATTCGAGGGAGCTTAGTATCTC 59.758 44.000 0.00 0.00 0.00 2.75
178 179 4.440826 TTCGAGGGAGCTTAGTATCTCT 57.559 45.455 0.00 0.00 0.00 3.10
179 180 5.563876 TTCGAGGGAGCTTAGTATCTCTA 57.436 43.478 0.00 0.00 0.00 2.43
180 181 5.765576 TCGAGGGAGCTTAGTATCTCTAT 57.234 43.478 0.00 0.00 0.00 1.98
181 182 6.870895 TCGAGGGAGCTTAGTATCTCTATA 57.129 41.667 0.00 0.00 0.00 1.31
182 183 6.880484 TCGAGGGAGCTTAGTATCTCTATAG 58.120 44.000 0.00 0.00 0.00 1.31
279 280 1.606350 GACGGTTGAAGCACTCGTCG 61.606 60.000 0.00 0.00 40.22 5.12
289 290 1.132643 AGCACTCGTCGGTGTAGAATC 59.867 52.381 13.14 0.00 39.21 2.52
296 297 2.094906 CGTCGGTGTAGAATCTGTCCAA 60.095 50.000 0.00 0.00 0.00 3.53
312 313 5.661312 TCTGTCCAACCTTGCATATAGTAGT 59.339 40.000 0.00 0.00 0.00 2.73
330 331 6.174720 AGTAGTGGATCAAGTTGAACTCAA 57.825 37.500 10.14 0.00 0.00 3.02
344 345 5.964958 TGAACTCAATCAAGAAATGACCC 57.035 39.130 0.00 0.00 41.93 4.46
372 373 2.306847 TCTTGGACCAAGCAAAGAACC 58.693 47.619 26.79 0.00 40.84 3.62
458 459 1.949799 AGGTCTGACAGAGGCATTCT 58.050 50.000 5.10 0.00 36.25 2.40
461 462 1.474478 GTCTGACAGAGGCATTCTCGA 59.526 52.381 5.10 0.00 46.82 4.04
468 469 4.074970 ACAGAGGCATTCTCGATTGTTTT 58.925 39.130 0.00 0.00 46.82 2.43
497 580 0.248539 CTAGTCAGAACGGGCGCTAC 60.249 60.000 7.64 0.00 0.00 3.58
543 626 4.199310 ACAAGTGGCGTATGATATGCTTT 58.801 39.130 15.53 6.28 40.50 3.51
558 641 3.890527 CTTTAGGAGCATGGGCACT 57.109 52.632 0.00 0.00 44.61 4.40
565 648 2.359850 GCATGGGCACTTCGTGGA 60.360 61.111 0.00 0.00 40.72 4.02
600 683 1.671379 GACCAGCTTCCGTGGGAAC 60.671 63.158 0.00 0.00 36.71 3.62
648 731 1.746615 CAGGGGAAGATGGTGCACG 60.747 63.158 11.45 0.00 0.00 5.34
705 788 5.375417 TGAACAGTAGTTGCATGGAATTG 57.625 39.130 1.94 2.90 38.30 2.32
713 796 6.765036 AGTAGTTGCATGGAATTGTCTATGAG 59.235 38.462 1.94 0.00 43.58 2.90
721 804 0.394565 ATTGTCTATGAGAGGGGCGC 59.605 55.000 0.00 0.00 0.00 6.53
722 805 2.016393 TTGTCTATGAGAGGGGCGCG 62.016 60.000 0.00 0.00 0.00 6.86
723 806 3.606662 TCTATGAGAGGGGCGCGC 61.607 66.667 25.94 25.94 0.00 6.86
737 820 2.202878 GCGCGGAGGCTTGATGTA 60.203 61.111 8.83 0.00 36.88 2.29
743 826 2.866762 GCGGAGGCTTGATGTAGTTTAG 59.133 50.000 0.00 0.00 35.83 1.85
749 832 5.026790 AGGCTTGATGTAGTTTAGACCTCT 58.973 41.667 0.00 0.00 0.00 3.69
944 1028 3.597002 CCAGCCATAGATGGGAACGGG 62.597 61.905 10.55 0.80 46.32 5.28
983 1068 6.653740 CGCGTATATATATGTGGAGGGATCTA 59.346 42.308 15.10 0.00 0.00 1.98
1076 1165 1.078143 GAGGACATGGCTGGTGGTC 60.078 63.158 0.00 0.00 0.00 4.02
1164 1253 2.355445 TATGAAGCGCTCGCAGGAGG 62.355 60.000 12.06 0.00 44.88 4.30
1282 1371 3.732219 CGTGCGTTTAGTTAGACAAGACA 59.268 43.478 0.00 0.00 0.00 3.41
1288 1377 2.814280 AGTTAGACAAGACACGTGGG 57.186 50.000 21.57 8.78 0.00 4.61
1509 1601 9.507280 ACTGATTGATTTCTTATTATTTGCGTG 57.493 29.630 0.00 0.00 0.00 5.34
1804 1900 7.826260 TTCAAAGTGTGAGAAAATTCCAAAC 57.174 32.000 0.00 0.00 37.61 2.93
1810 1906 8.791327 AGTGTGAGAAAATTCCAAACAAAAAT 57.209 26.923 7.32 0.00 0.00 1.82
1827 1923 3.338818 AAATTTGGCGCATACATCTCG 57.661 42.857 10.83 0.00 0.00 4.04
1835 1931 3.061295 GGCGCATACATCTCGACATTATG 59.939 47.826 10.83 0.00 0.00 1.90
1836 1932 3.675225 GCGCATACATCTCGACATTATGT 59.325 43.478 0.30 0.00 37.58 2.29
1837 1933 4.433413 GCGCATACATCTCGACATTATGTG 60.433 45.833 1.24 8.83 35.54 3.21
1847 1943 7.090953 TCTCGACATTATGTGTGTACATGTA 57.909 36.000 1.24 0.08 46.63 2.29
1861 1957 5.873164 GTGTACATGTAAAGGTTCGGAGAAT 59.127 40.000 7.25 0.00 45.90 2.40
1863 1959 7.009907 GTGTACATGTAAAGGTTCGGAGAATAC 59.990 40.741 7.25 0.00 45.90 1.89
1865 1961 5.046159 ACATGTAAAGGTTCGGAGAATACCA 60.046 40.000 0.00 0.00 45.90 3.25
1868 1964 4.360951 AAAGGTTCGGAGAATACCAACA 57.639 40.909 0.00 0.00 45.90 3.33
1873 1969 6.478129 AGGTTCGGAGAATACCAACATTTTA 58.522 36.000 0.00 0.00 45.90 1.52
1949 2047 7.227049 ACACCGGATTTTATCTTTTTCACAT 57.773 32.000 9.46 0.00 0.00 3.21
1952 2050 8.240682 CACCGGATTTTATCTTTTTCACATGTA 58.759 33.333 9.46 0.00 0.00 2.29
1965 2063 7.922505 TTTTCACATGTAACACATAAGTTGC 57.077 32.000 0.00 0.00 36.53 4.17
1993 2091 1.531149 CCGCGAAATGACTTTGTGAGT 59.469 47.619 8.23 0.00 42.70 3.41
1999 2097 6.241385 GCGAAATGACTTTGTGAGTATGTAC 58.759 40.000 0.00 0.00 39.19 2.90
2022 2120 0.595053 ATCGAGATGTACGCGCCAAG 60.595 55.000 5.73 0.00 41.27 3.61
2031 2129 0.308376 TACGCGCCAAGTTTTTGTCC 59.692 50.000 5.73 0.00 32.21 4.02
2033 2131 1.660264 GCGCCAAGTTTTTGTCCGG 60.660 57.895 0.00 0.00 32.21 5.14
2035 2133 0.382515 CGCCAAGTTTTTGTCCGGAA 59.617 50.000 5.23 0.00 32.21 4.30
2119 2217 2.032178 GTGCCGAAATGCCATTCTCTAC 59.968 50.000 0.00 0.00 0.00 2.59
2120 2218 2.288666 GCCGAAATGCCATTCTCTACA 58.711 47.619 0.00 0.00 0.00 2.74
2121 2219 2.032178 GCCGAAATGCCATTCTCTACAC 59.968 50.000 0.00 0.00 0.00 2.90
2122 2220 3.270027 CCGAAATGCCATTCTCTACACA 58.730 45.455 0.00 0.00 0.00 3.72
2400 2523 1.341877 CCCCTACATGATTTGCACCCA 60.342 52.381 0.00 0.00 0.00 4.51
2492 2617 3.249799 TCAACAAGATGTTAGTTGCACCG 59.750 43.478 10.82 0.00 38.77 4.94
2513 2638 3.559655 CGACACCAACACAATCTCAAGAA 59.440 43.478 0.00 0.00 0.00 2.52
2531 2656 9.948964 TCTCAAGAATTATTCAAGACATCAAGA 57.051 29.630 7.74 0.00 0.00 3.02
2638 2764 1.282157 ACCCAGGCAACAAGATAGGTC 59.718 52.381 0.00 0.00 41.41 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.757227 AGCACTTATTAAAATTTGTGCACTTTA 57.243 25.926 23.13 11.31 42.91 1.85
15 16 8.661352 AGCACTTATTAAAATTTGTGCACTTT 57.339 26.923 23.13 12.34 42.91 2.66
16 17 9.757227 TTAGCACTTATTAAAATTTGTGCACTT 57.243 25.926 23.13 5.94 42.91 3.16
17 18 9.927668 ATTAGCACTTATTAAAATTTGTGCACT 57.072 25.926 23.13 11.55 42.91 4.40
18 19 9.956797 CATTAGCACTTATTAAAATTTGTGCAC 57.043 29.630 23.13 10.75 42.91 4.57
19 20 9.920133 TCATTAGCACTTATTAAAATTTGTGCA 57.080 25.926 23.13 10.16 42.91 4.57
100 101 1.535930 TAGGGCCCCACACACGTAA 60.536 57.895 21.43 0.00 0.00 3.18
101 102 1.985662 CTAGGGCCCCACACACGTA 60.986 63.158 21.43 0.00 0.00 3.57
102 103 3.319198 CTAGGGCCCCACACACGT 61.319 66.667 21.43 0.00 0.00 4.49
103 104 3.319198 ACTAGGGCCCCACACACG 61.319 66.667 21.43 1.24 0.00 4.49
104 105 2.221299 TCACTAGGGCCCCACACAC 61.221 63.158 21.43 0.00 0.00 3.82
105 106 2.205749 TCACTAGGGCCCCACACA 59.794 61.111 21.43 0.00 0.00 3.72
106 107 2.669240 GTCACTAGGGCCCCACAC 59.331 66.667 21.43 4.49 0.00 3.82
107 108 2.609610 GGTCACTAGGGCCCCACA 60.610 66.667 21.43 2.52 0.00 4.17
108 109 2.285442 AGGTCACTAGGGCCCCAC 60.285 66.667 21.43 7.56 0.00 4.61
109 110 2.040606 GAGGTCACTAGGGCCCCA 59.959 66.667 21.43 2.83 0.00 4.96
110 111 2.768769 GGAGGTCACTAGGGCCCC 60.769 72.222 21.43 0.29 0.00 5.80
111 112 2.040606 TGGAGGTCACTAGGGCCC 59.959 66.667 16.46 16.46 0.00 5.80
112 113 1.198759 TTGTGGAGGTCACTAGGGCC 61.199 60.000 0.00 0.00 46.20 5.80
113 114 0.036294 GTTGTGGAGGTCACTAGGGC 60.036 60.000 0.00 0.00 46.20 5.19
114 115 0.613777 GGTTGTGGAGGTCACTAGGG 59.386 60.000 0.00 0.00 46.20 3.53
115 116 0.613777 GGGTTGTGGAGGTCACTAGG 59.386 60.000 0.00 0.00 46.20 3.02
116 117 1.550976 GAGGGTTGTGGAGGTCACTAG 59.449 57.143 0.00 0.00 46.20 2.57
117 118 1.640917 GAGGGTTGTGGAGGTCACTA 58.359 55.000 0.00 0.00 46.20 2.74
118 119 1.472662 CGAGGGTTGTGGAGGTCACT 61.473 60.000 0.00 0.00 46.20 3.41
119 120 1.004918 CGAGGGTTGTGGAGGTCAC 60.005 63.158 0.00 0.00 46.23 3.67
120 121 0.761323 TTCGAGGGTTGTGGAGGTCA 60.761 55.000 0.00 0.00 0.00 4.02
121 122 0.037232 CTTCGAGGGTTGTGGAGGTC 60.037 60.000 0.00 0.00 0.00 3.85
122 123 2.058675 CTTCGAGGGTTGTGGAGGT 58.941 57.895 0.00 0.00 0.00 3.85
123 124 1.376037 GCTTCGAGGGTTGTGGAGG 60.376 63.158 0.00 0.00 0.00 4.30
124 125 0.951040 GTGCTTCGAGGGTTGTGGAG 60.951 60.000 0.00 0.00 0.00 3.86
125 126 1.070786 GTGCTTCGAGGGTTGTGGA 59.929 57.895 0.00 0.00 0.00 4.02
126 127 1.966451 GGTGCTTCGAGGGTTGTGG 60.966 63.158 0.00 0.00 0.00 4.17
127 128 1.227823 TGGTGCTTCGAGGGTTGTG 60.228 57.895 0.00 0.00 0.00 3.33
128 129 1.227853 GTGGTGCTTCGAGGGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
129 130 0.817634 TTGTGGTGCTTCGAGGGTTG 60.818 55.000 0.00 0.00 0.00 3.77
130 131 0.818040 GTTGTGGTGCTTCGAGGGTT 60.818 55.000 0.00 0.00 0.00 4.11
131 132 1.227853 GTTGTGGTGCTTCGAGGGT 60.228 57.895 0.00 0.00 0.00 4.34
132 133 2.317609 CGTTGTGGTGCTTCGAGGG 61.318 63.158 0.00 0.00 0.00 4.30
133 134 2.954753 GCGTTGTGGTGCTTCGAGG 61.955 63.158 0.00 0.00 0.00 4.63
134 135 1.956170 AGCGTTGTGGTGCTTCGAG 60.956 57.895 0.00 0.00 38.57 4.04
135 136 2.108157 AGCGTTGTGGTGCTTCGA 59.892 55.556 0.00 0.00 38.57 3.71
139 140 1.001378 GAATTGAAGCGTTGTGGTGCT 60.001 47.619 0.00 0.00 44.97 4.40
140 141 1.408422 GAATTGAAGCGTTGTGGTGC 58.592 50.000 0.00 0.00 0.00 5.01
141 142 1.262950 TCGAATTGAAGCGTTGTGGTG 59.737 47.619 0.00 0.00 0.00 4.17
142 143 1.531149 CTCGAATTGAAGCGTTGTGGT 59.469 47.619 0.00 0.00 0.00 4.16
143 144 1.135972 CCTCGAATTGAAGCGTTGTGG 60.136 52.381 0.00 0.00 0.00 4.17
144 145 1.135972 CCCTCGAATTGAAGCGTTGTG 60.136 52.381 0.00 0.00 0.00 3.33
145 146 1.156736 CCCTCGAATTGAAGCGTTGT 58.843 50.000 0.00 0.00 0.00 3.32
146 147 1.394917 CTCCCTCGAATTGAAGCGTTG 59.605 52.381 0.00 0.00 0.00 4.10
147 148 1.726853 CTCCCTCGAATTGAAGCGTT 58.273 50.000 0.00 0.00 0.00 4.84
148 149 0.741221 GCTCCCTCGAATTGAAGCGT 60.741 55.000 0.00 0.00 0.00 5.07
149 150 0.460987 AGCTCCCTCGAATTGAAGCG 60.461 55.000 0.00 0.00 0.00 4.68
150 151 1.743996 AAGCTCCCTCGAATTGAAGC 58.256 50.000 0.00 0.00 0.00 3.86
151 152 4.130286 ACTAAGCTCCCTCGAATTGAAG 57.870 45.455 0.00 0.00 0.00 3.02
152 153 5.598830 AGATACTAAGCTCCCTCGAATTGAA 59.401 40.000 0.00 0.00 0.00 2.69
153 154 5.141182 AGATACTAAGCTCCCTCGAATTGA 58.859 41.667 0.00 0.00 0.00 2.57
154 155 5.242838 AGAGATACTAAGCTCCCTCGAATTG 59.757 44.000 0.00 0.00 39.02 2.32
155 156 5.390387 AGAGATACTAAGCTCCCTCGAATT 58.610 41.667 0.00 0.00 39.02 2.17
156 157 4.993028 AGAGATACTAAGCTCCCTCGAAT 58.007 43.478 0.00 0.00 39.02 3.34
157 158 4.440826 AGAGATACTAAGCTCCCTCGAA 57.559 45.455 0.00 0.00 39.02 3.71
158 159 5.765576 ATAGAGATACTAAGCTCCCTCGA 57.234 43.478 0.00 0.00 39.02 4.04
159 160 6.880484 TCTATAGAGATACTAAGCTCCCTCG 58.120 44.000 0.00 0.00 39.02 4.63
160 161 8.491134 TCATCTATAGAGATACTAAGCTCCCTC 58.509 40.741 8.70 0.00 40.68 4.30
161 162 8.272173 GTCATCTATAGAGATACTAAGCTCCCT 58.728 40.741 8.70 0.00 40.68 4.20
162 163 8.050325 TGTCATCTATAGAGATACTAAGCTCCC 58.950 40.741 8.70 0.00 40.68 4.30
163 164 8.889717 GTGTCATCTATAGAGATACTAAGCTCC 58.110 40.741 8.70 0.00 40.68 4.70
164 165 9.667107 AGTGTCATCTATAGAGATACTAAGCTC 57.333 37.037 19.99 0.00 40.68 4.09
165 166 9.448438 CAGTGTCATCTATAGAGATACTAAGCT 57.552 37.037 20.49 9.72 40.68 3.74
166 167 8.673711 CCAGTGTCATCTATAGAGATACTAAGC 58.326 40.741 20.49 8.39 40.68 3.09
167 168 9.733556 ACCAGTGTCATCTATAGAGATACTAAG 57.266 37.037 20.49 18.07 40.68 2.18
170 171 7.827236 GCTACCAGTGTCATCTATAGAGATACT 59.173 40.741 17.71 17.71 40.68 2.12
171 172 7.827236 AGCTACCAGTGTCATCTATAGAGATAC 59.173 40.741 8.70 12.82 40.68 2.24
172 173 7.923461 AGCTACCAGTGTCATCTATAGAGATA 58.077 38.462 8.70 2.22 40.68 1.98
173 174 6.789268 AGCTACCAGTGTCATCTATAGAGAT 58.211 40.000 8.70 0.00 43.63 2.75
174 175 6.043822 AGAGCTACCAGTGTCATCTATAGAGA 59.956 42.308 8.70 3.51 35.71 3.10
175 176 6.237901 AGAGCTACCAGTGTCATCTATAGAG 58.762 44.000 8.70 1.17 0.00 2.43
176 177 6.194285 AGAGCTACCAGTGTCATCTATAGA 57.806 41.667 4.57 4.57 0.00 1.98
177 178 6.892658 AAGAGCTACCAGTGTCATCTATAG 57.107 41.667 0.00 0.00 0.00 1.31
178 179 7.445707 CACTAAGAGCTACCAGTGTCATCTATA 59.554 40.741 11.20 0.00 34.91 1.31
179 180 6.264292 CACTAAGAGCTACCAGTGTCATCTAT 59.736 42.308 11.20 0.00 34.91 1.98
180 181 5.590663 CACTAAGAGCTACCAGTGTCATCTA 59.409 44.000 11.20 0.00 34.91 1.98
181 182 4.400884 CACTAAGAGCTACCAGTGTCATCT 59.599 45.833 11.20 0.00 34.91 2.90
182 183 4.399618 TCACTAAGAGCTACCAGTGTCATC 59.600 45.833 16.42 0.00 39.50 2.92
220 221 4.694509 GCAACATGAGACTGAAGATCAACT 59.305 41.667 0.00 0.00 0.00 3.16
279 280 3.983044 AGGTTGGACAGATTCTACACC 57.017 47.619 0.00 0.00 0.00 4.16
289 290 5.755375 CACTACTATATGCAAGGTTGGACAG 59.245 44.000 0.00 0.00 0.00 3.51
296 297 6.327626 ACTTGATCCACTACTATATGCAAGGT 59.672 38.462 0.00 0.00 35.71 3.50
312 313 6.298361 TCTTGATTGAGTTCAACTTGATCCA 58.702 36.000 10.11 1.61 38.86 3.41
330 331 6.653989 AGAAGTAATCGGGTCATTTCTTGAT 58.346 36.000 0.00 0.00 36.54 2.57
344 345 3.334691 TGCTTGGTCCAAGAAGTAATCG 58.665 45.455 31.94 6.58 43.42 3.34
372 373 0.530744 ATGAAGCAGCAACATGCCAG 59.469 50.000 0.00 0.00 46.52 4.85
468 469 5.297776 GCCCGTTCTGACTAGTACTACATTA 59.702 44.000 0.00 0.00 0.00 1.90
503 586 3.685139 TGTTGGTCAGTTCAGAGATCC 57.315 47.619 0.00 0.00 0.00 3.36
543 626 1.264749 ACGAAGTGCCCATGCTCCTA 61.265 55.000 0.00 0.00 42.51 2.94
558 641 1.228894 ACCTCTGCTCCTCCACGAA 60.229 57.895 0.00 0.00 0.00 3.85
600 683 2.574322 CAAACGAACGAGGCAAATCAG 58.426 47.619 0.14 0.00 0.00 2.90
705 788 2.336809 CGCGCCCCTCTCATAGAC 59.663 66.667 0.00 0.00 0.00 2.59
721 804 0.460284 AACTACATCAAGCCTCCGCG 60.460 55.000 0.00 0.00 41.18 6.46
722 805 1.739067 AAACTACATCAAGCCTCCGC 58.261 50.000 0.00 0.00 0.00 5.54
723 806 4.113354 GTCTAAACTACATCAAGCCTCCG 58.887 47.826 0.00 0.00 0.00 4.63
724 807 4.162509 AGGTCTAAACTACATCAAGCCTCC 59.837 45.833 0.00 0.00 0.00 4.30
743 826 7.158021 AGCAGACTATTTATTGCATAGAGGTC 58.842 38.462 0.00 0.00 38.97 3.85
854 938 4.154015 TGACAATTCATTCACGTGTGGATC 59.846 41.667 16.51 6.80 0.00 3.36
957 1041 3.317149 TCCCTCCACATATATATACGCGC 59.683 47.826 5.73 0.00 0.00 6.86
983 1068 4.075793 TGCTAGGCCGACTCCCCT 62.076 66.667 0.00 0.00 35.22 4.79
1259 1348 2.727798 TCTTGTCTAACTAAACGCACGC 59.272 45.455 0.00 0.00 0.00 5.34
1263 1352 3.732721 ACGTGTCTTGTCTAACTAAACGC 59.267 43.478 0.00 0.00 32.06 4.84
1267 1356 3.638160 ACCCACGTGTCTTGTCTAACTAA 59.362 43.478 15.65 0.00 0.00 2.24
1282 1371 1.618837 CTAGCTGCCATATACCCACGT 59.381 52.381 0.00 0.00 0.00 4.49
1288 1377 4.559862 ATGGAACCTAGCTGCCATATAC 57.440 45.455 0.00 0.00 39.25 1.47
1509 1601 5.041287 ACAGATACACACATACATGTACGC 58.959 41.667 7.96 0.00 39.39 4.42
1574 1670 4.082517 TCCGCAGAGAAGCAGCTATAATAG 60.083 45.833 0.00 0.00 0.00 1.73
1736 1832 7.484641 CACCAACTGATTTCCGTACAAAATATG 59.515 37.037 3.82 3.45 0.00 1.78
1747 1843 0.804989 GGAGCACCAACTGATTTCCG 59.195 55.000 0.00 0.00 35.97 4.30
1804 1900 4.027458 CGAGATGTATGCGCCAAATTTTTG 60.027 41.667 4.18 0.00 37.90 2.44
1810 1906 1.286501 GTCGAGATGTATGCGCCAAA 58.713 50.000 4.18 0.00 0.00 3.28
1814 1910 3.675225 ACATAATGTCGAGATGTATGCGC 59.325 43.478 17.01 0.00 32.07 6.09
1827 1923 8.263940 ACCTTTACATGTACACACATAATGTC 57.736 34.615 4.68 0.00 43.73 3.06
1835 1931 4.309099 TCCGAACCTTTACATGTACACAC 58.691 43.478 4.68 0.00 0.00 3.82
1836 1932 4.281435 TCTCCGAACCTTTACATGTACACA 59.719 41.667 4.68 0.00 0.00 3.72
1837 1933 4.813027 TCTCCGAACCTTTACATGTACAC 58.187 43.478 4.68 0.00 0.00 2.90
1847 1943 4.360951 TGTTGGTATTCTCCGAACCTTT 57.639 40.909 0.00 0.00 34.23 3.11
1861 1957 5.777802 CACAAGGCACATAAAATGTTGGTA 58.222 37.500 0.00 0.00 42.70 3.25
1863 1959 3.432933 GCACAAGGCACATAAAATGTTGG 59.567 43.478 0.00 0.00 42.70 3.77
1949 2047 3.128852 ACCGGCAACTTATGTGTTACA 57.871 42.857 0.00 0.00 0.00 2.41
1952 2050 3.243602 GGAAAACCGGCAACTTATGTGTT 60.244 43.478 0.00 0.00 0.00 3.32
1965 2063 0.453782 GTCATTTCGCGGAAAACCGG 60.454 55.000 2.72 0.00 35.11 5.28
1976 2074 7.346208 TGTACATACTCACAAAGTCATTTCG 57.654 36.000 0.00 0.00 39.55 3.46
1993 2091 6.245724 CGCGTACATCTCGATATTGTACATA 58.754 40.000 22.09 0.00 43.67 2.29
1999 2097 1.649171 GGCGCGTACATCTCGATATTG 59.351 52.381 8.43 0.00 0.00 1.90
2103 2201 6.203723 GGATACTGTGTAGAGAATGGCATTTC 59.796 42.308 14.93 13.03 0.00 2.17
2137 2235 2.307392 TGGGGCATGTGTGTGTATAACT 59.693 45.455 0.00 0.00 0.00 2.24
2220 2320 5.387788 TGACATGCCCATAATAAGCAGATT 58.612 37.500 0.00 0.00 40.40 2.40
2227 2327 7.335673 CGTAATGGTATGACATGCCCATAATAA 59.664 37.037 18.68 0.00 36.69 1.40
2228 2328 6.821160 CGTAATGGTATGACATGCCCATAATA 59.179 38.462 18.68 7.79 36.69 0.98
2229 2329 5.647658 CGTAATGGTATGACATGCCCATAAT 59.352 40.000 18.68 3.97 36.69 1.28
2437 2560 3.486383 TCGCTTTGTCCAGAAAAAGGAT 58.514 40.909 11.39 0.00 37.52 3.24
2440 2563 9.573133 AAATATATTCGCTTTGTCCAGAAAAAG 57.427 29.630 6.02 6.02 36.64 2.27
2492 2617 5.695851 ATTCTTGAGATTGTGTTGGTGTC 57.304 39.130 0.00 0.00 0.00 3.67
2513 2638 6.608405 TGGGCATTCTTGATGTCTTGAATAAT 59.392 34.615 0.00 0.00 40.30 1.28
2531 2656 8.083828 TGTATATTAATTTGGTTGTGGGCATT 57.916 30.769 0.00 0.00 0.00 3.56
2561 2686 4.429108 CAGTGGTTTCGTTGGTCATTTTT 58.571 39.130 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.