Multiple sequence alignment - TraesCS6A01G395200

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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 TraesCS6A01G395200 chr6A 100.000 2708 0 0 1 2708 608126808 608124101 0.000000e+00 5001
1 TraesCS6A01G395200 chr6B 92.884 2122 129 12 187 2294 703349233 703347120 0.000000e+00 3062
2 TraesCS6A01G395200 chr6B 90.975 1806 107 23 184 1962 703307674 703305898 0.000000e+00 2381
3 TraesCS6A01G395200 chr6B 96.651 418 10 4 2292 2708 703343695 703343281 0.000000e+00 691
4 TraesCS6A01G395200 chr6B 85.593 118 16 1 1 118 646438021 646438137 3.660000e-24 122
5 TraesCS6A01G395200 chr6B 83.051 118 19 1 1 118 166254433 166254317 3.690000e-19 106
6 TraesCS6A01G395200 chr6D 92.647 1768 93 13 929 2685 461461421 461459680 0.000000e+00 2510
7 TraesCS6A01G395200 chr6D 87.936 746 57 16 184 918 461462217 461461494 0.000000e+00 848
8 TraesCS6A01G395200 chr7D 85.864 382 47 6 391 769 37116214 37115837 1.510000e-107 399
9 TraesCS6A01G395200 chr7D 86.667 120 14 2 1 120 631387423 631387540 6.080000e-27 132
10 TraesCS6A01G395200 chr2D 83.246 382 53 8 390 769 577685743 577685371 9.290000e-90 340
11 TraesCS6A01G395200 chr2B 81.414 382 57 10 392 769 694543576 694543947 1.580000e-77 300
12 TraesCS6A01G395200 chr2A 86.809 235 29 2 390 623 715634507 715634740 7.440000e-66 261
13 TraesCS6A01G395200 chr2A 74.430 395 81 16 385 769 718105831 718106215 4.670000e-33 152
14 TraesCS6A01G395200 chr3D 73.711 388 84 15 391 769 594972914 594972536 4.700000e-28 135
15 TraesCS6A01G395200 chr3B 84.874 119 16 2 1 118 455026224 455026107 4.740000e-23 119
16 TraesCS6A01G395200 chr3B 85.981 107 15 0 12 118 479851219 479851113 6.130000e-22 115
17 TraesCS6A01G395200 chr3B 83.051 118 20 0 1 118 427962429 427962312 1.030000e-19 108
18 TraesCS6A01G395200 chrUn 87.255 102 11 2 18 118 325273434 325273534 6.130000e-22 115
19 TraesCS6A01G395200 chrUn 87.255 102 11 2 18 118 340616542 340616642 6.130000e-22 115
20 TraesCS6A01G395200 chrUn 82.443 131 11 8 1 123 137866073 137866199 1.330000e-18 104


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 TraesCS6A01G395200 chr6A 608124101 608126808 2707 True 5001.0 5001 100.0000 1 2708 1 chr6A.!!$R1 2707
1 TraesCS6A01G395200 chr6B 703305898 703307674 1776 True 2381.0 2381 90.9750 184 1962 1 chr6B.!!$R2 1778
2 TraesCS6A01G395200 chr6B 703343281 703349233 5952 True 1876.5 3062 94.7675 187 2708 2 chr6B.!!$R3 2521
3 TraesCS6A01G395200 chr6D 461459680 461462217 2537 True 1679.0 2510 90.2915 184 2685 2 chr6D.!!$R1 2501

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
137 138 0.036858 GCTTCTCGCTGGAGGAACTT 60.037 55.0 0.0 0.0 40.85 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1898 0.675083 CATGTGCAGCAAAACCAGGA 59.325 50.0 0.0 0.0 0.0 3.86 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
61 62 9.212641 AGTTATAGTGATCACATGTCATATTGC 57.787 33.333 27.02 10.74 0.00 3.56
62 63 9.212641 GTTATAGTGATCACATGTCATATTGCT 57.787 33.333 27.02 4.73 0.00 3.91
63 64 9.783081 TTATAGTGATCACATGTCATATTGCTT 57.217 29.630 27.02 4.30 0.00 3.91
65 66 9.955102 ATAGTGATCACATGTCATATTGCTTAT 57.045 29.630 27.02 8.37 0.00 1.73
66 67 8.320396 AGTGATCACATGTCATATTGCTTATC 57.680 34.615 27.02 0.00 0.00 1.75
67 68 7.935210 AGTGATCACATGTCATATTGCTTATCA 59.065 33.333 27.02 0.00 0.00 2.15
68 69 8.562052 GTGATCACATGTCATATTGCTTATCAA 58.438 33.333 21.07 0.00 39.32 2.57
69 70 9.292195 TGATCACATGTCATATTGCTTATCAAT 57.708 29.630 0.00 0.00 46.48 2.57
80 81 9.627657 CATATTGCTTATCAATTTTTCTTTGCG 57.372 29.630 0.00 0.00 42.48 4.85
81 82 7.887996 ATTGCTTATCAATTTTTCTTTGCGA 57.112 28.000 0.00 0.00 42.48 5.10
82 83 6.689178 TGCTTATCAATTTTTCTTTGCGAC 57.311 33.333 0.00 0.00 0.00 5.19
83 84 5.341993 TGCTTATCAATTTTTCTTTGCGACG 59.658 36.000 0.00 0.00 0.00 5.12
84 85 5.220024 GCTTATCAATTTTTCTTTGCGACGG 60.220 40.000 0.00 0.00 0.00 4.79
85 86 3.972950 TCAATTTTTCTTTGCGACGGA 57.027 38.095 0.00 0.00 0.00 4.69
86 87 3.623863 TCAATTTTTCTTTGCGACGGAC 58.376 40.909 0.00 0.00 0.00 4.79
87 88 2.699251 ATTTTTCTTTGCGACGGACC 57.301 45.000 0.00 0.00 0.00 4.46
88 89 1.380524 TTTTTCTTTGCGACGGACCA 58.619 45.000 0.00 0.00 0.00 4.02
89 90 0.658897 TTTTCTTTGCGACGGACCAC 59.341 50.000 0.00 0.00 0.00 4.16
90 91 1.161563 TTTCTTTGCGACGGACCACC 61.162 55.000 0.00 0.00 0.00 4.61
91 92 2.999739 TTCTTTGCGACGGACCACCC 63.000 60.000 0.00 0.00 0.00 4.61
92 93 3.530910 CTTTGCGACGGACCACCCT 62.531 63.158 0.00 0.00 0.00 4.34
93 94 3.818121 TTTGCGACGGACCACCCTG 62.818 63.158 0.00 0.00 0.00 4.45
95 96 4.309950 GCGACGGACCACCCTGTT 62.310 66.667 0.00 0.00 0.00 3.16
96 97 2.048503 CGACGGACCACCCTGTTC 60.049 66.667 0.00 0.00 0.00 3.18
97 98 2.571216 CGACGGACCACCCTGTTCT 61.571 63.158 0.00 0.00 0.00 3.01
98 99 1.292541 GACGGACCACCCTGTTCTC 59.707 63.158 0.00 0.00 0.00 2.87
99 100 1.458777 ACGGACCACCCTGTTCTCA 60.459 57.895 0.00 0.00 0.00 3.27
100 101 1.052124 ACGGACCACCCTGTTCTCAA 61.052 55.000 0.00 0.00 0.00 3.02
101 102 0.107831 CGGACCACCCTGTTCTCAAA 59.892 55.000 0.00 0.00 0.00 2.69
102 103 1.271379 CGGACCACCCTGTTCTCAAAT 60.271 52.381 0.00 0.00 0.00 2.32
103 104 2.162681 GGACCACCCTGTTCTCAAATG 58.837 52.381 0.00 0.00 0.00 2.32
104 105 1.541588 GACCACCCTGTTCTCAAATGC 59.458 52.381 0.00 0.00 0.00 3.56
105 106 1.145738 ACCACCCTGTTCTCAAATGCT 59.854 47.619 0.00 0.00 0.00 3.79
106 107 2.375174 ACCACCCTGTTCTCAAATGCTA 59.625 45.455 0.00 0.00 0.00 3.49
107 108 3.012518 CCACCCTGTTCTCAAATGCTAG 58.987 50.000 0.00 0.00 0.00 3.42
108 109 2.421424 CACCCTGTTCTCAAATGCTAGC 59.579 50.000 8.10 8.10 0.00 3.42
109 110 2.307098 ACCCTGTTCTCAAATGCTAGCT 59.693 45.455 17.23 0.00 0.00 3.32
110 111 2.941720 CCCTGTTCTCAAATGCTAGCTC 59.058 50.000 17.23 0.00 0.00 4.09
111 112 2.941720 CCTGTTCTCAAATGCTAGCTCC 59.058 50.000 17.23 0.00 0.00 4.70
112 113 2.606725 CTGTTCTCAAATGCTAGCTCCG 59.393 50.000 17.23 1.98 0.00 4.63
113 114 1.328986 GTTCTCAAATGCTAGCTCCGC 59.671 52.381 17.23 0.00 0.00 5.54
114 115 0.179073 TCTCAAATGCTAGCTCCGCC 60.179 55.000 17.23 0.00 0.00 6.13
115 116 0.462581 CTCAAATGCTAGCTCCGCCA 60.463 55.000 17.23 0.00 0.00 5.69
116 117 0.744414 TCAAATGCTAGCTCCGCCAC 60.744 55.000 17.23 0.00 0.00 5.01
117 118 0.745845 CAAATGCTAGCTCCGCCACT 60.746 55.000 17.23 0.00 0.00 4.00
118 119 0.745845 AAATGCTAGCTCCGCCACTG 60.746 55.000 17.23 0.00 0.00 3.66
119 120 3.746949 ATGCTAGCTCCGCCACTGC 62.747 63.158 17.23 0.00 0.00 4.40
120 121 4.154347 GCTAGCTCCGCCACTGCT 62.154 66.667 7.70 0.00 40.43 4.24
121 122 2.581354 CTAGCTCCGCCACTGCTT 59.419 61.111 0.00 0.00 38.15 3.91
122 123 1.520342 CTAGCTCCGCCACTGCTTC 60.520 63.158 0.00 0.00 38.15 3.86
123 124 1.954362 CTAGCTCCGCCACTGCTTCT 61.954 60.000 0.00 0.00 38.15 2.85
124 125 1.949847 TAGCTCCGCCACTGCTTCTC 61.950 60.000 0.00 0.00 38.15 2.87
125 126 2.507992 CTCCGCCACTGCTTCTCG 60.508 66.667 0.00 0.00 34.43 4.04
126 127 4.742201 TCCGCCACTGCTTCTCGC 62.742 66.667 0.00 0.00 39.77 5.03
127 128 4.749310 CCGCCACTGCTTCTCGCT 62.749 66.667 0.00 0.00 40.11 4.93
128 129 3.485431 CGCCACTGCTTCTCGCTG 61.485 66.667 0.00 0.00 42.62 5.18
129 130 3.123620 GCCACTGCTTCTCGCTGG 61.124 66.667 0.00 0.00 41.39 4.85
130 131 2.659016 CCACTGCTTCTCGCTGGA 59.341 61.111 0.00 0.00 41.39 3.86
131 132 1.447489 CCACTGCTTCTCGCTGGAG 60.447 63.158 0.00 0.00 41.39 3.86
132 133 1.447489 CACTGCTTCTCGCTGGAGG 60.447 63.158 0.00 0.00 41.39 4.30
133 134 1.607756 ACTGCTTCTCGCTGGAGGA 60.608 57.895 0.00 0.00 41.39 3.71
134 135 1.188219 ACTGCTTCTCGCTGGAGGAA 61.188 55.000 0.00 0.00 41.39 3.36
135 136 0.739112 CTGCTTCTCGCTGGAGGAAC 60.739 60.000 0.00 0.00 40.85 3.62
136 137 1.188219 TGCTTCTCGCTGGAGGAACT 61.188 55.000 0.00 0.00 40.85 3.01
137 138 0.036858 GCTTCTCGCTGGAGGAACTT 60.037 55.000 0.00 0.00 40.85 2.66
138 139 1.719600 CTTCTCGCTGGAGGAACTTG 58.280 55.000 0.00 0.00 41.55 3.16
139 140 1.001406 CTTCTCGCTGGAGGAACTTGT 59.999 52.381 0.00 0.00 41.55 3.16
140 141 1.919240 TCTCGCTGGAGGAACTTGTA 58.081 50.000 0.00 0.00 41.55 2.41
141 142 2.457598 TCTCGCTGGAGGAACTTGTAT 58.542 47.619 0.00 0.00 41.55 2.29
142 143 2.427453 TCTCGCTGGAGGAACTTGTATC 59.573 50.000 0.00 0.00 41.55 2.24
143 144 1.134367 TCGCTGGAGGAACTTGTATCG 59.866 52.381 0.00 0.00 41.55 2.92
144 145 1.802880 CGCTGGAGGAACTTGTATCGG 60.803 57.143 0.00 0.00 41.55 4.18
145 146 1.207329 GCTGGAGGAACTTGTATCGGT 59.793 52.381 0.00 0.00 41.55 4.69
146 147 2.354805 GCTGGAGGAACTTGTATCGGTT 60.355 50.000 0.00 0.00 41.55 4.44
147 148 3.868754 GCTGGAGGAACTTGTATCGGTTT 60.869 47.826 0.00 0.00 41.55 3.27
148 149 4.324267 CTGGAGGAACTTGTATCGGTTTT 58.676 43.478 0.00 0.00 41.55 2.43
149 150 4.320870 TGGAGGAACTTGTATCGGTTTTC 58.679 43.478 0.00 0.00 41.55 2.29
150 151 3.688185 GGAGGAACTTGTATCGGTTTTCC 59.312 47.826 0.00 0.00 41.55 3.13
151 152 3.682696 AGGAACTTGTATCGGTTTTCCC 58.317 45.455 0.00 0.00 34.23 3.97
152 153 2.751259 GGAACTTGTATCGGTTTTCCCC 59.249 50.000 0.00 0.00 36.42 4.81
153 154 3.414269 GAACTTGTATCGGTTTTCCCCA 58.586 45.455 0.00 0.00 36.42 4.96
154 155 3.512219 ACTTGTATCGGTTTTCCCCAA 57.488 42.857 0.00 0.00 36.42 4.12
155 156 3.151554 ACTTGTATCGGTTTTCCCCAAC 58.848 45.455 0.00 0.00 36.42 3.77
156 157 3.181437 ACTTGTATCGGTTTTCCCCAACT 60.181 43.478 0.00 0.00 36.42 3.16
157 158 4.041938 ACTTGTATCGGTTTTCCCCAACTA 59.958 41.667 0.00 0.00 36.42 2.24
158 159 3.941573 TGTATCGGTTTTCCCCAACTAC 58.058 45.455 0.00 0.00 36.42 2.73
159 160 3.327172 TGTATCGGTTTTCCCCAACTACA 59.673 43.478 0.00 0.00 36.42 2.74
160 161 3.512219 ATCGGTTTTCCCCAACTACAA 57.488 42.857 0.00 0.00 36.42 2.41
161 162 2.853705 TCGGTTTTCCCCAACTACAAG 58.146 47.619 0.00 0.00 36.42 3.16
162 163 2.173143 TCGGTTTTCCCCAACTACAAGT 59.827 45.455 0.00 0.00 36.42 3.16
163 164 3.390639 TCGGTTTTCCCCAACTACAAGTA 59.609 43.478 0.00 0.00 36.42 2.24
164 165 4.041938 TCGGTTTTCCCCAACTACAAGTAT 59.958 41.667 0.00 0.00 36.42 2.12
165 166 4.393990 CGGTTTTCCCCAACTACAAGTATC 59.606 45.833 0.00 0.00 36.42 2.24
166 167 5.318630 GGTTTTCCCCAACTACAAGTATCA 58.681 41.667 0.00 0.00 0.00 2.15
167 168 5.414765 GGTTTTCCCCAACTACAAGTATCAG 59.585 44.000 0.00 0.00 0.00 2.90
168 169 5.836024 TTTCCCCAACTACAAGTATCAGT 57.164 39.130 0.00 0.00 0.00 3.41
169 170 5.836024 TTCCCCAACTACAAGTATCAGTT 57.164 39.130 0.00 0.00 32.82 3.16
170 171 5.836024 TCCCCAACTACAAGTATCAGTTT 57.164 39.130 0.00 0.00 30.20 2.66
171 172 6.195600 TCCCCAACTACAAGTATCAGTTTT 57.804 37.500 0.00 0.00 30.20 2.43
172 173 6.235664 TCCCCAACTACAAGTATCAGTTTTC 58.764 40.000 0.00 0.00 30.20 2.29
173 174 5.414765 CCCCAACTACAAGTATCAGTTTTCC 59.585 44.000 0.00 0.00 30.20 3.13
174 175 5.414765 CCCAACTACAAGTATCAGTTTTCCC 59.585 44.000 0.00 0.00 30.20 3.97
175 176 5.414765 CCAACTACAAGTATCAGTTTTCCCC 59.585 44.000 0.00 0.00 30.20 4.81
176 177 5.836024 ACTACAAGTATCAGTTTTCCCCA 57.164 39.130 0.00 0.00 0.00 4.96
177 178 6.195600 ACTACAAGTATCAGTTTTCCCCAA 57.804 37.500 0.00 0.00 0.00 4.12
178 179 6.002082 ACTACAAGTATCAGTTTTCCCCAAC 58.998 40.000 0.00 0.00 0.00 3.77
179 180 5.061721 ACAAGTATCAGTTTTCCCCAACT 57.938 39.130 0.00 0.00 37.49 3.16
180 181 6.195600 ACAAGTATCAGTTTTCCCCAACTA 57.804 37.500 0.00 0.00 35.10 2.24
181 182 6.002082 ACAAGTATCAGTTTTCCCCAACTAC 58.998 40.000 0.00 0.00 35.10 2.73
182 183 5.836024 AGTATCAGTTTTCCCCAACTACA 57.164 39.130 0.00 0.00 35.10 2.74
343 347 2.748465 CGGGAGTCAAAAGACCCAACTT 60.748 50.000 0.00 0.00 42.16 2.66
376 380 6.144563 GGTTCTTTTTGCAGAGAAATAGTTGC 59.855 38.462 9.83 0.00 34.00 4.17
388 392 9.499479 CAGAGAAATAGTTGCCATAGTGATATT 57.501 33.333 0.00 0.00 0.00 1.28
522 529 6.446318 TGAACAAATGTTTTAGAGACATGCC 58.554 36.000 0.00 0.00 37.76 4.40
579 587 9.480053 CTCTCACCAAAAATAACAAAATCACAT 57.520 29.630 0.00 0.00 0.00 3.21
635 643 2.623416 TGTCTTTTCTGTCGAGAGCTCA 59.377 45.455 17.77 0.00 0.00 4.26
639 647 2.001812 TTCTGTCGAGAGCTCATTGC 57.998 50.000 17.77 3.99 43.29 3.56
659 667 7.876582 TCATTGCATGTTATTTGTGGATGAAAA 59.123 29.630 0.00 0.00 0.00 2.29
678 686 5.934625 TGAAAAGTTTGCAGCAACCTAAAAA 59.065 32.000 7.54 0.00 0.00 1.94
800 814 4.778534 TTAGTAGGAAACTGAGACCACG 57.221 45.455 0.00 0.00 43.88 4.94
882 903 4.856115 CACAAATTGTGTTTGGTCCAAC 57.144 40.909 17.29 0.56 43.08 3.77
990 1073 5.522456 TGAAGCTGATTGATGTTTGTTGTC 58.478 37.500 0.00 0.00 0.00 3.18
1004 1087 5.238432 TGTTTGTTGTCGCAGAGAATATGTT 59.762 36.000 0.00 0.00 43.15 2.71
1026 1109 2.099592 TGAAGCAGACAAAGCAAACAGG 59.900 45.455 0.00 0.00 0.00 4.00
1518 1601 3.087031 CAACAAGGAGACCGTAGTCCTA 58.913 50.000 2.88 0.00 42.76 2.94
1558 1641 1.004560 CTTGTCGGCCTCTGCTTCA 60.005 57.895 0.00 0.00 37.74 3.02
1680 1763 2.027192 GCACTGGGTTCTGGACTTCATA 60.027 50.000 0.00 0.00 0.00 2.15
1719 1802 4.033358 CGTGCTACATGAAGTGAAAGATCC 59.967 45.833 0.00 0.00 0.00 3.36
1812 1898 3.433173 GGCTTGTATCCGTAAATCCCTGT 60.433 47.826 0.00 0.00 0.00 4.00
1921 2023 0.032267 GGGCGTATACTCAGCAGTCC 59.968 60.000 0.56 0.00 33.62 3.85
1975 2077 8.666821 AGAGTTAATTTAAGGGAAAGTAGTGGT 58.333 33.333 0.00 0.00 29.84 4.16
2007 2114 6.363357 CAGGTGCAGCTTCTTGTTTTATTAAC 59.637 38.462 17.45 0.00 0.00 2.01
2050 2157 6.542005 TCTCGAGAGCATCAATATCTCCTATC 59.458 42.308 12.08 0.00 36.87 2.08
2118 2231 4.919754 GCACAAGCTCCACAAATAGAAAAG 59.080 41.667 0.00 0.00 37.91 2.27
2176 2289 8.992835 AGAATTTGGAATGAGAAAAATGCTAC 57.007 30.769 0.00 0.00 28.11 3.58
2221 2334 2.094803 CACCGCCAATCATGCTAAACAA 60.095 45.455 0.00 0.00 0.00 2.83
2294 2407 9.319143 CTATTGGTTGTTTTATCAGGAGAGTAG 57.681 37.037 0.00 0.00 0.00 2.57
2445 5988 5.047660 ACGGGAATTGAATCAAATTCGGAAA 60.048 36.000 0.00 0.00 44.20 3.13
2476 6019 3.445096 AGCATGTTCAGGGCAAGTTATTC 59.555 43.478 0.00 0.00 0.00 1.75
2566 6109 8.196103 TGAATCAACTGAACATTGTCATTGAAA 58.804 29.630 1.79 0.00 33.17 2.69
2589 6132 8.607441 AAAGTTTCTCTGGAAAAATATTTGGC 57.393 30.769 0.39 0.00 42.22 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.212641 GCAATATGACATGTGATCACTATAACT 57.787 33.333 25.55 9.90 0.00 2.24
36 37 9.212641 AGCAATATGACATGTGATCACTATAAC 57.787 33.333 25.55 13.61 0.00 1.89
37 38 9.783081 AAGCAATATGACATGTGATCACTATAA 57.217 29.630 25.55 6.73 0.00 0.98
39 40 9.955102 ATAAGCAATATGACATGTGATCACTAT 57.045 29.630 25.55 14.66 0.00 2.12
40 41 9.428097 GATAAGCAATATGACATGTGATCACTA 57.572 33.333 25.55 13.07 0.00 2.74
41 42 7.935210 TGATAAGCAATATGACATGTGATCACT 59.065 33.333 25.55 6.60 0.00 3.41
42 43 8.091385 TGATAAGCAATATGACATGTGATCAC 57.909 34.615 19.27 19.27 0.00 3.06
43 44 8.680039 TTGATAAGCAATATGACATGTGATCA 57.320 30.769 1.15 0.00 0.00 2.92
54 55 9.627657 CGCAAAGAAAAATTGATAAGCAATATG 57.372 29.630 0.00 0.00 46.25 1.78
55 56 9.585099 TCGCAAAGAAAAATTGATAAGCAATAT 57.415 25.926 0.00 0.00 46.25 1.28
56 57 8.859156 GTCGCAAAGAAAAATTGATAAGCAATA 58.141 29.630 0.00 0.00 46.25 1.90
58 59 6.129221 CGTCGCAAAGAAAAATTGATAAGCAA 60.129 34.615 0.00 0.00 41.53 3.91
59 60 5.341993 CGTCGCAAAGAAAAATTGATAAGCA 59.658 36.000 0.00 0.00 0.00 3.91
60 61 5.220024 CCGTCGCAAAGAAAAATTGATAAGC 60.220 40.000 0.00 0.00 0.00 3.09
61 62 6.032460 GTCCGTCGCAAAGAAAAATTGATAAG 59.968 38.462 0.00 0.00 0.00 1.73
62 63 5.854338 GTCCGTCGCAAAGAAAAATTGATAA 59.146 36.000 0.00 0.00 0.00 1.75
63 64 5.387279 GTCCGTCGCAAAGAAAAATTGATA 58.613 37.500 0.00 0.00 0.00 2.15
64 65 4.226761 GTCCGTCGCAAAGAAAAATTGAT 58.773 39.130 0.00 0.00 0.00 2.57
65 66 3.549221 GGTCCGTCGCAAAGAAAAATTGA 60.549 43.478 0.00 0.00 0.00 2.57
66 67 2.724174 GGTCCGTCGCAAAGAAAAATTG 59.276 45.455 0.00 0.00 0.00 2.32
67 68 2.359531 TGGTCCGTCGCAAAGAAAAATT 59.640 40.909 0.00 0.00 0.00 1.82
68 69 1.950909 TGGTCCGTCGCAAAGAAAAAT 59.049 42.857 0.00 0.00 0.00 1.82
69 70 1.064357 GTGGTCCGTCGCAAAGAAAAA 59.936 47.619 0.00 0.00 0.00 1.94
70 71 0.658897 GTGGTCCGTCGCAAAGAAAA 59.341 50.000 0.00 0.00 0.00 2.29
71 72 1.161563 GGTGGTCCGTCGCAAAGAAA 61.162 55.000 0.00 0.00 0.00 2.52
72 73 1.595929 GGTGGTCCGTCGCAAAGAA 60.596 57.895 0.00 0.00 0.00 2.52
73 74 2.029964 GGTGGTCCGTCGCAAAGA 59.970 61.111 0.00 0.00 0.00 2.52
74 75 3.047877 GGGTGGTCCGTCGCAAAG 61.048 66.667 0.00 0.00 33.83 2.77
75 76 3.552384 AGGGTGGTCCGTCGCAAA 61.552 61.111 0.00 0.00 41.52 3.68
76 77 4.308458 CAGGGTGGTCCGTCGCAA 62.308 66.667 0.00 0.00 41.52 4.85
78 79 4.309950 AACAGGGTGGTCCGTCGC 62.310 66.667 0.00 0.00 41.52 5.19
79 80 2.048503 GAACAGGGTGGTCCGTCG 60.049 66.667 0.00 0.00 41.52 5.12
80 81 1.292541 GAGAACAGGGTGGTCCGTC 59.707 63.158 0.00 0.00 33.71 4.79
81 82 1.052124 TTGAGAACAGGGTGGTCCGT 61.052 55.000 0.00 0.00 33.71 4.69
82 83 0.107831 TTTGAGAACAGGGTGGTCCG 59.892 55.000 0.00 0.00 33.71 4.79
83 84 2.162681 CATTTGAGAACAGGGTGGTCC 58.837 52.381 0.00 0.00 33.71 4.46
84 85 1.541588 GCATTTGAGAACAGGGTGGTC 59.458 52.381 0.00 0.00 33.32 4.02
85 86 1.145738 AGCATTTGAGAACAGGGTGGT 59.854 47.619 0.00 0.00 0.00 4.16
86 87 1.915141 AGCATTTGAGAACAGGGTGG 58.085 50.000 0.00 0.00 0.00 4.61
87 88 2.421424 GCTAGCATTTGAGAACAGGGTG 59.579 50.000 10.63 0.00 0.00 4.61
88 89 2.307098 AGCTAGCATTTGAGAACAGGGT 59.693 45.455 18.83 0.00 0.00 4.34
89 90 2.941720 GAGCTAGCATTTGAGAACAGGG 59.058 50.000 18.83 0.00 0.00 4.45
90 91 2.941720 GGAGCTAGCATTTGAGAACAGG 59.058 50.000 18.83 0.00 0.00 4.00
91 92 2.606725 CGGAGCTAGCATTTGAGAACAG 59.393 50.000 18.83 0.00 0.00 3.16
92 93 2.621338 CGGAGCTAGCATTTGAGAACA 58.379 47.619 18.83 0.00 0.00 3.18
119 120 1.001406 ACAAGTTCCTCCAGCGAGAAG 59.999 52.381 0.00 0.00 38.52 2.85
120 121 1.048601 ACAAGTTCCTCCAGCGAGAA 58.951 50.000 0.00 0.00 38.52 2.87
121 122 1.919240 TACAAGTTCCTCCAGCGAGA 58.081 50.000 0.00 0.00 38.52 4.04
122 123 2.796383 CGATACAAGTTCCTCCAGCGAG 60.796 54.545 0.00 0.00 35.72 5.03
123 124 1.134367 CGATACAAGTTCCTCCAGCGA 59.866 52.381 0.00 0.00 0.00 4.93
124 125 1.560923 CGATACAAGTTCCTCCAGCG 58.439 55.000 0.00 0.00 0.00 5.18
125 126 1.207329 ACCGATACAAGTTCCTCCAGC 59.793 52.381 0.00 0.00 0.00 4.85
126 127 3.611766 AACCGATACAAGTTCCTCCAG 57.388 47.619 0.00 0.00 0.00 3.86
127 128 4.320870 GAAAACCGATACAAGTTCCTCCA 58.679 43.478 0.00 0.00 0.00 3.86
128 129 3.688185 GGAAAACCGATACAAGTTCCTCC 59.312 47.826 0.00 0.00 33.28 4.30
129 130 3.688185 GGGAAAACCGATACAAGTTCCTC 59.312 47.826 0.00 0.00 35.81 3.71
130 131 3.560668 GGGGAAAACCGATACAAGTTCCT 60.561 47.826 0.00 0.00 41.60 3.36
131 132 2.751259 GGGGAAAACCGATACAAGTTCC 59.249 50.000 0.00 0.00 41.60 3.62
132 133 3.414269 TGGGGAAAACCGATACAAGTTC 58.586 45.455 0.00 0.00 41.60 3.01
133 134 3.512219 TGGGGAAAACCGATACAAGTT 57.488 42.857 0.00 0.00 41.60 2.66
134 135 3.151554 GTTGGGGAAAACCGATACAAGT 58.848 45.455 0.00 0.00 41.60 3.16
135 136 3.418047 AGTTGGGGAAAACCGATACAAG 58.582 45.455 0.00 0.00 41.60 3.16
136 137 3.512219 AGTTGGGGAAAACCGATACAA 57.488 42.857 0.00 0.00 41.60 2.41
137 138 3.327172 TGTAGTTGGGGAAAACCGATACA 59.673 43.478 0.00 0.00 41.60 2.29
138 139 3.941573 TGTAGTTGGGGAAAACCGATAC 58.058 45.455 0.00 0.00 41.60 2.24
139 140 4.041938 ACTTGTAGTTGGGGAAAACCGATA 59.958 41.667 0.00 0.00 41.60 2.92
140 141 3.181437 ACTTGTAGTTGGGGAAAACCGAT 60.181 43.478 0.00 0.00 41.60 4.18
141 142 2.173143 ACTTGTAGTTGGGGAAAACCGA 59.827 45.455 0.00 0.00 41.60 4.69
142 143 2.578786 ACTTGTAGTTGGGGAAAACCG 58.421 47.619 0.00 0.00 41.60 4.44
143 144 5.318630 TGATACTTGTAGTTGGGGAAAACC 58.681 41.667 0.00 0.00 39.11 3.27
144 145 6.002082 ACTGATACTTGTAGTTGGGGAAAAC 58.998 40.000 0.00 0.00 0.00 2.43
145 146 6.195600 ACTGATACTTGTAGTTGGGGAAAA 57.804 37.500 0.00 0.00 0.00 2.29
146 147 5.836024 ACTGATACTTGTAGTTGGGGAAA 57.164 39.130 0.00 0.00 0.00 3.13
147 148 5.836024 AACTGATACTTGTAGTTGGGGAA 57.164 39.130 0.00 0.00 33.69 3.97
148 149 5.836024 AAACTGATACTTGTAGTTGGGGA 57.164 39.130 0.00 0.00 35.06 4.81
149 150 5.414765 GGAAAACTGATACTTGTAGTTGGGG 59.585 44.000 0.00 0.00 35.06 4.96
150 151 5.414765 GGGAAAACTGATACTTGTAGTTGGG 59.585 44.000 0.00 0.00 35.06 4.12
151 152 5.414765 GGGGAAAACTGATACTTGTAGTTGG 59.585 44.000 0.00 0.00 35.06 3.77
152 153 6.001460 TGGGGAAAACTGATACTTGTAGTTG 58.999 40.000 0.00 0.00 35.06 3.16
153 154 6.195600 TGGGGAAAACTGATACTTGTAGTT 57.804 37.500 0.00 0.00 36.29 2.24
154 155 5.836024 TGGGGAAAACTGATACTTGTAGT 57.164 39.130 0.00 0.00 0.00 2.73
155 156 6.238648 AGTTGGGGAAAACTGATACTTGTAG 58.761 40.000 0.00 0.00 38.95 2.74
156 157 6.195600 AGTTGGGGAAAACTGATACTTGTA 57.804 37.500 0.00 0.00 38.95 2.41
157 158 5.061721 AGTTGGGGAAAACTGATACTTGT 57.938 39.130 0.00 0.00 38.95 3.16
158 159 6.001460 TGTAGTTGGGGAAAACTGATACTTG 58.999 40.000 0.00 0.00 40.58 3.16
159 160 6.195600 TGTAGTTGGGGAAAACTGATACTT 57.804 37.500 0.00 0.00 40.58 2.24
160 161 5.836024 TGTAGTTGGGGAAAACTGATACT 57.164 39.130 0.00 0.00 40.58 2.12
161 162 6.002082 AGTTGTAGTTGGGGAAAACTGATAC 58.998 40.000 0.00 0.00 40.58 2.24
162 163 6.195600 AGTTGTAGTTGGGGAAAACTGATA 57.804 37.500 0.00 0.00 40.58 2.15
163 164 5.061721 AGTTGTAGTTGGGGAAAACTGAT 57.938 39.130 0.00 0.00 40.58 2.90
164 165 4.513406 AGTTGTAGTTGGGGAAAACTGA 57.487 40.909 0.00 0.00 40.58 3.41
165 166 6.894339 AATAGTTGTAGTTGGGGAAAACTG 57.106 37.500 0.00 0.00 40.58 3.16
166 167 7.295340 AGAAATAGTTGTAGTTGGGGAAAACT 58.705 34.615 0.00 0.00 42.89 2.66
167 168 7.520451 AGAAATAGTTGTAGTTGGGGAAAAC 57.480 36.000 0.00 0.00 0.00 2.43
168 169 8.442374 AGTAGAAATAGTTGTAGTTGGGGAAAA 58.558 33.333 0.00 0.00 0.00 2.29
169 170 7.981142 AGTAGAAATAGTTGTAGTTGGGGAAA 58.019 34.615 0.00 0.00 0.00 3.13
170 171 7.563724 AGTAGAAATAGTTGTAGTTGGGGAA 57.436 36.000 0.00 0.00 0.00 3.97
171 172 8.849543 ATAGTAGAAATAGTTGTAGTTGGGGA 57.150 34.615 0.00 0.00 0.00 4.81
213 214 2.192664 ACATGTGGGCGTCATACAAA 57.807 45.000 0.00 0.00 0.00 2.83
343 347 4.776349 TCTGCAAAAAGAACCTCTACACA 58.224 39.130 0.00 0.00 0.00 3.72
376 380 6.423905 CACACCTTTCCGTAATATCACTATGG 59.576 42.308 0.00 0.00 0.00 2.74
388 392 1.340088 TGTAGCCACACCTTTCCGTA 58.660 50.000 0.00 0.00 0.00 4.02
434 441 9.900264 GTTTGATACATGTTTTGTCAGTTTTTC 57.100 29.630 2.30 0.00 39.87 2.29
522 529 9.138062 TCGAATGTTATTTGTGGATGAAATTTG 57.862 29.630 0.00 0.00 0.00 2.32
622 630 1.937278 ATGCAATGAGCTCTCGACAG 58.063 50.000 16.19 0.30 45.94 3.51
635 643 7.879160 ACTTTTCATCCACAAATAACATGCAAT 59.121 29.630 0.00 0.00 0.00 3.56
639 647 8.011106 GCAAACTTTTCATCCACAAATAACATG 58.989 33.333 0.00 0.00 0.00 3.21
687 697 9.563748 AAAATCAGAAATTTTGTGACATGGATT 57.436 25.926 10.79 0.00 35.64 3.01
688 698 9.563748 AAAAATCAGAAATTTTGTGACATGGAT 57.436 25.926 10.79 0.00 35.64 3.41
742 753 3.208594 ACACCCGAGTTTACAAGAAACC 58.791 45.455 0.00 0.00 0.00 3.27
747 758 4.083324 TCGTACTACACCCGAGTTTACAAG 60.083 45.833 0.00 0.00 0.00 3.16
800 814 7.802251 GCACATCACAATAAGAGCTAAATGATC 59.198 37.037 0.00 0.00 0.00 2.92
876 897 6.834168 TTGAAGGATCTTAATTGGTTGGAC 57.166 37.500 0.00 0.00 0.00 4.02
969 1052 4.539870 CGACAACAAACATCAATCAGCTT 58.460 39.130 0.00 0.00 0.00 3.74
990 1073 4.330894 TCTGCTTCAAACATATTCTCTGCG 59.669 41.667 0.00 0.00 0.00 5.18
1004 1087 3.429272 CCTGTTTGCTTTGTCTGCTTCAA 60.429 43.478 0.00 0.00 0.00 2.69
1026 1109 1.381327 TCCTGACGAGATCCCCACC 60.381 63.158 0.00 0.00 0.00 4.61
1050 1133 3.889134 TTGTGGCTGAGGCTGCGAG 62.889 63.158 7.74 0.00 38.73 5.03
1231 1314 5.704053 GGTTCTTCTTTTCGGAAATGGAGTA 59.296 40.000 18.80 10.66 0.00 2.59
1382 1465 2.355445 ATCGCGCATGATCGAGGTGT 62.355 55.000 8.75 0.00 38.17 4.16
1558 1641 2.292918 TGTAGCTAGTCCCCAAGGTCAT 60.293 50.000 0.00 0.00 0.00 3.06
1680 1763 2.434884 CGGCGTTGCATCCAGACT 60.435 61.111 0.00 0.00 0.00 3.24
1719 1802 2.111043 CCGATGGTTCCGGGGATG 59.889 66.667 0.00 0.00 43.05 3.51
1812 1898 0.675083 CATGTGCAGCAAAACCAGGA 59.325 50.000 0.00 0.00 0.00 3.86
1921 2023 2.681848 GGATGTCTGATTTGTGAGCCAG 59.318 50.000 0.00 0.00 0.00 4.85
2007 2114 7.187480 TCTCGAGATCTACAAACAAAGATACG 58.813 38.462 12.08 0.00 35.44 3.06
2050 2157 4.913126 GGAGTAGTCCAAGTGCCG 57.087 61.111 12.02 0.00 43.31 5.69
2118 2231 2.787994 CATCATAAGGGAGGCCATGAC 58.212 52.381 5.01 0.00 30.64 3.06
2176 2289 4.298332 AGCACTTTTATGGCGAAAAACTG 58.702 39.130 0.00 0.96 0.00 3.16
2221 2334 1.599047 CTCGCCTCCACCTTGATGT 59.401 57.895 0.00 0.00 0.00 3.06
2255 2368 4.959839 ACAACCAATAGTGTTTTGGAACCT 59.040 37.500 9.31 0.00 45.35 3.50
2266 2379 7.607991 ACTCTCCTGATAAAACAACCAATAGTG 59.392 37.037 0.00 0.00 0.00 2.74
2294 2407 4.457949 CACCCCCTTTACAACATACAAGAC 59.542 45.833 0.00 0.00 0.00 3.01
2445 5988 2.756760 CCCTGAACATGCTGCATAAACT 59.243 45.455 15.78 0.00 0.00 2.66
2476 6019 4.020839 AGGGATGGCTGATTTTTCTTTGTG 60.021 41.667 0.00 0.00 0.00 3.33
2566 6109 6.498303 AGGCCAAATATTTTTCCAGAGAAACT 59.502 34.615 5.01 0.00 41.69 2.66
2681 6224 8.095169 ACCTTGATAAGAACTTTGACGAGTAAT 58.905 33.333 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.