Multiple sequence alignment - TraesCS1B01G080600

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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 TraesCS1B01G080600 chr1B 100.000 2648 0 0 1 2648 63092482 63089835 0.000000e+00 4891.0
1 TraesCS1B01G080600 chr1A 91.794 2352 116 36 328 2648 42604591 42602286 0.000000e+00 3203.0
2 TraesCS1B01G080600 chr1A 94.203 345 15 4 1 343 42629454 42629113 3.020000e-144 521.0
3 TraesCS1B01G080600 chr2D 90.494 1925 102 37 750 2647 4496696 4498566 0.000000e+00 2466.0
4 TraesCS1B01G080600 chr2D 78.649 459 62 23 1 432 4495801 4496250 3.360000e-69 272.0
5 TraesCS1B01G080600 chrUn 78.649 459 62 23 1 432 270954499 270954050 3.360000e-69 272.0
6 TraesCS1B01G080600 chr6D 97.872 47 1 0 432 478 38154748 38154794 6.070000e-12 82.4


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 TraesCS1B01G080600 chr1B 63089835 63092482 2647 True 4891 4891 100.0000 1 2648 1 chr1B.!!$R1 2647
1 TraesCS1B01G080600 chr1A 42602286 42604591 2305 True 3203 3203 91.7940 328 2648 1 chr1A.!!$R1 2320
2 TraesCS1B01G080600 chr2D 4495801 4498566 2765 False 1369 2466 84.5715 1 2647 2 chr2D.!!$F1 2646

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
53 54 0.042281 GGTAGGAGGGTGGTGGTACT 59.958 60.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 2042 0.250513 AGTAGTAGCAGTTGGCCAGC 59.749 55.0 12.39 12.39 46.5 4.85 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
24 25 5.863935 GTCAAAAATATGAGAACCAACCAGC 59.136 40.000 0.00 0.00 0.00 4.85
26 27 2.332063 ATATGAGAACCAACCAGCGG 57.668 50.000 0.00 0.00 0.00 5.52
27 28 0.981183 TATGAGAACCAACCAGCGGT 59.019 50.000 0.00 0.00 38.85 5.68
52 53 0.979709 GGGTAGGAGGGTGGTGGTAC 60.980 65.000 0.00 0.00 0.00 3.34
53 54 0.042281 GGTAGGAGGGTGGTGGTACT 59.958 60.000 0.00 0.00 0.00 2.73
54 55 1.554118 GGTAGGAGGGTGGTGGTACTT 60.554 57.143 0.00 0.00 0.00 2.24
56 57 0.840722 AGGAGGGTGGTGGTACTTGG 60.841 60.000 0.00 0.00 0.00 3.61
87 88 3.831911 GGGATCAAATTCCAGGTTTGACA 59.168 43.478 7.27 0.00 45.27 3.58
100 103 5.922544 CCAGGTTTGACATTTTTGTCTCATC 59.077 40.000 7.55 0.00 39.41 2.92
105 108 7.285788 GTTTGACATTTTTGTCTCATCAATGC 58.714 34.615 7.55 0.00 39.41 3.56
107 110 6.693466 TGACATTTTTGTCTCATCAATGCAT 58.307 32.000 0.00 0.00 39.41 3.96
146 149 2.493713 ATGACGTTCACCTCGATAGC 57.506 50.000 0.00 0.00 0.00 2.97
158 161 0.744281 TCGATAGCGAGGCACATGAA 59.256 50.000 0.00 0.00 42.51 2.57
159 162 1.341209 TCGATAGCGAGGCACATGAAT 59.659 47.619 0.00 0.00 42.51 2.57
174 179 5.535333 CACATGAATTTCAACCTTGAAGCT 58.465 37.500 0.00 0.00 46.68 3.74
181 186 0.883833 CAACCTTGAAGCTCCGCAAT 59.116 50.000 0.00 0.00 0.00 3.56
184 189 1.271597 ACCTTGAAGCTCCGCAATTCT 60.272 47.619 0.00 0.00 0.00 2.40
185 190 1.399791 CCTTGAAGCTCCGCAATTCTC 59.600 52.381 0.00 0.00 0.00 2.87
192 197 1.875576 GCTCCGCAATTCTCATCCGAT 60.876 52.381 0.00 0.00 0.00 4.18
193 198 2.064762 CTCCGCAATTCTCATCCGATC 58.935 52.381 0.00 0.00 0.00 3.69
195 200 2.103094 TCCGCAATTCTCATCCGATCTT 59.897 45.455 0.00 0.00 0.00 2.40
197 202 3.126073 CGCAATTCTCATCCGATCTTCA 58.874 45.455 0.00 0.00 0.00 3.02
198 203 3.060003 CGCAATTCTCATCCGATCTTCAC 60.060 47.826 0.00 0.00 0.00 3.18
199 204 4.125703 GCAATTCTCATCCGATCTTCACT 58.874 43.478 0.00 0.00 0.00 3.41
200 205 5.292765 GCAATTCTCATCCGATCTTCACTA 58.707 41.667 0.00 0.00 0.00 2.74
201 206 5.176590 GCAATTCTCATCCGATCTTCACTAC 59.823 44.000 0.00 0.00 0.00 2.73
202 207 6.276091 CAATTCTCATCCGATCTTCACTACA 58.724 40.000 0.00 0.00 0.00 2.74
203 208 4.902443 TCTCATCCGATCTTCACTACAC 57.098 45.455 0.00 0.00 0.00 2.90
204 209 3.312697 TCTCATCCGATCTTCACTACACG 59.687 47.826 0.00 0.00 0.00 4.49
209 214 2.095415 CCGATCTTCACTACACGTGTGA 60.095 50.000 30.83 18.15 44.16 3.58
211 216 2.417339 TCTTCACTACACGTGTGAGC 57.583 50.000 30.83 0.00 43.98 4.26
212 217 1.053048 CTTCACTACACGTGTGAGCG 58.947 55.000 30.83 17.48 43.98 5.03
213 218 0.937699 TTCACTACACGTGTGAGCGC 60.938 55.000 30.83 0.00 43.98 5.92
220 225 3.756677 CGTGTGAGCGCGTCAGTG 61.757 66.667 8.43 0.00 42.94 3.66
223 228 3.406361 GTGAGCGCGTCAGTGTGG 61.406 66.667 8.43 0.00 35.13 4.17
224 229 3.911698 TGAGCGCGTCAGTGTGGT 61.912 61.111 8.43 0.00 0.00 4.16
235 240 0.676466 CAGTGTGGTGTGTGGTGTGT 60.676 55.000 0.00 0.00 0.00 3.72
238 243 2.043405 GTGGTGTGTGGTGTGTGCA 61.043 57.895 0.00 0.00 0.00 4.57
240 245 1.100463 TGGTGTGTGGTGTGTGCATC 61.100 55.000 0.00 0.00 0.00 3.91
242 247 1.542328 GGTGTGTGGTGTGTGCATCTA 60.542 52.381 0.00 0.00 0.00 1.98
244 249 2.160219 GTGTGTGGTGTGTGCATCTATG 59.840 50.000 0.00 0.00 0.00 2.23
245 250 2.224499 TGTGTGGTGTGTGCATCTATGT 60.224 45.455 0.00 0.00 0.00 2.29
247 252 3.253188 GTGTGGTGTGTGCATCTATGTTT 59.747 43.478 0.00 0.00 0.00 2.83
248 253 3.501828 TGTGGTGTGTGCATCTATGTTTC 59.498 43.478 0.00 0.00 0.00 2.78
250 255 4.216257 GTGGTGTGTGCATCTATGTTTCTT 59.784 41.667 0.00 0.00 0.00 2.52
251 256 5.411361 GTGGTGTGTGCATCTATGTTTCTTA 59.589 40.000 0.00 0.00 0.00 2.10
252 257 5.411361 TGGTGTGTGCATCTATGTTTCTTAC 59.589 40.000 0.00 0.00 0.00 2.34
253 258 5.163754 GGTGTGTGCATCTATGTTTCTTACC 60.164 44.000 0.00 0.00 0.00 2.85
254 259 5.411361 GTGTGTGCATCTATGTTTCTTACCA 59.589 40.000 0.00 0.00 0.00 3.25
255 260 6.000840 TGTGTGCATCTATGTTTCTTACCAA 58.999 36.000 0.00 0.00 0.00 3.67
256 261 6.488344 TGTGTGCATCTATGTTTCTTACCAAA 59.512 34.615 0.00 0.00 0.00 3.28
257 262 7.013750 TGTGTGCATCTATGTTTCTTACCAAAA 59.986 33.333 0.00 0.00 0.00 2.44
258 263 7.538678 GTGTGCATCTATGTTTCTTACCAAAAG 59.461 37.037 0.00 0.00 0.00 2.27
260 265 7.965107 GTGCATCTATGTTTCTTACCAAAAGAG 59.035 37.037 0.00 0.00 0.00 2.85
312 329 9.524106 TGTATATGTCCTATGTTTTTGTAGTCG 57.476 33.333 0.00 0.00 0.00 4.18
326 343 6.417191 TTTGTAGTCGAATTTACCATCAGC 57.583 37.500 0.00 0.00 0.00 4.26
342 368 6.963322 ACCATCAGCTAGGATTTCTTACTTT 58.037 36.000 6.08 0.00 0.00 2.66
423 449 8.816144 GTGCAAAGTTGTCAAATTTCTCAAATA 58.184 29.630 7.99 0.00 0.00 1.40
470 496 5.163426 TGTTTGAGGTACTTTGTACTTCCGA 60.163 40.000 14.41 4.25 41.55 4.55
490 516 7.519032 TCCGATGAATTTTGTTACTCCTTTT 57.481 32.000 0.00 0.00 0.00 2.27
513 539 4.396790 TCGCAAAAGAAACACTACCAACTT 59.603 37.500 0.00 0.00 0.00 2.66
515 541 5.407502 GCAAAAGAAACACTACCAACTTGT 58.592 37.500 0.00 0.00 0.00 3.16
547 574 2.624316 TCTAGTGCAAACCGTCTACG 57.376 50.000 0.00 0.00 39.44 3.51
549 576 0.314618 TAGTGCAAACCGTCTACGCA 59.685 50.000 0.00 0.00 38.18 5.24
555 582 3.062909 TGCAAACCGTCTACGCATTATTC 59.937 43.478 0.00 0.00 38.18 1.75
573 601 8.082242 GCATTATTCATAGGTGGTCCAAATTAC 58.918 37.037 0.00 0.00 35.89 1.89
585 613 8.837389 GGTGGTCCAAATTACAATTATCTACTC 58.163 37.037 0.00 0.00 0.00 2.59
606 635 4.513442 TCCCTCGTCTCAAAATGGTATTG 58.487 43.478 0.00 0.00 0.00 1.90
608 637 4.094887 CCCTCGTCTCAAAATGGTATTGTG 59.905 45.833 0.00 0.00 0.00 3.33
613 642 7.136119 TCGTCTCAAAATGGTATTGTGTTTTC 58.864 34.615 0.00 0.00 0.00 2.29
614 643 7.012894 TCGTCTCAAAATGGTATTGTGTTTTCT 59.987 33.333 0.00 0.00 0.00 2.52
615 644 8.286800 CGTCTCAAAATGGTATTGTGTTTTCTA 58.713 33.333 0.00 0.00 0.00 2.10
616 645 9.394477 GTCTCAAAATGGTATTGTGTTTTCTAC 57.606 33.333 0.00 0.00 0.00 2.59
617 646 9.126151 TCTCAAAATGGTATTGTGTTTTCTACA 57.874 29.630 0.00 0.00 0.00 2.74
690 723 8.225603 TCTAATCCACCAAGAAATAGCAAATC 57.774 34.615 0.00 0.00 0.00 2.17
707 740 4.978580 GCAAATCACTTTGTCAAGAACTCC 59.021 41.667 0.62 0.00 43.07 3.85
726 759 5.707495 ACTCCTAATACAGACCCTCCTAAG 58.293 45.833 0.00 0.00 0.00 2.18
732 765 2.986050 ACAGACCCTCCTAAGAACCAA 58.014 47.619 0.00 0.00 0.00 3.67
858 1200 1.660560 GCAGCTCGGCCATCAAATGT 61.661 55.000 2.24 0.00 0.00 2.71
924 1270 4.768448 CACGGACACCCTATATATACACCA 59.232 45.833 0.00 0.00 0.00 4.17
1564 1914 4.111016 CCACGGACGCGCTCTACA 62.111 66.667 5.73 0.00 0.00 2.74
1565 1915 2.874780 CACGGACGCGCTCTACAC 60.875 66.667 5.73 0.00 0.00 2.90
1682 2032 3.104766 CGCACTGGATGATGCACC 58.895 61.111 0.00 0.00 42.17 5.01
1683 2033 1.746239 CGCACTGGATGATGCACCA 60.746 57.895 0.00 0.00 42.17 4.17
1692 2042 3.201290 GGATGATGCACCAGTTACTCAG 58.799 50.000 0.00 0.00 0.00 3.35
1730 2083 2.159476 ACTACGTACGCATGATTCGTGT 60.159 45.455 16.72 0.00 40.69 4.49
1793 2146 3.650647 GGGTTGACCTGCTTGATGA 57.349 52.632 0.00 0.00 35.85 2.92
1794 2147 1.909700 GGGTTGACCTGCTTGATGAA 58.090 50.000 0.00 0.00 35.85 2.57
1795 2148 2.450476 GGGTTGACCTGCTTGATGAAT 58.550 47.619 0.00 0.00 35.85 2.57
1796 2149 2.827921 GGGTTGACCTGCTTGATGAATT 59.172 45.455 0.00 0.00 35.85 2.17
1817 2170 7.498239 TGAATTTGCTTGATGAATTTGTTGGAA 59.502 29.630 0.00 0.00 0.00 3.53
1872 2225 9.495754 TTTGTTTTGTTGCAAAAATAATACTGC 57.504 25.926 2.11 0.00 32.45 4.40
1873 2226 8.430801 TGTTTTGTTGCAAAAATAATACTGCT 57.569 26.923 2.11 0.00 35.78 4.24
1874 2227 9.534565 TGTTTTGTTGCAAAAATAATACTGCTA 57.465 25.926 2.11 0.00 35.78 3.49
1875 2228 9.791838 GTTTTGTTGCAAAAATAATACTGCTAC 57.208 29.630 2.11 0.00 39.80 3.58
1876 2229 7.789341 TTGTTGCAAAAATAATACTGCTACG 57.211 32.000 0.00 0.00 41.45 3.51
1877 2230 6.904498 TGTTGCAAAAATAATACTGCTACGT 58.096 32.000 0.00 0.00 41.45 3.57
1878 2231 8.030744 TGTTGCAAAAATAATACTGCTACGTA 57.969 30.769 0.00 0.00 41.45 3.57
1879 2232 7.958567 TGTTGCAAAAATAATACTGCTACGTAC 59.041 33.333 0.00 0.00 41.45 3.67
1880 2233 7.837202 TGCAAAAATAATACTGCTACGTACT 57.163 32.000 0.00 0.00 35.78 2.73
1943 2296 7.824289 CCAACAAGTTATGAGAAGTCCTAATCA 59.176 37.037 0.00 0.00 0.00 2.57
1969 2322 5.876357 ACAGAAAGTTGTATCCTTGCCTTA 58.124 37.500 0.00 0.00 0.00 2.69
2068 2421 4.209452 TGCACGTCATTTTCAAGAAGAC 57.791 40.909 0.00 0.00 0.00 3.01
2069 2422 3.003275 TGCACGTCATTTTCAAGAAGACC 59.997 43.478 0.00 0.00 0.00 3.85
2092 2445 5.104109 CCATCTTTAGTTCCTTACATCCCCA 60.104 44.000 0.00 0.00 0.00 4.96
2195 2548 8.250143 TGTCTAATATACATCATGTGGAGTGT 57.750 34.615 0.00 0.00 0.00 3.55
2253 2606 9.359653 AGCTTGATTTTAACATATTATCCTGCT 57.640 29.630 0.00 0.00 0.00 4.24
2284 2637 9.956720 CTTAATGAATCGGCATCTCTTTATTTT 57.043 29.630 0.00 0.00 0.00 1.82
2294 2647 6.258899 GCATCTCTTTATTTTCTCCCGAAAC 58.741 40.000 0.00 0.00 38.77 2.78
2298 2651 6.768861 TCTCTTTATTTTCTCCCGAAACAACA 59.231 34.615 0.00 0.00 38.77 3.33
2306 2659 3.625764 TCTCCCGAAACAACAAGACAAAG 59.374 43.478 0.00 0.00 0.00 2.77
2321 2674 9.463443 AACAAGACAAAGTAGACAATAATTTGC 57.537 29.630 7.49 2.52 36.37 3.68
2519 2880 5.796350 AACCGTCTTCATTATCCTTTTCG 57.204 39.130 0.00 0.00 0.00 3.46
2570 2937 3.997021 TCTTTGAATTTGACCGAGAGAGC 59.003 43.478 0.00 0.00 0.00 4.09
2571 2938 2.386661 TGAATTTGACCGAGAGAGCC 57.613 50.000 0.00 0.00 0.00 4.70
2572 2939 1.902508 TGAATTTGACCGAGAGAGCCT 59.097 47.619 0.00 0.00 0.00 4.58
2597 2964 4.394920 ACGAGCCAATGGTAATTGTTAGTG 59.605 41.667 0.00 0.00 41.46 2.74
2634 3001 7.303182 TGAGAGAAAGGAAGACATGACTTAA 57.697 36.000 10.43 0.00 0.00 1.85
2635 3002 7.735917 TGAGAGAAAGGAAGACATGACTTAAA 58.264 34.615 10.43 0.00 0.00 1.52
2642 3009 6.769512 AGGAAGACATGACTTAAAGCTTACA 58.230 36.000 10.43 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.910580 CTACCCATCCAACCGCTGGT 61.911 60.000 2.10 0.00 46.51 4.00
21 22 1.153168 CCTACCCATCCAACCGCTG 60.153 63.158 0.00 0.00 0.00 5.18
22 23 1.306654 TCCTACCCATCCAACCGCT 60.307 57.895 0.00 0.00 0.00 5.52
23 24 1.146263 CTCCTACCCATCCAACCGC 59.854 63.158 0.00 0.00 0.00 5.68
24 25 1.696097 CCCTCCTACCCATCCAACCG 61.696 65.000 0.00 0.00 0.00 4.44
26 27 0.546598 CACCCTCCTACCCATCCAAC 59.453 60.000 0.00 0.00 0.00 3.77
27 28 0.623324 CCACCCTCCTACCCATCCAA 60.623 60.000 0.00 0.00 0.00 3.53
28 29 1.004230 CCACCCTCCTACCCATCCA 59.996 63.158 0.00 0.00 0.00 3.41
29 30 1.004361 ACCACCCTCCTACCCATCC 59.996 63.158 0.00 0.00 0.00 3.51
30 31 1.345715 CCACCACCCTCCTACCCATC 61.346 65.000 0.00 0.00 0.00 3.51
32 33 1.453940 TACCACCACCCTCCTACCCA 61.454 60.000 0.00 0.00 0.00 4.51
33 34 0.979709 GTACCACCACCCTCCTACCC 60.980 65.000 0.00 0.00 0.00 3.69
72 73 6.888105 AGACAAAAATGTCAAACCTGGAATT 58.112 32.000 11.17 0.00 41.02 2.17
73 74 6.098124 TGAGACAAAAATGTCAAACCTGGAAT 59.902 34.615 11.17 0.00 41.02 3.01
74 75 5.420421 TGAGACAAAAATGTCAAACCTGGAA 59.580 36.000 11.17 0.00 41.02 3.53
75 76 4.952957 TGAGACAAAAATGTCAAACCTGGA 59.047 37.500 11.17 0.00 41.02 3.86
76 77 5.261209 TGAGACAAAAATGTCAAACCTGG 57.739 39.130 11.17 0.00 41.02 4.45
126 129 2.794981 CGCTATCGAGGTGAACGTCATT 60.795 50.000 0.00 0.00 38.10 2.57
130 133 2.474561 TCGCTATCGAGGTGAACGT 58.525 52.632 0.00 0.00 40.21 3.99
146 149 2.489329 AGGTTGAAATTCATGTGCCTCG 59.511 45.455 0.00 0.00 0.00 4.63
174 179 1.688735 AGATCGGATGAGAATTGCGGA 59.311 47.619 0.00 0.00 0.00 5.54
181 186 4.201920 CGTGTAGTGAAGATCGGATGAGAA 60.202 45.833 0.00 0.00 0.00 2.87
184 189 3.014623 ACGTGTAGTGAAGATCGGATGA 58.985 45.455 0.00 0.00 0.00 2.92
185 190 3.422417 ACGTGTAGTGAAGATCGGATG 57.578 47.619 0.00 0.00 0.00 3.51
197 202 2.428569 CGCGCTCACACGTGTAGT 60.429 61.111 22.90 0.00 38.69 2.73
202 207 4.266070 ACTGACGCGCTCACACGT 62.266 61.111 5.73 1.27 46.91 4.49
203 208 3.756677 CACTGACGCGCTCACACG 61.757 66.667 5.73 0.62 0.00 4.49
204 209 2.658593 ACACTGACGCGCTCACAC 60.659 61.111 5.73 0.00 0.00 3.82
209 214 4.221422 ACACCACACTGACGCGCT 62.221 61.111 5.73 0.00 0.00 5.92
211 216 2.584970 ACACACCACACTGACGCG 60.585 61.111 3.53 3.53 0.00 6.01
212 217 2.534019 CCACACACCACACTGACGC 61.534 63.158 0.00 0.00 0.00 5.19
213 218 1.153449 ACCACACACCACACTGACG 60.153 57.895 0.00 0.00 0.00 4.35
216 221 0.676466 ACACACCACACACCACACTG 60.676 55.000 0.00 0.00 0.00 3.66
217 222 0.676466 CACACACCACACACCACACT 60.676 55.000 0.00 0.00 0.00 3.55
218 223 1.800032 CACACACCACACACCACAC 59.200 57.895 0.00 0.00 0.00 3.82
220 225 1.383456 ATGCACACACCACACACCAC 61.383 55.000 0.00 0.00 0.00 4.16
223 228 1.877637 TAGATGCACACACCACACAC 58.122 50.000 0.00 0.00 0.00 3.82
224 229 2.224499 ACATAGATGCACACACCACACA 60.224 45.455 0.00 0.00 0.00 3.72
235 240 7.665559 ACTCTTTTGGTAAGAAACATAGATGCA 59.334 33.333 0.00 0.00 0.00 3.96
291 308 8.561738 AATTCGACTACAAAAACATAGGACAT 57.438 30.769 0.00 0.00 0.00 3.06
293 310 9.750882 GTAAATTCGACTACAAAAACATAGGAC 57.249 33.333 0.00 0.00 0.00 3.85
299 316 8.155821 TGATGGTAAATTCGACTACAAAAACA 57.844 30.769 0.00 0.00 0.00 2.83
300 317 7.270579 GCTGATGGTAAATTCGACTACAAAAAC 59.729 37.037 0.00 0.00 0.00 2.43
308 325 4.649674 TCCTAGCTGATGGTAAATTCGACT 59.350 41.667 0.00 0.00 0.00 4.18
312 329 8.457238 AAGAAATCCTAGCTGATGGTAAATTC 57.543 34.615 0.00 1.42 0.00 2.17
323 340 9.039870 CACATAGAAAGTAAGAAATCCTAGCTG 57.960 37.037 0.00 0.00 0.00 4.24
445 471 5.699458 CGGAAGTACAAAGTACCTCAAACAT 59.301 40.000 7.87 0.00 0.00 2.71
470 496 6.744112 TGCGAAAAGGAGTAACAAAATTCAT 58.256 32.000 0.00 0.00 0.00 2.57
490 516 3.942748 AGTTGGTAGTGTTTCTTTTGCGA 59.057 39.130 0.00 0.00 0.00 5.10
513 539 6.214191 TGCACTAGATTTTGGAAAAACACA 57.786 33.333 0.00 0.00 0.00 3.72
515 541 6.536941 GGTTTGCACTAGATTTTGGAAAAACA 59.463 34.615 0.00 0.00 35.20 2.83
547 574 6.655078 ATTTGGACCACCTATGAATAATGC 57.345 37.500 0.00 0.00 37.04 3.56
549 576 9.707957 TTGTAATTTGGACCACCTATGAATAAT 57.292 29.630 0.00 0.00 37.04 1.28
555 582 9.354673 AGATAATTGTAATTTGGACCACCTATG 57.645 33.333 0.00 0.00 37.04 2.23
573 601 6.392625 TTGAGACGAGGGAGTAGATAATTG 57.607 41.667 0.00 0.00 0.00 2.32
585 613 4.094887 CACAATACCATTTTGAGACGAGGG 59.905 45.833 0.00 0.00 0.00 4.30
608 637 9.668497 AAATATTCCCTCTGTAGTGTAGAAAAC 57.332 33.333 0.00 0.00 0.00 2.43
619 648 9.998106 GCACTCTAAATAAATATTCCCTCTGTA 57.002 33.333 0.00 0.00 0.00 2.74
659 692 8.854117 GCTATTTCTTGGTGGATTAGATTGAAT 58.146 33.333 0.00 0.00 0.00 2.57
676 709 8.632679 TCTTGACAAAGTGATTTGCTATTTCTT 58.367 29.630 0.79 0.00 35.42 2.52
690 723 7.872993 TCTGTATTAGGAGTTCTTGACAAAGTG 59.127 37.037 0.00 0.00 34.78 3.16
707 740 5.897824 TGGTTCTTAGGAGGGTCTGTATTAG 59.102 44.000 0.00 0.00 0.00 1.73
726 759 5.306394 AGAAGCTAGGTGTAGTTTTGGTTC 58.694 41.667 0.00 0.00 30.40 3.62
732 765 7.452189 AGAAAGAGTAGAAGCTAGGTGTAGTTT 59.548 37.037 0.00 0.00 32.75 2.66
826 1164 1.518903 GAGCTGCACGAAGCCCTTTT 61.519 55.000 1.02 0.00 44.68 2.27
835 1173 4.819761 GATGGCCGAGCTGCACGA 62.820 66.667 20.67 1.30 0.00 4.35
858 1200 3.367703 GCTAGGTGTAGTTGCGGAAAGTA 60.368 47.826 0.00 0.00 0.00 2.24
924 1270 0.534203 AATTCTGTCGCCGTTGGTGT 60.534 50.000 0.00 0.00 34.40 4.16
1035 1385 4.410743 GACGTCGGGGTCGGTGAC 62.411 72.222 0.00 0.00 36.95 3.67
1329 1679 1.913722 CCTCTGGAGCTGGCAGATT 59.086 57.895 20.86 4.98 0.00 2.40
1496 1846 1.001120 TGGGACTGTGATCCGCCTA 59.999 57.895 0.00 0.00 39.97 3.93
1549 1899 4.112341 GGTGTAGAGCGCGTCCGT 62.112 66.667 8.43 0.00 36.67 4.69
1635 1985 2.491621 CGCGCTCATGTCCAGAGA 59.508 61.111 5.56 0.00 35.09 3.10
1682 2032 1.160137 GTTGGCCAGCTGAGTAACTG 58.840 55.000 17.39 0.00 0.00 3.16
1683 2033 1.059913 AGTTGGCCAGCTGAGTAACT 58.940 50.000 22.70 17.70 0.00 2.24
1686 2036 1.003355 GCAGTTGGCCAGCTGAGTA 60.003 57.895 43.14 10.60 41.41 2.59
1692 2042 0.250513 AGTAGTAGCAGTTGGCCAGC 59.749 55.000 12.39 12.39 46.50 4.85
1784 2137 5.394224 TCATCAAGCAAATTCATCAAGCA 57.606 34.783 0.00 0.00 0.00 3.91
1785 2138 6.903883 ATTCATCAAGCAAATTCATCAAGC 57.096 33.333 0.00 0.00 0.00 4.01
1786 2139 8.717821 ACAAATTCATCAAGCAAATTCATCAAG 58.282 29.630 0.00 0.00 0.00 3.02
1787 2140 8.610248 ACAAATTCATCAAGCAAATTCATCAA 57.390 26.923 0.00 0.00 0.00 2.57
1788 2141 8.499967 CAACAAATTCATCAAGCAAATTCATCA 58.500 29.630 0.00 0.00 0.00 3.07
1789 2142 7.960738 CCAACAAATTCATCAAGCAAATTCATC 59.039 33.333 0.00 0.00 0.00 2.92
1790 2143 7.662258 TCCAACAAATTCATCAAGCAAATTCAT 59.338 29.630 0.00 0.00 0.00 2.57
1791 2144 6.990939 TCCAACAAATTCATCAAGCAAATTCA 59.009 30.769 0.00 0.00 0.00 2.57
1792 2145 7.424227 TCCAACAAATTCATCAAGCAAATTC 57.576 32.000 0.00 0.00 0.00 2.17
1793 2146 7.804843 TTCCAACAAATTCATCAAGCAAATT 57.195 28.000 0.00 0.00 0.00 1.82
1794 2147 7.989416 ATTCCAACAAATTCATCAAGCAAAT 57.011 28.000 0.00 0.00 0.00 2.32
1795 2148 7.804843 AATTCCAACAAATTCATCAAGCAAA 57.195 28.000 0.00 0.00 0.00 3.68
1796 2149 7.498239 TGAAATTCCAACAAATTCATCAAGCAA 59.502 29.630 0.00 0.00 0.00 3.91
1817 2170 5.130145 ACTCGATCTTCCTCCATCTTGAAAT 59.870 40.000 0.00 0.00 0.00 2.17
1927 2280 7.487822 TTCTGTCTTGATTAGGACTTCTCAT 57.512 36.000 1.46 0.00 34.01 2.90
1943 2296 4.762251 GGCAAGGATACAACTTTCTGTCTT 59.238 41.667 0.00 0.00 41.41 3.01
1969 2322 4.090761 TCCTTCTTCACAACTGCAGAAT 57.909 40.909 23.35 5.76 0.00 2.40
2051 2404 5.869753 AGATGGTCTTCTTGAAAATGACG 57.130 39.130 0.00 0.00 0.00 4.35
2068 2421 5.104109 TGGGGATGTAAGGAACTAAAGATGG 60.104 44.000 0.00 0.00 38.49 3.51
2069 2422 6.001449 TGGGGATGTAAGGAACTAAAGATG 57.999 41.667 0.00 0.00 38.49 2.90
2092 2445 7.994425 TGGACAATCACTGTTACATTTACAT 57.006 32.000 0.00 0.00 38.84 2.29
2140 2493 8.471457 CAAAGAATTTCACATTCACGTTAAGTG 58.529 33.333 0.00 0.00 44.56 3.16
2203 2556 9.347934 GCTGATATCAAGTAGTATATCACACAC 57.652 37.037 6.90 0.00 39.18 3.82
2246 2599 4.993584 CGATTCATTAAGTGCTAGCAGGAT 59.006 41.667 20.03 9.86 0.00 3.24
2251 2604 2.872245 TGCCGATTCATTAAGTGCTAGC 59.128 45.455 8.10 8.10 0.00 3.42
2253 2606 4.960938 AGATGCCGATTCATTAAGTGCTA 58.039 39.130 0.00 0.00 0.00 3.49
2284 2637 2.992124 TGTCTTGTTGTTTCGGGAGA 57.008 45.000 0.00 0.00 0.00 3.71
2330 2683 5.003160 ACTTCCATCATGTTGTTCGAATGA 58.997 37.500 0.00 0.24 34.96 2.57
2332 2685 5.964958 AACTTCCATCATGTTGTTCGAAT 57.035 34.783 0.00 0.00 0.00 3.34
2336 2690 6.317789 TGAGAAACTTCCATCATGTTGTTC 57.682 37.500 3.19 0.65 0.00 3.18
2392 2747 7.773149 AGTTCTTCATCTATAGTACTTTGCGT 58.227 34.615 0.00 0.00 0.00 5.24
2555 2919 2.159226 CGTTAGGCTCTCTCGGTCAAAT 60.159 50.000 0.00 0.00 0.00 2.32
2570 2937 3.945285 ACAATTACCATTGGCTCGTTAGG 59.055 43.478 1.54 0.00 43.82 2.69
2571 2938 5.560966 AACAATTACCATTGGCTCGTTAG 57.439 39.130 1.54 0.00 43.82 2.34
2572 2939 6.092944 CACTAACAATTACCATTGGCTCGTTA 59.907 38.462 1.54 3.60 43.82 3.18
2597 2964 5.186021 TCCTTTCTCTCATCCTCACACTAAC 59.814 44.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.