Multiple sequence alignment - TraesCS7D01G433900

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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 TraesCS7D01G433900 chr7D 100.000 2516 0 0 1 2516 553846970 553849485 0.000000e+00 4647.0
1 TraesCS7D01G433900 chr7B 87.315 1963 163 44 520 2445 600833216 600831303 0.000000e+00 2167.0
2 TraesCS7D01G433900 chr7B 90.314 1528 99 29 332 1847 600839594 600838104 0.000000e+00 1956.0
3 TraesCS7D01G433900 chr7B 83.801 321 20 13 1 303 600841659 600841353 2.470000e-70 276.0
4 TraesCS7D01G433900 chr7B 88.372 215 23 2 2230 2442 600836475 600836261 8.930000e-65 257.0
5 TraesCS7D01G433900 chr7A 91.696 1409 92 12 368 1753 640544397 640542991 0.000000e+00 1930.0
6 TraesCS7D01G433900 chr7A 93.095 391 23 3 2054 2444 640541861 640541475 1.010000e-158 569.0
7 TraesCS7D01G433900 chr7A 91.746 315 22 4 1744 2055 640542255 640541942 3.840000e-118 435.0
8 TraesCS7D01G433900 chr5B 88.535 157 18 0 516 672 626170604 626170760 9.190000e-45 191.0
9 TraesCS7D01G433900 chr5B 88.535 157 18 0 516 672 626182208 626182364 9.190000e-45 191.0
10 TraesCS7D01G433900 chrUn 80.729 192 15 5 511 702 271389238 271389407 2.030000e-26 130.0
11 TraesCS7D01G433900 chrUn 80.729 192 15 5 511 702 271397384 271397553 2.030000e-26 130.0
12 TraesCS7D01G433900 chr1B 87.879 66 8 0 604 669 24204219 24204284 7.460000e-11 78.7


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 TraesCS7D01G433900 chr7D 553846970 553849485 2515 False 4647 4647 100.0000 1 2516 1 chr7D.!!$F1 2515
1 TraesCS7D01G433900 chr7B 600831303 600841659 10356 True 1164 2167 87.4505 1 2445 4 chr7B.!!$R1 2444
2 TraesCS7D01G433900 chr7A 640541475 640544397 2922 True 978 1930 92.1790 368 2444 3 chr7A.!!$R1 2076

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
143 154 0.108963 ATGGAACCCGTTTCGTCCAA 59.891 50.0 4.61 0.0 34.67 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 10471 0.040058 TGCATGGTGGCAAGGAGAAT 59.96 50.0 0.0 0.0 41.65 2.4 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
39 50 1.004560 CGCTCTTCCAACAGCCAGA 60.005 57.895 0.00 0.00 31.37 3.86
75 86 7.653713 GGGACAGTGTATATTTGATGTCTACTG 59.346 40.741 0.00 0.00 37.71 2.74
89 100 3.005050 TGTCTACTGGTGTAGGAAACGTG 59.995 47.826 0.00 0.00 44.61 4.49
93 104 0.882927 TGGTGTAGGAAACGTGCTGC 60.883 55.000 0.00 0.00 0.00 5.25
105 116 1.154150 GTGCTGCGCAATGTCTTCC 60.154 57.895 13.05 0.00 41.47 3.46
106 117 1.600356 TGCTGCGCAATGTCTTCCA 60.600 52.632 13.05 0.00 34.76 3.53
122 133 0.383949 TCCAGTGCAAAACGCCTTTC 59.616 50.000 0.00 0.00 41.33 2.62
131 142 3.833442 CAAAACGCCTTTCTATGGAACC 58.167 45.455 0.00 0.00 0.00 3.62
143 154 0.108963 ATGGAACCCGTTTCGTCCAA 59.891 50.000 4.61 0.00 34.67 3.53
152 163 1.219646 GTTTCGTCCAACGGCTAACA 58.780 50.000 0.00 0.00 42.81 2.41
153 164 1.070376 GTTTCGTCCAACGGCTAACAC 60.070 52.381 0.00 0.00 42.81 3.32
154 165 0.390124 TTCGTCCAACGGCTAACACT 59.610 50.000 0.00 0.00 42.81 3.55
155 166 1.246649 TCGTCCAACGGCTAACACTA 58.753 50.000 0.00 0.00 42.81 2.74
156 167 1.612950 TCGTCCAACGGCTAACACTAA 59.387 47.619 0.00 0.00 42.81 2.24
157 168 2.035704 TCGTCCAACGGCTAACACTAAA 59.964 45.455 0.00 0.00 42.81 1.85
216 234 3.738281 GCGTCTTGTACATATGCCACTCT 60.738 47.826 1.58 0.00 0.00 3.24
219 237 4.568359 GTCTTGTACATATGCCACTCTGTG 59.432 45.833 1.58 0.00 0.00 3.66
234 252 5.494724 CACTCTGTGGTACTACCTACTACA 58.505 45.833 6.93 2.00 42.78 2.74
235 253 5.353678 CACTCTGTGGTACTACCTACTACAC 59.646 48.000 6.93 0.00 40.80 2.90
236 254 5.250313 ACTCTGTGGTACTACCTACTACACT 59.750 44.000 6.93 0.00 40.80 3.55
237 255 6.131972 TCTGTGGTACTACCTACTACACTT 57.868 41.667 6.93 0.00 40.80 3.16
238 256 6.546484 TCTGTGGTACTACCTACTACACTTT 58.454 40.000 6.93 0.00 40.80 2.66
239 257 6.432162 TCTGTGGTACTACCTACTACACTTTG 59.568 42.308 6.93 0.00 40.80 2.77
240 258 5.047802 TGTGGTACTACCTACTACACTTTGC 60.048 44.000 6.93 0.00 40.80 3.68
243 261 5.184671 GGTACTACCTACTACACTTTGCTGT 59.815 44.000 0.00 0.00 34.73 4.40
244 262 6.375455 GGTACTACCTACTACACTTTGCTGTA 59.625 42.308 0.00 0.00 34.73 2.74
245 263 6.512342 ACTACCTACTACACTTTGCTGTAG 57.488 41.667 8.81 8.81 46.32 2.74
246 264 4.189639 ACCTACTACACTTTGCTGTAGC 57.810 45.455 9.99 0.00 45.25 3.58
296 1035 5.241949 GTGACATTTGGTTTATGGTGGTGTA 59.758 40.000 0.00 0.00 0.00 2.90
307 1046 4.650972 ATGGTGGTGTACTATTTGTGGT 57.349 40.909 0.00 0.00 0.00 4.16
309 1048 4.794334 TGGTGGTGTACTATTTGTGGTTT 58.206 39.130 0.00 0.00 0.00 3.27
316 1055 9.961264 TGGTGTACTATTTGTGGTTTCATTATA 57.039 29.630 0.00 0.00 0.00 0.98
344 2092 2.282147 TTATGCCAACATGCGCCTGC 62.282 55.000 12.92 2.94 37.04 4.85
371 2119 3.130693 AGGAATGTAGTCTAGCGGACAAC 59.869 47.826 13.62 0.00 46.72 3.32
377 2126 0.737715 GTCTAGCGGACAACTGGCTG 60.738 60.000 7.76 0.00 43.94 4.85
384 2133 1.456287 GACAACTGGCTGGGAAGGT 59.544 57.895 0.00 0.00 0.00 3.50
449 2198 8.638873 AGGTTTTCTTTTTCATTTCCTTCGTAT 58.361 29.630 0.00 0.00 0.00 3.06
529 2285 1.133025 CAATGCCCTGAAATCGACACC 59.867 52.381 0.00 0.00 0.00 4.16
609 2365 3.125316 CGCTAGGAAAATAATGATCCCGC 59.875 47.826 0.00 0.00 33.55 6.13
630 2386 3.292460 CCCGGAATCACTCTCTACTCTT 58.708 50.000 0.73 0.00 0.00 2.85
638 2394 7.201696 GGAATCACTCTCTACTCTTACTGACTG 60.202 44.444 0.00 0.00 0.00 3.51
648 2404 1.278985 CTTACTGACTGCATGGGTCCA 59.721 52.381 2.46 0.00 33.22 4.02
671 2427 6.996879 CCACATGTCATATCCATCTTCTTTCT 59.003 38.462 0.00 0.00 0.00 2.52
744 2500 6.260870 ACAATAATACAATGTTTGCCACGA 57.739 33.333 0.00 0.00 0.00 4.35
746 2502 3.569250 AATACAATGTTTGCCACGACC 57.431 42.857 0.00 0.00 0.00 4.79
768 2524 1.971357 AGTCGAAATCAGTGGACACCT 59.029 47.619 0.00 0.00 31.93 4.00
791 2547 7.722728 ACCTTGAACCGTGACATATCTATACTA 59.277 37.037 0.00 0.00 0.00 1.82
798 8738 9.696572 ACCGTGACATATCTATACTATATGGTT 57.303 33.333 0.00 0.00 40.24 3.67
822 8762 9.726034 GTTAGAACGAAAAACGAAACGAATATA 57.274 29.630 0.00 0.00 45.77 0.86
997 8940 4.376413 CGTGATGTTTTCCTTCAGAACTCG 60.376 45.833 0.00 0.00 32.95 4.18
1017 8960 0.519999 CAGAGCAAAGCAACGATCGC 60.520 55.000 16.60 0.00 0.00 4.58
1040 8983 5.689819 CCAAGTCTTTCCTTCAATACAACG 58.310 41.667 0.00 0.00 0.00 4.10
1042 8985 6.363473 CAAGTCTTTCCTTCAATACAACGAC 58.637 40.000 0.00 0.00 0.00 4.34
1058 9001 6.627395 ACAACGACTATCTAAGATGAGGAG 57.373 41.667 0.00 0.00 0.00 3.69
1121 9064 3.119495 GCATCAGGTACCCATTTGTTCAC 60.119 47.826 8.74 0.00 0.00 3.18
1402 9347 4.953940 TTCCTCCCAAAAATGGAAACTG 57.046 40.909 0.00 0.00 35.87 3.16
1522 9468 5.916883 ACGATGAATTTTGTCTTGCTTCTTG 59.083 36.000 0.00 0.00 0.00 3.02
1668 9625 7.059945 CACATTAGCTTTGCTTTTAGACGAAAG 59.940 37.037 0.00 0.00 40.44 2.62
1754 9713 5.407691 TGACTCGTGAGTTGTACTAGTACTG 59.592 44.000 28.56 12.74 42.66 2.74
1760 9719 7.116948 TCGTGAGTTGTACTAGTACTGTTACTC 59.883 40.741 28.56 28.26 39.43 2.59
1762 10467 6.369890 TGAGTTGTACTAGTACTGTTACTCGG 59.630 42.308 28.56 0.00 39.43 4.63
1763 10468 5.123027 AGTTGTACTAGTACTGTTACTCGGC 59.877 44.000 28.56 10.12 39.43 5.54
1764 10469 4.836825 TGTACTAGTACTGTTACTCGGCT 58.163 43.478 28.56 0.00 39.43 5.52
1766 10471 6.406370 TGTACTAGTACTGTTACTCGGCTAA 58.594 40.000 28.56 5.41 39.43 3.09
1826 10531 4.142752 CGACCAAGTTACTATCGTCAGTGA 60.143 45.833 0.00 0.00 0.00 3.41
1864 10569 2.683211 AGGTGGTCAAAAGCTGGAAT 57.317 45.000 0.00 0.00 0.00 3.01
1900 10605 7.946237 GCATCACATTTGTTTTTCGTGAATAAG 59.054 33.333 0.00 0.00 39.80 1.73
1992 10708 9.177608 TGGCATTAGATAGGATATTATTTGCAC 57.822 33.333 0.00 0.00 0.00 4.57
2006 10722 6.570672 TTATTTGCACGTTGGTATTTGGTA 57.429 33.333 0.00 0.00 0.00 3.25
2007 10723 4.491234 TTTGCACGTTGGTATTTGGTAG 57.509 40.909 0.00 0.00 0.00 3.18
2009 10725 2.038689 TGCACGTTGGTATTTGGTAGGA 59.961 45.455 0.00 0.00 0.00 2.94
2010 10726 3.275999 GCACGTTGGTATTTGGTAGGAT 58.724 45.455 0.00 0.00 0.00 3.24
2011 10727 4.081031 TGCACGTTGGTATTTGGTAGGATA 60.081 41.667 0.00 0.00 0.00 2.59
2013 10729 5.529800 GCACGTTGGTATTTGGTAGGATATT 59.470 40.000 0.00 0.00 0.00 1.28
2014 10730 6.707161 GCACGTTGGTATTTGGTAGGATATTA 59.293 38.462 0.00 0.00 0.00 0.98
2020 10736 8.213489 TGGTATTTGGTAGGATATTAGATGCA 57.787 34.615 0.00 0.00 0.00 3.96
2021 10737 8.321353 TGGTATTTGGTAGGATATTAGATGCAG 58.679 37.037 0.00 0.00 0.00 4.41
2025 10741 6.114187 TGGTAGGATATTAGATGCAGGTTG 57.886 41.667 0.00 0.00 0.00 3.77
2037 10753 5.784177 AGATGCAGGTTGATATTAGGTACG 58.216 41.667 0.00 0.00 0.00 3.67
2127 10926 7.735500 TCAATGTGTTTATAACTAACGTCAGC 58.264 34.615 0.00 0.00 0.00 4.26
2156 10977 6.073927 GGGTAATTAGAACGCTAAGCATGTAC 60.074 42.308 0.00 0.00 39.79 2.90
2214 11035 8.190784 ACGGATAAAATGAATTTGATTCTCCAC 58.809 33.333 2.74 0.00 39.96 4.02
2335 11158 2.745968 AGGGAAAACCAGCAGAAAACA 58.254 42.857 0.00 0.00 43.89 2.83
2377 11200 3.992427 AGAAAACCTAGCGAAAACCGTAG 59.008 43.478 0.00 0.00 41.15 3.51
2381 11204 3.022406 ACCTAGCGAAAACCGTAGAGAT 58.978 45.455 0.00 0.00 41.15 2.75
2395 11218 3.508012 CGTAGAGATCCGAAGAATCCCAT 59.492 47.826 0.00 0.00 0.00 4.00
2416 11239 5.276773 CCATGAAAACATCACAACCAAAACG 60.277 40.000 0.00 0.00 41.93 3.60
2445 11268 0.458260 ACAAACGGAAAACCAGCACC 59.542 50.000 0.00 0.00 0.00 5.01
2446 11269 0.744281 CAAACGGAAAACCAGCACCT 59.256 50.000 0.00 0.00 0.00 4.00
2447 11270 0.744281 AAACGGAAAACCAGCACCTG 59.256 50.000 0.00 0.00 0.00 4.00
2448 11271 0.106918 AACGGAAAACCAGCACCTGA 60.107 50.000 0.00 0.00 32.44 3.86
2449 11272 0.818040 ACGGAAAACCAGCACCTGAC 60.818 55.000 0.00 0.00 32.44 3.51
2450 11273 0.817634 CGGAAAACCAGCACCTGACA 60.818 55.000 0.00 0.00 32.44 3.58
2451 11274 1.398692 GGAAAACCAGCACCTGACAA 58.601 50.000 0.00 0.00 32.44 3.18
2452 11275 1.963515 GGAAAACCAGCACCTGACAAT 59.036 47.619 0.00 0.00 32.44 2.71
2453 11276 2.365293 GGAAAACCAGCACCTGACAATT 59.635 45.455 0.00 0.00 32.44 2.32
2454 11277 3.572255 GGAAAACCAGCACCTGACAATTA 59.428 43.478 0.00 0.00 32.44 1.40
2455 11278 4.321230 GGAAAACCAGCACCTGACAATTAG 60.321 45.833 0.00 0.00 32.44 1.73
2456 11279 3.508845 AACCAGCACCTGACAATTAGT 57.491 42.857 0.00 0.00 32.44 2.24
2457 11280 2.783135 ACCAGCACCTGACAATTAGTG 58.217 47.619 0.00 0.00 32.44 2.74
2458 11281 2.371841 ACCAGCACCTGACAATTAGTGA 59.628 45.455 0.00 0.00 32.44 3.41
2459 11282 3.181445 ACCAGCACCTGACAATTAGTGAA 60.181 43.478 0.00 0.00 32.44 3.18
2460 11283 3.438087 CCAGCACCTGACAATTAGTGAAG 59.562 47.826 0.00 0.00 32.44 3.02
2461 11284 3.077359 AGCACCTGACAATTAGTGAAGC 58.923 45.455 0.00 0.00 31.79 3.86
2462 11285 2.813754 GCACCTGACAATTAGTGAAGCA 59.186 45.455 0.00 0.00 31.79 3.91
2463 11286 3.253188 GCACCTGACAATTAGTGAAGCAA 59.747 43.478 0.00 0.00 31.79 3.91
2464 11287 4.614535 GCACCTGACAATTAGTGAAGCAAG 60.615 45.833 0.00 0.00 31.79 4.01
2465 11288 4.074970 ACCTGACAATTAGTGAAGCAAGG 58.925 43.478 0.00 0.00 0.00 3.61
2466 11289 3.119708 CCTGACAATTAGTGAAGCAAGGC 60.120 47.826 0.00 0.00 0.00 4.35
2467 11290 2.819608 TGACAATTAGTGAAGCAAGGCC 59.180 45.455 0.00 0.00 0.00 5.19
2468 11291 2.164422 GACAATTAGTGAAGCAAGGCCC 59.836 50.000 0.00 0.00 0.00 5.80
2469 11292 1.133025 CAATTAGTGAAGCAAGGCCCG 59.867 52.381 0.00 0.00 0.00 6.13
2470 11293 0.394352 ATTAGTGAAGCAAGGCCCGG 60.394 55.000 0.00 0.00 0.00 5.73
2471 11294 2.478335 TTAGTGAAGCAAGGCCCGGG 62.478 60.000 19.09 19.09 0.00 5.73
2472 11295 4.344865 GTGAAGCAAGGCCCGGGA 62.345 66.667 29.31 0.00 0.00 5.14
2473 11296 4.033776 TGAAGCAAGGCCCGGGAG 62.034 66.667 29.31 11.80 0.00 4.30
2474 11297 3.717294 GAAGCAAGGCCCGGGAGA 61.717 66.667 29.31 0.00 0.00 3.71
2475 11298 3.256960 AAGCAAGGCCCGGGAGAA 61.257 61.111 29.31 0.00 0.00 2.87
2476 11299 2.764637 GAAGCAAGGCCCGGGAGAAA 62.765 60.000 29.31 0.00 0.00 2.52
2477 11300 2.282887 GCAAGGCCCGGGAGAAAA 60.283 61.111 29.31 0.00 0.00 2.29
2478 11301 2.343426 GCAAGGCCCGGGAGAAAAG 61.343 63.158 29.31 9.34 0.00 2.27
2479 11302 1.678970 CAAGGCCCGGGAGAAAAGG 60.679 63.158 29.31 1.54 0.00 3.11
2484 11307 4.715523 CCGGGAGAAAAGGGCGCA 62.716 66.667 10.83 0.00 0.00 6.09
2485 11308 2.438434 CGGGAGAAAAGGGCGCAT 60.438 61.111 10.83 0.00 0.00 4.73
2486 11309 2.472909 CGGGAGAAAAGGGCGCATC 61.473 63.158 10.83 0.00 0.00 3.91
2487 11310 2.121538 GGGAGAAAAGGGCGCATCC 61.122 63.158 10.83 1.02 0.00 3.51
2488 11311 1.077429 GGAGAAAAGGGCGCATCCT 60.077 57.895 10.83 4.10 39.17 3.24
2489 11312 1.379642 GGAGAAAAGGGCGCATCCTG 61.380 60.000 10.83 0.00 37.20 3.86
2490 11313 0.392998 GAGAAAAGGGCGCATCCTGA 60.393 55.000 10.83 0.00 37.20 3.86
2491 11314 0.257039 AGAAAAGGGCGCATCCTGAT 59.743 50.000 10.83 0.00 37.20 2.90
2492 11315 0.665298 GAAAAGGGCGCATCCTGATC 59.335 55.000 10.83 6.02 37.20 2.92
2493 11316 1.097547 AAAAGGGCGCATCCTGATCG 61.098 55.000 10.83 0.00 37.20 3.69
2494 11317 2.257409 AAAGGGCGCATCCTGATCGT 62.257 55.000 10.83 0.00 37.20 3.73
2495 11318 2.650813 AAGGGCGCATCCTGATCGTC 62.651 60.000 10.83 0.00 37.20 4.20
2496 11319 2.106938 GGCGCATCCTGATCGTCA 59.893 61.111 10.83 0.00 0.00 4.35
2497 11320 1.521457 GGCGCATCCTGATCGTCAA 60.521 57.895 10.83 0.00 0.00 3.18
2498 11321 1.089481 GGCGCATCCTGATCGTCAAA 61.089 55.000 10.83 0.00 0.00 2.69
2499 11322 0.940126 GCGCATCCTGATCGTCAAAT 59.060 50.000 0.30 0.00 0.00 2.32
2500 11323 1.070309 GCGCATCCTGATCGTCAAATC 60.070 52.381 0.30 0.00 0.00 2.17
2501 11324 1.528586 CGCATCCTGATCGTCAAATCC 59.471 52.381 0.00 0.00 0.00 3.01
2502 11325 2.564771 GCATCCTGATCGTCAAATCCA 58.435 47.619 0.00 0.00 0.00 3.41
2503 11326 3.144506 GCATCCTGATCGTCAAATCCAT 58.855 45.455 0.00 0.00 0.00 3.41
2504 11327 3.058432 GCATCCTGATCGTCAAATCCATG 60.058 47.826 0.00 0.00 0.00 3.66
2505 11328 3.198409 TCCTGATCGTCAAATCCATGG 57.802 47.619 4.97 4.97 0.00 3.66
2506 11329 1.605710 CCTGATCGTCAAATCCATGGC 59.394 52.381 6.96 0.00 0.00 4.40
2507 11330 1.605710 CTGATCGTCAAATCCATGGCC 59.394 52.381 6.96 0.00 0.00 5.36
2508 11331 0.588252 GATCGTCAAATCCATGGCCG 59.412 55.000 6.96 2.30 0.00 6.13
2509 11332 0.819259 ATCGTCAAATCCATGGCCGG 60.819 55.000 6.96 0.00 0.00 6.13
2510 11333 2.807622 GTCAAATCCATGGCCGGC 59.192 61.111 21.18 21.18 0.00 6.13
2511 11334 2.828095 TCAAATCCATGGCCGGCG 60.828 61.111 22.54 6.52 0.00 6.46
2512 11335 3.903282 CAAATCCATGGCCGGCGG 61.903 66.667 24.35 24.35 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 50 4.657814 ATACACTGTCCCATTCCAAACT 57.342 40.909 0.00 0.00 0.00 2.66
48 59 6.560003 AGACATCAAATATACACTGTCCCA 57.440 37.500 0.00 0.00 34.88 4.37
52 63 7.981789 CACCAGTAGACATCAAATATACACTGT 59.018 37.037 0.00 0.00 31.21 3.55
75 86 1.866925 GCAGCACGTTTCCTACACC 59.133 57.895 0.00 0.00 0.00 4.16
106 117 7.503011 GTTCCATAGAAAGGCGTTTTGCACT 62.503 44.000 5.76 1.28 38.59 4.40
114 125 0.107848 CGGGTTCCATAGAAAGGCGT 60.108 55.000 0.00 0.00 32.58 5.68
122 133 1.066716 TGGACGAAACGGGTTCCATAG 60.067 52.381 0.00 0.00 31.99 2.23
143 154 3.679083 GCATCCTCTTTAGTGTTAGCCGT 60.679 47.826 0.00 0.00 0.00 5.68
152 163 1.134670 GGACGCAGCATCCTCTTTAGT 60.135 52.381 0.00 0.00 33.03 2.24
153 164 1.576356 GGACGCAGCATCCTCTTTAG 58.424 55.000 0.00 0.00 33.03 1.85
154 165 0.178068 GGGACGCAGCATCCTCTTTA 59.822 55.000 7.60 0.00 36.40 1.85
155 166 1.078143 GGGACGCAGCATCCTCTTT 60.078 57.895 7.60 0.00 36.40 2.52
156 167 2.586792 GGGACGCAGCATCCTCTT 59.413 61.111 7.60 0.00 36.40 2.85
184 202 1.134965 GTACAAGACGCAGCATCCTCT 60.135 52.381 0.00 0.00 0.00 3.69
188 206 3.363378 GCATATGTACAAGACGCAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
216 234 5.047802 GCAAAGTGTAGTAGGTAGTACCACA 60.048 44.000 21.49 13.35 41.95 4.17
219 237 5.184671 ACAGCAAAGTGTAGTAGGTAGTACC 59.815 44.000 11.73 11.73 38.99 3.34
220 238 6.264841 ACAGCAAAGTGTAGTAGGTAGTAC 57.735 41.667 0.00 0.00 33.69 2.73
221 239 7.621428 CTACAGCAAAGTGTAGTAGGTAGTA 57.379 40.000 3.32 0.00 43.39 1.82
222 240 6.512342 CTACAGCAAAGTGTAGTAGGTAGT 57.488 41.667 3.32 0.00 43.39 2.73
239 257 4.872691 ACTAGTTCACAATGATGCTACAGC 59.127 41.667 0.00 0.00 42.50 4.40
240 258 6.101997 TCACTAGTTCACAATGATGCTACAG 58.898 40.000 0.00 0.00 0.00 2.74
243 261 6.643388 ACATCACTAGTTCACAATGATGCTA 58.357 36.000 14.06 0.00 46.91 3.49
244 262 5.494724 ACATCACTAGTTCACAATGATGCT 58.505 37.500 14.06 3.35 46.91 3.79
245 263 5.220739 GGACATCACTAGTTCACAATGATGC 60.221 44.000 14.06 8.89 46.91 3.91
247 265 6.053632 TGGACATCACTAGTTCACAATGAT 57.946 37.500 0.00 0.00 0.00 2.45
248 266 5.482163 TGGACATCACTAGTTCACAATGA 57.518 39.130 0.00 0.00 0.00 2.57
249 267 5.645067 ACATGGACATCACTAGTTCACAATG 59.355 40.000 0.00 0.00 0.00 2.82
250 268 5.645067 CACATGGACATCACTAGTTCACAAT 59.355 40.000 0.00 0.00 0.00 2.71
321 1060 0.108898 GCGCATGTTGGCATAAACCA 60.109 50.000 0.30 0.00 38.16 3.67
322 1061 0.805711 GGCGCATGTTGGCATAAACC 60.806 55.000 10.83 0.00 33.30 3.27
324 1063 0.173029 CAGGCGCATGTTGGCATAAA 59.827 50.000 15.06 0.00 33.30 1.40
325 1064 1.808546 CAGGCGCATGTTGGCATAA 59.191 52.632 15.06 0.00 33.30 1.90
326 1065 2.773745 GCAGGCGCATGTTGGCATA 61.774 57.895 24.27 0.00 38.36 3.14
327 1066 4.137872 GCAGGCGCATGTTGGCAT 62.138 61.111 24.27 2.25 38.36 4.40
344 2092 2.224066 CGCTAGACTACATTCCTTGGGG 60.224 54.545 0.00 0.00 0.00 4.96
371 2119 2.067932 TTGGACACCTTCCCAGCCAG 62.068 60.000 0.00 0.00 45.17 4.85
377 2126 0.613777 AGACGATTGGACACCTTCCC 59.386 55.000 0.00 0.00 45.17 3.97
384 2133 6.664515 GTCACAAAAATAAGACGATTGGACA 58.335 36.000 0.00 0.00 0.00 4.02
490 2239 6.228258 GCATTGAAGGCCATATGAATTCAAT 58.772 36.000 23.12 23.12 46.26 2.57
491 2240 5.603596 GCATTGAAGGCCATATGAATTCAA 58.396 37.500 21.59 21.59 42.26 2.69
504 2253 1.202336 CGATTTCAGGGCATTGAAGGC 60.202 52.381 0.00 0.00 38.25 4.35
529 2285 3.450457 AGACTAGGATCAAAGACTGCAGG 59.550 47.826 19.93 0.00 0.00 4.85
609 2365 2.938838 AGAGTAGAGAGTGATTCCGGG 58.061 52.381 0.00 0.00 0.00 5.73
614 2370 6.094881 GCAGTCAGTAAGAGTAGAGAGTGATT 59.905 42.308 0.00 0.00 0.00 2.57
630 2386 0.613260 GTGGACCCATGCAGTCAGTA 59.387 55.000 14.02 0.61 35.89 2.74
638 2394 2.346766 TATGACATGTGGACCCATGC 57.653 50.000 17.89 12.93 44.88 4.06
648 2404 7.799081 TGAGAAAGAAGATGGATATGACATGT 58.201 34.615 0.00 0.00 0.00 3.21
671 2427 8.981659 TCTTGTGGAGAGAGATAAACATTATGA 58.018 33.333 0.00 0.00 0.00 2.15
733 2489 3.599412 GACTAGGTCGTGGCAAACA 57.401 52.632 0.00 0.00 0.00 2.83
744 2500 3.056749 GTGTCCACTGATTTCGACTAGGT 60.057 47.826 0.00 0.00 0.00 3.08
746 2502 3.193691 AGGTGTCCACTGATTTCGACTAG 59.806 47.826 0.00 0.00 0.00 2.57
791 2547 7.011189 CGTTTCGTTTTTCGTTCTAACCATAT 58.989 34.615 0.00 0.00 40.80 1.78
794 2550 4.328440 TCGTTTCGTTTTTCGTTCTAACCA 59.672 37.500 0.00 0.00 40.80 3.67
795 2551 4.821012 TCGTTTCGTTTTTCGTTCTAACC 58.179 39.130 0.00 0.00 40.80 2.85
798 8738 9.726034 GTTATATTCGTTTCGTTTTTCGTTCTA 57.274 29.630 0.00 0.00 40.80 2.10
804 8744 8.491605 TGGTTGTTATATTCGTTTCGTTTTTC 57.508 30.769 0.00 0.00 0.00 2.29
880 8820 3.016736 AGTCTCCAAATATTGTTGCCCG 58.983 45.455 0.00 0.00 0.00 6.13
943 8886 8.520351 GGCCATTTTATACTGGATTTATGGTAC 58.480 37.037 0.00 0.00 34.24 3.34
997 8940 0.519999 CGATCGTTGCTTTGCTCTGC 60.520 55.000 7.03 0.00 0.00 4.26
1017 8960 5.468746 TCGTTGTATTGAAGGAAAGACTTGG 59.531 40.000 0.00 0.00 0.00 3.61
1040 8983 6.242396 TGGCTACTCCTCATCTTAGATAGTC 58.758 44.000 0.00 0.00 35.26 2.59
1042 8985 6.480763 TCTGGCTACTCCTCATCTTAGATAG 58.519 44.000 0.00 0.00 35.26 2.08
1058 9001 1.661341 CAGGAGCAACATCTGGCTAC 58.339 55.000 0.00 0.00 41.22 3.58
1121 9064 6.091437 ACGAGATTTTGAAGGAACGTAGTAG 58.909 40.000 0.00 0.00 45.00 2.57
1402 9347 7.918536 ACATGACATCCAATCATAGCTAATC 57.081 36.000 0.00 0.00 34.99 1.75
1477 9422 3.637998 TCTTCATACGGCTTATCGGTC 57.362 47.619 0.00 0.00 0.00 4.79
1634 9591 3.384467 AGCAAAGCTAATGTGTTGGTGTT 59.616 39.130 0.00 0.00 36.99 3.32
1635 9592 2.958355 AGCAAAGCTAATGTGTTGGTGT 59.042 40.909 0.00 0.00 36.99 4.16
1642 9599 5.927030 TCGTCTAAAAGCAAAGCTAATGTG 58.073 37.500 0.00 0.00 38.25 3.21
1668 9625 3.973425 TGTACTACCCCAAGGAGTAGTC 58.027 50.000 15.55 9.18 44.54 2.59
1754 9713 3.556365 GCAAGGAGAATTAGCCGAGTAAC 59.444 47.826 0.00 0.00 0.00 2.50
1762 10467 2.128771 TGGTGGCAAGGAGAATTAGC 57.871 50.000 0.00 0.00 0.00 3.09
1763 10468 2.360165 GCATGGTGGCAAGGAGAATTAG 59.640 50.000 0.00 0.00 0.00 1.73
1764 10469 2.291475 TGCATGGTGGCAAGGAGAATTA 60.291 45.455 0.00 0.00 41.65 1.40
1766 10471 0.040058 TGCATGGTGGCAAGGAGAAT 59.960 50.000 0.00 0.00 41.65 2.40
1826 10531 2.091665 CCTAAAGGCCAATGAGACCCAT 60.092 50.000 5.01 0.00 36.99 4.00
1885 10590 4.066710 AGCTCGCTTATTCACGAAAAAC 57.933 40.909 0.00 0.00 37.94 2.43
1992 10708 9.151471 CATCTAATATCCTACCAAATACCAACG 57.849 37.037 0.00 0.00 0.00 4.10
2007 10723 9.553064 CCTAATATCAACCTGCATCTAATATCC 57.447 37.037 0.00 0.00 0.00 2.59
2011 10727 8.035394 CGTACCTAATATCAACCTGCATCTAAT 58.965 37.037 0.00 0.00 0.00 1.73
2013 10729 6.717997 TCGTACCTAATATCAACCTGCATCTA 59.282 38.462 0.00 0.00 0.00 1.98
2014 10730 5.538813 TCGTACCTAATATCAACCTGCATCT 59.461 40.000 0.00 0.00 0.00 2.90
2087 10885 2.156917 CATTGAGCCACGCCATATGAT 58.843 47.619 3.65 0.00 0.00 2.45
2127 10926 4.150098 GCTTAGCGTTCTAATTACCCATCG 59.850 45.833 0.00 0.00 34.54 3.84
2156 10977 1.621107 ACTATACGGTTCACAACGCG 58.379 50.000 3.53 3.53 0.00 6.01
2223 11044 4.634883 GGGCTGGCTTTTTAACTAGTACTC 59.365 45.833 0.00 0.00 0.00 2.59
2226 11047 4.287585 TCAGGGCTGGCTTTTTAACTAGTA 59.712 41.667 0.00 0.00 0.00 1.82
2227 11048 3.073946 TCAGGGCTGGCTTTTTAACTAGT 59.926 43.478 0.00 0.00 0.00 2.57
2228 11049 3.686016 TCAGGGCTGGCTTTTTAACTAG 58.314 45.455 0.00 0.00 0.00 2.57
2351 11174 3.004419 GGTTTTCGCTAGGTTTTCTTGCT 59.996 43.478 0.00 0.00 41.08 3.91
2353 11176 3.002965 ACGGTTTTCGCTAGGTTTTCTTG 59.997 43.478 0.00 0.00 43.89 3.02
2377 11200 4.342862 TTCATGGGATTCTTCGGATCTC 57.657 45.455 0.00 0.00 0.00 2.75
2381 11204 4.027674 TGTTTTCATGGGATTCTTCGGA 57.972 40.909 0.00 0.00 0.00 4.55
2395 11218 4.177026 CCGTTTTGGTTGTGATGTTTTCA 58.823 39.130 0.00 0.00 0.00 2.69
2416 11239 4.805192 GGTTTTCCGTTTGTTACTTTTCCC 59.195 41.667 0.00 0.00 0.00 3.97
2445 11268 3.119708 GGCCTTGCTTCACTAATTGTCAG 60.120 47.826 0.00 0.00 0.00 3.51
2446 11269 2.819608 GGCCTTGCTTCACTAATTGTCA 59.180 45.455 0.00 0.00 0.00 3.58
2447 11270 2.164422 GGGCCTTGCTTCACTAATTGTC 59.836 50.000 0.84 0.00 0.00 3.18
2448 11271 2.171003 GGGCCTTGCTTCACTAATTGT 58.829 47.619 0.84 0.00 0.00 2.71
2449 11272 1.133025 CGGGCCTTGCTTCACTAATTG 59.867 52.381 0.84 0.00 0.00 2.32
2450 11273 1.463674 CGGGCCTTGCTTCACTAATT 58.536 50.000 0.84 0.00 0.00 1.40
2451 11274 0.394352 CCGGGCCTTGCTTCACTAAT 60.394 55.000 0.84 0.00 0.00 1.73
2452 11275 1.002624 CCGGGCCTTGCTTCACTAA 60.003 57.895 0.84 0.00 0.00 2.24
2453 11276 2.668632 CCGGGCCTTGCTTCACTA 59.331 61.111 0.84 0.00 0.00 2.74
2454 11277 4.351054 CCCGGGCCTTGCTTCACT 62.351 66.667 8.08 0.00 0.00 3.41
2455 11278 4.344865 TCCCGGGCCTTGCTTCAC 62.345 66.667 18.49 0.00 0.00 3.18
2456 11279 4.033776 CTCCCGGGCCTTGCTTCA 62.034 66.667 18.49 0.00 0.00 3.02
2457 11280 2.764637 TTTCTCCCGGGCCTTGCTTC 62.765 60.000 18.49 0.00 0.00 3.86
2458 11281 2.366153 TTTTCTCCCGGGCCTTGCTT 62.366 55.000 18.49 0.00 0.00 3.91
2459 11282 2.771328 CTTTTCTCCCGGGCCTTGCT 62.771 60.000 18.49 0.00 0.00 3.91
2460 11283 2.282887 TTTTCTCCCGGGCCTTGC 60.283 61.111 18.49 0.00 0.00 4.01
2461 11284 1.678970 CCTTTTCTCCCGGGCCTTG 60.679 63.158 18.49 5.91 0.00 3.61
2462 11285 2.763902 CCTTTTCTCCCGGGCCTT 59.236 61.111 18.49 0.00 0.00 4.35
2463 11286 3.339093 CCCTTTTCTCCCGGGCCT 61.339 66.667 18.49 0.00 0.00 5.19
2467 11290 3.995506 ATGCGCCCTTTTCTCCCGG 62.996 63.158 4.18 0.00 0.00 5.73
2468 11291 2.438434 ATGCGCCCTTTTCTCCCG 60.438 61.111 4.18 0.00 0.00 5.14
2469 11292 2.121538 GGATGCGCCCTTTTCTCCC 61.122 63.158 4.18 0.00 0.00 4.30
2470 11293 1.077429 AGGATGCGCCCTTTTCTCC 60.077 57.895 4.18 0.00 37.37 3.71
2471 11294 0.392998 TCAGGATGCGCCCTTTTCTC 60.393 55.000 4.18 0.00 37.37 2.87
2472 11295 0.257039 ATCAGGATGCGCCCTTTTCT 59.743 50.000 4.18 0.00 37.37 2.52
2473 11296 0.665298 GATCAGGATGCGCCCTTTTC 59.335 55.000 4.18 0.42 37.37 2.29
2474 11297 1.097547 CGATCAGGATGCGCCCTTTT 61.098 55.000 4.18 0.00 37.37 2.27
2475 11298 1.524621 CGATCAGGATGCGCCCTTT 60.525 57.895 4.18 0.00 37.37 3.11
2476 11299 2.109799 CGATCAGGATGCGCCCTT 59.890 61.111 4.18 0.00 37.37 3.95
2477 11300 3.157217 GACGATCAGGATGCGCCCT 62.157 63.158 4.18 0.98 37.37 5.19
2478 11301 2.663188 GACGATCAGGATGCGCCC 60.663 66.667 4.18 0.00 37.37 6.13
2479 11302 1.089481 TTTGACGATCAGGATGCGCC 61.089 55.000 4.18 0.00 34.76 6.53
2480 11303 0.940126 ATTTGACGATCAGGATGCGC 59.060 50.000 0.00 0.00 34.76 6.09
2481 11304 1.528586 GGATTTGACGATCAGGATGCG 59.471 52.381 0.00 0.00 34.76 4.73
2482 11305 2.564771 TGGATTTGACGATCAGGATGC 58.435 47.619 0.00 0.00 34.76 3.91
2483 11306 3.501062 CCATGGATTTGACGATCAGGATG 59.499 47.826 5.56 0.00 37.54 3.51
2484 11307 3.748083 CCATGGATTTGACGATCAGGAT 58.252 45.455 5.56 0.00 0.00 3.24
2485 11308 2.746142 GCCATGGATTTGACGATCAGGA 60.746 50.000 18.40 0.00 0.00 3.86
2486 11309 1.605710 GCCATGGATTTGACGATCAGG 59.394 52.381 18.40 0.00 0.00 3.86
2487 11310 1.605710 GGCCATGGATTTGACGATCAG 59.394 52.381 18.40 0.00 0.00 2.90
2488 11311 1.679139 GGCCATGGATTTGACGATCA 58.321 50.000 18.40 0.00 0.00 2.92
2489 11312 0.588252 CGGCCATGGATTTGACGATC 59.412 55.000 18.40 0.00 0.00 3.69
2490 11313 0.819259 CCGGCCATGGATTTGACGAT 60.819 55.000 18.40 0.00 0.00 3.73
2491 11314 1.451207 CCGGCCATGGATTTGACGA 60.451 57.895 18.40 0.00 0.00 4.20
2492 11315 3.110139 CCGGCCATGGATTTGACG 58.890 61.111 18.40 9.01 0.00 4.35
2493 11316 2.807622 GCCGGCCATGGATTTGAC 59.192 61.111 18.11 0.00 0.00 3.18
2494 11317 2.828095 CGCCGGCCATGGATTTGA 60.828 61.111 23.46 0.00 0.00 2.69
2495 11318 3.903282 CCGCCGGCCATGGATTTG 61.903 66.667 23.46 2.52 0.00 2.32


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

AutoCloner maintained by Alex Coulton.