Multiple sequence alignment - TraesCS6D01G189400

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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 TraesCS6D01G189400 chr6D 100.000 2839 0 0 1 2839 262271110 262273948 0.000000e+00 5243.0
1 TraesCS6D01G189400 chr6A 92.147 2254 85 27 2 2235 322997869 322995688 0.000000e+00 3097.0
2 TraesCS6D01G189400 chr6A 93.296 537 22 4 2303 2839 322995703 322995181 0.000000e+00 780.0
3 TraesCS6D01G189400 chr6B 91.583 1497 59 25 776 2235 348696757 348695291 0.000000e+00 2004.0
4 TraesCS6D01G189400 chr6B 92.393 723 22 11 2 720 348704458 348703765 0.000000e+00 1000.0
5 TraesCS6D01G189400 chr6B 91.387 476 23 7 2303 2770 348695306 348694841 1.110000e-178 636.0
6 TraesCS6D01G189400 chr6B 100.000 39 0 0 2801 2839 348694841 348694803 3.920000e-09 73.1
7 TraesCS6D01G189400 chr7A 100.000 28 0 0 2648 2675 567598054 567598027 5.000000e-03 52.8
8 TraesCS6D01G189400 chr5D 100.000 28 0 0 2648 2675 105114145 105114172 5.000000e-03 52.8
9 TraesCS6D01G189400 chr5B 100.000 28 0 0 2648 2675 115090631 115090658 5.000000e-03 52.8
10 TraesCS6D01G189400 chr5A 100.000 28 0 0 2648 2675 109290414 109290441 5.000000e-03 52.8
11 TraesCS6D01G189400 chr3A 100.000 28 0 0 2648 2675 528530998 528531025 5.000000e-03 52.8
12 TraesCS6D01G189400 chr1D 100.000 28 0 0 2648 2675 17195743 17195770 5.000000e-03 52.8
13 TraesCS6D01G189400 chr1A 100.000 28 0 0 2648 2675 548797139 548797166 5.000000e-03 52.8


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 TraesCS6D01G189400 chr6D 262271110 262273948 2838 False 5243.000000 5243 100.000000 1 2839 1 chr6D.!!$F1 2838
1 TraesCS6D01G189400 chr6A 322995181 322997869 2688 True 1938.500000 3097 92.721500 2 2839 2 chr6A.!!$R1 2837
2 TraesCS6D01G189400 chr6B 348703765 348704458 693 True 1000.000000 1000 92.393000 2 720 1 chr6B.!!$R1 718
3 TraesCS6D01G189400 chr6B 348694803 348696757 1954 True 904.366667 2004 94.323333 776 2839 3 chr6B.!!$R2 2063

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
291 292 0.178947 GAACCCACCCAACCCAATGA 60.179 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2342 0.02877 CAGTTTTGCTCCGTTTGCGA 59.971 50.0 0.0 0.0 41.33 5.1 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
54 55 5.508825 CCTTCCAGTCTATGTGTATCTGCTC 60.509 48.000 0.00 0.00 0.00 4.26
56 57 5.143369 TCCAGTCTATGTGTATCTGCTCAT 58.857 41.667 0.00 0.00 0.00 2.90
81 82 4.879598 ACGAGTTCTTTTCTCAACCGTAT 58.120 39.130 0.00 0.00 31.78 3.06
138 139 0.260230 TTGTGCACAAAGGGGGAGAA 59.740 50.000 29.36 2.82 32.11 2.87
249 250 5.305128 ACATTTTTCATCCAGTTCACCATGT 59.695 36.000 0.00 0.00 0.00 3.21
250 251 6.493115 ACATTTTTCATCCAGTTCACCATGTA 59.507 34.615 0.00 0.00 0.00 2.29
251 252 6.573664 TTTTTCATCCAGTTCACCATGTAG 57.426 37.500 0.00 0.00 0.00 2.74
252 253 5.497464 TTTCATCCAGTTCACCATGTAGA 57.503 39.130 0.00 0.00 0.00 2.59
254 255 5.089970 TCATCCAGTTCACCATGTAGAAG 57.910 43.478 0.00 0.00 0.00 2.85
255 256 4.532126 TCATCCAGTTCACCATGTAGAAGT 59.468 41.667 0.00 0.00 0.00 3.01
256 257 5.719563 TCATCCAGTTCACCATGTAGAAGTA 59.280 40.000 4.86 0.00 0.00 2.24
257 258 5.661056 TCCAGTTCACCATGTAGAAGTAG 57.339 43.478 4.86 0.00 0.00 2.57
258 259 5.084519 TCCAGTTCACCATGTAGAAGTAGT 58.915 41.667 4.86 0.00 0.00 2.73
259 260 6.250711 TCCAGTTCACCATGTAGAAGTAGTA 58.749 40.000 4.86 0.00 0.00 1.82
260 261 6.377429 TCCAGTTCACCATGTAGAAGTAGTAG 59.623 42.308 4.86 0.00 0.00 2.57
261 262 6.153000 CCAGTTCACCATGTAGAAGTAGTAGT 59.847 42.308 4.86 0.00 0.00 2.73
262 263 7.338703 CCAGTTCACCATGTAGAAGTAGTAGTA 59.661 40.741 4.86 0.00 0.00 1.82
263 264 8.904834 CAGTTCACCATGTAGAAGTAGTAGTAT 58.095 37.037 4.86 0.00 0.00 2.12
276 277 9.122779 AGAAGTAGTAGTATCATGTAGTGAACC 57.877 37.037 0.00 0.00 40.97 3.62
278 279 7.351952 AGTAGTAGTATCATGTAGTGAACCCA 58.648 38.462 0.00 0.00 40.97 4.51
279 280 6.466885 AGTAGTATCATGTAGTGAACCCAC 57.533 41.667 0.00 0.00 40.97 4.61
280 281 4.755266 AGTATCATGTAGTGAACCCACC 57.245 45.455 0.00 0.00 44.22 4.61
281 282 3.454812 AGTATCATGTAGTGAACCCACCC 59.545 47.826 0.00 0.00 44.22 4.61
282 283 1.735926 TCATGTAGTGAACCCACCCA 58.264 50.000 0.00 0.00 44.22 4.51
284 285 2.159382 CATGTAGTGAACCCACCCAAC 58.841 52.381 0.00 0.00 44.22 3.77
285 286 0.475044 TGTAGTGAACCCACCCAACC 59.525 55.000 0.00 0.00 44.22 3.77
286 287 0.251033 GTAGTGAACCCACCCAACCC 60.251 60.000 0.00 0.00 44.22 4.11
287 288 0.698198 TAGTGAACCCACCCAACCCA 60.698 55.000 0.00 0.00 44.22 4.51
288 289 1.075896 GTGAACCCACCCAACCCAA 60.076 57.895 0.00 0.00 37.33 4.12
289 290 0.471022 GTGAACCCACCCAACCCAAT 60.471 55.000 0.00 0.00 37.33 3.16
290 291 0.470833 TGAACCCACCCAACCCAATG 60.471 55.000 0.00 0.00 0.00 2.82
291 292 0.178947 GAACCCACCCAACCCAATGA 60.179 55.000 0.00 0.00 0.00 2.57
292 293 0.266152 AACCCACCCAACCCAATGAA 59.734 50.000 0.00 0.00 0.00 2.57
629 631 1.868713 TGGCCACCCGTTCTATTCTA 58.131 50.000 0.00 0.00 0.00 2.10
630 632 2.404559 TGGCCACCCGTTCTATTCTAT 58.595 47.619 0.00 0.00 0.00 1.98
631 633 2.775384 TGGCCACCCGTTCTATTCTATT 59.225 45.455 0.00 0.00 0.00 1.73
767 773 9.887406 AGTTAAAACAACATTCTGGTAAATACG 57.113 29.630 0.00 0.00 0.00 3.06
768 774 9.667989 GTTAAAACAACATTCTGGTAAATACGT 57.332 29.630 0.00 0.00 0.00 3.57
771 777 8.611654 AAACAACATTCTGGTAAATACGTACT 57.388 30.769 0.00 0.00 0.00 2.73
772 778 7.823149 ACAACATTCTGGTAAATACGTACTC 57.177 36.000 0.00 0.00 0.00 2.59
773 779 6.815142 ACAACATTCTGGTAAATACGTACTCC 59.185 38.462 0.00 0.00 0.00 3.85
774 780 6.786967 ACATTCTGGTAAATACGTACTCCT 57.213 37.500 0.00 0.00 0.00 3.69
804 810 5.794894 TGATGGTTAAAGAGGAGAAGTGAC 58.205 41.667 0.00 0.00 0.00 3.67
840 846 1.139095 GTCTAGAGTTGCGGTCCCG 59.861 63.158 0.24 0.24 43.09 5.14
912 918 1.482621 CGATTGACATCTGACGGCGG 61.483 60.000 13.24 0.00 0.00 6.13
929 935 0.882042 CGGGATGCTCTTATTGCGCT 60.882 55.000 9.73 0.00 0.00 5.92
930 936 0.871057 GGGATGCTCTTATTGCGCTC 59.129 55.000 9.73 0.00 0.00 5.03
1008 1014 3.130340 TGATCCAATCTCGAATGTCGTCA 59.870 43.478 0.00 0.00 41.35 4.35
1135 1141 0.243095 GTCTTCGGCCTACTCGTTGT 59.757 55.000 0.00 0.00 0.00 3.32
1242 1261 1.352156 CTTCCGTCCTTTTCGGCTCG 61.352 60.000 0.00 0.00 46.49 5.03
1437 1465 8.118607 GCTTGGAATTTTCTTTTTCTTTGTCAG 58.881 33.333 0.00 0.00 0.00 3.51
1460 1488 4.378874 GGAAGAAACGGAAGCAGAATTCTG 60.379 45.833 27.82 27.82 46.40 3.02
1603 1637 2.202676 GAGAGGTTCAGCGAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
1686 1720 5.121221 GCACAATTGCCACTTTACTTACT 57.879 39.130 5.05 0.00 43.66 2.24
1724 1764 7.679164 GCCATCTCTTCTTTTCATCATCTCAAC 60.679 40.741 0.00 0.00 0.00 3.18
1729 1769 8.103948 TCTTCTTTTCATCATCTCAACCTTTC 57.896 34.615 0.00 0.00 0.00 2.62
1732 1772 6.656693 TCTTTTCATCATCTCAACCTTTCCTC 59.343 38.462 0.00 0.00 0.00 3.71
1738 1782 4.709397 TCATCTCAACCTTTCCTCTCTCTC 59.291 45.833 0.00 0.00 0.00 3.20
1740 1784 4.340617 TCTCAACCTTTCCTCTCTCTCTC 58.659 47.826 0.00 0.00 0.00 3.20
1742 1786 4.340617 TCAACCTTTCCTCTCTCTCTCTC 58.659 47.826 0.00 0.00 0.00 3.20
1744 1788 4.236527 ACCTTTCCTCTCTCTCTCTCTC 57.763 50.000 0.00 0.00 0.00 3.20
1745 1789 3.852578 ACCTTTCCTCTCTCTCTCTCTCT 59.147 47.826 0.00 0.00 0.00 3.10
1746 1790 4.080299 ACCTTTCCTCTCTCTCTCTCTCTC 60.080 50.000 0.00 0.00 0.00 3.20
1749 1793 3.724478 TCCTCTCTCTCTCTCTCTCTGT 58.276 50.000 0.00 0.00 0.00 3.41
1751 1795 3.198635 CCTCTCTCTCTCTCTCTCTGTGT 59.801 52.174 0.00 0.00 0.00 3.72
1918 1963 3.246699 TGCACTAGCGTTGTTTACTGAAC 59.753 43.478 0.00 0.00 46.23 3.18
1958 2004 9.016623 CGTCTCAAAATATTCGTGATGTACTAA 57.983 33.333 0.00 0.00 0.00 2.24
1999 2054 2.985957 AAATGGTGCCATATGGTTGC 57.014 45.000 22.79 12.62 35.31 4.17
2145 2201 0.920664 GTTGCCGTTTCACTTTGCAC 59.079 50.000 0.00 0.00 0.00 4.57
2220 2276 9.886132 TTCTAATCCTAGACCAAGAAAACATAC 57.114 33.333 0.00 0.00 33.73 2.39
2221 2277 9.268282 TCTAATCCTAGACCAAGAAAACATACT 57.732 33.333 0.00 0.00 0.00 2.12
2222 2278 9.319143 CTAATCCTAGACCAAGAAAACATACTG 57.681 37.037 0.00 0.00 0.00 2.74
2223 2279 5.488341 TCCTAGACCAAGAAAACATACTGC 58.512 41.667 0.00 0.00 0.00 4.40
2224 2280 4.636206 CCTAGACCAAGAAAACATACTGCC 59.364 45.833 0.00 0.00 0.00 4.85
2225 2281 4.373156 AGACCAAGAAAACATACTGCCT 57.627 40.909 0.00 0.00 0.00 4.75
2226 2282 4.074970 AGACCAAGAAAACATACTGCCTG 58.925 43.478 0.00 0.00 0.00 4.85
2227 2283 2.558359 ACCAAGAAAACATACTGCCTGC 59.442 45.455 0.00 0.00 0.00 4.85
2228 2284 2.557924 CCAAGAAAACATACTGCCTGCA 59.442 45.455 0.00 0.00 0.00 4.41
2229 2285 3.005684 CCAAGAAAACATACTGCCTGCAA 59.994 43.478 0.00 0.00 0.00 4.08
2230 2286 3.923017 AGAAAACATACTGCCTGCAAC 57.077 42.857 0.00 0.00 0.00 4.17
2231 2287 3.490348 AGAAAACATACTGCCTGCAACT 58.510 40.909 0.00 0.00 0.00 3.16
2232 2288 4.651778 AGAAAACATACTGCCTGCAACTA 58.348 39.130 0.00 0.00 0.00 2.24
2233 2289 4.455877 AGAAAACATACTGCCTGCAACTAC 59.544 41.667 0.00 0.00 0.00 2.73
2234 2290 3.703001 AACATACTGCCTGCAACTACT 57.297 42.857 0.00 0.00 0.00 2.57
2235 2291 3.703001 ACATACTGCCTGCAACTACTT 57.297 42.857 0.00 0.00 0.00 2.24
2236 2292 4.021102 ACATACTGCCTGCAACTACTTT 57.979 40.909 0.00 0.00 0.00 2.66
2237 2293 4.398319 ACATACTGCCTGCAACTACTTTT 58.602 39.130 0.00 0.00 0.00 2.27
2238 2294 4.827284 ACATACTGCCTGCAACTACTTTTT 59.173 37.500 0.00 0.00 0.00 1.94
2259 2315 4.529716 TTTGGAAATGGAGGTATACCCC 57.470 45.455 18.65 18.25 36.42 4.95
2260 2316 2.424793 TGGAAATGGAGGTATACCCCC 58.575 52.381 18.65 17.04 36.42 5.40
2261 2317 1.350019 GGAAATGGAGGTATACCCCCG 59.650 57.143 18.65 0.00 36.42 5.73
2262 2318 1.350019 GAAATGGAGGTATACCCCCGG 59.650 57.143 18.65 0.00 36.42 5.73
2263 2319 1.131928 AATGGAGGTATACCCCCGGC 61.132 60.000 18.65 3.34 36.42 6.13
2264 2320 2.926779 GGAGGTATACCCCCGGCC 60.927 72.222 18.65 8.67 36.42 6.13
2265 2321 2.122725 GAGGTATACCCCCGGCCA 60.123 66.667 18.65 0.00 36.42 5.36
2266 2322 2.447186 AGGTATACCCCCGGCCAC 60.447 66.667 18.65 0.00 36.42 5.01
2267 2323 2.447186 GGTATACCCCCGGCCACT 60.447 66.667 11.17 0.00 0.00 4.00
2268 2324 2.814835 GGTATACCCCCGGCCACTG 61.815 68.421 11.17 0.00 0.00 3.66
2269 2325 3.165685 TATACCCCCGGCCACTGC 61.166 66.667 2.24 0.00 0.00 4.40
2274 2330 4.511246 CCCCGGCCACTGCATCAT 62.511 66.667 2.24 0.00 40.13 2.45
2275 2331 3.214123 CCCGGCCACTGCATCATG 61.214 66.667 2.24 0.00 40.13 3.07
2276 2332 2.124612 CCGGCCACTGCATCATGA 60.125 61.111 2.24 0.00 40.13 3.07
2277 2333 1.527611 CCGGCCACTGCATCATGAT 60.528 57.895 2.24 1.18 40.13 2.45
2278 2334 1.652563 CGGCCACTGCATCATGATG 59.347 57.895 28.04 28.04 41.60 3.07
2279 2335 0.816421 CGGCCACTGCATCATGATGA 60.816 55.000 34.65 19.93 41.20 2.92
2280 2336 1.617322 GGCCACTGCATCATGATGAT 58.383 50.000 34.65 18.39 41.20 2.45
2281 2337 2.786777 GGCCACTGCATCATGATGATA 58.213 47.619 34.65 22.08 41.20 2.15
2282 2338 2.486982 GGCCACTGCATCATGATGATAC 59.513 50.000 34.65 19.58 41.20 2.24
2283 2339 3.143728 GCCACTGCATCATGATGATACA 58.856 45.455 34.65 22.61 41.20 2.29
2285 2341 3.188667 CCACTGCATCATGATGATACAGC 59.811 47.826 34.65 20.45 46.95 4.40
2286 2342 4.065789 CACTGCATCATGATGATACAGCT 58.934 43.478 34.65 19.45 46.95 4.24
2287 2343 4.152580 CACTGCATCATGATGATACAGCTC 59.847 45.833 34.65 16.97 46.95 4.09
2288 2344 3.323243 TGCATCATGATGATACAGCTCG 58.677 45.455 34.65 8.71 41.20 5.03
2289 2345 2.093941 GCATCATGATGATACAGCTCGC 59.906 50.000 34.65 14.53 41.20 5.03
2290 2346 3.323243 CATCATGATGATACAGCTCGCA 58.677 45.455 28.37 0.00 41.20 5.10
2291 2347 3.457610 TCATGATGATACAGCTCGCAA 57.542 42.857 0.00 0.00 0.00 4.85
2292 2348 3.795877 TCATGATGATACAGCTCGCAAA 58.204 40.909 0.00 0.00 0.00 3.68
2293 2349 3.557185 TCATGATGATACAGCTCGCAAAC 59.443 43.478 0.00 0.00 0.00 2.93
2294 2350 1.926510 TGATGATACAGCTCGCAAACG 59.073 47.619 0.00 0.00 42.01 3.60
2295 2351 1.258982 GATGATACAGCTCGCAAACGG 59.741 52.381 0.00 0.00 40.63 4.44
2296 2352 0.245266 TGATACAGCTCGCAAACGGA 59.755 50.000 0.00 0.00 40.63 4.69
2297 2353 0.924090 GATACAGCTCGCAAACGGAG 59.076 55.000 0.00 0.00 40.63 4.63
2298 2354 1.084370 ATACAGCTCGCAAACGGAGC 61.084 55.000 5.69 5.69 40.47 4.70
2299 2355 2.428960 TACAGCTCGCAAACGGAGCA 62.429 55.000 15.27 0.00 41.70 4.26
2300 2356 2.280797 AGCTCGCAAACGGAGCAA 60.281 55.556 15.27 0.00 41.70 3.91
2301 2357 1.891919 AGCTCGCAAACGGAGCAAA 60.892 52.632 15.27 0.00 41.70 3.68
2467 2528 5.109210 TGAGTATCTGGTAATTTGCTGTCG 58.891 41.667 0.00 0.00 34.92 4.35
2486 2547 6.183360 GCTGTCGGTAGTTCTTTTACACATAC 60.183 42.308 0.00 0.00 0.00 2.39
2489 2550 8.239314 TGTCGGTAGTTCTTTTACACATACTAG 58.761 37.037 0.00 0.00 0.00 2.57
2538 2599 9.255304 GCAAAATGTTTACTAACAAAATGGAGA 57.745 29.630 0.00 0.00 46.62 3.71
2601 2665 6.645700 TCAGCAAACAAACACAAATTTCTC 57.354 33.333 0.00 0.00 0.00 2.87
2615 2679 7.505585 ACACAAATTTCTCCTGGATTCTGTTTA 59.494 33.333 0.00 0.00 0.00 2.01
2623 2687 5.800296 TCCTGGATTCTGTTTACGAAATGA 58.200 37.500 0.00 0.00 0.00 2.57
2625 2689 5.065218 CCTGGATTCTGTTTACGAAATGAGG 59.935 44.000 0.00 0.00 0.00 3.86
2626 2690 4.941263 TGGATTCTGTTTACGAAATGAGGG 59.059 41.667 0.00 0.00 0.00 4.30
2627 2691 5.183228 GGATTCTGTTTACGAAATGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
2628 2692 5.294552 GGATTCTGTTTACGAAATGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
2629 2693 5.477607 TTCTGTTTACGAAATGAGGGAGA 57.522 39.130 0.00 0.00 0.00 3.71
2630 2694 5.073311 TCTGTTTACGAAATGAGGGAGAG 57.927 43.478 0.00 0.00 0.00 3.20
2631 2695 4.081642 TCTGTTTACGAAATGAGGGAGAGG 60.082 45.833 0.00 0.00 0.00 3.69
2632 2696 3.055385 TGTTTACGAAATGAGGGAGAGGG 60.055 47.826 0.00 0.00 0.00 4.30
2633 2697 2.840640 TACGAAATGAGGGAGAGGGA 57.159 50.000 0.00 0.00 0.00 4.20
2634 2698 1.196012 ACGAAATGAGGGAGAGGGAC 58.804 55.000 0.00 0.00 0.00 4.46
2635 2699 0.466124 CGAAATGAGGGAGAGGGACC 59.534 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.251527 GCAGGGACTTGACGAGAGGA 61.252 60.000 0.00 0.00 34.60 3.71
54 55 5.444122 GGTTGAGAAAAGAACTCGTTCATG 58.556 41.667 11.90 0.00 41.84 3.07
56 57 3.554324 CGGTTGAGAAAAGAACTCGTTCA 59.446 43.478 11.90 0.00 41.84 3.18
81 82 1.000163 GTGGCGTCTGAGAAGAAGTCA 60.000 52.381 0.00 0.00 30.14 3.41
138 139 2.765807 CCATCCACTCCGCCTCCT 60.766 66.667 0.00 0.00 0.00 3.69
250 251 9.122779 GGTTCACTACATGATACTACTACTTCT 57.877 37.037 0.00 0.00 37.11 2.85
251 252 8.351461 GGGTTCACTACATGATACTACTACTTC 58.649 40.741 0.00 0.00 37.11 3.01
252 253 7.837689 TGGGTTCACTACATGATACTACTACTT 59.162 37.037 0.00 0.00 37.11 2.24
254 255 7.424001 GTGGGTTCACTACATGATACTACTAC 58.576 42.308 0.00 0.00 40.58 2.73
255 256 6.548622 GGTGGGTTCACTACATGATACTACTA 59.451 42.308 0.00 0.00 43.17 1.82
256 257 5.363005 GGTGGGTTCACTACATGATACTACT 59.637 44.000 0.00 0.00 43.17 2.57
257 258 5.452917 GGGTGGGTTCACTACATGATACTAC 60.453 48.000 0.00 0.00 43.17 2.73
258 259 4.652421 GGGTGGGTTCACTACATGATACTA 59.348 45.833 0.00 0.00 43.17 1.82
259 260 3.454812 GGGTGGGTTCACTACATGATACT 59.545 47.826 0.00 0.00 43.17 2.12
260 261 3.199071 TGGGTGGGTTCACTACATGATAC 59.801 47.826 0.00 0.00 43.17 2.24
261 262 3.455849 TGGGTGGGTTCACTACATGATA 58.544 45.455 0.00 0.00 43.17 2.15
262 263 2.274542 TGGGTGGGTTCACTACATGAT 58.725 47.619 0.00 0.00 43.17 2.45
263 264 1.735926 TGGGTGGGTTCACTACATGA 58.264 50.000 0.00 0.00 43.17 3.07
273 274 0.266152 TTCATTGGGTTGGGTGGGTT 59.734 50.000 0.00 0.00 0.00 4.11
274 275 0.178935 CTTCATTGGGTTGGGTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
275 276 0.114168 TCTTCATTGGGTTGGGTGGG 59.886 55.000 0.00 0.00 0.00 4.61
276 277 2.008242 TTCTTCATTGGGTTGGGTGG 57.992 50.000 0.00 0.00 0.00 4.61
278 279 4.132122 AGAATTCTTCATTGGGTTGGGT 57.868 40.909 0.88 0.00 0.00 4.51
392 393 4.791974 GCAATGCTGCTTTATCCTGTATC 58.208 43.478 0.00 0.00 45.74 2.24
516 517 3.507009 GACGGAGACCTCGACGGG 61.507 72.222 0.00 0.00 36.97 5.28
524 525 2.544698 CGGGATCGAGACGGAGACC 61.545 68.421 0.00 0.00 39.00 3.85
611 613 3.487120 AATAGAATAGAACGGGTGGCC 57.513 47.619 0.00 0.00 0.00 5.36
629 631 6.545504 AAAATGAATCGCTCGCTACATAAT 57.454 33.333 0.00 0.00 0.00 1.28
630 632 5.984233 AAAATGAATCGCTCGCTACATAA 57.016 34.783 0.00 0.00 0.00 1.90
631 633 5.050363 GGAAAAATGAATCGCTCGCTACATA 60.050 40.000 0.00 0.00 0.00 2.29
767 773 9.352191 TCTTTAACCATCATAGAGTAGGAGTAC 57.648 37.037 0.00 0.00 0.00 2.73
768 774 9.575868 CTCTTTAACCATCATAGAGTAGGAGTA 57.424 37.037 0.00 0.00 0.00 2.59
769 775 7.507616 CCTCTTTAACCATCATAGAGTAGGAGT 59.492 40.741 0.00 0.00 32.39 3.85
770 776 7.726291 TCCTCTTTAACCATCATAGAGTAGGAG 59.274 40.741 0.00 0.00 32.39 3.69
771 777 7.592736 TCCTCTTTAACCATCATAGAGTAGGA 58.407 38.462 0.00 0.00 32.39 2.94
772 778 7.726291 TCTCCTCTTTAACCATCATAGAGTAGG 59.274 40.741 0.00 0.00 32.39 3.18
773 779 8.698973 TCTCCTCTTTAACCATCATAGAGTAG 57.301 38.462 0.00 0.00 32.39 2.57
774 780 9.137459 CTTCTCCTCTTTAACCATCATAGAGTA 57.863 37.037 0.00 0.00 32.39 2.59
785 791 2.994578 GCGTCACTTCTCCTCTTTAACC 59.005 50.000 0.00 0.00 0.00 2.85
840 846 3.085952 TCCCACATCAAAATCTGGTCC 57.914 47.619 0.00 0.00 0.00 4.46
912 918 1.586422 TGAGCGCAATAAGAGCATCC 58.414 50.000 11.47 0.00 46.42 3.51
1111 1117 1.338337 CGAGTAGGCCGAAGACATCAT 59.662 52.381 0.00 0.00 0.00 2.45
1238 1257 1.005340 CTCTGAACATCTTGCCGAGC 58.995 55.000 0.00 0.00 0.00 5.03
1242 1261 1.372087 CGCCCTCTGAACATCTTGCC 61.372 60.000 0.00 0.00 0.00 4.52
1396 1424 0.321387 CAAGCAAGCAGGCAGAGAGA 60.321 55.000 2.37 0.00 35.83 3.10
1437 1465 3.753797 AGAATTCTGCTTCCGTTTCTTCC 59.246 43.478 7.30 0.00 0.00 3.46
1460 1488 4.424626 TCGCAGACAAGATGAATCACTAC 58.575 43.478 0.00 0.00 0.00 2.73
1642 1676 3.690487 CCAACCGTTGGTGTAGTCA 57.310 52.632 20.55 0.00 45.93 3.41
1675 1709 7.283580 TGGCAATGTTGTGTAAGTAAGTAAAGT 59.716 33.333 0.00 0.00 0.00 2.66
1683 1717 5.804639 AGAGATGGCAATGTTGTGTAAGTA 58.195 37.500 0.00 0.00 0.00 2.24
1684 1718 4.655963 AGAGATGGCAATGTTGTGTAAGT 58.344 39.130 0.00 0.00 0.00 2.24
1685 1719 5.413833 AGAAGAGATGGCAATGTTGTGTAAG 59.586 40.000 0.00 0.00 0.00 2.34
1686 1720 5.316167 AGAAGAGATGGCAATGTTGTGTAA 58.684 37.500 0.00 0.00 0.00 2.41
1724 1764 4.164988 AGAGAGAGAGAGAGAGAGGAAAGG 59.835 50.000 0.00 0.00 0.00 3.11
1729 1769 3.198635 ACACAGAGAGAGAGAGAGAGAGG 59.801 52.174 0.00 0.00 0.00 3.69
1732 1772 2.679837 GCACACAGAGAGAGAGAGAGAG 59.320 54.545 0.00 0.00 0.00 3.20
1738 1782 3.382227 AGATCATGCACACAGAGAGAGAG 59.618 47.826 0.00 0.00 0.00 3.20
1740 1784 3.491276 GGAGATCATGCACACAGAGAGAG 60.491 52.174 0.00 0.00 0.00 3.20
1742 1786 2.431419 AGGAGATCATGCACACAGAGAG 59.569 50.000 0.00 0.00 0.00 3.20
1744 1788 2.983907 AGGAGATCATGCACACAGAG 57.016 50.000 0.00 0.00 0.00 3.35
1745 1789 2.417787 CGAAGGAGATCATGCACACAGA 60.418 50.000 0.00 0.00 0.00 3.41
1746 1790 1.931841 CGAAGGAGATCATGCACACAG 59.068 52.381 0.00 0.00 0.00 3.66
1749 1793 0.249955 TGCGAAGGAGATCATGCACA 59.750 50.000 0.00 0.00 0.00 4.57
1751 1795 1.660167 CTTGCGAAGGAGATCATGCA 58.340 50.000 0.00 0.00 0.00 3.96
1868 1912 7.717436 CAGAAAGAAGGAAAGGTAGAAGAAAGT 59.283 37.037 0.00 0.00 0.00 2.66
1918 1963 0.389166 GAGACGTGTCTGGAGCAAGG 60.389 60.000 7.35 0.00 40.61 3.61
1999 2054 2.775911 TCATCCAAGCCTGTCTCTTG 57.224 50.000 0.00 0.00 40.31 3.02
2145 2201 6.536582 GTCGGAATCCTGATATATCAACCATG 59.463 42.308 16.08 4.65 36.18 3.66
2236 2292 5.274015 GGGGTATACCTCCATTTCCAAAAA 58.726 41.667 21.25 0.00 40.03 1.94
2237 2293 4.874199 GGGGTATACCTCCATTTCCAAAA 58.126 43.478 21.25 0.00 40.03 2.44
2238 2294 4.529716 GGGGTATACCTCCATTTCCAAA 57.470 45.455 21.25 0.00 40.03 3.28
2248 2304 2.122725 TGGCCGGGGGTATACCTC 60.123 66.667 21.25 17.88 40.03 3.85
2249 2305 2.447186 GTGGCCGGGGGTATACCT 60.447 66.667 21.25 0.00 40.03 3.08
2250 2306 2.447186 AGTGGCCGGGGGTATACC 60.447 66.667 13.99 13.99 39.11 2.73
2251 2307 2.826702 CAGTGGCCGGGGGTATAC 59.173 66.667 2.18 0.00 0.00 1.47
2252 2308 3.165685 GCAGTGGCCGGGGGTATA 61.166 66.667 2.18 0.00 0.00 1.47
2257 2313 4.511246 ATGATGCAGTGGCCGGGG 62.511 66.667 2.18 0.00 40.13 5.73
2258 2314 2.971095 ATCATGATGCAGTGGCCGGG 62.971 60.000 7.59 0.00 40.13 5.73
2259 2315 1.527611 ATCATGATGCAGTGGCCGG 60.528 57.895 7.59 0.00 40.13 6.13
2260 2316 0.816421 TCATCATGATGCAGTGGCCG 60.816 55.000 27.68 4.34 40.13 6.13
2261 2317 1.617322 ATCATCATGATGCAGTGGCC 58.383 50.000 27.68 0.00 35.43 5.36
2262 2318 3.143728 TGTATCATCATGATGCAGTGGC 58.856 45.455 27.68 15.14 42.97 5.01
2267 2323 3.323243 CGAGCTGTATCATCATGATGCA 58.677 45.455 27.68 16.60 45.03 3.96
2268 2324 2.093941 GCGAGCTGTATCATCATGATGC 59.906 50.000 27.68 16.47 37.70 3.91
2269 2325 3.323243 TGCGAGCTGTATCATCATGATG 58.677 45.455 26.79 26.79 37.70 3.07
2270 2326 3.672767 TGCGAGCTGTATCATCATGAT 57.327 42.857 5.24 5.24 40.72 2.45
2271 2327 3.457610 TTGCGAGCTGTATCATCATGA 57.542 42.857 0.00 0.00 0.00 3.07
2272 2328 3.603173 CGTTTGCGAGCTGTATCATCATG 60.603 47.826 0.00 0.00 41.33 3.07
2273 2329 2.541346 CGTTTGCGAGCTGTATCATCAT 59.459 45.455 0.00 0.00 41.33 2.45
2274 2330 1.926510 CGTTTGCGAGCTGTATCATCA 59.073 47.619 0.00 0.00 41.33 3.07
2275 2331 1.258982 CCGTTTGCGAGCTGTATCATC 59.741 52.381 0.00 0.00 41.33 2.92
2276 2332 1.134818 TCCGTTTGCGAGCTGTATCAT 60.135 47.619 0.00 0.00 41.33 2.45
2277 2333 0.245266 TCCGTTTGCGAGCTGTATCA 59.755 50.000 0.00 0.00 41.33 2.15
2278 2334 0.924090 CTCCGTTTGCGAGCTGTATC 59.076 55.000 0.00 0.00 41.33 2.24
2279 2335 1.084370 GCTCCGTTTGCGAGCTGTAT 61.084 55.000 0.00 0.00 41.33 2.29
2280 2336 1.736645 GCTCCGTTTGCGAGCTGTA 60.737 57.895 0.00 0.00 41.33 2.74
2281 2337 3.044305 GCTCCGTTTGCGAGCTGT 61.044 61.111 0.00 0.00 41.33 4.40
2282 2338 2.116736 TTTGCTCCGTTTGCGAGCTG 62.117 55.000 10.82 0.00 39.85 4.24
2283 2339 1.444119 TTTTGCTCCGTTTGCGAGCT 61.444 50.000 10.82 0.00 39.85 4.09
2284 2340 1.008995 TTTTGCTCCGTTTGCGAGC 60.009 52.632 2.88 2.88 41.33 5.03
2285 2341 0.307760 AGTTTTGCTCCGTTTGCGAG 59.692 50.000 0.00 0.00 41.33 5.03
2286 2342 0.028770 CAGTTTTGCTCCGTTTGCGA 59.971 50.000 0.00 0.00 41.33 5.10
2287 2343 1.539776 GCAGTTTTGCTCCGTTTGCG 61.540 55.000 0.00 0.00 46.95 4.85
2288 2344 2.216203 GCAGTTTTGCTCCGTTTGC 58.784 52.632 0.00 0.00 46.95 3.68
2298 2354 4.829064 TTAGTAGTTGCAGGCAGTTTTG 57.171 40.909 0.00 0.00 0.00 2.44
2299 2355 5.070001 TCATTAGTAGTTGCAGGCAGTTTT 58.930 37.500 0.00 0.00 0.00 2.43
2300 2356 4.651778 TCATTAGTAGTTGCAGGCAGTTT 58.348 39.130 0.00 0.00 0.00 2.66
2301 2357 4.286297 TCATTAGTAGTTGCAGGCAGTT 57.714 40.909 0.00 0.00 0.00 3.16
2489 2550 7.974675 TGCTTCAATTACTACTGATAGCAAAC 58.025 34.615 0.00 0.00 35.12 2.93
2538 2599 5.191722 TCCAAGTGCTACTGGATATTCCTTT 59.808 40.000 0.00 0.00 37.46 3.11
2601 2665 5.065218 CCTCATTTCGTAAACAGAATCCAGG 59.935 44.000 0.00 0.00 0.00 4.45
2615 2679 1.196012 GTCCCTCTCCCTCATTTCGT 58.804 55.000 0.00 0.00 0.00 3.85
2630 2694 0.252284 TCTCTCAGTCAAGGGGTCCC 60.252 60.000 0.00 0.00 0.00 4.46
2631 2695 0.899019 GTCTCTCAGTCAAGGGGTCC 59.101 60.000 0.00 0.00 0.00 4.46
2632 2696 0.528470 CGTCTCTCAGTCAAGGGGTC 59.472 60.000 0.00 0.00 0.00 4.46
2633 2697 0.178958 ACGTCTCTCAGTCAAGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
2634 2698 0.969894 AACGTCTCTCAGTCAAGGGG 59.030 55.000 0.00 0.00 0.00 4.79
2635 2699 2.821991 AAACGTCTCTCAGTCAAGGG 57.178 50.000 0.00 0.00 0.00 3.95
2636 2700 3.303395 GCAAAAACGTCTCTCAGTCAAGG 60.303 47.826 0.00 0.00 0.00 3.61
2637 2701 3.309682 TGCAAAAACGTCTCTCAGTCAAG 59.690 43.478 0.00 0.00 0.00 3.02
2638 2702 3.266636 TGCAAAAACGTCTCTCAGTCAA 58.733 40.909 0.00 0.00 0.00 3.18
2639 2703 2.866156 CTGCAAAAACGTCTCTCAGTCA 59.134 45.455 0.00 0.00 0.00 3.41
2640 2704 2.866762 ACTGCAAAAACGTCTCTCAGTC 59.133 45.455 0.00 0.00 0.00 3.51
2641 2705 2.906354 ACTGCAAAAACGTCTCTCAGT 58.094 42.857 0.00 0.00 0.00 3.41
2642 2706 3.951979 AACTGCAAAAACGTCTCTCAG 57.048 42.857 0.00 0.00 0.00 3.35
2681 2745 5.878116 TCTAAATGTAAGCCGTATTTGCAGT 59.122 36.000 0.00 0.00 0.00 4.40
2689 2753 5.640357 CCTGTGTTTCTAAATGTAAGCCGTA 59.360 40.000 0.00 0.00 0.00 4.02
2731 2795 4.469657 AGTTGCCACTTGTAATGGAGAAA 58.530 39.130 0.00 0.00 39.87 2.52
2742 2806 5.234752 TGTACTGTGTATAGTTGCCACTTG 58.765 41.667 0.00 0.00 34.06 3.16


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

AutoCloner maintained by Alex Coulton.