Multiple sequence alignment - TraesCS5A01G251800

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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 TraesCS5A01G251800 chr5A 100.000 2846 0 0 1 2846 467584704 467587549 0.000000e+00 5256.0
1 TraesCS5A01G251800 chr5B 86.242 2922 174 107 1 2846 432322363 432325132 0.000000e+00 2959.0
2 TraesCS5A01G251800 chr5B 92.857 56 4 0 1601 1656 432323788 432323843 6.530000e-12 82.4
3 TraesCS5A01G251800 chr5D 86.322 2610 149 98 325 2846 365991842 365994331 0.000000e+00 2651.0
4 TraesCS5A01G251800 chr5D 90.187 214 12 4 1 206 365991579 365991791 1.300000e-68 270.0
5 TraesCS5A01G251800 chr5D 82.500 160 18 7 1469 1620 365992972 365993129 6.400000e-27 132.0
6 TraesCS5A01G251800 chr5D 92.000 50 4 0 1601 1650 365992945 365992994 1.410000e-08 71.3
7 TraesCS5A01G251800 chr6D 91.391 151 13 0 1139 1289 358326157 358326007 1.030000e-49 207.0
8 TraesCS5A01G251800 chr6A 91.391 151 13 0 1139 1289 500083776 500083626 1.030000e-49 207.0
9 TraesCS5A01G251800 chr6A 86.441 177 18 3 1139 1309 520355710 520355534 3.740000e-44 189.0
10 TraesCS5A01G251800 chr6B 90.728 151 14 0 1139 1289 539727701 539727551 4.810000e-48 202.0
11 TraesCS5A01G251800 chr6B 100.000 28 0 0 1291 1318 7280644 7280671 5.000000e-03 52.8
12 TraesCS5A01G251800 chr3D 89.677 155 14 2 1135 1288 61703553 61703400 2.240000e-46 196.0
13 TraesCS5A01G251800 chr3A 83.036 224 27 9 1066 1288 70730713 70730500 2.890000e-45 193.0
14 TraesCS5A01G251800 chr3B 89.032 155 15 2 1135 1288 99171525 99171372 1.040000e-44 191.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G251800 chr5A 467584704 467587549 2845 False 5256.000 5256 100.00000 1 2846 1 chr5A.!!$F1 2845
1 TraesCS5A01G251800 chr5B 432322363 432325132 2769 False 1520.700 2959 89.54950 1 2846 2 chr5B.!!$F1 2845
2 TraesCS5A01G251800 chr5D 365991579 365994331 2752 False 781.075 2651 87.75225 1 2846 4 chr5D.!!$F1 2845

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
590 628 0.099082 GACCCGTCTCGTCTCATCAC 59.901 60.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 2677 0.028902 GACAATAATTCGTGGCCGGC 59.971 55.0 21.18 21.18 33.95 6.13 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
214 215 4.339809 CGCGCACGCACCATATCG 62.340 66.667 16.04 0.00 42.06 2.92
215 216 4.000557 GCGCACGCACCATATCGG 62.001 66.667 10.65 0.00 41.49 4.18
411 449 2.397413 CTGCCACGGTGAGGTTCCTT 62.397 60.000 10.28 0.00 0.00 3.36
583 621 4.808238 GCGTCGACCCGTCTCGTC 62.808 72.222 10.58 0.00 35.10 4.20
584 622 3.117171 CGTCGACCCGTCTCGTCT 61.117 66.667 10.58 0.00 35.10 4.18
585 623 2.783935 GTCGACCCGTCTCGTCTC 59.216 66.667 3.51 0.00 35.10 3.36
586 624 2.031516 GTCGACCCGTCTCGTCTCA 61.032 63.158 3.51 0.00 35.10 3.27
587 625 1.078637 TCGACCCGTCTCGTCTCAT 60.079 57.895 0.00 0.00 35.10 2.90
588 626 1.088340 TCGACCCGTCTCGTCTCATC 61.088 60.000 0.00 0.00 35.10 2.92
589 627 1.366854 CGACCCGTCTCGTCTCATCA 61.367 60.000 0.00 0.00 0.00 3.07
590 628 0.099082 GACCCGTCTCGTCTCATCAC 59.901 60.000 0.00 0.00 0.00 3.06
591 629 1.062685 CCCGTCTCGTCTCATCACG 59.937 63.158 0.00 0.00 41.36 4.35
592 630 1.062685 CCGTCTCGTCTCATCACGG 59.937 63.158 0.00 0.00 43.71 4.94
593 631 1.062685 CGTCTCGTCTCATCACGGG 59.937 63.158 0.00 0.00 41.98 5.28
596 634 1.064946 CTCGTCTCATCACGGGAGC 59.935 63.158 0.00 0.00 43.40 4.70
598 636 2.105128 GTCTCATCACGGGAGCGG 59.895 66.667 0.00 0.00 32.38 5.52
632 674 2.831742 CTCGGGTGGCGGCTAGTA 60.832 66.667 11.43 0.00 0.00 1.82
633 675 2.831742 TCGGGTGGCGGCTAGTAG 60.832 66.667 11.43 0.00 0.00 2.57
634 676 4.587189 CGGGTGGCGGCTAGTAGC 62.587 72.222 14.09 14.09 41.46 3.58
635 677 3.155167 GGGTGGCGGCTAGTAGCT 61.155 66.667 21.20 0.00 41.99 3.32
636 678 2.417936 GGTGGCGGCTAGTAGCTC 59.582 66.667 21.20 13.06 41.99 4.09
637 679 2.026301 GTGGCGGCTAGTAGCTCG 59.974 66.667 21.20 21.38 41.99 5.03
639 681 2.026301 GGCGGCTAGTAGCTCGTG 59.974 66.667 24.38 13.97 41.99 4.35
646 688 1.955080 GCTAGTAGCTCGTGGTGGTAT 59.045 52.381 15.16 0.00 38.45 2.73
647 689 3.144506 GCTAGTAGCTCGTGGTGGTATA 58.855 50.000 15.16 0.00 38.45 1.47
658 701 4.197107 GTGGTGGTATACTACGTCGTAC 57.803 50.000 12.62 0.00 30.83 3.67
659 702 3.871594 GTGGTGGTATACTACGTCGTACT 59.128 47.826 12.62 0.00 30.83 2.73
660 703 5.047847 GTGGTGGTATACTACGTCGTACTA 58.952 45.833 12.62 0.00 30.83 1.82
661 704 5.175856 GTGGTGGTATACTACGTCGTACTAG 59.824 48.000 12.62 0.00 30.83 2.57
776 819 3.792047 CCACCTCACGCACGCATG 61.792 66.667 0.00 0.00 0.00 4.06
811 854 4.746951 GCCGCCGCACCGTAAAAC 62.747 66.667 0.00 0.00 34.03 2.43
812 855 3.347405 CCGCCGCACCGTAAAACA 61.347 61.111 0.00 0.00 0.00 2.83
852 895 4.087892 CTGGACCTGCTCCACCGG 62.088 72.222 0.00 0.00 44.99 5.28
868 911 4.501285 GGCCCGCCCCCTTAAGAC 62.501 72.222 3.36 0.00 0.00 3.01
947 990 1.670015 GTCCGTCCGTTCCTTTCCT 59.330 57.895 0.00 0.00 0.00 3.36
963 1006 4.452733 CTTCCCTCCACCGCCGAC 62.453 72.222 0.00 0.00 0.00 4.79
979 1022 3.077556 ACCGATCGGAGCCAGCTT 61.078 61.111 39.55 12.74 38.96 3.74
980 1023 2.187946 CCGATCGGAGCCAGCTTT 59.812 61.111 30.62 0.00 37.50 3.51
1308 1356 2.435586 TCCTCCTCGTCGTCGTCC 60.436 66.667 1.33 0.00 38.33 4.79
1314 1362 3.081159 CTCGTCGTCGTCCTCGTCC 62.081 68.421 1.33 0.00 38.33 4.79
1459 1516 2.258591 CCACCGAGGACGTCACAG 59.741 66.667 18.91 7.14 41.22 3.66
1467 1524 1.735920 GGACGTCACAGCAGCTGAG 60.736 63.158 29.70 21.35 35.18 3.35
1512 1569 0.745128 ACGGGTGTTTCGCTTTCACA 60.745 50.000 0.00 0.00 34.27 3.58
1657 1714 4.680237 CACCCGCGGCTGACAGAA 62.680 66.667 22.85 0.00 0.00 3.02
1668 1725 2.359975 GACAGAAACGGGGGCCTG 60.360 66.667 0.84 0.00 0.00 4.85
1859 1937 2.604174 CGTGAACCGTGGTTGAGCC 61.604 63.158 9.42 0.00 38.60 4.70
1886 1964 2.752238 ACGGTCCGAGGAGAGCTG 60.752 66.667 20.51 0.00 32.00 4.24
1887 1965 2.438614 CGGTCCGAGGAGAGCTGA 60.439 66.667 4.91 0.00 32.00 4.26
1888 1966 2.477176 CGGTCCGAGGAGAGCTGAG 61.477 68.421 4.91 0.00 32.00 3.35
1889 1967 2.781158 GGTCCGAGGAGAGCTGAGC 61.781 68.421 0.00 0.00 0.00 4.26
1890 1968 1.752694 GTCCGAGGAGAGCTGAGCT 60.753 63.158 6.69 6.69 43.88 4.09
1891 1969 1.752310 TCCGAGGAGAGCTGAGCTG 60.752 63.158 13.71 0.00 39.88 4.24
1892 1970 1.752310 CCGAGGAGAGCTGAGCTGA 60.752 63.158 13.71 0.00 39.88 4.26
1893 1971 1.727511 CCGAGGAGAGCTGAGCTGAG 61.728 65.000 13.71 0.00 39.88 3.35
1894 1972 1.438814 GAGGAGAGCTGAGCTGAGC 59.561 63.158 18.32 18.32 39.88 4.26
1919 2000 4.412199 CCCCCAACCTTCTTACTATCATCA 59.588 45.833 0.00 0.00 0.00 3.07
1920 2001 5.073691 CCCCCAACCTTCTTACTATCATCAT 59.926 44.000 0.00 0.00 0.00 2.45
1921 2002 6.234177 CCCCAACCTTCTTACTATCATCATC 58.766 44.000 0.00 0.00 0.00 2.92
1927 2008 5.861251 CCTTCTTACTATCATCATCGTCTGC 59.139 44.000 0.00 0.00 0.00 4.26
1960 2044 6.394809 CGGCCAGTAGTATTTGGAAATTTTT 58.605 36.000 2.24 0.00 36.55 1.94
1981 2065 2.971901 TGTCACTACTCACCAGAGGA 57.028 50.000 0.00 0.00 46.44 3.71
2004 2088 3.303760 GTCGATCTAAGAAGCCGTTTGTC 59.696 47.826 0.00 0.00 0.00 3.18
2055 2139 2.238898 AGGTGAGGTGCCTGTATAAACC 59.761 50.000 0.00 0.00 34.56 3.27
2056 2140 2.026636 GGTGAGGTGCCTGTATAAACCA 60.027 50.000 0.00 0.00 35.01 3.67
2057 2141 3.560453 GGTGAGGTGCCTGTATAAACCAA 60.560 47.826 0.00 0.00 35.01 3.67
2073 2157 0.462047 CCAATCAGTACCCGGTCTGC 60.462 60.000 0.00 0.00 0.00 4.26
2138 2222 3.077484 AGCGAACTACCACTACCACTA 57.923 47.619 0.00 0.00 0.00 2.74
2139 2223 2.751806 AGCGAACTACCACTACCACTAC 59.248 50.000 0.00 0.00 0.00 2.73
2140 2224 2.159324 GCGAACTACCACTACCACTACC 60.159 54.545 0.00 0.00 0.00 3.18
2141 2225 3.084039 CGAACTACCACTACCACTACCA 58.916 50.000 0.00 0.00 0.00 3.25
2142 2226 3.119708 CGAACTACCACTACCACTACCAC 60.120 52.174 0.00 0.00 0.00 4.16
2143 2227 3.822097 ACTACCACTACCACTACCACT 57.178 47.619 0.00 0.00 0.00 4.00
2144 2228 3.694926 ACTACCACTACCACTACCACTC 58.305 50.000 0.00 0.00 0.00 3.51
2145 2229 2.688902 ACCACTACCACTACCACTCA 57.311 50.000 0.00 0.00 0.00 3.41
2156 2240 7.820578 ACCACTACCACTCATTATACTACTC 57.179 40.000 0.00 0.00 0.00 2.59
2157 2241 6.776603 ACCACTACCACTCATTATACTACTCC 59.223 42.308 0.00 0.00 0.00 3.85
2158 2242 6.776116 CCACTACCACTCATTATACTACTCCA 59.224 42.308 0.00 0.00 0.00 3.86
2159 2243 7.040340 CCACTACCACTCATTATACTACTCCAG 60.040 44.444 0.00 0.00 0.00 3.86
2160 2244 7.502895 CACTACCACTCATTATACTACTCCAGT 59.497 40.741 0.00 0.00 41.62 4.00
2161 2245 6.716934 ACCACTCATTATACTACTCCAGTG 57.283 41.667 0.00 0.00 38.24 3.66
2179 2263 0.843309 TGCTTGTTTGACTCCTCCCA 59.157 50.000 0.00 0.00 0.00 4.37
2180 2264 1.239347 GCTTGTTTGACTCCTCCCAC 58.761 55.000 0.00 0.00 0.00 4.61
2181 2265 1.897560 CTTGTTTGACTCCTCCCACC 58.102 55.000 0.00 0.00 0.00 4.61
2182 2266 1.142870 CTTGTTTGACTCCTCCCACCA 59.857 52.381 0.00 0.00 0.00 4.17
2183 2267 0.472471 TGTTTGACTCCTCCCACCAC 59.528 55.000 0.00 0.00 0.00 4.16
2184 2268 0.472471 GTTTGACTCCTCCCACCACA 59.528 55.000 0.00 0.00 0.00 4.17
2194 2278 2.044555 CCCACCACATGCTCTGCTG 61.045 63.158 0.00 0.00 0.00 4.41
2195 2279 2.697761 CCACCACATGCTCTGCTGC 61.698 63.158 0.00 0.00 0.00 5.25
2196 2280 1.674651 CACCACATGCTCTGCTGCT 60.675 57.895 0.00 0.00 0.00 4.24
2197 2281 1.376942 ACCACATGCTCTGCTGCTC 60.377 57.895 0.00 0.00 0.00 4.26
2199 2283 0.748367 CCACATGCTCTGCTGCTCAT 60.748 55.000 0.00 0.00 0.00 2.90
2200 2284 0.378610 CACATGCTCTGCTGCTCATG 59.621 55.000 17.01 17.01 41.35 3.07
2202 2286 1.095600 CATGCTCTGCTGCTCATGTT 58.904 50.000 0.00 0.00 33.55 2.71
2203 2287 2.285977 CATGCTCTGCTGCTCATGTTA 58.714 47.619 0.00 0.00 33.55 2.41
2204 2288 1.730501 TGCTCTGCTGCTCATGTTAC 58.269 50.000 0.00 0.00 0.00 2.50
2213 2303 4.091424 GCTGCTCATGTTACGATTTTCAC 58.909 43.478 0.00 0.00 0.00 3.18
2215 2305 3.124466 TGCTCATGTTACGATTTTCACCG 59.876 43.478 0.00 0.00 0.00 4.94
2218 2308 2.953640 TGTTACGATTTTCACCGTGC 57.046 45.000 0.00 0.00 39.54 5.34
2224 2314 0.874390 GATTTTCACCGTGCTGCTCA 59.126 50.000 0.00 0.00 0.00 4.26
2227 2317 0.534877 TTTCACCGTGCTGCTCATGT 60.535 50.000 0.00 0.00 0.00 3.21
2228 2318 0.950555 TTCACCGTGCTGCTCATGTC 60.951 55.000 0.00 0.00 0.00 3.06
2244 2334 0.179092 TGTCGATCATGGCTGCTGAG 60.179 55.000 0.00 0.00 0.00 3.35
2252 2342 0.987081 ATGGCTGCTGAGACCTGGAT 60.987 55.000 0.00 0.00 0.00 3.41
2259 2349 3.894427 CTGCTGAGACCTGGATATGTACT 59.106 47.826 0.00 0.00 0.00 2.73
2269 2359 5.775701 ACCTGGATATGTACTTGTAGCTAGG 59.224 44.000 14.65 14.65 39.82 3.02
2271 2361 4.527038 TGGATATGTACTTGTAGCTAGGCC 59.473 45.833 0.00 0.00 0.00 5.19
2273 2363 0.458669 TGTACTTGTAGCTAGGCCGC 59.541 55.000 0.00 0.00 0.00 6.53
2274 2364 0.458669 GTACTTGTAGCTAGGCCGCA 59.541 55.000 5.37 0.00 0.00 5.69
2275 2365 0.458669 TACTTGTAGCTAGGCCGCAC 59.541 55.000 5.37 2.55 0.00 5.34
2276 2366 1.258445 ACTTGTAGCTAGGCCGCACT 61.258 55.000 5.37 2.64 0.00 4.40
2277 2367 0.108138 CTTGTAGCTAGGCCGCACTT 60.108 55.000 5.37 0.00 0.00 3.16
2278 2368 0.108329 TTGTAGCTAGGCCGCACTTC 60.108 55.000 5.37 0.00 0.00 3.01
2282 2372 1.227292 GCTAGGCCGCACTTCTACC 60.227 63.158 0.00 0.00 0.00 3.18
2289 2379 1.517257 CGCACTTCTACCTCGCTGG 60.517 63.158 0.00 0.00 42.93 4.85
2299 2389 1.227674 CCTCGCTGGTAGCATTCCC 60.228 63.158 0.00 0.00 42.58 3.97
2300 2390 1.690219 CCTCGCTGGTAGCATTCCCT 61.690 60.000 0.00 0.00 42.58 4.20
2301 2391 0.531532 CTCGCTGGTAGCATTCCCTG 60.532 60.000 0.00 0.00 42.58 4.45
2302 2392 0.975556 TCGCTGGTAGCATTCCCTGA 60.976 55.000 0.00 0.00 42.58 3.86
2305 2395 0.531532 CTGGTAGCATTCCCTGAGCG 60.532 60.000 0.00 0.00 0.00 5.03
2308 2398 0.872021 GTAGCATTCCCTGAGCGTCG 60.872 60.000 0.00 0.00 0.00 5.12
2348 2482 2.736995 CCACGTACAGGCACGGTG 60.737 66.667 3.15 3.15 46.12 4.94
2358 2492 2.048222 GCACGGTGCACTAGAGCA 60.048 61.111 27.10 11.06 44.26 4.26
2386 2520 4.024218 GCATGTCCAGATTGCTCATAACTC 60.024 45.833 0.00 0.00 33.61 3.01
2388 2522 3.126831 GTCCAGATTGCTCATAACTCCG 58.873 50.000 0.00 0.00 0.00 4.63
2389 2523 2.766263 TCCAGATTGCTCATAACTCCGT 59.234 45.455 0.00 0.00 0.00 4.69
2390 2524 3.126831 CCAGATTGCTCATAACTCCGTC 58.873 50.000 0.00 0.00 0.00 4.79
2391 2525 2.791560 CAGATTGCTCATAACTCCGTCG 59.208 50.000 0.00 0.00 0.00 5.12
2392 2526 1.523095 GATTGCTCATAACTCCGTCGC 59.477 52.381 0.00 0.00 0.00 5.19
2393 2527 0.800683 TTGCTCATAACTCCGTCGCG 60.801 55.000 0.00 0.00 0.00 5.87
2394 2528 1.226603 GCTCATAACTCCGTCGCGT 60.227 57.895 5.77 0.00 0.00 6.01
2395 2529 0.028505 GCTCATAACTCCGTCGCGTA 59.971 55.000 5.77 0.00 0.00 4.42
2405 2546 2.206487 CGTCGCGTACAGTACAGCG 61.206 63.158 28.64 28.64 45.63 5.18
2414 2555 1.448365 CAGTACAGCGCAGGCATGA 60.448 57.895 11.47 0.00 43.41 3.07
2415 2556 1.020861 CAGTACAGCGCAGGCATGAA 61.021 55.000 11.47 0.00 43.41 2.57
2423 2564 0.806868 CGCAGGCATGAACAGATTGT 59.193 50.000 0.62 0.00 0.00 2.71
2434 2575 6.749118 GCATGAACAGATTGTTTCCATAACTC 59.251 38.462 0.00 0.00 41.28 3.01
2450 2596 2.918712 ACTCCATCATGATCCGGAAC 57.081 50.000 9.01 6.48 0.00 3.62
2460 2606 3.750373 ATCCGGAACCAATCGGCGG 62.750 63.158 9.01 0.00 45.31 6.13
2550 2696 0.028902 GCCGGCCACGAATTATTGTC 59.971 55.000 18.11 0.00 44.60 3.18
2551 2697 0.303493 CCGGCCACGAATTATTGTCG 59.697 55.000 2.24 0.00 44.60 4.35
2552 2698 0.315869 CGGCCACGAATTATTGTCGC 60.316 55.000 2.24 0.00 44.60 5.19
2553 2699 0.028902 GGCCACGAATTATTGTCGCC 59.971 55.000 0.00 0.00 39.60 5.54
2703 2849 1.319614 ATTTCAATTCACGGGCGGGG 61.320 55.000 0.00 0.00 0.00 5.73
2810 2960 4.899239 CGCGTCAGGGATGGGCTC 62.899 72.222 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.091771 AATCTCTGTTCGCGCCATGG 61.092 55.000 7.63 7.63 0.00 3.66
198 199 4.000557 CCGATATGGTGCGTGCGC 62.001 66.667 9.85 9.85 42.35 6.09
572 610 1.645704 CGTGATGAGACGAGACGGGT 61.646 60.000 0.00 0.00 42.10 5.28
574 612 1.062685 CCGTGATGAGACGAGACGG 59.937 63.158 0.00 0.00 42.10 4.79
576 614 0.378962 CTCCCGTGATGAGACGAGAC 59.621 60.000 0.00 0.00 42.10 3.36
577 615 1.377366 GCTCCCGTGATGAGACGAGA 61.377 60.000 0.00 0.00 42.10 4.04
578 616 1.064946 GCTCCCGTGATGAGACGAG 59.935 63.158 0.00 0.00 42.10 4.18
579 617 2.761195 CGCTCCCGTGATGAGACGA 61.761 63.158 0.00 0.00 42.10 4.20
580 618 2.278206 CGCTCCCGTGATGAGACG 60.278 66.667 0.00 0.00 39.13 4.18
581 619 2.105128 CCGCTCCCGTGATGAGAC 59.895 66.667 0.00 0.00 31.26 3.36
582 620 2.561467 TACCCGCTCCCGTGATGAGA 62.561 60.000 0.00 0.00 31.26 3.27
583 621 1.672854 TTACCCGCTCCCGTGATGAG 61.673 60.000 0.00 0.00 0.00 2.90
584 622 1.259142 TTTACCCGCTCCCGTGATGA 61.259 55.000 0.00 0.00 0.00 2.92
585 623 0.391927 TTTTACCCGCTCCCGTGATG 60.392 55.000 0.00 0.00 0.00 3.07
586 624 0.325602 TTTTTACCCGCTCCCGTGAT 59.674 50.000 0.00 0.00 0.00 3.06
587 625 1.753470 TTTTTACCCGCTCCCGTGA 59.247 52.632 0.00 0.00 0.00 4.35
588 626 4.382788 TTTTTACCCGCTCCCGTG 57.617 55.556 0.00 0.00 0.00 4.94
613 655 4.514577 CTAGCCGCCACCCGAGTG 62.515 72.222 0.00 0.00 44.12 3.51
614 656 3.650298 TACTAGCCGCCACCCGAGT 62.650 63.158 0.00 0.00 40.02 4.18
629 671 3.294038 AGTATACCACCACGAGCTACT 57.706 47.619 0.00 0.00 0.00 2.57
632 674 1.945394 CGTAGTATACCACCACGAGCT 59.055 52.381 9.91 0.00 43.83 4.09
633 675 1.672881 ACGTAGTATACCACCACGAGC 59.327 52.381 18.17 0.00 43.83 5.03
646 688 6.800632 GTACGGGCCTAGTACGACGTAGTA 62.801 54.167 18.89 18.89 36.67 1.82
704 747 1.362355 GCCACCTTTGTTTGACCCG 59.638 57.895 0.00 0.00 0.00 5.28
778 821 4.776647 GCATTTGACGGTGCGGCC 62.777 66.667 0.00 0.00 31.60 6.13
779 822 4.776647 GGCATTTGACGGTGCGGC 62.777 66.667 0.00 0.00 42.15 6.53
780 823 4.459331 CGGCATTTGACGGTGCGG 62.459 66.667 0.00 0.00 44.21 5.69
811 854 1.277273 TCCATCTCAAGTGGAGCAGTG 59.723 52.381 0.00 0.00 43.70 3.66
812 855 1.277557 GTCCATCTCAAGTGGAGCAGT 59.722 52.381 0.00 0.00 45.91 4.40
852 895 4.501285 GGTCTTAAGGGGGCGGGC 62.501 72.222 1.85 0.00 0.00 6.13
855 898 2.271173 GTGGGTCTTAAGGGGGCG 59.729 66.667 1.85 0.00 0.00 6.13
901 944 2.363788 TGGTTTGTGTAGCTAGCGAG 57.636 50.000 9.55 0.00 0.00 5.03
902 945 2.803956 GTTTGGTTTGTGTAGCTAGCGA 59.196 45.455 9.55 0.00 0.00 4.93
903 946 2.411031 CGTTTGGTTTGTGTAGCTAGCG 60.411 50.000 9.55 0.00 0.00 4.26
904 947 2.664698 GCGTTTGGTTTGTGTAGCTAGC 60.665 50.000 6.62 6.62 0.00 3.42
905 948 2.095919 GGCGTTTGGTTTGTGTAGCTAG 60.096 50.000 0.00 0.00 0.00 3.42
906 949 1.874872 GGCGTTTGGTTTGTGTAGCTA 59.125 47.619 0.00 0.00 0.00 3.32
963 1006 2.176273 CAAAGCTGGCTCCGATCGG 61.176 63.158 28.62 28.62 0.00 4.18
971 1014 1.072159 AACGAGAGCAAAGCTGGCT 59.928 52.632 12.56 12.56 46.07 4.75
979 1022 0.320374 CCACCTACCAACGAGAGCAA 59.680 55.000 0.00 0.00 0.00 3.91
980 1023 1.972198 CCACCTACCAACGAGAGCA 59.028 57.895 0.00 0.00 0.00 4.26
1146 1194 2.262915 GTGTCCCTGGACTCGCAG 59.737 66.667 16.81 0.00 44.80 5.18
1155 1203 0.109342 AGCAGAACTTGGTGTCCCTG 59.891 55.000 0.00 0.00 35.85 4.45
1156 1204 1.348036 GTAGCAGAACTTGGTGTCCCT 59.652 52.381 0.00 0.00 38.18 4.20
1308 1356 3.003173 TTGGGGCTGGAGGACGAG 61.003 66.667 0.00 0.00 0.00 4.18
1459 1516 4.925861 GGCGGGATCCTCAGCTGC 62.926 72.222 20.66 12.00 0.00 5.25
1486 1543 4.974989 GAAACACCCGTCCGCCGT 62.975 66.667 0.00 0.00 33.66 5.68
1491 1548 1.161563 TGAAAGCGAAACACCCGTCC 61.162 55.000 0.00 0.00 0.00 4.79
1540 1597 1.349357 GAGAGTGAAGCACCCTTCCTT 59.651 52.381 1.43 0.00 45.53 3.36
1541 1598 0.980423 GAGAGTGAAGCACCCTTCCT 59.020 55.000 1.43 0.00 45.53 3.36
1551 1608 2.125912 CCGGCCGTGAGAGTGAAG 60.126 66.667 26.12 0.00 0.00 3.02
1650 1707 2.852075 AGGCCCCCGTTTCTGTCA 60.852 61.111 0.00 0.00 0.00 3.58
1657 1714 4.678743 GAAAGCCAGGCCCCCGTT 62.679 66.667 8.22 0.00 0.00 4.44
1668 1725 2.106683 CGGGTGATCGGTGAAAGCC 61.107 63.158 0.00 0.00 0.00 4.35
1875 1953 1.729276 CTCAGCTCAGCTCTCCTCG 59.271 63.158 0.00 0.00 36.40 4.63
1887 1965 3.334054 GGTTGGGGGAGCTCAGCT 61.334 66.667 17.19 0.00 43.88 4.24
1888 1966 2.828480 GAAGGTTGGGGGAGCTCAGC 62.828 65.000 17.19 3.93 0.00 4.26
1889 1967 1.204113 AGAAGGTTGGGGGAGCTCAG 61.204 60.000 17.19 0.00 0.00 3.35
1890 1968 0.772124 AAGAAGGTTGGGGGAGCTCA 60.772 55.000 17.19 0.00 0.00 4.26
1891 1969 1.065345 GTAAGAAGGTTGGGGGAGCTC 60.065 57.143 4.71 4.71 0.00 4.09
1892 1970 0.992695 GTAAGAAGGTTGGGGGAGCT 59.007 55.000 0.00 0.00 0.00 4.09
1893 1971 0.992695 AGTAAGAAGGTTGGGGGAGC 59.007 55.000 0.00 0.00 0.00 4.70
1894 1972 4.037927 TGATAGTAAGAAGGTTGGGGGAG 58.962 47.826 0.00 0.00 0.00 4.30
1895 1973 4.083080 TGATAGTAAGAAGGTTGGGGGA 57.917 45.455 0.00 0.00 0.00 4.81
1896 1974 4.412199 TGATGATAGTAAGAAGGTTGGGGG 59.588 45.833 0.00 0.00 0.00 5.40
1919 2000 2.822399 GGAATCCGGGCAGACGAT 59.178 61.111 0.00 0.00 35.47 3.73
1920 2001 3.833645 CGGAATCCGGGCAGACGA 61.834 66.667 14.91 0.00 44.15 4.20
1960 2044 4.018324 ACTCCTCTGGTGAGTAGTGACATA 60.018 45.833 0.00 0.00 41.17 2.29
1981 2065 3.056749 ACAAACGGCTTCTTAGATCGACT 60.057 43.478 0.00 0.00 0.00 4.18
2004 2088 2.231215 CCTTCCGATCAGGCACTAAG 57.769 55.000 0.00 0.00 40.77 2.18
2055 2139 0.537188 AGCAGACCGGGTACTGATTG 59.463 55.000 23.02 8.22 36.31 2.67
2056 2140 0.824759 GAGCAGACCGGGTACTGATT 59.175 55.000 23.02 13.26 36.31 2.57
2057 2141 0.324368 TGAGCAGACCGGGTACTGAT 60.324 55.000 23.02 18.86 36.31 2.90
2073 2157 1.082756 GCTTGAAACACGCCGTGAG 60.083 57.895 25.94 11.41 36.96 3.51
2138 2222 5.069251 GCACTGGAGTAGTATAATGAGTGGT 59.931 44.000 0.00 0.00 37.60 4.16
2139 2223 5.303078 AGCACTGGAGTAGTATAATGAGTGG 59.697 44.000 0.00 0.00 37.60 4.00
2140 2224 6.398234 AGCACTGGAGTAGTATAATGAGTG 57.602 41.667 0.00 0.00 37.60 3.51
2141 2225 6.381420 ACAAGCACTGGAGTAGTATAATGAGT 59.619 38.462 0.00 0.00 37.60 3.41
2142 2226 6.810911 ACAAGCACTGGAGTAGTATAATGAG 58.189 40.000 0.00 0.00 37.60 2.90
2143 2227 6.791867 ACAAGCACTGGAGTAGTATAATGA 57.208 37.500 0.00 0.00 37.60 2.57
2144 2228 7.549134 TCAAACAAGCACTGGAGTAGTATAATG 59.451 37.037 0.00 0.00 37.60 1.90
2145 2229 7.549488 GTCAAACAAGCACTGGAGTAGTATAAT 59.451 37.037 0.00 0.00 37.60 1.28
2156 2240 1.876156 GAGGAGTCAAACAAGCACTGG 59.124 52.381 0.00 0.00 0.00 4.00
2157 2241 1.876156 GGAGGAGTCAAACAAGCACTG 59.124 52.381 0.00 0.00 0.00 3.66
2158 2242 1.202818 GGGAGGAGTCAAACAAGCACT 60.203 52.381 0.00 0.00 0.00 4.40
2159 2243 1.239347 GGGAGGAGTCAAACAAGCAC 58.761 55.000 0.00 0.00 0.00 4.40
2160 2244 0.843309 TGGGAGGAGTCAAACAAGCA 59.157 50.000 0.00 0.00 0.00 3.91
2161 2245 1.239347 GTGGGAGGAGTCAAACAAGC 58.761 55.000 0.00 0.00 0.00 4.01
2179 2263 1.376942 GAGCAGCAGAGCATGTGGT 60.377 57.895 0.00 0.00 42.57 4.16
2180 2264 0.748367 ATGAGCAGCAGAGCATGTGG 60.748 55.000 0.00 0.00 36.85 4.17
2181 2265 0.378610 CATGAGCAGCAGAGCATGTG 59.621 55.000 0.00 0.00 34.82 3.21
2182 2266 0.035343 ACATGAGCAGCAGAGCATGT 60.035 50.000 13.97 13.97 44.54 3.21
2183 2267 1.095600 AACATGAGCAGCAGAGCATG 58.904 50.000 0.00 13.00 42.75 4.06
2184 2268 2.286872 GTAACATGAGCAGCAGAGCAT 58.713 47.619 0.00 0.00 36.85 3.79
2194 2278 3.124636 ACGGTGAAAATCGTAACATGAGC 59.875 43.478 0.00 0.00 37.88 4.26
2195 2279 4.637968 CACGGTGAAAATCGTAACATGAG 58.362 43.478 0.74 0.00 37.88 2.90
2196 2280 3.120477 GCACGGTGAAAATCGTAACATGA 60.120 43.478 13.29 0.00 37.88 3.07
2197 2281 3.120338 AGCACGGTGAAAATCGTAACATG 60.120 43.478 13.29 0.00 37.88 3.21
2199 2283 2.222213 CAGCACGGTGAAAATCGTAACA 59.778 45.455 13.29 0.00 37.88 2.41
2200 2284 2.834689 CAGCACGGTGAAAATCGTAAC 58.165 47.619 13.29 0.00 37.88 2.50
2202 2286 0.793861 GCAGCACGGTGAAAATCGTA 59.206 50.000 13.29 0.00 37.88 3.43
2203 2287 0.884704 AGCAGCACGGTGAAAATCGT 60.885 50.000 13.29 0.00 40.49 3.73
2204 2288 0.179215 GAGCAGCACGGTGAAAATCG 60.179 55.000 13.29 0.00 0.00 3.34
2213 2303 1.485838 GATCGACATGAGCAGCACGG 61.486 60.000 0.00 0.00 31.75 4.94
2215 2305 3.055144 TGATCGACATGAGCAGCAC 57.945 52.632 0.00 0.00 38.27 4.40
2224 2314 0.466963 TCAGCAGCCATGATCGACAT 59.533 50.000 0.00 0.00 40.17 3.06
2227 2317 0.103755 GTCTCAGCAGCCATGATCGA 59.896 55.000 0.00 0.00 0.00 3.59
2228 2318 0.879400 GGTCTCAGCAGCCATGATCG 60.879 60.000 0.00 0.00 0.00 3.69
2235 2325 1.055040 ATATCCAGGTCTCAGCAGCC 58.945 55.000 0.00 0.00 0.00 4.85
2237 2327 3.894427 AGTACATATCCAGGTCTCAGCAG 59.106 47.826 0.00 0.00 0.00 4.24
2244 2334 5.793030 AGCTACAAGTACATATCCAGGTC 57.207 43.478 0.00 0.00 0.00 3.85
2252 2342 2.295349 GCGGCCTAGCTACAAGTACATA 59.705 50.000 0.00 0.00 0.00 2.29
2259 2349 0.108329 GAAGTGCGGCCTAGCTACAA 60.108 55.000 0.00 0.00 38.13 2.41
2269 2359 2.886124 GCGAGGTAGAAGTGCGGC 60.886 66.667 0.00 0.00 0.00 6.53
2271 2361 1.517257 CCAGCGAGGTAGAAGTGCG 60.517 63.158 0.00 0.00 0.00 5.34
2282 2372 0.531532 CAGGGAATGCTACCAGCGAG 60.532 60.000 0.00 0.00 46.26 5.03
2289 2379 0.872021 CGACGCTCAGGGAATGCTAC 60.872 60.000 0.00 0.00 0.00 3.58
2296 2386 1.587043 CTCTTCACGACGCTCAGGGA 61.587 60.000 0.00 0.00 0.00 4.20
2299 2389 0.179176 CCTCTCTTCACGACGCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
2300 2390 0.605589 TCCTCTCTTCACGACGCTCA 60.606 55.000 0.00 0.00 0.00 4.26
2301 2391 0.098025 CTCCTCTCTTCACGACGCTC 59.902 60.000 0.00 0.00 0.00 5.03
2302 2392 0.321741 TCTCCTCTCTTCACGACGCT 60.322 55.000 0.00 0.00 0.00 5.07
2305 2395 0.098025 CGCTCTCCTCTCTTCACGAC 59.902 60.000 0.00 0.00 0.00 4.34
2308 2398 0.457681 GCACGCTCTCCTCTCTTCAC 60.458 60.000 0.00 0.00 0.00 3.18
2348 2482 0.661552 CATGCCATGTGCTCTAGTGC 59.338 55.000 9.86 9.86 42.00 4.40
2351 2485 1.590932 GGACATGCCATGTGCTCTAG 58.409 55.000 20.54 0.00 46.53 2.43
2352 2486 3.786656 GGACATGCCATGTGCTCTA 57.213 52.632 20.54 0.00 46.53 2.43
2361 2495 0.328926 TGAGCAATCTGGACATGCCA 59.671 50.000 8.33 8.33 46.96 4.92
2386 2520 1.866496 GCTGTACTGTACGCGACGG 60.866 63.158 15.93 14.41 40.66 4.79
2388 2522 2.494591 GCGCTGTACTGTACGCGAC 61.495 63.158 36.43 28.47 46.45 5.19
2389 2523 2.202388 GCGCTGTACTGTACGCGA 60.202 61.111 36.43 15.31 46.45 5.87
2392 2526 2.158959 GCCTGCGCTGTACTGTACG 61.159 63.158 9.73 8.93 0.00 3.67
2393 2527 0.460284 ATGCCTGCGCTGTACTGTAC 60.460 55.000 9.73 10.98 35.36 2.90
2394 2528 0.460109 CATGCCTGCGCTGTACTGTA 60.460 55.000 9.73 0.00 35.36 2.74
2395 2529 1.742880 CATGCCTGCGCTGTACTGT 60.743 57.895 9.73 0.00 35.36 3.55
2405 2546 3.248266 GAAACAATCTGTTCATGCCTGC 58.752 45.455 0.00 0.00 40.14 4.85
2423 2564 5.308014 CGGATCATGATGGAGTTATGGAAA 58.692 41.667 14.30 0.00 0.00 3.13
2434 2575 2.346766 TTGGTTCCGGATCATGATGG 57.653 50.000 14.30 9.40 0.00 3.51
2528 2674 4.841861 TAATTCGTGGCCGGCGGG 62.842 66.667 29.48 12.23 33.95 6.13
2529 2675 2.184167 AATAATTCGTGGCCGGCGG 61.184 57.895 24.35 24.35 33.95 6.13
2530 2676 1.010125 CAATAATTCGTGGCCGGCG 60.010 57.895 22.54 6.96 33.95 6.46
2531 2677 0.028902 GACAATAATTCGTGGCCGGC 59.971 55.000 21.18 21.18 33.95 6.13
2553 2699 4.841861 TAATTCGTGGGCGGGCGG 62.842 66.667 0.00 0.00 38.89 6.13
2628 2774 1.578583 CGAACACGAACATATCCCCC 58.421 55.000 0.00 0.00 0.00 5.40
2630 2776 2.304751 ACCGAACACGAACATATCCC 57.695 50.000 0.00 0.00 0.00 3.85
2635 2781 1.223187 GTCCAACCGAACACGAACAT 58.777 50.000 0.00 0.00 0.00 2.71
2636 2782 1.146957 CGTCCAACCGAACACGAACA 61.147 55.000 0.00 0.00 34.06 3.18


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

AutoCloner maintained by Alex Coulton.