Multiple sequence alignment - TraesCS1B01G386500

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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 TraesCS1B01G386500 chr1B 100.000 2462 0 0 1 2462 620785153 620787614 0.000000e+00 4547.0
1 TraesCS1B01G386500 chr1B 87.723 1629 143 32 3 1616 621058358 621059944 0.000000e+00 1847.0
2 TraesCS1B01G386500 chr1B 89.455 1394 91 28 823 2185 621272360 621270992 0.000000e+00 1709.0
3 TraesCS1B01G386500 chr1B 94.753 648 28 5 823 1467 620899932 620900576 0.000000e+00 1003.0
4 TraesCS1B01G386500 chr1B 88.998 818 66 17 823 1637 610558246 610559042 0.000000e+00 990.0
5 TraesCS1B01G386500 chr1B 84.993 693 100 4 3 693 621273322 621272632 0.000000e+00 701.0
6 TraesCS1B01G386500 chr1B 95.050 101 5 0 2345 2445 620901710 620901810 2.530000e-35 159.0
7 TraesCS1B01G386500 chr1A 89.435 2035 148 32 1 2012 546215467 546217457 0.000000e+00 2505.0
8 TraesCS1B01G386500 chr1A 89.318 777 38 25 899 1640 542167886 542168652 0.000000e+00 933.0
9 TraesCS1B01G386500 chr1A 77.124 306 30 21 1432 1720 557098441 557098159 9.180000e-30 141.0
10 TraesCS1B01G386500 chr1D 89.554 1771 109 31 229 1982 451624403 451626114 0.000000e+00 2176.0
11 TraesCS1B01G386500 chr1D 89.222 835 65 21 823 1640 446434638 446435464 0.000000e+00 1020.0
12 TraesCS1B01G386500 chr1D 91.837 637 17 22 991 1611 451524632 451525249 0.000000e+00 856.0
13 TraesCS1B01G386500 chr1D 85.294 272 39 1 1 272 451624130 451624400 1.860000e-71 279.0
14 TraesCS1B01G386500 chr1D 90.698 172 14 2 2059 2230 451626109 451626278 6.850000e-56 228.0
15 TraesCS1B01G386500 chr1D 75.911 494 80 22 1381 1854 202283329 202282855 1.480000e-52 217.0
16 TraesCS1B01G386500 chr1D 93.069 101 7 0 2345 2445 451526186 451526286 5.490000e-32 148.0
17 TraesCS1B01G386500 chr3A 82.576 660 76 25 823 1465 57013710 57013073 1.660000e-151 545.0
18 TraesCS1B01G386500 chr3D 81.399 672 63 39 825 1465 45064794 45064154 2.200000e-135 492.0
19 TraesCS1B01G386500 chr3D 75.735 544 82 28 1381 1905 118253860 118254372 6.850000e-56 228.0
20 TraesCS1B01G386500 chr7A 82.993 147 10 10 1497 1640 3098439 3098305 4.300000e-23 119.0
21 TraesCS1B01G386500 chr5B 87.273 55 5 2 713 766 526527101 526527154 7.350000e-06 62.1


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 TraesCS1B01G386500 chr1B 620785153 620787614 2461 False 4547.000000 4547 100.000000 1 2462 1 chr1B.!!$F2 2461
1 TraesCS1B01G386500 chr1B 621058358 621059944 1586 False 1847.000000 1847 87.723000 3 1616 1 chr1B.!!$F3 1613
2 TraesCS1B01G386500 chr1B 621270992 621273322 2330 True 1205.000000 1709 87.224000 3 2185 2 chr1B.!!$R1 2182
3 TraesCS1B01G386500 chr1B 610558246 610559042 796 False 990.000000 990 88.998000 823 1637 1 chr1B.!!$F1 814
4 TraesCS1B01G386500 chr1B 620899932 620901810 1878 False 581.000000 1003 94.901500 823 2445 2 chr1B.!!$F4 1622
5 TraesCS1B01G386500 chr1A 546215467 546217457 1990 False 2505.000000 2505 89.435000 1 2012 1 chr1A.!!$F2 2011
6 TraesCS1B01G386500 chr1A 542167886 542168652 766 False 933.000000 933 89.318000 899 1640 1 chr1A.!!$F1 741
7 TraesCS1B01G386500 chr1D 446434638 446435464 826 False 1020.000000 1020 89.222000 823 1640 1 chr1D.!!$F1 817
8 TraesCS1B01G386500 chr1D 451624130 451626278 2148 False 894.333333 2176 88.515333 1 2230 3 chr1D.!!$F3 2229
9 TraesCS1B01G386500 chr1D 451524632 451526286 1654 False 502.000000 856 92.453000 991 2445 2 chr1D.!!$F2 1454
10 TraesCS1B01G386500 chr3A 57013073 57013710 637 True 545.000000 545 82.576000 823 1465 1 chr3A.!!$R1 642
11 TraesCS1B01G386500 chr3D 45064154 45064794 640 True 492.000000 492 81.399000 825 1465 1 chr3D.!!$R1 640
12 TraesCS1B01G386500 chr3D 118253860 118254372 512 False 228.000000 228 75.735000 1381 1905 1 chr3D.!!$F1 524

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
29 30 0.035458 CCAGGTTGTCCTCCACTGTC 59.965 60.0 0.0 0.0 43.07 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2491 0.95396 AGCCCGACCGATTGAACAAC 60.954 55.0 0.0 0.0 0.0 3.32 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
29 30 0.035458 CCAGGTTGTCCTCCACTGTC 59.965 60.000 0.00 0.00 43.07 3.51
38 39 2.606213 TCCACTGTCGGGATGCCA 60.606 61.111 3.39 0.00 0.00 4.92
74 75 3.312421 GTGTAGTGAAATATGCGTGCCAT 59.688 43.478 0.00 0.00 37.97 4.40
76 77 2.368439 AGTGAAATATGCGTGCCATGT 58.632 42.857 0.00 0.00 35.34 3.21
82 83 0.248843 TATGCGTGCCATGTCTGTCA 59.751 50.000 0.00 0.00 35.34 3.58
113 114 5.125417 AACACATTGCATAAGTATGTGGTCC 59.875 40.000 24.84 0.00 44.54 4.46
122 123 6.015010 GCATAAGTATGTGGTCCAGAGTATCT 60.015 42.308 0.00 0.00 40.35 1.98
175 176 1.078497 CGTCTTGTAGCCCATGCCA 60.078 57.895 0.00 0.00 38.69 4.92
180 181 2.025037 TCTTGTAGCCCATGCCAGAATT 60.025 45.455 0.00 0.00 38.69 2.17
203 204 2.750637 GCGGAGGTCCAGACTCGA 60.751 66.667 10.90 0.00 35.82 4.04
209 210 2.288518 GGAGGTCCAGACTCGATATTGC 60.289 54.545 0.00 0.00 35.82 3.56
213 214 4.588951 AGGTCCAGACTCGATATTGCATAA 59.411 41.667 0.00 0.00 0.00 1.90
217 218 6.257849 GTCCAGACTCGATATTGCATAACAAA 59.742 38.462 0.00 0.00 42.86 2.83
227 228 9.676195 CGATATTGCATAACAAACCATATGAAA 57.324 29.630 3.65 0.00 42.86 2.69
244 291 8.602328 CCATATGAAAATTTTGCATTTAAGCGA 58.398 29.630 8.47 0.00 37.31 4.93
258 305 3.717842 AGCGACACCCAGCTTTTTA 57.282 47.368 0.00 0.00 41.52 1.52
266 313 5.180492 CGACACCCAGCTTTTTAAGATACAA 59.820 40.000 0.00 0.00 0.00 2.41
291 339 2.756829 CAGTGGCAAACAAATCATGCA 58.243 42.857 0.00 0.00 41.80 3.96
310 358 2.419021 GCACTGGCATGGCATTTTGTAT 60.419 45.455 23.59 0.00 40.72 2.29
312 360 2.168936 ACTGGCATGGCATTTTGTATGG 59.831 45.455 23.59 10.00 0.00 2.74
313 361 2.168936 CTGGCATGGCATTTTGTATGGT 59.831 45.455 23.59 0.00 0.00 3.55
329 377 2.514013 GGTGATTGCGCCGAGTACG 61.514 63.158 4.18 0.00 34.49 3.67
408 456 4.139859 TGTTCCTAACGACAGACCAAAA 57.860 40.909 0.00 0.00 0.00 2.44
447 495 3.958147 CTTGCGGACCGGCACTCAT 62.958 63.158 17.22 0.00 43.82 2.90
473 521 6.259550 AGAAGAACACTATTCAATTGGCAC 57.740 37.500 5.42 0.00 0.00 5.01
507 555 3.711190 TCAGTAGGCCTATTCATGAGCAA 59.289 43.478 17.38 0.00 0.00 3.91
529 577 4.680537 ACCCGACGAGCCTGACCT 62.681 66.667 0.00 0.00 0.00 3.85
565 613 2.028190 CTAGGCATGGGCTCGACG 59.972 66.667 0.00 0.00 39.70 5.12
584 632 1.373748 TTTTCGTCCGAAGCCCGAG 60.374 57.895 2.12 0.00 41.76 4.63
802 949 4.532126 TCTGGTTCTAGGAAGAATGCTTGA 59.468 41.667 0.00 0.00 43.50 3.02
812 959 5.477984 AGGAAGAATGCTTGATTTGCAGTTA 59.522 36.000 0.00 0.00 44.04 2.24
896 1146 0.853586 TCCCCATAAAACCCAGCCCT 60.854 55.000 0.00 0.00 0.00 5.19
897 1147 0.687427 CCCCATAAAACCCAGCCCTG 60.687 60.000 0.00 0.00 0.00 4.45
938 1188 1.577736 CATCTCAGTCCCCACTTCCT 58.422 55.000 0.00 0.00 0.00 3.36
939 1189 1.209019 CATCTCAGTCCCCACTTCCTG 59.791 57.143 0.00 0.00 0.00 3.86
946 1202 1.065410 TCCCCACTTCCTGCTTCCAA 61.065 55.000 0.00 0.00 0.00 3.53
973 1251 1.147376 CACAACCCACCACCGAAGA 59.853 57.895 0.00 0.00 0.00 2.87
1499 1874 3.664107 TGGTTTCTGCATCTGTAGTGTC 58.336 45.455 0.00 0.00 0.00 3.67
1590 1968 1.403679 CTTTGTTGGCTCGTTGGTTGA 59.596 47.619 0.00 0.00 0.00 3.18
1591 1969 1.686355 TTGTTGGCTCGTTGGTTGAT 58.314 45.000 0.00 0.00 0.00 2.57
1592 1970 1.686355 TGTTGGCTCGTTGGTTGATT 58.314 45.000 0.00 0.00 0.00 2.57
1593 1971 1.336440 TGTTGGCTCGTTGGTTGATTG 59.664 47.619 0.00 0.00 0.00 2.67
1777 2238 8.472007 ACTGAATTTGTTGGAATTTGGTAGTA 57.528 30.769 0.00 0.00 29.75 1.82
1811 2272 1.621317 TCAGTGGTGCAAACCGAGATA 59.379 47.619 0.00 0.00 0.00 1.98
1908 2382 4.875536 TGTGCTTTCATATCGTAGCAATGT 59.124 37.500 0.00 0.00 44.39 2.71
1910 2384 6.705825 TGTGCTTTCATATCGTAGCAATGTAT 59.294 34.615 0.00 0.00 44.39 2.29
1984 2491 0.392998 ATTAGGCGCAGAACCCAGTG 60.393 55.000 10.83 0.00 0.00 3.66
2026 2533 2.425143 TTTCCTGCTGCTATTGAGGG 57.575 50.000 0.00 0.00 0.00 4.30
2028 2535 0.543277 TCCTGCTGCTATTGAGGGTG 59.457 55.000 0.00 0.00 0.00 4.61
2031 2538 2.369860 CCTGCTGCTATTGAGGGTGATA 59.630 50.000 0.00 0.00 0.00 2.15
2032 2539 3.181451 CCTGCTGCTATTGAGGGTGATAA 60.181 47.826 0.00 0.00 0.00 1.75
2041 2548 9.639563 TGCTATTGAGGGTGATAATCATTTAAA 57.360 29.630 0.00 0.00 0.00 1.52
2048 2555 6.667414 AGGGTGATAATCATTTAAAGTGGCAA 59.333 34.615 0.00 0.00 0.00 4.52
2050 2557 6.980397 GGTGATAATCATTTAAAGTGGCAAGG 59.020 38.462 0.00 0.00 0.00 3.61
2067 2574 3.207778 CAAGGTAAGAACAACCCAACGA 58.792 45.455 0.00 0.00 37.77 3.85
2076 2583 1.068434 ACAACCCAACGATTTGCCTTG 59.932 47.619 0.00 0.00 0.00 3.61
2089 2596 1.180456 TGCCTTGCCATGTCCTGTTG 61.180 55.000 0.00 0.00 0.00 3.33
2100 2607 5.253330 CCATGTCCTGTTGTTAAGGTACAT 58.747 41.667 0.00 0.00 36.67 2.29
2122 2629 8.084590 ACATTAGTTTACTCTGCAGTTTGTAC 57.915 34.615 14.67 8.11 33.62 2.90
2135 2642 2.154462 GTTTGTACATCAGCTGGCAGT 58.846 47.619 17.16 12.36 0.00 4.40
2191 2708 4.825422 TGGCAAATGTGAGTTGTTTTTGA 58.175 34.783 0.00 0.00 30.69 2.69
2193 2710 5.108517 GGCAAATGTGAGTTGTTTTTGAGA 58.891 37.500 0.00 0.00 30.69 3.27
2226 2743 4.025229 GTGTGTGTTGCTGTCGATTTCTTA 60.025 41.667 0.00 0.00 0.00 2.10
2227 2744 4.211164 TGTGTGTTGCTGTCGATTTCTTAG 59.789 41.667 0.00 0.00 0.00 2.18
2228 2745 4.211374 GTGTGTTGCTGTCGATTTCTTAGT 59.789 41.667 0.00 0.00 0.00 2.24
2229 2746 5.404366 GTGTGTTGCTGTCGATTTCTTAGTA 59.596 40.000 0.00 0.00 0.00 1.82
2231 2748 7.274904 GTGTGTTGCTGTCGATTTCTTAGTATA 59.725 37.037 0.00 0.00 0.00 1.47
2232 2749 7.274904 TGTGTTGCTGTCGATTTCTTAGTATAC 59.725 37.037 0.00 0.00 0.00 1.47
2234 2751 7.488150 TGTTGCTGTCGATTTCTTAGTATACAG 59.512 37.037 5.50 0.00 36.92 2.74
2240 2785 9.784680 TGTCGATTTCTTAGTATACAGAGTTTC 57.215 33.333 5.50 0.00 0.00 2.78
2247 2794 8.079211 TCTTAGTATACAGAGTTTCATTGCCT 57.921 34.615 5.50 0.00 0.00 4.75
2249 2796 5.352284 AGTATACAGAGTTTCATTGCCTCG 58.648 41.667 5.50 0.00 0.00 4.63
2253 2800 1.002430 AGAGTTTCATTGCCTCGCTGA 59.998 47.619 0.00 0.00 0.00 4.26
2255 2802 0.874390 GTTTCATTGCCTCGCTGACA 59.126 50.000 0.00 0.00 0.00 3.58
2268 2815 1.939934 CGCTGACAACTGAAGAAACCA 59.060 47.619 0.00 0.00 0.00 3.67
2271 2818 4.393062 CGCTGACAACTGAAGAAACCATAT 59.607 41.667 0.00 0.00 0.00 1.78
2272 2819 5.634896 GCTGACAACTGAAGAAACCATATG 58.365 41.667 0.00 0.00 0.00 1.78
2274 2821 4.458989 TGACAACTGAAGAAACCATATGCC 59.541 41.667 0.00 0.00 0.00 4.40
2283 2830 0.546122 AACCATATGCCTGCCTTCGA 59.454 50.000 0.00 0.00 0.00 3.71
2291 2838 2.020131 CCTGCCTTCGATGCACATC 58.980 57.895 6.08 0.31 34.46 3.06
2304 2851 4.709840 ACATCTGGTGTGCTGCTC 57.290 55.556 0.00 0.00 40.28 4.26
2305 2852 1.002868 ACATCTGGTGTGCTGCTCC 60.003 57.895 0.00 1.75 40.28 4.70
2306 2853 1.298993 CATCTGGTGTGCTGCTCCT 59.701 57.895 0.00 0.00 0.00 3.69
2307 2854 0.322277 CATCTGGTGTGCTGCTCCTT 60.322 55.000 0.00 0.00 0.00 3.36
2308 2855 0.322277 ATCTGGTGTGCTGCTCCTTG 60.322 55.000 0.00 0.06 0.00 3.61
2309 2856 2.595463 TGGTGTGCTGCTCCTTGC 60.595 61.111 0.00 0.00 43.25 4.01
2310 2857 3.730761 GGTGTGCTGCTCCTTGCG 61.731 66.667 0.00 0.00 46.63 4.85
2317 2864 4.314440 TGCTCCTTGCGGCTCGTT 62.314 61.111 0.00 0.00 46.63 3.85
2318 2865 3.491652 GCTCCTTGCGGCTCGTTC 61.492 66.667 0.00 0.00 0.00 3.95
2319 2866 2.815647 CTCCTTGCGGCTCGTTCC 60.816 66.667 0.00 0.00 0.00 3.62
2320 2867 3.589654 CTCCTTGCGGCTCGTTCCA 62.590 63.158 0.00 0.00 0.00 3.53
2321 2868 3.121030 CCTTGCGGCTCGTTCCAG 61.121 66.667 0.00 0.00 0.00 3.86
2322 2869 3.121030 CTTGCGGCTCGTTCCAGG 61.121 66.667 0.00 0.00 0.00 4.45
2327 2874 4.821589 GGCTCGTTCCAGGCTCCG 62.822 72.222 0.00 0.00 36.04 4.63
2329 2876 4.821589 CTCGTTCCAGGCTCCGGC 62.822 72.222 0.00 0.00 37.82 6.13
2333 2880 4.161295 TTCCAGGCTCCGGCGATG 62.161 66.667 9.30 0.80 39.81 3.84
2338 2885 3.606662 GGCTCCGGCGATGCTCTA 61.607 66.667 9.30 0.00 39.81 2.43
2339 2886 2.653702 GCTCCGGCGATGCTCTAT 59.346 61.111 9.30 0.00 0.00 1.98
2340 2887 1.595993 GGCTCCGGCGATGCTCTATA 61.596 60.000 9.30 0.00 39.81 1.31
2341 2888 0.179150 GCTCCGGCGATGCTCTATAG 60.179 60.000 9.30 0.00 0.00 1.31
2342 2889 1.169577 CTCCGGCGATGCTCTATAGT 58.830 55.000 9.30 0.00 0.00 2.12
2343 2890 1.542030 CTCCGGCGATGCTCTATAGTT 59.458 52.381 9.30 0.00 0.00 2.24
2346 3291 2.747989 CCGGCGATGCTCTATAGTTAGA 59.252 50.000 9.30 0.00 33.39 2.10
2366 3311 4.437239 AGATGCCAGTTCTGTAAATCTCG 58.563 43.478 0.00 0.00 0.00 4.04
2382 3327 7.662258 TGTAAATCTCGGTCAACCAAGAATTAA 59.338 33.333 0.32 0.00 35.14 1.40
2395 3340 9.185192 CAACCAAGAATTAACAAAATCTGAGTC 57.815 33.333 0.00 0.00 0.00 3.36
2449 3394 9.836179 ATCTTGGATTACTTCATATCTAGGAGT 57.164 33.333 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.964860 TTGTCCATGTTGGCATCCCG 60.965 55.000 0.00 0.00 37.47 5.14
38 39 3.135712 TCACTACACTGGTTGTCCATGTT 59.864 43.478 0.00 0.00 43.43 2.71
74 75 5.701855 CAATGTGTTTATGCATGACAGACA 58.298 37.500 10.16 8.14 0.00 3.41
76 77 4.217983 TGCAATGTGTTTATGCATGACAGA 59.782 37.500 10.16 12.81 44.52 3.41
113 114 6.707440 TTCTGCTAGGAAGAAGATACTCTG 57.293 41.667 0.00 0.00 37.25 3.35
122 123 5.316167 TGCTTCAATTTCTGCTAGGAAGAA 58.684 37.500 0.00 0.19 35.04 2.52
135 136 2.702270 ACCTCCCCTTGCTTCAATTT 57.298 45.000 0.00 0.00 0.00 1.82
138 139 0.328258 GCTACCTCCCCTTGCTTCAA 59.672 55.000 0.00 0.00 0.00 2.69
175 176 0.181350 GACCTCCGCCCATCAATTCT 59.819 55.000 0.00 0.00 0.00 2.40
180 181 3.083349 CTGGACCTCCGCCCATCA 61.083 66.667 0.00 0.00 39.43 3.07
186 187 0.818445 TATCGAGTCTGGACCTCCGC 60.818 60.000 0.00 0.00 39.43 5.54
217 218 8.389603 CGCTTAAATGCAAAATTTTCATATGGT 58.610 29.630 0.00 0.00 0.00 3.55
227 228 3.993736 GGGTGTCGCTTAAATGCAAAATT 59.006 39.130 0.00 0.00 0.00 1.82
244 291 6.719370 TCATTGTATCTTAAAAAGCTGGGTGT 59.281 34.615 0.00 0.00 0.00 4.16
258 305 3.354948 TGCCACTGCTCATTGTATCTT 57.645 42.857 0.00 0.00 38.71 2.40
266 313 2.629137 TGATTTGTTTGCCACTGCTCAT 59.371 40.909 0.00 0.00 38.71 2.90
291 339 2.168936 CCATACAAAATGCCATGCCAGT 59.831 45.455 0.00 0.00 0.00 4.00
299 347 2.859538 CGCAATCACCATACAAAATGCC 59.140 45.455 0.00 0.00 0.00 4.40
310 358 1.447140 GTACTCGGCGCAATCACCA 60.447 57.895 10.83 0.00 0.00 4.17
312 360 2.995482 CGTACTCGGCGCAATCAC 59.005 61.111 10.83 0.00 0.00 3.06
332 380 0.178973 TGGAGGTGGAGTTCGACTGA 60.179 55.000 0.00 0.00 0.00 3.41
394 442 2.864343 CTCGAACTTTTGGTCTGTCGTT 59.136 45.455 0.00 0.00 32.98 3.85
408 456 5.470047 AGGTCTACAACAATTCTCGAACT 57.530 39.130 0.00 0.00 0.00 3.01
444 492 9.166173 CCAATTGAATAGTGTTCTTCTACATGA 57.834 33.333 7.12 0.00 0.00 3.07
447 495 6.939730 TGCCAATTGAATAGTGTTCTTCTACA 59.060 34.615 7.12 0.00 0.00 2.74
473 521 1.935933 CCTACTGAAAACGGATCGGG 58.064 55.000 5.18 0.00 0.00 5.14
565 613 1.623973 CTCGGGCTTCGGACGAAAAC 61.624 60.000 8.59 3.93 39.77 2.43
584 632 2.438868 AAAACTCATTCGGCCTTTGC 57.561 45.000 0.00 0.00 0.00 3.68
687 829 6.536941 GGCCAGAAACATTTGAACAGTAAAAA 59.463 34.615 0.00 0.00 0.00 1.94
688 830 6.045955 GGCCAGAAACATTTGAACAGTAAAA 58.954 36.000 0.00 0.00 0.00 1.52
689 831 5.596845 GGCCAGAAACATTTGAACAGTAAA 58.403 37.500 0.00 0.00 0.00 2.01
690 832 4.261405 CGGCCAGAAACATTTGAACAGTAA 60.261 41.667 2.24 0.00 0.00 2.24
723 865 1.550524 GAAGCAAGAATCCCAAACCCC 59.449 52.381 0.00 0.00 0.00 4.95
802 949 3.412386 GACACACTCCCTAACTGCAAAT 58.588 45.455 0.00 0.00 0.00 2.32
812 959 1.456892 TGACGTGGACACACTCCCT 60.457 57.895 0.00 0.00 45.50 4.20
896 1146 3.407967 GGGAATGGAGCGGGGTCA 61.408 66.667 0.00 0.00 0.00 4.02
897 1147 4.191015 GGGGAATGGAGCGGGGTC 62.191 72.222 0.00 0.00 0.00 4.46
938 1188 2.441410 TGTGTGAGTTTGTTGGAAGCA 58.559 42.857 0.00 0.00 0.00 3.91
939 1189 3.179048 GTTGTGTGAGTTTGTTGGAAGC 58.821 45.455 0.00 0.00 0.00 3.86
946 1202 1.272203 TGGTGGGTTGTGTGAGTTTGT 60.272 47.619 0.00 0.00 0.00 2.83
973 1251 1.991230 CTTCGGGTGGAGTTGGGAT 59.009 57.895 0.00 0.00 0.00 3.85
1436 1783 1.691976 AGGATGTGAACTTGGTGACGA 59.308 47.619 0.00 0.00 0.00 4.20
1499 1874 6.093357 TGCAGATAGATAGATAAGCAGAGTCG 59.907 42.308 0.00 0.00 0.00 4.18
1590 1968 4.823989 AGCAGCAACTTCAGTTCTTACAAT 59.176 37.500 0.00 0.00 35.83 2.71
1591 1969 4.199310 AGCAGCAACTTCAGTTCTTACAA 58.801 39.130 0.00 0.00 35.83 2.41
1592 1970 3.808728 AGCAGCAACTTCAGTTCTTACA 58.191 40.909 0.00 0.00 35.83 2.41
1593 1971 4.061596 AGAGCAGCAACTTCAGTTCTTAC 58.938 43.478 0.00 0.00 35.83 2.34
1655 2043 3.087031 CCAACATCAGGCAGACATTTCT 58.913 45.455 0.00 0.00 0.00 2.52
1656 2044 3.498927 CCAACATCAGGCAGACATTTC 57.501 47.619 0.00 0.00 0.00 2.17
1666 2078 3.165071 AGGGTAAAAAGCCAACATCAGG 58.835 45.455 0.00 0.00 0.00 3.86
1745 2166 8.299570 CAAATTCCAACAAATTCAGTAGTAGCT 58.700 33.333 0.00 0.00 0.00 3.32
1910 2384 8.739039 CAGGAATCTGGAAACACAAATTACATA 58.261 33.333 0.00 0.00 37.36 2.29
1984 2491 0.953960 AGCCCGACCGATTGAACAAC 60.954 55.000 0.00 0.00 0.00 3.32
2026 2533 7.547227 ACCTTGCCACTTTAAATGATTATCAC 58.453 34.615 0.00 0.00 0.00 3.06
2028 2535 9.736023 CTTACCTTGCCACTTTAAATGATTATC 57.264 33.333 0.00 0.00 0.00 1.75
2031 2538 7.775053 TCTTACCTTGCCACTTTAAATGATT 57.225 32.000 0.00 0.00 0.00 2.57
2032 2539 7.232534 TGTTCTTACCTTGCCACTTTAAATGAT 59.767 33.333 0.00 0.00 0.00 2.45
2041 2548 2.583143 GGTTGTTCTTACCTTGCCACT 58.417 47.619 0.00 0.00 32.75 4.00
2048 2555 3.782656 ATCGTTGGGTTGTTCTTACCT 57.217 42.857 0.00 0.00 35.92 3.08
2050 2557 3.978855 GCAAATCGTTGGGTTGTTCTTAC 59.021 43.478 0.00 0.00 35.10 2.34
2067 2574 0.899720 CAGGACATGGCAAGGCAAAT 59.100 50.000 0.00 0.00 0.00 2.32
2076 2583 2.514803 ACCTTAACAACAGGACATGGC 58.485 47.619 0.00 0.00 35.14 4.40
2089 2596 8.767478 TGCAGAGTAAACTAATGTACCTTAAC 57.233 34.615 0.00 0.00 0.00 2.01
2100 2607 7.929245 TGATGTACAAACTGCAGAGTAAACTAA 59.071 33.333 23.35 0.00 0.00 2.24
2122 2629 0.107800 ACTGCTACTGCCAGCTGATG 60.108 55.000 17.39 7.16 41.54 3.07
2135 2642 4.530553 TCAGAGGATAACACCAAACTGCTA 59.469 41.667 0.00 0.00 32.62 3.49
2191 2708 7.096551 ACAGCAACACACACTTAAATTTTTCT 58.903 30.769 0.00 0.00 0.00 2.52
2193 2710 6.034470 CGACAGCAACACACACTTAAATTTTT 59.966 34.615 0.00 0.00 0.00 1.94
2198 2715 3.263261 TCGACAGCAACACACACTTAAA 58.737 40.909 0.00 0.00 0.00 1.52
2207 2724 4.992381 ACTAAGAAATCGACAGCAACAC 57.008 40.909 0.00 0.00 0.00 3.32
2226 2743 5.352284 CGAGGCAATGAAACTCTGTATACT 58.648 41.667 4.17 0.00 0.00 2.12
2227 2744 4.025647 GCGAGGCAATGAAACTCTGTATAC 60.026 45.833 0.00 0.00 0.00 1.47
2228 2745 4.119862 GCGAGGCAATGAAACTCTGTATA 58.880 43.478 0.00 0.00 0.00 1.47
2229 2746 2.939103 GCGAGGCAATGAAACTCTGTAT 59.061 45.455 0.00 0.00 0.00 2.29
2231 2748 1.160137 GCGAGGCAATGAAACTCTGT 58.840 50.000 0.00 0.00 0.00 3.41
2232 2749 1.129998 CAGCGAGGCAATGAAACTCTG 59.870 52.381 0.00 0.00 0.00 3.35
2234 2751 1.129437 GTCAGCGAGGCAATGAAACTC 59.871 52.381 0.00 0.00 0.00 3.01
2240 2785 0.167470 CAGTTGTCAGCGAGGCAATG 59.833 55.000 2.68 0.28 44.87 2.82
2244 2789 0.319900 TCTTCAGTTGTCAGCGAGGC 60.320 55.000 0.00 0.00 0.00 4.70
2245 2792 2.154854 TTCTTCAGTTGTCAGCGAGG 57.845 50.000 0.00 0.00 0.00 4.63
2247 2794 2.210116 GGTTTCTTCAGTTGTCAGCGA 58.790 47.619 0.00 0.00 0.00 4.93
2249 2796 5.634896 CATATGGTTTCTTCAGTTGTCAGC 58.365 41.667 0.00 0.00 0.00 4.26
2253 2800 4.460382 CAGGCATATGGTTTCTTCAGTTGT 59.540 41.667 4.56 0.00 0.00 3.32
2255 2802 3.445096 GCAGGCATATGGTTTCTTCAGTT 59.555 43.478 4.56 0.00 0.00 3.16
2268 2815 0.109153 TGCATCGAAGGCAGGCATAT 59.891 50.000 10.67 0.00 36.11 1.78
2271 2818 2.747460 GTGCATCGAAGGCAGGCA 60.747 61.111 14.52 3.66 42.85 4.75
2272 2819 2.056481 GATGTGCATCGAAGGCAGGC 62.056 60.000 14.52 5.88 42.85 4.85
2274 2821 0.656259 CAGATGTGCATCGAAGGCAG 59.344 55.000 14.52 0.67 42.85 4.85
2291 2838 2.623915 GCAAGGAGCAGCACACCAG 61.624 63.158 0.00 0.00 44.79 4.00
2305 2852 3.121030 CCTGGAACGAGCCGCAAG 61.121 66.667 0.00 0.00 0.00 4.01
2309 2856 4.821589 GGAGCCTGGAACGAGCCG 62.822 72.222 0.00 0.00 0.00 5.52
2310 2857 4.821589 CGGAGCCTGGAACGAGCC 62.822 72.222 0.00 0.00 0.00 4.70
2311 2858 4.821589 CCGGAGCCTGGAACGAGC 62.822 72.222 0.00 0.00 0.00 5.03
2312 2859 4.821589 GCCGGAGCCTGGAACGAG 62.822 72.222 5.05 0.00 0.00 4.18
2315 2862 4.162690 ATCGCCGGAGCCTGGAAC 62.163 66.667 5.05 0.00 34.57 3.62
2320 2867 3.950400 TATAGAGCATCGCCGGAGCCT 62.950 57.143 5.05 0.00 42.67 4.58
2321 2868 1.595993 TATAGAGCATCGCCGGAGCC 61.596 60.000 5.05 0.00 42.67 4.70
2322 2869 0.179150 CTATAGAGCATCGCCGGAGC 60.179 60.000 5.05 2.48 42.67 4.70
2323 2870 1.169577 ACTATAGAGCATCGCCGGAG 58.830 55.000 5.05 0.00 42.67 4.63
2327 2874 4.109050 GCATCTAACTATAGAGCATCGCC 58.891 47.826 6.78 0.00 41.36 5.54
2329 2876 5.105957 ACTGGCATCTAACTATAGAGCATCG 60.106 44.000 6.78 0.00 41.36 3.84
2331 2878 6.496565 AGAACTGGCATCTAACTATAGAGCAT 59.503 38.462 6.78 0.00 41.36 3.79
2333 2880 6.155827 CAGAACTGGCATCTAACTATAGAGC 58.844 44.000 6.78 0.74 41.36 4.09
2334 2881 7.283625 ACAGAACTGGCATCTAACTATAGAG 57.716 40.000 6.78 0.00 36.92 2.43
2335 2882 8.762481 TTACAGAACTGGCATCTAACTATAGA 57.238 34.615 6.78 0.00 37.45 1.98
2336 2883 9.988815 ATTTACAGAACTGGCATCTAACTATAG 57.011 33.333 6.76 0.00 34.19 1.31
2337 2884 9.982651 GATTTACAGAACTGGCATCTAACTATA 57.017 33.333 6.76 0.00 34.19 1.31
2338 2885 8.709308 AGATTTACAGAACTGGCATCTAACTAT 58.291 33.333 6.76 0.00 34.19 2.12
2339 2886 8.079211 AGATTTACAGAACTGGCATCTAACTA 57.921 34.615 6.76 0.00 34.19 2.24
2340 2887 6.951971 AGATTTACAGAACTGGCATCTAACT 58.048 36.000 6.76 0.00 34.19 2.24
2341 2888 6.019479 CGAGATTTACAGAACTGGCATCTAAC 60.019 42.308 6.76 0.20 30.11 2.34
2342 2889 6.042777 CGAGATTTACAGAACTGGCATCTAA 58.957 40.000 6.76 0.00 30.11 2.10
2343 2890 5.451937 CCGAGATTTACAGAACTGGCATCTA 60.452 44.000 6.76 0.00 30.11 1.98
2346 3291 3.055094 ACCGAGATTTACAGAACTGGCAT 60.055 43.478 6.76 0.00 34.19 4.40
2366 3311 8.141268 TCAGATTTTGTTAATTCTTGGTTGACC 58.859 33.333 0.00 0.00 0.00 4.02
2382 3327 5.078411 ACATCTAGCGACTCAGATTTTGT 57.922 39.130 0.00 0.00 28.88 2.83


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

AutoCloner maintained by Alex Coulton.