Multiple sequence alignment - TraesCS7B01G398800

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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 TraesCS7B01G398800 chr7B 100.000 2914 0 0 1 2914 665387169 665384256 0.000000e+00 5382.0
1 TraesCS7B01G398800 chr7B 85.886 333 43 4 2582 2913 579604768 579605097 4.620000e-93 351.0
2 TraesCS7B01G398800 chr7D 93.285 2919 108 28 49 2914 590418964 590416081 0.000000e+00 4224.0
3 TraesCS7B01G398800 chr7D 96.000 50 2 0 1 50 590419037 590418988 6.690000e-12 82.4
4 TraesCS7B01G398800 chr7D 100.000 29 0 0 106 134 197348965 197348937 1.000000e-03 54.7
5 TraesCS7B01G398800 chr2A 87.087 333 39 4 2581 2913 398444788 398445116 9.860000e-100 374.0
6 TraesCS7B01G398800 chr2A 86.787 333 41 3 2581 2913 398871196 398870867 4.590000e-98 368.0
7 TraesCS7B01G398800 chr5A 86.787 333 38 4 2585 2914 236882417 236882746 1.650000e-97 366.0
8 TraesCS7B01G398800 chrUn 86.890 328 40 3 2586 2913 329570578 329570254 5.930000e-97 364.0
9 TraesCS7B01G398800 chr1D 87.415 294 36 1 2620 2913 88216532 88216824 1.290000e-88 337.0
10 TraesCS7B01G398800 chr1D 80.412 97 17 2 2818 2913 376903190 376903095 4.030000e-09 73.1
11 TraesCS7B01G398800 chr1D 96.970 33 1 0 676 708 315977829 315977861 4.060000e-04 56.5
12 TraesCS7B01G398800 chr1B 86.395 294 39 1 2620 2913 142103585 142103877 1.300000e-83 320.0
13 TraesCS7B01G398800 chr3D 85.156 128 16 3 2580 2707 68293546 68293670 8.480000e-26 128.0
14 TraesCS7B01G398800 chr3D 91.111 45 3 1 678 721 47784241 47784197 3.140000e-05 60.2
15 TraesCS7B01G398800 chr3D 100.000 28 0 0 105 132 293756435 293756462 5.000000e-03 52.8
16 TraesCS7B01G398800 chr1A 73.333 315 59 19 2582 2881 299426438 299426742 3.090000e-15 93.5
17 TraesCS7B01G398800 chr2D 79.167 144 17 8 2585 2715 27975626 27975483 1.440000e-13 87.9
18 TraesCS7B01G398800 chr5B 97.222 36 1 0 676 711 116684119 116684084 8.720000e-06 62.1
19 TraesCS7B01G398800 chr5B 100.000 28 0 0 676 703 545083440 545083413 5.000000e-03 52.8
20 TraesCS7B01G398800 chr6A 92.683 41 2 1 670 709 560572933 560572973 1.130000e-04 58.4
21 TraesCS7B01G398800 chr3A 100.000 31 0 0 676 706 592213374 592213404 1.130000e-04 58.4
22 TraesCS7B01G398800 chr3A 94.286 35 1 1 99 132 388090772 388090806 5.000000e-03 52.8
23 TraesCS7B01G398800 chr3B 92.500 40 2 1 683 721 75322079 75322040 4.060000e-04 56.5
24 TraesCS7B01G398800 chr6D 90.476 42 3 1 670 710 417896932 417896973 1.000000e-03 54.7


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 TraesCS7B01G398800 chr7B 665384256 665387169 2913 True 5382.0 5382 100.0000 1 2914 1 chr7B.!!$R1 2913
1 TraesCS7B01G398800 chr7D 590416081 590419037 2956 True 2153.2 4224 94.6425 1 2914 2 chr7D.!!$R2 2913

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
51 52 0.467804 GCACCCAAGCCTTCCAAAAA 59.532 50.000 0.00 0.00 0.0 1.94 F
52 53 1.072173 GCACCCAAGCCTTCCAAAAAT 59.928 47.619 0.00 0.00 0.0 1.82 F
1647 1719 0.251742 CCTTGGGGTTGGCAATCTCA 60.252 55.000 9.48 9.48 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1218 0.100146 GAGGCCTACGTACGTTCCTG 59.900 60.0 28.97 17.08 0.00 3.86 R
1856 1928 0.106335 AGGCTGATCCGCTGATGAAG 59.894 55.0 9.11 0.00 40.77 3.02 R
2730 2808 0.317854 GGAGAGTTTTGCCGTGTTGC 60.318 55.0 0.00 0.00 0.00 4.17 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
50 51 2.132300 GCACCCAAGCCTTCCAAAA 58.868 52.632 0.00 0.00 0.00 2.44
51 52 0.467804 GCACCCAAGCCTTCCAAAAA 59.532 50.000 0.00 0.00 0.00 1.94
52 53 1.072173 GCACCCAAGCCTTCCAAAAAT 59.928 47.619 0.00 0.00 0.00 1.82
53 54 2.301583 GCACCCAAGCCTTCCAAAAATA 59.698 45.455 0.00 0.00 0.00 1.40
54 55 3.055167 GCACCCAAGCCTTCCAAAAATAT 60.055 43.478 0.00 0.00 0.00 1.28
191 240 3.334691 TCTAAACTGAAGTTGGCGGATG 58.665 45.455 0.00 0.00 38.44 3.51
207 256 2.675317 CGGATGTCTTGACCTTGGAGAC 60.675 54.545 0.00 0.00 40.09 3.36
266 315 8.848474 TTACTTTTGACTTAGATTTCCTCTGG 57.152 34.615 0.00 0.00 35.28 3.86
288 337 4.439837 GGAAACTATGTACTCAGGGTCGTC 60.440 50.000 0.00 0.00 0.00 4.20
298 347 4.176752 GGGTCGTCCATGGAGCCC 62.177 72.222 24.88 24.88 44.37 5.19
375 426 6.769608 AATACACACGTGCATATAGATGTG 57.230 37.500 17.22 4.63 42.44 3.21
472 541 5.894807 ACTATTGCATCTGTACCAAAATGC 58.105 37.500 10.28 10.28 43.71 3.56
594 663 7.714703 TCACACAAAAATGAGTTTCATCATCA 58.285 30.769 0.00 0.00 39.00 3.07
605 674 7.819644 TGAGTTTCATCATCAACATTTACAGG 58.180 34.615 0.00 0.00 0.00 4.00
723 795 7.713073 CAGAGGGAGTATTTGATAAGAAACCTC 59.287 40.741 0.00 0.00 39.80 3.85
777 849 1.474143 CGGGAGCAAGAAATCCTCTCC 60.474 57.143 0.00 0.00 41.87 3.71
910 982 1.602605 GTCAAACGGAAGGGGTGGG 60.603 63.158 0.00 0.00 0.00 4.61
929 1001 3.541115 TGGGGGACGGGGGAATATATATA 59.459 47.826 0.00 0.00 0.00 0.86
930 1002 4.175268 TGGGGGACGGGGGAATATATATAT 59.825 45.833 0.00 0.00 0.00 0.86
941 1013 6.003950 GGGAATATATATATGCGTGGCCATT 58.996 40.000 9.72 0.00 0.00 3.16
1156 1228 1.445582 CACCTCGCCAGGAACGTAC 60.446 63.158 3.62 0.00 43.65 3.67
1179 1251 1.144913 AGGCCTCTCTCGCTCTTCTAT 59.855 52.381 0.00 0.00 0.00 1.98
1211 1283 4.465886 AGACGACTATATCCTGCTCTGTT 58.534 43.478 0.00 0.00 0.00 3.16
1213 1285 5.009210 AGACGACTATATCCTGCTCTGTTTC 59.991 44.000 0.00 0.00 0.00 2.78
1223 1295 2.555757 CTGCTCTGTTTCCCTTTTCCTG 59.444 50.000 0.00 0.00 0.00 3.86
1279 1351 0.889186 CGGTCAGGTCCCAGTTTTGG 60.889 60.000 0.00 0.00 44.60 3.28
1370 1442 6.474819 TGAACTACCAAAATGTCACATACG 57.525 37.500 0.00 0.00 0.00 3.06
1371 1443 5.992829 TGAACTACCAAAATGTCACATACGT 59.007 36.000 0.00 0.00 0.00 3.57
1372 1444 7.153315 TGAACTACCAAAATGTCACATACGTA 58.847 34.615 0.00 0.00 0.00 3.57
1521 1593 2.904434 AGCCTCGGGAGAAAACTTTCTA 59.096 45.455 4.71 0.00 46.84 2.10
1522 1594 3.001414 GCCTCGGGAGAAAACTTTCTAC 58.999 50.000 5.94 5.94 46.84 2.59
1541 1613 9.185192 CTTTCTACTGAAATTGAACATGTTTCC 57.815 33.333 13.36 1.09 40.85 3.13
1552 1624 1.912043 ACATGTTTCCAGCCTAGCTCT 59.088 47.619 0.00 0.00 36.40 4.09
1583 1655 7.596621 ACATATATTGTCTATGCAACAGAGTCG 59.403 37.037 1.80 0.00 30.89 4.18
1647 1719 0.251742 CCTTGGGGTTGGCAATCTCA 60.252 55.000 9.48 9.48 0.00 3.27
1684 1756 2.826777 GATGTGTGGCTGGAGGTGGG 62.827 65.000 0.00 0.00 0.00 4.61
1698 1770 2.204385 TGGGGGCCCACCAATACT 60.204 61.111 25.09 0.00 41.89 2.12
1775 1847 1.153349 GGTTGATGAGAGGGCCGTC 60.153 63.158 17.88 17.88 0.00 4.79
1832 1904 5.163364 GGATGTGTATGAGTCCAGATTGTCT 60.163 44.000 0.00 0.00 0.00 3.41
1850 1922 3.288964 GTCTAGCTCCAAGTACCTAGCA 58.711 50.000 0.00 0.00 37.44 3.49
1856 1928 2.691011 CTCCAAGTACCTAGCAGGAGAC 59.309 54.545 8.91 6.56 44.12 3.36
1860 1932 3.741245 AGTACCTAGCAGGAGACTTCA 57.259 47.619 8.91 0.00 40.21 3.02
1861 1933 4.258457 AGTACCTAGCAGGAGACTTCAT 57.742 45.455 8.91 0.00 40.21 2.57
1862 1934 4.211920 AGTACCTAGCAGGAGACTTCATC 58.788 47.826 8.91 0.00 40.21 2.92
1863 1935 3.107402 ACCTAGCAGGAGACTTCATCA 57.893 47.619 8.91 0.00 40.21 3.07
1864 1936 3.030291 ACCTAGCAGGAGACTTCATCAG 58.970 50.000 8.91 0.00 40.21 2.90
1865 1937 2.224018 CCTAGCAGGAGACTTCATCAGC 60.224 54.545 0.00 0.00 40.21 4.26
1866 1938 0.175302 AGCAGGAGACTTCATCAGCG 59.825 55.000 0.00 0.00 40.21 5.18
1867 1939 0.809241 GCAGGAGACTTCATCAGCGG 60.809 60.000 0.00 0.00 40.21 5.52
2026 2098 3.132824 TGTCGGATCTAATGCACATGTCT 59.867 43.478 0.00 0.00 0.00 3.41
2061 2133 7.930325 TGATCTAAAATGATTTTGTTGGCAACA 59.070 29.630 28.09 28.09 38.39 3.33
2062 2134 7.475771 TCTAAAATGATTTTGTTGGCAACAC 57.524 32.000 31.20 20.09 41.97 3.32
2063 2135 6.481644 TCTAAAATGATTTTGTTGGCAACACC 59.518 34.615 31.20 19.84 41.97 4.16
2064 2136 6.352516 TAAAATGATTTTGTTGGCAACACCT 58.647 32.000 31.20 18.59 41.97 4.00
2065 2137 7.500992 TAAAATGATTTTGTTGGCAACACCTA 58.499 30.769 31.20 19.27 41.97 3.08
2066 2138 7.655328 TAAAATGATTTTGTTGGCAACACCTAG 59.345 33.333 31.20 0.00 41.97 3.02
2110 2182 4.866921 ACTTTTTCGGTATTTGGTCAAGC 58.133 39.130 0.00 0.00 0.00 4.01
2186 2259 3.936453 TGGGAAATCAAGTCGAAATACGG 59.064 43.478 0.00 0.00 42.82 4.02
2233 2307 6.652481 CACATTTCAAGTGATTCCTGTAGTCT 59.348 38.462 0.00 0.00 39.30 3.24
2234 2308 7.819415 CACATTTCAAGTGATTCCTGTAGTCTA 59.181 37.037 0.00 0.00 39.30 2.59
2235 2309 8.037758 ACATTTCAAGTGATTCCTGTAGTCTAG 58.962 37.037 0.00 0.00 0.00 2.43
2236 2310 7.776618 TTTCAAGTGATTCCTGTAGTCTAGA 57.223 36.000 0.00 0.00 0.00 2.43
2238 2312 6.486056 TCAAGTGATTCCTGTAGTCTAGAGT 58.514 40.000 5.21 5.21 0.00 3.24
2239 2313 6.600032 TCAAGTGATTCCTGTAGTCTAGAGTC 59.400 42.308 2.53 0.00 0.00 3.36
2240 2314 5.120399 AGTGATTCCTGTAGTCTAGAGTCG 58.880 45.833 2.53 0.00 0.00 4.18
2241 2315 4.273969 GTGATTCCTGTAGTCTAGAGTCGG 59.726 50.000 2.53 3.94 0.00 4.79
2242 2316 3.996921 TTCCTGTAGTCTAGAGTCGGT 57.003 47.619 2.53 0.00 0.00 4.69
2243 2317 3.540314 TCCTGTAGTCTAGAGTCGGTC 57.460 52.381 2.53 0.00 0.00 4.79
2244 2318 2.836372 TCCTGTAGTCTAGAGTCGGTCA 59.164 50.000 2.53 0.00 0.00 4.02
2276 2350 9.506018 AAATAAAATTGAAGCCTTAATGCAACT 57.494 25.926 5.50 0.00 0.00 3.16
2313 2388 7.454260 AAAATGACTTGGTCCTATGAGAAAC 57.546 36.000 0.00 0.00 0.00 2.78
2356 2431 4.715896 TCACACTAGCTAAACGTTAGTCG 58.284 43.478 0.00 0.00 37.53 4.18
2360 2435 1.992170 AGCTAAACGTTAGTCGCCTG 58.008 50.000 0.00 0.00 44.19 4.85
2376 2451 2.736400 CGCCTGAAAATCTGATTTGGGC 60.736 50.000 26.91 26.91 38.56 5.36
2393 2468 2.086094 GGGCCGGTCGATTTTCTAAAA 58.914 47.619 1.90 0.00 0.00 1.52
2395 2470 2.485038 GGCCGGTCGATTTTCTAAAACA 59.515 45.455 1.90 0.00 0.00 2.83
2397 2472 4.380128 GGCCGGTCGATTTTCTAAAACAAT 60.380 41.667 1.90 0.00 0.00 2.71
2425 2500 3.672295 GAGCTGCCGGAGTGAAGGG 62.672 68.421 5.05 0.00 0.00 3.95
2433 2508 1.338200 CCGGAGTGAAGGGAGAAACAG 60.338 57.143 0.00 0.00 0.00 3.16
2438 2513 0.603707 TGAAGGGAGAAACAGCTGCG 60.604 55.000 15.27 0.00 0.00 5.18
2499 2574 2.587150 TATTAGGGTGGGGGTGGGGG 62.587 65.000 0.00 0.00 0.00 5.40
2521 2596 0.748450 AAAGAACGTCGGGTCAGTCA 59.252 50.000 0.00 0.00 0.00 3.41
2526 2601 0.966920 ACGTCGGGTCAGTCATCTTT 59.033 50.000 0.00 0.00 0.00 2.52
2557 2632 5.955959 ACAAATCCCCAAAATTCTAGGGTAC 59.044 40.000 8.50 0.00 41.16 3.34
2579 2654 4.201910 ACAAATCCCGTAAATGATGCTTCG 60.202 41.667 0.00 0.00 0.00 3.79
2626 2704 6.866010 AAGCTTGCGTATCATTCATTGATA 57.134 33.333 0.00 0.00 43.43 2.15
2627 2705 6.477669 AGCTTGCGTATCATTCATTGATAG 57.522 37.500 0.00 0.00 45.74 2.08
2630 2708 7.014115 GCTTGCGTATCATTCATTGATAGAAG 58.986 38.462 0.00 1.83 45.74 2.85
2631 2709 7.095481 GCTTGCGTATCATTCATTGATAGAAGA 60.095 37.037 10.34 0.00 45.74 2.87
2632 2710 8.661352 TTGCGTATCATTCATTGATAGAAGAA 57.339 30.769 0.00 0.00 45.74 2.52
2702 2780 3.062466 CGGAGCAGAGGGACACGA 61.062 66.667 0.00 0.00 0.00 4.35
2711 2789 1.816863 GAGGGACACGAGGTGCTCAA 61.817 60.000 0.00 0.00 38.05 3.02
2722 2800 1.632589 GGTGCTCAACCCAAGGAAAT 58.367 50.000 0.00 0.00 44.02 2.17
2730 2808 5.776744 CTCAACCCAAGGAAATGAAAAGAG 58.223 41.667 0.00 0.00 0.00 2.85
2755 2833 0.744771 CGGCAAAACTCTCCTAGCCC 60.745 60.000 0.00 0.00 38.90 5.19
2768 2846 2.567615 TCCTAGCCCTGAGAAACAACTC 59.432 50.000 0.00 0.00 37.42 3.01
2769 2847 2.303022 CCTAGCCCTGAGAAACAACTCA 59.697 50.000 0.00 0.00 43.39 3.41
2778 2856 6.039270 CCCTGAGAAACAACTCAAACACAATA 59.961 38.462 0.00 0.00 44.62 1.90
2803 2881 2.618045 CCAACCAGTATCCAACTCCACC 60.618 54.545 0.00 0.00 35.76 4.61
2804 2882 0.902531 ACCAGTATCCAACTCCACCG 59.097 55.000 0.00 0.00 35.76 4.94
2807 2885 0.815734 AGTATCCAACTCCACCGTCG 59.184 55.000 0.00 0.00 30.33 5.12
2832 2910 2.307309 CCGCGAGCGAACAAGACAA 61.307 57.895 19.72 0.00 42.83 3.18
2846 2924 4.843728 ACAAGACAACACCTTCAAGAAGA 58.156 39.130 11.25 0.00 40.79 2.87
2862 2940 0.319641 AAGAGGAACGGCGTCAAGAC 60.320 55.000 15.17 4.52 33.89 3.01
2898 2976 4.332543 AGGAGCCCGGACCAAGGA 62.333 66.667 0.73 0.00 0.00 3.36
2904 2982 1.076995 CCCGGACCAAGGATTTCCC 60.077 63.158 0.73 0.00 36.42 3.97
2905 2983 1.076995 CCGGACCAAGGATTTCCCC 60.077 63.158 0.00 0.00 36.42 4.81
2906 2984 1.571773 CCGGACCAAGGATTTCCCCT 61.572 60.000 0.00 0.00 38.42 4.79
2907 2985 0.394352 CGGACCAAGGATTTCCCCTG 60.394 60.000 0.00 0.00 36.49 4.45
2908 2986 0.999712 GGACCAAGGATTTCCCCTGA 59.000 55.000 0.00 0.00 36.49 3.86
2909 2987 1.570979 GGACCAAGGATTTCCCCTGAT 59.429 52.381 0.00 0.00 36.49 2.90
2910 2988 2.659428 GACCAAGGATTTCCCCTGATG 58.341 52.381 0.00 0.00 36.49 3.07
2911 2989 1.342374 ACCAAGGATTTCCCCTGATGC 60.342 52.381 0.00 0.00 36.49 3.91
2913 2991 2.625087 CCAAGGATTTCCCCTGATGCTT 60.625 50.000 0.00 0.00 36.49 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.268566 CCCTGAAAGTCAAGTTCTTTTCTTG 58.731 40.000 0.00 0.00 42.25 3.02
9 10 5.163509 GCCCTGAAAGTCAAGTTCTTTTCTT 60.164 40.000 0.00 0.00 35.62 2.52
50 51 9.337396 TCTTATACGGCACAATTCTTTGATATT 57.663 29.630 0.00 0.00 36.64 1.28
51 52 8.902540 TCTTATACGGCACAATTCTTTGATAT 57.097 30.769 0.00 0.00 36.64 1.63
52 53 7.441157 CCTCTTATACGGCACAATTCTTTGATA 59.559 37.037 0.00 0.00 36.64 2.15
53 54 6.260936 CCTCTTATACGGCACAATTCTTTGAT 59.739 38.462 0.00 0.00 36.64 2.57
54 55 5.584649 CCTCTTATACGGCACAATTCTTTGA 59.415 40.000 0.00 0.00 36.64 2.69
116 142 3.691118 CCATTCACCGAAGATGACATTGT 59.309 43.478 0.00 0.00 0.00 2.71
191 240 1.056660 TGGGTCTCCAAGGTCAAGAC 58.943 55.000 0.00 0.00 40.73 3.01
207 256 2.548875 CTCTCTTCGAGAATGCTTGGG 58.451 52.381 0.00 0.00 42.62 4.12
266 315 4.439837 GGACGACCCTGAGTACATAGTTTC 60.440 50.000 0.00 0.00 0.00 2.78
288 337 1.000896 AAAAGTCCGGGCTCCATGG 60.001 57.895 10.20 4.97 0.00 3.66
472 541 6.421801 CCTATGCAAAACTCAAAAAGGTCTTG 59.578 38.462 0.00 0.00 0.00 3.02
560 629 8.565896 AACTCATTTTTGTGTGAGCTATATCA 57.434 30.769 2.52 0.00 44.38 2.15
561 630 9.495754 GAAACTCATTTTTGTGTGAGCTATATC 57.504 33.333 2.52 0.00 44.38 1.63
594 663 7.065324 CGTGTATACCACAATCCTGTAAATGTT 59.935 37.037 0.00 0.00 44.78 2.71
605 674 6.956299 AAAGTACACGTGTATACCACAATC 57.044 37.500 29.58 14.21 44.78 2.67
680 750 9.892130 ACTCCCTCTGTAACTTTTTATAAGATG 57.108 33.333 0.00 0.00 0.00 2.90
777 849 4.081309 TGTTCCACGAGGAGGGTTTTATAG 60.081 45.833 0.78 0.00 46.74 1.31
810 882 4.799564 TGGTCAAAATATTTGTCTGCCC 57.200 40.909 0.39 0.00 0.00 5.36
888 960 1.971695 CCCCTTCCGTTTGACTGCC 60.972 63.158 0.00 0.00 0.00 4.85
910 982 4.322499 CGCATATATATATTCCCCCGTCCC 60.322 50.000 2.28 0.00 0.00 4.46
929 1001 1.682854 CCTGAAATAATGGCCACGCAT 59.317 47.619 8.16 0.00 0.00 4.73
930 1002 1.102154 CCTGAAATAATGGCCACGCA 58.898 50.000 8.16 0.00 0.00 5.24
941 1013 8.128582 CGCTACAAAATATCTTTGCCTGAAATA 58.871 33.333 9.08 0.00 32.93 1.40
960 1032 1.268625 TCGCTCTTCAAGTCGCTACAA 59.731 47.619 0.00 0.00 0.00 2.41
1143 1215 1.226491 CCTACGTACGTTCCTGGCG 60.226 63.158 27.92 6.49 0.00 5.69
1146 1218 0.100146 GAGGCCTACGTACGTTCCTG 59.900 60.000 28.97 17.08 0.00 3.86
1156 1228 1.098712 AAGAGCGAGAGAGGCCTACG 61.099 60.000 4.42 11.03 0.00 3.51
1179 1251 6.010850 AGGATATAGTCGTCTCATAGGCAAA 58.989 40.000 0.00 0.00 0.00 3.68
1211 1283 0.106419 ACCAACGCAGGAAAAGGGAA 60.106 50.000 0.10 0.00 0.00 3.97
1213 1285 1.834188 ATACCAACGCAGGAAAAGGG 58.166 50.000 0.10 0.00 0.00 3.95
1279 1351 0.250338 AGGCAAAAGTCACCGTCCTC 60.250 55.000 0.00 0.00 0.00 3.71
1368 1440 0.397535 TCCCCCGCTCCTAAATACGT 60.398 55.000 0.00 0.00 0.00 3.57
1369 1441 0.754472 TTCCCCCGCTCCTAAATACG 59.246 55.000 0.00 0.00 0.00 3.06
1370 1442 1.767088 ACTTCCCCCGCTCCTAAATAC 59.233 52.381 0.00 0.00 0.00 1.89
1371 1443 2.185663 ACTTCCCCCGCTCCTAAATA 57.814 50.000 0.00 0.00 0.00 1.40
1372 1444 2.185663 TACTTCCCCCGCTCCTAAAT 57.814 50.000 0.00 0.00 0.00 1.40
1438 1510 5.887214 TCCATGCTAAATTACTCTGCCTA 57.113 39.130 0.00 0.00 0.00 3.93
1500 1572 1.700186 AGAAAGTTTTCTCCCGAGGCT 59.300 47.619 1.35 0.00 43.72 4.58
1505 1577 6.803154 ATTTCAGTAGAAAGTTTTCTCCCG 57.197 37.500 10.20 1.66 46.13 5.14
1521 1593 5.291971 GCTGGAAACATGTTCAATTTCAGT 58.708 37.500 12.39 0.00 41.51 3.41
1522 1594 4.687483 GGCTGGAAACATGTTCAATTTCAG 59.313 41.667 12.39 11.39 41.51 3.02
1541 1613 4.804868 ATATGTGATGAGAGCTAGGCTG 57.195 45.455 0.00 0.00 39.88 4.85
1552 1624 9.211485 CTGTTGCATAGACAATATATGTGATGA 57.789 33.333 0.00 0.00 44.12 2.92
1583 1655 2.570468 TATATTTCGTGATTGCGCGC 57.430 45.000 27.26 27.26 46.94 6.86
1647 1719 0.911769 TCGACCATTGCTGATCCCTT 59.088 50.000 0.00 0.00 0.00 3.95
1684 1756 2.442087 GCCAGTATTGGTGGGCCC 60.442 66.667 17.59 17.59 46.80 5.80
1716 1788 4.469227 CCGGATCCTGATCTCCATAAGAAT 59.531 45.833 10.75 0.00 37.61 2.40
1775 1847 2.414481 CAGCTTGTCAATGTTCTCCTCG 59.586 50.000 0.00 0.00 0.00 4.63
1832 1904 2.243994 TCCTGCTAGGTACTTGGAGCTA 59.756 50.000 1.96 0.00 46.50 3.32
1850 1922 1.686052 GATCCGCTGATGAAGTCTCCT 59.314 52.381 0.00 0.00 0.00 3.69
1856 1928 0.106335 AGGCTGATCCGCTGATGAAG 59.894 55.000 9.11 0.00 40.77 3.02
1860 1932 2.733301 CGAGGCTGATCCGCTGAT 59.267 61.111 9.11 0.00 40.77 2.90
1861 1933 4.212913 GCGAGGCTGATCCGCTGA 62.213 66.667 10.63 0.00 44.83 4.26
1865 1937 4.933064 GTCGGCGAGGCTGATCCG 62.933 72.222 11.20 11.16 46.06 4.18
1866 1938 4.593864 GGTCGGCGAGGCTGATCC 62.594 72.222 11.20 1.41 46.06 3.36
1867 1939 3.492311 GAGGTCGGCGAGGCTGATC 62.492 68.421 11.20 1.73 46.06 2.92
1996 2068 3.321111 GCATTAGATCCGACACCTTCCTA 59.679 47.826 0.00 0.00 0.00 2.94
2050 2122 1.142870 AGAGCTAGGTGTTGCCAACAA 59.857 47.619 12.63 0.00 44.16 2.83
2061 2133 7.448469 ACAAACACATTAATGAAAGAGCTAGGT 59.552 33.333 22.16 0.00 0.00 3.08
2062 2134 7.820648 ACAAACACATTAATGAAAGAGCTAGG 58.179 34.615 22.16 3.69 0.00 3.02
2063 2135 9.760660 GTACAAACACATTAATGAAAGAGCTAG 57.239 33.333 22.16 5.25 0.00 3.42
2064 2136 9.502091 AGTACAAACACATTAATGAAAGAGCTA 57.498 29.630 22.16 0.86 0.00 3.32
2065 2137 8.396272 AGTACAAACACATTAATGAAAGAGCT 57.604 30.769 22.16 7.25 0.00 4.09
2066 2138 9.463443 AAAGTACAAACACATTAATGAAAGAGC 57.537 29.630 22.16 5.29 0.00 4.09
2203 2277 4.529377 AGGAATCACTTGAAATGTGGCAAT 59.471 37.500 0.00 0.00 41.82 3.56
2233 2307 5.925506 TTATTTCACCATGACCGACTCTA 57.074 39.130 0.00 0.00 0.00 2.43
2234 2308 4.819105 TTATTTCACCATGACCGACTCT 57.181 40.909 0.00 0.00 0.00 3.24
2235 2309 5.873179 TTTTATTTCACCATGACCGACTC 57.127 39.130 0.00 0.00 0.00 3.36
2236 2310 6.432783 TCAATTTTATTTCACCATGACCGACT 59.567 34.615 0.00 0.00 0.00 4.18
2238 2312 6.825944 TCAATTTTATTTCACCATGACCGA 57.174 33.333 0.00 0.00 0.00 4.69
2239 2313 6.034898 GCTTCAATTTTATTTCACCATGACCG 59.965 38.462 0.00 0.00 0.00 4.79
2240 2314 6.313658 GGCTTCAATTTTATTTCACCATGACC 59.686 38.462 0.00 0.00 0.00 4.02
2241 2315 7.099120 AGGCTTCAATTTTATTTCACCATGAC 58.901 34.615 0.00 0.00 0.00 3.06
2242 2316 7.243604 AGGCTTCAATTTTATTTCACCATGA 57.756 32.000 0.00 0.00 0.00 3.07
2243 2317 7.910441 AAGGCTTCAATTTTATTTCACCATG 57.090 32.000 0.00 0.00 0.00 3.66
2339 2414 3.106672 CAGGCGACTAACGTTTAGCTAG 58.893 50.000 5.91 0.00 44.60 3.42
2343 2418 4.977741 TTTTCAGGCGACTAACGTTTAG 57.022 40.909 5.91 4.68 44.60 1.85
2356 2431 2.419159 GGCCCAAATCAGATTTTCAGGC 60.419 50.000 22.62 22.62 38.59 4.85
2360 2435 1.824852 ACCGGCCCAAATCAGATTTTC 59.175 47.619 5.58 0.00 0.00 2.29
2376 2451 7.298507 TCTATTGTTTTAGAAAATCGACCGG 57.701 36.000 0.00 0.00 0.00 5.28
2393 2468 3.615155 GGCAGCTCCTTTCTTCTATTGT 58.385 45.455 0.00 0.00 0.00 2.71
2395 2470 2.420687 CCGGCAGCTCCTTTCTTCTATT 60.421 50.000 0.00 0.00 0.00 1.73
2397 2472 0.537188 CCGGCAGCTCCTTTCTTCTA 59.463 55.000 0.00 0.00 0.00 2.10
2410 2485 1.544825 TTCTCCCTTCACTCCGGCAG 61.545 60.000 0.00 0.00 0.00 4.85
2425 2500 2.383527 CGGACCGCAGCTGTTTCTC 61.384 63.158 16.64 5.03 0.00 2.87
2458 2533 1.415659 AGATCATGGGGAAGCTTCTCG 59.584 52.381 25.05 9.74 0.00 4.04
2465 2540 6.126652 CCACCCTAATATAGATCATGGGGAAG 60.127 46.154 0.00 0.00 37.56 3.46
2499 2574 1.137513 CTGACCCGACGTTCTTTCAC 58.862 55.000 0.00 0.00 0.00 3.18
2500 2575 0.748450 ACTGACCCGACGTTCTTTCA 59.252 50.000 0.00 0.00 0.00 2.69
2502 2577 0.748450 TGACTGACCCGACGTTCTTT 59.252 50.000 0.00 0.00 0.00 2.52
2521 2596 7.625498 TTTGGGGATTTGTTTCCTAAAAGAT 57.375 32.000 0.00 0.00 35.97 2.40
2526 2601 7.625498 AGAATTTTGGGGATTTGTTTCCTAA 57.375 32.000 0.00 0.00 35.97 2.69
2557 2632 4.035091 TCGAAGCATCATTTACGGGATTTG 59.965 41.667 0.00 0.00 0.00 2.32
2626 2704 7.574607 ACCCCGTATTTATTCATTCTTCTTCT 58.425 34.615 0.00 0.00 0.00 2.85
2627 2705 7.803279 ACCCCGTATTTATTCATTCTTCTTC 57.197 36.000 0.00 0.00 0.00 2.87
2630 2708 7.881232 TCCATACCCCGTATTTATTCATTCTTC 59.119 37.037 0.00 0.00 0.00 2.87
2631 2709 7.751646 TCCATACCCCGTATTTATTCATTCTT 58.248 34.615 0.00 0.00 0.00 2.52
2632 2710 7.324388 TCCATACCCCGTATTTATTCATTCT 57.676 36.000 0.00 0.00 0.00 2.40
2636 2714 6.249911 TGTTCCATACCCCGTATTTATTCA 57.750 37.500 0.00 0.00 0.00 2.57
2637 2715 6.543100 TGTTGTTCCATACCCCGTATTTATTC 59.457 38.462 0.00 0.00 0.00 1.75
2638 2716 6.319405 GTGTTGTTCCATACCCCGTATTTATT 59.681 38.462 0.00 0.00 0.00 1.40
2639 2717 5.824097 GTGTTGTTCCATACCCCGTATTTAT 59.176 40.000 0.00 0.00 0.00 1.40
2640 2718 5.184711 GTGTTGTTCCATACCCCGTATTTA 58.815 41.667 0.00 0.00 0.00 1.40
2641 2719 4.011698 GTGTTGTTCCATACCCCGTATTT 58.988 43.478 0.00 0.00 0.00 1.40
2647 2725 1.476488 GCATGTGTTGTTCCATACCCC 59.524 52.381 0.00 0.00 0.00 4.95
2702 2780 0.555769 TTTCCTTGGGTTGAGCACCT 59.444 50.000 0.00 0.00 46.38 4.00
2711 2789 3.575805 TGCTCTTTTCATTTCCTTGGGT 58.424 40.909 0.00 0.00 0.00 4.51
2722 2800 1.098869 TTGCCGTGTTGCTCTTTTCA 58.901 45.000 0.00 0.00 0.00 2.69
2730 2808 0.317854 GGAGAGTTTTGCCGTGTTGC 60.318 55.000 0.00 0.00 0.00 4.17
2755 2833 7.645340 CCTTATTGTGTTTGAGTTGTTTCTCAG 59.355 37.037 0.00 0.00 43.85 3.35
2768 2846 3.069443 ACTGGTTGGCCTTATTGTGTTTG 59.931 43.478 3.32 0.00 35.27 2.93
2769 2847 3.304829 ACTGGTTGGCCTTATTGTGTTT 58.695 40.909 3.32 0.00 35.27 2.83
2778 2856 1.710809 AGTTGGATACTGGTTGGCCTT 59.289 47.619 3.32 0.00 35.19 4.35
2819 2897 1.940613 GAAGGTGTTGTCTTGTTCGCT 59.059 47.619 0.00 0.00 0.00 4.93
2832 2910 2.224305 CCGTTCCTCTTCTTGAAGGTGT 60.224 50.000 10.08 0.00 0.00 4.16
2846 2924 2.049433 CGTCTTGACGCCGTTCCT 60.049 61.111 10.23 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.