Multiple sequence alignment - TraesCS5B01G396800

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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 TraesCS5B01G396800 chr5B 100.000 3409 0 0 1 3409 574670537 574673945 0.000000e+00 6296.0
1 TraesCS5B01G396800 chr5B 88.991 109 10 2 2884 2991 256900859 256900966 2.130000e-27 134.0
2 TraesCS5B01G396800 chr5D 92.101 2823 155 24 1 2792 467596722 467599507 0.000000e+00 3916.0
3 TraesCS5B01G396800 chr5D 91.414 594 38 5 2828 3409 467599509 467600101 0.000000e+00 802.0
4 TraesCS5B01G396800 chr5D 91.071 112 9 1 1 111 442888844 442888733 2.120000e-32 150.0
5 TraesCS5B01G396800 chr5A 92.593 1377 69 14 1608 2959 588372217 588373585 0.000000e+00 1947.0
6 TraesCS5B01G396800 chr5A 90.702 527 20 8 1006 1521 588371681 588372189 0.000000e+00 675.0
7 TraesCS5B01G396800 chr5A 91.546 414 25 3 3006 3409 588373577 588373990 2.300000e-156 562.0
8 TraesCS5B01G396800 chr5A 92.593 108 7 1 1 107 295073338 295073231 1.640000e-33 154.0
9 TraesCS5B01G396800 chr5A 90.351 114 7 4 1 111 680902653 680902765 2.740000e-31 147.0
10 TraesCS5B01G396800 chr5A 89.899 99 9 1 2894 2991 311937039 311937137 3.570000e-25 126.0
11 TraesCS5B01G396800 chr5A 93.182 88 3 3 930 1017 588371579 588371663 3.570000e-25 126.0
12 TraesCS5B01G396800 chr5A 86.364 110 14 1 2884 2992 82869901 82869792 5.980000e-23 119.0
13 TraesCS5B01G396800 chr4D 96.000 100 3 1 1 100 401613314 401613412 9.790000e-36 161.0
14 TraesCS5B01G396800 chr4D 84.800 125 16 3 2874 2995 293386169 293386045 4.620000e-24 122.0
15 TraesCS5B01G396800 chr2A 92.793 111 8 0 1 111 52550280 52550390 9.790000e-36 161.0
16 TraesCS5B01G396800 chr2A 87.826 115 13 1 2874 2987 186406117 186406003 2.130000e-27 134.0
17 TraesCS5B01G396800 chr2B 91.150 113 8 1 1 111 488002190 488002078 5.890000e-33 152.0
18 TraesCS5B01G396800 chr1B 89.655 116 10 2 1 114 8837384 8837269 2.740000e-31 147.0
19 TraesCS5B01G396800 chr7A 87.402 127 13 2 1 124 680421168 680421042 3.550000e-30 143.0
20 TraesCS5B01G396800 chr7D 86.555 119 14 2 2874 2991 530123885 530124002 2.760000e-26 130.0
21 TraesCS5B01G396800 chr1D 90.000 100 9 1 2893 2991 110338929 110339028 9.930000e-26 128.0
22 TraesCS5B01G396800 chr4A 83.871 124 17 3 2874 2995 231025452 231025330 7.730000e-22 115.0
23 TraesCS5B01G396800 chr7B 97.143 35 0 1 621 654 650242020 650241986 1.320000e-04 58.4
24 TraesCS5B01G396800 chr6A 100.000 28 0 0 502 529 591774393 591774420 6.000000e-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 TraesCS5B01G396800 chr5B 574670537 574673945 3408 False 6296.0 6296 100.00000 1 3409 1 chr5B.!!$F2 3408
1 TraesCS5B01G396800 chr5D 467596722 467600101 3379 False 2359.0 3916 91.75750 1 3409 2 chr5D.!!$F1 3408
2 TraesCS5B01G396800 chr5A 588371579 588373990 2411 False 827.5 1947 92.00575 930 3409 4 chr5A.!!$F3 2479

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
186 188 0.381089 GGTCGATGGTACCGAGACTG 59.619 60.0 24.06 6.99 36.66 3.51 F
1947 2012 0.180406 AAGGTATGGATGGCACCGAC 59.820 55.0 0.00 0.00 37.42 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2094 0.107312 ATCTCAGGCATGTCAGGTGC 60.107 55.0 0.0 0.0 41.78 5.01 R
3331 3427 0.035317 TCTGCAACGAAGCATGACCT 59.965 50.0 0.0 0.0 44.68 3.85 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
69 70 1.466856 AATGGTTGCATGCATCGTCT 58.533 45.000 23.37 5.91 0.00 4.18
139 141 7.004555 AGATATTTTGCATATCGTCACCCTA 57.995 36.000 0.00 0.00 36.42 3.53
150 152 2.435069 TCGTCACCCTAACAAACCTCAA 59.565 45.455 0.00 0.00 0.00 3.02
180 182 1.141019 CACTGGGTCGATGGTACCG 59.859 63.158 7.57 0.00 37.93 4.02
186 188 0.381089 GGTCGATGGTACCGAGACTG 59.619 60.000 24.06 6.99 36.66 3.51
210 212 5.007430 GTCTTGTGGTCGACGATAGAGATAA 59.993 44.000 9.92 0.00 41.38 1.75
213 215 4.820173 TGTGGTCGACGATAGAGATAACAT 59.180 41.667 9.92 0.00 41.38 2.71
225 227 8.148351 CGATAGAGATAACATTGAAAGGGGTTA 58.852 37.037 0.00 0.00 39.76 2.85
232 234 9.586435 GATAACATTGAAAGGGGTTATGAAAAG 57.414 33.333 0.00 0.00 36.77 2.27
235 237 6.553100 ACATTGAAAGGGGTTATGAAAAGACA 59.447 34.615 0.00 0.00 0.00 3.41
241 243 5.892348 AGGGGTTATGAAAAGACACAGATT 58.108 37.500 0.00 0.00 0.00 2.40
251 253 0.539986 GACACAGATTTAGGGGGCGA 59.460 55.000 0.00 0.00 0.00 5.54
276 278 2.903678 CGAATGTTTCAAGACGTGTGG 58.096 47.619 0.00 0.00 0.00 4.17
280 282 1.890041 TTTCAAGACGTGTGGGCGG 60.890 57.895 0.00 0.00 35.98 6.13
314 316 1.430228 GAGGTCCTCGACGAAGAGC 59.570 63.158 16.01 16.01 36.95 4.09
384 386 1.499056 GCGTCGTTCGTCTCCTACA 59.501 57.895 0.00 0.00 42.13 2.74
388 390 1.265095 GTCGTTCGTCTCCTACACACA 59.735 52.381 0.00 0.00 0.00 3.72
419 421 4.150454 AGAGGAGGGAGGAGGCGG 62.150 72.222 0.00 0.00 0.00 6.13
465 467 2.352422 GACATGGTGGGAGCTGCA 59.648 61.111 7.79 0.00 0.00 4.41
467 469 2.034532 CATGGTGGGAGCTGCACA 59.965 61.111 7.79 3.06 0.00 4.57
490 492 5.365021 AGCAGCTCCTCTTAAATACACAT 57.635 39.130 0.00 0.00 0.00 3.21
513 515 8.592809 ACATTGTTGATATAATTGTGGTGGTTT 58.407 29.630 0.00 0.00 0.00 3.27
514 516 9.434420 CATTGTTGATATAATTGTGGTGGTTTT 57.566 29.630 0.00 0.00 0.00 2.43
517 519 7.869937 TGTTGATATAATTGTGGTGGTTTTGTG 59.130 33.333 0.00 0.00 0.00 3.33
551 553 9.559958 CTCTTAAATATACACTTTTGCTTGTGG 57.440 33.333 0.00 0.00 38.39 4.17
553 555 9.128107 CTTAAATATACACTTTTGCTTGTGGTG 57.872 33.333 0.00 0.00 38.39 4.17
559 561 2.164219 ACTTTTGCTTGTGGTGTGACAG 59.836 45.455 0.00 0.00 0.00 3.51
560 562 2.121291 TTTGCTTGTGGTGTGACAGA 57.879 45.000 0.00 0.00 0.00 3.41
569 571 7.013750 TGCTTGTGGTGTGACAGAAAAATATTA 59.986 33.333 0.00 0.00 0.00 0.98
681 683 6.749139 TCCACTATGAACTACATGTAGATGC 58.251 40.000 34.16 22.58 39.77 3.91
720 722 9.979578 TTTTTAGTGCAGATTCATACATTTGTT 57.020 25.926 0.00 0.00 0.00 2.83
723 726 9.624697 TTAGTGCAGATTCATACATTTGTTTTC 57.375 29.630 0.00 0.00 0.00 2.29
755 758 6.254589 GTCCATAGTGAAATCTCTGAAACGAG 59.745 42.308 0.00 0.00 0.00 4.18
761 764 8.690680 AGTGAAATCTCTGAAACGAGTTATAC 57.309 34.615 0.00 0.00 32.83 1.47
762 765 8.524487 AGTGAAATCTCTGAAACGAGTTATACT 58.476 33.333 0.00 0.00 32.83 2.12
763 766 9.141400 GTGAAATCTCTGAAACGAGTTATACTT 57.859 33.333 0.00 0.00 32.83 2.24
777 780 8.778358 ACGAGTTATACTTATACTTAGGAACGG 58.222 37.037 0.00 0.00 0.00 4.44
778 781 8.993121 CGAGTTATACTTATACTTAGGAACGGA 58.007 37.037 0.00 0.00 0.00 4.69
790 793 2.181975 AGGAACGGATTTAGGAACGGA 58.818 47.619 0.00 0.00 0.00 4.69
791 794 2.770232 AGGAACGGATTTAGGAACGGAT 59.230 45.455 0.00 0.00 0.00 4.18
792 795 3.199289 AGGAACGGATTTAGGAACGGATT 59.801 43.478 0.00 0.00 0.00 3.01
862 871 3.213206 AGCAAACATCACTCTGTTCCA 57.787 42.857 0.00 0.00 38.38 3.53
897 906 0.960861 AAAAAGCTACCTCTGCGGGC 60.961 55.000 0.00 0.00 36.97 6.13
1000 1009 2.001269 CTCCCCGAAATCCCCACCT 61.001 63.158 0.00 0.00 0.00 4.00
1003 1012 0.693092 CCCCGAAATCCCCACCTAGA 60.693 60.000 0.00 0.00 0.00 2.43
1049 1085 2.802667 CGGCGGCAGATTCAAGACG 61.803 63.158 10.53 0.56 39.81 4.18
1081 1117 2.022035 TCCAGAATCCAGATACCCACCT 60.022 50.000 0.00 0.00 0.00 4.00
1141 1177 1.404391 CGTACAGCAGTATTCCCTCGT 59.596 52.381 0.00 0.00 31.84 4.18
1360 1408 1.761198 GGCTGGTTGGTAGGTAGGTAG 59.239 57.143 0.00 0.00 0.00 3.18
1361 1409 1.761198 GCTGGTTGGTAGGTAGGTAGG 59.239 57.143 0.00 0.00 0.00 3.18
1373 1421 4.057274 AGGTAGGTAGGTAGGGTGTATGA 58.943 47.826 0.00 0.00 0.00 2.15
1444 1492 0.533755 GACCGAATGCCTGGGAGATG 60.534 60.000 0.00 0.00 0.00 2.90
1477 1525 0.250467 GTTGGTGAGAAGGCTGCAGA 60.250 55.000 20.43 0.00 0.00 4.26
1489 1537 1.424493 GCTGCAGAAATCGAGACCGG 61.424 60.000 20.43 0.00 36.24 5.28
1505 1553 2.955402 GGACGTCTCTGCGAGTGT 59.045 61.111 16.46 5.93 35.59 3.55
1611 1665 2.452600 TTGTGGAGGTTGCTTTCCTT 57.547 45.000 0.00 0.00 35.20 3.36
1680 1734 6.902341 TCAAATAGAATTTGTGTCAGCAGAC 58.098 36.000 1.64 1.64 45.19 3.51
1699 1753 5.118357 GCAGACAGAGAATAGATACGCATTG 59.882 44.000 0.00 0.00 0.00 2.82
1702 1756 4.987285 ACAGAGAATAGATACGCATTGCAG 59.013 41.667 9.69 4.31 0.00 4.41
1851 1909 2.095532 CCGTGACTGGTACTACTTCTCG 59.904 54.545 0.00 0.00 0.00 4.04
1890 1955 8.351495 TGTTCTTGTTCAGCACATTTTATTTC 57.649 30.769 0.00 0.00 34.43 2.17
1947 2012 0.180406 AAGGTATGGATGGCACCGAC 59.820 55.000 0.00 0.00 37.42 4.79
2029 2094 1.608283 GGGAGTTGGACTTGGACGAAG 60.608 57.143 0.00 0.00 37.73 3.79
2138 2203 2.182842 CCATTCCGGTAGCAGCAGC 61.183 63.158 0.00 0.00 42.56 5.25
2175 2240 2.287547 GGTTGCCATATTGTATGCACGG 60.288 50.000 0.00 0.00 32.63 4.94
2226 2291 4.547671 TGAAGAACCATTTTGGGGTAACA 58.452 39.130 0.00 0.00 43.37 2.41
2280 2345 6.116126 AGATTATGTACTTCTGTCCAAAGGC 58.884 40.000 0.00 0.00 0.00 4.35
2282 2347 1.270625 TGTACTTCTGTCCAAAGGCGG 60.271 52.381 0.00 0.00 0.00 6.13
2287 2352 1.118965 TCTGTCCAAAGGCGGAGACA 61.119 55.000 0.00 0.00 39.87 3.41
2288 2353 0.951040 CTGTCCAAAGGCGGAGACAC 60.951 60.000 0.00 0.00 39.87 3.67
2289 2354 1.371558 GTCCAAAGGCGGAGACACT 59.628 57.895 0.00 0.00 39.87 3.55
2290 2355 0.951040 GTCCAAAGGCGGAGACACTG 60.951 60.000 0.00 0.00 39.87 3.66
2291 2356 1.071471 CCAAAGGCGGAGACACTGT 59.929 57.895 0.00 0.00 39.87 3.55
2301 2376 1.555075 GGAGACACTGTATTGAGCCCA 59.445 52.381 0.00 0.00 0.00 5.36
2313 2388 5.606749 TGTATTGAGCCCATAGGTACTTGAT 59.393 40.000 0.00 0.00 41.75 2.57
2421 2496 5.071250 TGTGTGTGATGTAAACCCTCTTACT 59.929 40.000 0.00 0.00 33.67 2.24
2435 2510 2.235898 CTCTTACTCCTTGAGGCAGCTT 59.764 50.000 0.00 0.00 33.35 3.74
2457 2532 1.004161 TGGCACGGATTTCTTCCATGA 59.996 47.619 0.00 0.00 40.23 3.07
2492 2567 9.639601 CTTCTATTTTTGTTATTTTCCTGGGAC 57.360 33.333 0.00 0.00 0.00 4.46
2494 2569 6.658188 ATTTTTGTTATTTTCCTGGGACGA 57.342 33.333 0.00 0.00 0.00 4.20
2526 2601 5.316167 ACTGCTGTTTCTGGATATTGTGAA 58.684 37.500 0.00 0.00 0.00 3.18
2533 2608 9.350357 CTGTTTCTGGATATTGTGAATTTTCAG 57.650 33.333 0.00 0.00 37.98 3.02
2554 2629 3.055963 AGTCTCTCACTTGCTCCTGAATG 60.056 47.826 0.00 0.00 26.56 2.67
2577 2652 3.875134 ACCCTGAAGACTTTTGTGTAACG 59.125 43.478 0.00 0.00 42.39 3.18
2630 2705 1.550524 GATTTGTTGGCCCCTCCTTTC 59.449 52.381 0.00 0.00 35.26 2.62
2678 2753 3.978855 CGTGCAAGCATTTCATCCATATG 59.021 43.478 0.00 0.00 0.00 1.78
2715 2790 0.320771 CTTCCCCTTGTGTCACCTCG 60.321 60.000 0.00 0.00 0.00 4.63
2801 2876 7.147479 CCTCTCTTGATATTTCTAAACTGGGGA 60.147 40.741 0.00 0.00 0.00 4.81
2815 2890 4.488790 GGGATGCTTCGCCATCAT 57.511 55.556 5.44 0.00 42.63 2.45
2816 2891 2.251600 GGGATGCTTCGCCATCATC 58.748 57.895 5.44 5.84 42.63 2.92
2819 2894 1.590932 GATGCTTCGCCATCATCACT 58.409 50.000 5.90 0.00 40.96 3.41
2820 2895 2.548707 GGATGCTTCGCCATCATCACTA 60.549 50.000 11.01 0.00 42.63 2.74
2821 2896 2.229675 TGCTTCGCCATCATCACTAG 57.770 50.000 0.00 0.00 0.00 2.57
2822 2897 1.202568 TGCTTCGCCATCATCACTAGG 60.203 52.381 0.00 0.00 0.00 3.02
2825 2900 3.492656 GCTTCGCCATCATCACTAGGTAA 60.493 47.826 0.00 0.00 0.00 2.85
2872 2947 4.142227 GCTACTGCTGTGCTTAGTAACCTA 60.142 45.833 6.48 0.00 36.03 3.08
2882 2957 4.028825 GCTTAGTAACCTAAGGACCTGGA 58.971 47.826 0.00 0.00 46.87 3.86
2892 2967 1.348064 AGGACCTGGATTCGACACAA 58.652 50.000 0.00 0.00 0.00 3.33
2898 2973 2.611518 CTGGATTCGACACAACCTCTC 58.388 52.381 0.00 0.00 0.00 3.20
2946 3028 2.105821 TGCCTTGTATAATCCTTCCCCG 59.894 50.000 0.00 0.00 0.00 5.73
2963 3045 4.394712 GGGCCTCACCTGGTGTCG 62.395 72.222 25.15 16.99 39.10 4.35
2987 3069 2.028567 GCTTCTAGCACTTGGTCTGTCT 60.029 50.000 0.00 0.00 41.89 3.41
2988 3070 3.556004 GCTTCTAGCACTTGGTCTGTCTT 60.556 47.826 0.00 0.00 41.89 3.01
3045 3134 3.181471 CCTTACCTGATAGTGCAGAGGTG 60.181 52.174 10.20 0.00 39.25 4.00
3112 3201 1.302832 GTGGAAGGTGGTGCTGAGG 60.303 63.158 0.00 0.00 0.00 3.86
3181 3270 0.535335 GCTACGGGTGAACCATCTCA 59.465 55.000 1.16 0.00 40.22 3.27
3263 3357 5.011840 CACCATATGTCCACTGATCTCTGAT 59.988 44.000 1.24 0.00 0.00 2.90
3268 3362 4.860022 TGTCCACTGATCTCTGATACTCA 58.140 43.478 0.00 0.00 0.00 3.41
3282 3376 1.342074 TACTCAGCAGAGGCAACACT 58.658 50.000 11.18 0.00 46.44 3.55
3331 3427 0.899717 GGCTCCCTTCAACAATGGCA 60.900 55.000 0.00 0.00 0.00 4.92
3354 3450 2.004733 TCATGCTTCGTTGCAGATGAG 58.995 47.619 10.32 0.00 46.71 2.90
3363 3459 2.096496 CGTTGCAGATGAGGATGTTTCC 59.904 50.000 0.00 0.00 42.96 3.13
3364 3460 3.084039 GTTGCAGATGAGGATGTTTCCA 58.916 45.455 0.00 0.00 45.30 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.448119 CGGCCTCTGCATCTAGACGA 61.448 60.000 0.00 0.00 40.13 4.20
69 70 2.844362 CCCCGGCCTCTGCATCTA 60.844 66.667 0.00 0.00 40.13 1.98
125 127 4.766375 AGGTTTGTTAGGGTGACGATATG 58.234 43.478 0.00 0.00 0.00 1.78
139 141 5.014123 TGGTGGATAGAGATTGAGGTTTGTT 59.986 40.000 0.00 0.00 0.00 2.83
180 182 1.663445 CGTCGACCACAAGACAGTCTC 60.663 57.143 10.58 0.00 37.23 3.36
186 188 2.676839 TCTCTATCGTCGACCACAAGAC 59.323 50.000 10.58 0.00 0.00 3.01
210 212 6.553100 TGTCTTTTCATAACCCCTTTCAATGT 59.447 34.615 0.00 0.00 0.00 2.71
213 215 5.894393 TGTGTCTTTTCATAACCCCTTTCAA 59.106 36.000 0.00 0.00 0.00 2.69
225 227 5.264395 CCCCCTAAATCTGTGTCTTTTCAT 58.736 41.667 0.00 0.00 0.00 2.57
232 234 0.539986 TCGCCCCCTAAATCTGTGTC 59.460 55.000 0.00 0.00 0.00 3.67
235 237 2.654863 CAAATCGCCCCCTAAATCTGT 58.345 47.619 0.00 0.00 0.00 3.41
241 243 0.106918 ATTCGCAAATCGCCCCCTAA 60.107 50.000 0.00 0.00 37.30 2.69
251 253 3.974401 CACGTCTTGAAACATTCGCAAAT 59.026 39.130 0.00 0.00 0.00 2.32
360 362 3.467119 GACGAACGACGCGTGCAT 61.467 61.111 20.70 0.45 46.94 3.96
384 386 3.049674 CCCAATCGTGCGCTGTGT 61.050 61.111 9.73 0.00 0.00 3.72
388 390 2.185350 CTCTCCCAATCGTGCGCT 59.815 61.111 9.73 0.00 0.00 5.92
428 430 2.665185 GTCACCTTCGCACCGCTT 60.665 61.111 0.00 0.00 0.00 4.68
433 435 2.737376 GTCGGGTCACCTTCGCAC 60.737 66.667 0.00 0.00 33.28 5.34
438 440 1.374947 CACCATGTCGGGTCACCTT 59.625 57.895 0.00 0.00 39.79 3.50
448 450 2.042831 GTGCAGCTCCCACCATGTC 61.043 63.158 3.20 0.00 0.00 3.06
465 467 4.938226 GTGTATTTAAGAGGAGCTGCTTGT 59.062 41.667 9.91 2.79 0.00 3.16
467 469 5.165961 TGTGTATTTAAGAGGAGCTGCTT 57.834 39.130 9.91 3.72 0.00 3.91
471 473 7.168219 TCAACAATGTGTATTTAAGAGGAGCT 58.832 34.615 0.00 0.00 0.00 4.09
490 492 8.424918 ACAAAACCACCACAATTATATCAACAA 58.575 29.630 0.00 0.00 0.00 2.83
504 506 4.438148 AGTAAAATGCACAAAACCACCAC 58.562 39.130 0.00 0.00 0.00 4.16
652 654 9.286170 TCTACATGTAGTTCATAGTGGAGTATC 57.714 37.037 27.83 0.00 34.67 2.24
654 656 9.067986 CATCTACATGTAGTTCATAGTGGAGTA 57.932 37.037 27.83 7.96 34.67 2.59
697 699 9.624697 GAAAACAAATGTATGAATCTGCACTAA 57.375 29.630 0.00 0.00 0.00 2.24
698 700 9.013229 AGAAAACAAATGTATGAATCTGCACTA 57.987 29.630 0.00 0.00 0.00 2.74
701 703 9.791820 CATAGAAAACAAATGTATGAATCTGCA 57.208 29.630 0.00 0.00 0.00 4.41
761 764 9.473640 GTTCCTAAATCCGTTCCTAAGTATAAG 57.526 37.037 0.00 0.00 0.00 1.73
762 765 8.137437 CGTTCCTAAATCCGTTCCTAAGTATAA 58.863 37.037 0.00 0.00 0.00 0.98
763 766 7.255590 CCGTTCCTAAATCCGTTCCTAAGTATA 60.256 40.741 0.00 0.00 0.00 1.47
764 767 6.462067 CCGTTCCTAAATCCGTTCCTAAGTAT 60.462 42.308 0.00 0.00 0.00 2.12
765 768 5.163519 CCGTTCCTAAATCCGTTCCTAAGTA 60.164 44.000 0.00 0.00 0.00 2.24
766 769 4.382362 CCGTTCCTAAATCCGTTCCTAAGT 60.382 45.833 0.00 0.00 0.00 2.24
767 770 4.117685 CCGTTCCTAAATCCGTTCCTAAG 58.882 47.826 0.00 0.00 0.00 2.18
768 771 3.768757 TCCGTTCCTAAATCCGTTCCTAA 59.231 43.478 0.00 0.00 0.00 2.69
769 772 3.364549 TCCGTTCCTAAATCCGTTCCTA 58.635 45.455 0.00 0.00 0.00 2.94
770 773 2.181975 TCCGTTCCTAAATCCGTTCCT 58.818 47.619 0.00 0.00 0.00 3.36
771 774 2.678471 TCCGTTCCTAAATCCGTTCC 57.322 50.000 0.00 0.00 0.00 3.62
772 775 4.186159 TCAATCCGTTCCTAAATCCGTTC 58.814 43.478 0.00 0.00 0.00 3.95
773 776 4.210724 TCAATCCGTTCCTAAATCCGTT 57.789 40.909 0.00 0.00 0.00 4.44
774 777 3.899052 TCAATCCGTTCCTAAATCCGT 57.101 42.857 0.00 0.00 0.00 4.69
775 778 4.574828 ACATTCAATCCGTTCCTAAATCCG 59.425 41.667 0.00 0.00 0.00 4.18
776 779 5.357032 ACACATTCAATCCGTTCCTAAATCC 59.643 40.000 0.00 0.00 0.00 3.01
777 780 6.436843 ACACATTCAATCCGTTCCTAAATC 57.563 37.500 0.00 0.00 0.00 2.17
778 781 6.834168 AACACATTCAATCCGTTCCTAAAT 57.166 33.333 0.00 0.00 0.00 1.40
883 892 1.005630 CATAGCCCGCAGAGGTAGC 60.006 63.158 0.00 0.00 38.74 3.58
897 906 0.883833 GCCGAATTGATGGCCCATAG 59.116 55.000 0.00 0.00 45.73 2.23
1000 1009 4.815269 GCAGAGAAAGAAGAACTGCTCTA 58.185 43.478 0.00 0.00 46.66 2.43
1049 1085 3.309296 TGGATTCTGGACCAGGTATCTC 58.691 50.000 21.56 16.06 31.51 2.75
1081 1117 2.508526 GGCTTGCAGAGGAAGAAGAAA 58.491 47.619 2.32 0.00 0.00 2.52
1342 1390 3.111741 ACCTACCTACCTACCAACCAG 57.888 52.381 0.00 0.00 0.00 4.00
1343 1391 3.052642 CCTACCTACCTACCTACCAACCA 60.053 52.174 0.00 0.00 0.00 3.67
1360 1408 1.149964 GCGCGTTCATACACCCTACC 61.150 60.000 8.43 0.00 0.00 3.18
1361 1409 0.179119 AGCGCGTTCATACACCCTAC 60.179 55.000 8.43 0.00 0.00 3.18
1461 1509 1.742268 GATTTCTGCAGCCTTCTCACC 59.258 52.381 9.47 0.00 0.00 4.02
1505 1553 0.752009 CCTAGACTAGCAGGCCACGA 60.752 60.000 5.01 0.00 0.00 4.35
1680 1734 4.987285 ACTGCAATGCGTATCTATTCTCTG 59.013 41.667 0.00 0.00 0.00 3.35
1683 1737 6.090483 AGTACTGCAATGCGTATCTATTCT 57.910 37.500 11.59 3.01 0.00 2.40
1684 1738 6.346919 CCAAGTACTGCAATGCGTATCTATTC 60.347 42.308 11.59 1.22 0.00 1.75
1685 1739 5.466728 CCAAGTACTGCAATGCGTATCTATT 59.533 40.000 11.59 4.67 0.00 1.73
1686 1740 4.991056 CCAAGTACTGCAATGCGTATCTAT 59.009 41.667 11.59 0.05 0.00 1.98
1699 1753 3.694072 TGGAACATATTGCCAAGTACTGC 59.306 43.478 0.00 0.00 0.00 4.40
1702 1756 6.113411 AGTAGTGGAACATATTGCCAAGTAC 58.887 40.000 0.00 0.00 44.52 2.73
1851 1909 4.936891 ACAAGAACATGAAAACAAGAGGC 58.063 39.130 0.00 0.00 0.00 4.70
1947 2012 0.248621 GGCCCGCATCTTCAAATTCG 60.249 55.000 0.00 0.00 0.00 3.34
2029 2094 0.107312 ATCTCAGGCATGTCAGGTGC 60.107 55.000 0.00 0.00 41.78 5.01
2096 2161 1.548719 AGTACTGCACAGCGTAATCCA 59.451 47.619 0.00 0.00 0.00 3.41
2099 2164 1.405526 CCCAGTACTGCACAGCGTAAT 60.406 52.381 17.86 0.00 0.00 1.89
2175 2240 5.364157 ACCTATAACCAGTCATCACTTCCTC 59.636 44.000 0.00 0.00 0.00 3.71
2226 2291 8.632679 CATCCATAACCAGCTATAAATGTGTTT 58.367 33.333 0.00 0.00 0.00 2.83
2280 2345 1.471676 GGGCTCAATACAGTGTCTCCG 60.472 57.143 0.00 0.00 0.00 4.63
2282 2347 3.550437 ATGGGCTCAATACAGTGTCTC 57.450 47.619 0.00 0.00 0.00 3.36
2287 2352 4.557705 AGTACCTATGGGCTCAATACAGT 58.442 43.478 0.00 0.00 35.63 3.55
2288 2353 5.070446 TCAAGTACCTATGGGCTCAATACAG 59.930 44.000 0.00 0.00 35.63 2.74
2289 2354 4.966168 TCAAGTACCTATGGGCTCAATACA 59.034 41.667 0.00 0.00 35.63 2.29
2290 2355 5.546621 TCAAGTACCTATGGGCTCAATAC 57.453 43.478 0.00 0.00 35.63 1.89
2291 2356 6.328934 TGAATCAAGTACCTATGGGCTCAATA 59.671 38.462 0.00 0.00 35.63 1.90
2353 2428 9.810870 TGAATCCATCCATTGAATGACATATTA 57.189 29.630 6.76 0.00 0.00 0.98
2421 2496 1.681666 CCAGAAGCTGCCTCAAGGA 59.318 57.895 0.00 0.00 37.39 3.36
2435 2510 3.551259 GGAAGAAATCCGTGCCAGA 57.449 52.632 0.00 0.00 38.79 3.86
2486 2561 1.215647 GTACTGTGGCTCGTCCCAG 59.784 63.158 0.00 5.58 38.39 4.45
2492 2567 4.175599 CAGCAGTACTGTGGCTCG 57.824 61.111 23.44 6.71 41.86 5.03
2509 2584 9.346725 GACTGAAAATTCACAATATCCAGAAAC 57.653 33.333 0.00 0.00 32.90 2.78
2516 2591 9.160496 AGTGAGAGACTGAAAATTCACAATATC 57.840 33.333 5.38 0.00 37.87 1.63
2526 2601 4.041444 AGGAGCAAGTGAGAGACTGAAAAT 59.959 41.667 0.00 0.00 34.02 1.82
2533 2608 3.056250 TCATTCAGGAGCAAGTGAGAGAC 60.056 47.826 0.00 0.00 0.00 3.36
2554 2629 4.025145 CGTTACACAAAAGTCTTCAGGGTC 60.025 45.833 0.00 0.00 0.00 4.46
2577 2652 7.487829 TGCATCTTGAAAGTTACAAAAGAACAC 59.512 33.333 0.00 0.00 31.14 3.32
2608 2683 1.149133 AGGAGGGGCCAACAAATCCT 61.149 55.000 4.39 4.38 40.02 3.24
2630 2705 3.059597 AGCTTTCAACAAATGTCGACTCG 60.060 43.478 17.92 4.91 0.00 4.18
2678 2753 6.015688 AGGGGAAGAAAAACGAATAGGAAAAC 60.016 38.462 0.00 0.00 0.00 2.43
2715 2790 2.289565 GCCCAACTATCTACACCTTGC 58.710 52.381 0.00 0.00 0.00 4.01
2872 2947 1.348064 TGTGTCGAATCCAGGTCCTT 58.652 50.000 0.00 0.00 0.00 3.36
2882 2957 1.344438 TGCAGAGAGGTTGTGTCGAAT 59.656 47.619 0.00 0.00 0.00 3.34
2892 2967 1.816835 CACAATGCAATGCAGAGAGGT 59.183 47.619 14.98 4.24 43.65 3.85
2946 3028 4.394712 CGACACCAGGTGAGGCCC 62.395 72.222 27.39 8.34 36.96 5.80
2963 3045 1.552792 AGACCAAGTGCTAGAAGCTCC 59.447 52.381 0.00 0.00 42.97 4.70
2995 3077 6.171213 ACATTTCCAGGTTACTAAGCAGTAC 58.829 40.000 1.00 0.00 36.98 2.73
3045 3134 2.795329 ACACCATCCATTCCAAGTGAC 58.205 47.619 0.00 0.00 0.00 3.67
3146 3235 1.036707 TAGCTGTTGGTTTGTTGGCC 58.963 50.000 0.00 0.00 0.00 5.36
3181 3270 1.002888 CAGTGCAGTGGAAGGATCAGT 59.997 52.381 14.08 0.00 0.00 3.41
3241 3335 5.741962 ATCAGAGATCAGTGGACATATGG 57.258 43.478 7.80 0.00 0.00 2.74
3263 3357 1.001293 CAGTGTTGCCTCTGCTGAGTA 59.999 52.381 18.11 5.45 38.61 2.59
3268 3362 0.181114 TTCACAGTGTTGCCTCTGCT 59.819 50.000 0.00 0.00 35.98 4.24
3288 3382 4.669751 GCTATTGCTTGGGCTTGGAAGC 62.670 54.545 2.56 2.56 44.10 3.86
3299 3393 0.672342 GGGAGCCATGCTATTGCTTG 59.328 55.000 7.84 7.84 39.88 4.01
3331 3427 0.035317 TCTGCAACGAAGCATGACCT 59.965 50.000 0.00 0.00 44.68 3.85
3363 3459 1.286880 CGCTGTTTCCAAGCCCTTG 59.713 57.895 1.05 1.05 40.13 3.61
3364 3460 1.152756 ACGCTGTTTCCAAGCCCTT 60.153 52.632 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.