Multiple sequence alignment - TraesCS5A01G173500

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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 TraesCS5A01G173500 chr5A 100.000 2904 0 0 1 2904 366762688 366759785 0.000000e+00 5363
1 TraesCS5A01G173500 chr5D 88.986 2279 135 42 692 2904 277633356 277631128 0.000000e+00 2712
2 TraesCS5A01G173500 chr5D 95.222 293 11 2 252 544 277633877 277633588 7.330000e-126 460
3 TraesCS5A01G173500 chr5D 94.488 254 10 4 7 259 277634168 277633918 3.510000e-104 388
4 TraesCS5A01G173500 chr5B 93.793 1305 57 7 692 1982 315834787 315833493 0.000000e+00 1940
5 TraesCS5A01G173500 chr5B 83.442 918 84 28 2013 2904 315833106 315832231 0.000000e+00 791
6 TraesCS5A01G173500 chr5B 94.133 375 18 4 252 625 315835481 315835110 4.200000e-158 568
7 TraesCS5A01G173500 chr5B 93.462 260 12 5 1 259 315835781 315835526 5.870000e-102 381
8 TraesCS5A01G173500 chr5B 78.889 270 42 10 2643 2904 420009969 420009707 4.980000e-38 169
9 TraesCS5A01G173500 chr5B 95.349 86 4 0 609 694 315834936 315834851 1.400000e-28 137
10 TraesCS5A01G173500 chr6D 82.727 220 33 4 2687 2902 83058754 83058972 1.060000e-44 191
11 TraesCS5A01G173500 chr6B 85.083 181 26 1 2725 2904 229671957 229671777 1.780000e-42 183
12 TraesCS5A01G173500 chr6A 82.723 191 29 2 2713 2901 100094453 100094641 1.790000e-37 167
13 TraesCS5A01G173500 chr4B 84.667 150 20 2 2754 2903 2458147 2458001 2.330000e-31 147
14 TraesCS5A01G173500 chr4D 84.762 105 16 0 2800 2904 507667540 507667644 3.960000e-19 106


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 TraesCS5A01G173500 chr5A 366759785 366762688 2903 True 5363.000000 5363 100.000000 1 2904 1 chr5A.!!$R1 2903
1 TraesCS5A01G173500 chr5D 277631128 277634168 3040 True 1186.666667 2712 92.898667 7 2904 3 chr5D.!!$R1 2897
2 TraesCS5A01G173500 chr5B 315832231 315835781 3550 True 763.400000 1940 92.035800 1 2904 5 chr5B.!!$R2 2903

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
46 48 0.316204 AGCATTGTTTGGTCAGCAGC 59.684 50.0 0.0 0.0 0.00 5.25 F
731 1077 0.327259 ATGGCTGTGTGCATCACTCT 59.673 50.0 16.7 0.3 46.27 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1322 1673 0.036952 TGGCTCCTTGCTCTTCTTCG 60.037 55.0 0.0 0.0 42.39 3.79 R
2374 3116 0.179124 TGTTGCCTTTGTTTGACGCC 60.179 50.0 0.0 0.0 0.00 5.68 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
46 48 0.316204 AGCATTGTTTGGTCAGCAGC 59.684 50.000 0.00 0.00 0.00 5.25
88 90 5.163540 GGTGAATATGACTACGAGGAAGTGT 60.164 44.000 0.00 0.00 0.00 3.55
103 105 3.119849 GGAAGTGTTGGAATCATGTTCCG 60.120 47.826 17.01 0.00 41.43 4.30
118 120 3.764218 TGTTCCGTCTCTAGAAGAACCT 58.236 45.455 15.97 0.00 38.13 3.50
198 200 3.478540 GCTAGAGGCGGGAAACATT 57.521 52.632 0.00 0.00 0.00 2.71
263 316 2.028112 TCTTGGTCTTCACTGGATTCGG 60.028 50.000 0.00 0.00 0.00 4.30
299 352 3.932601 TCTCAATCCTGATCCTGGATCA 58.067 45.455 31.61 31.61 45.35 2.92
416 469 4.170256 TGCTTTCGTTCAAACAAAGAACC 58.830 39.130 15.62 5.38 41.72 3.62
443 496 2.521547 ATCCCCCAGCTTTCAAGAAG 57.478 50.000 0.00 0.00 0.00 2.85
445 498 1.780309 TCCCCCAGCTTTCAAGAAGAA 59.220 47.619 0.00 0.00 0.00 2.52
512 565 2.716017 GCTGTCGAGGACTGAGGGG 61.716 68.421 6.80 0.00 34.21 4.79
581 663 4.639334 TGCCTCTCTATTCTGCATCAATC 58.361 43.478 0.00 0.00 0.00 2.67
605 687 7.798801 TCGAAATCGAAGTAGCACAAAATTAA 58.201 30.769 2.51 0.00 46.30 1.40
649 921 6.915737 AGCAGCTAGCCATGAGAAACTCATA 61.916 44.000 12.13 0.00 46.11 2.15
731 1077 0.327259 ATGGCTGTGTGCATCACTCT 59.673 50.000 16.70 0.30 46.27 3.24
756 1102 0.469917 GGAGGCCGAGAATCATTCCA 59.530 55.000 0.00 0.00 33.17 3.53
882 1228 3.773860 AGATCACGAAGCTAGACAGTG 57.226 47.619 0.00 0.00 0.00 3.66
936 1282 8.974060 AGACCAACAAAGTATTCTCTTAAACA 57.026 30.769 0.00 0.00 0.00 2.83
1081 1432 3.801114 TGGATCACCTACTCAACATCG 57.199 47.619 0.00 0.00 37.04 3.84
1095 1446 1.456518 CATCGAGCCTCCTCTCCCA 60.457 63.158 0.00 0.00 35.90 4.37
1096 1447 1.456705 ATCGAGCCTCCTCTCCCAC 60.457 63.158 0.00 0.00 35.90 4.61
1097 1448 1.943730 ATCGAGCCTCCTCTCCCACT 61.944 60.000 0.00 0.00 35.90 4.00
1098 1449 2.124693 CGAGCCTCCTCTCCCACTC 61.125 68.421 0.00 0.00 35.90 3.51
1099 1450 1.760480 GAGCCTCCTCTCCCACTCC 60.760 68.421 0.00 0.00 35.16 3.85
1100 1451 2.766229 GCCTCCTCTCCCACTCCC 60.766 72.222 0.00 0.00 0.00 4.30
1101 1452 2.780693 CCTCCTCTCCCACTCCCA 59.219 66.667 0.00 0.00 0.00 4.37
1120 1471 3.289211 TCCCAGCCCCCTCTACCA 61.289 66.667 0.00 0.00 0.00 3.25
1140 1491 2.032681 ACCGGCAACCTCAAGCTC 59.967 61.111 0.00 0.00 0.00 4.09
1149 1500 1.523258 CCTCAAGCTCAGGGCATCG 60.523 63.158 0.00 0.00 44.79 3.84
1322 1673 2.737376 GTCGTCGACCAAGGCCAC 60.737 66.667 14.60 0.00 0.00 5.01
1476 1833 2.202892 GGCGTGGCCTGCTACTAC 60.203 66.667 18.09 0.00 46.69 2.73
1477 1834 2.722201 GGCGTGGCCTGCTACTACT 61.722 63.158 18.09 0.00 46.69 2.57
1558 1915 3.775654 GTCTGGAGTGGCCCGAGG 61.776 72.222 0.00 0.00 34.97 4.63
1559 1916 3.992641 TCTGGAGTGGCCCGAGGA 61.993 66.667 0.00 0.00 34.97 3.71
1593 1950 2.975799 GAGGGCGGTTGCAACGAA 60.976 61.111 22.67 0.00 45.35 3.85
1750 2110 6.480320 ACTTGGTCATGATTTCGATTACTAGC 59.520 38.462 0.00 0.00 0.00 3.42
1797 2160 3.274095 AGGGTTGCTCTCTTGATAAGC 57.726 47.619 0.00 0.00 36.56 3.09
1817 2180 1.002134 CTGTAGTTGGGGTGGCCAG 60.002 63.158 5.11 0.00 0.00 4.85
1818 2181 1.462432 TGTAGTTGGGGTGGCCAGA 60.462 57.895 5.11 0.00 0.00 3.86
1904 2277 8.044908 AGTATGTAACTTTTCACCATTATCCGT 58.955 33.333 0.00 0.00 33.35 4.69
1905 2278 7.696992 ATGTAACTTTTCACCATTATCCGTT 57.303 32.000 0.00 0.00 0.00 4.44
1982 2355 6.624526 GCAATCTTTTCAACGTTTCAACATTG 59.375 34.615 0.00 4.82 33.74 2.82
1983 2356 6.826893 ATCTTTTCAACGTTTCAACATTGG 57.173 33.333 0.00 0.00 33.32 3.16
1984 2357 5.105752 TCTTTTCAACGTTTCAACATTGGG 58.894 37.500 0.00 0.00 33.32 4.12
1985 2358 4.720649 TTTCAACGTTTCAACATTGGGA 57.279 36.364 0.00 0.00 33.32 4.37
1986 2359 4.720649 TTCAACGTTTCAACATTGGGAA 57.279 36.364 0.00 0.00 33.32 3.97
1987 2360 4.927978 TCAACGTTTCAACATTGGGAAT 57.072 36.364 0.00 0.00 33.32 3.01
1988 2361 5.269505 TCAACGTTTCAACATTGGGAATT 57.730 34.783 0.00 0.00 33.32 2.17
1992 2365 5.768317 ACGTTTCAACATTGGGAATTACAG 58.232 37.500 0.00 0.00 0.00 2.74
2000 2373 9.051679 TCAACATTGGGAATTACAGTATAATCG 57.948 33.333 0.00 0.00 0.00 3.34
2002 2375 8.378172 ACATTGGGAATTACAGTATAATCGTG 57.622 34.615 0.00 0.00 0.00 4.35
2023 2757 6.040054 TCGTGCAGTACTTATTATTCCTGCTA 59.960 38.462 10.37 0.00 44.20 3.49
2043 2777 4.023365 GCTATCAGATTTGACCTGCAATCC 60.023 45.833 0.00 0.00 35.83 3.01
2055 2789 2.548493 CCTGCAATCCTTTTTGTGTGGG 60.548 50.000 0.00 0.00 0.00 4.61
2099 2837 0.608308 GTACCTTTTGAGGCCGCCTT 60.608 55.000 14.70 0.00 31.76 4.35
2100 2838 0.608035 TACCTTTTGAGGCCGCCTTG 60.608 55.000 14.70 2.17 31.76 3.61
2101 2839 1.603455 CCTTTTGAGGCCGCCTTGA 60.603 57.895 14.70 2.16 31.76 3.02
2102 2840 1.178534 CCTTTTGAGGCCGCCTTGAA 61.179 55.000 14.70 8.79 31.76 2.69
2103 2841 0.673437 CTTTTGAGGCCGCCTTGAAA 59.327 50.000 14.70 15.58 31.76 2.69
2104 2842 1.273327 CTTTTGAGGCCGCCTTGAAAT 59.727 47.619 14.70 0.00 31.76 2.17
2105 2843 0.602562 TTTGAGGCCGCCTTGAAATG 59.397 50.000 14.70 0.00 31.76 2.32
2106 2844 1.250154 TTGAGGCCGCCTTGAAATGG 61.250 55.000 14.70 0.00 31.76 3.16
2107 2845 1.378514 GAGGCCGCCTTGAAATGGA 60.379 57.895 14.70 0.00 31.76 3.41
2108 2846 1.379044 AGGCCGCCTTGAAATGGAG 60.379 57.895 5.94 0.00 31.60 3.86
2109 2847 2.491621 GCCGCCTTGAAATGGAGC 59.508 61.111 0.00 0.00 31.60 4.70
2110 2848 3.068729 GCCGCCTTGAAATGGAGCC 62.069 63.158 0.00 0.00 31.60 4.70
2111 2849 1.379044 CCGCCTTGAAATGGAGCCT 60.379 57.895 0.00 0.00 31.60 4.58
2112 2850 0.967380 CCGCCTTGAAATGGAGCCTT 60.967 55.000 0.00 0.00 31.60 4.35
2131 2869 7.288810 AGCCTTGAAAGTTCACAAATCATTA 57.711 32.000 0.00 0.00 36.83 1.90
2178 2916 3.622612 CCACAAAGATCGATGCACACATA 59.377 43.478 0.54 0.00 36.35 2.29
2179 2917 4.260497 CCACAAAGATCGATGCACACATAG 60.260 45.833 0.54 0.00 36.35 2.23
2180 2918 3.873361 ACAAAGATCGATGCACACATAGG 59.127 43.478 0.54 0.00 36.35 2.57
2268 3010 1.824230 TGATTGTGGTATTTGCTGCCC 59.176 47.619 0.00 0.00 0.00 5.36
2286 3028 1.699634 CCCTTGACTTCCTGTCTTGGA 59.300 52.381 0.00 0.00 45.54 3.53
2293 3035 2.982488 ACTTCCTGTCTTGGAGTCCATT 59.018 45.455 14.00 0.00 37.43 3.16
2294 3036 3.395941 ACTTCCTGTCTTGGAGTCCATTT 59.604 43.478 14.00 0.00 37.43 2.32
2295 3037 4.141158 ACTTCCTGTCTTGGAGTCCATTTT 60.141 41.667 14.00 0.00 37.43 1.82
2320 3062 5.467035 TTTGTTGGAAAATGAGGATGACC 57.533 39.130 0.00 0.00 0.00 4.02
2331 3073 2.051334 AGGATGACCTCTCGACTCTG 57.949 55.000 0.00 0.00 44.13 3.35
2333 3075 2.506231 AGGATGACCTCTCGACTCTGTA 59.494 50.000 0.00 0.00 44.13 2.74
2334 3076 3.137544 AGGATGACCTCTCGACTCTGTAT 59.862 47.826 0.00 0.00 44.13 2.29
2335 3077 3.500680 GGATGACCTCTCGACTCTGTATC 59.499 52.174 0.00 0.00 0.00 2.24
2337 3079 3.536570 TGACCTCTCGACTCTGTATCAG 58.463 50.000 0.00 0.00 0.00 2.90
2338 3080 3.197983 TGACCTCTCGACTCTGTATCAGA 59.802 47.826 0.00 0.00 38.25 3.27
2349 3091 3.725490 TCTGTATCAGAGTGATGCATGC 58.275 45.455 11.82 11.82 45.80 4.06
2350 3092 3.133362 TCTGTATCAGAGTGATGCATGCA 59.867 43.478 25.04 25.04 45.80 3.96
2351 3093 3.875134 CTGTATCAGAGTGATGCATGCAA 59.125 43.478 26.68 6.15 45.80 4.08
2374 3116 5.560724 ACAATAGTAAATCATCCCCATCCG 58.439 41.667 0.00 0.00 0.00 4.18
2376 3118 1.073923 AGTAAATCATCCCCATCCGGC 59.926 52.381 0.00 0.00 0.00 6.13
2441 3197 1.067846 GTGTGTGTGTGATCCGCTAGA 60.068 52.381 0.00 0.00 0.00 2.43
2470 3226 2.222027 AGGTTGTTTTCCTCTGCTTCG 58.778 47.619 0.00 0.00 0.00 3.79
2505 3261 4.886247 AGCTAGCTACTCTGTAGTTTCG 57.114 45.455 17.69 0.00 37.15 3.46
2511 3267 4.022242 AGCTACTCTGTAGTTTCGCAAAGA 60.022 41.667 6.60 0.00 37.15 2.52
2522 3278 5.587289 AGTTTCGCAAAGACATTTTAAGCA 58.413 33.333 0.00 0.00 0.00 3.91
2576 3332 5.785599 CGCTTATATTTTCTAAGATGCGTGC 59.214 40.000 0.00 0.00 35.82 5.34
2579 3335 5.984233 ATATTTTCTAAGATGCGTGCGAA 57.016 34.783 0.00 0.00 0.00 4.70
2633 3389 3.751698 ACCTTTTACGCATTTCAGAGTCC 59.248 43.478 0.00 0.00 0.00 3.85
2637 3393 5.957842 TTTACGCATTTCAGAGTCCAATT 57.042 34.783 0.00 0.00 0.00 2.32
2679 3447 3.190079 ACACGTGCATGATACACATCTC 58.810 45.455 17.22 0.00 37.93 2.75
2687 3455 5.241285 TGCATGATACACATCTCTCTCTCTC 59.759 44.000 0.00 0.00 37.07 3.20
2688 3456 5.474532 GCATGATACACATCTCTCTCTCTCT 59.525 44.000 0.00 0.00 37.07 3.10
2689 3457 6.348786 GCATGATACACATCTCTCTCTCTCTC 60.349 46.154 0.00 0.00 37.07 3.20
2690 3458 6.499106 TGATACACATCTCTCTCTCTCTCT 57.501 41.667 0.00 0.00 31.93 3.10
2691 3459 6.524734 TGATACACATCTCTCTCTCTCTCTC 58.475 44.000 0.00 0.00 31.93 3.20
2692 3460 6.327365 TGATACACATCTCTCTCTCTCTCTCT 59.673 42.308 0.00 0.00 31.93 3.10
2772 3540 9.320352 TCTTTTCCATAATTTGCATGATTCATG 57.680 29.630 20.14 20.14 43.91 3.07
2835 3604 4.890158 TTGAACTCCTAGCATCAAGACA 57.110 40.909 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.036098 CCATGTCCCCTGCAGCAA 59.964 61.111 8.66 0.00 0.00 3.91
17 18 0.837260 AAACAATGCTGGGGCCATGT 60.837 50.000 4.39 0.00 37.69 3.21
46 48 3.745975 TCACCAAACGATGCTTTGTAGAG 59.254 43.478 0.00 0.00 30.33 2.43
88 90 3.981071 AGAGACGGAACATGATTCCAA 57.019 42.857 20.14 0.00 38.49 3.53
103 105 3.065648 CCACGCTAGGTTCTTCTAGAGAC 59.934 52.174 9.05 0.00 38.76 3.36
118 120 5.577945 GTGCTAGTAATTGTTTACCACGCTA 59.422 40.000 0.00 0.00 38.81 4.26
220 222 4.460263 AGGTGCACAAATCTGAACAGTAA 58.540 39.130 20.43 0.00 0.00 2.24
221 223 4.065088 GAGGTGCACAAATCTGAACAGTA 58.935 43.478 20.43 0.00 0.00 2.74
263 316 5.412904 AGGATTGAGAACGGAGAAATTTCAC 59.587 40.000 19.99 13.54 0.00 3.18
299 352 5.698741 TCTCATATTCACCATGTCCAACT 57.301 39.130 0.00 0.00 0.00 3.16
458 511 2.922955 TGGTCATACAAAATCAGGGGGA 59.077 45.455 0.00 0.00 0.00 4.81
512 565 3.261897 TCTTCTGTCATCTTTCCCACTCC 59.738 47.826 0.00 0.00 0.00 3.85
562 644 7.410620 CGATTTCGATTGATGCAGAATAGAGAG 60.411 40.741 0.00 0.00 43.02 3.20
581 663 8.601243 ATTAATTTTGTGCTACTTCGATTTCG 57.399 30.769 0.00 0.00 41.45 3.46
605 687 9.927668 AGCTGCTACAAATGTTTAATTGTTTAT 57.072 25.926 0.00 0.00 40.14 1.40
626 898 1.939255 GAGTTTCTCATGGCTAGCTGC 59.061 52.381 15.72 0.00 41.94 5.25
649 921 1.981256 AAACTGCCCGTTCATGACTT 58.019 45.000 0.00 0.00 33.90 3.01
707 1045 2.512705 TGATGCACACAGCCATACAAA 58.487 42.857 0.00 0.00 44.83 2.83
737 1083 0.469917 TGGAATGATTCTCGGCCTCC 59.530 55.000 0.00 0.00 0.00 4.30
789 1135 9.170890 TCTTTTGTCCTCTGGAATATATATGGT 57.829 33.333 0.00 0.00 31.38 3.55
882 1228 8.655651 TTTTCATCAAACATTTTCCCACTTAC 57.344 30.769 0.00 0.00 0.00 2.34
976 1322 1.611519 AGCTATACGACTCTCTGGGC 58.388 55.000 0.00 0.00 0.00 5.36
1081 1432 1.760480 GGAGTGGGAGAGGAGGCTC 60.760 68.421 5.78 5.78 0.00 4.70
1099 1450 3.332393 TAGAGGGGGCTGGGAGTGG 62.332 68.421 0.00 0.00 0.00 4.00
1100 1451 2.066999 GTAGAGGGGGCTGGGAGTG 61.067 68.421 0.00 0.00 0.00 3.51
1101 1452 2.369001 GTAGAGGGGGCTGGGAGT 59.631 66.667 0.00 0.00 0.00 3.85
1120 1471 2.113139 CTTGAGGTTGCCGGTGGT 59.887 61.111 1.90 0.00 0.00 4.16
1140 1491 4.899239 GCCTCCGTCGATGCCCTG 62.899 72.222 0.00 0.00 0.00 4.45
1322 1673 0.036952 TGGCTCCTTGCTCTTCTTCG 60.037 55.000 0.00 0.00 42.39 3.79
1426 1777 3.631046 GGGCGATGGCTCCCCTAG 61.631 72.222 0.00 0.00 39.81 3.02
1469 1826 0.579156 CGACGGGTCGTAGTAGTAGC 59.421 60.000 12.77 0.00 46.99 3.58
1495 1852 3.000819 TTCGGCAGGGATCACCGT 61.001 61.111 13.25 0.00 46.92 4.83
1558 1915 1.755008 CCTCCTCCACTCCGTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
1559 1916 2.218115 CTCCTCCTCCACTCCGTCCT 62.218 65.000 0.00 0.00 0.00 3.85
1566 1923 4.787280 CCGCCCTCCTCCTCCACT 62.787 72.222 0.00 0.00 0.00 4.00
1797 2160 1.303317 GGCCACCCCAACTACAGTG 60.303 63.158 0.00 0.00 0.00 3.66
1817 2180 4.507710 TCAGTGACATCCATAAGCACTTC 58.492 43.478 0.00 0.00 37.69 3.01
1818 2181 4.019860 ACTCAGTGACATCCATAAGCACTT 60.020 41.667 0.00 0.00 37.69 3.16
1894 2267 6.738114 AGCATAACAAATCAACGGATAATGG 58.262 36.000 0.00 0.00 32.09 3.16
1900 2273 4.260579 CGCATAGCATAACAAATCAACGGA 60.261 41.667 0.00 0.00 0.00 4.69
1901 2274 3.968096 CGCATAGCATAACAAATCAACGG 59.032 43.478 0.00 0.00 0.00 4.44
1904 2277 6.918892 ACTACGCATAGCATAACAAATCAA 57.081 33.333 0.00 0.00 30.75 2.57
1905 2278 6.714492 CAACTACGCATAGCATAACAAATCA 58.286 36.000 0.00 0.00 30.75 2.57
1982 2355 5.989777 ACTGCACGATTATACTGTAATTCCC 59.010 40.000 0.00 0.00 0.00 3.97
1983 2356 7.866393 AGTACTGCACGATTATACTGTAATTCC 59.134 37.037 0.00 0.00 0.00 3.01
1984 2357 8.798748 AGTACTGCACGATTATACTGTAATTC 57.201 34.615 0.00 0.00 0.00 2.17
2015 2749 4.774124 CAGGTCAAATCTGATAGCAGGAA 58.226 43.478 8.37 0.00 42.53 3.36
2023 2757 4.246712 AGGATTGCAGGTCAAATCTGAT 57.753 40.909 3.94 0.00 38.34 2.90
2033 2767 2.102925 CCACACAAAAAGGATTGCAGGT 59.897 45.455 0.00 0.00 33.52 4.00
2043 2777 0.821711 TCCGAGGCCCACACAAAAAG 60.822 55.000 0.00 0.00 0.00 2.27
2055 2789 1.880340 CGCAGAATGTCTCCGAGGC 60.880 63.158 0.00 0.00 39.31 4.70
2099 2837 4.037923 GTGAACTTTCAAGGCTCCATTTCA 59.962 41.667 0.00 0.00 39.21 2.69
2100 2838 4.037923 TGTGAACTTTCAAGGCTCCATTTC 59.962 41.667 0.00 0.00 39.21 2.17
2101 2839 3.960102 TGTGAACTTTCAAGGCTCCATTT 59.040 39.130 0.00 0.00 39.21 2.32
2102 2840 3.565307 TGTGAACTTTCAAGGCTCCATT 58.435 40.909 0.00 0.00 39.21 3.16
2103 2841 3.228188 TGTGAACTTTCAAGGCTCCAT 57.772 42.857 0.00 0.00 39.21 3.41
2104 2842 2.727123 TGTGAACTTTCAAGGCTCCA 57.273 45.000 0.00 0.00 39.21 3.86
2105 2843 4.037923 TGATTTGTGAACTTTCAAGGCTCC 59.962 41.667 0.00 0.00 39.21 4.70
2106 2844 5.186996 TGATTTGTGAACTTTCAAGGCTC 57.813 39.130 0.00 0.00 39.21 4.70
2107 2845 5.796424 ATGATTTGTGAACTTTCAAGGCT 57.204 34.783 0.00 0.00 39.21 4.58
2108 2846 7.327032 GTCTAATGATTTGTGAACTTTCAAGGC 59.673 37.037 0.00 0.00 39.21 4.35
2109 2847 8.571336 AGTCTAATGATTTGTGAACTTTCAAGG 58.429 33.333 0.00 0.00 39.21 3.61
2110 2848 9.390795 CAGTCTAATGATTTGTGAACTTTCAAG 57.609 33.333 0.00 0.00 39.21 3.02
2111 2849 8.902806 ACAGTCTAATGATTTGTGAACTTTCAA 58.097 29.630 0.00 0.00 39.21 2.69
2112 2850 8.450578 ACAGTCTAATGATTTGTGAACTTTCA 57.549 30.769 0.00 0.00 34.20 2.69
2131 2869 1.924731 TCGACAGGGAATGACAGTCT 58.075 50.000 2.53 0.00 0.00 3.24
2234 2976 1.198408 ACAATCATGTTGTGCTCGCTG 59.802 47.619 11.32 0.00 35.91 5.18
2237 2979 1.536766 ACCACAATCATGTTGTGCTCG 59.463 47.619 24.07 17.26 46.11 5.03
2268 3010 7.262944 ATGGACTCCAAGACAGGAAGTCAAG 62.263 48.000 0.66 0.00 41.98 3.02
2297 3039 5.602145 AGGTCATCCTCATTTTCCAACAAAA 59.398 36.000 0.00 0.00 40.58 2.44
2298 3040 5.147032 AGGTCATCCTCATTTTCCAACAAA 58.853 37.500 0.00 0.00 40.58 2.83
2300 3042 4.387026 AGGTCATCCTCATTTTCCAACA 57.613 40.909 0.00 0.00 40.58 3.33
2312 3054 8.862081 CTGATACAGAGTCGAGAGGTCATCCT 62.862 50.000 0.00 0.00 39.30 3.24
2313 3055 1.757682 ACAGAGTCGAGAGGTCATCC 58.242 55.000 0.00 0.00 0.00 3.51
2314 3056 4.130857 TGATACAGAGTCGAGAGGTCATC 58.869 47.826 0.00 0.00 0.00 2.92
2315 3057 4.133820 CTGATACAGAGTCGAGAGGTCAT 58.866 47.826 0.00 0.00 32.44 3.06
2316 3058 3.197983 TCTGATACAGAGTCGAGAGGTCA 59.802 47.826 0.00 0.00 35.39 4.02
2317 3059 3.799366 TCTGATACAGAGTCGAGAGGTC 58.201 50.000 0.00 0.00 35.39 3.85
2318 3060 3.916359 TCTGATACAGAGTCGAGAGGT 57.084 47.619 0.00 0.00 35.39 3.85
2328 3070 3.133362 TGCATGCATCACTCTGATACAGA 59.867 43.478 18.46 0.00 34.00 3.41
2329 3071 3.463944 TGCATGCATCACTCTGATACAG 58.536 45.455 18.46 0.00 34.00 2.74
2330 3072 3.547054 TGCATGCATCACTCTGATACA 57.453 42.857 18.46 0.00 34.28 2.29
2331 3073 3.624410 TGTTGCATGCATCACTCTGATAC 59.376 43.478 24.14 14.61 34.28 2.24
2333 3075 2.718563 TGTTGCATGCATCACTCTGAT 58.281 42.857 24.14 0.00 37.65 2.90
2334 3076 2.188062 TGTTGCATGCATCACTCTGA 57.812 45.000 24.14 3.84 0.00 3.27
2335 3077 3.503827 ATTGTTGCATGCATCACTCTG 57.496 42.857 26.94 0.00 0.00 3.35
2337 3079 4.627611 ACTATTGTTGCATGCATCACTC 57.372 40.909 26.94 13.63 0.00 3.51
2338 3080 6.513806 TTTACTATTGTTGCATGCATCACT 57.486 33.333 26.94 23.71 0.00 3.41
2340 3082 7.098074 TGATTTACTATTGTTGCATGCATCA 57.902 32.000 24.14 24.14 0.00 3.07
2342 3084 7.149973 GGATGATTTACTATTGTTGCATGCAT 58.850 34.615 23.37 9.20 0.00 3.96
2343 3085 6.461370 GGGATGATTTACTATTGTTGCATGCA 60.461 38.462 18.46 18.46 0.00 3.96
2344 3086 5.922544 GGGATGATTTACTATTGTTGCATGC 59.077 40.000 11.82 11.82 0.00 4.06
2345 3087 6.040729 TGGGGATGATTTACTATTGTTGCATG 59.959 38.462 0.00 0.00 0.00 4.06
2347 3089 5.514169 TGGGGATGATTTACTATTGTTGCA 58.486 37.500 0.00 0.00 0.00 4.08
2348 3090 6.294731 GGATGGGGATGATTTACTATTGTTGC 60.295 42.308 0.00 0.00 0.00 4.17
2349 3091 6.072508 CGGATGGGGATGATTTACTATTGTTG 60.073 42.308 0.00 0.00 0.00 3.33
2350 3092 6.003950 CGGATGGGGATGATTTACTATTGTT 58.996 40.000 0.00 0.00 0.00 2.83
2351 3093 5.514834 CCGGATGGGGATGATTTACTATTGT 60.515 44.000 0.00 0.00 0.00 2.71
2374 3116 0.179124 TGTTGCCTTTGTTTGACGCC 60.179 50.000 0.00 0.00 0.00 5.68
2376 3118 1.587946 GCTTGTTGCCTTTGTTTGACG 59.412 47.619 0.00 0.00 35.15 4.35
2441 3197 3.826729 GAGGAAAACAACCTAACCTGCAT 59.173 43.478 0.00 0.00 37.93 3.96
2470 3226 2.969262 AGCTAGCTTCCCAGGATTAGAC 59.031 50.000 12.68 0.00 0.00 2.59
2505 3261 6.755190 GCATTACTGCTTAAAATGTCTTTGC 58.245 36.000 0.00 0.00 45.32 3.68
2538 3294 9.632807 GAAAATATAAGCGATGTGAGATCTAGT 57.367 33.333 0.00 0.00 0.00 2.57
2539 3295 9.853555 AGAAAATATAAGCGATGTGAGATCTAG 57.146 33.333 0.00 0.00 0.00 2.43
2566 3322 1.290203 CCATAGTTCGCACGCATCTT 58.710 50.000 0.00 0.00 0.00 2.40
2576 3332 1.410004 TCTAGGTGGGCCATAGTTCG 58.590 55.000 10.70 0.00 37.19 3.95
2579 3335 2.496679 ACATCTAGGTGGGCCATAGT 57.503 50.000 10.70 0.00 37.19 2.12
2648 3416 4.630894 TCATGCACGTGTTCTTTTTCTT 57.369 36.364 18.38 0.00 0.00 2.52
2662 3430 5.009911 AGAGAGAGAGATGTGTATCATGCAC 59.990 44.000 0.00 0.00 36.83 4.57
2679 3447 5.939883 TGAGTGAGAAAAGAGAGAGAGAGAG 59.060 44.000 0.00 0.00 0.00 3.20
2687 3455 4.375272 TGTGCTTGAGTGAGAAAAGAGAG 58.625 43.478 0.00 0.00 0.00 3.20
2688 3456 4.406648 TGTGCTTGAGTGAGAAAAGAGA 57.593 40.909 0.00 0.00 0.00 3.10
2689 3457 5.931146 AGTATGTGCTTGAGTGAGAAAAGAG 59.069 40.000 0.00 0.00 0.00 2.85
2690 3458 5.858381 AGTATGTGCTTGAGTGAGAAAAGA 58.142 37.500 0.00 0.00 0.00 2.52
2691 3459 5.931146 AGAGTATGTGCTTGAGTGAGAAAAG 59.069 40.000 0.00 0.00 0.00 2.27
2692 3460 5.858381 AGAGTATGTGCTTGAGTGAGAAAA 58.142 37.500 0.00 0.00 0.00 2.29
2824 3593 8.579006 TGATTTTGTTCTAAATGTCTTGATGCT 58.421 29.630 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.