Multiple sequence alignment - TraesCS7A01G394700

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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 TraesCS7A01G394700 chr7A 100.000 2603 0 0 1 2603 573070674 573068072 0.000000e+00 4807.0
1 TraesCS7A01G394700 chr7A 85.775 1181 99 35 691 1856 572876118 572874992 0.000000e+00 1186.0
2 TraesCS7A01G394700 chr7A 88.649 370 34 6 2237 2603 573029559 573029195 6.610000e-121 444.0
3 TraesCS7A01G394700 chr7A 80.606 165 14 12 15 162 573039188 573039025 7.610000e-21 111.0
4 TraesCS7A01G394700 chr7B 89.479 1055 71 17 816 1863 533373137 533372116 0.000000e+00 1297.0
5 TraesCS7A01G394700 chr7B 85.972 1162 106 33 682 1827 533309735 533308615 0.000000e+00 1190.0
6 TraesCS7A01G394700 chr7B 88.420 924 71 21 884 1803 533552703 533551812 0.000000e+00 1081.0
7 TraesCS7A01G394700 chr7B 84.431 668 42 22 11 658 533555473 533554848 3.710000e-168 601.0
8 TraesCS7A01G394700 chr7B 77.904 353 44 14 265 616 533324740 533324421 3.420000e-44 189.0
9 TraesCS7A01G394700 chr7B 84.324 185 25 4 678 860 533553266 533553084 7.400000e-41 178.0
10 TraesCS7A01G394700 chr7B 89.362 47 4 1 714 760 533373256 533373211 1.010000e-04 58.4
11 TraesCS7A01G394700 chr7D 87.697 1081 94 17 758 1831 505329779 505328731 0.000000e+00 1223.0
12 TraesCS7A01G394700 chr7D 86.384 1131 101 34 691 1803 505143729 505142634 0.000000e+00 1186.0
13 TraesCS7A01G394700 chr7D 87.765 989 76 24 723 1685 505590033 505589064 0.000000e+00 1114.0
14 TraesCS7A01G394700 chr7D 85.201 696 73 17 1929 2603 505328363 505327677 0.000000e+00 688.0
15 TraesCS7A01G394700 chr7D 83.010 671 48 18 11 654 505590692 505590061 4.900000e-152 547.0
16 TraesCS7A01G394700 chr7D 83.261 460 46 13 1932 2372 505588806 505588359 6.750000e-106 394.0
17 TraesCS7A01G394700 chr7D 76.812 621 72 42 11 610 505353732 505353163 1.520000e-72 283.0
18 TraesCS7A01G394700 chr7D 76.490 621 74 42 11 610 505145862 505145293 3.300000e-69 272.0
19 TraesCS7A01G394700 chr7D 79.179 341 45 14 691 1018 505351743 505351416 2.030000e-51 213.0
20 TraesCS7A01G394700 chr7D 88.344 163 15 3 1704 1863 505588967 505588806 2.640000e-45 193.0
21 TraesCS7A01G394700 chr7D 82.778 180 17 9 13 178 505333621 505333442 5.800000e-32 148.0
22 TraesCS7A01G394700 chr2A 97.101 69 1 1 1856 1923 62534323 62534391 5.890000e-22 115.0
23 TraesCS7A01G394700 chr5A 94.118 68 3 1 1857 1923 588850143 588850210 4.580000e-18 102.0


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 TraesCS7A01G394700 chr7A 573068072 573070674 2602 True 4807.000000 4807 100.000000 1 2603 1 chr7A.!!$R4 2602
1 TraesCS7A01G394700 chr7A 572874992 572876118 1126 True 1186.000000 1186 85.775000 691 1856 1 chr7A.!!$R1 1165
2 TraesCS7A01G394700 chr7B 533308615 533309735 1120 True 1190.000000 1190 85.972000 682 1827 1 chr7B.!!$R1 1145
3 TraesCS7A01G394700 chr7B 533372116 533373256 1140 True 677.700000 1297 89.420500 714 1863 2 chr7B.!!$R3 1149
4 TraesCS7A01G394700 chr7B 533551812 533555473 3661 True 620.000000 1081 85.725000 11 1803 3 chr7B.!!$R4 1792
5 TraesCS7A01G394700 chr7D 505142634 505145862 3228 True 729.000000 1186 81.437000 11 1803 2 chr7D.!!$R1 1792
6 TraesCS7A01G394700 chr7D 505327677 505333621 5944 True 686.333333 1223 85.225333 13 2603 3 chr7D.!!$R2 2590
7 TraesCS7A01G394700 chr7D 505588359 505590692 2333 True 562.000000 1114 85.595000 11 2372 4 chr7D.!!$R4 2361
8 TraesCS7A01G394700 chr7D 505351416 505353732 2316 True 248.000000 283 77.995500 11 1018 2 chr7D.!!$R3 1007

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
930 6862 0.179145 GGCGCGTCGTGGCTATATAT 60.179 55.0 23.46 0.0 35.7 0.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 8558 0.577269 CGCATAGGAAAGTACGCTGC 59.423 55.0 0.0 0.0 0.0 5.25 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
259 302 7.902920 ATATACGTAGGAGTACCCTCAAAAA 57.097 36.000 0.08 0.00 43.31 1.94
492 3394 3.195661 GAGGTGCTATTTTACAGGACGG 58.804 50.000 0.00 0.00 35.39 4.79
495 3397 2.093341 GTGCTATTTTACAGGACGGGGA 60.093 50.000 0.00 0.00 0.00 4.81
532 3435 2.064581 GGGGAGAGGCTAGGCGAAA 61.065 63.158 11.10 0.00 0.00 3.46
533 3436 1.623542 GGGGAGAGGCTAGGCGAAAA 61.624 60.000 11.10 0.00 0.00 2.29
588 3514 0.668535 GGTTCACCAGGTTGACTTGC 59.331 55.000 0.00 0.00 35.64 4.01
592 3518 3.719268 TCACCAGGTTGACTTGCATAT 57.281 42.857 0.00 0.00 0.00 1.78
672 4872 1.278413 ACAGCTGCATGTCATGAGTCT 59.722 47.619 17.24 6.22 0.00 3.24
773 6316 7.639945 ACAAGAAATAAACAAAGGAGTTCTCG 58.360 34.615 0.00 0.00 0.00 4.04
803 6348 5.986135 ACGCCATGAGAAACTGATAATCTAC 59.014 40.000 0.00 0.00 0.00 2.59
814 6359 9.871238 GAAACTGATAATCTACAAGGAGTAACA 57.129 33.333 0.00 0.00 30.92 2.41
844 6393 6.015519 TCACAATAACAGAAAACCAAGGGATG 60.016 38.462 0.00 0.00 0.00 3.51
884 6443 1.339151 ACTCGTTTCCTGATTCAGCCC 60.339 52.381 8.23 0.00 0.00 5.19
930 6862 0.179145 GGCGCGTCGTGGCTATATAT 60.179 55.000 23.46 0.00 35.70 0.86
931 6863 1.064505 GGCGCGTCGTGGCTATATATA 59.935 52.381 23.46 0.00 35.70 0.86
939 6871 6.200100 CGTCGTGGCTATATATACATCTTCC 58.800 44.000 0.00 0.00 0.00 3.46
945 6877 7.345914 GTGGCTATATATACATCTTCCTTCCCT 59.654 40.741 0.00 0.00 0.00 4.20
1182 7120 4.048470 GGCGGCCCCTTCTTCCTT 62.048 66.667 8.12 0.00 0.00 3.36
1516 7454 1.287425 CTCTGGTAATCCGGCGAAAC 58.713 55.000 9.30 0.00 39.81 2.78
1529 7467 1.228657 GCGAAACTCGGCAAGAAGGT 61.229 55.000 0.00 0.00 40.84 3.50
1614 7552 1.945819 GCGGAGTGAGGAAATGCTCAA 60.946 52.381 6.18 0.00 0.00 3.02
1622 7565 5.009410 AGTGAGGAAATGCTCAAAAGAACAG 59.991 40.000 6.18 0.00 0.00 3.16
1627 7570 1.441016 GCTCAAAAGAACAGCGCCG 60.441 57.895 2.29 0.00 0.00 6.46
1661 7604 8.034804 CCGAGTGATAAAAATGGAAGGAAATTT 58.965 33.333 0.00 0.00 0.00 1.82
1725 7758 8.506168 TGATATTAACCATTCTTGGAACAGTC 57.494 34.615 0.00 0.00 46.92 3.51
1781 7817 7.376615 AGTAGTATATAAGAATGTCGGTTGGC 58.623 38.462 0.00 0.00 0.00 4.52
1806 7848 9.097257 GCTAATTTGCCATTGTACATGTATTTT 57.903 29.630 9.18 0.00 0.00 1.82
1871 8252 8.726988 TGTTCATACTTACAACTGAAAATAGGC 58.273 33.333 0.00 0.00 30.06 3.93
1872 8253 8.947115 GTTCATACTTACAACTGAAAATAGGCT 58.053 33.333 0.00 0.00 30.06 4.58
1878 8259 8.244113 ACTTACAACTGAAAATAGGCTATTTGC 58.756 33.333 28.10 26.57 38.32 3.68
1879 8260 6.588719 ACAACTGAAAATAGGCTATTTGCA 57.411 33.333 29.96 29.96 40.51 4.08
1880 8261 6.389906 ACAACTGAAAATAGGCTATTTGCAC 58.610 36.000 28.95 22.42 38.47 4.57
1881 8262 6.015519 ACAACTGAAAATAGGCTATTTGCACA 60.016 34.615 28.95 24.72 38.47 4.57
1882 8263 6.780457 ACTGAAAATAGGCTATTTGCACAT 57.220 33.333 28.95 19.92 38.47 3.21
1883 8264 7.174107 ACTGAAAATAGGCTATTTGCACATT 57.826 32.000 28.95 20.11 38.47 2.71
1884 8265 7.037438 ACTGAAAATAGGCTATTTGCACATTG 58.963 34.615 28.95 22.62 38.47 2.82
1885 8266 6.934056 TGAAAATAGGCTATTTGCACATTGT 58.066 32.000 28.95 14.33 38.47 2.71
1886 8267 7.035004 TGAAAATAGGCTATTTGCACATTGTC 58.965 34.615 28.95 20.57 38.47 3.18
1887 8268 6.780457 AAATAGGCTATTTGCACATTGTCT 57.220 33.333 27.14 6.64 45.15 3.41
1888 8269 5.762825 ATAGGCTATTTGCACATTGTCTG 57.237 39.130 10.98 0.00 45.15 3.51
1889 8270 3.689347 AGGCTATTTGCACATTGTCTGA 58.311 40.909 0.53 0.00 45.15 3.27
1890 8271 4.081406 AGGCTATTTGCACATTGTCTGAA 58.919 39.130 0.53 0.00 45.15 3.02
1891 8272 4.523943 AGGCTATTTGCACATTGTCTGAAA 59.476 37.500 0.53 0.00 45.15 2.69
1892 8273 5.186409 AGGCTATTTGCACATTGTCTGAAAT 59.814 36.000 0.53 0.00 45.15 2.17
1893 8274 6.377996 AGGCTATTTGCACATTGTCTGAAATA 59.622 34.615 0.53 0.00 45.15 1.40
1894 8275 7.069085 AGGCTATTTGCACATTGTCTGAAATAT 59.931 33.333 0.53 0.00 45.15 1.28
1895 8276 7.380602 GGCTATTTGCACATTGTCTGAAATATC 59.619 37.037 0.00 0.00 45.15 1.63
1896 8277 8.133627 GCTATTTGCACATTGTCTGAAATATCT 58.866 33.333 0.00 0.00 42.31 1.98
1901 8282 9.844790 TTGCACATTGTCTGAAATATCTTTAAG 57.155 29.630 0.00 0.00 0.00 1.85
1902 8283 8.461222 TGCACATTGTCTGAAATATCTTTAAGG 58.539 33.333 0.00 0.00 0.00 2.69
1903 8284 7.433425 GCACATTGTCTGAAATATCTTTAAGGC 59.567 37.037 0.00 0.00 29.29 4.35
1904 8285 7.917505 CACATTGTCTGAAATATCTTTAAGGCC 59.082 37.037 0.00 0.00 27.62 5.19
1905 8286 7.836183 ACATTGTCTGAAATATCTTTAAGGCCT 59.164 33.333 0.00 0.00 27.62 5.19
1906 8287 8.689972 CATTGTCTGAAATATCTTTAAGGCCTT 58.310 33.333 24.18 24.18 27.62 4.35
1907 8288 9.920946 ATTGTCTGAAATATCTTTAAGGCCTTA 57.079 29.630 21.68 21.68 27.62 2.69
1908 8289 9.920946 TTGTCTGAAATATCTTTAAGGCCTTAT 57.079 29.630 25.70 14.42 27.62 1.73
1920 8301 9.832445 TCTTTAAGGCCTTATAATAGTGAACAG 57.168 33.333 25.70 5.31 0.00 3.16
1921 8302 9.832445 CTTTAAGGCCTTATAATAGTGAACAGA 57.168 33.333 25.70 2.85 0.00 3.41
1922 8303 9.832445 TTTAAGGCCTTATAATAGTGAACAGAG 57.168 33.333 25.70 0.00 0.00 3.35
1923 8304 7.676683 AAGGCCTTATAATAGTGAACAGAGA 57.323 36.000 18.87 0.00 0.00 3.10
1924 8305 7.296628 AGGCCTTATAATAGTGAACAGAGAG 57.703 40.000 0.00 0.00 0.00 3.20
1925 8306 7.069986 AGGCCTTATAATAGTGAACAGAGAGA 58.930 38.462 0.00 0.00 0.00 3.10
1926 8307 7.565398 AGGCCTTATAATAGTGAACAGAGAGAA 59.435 37.037 0.00 0.00 0.00 2.87
1927 8308 7.654116 GGCCTTATAATAGTGAACAGAGAGAAC 59.346 40.741 0.00 0.00 0.00 3.01
1981 8362 4.854173 TCTTAATTGTGCTGGGCTAATGA 58.146 39.130 0.00 0.00 0.00 2.57
1997 8378 0.324645 ATGATCAAAGGTGGTGGCCC 60.325 55.000 0.00 0.00 0.00 5.80
2021 8402 1.067915 GTGAGCCTATCTCTCCATCGC 60.068 57.143 0.00 0.00 42.38 4.58
2040 8421 2.781945 CTGAAGGAGCAAACCACAAC 57.218 50.000 0.00 0.00 0.00 3.32
2044 8425 2.159179 AGGAGCAAACCACAACCTTT 57.841 45.000 0.00 0.00 0.00 3.11
2045 8426 2.466846 AGGAGCAAACCACAACCTTTT 58.533 42.857 0.00 0.00 0.00 2.27
2094 8475 3.173151 TGAGTTGAAGCATCCTAGACCA 58.827 45.455 0.00 0.00 0.00 4.02
2107 8488 1.264749 TAGACCAGCAGTTCCCGCAT 61.265 55.000 0.00 0.00 0.00 4.73
2114 8495 1.450312 CAGTTCCCGCATCTCCCAC 60.450 63.158 0.00 0.00 0.00 4.61
2119 8500 2.124983 CCGCATCTCCCACACCTG 60.125 66.667 0.00 0.00 0.00 4.00
2130 8511 1.172180 CCACACCTGTTCGGCAACAT 61.172 55.000 3.58 0.00 41.82 2.71
2138 8519 4.126437 CCTGTTCGGCAACATATGTCATA 58.874 43.478 9.23 0.00 41.82 2.15
2172 8553 1.066502 GCGGGTGTGGCCAAAATAAAT 60.067 47.619 7.24 0.00 39.65 1.40
2176 8557 4.322049 CGGGTGTGGCCAAAATAAATGTTA 60.322 41.667 7.24 0.00 39.65 2.41
2177 8558 5.175127 GGGTGTGGCCAAAATAAATGTTAG 58.825 41.667 7.24 0.00 39.65 2.34
2179 8560 5.233988 GTGTGGCCAAAATAAATGTTAGCA 58.766 37.500 7.24 0.00 0.00 3.49
2183 8564 4.173256 GCCAAAATAAATGTTAGCAGCGT 58.827 39.130 0.00 0.00 0.00 5.07
2188 8569 7.540745 CCAAAATAAATGTTAGCAGCGTACTTT 59.459 33.333 0.00 0.00 0.00 2.66
2190 8571 4.680171 AAATGTTAGCAGCGTACTTTCC 57.320 40.909 0.00 0.00 0.00 3.13
2193 8574 4.730949 TGTTAGCAGCGTACTTTCCTAT 57.269 40.909 0.00 0.00 0.00 2.57
2194 8575 4.430007 TGTTAGCAGCGTACTTTCCTATG 58.570 43.478 0.00 0.00 0.00 2.23
2195 8576 1.941325 AGCAGCGTACTTTCCTATGC 58.059 50.000 0.00 0.00 0.00 3.14
2198 8579 0.822164 AGCGTACTTTCCTATGCGGT 59.178 50.000 0.00 0.00 34.34 5.68
2199 8580 0.928229 GCGTACTTTCCTATGCGGTG 59.072 55.000 0.00 0.00 0.00 4.94
2207 8608 4.202223 ACTTTCCTATGCGGTGGTATGTAG 60.202 45.833 0.00 0.00 0.00 2.74
2218 8619 5.279306 GCGGTGGTATGTAGGAATCATAAGA 60.279 44.000 0.00 0.00 31.00 2.10
2263 8665 5.465724 GCTATAGTCTTCCCCAACATTAACG 59.534 44.000 0.84 0.00 0.00 3.18
2269 8671 1.706305 TCCCCAACATTAACGACCCTT 59.294 47.619 0.00 0.00 0.00 3.95
2300 8702 2.345244 CCCTGCGTGCTGAGAAGT 59.655 61.111 0.00 0.00 0.00 3.01
2310 8712 1.977854 TGCTGAGAAGTTCAAGCCCTA 59.022 47.619 21.29 6.57 34.81 3.53
2382 8784 6.803154 ACAATGGTAGAAGAAGTTAAGCAC 57.197 37.500 0.00 0.00 0.00 4.40
2387 8789 4.388165 GGTAGAAGAAGTTAAGCACGGAAC 59.612 45.833 0.00 0.00 0.00 3.62
2390 8792 5.471257 AGAAGAAGTTAAGCACGGAACTAG 58.529 41.667 0.00 0.00 34.81 2.57
2402 8804 4.112634 CACGGAACTAGTGACATGTATGG 58.887 47.826 0.00 0.00 41.83 2.74
2423 8825 7.574021 ATGGTGCTATAATTAGGGAGATCAA 57.426 36.000 0.00 0.00 0.00 2.57
2428 8830 6.216251 TGCTATAATTAGGGAGATCAAGGCAT 59.784 38.462 0.00 0.00 0.00 4.40
2447 8849 4.153835 GGCATCTCAACTTCTGTTTGAGAG 59.846 45.833 17.24 11.59 40.26 3.20
2448 8850 4.754114 GCATCTCAACTTCTGTTTGAGAGT 59.246 41.667 17.24 6.23 40.26 3.24
2463 8865 6.706270 TGTTTGAGAGTTGTGAGGTTATCTTC 59.294 38.462 0.00 0.00 0.00 2.87
2470 8872 4.451629 TGTGAGGTTATCTTCGAAGGTC 57.548 45.455 24.37 6.95 0.00 3.85
2496 8898 5.557891 AGAACAACTCAAATGCTCATAGC 57.442 39.130 0.00 0.00 42.82 2.97
2524 8926 3.887621 AGCACTCAGTTCCGCTTAATA 57.112 42.857 0.00 0.00 0.00 0.98
2530 8932 4.466726 ACTCAGTTCCGCTTAATAAGGTCT 59.533 41.667 1.88 0.00 0.00 3.85
2540 8942 5.220854 CGCTTAATAAGGTCTCCATTTGTGG 60.221 44.000 1.88 0.00 0.00 4.17
2550 8952 2.749621 CTCCATTTGTGGCTTGGTACTC 59.250 50.000 0.00 0.00 0.00 2.59
2552 8954 2.513753 CATTTGTGGCTTGGTACTCCA 58.486 47.619 0.00 0.00 42.66 3.86
2553 8955 2.969821 TTTGTGGCTTGGTACTCCAT 57.030 45.000 0.00 0.00 43.91 3.41
2554 8956 2.198827 TTGTGGCTTGGTACTCCATG 57.801 50.000 0.00 0.00 43.91 3.66
2566 8968 0.988832 ACTCCATGCGACCCCTTTTA 59.011 50.000 0.00 0.00 0.00 1.52
2568 8970 2.025321 ACTCCATGCGACCCCTTTTATT 60.025 45.455 0.00 0.00 0.00 1.40
2571 8973 3.835395 TCCATGCGACCCCTTTTATTTTT 59.165 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.066481 GTGTTCGTATCAGGTACTCCCTC 59.934 52.174 0.00 0.00 43.86 4.30
2 3 2.223433 CGTGTTCGTATCAGGTACTCCC 60.223 54.545 0.00 0.00 34.60 4.30
3 4 2.679837 TCGTGTTCGTATCAGGTACTCC 59.320 50.000 0.00 0.00 35.55 3.85
4 5 4.548991 ATCGTGTTCGTATCAGGTACTC 57.451 45.455 0.00 0.00 35.55 2.59
5 6 4.025396 CGTATCGTGTTCGTATCAGGTACT 60.025 45.833 0.00 0.00 37.52 2.73
6 7 4.206843 CGTATCGTGTTCGTATCAGGTAC 58.793 47.826 0.00 0.00 38.33 3.34
7 8 3.303329 GCGTATCGTGTTCGTATCAGGTA 60.303 47.826 0.00 0.00 38.33 3.08
8 9 2.540361 GCGTATCGTGTTCGTATCAGGT 60.540 50.000 0.00 0.00 38.33 4.00
9 10 2.041966 GCGTATCGTGTTCGTATCAGG 58.958 52.381 0.00 0.00 38.33 3.86
20 21 0.657659 CTCCACTAGCGCGTATCGTG 60.658 60.000 8.43 9.41 41.07 4.35
115 132 1.754234 GGTTCCCTCCGTACCGCTA 60.754 63.158 0.00 0.00 0.00 4.26
260 303 5.904362 ACGACCTACTCCTACGTATTTTT 57.096 39.130 0.00 0.00 35.49 1.94
469 3371 2.608090 GTCCTGTAAAATAGCACCTCGC 59.392 50.000 0.00 0.00 42.91 5.03
492 3394 0.038890 AGAAAGAAGGCCAGCTTCCC 59.961 55.000 5.01 3.91 0.00 3.97
495 3397 1.625511 CCAAGAAAGAAGGCCAGCTT 58.374 50.000 5.01 4.66 0.00 3.74
556 3463 8.316214 CAACCTGGTGAACCTTACTATAGTTTA 58.684 37.037 11.40 0.00 36.82 2.01
557 3464 6.947376 ACCTGGTGAACCTTACTATAGTTT 57.053 37.500 11.40 0.00 36.82 2.66
558 3465 6.499350 TCAACCTGGTGAACCTTACTATAGTT 59.501 38.462 11.40 0.00 36.82 2.24
559 3466 6.021030 TCAACCTGGTGAACCTTACTATAGT 58.979 40.000 10.87 10.87 36.82 2.12
570 3496 1.388547 TGCAAGTCAACCTGGTGAAC 58.611 50.000 0.00 1.55 0.00 3.18
588 3514 7.201513 CCGTGGCCAGAAAACAAATTTTATATG 60.202 37.037 5.11 0.00 38.17 1.78
592 3518 4.372656 CCGTGGCCAGAAAACAAATTTTA 58.627 39.130 5.11 0.00 38.17 1.52
620 3546 3.073274 ACAGTATTCCAAAGTCAGCCC 57.927 47.619 0.00 0.00 0.00 5.19
664 4864 8.955061 AAATTATTTGAAACACGAGACTCATG 57.045 30.769 2.82 0.00 0.00 3.07
672 4872 6.579292 CCTGCGTAAAATTATTTGAAACACGA 59.421 34.615 10.74 0.00 30.74 4.35
773 6316 1.377202 TTTCTCATGGCGTGGGAGC 60.377 57.895 9.61 0.00 38.89 4.70
781 6326 7.041508 CCTTGTAGATTATCAGTTTCTCATGGC 60.042 40.741 0.00 0.00 0.00 4.40
803 6348 5.695851 ATTGTGAGCTTTGTTACTCCTTG 57.304 39.130 0.00 0.00 31.65 3.61
813 6358 6.272318 TGGTTTTCTGTTATTGTGAGCTTTG 58.728 36.000 0.00 0.00 0.00 2.77
814 6359 6.463995 TGGTTTTCTGTTATTGTGAGCTTT 57.536 33.333 0.00 0.00 0.00 3.51
884 6443 1.686741 GGAGGACAGTAGGAGGGACAG 60.687 61.905 0.00 0.00 0.00 3.51
921 6853 7.922699 AGGGAAGGAAGATGTATATATAGCC 57.077 40.000 0.00 0.00 0.00 3.93
930 6862 3.116862 ACGGGATAGGGAAGGAAGATGTA 60.117 47.826 0.00 0.00 0.00 2.29
931 6863 2.330216 CGGGATAGGGAAGGAAGATGT 58.670 52.381 0.00 0.00 0.00 3.06
939 6871 0.384669 GTGACGACGGGATAGGGAAG 59.615 60.000 0.00 0.00 0.00 3.46
945 6877 0.967662 TGTTTGGTGACGACGGGATA 59.032 50.000 0.00 0.00 0.00 2.59
1098 7030 4.821589 GAGGAGGCGGTGGCGAAG 62.822 72.222 0.00 0.00 41.24 3.79
1167 7105 2.343426 GCAAAGGAAGAAGGGGCCG 61.343 63.158 0.00 0.00 0.00 6.13
1435 7373 1.153369 CGTTGATCTGGGCGTCCAT 60.153 57.895 10.40 0.00 43.11 3.41
1447 7385 0.666274 TCGTTGAGCTTCGCGTTGAT 60.666 50.000 5.77 0.00 0.00 2.57
1627 7570 0.524816 TTTATCACTCGGCGTCGCTC 60.525 55.000 18.11 6.41 36.13 5.03
1714 7746 3.278574 TCACCAACAAGACTGTTCCAAG 58.721 45.455 0.00 0.00 44.15 3.61
1725 7758 7.201635 CCTTTTTGAATTTTCCTCACCAACAAG 60.202 37.037 0.00 0.00 0.00 3.16
1806 7848 5.226396 CGCATTTCATTTCCCTTTGTTACA 58.774 37.500 0.00 0.00 0.00 2.41
1856 8237 6.015519 TGTGCAAATAGCCTATTTTCAGTTGT 60.016 34.615 9.36 0.00 44.83 3.32
1857 8238 6.389091 TGTGCAAATAGCCTATTTTCAGTTG 58.611 36.000 9.36 0.00 44.83 3.16
1858 8239 6.588719 TGTGCAAATAGCCTATTTTCAGTT 57.411 33.333 9.36 0.00 44.83 3.16
1859 8240 6.780457 ATGTGCAAATAGCCTATTTTCAGT 57.220 33.333 9.36 0.73 44.83 3.41
1860 8241 7.037438 ACAATGTGCAAATAGCCTATTTTCAG 58.963 34.615 9.36 2.18 44.83 3.02
1861 8242 6.934056 ACAATGTGCAAATAGCCTATTTTCA 58.066 32.000 6.97 6.23 44.83 2.69
1862 8243 7.221452 CAGACAATGTGCAAATAGCCTATTTTC 59.779 37.037 6.97 3.59 44.83 2.29
1863 8244 7.037438 CAGACAATGTGCAAATAGCCTATTTT 58.963 34.615 6.97 0.00 44.83 1.82
1864 8245 6.377996 TCAGACAATGTGCAAATAGCCTATTT 59.622 34.615 3.83 3.83 44.83 1.40
1865 8246 5.887598 TCAGACAATGTGCAAATAGCCTATT 59.112 36.000 0.00 0.00 44.83 1.73
1866 8247 5.439721 TCAGACAATGTGCAAATAGCCTAT 58.560 37.500 0.00 0.00 44.83 2.57
1867 8248 4.842574 TCAGACAATGTGCAAATAGCCTA 58.157 39.130 0.00 0.00 44.83 3.93
1868 8249 3.689347 TCAGACAATGTGCAAATAGCCT 58.311 40.909 0.00 0.00 44.83 4.58
1869 8250 4.439305 TTCAGACAATGTGCAAATAGCC 57.561 40.909 0.00 0.00 44.83 3.93
1870 8251 8.133627 AGATATTTCAGACAATGTGCAAATAGC 58.866 33.333 0.00 0.00 45.96 2.97
1875 8256 9.844790 CTTAAAGATATTTCAGACAATGTGCAA 57.155 29.630 0.00 0.00 0.00 4.08
1876 8257 8.461222 CCTTAAAGATATTTCAGACAATGTGCA 58.539 33.333 0.00 0.00 0.00 4.57
1877 8258 7.433425 GCCTTAAAGATATTTCAGACAATGTGC 59.567 37.037 0.00 0.00 0.00 4.57
1878 8259 7.917505 GGCCTTAAAGATATTTCAGACAATGTG 59.082 37.037 0.00 0.00 0.00 3.21
1879 8260 7.836183 AGGCCTTAAAGATATTTCAGACAATGT 59.164 33.333 0.00 0.00 0.00 2.71
1880 8261 8.230472 AGGCCTTAAAGATATTTCAGACAATG 57.770 34.615 0.00 0.00 0.00 2.82
1881 8262 8.829373 AAGGCCTTAAAGATATTTCAGACAAT 57.171 30.769 18.87 0.00 0.00 2.71
1882 8263 9.920946 ATAAGGCCTTAAAGATATTTCAGACAA 57.079 29.630 28.50 1.59 0.00 3.18
1894 8275 9.832445 CTGTTCACTATTATAAGGCCTTAAAGA 57.168 33.333 28.50 18.29 0.00 2.52
1895 8276 9.832445 TCTGTTCACTATTATAAGGCCTTAAAG 57.168 33.333 28.50 22.52 0.00 1.85
1896 8277 9.832445 CTCTGTTCACTATTATAAGGCCTTAAA 57.168 33.333 28.50 21.71 0.00 1.52
1897 8278 9.209048 TCTCTGTTCACTATTATAAGGCCTTAA 57.791 33.333 28.50 16.04 0.00 1.85
1898 8279 8.777578 TCTCTGTTCACTATTATAAGGCCTTA 57.222 34.615 27.11 27.11 0.00 2.69
1899 8280 7.565398 TCTCTCTGTTCACTATTATAAGGCCTT 59.435 37.037 24.18 24.18 0.00 4.35
1900 8281 7.069986 TCTCTCTGTTCACTATTATAAGGCCT 58.930 38.462 0.00 0.00 0.00 5.19
1901 8282 7.291411 TCTCTCTGTTCACTATTATAAGGCC 57.709 40.000 0.00 0.00 0.00 5.19
1902 8283 8.198109 TGTTCTCTCTGTTCACTATTATAAGGC 58.802 37.037 0.00 0.00 0.00 4.35
1903 8284 9.522804 GTGTTCTCTCTGTTCACTATTATAAGG 57.477 37.037 0.00 0.00 0.00 2.69
1904 8285 9.522804 GGTGTTCTCTCTGTTCACTATTATAAG 57.477 37.037 0.00 0.00 0.00 1.73
1905 8286 8.188799 CGGTGTTCTCTCTGTTCACTATTATAA 58.811 37.037 0.00 0.00 0.00 0.98
1906 8287 7.338703 ACGGTGTTCTCTCTGTTCACTATTATA 59.661 37.037 0.00 0.00 0.00 0.98
1907 8288 6.153000 ACGGTGTTCTCTCTGTTCACTATTAT 59.847 38.462 0.00 0.00 0.00 1.28
1908 8289 5.475909 ACGGTGTTCTCTCTGTTCACTATTA 59.524 40.000 0.00 0.00 0.00 0.98
1909 8290 4.281182 ACGGTGTTCTCTCTGTTCACTATT 59.719 41.667 0.00 0.00 0.00 1.73
1910 8291 3.827302 ACGGTGTTCTCTCTGTTCACTAT 59.173 43.478 0.00 0.00 0.00 2.12
1911 8292 3.220110 ACGGTGTTCTCTCTGTTCACTA 58.780 45.455 0.00 0.00 0.00 2.74
1912 8293 2.032620 ACGGTGTTCTCTCTGTTCACT 58.967 47.619 0.00 0.00 0.00 3.41
1913 8294 2.510768 ACGGTGTTCTCTCTGTTCAC 57.489 50.000 0.00 0.00 0.00 3.18
1914 8295 2.693591 AGAACGGTGTTCTCTCTGTTCA 59.306 45.455 17.84 0.00 46.81 3.18
1915 8296 3.372660 AGAACGGTGTTCTCTCTGTTC 57.627 47.619 6.38 11.54 45.76 3.18
1916 8297 3.821421 AAGAACGGTGTTCTCTCTGTT 57.179 42.857 12.19 0.00 38.72 3.16
1917 8298 3.821421 AAAGAACGGTGTTCTCTCTGT 57.179 42.857 12.19 0.00 0.00 3.41
1918 8299 4.119862 TCAAAAGAACGGTGTTCTCTCTG 58.880 43.478 12.19 9.87 0.00 3.35
1919 8300 4.372656 CTCAAAAGAACGGTGTTCTCTCT 58.627 43.478 12.19 0.00 0.00 3.10
1920 8301 3.495001 CCTCAAAAGAACGGTGTTCTCTC 59.505 47.826 12.19 0.00 0.00 3.20
1921 8302 3.467803 CCTCAAAAGAACGGTGTTCTCT 58.532 45.455 12.19 0.00 0.00 3.10
1922 8303 2.548480 CCCTCAAAAGAACGGTGTTCTC 59.452 50.000 12.19 0.00 0.00 2.87
1923 8304 2.171870 TCCCTCAAAAGAACGGTGTTCT 59.828 45.455 6.38 6.38 0.00 3.01
1924 8305 2.289820 GTCCCTCAAAAGAACGGTGTTC 59.710 50.000 1.49 1.49 0.00 3.18
1925 8306 2.294979 GTCCCTCAAAAGAACGGTGTT 58.705 47.619 0.00 0.00 0.00 3.32
1926 8307 1.210967 TGTCCCTCAAAAGAACGGTGT 59.789 47.619 0.00 0.00 0.00 4.16
1927 8308 1.961793 TGTCCCTCAAAAGAACGGTG 58.038 50.000 0.00 0.00 0.00 4.94
1981 8362 1.077265 CAGGGCCACCACCTTTGAT 59.923 57.895 6.18 0.00 40.13 2.57
1997 8378 2.942804 TGGAGAGATAGGCTCACTCAG 58.057 52.381 18.37 0.00 46.45 3.35
2021 8402 1.338020 GGTTGTGGTTTGCTCCTTCAG 59.662 52.381 0.00 0.00 0.00 3.02
2040 8421 5.163513 GCAATGTACCTCAACATGAAAAGG 58.836 41.667 0.00 5.08 39.98 3.11
2044 8425 2.746904 CGGCAATGTACCTCAACATGAA 59.253 45.455 0.00 0.00 39.98 2.57
2045 8426 2.027653 TCGGCAATGTACCTCAACATGA 60.028 45.455 0.00 0.00 39.98 3.07
2107 8488 2.879233 GCCGAACAGGTGTGGGAGA 61.879 63.158 4.97 0.00 43.70 3.71
2114 8495 2.083774 ACATATGTTGCCGAACAGGTG 58.916 47.619 1.41 0.00 45.29 4.00
2119 8500 3.559655 TGCTATGACATATGTTGCCGAAC 59.440 43.478 10.30 0.00 0.00 3.95
2130 8511 2.682594 AGAGGTGGCTGCTATGACATA 58.317 47.619 0.00 0.00 0.00 2.29
2138 8519 4.711949 CCGCAAGAGGTGGCTGCT 62.712 66.667 0.00 0.00 41.01 4.24
2172 8553 4.430007 CATAGGAAAGTACGCTGCTAACA 58.570 43.478 0.00 0.00 0.00 2.41
2176 8557 1.802880 CGCATAGGAAAGTACGCTGCT 60.803 52.381 0.00 0.00 0.00 4.24
2177 8558 0.577269 CGCATAGGAAAGTACGCTGC 59.423 55.000 0.00 0.00 0.00 5.25
2179 8560 0.822164 ACCGCATAGGAAAGTACGCT 59.178 50.000 0.00 0.00 45.00 5.07
2183 8564 3.707611 ACATACCACCGCATAGGAAAGTA 59.292 43.478 0.00 0.00 45.00 2.24
2188 8569 2.158430 TCCTACATACCACCGCATAGGA 60.158 50.000 0.00 0.00 45.00 2.94
2190 8571 4.021456 TGATTCCTACATACCACCGCATAG 60.021 45.833 0.00 0.00 0.00 2.23
2193 8574 2.112190 TGATTCCTACATACCACCGCA 58.888 47.619 0.00 0.00 0.00 5.69
2194 8575 2.902705 TGATTCCTACATACCACCGC 57.097 50.000 0.00 0.00 0.00 5.68
2195 8576 6.015350 ACTCTTATGATTCCTACATACCACCG 60.015 42.308 0.00 0.00 31.26 4.94
2198 8579 9.601810 ACATACTCTTATGATTCCTACATACCA 57.398 33.333 0.00 0.00 37.86 3.25
2207 8608 7.509546 TCCCAGAAACATACTCTTATGATTCC 58.490 38.462 9.70 0.00 43.56 3.01
2218 8619 3.135530 GCTGAGGATCCCAGAAACATACT 59.864 47.826 25.77 0.00 33.65 2.12
2226 8628 3.660177 AGACTATAGCTGAGGATCCCAGA 59.340 47.826 25.77 12.10 33.65 3.86
2263 8665 3.256281 CCTCAAGGCTTGAAGGGTC 57.744 57.895 28.27 0.00 39.58 4.46
2293 8695 2.770164 GCTAGGGCTTGAACTTCTCA 57.230 50.000 0.00 0.00 35.22 3.27
2310 8712 4.771903 TCTGTAGAAGTAGATCGTGAGCT 58.228 43.478 0.00 0.00 0.00 4.09
2382 8784 4.112634 CACCATACATGTCACTAGTTCCG 58.887 47.826 0.00 0.00 0.00 4.30
2390 8792 7.334421 CCCTAATTATAGCACCATACATGTCAC 59.666 40.741 0.00 0.00 0.00 3.67
2402 8804 5.877564 GCCTTGATCTCCCTAATTATAGCAC 59.122 44.000 0.00 0.00 0.00 4.40
2423 8825 4.070716 CTCAAACAGAAGTTGAGATGCCT 58.929 43.478 8.18 0.00 38.17 4.75
2428 8830 5.582269 CACAACTCTCAAACAGAAGTTGAGA 59.418 40.000 18.03 14.33 42.02 3.27
2433 8835 4.080863 ACCTCACAACTCTCAAACAGAAGT 60.081 41.667 0.00 0.00 0.00 3.01
2437 8839 6.226787 AGATAACCTCACAACTCTCAAACAG 58.773 40.000 0.00 0.00 0.00 3.16
2447 8849 4.566987 ACCTTCGAAGATAACCTCACAAC 58.433 43.478 26.61 0.00 35.04 3.32
2448 8850 4.617530 CGACCTTCGAAGATAACCTCACAA 60.618 45.833 26.61 0.00 43.74 3.33
2463 8865 1.192534 GAGTTGTTCTTGCGACCTTCG 59.807 52.381 0.00 0.00 43.89 3.79
2470 8872 2.975851 GAGCATTTGAGTTGTTCTTGCG 59.024 45.455 0.00 0.00 34.36 4.85
2483 8885 4.856664 CTTAGCCAAGCTATGAGCATTTG 58.143 43.478 0.64 0.00 45.56 2.32
2496 8898 2.079925 GGAACTGAGTGCTTAGCCAAG 58.920 52.381 0.29 0.00 34.66 3.61
2506 8908 4.504858 ACCTTATTAAGCGGAACTGAGTG 58.495 43.478 0.00 0.00 0.00 3.51
2510 8912 4.120589 GGAGACCTTATTAAGCGGAACTG 58.879 47.826 0.00 0.00 0.00 3.16
2515 8917 4.881850 ACAAATGGAGACCTTATTAAGCGG 59.118 41.667 0.00 0.00 0.00 5.52
2530 8932 2.554344 GGAGTACCAAGCCACAAATGGA 60.554 50.000 0.00 0.00 41.53 3.41
2550 8952 3.885724 AAAATAAAAGGGGTCGCATGG 57.114 42.857 0.00 0.00 0.00 3.66
2552 8954 5.476091 TTGAAAAATAAAAGGGGTCGCAT 57.524 34.783 0.00 0.00 0.00 4.73
2553 8955 4.939052 TTGAAAAATAAAAGGGGTCGCA 57.061 36.364 0.00 0.00 0.00 5.10
2554 8956 5.474825 TCATTGAAAAATAAAAGGGGTCGC 58.525 37.500 0.00 0.00 0.00 5.19
2555 8957 6.926272 TGTTCATTGAAAAATAAAAGGGGTCG 59.074 34.615 0.00 0.00 0.00 4.79
2556 8958 8.846943 ATGTTCATTGAAAAATAAAAGGGGTC 57.153 30.769 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.